Modified sequence Experiment N duplicates Sequence Length Missed cleavages Proteins Leading proteins Gene names Protein names Phospho (STY) Acetyl (K) All Phospho (STY) Probabilities All Acetyl (K) Probabilities Max Score Min PEP Intensity Reporter intensity corrected 1 Reporter intensity corrected 2 Reporter intensity corrected 3 Reporter intensity corrected 4 Reporter intensity corrected 5 Reporter intensity corrected 6 Reporter intensity corrected 7 Reporter intensity corrected 8 Reporter intensity corrected 9 Reporter intensity corrected 10 Phosphoproteome Acetylproteome Fullproteome TMT Channel Normal 1 TMT Channel Normal 2 TMT Channel Normal 3 TMT Channel Normal 4 TMT Channel Normal 5 TMT Channel Normal 6 TMT Channel Normal 7 TMT Channel Normal 8 TMT Channel Normal 9 TMT Channel Normal 10 TMT Channel Ratio 1 TMT Channel Ratio 2 TMT Channel Ratio 3 TMT Channel Ratio 4 TMT Channel Ratio 5 TMT Channel Ratio 6 TMT Channel Ratio 7 TMT Channel Ratio 8 TMT Channel Ratio 9 TMT Channel Ratio 10 Curve signal Log EC50 Curve slope Curve top Curve bottom R2 Curve RMSE Log EC50 error Curve slope error Curve top error Curve bottom error EC50 pEC50 Curve effect size Regulation (ac)AAAAAAAAAAGAAGGRGS(ph)GPGR ddPTM_HeLa_Romidepsin_16h_R1 2 AAAAAAAAAAGAAGGRGSGPGR 22 1 Q86U42-2;Q86U42 Q86U42-2 PABPN1 Polyadenylate-binding protein 2 1 0 AAAAAAAAAAGAAGGRGS(1)GPGR;AAAAAAAAAAGAAGGRGS(1)GPGR ; 83.776 1.40E-05 15185600 965.7 947.79 875.67 352.318 925.52 713.83 948.31 974.35 1158.67 967.03 TRUE FALSE FALSE 953.929677 961.1330125 890.910669 393.0546649 878.2872608 668.2185668 1028.859428 1002.54128 1055.035653 941.9064212 1.012764809 1.020412422 0.945859004 0.417296937 0.932457027 0.709432011 1.092315972 1.06437461 1.120106658 1 9.879439924 -9.512619562 24.93211922 1.006125617 0.837249546 0.195366651 0.182121951 659.4638492 1602646.506 0.027488195 0.040295226 3.07E-10 9.512619562 -0.168876071 (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVR ddPTM_HeLa_Romidepsin_16h_R1 3 AAAAAAAGDSDSWDADAFSVEDPVR 25 0 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 AAAAAAAGDS(0.994)DS(0.006)WDADAFSVEDPVR;AAAAAAAGDS(0.902)DS(0.098)WDADAFSVEDPVR;AAAAAAAGDS(1)DSWDADAFSVEDPVR ;; 210.39 6.06E-113 2265300 0 0 97.629 185.193 141.57 61.698 44.988 64.21 174.067 294.275 TRUE FALSE FALSE 0 0 99.32819179 206.605886 134.3451546 57.75569692 48.8092796 66.06781504 158.4980116 286.6296931 0 0 0.346538388 0.720811176 0.468706341 0.20149935 0.170286892 0.230498851 0.552971361 1 8.163044261 -12.41881032 1.141920873 1.000804378 0.2537699 0.369072207 0.241615256 0.276653296 0.644182171 0.163426755 0.041077359 3.81E-13 12.41881032 -0.747034478 (ac)AAAAAAAGDS(ph)DSWDADAFSVEDPVRK ddPTM_HeLa_Romidepsin_16h_R1 4 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 AAAAAAAGDS(0.972)DS(0.028)WDADAFSVEDPVRK;AAAAAAAGDS(0.949)DS(0.051)WDADAFSVEDPVRK;AAAAAAAGDS(0.875)DS(0.125)WDADAFSVEDPVRK;AAAAAAAGDS(0.961)DS(0.039)WDADAFSVEDPVRK ;;; 128.04 1.20E-11 252851000 10227.7 10997.5 9631.9 9686.2 10438.5 10396 8520.2 9228 11102.7 11260.1 TRUE FALSE FALSE 10103.04086 11152.32309 9799.539179 10806.16402 9905.784394 9731.729152 9243.905575 9494.997621 10109.6467 10967.56098 0.921174806 1.016846235 0.893502138 0.985284152 0.903189361 0.887319357 0.842840591 0.865734655 0.921777114 1 13.42095511 -4 0.185489326 0.991021215 0.336622458 0.450096482 0.041191298 30.23358225 0.333725996 0.044759427 5.660966769 1.00E-04 4 -0.654398756 (ac)AAAAAAAGDSDS(ph)WDADAFSVEDPVRK ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAAAGDSDSWDADAFSVEDPVRK 26 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 AAAAAAAGDS(0.385)DS(0.615)WDADAFSVEDPVRK 98.376 1.63E-08 29672000 2946.8 2713.1 2623.2 2459 2891.5 2810.9 2434 2532.2 3531 2720.8 TRUE FALSE FALSE 2910.883268 2751.295093 2668.855696 2743.32115 2743.935965 2631.292562 2640.743899 2605.465212 3215.178516 2650.113224 1.098399586 1.038180206 1.007072329 1.0351713 1.035403295 0.992898167 0.996464557 0.983152413 1.213223076 1 11.37183828 -8.265778213 0.906389704 1.044730543 0.980630796 0.199355103 0.059011431 0.838167261 1.095797526 0.006370408 0.037573685 5.42E-09 8.265778213 -0.064099747 (ac)AAADGDDSLYPIAVLIDELR ddPTM_HeLa_Romidepsin_16h_R1 4 AAADGDDSLYPIAVLIDELR 20 0 C9J9C1;P30153;M0QXG4;M0R0K6 C9J9C1 PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform 0 0 ;;; ;;; 149.32 2.18E-42 33323740 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 (ac)AAAEPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAEPSPR 8 0 F8WEI0;Q53H96-2;Q53H96 F8WEI0 PYCRL Pyrroline-5-carboxylate reductase 3 1 0 AAAEPS(1)PR 59.35 0.025341 6164900 0 0 0 0 54.659 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 51.86954727 0 0 0 0 0 0 (ac)AAAMDVDT(ph)PSGTNSGAGKK ddPTM_HeLa_Romidepsin_16h_R1 1 AAAMDVDTPSGTNSGAGKK 19 1 P62877 P62877 RBX1 "E3 ubiquitin-protein ligase RBX1;E3 ubiquitin-protein ligase RBX1, N-terminally processed" 1 0 AAAMDVDT(0.991)PS(0.008)GTNSGAGKK 84.365 0.0004454 3006300 1053.8 711.87 1078.9 915.74 664.34 891.14 585.89 839 1001.3 728.13 TRUE FALSE FALSE 1040.95588 721.8917245 1097.677802 1021.622167 630.4362508 834.19903 635.655482 863.2751413 911.7412202 709.2130776 1.467761824 1.017877063 1.547740498 1.440501028 0.888923612 1.176231878 0.896282799 1.217229587 1.285567411 1 9.470075329 -8.755343396 24.99824675 1.250076795 1.043465627 0.263447105 0.195789048 218.1398758 894533.1054 0.033538584 0.065732465 1.76E-09 8.755343396 -0.206611168 (ac)AAAPQAPGRGS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAPQAPGRGSLR 13 1 P78345;Q5VUC9;Q5VUC3 P78345 RPP38 Ribonuclease P protein subunit p38 1 0 AAAPQAPGRGS(1)LR 71.879 0.0021252 0 1216.6 759.44 1086.3 408.41 954.34 757.36 1182.5 849.99 1539.7 1143.7 TRUE FALSE FALSE 1201.771611 770.1314163 1105.206596 455.6322858 905.6364687 708.9671403 1282.94152 874.5831196 1401.985376 1113.986509 1.078802662 0.691329213 0.992118474 0.409010596 0.812968973 0.636423453 1.151667017 0.785093098 1.258529941 1 10.12151605 -10.2690289 24.59445205 1.037212373 0.78607773 0.344292816 0.200619474 431.2867809 1397617.282 0.030667398 0.035439627 5.38E-11 10.2690289 -0.251134643 (ac)AAAPQAPGRGS(ph)LRK ddPTM_HeLa_Romidepsin_16h_R1 2 AAAPQAPGRGSLRK 14 2 P78345;Q5VUC9;Q5VUC3 P78345 RPP38 Ribonuclease P protein subunit p38 1 0 AAAPQAPGRGS(1)LRK;AAAPQAPGRGS(1)LRK ; 83.53 0.0034516 8574000 2092.3 2385.7 1792.84 2025.5 2262.3 2533.2 2611.8 2344.9 2474.4 2003.57 TRUE FALSE FALSE 2066.798243 2419.285947 1824.043628 2259.69784 2146.846389 2371.336696 2833.646227 2412.745982 2253.083467 1951.516963 1.059072651 1.239695065 0.934679874 1.157918626 1.100091073 1.215124819 1.45202234 1.236343843 1.154529276 1 10.93038029 -8.232392995 1.537121324 1.045124825 1.349416218 0.456084567 0.101770263 0.201842821 0.884923206 0.013754391 0.052423712 5.86E-09 8.232392995 0.304291393 (ac)AAAVAAAGAGEPQS(ph)PDELLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AAAVAAAGAGEPQSPDELLPK 21 0 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 1 0 AAAVAAAGAGEPQS(1)PDELLPK 110.77 1.18E-10 4035900 1028.6 1225.5 1250.7 1103.1 1428.4 2240 1281.8 1705.9 1313.1 1216.5 TRUE FALSE FALSE 1016.063028 1242.752621 1272.467909 1230.645612 1355.503418 2096.871229 1390.67606 1755.257525 1195.653047 1184.895155 0.857513024 1.048829187 1.073907598 1.038611397 1.143985957 1.769668161 1.173670138 1.481361045 1.009079194 1 10.21054369 -8.514989667 4.19918357 0.96146199 1.450058901 0.654485005 0.149837524 0.087679381 3.655022623 0.021403007 0.046969664 3.05E-09 8.514989667 0.488596911 (ac)AADS(ph)DDGAVSAPAASDGGVSK ddPTM_HeLa_Romidepsin_16h_R1 1 AADSDDGAVSAPAASDGGVSK 21 0 Q96GM8 Q96GM8 TOE1 Target of EGR1 protein 1 1 0 AADS(1)DDGAVSAPAASDGGVSK 113.72 8.79E-16 0 1210.4 1125.8 1083.8 809.36 1089.7 971.29 925.19 841.8 1261.2 988.46 TRUE FALSE FALSE 1195.647179 1141.649042 1102.663084 902.9420114 1034.088543 909.2277037 1003.775616 866.1561549 1148.395113 962.7796667 1.241869994 1.18578433 1.145291205 0.937849066 1.074065623 0.944377759 1.042580821 0.899641096 1.192791199 1 9.911061863 -9.268863378 24.79218232 1.125742521 0.98647596 0.541622504 0.077637815 480.6739032 1605192.292 0.015730074 0.024322593 5.38E-10 9.268863378 -0.139266561 (ac)AADVS(ph)VTHRPPLSPK ddPTM_HeLa_Romidepsin_16h_R1 1 AADVSVTHRPPLSPK 15 1 A0A087WZ13;Q8IY67-2;Q8IY67;Q8IY67-3 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 0 AADVS(0.853)VT(0.146)HRPPLS(0.001)PK 83.883 0.0021606 32357000 2017.7 2034.5 1896.9 1295 2272.7 2704.2 2206.8 1969.2 2511.1 2314.8 TRUE FALSE FALSE 1993.107496 2063.141744 1929.914749 1444.733993 2156.715638 2531.410347 2394.245537 2026.175695 2286.500927 2254.661162 0.883994247 0.915056231 0.855966644 0.640776547 0.95655865 1.122745355 1.061909247 0.89866084 1.014121751 1 11.13869492 -8.514236578 24.98947115 0.910313063 1.032596648 0.234413743 0.110482331 532.1574887 1538771.423 0.016909744 0.035232571 3.06E-09 8.514236578 0.122283584 (ac)AAGGAAPETPAIS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 4 AAGGAAPETPAISPSKR 17 1 H0YNW5;H0YMM5 H0YNW5 DUT 1 0 AAGGAAPET(0.225)PAIS(0.642)PS(0.132)KR;AAGGAAPET(0.001)PAIS(0.945)PS(0.054)KR;AAGGAAPET(0.001)PAIS(0.901)PS(0.098)KR;AAGGAAPET(0.003)PAIS(0.939)PS(0.059)KR ;;; 145.94 1.07E-14 75227000 10080 9646.3 9069.6 8724 7445.7 6659.7 5594.4 5981.9 10298.7 9473.1 TRUE FALSE FALSE 9957.141083 9782.100865 9227.452583 9732.709928 7065.718145 6234.166663 6069.588196 6154.976839 9377.558478 9226.987496 1.079132391 1.060161929 1.000050405 1.054809051 0.765766524 0.675644859 0.657808217 0.667062445 1.016318542 1 13.17164399 -8.654370727 3.271986481 1.03883462 0.670399921 0.974817508 0.02732338 0.032796714 0.693835793 0.005253625 0.011091919 2.22E-09 8.654370727 -0.368434698 (ac)AAGGDHGS(ph)PDSYR ddPTM_HeLa_Romidepsin_16h_R1 4 AAGGDHGSPDSYR 13 0 A0A1B0GTG9;A0A1B0GWF8;A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566-2;P30566;B4DEP1;A0A1W2PRX2;A0A096LP72;A0A096LNY4;A0A096LNY5 A0A1B0GTG9 ADSL Adenylosuccinate lyase 1 0 AAGGDHGS(0.845)PDS(0.155)YR;AAGGDHGS(0.974)PDS(0.026)YR;AAGGDHGS(0.986)PDS(0.014)YR;AAGGDHGS(0.981)PDS(0.019)YR ;;; 106.29 7.03E-08 71569100 656.23 671.703 856.27 661.29 624.72 562.34 435.75 611.787 929.92 571.35 TRUE FALSE FALSE 648.2316163 681.1592525 871.1730202 737.7514613 592.8382072 526.4082889 472.7625941 629.4880916 846.7456262 556.5062446 1.164823616 1.22399211 1.565432605 1.325684066 1.065285813 0.94591623 0.849518938 1.131142908 1.521538409 1 9.120254066 -8.520804801 24.90887908 1.14985092 0.970037909 0.178875237 0.202735028 112.4076225 1350056.343 0.028589082 0.057916047 3.01E-09 8.520804801 -0.179813012 (ac)AAGTAAALAFLS(ph)QESR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGTAAALAFLSQESR 16 0 O75607 O75607 NPM3 Nucleoplasmin-3 1 0 AAGTAAALAFLS(0.871)QES(0.129)R 73.597 2.06E-07 0 379.98 183.21 321.15 210.11 275.49 262.34 253.35 380.45 218.42 269.8 TRUE FALSE FALSE 375.3486576 185.7892352 326.739481 234.4039068 261.4307173 245.5773207 274.8695427 391.4577205 198.8839682 262.7905571 1.428318665 0.706985963 1.243345593 0.891979945 0.994825386 0.934498269 1.045964306 1.489618671 0.756815505 1 8.037769626 -10.2887515 24.99441474 1.202261564 1.039702499 0 0.260762779 1383.710038 1266284.194 0.040982714 0.046871479 5.14E-11 10.2887515 -0.162559065 (ac)AAGTLYTYPENWR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGTLYTYPENWR 13 0 P26641 P26641 EEF1G Elongation factor 1-gamma 0 0 92.239 0.0021487 1599400 373.94 435.07 328.15 396.01 259.66 517.04 246.56 476.08 471.07 385.03 FALSE FALSE TRUE 369.3822754 441.1949269 333.8613131 441.7985395 246.4085813 484.0028127 267.5028002 489.8546237 428.9363194 375.0268651 0.984948839 1.176435525 0.890233058 1.178045043 0.657042479 1.29058171 0.7132897 1.306185421 1.143748247 1 8.550850137 -7.20437188 22.32686469 0.993971674 1.306193886 0.176150527 0.195133215 20286.12573 7935640.336 0.021508641 40.80207256 6.25E-08 7.20437188 0.312222212 (ac)AAIPS(ph)SGSLVATHDYYR ddPTM_HeLa_Romidepsin_16h_R1 1 AAIPSSGSLVATHDYYR 17 0 X6R7I6;Q9H3Y8-2;Q9H3Y8 X6R7I6 PPDPF Pancreatic progenitor cell differentiation and proliferation factor 1 0 AAIPS(0.54)S(0.309)GS(0.152)LVATHDYYR 112.64 0.0011594 3218500 264.25 131.53 375.29 149.34 246.19 447.15 291.42 250.38 333.21 331.91 TRUE FALSE FALSE 261.0292194 133.3816828 381.821765 166.6073935 233.6260056 418.5785581 316.1732075 257.6243503 303.4068631 323.2869304 0.807422741 0.41257988 1.181061556 0.515354559 0.722658368 1.294758677 0.977995637 0.796890706 0.938506431 1 8.336671374 -6.964296403 13.00806294 0.883035817 0.545908716 0.00601557 0.259242472 1562494.13 19190639.96 0.034408636 11350173.38 1.09E-07 6.964296403 -0.337127101 (ac)AAIPSSGS(ph)LVATHDYYR ddPTM_HeLa_Romidepsin_16h_R1 1 AAIPSSGSLVATHDYYR 17 0 X6R7I6;Q9H3Y8-2;Q9H3Y8 X6R7I6 PPDPF Pancreatic progenitor cell differentiation and proliferation factor 1 0 AAIPS(0.08)S(0.047)GS(0.873)LVATHDYYR 81.713 0.0084968 4875900 218.13 140.78 287.09 137.85 163.74 224.74 0 252.29 174.47 156.44 TRUE FALSE FALSE 215.4713477 142.7619045 292.086681 153.7888656 155.3837368 210.3798393 0 259.5896131 158.8649662 152.3756662 1.414079774 0.9369075 1.916885341 1.009274443 1.019741148 1.380665591 0 1.703615935 1.042587509 1 7.251488719 (ac)AALHT(ph)TPDSPAAQLER ddPTM_HeLa_Romidepsin_16h_R1 2 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 0 AALHT(0.588)T(0.356)PDS(0.056)PAAQLER;AALHT(0.782)T(0.02)PDS(0.198)PAAQLER ; 96.673 1.05E-06 19971000 363.49 148.9 252.4 204.658 54.529 203.41 177.79 268.128 272.35 328.12 TRUE FALSE FALSE 359.0596441 150.9962181 256.7929161 228.3215209 51.74618165 190.4127575 192.8914782 275.8858606 247.9903339 319.5953951 1.123481907 0.472460556 0.803493793 0.714408043 0.161911537 0.595793182 0.603548991 0.86323478 0.775950898 1 8.320102811 -10.26594583 24.97494703 1.058310908 0.597065696 0.376475236 0.204824717 196.9909619 1091730.284 0.031507345 0.036678734 5.42E-11 10.26594583 -0.461245211 (ac)AALHTTPDS(ph)PAAQLER ddPTM_HeLa_Romidepsin_16h_R1 2 AALHTTPDSPAAQLER 16 0 A6NFI3 A6NFI3 ZNF316 Zinc finger protein 316 1 0 AALHT(0.128)T(0.077)PDS(0.795)PAAQLER;AALHT(0.081)T(0.04)PDS(0.879)PAAQLER ; 129.36 5.61E-36 19456700 284.37 561.5 427.52 433.29 488.66 325.56 408.61 488.58 426.66 498.29 TRUE FALSE FALSE 280.9039891 569.4048117 434.9608063 483.3890285 463.7218568 304.7577667 443.3173232 502.7162914 388.498461 485.344354 0.578772549 1.17319756 0.896190102 0.995971262 0.955449163 0.6279207 0.913407809 1.035793014 0.800459422 1 8.922864899 -10.26709285 24.95882571 0.801087047 0.930104916 0.150835685 0.160305818 902.3042926 3983469.153 0.03387391 0.039292494 5.41E-11 10.26709285 0.129017868 (ac)AAPAQQTTQPGGGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AAPAQQTTQPGGGKR 15 1 H3BNW0;Q9NXG2 H3BNW0 THUMPD1 THUMP domain-containing protein 1 0 1 ; AAPAQQTTQPGGGK(1)R;AAPAQQTTQPGGGK(1)R 80.17 1.91E-05 1076180 0 0 0 0 0 0 0 0 0 57.207 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 55.72075389 0 0 0 0 0 0 0 0 0 1 5.800142872 -12.15782943 0.67715094 1.083625667 2.50E-23 0 0.307667284 0.06659167 0.049088893 0.041658112 0.0090835 6.95E-13 12.15782943 -1.083625667 (ac)AARDS(ph)DSEEDLVS(ph)YGTGLEPLEEGERPK ddPTM_HeLa_Romidepsin_16h_R1 1 AARDSDSEEDLVSYGTGLEPLEEGERPK 28 2 Q9BRR8;K7EQ19 Q9BRR8 GPATCH1 G patch domain-containing protein 1 2 0 AARDS(0.678)DS(0.331)EEDLVS(0.701)Y(0.224)GT(0.066)GLEPLEEGERPK 55.789 0.00039195 0 458.7 422.34 325.47 350.01 480.04 517.88 518.24 286.09 364.64 374.46 TRUE FALSE FALSE 453.109188 428.2857136 331.1346688 390.479803 455.5417675 484.7891394 562.2592927 294.3675628 332.0256851 364.7314752 1.242308983 1.174249394 0.907886188 1.0705953 1.248978491 1.32916727 1.541570528 0.80708023 0.910329126 1 8.510690895 -12.44964405 1.056347445 0.994712167 1.180972907 0.137141042 0.199145172 1.066422982 2.028939479 0.154828904 0.034308239 3.55E-13 12.44964405 0.18626074 (ac)AARDS(ph)DSEEDLVSYGTGLEPLEEGERPK ddPTM_HeLa_Romidepsin_16h_R1 1 AARDSDSEEDLVSYGTGLEPLEEGERPK 28 2 Q9BRR8;K7EQ19 Q9BRR8 GPATCH1 G patch domain-containing protein 1 1 0 AARDS(0.472)DS(0.472)EEDLVS(0.029)Y(0.026)GT(0.002)GLEPLEEGERPK 63.115 2.13E-08 2492900 188.83 258.62 164.06 203.24 226.71 301.05 270.03 193.38 158.72 222.22 TRUE FALSE FALSE 186.5284673 262.2608591 166.9153955 226.7395651 215.1401427 281.8138766 292.9663415 198.9751452 144.5236857 216.4466924 0.86177555 1.211664897 0.771161683 1.047553846 0.993963642 1.302001308 1.353526535 0.919280138 0.667710299 1 7.757867944 -8.390375082 4.909308978 0.952163573 1.206526802 0.301440582 0.17730676 0.178824878 6.380891132 0.020775315 0.04747473 4.07E-09 8.390375082 0.254363229 (ac)AAS(ph)PGSGSANPR ddPTM_HeLa_Romidepsin_16h_R1 2 AASPGSGSANPR 12 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 0 AAS(0.997)PGS(0.003)GSANPR;AAS(0.992)PGS(0.008)GS(0.001)ANPR ; 94.538 0.007564 9969600 68.71 62.273 0 132.98 119.12 0 0 0 0 0 TRUE FALSE FALSE 67.87253609 63.14968093 0 148.3557733 113.0408619 0 0 0 0 0 0 (ac)AASAAAAS(ph)AAAASAASGSPGPGEGSAGGEKR ddPTM_HeLa_Romidepsin_16h_R1 3 AASAAAASAAAASAASGSPGPGEGSAGGEKR 31 1 Q13263-2;Q13263 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 1 0 AAS(0.024)AAAAS(0.717)AAAAS(0.213)AAS(0.023)GS(0.023)PGPGEGSAGGEKR;AAS(0.028)AAAAS(0.496)AAAAS(0.159)AAS(0.115)GS(0.201)PGPGEGSAGGEKR;AAS(0.012)AAAAS(0.746)AAAAS(0.192)AAS(0.039)GS(0.011)PGPGEGSAGGEKR ;; 75.297 5.34E-13 671431000 3722.01 4218.8 4150.5 4315.2 5345.6 5570.9 5212.2 5305.5 4702.1 4477.2 TRUE FALSE FALSE 3676.64471 4278.192377 4222.737711 4814.143728 5072.794085 5214.937469 5654.924138 5459.006272 4281.532399 4360.881699 0.843096641 0.981038394 0.968322005 1.103938162 1.163249644 1.195844746 1.296738717 1.251812512 0.981804299 1 12.09040414 -8.91215614 1.094037956 0.92641413 1.263647514 0.885210122 0.046925586 0.140703372 0.331456621 0.010604062 0.02759646 1.22E-09 8.91215614 0.337233384 (ac)AASAAAASAAAASAAS(ph)GSPGPGEGSAGGEK ddPTM_HeLa_Romidepsin_16h_R1 1 AASAAAASAAAASAASGSPGPGEGSAGGEK 30 0 Q13263-2;Q13263 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 1 0 AAS(0.033)AAAAS(0.031)AAAAS(0.045)AAS(0.52)GS(0.371)PGPGEGS(0.001)AGGEK 49.643 1.05E-08 0 1252.2 1141.3 895.03 1826.5 1015 1397.8 915.04 1248.2 1163.8 1565.4 TRUE FALSE FALSE 1236.937705 1157.367251 910.6076217 2037.688524 963.2007625 1308.485091 992.7634748 1284.314698 1059.706813 1524.730682 0.81124996 0.759063397 0.597225223 1.336425211 0.63171862 0.858174566 0.651107429 0.842322328 0.695012454 1 10.57433872 -12.07856629 0.767713751 1.005763036 0.809855575 0 0.217762706 1.208175402 1.246205985 0.141361756 0.038157372 8.35E-13 12.07856629 -0.195907461 (ac)AASAAAASAAAASAASGS(ph)PGPGEGSAGGEK ddPTM_HeLa_Romidepsin_16h_R1 1 AASAAAASAAAASAASGSPGPGEGSAGGEK 30 0 Q13263-2;Q13263 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 1 0 AAS(0.125)AAAAS(0.125)AAAAS(0.076)AAS(0.042)GS(0.631)PGPGEGSAGGEK 62.173 2.07E-08 15717000 2065.4 2074.7 2342.1 1629.8 2273.1 2474.7 2470.6 2329.2 2574.2 2334.6 TRUE FALSE FALSE 2040.22611 2103.907681 2382.863268 1818.245144 2157.095225 2316.574657 2680.452702 2396.591727 2343.957105 2273.946755 0.897218066 0.925222931 1.047897565 0.799598821 0.948612899 1.018746218 1.178766695 1.053934848 1.030788034 1 11.15098276 -7.999301031 3.889713919 0.944576832 1.116013263 0.44990457 0.072833486 0.129535945 4.422891599 0.009788217 0.030030055 1.00E-08 7.999301031 0.171436431 (ac)AATLGAGT(ph)PPRPQAR ddPTM_HeLa_Romidepsin_16h_R1 1 AATLGAGTPPRPQAR 15 1 A0A075B730 A0A075B730 EPPK1 1 0 AAT(0.002)LGAGT(0.998)PPRPQAR 79.639 0.0027713 29187000 305.93 415.85 323.83 757.41 465.7 420.09 274.89 477.06 379.71 441.72 TRUE FALSE FALSE 302.2012075 421.7043472 329.4661253 844.9853079 441.9335912 393.2476048 298.2391497 490.8629784 345.7477866 430.2440507 0.702394855 0.98015149 0.765765674 1.963967442 1.027169558 0.914010558 0.693185993 1.140894285 0.803608524 1 8.749011433 (ac)AAVK(ac)TLNPK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVKTLNPK 9 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 1 AAVK(1)TLNPK 43.769 0.0016564 748220 1453.3 1273.1 1267.4 1369.9 906.09 866.87 1593.2 933.24 1931.5 1779.4 FALSE TRUE FALSE 1435.586621 1291.022735 1289.458565 1528.294284 859.8488462 811.4798047 1728.526368 960.241827 1758.741802 1733.170931 0.828300657 0.7448906 0.74398811 0.881790858 0.496113125 0.468205294 0.997320193 0.554037579 1.014753808 1 10.75919823 -10.81283729 0.40609674 1.012197515 0.655534266 0.408243623 0.152757006 0.81052251 0.356050553 0.11216249 0.077767328 1.54E-11 10.81283729 -0.356663249 (ac)ADAAPQLGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ADAAPQLGKR 10 1 Q96C86 Q96C86 DCPS m7GpppX diphosphatase 0 1 ; ADAAPQLGK(1)R;ADAAPQLGK(1)R 47.603 0.0016214 7681000 289.3 186.937 353.3 906.88 2225.9 3235.6 3426 3542.6 262.89 172.121 FALSE TRUE FALSE 285.7739003 189.568704 359.4490383 1011.737733 2112.304017 3028.855602 3717.004354 3645.099542 239.37646 167.6492716 1.704593749 1.130745766 2.144053683 6.034847172 12.59954187 18.06661952 22.17131228 21.74241204 1.42784074 1 7.389302405 -8.548136164 1.173571081 1.255706338 22.49673056 0.996934039 0.47078589 0.018521217 0.048458302 0.079273735 0.269832906 2.83E-09 8.548136164 21.24102422 (ac)ADAWEEIRR ddPTM_HeLa_Romidepsin_16h_R1 2 ADAWEEIRR 9 1 O94874;O94874-3 O94874 UFL1 E3 UFM1-protein ligase 1 0 0 ; ; 94.302 0.0035968 6976200 794.64 858.98 880.5 1006.01 638.61 932.31 845.97 718.2 728.36 721.24 FALSE FALSE TRUE 784.954622 871.072743 895.8247331 1122.32961 606.0193487 872.7383999 917.8266707 738.9799839 663.2136574 702.5020808 1.117369818 1.239957527 1.275191573 1.597617488 0.862658439 1.242328562 1.306510964 1.051925687 0.944073584 1 9.456358688 -10.73509827 1.319886253 1.033446485 1.230095668 0.219038788 0.179681574 0.459442892 1.663235321 0.038402877 0.03689006 1.84E-11 10.73509827 0.196649183 (ac)ADDVDQQQTTNTVEEPLDLIR ddPTM_HeLa_Romidepsin_16h_R1 2 ADDVDQQQTTNTVEEPLDLIR 21 0 P62310 P62310 LSM3 U6 snRNA-associated Sm-like protein LSm3 0 0 ; ; 249.28 2.26E-243 9892100 0 0 0 0 0 0 0 62.121 58.519 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 63.91837312 53.28491408 0 0 (ac)ADEAALALQPGGS(ph)PSAAGADR ddPTM_HeLa_Romidepsin_16h_R1 4 ADEAALALQPGGSPSAAGADR 21 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 ADEAALALQPGGS(0.894)PS(0.106)AAGADR;ADEAALALQPGGS(0.85)PS(0.15)AAGADR;ADEAALALQPGGS(0.638)PS(0.362)AAGADR;ADEAALALQPGGS(0.875)PS(0.125)AAGADR ;;; 137.12 2.21E-13 36149600 851.95 773.12 933.28 698.85 1003.18 512.54 966.948 763.44 1059.09 819.17 TRUE FALSE FALSE 841.5661057 784.0040037 949.5233469 779.6543252 951.9839812 479.7903481 1049.080539 785.5289319 964.3623379 797.8878453 1.054742356 0.982599257 1.190046136 0.977147766 1.193130071 0.601325551 1.314822058 0.984510463 1.208643976 1 9.640042159 (ac)ADEAALALQPGGSPS(ph)AAGADREAASSPAGEPLR ddPTM_HeLa_Romidepsin_16h_R1 1 ADEAALALQPGGSPSAAGADREAASSPAGEPLR 33 1 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 ADEAALALQPGGS(0.335)PS(0.654)AAGADREAAS(0.005)S(0.006)PAGEPLR 48.163 3.40E-11 17509000 742.54 926.87 522.59 586.13 821.07 703.8 677.51 624.24 921.39 728.62 TRUE FALSE FALSE 733.4896369 939.9185002 531.6854597 653.9011084 779.1677341 658.8294514 735.0576825 642.3013995 838.9785707 709.6903474 1.033534752 1.324406488 0.7491795 0.921389323 1.097898171 0.928333679 1.03574423 0.905044576 1.182175542 1 9.471045874 (ac)ADEELEALRR ddPTM_HeLa_Romidepsin_16h_R1 2 ADEELEALRR 10 1 O14737;Q3HM38;X6R2P6;K7ESJ4;O14737-2 O14737 PDCD5 Programmed cell death protein 5 0 0 ; ; 76.478 0.00862 41125000 2061.5 1792.53 1587.85 1558.36 1690.41 1602.69 1524.79 1919.32 1938.95 1803.19 FALSE FALSE TRUE 2036.373645 1817.765284 1615.485863 1738.544916 1604.14207 1500.283281 1654.305625 1974.852496 1765.525456 1756.342864 1.159439701 1.034971771 0.919800966 0.989866473 0.913342208 0.854208658 0.941903576 1.124411717 1.005228246 1 10.77835879 -9.922774285 5.237342002 1.076351022 0.951956003 0.238910125 0.078274283 0.189332286 9.275017293 0.014141582 0.018659532 1.19E-10 9.922774285 -0.124395019 (ac)ADEK(ac)PKEGVK ddPTM_HeLa_Romidepsin_16h_R1 1 ADEKPKEGVK 10 2 P61956-2;P61956 P61956-2 SUMO2 Small ubiquitin-related modifier 2 0 1 ADEK(0.978)PK(0.022)EGVK 75.378 0.0054924 29661000 7548 6335.5 5584.4 8928 6102.4 5653.9 5866.2 6426.9 6787.5 5763 FALSE TRUE FALSE 7456.002073 6424.691335 5681.594139 9960.297368 5790.971757 5292.634037 6364.474882 6612.852212 6180.409 5613.276429 1.328279868 1.144552814 1.012170737 1.774417756 1.031656258 0.942877855 1.133825309 1.1780735 1.101034143 1 12.45462739 -6.914986564 15.86563405 1.165243778 1.465184998 0.000309782 0.22830701 81328729.78 198616861.9 0.031997218 841788991 1.22E-07 6.914986564 0.29994122 (ac)ADELS(ph)EKQVYDAHTK ddPTM_HeLa_Romidepsin_16h_R1 1 ADELSEKQVYDAHTK 15 1 C9JKI3;Q03135-2 C9JKI3 CAV1 Caveolin 1 0 ADELS(0.999)EKQVY(0.001)DAHTK 55.335 0.0099091 10078000 3601.8 4877 3454.2 5077 4169 5118.4 2664.9 4406.2 4275 4272.6 TRUE FALSE FALSE 3557.899876 4945.658534 3514.318902 5664.026628 3956.240373 4791.350759 2891.256539 4533.686445 3892.633293 4161.597236 0.85493614 1.188403936 0.844463965 1.361022297 0.950654316 1.151324957 0.694746842 1.089410192 0.935370021 1 12.02292163 -10.29844171 24.98602136 0.931497631 1.032395965 0.073122262 0.177849604 1211.252805 817901.1647 0.028867792 0.033012005 5.03E-11 10.29844171 0.100898334 (ac)ADFDTYDDR ddPTM_HeLa_Romidepsin_16h_R1 1 ADFDTYDDR 9 0 Q15056;Q15056-2 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 0 112.41 0.00039187 23878000 254.11 203.25 179.14 0 146.7 113.75 112.68 111.21 169.97 230.62 FALSE FALSE TRUE 251.0128096 206.1113588 182.2578566 0 139.2133516 106.4817421 122.2510364 114.4276859 154.7674575 224.6284592 1.117457737 0.917565653 0.811374735 0 0.619749395 0.474034958 0.544236633 0.509408676 0.688993096 1 7.81139691 -9.548921572 3.692323684 1.045054544 0.444209685 0.560299326 0.201363794 0.08136918 2.393172249 0.0255092 0.037657769 2.83E-10 9.548921572 -0.600844859 (ac)ADGGS(ph)PFLGRR ddPTM_HeLa_Romidepsin_16h_R1 1 ADGGSPFLGRR 11 1 O60504-2;E5RIA0;E5RJP2 O60504-2 SORBS3 Vinexin 1 0 ADGGS(1)PFLGRR 64.224 0.0099512 42510000 434.86 436.9 334.96 440.16 364.82 333.95 235.3 456 363.57 333.6 TRUE FALSE FALSE 429.5597591 443.0506897 340.7898383 491.0533702 346.2018741 312.6116728 255.2863761 469.1936406 331.0513886 324.9330239 1.321994773 1.363513885 1.048800255 1.511244885 1.065456105 0.962080336 0.785658451 1.443970314 1.018829618 1 8.343998566 -8.546056683 24.99621197 1.191111951 1.03235992 0.089278485 0.21702981 408.3409522 440372.9719 0.031756674 0.063515919 2.84E-09 8.546056683 -0.158752031 (ac)ADGS(ph)LTGGGLEAAAMAPER ddPTM_HeLa_Romidepsin_16h_R1 2 ADGSLTGGGLEAAAMAPER 19 0 Q8NEM2 Q8NEM2 SHCBP1 SHC SH2 domain-binding protein 1 1 0 ADGS(0.782)LT(0.218)GGGLEAAAMAPER;ADGS(0.74)LT(0.26)GGGLEAAAMAPER ; 62.077 0.018003 5185400 166.82 238.625 132.4 276.66 315.3 145.06 316.94 147.72 262.31 134.3 TRUE FALSE FALSE 164.7867337 241.984369 134.7043665 308.6487309 299.2090645 135.7911342 343.8608757 151.9940451 238.8483366 130.8108666 1.259732757 1.849879717 1.029764345 2.359503754 2.287341045 1.038072277 2.628687391 1.161937452 1.825905926 1 7.031338582 -10.22885729 0.83403198 1.063332217 1.863973108 0.031073486 0.583186256 0.483008139 0.680032214 0.116069023 0.140862177 5.90E-11 10.22885729 0.800640891 (ac)ADHNPDSDST(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ADHNPDSDSTPR 12 0 Q96BT3;H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2;H3BQ71 Q96BT3 CENPT Centromere protein T 1 0 ADHNPDS(0.001)DS(0.065)T(0.934)PR;ADHNPDS(0.001)DS(0.18)T(0.819)PR ; 108.32 2.56E-05 6302800 298.19 199.46 154.37 224.7 275.4 55.733 222.534 198.88 183.04 197.292 TRUE FALSE FALSE 294.5555456 202.2680031 157.0567451 250.6808712 261.3453103 52.17184117 241.4360324 204.634279 166.668444 192.1663254 1.532815622 1.052567367 0.817295875 1.304499478 1.359995357 0.271493151 1.256390951 1.064881053 0.867313478 1 7.586211735 -9.039328985 0.929876033 1.231836248 0.954299122 0 0.344052733 1.103566986 1.863631706 0.063032359 0.163482307 9.13E-10 9.039328985 -0.277537126 (ac)ADHS(ph)FS(ph)DGVPSDSVEAAK ddPTM_HeLa_Romidepsin_16h_R1 2 ADHSFSDGVPSDSVEAAK 18 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;E9PNW0;E9PJJ2;E9PKI2;E9PP22;C9J1B1 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 2 0 ADHS(0.999)FS(0.632)DGVPS(0.308)DS(0.06)VEAAK;ADHS(0.996)FS(0.996)DGVPS(0.002)DS(0.006)VEAAK ; 84.842 6.30E-21 16028700 2496.78 2972.83 2589.5 2664.7 3637.6 4109.4 3357.87 3451.22 2925.87 2906.9 TRUE FALSE FALSE 2466.348285 3014.681579 2634.569161 2972.805152 3451.959698 3846.822602 3643.087394 3551.075606 2664.172859 2831.378319 0.871076913 1.064739939 0.930489982 1.049949818 1.219179957 1.358639563 1.286683369 1.254186197 0.94094556 1 11.46728881 -8.803828555 2.164453005 0.948183082 1.299937958 0.886710133 0.054257167 0.078959222 0.754108705 0.009760519 0.020724329 1.57E-09 8.803828555 0.351754877 (ac)ADHS(ph)FSDGVPSDSVEAAK ddPTM_HeLa_Romidepsin_16h_R1 6 ADHSFSDGVPSDSVEAAK 18 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;E9PNW0;E9PJJ2;E9PKI2;E9PP22;C9J1B1 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 ADHS(0.718)FS(0.282)DGVPS(0.001)DSVEAAK;ADHS(0.964)FS(0.036)DGVPSDSVEAAK;ADHS(1)FSDGVPSDSVEAAK;ADHS(0.768)FS(0.229)DGVPS(0.001)DS(0.002)VEAAK;ADHS(0.973)FS(0.027)DGVPSDSVEAAK;ADHS(0.987)FS(0.013)DGVPSDSVEAAK ;;;;; 141.13 1.52E-76 355402500 9988.08 9462.72 9027.53 9559.37 10668.24 10952.42 7835.78 9872.08 10431.53 10045.61 TRUE FALSE FALSE 9866.341439 9595.936421 9184.650373 10664.66934 10123.7999 10252.59571 8501.350958 10157.71306 9498.507831 9784.623604 1.008351659 0.980715949 0.938682033 1.089941705 1.034664215 1.047827298 0.868848032 1.03813018 0.970758633 1 13.25630064 -7.801965367 24.99999022 1.008389763 0.953487622 0.139183432 0.055078269 174.8637527 107870.9906 0.006892698 0.020678418 1.58E-08 7.801965367 -0.054902141 (ac)ADHSFS(ph)DGVPSDSVEAAK ddPTM_HeLa_Romidepsin_16h_R1 1 ADHSFSDGVPSDSVEAAK 18 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;E9PNW0;E9PJJ2;E9PKI2;E9PP22;C9J1B1 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 ADHS(0.413)FS(0.581)DGVPSDS(0.005)VEAAK 89.311 8.56E-11 119100000 3473 3039 3114.1 3465.9 3301.3 2883.7 2207.2 2983 3831.9 3422.4 TRUE FALSE FALSE 3430.66974 3081.783122 3168.299604 3866.643666 3132.822342 2699.440877 2394.679513 3069.308399 3489.165267 3333.485555 1.029153924 0.924492718 0.950446478 1.159940129 0.939803785 0.809795283 0.718371048 0.920750472 1.046701781 1 11.70281576 -8.380746817 3.929261633 1.011583073 0.806740294 0.585613698 0.075377015 0.113232836 3.037481908 0.010106995 0.02373332 4.16E-09 8.380746817 -0.204842779 (ac)ADK(ac)EAAFDDAVEER ddPTM_HeLa_Romidepsin_16h_R1 1 ADKEAAFDDAVEER 14 1 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 1 ADK(1)EAAFDDAVEER 74.698 0.0032565 0 277.27 200.63 120.61 167.77 126.38 61.948 183.76 113.36 62.963 176.11 FALSE TRUE FALSE 273.8905266 203.4544744 122.7091665 187.1683568 119.930357 57.98972273 199.3685698 116.6398927 57.33143159 171.5346368 1.596706832 1.18608392 0.715360867 1.09114031 0.699161168 0.338064217 1.162264214 0.679978662 0.33422656 1 7.422356109 -9.842932357 5.05684973 1.286515945 0.788816713 0 0.393374239 0.163842287 7.356288675 0.048619823 0.064680829 1.44E-10 9.842932357 -0.497699232 (ac)ADKEAAFDDAVEER ddPTM_HeLa_Romidepsin_16h_R1 2 ADKEAAFDDAVEER 14 1 Q09028-3;Q09028;E9PNS2;E9PIC4;E9PNS6 Q09028-3 RBBP4 Histone-binding protein RBBP4 0 0 ; ; 144.7 2.04E-16 77042000 7535.3 7021.9 6440.4 7476.6 6493.3 6438.9 5845.8 6730.8 7950.7 6834.7 FALSE FALSE TRUE 7443.456865 7120.754493 6552.49246 8341.07967 6161.922671 6027.475071 6342.342106 6925.545079 7239.569479 6657.133509 1.118117408 1.069642735 0.984281366 1.252953641 0.925612001 0.905415982 0.952713671 1.040319391 1.087490505 1 12.70068539 (ac)ADKPDMGEIASFDK ddPTM_HeLa_Romidepsin_16h_R1 5 ADKPDMGEIASFDK 14 1 P63313 P63313 TMSB10 Thymosin beta-10 0 0 ;;;; ;;;; 78.342 0.0024227 215641000 10993.98 9957.27 10143.28 9831.58 10881.5 10994.87 9710 11118.17 11889.09 10751.47 FALSE FALSE TRUE 10859.98114 10097.44871 10319.81953 10968.35354 10326.17645 10292.33329 10534.76716 11439.85671 10825.70001 10472.14526 1.037034998 0.964219695 0.9854542 1.047383632 0.986061231 0.9828295 1.005979854 1.092408138 1.033761445 1 13.35426939 (ac)ADLDS(ph)PPKLSGVQQPSEGVGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 ADLDSPPKLSGVQQPSEGVGGGR 23 1 E9PRT5;H3BSD2;H3BMV9;A0A6I8PIQ6;Q9H9E3-2;Q9H9E3 E9PRT5 COG4 Conserved oligomeric Golgi complex subunit 4 1 0 ADLDS(0.997)PPKLS(0.003)GVQQPSEGVGGGR;ADLDS(0.991)PPKLS(0.009)GVQQPSEGVGGGR ; 68.401 4.85E-06 16549900 893.84 861.99 587.67 685.93 899.9 964.2 730.44 867.08 987.95 845.22 TRUE FALSE FALSE 882.9455343 874.1251178 597.8981498 765.240454 853.974745 902.5907318 792.4835554 892.1675918 899.5852776 823.2610626 1.072497625 1.061783628 0.726255834 0.929523439 1.037307343 1.096360283 0.962615131 1.083699488 1.092709614 1 9.685206183 -7.23083358 21.61759429 1.009962084 1.083700244 0.045599369 0.105335808 5263.720351 3717504.608 0.014659716 1.690909311 5.88E-08 7.23083358 0.07373816 (ac)ADLEEQLS(ph)DEEKVR ddPTM_HeLa_Romidepsin_16h_R1 2 ADLEEQLSDEEKVR 14 1 C9JUG7;F8W9N7;P47755-2;P47755 C9JUG7 CAPZA2 F-actin-capping protein subunit alpha-2 1 0 ADLEEQLS(1)DEEKVR;ADLEEQLS(1)DEEKVR ; 142.39 3.30E-11 45422000 1915.44 1521.72 1796.72 1726.98 2098.44 1756.72 1684.92 1502.01 1836.19 2086.61 TRUE FALSE FALSE 1892.093881 1543.142814 1827.991158 1926.661553 1991.348776 1644.471262 1828.037063 1545.46829 1671.956568 2032.399571 0.930965499 0.759271374 0.899425085 0.947973804 0.979801809 0.809127932 0.899447672 0.760415575 0.822651506 1 10.98896835 -16.52287875 0.029449657 1.839244732 0.313046981 0 0.089489221 978.2906374 2.314135132 90.41692958 39.40016165 3.00E-17 16.52287875 -1.526197751 (ac)ADLEEQLSDEEKVR ddPTM_HeLa_Romidepsin_16h_R1 2 ADLEEQLSDEEKVR 14 1 C9JUG7;F8W9N7;P47755-2;P47755 C9JUG7 CAPZA2 F-actin-capping protein subunit alpha-2 0 0 ; ; 130.01 6.41E-07 5094800 1382.16 1590.53 1459.52 1705.85 1778.64 1466.12 1389.77 1435.75 1725.73 1724.7 FALSE FALSE TRUE 1365.313702 1612.921523 1484.922333 1903.088403 1687.869364 1372.439664 1507.817029 1477.291161 1571.376387 1679.892045 0.812738953 0.960134032 0.883939142 1.132863513 1.004748709 0.816980869 0.897567813 0.879396486 0.935403195 1 10.71415281 -8.250419728 24.90845813 0.933678732 0.86794034 0.168037492 0.083984074 1525.584547 3448374.916 0.014436552 0.03643344 5.62E-09 8.250419728 -0.065738393 (ac)ADQLTEEQVTEFK ddPTM_HeLa_Romidepsin_16h_R1 2 ADQLTEEQVTEFK 13 0 P27482 P27482 CALML3 Calmodulin-like protein 3 0 0 ; ; 137.98 1.73E-06 14361200 6699.4 6531.3 6765.9 6038.1 7586.3 7736.1 6936.8 7760.8 7553.8 7140.9 FALSE FALSE TRUE 6617.745136 6623.247813 6883.657651 6736.253532 7199.142803 7241.788177 7526.011619 7985.346503 6878.169209 6955.378389 0.951457242 0.952248381 0.989688449 0.968495624 1.035046895 1.041178175 1.082042011 1.148082255 0.988899356 1 12.76391329 -7.559844906 0.784475851 0.974374863 1.201497499 0.900464789 0.018657457 0.462858114 0.264332211 0.003803774 0.083395236 2.76E-08 7.559844906 0.227122636 (ac)ADSGT(ph)AGGAALAAPAPGPGSGGPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 ADSGTAGGAALAAPAPGPGSGGPGPR 26 0 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 1 0 ADS(0.002)GT(0.998)AGGAALAAPAPGPGSGGPGPR 171.26 9.73E-49 0 0 67.014 0 0 131 0 108.12 0 0 126.04 TRUE FALSE FALSE 0 67.95742485 0 0 124.3145812 0 117.3037101 0 0 122.7654626 0 0.553554912 0 0 1.012618521 0 0.955510675 0 0 1 6.939760937 -12.48949435 1.217616476 1.002144981 0.300143708 0 0.488520409 0.432483101 1.141686355 0.254308394 0.061207988 3.24E-13 12.48949435 -0.702001273 (ac)ADSS(ph)PALSLR ddPTM_HeLa_Romidepsin_16h_R1 1 ADSSPALSLR 10 0 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 0 ADS(0.224)S(0.776)PALSLR 118.23 2.68E-13 9679500 355.19 73.746 131.59 91.096 279.48 288.9 136.08 258.84 269.1 191.3 TRUE FALSE FALSE 350.8608077 74.78419812 133.8802688 101.6289481 265.2170927 270.4402224 147.6386318 266.329127 245.031022 186.3299984 1.883007624 0.401353506 0.718511619 0.54542451 1.423373021 1.45140463 0.792350309 1.429341111 1.315037965 1 7.541716151 -10.26955321 24.97720067 1.416975804 0.969859235 0.192690001 0.405975252 832.9513783 2564110.802 0.081916104 0.094527705 5.38E-11 10.26955321 -0.447116568 (ac)AEAPAS(ph)PAPLSPLEVELDPEFEPQSRPR ddPTM_HeLa_Romidepsin_16h_R1 2 AEAPASPAPLSPLEVELDPEFEPQSRPR 28 1 O43524 O43524 FOXO3 Forkhead box protein O3 1 0 AEAPAS(0.854)PAPLS(0.146)PLEVELDPEFEPQSRPR;AEAPAS(0.528)PAPLS(0.472)PLEVELDPEFEPQSRPR ; 71.651 0.00018988 6744100 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)AEAPASPAPLS(ph)PLEVELDPEFEPQSRPR ddPTM_HeLa_Romidepsin_16h_R1 1 AEAPASPAPLSPLEVELDPEFEPQSRPR 28 1 O43524 O43524 FOXO3 Forkhead box protein O3 1 0 AEAPAS(0.02)PAPLS(0.98)PLEVELDPEFEPQSRPR 103.67 1.08E-09 1374600 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)AEAS(ph)PHPGR ddPTM_HeLa_Romidepsin_16h_R1 4 AEASPHPGR 9 0 U3KQF4;K7EIY6;Q9BV68 U3KQF4 RNF126 E3 ubiquitin-protein ligase RNF126 1 0 AEAS(1)PHPGR;AEAS(1)PHPGR;AEAS(1)PHPGR;AEAS(1)PHPGR ;;; 85.533 0.0032324 19533100 324.83 207.14 223.95 764.066 115.67 210.781 192.28 218.99 268.35 364.21 TRUE FALSE FALSE 320.870847 210.0561224 227.8477558 852.410906 109.7669283 197.3127744 208.6122584 225.3261301 244.3481039 354.7477717 0.904504193 0.592128095 0.642281006 2.402864722 0.30942246 0.556205818 0.588057981 0.635172785 0.688793908 1 8.470649812 (ac)AEDLDELLDEVESK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDLDELLDEVESK 14 0 Q96NL8 Q96NL8 C8orf37 Protein C8orf37 0 0 146.71 1.19E-42 1854300 638.91 560.12 402.87 566.83 551.77 623.55 410.74 412.46 640.52 490.92 FALSE FALSE TRUE 631.1227192 568.0053841 409.8817834 632.3695516 523.611118 583.7071674 445.6282453 424.3938793 583.230287 478.1658276 1.319882523 1.187883682 0.857195892 1.322490055 1.095040858 1.220721209 0.931953351 0.887545397 1.219723898 1 8.901367221 -7.690071894 6.419143979 1.147569283 0.902539828 0.342050082 0.134916956 0.202975051 14.091298 0.021110067 0.080412723 2.04E-08 7.690071894 -0.245029455 (ac)AEDVSSAAPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 AEDVSSAAPSPR 12 0 E5RFJ5;P54274-2;P54274 E5RFJ5 TERF1 Telomeric repeat-binding factor 1 1 0 AEDVSSAAPS(1)PR;AEDVSSAAPS(1)PR ; 102.5 0.0007576 13541600 1337.35 941.98 1184.5 1256.35 1168.65 1172.32 1339.79 957.79 1028.63 1355.13 TRUE FALSE FALSE 1321.049864 955.2412192 1205.115726 1401.615098 1109.00943 1097.412535 1453.591729 985.5021425 936.6267565 1319.923527 1.000853335 0.723709518 0.913019354 1.061891139 0.840207335 0.8314213 1.101269656 0.746635788 0.709606835 1 10.36623863 (ac)AEEES(ph)DQEAER ddPTM_HeLa_Romidepsin_16h_R1 1 AEEESDQEAER 11 0 A0A1B0GWA0 A0A1B0GWA0 1 0 AEEES(1)DQEAER 114.71 0.0038812 1737900 0 0 66.106 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 67.2565472 0 0 0 0 0 0 0 0 (ac)AEEGIAAGGVMDVNTALQEVLK ddPTM_HeLa_Romidepsin_16h_R1 2 AEEGIAAGGVMDVNTALQEVLK 22 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 0 ; ; 130.47 1.48E-23 12166300 3121.9 2793.9 2723.3 3661.6 2675.2 3456 2220.8 3037.8 3511.1 3062.2 FALSE FALSE TRUE 3083.849082 2833.232598 2770.697894 4084.97142 2538.674561 3235.172754 2409.434697 3125.69395 3197.058422 2982.643603 1.033931469 0.949906518 0.928940317 1.369580803 0.851149148 1.084666217 0.807818505 1.047960925 1.071887509 1 11.54237588 -7.786220373 24.97238591 1.022554854 0.927889375 0.079703095 0.141284224 387.0869654 390076.6041 0.01759316 0.052812118 1.64E-08 7.786220373 -0.094665479 (ac)AENDVDNELLDYEDDEVETAAGGDGAEAPAKK ddPTM_HeLa_Romidepsin_16h_R1 4 AENDVDNELLDYEDDEVETAAGGDGAEAPAKK 32 1 Q5STU3;Q13838;Q13838-2;A0A0G2JHN7;F6U6E2;F6S2B7;F6R6M7;F6S4E6;A0A0A0MT12;F6TRA5;F6WLT2 Q5STU3 DDX39B Spliceosome RNA helicase DDX39B 0 0 ;;; ;;; 147.87 8.66E-25 42136700 17839.3 17536.7 17627.7 17694.5 17307.9 17721.8 15289.61 17218.7 19085.7 16263.9 FALSE FALSE TRUE 17621.86775 17783.58212 17934.50272 19740.42135 16424.61328 16589.43417 16588.30909 17716.89592 17378.62719 15841.36153 1.112396034 1.122604398 1.132131395 1.24613161 1.036818284 1.047222749 1.047151727 1.118394772 1.097041258 1 13.95140872 -12.10764422 0.877997665 1.0001304 1.10702033 0.042435017 0.064024604 0.58610956 0.818865215 0.039655115 0.011717609 7.80E-13 12.10764422 0.106889929 (ac)AENHCELLS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 AENHCELLSPAR 12 0 H3BSS5;Q9NXV2 H3BSS5 KCTD5 BTB/POZ domain-containing protein KCTD5 1 0 AENHCELLS(1)PAR;AENHCELLS(1)PAR ; 65.234 0.00073046 11150800 1172.27 796.3 832.4 896.69 920.55 867.22 985.1 874.76 844.25 893.65 TRUE FALSE FALSE 1157.981922 807.5103323 846.8875728 1000.369517 873.5708985 811.8074408 1068.774369 900.0698005 768.7381655 870.4328442 1.330351824 0.927711239 0.972949928 1.149278228 1.003605165 0.932647988 1.227865397 1.034048527 0.883167691 1 9.765589185 -10.24051202 24.86817869 1.155999491 1.039641017 0 0.143657188 1230.922044 1462718.157 0.024476299 0.029960315 5.75E-11 10.24051202 -0.116358474 (ac)AENVVEPGPPSAK(ac)RPK ddPTM_HeLa_Romidepsin_16h_R1 2 AENVVEPGPPSAKRPK 16 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 1 ; AENVVEPGPPSAK(1)RPK;AENVVEPGPPSAK(1)RPK 116.24 5.40E-11 13593600 2671.1 2858.3 2871.6 3682.2 3672.4 3390.5 3041.2 3299.4 2920.8 2833.8 FALSE TRUE FALSE 2638.543606 2898.539222 2921.578993 4107.953289 3484.983724 3173.857992 3299.519452 3394.862933 2659.556333 2760.177467 0.955932594 1.050127847 1.058475054 1.488293176 1.262594078 1.149874611 1.195401198 1.229943717 0.963545411 1 11.43054531 -9.492048597 14.39772965 0.98727561 1.256658635 0.69513937 0.086727513 1.758952647 820.9926362 0.013631444 0.020723758 3.22E-10 9.492048597 0.269383025 (ac)AEQDVENDLLDYDEEEEPQAPQESTPAPPK ddPTM_HeLa_Romidepsin_16h_R1 2 AEQDVENDLLDYDEEEEPQAPQESTPAPPK 30 0 O00148;K7ENP6;K7EL56;K7EIL8;K7EN69;K7EQN7;O00148-3;O00148-2 O00148 DDX39A ATP-dependent RNA helicase DDX39A 0 0 ; ; 72.848 2.22E-09 11570700 21172.6 20671.1 20272.9 16712.8 20666 21677.6 17665.6 20362.9 22573.3 20757.5 FALSE FALSE TRUE 20914.54021 20962.10829 20625.74132 18645.21257 19611.3369 20292.47132 19166.11562 20952.06838 20554.28751 20218.21716 1.034440378 1.036793112 1.020156286 0.92219865 0.969983493 1.003672637 0.947962695 1.036296535 1.016622156 1 14.30336817 (ac)AES(ph)DWDTVTVLR ddPTM_HeLa_Romidepsin_16h_R1 1 AESDWDTVTVLR 12 0 O60869-2;O60869-3;O60869 O60869-2 EDF1 Endothelial differentiation-related factor 1 1 0 AES(0.99)DWDT(0.007)VT(0.003)VLR 59.155 0.0022094 0 127.59 134.19 135.04 148.79 0 57.125 0 148.32 76.482 115.36 TRUE FALSE FALSE 126.034884 136.0791303 137.3903146 165.9937999 0 53.47489686 0 152.6114052 69.64125837 112.3629306 1.121676725 1.211067829 1.222737017 1.477300379 0 0.475912266 0 1.358200649 0.619788555 1 6.812022347 -8.764560143 24.9999996 1.111610444 0.427017936 0.380636831 0.405536524 53.22525233 426384.9257 0.050690826 0.094780674 1.72E-09 8.764560143 -0.684592508 (ac)AESDWDTVTVLR ddPTM_HeLa_Romidepsin_16h_R1 1 AESDWDTVTVLR 12 0 O60869-2;O60869-3;O60869 O60869-2 EDF1 Endothelial differentiation-related factor 1 0 0 135.55 3.53E-06 1105400 212.37 153.44 108.45 126.25 110.89 50.714 198.15 261.63 195.38 201.63 FALSE FALSE TRUE 209.7815528 155.6001323 110.3375268 140.847619 105.2308695 47.47353907 214.9808561 269.1998513 177.9047235 196.3916235 1.068179737 0.792295158 0.561823996 0.717177324 0.535821577 0.24172894 1.094653897 1.370729802 0.905867166 1 7.617589587 -10.17958851 4.752469647 1.032128477 0.730861184 0.108132717 0.294502715 0.295019137 11.96781761 0.05047693 0.06189838 6.61E-11 10.17958851 -0.301267293 (ac)AESSESFTMAS(ph)SPAQR ddPTM_HeLa_Romidepsin_16h_R1 1 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 0 AESSES(0.001)FT(0.004)MAS(0.574)S(0.42)PAQR 102.39 0.0046524 71610000 274.92 118.45 144.79 218.55 248.14 283.56 161.9 51.529 262.25 202.55 TRUE FALSE FALSE 271.5691693 120.1175422 147.3100092 243.8197793 235.4764899 265.4414311 175.651782 53.01991032 238.7937032 197.2877218 1.376513281 0.608844489 0.746676011 1.235858862 1.193568904 1.345453375 0.890333065 0.268744095 1.210382993 1 7.624157363 -7.327408482 3.160933877 1.124224334 0.200221127 0.511543379 0.23812479 0.191020731 3.022030707 0.036766956 0.394336022 4.71E-08 7.327408482 -0.924003207 (ac)AESSESFTMASS(ph)PAQR ddPTM_HeLa_Romidepsin_16h_R1 1 AESSESFTMASSPAQR 16 0 P49736;F8WDM3 P49736 MCM2 DNA replication licensing factor MCM2 1 0 AES(0.002)S(0.002)ESFT(0.002)MAS(0.285)S(0.709)PAQR 89.232 0.0049469 94762000 216.09 207.59 206.54 187.66 93.564 176.19 124.91 153.84 189.09 165.49 TRUE FALSE FALSE 213.456212 210.5124575 210.1347421 209.3581322 88.78907994 164.9320276 135.5198523 158.2911177 172.1773168 161.1905459 1.324247714 1.305985139 1.303641853 1.298823892 0.550833049 1.023211545 0.840743181 0.982012417 1.068160144 1 7.33262332 -8.786256135 24.9997498 1.191071653 0.861025145 0.566803361 0.156336944 155.574622 156721.3271 0.026340676 0.047761192 1.64E-09 8.786256135 -0.330046507 (ac)AGEK(ac)VEKPDTK ddPTM_HeLa_Romidepsin_16h_R1 1 AGEKVEKPDTK 11 2 Q02878;F8VZA3;F8VWR1;F8VU16;F8VZ45;U3KQR5 Q02878 RPL6 60S ribosomal protein L6 0 1 AGEK(1)VEKPDTK 71.221 0.012855 929360 450.33 538.12 555.25 508.12 535.27 539.26 505.16 437.66 769.11 492.5 FALSE TRUE FALSE 444.8412047 545.6956675 564.9138933 566.8712252 507.9531745 504.8030264 548.0682778 450.3230016 700.3188753 479.704779 0.927322854 1.137565627 1.177628237 1.181708522 1.058887042 1.052320195 1.142511607 0.938750292 1.459895557 1 8.906003002 -10.26044973 24.99881253 0.965680236 1.103121931 0 0.171148607 60.75435993 1534677.501 0.012028274 0.014278179 5.49E-11 10.26044973 0.137441695 AYTPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 AYTPSKR 7 1 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 0 1 AYTPSK(1)R 87.754 0.027223 4028600 1278.5 1208.2 2847.1 2468.2 2975 3569.1 2514.9 1833.2 1280.3 890.42 FALSE TRUE FALSE 1262.91715 1225.209071 2896.652581 2753.584897 2823.174649 3341.046029 2728.515543 1886.24075 1165.786761 867.28676 1.456170218 1.412692004 3.339901766 3.174941696 3.255180154 3.852296821 3.1460362 2.174875527 1.344176823 1 9.760365275 -9.791407374 5.980882624 1.230090341 3.195968426 0.833882803 0.404908922 0.049448054 5.103398147 0.067989948 0.091108779 1.62E-10 9.791407374 1.965878085 (ac)AGITTIEAVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 AGITTIEAVKR 11 1 P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8;D6R904;Q5VU61 P06753-4 TPM3 Tropomyosin alpha-3 chain 0 1 AGITTIEAVK(1)R 61.78 0.0047071 578120 521.1 354.81 563.9 499.11 1147.5 1036.4 970.69 794.98 845.75 598.51 FALSE TRUE FALSE 514.7486328 359.8050245 573.714443 556.8194466 1088.938793 970.1773848 1053.140384 817.981492 770.1040018 582.9606239 0.882990397 0.617202963 0.98413927 0.955157902 1.867945704 1.664224555 1.806537768 1.403150502 1.32102233 1 9.18725463 -8.771153785 24.98466242 0.920097216 1.692595558 0.760830342 0.198467076 50.06557998 128764.7552 0.022317431 0.04082177 1.69E-09 8.771153785 0.772498342 (ac)AGITTIEAVKR ddPTM_HeLa_Romidepsin_16h_R1 2 AGITTIEAVKR 11 1 P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8;D6R904;Q5VU61 P06753-4 TPM3 Tropomyosin alpha-3 chain 0 0 ; ; 80.455 0.012601 1230520 373.7 293.86 362.46 137.35 686.33 508.55 388.08 493.1 449.44 258.626 FALSE FALSE TRUE 369.1452007 297.9969688 368.7684643 153.2310533 651.304019 476.0552963 421.0435055 507.3670705 409.2409608 251.9068592 1.46540353 1.182964885 1.463907991 0.608284561 2.585495373 1.889806803 1.671425331 2.014105817 1.624572519 1 7.976746596 -4.0000011 0.141709802 0.903739767 4.965545272 0.200040449 0.470054179 63.43958765 0.591833265 1.125647364 52.53900963 1.00E-04 4.0000011 4.061805505 (ac)AGLS(ph)DLELRR ddPTM_HeLa_Romidepsin_16h_R1 1 AGLSDLELRR 10 1 D6RBV0;Q8NC56 D6RBV0 LEMD2 LEM domain-containing protein 2 1 0 AGLS(1)DLELRR 52.167 0.023221 1255600 138.21 263.93 183.39 198.3 210.07 151.53 102.57 183.81 242.31 166.04 TRUE FALSE FALSE 136.5254434 267.6456135 186.581826 221.228379 199.349344 141.847722 111.2822932 189.1282523 220.6371867 161.7262569 0.844176116 1.654929871 1.153689139 1.367918749 1.232634378 0.877085297 0.688090452 1.169434426 1.364263237 1 7.337410115 -5.687530796 20.32866465 1.025013514 1.016343924 0 0.296431776 0 0 0.038734026 0 2.05E-06 5.687530796 -0.008669591 (ac)AGS(ph)PELVVLDPPWDK ddPTM_HeLa_Romidepsin_16h_R1 4 AGSPELVVLDPPWDK 15 0 Q5SY74;Q96IY1-2;Q96IY1 Q5SY74 NSL1 Kinetochore-associated protein NSL1 homolog 1 0 AGS(1)PELVVLDPPWDK;AGS(1)PELVVLDPPWDK;AGS(1)PELVVLDPPWDK;AGS(1)PELVVLDPPWDK ;;; 91.313 0.00017877 14581600 12169.5 12598.9 12161.1 7300.57 12820.2 14511.2 12495.3 13393.6 12991.8 13444.3 TRUE FALSE FALSE 12021.17345 12776.26764 12372.75884 8144.696254 12165.93736 13583.98115 13556.65047 13781.12268 11829.78087 13095.01515 0.917996147 0.975658867 0.944844943 0.621969212 0.929051033 1.037339858 1.035252752 1.052394558 0.903380465 1 13.67673011 -8.255885445 10.26514848 0.932320051 1.041078679 0.251344688 0.102059862 0.275414564 437.3992231 0.015580127 0.03777543 5.55E-09 8.255885445 0.108758627 (ac)AGTVVLDDVELR ddPTM_HeLa_Romidepsin_16h_R1 1 AGTVVLDDVELR 12 0 P25205 P25205 MCM3 DNA replication licensing factor MCM3 0 0 79.07 0.012057 798410 0 0 0 102.58 0 54.459 0 0 0 180.14 FALSE FALSE TRUE 0 0 0 114.4407823 0 50.97924566 0 0 0 175.4599368 0 0 0 0.652233121 0 0.290546358 0 0 0 1 7.454997844 -12.26008482 0.873437435 1.029115238 0.119692167 0 0.36549914 0.264409477 0.344137392 0.160684939 0.038826608 5.49E-13 12.26008482 -0.909423071 (ac)AHS(ph)PVAVQVPGMQNNIADPEELFTK ddPTM_HeLa_Romidepsin_16h_R1 2 AHSPVAVQVPGMQNNIADPEELFTK 25 0 Q8NBY1;B4E0Y9;Q9P289-3;Q9P289 Q8NBY1 STK26 Serine/threonine-protein kinase 26 1 0 AHS(1)PVAVQVPGMQNNIADPEELFTK;AHS(1)PVAVQVPGMQNNIADPEELFTK ; 57.278 2.17E-07 51521400 4911.7 4733.7 4842.4 4478.2 4921 5061.5 4130 4713.4 5347.3 5180.7 TRUE FALSE FALSE 4851.834311 4800.341153 4926.679941 4995.990555 4669.863007 4738.086485 4480.802097 4849.774792 4869.024095 5046.104667 0.961500926 0.95129639 0.976333284 0.990068753 0.925439188 0.938959217 0.887972484 0.961092786 0.964907472 1 12.30095442 -4.000000004 0.066642766 1.064738515 0.702948191 0.291372077 0.02597236 154.754519 0.772394879 0.786493498 5.333686771 1.00E-04 4.000000004 -0.361790324 (ac)AHS(ph)PVQSGLPGMQNLK ddPTM_HeLa_Romidepsin_16h_R1 1 AHSPVQSGLPGMQNLK 16 0 B4DR80;Q9Y6E0-2 B4DR80 STK24 1 0 AHS(0.926)PVQS(0.074)GLPGMQNLK 68.786 0.0026255 33430000 619.76 595.87 560.45 717.23 854.12 557.18 533.22 612.04 681.57 712.27 TRUE FALSE FALSE 612.2061267 604.2586735 570.2043972 800.1595073 810.5310692 521.5779962 578.5116935 629.7484118 620.6086722 693.7651227 0.882440046 0.870984507 0.821898332 1.153357932 1.168307605 0.75180775 0.833872552 0.907725671 0.894551559 1 9.438303504 -9.182016756 0.00961019 1.846536851 1.53E-05 0 0.131116768 9178.074323 33.47048209 3130.553915 3299.567669 6.58E-10 9.182016756 -1.84652157 DAVTYTEHAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 DAVTYTEHAKR 11 1 P62805 P62805 HIST1H4A Histone H4 0 1 ; DAVTYTEHAK(1)R;DAVTYTEHAK(1)R 145.09 3.95E-11 2248200 477.32 410.01 780.92 731.86 1250.81 1114.23 824.06 777.98 669.79 279.12 FALSE TRUE FALSE 471.5022402 415.7821315 794.511585 816.4810967 1186.976498 1043.034299 894.0556358 800.4896239 609.8823049 271.8684222 1.734303074 1.529350589 2.922412168 3.003221522 4.365996201 3.836540819 3.288560064 2.944400889 2.243299534 1 8.08676478 -9.652888935 1.434733443 1.320203164 3.591057268 0.741482994 0.508817705 0.112013633 0.465705657 0.08132931 0.126442193 2.22E-10 9.652888935 2.270854105 (ac)AMS(ph)SGGSGGGVPEQEDSVLFR ddPTM_HeLa_Romidepsin_16h_R1 2 AMSSGGSGGGVPEQEDSVLFR 21 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 0 AMS(0.808)S(0.192)GGSGGGVPEQEDSVLFR;AMS(0.5)S(0.5)GGS(0.001)GGGVPEQEDSVLFR ; 138.55 6.11E-26 16250900 151.14 153.34 350.24 66.254 48.904 201.34 54.536 308.9 319.04 191.67 TRUE FALSE FALSE 149.2978475 155.4987245 356.3357803 73.91459921 46.40824639 188.4750238 59.16828648 317.8375341 290.5042633 186.6903858 0.799708281 0.832923045 1.908699148 0.395920759 0.248584019 1.009559346 0.316932692 1.702484747 1.556075114 1 7.544503823 (ac)AMS(ph)YVKDDIFRIY(ph)IK ddPTM_HeLa_Romidepsin_16h_R1 1 AMSYVKDDIFRIYIK 15 2 Q13501-2;C9JRJ8;E9PFW8 Q13501-2 SQSTM1 Sequestosome-1 2 0 AMS(0.568)Y(0.432)VKDDIFRIY(1)IK 56.548 0.0040131 0 694.78 559.72 528.82 572.23 840.8 762.72 719.59 641.76 616.78 555.46 TRUE FALSE FALSE 686.3117541 567.5997529 538.0238903 638.393925 797.8908385 713.9846536 780.7119566 660.3283131 561.613652 541.0290691 1.268530276 1.049111379 0.994445439 1.179962337 1.474765191 1.319678912 1.443012957 1.220504314 1.038047092 1 9.079562301 -8.919376361 6.07771252 1.112833499 1.365443359 0.642999937 0.100979651 0.1349948 8.02151721 0.01805955 0.032990136 1.20E-09 8.919376361 0.25260986 (ac)ANDSGGPGGPS(ph)PSERDR ddPTM_HeLa_Romidepsin_16h_R1 1 ANDSGGPGGPSPSERDR 17 1 Q9GZT9-3;Q9GZT9-2;Q9GZT9 Q9GZT9-3 EGLN1 Egl nine homolog 1 1 0 ANDSGGPGGPS(0.865)PS(0.135)ERDR 54.393 0.0022746 2303100 560.45 253.81 428.12 432.37 304.17 212.63 418.46 401.49 802.15 619.65 TRUE FALSE FALSE 553.6190198 257.3831438 435.571249 482.3626538 288.6470699 199.0436292 454.003982 413.1064797 730.403695 603.5514037 0.917269045 0.42644776 0.721680451 0.799207244 0.478247699 0.329787369 0.752220903 0.68445948 1.21017645 1 9.237332838 -10.38147542 5.992538642 0.96374034 0.602802589 0.598623677 0.162959813 0.124681793 5.656410285 0.025245762 0.028737425 4.15E-11 10.38147542 -0.360937751 (ac)AQDQGEK(ac)ENPMR ddPTM_HeLa_Romidepsin_16h_R1 2 AQDQGEKENPMR 12 1 P62913 P62913 RPL11 60S ribosomal protein L11 0 1 ; AQDQGEK(1)ENPMR;AQDQGEK(1)ENPMR 73.841 1.61E-05 1723110 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)AQES(ph)PKNSAAEIPVTSNGEVDDSREHSFNR ddPTM_HeLa_Romidepsin_16h_R1 1 AQESPKNSAAEIPVTSNGEVDDSREHSFNR 30 2 P53367-3;P53367-2;P53367 P53367-3 ARFIP1 Arfaptin-1 1 0 AQES(0.498)PKNS(0.498)AAEIPVT(0.003)S(0.001)NGEVDDSREHSFNR 52.97 4.84E-06 10949000 218.49 246.1 0 233.19 263.7 285.51 228.23 233.69 284.99 242.24 TRUE FALSE FALSE 215.8269598 249.5646023 0 260.152525 250.242405 267.2668324 247.6158505 240.4514514 259.4997806 235.9465699 0.91472811 1.057716594 0 1.102590833 1.06058929 1.13274303 1.049457301 1.019092804 1.099824341 1 7.882316388 (ac)AQESPKNS(ph)AAEIPVTSNGEVDDSR ddPTM_HeLa_Romidepsin_16h_R1 1 AQESPKNSAAEIPVTSNGEVDDSR 24 1 P53367-3;P53367-2;P53367 P53367-3 ARFIP1 Arfaptin-1 1 0 AQES(0.449)PKNS(0.551)AAEIPVTSNGEVDDSR 50.945 3.98E-06 16616000 521.36 670.07 524.08 448.92 450.95 527.8 550.12 587.25 604.23 654.21 TRUE FALSE FALSE 515.0054638 679.503263 533.2013926 500.8262426 427.9363388 494.0752834 596.8471791 604.2411522 550.1861555 637.2135299 0.808214891 1.066366659 0.836770356 0.785962977 0.67157447 0.775368476 0.936651768 0.948255371 0.8634251 1 9.31563309 -9.548813307 24.97639727 0.920240603 0.81798829 0.218031426 0.099409133 311.8488735 300326.0713 0.017989796 0.025441835 2.83E-10 9.548813307 -0.102252313 (ac)AQSS(ph)PQLDIQVLHDLR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSSPQLDIQVLHDLR 16 0 F6SS63;Q8N5C8-2;Q8N5C8;A0A0A0MQY2 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 0 AQS(0.106)S(0.894)PQLDIQVLHDLR 154.13 9.96E-05 1491700 0 0 60.177 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 61.22435544 0 0 0 0 0 0 0 0 (ac)AQSVLVPPGPDS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSVLVPPGPDSFR 14 0 A0A1B0GTX0;F6U291;A0A1B0GTS6;A0A1B0GW67;A0A1B0GW40;Q99250-2;Q99250 A0A1B0GTX0 SCN2A Sodium channel protein type 2 subunit alpha 1 0 AQS(0.028)VLVPPGPDS(0.972)FR 57.267 0.0096481 1214400 149.46 189.11 166.35 0 179.75 207.46 166.31 232.21 143.05 128.96 TRUE FALSE FALSE 147.638324 191.7722955 169.245252 0 170.5766868 194.2039755 180.4363672 238.92863 130.2552497 125.6096006 1.17537452 1.526732786 1.347391053 0 1.357990838 1.546091816 1.436485479 1.902152613 1.036984825 1 6.972802926 -8.527753507 24.99950577 1.060224583 1.582896645 0.324430165 0.395766654 132.4586313 679293.9614 0.056781375 0.113885154 2.97E-09 8.527753507 0.522672063 (ac)AS(ph)AVSPANLPAVLLQPR ddPTM_HeLa_Romidepsin_16h_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 0 AS(0.998)AVS(0.002)PANLPAVLLQPR;AS(0.767)AVS(0.233)PANLPAVLLQPR ; 152.07 4.52E-88 46961000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)AS(ph)EAPSPPRS(ph)PPPPTSPEPELAQLR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEAPSPPRSPPPPTSPEPELAQLR 25 1 Q8N302-2;Q8N302-3;Q8N302 Q8N302-2 AGGF1 Angiogenic factor with G patch and FHA domains 1 2 0 AS(0.609)EAPS(0.439)PPRS(0.951)PPPPT(0.001)SPEPELAQLR 67.877 6.95E-06 4304400 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)AS(ph)EDNRVPSPPPTGDDGGGGGR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDNRVPSPPPTGDDGGGGGR 22 1 E9PEM5;A0A494C1L5;P50851-2;P50851;A0A494C0R9 E9PEM5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 0 AS(0.669)EDNRVPS(0.331)PPPT(0.001)GDDGGGGGR 77.192 3.74E-05 8987300 0 0 0 0 0 0 0 0 110.09 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 100.2432747 0 0 (ac)AS(ph)GVAVSDGVIK ddPTM_HeLa_Romidepsin_16h_R1 25 ASGVAVSDGVIK 12 0 E9PP50;P23528;E9PS23 E9PP50 CFL1 Cofilin-1 1 0 AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(1)GVAVSDGVIK;AS(0.994)GVAVS(0.006)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.99)GVAVS(0.01)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.998)GVAVS(0.002)DGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK;AS(0.998)GVAVS(0.002)DGVIK;AS(0.829)GVAVS(0.171)DGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK;AS(0.999)GVAVS(0.001)DGVIK ;;;;;;;;;;;;;;;;;;;;;;;; 120.31 1.27E-63 4005802300 152191.29 159618.12 159953.809 132577.6 150030.99 112278.08 81871.83 113658.27 138064.22 131658.4 TRUE FALSE FALSE 150336.324 161865.2281 162737.7379 147906.8459 142374.3487 105103.873 88826.0212 116946.7927 125715.4104 128237.8958 1.172323696 1.26222617 1.269030008 1.153378609 1.110236158 0.81960073 0.692665929 0.9119519 0.980329641 1 16.96846313 -8.24988073 5.11473631 1.119154952 0.792802747 0.680435484 0.102353783 0.09028782 7.486882283 0.016381382 0.040854526 5.62E-09 8.24988073 -0.326352205 (ac)AS(ph)GVQVADEVCR ddPTM_HeLa_Romidepsin_16h_R1 2 ASGVQVADEVCR 12 0 F6RFD5;P60981 F6RFD5 DSTN Destrin 1 0 AS(1)GVQVADEVCR;AS(1)GVQVADEVCR ; 127.4 0.00076329 73686000 662.2 296.69 405.81 398.94 563.38 179.76 337.84 493.85 448.08 522.61 TRUE FALSE FALSE 654.1288517 300.8668096 412.8729528 445.0673199 534.6286163 168.2739161 366.5361212 508.1387706 408.0026026 509.0325169 1.285043352 0.59105617 0.811093475 0.874339664 1.05028382 0.330575966 0.720064257 0.998244226 0.801525618 1 8.991614008 -10.26374315 24.98869184 1.134603806 0.765897304 0.173085357 0.228589013 154.2083527 1672674.804 0.036304996 0.042583893 5.45E-11 10.26374315 -0.368706502 (ac)AS(ph)GVTVNDEVIK ddPTM_HeLa_Romidepsin_16h_R1 4 ASGVTVNDEVIK 12 0 Q9Y281;G3V2U0;F8WDN3 Q9Y281 CFL2 Cofilin-2 1 0 AS(1)GVTVNDEVIK;AS(1)GVTVNDEVIK;AS(1)GVTVNDEVIK;AS(1)GVTVNDEVIK ;;; 154.85 6.18E-05 304724000 21921.3 24600.2 24087.6 20847 18276.7 13270 8827.3 11090.5 21954.4 19270.4 TRUE FALSE FALSE 21654.11476 24946.52226 24506.83457 23257.42823 17343.9718 12422.08983 9577.090642 11411.38612 19990.74348 18769.75223 1.153670784 1.329081064 1.305655731 1.239090849 0.924038399 0.661814268 0.510240653 0.607966796 1.065051005 1 14.19612199 -8.347844363 2.531109177 1.124824555 0.566721592 0.849626312 0.109426108 0.104243877 1.293043968 0.020075911 0.053340795 4.49E-09 8.347844363 -0.558102963 (ac)AS(ph)LSLAPVNIFK ddPTM_HeLa_Romidepsin_16h_R1 1 ASLSLAPVNIFK 12 0 F8VQ14;F5GWF6;P78371 F8VQ14 CCT2 T-complex protein 1 subunit beta 1 0 AS(0.899)LS(0.101)LAPVNIFK 68.846 0.0014258 1973300 1102.2 1016.6 1118.2 821.34 956.18 847.02 860.05 854.59 1030.7 1036.5 TRUE FALSE FALSE 1088.765962 1030.911721 1137.661802 916.3071953 907.3825666 792.8981556 933.1026255 879.3162133 938.5116106 1009.571581 1.078443553 1.021137819 1.126875819 0.907619839 0.898779823 0.78538082 0.924256034 0.870979562 0.929613738 1 9.979527489 -9.10004851 5.369452796 1.042491048 0.871503121 0.632835657 0.058747954 0.087262653 3.78054577 0.007483839 0.012590684 7.94E-10 9.10004851 -0.170987927 (ac)AS(ph)NPERGEILLTELQGDSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASNPERGEILLTELQGDSR 19 1 Q16513-3;Q16513-2;Q16513;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 AS(1)NPERGEILLTELQGDSR 65.565 0.0024254 1510300 68.131 277.07 205.1 229.06 125.05 156.59 59.395 133.94 190.04 163.78 TRUE FALSE FALSE 67.30059317 280.9705987 208.6696795 255.544995 118.6682319 146.5844044 64.44000982 137.8153426 173.0423464 159.524972 0.421881241 1.761295396 1.308069056 1.601912176 0.743884988 0.918880615 0.403949357 0.863910777 1.084735163 1 7.31763847 -7.801695046 23.79284478 0.910913578 0.633929737 0.029382243 0.420643332 209.4194177 123775.5427 0.068092121 0.204282265 1.58E-08 7.801695046 -0.27698384 (ac)AS(ph)PGIEVELLGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPGIEVELLGK 12 0 Q8TCY9 Q8TCY9 URGCP Up-regulator of cell proliferation 1 0 AS(1)PGIEVELLGK 78.939 0.00010965 2258200 3487.4 3607.9 3610.2 2573.6 2146.5 1947.1 1540.3 1602.2 3727.3 3498.2 TRUE FALSE FALSE 3444.894227 3658.692111 3673.034017 2871.171741 2036.956095 1822.686594 1671.133044 1648.557129 3393.920953 3407.31626 1.011028612 1.073775321 1.077984471 0.84264903 0.597818324 0.534933201 0.490454339 0.483828622 0.996068663 1 11.73442015 -8.825703988 2.174202732 1.016579473 0.504934838 0.979892831 0.034231229 0.031849379 0.306706852 0.00576091 0.012085237 1.49E-09 8.825703988 -0.511644635 (ac)AS(ph)PPESDGFSDVRK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPPESDGFSDVRK 14 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 0 AS(1)PPESDGFSDVRK;AS(0.999)PPES(0.001)DGFSDVRK ; 109.83 0.00038766 27201000 7021.3 6135.4 5414.2 5787.7 5572.4 4777.9 3923.6 4584.3 6927.2 6652.1 TRUE FALSE FALSE 6935.721695 6221.774322 5508.43188 6456.901106 5288.019635 4472.60761 4256.870486 4716.939488 6307.613883 6479.277483 1.070446776 0.960257427 0.850161441 0.99654647 0.816143412 0.690294191 0.656997713 0.728003933 0.97350575 1 12.66161723 -8.706353348 0.800570897 1.029197626 0.654033814 0.801617057 0.061860307 0.206558905 0.236751938 0.011381691 0.044609786 1.97E-09 8.706353348 -0.375163811 (ac)AS(ph)PSRQPPPGGSGLLQGSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSRQPPPGGSGLLQGSR 19 1 Q96S90 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 0 AS(0.583)PS(0.417)RQPPPGGSGLLQGSR 88.163 1.38E-07 13441000 960.73 902.67 902.28 875.37 647.61 645.77 349.26 487.67 1097.6 1030.1 TRUE FALSE FALSE 949.0202532 915.377812 917.9838049 976.5843981 614.5600451 604.5073811 378.9261357 501.779962 999.427907 1003.337854 0.945863101 0.912332579 0.914929903 0.973335547 0.612515558 0.602496337 0.377665543 0.500110666 0.996103061 1 9.97059177 -8.554286379 1.547490439 0.968074038 0.454201042 0.920592486 0.062717383 0.067640233 0.318732502 0.009022215 0.025502564 2.79E-09 8.554286379 -0.513872996 (ac)AS(ph)PTDGTDLEASLLSFEK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPTDGTDLEASLLSFEK 18 0 G3V5T8 G3V5T8 LIN52 1 0 AS(0.5)PT(0.5)DGTDLEASLLSFEK;AS(0.986)PT(0.014)DGTDLEASLLSFEK ; 182.1 5.84E-125 37179000 16697.4 16448.5 16241.9 14923.5 17748.7 16260.3 15079.2 16484.2 18217.2 16480.8 TRUE FALSE FALSE 16493.88567 16680.06241 16524.58346 16649.02529 16842.91761 15221.31931 16360.02687 16961.14432 16587.80801 16052.62644 1.027488288 1.039086188 1.02940061 1.037152727 1.049231269 0.948213637 1.019149541 1.056596214 1.03333919 1 13.97052174 -7.269922521 6.392449745 1.01604038 1.057330745 0.119192741 0.027476748 0.159968162 36.77501767 0.003759014 0.028194896 5.37E-08 7.269922521 0.041290365 (ac)ASEAPS(ph)PPRS(ph)PPPPTSPEPELAQLR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEAPSPPRSPPPPTSPEPELAQLR 25 1 Q8N302-2;Q8N302-3;Q8N302 Q8N302-2 AGGF1 Angiogenic factor with G patch and FHA domains 1 2 0 AS(0.398)EAPS(0.861)PPRS(0.742)PPPPTSPEPELAQLR 88.627 4.62E-06 4435300 0 0 0 61.249 0 0 0 0 61.812 0 TRUE FALSE FALSE 0 0 0 68.33089757 0 0 0 0 56.28337991 0 0 (ac)ASEAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEAVK 6 0 Q9P2E2;Q9P2E2-3 Q9P2E2 KIF17 Kinesin-like protein KIF17 0 0 49.211 0.023541 2988100 0 0 0 0 154.25 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 146.3780469 0 0 0 0 0 0 (ac)ASEDNRVPS(ph)PPPTGDDGGGGGR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDNRVPSPPPTGDDGGGGGR 22 1 E9PEM5;A0A494C1L5;P50851-2;P50851;A0A494C0R9 E9PEM5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 0 AS(0.426)EDNRVPS(0.563)PPPT(0.011)GDDGGGGGR 88.57 6.74E-06 9245200 109.98 0 0 116.65 168.61 0 48.599 0 62.557 194.7 TRUE FALSE FALSE 108.6395215 0 0 130.1376219 160.0052025 0 52.72699785 0 56.96174524 189.6416659 0.572867365 0 0 0.686229058 0.843723882 0 0.27803488 0 0.300365138 1 7.567132162 -11.11037193 0.90430665 0.932232606 0.282789626 0.049564742 0.354647789 0.341057286 0.595508225 0.097093073 0.069614256 7.76E-12 11.11037193 -0.64944298 (ac)ASESDT(ph)EEFYDAPEDVHLGGGYPVGS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASESDTEEFYDAPEDVHLGGGYPVGSPGK 29 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 2 0 AS(0.258)ES(0.28)DT(0.325)EEFY(0.368)DAPEDVHLGGGY(0.002)PVGS(0.767)PGK 52.057 2.47E-05 8062900 2120 2335.9 2301.8 2203.8 2277.9 2162.2 1894.7 2074.7 2604 2156 TRUE FALSE FALSE 2094.160625 2368.784862 2341.861863 2458.613725 2161.650263 2024.042398 2055.635771 2134.728171 2371.091718 2099.986809 0.997225609 1.127999877 1.115179321 1.170775795 1.029363734 0.963835768 0.978880325 1.01654361 1.129098387 1 11.03616455 -5.896864369 12.39837594 1.024122272 0.582787015 0 0.076603331 0 0 0.010194923 0 1.27E-06 5.896864369 -0.441335258 (ac)ASESDT(ph)EEFYDAPEDVHLGGGYPVGSPGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASESDTEEFYDAPEDVHLGGGYPVGSPGK 29 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 AS(0.3)ES(0.3)DT(0.34)EEFY(0.058)DAPEDVHLGGGYPVGS(0.001)PGK 78.236 3.87E-09 8004500 2784.4 2921.9 2304.1 2371.5 3349.9 3026.1 3444.1 3022.6 3181.1 2901.9 TRUE FALSE FALSE 2750.462662 2963.034585 2344.201894 2645.703988 3178.942103 2832.741976 3736.641768 3110.054162 2896.574449 2826.50822 0.973095582 1.048302129 0.829363197 0.936032653 1.124688788 1.002205462 1.321999258 1.100316688 1.024788971 1 11.46480518 -8.122814186 1.600101258 0.97883845 1.202840924 0.436897855 0.092868691 0.253719163 1.197615174 0.012531719 0.052347139 7.54E-09 8.122814186 0.224002473 (ac)ASESDTEEFYDAPEDVHLGGGYPVGS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASESDTEEFYDAPEDVHLGGGYPVGSPGK 29 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 AS(0.047)ES(0.047)DT(0.047)EEFY(0.047)DAPEDVHLGGGY(0.044)PVGS(0.766)PGK 51.544 2.07E-07 7936800 2736.6 2564.2 2125.7 2026.5 2189.2 2728.5 2799 2620.1 2879 2686.4 TRUE FALSE FALSE 2703.245267 2600.298875 2162.696917 2260.813465 2077.476955 2554.157656 3036.74699 2695.90846 2621.495029 2616.606941 1.033110944 0.993767476 0.826527241 0.864024867 0.79395836 0.976133486 1.160566741 1.030307005 1.001868102 1 11.35348151 -7.786336382 22.11758509 0.972098289 1.095436645 0.277044948 0.088860318 67.72695825 60166.82195 0.0145189 0.043606968 1.64E-08 7.786336382 0.123338356 (ac)ASGEHS(ph)PGSGAAR ddPTM_HeLa_Romidepsin_16h_R1 3 ASGEHSPGSGAAR 13 0 A6NKB8;Q9H4A4 A6NKB8 RNPEP Aminopeptidase B 1 0 AS(0.002)GEHS(0.995)PGS(0.004)GAAR;AS(0.001)GEHS(0.992)PGS(0.007)GAAR;AS(0.002)GEHS(0.992)PGS(0.006)GAAR ;; 123.95 7.84E-25 92929900 0 130.93 0 180.73 54.736 121 0 0 0 166.62 TRUE FALSE FALSE 0 132.773236 0 201.626853 51.94261767 113.2684905 0 0 0 162.2911884 0 0.818117344 0 1.242377081 0.320058151 0.697933706 0 0 0 1 7.34244086 -12.57091001 1.346410253 1.000404329 0.356676709 0 0.506312894 0.481960271 1.56462956 0.281004444 0.065694767 2.69E-13 12.57091001 -0.64372762 (ac)ASGVAVSDGVIK ddPTM_HeLa_Romidepsin_16h_R1 3 ASGVAVSDGVIK 12 0 E9PP50;P23528;E9PS23 E9PP50 CFL1 Cofilin-1 0 0 ;; ;; 122.96 1.04E-06 27114000 13350 13899.6 14327.1 12043.2 14006.6 10014.8 6498.92 9903.51 11984.6 11547.71 FALSE FALSE TRUE 13187.28507 14095.27893 14576.45717 13435.69145 13291.79094 9374.886601 7050.938103 10190.05244 10912.66736 11247.69883 1.172442938 1.253170017 1.295950166 1.194528023 1.18173425 0.833493743 0.626878281 0.905967753 0.970213332 1 13.45734225 -8.171840187 4.675489356 1.12725152 0.760439152 0.67002988 0.116326255 0.111782402 4.202696338 0.018026766 0.047724188 6.73E-09 8.171840187 -0.366812368 (ac)ASIWVGHR ddPTM_HeLa_Romidepsin_16h_R1 3 ASIWVGHR 8 0 P12429;D6RFG5;D6RAZ8;D6RCA8 P12429 ANXA3 Annexin A3;Annexin 0 0 ;; ;; 95.62 0.00061333 1610010 361.48 314.04 672.2 122.14 372.29 545.36 446.06 642.44 302.67 219.41 FALSE FALSE TRUE 357.0741427 318.4610634 683.899359 136.2624015 353.2906521 510.5132561 483.9483253 661.0279878 275.5984371 213.7096966 1.670837348 1.490157295 3.200132563 0.637605142 1.653133469 2.388816531 2.264512715 3.093111817 1.289592571 1 7.739508558 -4 0.136774606 0.820797665 7.281391907 0.358287538 0.647509972 60.51758416 0.550584952 1.841771285 76.39813624 1.00E-04 4 6.460594243 (ac)ASLEVSRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 ASLEVSRSPR 10 1 Q5QPJ9;Q5QPK2;O60762 Q5QPJ9 DPM1 Dolichol-phosphate mannosyltransferase subunit 1 1 0 ASLEVS(0.083)RS(0.917)PR;ASLEVS(0.201)RS(0.799)PR;ASLEVS(0.005)RS(0.995)PR;ASLEVS(0.022)RS(0.978)PR ;;; 101.56 1.98E-05 691869300 1647.996 1632.72 1910.086 1637.82 1370.916 1269.35 1432.06 1285.56 1535.64 1639.97 TRUE FALSE FALSE 1627.909591 1655.705475 1943.330246 1827.192455 1300.953041 1188.242632 1553.699141 1322.75565 1398.288512 1597.363343 1.019122918 1.036524021 1.216586229 1.143880297 0.814437771 0.743877488 0.972664828 0.828086895 0.875372856 1 10.6414768 -8.746568374 24.99953044 1.037256135 0.842410184 0.511668257 0.099556106 152.4285452 256245.0951 0.013501868 0.026915382 1.79E-09 8.746568374 -0.194845952 (ac)ASLSTWSS(ph)PAEPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASLSTWSSPAEPR 13 0 Q92888-3;Q92888-4 Q92888-3 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 0 AS(0.015)LS(0.004)T(0.005)WS(0.134)S(0.841)PAEPR 84.566 0.0052242 1798400 245.26 258.76 305.42 421.18 283.23 323.94 185.69 182.98 224.85 298.11 TRUE FALSE FALSE 242.2706768 262.4028301 310.735707 469.8788133 268.7757162 303.2412795 201.462504 188.2742376 204.7388529 290.3650592 0.834365806 0.903699745 1.0701553 1.618234696 0.925647586 1.044344937 0.693824885 0.64840528 0.705108436 1 8.181724048 -7.731511753 8.370532523 0.98611447 0.668887023 0.256918718 0.228837899 0.262498478 62.45011668 0.031443335 0.11562495 1.86E-08 7.731511753 -0.317227447 (ac)ASPS(ph)RQPPPGGSGLLQGSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSRQPPPGGSGLLQGSR 19 1 Q96S90 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 0 AS(0.309)PS(0.691)RQPPPGGSGLLQGSR 81.789 3.01E-05 14014000 798.14 611.33 504.53 569 534.42 392.79 436.34 610.66 694.89 608.33 TRUE FALSE FALSE 788.4119627 619.9363198 513.311133 634.7904572 507.1465532 367.6919867 473.4027087 628.3284836 632.737298 592.5254989 1.330595838 1.046260998 0.866310621 1.071330193 0.855906715 0.620550487 0.798957529 1.060424378 1.067865095 1 9.21073343 -9.898348128 3.813848433 1.157536331 0.871029964 0.387009909 0.144339491 0.183245555 5.10648546 0.028368059 0.03777141 1.26E-10 9.898348128 -0.286506368 (ac)AT(ph)AAETSASEPEAESK ddPTM_HeLa_Romidepsin_16h_R1 1 ATAAETSASEPEAESK 16 0 A0A494C0L2;F8W667;A0A499FI31;Q15020-3;Q15020-2;Q15020-4;Q15020 A0A494C0L2 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 1 0 AT(0.333)AAET(0.333)S(0.333)ASEPEAESK 95.477 0.00091649 7709100 3361.4 3215.5 2727.8 3028.9 3203.5 3138.6 2629.9 2909.3 3386.3 3807.3 TRUE FALSE FALSE 3320.429964 3260.767893 2775.276215 3379.115669 3040.013441 2938.053589 2853.28364 2993.476005 3083.420847 3708.385797 0.895384177 0.879295756 0.748378504 0.911209312 0.819767308 0.792272905 0.769413917 0.807218064 0.83147251 1 11.85657563 -10.94751388 0.276683757 1.042056031 0.766468081 0.131072635 0.067346911 0.671307323 0.156319324 0.073145437 0.044536597 1.13E-11 10.94751388 -0.275587951 SSGSSSSGLGTVSNS(ph)PASQR ddPTM_HeLa_Romidepsin_16h_R1 4 SSGSSSSGLGTVSNSPASQR 20 0 H0Y589;H0Y3N9;Q9UPP1-5;Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1 H0Y589 PHF8 Histone lysine demethylase PHF8 1 0 SSGSSSSGLGTVSNS(0.981)PAS(0.019)QR;SSGSSSSGLGTVSNS(1)PASQR;SSGSSSSGLGTVSNS(0.998)PAS(0.002)QR;SSGSSSSGLGTVSNS(0.832)PAS(0.168)QR ;;; 370.35 4.10E-301 22015800 5535.07 4423.01 4534 3394.06 3142.69 2918.58 3186.57 2730.91 6408.3 6192.88 TRUE FALSE FALSE 5467.606438 4485.277251 4612.912368 3786.497187 2982.306802 2732.092157 3457.237176 2809.924572 5835.125598 6031.988085 0.906435219 0.743581915 0.764741625 0.627736185 0.494415234 0.452933945 0.573150531 0.465837222 0.967363582 1 12.55841786 -9.627940104 0.679522899 0.978548963 0.473466722 0.94526123 0.046182695 0.099947736 0.093546376 0.011062433 0.02090173 2.36E-10 9.627940104 -0.505082241 down (ac)AT(ph)SPQKSPSVPK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSPQKSPSVPK 12 1 Q9NVD7-2;Q9NVD7 Q9NVD7-2 PARVA Alpha-parvin 1 0 AT(0.495)S(0.495)PQKS(0.004)PS(0.006)VPK 50.034 0.0020468 281280000 4511.3 4429.5 3636.9 4794.9 3374.6 3600.4 3328.8 3402.4 4466.4 3785.4 TRUE FALSE FALSE 4456.31454 4491.858617 3700.198719 5349.308899 3202.38157 3370.34606 3611.548189 3500.843076 4066.913998 3687.054762 1.208638013 1.218278248 1.003564893 1.450835218 0.86854733 0.914102523 0.979521168 0.949495818 1.103025114 1 11.84825313 (ac)ATAAETS(ph)ASEPEAESK ddPTM_HeLa_Romidepsin_16h_R1 1 ATAAETSASEPEAESK 16 0 A0A494C0L2;F8W667;A0A499FI31;Q15020-3;Q15020-2;Q15020-4;Q15020 A0A494C0L2 SART3 Squamous cell carcinoma antigen recognized by T-cells 3 1 0 AT(0.001)AAET(0.121)S(0.865)AS(0.013)EPEAESK 121.99 7.87E-06 6280800 1688.9 1742.9 1563.7 1502.2 1832.4 1374.5 1305.8 1594.2 1945.8 1689.1 TRUE FALSE FALSE 1668.315037 1767.436592 1590.915543 1675.891432 1738.88579 1286.673886 1416.714619 1640.325662 1771.762775 1645.216939 1.014039546 1.074287865 0.966994386 1.01864465 1.056934043 0.782069438 0.861111131 0.997026972 1.076917416 1 10.68406212 -8.275581345 24.99010419 1.012754261 0.878173369 0.556878278 0.059834279 402.9088601 711974.9 0.007594466 0.017056984 5.30E-09 8.275581345 -0.134580892 (ac)ATAT(ph)PVPPR ddPTM_HeLa_Romidepsin_16h_R1 1 ATATPVPPR 9 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 0 AT(0.039)AT(0.961)PVPPR 50.353 0.027225 7604100 298.5 251.52 246.55 342.29 348.24 195.47 214.23 197.73 175.12 296.2 TRUE FALSE FALSE 294.8617672 255.0609052 250.8410993 381.8671803 330.4680133 182.9800979 232.4266909 203.4510056 159.4568286 288.5046813 1.022034602 0.884078913 0.869452441 1.323608264 1.14545113 0.634236148 0.805625371 0.70519135 0.55270101 1 8.172450918 -8.257496913 24.99991158 1.021952591 0.72407839 0.236863462 0.19602825 206.5550268 1309797.066 0.018444577 0.045158312 5.53E-09 8.257496913 -0.297874202 (ac)ATDELATKLS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 ATDELATKLSR 11 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 ATDELAT(0.001)KLS(0.999)R;ATDELAT(0.001)KLS(0.999)R ; 80.17 0.0024847 21566000 4621.9 4800.5 4321.9 3906.4 5975.1 6042.8 3950.3 5813.4 4847.7 4769.8 TRUE FALSE FALSE 4565.566505 4868.081565 4397.120857 4358.076348 5670.168351 5656.684582 4285.838383 5981.601557 4414.109571 4645.879908 0.982712983 1.04782768 0.946455988 0.938051873 1.220472432 1.217570125 0.92250305 1.28750671 0.950112714 1 12.18173615 -8.765920413 24.996264 0.989169247 1.148873584 0.471507023 0.094800335 78.95410709 440427.3594 0.012696497 0.023591499 1.71E-09 8.765920413 0.159704337 (ac)ATDT(ph)SQGELVHPK ddPTM_HeLa_Romidepsin_16h_R1 1 ATDTSQGELVHPK 13 0 Q5SSJ5;B0QZK9;B0QZK8;Q5SSJ5-5 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 1 0 AT(0.046)DT(0.477)S(0.477)QGELVHPK 56.122 0.003452 10458000 6048 6491 5067 4759.1 3465 4261.3 3395.4 3484.3 5961.1 5619.3 TRUE FALSE FALSE 5974.28465 6582.380468 5155.189009 5309.369534 3288.16812 3989.016683 3683.805191 3585.112723 5427.924286 5473.309776 1.091530517 1.202632546 0.941877807 0.97004733 0.600764118 0.728812519 0.673048912 0.655017324 0.991707853 1 12.4181978 -8.876109012 3.913643597 1.048924482 0.669554366 0.860313037 0.073012056 0.061149579 1.750312238 0.011278299 0.021248695 1.33E-09 8.876109012 -0.379370116 (ac)ATEEK(ac)KPETEAAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATEEKKPETEAAR 13 2 V9GYQ5;V9GZ59;P61964 V9GYQ5 WDR5 WD repeat-containing protein 5 0 1 ATEEK(0.973)K(0.027)PETEAAR 62.466 4.24E-05 2130900 526.21 480.9 404.65 483.93 590.3 493.66 451.76 463.96 548.47 653.53 FALSE TRUE FALSE 519.7963501 487.6701228 411.6927635 539.8842636 560.1747883 462.1167192 490.1324831 477.3839506 499.4134695 636.5511964 0.816582159 0.766112962 0.646755148 0.848139579 0.880015294 0.725969446 0.769981246 0.74995374 0.784561356 1 9.314132741 -11.71613781 0.637659222 1.004138821 0.770069947 0.039898999 0.089127102 0.374628203 0.292452649 0.044520788 0.015388385 1.92E-12 11.71613781 -0.234068875 (ac)ATEIGS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 ATEIGSPPR 9 0 Q9C0J8;B9A053;Q9C0J8-3;Q9C0J8-2 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 0 AT(0.001)EIGS(0.999)PPR 80.916 0.0039944 12400000 130.14 127.24 197.18 271.71 291.45 175.57 145.95 134.97 147.86 194.98 TRUE FALSE FALSE 128.5538036 129.0312881 200.6118352 303.1263886 276.576219 164.3516436 158.3469894 138.875144 134.6350313 189.9143915 0.67690396 0.679418169 1.056327715 1.596121212 1.456320486 0.865398574 0.833780885 0.731251291 0.708924849 1 7.569205425 -9.618404214 7.387383572 0.831145918 1.112133171 0.243864465 0.26956043 0.320540445 21.60820358 0.047830437 0.067718782 2.41E-10 9.618404214 0.280987254 (ac)ATSATS(ph)PHAPGFPAEGR ddPTM_HeLa_Romidepsin_16h_R1 1 ATSATSPHAPGFPAEGR 17 0 Q5VVL2;Q9NUP7-2;Q9NUP7 Q5VVL2 TRMT13 tRNA:m(4)X modification enzyme TRM13 homolog 1 0 AT(0.155)S(0.155)AT(0.139)S(0.551)PHAPGFPAEGR 77.324 0.0010188 15084000 371.01 438.04 304.77 628.27 2004.1 2703.8 2526 2970.1 447.97 268.62 TRUE FALSE FALSE 366.4879874 444.2067386 310.074394 700.9135335 1901.823299 2531.035906 2740.558377 3056.035157 407.9024412 261.6412137 1.400727287 1.697770517 1.185112963 2.678911031 7.268821574 9.67368967 10.47449038 11.68025142 1.559014482 1 8.031446002 -8.595441433 1.49373885 1.196871266 11.03643712 0.990196948 0.411860076 0.02447188 0.107930268 0.061729856 0.1722045 2.54E-09 8.595441433 9.839565857 up (ac)ATTAELFEEPFVADEYIER ddPTM_HeLa_Romidepsin_16h_R1 1 ATTAELFEEPFVADEYIER 19 0 G3V377;F8W9B8;A0A0A0MSI8;O00471 G3V377 EXOC5 Exocyst complex component 5 0 0 75.669 0.0017697 1068000 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 (ac)ATTATMATSGS(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 1 ATTATMATSGSAR 13 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 1 0 ATTATMAT(0.002)S(0.004)GS(0.994)AR 102.63 0.0010681 30628000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)ATTATMATSGS(ph)ARK ddPTM_HeLa_Romidepsin_16h_R1 1 ATTATMATSGSARK 14 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 1 0 ATTATMAT(0.01)S(0.007)GS(0.983)ARK 70.889 0.0014337 2379900 1011 1038 825.61 749.59 1307.9 1288.2 843.27 1258.8 1056.4 713.29 TRUE FALSE FALSE 998.6775431 1052.612991 839.9793957 836.2611227 1241.152983 1205.888177 914.8973328 1295.221392 961.9129382 694.758623 1.437445337 1.515077261 1.209023347 1.203671455 1.786452073 1.735693718 1.316856391 1.864275374 1.384528247 1 9.440368025 -14.1659056 0.111098715 1.40E-12 1.900483506 0.27789107 0.227045778 33.1964119 0.491597397 9.868352957 1.579853774 6.82E-15 14.1659056 1.900483506 (ac)ATVVVEATEPEPSGSIANPAAST(ph)SPSLSHR ddPTM_HeLa_Romidepsin_16h_R1 1 ATVVVEATEPEPSGSIANPAASTSPSLSHR 30 0 P46821;D6RA32;D6RCL2;D6RGJ3 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 ATVVVEATEPEPSGSIANPAAS(0.056)T(0.384)S(0.384)PS(0.164)LS(0.011)HR 62.51 7.13E-07 21749000 411.29 296.16 383.58 320.32 283.46 290.91 359.55 372.35 386.11 278.81 TRUE FALSE FALSE 406.2770393 300.3293483 390.256049 357.3569056 268.9939785 272.3217899 390.090168 383.1233598 351.5753546 271.566476 1.496050047 1.105914665 1.43705532 1.3159095 0.99052719 1.002781322 1.43644449 1.410790335 1.294619865 1 8.085161584 -12.63363932 1.468306849 1.000617546 1.297245559 0 0.196922584 0.469427628 1.824547413 0.134651383 0.030923575 2.32E-13 12.63363932 0.296628013 (ac)ATVVVEATEPEPSGSIANPAASTS(ph)PSLSHR ddPTM_HeLa_Romidepsin_16h_R1 1 ATVVVEATEPEPSGSIANPAASTSPSLSHR 30 0 P46821;D6RA32;D6RCL2;D6RGJ3 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 ATVVVEATEPEPS(0.001)GS(0.004)IANPAAS(0.18)T(0.18)S(0.444)PS(0.18)LS(0.011)HR 60.078 5.03E-07 19292000 262.02 180.04 236.44 179.01 254.5 206.63 233.11 277.45 351.41 259.41 TRUE FALSE FALSE 258.8263995 182.5746078 240.555139 199.7079785 241.5119153 193.4270099 252.9103576 285.477578 319.9790095 252.6704908 1.024363386 0.72257986 0.952050785 0.790389008 0.955837441 0.765530669 1.000949326 1.129841388 1.266388522 1 7.981113373 (ac)ATVWDEAEQDGIGEEVLK ddPTM_HeLa_Romidepsin_16h_R1 2 ATVWDEAEQDGIGEEVLK 18 0 R4GNH3;E9PN50 R4GNH3 PSMC3 0 0 ; ; 234.49 9.06E-236 7258900 4459.7 4304.6 4064.5 4309.2 4305.3 4222.5 3677.8 3585.7 5089.2 4452.4 FALSE FALSE TRUE 4405.343461 4365.200272 4135.240918 4807.449979 4085.584476 3952.695877 3990.19224 3689.446572 4634.009206 4336.726006 1.01582241 1.006565844 0.953539816 1.108543628 0.942089602 0.911446993 0.92009323 0.850744679 1.068550146 1 12.08239058 -8.531916212 24.99932065 1.010029807 0.901707031 0.637839404 0.044155354 88.16589362 243882.8946 0.005341516 0.010694737 2.94E-09 8.531916212 -0.108322777 (ac)AVADLALIPDVDIDSDGVFK ddPTM_HeLa_Romidepsin_16h_R1 2 AVADLALIPDVDIDSDGVFK 20 0 Q9NRX4-2;Q9NRX4 Q9NRX4-2 PHPT1 14 kDa phosphohistidine phosphatase 0 0 ; ; 196.7 9.79E-80 12631700 7246.8 6142.7 6056.6 6020.2 7321.8 7149.5 6092.4 6597.1 7712.9 6379 FALSE FALSE TRUE 7158.473214 6229.177092 6162.012582 6716.28385 6948.141225 6692.670024 6609.888304 6787.97668 7023.038907 6213.27266 1.152126038 1.002559751 0.991749907 1.080957527 1.118273993 1.077156981 1.063833613 1.092496185 1.130328458 1 12.60113765 -9.020515228 24.75402543 1.060792716 1.087219037 0.080060479 0.051644088 2178.091839 2628123.434 0.009837194 0.016474916 9.54E-10 9.020515228 0.026426321 (ac)AVAVGRPS(ph)NEELR ddPTM_HeLa_Romidepsin_16h_R1 1 AVAVGRPSNEELR 13 1 D6RGI3;D6RER5;Q9NVA2 D6RGI3 Sep-11 Septin-11 1 0 AVAVGRPS(1)NEELR 78.964 0.00096648 10305000 169.6 125.02 142.31 181.91 187.98 198.06 198.55 130.23 250.68 133.24 TRUE FALSE FALSE 167.53285 126.7800348 144.7868459 202.9432901 178.3866791 185.4046052 215.414832 133.9979996 228.258553 129.7784056 1.290914688 0.976896228 1.115646669 1.563767787 1.374548241 1.428624465 1.659866532 1.032513837 1.758833081 1 7.019906537 -9.278168861 24.14235009 1.124795195 1.424500097 0.040631934 0.264213865 394.5320706 569348.9417 0.027337641 0.041835276 5.27E-10 9.278168861 0.299704901 (ac)DDDIAALVVDNGSGMCK ddPTM_HeLa_Romidepsin_16h_R1 1 DDDIAALVVDNGSGMCK 17 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7 P60709 ACTB "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed" 0 0 95.094 1.07E-94 0 75 64.082 0 0 0 71.845 0 0 0 0 FALSE FALSE TRUE 74.08587115 64.98414808 0 0 0 67.25433637 0 0 0 0 0 (ac)DDS(ph)KQES(ph)TTS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DDSKQESTTSK 11 1 E9PJY3;Q9C0D2-4 E9PJY3 CEP295 3 0 DDS(0.904)KQES(0.761)T(0.191)T(0.267)S(0.877)K 42.19 0.004258 0 902.1 640.42 897.41 511.41 825.42 932.23 679.49 703.16 730.97 692.65 TRUE FALSE FALSE 891.1048582 649.4358496 913.0290446 570.5416305 783.2957373 872.6635116 737.2058636 723.5048252 665.5902125 674.6548531 1.320830724 0.962619399 1.353327617 0.84567928 1.161031798 1.293496234 1.092715572 1.072407353 0.986564032 1 9.398005812 -10.24659896 24.85463834 1.151503411 1.118849346 0 0.16369499 5055.712019 8467289.925 0.028598704 0.034937402 5.67E-11 10.24659896 -0.032654066 (ac)DFSS(ph)NGK ddPTM_HeLa_Romidepsin_16h_R1 1 DFSSNGK 7 0 A0A087WXC6 A0A087WXC6 TBL2 1 0 DFS(0.002)S(0.998)NGK 47.045 0.030158 9424400 17658 16140 19830 7178.5 13600 15861 12931 8099.9 19818 19914 TRUE FALSE FALSE 17442.7775 16367.21934 20175.13283 8008.511946 12905.94125 14847.53329 14029.35882 8334.257827 18045.42844 19396.63141 0.89926839 0.84381762 1.040135908 0.412881586 0.665370238 0.765469683 0.723288416 0.429675527 0.930338267 1 14.2435185 -9.273963074 24.99951213 0.947329759 0.619121367 0.680331092 0.117274334 348.0496381 694767.4929 0.017962325 0.027555125 5.32E-10 9.273963074 -0.328208392 (ac)DQS(ph)S(ph)EGCMK ddPTM_HeLa_Romidepsin_16h_R1 1 DQSSEGCMK 9 0 Q4G0S7-2;Q4G0S7 Q4G0S7-2 CCDC152 Coiled-coil domain-containing protein 152 2 0 DQS(1)S(1)EGCMK 44.135 0.0043107 0 493.62 455.34 316.99 896.67 622.28 584.43 642.82 576.24 625.55 602.6 TRUE FALSE FALSE 487.6035696 461.7502885 322.507078 1000.347204 590.5227296 547.0868092 697.4211148 592.9125952 569.5992413 586.9443651 0.830749213 0.78670197 0.549467883 1.704330536 1.006096599 0.932093128 1.188223546 1.010168306 0.970448436 1 9.19707995 -9.304798551 24.99998566 0.880652281 1.147176538 0.336350674 0.232454093 506.2362896 291883.8988 0.035263079 0.053865474 4.96E-10 9.304798551 0.266524256 (ac)EEEIAALVIDNGSGMCK ddPTM_HeLa_Romidepsin_16h_R1 1 EEEIAALVIDNGSGMCK 17 0 P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65 P63261 ACTG1 "Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 0 114.72 2.58E-29 446440 122.45 0 47.457 0 137.62 125.13 61.06 122.86 65.695 0 FALSE FALSE TRUE 120.9575323 0 48.28296918 0 130.5967379 117.1345968 66.24643488 126.4147603 59.81907466 0 0 (ac)GDS(ph)DDEYDR ddPTM_HeLa_Romidepsin_16h_R1 2 GDSDDEYDR 9 0 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;A0A087X0F4 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 1 0 GDS(1)DDEYDR;GDS(1)DDEYDR ; 112.36 0.0069701 8224800 180.148 318.4 291.45 288.33 343.78 222.252 423.64 178.91 260.13 240.92 TRUE FALSE FALSE 177.9522869 322.8824436 296.522565 321.6680712 326.2356238 208.0508145 459.623971 184.0864786 236.8633213 234.6608637 0.758338157 1.375953529 1.263621724 1.370778519 1.390243003 0.8866021 1.958673312 0.784478825 1.009385705 1 7.874433442 -10.2566208 24.93867107 0.885881906 1.306191228 0.228734469 0.306011516 333.7064566 1727106.111 0.045991224 0.055374811 5.54E-11 10.2566208 0.420309322 (ac)GK(ac)FMKPGK ddPTM_HeLa_Romidepsin_16h_R1 1 GKFMKPGK 8 2 P61353;K7EQQ9;K7ERY7 P61353 RPL27 60S ribosomal protein L27 0 1 GK(0.999)FMK(0.001)PGK 41.979 0.021625 2378600 783.72 695.17 971.21 814.25 560.1 699.54 834.35 498.3 1115.8 770.32 FALSE TRUE FALSE 774.1677192 704.9566215 988.1135026 908.3974162 531.516007 654.8416517 905.2196682 512.7175243 1016.000053 750.3069754 1.031801309 0.939557601 1.316945644 1.210701014 0.708398062 0.872764979 1.206465751 0.683343673 1.354112499 1 9.55133716 -8.765895497 24.99999636 1.046469562 0.892296306 0.242630714 0.196250351 159.2197224 893271.6324 0.02480328 0.04608963 1.71E-09 8.765895497 -0.154173256 (ac)GTRDDEYDYLFK ddPTM_HeLa_Romidepsin_16h_R1 2 GTRDDEYDYLFK 12 1 B4DQU5;H3BMH2;H3BSC1;P62491-2;Q15907-2;P62491;Q15907 B4DQU5 RAB11A;RAB11B Ras-related protein Rab-11A;Ras-related protein Rab-11B 0 0 ; ; 99.013 0.00017313 25909000 4046.4 4595.6 4182.5 3640.5 4044 4749.4 3534.4 5263.9 4452.2 3719.4 FALSE FALSE TRUE 3997.08092 4660.296977 4255.294658 4061.431739 3837.61959 4445.928668 3834.611848 5416.202641 4053.984081 3622.769452 1.103321913 1.286390713 1.174597146 1.121084792 1.059305496 1.227218217 1.058475263 1.495044803 1.119029001 1 11.82287728 -4.00000001 0.051243915 0.643923896 2.114739733 0.210162249 0.120950431 348.02617 1.358652149 9.154991038 40.38545951 1.00E-04 4.00000001 1.470815837 (ac)GY(ph)S(ph)AVPK ddPTM_HeLa_Romidepsin_16h_R1 1 GYSAVPK 7 0 Q96CP7-2 Q96CP7-2 2 0 GY(1)S(1)AVPK 42.474 0.023648 982590 1072.7 962.9 994.68 1020.6 640.82 636.3 547.12 509.87 1239.8 1106.4 TRUE FALSE FALSE 1059.62552 976.4557315 1011.991988 1138.606574 608.1165642 595.6424836 593.5923591 524.622284 1128.909183 1077.655569 0.983269192 0.906092596 0.939068119 1.056558893 0.564295849 0.552720647 0.550818254 0.486818144 1.047560293 1 10.07368043 -8.75377888 24.90916535 0.984357607 0.540535409 0.957954347 0.046189126 21.11690588 68663.90836 0.006142402 0.012100247 1.76E-09 8.75377888 -0.443822198 (ac)IKSS(ph)WFYVK ddPTM_HeLa_Romidepsin_16h_R1 1 IKSSWFYVK 9 1 A0A590UK55 A0A590UK55 1 0 IKS(0.356)S(0.636)WFY(0.008)VK 43.635 0.0034319 0 974 769.93 796.72 5533.8 748.57 773.66 823.5 588.88 983.28 880.65 TRUE FALSE FALSE 962.1285134 780.7690947 810.5865774 6173.643993 710.3676796 724.2256229 893.4480694 605.9183137 895.3329741 857.770586 1.121661816 0.910230669 0.944992275 7.197313703 0.828155793 0.844311561 1.04159327 0.706387376 1.043790716 1 9.744448035 (ac)LFT(ph)SFVEQKK ddPTM_HeLa_Romidepsin_16h_R1 1 LFTSFVEQKK 10 1 Q8NC67-2 Q8NC67-2 1 0 LFT(0.999)S(0.001)FVEQKK 61.999 0.0030393 0 945.51 2059.2 796.13 1282.6 988.98 835.4 617.64 831.53 1026.3 1096.4 TRUE FALSE FALSE 933.9857604 2088.189472 809.9863087 1430.900247 938.5086602 782.0206361 670.1023262 855.5890086 934.5051576 1067.91537 0.874587806 1.955388536 0.758474249 1.339900414 0.878823067 0.732287088 0.627486358 0.80117679 0.875074171 1 10.06058161 -8.523537154 24.98400831 1.03672913 0.726787226 0.215693462 0.329009056 30.86481637 1171204.867 0.046916996 0.094514621 3.00E-09 8.523537154 -0.309941904 (ac)MAAAGEGTPS(ph)S(ph)RGPRR ddPTM_HeLa_Romidepsin_16h_R1 1 MAAAGEGTPSSRGPRR 16 2 B4DRE3;Q5T089-2;Q5T089 B4DRE3 MORN1 MORN repeat-containing protein 1 2 0 MAAAGEGT(0.518)PS(0.588)S(0.894)RGPRR 41.621 0.0042767 0 135.11 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 133.4632274 0 0 0 0 0 0 0 0 0 0 (ac)MAPMPTGQK ddPTM_HeLa_Romidepsin_16h_R1 1 MAPMPTGQK 9 0 P85299-2 P85299-2 0 0 42.109 0.029332 5445600 185.79 236.44 268.18 200.79 418 257.01 184.91 162.5 165.14 215.11 FALSE FALSE TRUE 183.52552 239.7686085 272.8475604 224.0062845 396.6679002 240.5878905 200.6162508 167.2016811 150.3694648 209.5214112 0.875927281 1.144363276 1.302241899 1.069133141 1.893209376 1.14827353 0.957497612 0.798017158 0.717680661 1 7.710953872 -10.13070304 4.771616951 0.9418875 1.208830028 0.202959297 0.281234908 0.314588184 10.9607712 0.046461742 0.057282255 7.40E-11 10.13070304 0.266942529 (ac)MAPS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 MAPSPTK 7 0 H3BMS0;Q15287-3;Q15287-2 H3BMS0 RNPS1 RNA-binding protein with serine-rich domain 1 1 0 MAPS(0.988)PT(0.012)K 93.178 0.0055693 3777800 7181 7353.3 6377 6489.4 7235.8 6728.5 5990.3 6859.8 7422.3 6734.5 TRUE FALSE FALSE 7093.47521 7456.81995 6487.98901 7239.734962 6866.530126 6298.570565 6499.115932 7058.27749 6758.430899 6559.536719 1.081398811 1.136790641 0.989092567 1.10369608 1.046801081 0.960215764 0.990788864 1.076032926 1.030321376 1 12.67937821 -8.468733883 24.89303494 1.048605956 1.006576491 0.14171579 0.050347098 525.9279987 241794.0028 0.007730786 0.017286404 3.40E-09 8.468733883 -0.042029465 (ac)MAPSSPR ddPTM_HeLa_Romidepsin_16h_R1 1 MAPSSPR 7 0 K7EKL8;E7ESS4;P05362 K7EKL8 ICAM1 Intercellular adhesion molecule 1 0 0 40.921 0.02902 7154800 419.72 403.62 494.55 253.01 503.6 373.55 482.72 579.03 497.8 468.6 FALSE FALSE TRUE 414.6042912 409.302173 503.1574353 282.2642066 477.8994128 349.6813606 523.7222248 595.7833195 453.2755212 456.4257044 0.908371915 0.896755308 1.102386282 0.618423117 1.047047544 0.766129859 1.147442442 1.305323766 0.993098147 1 8.834236232 -7.55990097 5.979086916 0.934171687 1.269926319 0.473231988 0.13430681 0.093390332 8.934466916 0.016776602 0.067405445 2.75E-08 7.55990097 0.335754632 (ac)MATART(ph)FGPER ddPTM_HeLa_Romidepsin_16h_R1 1 MATARTFGPER 11 1 C9J715;Q9Y2I1-4;Q9Y2I1-3;Q9Y2I1 C9J715 NISCH Nischarin 1 0 MAT(0.118)ART(0.882)FGPER 48.004 0.027191 1637600 1427.8 1112.1 1095.6 1215.9 1384.8 1405.9 1498 1044.7 1432.3 1253.3 TRUE FALSE FALSE 1410.397424 1127.756173 1114.668458 1356.488079 1314.128489 1316.067527 1625.240083 1074.926746 1304.191501 1220.739085 1.155363535 0.923830642 0.913109502 1.1112023 1.076502346 1.078090759 1.331357456 0.880554051 1.068362205 1 10.25353916 -8.64113292 2.121818627 1.051071923 1.115650887 0.039353277 0.124580224 0.882114337 8.023433026 0.019083811 0.044529771 2.28E-09 8.64113292 0.064578964 (ac)MATFHRAHAT(ph)S(ph)SVK ddPTM_HeLa_Romidepsin_16h_R1 1 MATFHRAHATSSVK 14 1 Q9Y4M8 Q9Y4M8 LINC00588 Putative uncharacterized protein encoded by LINC00588 2 0 MAT(0.034)FHRAHAT(0.951)S(0.558)S(0.458)VK 43.305 0.023806 6571500 1596.6 922.76 1048.3 14422 0 380.52 1139.6 1074.3 1093.7 1739.1 TRUE FALSE FALSE 1577.140025 935.7506395 1066.545222 16089.5395 0 356.2060001 1236.397596 1105.383176 995.8767328 1693.917931 0.93106047 0.552417931 0.629632169 9.498417367 0 0.210285276 0.729904072 0.652560053 0.587913213 1 10.72614826 (ac)MDDREDLVYQAK ddPTM_HeLa_Romidepsin_16h_R1 1 MDDREDLVYQAK 12 1 P62258;I3L0W5;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 0 53.751 0.020015 68718000 3175 3505.2 2872.6 2665.9 3420.5 3160.9 3059.6 3200.3 3607.9 2975.6 FALSE FALSE TRUE 3136.301879 3554.546298 2922.596398 2974.143901 3245.939121 2958.928691 3319.482348 3292.895631 3285.200388 2898.293483 1.082120185 1.226427316 1.00838525 1.026170717 1.11994839 1.020921004 1.145323055 1.136149824 1.13349473 1 11.50098798 -11.80306928 0.894691373 1.004465614 1.093246174 0 0.075111492 0.607389087 0.955501717 0.030500616 0.012709461 1.57E-12 11.80306928 0.088780559 (ac)MDEMATTQISKDELDELKEAFAK ddPTM_HeLa_Romidepsin_16h_R1 1 MDEMATTQISKDELDELKEAFAK 23 2 P13797;U3KQI3;F2Z2Z9 P13797 PLS3 Plastin-3 0 0 61.139 0.0068123 6930100 580.3 484.14 500.27 596.74 488.86 758.88 569.75 694 587.09 603.61 FALSE FALSE TRUE 573.2270804 490.9557356 508.9769895 665.7378865 463.91165 710.3900172 618.1445508 714.079795 534.5792 587.9281252 0.974995167 0.835060809 0.865712946 1.132345704 0.789061843 1.208293985 1.051394761 1.214569884 0.909259444 1 9.199495985 -8.234927382 24.99542581 0.966337995 1.147417078 0.479930167 0.104041505 555.4558073 523681.5862 0.013483607 0.034366098 5.82E-09 8.234927382 0.181079083 (ac)MDEPS(ph)PLAQPLELNQHSR ddPTM_HeLa_Romidepsin_16h_R1 2 MDEPSPLAQPLELNQHSR 18 0 A0A087X2F8;A0A087X126;A0A0C4DGT1;Q13085 A0A087X2F8 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 0 MDEPS(1)PLAQPLELNQHSR;MDEPS(1)PLAQPLELNQHSR ; 160.56 7.29E-49 68342000 374.96 551.21 345.51 304.37 315.08 195.46 324.27 643.47 546.43 516.33 TRUE FALSE FALSE 370.3898433 558.9699488 351.5234566 339.5626915 299.0002919 182.9707368 351.8134857 662.0877892 497.5559322 502.9156722 0.736484989 1.1114586 0.698970973 0.675188129 0.594533653 0.363819914 0.699547668 1.316498622 0.989342667 1 8.974172702 -9.617640208 23.95541405 0.890515512 0.698942777 0.153988281 0.24483553 18.94181437 4773.42446 0.039243834 0.055499167 2.41E-10 9.617640208 -0.191572735 (ac)MDGFAGS(ph)LDDSISAASTSDVQDR ddPTM_HeLa_Romidepsin_16h_R1 1 MDGFAGSLDDSISAASTSDVQDR 23 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 MDGFAGS(0.59)LDDS(0.308)IS(0.091)AAS(0.009)T(0.001)S(0.001)DVQDR 48.919 0.0025391 0 0 0 143.52 231.54 0 151.06 152.66 120.81 183.04 139.45 TRUE FALSE FALSE 0 0 146.0179054 258.3117442 0 141.4077535 165.6269366 124.3054467 166.668444 135.8270689 0 0 1.075028023 1.901769259 0 1.04108669 1.219395647 0.91517433 1.22706354 1 7.085627212 -9.725532809 24.91881515 0.474999858 1.02816461 0.136519024 0.562537289 228.3242149 158454.4435 0.091522287 0.129429457 1.88E-10 9.725532809 0.553164752 (ac)MDGFAGSLDDSISAAS(ph)TSDVQDR ddPTM_HeLa_Romidepsin_16h_R1 1 MDGFAGSLDDSISAASTSDVQDR 23 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 MDGFAGSLDDSIS(0.001)AAS(0.863)T(0.12)S(0.017)DVQDR 184.97 3.66E-113 6640000 0 0 0 72.001 0 0 0 204.33 0 0 TRUE FALSE FALSE 0 0 0 80.32609439 0 0 0 210.2419662 0 0 0 (ac)MDHTEGS(ph)PAEEPPAHAPSPGK ddPTM_HeLa_Romidepsin_16h_R1 1 MDHTEGSPAEEPPAHAPSPGK 21 0 D6R946;Q06330 D6R946 RBPJ Recombining binding protein suppressor of hairless 1 0 MDHT(0.181)EGS(0.819)PAEEPPAHAPSPGK 47.814 0.0014951 3349600 2631 2442 2172.2 2152.9 2749.2 2668.3 2199.5 2544.9 2950 2775 TRUE FALSE FALSE 2598.93236 2476.37854 2210.00623 2401.828428 2608.898065 2497.804242 2386.325475 2618.532666 2686.144612 2702.9051 0.961532967 0.916191449 0.817641074 0.888609973 0.965220002 0.924118365 0.88287431 0.968784537 0.993799084 1 11.40029514 -10.45125756 2.258486693 0.985200372 0.90652717 0.42644185 0.041104499 0.216489321 2.138477991 0.008001787 0.008860654 3.54E-11 10.45125756 -0.078673202 (ac)MDK(ac)SELVQK ddPTM_HeLa_Romidepsin_16h_R1 1 MDKSELVQK 9 1 P31946-2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 1 MDK(1)SELVQK 57.047 0.0082444 416670 264.13 161.64 170.22 184.14 582.54 340.14 331.18 350.14 651.71 292.28 FALSE TRUE FALSE 260.910682 163.9155722 173.1826077 205.4311332 552.81081 318.4061518 359.3104209 360.2707485 593.4194254 284.6865235 0.916484134 0.575775664 0.608327383 0.721604699 1.941822898 1.118444765 1.262126554 1.265499835 2.084466163 1 8.15323039 -8.80536581 24.99999921 0.883290347 1.367450524 0.142506257 0.454670785 91.26551176 51941.93208 0.038404501 0.069614359 1.57E-09 8.80536581 0.484160176 (ac)MDLAAAAEPGAGS(ph)QHLEVR ddPTM_HeLa_Romidepsin_16h_R1 2 MDLAAAAEPGAGSQHLEVR 19 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 MDLAAAAEPGAGS(1)QHLEVR;MDLAAAAEPGAGS(1)QHLEVR ; 191.07 8.86E-29 79557000 0 0 0 0 0 0 60.295 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 65.4164558 0 0 0 0 (ac)MDLAAAAEPGAGS(ph)QHLEVRDEVAEK ddPTM_HeLa_Romidepsin_16h_R1 2 MDLAAAAEPGAGSQHLEVRDEVAEK 25 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 MDLAAAAEPGAGS(1)QHLEVRDEVAEK;MDLAAAAEPGAGS(1)QHLEVRDEVAEK ; 60.379 6.84E-07 36329000 5233.6 5991.3 5133.1 7433.6 4385.3 4063.5 2998.3 4647 6466.7 5186.4 TRUE FALSE FALSE 5169.81087 6075.645679 5222.439452 8293.107808 4161.501777 3803.855464 3252.975527 4781.453613 5888.302156 5051.65658 1.023389217 1.202703624 1.0338073 1.641661043 0.823789525 0.752991698 0.643942334 0.946512008 1.165618063 1 12.30254085 -8.549960687 24.99983227 1.075149657 0.770921157 0.423180333 0.200674546 181.8090541 167830.5651 0.028980181 0.057961414 2.82E-09 8.549960687 -0.3042285 (ac)MDLFGDLPEPERS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 MDLFGDLPEPERSPR 15 1 F8SNU6;E9PC05;F8SNU7;Q9H0C8 F8SNU6 ILKAP2;ILKAP;ILKAP3 Integrin-linked kinase-associated serine/threonine phosphatase 2C 1 0 MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR;MDLFGDLPEPERS(1)PR ;; 77.42 0.0057168 30938800 1005.98 1078.66 939.59 1163.89 1259.08 1404.51 1078.69 1211.71 940.421 973.84 TRUE FALSE FALSE 993.7187288 1093.845404 955.9431698 1298.464438 1194.824449 1314.766344 1170.313902 1246.768917 856.3073904 948.5394964 1.047630312 1.153189095 1.00780534 1.368909195 1.259646492 1.386095517 1.23380619 1.31440907 0.902764085 1 9.889564037 -9.265677756 24.99938169 1.033943588 1.309341536 0.804278011 0.071477698 99.65241412 587783.3347 0.008894768 0.013894704 5.42E-10 9.265677756 0.275397949 (ac)MDNYADLS(ph)DTELTTLLR ddPTM_HeLa_Romidepsin_16h_R1 3 MDNYADLSDTELTTLLR 17 0 P50402;Q5HY57;F8WEQ1 P50402 EMD Emerin 1 0 MDNYADLS(0.999)DT(0.001)ELTTLLR;MDNY(0.088)ADLS(0.911)DT(0.001)ELTTLLR;MDNYADLS(0.986)DT(0.011)ELTT(0.002)LLR ;; 184.87 3.35E-46 22290300 328.74 451.73 426.22 702.89 433.993 469.884 468.567 553.917 343.366 209.02 TRUE FALSE FALSE 324.7331904 458.0894668 433.6381803 784.161449 411.8447178 439.8599289 508.3670693 569.9437145 312.654485 203.5896303 1.595037969 2.250062865 2.129962021 3.851676767 2.022915987 2.160522264 2.497018481 2.799473204 1.535709282 1 7.66952027 -10.3818067 1.072350754 1.173524244 2.600131302 0.536310075 0.503198313 0.221205466 0.503565868 0.107973844 0.121040603 4.15E-11 10.3818067 1.426607059 (ac)MDRNPS(ph)PPPPGR ddPTM_HeLa_Romidepsin_16h_R1 1 MDRNPSPPPPGR 12 1 E9PL53;E9PMD2;J3KND1;E9PRZ1;Q96ER3 E9PL53 SAAL1 Protein SAAL1 1 0 MDRNPS(1)PPPPGR 57.55 0.019643 88650000 484.52 170.6 268.71 262.94 284.58 176.04 332.01 371.36 544.49 328.35 TRUE FALSE FALSE 478.6144839 173.0017113 273.3867848 293.34236 270.0568207 164.7916121 360.2109211 382.1047157 495.7894507 319.8194197 1.496514766 0.540935605 0.854816087 0.91721247 0.844404073 0.515264559 1.126294712 1.194751451 1.550216842 1 8.321113733 -10.26626892 24.99961983 1.234465301 0.855347262 0.42733372 0.251079482 373.245021 1932060.796 0.045745829 0.053196229 5.42E-11 10.26626892 -0.37911804 (ac)MDS(ph)AGQDINLNSPNK ddPTM_HeLa_Romidepsin_16h_R1 1 MDSAGQDINLNSPNK 15 0 O43399;O43399-5;O43399-7;A0A087WYR3;O43399-2;O43399-4;O43399-3;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 0 MDS(0.998)AGQDINLNS(0.002)PNK 185.61 1.62E-34 12827000 4203 3755.4 4268 2135.8 3500.9 3758.6 2826.6 3696.5 4108.3 3818.2 TRUE FALSE FALSE 4151.772219 3808.26862 4342.28275 2382.751245 3322.236009 3518.43759 3066.691333 3803.452395 3740.843359 3719.002614 1.116367115 1.024002674 1.167593358 0.640696308 0.893313707 0.946070212 0.824600478 1.022707643 1.005872743 1 11.86070005 -9.28756342 24.99889183 1.061213607 0.869230463 0.476506906 0.103350027 498.0982093 476643.8959 0.015426186 0.023568574 5.16E-10 9.28756342 -0.191983144 (ac)MDS(ph)AGQDINLNSPNKGLLSDSMTDVPVDTGVAAR ddPTM_HeLa_Romidepsin_16h_R1 1 MDSAGQDINLNSPNKGLLSDSMTDVPVDTGVAAR 34 1 O43399;O43399-5;O43399-7;A0A087WYR3;O43399-2;O43399-4;O43399-3;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 0 MDS(0.439)AGQDINLNS(0.439)PNKGLLS(0.071)DS(0.028)MT(0.022)DVPVDTGVAAR 40.064 8.48E-05 32350000 634.67 328.28 354.1 423.58 395.98 432.6 290.22 153.62 337.58 451.13 TRUE FALSE FALSE 626.9343979 332.9015345 360.262962 472.5563126 375.771663 404.9582562 314.8712796 158.0647523 307.3859993 439.4095776 1.426765437 0.757611011 0.81987963 1.075434712 0.855174038 0.921596335 0.716578099 0.359720772 0.699543239 1 8.779422505 -7.311906393 0.454397639 1.169767861 3.44E-15 0.194084928 0.23745482 2.88003044 0.410507995 0.054688812 1.792019428 4.88E-08 7.311906393 -1.169767861 (ac)MDSAGQDINLNS(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 3 MDSAGQDINLNSPNK 15 0 O43399;O43399-5;O43399-7;A0A087WYR3;O43399-2;O43399-4;O43399-3;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 0 MDSAGQDINLNS(1)PNK;MDSAGQDINLNS(1)PNK;MDSAGQDINLNS(1)PNK ;; 235.38 3.15E-134 61732000 17239.2 16421.5 18676.9 9285.7 16174.9 17714.2 14876.9 15529.5 18312.8 18732 TRUE FALSE FALSE 17029.082 16652.68231 19001.96361 10359.35632 15349.4345 16582.31979 16140.54351 15978.82158 16674.8573 18245.33994 0.933338708 0.912708799 1.04146942 0.567780943 0.841279721 0.908852334 0.884639232 0.875775493 0.913924178 1 14.15524041 (ac)MDTDLYDEFGNYIGPELDS(ph)DEDDDELGR ddPTM_HeLa_Romidepsin_16h_R1 1 MDTDLYDEFGNYIGPELDSDEDDDELGR 28 0 Q15029-3;Q15029;K7EIV5;K7EIT3 Q15029-3 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 1 0 MDT(0.013)DLY(0.003)DEFGNY(0.001)IGPELDS(0.984)DEDDDELGR 86.191 3.60E-16 0 67.318 0 56.377 0 129.99 0 133.32 0 0 128.54 TRUE FALSE FALSE 66.49750232 0 57.35821804 0 123.3561252 0 144.6441975 0 0 125.2005123 0.531128037 0 0.458130857 0 0.985268534 0 1.155300365 0 0 1 6.968096655 -11.57536225 0.883704546 0.957877855 0.403793929 0 0.4981619 0.520995822 0.829335044 0.149440665 0.075467718 2.66E-12 11.57536225 -0.554083926 (ac)MDVAES(ph)PERDPHSPEDEEQPQGLSDDDILR ddPTM_HeLa_Romidepsin_16h_R1 2 MDVAESPERDPHSPEDEEQPQGLSDDDILR 30 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 MDVAES(0.859)PERDPHS(0.141)PEDEEQPQGLSDDDILR;MDVAES(0.635)PERDPHS(0.357)PEDEEQPQGLS(0.008)DDDILR ; 49.968 0.0051439 27567000 479.02 413.192 282.08 423.82 270.93 209.53 409.29 279.73 395.15 297.57 TRUE FALSE FALSE 473.18152 419.0089278 286.9894841 472.8240625 257.1034311 196.1417092 444.0550824 287.8235462 359.8067943 289.8390885 1.632566271 1.445660521 0.990168323 1.631332975 0.887055754 0.676726215 1.53207452 0.993045996 1.241401897 1 8.179108364 -8.736562631 24.99680245 1.312989834 1.033964906 0.207518787 0.287639342 360.3283108 362065.5347 0.047858755 0.095685917 1.83E-09 8.736562631 -0.279024928 (ac)MEDKVT(ph)SPEKAEEAK ddPTM_HeLa_Romidepsin_16h_R1 1 MEDKVTSPEKAEEAK 15 2 H3BTD3;P56211-2 H3BTD3 ARPP19 cAMP-regulated phosphoprotein 19 1 0 MEDKVT(0.975)S(0.025)PEKAEEAK 89.26 0.00020755 0 3255.8 3077.3 2822.8 3072.5 2553.1 2355.3 1906.6 2195.6 3540.1 2968.6 TRUE FALSE FALSE 3216.117057 3120.62231 2871.92965 3427.756907 2422.80578 2204.803931 2068.546556 2259.126222 3223.46459 2891.475344 1.112275456 1.079249151 0.993240235 1.185469872 0.837913346 0.762518669 0.715394845 0.781305719 1.114816558 1 11.49759008 -8.601719557 5.407014325 1.059386187 0.756714767 0.873556637 0.057397966 0.05507418 2.779337063 0.008852323 0.017996634 2.50E-09 8.601719557 -0.30267142 (ac)MEDLDQSPLVS(ph)SSDSPPRPQPAFK ddPTM_HeLa_Romidepsin_16h_R1 1 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-2;Q9NQC3-4 Q9NQC3-5 RTN4 Reticulon-4 1 0 MEDLDQS(0.076)PLVS(0.452)S(0.452)S(0.02)DS(0.001)PPRPQPAFK 47.392 0.0070586 210630000 976.98 867.99 1218.9 860.83 756.84 1095 810 907.39 941.1 1189.5 TRUE FALSE FALSE 965.072192 880.209586 1240.114443 960.3632149 718.2156306 1025.033034 878.8013798 933.643898 856.925659 1158.596619 0.832966519 0.759720486 1.070359108 0.828902139 0.61990137 0.884719511 0.758505045 0.805840344 0.739623822 1 10.17816264 -16.52287875 0.148884836 1.689680316 0.751756294 0 0.133033586 61.08216985 0.6213906 12.28670626 0.252285722 3.00E-17 16.52287875 -0.937924022 (ac)MEDLDQSPLVSSSDS(ph)PPRPQPAFK ddPTM_HeLa_Romidepsin_16h_R1 1 MEDLDQSPLVSSSDSPPRPQPAFK 24 1 Q9NQC3-5;Q9NQC3;Q9NQC3-2;Q9NQC3-4 Q9NQC3-5 RTN4 Reticulon-4 1 0 MEDLDQS(0.003)PLVS(0.044)S(0.044)S(0.044)DS(0.864)PPRPQPAFK 48.315 0.024597 242380000 782.59 743.29 962.58 681.35 724.76 849.38 659.03 690.38 620.31 1011.1 TRUE FALSE FALSE 773.0514921 753.7540561 979.3333011 760.1308928 687.7727927 795.1073592 715.0079918 710.3550561 564.82792 984.8314762 0.784958148 0.76536349 0.994417141 0.771838544 0.698365974 0.807353723 0.726020653 0.721296052 0.573527485 1 9.943733062 -16.52287875 0.166039679 1.874912686 0.718670012 0 0.152445105 32.959881 0.360360772 9.352609745 0.130498507 3.00E-17 16.52287875 -1.156242673 SSS(ph)SGDQSSDSLNSPTLLAL ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSGDQSSDSLNSPTLLAL 20 0 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 0 S(0.274)S(0.274)S(0.441)S(0.012)GDQSSDSLNSPTLLAL 210.91 6.41E-32 1402600 497.48 491.06 260.75 344.66 206.88 307.96 135.07 225.64 490.69 590.95 TRUE FALSE FALSE 491.4165224 497.9731556 265.2882444 384.5112109 196.3221416 288.2823499 146.5428424 232.1685374 446.8014574 575.5970338 0.853750964 0.865141977 0.460892306 0.668021529 0.341075666 0.500840576 0.254592769 0.40335256 0.776240028 1 9.168915347 -9.549351223 0.591177724 0.970777951 0.322125227 0.754492619 0.119641769 0.189835345 0.134806124 0.024269333 0.051218478 2.82E-10 9.549351223 -0.648652724 down (ac)MEDMNEYSNIEEFAEGSK ddPTM_HeLa_Romidepsin_16h_R1 2 MEDMNEYSNIEEFAEGSK 18 0 O14979-3;O14979-2;A0A087WU03 O14979-3 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 0 0 ; ; 156 2.15E-21 2203300 2001.7 1997.13 1645.6 1524.37 1937.99 1813.42 1771.17 1717.02 1927.82 2025.36 FALSE FALSE TRUE 1977.30251 2025.245649 1674.240978 1700.624832 1839.087139 1697.548315 1921.613136 1766.699265 1755.390951 1972.740855 1.002312344 1.02661515 0.84868774 0.862061952 0.932249735 0.860502438 0.974082901 0.895555673 0.889823388 1 10.94598574 -9.769975952 24.99975787 1.003036696 0.897650832 0.367404591 0.050468059 77.17146318 225999.8917 0.005537206 0.00734171 1.70E-10 9.769975952 -0.105385864 (ac)MEEEEEAIGLLDK ddPTM_HeLa_Romidepsin_16h_R1 1 MEEEEEAIGLLDK 13 0 Q12979-2 Q12979-2 0 0 119.34 2.64E-06 1112700 578.4 644.68 650.25 576.1 758.45 766.77 524.02 592.76 766.38 596.31 FALSE FALSE TRUE 571.3502383 653.755822 661.5673285 642.7113926 719.7434663 717.7758716 568.5302457 609.9105754 697.8330534 580.8177802 0.983699635 1.125578183 1.139027335 1.106562875 1.239189796 1.235802167 0.978844424 1.050089367 1.20146641 1 9.181941808 -10.25845593 23.45413349 0.992302602 1.127873435 0 0.09836998 80.95624067 636428.3092 0.012787408 0.015290327 5.51E-11 10.25845593 0.135570833 (ac)MEEGGRDKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 MEEGGRDKAPVQPQQSPAAAPGGTDEKPSGK 31 3 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 0 MEEGGRDKAPVQPQQS(0.997)PAAAPGGT(0.003)DEKPS(0.001)GK 41.205 0.0044414 16502000 3235.4 3001.3 2146 5743.2 2870.3 2881.1 2550.6 3314.9 2949.8 2275.2 TRUE FALSE FALSE 3195.9657 3043.55238 2183.35023 6407.255807 2723.81788 2697.007008 2767.2479 3410.811401 2685.9625 2216.089976 1.442164233 1.373388451 0.985226346 2.891243531 1.229109788 1.21701151 1.248707377 1.539112328 1.212027729 1 11.11380074 -11.88394274 0.582965902 0.967463121 1.5088334 0.085644902 0.496561384 1.6316792 0.971210014 0.44994637 0.121072987 1.31E-12 11.88394274 0.541370278 (ac)MEES(ph)DSEKTTEKENLGPR ddPTM_HeLa_Romidepsin_16h_R1 1 MEESDSEKTTEKENLGPR 18 2 Q5VZM2-2;Q5VZM2 Q5VZM2-2 RRAGB Ras-related GTP-binding protein B 1 0 MEES(0.972)DS(0.022)EKT(0.005)TEKENLGPR 65.943 0.0046658 7028400 1054.2 1407.3 1262.9 1356.3 1313.8 1616.5 971.46 1393.8 1211.8 1463.8 TRUE FALSE FALSE 1041.351005 1427.112006 1284.880245 1513.121788 1246.751884 1513.210867 1053.975788 1434.127404 1103.413573 1425.770265 0.730377839 1.000941064 0.901183224 1.061266197 0.874440935 1.061328676 0.73923255 1.005861491 0.773906989 1 10.47752582 (ac)MEGAAAPVAGDRPDLGLGAPGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MEGAAAPVAGDRPDLGLGAPGSPR 24 1 O60285;O60285-2 O60285 NUAK1 NUAK family SNF1-like kinase 1 1 0 MEGAAAPVAGDRPDLGLGAPGS(1)PR 41.41 0.0017645 12302000 201.92 0 108.8 120.05 0 123.89 116.56 0 238.98 0 TRUE FALSE FALSE 199.4589214 0 110.6936184 133.9307459 0 115.9738288 126.4606035 0 217.6050303 0 0 (ac)MEGIS(ph)NFKTPSK ddPTM_HeLa_Romidepsin_16h_R1 1 MEGISNFKTPSK 12 1 Q96KB5;Q96KB5-2;E5RIE1 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 1 0 MEGIS(0.757)NFKT(0.223)PS(0.02)K 77.124 0.02225 46548000 5270.3 5750.5 6179.3 4924.2 6737.1 6877.1 5267.8 5992.6 6083.4 5695.3 TRUE FALSE FALSE 5206.063556 5831.45569 6286.848124 5493.559173 6393.280647 6437.675505 5715.246801 6165.986426 5539.285468 5547.335285 0.938480061 1.051217457 1.133309562 0.990305956 1.152495805 1.160498721 1.03026886 1.111522219 0.998548886 1 12.43757921 -10.07186134 4.599144058 0.971286524 1.094118768 0.500096353 0.05221313 0.124091816 4.97877456 0.008710468 0.010840977 8.47E-11 10.07186134 0.122832244 (ac)MEGQS(ph)VEELLAK ddPTM_HeLa_Romidepsin_16h_R1 1 MEGQSVEELLAK 12 0 Q15050 Q15050 RRS1 Ribosome biogenesis regulatory protein homolog 1 0 MEGQS(1)VEELLAK 101.39 1.99E-05 0 880.18 643.32 939.92 710.35 673.65 804.51 757.56 1056.2 900.87 912.51 TRUE FALSE FALSE 869.4520276 652.3766758 956.2789133 792.4840093 639.2711268 753.1044074 821.9071275 1086.759481 820.2939309 888.8028587 0.978228208 0.733994799 1.075917909 0.891630806 0.719249629 0.847324466 0.924735018 1.222722756 0.922919996 1 9.795719647 -10.49199129 24.68767011 0.990394883 0.907778829 0.016275844 0.142145241 706.1247468 564396.706 0.023886116 0.026101634 3.22E-11 10.49199129 -0.082616053 (ac)MEGSAS(ph)PPEKPR ddPTM_HeLa_Romidepsin_16h_R1 1 MEGSASPPEKPR 12 1 Q96NT5-2;Q96NT5 Q96NT5-2 SLC46A1 Proton-coupled folate transporter 1 0 MEGS(0.444)AS(0.556)PPEKPR 67.519 0.001536 0 859.73 1420.1 875.43 2689.9 1303.1 2289.3 925.61 1572.2 889.87 1098 TRUE FALSE FALSE 849.2512801 1440.092205 890.6664919 3000.918894 1236.597944 2143.021118 1004.23129 1617.689126 810.2777985 1069.473802 0.794083295 1.34654276 0.832808144 2.805977004 1.156267636 2.003808896 0.93899569 1.512602856 0.757641559 1 10.06268543 (ac)MENSKEEGTSS(ph)SEK ddPTM_HeLa_Romidepsin_16h_R1 1 MENSKEEGTSSSEK 14 1 A0A096LNN3;A0A096LNL7 A0A096LNN3 ATRX 1 0 MENS(0.001)KEEGT(0.026)S(0.156)S(0.661)S(0.156)EK 49.298 0.0043469 0 1288.7 1559.6 1224.2 1187.3 1081.5 1154.3 1277.8 1069.1 1217.8 1183.1 TRUE FALSE FALSE 1272.992829 1581.55609 1245.506687 1324.581212 1026.307019 1080.543955 1386.3363 1100.032722 1108.876918 1152.362891 1.104680512 1.372446216 1.080828528 1.149447993 0.890610959 0.937676806 1.203037958 0.95458881 0.962263646 1 10.17037939 -8.789753094 24.99959585 1.086368573 1.007032506 0.140444001 0.129838261 453.7447983 400632.4304 0.019759245 0.03582135 1.62E-09 8.789753094 -0.079336067 (ac)MEPAPARS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MEPAPARSPR 10 1 P29590-12;P29590-11;H3BT57;P29590-13;P29590-14;P29590-10;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 MEPAPARS(1)PR 113.67 0.0055379 11195000 167.73 0 55.852 0 53.119 0 148.17 62.79 134.15 121.23 TRUE FALSE FALSE 165.6856422 0 56.82408063 0 50.40813922 0 160.7555561 64.60672958 122.151288 118.0804271 1.403159239 0 0.481232004 0 0.426896654 0 1.361407305 0.547141733 1.034475323 1 6.883626035 -10.27056141 24.97238691 1.19038076 0.412291114 0.428445911 0.392396558 428.295029 1172493.5 0.068321398 0.07871002 5.36E-11 10.27056141 -0.778089646 (ac)MEPETALWGPDLQGPEQS(ph)PNDAHR ddPTM_HeLa_Romidepsin_16h_R1 2 MEPETALWGPDLQGPEQSPNDAHR 24 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 0 MEPET(0.003)ALWGPDLQGPEQS(0.997)PNDAHR;MEPETALWGPDLQGPEQS(1)PNDAHR ; 90.454 6.80E-05 5380800 145.75 0 523.81 493.55 118.64 442.527 246.01 311.56 218.21 0 TRUE FALSE FALSE 143.9735429 0 532.9266933 550.6165732 112.5853581 414.2509529 266.9060833 320.574497 198.6927511 0 0 (ac)MEPS(ph)SWSGSESPAENMER ddPTM_HeLa_Romidepsin_16h_R1 1 MEPSSWSGSESPAENMER 18 0 P28347 P28347 TEAD1 Transcriptional enhancer factor TEF-1 1 0 MEPS(0.467)S(0.467)WS(0.028)GS(0.012)ES(0.026)PAENMER 53.869 0.0085911 8130800 0 0 0 65.119 0 0 0 0 0 145.99 TRUE FALSE FALSE 0 0 0 72.64836517 0 0 0 0 0 142.1971588 0 0 0 0.510898852 0 0 0 0 0 1 7.151748828 -12.22853334 0.740902503 1.06932503 0.059259848 0 0.343370447 0.246338567 0.217835138 0.152840538 0.032922563 5.91E-13 12.22853334 -1.010065182 (ac)MES(ph)PASSQPASMPQSK ddPTM_HeLa_Romidepsin_16h_R1 3 MESPASSQPASMPQSK 16 0 X6RB39;J3QL77;E9PMA8;J3QR49;P46734 X6RB39 MAP2K3 Dual specificity mitogen-activated protein kinase kinase 3 1 0 MES(0.899)PAS(0.078)S(0.023)QPASMPQSK;MES(0.914)PAS(0.08)S(0.007)QPASMPQSK;MES(0.995)PAS(0.003)S(0.001)QPASMPQSK ;; 77.279 4.13E-05 6969100 2319.33 2181.41 1740.13 2478.02 4182.2 5022.8 4656.1 4884.6 2441.64 2209.63 TRUE FALSE FALSE 2291.061114 2212.119947 1770.416233 2764.540332 3968.766728 4701.85929 5051.589018 5025.928194 2223.253603 2152.223494 1.064508923 1.027830034 0.822598693 1.2845043 1.844030947 2.184651967 2.347148905 2.335225969 1.033003129 1 11.07161218 -8.639337441 1.785383054 1.014771582 2.31753749 0.982386762 0.077249225 0.032213195 0.206399904 0.012499765 0.031030122 2.29E-09 8.639337441 1.302765908 up (ac)MESQEPTESS(ph)QNGK ddPTM_HeLa_Romidepsin_16h_R1 1 MESQEPTESSQNGK 14 0 C9JYY9;A6NCQ0;A6NJU6;A6NFX8;Q9UKK9 C9JYY9 NUDT5 ADP-sugar pyrophosphatase 1 0 MESQEPT(0.093)ES(0.175)S(0.731)QNGK 113.35 0.0031858 2915200 1125.1 1063.9 1063.1 649.54 1298.4 835.22 803.83 1207.5 1164.3 1170.3 TRUE FALSE FALSE 1111.386848 1078.877612 1081.60281 724.642871 1232.137803 781.8521375 872.1073001 1242.437107 1060.162092 1139.895437 0.974990172 0.946470682 0.948861426 0.63570995 1.080921778 0.68589812 0.765076578 1.089957084 0.930052053 1 10.15468578 -9.503011073 24.45540148 0.982965905 0.844457919 0.124228855 0.139888837 695.0802022 855585.1397 0.01946133 0.029465107 3.14E-10 9.503011073 -0.138507986 (ac)MESSTGPR ddPTM_HeLa_Romidepsin_16h_R1 1 MESSTGPR 8 0 E9PNY9;Q9NQ32-2;Q9NQ32 E9PNY9 C11orf16 Uncharacterized protein C11orf16 0 0 55.441 0.013127 9003200 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 (ac)MESYHKPDQQK ddPTM_HeLa_Romidepsin_16h_R1 1 MESYHKPDQQK 11 1 P29401;P29401-2;E9PFF2;F8WAX4;F8W888 P29401 TKT Transketolase 0 0 45.158 0.0022935 0 929.42 773.36 816.37 361.58 965.55 1046.1 1115.3 797.17 1149.3 891.42 FALSE FALSE TRUE 918.0918715 784.2473824 830.5785774 403.3875809 916.2743805 979.2575861 1210.033554 820.2348562 1046.50373 868.2607799 1.057391849 0.903239442 0.956600363 0.464592655 1.055298594 1.127838098 1.393629175 0.944687213 1.205287344 1 9.761984607 -8.302158848 4.131412484 0.969811991 1.182218798 0.170337362 0.207621566 0.282722184 10.67928793 0.028305412 0.068518755 4.99E-09 8.302158848 0.212406807 (ac)MET(ph)MASPGKDNYR ddPTM_HeLa_Romidepsin_16h_R1 3 METMASPGKDNYR 13 1 S4R3E5;O60684 S4R3E5 KPNA6 Importin subunit alpha-7 1 0 MET(1)MASPGKDNYR;MET(0.905)MAS(0.095)PGKDNYR;MET(0.992)MAS(0.008)PGKDNYR ;; 130.41 0.00047198 1072560000 19600.1 17948.4 18121.3 18032.5 17996 17871.6 14798.3 14333.5 19826 17437.6 TRUE FALSE FALSE 19361.20644 18201.07805 18436.69362 20117.5025 17077.59697 16729.66244 16055.26723 14748.21721 18052.7129 16984.56864 1.139929241 1.071624392 1.085496725 1.184457664 1.005477227 0.984991894 0.945285546 0.868330396 1.062889102 1 14.05193696 -7.92174244 1.389388085 1.07618648 0.879963595 0.664389859 0.051308612 0.317093454 1.026847205 0.009770936 0.061631684 1.20E-08 7.92174244 -0.196222885 (ac)MET(ph)PSQRR ddPTM_HeLa_Romidepsin_16h_R1 4 METPSQRR 8 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 MET(0.665)PS(0.335)QRR;MET(0.943)PS(0.057)QRR;MET(0.868)PS(0.132)QRR;MET(0.947)PS(0.053)QRR ;;; 58.433 0.015997 63240900 0 0 0 0 57.106 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 54.19166773 0 0 0 0 0 0 (ac)METMAS(ph)PGKDNYR ddPTM_HeLa_Romidepsin_16h_R1 1 METMASPGKDNYR 13 1 S4R3E5;O60684 S4R3E5 KPNA6 Importin subunit alpha-7 1 0 MET(0.055)MAS(0.945)PGKDNYR 58.754 0.011241 6892700 1588 1371.5 1465 1199.4 1468.6 1199.7 1470.6 1209.6 1566.4 1377.5 TRUE FALSE FALSE 1568.644845 1390.808013 1490.49771 1338.080271 1393.651862 1123.043042 1595.512727 1244.597868 1426.297261 1341.712351 1.169136472 1.036591794 1.110892144 0.997292952 1.03871136 0.837022213 1.189161541 0.927618998 1.063042506 1 10.38985969 -9.248723183 23.81185561 1.080079548 1.001906452 0.147901059 0.093070149 673.5117092 1261189.967 0.014693052 0.024238199 5.64E-10 9.248723183 -0.078173095 (ac)MEVAEPS(ph)SPTEEEEEEEEHSAEPR ddPTM_HeLa_Romidepsin_16h_R1 1 MEVAEPSSPTEEEEEEEEHSAEPR 24 0 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R3H9 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 MEVAEPS(0.497)S(0.497)PT(0.007)EEEEEEEEHSAEPR 127.5 2.41E-07 3545900 482.04 309.3 404.71 540.05 379.89 437.36 390.89 332.76 436.85 635.41 TRUE FALSE FALSE 476.1647111 313.6543335 411.7538078 602.493122 360.5027957 409.4141075 424.0921868 342.3878856 397.7770419 618.9019566 0.769370182 0.506791633 0.665297311 0.973487183 0.58248773 0.661516906 0.68523323 0.553218296 0.642714145 1 9.273567073 -11.54673632 0.558387304 1.013501249 0.662377829 0 0.164037741 0.548657282 0.344641469 0.090807831 0.034148046 2.84E-12 11.54673632 -0.35112342 (ac)MEVAEPS(ph)SPTEEEEEEEEHSAEPRPR ddPTM_HeLa_Romidepsin_16h_R1 3 MEVAEPSSPTEEEEEEEEHSAEPRPR 26 1 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R3H9 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 MEVAEPS(0.361)S(0.361)PT(0.277)EEEEEEEEHSAEPRPR;MEVAEPS(0.438)S(0.438)PT(0.125)EEEEEEEEHSAEPRPR;MEVAEPS(0.408)S(0.408)PT(0.183)EEEEEEEEHSAEPRPR ;; 88.872 2.82E-07 205613000 124.5 140.57 136.35 115.55 40.879 57.427 230.18 115.57 255.35 246.814 TRUE FALSE FALSE 122.9825461 142.5489481 138.7231146 128.9104347 38.79279209 53.75760004 249.7314835 118.9138356 232.5108565 240.4017367 0.511570955 0.592961391 0.577047057 0.536229216 0.161366522 0.223615689 1.038808982 0.494646325 0.967176276 1 7.909303508 -12.21270227 0.604240564 1.066244965 0.506191464 0.413321692 0.222511733 0.925137821 0.503851858 0.284853016 0.052751665 6.13E-13 12.21270227 -0.5600535 (ac)MEVKPPPGRPQPDS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 MEVKPPPGRPQPDSGR 16 2 P51991 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 MEVKPPPGRPQPDS(1)GR 60.669 0.0061058 60092000 3697.3 3412.4 3341.8 2124.7 3845.5 4832.7 3882 4092 3878.8 3515 TRUE FALSE FALSE 3652.235885 3460.439857 3399.962627 2370.367811 3649.249785 4523.906067 4211.736983 4210.395564 3531.870413 3423.679793 1.066757438 1.010737004 0.99307261 0.692345066 1.065885248 1.32135782 1.230178415 1.229786609 1.031600683 1 11.74133206 -8.386124176 5.385390167 1.001736137 1.255405085 0.605048314 0.103739317 0.13512715 5.377949352 0.015675778 0.035606281 4.11E-09 8.386124176 0.253668948 (ac)MEVS(ph)PLQPVNENMQVNK ddPTM_HeLa_Romidepsin_16h_R1 2 MEVSPLQPVNENMQVNK 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 MEVS(1)PLQPVNENMQVNK;MEVS(1)PLQPVNENMQVNK ; 110.93 0.00036968 26338200 2011.04 1880.17 1855.48 1694.71 2419.5 2328.7 1580.36 2162.58 2033.02 1557.68 TRUE FALSE FALSE 1986.528671 1906.639083 1887.773851 1890.660344 2296.023887 2179.903586 1714.595739 2225.15084 1851.181599 1517.211249 1.309328989 1.256673442 1.244239292 1.246141792 1.513318523 1.436783168 1.130096906 1.466605815 1.220121193 1 10.56720626 -13.49374011 0.275372509 0.631978514 1.367106845 0.257456597 0.128412605 5.003157865 0.282445375 1.261839081 0.064061403 3.21E-14 13.49374011 0.735128331 (ac)MFAVHLMAFYFS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MFAVHLMAFYFSK 13 0 Q2TB90-3;Q2TB90-2;Q2TB90 Q2TB90-3 HKDC1 Putative hexokinase HKDC1 1 0 MFAVHLMAFY(0.006)FS(0.994)K 48.568 0.023346 7891000 3634.8 3622.8 3863.5 191.15 5605.1 6303 5357.8 5737.5 4119.8 3962.3 TRUE FALSE FALSE 3590.49766 3673.801873 3930.742597 213.2516624 5319.050831 5900.258642 5812.891398 5903.50551 3751.31477 3859.358875 0.930335264 0.951920252 1.018496264 0.055255722 1.378221359 1.528818344 1.506180583 1.529659641 0.972004649 1 11.91414549 -8.54524495 24.99989596 0.904538874 1.50893346 0.57876235 0.274167034 131.8913855 147421.4898 0.038540765 0.077085516 2.85E-09 8.54524495 0.604394586 (ac)MFGAGDEDDTDFLSPSGGAR ddPTM_HeLa_Romidepsin_16h_R1 1 MFGAGDEDDTDFLSPSGGAR 20 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 0 0 124.42 1.00E-05 1112100 127.19 0 60.339 131.4 0 0 0 119.08 0 102.92 FALSE FALSE TRUE 125.6397594 0 61.38917498 146.5930863 0 0 0 122.5253919 0 100.2461236 1.253312895 0 0.612384527 1.46233172 0 0 0 1.222245685 0 1 6.64740264 -10.280428 24.83341342 1.119619997 0.460215448 0 0.611637758 724.9945692 948148.84 0.085096134 0.097396201 5.24E-11 10.280428 -0.65940455 (ac)MFPTGFS(ph)SPSPSAAAAAQEVR ddPTM_HeLa_Romidepsin_16h_R1 1 MFPTGFSSPSPSAAAAAQEVR 21 0 A0A669KAU9;A0A669KAX4;Q13620-1 A0A669KAU9 CUL4B Cullin-4B 1 0 MFPT(0.005)GFS(0.497)S(0.497)PS(0.002)PSAAAAAQEVR 178.57 6.91E-32 3874400 239.6 187.11 128.39 53.412 253.84 307.6 0 119.9 165.81 120.44 TRUE FALSE FALSE 236.679663 189.7441395 130.6245741 59.58774675 240.8855976 287.9453527 0 123.3691173 150.9795383 117.3109514 2.017541075 1.617446088 1.113490024 0.507947008 2.053393947 2.454547928 0 1.051641947 1.287002931 1 6.874193891 -9.759151709 24.97404169 1.504201942 1.207225059 0.037898282 0.694904819 196.8403663 2148848.299 0.120644608 0.165958886 1.74E-10 9.759151709 -0.296976883 (ac)MFSS(ph)TDRAMRIR ddPTM_HeLa_Romidepsin_16h_R1 1 MFSSTDRAMRIR 12 2 E9PPN3;E9PS17;Q96KG9-3;Q96KG9-2;Q96KG9;A0A0A0MQX4;E9PK59;Q96KG9-5;Q96KG9-4;Q96KG9-6 E9PPN3 SCYL1 N-terminal kinase-like protein 1 0 MFS(0.051)S(0.474)T(0.474)DRAMRIR 57.96 0.025769 10162000 117.55 202.69 0 141.31 69.208 137.48 0 0 106.02 118.1 TRUE FALSE FALSE 116.1172554 205.5434751 0 157.6489271 65.67605751 128.6954717 0 0 96.53730567 115.031745 1.009436616 1.786841321 0 1.370481923 0.570938549 1.118782226 0 0 0.83922317 1 6.845888242 -7.756892304 24.99342483 0.989986676 3.23E-07 0.427394356 0.444435104 66.71420328 366686.815 0.053858788 0.188690694 1.75E-08 7.756892304 -0.989986353 (ac)MGGSAPPDSS(ph)WRGS(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 MGGSAPPDSSWRGSLK 16 1 Q9HBA9;Q04609-10;Q04609-6;Q04609-9;Q04609-8;Q04609-7;Q04609 Q9HBA9 FOLH1B;FOLH1 Putative N-acetylated-alpha-linked acidic dipeptidase;Glutamate carboxypeptidase 2 2 0 MGGS(0.035)APPDS(0.195)S(0.912)WRGS(0.858)LK 47.088 0.004219 0 648.17 820.82 1037.2 792.79 756 778.72 954.73 921.53 817.74 881.82 TRUE FALSE FALSE 640.2698547 832.3755255 1055.252031 884.45611 717.418499 728.9623052 1035.824742 948.1930166 744.5992863 858.9101893 0.745444475 0.969106591 1.228594146 1.029742249 0.835266024 0.848706086 1.205975613 1.103948967 0.866911693 1 9.746363476 -10.00515358 24.94169138 0.878608078 1.036420412 0.246769396 0.13363739 290.7245025 1407022.828 0.025449934 0.032921701 9.88E-11 10.00515358 0.157812334 (ac)MGS(ph)FSSHMTEFPRKRK ddPTM_HeLa_Romidepsin_16h_R1 1 MGSFSSHMTEFPRKRK 16 3 Q8WYA1-6;Q8WYA1-8;Q8WYA1-7 Q8WYA1-6 1 0 MGS(0.487)FS(0.487)S(0.026)HMT(0.001)EFPRKRK 52.5 0.0042176 0 705.41 1043.1 558.39 775.3 1128.3 926.14 918.15 833.28 1076.5 1039.9 TRUE FALSE FALSE 696.8121916 1057.784789 568.1085437 864.9438339 1070.718641 866.962643 996.1376381 857.3896421 980.2151439 1012.883248 0.687949172 1.044330421 0.560882555 0.853942284 1.057099762 0.855935415 0.983467384 0.846484176 0.967747414 1 9.984252173 -8.968637114 24.96986028 0.840388646 0.936212859 0.068759946 0.146966688 427.4318609 340302.3591 0.023419894 0.042451885 1.07E-09 8.968637114 0.095824213 (ac)MHPAGLAAAAAGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 MHPAGLAAAAAGTPR 15 0 Q5BJH7-4;Q5BJH7-5;Q5BJH7-3;Q5BJH7 Q5BJH7-4 YIF1B Protein YIF1B 1 0 MHPAGLAAAAAGT(1)PR;MHPAGLAAAAAGT(1)PR ; 66.738 0.00075358 5071800 1751.91 1339.91 1550.55 1028.93 1251.53 1053.2 1675.18 853.08 1969.11 1572.55 TRUE FALSE FALSE 1730.557047 1358.773288 1577.536672 1147.899728 1187.659754 985.903919 1817.469747 877.7625239 1792.98787 1531.694924 1.129831417 0.887104388 1.029928772 0.749431045 0.775389234 0.643668594 1.186574244 0.573066157 1.170590724 1 10.58091326 -9.54619253 1.635415932 1.055822203 0.800842029 0.360312791 0.168507491 0.306119397 1.642857629 0.026056645 0.041715944 2.84E-10 9.54619253 -0.254980174 (ac)MIEEAY(ph)MT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MIEEAYMTK 9 0 E9PMW8;E9PJB5 E9PMW8 RFWD2 2 0 MIEEAY(1)MT(1)K 60.019 0.004166 0 0 264.66 228.02 210.03 288.19 287.72 269 379 309.89 427.61 TRUE FALSE FALSE 0 268.3858904 231.9885925 234.3146568 273.4825889 269.3356206 291.8488533 389.965767 282.1726623 416.5006306 0 0.644382915 0.556994577 0.562579357 0.656619868 0.646663176 0.700716474 0.93629094 0.677484358 1 8.70217487 -6.868791738 0.750632615 0.533619348 1.403560471 0.156278093 0.233329939 8.214414008 2.202810337 0.059657673 6.884643438 1.35E-07 6.868791738 0.869941122 (ac)MKDCKHPNIVAY(ph)FGSYLRR ddPTM_HeLa_Romidepsin_16h_R1 1 MKDCKHPNIVAYFGSYLRR 19 3 F5H5A3 F5H5A3 MAP4K3 Mitogen-activated protein kinase kinase kinase kinase 1 0 MKDCKHPNIVAY(0.708)FGS(0.159)Y(0.133)LRR 62.813 0.018485 12809000 1632.2 1896.6 1628.3 1158.6 1597.5 1934.8 1412.1 1711.9 2408 2045.8 TRUE FALSE FALSE 1612.306119 1923.300385 1656.639878 1292.562783 1515.973614 1811.172524 1532.043739 1761.431126 2192.622449 1992.649821 0.809126672 0.965197379 0.831375318 0.648665295 0.760782752 0.908926649 0.768847453 0.88396421 1.100355128 1 10.96047248 -12.6283955 0.433944739 1.077502961 0.8079559 0.504782072 0.088184286 2.132660838 0.427205083 0.268077848 0.025370458 2.35E-13 12.6283955 -0.269547061 (ac)MMEGLDDGPDFLSEEDR ddPTM_HeLa_Romidepsin_16h_R1 2 MMEGLDDGPDFLSEEDR 17 0 G3V5X9;Q9UNH7;G3V2U1;H0YJF8;G3V4Z5 G3V5X9 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 0 ; ; 289.71 3.03E-230 24657000 0 66.228 171.358 50.709 194.26 328.07 0 128.01 0 203.03 FALSE FALSE TRUE 0 67.16035952 174.3404141 56.57221317 184.3461873 307.1073858 0 131.7137674 0 197.7552513 0 0.339613533 0.881596888 0.286071863 0.932193639 1.552967032 0 0.666044348 0 1 7.627572195 (ac)MMPQEQYT(ph)HHRS(ph)T(ph)MPGSVGPQVYK ddPTM_HeLa_Romidepsin_16h_R1 1 MMPQEQYTHHRSTMPGSVGPQVYK 24 1 E5RI34;Q92629-3;Q92629-2 E5RI34 SGCD 3 0 MMPQEQY(0.515)T(0.553)HHRS(0.942)T(0.972)MPGS(0.017)VGPQVYK 54.271 0.0039043 0 1014.8 854.06 742.36 676.92 715.65 944.82 650.09 695.59 923.19 790.39 TRUE FALSE FALSE 1002.431227 866.0834791 755.2804644 755.1886754 679.12771 884.4490513 705.3086284 715.7157992 840.6175742 769.8555539 1.302103001 1.12499478 0.981067761 0.980948532 0.882149524 1.148850647 0.916157096 0.929675438 1.09191597 1 9.588443972 -9.778195676 5.108370838 1.14599116 0.974022968 0.384750056 0.096473384 0.178253585 12.58051564 0.020601515 0.027996906 1.67E-10 9.778195676 -0.171968192 (ac)MNLLPNIES(ph)PVTR ddPTM_HeLa_Romidepsin_16h_R1 5 MNLLPNIESPVTR 13 0 E9PM69;P17980 E9PM69 PSMC3 26S protease regulatory subunit 6A 1 0 MNLLPNIES(0.782)PVT(0.218)R;MNLLPNIES(0.854)PVT(0.146)R;MNLLPNIES(0.994)PVT(0.006)R;MNLLPNIES(0.956)PVT(0.044)R;MNLLPNIES(0.979)PVT(0.021)R ;;;; 127.07 0.0022604 39877900 871.103 1035 784.35 879.81 841.173 1113.417 811.49 942.56 1160.73 822.41 TRUE FALSE FALSE 860.4856616 1049.570757 798.0012827 981.5377718 798.244803 1042.273247 880.4179403 969.8314865 1056.911402 801.0436696 1.074205682 1.310254106 0.996201971 1.225323673 0.996505975 1.301144103 1.099088569 1.210709882 1.319417957 1 9.645737084 -10.49425267 8.78953526 1.03251114 1.157875885 0 0.137878732 0.263496567 72.70149532 0.016356777 0.018050524 3.20E-11 10.49425267 0.125364744 (ac)MNTAPSRPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 MNTAPSRPSPTR 12 1 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 0 MNTAPS(0.002)RPS(0.499)PT(0.499)R;MNTAPS(0.003)RPS(0.631)PT(0.365)R;MNTAPS(0.074)RPS(0.701)PT(0.225)R ;; 80.905 0.00037128 100644600 1161.75 1039.85 941.99 1133.69 894.3 846.611 1213.2 820.447 1221.09 1082.3 TRUE FALSE FALSE 1147.590144 1054.489036 958.3849408 1264.772572 848.6605339 792.5152894 1316.249178 844.1853395 1111.872652 1054.18169 1.088607548 1.000291549 0.909126908 1.19976716 0.805041998 0.751782446 1.248598027 0.800796815 1.054725824 1 10.04190782 -8.746043358 24.99967286 1.038164834 0.915645645 0.180193531 0.145467425 360.3118318 585062.3905 0.019949732 0.039782533 1.79E-09 8.746043358 -0.122519189 (ac)MNVDHEVNLLVEEIHR ddPTM_HeLa_Romidepsin_16h_R1 1 MNVDHEVNLLVEEIHR 16 0 Q5SZC9;Q9P1F3 Q5SZC9 ABRACL Costars family protein ABRACL 0 0 47.64 0.0011797 2722100 636.07 809.85 767.26 980.48 680.03 781.39 663.76 840.73 803.96 834.82 FALSE FALSE TRUE 628.3173342 821.2510896 780.6138384 1093.847711 645.3255316 731.4617008 720.1397578 865.0551961 732.051804 813.1312561 0.772713298 1.009985883 0.960009633 1.345228956 0.793630213 0.899561658 0.885637777 1.063856775 0.900287375 1 9.667344441 STPENHPET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 STPENHPETPK 11 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 STPENHPET(1)PK 119.32 0.021344 4284600 1810.6 1495.2 1583.6 755.41 884.65 1054.2 908.91 542.34 2049.4 2016.1 TRUE FALSE FALSE 1788.531711 1516.249465 1611.161894 842.7540585 839.5030094 986.8400223 986.1127927 558.0317522 1866.096531 1963.721431 0.910786878 0.772130629 0.820463569 0.429161716 0.427506161 0.502535648 0.502165316 0.284170526 0.950285769 1 10.93937457 -9.524521138 0.971518064 0.966652565 0.410552697 0.891706856 0.080565692 0.107047321 0.201724579 0.015013856 0.027199626 2.99E-10 9.524521138 -0.556099868 down (ac)MQHPSGGRPCGARKSADPK ddPTM_HeLa_Romidepsin_16h_R1 1 MQHPSGGRPCGARKSADPK 19 3 A0A2R8YE36 A0A2R8YE36 0 0 43.382 0.0040787 0 579.96 432.29 434.08 551.84 480.44 463.35 467.15 415.99 581.26 536.9 FALSE FALSE TRUE 572.8912244 438.37579 441.6349803 615.6463373 455.921354 433.7434304 506.8297093 428.0260143 529.2706498 522.9512606 1.095496402 0.838272747 0.84450505 1.177253759 0.871823798 0.829414638 0.969171981 0.818481657 1.012084088 1 9.030532682 -8.903192604 0.486908039 1.039636843 0.850658874 0.140452734 0.110053157 1.559980124 0.611264129 0.03127326 0.132082683 1.25E-09 8.903192604 -0.188977969 (ac)MS(ph)PISGASPSWRAAPK ddPTM_HeLa_Romidepsin_16h_R1 1 MSPISGASPSWRAAPK 16 1 A0A0C4DFW6 A0A0C4DFW6 FOXP3 1 0 MS(0.994)PIS(0.005)GAS(0.001)PSWRAAPK 63.408 0.0036641 0 943.67 844.79 789.95 878.65 766.18 918.55 813.5 635.07 695.93 903.07 TRUE FALSE FALSE 932.1681871 856.6829758 803.6987484 980.2436472 727.0789756 859.8576195 882.5986697 653.4447485 633.6842778 879.6081112 1.059753969 0.973937103 0.913700929 1.114409513 0.826594214 0.97754626 1.003399876 0.742881677 0.720416592 1 9.780717098 -6.026120097 0.595950507 1.017736174 4.43E-48 0.00483066 0.124242777 9.261040979 0.743768448 0.013839149 9.104960457 9.42E-07 6.026120097 -1.017736174 (ac)MS(ph)PTPPLFSLPEAR ddPTM_HeLa_Romidepsin_16h_R1 4 MSPTPPLFSLPEAR 14 0 A0A087WWS1;Q96FV9;J3KRD7;J3QQZ3;J3KT14;Q96FV9-2 A0A087WWS1 THOC1 THO complex subunit 1 1 0 MS(1)PTPPLFSLPEAR;MS(0.997)PT(0.003)PPLFSLPEAR;MS(0.922)PT(0.078)PPLFSLPEAR;MS(0.998)PT(0.002)PPLFSLPEAR ;;; 141.71 0.0056994 13702900 770.36 762.42 648.6 816.24 772.938 855.24 656.987 1002.53 911.78 790.69 TRUE FALSE FALSE 760.970556 773.1533688 659.8886109 910.6175093 733.4920896 800.5929242 712.7914594 1031.536624 830.2281132 770.1477598 0.98808384 1.003902639 0.856833773 1.182393246 0.952404367 1.039531589 0.925525589 1.339400928 1.078011463 1 9.588991456 -7.254308181 24.92943773 0.995039138 1.339401095 0.591828555 0.083586891 355.4623529 1242602.909 0.009504896 0.128935081 5.57E-08 7.254308181 0.344361956 (ac)MS(ph)QKS(ph)WIES(ph)T(ph)LTK ddPTM_HeLa_Romidepsin_16h_R1 1 MSQKSWIESTLTK 13 1 H0YLN8;Q96QT4 H0YLN8 TRPM7 Transient receptor potential cation channel subfamily M member 7 4 0 MS(1)QKS(1)WIES(0.895)T(0.633)LT(0.472)K 49.988 0.0041656 0 2250.2 2432.8 2405.2 2021.2 2862.7 2855.1 2687.6 2765.9 2886.7 2867.2 TRUE FALSE FALSE 2222.773697 2467.049022 2447.061497 2254.900654 2716.605737 2672.668324 2915.884677 2845.926953 2628.506322 2792.709731 0.79592006 0.883388988 0.876231951 0.807423926 0.97274905 0.957016154 1.044105889 1.019055766 0.941202837 1 11.44744991 -8.217997689 1.834626111 0.892256963 1.027602293 0.460497447 0.059941919 0.345966293 2.20616375 0.012286426 0.042139577 6.05E-09 8.217997689 0.13534533 VSGTLDTPEKT(ph)VDSQGPTPVCTPTFLER ddPTM_HeLa_Romidepsin_16h_R1 1 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 H7BZL0;Q9BYG3;C9J808 H7BZL0 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 0 VSGT(0.001)LDT(0.024)PEKT(0.803)VDS(0.167)QGPT(0.004)PVCT(0.001)PTFLER 58.294 0.0015829 15114000 1843.3 1978.9 1503.6 301.02 952.97 912.77 839.79 742.37 2189 1992.6 TRUE FALSE FALSE 1820.833151 2006.759006 1529.769527 335.8253487 904.3363849 854.4469428 911.1217416 763.8493047 1993.210358 1940.831965 0.938171456 1.033968444 0.788202974 0.173031646 0.465952953 0.440247769 0.46944906 0.393567974 1.026987598 1 10.9224595 -9.458864519 4.824525236 0.972876888 0.401991802 0.920034494 0.08542853 0.04108512 1.898883512 0.012582993 0.019188955 3.48E-10 9.458864519 -0.570885086 down (ac)MSDNT(ph)TLPAPASNQGPTTPRK ddPTM_HeLa_Romidepsin_16h_R1 1 MSDNTTLPAPASNQGPTTPRK 21 1 Q13956 Q13956 PDE6H "Retinal cone rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit gamma" 1 0 MS(0.16)DNT(0.699)T(0.129)LPAPAS(0.012)NQGPTTPRK 62.68 0.026028 2468300 839.07 832.65 811.36 553.45 901.75 935.28 813.91 931.26 908.55 793.12 TRUE FALSE FALSE 828.8430921 844.3720686 825.4813805 617.4424931 855.7303326 875.5186265 883.0434951 958.2045388 827.2870125 772.5146281 1.072915725 1.093017579 1.068564077 0.799263173 1.107720555 1.133335984 1.14307673 1.240370737 1.07090142 1 9.593418441 -8.530400483 24.98539735 1.025271662 1.161207009 0.409847388 0.083610206 143.9033042 478011.7282 0.012145442 0.024329276 2.95E-09 8.530400483 0.135935347 (ac)MVLGT(ph)VLLPPNS(ph)Y(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 MVLGTVLLPPNSYGR 15 0 P42684-2;P42684-3;P42684-4;P42684-10 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 3 0 MVLGT(1)VLLPPNS(1)Y(1)GR 43.05 0.016576 36477000 1864.3 1750.5 1707.7 352.31 1540.1 1680 1081.2 1590.7 2027.4 1935.6 TRUE FALSE FALSE 1841.577195 1775.143585 1737.421802 393.0457399 1461.50295 1572.653422 1173.037101 1636.724395 1846.064266 1885.312833 0.97680192 0.941564473 0.921556238 0.20847773 0.775204478 0.834160461 0.62219759 0.868144727 0.979181934 1 10.88058822 -9.497866992 24.96930403 0.982625002 0.664307561 0.438920887 0.171547495 496.318277 495476.6873 0.02506586 0.038181285 3.18E-10 9.497866992 -0.31831744 (ac)MVMAS(ph)VMQK ddPTM_HeLa_Romidepsin_16h_R1 1 MVMASVMQK 9 0 B7Z6T3 B7Z6T3 TMEM161B 1 0 MVMAS(1)VMQK 53.166 0.0038103 0 1129.6 1300.1 1486.8 1372.4 1586.1 1293.1 1409.9 1405.8 1574.5 1337.2 TRUE FALSE FALSE 1115.832001 1318.402842 1512.67713 1531.083345 1505.155398 1210.475083 1529.656871 1446.474605 1433.672777 1302.459351 0.856711574 1.012241066 1.161400645 1.175532537 1.155625622 0.929376477 1.174437321 1.110571784 1.100742818 1 10.34702263 -9.970353764 5.039428172 0.932209646 1.115245019 0.258818032 0.091828143 0.115222227 7.541846217 0.013821095 0.018038099 1.07E-10 9.970353764 0.183035373 (ac)NSIYTISISSTAES(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 NSIYTISISSTAESGK 16 0 Q5JSG7 Q5JSG7 PCSK5 1 0 NSIYT(0.003)IS(0.003)IS(0.003)S(0.002)T(0.006)AES(0.984)GK 79.337 0.014734 634790000 657.53 513.15 531.59 243.01 555.07 501.18 474.21 521.51 586.08 341.65 TRUE FALSE FALSE 649.5157714 520.3741392 540.842101 271.1079596 526.7427066 469.1562155 514.4893856 536.599069 533.6595369 332.7738837 1.951823154 1.56374693 1.625254046 0.814691215 1.582884753 1.409834841 1.54606299 1.61250355 1.603670129 1 8.378398404 -12.64180218 1.491318581 1.00186888 1.564400149 0 0.327922019 0.388039155 1.559551692 0.213200401 0.04904966 2.28E-13 12.64180218 0.56253127 FVNVVPTFGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 FVNVVPTFGKK 11 1 E9PR30;P62861 E9PR30 FAU 40S ribosomal protein S30 0 1 ; FVNVVPTFGK(1)K;FVNVVPTFGK(1)K 160.36 0.00074123 16994600 1152.13 1077.2 1824.31 1679.14 2476.5 2259.6 2271.1 1806.76 1025.91 834.01 FALSE TRUE FALSE 1138.087396 1092.36485 1856.06135 1873.290067 2350.114964 2115.218853 2464.007177 1859.03575 934.1500402 812.3423 1.400994872 1.344710044 2.284826668 2.306035359 2.893010698 2.603851668 3.033212942 2.288488178 1.149946322 1 9.66594396 -9.6522544 1.11822913 1.155375988 2.730410376 0.89160514 0.232550438 0.09591674 0.240158743 0.042560469 0.069035954 2.23E-10 9.6522544 1.575034388 up (ac)PEPSK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PEPSKSAPAPKKGSK 15 3 P33778;U3KQK0;Q99877 P33778;U3KQK0 HIST1H2BB;HIST1H2BN Histone H2B type 1-B;Histone H2B;Histone H2B type 1-N 0 3 PEPSK(1)SAPAPK(1)K(1)GSK 60.157 0.0001173 691510 0 0 0 55.125 496.67 1015.8 1050.2 1492.7 0 0 FALSE TRUE FALSE 0 0 0 61.49881187 471.3230766 950.8936583 1139.403962 1535.888919 0 0 0 RFVNVVPTFGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RFVNVVPTFGKK 12 2 E9PR30;P62861 E9PR30 FAU 40S ribosomal protein S30 0 1 ; RFVNVVPTFGK(1)K;RFVNVVPTFGK(1)K 124.48 0.0046549 6475300 1753.92 2077.43 3322.1 2287.28 3660.3 4887.1 3657.5 3392.6 2110.87 1231.82 FALSE TRUE FALSE 1732.542548 2106.676114 3379.919757 2551.746076 3473.501233 4574.830082 3968.167959 3490.759528 1922.0685 1199.817139 1.444005501 1.755830989 2.817029068 2.126779151 2.895025517 3.812939434 3.307310615 2.909409622 1.601967865 1 10.22859883 -9.579470682 0.624704366 1.088441599 3.398064701 0.799773702 0.387196538 0.183865201 0.145756037 0.087337958 0.176424537 2.63E-10 9.579470682 2.309623102 up (ac)PLS(ph)TAGILS(ph)SSSAASNR ddPTM_HeLa_Romidepsin_16h_R1 1 PLSTAGILSSSSAASNR 17 0 A0A087X182;Q9UL16 A0A087X182 CFAP45 Cilia- and flagella-associated protein 45 2 0 PLS(0.79)T(0.211)AGILS(0.479)S(0.479)S(0.019)S(0.019)AAS(0.003)NR 42.257 0.029686 4724200 1610.4 1314.3 1503.5 1082.2 1527.4 1334.4 1106.7 1142.3 1415.6 1465.3 TRUE FALSE FALSE 1590.771825 1332.80275 1529.667787 1207.329056 1449.451078 1249.136147 1200.70307 1175.350648 1288.985191 1427.231295 1.114585864 0.933837952 1.071772874 0.845923895 1.015568453 0.875216338 0.84128135 0.823517991 0.90313686 1 10.47900344 -8.554626476 0.652840283 1.05041016 0.807785156 0.30397585 0.081251704 0.563046531 0.375868448 0.013859788 0.075086942 2.79E-09 8.554626476 -0.242625004 (ac)S(ph)AADEVDGLGVARPHYGSVLDNER ddPTM_HeLa_Romidepsin_16h_R1 1 SAADEVDGLGVARPHYGSVLDNER 24 1 P46940;H0YLE8;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 0 S(1)AADEVDGLGVARPHYGSVLDNER 71.001 0.00045251 6321500 312.7 350.3 120.49 147.92 241.51 342.97 130.18 197.23 263.12 190.33 TRUE FALSE FALSE 308.8886921 355.2315326 122.5870779 165.0232064 229.1848435 321.0553239 141.237486 202.9365389 239.5858882 185.3851992 1.666199316 1.916180656 0.661256014 0.89016387 1.236262898 1.731828244 0.761859558 1.094674978 1.292367941 1 7.534382256 -9.744690751 24.99976973 1.368503353 1.079466145 0.21494555 0.359467287 450.7559831 672817.8389 0.065668147 0.092725133 1.80E-10 9.744690751 -0.289037208 (ac)S(ph)AEVPEAASAEEQKEMEDKVTSPEKAEEAK ddPTM_HeLa_Romidepsin_16h_R1 1 SAEVPEAASAEEQKEMEDKVTSPEKAEEAK 30 3 P56211 P56211 ARPP19 cAMP-regulated phosphoprotein 19 1 0 S(0.531)AEVPEAAS(0.432)AEEQKEMEDKVT(0.019)S(0.019)PEKAEEAK 45.941 1.83E-06 295350000 2573.3 2579.9 2012 2800.4 1877.3 1874.1 1426.5 1300.6 2679.9 2256.2 TRUE FALSE FALSE 2541.93563 2616.2199 2047.018016 3124.195424 1781.494376 1754.351058 1547.666874 1338.230809 2440.203032 2197.583599 1.156695759 1.190498464 0.931485845 1.421650319 0.810660571 0.798309133 0.704258475 0.608955586 1.110402823 1 11.10170233 -8.5430809 24.81111282 1.096114505 0.720649759 0.69241946 0.131860524 97.73190588 120028.2453 0.018924534 0.037852466 2.86E-09 8.5430809 -0.375464747 (ac)S(ph)ASSLLEQRPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASSLLEQRPK 11 1 Q9Y5A9;S4R3J8;S4R3V3 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 0 S(0.795)AS(0.202)S(0.003)LLEQRPK 88.37 0.0028967 7577000 2027.7 2027.2 1537.1 1507.6 1628.6 1204.9 1312.9 1315.2 2285.4 1904 TRUE FALSE FALSE 2002.985612 2055.738975 1563.852581 1681.915805 1545.486465 1127.910779 1424.417693 1353.253237 2080.9881 1854.533806 1.080048046 1.108493665 0.843259139 0.906921082 0.833355779 0.608191005 0.768073189 0.729699956 1.122108475 1 10.85684085 -9.061073068 1.111061512 1.041783643 0.710715797 0.792879649 0.075400194 0.157415231 0.383571342 0.012390108 0.028702283 8.69E-10 9.061073068 -0.331067846 (ac)S(ph)DAAVDTSSEITTK ddPTM_HeLa_Romidepsin_16h_R1 7 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 0 S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK;S(1)DAAVDTSSEITTK ;;;;;; 147.74 3.79E-25 488274400 33433.2 32708.4 28290.8 27293.6 29122.9 24484.4 21887.31 25333 33663 30296.7 TRUE FALSE FALSE 33025.7033 33168.86971 28783.18951 30449.41445 27636.64974 22919.92586 23746.41757 26065.97039 30652.09697 29509.58737 1.119151647 1.124003169 0.975384344 1.031848195 0.936531216 0.776694217 0.804701783 0.883305146 1.038716556 1 14.84889613 -8.596758096 2.180342447 1.056871371 0.819248517 0.798736869 0.05090579 0.114755881 1.096251188 0.00918279 0.021820017 2.53E-09 8.596758096 -0.237622853 (ac)S(ph)DAAVDTSSEITTKDLK ddPTM_HeLa_Romidepsin_16h_R1 3 SDAAVDTSSEITTKDLK 17 1 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 0 S(0.995)DAAVDT(0.002)S(0.002)SEITTKDLK;S(0.744)DAAVDT(0.097)S(0.131)S(0.026)EIT(0.002)TKDLK;S(1)DAAVDTSSEITTKDLK ;; 99.531 6.44E-08 10432900 3316.39 3399.2 3137.97 3492.9 3440.57 3158.75 2393.77 2703.05 3394.43 3372.72 TRUE FALSE FALSE 3275.968563 3447.054027 3192.585052 3896.765533 3264.984874 2956.916069 2597.096764 2781.258487 3090.823679 3285.096248 0.997221486 1.049300771 0.971839121 1.18619524 0.993877996 0.900100285 0.790569459 0.846629224 0.940862442 1 11.68171992 -8.098512506 2.943459076 1.014718428 0.820863119 0.624522559 0.063780093 0.121056949 2.007445722 0.008460383 0.025816855 7.97E-09 8.098512506 -0.193855309 (ac)S(ph)DEASAITSYEK ddPTM_HeLa_Romidepsin_16h_R1 1 SDEASAITSYEK 12 0 Q6PEV8;Q6PEV8-2 Q6PEV8 FAM199X Protein FAM199X 1 0 S(0.997)DEAS(0.003)AITSYEK 73.466 0.0034057 2633400 1865.5 1632.4 2066.4 2067.2 2003.5 2435.4 1695.6 1864.9 2050.4 2034.3 TRUE FALSE FALSE 1842.762568 1655.38097 2102.364825 2306.21939 1901.253919 2279.7858 1839.624222 1918.857939 1867.007089 1981.448593 0.930007761 0.835439777 1.061024158 1.16390574 0.95952725 1.150565202 0.928423896 0.968411669 0.942243516 1 10.95233982 (ac)S(ph)DEFSLADALPEHS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 2 0 S(0.744)DEFS(0.256)LADALPEHS(1)PAK 73.783 1.85E-08 0 434.54 383.14 520.51 361.47 394 437.7 441.08 374.9 404.99 353.16 TRUE FALSE FALSE 429.2436593 388.533855 529.5692582 403.2648622 373.8927098 409.7323826 478.5453242 385.74714 368.7666801 343.9848523 1.247856283 1.129508618 1.539513309 1.172333199 1.086945275 1.191134958 1.391181388 1.121407345 1.072043369 1 8.426201226 -12.15006445 0.74506245 0.987603092 1.240313106 0.260610155 0.131823181 0.717889773 0.668410688 0.109301717 0.026237553 7.08E-13 12.15006445 0.252710014 (ac)S(ph)DEFSLADALPEHSPAK ddPTM_HeLa_Romidepsin_16h_R1 7 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 0 S(0.871)DEFS(0.129)LADALPEHSPAK;S(1)DEFSLADALPEHSPAK;S(1)DEFSLADALPEHSPAK;S(0.999)DEFS(0.001)LADALPEHSPAK;S(0.773)DEFS(0.015)LADALPEHS(0.212)PAK;S(0.893)DEFS(0.107)LADALPEHSPAK;S(0.595)DEFS(0.402)LADALPEHS(0.003)PAK ;;;;;; 211.63 2.94E-87 1941157400 34791.5 33371.1 32050.8 29419.6 25138.2 24111.1 20441.3 21469.8 33950.4 30342.2 TRUE FALSE FALSE 34367.44782 33840.89922 32608.63073 32821.23258 23855.30385 22570.47853 22177.58351 22090.99479 30913.79119 29553.90527 1.162873316 1.145056767 1.103361144 1.110554841 0.807179411 0.76370545 0.750411267 0.74748141 1.046013747 1 14.85106116 -8.70971748 4.785323457 1.088963375 0.7595008 0.927747645 0.04485498 0.055797283 2.688888809 0.009775264 0.019644042 1.95E-09 8.70971748 -0.329462574 (ac)S(ph)DKPDMAEIEKFDK ddPTM_HeLa_Romidepsin_16h_R1 1 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 1 0 S(1)DKPDMAEIEKFDK 59.198 0.0051283 62887000 8191.1 8038.8 7587.1 8700.3 7225.2 6171.5 5424.7 6229.5 8804.8 8160.3 TRUE FALSE FALSE 8091.263723 8151.970437 7719.150293 9706.269622 6856.471083 5777.161068 5885.473883 6409.740754 8017.276636 7948.29423 1.017987443 1.025625147 0.971170678 1.221176436 0.862634282 0.72684288 0.740470057 0.806429728 1.008678894 1 12.95642956 -8.530877897 24.99720413 1.02116596 0.762597913 0.777861826 0.0684302 60.48162438 189003.6412 0.009308811 0.018643821 2.95E-09 8.530877897 -0.258568047 (ac)S(ph)DNDDIEVES(ph)DADKR ddPTM_HeLa_Romidepsin_16h_R1 2 SDNDDIEVESDADKR 15 1 A0A494C130;Q6V3B1;G3V563;G3V2R5;P61244-2 A0A494C130 MAX Protein max 2 0 S(1)DNDDIEVES(1)DADKR;S(1)DNDDIEVES(1)DADKR ; 71.685 0.0030518 16965900 3921.7 4254.6 4040.6 4048.6 4437.5 4282.7 3616.6 4225.2 3782.1 4331 TRUE FALSE FALSE 3873.900812 4314.49637 4110.924948 4516.718181 4211.037816 4009.049292 3923.793914 4347.449496 3443.819504 4218.479996 0.918316743 1.022760894 0.974503838 1.070698021 0.998235815 0.950353989 0.930144013 1.030572505 0.816365019 1 12.04250754 -10.24463066 24.92970872 0.961427349 0.994451648 0.166375581 0.062290773 1512.459162 2243194.182 0.008044318 0.009838503 5.69E-11 10.24463066 0.033024299 (ac)S(ph)DNDDIEVES(ph)DEEQPR ddPTM_HeLa_Romidepsin_16h_R1 1 SDNDDIEVESDEEQPR 16 0 G3V5L1;P61244-6;P61244-5;P61244-3;P61244-4;P61244 G3V5L1 MAX Protein max 2 0 S(1)DNDDIEVES(1)DEEQPR 127.49 9.45E-09 3190500 63.089 142.14 164.46 156.56 0 55.542 120.9 149.12 149.7 194.13 TRUE FALSE FALSE 62.320047 144.1410507 167.3223573 174.6622038 0 51.99304545 131.169243 153.4345519 136.3104571 189.0864746 0.329584901 0.76230228 0.884898603 0.92371601 0 0.27496967 0.693699765 0.811451756 0.720889515 1 7.562902361 -8.815324696 24.99999967 0.714426497 0.450629224 0.244016265 0.269824725 150.5631193 69852.82865 0.049919772 0.090487333 1.53E-09 8.815324696 -0.263797273 (ac)S(ph)DNDDIEVESDADKR ddPTM_HeLa_Romidepsin_16h_R1 3 SDNDDIEVESDADKR 15 1 A0A494C130;Q6V3B1;G3V563;G3V2R5;P61244-2 A0A494C130 MAX Protein max 1 0 S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR;S(1)DNDDIEVESDADKR ;; 172.21 4.70E-26 402220000 3491.9 3153.7 3062.91 3243.93 4578.44 4732.23 4200.97 4604.53 3159.22 3547.18 TRUE FALSE FALSE 3449.33938 3198.097871 3116.218664 3619.00845 4344.785122 4429.855776 4557.800287 4737.754811 2876.651451 3455.023752 0.998354752 0.925637015 0.90193842 1.047462683 1.257526846 1.282149152 1.319180594 1.371265482 0.832599616 1 11.75447991 -8.746866125 2.73444664 0.985125445 1.319221805 0.887965194 0.062029633 0.049082764 0.750629782 0.006574444 0.013695223 1.79E-09 8.746866125 0.33409636 (ac)S(ph)DNGELEDKPPAPPVR ddPTM_HeLa_Romidepsin_16h_R1 4 SDNGELEDKPPAPPVR 16 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR;S(1)DNGELEDKPPAPPVR ;;; 85.924 0.00012603 101329200 5995 5937 5277.74 5490.16 5187.01 5061.36 4408.43 5042.5 6536.5 6483.7 TRUE FALSE FALSE 5921.930634 6020.581242 5369.596851 6124.958131 4922.297524 4737.955431 4782.881934 5188.396782 5951.859069 6315.252539 0.937718737 0.953339744 0.850258452 0.96986749 0.779430038 0.750240058 0.757354026 0.821566002 0.942457809 1 12.62462471 -9.052423575 0.599781336 0.979011862 0.750645624 0.696572207 0.049648559 0.336094597 0.220438929 0.010942463 0.036343497 8.86E-10 9.052423575 -0.228366238 (ac)S(ph)DQDHSMDEMTAVVK ddPTM_HeLa_Romidepsin_16h_R1 1 SDQDHSMDEMTAVVK 15 0 H3BUU5;P08047-3;P08047 H3BUU5 SP1 Transcription factor Sp1 1 0 S(0.656)DQDHS(0.332)MDEMT(0.012)AVVK 42.976 0.0015337 0 1076.5 1114.7 1231.3 934.67 909.35 756.08 796.58 629.06 1255.2 1196.8 TRUE FALSE FALSE 1063.379204 1130.392776 1252.73026 1042.740943 862.9424762 707.7689281 864.2414853 647.2608586 1142.931768 1165.706963 0.912218282 0.969705776 1.074652807 0.894513781 0.740273931 0.607158532 0.741388284 0.555251773 0.980462332 1 10.18698945 -8.719428415 2.580523436 0.96696195 0.647065282 0.869655323 0.060390412 0.075017454 1.01790854 0.009246916 0.01972142 1.91E-09 8.719428415 -0.319896668 (ac)S(ph)DQEAKPSTEDLGDK ddPTM_HeLa_Romidepsin_16h_R1 2 SDQEAKPSTEDLGDK 15 1 B8ZZJ0;B9A032;B8ZZN6;P63165 B8ZZJ0 SUMO1 Small ubiquitin-related modifier 1 1 0 S(0.965)DQEAKPS(0.018)T(0.018)EDLGDK;S(0.99)DQEAKPS(0.009)T(0.001)EDLGDK ; 91.123 0.0003338 38201000 5967 5648 5837.2 4649.8 6905.4 7339 6525.2 6901.6 6075.5 6450.8 TRUE FALSE FALSE 5894.271909 5727.512692 5938.794017 5187.431754 6552.99167 6870.061586 7079.450325 7101.286907 5532.092064 6283.207286 0.938099229 0.911558768 0.945185118 0.825602518 1.042937368 1.093400436 1.126725572 1.13020096 0.880456718 1 12.61728546 -8.528085051 24.95022613 0.953162176 1.109503708 0.737218437 0.051727155 61.68342755 295605.7324 0.007719088 0.015480055 2.96E-09 8.528085051 0.156341532 (ac)S(ph)DQEAKPSTEDLGDKK ddPTM_HeLa_Romidepsin_16h_R1 2 SDQEAKPSTEDLGDKK 16 2 B8ZZJ0;B9A032;B8ZZN6;P63165 B8ZZJ0 SUMO1 Small ubiquitin-related modifier 1 1 0 S(1)DQEAKPSTEDLGDKK;S(0.99)DQEAKPS(0.002)T(0.008)EDLGDKK ; 98.407 0.0016217 849999000 13408 15054.5 13522 12326.1 17251.9 17312.8 15238.1 17405 15955.6 15433.4 TRUE FALSE FALSE 13244.57814 15266.43765 13757.34474 13751.30168 16371.47117 16206.56795 16532.42383 17908.58621 14528.49117 15032.43804 0.881066538 1.015566311 0.915177212 0.914775211 1.089076244 1.078106419 1.099783268 1.191329455 0.966476039 1 13.87579139 -8.688154687 5.123451861 0.944335917 1.114386811 0.749446343 0.047030036 0.0920616 4.40627466 0.008187446 0.016514883 2.05E-09 8.688154687 0.170050894 (ac)S(ph)DSGEQNYGER ddPTM_HeLa_Romidepsin_16h_R1 2 SDSGEQNYGER 11 0 P62995;P62995-2 P62995 TRA2B Transformer-2 protein homolog beta 1 0 S(1)DSGEQNYGER;S(1)DSGEQNYGER ; 166.09 3.91E-48 94548000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)S(ph)DSGEQNYGERES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 0 S(0.905)DS(0.085)GEQNY(0.011)GERES(1)R 61.165 0.0035288 0 0 0 0 0 0 0 0 0 63.614 118.2 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 57.92420452 115.129147 0 0 0 0 0 0 0 0 0.503123718 1 6.847109313 -12.15782943 0.67715094 1.083625667 2.50E-23 0.780651779 0.150104457 0.06659167 0.049088893 0.041658112 0.0090835 6.95E-13 12.15782943 -1.083625667 (ac)S(ph)DTAVADTR ddPTM_HeLa_Romidepsin_16h_R1 1 SDTAVADTR 9 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 0 S(1)DTAVADTR 102.51 0.0013023 3360500 0 151.56 0 113.28 160.13 0 0 0 0 63.47 TRUE FALSE FALSE 0 153.6936657 0 126.3779666 151.9579686 0 0 0 0 61.82104025 0 2.486106106 0 2.044254935 2.458029952 0 0 0 0 1 5.950026025 -8.092580976 22.25936113 0.86951134 1.71E-09 0.201280678 0.938191126 32.3484615 7772.914044 0.136405223 0.347767262 8.08E-09 8.092580976 -0.869511338 (ac)S(ph)DTAVADTRR ddPTM_HeLa_Romidepsin_16h_R1 1 SDTAVADTRR 10 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 0 S(0.895)DT(0.105)AVADTRR 76.478 0.0037583 6802200 212.97 210.93 335.97 321.62 159.24 354.23 120.02 185.68 379.49 233.72 TRUE FALSE FALSE 210.3742397 213.8994781 341.8174169 358.8072177 151.1133886 331.5958462 130.2144958 191.0523578 345.5474639 227.6479207 0.924121068 0.939606553 1.501517852 1.576149769 0.66380307 1.456617065 0.571999496 0.839244906 1.51790301 1 7.830660472 -7.723331639 24.99768726 1.048720748 0.705622007 0.162399206 0.329149706 216.5769522 142066.0782 0.04029863 0.150777564 1.89E-08 7.723331639 -0.343098742 (ac)S(ph)DVEENNFEGR ddPTM_HeLa_Romidepsin_16h_R1 2 SDVEENNFEGR 11 0 Q13595;F8WEH2 Q13595 TRA2A Transformer-2 protein homolog alpha 1 0 S(1)DVEENNFEGR;S(1)DVEENNFEGR ; 133.57 5.89E-05 24151000 410.77 464.54 487.69 343.08 328.883 548.3 479.49 192.86 558.19 449.53 TRUE FALSE FALSE 405.7633772 471.0798063 496.1780399 382.7485238 312.0988733 513.2653996 520.2178686 198.4400998 508.2640884 437.8511458 0.926715349 1.075890313 1.133211697 0.874152158 0.712796749 1.172237196 1.18811581 0.453213613 1.160814796 1 8.774296677 (ac)S(ph)DVEENNFEGRES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 2 0 S(1)DVEENNFEGRES(1)R;S(1)DVEENNFEGRES(1)R ; 93.909 0.0025065 76008000 332.164 320.54 50.157 200.046 347.55 382.28 365.36 370.12 304 472.45 TRUE FALSE FALSE 328.1154574 325.0525705 51.02996155 223.1762598 329.8132266 357.8535418 396.3936693 380.8288382 276.8094786 460.1756809 0.713022159 0.706366251 0.110892348 0.484980561 0.716711552 0.777645488 0.861396388 0.827572716 0.601530003 1 8.846040933 -11.57063066 0.88563565 0.972683715 0.64247843 0 0.236076515 0.54484562 0.871646393 0.093001737 0.04721819 2.69E-12 11.57063066 -0.330205285 (ac)S(ph)EGESQTVLSSGSDPK ddPTM_HeLa_Romidepsin_16h_R1 4 SEGESQTVLSSGSDPK 16 0 F8W6G1;Q9UHY1;C9JDW7;C9JHZ6 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 0 S(0.828)EGES(0.172)QTVLSSGSDPK;S(0.862)EGES(0.123)QT(0.015)VLSSGSDPK;S(0.961)EGES(0.039)QTVLSSGSDPK;S(0.632)EGES(0.366)QT(0.002)VLSSGSDPK ;;; 132.08 4.03E-19 53166200 20765.1 20880.1 18053.5 19587.7 24730.3 24219.1 21006.5 22476.5 22319.8 20256 TRUE FALSE FALSE 20512.00697 21174.0506 18367.71359 21852.52204 23468.22051 22671.57767 22790.79159 23126.82207 20323.46119 19729.7462 1.039648801 1.073204408 0.930965528 1.107592658 1.189484156 1.149106402 1.155148746 1.172180414 1.030092378 1 14.26808478 -9.028908916 6.738164791 1.01806424 1.162829569 0.803410505 0.035531627 0.060426579 9.897029768 0.005179409 0.008824449 9.36E-10 9.028908916 0.144765328 (ac)S(ph)EKS(ph)VEAAAELSAK ddPTM_HeLa_Romidepsin_16h_R1 1 SEKSVEAAAELSAK 14 1 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 2 0 S(1)EKS(1)VEAAAELSAK 77.124 0.003433 22115000 5154.3 4896.3 4100.3 4966.6 4745.2 3995.7 3146.7 4290.7 4969.8 4454.5 TRUE FALSE FALSE 5091.477409 4965.23024 4171.664002 5540.861661 4503.034737 3740.387666 3413.980619 4414.844635 4525.288641 4338.771448 1.173483662 1.144386216 0.961485077 1.27705774 1.037859401 0.862084512 0.786854219 1.017533347 1.042988481 1 12.08307088 -8.354901252 4.586601038 1.093209983 0.87905571 0.466692694 0.100131751 0.151148433 5.408701815 0.014986327 0.03470797 4.42E-09 8.354901252 -0.214154273 (ac)S(ph)EKSVEAAAELSAK ddPTM_HeLa_Romidepsin_16h_R1 4 SEKSVEAAAELSAK 14 1 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 1 0 S(0.725)EKS(0.275)VEAAAELSAK;S(0.865)EKS(0.135)VEAAAELSAK;S(0.834)EKS(0.166)VEAAAELSAK;S(0.821)EKS(0.179)VEAAAELSAK ;;; 74.962 8.61E-06 188523900 10300.4 9339.3 8700.5 10993.1 9982.1 8923 8158.8 8983.2 9951.8 9632.2 TRUE FALSE FALSE 10174.85476 9470.778911 8851.928553 12264.17395 9472.676189 8352.849098 8851.808268 9243.114719 9061.686083 9381.954055 1.084513386 1.009467628 0.943505852 1.307208911 1.009669855 0.890310169 0.943493031 0.985201448 0.965863404 1 13.19567272 -8.514419293 24.99977448 1.0514328 0.941707232 0.210228996 0.097174634 460.3214639 1360363.208 0.013413295 0.027917371 3.06E-09 8.514419293 -0.109725568 (ac)S(ph)ESGEMSEFGY(ph)IMELIAK ddPTM_HeLa_Romidepsin_16h_R1 1 SESGEMSEFGYIMELIAK 18 0 Q9NQ86-2;Q9NQ86-3;Q9NQ86 Q9NQ86-2 TRIM36 E3 ubiquitin-protein ligase TRIM36 2 0 S(0.464)ES(0.464)GEMS(0.076)EFGY(0.996)IMELIAK 53.252 0.011852 7868200 993.89 956.46 843.25 817.45 975.09 1200.8 832.08 701.67 1080.9 1095.7 TRUE FALSE FALSE 981.7760864 969.925069 857.9264125 911.9674152 925.3275187 1124.072755 902.7568544 721.9717144 984.2215968 1067.233556 0.919926178 0.908821751 0.803878783 0.854515312 0.867033756 1.053258445 0.845884998 0.676488956 0.922217626 1 10.05966022 -4 0.033054437 1.479795367 1.61E-09 0.214543964 0.087532459 912.7310894 2.332875269 32.05319307 84.08612099 1.00E-04 4 -1.479795365 (ac)S(ph)ET(ph)APAAPAAPAPAEKTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 2 0 S(0.63)ET(0.756)APAAPAAPAPAEKT(0.614)PVK 87.001 0.00021057 4182600 1184.9 1599.3 1429 1096.1 1045.6 1126.7 921.66 784.53 1217.9 1733.9 TRUE FALSE FALSE 1170.457983 1621.814987 1453.871146 1222.836239 992.2391303 1054.707506 999.9457774 807.2291378 1108.967974 1688.853028 0.693049048 0.96030558 0.860863036 0.724063148 0.587522486 0.624511126 0.59208573 0.47797477 0.656639717 1 10.72182807 -7.317772424 0.113859464 1.136693691 6.81E-21 0.364055614 0.129154355 20.32892181 0.390742235 0.860532229 3.874887803 4.81E-08 7.317772424 -1.136693691 (ac)S(ph)ETAPAAPAAAPPAEK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAAPPAEK 16 0 P16403 P16403 HIST1H1C Histone H1.2 1 0 S(0.5)ET(0.5)APAAPAAAPPAEK;S(0.5)ET(0.5)APAAPAAAPPAEK ; 50.467 0.0016387 40191000 7275.7 13723.7 7825.5 7635.8 8054.7 9136.9 6793.7 8701.6 10406.9 10307.1 TRUE FALSE FALSE 7187.02097 13916.90261 7961.699545 8518.687124 7643.638603 8553.081578 7370.756708 8953.367067 9476.080799 10039.32006 0.715887224 1.386239559 0.793051671 0.848532279 0.761370149 0.851958253 0.734188836 0.891830026 0.943896673 1 13.29337394 (ac)S(ph)ETAPAAPAAAPPAEKAPVK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAAPPAEKAPVK 20 1 P16403 P16403 HIST1H1C Histone H1.2 1 0 S(0.5)ET(0.5)APAAPAAAPPAEKAPVK;S(0.5)ET(0.5)APAAPAAAPPAEKAPVK ; 62.68 0.00015222 13250700 4478.6 8131.1 2810.7 8487.3 4146.6 3535.4 3369.4 3977.3 5070.5 4615.8 TRUE FALSE FALSE 4424.013101 8245.569839 2859.619054 9468.64156 3934.983529 3309.49935 3655.596752 4092.3769 4616.981781 4495.880851 0.984014757 1.834027661 0.636053123 2.106070395 0.875241951 0.736118118 0.813099117 0.910250302 1.026935974 1 12.13438809 -8.547632646 24.99968016 1.117842148 0.816903973 0.152073333 0.421539116 389.9428365 393813.0595 0.058831607 0.117666831 2.83E-09 8.547632646 -0.300938175 (ac)S(ph)ETAPAAPAAPAPAEKTPVK ddPTM_HeLa_Romidepsin_16h_R1 4 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 0 S(0.499)ET(0.499)APAAPAAPAPAEKT(0.001)PVK;S(0.5)ET(0.5)APAAPAAPAPAEKTPVK;S(0.5)ET(0.5)APAAPAAPAPAEKTPVK;S(0.5)ET(0.5)APAAPAAPAPAEKTPVK ;;; 150.51 5.63E-10 1448098000 17298.3 31227.7 16294.7 16180.7 16589.9 17025 13528.5 15330.4 20215.1 21655.4 TRUE FALSE FALSE 17087.46167 31667.32438 16578.30242 18051.58867 15743.2555 15937.15745 14677.61045 15773.96094 18407.01083 21092.78959 0.810109142 1.501334105 0.785970123 0.855817984 0.746380911 0.755573718 0.695859141 0.747836642 0.872668395 1 14.36446229 -9.145105943 2.2590798 0.954378398 0.739168311 0.287093017 0.188696075 0.379364364 3.785723374 0.030178495 0.054384717 7.16E-10 9.145105943 -0.215210086 (ac)S(ph)ETAPAETATPAPVEK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAETATPAPVEK 16 0 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.966)ET(0.034)APAETATPAPVEK 98.676 0.0035822 27307000 5195.1 9645.4 4494 5706.8 6954.3 9723.8 7245.9 9059.6 6368.3 6523 TRUE FALSE FALSE 5131.780123 9781.188194 4572.216185 6366.647067 6599.396121 9102.480562 7861.366565 9321.725232 5798.703298 6353.53152 0.807705149 1.539488419 0.719633824 1.002064293 1.038697314 1.432664737 1.237322352 1.467172265 0.912674043 1 12.633343 -8.38055679 3.614935199 0.951214377 1.365578081 0.380921147 0.214552054 0.174351085 4.116617556 0.030449876 0.07249922 4.16E-09 8.38055679 0.414363704 (ac)S(ph)ETAPAETATPAPVEKS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 2 0 S(0.92)ET(0.079)APAET(0.001)AT(0.027)PAPVEKS(0.973)PAK;S(0.681)ET(0.205)APAET(0.084)AT(0.033)PAPVEKS(0.996)PAK ; 77.63 0.0014773 7984000 5866.6 8489.3 4937.7 5260.8 4153 4660.3 3866.9 4102 7288.1 7464.9 TRUE FALSE FALSE 5795.095623 8608.812588 5023.638597 5869.078449 3941.056913 4362.52187 4195.354389 4220.684898 6636.234083 7270.960822 0.797019234 1.183999309 0.690918122 0.807194344 0.542026977 0.599992488 0.577001375 0.580485166 0.91270387 1 12.82793031 -9.118780443 1.553192557 0.919250225 0.575614435 0.656961669 0.118167934 0.193607942 0.918602917 0.019914156 0.039237301 7.61E-10 9.118780443 -0.34363579 (ac)S(ph)ETAPAETATPAPVEKSPAK ddPTM_HeLa_Romidepsin_16h_R1 4 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.857)ET(0.037)APAET(0.027)AT(0.005)PAPVEKS(0.074)PAK;S(0.944)ET(0.054)APAETAT(0.001)PAPVEKSPAK;S(0.965)ET(0.031)APAET(0.003)AT(0.001)PAPVEKSPAK;S(0.561)ET(0.071)APAET(0.324)AT(0.043)PAPVEKS(0.001)PAK ;;; 86.548 0.00057834 2797550000 26764.6 48519.9 23492.5 25219.6 19775.5 17731.1 15334.6 17442.6 32037.1 32558.9 TRUE FALSE FALSE 26438.38276 49202.96443 23901.37711 28135.60881 18766.28244 16598.13993 16637.12054 17947.27411 29171.62154 31713.01508 0.833676101 1.551506985 0.753677222 0.887194382 0.591753335 0.523385742 0.52461491 0.565927713 0.919862759 1 14.95278743 -8.821046134 2.00601347 0.964572563 0.531780805 0.532988831 0.202519151 0.214468315 1.756377062 0.031201978 0.066909906 1.51E-09 8.821046134 -0.432791758 (ac)S(ph)ETAPAETATPAPVEKSPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.717)ET(0.048)APAET(0.061)AT(0.061)PAPVEKS(0.113)PAKK 49.125 0.010933 269020000 2563.2 4224.2 2302.7 2490.6 1605.7 1581.5 1428.6 1695 3133 2900.6 TRUE FALSE FALSE 2531.958732 4283.668398 2342.777528 2778.574891 1523.755137 1480.447254 1549.945248 1744.042151 2852.776633 2825.241994 0.896191809 1.516212915 0.829230746 0.983482086 0.539336149 0.524007238 0.548606191 0.617307174 1.00974594 1 11.46415873 -8.763106717 24.36801399 0.988826562 0.554313053 0.630270359 0.178303955 17.18580832 251178.4192 0.026042224 0.04907372 1.73E-09 8.763106717 -0.434513508 (ac)S(ph)FEGGDGAGPAMLATGTAR ddPTM_HeLa_Romidepsin_16h_R1 2 SFEGGDGAGPAMLATGTAR 19 0 Q96B36-3 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 S(1)FEGGDGAGPAMLATGTAR;S(1)FEGGDGAGPAMLATGTAR ; 116.06 5.43E-10 14232700 137.82 66.302 229.428 299.2 179.095 246.773 177.36 152.68 307.46 308.83 TRUE FALSE FALSE 136.1401968 67.2354013 233.4210981 333.7949118 169.9551139 231.0050017 192.424954 157.0975549 279.9600076 300.8065521 0.452583881 0.223517077 0.775984088 1.10966636 0.564998045 0.767952028 0.639696684 0.522254432 0.930697838 1 8.232692181 -12.48977626 1.278638754 0.996781823 0.621312764 0.265133533 0.220751326 0.491116694 1.455979008 0.156940678 0.039658295 3.24E-13 12.48977626 -0.37546906 (ac)S(ph)FLFSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SFLFSSR 7 0 Q9H8S9-2;Q9H8S9 Q9H8S9-2 MOB1A MOB kinase activator 1A 1 0 S(1)FLFSSR 72.138 0.0057945 1735800 160.32 149.41 54.947 0 55.13 0 58.137 174.4 166.13 56.198 TRUE FALSE FALSE 158.3659582 151.5133979 55.90332949 0 52.31651038 0 63.07515533 179.4459888 151.2709167 54.73796786 2.893164733 2.767976303 1.021289823 0 0.955762744 0 1.152310869 3.278272758 2.763546449 1 5.774469971 -12.95187855 2.258633333 0.990886028 1.738614725 0 1.236723236 0.961439784 8.90204448 1.015447266 0.189603003 1.12E-13 12.95187855 0.747728697 (ac)S(ph)GDEMIFDPTMSK ddPTM_HeLa_Romidepsin_16h_R1 6 SGDEMIFDPTMSK 13 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 0 S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(1)GDEMIFDPTMSK;S(0.999)GDEMIFDPT(0.001)MSK;S(0.982)GDEMIFDPT(0.017)MS(0.001)K ;;;;; 70.808 0.0020922 1190987000 34452.7 33760.2 32916.5 28443.1 30688.2 29641.5 28704 30437.5 35925.1 35118.4 TRUE FALSE FALSE 34032.77724 34235.47698 33489.39787 31731.82505 29122.06664 27747.50381 31142.11704 31318.16104 32711.86908 34206.01891 0.994935346 1.000861196 0.979049856 0.92766788 0.851372582 0.811187759 0.91042799 0.91557457 0.956319096 1 15.06196258 -9.110965098 2.443825711 0.997282608 0.871060024 0.745617786 0.031052992 0.092734446 1.08368684 0.004498721 0.008128936 7.75E-10 9.110965098 -0.126222584 (ac)S(ph)GDEMIFDPTMSKK ddPTM_HeLa_Romidepsin_16h_R1 7 SGDEMIFDPTMSKK 14 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 0 S(0.999)GDEMIFDPTMSKK;S(0.998)GDEMIFDPT(0.002)MSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK;S(1)GDEMIFDPTMSKK ;;;;;; 68.069 0.0056372 1597342400 21857.7 21176.8 16720.2 24357.7 19734.9 17556.2 17887.5 18639.5 22335.6 20559.2 TRUE FALSE FALSE 21591.28995 21474.92755 17011.20807 27174.05188 18727.75441 16434.41548 19406.8638 19178.80452 20337.848 20025.06902 1.07821301 1.072402174 0.849495602 1.357001659 0.935215474 0.820692077 0.969128435 0.957739746 1.015619371 1 14.28951959 -8.552058493 24.99999821 1.04917293 0.913975893 0.23577436 0.123780149 225.3914072 193105.1575 0.016708819 0.033417982 2.81E-09 8.552058493 -0.135197037 (ac)S(ph)GDGATEQAAEYVPEK ddPTM_HeLa_Romidepsin_16h_R1 2 SGDGATEQAAEYVPEK 16 0 Q12996;E9PJ06;Q12996-3;Q12996-2 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 0 S(0.993)GDGAT(0.007)EQAAEYVPEK;S(0.995)GDGAT(0.005)EQAAEYVPEK ; 107.74 9.49E-09 4379400 2560.1 2444.03 2259.54 2769.3 2498.7 2826.5 2386.5 2595.46 2728.2 2465.06 TRUE FALSE FALSE 2528.896516 2478.437118 2298.866346 3089.499496 2371.182015 2645.895772 2589.20925 2670.55554 2484.182959 2401.017386 1.053260393 1.032244553 0.957455102 1.286745991 0.987573863 1.101989427 1.078380051 1.112259976 1.034637639 1 11.22943013 (ac)S(ph)GEDEQQEQTIAEDLVVTK ddPTM_HeLa_Romidepsin_16h_R1 11 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 1 0 S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK;S(1)GEDEQQEQTIAEDLVVTK ;;;;;;;;;; 144.73 6.09E-63 865337900 51711.45 51971.02 45829.38 46755.12 47975.8 49348.5 41965.99 50231.14 53405.47 52591.16 TRUE FALSE FALSE 51081.17096 52702.66938 46627.02113 52161.16696 45527.4159 46195.29011 45530.58014 51684.49878 48628.75101 51224.83408 0.99719544 1.028849977 0.910242502 1.018278886 0.888776249 0.901814343 0.888838021 1.008973474 0.949319834 1 15.64455579 -9.279491257 1.198223785 0.999922102 0.923190532 0.18835253 0.049035757 0.360594905 1.021838521 0.007324601 0.014366887 5.25E-10 9.279491257 -0.07673157 (ac)S(ph)GEENPASKPTPVQDVQGDGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGEENPASKPTPVQDVQGDGR 21 1 M0QXS6;M0R323;M0QZT2;M0R389;Q15102 M0QXS6 PAFAH1B3 Platelet-activating factor acetylhydrolase IB subunit gamma 1 0 S(0.724)GEENPAS(0.27)KPT(0.007)PVQDVQGDGR 58.885 8.17E-06 0 309.46 233.95 365.8 158.33 335.2 443.69 259.44 223.6 281.81 260.54 TRUE FALSE FALSE 305.6881825 237.2435542 372.1665956 176.6368596 318.0934932 415.3396409 281.4768271 230.0695132 256.6042078 253.7711332 1.204582171 0.934872108 1.466544247 0.696047881 1.253466023 1.636670159 1.109175908 0.906602379 1.011163896 1 7.98738416 (ac)S(ph)KSESPKEPEQLR ddPTM_HeLa_Romidepsin_16h_R1 3 SKSESPKEPEQLR 13 2 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 S(0.931)KS(0.069)ES(0.001)PKEPEQLR;S(0.948)KS(0.052)ESPKEPEQLR;S(0.999)KS(0.001)ESPKEPEQLR ;; 112.3 0.0019689 38897100 6277 6520.9 5284.8 5705.1 5788.7 5354.3 4524.5 5089.1 7144 7059.3 TRUE FALSE FALSE 6200.49351 6612.701401 5376.779727 6364.750505 5493.281038 5012.17751 4908.810917 5236.345079 6505.022748 6875.898368 0.901772129 0.961721807 0.781974869 0.925660934 0.7989183 0.728948748 0.713915572 0.76155068 0.946061503 1 12.74733251 -8.087574842 0.228125018 1.012602444 0.545197723 0.725114465 0.05264008 2.623654346 0.164870519 0.051808141 0.350338614 8.17E-09 8.087574842 -0.46740472 (ac)S(ph)KSESPKEPEQLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSESPKEPEQLRK 14 3 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 S(0.478)KS(0.478)ES(0.044)PKEPEQLRK 51.606 0.02299 47006000 1879.2 1752.6 1212 4939.6 1627.1 1591.1 1981.2 1950.9 2037.3 1386.4 TRUE FALSE FALSE 1856.295588 1777.273149 1233.094352 5510.739794 1544.063015 1489.433845 2149.483079 2007.346213 1855.078785 1350.381128 1.374645683 1.316127064 0.913145427 4.080877375 1.143427573 1.102972941 1.591760307 1.486503456 1.373744602 1 10.39915093 (ac)S(ph)LSHLYR ddPTM_HeLa_Romidepsin_16h_R1 2 SLSHLYR 7 0 Q9UBB9;F6XM96;F6UKU9;F6SQZ1;F6UQ07 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 S(1)LSHLYR;S(0.999)LS(0.001)HLYR ; 75.311 0.014209 2885500 1728.36 1391.7 1459.63 1148 1357.97 1568.07 1080.45 1178.82 1680.05 1567.6 TRUE FALSE FALSE 1707.294084 1411.292389 1485.034248 1280.737162 1288.667724 1467.875388 1172.223396 1212.927297 1529.78212 1526.873526 1.118163394 0.924302089 0.972598072 0.83879715 0.843991137 0.961360167 0.767727894 0.794386225 1.001904935 1 10.57636485 -9.648022766 1.399742613 1.05374037 0.841653851 0.610797793 0.064880248 0.185266292 0.732310269 0.012390424 0.019377591 2.25E-10 9.648022766 -0.212086519 (ac)S(ph)MPDAMPLPGVGEELK ddPTM_HeLa_Romidepsin_16h_R1 1 SMPDAMPLPGVGEELK 16 0 O43865 O43865 AHCYL1 Putative adenosylhomocysteinase 2 1 0 S(1)MPDAMPLPGVGEELK 69.03 0.0035515 2973400 2252.8 2302.1 1871.5 2098.3 1855.2 2091.4 1820.6 2130.4 2106 1739.7 TRUE FALSE FALSE 2225.342007 2334.509024 1904.072672 2340.915319 1760.522221 1957.76629 1975.241719 2192.039763 1917.634085 1694.502343 1.31327172 1.377695955 1.123676624 1.38147659 1.03896122 1.155363578 1.165676593 1.293618608 1.131679807 1 10.72664592 -12.41349641 1.161138904 1.000996224 1.233657788 0.227409925 0.113133821 0.389759955 0.946144675 0.071915553 0.018522196 3.86E-13 12.41349641 0.232661564 (ac)S(ph)QERPTFYR ddPTM_HeLa_Romidepsin_16h_R1 1 SQERPTFYR 9 1 Q16539-5;Q16539-3;Q16539-4;Q16539-2;Q16539;B5TY33 Q16539-5 MAPK14 Mitogen-activated protein kinase 14 1 0 S(0.8)QERPT(0.2)FYR 59.153 0.017784 42506000 64.348 253.69 139.43 153.93 193.64 203.66 166.69 0 297.95 230.72 TRUE FALSE FALSE 63.56370183 257.2614545 141.8567207 171.7281109 183.7578282 190.6467833 180.8486444 0 271.3006058 224.7258611 0.282849964 1.144779035 0.631243418 0.764167106 0.817697738 0.848352665 0.804752259 0 1.207251379 1 7.812022347 -12.74470067 1.684425835 1.000166801 0.62304419 0.218699058 0.311222019 0.555356002 2.848366166 0.227722429 0.049169166 1.80E-13 12.74470067 -0.377122611 (ac)S(ph)QGDSNPAAIPHAAEDIQGDDR ddPTM_HeLa_Romidepsin_16h_R1 2 SQGDSNPAAIPHAAEDIQGDDR 22 0 P68402-3;P68402-2;P68402-4;P68402 P68402-3 PAFAH1B2 Platelet-activating factor acetylhydrolase IB subunit beta 1 0 S(0.5)QGDS(0.5)NPAAIPHAAEDIQGDDR;S(0.81)QGDS(0.19)NPAAIPHAAEDIQGDDR ; 95.067 3.31E-17 18443000 5387.8 4586.1 4486.9 4101.2 5138.1 5256.6 4399.8 4686.8 4947.8 4488.9 TRUE FALSE FALSE 5322.131421 4650.663236 4564.992612 4575.400041 4875.883584 4920.720225 4773.518902 4822.405163 4505.256376 4372.277731 1.217244592 1.063670591 1.044076542 1.046456864 1.115181579 1.125436335 1.09176937 1.102950329 1.030414044 1 12.09416933 -12.72082854 1.638219637 1.000103689 1.117541443 0.272276985 0.049892513 0.361608528 1.755047504 0.045011389 0.009883088 1.90E-13 12.72082854 0.117437753 (ac)S(ph)QKQEEENPAEETGEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SQKQEEENPAEETGEEK 17 1 O43768-2;O43768;A6NMQ3;Q5T5H1;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-8 O43768-2 ENSA Alpha-endosulfine 1 0 S(1)QKQEEENPAEETGEEK;S(1)QKQEEENPAEETGEEK ; 156.36 8.62E-27 15594500 5191.8 4479.2 4803 3221.5 4181.8 4417.2 3208 4093.6 5162.2 4978.3 TRUE FALSE FALSE 5128.520345 4542.258295 4886.5942 3593.984988 3968.387142 4134.955176 3480.48744 4212.041857 4700.479903 4848.963048 1.057653006 0.936748383 1.00776066 0.741186301 0.81839913 0.852750399 0.717779741 0.868647959 0.969378371 1 12.24346054 -9.273226731 23.86200489 1.018364322 0.799178884 0.759122173 0.053952119 121.5499879 246062.3032 0.007902157 0.012138255 5.33E-10 9.273226731 -0.219185438 (ac)S(ph)QKQEEENPAEETGEEKQDTQEK ddPTM_HeLa_Romidepsin_16h_R1 4 SQKQEEENPAEETGEEKQDTQEK 23 2 O43768-2;O43768;A6NMQ3;Q5T5H1;O43768-9;O43768-3;O43768-4;A0A1W2PRU0;O43768-8 O43768-2 ENSA Alpha-endosulfine 1 0 S(0.981)QKQEEENPAEET(0.019)GEEKQDTQEK;S(1)QKQEEENPAEETGEEKQDTQEK;S(1)QKQEEENPAEETGEEKQDTQEK;S(0.999)QKQEEENPAEET(0.001)GEEKQDTQEK ;;; 93.029 1.09E-05 131353000 5976 5594.7 5744.9 4654.4 5818.4 5338.52 4008.18 4651.88 5595.9 5884.15 TRUE FALSE FALSE 5903.162213 5673.462333 5844.887575 5192.563628 5521.465337 4997.405801 4348.634709 4786.474808 5095.388689 5731.278935 1.029990388 0.989912094 1.019822563 0.906004347 0.963391487 0.87195299 0.758754679 0.835149512 0.889049154 1 12.4846414 -8.318222195 0.868559396 1.013341358 0.776449159 0.6116248 0.052690611 0.201208437 0.242638049 0.005597075 0.032107387 4.81E-09 8.318222195 -0.236892199 (ac)S(ph)RLSWGYR ddPTM_HeLa_Romidepsin_16h_R1 2 SRLSWGYR 8 1 Q8N1Q1 Q8N1Q1 CA13 Carbonic anhydrase 13 1 0 S(0.999)RLS(0.001)WGYR;S(1)RLSWGYR ; 88.643 0.020781 23308000 1068.33 997.23 1011 1096.27 1023.02 1301.37 1140.02 1299.61 1152.53 1190.97 TRUE FALSE FALSE 1055.308783 1011.26903 1028.596031 1223.025896 970.811472 1218.216657 1236.85327 1337.212165 1049.44483 1160.028428 0.909726657 0.871762283 0.886698986 1.054306831 0.836885932 1.050161037 1.06622669 1.152740858 0.904671649 1 10.17994445 -7.906097891 2.546792305 0.944887444 1.119110181 0.562091337 0.065905074 0.17479362 2.23568608 0.009475039 0.037352237 1.24E-08 7.906097891 0.174222737 (ac)S(ph)SDASQGVITTPPPPSMPHK ddPTM_HeLa_Romidepsin_16h_R1 1 SSDASQGVITTPPPPSMPHK 20 0 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 0 S(0.226)S(0.226)DAS(0.226)QGVIT(0.161)T(0.161)PPPPSMPHK 41.227 0.0029739 11726000 757.62 514.63 694.96 671.26 944.51 1022.5 831.3 792.82 742.25 806.85 TRUE FALSE FALSE 748.385836 521.8749746 707.0554873 748.8742396 896.3081302 957.16555 901.9106013 815.7589958 675.861301 785.8879207 0.95228062 0.664057763 0.89968998 0.952902087 1.140503762 1.217941547 1.147632604 1.038009332 0.85999706 1 9.618179767 -8.767483587 6.45146186 0.942528226 1.14340529 0.549370586 0.103099832 0.108093778 19.07056762 0.016248047 0.030939919 1.71E-09 8.767483587 0.200877063 (ac)S(ph)SILPFTPPVVKR ddPTM_HeLa_Romidepsin_16h_R1 2 SSILPFTPPVVKR 13 1 K7ESI8;K7EL92;K7ERC7;K7EJX0;B7Z5N5;Q15796-2;Q15796 K7ESI8 SMAD2 Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 2 1 0 S(0.5)S(0.5)ILPFTPPVVKR;S(0.5)S(0.5)ILPFTPPVVKR ; 109.44 0.0026042 239670000 4013.1 3711.9 2878 6172.7 3744.6 3266.3 2877.4 3244 3923.6 3453.1 TRUE FALSE FALSE 3964.186794 3764.156226 2928.090383 6886.416617 3553.499089 3057.593972 3121.806284 3337.860022 3572.663389 3363.387964 1.17862906 1.11915612 0.870577648 2.047464251 1.056523698 0.909081558 0.928173115 0.992410051 1.062221613 1 11.71569949 -8.520078278 24.99954635 1.148412736 0.948564308 0.119071919 0.303415116 227.969917 2035062.194 0.044000942 0.089327885 3.02E-09 8.520078278 -0.199848428 (ac)S(ph)SLSMCMKSDK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSMCMKSDK 11 1 A0A1B0GVS0 A0A1B0GVS0 1 0 S(0.37)S(0.37)LS(0.259)MCMKSDK 46.129 0.0033828 0 368.33 280.83 325.18 268.07 153.01 275.71 203.73 286.68 280.61 334.82 TRUE FALSE FALSE 363.8406523 284.7835321 330.8396215 299.0655147 145.2013287 258.0930208 221.0348211 294.9746335 255.5115388 326.1213281 1.115660403 0.87324412 1.014467908 0.917037584 0.445237144 0.791401845 0.677768677 0.904493537 0.783486135 1 8.349264985 -8.989640296 24.94949409 1.033690724 0.705509238 0.356307864 0.145620209 103.4243055 249077.117 0.017825781 0.032287981 1.02E-09 8.989640296 -0.328181487 (ac)S(ph)SPASTPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPASTPSR 9 0 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;E5RG53;A0A3B3IS88 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 S(0.488)S(0.488)PAS(0.023)T(0.001)PSR 70.525 0.014806 482160 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)S(ph)SPASTPSRR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPASTPSRR 10 1 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;E5RG53;A0A3B3IS88 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 S(0.5)S(0.5)PASTPSRR 80.219 0.029816 802350 0 60.489 0 115.53 0 0 0 0 0 0 TRUE FALSE FALSE 0 61.34056573 0 128.8881222 0 0 0 0 0 0 0 (ac)S(ph)SPPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPPEGK 7 0 P51397;B4DQ75 P51397 DAP Death-associated protein 1 1 0 S(0.993)S(0.007)PPEGK 80.462 0.012506 74010000 19281 22116 29838 17546 16814 16639 21967 6833.4 31365 31467 TRUE FALSE FALSE 19045.99576 22427.34963 30357.31787 19574.75108 15955.91884 15575.8216 23832.87643 7031.113648 28559.63584 30649.4828 0.621413284 0.731736642 0.990467541 0.638664972 0.520593412 0.508191988 0.777594734 0.22940399 0.931814609 1 14.90357511 -16.52287875 0.059582316 2.396395916 1.36E-13 0.498657745 0.163813734 213.6408708 0.999745154 45.23036826 8.607084499 3.00E-17 16.52287875 -2.396395916 (ac)S(ph)SPPEGKLETK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPPEGKLETK 11 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 1 0 S(0.5)S(0.5)PPEGKLETK 58.699 0.01198 1205500000 12699 10934 8382.3 21893 11680 8698.9 7419.6 8040.3 12124 9903.3 TRUE FALSE FALSE 12544.2197 11087.92914 8528.190415 24424.37167 11083.92602 8143.068364 8049.820639 8272.933395 11039.59907 9646.010838 1.300456729 1.14948338 0.884115782 2.53206969 1.149068377 0.844190257 0.834523284 0.857653338 1.144473012 1 13.23571672 -8.300732012 5.734220496 1.234006053 0.843452463 0.180056946 0.434327177 0.300021348 27.34468947 0.06311698 0.145901622 5.00E-09 8.300732012 -0.39055359 (ac)S(ph)SSAGSGHQPSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSAGSGHQPSQSR 14 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 0 S(0.333)S(0.333)S(0.333)AGSGHQPSQSR 113.93 0.00098227 220980 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)S(ph)SSPVNVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPVNVK 8 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 0 S(0.958)S(0.021)S(0.021)PVNVK 75.189 0.0046016 3176600 3709.6 3758.9 3427.1 2831.6 2943.5 3278.3 2703.1 3235 4037.3 4063.5 TRUE FALSE FALSE 3664.385968 3811.817893 3486.747238 3159.002915 2793.282211 3068.82721 2932.701247 3328.599621 3676.193776 3957.929684 0.925834025 0.963083783 0.880952295 0.798145285 0.705743263 0.775361731 0.740968506 0.840995138 0.928817354 1 11.95053027 -9.430761726 1.965796449 0.964715198 0.763391958 0.836041214 0.038176058 0.091907355 0.700321314 0.006632053 0.010843714 3.71E-10 9.430761726 -0.201323241 (ac)S(ph)TGGDFGNPLRK ddPTM_HeLa_Romidepsin_16h_R1 1 STGGDFGNPLRK 12 1 F5H3K7;F5GX61;P20340-3;P20340-2;P20340 F5H3K7 RAB6A Ras-related protein Rab-6A 1 0 S(0.5)T(0.5)GGDFGNPLRK 116.37 0.00033639 6072300 2207.4 2630.4 1967.3 2079.6 2638.7 2439.1 1909.7 2948.8 2301.2 2533.6 TRUE FALSE FALSE 2180.49536 2667.43084 2001.540031 2320.053137 2504.037293 2283.249382 2071.90987 3034.118876 2095.374909 2467.776707 0.883586977 1.080904457 0.811070153 0.940139005 1.014693625 0.925225275 0.839585634 1.2294949 0.849094208 1 11.26899614 -7.248439283 24.84103812 0.941857543 1.229495101 0.542044814 0.082380009 1129.489759 2158229.85 0.010474525 0.258263337 5.64E-08 7.248439283 0.287637558 (ac)S(ph)VELEEALPVTTAEGMAK ddPTM_HeLa_Romidepsin_16h_R1 1 SVELEEALPVTTAEGMAK 18 0 Q92522 Q92522 H1FX Histone H1x 1 0 S(0.998)VELEEALPVT(0.002)TAEGMAK 62.162 0.0016712 983120 329.59 358.27 350.57 361.99 420.43 755.55 538.31 573.39 414.62 229.39 TRUE FALSE FALSE 325.5728303 363.3137345 356.6715238 403.844987 398.9738883 707.2727934 584.034038 589.980135 377.5353488 223.4304147 1.457155377 1.626071074 1.596342755 1.807475439 1.785674026 3.165517077 2.61394152 2.640554267 1.689722275 1 7.803681778 -8.490273651 0.391287345 1.09082548 3.332683265 0.711689819 0.334644135 0.715417535 0.143360514 0.098037016 0.660108724 3.23E-09 8.490273651 2.241857785 up (ac)S(ph)VNYAAGLSPYADKGK ddPTM_HeLa_Romidepsin_16h_R1 2 SVNYAAGLSPYADKGK 16 1 M0R0B2;M0QXA0;Q8N6T7-2;Q8N6T7 M0R0B2 SIRT6 NAD-dependent protein deacetylase sirtuin-6 1 0 S(0.981)VNY(0.019)AAGLSPYADKGK;S(0.601)VNY(0.399)AAGLSPYADKGK ; 126.19 0.0002177 18102600 2366.3 2125.98 2285.8 2723 2890.1 3133.3 2820.3 2917.5 2165 2260.7 TRUE FALSE FALSE 2337.458625 2155.909602 2325.58339 3037.846072 2742.607413 2933.092242 3059.856212 3001.913259 1971.356978 2201.966688 1.061532238 0.979083659 1.056139224 1.379605826 1.245526296 1.332032977 1.389601499 1.363287318 0.895271027 1 11.10457693 -9.299716811 6.071972237 1.026379668 1.338887248 0.891074805 0.059684232 0.038304612 4.10372566 0.00700764 0.010866629 5.02E-10 9.299716811 0.31250758 (ac)S(ph)VPAFIDISEEDQAAELR ddPTM_HeLa_Romidepsin_16h_R1 1 SVPAFIDISEEDQAAELR 18 0 E9PRI2;E7ESM3;Q7L2H7 E9PRI2 EIF3M Eukaryotic translation initiation factor 3 subunit M 1 0 S(1)VPAFIDISEEDQAAELR 104.41 0.00037417 0 0 0 0 134.02 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 149.516023 0 0 0 0 0 0 0 (ac)S(ph)Y(ph)EQLMQLYS(ph)ARQR ddPTM_HeLa_Romidepsin_16h_R1 1 SYEQLMQLYSARQR 14 1 A0A0B4J2B4 A0A0B4J2B4 RPS15 3 0 S(0.912)Y(0.977)EQLMQLY(0.12)S(0.992)ARQR 52.79 0.0040526 0 0 0 0 75.753 0 62.246 0 0 0 71.989 TRUE FALSE FALSE 0 0 0 84.51191829 0 58.26868149 0 0 0 70.1187154 0 0 0 1.205269061 0 0.831000413 0 0 0 1 6.131727661 -12.41017432 1.139469068 0.999640279 0.249111778 0 0.505365329 0.460718065 1.070797973 0.272076456 0.069116865 3.89E-13 12.41017432 -0.750528502 (ac)S(ph)YDYHQNWGR ddPTM_HeLa_Romidepsin_16h_R1 2 SYDYHQNWGR 10 0 Q9H2U1-3;Q9H2U1-2;Q9H2U1 Q9H2U1-3 DHX36 ATP-dependent RNA helicase DHX36 1 0 S(0.636)Y(0.364)DYHQNWGR;S(0.656)Y(0.344)DYHQNWGR ; 111.82 1.10E-05 2743300 1094.07 1385.91 858.84 1164.88 1015.97 1095.76 966.76 1289.38 1475.92 1336.78 TRUE FALSE FALSE 1080.735054 1405.420877 873.7877499 1299.568907 964.1212598 1025.744472 1048.87657 1326.686176 1343.910019 1302.050263 0.830025603 1.079390648 0.671086036 0.99809427 0.740463934 0.787791763 0.805557666 1.018920862 1.032149109 1 10.34656943 -13.19299739 0.432051753 1.109981798 0.851826753 0.188698341 0.12334823 5.747665212 0.808583107 0.743500024 0.032221987 6.41E-14 13.19299739 -0.258155045 (ac)SAEQEKDPISLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SAEQEKDPISLKR 13 2 Q9Y3Y4-2 Q9Y3Y4-2 0 1 SAEQEKDPISLK(1)R 86.344 2.27E-05 2570500 1607.5 1919.7 1392.4 1563.9 1511 1125.6 1041.6 1083.5 1805.8 1865.2 FALSE TRUE FALSE 1587.907172 1946.725587 1416.634138 1744.725476 1433.888032 1053.677793 1130.073478 1114.849363 1644.284725 1816.741835 0.874041177 1.071547729 0.779766344 0.960359608 0.789263507 0.579982126 0.622033057 0.613653157 0.905073409 1 10.82713771 -8.491929639 2.698313792 0.938267705 0.605686117 0.79441451 0.074154578 0.090304428 1.304999664 0.011193855 0.026728827 3.22E-09 8.491929639 -0.332581587 (ac)SDAAVDT(ph)SSEITTK ddPTM_HeLa_Romidepsin_16h_R1 2 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 0 S(0.001)DAAVDT(0.825)S(0.087)S(0.087)EITTK;SDAAVDT(0.692)S(0.274)S(0.034)EITTK ; 145.61 4.63E-17 35044000 6797.4 6199.6 6281.7 5153.6 5096.1 4989.06 3663.4 4192.5 6731.3 6371.7 TRUE FALSE FALSE 6714.550674 6286.878132 6391.030353 5749.48348 4836.027001 4670.275167 3974.569105 4313.803373 6129.235669 6206.162315 1.081916704 1.013005753 1.029787819 0.926415261 0.779229861 0.75252224 0.640423003 0.695083878 0.987604796 1 12.59948571 -8.735993702 1.300829138 1.039282223 0.675426091 0.949381155 0.03381563 0.066710257 0.224107799 0.005864001 0.015826931 1.84E-09 8.735993702 -0.363856132 (ac)SDAAVDTS(ph)SEITTK ddPTM_HeLa_Romidepsin_16h_R1 2 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 1 0 SDAAVDT(0.031)S(0.733)S(0.233)EITT(0.003)K;S(0.08)DAAVDT(0.193)S(0.651)S(0.077)EITTK ; 145.61 3.39E-43 36347000 7581.9 7089.2 6511.1 6443.3 5548.2 5462.8 4851.9 4571.2 7810.4 7549.5 TRUE FALSE FALSE 7489.488887 7189.001944 6624.422964 7188.304663 5265.054651 5113.74471 5264.020265 4703.46046 7111.818262 7353.362902 1.018512072 0.977648192 0.900869854 0.977553367 0.716006366 0.695429395 0.715865698 0.639633937 0.967151813 1 12.84418847 -8.778659808 1.441270484 1.0030264 0.672342802 0.900572336 0.044891405 0.074268747 0.309729433 0.006526695 0.016177869 1.66E-09 8.778659808 -0.330683598 (ac)SDAAVDTSSEITTK ddPTM_HeLa_Romidepsin_16h_R1 2 SDAAVDTSSEITTK 14 0 B8ZZQ6;P06454-2;P06454 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 0 ; ; 116.55 6.92E-07 9111300 4841.8 5517.3 5057.1 5138.2 5280.2 5116.5 5184 5269.7 6154.5 6047.4 FALSE FALSE TRUE 4782.786279 5594.972694 5145.116704 5732.30286 5010.731691 4789.572163 5624.328831 5422.170455 5604.026106 5890.287676 0.811978386 0.949864082 0.873491583 0.973178761 0.850676905 0.813130432 0.954847902 0.920527274 0.951401088 1 12.52412238 -12.60470739 1.41225016 0.999856341 0.883555907 0.225598494 0.056594983 0.373854097 1.34084053 0.040797267 0.009462307 2.48E-13 12.60470739 -0.116300434 (ac)SDEFS(ph)LADALPEHSPAK ddPTM_HeLa_Romidepsin_16h_R1 3 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 0 S(0.435)DEFS(0.561)LADALPEHS(0.004)PAK;S(0.058)DEFS(0.904)LADALPEHS(0.038)PAK;S(0.418)DEFS(0.576)LADALPEHS(0.006)PAK ;; 96.015 7.95E-07 18821400 8758.8 8822.1 7443.6 8084.2 5509.2 5180.3 4654.23 5639.8 7867.1 7910.5 TRUE FALSE FALSE 8652.044377 8946.297755 7573.152736 9018.933241 5228.044966 4849.295549 5049.56018 5802.978715 7163.446872 7704.98407 1.122915284 1.161105289 0.982890122 1.170532367 0.67852768 0.629371262 0.655362832 0.753146102 0.929715987 1 12.91157626 -8.751835887 24.99982559 1.068751122 0.673854008 0.849733455 0.078665004 48.59579199 126503.7487 0.010400981 0.02058974 1.77E-09 8.751835887 -0.394897114 (ac)SDEFSLADALPEHS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SDEFSLADALPEHSPAK 17 0 Q8NDC0 Q8NDC0 MAPK1IP1L MAPK-interacting and spindle-stabilizing protein-like 1 0 SDEFSLADALPEHS(1)PAK 78.708 0.00030746 7610200 4074.1 3905.9 4043.8 3248.7 2982 3370.2 2949.4 2426.4 3563.3 3524.3 TRUE FALSE FALSE 4024.443302 3960.887363 4114.180643 3624.32998 2829.817413 3154.855097 3199.921962 2496.604056 3244.589524 3432.738178 1.172371178 1.15385653 1.198512799 1.055813112 0.824361564 0.919049148 0.932177695 0.727292303 0.94518992 1 11.74514411 -8.838342151 5.163545227 1.09896584 0.861616253 0.627166804 0.089484158 0.105492714 5.001644969 0.013564451 0.025164285 1.45E-09 8.838342151 -0.237349587 (ac)SDKPDMAEIEKFDK ddPTM_HeLa_Romidepsin_16h_R1 1 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 0 75.483 8.55E-06 817740 814.19 744.6 833.24 591.78 879.74 843.79 643.28 558.48 912.79 614.01 FALSE FALSE TRUE 804.2663391 755.0824983 847.7421927 660.204388 834.843585 789.8745422 697.9201871 574.6387377 831.1477763 598.0579317 1.34479671 1.262557452 1.417491764 1.103913773 1.395924276 1.320732492 1.166977562 0.960841262 1.389744592 1 9.22414143 -12.40704399 1.119630587 0.999221828 1.260442683 0 0.178648996 0.451233827 1.006934399 0.09205603 0.023086866 3.92E-13 12.40704399 0.261220854 (ac)SDQDHS(ph)MDEMTAVVK ddPTM_HeLa_Romidepsin_16h_R1 1 SDQDHSMDEMTAVVK 15 0 H3BUU5;P08047-3;P08047 H3BUU5 SP1 Transcription factor Sp1 1 0 S(0.412)DQDHS(0.517)MDEMT(0.071)AVVK 42.041 0.024301 41670000 2120.3 1985 1866.5 1355.7 1233 1414.7 830.55 1394.5 1882.3 1951.9 TRUE FALSE FALSE 2094.456968 2012.944882 1898.98565 1512.452413 1170.075409 1324.305236 901.0968963 1434.847657 1713.942374 1901.189357 1.101656161 1.058781901 0.99884088 0.795529602 0.615443909 0.696566721 0.473964833 0.754710546 0.901510608 1 10.89268651 -9.106755234 2.021455678 1.050334304 0.62434049 0.809167269 0.085734444 0.075138756 0.603116289 0.011113566 0.020734659 7.82E-10 9.106755234 -0.425993815 (ac)SDS(ph)GEQNYGERES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 2 0 S(0.145)DS(0.852)GEQNY(0.003)GERES(1)R 75.376 0.00093066 0 0 0 0 0 0 0 0 0 55.396 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 50.44124302 0 0 (ac)SDSGEQNYGERES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 3 SDSGEQNYGERESR 14 1 P62995 P62995 TRA2B Transformer-2 protein homolog beta 1 0 SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R;SDSGEQNYGERES(1)R ;; 115.8 2.67E-07 123957700 141.86 0 239.438 0 0 0 0 119.96 161.68 0 TRUE FALSE FALSE 140.1309558 0 243.605318 0 0 0 0 123.4308533 147.2189359 0 0 (ac)SDSTWMSADPHLASSLS(ph)PSQDER ddPTM_HeLa_Romidepsin_16h_R1 1 SDSTWMSADPHLASSLSPSQDER 23 0 A0A087WTU5;Q96MY1-2;Q96MY1;Q5JYB6;A0A1W2PQU1 A0A087WTU5 NOL4L Nucleolar protein 4-like 1 0 SDSTWMSADPHLAS(0.026)S(0.047)LS(0.767)PS(0.16)QDER 67.848 0.00010479 1490300 563.05 540.23 481.09 616.17 577.84 561.65 530.77 618.17 852.56 767.26 TRUE FALSE FALSE 556.18733 547.8353721 489.4631696 687.4144746 548.3506686 525.7623776 575.8535906 636.0557736 776.3048983 747.3264746 0.744236085 0.733060303 0.654952268 0.919831557 0.733749823 0.703524357 0.770551573 0.851108311 1.038776124 1 9.545594822 -12.17356709 0.831308513 1.006442558 0.761115969 0.656695582 0.072931435 0.342184529 0.410074358 0.053343342 0.013780855 6.71E-13 12.17356709 -0.245326589 (ac)SDVEENNFEGRES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SDVEENNFEGRESR 14 1 Q13595 Q13595 TRA2A Transformer-2 protein homolog alpha 1 0 SDVEENNFEGRES(1)R;SDVEENNFEGRES(1)R ; 92.151 0.00043175 10741300 397.74 425.53 420.19 379.91 285.906 400.91 361.79 127.02 448.5 321.675 TRUE FALSE FALSE 392.8921919 431.5206225 427.5032307 423.8369817 271.31515 375.2931449 392.5204336 130.6951233 408.3850367 313.3178371 1.253973267 1.37726159 1.364439493 1.352738119 0.865942241 1.197803318 1.252786746 0.417132725 1.303420962 1 8.291483094 -7.257339909 24.65071414 1.166043639 0.417132366 0.670753502 0.164802104 175.8008494 1057064.884 0.024810767 0.253992693 5.53E-08 7.257339909 -0.748911273 (ac)SET(ph)APAETATPAPVEKS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 2 0 S(0.136)ET(0.539)APAET(0.214)AT(0.111)PAPVEKS(0.999)PAK 49.959 0.0022683 13109000 2447.1 3596.1 2344.4 2142.5 2531.1 4277.8 3452 4642.7 2562.5 2683.6 TRUE FALSE FALSE 2417.273804 3646.72599 2385.203299 2390.225931 2401.928522 4004.462386 3745.212794 4777.0292 2333.303582 2613.879685 0.924783883 1.395139191 0.912514571 0.914436094 0.918913191 1.531999506 1.432817591 1.827562771 0.892659136 1 11.35197702 -8.219156142 5.388119939 0.986183435 1.589949514 0.733006341 0.166918711 0.076175715 5.644139841 0.022607767 0.05807183 6.04E-09 8.219156142 0.603766079 GK(ac)GGK(ac)GLGK(ac)GGAK ddPTM_HeLa_Romidepsin_16h_R1 1 GKGGKGLGKGGAK 13 3 P62805 P62805 HIST1H4A Histone H4 0 3 GK(1)GGK(1)GLGK(1)GGAK 206.97 5.57E-22 150100000 1213.3 1207.2 2362.1 4459.1 6732 5217.8 4236.2 3376.3 1244.5 921.15 FALSE TRUE FALSE 1198.511833 1224.194993 2403.21136 4974.682123 6388.440919 4884.39942 4596.022722 3473.987914 1133.188803 897.2183902 1.335808367 1.364433684 2.678513265 5.544561031 7.12027416 5.443935917 5.122523983 3.87195353 1.263002203 1 9.809315381 -9.433066261 2.723383629 1.181978044 5.511405981 0.874661305 0.751042945 0.068096707 0.987003537 0.124880537 0.196495586 3.69E-10 9.433066261 4.329427937 up QIASDK(ac)DAR ddPTM_HeLa_Romidepsin_16h_R1 2 QIASDKDAR 9 1 E7EVK1;A0A088AWL3;O75376 E7EVK1 NCOR1 Nuclear receptor corepressor 1 0 1 ; QIASDK(1)DAR;QIASDK(1)DAR 122.96 0.0059718 1413150 1175.03 1053.75 1319.76 1865.95 2618.5 2286.6 2125.9 1565.54 1091.98 781.48 FALSE TRUE FALSE 1160.708282 1068.58472 1342.729869 2081.699919 2484.868174 2140.49364 2306.473893 1610.83643 994.3105739 761.1770369 1.524886099 1.403858325 1.764017836 2.734843299 3.264507537 2.812083833 3.030141191 2.116244122 1.306280308 1 9.572088229 -9.40785562 2.258871434 1.263166489 2.850047315 0.846369411 0.301059294 0.086825589 0.868956721 0.052835234 0.085572494 3.91E-10 9.40785562 1.586880826 up (ac)SETAPAAPAAPAPAEK(ac)TPVK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 0 1 ; SETAPAAPAAPAPAEK(1)TPVK;SETAPAAPAAPAPAEK(1)TPVK 63.754 1.60E-19 5428400 1931.88 3971.6 2355.3 2808.7 5029.2 6703.9 4640 6864.1 3157.2 3391.7 FALSE TRUE FALSE 1908.333503 4027.512289 2396.293008 3133.455109 4772.541157 6275.542426 5034.121484 7062.701904 2874.812125 3303.583145 0.57765566 1.219134531 0.725361798 0.948501966 1.444655983 1.899616916 1.523836775 2.137891372 0.870210314 1 11.68981594 -8.629039785 2.158088669 0.826362 1.829073852 0.804245684 0.214334019 0.102494094 0.963240004 0.034695379 0.081119809 2.35E-09 8.629039785 1.002711852 (ac)SETAPAAPAAPAPAEK(ac)TPVKK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 0 1 ; SETAPAAPAAPAPAEK(0.996)TPVK(0.004)K;SETAPAAPAAPAPAEK(0.973)TPVK(0.027)K 59.673 0.000388 2205000 1024.51 1758.91 903.6 1178.16 2432.1 2773.8 2249.8 3056.9 1418.02 1384.38 FALSE TRUE FALSE 1012.022878 1783.671981 919.326779 1314.384403 2307.980862 2596.563132 2440.897956 3145.346579 1291.18874 1348.413608 0.750528526 1.322792925 0.681783967 0.974763526 1.711626795 1.925642931 1.810199735 2.332627437 0.957561339 1 10.39704738 -8.671741735 2.706445484 0.900183183 1.993640184 0.853879798 0.204544969 0.070354218 1.042463452 0.030183369 0.065270411 2.13E-09 8.671741735 1.093457001 (ac)SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 0 S(0.005)ET(0.005)APAAPAAPAPAEKT(0.989)PVKK;S(0.001)ET(0.001)APAAPAAPAPAEKT(0.998)PVKK ; 48.477 0.0024977 264750000 5536.8 9482.4 4928.2 6036.8 5129.8 5484.1 4705.6 5274.8 6841 7020.4 TRUE FALSE FALSE 5469.315352 9615.893476 5013.973254 6734.80322 4868.007164 5133.683709 5105.293547 5427.418016 6229.123826 6838.008996 0.799840327 1.406241712 0.733250462 0.984907043 0.711904177 0.750757086 0.746605269 0.793713202 0.910955781 1 12.73936061 -8.759421651 24.99512237 0.935621164 0.750450094 0.273804846 0.170712784 65.07814801 806151.7618 0.024936921 0.047958545 1.74E-09 8.759421651 -0.18517107 (ac)SETAPAAPAAPAPAEKT(ph)PVKKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAAPAAPAPAEKTPVKKK 22 3 P10412 P10412 HIST1H1E Histone H1.4 1 0 S(0.004)ET(0.004)APAAPAAPAPAEKT(0.991)PVKKK 43.162 0.0024299 31591000 2837.8 4047.8 1986 4717 2153.5 2024.9 1712.2 2075.8 3030.4 2136.5 TRUE FALSE FALSE 2803.211802 4104.785035 2020.565497 5262.401734 2043.598859 1895.515425 1857.634225 2135.859998 2759.353434 2080.993422 1.347054619 1.972512258 0.970961982 2.528793065 0.982030427 0.910870455 0.892667034 1.026365569 1.325978932 1 11.02305669 -8.559030681 24.99999258 1.322361469 0.939601382 0.20318044 0.460081615 272.3378896 188327.6603 0.068931175 0.137862658 2.76E-09 8.559030681 -0.382760087 (ac)SETAPAET(ph)ATPAPVEKSPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.26)ET(0.034)APAET(0.482)AT(0.008)PAPVEKS(0.215)PAKK 51.798 0.0010067 272050000 2783 4394 2595.6 2490.4 1915.3 1935.5 1719.6 1742.7 3312.5 3479.3 TRUE FALSE FALSE 2749.079726 4455.858847 2640.775329 2778.351766 1817.555094 1811.827797 1865.662781 1793.122275 3016.221704 3388.907284 0.81119945 1.314836457 0.779240949 0.819837054 0.536324821 0.534634808 0.550520455 0.529115176 0.890027803 1 11.72660445 -8.933924418 2.014386082 0.937169852 0.531536757 0.674563634 0.137882266 0.159160682 1.30183161 0.022073563 0.044652171 1.16E-09 8.933924418 -0.405633095 (ac)SETAPAETATPAPVEKS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.28)ET(0.061)APAET(0.18)AT(0.003)PAPVEKS(0.476)PAK 63.578 0.00024157 0 598.07 1318.5 623.27 750.55 439.05 406.13 501.79 572.9 953.93 853.98 TRUE FALSE FALSE 590.7804928 1337.061878 634.1177529 837.3321224 416.6436402 380.1796037 544.4120301 589.4759576 868.6081116 831.7934765 0.71024901 1.607444534 0.762349995 1.006658679 0.500897942 0.457060093 0.654503847 0.708680669 1.044259346 1 9.70008156 -8.76061574 24.99994079 0.922575764 0.576785082 0.4007527 0.247224842 21.3834942 649015.2395 0.037171877 0.071009759 1.74E-09 8.76061574 -0.345790682 (ac)SETAPAETATPAPVEKS(ph)PAKK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAETATPAPVEKSPAKK 21 2 P16401 P16401 HIST1H1B Histone H1.5 1 0 S(0.255)ET(0.033)APAET(0.224)AT(0.008)PAPVEKS(0.48)PAKK;SETAPAETATPAPVEKS(1)PAKK ; 61.37 0.0011181 56757000 6957.9 11249.1 6821.7 6099.1 5073.1 5311 4229.6 4335.4 8656.9 8187.8 TRUE FALSE FALSE 6873.094439 11407.46513 6940.428827 6804.306639 4814.200777 4971.64424 4588.862118 4460.837959 7882.605182 7975.079776 0.861821403 1.430388842 0.870264502 0.85319606 0.603655501 0.623397431 0.575400152 0.559347127 0.988404556 1 12.96128324 -8.895476622 2.211277911 0.973172901 0.583515955 0.638322652 0.153230646 0.173847677 1.723731675 0.024387151 0.049276566 1.27E-09 8.895476622 -0.389656946 (ac)SETAPLAPT(ph)IPAPAEKTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 0 S(0.085)ET(0.085)APLAPT(0.547)IPAPAEKT(0.282)PVK 56.746 0.00067221 29931000 2870.7 4480.4 2667.9 3080.8 3547.3 3706.8 2562.4 3168.8 3180.5 3384.5 TRUE FALSE FALSE 2835.710804 4543.475189 2714.33368 3437.016592 3366.268044 3469.947443 2780.050192 3260.484228 2896.028114 3296.570202 0.860200339 1.378243116 0.823381125 1.042603791 1.021142532 1.05259322 0.843315938 0.989053479 0.878497328 1 11.68675009 (ac)SETAPLAPT(ph)IPAPAEKTPVKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPLAPTIPAPAEKTPVKK 21 2 P16402 P16402 HIST1H1D Histone H1.3 1 0 S(0.205)ET(0.183)APLAPT(0.601)IPAPAEKT(0.011)PVKK 59.9 0.00027826 53080000 2721.8 4349.9 2187.7 3404.8 3232.9 3699.2 2375.1 2406 3231.5 3234.2 TRUE FALSE FALSE 2688.625655 4411.138006 2225.776001 3798.478996 3067.913049 3462.833059 2576.840935 2475.613814 2942.466547 3150.175018 0.853484533 1.40028347 0.706556299 1.205799352 0.97388654 1.099251006 0.817999292 0.785865484 0.934064466 1 11.62121627 -7.632057245 7.854668869 0.978575393 0.794254338 0.157336593 0.183375213 0.320323281 20.61498609 0.023780803 0.089844659 2.33E-08 7.632057245 -0.184321055 (ac)SETAPLAPTIPAPAEKT(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPLAPTIPAPAEKTPVK 20 1 P16402 P16402 HIST1H1D Histone H1.3 1 0 SETAPLAPT(0.029)IPAPAEKT(0.971)PVK 56.72 0.0017418 33098000 2976.3 6138.7 3596.8 4442.4 4825.6 4855.8 3479.7 4060.6 3906.1 4423.4 TRUE FALSE FALSE 2940.023711 6225.12078 3659.400795 4956.05119 4579.331625 4545.530051 3775.265631 4178.087054 3556.728633 4308.47943 0.682380816 1.444853313 0.849348559 1.150301695 1.062864915 1.055019555 0.876240839 0.969735871 0.825518304 1 12.07296308 (ac)SETAPLAPTIPAPAEKT(ph)PVKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPLAPTIPAPAEKTPVKK 21 2 P16402 P16402 HIST1H1D Histone H1.3 1 0 S(0.016)ET(0.016)APLAPT(0.083)IPAPAEKT(0.884)PVKK 48.685 0.00096414 58898000 3174.1 5617.8 3668.1 4600.6 4207.8 4181.9 3292.8 3573.1 4237.6 3750.7 TRUE FALSE FALSE 3135.412848 5696.887536 3731.941742 5132.543018 3993.060265 3914.690086 3572.49035 3676.482011 3858.578443 3653.256273 0.858251547 1.559399919 1.021538448 1.404922796 1.093014003 1.07156186 0.977892073 1.006357544 1.056202509 1 11.83496725 (ac)SGEDEQQEQTIAEDLVVTK ddPTM_HeLa_Romidepsin_16h_R1 2 SGEDEQQEQTIAEDLVVTK 19 0 Q9UQ80;F8VR77 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 0 ; ; 135.81 1.53E-75 5875400 6812.62 6947.26 6424.69 6636.22 6415.62 6588.76 5924.53 6458.4 7500.55 6467.72 FALSE FALSE TRUE 6729.585167 7045.063709 6536.509034 7403.530981 6088.206971 6167.7595 6427.75943 6645.263614 6829.682023 6299.687702 1.068241076 1.118319517 1.037592551 1.175221905 0.966429966 0.979057977 1.020329854 1.054856039 1.084130253 1 12.6210646 -6.892279844 15.49186805 1.039854842 1.754663993 0 0.061894475 10828550.51 10352959.85 0.008548636 268516765.3 1.28E-07 6.892279844 0.714809151 (ac)SGNGNAAATAEENS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SGNGNAAATAEENSPK 16 0 F5H226;A0A3F2YNY7;P08397-3;P08397;F5H4X2 F5H226 HMBS Porphobilinogen deaminase 1 0 S(0.02)GNGNAAAT(0.001)AEENS(0.979)PK 99.392 4.23E-07 0 1287.5 1199.6 1194 805.61 1237.1 983.4 992.55 1214.3 1462.6 1382.4 TRUE FALSE FALSE 1271.807455 1216.488 1214.781069 898.7584187 1173.966171 920.5639138 1076.857172 1249.433855 1331.781393 1346.485049 0.944538861 0.903454518 0.902186824 0.667484886 0.871874643 0.683679269 0.799754274 0.927922561 0.989079971 1 10.39498249 -9.805426217 1.487216197 0.97545187 0.790488647 0.515343887 0.077147098 0.20977985 0.936514495 0.013066087 0.0188414 1.57E-10 9.805426217 -0.184963223 (ac)SGYSS(ph)DRDR ddPTM_HeLa_Romidepsin_16h_R1 5 SGYSSDRDR 9 1 P17844;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3QKN9;J3QS79 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 1 0 SGYS(0.004)S(0.996)DRDR;SGYS(0.034)S(0.966)DRDR;SGYS(0.007)S(0.993)DRDR;SGYS(0.007)S(0.993)DRDR;SGYS(0.199)S(0.801)DRDR ;;;; 81.525 0.0012389 626912000 433.523 129.69 288.612 378.07 237.667 112.111 187.417 285.36 267.41 266.368 TRUE FALSE FALSE 428.2390549 131.5157792 293.6351708 421.7842323 225.5379661 104.9474689 203.3361953 293.6164414 243.4921799 259.447721 1.650579367 0.506906666 1.131770091 1.625700279 0.86930024 0.404503337 0.783727044 1.131697902 0.938501903 1 8.019300053 -8.554545643 16.17982517 1.252753917 0.751444976 0.143763113 0.360127908 4.442269753 2269.246953 0.056144184 0.112312865 2.79E-09 8.554545643 -0.501308941 (ac)SGYSSDRDR ddPTM_HeLa_Romidepsin_16h_R1 1 SGYSSDRDR 9 1 P17844;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3QKN9;J3QS79 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 0 58.815 0.026746 3863500 0 53.522 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 54.27548412 0 0 0 0 0 0 0 0 0 (ac)SHTILLVQPTK ddPTM_HeLa_Romidepsin_16h_R1 2 SHTILLVQPTK 11 0 G3V279;P84090 G3V279 ERH Enhancer of rudimentary homolog 0 0 ; ; 80.916 7.52E-07 4653500 4923.8 5231.8 4953.8 4617.4 4583.8 5128.8 4478.9 5106.1 5334.2 5222.3 FALSE FALSE TRUE 4863.786832 5305.453418 5040.018811 5151.285514 4349.871581 4801.086232 4859.337654 5253.836947 4857.095792 5086.623893 0.956191559 1.043020583 0.990837718 1.01271209 0.855158878 0.943864994 0.955316877 1.032873092 0.954876141 1 12.31249271 (ac)SILK(ac)IHAR ddPTM_HeLa_Romidepsin_16h_R1 2 SILKIHAR 8 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y798;A0A2R8YEG5 P06733 ENO1 Alpha-enolase;Enolase 0 1 ; SILK(1)IHAR;SILK(1)IHAR 54.549 0.00068599 6251800 687.87 328.95 409.5 330.34 699.03 466.42 600.94 786.67 535.12 576.5 FALSE TRUE FALSE 679.4859759 333.5809667 416.6271757 368.5354651 663.3558907 436.6172673 651.9838286 809.4310553 487.257527 561.5224469 1.210078029 0.594065239 0.741959966 0.656314751 1.181352401 0.777559775 1.161100206 1.441493675 0.867743631 1 9.133199885 -7.401093051 3.593939988 0.995843671 1.440239109 0.301731556 0.221209128 0.281795687 5.87408137 0.034097621 0.25773092 3.97E-08 7.401093051 0.444395439 (ac)SKS(ph)ES(ph)PKEPEQLR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSESPKEPEQLR 13 2 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 2 0 S(0.416)KS(0.59)ES(0.994)PKEPEQLR 61.265 0.029054 11543000 7888.6 7564.2 7083.6 6372.4 6700.5 7638.5 6108.5 6765.4 8438.1 8543.1 TRUE FALSE FALSE 7792.450709 7670.689006 7206.887087 7109.206871 6358.548482 7150.424502 6627.355838 6961.146175 7683.375202 8321.14903 0.936463303 0.921830504 0.866092779 0.854353989 0.764143084 0.859307348 0.796447199 0.83656069 0.923355077 1 13.02256704 -9.969331883 0.626170848 0.986244797 0.808585913 0.743824925 0.033807541 0.168377933 0.139905228 0.007514793 0.011133896 1.07E-10 9.969331883 -0.177658884 (ac)SKSES(ph)PKEPEQLR ddPTM_HeLa_Romidepsin_16h_R1 2 SKSESPKEPEQLR 13 2 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 S(0.003)KS(0.003)ES(0.994)PKEPEQLR;S(0.067)KS(0.096)ES(0.838)PKEPEQLR ; 74.783 0.0069123 76332000 6155 4612.5 3296.03 13113.6 5035.2 4704.93 4891.2 4888.6 6066.3 4426.9 TRUE FALSE FALSE 6079.980493 4677.434896 3353.39602 14629.85613 4778.234955 4404.300157 5306.658406 5030.043928 5523.714935 4311.8885 1.41005049 1.084776403 0.777709354 3.392911513 1.108153644 1.021431829 1.230703996 1.166552412 1.281043082 1 12.07410416 -12.10483823 0.576295678 0.95276959 1.423664225 0.01649103 0.695369773 3.281593561 1.697342874 0.812631834 0.166843427 7.86E-13 12.10483823 0.470894636 (ac)SLLDGLAS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 SLLDGLASSPR 11 0 E9PI10;E9PK87;F8W6N5;Q3YBR2 E9PI10 TBRG1 Transforming growth factor beta regulator 1 1 0 SLLDGLAS(0.669)S(0.331)PR 79.23 0.0058407 2590500 0 108.61 0 146.27 0 45.973 0 0 63.949 0 TRUE FALSE FALSE 0 110.1390144 0 163.1824256 0 43.03547367 0 0 58.22924128 0 0 (ac)SLLDGLASS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 SLLDGLASSPR 11 0 E9PI10;E9PK87;F8W6N5;Q3YBR2 E9PI10 TBRG1 Transforming growth factor beta regulator 1 1 0 SLLDGLAS(0.228)S(0.772)PR;SLLDGLAS(0.044)S(0.956)PR;SLLDGLAS(0.23)S(0.77)PR ;; 128.21 0.00018 4806200 416.44 212.28 184.81 251.7 379.508 229.348 168.52 116.321 292.571 127.03 TRUE FALSE FALSE 411.3642691 215.2684834 188.0265405 280.8027383 360.1402906 214.693403 182.8340846 119.6865646 266.402717 123.7297423 3.324699959 1.739828108 1.519655154 2.269484548 2.910701049 1.735180232 1.477689044 0.967322508 2.153101688 1 6.951048528 -7.678237861 2.313242605 2.111651998 1.041966026 0.255946003 0.62836441 0.500946769 4.939106563 0.128151499 0.75958669 2.10E-08 7.678237861 -1.069685972 (ac)SLY(ph)PSLEDLK ddPTM_HeLa_Romidepsin_16h_R1 2 SLYPSLEDLK 10 0 B4DHN5;E9PBU7;O00560-2;O00560;O00560-3 B4DHN5 SDCBP Syntenin-1 1 0 S(0.022)LY(0.975)PS(0.003)LEDLK;S(0.067)LY(0.928)PS(0.005)LEDLK ; 83.998 6.95E-05 0 2322.8 2142.97 2250 2128.6 3088 2623.8 1940.77 1687.74 2877.1 2527.5 TRUE FALSE FALSE 2294.48882 2173.138788 2289.160306 2374.718747 2930.407837 2456.147648 2105.618955 1736.572094 2619.76497 2461.835186 0.932023733 0.882731224 0.929859285 0.964613213 1.190334696 0.997689716 0.855304599 0.705397382 1.064151242 1 11.26551846 -7.465344549 2.904818505 0.975362095 0.705508725 0.542147971 0.082811777 0.185109278 2.698592162 0.011631818 0.091571669 3.42E-08 7.465344549 -0.26985337 (ac)SLY(ph)PSLEDLKVDK ddPTM_HeLa_Romidepsin_16h_R1 1 SLYPSLEDLKVDK 13 1 B4DHN5;E9PBU7;O00560-2;O00560 B4DHN5 SDCBP Syntenin-1 1 0 S(0.18)LY(0.81)PS(0.01)LEDLKVDK 67.214 0.030294 10118000 2199.2 1782.6 1904.9 2690.5 2426.1 2052 1711.1 1568 2378.1 1924.3 TRUE FALSE FALSE 2172.395305 1807.69549 1938.053985 3001.588269 2302.287064 1920.883823 1856.440791 1613.367606 2165.39678 1874.306409 1.159039576 0.96446103 1.034011289 1.601439474 1.228340816 1.02485048 0.990468145 0.860781139 1.155305648 1 10.87214111 -7.625769846 2.12748839 1.113301168 0.872468778 0.209702622 0.173754949 0.553192241 4.349789484 0.026544447 0.190543643 2.37E-08 7.625769846 -0.24083239 (ac)SQPGQKPAAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 SQPGQKPAASPR 12 1 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6 CAST Calpastatin 1 0 SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR;SQPGQKPAAS(1)PR ;;; 109.16 0.0010624 225409000 11509.4 11369.3 10607.1 9213.3 10051.5 10264.6 8680.8 8211.2 10704.5 10405.5 TRUE FALSE FALSE 11369.11901 11529.3573 10791.71213 10278.5851 9538.534448 9608.725187 9418.146935 8448.778117 9747.06271 10135.16361 1.121749924 1.137560058 1.064779272 1.01415088 0.941132755 0.948058222 0.929254554 0.833610432 0.961707485 1 13.30708176 -8.644258758 1.290320401 1.06671951 0.89355215 0.611075883 0.055160076 0.233517379 0.76299763 0.009345822 0.027312567 2.27E-09 8.644258758 -0.17316736 (ac)SQPGQKPAAS(ph)PRPR ddPTM_HeLa_Romidepsin_16h_R1 4 SQPGQKPAASPRPR 14 2 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;F8W7E0;E9PSG1 P20810-6 CAST Calpastatin 1 0 SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;SQPGQKPAAS(1)PRPR;S(0.001)QPGQKPAAS(0.999)PRPR ;;; 86.738 0.0011944 1111927800 13046.42 12765.13 11016.19 13288.06 12337.8 11203.93 8202.47 9814.17 12287.02 11914.7 TRUE FALSE FALSE 12887.40521 12944.83784 11207.92217 14824.48802 11708.15603 10488.03503 8899.187597 10098.12752 11188.03816 11605.15438 1.11048977 1.115438659 0.965771053 1.277405499 1.008875509 0.903739381 0.766830609 0.870141594 0.964057676 1 13.50247809 -8.193714986 2.908401507 1.067394634 0.822707587 0.558309874 0.090516562 0.138449154 2.287358692 0.012297437 0.035205723 6.40E-09 8.193714986 -0.244687046 (ac)SS(ph)PASTPSRR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPASTPSRR 10 1 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;E5RG53;A0A3B3IS88 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 S(0.18)S(0.82)PAS(0.001)TPSRR 100.02 0.0061908 140820000 0 0 0 0 0 99.713 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 93.34166111 0 0 0 0 0 (ac)SS(ph)SPLSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPLSK 7 0 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 0 S(0.031)S(0.484)S(0.484)PLSK 67.993 0.009386 4186300 8072 7504.4 7477.8 6914.1 7108.3 6936.6 6109.8 5481.6 8688.9 7964.2 TRUE FALSE FALSE 7973.615359 7610.04714 7607.947972 7713.540774 6745.536926 6493.373647 6628.766259 5640.201447 7911.743022 7757.288936 1.027886859 0.98101891 0.980748305 0.99436038 0.86957402 0.837067396 0.854520995 0.7270841 1.019910833 1 12.92133682 -8.174990179 0.691282384 1.013817346 0.727820181 0.904714702 0.029452961 0.252984557 0.160649092 0.005278319 0.044744273 6.68E-09 8.174990179 -0.285997165 (ac)SS(ph)SPVNVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPVNVK 8 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 0 S(0.222)S(0.389)S(0.389)PVNVK 46.819 0.0094696 2642000 2976.7 2822.3 2484.7 2405.5 1674.4 2052.9 1346.4 1920.4 2823.4 2628.9 TRUE FALSE FALSE 2940.418835 2862.032413 2527.945161 2683.635228 1588.94912 1921.726315 1460.763182 1975.963744 2570.868033 2560.600799 1.148331609 1.117719097 0.987246884 1.048049047 0.620537618 0.75049821 0.570476735 0.771679734 1.004009697 1 11.32226664 -8.768226677 24.65932416 1.067374621 0.675753686 0.861367801 0.073046284 34.46355007 125212.1011 0.011516811 0.02122454 1.71E-09 8.768226677 -0.391620935 (ac)SSAPRS(ph)PTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSAPRSPTPR 10 1 Q9HBI1 Q9HBI1 PARVB Beta-parvin 1 0 S(0.023)S(0.023)APRS(0.935)PT(0.018)PR 51.346 0.025006 5792000 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 (ac)SSAPTT(ph)PPSVDKVDGFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSAPTTPPSVDKVDGFSR 18 1 Q16537-2;Q16537 Q16537-2 PPP2R5E Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform 1 0 S(0.022)S(0.022)APT(0.236)T(0.689)PPS(0.029)VDKVDGFS(0.001)R 57.788 0.011351 25918000 2063.9 1882.5 2106.7 2097.6 2397.7 2629.6 2279.1 2286.6 2217.9 2376.4 TRUE FALSE FALSE 2038.744393 1909.001884 2143.36623 2340.134382 2275.336422 2461.577047 2472.686697 2352.759163 2019.525469 2314.660785 0.880796187 0.824743693 0.925995828 1.011005326 0.983010745 1.063472048 1.068271737 1.016459594 0.872493059 1 11.17658507 -8.863685483 1.707852791 0.931152487 1.045916881 0.570431632 0.052234257 0.283762662 1.673071376 0.009948616 0.02184209 1.37E-09 8.863685483 0.114764394 (ac)SSNSASAANGNDSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SSNSASAANGNDSKK 15 1 A6NLN1;K7ES59 A6NLN1 PTBP1 0 1 ; SSNSASAANGNDSK(1)K;SSNSASAANGNDSK(1)K 136.7 5.15E-45 456970 401.39 297.4 44.5 313.86 132.152 218.236 197.126 269.92 240.53 196.39 FALSE TRUE FALSE 396.4977043 301.586805 45.27450383 350.14997 125.4077903 204.2914239 213.8698775 277.7297093 219.0163944 191.2877595 2.072781371 1.576613192 0.236682702 1.830488113 0.65559757 1.067979595 1.118053126 1.451894832 1.144957706 1 7.579600748 (ac)SSPAS(ph)TPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPASTPSR 9 0 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;E5RG53;A0A3B3IS88 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 S(0.101)S(0.051)PAS(0.606)T(0.167)PS(0.075)R 71.221 0.024674 5110700 0 0 0 0 125.96 0 0 65.021 0 0 TRUE FALSE FALSE 0 0 0 0 119.5317912 0 0 66.90228005 0 0 0 (ac)SSS(ph)PLSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPLSK 7 0 P22314;Q5JRR9 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 0 S(0.01)S(0.152)S(0.837)PLS(0.001)K 78.334 0.013179 1416700000 5914.9 5900.5 5932.9 5509.2 5442.1 5850.1 5103 4278.3 6072.8 6406.4 TRUE FALSE FALSE 5842.806924 5983.567394 6036.159636 6146.199626 5164.36933 5476.29749 5536.448693 4402.08586 5529.633558 6239.960804 0.936353145 0.958911054 0.967339351 0.984974076 0.827628489 0.87761729 0.887256966 0.705466909 0.88616479 1 12.60732125 -5.690665635 0.398859054 0.975897354 2.58E-13 0.64013105 0.050327305 6.162586314 0.255326274 0.010772437 3.782505952 2.04E-06 5.690665635 -0.975897354 (ac)SSSPVNVKK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPVNVKK 9 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 56.011 0.017771 91257000 12939.2 12569.2 11569.1 11830.2 10688.7 10252.8 9482.1 9768.8 13319.5 11527.2 FALSE FALSE TRUE 12781.49205 12746.14953 11770.45533 13198.06339 10143.21575 9597.679169 10287.50934 10051.44482 12128.17056 11227.72168 1.138386969 1.135239177 1.048338716 1.175489005 0.903408193 0.854819833 0.916259739 0.89523459 1.080198717 1 13.45477759 -8.68811507 8.544119301 1.078085973 0.890363026 0.793472426 0.050448175 0.128876677 13.53860919 0.009367944 0.018751805 2.05E-09 8.68811507 -0.187722947 (ac)STGPTAAT(ph)GSNRR ddPTM_HeLa_Romidepsin_16h_R1 1 STGPTAATGSNRR 13 1 Q15836 Q15836 VAMP3 Vesicle-associated membrane protein 3 1 0 STGPTAAT(0.657)GS(0.343)NRR 84.892 0.0063349 3229400 844.87 502.32 897.23 512.75 409.55 507.45 723.58 410.94 660.83 620.02 TRUE FALSE FALSE 834.5723995 509.3916741 912.8459118 572.0365676 388.6491353 475.0255827 785.0408671 422.8299005 601.7237097 603.911791 1.381944204 0.843486883 1.511555041 0.947218743 0.643552819 0.78658107 1.299926378 0.700151755 0.99637682 1 9.238194031 -9.02026739 24.4158224 1.17918223 0.872994672 0.234127819 0.245368252 587.8545942 708179.6702 0.03697062 0.061845716 9.54E-10 9.02026739 -0.306187558 (ac)STNENANT(ph)PAAR ddPTM_HeLa_Romidepsin_16h_R1 4 STNENANTPAAR 12 0 J3QLL0;J3KS65;P52292;J3QL07 J3QLL0 KPNA2 Importin subunit alpha-1 1 0 STNENANT(1)PAAR;STNENANT(1)PAAR;STNENANT(1)PAAR;STNENANT(1)PAAR ;;; 222.72 8.85E-77 54780600 0 0 0 0 0 0 0 51.964 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 53.46749635 0 0 0 (ac)STVHEILCKLSLEGDHS(ph)TPPSAYGSVK ddPTM_HeLa_Romidepsin_16h_R1 1 STVHEILCKLSLEGDHSTPPSAYGSVK 27 1 P07355;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YNB8;H0YKN4 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 0 S(0.01)T(0.01)VHEILCKLS(0.102)LEGDHS(0.437)T(0.437)PPS(0.002)AY(0.002)GSVK 43.696 1.93E-05 13918000 1343 1187.1 1048.8 322.24 3285.9 3089.8 1804.2 1945.6 2272.3 1971.6 TRUE FALSE FALSE 1326.630999 1203.812025 1067.053924 359.498905 3118.208262 2892.371752 1957.448703 2001.892866 2069.059797 1920.377548 0.690817803 0.626862164 0.55564799 0.187202202 1.62374751 1.506147453 1.019304097 1.042447548 1.077423447 1 10.90717426 -8.743800573 24.99976011 0.765132582 1.292884999 0.501738791 0.291158821 190.385156 269834.5624 0.044784708 0.089411917 1.80E-09 8.743800573 0.527752417 (ac)SVAGLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SVAGLKK 7 1 Q99961-3;Q99961-2;Q99961;H3BRH8;Q99963-4;Q99963;Q99962 Q99961-3 SH3GL1;SH3GL3;SH3GL2 Endophilin-A2;Endophilin-A3;Endophilin-A1 0 1 SVAGLK(1)K 41.502 0.0024344 1057100 1149.7 1197.7 1612.4 1744.5 2227 2082.2 2175.6 1074.4 1486.1 883.83 FALSE TRUE FALSE 1135.687014 1214.561252 1640.463146 1946.207298 2113.34788 1949.15414 2360.39541 1105.486069 1353.179494 860.8679692 1.319234836 1.410856595 1.905592035 2.260750043 2.454903604 2.264173148 2.741878539 1.284152865 1.571878084 1 9.749648179 -9.780455657 1.408655755 1.135264125 2.25931171 0.526482782 0.382580764 0.164337354 0.657362293 0.060246212 0.088369375 1.66E-10 9.780455657 1.124047586 (ac)SVPAFIDISEEDQAAELR ddPTM_HeLa_Romidepsin_16h_R1 2 SVPAFIDISEEDQAAELR 18 0 E9PRI2;E7ESM3;Q7L2H7 E9PRI2 EIF3M Eukaryotic translation initiation factor 3 subunit M 0 0 ; ; 171.26 4.09E-14 4375100 0 0 0 0 136.81 74.625 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 129.8280752 69.85670334 0 0 0 0 0 (ac)T(ph)TSGALFPSLVPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSGALFPSLVPGSR 15 0 Q16186;A0A087WX59;A0A087WUX6 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 0 T(0.876)T(0.062)S(0.062)GALFPSLVPGSR 50.484 2.23E-05 0 942.48 937.18 1183.1 588.17 595.23 607.16 412.96 445.68 537.05 985.93 TRUE FALSE FALSE 930.9926912 950.3736446 1203.691359 656.1769828 564.853192 568.3644355 448.0368121 458.5750476 489.0149029 960.3153965 0.969465547 0.98964741 1.253433365 0.683293203 0.588195497 0.591851841 0.466551733 0.477525456 0.509223225 1 9.907364498 -9.054818214 5.054954512 1.003862625 0.540344084 0.530356653 0.179970103 0.054469323 2.994987313 0.013647143 0.02329997 8.81E-10 9.054818214 -0.463518541 (ac)TEVMMNTQPMEEIGLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TEVMMNTQPMEEIGLSPR 18 0 B5MBX5 B5MBX5 LBH 1 0 TEVMMNTQPMEEIGLS(1)PR 66.261 0.0041465 11705000 70.364 68.593 63.282 61.867 0 0 67.916 143.75 0 55.957 TRUE FALSE FALSE 69.5063765 69.55865405 64.38339666 69.02035363 0 0 73.68478334 147.9091795 0 54.50322907 1.275270799 1.276229964 1.181276738 1.266353477 0 0 1.351934272 2.71376911 0 1 5.768269801 DGSASAAAK(ac)K(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DGSASAAAKKK 11 2 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2;Q68E03 D6REM6 MATR3;DKFZp686L22104 Matrin-3 0 2 ; DGSASAAAK(1)K(1)K;DGSASAAAK(1)K(1)K 155.11 0.00244 4049500 1486.24 1393.76 1971.02 2930.2 4126.5 4034.4 3296.6 2956.8 1562.97 1233.94 FALSE TRUE FALSE 1468.125135 1413.38139 2005.324776 3269.003511 3915.909307 3776.61486 3576.613122 3042.350343 1423.174049 1201.882061 1.221521797 1.175973447 1.668487152 2.719903739 3.258147729 3.142250794 2.975843669 2.531321867 1.184121217 1 10.23107962 -9.353116575 2.192755654 1.111127673 2.998487969 0.953875854 0.187524712 0.045213557 0.425014111 0.031907094 0.052993387 4.43E-10 9.353116575 1.887360296 up (ac)VNPTVFFDIAVDGEPLGR ddPTM_HeLa_Romidepsin_16h_R1 1 VNPTVFFDIAVDGEPLGR 18 0 F8WE65;C9J5S7;P62937;E5RIZ5 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 0 88.092 0.0039737 937890 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLS(ph)GPAEVGPGAVGERTPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPR 55 1 R4GMQ1;O60341;O60341-2 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 0 AAAAAAAAAAAAT(0.002)GT(0.002)EAGPGT(0.008)AGGS(0.031)ENGS(0.031)EVAAQPAGLS(0.745)GPAEVGPGAVGERT(0.181)PR 69.344 2.95E-11 9890300 2306 2453.1 2113.4 2663.7 2018.9 1810.6 1273.7 1389.8 2681.8 1842.7 TRUE FALSE FALSE 2277.893585 2487.634806 2150.18284 2971.689527 1915.867999 1694.908503 1381.888046 1430.01167 2441.933091 1794.826388 1.269144247 1.386003026 1.197989318 1.655697479 1.067439175 0.944330056 0.769928532 0.796740944 1.360539998 1 10.80962859 -8.167944846 2.624097598 1.194038449 0.794808096 0.532074925 0.182635477 0.218216477 2.901030695 0.029453095 0.088916459 6.79E-09 8.167944846 -0.399230353 AAAAAAGSGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAAGSGTPR 12 0 Q9NR33 Q9NR33 POLE4 DNA polymerase epsilon subunit 4 1 0 AAAAAAGS(0.029)GT(0.971)PR 105.13 0.026976 6453500 1546.6 1729.5 2028 1572.6 1021.8 1376.4 2569.4 885.39 2804.1 2471 TRUE FALSE FALSE 1527.749444 1753.847946 2063.296489 1754.431411 969.6537331 1288.452482 2787.644772 911.0073627 2553.294273 2406.803064 0.634762963 0.728704385 0.857276825 0.728946808 0.40288038 0.535337727 1.158235509 0.378513463 1.060865474 1 11.23290238 -12.38687538 0.744887196 1.036909825 0.683100592 0.297688911 0.214648117 1.045862837 0.85951568 0.237914977 0.041154072 4.10E-13 12.38687538 -0.353809233 AAAAAATAPPS(ph)PGPAQPGPR ddPTM_HeLa_Romidepsin_16h_R1 4 AAAAAATAPPSPGPAQPGPR 20 0 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 0 AAAAAAT(0.02)APPS(0.98)PGPAQPGPR;AAAAAAT(0.012)APPS(0.988)PGPAQPGPR;AAAAAATAPPS(1)PGPAQPGPR;AAAAAAT(0.002)APPS(0.998)PGPAQPGPR ;;; 211.26 6.17E-32 181579000 17207.2 17138.4 16391.2 19670.7 13846.6 11708 9619.7 10107.7 16962.5 16467 TRUE FALSE FALSE 16997.47203 17379.67485 16676.48196 21945.11889 13139.95633 10959.89659 10436.79708 10400.15035 15445.33152 16039.18497 1.059746618 1.083575935 1.039733752 1.368219079 0.8192409 0.683320045 0.650706199 0.648421374 0.962974836 1 13.96931321 -8.531583007 24.99858657 1.057215922 0.675050795 0.768637631 0.105477512 68.78080464 197537.7124 0.014956841 0.029949629 2.94E-09 8.531583007 -0.382165127 AAAAAPAS(ph)ED ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAPASED 10 0 C9JWL1 C9JWL1 NCL 1 0 AAAAAPAS(1)ED 114.86 0.024637 5292300 7989.2 9713.2 7632.6 9471.9 6295.5 7094.7 5481 6836.2 8420.2 8625.5 TRUE FALSE FALSE 7891.824557 9849.942685 7765.442201 10567.08564 5974.217143 6641.371567 5946.556003 7033.994661 7667.076223 8401.408267 0.939345442 1.172415668 0.924302445 1.257775519 0.711097111 0.790506943 0.70780467 0.837239953 0.912594172 1 13.03641546 -8.71660453 24.99999398 1.001425726 0.759875258 0.579775577 0.111652324 74.33428389 41448.57887 0.014914296 0.029828484 1.92E-09 8.71660453 -0.241550468 AAAAAWEEPS(ph)SGNGTAR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAWEEPSSGNGTAR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 1 0 AAAAAWEEPS(0.715)S(0.281)GNGT(0.004)AR 150.9 0.00010075 6171200 2194.4 2248.1 2274 2269 2134.6 2330.2 1700.6 2006 2554.9 2566.2 TRUE FALSE FALSE 2167.653809 2279.748811 2313.578016 2531.352456 2025.663397 2181.30774 1845.048922 2064.040445 2326.383345 2499.529754 0.867224647 0.912071083 0.925605311 1.012731476 0.810417797 0.872687247 0.738158415 0.825771504 0.930728407 1 11.28744099 -4 0.105616447 1.037744195 0.315333146 0.431759777 0.060731424 80.42859626 0.5999027 0.443003937 8.480501837 1.00E-04 4 -0.722411049 AAAAAWEEPSS(ph)GNGTAR ddPTM_HeLa_Romidepsin_16h_R1 1 AAAAAWEEPSSGNGTAR 17 0 Q9P258 Q9P258 RCC2 Protein RCC2 1 0 AAAAAWEEPS(0.093)S(0.884)GNGT(0.023)AR 188 3.79E-13 5614800 1871.3 1787 1537 1432.5 1446.1 1400.9 1134.7 1361.6 1731.3 1746.1 TRUE FALSE FALSE 1848.491876 1812.157433 1563.75084 1598.13239 1372.300121 1311.387011 1231.08139 1400.995748 1576.448192 1700.73607 1.086877563 1.065513612 0.919455327 0.939671015 0.806885998 0.771070264 0.723852108 0.823758473 0.926921125 1 10.73194356 -9.030553323 1.214835498 1.042656231 0.76379599 0.772760096 0.055738748 0.114030001 0.333034763 0.007987792 0.01810004 9.32E-10 9.030553323 -0.278860241 AAAGEEETAAAGS(ph)PGRK ddPTM_HeLa_Romidepsin_16h_R1 2 AAAGEEETAAAGSPGRK 17 1 Q9NS37;E9PIM0 Q9NS37 CREBZF CREB/ATF bZIP transcription factor 1 0 AAAGEEETAAAGS(1)PGRK;AAAGEEETAAAGS(1)PGRK ; 177.39 1.25E-08 6546900 4168.1 3894.4 4081.1 2885.1 3355.1 3386.8 3257.3 2290.3 4145 4071.9 TRUE FALSE FALSE 4117.297594 3949.225465 4152.129834 3218.688837 3183.876727 3170.39441 3533.974981 2356.566217 3774.260819 3966.111451 1.038119489 0.995742433 1.046901955 0.811547753 0.802770363 0.799370983 0.891042782 0.594175491 0.951627524 1 11.9535095 -9.212815244 5.249799857 1.018477056 0.786138345 0.698206694 0.074321685 0.07777387 5.051056272 0.009855397 0.016364373 6.13E-10 9.212815244 -0.232338711 AAAGPLDMS(ph)LPST(ph)PDIK ddPTM_HeLa_Romidepsin_16h_R1 2 AAAGPLDMSLPSTPDIK 17 0 K7ELQ4;P17544-4;P17544-2;P17544 K7ELQ4 ATF7 Cyclic AMP-dependent transcription factor ATF-7 2 0 AAAGPLDMS(0.999)LPS(0.31)T(0.691)PDIK;AAAGPLDMS(0.879)LPS(0.323)T(0.798)PDIK ; 103.83 0.0044295 16976300 6720.4 6127.5 6444.5 5828.7 5724.8 5255.6 4499.1 5237.5 7183.7 6004.6 TRUE FALSE FALSE 6638.48918 6213.763106 6556.663819 6502.641719 5432.642094 4919.784122 4881.253442 5389.038799 6541.17188 5848.599626 1.135056185 1.062436054 1.121065595 1.111828837 0.928879123 0.841190103 0.834602085 0.921423784 1.118416766 1 12.51387552 -8.613075717 4.215786953 1.072718622 0.865190575 0.839311597 0.045098396 0.08389625 2.766135701 0.008552409 0.017726415 2.44E-09 8.613075717 -0.207528047 AAAGPLDMSLPST(ph)PDIK ddPTM_HeLa_Romidepsin_16h_R1 4 AAAGPLDMSLPSTPDIK 17 0 K7ELQ4;P17544-4;P17544-2;P17544 K7ELQ4 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 0 AAAGPLDMS(0.018)LPS(0.156)T(0.827)PDIK;AAAGPLDMS(0.083)LPS(0.368)T(0.549)PDIK;AAAGPLDMS(0.027)LPS(0.209)T(0.765)PDIK;AAAGPLDMS(0.021)LPS(0.261)T(0.718)PDIK ;;; 124.81 0.0053558 57141700 15951.3 15895.5 14277.8 13291.7 10541.7 9238.2 8879.4 8425.4 16423 16081.6 TRUE FALSE FALSE 15756.87942 16119.27727 14526.29912 14828.54889 10003.71771 8647.908835 9633.616014 8669.175656 14954.08575 15663.79771 1.005942474 1.029078488 0.927380408 0.946676481 0.638652126 0.552095283 0.615024287 0.553452989 0.954690939 1 13.93514642 -8.75978422 2.821948912 0.999061828 0.576213934 0.97061892 0.033152355 0.025709626 0.419610829 0.004450373 0.009167197 1.74E-09 8.75978422 -0.422847893 AAAPPQPS(ph)PPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 AAAPPQPSPPPTK 13 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 0 AAAPPQPS(0.975)PPPT(0.025)K 171.36 7.64E-05 11293000 4012.6 4427 3997.8 4416.6 4385.3 4521.7 4148.2 4654.4 4524.9 3749.7 TRUE FALSE FALSE 3963.692888 4489.323422 4067.380032 4927.268073 4161.501777 4232.777963 4500.548004 4789.067721 4120.181611 3652.282253 1.085264668 1.229183045 1.113654354 1.349092904 1.139425019 1.158940539 1.232256352 1.311253454 1.1281115 1 11.83458255 -10.5015076 0.706740149 1.013141505 1.230644869 0.392146412 0.078450492 0.279192732 0.301599898 0.019868236 0.020062046 3.15E-11 10.5015076 0.217503364 AAAS(ph)VTPPGSLELLQPGFS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AAASVTPPGSLELLQPGFSK 20 0 B1AMY1;B1AMX7;B1AMX8;Q12933-4;Q12933-3;Q12933;Q12933-2 B1AMY1 TRAF2 TNF receptor-associated factor 2 2 0 AAAS(0.707)VT(0.235)PPGS(0.06)LELLQPGFS(0.997)K 85.522 0.0024832 0 2415 2800.3 2656.1 2396.5 3446.9 3861.8 2644.5 3808.1 3327.8 2942.9 TRUE FALSE FALSE 2385.565051 2839.722697 2702.328306 2673.594606 3270.991831 3615.043443 2869.123764 3918.281365 3030.153233 2866.443034 0.832238779 0.990678225 0.94274621 0.932722044 1.141132683 1.261160051 1.000935211 1.366948974 1.057112665 1 11.48504589 -8.713594758 3.989876397 0.926674371 1.190427351 0.539229289 0.103933917 0.111186569 3.67544662 0.014423108 0.029198448 1.93E-09 8.713594758 0.26375298 AAASK(ac)LEQGKR ddPTM_HeLa_Romidepsin_16h_R1 2 AAASKLEQGKR 11 2 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 0 1 ; AAASK(1)LEQGKR;AAASK(1)LEQGKR 111.63 0.0075613 11736500 3617.1 4093.9 3236.5 4066.2 5218.3 5215.2 5691.5 3754.5 3954.7 3445.4 FALSE TRUE FALSE 3573.013394 4151.534032 3292.829925 4536.353176 4951.990679 4881.965551 6174.935868 3863.130534 3600.981727 3355.888011 1.06469983 1.237089562 0.981209717 1.351759403 1.475612613 1.454746265 1.840030373 1.151150015 1.073033938 1 11.71247886 -9.069346356 2.459979008 1.045428781 1.507193628 0.560957587 0.170223098 0.135113197 1.612464034 0.02404048 0.0441441 8.52E-10 9.069346356 0.461764847 AAASK(ac)LGEFAK ddPTM_HeLa_Romidepsin_16h_R1 1 AAASKLGEFAK 11 1 C9J9C1;P30153;B3KQV6;P30154-4;P30154;P30154-3;P30154-2 C9J9C1 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 1 AAASK(1)LGEFAK 142.07 0.0037683 2156000 1105.8 682.07 1042.9 1163.8 785.8 538.04 1432.4 601.91 1625 888.75 FALSE TRUE FALSE 1092.322084 691.6721994 1061.051237 1298.364032 745.6976938 503.6609804 1554.06802 619.3253162 1479.65593 865.6601469 1.261837094 0.799011254 1.225713394 1.499854229 0.861420843 0.581822996 1.795240344 0.71543702 1.709280409 1 9.757656932 -7.768306375 24.99970288 1.089331052 1.255338667 0.015010299 0.398244408 416.6417435 1516832.518 0.045008326 0.139454762 1.70E-08 7.768306375 0.166007615 AAAT(ph)PESQEPQAK ddPTM_HeLa_Romidepsin_16h_R1 2 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 AAAT(1)PESQEPQAK;AAAT(0.994)PES(0.006)QEPQAK ; 181.76 9.74E-07 25343500 11698.8 11824.3 10669.9 10948.6 11910.7 14641.3 13317.4 14473.1 12796 11212.9 TRUE FALSE FALSE 11556.21053 11990.76281 10855.60513 12214.52865 11302.85253 13705.76818 14448.57962 14891.85631 11651.49371 10921.58724 1.058107239 1.097895621 0.993958561 1.11838402 1.03490933 1.254924571 1.322937711 1.363524915 1.066831538 1 13.41489492 -8.109822531 1.842187049 1.035699328 1.356369704 0.894501644 0.041356987 0.075546352 0.483828113 0.006114824 0.023373844 7.77E-09 8.109822531 0.320670376 AAATPES(ph)QEPQAK ddPTM_HeLa_Romidepsin_16h_R1 2 AAATPESQEPQAK 13 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 AAAT(0.217)PES(0.783)QEPQAK;AAAT(0.001)PES(0.999)QEPQAK ; 133.13 0.0018925 25321900 6256.8 6123.4 5726.7 5350.6 6373.4 7081.4 6175.1 6039.6 5976 5756.5 TRUE FALSE FALSE 6180.539715 6209.605386 5826.370811 5969.261547 6048.141616 6628.921394 6699.61284 6214.346297 5441.491593 5606.9453 1.102300697 1.107484567 1.039134591 1.064619187 1.078687466 1.182269674 1.19487751 1.108330109 0.970491293 1 12.45299928 -16.52287767 0.03025104 0.295242817 1.592641727 0.616490021 0.041900903 658.9287452 1.600451645 52.31894352 22.29360317 3.00E-17 16.52287767 1.29739891 AADAEAEVAS(ph)LNRR ddPTM_HeLa_Romidepsin_16h_R1 2 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;P06753;A0A494C0P6 J3KN67 TPM3 Tropomyosin alpha-3 chain 1 0 AADAEAEVAS(1)LNRR;AADAEAEVAS(1)LNRR ; 116.96 0.0013591 13975900 4537.6 4243.3 4053.9 4256.1 5068.7 5039 4862.6 4896.6 5000.6 4692.3 TRUE FALSE FALSE 4482.293986 4303.037289 4124.456429 4748.210308 4810.025325 4717.024163 5275.629123 5038.275395 4553.333812 4570.39337 0.980723895 0.941502611 0.902429199 1.038906266 1.052431363 1.032082751 1.154305263 1.102372375 0.996267376 1 12.15810263 -8.244387304 1.155777765 0.981764364 1.129219157 0.672017644 0.040035125 0.269147825 0.624886894 0.006448024 0.030929329 5.70E-09 8.244387304 0.147454793 AADAEAEVASLNRR ddPTM_HeLa_Romidepsin_16h_R1 2 AADAEAEVASLNRR 14 1 J3KN67;A0A2R2Y2Q3;P06753;A0A494C0P6 J3KN67 TPM3 Tropomyosin alpha-3 chain 0 0 ; ; 144.51 0.0003992 19528200 5710 5197.1 4672.9 5505.6 5447.9 6132.6 5071.5 6423.8 5560.7 5016 FALSE FALSE TRUE 5640.404324 5270.26491 4754.229864 6142.183377 5169.873334 5740.746652 5502.273083 6609.662518 5063.337065 4885.683597 1.154475973 1.078715968 0.973094096 1.257179933 1.058167855 1.175014005 1.126203319 1.352863399 1.036362049 1 12.25434472 -4 0.438858195 1.068856385 6.085629883 0.496239522 0.079603078 52.5731642 0.58028458 0.01848848 236.7526205 1.00E-04 4 5.016773498 AADEEAFEDNSEEYIR ddPTM_HeLa_Romidepsin_16h_R1 1 AADEEAFEDNSEEYIR 16 0 P55060-4;P55060-3;P55060 P55060-4 CSE1L Exportin-2 0 0 195.1 5.99E-16 0 393.1 383.8 414.84 408.61 393.61 424.68 260.19 456.9 505.22 465.82 FALSE FALSE TRUE 388.308746 389.2031465 422.0601162 455.8554108 373.5226129 397.5443186 282.2905321 470.1196806 460.0318579 453.7179292 0.855837341 0.857808611 0.930225783 1.004711036 0.823248518 0.876192658 0.622171869 1.036149666 1.013915978 1 8.825651861 -16.52287875 0.221892533 1.710371213 0.848397728 0.191071054 0.106694971 60.77344761 0.772441957 18.75965107 0.080882145 3.00E-17 16.52287875 -0.861973484 AADEEAFEDNSEEYIRR ddPTM_HeLa_Romidepsin_16h_R1 2 AADEEAFEDNSEEYIRR 17 1 P55060-4;P55060-3;P55060 P55060-4 CSE1L Exportin-2 0 0 ; ; 202.32 2.70E-19 39569000 3718.6 3819.6 3531.7 4849.1 3545.9 3811.6 2746.5 3663 4162.4 3443.1 FALSE FALSE TRUE 3673.276273 3873.372429 3593.167757 5409.775758 3364.939491 3568.051061 2979.787641 3768.983126 3790.104519 3353.647766 1.095307716 1.154972943 1.071420736 1.613101952 1.003366998 1.06393137 0.88852135 1.123845851 1.130143886 1 11.71151545 -6.370181889 13.60869946 1.082317779 1.116998492 0 0.184990424 3227073.948 0.122756838 0.024369448 9201913.982 4.26E-07 6.370181889 0.034680714 AADIS(ph)LDNLVEGK ddPTM_HeLa_Romidepsin_16h_R1 4 AADISLDNLVEGK 13 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK;AADIS(1)LDNLVEGK ;;; 162.7 0.00031066 90930500 9628.72 9297.46 9851.89 7776.79 13018.2 15933.9 14410.4 14856.7 10107.7 9515.5 TRUE FALSE FALSE 9511.361457 9428.349886 10023.35801 8675.979051 12353.83268 14915.77521 15634.41902 15286.55517 9203.641997 9268.285938 1.026226588 1.01727007 1.081468362 0.936093158 1.332914496 1.609334813 1.686872753 1.649340048 0.993025254 1 13.17808684 -8.470648395 2.421598814 1.013627026 1.661856301 0.9763134 0.044691622 0.026960116 0.310557089 0.006052753 0.015065677 3.38E-09 8.470648395 0.648229275 AADK(ac)LAPAQYIR ddPTM_HeLa_Romidepsin_16h_R1 1 AADKLAPAQYIR 12 1 Q13573;G3V3A4;G3V4X8 Q13573 SNW1 SNW domain-containing protein 1 0 1 AADK(1)LAPAQYIR 137.01 0.0020844 2388600 598.06 666.16 575.32 621.36 575.93 600.77 925.73 385.39 790.09 700.71 FALSE TRUE FALSE 590.7706147 675.538218 585.3332033 693.2045668 546.538143 562.3827359 1004.361483 396.5406516 719.4223716 682.5054532 0.865591054 0.989791678 0.857624215 1.015676232 0.80078209 0.823997425 1.471580159 0.581007301 1.054090291 1 9.414696763 AADK(ac)LIQNLDANHDGR ddPTM_HeLa_Romidepsin_16h_R1 1 AADKLIQNLDANHDGR 16 1 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 1 AADK(1)LIQNLDANHDGR 128.82 1.86E-05 764120 1286.5 907.41 944.73 970.12 1340.8 384.61 708.86 985.64 1164.2 1155 FALSE TRUE FALSE 1270.819643 920.1845418 961.1726294 1082.289839 1272.373973 360.0346623 769.0705507 1014.157938 1060.071036 1124.992933 1.129624556 0.817946953 0.854381037 0.962041455 1.131006191 0.320032821 0.683622561 0.901479385 0.942291284 1 10.13570022 -8.283160532 24.98916416 1.024302667 0.639902634 0.452213528 0.166666721 451.2727395 519167.0231 0.024167051 0.05408317 5.21E-09 8.283160532 -0.384400033 SSVAGS(ph)LS(ph)LRRAVDPGENS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SSVAGSLSLRRAVDPGENSR 20 2 O94972-2;O94972-3;O94972 O94972-2 TRIM37 E3 ubiquitin-protein ligase TRIM37 3 0 S(0.056)S(0.064)VAGS(0.916)LS(0.965)LRRAVDPGENS(1)R 69.255 0.0014865 0 1634.6 1313 1071.6 892.28 772.06 679.68 681.88 685.71 1483.2 1497.3 TRUE FALSE FALSE 1614.676866 1331.484448 1090.250748 995.4496119 732.6588972 636.2506416 739.7988702 705.549937 1350.538877 1458.39993 1.107156434 0.912976215 0.747566375 0.682562849 0.502371731 0.436266232 0.507267489 0.483783578 0.926041513 1 10.51017068 -9.440055235 1.152189655 1.051839043 0.47660436 0.92916443 0.061729552 0.067558648 0.178393008 0.010486646 0.019020281 3.63E-10 9.440055235 -0.575234683 down AADPPAENS(ph)SAPEAEQGGAE ddPTM_HeLa_Romidepsin_16h_R1 1 AADPPAENSSAPEAEQGGAE 20 0 H0Y449;P67809 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 AADPPAENS(0.864)S(0.136)APEAEQGGAE 111.7 0.00032739 34633000 4975.9 5405.9 5049.9 5017.2 5327 4643.3 4237.2 4399.8 5316.6 5510.7 TRUE FALSE FALSE 4915.251817 5482.004402 5137.791391 5597.312271 5055.143312 4346.608116 4597.107662 4527.101271 4841.06998 5367.53122 0.915737909 1.021326971 0.957198232 1.042809448 0.941800449 0.809796522 0.856465938 0.84342337 0.901917433 1 12.39004296 -8.369465815 4.961406651 0.970002142 0.839147632 0.674409472 0.042386495 0.101899811 3.831632106 0.006162383 0.014111088 4.27E-09 8.369465815 -0.130854509 AADPPAENSSAPEAEQGGAE ddPTM_HeLa_Romidepsin_16h_R1 1 AADPPAENSSAPEAEQGGAE 20 0 H0Y449;P67809 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 0 0 137.62 0.0023431 9174400 3711.9 3743.9 3321.1 3734 3466 3298.3 2783.6 3220.6 4180.9 3809.9 FALSE FALSE TRUE 3666.657935 3796.606722 3378.902352 4165.742649 3289.117087 3087.549275 3020.038915 3313.78298 3806.949833 3710.918249 0.988072948 1.023090908 0.910529989 1.122563843 0.886335097 0.832017595 0.813825235 0.892981941 1.025878119 1 11.8575605 -8.540553164 24.83573278 0.99792776 0.845721006 0.67351425 0.053034952 86.85181784 122042.0353 0.006671184 0.013344611 2.88E-09 8.540553164 -0.152206755 AADRLPNLS(ph)SPSAEGPPGPPSGPAPR ddPTM_HeLa_Romidepsin_16h_R1 3 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784-3;O60784-4;O60784;O60784-2 O60784-3 TOM1 Target of Myb protein 1 1 0 AADRLPNLS(0.604)S(0.392)PS(0.005)AEGPPGPPSGPAPR;AADRLPNLS(0.5)S(0.5)PS(0.001)AEGPPGPPSGPAPR;AADRLPNLS(0.788)S(0.192)PS(0.019)AEGPPGPPSGPAPR ;; 111.8 3.75E-07 96798000 1584.23 1295.36 1350.63 1342.27 1434.08 1820.13 1823.66 2323.66 1273.91 1434.11 TRUE FALSE FALSE 1564.920795 1313.596112 1374.137149 1497.469573 1360.893546 1703.829567 1978.561635 2390.891436 1159.968299 1396.851615 1.120319995 0.940397747 0.983738812 1.072031958 0.974257775 1.219764181 1.416443674 1.711628787 0.830416263 1 10.44796306 -7.556128342 1.455822601 1.039243156 1.793262526 0.876269736 0.087586171 0.139106148 0.389401371 0.009847543 0.129013886 2.78E-08 7.556128342 0.75401937 AADRLPNLSSPS(ph)AEGPPGPPSGPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 AADRLPNLSSPSAEGPPGPPSGPAPR 26 1 O60784-3;O60784-4;O60784;O60784-2 O60784-3 TOM1 Target of Myb protein 1 1 0 AADRLPNLS(0.284)S(0.284)PS(0.431)AEGPPGPPSGPAPR 86.825 1.12E-05 24359000 219.03 174.46 316 199.17 347.64 389.21 295.22 301.87 267.68 261.21 TRUE FALSE FALSE 216.3603781 176.9160525 321.4998474 222.1989725 329.8986336 364.3407371 320.2959794 310.6041322 243.7380304 254.4237265 0.850393873 0.695359882 1.263639409 0.873342182 1.296650427 1.432023428 1.258907665 1.220814334 0.958000394 1 7.991089407 -8.754702575 24.61279045 0.932564858 1.30829431 0.602817138 0.143828615 66.60708777 243344.8213 0.020913729 0.041065602 1.76E-09 8.754702575 0.375729452 AADS(ph)DDGAVSAPAASDGGVSK ddPTM_HeLa_Romidepsin_16h_R1 2 AADSDDGAVSAPAASDGGVSK 21 0 Q96GM8 Q96GM8 TOE1 Target of EGR1 protein 1 1 0 AADS(1)DDGAVSAPAASDGGVSK;AADS(1)DDGAVSAPAASDGGVSK ; 255.22 2.69E-76 5271500 4430.2 4681.9 3972.2 3790.8 3499.5 4164.1 3268.2 3700.5 4426.6 4117.2 TRUE FALSE FALSE 4376.203018 4747.811911 4041.334475 4229.110132 3320.907457 3898.027449 3545.800826 3807.568129 4030.673809 4010.23455 1.091258619 1.183923746 1.007755138 1.054579247 0.828108036 0.972019816 0.88418789 0.949462701 1.005096774 1 11.9694709 -8.784386633 24.91834506 1.053606451 0.911253087 0.578745266 0.062071423 129.853843 141007.4655 0.009561998 0.017340833 1.64E-09 8.784386633 -0.142353364 AADSQNS(ph)GEGNTGAAESSFSQEVSR ddPTM_HeLa_Romidepsin_16h_R1 1 AADSQNSGEGNTGAAESSFSQEVSR 25 0 P12270 P12270 TPR Nucleoprotein TPR 1 0 AADS(0.017)QNS(0.82)GEGNT(0.163)GAAESSFSQEVSR 81.839 6.67E-05 4291500 750.77 471.77 539.54 601.32 808.28 555.64 640.08 664.65 775.98 501.24 TRUE FALSE FALSE 741.6193265 478.4115904 548.9304674 670.8474477 767.0304555 520.1363972 694.4483792 683.8805991 706.5744053 488.2177125 1.519034044 0.979914448 1.124355904 1.374074374 1.57108281 1.065377974 1.422415372 1.400769742 1.447252705 1 8.931380827 -9.236406398 23.20612428 1.21898496 1.364446539 0.128757692 0.198270629 660.3099233 612120.698 0.035304737 0.058522158 5.80E-10 9.236406398 0.145461579 AADTEEMDIEMDS(ph)GDEA ddPTM_HeLa_Romidepsin_16h_R1 2 AADTEEMDIEMDSGDEA 17 0 Q9UBB5 Q9UBB5 MBD2 Methyl-CpG-binding domain protein 2 1 0 AADTEEMDIEMDS(1)GDEA;AADTEEMDIEMDS(1)GDEA ; 99.568 0.0024848 55414000 5101.1 4535.9 3899.1 4653.4 5128.7 4987.2 3792.8 4926.4 4520.8 4593 TRUE FALSE FALSE 5038.925831 4599.756519 3966.9622 5191.448003 4866.963301 4668.534015 4114.960337 5068.937611 4116.448325 4473.673198 1.1263509 1.0281834 0.88673491 1.160444175 1.087912122 1.043557231 0.919816928 1.133059432 0.920149538 1 12.12724416 AAEAAAAPAESAAPAAGEEPS(ph)KEEGEPK ddPTM_HeLa_Romidepsin_16h_R1 2 AAEAAAAPAESAAPAAGEEPSKEEGEPK 28 1 P80723 P80723 BASP1 Brain acid soluble protein 1 1 0 AAEAAAAPAES(0.016)AAPAAGEEPS(0.984)KEEGEPK;AAEAAAAPAESAAPAAGEEPS(1)KEEGEPK ; 98.135 2.47E-08 9361300 3747.5 4801.3 4200.6 3709.8 5896.9 5680.7 3894.7 5644.8 4228.8 4822.7 TRUE FALSE FALSE 3701.824029 4868.892827 4273.709681 4138.744531 5595.959189 5317.721604 4225.515721 5808.123382 3850.565537 4697.405559 0.788057148 1.036506805 0.909802151 0.881070301 1.191287216 1.132055033 0.899542453 1.236453465 0.819721757 1 12.19764844 -8.773288638 24.99037936 0.908614059 1.100686574 0.472664392 0.107697692 167.8062363 353907.4289 0.016934141 0.030873484 1.69E-09 8.773288638 0.192072515 AAEAGGAEEQYGFLT(ph)TPTK ddPTM_HeLa_Romidepsin_16h_R1 3 AAEAGGAEEQYGFLTTPTK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 AAEAGGAEEQYGFLT(0.716)T(0.284)PTK;AAEAGGAEEQYGFLT(0.5)T(0.5)PT(0.001)K;AAEAGGAEEQYGFLT(0.494)T(0.494)PT(0.012)K ;; 200.71 9.95E-21 390978000 20619.4 21874.7 20956.7 21120.1 17617.4 16498.4 13884.1 15699.2 21346.4 19806.7 TRUE FALSE FALSE 20368.08282 22182.6526 21321.44257 23562.10534 16718.31834 15444.20549 15063.41511 16153.43158 19437.12452 19292.11908 1.055772191 1.149829757 1.105189248 1.22133319 0.866587972 0.800544794 0.780806662 0.837307271 1.007516305 1 14.235724 -8.586442011 8.035581663 1.055897144 0.808513586 0.786739906 0.067665812 0.101661765 11.33924648 0.01102484 0.022118504 2.59E-09 8.586442011 -0.247383558 AAEAGGAEEQYGFLTT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 3 AAEAGGAEEQYGFLTTPTK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 AAEAGGAEEQYGFLT(0.376)T(0.623)PT(0.001)K;AAEAGGAEEQYGFLT(0.116)T(0.884)PTK;AAEAGGAEEQYGFLT(0.102)T(0.898)PTK ;; 204.9 5.07E-21 300417000 7236.6 8272.2 6866.3 6744 6367.4 5602.4 4814.66 4962.7 7491.3 6772.9 TRUE FALSE FALSE 7148.397536 8388.656249 6985.805071 7523.773011 6042.447818 5244.424721 5223.6171 5106.287895 6821.259366 6596.939082 1.08359308 1.271598259 1.058946427 1.140494541 0.915947191 0.794978498 0.791824365 0.774038964 1.034003692 1 12.68758107 -8.509286142 3.290074024 1.067513557 0.789536294 0.778656876 0.073911335 0.104381128 2.332188268 0.01228147 0.027928156 3.10E-09 8.509286142 -0.277977262 AAEDDEDDDVDTK ddPTM_HeLa_Romidepsin_16h_R1 5 AAEDDEDDDVDTK 13 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 0 ;;;; ;;;; 363.35 1.41E-275 1199726680 19365.74 18264.35 17006.89 16563.26 17477.01 16342.85 14759.68 14378.64 19282.44 17529.92 FALSE FALSE TRUE 19129.70291 18521.476 17302.88779 18478.38205 16585.09296 15298.59463 16013.36685 14794.66326 17557.77027 17074.49015 1.120367445 1.084745479 1.013376542 1.0822216 0.971337523 0.8959913 0.937853295 0.866477601 1.02830422 1 14.05955488 -8.542896856 3.117233783 1.058466965 0.904626105 0.769791116 0.038004445 0.115214914 2.297483177 0.007358479 0.016545384 2.86E-09 8.542896856 -0.153840859 AAEDDEDDDVDTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 3 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 1 ;; AAEDDEDDDVDTK(1)K;AAEDDEDDDVDTK(1)K;AAEDDEDDDVDTK(1)K 366.15 1.04E-286 11310440 3848.6 3746.31 3402.2 2306.79 4449.42 3263.29 3413.27 2560.46 5736.98 4706.96 FALSE TRUE FALSE 3801.691783 3799.050651 3461.413864 2573.511914 4222.349494 3054.776301 3703.193069 2634.54287 5223.85014 4584.672501 0.829217743 0.828641664 0.754996974 0.561329498 0.920970799 0.666301966 0.807733392 0.574641454 1.139416205 1 12.16260297 -11.61024692 0.228982637 1.125049302 0.653783725 0.599889461 0.109290638 2.372465203 0.27055792 0.367727184 0.133205112 2.45E-12 11.61024692 -0.471265576 AAEDDEDDDVDTKK ddPTM_HeLa_Romidepsin_16h_R1 11 AAEDDEDDDVDTKK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 0 ;;;;;;;;;; ;;;;;;;;;; 251.03 1.62E-54 1362097100 30392.1 27768.5 28670.7 27318.3 28276.3 27448.5 25823 20200.39 32541.6 30681.3 FALSE FALSE TRUE 30021.6694 28159.42567 29169.70151 30476.97038 26833.2549 25694.62944 28016.40498 20784.85641 29630.99779 29884.1954 1.004600224 0.942284886 0.976091245 1.019835735 0.897907892 0.859806633 0.937499056 0.695513335 0.991527374 1 14.86709508 -6.053440204 0.497095613 0.999887711 7.74E-13 0.75737146 0.045554651 3.988894289 0.271166822 0.008544951 3.061263222 8.84E-07 6.053440204 -0.999887711 AAEDS(ph)PYWVSPAYSK ddPTM_HeLa_Romidepsin_16h_R1 1 AAEDSPYWVSPAYSK 15 0 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 0 AAEDS(0.897)PYWVS(0.103)PAYSK 212.43 1.40E-25 8946800 2612 2419.6 2548.3 2321.8 4259.3 5340.8 4515.2 5117 3085.4 2767.8 TRUE FALSE FALSE 2580.163939 2453.663192 2592.652093 2590.25744 4041.932027 4999.540117 4898.720975 5265.052322 2809.434096 2695.892157 0.957072386 0.910148867 0.961704676 0.960816416 1.499292921 1.854503009 1.817105689 1.952990704 1.042116647 1 11.39654707 -8.563009857 2.4055095 0.96826219 1.873948873 0.984037786 0.052036306 0.02287558 0.26541637 0.007358466 0.017339623 2.74E-09 8.563009857 0.905686683 AAEDSPYWVS(ph)PAYSK ddPTM_HeLa_Romidepsin_16h_R1 3 AAEDSPYWVSPAYSK 15 0 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 0 AAEDSPYWVS(1)PAYSK;AAEDS(0.039)PYWVS(0.961)PAYSK;AAEDSPYWVS(0.998)PAYS(0.002)K ;; 217.01 5.78E-26 61951100 9289.5 8965.2 8778.2 8612 14246.5 17866.7 15741.7 17489.8 9556.1 8689.8 TRUE FALSE FALSE 9176.276001 9091.412321 8930.980889 9607.759961 13519.44794 16725.07553 17078.79961 17995.83977 8701.378482 8464.037743 1.084148757 1.074122375 1.055167895 1.135127259 1.59728115 1.97601618 2.017807591 2.126153062 1.028041078 1 13.04713035 -8.534290751 1.688619079 1.042064501 2.075634773 0.993637102 0.035424405 0.022720256 0.127673656 0.006477901 0.017769531 2.92E-09 8.534290751 1.033570271 up AAEEAFVNDIDESS(ph)PGTEWER ddPTM_HeLa_Romidepsin_16h_R1 2 AAEEAFVNDIDESSPGTEWER 21 0 P09496-5;P09496-2 P09496-5 1 0 AAEEAFVNDIDES(0.006)S(0.994)PGTEWER;AAEEAFVNDIDES(0.25)S(0.733)PGT(0.017)EWER ; 239.27 5.03E-54 19149200 5578.9 5406.1 5171.4 5681.9 5527.5 6203.2 5788.8 6227 6380.1 5767 TRUE FALSE FALSE 5510.902221 5482.207218 5261.406048 6338.868012 5245.411049 5806.83554 6280.500528 6407.16842 5809.447877 5617.172509 0.981081178 0.975972735 0.936664494 1.12848021 0.933816977 1.033764858 1.118089309 1.140639425 1.03422992 1 12.45562839 -7.819692415 3.113113403 0.992493966 1.135419492 0.489569205 0.052440472 0.127944332 2.459777958 0.006514657 0.025424443 1.51E-08 7.819692415 0.142925527 AAEEAFVNDIDESSPGTEWER ddPTM_HeLa_Romidepsin_16h_R1 2 AAEEAFVNDIDESSPGTEWER 21 0 P09496-5;P09496-2 P09496-5 0 0 ; ; 216.01 1.94E-31 4198500 1844.92 2005.45 1791.9 1945.27 2168.67 2214.18 1526.63 2211.1 2268.15 1877.26 FALSE FALSE TRUE 1822.433405 2033.682778 1823.087268 2170.19127 2057.994677 2072.701044 1656.301914 2275.07469 2065.280983 1828.488515 0.996688462 1.112220701 0.997046059 1.186877168 1.125516874 1.133559783 0.905831183 1.244237889 1.129501753 1 10.83643585 -10.11617264 1.407023678 0.996948365 1.101229118 0 0.098638438 0.430835252 1.642058443 0.015688513 0.019784326 7.65E-11 10.11617264 0.104280753 AAEEEDEADPK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 1 ; AAEEEDEADPK(1)R;AAEEEDEADPK(1)R 124.1 0.002915 1081080 633.27 605.54 628.38 408.14 1345.41 1162.45 872.52 682.88 1317.11 956.79 FALSE TRUE FALSE 625.5514617 614.064808 639.3166903 455.3310672 1276.748707 1088.173197 946.631827 702.6380554 1199.304383 931.9324579 0.6712412 0.658915571 0.686011829 0.488588055 1.370001331 1.167652427 1.015772998 0.753958132 1.28690054 1 9.864081589 -8.760170466 24.99991453 0.790162832 1.078969953 0.228409799 0.250226641 34.88449021 687260.5619 0.032989428 0.063179393 1.74E-09 8.760170466 0.288807121 AAEEEDEADPKR ddPTM_HeLa_Romidepsin_16h_R1 3 AAEEEDEADPKR 12 1 P20962 P20962 PTMS Parathymosin 0 0 ;; ;; 99.343 0.010275 121231900 10049.3 9973.3 9077.5 9597.1 9761 9840.5 10178 5652.1 11431.3 10245.2 FALSE FALSE TRUE 9926.815266 10113.70438 9235.49008 10706.76186 9262.859747 9211.723809 11042.51907 5815.634596 10408.8559 9979.028227 0.994767731 1.013495919 0.925489924 1.072926302 0.928232643 0.923108303 1.106572585 0.582785664 1.043073099 1 13.28468362 -7.251736202 24.9547539 0.994642488 0.582785438 0.814711407 0.059746043 350.9075585 902450.2733 0.006971572 0.122841014 5.60E-08 7.251736202 -0.41185705 AAEEQGDDQDSEKS(ph)KPAGSDGER ddPTM_HeLa_Romidepsin_16h_R1 2 AAEEQGDDQDSEKSKPAGSDGER 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 AAEEQGDDQDS(0.382)EKS(0.471)KPAGS(0.147)DGER;AAEEQGDDQDS(0.03)EKS(0.944)KPAGS(0.026)DGER ; 55.209 0.0053822 29195600 4833.1 4243.2 4365.5 3572 4279.2 4435 4148.5 4279.6 5314.2 4768.6 TRUE FALSE FALSE 4774.192318 4302.935881 4441.479696 3985.011447 4060.816456 4151.617813 4500.873486 4403.423474 4838.884642 4644.711085 1.027877134 0.926416262 0.956244558 0.857967562 0.874288278 0.893837687 0.96903196 0.948051105 1.041805304 1 12.18137314 -10.19900006 4.856355072 1.013181871 0.915623865 0.65025104 0.035141399 0.108031875 5.213025421 0.00619311 0.007566483 6.32E-11 10.19900006 -0.097558005 AAEK(ac)RPAEDYVPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAEKRPAEDYVPR 13 2 Q969E4;Q5H9L2 Q969E4 TCEAL3;TCEAL5 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5 0 1 AAEK(1)RPAEDYVPR 92.906 0.024301 8251700 1505.5 1699 1516.3 1243.7 1269.6 1325.1 1513.4 1581.3 2049.1 1925.6 FALSE TRUE FALSE 1487.150387 1722.918567 1542.690565 1387.502446 1204.807574 1240.430387 1641.948158 1627.052421 1865.823364 1875.572634 0.792904716 0.918609354 0.822517101 0.739775373 0.642367857 0.66136089 0.875438321 0.867496353 0.994801977 1 10.87311542 -12.47500352 0.370533938 1.092443249 0.764998903 0.512560935 0.08277819 2.207503222 0.351746798 0.296699727 0.035227957 3.35E-13 12.47500352 -0.327444346 AAEK(ac)VSEAR ddPTM_HeLa_Romidepsin_16h_R1 2 AAEKVSEAR 9 1 O75348 O75348 ATP6V1G1 V-type proton ATPase subunit G 1 0 1 ; AAEK(1)VSEAR;AAEK(1)VSEAR 134.25 0.011036 1729830 961.17 945.41 661.47 590.96 1190.44 1274.86 1156.99 688.29 1035.52 1041.41 FALSE TRUE FALSE 949.4548903 958.7195068 672.9826079 659.2895758 1129.687405 1193.40056 1255.264702 708.2045852 942.9004977 1014.354018 0.936019253 0.945152767 0.663459301 0.649960038 1.113701316 1.176512873 1.237501582 0.698182856 0.929557611 1 9.986345538 AAEKGY(ph)S(ph)VGGLLQEVMK ddPTM_HeLa_Romidepsin_16h_R1 1 AAEKGYSVGGLLQEVMK 17 1 Q5JQC9-2;Q5JQC9 Q5JQC9-2 AKAP4 A-kinase anchor protein 4 2 0 AAEKGY(1)S(1)VGGLLQEVMK 65.467 0.016743 37384000 647.03 764.15 477.1 756.09 670.82 651.59 382.63 530.47 495.54 386.2 TRUE FALSE FALSE 639.1437495 774.9077238 485.4037254 843.5126833 636.5855522 609.9555019 415.1305826 545.8183125 451.2176613 376.1664683 1.699098148 2.060012758 1.290396051 2.242392011 1.692297442 1.621504183 1.103582104 1.451002039 1.199515904 1 8.555227442 -12.14417643 0.923003029 1.003865246 1.64705438 0.3096574 0.320393164 0.489413096 0.75883888 0.205402782 0.060837516 7.18E-13 12.14417643 0.643189133 AAEPHFGT(ph)LPK ddPTM_HeLa_Romidepsin_16h_R1 1 AAEPHFGTLPK 11 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 AAEPHFGT(1)LPK 93.649 0.021358 5740300 6009.9 5663.9 6303 5443.9 7019.9 6053.6 4949.8 6168.3 5857.1 4880.5 TRUE FALSE FALSE 5936.649027 5743.636533 6412.701071 6073.349332 6661.648308 5666.794497 5370.235888 6346.770029 5333.226307 4753.703906 1.248847035 1.208244486 1.348990429 1.277603623 1.401359538 1.19207982 1.129695074 1.335121024 1.121909654 1 12.21483633 -12.00955853 0.616493544 0.979016315 1.272061216 0.47576181 0.083695019 0.474714103 0.302052282 0.07436849 0.018027101 9.78E-13 12.00955853 0.293044901 AAES(ph)AEIEPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAESAEIEPR 10 0 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 0 AAES(1)AEIEPR 97.163 0.028142 7099400 1096.8 1271.1 949.11 812.49 1089.9 1142 1098 773.39 1207.8 1110.6 TRUE FALSE FALSE 1083.43178 1288.994579 965.6288614 906.4339167 1034.278336 1069.029886 1191.264093 795.7668194 1099.771343 1081.746452 1.001557969 1.191586602 0.892657295 0.83793565 0.956119 0.988244411 1.101241507 0.73563155 1.016662769 1 10.07914667 AAESET(ph)PGKSPEK ddPTM_HeLa_Romidepsin_16h_R1 1 AAESETPGKSPEK 13 1 J3QSV6;O76021-2;O76021 J3QSV6 RSL1D1 Ribosomal L1 domain-containing protein 1 1 0 AAES(0.046)ET(0.521)PGKS(0.432)PEK 133.04 0.008052 21503000 2276.8 2695.6 3042.4 1616.4 1500.1 1415.2 1465.7 678.79 2613.5 3057.8 TRUE FALSE FALSE 2249.049486 2733.548728 3095.351696 1803.295773 1423.544299 1324.773287 1590.196521 698.4297177 2379.742014 2978.357915 0.755130696 0.917803973 1.039281303 0.605466443 0.477962804 0.444799895 0.533917201 0.234501607 0.799011429 1 11.54030142 -9.026809458 3.346404847 0.894692776 0.435041745 0.814712167 0.107985522 0.088477545 2.045944623 0.018602917 0.033480914 9.40E-10 9.026809458 -0.459651031 AAFTTPDHAPLS(ph)PQSSVASSGSEQTEEQGSSR ddPTM_HeLa_Romidepsin_16h_R1 2 AAFTTPDHAPLSPQSSVASSGSEQTEEQGSSR 32 0 M0QZ22;Q5PRF9;A0A087WZT0;M0R0X3 M0QZ22 SAMD4B Protein Smaug homolog 2 1 0 AAFTTPDHAPLS(0.593)PQS(0.23)S(0.08)VAS(0.07)S(0.022)GS(0.002)EQT(0.001)EEQGSSR;AAFTTPDHAPLS(0.984)PQS(0.012)S(0.003)VASSGSEQTEEQGSSR ; 99.987 7.51E-13 55572000 3460.07 3360.93 3263.41 3432.65 5862.1 5676.7 5165.9 5601.2 3915.1 3861.4 TRUE FALSE FALSE 3417.897336 3408.245261 3320.208282 3829.549144 5562.935162 5313.977191 5604.691417 5763.261885 3564.92365 3761.080271 0.908754158 0.906187854 0.882780489 1.018204576 1.479079084 1.412885875 1.490181281 1.532342165 0.94784567 1 11.87693138 -8.796357959 4.514222826 0.946569458 1.478277055 0.973944755 0.042964811 0.026745889 1.227549652 0.007757623 0.014816485 1.60E-09 8.796357959 0.531707597 AAGARPLT(ph)SPESLSR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGARPLTSPESLSR 15 1 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 AAGARPLT(0.962)S(0.037)PES(0.001)LSR 134.4 0.006046 34560000 3370.2 3272.6 2965.6 3922.1 3685.4 4045.1 4128.7 4240.8 4208.8 3035.9 TRUE FALSE FALSE 3329.122706 3318.671749 3017.215024 4375.591656 3497.320286 3786.631165 4479.391675 4363.500857 3832.354387 2957.02688 1.125834441 1.122300163 1.020354277 1.47972671 1.182715081 1.280553515 1.514829542 1.475637873 1.29601608 1 11.52993164 -4 0.192117949 0.979685987 3.534490173 0.414393255 0.138668785 20.52265738 0.230760853 0.10755747 15.70600388 1.00E-04 4 2.554804186 AAGDGGSGPPEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AAGDGGSGPPEKK 13 1 H3BP71;O75150-3;O75150-4;O75150;H3BQ99;H3BUL6;I3L332 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 1 ; AAGDGGSGPPEK(1)K;AAGDGGSGPPEK(1)K 226.33 5.70E-31 31062000 3434.3 3127.7 3213.5 4952.1 5278 4716.7 5008.1 4321.7 3539.5 3266.5 FALSE TRUE FALSE 3392.441431 3171.731843 3269.42962 5524.685102 5008.643965 4415.318092 5433.487889 4446.741571 3222.918255 3181.635859 1.066256976 0.996887131 1.027593906 1.736429103 1.574235452 1.387750921 1.70776548 1.397627437 1.012975211 1 11.63555301 -9.273376187 24.93147545 1.028703526 1.560065388 0.866068151 0.106157293 170.9091257 356963.929 0.015086971 0.023155267 5.33E-10 9.273376187 0.531361862 AAGEPGTSMPPEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AAGEPGTSMPPEKK 14 1 C9J0A5;C9JXC9;Q5VTR2;C9JWJ4 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 0 1 ; AAGEPGTSMPPEK(1)K;AAGEPGTSMPPEK(1)K 163.71 5.02E-07 4178400 1793.2 2030.79 1714.66 1598.29 1793.92 1945.4 2089.04 2144.9 2022.2 1901.47 FALSE TRUE FALSE 1771.343789 2059.379515 1744.502938 1783.09181 1702.369568 1821.095218 2266.483005 2206.959297 1841.329367 1852.069535 0.95641322 1.111934231 0.941920865 0.962756406 0.919171519 0.983275835 1.223756971 1.191617947 0.994200991 1 10.85492255 -7.764328774 24.9844559 0.980507088 1.207687511 0.76587995 0.049508858 22.16424875 191662.152 0.006783106 0.021735447 1.72E-08 7.764328774 0.227180423 AAGGAPS(ph)PPPPVR ddPTM_HeLa_Romidepsin_16h_R1 3 AAGGAPSPPPPVR 13 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR;AAGGAPS(1)PPPPVR ;; 173.76 3.97E-05 225141700 9328.3 9205.7 8385.3 7711.5 12087.8 13798 11307.2 13086.4 9742.7 9014.1 TRUE FALSE FALSE 9214.603092 9335.298086 8531.242629 8603.139914 11470.91446 12916.35233 12267.63329 13465.03434 8871.288511 8779.912383 1.049509686 1.063256406 0.971677422 0.97986626 1.306495323 1.471125425 1.397238691 1.533618304 1.010407408 1 13.09999083 -8.602169915 3.307551556 1.020093873 1.455602482 0.957292268 0.04375286 0.034937108 0.76511592 0.006621141 0.014262267 2.50E-09 8.602169915 0.435508609 AAGIGK(ac)DFK ddPTM_HeLa_Romidepsin_16h_R1 2 AAGIGKDFK 9 1 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 1 ; AAGIGK(1)DFK;AAGIGK(1)DFK 126.07 0.0074684 1616220 1977.91 1877.16 2008.67 1318.75 1454.28 1474.09 1178.94 1530.04 2767.5 2095.8 FALSE TRUE FALSE 1953.802472 1903.586708 2043.630059 1471.23008 1380.062665 1379.900406 1279.079134 1574.309293 2519.967869 2041.350814 0.957112545 0.932513263 1.001116538 0.720713985 0.676053648 0.675974162 0.626584674 0.771209575 1.234460952 1 10.99530842 -9.212862088 4.804512802 0.976609244 0.6849738 0.762697015 0.090336226 0.037133085 1.950336855 0.005827925 0.009688775 6.13E-10 9.212862088 -0.291635444 AAGISLIVPGKS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGISLIVPGKSPTR 15 1 F2Z357;J3KPC5;P47736;P47736-3;P47736-4 F2Z357 RAP1GAP Rap1 GTPase-activating protein 1 1 0 AAGIS(0.135)LIVPGKS(0.795)PT(0.07)R 124.77 0.0010742 71636000 2645.4 2656.9 2499.9 2732.9 3790.8 3888.9 4359.1 4088 2564.6 2893.4 TRUE FALSE FALSE 2613.156847 2694.303908 2543.409711 3048.890757 3597.341331 3640.411841 4729.361845 4206.27983 2335.215753 2818.229051 0.927233663 0.956027299 0.902485094 1.08184633 1.276454563 1.291737391 1.678132529 1.492525893 0.828611057 1 11.46057316 -8.3633558 1.127411622 0.958628098 1.594999642 0.892451374 0.087436601 0.106441804 0.242369792 0.011641105 0.049656242 4.33E-09 8.3633558 0.636371545 AAGISLIVPGKSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AAGISLIVPGKSPTR 15 1 F2Z357;J3KPC5;P47736;P47736-3;P47736-4 F2Z357 RAP1GAP Rap1 GTPase-activating protein 1 1 0 AAGIS(0.001)LIVPGKS(0.233)PT(0.766)R 107.63 0.0028259 46299000 2424 2532.9 1921.8 2473.6 3914.3 3693.9 3475.9 3952.7 2430.5 2282.8 TRUE FALSE FALSE 2394.455356 2568.558233 1955.248123 2759.609271 3714.538665 3457.871712 3771.142859 4067.065138 2213.109993 2223.492527 1.07688932 1.155190855 0.879358981 1.241114705 1.670587429 1.555153287 1.696044765 1.829133711 0.995330529 1 11.11861184 -8.865118968 3.161159678 1.03725908 1.685645878 0.921117362 0.091969446 0.047202339 0.941991631 0.013440654 0.026019366 1.36E-09 8.865118968 0.648386799 AAGMS(ph)SPGAQSHPEELPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGMSSPGAQSHPEELPR 18 0 M0R300;M0R0P8;Q13459-2;Q13459;M0QZY4;M0R2J3 M0R300 MYO9B Unconventional myosin-IXb 1 0 AAGMS(0.5)S(0.5)PGAQSHPEELPR 93.029 0.0015356 12543000 2012.2 1852.5 2189.6 1669.8 3004.3 3547.2 2546.3 2915.6 1932 2100.4 TRUE FALSE FALSE 1987.674532 1878.579544 2227.70907 1862.870133 2850.97936 3320.545368 2762.582658 2999.958286 1759.197081 2045.831305 0.971573036 0.91824753 1.088901643 0.910568788 1.393555448 1.623078775 1.350347241 1.466376176 0.859893519 1 10.99847147 -8.694202911 5.318575291 0.984391109 1.471260796 0.886440033 0.087612746 0.040069708 2.133860041 0.010336275 0.020800923 2.02E-09 8.694202911 0.486869688 AAGMSS(ph)PGAQSHPEELPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAGMSSPGAQSHPEELPR 18 0 M0R300;M0R0P8;Q13459-2;Q13459;M0QZY4;M0R2J3 M0R300 MYO9B Unconventional myosin-IXb 1 0 AAGMS(0.274)S(0.723)PGAQS(0.003)HPEELPR 54.457 0.021294 14472000 1592.8 1628.9 1325.1 2134.3 2017.3 2746.8 2054.5 2208.8 1671.1 1366.3 TRUE FALSE FALSE 1573.386341 1651.831697 1348.16281 2381.077808 1914.349653 2571.288345 2229.009179 2272.708143 1521.632631 1330.803329 1.182283142 1.241229009 1.013044362 1.789203375 1.438491783 1.932132486 1.674935079 1.707771609 1.143394067 1 10.37808166 -9.261484815 24.99999656 1.097389669 1.704064588 0.831676019 0.133141566 1.198337876 659357.0314 0.020559333 0.032689839 5.48E-10 9.261484815 0.60667492 AAGS(ph)PSPLPAPDPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 AAGSPSPLPAPDPAPK 16 0 J3KRY8;Q9BZE9-3;Q9BZE9;Q9BZE9-2;J3KRF7 J3KRY8 ASPSCR1 Tether containing UBX domain for GLUT4 1 0 AAGS(0.788)PS(0.212)PLPAPDPAPK;AAGS(0.99)PS(0.01)PLPAPDPAPK ; 171.08 1.04E-05 27420000 9664.4 9557.1 8192.4 8620.3 10803.2 11865.7 10749 12745 9967.2 8510.1 TRUE FALSE FALSE 9546.606575 9691.645105 8334.985285 9617.019646 10251.87239 11107.52006 11662.01979 13113.75647 9075.708669 8289.006375 1.151719053 1.169216751 1.005546975 1.160213807 1.236803536 1.340030344 1.406926146 1.582066158 1.094909119 1 13.01698346 -4 0.31460619 1.046698387 6.225915986 0.898848458 0.055205944 11.87289458 0.151607488 0.02234317 35.66629579 1.00E-04 4 5.179217598 AAGSPS(ph)PLPAPDPAPK ddPTM_HeLa_Romidepsin_16h_R1 1 AAGSPSPLPAPDPAPK 16 0 J3KRY8;Q9BZE9-3;Q9BZE9;Q9BZE9-2;J3KRF7 J3KRY8 ASPSCR1 Tether containing UBX domain for GLUT4 1 0 AAGS(0.039)PS(0.961)PLPAPDPAPK 93.237 0.010172 5023800 3443.8 3871.3 3118.5 3513 3823 3414 3515.9 3723.4 4142.5 3263.5 TRUE FALSE FALSE 3401.825641 3925.800263 3172.776184 3919.189589 3627.898044 3195.856418 3814.540458 3831.130704 3771.984425 3178.7138 1.070189346 1.235027911 0.99813207 1.232948241 1.141310062 1.005392942 1.200026394 1.205245563 1.186638579 1 11.63422741 -10.93359573 0.692804706 1.006659669 1.144797921 0 0.099192779 0.522711273 0.560327703 0.028649787 0.020966091 1.17E-11 10.93359573 0.138138252 AAGSPSSSDQDEKLPGQDES(ph)TAGTSEQNDILK ddPTM_HeLa_Romidepsin_16h_R1 1 AAGSPSSSDQDEKLPGQDESTAGTSEQNDILK 32 1 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 1 0 AAGS(0.064)PS(0.068)S(0.064)S(0.064)DQDEKLPGQDES(0.353)T(0.353)AGT(0.024)S(0.012)EQNDILK 50.224 0.0046588 7657400 1800 1922.9 1759.4 2051.9 2055 2167.8 2228.2 2127.9 2262.7 2316.9 TRUE FALSE FALSE 1778.060908 1949.970637 1790.021619 2289.150332 1950.125682 2029.284576 2417.463252 2189.467429 2060.318445 2256.706604 0.787900786 0.864078048 0.79320086 1.014376582 0.864146752 0.899223928 1.071235068 0.970204733 0.912975768 1 11.14000315 -7.779657706 22.69668675 0.8932695 1.020719789 0.327572072 0.073757887 77.85276592 96991.70154 0.012890017 0.038827464 1.66E-08 7.779657706 0.127450288 AAHVPENS(ph)DTEQDVLTVKPVR ddPTM_HeLa_Romidepsin_16h_R1 2 AAHVPENSDTEQDVLTVKPVR 21 1 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BS99 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 AAHVPENS(0.985)DT(0.015)EQDVLTVKPVR;AAHVPENS(0.908)DT(0.092)EQDVLTVKPVR ; 95.094 0.00028775 34763000 7729.7 7482 6890.6 5850.8 7359.1 7747.1 7316.3 7608 8540.2 7743.2 TRUE FALSE FALSE 7635.487443 7587.331792 7010.528003 6527.297025 6983.537666 7252.085313 7937.746339 7828.125477 7776.343123 7542.030548 1.012391477 1.006006505 0.929527925 0.86545619 0.925949268 0.961556078 1.052468071 1.037933409 1.031067572 1 12.88073728 -9.791933743 23.05024778 1.006026689 0.960186486 0.182135616 0.051334388 132.9363991 100483.9342 0.009064886 0.011914907 1.61E-10 9.791933743 -0.045840202 AAIDWFDGKEFSGNPIK ddPTM_HeLa_Romidepsin_16h_R1 1 AAIDWFDGKEFSGNPIK 17 1 H3BPE7;P35637-2;P35637 H3BPE7 FUS RNA-binding protein FUS 0 0 92.575 0.0086736 10001000 1491.7 1435.2 1271.2 1846.9 1424.6 1209.3 1171.6 1270 1443.8 1154.5 FALSE FALSE TRUE 1473.518587 1455.404783 1293.324703 2060.447268 1351.897346 1132.029633 1271.115675 1306.745446 1314.662912 1124.505924 1.310369786 1.294261553 1.15012707 1.832313396 1.202214517 1.00669068 1.130377038 1.162061861 1.1691027 1 10.13507555 -5.742984914 16.05546125 1.195887168 1.216482934 0 0.22589298 0 0 0.031828765 0 1.81E-06 5.742984914 0.020595766 AAIPPPVYEEQDRPRSPTGPS(ph)NSFLANMGGTVAHK ddPTM_HeLa_Romidepsin_16h_R1 1 AAIPPPVYEEQDRPRSPTGPSNSFLANMGGTVAHK 35 2 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 0 AAIPPPVY(0.001)EEQDRPRS(0.109)PT(0.109)GPS(0.386)NS(0.386)FLANMGGT(0.007)VAHK 47.803 0.0040113 74652000 2252.8 1923.9 1534.8 2137 2375.5 2240.2 2020.1 1777 2366.8 1684.3 TRUE FALSE FALSE 2225.342007 1950.984715 1561.51255 2384.089995 2254.269371 2097.05845 2191.687244 1828.414691 2155.10748 1640.541643 1.356467857 1.189232058 0.951827439 1.453233452 1.37410067 1.278272002 1.335953435 1.114518914 1.313656065 1 10.6799565 -9.244755473 24.98504984 1.159746172 1.314253402 0.219903725 0.140200835 1146.147858 1716419.434 0.024890508 0.041207668 5.69E-10 9.244755473 0.15450723 AAK(ac)LQSSQEPEAPPPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAKLQSSQEPEAPPPR 16 1 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 0 1 AAK(1)LQSSQEPEAPPPR 134.21 1.19E-15 0 0 0 0 0 0 0 0 71.369 0 181.87 FALSE TRUE FALSE 0 0 0 0 0 0 0 73.43394941 0 177.1449912 0 0 0 0 0 0 0 0.414541495 0 1 7.468786863 -12.16594663 0.747620122 1.05331903 0.034719265 0 0.330610719 0.180267731 0.167984959 0.111300525 0.026259792 6.82E-13 12.16594663 -1.018599766 AAKLS(ph)EGSQPAEEEEDQETPSR ddPTM_HeLa_Romidepsin_16h_R1 2 AAKLSEGSQPAEEEEDQETPSR 22 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 AAKLS(0.998)EGS(0.002)QPAEEEEDQETPSR;AAKLS(0.971)EGS(0.029)QPAEEEEDQETPSR ; 124.1 2.92E-05 31222000 3264.6 3200.2 2822.1 3760.4 2450.5 2566.6 2230.67 2538.2 3898.2 2992.1 TRUE FALSE FALSE 3224.8098 3245.2525 2871.217467 4195.195141 2325.441841 2402.602543 2420.143054 2611.638812 3549.535229 2914.364811 1.10652235 1.113536812 0.985194941 1.439488675 0.797924073 0.824400066 0.830418706 0.896126251 1.217944718 1 11.50896577 AAKPGPAEAPS(ph)PTASPSGDAS(ph)PPATAPYDPR ddPTM_HeLa_Romidepsin_16h_R1 1 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 0 AAKPGPAEAPS(0.78)PT(0.224)AS(0.056)PS(0.051)GDAS(0.782)PPAT(0.101)APY(0.006)DPR 60.62 0.0018507 11489000 985.07 1054.2 1352.4 917.23 1113.4 1117.7 718.28 979.72 1219.4 1257.9 TRUE FALSE FALSE 973.0635879 1069.041055 1375.937955 1023.284448 1056.579043 1046.282577 779.2906853 1008.066652 1110.33381 1225.219577 0.794195266 0.872530178 1.123013361 0.83518454 0.86235893 0.853955158 0.636041653 0.822764076 0.906232508 1 10.25882461 -7.94367763 5.537846322 0.906228725 0.729528443 0.357856929 0.096982812 0.179728422 11.48272581 0.015285399 0.047051844 1.14E-08 7.94367763 -0.176700283 AAKPGPAEAPSPT(ph)ASPSGDASPPATAPYDPR ddPTM_HeLa_Romidepsin_16h_R1 4 AAKPGPAEAPSPTASPSGDASPPATAPYDPR 31 1 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 0 AAKPGPAEAPS(0.163)PT(0.817)AS(0.006)PS(0.013)GDAS(0.001)PPATAPYDPR;AAKPGPAEAPS(0.044)PT(0.94)AS(0.017)PSGDASPPATAPYDPR;AAKPGPAEAPS(0.063)PT(0.687)AS(0.232)PS(0.007)GDAS(0.008)PPAT(0.001)APY(0.001)DPR;AAKPGPAEAPS(0.006)PT(0.319)AS(0.319)PS(0.101)GDAS(0.245)PPAT(0.008)APY(0.001)DPR ;;; 104.83 7.11E-13 165468000 7666.4 7890.5 7066.3 8359.5 6334.3 5784.24 4819.96 4797.12 8185.8 7057.4 TRUE FALSE FALSE 7572.958968 8001.582666 7189.285987 9326.064723 6011.037034 5414.645732 5229.367282 4935.917099 7453.641546 6874.047731 1.101673899 1.164027801 1.045859189 1.356706425 0.874453782 0.787693939 0.760740613 0.718051037 1.084316234 1 12.74694415 -8.534357816 24.97407582 1.079419171 0.768528719 0.743403655 0.097455492 93.65180531 203750.1358 0.014902771 0.029824498 2.92E-09 8.534357816 -0.310890452 AALAPAKES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 AALAPAKESPR 11 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;H0YAB7;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 AALAPAKES(1)PR;AALAPAKES(1)PR;AALAPAKES(1)PR ;; 110.8 0.0052474 1018510000 22757.9 24144.1 22815.2 21615.4 19686.9 15344.7 14641.3 13538.3 26631.6 24314.8 TRUE FALSE FALSE 22480.51796 24484.00127 23212.28899 24114.67425 18682.20403 14364.22319 15884.93166 13930.00935 24249.603 23683.09799 0.949222014 1.033817505 0.980120464 1.018222965 0.788841225 0.606517914 0.670728621 0.58818358 1.023920224 1 14.53157019 -8.539508571 3.000044157 0.983282964 0.628097095 0.959079712 0.03519898 0.035454289 0.6503358 0.005097663 0.011569373 2.89E-09 8.539508571 -0.35518587 AALAPAKESPR ddPTM_HeLa_Romidepsin_16h_R1 1 AALAPAKESPR 11 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;H0YAB7;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 0 0 104.42 0.019509 5605500 2001.4 1910.8 2044.6 2288 1913.4 1795.6 1339.7 1351.7 1898.1 2295.4 FALSE FALSE TRUE 1977.006167 1937.700293 2080.185405 2552.549325 1815.752058 1680.866955 1453.494085 1390.809307 1728.329182 2235.765177 0.88426378 0.866683278 0.930413188 1.141689365 0.812138983 0.751808362 0.650110351 0.62207307 0.77303699 1 11.12655295 -8.243827091 2.119193854 0.948245745 0.645059851 0.588604901 0.095984689 0.136570058 1.177919333 0.01229636 0.038098769 5.70E-09 8.243827091 -0.303185894 AALDGGVASAAS(ph)PESKPSPGTK ddPTM_HeLa_Romidepsin_16h_R1 1 AALDGGVASAASPESKPSPGTK 22 1 A0A494C1M5;A0A0J9YWL0;Q9Y4K1 A0A494C1M5 AIM1 Absent in melanoma 1 protein 1 0 AALDGGVAS(0.005)AAS(0.972)PES(0.022)KPS(0.001)PGTK 88.471 0.00025292 13523000 3795.4 3712 3778.8 3865.7 3772.9 3448.1 2482.1 2665.2 4055 3679.4 TRUE FALSE FALSE 3749.140205 3764.257633 3844.568429 4312.670423 3580.354834 3227.777538 2692.929512 2742.313357 3692.310644 3583.808658 1.046132917 1.050351175 1.072760517 1.203376306 0.99903627 0.900655656 0.751415538 0.765195249 1.030275608 1 11.8072779 -8.025478694 2.323955908 1.041433888 0.755043242 0.824044075 0.055611946 0.103940942 1.092322549 0.008943115 0.032462042 9.43E-09 8.025478694 -0.286390646 AALLELWELRR ddPTM_HeLa_Romidepsin_16h_R1 2 AALLELWELRR 11 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 ; ; 160.53 0.00084637 14544300 3964.2 3398.2 3937.9 2311.3 3818.5 3924.3 2864.9 3244.8 3737.4 2640 FALSE FALSE TRUE 3915.882806 3446.039949 4006.437498 2578.543381 3623.627696 3673.549895 3108.244534 3338.683169 3403.117584 2571.412419 1.522852879 1.340135065 1.558068814 1.002773169 1.4091974 1.428611711 1.208769356 1.298384943 1.323442929 1 11.3283453 -12.49756114 1.247855073 1.000282286 1.361696375 0.032809892 0.179385325 0.344544085 0.961303801 0.105609969 0.025729895 3.18E-13 12.49756114 0.361414089 AALLNQHYQVNFK ddPTM_HeLa_Romidepsin_16h_R1 2 AALLNQHYQVNFK 13 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 0 ; ; 120.77 0.0005872 1364580 735.06 631.79 715.95 663.39 806.37 960.27 530.55 858.09 1041.84 614.7 FALSE FALSE TRUE 726.100806 640.6843562 728.4108094 740.0942731 765.2179299 898.9118461 575.6149038 882.9174803 948.6552211 598.7300054 1.212734955 1.070072237 1.216593127 1.23610687 1.27806845 1.501364284 0.961393113 1.474650464 1.584445764 1 9.225761763 -16.52287874 0.108606155 0.161454753 1.404827748 0 0.232804637 88.64327602 0.708859099 16.51470257 0.884422993 3.00E-17 16.52287874 1.243372995 AALQELLS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AALQELLSK 9 0 P62851 P62851 RPS25 40S ribosomal protein S25 1 0 AALQELLS(1)K 115.29 0.016138 6719000 1291.9 1266.2 1263.9 753.32 1133.6 1341.4 1414.8 1453.5 1447 1308 TRUE FALSE FALSE 1276.153826 1284.025597 1285.897649 840.4224029 1075.748162 1255.688869 1534.973077 1495.554729 1317.576696 1274.017971 1.001676471 1.007855168 1.009324576 0.65966291 0.844374401 0.985613152 1.204828433 1.173888252 1.034190039 1 10.31516991 -7.786037245 6.535638363 0.965207292 1.190203401 0.438038569 0.109445074 0.119862152 17.79977839 0.01640932 0.052637547 1.64E-08 7.786037245 0.224996109 AALQTAPESADDS(ph)PSQLSK ddPTM_HeLa_Romidepsin_16h_R1 2 AALQTAPESADDSPSQLSK 19 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 0 AALQTAPESADDS(0.996)PS(0.004)QLSK;AALQTAPES(0.002)ADDS(0.928)PS(0.049)QLS(0.021)K ; 192.62 2.44E-20 7271400 4415.9 4332.5 3881.3 4909.1 3720.4 3286.5 2623.52 2984.6 4628.9 4085.2 TRUE FALSE FALSE 4362.077312 4393.493049 3948.852398 5476.71324 3530.534105 3076.503257 2846.361723 3070.954692 4214.879591 3979.065915 1.09625661 1.104151864 0.992406882 1.376381632 0.88727711 0.773172227 0.715334147 0.771777788 1.059263576 1 11.95821408 -8.529604628 24.99862029 1.070233161 0.763052955 0.694859796 0.104460591 75.06562883 279001.9889 0.015175128 0.030407507 2.95E-09 8.529604628 -0.307180205 AALRPLVK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AALRPLVKPK 10 2 D3YTB1;F8W727;P62910;D3YTI8 D3YTB1 RPL32 60S ribosomal protein L32 0 1 AALRPLVK(1)PK 81.525 0.021676 0 398.19 569.91 446.72 385.77 958.23 835.42 591.56 827.38 988.1 892.97 FALSE TRUE FALSE 393.3367071 577.9332079 454.4949742 430.3745425 909.3279475 782.0393582 641.8070916 851.3189349 899.7218613 869.7705107 0.452230447 0.664466317 0.522545854 0.494813905 1.045480315 0.899132988 0.737903946 0.978785696 1.034435923 1 9.764490985 -8.751678022 24.99989818 0.695263295 0.901496091 0.228621293 0.197838444 310.2527506 794585.6071 0.034351011 0.068031581 1.77E-09 8.751678022 0.206232796 AALSS(ph)SELLELGDSLMR ddPTM_HeLa_Romidepsin_16h_R1 1 AALSSSELLELGDSLMR 17 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 0 AALS(0.123)S(0.672)S(0.165)ELLELGDS(0.04)LMR 81.128 0.024287 6170900 1574.1 1822.9 1520.4 1552.1 1482.3 1393.5 1142.9 1838.9 1643.2 1535.8 TRUE FALSE FALSE 1554.914264 1848.562834 1546.861924 1731.561105 1406.6527 1304.459847 1239.977897 1892.10567 1496.228077 1495.899695 1.039450887 1.2357532 1.034067946 1.157538243 0.940338918 0.872023607 0.828917809 1.264861325 1.000219521 1 10.54679773 AAMYDIIS(ph)SPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AAMYDIISSPSK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 AAMYDIIS(0.704)S(0.296)PSK 120.86 0.0099933 10289000 4206.1 3798.3 4946.6 2216.8 2626.9 2577.2 2009.9 2245.6 4603.3 4212.1 TRUE FALSE FALSE 4154.834435 3851.772567 5032.693498 2473.116846 2492.839491 2412.525238 2180.620856 2310.572893 4191.569319 4102.669035 1.012714991 0.93884555 1.226687665 0.602806813 0.607614085 0.588037986 0.531512739 0.563187738 1.02166889 1 12.00234706 -9.197464003 8.59486487 1.014990607 0.57708369 0.906142772 0.074026021 0.079001234 10.02479653 0.010266773 0.017042238 6.35E-10 9.197464003 -0.437906917 AAMYDIIS(ph)SPSKDSTK ddPTM_HeLa_Romidepsin_16h_R1 2 AAMYDIISSPSKDSTK 16 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 AAMYDIIS(0.462)S(0.462)PS(0.076)KDSTK;AAMYDIIS(0.923)S(0.066)PS(0.011)KDSTK ; 206.63 2.50E-18 110525000 15776.6 15344.9 14461.7 11501.5 9214 7683.2 6390.5 7073.2 16112.5 14279.3 TRUE FALSE FALSE 15584.30873 15560.9259 14713.39982 12831.35755 8743.775198 7192.268316 6933.30891 7277.851882 14671.35765 13908.32173 1.120502461 1.11882125 1.057884633 0.922566921 0.628672198 0.517119783 0.498500757 0.52327319 1.054861825 1 13.76366072 -8.781685323 2.0409858 1.064399406 0.509891565 0.982824857 0.033364758 0.0416736 0.353686869 0.007799414 0.017002309 1.65E-09 8.781685323 -0.554507841 AAMYDIISS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 AAMYDIISSPSK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 AAMYDIIS(0.187)S(0.812)PSK 126.12 0.0074312 13259000 3834.1 4187.8 4745.5 1646.8 2507.8 2046 1541.7 1627.1 3527.5 3696.1 TRUE FALSE FALSE 3787.368514 4246.755958 4828.093437 1837.210764 2379.817608 1915.267203 1672.65196 1674.177571 3211.991565 3600.074789 1.052024954 1.179629926 1.341109205 0.510325722 0.661046714 0.532007615 0.464615892 0.465039664 0.892201344 1 11.81381116 -9.242782128 24.95201775 1.060870373 0.53093201 0.840702383 0.122868063 240.1388527 321159.4879 0.018158077 0.030076642 5.72E-10 9.242782128 -0.529938363 AANGS(ph)S(ph)ERGGAVSTPDY(ph)GEKK ddPTM_HeLa_Romidepsin_16h_R1 1 AANGSSERGGAVSTPDYGEKK 21 2 Q9Y661 Q9Y661 HS3ST4 Heparan sulfate glucosamine 3-O-sulfotransferase 4 3 0 AANGS(0.969)S(0.969)ERGGAVS(0.069)T(0.189)PDY(0.804)GEKK 40.689 0.029318 2299500 1481.3 1250 1239.5 1032.1 1128.9 1237.9 1114.2 1508.6 1491.2 1793.9 TRUE FALSE FALSE 1463.245346 1267.597533 1261.072978 1151.436258 1071.28802 1158.802185 1208.84012 1552.248961 1357.823337 1747.294219 0.837435006 0.72546313 0.721729039 0.658982469 0.613112553 0.663198088 0.691835472 0.888372973 0.777100572 1 10.77090684 -10.85174452 0.728698307 0.975844128 0.692405589 0.303444863 0.094708143 0.227171678 0.266549064 0.024747354 0.019613763 1.41E-11 10.85174452 -0.283438539 AANGVVLATEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AANGVVLATEKK 12 1 A0A024RA52;P25787 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 1 AANGVVLATEK(1)K 169.52 0.00017516 694410 382.49 403.41 469.76 310.74 721.54 738.27 590.41 499.41 771.44 506.9 FALSE TRUE FALSE 377.8280648 409.0892166 477.9359757 346.6692209 684.7171214 691.0969297 640.5594107 513.8596404 702.4404743 493.7306649 0.765251364 0.828567569 0.968009503 0.702142373 1.386823161 1.399744798 1.29738632 1.040769142 1.422719965 1 8.947580441 -8.754799881 24.99999341 0.876401246 1.29080729 0.343464731 0.212318252 69.17455237 260463.5854 0.01996547 0.039204353 1.76E-09 8.754799881 0.414406044 AANMLQQS(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 AANMLQQSGSK 11 0 P46063 P46063 RECQL ATP-dependent DNA helicase Q1 1 0 AANMLQQS(0.991)GS(0.009)K;AANMLQQS(0.998)GS(0.002)K ; 110.64 0.019676 10874100 9346.7 7871 8290 7177.9 9463.9 10162.3 7446.8 8572.9 8604.9 8476.6 TRUE FALSE FALSE 9232.778825 7981.808145 8434.283973 8007.842571 8980.921868 9512.961827 8079.331006 8820.943336 7835.256193 8256.37671 1.118260364 0.966744666 1.021547862 0.969897917 1.087755826 1.15219571 0.978556489 1.068379465 0.948994513 1 13.01129308 -6.870417506 18.80514969 1.046836451 6.959170318 0 0.068759683 2217.125907 323716.6549 0.009091754 3451.888815 1.35E-07 6.870417506 5.912333867 AANQVEETLHTHLPQT(ph)PETNFR ddPTM_HeLa_Romidepsin_16h_R1 1 AANQVEETLHTHLPQTPETNFR 22 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 0 AANQVEET(0.017)LHT(0.212)HLPQT(0.739)PET(0.032)NFR 80.191 0.00052545 4416200 1500 1415 1617.9 1478.2 1714.9 1710.3 1393.1 2014.7 1757.4 1296.8 TRUE FALSE FALSE 1481.717423 1434.920407 1646.058871 1649.116439 1627.382254 1601.01735 1511.429879 2072.992166 1600.213743 1263.108949 1.173071748 1.136022675 1.303180436 1.305601105 1.288394208 1.267521183 1.196595021 1.641182392 1.26688497 1 10.30276337 -4 0.084329685 0.765586489 2.576319499 0.330840312 0.127950456 72.27450582 0.445591061 1.392300071 15.26599992 1.00E-04 4 1.81073301 AAPEAS(ph)GTPSSDAVSR ddPTM_HeLa_Romidepsin_16h_R1 2 AAPEASGTPSSDAVSR 16 0 P31146 P31146 CORO1A Coronin-1A 1 0 AAPEAS(0.596)GT(0.403)PSSDAVSR;AAPEAS(0.524)GT(0.216)PS(0.216)S(0.043)DAVSR ; 158.65 0.00016816 8135200 1625.53 1636.3 1961.93 810.65 1987 2138.7 2834.7 2220.42 1723.34 1544.74 TRUE FALSE FALSE 1605.717415 1659.335874 1996.076569 904.3811672 1885.595975 2002.043972 3075.479347 2284.664349 1569.200154 1504.607432 1.067200242 1.10283642 1.326642768 0.601074505 1.253214583 1.330608855 2.044041045 1.518445477 1.04292995 1 10.55517141 -8.060267236 2.552522148 1.038292584 1.776464086 0.623532632 0.220540798 0.117596648 1.491056399 0.028289831 0.094600816 8.70E-09 8.060267236 0.738171502 AAPEAS(ph)SPPAS(ph)PLQHLLPGK ddPTM_HeLa_Romidepsin_16h_R1 2 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 2 0 AAPEAS(0.5)S(0.5)PPAS(1)PLQHLLPGK;AAPEAS(0.603)S(0.398)PPAS(0.999)PLQHLLPGK ; 106.58 0.002053 167878000 21690.9 20195.6 20377.7 20208.5 27422 29223.7 23837.4 28972.5 23737.9 21950.9 TRUE FALSE FALSE 21426.52297 20479.91419 20732.36532 22545.10185 26022.55301 27356.39989 25862.14816 29810.77358 21614.72277 21380.61245 1.002147296 0.957873131 0.96968061 1.054464735 1.217109803 1.279495615 1.209607452 1.394289974 1.010949654 1 14.38401556 -8.732792296 2.192537261 0.994719011 1.286722216 0.904375653 0.044854745 0.061379773 0.601139002 0.006268067 0.013767376 1.85E-09 8.732792296 0.292003205 AAPEAS(ph)SPPASPLQHLLPGK ddPTM_HeLa_Romidepsin_16h_R1 2 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 1 0 AAPEAS(0.843)S(0.139)PPAS(0.018)PLQHLLPGK;AAPEAS(0.574)S(0.424)PPAS(0.002)PLQHLLPGK ; 90.464 0.00068241 430801000 5082.7 4974.8 4707.3 4796.9 9290.5 9575.4 7704.3 9475.6 7948.8 6242.1 TRUE FALSE FALSE 5020.750097 5044.835365 4789.228582 5351.540148 8816.371117 8963.562843 8358.70305 9749.761536 7237.83942 6079.929342 0.825790863 0.829752302 0.787711224 0.880197753 1.450077891 1.474287338 1.374802663 1.603597836 1.19044795 1 12.56983884 -8.755510345 9.129047502 0.895185232 1.469058091 0.834909363 0.120986916 0.028091521 23.92116007 0.013839561 0.026676523 1.76E-09 8.755510345 0.573872859 AAPEASS(ph)PPAS(ph)PLQHLLPGK ddPTM_HeLa_Romidepsin_16h_R1 1 AAPEASSPPASPLQHLLPGK 20 0 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 2 0 AAPEAS(0.398)S(0.602)PPAS(1)PLQHLLPGK 105.72 0.0021785 80464000 12805 13024 12908 13021 17357 18802 16558 18079 14533 13819 TRUE FALSE FALSE 12648.92773 13207.35221 13132.65833 14526.54929 16471.20752 17600.61288 17964.43611 18602.08734 13233.13208 13459.98039 0.9397434 0.981231163 0.975681832 1.079240004 1.223717052 1.307625448 1.334655444 1.382029305 0.983146461 1 13.71638869 -8.690333802 1.33699546 0.969910305 1.357354391 0.986395264 0.019096788 0.043036808 0.152498629 0.00404956 0.011154024 2.04E-09 8.690333802 0.387444086 TVVVEAGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TVVVEAGKK 9 1 O94842-3;O94842-2;O94842 O94842-3 TOX4 TOX high mobility group box family member 4 0 1 ; TVVVEAGK(1)K;TVVVEAGK(1)K 156.92 0.0021745 10072300 7453.3 7108.2 9986.3 14218 19731.9 20592.5 18977.3 14588.3 8352.5 5251.9 FALSE TRUE FALSE 7362.456313 7208.269426 10160.10736 15861.95206 18724.90751 19276.70571 20589.23139 15010.38944 7605.431481 5115.454881 1.439257404 1.409116021 1.98615912 3.10079014 3.660457955 3.768326798 4.02490724 2.93432154 1.486755657 1 12.32064682 -9.336747753 1.528254778 1.207655756 3.66639689 0.926307368 0.293413822 0.063503962 0.291101983 0.048034754 0.08555787 4.61E-10 9.336747753 2.458741134 up AAPGAEFAPNKR ddPTM_HeLa_Romidepsin_16h_R1 1 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 0 87.667 0.020747 5114300 1843.3 1789.6 1816.6 1566.6 2155.7 1882 1692 1349.9 1954 1935.4 FALSE FALSE TRUE 1820.833151 1814.794036 1848.217161 1747.737663 2045.686585 1761.746274 1835.718438 1388.957227 1779.229346 1885.118029 0.965898751 0.962695178 0.980425168 0.927123732 1.085176924 0.934554891 0.973794961 0.7368012 0.94382915 1 10.88043914 -7.256724914 4.887866436 0.981554908 0.723077625 0.734627545 0.042766718 0.061175792 4.278302077 0.005207088 0.053445899 5.54E-08 7.256724914 -0.258477283 AAPPPPPPPPPLES(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 4 AAPPPPPPPPPLESSPR 17 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 AAPPPPPPPPPLES(0.5)S(0.5)PR;AAPPPPPPPPPLES(0.5)S(0.5)PR;AAPPPPPPPPPLES(0.5)S(0.5)PR;AAPPPPPPPPPLES(0.5)S(0.5)PR ;;; 181.81 4.49E-09 107229000 1157.51 1474.68 1404.73 1404.44 1298.56 1049.6 1241.64 1404.52 1342.4 1312.3 TRUE FALSE FALSE 1143.401823 1495.440584 1429.178736 1566.827961 1232.289638 982.5339474 1347.104871 1445.15757 1222.332382 1278.206257 0.894536243 1.169952483 1.118112768 1.225802137 0.964077301 0.768681848 1.053902579 1.130613751 0.956287278 1 10.31990494 -10.28403436 24.84554689 0.950197672 1.054769447 0.14796284 0.121643555 1188.834221 1307243.785 0.022614345 0.025870423 5.20E-11 10.28403436 0.104571775 AAPQS(ph)PSVPK ddPTM_HeLa_Romidepsin_16h_R1 3 AAPQSPSVPK 10 0 E9PF10;O75694-2;O75694 E9PF10 NUP155 Nuclear pore complex protein Nup155 1 0 AAPQS(0.671)PS(0.329)VPK;AAPQS(0.779)PS(0.221)VPK;AAPQS(0.541)PS(0.459)VPK ;; 135.1 0.0058365 558891000 23470.1 23113.5 22436 17865.9 25695.3 25415.2 23427.4 24593.1 24085.7 22241.7 TRUE FALSE FALSE 23184.03739 23438.89246 22826.48917 19931.63942 24383.97296 23791.25074 25417.32277 25304.66255 21931.41467 21663.85743 1.07017125 1.081935317 1.053666885 0.920041109 1.125560074 1.098200116 1.173259326 1.168058949 1.012350397 1 14.40300253 -8.282176945 1.944789973 1.033319015 1.162751236 0.55279816 0.049720339 0.208556345 1.508009144 0.007597014 0.023765315 5.22E-09 8.282176945 0.129432221 AAPQSPS(ph)VPK ddPTM_HeLa_Romidepsin_16h_R1 1 AAPQSPSVPK 10 0 E9PF10;O75694-2;O75694 E9PF10 NUP155 Nuclear pore complex protein Nup155 1 0 AAPQS(0.172)PS(0.828)VPK 134.38 0.0059797 508620000 10755 10750 10050 8043.4 11323 11196 10609 10823 10408 9247.8 TRUE FALSE FALSE 10623.91392 10901.33878 10224.91603 8973.415753 10745.14506 10480.61173 11510.1282 11136.14643 9477.082413 9007.540823 1.179446658 1.210245837 1.135150674 0.9962115 1.192905508 1.163537523 1.277832476 1.236313734 1.052127612 1 13.13691757 -16.52287875 0.186293502 0.23417257 1.213685579 0.425133362 0.070290567 37.20215952 0.435277581 10.36004815 0.09308436 3.00E-17 16.52287875 0.979513009 AAPSTAPAEAT(ph)PPKPGEAEAPPK ddPTM_HeLa_Romidepsin_16h_R1 2 AAPSTAPAEATPPKPGEAEAPPK 23 1 O95817 O95817 BAG3 BAG family molecular chaperone regulator 3 1 0 AAPS(0.01)T(0.036)APAEAT(0.954)PPKPGEAEAPPK;AAPS(0.005)T(0.004)APAEAT(0.991)PPKPGEAEAPPK ; 100.01 1.96E-05 107457000 7404.3 5920 8082.8 5511.3 6135.3 6804.2 5202.7 6115.5 7004.1 7378 TRUE FALSE FALSE 7314.053544 6003.341915 8223.477743 6148.542437 5822.192747 6369.43358 5644.617208 6292.442344 6377.635754 7186.318496 1.017774755 0.835384894 1.144324141 0.855590027 0.810177388 0.886327761 0.785467164 0.875614175 0.88746912 1 12.81103716 -9.083161487 11.13009407 1.002125117 0.838144827 0.38036423 0.0828864 0.370296687 48.47763585 0.01008531 0.016733459 8.26E-10 9.083161487 -0.16398029 AAPSTAPAEAT(ph)PPKPGEAEAPPKHPGVLK ddPTM_HeLa_Romidepsin_16h_R1 1 AAPSTAPAEATPPKPGEAEAPPKHPGVLK 29 2 O95817 O95817 BAG3 BAG family molecular chaperone regulator 3 1 0 AAPS(0.068)T(0.183)APAEAT(0.749)PPKPGEAEAPPKHPGVLK 57.738 0.00072018 30447000 4987.5 5178.3 4694 5568.8 4396.3 4121.9 3854.7 3913 4897.3 5019.8 TRUE FALSE FALSE 4926.710432 5251.200243 4775.697101 6212.690858 4171.940406 3858.523893 4182.118122 4026.216481 4459.273222 4889.384872 1.007633999 1.074000182 0.976748042 1.270648767 0.853264882 0.789163462 0.855346476 0.823460739 0.912031542 1 12.25543726 -8.554361576 24.99976593 1.025525329 0.825140321 0.565132569 0.089931409 97.90169566 77741.04838 0.011391697 0.022783549 2.79E-09 8.554361576 -0.200385008 AAQASDLEK(ac)IHLDEK ddPTM_HeLa_Romidepsin_16h_R1 1 AAQASDLEKIHLDEK 15 1 P37837 P37837 TALDO1 Transaldolase 0 1 AAQASDLEK(1)IHLDEK 101.2 0.015168 642110 262.74 134.07 145.41 146.55 195.86 212.09 303.72 193.3 303.87 329.99 FALSE TRUE FALSE 259.5376238 135.957441 147.9408001 163.4948005 185.8645333 198.5381335 329.5179692 198.8928305 276.6911061 321.4168122 0.807479926 0.42299418 0.460277106 0.5086691 0.57826637 0.617696791 1.025204522 0.618800333 0.860848268 1 8.328301583 -10.67813894 2.074735655 0.933736045 0.612677746 0.386272562 0.162673578 0.214401058 1.926671824 0.034966903 0.035433362 2.10E-11 10.67813894 -0.321058299 AAQDRDQIYR ddPTM_HeLa_Romidepsin_16h_R1 1 AAQDRDQIYR 10 1 P62995;H7C2L4;P62995-3 P62995 TRA2B Transformer-2 protein homolog beta 0 0 122.94 0.00073194 0 2321.5 2513.4 2508.5 2150.6 2629.9 2751.6 2342.7 2122 2407.1 2350.1 FALSE FALSE TRUE 2293.204665 2548.783711 2552.15939 2399.262491 2495.686389 2575.78164 2541.68888 2183.396722 2191.802947 2289.044063 1.001817615 1.113470794 1.114945506 1.048150418 1.090274508 1.125265206 1.110371321 0.953846524 0.957518897 1 11.16052952 -10.27640687 23.39428315 1.00085831 1.082999221 0.418037733 0.049307685 240.138821 375337.3658 0.007664576 0.008787299 5.29E-11 10.27640687 0.08214091 AAQEEYVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AAQEEYVKR 9 1 H3BQN4;J3KPS3;P04075;P04075-2;H3BR68 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 1 ; AAQEEYVK(1)R;AAQEEYVK(1)R 136.99 0.0032634 31193000 6161.3 5880.5 7034.3 4629.5 15789.6 14379.5 16289.3 7279.2 16899 11133.2 FALSE TRUE FALSE 6086.203706 5963.285833 7156.729041 5164.784572 14983.79779 13460.69636 17672.91274 7489.812167 15387.51112 10843.95786 0.561252984 0.549917835 0.659973889 0.476282243 1.381764664 1.241308435 1.629747456 0.6906899 1.418993998 1 13.40460379 -8.751761332 24.99876972 0.736895148 1.264399163 0.298792919 0.339272692 143.4027776 370412.3311 0.04083569 0.080853304 1.77E-09 8.751761332 0.527504015 AAQK(ac)TLLVSTSAVDNNEAQK ddPTM_HeLa_Romidepsin_16h_R1 1 AAQKTLLVSTSAVDNNEAQK 20 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 0 1 AAQK(1)TLLVSTSAVDNNEAQK 124.73 6.25E-06 660880 0 150.83 0 135.31 120.63 122.42 0 175.12 73.518 0 FALSE TRUE FALSE 0 152.9533887 0 150.9551789 114.473801 114.5977571 0 180.1868209 66.94236595 0 0 AAQK(ac)TLLVSTSAVDNNEAQKK ddPTM_HeLa_Romidepsin_16h_R1 2 AAQKTLLVSTSAVDNNEAQKK 21 2 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 0 1 ; AAQK(1)TLLVSTSAVDNNEAQKK;AAQK(1)TLLVSTSAVDNNEAQKK 211.11 1.78E-41 3844400 828.5 1025.4 710.99 636.58 599.88 342.12 473.85 541.78 1159.92 700.68 FALSE TRUE FALSE 818.4019233 1039.835608 723.3644827 710.1843748 569.2658851 320.2596361 514.0988072 557.4555495 1056.17385 682.4762326 1.199165457 1.523621715 1.05991161 1.040599424 0.834118256 0.46926123 0.753284558 0.816813133 1.547561365 1 9.414634994 -8.726596409 2.624446257 1.130362192 0.682928209 0.578244314 0.207060778 0.151201581 2.123986522 0.026369398 0.055866278 1.88E-09 8.726596409 -0.447433983 AAQQAASSSGQGQQAQT(ph)PTGK ddPTM_HeLa_Romidepsin_16h_R1 4 AAQQAASSSGQGQQAQTPTGK 21 0 H0Y9X2;U3KQK7;U3KPX3;A0A590UJ43;P48729;P48729-2 H0Y9X2 CSNK1A1 Casein kinase I isoform alpha 1 0 AAQQAASSSGQGQQAQT(0.998)PT(0.002)GK;AAQQAASSSGQGQQAQT(0.999)PT(0.001)GK;AAQQAASSSGQGQQAQT(0.955)PT(0.045)GK;AAQQAASSS(0.013)GQGQQAQT(0.978)PT(0.009)GK ;;; 179.78 6.60E-13 9739900 3420.97 3174.57 3144.16 3738.42 4152.14 4917 3970.65 4541.72 3558.56 3285.27 TRUE FALSE FALSE 3379.273902 3219.26168 3198.882786 4170.67371 3940.240802 4602.819569 4307.916912 4673.127503 3240.273481 3199.918212 1.056050086 1.006044988 0.999676421 1.303368847 1.231356723 1.43841788 1.346258444 1.46038967 1.012611344 1 11.64381932 -8.956122609 1.313102605 1.021081522 1.403762153 0.887734869 0.060789452 0.093347116 0.320242103 0.009303362 0.021358679 1.11E-09 8.956122609 0.382680631 AAQQQQPSAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 AAQQQQPSASPR 12 0 Q86U86-8;Q86U86 Q86U86-8 PBRM1 Protein polybromo-1 1 0 AAQQQQPSAS(1)PR;AAQQQQPSAS(1)PR;AAQQQQPS(0.001)AS(0.999)PR ;; 212.1 5.05E-21 26837000 3550.67 3288.38 3447.16 3545.72 3029.65 3002.57 2747.08 2121.91 3969.73 3914.1 TRUE FALSE FALSE 3507.393068 3334.6739 3507.156374 3955.69283 2875.035655 2810.715467 2980.416907 2183.304118 3614.667406 3812.411118 0.9199934 0.874688956 0.919931315 1.037582965 0.754125294 0.737254032 0.781766922 0.572683284 0.948131588 1 11.89648799 -6.374603046 0.372785005 0.973009748 1.42E-11 0.744251447 0.068030922 3.871286093 0.226357165 0.019495864 1.939350748 4.22E-07 6.374603046 -0.973009748 SGSS(ph)QELDVKPSASPQER ddPTM_HeLa_Romidepsin_16h_R1 2 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.144)GS(0.208)S(0.436)QELDVKPS(0.21)AS(0.002)PQER;S(0.001)GS(0.071)S(0.497)QELDVKPS(0.407)AS(0.024)PQER ; 171.85 1.44E-06 15628100 4739.4 4657.8 3787 2628.7 2157.41 2313.6 1933.12 2553.3 5436.2 5510.9 TRUE FALSE FALSE 4681.63437 4723.372631 3852.911146 2932.642662 2047.309317 2165.768427 2097.319165 2627.175707 4949.972657 5367.726024 0.872182065 0.879957846 0.717792065 0.546347308 0.381410919 0.403479689 0.390727685 0.489439233 0.92217312 1 12.39009532 -9.426633115 1.200959421 0.944345483 0.404579254 0.965737261 0.04297421 0.063776178 0.182721059 0.009469431 0.017108085 3.74E-10 9.426633115 -0.539766228 down AAS(ph)ALLLR ddPTM_HeLa_Romidepsin_16h_R1 2 AASALLLR 8 0 F5H672;F5H5N2;B4DNC9;B3KQ30;Q9H1K1 F5H672 ISCU "Iron-sulfur cluster assembly enzyme ISCU, mitochondrial" 1 0 AAS(1)ALLLR;AAS(1)ALLLR ; 113.62 0.021129 29155000 5046.6 5386.9 4629.9 4463.1 5818.1 6074.6 5799.9 6251.9 5665.5 4860.5 TRUE FALSE FALSE 4985.090098 5462.73692 4710.481467 4979.144622 5521.180647 5686.452665 6292.543361 6432.788863 5158.76349 4734.223509 1.052990018 1.153882344 0.994985019 1.051734168 1.166227289 1.201137347 1.3291606 1.35878436 1.089674681 1 12.2089121 -7.888316562 0.712003165 1.028712991 1.453764259 0.832822715 0.049537829 0.370911659 0.212542106 0.008324295 0.106477655 1.29E-08 7.888316562 0.425051268 AAS(ph)DSNPAGPLR ddPTM_HeLa_Romidepsin_16h_R1 1 AASDSNPAGPLR 12 0 Q9BUU2-2;Q9BUU2 Q9BUU2-2 METTL22 Methyltransferase-like protein 22 1 0 AAS(0.613)DS(0.387)NPAGPLR 143.58 0.0015298 9653000 1802 1589 1652 1557.9 1466 1537.8 1135.3 1131.9 1639.3 1270 TRUE FALSE FALSE 1780.036531 1611.369984 1680.752367 1738.031728 1391.18455 1439.539543 1231.732354 1164.649741 1492.676902 1237.005217 1.438988702 1.302637985 1.358726984 1.40503185 1.124639194 1.163729565 0.995737396 0.941507542 1.20668602 1 10.27263587 -7.826632247 1.560630101 1.242372042 0.928597887 0.469360285 0.124066688 0.512135818 2.124749377 0.026830387 0.1771397 1.49E-08 7.826632247 -0.313774154 AAS(ph)DTERDGLAPEK ddPTM_HeLa_Romidepsin_16h_R1 1 AASDTERDGLAPEK 14 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 0 AAS(0.74)DT(0.26)ERDGLAPEK 122.75 0.024779 4160800 1608.6 1650.8 1646.9 1483 1365.1 1352.5 1264 1309 1720 1589.3 TRUE FALSE FALSE 1588.993764 1674.040006 1675.563604 1654.471438 1295.433853 1266.079615 1371.364128 1346.87385 1566.158892 1548.009757 1.02647529 1.081414376 1.082398606 1.068773262 0.8368383 0.817875733 0.885888556 0.870068062 1.011724174 1 10.59619885 -8.756414876 24.99935323 1.027877647 0.852555415 0.884113246 0.033791643 38.30143133 190566.0915 0.00589292 0.011497468 1.75E-09 8.756414876 -0.175322232 AAS(ph)LDSVATSR ddPTM_HeLa_Romidepsin_16h_R1 2 AASLDSVATSR 11 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4;Q9Y2J4-3 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 0 AAS(0.918)LDS(0.078)VAT(0.003)SR;AAS(0.655)LDS(0.344)VATSR ; 142.12 0.0027723 38686000 3007.2 2977.9 2704.3 2347.9 1769.8 1535.09 1452 1498.24 3530.3 3234.6 TRUE FALSE FALSE 2970.54709 3019.822954 2751.367207 2619.375245 1679.480502 1437.002703 1575.332844 1541.589211 3214.541126 3150.564626 0.942861818 0.958502146 0.873293372 0.831398672 0.533072862 0.456109578 0.500016039 0.489305694 1.02030636 1 11.62139469 -8.882892824 1.646904453 0.968246777 0.472624793 0.971737371 0.037623359 0.039502611 0.216013803 0.00586063 0.012879664 1.31E-09 8.882892824 -0.495621984 AAS(ph)LGSSQSSR ddPTM_HeLa_Romidepsin_16h_R1 1 AASLGSSQSSR 11 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;H0YA91;E9PSG1;H0Y944;D6RGF7;D6RBR1;E7EN75 P20810-6 CAST Calpastatin 1 0 AAS(0.68)LGS(0.159)S(0.159)QS(0.002)SR 132.03 0.004703 10243000 2016.8 1850.5 2285.3 2027.9 2263.1 2303.5 2693.8 1157.6 2603.7 1898.3 TRUE FALSE FALSE 1992.218466 1876.551388 2325.074688 2262.37534 2147.605562 2156.313784 2922.611305 1191.09333 2370.818551 1848.981892 1.077467808 1.014910636 1.257489161 1.223578959 1.161507082 1.166216821 1.580659777 0.644188748 1.282229188 1 10.85251538 -9.771523323 24.90903451 1.0359788 1.192403832 0 0.228523472 305.9215005 755676.1123 0.030954782 0.040945888 1.69E-10 9.771523323 0.156425032 AAS(ph)LNYLNQPSAAPLQVSR ddPTM_HeLa_Romidepsin_16h_R1 2 AASLNYLNQPSAAPLQVSR 19 0 Q9NSK0-5;Q9NSK0;Q9NSK0-3 Q9NSK0-5 KLC4 Kinesin light chain 4 1 0 AAS(0.91)LNY(0.002)LNQPS(0.088)AAPLQVSR;AAS(0.999)LNYLNQPS(0.001)AAPLQVSR ; 200.4 5.00E-21 153484000 3306.94 2790.89 2549.6 2296.35 2767.6 2131.94 2462.46 2322.97 2688.3 2462.97 TRUE FALSE FALSE 3266.633743 2830.180223 2593.974718 2561.864792 2626.359045 1995.715915 2671.621291 2390.181472 2447.851715 2398.981684 1.361675149 1.179742322 1.081281585 1.06789677 1.094780782 0.831901272 1.113648057 0.996331688 1.020371156 1 11.22820643 -9.212378269 1.533371482 1.174004187 1.004247702 0.166255192 0.118710559 0.481344785 2.215596161 0.024630823 0.046497676 6.13E-10 9.212378269 -0.169756485 AAS(ph)LSSIPSGIER ddPTM_HeLa_Romidepsin_16h_R1 1 AASLSSIPSGIER 13 0 A0A494C1D7;Q03001-13 A0A494C1D7 DST Dystonin 1 0 AAS(1)LSSIPSGIER 119.21 0.0050344 5107600 1168.9 1762.3 1051.9 978.14 1191.7 1474.8 699.8 1351.4 1154.2 1256 TRUE FALSE FALSE 1154.652997 1787.109706 1070.207878 1091.237149 1130.883102 1380.56504 759.2409945 1390.500627 1050.965461 1223.368939 0.943830565 1.460810103 0.874803867 0.891993506 0.924400699 1.128494435 0.620614902 1.136615932 0.859074828 1 10.25664384 AAS(ph)LTEDR ddPTM_HeLa_Romidepsin_16h_R1 2 AASLTEDR 8 0 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 AAS(0.933)LT(0.067)EDR;AAS(0.869)LT(0.131)EDR ; 120.31 0.018687 33208000 3121.5 2893 3395.5 2105.6 6437.4 6991 6372.8 5353.7 3518.7 3775.5 TRUE FALSE FALSE 3083.453957 2933.72773 3454.597253 2349.059379 6108.875457 6544.297662 6914.105473 5508.600863 3203.978659 3677.411966 0.838484778 0.79776967 0.939409913 0.638780588 1.661188769 1.779593291 1.880155266 1.497955876 0.871259105 1 11.84447509 -8.718123697 8.674785399 0.895090591 1.725348848 0.909323761 0.132033238 0.06200974 11.33756719 0.019409299 0.038732501 1.91E-09 8.718123697 0.830258257 AAS(ph)PAKPSSLDLVPNLPK ddPTM_HeLa_Romidepsin_16h_R1 2 AASPAKPSSLDLVPNLPK 18 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 0 AAS(0.993)PAKPS(0.005)S(0.002)LDLVPNLPK;AAS(0.369)PAKPS(0.369)S(0.263)LDLVPNLPK ; 76.051 0.0062817 591870000 9054.4 10181.5 9258.6 8417.3 6068.1 5977.8 5135.7 5371.3 9797 8838.7 TRUE FALSE FALSE 8944.04149 10324.83542 9419.742049 9390.547831 5758.422214 5595.837872 5571.92623 5526.710091 8920.731783 8609.0693 1.038909222 1.199297516 1.09416497 1.090773869 0.668878599 0.649993359 0.647215865 0.641963713 1.036201646 1 13.07164157 -8.755743741 24.80929635 1.044719539 0.651525878 0.932279926 0.055659536 28.41612482 123774.6652 0.00969123 0.018958063 1.75E-09 8.755743741 -0.393193661 AAS(ph)PESASSTPESLQAR ddPTM_HeLa_Romidepsin_16h_R1 4 AASPESASSTPESLQAR 17 0 Q96BT3 Q96BT3 CENPT Centromere protein T 1 0 AAS(0.983)PES(0.016)ASSTPESLQAR;AAS(1)PESASSTPESLQAR;AAS(0.998)PES(0.002)ASSTPESLQAR;AAS(0.998)PES(0.002)ASSTPESLQAR ;;; 257.37 1.26E-72 59095900 3374.39 3225.62 2917.95 2567.42 3785.35 4087.83 3712.77 3828.83 3396.43 3372.45 TRUE FALSE FALSE 3333.261637 3271.030363 2968.735696 2864.27718 3592.169464 3826.630856 4028.132591 3939.611155 3092.644794 3284.833263 1.014743023 0.995797991 0.90377059 0.871970341 1.093562192 1.164939146 1.226282209 1.199333677 0.941492169 1 11.68160443 -8.40673978 3.031576239 0.989087054 1.202219456 0.801336555 0.052594728 0.09824754 1.714667749 0.008115981 0.019784446 3.92E-09 8.40673978 0.213132402 ALQESATGQPEPTS(ph)SPDNKPFK ddPTM_HeLa_Romidepsin_16h_R1 1 ALQESATGQPEPTSSPDNKPFK 22 1 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 ALQESATGQPEPT(0.005)S(0.597)S(0.399)PDNKPFK 130.15 4.42E-05 14392000 3773 3086.6 2742.8 2658.6 1799.3 1793.3 1971 1559.5 3623.5 3894.2 TRUE FALSE FALSE 3727.013225 3130.053236 2790.537283 2965.999841 1707.475007 1678.713918 2138.416691 1604.621672 3299.405085 3793.028123 0.982595727 0.825212241 0.735701712 0.781960941 0.450161441 0.442578822 0.563775596 0.423045024 0.869860433 1 11.88913435 -9.322161501 0.790119879 0.999405669 0.450244111 0.855988415 0.080122296 0.11762974 0.145097419 0.013356586 0.030215669 4.76E-10 9.322161501 -0.549161559 down AAS(ph)PPASASDLIEQQQK ddPTM_HeLa_Romidepsin_16h_R1 2 AASPPASASDLIEQQQK 17 0 Q5VSL9;Q5VSL9-3;Q5VSL9-2 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 0 AAS(1)PPASASDLIEQQQK;AAS(0.998)PPAS(0.002)ASDLIEQQQK ; 165.89 5.25E-06 152256000 6441.9 5562.2 5954.9 4693.4 5641.3 5344.9 4511.8 4998.7 6719.3 6799.9 TRUE FALSE FALSE 6363.383645 5640.504798 6058.542537 5236.072991 5353.40341 5003.37814 4895.032179 5143.329498 6118.308979 6623.237618 0.960766322 0.851623499 0.914740326 0.790560945 0.80827591 0.755427848 0.739069389 0.776558202 0.923764076 1 12.6933209 -9.597067493 0.596189854 0.994610673 0.743363839 0.828338159 0.036185697 0.13399813 0.097427503 0.006848699 0.01383839 2.53E-10 9.597067493 -0.251246834 AAS(ph)PPASASDLIEQQQKR ddPTM_HeLa_Romidepsin_16h_R1 2 AASPPASASDLIEQQQKR 18 1 Q5VSL9;Q5VSL9-3;Q5VSL9-2 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 0 AAS(0.946)PPAS(0.053)AS(0.001)DLIEQQQKR;AAS(0.994)PPAS(0.006)AS(0.001)DLIEQQQKR ; 118.02 0.00044785 80527000 7517.6 8751.1 6126 11612.1 6862 6484.4 5204.8 6271.8 8192.9 6866.3 TRUE FALSE FALSE 7425.9726 8874.298216 6232.62046 12954.74564 6511.806534 6070.067767 5646.895582 6453.264638 7460.106505 6687.912536 1.110357314 1.32691601 0.931923141 1.937038735 0.973668017 0.907617696 0.844343515 0.964914628 1.115461134 1 12.70734026 -8.538048772 24.99896856 1.134872166 0.906354382 0.192275949 0.273493119 371.3542043 611959.9657 0.040013138 0.080048589 2.90E-09 8.538048772 -0.228517783 AAS(ph)PPSYTLDLGESQLAPPPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AASPPSYTLDLGESQLAPPPSK 22 0 Q9ULQ0-2;Q9ULQ0 Q9ULQ0-2 STRIP2 Striatin-interacting protein 2 1 0 AAS(0.964)PPS(0.036)YTLDLGESQLAPPPSK 186.69 1.23E-21 0 2055.5 1996.3 1651.5 2191.1 2883 2968.9 2327.2 2816.7 1941.6 2136.5 TRUE FALSE FALSE 2030.446775 2024.403964 1680.243665 2444.445291 2735.869752 2779.196872 2524.87231 2898.19677 1767.938433 2080.993422 0.975710328 0.972806517 0.807423823 1.17465306 1.314694089 1.335514491 1.213301437 1.39269867 0.849564643 1 11.02305669 -9.025640794 4.826511508 0.974335788 1.303668865 0.843376706 0.078700455 0.052569792 3.173740267 0.009930564 0.017309623 9.43E-10 9.025640794 0.329333078 AAS(ph)PSPQSVR ddPTM_HeLa_Romidepsin_16h_R1 3 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 AAS(0.999)PS(0.001)PQSVR;AAS(0.997)PS(0.003)PQSVR;AAS(0.966)PS(0.032)PQS(0.002)VR ;; 158.06 0.0028193 673550000 10377.5 10166.5 10240.8 10668.9 11357.3 11155.7 9874.2 10158.3 11176.5 9558 TRUE FALSE FALSE 10251.01504 10309.62425 10419.03683 11902.48842 10777.6946 10442.88677 10712.9143 10452.21438 10176.84585 9309.681782 1.101113365 1.107408878 1.119161436 1.278506473 1.157686681 1.121723279 1.150728301 1.122725205 1.093146478 1 13.18451614 -11.14793006 0.559874018 1.00364295 1.160835767 0.366667136 0.052102824 0.384169382 0.273513283 0.025772709 0.014308225 7.11E-12 11.14793006 0.157192817 AAS(ph)PVLLSSNSQK ddPTM_HeLa_Romidepsin_16h_R1 2 AASPVLLSSNSQK 13 0 G3V1Z7;P41970 G3V1Z7 ELK3 ETS domain-containing protein Elk-3 1 0 AAS(0.999)PVLLS(0.001)SNSQK;AAS(1)PVLLSSNSQK ; 198.48 4.15E-16 19291400 7015 6292.3 6531.3 6364.8 3112.6 2514.4 2412.9 2567.26 6543.7 5626.6 TRUE FALSE FALSE 6929.498482 6380.883165 6644.974537 7100.728123 2953.752407 2353.737955 2617.851666 2641.539618 5958.415083 5480.420121 1.264410087 1.164305477 1.212493639 1.295653977 0.538964594 0.429481299 0.477673537 0.481995825 1.087218671 1 12.42007078 -8.715746728 7.057256921 1.148925789 0.473234768 0.941540877 0.083982359 0.048054665 5.789748806 0.01675502 0.03343453 1.92E-09 8.715746728 -0.675691021 AAS(ph)SSS(ph)PGSPVASSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 AASSSSPGSPVASSPSR 17 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 2 0 AAS(0.589)S(0.286)S(0.142)S(0.525)PGS(0.43)PVAS(0.028)S(0.001)PSR 158.65 0.00044297 14300000 3603.4 3445.7 3900.2 3322 4681.2 5881.3 4645.4 6052.9 3712.9 3705.4 TRUE FALSE FALSE 3559.480375 3494.208655 3968.081345 3706.10527 4442.300896 5505.503911 5039.98016 6228.031112 3380.808925 3609.133174 0.986242459 0.968157307 1.099455507 1.026868528 1.230849814 1.52543662 1.396451701 1.725630729 0.936737095 1 11.81743666 -8.27432174 0.957741252 0.991214815 1.654624087 0.908986501 0.078059405 0.129340551 0.194174885 0.011088435 0.061338415 5.32E-09 8.27432174 0.663409271 AAS(ph)YTEEDENHTAK ddPTM_HeLa_Romidepsin_16h_R1 1 AASYTEEDENHTAK 14 0 Q14126 Q14126 DSG2 Desmoglein-2 1 0 AAS(0.978)YT(0.022)EEDENHTAK 95.873 0.0057753 10415000 3788.1 5241.9 4932.5 3146.4 3606.4 3510.6 1732.3 2346.5 4619.8 4284.6 TRUE FALSE FALSE 3741.92918 5315.695606 5018.348093 3510.201572 3422.351951 3286.28399 1879.441519 2414.392275 4206.593517 4173.285474 0.89663868 1.273743586 1.202493365 0.841112259 0.820061789 0.787457271 0.450350576 0.578535135 1.007981252 1 12.0269679 -8.164411061 1.278344591 0.991229094 0.499082206 0.688753903 0.134231277 0.262217681 0.750972457 0.022457286 0.108297375 6.85E-09 8.164411061 -0.492146888 AASADS(ph)TTEGTPADGFTVLSTK ddPTM_HeLa_Romidepsin_16h_R1 2 AASADSTTEGTPADGFTVLSTK 22 0 O75367-2;O75367-3;O75367 O75367-2 H2AFY Core histone macro-H2A.1 1 0 AAS(0.14)ADS(0.405)T(0.344)T(0.102)EGT(0.009)PADGFTVLSTK;AAS(0.238)ADS(0.563)T(0.155)T(0.044)EGTPADGFTVLSTK ; 100.81 9.87E-05 10603100 3810.7 3266.8 3188.4 3218 3451.9 3232.6 2696.8 3274 3260.4 3923.2 TRUE FALSE FALSE 3764.253723 3312.790096 3243.892765 3590.080301 3275.736662 3026.047293 2925.866125 3368.728024 2968.781658 3821.274698 0.985078022 0.866933251 0.848903316 0.939498095 0.857236635 0.791894729 0.765678041 0.881571803 0.776908726 1 11.89983826 -9.813739121 0.607088886 1.003231106 0.814128213 0 0.084557166 0.290120676 0.224456004 0.01264522 0.021275201 1.54E-10 9.813739121 -0.189102893 AASAPAKES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 AASAPAKESPR 11 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 AASAPAKES(1)PR;AASAPAKES(1)PR ; 112.5 0.0049632 159866000 10629.1 12689.9 18484.7 13309.1 10721.5 11892 20566.1 2755.9 23423.1 17564 TRUE FALSE FALSE 10499.54844 12868.54875 18806.41845 14847.96076 10174.34185 11132.13958 22312.98402 2835.637618 21328.07927 17107.68475 0.613732869 0.752208667 1.099296528 0.867911759 0.594723482 0.650709885 1.304266729 0.165752272 1.246695832 1 14.06235691 -12.59209866 1.394472651 0.999569044 0.757614725 0.165348158 0.30064951 0.839306016 2.936203583 0.188344337 0.044052852 2.56E-13 12.59209866 -0.241954319 AASDPLLSS(ph)VSPAVSK ddPTM_HeLa_Romidepsin_16h_R1 1 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 0 AASDPLLS(0.002)S(0.988)VS(0.011)PAVSK 250.52 9.83E-59 65950000 5706.7 5540.6 4725 4478.3 4133.1 4002.7 3878.6 4110 5687.7 5427.5 TRUE FALSE FALSE 5637.144545 5618.600712 4807.236643 4996.102117 3922.172484 3746.940388 4208.048187 4228.916365 5178.977867 5286.492768 1.066329756 1.06282198 0.909343274 0.945069318 0.741923361 0.708776225 0.795999989 0.799947442 0.979662338 1 12.36809519 -9.091232805 1.513324821 1.032361854 0.759134559 0.83315742 0.050855408 0.102110207 0.461138322 0.008187503 0.016486643 8.11E-10 9.091232805 -0.273227295 AASDPLLSSVS(ph)PAVSK ddPTM_HeLa_Romidepsin_16h_R1 1 AASDPLLSSVSPAVSK 16 0 P19532 P19532 TFE3 Transcription factor E3 1 0 AASDPLLS(0.001)S(0.226)VS(0.773)PAVSK 244.54 3.16E-58 63186000 4621 4745.7 4012.7 3698.4 3915.2 3610.7 3003.3 3363.4 4494.7 4393.1 TRUE FALSE FALSE 4564.677475 4812.510089 4082.53936 4126.026409 3715.392734 3379.987923 3258.400227 3460.714672 4092.682775 4278.966629 1.066770992 1.124689792 0.954094695 0.964257674 0.868292057 0.789907521 0.76149232 0.808773466 0.956465224 1 12.06304671 -8.769305964 1.327458591 1.03725122 0.778212612 0.825154752 0.047765027 0.11180112 0.392764877 0.007198963 0.018728548 1.70E-09 8.769305964 -0.259038608 AASDS(ph)NPAGPLR ddPTM_HeLa_Romidepsin_16h_R1 1 AASDSNPAGPLR 12 0 Q9BUU2-2;Q9BUU2 Q9BUU2-2 METTL22 Methyltransferase-like protein 22 1 0 AAS(0.111)DS(0.889)NPAGPLR 116.98 0.008459 3756800 841.94 811.61 929 1045.9 820.49 985.87 704.81 815.57 1023.1 786.88 TRUE FALSE FALSE 831.6781114 823.0358669 945.1688553 1166.831879 778.6173336 922.8760887 764.6765438 839.1672312 931.5913736 766.4367442 1.085122964 1.073847089 1.233198777 1.522411194 1.015892492 1.204112532 0.997703398 1.094894311 1.215483705 1 9.582022918 -9.908546822 5.258118419 1.042035625 1.178929685 0.031986088 0.148960312 0.284139071 12.91462859 0.023055281 0.030459821 1.23E-10 9.908546822 0.13689406 AASEQQADT(ph)SGGDSPKDESKPPFSYAQLIVQAISSAQDR ddPTM_HeLa_Romidepsin_16h_R1 1 AASEQQADTSGGDSPKDESKPPFSYAQLIVQAISSAQDR 39 2 P85037-2;P85037 P85037-2 FOXK1 Forkhead box protein K1 1 0 AASEQQADT(0.366)S(0.322)GGDS(0.095)PKDES(0.095)KPPFS(0.095)Y(0.025)AQLIVQAISSAQDR 48.627 0.0031747 3518400 204.93 249.24 220.15 268.06 145.9 268.26 264.46 308.58 117.34 67.65 TRUE FALSE FALSE 202.4322343 252.7488073 223.9816184 299.0543585 138.4541786 251.1190518 286.9232258 317.5082754 106.8448165 65.89244325 3.072161607 3.83577835 3.399200384 4.538522837 2.101214824 3.811044778 4.35441777 4.818584041 1.621503336 1 6.042041117 -11.92604132 0.299900682 1.04E-15 4.22535697 0.669337121 0.706289674 1.283405675 0.188671977 1.954331444 0.458829444 1.19E-12 11.92604132 4.22535697 AASEQQADTSGGDS(ph)PKV ddPTM_HeLa_Romidepsin_16h_R1 3 AASEQQADTSGGDSPKV 17 1 U3KQ26 U3KQ26 FOXK1 1 0 AASEQQADTSGGDS(1)PKV;AASEQQADTSGGDS(1)PKV;AASEQQADT(0.011)S(0.143)GGDS(0.847)PKV ;; 236.68 2.60E-46 39033300 13226.6 13283.6 11836.6 12341.4 12828.8 12808.7 11471.7 12246 14015.4 12637.7 TRUE FALSE FALSE 13065.38911 13470.60687 12042.61106 13768.37074 12174.09847 11990.26541 12446.10591 12600.31869 12761.82752 12309.37073 1.061418118 1.094337571 0.978328732 1.118527586 0.989010627 0.974076228 1.011108218 1.023636298 1.036757102 1 13.58746939 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(ph)PFAK ddPTM_HeLa_Romidepsin_16h_R1 2 AASGEDSTEEALAAAAAPWEGGPVPGVDRSPFAK 34 1 F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 F8W7U3 FAM21A WASH complex subunit FAM21A 1 0 AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK;AASGEDSTEEALAAAAAPWEGGPVPGVDRS(1)PFAK ; 110.33 1.13E-14 45418000 6179 6017.5 6168 5692 6917.7 6731.2 5083.8 5439.8 6606.6 6480.5 TRUE FALSE FALSE 6103.687971 6102.214523 6275.351453 6350.135822 6564.663956 6301.098044 5515.617845 5597.19203 6015.689149 6312.135676 0.966976676 0.966743245 0.99417246 1.006020173 1.040006789 0.998251363 0.873811675 0.886735064 0.953035464 1 12.6239125 -7.760804124 24.99998452 0.989787591 0.880273332 0.780941954 0.023379969 5.392364744 212160.5412 0.00336367 0.011246526 1.73E-08 7.760804124 -0.109514259 AASGEDSTEEALAAAAAPWEGGPVPGVDT(ph)SPFAK ddPTM_HeLa_Romidepsin_16h_R1 1 AASGEDSTEEALAAAAAPWEGGPVPGVDTSPFAK 34 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;Q5SRD0 A0A0A0MR88 FAM21C;FAM21D WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 0 AASGEDSTEEALAAAAAPWEGGPVPGVDT(0.594)S(0.406)PFAK 110.2 2.96E-14 3418300 1441.9 1420.3 1365.8 1100.6 1374 1346.4 1079.8 1366.5 1559.2 1383.8 TRUE FALSE FALSE 1424.325568 1440.295021 1389.571176 1227.85655 1303.879653 1260.369385 1171.518185 1406.037522 1419.741247 1347.848677 1.056739969 1.068588074 1.030954884 0.910975076 0.967378368 0.935097098 0.869176344 1.043171645 1.053338755 1 10.39644282 -9.274501562 24.09959081 1.03155765 0.941613746 0.524442216 0.045477756 306.1613797 564863.6164 0.006898836 0.010580783 5.31E-10 9.274501562 -0.089943904 AASLNYLNQPS(ph)AAPLQVSR ddPTM_HeLa_Romidepsin_16h_R1 2 AASLNYLNQPSAAPLQVSR 19 0 Q9NSK0-5;Q9NSK0;Q9NSK0-3 Q9NSK0-5 KLC4 Kinesin light chain 4 1 0 AAS(0.001)LNY(0.26)LNQPS(0.739)AAPLQVSR;AASLNY(0.003)LNQPS(0.997)AAPLQVSR ; 171.99 1.01E-07 155915400 2037.25 1956.67 2080.34 1784.58 1661.46 1914.6 1815.77 2013.71 2274.43 1993.31 TRUE FALSE FALSE 2012.419213 1984.216052 2116.547445 1990.921536 1576.669496 1792.263239 1970.001458 2071.973522 2070.999284 1941.523519 1.036515496 1.021989192 1.090147724 1.025442915 0.812078495 0.923122085 1.014667831 1.067189504 1.066687714 1 10.92297347 AASLT(ph)EDRDR ddPTM_HeLa_Romidepsin_16h_R1 1 AASLTEDRDR 10 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 AAS(0.006)LT(0.994)EDRDR 172.61 0.0024142 82274000 2624.8 2505 2352.4 2952.7 5763.7 6367.6 5373.8 4654.9 2974.8 2978.9 TRUE FALSE FALSE 2592.807928 2540.265456 2393.342535 3294.105067 5469.556882 5960.73091 5830.250438 4789.582187 2708.726437 2901.507749 0.893607101 0.875498422 0.824861673 1.135308037 1.885074022 2.054356365 2.009386479 1.650721832 0.93355823 1 11.50258707 -8.814505397 3.653742344 0.934761174 1.929051099 0.947308288 0.111353422 0.035307556 0.962942634 0.016760039 0.032497102 1.53E-09 8.814505397 0.994289926 AASLTEDRDR ddPTM_HeLa_Romidepsin_16h_R1 1 AASLTEDRDR 10 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 0 104.42 0.024652 3585700 940.41 985.59 1041.6 903.27 731.73 787.37 886.6 208.69 1142.6 847.55 FALSE FALSE TRUE 928.9479212 999.4651619 1059.728611 1007.710327 694.3870876 737.0595981 961.9077819 214.7281159 1040.402994 825.5305288 1.125273856 1.210694368 1.28369403 1.220682085 0.84114041 0.892831425 1.165199527 0.260109237 1.260284094 1 9.689177758 -7.257598696 24.89293763 1.075778292 0.260108903 0.743320617 0.148722442 139.3961386 903439.8723 0.020142309 0.203058199 5.53E-08 7.257598696 -0.815669389 AASPAKPS(ph)SLDLVPNLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AASPAKPSSLDLVPNLPK 18 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 0 AAS(0.409)PAKPS(0.567)S(0.024)LDLVPNLPK 142.72 0.0012147 27038000 15467 15695 14944 14363 11127 9285.1 7875.5 8674.5 15113 14532 TRUE FALSE FALSE 15278.48225 15915.95462 15204.09405 16023.71764 10559.14767 8691.812076 8544.444773 8925.482971 13761.25543 14154.45655 1.079411435 1.124448302 1.074155974 1.132061665 0.745994566 0.614068936 0.603657565 0.630577581 0.972220684 1 13.78896874 -8.620652443 4.041036759 1.054318644 0.622348579 0.945835898 0.049248551 0.037550962 1.142775364 0.007805151 0.016220441 2.40E-09 8.620652443 -0.431970065 AASPS(ph)PQSVR ddPTM_HeLa_Romidepsin_16h_R1 1 AASPSPQSVR 10 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 AAS(0.313)PS(0.685)PQS(0.001)VR 99.732 0.024658 241330000 1629.6 1483.2 1357.5 1439.7 1552.5 1383.4 1403 1274.5 1509.4 1369.7 TRUE FALSE FALSE 1609.737808 1504.080529 1381.126718 1606.164888 1473.270132 1295.005205 1522.170785 1311.375647 1374.395484 1334.114997 1.206595993 1.127399461 1.035238133 1.203917872 1.104305203 0.970684842 1.140959204 0.98295548 1.030192665 1 10.38166731 -8.457736042 24.95840269 1.105785196 1.041645539 0.13823364 0.077771968 384.9582427 147489.7321 0.01310612 0.029306159 3.49E-09 8.457736042 -0.064139657 AASPYSQRPAS(ph)PTAIR ddPTM_HeLa_Romidepsin_16h_R1 3 AASPYSQRPASPTAIR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 AASPY(0.002)S(0.014)QRPAS(0.825)PT(0.159)AIR;AASPY(0.014)S(0.101)QRPAS(0.865)PT(0.02)AIR;AASPYSQRPAS(0.998)PT(0.001)AIR ;; 180.93 1.38E-07 37781600 2924.46 3373.7 3300.02 2846.71 3564.42 4630.7 3673.65 4126.72 3483.1 3556.58 TRUE FALSE FALSE 2888.815557 3421.195037 3357.455464 3175.860004 3382.514347 4334.813215 3985.689739 4246.120132 3171.562812 3464.179539 0.833910461 0.987591722 0.969192106 0.916771192 0.97642582 1.25132464 1.150543641 1.225721729 0.915530727 1 11.75829799 -8.350699773 4.554946984 0.929653856 1.203049044 0.852695486 0.050762311 0.077427791 2.794484998 0.00982694 0.022806096 4.46E-09 8.350699773 0.273395188 AASQGSDS(ph)PLLPAQR ddPTM_HeLa_Romidepsin_16h_R1 1 AASQGSDSPLLPAQR 15 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 0 AAS(0.001)QGS(0.038)DS(0.961)PLLPAQR 139.49 0.00088871 6984400 1339.7 1304.6 1385 1287.3 875.42 871.1 699.4 738.4 1429 1466.6 TRUE FALSE FALSE 1323.371221 1322.966193 1409.105344 1436.143683 830.7440508 815.4395213 758.8070185 759.764439 1301.186661 1428.497521 0.926407783 0.926124249 0.986424774 1.005352591 0.581550922 0.570837198 0.531192395 0.531862624 0.910877788 1 10.48028282 -8.740365151 7.711482496 0.965533434 0.552017564 0.972230767 0.03355277 0.021087447 5.462881113 0.005354862 0.010534304 1.82E-09 8.740365151 -0.41351587 AASSDQLRDNS(ph)PPPAFKPEPPK ddPTM_HeLa_Romidepsin_16h_R1 2 AASSDQLRDNSPPPAFKPEPPK 22 2 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 AASSDQLRDNS(1)PPPAFKPEPPK;AAS(0.016)S(0.078)DQLRDNS(0.906)PPPAFKPEPPK ; 83.312 0.0012301 62894000 4476.3 4696.7 4396.9 4943 5489.4 4204.4 3141 3955.7 4739.5 4311.7 TRUE FALSE FALSE 4421.741134 4762.820266 4473.4262 5514.532918 5209.255434 3935.752409 3407.796462 4070.151938 4315.58725 4199.681412 1.052875373 1.134090851 1.065182275 1.313083631 1.240393002 0.937154994 0.811441661 0.96915731 1.027598721 1 12.03606417 -8.017429622 24.33796855 1.072220576 0.886299164 0.424996777 0.104987962 447.3944612 624725.3929 0.016739487 0.0438019 9.61E-09 8.017429622 -0.185921412 AASSLNLS(ph)NGETESVK ddPTM_HeLa_Romidepsin_16h_R1 2 AASSLNLSNGETESVK 16 0 C9J840;E7EX83;A0A0D9SG62;H7C0P6;E7ENQ1;G3XAA2;H7C360;G5E948;A0A0D9SEY1;O95819-4;O95819-2;O95819;O95819-5;O95819-3;E7EN19;O95819-6 C9J840 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 0 AASSLNLS(0.997)NGET(0.003)ESVK;AASSLNLS(0.998)NGET(0.002)ESVK ; 331.4 2.64E-203 33801000 7495.4 7403.2 7363.9 6072.7 6814.4 6959.1 5473.2 6132.2 8184.8 7342.1 TRUE FALSE FALSE 7404.043182 7507.422444 7492.06559 6774.854147 6466.63574 6514.435969 5938.093471 6309.625532 7452.730989 7151.351184 1.035334861 1.049790767 1.047643361 0.947353021 0.904253696 0.91093778 0.830345667 0.882298376 1.042143058 1 12.80400014 -8.875417058 1.865201445 1.02219947 0.872901905 0.886185187 0.02570134 0.088834764 0.625800806 0.004295482 0.009125272 1.33E-09 8.875417058 -0.149297565 AASSPDGFFWT(ph)QGSPKPGTASPK ddPTM_HeLa_Romidepsin_16h_R1 1 AASSPDGFFWTQGSPKPGTASPK 23 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 AAS(0.008)S(0.031)PDGFFWT(0.526)QGS(0.434)PKPGTASPK 82.406 0.00020628 15089000 953.85 933.54 1198.1 1260.9 1459.4 1296.6 1100.3 1233.4 1310.7 948.85 TRUE FALSE FALSE 942.2241093 946.6824006 1218.952428 1406.691191 1384.921372 1213.751445 1193.759455 1269.086483 1193.467709 924.1987402 1.01950378 1.024327733 1.3189289 1.522065687 1.498510344 1.313301341 1.291669641 1.373174868 1.291353967 1 9.852059313 -9.713442484 3.919653842 1.009331032 1.396405474 0.618153602 0.111806433 0.055205693 1.763155723 0.01169732 0.016477267 1.93E-10 9.713442484 0.387074442 AASSS(ph)S(ph)PGSPVASSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 AASSSSPGSPVASSPSR 17 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 2 0 AAS(0.019)S(0.216)S(0.758)S(0.506)PGS(0.089)PVAS(0.406)S(0.006)PSR 158.89 0.00042904 13595000 2725.9 2633.5 2723.8 2608.3 3607.7 4543 3661.5 4985.9 2760.3 2492.3 TRUE FALSE FALSE 2692.675682 2670.574482 2771.206596 2909.883918 3423.585607 4252.716962 3972.507719 5130.15915 2513.411855 2427.549687 1.109215476 1.100111152 1.141565345 1.198691806 1.41030506 1.751855785 1.636426945 2.113307578 1.035369891 1 11.24528511 -7.405455554 0.481035361 1.031024923 2.681321293 0.945907046 0.08183525 0.574671713 0.097295995 0.017709669 0.521492604 3.93E-08 7.405455554 1.65029637 up AASSSSPGS(ph)PVASS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 AASSSSPGSPVASSPSR 17 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 2 0 AAS(0.01)S(0.003)S(0.02)S(0.177)PGS(0.787)PVAS(0.015)S(0.887)PS(0.1)R 132.15 2.70E-06 0 1073.6 707.84 805.52 989.45 1045.2 1428.5 1356.8 1304.8 1090 920.63 TRUE FALSE FALSE 1060.51455 717.8049901 819.5397377 1103.854865 991.8595438 1337.22346 1472.046558 1342.552329 992.50767 896.7118999 1.182670321 0.80048563 0.913938733 1.231002806 1.106107261 1.491252051 1.641604799 1.497194728 1.106830042 1 9.808500733 -8.252524501 2.433080955 1.060049394 1.579158944 0.77487536 0.122656957 0.114868289 1.322827343 0.01959382 0.056814801 5.59E-09 8.252524501 0.51910955 AASSSSPGS(ph)PVASSPSR ddPTM_HeLa_Romidepsin_16h_R1 2 AASSSSPGSPVASSPSR 17 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 AAS(0.17)S(0.17)S(0.17)S(0.17)PGS(0.32)PVAS(0.001)SPSR;AAS(0.206)S(0.018)S(0.018)S(0.033)PGS(0.708)PVAS(0.018)SPSR ; 262.73 2.73E-73 63744000 3826.3 4323.9 4071.4 3971.5 6220.8 7672.9 5979.7 7544 4385.2 3569.3 TRUE FALSE FALSE 3779.663584 4384.771978 4142.261009 4430.703516 5903.329363 7182.626453 6487.615569 7762.273738 3992.976729 3476.569071 1.087182077 1.261235398 1.191479566 1.274447142 1.698033102 2.066009996 1.866097131 2.232739686 1.14853945 1 11.76344854 -8.616593849 0.837992273 1.044363266 2.175688353 0.930316457 0.111199377 0.111447501 0.138291083 0.018252945 0.07594668 2.42E-09 8.616593849 1.131325087 up AASSSSPGSPVASS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 AASSSSPGSPVASSPSR 17 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 AASSSSPGSPVAS(0.086)S(0.914)PSR;AASSSSPGSPVAS(0.005)S(0.995)PSR ; 241.39 2.54E-47 61805000 6966.5 6763.1 7071.3 5893.4 7267.2 7114 6146.5 7715.5 7484.5 6532.8 TRUE FALSE FALSE 6881.589618 6858.311099 7194.37301 6574.822637 6896.327666 6659.438359 6668.583557 7938.735819 6815.067575 6363.076914 1.081487732 1.077829357 1.130643729 1.033277253 1.083803914 1.046575179 1.048012408 1.247625312 1.071033349 1 12.63550885 -16.52287875 0.112698686 0.701377615 1.144274655 0.146372335 0.059481423 94.4491688 0.778462294 6.519549204 0.315665465 3.00E-17 16.52287875 0.44289704 AASVAAATTS(ph)PTPR ddPTM_HeLa_Romidepsin_16h_R1 1 AASVAAATTSPTPR 14 0 Q9Y2D9 Q9Y2D9 ZNF652 Zinc finger protein 652 1 0 AASVAAAT(0.057)T(0.353)S(0.581)PT(0.009)PR 180.85 2.84E-07 13158000 4555.7 4157.5 4099 2821.2 3065.9 3300.7 2559.7 3070.7 5184.4 4212.8 TRUE FALSE FALSE 4500.173376 4216.029394 4170.341376 3147.400418 2909.435683 3089.795923 2777.120854 3159.54586 4720.694279 4103.350849 1.096706946 1.027460129 1.01632581 0.767031759 0.709038976 0.752993355 0.67679342 0.769991643 1.15044861 1 12.0025868 -9.249306411 3.292006764 1.045096704 0.725773548 0.924040648 0.046410704 0.043616275 0.987091746 0.006399645 0.010621851 5.63E-10 9.249306411 -0.319323156 KAPAGQEEPGT(ph)PPSSPLSAEQLDR ddPTM_HeLa_Romidepsin_16h_R1 2 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 0 KAPAGQEEPGT(0.949)PPS(0.021)S(0.023)PLS(0.007)AEQLDR;KAPAGQEEPGT(0.997)PPS(0.002)S(0.001)PLSAEQLDR ; 87.868 4.47E-05 114918000 4839.5 4998.1 4197.3 2472.3 2174.6 1936.8 2016.99 2484.2 6158.7 5651 TRUE FALSE FALSE 4780.514313 5068.463383 4270.352246 2758.158959 2063.622047 1813.044731 2188.31308 2556.076408 5607.850447 5504.186205 0.868523363 0.920837921 0.775837169 0.501102044 0.374918647 0.329393786 0.397572502 0.464387706 1.018833709 1 12.42631356 -9.318949801 1.786554802 0.93724774 0.384430181 0.962726577 0.050786531 0.051653254 0.322158041 0.009526973 0.016574824 4.80E-10 9.318949801 -0.552817559 down AATAARPPAPPPAPQPPS(ph)PTPS(ph)PPRPTLAR ddPTM_HeLa_Romidepsin_16h_R1 2 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36-3;Q96B36;H9KV91 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 2 0 AATAARPPAPPPAPQPPS(0.823)PT(0.316)PS(0.78)PPRPT(0.081)LAR;AATAARPPAPPPAPQPPS(0.982)PT(0.061)PS(0.91)PPRPT(0.047)LAR ; 68.487 6.71E-05 117619000 3016.29 2183.89 2413.19 1845.62 2354.85 2385.1 2069.32 2341.59 2724.85 2692.87 TRUE FALSE FALSE 2979.526297 2214.634861 2455.19056 2059.019268 2234.673217 2232.699808 2245.087989 2409.340212 2481.132591 2622.908849 1.135962578 0.844343051 0.936056379 0.785013657 0.851982797 0.851230422 0.855953492 0.918575654 0.945946937 1 11.35695196 -10.25189651 24.99170013 1.064204551 0.861911651 0.576776788 0.061995716 264.6001003 692958.6001 0.010238272 0.012451188 5.60E-11 10.25189651 -0.202292899 AATAARPPAPPPAPQPPS(ph)PTPSPPRPTLAR ddPTM_HeLa_Romidepsin_16h_R1 3 AATAARPPAPPPAPQPPSPTPSPPRPTLAR 30 2 Q96B36-3;Q96B36;H9KV91 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 AATAARPPAPPPAPQPPS(0.56)PT(0.398)PS(0.039)PPRPT(0.003)LAR;AATAARPPAPPPAPQPPS(0.543)PT(0.113)PS(0.172)PPRPT(0.172)LAR;AATAARPPAPPPAPQPPS(0.924)PT(0.03)PS(0.039)PPRPT(0.007)LAR ;; 100.04 2.69E-09 102426000 2743.1 3034.6 2668.7 2114.65 2253.39 2136.43 1597.82 2299.99 2961.38 3255.99 TRUE FALSE FALSE 2709.666042 3077.321178 2715.147604 2359.155783 2138.3911 1999.919018 1733.538791 2366.536582 2696.506756 3171.39891 0.854407193 0.970335573 0.85613563 0.743884907 0.67427377 0.630610994 0.546616443 0.746212208 0.85025783 1 11.63090364 -9.151500134 1.404654858 0.93407465 0.632103491 0.785775849 0.063928855 0.13194047 0.511914013 0.011290538 0.022540055 7.06E-10 9.151500134 -0.301971159 AATEALGEKSPDS(ph)ATVSGYDIMK ddPTM_HeLa_Romidepsin_16h_R1 1 AATEALGEKSPDSATVSGYDIMK 23 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;H0Y2S9;H0Y7E2;K7EL39;J3QRL2;H7C3G6 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 AATEALGEKS(0.039)PDS(0.431)AT(0.284)VS(0.071)GY(0.174)DIMK 57.39 0.012483 77104000 1539.9 1598.8 1382.9 1767.9 1644.9 1901.3 1855.8 1580.2 1895.7 1666.1 TRUE FALSE FALSE 1521.131106 1621.307948 1406.968794 1972.312916 1560.954615 1779.813066 2013.431606 1625.920594 1726.143844 1622.814482 0.937341343 0.999071654 0.866992999 1.215365612 0.961881122 1.096744629 1.240703499 1.001914028 1.063672936 1 10.66428237 -9.265095092 24.9953584 0.96521386 1.102730883 0.331919473 0.09178039 240.4023337 1643714.464 0.01239498 0.019407957 5.43E-10 9.265095092 0.137517023 AATEALGEKSPDSATVSGY(ph)DIMK ddPTM_HeLa_Romidepsin_16h_R1 1 AATEALGEKSPDSATVSGYDIMK 23 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;H0Y2S9;H0Y7E2;K7EL39;J3QRL2;H7C3G6 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 AATEALGEKS(0.032)PDS(0.132)AT(0.142)VS(0.23)GY(0.464)DIMK 47.089 0.021521 78799000 2959.6 2786.3 2998.6 2878.3 3539.3 3627.1 3032.5 3548.4 3310 3153.8 TRUE FALSE FALSE 2923.527257 2825.525605 3050.789375 3211.102589 3358.676314 3395.340016 3290.080474 3651.067356 3013.94531 3071.863821 0.951711217 0.919808224 0.993139525 1.045327129 1.093367581 1.105302908 1.071037216 1.188551175 0.981145482 1 11.58489855 -8.975756667 1.705257042 0.971826021 1.116036081 0.803942236 0.034130672 0.127767578 0.742494119 0.005722383 0.011819427 1.06E-09 8.975756667 0.14421006 AATS(ph)PAPGPSDATAR ddPTM_HeLa_Romidepsin_16h_R1 1 AATSPAPGPSDATAR 15 0 Q8IXZ2-2;Q8IXZ2 Q8IXZ2-2 ZC3H3 Zinc finger CCCH domain-containing protein 3 1 0 AAT(0.323)S(0.64)PAPGPS(0.003)DAT(0.035)AR 134.06 0.0014651 3394200 1221 1252.3 1083.8 1002.6 1329.4 1387.7 1446.8 1341.6 1253.7 1369.2 TRUE FALSE FALSE 1206.117982 1269.929912 1102.663084 1118.525329 1261.555757 1299.030449 1569.691156 1380.417079 1141.565932 1333.627987 0.904388626 0.952236999 0.826814596 0.838708651 0.945957771 0.974057579 1.17700826 1.035084066 0.855985285 1 10.38114057 -7.90632228 5.637268747 0.935249349 1.104470024 0.569932167 0.065691354 0.124225742 6.020865093 0.00968772 0.030026957 1.24E-08 7.90632228 0.169220674 AATTATPAATTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 AATTATPAATTSPK 14 0 A0A087X055;Q92766;Q92766-2;Q92766-5;Q92766-3 A0A087X055 RREB1 Ras-responsive element-binding protein 1 1 0 AATTATPAATT(0.021)S(0.979)PK;AATTATPAAT(0.008)T(0.057)S(0.936)PK;AATTATPAATT(0.025)S(0.975)PK ;; 195.71 1.56E-11 24418400 13310.7 13056.4 12864.6 5443.29 6353.5 8259.7 7680.1 7644.1 16062.9 13889.8 TRUE FALSE FALSE 13148.46407 13240.20834 13088.50297 6072.668801 6029.257187 7731.931827 8332.447502 7865.269973 14626.19399 13528.94099 0.971876814 0.978658148 0.967444752 0.448865052 0.445656256 0.5715105 0.615897985 0.581366271 1.081104131 1 13.72376129 -9.269611153 24.69196687 0.984335229 0.534608495 0.938775153 0.059584235 82.68097691 249829.9735 0.008566106 0.013225809 5.38E-10 9.269611153 -0.449726734 AAVEEGIVLGGGCALLR ddPTM_HeLa_Romidepsin_16h_R1 1 AAVEEGIVLGGGCALLR 17 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 125.36 0.00018534 344090 0 0 0 116.57 68.615 142.61 0 0 167.54 62.263 FALSE FALSE TRUE 0 0 0 130.0483719 65.11332051 133.4976813 0 0 152.5548028 60.64539828 0 0 0 2.144406263 1.073672898 2.20128295 0 0 2.515521492 1 5.922326274 AAVEWFDGKDFQGSK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVEWFDGKDFQGSK 15 1 H7BY36;A0A0D9SFL3;B0QYK0;C9JGE3;Q01844-2;Q01844-6;Q01844-3;Q01844;Q01844-5 H7BY36 EWSR1 RNA-binding protein EWS 0 0 88.092 0.0038747 0 1893.9 1848.8 1289.2 799 1228.5 1141.5 1310.8 1529.1 1807.2 1865 FALSE FALSE TRUE 1870.816418 1874.827455 1311.637985 891.3841394 1165.805061 1068.561834 1422.139319 1573.342096 1645.559506 1816.547031 1.029875025 1.03208308 0.722050111 0.490702483 0.64176982 0.588237913 0.782880539 0.866116907 0.905872228 1 10.826983 -9.715945936 5.077647691 1.016192762 0.668202776 0.686108089 0.102367529 0.073713941 4.242451246 0.015803217 0.022211708 1.92E-10 9.715945936 -0.347989986 AAVGEEKDINTFVGT(ph)PVEK ddPTM_HeLa_Romidepsin_16h_R1 4 AAVGEEKDINTFVGTPVEK 19 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 AAVGEEKDINT(0.001)FVGT(0.999)PVEK;AAVGEEKDINT(0.003)FVGT(0.997)PVEK;AAVGEEKDINTFVGT(1)PVEK;AAVGEEKDINT(0.015)FVGT(0.985)PVEK ;;; 116.35 0.0004545 68562000 9805.8 7973.7 9194.8 8594.6 6970.73 8039.7 7913.9 7247.15 11074.3 9438.7 TRUE FALSE FALSE 9686.283138 8085.953958 9354.831637 9588.348091 6614.987637 7525.989117 8586.106468 7456.834851 10083.78687 9193.481213 1.053603408 0.879531243 1.017550525 1.042950746 0.719530228 0.818622341 0.933934194 0.811100244 1.096840972 1 13.16639554 -8.777577156 24.99977165 1.014209194 0.828722673 0.639323288 0.071387867 111.5254665 172769.0216 0.00999825 0.018163145 1.67E-09 8.777577156 -0.185486521 AAVGQES(ph)PGGLEAGNAK ddPTM_HeLa_Romidepsin_16h_R1 2 AAVGQESPGGLEAGNAK 17 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 0 AAVGQES(1)PGGLEAGNAK;AAVGQES(1)PGGLEAGNAK ; 190.18 2.99E-13 307210000 6181.8 5927.2 6426.5 5952.7 5714.4 6310.5 4979.2 5359.8 6219.4 5741.2 TRUE FALSE FALSE 6106.453844 6010.643277 6538.350537 6640.979182 5422.772845 5907.279416 5402.133124 5514.877357 5663.121287 5592.042796 1.091989827 1.074856452 1.16922398 1.187576602 0.969730212 1.056372355 0.966039303 0.98620085 1.012710649 1 12.44915969 AAVLS(ph)DS(ph)EDEEK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVLSDSEDEEK 12 0 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 2 0 AAVLS(1)DS(1)EDEEK 116.19 0.0026775 0 2975.3 2855 3786.4 1878.5 3208.3 3312.9 2527 3011.4 3336.9 3192.8 TRUE FALSE FALSE 2939.035899 2895.192765 3852.300704 2095.701009 3044.568479 3101.216382 2741.643317 3098.530108 3038.439307 3109.850596 0.945073022 0.930974873 1.238741407 0.673891219 0.979007957 0.997223592 0.881599689 0.996359797 0.977037068 1 11.60262956 -9.255929483 24.99890038 0.987532683 0.9134488 0.155636914 0.120401702 918.8784468 4169030.934 0.017100318 0.027813547 5.55E-10 9.255929483 -0.074083883 AAVLS(ph)DS(ph)EDEEKASAK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVLSDSEDEEKASAK 16 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 2 0 AAVLS(0.995)DS(1)EDEEKAS(0.005)AK 85.469 0.0016788 0 1601.2 1714.5 1811.3 1466.2 1635.7 1578.6 1675.1 1486.6 1993.5 1722.4 TRUE FALSE FALSE 1581.683959 1738.636776 1842.824917 1635.728943 1552.224125 1477.732555 1817.382952 1529.612426 1815.196367 1677.6518 0.942796329 1.036351391 1.098454946 0.97501099 0.92523617 0.880833886 1.083289722 0.911757986 1.081986362 1 10.7122276 -7.739332647 24.9997079 0.977732991 0.997523627 0 0.075801984 1266.461927 1432173.953 0.0094013 0.035120731 1.82E-08 7.739332647 0.019790636 AAVLS(ph)DSEDEEK ddPTM_HeLa_Romidepsin_16h_R1 2 AAVLSDSEDEEK 12 0 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 AAVLS(0.765)DS(0.235)EDEEK;AAVLS(0.978)DS(0.022)EDEEK ; 211.38 5.50E-21 10408900 4449.6 4316.2 4113.6 2394.2 3666 4101.8 4193.7 4587.7 4957.9 4686.4 TRUE FALSE FALSE 4395.366564 4376.963577 4185.195482 2671.028669 3478.91034 3839.708218 4549.912773 4720.437861 4514.453007 4564.646652 0.962914963 0.958883329 0.916871732 0.585155626 0.762142309 0.841184107 0.996772175 1.03412996 0.989003827 1 12.15628747 -9.518158886 23.10681862 0.978211337 0.838013953 0.228203049 0.116003589 87.768701 429686.41 0.019379234 0.027869475 3.03E-10 9.518158886 -0.140197384 AAVLS(ph)DSEDEEKASAK ddPTM_HeLa_Romidepsin_16h_R1 2 AAVLSDSEDEEKASAK 16 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 AAVLS(0.665)DS(0.335)EDEEKASAK;AAVLS(0.922)DS(0.078)EDEEKASAK ; 82.482 0.0080044 25517000 4050.3 3760.9 3900.9 3767.8 4136.9 4240.3 3661 4698.6 3997.1 4040.1 TRUE FALSE FALSE 4000.933386 3813.846049 3968.793528 4203.450764 3925.778556 3969.358515 3971.965249 4834.546578 3639.589365 3935.13762 1.016720067 0.969177299 1.008552664 1.068183929 0.997621668 1.008696239 1.009358664 1.228558451 0.924895065 1 11.94219838 -7.261439191 10.4511679 1.008952474 1.22896512 0.788070927 0.035249359 0.01564116 69.96263046 0.003116415 0.024111232 5.48E-08 7.261439191 0.220012646 AAVLSDS(ph)EDEEK ddPTM_HeLa_Romidepsin_16h_R1 2 AAVLSDSEDEEK 12 0 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 AAVLS(0.016)DS(0.984)EDEEK;AAVLS(0.138)DS(0.862)EDEEK ; 208.33 1.12E-15 13044100 4171.6 4316.4 4443.3 2573.79 3809.6 4179 3907.8 4297.5 4264.5 4641.3 TRUE FALSE FALSE 4120.754935 4377.166392 4520.633773 2871.38371 3615.181896 3911.975387 4239.728434 4421.841382 3883.072439 4520.718357 0.911526578 0.968245762 0.99998129 0.635160938 0.79969191 0.865343753 0.937843966 0.978128039 0.858950311 1 12.14233632 -10.85888586 0.580737471 0.988353899 0.866288794 0.00041636 0.10731203 0.980374228 0.770840838 0.045945005 0.033488943 1.38E-11 10.85888586 -0.122065106 AAVLSDS(ph)EDEEKASAK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVLSDSEDEEKASAK 16 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 AAVLS(0.201)DS(0.799)EDEEKASAK 90.379 0.0045374 15117000 1677 2153.1 1601 1962.3 2034.7 1744.3 2028.7 1674.7 1746.2 2106.6 TRUE FALSE FALSE 1656.560079 2183.411398 1628.864733 2189.190359 1930.861666 1632.844859 2201.017727 1723.154802 1590.015499 2051.870228 0.807341544 1.064107938 0.793843934 1.066924374 0.941025236 0.795783689 1.072688563 0.839797166 0.774910361 1 11.00272377 -9.268333764 24.90152571 0.912957083 0.942119698 0.031340328 0.118039103 2585.151961 9337196.516 0.017429149 0.027017176 5.39E-10 9.268333764 0.029162615 AAVPAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AAVPAKR 7 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2;S4R3C2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ; AAVPAK(1)R;AAVPAK(1)R 97.596 0.014336 4156300 54.655 255.68 618.62 248.46 927.46 2912.4 2272.76 992.07 118.13 0 FALSE TRUE FALSE 53.98884384 259.2794698 629.3868216 277.1881142 880.1282554 2726.307039 2465.808178 1020.77398 107.5641569 0 0 AAVPQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AAVPQKK 7 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4;A8MXE8;Q7Z5J4-4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 0 1 AAVPQK(1)K 88.643 0.021123 0 2282.5 2837.9 2162.8 2930.7 3273 4004.5 3255.7 1515.2 2916.1 2532.7 FALSE TRUE FALSE 2254.680012 2877.852031 2200.442627 3269.561323 3105.966597 3748.625374 3532.239077 1559.039921 2655.276712 2466.900089 0.913972975 1.166586374 0.891986926 1.325372413 1.259056502 1.519569192 1.431853318 0.631983406 1.076361675 1 11.26848357 -9.259373846 24.90189232 0.972586813 1.261887977 0.170691242 0.235625629 174.6972734 2106128.143 0.033550157 0.053884487 5.50E-10 9.259373846 0.289301164 AAVPS(ph)GASTGIYEALELR ddPTM_HeLa_Romidepsin_16h_R1 1 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y798;A0A2R8YEG5;E5RI09;F5H1C3;P09104-2;K7EPM1;K7EKN2;E5RGZ4;F5H0C8;P09104;E5RG95;P13929-3;P13929-2;P13929 P06733;P13929-3 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Gamma-enolase;Beta-enolase 1 0 AAVPS(0.94)GAS(0.051)T(0.009)GIYEALELR 106.67 0.0015518 4039100 714.92 699.45 867.64 510.47 576.19 711.65 762.43 602.55 680.77 848.45 TRUE FALSE FALSE 706.2062801 709.2968755 882.7409102 569.4929432 546.7848742 666.1778617 827.1907852 619.9838336 619.8802262 826.4071467 0.854550064 0.858289861 1.068167082 0.689119093 0.661641028 0.806113384 1.000948247 0.750215963 0.750090592 1 9.69070892 -9.252411348 24.99487456 0.93226277 0.788489772 0.200151894 0.118589843 675.2685606 1869538.673 0.017087181 0.028072501 5.59E-10 9.252411348 -0.143772998 AAVPSGASTGIYEALELR ddPTM_HeLa_Romidepsin_16h_R1 1 AAVPSGASTGIYEALELR 18 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y798;A0A2R8YEG5;E5RI09;F5H1C3;P09104-2;K7EPM1;K7EKN2;E5RGZ4;F5H0C8;P09104;E5RG95;P13929-3;P13929-2;P13929 P06733;P13929-3 ENO1;ENO3;ENO2 Alpha-enolase;Enolase;Gamma-enolase;Beta-enolase 0 0 152.99 3.11E-13 451680 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 AAVQELSS(ph)SILAGEDPEER ddPTM_HeLa_Romidepsin_16h_R1 1 AAVQELSSSILAGEDPEER 19 0 E7ES96;P49768-7;P49768-2;P49768 E7ES96 PSEN1 Presenilin;Presenilin-1;Presenilin-1 NTF subunit;Presenilin-1 CTF subunit;Presenilin-1 CTF12 1 0 AAVQELS(0.036)S(0.958)S(0.007)ILAGEDPEER 186.17 3.79E-11 2184800 840.72 1282 1078.1 634.61 1075.5 1646.5 724.84 1152.3 1161.3 1183.7 TRUE FALSE FALSE 830.4729813 1300.04803 1096.863878 707.9865941 1020.613222 1541.293964 786.4078915 1185.639982 1057.430419 1152.947303 0.72030437 1.127586687 0.951356471 0.614066742 0.885221049 1.336829497 0.682084853 1.028355744 0.917154163 1 10.17111086 -8.484082526 24.94866956 0.872454678 1.003828759 0.075794405 0.198622238 1115.786816 717528.4313 0.028882654 0.064571388 3.28E-09 8.484082526 0.131374082 AAVVT(ph)SPPPTTAPHKER ddPTM_HeLa_Romidepsin_16h_R1 1 AAVVTSPPPTTAPHKER 17 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 E7EV99 ADD1 Alpha-adducin 1 0 AAVVT(0.499)S(0.499)PPPT(0.001)TAPHKER 60.968 0.015009 9570800 7526.1 7902.2 5190.1 12299 8182.1 7308.1 6575.4 7005 7957.4 6360.9 TRUE FALSE FALSE 7434.368998 8013.447379 5280.431513 13721.06825 7764.536905 6841.135996 7133.914312 7207.678623 7245.670214 6195.642901 1.199935038 1.29340046 0.85228145 2.214631874 1.253225376 1.104185006 1.151440525 1.163346361 1.169478346 1 12.59703828 -11.1723237 0.699696864 1.021248914 1.30187455 0.050824544 0.337436316 1.118316824 1.20227091 0.13689344 0.083211538 6.72E-12 11.1723237 0.280625637 AAVVTS(ph)PPPTTAPHK ddPTM_HeLa_Romidepsin_16h_R1 1 AAVVTSPPPTTAPHK 15 0 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 E7EV99 ADD1 Alpha-adducin 1 0 AAVVT(0.104)S(0.896)PPPTTAPHK 75.589 0.01663 191440000 3949 3444.5 3236.1 3456.1 4651.3 4462.4 3549.7 4045.9 4119.2 3633.3 TRUE FALSE FALSE 3900.868069 3492.991761 3292.422963 3855.710543 4413.926805 4177.267042 3851.211429 4162.961733 3750.768435 3538.906342 1.102280674 0.987025771 0.930350409 1.089520369 1.24725731 1.180383609 1.08824904 1.176341313 1.059866544 1 11.78908787 -8.993664597 24.37563513 1.034784287 1.167631545 0.620134353 0.056975836 79.33251414 305229.2638 0.009616957 0.017396694 1.01E-09 8.993664597 0.132847258 YLTNQK(ac)NSNSK(ac)NDRR ddPTM_HeLa_Romidepsin_16h_R1 2 YLTNQKNSNSKNDRR 15 3 B1AK63;Q9HAF1-2;Q9HAF1;Q9HAF1-4;Q9HAF1-3 B1AK63 MEAF6 Chromatin modification-related protein MEAF6 0 2 ; YLTNQK(1)NSNSK(1)NDRR;YLTNQK(1)NSNSK(1)NDRR 192.4 1.48E-13 65623000 2530.6 2945.1 3150.4 7292.7 8835.5 8189.9 7263.4 7447.8 2926.7 2079.28 FALSE TRUE FALSE 2499.756074 2986.561195 3205.23139 8135.916287 8384.591465 7666.591822 7880.353015 7663.290342 2664.928622 2025.260006 1.234288964 1.474655692 1.58262711 4.017220635 4.140007427 3.785485221 3.891032752 3.783855071 1.315845182 1 10.98389142 -9.322087375 3.723005937 1.154842342 3.939497449 0.982342981 0.174393654 0.023226322 0.648362643 0.031757969 0.050405238 4.76E-10 9.322087375 2.784655107 up AAYEAELGDAR ddPTM_HeLa_Romidepsin_16h_R1 3 AAYEAELGDAR 11 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ;; ;; 182.16 7.22E-05 70564100 6109.6 5932.9 6156.6 4676.2 6557.8 7149.4 6229 7388.8 7346.9 5914.8 FALSE FALSE TRUE 6035.133845 6016.423522 6263.75304 5216.884246 6223.130995 6692.576414 6758.091105 7602.58327 6689.774863 5761.132643 1.047560301 1.044312619 1.08724333 0.905531007 1.080192278 1.161677196 1.173049038 1.319633437 1.161190911 1 12.49213676 -7.628249308 1.031219843 1.022512761 1.360010488 0.606535863 0.067357292 0.37765721 0.458411327 0.007816959 0.12092121 2.35E-08 7.628249308 0.337497727 AAYEAELGDARK ddPTM_HeLa_Romidepsin_16h_R1 1 AAYEAELGDARK 12 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 89.266 0.018987 9530200 3372.4 3722.2 2555.6 5639.4 3995.6 3129.9 3013.3 3395 3434.5 2936.2 FALSE FALSE TRUE 3331.295892 3774.601229 2600.079146 6291.453962 3791.689622 2929.909491 3269.249627 3493.228969 3127.309718 2859.917101 1.164822537 1.319828896 0.909144935 2.199872843 1.325804032 1.024473573 1.14312741 1.221444135 1.093496632 1 11.48175761 -10.71171288 0.935377758 1.038879397 1.317730738 0.092853028 0.327929564 0.81280455 1.498185346 0.085352901 0.079063014 1.94E-11 10.71171288 0.278851341 AAYGDLS(ph)S(ph)EEEEENEPESLGVVYK ddPTM_HeLa_Romidepsin_16h_R1 2 AAYGDLSSEEEEENEPESLGVVYK 24 0 O15541 O15541 RNF113A RING finger protein 113A 2 0 AAY(0.002)GDLS(0.776)S(0.801)EEEEENEPES(0.417)LGVVY(0.002)K;AAY(0.005)GDLS(0.992)S(0.995)EEEEENEPES(0.006)LGVVY(0.001)K ; 64.289 0.00087177 4109600 1780.98 2258.4 2217.89 1701.8 2787.3 2627.4 2058.09 2597.1 3000.6 2176 TRUE FALSE FALSE 1759.272731 2290.193814 2256.491445 1898.570123 2645.05368 2459.51762 2232.904113 2672.242991 2732.218821 2119.467206 0.830054235 1.080551663 1.064650323 0.89577707 1.24798047 1.16044146 1.053521426 1.260808841 1.289106438 1 11.04948593 -9.094260222 0.911028522 0.927319087 1.174369697 0 0.152565073 0.387226532 0.629128808 0.019828747 0.049827222 8.05E-10 9.094260222 0.24705061 AAYWEEEPAEVRR ddPTM_HeLa_Romidepsin_16h_R1 1 AAYWEEEPAEVRR 13 1 Q9Y6Y8;H7C4C4;H7C0V8;A0A0C4DH82;Q9Y6Y8-2 Q9Y6Y8 SEC23IP SEC23-interacting protein 0 0 103.43 0.0020032 0 465.25 421.2 581.54 1054 410.42 607.82 584.83 570 486.37 574.2 FALSE FALSE TRUE 459.579354 427.1296647 591.6614598 1175.868439 389.4747359 568.9822636 634.5054456 586.4920507 442.8678491 559.2822012 0.821730699 0.763710456 1.057894312 2.102459969 0.696383212 1.017343771 1.134499622 1.048651377 0.791850426 1 9.127432608 -9.524394874 24.99193478 0.902473517 1.200329707 0.18536233 0.342950189 73.05664928 1204259.604 0.052551611 0.074639878 2.99E-10 9.524394874 0.29785619 ACANPAAGSVILLENLR ddPTM_HeLa_Romidepsin_16h_R1 1 ACANPAAGSVILLENLR 17 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 0 146.79 3.20E-23 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 ACARPLISVYS(ph)EKGES(ph)S(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 ACARPLISVYSEKGESSGK 19 2 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 3 0 ACARPLIS(0.03)VY(0.155)S(0.834)EKGES(0.99)S(0.99)GK 40.962 0.029635 7740200 4180.1 1454.6 2577.2 2439.5 3037.4 2066.4 3312 2593.3 3752.4 3256.9 TRUE FALSE FALSE 4129.151333 1475.077897 2622.055085 2721.566468 2882.390144 1934.363709 3593.321197 2668.333044 3416.775946 3172.285268 1.301633045 0.464989045 0.82655085 0.857919839 0.908616313 0.609769786 1.132723224 0.841139058 1.077070836 1 11.6313068 -10.28536519 24.93767576 1.142437824 0.81771935 0.394960525 0.180913952 571.363351 595525.3311 0.032833799 0.03755704 5.18E-11 10.28536519 -0.324718474 ACLISLGYDVENDR ddPTM_HeLa_Romidepsin_16h_R1 1 ACLISLGYDVENDR 14 0 O43707;O43707-2;O43707-3;F5GXS2 O43707 ACTN4 Alpha-actinin-4 0 0 144.7 0.0062918 6690700 1918.8 1807.2 1797.7 1038.1 1949.6 1796 1502.5 1775.8 2001.5 1787.4 FALSE FALSE TRUE 1895.412928 1832.641809 1828.988214 1158.130006 1850.104637 1681.241396 1630.122312 1827.179971 1822.480827 1740.96309 1.08871517 1.052659772 1.050561166 0.665223756 1.062690328 0.965696175 0.936333643 1.049522521 1.046823357 1 10.7656699 ACS(ph)TPGSCS(ph)SGMT(ph)S(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ACSTPGSCSSGMTSTK 16 0 D6RHU4;Q53FE4-2;Q53FE4 D6RHU4 C4orf17 Uncharacterized protein C4orf17 5 0 ACS(0.796)T(0.174)PGS(0.41)CS(0.48)S(0.435)GMT(0.947)S(0.828)T(0.93)K 55.353 0.0040627 0 1262.7 1348.9 1488.3 918.64 1580.2 1287.8 1337 1347 1467 1441.7 TRUE FALSE FALSE 1247.309727 1367.88985 1514.203237 1024.857479 1499.556497 1205.513736 1450.564747 1385.97332 1335.787846 1404.244426 0.888242605 0.974110934 1.078304609 0.729828412 1.067874274 0.858478562 1.032985939 0.986988657 0.951250239 1 10.45557836 ADAASSLT(ph)VDVTPPTAK ddPTM_HeLa_Romidepsin_16h_R1 1 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8-2;Q9H8Y8;Q9H8Y8-3 Q9H8Y8-2 GORASP2 Golgi reassembly-stacking protein 2 1 0 ADAAS(0.334)S(0.009)LT(0.628)VDVT(0.007)PPT(0.021)AK 268.17 9.54E-87 89688000 15289 16050 14903 14682 15678 14932 13963 14722 16206 15434 TRUE FALSE FALSE 15102.65179 16275.95232 15162.38046 16379.60192 14877.89316 13977.89339 15149.01687 15147.95784 14756.49477 15033.02246 1.004631759 1.082679971 1.008604924 1.089574766 0.989680765 0.92981258 1.007715974 1.007645528 0.981605317 1 13.87584748 -8.540619853 24.99920531 1.015929819 0.980227598 0.199094757 0.039422607 342.8034691 483047.1158 0.005726503 0.011454699 2.88E-09 8.540619853 -0.035702221 ADAASSLTVDVT(ph)PPTAK ddPTM_HeLa_Romidepsin_16h_R1 1 ADAASSLTVDVTPPTAK 17 0 Q9H8Y8-2;Q9H8Y8;Q9H8Y8-3 Q9H8Y8-2 GORASP2 Golgi reassembly-stacking protein 2 1 0 ADAASSLTVDVT(0.957)PPT(0.043)AK 193.32 3.77E-13 84981000 4367.4 4741.8 4208.4 4027.6 4714.1 4507.6 3437.3 4024.3 4862.9 4330.4 TRUE FALSE FALSE 4314.168449 4808.555185 4281.645437 4493.290062 4473.521886 4219.578908 3729.264176 4140.736771 4427.950045 4217.895584 1.022824857 1.140036563 1.015114137 1.065291915 1.060605176 1.000399091 0.884152797 0.981706799 1.049800773 1 12.04230767 -7.942950502 6.800383421 1.028446125 0.933867175 0.468610868 0.04592716 0.15604399 14.57752711 0.006615714 0.020094541 1.14E-08 7.942950502 -0.09457895 ADADPSPT(ph)SPPTAR ddPTM_HeLa_Romidepsin_16h_R1 1 ADADPSPTSPPTAR 14 0 Q9NWZ5;Q9NWZ5-3;Q9NWZ5-2 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 0 ADADPS(0.195)PT(0.551)S(0.254)PPTAR 132.31 0.0037365 22959000 4448.7 4712.6 4608.5 3480.1 4591.5 4342.4 3989.2 4508.1 4894.2 4458.2 TRUE FALSE FALSE 4394.477533 4778.944106 4688.709009 3882.485536 4357.178622 4064.934654 4328.042548 4638.534761 4456.450494 4342.375321 1.011998551 1.100536861 1.079756737 0.894092576 1.003409033 0.936108547 0.996699324 1.068202175 1.026270224 1 12.08426871 -9.287219178 24.99787144 1.019486167 0.979541736 0.20355326 0.053475477 1342.801751 1302068.854 0.008468862 0.012939338 5.16E-10 9.287219178 -0.039944431 ADAEGESDLENSR ddPTM_HeLa_Romidepsin_16h_R1 2 ADAEGESDLENSR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 ; ; 276.17 2.55E-93 6756300 2154.8 2127.1 2442.3 2127.5 2420.8 2309.9 2043.4 2486.3 2380.7 2253.8 FALSE FALSE TRUE 2128.536469 2157.04537 2484.807207 2373.49156 2297.257543 2162.304845 2216.966345 2558.237168 2167.764229 2195.245951 0.969611841 0.982598496 1.131903788 1.081196191 1.046469322 0.984994344 1.009894287 1.165353325 0.987481256 1 11.10016687 -9.805983234 24.98871043 0.985020164 1.062817667 0.403359723 0.050222092 107.5307549 60323.31792 0.008174631 0.010743599 1.56E-10 9.805983234 0.077797503 ADAGHAGVSANMMK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ADAGHAGVSANMMKK 15 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 0 1 ; ADAGHAGVSANMMK(1)K;ADAGHAGVSANMMK(1)K 124.42 0.000495 1975510 275.03 355.9 139.9 169.74 414.86 802.25 698.34 409.77 387.929 485.5 FALSE TRUE FALSE 271.6778286 360.9103695 142.3349008 189.3661375 393.6881461 750.9888141 757.6569822 421.6260484 353.2316587 472.88664 0.574509419 0.763206949 0.300991588 0.400447214 0.832521185 1.5880948 1.602195787 0.891600677 0.746968996 1 8.885350573 -8.362292308 5.583901342 0.721639808 1.381688621 0.585177175 0.267784027 0.142324707 6.433037397 0.043432338 0.098656367 4.34E-09 8.362292308 0.660048814 ADALQAGASQFETS(ph)AAK ddPTM_HeLa_Romidepsin_16h_R1 2 ADALQAGASQFETSAAK 17 0 Q15836;K7ENK9;K7EKX0;J3QRU4;F8WCA0;L7N2F9;P63027 Q15836 VAMP3;VAMP2 Vesicle-associated membrane protein 3;Vesicle-associated membrane protein 2 1 0 ADALQAGASQFET(0.188)S(0.812)AAK;ADALQAGASQFET(0.259)S(0.741)AAK ; 227 8.12E-36 10724100 5061.6 6830 5660.4 3168.3 4250.5 5604.4 2661.7 5394.2 5605.4 6164.8 TRUE FALSE FALSE 4999.907272 6926.152919 5758.916888 3534.633753 4033.581124 5246.296927 2887.784732 5550.272666 5104.038985 6004.637607 0.832674276 1.153467265 0.959078177 0.588650637 0.671744306 0.873707503 0.480925731 0.924330997 0.850016157 1 12.55186146 -9.276654672 24.5689218 0.942710021 0.702469726 0.426382971 0.144980718 477.0646158 770339.3353 0.021500345 0.032922106 5.29E-10 9.276654672 -0.240240295 ADAPDAGAQS(ph)DSELPSYHQNDVSLDR ddPTM_HeLa_Romidepsin_16h_R1 3 ADAPDAGAQSDSELPSYHQNDVSLDR 26 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 ADAPDAGAQS(0.591)DS(0.409)ELPSYHQNDVSLDR;ADAPDAGAQS(0.907)DS(0.093)ELPSYHQNDVSLDR;ADAPDAGAQS(0.905)DS(0.095)ELPSYHQNDVSLDR ;; 168.78 4.03E-15 107795000 8290.6 8250.8 8003.2 8778.4 18872 21595.5 14750.6 17904.5 13795.2 11897.7 TRUE FALSE FALSE 8189.550978 8366.954979 8142.492339 9793.399912 17908.89142 20215.61725 16003.5156 18422.53846 12561.32276 11588.59604 0.706690522 0.72199902 0.70262975 0.845089421 1.545389222 1.744440584 1.380971046 1.589712714 1.083938272 1 13.50041817 -8.759823641 7.010557371 0.831758715 1.567109601 0.860338497 0.142446039 0.036659434 9.527075845 0.021866233 0.041949379 1.74E-09 8.759823641 0.735350887 ADAPDAGAQSDS(ph)ELPSYHQNDVSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 ADAPDAGAQSDSELPSYHQNDVSLDR 26 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 ADAPDAGAQS(0.386)DS(0.614)ELPSYHQNDVSLDR 130.3 2.61E-07 26930000 1835.7 1773.7 1637.4 1685.8 4632.2 4577.5 3508.6 3460.7 2970.7 2422.9 TRUE FALSE FALSE 1813.325782 1798.670195 1665.89826 1880.720128 4395.801549 4285.012523 3806.620396 3560.829894 2704.993152 2359.952709 0.76837378 0.762163661 0.705903239 0.796931278 1.8626651 1.815719657 1.613007067 1.508856462 1.146206507 1 11.20454223 -8.765622679 24.99987899 0.85612057 1.702105167 0.878943138 0.152124557 24.22374472 144765.0031 0.021874714 0.040700798 1.72E-09 8.765622679 0.845984597 ADDADEFGYSR ddPTM_HeLa_Romidepsin_16h_R1 1 ADDADEFGYSR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 0 228.2 1.35E-26 61244000 2756.8 2831.9 2873.1 3011.5 3205.9 3440.1 2908.4 3356.2 3491 2680.7 FALSE FALSE TRUE 2723.199061 2871.767563 2923.1051 3359.7038 3042.29096 3220.288712 3155.439423 3453.306352 3178.756217 2611.055028 1.042949701 1.099849498 1.119511105 1.286722709 1.165157734 1.233328551 1.208492119 1.322571265 1.217422147 1 11.35041715 -9.716548617 0.836484778 1.011753414 1.24929913 0.364717363 0.078571552 0.147307531 0.206625636 0.008747163 0.014582685 1.92E-10 9.716548617 0.237545716 ADDITSLVT(ph)DT(ph)T(ph)LLVHFFGKK ddPTM_HeLa_Romidepsin_16h_R1 1 ADDITSLVTDTTLLVHFFGKK 21 1 H0YAN7;Q86XE3 H0YAN7 MICU3 "Calcium uptake protein 3, mitochondrial" 3 0 ADDIT(0.314)S(0.318)LVT(0.766)DT(0.798)T(0.803)LLVHFFGKK 42.041 0.024818 21917000 612.86 704.37 858.65 905.83 731.79 660.75 581.2 749.93 757.29 744.02 TRUE FALSE FALSE 605.3902266 714.2861393 873.5944431 1010.566327 694.4440256 618.5302075 630.5671135 771.6280414 689.5560857 724.6902531 0.835377907 0.985643365 1.205472875 1.394480362 0.958263234 0.853509765 0.87011949 1.064769449 0.951518366 1 9.50122068 -6.011958725 20.40567374 0.973454172 1.003816132 0 0.168857687 0 0 0.024671249 0 9.73E-07 6.011958725 0.03036196 ADDTDSQSWRS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 2 ADDTDSQSWRSPLK 14 1 O75369-8 O75369-8 FLNB Filamin-B 1 0 ADDT(0.117)DS(0.252)QS(0.034)WRS(0.597)PLK;ADDTDSQS(0.001)WRS(0.998)PLK ; 142.95 0.0043536 205537000 6404 6538.4 5939.4 8637.4 8852.8 9095.1 7779.9 8082.6 7338.9 6826.7 TRUE FALSE FALSE 6325.945585 6630.447767 6042.772766 9636.096828 8401.008582 8513.952463 8440.724512 8316.457279 6682.490403 6649.34135 0.951364241 0.997158578 0.908777644 1.449180651 1.263434698 1.280420423 1.26940761 1.250718957 1.004985314 1 12.69899573 -9.271006008 24.99998478 0.973625532 1.297374988 0.887939244 0.058631923 148.8571995 389000.436 0.008551598 0.013167129 5.36E-10 9.271006008 0.323749456 ADEEEMLDNLPEAGDSR ddPTM_HeLa_Romidepsin_16h_R1 1 ADEEEMLDNLPEAGDSR 17 0 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 0 109.15 0.0051872 3387900 850.66 548.01 487.52 780.81 673.99 611.03 706.17 614.36 853.7 656.31 FALSE FALSE TRUE 840.2918287 555.7248992 496.0050811 871.090926 639.5937753 571.987155 766.1520622 632.1355373 777.3429339 639.2589716 1.31447796 0.869326711 0.775906328 1.362657334 1.000523737 0.894765941 1.198500289 0.988856732 1.216006295 1 9.320256693 -10.25713249 24.98860549 1.14850348 1.01938327 0.150702134 0.173980596 708.5758915 4111170.336 0.032014679 0.038490214 5.53E-11 10.25713249 -0.129120209 ADEGIS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 ADEGISFR 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 1 0 ADEGIS(1)FR 123.96 0.016221 18969000 2691.9 2841.8 2658.1 1794.1 2744.1 3341.1 2774.4 2848 3204.9 2784.3 TRUE FALSE FALSE 2659.090087 2881.806935 2704.363115 2001.542283 2604.058337 3127.614493 3010.057467 2930.402387 2918.245717 2711.963485 0.980503647 1.062627484 0.997197466 0.738041753 0.960211431 1.15326571 1.10991814 1.080546402 1.076063794 1 11.40512204 -8.267545764 24.81901274 0.975407051 1.114110892 0.348407693 0.088371514 366.7690259 1490711.524 0.012241603 0.02806692 5.40E-09 8.267545764 0.138703841 ADEGKKETS(ph)PESSLIQDEIAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ADEGKKETSPESSLIQDEIAVK 22 2 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 ADEGKKET(0.116)S(0.671)PES(0.095)S(0.118)LIQDEIAVK 63.606 0.0082487 18786000 1330.9 1200.2 900.73 1944 1310 1155 1275.2 1426.7 1336.3 1015.9 TRUE FALSE FALSE 1314.678479 1217.096447 916.4068278 2168.774427 1243.145812 1081.199228 1383.515456 1467.979314 1216.777981 989.5067715 1.328619992 1.230003151 0.926124868 2.191773204 1.256328756 1.092664809 1.398186951 1.483546506 1.229681308 1 9.95056577 -12.36298528 0.33502572 0.839567392 1.40916375 0.0822143 0.320905986 4.829698149 0.676576771 1.048392965 0.147716518 4.34E-13 12.36298528 0.569596358 ADEHVIDQGDDGDNFYVIER ddPTM_HeLa_Romidepsin_16h_R1 3 ADEHVIDQGDDGDNFYVIER 20 0 P13861;P13861-2;H7C1L0 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 0 0 ;; ;; 149.12 9.78E-06 23076000 3643.37 3507.1 3431.22 3332.05 3432.2 3996.5 3450.29 3806.4 3885 3751.78 FALSE FALSE TRUE 3598.963205 3556.473046 3490.938945 3717.317299 3257.042027 3741.136548 3743.357546 3916.532178 3537.51587 3654.308215 0.98485486 0.973227445 0.955294064 1.017242411 0.891288265 1.023760539 1.024368314 1.071757484 0.968039821 1 11.8353826 -7.647815182 2.155035282 0.9841593 1.065442878 0.426214766 0.035185431 0.277193742 2.280367646 0.004721601 0.031868304 2.25E-08 7.647815182 0.081283578 ADEK(ac)PK(ac)EGVKTENNDHINLK ddPTM_HeLa_Romidepsin_16h_R1 1 ADEKPKEGVKTENNDHINLK 20 3 P61956-2;P61956 P61956-2 SUMO2 Small ubiquitin-related modifier 2 0 2 ADEK(0.914)PK(0.543)EGVK(0.543)TENNDHINLK 46.663 0.020851 880880 751.67 623.97 371.02 649.43 607.19 596.45 751.34 802.89 804.7 778.73 FALSE TRUE FALSE 742.5083569 632.754266 377.4774475 724.5201523 576.2028286 558.33877 815.1588008 826.1203554 732.7256166 758.4984823 0.978918711 0.834219555 0.497664077 0.955203167 0.759662467 0.736110596 1.074700635 1.089152285 0.966021203 1 9.567002484 -10.27850776 6.99737443 0.990243835 0.840823967 0.119177635 0.162966597 0.245622602 61.54719674 0.028216423 0.032798209 5.27E-11 10.27850776 -0.149419868 ADEVAPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ADEVAPAKK 9 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 1 ; ADEVAPAK(1)K;ADEVAPAK(1)K 107.69 0.0031065 24119000 9662 8973.1 9717.4 12281.5 16572 18247.7 18330.3 16248.8 11487.8 10039.3 FALSE TRUE FALSE 9544.235828 9099.423537 9886.527271 13701.54482 15726.269 17081.73086 19887.27522 16718.93339 10460.3024 9778.477539 0.976045176 0.930556265 1.01104975 1.401194078 1.608253324 1.746870184 2.033780325 1.709768553 1.069727098 1 13.25539415 -8.872301208 1.39632425 0.979227348 1.857074704 0.942089672 0.091809064 0.056075098 0.218960393 0.013117821 0.030953733 1.34E-09 8.872301208 0.877847357 ADFDNTVAIHPTS(ph)SEELVTLR ddPTM_HeLa_Romidepsin_16h_R1 1 ADFDNTVAIHPTSSEELVTLR 21 0 P00390-5;P00390-4;P00390-2;P00390-3;P00390 P00390-5 GSR "Glutathione reductase, mitochondrial" 1 0 ADFDNTVAIHPT(0.379)S(0.504)S(0.079)EELVT(0.038)LR 75.529 0.00081866 0 837.63 524.13 561.09 768.49 598.32 662.61 662.02 687.11 853.5 605.99 TRUE FALSE FALSE 827.4206434 531.5087159 570.8555361 857.3464297 567.7854978 620.2713595 718.2519623 706.9904438 777.1608224 590.2462924 1.401822687 0.900486327 0.967148025 1.452523194 0.961946742 1.050868709 1.216868232 1.197788877 1.316672095 1 9.205173264 -10.26085559 24.99876121 1.189749595 1.111240211 0.083386545 0.179812204 177.4948889 7600659.457 0.034779765 0.041218235 5.48E-11 10.26085559 -0.078509384 ADGGTGDSS(ph)PSPGSSLPSPLSDPR ddPTM_HeLa_Romidepsin_16h_R1 2 ADGGTGDSSPSPGSSLPSPLSDPR 24 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 0 ADGGT(0.003)GDS(0.108)S(0.889)PSPGSSLPSPLSDPR;ADGGT(0.007)GDS(0.209)S(0.665)PS(0.036)PGS(0.081)S(0.001)LPSPLSDPR ; 205 1.90E-39 10366000 5687.1 5804.7 5318.9 4797.5 5882.3 6456.6 5320.2 5522.1 6259.4 5558.1 TRUE FALSE FALSE 5617.783438 5886.418719 5411.473223 5352.209523 5582.104281 6044.044098 5772.097655 5681.873251 5699.543587 5413.699761 1.037697635 1.08731902 0.999588722 0.988641735 1.031107104 1.116435038 1.066202026 1.049536085 1.052800088 1 12.40239916 -8.453783029 9.091774905 1.020241232 1.076026797 0.319725902 0.031828506 0.345296644 43.34031675 0.004593498 0.010274177 3.52E-09 8.453783029 0.055785564 ADGGTGDSSPSPGSS(ph)LPSPLSDPR ddPTM_HeLa_Romidepsin_16h_R1 1 ADGGTGDSSPSPGSSLPSPLSDPR 24 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 0 ADGGTGDS(0.049)S(0.049)PS(0.065)PGS(0.131)S(0.544)LPS(0.131)PLS(0.03)DPR 82.529 0.00024395 9086300 1938.9 1853.2 1774.7 1938.2 2106.7 2397.1 2084.4 1946 2214.8 2330.4 TRUE FALSE FALSE 1915.267941 1879.289398 1805.587909 2162.303804 1999.187238 2243.933046 2261.448884 2002.30444 2016.702741 2269.855872 0.843783944 0.82793336 0.795463682 0.952617226 0.880755145 0.988579528 0.996296246 0.882128449 0.888471716 1 11.14838498 -6.937791192 14.05292124 0.916722979 0.623226415 0 0.070511037 1412158.89 8705985.393 0.011580672 11507875.77 1.15E-07 6.937791192 -0.293496564 ADGGTGDSSPSPGSSLPS(ph)PLSDPR ddPTM_HeLa_Romidepsin_16h_R1 1 ADGGTGDSSPSPGSSLPSPLSDPR 24 0 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 0 ADGGTGDSSPSPGS(0.033)S(0.281)LPS(0.676)PLS(0.01)DPR 184.62 2.23E-18 2351800 533.65 483.37 591.43 628.53 749.98 559.36 561.19 799.19 949.4 696.88 TRUE FALSE FALSE 527.1456685 490.1748955 601.7235911 701.2035959 711.705722 523.6187013 608.8574646 822.3133017 864.4832862 678.7749571 0.776613313 0.722146406 0.886484666 1.03304282 1.048514997 0.771417236 0.89699459 1.211466765 1.273593372 1 9.406789529 -9.363026854 7.398288593 0.875301896 0.977647438 0 0.178669426 0.496699192 31.96236182 0.02221423 0.03398372 4.33E-10 9.363026854 0.102345541 ADGYEPPVQES(ph)V ddPTM_HeLa_Romidepsin_16h_R1 2 ADGYEPPVQESV 12 0 D6RAT0;P61247;D6R9B6;H0Y9Y4 D6RAT0 RPS3A 40S ribosomal protein S3a 1 0 ADGYEPPVQES(1)V;ADGYEPPVQES(1)V ; 145.81 0.001505 62008000 10638 11208.5 10197.6 9710.6 10914.9 10785.2 8915.8 10237.8 11607.7 10726.1 TRUE FALSE FALSE 10508.33996 11366.29356 10375.08495 10833.38526 10357.87192 10096.06053 9673.107829 10534.01459 10569.47824 10447.43438 1.005829717 1.087950701 0.99307491 1.036942169 0.991427326 0.966367451 0.925883569 1.008287223 1.011681707 1 13.35086108 -8.40718354 3.543096905 1.011324928 0.962835784 0.343142768 0.032428512 0.226580722 5.179781703 0.004591433 0.010860273 3.92E-09 8.40718354 -0.048489145 ADHGEPIGR ddPTM_HeLa_Romidepsin_16h_R1 1 ADHGEPIGR 9 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 81.95 0.026691 5348500 2171.2 2485.3 3990.6 2694 2317.1 2582.9 5982 481.94 3863.6 3035.6 FALSE FALSE TRUE 2144.736579 2520.288119 4060.054719 3005.492956 2198.849741 2417.861026 6490.110931 495.8841735 3518.029939 2956.734674 0.725373365 0.852389002 1.373154904 1.016490584 0.743675028 0.817747039 2.195026489 0.16771345 1.189836197 1 11.52978907 ADIDVSGPKVDIDT(ph)PDIDIHGPEGK ddPTM_HeLa_Romidepsin_16h_R1 2 ADIDVSGPKVDIDTPDIDIHGPEGK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ADIDVS(0.081)GPKVDIDT(0.919)PDIDIHGPEGK;ADIDVS(0.004)GPKVDIDT(0.996)PDIDIHGPEGK ; 67.785 0.00027931 40697000 10716.4 14714.3 7397.2 14855 11661.5 7893.5 6407 7792.3 9202.1 8674.7 TRUE FALSE FALSE 10585.78439 14921.4483 7525.945163 16572.60499 11066.37014 7389.130825 6951.21042 8017.757906 8379.041129 8449.330043 1.252854882 1.765991886 0.890715018 1.961410539 1.309733444 0.874522688 0.822693679 0.948922325 0.991681126 1 13.04462124 -8.253072453 23.342676 1.229866498 0.876110889 0.242347988 0.325921213 330.1466025 921058.5699 0.046749127 0.116812758 5.58E-09 8.253072453 -0.353755609 ADIEISGPK ddPTM_HeLa_Romidepsin_16h_R1 1 ADIEISGPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 117.89 0.012426 453530 620.28 434.53 383.11 326.46 510.01 459.03 509.88 514.91 557.73 589.4 FALSE FALSE TRUE 612.7197888 440.6473247 389.7778688 364.2068412 483.9822866 429.6994645 553.1891945 529.8081085 507.8452319 574.087303 1.067293747 0.767561523 0.678952255 0.634410201 0.843046491 0.748491496 0.963597682 0.922870277 0.884613245 1 9.165126338 -10.25958602 24.99999912 1.031777605 0.790203376 0.377546236 0.106436796 93.11213418 1255988.712 0.017475064 0.020829957 5.50E-11 10.25958602 -0.241574229 ADIKS(ph)PSLDVTVPEAELNLETPEISVGGK ddPTM_HeLa_Romidepsin_16h_R1 1 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ADIKS(0.65)PS(0.285)LDVT(0.065)VPEAELNLETPEISVGGK 70.54 3.67E-05 65468000 5133 5404.5 5041.5 5382.9 7665.7 7951.9 6822.2 8292.9 5367.3 5803.1 TRUE FALSE FALSE 5070.437022 5480.584693 5129.245193 6005.296225 7274.490724 7443.799254 7401.677498 8532.841977 4887.235245 5652.334625 0.897051813 0.969614337 0.907456039 1.062445277 1.286988688 1.316942422 1.309490324 1.509613734 0.864640112 1 12.46463116 -8.755381238 1.785833063 0.947611935 1.378333055 0.911356289 0.063453788 0.072333976 0.468156036 0.009584179 0.022095203 1.76E-09 8.755381238 0.43072112 ADIKSPS(ph)LDVTVPEAELNLETPEISVGGK ddPTM_HeLa_Romidepsin_16h_R1 1 ADIKSPSLDVTVPEAELNLETPEISVGGK 29 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ADIKS(0.363)PS(0.505)LDVT(0.132)VPEAELNLETPEISVGGK 86.004 4.02E-07 56762000 6077.7 5213.4 5540.4 5945.2 8169 8945.2 7957 8425 6313.6 5873.1 TRUE FALSE FALSE 6003.622655 5286.794382 5636.828338 6632.611997 7752.105447 8373.630589 8632.867381 8668.764083 5748.895803 5720.516015 1.049489703 0.924181379 0.985370607 1.159442956 1.355140939 1.46378938 1.509106409 1.51538149 1.004961054 1 12.48192957 -8.736317422 1.722368832 1.011978348 1.502422782 0.974708381 0.03602154 0.044107703 0.2649683 0.006460789 0.01527089 1.84E-09 8.736317422 0.490444433 ADILEDK(ac)DGK ddPTM_HeLa_Romidepsin_16h_R1 2 ADILEDKDGK 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0QZM1;M0QYQ7;M0R0N3;M0R019 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 1 ; ADILEDK(1)DGK;ADILEDK(1)DGK 152.04 0.0090369 4718700 2915.9 3087.1 2760.7 2114.86 4842.9 3423.4 3431 3718.4 4584.3 3848.6 FALSE TRUE FALSE 2880.359889 3130.560275 2808.748825 2359.390064 4595.748742 3204.655789 3722.429054 3825.986037 4174.268726 3748.612817 0.768380206 0.835124999 0.749276856 0.62940351 1.225986509 0.854891114 0.993015079 1.020640494 1.113550246 1 11.87214111 -8.759327993 24.99999965 0.855347128 1.009393215 0.238960685 0.151342444 69.65661373 824753.4494 0.021212594 0.040820308 1.74E-09 8.759327993 0.154046088 ADINTK(ac)WAATR ddPTM_HeLa_Romidepsin_16h_R1 1 ADINTKWAATR 11 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 1 ADINTK(1)WAATR 142.19 0.0037453 1901300 271.78 362.78 307.64 214.56 646.61 487.89 423.1 311.51 666.02 1143.8 FALSE TRUE FALSE 268.4674408 367.8872264 312.9943452 239.3684367 613.6110789 456.7154036 459.0381034 320.5230504 606.4495031 1114.083911 0.240975961 0.330215007 0.280943241 0.21485674 0.550776358 0.409947042 0.412031894 0.287700996 0.544348138 1 10.12164218 -12.27335581 0.889421504 1.020428584 0.340642081 0.437786466 0.165578562 0.177248708 0.239694853 0.081513556 0.019687919 5.33E-13 12.27335581 -0.679786503 ADK(ac)PDMGEIASFDK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 ADKPDMGEIASFDKAK 16 2 P63313 P63313 TMSB10 Thymosin beta-10 0 2 ; ADK(1)PDMGEIASFDK(1)AK;ADK(1)PDMGEIASFDK(1)AK 65.038 0.019366 2958060 1987.03 1851.65 1679.75 1781.5 1794.69 1847.15 1783.21 1810.27 2694.9 2333.8 FALSE TRUE FALSE 1962.811314 1877.717577 1708.985344 1987.485412 1703.100272 1729.123076 1934.675813 1862.647306 2453.861394 2273.16754 0.863469709 0.826035717 0.751807913 0.87432421 0.749218983 0.760666799 0.851092486 0.819406082 1.079489898 1 11.1504883 -11.40756416 0.545437831 1.003628009 0.797456674 0.766348406 0.049450701 0.293550447 0.184989811 0.027564191 0.011770754 3.91E-12 11.40756416 -0.206171335 ADLAEEYSKDR ddPTM_HeLa_Romidepsin_16h_R1 1 ADLAEEYSKDR 11 1 P68036-2;P68036;P68036-3 P68036-2 UBE2L3 Ubiquitin-conjugating enzyme E2 L3 0 0 106.16 0.0186 16625000 3990.9 4251.4 3228.8 3359.4 3856.2 4107.7 3675.8 4013.9 4502.6 3827.3 FALSE FALSE TRUE 3942.257376 4311.251321 3284.99591 3747.829634 3659.403725 3845.231227 3988.02236 4130.035864 4099.876179 3727.866194 1.057510428 1.156493044 0.881200059 1.005355192 0.981634944 1.031483167 1.069786884 1.107882002 1.099791668 1 11.86413436 -7.585194834 2.49275975 1.021737226 1.105999237 0.123843571 0.069061397 0.460610727 5.136792434 0.009082061 0.060739584 2.60E-08 7.585194834 0.084262011 ADLDVSGPK ddPTM_HeLa_Romidepsin_16h_R1 1 ADLDVSGPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 104.2 0.0059872 0 1720.5 1364.2 1734.9 1154.4 1771.2 2026.8 1871.5 1730.9 1512.8 1633.1 FALSE FALSE TRUE 1699.529884 1383.405243 1765.095207 1287.87716 1680.809055 1897.294021 2030.465163 1780.980861 1377.491379 1590.671827 1.068435271 0.869698715 1.109653907 0.809643534 1.056666137 1.192762699 1.27648276 1.119640664 0.865980874 1 10.63542051 -8.309071059 4.282789955 1.009665038 1.205923501 0.47908986 0.103436882 0.135968304 5.434806719 0.012756389 0.030513084 4.91E-09 8.309071059 0.196258462 ADLLQREEEEEEEEDQEGDRETTIR ddPTM_HeLa_Romidepsin_16h_R1 1 ADLLQREEEEEEEEDQEGDRETTIR 25 2 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 0 85.61 3.27E-05 3747800 669.31 746.82 593.25 839.09 604.82 591.5 541.15 769.63 739.46 655.87 FALSE FALSE TRUE 661.1521923 757.3337516 603.5752674 936.1095338 573.9537785 553.705059 587.1152675 791.8980298 673.3208456 638.8304029 1.034941652 1.185500484 0.944812997 1.465349066 0.898444683 0.866748133 0.91904716 1.239606046 1.053989983 1 9.319289164 -7.239204346 23.21288898 1.030491881 1.239606639 0.110220587 0.166924965 3443.330133 3594616.023 0.021765208 1.273903019 5.76E-08 7.239204346 0.209114758 ADLNQGIGEPQS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 ADLNQGIGEPQSPSR 15 0 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 ADLNQGIGEPQS(0.994)PS(0.006)R;ADLNQGIGEPQS(0.945)PS(0.055)R ; 186.96 1.88E-09 182506000 6408.9 5883.9 7288.5 4995.8 6640.4 7309 5915.8 6371.9 7355.8 6665.7 TRUE FALSE FALSE 6330.785862 5966.733699 7415.353285 5573.437902 6301.515609 6841.978489 6418.287904 6556.260873 6697.878825 6492.524153 0.975088535 0.919016019 1.142137189 0.858439302 0.970580234 1.05382411 0.988565888 1.00981694 1.031629404 1 12.66456376 -8.305291586 24.92277223 0.983494315 1.014518803 0.040672844 0.070732733 1152.497197 655002.73 0.009085035 0.020314891 4.95E-09 8.305291586 0.031024489 ADLNQGIGEPQS(ph)PSRR ddPTM_HeLa_Romidepsin_16h_R1 2 ADLNQGIGEPQSPSRR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 ADLNQGIGEPQS(0.844)PS(0.156)RR;ADLNQGIGEPQS(0.947)PS(0.053)RR ; 168.68 2.33E-05 42490000 3900.7 3949.7 3879.1 4239.9 4402.4 4400.3 3700.3 3208.7 4432.1 3963.1 TRUE FALSE FALSE 3853.156768 4005.30398 3946.614108 4730.137187 4177.7291 4119.135031 4014.60339 3301.538672 4035.681876 3860.138091 0.998191432 1.037606398 1.022402312 1.225380304 1.08227452 1.067095253 1.040015485 0.855290302 1.045476038 1 11.91443674 -10.01119219 2.342107133 0.999153832 1.058523098 0.01550159 0.085715983 0.569048921 6.219461135 0.014558128 0.0189033 9.75E-11 10.01119219 0.059369266 ADNPSPNLMPAS(ph)AQAQNAQR ddPTM_HeLa_Romidepsin_16h_R1 1 ADNPSPNLMPASAQAQNAQR 20 0 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 0 ADNPSPNLMPAS(1)AQAQNAQR 161.25 6.37E-08 7557600 2857.2 2892.4 2449 2325.1 2004.9 1911.7 1309.8 1699.4 3016.9 3166.3 TRUE FALSE FALSE 2822.375347 2933.119283 2491.623818 2593.939002 1902.582472 1789.54854 1421.054379 1748.569458 2747.060908 3084.03907 0.91515551 0.951064243 0.807909291 0.841085 0.616912571 0.580261306 0.460777035 0.566973835 0.890734795 1 11.59060533 -8.826298946 0.801339245 0.96505973 0.483486972 0.912966341 0.053071378 0.113316686 0.134267086 0.008724409 0.030229933 1.49E-09 8.826298946 -0.481572758 ADNSSDSPT(ph)TLK ddPTM_HeLa_Romidepsin_16h_R1 2 ADNSSDSPTTLK 12 0 Q5VWN6;A0A2R8YH03;J3KPH3 Q5VWN6 FAM208B Protein FAM208B 1 0 ADNSSDS(0.12)PT(0.726)T(0.153)LK;ADNS(0.003)S(0.072)DS(0.249)PT(0.546)T(0.13)LK ; 138.55 0.0046304 9026700 2553.1 2192.25 2481.7 2431.2 3177.6 3588.6 3296.5 3252.1 2653.4 2383.1 TRUE FALSE FALSE 2521.981835 2223.112553 2524.892947 2712.306783 3015.435215 3359.300042 3576.504628 3346.194383 2416.073258 2321.186718 1.08650537 0.957748265 1.087759519 1.168500044 1.299092051 1.447233872 1.540808673 1.441587769 1.040878461 1 11.18064686 -8.658076826 1.288005843 1.035518072 1.5015983 0.954341713 0.042491534 0.06933717 0.226141934 0.007501956 0.021694938 2.20E-09 8.658076826 0.466080228 ADNSSDSPTT(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 ADNSSDSPTTLK 12 0 Q5VWN6;A0A2R8YH03;J3KPH3 Q5VWN6 FAM208B Protein FAM208B 1 0 ADNSSDS(0.005)PT(0.299)T(0.696)LK 135.91 0.0054424 4530100 1680.3 1633.3 1579 1473.8 1956.4 2127.6 1945.4 2202.3 1782.3 1737.2 TRUE FALSE FALSE 1659.819857 1656.29364 1606.481833 1644.20769 1856.557608 1991.653227 2110.642227 2266.020076 1622.886624 1692.067294 0.980941989 0.97885802 0.949419588 0.971715307 1.097212631 1.177053202 1.247374874 1.339202102 0.959114706 1 10.72457123 -8.082031548 1.188336867 0.984494547 1.331128979 0.963193728 0.025289658 0.079186117 0.18560019 0.004035433 0.023351813 8.28E-09 8.082031548 0.346634432 ADQEQQDPLEY(ph)LQSDEEDDEKR ddPTM_HeLa_Romidepsin_16h_R1 1 ADQEQQDPLEYLQSDEEDDEKR 22 1 Q7RTV3 Q7RTV3 ZNF367 Zinc finger protein 367 1 0 ADQEQQDPLEY(0.801)LQS(0.199)DEEDDEKR 84.166 0.00031551 9838600 1097.7 840.3 755.95 995.34 537.86 516.6 457.55 466.63 1090.1 930.46 TRUE FALSE FALSE 1084.32081 852.1297655 769.1069926 1110.425894 510.4109972 483.5909273 496.4142856 480.1312028 992.5987258 906.2865151 1.196443721 0.940243236 0.848635591 1.22524817 0.563189443 0.533596075 0.547745418 0.529778602 1.095237223 1 9.823823408 -8.749331506 24.78012718 1.070150968 0.543161941 0.845857194 0.105921357 61.2536735 125361.6672 0.017385992 0.034558255 1.78E-09 8.749331506 -0.526989027 APAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_HeLa_Romidepsin_16h_R1 1 APAGQEEPGTPPSSPLSAEQLDR 23 0 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 0 APAGQEEPGT(0.969)PPS(0.569)S(0.39)PLS(0.072)AEQLDR 62.108 0.0072758 5781400 578.61 498.93 355.99 396.91 220.57 261.78 267.2 166.94 593.64 570.17 TRUE FALSE FALSE 571.5576788 505.9539496 362.1858566 442.8026017 209.3134898 245.0531029 289.8959613 171.7701455 540.5433516 555.3569012 1.029171831 0.911042878 0.652167743 0.797329791 0.376899052 0.441253368 0.521999386 0.30929686 0.973326073 1 9.11727141 -9.289451479 0.882467054 1.019590969 0.399477285 0.866942517 0.095471163 0.122944504 0.189428742 0.016720035 0.036841204 5.14E-10 9.289451479 -0.620113685 down ADRDESSPYAAMLAAQDVAQR ddPTM_HeLa_Romidepsin_16h_R1 1 ADRDESSPYAAMLAAQDVAQR 21 1 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 0 67.312 0.010792 10500000 2538.4 4057.2 3059.6 2489.1 3390.2 3933.7 2271.2 3749.5 3049 2743.2 FALSE FALSE TRUE 2507.461004 4114.317368 3112.851055 2776.901454 3217.185443 3682.349265 2464.115671 3857.985867 2776.289804 2671.931269 0.938445174 1.539829043 1.165019135 1.039286259 1.20406744 1.378160175 0.922222701 1.443894127 1.039057343 1 11.38366718 ADREVQAEQPSSS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 ADREVQAEQPSSSSPR 16 1 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 0 ADREVQAEQPS(0.002)S(0.015)S(0.492)S(0.492)PR 70.272 0.01501 8904500 2827.6 2232.4 2463 1105.1 2564.2 3068.7 2653.6 2306.7 3062 2444.4 TRUE FALSE FALSE 2793.136124 2263.827786 2505.867482 1232.876862 2433.339306 2872.619974 2878.996718 2373.440725 2788.127051 2380.894136 1.173145871 0.95083093 1.052490089 0.517820949 1.02202751 1.206529904 1.209208202 0.996869491 1.171042009 1 11.21728776 -10.23964451 24.24211702 1.08176334 0.995208001 0.073350002 0.186368115 1608.959072 1789624.29 0.032895992 0.040265937 5.76E-11 10.23964451 -0.086555339 ADREVQAEQPSSSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ADREVQAEQPSSSSPR 16 1 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 0 ADREVQAEQPS(0.003)S(0.027)S(0.479)S(0.49)PR 61.757 0.024069 9392200 4216.3 3643.2 3210.3 3429.4 4029.9 3975.5 3742 3244.8 4039.8 3792 TRUE FALSE FALSE 4164.910114 3694.489065 3266.173925 3825.923364 3824.239165 3721.47838 4059.845387 3338.683169 3678.47017 3693.483293 1.127637458 1.00027231 0.884307215 1.035857769 1.035401777 1.007579589 1.099191485 0.903938885 0.99593524 1 11.85076634 -10.06033488 24.94936893 1.060467042 0.998393256 0.064421867 0.068765999 356.2554611 147315.9074 0.012145642 0.014875327 8.70E-11 10.06033488 -0.062073786 ADS(ph)LLAVVK ddPTM_HeLa_Romidepsin_16h_R1 2 ADSLLAVVK 9 0 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 ADS(1)LLAVVK;ADS(1)LLAVVK ; 129.89 0.0083308 28709000 6398.5 5906.4 6773.1 5944.3 6036.6 5736 5079.7 4875.9 6070.6 5722.9 TRUE FALSE FALSE 6320.512621 5989.550454 6890.982964 6631.607935 5728.529776 5369.488112 5511.169591 5016.976474 5527.630332 5574.218233 1.133883238 1.074509501 1.236224108 1.189692914 1.027683083 0.963271958 0.988689241 0.900032303 0.991642254 1 12.44455377 -8.422081345 3.76016644 1.088520816 0.955029785 0.447548417 0.075067494 0.215166605 5.501290341 0.012338542 0.028779905 3.78E-09 8.422081345 -0.133491031 ADS(ph)PAGPESSRR ddPTM_HeLa_Romidepsin_16h_R1 1 ADSPAGPESSRR 12 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 ADS(1)PAGPESSRR 86.738 0.010141 4453700 1607.1 1897.9 1387.5 1508.6 1130.8 1159.2 1534.6 1049.3 1647.1 1452.8 TRUE FALSE FALSE 1587.512047 1924.618686 1411.648855 1683.03143 1073.091056 1085.130861 1664.948886 1079.65984 1499.779251 1415.056047 1.121872205 1.360100676 0.997592186 1.189374396 0.758338201 0.76684656 1.176595718 0.762980267 1.059872684 1 10.46664348 -8.764974952 24.99987783 1.087345714 0.881266038 0.390437533 0.152266625 87.73367377 620366.6107 0.022418522 0.041837861 1.72E-09 8.764974952 -0.206079677 ADS(ph)PLEQPEGSPLTQDDR ddPTM_HeLa_Romidepsin_16h_R1 2 ADSPLEQPEGSPLTQDDR 18 0 P09603-3;P09603-2;P09603 P09603-3 CSF1 Macrophage colony-stimulating factor 1;Processed macrophage colony-stimulating factor 1 1 0 ADS(1)PLEQPEGSPLTQDDR;ADS(0.999)PLEQPEGS(0.001)PLTQDDR ; 218.11 2.92E-29 5062100 1294.72 1510.96 1539.45 1055.74 1190.73 1063.75 656.11 1192.71 1701.82 1625.26 TRUE FALSE FALSE 1278.939455 1532.231335 1566.243481 1177.809626 1129.962605 995.7798081 711.839967 1227.219182 1549.604957 1583.035511 0.8079032 0.967907115 0.989392512 0.744019713 0.713794856 0.629031883 0.449667719 0.775231619 0.978881994 1 10.6284779 -8.860764687 1.812520306 0.917306121 0.609435187 0.689304316 0.096376077 0.166223924 1.106151943 0.016238843 0.035057984 1.38E-09 8.860764687 -0.307870935 ADS(ph)PVNGLPK ddPTM_HeLa_Romidepsin_16h_R1 1 ADSPVNGLPK 10 0 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 0 ADS(1)PVNGLPK 104.59 0.021547 93865000 10365 9137.9 9026.1 7882.3 9145.4 9137.2 8759.3 9484.7 9645.5 9590 TRUE FALSE FALSE 10238.66739 9266.543596 9183.195484 8793.688613 8678.676112 8553.362409 9503.314723 9759.12483 8782.782322 9340.850418 1.096117263 0.992044962 0.983121994 0.941422699 0.929109848 0.915694185 1.017392882 1.044779051 0.940255108 1 13.18933819 -10.05208637 6.084401875 1.045495896 0.969483431 0 0.054021692 0.194718945 16.69749693 0.00868533 0.01075771 8.87E-11 10.05208637 -0.076012465 ADS(ph)VPGTYR ddPTM_HeLa_Romidepsin_16h_R1 1 ADSVPGTYR 9 0 A0A0U1RQC1;H0YMA4;A0A0U1RQM0;Q15004-2;Q15004;H0YKX3 A0A0U1RQC1 KIAA0101 PCNA-associated factor 1 0 ADS(0.997)VPGT(0.003)YR 108.47 0.020637 5314500 2190.7 2479.6 2583.1 1643.5 2136.4 1989.2 1518.9 1800.3 2662.4 2558.9 TRUE FALSE FALSE 2163.998906 2514.507874 2628.057772 1833.529203 2027.371536 1862.09654 1647.915328 1852.38884 2424.268276 2492.419409 0.868232248 1.008862258 1.054420361 0.735642323 0.813415081 0.747104012 0.661170958 0.743209122 0.972656635 1 11.28333114 -9.243318262 24.55625339 0.950611148 0.740184117 0.797778845 0.059636075 295.2618386 400114.7378 0.010877911 0.018013775 5.71E-10 9.243318262 -0.210427031 ADSEGSNSGGT(ph)WPK ddPTM_HeLa_Romidepsin_16h_R1 1 ADSEGSNSGGTWPK 14 0 Q8TDM6-4;Q8TDM6;Q8TDM6-3 Q8TDM6-4 DLG5 Disks large homolog 5 1 0 ADSEGSNS(0.001)GGT(0.999)WPK 109.55 0.011905 6333000 1657.3 1827.9 1682.7 4754.3 1210.6 1361.6 1130.1 1322.3 1843.7 1559.4 TRUE FALSE FALSE 1637.10019 1853.633224 1711.986688 5304.014536 1148.818565 1274.598154 1226.090666 1360.558664 1678.794854 1518.886563 1.077829135 1.220389507 1.127132683 3.492041252 0.756355736 0.839166127 0.807229911 0.895760551 1.105279943 1 10.56879841 -5.97376738 12.72119811 1.157146838 0.837972726 0 0.770896809 0 0 0.098984142 0 1.06E-06 5.97376738 -0.319174112 ADSGPTQPPLS(ph)LSPAPETK ddPTM_HeLa_Romidepsin_16h_R1 3 ADSGPTQPPLSLSPAPETK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;A0A0C4DH09;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 ADSGPT(0.002)QPPLS(0.843)LS(0.138)PAPET(0.018)K;ADSGPTQPPLS(0.499)LS(0.499)PAPET(0.001)K;ADSGPTQPPLS(0.68)LS(0.32)PAPETK ;; 216.75 2.29E-29 818300000 15249.9 16348.6 12988.7 12703.9 17599.9 17208.5 16753.2 19645.4 16166.9 14928.2 TRUE FALSE FALSE 15064.02835 16578.75602 13214.76287 14172.78469 16701.71143 16108.93239 18176.21639 20213.80865 14720.89197 14540.36321 1.036014585 1.140188576 0.908833066 0.974720128 1.14864472 1.107876891 1.250052432 1.390185951 1.012415698 1 13.82777569 -7.371557255 0.871475561 1.017604674 1.56320821 0.783382013 0.063248753 0.631640906 0.392289281 0.009884437 0.31599272 4.25E-08 7.371557255 0.545603535 ADSGPTQPPLSLS(ph)PAPETK ddPTM_HeLa_Romidepsin_16h_R1 2 ADSGPTQPPLSLSPAPETK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;A0A0C4DH09;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 ADSGPTQPPLS(0.313)LS(0.662)PAPET(0.025)K;ADSGPTQPPLS(0.001)LS(0.999)PAPETK ; 125.79 0.00037678 99207800 6032.8 6263.7 5346.7 5133.7 7510.9 7602.4 6239.7 8077.4 7083.7 6163 TRUE FALSE FALSE 5959.269913 6351.880533 5439.757071 5727.282549 7127.590746 7116.631176 6769.699962 8311.106825 6450.116131 6002.884372 0.992734416 1.058138078 0.906190547 0.954088434 1.187360993 1.185535275 1.12774119 1.384518893 1.074502811 1 12.55144016 -6.839585229 0.555001819 0.991096124 1.775270486 0.690246812 0.074203701 2.09624505 0.315114221 0.013101308 1.175096978 1.45E-07 6.839585229 0.784174362 ADSLLAVVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 ADSLLAVVKR 10 1 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 1 ADSLLAVVK(1)R 128.86 0.0022847 5777100 858.4 946.19 1200.1 907.5 863.12 1059.3 1065 658.62 1005.4 981.02 FALSE TRUE FALSE 847.9374906 959.5104877 1220.987237 1012.42942 819.0717657 991.6141487 1155.461073 677.6761306 915.4745059 955.532959 0.887397428 1.004162628 1.277807558 1.059544216 0.857188397 1.037760278 1.209232044 0.709212722 0.958077372 1 9.900161826 -10.00959453 24.70590253 0.946771477 1.037413762 0.044221267 0.153128723 853.9524163 2198928.794 0.024316793 0.030984082 9.78E-11 10.00959453 0.090642285 ADT(ph)PGPEDGGVK ddPTM_HeLa_Romidepsin_16h_R1 2 ADTPGPEDGGVK 12 0 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 ADT(1)PGPEDGGVK;ADT(1)PGPEDGGVK ; 161.25 0.0014309 11849300 12361.1 12099.6 11417.8 8135.3 7934.4 7742 5888.3 6626.1 12841.3 12708.1 TRUE FALSE FALSE 12210.43816 12269.93849 11616.52202 9075.941664 7529.477961 7247.311186 6388.452055 6817.815749 11692.74197 12377.94173 0.986467575 0.991274539 0.938485757 0.733235126 0.608298062 0.585502125 0.516115861 0.550803671 0.944643481 1 13.59548382 -9.056687279 1.482653323 0.99532279 0.546288074 0.986176081 0.022897114 0.020766668 0.090312038 0.002687307 0.00554753 8.78E-10 9.056687279 -0.449034716 ADVLEAHEAEAEEPEAGKS(ph)EAEDDEDEVDDLPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ADVLEAHEAEAEEPEAGKSEAEDDEDEVDDLPSSR 35 1 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 ADVLEAHEAEAEEPEAGKS(0.999)EAEDDEDEVDDLPS(0.001)S(0.001)R 77.876 1.56E-08 59428000 3352 3041.8 3181 3136.9 3110.9 3223.7 2974.1 3448.6 3621.7 3062.9 TRUE FALSE FALSE 3311.144535 3084.62254 3236.363971 3499.603138 2952.139165 3017.715974 3226.71998 3548.3798 3297.766081 2983.325416 1.109883795 1.033954433 1.084817618 1.173054444 0.98954648 1.011527592 1.081584986 1.189404207 1.105399385 1 11.54270564 -12.43554555 1.062120458 0.99803841 1.08259937 0 0.068426856 0.714870753 1.387443098 0.046924301 0.010687913 3.67E-13 12.43554555 0.084560959 ADVVPQQADPEFPRAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ADVVPQQADPEFPRASPR 18 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 ADVVPQQADPEFPRAS(1)PR;ADVVPQQADPEFPRAS(1)PR ; 144.33 3.59E-05 111518000 13695.4 12668.4 11781.2 12942.7 10032.5 8938.8 8492.7 9537.6 13301.1 12775.4 TRUE FALSE FALSE 13528.4752 12846.74607 11986.24684 14439.19587 9520.504089 8367.639529 9214.069726 9813.555408 12111.4163 12443.49327 1.087192712 1.03240672 0.963254175 1.160381218 0.765098987 0.672451003 0.740472915 0.788649553 0.973313204 1 13.60310393 -8.688971558 7.17718963 1.042185006 0.733669328 0.851550187 0.060210974 0.05659999 4.675110289 0.008318988 0.016671086 2.05E-09 8.688971558 -0.308515677 S(ph)LNDDGSSDPR ddPTM_HeLa_Romidepsin_16h_R1 1 SLNDDGSSDPR 11 0 P54259 P54259 ATN1 Atrophin-1 1 0 S(0.985)LNDDGS(0.014)SDPR 94.688 0.026798 3424300 2674.6 2503.8 2168.5 1084.5 1463 978.48 875.94 1038 2569.3 2315.7 TRUE FALSE FALSE 2642.000946 2539.048562 2206.241833 1209.894993 1388.337651 915.9582859 950.3423217 1068.032892 2339.495373 2255.53778 1.1713397 1.125695426 0.978144482 0.536410874 0.615524006 0.406093081 0.421337355 0.473515851 1.037222871 1 11.13925574 -9.275597337 2.448038758 1.087411988 0.472251826 0.946491656 0.068429775 0.055430664 0.653110367 0.013356447 0.022565349 5.30E-10 9.275597337 -0.615160162 down HS(ph)YPPALGSPGALAGAGVGAAGPLER ddPTM_HeLa_Romidepsin_16h_R1 3 HSYPPALGSPGALAGAGVGAAGPLER 26 0 Q96IF1;H0YJL9 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 0 HS(0.989)Y(0.01)PPALGSPGALAGAGVGAAGPLER;HS(0.999)Y(0.001)PPALGSPGALAGAGVGAAGPLER;HS(0.989)Y(0.011)PPALGSPGALAGAGVGAAGPLER ;; 141.3 8.82E-08 55142000 3614.42 3549.07 3577.97 1719.22 1920.94 1633.88 1394.22 1661.7 3795.58 3823.77 TRUE FALSE FALSE 3570.366059 3599.033901 3640.243067 1918.004306 1822.907264 1529.480341 1512.645012 1709.778668 3456.093819 3724.427904 0.958634762 0.966332009 0.977396572 0.514979577 0.489446248 0.41066182 0.406141574 0.45907149 0.927952939 1 11.86280312 -9.218617896 3.694022731 0.980034018 0.442724176 0.985438171 0.031052782 0.018392082 0.528030643 0.004776423 0.00798582 6.04E-10 9.218617896 -0.537309843 down ADYDTLS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 2 ADYDTLSLR 9 0 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71;E9PQ15 E9PKC4 PKP3 Plakophilin-3 1 0 ADYDTLS(1)LR;ADYDTLS(1)LR ; 116.55 0.015426 13654700 10249.2 8640.2 10598.5 7770.1 7511.7 5492.1 3703.9 4693.6 8440.5 8143.4 TRUE FALSE FALSE 10124.27881 8761.836962 10782.96245 8668.515521 7128.349919 5141.172535 4018.509174 4829.401911 7685.56054 7931.833294 1.276410942 1.104642097 1.359453993 1.092876665 0.898701429 0.648169514 0.506630564 0.608863264 0.968951345 1 12.95343864 -8.434856502 1.955672951 1.149278329 0.558821068 0.827187817 0.112159453 0.106915657 0.795290932 0.018747632 0.051716538 3.67E-09 8.434856502 -0.590457262 AEAAVVAVAEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AEAAVVAVAEKR 12 1 A0A087WYP2;Q8IZQ5 A0A087WYP2 C11orf31;SELH Selenoprotein H 0 1 ; AEAAVVAVAEK(1)R;AEAAVVAVAEK(1)R 164.04 0.00028636 11318900 3361.3 3790.1 3488.9 4040.4 4587.6 5374.8 4591.6 4898 3540.6 3207.5 FALSE TRUE FALSE 3320.331183 3843.457127 3549.622841 4507.570059 4353.477653 5031.367626 4981.610389 5039.715902 3223.919868 3124.168688 1.062788701 1.230233547 1.136181556 1.442806234 1.393483544 1.610466057 1.594539504 1.613138216 1.031928872 1 11.60925664 -9.095057483 0.620092591 1.013101147 1.662528597 0.939105677 0.058334907 0.118431577 0.084532533 0.011633102 0.036420052 8.03E-10 9.095057483 0.64942745 AEADKIYSFTDNAPS(ph)PSIGGSSR ddPTM_HeLa_Romidepsin_16h_R1 2 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 AEADKIYSFTDNAPS(0.837)PS(0.161)IGGS(0.001)SR;AEADKIYSFT(0.001)DNAPS(0.697)PS(0.184)IGGS(0.067)S(0.051)R ; 160.64 3.67E-17 14083000 2783.2 2681.83 2468.02 2861.67 2287.38 1882.57 2013.35 1723.36 2925.47 2884.78 TRUE FALSE FALSE 2749.277288 2719.584873 2510.974853 3192.54975 2170.646463 1762.279853 2184.363899 1773.222703 2663.808636 2809.833 0.978448644 0.96788132 0.893638466 1.136206227 0.772517962 0.627183129 0.777399902 0.631077613 0.948030946 1 11.45626867 -8.591387445 6.273037272 0.988522816 0.690024707 0.806137553 0.069585469 0.055570677 3.895514782 0.008839234 0.01785356 2.56E-09 8.591387445 -0.298498109 AEADKIYSFTDNAPSPSIGGSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AEADKIYSFTDNAPSPSIGGSSR 23 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 AEADKIYSFT(0.004)DNAPS(0.201)PS(0.08)IGGS(0.203)S(0.512)R 80.832 0.00016191 31376000 1396 1370.8 1285.1 1376.6 1137.1 1033 961.3 712.91 1395.2 1263.1 TRUE FALSE FALSE 1378.985015 1390.098158 1307.466626 1535.768969 1079.069544 966.9946339 1042.952798 733.5369261 1270.409818 1230.28448 1.120866789 1.129899776 1.062735203 1.248303944 0.877089455 0.785992711 0.847733037 0.596233585 1.032614683 1 10.26477623 -8.557847352 5.783180175 1.077032065 0.764813225 0.767321782 0.088464587 0.071217745 6.457386665 0.013363949 0.027403951 2.77E-09 8.557847352 -0.31221884 AEAEAGS(ph)PRPDPR ddPTM_HeLa_Romidepsin_16h_R1 2 AEAEAGSPRPDPR 13 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 AEAEAGS(1)PRPDPR;AEAEAGS(1)PRPDPR ; 97.45 0.0055614 295495000 12475.5 11920.9 11523 12056.7 16097.4 21231.4 18946.5 20301.7 12904.5 12328.5 TRUE FALSE FALSE 12323.44381 12088.72274 11723.55298 13450.75238 15275.88961 19874.78206 20555.81524 20889.09766 11750.2892 12008.20379 1.026252054 1.006705328 0.976295305 1.120130256 1.272121116 1.65510033 1.711814322 1.739568883 0.978521801 1 13.55173275 -8.416765151 1.596975758 1.010386739 1.74488327 0.99210447 0.027456085 0.020875198 0.102250352 0.003863533 0.012021181 3.83E-09 8.416765151 0.734496531 AEAESDALPDDT(ph)VIESEALPSDIAAEAR ddPTM_HeLa_Romidepsin_16h_R1 1 AEAESDALPDDTVIESEALPSDIAAEAR 28 0 G3V529;Q9GZR7-2;Q9GZR7;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 0 AEAES(0.175)DALPDDT(0.822)VIES(0.002)EALPSDIAAEAR 61.101 0.00046576 0 488.37 390.73 575.18 323.32 455.99 603.3 545.77 621.29 557.32 501.46 TRUE FALSE FALSE 482.4175586 396.2307072 585.1907666 360.7037797 432.7191288 564.7510771 592.1276902 639.2660459 507.4719034 488.4319969 0.987686232 0.811230038 1.198100801 0.738493346 0.885935261 1.156253236 1.212303236 1.308812793 1.038981694 1 8.932013903 -8.038097545 3.441678181 0.970093271 1.254157695 0.518619541 0.12243209 0.142066147 3.432570081 0.016232266 0.049379905 9.16E-09 8.038097545 0.284064424 AEAGAGS(ph)ATEFQFR ddPTM_HeLa_Romidepsin_16h_R1 2 AEAGAGSATEFQFR 14 0 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 0 AEAGAGS(0.996)AT(0.004)EFQFR;AEAGAGS(0.958)AT(0.042)EFQFR ; 148.57 0.0006169 44596000 3022.4 3096.7 2927.3 2695.4 2504.3 2122.6 1746.63 1908.69 3170.5 2919.5 TRUE FALSE FALSE 2985.561826 3140.295424 2978.248429 3007.05483 2376.496226 1986.97271 1894.988709 1963.914934 2886.922539 2843.650969 1.049904457 1.104318166 1.047332623 1.057462699 0.835720084 0.698740011 0.666392862 0.6906315 1.015216906 1 11.47352868 -8.535690597 2.556083098 1.035341571 0.682202951 0.96596873 0.030552437 0.042560035 0.556734299 0.005499592 0.012963281 2.91E-09 8.535690597 -0.35313862 AEAGEQPGT(ph)AER ddPTM_HeLa_Romidepsin_16h_R1 1 AEAGEQPGTAER 12 0 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 0 AEAGEQPGT(1)AER 119.96 0.015535 3309300 2180.1 1908.7 1916.6 1863.2 2072.4 2518 2694.4 2332.7 2495.1 2256.2 TRUE FALSE FALSE 2153.528103 1935.570729 1949.957619 2078.631951 1966.637695 2357.107926 2923.262269 2400.192994 2271.932007 2197.583599 0.979952755 0.880772285 0.887318972 0.945871616 0.894909161 1.072590789 1.330216639 1.092196445 1.033831891 1 11.10170233 -7.984288055 6.552979525 0.965522878 1.210778669 0.675773457 0.072889005 0.064679775 11.6443014 0.009799322 0.02891719 1.04E-08 7.984288055 0.245255791 AEAIK(ac)ALVKPK ddPTM_HeLa_Romidepsin_16h_R1 1 AEAIKALVKPK 11 2 A0A3B3ITT5;P47914 A0A3B3ITT5 RPL29 60S ribosomal protein L29 0 1 AEAIK(1)ALVKPK 84.605 0.021711 0 166.5 0 157.91 178.22 0 189.62 70.004 192.05 138.34 146.16 FALSE TRUE FALSE 164.470634 0 160.6583573 198.826635 0 177.503894 75.95013801 197.6066637 125.9665239 142.3627421 1.15529268 0 1.128514068 1.396619874 0 1.246842336 0.533497296 1.388050418 0.884827884 1 7.153427817 AEAPAGPALGLPS(ph)PEAESGVDR ddPTM_HeLa_Romidepsin_16h_R1 2 AEAPAGPALGLPSPEAESGVDR 22 0 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 0 AEAPAGPALGLPS(0.773)PEAES(0.227)GVDR;AEAPAGPALGLPS(1)PEAESGVDR ; 139.2 5.95E-05 41505000 4913.9 5612.6 5450.7 3045.39 5135.2 5581.7 4329.5 5069.3 5836.4 5739.8 TRUE FALSE FALSE 4854.007497 5691.61433 5545.567147 3397.512321 4873.131582 5225.047384 4697.247622 5215.972197 5314.377766 5590.679169 0.868232168 1.018054186 0.991930851 0.607710122 0.871652877 0.934599756 0.840192664 0.932976485 0.950578205 1 12.44880784 AEAPAGPALGLPS(ph)PEAESGVDRGEPEPMEVEEGELEIVPVRR ddPTM_HeLa_Romidepsin_16h_R1 1 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 0 AEAPAGPALGLPS(0.5)PEAES(0.5)GVDRGEPEPMEVEEGELEIVPVRR 54.376 0.00049124 52566000 1493.1 1587.4 1256.6 1671.1 1297.6 1578.1 1376.4 1701.9 1525.2 1061.8 TRUE FALSE FALSE 1474.901523 1609.747459 1278.470596 1864.320445 1231.37863 1477.264503 1493.311382 1751.141791 1388.782292 1034.214283 1.426108252 1.556493161 1.23617573 1.802644264 1.190641679 1.428393059 1.443909068 1.693209831 1.342838051 1 10.01431942 -12.11881942 0.517593776 0.919502839 1.483327353 0.183187798 0.203798562 0.811560363 0.325041834 0.227227029 0.042956003 7.61E-13 12.11881942 0.563824514 AEAPAGPALGLPSPEAES(ph)GVDRGEPEPMEVEEGELEIVPVRR ddPTM_HeLa_Romidepsin_16h_R1 1 AEAPAGPALGLPSPEAESGVDRGEPEPMEVEEGELEIVPVRR 42 2 Q53F19 Q53F19 C17orf85 Uncharacterized protein C17orf85 1 0 AEAPAGPALGLPS(0.224)PEAES(0.776)GVDRGEPEPMEVEEGELEIVPVRR 74.465 6.62E-07 63644000 1470.5 1561.8 1267.3 1125 1479.7 1476.9 1316.6 1713.8 1426.8 1438.5 TRUE FALSE FALSE 1452.57698 1583.787061 1289.356825 1255.077793 1404.185387 1382.530856 1428.431971 1763.386099 1299.183435 1401.127563 1.03672001 1.130366073 0.920228007 0.895762689 1.002182403 0.986727328 1.019487454 1.258547863 0.927241366 1 10.45237259 -7.262221437 5.155292537 1.007268923 1.269704244 0.591584439 0.065526727 0.085811273 7.549987897 0.008597572 0.079645863 5.47E-08 7.262221437 0.262435321 AEAPLPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 AEAPLPSPK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 AEAPLPS(1)PK;AEAPLPS(1)PK ; 100.09 0.028256 297250000 15910.5 16172.8 16843.2 11280 17811.2 17074.9 13605 17941.1 15716.1 14966.2 TRUE FALSE FALSE 15716.57671 16400.4811 17136.34883 12584.24667 16902.228 15983.869 14760.60836 18460.19742 14310.41265 14577.37597 1.078148546 1.125064013 1.175544136 0.863272423 1.159483575 1.096484651 1.012569642 1.266359423 0.981686463 1 13.83144343 -16.52287434 0.015763215 5.71E-07 1.91751119 0.174555467 0.0994816 6425.565574 8.179097617 620.930214 397.4991771 3.00E-17 16.52287434 1.917510619 AEDEALLS(ph)EEDDPIDR ddPTM_HeLa_Romidepsin_16h_R1 1 AEDEALLSEEDDPIDR 16 0 Q04721 Q04721 NOTCH2 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain 1 0 AEDEALLS(1)EEDDPIDR 92.952 0.010383 8545300 876.72 1284 1253.8 630.39 1507.6 1802.8 850.99 1543.1 1337.1 1508 TRUE FALSE FALSE 866.0341994 1302.076186 1275.621863 703.2786579 1430.661546 1687.606898 923.2730694 1587.747164 1217.506427 1468.821943 0.589611426 0.886476535 0.868465963 0.478804569 0.974019726 1.148952674 0.628580662 1.080966398 0.828899945 1 10.5204438 AEDGAT(ph)PS(ph)PSNETPK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 AEDGAT(1)PS(0.499)PS(0.499)NET(0.002)PK 111.07 0.017299 16760000 4125.9 3961.5 4171.5 3829.4 4033.7 3860.1 3275.5 2903.6 4175.5 4129.7 TRUE FALSE FALSE 4075.611944 4017.270101 4244.103208 4272.173246 3827.845237 3613.452068 3553.720888 2987.611085 3802.032822 4022.409799 1.013226436 0.998722234 1.055114576 1.062092989 0.951629851 0.898330167 0.883480567 0.742741599 0.945212699 1 11.97384435 -7.471699645 0.930408191 1.012534743 0.667432131 0.829604815 0.037449368 0.382932453 0.308019881 0.005083824 0.123086146 3.38E-08 7.471699645 -0.345102613 AEDGAT(ph)PSPS(ph)NETPK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 AEDGAT(0.943)PS(0.247)PS(0.588)NET(0.222)PK 107.69 0.021472 15078000 5203.7 4768.8 4735.3 4020 4255 4449.2 3718.2 3496 5797.4 5510 TRUE FALSE FALSE 5140.275303 4835.935292 4817.71591 4484.811315 4037.851472 4164.910479 4034.023815 3597.151244 5278.866024 5366.849406 0.957782661 0.901075273 0.897680472 0.835650672 0.752369066 0.776043851 0.751655862 0.670253807 0.983606139 1 12.38985969 -8.957846502 0.460804403 0.996745863 0.664932107 0.957882737 0.021909052 0.17827677 0.063449547 0.006358753 0.025681873 1.10E-09 8.957846502 -0.331813756 AEDGAT(ph)PSPSNET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 AEDGAT(1)PSPS(0.002)NET(0.998)PK 139.29 0.018061 9365200 16634 17729 18173 10119 13637 14494 9326.2 9795.3 14603 14902 TRUE FALSE FALSE 16431.25841 17978.58933 18489.29344 11289.00639 12941.053 13567.88018 10118.3672 10078.71155 13296.87111 14514.84389 1.132031356 1.238634701 1.273819655 0.777755963 0.891573695 0.934758946 0.697104789 0.694372714 0.916087779 1 13.82524144 -9.241134271 24.89601353 1.094376414 0.806118628 0.627768205 0.12006186 433.9810374 532102.834 0.018530873 0.030703998 5.74E-10 9.241134271 -0.288257786 AEDGAT(ph)PSPSNET(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 AEDGAT(0.883)PS(0.116)PS(0.002)NET(0.999)PKK 81.788 0.0064141 6619500 5085.6 4400.1 4852.6 4574.7 4794.8 4811.9 3577 3329.2 4889.7 5185.4 TRUE FALSE FALSE 5023.614751 4462.044723 4937.057467 5103.648339 4550.103464 4504.43512 3880.830291 3425.525149 4452.352986 5050.68256 0.994640762 0.883453804 0.977503022 1.010486855 0.900888822 0.891846808 0.768377391 0.678230142 0.881534908 1 12.30226265 -6.4084442 0.525433694 0.993832198 5.48E-14 0.739189202 0.05216666 1.961785095 0.191174169 0.007410369 1.467812029 3.90E-07 6.4084442 -0.993832198 AEDGATPS(ph)PSNET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 AEDGATPS(0.987)PS(0.013)NET(1)PK 170.35 8.85E-05 13018000 2424.6 2789.5 2502.4 1582.2 2500.3 2739.2 1681.9 1775.7 2977.2 2356.8 TRUE FALSE FALSE 2395.048043 2828.770654 2545.953222 1765.141408 2372.700361 2564.17396 1824.760544 1827.077078 2710.911775 2295.569996 1.043334791 1.232273753 1.109072355 0.768933821 1.033599657 1.117009703 0.794905207 0.79591434 1.180931873 1 11.16463671 -9.28773167 24.98483775 1.046280415 0.915366781 0.349992736 0.127937216 919.2475526 873532.9423 0.019538667 0.029851523 5.16E-10 9.28773167 -0.130913634 AEDGATPS(ph)PSNETPK ddPTM_HeLa_Romidepsin_16h_R1 2 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGAT(0.006)PS(0.83)PS(0.163)NET(0.001)PK;AEDGATPS(0.953)PS(0.047)NETPK ; 225.7 9.31E-35 537899000 16327.2 16565.7 15744.8 14618.4 13092.5 12792.7 10925.8 10402.9 17485.6 16062.7 TRUE FALSE FALSE 16128.19781 16798.91236 16018.83164 16308.64819 12424.34087 11975.28776 11853.83718 10703.8915 15921.64414 15645.38874 1.030859512 1.073729304 1.023869199 1.042393287 0.794121583 0.765419636 0.757656929 0.684156315 1.017657305 1 13.93344988 -8.689630185 4.188739673 1.022618666 0.744140673 0.957146269 0.029227207 0.034284359 1.166141281 0.004714157 0.009595344 2.04E-09 8.689630185 -0.278477993 AEDGATPS(ph)PSNETPKK ddPTM_HeLa_Romidepsin_16h_R1 2 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGAT(0.104)PS(0.403)PS(0.36)NET(0.134)PKK;AEDGAT(0.382)PS(0.567)PS(0.029)NET(0.022)PKK ; 164.01 7.73E-05 76842400 6569.6 8472.1 6302 6669.2 6496.2 5553.2 4483.17 4495.74 7641.4 7762.2 TRUE FALSE FALSE 6489.527188 8591.370446 6411.683666 7440.324284 6164.674673 5198.368442 4863.970348 4625.817144 6957.934046 7560.536925 0.858342106 1.136343957 0.848046075 0.984099986 0.815375248 0.687566041 0.64333663 0.611837121 0.920296285 1 12.88427298 -8.367926531 1.855839247 0.945351211 0.628242818 0.759902006 0.078170088 0.138700469 0.918253572 0.012284544 0.0366164 4.29E-09 8.367926531 -0.317108393 AEDGATPSPS(ph)NETPKKK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPKKK 17 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGAT(0.001)PS(0.142)PS(0.726)NET(0.13)PKKK 67.136 0.013213 177120000 2944.7 3099.2 2192.9 4515.6 2541.7 2100.3 1506.1 1365.7 3060.1 2810.8 TRUE FALSE FALSE 2908.808864 3142.830619 2231.066505 5037.714919 2411.987565 1966.097608 1634.028096 1405.214375 2786.396992 2737.775011 1.062471844 1.147950656 0.814919596 1.840076302 0.881002842 0.718137028 0.596845281 0.513268756 1.01775967 1 11.41878818 -8.284370276 3.266539323 1.08017 0.590782278 0.440699047 0.263618429 0.1839214 4.046428095 0.036325955 0.093890705 5.20E-09 8.284370276 -0.489387722 AEDGATPSPSNET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 10 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGATPSPSNET(1)PK;AEDGATPSPSNET(1)PK;AEDGATPSPS(0.001)NET(0.999)PK;AEDGATPS(0.014)PS(0.259)NET(0.727)PK;AEDGAT(0.001)PS(0.008)PS(0.214)NET(0.777)PK;AEDGATPS(0.001)PS(0.013)NET(0.986)PK;AEDGAT(0.001)PS(0.247)PS(0.24)NET(0.512)PK;AEDGAT(0.058)PS(0.022)PS(0.074)NET(0.846)PK;AEDGATPSPS(0.001)NET(0.999)PK;AEDGATPS(0.002)PS(0.002)NET(0.996)PK ;;;;;;;;; 238.12 2.86E-45 6729899200 56379 62166.8 55683.5 42335.5 40530.2 37829.7 29771.6 30920.4 54386.9 54557.3 TRUE FALSE FALSE 55691.83106 63041.98584 56652.64796 47230.5297 38461.79265 35412.50426 32300.39896 31815.03299 49522.39945 53139.89348 1.048023009 1.186340087 1.066103905 0.888796093 0.723783774 0.666401491 0.607837104 0.598703364 0.931925079 1 15.69750772 -8.803297152 1.859863796 1.040952215 0.623464699 0.899340421 0.063170683 0.071398053 0.5019641 0.009518079 0.02105493 1.57E-09 8.803297152 -0.417487516 AEDGATPSPSNET(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 5 AEDGATPSPSNETPKK 16 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGATPS(0.019)PS(0.059)NET(0.922)PKK;AEDGATPS(0.005)PS(0.003)NET(0.992)PKK;AEDGAT(0.003)PS(0.111)PS(0.006)NET(0.88)PKK;AEDGATPSPS(0.287)NET(0.712)PKK;AEDGATPSPSNET(1)PKK ;;;; 246.03 6.45E-58 1003509000 43355.6 45695.1 39845 45208.6 36225.2 34382.7 27476.1 27778.8 49035.8 46913.1 TRUE FALSE FALSE 42827.16527 46338.39682 40538.48551 50435.83104 34376.49287 32185.75644 29809.91925 28582.53575 44649.91524 45694.2909 0.937254183 1.014095982 0.887167406 1.103766577 0.752314834 0.704371505 0.652377325 0.625516562 0.977144286 1 15.4797263 -8.59852593 5.271549525 0.974430144 0.669756036 0.875301262 0.056589765 0.049312486 2.447091014 0.00799166 0.016284386 2.52E-09 8.59852593 -0.304674108 AEDGATPSPSNET(ph)PKKK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDGATPSPSNETPKKK 17 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 AEDGATPS(0.005)PS(0.233)NET(0.762)PKKK 62.556 0.015416 19126000 8037.3 8097.2 6693.4 13708 6351 4742.9 4140.6 4043.6 8100.9 6556.7 TRUE FALSE FALSE 7939.338296 8211.192594 6809.895819 15292.98346 6026.884771 4439.843997 4492.302461 4160.595186 7376.335215 6386.355989 1.243171898 1.285739882 1.066319483 2.394633729 0.943712624 0.695207722 0.703421868 0.651481877 1.155014726 1 12.64077726 -8.525999679 24.99992851 1.226151543 0.7077229 0.36495309 0.381350301 94.6884807 758492.542 0.057139323 0.114762075 2.98E-09 8.525999679 -0.518428644 AEDGATPSPSNETPK ddPTM_HeLa_Romidepsin_16h_R1 2 AEDGATPSPSNETPK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 0 ; ; 301.35 1.44E-133 15058600 10334.8 11041.9 9774.9 7296.7 7823.2 7126.7 5218.6 5359.5 9578.3 9349.5 FALSE FALSE TRUE 10208.83548 11197.34816 9945.028034 8140.378786 7423.952912 6671.32687 5661.867754 5514.568677 8721.592859 9106.598642 1.12103716 1.229586215 1.092068337 0.89389893 0.815227859 0.732581629 0.621732436 0.605557453 0.957722329 1 13.15269659 -8.64261626 1.276677432 1.075864822 0.626609215 0.857479239 0.076124811 0.127331572 0.406647928 0.013087472 0.038559499 2.28E-09 8.64261626 -0.449255607 AEDGENYDIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AEDGENYDIKK 11 1 E5RJD8;E5RHG6;O75347;E5RIW3;A0A494C144;E5RIX8;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 1 ; AEDGENYDIK(1)K;AEDGENYDIK(1)K 244.16 2.80E-51 5375400 1887.24 2115.64 2388.1 1209.98 5003.8 3629 3552.2 3583.2 4850 4273.2 FALSE TRUE FALSE 1864.237593 2145.424035 2429.663879 1349.883581 4748.437414 3397.118612 3853.923779 3686.874239 4416.203853 4162.181648 0.447899143 0.515456608 0.58374768 0.32432116 1.140852999 0.816187014 0.925938391 0.8858033 1.061031023 1 12.02312421 -8.739658831 24.99996921 0.675665847 0.932033492 0.271346927 0.228546824 323.1837616 370952.366 0.037735332 0.07541883 1.82E-09 8.739658831 0.256367645 AEDGS(ph)VIDYELIDQDAR ddPTM_HeLa_Romidepsin_16h_R1 2 AEDGSVIDYELIDQDAR 17 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33;H0YNA0 P07355 ANXA2 Annexin A2;Annexin 1 0 AEDGS(1)VIDYELIDQDAR;AEDGS(0.992)VIDY(0.008)ELIDQDAR ; 284.07 3.26E-103 23828000 3595.7 3868.2 3871.1 3399.98 3243.7 3412.5 2561.43 3004.4 3982.5 3638.9 TRUE FALSE FALSE 3551.874225 3922.656621 3938.474872 3793.101685 3078.161885 3194.452263 2778.9978 3091.327574 3626.295226 3544.360853 1.00211981 1.106731731 1.111194665 1.070179319 0.868467408 0.90127738 0.784061758 0.872181954 1.023116826 1 11.79130978 -8.712514394 7.534585544 1.023299907 0.853508321 0.773062199 0.050513983 0.105775385 13.61923534 0.008482324 0.016942107 1.94E-09 8.712514394 -0.169791586 AEDGSVIDYELIDQDAR ddPTM_HeLa_Romidepsin_16h_R1 5 AEDGSVIDYELIDQDAR 17 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33;H0YNA0 P07355 ANXA2 Annexin A2;Annexin 0 0 ;;;; ;;;; 435.07 0 248432700 15716.2 19105.2 17192.5 16562.6 19718.4 20728.8 16326.5 17871.2 18080 16527.9 FALSE FALSE TRUE 15524.64491 19374.16351 17491.72825 18477.64574 18712.09647 19404.29658 17713.2725 18388.27498 16462.87952 16098.50278 0.964353339 1.203476111 1.086543792 1.147786598 1.16235011 1.205347904 1.100305584 1.142235103 1.022634201 1 13.9746389 -10.269325 24.96651349 0.983166851 1.147941139 0.768650513 0.03854041 164.3428762 520321.8582 0.006127614 0.007076578 5.38E-11 10.269325 0.164774287 AEDK(ac)EWMPVTK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDKEWMPVTK 11 1 E9PQD7;P15880;E9PPT0;E9PMM9 E9PQD7 RPS2 40S ribosomal protein S2 0 1 AEDK(1)EWMPVTK 116.74 0.004769 697560 156.45 300.79 177.06 0 337.76 243.34 177.33 346.09 323.19 262.87 FALSE TRUE FALSE 154.5431272 305.0245295 180.141655 0 320.5228468 227.7913593 192.3924058 356.1035681 294.283077 256.0405995 0.603588367 1.191313136 0.70356676 0 1.251843838 0.889668903 0.751413667 1.390808992 1.14936099 1 8.000228781 AEDNADTLALVFEAPNQEK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDNADTLALVFEAPNQEK 19 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 0 158.14 1.13E-10 0 2375.9 2420.4 2006.9 1625.2 2622.7 2679.9 1943.5 2512.2 2184.6 2427.2 FALSE FALSE TRUE 2346.941617 2454.474455 2041.829253 1813.113271 2488.853832 2508.663039 2108.580841 2584.886543 1989.203905 2364.140994 0.992724894 1.038209845 0.863666447 0.766922648 1.052751861 1.061130891 0.891901476 1.093372413 0.841406629 1 11.20710036 -7.224705027 22.72316165 0.97792466 1.093373223 0.092075002 0.100238222 9378.323711 5800895.181 0.012503799 3.160622681 5.96E-08 7.224705027 0.115448562 AEDRS(ph)IFS(ph)AVLDELK ddPTM_HeLa_Romidepsin_16h_R1 1 AEDRSIFSAVLDELK 15 1 P31327;P31327-3;P31327-2;A0A669KBF2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 2 0 AEDRS(1)IFS(1)AVLDELK 76.358 0.0039739 0 458.17 601.36 591.32 644.53 837.89 700.62 383.82 502.38 668.31 748.37 TRUE FALSE FALSE 452.5856478 609.8259619 601.6116766 719.0535912 795.1293467 655.8526431 416.4216612 516.9155727 608.5346798 728.9272395 0.620892763 0.836607454 0.825338448 0.986454549 1.090821283 0.899750493 0.571280148 0.709145638 0.834835971 1 9.509631004 -12.71177937 1.621547473 0.999704602 0.792689636 0.001690484 0.158315643 0.572430543 2.722602728 0.124422043 0.027495064 1.94E-13 12.71177937 -0.207014966 AEDS(ph)DSEPEPEDNVR ddPTM_HeLa_Romidepsin_16h_R1 1 AEDSDSEPEPEDNVR 15 0 Q9H0D6-2;Q9H0D6 Q9H0D6-2 XRN2 5-3 exoribonuclease 2 1 0 AEDS(0.999)DS(0.001)EPEPEDNVR 205.28 1.82E-20 0 714.61 806.65 741.9 817.02 792.28 1171 896.33 929.82 1103.4 1127.7 TRUE FALSE FALSE 705.9000585 818.0060399 754.8124583 911.4876966 751.8469952 1096.176879 972.4642478 956.7228747 1004.70914 1098.402191 0.642660825 0.744723605 0.687191326 0.829830552 0.684491529 0.997974046 0.885344417 0.871013261 0.914700597 1 10.10119069 -8.250799873 24.97394299 0.801314448 0.91483395 0.228412659 0.108578491 1289.241757 3026210.893 0.020836467 0.052529675 5.61E-09 8.250799873 0.113519502 AEEAQKTESVDNEGE ddPTM_HeLa_Romidepsin_16h_R1 1 AEEAQKTESVDNEGE 15 1 Q15651 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 0 0 138.45 0.013008 10419000 3943 4359.4 3619.4 3052.4 3980 4506.8 4478.1 4622.9 4301.9 4371.3 FALSE FALSE TRUE 3894.941199 4420.771748 3682.394139 3405.33285 3776.885749 4218.830025 4858.469702 4756.656318 3917.12729 4257.732996 0.914792262 1.038292385 0.86487202 0.79979953 0.88706496 0.990862985 1.14109309 1.11718051 0.920003038 1 12.05586977 -7.859985036 4.025905969 0.941082522 1.129987336 0.602973808 0.065878518 0.130561158 3.871287633 0.010464468 0.03532262 1.38E-08 7.859985036 0.188904815 AEEDEILNRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 5 AEEDEILNRSPR 12 1 P27824-3;P27824;P27824-2 P27824-3 CANX Calnexin 1 0 AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR;AEEDEILNRS(1)PR ;;;; 161.87 0.00073213 2951700000 22632.9 37699.6 26748 16979.1 21608 32411.1 16388.2 33164.7 31480.9 35213.9 TRUE FALSE FALSE 22357.04151 38230.33596 27213.53772 18942.30343 20505.26313 30340.13531 17780.2133 34124.26827 28665.16946 34299.0378 0.651827076 1.114618322 0.793419859 0.552269237 0.597837853 0.884576864 0.518388108 0.994904535 0.835742671 1 15.06588048 -9.516043078 24.99292329 0.856780483 0.699521077 0.187478068 0.177699026 504.958153 1846255.67 0.030095099 0.04351278 3.05E-10 9.516043078 -0.157259406 AEEDTQFNYHR ddPTM_HeLa_Romidepsin_16h_R1 1 AEEDTQFNYHR 11 0 H0Y7K8;G8JLG1;Q14683 H0Y7K8 SMC1A Structural maintenance of chromosomes protein;Structural maintenance of chromosomes protein 1A 0 0 95.477 0.011959 3875200 3404.2 3207.1 3021.1 2136.7 3340.6 2957.1 2510.5 2972.4 3210 3619.5 FALSE FALSE TRUE 3362.708301 3252.249638 3073.680978 2383.755307 3170.116717 2768.150854 2723.741807 3058.401704 2922.88956 3525.464868 0.953834012 0.922502353 0.871851257 0.676153471 0.899205306 0.785187474 0.772590824 0.867517283 0.829079191 1 11.78359779 -9.809994554 1.995617433 0.978197335 0.802066614 0.319240046 0.074709576 0.136070856 1.108070705 0.009361844 0.013175765 1.55E-10 9.809994554 -0.176130721 AEEFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AEEFKK 6 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 1 AEEFK(1)K 107.43 0.0107 2272400 1801.4 2158.6 1980.3 1571.1 2167.6 2558.4 2052.9 1155.5 2166 1583.4 FALSE TRUE FALSE 1779.443844 2188.988827 2014.766291 1752.757974 2056.979284 2394.926497 2227.273275 1188.932569 1972.267535 1542.26304 1.153787517 1.419335594 1.30637008 1.136484458 1.333740893 1.552865131 1.444159146 0.770901292 1.278813979 1 10.59083313 -10.87773296 1.130446948 1.035998069 1.293921644 0.01220211 0.218252582 0.452289658 1.215163454 0.049535594 0.043365877 1.33E-11 10.87773296 0.257923574 AEEILEK(ac)GLK ddPTM_HeLa_Romidepsin_16h_R1 2 AEEILEKGLK 10 1 P62913;Q5VVC8;P62913-2 P62913 RPL11 60S ribosomal protein L11 0 1 ; AEEILEK(1)GLK;AEEILEK(1)GLK 156.12 0.0095502 516930 425.56 320.947 175.45 237.39 343.67 471.029 322.767 222.78 256.05 398.47 FALSE TRUE FALSE 420.373111 325.4653003 178.5036337 264.8381488 326.1312375 440.9317671 350.1828209 229.2257878 233.1482467 388.117692 1.083107314 0.838573729 0.459921404 0.682365567 0.840289542 1.136077474 0.902259361 0.590608964 0.600715328 1 8.600350388 -10.17094937 5.268771649 1.038983005 0.780771162 0 0.221384205 0.212145904 9.562321787 0.030795608 0.037805318 6.75E-11 10.17094937 -0.258211843 AEEKENDTVTIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 AEEKENDTVTISPK 14 1 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 AEEKENDT(0.002)VT(0.006)IS(0.992)PK;AEEKENDTVT(0.013)IS(0.987)PK;AEEKENDTVT(0.002)IS(0.998)PK;AEEKENDTVTIS(1)PK ;;; 164.7 0.00085799 72017600 15159.7 12781.3 12801 10423.7 11578.2 11212.9 9962.3 10735.2 15440.3 14526.7 TRUE FALSE FALSE 14974.92775 12961.23548 13023.79604 11628.93724 10987.32125 10496.43188 10808.49751 11045.80607 14059.2809 14149.29424 1.058351568 0.916034062 0.920455523 0.821874013 0.776527865 0.741834306 0.763889515 0.780661275 0.993638316 1 13.78844247 -9.490763172 1.146610391 1.026896916 0.76048069 0.926908834 0.029431493 0.080689736 0.211551729 0.005866189 0.010355104 3.23E-10 9.490763172 -0.266416226 AEELS(ph)PAALSPSLEPIR ddPTM_HeLa_Romidepsin_16h_R1 1 AEELSPAALSPSLEPIR 17 0 A0A2R8YFR7;A0A2R8YF49;Q12774;A0A5F9ZGZ6 A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 0 AEELS(0.869)PAALS(0.099)PS(0.032)LEPIR 103.77 0.0027629 2673000 659.98 688.45 728.28 681.41 702.01 737.84 705.48 712.32 837.61 878.79 TRUE FALSE FALSE 651.9359099 698.1420172 740.9554079 760.1978303 666.1838101 690.6944053 765.4034536 732.9298553 762.6920638 855.9589091 0.761643933 0.815625621 0.865643666 0.88812421 0.778289475 0.806924723 0.894205838 0.85626757 0.891038174 1 9.741397731 -12.45660748 1.175696164 1.000562247 0.827838196 0.357319279 0.052891246 0.238874317 0.587588095 0.033578098 0.008208632 3.49E-13 12.45660748 -0.172724051 AEELSPAALS(ph)PSLEPIR ddPTM_HeLa_Romidepsin_16h_R1 2 AEELSPAALSPSLEPIR 17 0 A0A2R8YFR7;A0A2R8YF49;Q12774;A0A5F9ZGZ6 A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 0 AEELSPAALS(0.715)PS(0.285)LEPIR;AEELSPAALS(0.715)PS(0.285)LEPIR ; 187.75 3.88E-13 8307000 2556.6 2478.5 2793.61 2441.88 2353.69 2485.82 2000.4 2290.8 2675.93 2355.61 TRUE FALSE FALSE 2525.439176 2513.392388 2842.23161 2724.221655 2233.572416 2326.984125 2170.313926 2357.080684 2436.588119 2294.410913 1.100691756 1.095441263 1.238763115 1.187329454 0.973484045 1.014196765 0.945913356 1.027314101 1.061966758 1 11.16390808 -8.657488154 21.36000062 1.077460998 0.98876296 0.367883931 0.070284359 5.134510273 1039.679849 0.012454608 0.024909225 2.20E-09 8.657488154 -0.088698039 AEENTDQAS(ph)PQEDYAGFER ddPTM_HeLa_Romidepsin_16h_R1 2 AEENTDQASPQEDYAGFER 19 0 Q9NU22 Q9NU22 MDN1 Midasin 1 0 AEENTDQAS(1)PQEDYAGFER;AEENTDQAS(1)PQEDYAGFER ; 342.81 1.70E-236 30494000 5403.5 5678.5 5323.3 4867.3 5147 5400.8 4582.4 6036.8 5729.7 5358.6 TRUE FALSE FALSE 5337.640064 5758.442072 5415.949803 5430.080127 4884.329384 5055.70631 4971.628942 6211.465284 5217.221282 5219.3828 1.022657327 1.103280271 1.037660967 1.040368246 0.935805932 0.968640643 0.952531963 1.19007659 0.999585867 1 12.3496635 AEEPLK(ac)TVQEK ddPTM_HeLa_Romidepsin_16h_R1 1 AEEPLKTVQEK 11 1 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8 BCAR2;TRERF1 Transcriptional-regulating factor 1 0 1 AEEPLK(1)TVQEK 231.07 4.52E-29 948550 510.46 661.53 500.99 447.36 347.38 502.23 246.64 281.12 767.52 715.61 FALSE TRUE FALSE 504.2383172 670.8430367 509.7095208 499.0858681 329.6519023 470.1391239 267.5895954 289.2537637 698.8710889 697.018349 0.72342187 0.962446738 0.731271309 0.716029741 0.472945802 0.674500355 0.383906099 0.414987301 1.002658093 1 9.445052825 -7.682025727 0.21396074 0.998867664 1.18E-22 0.788457921 0.101284353 4.051205189 0.193607836 0.124527526 1.092682446 2.08E-08 7.682025727 -0.998867664 AEEPPS(ph)PPVPK ddPTM_HeLa_Romidepsin_16h_R1 1 AEEPPSPPVPK 11 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 0 AEEPPS(1)PPVPK 95.401 0.025679 7416500 1811 1849.1 1716.4 2306.2 1962.3 1527.3 1426.4 1814.3 2336.7 1959.3 TRUE FALSE FALSE 1788.926835 1875.131678 1746.273222 2572.853695 1862.156509 1429.710459 1547.55838 1866.793908 2127.6997 1908.397104 0.937397585 0.982568919 0.915047093 1.348175225 0.97576993 0.749168219 0.810920525 0.978199927 1.114914551 1 10.89814569 -8.391169553 7.678046253 0.996398839 0.843406248 0.271781062 0.132771258 0.308518942 17.82306829 0.018309164 0.041069827 4.06E-09 8.391169553 -0.152992591 AEEQQLPPPLS(ph)PPSPSTPNHR ddPTM_HeLa_Romidepsin_16h_R1 3 AEEQQLPPPLSPPSPSTPNHR 21 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 AEEQQLPPPLS(0.866)PPS(0.036)PS(0.054)T(0.044)PNHR;AEEQQLPPPLS(0.985)PPS(0.004)PS(0.006)T(0.005)PNHR;AEEQQLPPPLS(0.911)PPS(0.031)PS(0.027)T(0.031)PNHR ;; 65.836 0.0022828 8785600 3880.3 3242.15 3514.28 2735.19 4946.88 5018.44 4245.07 4478.58 4921.12 4565.42 TRUE FALSE FALSE 3833.005411 3287.793073 3575.444569 3051.445537 4694.422254 4697.77788 4605.64614 4608.160646 4480.962702 4446.80973 0.861967488 0.739359962 0.804047123 0.686210052 1.055683184 1.056437798 1.035719183 1.036284646 1.007680331 1 12.11855496 AEES(ph)IEDIYANIPDLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AEESIEDIYANIPDLPK 17 0 S4R313;Q9NP74-2;Q9NP74 S4R313 PALMD Palmdelphin 1 0 AEES(1)IEDIYANIPDLPK 172.95 1.54E-08 0 484.07 556.22 671.34 302.35 351.99 407.45 264.67 272.87 647.66 577.86 TRUE FALSE FALSE 478.1699686 564.0504798 683.0243911 337.3091296 334.0266368 381.41526 287.1510632 280.7650629 589.7316675 562.8471139 0.849555691 1.002137998 1.213516733 0.599290858 0.593458914 0.677653399 0.510175954 0.498830066 1.047765286 1 9.136599286 -9.154397527 8.370966694 0.95305062 0.576758418 0.807442744 0.10643437 0.123006107 8.761290316 0.01697819 0.028208053 7.01E-10 9.154397527 -0.376292202 VSLPS(ph)SPVPASPASSSGADQR ddPTM_HeLa_Romidepsin_16h_R1 1 VSLPSSPVPASPASSSGADQR 21 0 Q5T6S3-2 Q5T6S3-2 1 0 VSLPS(0.5)S(0.5)PVPASPASSSGADQR 310.9 9.02E-170 10603000 6704.5 5774.6 4588.3 3148.1 2454.7 2057.1 1904.2 1946.9 6473 5633.9 TRUE FALSE FALSE 6622.782975 5855.89497 4668.157437 3512.098134 2329.427499 1925.657949 2065.9427 2003.23048 5894.038668 5487.530466 1.20687858 1.067127555 0.850684559 0.64001433 0.424494682 0.350915218 0.376479495 0.365051364 1.074078532 1 12.42194133 -9.217686809 1.40477122 1.100120419 0.363352074 0.97203779 0.054182917 0.064889555 0.251307833 0.013714859 0.026450164 6.06E-10 9.217686809 -0.736768345 down AEFEDQDDEAR ddPTM_HeLa_Romidepsin_16h_R1 1 AEFEDQDDEAR 11 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 0 208.84 2.37E-13 9212500 1400.1 1550.3 1212.2 1418.3 1403.2 1339.4 1151.8 1235.4 1504.5 1435.6 FALSE FALSE TRUE 1383.035043 1572.125164 1233.297833 1582.290519 1331.589468 1253.816663 1249.633863 1271.14435 1369.933752 1398.302905 0.989081148 1.124309446 0.881996188 1.131579226 0.95228971 0.896670284 0.893678944 0.909062225 0.979711726 1 10.4494612 -8.524563891 24.96387031 1.006145796 0.903406092 0.373446495 0.06805074 42.28590907 626427.826 0.008801335 0.017708525 2.99E-09 8.524563891 -0.102739704 AEGAAT(ph)EEEGTPK ddPTM_HeLa_Romidepsin_16h_R1 3 AEGAATEEEGTPK 13 0 P80723;P80723-2;U3KQP0 P80723 BASP1 Brain acid soluble protein 1 1 0 AEGAAT(0.986)EEEGT(0.014)PK;AEGAAT(0.996)EEEGT(0.004)PK;AEGAAT(0.998)EEEGT(0.002)PK ;; 187.74 2.72E-10 38010000 11679.4 13836.3 11407.7 6798.2 12563 14984.2 10937.1 13553.3 12163.2 12068.9 TRUE FALSE FALSE 11537.04698 14031.08779 11606.24623 7584.23987 11921.86323 14026.75798 11866.097 13945.44335 11075.29293 11755.34824 0.981429622 1.193591845 0.987316241 0.64517356 1.014165041 1.193223518 1.009421138 1.186306273 0.942149284 1 13.52102966 -8.503816144 24.51690888 0.97968451 1.115305242 0.233408209 0.134855727 809.1338147 1040647.721 0.019212676 0.042301511 3.13E-09 8.503816144 0.135620732 AEGAATEEEGT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 AEGAATEEEGTPK 13 0 P80723;P80723-2;U3KQP0 P80723 BASP1 Brain acid soluble protein 1 1 0 AEGAATEEEGT(1)PK;AEGAAT(0.017)EEEGT(0.983)PK;AEGAATEEEGT(1)PK ;; 173.72 8.30E-05 105727000 11119.5 13316.3 12269.3 6364.1 12225 13939.9 10207 11680.3 11720 11793.6 TRUE FALSE FALSE 10983.97126 13503.76722 12482.84202 7099.947186 11601.11263 13049.18538 11073.98233 12018.25105 10671.73385 11487.20057 0.956192171 1.175549007 1.086673985 0.618074625 1.009916433 1.135976106 0.964027942 1.046229756 0.929010839 1 13.48773964 -8.52251672 24.99985253 0.974851339 1.045718521 0.068616082 0.140703766 34.06452693 2352282.761 0.020190181 0.040737611 3.00E-09 8.52251672 0.070867182 AEGAATEEEGT(ph)PKESEPQAAAEPAEAK ddPTM_HeLa_Romidepsin_16h_R1 4 AEGAATEEEGTPKESEPQAAAEPAEAK 27 1 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 AEGAATEEEGT(0.862)PKES(0.138)EPQAAAEPAEAK;AEGAATEEEGT(0.976)PKES(0.024)EPQAAAEPAEAK;AEGAAT(0.002)EEEGT(0.89)PKES(0.108)EPQAAAEPAEAK;AEGAAT(0.017)EEEGT(0.888)PKES(0.095)EPQAAAEPAEAK ;;; 109.5 4.33E-09 131452100 7024.95 7330.46 6226.96 6773.47 7576.24 9103.7 6484.22 8316.79 7857.12 7821.8 TRUE FALSE FALSE 6939.327207 7433.658408 6335.337627 7556.650472 7189.596202 8522.002951 7034.989485 8557.423197 7154.359509 7618.588508 0.910841582 0.975726462 0.831563172 0.991870143 0.943691367 1.118580291 0.923398012 1.123229478 0.939066272 1 12.89530802 -8.29696626 24.62124641 0.95043964 1.04190216 0.354125744 0.068719399 464.0115217 321573.6625 0.009519918 0.021288377 5.05E-09 8.29696626 0.09146252 AEGDEEGPSGAS(ph)EEEDT ddPTM_HeLa_Romidepsin_16h_R1 1 AEGDEEGPSGASEEEDT 17 0 Q96DX7 Q96DX7 TRIM44 Tripartite motif-containing protein 44 1 0 AEGDEEGPS(0.029)GAS(0.796)EEEDT(0.175) 114.31 2.96E-05 0 2608.3 2935.8 2093 1871.6 2035.8 1629.4 1547 1290.7 3276.1 2912.4 TRUE FALSE FALSE 2576.509036 2977.130269 2129.427787 2088.003198 1931.905529 1525.286599 1678.402141 1328.044368 2983.077411 2836.735428 0.90826554 1.049491694 0.7506614 0.736058491 0.681031269 0.53769082 0.591666789 0.468159404 1.051588168 1 11.47001589 -8.961161813 0.729584965 0.970345224 0.497615086 0.88919163 0.067827917 0.163584632 0.161894678 0.012313978 0.039903319 1.09E-09 8.961161813 -0.472730138 AEGDS(ph)AGTAGTPGGTPAGDK ddPTM_HeLa_Romidepsin_16h_R1 1 AEGDSAGTAGTPGGTPAGDK 20 0 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 1 0 AEGDS(0.688)AGT(0.046)AGT(0.207)PGGT(0.059)PAGDK 162.82 2.84E-08 9093400 2390.2 2254.8 2393.7 1644.6 3605.4 5354.8 3848.3 4453.9 2331.6 2711.6 TRUE FALSE FALSE 2361.067323 2286.543134 2435.361344 1834.75639 3421.402984 5012.645562 4175.174506 4582.766569 2123.055856 2641.152241 0.893953513 0.865736968 0.92208291 0.694680284 1.295420586 1.897901031 1.58081554 1.735139118 0.803836986 1 11.36695175 -8.504463628 4.433963334 0.924159582 1.713796783 0.919270697 0.115513588 0.039210407 1.877655679 0.015819795 0.034844776 3.13E-09 8.504463628 0.789637201 AEGDSAGTAGTPGGT(ph)PAGDKVASWELR ddPTM_HeLa_Romidepsin_16h_R1 1 AEGDSAGTAGTPGGTPAGDKVASWELR 27 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 1 0 AEGDS(0.007)AGT(0.068)AGT(0.176)PGGT(0.728)PAGDKVAS(0.021)WELR 51.811 0.011714 6528800 1079.7 934.35 1167.3 970.09 1445.7 1460.1 1511.7 1814.3 1193.9 1182.5 TRUE FALSE FALSE 1066.540201 947.5038038 1187.616367 1082.25637 1371.920534 1366.804322 1640.10376 1866.793908 1087.114594 1151.77848 0.925994208 0.822644129 1.03111526 0.93963934 1.191132287 1.186690276 1.423975 1.620792488 0.943857359 1 10.16964756 -7.606778163 0.804236755 0.953185802 1.825029821 0.920531076 0.066907339 0.315968371 0.199468989 0.011184301 0.219605815 2.47E-08 7.606778163 0.871844019 AEGEAEEESDFDVFPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 AEGEAEEESDFDVFPSSPR 19 0 B1AL69;Q7L3B6 B1AL69 CDC37L1 Hsp90 co-chaperone Cdc37-like 1 1 0 AEGEAEEES(0.155)DFDVFPS(0.509)S(0.337)PR 65.477 0.021627 12326000 904.78 936.88 951.01 1032.8 962.97 1185.4 726.75 1000.6 1121.7 1167.2 TRUE FALSE FALSE 893.7521933 950.0694212 967.5619301 1152.217195 913.8260476 1109.656766 788.4801269 1029.550782 1021.372343 1136.875976 0.786147489 0.835684315 0.851070786 1.013494189 0.80380452 0.97605789 0.693549819 0.905596392 0.898402609 1 10.15085916 -12.49175171 1.237236976 0.999971125 0.851125729 0.095681566 0.092438242 0.463839925 1.270976327 0.058208864 0.014188221 3.22E-13 12.49175171 -0.148845396 AEGEPQEES(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 2 AEGEPQEESPLK 12 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 AEGEPQEES(1)PLK;AEGEPQEES(1)PLK ; 151.56 0.0014412 175226000 9624.4 9283.5 9475.1 5672.6 7520.4 8208.6 6506.1 7190.6 8564.2 9222.4 TRUE FALSE FALSE 9507.094111 9414.193357 9640.010141 6328.492702 7136.605926 7684.096952 7058.727972 7398.648666 7798.196503 8982.800719 1.058366361 1.048024291 1.073163086 0.704512201 0.79447448 0.855423291 0.785804806 0.823646087 0.868125293 1 13.13294961 -9.269104973 24.99980025 1.033231388 0.795960286 0.724505155 0.066015111 138.1633058 450591.5576 0.006657418 0.010290551 5.38E-10 9.269104973 -0.237271102 AEGEPQEES(ph)PLKSK ddPTM_HeLa_Romidepsin_16h_R1 2 AEGEPQEESPLKSK 14 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 AEGEPQEES(0.758)PLKS(0.242)K;AEGEPQEES(0.885)PLKS(0.115)K ; 69.612 0.021577 278710000 11178.9 11093.8 9927.7 12909.8 9945.3 9846 10081 10369.7 12413.6 11812.5 TRUE FALSE FALSE 11042.64727 11249.97881 10100.48745 14402.49182 9437.75423 9216.872377 10937.27989 10669.73091 11303.29653 11505.60955 0.959762038 0.977782078 0.877875041 1.251779991 0.820274162 0.801076409 0.950604124 0.927350339 0.982416141 1 13.4900498 AEGEWEDQEALDYFS(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 1 AEGEWEDQEALDYFSDK 17 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 AEGEWEDQEALDYFS(1)DK 115.2 0.0021108 2577500 1347.1 1380.1 1351.5 654.18 1200.6 1220.4 986.47 1197.8 1205.7 1285.8 TRUE FALSE FALSE 1330.681027 1399.529084 1375.022291 729.8193696 1139.328902 1142.420379 1070.260737 1232.456453 1097.859172 1252.394731 1.062509283 1.117482412 1.097914465 0.582739093 0.909720294 0.912188746 0.854571415 0.984079878 0.876607946 1 10.29047363 AEGEWEDQEALDYFS(ph)DKESGK ddPTM_HeLa_Romidepsin_16h_R1 7 AEGEWEDQEALDYFSDKESGK 21 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 AEGEWEDQEALDY(0.421)FS(0.563)DKES(0.016)GK;AEGEWEDQEALDY(0.333)FS(0.542)DKES(0.126)GK;AEGEWEDQEALDY(0.006)FS(0.971)DKES(0.023)GK;AEGEWEDQEALDY(0.003)FS(0.556)DKES(0.442)GK;AEGEWEDQEALDY(0.05)FS(0.83)DKES(0.12)GK;AEGEWEDQEALDY(0.005)FS(0.967)DKES(0.028)GK;AEGEWEDQEALDY(0.045)FS(0.905)DKES(0.05)GK ;;;;;; 84.68 0.00077533 1337007100 23123.53 23542.57 21754.85 18813.7 21876.64 23027.56 19179.36 20986.65 24154.98 23159.01 TRUE FALSE FALSE 22841.69152 23874.00292 22133.48404 20989.02852 20760.19343 21556.17323 20808.45436 21593.86561 21994.49809 22557.33558 1.012605919 1.058369808 0.981210035 0.930474632 0.920330034 0.955616995 0.922469513 0.957287953 0.975048583 1 14.46130905 -9.436651509 4.302271999 1.010438949 0.936966396 0.708525016 0.022465038 0.081545368 2.714428557 0.003054101 0.004687908 3.66E-10 9.436651509 -0.073472553 AEGEWEDQEALDYFS(ph)DKESGKQK ddPTM_HeLa_Romidepsin_16h_R1 1 AEGEWEDQEALDYFSDKESGKQK 23 2 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 AEGEWEDQEALDY(0.46)FS(0.53)DKES(0.01)GKQK 71.527 0.0014187 7220400 1928.8 1526.2 1235.1 3508.6 1364.2 1325.2 1570.4 1623.5 1864.5 1627 TRUE FALSE FALSE 1905.291044 1547.685884 1256.596397 3914.28084 1294.579783 1240.523997 1703.789737 1670.473411 1697.73445 1584.730305 1.202280942 0.976624148 0.79294022 2.469998098 0.81690858 0.782798179 1.075129144 1.054105803 1.071308124 1 10.63002162 -5.682350476 10.64683281 1.116577627 0.616984105 0 0.467535112 0 0 0.057681675 0 2.08E-06 5.682350476 -0.499593523 AEGFVDALHR ddPTM_HeLa_Romidepsin_16h_R1 2 AEGFVDALHR 10 0 Q96I24;A0A494C1K6 Q96I24 FUBP3 Far upstream element-binding protein 3 0 0 ; ; 103.31 0.010465 9172200 17667.5 15886.3 18236.5 15703.5 21954.4 22487.5 19415.4 19194.3 17918.7 14933.2 FALSE FALSE TRUE 17452.16171 16109.94775 18553.89863 17519.21256 20833.98504 21050.62133 21064.54359 19749.65679 16316.00659 14545.23331 1.199854367 1.107575754 1.275599933 1.204464183 1.432358258 1.447252229 1.448209399 1.357809556 1.121742515 1 13.82825882 -9.318236777 0.227042341 0.957974768 1.596342775 0.755374985 0.074461064 1.173561441 0.143423918 0.103660023 0.249008806 4.81E-10 9.318236777 0.638368007 AEHLES(ph)PQLGGK ddPTM_HeLa_Romidepsin_16h_R1 2 AEHLESPQLGGK 12 0 Q9NYD6;D6RAG4 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 0 AEHLES(1)PQLGGK;AEHLES(1)PQLGGK ; 96.23 0.0099574 45363000 8918.5 8860 7860.6 6979.4 6388.8 6845.4 5735.3 6257.3 9634.6 8547.4 TRUE FALSE FALSE 8809.797892 8984.731313 7997.410446 7786.391067 6062.755696 6408.001033 6222.456239 6438.345103 8772.857246 8325.337316 1.058191105 1.079203277 0.960610981 0.935264335 0.728229436 0.769698667 0.747411907 0.773343453 1.05375397 1 13.02329301 -8.989427375 2.015300334 1.029986476 0.752594446 0.931533039 0.035143345 0.060111614 0.488182768 0.005730167 0.011284888 1.02E-09 8.989427375 -0.27739203 AEHMETNAVGPS(ph)PSSDTR ddPTM_HeLa_Romidepsin_16h_R1 2 AEHMETNAVGPSPSSDTR 18 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 AEHMET(0.134)NAVGPS(0.594)PS(0.123)S(0.123)DT(0.027)R;AEHMETNAVGPS(0.541)PS(0.194)S(0.194)DT(0.07)R ; 105.65 0.00049447 58755000 2490.3 2258.9 2427 1925.06 3483.5 3565.5 2549.2 2813.4 2777.6 2872 TRUE FALSE FALSE 2459.947266 2290.700853 2469.240917 2147.644495 3305.723996 3337.676057 2765.728984 2894.80129 2529.164499 2797.385026 0.879373859 0.818872208 0.882696123 0.767732892 1.181719343 1.193141461 0.988683702 1.034824046 0.904117408 1 11.44986312 -8.748691089 24.99993777 0.91537919 1.098352199 0.604024557 0.085301401 164.5242993 322637.2362 0.014282918 0.028416933 1.78E-09 8.748691089 0.182973009 AEIAFEDRK ddPTM_HeLa_Romidepsin_16h_R1 1 AEIAFEDRK 9 1 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 0 0 93.178 0.023796 4811500 2878.7 2997.9 3012.5 2389.6 3251.2 2980.3 2242.8 2879.6 3101.8 3131.1 FALSE FALSE TRUE 2843.613297 3040.104515 3064.931299 2665.896795 3085.279132 2789.868448 2433.303376 2962.916683 2824.367239 3049.753571 0.932407564 0.99683612 1.004976706 0.87413515 1.011648666 0.914784878 0.797868851 0.971526589 0.926096871 1 11.57447696 -8.00609132 24.98040192 0.967564958 0.877605003 0.24458914 0.056670748 229.176825 939866.1686 0.007271784 0.020836003 9.86E-09 8.00609132 -0.089959954 AEIIADK(ac)QSGK ddPTM_HeLa_Romidepsin_16h_R1 1 AEIIADKQSGK 11 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 1 AEIIADK(1)QSGK 178.67 9.68E-05 1098700 821.24 604.14 564.71 527.71 427.11 700.02 514.73 472.83 763.59 463.74 FALSE TRUE FALSE 811.230411 612.6450988 574.5385407 588.7263132 405.3129829 655.2909812 558.4511534 486.51059 695.292598 451.6919679 1.795981484 1.356333834 1.271969797 1.30338008 0.897321652 1.450747473 1.23635396 1.077084882 1.539306978 1 8.81919545 -9.419833914 2.295187922 1.383040562 1.190924735 0.177576716 0.22858683 0.692694441 7.165521893 0.051575198 0.082993668 3.80E-10 9.419833914 -0.192115827 AEISFEDR ddPTM_HeLa_Romidepsin_16h_R1 1 AEISFEDR 8 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 0 168.23 0.016302 23745000 2751.8 2615.8 2750.5 1349.1 2819.4 2925.8 2511.6 2849.6 3049.8 2706.4 FALSE FALSE TRUE 2718.260003 2652.625301 2798.371299 1505.08929 2675.515497 2738.850823 2724.935241 2932.04868 2777.01825 2636.087338 1.031172209 1.006273678 1.061562437 0.570955775 1.014957076 1.038983338 1.033704461 1.112272965 1.053462156 1 11.36418245 AEITFDDHK ddPTM_HeLa_Romidepsin_16h_R1 2 AEITFDDHK 9 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3 O75369-8 FLNB Filamin-B 0 0 ; ; 128.35 0.0042676 52873000 11105.1 11108.4 11094.1 8097.3 13440.8 14709.3 12718.2 13342.3 10798.7 10272.7 FALSE FALSE TRUE 10969.74677 11264.78435 11287.18816 9033.547925 12754.86582 13769.4232 13798.48359 13728.3384 9832.837226 10005.81377 1.096337291 1.125823906 1.128062985 0.902829908 1.274745474 1.376142262 1.379046613 1.372036169 0.982712396 1 13.28855089 -8.586054967 5.728965921 1.051514734 1.368735472 0.845919077 0.065927826 0.05641883 3.58629613 0.009792092 0.019891703 2.59E-09 8.586054967 0.317220738 AEKDEPGAWEETFK ddPTM_HeLa_Romidepsin_16h_R1 2 AEKDEPGAWEETFK 14 1 F5H6X6;Q14697;Q14697-2;E9PKU7 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 ; ; 134.88 0.0017431 23304000 4004.8 4608.5 4222.2 4552.8 4164.5 4198.9 3715.1 4746.5 4492.3 4595.4 FALSE FALSE TRUE 3955.987957 4673.378584 4295.68562 5079.216158 3951.970025 3930.603841 4030.660501 4883.832489 4090.497437 4476.010846 0.883820012 1.044094562 0.959712961 1.134764042 0.882922352 0.878148864 0.900502845 1.091112747 0.913871208 1 12.12799782 -7.246424246 23.47571137 0.953480666 1.091112981 0.207795158 0.079472609 1486.565186 2324109.476 0.011332004 0.321977447 5.67E-08 7.246424246 0.137632315 AELEEMEEVHPS(ph)DEEEEDATK ddPTM_HeLa_Romidepsin_16h_R1 1 AELEEMEEVHPSDEEEEDATK 21 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 AELEEMEEVHPS(0.991)DEEEEDAT(0.009)K 87.952 0.00040948 9564700 1632.7 1519.8 1728.5 623.96 3212.7 4262.1 3744.3 3964.9 1694.3 1461.2 TRUE FALSE FALSE 1612.800024 1541.195784 1758.583817 696.105191 3048.743931 3989.765565 4062.340749 4079.618126 1542.757565 1423.237813 1.13319082 1.082880015 1.235621904 0.489099702 2.142118416 2.80330211 2.854295122 2.86643461 1.083977358 1 10.47496103 -8.5580967 4.073720897 1.045880535 2.808307428 0.945525474 0.20009254 0.032600348 1.188822869 0.028509999 0.060812459 2.77E-09 8.5580967 1.762426893 up AELEEMEEVHPS(ph)DEEEEDATKAEGFYQK ddPTM_HeLa_Romidepsin_16h_R1 2 AELEEMEEVHPSDEEEEDATKAEGFYQK 28 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 AELEEMEEVHPS(0.701)DEEEEDAT(0.13)KAEGFY(0.168)QK;AELEEMEEVHPS(1)DEEEEDATKAEGFYQK ; 104.97 5.83E-09 28858500 1521.06 1825.5 2057.5 1800.2 4281.7 5900.7 4633.8 5529.5 1880.17 2050.42 TRUE FALSE FALSE 1502.520736 1851.199437 2093.309924 2008.347594 4063.188872 5523.664314 5027.394856 5689.487358 1712.002886 1997.149793 0.75233252 0.926920676 1.048148683 1.005606891 2.0344938 2.765773671 2.51728482 2.848803519 0.857223075 1 10.96372683 -8.621165459 2.268908777 0.894229767 2.70088143 0.979705907 0.116466574 0.03129733 0.325042545 0.019671691 0.045537143 2.39E-09 8.621165459 1.806651663 up AELNPWPEYIYTR ddPTM_HeLa_Romidepsin_16h_R1 1 AELNPWPEYIYTR 13 0 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 154.67 0.0076214 24644000 1582.6 1353.6 1563 1301.7 1249.5 1655.1 1343.1 990.68 1457.2 1472.5 FALSE FALSE TRUE 1563.310662 1372.656016 1590.203359 1452.208679 1185.733352 1549.344452 1457.18288 1019.343763 1326.864382 1434.244238 1.089989153 0.957058763 1.108739584 1.012525371 0.826730428 1.080251474 1.01599354 0.710718395 0.925131402 1 10.48607501 -8.980779339 24.60992164 1.041207037 0.927286348 0.163804183 0.108385106 231.4895986 296394.88 0.014476943 0.026238908 1.05E-09 8.980779339 -0.113920689 AELPGSS(ph)SPLLAQPR ddPTM_HeLa_Romidepsin_16h_R1 1 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 AELPGS(0.088)S(0.456)S(0.456)PLLAQPR 86.189 0.021153 16953000 1492.2 1531.6 1576.8 1867 2097.1 2268.9 2000.7 2519.9 1533.7 1611.5 TRUE FALSE FALSE 1474.012492 1553.161905 1604.243543 2082.871324 1990.077162 2123.924613 2170.639408 2592.809331 1396.522031 1569.632998 0.939080979 0.989506405 1.022050087 1.326979827 1.267861446 1.353134533 1.382896136 1.651857048 0.889712457 1 10.61621156 -8.495285907 0.618901498 0.961715123 1.604510965 0.887969895 0.079136257 0.275575441 0.157394613 0.015915692 0.095882284 3.20E-09 8.495285907 0.642795842 AELPGSSS(ph)PLLAQPR ddPTM_HeLa_Romidepsin_16h_R1 1 AELPGSSSPLLAQPR 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 AELPGS(0.027)S(0.223)S(0.75)PLLAQPR 162.64 3.85E-05 0 2219.4 2135 1984.2 2250.1 3143.1 3362.5 2585.7 3025.7 2345.9 1976.7 TRUE FALSE FALSE 2192.349099 2165.056586 2018.734169 2510.267149 2982.695878 3147.647102 2805.329293 3113.243856 2136.076829 1925.345049 1.138678545 1.124503157 1.048505134 1.303801181 1.549174721 1.634848311 1.457052747 1.616979698 1.109451436 1 10.9109013 -8.975063592 2.447227889 1.070867606 1.566037435 0.934803078 0.059648402 0.056383088 0.680453663 0.010711365 0.020505973 1.06E-09 8.975063592 0.495169829 AELVLIDEDDEKS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 AELVLIDEDDEKSLR 15 1 B1ALY0;Q8IXS6-2;C9JA33;Q8IXS6 B1ALY0 PALM2-AKAP2;PALM2 Paralemmin-2 1 0 AELVLIDEDDEKS(1)LR 85.054 0.0085241 2344100 971.17 1457.8 1372 688.56 990.62 1494.6 867.09 1290.3 1290.3 1130.5 TRUE FALSE FALSE 959.3330065 1478.322947 1395.879084 768.174547 940.0649649 1399.099884 940.740603 1327.632795 1174.892336 1101.129447 0.871226366 1.34255146 1.267679371 0.697624198 0.853727931 1.270604367 0.854341518 1.205700927 1.06698839 1 10.10476836 AENFIFMGDFNAGCSY(ph)VPK ddPTM_HeLa_Romidepsin_16h_R1 1 AENFIFMGDFNAGCSYVPK 19 0 H7C4R7;A0A0A0MT68;Q13609-2;Q13609 H7C4R7 DNASE1L3 Deoxyribonuclease;Deoxyribonuclease gamma 1 0 AENFIFMGDFNAGCS(0.276)Y(0.724)VPK 55.322 0.0040495 0 1149.2 1088.7 931.18 1123.9 1160 975.07 848.28 1147.2 1210.9 1159.3 TRUE FALSE FALSE 1135.193108 1104.026747 947.3867973 1253.850606 1100.800871 912.7661739 920.332882 1180.392422 1102.594071 1129.181219 1.005324114 0.977723264 0.839003325 1.110406891 0.974866437 0.80834339 0.815044447 1.045352511 0.97645449 1 10.14106132 -8.435833565 8.010814166 0.995535528 0.882921697 0.191138948 0.086635715 0.307321256 25.59660644 0.011548554 0.025871599 3.67E-09 8.435833565 -0.112613831 AENGERS(ph)DLEEDNER ddPTM_HeLa_Romidepsin_16h_R1 4 AENGERSDLEEDNER 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 0 AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER;AENGERS(1)DLEEDNER ;;; 100.07 0.0029158 55693300 5452 4869.5 5485.9 3541.53 5218.22 5874.4 4948.3 5262.1 5410.55 5697.2 TRUE FALSE FALSE 5385.548927 4938.052949 5581.379788 3951.018362 4951.914762 5499.044799 5368.608478 5414.350561 4926.616857 5549.185923 0.970511531 0.889869797 1.005801547 0.711999637 0.892367787 0.990964238 0.96745875 0.975701776 0.887808937 1 12.43806043 -10.49836658 1.944858767 0.989619911 0.917552168 0 0.085855742 0.477585115 3.57673864 0.015529955 0.016856234 3.17E-11 10.49836658 -0.072067743 AENNS(ph)EVGASGYGVPGPTWDR ddPTM_HeLa_Romidepsin_16h_R1 2 AENNSEVGASGYGVPGPTWDR 21 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 0 AENNS(0.857)EVGAS(0.143)GYGVPGPTWDR;AENNS(0.992)EVGAS(0.008)GYGVPGPTWDR ; 239.9 9.45E-54 22435000 2615.27 2965.2 2089.57 1976.61 2197.52 2295.08 1766.01 2653.66 2994.2 2651.71 TRUE FALSE FALSE 2583.394083 3006.944163 2125.938089 2205.154948 2085.372354 2148.431795 1916.014845 2730.439465 2726.391253 2582.818192 1.00022297 1.164210541 0.823107912 0.853778619 0.807401915 0.83181689 0.741831094 1.057155116 1.055587753 1 11.33473038 -9.72542563 24.9987154 1.012416192 0.844550048 0.522212794 0.091130325 110.8329419 76933.82219 0.013071748 0.018485906 1.88E-10 9.72542563 -0.167866145 AENYDIPSADR ddPTM_HeLa_Romidepsin_16h_R1 1 AENYDIPSADR 11 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 141.08 0.030133 7382700 2500.2 2273.2 2059.6 1779.1 2524.1 2528 2193.3 2610.6 2577.6 2127.6 FALSE FALSE TRUE 2469.726601 2305.202169 2095.446474 1984.807913 2395.285758 2366.468959 2379.598847 2686.133592 2347.053 2072.324645 1.191766264 1.11237502 1.011157436 0.957768812 1.155844845 1.141939302 1.148275128 1.296193431 1.132570134 1 11.01703431 -16.52287526 0.017689687 4.75E-12 1.965517436 0.159380735 0.08759207 4671.243734 6.669023207 475.0217624 288.0095655 3.00E-17 16.52287526 1.965517436 AEPAK(ac)IEAFR ddPTM_HeLa_Romidepsin_16h_R1 1 AEPAKIEAFR 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 1 AEPAK(1)IEAFR 134.84 0.0084202 1953100 419.52 483.91 498.69 549.04 663.8 747.29 639.8 703.05 862.75 494.63 FALSE TRUE FALSE 414.4067289 490.7224977 507.3694903 612.5225881 629.923809 699.5405808 694.144596 723.3916425 785.5834792 481.7794413 0.860158598 1.018562553 1.053115693 1.271375521 1.307494166 1.451993424 1.44079331 1.501499609 1.630587385 1 8.912229021 -9.076695966 1.066142747 0.933729094 1.468995508 0.150858227 0.224915255 0.08472836 0.189897324 0.010515435 0.024599628 8.38E-10 9.076695966 0.535266414 AEPEAGEEQAGDDRDS(ph)GGPVLQFDYEAVANR ddPTM_HeLa_Romidepsin_16h_R1 1 AEPEAGEEQAGDDRDSGGPVLQFDYEAVANR 31 1 P56182 P56182 RRP1 Ribosomal RNA processing protein 1 homolog A 1 0 AEPEAGEEQAGDDRDS(0.999)GGPVLQFDY(0.001)EAVANR 65.299 7.75E-05 2763900 482.8 435.2 506.8 314.84 366.54 486.85 395.03 517.19 508.23 386.44 TRUE FALSE FALSE 476.9154479 441.326757 515.6206414 351.2432822 347.8340961 455.7418562 428.5838383 532.1540767 462.7726359 376.4002331 1.267043445 1.172493315 1.369873332 0.933164359 0.924107016 1.210790579 1.13863861 1.413798478 1.229469578 1 8.556123711 -12.52379598 1.29552645 1.000522052 1.179635466 0 0.166164245 0.680732701 2.055095092 0.106186764 0.025776788 2.99E-13 12.52379598 0.179113414 AEPEDHYFLLTEPPLNTPENR ddPTM_HeLa_Romidepsin_16h_R1 1 AEPEDHYFLLTEPPLNTPENR 21 0 P61158;B4DXW1;F8WDR7 P61158 ACTR3 Actin-related protein 3 0 0 142.88 1.81E-05 5723900 1466.1 1522.2 1150.9 1354.3 1255.6 1520.5 1252.9 1462.9 1970.6 1615.2 FALSE FALSE TRUE 1448.230609 1543.629572 1170.930932 1510.890538 1191.522047 1423.344957 1359.321295 1505.226703 1794.344601 1573.236871 0.920541996 0.981180647 0.744281394 0.960370664 0.75736977 0.904723874 0.864028373 0.956770548 1.140543191 1 10.61952019 -10.97005909 0.623449615 0.991452475 0.870671718 0.351619588 0.089073378 0.602750847 0.533923278 0.029233144 0.019914956 1.07E-11 10.97005909 -0.120780757 AEPGEGTRPATVGDS(ph)SAR ddPTM_HeLa_Romidepsin_16h_R1 1 AEPGEGTRPATVGDSSAR 18 1 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 AEPGEGTRPAT(0.003)VGDS(0.749)S(0.247)AR 102.03 0.012542 25266000 8789.1 9434.9 8469.8 6413.4 6602.4 5766.1 4501.1 4459.2 8159 8437.2 TRUE FALSE FALSE 8681.975069 9567.72477 8617.213316 7154.947484 6265.454891 5397.664819 4883.423322 4588.219917 7429.238605 8218.000328 1.05645835 1.164240008 1.048577874 0.870643368 0.76240626 0.656810003 0.594234987 0.558313426 0.904020237 1 13.00457167 -8.690375013 1.364195097 1.041493838 0.586087915 0.892946235 0.065503747 0.08062057 0.298023851 0.009066873 0.024688002 2.04E-09 8.690375013 -0.455405923 AEPSEVDMNS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 AEPSEVDMNSPK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 AEPSEVDMNS(1)PK;AEPS(0.001)EVDMNS(0.999)PK ; 79.022 0.01547 19637200 15283.5 13685.9 14885.7 11265.1 13651.3 14643.6 13153.8 12922.3 14826.4 15309.6 TRUE FALSE FALSE 15097.21882 13878.57046 15144.77936 12567.62387 12954.62322 13707.92122 14271.08344 13296.18636 13500.28965 14911.85438 1.012430677 0.930707215 1.015620122 0.842794165 0.868746628 0.91926335 0.957029426 0.891652106 0.905339423 1 13.86417206 -9.276253794 24.98650158 0.999850943 0.899083134 0.334818158 0.046935286 377.5070873 636715.2815 0.005747598 0.008802145 5.29E-10 9.276253794 -0.100767809 AEPTAGAVDRAEK ddPTM_HeLa_Romidepsin_16h_R1 1 AEPTAGAVDRAEK 13 1 A0A0B4J1R9;Q8N0S2 A0A0B4J1R9 SYCE1 Synaptonemal complex central element protein 1 0 0 108.31 0.028813 1170900 165.5 231.94 292.56 160.61 1878.1 2818.4 1417.3 1516.9 318.88 313.12 FALSE FALSE TRUE 163.4828223 235.2052574 297.6518841 179.1804839 1782.253549 2638.313336 1537.685427 1560.789108 290.3585742 304.9850973 0.536035445 0.77120246 0.975955503 0.587505703 5.843739792 8.650630341 5.041837914 5.117591391 0.952041843 1 8.252594939 -8.742394824 6.338922731 0.77520317 6.296417287 0.886361103 0.940223529 0.036504071 5.220478988 0.133948269 0.262828655 1.81E-09 8.742394824 5.521214117 AEQDMRELT(ph)Y(ph)ELNALQLEK ddPTM_HeLa_Romidepsin_16h_R1 1 AEQDMRELTYELNALQLEK 19 1 Q03001-3 Q03001-3 DST Dystonin 2 0 AEQDMRELT(1)Y(1)ELNALQLEK 42.913 0.004236 0 430.07 270.99 365.07 267.39 456.61 540.05 298.45 406.29 498.76 342.13 TRUE FALSE FALSE 424.8281414 274.8050043 371.4238902 298.3068899 433.3074879 505.5425479 323.8003356 418.0453601 454.1496564 333.2414133 1.274835973 0.824642417 1.114579027 0.895167521 1.300281029 1.517045985 0.971668954 1.254482017 1.362824782 1 8.380423891 -8.705195348 24.99998679 1.091445362 1.258510959 0.172729535 0.194104401 127.0735316 56482.19966 0.027106893 0.054213769 1.97E-09 8.705195348 0.167065597 AEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_HeLa_Romidepsin_16h_R1 4 AEQGSEEEGEGEEEEEEGGESK 22 0 Q8NE71;Q5STZ8 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 AEQGS(1)EEEGEGEEEEEEGGESK;AEQGS(1)EEEGEGEEEEEEGGESK;AEQGS(1)EEEGEGEEEEEEGGESK;AEQGS(1)EEEGEGEEEEEEGGESK ;;; 176.28 1.66E-13 55452000 16720.4 16537.7 16561 8591.6 15013.6 16523 13680.3 14801.3 17273.9 16803.5 TRUE FALSE FALSE 16516.60533 16770.51817 16849.23726 9585.001217 14247.39997 15467.23363 14842.30434 15229.55226 15728.87912 16366.94265 1.009144205 1.024657967 1.029467606 0.585631747 0.870498558 0.945028889 0.906846481 0.930506851 0.961015106 1 13.99849723 AEQGS(ph)EEEGEGEEEEEEGGESKADDPYAHLSK ddPTM_HeLa_Romidepsin_16h_R1 1 AEQGSEEEGEGEEEEEEGGESKADDPYAHLSK 32 1 Q8NE71;Q5STZ8 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 AEQGS(0.982)EEEGEGEEEEEEGGES(0.017)KADDPY(0.001)AHLSK 73.562 4.94E-06 15343000 2901.6 2479 2032.6 2516.7 4682.5 5294.6 3938.9 3940 4288.9 3465.4 TRUE FALSE FALSE 2866.234183 2513.899427 2067.97655 2807.692695 4443.534552 4956.292148 4273.470068 4053.997684 3905.290042 3375.368408 0.84916188 0.744777791 0.612666915 0.831818147 1.316459128 1.468370722 1.266075151 1.201053394 1.15699668 1 11.72082926 -8.757322316 24.89318462 0.879378055 1.320737318 0.681892876 0.149390405 43.84619716 265105.2794 0.021367401 0.041529325 1.75E-09 8.757322316 0.441359263 AEQLVLSGADS(ph)DEDTSR ddPTM_HeLa_Romidepsin_16h_R1 3 AEQLVLSGADSDEDTSR 17 0 H7C1N2;J3KR05;O75128-2 H7C1N2 COBL Protein cordon-bleu 1 0 AEQLVLS(0.097)GADS(0.902)DEDT(0.001)SR;AEQLVLS(0.125)GADS(0.875)DEDTSR;AEQLVLS(0.425)GADS(0.571)DEDT(0.004)SR ;; 167.9 4.23E-06 46090900 10842.4 11202.6 9930.8 11092.2 10411.7 9860.6 8439.8 8630.9 11983.3 10410.4 TRUE FALSE FALSE 10710.24866 11360.3105 10103.64141 12374.73235 9880.352098 9230.539484 9156.676401 8880.621474 10911.48364 10139.93631 1.056244175 1.12035324 0.996420599 1.220395472 0.974399819 0.910315332 0.903030958 0.875806436 1.076089958 1 13.30776097 -8.523492382 24.99908333 1.046709443 0.904600335 0.594149232 0.064899402 13.00015796 529618.2066 0.00959219 0.019325216 3.00E-09 8.523492382 -0.142109109 AES(ph)PAEKVPEESVLPLVQK ddPTM_HeLa_Romidepsin_16h_R1 3 AESPAEKVPEESVLPLVQK 19 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 AES(0.943)PAEKVPEES(0.057)VLPLVQK;AES(0.999)PAEKVPEES(0.001)VLPLVQK;AES(0.996)PAEKVPEES(0.004)VLPLVQK ;; 110.57 0.0002939 278066000 14174.2 14848 15521.3 8381.6 13542 13874.1 12328.1 13290.5 14808.3 15201.1 TRUE FALSE FALSE 14001.4394 15057.03053 15791.44172 9350.720029 12850.90121 12987.58979 13375.24851 13675.03965 13483.80856 14806.17323 0.945648763 1.016942751 1.066544439 0.631541985 0.867942108 0.877173972 0.903356208 0.923603921 0.910688289 1 13.85391119 AES(ph)PEEVACR ddPTM_HeLa_Romidepsin_16h_R1 1 AESPEEVACR 10 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 AES(1)PEEVACR 161.19 0.0022838 15603000 1831.8 1692.9 1645.8 208.17 1866.5 1674.9 1343.2 1674 1593.9 1715.3 TRUE FALSE FALSE 1809.473317 1716.732691 1674.444459 232.2395949 1771.24554 1567.879295 1457.291374 1722.434549 1451.337592 1670.736259 1.083039473 1.027530636 1.0022195 0.139004342 1.060158676 0.938436146 0.872245016 1.030943418 0.868681448 1 10.70626829 -9.49350669 24.99898309 1.038263256 0.806721369 0.116452745 0.247858088 922.3949052 785064.9904 0.036012278 0.054951922 3.21E-10 9.49350669 -0.231541888 VSLPSS(ph)PVPASPASSSGADQR ddPTM_HeLa_Romidepsin_16h_R1 1 VSLPSSPVPASPASSSGADQR 21 0 Q5T6S3-2 Q5T6S3-2 1 0 VSLPS(0.031)S(0.966)PVPAS(0.001)PAS(0.001)S(0.001)SGADQR 195.25 3.44E-18 9712200 2427.5 2194.9 2137.2 1350 877.21 829.96 831.7 737.75 2234.9 2806.4 TRUE FALSE FALSE 2397.912696 2225.79986 2174.397069 1506.093352 832.4427004 776.9282346 902.3445772 759.0956323 2035.004947 2733.489323 0.877235069 0.814270552 0.795465726 0.550978319 0.304534828 0.284225816 0.330107226 0.277702066 0.744471518 1 11.41652803 -9.1994783 1.057433073 0.944181504 0.271259764 0.915826359 0.077194491 0.061055711 0.134857204 0.009841937 0.021273652 6.32E-10 9.1994783 -0.672921739 down AES(ph)PESSAIESTQS(ph)TPQKGR ddPTM_HeLa_Romidepsin_16h_R1 2 AESPESSAIESTQSTPQKGR 20 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 AES(0.492)PES(0.458)S(0.051)AIES(0.003)T(0.006)QS(0.542)T(0.448)PQKGR;AES(0.833)PES(0.148)S(0.029)AIES(0.011)T(0.072)QS(0.492)T(0.415)PQKGR ; 76.241 0.011922 21423700 7791.1 7370.3 6003.9 7565.5 4694.5 3741 3670.6 3447.6 8167.4 6773 TRUE FALSE FALSE 7696.139076 7474.059277 6108.395361 8440.258707 4454.922147 3501.962174 3982.380672 3547.350867 7436.887288 6597.036484 1.166605505 1.132941935 0.925930208 1.279401551 0.675291422 0.530838685 0.603662066 0.537718849 1.127307285 1 12.68760237 -8.634395573 5.630428918 1.084214398 0.568884852 0.882387546 0.093129047 0.052731029 2.416687755 0.014052078 0.028405121 2.32E-09 8.634395573 -0.515329547 AES(ph)PESSAIESTQST(ph)PQKGR ddPTM_HeLa_Romidepsin_16h_R1 1 AESPESSAIESTQSTPQKGR 20 1 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 AES(0.91)PES(0.039)S(0.051)AIEST(0.002)QS(0.312)T(0.685)PQKGR 133.98 0.00032228 13449000 2265.7 2403.1 1950.3 2443 1185.1 1014.9 1274.3 1013.4 2132.4 1818 TRUE FALSE FALSE 2238.084777 2436.930905 1984.244153 2725.471155 1124.619925 950.0511654 1382.53901 1042.72113 1941.672803 1770.768098 1.2639062 1.376199914 1.120555625 1.539146294 0.635102883 0.536519246 0.780756674 0.588852448 1.096514448 1 10.79015957 -8.732924156 24.98891467 1.174057749 0.638640264 0.766584554 0.159534512 92.88694998 81399.77389 0.025530832 0.051054158 1.85E-09 8.732924156 -0.535417485 AES(ph)PESSAIESTQSTPQK ddPTM_HeLa_Romidepsin_16h_R1 3 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 AES(0.893)PES(0.087)S(0.02)AIESTQSTPQK;AES(0.872)PES(0.119)S(0.009)AIESTQSTPQK;AES(0.943)PES(0.028)S(0.028)AIESTQSTPQK ;; 308.29 3.59E-164 284433000 14010.9 13070.9 12415.7 11162.9 13462.7 13889.6 13159.1 15399.2 14838.5 12740.1 TRUE FALSE FALSE 13840.12976 13254.91247 12631.79005 12453.60702 12775.64818 13002.09939 14276.83363 15844.75156 13511.3074 12409.11037 1.115320064 1.06815977 1.017944855 1.003585805 1.0295378 1.047786586 1.150512261 1.276864424 1.088821599 1 13.59911207 -7.434324649 2.178636075 1.047845447 1.297423771 0.808645799 0.035231479 0.192096857 1.326512729 0.006747923 0.080032584 3.68E-08 7.434324649 0.249578323 AES(ph)PSPAPPPGLR ddPTM_HeLa_Romidepsin_16h_R1 2 AESPSPAPPPGLR 13 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 0 AES(0.991)PS(0.009)PAPPPGLR;AES(0.914)PS(0.086)PAPPPGLR ; 160.56 0.00042774 132851400 5142.2 4956.1 5221.1 4210.9 4348.5 4547.7 3835.5 4574 5149.3 5091.7 TRUE FALSE FALSE 5079.524889 5025.872106 5311.971055 4697.784071 4126.579819 4257.116647 4161.287274 4706.341473 4688.733711 4959.4169 1.024218167 1.013399802 1.071087824 0.947245244 0.832069556 0.858390559 0.83906785 0.948970729 0.94542036 1 12.27595479 -8.980616132 4.838238656 1.015922255 0.867715209 0.71879814 0.041513216 0.057999195 3.587508205 0.00501606 0.009042831 1.05E-09 8.980616132 -0.148207046 AES(ph)PTPGMAQGMEPGAGQEGAMFVHAR ddPTM_HeLa_Romidepsin_16h_R1 1 AESPTPGMAQGMEPGAGQEGAMFVHAR 27 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 0 AES(0.942)PT(0.058)PGMAQGMEPGAGQEGAMFVHAR 52.532 0.0041062 21583000 1973.9 1783.8 1517.4 1359.4 1642.4 1672 1490.2 1659.6 1901.5 1873.2 TRUE FALSE FALSE 1949.841348 1808.912383 1543.80971 1516.580224 1558.582199 1565.164596 1616.777551 1707.617908 1731.425078 1824.533994 1.068679101 0.991438027 0.846139187 0.83121511 0.854235769 0.857843483 0.886131777 0.935920028 0.948968385 1 10.83331232 -9.866628277 4.39345108 1.032279759 0.866661146 0.708989581 0.040846581 0.065175403 2.230036205 0.006132083 0.008172761 1.36E-10 9.866628277 -0.165618613 AES(ph)Y(ph)S(ph)LIS(ph)MK ddPTM_HeLa_Romidepsin_16h_R1 1 AESYSLISMK 10 0 O75969 O75969 AKAP3 A-kinase anchor protein 3 4 0 AES(1)Y(1)S(1)LIS(1)MK 48.64 0.026399 1338700 725.13 688.55 538.39 1683.9 725.74 783.3 783.36 658.3 745.54 819.19 TRUE FALSE FALSE 716.2918366 698.243425 547.7604521 1878.600441 688.7027797 733.249658 849.8985788 677.3468719 678.8570352 797.9073257 0.897713072 0.875093388 0.686496332 2.354409316 0.863136304 0.918965943 1.065159513 0.84890419 0.850796845 1 9.640077382 AESGDS(ph)LGSEDRDLLYSIDAYR ddPTM_HeLa_Romidepsin_16h_R1 2 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 0 AES(0.023)GDS(0.953)LGS(0.023)EDRDLLYSIDAYR;AES(0.053)GDS(0.577)LGS(0.37)EDRDLLYSIDAYR ; 93.104 0.00018511 38549000 1026.12 1203.94 1260.35 1262.06 1249.22 1375.79 947.12 1007.31 1206.73 1201.56 TRUE FALSE FALSE 1013.613255 1220.889099 1282.285863 1407.985315 1185.467642 1287.881459 1027.568349 1036.454926 1098.797046 1170.343298 0.866081992 1.043188867 1.095649341 1.203053256 1.012922998 1.100430499 0.878005924 0.885599061 0.938867295 1 10.19271606 -13.26914177 4.581667732 1.001416797 0.975536602 0 0.110023718 1.875711254 69.26938292 0.129812591 0.017640393 5.38E-14 13.26914177 -0.025880195 AESGDSLGS(ph)EDRDLLYSIDAYR ddPTM_HeLa_Romidepsin_16h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 0 AES(0.007)GDS(0.095)LGS(0.897)EDRDLLY(0.001)SIDAYR 85.166 0.00041022 17002000 2380.5 2793.6 2880.3 2798.4 2613.6 2619.5 2076.1 1717.5 2537.9 2332 TRUE FALSE FALSE 2351.48555 2832.928374 2930.430413 3121.964175 2480.218239 2452.122404 2252.443882 1767.193153 2310.903868 2271.414304 1.035251714 1.247209005 1.290134701 1.37445827 1.091926838 1.079557525 0.99164819 0.778014451 1.017385452 1 11.14937516 -7.295329782 2.077277243 1.087511826 0.704792993 0.389508392 0.128190433 0.682331614 3.380706397 0.021949067 0.475432299 5.07E-08 7.295329782 -0.382718833 AESGDSLGSEDRDLLYSIDAYR ddPTM_HeLa_Romidepsin_16h_R1 1 AESGDSLGSEDRDLLYSIDAYR 22 1 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 0 89.557 0.0007304 4969900 913.44 816.78 1087 882.02 1091.7 1275 976.35 1141 1100.9 1069.8 FALSE FALSE TRUE 902.3066419 828.2786503 1105.918779 984.0033024 1035.986475 1193.531615 1059.281145 1174.013035 1002.432747 1042.006442 0.865931923 0.794888224 1.061335837 0.944335143 0.994222717 1.145416734 1.016578307 1.126685007 0.962021641 1 10.02514848 -8.627040621 1.389253904 0.930299951 1.092114658 0.458281364 0.075443091 0.32739232 1.24710953 0.01295416 0.036716211 2.36E-09 8.627040621 0.161814707 AESPES(ph)SAIESTQSTPQK ddPTM_HeLa_Romidepsin_16h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 AES(0.205)PES(0.792)S(0.003)AIESTQSTPQK 261.59 5.32E-76 5667400 2894.2 2535.2 2646.3 2135.9 2493.1 2479.9 2866.3 3003.2 2677 2244.9 TRUE FALSE FALSE 2858.924377 2570.890612 2692.357741 2382.862808 2365.867804 2321.442394 3109.76345 3090.092854 2437.562415 2186.577174 1.307488439 1.17576029 1.231311555 1.089768445 1.081996022 1.061678692 1.422206125 1.413210057 1.114784534 1 11.09445855 -12.45863307 1.152193641 0.998034847 1.222918102 0.197029867 0.12653229 0.524206849 1.227395076 0.095364891 0.022771011 3.48E-13 12.45863307 0.224883255 ATSDTLES(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSDTLESPPK 11 0 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 ATSDT(0.003)LES(0.997)PPK 134.99 0.0040816 11548000 2338.1 2747.7 2821.9 1084.2 920.27 934.88 689.48 770 3001.6 3020.6 TRUE FALSE FALSE 2309.602338 2786.382193 2871.013986 1209.560305 873.3051879 875.1441852 748.044414 792.2787351 2733.129378 2942.124377 0.785011795 0.947064718 0.975830257 0.411118005 0.2968281 0.297453157 0.254253158 0.269287982 0.928964594 1 11.52264252 -9.163233444 3.904407429 0.905772884 0.286095519 0.964269126 0.060056651 0.045317377 1.254683844 0.013382353 0.022711179 6.87E-10 9.163233444 -0.619677366 down AESSSGGGTVPSSAGILEQGPS(ph)PGDGSPPKPK ddPTM_HeLa_Romidepsin_16h_R1 1 AESSSGGGTVPSSAGILEQGPSPGDGSPPKPK 32 1 Q68EM7-7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7 Q68EM7-7 ARHGAP17 Rho GTPase-activating protein 17 1 0 AESSSGGGTVPSSAGILEQGPS(0.543)PGDGS(0.457)PPKPK 81.441 1.89E-08 126840000 4299.2 3585.3 4633.9 2967.7 3909.4 3837.8 3767.4 3756.9 3914 4156.5 TRUE FALSE FALSE 4246.799697 3635.773948 4714.551086 3310.839437 3709.88873 3592.576966 4087.402862 3865.599974 3563.922037 4048.513531 1.048977523 0.898051574 1.164514099 0.817791373 0.916358239 0.887381736 1.00960583 0.954819576 0.880303847 1 11.98317658 -9.247058917 24.98929976 1.021985096 0.920623126 0.149141185 0.088172803 740.6006391 1286961.601 0.010753216 0.01777695 5.66E-10 9.247058917 -0.10136197 AESSSGGGTVPSSAGILEQGPSPGDGS(ph)PPKPK ddPTM_HeLa_Romidepsin_16h_R1 2 AESSSGGGTVPSSAGILEQGPSPGDGSPPKPK 32 1 Q68EM7-7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7 Q68EM7-7 ARHGAP17 Rho GTPase-activating protein 17 1 0 AESSSGGGTVPSSAGILEQGPS(0.012)PGDGS(0.988)PPKPK;AESSSGGGTVPS(0.006)S(0.006)AGILEQGPS(0.095)PGDGS(0.892)PPKPK ; 71.682 8.61E-06 153450000 6790.6 6312 6799.2 4218.8 6563.4 7617.3 5862.6 6846.9 7816.2 6928.1 TRUE FALSE FALSE 6707.833555 6400.860502 6917.537224 4706.597506 6228.445207 7130.579114 6360.569098 7045.004249 7117.099496 6748.106963 0.994031895 0.948541648 1.025107821 0.69746931 0.922991476 1.056678436 0.942570877 1.043997122 1.054680896 1 12.72026713 -9.956892554 1.968971083 0.996901321 0.939862588 0.082770398 0.096890974 0.737755561 5.724291653 0.016620621 0.022124761 1.10E-10 9.956892554 -0.057038733 AESSSGGGTVPSSAGILEQGPSPGDGS(ph)PPKPKDPVSAAVPAPGR ddPTM_HeLa_Romidepsin_16h_R1 1 AESSSGGGTVPSSAGILEQGPSPGDGSPPKPKDPVSAAVPAPGR 44 2 Q68EM7-7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7 Q68EM7-7 ARHGAP17 Rho GTPase-activating protein 17 1 0 AESSSGGGTVPS(0.001)S(0.004)AGILEQGPS(0.489)PGDGS(0.494)PPKPKDPVS(0.011)AAVPAPGR 63.394 5.53E-05 71078000 2474.4 1877 2117.1 2510.6 2155.2 2265.1 2141.8 2260.2 2446.1 1901.7 TRUE FALSE FALSE 2444.241061 1903.424455 2153.947237 2800.887385 2045.212102 2120.36742 2323.724439 2325.595321 2227.31469 1852.29356 1.319575425 1.027604099 1.162854142 1.512118514 1.10415117 1.144725364 1.254511968 1.255522003 1.202463118 1 10.85509705 -12.48380556 1.129724118 0.995304702 1.228914401 0.03232014 0.139496434 0.507870411 1.121194527 0.09646478 0.021697806 3.28E-13 12.48380556 0.233609698 AESVERLEEAAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AESVERLEEAASR 13 1 Q15814 Q15814 TBCC Tubulin-specific chaperone C 1 0 AES(0.073)VERLEEAAS(0.927)R 132.51 0.012963 2202500 855.76 818.41 895.67 689.05 809.91 1003.4 905.2 872.67 924.25 905.16 TRUE FALSE FALSE 845.329668 829.9315975 911.2587606 768.7212031 768.5772705 939.2859783 982.0876654 897.9193296 841.5827652 881.6438127 0.958810866 0.941345683 1.033590604 0.871918106 0.871754851 1.065380332 1.113927928 1.018460422 0.954560961 1 9.784052109 -8.103495299 11.38685897 0.966575772 1.072039139 0.480545414 0.053875924 0.412554889 43.15481285 0.007822826 0.019962549 7.88E-09 8.103495299 0.105463367 AET(ph)PPLPIPPPPPDIQPLER ddPTM_HeLa_Romidepsin_16h_R1 2 AETPPLPIPPPPPDIQPLER 20 0 U3KPW8;A0A669KB72;Q8IX15;Q8IX15-3 U3KPW8 HOMEZ Homeobox and leucine zipper protein Homez 1 0 AET(1)PPLPIPPPPPDIQPLER;AET(1)PPLPIPPPPPDIQPLER ; 156 2.18E-07 19541500 4232.51 4628.7 4213.17 3873.76 4831.1 5155 4450.7 4706.1 4331.3 4446.1 TRUE FALSE FALSE 4180.92254 4693.86296 4286.498457 4321.662358 4584.55094 4825.612137 4828.742347 4842.263579 3943.89768 4330.589681 0.965439547 1.083885407 0.989818656 0.997938543 1.058643575 1.114308326 1.11503114 1.118153401 0.910706848 1 12.08034777 -8.536787956 1.98569656 0.992344125 1.118229858 0.664743039 0.039899004 0.126063176 0.986008497 0.004926846 0.012565074 2.91E-09 8.536787956 0.125885732 AET(ph)PTESVSEPEVATK ddPTM_HeLa_Romidepsin_16h_R1 2 AETPTESVSEPEVATK 16 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 AET(0.999)PT(0.001)ESVSEPEVATK;AET(0.994)PT(0.006)ESVSEPEVATK ; 290.63 1.09E-118 48702000 14999.6 16145.9 14841.1 10973.2 13629.3 12191.1 9676.3 10462.3 15370.8 14536 TRUE FALSE FALSE 14816.77911 16373.2024 15099.40312 12241.97301 12933.74596 11412.12805 10498.20468 10765.01014 13995.99715 14158.35262 1.046504456 1.156434144 1.066466101 0.86464671 0.913506416 0.806035021 0.7414849 0.760329286 0.988532884 1 13.78936579 -8.659084743 1.216672398 1.035888679 0.755380223 0.806014543 0.058403819 0.160336953 0.463164727 0.009925829 0.029748976 2.19E-09 8.659084743 -0.280508456 AETNSRVS(ph)GVDGYETEGIR ddPTM_HeLa_Romidepsin_16h_R1 2 AETNSRVSGVDGYETEGIR 19 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 AET(0.002)NS(0.031)RVS(0.966)GVDGYET(0.001)EGIR;AET(0.014)NS(0.185)RVS(0.797)GVDGY(0.001)ET(0.003)EGIR ; 76.049 0.0042059 12803400 2480.7 2152.5 1932.87 1871.54 1912.31 2124.04 1299.9 1643.23 2828.8 2451.9 TRUE FALSE FALSE 2450.464274 2182.802951 1966.510792 2087.936261 1814.717685 1988.320699 1410.313474 1690.774267 2575.785043 2388.199285 1.026071941 0.913995313 0.823428264 0.874272208 0.759868616 0.832560629 0.59053425 0.707970343 1.078546945 1 11.22170751 -8.916131163 0.541163876 1.019709917 0.637297625 0.817803182 0.061248657 0.314776456 0.156842728 0.014055118 0.056394908 1.21E-09 8.916131163 -0.382412292 AETSEGSGSAPAVPEAS(ph)ASPK ddPTM_HeLa_Romidepsin_16h_R1 1 AETSEGSGSAPAVPEASASPK 21 0 A0A087WVW7;A0A0D9SFX7;B5MCB4;I6LM39;A0A087X1U4;P51608;P51608-2 A0A087WVW7 MECP2 Methyl-CpG-binding protein 2 1 0 AETSEGSGSAPAVPEAS(0.749)AS(0.251)PK 162.37 2.21E-08 19710000 3694.6 2948.2 3377.5 1862.6 2298.3 2532.3 2100.2 2246.7 3232.8 3554.4 TRUE FALSE FALSE 3649.568794 2989.704837 3436.283971 2077.962576 2181.009175 2370.494203 2278.590936 2311.70472 2943.650271 3462.056176 1.054162211 0.863563352 0.99255581 0.600210531 0.629975097 0.68470703 0.658161168 0.667725942 0.85026069 1 11.75741342 -9.268190367 23.96923286 1.009246393 0.649732361 0.800942127 0.07303582 63.36269782 224967.827 0.008920685 0.013828175 5.39E-10 9.268190367 -0.359514032 AETSEGSGSAPAVPEASAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AETSEGSGSAPAVPEASASPK 21 0 A0A087WVW7;A0A0D9SFX7;B5MCB4;I6LM39;A0A087X1U4;P51608;P51608-2 A0A087WVW7 MECP2 Methyl-CpG-binding protein 2 1 0 AETSEGSGSAPAVPEAS(0.081)AS(0.919)PK 272.51 1.77E-95 19145000 5874.5 4817.9 4619.5 2815.4 3240 3471.3 3294.8 3359.8 5085.8 5290.5 TRUE FALSE FALSE 5802.899334 4885.726523 4699.90046 3140.929795 3074.65071 3249.495133 3574.66023 3457.010512 4630.91331 5153.052047 1.126109203 0.948122875 0.912061515 0.609528056 0.596665953 0.630596218 0.693697676 0.670866601 0.898673886 1 12.33121145 -9.501057343 2.056017088 1.055852795 0.638357443 0.840354955 0.071934998 0.066805048 0.563184759 0.010395866 0.016432588 3.15E-10 9.501057343 -0.417495352 AEVVETTQVYTEEETRR ddPTM_HeLa_Romidepsin_16h_R1 1 AEVVETTQVYTEEETRR 17 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 116.58 0.0013921 3730800 1056.7 1074.6 1229.4 927.54 1318.5 1541.7 1301.6 1310.8 1416.5 1497.3 FALSE FALSE TRUE 1043.820534 1089.728247 1250.797191 1034.786539 1251.212025 1443.190346 1412.157872 1348.72593 1289.804692 1458.39993 0.715729967 0.747208104 0.857650337 0.709535511 0.857934781 0.989571047 0.968292608 0.924798405 0.884397116 1 10.51017068 -8.328708118 6.079078733 0.840317573 0.961387084 0.343767916 0.084494029 0.302802192 21.32527754 0.017293274 0.03927419 4.69E-09 8.328708118 0.121069511 AEVYGS(ph)ENESER ddPTM_HeLa_Romidepsin_16h_R1 2 AEVYGSENESER 12 0 Q9BVS4;Q9BVS4-2 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 1 0 AEVYGS(1)ENESER;AEVYGS(1)ENESER ; 143.76 0.0015278 35257000 2807.1 3097.4 3470.9 2537.42 3018.8 3846.7 2980.8 3274.6 3247.2 2733.8 TRUE FALSE FALSE 2772.885985 3141.005279 3531.309559 2830.808439 2864.739371 3600.908285 3233.989078 3369.345385 2956.762299 2662.775482 1.041351779 1.179598242 1.326176233 1.063104441 1.075847134 1.352313895 1.214518122 1.265350912 1.110406161 1 11.37871507 -10.25825959 3.48466834 1.017871516 1.212039952 0.379225763 0.092415274 0.14565212 3.736278799 0.015311479 0.018155292 5.52E-11 10.25825959 0.194168435 AFAAVPTSHPPEDAPAQPPTPGPAAS(ph)PEQLSFR ddPTM_HeLa_Romidepsin_16h_R1 2 AFAAVPTSHPPEDAPAQPPTPGPAASPEQLSFR 33 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 AFAAVPTSHPPEDAPAQPPT(0.015)PGPAAS(0.938)PEQLS(0.047)FR;AFAAVPTSHPPEDAPAQPPTPGPAAS(0.965)PEQLS(0.035)FR ; 136.96 7.53E-16 125396000 4596 6018.3 4648.5 3878.3 6294 7835.2 5958.5 7103.5 5390 5274.4 TRUE FALSE FALSE 4539.982184 6103.025785 4729.405193 4326.727294 5972.793694 7334.556007 6464.614841 7309.028565 4907.9049 5137.370328 0.883717134 1.187966877 0.920588724 0.842206619 1.162616925 1.42768684 1.258350952 1.422717869 0.955334069 1 12.32681436 -8.523640699 4.292213618 0.955984675 1.353803619 0.774424814 0.097825079 0.070638627 3.149589148 0.014396737 0.031293676 2.99E-09 8.523640699 0.397818945 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR ddPTM_HeLa_Romidepsin_16h_R1 1 AFAMIIDKLEEDINSSMTNSTAASRPPVTLR 31 2 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 0 0 40.718 0.013961 16309000 673.22 621.95 621.71 818.63 481.89 714.39 537.39 665.52 900.68 739.26 FALSE FALSE TRUE 665.0145357 630.7058284 632.5306018 913.2838524 457.2973551 668.7427846 583.0358932 684.7757712 820.120925 720.0539186 0.923562137 0.875914723 0.87844894 1.268354812 0.635087656 0.928739873 0.809711437 0.951006242 1.138971546 1 9.491961131 -9.284433267 0.017469178 1.829036594 4.10E-05 0.115344526 0.154365902 1422.252741 10.14342954 507.5006743 553.7733459 5.19E-10 9.284433267 -1.828995547 AFDGAGSS(ph)LGR ddPTM_HeLa_Romidepsin_16h_R1 2 AFDGAGSSLGR 11 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 AFDGAGS(0.053)S(0.947)LGR;AFDGAGS(0.288)S(0.712)LGR ; 112.64 0.003206 2891900 5898.1 5387.8 6178.7 4790.8 6097.4 5036.9 3947.3 5120.1 5603 5795.4 TRUE FALSE FALSE 5826.211689 5463.64959 6286.237682 5344.734837 5786.226925 4715.058346 4282.583563 5268.242015 5101.853647 5644.834673 1.032131502 0.9679025 1.113626536 0.946836382 1.025048077 0.835287235 0.758672984 0.933285441 0.903809224 1 12.46271561 -8.259172824 24.51049494 1.014749481 0.834040979 0.521436456 0.067118057 59.70885476 645681.9809 0.007245662 0.017540261 5.51E-09 8.259172824 -0.180708502 AFEDDDITHVEGSVDPIR ddPTM_HeLa_Romidepsin_16h_R1 2 AFEDDDITHVEGSVDPIR 18 0 J3KQ32;Q9NTK5-3;Q9NTK5 J3KQ32 OLA1 Obg-like ATPase 1 0 0 ; ; 104.26 0.00081012 3891800 1935.85 1755.12 2074.9 1078.98 2285.5 2614.4 2114 2110.7 2069.37 2104.4 FALSE FALSE TRUE 1912.255116 1779.828625 2111.012764 1203.736744 2168.862407 2447.348278 2293.563107 2171.769774 1884.280364 2049.727385 0.932931438 0.868324558 1.029899283 0.587266752 1.058122374 1.193987208 1.118960075 1.059540791 0.919283403 1 11.00121633 -8.533611263 24.99519306 0.935857021 1.124044566 0.413298667 0.121817849 178.5357149 415794.9407 0.017416705 0.034859463 2.93E-09 8.533611263 0.188187545 AFEDEMSGR ddPTM_HeLa_Romidepsin_16h_R1 1 AFEDEMSGR 9 0 A0A087WUZ3;Q01082;Q01082-2;F8W6C1;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 124.08 0.027965 7355400 2499.6 1951.1 2468.8 1695.5 2809.2 2607.5 1992.1 2172 2379.2 2387.8 FALSE FALSE TRUE 2469.133914 1978.567637 2511.768428 1891.541688 2665.836041 2440.889165 2161.308924 2234.843393 2166.398393 2325.764612 1.061643943 0.850717062 1.07997534 0.813298851 1.146219195 1.049499658 0.929289625 0.960906956 0.931477924 1 11.18348938 AFFDEEEDHWK ddPTM_HeLa_Romidepsin_16h_R1 2 AFFDEEEDHWK 11 0 O15066-2;O15066 O15066-2 KIF3B "Kinesin-like protein KIF3B;Kinesin-like protein KIF3B, N-terminally processed" 0 0 ; ; 93.561 0.013365 6627600 5119.2 4969.2 4857.3 4332.6 7169.9 8082 8688.4 8289.7 5377.8 4845.2 FALSE FALSE TRUE 5056.805221 5039.156528 4941.839269 4833.555597 6803.993248 7565.586283 9426.392479 8529.549391 4896.796099 4719.321006 1.07151118 1.067771512 1.047150483 1.024205726 1.441731393 1.603109065 1.997404387 1.80736792 1.037606065 1 12.20436359 -8.3551012 1.47543108 1.03421647 1.905118341 0.95260493 0.077270646 0.054296614 0.222688616 0.010799852 0.037450556 4.41E-09 8.3551012 0.870901871 AFGALVWIR ddPTM_HeLa_Romidepsin_16h_R1 1 AFGALVWIR 9 0 Q9P2P1 Q9P2P1 NYNRIN Protein NYNRIN 0 0 74.127 0.018813 2703300 398.49 352.94 817.57 950.89 618.82 824.44 841.3 529.37 473.45 399.16 FALSE FALSE TRUE 393.6330506 357.9086986 831.7994629 1060.836376 587.2393063 771.7609448 912.760001 544.6864857 431.1034462 388.7897657 1.012457337 0.920571296 2.139458227 2.728560445 1.510428921 1.985034106 2.347695546 1.400979485 1.108834348 1 8.602846432 -9.76207651 25 0.999648598 2.041281407 0.653940411 0.359050803 7.102894832 278711.0736 0.053692815 0.072975003 1.73E-10 9.76207651 1.041632808 AFGFSHLEALLDDSKELQR ddPTM_HeLa_Romidepsin_16h_R1 1 AFGFSHLEALLDDSKELQR 19 1 F5GYN4;J3KR44;F5H6Q1;F5GYJ8;Q96FW1 F5GYN4 OTUB1 Ubiquitin thioesterase OTUB1 0 0 59.634 0.015271 6880600 2443.1 2182.3 2004 2798.8 2312.8 2415.3 2244.8 2273.3 2961.9 2358.6 FALSE FALSE TRUE 2413.322557 2213.022477 2038.878779 3122.410425 2194.769186 2260.970125 2435.473256 2339.074349 2696.980246 2297.323232 1.050493254 0.963304791 0.88750192 1.359151547 0.955359331 0.984175885 1.060135214 1.01817381 1.173966383 1 11.16573814 -16.52264663 0.287212348 0.69777114 1.040724733 0 0.13130856 237.7740121 3.214704998 41.40707715 0.051990213 3.00E-17 16.52264663 0.342953593 AFGGQSLK(ac)FGK ddPTM_HeLa_Romidepsin_16h_R1 1 AFGGQSLKFGK 11 1 D6RFM5;P31040-2;P31040;A0A494C1T6 D6RFM5 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 1 AFGGQSLK(1)FGK 121.9 0.019244 353360 104.47 115.42 118.45 0 102.44 176.54 105.96 168.84 109.96 0 FALSE TRUE FALSE 103.1966795 117.0448858 120.5115726 0 97.21210454 165.2596638 114.9602398 173.725119 100.1249022 0 0 AFGPGLQGGSAGS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 6 AFGPGLQGGSAGSPAR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGS(0.004)AGS(0.996)PAR;AFGPGLQGGS(0.071)AGS(0.929)PAR;AFGPGLQGGSAGS(1)PAR;AFGPGLQGGSAGS(1)PAR ;;;;; 236.31 7.90E-46 3377942000 7475.83 7890.96 7267.77 6856.51 8944.58 9999.1 8537.14 9792.39 7137.92 6482.91 TRUE FALSE FALSE 7384.711708 8002.049142 7394.262488 7649.291947 8488.104706 9360.189781 9262.284459 10075.71735 6499.486558 6314.483064 1.169487927 1.267253243 1.171000447 1.211388465 1.344227963 1.482336667 1.466831784 1.595651972 1.02929828 1 12.62444892 -4 0.164755874 0.956356897 3.533921522 0.937669658 0.046669274 10.51530198 0.108359501 0.083526847 6.659743641 1.00E-04 4 2.577564625 AFGS(ph)GYRR ddPTM_HeLa_Romidepsin_16h_R1 2 AFGSGYRR 8 1 E7EX17;P23588-2;P23588;F8VP89;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 AFGS(1)GYRR;AFGS(1)GYRR ; 72.325 0.023127 11305400 2600.9 2844.7 2503.8 2006.34 2326.36 2669.8 2153.4 2259.2 2913.9 2502.4 TRUE FALSE FALSE 2569.19923 2884.747761 2547.377589 2238.322471 2207.637168 2499.208396 2336.309742 2324.566388 2653.273486 2437.387287 1.054079195 1.183540989 1.045126313 0.918328606 0.905739182 1.025363679 0.958530372 0.953712362 1.088572793 1 11.25111979 -9.275656566 23.82322299 1.041885651 0.954147548 0.492525484 0.057338487 383.6964643 642945.3627 0.00952619 0.014602005 5.30E-10 9.275656566 -0.087738103 AFHNEAQVNPER ddPTM_HeLa_Romidepsin_16h_R1 1 AFHNEAQVNPER 12 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 0 0 158.01 0.00048113 6683300 3238.4 3427.9 3345.9 2446.9 3484.8 3776.9 3216.2 2817.1 3462 3231.8 FALSE FALSE TRUE 3198.929135 3476.158066 3404.133986 2729.822091 3306.957652 3535.568279 3489.383948 2898.608344 3152.350049 3147.83737 1.016230751 1.1043004 1.081419904 0.867205567 1.05054908 1.123173742 1.108501977 0.920825317 1.001433581 1 11.62014529 -8.54491855 24.99905698 1.011088133 1.061644115 0.051762425 0.077711884 446.0752465 505967.4318 0.010897535 0.021795997 2.85E-09 8.54491855 0.050555982 AFLAELEQNS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 AFLAELEQNSPK 12 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 AFLAELEQNS(1)PK;AFLAELEQNS(1)PK ; 172.57 9.48E-05 181178000 13657.5 13385 14348.7 12615.4 13057.4 13851.3 12507.2 13283.7 13832.4 13438.7 TRUE FALSE FALSE 13491.03714 13573.43438 14598.4331 14074.05191 12391.03215 12966.24663 13569.56126 13668.0429 12595.1955 13089.56064 1.030671503 1.036966386 1.115272965 1.075211941 0.946634688 0.99057921 1.036670491 1.04419417 0.962232106 1 13.67612905 -7.540299849 24.63610791 1.021507213 1.042313298 0.029555582 0.047477634 606.748578 858034.6684 0.006452001 0.024152621 2.88E-08 7.540299849 0.020806086 AFLASLS(ph)PAMVVPEDQLTR ddPTM_HeLa_Romidepsin_16h_R1 1 AFLASLSPAMVVPEDQLTR 19 0 H3BSY1;Q9H211 H3BSY1 CDT1 DNA replication factor Cdt1 1 0 AFLAS(0.019)LS(0.968)PAMVVPEDQLT(0.013)R 106.87 0.0013503 17241000 1607.7 1312.8 1273.7 1559.1 1634 1606.6 1538.1 1787.7 1499.2 1427.9 TRUE FALSE FALSE 1588.104734 1331.281633 1295.868214 1739.370478 1550.610883 1503.943445 1668.746176 1839.424279 1365.107797 1390.802952 1.14186178 0.957203629 0.931741058 1.250623228 1.114903359 1.081349046 1.199843711 1.322562823 0.981524949 1 10.44170232 -4 0.483515873 1.054903597 8.614478166 0.505540092 0.088168907 63.32334762 0.63357884 0.018785037 485.3912931 1.00E-04 4 7.559574569 AFLASLSPAMVVPEDQLT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AFLASLSPAMVVPEDQLTR 19 0 H3BSY1;Q9H211 H3BSY1 CDT1 DNA replication factor Cdt1 1 0 AFLAS(0.014)LS(0.36)PAMVVPEDQLT(0.625)R 80.834 0.021026 19004000 1048.4 1050.9 1401.3 1130.9 1372.3 1439.6 1468.4 1534.3 1225.6 1261.1 TRUE FALSE FALSE 1035.621698 1065.694598 1425.689039 1261.659979 1302.26641 1347.614206 1593.125859 1578.69255 1115.979266 1228.33644 0.843109155 0.867591779 1.160666567 1.027129 1.060187069 1.097105127 1.296978423 1.285228133 0.908528991 1 10.26249005 -7.973660178 0.597182192 0.92704102 1.404597376 0.718083292 0.08048838 0.813638683 0.319998773 0.018378115 0.227492795 1.06E-08 7.973660178 0.477556356 AFLS(ph)PPTLLEGPLR ddPTM_HeLa_Romidepsin_16h_R1 1 AFLSPPTLLEGPLR 14 0 G3V599;Q96PC5-6;Q96PC5-11;Q96PC5-13;Q96PC5-10;Q96PC5-9;Q96PC5-14;Q96PC5-7;Q96PC5-12;Q96PC5 G3V599 MIA2 Melanoma inhibitory activity protein 2 1 0 AFLS(0.673)PPT(0.327)LLEGPLR 99.834 0.01032 7880600 2101.1 2320.1 2378.7 1615.8 2269.9 2506.6 1778.5 2543.2 2019.3 1947.6 TRUE FALSE FALSE 2075.490985 2352.762429 2420.100276 1802.626399 2154.058533 2346.43635 1929.565746 2616.783479 1838.688751 1897.001071 1.094090571 1.240253611 1.275750611 0.950250596 1.135507283 1.236918832 1.017166397 1.379431735 0.969260787 1 10.88950478 -16.52287875 0.094552175 0.42548226 1.292010141 0.282237097 0.118653086 140.2854448 0.998095112 15.82599639 1.205315222 3.00E-17 16.52287875 0.866527881 AFNQGK(ac)IFK ddPTM_HeLa_Romidepsin_16h_R1 1 AFNQGKIFK 9 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 1 AFNQGK(1)IFK 179.21 0.00012461 3546100 1599.6 1390.3 1569.3 1312 2050.1 2300.5 1021 1425.8 1257.6 1066.4 FALSE TRUE FALSE 1580.10346 1409.87268 1596.613008 1463.699613 1945.475747 2153.505475 1107.723715 1467.053273 1145.117106 1038.694774 1.521239443 1.357350316 1.537133957 1.40917202 1.873000419 2.073280359 1.066457387 1.412400745 1.102457752 1 10.02055606 -12.28572916 0.471638549 0.862454157 1.565263985 0.350992689 0.262281943 1.547203262 0.455852662 0.519366945 0.076895216 5.18E-13 12.28572916 0.702809828 AFS(ph)DPFVEAEK ddPTM_HeLa_Romidepsin_16h_R1 2 AFSDPFVEAEK 11 0 A0A087WYC1;P34932;A0A087WTS8;P34932-2 A0A087WYC1 HSPA4 Heat shock 70 kDa protein 4 1 0 AFS(1)DPFVEAEK;AFS(1)DPFVEAEK ; 158.34 0.0016346 18915000 10034.4 9803.4 9800.9 8665.9 10269.7 10922.2 9802.8 10965.1 10380.1 10472.5 TRUE FALSE FALSE 9912.096873 9941.412523 9971.480553 9667.892132 9745.598887 10224.30667 10635.44959 11282.35787 9451.677859 10200.42294 0.971733911 0.974607875 0.977555599 0.947793262 0.955411255 1.002341445 1.042647903 1.106067654 0.926596663 1 13.31634135 -7.502372994 1.831625758 0.980009982 1.116643196 0.785794377 0.022775788 0.164299847 0.788493814 0.002768712 0.03255624 3.15E-08 7.502372994 0.136633214 AFS(ph)EGEQEK ddPTM_HeLa_Romidepsin_16h_R1 2 AFSEGEQEK 9 0 Q7Z333-3;Q7Z333;Q7Z333-4;X6RI79 Q7Z333-3 SETX Probable helicase senataxin 1 0 AFS(1)EGEQEK;AFS(1)EGEQEK ; 106.62 0.022319 17546500 5525.2 4972.3 4700.8 4207.9 6694 7288.9 6606.2 8728.6 5748.4 5606.4 TRUE FALSE FALSE 5457.856737 5042.30017 4782.615452 4694.437197 6352.380201 6823.162814 7167.330463 8981.14827 5234.248707 5460.74492 0.999471101 0.923372222 0.875817406 0.859669746 1.163280888 1.249493048 1.312518817 1.644674564 0.958522836 1 12.41488205 -7.526160259 0.931598501 0.977145633 1.803530976 0.88881362 0.078022538 0.372385433 0.316669947 0.01324544 0.281387884 2.98E-08 7.526160259 0.826385343 AFSIGK(ac)MSTAK ddPTM_HeLa_Romidepsin_16h_R1 2 AFSIGKMSTAK 11 1 O15042-2;O15042;U3KPT1;C9JDJ7;C9J5L1;E7EW00;H0Y8D9;E7ET15 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 0 1 ; AFSIGK(1)MSTAK;AFSIGK(1)MSTAK 150.46 0.0014137 2673400 827.93 685.81 2342.08 722.22 1173.49 1738.15 1883.76 610.08 1002.4 534.74 FALSE TRUE FALSE 817.8388707 695.4648512 2382.84292 805.7264745 1113.602426 1627.087825 2043.766527 627.7317023 912.7428334 520.8473777 1.570208291 1.335256509 4.574935042 1.546953117 2.138059005 3.123924386 3.923925923 1.20521237 1.752418986 1 9.024716876 -9.943960332 24.99982763 1.278914007 2.757589261 0.309061906 0.971775299 66.92827905 29857.08112 0.14569284 0.191477894 1.14E-10 9.943960332 1.478675253 AFSS(ph)PQEEEEAGFTGR ddPTM_HeLa_Romidepsin_16h_R1 2 AFSSPQEEEEAGFTGR 16 0 A0A024RAC6;Q14241 A0A024RAC6 TCEB3 Transcription elongation factor B polypeptide 3 1 0 AFS(0.163)S(0.837)PQEEEEAGFTGR;AFS(0.17)S(0.83)PQEEEEAGFTGR ; 142.95 0.00037257 33255000 3625.8 3393.2 3335.2 2280.2 3778.1 4609.4 4860.4 4919.2 4282.3 3866.9 TRUE FALSE FALSE 3581.607355 3440.969559 3393.247757 2543.847453 3585.289459 4314.874216 5273.242255 5061.529291 3899.280363 3766.437381 0.950927095 0.913587354 0.900917077 0.675398844 0.951904704 1.145611563 1.400061045 1.343850642 1.035270195 1 11.87898483 -7.997275604 2.79506504 0.941419337 1.37303305 0.787196493 0.094316347 0.097157311 1.518252702 0.014463925 0.049436035 1.01E-08 7.997275604 0.431613714 AFT(ph)QFASLT(ph)RHKRIHT(ph)GEK ddPTM_HeLa_Romidepsin_16h_R1 1 AFTQFASLTRHKRIHTGEK 19 3 Q5SXM1 Q5SXM1 ZNF678 Zinc finger protein 678 3 0 AFT(0.958)QFAS(0.249)LT(0.794)RHKRIHT(1)GEK 44.391 0.024668 10154000 1047 880.12 1079.5 862.42 780.66 939.56 729.8 1028.4 977.3 1050.6 TRUE FALSE FALSE 1034.238761 892.5103525 1098.288245 962.1370582 740.8200072 879.5251483 791.7891938 1058.155131 889.8878403 1023.305261 1.010684496 0.87218388 1.073275285 0.940224873 0.723948206 0.859494407 0.773756595 1.034056183 0.869621094 1 9.999020862 -8.99062574 24.49881061 0.998138752 0.841949351 0.214653941 0.096940787 110.3152287 288296.219 0.011785355 0.021341376 1.02E-09 8.99062574 -0.156189401 AFTHTAQYDEAISDYFR ddPTM_HeLa_Romidepsin_16h_R1 1 AFTHTAQYDEAISDYFR 17 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 0 161.94 1.15E-05 16665000 985.87 1213.1 1133 1118.4 1053.2 1075.1 795.96 977.75 1205.8 1148.9 FALSE FALSE TRUE 973.8538372 1230.178054 1152.71939 1247.71467 999.451274 1006.40458 863.5688225 1006.039654 1097.950228 1119.051412 0.870249415 1.099304322 1.030086176 1.114975287 0.893123643 0.899337214 0.771697183 0.899011111 0.981143686 1 10.1280606 -8.312790008 2.735140711 0.969502933 0.842121288 0.378784254 0.080993547 0.297103557 4.353196395 0.013642037 0.036242298 4.87E-09 8.312790008 -0.127381645 AFVEDS(ph)EDEDGAGEGGSSLLQK ddPTM_HeLa_Romidepsin_16h_R1 4 AFVEDSEDEDGAGEGGSSLLQK 22 0 A0A494C108;Q8N9T8;F8WFC1;H0YFD2 A0A494C108 KRI1 Protein KRI1 homolog 1 0 AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK;AFVEDS(1)EDEDGAGEGGSSLLQK ;;; 174.28 1.22E-11 89576000 22127.9 20621.8 19902.6 18827.9 20000.1 21077.9 18610.1 19726.2 22401.8 21671.5 TRUE FALSE FALSE 21858.19664 20912.11424 20248.9964 21004.87039 18979.42027 19731.09022 20190.84143 20296.94647 20398.1269 21108.47131 1.035517747 0.990697713 0.95928294 0.995091974 0.899137602 0.934747473 0.956527886 0.961554543 0.966347899 1 14.36553448 -9.630946972 1.403349173 1.016605292 0.944002776 0.364732552 0.028622046 0.196314393 0.779431104 0.00448193 0.007064464 2.34E-10 9.630946972 -0.072602516 AFVHWYVGEGMEEGEFSEAR ddPTM_HeLa_Romidepsin_16h_R1 4 AFVHWYVGEGMEEGEFSEAR 20 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;Q9NY65;C9J2C0;Q9NY65-2;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA8;TUBA1A;TUBA1B;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 ;;; ;;; 100.58 0.0027698 101989800 10026.3 9442.83 9669.4 8603.9 9583.85 10452.8 8814.51 10412.32 11085.9 9465.66 FALSE FALSE TRUE 9904.095599 9575.766409 9837.691851 9598.723401 9094.750372 9784.899815 9563.214259 10713.58405 10094.34934 9219.740789 1.07422712 1.038615578 1.067024776 1.04110556 0.986443175 1.061298798 1.037254135 1.162026601 1.094862596 1 13.17051047 AGAAAAS(ph)AAAY(ph)AAYGY(ph)NVSK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAAAASAAAYAAYGYNVSK 20 0 Q9ULG1 Q9ULG1 INO80 DNA helicase INO80 3 0 AGAAAAS(0.86)AAAY(0.963)AAY(0.211)GY(0.921)NVS(0.045)K 52.071 0.015054 5129300 1396.5 1162.4 1245.9 1182 1244.9 1119.1 1013.2 1301.3 1373.5 1367.4 TRUE FALSE FALSE 1379.478921 1178.764298 1267.584367 1318.668401 1181.368108 1047.593122 1099.261183 1338.951062 1250.65072 1331.874751 1.035742227 0.885041403 0.951729407 0.990084391 0.886996399 0.786555283 0.825348766 1.005313046 0.939015263 1 10.3792427 -9.486540961 0.796004842 1.015781279 0.870827556 0.175478586 0.071100967 0.43301829 0.547780603 0.014001931 0.027860257 3.26E-10 9.486540961 -0.144953723 AGAAAGDS(ph)DEESRADDK ddPTM_HeLa_Romidepsin_16h_R1 3 AGAAAGDSDEESRADDK 17 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 0 AGAAAGDS(0.999)DEES(0.001)RADDK;AGAAAGDS(0.999)DEES(0.001)RADDK;AGAAAGDS(0.99)DEES(0.01)RADDK ;; 227.63 4.57E-35 22218600 5315.5 5245.6 5546.2 2894.9 3683.99 4256.61 3720.04 3873.12 6425.3 6219.5 TRUE FALSE FALSE 5250.712641 5319.447694 5642.729284 3229.621959 3495.982243 3984.626359 4036.020105 3985.182616 5850.605076 6057.916493 0.866752232 0.878098551 0.931463696 0.533124212 0.577093172 0.657755247 0.66623898 0.65784707 0.965778429 1 12.56460598 -9.271437428 24.88542449 0.929734678 0.62095908 0.898029986 0.052226984 180.3444295 448881.8104 0.010261783 0.01578958 5.35E-10 9.271437428 -0.308775597 AGAAAGDSDEES(ph)RADDKGVMDYYLK ddPTM_HeLa_Romidepsin_16h_R1 2 AGAAAGDSDEESRADDKGVMDYYLK 25 2 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 0 AGAAAGDS(0.003)DEES(0.55)RADDKGVMDY(0.204)Y(0.243)LK;AGAAAGDS(0.012)DEES(0.979)RADDKGVMDY(0.004)Y(0.005)LK ; 64.377 0.0018174 51667000 5549.4 4321.7 4491.2 3900.4 3393.3 3937 3186.2 2997.5 5819.9 4805.8 TRUE FALSE FALSE 5481.761778 4382.541006 4569.367452 4351.3826 3220.127239 3685.438406 3456.835748 3084.227933 5299.353568 4680.944623 1.171080245 0.936251411 0.976163535 0.929594975 0.687922524 0.787327923 0.738491058 0.658890071 1.132111998 1 12.19258398 -9.118148429 1.084475946 1.075638382 0.70894908 0.828626801 0.070157106 0.163835825 0.380229719 0.014284067 0.032211024 7.62E-10 9.118148429 -0.366689302 AGAAGGPEEEAEK(ac)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 AGAAGGPEEEAEKPVK 16 1 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 1 ; AGAAGGPEEEAEK(1)PVK;AGAAGGPEEEAEK(1)PVK 228.62 2.21E-94 1332700 188.15 249.29 261.144 379.25 769.31 595.2 445.48 539.01 586.94 506.62 FALSE TRUE FALSE 185.8567554 252.7995112 265.6891018 423.1006694 730.04924 557.1686409 483.3190601 554.6054039 534.4426164 493.4579394 0.376641534 0.512302044 0.538422995 0.857419925 1.47945586 1.129110703 0.979453407 1.123916265 1.08305607 1 8.946783309 -8.990509103 22.20103914 0.670431876 1.161328463 0.478776971 0.233310793 39.21643978 91731.32937 0.039995398 0.072387439 1.02E-09 8.990509103 0.490896587 AGAAGKDLLNELES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAAGKDLLNELESPK 16 1 Q9BZH6 Q9BZH6 WDR11 WD repeat-containing protein 11 1 0 AGAAGKDLLNELES(1)PK 66.777 0.017211 7312000 3811.7 3708.3 3843.7 2705.2 2598.7 2484.7 2065.7 2270.8 4153.9 3988.4 TRUE FALSE FALSE 3765.241534 3760.505545 3910.597986 3017.987952 2466.078642 2325.935689 2241.160506 2336.502015 3782.36478 3884.780793 0.969228828 0.968009714 1.006645727 0.77687471 0.634805095 0.598730228 0.576907843 0.601450156 0.973636604 1 11.92361748 -8.988838858 2.120757128 0.985943418 0.593721925 0.988256106 0.019569993 0.023080422 0.207784809 0.003203706 0.006246878 1.03E-09 8.988838858 -0.392221493 AGAAS(ph)PLNS(ph)PLSSAVPSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAASPLNSPLSSAVPSLGK 20 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 2 0 AGAAS(0.932)PLNS(0.966)PLS(0.076)S(0.025)AVPSLGK 112.44 0.0032335 13004000 1169 1608.9 1396.6 1233.5 1766.1 1674.2 1449.2 1427.1 1650.9 1440.8 TRUE FALSE FALSE 1154.751778 1631.550136 1420.907237 1376.123074 1675.969327 1567.224023 1572.295012 1468.390887 1503.239369 1403.367808 0.822843286 1.162596239 1.012498098 0.980586177 1.194248092 1.11675928 1.120372722 1.046333597 1.071165635 1 10.45467746 -10.25734063 24.98718516 0.916342663 1.0894095 0.253145256 0.087965008 232.6473432 1418288.453 0.014826849 0.017812917 5.53E-11 10.25734063 0.173066837 AGAAS(ph)PLNSPLSSAVPSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAASPLNSPLSSAVPSLGK 20 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 AGAAS(0.826)PLNS(0.174)PLSSAVPSLGK 190.37 1.37E-17 22780000 4313.5 3896 4579.5 3003.8 3306.3 3320.1 3016.8 3133.2 4321.2 4290.4 TRUE FALSE FALSE 4260.925403 3950.84799 4659.204276 3351.113489 3137.567173 3107.956325 3273.046917 3223.854199 3934.701049 4178.93479 1.019619979 0.945419871 1.114926294 0.801906145 0.750805488 0.743719747 0.783225171 0.771453579 0.941555982 1 12.02891953 -9.143274669 5.732047531 1.010624804 0.764436291 0.864999695 0.0463501 0.046388631 2.021370452 0.005587805 0.009348351 7.19E-10 9.143274669 -0.246188513 AGAASPLNS(ph)PLSSAVPSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAASPLNSPLSSAVPSLGK 20 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 AGAAS(0.147)PLNS(0.424)PLS(0.424)S(0.005)AVPSLGK 212.41 5.38E-32 24510000 3754.7 3857.9 4132 2776.3 3094.1 3529.2 2509.4 3268.2 3931.3 4447.2 TRUE FALSE FALSE 3708.936272 3912.211617 4203.915727 3097.308869 2936.196531 3303.69551 2722.548373 3362.760211 3579.674682 4331.661103 0.856238792 0.903166597 0.970508917 0.715039518 0.677845395 0.762685591 0.62852294 0.776321169 0.826397679 1 12.08070466 -9.253761434 24.22151336 0.930374805 0.708349856 0.716853373 0.061988852 147.2276182 464456.2054 0.009760213 0.015978813 5.57E-10 9.253761434 -0.222024949 AGAASPLNSPLSSAVPS(ph)LGKEPFPPSSPLQK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAASPLNSPLSSAVPSLGKEPFPPSSPLQK 31 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 AGAAS(0.017)PLNS(0.053)PLS(0.169)S(0.169)AVPS(0.511)LGKEPFPPS(0.041)S(0.041)PLQK 47.286 0.0088548 12005000 1043.5 1101.3 1014.4 1179.2 1030.4 889.71 1124 1047.5 1149.4 984.47 TRUE FALSE FALSE 1030.781421 1116.80413 1032.055206 1315.544652 977.814843 832.8604024 1219.472532 1077.80776 1046.594785 958.8933275 1.074969854 1.16468026 1.076298246 1.371940564 1.01973266 0.868564186 1.27174994 1.12401216 1.09146112 1 9.905226521 -11.03545113 0.9937276 1.01455511 1.126128487 0.04590705 0.130710965 0.746306776 1.562253168 0.036164747 0.028088501 9.22E-12 11.03545113 0.111573377 AGAASPLNSPLSSAVPSLGKEPFPPS(ph)SPLQK ddPTM_HeLa_Romidepsin_16h_R1 2 AGAASPLNSPLSSAVPSLGKEPFPPSSPLQK 31 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 AGAASPLNSPLSSAVPSLGKEPFPPS(0.595)S(0.405)PLQK;AGAASPLNSPLSSAVPSLGKEPFPPS(0.5)S(0.5)PLQK ; 111.45 3.30E-14 27164000 7766.1 7259.8 6954 9764.5 6495.7 6176.7 5330.8 5676.4 7199.8 6873 TRUE FALSE FALSE 7671.443786 7362.003655 7075.031453 10893.51743 6164.20019 5782.028804 5783.598019 5840.637678 6555.831856 6694.438469 1.145942833 1.09971937 1.056852115 1.62724887 0.920794211 0.863706318 0.863940724 0.872461179 0.979295259 1 12.70874733 -8.546306191 24.99993481 1.113660912 0.870730053 0.362478529 0.173005108 210.2083361 224317.0763 0.025060277 0.05012256 2.84E-09 8.546306191 -0.242930859 AGAGK(ac)IGR ddPTM_HeLa_Romidepsin_16h_R1 2 AGAGKIGR 8 1 A0A669KBF4;O00327-4;O00327-9;O00327-1;O00327-7;O00327-8;O00327 A0A669KBF4 ARNTL Aryl hydrocarbon receptor nuclear translocator-like protein 1 0 1 ; AGAGK(1)IGR;AGAGK(1)IGR 107.43 0.016648 1003800 1032.61 1123.66 1370.71 1562.23 623.85 699.48 564.22 255.12 1176.64 1115.05 FALSE TRUE FALSE 1020.024152 1139.478915 1394.566633 1742.862383 592.0126066 654.7854855 612.1448327 262.5014947 1071.398371 1086.08084 0.939178848 1.049165838 1.284035756 1.604726203 0.545090738 0.60288835 0.563627319 0.241696092 0.986481238 1 10.08491578 -8.562701768 24.99933444 1.044040632 0.494686248 0.675137371 0.216496069 82.30317147 51666.41493 0.033537878 0.067075825 2.74E-09 8.562701768 -0.549354383 AGAGMITQHSS(ph)NASPINR ddPTM_HeLa_Romidepsin_16h_R1 1 AGAGMITQHSSNASPINR 18 0 Q9NWH9;H7C3F4;Q9NWH9-3;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 1 0 AGAGMIT(0.016)QHS(0.236)S(0.634)NAS(0.115)PINR 76.678 0.0049561 4410400 1301.8 774.41 1381.5 932.94 1082.7 1592.9 1413.4 947.82 1437.3 1311.8 TRUE FALSE FALSE 1285.933161 785.3121643 1405.544428 1040.810912 1027.445779 1491.118831 1533.454161 975.2436763 1308.744288 1277.719247 1.006428575 0.614620282 1.100041681 0.814584984 0.804124835 1.167016021 1.200149536 0.763269144 1.024281579 1 10.31935515 -6.985269721 13.27015614 0.978731733 0.425332472 0.11457919 0.17102516 307870.1537 5951561.455 0.022603915 3110841.066 1.03E-07 6.985269721 -0.553399261 AGAIASRMS(ph)FS(ph)S(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAIASRMSFSSLK 14 1 A0A5F9ZHD8;P35240-9;P35240-10;P35240-7;P35240-4;P35240-6;P35240-5;P35240-8;P35240-3;P35240;P35240-2 A0A5F9ZHD8 NF2 Merlin 3 0 AGAIAS(0.091)RMS(0.922)FS(0.987)S(1)LK 85.457 0.0024295 0 3437.4 3880.7 2788.1 1725.6 2916.9 2461.5 2221.9 2192.4 3528.4 3686.1 TRUE FALSE FALSE 3395.503647 3935.332596 2836.625711 1925.121991 2768.039709 2304.218094 2410.628131 2255.833635 3212.811067 3590.334591 0.9457346 1.096090767 0.790072802 0.536195706 0.770969847 0.641783666 0.671421582 0.628307356 0.894850044 1 11.80990258 -9.555198584 5.527579918 0.9820906 0.657182902 0.82818597 0.071725058 0.045481871 3.762723573 0.00975115 0.014022094 2.78E-10 9.555198584 -0.324907698 AGAPGALS(ph)PSYDGGLHGLQSK ddPTM_HeLa_Romidepsin_16h_R1 4 AGAPGALSPSYDGGLHGLQSK 21 0 K7ENH8;A0A0A0MRB7;P15923-2;X6REB3;P15923;P15923-3 K7ENH8 TCF3 Transcription factor E2-alpha 1 0 AGAPGALS(0.992)PS(0.008)YDGGLHGLQSK;AGAPGALS(0.996)PS(0.004)YDGGLHGLQSK;AGAPGALS(0.965)PS(0.035)YDGGLHGLQSK;AGAPGALS(0.643)PS(0.357)YDGGLHGLQSK ;;; 261.76 4.82E-90 80494000 16220.9 15687.3 14183 14161.7 15003.7 11881.4 9780.1 10781.3 19868.5 17949.6 TRUE FALSE FALSE 16023.19343 15908.14622 14429.84917 15799.14239 14238.0052 11122.21689 10610.82145 11093.23991 18091.4116 17483.2668 0.916487383 0.909906964 0.825351997 0.903672212 0.814378992 0.636163539 0.606912974 0.634506127 1.034784391 1 14.09368716 -7.936112448 0.387809765 0.981029356 0.410551678 0.891748946 0.048346384 0.77774229 0.11469024 0.014838017 0.189540307 1.16E-08 7.936112448 -0.570477678 AGAPVGGS(ph)PGLAK ddPTM_HeLa_Romidepsin_16h_R1 1 AGAPVGGSPGLAK 13 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 AGAPVGGS(1)PGLAK 101.56 0.01183 40657000 3456.8 3154.3 3494.7 3037 2701.3 2747.9 1866.6 2282.8 3757 3203.5 TRUE FALSE FALSE 3414.667192 3198.706318 3555.523788 3388.15223 2563.442581 2572.318058 2025.148957 2348.849216 3420.96451 3120.272608 1.094348995 1.025136813 1.139491395 1.085851352 0.82154443 0.824388886 0.649029496 0.752770514 1.09636719 1 11.60745636 -8.587324069 2.558971847 1.054745894 0.733477661 0.873119083 0.058151518 0.077409429 1.02120094 0.009247509 0.021146658 2.59E-09 8.587324069 -0.321268233 AGASIPSSGAAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 AGASIPSSGAASPR 14 0 Q9P270 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 0 AGASIPSSGAAS(1)PR;AGASIPSSGAAS(1)PR;AGASIPSSGAAS(1)PR;AGASIPSSGAAS(1)PR ;;; 206.46 4.72E-17 158452600 11023 10570.9 10020.7 9212.1 11156.7 9677.5 7975.7 8431 11279.1 11156.3 TRUE FALSE FALSE 10888.64744 10719.71741 10195.10608 10277.24635 10587.33197 9059.138983 8653.155759 8674.937683 10270.26905 10866.45772 1.002042038 0.986496031 0.938217986 0.945777052 0.974313087 0.833679127 0.796317989 0.798322499 0.945134957 1 13.4075941 -8.112970304 0.762487486 0.998805097 0.747852634 0.841422709 0.030754001 0.226761083 0.177665743 0.004431957 0.037953104 7.71E-09 8.112970304 -0.250952463 AGDLLEDS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 AGDLLEDSPK 10 0 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK;AGDLLEDS(1)PK ;;; 138.42 0.0051721 2541446000 40002.6 42589.4 40778.6 17282.1 30308.7 34903.5 30780.1 34513.3 37150.8 41381.5 TRUE FALSE FALSE 39515.03292 43188.97469 41488.33443 19280.33772 28761.93394 32673.279 33394.56093 35511.88788 33827.9394 40306.40266 0.980366153 1.07151648 1.029323673 0.478344294 0.713582261 0.810622552 0.828517524 0.881048308 0.839269624 1 15.29872141 -9.331104959 24.99996293 1.000468952 0.749389784 0.518055725 0.115914883 86.96654976 31208.23689 0.016144966 0.024661556 4.67E-10 9.331104959 -0.251079168 AGDLLEDS(ph)PKRPK ddPTM_HeLa_Romidepsin_16h_R1 1 AGDLLEDSPKRPK 13 2 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 AGDLLEDS(1)PKRPK 95.755 0.015234 43389000 4902.6 4832.1 4091.3 4624.2 3558.8 3929.5 3358.6 4157.4 4830.6 5708.7 TRUE FALSE FALSE 4842.845225 4900.126431 4162.50736 5158.871762 3377.181156 3678.417632 3643.8794 4277.68781 4398.539038 5560.387151 0.870954682 0.88125634 0.748600277 0.92779003 0.607364391 0.661539841 0.655328361 0.769314743 0.791049062 1 12.44096962 -9.762666251 0.358606962 0.99654748 0.638737563 0.34636634 0.098384338 0.587751702 0.185893772 0.043793991 0.080843859 1.73E-10 9.762666251 -0.357809916 AGDPGEMPQS(ph)PTGLGQPK ddPTM_HeLa_Romidepsin_16h_R1 2 AGDPGEMPQSPTGLGQPK 18 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9;H0YHL2 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 AGDPGEMPQS(0.759)PT(0.241)GLGQPK;AGDPGEMPQS(0.996)PT(0.004)GLGQPK ; 119.04 0.0020245 25863000 8445.1 7644.8 7681.8 7701.6 9601.9 8584.9 7332 8025.6 8455 7802.5 TRUE FALSE FALSE 8342.167873 7752.423695 7815.498507 8592.095229 9111.879213 8036.352596 7954.779897 8257.808074 7698.763624 7599.789925 1.097684009 1.020083946 1.028383493 1.130570097 1.198964617 1.057444045 1.046710498 1.086583729 1.013023215 1 12.89174382 -13.44558271 0.371581143 0.913048408 1.090274615 0.282858252 0.049646732 6.440696544 0.595990398 0.517079776 0.018059388 3.58E-14 13.44558271 0.177226207 AGDPGEMPQSPT(ph)GLGQPK ddPTM_HeLa_Romidepsin_16h_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 0 AGDPGEMPQS(0.101)PT(0.899)GLGQPK 114.76 0.003499 15222000 5503.5 5283.2 5192.3 5430.7 5914.7 5898.1 5388.4 5572.4 6223.9 6002.4 TRUE FALSE FALSE 5436.421225 5357.577028 5282.669803 6058.623086 5612.850788 5521.230445 5846.090562 5733.628602 5667.218796 5846.456783 0.929865973 0.916380165 0.90356775 1.036289724 0.96004315 0.944372062 0.99993736 0.980701443 0.969342459 1 12.51334684 -9.263073051 24.9979123 0.957132079 0.981576875 0.202940015 0.035269419 332.5447142 5088471.969 0.006468136 0.010252809 5.46E-10 9.263073051 0.024444796 SSFASSSASDASKPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 3 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 0 SSFASSSASDAS(0.001)KPS(0.5)S(0.5)PR;SSFASS(0.001)S(0.003)AS(0.001)DAS(0.096)KPS(0.893)S(0.007)PR;SSFAS(0.008)S(0.066)S(0.066)AS(0.008)DAS(0.244)KPS(0.551)S(0.057)PR ;; 153.58 5.23E-06 28224500 3676.26 3106.36 3389.69 2332.55 1957.24 1699.36 1954.62 1644.89 4431.5 3935.06 TRUE FALSE FALSE 3631.452329 3150.091418 3448.686133 2602.250406 1857.354739 1590.77638 2120.645374 1692.482297 4035.135541 3832.826574 0.947460643 0.821871628 0.899776201 0.678937686 0.484591385 0.41504001 0.55328498 0.441575496 1.05278323 1 11.90419301 -9.15907843 1.177995792 0.971012871 0.457438523 0.929466337 0.061606364 0.07451515 0.204008915 0.009729493 0.020610513 6.93E-10 9.15907843 -0.513574348 down AGEAPTENPAPPTQQSS(ph)AE ddPTM_HeLa_Romidepsin_16h_R1 1 AGEAPTENPAPPTQQSSAE 19 0 P16989-2;P16989 P16989-2 YBX3 Y-box-binding protein 3 1 0 AGEAPTENPAPPT(0.004)QQS(0.188)S(0.808)AE 94.639 0.0026903 3685300 2189.3 2281.9 1757.8 1834.9 1766.9 1896.1 2090.2 1728.8 2193.3 2081.5 TRUE FALSE FALSE 2162.61597 2314.024648 1788.393772 2047.059771 1676.7285 1774.945329 2267.741536 1778.8201 1997.125755 2027.42233 1.066682525 1.141362909 0.882102237 1.009685916 0.827024777 0.875468965 1.118534359 0.877380146 0.985056604 1 10.98543093 -9.744787601 24.99967088 1.040609367 0.936422879 0.297301764 0.087303219 254.0976314 381481.3575 0.013343203 0.01883991 1.80E-10 9.744787601 -0.104186488 AGEK(ac)GSHEEEPVK ddPTM_HeLa_Romidepsin_16h_R1 2 AGEKGSHEEEPVK 13 1 C9JQA7;C9J8X5;Q9P0W2-3;Q9P0W2 C9JQA7 HMG20B SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related 0 1 ; AGEK(1)GSHEEEPVK;AGEK(1)GSHEEEPVK 164.22 7.53E-05 1881580 3863.8 3990.9 2727 3105.9 2901.3 2277.3 2916.3 2396.47 4260 3840.6 FALSE TRUE FALSE 3816.706519 4047.083995 2774.462291 3465.018772 2753.235835 2131.78788 3164.010449 2465.808078 3878.974931 3740.820658 1.020285886 1.081870628 0.741672094 0.926272358 0.735997816 0.569871714 0.845806506 0.659162335 1.036931541 1 11.86913909 -9.295367319 1.110554599 1.014626982 0.704675091 0.658690108 0.098501309 0.203648473 0.496930892 0.016032421 0.031997812 5.07E-10 9.295367319 -0.309951891 AGEK(ac)VEKPDTK ddPTM_HeLa_Romidepsin_16h_R1 1 AGEKVEKPDTK 11 2 Q02878;F8VZA3;F8VWR1;F8VU16;F8VZ45;U3KQR5 Q02878 RPL6 60S ribosomal protein L6 0 1 AGEK(1)VEKPDTK 116.84 0.0071352 10490000 4606.8 4162.8 3886 3515 3836.8 4255.3 4618 5407.3 5459 6246.4 FALSE TRUE FALSE 4550.65055 4221.404008 3953.6342 3921.420839 3640.993779 3983.400063 5010.252805 5563.751694 4970.733368 6084.117628 0.747955715 0.693839973 0.649828692 0.644534028 0.598442371 0.65472108 0.823497031 0.914471421 0.817001523 1 12.57083233 -11.78389314 0.717966109 0.998357144 0.705589182 0.303378201 0.104115608 0.391585661 0.386297676 0.06127673 0.021702245 1.64E-12 11.78389314 -0.292767962 AGELTEDEVER ddPTM_HeLa_Romidepsin_16h_R1 2 AGELTEDEVER 11 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 0 ; ; 223.87 3.27E-26 91785000 6370.7 6019.8 5691.2 6081.9 6185.2 6216.1 5149.8 6290.9 5790.8 5594.6 FALSE FALSE TRUE 6293.051458 6104.546902 5790.252949 6785.117894 5869.546164 5818.911272 5587.223883 6472.917266 5272.856345 5449.251485 1.15484695 1.120254207 1.06257767 1.245146771 1.077128883 1.067836801 1.025319514 1.187854384 0.967629473 1 12.41184236 -12.40981331 1.094470989 0.998900174 1.117425109 0.409594551 0.063094131 0.476427301 1.005627533 0.043808388 0.010695767 3.89E-13 12.40981331 0.118524935 AGEPDGES(ph)LDEQPSSSSSK ddPTM_HeLa_Romidepsin_16h_R1 2 AGEPDGESLDEQPSSSSSK 19 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 0 AGEPDGES(0.998)LDEQPS(0.002)SSSSK;AGEPDGES(1)LDEQPSSSSSK ; 324.29 3.06E-187 83642000 10488.8 11201.4 10567.7 8794.3 9376.1 8317.6 6599.3 7089.1 12283.5 11031.7 TRUE FALSE FALSE 10360.95847 11359.0936 10751.62639 9811.138344 8897.60263 7786.132204 7159.844377 7294.211924 11184.833 10745.09484 0.964250071 1.057142237 1.000607863 0.913080665 0.828061805 0.724622008 0.66633608 0.678841093 1.040924548 1 13.3913906 -8.541171878 1.386397706 0.990647771 0.669950172 0.955077143 0.030481508 0.060962596 0.227770338 0.004599169 0.014028103 2.88E-09 8.541171878 -0.320697599 AGEPDGES(ph)LDEQPSSSSSKR ddPTM_HeLa_Romidepsin_16h_R1 4 AGEPDGESLDEQPSSSSSKR 20 1 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 0 AGEPDGES(1)LDEQPSSSSSKR;AGEPDGES(1)LDEQPSSSSSKR;AGEPDGES(1)LDEQPSSSSSKR;AGEPDGES(1)LDEQPSSSSSKR ;;; 84.03 0.00097482 91714300 9205 8770.3 7780.9 11080.6 7188.1 6721.6 5880.2 5804.6 9860.3 8392.4 TRUE FALSE FALSE 9092.805919 8893.768514 7916.323301 12361.79111 6821.264435 6292.111453 6379.664041 5972.546943 8978.370072 8174.364238 1.112356344 1.088007367 0.968432904 1.512263309 0.834470331 0.769737104 0.780447733 0.730643603 1.098356987 1 12.99689081 -8.546006724 24.99993751 1.082633994 0.768928131 0.58014009 0.143947969 132.1684513 142865.541 0.020258242 0.040518257 2.84E-09 8.546006724 -0.313705863 AGEPNS(ph)PDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_HeLa_Romidepsin_16h_R1 4 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 2 0 AGEPNS(0.994)PDAEEANS(0.979)PDVT(0.027)AGCDPAGVHPPR;AGEPNS(1)PDAEEANS(0.999)PDVT(0.001)AGCDPAGVHPPR;AGEPNS(0.896)PDAEEANS(0.836)PDVT(0.268)AGCDPAGVHPPR;AGEPNS(0.987)PDAEEANS(0.78)PDVT(0.232)AGCDPAGVHPPR ;;; 130.64 4.51E-20 54250000 4898.13 4796.08 4677.89 1117.673 5487.46 6040.11 6669.73 5646.86 8148.17 6380.52 TRUE FALSE FALSE 4838.429708 4863.59934 4759.306713 1246.903611 5207.41444 5654.166465 7236.2567 5810.242985 7419.377268 6214.753171 0.77853932 0.782589301 0.765807842 0.200636063 0.837911707 0.90979743 1.164367514 0.934911303 1.193832975 1 12.60148138 -12.12034731 0.929935204 0.997244263 0.793657687 0.173598248 0.238519478 1.154813301 1.835324909 0.152305457 0.046760274 7.58E-13 12.12034731 -0.203586576 AGEPNS(ph)PDAEEANSPDVTAGCDPAGVHPPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 AGEPNS(0.971)PDAEEANS(0.028)PDVTAGCDPAGVHPPR 63.085 0.00030491 6435300 2110.4 2044.9 2223.3 1198.1 2129.4 2086.1 1826.9 2143.4 2466.8 1933.3 TRUE FALSE FALSE 2084.677633 2073.688156 2261.995604 1336.629959 2020.728772 1952.804943 1982.07684 2205.415897 2246.16323 1883.072587 1.10706175 1.101225821 1.201225921 0.709813296 1.0731019 1.037031156 1.052575909 1.171179439 1.192818187 1 10.8788729 -12.68588422 1.582964094 1.000235476 1.060262619 0 0.139886262 1.409590846 6.404290252 0.086636255 0.019590828 2.06E-13 12.68588422 0.060027143 AGEPNSPDAEEANS(ph)PDVTAGCDPAGVHPPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGEPNSPDAEEANSPDVTAGCDPAGVHPPR 30 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 AGEPNS(0.313)PDAEEANS(0.684)PDVT(0.004)AGCDPAGVHPPR 86.527 1.49E-07 7090500 3155.1 2964.1 2512.3 1004.2 3516.4 3311.6 2858.8 3251.1 3499.4 3046.6 TRUE FALSE FALSE 3116.644428 3005.828678 2556.025528 1120.310329 3336.944987 3099.999448 3101.626401 3345.165449 3186.4049 2967.448893 1.050277373 1.012933596 0.861354524 0.37753315 1.124516414 1.044668185 1.045216451 1.127286626 1.07378594 1 11.53500747 -9.878755071 7.918819532 1.024104767 0.924421863 0.057691552 0.204221052 0.647998306 42.548463 0.033826626 0.044528774 1.32E-10 9.878755071 -0.099682905 AGEQQLS(ph)EPEDMEMEAGDTDDPPR ddPTM_HeLa_Romidepsin_16h_R1 2 AGEQQLSEPEDMEMEAGDTDDPPR 24 0 Q93009;H3BMF6 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 1 0 AGEQQLS(0.999)EPEDMEMEAGDT(0.001)DDPPR;AGEQQLS(0.506)EPEDMEMEAGDT(0.494)DDPPR ; 77.657 0.00010073 33632000 4854.3 4819.7 4942 4392.4 5200.7 4951.7 4358.3 4992.7 5265.5 5213.2 TRUE FALSE FALSE 4795.133924 4887.551863 5028.013437 4900.269955 4935.288873 4635.302351 4728.493893 5137.155897 4794.540492 5077.760312 0.944340345 0.962540877 0.990202989 0.965045542 0.971942071 0.912863559 0.931216442 1.011697201 0.944223476 1 12.30997658 -12.44104271 1.098183815 1.000683517 0.958658604 0 0.03164103 0.60336211 1.267248404 0.019986612 0.004670143 3.62E-13 12.44104271 -0.042024913 AGEVFIHK ddPTM_HeLa_Romidepsin_16h_R1 1 AGEVFIHK 8 0 Q15233;Q15233-2;H7C367;C9JYS8;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 0 82.452 0.025808 13862000 10816 10308 9916.4 9210.3 10425 9761 8450.6 8462.8 10422 10620 FALSE FALSE TRUE 10684.17043 10453.11629 10088.99078 10275.23822 9892.973349 9137.303602 9168.393753 8707.657766 9489.830218 10344.09087 1.032876699 1.010539875 0.975338569 0.99334377 0.956388867 0.883335589 0.886341184 0.8418002 0.917415589 1 13.33651923 -8.290976258 0.875780933 1.014861607 0.839458089 0.681599834 0.034258186 0.144269869 0.17536323 0.002928314 0.017265829 5.12E-09 8.290976258 -0.175403519 TPSSS(ph)PPIT(ph)PPASETK ddPTM_HeLa_Romidepsin_16h_R1 2 TPSSSPPITPPASETK 16 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 2 0 T(0.516)PS(0.05)S(0.141)S(0.492)PPIT(0.799)PPAS(0.002)ETK;T(0.322)PS(0.156)S(0.412)S(0.709)PPIT(0.4)PPASETK ; 121.32 0.011986 14586000 7922.3 7284 6235.7 5271.6 3883.1 3596.8 3437.7 3579.7 8194.8 7931 TRUE FALSE FALSE 7825.73996 7386.544343 6344.229743 5881.127196 3684.930917 3366.976088 3729.698152 3683.272972 7461.836564 7724.951477 1.013047135 0.956192976 0.821264672 0.761315746 0.477016707 0.435857248 0.482811855 0.476802085 0.965939603 1 12.91531016 -9.11890394 1.192623155 1.005657907 0.44881768 0.968495746 0.041401246 0.045837468 0.128690234 0.006476025 0.013989424 7.60E-10 9.11890394 -0.556840227 down AGFSPDS(ph)SKADSDAASSGGSDSK ddPTM_HeLa_Romidepsin_16h_R1 2 AGFSPDSSKADSDAASSGGSDSK 23 1 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 0 AGFS(0.037)PDS(0.479)S(0.479)KADS(0.005)DAASSGGSDSK;AGFS(0.129)PDS(0.43)S(0.43)KADS(0.007)DAAS(0.001)S(0.001)GGS(0.001)DS(0.002)K ; 81.226 0.00015636 21588800 4054.5 4238.9 3176.4 3551.5 6071.2 5449.1 4723.6 5231.7 4463.9 4567.9 TRUE FALSE FALSE 4005.082194 4298.575345 3231.68391 3962.14114 5761.364009 5100.920096 5124.822466 5383.070985 4064.637604 4449.225299 0.900175182 0.966140183 0.726347553 0.890523827 1.294913973 1.146473769 1.151846023 1.209889503 0.913560751 1 12.11933844 -8.769767473 24.99997518 0.930097397 1.193406405 0.765559165 0.080585241 79.40293233 238358.9367 0.013105503 0.024043031 1.70E-09 8.769767473 0.263309008 AGGAGVPAFYTPTGYGTLVQEGGS(ph)PIKYNK ddPTM_HeLa_Romidepsin_16h_R1 2 AGGAGVPAFYTPTGYGTLVQEGGSPIKYNK 30 1 P55809 P55809 OXCT1 "Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial" 1 0 AGGAGVPAFYTPT(0.001)GY(0.005)GT(0.005)LVQEGGS(0.988)PIKYNK;AGGAGVPAFY(0.001)T(0.003)PT(0.046)GY(0.109)GT(0.109)LVQEGGS(0.733)PIKYNK ; 110.21 3.32E-10 56545000 16357.8 16399.7 15409.6 16572.5 13420 12511.3 10183.2 10265.5 16011.2 14225.4 TRUE FALSE FALSE 16158.42484 16630.57541 15677.79762 18488.69043 12735.12732 11711.86831 11048.16075 10562.51605 14579.11817 13855.82206 1.166183051 1.20025902 1.131495306 1.334362577 0.919117413 0.84526694 0.797365953 0.762316087 1.052201602 1 13.75820469 -8.533706034 24.51708282 1.111497625 0.814716404 0.74981481 0.089925347 79.96648755 181074.0041 0.015475544 0.030976502 2.93E-09 8.533706034 -0.296781221 AGGAS(ph)PAASSTAQPPTQHR ddPTM_HeLa_Romidepsin_16h_R1 3 AGGASPAASSTAQPPTQHR 19 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 AGGAS(0.895)PAAS(0.015)S(0.021)T(0.021)AQPPT(0.049)QHR;AGGAS(0.891)PAAS(0.075)S(0.027)T(0.006)AQPPTQHR;AGGAS(1)PAASSTAQPPTQHR ;; 206.62 1.49E-21 15971300 648.63 888.95 625.71 581.992 813.5 761.67 585.39 925.58 866.95 866.9 TRUE FALSE FALSE 640.7242481 901.4646614 636.6002201 649.2846534 771.9840594 713.0017452 635.113012 952.360197 789.4078207 844.377813 0.758812274 1.067608181 0.753928171 0.768950396 0.91426379 0.844410801 0.752166864 1.127883966 0.93489882 1 9.721744861 -12.62037289 1.428290792 1.000084853 0.852911826 0.054047405 0.128383565 0.609695968 2.231447182 0.085312659 0.019484973 2.40E-13 12.62037289 -0.147173027 TLYSFFS(ph)PSPAR ddPTM_HeLa_Romidepsin_16h_R1 1 TLYSFFSPSPAR 12 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 0 TLYSFFS(1)PSPAR 206.74 3.05E-15 17372000 2184.3 2411.4 1724.6 1091.1 537 579.04 394.13 531.16 2154.5 2085.4 TRUE FALSE FALSE 2157.676911 2445.347752 1754.61594 1217.258116 509.5948862 542.0412128 427.6073924 546.5282766 1961.796124 2031.221007 1.062256103 1.203880692 0.863823254 0.599274088 0.250881063 0.266854867 0.210517413 0.269063915 0.965821108 1 10.98813151 -9.099129792 1.850173269 1.042769146 0.239347802 0.963384613 0.071287813 0.041461631 0.279193438 0.011003256 0.020964356 7.96E-10 9.099129792 -0.803421344 down AGGEESQFEMDI ddPTM_HeLa_Romidepsin_16h_R1 2 AGGEESQFEMDI 12 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 0 0 ; ; 146.23 0.0037093 5997900 8697.7 8128.1 7977.8 7796 7986.6 8413.4 7223.7 8143.7 9042.4 8396.2 FALSE FALSE TRUE 8591.689087 8242.527605 8116.650262 8697.410201 7579.014 7875.810893 7837.280898 8379.325111 8233.625097 8178.065514 1.05057719 1.007882315 0.992490247 1.063504589 0.926748996 0.963040817 0.958329434 1.024609683 1.006793732 1 12.9975439 -8.76133 24.99999999 1.022966529 0.967111221 0.407298287 0.030626657 2.215544448 506126.1397 0.004654287 0.008857978 1.73E-09 8.76133 -0.055855308 AGGGATPVSS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 AGGGATPVSSPSR 13 0 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;Q9Y4B5-4 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 AGGGATPVS(0.023)S(0.977)PS(0.001)R;AGGGATPVS(0.026)S(0.971)PS(0.003)R ; 178.22 7.74E-07 12805800 8311.6 6660 9284.5 8725.3 7089.1 6813.4 5735.5 4735.3 8223.7 6874.9 TRUE FALSE FALSE 8210.295022 6753.759655 9446.092828 9734.16024 6727.316774 6378.045729 6222.673227 4872.308434 7488.151675 6696.289107 1.226096259 1.008582447 1.410645908 1.453664871 1.004633561 0.952474666 0.929271889 0.727613213 1.11825394 1 12.7091461 -7.955422228 1.581763484 1.146234755 0.789300299 0.469112869 0.154906869 0.374401846 1.677601126 0.025936562 0.136617024 1.11E-08 7.955422228 -0.356934456 AGGGGGLGAGS(ph)PALSGGQGR ddPTM_HeLa_Romidepsin_16h_R1 4 AGGGGGLGAGSPALSGGQGR 20 0 A0A3B3ITT1;Q6IQ22 A0A3B3ITT1 RAB12 Ras-related protein Rab-12 1 0 AGGGGGLGAGS(0.978)PALS(0.022)GGQGR;AGGGGGLGAGS(0.987)PALS(0.013)GGQGR;AGGGGGLGAGS(0.996)PALS(0.004)GGQGR;AGGGGGLGAGS(0.987)PALS(0.013)GGQGR ;;; 195.25 5.26E-18 104299000 7801.1 9949.6 10121.5 6983.8 7325.3 8645 5833.6 7694.6 9447.7 9199.4 TRUE FALSE FALSE 7706.017193 10089.67073 10297.66046 7791.299816 6951.462607 8092.6124 6329.105838 7917.231111 8602.67405 8960.398262 0.860008335 1.126029272 1.14924138 0.869526062 0.775798397 0.903153204 0.706342023 0.883580269 0.960077197 1 13.12934714 -9.010585487 24.56362738 0.966320842 0.816340061 0.450890079 0.09861201 401.0077279 930541.9624 0.016565665 0.02869602 9.76E-10 9.010585487 -0.149980781 AGGIETIANEYSDR ddPTM_HeLa_Romidepsin_16h_R1 1 AGGIETIANEYSDR 14 0 A0A087WYC1;P34932;A0A087WTS8;P34932-2 A0A087WYC1 HSPA4 Heat shock 70 kDa protein 4 0 0 150.15 0.0062693 6670400 1903.5 1764.5 1523.3 1853.8 1981.6 1708.6 1564.9 1547.6 1624.7 1699.1 FALSE FALSE TRUE 1880.29941 1789.340677 1549.812398 2068.145078 1880.471558 1599.425974 1697.822567 1592.377364 1479.382763 1654.957137 1.136161999 1.081200617 0.93646679 1.249666854 1.136266019 0.966445558 1.025901233 0.962186469 0.893910017 1 10.69257814 -8.244558352 24.3656669 1.075558676 0.988950095 0.101748346 0.099168379 844.4312083 1218829.033 0.012404075 0.031523551 5.69E-09 8.244558352 -0.086608581 AGGK(ac)AGK(ac)DSGK ddPTM_HeLa_Romidepsin_16h_R1 2 AGGKAGKDSGK 11 2 P0C0S5;A0A494C189;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;Q71UI9-5 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V;Histone H2A 0 2 ; AGGK(1)AGK(1)DSGK;AGGK(1)AGK(1)DSGK 134.75 0.0016729 696350 68.343 142.77 567.88 1220.28 1188.86 1645.47 3641.5 499.99 208.37 59.707 FALSE TRUE FALSE 67.51000923 144.7799198 577.7637132 1361.374515 1128.188038 1540.329778 3950.808919 514.4564218 189.7328653 58.15580353 1.16084733 2.489518002 9.934755916 23.40909131 19.3994059 26.48626077 67.93490381 8.846175111 3.262492371 1 5.861851264 -8.932491063 0.912942921 0.843374967 37.96872609 0.475674533 14.02229049 0.312041482 0.501810671 2.234255623 6.405386224 1.17E-09 8.932491063 37.12535113 KSNVSYK(ac)NPSLMPK ddPTM_HeLa_Romidepsin_16h_R1 1 KSNVSYKNPSLMPK 14 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 1 K(0.054)SNVSYK(0.946)NPSLMPK 97.86 0.0014699 0 447.95 362.41 508.64 598.22 809.75 729.6 812.62 681.27 506.16 358.07 FALSE TRUE FALSE 442.4902131 367.5120175 517.4926658 667.3890111 768.4254359 682.9809147 881.6439225 700.9814726 460.8877819 348.7672898 1.268726243 1.053745659 1.483776378 1.913565379 2.203261196 1.95827113 2.527885924 2.009883074 1.321476513 1 8.446120929 -9.292780885 1.58419186 1.119502834 2.198609316 0.876953105 0.17270205 0.080136038 0.393516584 0.026910516 0.048528612 5.10E-10 9.292780885 1.079106483 up AGGKPSQSPS(ph)QEAAGEAVLGAK ddPTM_HeLa_Romidepsin_16h_R1 1 AGGKPSQSPSQEAAGEAVLGAK 22 1 P00519;P00519-2 P00519 ABL1 Tyrosine-protein kinase ABL1 1 0 AGGKPS(0.015)QS(0.165)PS(0.82)QEAAGEAVLGAK 77.66 0.00043493 0 1533.1 1511.2 1317.7 1220 1613.6 1472.4 1650.6 1615.4 1552.7 1424.7 TRUE FALSE FALSE 1514.413988 1532.474713 1340.634016 1361.06214 1531.251971 1378.318392 1790.801923 1662.13905 1413.822623 1387.686089 1.091323175 1.104338168 0.966093144 0.980814142 1.103457031 0.993249412 1.290494974 1.197777411 1.018834616 1 10.43846553 -7.761365447 25 1.040042412 1.244136233 0.71595814 0.053200208 0.782012189 263866.9577 0.007819771 0.025964807 1.73E-08 7.761365447 0.204093821 AGGLDWPEATEVS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 3 AGGLDWPEATEVSPSR 16 0 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71 E9PKC4 PKP3 Plakophilin-3 1 0 AGGLDWPEAT(0.216)EVS(0.736)PS(0.048)R;AGGLDWPEATEVS(0.998)PS(0.002)R;AGGLDWPEATEVS(0.977)PS(0.023)R ;; 284.53 1.12E-102 154450200 11262.7 10053.2 10668 9455.5 9549.3 8600.7 7198.6 7617.3 11276.4 10139 TRUE FALSE FALSE 11125.42588 10194.72921 10853.67206 10548.7894 9061.963588 8051.143027 7810.048904 7837.694557 10267.81054 9875.587318 1.126558403 1.032316245 1.099040666 1.068168308 0.917612623 0.815257135 0.790843993 0.793643386 1.039716445 1 13.26965083 -8.521309133 2.315154069 1.063147917 0.796006734 0.922195406 0.034196842 0.080175556 0.853709126 0.007327193 0.017907832 3.01E-09 8.521309133 -0.267141183 AGGPAIPSHLLS(ph)TPYPFGLSPSSVVQDSR ddPTM_HeLa_Romidepsin_16h_R1 1 AGGPAIPSHLLSTPYPFGLSPSSVVQDSR 29 0 Q14687-2;Q14687-3;Q14687;C9JLW9 Q14687-2 GSE1 Genetic suppressor element 1 1 0 AGGPAIPS(0.004)HLLS(0.759)T(0.108)PY(0.025)PFGLS(0.084)PS(0.008)S(0.008)VVQDS(0.005)R 52.366 0.0058867 5712300 810.07 901.96 877.58 793.92 800.16 880.18 537.3 620.41 964.08 908.6 TRUE FALSE FALSE 800.1965553 914.6578166 892.8539118 885.7167659 759.3248494 823.9393387 582.9382486 638.3605845 877.8502702 884.994441 0.904182578 1.033518149 1.008880814 1.000816191 0.857999569 0.93101075 0.658691424 0.721315926 0.99192744 1 9.789524583 -7.805134724 5.54706027 0.959306422 0.689162315 0.811960982 0.053113412 0.057331781 4.121813383 0.008202709 0.026438887 1.57E-08 7.805134724 -0.270144108 AGGPATPLS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 AGGPATPLSPTR 12 0 Q03252 Q03252 LMNB2 Lamin-B2 1 0 AGGPATPLS(0.975)PT(0.025)R 113.95 0.0094044 78891000 2276.6 2062.1 2124.9 2013.7 3387.5 3674.7 3288.1 2831.1 2391.9 2227.7 TRUE FALSE FALSE 2248.851924 2091.130298 2161.882993 2246.533469 3214.623234 3439.89853 3567.391132 2913.013412 2177.962473 2169.824033 1.036421336 0.963732665 0.996340238 1.035352837 1.481513333 1.585335252 1.644092368 1.342511359 1.003750738 1 11.08336233 -8.747205659 4.583039492 1.011129052 1.535069151 0.918460698 0.074141432 0.034940537 1.790060273 0.010131327 0.019987346 1.79E-09 8.747205659 0.523940099 AGGPS(ph)DDDNADKPK ddPTM_HeLa_Romidepsin_16h_R1 3 AGGPSDDDNADKPK 14 1 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 0 AGGPS(1)DDDNADKPK;AGGPS(1)DDDNADKPK;AGGPS(1)DDDNADKPK ;; 132.4 0.00066471 83301200 8102.4 8587.4 10845.9 9289.2 8737.4 9086.4 12533.2 2672.64 12062.7 11197 TRUE FALSE FALSE 8003.644832 8708.293643 11034.66834 10363.26101 8291.497874 8505.808365 13597.7697 2749.968622 10983.7819 10906.10033 0.733868623 0.798479143 1.011788633 0.950226085 0.760262388 0.779912903 1.246804017 0.25214958 1.007122764 1 13.41284771 -12.54889504 1.325027493 0.999727066 0.825219778 0.087569361 0.239228339 0.973028208 3.068205655 0.15107467 0.036031437 2.83E-13 12.54889504 -0.174507287 AGGPTT(ph)PLS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 2 0 AGGPT(0.011)T(0.989)PLS(0.952)PT(0.048)R 126.5 0.021879 151760000 6777.5 6780.5 6654.6 5752.4 8766.4 11126 7859 9090.2 7155.3 6048.5 TRUE FALSE FALSE 6694.893223 6875.956057 6770.420522 6417.519554 8319.017896 10415.08451 8526.543264 9353.210595 6515.312047 5891.359098 1.136391979 1.167125606 1.149211991 1.089310539 1.412071096 1.767857694 1.447296476 1.587615088 1.105909848 1 12.52438478 -8.642583678 3.395023612 1.082196385 1.587676813 0.865971309 0.087650627 0.06212506 1.401797098 0.013894864 0.029314156 2.28E-09 8.642583678 0.505480428 AGGPTT(ph)PLSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 0 AGGPT(0.035)T(0.965)PLSPTR 112.64 0.020239 49355000 5885.2 5987 5314.7 4543.7 3961.1 3344.2 2497.3 2676.4 5746.7 5603.9 TRUE FALSE FALSE 5813.468919 6071.285143 5407.200124 5069.063973 3758.950286 3130.516413 2709.4206 2753.837411 5232.700759 5458.30987 1.065067586 1.112301296 0.990636342 0.928687468 0.688665608 0.57353219 0.496384534 0.504522 0.958666855 1 12.41423858 -8.659597227 1.47566039 1.038022099 0.503298168 0.967661842 0.040963786 0.043935523 0.190689894 0.006110738 0.01632761 2.19E-09 8.659597227 -0.53472393 AGGPTTPLS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 4 AGGPTTPLSPTR 12 0 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 1 0 AGGPTT(0.008)PLS(0.961)PT(0.031)R;AGGPT(0.001)T(0.018)PLS(0.69)PT(0.291)R;AGGPTT(0.001)PLS(0.499)PT(0.499)R;AGGPTT(0.005)PLS(0.6)PT(0.394)R ;;; 111.31 0.010225 541891000 9955.3 10321.6 11109.4 7860.7 8872.8 9277.2 7174.3 6691.46 11170.9 9017.8 TRUE FALSE FALSE 9833.960974 10466.90776 11302.75445 8769.59112 8419.987907 8684.416861 7783.684863 6885.066838 10171.74673 8783.516256 1.119592733 1.191653485 1.286814314 0.998414629 0.958612435 0.988717571 0.886169574 0.783862253 1.158049513 1 13.10058289 -7.77456169 0.963732861 1.081910215 0.752337002 0.602834958 0.090443689 0.69092007 0.792640248 0.016140615 0.195685318 1.68E-08 7.77456169 -0.329573212 AGGQTEINSLR ddPTM_HeLa_Romidepsin_16h_R1 2 AGGQTEINSLR 11 0 O43586-2;H0YNS1;B4E1Z9;H0YLI2;H0YLM9;H0YLW8;H0YLX8;J3KPG6;H0YKY3;O43586 O43586-2 PSTPIP1 Proline-serine-threonine phosphatase-interacting protein 1 0 0 ; ; 84.817 0.0034864 3124200 2404.77 2687.2 2637.65 1707.48 2593.59 2221.99 2047.64 2618.9 3264.68 3901 FALSE FALSE TRUE 2375.459738 2725.030472 2683.557192 1904.906872 2461.229424 2080.01201 2221.56649 2694.67374 2972.678844 3799.651458 0.625178326 0.717179063 0.706264041 0.501337265 0.647751367 0.547421792 0.584676388 0.709189716 0.782355665 1 11.89165137 -12.50850167 0.444597842 1.137867521 0.605746259 0.495441503 0.094871195 0.694978727 0.157504837 0.173392635 0.019157219 3.10E-13 12.50850167 -0.532121262 AGGS(ph)AALSPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 0 AGGS(0.809)AALS(0.191)PS(0.001)K 144.7 0.0025112 119870000 5213.5 5722 11327 9569.5 9871.5 11319 7425.2 3947.6 6854.6 4008.2 TRUE FALSE FALSE 5149.955857 5802.554466 11524.14168 10675.97062 9367.720519 10595.75243 8055.896303 4061.817578 6241.507408 3904.066386 1.319126098 1.486284784 2.951830359 2.73457712 2.399477773 2.714029779 2.06346294 1.040406893 1.598719589 1 11.93076187 -9.93323542 5.931375148 1.162559801 2.344679981 0.449468088 0.518348904 0.115999642 7.597071634 0.083367398 0.109795229 1.17E-10 9.93323542 1.18212018 AGGS(ph)PAPGPETPAISPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AGGSPAPGPETPAISPSK 18 0 P33316;H0YKI0 P33316 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 0 AGGS(0.999)PAPGPET(0.001)PAISPSK 92.427 0.0053365 3947400 1562.7 1699.6 1826 1309.9 1681 1900.8 1559 1651.4 1680.8 1560.1 TRUE FALSE FALSE 1543.653211 1723.527013 1857.780764 1461.356801 1595.212297 1779.345015 1691.421421 1699.180654 1530.465038 1519.568377 1.015849786 1.134221427 1.222571351 0.961692033 1.049779873 1.170954227 1.113093327 1.118199536 1.007170892 1 10.56944588 -10.30703302 7.258603169 1.007302638 1.108801736 0.339656204 0.065423754 0.215879496 29.74612006 0.011269594 0.012906146 4.93E-11 10.30703302 0.101499098 AGGSAALS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 AGGSAALSPSK 11 0 Q92522 Q92522 H1FX Histone H1x 1 0 AGGSAALS(0.991)PS(0.009)K;AGGS(0.036)AALS(0.952)PS(0.012)K ; 136.38 0.0038269 523500000 8418.7 10407.7 19902 16299.2 16387.1 17974.9 13657.3 5334.7 12120.1 6958.6 TRUE FALSE FALSE 8316.089646 10554.21987 20248.38596 18183.79019 15550.80514 16826.3619 14817.35072 5489.051128 11036.0479 6777.814569 1.226957386 1.557171529 2.987450565 2.682839728 2.294368632 2.48256451 2.186154633 0.809855606 1.628260524 1 12.72660445 -9.97299437 6.292077409 1.120284297 2.275189554 0.369809494 0.562055413 0.106215186 13.72770754 0.087589226 0.114393844 1.06E-10 9.97299437 1.154905257 AGGSPAPGPETPAIS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 3 AGGSPAPGPETPAISPSKR 19 1 P33316;H0YKI0 P33316 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 0 AGGSPAPGPETPAIS(0.79)PS(0.21)KR;AGGSPAPGPETPAIS(0.818)PS(0.182)KR;AGGSPAPGPET(0.001)PAIS(0.909)PS(0.09)KR ;; 144.4 1.99E-05 89551000 10718 10754.8 10869.7 10666.3 9104.2 7508.7 6950.2 8426.4 11505.1 10861.1 TRUE FALSE FALSE 10587.36489 10906.20636 11058.88257 11899.58779 8639.578702 7028.918303 7540.549815 8670.204589 10476.05504 10578.92706 1.000797608 1.030936909 1.045369016 1.124838817 0.816678162 0.664426389 0.71278966 0.819573152 0.990275761 1 13.36890569 -8.592838228 5.534817383 1.014025867 0.731532015 0.873338514 0.052409981 0.050077155 2.811346953 0.007630174 0.01551293 2.55E-09 8.592838228 -0.282493852 AGGTEIGK(ac)TLAEK ddPTM_HeLa_Romidepsin_16h_R1 2 AGGTEIGKTLAEK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 1 ; AGGTEIGK(1)TLAEK;AGGTEIGK(1)TLAEK 251.75 3.30E-53 7352800 5129.3 4612.5 3626.6 3616.4 3837.8 3199.3 3218.6 3315.2 4982.8 4101.2 FALSE TRUE FALSE 5066.782119 4677.434896 3689.719452 4034.545184 3641.942745 2994.875055 3491.987804 3411.120081 4537.125888 3994.650233 1.26839193 1.170924768 0.923665211 1.009987095 0.911705039 0.749721473 0.874166097 0.853922091 1.135800539 1 11.96385347 -9.177161816 1.264184976 1.129899946 0.837731411 0.679128417 0.086315535 0.253711806 0.798703571 0.019794584 0.040380893 6.65E-10 9.177161816 -0.292168535 AGGVMVMPEGADTVS(ph)RPSPDYPMLPTIPLSAFSDPKK ddPTM_HeLa_Romidepsin_16h_R1 1 AGGVMVMPEGADTVSRPSPDYPMLPTIPLSAFSDPKK 37 2 Q03111 Q03111 MLLT1 Protein ENL 1 0 AGGVMVMPEGADT(0.232)VS(0.259)RPS(0.259)PDY(0.232)PMLPT(0.018)IPLSAFSDPKK 55.484 0.0052666 16205000 2223.1 1991.6 1763.3 1412.1 3331.2 2834.7 2218.5 3267.1 2158.2 2185 TRUE FALSE FALSE 2196.004002 2019.637797 1793.989497 1575.373646 3161.196434 2653.571819 2406.939335 3361.628384 1965.165187 2128.233385 1.031843602 0.948973835 0.842947728 0.740225981 1.485361735 1.246842493 1.130956479 1.579539353 0.923378611 1 11.05544065 -8.752620295 24.99999925 0.9783656 1.336135659 0.678255131 0.146236014 103.5624296 293572.5406 0.021128273 0.041752649 1.77E-09 8.752620295 0.357770059 AGK(ac)DSGK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 AGKDSGKAK 9 2 P0C0S5;A0A494C189;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;Q71UI9-5 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V;Histone H2A 0 2 ; AGK(1)DSGK(1)AK;AGK(1)DSGK(1)AK 153.97 0.0033006 5264400 1038.23 1079.21 5366.3 13693.5 7127.8 5162.5 15374 783.36 1731.05 1081.34 FALSE TRUE FALSE 1025.575653 1094.403147 5459.6982 15276.8069 6764.041769 4832.632911 16679.86718 806.0252857 1576.220553 1053.246631 0.973727922 1.039075858 5.183684467 14.50449159 6.422087259 4.588320313 15.83662049 0.765276871 1.4965351 1 10.04062759 -9.593064168 4.149386583 1.007110986 8.626177467 0.406433624 4.132942849 0.140379218 4.792191061 0.588515172 0.849014781 2.55E-10 9.593064168 7.619066481 AGK(ac)DSGK(ac)AK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 AGKDSGKAKAK 11 3 Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;Q71UI9-5 Q71UI9 H2AFV Histone H2A.V;Histone H2A 0 3 ; AGK(1)DSGK(1)AK(1)AK;AGK(1)DSGK(1)AK(1)AK 169.65 0.00016697 8381300 2203.2 1936.5 2421.5 13737.6 11240.5 6637.6 5700.9 6232.9 2506.28 2352.6 FALSE TRUE FALSE 2176.346551 1963.762098 2463.645192 15326.00595 10666.85534 6213.478782 6185.134304 6413.239128 2282.11204 2291.479113 0.949756225 0.856984507 1.075133165 6.688259065 4.655008759 2.711558114 2.699188602 2.7987334 0.995912215 1 11.16206342 -9.466605426 24.9450033 0.966634781 3.824371665 0.633157473 1.116351749 146.6477812 65006.4704 0.176486497 0.269586944 3.42E-10 9.466605426 2.857736884 AGK(ac)DSGK(ac)AK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 AGKDSGKAKTK 11 3 P0C0S5;A0A494C189 P0C0S5 H2AFZ Histone H2A.Z 0 3 ; AGK(1)DSGK(1)AK(1)TK;AGK(1)DSGK(1)AK(1)TK 180.24 5.94E-08 76701000 3963.8 4535.4 8035.5 49565 32572 19265 16013.9 15188.9 3702.1 3263.7 FALSE TRUE FALSE 3915.487681 4599.24948 8175.354507 55295.93851 30909.7293 18034.02867 17374.12027 15628.36686 3370.974904 3178.908604 1.231708164 1.44680142 2.571748838 17.39462986 9.723377785 5.673025218 5.465435605 4.916268068 1.060418944 1 11.63431582 -9.497629858 24.96752006 1.179278072 8.517321852 0.540122474 3.327962973 446.5448661 441569.3383 0.521451076 0.794405414 3.18E-10 9.497629858 7.33804378 AGKSGTST(ph)PTTPGSTAIT(ph)PGTPPSYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 AGKSGTSTPTTPGSTAITPGTPPSYSSR 28 1 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 2 0 AGKS(0.148)GT(0.179)S(0.198)T(0.218)PT(0.221)T(0.036)PGS(0.031)T(0.029)AIT(0.502)PGT(0.39)PPS(0.018)YS(0.015)S(0.015)R 64.936 0.00061908 8581700 333.45 365.25 305.48 703.18 816.83 503.7 707.69 644.91 463.95 433.86 TRUE FALSE FALSE 329.3857831 370.3919991 310.7967513 784.4849802 775.1441171 471.5151956 767.8011709 663.5694534 422.45315 422.5882547 0.779448505 0.876484367 0.735459985 1.85638141 1.834277476 1.115779226 1.816901351 1.570250583 0.999680292 1 8.72310886 -9.265202507 24.99815302 0.880508868 1.630429352 0.760348705 0.213451428 118.8460898 789484.8109 0.032255129 0.050460912 5.43E-10 9.265202507 0.749920484 AGLAS(ph)PEEEDAVGKEPLK ddPTM_HeLa_Romidepsin_16h_R1 2 AGLASPEEEDAVGKEPLK 18 1 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 0 AGLAS(1)PEEEDAVGKEPLK;AGLAS(1)PEEEDAVGKEPLK ; 83.393 0.0040618 26681900 5523.2 5342.1 5303 5446.5 6001.4 6310.1 5663 6398.4 6151.7 6410.5 TRUE FALSE FALSE 5455.881114 5417.306224 5395.29649 6076.249957 5695.126164 5906.904975 6144.015079 6583.527609 5601.476545 6243.954286 0.873786204 0.867608246 0.864083279 0.973141327 0.912102476 0.946019895 0.983994244 1.054384338 0.897104029 1 12.60824426 -7.338020045 1.482367093 0.928306632 1.092747775 0.489430002 0.043863337 0.938096039 2.074380238 0.008442527 0.216018025 4.59E-08 7.338020045 0.164441143 AGLES(ph)GAEPGDGDSDT(ph)TK ddPTM_HeLa_Romidepsin_16h_R1 1 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 0 AGLES(0.996)GAEPGDGDS(0.016)DT(0.589)T(0.399)K 167.9 1.71E-06 9099800 3257.1 3676.6 3233.4 2611.1 3366.2 2947.4 2435.8 3102.8 3425.3 3544.7 TRUE FALSE FALSE 3217.401212 3728.359271 3289.675971 2913.007668 3194.410253 2759.070652 2642.696791 3192.574623 3118.932589 3452.608183 0.931875568 1.079867472 0.952808948 0.843712206 0.925216556 0.799126488 0.765420416 0.924684891 0.903355499 1 11.7534709 -9.313400322 4.503348694 0.976907586 0.847587554 0.484316392 0.063128363 0.133015854 5.854609384 0.009304076 0.014592332 4.86E-10 9.313400322 -0.129320032 AGLESGAEPGDGDS(ph)DTTK ddPTM_HeLa_Romidepsin_16h_R1 2 AGLESGAEPGDGDSDTTK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 AGLESGAEPGDGDS(0.929)DT(0.068)T(0.003)K;AGLESGAEPGDGDS(0.995)DT(0.004)TK ; 222.51 4.05E-38 497270000 8175.2 8547.2 7767.2 5025.7 6346.6 6711.4 6160.2 6780.3 9472 7741.3 TRUE FALSE FALSE 8075.557518 8667.527706 7902.384858 5606.795081 6022.70932 6282.5632 6683.447234 6976.477283 8624.800597 7540.17991 1.071003294 1.149512055 1.048036645 0.743589032 0.798748756 0.833211313 0.886377688 0.925240162 1.143845465 1 12.88038323 -9.278296315 24.47803206 1.045914043 0.837768815 0.767327727 0.065948784 249.7206084 362619.636 0.010106153 0.015463673 5.27E-10 9.278296315 -0.208145228 AGLESGAEPGDGDS(ph)DTTKK ddPTM_HeLa_Romidepsin_16h_R1 2 AGLESGAEPGDGDSDTTKK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 AGLESGAEPGDGDS(0.426)DT(0.148)T(0.426)KK;AGLESGAEPGDGDS(0.758)DT(0.141)T(0.101)KK ; 87.729 0.0014172 107311000 9472.7 9326.1 9300.1 9341.5 9033.8 9239.2 8471.5 9542 9714.7 9992.2 TRUE FALSE FALSE 9357.243089 9457.393081 9461.964339 10421.60818 8572.771476 8648.844938 9191.068999 9818.082715 8845.792901 9732.601204 0.961432909 0.971723066 0.972192751 1.070793713 0.880830448 0.888646802 0.944358944 1.008783008 0.908882704 1 13.24860973 -8.733558664 24.99999762 0.985288315 0.928633134 0.192127433 0.049845113 223.4915888 200398.8512 0.006382748 0.01276342 1.85E-09 8.733558664 -0.056655181 AGLQFPVGR ddPTM_HeLa_Romidepsin_16h_R1 2 AGLQFPVGR 9 0 P0C0S5;A0A494C189;P16104;Q71UI9;C9J0D1;Q71UI9-2;Q71UI9-5;A0A0U1RR32;A0A0U1RRH7;Q99878;Q96KK5;Q16777;Q6FI13;P20671;P0C0S8;A0A3B3IS11;Q9BTM1;Q96QV6;Q9BTM1-2;Q8IUE6;Q93077;Q7L7L0;P04908 P0C0S5;Q71UI9;A0A0U1RR32;Q93077 H2AFZ;H2AFX;H2AFV;HIST1H2AJ;HIST1H2AH;HIST2H2AC;HIST2H2AA3;HIST1H2AD;HIST1H2AG;H2AFJ;HIST1H2AA;HIST2H2AB;HIST1H2AC;HIST3H2A;HIST1H2AB Histone H2A.Z;Histone H2AX;Histone H2A.V;Histone H2A;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-C;Histone H2A type 2-A;Histone H2A type 1-D;Histone H2A type 1;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 2-B;Histone H2A type 1-C;Histone H2A type 3;Histone H2A type 1-B/E 0 0 ; ; 166.17 0.010698 4486600 3266.2 2199.1 3956.3 2796 3372.2 4021 3711.8 2875.3 2514.4 2334.36 FALSE FALSE TRUE 3226.390298 2230.058988 4025.157742 3119.286676 3200.104051 3764.071077 4027.080199 2958.492269 2289.505767 2273.712991 1.41899629 0.980800566 1.770301598 1.371891126 1.407435355 1.655473269 1.771147113 1.301172259 1.006945809 1 11.15083444 -14.6584308 0.146094455 8.64E-10 1.694229352 0.460564167 0.211769718 25.79877198 0.438636946 8.553175012 0.614597317 2.20E-15 14.6584308 1.694229351 AGLS(ph)PAEPLLSR ddPTM_HeLa_Romidepsin_16h_R1 2 AGLSPAEPLLSR 12 0 O95402;B8ZZF3 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 0 AGLS(1)PAEPLLSR;AGLS(1)PAEPLLSR ; 133.98 0.0029269 45988000 5654.7 4980.2 4655.9 5294.3 9597.6 10414.1 9252.7 9639.7 5100.4 5214.5 TRUE FALSE FALSE 5585.778341 5050.311386 4736.933986 5906.451876 9107.798658 9748.67262 10038.62411 9918.609511 4644.20745 5079.026538 1.099773411 0.994346328 0.93264604 1.162910221 1.793217379 1.91939785 1.976485854 1.952856406 0.914389286 1 12.3103363 -8.747616034 3.023426683 1.034960963 1.944024884 0.982559246 0.058780396 0.021858526 0.411108655 0.008454723 0.017336458 1.79E-09 8.747616034 0.909063921 AGLVDDFEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AGLVDDFEKK 10 1 F5H608;O75947-2;O75947 F5H608 ATP5H "ATP synthase subunit d, mitochondrial" 0 1 AGLVDDFEK(1)K 101.38 0.0088087 490910 67.022 241.42 298.21 135.63 440.64 549.52 276.94 384.51 224.8 227.87 FALSE TRUE FALSE 66.20511008 244.8187171 303.40022 151.3121788 418.1524965 514.4074455 300.4632767 395.6351902 204.693325 221.9499046 0.298288527 1.10303592 1.366976123 0.681740229 1.883994937 2.31767365 1.353743663 1.782542736 0.922250115 1 7.794090278 -9.059668257 1.13768685 0.699255278 1.835731862 0.51818842 0.396667417 0.269638516 0.689286686 0.074072262 0.169790364 8.72E-10 9.059668257 1.136476584 AGMS(ph)SNQSIS(ph)SPVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 AGMS(0.557)S(0.058)NQS(0.414)IS(0.82)S(0.151)PVLDAVPR 76.068 0.025499 16124000 1549.8 1891.8 1377 1095.1 1486.7 1356.2 1146.9 1029.6 1274.6 1785.4 TRUE FALSE FALSE 1530.910441 1918.43281 1400.966107 1221.720615 1410.828151 1269.543197 1244.317657 1059.389852 1160.596584 1739.015051 0.88033191 1.103172057 0.805608961 0.702535964 0.811280012 0.730035773 0.715530125 0.609189582 0.667387314 1 10.7640547 -9.552018568 8.593547259 0.954071602 0.723410875 0.377131094 0.115449351 0.10491942 27.7149666 0.012038894 0.017102004 2.81E-10 9.552018568 -0.230660727 AGMS(ph)SNQSISSPVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMS(0.641)S(0.072)NQS(0.085)IS(0.055)S(0.147)PVLDAVPR;AGMS(0.479)S(0.395)NQS(0.11)IS(0.008)S(0.008)PVLDAVPR ; 97.836 0.0024846 381670000 5193.3 4902.1 5300 3786.5 4227.1 4790.8 4233 4257.7 5614 5843.4 TRUE FALSE FALSE 5130.002062 4971.111892 5392.244277 4224.312946 4011.375314 4484.683342 4592.550914 4380.889832 5111.869779 5691.587626 0.901330595 0.873413926 0.947406002 0.742202918 0.704790223 0.78794945 0.806901557 0.769713149 0.898144791 1 12.47461542 -10.01459339 0.48237429 0.985704281 0.752433578 0.598153637 0.0573628 0.35724291 0.194096618 0.020879387 0.030589117 9.67E-11 10.01459339 -0.233270703 AGMSSNQS(ph)ISS(ph)PVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 AGMS(0.031)S(0.146)NQS(0.824)IS(0.329)S(0.671)PVLDAVPR 77.137 0.023597 14800000 2629 2527.3 2416.4 1236.3 2080.9 2659.1 1781.8 1798.1 2424.9 2508.5 TRUE FALSE FALSE 2596.956737 2562.879396 2458.456428 1379.246823 1974.703908 2489.192092 1933.146048 1850.125187 2208.010871 2443.328808 1.062876486 1.04892939 1.006191398 0.56449497 0.808202278 1.018770819 0.791193572 0.757214985 0.903689615 1 11.25463231 -9.486591458 24.96071502 1.031754437 0.800424098 0.477081016 0.111365649 336.572337 231516.3446 0.016036819 0.024491604 3.26E-10 9.486591458 -0.231330339 AGMSSNQS(ph)ISSPVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMS(0.002)S(0.002)NQS(0.332)IS(0.332)S(0.332)PVLDAVPR;AGMS(0.014)S(0.012)NQS(0.765)IS(0.062)S(0.148)PVLDAVPR ; 95.767 0.003276 381429000 5937 5249.9 4996.8 3476.8 4313 4938.3 4422.8 5251.9 6218.2 6414.3 TRUE FALSE FALSE 5864.63756 5323.80823 5083.767208 3878.803975 4092.891516 4622.758568 4798.472522 5403.85544 5662.028618 6247.655561 0.938694123 0.852128959 0.813707983 0.62084152 0.65510838 0.739918922 0.768043704 0.864941319 0.906264528 1 12.6090992 -10.00290897 1.494813856 0.975656244 0.729977796 0.649421673 0.068238816 0.148144913 0.64894111 0.01274745 0.016832107 9.93E-11 10.00290897 -0.245678448 AGMSSNQSIS(ph)SPVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMS(0.004)S(0.012)NQS(0.036)IS(0.474)S(0.474)PVLDAVPR 48.5 0.026914 13241000 1639.2 1651.6 1526.1 1330.3 1687.6 1739.1 1362.7 1649.2 1817.3 1969.7 TRUE FALSE FALSE 1619.2208 1674.851268 1552.66113 1484.115545 1601.475475 1627.977123 1478.447704 1696.917 1654.756136 1918.52691 0.843991706 0.872988155 0.809298594 0.773570356 0.834742253 0.848555793 0.770616089 0.884489548 0.862513905 1 10.90578329 -12.05550875 0.491660112 1.029670313 0.818576027 0.224486209 0.054603062 0.463411915 0.171376734 0.04686576 0.009332918 8.80E-13 12.05550875 -0.211094286 AGMSSNQSIS(ph)SPVLDAVPRT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 AGMSSNQS(0.003)IS(0.537)S(0.459)PVLDAVPRT(0.822)PS(0.177)R;AGMS(0.048)S(0.132)NQS(0.062)IS(0.499)S(0.26)PVLDAVPRT(0.788)PS(0.211)R ; 72.469 0.0023301 93195000 4049.3 3717 3457 2966.3 2956.8 3230.7 2210.77 2962.89 3953.8 3731.2 TRUE FALSE FALSE 3999.945574 3769.328024 3517.167635 3309.277563 2805.903463 3024.268697 2398.552749 3048.616547 3600.162226 3634.262886 1.100620869 1.037164383 0.967780192 0.910577376 0.772069482 0.832154633 0.659983282 0.838854162 0.990616898 1 11.82744707 -9.078588036 1.352903082 1.048099249 0.761394249 0.80827637 0.055918022 0.118374425 0.428057906 0.009266321 0.019507338 8.34E-10 9.078588036 -0.286705 AGMSSNQSISS(ph)PVLDAVPR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPR 19 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMSS(0.001)NQS(0.243)IS(0.248)S(0.508)PVLDAVPR;AGMSSNQS(0.071)IS(0.223)S(0.706)PVLDAVPR ; 120.59 0.0011861 335055000 4587.6 4474.6 5055.7 3124.26 4001.7 4092.2 3562.3 4285.9 5368 5438.2 TRUE FALSE FALSE 4531.684567 4537.593536 5143.692338 3485.501641 3797.478317 3830.721627 3864.881673 4409.905754 4887.872636 5296.91478 0.855532844 0.856648393 0.971073266 0.658024867 0.716922676 0.723198652 0.729647697 0.832542327 0.922777284 1 12.37093658 -9.266345749 24.99881869 0.92589556 0.730598759 0.729065642 0.057611174 195.5506569 996364.883 0.010937844 0.017043619 5.42E-10 9.266345749 -0.195296802 AGMSSNQSISS(ph)PVLDAVPRT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 AGMSSNQSIS(0.453)S(0.546)PVLDAVPRT(0.836)PS(0.164)R;AGMS(0.001)S(0.002)NQS(0.019)IS(0.453)S(0.525)PVLDAVPRT(0.574)PS(0.426)R ; 87.704 0.00029187 61792000 2799.4 2756.6 2944.2 2530.38 2384.77 2629.3 2267.42 2591.2 3254.1 2997.3 TRUE FALSE FALSE 2765.279836 2795.407487 2995.442566 2822.954441 2263.066288 2461.296216 2460.014598 2666.172284 2963.045146 2919.429714 0.947198634 0.957518338 1.026036884 0.966954069 0.775174096 0.843074318 0.842635322 0.913251061 1.01493971 1 11.51147086 -8.837461634 8.321997494 0.977019687 0.843645171 0.758840411 0.039033687 0.099627831 9.710166078 0.005731646 0.010424367 1.45E-09 8.837461634 -0.133374516 AGMSSNQSISSPVLDAVPRT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMSSNQSISSPVLDAVPRT(0.756)PS(0.244)R;AGMSSNQSISSPVLDAVPRT(0.5)PS(0.5)R ; 105.75 1.17E-05 9244100 2747 3092.6 2673.2 2203.29 2577 2598.1 2066.4 2791.9 2912.1 2990.1 TRUE FALSE FALSE 2713.518507 3136.137704 2719.725925 2458.044757 2445.486074 2432.089795 2241.919964 2872.679222 2651.634483 2912.416771 0.931706799 1.076816249 0.933838162 0.843987983 0.839675866 0.835076154 0.769779925 0.986355816 0.910458458 1 11.50800111 -9.380643447 4.134040726 0.976085131 0.848449934 0.445696946 0.065457736 0.148530262 4.321031421 0.009428012 0.014625617 4.16E-10 9.380643447 -0.127635196 AGMSSNQSISSPVLDAVPRTPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AGMSSNQSISSPVLDAVPRTPSR 23 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AGMSSNQSISSPVLDAVPRT(0.236)PS(0.764)R 62.107 0.0073329 17872000 1004.1 829.22 957.27 763.31 760.23 740.22 737.2 684.36 979.19 983.46 TRUE FALSE FALSE 991.861643 840.8937809 973.9308828 851.5674937 721.4326263 692.922331 799.8177496 704.1608769 891.608794 957.9095674 1.035443926 0.877842554 1.01672529 0.888985268 0.75313229 0.723369256 0.834961646 0.735101622 0.930785978 1 9.903745653 -9.003640108 2.468817843 1.005157021 0.762980919 0.747031272 0.055910621 0.084461488 1.03238113 0.007892785 0.01490032 9.92E-10 9.003640108 -0.242176102 AGMTSS(ph)PDATTGQTFG ddPTM_HeLa_Romidepsin_16h_R1 2 AGMTSSPDATTGQTFG 16 0 Q9UQR1;G5E9X2;Q9UQR1-2 Q9UQR1 ZNF148 Zinc finger protein 148 1 0 AGMT(0.022)S(0.16)S(0.818)PDATTGQTFG;AGMT(0.021)S(0.129)S(0.85)PDATTGQTFG ; 120.6 0.0039828 22603000 5407.8 6205.4 5503.6 3601.2 3805.4 3689.6 3708.4 3754.9 6705.3 6188.3 TRUE FALSE FALSE 5341.887654 6292.759784 5599.387849 4017.587688 3611.196238 3453.846468 4023.391403 3863.542107 6105.561174 6027.527074 0.886248637 1.04400357 0.92896934 0.666539966 0.599117382 0.573012186 0.667502834 0.640982954 1.012946288 1 12.55735051 -9.240357591 3.868068341 0.953801327 0.621916605 0.925728986 0.048861397 0.050603532 1.706933389 0.008482162 0.014003143 5.75E-10 9.240357591 -0.331884723 AGNALT(ph)PELAPVQIK ddPTM_HeLa_Romidepsin_16h_R1 2 AGNALTPELAPVQIK 15 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 0 AGNALT(1)PELAPVQIK;AGNALT(1)PELAPVQIK ; 168.1 6.04E-05 20363100 7752.2 6790.2 7635.7 5751.5 6978 8054.2 6369.8 7682.3 7834.1 7558.2 TRUE FALSE FALSE 7657.713205 6885.792614 7768.596155 6416.515492 6621.886621 7539.562614 6910.850653 7904.57523 7133.398475 7361.836874 1.040190558 0.935336212 1.055252417 0.871591642 0.899488366 1.024141494 0.938739987 1.073723225 0.968969918 1 12.84585007 -10.26997308 24.87249482 1.018978874 0.96861669 0.031230901 0.06414044 903.9793789 2634749.831 0.010219786 0.011784896 5.37E-11 10.26997308 -0.050362185 AGNLGGGVVTIER ddPTM_HeLa_Romidepsin_16h_R1 1 AGNLGGGVVTIER 13 0 K7ERI7;P35268;K7EP65;K7EKS7;K7ELC4;K7EMH1;K7EJT5 K7ERI7 RPL22 60S ribosomal protein L22 0 0 124.42 0.01075 1152000 103.53 61.368 120.45 55.87 183.46 59.819 114.27 253.71 139.71 97.414 FALSE FALSE TRUE 102.2681365 62.23194031 122.5463817 62.32995228 174.0973516 55.99675896 123.9760909 261.0506986 127.2139877 94.88317024 1.077832204 0.655879648 1.291550245 0.656912623 1.834860188 0.590165346 1.306618346 2.751285585 1.340743436 1 6.568080309 -7.280878403 3.701279059 1.032052436 2.903150607 0.662788213 0.359908941 0.090616502 2.311199861 0.041014158 0.449553646 5.24E-08 7.280878403 1.871098171 AGNNMLLVGVHGPR ddPTM_HeLa_Romidepsin_16h_R1 2 AGNNMLLVGVHGPR 14 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 173.72 9.56E-08 20384500 3911.7 3642.9 4327.6 3826.3 4236.4 4833.1 3449.2 3933.8 3934.7 2797.93 FALSE FALSE TRUE 3864.022696 3694.184842 4402.920063 4268.714809 4020.2007 4524.280508 3742.174962 4047.618296 3582.770577 2725.239375 1.417865429 1.355545085 1.61560856 1.566363252 1.475173424 1.660140591 1.373154592 1.485234043 1.314662708 1 11.41216724 -11.8391658 0.486872533 0.938365733 1.527407809 0.476930985 0.128990568 0.371525464 0.151562124 0.102189789 0.026027924 1.45E-12 11.8391658 0.589042076 AGNSDS(ph)EEDDANGRVELILEPK ddPTM_HeLa_Romidepsin_16h_R1 1 AGNSDSEEDDANGRVELILEPK 22 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;A0A0A0MT65;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 AGNS(0.223)DS(0.777)EEDDANGRVELILEPK 58.345 0.0060821 8466400 1128.6 1311.9 952.62 1106.5 1090.4 997.77 1083.7 1188.4 1268.1 1496 TRUE FALSE FALSE 1114.844189 1330.368963 969.1999515 1234.438736 1034.752819 934.0157172 1175.749451 1222.784479 1154.67796 1457.133704 0.765093955 0.913004043 0.6651414 0.84716916 0.710128944 0.640995205 0.806891946 0.83917109 0.792431028 1 10.50891755 -12.60502952 0.425139675 1.098631716 0.75608022 0.038324721 0.102551244 1.541685944 0.300148385 0.24196869 0.023663253 2.48E-13 12.60502952 -0.342551496 AGPDLPSLPSHALEDEGWAAAAPS(ph)PGSAR ddPTM_HeLa_Romidepsin_16h_R1 4 AGPDLPSLPSHALEDEGWAAAAPSPGSAR 29 0 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 0 AGPDLPSLPSHALEDEGWAAAAPS(0.633)PGS(0.367)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.5)PGS(0.5)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.857)PGS(0.143)AR;AGPDLPSLPSHALEDEGWAAAAPS(0.884)PGS(0.116)AR ;;; 169.14 2.76E-18 180743000 12972.1 12058.5 11483.3 11939 12197.8 9691.5 9250.3 8918.8 14619.8 13620 TRUE FALSE FALSE 12813.99106 12228.25988 11683.16202 13319.44335 11575.30075 9072.244428 10036.02025 9176.851406 13312.16847 13266.15044 0.965916308 0.921763999 0.880674622 1.00401721 0.872544059 0.68386413 0.756513376 0.691749385 1.003468831 1 13.69546217 -8.4540399 3.294933588 0.970781834 0.715666102 0.87686359 0.042010186 0.061526459 1.298845978 0.006445189 0.015115224 3.52E-09 8.4540399 -0.255115731 AGPEEPGDS(ph)PPLR ddPTM_HeLa_Romidepsin_16h_R1 1 AGPEEPGDSPPLR 13 0 A0A0A0MTG6;Q12770-4;Q12770-2;Q12770 A0A0A0MTG6 SCAP Sterol regulatory element-binding protein cleavage-activating protein 1 0 AGPEEPGDS(1)PPLR 91.712 0.020887 2270200 1106.7 1172.2 1070.9 792.2 983.08 1324.2 771.57 1692.5 1147.2 1238.6 TRUE FALSE FALSE 1093.211115 1188.702262 1089.538565 883.7978914 932.9097592 1239.587894 837.1071365 1741.469817 1044.591559 1206.420993 0.906160553 0.985312978 0.903116384 0.732578342 0.773287073 1.027491979 0.693876467 1.443500923 0.865859898 1 10.23651772 -7.245538759 24.8869578 0.917994442 1.443501341 0.674981886 0.114836433 1401.472727 2193489.551 0.015939539 0.545152259 5.68E-08 7.245538759 0.525506899 AGPGS(ph)SPLFSLLPGYR ddPTM_HeLa_Romidepsin_16h_R1 1 AGPGSSPLFSLLPGYR 16 0 Q9H0W8-2;Q9H0W8 Q9H0W8-2 SMG9 Protein SMG9 1 0 AGPGS(0.499)S(0.499)PLFS(0.002)LLPGYR 219.95 2.77E-27 34282000 1578.9 1320.5 1366.8 989.02 988.56 726.31 799.79 860.15 1572.1 1627.3 TRUE FALSE FALSE 1559.655759 1339.090034 1390.588581 1103.375146 938.1100944 679.9011351 867.7241426 885.0370832 1431.487439 1585.022511 0.983995967 0.844839757 0.877330493 0.696125852 0.591859161 0.428953614 0.547452252 0.558375087 0.903133822 1 10.63028762 -9.222155894 0.981576101 0.992720894 0.502245587 0.916755924 0.055810458 0.075857168 0.144425599 0.008543861 0.018806894 6.00E-10 9.222155894 -0.490475307 AGPLSGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AGPLSGKK 8 1 P17844;J3KTA4;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3QKN9;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 1 ; AGPLSGK(1)K;AGPLSGK(1)K 169.06 0.00020809 18658400 8140.3 7874.2 15821.7 8647.3 10777 12070.9 12913.4 4314.7 10022.6 5086 FALSE TRUE FALSE 8041.082893 7985.053194 16097.07005 9647.141513 10227.00948 11299.60845 14010.26387 4439.539037 9126.153554 4953.864987 1.623193792 1.611883492 3.249396198 1.947396939 2.064450586 2.280968189 2.828148105 0.896176833 1.842228962 1 12.27433883 -10.70315077 0.955479253 1.149124467 2.203527644 0.146394338 0.641804434 0.367581861 0.704782645 0.146198791 0.136619623 1.98E-11 10.70315077 1.054403176 AGPSAQEPGSQT(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 2 AGPSAQEPGSQTPLK 15 0 O60271;A0A087X2D8;O60271-9;O60271-4;O60271-2 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 AGPSAQEPGS(0.002)QT(0.998)PLK;AGPSAQEPGS(0.031)QT(0.968)PLK ; 194.77 2.03E-12 12584500 3849.9 3500.8 3915.6 3195.3 4480.6 4807.7 4729 4861.3 3930.5 4051.3 TRUE FALSE FALSE 3802.975938 3550.084354 3983.749375 3564.75562 4251.938263 4500.503486 5130.681142 5001.954046 3578.946236 3946.046642 0.963743281 0.899655954 1.009554559 0.903373919 1.077518501 1.14050945 1.300207932 1.267586144 0.906970079 1 11.94619229 -8.14000468 1.674890319 0.973262157 1.290191906 0.880605328 0.048243684 0.084539901 0.441705446 0.006250441 0.02471871 7.24E-09 8.14000468 0.316929749 AGQAVDDFIEK ddPTM_HeLa_Romidepsin_16h_R1 1 AGQAVDDFIEK 11 0 P52209-2;P52209;K7EMN2;K7EM49;K7EPF6 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 180.97 8.90E-05 5799200 2364 1946.4 2834.7 2106.5 2092.9 2299.5 2022.8 2121 2283.6 2217.8 FALSE FALSE TRUE 2335.186659 1973.80147 2884.036764 2350.063441 1986.091503 2152.569371 2194.616582 2182.367789 2079.349097 2160.181236 1.081014231 0.913720311 1.335090184 1.087901053 0.919409663 0.996476284 1.015940952 1.01027069 0.962580853 1 11.07693664 -8.783152166 24.99478245 1.05660836 0.988479239 0.107958047 0.108468092 465.5987184 535974.4887 0.015613515 0.028318898 1.65E-09 8.783152166 -0.06812912 AGQEPS(ph)PKPGTDVIPAAPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGQEPSPKPGTDVIPAAPR 19 1 I3L0R3;I3L231;Q4VC44-2;Q4VC44;Q4VC44-3 I3L0R3 FLYWCH1 FLYWCH-type zinc finger-containing protein 1 1 0 AGQEPS(0.764)PKPGT(0.236)DVIPAAPR 55.302 0.01872 18971000 3453.8 3104.5 3329 2772.6 2757.6 3585.7 3359.5 3390.5 4255.7 3515.6 TRUE FALSE FALSE 3411.703757 3148.205232 3386.939849 3093.181057 2616.869382 3356.585342 3644.855846 3488.598768 3875.059533 3424.264205 0.996331928 0.919381521 0.989100036 0.903312616 0.764213631 0.980235502 1.064420158 1.01878785 1.131647356 1 11.7415783 -10.29501584 16.88878988 0.998268295 0.946909292 0.143590524 0.087005116 26.54507601 13351.15154 0.013826826 0.015816354 5.07E-11 10.29501584 -0.051359003 AGQTQPNPGILPIQPALT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 AGQTQPNPGILPIQPALTPR 20 0 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 AGQTQPNPGILPIQPALT(1)PR;AGQTQPNPGILPIQPALT(1)PR ; 198.6 1.87E-23 34200000 4916.6 5762.8 4866.2 5202.4 5322.7 5262.2 4404.7 4976.3 5080.3 5541.1 TRUE FALSE FALSE 4856.674588 5843.92885 4950.89417 5803.925966 5051.062757 4925.962403 4778.835108 5120.281389 4625.905244 5397.141423 0.899860539 1.082782234 0.917317851 1.075370369 0.935877414 0.912698411 0.885438185 0.948702468 0.85710284 1 12.39797978 -8.53036639 24.99761041 0.968704975 0.914544248 0.122225158 0.068719058 272.4326932 909519.4558 0.009123493 0.018274919 2.95E-09 8.53036639 -0.054160727 AGRPDPEPS(ph)EPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AGRPDPEPSEPSK 13 1 F5H1N7;Q6ZU35 F5H1N7 KIAA1211 Uncharacterized protein KIAA1211 1 0 AGRPDPEPS(1)EPSK 106.88 0.0025577 0 1144.9 1204.8 1331.5 1019.8 1545.4 1605.8 1275.7 1458 1157.9 1190.5 TRUE FALSE FALSE 1130.945518 1221.761206 1354.674199 1137.714074 1466.532471 1503.194562 1384.057926 1500.18493 1054.334524 1159.570638 0.975314035 1.05363241 1.168255002 0.981151158 1.264720253 1.296337207 1.193595181 1.293741735 0.90924562 1 10.17937499 -9.002943598 0.774122165 0.988448867 1.280864576 0.718294295 0.073734547 0.252815224 0.287407557 0.012761069 0.038269535 9.93E-10 9.002943598 0.292415709 AGRPVMPPPQVPLPTSSIS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 AGRPVMPPPQVPLPTSSISPAK 22 1 P42684-2;P42684-3;P42684-4;P42684-10;P42684-6;P42684;P42684-7;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 AGRPVMPPPQVPLPT(0.018)S(0.061)S(0.205)IS(0.716)PAK 63.701 0.0097744 9721300 5314 4015.3 4336.1 3658.1 3818.9 3719.7 3461 4114 5785.6 4720.1 TRUE FALSE FALSE 5249.230924 4071.827499 4411.568002 4081.066734 3624.007283 3482.023175 3754.977254 4233.032099 5268.121446 4597.471122 1.14176485 0.885666792 0.959564048 0.887676426 0.788261022 0.757377933 0.816748415 0.920730547 1.145873744 1 12.1666248 -9.681713229 1.300000063 1.063956035 0.823220367 0.685440799 0.071775384 0.191749076 0.652297982 0.014134763 0.021984708 2.08E-10 9.681713229 -0.240735667 LTPVS(ph)PESSS(ph)TEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTPVSPESSSTEEK 14 0 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 LTPVS(0.992)PES(0.008)S(0.047)S(0.892)T(0.06)EEK 171.11 0.00049333 14332000 3902.2 3206.6 3385.6 1876.9 1890.8 1599.3 1124.7 1450 3420.8 3379.3 TRUE FALSE FALSE 3854.638485 3251.742599 3444.524948 2093.916009 1794.30542 1497.109892 1220.23199 1491.953462 3114.83508 3291.505299 1.171086824 0.9879196 1.046489261 0.636157569 0.545132168 0.454840493 0.370721563 0.453273906 0.946325404 1 11.6845318 -9.094864157 1.605452522 1.07959641 0.429546818 0.931718895 0.073703487 0.061585212 0.312732221 0.012178366 0.024064262 8.04E-10 9.094864157 -0.650049592 down AGS(ph)ISTLDSLDFAR ddPTM_HeLa_Romidepsin_16h_R1 4 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 0 AGS(0.788)IS(0.204)T(0.008)LDSLDFAR;AGS(0.986)IS(0.013)T(0.001)LDSLDFAR;AGS(0.915)IS(0.066)T(0.019)LDSLDFAR;AGS(0.76)IS(0.224)T(0.016)LDSLDFAR ;;; 259.27 6.96E-68 46177600 8895.26 9007.15 8579.57 3029.21 13776.6 17217.7 13403.6 16359.6 9715.02 9277.6 TRUE FALSE FALSE 8786.84115 9133.952894 8728.893817 3379.461513 13073.52869 16117.54454 14542.10145 16832.93921 8846.084279 9036.566615 0.972365006 1.010776912 0.965952467 0.373976274 1.446736272 1.783591626 1.609250733 1.862758272 0.978920939 1 13.14155902 -8.533572667 24.92971013 0.947042524 1.717198433 0.805110712 0.19352906 65.59484782 152914.6353 0.027086096 0.0542135 2.93E-09 8.533572667 0.770155909 AGS(ph)PSPQPSGELPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSPSPQPSGELPR 14 0 Q92619 Q92619 HMHA1 Minor histocompatibility protein HA-1;Minor histocompatibility antigen HA-1 1 0 AGS(0.999)PS(0.001)PQPS(0.001)GELPR 113.67 0.0049854 68999000 974.58 937.2 816.07 838.34 1075.7 818.83 862.6 875.38 848.38 715.19 TRUE FALSE FALSE 962.7014441 950.3939262 830.273356 935.2728153 1020.803015 766.5094057 935.8692225 900.7077392 772.498768 696.6092607 1.381981978 1.364314229 1.191878149 1.342607496 1.465388235 1.100343405 1.343463654 1.292988466 1.108941284 1 9.444205842 -12.33306415 0.975009648 0.993551167 1.313026853 0.494910423 0.101350113 0.310842583 0.512177015 0.071334502 0.017353411 4.64E-13 12.33306415 0.319475686 AGS(ph)SPAQGAQNEPPR ddPTM_HeLa_Romidepsin_16h_R1 3 AGSSPAQGAQNEPPR 15 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 AGS(0.894)S(0.106)PAQGAQNEPPR;AGS(0.894)S(0.106)PAQGAQNEPPR;AGS(0.625)S(0.375)PAQGAQNEPPR ;; 192.4 1.65E-12 24610200 10136.3 9067.7 8645.9 10042.7 8434.9 8424.5 8031 8889.4 11132 9349.8 TRUE FALSE FALSE 10012.75488 9195.355319 8796.378263 11203.88423 8004.435578 7886.201639 8713.15294 9146.600764 10136.32604 9106.890848 1.099470175 1.009714015 0.965903557 1.230264468 0.878942738 0.865959829 0.956764837 1.004360425 1.113039149 1 13.15274288 AGS(ph)STPGDAPPAVAEVQGR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 AGS(0.709)S(0.049)T(0.242)PGDAPPAVAEVQGR 88.637 0.0043563 85578000 999.03 929.4 903.3 643.47 738.99 835.24 630.24 957.53 858.4 752.16 TRUE FALSE FALSE 986.8534381 942.4841176 919.0215576 717.871029 701.2765827 781.8708596 683.7725699 985.2346198 781.6225541 732.6187748 1.347021769 1.286459138 1.254433532 0.979869823 0.957218961 1.06722744 0.933326572 1.344812137 1.066888511 1 9.516918863 -9.260396321 24.99999994 1.185352932 1.044729876 0.178346676 0.142951787 150.4685006 3606422.368 0.025786516 0.041189148 5.49E-10 9.260396321 -0.140623055 AGSFT(ph)GTSDPEAAPAR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSFTGTSDPEAAPAR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 AGS(0.085)FT(0.91)GT(0.004)S(0.001)DPEAAPAR 203.74 1.05E-21 0 1320.6 1314.8 1181.3 1283.5 1064.2 998.12 847.18 931.07 1246.6 1291.6 TRUE FALSE FALSE 1304.504019 1333.309789 1201.860031 1431.904309 1009.889903 934.3433533 919.1394481 958.0090415 1135.100974 1258.044046 1.036930323 1.05982759 0.955340185 1.138198868 0.802746061 0.742695263 0.730609911 0.761506757 0.90227443 1 10.29696672 -8.632771718 5.851679231 1.023419079 0.748344939 0.817351252 0.0596006 0.043481367 2.086592704 0.006180621 0.012475456 2.33E-09 8.632771718 -0.27507414 AGSFTGTS(ph)DPEAAPAR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSFTGTSDPEAAPAR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 AGS(0.026)FT(0.147)GT(0.232)S(0.595)DPEAAPAR 155.39 0.00024014 5852000 1196.6 1294.2 1209 1307.7 1048.5 1203.1 1054.8 1256.2 1484.6 1219.3 TRUE FALSE FALSE 1182.015379 1312.419782 1230.042138 1458.902427 994.9911325 1126.225793 1144.394686 1292.546165 1351.813658 1187.62241 0.995278776 1.105081691 1.035718194 1.228422783 0.837800907 0.948302914 0.963601458 1.088347739 1.138252062 1 10.21386051 -5.936768267 9.501889304 1.010246444 1.080614718 0 0.107614097 0 0 0.012475101 0 1.16E-06 5.936768267 0.070368274 AGSIS(ph)TLDSLDFAR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSISTLDSLDFAR 14 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 0 AGS(0.013)IS(0.428)T(0.319)LDS(0.24)LDFAR 86.803 0.0043284 0 1781.8 1550.5 1851.5 1069.1 1640.8 2227.5 1867.6 2193.7 2058.6 1931.9 TRUE FALSE FALSE 1760.082736 1572.32798 1883.724581 1192.714372 1557.063853 2085.169939 2026.233897 2257.171248 1874.47366 1881.708959 0.935363956 0.835585106 1.001071165 0.633846359 0.827473263 1.108125637 1.076805149 1.199532604 0.996154932 1 10.87782779 -8.165896316 6.864667022 0.927064802 1.125949579 0.461647587 0.113089042 0.219070459 13.54399812 0.017069424 0.043973293 6.83E-09 8.165896316 0.198884778 AGSISS(ph)EEVDGSQGNMMR ddPTM_HeLa_Romidepsin_16h_R1 2 AGSISSEEVDGSQGNMMR 18 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 AGS(0.002)IS(0.055)S(0.941)EEVDGS(0.002)QGNMMR;AGS(0.014)IS(0.122)S(0.858)EEVDGS(0.005)QGNMMR ; 109.48 0.0010161 14147300 3438.8 3766.8 3283.6 3252.2 3487.6 3513 3751.9 3771.4 3764.5 3844.9 TRUE FALSE FALSE 3396.886583 3819.829109 3340.749681 3628.234666 3309.614758 3288.530638 4070.586292 3880.519509 3427.793692 3745.008944 0.90704365 1.019978635 0.892053859 0.968818692 0.883740148 0.878110223 1.086936334 1.03618431 0.91529653 1 11.87075345 -7.747654432 24.99763695 0.946776457 1.061560369 0.506953959 0.049211729 166.4843981 301897.7184 0.007290411 0.026990135 1.79E-08 7.747654432 0.114783911 AGSNEDPILAPS(ph)GTPPPTIPPDETFGGR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 0 AGSNEDPILAPS(0.57)GT(0.424)PPPT(0.007)IPPDETFGGR 60.379 0.00092819 50066000 4088.7 4202.6 3707.2 4201.2 4318 3783.6 3168 4131.2 4453.7 4116.7 TRUE FALSE FALSE 4038.865352 4261.764313 3771.722261 4686.962511 4097.636347 3541.840171 3437.089841 4250.729754 4055.349918 4009.747541 1.007261757 1.062851032 0.940638338 1.168892172 1.021918788 0.883307524 0.857183602 1.060099099 1.01137288 1 11.96929569 -8.277188644 24.2701336 1.017038352 0.925895429 0.246209394 0.074821669 554.4221682 854382.36 0.010086706 0.022635704 5.28E-09 8.277188644 -0.091142923 AGSNEDPILAPSGT(ph)PPPTIPPDETFGGR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSNEDPILAPSGTPPPTIPPDETFGGR 28 0 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 0 AGSNEDPILAPS(0.082)GT(0.918)PPPTIPPDETFGGR 117.05 1.11E-09 46380000 6883.6 6931.3 6567.4 7419.1 7456.5 7181.6 5984.2 7694.7 7874.9 7371.4 TRUE FALSE FALSE 6799.700036 7028.879023 6681.702842 8276.93125 7075.966981 6722.718938 6492.497799 7917.334004 7170.549221 7179.889965 0.947047945 0.978967513 0.930613543 1.152793607 0.985525825 0.936326179 0.904261462 1.102709657 0.998699041 1 12.80974602 -7.236237463 23.61110545 0.978275903 1.102709989 0.23834319 0.06471732 4040.139277 3784993.76 0.008743344 0.752127122 5.80E-08 7.236237463 0.124434086 AGSQEAEVGS(ph)DGER ddPTM_HeLa_Romidepsin_16h_R1 2 AGSQEAEVGSDGER 14 0 J3KN78;Q9UK96 J3KN78 FBXO10 F-box only protein 10 1 0 AGSQEAEVGS(1)DGER;AGSQEAEVGS(1)DGER ; 140.49 0.00092528 9483500 1486.96 1396.71 1384.52 1572.52 1624.72 1668.46 1865.11 1391.74 1450.16 1400.76 TRUE FALSE FALSE 1468.83636 1416.37292 1408.61699 1754.342161 1541.804476 1561.850791 2023.532397 1432.007801 1320.454058 1364.368053 1.076569006 1.03811645 1.032431818 1.285827645 1.130050262 1.144743009 1.483127952 1.049575881 0.967813673 1 10.41401716 -9.272646323 24.32259351 1.03700007 1.224327525 0.432189117 0.11147356 355.2063764 770908.5304 0.015695388 0.024120528 5.34E-10 9.272646323 0.187327455 AGSS(ph)PAQGAQNEPPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSSPAQGAQNEPPR 15 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 AGS(0.238)S(0.762)PAQGAQNEPPR 115.26 0.0038803 3244000 935.11 961.65 860.86 821.02 817.72 751.7 853.65 823.07 1048.8 876.93 TRUE FALSE FALSE 923.7125196 975.1881339 875.8429072 915.9501954 775.9886971 703.668796 926.1590097 846.8842319 954.9927012 854.1472322 1.081444141 1.141709646 1.025400393 1.072356335 0.908495243 0.823826115 1.084308389 0.991496782 1.118065674 1 9.738340963 -8.768906047 24.99987762 1.048989664 0.952322432 0.36438044 0.074371559 170.9871041 572500.3285 0.01118869 0.020570101 1.70E-09 8.768906047 -0.096667231 AGSS(ph)TPGDAPPAVAEVQGR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 AGSS(0.5)T(0.5)PGDAPPAVAEVQGR 229.69 3.43E-39 7165200 2154.9 2152.8 2002.2 2320.8 2011.4 1881.5 1795.1 1841.9 2303.9 1987.6 TRUE FALSE FALSE 2128.63525 2183.107175 2037.047451 2589.141816 1908.750752 1761.278222 1947.575749 1895.19247 2097.833414 1935.961865 1.099523337 1.127660216 1.052214657 1.337392984 0.985944396 0.909769068 1.005999025 0.978941013 1.083612984 1 10.91883482 -8.548800071 24.99989325 1.076928702 0.965486345 0.339584557 0.090788796 247.5436521 238743.1954 0.014115184 0.028231004 2.83E-09 8.548800071 -0.111442358 AGSST(ph)PGDAPPAVAEVQGR ddPTM_HeLa_Romidepsin_16h_R1 3 AGSSTPGDAPPAVAEVQGR 19 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 AGS(0.002)S(0.008)T(0.99)PGDAPPAVAEVQGR;AGS(0.002)S(0.009)T(0.99)PGDAPPAVAEVQGR;AGS(0.003)S(0.013)T(0.984)PGDAPPAVAEVQGR ;; 129.05 0.0017551 74116000 8197.8 8739.6 7665.1 7510.7 8085.6 7940.6 6027.5 7317.3 8871.5 7990.4 TRUE FALSE FALSE 8097.88206 8862.636318 7798.50785 8379.122473 7672.96166 7433.221287 6539.4757 7529.014531 8078.010821 7782.808256 1.040483306 1.138745299 1.002017215 1.076619415 0.985885995 0.955082156 0.840246282 0.967390469 1.037930083 1 12.9260751 -8.250408295 2.408976699 1.031414581 0.904484644 0.556041462 0.050219366 0.17523189 1.975911104 0.007254515 0.021152406 5.62E-09 8.250408295 -0.126929937 AGT(ph)EDEEEEEEGRR ddPTM_HeLa_Romidepsin_16h_R1 2 AGTEDEEEEEEGRR 14 1 F8WBH7;O95456-2;O95456 F8WBH7 PSMG1 Proteasome assembly chaperone 1 1 0 AGT(1)EDEEEEEEGRR;AGT(1)EDEEEEEEGRR ; 144.29 0.00025586 36693000 6934.5 6794.2 6534 4712.4 6408.5 6207 5567.7 5696.2 7051.9 6449.8 TRUE FALSE FALSE 6849.979647 6889.848926 6647.721529 5257.269861 6081.450332 5810.392732 6040.620299 5861.01056 6421.160402 6282.233266 1.090373336 1.096719691 1.058178079 0.836847286 0.968039561 0.924892866 0.961540274 0.932950165 1.022114291 1 12.6170618 -9.291732668 24.72461425 1.049730306 0.929293502 0.692540199 0.042763451 310.0629825 253064.6402 0.007543397 0.011523724 5.11E-10 9.291732668 -0.120436803 AGT(ph)EDEEEEEEGRRETPEDR ddPTM_HeLa_Romidepsin_16h_R1 1 AGTEDEEEEEEGRRETPEDR 20 2 F8WBH7;O95456-2;O95456 F8WBH7 PSMG1 Proteasome assembly chaperone 1 1 0 AGT(1)EDEEEEEEGRRETPEDR 56.404 0.010044 6223000 1780.7 1803.9 1535.7 1805.4 1763.3 1850 1677.6 1623.9 1886.1 1542.8 TRUE FALSE FALSE 1758.996143 1829.295352 1562.428214 2014.148843 1673.312221 1731.790971 1820.095302 1670.884984 1717.402492 1502.717834 1.170543201 1.217324577 1.039734925 1.340337353 1.113523899 1.152439222 1.211202304 1.111908668 1.142864252 1 10.55335842 -12.12675048 0.674624811 0.986517403 1.173515142 0.077417868 0.087203306 0.622738505 0.462183882 0.066616069 0.015064574 7.47E-13 12.12675048 0.186997739 AGT(ph)PVSELTK ddPTM_HeLa_Romidepsin_16h_R1 2 AGTPVSELTK 10 0 O75113 O75113 N4BP1 NEDD4-binding protein 1 1 0 AGT(1)PVSELTK;AGT(0.959)PVS(0.005)ELT(0.036)K ; 140.78 0.0096986 125450000 13061.5 12792.2 13212.1 10112 10593.7 10511.3 8119.5 9114.2 12599 12492.1 TRUE FALSE FALSE 12902.30141 12972.28893 13442.05106 11281.19702 10053.06396 9839.661854 8809.170127 9377.904997 11472.11389 12167.55344 1.060385843 1.066137822 1.104745594 0.927154097 0.82621901 0.808680389 0.723988612 0.770730537 0.94284475 1 13.57075149 -8.823673054 2.071854637 1.037791525 0.767400059 0.86720972 0.046661049 0.068461798 0.598349681 0.006351675 0.013490964 1.50E-09 8.823673054 -0.270391466 AGTEDEEEEEEGRR ddPTM_HeLa_Romidepsin_16h_R1 2 AGTEDEEEEEEGRR 14 1 F8WBH7;O95456-2;O95456 F8WBH7 PSMG1 Proteasome assembly chaperone 1 0 0 ; ; 201.09 8.90E-17 10307800 3928.5 3500.1 3646 2590.9 4065.1 4148.9 3224.4 4090.2 4175.4 4034.6 FALSE FALSE TRUE 3880.617931 3549.3745 3709.457101 2890.472049 3857.642778 3883.79868 3498.280456 4208.543484 3801.941767 3929.78051 0.987489739 0.903199171 0.943934932 0.73553015 0.981643318 0.988299135 0.890197416 1.070936016 0.967469241 1 11.94023302 -10.33907903 6.109224558 0.994406156 0.926254578 0.080110793 0.081950251 0.349798556 22.03879252 0.013496035 0.015400034 4.58E-11 10.33907903 -0.068151579 AGTFIAPPVYSNITPYQS(ph)HLRSPVR ddPTM_HeLa_Romidepsin_16h_R1 1 AGTFIAPPVYSNITPYQSHLRSPVR 25 1 A0A1C7CYX1;Q6PJG2;A0A0A0MSU2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 0 AGTFIAPPVYSNIT(0.005)PY(0.006)QS(0.495)HLRS(0.495)PVR 89.968 1.88E-05 25772000 2261.6 2348.7 1680.8 2108.2 3383.2 2876.2 2769.9 3021.8 2455.6 2193.4 TRUE FALSE FALSE 2234.034749 2381.76506 1710.053619 2351.960003 3210.54268 2692.420103 3005.175237 3109.231015 2235.964986 2136.415152 1.045693178 1.114841869 0.800431329 1.100890902 1.502770974 1.260251361 1.406643851 1.455349637 1.046596671 1 11.06097631 -8.880493281 5.415012206 1.013093928 1.394140836 0.798127447 0.096382892 0.066150867 2.893123952 0.01331969 0.024499243 1.32E-09 8.880493281 0.381046907 AGTFQAFEQFGQQLLAHGHYAS(ph)PEIK ddPTM_HeLa_Romidepsin_16h_R1 1 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 0 AGTFQAFEQFGQQLLAHGHY(0.003)AS(0.997)PEIK 66.01 0.00027662 2416200 1255.8 1258.3 1322.9 1272 1226 1212.7 1254.1 1421.7 1625 1301 TRUE FALSE FALSE 1240.493827 1276.01438 1345.92452 1419.074625 1163.432645 1135.212384 1360.623223 1462.834646 1479.65593 1267.199832 0.978925182 1.006955926 1.062124919 1.119850704 0.918113004 0.895843224 1.073724276 1.154383554 1.167657928 1 10.30742833 -7.527512257 24.76993322 0.994929799 1.134218774 0.162295078 0.081552126 69.58760896 372007.4746 0.008543409 0.032233345 2.97E-08 7.527512257 0.139288975 AGTFQAFEQFGQQLLAHGHYASPEIK ddPTM_HeLa_Romidepsin_16h_R1 1 AGTFQAFEQFGQQLLAHGHYASPEIK 26 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 140.07 1.06E-07 1931100 663.47 775.08 818.42 711.18 746.52 796.33 501.36 628.95 778.35 708.51 FALSE FALSE TRUE 655.3833724 785.9915966 832.6642568 793.4099778 708.4222987 745.447083 543.9455059 647.1476759 708.7324266 690.1028081 0.949689473 1.138948556 1.206580015 1.149698231 1.026546031 1.080197145 0.788209379 0.93775546 1.026995425 1 9.430667493 -7.765733194 24.99999435 1.025394525 0.86298241 0.391085388 0.090409913 99.19032404 577534.7983 0.015098242 0.047729729 1.72E-08 7.765733194 -0.162412115 AGTGYAS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 AGTGYASPDR 10 0 O43379;O43379-4 O43379 WDR62 WD repeat-containing protein 62 1 0 AGTGYAS(1)PDR 97.163 0.028142 4850300 1760.6 2032.2 1934.1 1053.2 1688.7 1557.7 1514.6 990.41 2098 2185.4 TRUE FALSE FALSE 1739.14113 2060.809365 1967.762199 1174.975939 1602.519338 1458.167997 1643.250086 1019.065951 1910.349625 2128.622993 0.817026376 0.96814202 0.924429646 0.551988747 0.752843196 0.685028773 0.771977984 0.478744218 0.897457949 1 11.05570474 -9.276745648 24.53505936 0.91709846 0.662866598 0.681737977 0.093069455 319.2861915 511796.1935 0.015488957 0.023717789 5.29E-10 9.276745648 -0.254231862 AGTLSITEFADMLS(ph)GNAGGFRSR ddPTM_HeLa_Romidepsin_16h_R1 1 AGTLSITEFADMLSGNAGGFRSR 23 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 AGTLSITEFADMLS(0.5)GNAGGFRS(0.5)R 53.768 0.025738 8362800 978.4 940.68 899.57 2330.4 819.66 919.33 685.84 727.43 1095.4 811.03 TRUE FALSE FALSE 966.4748845 953.9229177 915.2266385 2599.851813 777.8296916 860.58778 744.0952325 748.4770394 997.4246805 789.9593237 1.223448924 1.20755954 1.158574386 3.291121118 0.984645245 1.089407713 0.941941199 0.947488076 1.262627898 1 9.625634558 -5.554846445 20.2466663 1.227461589 1.164729822 0 0.674888839 0 0 0.08742097 0 2.79E-06 5.554846445 -0.062731768 AGTLSITEFADMLSGNAGGFRS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 AGTLSITEFADMLSGNAGGFRSR 23 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 AGTLSITEFADMLS(0.028)GNAGGFRS(0.972)R;AGTLSITEFADMLS(0.045)GNAGGFRS(0.955)R ; 85.17 0.00029755 207584000 7594.4 6672.6 5464.2 16084 5960.7 5198.2 5167.7 6186.3 8202.3 6242.7 TRUE FALSE FALSE 7501.836532 6766.537038 5559.302109 17943.70776 5656.503237 4866.051796 5606.644309 6365.29083 7468.665745 6080.513754 1.233750442 1.112823244 0.914281644 2.951018365 0.93026732 0.800269844 0.922067532 1.046834377 1.228295181 1 12.56997751 -5.345023905 13.25825066 1.169787845 0.566496115 0 0.595655045 0 0 0.07543133 0 4.52E-06 5.345023905 -0.603291731 AGTQIENIDEDFRDGLK ddPTM_HeLa_Romidepsin_16h_R1 2 AGTQIENIDEDFRDGLK 17 1 O43707;O43707-3;F5GXS2;K7EP19 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 139.08 0.00096609 39420000 5452.8 4711.6 5749.4 3797 5828.3 5888.2 5021.2 5378.8 5653.5 5301.5 FALSE FALSE TRUE 5386.339176 4777.930028 5849.465895 4236.027005 5530.860103 5511.963023 5447.700603 5534.427092 5147.836801 5163.766266 1.043102824 0.925280073 1.132790602 0.820336705 1.071090328 1.067430774 1.0549859 1.071781101 0.996915146 1 12.33420798 AGTQIENIEEDFRDGLK ddPTM_HeLa_Romidepsin_16h_R1 1 AGTQIENIEEDFRDGLK 17 1 P12814-2;P12814;P12814-3;P12814-4;G3V2N5;G3V5M4;G3V380 P12814-2 ACTN1 Alpha-actinin-1 0 0 84.653 0.016 6423900 943.27 1033.2 981.05 1015.8 1017.5 862.55 938.06 1056.2 1211.6 1361.9 FALSE FALSE TRUE 931.7730624 1047.745417 998.1247637 1133.251575 965.5731782 807.4358388 1017.738793 1086.759481 1103.231461 1326.517642 0.702420408 0.789846576 0.752439871 0.854305695 0.727900744 0.608688353 0.767225977 0.819257465 0.831674926 1 10.37342815 -12.34283376 0.856662481 1.014958466 0.748324466 0.315444027 0.081463881 0.330989503 0.395049906 0.060188351 0.012693425 4.54E-13 12.34283376 -0.266634001 AGVLAHLEEER ddPTM_HeLa_Romidepsin_16h_R1 2 AGVLAHLEEER 11 0 P35579;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35579-2;P35580 MYH9;MYH10 Myosin-9;Myosin-10 0 0 ; ; 133.91 0.0020023 58876000 5729.2 5976.2 6910.7 4917.7 7259.8 6518 7197.5 6164.2 6567.9 7116.5 FALSE FALSE TRUE 5659.370307 6060.3331 7030.977835 5486.307612 6889.305316 6101.520836 7808.85547 6342.551402 5980.450574 6931.612304 0.816457998 0.874303529 1.014335125 0.791490835 0.993896516 0.880245543 1.126556871 0.915018198 0.86277915 1 12.75897525 -7.790432281 24.97124706 0.911305074 1.020787815 0.219927979 0.087015901 224.3861897 193261.0305 0.012844722 0.038543649 1.62E-08 7.790432281 0.109482741 AGVLT(ph)PPDLGPHPPPPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 AGVLTPPDLGPHPPPPAPR 19 0 I3L2J0 I3L2J0 CIC 1 0 AGVLT(1)PPDLGPHPPPPAPR 118.84 0.00063815 8518700 1752.7 1784.7 1560.9 1432.7 1853.1 1557.9 1757.7 1644.4 2153.3 1585 TRUE FALSE FALSE 1731.337418 1809.825053 1588.06681 1598.355515 1758.529392 1458.355218 1906.998994 1691.97812 1960.703455 1543.821472 1.121462196 1.172302035 1.028659621 1.035324061 1.139075615 0.944639808 1.235245804 1.095967475 1.270032508 1 10.59229021 -12.33782516 1.061042832 0.999975264 1.09723471 0 0.113648771 0.688856136 1.387951388 0.049730307 0.013064049 4.59E-13 12.33782516 0.097259446 AGVVNGTGAPGQS(ph)PGAGR ddPTM_HeLa_Romidepsin_16h_R1 4 AGVVNGTGAPGQSPGAGR 18 0 H0Y4T7;E7ESY4;Q13330-3;Q13330;Q13330-2 H0Y4T7 MTA1 Metastasis-associated protein MTA1 1 0 AGVVNGT(0.025)GAPGQS(0.975)PGAGR;AGVVNGTGAPGQS(1)PGAGR;AGVVNGTGAPGQS(1)PGAGR;AGVVNGTGAPGQS(1)PGAGR ;;; 174.87 6.99E-08 30674400 9553.9 8797.6 8011.8 4653.29 8330.7 9157.3 8576.4 8081.2 9062 8715.5 TRUE FALSE FALSE 9437.453392 8921.452844 8151.242018 5191.325284 7905.553293 8572.178084 9304.879202 8315.016772 8251.472024 8489.070054 1.111718166 1.050934058 0.960204353 0.611530504 0.931262582 1.009790004 1.096101121 0.979496779 0.972011301 1 13.05139081 -9.705273585 5.126947462 1.054186727 0.92635533 0.136890993 0.122955153 0.269436011 14.61166931 0.020773752 0.029284953 1.97E-10 9.705273585 -0.127831397 AGY(ph)RKDLGAPKGMGSGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AGYRKDLGAPKGMGSGSK 18 3 Q86VF2-5 Q86VF2-5 2 0 AGY(1)RKDLGAPKGMGS(0.415)GS(0.585)K 44.312 0.025236 21317000 5115.3 4838.6 4721.7 4100.3 3899.7 3870.3 3616.6 4104 5081 4858 TRUE FALSE FALSE 5052.952756 4906.717938 4803.879208 4574.395978 3700.683757 3623.000321 3923.793914 4222.742765 4626.542634 4731.78846 1.067873765 1.036968998 1.015235412 0.966737211 0.782089856 0.765672505 0.829241194 0.892420023 0.977757707 1 12.20816986 -8.911859888 3.591183653 1.031217355 0.81471219 0.85172376 0.03975278 0.062013802 1.577329194 0.006303942 0.011850779 1.23E-09 8.911859888 -0.216505165 AHADDELAALR ddPTM_HeLa_Romidepsin_16h_R1 2 AHADDELAALR 11 0 P48681 P48681 NES Nestin 0 0 ; ; 181.87 3.51E-06 4788100 1614.15 1236 1183 1276.15 1705.86 1375.47 1158.47 1254.8 1422.32 1398.28 FALSE FALSE TRUE 1594.476119 1253.40044 1203.589619 1423.704467 1618.803599 1287.581906 1256.870413 1291.105658 1295.104137 1361.952484 1.170728155 0.920296747 0.883723649 1.045340777 1.188590364 0.945394146 0.922844539 0.947981426 0.950917269 1 10.41146066 -10.25129861 24.95770272 1.08062163 0.982631096 0.029915014 0.09880479 951.6841653 2342217.571 0.017644287 0.021479955 5.61E-11 10.25129861 -0.097990534 AHAS(ph)PFSGALTPSAPPGPEMNR ddPTM_HeLa_Romidepsin_16h_R1 2 AHASPFSGALTPSAPPGPEMNR 22 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 AHAS(0.861)PFS(0.126)GALT(0.005)PS(0.007)APPGPEMNR;AHAS(0.927)PFS(0.041)GALT(0.006)PS(0.026)APPGPEMNR ; 152.66 1.07E-11 7207800 3248.2 3698.1 3145.45 2962.38 5284.5 6501.9 5106.4 5842 4943.1 4217.9 TRUE FALSE FALSE 3208.609689 3750.161949 3200.195238 3304.904314 5014.812246 6086.449574 5540.137489 6011.029053 4500.976756 4108.31835 0.781003178 0.912821653 0.778955029 0.804442118 1.220648406 1.481494143 1.348517086 1.46313614 1.095576431 1 12.00433226 -8.589240604 3.725783109 0.880368554 1.417081445 0.852643675 0.100810696 0.057734169 1.613744032 0.014441006 0.030699545 2.57E-09 8.589240604 0.536712891 AHAWPS(ph)PYKDYEVK ddPTM_HeLa_Romidepsin_16h_R1 1 AHAWPSPYKDYEVK 14 1 Q8NFJ5 Q8NFJ5 GPRC5A Retinoic acid-induced protein 3 1 0 AHAWPS(0.75)PY(0.249)KDY(0.001)EVK 64.588 0.026723 26594000 2059.1 3093.7 2721.1 1733.7 3177.3 4716.1 2107.8 4026.7 2411.6 2633.1 TRUE FALSE FALSE 2034.002897 3137.25319 2768.459604 1934.158551 3015.150525 4414.756431 2286.836479 4143.206211 2195.900456 2564.691682 0.793078915 1.223247695 1.079451235 0.754148565 1.175638595 1.721359515 0.891661362 1.615479256 0.85620446 1 11.32456969 -8.530643652 11.70726051 0.933525619 1.372857071 0.419773852 0.240707637 0.22032976 323.0658179 0.032747639 0.066434652 2.95E-09 8.530643652 0.439331453 AHFNAMFQPSS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 AHFNAMFQPSSPTR 14 0 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 0 AHFNAMFQPS(0.311)S(0.506)PT(0.183)R 64.588 0.021975 48675000 5171.8 2905.5 4407.8 1155.5 4510.5 3300.1 4791.6 3321 5443.1 4355.7 TRUE FALSE FALSE 5108.764112 2946.403705 4484.51591 1289.104347 4280.312354 3089.234261 5198.598384 3417.087895 4956.255504 4242.538286 1.204176313 0.694490776 1.05703605 0.303852142 1.008903648 0.728157073 1.225350965 0.805434781 1.168228822 1 12.05071196 -10.26630946 24.98529872 1.096416592 0.838191391 0.235975522 0.239236785 465.6982825 2389198.544 0.03899072 0.045334672 5.42E-11 10.26630946 -0.258225201 AHGELHEQFK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AHGELHEQFKR 11 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 0 1 ; AHGELHEQFK(1)R;AHGELHEQFK(1)R 105.17 0.0019196 4646600 1122.79 1147.31 1344.57 1037.31 1279.91 1080.35 1109.21 1126.93 1241.28 1142.33 FALSE TRUE FALSE 1109.105004 1163.46186 1367.971677 1157.248663 1214.591417 1011.319122 1203.42627 1159.535942 1130.256808 1112.652102 0.996812033 1.04566545 1.229469368 1.040081316 1.091618319 0.908926627 1.081583603 1.042137016 1.015822292 1 10.11978685 -10.18799487 5.148102 0.998504308 1.064888291 0.11859183 0.073497731 0.317710119 15.68676721 0.012153588 0.01488864 6.49E-11 10.18799487 0.066383983 AHGGYSVFAGVGER ddPTM_HeLa_Romidepsin_16h_R1 2 AHGGYSVFAGVGER 14 0 H0YH81;P06576;F8W0P7;H0YI37;F8W079 H0YH81 ATP5B "ATP synthase subunit beta;ATP synthase subunit beta, mitochondrial" 0 0 ; ; 107.99 0.0015785 2099050 785.39 867.56 804.06 554.33 1634.58 1773.74 1318.6 1268.35 1481.62 915.38 FALSE FALSE TRUE 775.8173646 879.7735325 818.054327 618.4242428 1551.161283 1660.403738 1430.601851 1305.047706 1349.100196 891.5982956 0.87014227 0.986737566 0.917514458 0.693613083 1.739753531 1.862277829 1.604536323 1.463717139 1.513125589 1 9.800250049 -8.753562815 24.99786335 0.924175166 1.676976488 0.676199401 0.223976322 40.45296323 128384.5712 0.018747301 0.036955914 1.76E-09 8.753562815 0.752801322 AHLDHIPDYTPPLLT(ph)TISPEQESDER ddPTM_HeLa_Romidepsin_16h_R1 1 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 0 AHLDHIPDY(0.003)T(0.072)PPLLT(0.607)T(0.101)IS(0.208)PEQES(0.009)DER 128.71 4.17E-07 6836800 1458.4 1425.2 1719.2 1240.5 1379.3 1388.8 1492.8 1441.9 1613 1379.2 TRUE FALSE FALSE 1440.62446 1445.264003 1749.121955 1383.932447 1308.909174 1300.060162 1619.598395 1483.619102 1468.72924 1343.368185 1.072397334 1.075850998 1.302042116 1.030195937 0.974348796 0.967761613 1.205625094 1.10440244 1.093318464 1 10.39163905 -11.55338275 0.901395263 1.007267206 1.091410227 0.002699765 0.099115627 0.911715883 1.513808426 0.039503388 0.020577019 2.80E-12 11.55338275 0.084143021 AHLDHIPDYTPPLLTTIS(ph)PEQESDER ddPTM_HeLa_Romidepsin_16h_R1 1 AHLDHIPDYTPPLLTTISPEQESDER 26 0 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;K7EM61 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 0 AHLDHIPDYTPPLLT(0.002)T(0.006)IS(0.882)PEQES(0.11)DER 98.033 2.18E-06 7598700 1247.4 1359 1109.3 1239.5 1314.6 1461.8 1079.6 1306.8 1218.7 1431.9 TRUE FALSE FALSE 1232.196209 1378.132038 1128.606901 1382.816822 1247.511057 1368.395698 1171.301197 1344.610196 1109.69642 1394.699032 0.883485384 0.988121456 0.809211791 0.991480449 0.894466138 0.981140495 0.839823625 0.964086277 0.795652965 1 10.44573811 -12.46090263 1.125508589 1.001293859 0.915188592 0 0.087438106 0.577963016 1.277440626 0.039962701 0.009284419 3.46E-13 12.46090263 -0.086105267 AHLGTALK(ac)ANPFGGASHAK ddPTM_HeLa_Romidepsin_16h_R1 1 AHLGTALKANPFGGASHAK 19 1 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 1 AHLGTALK(1)ANPFGGASHAK 67.846 0.0049035 823020 269.6 231.13 356.23 174.93 513.87 530.17 283.56 330.01 457.67 433.89 FALSE TRUE FALSE 266.3140115 234.3838542 362.4300337 195.1562297 487.6452964 496.293848 307.6455793 339.5583187 416.7348489 422.6174753 0.630153808 0.554600479 0.857584116 0.461779839 1.15386922 1.174333474 0.727952812 0.803464926 0.986080494 1 8.723208614 AHLMEIQVNGGTVAEK ddPTM_HeLa_Romidepsin_16h_R1 1 AHLMEIQVNGGTVAEK 16 0 B5MCW2;G5E9G0;P39023;H7C3M2;H7C422 B5MCW2 RPL3 60S ribosomal protein L3 0 0 101.04 0.00069044 0 810.83 898.03 732.31 660.57 876.21 619.27 639.89 721.33 873.57 785.31 FALSE FALSE TRUE 800.9472921 910.6724899 745.0555484 736.9482115 831.4937341 579.7006456 694.2422406 742.2005455 795.4357113 764.907533 1.047116491 1.190565461 0.974046556 0.963447449 1.087051308 0.757870227 0.907615902 0.970314075 1.03991094 1 9.579141546 -8.278416986 24.97188818 1.031182474 0.881501637 0.475744994 0.078443344 536.8127926 789581.7848 0.011057354 0.024784152 5.27E-09 8.278416986 -0.149680837 AHLS(ph)ENELEALEK ddPTM_HeLa_Romidepsin_16h_R1 2 AHLSENELEALEK 13 0 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 0 AHLS(1)ENELEALEK;AHLS(1)ENELEALEK ; 140.68 0.00044397 12683800 10677.4 9882.1 11306.2 7010.1 10106 10617.2 8700.1 9009.1 11224.9 11145.5 TRUE FALSE FALSE 10547.25974 10021.22046 11502.97967 7820.640746 9590.253109 9938.795185 9439.086277 9269.764094 10220.91683 10855.9383 0.971565925 0.923109563 1.059602528 0.720402099 0.883410797 0.915516919 0.869485991 0.853888797 0.94150469 1 13.40619681 -9.279051262 24.99160763 0.985441646 0.855362628 0.550021917 0.058771852 436.8744693 619932.1116 0.008389634 0.012833108 5.26E-10 9.279051262 -0.130079018 AHPEVNGDTK(ac)WHSFK ddPTM_HeLa_Romidepsin_16h_R1 1 AHPEVNGDTKWHSFK 15 1 D6RE87;E7EPB1;E7EQS8;Q6N021-2;Q6N021-3;Q6N021 D6RE87 TET2 Methylcytosine dioxygenase TET2 0 1 AHPEVNGDTK(1)WHSFK 101.43 0.0032585 1628800 2716.3 2822.8 1868.9 2028.1 1638.7 1263.4 984.57 803.16 3358.9 2850 FALSE TRUE FALSE 2683.192691 2862.539452 1901.427421 2262.598464 1555.071024 1182.672817 1068.199351 826.3981674 3058.471571 2775.956589 0.966583088 1.03119028 0.684962952 0.81506983 0.560192847 0.426041539 0.384804055 0.29769852 1.101772118 1 11.43876929 -8.694564273 0.700023461 0.994634997 0.268082847 0.923403611 0.07799721 0.136695344 0.113982926 0.012403711 0.054483967 2.02E-09 8.694564273 -0.72655215 down AHQGTGAGIS(ph)PVILNSGEGK ddPTM_HeLa_Romidepsin_16h_R1 1 AHQGTGAGISPVILNSGEGK 20 0 F5GZK9;Q8IZD4-2;Q8IZD4 F5GZK9 DCP1B mRNA-decapping enzyme 1B 1 0 AHQGTGAGIS(1)PVILNSGEGK 129.29 0.00014358 12407000 3819.9 5847.1 3151.6 3072.6 2756.9 2371.2 2375.2 2305.9 3902.3 4277 TRUE FALSE FALSE 3773.34159 5929.415627 3206.452276 3427.868469 2616.205106 2219.687973 2576.949429 2372.617578 3553.268515 4165.882923 0.905772356 1.423327476 0.769693324 0.822843208 0.628007353 0.532825337 0.618584218 0.569535347 0.852944881 1 12.02440658 -9.018132609 1.74312009 0.986881599 0.578555279 0.591278375 0.160394006 0.187654965 1.133448098 0.024243884 0.048705593 9.59E-10 9.018132609 -0.40832632 AHS(ph)DSNLSASAAER ddPTM_HeLa_Romidepsin_16h_R1 2 AHSDSNLSASAAER 14 0 Q6PEV8 Q6PEV8 FAM199X Protein FAM199X 1 0 AHS(0.999)DS(0.001)NLSASAAER;AHS(0.998)DS(0.002)NLSASAAER ; 91.789 0.017572 3290800 2104.74 1655.22 2179.57 1792.68 2334.17 2144.99 2224.81 2323.7 2280.98 2542.05 TRUE FALSE FALSE 2079.086619 1678.522231 2217.504502 1999.958096 2215.048595 2007.932062 2413.785306 2390.932593 2076.963436 2476.007175 0.839693294 0.67791493 0.895596961 0.807735178 0.894605079 0.810955672 0.974870077 0.965640414 0.838835791 1 11.27379978 -12.15971437 1.040504561 0.995585274 0.85644533 0 0.094329431 0.497167478 1.010007771 0.047064062 0.015271359 6.92E-13 12.15971437 -0.139139944 AHS(ph)LLFENSDSFSEDSSTLGR ddPTM_HeLa_Romidepsin_16h_R1 3 AHSLLFENSDSFSEDSSTLGR 21 0 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 AHS(0.999)LLFENS(0.001)DSFSEDSSTLGR;AHS(1)LLFENSDSFSEDSSTLGR;AHS(0.497)LLFENS(0.45)DS(0.051)FS(0.002)EDSSTLGR ;; 124.08 7.98E-09 13214700 2864.68 2458.32 2744.11 2363.89 4195.2 4742.5 3874.7 4148 3789.75 3385.09 TRUE FALSE FALSE 2829.764178 2492.928293 2791.870083 2637.214084 3981.10329 4439.469556 4203.816921 4268.015836 3450.785268 3297.144874 0.858246843 0.756086975 0.84675384 0.799847803 1.207439601 1.346458747 1.274987021 1.294458084 1.046598011 1 11.68700156 -8.641458173 4.971176583 0.901668004 1.298132981 0.841878872 0.084552248 0.066466584 2.622424942 0.013443201 0.027328815 2.28E-09 8.641458173 0.396464976 AHS(ph)PAEGASVESSSPGPK ddPTM_HeLa_Romidepsin_16h_R1 3 AHSPAEGASVESSSPGPK 18 0 C9J4C4;Q8NFG4-3;Q8NFG4-2;Q8NFG4 C9J4C4 FLCN Folliculin 1 0 AHS(1)PAEGASVESSSPGPK;AHS(1)PAEGASVESSSPGPK;AHS(1)PAEGASVESSSPGPK ;; 131.31 0.00064689 24131600 12860.5 11122.6 11860.6 10194.8 17107.6 21082.9 17679.4 21109.3 14756.4 13057.3 TRUE FALSE FALSE 12703.75128 11279.18425 12067.02877 11373.57074 16234.53533 19735.77073 19181.08779 21720.06429 13436.55063 12718.06946 0.998874186 0.886862923 0.948809786 0.89428437 1.276493683 1.551789821 1.508176052 1.707811422 1.056492942 1 13.63459207 -8.464716731 2.514140849 0.979238106 1.589838476 0.939215851 0.071251241 0.046249753 0.573486643 0.009991728 0.024693544 3.43E-09 8.464716731 0.610600369 AHSPAEGASVESS(ph)SPGPK ddPTM_HeLa_Romidepsin_16h_R1 1 AHSPAEGASVESSSPGPK 18 0 C9J4C4;Q8NFG4-3;Q8NFG4-2;Q8NFG4 C9J4C4 FLCN Folliculin 1 0 AHS(0.003)PAEGAS(0.09)VES(0.122)S(0.433)S(0.351)PGPK 69.986 0.0040007 0 2925.5 2540.9 2620.4 3322.1 3940.3 4043.6 3078.7 3578 3205 3141.6 TRUE FALSE FALSE 2889.842881 2576.670857 2666.006963 3706.216833 3739.211788 3785.22701 3340.204701 3681.523785 2918.336773 3059.980779 0.94439903 0.842054589 0.871249578 1.211189579 1.221972312 1.237010061 1.09157702 1.203119905 0.953710818 1 11.57930688 -9.25197239 24.98970833 0.954117037 1.191398124 0.835238259 0.05927348 251.6837415 664361.6299 0.010178588 0.016734047 5.60E-10 9.25197239 0.237281087 AHT(ph)EY(ph)T(ph)FCVT(ph)SLRNSR ddPTM_HeLa_Romidepsin_16h_R1 1 AHTEYTFCVTSLRNSR 16 1 Q5R3F8 Q5R3F8 ELFN2 Protein phosphatase 1 regulatory subunit 29 4 0 AHT(0.958)EY(0.951)T(0.983)FCVT(0.525)S(0.525)LRNS(0.058)R 40.242 0.030128 1031600 730.25 591.53 574.92 486.93 804.72 873.32 550.57 559.38 800.01 745.11 TRUE FALSE FALSE 721.3494321 599.8575749 584.9262414 543.2311377 763.6521356 817.5176705 597.3354021 575.5647777 728.4551019 725.7519348 0.993933874 0.826532519 0.805958914 0.748508012 1.052221977 1.126442289 0.823057264 0.793059929 1.003724643 1 9.503332703 -10.2912151 19.77053792 0.997135613 0.887828189 0.183193287 0.112725342 75.35979449 50036.86348 0.020450463 0.023392387 5.11E-11 10.2912151 -0.109307424 AHT(ph)PLNTPDPSTK ddPTM_HeLa_Romidepsin_16h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 AHT(1)PLNTPDPSTK 218.45 1.43E-23 12766000 4940.2 4121.1 3510.1 3485.7 2660.1 3116 2636.4 2924 4904.5 4712.2 TRUE FALSE FALSE 4879.986942 4179.116954 3571.191818 3888.733035 2524.345171 2916.897656 2860.33575 3008.601327 4465.829236 4589.776365 1.063229786 0.910527359 0.778075343 0.847259807 0.549993065 0.63552065 0.623197194 0.655500636 0.972994953 1 12.16420815 -9.469257766 1.059580525 1.03109269 0.620939324 0.858248651 0.064743796 0.107663872 0.240906558 0.011475035 0.020960431 3.39E-10 9.469257766 -0.410153367 AHTDFFEAFK ddPTM_HeLa_Romidepsin_16h_R1 1 AHTDFFEAFK 10 0 B4DIH5;P61201;P61201-2;H0YKU5 B4DIH5 COPS2 COP9 signalosome complex subunit 2 0 0 112.3 0.0077881 6934500 4945 4330.6 5072 14086 5198.2 5250.6 4390.1 4622.8 5190.1 4723.8 FALSE FALSE TRUE 4884.728438 4391.5663 5160.276032 15714.6896 4932.916457 4915.103606 4762.994984 4756.553424 4725.884457 4601.074995 1.061649385 0.954465273 1.12153704 3.415438699 1.072122594 1.068251139 1.035191774 1.033791762 1.027126153 1 12.16775526 -9.497837192 24.98336821 1.024978062 1.529346304 0.12064893 0.669007859 1297.53738 1294524.493 0.102962533 0.156841578 3.18E-10 9.497837192 0.504368242 AHTPLNT(ph)PDPSTK ddPTM_HeLa_Romidepsin_16h_R1 1 AHTPLNTPDPSTK 13 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 AHT(0.23)PLNT(0.766)PDPS(0.003)T(0.001)K 132.24 0.0041301 12268000 3633.3 3449.4 2979 2378.7 2210.6 2044.9 1734.3 2108.5 3451.2 3311 TRUE FALSE FALSE 3589.015942 3497.960744 3030.848245 2653.736486 2097.784833 1914.23749 1881.611399 2169.506121 3142.516028 3224.979743 1.112880151 1.084645803 0.939803809 0.822869195 0.650480003 0.593565741 0.58344906 0.672719302 0.974429695 1 11.65507438 -9.0895563 1.549391116 1.056569175 0.610184329 0.939247397 0.047957279 0.063752481 0.301775389 0.008469036 0.016949247 8.14E-10 9.0895563 -0.446384846 AHTPT(ph)PGIYMGRPTHSGGGGGGGGGGGGGGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 AHTPTPGIYMGRPTHSGGGGGGGGGGGGGGGGR 33 1 Q13595;Q13595-4;Q13595-3 Q13595 TRA2A Transformer-2 protein homolog alpha 1 0 AHT(0.16)PT(0.701)PGIY(0.131)MGRPT(0.007)HSGGGGGGGGGGGGGGGGR;AHT(0.037)PT(0.859)PGIY(0.102)MGRPT(0.002)HSGGGGGGGGGGGGGGGGR ; 66.501 1.08E-05 14964200 3848.4 2566.4 3421.6 1784.11 3710 3527 5219.4 3028.1 4349.6 3393.6 TRUE FALSE FALSE 3801.494221 2602.529847 3481.151513 1990.397193 3520.664856 3301.636083 5662.735706 3115.713296 3960.560882 3305.433783 1.150074232 0.787348959 1.053160263 0.602159149 1.06511432 0.998851074 1.713159627 0.942603453 1.198197012 1 11.6906239 AIAELGIYPAVDPLDSTSR ddPTM_HeLa_Romidepsin_16h_R1 1 AIAELGIYPAVDPLDSTSR 19 0 H0YH81;P06576 H0YH81 ATP5B "ATP synthase subunit beta;ATP synthase subunit beta, mitochondrial" 0 0 126.48 1.16E-08 0 1431.7 1227.8 1205.2 1167.6 1309.9 1466.4 1427.4 1506.8 1325.8 1193.4 FALSE FALSE TRUE 1414.24989 1245.085001 1226.176 1302.603406 1243.050915 1372.701773 1548.64332 1550.396881 1207.217127 1162.395296 1.216668628 1.071137336 1.054870064 1.120619991 1.069387427 1.180925093 1.332286293 1.333794868 1.038559887 1 10.18288505 -7.888974938 2.886713319 1.098168094 1.338856476 0.755692399 0.056202133 0.138861638 2.284395254 0.011431508 0.043018179 1.29E-08 7.888974938 0.240688382 AIAIASDMQDDFIS(ph)PCGACR ddPTM_HeLa_Romidepsin_16h_R1 1 AIAIASDMQDDFISPCGACR 20 0 P32320 P32320 CDA Cytidine deaminase 1 0 AIAIASDMQDDFIS(1)PCGACR 63.537 0.017535 3015500 1508.6 1413.7 1276.5 247.79 1467.1 1337.7 1245.3 1618.6 1582.4 1536.6 TRUE FALSE FALSE 1490.212603 1433.602106 1298.716947 276.4406457 1392.228412 1252.225287 1351.075751 1665.431637 1440.866181 1496.67891 0.995679563 0.957855486 0.86773251 0.184702707 0.930211819 0.836669294 0.902715834 1.112751456 0.962708949 1 10.54754903 -9.704907867 4.382901755 0.995490027 0.785468837 0.124951747 0.225889139 0.298512036 11.72454136 0.035881872 0.050603803 1.97E-10 9.704907867 -0.210021191 AIAK(ac)IK(ac)MLGNIK ddPTM_HeLa_Romidepsin_16h_R1 1 AIAKIKMLGNIK 12 2 H0Y3P2;D3DQV9;P78344-2;P78344;H0YCH5;H0YEC5;H0YD77 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 2 AIAK(1)IK(1)MLGNIK 53.327 0.027886 0 52.108 138.07 112.01 294.33 1200.8 1312.9 887.9 1302.4 133.32 143.43 FALSE TRUE FALSE 51.47288765 140.0137531 113.9594871 328.3618195 1139.518695 1229.009927 963.3182038 1340.082889 121.3955253 139.7036679 0.368443352 1.002219592 0.815722942 2.350416595 8.15668416 8.797263132 6.895439598 9.592324304 0.868950165 1 7.126226089 -8.827145949 3.353314316 0.750596376 8.372115307 0.967502613 0.659371057 0.027475364 0.62347945 0.09510836 0.185432238 1.49E-09 8.827145949 7.621518931 AICCNS(ph)CELTNITIAIEK ddPTM_HeLa_Romidepsin_16h_R1 1 AICCNSCELTNITIAIEK 18 0 P01225 P01225 FSHB Follitropin subunit beta 1 0 AICCNS(0.999)CELT(0.001)NITIAIEK 58.914 0.022314 12717000 2246.2 2357.8 2171.6 2048.2 2245.8 2187.2 2133.9 2424.7 2756.6 2612.1 TRUE FALSE FALSE 2218.82245 2390.99317 2209.395787 2285.022521 2131.188446 2047.444979 2315.153413 2494.854869 2510.042792 2544.237265 0.8720973 0.939768159 0.868392196 0.898116914 0.837653184 0.804738224 0.909959713 0.980590491 0.98656003 1 11.3130175 -12.38454662 0.652892266 1.018607525 0.883523292 0.436539618 0.047149086 0.830255066 0.492968526 0.066727114 0.01035892 4.13E-13 12.38454662 -0.135084233 AIDS(ph)PGGAVR ddPTM_HeLa_Romidepsin_16h_R1 1 AIDSPGGAVR 10 0 O60346 O60346 PHLPP1 PH domain leucine-rich repeat-containing protein phosphatase 1 1 0 AIDS(1)PGGAVR 113.67 0.015786 5524700 3434.4 3175.9 3922.5 3551.4 4530.4 4162.1 3559.4 3627.5 4338.6 4518.5 TRUE FALSE FALSE 3392.540212 3220.610404 3990.769467 3962.029578 4299.196783 3896.155243 3861.735347 3732.455989 3950.54475 4401.108719 0.770837629 0.731772517 0.906764573 0.900234425 0.976844031 0.885266757 0.877446024 0.848071754 0.897624895 1 12.1036513 -12.5682516 1.383693811 0.999039619 0.8532388 0.125287921 0.072537887 0.391819235 1.358678821 0.052106502 0.012582051 2.70E-13 12.5682516 -0.145800818 AIEEGTLEEIEEEVR ddPTM_HeLa_Romidepsin_16h_R1 2 AIEEGTLEEIEEEVR 15 0 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8Y6N0;A0A2R8YG32;A0A2R8Y7F3;A0A2R8YF80;A0A2R8YF58;A0A2R8Y526;A0A2R8Y7Y7;A0A2R8Y6V2;A0A2R8YDA1;A0A2R8Y523;A0A2R8Y5K3;K7EQF0;A0A2R8YFK5;K7EP28 P51532 SMARCA4 Transcription activator BRG1 0 0 ; ; 188.15 2.91E-11 3192300 912.47 907.86 851.15 809.1 854.96 871.82 975.05 918.04 1054.68 704.64 FALSE FALSE TRUE 901.3484647 920.6408769 865.9639087 902.6519489 811.3282009 816.1135157 1057.870723 944.602039 960.3467793 686.3333512 1.313280876 1.341390267 1.261724943 1.315180076 1.182119737 1.189092027 1.541336613 1.376302109 1.399242478 1 9.422765652 -15.35138075 0.235905976 1.19E-13 1.358212981 0 0.160277837 14.35907017 0.303639716 6.744356864 0.07319322 4.45E-16 15.35138075 1.358212981 AIENLIGKPTEK(ac)SQTPK ddPTM_HeLa_Romidepsin_16h_R1 1 AIENLIGKPTEKSQTPK 17 2 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 0 1 AIENLIGKPTEK(1)SQTPK 143.93 8.27E-09 908050 462.94 419.18 402.25 363.72 582.06 477.04 305.99 416.4 449.42 548.97 FALSE TRUE FALSE 457.2975092 425.081227 409.2509925 405.7750178 552.3553062 446.5586836 331.980783 428.447877 409.2227496 534.7076803 0.85522899 0.79497872 0.76537332 0.758872619 1.03300425 0.835145445 0.620864063 0.801274964 0.765320501 1 9.062606589 -16.52287874 0.128516423 1.702476283 0.715736161 0 0.121588341 64.64213649 0.590813859 11.50057876 0.379921219 3.00E-17 16.52287874 -0.986740122 AIEPPPLDAVIEAEHTLR ddPTM_HeLa_Romidepsin_16h_R1 2 AIEPPPLDAVIEAEHTLR 18 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 ; ; 190.24 8.09E-15 9915400 5227.5 4882.8 4443.4 4325.8 4692.8 4458.5 4043.9 4351.9 5281.3 5112.2 FALSE FALSE TRUE 5163.785219 4951.540187 4520.735513 4825.96935 4453.308905 4173.616239 4387.388765 4477.81536 4808.927301 4979.384307 1.037032874 0.99440812 0.907890461 0.969189974 0.894349307 0.838179177 0.881110695 0.899270891 0.965767453 1 12.28175165 -9.359143208 0.988395567 1.017927814 0.874853059 0.681004538 0.033927581 0.16840785 0.326749852 0.005816128 0.011646657 4.37E-10 9.359143208 -0.143074755 AIESLVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AIESLVKK 8 1 K7ENG1;K7EL15;K7EL18;K7EIJ2;K7ES96;K7EIU8;Q13485 K7ENG1 SMAD4 Mothers against decapentaplegic homolog;Mothers against decapentaplegic homolog 4 0 1 ; AIESLVK(1)K;AIESLVK(1)K 128.69 0.0017355 2469400 1820.95 1637.13 1844.15 1961.69 1961.7 1489.3 1234.94 1454.04 1888.38 1666.31 FALSE TRUE FALSE 1798.755561 1660.177559 1876.246657 2188.509828 1861.587129 1394.138536 1339.835773 1496.110353 1719.478563 1623.019026 1.108277557 1.0228947 1.156022589 1.348419084 1.14699033 0.858978554 0.825520682 0.921807033 1.059432167 1 10.6644642 -8.252382669 24.25583859 1.086525241 0.864443916 0.568720069 0.097289454 311.8321824 835150.5256 0.015960029 0.040014428 5.59E-09 8.252382669 -0.222081325 AIET(ph)MYNQCMEVGYK ddPTM_HeLa_Romidepsin_16h_R1 1 AIETMYNQCMEVGYK 15 0 O60507 O60507 TPST1 Protein-tyrosine sulfotransferase 1 1 0 AIET(0.982)MY(0.018)NQCMEVGYK 77.185 0.0033407 0 1844.7 1776 1381.5 2130.5 1660.2 1502.7 1654 1528.4 2009.4 1740 TRUE FALSE FALSE 1822.216087 1801.002575 1405.544428 2376.838434 1575.473799 1406.68232 1794.490719 1572.621843 1829.674231 1694.794549 1.075184062 1.062667198 0.829330274 1.402434552 0.929595743 0.830001678 1.058824929 0.927912969 1.07958468 1 10.72689468 AIGGEFSDTNAAVEGT(ph)PLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AIGGEFSDTNAAVEGTPLPK 20 0 E5RJU4;E5RFM9;H0YAY0;R4GMT7;E7EVI4;E7ET87;O75410-3;O75410-7;O75410-9;O75410;O75410-2 E5RJU4 TACC1 Transforming acidic coiled-coil-containing protein 1 1 0 AIGGEFSDTNAAVEGT(1)PLPK 195.25 3.44E-20 0 1416.2 1303.4 1566 1445.6 3056.5 3049.1 1831.1 2395.6 1148.1 1015.3 TRUE FALSE FALSE 1398.93881 1321.749299 1593.255573 1612.747074 2900.5154 2854.272351 1986.633588 2464.912906 1045.411061 988.9223596 1.414609343 1.336555177 1.61110279 1.63081263 2.933006187 2.886245136 2.00888732 2.492524193 1.057121472 1 9.949713449 -8.979724588 2.80658306 1.24233656 2.557445347 0.803897722 0.300102655 0.091163696 1.460383158 0.049699526 0.093189647 1.05E-09 8.979724588 1.315108787 up AIGGIILTAS(ph)HNPGGPNGDFGIK ddPTM_HeLa_Romidepsin_16h_R1 3 AIGGIILTASHNPGGPNGDFGIK 23 0 A0A3B3ITK7;P36871;P36871-2 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 1 0 AIGGIILTAS(1)HNPGGPNGDFGIK;AIGGIILT(0.004)AS(0.996)HNPGGPNGDFGIK;AIGGIILT(0.001)AS(0.999)HNPGGPNGDFGIK ;; 237.05 1.30E-55 3105500000 19558.3 19463.1 18733.4 18285.2 19649.9 16612.8 14714.89 17137.47 18823.2 17462.84 TRUE FALSE FALSE 19319.91592 19737.10203 19059.44697 20399.42086 18647.09228 15551.2957 15964.77239 17633.31566 17139.60585 17009.1529 1.135854092 1.160381246 1.120540634 1.199320212 1.096297528 0.914289841 0.938598911 1.036695699 1.007669574 1 14.05402367 -8.272850037 24.23292527 1.089523746 0.960735228 0.477971558 0.065850039 386.6846452 821205.908 0.011208117 0.025281804 5.34E-09 8.272850037 -0.128788519 AIGLSPMS(ph)FPTADLTLK ddPTM_HeLa_Romidepsin_16h_R1 2 AIGLSPMSFPTADLTLK 17 0 Q5JSZ5;Q5JSZ5-5;A0A494C0D3;A0A494C065;H0Y412 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 AIGLS(0.029)PMS(0.917)FPT(0.054)ADLTLK;AIGLS(0.217)PMS(0.715)FPT(0.067)ADLTLK ; 103.21 0.0039015 55738000 6161.1 6944.8 6198.5 6629.1 6711.5 6105.4 4937.1 5627.1 6376.6 6282.1 TRUE FALSE FALSE 6086.006143 7042.569077 6306.382292 7395.587733 6368.987111 5715.284644 5356.457151 5789.91126 5806.260926 6118.890136 0.994625824 1.150955307 1.03064153 1.208648557 1.040872931 0.934039428 0.87539685 0.946235532 0.94890753 1 12.57905428 -8.185060776 4.710243903 1.030481967 0.910652378 0.374869431 0.076099786 0.211120879 8.670378885 0.011281356 0.029730016 6.53E-09 8.185060776 -0.119829589 AIGNNSATS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 AIGNNSATSPR 11 0 A0A1B0GV57;Q9NYJ8-2;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 0 AIGNNS(0.009)AT(0.079)S(0.911)PR;AIGNNS(0.004)AT(0.11)S(0.886)PR ; 110.64 0.014279 7215700 6078.5 7998 4528.6 4927.5 6158.1 4101.8 2949.9 3324.3 5422.2 5759.2 TRUE FALSE FALSE 6004.412904 8110.596054 4607.418383 5497.240735 5843.829178 3839.708218 3200.464432 3420.483376 4937.224852 5609.575154 1.070386391 1.445848541 0.8213489 0.979974523 1.041759673 0.684491804 0.570535975 0.609758009 0.880142384 1 12.4536758 -8.194837306 3.132543115 1.047327685 0.593409225 0.593835848 0.157171343 0.121519756 2.33960373 0.020933911 0.058700766 6.39E-09 8.194837306 -0.453918461 AIGSGESET(ph)PPSTPTAQEPSSSGGFEFFR ddPTM_HeLa_Romidepsin_16h_R1 1 AIGSGESETPPSTPTAQEPSSSGGFEFFR 29 0 H0YFN7;Q4ADV7-2;Q4ADV7-3;Q4ADV7 H0YFN7 RIC1 RAB6A-GEF complex partner protein 1 1 0 AIGSGES(0.011)ET(0.95)PPS(0.035)T(0.004)PTAQEPSSSGGFEFFR 132.48 3.14E-10 6783800 2312 1934.7 2447.8 1973.1 2692.2 2965.2 2725.2 3185.5 2701 2514.2 TRUE FALSE FALSE 2283.820455 1961.936757 2490.402932 2201.239106 2554.806988 2775.73329 2956.67842 3277.667417 2459.415795 2448.880722 0.93259767 0.80115652 1.016955587 0.898875591 1.043254972 1.133470187 1.207359098 1.338434897 1.004301995 1 11.25790679 -7.868106866 1.126834589 0.952784028 1.352069125 0.815352493 0.063396903 0.234032825 0.431606394 0.009871278 0.08539734 1.35E-08 7.868106866 0.399285097 AIGSGESETPPST(ph)PTAQEPSSSGGFEFFR ddPTM_HeLa_Romidepsin_16h_R1 1 AIGSGESETPPSTPTAQEPSSSGGFEFFR 29 0 H0YFN7;Q4ADV7-2;Q4ADV7-3;Q4ADV7 H0YFN7 RIC1 RAB6A-GEF complex partner protein 1 1 0 AIGSGES(0.001)ET(0.21)PPS(0.063)T(0.709)PT(0.016)AQEPSSSGGFEFFR 104.03 9.27E-09 6542300 946.54 919.2 962.73 964.78 1230.8 1313.3 1014 1692.1 1122.7 1196.5 TRUE FALSE FALSE 935.0032064 932.1405217 979.4859118 1076.332403 1167.987683 1229.384368 1100.129135 1741.058244 1022.2829 1165.414758 0.802292231 0.799835866 0.840461222 0.923561673 1.002207734 1.054889996 0.943980782 1.493938731 0.877183761 1 10.18662777 -4.41983326 0.98421077 0.899597647 200 0.81519794 0.08255814 218.9953033 0.789428037 0.015322341 97646.08143 3.80E-05 4.41983326 199.1004024 AIGSTSKPQES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AIGSTSKPQESPK 13 1 P18887;F5H8D7;M0QYS5 P18887 XRCC1 DNA repair protein XRCC1 1 0 AIGST(0.001)S(0.001)KPQES(0.998)PK 130.47 0.016065 22059000 2721.4 2553 2467 1601.2 1448.4 1539.7 1087.4 1231.6 1972.4 2254.1 TRUE FALSE FALSE 2688.23053 2588.941201 2509.9371 1786.338278 1374.482743 1441.318139 1179.763729 1267.234403 1795.983604 2195.538157 1.224406199 1.179182968 1.143199034 0.81362206 0.626034551 0.656476015 0.537346037 0.577186235 0.818015209 1 11.10035889 -9.030607351 2.410936708 1.118548932 0.594855951 0.789111735 0.114214879 0.073242736 0.847676898 0.01461336 0.02736173 9.32E-10 9.030607351 -0.523692981 AIGSVPERS(ph)PAGVDLSLTGLPPPVSR ddPTM_HeLa_Romidepsin_16h_R1 2 AIGSVPERSPAGVDLSLTGLPPPVSR 26 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 AIGS(0.006)VPERS(0.993)PAGVDLSLT(0.001)GLPPPVSR;AIGS(0.004)VPERS(0.993)PAGVDLS(0.001)LT(0.001)GLPPPVSR ; 98.533 2.19E-06 47852000 1286.43 1620.43 1343.13 1534.91 2487.44 3434.81 2782.42 2821.74 1429.81 1353.98 TRUE FALSE FALSE 1270.750496 1643.242456 1366.506614 1712.383516 2360.496655 3215.336726 3018.758685 2903.382595 1301.924213 1318.803404 0.963563251 1.246010171 1.036171585 1.298437288 1.789877587 2.438071297 2.289013416 2.20152798 0.987201131 1 10.3650138 -8.677940077 1.772433709 1.008398908 2.320433758 0.964116386 0.107047882 0.042040366 0.26659576 0.016536321 0.040134314 2.10E-09 8.677940077 1.31203485 up AIK(ac)LRPIAVIK ddPTM_HeLa_Romidepsin_16h_R1 1 AIKLRPIAVIK 11 2 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 1 AIK(1)LRPIAVIK 105.4 0.00093389 0 665.83 648.9 868.84 543.85 656.8 927.92 821.43 833.33 653.73 492.97 FALSE TRUE FALSE 657.7146079 658.0352312 883.9617957 606.7324959 623.2810451 868.6289067 891.2022437 857.4410888 595.2587515 480.1625683 1.369774846 1.370442585 1.840963569 1.263598073 1.298062544 1.809030866 1.856042729 1.785730803 1.239702532 1 8.907379131 -4 0.055567633 4.66E-10 4.466373986 0.550330345 0.197284522 158.0716074 0.666223745 11.80039274 58.79566684 1.00E-04 4 4.466373986 AIK(ac)LRPIAVIKG ddPTM_HeLa_Romidepsin_16h_R1 1 AIKLRPIAVIKG 12 3 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 1 AIK(1)LRPIAVIKG 59.198 0.028618 0 0 0 0 64.043 0 62.363 0 0 0 0 FALSE TRUE FALSE 0 0 0 71.44795299 0 58.37820557 0 0 0 0 0 AILDAEPGPRPALQPS(ph)PSIR ddPTM_HeLa_Romidepsin_16h_R1 1 AILDAEPGPRPALQPSPSIR 20 1 B5MD46;Q9BXI6;Q9BXI6-2 B5MD46 TBC1D10A TBC1 domain family member 10A 1 0 AILDAEPGPRPALQPS(0.835)PS(0.165)IR 63.46 0.0065423 27093000 1292 1379.8 1370.9 1073.1 2005.4 2602.7 2174.9 2535.9 1434 1291.1 TRUE FALSE FALSE 1276.252607 1399.224861 1394.759939 1197.176871 1903.056955 2436.39587 2359.635952 2609.272266 1305.739448 1257.557036 1.014866579 1.1126532 1.109102728 0.951986142 1.513296734 1.937403871 1.876364956 2.074873895 1.038314296 1 10.29640812 -8.508327979 2.401373576 1.019489718 1.964789513 0.969459356 0.073674745 0.03216816 0.367913835 0.010603908 0.025845654 3.10E-09 8.508327979 0.945299795 AILGSYDSELTPAEYS(ph)PQLTR ddPTM_HeLa_Romidepsin_16h_R1 3 AILGSYDSELTPAEYSPQLTR 21 0 C9J9H5;C9JX80;Q9Y6D9-3;Q9Y6D9 C9J9H5 MAD1L1 Mitotic spindle assembly checkpoint protein MAD1 1 0 AILGSYDSELT(0.001)PAEYS(0.993)PQLT(0.006)R;AILGSYDSELTPAEY(0.258)S(0.715)PQLT(0.027)R;AILGSYDSELT(0.005)PAEY(0.022)S(0.893)PQLT(0.08)R ;; 122.44 5.65E-05 43115000 5745.9 5811.9 5565.9 4809.7 6697.1 7742.7 7256.7 8193.7 5957.3 5395.8 TRUE FALSE FALSE 5675.866761 5893.720081 5662.772155 5365.820144 6355.321997 7247.966458 7873.083917 8430.771782 5424.464168 5255.616338 1.079962158 1.121413684 1.077470612 1.020968769 1.2092439 1.379089719 1.498032469 1.604145211 1.032127122 1 12.35964425 -8.111679176 1.15568982 1.044428501 1.612523515 0.962982053 0.039434905 0.088510543 0.19607605 0.007302817 0.041682855 7.73E-09 8.111679176 0.568095014 AILILDNDGDR ddPTM_HeLa_Romidepsin_16h_R1 1 AILILDNDGDR 11 0 F8VXB1;F8VUC5;F8W156;F8W651;F8VXR1;F8VYZ4;F8VVA7;P61923-5;P61923;P61923-4 F8VXB1 COPZ1 Coatomer subunit zeta-1 0 0 178.55 0.00012302 10103000 3805.4 3535.7 3506.4 2534.6 3632.4 3510.5 3460.2 3611.7 4148.9 3394.3 FALSE FALSE TRUE 3759.018321 3585.475677 3567.427421 2827.662378 3447.025074 3286.19038 3754.109302 3716.198841 3777.811993 3306.115597 1.13698938 1.084497977 1.079038926 0.855282368 1.042620856 0.993973224 1.13550455 1.124037782 1.142673897 1 11.69092145 -11.15530004 0.002919696 4.67E-05 2.108482213 0 0.086568212 139942.3278 209.9140167 76190.24972 75392.64521 6.99E-12 11.15530004 2.108435475 AILVDLEPGTMDS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 2 AILVDLEPGTMDSVR 15 0 Q5JP53;P07437;G3V5W4;G3V2R8;G3V3R4;G3V2N6;A0A0B4J269;Q13509;Q9BVA1;Q13885 Q5JP53;A0A0B4J269;Q9BVA1 TUBB;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 1 0 AILVDLEPGT(0.493)MDS(0.507)VR;AILVDLEPGT(0.222)MDS(0.778)VR ; 112.02 0.0056407 27113000 8633.7 8708.6 8740.6 6781.9 8696.7 7797.2 7636 7627.5 10204.1 8091.1 TRUE FALSE FALSE 8528.469144 8831.199899 8892.726476 7566.055188 8252.874947 7298.984084 8284.601649 7848.189678 9291.419739 7880.892056 1.082170531 1.120583791 1.128390849 0.960050605 1.047200607 0.92616217 1.051226383 0.995850422 1.178980714 1 12.94414323 -9.233258024 24.98778435 1.053331314 0.998114434 0.280545946 0.064406504 984.705401 873117.958 0.008683012 0.014397892 5.84E-10 9.233258024 -0.05521688 AILVDLEPGTMDSVR ddPTM_HeLa_Romidepsin_16h_R1 1 AILVDLEPGTMDSVR 15 0 Q5JP53;P07437;G3V5W4;G3V2R8;G3V3R4;G3V2N6;A0A0B4J269;Q13509;Q9BVA1;Q13885 Q5JP53;A0A0B4J269;Q9BVA1 TUBB;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 0 106.01 0.018521 1509900 288.81 178.46 247.99 264.75 325.68 187.61 167.39 246.21 420.69 349.74 FALSE FALSE TRUE 285.2898726 180.9723646 252.3061619 295.3616407 309.0593343 175.6223265 181.6081024 253.3336979 383.0624328 340.6537044 0.837477676 0.531250247 0.740652923 0.867043678 0.907253702 0.515545037 0.533116476 0.743669288 1.124492198 1 8.412162085 -12.18618175 0.141369197 1.333448847 0.504268755 0.507765598 0.13851486 10.9048781 0.457478732 2.074790586 0.711683921 6.51E-13 12.18618175 -0.829180092 AILVVFANK ddPTM_HeLa_Romidepsin_16h_R1 1 AILVVFANK 9 0 B4DZG7;F8VYN9;P40616-2;P40616 B4DZG7 ARL1 ADP-ribosylation factor-like protein 1 0 0 138.37 3.34E-07 0 0 0 60.341 138.43 137.14 127.28 178.32 69.618 0 0 FALSE FALSE TRUE 0 0 61.39120979 154.4359279 130.1412341 119.1472188 193.4664963 71.63228699 0 0 0 AIMTYVSSFYHAFSGAQK ddPTM_HeLa_Romidepsin_16h_R1 1 AIMTYVSSFYHAFSGAQK 18 0 O43707;P12814-2;P12814;P12814-3;P12814-4;H9KV75;G3V2N5;G3V2W4 O43707;P12814-2 ACTN4;ACTN1 Alpha-actinin-4;Alpha-actinin-1 0 0 134.25 8.91E-10 997600 1118.9 705.58 664.78 403.43 738.71 658.82 746.98 1002.8 797.1 313.6 FALSE FALSE TRUE 1105.262416 715.5131738 676.350217 450.0764748 701.0108722 616.7235282 810.4284626 1031.814436 725.8053796 305.4526268 3.618441354 2.342468557 2.21425569 1.473473905 2.294990485 2.019048043 2.653205085 3.377985145 2.37616349 1 8.254804837 -7.392648927 2.704746401 2.205686698 3.453199862 0.253071621 0.639688894 0.593434802 6.683712939 0.135377383 1.420140129 4.05E-08 7.392648927 1.247513165 AIPGDQHPES(ph)PVHTEPMGIQGR ddPTM_HeLa_Romidepsin_16h_R1 1 AIPGDQHPESPVHTEPMGIQGR 22 0 Q14676-3;Q14676 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 AIPGDQHPES(0.953)PVHT(0.047)EPMGIQGR 47.392 0.01357 13568000 3437 3327.8 3016.9 2571.4 2484.3 2119.9 2091.4 2372.7 3566.8 3424.2 TRUE FALSE FALSE 3395.108522 3374.648856 3069.407879 2868.717367 2357.516901 1984.445232 2269.043464 2441.350331 3247.776475 3335.23879 1.017950658 1.011816265 0.920296288 0.860123532 0.706851008 0.594993449 0.680324141 0.731986669 0.973776296 1 11.70357434 -9.030078704 1.514509947 1.008029085 0.664322342 0.933854978 0.038620272 0.060044763 0.273179763 0.006000935 0.012482173 9.33E-10 9.030078704 -0.343706743 AIPTVNHSGTFS(ph)PQAPVPTTVPVVDVR ddPTM_HeLa_Romidepsin_16h_R1 2 AIPTVNHSGTFSPQAPVPTTVPVVDVR 27 0 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 AIPTVNHS(0.002)GT(0.151)FS(0.847)PQAPVPTTVPVVDVR;AIPTVNHS(0.016)GT(0.045)FS(0.89)PQAPVPT(0.025)T(0.025)VPVVDVR ; 84.481 1.57E-06 156431000 1923.02 2009.06 2256.3 2149.2 2888.9 3080.3 2382.4 2741.2 2407 2129.8 TRUE FALSE FALSE 1899.581493 2037.343599 2295.569955 2397.700616 2741.468653 2883.478771 2584.760997 2820.512297 2191.711892 2074.467489 0.915695957 0.982104376 1.106582758 1.155814988 1.321528859 1.389985038 1.24598771 1.35963196 1.056517831 1 11.01852533 -9.214520491 1.342335517 0.959837658 1.332140351 0.879049818 0.055677734 0.082390382 0.29178095 0.008561968 0.016769296 6.10E-10 9.214520491 0.372302693 AIPVS(ph)PSAVEEDEDEDGHTVVATAR ddPTM_HeLa_Romidepsin_16h_R1 1 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 AIPVS(0.832)PS(0.168)AVEEDEDEDGHTVVATAR 121.75 1.21E-11 0 911.18 1131.8 898.16 1124.4 973.49 1310 1259.5 1285.5 1411.5 1042.4 TRUE FALSE FALSE 900.0741877 1147.73351 913.792098 1254.408418 923.8091727 1226.295228 1366.481899 1322.693914 1285.251905 1015.318298 0.886494599 1.130417439 0.900005545 1.235482923 0.90987149 1.207793882 1.34586553 1.302738183 1.265861068 1 9.987716361 -7.875602385 0.627137491 0.955084453 1.464778092 0.236089693 0.14840043 0.888320686 0.369547467 0.019936761 0.280150794 1.33E-08 7.875602385 0.509693639 AIPVSPS(ph)AVEEDEDEDGHTVVATAR ddPTM_HeLa_Romidepsin_16h_R1 5 AIPVSPSAVEEDEDEDGHTVVATAR 25 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0Y3R8 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 AIPVS(0.429)PS(0.571)AVEEDEDEDGHTVVATAR;AIPVS(0.015)PS(0.985)AVEEDEDEDGHTVVATAR;AIPVS(0.146)PS(0.854)AVEEDEDEDGHTVVATAR;AIPVS(0.122)PS(0.878)AVEEDEDEDGHTVVATAR;AIPVS(0.145)PS(0.855)AVEEDEDEDGHTVVATAR ;;;; 212.86 1.82E-37 311002000 14979.03 14665.36 13407.02 13601.7 18107.64 19368.64 15826.24 18420.33 14984.32 15335.95 TRUE FALSE FALSE 14796.45982 14871.81932 13640.36356 15174.39255 17183.53956 18131.04641 17170.52043 18953.29319 13644.08489 14937.51981 0.990556666 0.995601647 0.913161203 1.015857569 1.150360956 1.213792293 1.149489383 1.268838029 0.91341033 1 13.86665301 -8.705891917 3.031704681 0.988768446 1.202477064 0.864617214 0.043690129 0.057381938 1.071581076 0.005175445 0.010812196 1.97E-09 8.705891917 0.213708618 AIS(ph)PTSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 AISPTSSSR 9 0 A0A0U1RRL2;B1AM27;O14795;O14795-2 A0A0U1RRL2 UNC13B Protein unc-13 homolog B 1 0 AIS(0.96)PT(0.04)SSSR 117.14 0.015093 34382000 3687.5 3499.5 3976 3237.3 3388.7 4159.4 4577.2 2122.1 4094.6 3792.1 TRUE FALSE FALSE 3642.555332 3548.766053 4045.200612 3611.611858 3215.761994 3893.627764 4965.987254 2183.499615 3728.368721 3693.580695 0.986185394 0.960792885 1.095197573 0.977807758 0.87063537 1.054160741 1.344491339 0.591160664 1.00941851 1 11.85080438 AIS(ph)SANLLVR ddPTM_HeLa_Romidepsin_16h_R1 1 AISSANLLVR 10 0 B7WPE2;Q32P44;G3V1D0;H0Y3M3;Q32P44-2 B7WPE2 EML3 Echinoderm microtubule-associated protein-like 3 1 0 AIS(0.65)S(0.35)ANLLVR 109.48 0.01842 44139000 2640.7 2353.3 3636 3111.4 2760.4 3180.3 2906.1 2816.1 3069.9 1996.3 TRUE FALSE FALSE 2608.514133 2386.429819 3699.283055 3471.154708 2619.526488 2977.089094 3152.944061 2897.57941 2795.320455 1944.435838 1.341527492 1.227312196 1.902496849 1.785173179 1.347191013 1.531081168 1.621521266 1.490190292 1.43759974 1 10.92513591 -10.91713189 0.653580669 1.041108039 1.590437158 0.244623016 0.217436407 0.33706788 0.325521867 0.07280794 0.052783416 1.21E-11 10.91713189 0.549329119 AISAPTS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 AISAPTSPTR 10 0 B0QY95;Q9NQG6-2;Q9NQG6 B0QY95 MIEF1 Mitochondrial dynamics protein MID51 1 0 AISAPT(0.261)S(0.709)PT(0.03)R 105.17 0.021181 75574000 4533 5235.2 4796.6 3708.5 4492.8 5276.3 4856.3 5805.9 5480.7 4292 TRUE FALSE FALSE 4477.750052 5308.901283 4880.082811 4137.294219 4263.515651 4939.161458 5268.794001 5973.884556 4990.492465 4180.493221 1.071105684 1.269922232 1.167346184 0.98966653 1.019859482 1.181478165 1.260328321 1.42899037 1.193756861 1 12.02945745 -4 0.540708214 1.050695172 17.52614654 0.47027866 0.097180557 57.98973122 0.497850451 0.017852415 1110.682225 1.00E-04 4 16.47545137 AISS(ph)ANLLVR ddPTM_HeLa_Romidepsin_16h_R1 2 AISSANLLVR 10 0 B7WPE2;Q32P44;G3V1D0;H0Y3M3;Q32P44-2 B7WPE2 EML3 Echinoderm microtubule-associated protein-like 3 1 0 AIS(0.285)S(0.715)ANLLVR;AIS(0.304)S(0.696)ANLLVR ; 128.36 0.0080499 72164000 3355.5 2550.96 4012.6 3293.2 3443.9 3753.6 3089.3 3291.1 3222.7 2808.7 TRUE FALSE FALSE 3314.601875 2586.872482 4082.43762 3673.975279 3268.144932 3513.757074 3351.705065 3386.322786 2934.453641 2735.729569 1.21159705 0.945587792 1.492266511 1.342959962 1.194615495 1.284394888 1.225159498 1.237813424 1.072640247 1 11.41770991 -11.81160333 0.397689528 0.954068892 1.273554259 0.317915553 0.126914283 1.470259938 0.397076923 0.198217655 0.049429311 1.54E-12 11.81160333 0.319485367 AISS(ph)PTVSR ddPTM_HeLa_Romidepsin_16h_R1 5 AISSPTVSR 9 0 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 0 AIS(0.15)S(0.584)PT(0.266)VSR;AIS(0.013)S(0.971)PT(0.016)VSR;AIS(0.198)S(0.776)PT(0.026)VSR;AIS(0.065)S(0.935)PTVSR;AIS(0.015)S(0.969)PT(0.015)VSR ;;;; 176.48 1.06E-05 250235300 5664.28 5195.87 5530.11 7264.7 24203.9 30117.4 27781.6 29831.1 6091.04 5561.76 TRUE FALSE FALSE 5595.241577 5269.017594 5626.359245 8104.678795 22968.68467 28192.99534 30141.36841 30694.21581 5546.242127 5417.264673 1.032853647 0.97263433 1.038597813 1.496083224 4.239904463 5.204286118 5.563946055 5.665998924 1.023808594 1 12.40334886 -8.671235178 2.147731177 1.005151454 5.512178766 0.996286984 0.123846896 0.013346517 0.124812635 0.020471299 0.046772972 2.13E-09 8.671235178 4.507027312 up AIST(ph)PETPLTK ddPTM_HeLa_Romidepsin_16h_R1 2 AISTPETPLTK 11 0 E9PIQ6;A0A3B3ITS5;Q14181 E9PIQ6 POLA2 DNA polymerase alpha subunit B 1 0 AIS(0.07)T(0.928)PET(0.002)PLTK;AIS(0.031)T(0.968)PET(0.001)PLTK ; 181.66 1.61E-05 148866000 28720 27019 27456 21069.2 24249.2 20820.1 17714.3 16771.3 31042 28609 TRUE FALSE FALSE 28369.94959 27399.37419 27933.86016 23505.32004 23011.67284 19489.7628 19218.9522 17256.5511 28265.52577 27865.73406 1.018094465 0.983264038 1.002444799 0.843520576 0.825805371 0.699416809 0.6896984 0.619274951 1.014347073 1 14.76620454 -8.624277894 0.895246531 1.010687115 0.631274381 0.970297276 0.02539741 0.068146838 0.098826541 0.004066936 0.015896676 2.38E-09 8.624277894 -0.379412734 AIST(ph)PETPLTKR ddPTM_HeLa_Romidepsin_16h_R1 1 AISTPETPLTKR 12 1 E9PIQ6;A0A3B3ITS5;Q14181 E9PIQ6 POLA2 DNA polymerase alpha subunit B 1 0 AIS(0.016)T(0.982)PET(0.001)PLTKR 134.98 0.0068437 7865000 2445.8 2179 1615.1 2861.3 1824 1318.7 1297.7 1254 2208.8 1902.1 TRUE FALSE FALSE 2415.989649 2209.676019 1643.210138 3192.136969 1730.914474 1234.439326 1407.926606 1290.282512 2011.239396 1852.683168 1.304049009 1.192689639 0.88693532 1.722980499 0.93427441 0.666298128 0.759939222 0.696439917 1.085581945 1 10.85540047 -8.525317253 24.99994771 1.172351567 0.727378564 0.52191833 0.211043776 48.40418383 496247.1787 0.030973829 0.062249841 2.98E-09 8.525317253 -0.444973003 AIT(ph)PPQQPYK ddPTM_HeLa_Romidepsin_16h_R1 1 AITPPQQPYK 10 0 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 AIT(1)PPQQPYK 136.02 0.01166 48852000 10706 9827.4 10371 10462 10633 9935.5 8690.4 8059.5 10508 9212.6 TRUE FALSE FALSE 10575.51115 9965.750395 10551.5029 11671.66567 10090.35833 9300.653615 9428.562359 8292.688917 9568.138162 8973.255324 1.178559037 1.11060591 1.175883503 1.300716991 1.124492502 1.036486011 1.050740452 0.92415613 1.066295098 1 13.13141575 -7.336279324 1.401949285 1.112025319 0.871919393 0.38160048 0.07916519 1.216569646 2.329394587 0.014570969 0.393211219 4.61E-08 7.336279324 -0.240105926 AITHLNNNFMFGQK ddPTM_HeLa_Romidepsin_16h_R1 2 AITHLNNNFMFGQK 14 0 P14866;M0QYT0;M0QXS5;A0A3B3ITJ4;P14866-2 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 0 ; ; 152.4 4.83E-07 1257520 600.41 498 539.58 289.11 585.36 606.07 404.79 348.53 472.61 475.49 FALSE FALSE TRUE 593.091972 505.0108571 548.9711636 322.5382585 555.4868949 567.344083 439.1728525 358.6141657 430.3385779 463.1367013 1.280598083 1.090414246 1.185332888 0.696421289 1.199401588 1.225003506 0.948257504 0.774316017 0.92918263 1 8.855294278 AITSLLGGGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AITSLLGGGSPK 12 0 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 AITSLLGGGS(1)PK 115.12 0.0090402 578240000 4296.2 4037.2 4121.6 3528.5 3197.7 3285.1 2953.6 3508.6 4189.2 4151.6 TRUE FALSE FALSE 4243.836262 4094.035808 4193.334719 3936.481772 3034.509437 3075.192712 3204.47871 3610.115805 3814.50746 4043.740834 1.049482753 1.012437734 1.036993935 0.973475288 0.750421345 0.760482147 0.792454028 0.892766365 0.943311557 1 11.98147482 -8.869847487 4.730018393 1.023122213 0.796375806 0.823837491 0.045977648 0.050781854 1.902343198 0.00597639 0.01109647 1.35E-09 8.869847487 -0.226746407 AITVFS(ph)PDGHLFQVEYAQEAVK ddPTM_HeLa_Romidepsin_16h_R1 1 AITVFSPDGHLFQVEYAQEAVK 22 0 O14818;O14818-4;F5GY34;Q8TAA3-5;Q8TAA3;Q8TAA3-2 O14818;Q8TAA3-5 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 1 0 AIT(0.191)VFS(0.809)PDGHLFQVEYAQEAVK 75.529 0.00111 9999000 1514.3 1117.7 1056.6 1177.4 1244.6 1107.2 1005.8 1083.1 1364.6 1151.1 TRUE FALSE FALSE 1495.843129 1133.43501 1074.98968 1313.536528 1181.083418 1036.453493 1091.232627 1114.43779 1242.546758 1121.194256 1.334151617 1.010917603 0.958789856 1.171551246 1.053415509 0.924419197 0.97327704 0.993973866 1.108235037 1 10.13082054 -8.876783815 0.858734107 1.145423492 0.962157485 0.167698705 0.10638432 0.808259777 1.128782226 0.026187639 0.082278083 1.33E-09 8.876783815 -0.183266007 AIVAIENPADVSVISSR ddPTM_HeLa_Romidepsin_16h_R1 2 AIVAIENPADVSVISSR 17 0 F8WD59;C9J9K3;A0A0C4DG17;P08865 F8WD59 RPSA 40S ribosomal protein SA 0 0 ; ; 186.49 4.45E-23 246580 0 0 0 118.38 129.33 0 198.39 100.71 0 129.8 FALSE FALSE TRUE 0 0 0 132.0676526 122.7298075 0 215.2412416 103.623885 0 126.4277773 0 0 0 1.044609463 0.970750338 0 1.702483792 0.819629097 0 1 6.982169661 -7.759569885 24.99972596 0.48323999 1.261056381 0.327999916 0.487561806 49.52950959 662275.0131 0.074304762 0.252311525 1.74E-08 7.759569885 0.777816391 AIYHDLEQSIR ddPTM_HeLa_Romidepsin_16h_R1 1 AIYHDLEQSIR 11 0 A0A0U1RR22;Q9UNF0-2;Q9UNF0 A0A0U1RR22 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 0 202.96 1.67E-13 3715400 2854.5 2749 3093 2427.3 4996.7 5265.3 4275.1 5006.6 3459.9 2768.3 FALSE FALSE TRUE 2819.708256 2787.700494 3146.832368 2707.955847 4741.699754 4928.864323 4638.226887 5151.458072 3150.437879 2696.379167 1.045738778 1.033868133 1.167058553 1.004293417 1.758543387 1.827956685 1.720168641 1.910509521 1.16839572 1 11.39680767 -8.748108926 7.140089596 1.033772067 1.802974589 0.956442932 0.076559042 0.016146683 3.92059976 0.009046154 0.017631233 1.79E-09 8.748108926 0.769202522 AK(ac)EAMEK(ac)EK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AKEAMEKEKK 10 3 Q5JYW6;H0Y5P0;H0YE38;B1AJZ9-4;B1AJZ9;B1AJZ9-3 Q5JYW6 FHAD1 Forkhead-associated domain-containing protein 1 0 3 AK(1)EAMEK(1)EK(1)K 67.704 0.015825 0 145.48 0 141.67 236.23 347.61 284.25 312.56 393.12 0 60.071 FALSE TRUE FALSE 143.7068338 0 144.1357069 263.5440241 329.8701646 266.0873424 339.1088386 404.494307 0 58.51034676 2.45609267 0 2.463422538 4.5042294 5.637809086 4.547697238 5.79570721 6.913209874 0 1 5.870619863 -9.202933269 2.348614462 1.568046796 5.634723787 0.837666143 0.955390622 0.091633199 0.989083224 0.141400812 0.247493908 6.27E-10 9.202933269 4.066676991 AK(ac)LAEQAER ddPTM_HeLa_Romidepsin_16h_R1 1 AKLAEQAER 9 1 P63104;E7EX29;E7ESK7;E5RGE1;E5RIR4;E9PD24;E7EVZ2;P31946-2;P31946;Q4VY20;Q4VY19;A0A0J9YWE8;E9PG15;P27348;P31947-2;P31947 P63104;P31946-2;E9PG15;P31947-2 YWHAZ;YWHAB;YWHAQ;SFN "14-3-3 protein zeta/delta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein theta;14-3-3 protein sigma" 0 1 AK(1)LAEQAER 103.26 0.022894 3005100 1492 1124.1 2430.4 1762.2 2290.2 2180.7 2111.1 2144.5 1536.6 1049.7 FALSE TRUE FALSE 1473.81493 1139.925109 2472.700092 1965.953855 2173.322548 2041.360308 2290.416781 2206.547724 1399.162648 1022.428643 1.441484392 1.11491899 2.418457376 1.922827446 2.125647167 1.996579734 2.240172747 2.158143495 1.368469729 1 9.997784443 -9.768913886 24.99999202 1.207286837 2.130486879 0.87340147 0.17003782 46.89780261 156858.9729 0.032024371 0.042550982 1.70E-10 9.768913886 0.923200041 AK(ac)LDSSETTMVK ddPTM_HeLa_Romidepsin_16h_R1 1 AKLDSSETTMVK 12 1 A0A590UK93;A0A590UKC5;B3KNJ4;Q9UBE0-2;Q9UBE0-3;Q9UBE0;M0R054;M0QX65 A0A590UK93 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 0 1 AK(1)LDSSETTMVK 96.745 0.01378 788060 244.65 113.88 144.89 122.99 267.04 267.5 218.22 260.2 239.35 186.21 FALSE TRUE FALSE 241.6681117 115.4832056 147.4117497 137.2106825 253.4119523 250.4076133 236.7556014 267.7284765 217.9419365 181.3722374 1.332442689 0.636719309 0.81275807 0.756514252 1.397192625 1.380628132 1.305357451 1.47612711 1.201627877 1 7.502809829 -8.706934946 24.99888653 1.063570936 1.383136863 0.459012595 0.212058278 96.77854761 44387.60792 0.036882996 0.073765959 1.96E-09 8.706934946 0.319565927 AK(ac)LVPSQEETK ddPTM_HeLa_Romidepsin_16h_R1 2 AKLVPSQEETK 11 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 0 1 ; AK(1)LVPSQEETK;AK(1)LVPSQEETK 123.01 0.01827 8694500 4308 4447.1 4632.8 3731.5 6106.4 6098.8 5147.7 5641 4407.1 4185.2 FALSE TRUE FALSE 4255.492439 4509.706391 4713.431941 4162.953587 5794.767622 5709.106363 5584.94551 5804.213435 4012.917938 4076.467901 1.043916582 1.10627791 1.156253908 1.021215839 1.421516804 1.400503206 1.370045256 1.42383396 0.984410533 1 11.99310394 -8.761608174 24.99999881 1.039672345 1.401303345 0.922470808 0.049907847 0.905864254 134195.8677 0.008060571 0.015312982 1.73E-09 8.761608174 0.361631 AKADS(ph)PVNGLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AKADSPVNGLPK 12 1 Q96S94;Q96S94-3;A0A0A0MSF3 Q96S94 CCNL2 Cyclin-L2 1 0 AKADS(1)PVNGLPK 81.526 0.016803 90198000 8495.7 8836.4 7549.9 6448.1 8178.6 8477.1 7674.7 8579.2 8870 8242.1 TRUE FALSE FALSE 8392.151141 8960.799071 7681.302842 7193.659661 7761.215523 7935.440669 8326.588826 8827.425616 8076.644985 8027.969054 1.045364162 1.11619751 0.956817695 0.896074663 0.966771978 0.988474247 1.037197424 1.099583912 1.006063293 1 12.97081934 AKAGLESGAEPGDGDS(ph)DTTK ddPTM_HeLa_Romidepsin_16h_R1 1 AKAGLESGAEPGDGDSDTTK 20 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 AKAGLESGAEPGDGDS(0.905)DT(0.07)T(0.025)K 114.64 0.00010464 8409400 1679.9 2092.7 1610.7 2415.5 1730.7 1763.3 1518.2 1593.3 2196 1809.6 TRUE FALSE FALSE 1659.424733 2122.161086 1638.733558 2694.791475 1642.375921 1650.630821 1647.15587 1639.399622 1999.58426 1762.586331 0.941471463 1.204004052 0.929732365 1.528884814 0.931798853 0.936482254 0.934510748 0.930110255 1.134460324 1 10.78347821 AKDDATLSGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AKDDATLSGKR 11 2 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 1 ; AKDDATLSGK(1)R;AKDDATLSGK(1)R 130.56 0.0030768 55971000 13952.3 13044.1 13167 12081.4 14493.7 13002.1 16656.1 11911.3 17213.4 12276.8 FALSE TRUE FALSE 13782.244 13227.73518 13396.16611 13478.30831 13754.03241 12171.30777 18070.86872 12255.93467 15673.79039 11957.84697 1.152569024 1.106197062 1.120282451 1.127151765 1.15020977 1.017851107 1.511214249 1.024928209 1.310753553 1 13.54567003 -16.52287874 0.11520403 0.465600221 1.253658417 0 0.159785523 112.8867471 0.947086634 14.19820248 0.64656 3.00E-17 16.52287874 0.788058196 AKEEELT(ph)T(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 AKEEELTTLR 10 1 Q8IUG5-2;Q8IUG5;Q8IUG5-3 Q8IUG5-2 MYO18B Unconventional myosin-XVIIIb 2 0 AKEEELT(1)T(1)LR 60.102 0.0040007 0 4909.1 4692.6 4238.8 3681.1 4372.8 4768.3 3939.5 3975.8 4961.9 4911.4 TRUE FALSE FALSE 4849.266001 4758.662546 4312.574536 4106.726102 4149.639699 4463.621019 4274.121032 4090.8335 4518.095237 4783.80112 1.0136847 0.994745063 0.901495365 0.858465057 0.867435664 0.933069939 0.893457091 0.855142887 0.944457164 1 12.2239417 -9.747409463 3.844590649 1.006416492 0.883874408 0.751004986 0.028644063 0.051058111 1.647514217 0.003455788 0.004811453 1.79E-10 9.747409463 -0.122542084 AKEGVVAAAEK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 AKEGVVAAAEKTK 13 2 D6RA31;H6UYS7;E7EPV7;A0A669KB41;A0A669KBH5;P37840-2;P37840-3;P37840 D6RA31 SNCA Alpha-synuclein 0 1 ; AKEGVVAAAEK(1)TK;AKEGVVAAAEK(1)TK 115.1 0.00379 4681800 4460 3911 3426.5 4538.1 4642.6 3842.1 4443.4 3782.8 4587.3 3712.5 FALSE TRUE FALSE 4405.639805 3966.059161 3486.136795 5062.816474 4405.670798 3596.60221 4820.822285 3892.24935 4177.000399 3616.048715 1.218357426 1.09679362 0.964073515 1.400096313 1.218365997 0.994622167 1.333174043 1.07638189 1.155128354 1 11.8201984 -12.43941069 0.95677902 0.990887314 1.168865478 0.004909287 0.139210012 0.847919221 1.268259282 0.112228788 0.022837671 3.64E-13 12.43941069 0.177978164 AKEQEAEPEEQEEDS(ph)SSDPR ddPTM_HeLa_Romidepsin_16h_R1 2 AKEQEAEPEEQEEDSSSDPR 20 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 0 AKEQEAEPEEQEEDS(0.333)S(0.333)S(0.333)DPR;AKEQEAEPEEQEEDS(0.333)S(0.333)S(0.333)DPR ; 86.573 0.0009012 8016200 1813.04 1542.13 1687.89 1794.45 1731.8 1905.54 1895.25 2117.18 1665.68 2067.29 TRUE FALSE FALSE 1790.941971 1563.840147 1717.267017 2001.932752 1643.419784 1783.782144 2056.232488 2178.437263 1516.697409 2013.581508 0.889431078 0.776646061 0.852842068 0.994214907 0.816167499 0.885875311 1.021181651 1.081871906 0.75323368 1 10.97554816 -7.600254741 4.267676247 0.918505166 1.069945303 0.316463174 0.087671032 0.184513555 6.201234889 0.011561438 0.050126623 2.51E-08 7.600254741 0.151440137 AKLDPEPEKAAESPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 AKLDPEPEKAAESPSPR 17 2 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 AKLDPEPEKAAES(0.098)PS(0.902)PR 83.063 0.0038631 0 1789 1985.1 1482.9 2813.9 1926.6 1512.5 1439.7 1462.2 1710.9 1526.1 TRUE FALSE FALSE 1767.19498 2013.04629 1508.709252 3139.256358 1828.278413 1415.856131 1561.988082 1504.50645 1557.872819 1486.451702 1.188868079 1.354262831 1.014973612 2.111912788 1.229961532 0.952507323 1.050816572 1.012146206 1.048048058 1 10.53765687 -5.829233279 18.81560092 1.160840652 1.198137283 0 0.329393499 0 0 0.04337004 0 1.48E-06 5.829233279 0.037296631 AKNWEDEDFYDS(ph)DDDTFLDR ddPTM_HeLa_Romidepsin_16h_R1 2 AKNWEDEDFYDSDDDTFLDR 20 1 A0A087WWF4;A0A087X0M4;Q9BWU0 A0A087WWF4 SLC4A1AP Kanadaptin 1 0 AKNWEDEDFYDS(0.985)DDDT(0.014)FLDR;AKNWEDEDFYDS(0.932)DDDT(0.068)FLDR ; 127.3 0.00011176 48239000 9006.2 8309 7366.3 8775.8 7914.5 7259.3 6645.2 7050.1 9253.2 8366.1 TRUE FALSE FALSE 8896.42897 8425.97432 7494.507361 9790.499287 7510.593532 6795.454158 7209.643122 7254.08352 8425.570617 8148.747516 1.091754156 1.034020787 0.919712796 1.201472897 0.921686863 0.833926213 0.884754756 0.890208404 1.033971245 1 12.99236262 -8.53860061 24.99864055 1.043881766 0.872252972 0.588453271 0.06827398 120.6177524 191788.4384 0.009726755 0.019458113 2.89E-09 8.53860061 -0.171628793 AKPAMPQDSVPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 AKPAMPQDSVPSPR 14 1 P53396 P53396 ACLY ATP-citrate synthase 1 0 AKPAMPQDSVPS(1)PR 86.222 0.026913 27627000 5144 4500.5 4594.8 5346.3 6021.8 6850 5847.7 6673.6 5466.3 5204.6 TRUE FALSE FALSE 5081.302949 4563.858157 4674.770567 5964.464361 5714.485076 6412.307107 6344.403492 6866.690087 4977.380437 5069.383742 1.002351214 0.900278691 0.922157565 1.176565962 1.12725439 1.264908603 1.251513757 1.354541387 0.981851186 1 12.30759466 -8.640915335 1.195393533 0.988303449 1.302980656 0.846292337 0.059007205 0.141611006 0.392711667 0.00959209 0.029561895 2.29E-09 8.640915335 0.314677207 AKS(ph)PTPESSTIASYVTLR ddPTM_HeLa_Romidepsin_16h_R1 1 AKSPTPESSTIASYVTLR 18 1 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 AKS(0.742)PT(0.082)PES(0.119)S(0.031)T(0.018)IAS(0.004)YVT(0.004)LR 54.171 0.026436 231320000 1688.9 2072.7 1631.6 1807.8 1583.9 1553.1 1508.6 1685 2159.3 2142.4 TRUE FALSE FALSE 1668.315037 2101.879525 1659.997314 2016.826342 1503.067673 1453.861922 1636.740446 1733.752817 1966.1668 2086.740139 0.799483848 1.007255041 0.795497859 0.966496165 0.720294609 0.696714409 0.784352788 0.830842702 0.942219284 1 11.02703524 -8.7556308 25 0.906275197 0.755548606 0.508690646 0.07666749 113.3639248 487910.9005 0.013243694 0.025923362 1.76E-09 8.7556308 -0.15072659 AKS(ph)PTPESSTIASYVTLRK ddPTM_HeLa_Romidepsin_16h_R1 1 AKSPTPESSTIASYVTLRK 19 2 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 AKS(0.994)PT(0.005)PESSTIASYVTLRK 66.606 0.017139 12249000 361.4 457.58 417.99 402.28 295.49 190.78 299.77 272.08 432.53 350.78 TRUE FALSE FALSE 356.9951178 464.0218233 425.2649406 448.7935064 280.4100427 178.5897737 325.2324563 279.9522055 393.8434335 341.666685 1.044863703 1.35811258 1.244677808 1.313541899 0.820712276 0.522701749 0.951899821 0.819372265 1.152712426 1 8.416445771 -8.602329055 8.774902268 1.08638939 0.764974347 0.566494652 0.161468744 0.204336447 20.37192053 0.025840416 0.051759338 2.50E-09 8.602329055 -0.321415042 AKSPT(ph)PESSTIASYVTLR ddPTM_HeLa_Romidepsin_16h_R1 1 AKSPTPESSTIASYVTLR 18 1 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 AKS(0.249)PT(0.459)PES(0.136)S(0.148)T(0.008)IASYVTLR 131.31 0.0065306 108990000 1634.4 1895.8 1672.7 1385.1 1526 1658.5 1155.5 1690.7 1903.2 1747.1 TRUE FALSE FALSE 1614.479304 1922.489122 1701.812642 1545.251779 1448.122526 1552.527203 1253.648141 1739.617737 1732.973025 1701.71009 0.948739338 1.129739509 1.000060264 0.908058187 0.850980748 0.912333547 0.736699011 1.022276207 1.018371481 1 10.73276956 -9.12529177 3.889196808 0.990687457 0.873187667 0.383987068 0.080661098 0.209895133 5.564130209 0.011671101 0.019973584 7.49E-10 9.12529177 -0.11749979 AKSPT(ph)PESSTIASYVTLRK ddPTM_HeLa_Romidepsin_16h_R1 1 AKSPTPESSTIASYVTLRK 19 2 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 AKS(0.281)PT(0.713)PES(0.005)S(0.002)T(0.001)IASYVTLRK 87.088 0.023124 30816000 1562.4 1541.2 835.73 2484.9 1345.9 838.17 859.22 1148.9 1374 1249.4 TRUE FALSE FALSE 1543.356868 1562.897054 850.2755301 2772.21583 1277.213701 784.6136421 932.2021254 1182.141609 1251.105999 1216.940408 1.268227152 1.284283967 0.698699398 2.27802102 1.049528549 0.644742862 0.766021178 0.971404681 1.028074991 1 10.24904281 -8.513943442 24.98326586 1.19843266 0.800566489 0.2105509 0.3937694 548.6518067 1534038.821 0.055051351 0.114927434 3.06E-09 8.513943442 -0.397866171 AKT(ph)QT(ph)PPVSPAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 2 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 AKT(0.613)QT(0.854)PPVS(0.533)PAPQPTEER;AKT(0.983)QT(0.954)PPVS(0.063)PAPQPTEER ; 79.393 0.012187 61242000 6102 6040.1 5965.9 5547.8 7971 6955.4 6212.1 7019 6692.2 6742 TRUE FALSE FALSE 6027.626477 6125.132686 6069.733987 6189.262739 7564.210126 6510.972388 6739.755619 7222.083691 6093.632871 6566.841868 0.917888172 0.932736437 0.924300312 0.942502174 1.151879439 0.991492184 1.026331341 1.099780357 0.927939639 1 12.680984 -8.797352017 24.99921876 0.953700817 1.059019628 0.634016818 0.046294694 104.710221 72889.707 0.007397134 0.013408751 1.59E-09 8.797352017 0.105318811 AKT(ph)QTPPVS(ph)PAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 2 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 AKT(0.709)QT(0.298)PPVS(0.993)PAPQPTEER;AKT(0.506)QT(0.507)PPVS(0.986)PAPQPT(0.001)EER ; 87.05 0.0075911 51657000 5583.5 5675.2 4995.6 4506.4 6569.6 6786 6021.2 6862.8 6422.7 6026 TRUE FALSE FALSE 5515.446154 5755.095615 5082.546322 5027.451171 6234.328797 6352.396501 6532.640578 7061.36429 5848.237626 5869.443651 0.939688066 0.980518079 0.865933234 0.856546458 1.062166905 1.08228256 1.112991446 1.203072167 0.996387047 1 12.51900805 -8.224652258 1.751581356 0.956673648 1.156211658 0.701895896 0.056274428 0.177807062 1.029009331 0.008962635 0.031437304 5.96E-09 8.224652258 0.199538009 AKTQT(ph)PPVSPAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 2 AKTQTPPVSPAPQPTEER 18 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 AKT(0.283)QT(0.707)PPVS(0.011)PAPQPTEER;AKT(0.364)QT(0.627)PPVS(0.01)PAPQPTEER ; 73.918 0.010557 548540000 6923.1 6304.4 5857.9 5929.2 5764.6 5333.3 4474.7 5490.7 6762.4 6676 TRUE FALSE FALSE 6838.718594 6393.153509 5959.854292 6614.762002 5470.410951 4992.519342 4854.780906 5649.564742 6157.554007 6502.556558 1.051696903 0.983175379 0.91654017 1.017255589 0.841270799 0.767777919 0.746595722 0.868822084 0.946943553 1 12.66679133 -8.682988911 3.364422522 1.012785961 0.790504743 0.746993805 0.050206779 0.073610513 1.660457726 0.007264438 0.015114819 2.07E-09 8.682988911 -0.222281218 AKTQTPPVS(ph)PAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 AKT(0.167)QT(0.29)PPVS(0.55)PAPQPT(0.209)EERLPS(0.322)S(0.322)PVY(0.132)EDAAS(0.007)FK 41.139 0.019938 33557000 1896 1886.6 1649.9 2962.2 2109 1679.3 2158 2117.7 2104.7 1742.2 TRUE FALSE FALSE 1872.890823 1913.159604 1678.615817 3304.703502 2001.36986 1571.99815 2341.300466 2178.972308 1916.450361 1696.937393 1.103688816 1.127419086 0.989203152 1.947451636 1.179401119 0.926373687 1.379721182 1.284061697 1.129358319 1 10.72871762 AKTQTPPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 1 AKTQTPPVSPAPQPTEERLPSSPVYEDAASFK 32 2 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 AKTQTPPVS(0.002)PAPQPT(0.323)EERLPS(0.323)S(0.323)PVY(0.027)EDAAS(0.001)FK 46.785 0.0069439 20633000 1639.3 1865.3 1370.9 3558.8 1713.8 1947.1 1914.7 1993.2 1684.9 1347.9 TRUE FALSE FALSE 1619.319581 1891.559742 1394.759939 3970.285201 1626.338391 1822.686594 2077.33457 2050.870097 1534.198324 1312.881364 1.233408917 1.440769741 1.062365556 3.024100509 1.238755028 1.388310204 1.582271352 1.562113801 1.168573465 1 10.35852084 ALAAFLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 ALAAFLKK 8 1 M0R2L9;M0QYF7;M0R140;P39019 M0R2L9 RPS19 40S ribosomal protein S19 0 1 ALAAFLK(1)K 119.89 0.0015704 290870 132.62 55.198 407.34 153.37 420 391.71 307.16 95.935 102.63 0 FALSE TRUE FALSE 131.0035764 55.97507889 414.4295818 171.103361 398.5658328 366.6809952 333.2501627 98.71072786 93.45051576 0 0 ALAAGADS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ALAAGADSPK 10 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 ALAAGADS(1)PK;ALAAGADS(1)PK ; 106.4 0.020391 65936000 12164.3 12844.2 13826.6 6912.8 12631.9 17436.2 16435.8 11146.6 13037.6 12679.5 TRUE FALSE FALSE 12016.03683 13025.02098 14067.24617 7712.090462 11987.24701 16322.08309 17831.85644 11469.10928 11871.4844 12350.08476 0.97295177 1.054650331 1.139040456 0.62445648 0.970620626 1.321617091 1.443865106 0.928666443 0.9612472 1 13.59223332 -8.270148342 23.65476161 0.974953504 1.252631104 0.332929733 0.174139276 236.0644415 641185.8615 0.023381536 0.053122164 5.37E-09 8.270148342 0.2776776 ALAAGADS(ph)PKTEEARPSPAPGPGTPTGTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 ALAAGADSPKTEEARPSPAPGPGTPTGTPTR 31 2 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 ALAAGADS(0.843)PKT(0.109)EEARPS(0.013)PAPGPGT(0.016)PT(0.006)GT(0.006)PT(0.006)R 41.986 0.019618 78060000 1791.4 1510.3 1321.8 1647.8 1065.8 1237.6 1394.7 1676.9 2089.7 1324 TRUE FALSE FALSE 1769.565728 1531.562043 1344.805375 1838.326389 1011.408249 1158.521354 1513.165783 1725.418456 1902.791998 1289.602289 1.372179425 1.187623546 1.042806287 1.425498702 0.784279198 0.898355535 1.173358481 1.337946179 1.475487454 1 10.33271049 -8.76706617 24.99940352 1.185363413 1.046680884 0.14625705 0.205709084 269.2994597 1196481.344 0.031078237 0.057465856 1.71E-09 8.76706617 -0.138682528 ALAEEAS(ph)EEELPS(ph)DVDLNDPYFAEEVK ddPTM_HeLa_Romidepsin_16h_R1 2 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 2 0 ALAEEAS(1)EEELPS(0.997)DVDLNDPY(0.003)FAEEVK;ALAEEAS(0.894)EEELPS(0.835)DVDLNDPY(0.272)FAEEVK ; 91.115 4.41E-07 6158800 2121.72 1693.21 1555.67 1574.99 1900.37 1847.01 1612.96 2081.77 1858.23 1888.82 TRUE FALSE FALSE 2095.859661 1717.047055 1582.745784 1757.097754 1803.387028 1728.992022 1749.964782 2142.00273 1692.025255 1839.748184 1.139210072 0.933305476 0.860305664 0.95507514 0.980235797 0.939798195 0.951197994 1.16429126 0.91970481 1 10.8452926 -10.24558777 24.92074156 1.065738091 0.963047743 0 0.091665039 854.8826054 1343985.262 0.014459532 0.017675109 5.68E-11 10.24558777 -0.102690348 ALAEEASEEELPS(ph)DVDLNDPYFAEEVK ddPTM_HeLa_Romidepsin_16h_R1 3 ALAEEASEEELPSDVDLNDPYFAEEVK 27 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 0 ALAEEAS(0.286)EEELPS(0.714)DVDLNDPYFAEEVK;ALAEEASEEELPS(1)DVDLNDPYFAEEVK;ALAEEAS(0.001)EEELPS(0.997)DVDLNDPY(0.002)FAEEVK ;; 136.57 2.73E-10 13914200 5760.15 5307.64 4986.64 5287.78 5447.54 5256.02 5957.63 6061.64 5902.9 6124.12 TRUE FALSE FALSE 5689.943076 5382.361095 5073.430377 5899.178003 5169.531706 4920.177285 6463.670943 6237.02399 5374.92984 5965.01448 0.953885878 0.902321547 0.850531108 0.988962898 0.866641938 0.824839118 1.083596857 1.045600813 0.901075741 1 12.54230992 -11.35039192 1.100877493 0.992250739 0.936130817 0 0.084192771 0.895035074 2.227191061 0.024862987 0.01659207 4.46E-12 11.35039192 -0.056119921 ALAITSK(ac)APPAK ddPTM_HeLa_Romidepsin_16h_R1 2 ALAITSKAPPAK 12 1 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 0 1 ; ALAITSK(1)APPAK;ALAITSK(1)APPAK 126.19 0.011319 2707300 3344.4 3538.1 2772.7 2525.2 4336.8 4426.1 5106.9 5289.9 3803.7 3377.6 FALSE TRUE FALSE 3303.637166 3587.909465 2820.95768 2817.175505 4115.476913 4143.286495 5540.679959 5442.95491 3463.487545 3289.849465 1.004190982 1.09059989 0.857473179 0.856323529 1.250962075 1.259415222 1.684174312 1.654469291 1.052779947 1 11.68380586 -8.016032254 1.455430923 0.991587503 1.714504347 0.872855163 0.099976078 0.106034736 0.396015129 0.014047674 0.073205308 9.64E-09 8.016032254 0.722916844 ALALDLGS(ph)PAALR ddPTM_HeLa_Romidepsin_16h_R1 1 ALALDLGSPAALR 13 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 ALALDLGS(1)PAALR 116.63 0.0055157 7290400 1593.9 1769.4 1663.9 1646.9 1911.1 2030.7 1703.6 1759.9 1943 1736 TRUE FALSE FALSE 1574.472934 1794.30966 1692.859482 1837.322327 1813.569436 1900.944824 1848.303741 1810.81993 1769.213214 1690.89847 0.931145756 1.061157539 1.001159745 1.086595298 1.072547801 1.124221742 1.093089724 1.070921739 1.046315462 1 10.72357432 -9.578795526 1.217170011 0.969354523 1.093896302 0.439917942 0.040151604 0.182423131 0.541419241 0.006551452 0.010873054 2.64E-10 9.578795526 0.124541779 ALAS(ph)PEQLAQLPSSGVPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALASPEQLAQLPSSGVPR 18 0 Q9Y3Q8;H7BZ77;Q9Y3Q8-2 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 0 ALAS(1)PEQLAQLPSSGVPR 69.069 0.024689 12060000 1212 1019.5 1062.4 1290.4 1524.5 1606.1 1362.7 1642.1 1453.8 1124.8 TRUE FALSE FALSE 1197.227678 1033.852548 1080.890626 1439.60212 1446.699076 1503.475393 1478.447704 1689.611573 1323.768487 1095.577534 1.092782246 0.943659865 0.98659437 1.314012085 1.320489907 1.372313092 1.349468804 1.542210862 1.20828371 1 10.09747587 -9.148605151 3.615984665 1.031863939 1.385218766 0.783621897 0.087987316 0.068305219 1.635163603 0.011145745 0.019077698 7.10E-10 9.148605151 0.353354827 ALASVPS(ph)PALPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALASVPSPALPR 12 0 O60336-4;O60336-3;O60336-6;O60336;O60336-2 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 0 ALAS(0.001)VPS(0.999)PALPR 110.31 0.010546 4694500 1223.1 1166.4 1292.5 1280.3 2436.3 2960.2 2091.8 2871.3 1321.1 1215.6 TRUE FALSE FALSE 1208.192387 1182.82061 1314.99542 1428.33431 2311.96652 2771.052774 2269.47744 2954.376535 1202.937507 1184.018537 1.020416783 0.998988253 1.110620636 1.206344551 1.952643855 2.340379553 1.916758369 2.495211387 1.01597861 1 10.20947595 -8.740735457 2.406078936 1.016614844 2.222972287 0.9406864 0.139439598 0.041482543 0.489882702 0.018562414 0.039735579 1.82E-09 8.740735457 1.206357443 up ALATPPK(ac)LHTCEK ddPTM_HeLa_Romidepsin_16h_R1 2 ALATPPKLHTCEK 13 1 E5RGS7;H0YBP7;B3KPU0;A0A087WVI1;Q96JY6;Q96JY6-3;Q96JY6-5 E5RGS7 PDLIM2 PDZ and LIM domain protein 2 0 1 ; ALATPPK(1)LHTCEK;ALATPPK(1)LHTCEK 136.3 0.00019391 45424000 4576.9 3964.2 4541 60.841 3784.2 4524.5 3656 4228.9 4931.8 3929 FALSE TRUE FALSE 4521.114982 4020.008112 4620.0342 67.87572269 3591.078153 4235.399052 3966.540549 4351.256549 4490.687456 3826.924014 1.181396591 1.050454124 1.207244822 0.017736365 0.938371951 1.10673717 1.036482704 1.137011483 1.173445681 1 11.90196954 ALDEYYDKHFTEFVPLR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDEYYDKHFTEFVPLR 17 1 P38606-2;P38606 P38606-2 ATP6V1A V-type proton ATPase catalytic subunit A 0 0 74.89 0.0099792 4957200 1553.6 1059.1 905.54 1419 1491 1732 1642.6 1704.1 1317.6 1494.3 FALSE FALSE TRUE 1534.664126 1074.010038 921.3005438 1583.071457 1414.908706 1621.33079 1782.122403 1753.405445 1199.750556 1455.477871 1.054405674 0.737908875 0.632988356 1.087664394 0.972126567 1.113950835 1.224424252 1.204693991 0.824300101 1 10.50727719 -8.063632533 2.183611569 0.974392434 1.219068935 0.381470794 0.146872586 0.318957239 2.928872579 0.022515664 0.081314586 8.64E-09 8.063632533 0.244676501 ALDGAFTEENR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDGAFTEENR 11 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 187.5 1.98E-07 6195100 1546 1270.4 1387.1 1298.4 1520.2 1603.6 1495 1864.2 1398.5 1338.3 FALSE FALSE TRUE 1527.156757 1288.284725 1411.241894 1448.527117 1442.618521 1501.135135 1621.985263 1918.137686 1273.414657 1303.530773 1.171554051 0.988304036 1.082630286 1.111233541 1.106700778 1.151591636 1.244301474 1.47149398 0.976896506 1 10.34820893 -4.000001022 0.670789662 1.074377491 42.71990588 0.832087174 0.057284708 78.59687226 0.435571355 0.011206267 4891.18998 1.00E-04 4.000001022 41.64552838 ALDIDS(ph)DEESEPK ddPTM_HeLa_Romidepsin_16h_R1 4 ALDIDSDEESEPK 13 0 Q96DR7-3;Q96DR7-4;Q96DR7 Q96DR7-3 ARHGEF26 Rho guanine nucleotide exchange factor 26 1 0 ALDIDS(0.984)DEES(0.016)EPK;ALDIDS(0.601)DEES(0.399)EPK;ALDIDS(0.996)DEES(0.004)EPK;ALDIDS(0.988)DEES(0.012)EPK ;;; 198.48 4.15E-16 28893000 12666.8 11684.2 14005.1 9342.1 14164.8 14412.4 12141.1 12994.9 12728.4 11794.5 TRUE FALSE FALSE 12512.41217 11848.69047 14248.85289 10422.27756 13441.9174 13491.49415 13172.36473 13370.88693 11589.94003 11488.07719 1.08916505 1.031390221 1.240316604 0.907225586 1.170075477 1.174390973 1.146611788 1.163892504 1.008866831 1 13.48784973 -4.000000278 0.033688208 0.585188389 1.888190677 0.28461591 0.082965074 874.4220204 2.276854876 26.77572287 71.53811278 1.00E-04 4.000000278 1.303002288 ALDISLS(ph)S(ph)GEEDEGDEEDSTAGTTK ddPTM_HeLa_Romidepsin_16h_R1 1 ALDISLSSGEEDEGDEEDSTAGTTK 25 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 2 0 ALDIS(0.049)LS(0.964)S(0.986)GEEDEGDEEDSTAGTTK 115.34 8.83E-06 4227100 3392 4150.5 3343.6 2815.5 3712.2 4092.6 3386 4238.4 4099.9 4317.7 TRUE FALSE FALSE 3350.656999 4208.930848 3401.793955 3141.041357 3522.752582 3831.096068 3673.606755 4361.031417 3733.194676 4205.525532 0.796727299 1.000809724 0.808886768 0.746884387 0.837648602 0.91096726 0.873519071 1.036976564 0.88768803 1 12.03807038 -7.258320416 23.82227221 0.886373925 1.036976673 0.264660167 0.079152075 211.8120585 1617628.389 0.013326627 0.125885231 5.52E-08 7.258320416 0.150602749 ALDQASEEIWNDFR ddPTM_HeLa_Romidepsin_16h_R1 2 ALDQASEEIWNDFR 14 0 F8VZX9;F8VY03;G3V1U3;F8VRR3;F8VQZ7;P50579-3;P50579-2;P50579 F8VZX9 METAP2 Methionine aminopeptidase 2 0 0 ; ; 258.78 7.77E-67 5886200 1486.63 1496.38 1400.9 1303.97 1458.98 1207.36 941.82 1224.78 1699.02 1668.45 FALSE FALSE TRUE 1468.510382 1517.446077 1425.282077 1454.741147 1384.522806 1130.213593 1021.818167 1260.217077 1547.055396 1625.103428 0.903641181 0.933753539 0.877040841 0.895168345 0.851959809 0.695471791 0.62877116 0.775468844 0.951973498 1 10.66631582 -8.570671123 1.06295995 0.949953521 0.678304562 0.80869336 0.048690402 0.179187131 0.378603763 0.008958286 0.032196804 2.69E-09 8.570671123 -0.271648959 ALDSNS(ph)LENDDLSAPGR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDSNSLENDDLSAPGR 17 0 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 ALDS(0.001)NS(0.999)LENDDLSAPGR 196.65 5.95E-14 6046100 1210.9 1139.1 1281.3 844.61 1098.3 1356.5 1321.3 1264.6 1284 1355.1 TRUE FALSE FALSE 1196.141085 1155.13628 1303.600489 942.2677822 1042.249653 1269.824028 1433.531189 1301.189206 1169.155824 1319.894307 0.906240052 0.875173318 0.98765521 0.713896391 0.789646298 0.962064933 1.086095441 0.985828334 0.885795035 1 10.36620669 -7.980270984 12.24257919 0.921110785 1.033064471 0.260525915 0.089159729 1.03879021 635.9918785 0.013921303 0.041529116 1.05E-08 7.980270984 0.111953686 ALDSNS(ph)LENDDLSAPGREPGHFNPESR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDSNSLENDDLSAPGREPGHFNPESR 27 1 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 ALDS(0.114)NS(0.794)LENDDLS(0.092)APGREPGHFNPESR 68.441 9.43E-05 7879200 371.93 293.88 350.23 195.42 314.31 385.05 340.05 403.79 436.69 452.75 TRUE FALSE FALSE 367.3967741 298.0172504 356.3256062 218.0153799 298.2695878 360.4465477 368.9338385 415.4730266 397.6313527 440.9874897 0.833122895 0.675795249 0.808017494 0.494379965 0.676367459 0.817362297 0.836608401 0.942142433 0.901683975 1 8.784593919 -11.22908877 0.881950459 0.976065902 0.747526445 0.293096817 0.118140599 0.396806196 0.655363228 0.041366998 0.027077717 5.90E-12 11.22908877 -0.228539456 ALDVS(ph)ASDDEIAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDVSASDDEIAR 13 0 C9JLK2;H7C393;H7C1U0;C9JIF9;P13798 C9JLK2 APEH Acylamino-acid-releasing enzyme 1 0 ALDVS(0.665)AS(0.335)DDEIAR 223.36 1.94E-31 67392000 3927.8 3756.1 3855.1 3167.9 4516.9 4618.1 3506.7 3513.6 3518 2906.1 TRUE FALSE FALSE 3879.926463 3808.978474 3922.196398 3534.187503 4286.385738 4323.018314 3804.55901 3615.260472 3203.341269 2830.599103 1.370708575 1.34564392 1.385641787 1.248565189 1.514303362 1.527244995 1.344082603 1.277206818 1.131683136 1 11.46689172 -12.26007389 0.516954643 0.919025794 1.394754505 0.631986474 0.092662904 0.590449409 0.217144599 0.14178994 0.022445762 5.49E-13 12.26007389 0.475728711 ALDVSAS(ph)DDEIAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALDVSASDDEIAR 13 0 C9JLK2;H7C393;H7C1U0;C9JIF9;P13798 C9JLK2 APEH Acylamino-acid-releasing enzyme 1 0 ALDVS(0.017)AS(0.983)DDEIAR 138.31 0.0013211 73782000 933.18 956.09 1008.3 982.73 1173.5 1248.4 1034.8 924.17 1134.9 719.3 TRUE FALSE FALSE 921.8060432 969.5498601 1025.849039 1096.357866 1113.611916 1168.631269 1122.695886 950.9094009 1033.391702 700.6124823 1.315714559 1.383860386 1.464217473 1.564856314 1.589483408 1.668013772 1.602449163 1.357254438 1.474983286 1 9.452472882 -10.89502953 0.46064068 0.996047292 1.587611257 0.208340867 0.163367502 0.232093325 0.122938354 0.054089877 0.035538998 1.27E-11 10.89502953 0.591563965 ALEATTEHIR ddPTM_HeLa_Romidepsin_16h_R1 1 ALEATTEHIR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 132.32 0.0029915 4648300 3954.4 3777.5 3762.7 3000.7 4515.6 5001.4 3998.5 3708.9 4262.5 4159 FALSE FALSE TRUE 3906.202252 3830.679744 3828.188215 3347.655053 4285.152082 4681.826681 4338.13249 3816.21117 3881.251324 4050.94858 0.964268535 0.945625368 0.94501032 0.82638794 1.057814484 1.155735895 1.070893003 0.942053718 0.958109254 1 11.98404406 -8.56519702 24.99999197 0.965654827 1.065874824 0.387834297 0.067002201 123.1361551 72743.57849 0.009941308 0.019882628 2.72E-09 8.56519702 0.100219997 ALEAVFGK ddPTM_HeLa_Romidepsin_16h_R1 1 ALEAVFGK 8 0 P38159;P38159-2;H0Y6E7;H3BT71;H3BR27;P38159-3;H3BNC1 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 0 0 113.5 0.017567 399250 812.77 504.36 503.12 526.8 473.13 574.54 390.07 441.95 801.72 543.25 FALSE FALSE TRUE 802.8636466 511.4603933 511.8765926 587.7110947 448.9844106 537.8287482 423.2025361 454.737126 730.0121553 529.1362867 1.51730975 0.966594819 0.967381383 1.110698906 0.848523191 1.016427642 0.799798741 0.859395089 1.379629736 1 9.047495547 -10.08364683 11.81584523 1.244288947 0.938160517 0.543278262 0.149220501 0.745450436 103.6265064 0.034079837 0.041747424 8.25E-11 10.08364683 -0.30612843 ALEEGDGSVSGSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ALEEGDGSVSGSSPR 15 0 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 0 ALEEGDGSVSGS(0.002)S(0.998)PR;ALEEGDGSVSGS(0.02)S(0.98)PR ; 263.98 4.11E-72 258970000 13908.4 12626.4 12864.6 11746.5 10686.4 9566.8 9734.4 10132.3 13894.8 13497.7 TRUE FALSE FALSE 13738.87907 12804.15479 13088.50297 13104.6856 10141.03313 8955.512355 10561.23969 10425.46211 12652.01429 13147.02781 1.045017876 0.973920112 0.995548436 0.996779332 0.77135557 0.681181518 0.803317666 0.792990041 0.962347876 1 13.68244906 -8.765760085 5.031497732 1.014867072 0.757247049 0.894952959 0.038900776 0.035647382 2.483320704 0.005541814 0.01071714 1.71E-09 8.765760085 -0.257620023 ALEESESSQLIS(ph)PPLAQAIR ddPTM_HeLa_Romidepsin_16h_R1 2 ALEESESSQLISPPLAQAIR 20 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 ALEES(0.017)ES(0.36)S(0.247)QLIS(0.376)PPLAQAIR;ALEESESSQLIS(0.999)PPLAQAIR ; 149.42 1.97E-05 16493000 3168.1 2765.8 2576.8 2830.9 3171.6 3713.9 3247.2 3601 2977.7 2831 TRUE FALSE FALSE 3129.485979 2804.737005 2621.648123 3158.221978 3009.741417 3476.593776 3523.017087 3705.189254 2711.367054 2757.450212 1.134920212 1.017148739 0.950750846 1.145341433 1.091494383 1.260800199 1.277635793 1.343701234 0.983287764 1 11.42911912 -8.198725843 1.360887161 1.055162267 1.330481801 0.788480462 0.059736365 0.191370791 0.637723481 0.010137705 0.044298038 6.33E-09 8.198725843 0.275319535 ALELDSNLYR ddPTM_HeLa_Romidepsin_16h_R1 1 ALELDSNLYR 10 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 121.73 8.93E-05 0 444.76 392.32 499.28 536.34 793.98 514.07 552.83 336.85 526.18 410.34 FALSE FALSE TRUE 439.339094 397.8430913 507.969759 598.3541544 753.4602379 481.2225861 599.7873664 346.5962233 479.117143 399.6793076 1.099229021 0.995405776 1.270943352 1.497085646 1.885161987 1.204021767 1.500671551 0.867185808 1.198753935 1 8.642699073 -9.587891316 3.933178466 1.04475938 1.412654151 0.262209289 0.247320163 0.187895403 5.883770579 0.037161691 0.053860759 2.58E-10 9.587891316 0.367894771 ALELTGLK ddPTM_HeLa_Romidepsin_16h_R1 1 ALELTGLK 8 0 P19338 P19338 NCL Nucleolin 0 0 101.28 0.017744 0 416.22 359.15 547.52 413.3 640.78 485.06 474.28 548.04 267.29 381.17 FALSE FALSE TRUE 411.1469505 364.2061231 557.0493559 461.0876906 608.0786055 454.0662315 514.5653314 563.8966727 243.382913 371.2671485 1.107415381 0.980981282 1.50040034 1.241929679 1.637846516 1.223017532 1.385970543 1.51884344 0.655546589 1 8.536313854 -9.763818217 24.99986002 1.046910503 1.409672216 0.629383959 0.172952795 25.11039666 263892.9881 0.018086889 0.024409887 1.72E-10 9.763818217 0.362761713 ALENDFFNS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 3 ALENDFFNSPPR 12 0 F5H148;Q9NYV6;H3BMT1;Q9NYV6-2;Q9NYV6-3;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 0 ALENDFFNS(1)PPR;ALENDFFNS(1)PPR;ALENDFFNS(1)PPR ;; 175.01 3.40E-05 32005500 9554 8659.4 7923.2 6317.9 7098.4 8407.4 6710.9 6970 9540.1 8366.3 TRUE FALSE FALSE 9437.552173 8781.30726 8061.099972 7048.405325 6736.14216 7870.194274 7280.923678 7171.665953 8686.809562 8148.94232 1.15813216 1.077600861 0.989220399 0.864947259 0.826627787 0.965793347 0.893480822 0.880073226 1.066004547 1 12.9923971 -9.514361664 3.11238267 1.076747927 0.888353559 0.772605469 0.048386848 0.122067285 2.427944511 0.010724008 0.016233397 3.06E-10 9.514361664 -0.188394368 ALENDFFNS(ph)PPRK ddPTM_HeLa_Romidepsin_16h_R1 2 ALENDFFNSPPRK 13 1 F5H148;Q9NYV6;H3BMT1;Q9NYV6-2;Q9NYV6-3;A6NIE6 F5H148 RRN3;RRN3P2 RNA polymerase I-specific transcription initiation factor RRN3;Putative RRN3-like protein RRN3P2 1 0 ALENDFFNS(1)PPRK;ALENDFFNS(1)PPRK ; 98 0.0058715 85915000 3540.8 3817.8 3215.3 2658.2 3171.4 3305.7 2962.5 3045.4 4410.1 3931.9 TRUE FALSE FALSE 3497.643368 3871.547089 3271.260948 2965.553591 3009.551624 3094.476439 3214.134676 3133.513844 4015.649611 3829.748671 0.913282742 1.010914141 0.854171182 0.77434679 0.785835281 0.808010317 0.839254727 0.81820352 1.04854129 1 11.903034 -9.599040888 5.001315802 0.961523051 0.806675713 0.819171514 0.040817302 0.067942028 3.109589096 0.006141516 0.008770645 2.52E-10 9.599040888 -0.154847337 ALES(ph)PERPFLAILGGAK ddPTM_HeLa_Romidepsin_16h_R1 2 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 1 0 ALES(1)PERPFLAILGGAK;ALES(1)PERPFLAILGGAK ; 117 2.65E-05 1166800 1115.29 1211.32 909.62 1134.08 1451.18 1166.85 1089.27 1216.4 1263.32 1107.33 TRUE FALSE FALSE 1101.696416 1228.372995 925.4515545 1265.207666 1377.12087 1092.292051 1181.792567 1251.594615 1150.325495 1078.561407 1.021449877 1.138899451 0.858042526 1.173051119 1.27681267 1.012730517 1.095711898 1.16042963 1.066536859 1 10.0748926 -9.200823511 24.99998634 1.011722803 1.141192434 0.329551229 0.090209237 205.3527897 84694.18798 0.012654926 0.020985816 6.30E-10 9.200823511 0.129469632 ALESPERPFLAILGGAK ddPTM_HeLa_Romidepsin_16h_R1 3 ALESPERPFLAILGGAK 17 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 0 ;; ;; 158.31 5.16E-05 15956070 4863 3728.3 4189.7 3883.56 4522.68 4621.06 4637.4 4803 4911.9 3965.1 FALSE FALSE TRUE 4803.727886 3780.787105 4262.619971 4332.59548 4291.870763 4325.78918 5031.30064 4941.967227 4472.567362 3862.08613 1.243816871 0.978949453 1.103709194 1.121827772 1.111283026 1.120065435 1.302741697 1.279610827 1.158070331 1 11.91516462 -16.52287873 0.023586922 2.16E-06 1.945678498 0.220140711 0.090682783 2135.029649 4.055766766 232.7249441 119.5233725 3.00E-17 16.52287873 1.945676335 ALEVAGPDGQASAISPAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ALEVAGPDGQASAISPASPR 20 0 K7EIN8;Q0VDD7-2;Q0VDD7 K7EIN8 C19orf57 Uncharacterized protein C19orf57 1 0 ALEVAGPDGQASAIS(0.04)PAS(0.96)PR 220.74 1.51E-41 8305900 1325.6 1448.5 1462 1640.9 1754.9 2107.5 1948.8 2785.7 1596.5 1370.4 TRUE FALSE FALSE 1309.443077 1468.892021 1487.445497 1830.628579 1665.340905 1972.837552 2114.331023 2866.299834 1453.705041 1334.79681 0.981005549 1.100461141 1.114360991 1.371466102 1.247636263 1.478005893 1.584009646 2.147367908 1.089083395 1 10.38240443 -4 0.361288558 0.977739384 15.3307039 0.939562753 0.083276397 7.504804139 0.093042272 0.02090806 75.11664854 1.00E-04 4 14.35296452 up ALFEEVPELLTEAEKK ddPTM_HeLa_Romidepsin_16h_R1 1 ALFEEVPELLTEAEKK 16 1 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 0 98.654 0.003984 2982000 583.56 336.65 455.22 572.78 578.58 382.43 331.05 279.1 533.19 340.98 FALSE FALSE TRUE 576.4473463 341.3893675 463.1429131 639.0075186 549.0529036 357.9939572 359.1693787 287.1753182 485.500151 332.1212904 1.735653097 1.0279057 1.394499318 1.924018535 1.653169849 1.077901259 1.081440393 0.864670006 1.461815803 1 8.375566399 -8.087084296 6.538712281 1.395775917 0.997955854 0.339825416 0.279673001 0.293224822 18.32271588 0.049841907 0.129335816 8.18E-09 8.087084296 -0.397820062 ALFLDALGPPAVT(ph)REGGDPGVR ddPTM_HeLa_Romidepsin_16h_R1 1 ALFLDALGPPAVTREGGDPGVR 22 1 P05111 P05111 INHA Inhibin alpha chain 1 0 ALFLDALGPPAVT(1)REGGDPGVR 73.36 0.013749 33087000 2726 2568.9 2278.9 2011.5 2493.2 2746.3 2392.8 2335.3 3015.8 2755.8 TRUE FALSE FALSE 2692.774463 2605.065042 2318.563299 2244.079094 2365.962701 2570.820293 2596.044372 2402.868221 2746.059295 2684.203919 1.003192956 0.970516816 0.86378061 0.836031525 0.881439254 0.957758938 0.967156167 0.895188404 1.023044216 1 11.39027856 -9.93522231 5.174169641 1.00089232 0.902372921 0.631482503 0.037681399 0.110961635 5.822565202 0.006673467 0.008792089 1.16E-10 9.93522231 -0.098519399 ALGITLIK ddPTM_HeLa_Romidepsin_16h_R1 1 ALGITLIK 8 0 C9K0P5;C9JFA7;Q8N335 C9K0P5 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein 0 0 92.47 0.020285 0 62.737 196.8 112.09 0 0 0 0 0 111.54 54.49 FALSE FALSE TRUE 61.97233731 199.5705556 114.0408794 0 0 0 0 0 101.563583 53.07434194 1.167651544 3.760207819 2.14870077 0 0 0 0 0 1.913609841 1 5.729942674 -9.238408323 22.63241214 1.397833162 1.17E-05 0.552605973 0.813750412 204.3173915 200780.1476 0.13715795 0.227292213 5.78E-10 9.238408323 -1.3978215 ALHSFIT(ph)PPT(ph)TPQLR ddPTM_HeLa_Romidepsin_16h_R1 2 ALHSFITPPTTPQLR 15 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QR75 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 2 0 ALHS(0.358)FIT(0.644)PPT(0.642)T(0.356)PQLR;ALHS(0.01)FIT(0.991)PPT(0.553)T(0.446)PQLR ; 61.957 0.004329 8206700 3837.2 3570.8 3315.8 2667.36 3133.6 3211.9 2164.59 2565.25 3422.4 4008.9 TRUE FALSE FALSE 3790.43073 3621.069816 3373.510108 2975.772714 2973.680699 3006.669956 2348.450221 2639.471461 3116.291972 3904.7482 0.970723472 0.927350403 0.863950743 0.762090809 0.761555047 0.770003545 0.601434484 0.675964576 0.798077574 1 11.9310138 -9.075824867 0.581732394 0.998029567 0.631188479 0.642316531 0.072355148 0.157273923 0.097127141 0.008167561 0.026901617 8.40E-10 9.075824867 -0.366841088 ALHSFIT(ph)PPTTPQLR ddPTM_HeLa_Romidepsin_16h_R1 1 ALHSFITPPTTPQLR 15 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;J3QR75 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 ALHS(0.001)FIT(0.998)PPT(0.001)T(0.001)PQLR 78.166 0.026095 37059000 2142.7 1918.6 2294 1897.5 1795.3 1573.4 1642.6 1508.8 2390.8 1756.5 TRUE FALSE FALSE 2116.583948 1945.610101 2333.926108 2116.897878 1703.679142 1472.864818 1782.122403 1552.454748 2176.96086 1710.865877 1.237141951 1.137207848 1.364178303 1.237325442 0.995799358 0.860888535 1.041649394 0.907408797 1.272432217 1 10.74051095 -8.603491678 6.233394058 1.14521908 0.944139448 0.532166715 0.109610329 0.178319245 10.92178222 0.018782126 0.037897235 2.49E-09 8.603491678 -0.201079632 ALIAAQYSGAQVR ddPTM_HeLa_Romidepsin_16h_R1 2 ALIAAQYSGAQVR 13 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 0 ; ; 197.73 2.68E-10 6014200 1901 1533.94 2680.9 2026.74 2964.8 3072.4 2128.58 1626.31 1659.29 1166.89 FALSE FALSE TRUE 1877.829881 1555.534848 2727.55994 2261.081215 2813.495193 2876.083556 2309.381532 1673.364714 1510.878947 1136.57403 1.6521844 1.368617272 2.399808432 1.989383143 2.475417456 2.53048502 2.031879554 1.47228836 1.329327353 1 10.15047594 -10.74714734 0.555989523 1.067641703 2.176119323 0.512850924 0.356565 0.38232283 0.279890294 0.155404187 0.122991717 1.79E-11 10.74714734 1.10847762 ALLELQLEPEELYQTFQR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLELQLEPEELYQTFQR 18 0 P13639 P13639 EEF2 Elongation factor 2 0 0 88.087 0.0041753 0 397.53 326.49 301.36 384.99 428.15 327.04 317.88 314.47 482.91 458.42 FALSE FALSE TRUE 392.6847515 331.0863348 306.6050444 429.5043552 406.2999079 306.1431995 344.8807193 323.5686933 439.7173201 446.5101823 0.879453072 0.741497838 0.68666977 0.96191391 0.909945448 0.685635427 0.772391611 0.724661399 0.98478677 1 8.802549265 -16.52287873 0.090877073 1.746753466 0.612192763 0.458891614 0.087813869 93.29555295 0.641346248 13.26437667 1.10936179 3.00E-17 16.52287873 -1.134560703 ALLETAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLETASPR 9 0 Q96BT3;H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2 Q96BT3 CENPT Centromere protein T 1 0 ALLETAS(1)PR 131.09 8.40E-05 0 5071.2 4547 5030 3810.4 3776.4 3113.2 3247.2 3039.7 5587.2 5159.7 TRUE FALSE FALSE 5009.390264 4611.012785 5117.54504 4250.976376 3583.676216 2914.276567 3523.017087 3127.648924 5087.466839 5025.65025 0.9967646 0.917495758 1.018285154 0.845855992 0.713077122 0.579880498 0.701007215 0.622337164 1.012300217 1 12.29509456 -8.88618447 1.956801482 0.99323625 0.639863022 0.938145718 0.040726248 0.048634412 0.377147557 0.005742833 0.011979888 1.30E-09 8.88618447 -0.353373228 ALLEVVQSGGK ddPTM_HeLa_Romidepsin_16h_R1 2 ALLEVVQSGGK 11 0 O14818;O14818-2;Q8TAA3-5;Q8TAA3;A0A087WYS6;Q8TAA3-2 O14818;Q8TAA3-5 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 0 ; ; 136.48 0.0071037 302580 481.02 188.929 408.43 352.01 454.37 457.04 380.59 495.42 559.69 247.05 FALSE FALSE TRUE 475.1571432 191.5887474 415.5385528 392.7110525 431.1818034 427.836619 412.9173051 509.7541961 509.6299246 240.6316054 1.974624831 0.79619112 1.726866062 1.632001132 1.791875189 1.777973506 1.715972864 2.118400844 2.117884406 1 7.910682333 -12.49913998 1.07320824 0.972861729 1.701218692 0 0.477444797 0.47754694 0.922053058 0.279013397 0.058044629 3.17E-13 12.49913998 0.728356963 ALLS(ph)PFSTPVR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLSPFSTPVR 11 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 0 ALLS(0.988)PFS(0.01)T(0.002)PVR 109.39 0.014851 12480000 1241 1343.5 1124 1292.3 1459.9 1232.6 1106.7 1214.3 1323.2 1507.6 TRUE FALSE FALSE 1225.874215 1362.413828 1143.562749 1441.721806 1385.395855 1153.840838 1200.70307 1249.433855 1204.849678 1468.432335 0.83481832 0.927801572 0.778764347 0.981810174 0.943452294 0.785763709 0.817676812 0.850862396 0.820500645 1 10.52006107 -12.37801669 0.874815188 1.008548731 0.863919693 0 0.084579535 0.588274419 0.726476847 0.059317391 0.012123525 4.19E-13 12.37801669 -0.144629038 ALLS(ph)PQYMVPDMDLWVPAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLSPQYMVPDMDLWVPAR 19 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 ALLS(0.944)PQY(0.056)MVPDMDLWVPAR 70.334 0.0015153 0 737.72 806.06 611.6 601.3 924.61 958.03 693.89 1065.3 848.55 652.94 TRUE FALSE FALSE 728.7283849 817.4077338 622.2446414 670.8251352 877.4237015 896.8149749 752.8289993 1096.122775 772.6535628 635.9765247 1.145841641 1.285279727 0.978408192 1.054795435 1.379647939 1.410138488 1.183737088 1.723527099 1.214908936 1 9.312829703 -4 0.317022977 1.0508481 6.308235444 0.540821735 0.144897017 24.90459389 0.317800285 0.046038337 76.72593206 1.00E-04 4 5.257387344 ALLSPQY(ph)MVPDMDLWVPAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLSPQYMVPDMDLWVPAR 19 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 ALLS(0.442)PQY(0.558)MVPDMDLWVPAR 98.368 0.00015213 0 1140.3 1324.1 1171.4 1284.6 1555.9 2388.8 1673.7 1767 1294.3 1131.8 TRUE FALSE FALSE 1126.401585 1342.740715 1191.787726 1433.131496 1476.496617 2236.163389 1815.864036 1818.125357 1178.534566 1102.395673 1.021776131 1.218020669 1.0810889 1.300015531 1.339352697 2.028458061 1.64719808 1.649249359 1.069066757 1 10.10642641 -8.73996991 1.402288944 1.030042364 1.762943793 0.80913593 0.140723843 0.112952276 0.444183045 0.021276538 0.054966617 1.82E-09 8.73996991 0.732901429 ALLSS(ph)PEGEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ALLSSPEGEEK 11 0 A0A499FJI4;O75592-2;O75592;H7C3U4 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 ALLS(0.081)S(0.919)PEGEEK 121.36 0.0094188 9101800 3936.1 3834 4160.6 2850.9 4329.9 4957.9 4064.3 4978.1 4759 3756.8 TRUE FALSE FALSE 3888.125299 3887.975153 4233.013498 3180.534472 4108.929046 4641.106191 4409.521541 5122.133469 4333.343121 3659.197794 1.062562211 1.062521178 1.156814618 0.869189 1.12290433 1.268339798 1.205051432 1.399796829 1.184233093 1 11.83731169 -8.35898619 3.318497076 1.032576246 1.285949444 0.54304605 0.094443533 0.108263913 2.252665546 0.011125656 0.027220538 4.38E-09 8.35898619 0.253373198 ALLSVESGSKPFTRQEVIGFVIGSISSVLYLLSRLPQIR ddPTM_HeLa_Romidepsin_16h_R1 1 ALLSVESGSKPFTRQEVIGFVIGSISSVLYLLSRLPQIR 39 3 A2A2E6;Q6ZP29-2;Q6ZP29-3;Q6ZP29 A2A2E6 PQLC2 Lysosomal amino acid transporter 1 homolog 0 0 24.473 0.023696 2248200 0 0 0 0 123.61 57.566 115.56 191.91 0 0 FALSE FALSE TRUE 0 0 0 0 117.3017204 53.88771839 125.3756635 197.4626131 0 0 0 ALNHEIEELEK ddPTM_HeLa_Romidepsin_16h_R1 1 ALNHEIEELEK 11 0 Q5T821;O95347-2;O95347 Q5T821 SMC2 Structural maintenance of chromosomes protein 2 0 0 87.667 0.0030788 0 2862.7 2420.4 2328.9 1947.1 2141 2476.6 2109.3 2436.1 2883 2802.3 FALSE FALSE TRUE 2827.808311 2454.474455 2369.433528 2172.232863 2031.736781 2318.353253 2288.463889 2506.58471 2625.137259 2729.495842 1.036018545 0.899240958 0.868084681 0.795836663 0.744363391 0.849370502 0.838419995 0.918332489 0.961766352 1 11.41441878 -10.01619016 2.303303611 1.017264922 0.829059416 0.700978276 0.047140057 0.098205116 1.035772937 0.007903914 0.01024809 9.63E-11 10.01619016 -0.188205506 ALNHSVEDIEPDLLT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ALNHSVEDIEPDLLTPR 17 0 I3L2K5;Q8IWR0 I3L2K5 ZC3H7A Zinc finger CCCH domain-containing protein 7A 1 0 ALNHSVEDIEPDLLT(1)PR;ALNHSVEDIEPDLLT(1)PR ; 205.84 1.54E-19 24413000 6053.8 5560 5407.3 5443.5 5564.4 6161.6 5130.6 5273.1 6658.3 5476.5 TRUE FALSE FALSE 5980.013957 5638.273826 5501.411788 6072.903082 5280.427904 5767.893646 5566.393036 5425.668829 6062.764972 5334.219741 1.121066294 1.057000667 1.0313433 1.138480111 0.989915707 1.081300345 1.043525259 1.017143855 1.136579531 1 12.38106154 -7.394675492 3.565797812 1.058850717 1.0169823 0.067394164 0.050761795 0.646276303 13.20078905 0.007281073 0.056103717 4.03E-08 7.394675492 -0.041868417 ALPAAHIPAPPHEGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ALPAAHIPAPPHEGSPR 17 0 P17029;E9PC66 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 0 ALPAAHIPAPPHEGS(1)PR;ALPAAHIPAPPHEGS(1)PR ; 124.08 0.00092972 14835400 4147.4 2831.1 4029.6 2410.2 3769.1 5372.5 5082.1 5452.2 4254.9 2886.1 TRUE FALSE FALSE 4096.849894 2870.9563 4099.733498 2688.878664 3576.748763 5029.214589 5513.773447 5609.950805 3874.331087 2811.118706 1.457373495 1.021286043 1.45839928 0.956515518 1.272357782 1.789043835 1.961416085 1.995629282 1.378216821 1 11.45692866 -8.192119559 2.976061296 1.204860692 1.964564491 0.776929862 0.172663126 0.102434304 1.77198883 0.028629123 0.081522848 6.43E-09 8.192119559 0.759703799 ALPDSQQVPSS(ph)PASK ddPTM_HeLa_Romidepsin_16h_R1 1 ALPDSQQVPSSPASK 15 0 O14924-7;O14924-6;O14924-2;O14924-3;O14924-5;O14924-4;O14924 O14924-7 RGS12 Regulator of G-protein signaling 12 1 0 ALPDSQQVPS(0.057)S(0.92)PAS(0.023)K 106.52 0.0012216 0 1686.6 1664.1 1861.8 1885.6 1733.4 2012 1751.2 1849.2 2053.1 1919.6 TRUE FALSE FALSE 1666.04307 1687.527243 1894.203848 2103.621944 1644.93813 1883.439693 1899.946884 1902.703684 1869.465594 1869.728515 0.891061487 0.902552017 1.013090314 1.125094861 0.879773783 1.007333245 1.016161902 1.017636341 0.99985938 1 10.86861309 -9.738399324 24.35753094 0.94366907 1.009347081 0.179309957 0.064116073 233.4450306 246793.151 0.010722289 0.015157154 1.83E-10 9.738399324 0.065678011 ALPNNTSSS(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALPNNTSSSPQPK 13 0 A0A087WXZ1;A0A087WT22;E7ESS1;A0A087X1Q1;J3KP33;A0A087WZU8;A0A0U1RQC9;P04637-8;P04637-9;P04637-7;P04637-5;P04637-6;P04637-2;P04637-3;P04637-4;P04637 A0A087WXZ1 TP53 Cellular tumor antigen p53 1 0 ALPNNT(0.012)S(0.012)S(0.051)S(0.924)PQPK 110.98 0.0065719 3446200 1456 1708.9 1348.6 1541.4 1364.2 1490.2 1354.3 1606.9 1959.3 1480.1 TRUE FALSE FALSE 1438.253712 1732.957939 1372.071817 1719.623921 1294.579783 1394.981029 1469.334208 1653.393116 1784.055301 1441.646789 0.997646388 1.202068324 0.951739239 1.192819166 0.897986798 0.967630241 1.019205411 1.146878091 1.237512069 1 10.49350202 ALPQT(ph)PRPR ddPTM_HeLa_Romidepsin_16h_R1 4 ALPQTPRPR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR;ALPQT(1)PRPR ;;; 97.452 0.017113 886236000 5250.5 4733.2 4332.92 3929.75 4023.66 4279.95 4217.15 3000.07 6011.1 5289.3 TRUE FALSE FALSE 5186.504886 4799.834114 4408.332655 4384.126185 3818.317616 4006.475008 4575.354616 3086.872292 5473.452161 5151.883224 1.006720196 0.931665938 0.855674025 0.850975458 0.741149877 0.777671937 0.888093619 0.599173576 1.062417746 1 12.33088418 -9.545125471 0.960224185 1.006452027 0.758151599 0.719904915 0.070165676 0.189867352 0.349668004 0.0118959 0.021345505 2.85E-10 9.545125471 -0.248300428 ALPQTPRPR ddPTM_HeLa_Romidepsin_16h_R1 2 ALPQTPRPR 9 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 0 ; ; 131.11 0.0087732 11481800 705.3 829.38 749.99 607.76 530.09 596.03 541.78 706.67 728.82 549.75 FALSE FALSE TRUE 696.7035323 841.0560334 763.0432613 678.0320708 503.0375293 557.9456066 587.7987797 727.1163815 663.6325138 535.4674157 1.301112844 1.570695076 1.425004097 1.266243381 0.939436303 1.041978634 1.097730249 1.357909669 1.239351815 1 9.064654977 -8.847778272 22.99561962 1.212532472 1.103399225 0.112382678 0.180419803 32.21004073 8568.920512 0.033088214 0.059977534 1.42E-09 8.847778272 -0.109133248 ALPS(ph)EDEEGQDDKDFYLR ddPTM_HeLa_Romidepsin_16h_R1 1 ALPSEDEEGQDDKDFYLR 18 1 Q8NF91;A0A0C4DG40;Q8NF91-4;Q8NF91-2;E7ENN3;H0Y326;A0A5F9ZHE1;Q5JV20;F8WAI0;A0A5F9ZH87;H0Y325;Q8NF91-11;Q8NF91-8;Q8NF91-3;Q8NF91-9;A0A5F9ZHB2;A0A5F9ZH86 Q8NF91 SYNE1 Nesprin-1 1 0 ALPS(1)EDEEGQDDKDFYLR 114.3 0.00051582 9408800 1380.6 1911.5 1614.1 1507.9 1700.8 1696.4 1360.8 1693.5 1909.6 2024.5 TRUE FALSE FALSE 1363.772716 1938.410147 1642.192733 1682.250493 1614.001829 1588.005515 1476.386318 1742.498751 1738.800593 1971.903198 0.691602264 0.98301486 0.832795816 0.853110079 0.818499524 0.805316162 0.748711356 0.883663433 0.881788008 1 10.94537302 -12.61090975 1.415649144 0.999991635 0.810067887 0.16544653 0.082208482 0.320308238 1.152371497 0.057341661 0.013191084 2.45E-13 12.61090975 -0.189923748 ALPSLNTGSSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 ALPSLNTGSSSPR 13 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 0 ALPSLNT(0.002)GS(0.023)S(0.443)S(0.532)PR;ALPSLNT(0.007)GS(0.012)S(0.044)S(0.936)PR;ALPSLNT(0.002)GS(0.03)S(0.338)S(0.63)PR;ALPS(0.001)LNT(0.046)GS(0.081)S(0.285)S(0.588)PR ;;; 180.3 5.97E-07 1382057000 8342 7814 7517.1 7261 14839.5 14532.1 14054.2 14129 7821.23 7315.2 TRUE FALSE FALSE 8240.324495 7924.005697 7647.931972 8100.550984 14082.18494 13603.54571 15247.9634 14537.80032 7121.6796 7125.150049 1.156512416 1.11211773 1.073371356 1.136895494 1.976405387 1.909229366 2.14001997 2.040350059 0.99951293 1 12.79870468 -8.762785115 4.887977876 1.080014822 2.026592728 0.978356433 0.068343325 0.020877386 1.326666079 0.011640448 0.022609989 1.73E-09 8.762785115 0.946577906 ALPTSKPEGSLHS(ph)SPVGPSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 ALPTSKPEGSLHSSPVGPSSSK 22 1 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 0 ALPTSKPEGS(0.003)LHS(0.55)S(0.437)PVGPS(0.004)S(0.005)S(0.001)K 62.1 0.0035377 17789000 2777.9 2231.2 2119.6 2244.2 4253.3 3856.7 2845.6 2576.7 4854.3 4110.7 TRUE FALSE FALSE 2744.041886 2262.610892 2156.490749 2503.684963 4036.23823 3610.269317 3087.305193 2651.252749 4420.11925 4003.903421 0.685341677 0.565101266 0.538597094 0.625311028 1.008075821 0.901687413 0.771073842 0.662167008 1.103952515 1 11.96719146 -12.19838884 1.010552792 0.995198946 0.723286916 0.447286188 0.143218464 0.504073354 0.948149511 0.094095721 0.028364159 6.33E-13 12.19838884 -0.27191203 ALQDEWDAVMLHSFTLR ddPTM_HeLa_Romidepsin_16h_R1 1 ALQDEWDAVMLHSFTLR 17 0 F5GY56;Q9UMS4 F5GY56 PRPF19 Pre-mRNA-processing factor 19 0 0 98.077 0.016921 5719100 1627.4 1312.5 1686.7 1703.3 1690.7 1869.7 1344.5 1521.3 1762.5 1325.6 FALSE FALSE TRUE 1607.564623 1330.977409 1716.056306 1900.24356 1604.41727 1750.232204 1458.701796 1565.316415 1604.857586 1291.160721 1.245053847 1.030837903 1.329080321 1.471732782 1.242616232 1.355549449 1.129760047 1.212332741 1.242957255 1 10.33445288 -12.19316298 0.452755041 0.93929582 1.272122809 0.025137407 0.135138451 1.400056881 0.398424101 0.21514569 0.03533125 6.41E-13 12.19316298 0.332826989 ALQEGEGDLSIS(ph)ADRLSEK ddPTM_HeLa_Romidepsin_16h_R1 1 ALQEGEGDLSISADRLSEK 19 1 B4DKY1;P49589-2;P49589;P49589-3 B4DKY1 CARS "Cysteine--tRNA ligase, cytoplasmic" 1 0 ALQEGEGDLS(0.059)IS(0.892)ADRLS(0.049)EK 78.272 0.0036389 6613000 808.34 801 1016.5 947.13 1391.4 1775.2 1709.2 1983.3 1123.6 1021.5 TRUE FALSE FALSE 798.4876412 812.276499 1034.191756 1056.641627 1320.391666 1661.770449 1854.379405 2040.683656 1023.102402 994.9612827 0.80253137 0.816390058 1.039429146 1.061992708 1.327078439 1.670186044 1.863770418 2.051018157 1.028283632 1 9.958496576 -8.261567025 0.978686261 0.899028459 2.079372467 0.967703678 0.075774688 0.091744865 0.144368082 0.014257103 0.078515192 5.48E-09 8.261567025 1.180344008 up GEADDEDDDEDGQDNQGTVTEGS(ph)SPAYLK ddPTM_HeLa_Romidepsin_16h_R1 1 GEADDEDDDEDGQDNQGTVTEGSSPAYLK 29 0 Q86U86-8;Q86U86;H0Y5B5;E7EVG2;Q86U86-6;Q86U86-5;Q86U86-4;Q86U86-7;Q86U86-3;Q86U86-9;Q86U86-2;C9JPI5 Q86U86-8 PBRM1 Protein polybromo-1 1 0 GEADDEDDDEDGQDNQGT(0.001)VTEGS(0.85)S(0.148)PAYLK 208.34 1.36E-36 9576300 6543.7 5268.8 5608.7 3464.1 3067.6 2677.2 2610.8 2255.5 6344.6 5667.3 TRUE FALSE FALSE 6463.942867 5342.974305 5706.317071 3864.635541 2911.048925 2506.13556 2832.561287 2320.759334 5777.123086 5520.062729 1.170990836 0.967919128 1.033741345 0.700107178 0.527357943 0.454004906 0.513139329 0.420422638 1.046568376 1 12.43046895 -9.087896922 1.671414283 1.076474561 0.465203836 0.956926556 0.056796155 0.060893793 0.335279746 0.011584239 0.022725611 8.17E-10 9.087896922 -0.611270725 down ALQESATGQPEPTSS(ph)PDNKPFK ddPTM_HeLa_Romidepsin_16h_R1 1 ALQESATGQPEPTSSPDNKPFK 22 1 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 ALQESATGQPEPT(0.277)S(0.209)S(0.514)PDNKPFK 90.464 0.00022375 9866300 8045.1 7275.9 6896.4 6844.6 4428.1 4279.5 3434.9 3690.5 8147.2 8038.9 TRUE FALSE FALSE 7947.043227 7378.330311 7016.428949 7636.004857 4202.117533 4006.053761 3726.66032 3797.278795 7418.494027 7830.048219 1.014941799 0.94230969 0.896090133 0.975218114 0.536665601 0.511625682 0.47594347 0.484962377 0.947439124 1 12.93480548 -8.749026558 4.602908248 0.991934832 0.494563042 0.970840654 0.038949888 0.02310335 1.203332066 0.006392033 0.012591547 1.78E-09 8.749026558 -0.49737179 ALQEVGSGGTLGLS(ph)SPKS ddPTM_HeLa_Romidepsin_16h_R1 1 ALQEVGSGGTLGLSSPKS 18 1 A0A0M3HER3 A0A0M3HER3 1 0 ALQEVGSGGTLGLS(0.496)S(0.496)PKS(0.009) 215.15 5.30E-35 0 2270.5 2490 1917.6 2180 2069.4 2203.8 1674.7 1622.8 2631.8 2158.9 TRUE FALSE FALSE 2242.826273 2525.054285 1950.975024 2432.061857 1963.790796 2062.984292 1816.948976 1669.753158 2396.405217 2102.811467 1.066584574 1.20079918 0.927793601 1.156576277 0.933888191 0.981060036 0.864057004 0.794057472 1.139619626 1 11.03810379 -7.682472375 1.085683167 1.044005192 0.751931907 0.551578998 0.084487667 0.535381656 0.78026027 0.011532979 0.150527344 2.08E-08 7.682472375 -0.292073285 ALQEVGSGGTLGLSS(ph)PKS ddPTM_HeLa_Romidepsin_16h_R1 1 ALQEVGSGGTLGLSSPKS 18 1 A0A0M3HER3 A0A0M3HER3 1 0 ALQEVGSGGTLGLS(0.223)S(0.776)PKS(0.001) 135.69 0.0016935 10941000 2464.7 2327.3 2409.1 2428.6 2290.2 2374.5 1882.4 1872.5 2260.6 2250 TRUE FALSE FALSE 2434.659288 2360.06379 2451.029375 2709.406159 2173.322548 2222.777113 2042.291009 1926.677833 2058.406274 2191.544676 1.110932994 1.076895131 1.118402651 1.236299761 0.991685258 1.014251335 0.931895677 0.879141482 0.939249059 1 11.09773237 -7.819922012 1.566839104 1.071353734 0.878494392 0.42390115 0.076790946 0.342147131 1.428991749 0.010991116 0.073161591 1.51E-08 7.819922012 -0.192859342 ALQS(ph)PALGLR ddPTM_HeLa_Romidepsin_16h_R1 1 ALQSPALGLR 10 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 1 0 ALQS(1)PALGLR 118.76 0.012604 15820000 1621.6 1122.7 1599.6 1268.5 2011.2 2284.7 1734.4 1824.5 1635.8 1444.7 TRUE FALSE FALSE 1601.835315 1138.5054 1627.440367 1415.169938 1908.560959 2138.715044 1881.719893 1877.289029 1489.489951 1407.166486 1.138341008 0.809076546 1.156537186 1.005687637 1.356314962 1.519873494 1.337240413 1.334091629 1.058503003 1 10.45857731 -8.718650099 6.059973746 1.049303175 1.396398119 0.744591496 0.102552835 0.077018533 6.927593301 0.015147611 0.030203829 1.91E-09 8.718650099 0.347094944 ALQTS(ph)PQPPEGPGLPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALQTSPQPPEGPGLPR 16 0 A0A2R8YGT1;F8W9A8;B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;Q6PFW1;H7C398;Q6PFW1-5 A0A2R8YGT1 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 0 ALQT(0.016)S(0.984)PQPPEGPGLPR 91.789 0.011241 4970900 1092 1183 1121.9 1123.7 1099 1200.7 957.94 1217.9 1305 1091.5 TRUE FALSE FALSE 1078.690284 1199.654305 1141.426199 1253.627481 1042.913929 1123.979145 1039.3074 1253.138015 1188.277532 1063.142673 1.0146242 1.128403869 1.073634074 1.179171445 0.980972692 1.057223244 0.977580363 1.178711049 1.11770279 1 10.0541195 -10.41152632 7.760889996 1.00641602 1.076708064 0 0.074422511 0.321372793 20.24791795 0.010618077 0.012106717 3.88E-11 10.41152632 0.070292044 ALRPGDLPPS(ph)PDDVKR ddPTM_HeLa_Romidepsin_16h_R1 1 ALRPGDLPPSPDDVKR 16 2 O75382-3;O75382-2;O75382;A0A1W2PPI7;O75382-4 O75382-3 TRIM3 Tripartite motif-containing protein 3 1 0 ALRPGDLPPS(1)PDDVKR 116.09 0.0026849 8286200 981.08 1218.8 960.82 1167.6 1289 1198.1 1209.3 1129.1 1176.6 1230.3 TRUE FALSE FALSE 969.1222196 1235.958298 977.5426691 1302.603406 1223.21752 1121.545277 1312.017912 1161.768727 1071.361949 1198.336629 0.808722855 1.031394909 0.815749636 1.087009589 1.020762856 0.93591838 1.0948659 0.96948445 0.894040893 1 10.22681752 -9.251543887 24.97216851 0.912041816 1.020870589 0.33438833 0.078714635 744.5581447 1878959.033 0.013607689 0.022388365 5.60E-10 9.251543887 0.108828773 ALS(ph)DREEEEEDDEEEEEEVEAAAQR ddPTM_HeLa_Romidepsin_16h_R1 3 ALSDREEEEEDDEEEEEEVEAAAQR 25 1 Q8N3E9 Q8N3E9 PLCD3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3" 1 0 ALS(1)DREEEEEDDEEEEEEVEAAAQR;ALS(1)DREEEEEDDEEEEEEVEAAAQR;ALS(1)DREEEEEDDEEEEEEVEAAAQR ;; 86.376 9.78E-06 27071000 2616.09 2885.41 2675.2 1976.77 2724.45 3514.47 2315.13 2762.92 3083.31 2779.93 TRUE FALSE FALSE 2584.204089 2926.030878 2721.760734 2205.333448 2585.41115 3289.906709 2511.777084 2842.860731 2807.531031 2707.707018 0.954388371 1.080630533 1.005190265 0.814465315 0.954834158 1.215015763 0.927639906 1.049914452 1.036866623 1 11.40285593 ALS(ph)DVTDEEEVQVDPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSDVTDEEEVQVDPR 16 0 Q16659 Q16659 MAPK6 Mitogen-activated protein kinase 6 1 0 ALS(0.674)DVT(0.326)DEEEVQVDPR 199.33 2.58E-18 2112000 715.72 482.55 624.55 722.76 780.98 615.19 474.41 689.31 1032.9 744.59 TRUE FALSE FALSE 706.9965293 489.3433516 635.4200308 806.3289119 741.1236764 575.8813444 514.7063736 709.2540973 940.5148371 725.2454445 0.974837601 0.674727922 0.876144808 1.111801416 1.021893598 0.794050275 0.709699561 0.977950434 1.296822813 1 9.502325518 -6.730593377 0.05405134 1.25172224 0.442647271 0.19082759 0.160522226 350.33166 2.584011768 12.18456587 29.75941485 1.86E-07 6.730593377 -0.80907497 ALS(ph)EGEEITAAPER ddPTM_HeLa_Romidepsin_16h_R1 1 ALSEGEEITAAPER 14 0 O43822-2;O43822-3;O43822;O43822-4 O43822-2 C21orf2 Protein C21orf2 1 0 ALS(1)EGEEITAAPER 137.73 0.0012237 2351200 598.99 531.03 532.15 563.29 661.84 622.35 659.83 707.23 831.57 586.28 TRUE FALSE FALSE 591.6892795 538.5058543 541.4118475 628.4202402 628.0638351 582.5838435 715.8759437 727.6925842 757.1922965 571.0483611 1.036145657 0.943012696 0.94810157 1.100467636 1.099843512 1.020200535 1.253617018 1.274309908 1.325968776 1 9.15746912 -7.456007308 0.864450783 1.010390134 1.41019462 0.253310139 0.113724341 0.640658075 0.42342354 0.008655664 0.226561517 3.50E-08 7.456007308 0.399804485 ALS(ph)IESLSPTDSSNGVNWR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSIESLSPTDSSNGVNWR 19 0 H3BRG5;Q9Y3M8-5;Q9Y3M8-3;Q9Y3M8-4;Q9Y3M8-2;Q9Y3M8 H3BRG5 STARD13 StAR-related lipid transfer protein 13 1 0 ALS(0.999)IES(0.001)LSPTDSSNGVNWR 326.09 2.12E-187 25969000 1748 1418.4 1318.2 1492.6 1795.6 1426.8 1308.1 1530 1723.8 1454 TRUE FALSE FALSE 1726.694704 1438.368272 1341.142718 1665.181435 1703.963832 1335.632085 1419.209981 1574.268136 1569.619011 1416.22487 1.219223543 1.015635513 0.9469843 1.175788866 1.203173216 0.943093228 1.002107794 1.111594754 1.108311994 1 10.46783464 -8.247487602 24.88909522 1.098253428 1.017249527 0.125288469 0.092599199 1450.70081 2587953.63 0.015611215 0.039574469 5.66E-09 8.247487602 -0.081003901 ALS(ph)ISPLSDASLDLQR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSISPLSDASLDLQR 16 0 P10070 P10070 GLI2 Zinc finger protein GLI2 1 0 ALS(0.472)IS(0.472)PLS(0.024)DAS(0.032)LDLQR;ALS(0.939)IS(0.046)PLS(0.008)DAS(0.008)LDLQR ; 142.19 0.00047384 6157200 2412.1 2620.47 2170.41 2083.28 2264.54 2104.97 1784.72 1823.86 2618.5 2057.49 TRUE FALSE FALSE 2382.700397 2657.361045 2208.185076 2324.158636 2148.972074 1970.46921 1936.314072 1876.630512 2384.294802 2004.036113 1.188950829 1.32600457 1.101868904 1.159738899 1.07232203 0.98325035 0.966207175 0.936425496 1.189746425 1 10.96869279 -8.285546349 2.488254414 1.116606409 0.954425881 0.490334918 0.084199078 0.280054165 3.379868888 0.01528545 0.042803035 5.18E-09 8.285546349 -0.162180529 ALS(ph)PAELR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSPAELR 8 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 ALS(1)PAELR 104.42 0.027283 18997000 2540.7 2719.3 2335.5 2498.5 3499.8 4437.2 3089 4394.5 2660.7 2457.9 TRUE FALSE FALSE 2509.732971 2757.582377 2376.148398 2787.388326 3321.192146 4153.67724 3351.379583 4521.647924 2422.720328 2394.043404 1.048323922 1.151851455 0.992525196 1.1643015 1.387273155 1.735004985 1.399882549 1.88870758 1.011978448 1 11.22523359 -8.640446889 1.726733168 1.031889781 1.660433637 0.835904326 0.122852517 0.091652846 0.548598216 0.01675999 0.042153422 2.29E-09 8.640446889 0.628543856 ALS(ph)PEGALRR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSPEGALRR 10 1 K7EPS7;I3L2Z9;I3L100;I3L2W2;Q96JN8-2;Q96JN8 K7EPS7 NEURL4 Neuralized-like protein 4 1 0 ALS(1)PEGALRR 59.975 0.0040113 0 1598.5 1258 1457.1 1596.9 1916.6 1647.3 1285 1515.6 1664.6 1329.6 TRUE FALSE FALSE 1579.016867 1275.710157 1482.460214 1781.541092 1818.78875 1542.042846 1394.147868 1559.451495 1515.714007 1295.0568 1.219264566 0.985061162 1.144706714 1.375647069 1.404408478 1.190714451 1.076514843 1.204156833 1.170384192 1 10.33879966 -13.08634893 0.350039219 0.844293376 1.221417454 0.061571919 0.127504405 5.38921803 0.548973793 0.835331418 0.049335495 8.20E-14 13.08634893 0.377124078 VEESSEIS(ph)PEPK ddPTM_HeLa_Romidepsin_16h_R1 2 VEESSEISPEPK 12 0 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 VEES(0.002)S(0.013)EIS(0.985)PEPK;VEES(0.001)S(0.019)EIS(0.98)PEPK ; 172.33 0.00010077 12995800 8030.9 7815.1 8089.7 4182.6 3246.28 2994.9 2027.57 2401.18 8288.9 8879.3 TRUE FALSE FALSE 7933.016302 7925.121183 8230.497835 4666.211892 3080.610218 2803.535556 2199.791745 2470.654355 7547.520024 8648.614506 0.917258631 0.916345754 0.951655069 0.53953288 0.356196963 0.324160078 0.254351925 0.285670538 0.872685448 1 13.07825332 -9.068967523 1.953984889 0.959481345 0.291482549 0.977452998 0.045015567 0.029877335 0.225220584 0.00677983 0.012949614 8.53E-10 9.068967523 -0.667998796 down ALS(ph)PVIPLIPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSPVIPLIPR 11 0 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 ALS(1)PVIPLIPR 123.67 0.0083974 142860000 3905.4 3516.7 3905.2 3298.3 3144.6 2753.9 2487 2536.1 4064.4 3870.7 TRUE FALSE FALSE 3857.799483 3566.208195 3973.168368 3679.664965 2984.119328 2577.934678 2698.245718 2609.478052 3700.869885 3770.138656 1.023251353 0.945909029 1.053852054 0.976002556 0.791514477 0.683777153 0.715688722 0.692143788 0.981626996 1 11.88040187 -8.67542375 2.665139568 1.008927346 0.700570026 0.959669052 0.028205009 0.031905269 0.458921078 0.003828306 0.008288656 2.11E-09 8.67542375 -0.30835732 ALS(ph)SAGPIPIRPPIVPVK ddPTM_HeLa_Romidepsin_16h_R1 2 ALSSAGPIPIRPPIVPVK 18 1 Q765P7;A0A087WXN9 Q765P7 MTSS1L MTSS1-like protein 1 0 ALS(0.5)S(0.5)AGPIPIRPPIVPVK;ALS(0.5)S(0.5)AGPIPIRPPIVPVK ; 87.323 0.0029642 55504000 4167.5 4116 4437.4 4636.9 4287.5 3618.7 2875.7 3072.1 3875.6 4528.7 TRUE FALSE FALSE 4116.704907 4173.945156 4514.631086 5173.040195 4068.692876 3387.476749 3119.961886 3160.986367 3528.956629 4411.043721 0.933272297 0.946248874 1.02348364 1.172747432 0.922387791 0.767953564 0.707306951 0.716607353 0.800027579 1 12.10690434 -8.266286766 3.27473413 0.985005761 0.719453061 0.617694958 0.087784716 0.096450964 2.152801022 0.010312359 0.027049554 5.42E-09 8.266286766 -0.2655527 ALS(ph)SDSILSPAPDAR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 ALS(0.851)S(0.146)DS(0.002)ILS(0.001)PAPDAR;ALS(0.66)S(0.141)DS(0.197)ILS(0.003)PAPDAR ; 125.22 0.0028334 809651400 3040.3 2546.32 2596.73 2734.9 2542 2601.6 2380.5 2421.3 3369.6 3056 TRUE FALSE FALSE 3003.243654 2582.16716 2641.924996 3051.122006 2412.272254 2435.366156 2582.699611 2491.356495 3068.214537 2976.604679 1.00894945 0.867487435 0.887563275 1.025034338 0.810410691 0.818169162 0.867666314 0.836979298 1.030776629 1 11.53945192 -9.45087665 0.561128966 1.009276929 0.828831346 0.553938495 0.057147686 0.467302796 0.294395046 0.015234052 0.03568917 3.54E-10 9.45087665 -0.180445583 ALS(ph)TPVVEK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSTPVVEK 9 0 E5RK24;E5RIW4;E5RH41;P29084 E5RK24 GTF2E2 Transcription initiation factor IIE subunit beta 1 0 ALS(0.98)T(0.02)PVVEK 91.855 0.0042955 0 1516.2 1652.6 1126.8 1223.9 1621.8 1577.8 1703 1914.3 1725.2 1596.1 TRUE FALSE FALSE 1497.719971 1675.865346 1146.411481 1365.413077 1539.033494 1476.983672 1847.652777 1969.68725 1570.893791 1554.633092 0.963391284 1.077981264 0.737416106 0.878286384 0.989965737 0.950052897 1.18848157 1.266978852 1.010459509 1 10.60235842 -7.681026306 3.833675541 0.962603179 1.250519411 0.617024754 0.087583451 0.111131006 3.073997474 0.01226519 0.052060348 2.08E-08 7.681026306 0.287916232 ALS(ph)TTSSSTTNGNR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSTTSSSTTNGNR 14 0 C9JUH3;A0A0A0MT72;Q9BSQ5-3;Q9BSQ5-4;Q9BSQ5;Q9BSQ5-2 C9JUH3 CCM2 Cerebral cavernous malformations 2 protein 1 0 ALS(0.758)T(0.239)T(0.003)SSSTTNGNR 89.747 0.019468 6653700 1328.9 1396.3 1414.3 1247.1 1780.9 2206.8 1628.4 1801.6 1647.7 1639.4 TRUE FALSE FALSE 1312.702856 1415.957148 1438.915298 1391.29557 1690.014028 2065.792602 1766.716255 1853.726454 1500.325585 1596.808152 0.822079255 0.886742184 0.90111971 0.871297888 1.058370115 1.293701188 1.106404832 1.160894909 0.93957786 1 10.64097528 -8.562288515 4.304330213 0.908121978 1.179895278 0.810851395 0.061688673 0.082147181 3.372781186 0.011462788 0.024202775 2.74E-09 8.562288515 0.2717733 ALSAAVADSLTNS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSAAVADSLTNSPR 15 0 Q14687-2;Q14687-3;Q14687;H7C3B5 Q14687-2 GSE1 Genetic suppressor element 1 1 0 ALSAAVADSLTNS(1)PR;ALSAAVADSLT(0.01)NS(0.99)PR ; 215.37 8.71E-26 50915000 5615.5 5549.6 5243.4 4921.6 4237.1 4087.1 3938.3 4240.6 5897 4933.1 TRUE FALSE FALSE 5547.056126 5627.727414 5334.659177 5490.658549 4020.864976 3825.947501 4272.819104 4363.29507 5369.557551 4804.937351 1.154449209 1.171238458 1.110245314 1.142711787 0.836819439 0.796253358 0.889255945 0.908085736 1.117508337 1 12.23030191 -8.756410174 24.99997087 1.090294925 0.855482296 0.83684109 0.055200634 53.14235665 264165.3855 0.010917546 0.021303522 1.75E-09 8.756410174 -0.234812629 ALSAIADLLTNEHER ddPTM_HeLa_Romidepsin_16h_R1 1 ALSAIADLLTNEHER 15 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22;O60716-25;O60716-27;O60716-29;O60716-26;O60716-28;O60716-30;O60716-31;O60716-32 O60716 CTNND1 Catenin delta-1 0 0 125.36 0.0013149 3779900 3103.8 3021.4 2837.5 3357 2876.1 3298.4 2593.1 2730.8 3020.3 3232.1 FALSE FALSE TRUE 3065.969692 3063.935349 2886.885497 3745.152135 2729.321885 3087.642885 2813.357849 2809.81139 2750.156804 3148.129576 0.973902 0.973255793 0.917016097 1.189643579 0.866966184 0.980786467 0.893660118 0.892533589 0.873584374 1 11.62027921 ALSAS(ph)HTDLAH ddPTM_HeLa_Romidepsin_16h_R1 2 ALSASHTDLAH 11 0 Q07866-6;H0YG16;Q07866-7;Q07866-4;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 0 ALS(0.001)AS(0.897)HT(0.102)DLAH;ALSAS(0.736)HT(0.264)DLAH ; 119.74 0.0042548 83465000 12092.7 11081.3 11331 8130.9 14375 12436.6 9839.6 10297.4 13668 11517.9 TRUE FALSE FALSE 11945.30952 11237.30283 11528.2113 9071.032915 13641.39011 11641.9414 10675.37538 10595.33902 12445.49985 11218.6633 1.064771195 1.001661476 1.027592236 0.808566286 1.215955034 1.037729816 0.951572847 0.944438632 1.109356749 1 13.45361317 -10.05220079 23.93305818 1.030724827 1.00002671 0.050334513 0.09959291 821.2157064 376509.2358 0.015715717 0.019247837 8.87E-11 10.05220079 -0.030698117 ALSDVT(ph)DEEEVQVDPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSDVTDEEEVQVDPR 16 0 Q16659 Q16659 MAPK6 Mitogen-activated protein kinase 6 1 0 ALS(0.058)DVT(0.942)DEEEVQVDPR 96.707 0.015701 2771100 479.58 378.38 360.65 415.21 334.56 429.65 354.63 271.19 554.49 403.47 TRUE FALSE FALSE 473.7346945 383.7068436 366.926962 463.2185338 317.4861548 402.1967516 384.7522633 279.0364548 504.8950257 392.9877912 1.205469241 0.976383623 0.933685397 1.178709731 0.807877908 1.023433197 0.979043807 0.710038482 1.284760079 1 8.618340683 -6.130515791 0.469745459 1.084007169 9.87E-16 0.410217489 0.128778613 8.949570651 0.604690341 0.025979206 6.83760433 7.40E-07 6.130515791 -1.084007169 ALSGGGSVAS(ph)PPPSPAMPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSGGGSVASPPPSPAMPK 19 0 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 0 ALSGGGSVAS(0.616)PPPS(0.384)PAMPK 134.14 0.0011076 15593000 1886.9 2141.4 1825.7 2061.9 1993.5 1624.7 1981.2 1718.7 2043.2 1981.3 TRUE FALSE FALSE 1863.901737 2171.546685 1857.475543 2300.30658 1891.764256 1520.886913 2149.483079 1768.427873 1860.451075 1929.82554 0.965839501 1.125255439 0.962509566 1.191976441 0.980277345 0.788095546 1.113822485 0.916366706 0.964051431 1 10.91425472 -8.519597055 24.99516149 1.009687077 0.944754129 0.121685719 0.103364454 275.6167195 2099245.719 0.014311305 0.029092447 3.02E-09 8.519597055 -0.064932948 ALSGTS(ph)PDDVQPGPSVGPPSK ddPTM_HeLa_Romidepsin_16h_R1 2 ALSGTSPDDVQPGPSVGPPSK 21 0 A0A075B797;M0R3B2;Q9Y314 A0A075B797 NOSIP Nitric oxide synthase-interacting protein 1 0 ALS(0.006)GT(0.271)S(0.723)PDDVQPGPSVGPPSK;ALS(0.021)GT(0.106)S(0.874)PDDVQPGPSVGPPSK ; 239.8 9.85E-54 29892000 7840.5 7057.1 7061.1 6463.5 11826.8 14078.3 13001.5 13992.5 7502.3 8188.4 TRUE FALSE FALSE 7744.93697 7156.450039 7183.995484 7210.840282 11223.23426 13178.74207 14105.84709 14397.35091 6831.275498 7975.664188 0.971071097 0.897285777 0.900739464 0.904105302 1.407184907 1.652369227 1.768610959 1.805160119 0.856514936 1 12.96138895 -8.496353305 2.217680991 0.965352615 1.760798081 0.967410155 0.067873655 0.036732148 0.356465877 0.009643514 0.024277837 3.19E-09 8.496353305 0.795445467 ALSGTS(ph)PDDVQPGPSVGPPSKDKDK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSGTSPDDVQPGPSVGPPSKDKDK 25 2 A0A075B797;M0R3B2;Q9Y314 A0A075B797 NOSIP Nitric oxide synthase-interacting protein 1 0 ALS(0.08)GT(0.36)S(0.56)PDDVQPGPSVGPPSKDKDK 91.691 1.62E-05 13591000 2407.5 2320.7 1395.5 2575.3 3418.4 3757.3 2958 3734.3 1677.7 1932.5 TRUE FALSE FALSE 2378.156464 2353.370876 1419.788092 2873.068303 3243.946292 3517.220656 3209.252446 3842.346079 1527.64231 1882.293371 1.263435605 1.250267844 0.754286294 1.52636584 1.723401007 1.868582608 1.704969318 2.041310955 0.811585661 1 10.87827579 -8.970894786 3.298965087 1.113320916 1.826935896 0.800949878 0.189723986 0.079906771 1.813517495 0.025920861 0.047976589 1.07E-09 8.970894786 0.71361498 ALSQY(ph)LT(ph)DRAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSQYLTDRAR 11 1 P14222 P14222 PRF1 Perforin-1 2 0 ALSQY(1)LT(1)DRAR 86.136 0.0024597 0 353.9 399.7 413.81 423.96 251.47 352.4 313.26 208.97 605.94 434.45 TRUE FALSE FALSE 349.5865307 405.3269871 421.0121895 472.98025 238.6365475 329.8827773 339.8682966 215.0162172 551.7432088 423.1629264 0.826127501 0.957850893 0.994917473 1.117726106 0.563935384 0.779564458 0.803161798 0.50811686 1.303855263 1 8.725069427 -8.752935098 24.99980202 0.938219728 0.681932985 0.517186452 0.159454491 114.8998402 337765.2367 0.017183637 0.03392972 1.77E-09 8.752935098 -0.256286743 ALSS(ph)DSILS(ph)PAPDAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 0 ALS(0.459)S(0.539)DS(0.002)ILS(1)PAPDAR 179.55 4.70E-07 9396700 3348.8 3202.6 3230.2 2966.2 3685.6 4408.6 3897.5 4658.4 3417.7 2699.8 TRUE FALSE FALSE 3307.983538 3247.686287 3286.420276 3309.166 3497.510079 4126.904688 4228.553553 4793.183454 3112.012352 2629.658807 1.257951613 1.235021927 1.24975159 1.258401277 1.330024287 1.569368877 1.60802365 1.822739681 1.183428186 1 11.36065991 -4 0.220460831 1.036740288 5.186112627 0.918053247 0.065836744 9.764873386 0.116909635 0.054977551 14.56344991 1.00E-04 4 4.149372339 ALSSDS(ph)ILSPAPDAR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSSDSILSPAPDAR 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 ALS(0.037)S(0.1)DS(0.82)ILS(0.043)PAPDAR;ALS(0.032)S(0.089)DS(0.878)ILS(0.001)PAPDAR ; 189.99 2.34E-12 770816000 3603.23 3054.7 3369.9 2464.97 2560.16 2645.59 1941.21 2284.72 3515.1 3249.78 TRUE FALSE FALSE 3559.312447 3097.704147 3428.551696 2749.981429 2429.505482 2476.545337 2106.096329 2350.824769 3200.700652 3165.350247 1.124460855 0.978629189 1.083150814 0.868776349 0.767531329 0.782392198 0.665359649 0.742674455 1.011167928 1 11.62814943 -8.994490419 1.827466558 1.056359946 0.727121216 0.884114613 0.05101425 0.085350514 0.568748117 0.009121437 0.01832216 1.01E-09 8.994490419 -0.32923873 ALSSGGS(ph)ITSPPLS(ph)PALPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSGGSITSPPLSPALPK 19 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JW88;F8WCD5;C9JPV7;C9JXQ0;C9J0V6;C9JHT0;C9JRZ2 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 2 0 ALSSGGS(0.513)IT(0.374)S(0.114)PPLS(0.999)PALPK 140.35 0.0031718 3629500 1541.1 1421.1 1284.7 1402.6 1474.4 1665.6 1327.6 1448.7 1744 1275.5 TRUE FALSE FALSE 1522.31648 1441.106283 1307.059665 1564.775211 1399.155866 1559.173535 1440.366311 1490.615849 1588.012272 1242.362326 1.225340183 1.159972621 1.052076063 1.259515987 1.126205968 1.255007096 1.159377003 1.199823769 1.278219919 1 10.27887027 -12.38575375 0.932881696 0.991604588 1.181309237 0 0.10411924 0.354888861 0.512219307 0.04848441 0.010444866 4.11E-13 12.38575375 0.18970465 ALSSGGSIT(ph)SPPLSPALPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSGGSITSPPLSPALPK 19 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JW88;F8WCD5;C9JPV7;C9JXQ0;C9J0V6;C9JHT0;C9JRZ2 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 0 ALSSGGS(0.013)IT(0.877)S(0.104)PPLS(0.006)PALPK 176.17 6.47E-09 400700000 5998.2 5226.7 5093.2 5124.2 6301.7 6367.5 5843.1 6841 6039.4 5127.6 TRUE FALSE FALSE 5925.091631 5300.28162 5181.84501 5716.684114 5980.100734 5960.6373 6339.412768 7038.933542 5499.220938 4994.384213 1.186350785 1.061248273 1.037534316 1.144622414 1.197364976 1.193467912 1.269308187 1.409369652 1.101080875 1 12.2860911 -4 0.332284477 1.068611184 4.512978531 0.805753491 0.050521616 22.65171014 0.287189864 0.022319907 48.68683277 1.00E-04 4 3.444367347 ALSSGGSITS(ph)PPLS(ph)PALPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSGGSITSPPLSPALPK 19 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JW88;F8WCD5;C9JPV7;C9JXQ0;C9J0V6;C9JHT0;C9JRZ2 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 2 0 ALSS(0.002)GGS(0.007)IT(0.111)S(0.88)PPLS(1)PALPK 116.61 0.0085354 120420000 5605.6 5316.1 5255.3 5276.2 6012.4 5681 5228.7 5286.4 5515.6 5064.4 TRUE FALSE FALSE 5537.276791 5390.940195 5346.766292 5886.259069 5705.564793 5318.002435 5672.825647 5439.353643 5022.270922 4932.826158 1.122536374 1.092870501 1.083915411 1.193283299 1.156652315 1.0780843 1.150015319 1.102685047 1.01813256 1 12.26819873 -12.37071385 0.476263667 0.964995906 1.129432154 0.639526742 0.034185415 0.887594642 0.253913064 0.070764031 0.009430781 4.26E-13 12.37071385 0.164436249 ALSSGGSITS(ph)PPLSPALPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSGGSITSPPLSPALPK 19 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JW88;F8WCD5;C9JPV7;C9JXQ0;C9J0V6;C9JHT0;C9JRZ2 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 0 ALSSGGS(0.021)IT(0.036)S(0.933)PPLS(0.01)PALPK 108.14 0.00091211 387930000 5660 5995 5774.6 5856.6 7487.3 6959.4 6955.3 7333.3 6719.6 5732.6 TRUE FALSE FALSE 5591.013743 6079.397767 5875.104491 6533.767648 7105.195142 6514.7168 7546.083008 7545.477465 6118.582146 5583.666226 1.001315895 1.088782445 1.052194786 1.170157274 1.272496395 1.166745385 1.351456678 1.351348229 1.095800125 1 12.44699699 -8.662012906 0.546903234 0.993022832 1.387892081 0.80635082 0.055213082 0.267524474 0.122908405 0.009824446 0.051925832 2.18E-09 8.662012906 0.394869249 ALSSGGSITSPPLS(ph)PALPK ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSGGSITSPPLSPALPK 19 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JW88;F8WCD5;C9JPV7;C9JXQ0;C9J0V6;C9JHT0;C9JRZ2 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 0 ALSSGGSITSPPLS(1)PALPK 139.49 0.00037832 7142500 3311.7 2722.6 3014.9 3462.7 2629.2 2391 2117.8 2414.3 3093.1 3017.7 TRUE FALSE FALSE 3271.335727 2760.928834 3067.37307 3863.073666 2495.022113 2238.222817 2297.685879 2484.153961 2816.445389 2939.299719 1.112964325 0.939315176 1.043572743 1.314283685 0.848849165 0.761481656 0.781712006 0.845151634 0.958202857 1 11.52125676 -8.54719677 24.99984402 1.061417907 0.796423162 0.607085058 0.100031474 104.9262067 107867.6745 0.01384656 0.027694042 2.84E-09 8.54719677 -0.264994745 ALSSLHGDDQDS(ph)EDEVLTIPEVK ddPTM_HeLa_Romidepsin_16h_R1 3 ALSSLHGDDQDSEDEVLTIPEVK 23 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 0 ALSSLHGDDQDS(1)EDEVLTIPEVK;ALSSLHGDDQDS(0.825)EDEVLT(0.175)IPEVK;ALSSLHGDDQDS(0.999)EDEVLT(0.001)IPEVK ;; 115.12 3.14E-06 115773000 9003.4 9704.1 9146.81 7925.75 20631 25184.3 12985.3 20829.7 16152.8 14223.1 TRUE FALSE FALSE 8893.663098 9840.714575 9306.006391 8842.162507 19578.12309 23575.10451 14088.27106 21432.37451 14708.05311 13853.58181 0.641975716 0.710337204 0.671740097 0.638258223 1.413217416 1.701733518 1.016940691 1.54706377 1.061678728 1 13.75797141 -8.752774634 24.98420435 0.791638472 1.411110195 0.684823247 0.210134643 86.46568798 249315.9718 0.031144003 0.061519652 1.77E-09 8.752774634 0.619471723 ALSSS(ph)VIR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSSSVIR 8 0 Q8NEJ9-2;Q8NEJ9;H0YJ17 Q8NEJ9-2 NGDN Neuroguidin 1 0 ALS(0.01)S(0.221)S(0.769)VIR 109.44 0.023086 12483000 3283.6 3107.4 2913.4 2182.6 3572.2 3979.8 3315.9 3171.2 3303.2 2745.9 TRUE FALSE FALSE 3243.57822 3151.146059 2964.106505 2434.962481 3389.897304 3725.503624 3597.552463 3262.953669 3007.753519 2674.561122 1.212751578 1.178191828 1.108259026 0.910415717 1.267459276 1.39294017 1.345100111 1.219995924 1.124578344 1 11.38508646 -4.000000098 0.025483464 1.05E-09 2.828946827 0.273603446 0.119338065 1496.099382 2.961044453 112.8384355 237.7307701 1.00E-04 4.000000098 2.828946826 ALSSSK(ac)QSSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSSSKQSSSSR 12 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 1 ; ALSSSK(1)QSSSSR;ALSSSK(1)QSSSSR 208.33 9.87E-15 1909170 63.343 252.2 0 0 140.35 293.65 271.82 59.048 0 0 FALSE TRUE FALSE 62.57095115 255.7504782 0 0 133.1874158 274.8867127 294.908384 60.75646072 0 0 0 ALSTGEK(ac)GFGYK ddPTM_HeLa_Romidepsin_16h_R1 2 ALSTGEKGFGYK 12 1 F8WE65;C9J5S7;P62937 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 1 ; ALSTGEK(1)GFGYK;ALSTGEK(1)GFGYK 196.11 1.62E-09 14602800 3635.8 3390.4 3105.5 3352.5 4018.3 3312.9 3320.1 3287.5 3604.4 3125.1 FALSE TRUE FALSE 3591.485471 3438.13014 3159.549925 3740.131824 3813.231157 3101.216382 3602.109211 3382.618626 3282.013437 3043.909451 1.179892348 1.129511306 1.037990773 1.228726374 1.252741324 1.018826753 1.183382511 1.111274392 1.078223084 1 11.57170973 -12.37462116 0.935783976 0.993839774 1.145492248 0.210256379 0.074499007 0.535575528 0.783214222 0.058323279 0.012815651 4.22E-13 12.37462116 0.151652474 ALSTGLDYS(ph)PPSAPR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSTGLDYSPPSAPR 15 0 P54253 P54253 ATXN1 Ataxin-1 1 0 ALSTGLDYS(0.997)PPS(0.003)APR;ALSTGLDYS(0.694)PPS(0.306)APR ; 137.93 0.0010538 15494100 2779.4 2845.6 3031.5 2490.3 3067 2493.2 2542.1 2384.24 3820.4 3216.5 TRUE FALSE FALSE 2745.523604 2885.660431 3084.261986 2778.240203 2910.479545 2333.892566 2758.025911 2453.224223 3478.693856 3132.934866 0.876342382 0.92107259 0.984464126 0.886785178 0.928994591 0.744954066 0.880332988 0.783043481 1.110362648 1 11.61329906 -4 0.072238791 1.11178926 0.33843879 0.535606588 0.068199812 144.9563056 0.778669569 1.442159149 11.40446041 1.00E-04 4 -0.773350471 ALSTPVVEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 ALSTPVVEKR 10 1 E5RK24;E5RIW4;E5RH41;P29084 E5RK24 GTF2E2 Transcription initiation factor IIE subunit beta 0 1 ALSTPVVEK(1)R 116.3 0.0033173 1598100 462.54 434.46 469.23 383.08 525.32 389.15 565.65 536.37 722.94 475.47 FALSE TRUE FALSE 456.9023846 440.5763393 477.3967513 427.373512 498.5109602 364.2845709 613.6962969 551.8890197 658.2784358 463.1172209 0.986580425 0.951327913 1.030833512 0.922819305 1.076425012 0.786592583 1.325142468 1.191683217 1.421407812 1 8.855233594 -7.743697709 24.99999971 0.982925853 1.25841297 0.231951889 0.159897582 93.18739958 131309.396 0.009366947 0.034892715 1.80E-08 7.743697709 0.275487117 ALSVGLVK ddPTM_HeLa_Romidepsin_16h_R1 2 ALSVGLVK 8 0 J3KNQ3;A0A087WUL9;Q9UNM6;Q9UNM6-2 J3KNQ3 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 0 ; ; 124.08 0.014682 2691900 3903.4 3859.1 4281 3763.8 4518.3 4334.9 4046.7 3871 3940.4 3410 FALSE FALSE TRUE 3855.823859 3913.428511 4355.509009 4198.988265 4287.714291 4057.91388 4390.426597 3983.001278 3587.960755 3321.407708 1.160900497 1.178243942 1.311344283 1.264219462 1.290932842 1.221745187 1.321857171 1.199190713 1.080253034 1 11.69757911 -11.06863022 0.524425073 1.002243984 1.275482079 0.764497238 0.047640256 0.210982616 0.135409773 0.023937779 0.013915303 8.54E-12 11.06863022 0.273238096 ALSYAS(ph)LDKEDLLSPINQNTLQR ddPTM_HeLa_Romidepsin_16h_R1 1 ALSYASLDKEDLLSPINQNTLQR 23 1 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 ALS(0.011)Y(0.018)AS(0.66)LDKEDLLS(0.199)PINQNT(0.113)LQR 63.674 0.0019021 14717000 1318.1 1001.2 1308.2 1374.7 1554.7 1386.8 1259.8 1543.7 1242.6 792.34 TRUE FALSE FALSE 1302.03449 1015.29492 1330.968672 1533.649282 1475.357858 1298.187956 1366.807381 1588.364524 1131.458744 771.7548926 1.687108825 1.315566548 1.724600239 1.987223271 1.911692264 1.682124685 1.77103818 2.058120446 1.466085612 1 9.591998914 -13.58714186 0.199947884 1.46E-12 1.987728647 0.508843474 0.214696061 5.441479237 0.191257981 2.783027914 0.227283617 2.59E-14 13.58714186 1.987728647 ALT(ph)TPTHYK ddPTM_HeLa_Romidepsin_16h_R1 1 ALTTPTHYK 9 0 P52948-6;P52948-2;P52948-5;P52948;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4;H0YCR0 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 0 ALT(0.882)T(0.118)PTHYK 99.568 0.021583 15377000 5942.3 5782.4 5852.9 6524.5 7498.5 8802.9 7699 7528.2 6045.8 5694.5 TRUE FALSE FALSE 5869.872962 5863.804779 5954.767269 7278.893389 7115.823564 8240.4231 8352.952868 7746.016589 5505.048506 5546.556069 1.058291468 1.057197422 1.073597237 1.312326658 1.282926464 1.485682827 1.50597105 1.39654526 0.992516516 1 12.43737655 -8.982688893 1.042297347 1.024844751 1.472001328 0.931805698 0.050240431 0.083377147 0.178005942 0.008223909 0.020855444 1.04E-09 8.982688893 0.447156577 ALTDDS(ph)DENEEEDAFTDQK ddPTM_HeLa_Romidepsin_16h_R1 1 ALTDDSDENEEEDAFTDQK 19 0 A0A2R8Y549;Q8NI35-4;Q8NI35-3;Q8NI35-2;Q8NI35;Q8NI35-5;A0A0U1RRD7;A0A0U1RQW4 A0A2R8Y549 INADL InaD-like protein 1 0 ALT(0.005)DDS(0.995)DENEEEDAFTDQK 153.1 2.50E-11 0 2124.5 1560.9 1990.7 2248 2334 2142.3 2036.9 2102.1 2383.4 2059.5 TRUE FALSE FALSE 2098.605777 1582.874391 2025.347298 2507.924337 2214.887271 2005.413944 2209.914235 2162.920947 2170.222735 2005.993893 1.04616758 0.789072388 1.009647789 1.25021534 1.104134603 0.999710892 1.101655515 1.078229079 1.081869064 1 10.9701015 -9.483506105 24.99372955 0.999927441 1.103360034 0.29354363 0.092874719 615.391146 390650.509 0.014200296 0.021689026 3.28E-10 9.483506105 0.103432593 ALTGGIAHLFK(ac)QNK ddPTM_HeLa_Romidepsin_16h_R1 1 ALTGGIAHLFKQNK 14 1 E9PEX6;P09622-2;P09622-3;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 1 ALTGGIAHLFK(1)QNK 102.62 0.011384 302350 123.68 0 564.36 56.255 320.52 585.42 476.4 0 150.58 120.8 FALSE TRUE FALSE 122.1725406 0 574.1824491 62.75946779 304.1626684 548.0135514 516.8654041 0 137.1117477 117.6615986 1.038338269 0 4.879947714 0.533389556 2.585063198 4.657539571 4.392813036 0 1.165305837 1 6.878499732 -9.782798624 24.99854658 0.942252261 2.877958326 0.289708288 1.558373052 228.6987299 267664.5899 0.237454258 0.312238739 1.65E-10 9.782798624 1.935706065 ALTGHLEEVVLALLK ddPTM_HeLa_Romidepsin_16h_R1 1 ALTGHLEEVVLALLK 15 0 P04083;Q5T3N1;Q5T3N0 P04083 ANXA1 Annexin A1;Annexin 0 0 69.258 0.024539 6483700 536.77 563.93 462.84 525.67 729.27 740.23 535.35 581.36 635.67 368.92 FALSE FALSE TRUE 530.2276408 571.8690213 470.895536 586.4504388 692.0526306 692.931692 580.8226156 598.1807344 578.8140831 359.3354052 1.475578618 1.591463054 1.310462396 1.632041904 1.92592386 1.928370213 1.616380148 1.664686323 1.610790573 1 8.48918728 -11.57650186 0.262173123 0.75956062 1.8395539 0.157055377 0.238192699 1.197785004 0.173047045 0.454714745 0.158534309 2.65E-12 11.57650186 1.07999328 ALTQTGGPHVK ddPTM_HeLa_Romidepsin_16h_R1 1 ALTQTGGPHVK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 118.61 0.0049905 6514200 2317.1 2379.6 2011.2 2450.9 2376.5 2432.9 2264.9 2135.9 2758.2 2483.2 FALSE FALSE TRUE 2288.858294 2413.100071 2046.204092 2734.28459 2255.218337 2277.445542 2457.280549 2197.698897 2511.499684 2418.686106 0.946323001 0.997690467 0.8459982 1.13048344 0.932414641 0.941604426 1.015956781 0.908633366 1.038373552 1 11.24000784 -8.96035113 0.003534776 1.931468065 6.30E-08 0.038956354 0.073230049 97915.80597 113.676221 30700.32802 31414.42804 1.10E-09 8.96035113 -1.931468002 ALTS(ph)ELANAR ddPTM_HeLa_Romidepsin_16h_R1 1 ALTSELANAR 10 0 P26038 P26038 MSN Moesin 1 0 ALT(0.038)S(0.962)ELANAR 127.51 0.008405 3213300 1762.9 2174.1 1735.9 1104.5 1667.4 1842.9 1936.2 1509.3 2041.3 1483.7 TRUE FALSE FALSE 1741.413097 2204.707037 1766.112611 1232.207487 1582.306356 1725.144638 2100.66078 1552.969214 1858.721015 1445.15326 1.205002365 1.525587007 1.222093642 0.852648311 1.094905571 1.19374511 1.453590313 1.074605204 1.286175707 1 10.49700678 -11.99649642 1.019096357 1.010409652 1.203160827 0 0.198181387 0.758031351 1.521222099 0.09197101 0.035128365 1.01E-12 11.99649642 0.192751175 ALTTPTHYK(ac)LTPR ddPTM_HeLa_Romidepsin_16h_R1 1 ALTTPTHYKLTPR 13 1 P52948-6;P52948-2;P52948-5;P52948;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4;H0YCR0 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 1 ALTTPTHYK(1)LTPR 95.428 0.018118 507380 164.25 0 57.487 0 0 242.11 107.05 173.87 165.45 0 FALSE TRUE FALSE 162.2480578 0 58.48753712 0 0 226.6399524 116.1428243 178.9006541 150.6517376 0 0 ALTVPELTQQVFDAK ddPTM_HeLa_Romidepsin_16h_R1 2 ALTVPELTQQVFDAK 15 0 Q5JP53;P07437;Q5ST81 Q5JP53 TUBB Tubulin beta chain 0 0 ; ; 166.6 0.00035241 11338700 3981.2 3681.8 3887.6 4325.3 3664.1 3505.7 3262.4 3204.3 4306 4044 FALSE FALSE TRUE 3932.675603 3733.632477 3955.262047 4825.411537 3477.107304 3281.697084 3539.508175 3297.011365 3920.860575 3938.936297 0.998410562 0.94787836 1.00414471 1.225054475 0.882752866 0.83314297 0.898594927 0.837030893 0.995411014 1 11.94359037 -8.553001665 24.99999699 1.011249078 0.860066179 0.548723921 0.072843139 120.6854063 100160.3386 0.010235901 0.020471995 2.80E-09 8.553001665 -0.151182899 GK(ac)GGKGLGK(ac)GGAK ddPTM_HeLa_Romidepsin_16h_R1 1 GKGGKGLGKGGAK 13 3 P62805 P62805 HIST1H4A Histone H4 0 2 GK(0.827)GGK(0.173)GLGK(1)GGAK 96.23 0.0044891 0 2111.2 2304.4 3751.2 6932.8 8381.5 9580 8775.6 9277.9 2024.2 1222.5 FALSE TRUE FALSE 2085.467882 2336.841404 3816.488062 7734.402956 7953.760779 8967.868918 9520.999245 9546.341398 1843.150482 1190.739274 1.751405978 1.962513083 3.205141668 6.495463051 6.679682912 7.531345539 7.995872358 8.017155064 1.547904334 1 10.21764184 -9.291612938 1.171767089 1.307476598 7.863394545 0.985580279 0.337530832 0.037448647 0.101583788 0.064330118 0.126264338 5.11E-10 9.291612938 6.555917947 up ALVATPGKK ddPTM_HeLa_Romidepsin_16h_R1 1 ALVATPGKK 9 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 0 99.136 0.0019935 0 3157.5 2687.4 2126.3 2813.6 3047.2 3061.6 2770.2 2479.9 2918.9 2605.5 FALSE FALSE TRUE 3119.015176 2725.233288 2163.30736 3138.92167 2891.690013 2865.973641 3005.500719 2551.651994 2657.826273 2537.808734 1.229019009 1.073852907 0.852431206 1.236862979 1.139443637 1.129310338 1.18428969 1.005454808 1.047291798 1 11.30936763 ALVEFESNPEET(ph)REPGSPPSVQR ddPTM_HeLa_Romidepsin_16h_R1 4 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 ALVEFES(0.084)NPEET(0.629)REPGS(0.274)PPS(0.013)VQR;ALVEFES(0.04)NPEET(0.632)REPGS(0.325)PPS(0.002)VQR;ALVEFES(0.003)NPEET(0.438)REPGS(0.438)PPS(0.121)VQR;ALVEFESNPEET(0.499)REPGS(0.499)PPS(0.003)VQR ;;; 82.367 0.0002071 1108237900 7066.6 6608.5 6693.8 6425.9 6954.9 6827.5 6032.6 6967.8 7840.6 7274.5 TRUE FALSE FALSE 6980.469561 6701.534636 6810.302781 7168.892793 6599.965501 6391.244785 6545.008893 7169.4023 7139.317099 7085.507441 0.985175673 0.945808708 0.961159499 1.011768437 0.931473935 0.902016523 0.923717736 1.011840346 1.007594327 1 12.79065546 -10.11495754 0.537555756 0.998779945 0.944781587 0.241601569 0.033629743 0.805110443 0.528435325 0.011577273 0.015487424 7.67E-11 10.11495754 -0.053998358 ALVEFESNPEETREPGS(ph)PPSVQR ddPTM_HeLa_Romidepsin_16h_R1 2 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 ALVEFESNPEET(0.108)REPGS(0.886)PPS(0.006)VQR;ALVEFESNPEET(0.082)REPGS(0.902)PPS(0.016)VQR ; 90.765 4.64E-05 1005550000 3853.7 3589.26 3473.6 3380.71 4026.16 4065.85 3062.69 4064.63 4467.79 3661.46 TRUE FALSE FALSE 3806.729622 3639.789696 3534.056551 3771.603597 3820.690032 3806.055307 3322.834812 4182.233656 4068.179673 3566.334741 1.067406707 1.020596764 0.990949198 1.057557372 1.071321205 1.067217629 0.931722638 1.172698011 1.140717282 1 11.80022641 ALVEFESNPEETREPGSPPSVQR ddPTM_HeLa_Romidepsin_16h_R1 1 ALVEFESNPEETREPGSPPSVQR 23 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 0 0 85.737 0.00028556 4749800 411.67 385.73 364.04 531.62 397.33 333.11 332.39 550.88 422.63 412.79 FALSE FALSE TRUE 406.6524077 391.1603171 370.3759635 593.0884057 377.0527675 311.8253461 360.6231983 566.8188437 384.8289143 402.0656563 1.011407966 0.97287672 0.921182791 1.475103373 0.937789044 0.775558273 0.896926143 1.409766875 0.957129534 1 8.651287299 -7.251852581 24.41575773 1.003769377 1.409767177 0.340045338 0.17321307 840.7194523 2141091.888 0.023011595 0.391770177 5.60E-08 7.251852581 0.4059978 ALVHERDEAAYGELR ddPTM_HeLa_Romidepsin_16h_R1 1 ALVHERDEAAYGELR 15 1 H0YM70;A0A087X1Z3;Q9UL46 H0YM70 PSME2 Proteasome activator complex subunit 2 0 0 88.706 0.0068752 3824700 1848.3 2235.9 1902.6 3701.9 2355.9 2238.4 1838.8 2280.1 2577.5 2116.4 FALSE FALSE TRUE 1825.772209 2267.377059 1935.713955 4129.931096 2235.669632 2095.373464 1994.987626 2346.071096 2346.961945 2061.415623 0.885688547 1.09991262 0.939021677 2.003444162 1.084531235 1.016473069 0.967775544 1.138087376 1.138519529 1 11.0094197 ALVIVMGK ddPTM_HeLa_Romidepsin_16h_R1 2 ALVIVMGK 8 0 C9J0J7;P35080-2;G5E9Q6 C9J0J7 PFN2 Profilin 0 0 ; ; 129.96 0.0049295 3768400 2114.7 2120.1 3136.1 2236.26 3283.2 3023.9 2496.2 1414.74 2078.17 1315.26 FALSE FALSE TRUE 2088.925223 2149.946823 3190.682505 2494.826903 3115.646053 2830.682549 2708.227166 1455.67327 1892.29327 1281.089356 1.630585106 1.678217693 2.490601058 1.947426143 2.432028679 2.20959025 2.114003332 1.136277703 1.477097021 1 10.32315539 -10.99183122 0.70557564 1.081022002 2.065381358 0.365627476 0.389497574 0.33950872 0.375712438 0.135974332 0.095811941 1.02E-11 10.99183122 0.984359356 ALVVPEPEPDS(ph)DS(ph)NQER ddPTM_HeLa_Romidepsin_16h_R1 1 ALVVPEPEPDSDSNQER 17 0 C9J0A5;C9JXC9;Q5VTR2 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 2 0 ALVVPEPEPDS(1)DS(1)NQER 102.03 0.030445 2372600 937.72 1083.1 1057.3 1047.6 1071.3 1006.2 881.62 732.68 1318.3 977.43 TRUE FALSE FALSE 926.290708 1098.34791 1075.701863 1168.728441 1016.627563 941.9070674 956.5047808 753.8789398 1200.387946 952.0362277 0.972957416 1.153682894 1.129895934 1.22760921 1.06784546 0.989360531 1.00469368 0.791859509 1.260863727 1 9.894872663 -7.089642471 1.959204542 1.032419222 0.629447206 0.294574236 0.110562661 1.269891229 3.43771099 0.014255408 1.072018977 8.13E-08 7.089642471 -0.402972016 ALVVPEPEPDS(ph)DSNQER ddPTM_HeLa_Romidepsin_16h_R1 4 ALVVPEPEPDSDSNQER 17 0 C9J0A5;C9JXC9;Q5VTR2 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 1 0 ALVVPEPEPDS(0.957)DS(0.043)NQER;ALVVPEPEPDS(0.999)DS(0.001)NQER;ALVVPEPEPDS(0.97)DS(0.03)NQER;ALVVPEPEPDS(0.628)DS(0.372)NQER ;;; 239.7 7.68E-47 116151000 10964.3 10404.4 9982.8 9751.2 11442.5 11982.8 10485.1 11251 10868.3 10106.8 TRUE FALSE FALSE 10830.66289 10550.87342 10156.54645 10878.67962 10858.54653 11217.13775 11375.70413 11576.52993 9896.212028 9844.223879 1.100204854 1.071783164 1.03172648 1.105082509 1.103037341 1.139463902 1.155571457 1.175971826 1.005281082 1 13.26506175 -4 0.061211313 0.853881852 1.623221667 0.820777114 0.024550448 112.9590204 0.521195321 1.329479702 7.756179548 1.00E-04 4 0.769339815 ALVVPEPEPDS(ph)DSNQERK ddPTM_HeLa_Romidepsin_16h_R1 1 ALVVPEPEPDSDSNQERK 18 1 C9J0A5;C9JXC9;Q5VTR2 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 1 0 ALVVPEPEPDS(0.623)DS(0.377)NQERK 116.73 0.00043624 11581000 4033.5 3774.9 4090.1 3050.4 3202 3408.7 2707 2860 4129.5 4028.1 TRUE FALSE FALSE 3984.338151 3828.043141 4161.286475 3403.101601 3038.589992 3190.895071 2936.932512 2942.749588 3760.147177 3923.449381 1.015519193 0.975683071 1.060619386 0.867374922 0.774469019 0.813288196 0.748558788 0.750041431 0.9583779 1 11.93790687 -9.03155476 3.216641087 1.008128843 0.773715281 0.922385469 0.031508515 0.038055913 0.802469104 0.003985581 0.007187865 9.30E-10 9.03155476 -0.234413562 ALVVPEPEPDSDS(ph)NQER ddPTM_HeLa_Romidepsin_16h_R1 1 ALVVPEPEPDSDSNQER 17 0 C9J0A5;C9JXC9;Q5VTR2 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 1 0 ALVVPEPEPDS(0.248)DS(0.752)NQER 88.108 0.010557 91474000 3409.1 3216.4 2921.7 3179.2 2686.1 2907.9 2295.2 2593.7 3647.1 3236.2 TRUE FALSE FALSE 3367.548578 3261.680564 2972.550963 3546.794063 2549.018294 2722.094575 2490.154231 2668.744617 3320.894242 3152.123057 1.068342992 1.034756735 0.943031382 1.125207994 0.808667126 0.86357497 0.789992708 0.846649883 1.053542067 1 11.62210814 -8.74804861 24.99997376 1.031603131 0.827158639 0.822349879 0.047828861 71.1995342 132925.6307 0.006797839 0.01353394 1.79E-09 8.74804861 -0.204444492 ALYDYAGQEADELS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 2 ALYDYAGQEADELSFR 16 0 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 ALYDYAGQEADELS(1)FR;ALYDYAGQEADELS(1)FR ; 167.18 1.81E-05 34382000 5390.9 5482.3 4841 4184.3 4640.4 4014.6 2866 3423.9 5099.1 5109.9 TRUE FALSE FALSE 5325.193637 5559.479963 4925.255574 4668.108454 4403.583072 3758.080017 3109.437968 3522.965144 4643.023725 4977.144061 1.069929576 1.117002019 0.989574646 0.937909049 0.884761023 0.755067559 0.624743413 0.707828647 0.932869065 1 12.28110243 -8.455202921 1.145177101 1.038802145 0.652724232 0.875446305 0.053569965 0.104133708 0.252228496 0.007474522 0.028474378 3.51E-09 8.455202921 -0.386077913 ALYDYEGQEHDELSFK ddPTM_HeLa_Romidepsin_16h_R1 2 ALYDYEGQEHDELSFK 16 0 A0A0U1RR22;Q9UNF0-2;Q9UNF0;H0Y923 A0A0U1RR22 PACSIN2 Protein kinase C and casein kinase substrate in neurons protein 2 0 0 ; ; 157.91 8.64E-05 14048000 4068.6 4593.6 3914.7 3667.9 5556.3 6654.3 6284.2 6630.8 4674.8 4040.9 FALSE FALSE TRUE 4019.010338 4658.268821 3982.833711 4091.999856 5272.741278 6229.111706 6817.979791 6822.651736 4256.67418 3935.916835 1.0211116 1.183528264 1.01192019 1.039656077 1.339647533 1.582632959 1.732246914 1.733433917 1.08149495 1 11.94248402 -8.397594386 1.538424342 1.022539485 1.741416306 0.957439109 0.059381128 0.050813891 0.229440905 0.00883897 0.028634657 4.00E-09 8.397594386 0.71887682 ALYETELADARR ddPTM_HeLa_Romidepsin_16h_R1 2 ALYETELADARR 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 0 ; ; 145.99 0.00097001 9917500 5092.3 5615.8 4559.7 6045.1 4877.8 4509.5 4068.8 4092.4 5228.4 4507.5 FALSE FALSE TRUE 5030.233089 5694.85938 4639.059666 6744.062905 4628.867664 4221.357504 4414.40377 4210.807137 4760.758809 4390.3945 1.145736013 1.297117919 1.056638456 1.536094969 1.054317024 0.961498449 1.005468591 0.959095393 1.084357866 1 12.10013486 -8.522729665 24.99999952 1.124739396 0.98328924 0.23795516 0.149247797 8.095254056 1357473.939 0.023476745 0.047362112 3.00E-09 8.522729665 -0.141450157 AMEVDERPTEQYSDIGGLDK ddPTM_HeLa_Romidepsin_16h_R1 1 AMEVDERPTEQYSDIGGLDK 20 1 E9PM69;P17980;E9PMD8;R4GNH3;E9PN50 E9PM69;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 0 69.763 0.013123 13534000 1264.3 1437.6 1406.7 1242 1111.2 1264.5 1137.3 1366.6 1435.4 1503.2 FALSE FALSE TRUE 1248.890225 1457.838571 1431.183023 1385.605884 1054.491318 1183.702531 1233.902234 1406.140415 1307.014229 1464.146647 0.852981652 0.995691636 0.977486119 0.946357311 0.720208812 0.808458998 0.842744978 0.960382225 0.892679863 1 10.51584434 -8.836194991 24.99999938 0.939280576 0.831893221 0.38281776 0.069027392 36.08304125 12065.8936 0.01166891 0.021151702 1.46E-09 8.836194991 -0.107387354 AMGEQLLPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AMGEQLLPGKK 11 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 0 1 ; AMGEQLLPGK(1)K;AMGEQLLPGK(1)K 97.813 0.0017768 0 1672.94 1351.67 1268.39 1133.18 1239.25 1136.69 983.43 1082.54 1669.96 1589.71 FALSE TRUE FALSE 1652.549564 1370.698846 1290.465796 1264.203603 1176.006448 1064.059177 1066.96252 1113.861587 1520.594595 1548.409105 1.067256424 0.885230422 0.833413981 0.816453222 0.759493369 0.687195118 0.689070166 0.719358717 0.982036718 1 10.59657098 -9.592457994 1.008413415 1.033182657 0.708328457 0.903869812 0.040075783 0.099857948 0.20296794 0.008523076 0.014653452 2.56E-10 9.592457994 -0.324854199 AMKPPGGESSNLFGS(ph)PEEATPSSRPNR ddPTM_HeLa_Romidepsin_16h_R1 1 AMKPPGGESSNLFGSPEEATPSSRPNR 27 2 A6NGP5;Q9H910;Q9H910-3;H3BMV3;H3BMM8;B4E1P3 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 0 AMKPPGGES(0.005)S(0.001)NLFGS(0.704)PEEAT(0.097)PS(0.097)S(0.097)RPNR 60.23 0.0019847 13529000 1153.7 1303.5 1326.2 1197.5 1471.8 1977.7 1529.8 1652.3 1318.5 1334.3 TRUE FALSE FALSE 1139.638261 1321.850707 1349.281955 1335.960584 1396.688554 1851.331353 1659.741174 1700.106694 1200.570058 1299.634694 0.876891227 1.017094045 1.038200935 1.027950847 1.0746778 1.424501332 1.277082846 1.308141974 0.923775014 1 10.34389045 -8.48672196 2.572542887 0.959275009 1.331153726 0.859030527 0.063633351 0.081107802 1.060961631 0.010900792 0.026420029 3.26E-09 8.48672196 0.371878717 AMLDS(ph)GIYPPGSPGK ddPTM_HeLa_Romidepsin_16h_R1 2 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 0 AMLDS(0.952)GIY(0.021)PPGS(0.027)PGK;AMLDS(0.835)GIYPPGS(0.164)PGK ; 140.31 0.0011052 55072000 16325.7 15962.5 15737 13488.5 13385.7 13155.3 11531.5 12205.6 17098.3 15208.3 TRUE FALSE FALSE 16126.71609 16187.22049 16010.89588 15048.10384 12702.57778 12314.71879 12510.98532 12558.74978 15568.98522 14813.18617 1.088673017 1.092757514 1.080854294 1.015858686 0.85751827 0.831334909 0.844584357 0.847808812 1.051022045 1 13.85459436 -8.788840627 3.716479835 1.050175885 0.841328139 0.938601304 0.026402816 0.057748605 1.692984644 0.005845742 0.011451421 1.63E-09 8.788840627 -0.208847747 AMLDSGIYPPGS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 AMLDSGIYPPGSPGK 15 0 O95295 O95295 SNAPIN SNARE-associated protein Snapin 1 0 AMLDS(0.002)GIY(0.006)PPGS(0.993)PGK;AMLDSGIY(0.001)PPGS(0.999)PGK ; 110.84 0.0057477 204056000 10316 11270.5 10519.1 9472.2 9380.4 9484.5 7131 8475.8 12113.7 10441.2 TRUE FALSE FALSE 10190.26462 11429.16639 10702.18052 10567.42033 8901.683185 8878.47106 7736.706962 8721.0339 11030.22033 10169.93612 1.001998882 1.123818897 1.052335078 1.039084239 0.875293913 0.873011488 0.760742926 0.857530844 1.084590916 1 13.312023 -8.62575508 3.174514556 1.017998519 0.827480671 0.792609186 0.0509116 0.091701681 1.838952185 0.007443761 0.015976237 2.37E-09 8.62575508 -0.190517848 AMRVGQY(ph)RRLANS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AMRVGQYRRLANSK 14 3 B2RXH2 B2RXH2 KDM4E Lysine-specific demethylase 4E 2 0 AMRVGQY(1)RRLANS(1)K 44.188 0.0043436 0 1665.4 1517 2055.2 1496.3 2318.3 2326.9 2332.4 2530.4 1993.6 2068 TRUE FALSE FALSE 1645.101464 1538.356366 2090.969894 1669.309246 2199.9885 2178.2186 2530.513998 2603.613132 1815.287423 2014.273062 0.816722169 0.763727816 1.038076681 0.828740292 1.092199733 1.081391913 1.256291436 1.292582014 0.901212183 1 10.97604356 -8.081875172 1.092180683 0.903055735 1.317216965 0.744230698 0.086990442 0.286364175 0.54545111 0.015401489 0.097181817 8.28E-09 8.081875172 0.414161229 AMS(ph)LNTLNVDAPR ddPTM_HeLa_Romidepsin_16h_R1 3 AMSLNTLNVDAPR 13 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 0 AMS(0.999)LNT(0.001)LNVDAPR;AMS(0.944)LNT(0.056)LNVDAPR;AMS(0.999)LNT(0.001)LNVDAPR ;; 95.428 0.023576 192758000 3382.21 3526.51 3912.3 3433.16 10050.4 14635.9 14158.9 16657.9 3677.58 3951 TRUE FALSE FALSE 3340.986324 3576.1563 3980.39194 3830.118113 9537.490585 13700.71323 15361.55661 17139.87005 3348.648034 3848.35245 0.868160172 0.929269433 1.034310654 0.995261781 2.478330846 3.560150325 3.991722902 4.453820245 0.870151078 1 11.91002522 -8.408323365 1.488588964 0.925854954 4.265119653 0.988558191 0.148579053 0.027435599 0.115860376 0.021625909 0.070891168 3.91E-09 8.408323365 3.3392647 up AMS(ph)TTSISSPQPGK ddPTM_HeLa_Romidepsin_16h_R1 3 AMSTTSISSPQPGK 14 0 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3;H0Y5J4;Q9UJU6-5;Q9UJU6 B4DDD6;H0Y5J4 DBNL Drebrin-like protein 1 0 AMS(0.923)T(0.071)T(0.006)SISSPQPGK;AMS(0.942)T(0.047)T(0.001)S(0.009)IS(0.001)SPQPGK;AMS(0.982)T(0.017)T(0.001)SISSPQPGK ;; 126.56 0.0041006 66290000 14062.2 12052.5 13675.7 15716.3 12944.7 17657.2 14888.1 19015.2 13381.1 11419.8 TRUE FALSE FALSE 13890.8045 12222.17541 13913.71982 17533.49255 12284.08366 16528.96191 16152.69484 19565.37481 12184.2609 11123.11195 1.248823581 1.09880899 1.250883735 1.576311794 1.104374721 1.486001578 1.452174078 1.758983898 1.095400366 1 13.44127285 -4 0.16488358 0.981524792 3.631244749 0.65727795 0.138523464 27.19887884 0.280417156 0.221673684 17.72569182 1.00E-04 4 2.649719957 AMST(ph)TSISSPQPGK ddPTM_HeLa_Romidepsin_16h_R1 1 AMSTTSISSPQPGK 14 0 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3;H0Y5J4;Q9UJU6-5;Q9UJU6 B4DDD6;H0Y5J4 DBNL Drebrin-like protein 1 0 AMS(0.11)T(0.837)T(0.044)S(0.009)IS(0.001)SPQPGK 117.48 0.011198 9421100 2077.3 1873 2123.6 2128.5 2218 2519.3 2221.8 2433.2 2032.9 1889.1 TRUE FALSE FALSE 2051.981069 1899.368143 2160.560367 2374.607185 2104.807184 2358.324861 2410.519637 2503.600803 1851.072333 1840.02091 1.115194429 1.032253565 1.174204247 1.290532718 1.143903948 1.281683729 1.310050133 1.360637148 1.00600614 1 10.84550645 -4 0.145360898 0.951301303 2.469711104 0.832735046 0.051959412 19.90567138 0.189005273 0.124888523 6.355822022 1.00E-04 4 1.518409801 AMSTTSIS(ph)SPQPGK ddPTM_HeLa_Romidepsin_16h_R1 4 AMSTTSISSPQPGK 14 0 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3;H0Y5J4;Q9UJU6-5;Q9UJU6 B4DDD6;H0Y5J4 DBNL Drebrin-like protein 1 0 AMSTT(0.015)S(0.037)IS(0.72)S(0.228)PQPGK;AMSTT(0.004)S(0.025)IS(0.697)S(0.274)PQPGK;AMS(0.003)T(0.004)T(0.006)S(0.093)IS(0.69)S(0.204)PQPGK;AMSTT(0.001)S(0.037)IS(0.735)S(0.227)PQPGK ;;; 116.98 0.0063048 507606000 29131.1 30428.9 26936.1 27358.9 33608.8 33602.2 30117.2 31756.6 26716.7 25400.7 TRUE FALSE FALSE 28776.03895 30857.27885 27404.91152 30522.26475 31893.61752 31455.12787 32675.35422 32675.42712 24327.09144 24740.78615 1.163101236 1.247223054 1.107681516 1.233682089 1.289110917 1.271387565 1.320708001 1.320710947 0.983278837 1 14.59460372 -13.7843526 0.045978394 3.12E-13 1.977688325 0.887906889 0.03989596 59.21254297 0.395734341 12.03194876 5.886310556 1.64E-14 13.7843526 1.977688325 AMSTTSISS(ph)PQPGK ddPTM_HeLa_Romidepsin_16h_R1 1 AMSTTSISSPQPGK 14 0 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3;H0Y5J4;Q9UJU6-5;Q9UJU6 B4DDD6;H0Y5J4 DBNL Drebrin-like protein 1 0 AMST(0.001)T(0.002)S(0.054)IS(0.376)S(0.568)PQPGK 103.11 0.012108 7199300 4885.1 5178.7 4424.4 4409 5594 5622.9 4829.4 4829.1 4448.3 4450.2 TRUE FALSE FALSE 4825.558522 5251.605875 4501.404826 4918.789325 5308.517306 5263.614837 5239.609115 4968.822389 4050.432907 4334.583162 1.113269337 1.211559607 1.038486207 1.134777934 1.224689228 1.214330107 1.208791923 1.146320696 0.934445771 1 12.08167755 -11.76389367 0.219988054 0.910026716 1.223662134 0.676333201 0.05471238 2.421945517 0.23590418 0.237507761 0.077504587 1.72E-12 11.76389367 0.313635418 AMSTTSISSPQPGK(ac)LR ddPTM_HeLa_Romidepsin_16h_R1 2 AMSTTSISSPQPGKLR 16 1 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3;H0Y5J4;Q9UJU6-5;Q9UJU6 B4DDD6;H0Y5J4 DBNL Drebrin-like protein 0 1 ; AMSTTSISSPQPGK(1)LR;AMSTTSISSPQPGK(1)LR 116.51 0.0015527 3794500 455.9 149.733 231.211 180.22 248.27 398 675.81 504.86 420.65 324.02 FALSE TRUE FALSE 450.3433154 151.8409451 235.2351305 201.0578844 235.5998555 372.5690845 733.2132845 519.4673276 383.0260105 315.6019137 1.426934679 0.481115413 0.745353942 0.637061677 0.746509591 1.180503249 2.323221922 1.645957471 1.213636527 1 8.301962143 -7.855870634 6.293602047 1.043556152 1.977701612 0.611836858 0.32746936 0.120753575 6.618241782 0.053147358 0.163770842 1.39E-08 7.855870634 0.93414546 AMT(ph)MPPVSPVGAEGPVVLR ddPTM_HeLa_Romidepsin_16h_R1 3 AMTMPPVSPVGAEGPVVLR 19 0 O15020;A4QPE4 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 1 0 AMT(0.684)MPPVS(0.316)PVGAEGPVVLR;AMT(0.749)MPPVS(0.251)PVGAEGPVVLR;AMT(0.984)MPPVS(0.016)PVGAEGPVVLR ;; 75.088 0.011223 41999700 2527.67 3413.9 2363.21 3178.8 3107.57 3122.31 3117.33 3191.47 2924.7 2849.61 TRUE FALSE FALSE 2496.861786 3461.960974 2404.340679 3546.347813 2948.979107 2922.804468 3382.115932 3283.810149 2663.107507 2775.576721 0.899583055 1.247294282 0.866249043 1.277697635 1.062474362 1.05304402 1.218527273 1.183109126 0.959478975 1 11.43857186 -9.817086442 1.036439978 0.956075233 1.144636463 0.248045572 0.121706396 0.426495566 0.911242432 0.022878822 0.034302891 1.52E-10 9.817086442 0.18856123 AMTLS(ph)PQEEVAAGQMASSSR ddPTM_HeLa_Romidepsin_16h_R1 4 AMTLSPQEEVAAGQMASSSR 20 0 A0A494BZT8;Q9Y6A5 A0A494BZT8 TACC3 Transforming acidic coiled-coil-containing protein 3 1 0 AMT(0.055)LS(0.945)PQEEVAAGQMASSSR;AMT(0.026)LS(0.973)PQEEVAAGQMASSSR;AMT(0.052)LS(0.937)PQEEVAAGQMAS(0.011)S(0.001)SR;AMT(0.006)LS(0.905)PQEEVAAGQMAS(0.022)S(0.065)S(0.003)R ;;; 108.25 0.0003165 113836000 10707.8 9935.2 9680.7 9146 13548.4 15840.1 13883.2 15386.7 10847.7 9766.9 TRUE FALSE FALSE 10577.28921 10075.06801 9849.188523 10203.50355 12856.97459 14827.96873 15062.43866 15831.88989 9877.454543 9513.15453 1.111859287 1.059066998 1.035323088 1.072567834 1.351494349 1.558680529 1.583327446 1.664210314 1.038294344 1 13.2157081 -8.507763572 1.853790097 1.051446449 1.618807373 0.980520894 0.034992923 0.043080434 0.291416552 0.007158873 0.019169567 3.11E-09 8.507763572 0.567360924 ANAEK(ac)TSGSNVK ddPTM_HeLa_Romidepsin_16h_R1 2 ANAEKTSGSNVK 12 1 P56381 P56381 ATP5E "ATP synthase subunit epsilon, mitochondrial" 0 1 ; ANAEK(1)TSGSNVK;ANAEK(1)TSGSNVK 193.49 2.99E-09 1032220 308.8 216.09 214.716 428.59 170.88 612.55 513.63 207.54 335.35 404.09 FALSE TRUE FALSE 305.0362268 219.1321207 218.4530419 478.1455924 162.159356 573.4100319 557.2577194 213.5448425 305.3554561 393.5916835 0.775006789 0.556749875 0.555024537 1.214826462 0.411998939 1.456865213 1.415826967 0.542554255 0.775817856 1 8.620555927 -8.24647676 24.96719999 0.836394652 1.166156576 0.198214522 0.324133347 1050.32534 1752610.936 0.043679691 0.110858124 5.67E-09 8.24647676 0.329761924 ANASNSPS(ph)SLR ddPTM_HeLa_Romidepsin_16h_R1 1 ANASNSPSSLR 11 0 Q5T5X7 Q5T5X7 BEND3 BEN domain-containing protein 3 1 0 ANAS(0.005)NS(0.275)PS(0.707)S(0.013)LR 117.48 0.011178 6236900 3259.3 3165.7 3254.4 2354.8 2396.7 2248.9 1591.4 1820 3741.9 3467.5 TRUE FALSE FALSE 3219.574398 3210.266808 3311.041467 2627.073056 2274.387456 2105.202548 1726.573476 1872.658829 3407.215092 3377.41385 0.95326618 0.950510346 0.980348164 0.777835697 0.673410946 0.623317912 0.5112117 0.554465313 1.008823687 1 11.72170325 -8.81190371 1.137609933 0.979808029 0.537981 0.971802175 0.03157583 0.052920835 0.134656847 0.005193732 0.014291493 1.54E-09 8.81190371 -0.441827029 ANDDIIVNWVNR ddPTM_HeLa_Romidepsin_16h_R1 1 ANDDIIVNWVNR 12 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 0 144.7 0.015436 20553000 1718.3 1321.7 1840.8 1338 1688.3 1488.4 1523.5 1318.1 1250.7 1283.4 FALSE FALSE TRUE 1697.356699 1340.306927 1872.838352 1492.705855 1602.139751 1393.296044 1652.906052 1356.237144 1138.83426 1250.057083 1.357823352 1.072196578 1.498202264 1.194110154 1.281653272 1.114585936 1.322264459 1.08494017 0.911025804 1 10.28777826 -12.47971135 1.180389331 0.997920087 1.254079154 0.416533826 0.13079329 0.402749243 0.99078889 0.085067467 0.02014513 3.31E-13 12.47971135 0.256159067 ANDEANQS(ph)DTSVSLSEPK ddPTM_HeLa_Romidepsin_16h_R1 2 ANDEANQSDTSVSLSEPK 18 0 O95684;O95684-2;A0A087WV25 O95684 FGFR1OP FGFR1 oncogene partner 1 0 ANDEANQS(0.792)DT(0.006)S(0.052)VS(0.146)LS(0.004)EPK;ANDEANQS(0.823)DT(0.163)S(0.014)VSLSEPK ; 258.38 1.19E-75 14679100 4136.1 3821.2 3806.6 3323.4 4144 4252.3 3619 3904.3 4141.9 4331.3 TRUE FALSE FALSE 4085.687622 3874.994954 3872.852276 3707.667145 3932.516217 3980.591754 3926.39777 4017.264761 3771.43809 4218.772202 0.968454192 0.918512489 0.918004597 0.878849809 0.932147087 0.943542709 0.930696796 0.952235525 0.893965806 1 12.04260747 -10.53054526 1.714698207 0.989218633 0.923811661 0 0.035913178 0.149944261 0.88226575 0.004256961 0.004546632 2.95E-11 10.53054526 -0.065406972 ANEAGGQVGPEAPRPPET(ph)SPEMR ddPTM_HeLa_Romidepsin_16h_R1 1 ANEAGGQVGPEAPRPPETSPEMR 23 1 Q8N3D4;E9PIH6 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 ANEAGGQVGPEAPRPPET(0.5)S(0.5)PEMR 55.02 0.0084486 72034000 1319 1018.6 1139.1 1161.1 1246.2 1551.9 1241 1480.7 1236.6 1308.1 TRUE FALSE FALSE 1302.923521 1032.939878 1158.925558 1295.351845 1182.601764 1452.738599 1346.410509 1523.541718 1125.995399 1274.115373 1.022610313 0.810711415 0.909592319 1.016667621 0.928174786 1.140193917 1.056741436 1.195764332 0.883746812 1 10.31528021 -8.251545559 24.81802824 0.983449912 1.123484061 0.508907137 0.078204014 474.7305175 1190828.303 0.010798713 0.027166369 5.60E-09 8.251545559 0.14003415 ANEFLEVGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 ANEFLEVGKK 10 1 Q14152 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 1 ANEFLEVGK(1)K 108.47 0.0050167 252580 0 96.371 181.22 178.24 152.14 251.45 276.62 306.45 226.51 264.74 FALSE TRUE FALSE 0 97.72771347 184.3740581 198.8489474 144.3757281 235.3831565 300.1160959 315.3166473 206.2503783 257.8620166 0 0.378992279 0.715010533 0.771144778 0.559895288 0.912826013 1.163863138 1.222811531 0.799847845 1 8.010455468 -7.963570627 0.995611713 0.523341913 1.330088754 0.439405895 0.261972429 0.770098683 1.09142167 0.060909283 0.508888237 1.09E-08 7.963570627 0.806746841 ANES(ph)SPKPVGPPPER ddPTM_HeLa_Romidepsin_16h_R1 1 ANESSPKPVGPPPER 15 1 A6PVM9;Q9BQI0-3;Q9BQI0;Q9BQI0-2 A6PVM9 AIF1L Allograft inflammatory factor 1-like 1 0 ANES(0.5)S(0.5)PKPVGPPPER 63.29 0.025944 18593000 1329.2 1185.4 983.28 907.72 1960.1 2411.7 2174.6 2183.4 1475.4 1391.8 TRUE FALSE FALSE 1312.999199 1202.088092 1000.393576 1012.674857 1860.068783 2257.600153 2359.31047 2246.573234 1343.436529 1355.640835 0.968545034 0.886730512 0.737948836 0.747008227 1.372095569 1.665337967 1.740365448 1.657203867 0.990997389 1 10.40475928 -8.532811417 3.532083009 0.941729339 1.682915627 0.927107123 0.100868383 0.052120803 1.385585788 0.017321837 0.038373038 2.93E-09 8.532811417 0.741186288 ANGLPAGPEPASEPGS(ph)PYPEGPR ddPTM_HeLa_Romidepsin_16h_R1 2 ANGLPAGPEPASEPGSPYPEGPR 23 0 Q5VTI5;A0A1B0GUN5;Q9Y2H5;A0A5F9ZH45 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 ANGLPAGPEPAS(0.058)EPGS(0.942)PYPEGPR;ANGLPAGPEPAS(0.062)EPGS(0.938)PYPEGPR ; 219.16 7.16E-35 15162400 14809.2 14619 12661.1 12208.1 12399.3 10265.2 8456.5 9078.1 13870.6 13870.2 TRUE FALSE FALSE 14628.69977 14824.80667 12881.46113 13619.65796 11766.51745 9609.286849 9174.794899 9340.760501 12629.9788 13509.8502 1.082817319 1.097333164 0.9534866 1.008127977 0.870958395 0.711280044 0.679118921 0.691403706 0.934871861 1 13.72172406 -8.499666529 1.487780131 1.04021865 0.674066148 0.889318017 0.050103027 0.075449036 0.324196962 0.006786321 0.020526853 3.16E-09 8.499666529 -0.366152501 ANK(ac)ITITNDK ddPTM_HeLa_Romidepsin_16h_R1 2 ANKITITNDK 10 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;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 1 ; ANK(1)ITITNDK;ANK(1)ITITNDK 164.33 0.013146 7430100 2693.7 2833.4 3423.6 2138.3 2859.8 3322.1 2718.3 2891.2 3418.8 3144.2 FALSE TRUE FALSE 2660.868148 2873.28868 3483.186322 2385.540307 2713.853735 3109.828532 2949.192334 2974.85231 3113.013965 3062.513231 0.868851152 0.938212658 1.137362049 0.778948572 0.886152493 1.015449827 0.962997418 0.97137615 1.016489965 1 11.58050036 -8.247659518 24.57407708 0.936843678 0.981246751 0.024919224 0.091796246 1840.057743 3281425.951 0.013048357 0.033068075 5.65E-09 8.247659518 0.044403073 ANK(ac)ITITNDKGR ddPTM_HeLa_Romidepsin_16h_R1 1 ANKITITNDKGR 12 2 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;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 1 ANK(1)ITITNDKGR 102.33 0.012399 1506600 179.65 238.5 349.31 91.304 311.99 419.08 259.34 308.33 107.04 143.98 FALSE TRUE FALSE 177.4603567 241.8576093 355.389594 101.8609981 296.0679861 392.3021405 281.3683331 317.2510421 97.46607431 140.2393788 1.265410316 1.724605537 2.534164063 0.726336632 2.111161562 2.797375058 2.006343264 2.262210833 0.694997904 1 7.131747701 -9.552105034 0.373187274 0.958265893 2.472571104 0.484881722 0.513309099 0.947840532 0.291268722 0.246862555 0.55847632 2.80E-10 9.552105034 1.514305211 GGK(ac)GLGK(ac)GGAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GGKGLGKGGAKR 12 3 P62805 P62805 HIST1H4A Histone H4 0 3 ; GGK(1)GLGK(1)GGAK(1)R;GGK(1)GLGK(1)GGAK(1)R 179.42 7.44E-09 10526900000 2543.68 3252.61 9207.8 20225.2 40052 32133.4 29139.8 22948.7 2856.26 1528.85 FALSE TRUE FALSE 2512.67665 3298.400329 9368.057897 22563.73279 38007.99699 30080.17945 31614.93388 23612.68443 2600.788952 1489.130257 1.687345105 2.214984428 6.29095934 15.15228952 25.52362147 20.19983095 21.23046909 15.85669509 1.746515418 1 10.54025424 -9.27224751 2.127687771 1.417902413 20.73229496 0.93219279 2.347466893 0.050729711 0.448485257 0.356145569 0.614024444 5.34E-10 9.27224751 19.31439255 up ANLPQSFQVDTSK ddPTM_HeLa_Romidepsin_16h_R1 1 ANLPQSFQVDTSK 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 130.56 0.0044116 727070 404.03 508.31 412.21 522.52 394.98 503.2 507.34 478.27 494.62 680.93 FALSE FALSE TRUE 399.105527 515.4660015 419.3843421 582.9362209 374.8226967 471.047144 550.4334469 492.1079879 450.3799484 663.2393404 0.60175189 0.777194551 0.632327301 0.878922864 0.565139421 0.71022196 0.829916764 0.741976475 0.679060968 1 9.373385773 -12.44889903 1.14476356 1.002299118 0.708962659 0 0.134924507 0.283262721 0.655627275 0.066742917 0.016071647 3.56E-13 12.44889903 -0.293336459 ANLQIDQINTDLNLER ddPTM_HeLa_Romidepsin_16h_R1 1 ANLQIDQINTDLNLER 16 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 188.63 1.99E-11 0 1618.9 1081.2 1342.8 981.72 1430.9 1658.6 1221.7 1232.1 1474.8 1608.3 FALSE FALSE TRUE 1599.168224 1096.421162 1366.170871 1095.231086 1357.875834 1552.620813 1325.471168 1267.74887 1342.890194 1566.516134 1.020843762 0.699910545 0.872107756 0.699150849 0.866812543 0.991129794 0.846126726 0.809279165 0.857246322 1 10.61334391 -10.29039796 24.85403298 1.009842902 0.831879989 0.250907792 0.093514389 376.7007906 323306.523 0.01362294 0.015579816 5.12E-11 10.29039796 -0.177962913 ANLQQAIVT(ph)PLKPVDNTYYK ddPTM_HeLa_Romidepsin_16h_R1 2 ANLQQAIVTPLKPVDNTYYK 20 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 ANLQQAIVT(1)PLKPVDNTYYK;ANLQQAIVT(0.947)PLKPVDNT(0.044)Y(0.008)Y(0.002)K ; 104.16 0.0003027 193197000 4850.6 4729.2 4870.3 4620.9 4429.2 5051.1 3771.2 3913.5 4806.7 4491.4 TRUE FALSE FALSE 4791.479021 4795.777802 4955.065529 5155.1902 4203.161396 4728.351012 4091.525634 4026.730948 4376.776713 4374.712781 1.095267109 1.096249752 1.132660766 1.178406551 0.960785681 1.080836903 0.93526726 0.920456073 1.000471787 1 12.09497259 -7.753569182 22.64229695 1.061245173 0.927861345 0.442026852 0.062641677 41.89575756 120521.6575 0.009255582 0.033206295 1.76E-08 7.753569182 -0.133383828 ANLVLLSGANEGK ddPTM_HeLa_Romidepsin_16h_R1 1 ANLVLLSGANEGK 13 0 F5H7V1;O43847;O43847-2;G3V1R5;H0Y5G9 F5H7V1 NRD1 Nardilysin 0 0 110.31 0.028916 197490 184.13 131.09 56.715 125.45 208.51 178.96 0 122.13 107.57 133.8 FALSE FALSE TRUE 181.8857527 132.9354885 57.70210078 139.9551193 197.8689566 167.5250336 0 125.6636389 97.94866979 130.3238567 1.395644338 1.020039552 0.442759309 1.073902529 1.518286534 1.28545178 0 0.964241253 0.751578968 1 7.025957393 -7.781294651 24.99967036 1.146391206 0.482120339 0.257381644 0.37125151 167.4921236 210888.8251 0.049714909 0.149428279 1.65E-08 7.781294651 -0.664270867 ANNS(ph)QEPS(ph)PQLASSVASTR ddPTM_HeLa_Romidepsin_16h_R1 1 ANNSQEPSPQLASSVASTR 19 0 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 2 0 ANNS(1)QEPS(0.506)PQLAS(0.413)S(0.081)VAS(0.001)TR 145.71 0.00060113 6020600 1808 1667.2 1528.4 1782.3 2879.2 3479.8 2713.9 3178.1 1942.9 1856.8 TRUE FALSE FALSE 1785.963401 1690.670885 1555.001161 1988.377912 2732.26368 3257.452011 2944.418598 3270.053309 1769.122158 1808.560068 0.987505713 0.934815998 0.859800671 1.099425973 1.510739802 1.801130119 1.628045786 1.808097705 0.978193751 1 10.8206258 -8.697028739 2.563061069 0.978781635 1.731271444 0.967938095 0.064672336 0.032660699 0.436067653 0.0093878 0.020269531 2.01E-09 8.697028739 0.752489809 ANNSQEPS(ph)PQLASSVASTR ddPTM_HeLa_Romidepsin_16h_R1 2 ANNSQEPSPQLASSVASTR 19 0 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 ANNSQEPS(0.989)PQLAS(0.008)S(0.003)VASTR;ANNSQEPS(0.991)PQLAS(0.007)S(0.002)VASTR ; 166.21 2.36E-07 26365800 4756.2 4478.4 4614 4585.8 7394.5 8631.1 7121.8 7538.8 4986.5 4463.6 TRUE FALSE FALSE 4698.229605 4541.447033 4694.304735 5116.031773 7017.131072 8079.600566 7726.725514 7756.923284 4540.494951 4347.635029 1.080640296 1.04457872 1.079737536 1.176739018 1.614011072 1.858389794 1.777224966 1.784170758 1.044359732 1 12.08601512 -8.733813633 2.253067396 1.042622344 1.80592707 0.991370865 0.031961722 0.022325307 0.230966279 0.006062928 0.013220271 1.85E-09 8.733813633 0.763304725 ANPEDLEFIR ddPTM_HeLa_Romidepsin_16h_R1 1 ANPEDLEFIR 10 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 0 0 91.087 0.017369 2919600 1351.8 1385.1 1631.5 996.94 1113.4 1153.6 1208 1273 1375.8 1363 FALSE FALSE TRUE 1335.323742 1404.599474 1659.895573 1112.210894 1056.579043 1079.888683 1310.60749 1309.832247 1252.745002 1327.589064 1.005826109 1.058007717 1.250308261 0.837767442 0.795863021 0.813420894 0.987208712 0.986624764 0.943624075 1 10.37459293 ANPFGGASHAK ddPTM_HeLa_Romidepsin_16h_R1 1 ANPFGGASHAK 11 0 D6RD47;P62266;D6RDJ2;D6RIX0;D6R9I7 D6RD47 RPS23 40S ribosomal protein S23 0 0 84.479 0.02147 4348600 2399.6 2189.1 2592.8 2506.5 3259.8 3129.2 2281.3 1904.6 2699.8 2133.2 FALSE FALSE TRUE 2370.352752 2219.918207 2637.926596 2796.313323 3093.440242 2929.254219 2475.073565 1959.706596 2458.323126 2077.779156 1.140810728 1.068409123 1.269589498 1.345818354 1.488820519 1.40980056 1.191211086 0.943173672 1.183149383 1 11.02082661 -9.740609556 5.086532781 1.068033845 1.291698397 0.249194886 0.145124397 0.164834734 11.24819436 0.024189446 0.033642571 1.82E-10 9.740609556 0.223664552 ANPQVGVAFPHIK ddPTM_HeLa_Romidepsin_16h_R1 2 ANPQVGVAFPHIK 13 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 0 ; ; 125.28 0.0003971 2083800 1730.07 1512.58 1706.94 1632.81 1342.27 1756.24 1358.22 1326.52 1674.9 1632.15 FALSE FALSE TRUE 1708.983241 1533.874141 1736.648575 1821.603175 1273.768953 1644.021932 1473.587173 1364.900763 1525.092749 1589.746508 1.075003614 0.964854543 1.092405969 1.145845055 0.80124029 1.03414093 0.926932165 0.858565033 0.959330775 1 10.63458102 -8.764453612 24.99999994 1.042013375 0.915979177 0.418479689 0.077141061 58.16586662 482432.2994 0.010521044 0.019684404 1.72E-09 8.764453612 -0.126034199 ANQEQYAEGK(ac)MR ddPTM_HeLa_Romidepsin_16h_R1 1 ANQEQYAEGKMR 12 1 H0YMJ0;B3KTM8;Q9UBU8-2;H0YNE0;Q9UBU8 H0YMJ0 MORF4L1 Mortality factor 4-like protein 1 0 1 ANQEQYAEGK(1)MR 88.021 0.025954 1053700 191.82 271.89 203.24 0 164.63 172.5 172.64 219.56 148.04 178.05 FALSE TRUE FALSE 189.4820241 275.7176746 206.7773069 0 156.2283168 161.4778067 187.3040373 225.9126222 134.7989316 173.4242353 1.09259253 1.589845122 1.192320707 0 0.900844778 0.931114422 1.080033808 1.302658892 0.777278512 1 7.438161713 ANQISPS(ph)NSSLK ddPTM_HeLa_Romidepsin_16h_R1 2 ANQISPSNSSLK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 ANQIS(0.013)PS(0.845)NS(0.13)S(0.011)LK;ANQIS(0.423)PS(0.533)NS(0.029)S(0.015)LK ; 123.1 0.0064731 31658000 7816 6539.5 8885.3 5359 6513.6 6655.2 5486.5 5379.6 7802.1 8130.7 TRUE FALSE FALSE 7720.735586 6631.563253 9039.944919 5978.632795 6181.186686 6229.954199 5952.523173 5535.250238 7104.260635 7919.463242 0.974906424 0.837375344 1.141484548 0.754929042 0.780505761 0.786663693 0.751632149 0.698942601 0.897063402 1 12.95118694 -9.231982478 24.41363515 0.984597058 0.757601132 0.660710396 0.076898682 200.7569274 166385.7723 0.009923265 0.016453948 5.86E-10 9.231982478 -0.226995926 ANQISPS(ph)NSSLKNPQAGVPPFSSLK ddPTM_HeLa_Romidepsin_16h_R1 2 ANQISPSNSSLKNPQAGVPPFSSLK 25 1 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 ANQIS(0.018)PS(0.327)NS(0.327)S(0.327)LKNPQAGVPPFSSLK;ANQIS(0.038)PS(0.427)NS(0.107)S(0.427)LKNPQAGVPPFS(0.001)SLK ; 91.733 1.62E-05 28765000 4404.4 4110.7 3872.2 4027.8 3227.2 2712.55 2610.63 2717.9 4866.1 4492.5 TRUE FALSE FALSE 4350.717479 4168.570542 3939.594017 4493.513187 3062.503942 2539.226809 2832.376847 2796.538148 4430.863829 4375.784202 0.99427149 0.952645366 0.900317254 1.02690466 0.699875451 0.580290684 0.647284399 0.639094164 1.012587373 1 12.09532588 -8.678191513 4.431307585 0.987398192 0.627418833 0.948127939 0.039101461 0.031761224 1.147464014 0.005718872 0.011635303 2.10E-09 8.678191513 -0.359979359 ANS(ph)FVGTAQYVSPELLTEK ddPTM_HeLa_Romidepsin_16h_R1 2 ANSFVGTAQYVSPELLTEK 19 0 E9PER6;Q6A1A2;O15530-4;O15530-5;O15530;O15530-2 E9PER6 PDPK1;PDPK2P Putative 3-phosphoinositide-dependent protein kinase 2;3-phosphoinositide-dependent protein kinase 1 1 0 ANS(0.985)FVGT(0.015)AQYVSPELLTEK;ANS(0.938)FVGT(0.04)AQYVSPELLT(0.022)EK ; 193.47 2.22E-20 26622000 28388.8 29069.8 28437.2 27457 42649.1 55299.6 42682.3 51820.4 28655.6 25616.1 TRUE FALSE FALSE 28042.78639 29479.04541 28932.13754 30631.70753 40472.55728 51766.13403 46307.7335 53319.74151 26092.57137 24950.59003 1.123932795 1.181496925 1.159577289 1.227694716 1.622108224 2.074745887 1.855977492 2.137013251 1.045769713 1 14.60678631 -8.628871906 1.602496194 1.074823857 2.031747327 0.95538045 0.087968012 0.053852178 0.276098036 0.014132532 0.037068487 2.35E-09 8.628871906 0.95692347 ANSGGVDLDS(ph)SGEFASIEK ddPTM_HeLa_Romidepsin_16h_R1 1 ANSGGVDLDSSGEFASIEK 19 0 A0A087X055;Q92766;Q92766-2;Q92766-5;Q92766-3 A0A087X055 RREB1 Ras-responsive element-binding protein 1 1 0 ANSGGVDLDS(0.5)S(0.5)GEFASIEK 156.08 3.15E-06 3513600 2008 1490.4 2008.7 1211.2 1029.5 951.27 1053.1 894.47 3030.8 1755.6 TRUE FALSE FALSE 1983.525724 1511.38189 2043.660581 1351.244643 976.9607734 890.4869171 1142.550288 920.3500782 2759.717657 1709.989259 1.15996385 0.88385461 1.195130654 0.790206509 0.571325678 0.520755854 0.66816226 0.538219801 1.613880112 1 10.73977155 -9.014827096 3.385983044 1.067847555 0.579681351 0.663878718 0.194264288 0.062731928 1.505865796 0.014138029 0.025562662 9.66E-10 9.014827096 -0.488166204 ANSPS(ph)LFGTEGKPK ddPTM_HeLa_Romidepsin_16h_R1 1 ANSPSLFGTEGKPK 14 1 Q5JPT2;Q96B97-2;Q96B97;Q96B97-3 Q5JPT2 SH3KBP1 SH3 domain-containing kinase-binding protein 1 1 0 ANS(0.015)PS(0.985)LFGTEGKPK 71.558 0.01994 122760000 6082 6235.6 5911.1 6644.6 5253.6 4475.4 3562.6 3948.5 5661.5 6169.6 TRUE FALSE FALSE 6007.870245 6323.38494 6013.980216 7412.879916 4985.489188 4189.436384 3865.207155 4062.743618 5155.121261 6009.312903 0.99975993 1.052264218 1.00077668 1.233565307 0.829627159 0.697157304 0.643202845 0.676074567 0.857855356 1 12.55298433 -8.521913675 5.104795162 1.019842364 0.680415186 0.76629189 0.087621574 0.051908892 4.041499076 0.010380442 0.022223076 3.01E-09 8.521913675 -0.339427178 ANSTS(ph)DSVFTETPSPVLK ddPTM_HeLa_Romidepsin_16h_R1 1 ANSTSDSVFTETPSPVLK 18 0 C9JEZ4;Q9UKI2 C9JEZ4 CDC42EP3 Cdc42 effector protein 3 1 0 ANS(0.002)T(0.007)S(0.967)DS(0.024)VFTETPSPVLK 335.14 6.72E-211 32574000 7176.3 9801.5 5392.2 8963.2 12571 8040.6 5537.5 8765.9 6832.8 6473.5 TRUE FALSE FALSE 7088.832495 9939.485774 5486.048979 9999.567357 11929.45496 7526.83161 6007.855112 9019.527486 6221.657255 6305.317537 1.124262569 1.576365618 0.870067042 1.585894334 1.891967358 1.193727606 0.952823561 1.430463642 0.986731789 1 12.62235331 -10.46118288 7.073493861 1.054132404 1.347050529 0.208982016 0.287676294 0.331542826 31.99453226 0.049958974 0.056501447 3.46E-11 10.46118288 0.292918125 ANSTSDS(ph)VFTETPSPVLK ddPTM_HeLa_Romidepsin_16h_R1 2 ANSTSDSVFTETPSPVLK 18 0 C9JEZ4;Q9UKI2 C9JEZ4 CDC42EP3 Cdc42 effector protein 3 1 0 ANS(0.013)T(0.199)S(0.023)DS(0.751)VFT(0.014)ETPSPVLK;ANS(0.191)T(0.191)S(0.191)DS(0.328)VFT(0.093)ET(0.005)PSPVLK ; 156.67 6.09E-06 35818000 5130.78 7084.36 4083.29 6489.29 9410.93 6119.78 4730.47 6802.76 5330.67 5888.2 TRUE FALSE FALSE 5068.24408 7184.093806 4154.35795 7239.612243 8930.655125 5728.745809 5132.276004 6999.587128 4853.881524 5735.223715 0.883704687 1.252626604 0.724358483 1.262306861 1.557158983 0.998870505 0.894869365 1.220455814 0.846328193 1 12.48563405 -9.23307111 24.93962104 0.956596933 1.180660197 0.259451844 0.206312802 834.201528 733378.9739 0.030649702 0.050820687 5.85E-10 9.23307111 0.224063264 ANSTSDSVFTETPS(ph)PVLK ddPTM_HeLa_Romidepsin_16h_R1 4 ANSTSDSVFTETPSPVLK 18 0 C9JEZ4;Q9UKI2 C9JEZ4 CDC42EP3 Cdc42 effector protein 3 1 0 ANSTSDSVFTET(0.055)PS(0.945)PVLK;ANSTSDSVFTET(0.088)PS(0.912)PVLK;ANSTSDSVFTET(0.026)PS(0.974)PVLK;ANSTSDSVFTET(0.072)PS(0.928)PVLK ;;; 222.93 3.86E-38 45818400 19619.7 17866.3 20282.5 27274.2 31096.1 28403.4 24857.2 26743.1 20202.7 19407.6 TRUE FALSE FALSE 19380.56755 18117.82224 20635.5084 30427.77133 29509.14998 26588.51441 26968.56995 27516.8694 18395.71991 18903.38775 1.025243084 0.958443136 1.091630171 1.609646468 1.561050874 1.406547586 1.426652741 1.455658095 0.973144082 1 14.20635719 -9.363023185 5.006442752 1.009338463 1.486338736 0.939023511 0.061676807 0.039680604 1.561645817 0.009778596 0.015077296 4.33E-10 9.363023185 0.477000273 ANSWQLVET(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 2 ANSWQLVETPEK 12 0 Q9Y2H0-3;Q9Y2H0-1;Q9Y2H0;F8WF49;A0A0B4J2C2 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 0 ANSWQLVET(1)PEK;ANSWQLVET(1)PEK ; 169.4 0.00035923 53935000 6818.3 5920.7 6540.1 4764.3 6946.1 6760.7 5721.1 6130.8 6792 7325.5 TRUE FALSE FALSE 6735.195937 6004.05177 6653.927697 5315.170783 6591.614598 6328.713089 6207.050091 6308.185025 6184.506509 7135.182454 0.943941655 0.841471372 0.932551864 0.744924298 0.923818647 0.886972846 0.869921706 0.884095826 0.86676221 1 12.80073461 -10.62106128 1.182808929 0.984719386 0.867851917 0.06870549 0.062801633 0.235908639 0.676027965 0.010732811 0.010774473 2.39E-11 10.62106128 -0.116867469 ANSWQLVET(ph)PEKR ddPTM_HeLa_Romidepsin_16h_R1 4 ANSWQLVETPEKR 13 1 Q9Y2H0-3;Q9Y2H0-1;Q9Y2H0;F8WF49;A0A0B4J2C2 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 1 0 ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR;ANSWQLVET(1)PEKR ;;; 127.88 0.0012642 113901000 9885.2 8948.3 9413.7 8808.9 10292.8 10428.2 8612.9 9376.2 10724.5 9568 TRUE FALSE FALSE 9764.71538 9074.274402 9577.5415 9827.426465 9767.520008 9761.871675 9344.479511 9647.485554 9765.27386 9319.421981 1.047781225 0.97369498 1.027696945 1.0545103 1.04808217 1.047476088 1.002688743 1.035202137 1.047841152 1 13.18602476 -12.56559402 1.276200615 0.999617414 1.031280833 0 0.027706999 0.645264683 1.845872608 0.01811902 0.004042877 2.72E-13 12.56559402 0.031663418 ANT(ph)MS(ph)NY(ph)TLLPPSLLDHRRGAFLRK ddPTM_HeLa_Romidepsin_16h_R1 1 ANTMSNYTLLPPSLLDHRRGAFLRK 25 3 O00204-2;O00204 O00204-2 SULT2B1 Sulfotransferase family cytosolic 2B member 1 3 0 ANT(0.961)MS(0.961)NY(0.958)T(0.108)LLPPS(0.011)LLDHRRGAFLRK 46.982 0.0037841 0 793.79 861.52 721.99 1129.6 855.39 923.46 794.43 997.91 934.79 1071.4 TRUE FALSE FALSE 784.1149822 873.6485012 734.5559331 1260.209667 811.7362564 864.4538863 861.9088644 1026.782951 851.1800412 1043.564874 0.751381157 0.837176991 0.70389101 1.207600695 0.777849348 0.828366217 0.82592744 0.983918659 0.815646504 1 10.02730457 -12.61395941 1.447220183 0.999338187 0.848079899 0 0.146660724 0.636531287 2.410200888 0.091549937 0.021433232 2.43E-13 12.61395941 -0.151258289 ANTPDS(ph)DIT(ph)EKTEDSSVPETPDNER ddPTM_HeLa_Romidepsin_16h_R1 2 ANTPDSDITEKTEDSSVPETPDNER 25 1 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 2 0 ANT(0.2)PDS(0.847)DIT(0.625)EKT(0.285)EDS(0.019)S(0.021)VPET(0.002)PDNER;ANT(0.202)PDS(0.791)DIT(0.807)EKT(0.176)EDS(0.012)S(0.012)VPETPDNER ; 62.677 0.0033968 14885300 1819.29 1930.67 1638.12 1340.63 1452.25 1450.04 1263.04 1384.23 2022.41 2112.15 TRUE FALSE FALSE 1797.115794 1957.850023 1666.630791 1495.639948 1378.136263 1357.387124 1370.322586 1424.280511 1841.520584 2057.276039 0.873541401 0.951671038 0.810115298 0.72700013 0.669883981 0.659798247 0.666085912 0.692313761 0.895125666 1 11.00651967 ANTPDS(ph)DITEKTEDSSVPETPDNER ddPTM_HeLa_Romidepsin_16h_R1 2 ANTPDSDITEKTEDSSVPETPDNER 25 1 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 0 ANT(0.044)PDS(0.506)DIT(0.192)EKT(0.224)EDS(0.016)S(0.016)VPET(0.001)PDNER;ANT(0.014)PDS(0.876)DIT(0.085)EKT(0.021)EDS(0.001)S(0.001)VPET(0.001)PDNER ; 44.625 0.024909 9335600 3154.6 2738.8 2670 2485.7 2963.71 2996.8 2108.5 2154.23 3529 3171.9 TRUE FALSE FALSE 3116.150522 2777.356898 2716.47023 2773.10833 2812.46082 2805.314152 2287.595937 2216.559246 3213.357401 3089.493581 1.008628256 0.898968334 0.879260681 0.897593168 0.910330689 0.908017472 0.740443661 0.717450672 1.04009195 1 11.59315466 -5.605528058 0.277914837 1.015075455 1.59E-16 0.823671805 0.042162481 6.081805373 0.16923214 0.021123137 2.520288562 2.48E-06 5.605528058 -1.015075455 ANTTAFLT(ph)PLEIK ddPTM_HeLa_Romidepsin_16h_R1 1 ANTTAFLTPLEIK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 0 ANTTAFLT(1)PLEIK 168.45 0.00024923 7315800 2745.3 2321.1 2425.7 2550 2462.4 2524.2 1567.5 2325 2747.7 2439 TRUE FALSE FALSE 2711.839228 2353.776507 2467.918291 2844.842998 2336.73454 2362.911766 1700.643411 2392.270207 2501.93883 2375.634428 1.141522111 0.990799122 1.038845986 1.197508743 0.983625474 0.99464452 0.715869155 1.007002668 1.053166599 1 11.21409713 -8.111259299 2.632719834 1.066489802 0.862597131 0.394162875 0.093085002 0.193212455 2.577029851 0.013216632 0.041685253 7.74E-09 8.111259299 -0.203892671 ANVGK(ac)LLK ddPTM_HeLa_Romidepsin_16h_R1 1 ANVGKLLK 8 1 A0A087WVB9;K7ERF1;Q9UBQ5;K7ES31;K7EQM4;Q9UBQ5-2 A0A087WVB9 EIF3K Eukaryotic translation initiation factor 3 subunit K 0 1 ANVGK(1)LLK 107.9 0.015832 723470 643.44 557.89 655.74 792.63 821.2 598.98 498.51 510.85 696.7 560.67 FALSE TRUE FALSE 635.5975058 565.7439901 667.1528796 884.27761 779.2910997 560.7071111 540.853427 525.6306388 634.3854071 546.1037126 1.163876918 1.035964373 1.221659667 1.619248486 1.427002018 1.026741072 0.990385918 0.962510649 1.161657378 1 9.093031154 -5.711737296 20.14368946 1.126895666 1.162868843 0 0.205934608 0 0 0.029678584 0 1.94E-06 5.711737296 0.035973178 ANVVTT(ph)PSTNRK ddPTM_HeLa_Romidepsin_16h_R1 1 ANVVTTPSTNRK 12 1 H0Y785;H0Y472;H0Y4P6;Q8IWZ3;Q8IWZ3-4;Q8IWZ3-6;E9PDP5 H0Y785 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 0 ANVVT(0.17)T(0.83)PSTNRK 102.52 0.0059365 33027000 2400 2293.1 1860.1 3027 2391 2773 1986.8 2626.4 2370.1 2369.6 TRUE FALSE FALSE 2370.747877 2325.382322 1892.47426 3376.995982 2268.978348 2595.814249 2155.558742 2702.39074 2158.11232 2308.03745 1.027170454 1.007514987 0.819949546 1.463146095 0.98307692 1.124684632 0.933935774 1.170860871 0.935042159 1 11.17245092 ANVVTTPS(ph)TNR ddPTM_HeLa_Romidepsin_16h_R1 2 ANVVTTPSTNR 11 0 H0Y785;H0Y472;H0Y4P6;Q8IWZ3;Q8IWZ3-4;Q8IWZ3-6;E9PDP5 H0Y785 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 0 ANVVT(0.252)T(0.252)PS(0.489)T(0.007)NR;ANVVT(0.171)T(0.171)PS(0.638)T(0.021)NR ; 101.35 0.018553 12341600 7151.1 7537 7897.7 5373.1 7934.6 8079.2 6510.4 6969 7178.5 7529 TRUE FALSE FALSE 7063.939643 7643.106084 8035.156156 5994.363103 7529.667754 7562.965194 7063.393213 7170.63702 6536.436981 7333.395495 0.963256332 1.042232904 1.095693824 0.817406222 1.026764172 1.031304694 0.963181819 0.977805851 0.89132476 1 12.84026563 APAGPSLEETSVS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 APAGPSLEETSVSSPK 16 0 A0A087WXZ7;K7EIX2;Q6AI08 A0A087WXZ7 HEATR6 HEAT repeat-containing protein 6 1 0 APAGPSLEETS(0.002)VS(0.499)S(0.499)PK;APAGPSLEETSVS(0.988)S(0.012)PK ; 165.64 2.12E-05 69941000 5862.5 5194.5 6557.6 4602.5 6593.9 6579 6450.2 6558.2 5995.2 5393.8 TRUE FALSE FALSE 5791.045595 5267.628307 6671.732277 5134.662705 6257.388678 6158.623133 6998.079827 6747.95117 5458.974297 5253.668298 1.102286111 1.002657193 1.269918826 0.977348095 1.191051342 1.172251993 1.332036861 1.284426573 1.039078599 1 12.3591094 -4 0.21700279 1.011051642 2.689126226 0.551720599 0.08327726 24.79748791 0.295006521 0.059356233 14.64432104 1.00E-04 4 1.678074584 APAGPSLEETSVSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 APAGPSLEETSVSSPK 16 0 A0A087WXZ7;K7EIX2;Q6AI08 A0A087WXZ7 HEATR6 HEAT repeat-containing protein 6 1 0 APAGPSLEETSVS(0.17)S(0.83)PK 139.86 0.0007855 3627500 660.13 692.49 750.15 559.28 860.36 992.86 701.94 800.82 734.54 944.29 TRUE FALSE FALSE 652.0840816 702.2388924 763.2060461 623.9465851 816.4526188 929.4194503 761.5627661 823.9904632 668.8409027 919.7572097 0.708974145 0.763504635 0.829790773 0.678381837 0.88768276 1.010505208 0.828004128 0.895878232 0.727192889 1 9.84510927 -7.241384049 20.46130886 0.848750135 0.895878784 0 0.110432095 1971.463924 2010961.886 0.018129121 0.663901839 5.74E-08 7.241384049 0.04712865 LGFSLT(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 LGFSLTPSK 9 0 P38432 P38432 COIL Coilin 1 0 LGFS(0.004)LT(0.993)PS(0.003)K;LGFS(0.001)LT(0.999)PSK ; 144.55 0.012381 249470000 26711.2 25001.4 28583.6 13642.5 12717.5 11265.3 9714.6 8292.5 27684.9 24602.3 TRUE FALSE FALSE 26385.63362 25353.37037 29081.08557 15219.91004 12068.47852 10545.48369 10539.75788 8532.430404 25208.69321 23963.1287 1.101093015 1.058015866 1.213576321 0.635138685 0.503626996 0.440071237 0.439832295 0.356064958 1.051978376 1 14.54852866 -9.068366414 3.379549729 1.060764766 0.441000283 0.95418437 0.067657034 0.040480894 0.90510596 0.01139586 0.020117854 8.54E-10 9.068366414 -0.619764484 down DSPAFPDS(ph)PWR ddPTM_HeLa_Romidepsin_16h_R1 2 DSPAFPDSPWR 11 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 DSPAFPDS(1)PWR;DSPAFPDS(1)PWR ; 201.09 4.62E-13 32947000 8100.5 7097.6 8256.5 3985.7 4844.5 3807.8 3129.5 2637.42 8078.7 8939.6 TRUE FALSE FALSE 8001.76799 7197.520199 8400.200919 4446.545387 4597.267088 3564.493869 3395.319652 2713.729587 7356.120839 8707.347903 0.9189673 0.826603034 0.964725541 0.510665869 0.527975583 0.409366194 0.389937291 0.311659717 0.844817609 1 13.08801765 -9.06586046 0.991493424 0.964472766 0.351067609 0.894870539 0.081586783 0.090824383 0.175456055 0.012189293 0.029861303 8.59E-10 9.06586046 -0.613405157 down APAPLGTVADS(ph)LRASDGQLQAK ddPTM_HeLa_Romidepsin_16h_R1 1 APAPLGTVADSLRASDGQLQAK 22 1 Q9BRG2;Q9BRG2-2 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 0 APAPLGT(0.13)VADS(0.847)LRAS(0.024)DGQLQAK 61.684 0.0043523 13167000 1016.1 950.84 1032.1 1207.7 836.06 748.04 854.39 702.25 904.37 808.1 TRUE FALSE FALSE 1003.715382 964.2259505 1050.063268 1347.339956 793.3927384 700.2426582 926.9618653 722.5684958 823.4808822 787.1054455 1.275198117 1.225027671 1.334082077 1.711765513 1.007987866 0.889642756 1.177684477 0.918007238 1.046214185 1 9.620413111 -8.584264938 24.99999999 1.200900916 1.002576117 0.267783384 0.199919989 97.9448832 39888.12148 0.03233343 0.064666864 2.60E-09 8.584264938 -0.198324799 APAPVVLGS(ph)PVVLGPPVGQAR ddPTM_HeLa_Romidepsin_16h_R1 1 APAPVVLGSPVVLGPPVGQAR 21 0 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 0 APAPVVLGS(1)PVVLGPPVGQAR 84.653 0.0021049 6761700 693.96 657.48 741.28 668.5 750.98 682.9 549.88 585.53 730.05 853.05 TRUE FALSE FALSE 685.5017486 666.7360207 754.1816674 745.7951154 712.6546883 639.264894 596.5867935 602.4713867 664.7524996 830.887638 0.825023405 0.802438248 0.907681897 0.897588412 0.857702842 0.769375863 0.718011397 0.725093694 0.800051017 1 9.698509583 -16.52287875 0.029530304 2.176247826 1.27E-10 0.209045525 0.073967849 556.1027576 1.319001299 73.36603263 31.89799957 3.00E-17 16.52287875 -2.176247826 APAQK(ac)APAPK ddPTM_HeLa_Romidepsin_16h_R1 1 APAQKAPAPK 10 1 P50914 P50914 RPL14 60S ribosomal protein L14 0 1 APAQK(1)APAPK 117.81 0.015425 3285500 1489.4 1868.1 4607.7 2269.5 4019.9 7016.5 4915 3282.3 1873.4 940.64 FALSE TRUE FALSE 1471.24662 1894.399161 4687.895086 2531.910268 3814.749503 6568.168295 5332.479977 3377.268172 1705.838412 916.2020372 1.605810247 2.067665301 5.11666084 2.763484652 4.163655338 7.168908197 5.820200961 3.68616095 1.861858349 1 9.839521961 -9.597620739 0.729094912 1.12163404 5.462003334 0.629806895 1.171011051 0.259064371 0.27720429 0.251225461 0.474709439 2.53E-10 9.597620739 4.340369294 APDVDVNIAGPDAALKVDVKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 APDVDVNIAGPDAALKVDVKSPK 23 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 APDVDVNIAGPDAALKVDVKS(1)PK 76.237 0.00069361 15748000 1082.5 912.56 968.67 1652.7 1045 1019.8 845.21 1136.7 1257.3 1177.4 TRUE FALSE FALSE 1069.306074 925.4070436 985.529295 1843.79295 991.6697506 954.6380713 917.0021163 1169.588621 1144.843939 1146.810978 0.932417019 0.806939471 0.859365069 1.607756627 0.864719443 0.832428438 0.799610514 1.019861724 0.998284775 1 10.16341191 APEAAVSEDGKS(ph)DDELLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 APEAAVSEDGKSDDELLSSK 20 1 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 APEAAVS(0.001)EDGKS(0.555)DDELLS(0.35)S(0.094)K 67.827 0.0038199 39354000 2297.2 1890.4 1953.7 1953.4 1961.2 1736.2 1375.4 1679.4 2236.7 2052.8 TRUE FALSE FALSE 2269.200843 1917.013101 1987.703329 2179.261299 1861.112646 1625.262423 1492.226442 1727.990789 2036.64395 1999.46796 1.134902328 0.9587616 0.994116119 1.08992059 0.930803935 0.812847445 0.746311755 0.864225296 1.018592941 1 10.96540045 -8.474815091 2.695233891 1.052312668 0.800326499 0.753292587 0.056798564 0.106344827 1.522589855 0.009920562 0.023935081 3.35E-09 8.474815091 -0.251986169 APEAAVSEDGKSDDELLS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 APEAAVSEDGKSDDELLSSK 20 1 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 APEAAVS(0.01)EDGKS(0.4)DDELLS(0.502)S(0.088)K 53.278 0.017989 26795000 1802.4 1230.8 1787.7 1643.7 1610.7 1504.5 1243 1236.8 1782.8 1714.8 TRUE FALSE FALSE 1780.431656 1248.127235 1818.814169 1833.752328 1528.499969 1408.367306 1348.580389 1272.584857 1623.341903 1670.249249 1.065967643 0.747270047 1.088947754 1.097891425 0.915132858 0.843207866 0.80741266 0.761913144 0.97191596 1 10.70584769 -8.35663854 2.344601475 1.016950642 0.794679438 0.427362003 0.096618862 0.192326124 2.044402342 0.014059302 0.038140354 4.40E-09 8.35663854 -0.222271205 APELPNTSSS(ph)PSLK ddPTM_HeLa_Romidepsin_16h_R1 1 APELPNTSSSPSLK 14 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 0 APELPNTSS(0.024)S(0.976)PS(0.001)LK 191.19 4.32E-11 15954000 3192.6 3635.5 2947.4 3429 2465 1989.1 1747.4 1361.6 3256.7 2998.6 TRUE FALSE FALSE 3153.687363 3686.680664 2998.698261 3825.477114 2339.201852 1862.00293 1895.824112 1400.995748 2965.412595 2920.69594 1.079772571 1.26226103 1.026706758 1.309782734 0.80090564 0.637520292 0.649100129 0.47967874 1.015310274 1 11.51209646 -8.526214153 4.377876576 1.073766192 0.606798018 0.817965265 0.111449849 0.068207403 3.220806577 0.016603027 0.035931351 2.98E-09 8.526214153 -0.466968174 APEPLS(ph)SLKSMAER ddPTM_HeLa_Romidepsin_16h_R1 1 APEPLSSLKSMAER 14 1 H7C3F5;A0A2H2FJL5;B7Z6J7;O75175;A0A2R8Y691;A0A2R8Y4W0;H0Y5X7 H7C3F5 CNOT3 CCR4-NOT transcription complex subunit 3 1 0 APEPLS(0.5)S(0.5)LKSMAER 66.393 0.024286 12272000 1667.2 1803.3 1820.2 2187.9 1933.7 1658.4 1784.5 1710.4 1955.6 1765.2 TRUE FALSE FALSE 1646.879525 1828.686905 1851.879817 2440.875292 1835.016073 1552.433592 1936.075385 1759.887725 1780.686238 1719.33985 0.957855729 1.063598279 1.077087708 1.419658419 1.067279441 0.90292422 1.126057414 1.023583398 1.035680199 1 10.74763902 -10.05308686 3.164858474 0.980265458 1.106441342 0.119843165 0.123808165 0.337758811 6.740879929 0.021214559 0.026942895 8.85E-11 10.05308686 0.126175884 APEPPKTDK(ac)PGAAPPSTEER ddPTM_HeLa_Romidepsin_16h_R1 2 APEPPKTDKPGAAPPSTEER 20 2 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 0 1 ; APEPPKTDK(1)PGAAPPSTEER;APEPPKTDK(1)PGAAPPSTEER 106.7 0.0026609 5573100 1860.83 2182.3 1943 1958.66 1850.48 1975.67 1828.11 2171.34 2033.98 2147.22 FALSE TRUE FALSE 1838.149488 2213.022477 1976.8171 2185.129485 1756.043101 1849.431063 1983.389618 2234.164297 1852.055735 2091.434915 0.878893947 1.058135953 0.945196566 1.04479918 0.839635548 0.884288127 0.948339154 1.068244716 0.885543089 1 11.03027739 -7.2625482 7.414651673 0.945839507 1.069621992 0.225051087 0.069658942 0.124226078 63.7526331 0.00984038 0.077698299 5.46E-08 7.2625482 0.123782485 APES(ph)DTGDEDQDQERDTVFLK ddPTM_HeLa_Romidepsin_16h_R1 2 APESDTGDEDQDQERDTVFLK 21 1 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 APES(0.945)DT(0.054)GDEDQDQERDTVFLK;APES(0.761)DT(0.239)GDEDQDQERDTVFLK ; 74.308 0.0018363 85604000 2903.49 2839.04 2102.39 2564.13 2852.4 2275.9 2234.61 2105.53 3665.5 2689.2 TRUE FALSE FALSE 2868.101147 2879.00808 2138.981216 2860.606775 2706.831384 2130.477335 2424.417718 2166.450189 3337.6485 2619.334196 1.094973353 1.099137362 0.816612565 1.092112178 1.033404362 0.813365984 0.925585487 0.82709957 1.274235454 1 11.35498443 -8.272386902 24.10530857 1.03540735 0.862373863 0.399334057 0.111639839 277.2813114 610545.1714 0.011833162 0.026722291 5.34E-09 8.272386902 -0.173033487 APGAPPRS(ph)PPQR ddPTM_HeLa_Romidepsin_16h_R1 1 APGAPPRSPPQR 12 1 H3BN50;Q15599-3 H3BN50 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 0 APGAPPRS(1)PPQR 67.214 0.028781 14072000 1725.6 1695.1 1535.1 1363.6 1154.2 1006.5 992.56 1229.4 1637.4 1452.4 TRUE FALSE FALSE 1704.567723 1718.963662 1561.817772 1521.265848 1095.296867 942.1878983 1076.868022 1264.970749 1490.946843 1414.666439 1.204925541 1.215101748 1.104018395 1.075353035 0.774243905 0.666014173 0.761216915 0.894183049 1.053921124 1 10.46624621 -8.777835697 4.875197606 1.109410238 0.762806424 0.812929603 0.078819429 0.072512012 4.436770221 0.014712146 0.028240373 1.67E-09 8.777835697 -0.346603814 APGASPGNPLS(ph)PSLSDKDR ddPTM_HeLa_Romidepsin_16h_R1 1 APGASPGNPLSPSLSDKDR 19 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 0 APGASPGNPLS(0.992)PS(0.003)LS(0.005)DKDR 94.671 0.00099065 9921300 1587.7 1715.4 1301 1162.8 1093.9 1038.9 817.87 747.49 1447.8 1379.2 TRUE FALSE FALSE 1568.348502 1739.549446 1323.643359 1297.248407 1038.074201 972.5176429 887.3398574 769.1174438 1318.305142 1343.368185 1.167474799 1.294916364 0.985316888 0.96566855 0.772739903 0.723939761 0.660533625 0.572529149 0.981343132 1 10.39163905 -8.713980617 1.284460144 1.096192845 0.630769187 0.821247221 0.091261739 0.145816078 0.475999888 0.016084835 0.044504204 1.93E-09 8.713980617 -0.465423658 APGYPS(ph)SPVTTASGTTLR ddPTM_HeLa_Romidepsin_16h_R1 2 APGYPSSPVTTASGTTLR 18 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 0 APGYPS(0.635)S(0.359)PVT(0.004)T(0.001)ASGTTLR;APGY(0.001)PS(0.599)S(0.4)PVTTASGTTLR ; 241.66 2.73E-50 94732000 2624.8 2526.01 2424.54 2469.29 2195.8 2525.9 2143.44 1846.15 2637.5 2693 TRUE FALSE FALSE 2592.807928 2561.571235 2466.738102 2754.800928 2083.740132 2364.503142 2325.50374 1899.565438 2401.595394 2623.035472 0.988476121 0.976567516 0.940413551 1.050233959 0.794400287 0.90143773 0.886569688 0.724185951 0.915578695 1 11.3570216 -5.653961571 0.371245771 0.999958857 3.68E-10 0.552229296 0.062492781 7.292251075 0.275807549 0.014450018 4.220081893 2.22E-06 5.653961571 -0.999958856 APGYPSS(ph)PVTTASGTTLR ddPTM_HeLa_Romidepsin_16h_R1 2 APGYPSSPVTTASGTTLR 18 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 0 APGYPS(0.316)S(0.682)PVT(0.002)TASGTTLR;APGYPS(0.14)S(0.849)PVT(0.01)T(0.001)ASGTTLR ; 230.96 1.29E-39 129935000 4599.3 4426.9 4621.1 4805 4029.1 3786.9 2824.9 3410.8 4506.9 4060.1 TRUE FALSE FALSE 4543.241963 4489.222014 4701.528307 5360.576708 3823.479992 3544.929312 3064.846935 3509.486117 4103.791576 3954.618017 1.148844703 1.135184737 1.188870401 1.355523261 0.966839269 0.896402458 0.775004545 0.887439976 1.037721357 1 11.94932263 -8.440406954 3.797990088 1.106545914 0.847805096 0.619961723 0.100106668 0.147085575 3.96580392 0.016553902 0.038314258 3.63E-09 8.440406954 -0.258740818 APIDTS(ph)DVEEK ddPTM_HeLa_Romidepsin_16h_R1 2 APIDTSDVEEK 11 0 D6RIY6;Q06265-3;Q06265-4;Q06265;Q06265-2 D6RIY6 EXOSC9 Exosome complex component RRP45 1 0 APIDT(0.226)S(0.774)DVEEK;APIDT(0.066)S(0.934)DVEEK ; 177.1 1.41E-05 230240000 23459.1 23958.1 23642.6 10046 19908.3 20288.7 16273.4 19081.3 21070.3 22654 TRUE FALSE FALSE 23173.17147 24295.38276 24054.08954 11207.56579 18892.30516 18992.31755 17655.66219 19633.38731 19185.7196 22065.44581 1.050201825 1.101060136 1.090124792 0.507923832 0.856194129 0.860726663 0.800149806 0.88977977 0.869491591 1 14.42950128 -9.323251128 24.99999162 1.03586933 0.792297468 0.511048791 0.116432603 119.2745833 48240.72692 0.01540678 0.023534249 4.75E-10 9.323251128 -0.243571861 APILIATDVAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 APILIATDVASR 12 0 P17844;J3KTA4;P17844-2;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 1 0 APILIAT(0.001)DVAS(0.999)R 115.37 0.0089601 3225500 627.89 547.1 787.69 633.54 561.27 467.71 598.54 865.34 717.28 668.11 TRUE FALSE FALSE 620.2370352 554.8020882 801.399414 706.7928757 532.6262975 437.8248405 649.3799727 890.3772476 653.1246803 650.7524059 0.953107556 0.852554801 1.23149666 1.086116424 0.818477646 0.672797882 0.997891006 1.368227362 1.003645433 1 9.34596493 -14.46083179 0.002962068 1.70E-07 1.939941385 0.00120954 0.189764526 1295337.456 464.3789656 156362.3602 147876.4493 3.46E-15 14.46083179 1.939941216 APILIATDVASR ddPTM_HeLa_Romidepsin_16h_R1 1 APILIATDVASR 12 0 P17844;J3KTA4;P17844-2;A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 P17844;A0A1X7SBZ2 DDX5;DDX17 Probable ATP-dependent RNA helicase DDX5;Probable ATP-dependent RNA helicase DDX17 0 0 144.77 6.71E-18 0 318.7 249.8 243.66 253.46 281.76 353.09 112.85 162.62 223.19 248.6 FALSE FALSE TRUE 314.8155618 253.316691 247.9008001 282.7662378 267.3807358 330.5286885 122.4354762 167.3251531 203.2273274 242.1413362 1.300131431 1.046152198 1.023785546 1.167773509 1.104234164 1.365023807 0.505636411 0.691022672 0.83929217 1 7.919705574 -7.752814425 24.99981613 1.14045034 0.598329334 0.638244285 0.15102953 72.64234554 210552.1806 0.018960069 0.068748764 1.77E-08 7.752814425 -0.542121006 APIQDIWYHEDR ddPTM_HeLa_Romidepsin_16h_R1 1 APIQDIWYHEDR 12 0 J3QLR8;Q9Y3D9 J3QLR8 MRPS23 "28S ribosomal protein S23, mitochondrial" 0 0 92.906 0.011483 6936400 2342.2 2521 2506.7 2562.7 2544.4 2669.6 2478 2149.3 2453.4 2485 FALSE FALSE TRUE 2313.652365 2556.490704 2550.328062 2859.011432 2414.549774 2499.021176 2688.481258 2211.486604 2233.961759 2420.439342 0.95588116 1.056209367 1.053663283 1.181195241 0.997566736 1.032465938 1.110741018 0.913671566 0.922957135 1 11.24105322 -10.25070911 23.68804861 0.979166104 1.054314301 0.249542126 0.068483916 385.3518282 850699.3642 0.010488551 0.012768457 5.61E-11 10.25070911 0.075148197 APITYVPPEDRMDLLT(ph)TVQAHYT(ph)CPK ddPTM_HeLa_Romidepsin_16h_R1 1 APITYVPPEDRMDLLTTVQAHYTCPK 26 1 F6S232;Q8IYX7 F6S232 SAXO1;FAM154A Protein FAM154A 2 0 APIT(0.01)Y(0.008)VPPEDRMDLLT(0.492)T(0.492)VQAHY(0.484)T(0.514)CPK 43.497 0.022646 2519800 476.21 301.89 203.56 463.61 331.34 361.27 451.07 266.76 403.69 363.04 TRUE FALSE FALSE 470.4057694 306.1400153 207.1028764 517.2147696 314.4304834 338.1860129 489.3838745 274.4782797 367.5829553 353.6081685 1.330302327 0.865760587 0.58568465 1.462677663 0.889205939 0.956386314 1.383972199 0.776221547 1.039520543 1 8.466007792 -10.25251646 24.86331342 1.1559761 1.001448219 0.047011418 0.261527004 1325.066497 3692241.422 0.043870427 0.053290256 5.59E-11 10.25251646 -0.154527881 APKPEDIDEEDDDVPDLVENFDEASKNEAN ddPTM_HeLa_Romidepsin_16h_R1 1 APKPEDIDEEDDDVPDLVENFDEASKNEAN 30 2 Q96K17-2;Q96K17 Q96K17-2 BTF3L4 Transcription factor BTF3 homolog 4 0 0 86.084 1.38E-07 4499500 1188.9 882.05 969.33 1106.2 1016.8 1252.9 921.44 969.51 1132.4 1044.4 FALSE FALSE TRUE 1174.40923 894.4675231 986.200782 1234.104049 964.9089018 1172.843734 999.7070906 997.5612422 1031.115308 1017.266337 1.154475663 0.879285483 0.969461729 1.213157266 0.948531241 1.152936739 0.982738791 0.980629365 1.013613908 1 9.990481735 -7.589813584 24.99959573 1.058910287 0.981145874 0.031745979 0.099868887 92.31418901 34477.38436 0.014008119 0.052413086 2.57E-08 7.589813584 -0.077764413 APKPPTDGSTSPT(ph)STPSEDQEALGK ddPTM_HeLa_Romidepsin_16h_R1 1 APKPPTDGSTSPTSTPSEDQEALGK 25 1 Q8NHM5-2;Q8NHM5-3;Q8NHM5;Q8NHM5-4;S4R3G4;F8WBN2;F6SRV7;Q8NHM5-5 Q8NHM5-2 KDM2B Lysine-specific demethylase 2B 1 0 APKPPTDGS(0.002)T(0.023)S(0.159)PT(0.759)S(0.053)T(0.004)PSEDQEALGK 101.16 6.32E-06 8570600 2203.9 2070.6 2055.3 1770.3 1549.4 1354 955.01 1349.1 2006.6 2164.8 TRUE FALSE FALSE 2177.038019 2099.749961 2091.071634 1974.990416 1470.328336 1267.48377 1036.128526 1388.13408 1827.12467 2108.558184 1.032477091 0.995822632 0.991706869 0.936654454 0.697314567 0.601113965 0.491391954 0.658333306 0.866527983 1 11.04204112 -8.701130561 1.882692631 1.013170914 0.570369149 0.893316163 0.061131209 0.040790432 0.293082337 0.005680253 0.013289807 1.99E-09 8.701130561 -0.442801765 APLATGEDDDDEVPDLVENFDEAS(ph)KNEAN ddPTM_HeLa_Romidepsin_16h_R1 1 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2 BTF3 Transcription factor BTF3 1 0 APLATGEDDDDEVPDLVENFDEAS(1)KNEAN 54.259 0.0026482 1056000 221.88 198.67 435.14 249.19 233.2 181.31 189.5 127.03 260.01 242.67 TRUE FALSE FALSE 219.1756412 201.4668815 442.7134292 278.0025203 221.2989338 169.7248762 205.5961253 130.7054126 236.7540544 236.3653984 0.927274646 0.852353529 1.873004391 1.176155741 0.93625774 0.718061431 0.869823276 0.552980316 1.001644301 1 7.884875044 -8.392119964 3.667028783 1.044488064 0.728684833 0.275844758 0.284755629 0.324270664 7.797805692 0.043380408 0.102593748 4.05E-09 8.392119964 -0.315803231 APLATGEDDDDEVPDLVENFDEASK ddPTM_HeLa_Romidepsin_16h_R1 2 APLATGEDDDDEVPDLVENFDEASK 25 0 P20290-2;P20290 P20290-2 BTF3 Transcription factor BTF3 0 0 ; ; 146.06 9.68E-08 26492000 4374.8 3970.1 4172.2 2520.3 3957.8 3751.5 3120.3 3243.7 4613.1 4946.9 FALSE FALSE TRUE 4321.478255 4025.991172 4244.815391 2811.708944 3755.818697 3511.791257 3385.338204 3337.551342 4200.492782 4818.378825 0.89687391 0.835548909 0.8809634 0.583538374 0.77947767 0.728832536 0.702588636 0.692671013 0.871764744 1 12.23433211 -10.03054605 0.590481018 0.981129787 0.691287723 0.62098771 0.071696705 0.245528521 0.185837109 0.018246187 0.025967611 9.32E-11 10.03054605 -0.289842063 APLATGEDDDDEVPDLVENFDEASKNEAN ddPTM_HeLa_Romidepsin_16h_R1 3 APLATGEDDDDEVPDLVENFDEASKNEAN 29 1 P20290-2;P20290 P20290-2 BTF3 Transcription factor BTF3 0 0 ;; ;; 107.58 7.50E-09 392003000 8134.2 7908.81 7127.3 5471.17 7575.55 7790.56 6339.47 7379.22 7837.7 6930.96 FALSE FALSE TRUE 8035.057242 8020.150435 7251.347667 6103.772418 7188.941415 7292.768359 6877.944424 7592.726088 7136.676482 6750.89266 1.190221449 1.188013325 1.074131679 0.904143011 1.064887531 1.080267266 1.018819995 1.124699572 1.057145602 1 12.72086256 -9.516927784 24.95494286 1.101194549 1.036035082 0.160798935 0.074823896 489.8705352 2054241.556 0.014596378 0.021036103 3.04E-10 9.516927784 -0.065159467 APLKPYPVS(ph)PSDKVLIQEK ddPTM_HeLa_Romidepsin_16h_R1 1 APLKPYPVSPSDKVLIQEK 19 2 J3KR24;A0A0A0MSX9;P41252;Q5TCC6 J3KR24 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 0 APLKPY(0.001)PVS(0.991)PS(0.007)DKVLIQEK 82.267 0.0069974 10894000 2203.3 1911.1 1798.2 3096.4 2262.6 2059.4 1869.1 2214.2 2015.2 2215.1 TRUE FALSE FALSE 2176.445332 1938.004516 1829.496917 3454.420337 2147.131079 1927.810986 2027.861307 2278.264384 1834.955465 2157.551383 1.008757126 0.898242578 0.847950566 1.601083694 0.99517031 0.893517995 0.939890157 1.055949074 0.85048054 1 11.0751792 APLKPYPVSPS(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 1 APLKPYPVSPSDK 13 1 J3KR24;A0A0A0MSX9;P41252;Q5TCC6 J3KR24 IARS "Isoleucine--tRNA ligase, cytoplasmic" 1 0 APLKPYPVS(0.047)PS(0.953)DK 154.13 0.0050823 34093000 3471.9 2902.9 3007.3 2616.9 2516 3085.2 2918.1 2634.6 3238.9 3271.7 TRUE FALSE FALSE 3429.583147 2943.767102 3059.640795 2919.478291 2387.599132 2888.065677 3165.963341 2710.827994 2949.204672 3186.700762 1.076217506 0.923766404 0.960128052 0.916144473 0.749238573 0.906287064 0.993492511 0.850669139 0.925472736 1 11.63784784 -9.870773096 1.66472116 1.035102132 0.88770867 0.244246485 0.073251998 0.22681153 1.267256323 0.012039009 0.016722575 1.35E-10 9.870773096 -0.147393462 APNPTAT(ph)SPPASAPR ddPTM_HeLa_Romidepsin_16h_R1 1 APNPTATSPPASAPR 15 0 Q8IV32 Q8IV32 CCDC71 Coiled-coil domain-containing protein 71 1 0 APNPT(0.064)AT(0.468)S(0.468)PPASAPR 114.21 0.0081483 6669000 684.51 798.27 798.99 584.99 936.89 1107.6 1244.8 886.32 902.95 1054.5 TRUE FALSE FALSE 676.1669288 809.508066 812.8960858 652.6292963 889.0770073 1036.827935 1350.533281 911.9642708 822.1878905 1027.103938 0.658323762 0.7881462 0.791444815 0.635407257 0.865615421 1.009467393 1.314894463 0.887898719 0.800491421 1 10.00436647 -8.196295847 3.389603483 0.812657603 1.110340066 0.468698634 0.136734668 0.197633433 4.482065629 0.023355166 0.064259686 6.36E-09 8.196295847 0.297682463 APPAPLAASEVT(ph)NSNSAER ddPTM_HeLa_Romidepsin_16h_R1 1 APPAPLAASEVTNSNSAER 19 0 Q9Y2U8 Q9Y2U8 LEMD3 Inner nuclear membrane protein Man1 1 0 APPAPLAAS(0.105)EVT(0.522)NS(0.025)NS(0.348)AER 81.676 0.016552 4788200 414.23 552.61 322.98 458.39 442.51 480.03 399.56 528.58 512.92 540.81 TRUE FALSE FALSE 409.1812054 560.3896581 328.6013314 511.3912086 419.9270635 449.3576322 433.4986164 543.8736283 467.0431506 526.7596782 0.776789155 1.063843117 0.62381641 0.970824514 0.79718908 0.85306004 0.822953302 1.032489104 0.886634209 1 9.041001106 -12.5582715 1.304895088 1.000678535 0.85391823 0.016177999 0.128097657 0.617573927 1.870078582 0.080665059 0.018647794 2.77E-13 12.5582715 -0.146760305 APPAPLAASEVTNSNS(ph)AER ddPTM_HeLa_Romidepsin_16h_R1 1 APPAPLAASEVTNSNSAER 19 0 Q9Y2U8 Q9Y2U8 LEMD3 Inner nuclear membrane protein Man1 1 0 APPAPLAASEVT(0.002)NS(0.382)NS(0.616)AER 117.27 0.00083919 3507000 194.79 176.83 255.87 189.98 303.21 295.72 226.48 490.64 233.94 361.56 TRUE FALSE FALSE 192.4158246 179.3194174 260.32331 211.9463815 287.7360623 276.8244464 245.7172055 504.8358943 213.0158205 352.1666191 0.546377238 0.509189139 0.739204956 0.601835523 0.817045247 0.786061005 0.697729973 1.433514328 0.604872265 1 8.460114356 -4.013341367 9.330687999 0.777176106 1.130897426 0 0.259878895 0 0 0.035153343 0 9.70E-05 4.013341367 0.35372132 APPEAPHPGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 APPEAPHPGKR 11 1 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2 A0A669KBI3 AFF1 AF4/FMR2 family member 1 0 1 ; APPEAPHPGK(1)R;APPEAPHPGK(1)R 112.13 0.0021869 2366900 1045.65 947.63 663.93 959.9 1122.98 1195.19 961.14 903.83 1024.41 1054.34 FALSE TRUE FALSE 1032.905216 960.97076 675.4854231 1070.888154 1065.67014 1118.821216 1042.779208 929.980895 932.7842039 1026.948095 1.0058008 0.935753973 0.657760043 1.042787031 1.037705942 1.089462283 1.015415689 0.905577312 0.908307059 1 10.00414755 -7.247025605 22.23422046 0.986742307 0.905577053 0 0.116031066 1555.631347 2399466.024 0.0157202 0.387170307 5.66E-08 7.247025605 -0.081165254 APPPESWNTVSGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 APPPESWNTVSGKK 14 1 Q01804-5;Q01804-3;Q01804;D6RI06 Q01804-5 OTUD4 OTU domain-containing protein 4 0 1 APPPESWNTVSGK(1)K 89.231 0.019565 909840 402.28 362.7 460.52 227.4 330.74 443.08 384.72 468.99 424.71 369.3 FALSE TRUE FALSE 397.3768566 367.8061001 468.5351574 253.6930579 313.8611036 414.768618 417.3981072 482.5594857 386.7228739 359.7055328 1.10472823 1.022519997 1.30255199 0.705279833 0.872550114 1.153078227 1.160388343 1.341540348 1.075109607 1 8.49067254 -7.519151432 1.816948322 1.03297913 1.354263673 0.306691858 0.149677704 0.524351122 2.512880915 0.021298509 0.240654856 3.03E-08 7.519151432 0.321284543 APPPPIS(ph)PTQLSDVSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 APPPPISPTQLSDVSSPR 18 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 0 APPPPIS(0.954)PT(0.041)QLS(0.004)DVS(0.001)S(0.001)PR;APPPPIS(0.91)PT(0.034)QLS(0.054)DVS(0.001)S(0.001)PR ; 87.419 0.0079515 13000000 286.07 179.37 438.25 443.71 255.105 345.44 182.956 268.23 379.78 170.61 TRUE FALSE FALSE 282.5832688 181.8951756 445.8775574 495.0138379 242.0860399 323.3674989 198.4962781 275.9908119 345.8115256 166.1775276 1.70049027 1.094583475 2.683139916 2.978825387 1.456791682 1.945915934 1.194483279 1.6608191 2.080976475 1 7.376581488 -11.55894235 0.661582217 1.022374928 1.882539314 0 0.647382754 0.808759655 0.71953668 0.341894522 0.142282864 2.76E-12 11.55894235 0.860164387 APPS(ph)PGSLAAPGR ddPTM_HeLa_Romidepsin_16h_R1 2 APPSPGSLAAPGR 13 0 Q9Y4B5 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 APPS(0.993)PGS(0.007)LAAPGR;APPS(0.989)PGS(0.011)LAAPGR ; 96.371 0.016151 28750000 4128.7 3968.2 3644 3049.4 4560.7 4644.3 3615.2 3783.5 3809.1 4186.1 TRUE FALSE FALSE 4078.377816 4024.064424 3707.422291 3401.985976 4327.950461 4347.544219 3922.274998 3892.969603 3468.404556 4077.344519 1.000253424 0.986932648 0.909273738 0.83436314 1.061463028 1.066268548 0.961968011 0.954780639 0.850652806 1 11.99341415 -9.991423345 24.66758503 0.99977617 0.966025855 0 0.078799557 431.2462005 1240313.399 0.01074378 0.014107559 1.02E-10 9.991423345 -0.033750315 APQFQESVGS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 APQFQESVGSFR 12 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 APQFQES(0.38)VGS(0.62)FR 90.614 0.027615 7032700 509.57 386.1 382.07 501.91 440.76 478.36 429.07 421.47 603.03 557.46 TRUE FALSE FALSE 503.3591648 391.5355259 388.7197681 559.9431958 418.2663725 447.7943398 465.5151951 433.6645695 549.0934865 542.9771088 0.927035701 0.721090299 0.715904523 1.031246413 0.770320453 0.824702059 0.857338528 0.798679286 1.011264522 1 9.084747567 -10.4785295 4.828334124 0.969089339 0.821012911 0.436719555 0.085270316 0.155870124 7.673821147 0.014809426 0.016461537 3.32E-11 10.4785295 -0.148076429 APQT(ph)SSS(ph)PPPVR ddPTM_HeLa_Romidepsin_16h_R1 1 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 2 0 APQT(0.819)S(0.244)S(0.314)S(0.623)PPPVR 131.08 0.015059 23728000 2236.2 2415 2039.5 1912.2 2372.7 2031.5 1959 2313.4 1990.2 1993.7 TRUE FALSE FALSE 2208.944334 2448.998433 2074.996642 2133.297561 2251.612265 1901.693706 2125.397411 2380.334579 1812.191527 1941.903387 1.137515053 1.261132995 1.068537527 1.098560091 1.159487275 0.979293676 1.09449184 1.225773947 0.933203753 1 10.92325571 -12.16522497 0.999313413 1.002542588 1.123823168 0.379526478 0.078756716 0.548345769 1.014767509 0.044850243 0.013938037 6.84E-13 12.16522497 0.121280579 APQTSS(ph)SPPPVRR ddPTM_HeLa_Romidepsin_16h_R1 1 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 APQT(0.06)S(0.169)S(0.479)S(0.291)PPPVRR 64.407 0.023929 142850000 841.71 650.69 827.47 905.64 879.25 700.18 800.51 709.26 869.15 874.71 TRUE FALSE FALSE 831.4509148 659.8504309 841.8717682 1010.354358 834.3785916 655.4407577 868.5052994 729.7813191 791.4110472 851.9849081 0.975898642 0.774486056 0.988129907 1.185882929 0.979334943 0.769310291 1.019390474 0.856566017 0.92890266 1 9.734684065 -8.480062803 24.96023896 0.986790148 0.891986307 0.12726141 0.109951202 720.8348162 420221.9518 0.015288381 0.03418349 3.31E-09 8.480062803 -0.094803842 APQTSSS(ph)PPPVR ddPTM_HeLa_Romidepsin_16h_R1 5 APQTSSSPPPVR 12 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 APQT(0.009)S(0.004)S(0.032)S(0.955)PPPVR;APQT(0.001)S(0.003)S(0.029)S(0.967)PPPVR;APQT(0.001)S(0.001)S(0.013)S(0.985)PPPVR;APQT(0.002)S(0.009)S(0.093)S(0.896)PPPVR;APQTS(0.004)S(0.031)S(0.964)PPPVR ;;;; 179.83 1.42E-06 2318442400 24177.2 24305.1 21334.3 21811.73 23843.7 24263 20346.3 21907.3 25588.7 24942.7 TRUE FALSE FALSE 23882.51899 24647.26784 21705.61454 24333.70485 22626.86702 22712.67261 22074.51421 22541.15316 23299.98258 24294.68506 0.983034723 1.014512754 0.893430579 1.001606104 0.931350498 0.934882364 0.908614957 0.927822407 0.959056787 1 14.56835311 -8.927690836 0.426359671 0.99822854 0.904202439 0.319489347 0.033186878 0.99382827 0.295953501 0.009315245 0.039247897 1.18E-09 8.927690836 -0.0940261 APQTSSS(ph)PPPVRR ddPTM_HeLa_Romidepsin_16h_R1 4 APQTSSSPPPVRR 13 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 APQT(0.002)S(0.009)S(0.043)S(0.946)PPPVRR;APQT(0.001)S(0.006)S(0.004)S(0.99)PPPVRR;APQT(0.001)S(0.119)S(0.391)S(0.488)PPPVRR;APQTS(0.001)S(0.003)S(0.996)PPPVRR ;;; 95.073 0.0051857 382049000 6324.69 5891.21 4621.21 5856.19 5387.96 4948.46 4785.47 4594.46 5472.1 5369.17 TRUE FALSE FALSE 6247.602246 5974.146609 4701.640222 6533.310242 5112.992296 4632.269376 5191.947702 4727.393451 4982.661671 5229.678189 1.194643727 1.142354537 0.899030505 1.249275769 0.977687749 0.885765664 0.992785314 0.903954943 0.952766402 1 12.35250646 -8.539592924 24.98189866 1.092878374 0.933646346 0.275960058 0.104771434 200.7406606 300036.7891 0.01506172 0.030129086 2.89E-09 8.539592924 -0.159232029 APQVVAEAAK(ac)TAK ddPTM_HeLa_Romidepsin_16h_R1 2 APQVVAEAAKTAK 13 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 1 ; APQVVAEAAK(1)TAK;APQVVAEAAK(1)TAK 147.18 0.00014782 1219210 692.99 643.4 499.63 220.79 388.7 526.38 517.45 400.98 431.65 620.22 FALSE TRUE FALSE 684.5435713 652.4578021 508.3258506 246.3187786 368.8631886 492.7460168 561.4021901 412.5817237 393.0421429 604.106595 1.133150303 1.080037542 0.84145059 0.407740589 0.610592885 0.815660714 0.929309818 0.682961794 0.650617203 1 9.238659326 -9.615668975 4.311177419 1.065307851 0.698492688 0.27299803 0.185154249 0.112183842 3.8299646 0.022735014 0.032577076 2.42E-10 9.615668975 -0.366815162 APRPS(ph)APSPPPR ddPTM_HeLa_Romidepsin_16h_R1 1 APRPSAPSPPPR 12 1 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 0 APRPS(0.5)APS(0.5)PPPR 70.272 0.026178 4006400 1443.4 1330.3 1354.7 1562.3 868.28 1396.3 1354.2 808.59 1661 1625.3 TRUE FALSE FALSE 1425.807286 1349.027998 1378.277985 1742.940477 823.9684316 1307.080936 1469.225714 831.9852759 1512.436 1583.074472 0.900657114 0.852157004 0.8706337 1.100984513 0.52048621 0.82565979 0.928083764 0.525550308 0.955378933 1 10.62851341 -5.226683372 0.192574284 1.00452124 1.60E-13 0.309689425 0.148647579 31.15343672 0.531223835 0.16081067 8.537211783 5.93E-06 5.226683372 -1.00452124 APRPSAPS(ph)PPPR ddPTM_HeLa_Romidepsin_16h_R1 3 APRPSAPSPPPR 12 1 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 0 APRPS(0.032)APS(0.968)PPPR;APRPS(0.463)APS(0.537)PPPR;APRPS(0.325)APS(0.675)PPPR ;; 79.337 0.01856 84887100 2917.29 3027.94 2656.05 2370.67 2230.96 2061.42 2065.23 1881.3 3041.51 2858.69 TRUE FALSE FALSE 2881.732947 3070.567419 2702.277436 2644.77802 2117.105786 1929.701915 2240.650585 1935.732447 2769.469728 2784.420822 1.034948785 1.102767008 0.970498933 0.949848528 0.760339734 0.693035298 0.80470975 0.69520111 0.994630448 1 11.44316155 -8.851405037 2.335004574 1.021424447 0.733314111 0.905158703 0.043453823 0.060336357 0.669449937 0.00643408 0.013132561 1.41E-09 8.851405037 -0.288110336 APS(ph)APPGTGALPPAAPSGR ddPTM_HeLa_Romidepsin_16h_R1 2 APSAPPGTGALPPAAPSGR 19 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 APS(0.998)APPGT(0.002)GALPPAAPSGR;APS(0.973)APPGT(0.021)GALPPAAPS(0.006)GR ; 135.95 0.00066012 32784000 5569.9 5381.9 5214.5 4400.6 4816.5 6222.4 4869.4 6613.5 5950.1 5249.1 TRUE FALSE FALSE 5502.011916 5457.666529 5305.256185 4909.418077 4570.696032 5824.808722 5283.006714 6804.851188 5417.908154 5112.727625 1.076140237 1.067466708 1.037656721 0.960234622 0.893983871 1.139276165 1.03330494 1.330962978 1.059690355 1 12.31987745 -6.650091064 1.53901666 1.028070646 2.383996557 0.659059767 0.064585922 3.038253052 1.720630802 0.009468391 9.967461611 2.24E-07 6.650091064 1.355925911 APS(ph)DSSLGTPSDGRPELR ddPTM_HeLa_Romidepsin_16h_R1 2 APSDSSLGTPSDGRPELR 18 1 M0R2H7;M0R0F9;W4VSQ9;Q15642-5;Q15642-4;Q15642-2;Q15642-3;Q15642 M0R2H7 TRIP10 Cdc42-interacting protein 4 1 0 APS(0.726)DS(0.255)S(0.019)LGTPSDGRPELR;APS(0.492)DS(0.376)S(0.131)LGTPSDGRPELR ; 146.28 2.94E-05 431600000 2489.5 2824 2459.5 2513.3 3036.6 3046.8 2565.3 2535.4 3180.7 2905.1 TRUE FALSE FALSE 2459.157016 2863.756346 2502.306566 2803.899571 2881.630971 2852.119313 2783.196518 2608.757799 2896.210226 2829.625083 0.869075211 1.012062115 0.884324422 0.990908509 1.018379074 1.007949544 0.983591973 0.921944682 1.023531436 1 11.4663952 APS(ph)EEEALEK ddPTM_HeLa_Romidepsin_16h_R1 2 APSEEEALEK 10 0 Q14147 Q14147 DHX34 Probable ATP-dependent RNA helicase DHX34 1 0 APS(1)EEEALEK;APS(1)EEEALEK ; 114.71 0.015136 7055600 2793.4 2388 2622.6 2303.2 2750.1 3463.3 2700.6 3198.9 2950.7 3087.1 TRUE FALSE FALSE 2759.352966 2421.618327 2668.245253 2569.506821 2609.752135 3242.006307 2929.988897 3291.455124 2686.782002 3006.896697 0.917674681 0.80535468 0.887375099 0.854537778 0.867922113 1.078190119 0.974422866 1.094635252 0.893539843 1 11.55405959 -8.253731642 24.99223482 0.929057323 1.04161676 0.50562742 0.064356775 564.7947248 1831334.188 0.010878466 0.027162509 5.58E-09 8.253731642 0.112559437 APS(ph)LTNDEVEEFR ddPTM_HeLa_Romidepsin_16h_R1 1 APSLTNDEVEEFR 13 0 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 0 APS(0.859)LT(0.141)NDEVEEFR 134.88 0.0016994 5862200 484.74 575.11 783.56 640.92 955.72 666.86 596.12 738.83 951.88 832.34 TRUE FALSE FALSE 478.8318024 583.2064137 797.1975331 715.026186 906.9460421 624.2497982 646.7544179 760.2068804 866.7414688 810.7156868 0.590628515 0.719372307 0.983325654 0.881969102 1.11869803 0.76999842 0.797757375 0.937698496 1.069106572 1 9.663052248 -9.760600833 24.99999728 0.794735756 0.910762004 0.006762716 0.157287673 44.72816464 1333481.791 0.028519346 0.039003964 1.74E-10 9.760600833 0.116026247 PSGGFVISGVLS(ph)PDTISSK ddPTM_HeLa_Romidepsin_16h_R1 1 PSGGFVISGVLSPDTISSK 19 0 H0Y8J2;Q03188;H0Y9W1 H0Y8J2 CENPC Centromere protein C 1 0 PSGGFVISGVLS(0.794)PDT(0.135)IS(0.069)S(0.001)K 169.67 2.44E-12 0 2097.7 2034.7 1665.4 1179.6 848.8 713.75 717.4 540.07 1844.9 1986.7 TRUE FALSE FALSE 2072.132426 2063.34456 1694.385588 1315.990902 805.4825687 668.1436785 778.3359381 555.6960734 1679.887523 1935.085248 1.070822295 1.066280962 0.875612891 0.680068697 0.416251723 0.345278679 0.402223075 0.287168782 0.868120681 1 10.91818141 -9.063626743 1.450827198 1.037439509 0.342148303 0.950116191 0.066503359 0.035812961 0.149049259 0.007087418 0.0146806 8.64E-10 9.063626743 -0.695291206 down APS(ph)PDGFSPYSPEETNR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPDGFSPYSPEETNR 17 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 0 APS(0.999)PDGFS(0.001)PYSPEETNR 99.055 0.0012507 0 268.51 305.13 266.05 194.2 229.91 229.38 276.41 271.03 270.35 378.97 TRUE FALSE FALSE 265.2372968 309.4256281 270.6804886 216.6543177 218.1768348 214.7233583 299.8882585 278.8718254 246.1692189 369.1243048 0.718558202 0.838269451 0.733304432 0.58694135 0.591066023 0.58171016 0.812431624 0.755495701 0.666900596 1 8.527962924 -12.24075284 0.418811138 1.087758247 0.675631889 0 0.133255493 1.090709545 0.255448522 0.198148762 0.03042604 5.74E-13 12.24075284 -0.412126358 APS(ph)PEPAAPR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPEPAAPR 10 0 P20749 P20749 BCL3 B-cell lymphoma 3 protein 1 0 APS(1)PEPAAPR 119.34 0.012243 60019000 3278.2 2732.8 2580.4 2057.6 1743.5 1354.4 1039.3 1423.7 3031.1 2693.9 TRUE FALSE FALSE 3238.244037 2771.27243 2625.31078 2295.509393 1654.522689 1267.858211 1127.578116 1464.892513 2759.990824 2623.91209 1.234128251 1.056160548 1.000533055 0.87484234 0.630555687 0.48319386 0.429731667 0.558285668 1.051861011 1 11.35750367 -8.88089708 1.34369065 1.108304108 0.473104746 0.937236499 0.06711779 0.09180732 0.331160105 0.015144327 0.036160899 1.32E-09 8.88089708 -0.635199362 APS(ph)PPEAALQPAPTEPR ddPTM_HeLa_Romidepsin_16h_R1 2 APSPPEAALQPAPTEPR 17 0 Q9NVR5-2;Q9NVR5 Q9NVR5-2 DNAAF2 Protein kintoun 1 0 APS(1)PPEAALQPAPTEPR;APS(1)PPEAALQPAPTEPR ; 151.73 9.28E-05 12457700 1068.95 879.56 727.13 849.43 534.42 740.35 706.18 639.61 1130.52 889.22 TRUE FALSE FALSE 1055.921226 891.9424688 739.7853926 947.6450933 507.1465532 693.0440244 766.1629116 658.1161062 1029.40346 866.1179362 1.219142546 1.029816416 0.854139329 1.094129395 0.585539835 0.800172812 0.88459421 0.759845835 1.188525738 1 9.758419675 -9.354580304 1.252603481 1.100849769 0.785455373 0.549990816 0.127840417 0.266407863 0.826192102 0.023239408 0.043141485 4.42E-10 9.354580304 -0.315394395 APS(ph)PPVEHPR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPPVEHPR 10 0 Q86WR7;Q86WR7-2 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 0 APS(1)PPVEHPR 101.89 0.0097565 50194000 122.22 0 0 166.82 156.74 148.25 150.56 0 195.81 117.31 TRUE FALSE FALSE 120.7303356 0 0 186.1085133 148.7409729 138.7773035 163.3485626 0 178.2962632 114.2622693 1.056607193 0 0 1.628783626 1.301750559 1.214550563 1.429593195 0 1.560412412 1 6.836205278 -7.243212877 23.49304121 0.981467456 1.92E-06 0.232925946 0.551766941 1961.669033 2528401.535 0.073354024 2.914236002 5.71E-08 7.243212877 -0.981465531 APS(ph)PSINR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPSINR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 0 APS(0.5)PS(0.5)INR 102.06 0.02926 49662000 2776.9 3113.1 2648.9 2591.2 2820.6 3247.2 2759.9 3087.7 2403.9 2311.3 TRUE FALSE FALSE 2743.054075 3156.926304 2695.002993 2890.806736 2676.654257 3039.7144 2994.325837 3177.037728 2188.889163 2251.252093 1.21845709 1.402297998 1.197112932 1.284088417 1.188962474 1.350232792 1.330071318 1.411231438 0.972298558 1 11.1365119 -16.21839668 0.131031835 8.26E-17 1.434206464 0.770442748 0.069734181 26.43669133 0.264710186 6.909016383 0.256445872 6.05E-17 16.21839668 1.434206464 APS(ph)PTAEQPPGGGDSAR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-3;Q15742-2 Q15742 NAB2 NGFI-A-binding protein 2 1 0 APS(0.956)PT(0.044)AEQPPGGGDSAR 150.92 0.00010058 23070000 1100.6 1102.6 794.31 752.79 700.54 895.77 862.51 622.65 952.02 1013.4 TRUE FALSE FALSE 1087.185464 1118.122432 808.1346324 839.8311218 664.7888297 838.533188 935.7715779 640.6653954 866.8689468 987.0717219 1.101424992 1.132767161 0.818719263 0.8508309 0.673495973 0.849515967 0.948027947 0.649056579 0.878222856 1 9.947011106 -9.747136284 23.22969544 1.055598768 0.804127591 0.531538397 0.104346355 46.22522068 75073.86895 0.013994683 0.019725203 1.79E-10 9.747136284 -0.251471177 APS(ph)PTAEQPPGGGDSARR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPTAEQPPGGGDSARR 18 1 Q15742;Q15742-3;Q15742-2 Q15742 NAB2 NGFI-A-binding protein 2 1 0 APS(0.542)PT(0.457)AEQPPGGGDS(0.001)ARR 59.728 0.014976 2374500 1041.2 892.31 822.76 1140.8 658.33 798.67 661.64 689.87 1162.7 774.65 TRUE FALSE FALSE 1028.509454 904.8719636 837.0797927 1272.704664 624.7329635 747.6375646 717.8396851 709.8303 1058.7052 754.5244813 1.363122708 1.199261238 1.109413695 1.686763909 0.827982364 0.990872507 0.951380244 0.940765101 1.403142279 1 9.559423901 APS(ph)PTSSAGEEGTK ddPTM_HeLa_Romidepsin_16h_R1 1 APSPTSSAGEEGTK 14 0 O94964-2;H0YDM2;O94964;O94964-3 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 0 APS(0.599)PT(0.395)S(0.006)SAGEEGTK 134.13 0.0016125 8871200 3572.4 3094.7 3437.7 2711.4 2105.7 1822.9 1468.4 1699.3 3762.4 3348.5 TRUE FALSE FALSE 3528.858215 3138.267268 3497.531726 3024.904826 1998.238272 1706.422573 1593.125859 1748.466564 3425.881521 3261.505487 1.081972184 0.962214315 1.072367267 0.927456611 0.612673589 0.52320089 0.488463339 0.536091867 1.050398822 1 11.67132234 -8.765303229 2.436739392 1.035266027 0.514507421 0.978741693 0.034836304 0.030787491 0.373247204 0.006018835 0.012695038 1.72E-09 8.765303229 -0.520758606 APS(ph)RNLAPTPR ddPTM_HeLa_Romidepsin_16h_R1 1 APSRNLAPTPR 11 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 APS(0.999)RNLAPT(0.001)PR 76.868 0.023549 5023500 1211.5 982.49 754.38 2606.8 967.75 866.55 963.2 508.07 1192.6 948.47 TRUE FALSE FALSE 1196.733772 996.32152 767.5096675 2908.210481 918.3621063 811.1802517 1045.014184 522.7702038 1085.930869 923.8286127 1.295406697 1.078470082 0.830792267 3.147997844 0.99408277 0.878063572 1.131177547 0.565873579 1.175467889 1 9.85148142 -8.540553369 24.99922435 1.270808696 0.894054525 0.120016788 0.632587208 521.233784 737237.8756 0.091841246 0.183710959 2.88E-09 8.540553369 -0.376754171 APS(ph)RQDVYGPQPQVR ddPTM_HeLa_Romidepsin_16h_R1 1 APSRQDVYGPQPQVR 15 1 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 APS(1)RQDVYGPQPQVR 66.939 0.021103 65392000 1325 1222.4 1334.9 1283.4 1133.2 1241.8 1054.7 1177.2 1095.3 1211.7 TRUE FALSE FALSE 1308.85039 1239.608979 1358.133375 1431.792747 1075.368575 1162.452988 1144.286192 1211.260425 997.3336248 1180.219859 1.108988618 1.050320387 1.150746078 1.213157646 0.911159533 0.984946134 0.969553412 1.026300663 0.845040538 1 10.20483992 -8.721327665 24.99999552 1.070948902 0.973598536 0.166108948 0.095578877 155.3642121 96831.46337 0.010699955 0.021399705 1.90E-09 8.721327665 -0.097350366 APS(ph)SSSLNSATSSQSK ddPTM_HeLa_Romidepsin_16h_R1 1 APSSSSLNSATSSQSK 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2;A0A2R8Y534;A0A2R8Y4Q0 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 1 0 APS(0.997)S(0.003)SSLNSATSSQSK 179.81 2.45E-08 4202600 393.78 712.87 717.23 751.74 691.39 860.78 677.07 814.73 620.03 441.19 TRUE FALSE FALSE 388.9804579 722.9058026 729.7130873 838.6597158 656.1057884 805.778936 734.5803089 838.3029271 564.5729639 429.7278202 0.905178673 1.682241104 1.698082025 1.951606753 1.526793839 1.875091391 1.709408315 1.950776486 1.31379198 1 8.747279369 -10.22064616 4.83213028 0.954218081 1.773047967 0.777166498 0.167945368 0.038322853 2.167923262 0.01945887 0.023602638 6.02E-11 10.22064616 0.818829886 APS(ph)VANVGSHCDLSLK ddPTM_HeLa_Romidepsin_16h_R1 2 APSVANVGSHCDLSLK 16 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 0 APS(1)VANVGSHCDLSLK;APS(1)VANVGSHCDLSLK ; 105 0.0043123 60346000 3641.1 3407.8 4060.9 253.56 3614.6 4078 2817.3 4244.4 3993.4 4434.1 TRUE FALSE FALSE 3596.720873 3455.775098 4131.578261 282.8778002 3430.133474 3817.428961 3056.601392 4367.205017 3636.220302 4318.901443 0.83278605 0.800151414 0.956627123 0.065497628 0.794214344 0.88388888 0.70772659 1.011184227 0.841931762 1 12.07644868 -10.96905361 0.762309804 0.973168608 0.72765686 0.067424363 0.2492028 0.82848119 1.056895749 0.082477634 0.060980257 1.07E-11 10.96905361 -0.245511748 APS(ph)VATVGSICDLNLK ddPTM_HeLa_Romidepsin_16h_R1 1 APSVATVGSICDLNLK 16 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-5;O75369-4;A0A0C4DGA1 O75369-8 FLNB Filamin-B 1 0 APS(1)VATVGSICDLNLK 276.63 6.50E-102 27128000 4132.3 3930.9 3898.9 326.27 4194 5180 3609 5152.2 3836.4 3992.9 TRUE FALSE FALSE 4081.933938 3986.239313 3966.758719 363.9948725 3979.96453 4849.014718 3915.54837 5301.270778 3493.262776 3889.163882 1.049565938 1.024960489 1.019951547 0.093592063 1.023347087 1.246801334 1.006784103 1.363087527 0.898204057 1 11.92524431 -9.469579349 24.99922787 1.024097192 0.92956605 0.001948998 0.319259812 1425.087058 668414.5021 0.04931345 0.075327262 3.39E-10 9.469579349 -0.094531142 APS(ph)VPAAEPEYPK ddPTM_HeLa_Romidepsin_16h_R1 2 APSVPAAEPEYPK 13 0 F8VPP1;G3V213;F8VZG5;A0A5F9ZHP2;F8VY04;A0A5K1VW67;F8W1A4;P54819-3;P54819-5;P54819-2;P54819 F8VPP1 AK2 "Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial;Adenylate kinase 2, mitochondrial, N-terminally processed" 1 0 APS(1)VPAAEPEYPK;APS(1)VPAAEPEYPK ; 118.52 0.0051634 15345800 3207.1 3513.9 2617.8 2971.8 3658.5 3265 2906.8 3270.5 3813.6 3597.3 TRUE FALSE FALSE 3168.010632 3563.368776 2663.361711 3315.413499 3471.793093 3056.377037 3153.703519 3365.126758 3472.502065 3503.841627 0.904153489 1.016989109 0.760126168 0.946222419 0.990853315 0.872293146 0.900070224 0.960410634 0.991055657 1 11.77472185 -12.36347976 0.735882887 1.009338706 0.916152282 0.171049059 0.06731253 1.236670385 0.999509335 0.073139964 0.012952986 4.33E-13 12.36347976 -0.093186424 APSAGLEEVAQPESVDVITSQSDS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 APSAGLEEVAQPESVDVITSQSDSPTR 27 0 A0A087WU78;A0A087WWC4;Q6T4R5-4;Q6T4R5-3;Q6T4R5-2;Q6T4R5 A0A087WU78 NHS Nance-Horan syndrome protein 1 0 APSAGLEEVAQPESVDVITSQS(0.171)DS(0.688)PT(0.141)R 142.12 9.86E-11 5303400 1389.7 1641.5 1576.8 1303.5 1330.1 1613.6 1076.9 1311.1 1637 1643.8 TRUE FALSE FALSE 1372.761802 1664.60908 1604.243543 1454.216803 1262.220034 1510.496168 1168.371859 1349.03461 1490.58262 1601.093839 0.857389972 1.039669905 1.00196722 0.908264567 0.788348567 0.94341514 0.72973353 0.842570608 0.930977675 1 10.64484215 -8.929518697 5.467150135 0.945817496 0.828287564 0.464435302 0.06912105 0.182540937 10.0506645 0.011634353 0.021294434 1.18E-09 8.929518697 -0.117529932 APSDS(ph)S(ph)LGTPSDGRPELR ddPTM_HeLa_Romidepsin_16h_R1 1 APSDSSLGTPSDGRPELR 18 1 M0R2H7;M0R0F9;W4VSQ9;Q15642-5;Q15642-4;Q15642-2;Q15642-3;Q15642 M0R2H7 TRIP10 Cdc42-interacting protein 4 2 0 APS(0.277)DS(0.738)S(0.949)LGT(0.016)PS(0.019)DGRPELR 82.942 0.022264 9957000 2306.5 2290.4 1963.1 2175.2 2105.9 1856.9 1532.4 1483.4 2407 2268.7 TRUE FALSE FALSE 2278.387491 2322.644311 1997.266932 2426.706859 1998.428065 1738.250083 1662.562018 1526.319839 2191.711892 2209.758847 1.031057074 1.05108497 0.903839319 1.098177234 0.904364776 0.786624335 0.752372604 0.690717831 0.991833066 1 11.10967322 -8.313066709 2.029588152 1.01433054 0.72513873 0.848487911 0.051016099 0.080273984 0.635111245 0.006816056 0.020328909 4.86E-09 8.313066709 -0.289191811 APSDSS(ph)LGTPSDGRPELR ddPTM_HeLa_Romidepsin_16h_R1 2 APSDSSLGTPSDGRPELR 18 1 M0R2H7;M0R0F9;W4VSQ9;Q15642-5;Q15642-4;Q15642-2;Q15642-3;Q15642 M0R2H7 TRIP10 Cdc42-interacting protein 4 1 0 APS(0.001)DS(0.371)S(0.628)LGTPSDGRPELR;APS(0.025)DS(0.2)S(0.727)LGT(0.047)PSDGRPELR ; 229.02 6.80E-38 97123000 5683.5 5537.7 5334.8 5413.4 6027.1 5842.7 5631.6 6098.1 6388.8 6031.4 TRUE FALSE FALSE 5614.227316 5615.659886 5427.649956 6039.322779 5719.514597 5469.370326 6109.947963 6274.538902 5817.369727 5874.703359 0.955661414 0.955905268 0.923901961 1.028021742 0.973583558 0.93100366 1.040043657 1.06806055 0.990240591 1 12.52030029 -7.605019792 6.118644053 0.97367118 1.061372349 0.564061997 0.029888084 0.106574124 6.083412825 0.004308725 0.016712989 2.48E-08 7.605019792 0.087701169 APSGSSLPS(ph)SPGSNSR ddPTM_HeLa_Romidepsin_16h_R1 1 APSGSSLPSSPGSNSR 16 0 Q96Q07-3;Q96Q07-2;Q96Q07 Q96Q07-3 BTBD9 BTB/POZ domain-containing protein 9 1 0 APS(0.001)GS(0.006)S(0.028)LPS(0.478)S(0.478)PGS(0.009)NSR 80.507 0.024318 8546800 859.19 775.39 816.49 907.78 1211.6 720.81 1041.8 1233.9 841.36 704.59 TRUE FALSE FALSE 848.7178618 786.3059608 830.7006659 1012.741795 1149.767531 674.7525673 1130.290466 1269.60095 766.1066544 686.2846502 1.236684897 1.145743185 1.210431656 1.475687668 1.67535079 0.983196356 1.646970343 1.84996262 1.116310345 1 9.422663277 -4 0.176350633 0.98354875 4.094966368 0.525281369 0.200041201 33.10941179 0.355322825 0.266925487 27.60945864 1.00E-04 4 3.111417618 APSGSSLPSS(ph)PGSNSR ddPTM_HeLa_Romidepsin_16h_R1 1 APSGSSLPSSPGSNSR 16 0 Q96Q07-3;Q96Q07-2;Q96Q07 Q96Q07-3 BTBD9 BTB/POZ domain-containing protein 9 1 0 APSGS(0.002)S(0.002)LPS(0.183)S(0.807)PGS(0.006)NSR 107.13 0.0038065 9089900 1411.8 1481 1103.9 1448.3 1585.4 1389.9 1825.5 1524.3 1618.8 1359 TRUE FALSE FALSE 1394.592439 1501.849557 1123.112916 1615.75926 1504.491122 1301.089876 1980.557924 1568.403216 1474.010474 1323.692984 1.053561857 1.134590555 0.848469343 1.220645029 1.136586157 0.982924206 1.496236626 1.184869327 1.11355918 1 10.37035283 -7.773223123 24.99952364 1.040608029 1.340552999 0.453375369 0.12096121 104.6250359 221966.3934 0.015131456 0.045924908 1.69E-08 7.773223123 0.29994497 APSLPAPPYAGAPGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 APSLPAPPYAGAPGSPR 17 0 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 0 APSLPAPPYAGAPGS(1)PR 96.805 0.004931 15311000 750.77 685.84 648.37 905.39 738.55 534.38 647.98 730.34 810.91 784.86 TRUE FALSE FALSE 741.6193265 695.4952735 659.6546079 1010.075452 700.8590376 500.2348426 703.019405 751.4712356 738.3801786 764.4692241 0.970110114 0.909775373 0.862892301 1.321276802 0.916791697 0.654355763 0.919617668 0.982997369 0.965872994 1 9.578314613 -8.524828591 24.99938623 0.995091023 0.846806434 0.196016242 0.139119003 74.59049363 956340.6559 0.0193892 0.03898711 2.99E-09 8.524828591 -0.148284589 APSLT(ph)NDEVEEFR ddPTM_HeLa_Romidepsin_16h_R1 2 APSLTNDEVEEFR 13 0 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 0 APS(0.261)LT(0.739)NDEVEEFR;APS(0.249)LT(0.751)NDEVEEFR ; 109.99 0.014232 25482000 772.81 699.79 745.92 677.11 824.97 558.03 790.29 799.05 798.44 817.33 TRUE FALSE FALSE 763.3906945 709.641662 758.9024247 755.4006441 782.8687025 522.373684 857.4172129 822.1692511 727.0255267 796.0956488 0.95891831 0.891402513 0.953280458 0.948881765 0.98338523 0.6561695 1.077027885 1.032751846 0.913238915 1 9.636797967 -11.14335353 0.909351251 0.993580221 0.932627942 0 0.109196495 1.213159707 2.136294963 0.03284009 0.023092194 7.19E-12 11.14335353 -0.060952279 APSPAPRPVPGS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPAPRPVPGSPAR 15 1 Q5TZA2-2;Q5TZA2 Q5TZA2-2 CROCC Rootletin 1 0 APSPAPRPVPGS(1)PAR 64.798 0.023788 4312500 1320.2 1333.3 1342.1 1435.7 1465.7 1290.4 1119.7 1267.9 1649.6 1418 TRUE FALSE FALSE 1304.108895 1352.070232 1365.458688 1601.702389 1390.89986 1207.947605 1214.80729 1304.584686 1502.055645 1381.160156 0.944212653 0.978938052 0.988631682 1.159678972 1.007051828 0.874589091 0.879555702 0.94455714 1.087531839 1 10.4316649 -8.263979615 24.99518712 0.990884194 0.897566148 0.362859019 0.066002597 209.0966569 2057466.1 0.009203478 0.021511638 5.45E-09 8.263979615 -0.093318047 APSPAPS(ph)SVPLGSEKPSNVSQDR ddPTM_HeLa_Romidepsin_16h_R1 2 APSPAPSSVPLGSEKPSNVSQDR 23 1 O75179-4;O75179-6;O75179-2;O75179;H0YM23;O75179-7 O75179-4 ANKRD17 Ankyrin repeat domain-containing protein 17 1 0 APS(0.134)PAPS(0.733)S(0.134)VPLGSEKPSNVSQDR;APS(0.089)PAPS(0.455)S(0.455)VPLGSEKPSNVSQDR ; 98.292 1.79E-05 230718000 3529.2 3629.7 3235.7 3161.3 3254 2693.3 2631.7 2577.1 3796.4 3556.8 TRUE FALSE FALSE 3486.184753 3680.799012 3292.016001 3526.82438 3087.936238 2521.206822 2855.236532 2651.664323 3456.840476 3464.393823 1.006289969 1.062465528 0.950243006 1.018020629 0.891335222 0.727748331 0.824166269 0.765404991 0.99781972 1 11.75838723 -8.53886631 3.302712349 1.004453277 0.778446723 0.900994151 0.034668577 0.047353333 1.074892496 0.004603364 0.010269668 2.89E-09 8.53886631 -0.226006554 APSPT(ph)AEQPPGGGDSAR ddPTM_HeLa_Romidepsin_16h_R1 1 APSPTAEQPPGGGDSAR 17 0 Q15742;Q15742-3;Q15742-2 Q15742 NAB2 NGFI-A-binding protein 2 1 0 APS(0.123)PT(0.877)AEQPPGGGDSAR 97.957 0.0086619 30245000 577.76 506.92 567.46 427.73 541.71 684.86 599.18 635.98 625.18 654.6 TRUE FALSE FALSE 570.7180389 514.0564331 577.3364033 477.1861551 514.0645173 641.0996563 650.0743342 654.3810779 569.262335 637.5933976 0.895112843 0.806244912 0.90549307 0.748417654 0.806257592 1.005499208 1.019575072 1.026329759 0.892829721 1 9.31649288 -8.034956595 23.01730232 0.910799669 1.020348671 0.3751312 0.075378304 259.0217268 170554.1648 0.013275199 0.03387305 9.23E-09 8.034956595 0.109549002 APSQVSISAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 APSQVSISASPR 12 0 A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-4;Q8IVL1-8;Q8IVL1-9;Q8IVL1-10;Q8IVL1-13;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;Q8IVL1-5;Q8IVL1-7;Q8IVL1-6 A0A0A0MTL4 NAV2 Neuron navigator 2 1 0 APSQVS(0.01)IS(0.093)AS(0.897)PR;APSQVSISAS(1)PR;APSQVSISAS(1)PR ;; 177.21 1.92E-06 51059200 3889.39 4073.81 3372.75 3317.11 2975.52 2666.8 1884.86 2448.48 4052.03 3520.12 TRUE FALSE FALSE 3841.984619 4131.161204 3431.451299 3700.649866 2823.668111 2496.400087 2044.959961 2519.322906 3689.606288 3428.666775 1.120547685 1.204888511 1.00081213 1.079326195 0.823546963 0.728096444 0.596430069 0.73478208 1.076105242 1 11.74343198 -8.556700098 2.088627685 1.06903946 0.671164443 0.877577094 0.066982779 0.087124169 0.7578455 0.011209021 0.027697135 2.78E-09 8.556700098 -0.397875016 APSSSSLNSATS(ph)SQSK ddPTM_HeLa_Romidepsin_16h_R1 1 APSSSSLNSATSSQSK 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2;A0A2R8Y534;A0A2R8Y4Q0 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 1 0 APSSSS(0.002)LNSAT(0.072)S(0.905)S(0.021)QS(0.001)K 273.84 3.91E-87 3003800 1140.3 1059.3 988.69 964.53 890.78 1126.5 1115.8 802 1126.8 911.32 TRUE FALSE FALSE 1126.401585 1074.212853 1005.897735 1076.053497 845.3201726 1054.520286 1210.576024 825.2046047 1026.016186 887.643775 1.26897931 1.21018463 1.133222316 1.212258258 0.952319158 1.187999415 1.363808386 0.929657401 1.155887322 1 9.793837007 -12.55643467 1.348067797 1.000636667 1.174903405 0 0.134357786 0.534115121 1.749320212 0.08363027 0.02005068 2.78E-13 12.55643467 0.174266738 APSTSPS(ph)FEGTQETYTVAHEENVR ddPTM_HeLa_Romidepsin_16h_R1 2 APSTSPSFEGTQETYTVAHEENVR 24 0 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 0 APS(0.023)T(0.081)S(0.388)PS(0.507)FEGT(0.002)QETYTVAHEENVR;APS(0.016)T(0.052)S(0.175)PS(0.755)FEGT(0.001)QETYTVAHEENVR ; 132.81 1.34E-06 11740000 1859.23 2007 1333.8 1130.72 1565.65 1785.27 1193.45 1602.09 2046.78 2006.86 TRUE FALSE FALSE 1836.56899 2035.254599 1357.014229 1261.459167 1485.749038 1671.197009 1294.821613 1648.443946 1863.710871 1954.721488 0.939555328 1.041199276 0.694223826 0.645339592 0.760082215 0.854954027 0.662407213 0.843313974 0.953440622 1 10.93274735 -9.758703207 24.99999391 0.975889848 0.741079329 0.742148737 0.06928359 26.85736065 245389.8479 0.010813058 0.014900854 1.74E-10 9.758703207 -0.23481052 APSYSGLS(ph)MVSGVK ddPTM_HeLa_Romidepsin_16h_R1 2 APSYSGLSMVSGVK 14 0 A0A2R8Y7K2;A0A2R8Y5N9;A0A2R8Y481;A0A2R8YFW8;A0A2R8YGN6;A0A2R8YCL5;A0A2R8Y4I8;A0A2U3TZR0;Q9UBP0-4;Q9UBP0-3;Q9UBP0-2;Q9UBP0 A0A2R8Y7K2 SPAST Spastin 1 0 APS(0.189)Y(0.001)S(0.002)GLS(0.808)MVSGVK;APS(0.31)Y(0.043)S(0.241)GLS(0.406)MVSGVK ; 94.409 0.020861 51090000 5989.7 6691.8 5735.1 5701.3 6918.5 6897.9 5317.8 6821.5 5610.2 5153.6 TRUE FALSE FALSE 5916.695233 6786.007336 5834.91701 6360.511131 6565.423129 6457.146452 5769.493799 7018.86934 5108.409661 5019.708729 1.178692939 1.351872729 1.162401511 1.26710761 1.307929102 1.286358791 1.149368242 1.398262274 1.017670534 1 12.29338794 -11.41215883 0.507270408 0.987113829 1.279881665 0.660806335 0.074179653 0.40663639 0.221181735 0.053437654 0.021901477 3.87E-12 11.41215883 0.292767836 APTLAELDSS(ph)ESEEETLHK ddPTM_HeLa_Romidepsin_16h_R1 2 APTLAELDSSESEEETLHK 19 0 J3KNG6;Q08AE8-4;Q08AE8-3;Q08AE8-5;Q08AE8-2;Q08AE8 J3KNG6 SPIRE1 Protein spire homolog 1 1 0 APTLAELDS(0.182)S(0.816)ES(0.002)EEET(0.001)LHK;APTLAELDS(0.158)S(0.749)ES(0.073)EEET(0.019)LHK ; 72.99 0.0057888 10384700 2584.8 2520.2 2651.2 2537.1 3498.3 3546.3 3371.7 4415.7 2499.6 2846.7 TRUE FALSE FALSE 2553.295463 2555.679442 2697.343024 2830.451439 3319.768697 3319.702875 3658.092114 4543.461313 2276.029516 2772.742324 0.92085566 0.921715451 0.972806958 1.020813011 1.197287129 1.19726339 1.319304748 1.638616497 0.820858648 1 11.43709783 -6.567257875 0.546003827 0.955043535 2.753906883 0.925102521 0.063085565 1.171154822 0.137621731 0.010371844 1.589824823 2.71E-07 6.567257875 1.798863348 APVASPAALGSTATAS(ph)PAAPAR ddPTM_HeLa_Romidepsin_16h_R1 1 APVASPAALGSTATASPAAPAR 22 0 A0A0C4DFM2;Q6ZN55;Q6ZN55-2 A0A0C4DFM2 ZNF574 Zinc finger protein 574 1 0 APVASPAALGS(0.001)T(0.02)AT(0.226)AS(0.753)PAAPAR 241.08 2.31E-54 6188900 744.67 641.77 738.93 788.45 850.25 1045.4 1040 1087.2 756.9 606.77 TRUE FALSE FALSE 735.5936756 650.8048549 751.7907667 879.6142988 806.8585698 978.6023139 1128.337574 1118.656417 689.2009683 591.0060279 1.244646655 1.101181416 1.272052621 1.488333887 1.365229002 1.65582459 1.90918116 1.89280035 1.166148797 1 9.207029035 -4.100796029 0.225595774 1.007993964 6.385484554 0.9000139 0.095917772 8.818094789 0.110931521 0.065404973 17.41446839 7.93E-05 4.100796029 5.377490591 APVHFVEPLS(ph)PTGVAGHR ddPTM_HeLa_Romidepsin_16h_R1 4 APVHFVEPLSPTGVAGHR 18 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 APVHFVEPLS(0.804)PT(0.196)GVAGHR;APVHFVEPLS(0.964)PT(0.036)GVAGHR;APVHFVEPLS(0.797)PT(0.203)GVAGHR;APVHFVEPLS(0.745)PT(0.255)GVAGHR ;;; 115.63 0.00043028 86783400 7394.6 6856.6 7216.8 6661.9 8113.6 8948.7 7954.8 8450.3 8157.7 7950.4 TRUE FALSE FALSE 7304.471771 6953.127395 7342.405377 7432.180223 7699.532716 8376.906951 8630.480513 8694.796098 7428.054881 7743.847462 0.943261319 0.897890542 0.948159867 0.959752921 0.994277425 1.081749995 1.11449516 1.122800538 0.959220196 1 12.91883482 -8.232118613 2.090666193 0.96329666 1.11941572 0.883343811 0.025208605 0.107526516 0.901188433 0.004917208 0.015494053 5.86E-09 8.232118613 0.156119061 APVHFVEPLS(ph)PTGVAGHRK ddPTM_HeLa_Romidepsin_16h_R1 1 APVHFVEPLSPTGVAGHRK 19 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 APVHFVEPLS(0.994)PT(0.006)GVAGHRK 60.454 0.0091617 11354000 4254.4 4137.7 4059.7 4628.9 4933.6 5028.9 4102.3 4480 4239.9 4015.2 TRUE FALSE FALSE 4202.545736 4195.950649 4130.357376 5164.115198 4681.819982 4707.56952 4450.74926 4609.621732 3860.672725 3910.884525 1.074576789 1.072890448 1.056118469 1.320446862 1.1971256 1.20370967 1.138041594 1.17866475 0.987161012 1 11.93327922 -9.399077093 7.853520158 1.040233551 1.202740224 0.739149541 0.050360853 0.118143318 7.093282022 0.008072787 0.012340916 3.99E-10 9.399077093 0.162506673 APVPEPGLDLS(ph)LSPRPDSPQPR ddPTM_HeLa_Romidepsin_16h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 0 APVPEPGLDLS(0.422)LS(0.374)PRPDS(0.204)PQPR 64.68 0.0027998 26436000 1156.7 1190.9 1070.7 953.92 877.95 945.49 649.11 657.51 1152.5 1163.9 TRUE FALSE FALSE 1142.601695 1207.665521 1089.335084 1064.216719 833.1449354 885.0762404 704.2453872 676.5340145 1049.417514 1133.66171 1.007885937 1.065278566 0.9608996 0.938742756 0.734914947 0.780723414 0.621212996 0.596768867 0.925688417 1 10.14677448 -8.480696403 0.941187139 1.010434808 0.596771472 0.89797996 0.050748683 0.109990378 0.171405027 0.006834523 0.029956612 3.31E-09 8.480696403 -0.413663335 APVPEPGLDLSLS(ph)PRPDSPQPR ddPTM_HeLa_Romidepsin_16h_R1 1 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 0 APVPEPGLDLS(0.273)LS(0.719)PRPDS(0.008)PQPR 64.152 0.0020059 0 853.08 579.75 582.97 613.91 793.59 553.97 584.92 668.08 828.37 639.3 TRUE FALSE FALSE 842.6823328 587.9117357 593.1163483 684.8931627 753.090141 518.5731049 634.6030902 687.4098407 754.2785125 622.6908938 1.353291563 0.944146994 0.952505254 1.099892691 1.209412485 0.832793783 1.019130192 1.103934308 1.21132093 1 9.282372371 -10.22773373 24.95754075 1.166832189 1.023045448 0.259784637 0.12616357 886.5297951 656437.6824 0.026607818 0.03258682 5.92E-11 10.22773373 -0.14378674 APVPEPGLDLSLSPRPDS(ph)PQPR ddPTM_HeLa_Romidepsin_16h_R1 3 APVPEPGLDLSLSPRPDSPQPR 22 1 Q8TAP8 Q8TAP8 PPP1R35 Protein phosphatase 1 regulatory subunit 35 1 0 APVPEPGLDLSLSPRPDS(1)PQPR;APVPEPGLDLS(0.326)LS(0.158)PRPDS(0.516)PQPR;APVPEPGLDLS(0.031)LS(0.109)PRPDS(0.86)PQPR ;; 136.96 3.10E-05 280830000 6857.45 6176.55 6145.16 6182.25 4818.55 4717.23 3951.61 3884.76 6429.73 5912.53 TRUE FALSE FALSE 6773.868762 6263.503633 6252.113932 6897.070833 4572.641413 4415.814227 4287.259655 3997.159401 5854.638845 5758.921618 1.176239097 1.087617448 1.085639699 1.19763235 0.79401001 0.76677797 0.744455288 0.69408123 1.016620686 1 12.49158297 -8.675903611 5.90215428 1.09261995 0.744478621 0.886650879 0.06041667 0.060865346 3.318741019 0.010944078 0.022023237 2.11E-09 8.675903611 -0.348141329 APVPGT(ph)PDSLSSGSSR ddPTM_HeLa_Romidepsin_16h_R1 4 APVPGTPDSLSSGSSR 16 0 A0A087WYB4;Q9UJZ1-2;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 1 0 APVPGT(0.996)PDS(0.004)LSSGSSR;APVPGT(0.917)PDS(0.067)LS(0.005)S(0.005)GS(0.005)S(0.002)R;APVPGT(1)PDSLSSGSSR;APVPGT(0.988)PDS(0.005)LS(0.005)S(0.001)GSSR ;;; 202.32 3.72E-18 166680000 7583.9 7580.3 6562.1 8168.6 7358.8 7341.7 6702.8 7789.9 7302 7300.8 TRUE FALSE FALSE 7491.46451 7687.015662 6676.310598 9113.091966 6983.252977 6872.589064 7272.135665 8015.288466 6648.890832 7111.124164 1.053485263 1.080984593 0.938854455 1.281526206 0.982018147 0.966456063 1.022642201 1.127147872 0.934998557 1 12.79586193 -12.05609569 0.736682591 0.998065793 1.054660288 0.102410629 0.094601225 2.103814905 1.987875713 0.069501211 0.01856029 8.79E-13 12.05609569 0.056594495 APVPSTCSSTFPEELS(ph)PPSHQAK ddPTM_HeLa_Romidepsin_16h_R1 1 APVPSTCSSTFPEELSPPSHQAK 23 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;Q14980-4;Q14980-3;F5H6Y5;F5H4J1;F5H0Z7;F5H763 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 APVPSTCSSTFPEELS(1)PPSHQAK 123.85 2.73E-09 0 1059.1 1313.7 1496.4 279.22 1167.4 1485.9 1245.9 1288.4 1524.9 1254.9 TRUE FALSE FALSE 1046.191282 1332.194303 1522.444214 311.5047302 1107.823222 1390.955786 1351.726715 1325.677821 1388.509125 1222.297517 0.855921956 1.089910013 1.245559443 0.254851806 0.906344983 1.137984628 1.105890093 1.084578675 1.135982938 1 10.25537978 -8.26567148 23.1193147 0.913209901 1.109125036 0.097290094 0.252398452 208.0035493 1136307.393 0.034200942 0.079240163 5.42E-09 8.26567148 0.195915135 APVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_HeLa_Romidepsin_16h_R1 2 APVQPQQSPAAAPGGTDEKPSGK 23 1 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 0 APVQPQQS(1)PAAAPGGTDEKPSGK;APVQPQQS(1)PAAAPGGTDEKPSGK ; 146.18 2.91E-07 179433000 8179.3 7803.8 7917.9 7537.6 7862.7 9114.8 7985.2 9036.9 8628.9 7679.5 TRUE FALSE FALSE 8079.607546 7913.662101 8055.707728 8409.132777 7461.437079 8532.393697 8663.462689 9298.368444 7857.109573 7479.985483 1.080163533 1.05797827 1.076968364 1.124217794 0.997520262 1.140696558 1.158219185 1.243099798 1.050417757 1 12.86881975 -4 0.329862414 1.031807933 3.118816513 0.700157241 0.039204473 21.93026842 0.278399469 0.013527624 28.28317822 1.00E-04 4 2.08700858 APVSSTESVIQSNT(ph)PT(ph)PPPSQPLNETAEEESR ddPTM_HeLa_Romidepsin_16h_R1 2 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 0 APVSSTESVIQS(0.129)NT(0.899)PT(0.97)PPPS(0.001)QPLNETAEEESR;APVSSTESVIQS(0.017)NT(0.992)PT(0.987)PPPS(0.003)QPLNETAEEESR ; 137.36 6.79E-16 10870900 1699.15 2153.49 1600.82 2394.95 1828.06 1979.97 1553.95 1914.09 2200.18 2326.71 TRUE FALSE FALSE 1678.440106 2183.806889 1628.681601 2671.865388 1734.767277 1853.456307 1685.942474 1969.471174 2003.39039 2266.261739 0.74062059 0.963616361 0.718664386 1.178974759 0.765475253 0.817847416 0.74393105 0.869039591 0.884006625 1 11.14609878 -12.59391975 1.389534135 0.999929979 0.837336856 0.038533526 0.135327487 0.588477267 2.039851492 0.088740023 0.02061622 2.55E-13 12.59391975 -0.162593123 APVSSTESVIQSNT(ph)PTPPPSQPLNETAEEESR ddPTM_HeLa_Romidepsin_16h_R1 2 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 APVSSTESVIQS(0.046)NT(0.708)PT(0.246)PPPS(0.001)QPLNETAEEESR;APVSSTES(0.001)VIQS(0.262)NT(0.533)PT(0.199)PPPS(0.005)QPLNETAEEESR ; 115.77 2.92E-14 24867000 1254.09 847.09 913.14 1190.35 1200.52 1371.77 1084.86 1273.53 1083.16 798.16 TRUE FALSE FALSE 1238.804669 859.0153553 929.0328187 1327.983868 1139.252985 1284.118324 1177.007981 1310.377581 986.2794568 777.4236881 1.593474302 1.104951352 1.195014807 1.708185495 1.465420982 1.651761252 1.51398523 1.685538531 1.268651151 1 9.602557257 -14.56515051 0.250182875 1.17E-15 1.574792276 0.359547466 0.195607843 11.85286533 0.367707377 6.390728206 0.129558709 2.72E-15 14.56515051 1.574792276 APVSSTESVIQSNTPT(ph)PPPSQPLNETAEEESR ddPTM_HeLa_Romidepsin_16h_R1 2 APVSSTESVIQSNTPTPPPSQPLNETAEEESR 32 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 APVSSTESVIQS(0.004)NT(0.056)PT(0.939)PPPS(0.001)QPLNETAEEESR;APVSSTESVIQSNT(0.083)PT(0.916)PPPSQPLNETAEEESR ; 138.78 1.52E-15 28918000 2199.3 2476.1 2271.89 2388.6 3283.5 2852.7 2378.7 3041.9 2694.4 2575.3 TRUE FALSE FALSE 2172.494086 2510.958601 2311.431292 2664.781171 3115.930743 2670.421677 2580.746719 3129.912577 2453.406116 2508.393335 0.866089881 1.001022673 0.921478805 1.062345819 1.242201811 1.064594472 1.028844513 1.247775831 0.978078709 1 11.29254788 -9.10160417 4.072644644 0.940239929 1.133883736 0.591793127 0.074650108 0.128761232 3.755675015 0.012053972 0.020659839 7.91E-10 9.10160417 0.193643806 APVVTGK(ac)FGERPPPK ddPTM_HeLa_Romidepsin_16h_R1 1 APVVTGKFGERPPPK 15 2 D6RIV8;Q06330-7 D6RIV8 RBPJ Recombining binding protein suppressor of hairless 0 1 APVVTGK(1)FGERPPPK 100.41 0.018168 2601700 580.33 560.35 776.12 772.83 771.16 780.05 694.82 589.38 768.74 461.49 FALSE TRUE FALSE 573.2567147 568.238622 789.628043 862.1882409 731.8048276 730.2073225 753.8379935 606.4327804 699.9819691 449.5004233 1.275319633 1.264155922 1.756679198 1.91810329 1.628040353 1.624486396 1.677057361 1.349126161 1.557244293 1 8.812178664 -10.15777711 1.367339941 1.105078505 1.664308638 0.341531738 0.212507638 0.170523597 0.611906068 0.033239469 0.041216866 6.95E-11 10.15777711 0.559230132 APYS(ph)PTTSK ddPTM_HeLa_Romidepsin_16h_R1 4 APYSPTTSK 9 0 Q96JH7 Q96JH7 VCPIP1 Deubiquitinating protein VCIP135 1 0 APYS(0.995)PT(0.005)TSK;APY(0.001)S(0.73)PT(0.242)T(0.021)S(0.005)K;APYS(0.987)PT(0.012)T(0.001)S(0.001)K;APY(0.003)S(0.985)PT(0.011)T(0.002)SK ;;; 135.8 0.0067894 238395000 18651.4 19040.2 18337.1 17238.1 27336.9 32069.5 27390.7 29768.2 19681.3 18803.2 TRUE FALSE FALSE 18424.06956 19308.24844 18656.24953 19231.25023 25941.79598 30020.36245 29717.26537 30629.4959 17920.95524 18314.69015 1.005972223 1.054249254 1.018649476 1.050045077 1.41644744 1.639141159 1.622591762 1.672400442 0.978501688 1 14.16071367 -8.619176031 2.221890829 1.007518537 1.64634199 0.992613679 0.024667345 0.016580316 0.165044744 0.00363385 0.008472126 2.40E-09 8.619176031 0.638823454 AQAEAQQPTFDALRDELR ddPTM_HeLa_Romidepsin_16h_R1 2 AQAEAQQPTFDALRDELR 18 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 114.58 0.0015647 29766000 4740.9 4663 4513.2 4886.1 4730.7 4895.1 4520.1 4472.8 5433.3 4693.6 FALSE FALSE TRUE 4683.116087 4728.645836 4591.750353 5451.053872 4489.274726 4582.318908 4904.037181 4602.213411 4947.33204 4571.659595 1.024379876 1.034339005 1.004394631 1.192357777 0.981979221 1.002331607 1.072703923 1.006683309 1.082174194 1 12.15850227 -10.73443703 0.92867993 1.005739536 1.044741556 0 0.06107484 0.962250314 1.753881541 0.014245273 0.0130027 1.84E-11 10.73443703 0.039002019 AQAVS(ph)EDAGGNEGR ddPTM_HeLa_Romidepsin_16h_R1 2 AQAVSEDAGGNEGR 14 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 0 AQAVS(1)EDAGGNEGR;AQAVS(1)EDAGGNEGR ; 167.92 7.77E-05 20995000 3769.9 3333.8 3333.6 3012.5 3470.6 3205.5 3377.3 3161 4266.9 4030.3 TRUE FALSE FALSE 3723.951009 3380.733324 3391.61991 3360.819424 3293.482331 3000.678895 3664.167778 3252.458548 3885.257777 3925.592225 0.948634192 0.861203388 0.863976622 0.856130548 0.838977189 0.764388842 0.933405093 0.828526847 0.989725258 1 11.9386946 -10.38810752 1.037690291 0.986274803 0.843213895 0.694226962 0.039935793 0.178351881 0.381904966 0.008659009 0.009664813 4.09E-11 10.38810752 -0.143060908 AQAVS(ph)EEEEEEEGK ddPTM_HeLa_Romidepsin_16h_R1 2 AQAVSEEEEEEEGK 14 0 G3V529;Q9GZR7-2;Q9GZR7 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 0 AQAVS(1)EEEEEEEGK;AQAVS(1)EEEEEEEGK ; 224.67 8.15E-33 104419000 6235.4 5784.6 6099.1 3667.3 7230.3 8893.3 7501.3 8811.5 6057.1 6591.5 TRUE FALSE FALSE 6159.400546 5866.035751 6205.252277 4091.330481 6861.310811 8325.046832 8138.460235 9066.44685 5515.337806 6420.25188 0.959370545 0.913676887 0.966512279 0.637253889 1.068698073 1.296685393 1.2676232 1.412163731 0.859053182 1 12.64841418 -8.339510221 3.686228558 0.949411389 1.323708791 0.741172004 0.111624098 0.097885758 2.548610369 0.015783423 0.038136018 4.58E-09 8.339510221 0.374297402 AQAVS(ph)EEEEEEEGKSSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 AQAVSEEEEEEEGKSSSPK 19 1 G3V529;Q9GZR7-2;Q9GZR7 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 0 AQAVS(0.912)EEEEEEEGKS(0.063)S(0.02)S(0.004)PK 87.652 0.001779 68633000 1905.3 2122.5 1797 2332.8 3681.1 3309.2 3559.1 3658.8 2574.3 1906.5 TRUE FALSE FALSE 1882.077471 2152.380611 1828.276031 2602.529312 3493.239731 3097.7528 3861.409865 3764.661605 2344.048161 1856.968855 1.013521291 1.159082773 0.98454857 1.401493248 1.881151491 1.668177036 2.079415524 2.027315426 1.262298048 1 10.8587339 -8.897475336 1.501849331 1.011192755 1.962048709 0.885289599 0.139430318 0.064166681 0.290493399 0.017217101 0.038784157 1.27E-09 8.897475336 0.950855954 SSQPS(ph)PTAVPASDSPPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 SSQPSPTAVPASDSPPTK 18 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 2 0 S(0.001)S(0.002)QPS(0.988)PT(0.009)AVPAS(0.002)DS(0.112)PPT(0.885)K 135.23 0.0048243 7034300 3483.6 2771.9 3540.3 1938.9 2095 1976.4 1334.9 1653.5 3390.2 3580.3 TRUE FALSE FALSE 3441.140543 2810.922881 3601.917436 2163.084741 1988.084332 1850.114419 1448.286373 1701.341414 3086.972021 3487.28329 0.986768283 0.80604948 1.032872049 0.620277896 0.570095449 0.530531725 0.415305053 0.487870148 0.885208274 1 11.76788785 -9.06145847 1.280313166 0.987695298 0.465980049 0.860742061 0.083056562 0.085234208 0.276311171 0.011667517 0.025348879 8.68E-10 9.06145847 -0.521715249 down AQEEAERLEADR ddPTM_HeLa_Romidepsin_16h_R1 2 AQEEAERLEADR 12 1 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 ; ; 123.26 0.0073041 17193300 4019.7 3974.4 3399.9 6952.6 4667.6 5041.8 4770.3 4609.5 4551.8 4269.6 FALSE FALSE TRUE 3970.70635 4030.351708 3459.073833 7756.492325 4429.394955 4719.645252 5175.489163 4742.86861 4144.675608 4158.675176 0.954800792 0.969143185 0.831773025 1.865135409 1.065097601 1.134891534 1.244504306 1.140475851 0.996633647 1 12.02190829 AQEES(ph)S(ph)AMMQWLQKMNKT(ph)ATK ddPTM_HeLa_Romidepsin_16h_R1 1 AQEESSAMMQWLQKMNKTATK 21 2 F6QMI7;E9PHM6;F8W9J4;Q03001-14;Q03001;Q03001-8 F6QMI7 DST Dystonin 3 0 AQEES(1)S(1)AMMQWLQKMNKT(0.531)AT(0.469)K 46.132 0.030146 3550900 411.48 489.95 145.59 361.13 288.97 289.23 194.53 183.36 333.77 279.65 TRUE FALSE FALSE 406.4647235 496.847529 148.1239329 402.8855498 274.2227826 270.7491364 211.0533733 188.6652323 303.9167753 272.3846527 1.492245321 1.824065798 0.543804254 1.479105176 1.006748287 0.993995564 0.774835775 0.692642667 1.115763213 1 8.089501608 -7.970008176 0.9449667 1.251170828 0.624034018 0.270727468 0.32321165 0.940210241 1.169363929 0.053591292 0.467392029 1.07E-08 7.970008176 -0.627136811 AQEK(ac)VLQK ddPTM_HeLa_Romidepsin_16h_R1 1 AQEKVLQK 8 1 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;S4R3J0;Q9UBW5-2;Q9UBW5;P49418-2;P49418;O00499-9;O00499-10 O00499-6;O00499-9 BIN1;BIN2;AMPH Myc box-dependent-interacting protein 1;Bridging integrator 2;Amphiphysin 0 1 AQEK(1)VLQK 126.41 0.0089829 1127300 1154.2 982.18 1064.7 1126.6 1233.9 1545.8 1068 910.93 1005.9 835.13 FALSE TRUE FALSE 1140.132166 996.0071558 1083.230657 1256.862793 1170.929479 1447.028369 1158.715893 937.2863223 915.9297847 813.4332022 1.401629738 1.224448613 1.331677455 1.54513338 1.439490637 1.778914808 1.424475778 1.15225973 1.126004916 1 9.667880069 -12.55474749 0.346104897 0.787671034 1.470141662 0.424176067 0.163732126 2.353251791 0.314625897 0.629646447 0.07035864 2.79E-13 12.55474749 0.682470627 AQENYEGSEEVS(ph)PPQTK ddPTM_HeLa_Romidepsin_16h_R1 3 AQENYEGSEEVSPPQTK 17 0 Q93008;Q93008-3 Q93008 USP9X Probable ubiquitin carboxyl-terminal hydrolase FAF-X 1 0 AQENYEGSEEVS(1)PPQTK;AQENYEGSEEVS(1)PPQTK;AQENYEGSEEVS(0.999)PPQTK ;; 220.78 1.67E-31 10236000 3960.3 4209.6 4531.9 3701.36 4378.6 5144.8 4207 4846.4 4277.6 4223.3 TRUE FALSE FALSE 3912.03034 4268.862859 4610.775818 4129.328659 4155.143703 4816.063884 4564.342475 4986.622938 3895.000743 4113.578057 0.95100428 1.037749327 1.120867467 1.00382893 1.010104499 1.170772456 1.109579644 1.212234913 0.94686443 1 12.0061781 -7.108948255 0.387252788 0.977019759 1.395584873 0.666682105 0.050295192 2.815003678 0.264769412 0.014981995 0.559172645 7.78E-08 7.108948255 0.418565114 AQGAGVTLPPT(ph)PSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 AQGAGVTLPPTPSGSR 16 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 0 AQGAGVTLPPT(0.953)PS(0.044)GS(0.003)R 163.91 2.35E-06 0 1408.9 1613.3 1237.8 1168.4 1713.8 1517.2 1095.5 1334.9 1482.4 1239.7 TRUE FALSE FALSE 1391.727785 1636.01208 1259.34339 1303.495905 1626.338391 1420.255817 1188.551743 1373.523225 1349.810431 1207.492415 1.152576834 1.354883939 1.042941035 1.079506495 1.346872552 1.176202681 0.984314044 1.137500499 1.117862451 1 10.23779841 -11.94704229 0.931344313 1.006234527 1.157854418 0.073592448 0.117033562 0.646187257 1.07669012 0.05918081 0.022084036 1.13E-12 11.94704229 0.151619891 AQGEPVAGHES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AQGEPVAGHESPK 13 0 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;D6RHZ5;H7BXG7;O94979-7;O94979-6;O94979-10;O94979-4;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 0 AQGEPVAGHES(1)PK 135.55 0.0016256 47659000 8080.8 9278 8235.2 3604.7 8586.3 9931.3 8627.4 8616.6 7817.3 8040.4 TRUE FALSE FALSE 7982.308101 9408.615928 8378.530201 4021.492375 8148.109071 9296.721982 9360.211141 8865.907726 7118.101109 7831.509249 1.019255401 1.201379661 1.069848727 0.51350158 1.040426412 1.187092001 1.195198887 1.132081626 0.908905408 1 12.93507465 -8.336363649 5.420248136 0.991632931 1.173475895 0.228427952 0.170281719 0.278028631 14.7186882 0.024308857 0.055588894 4.61E-09 8.336363649 0.181842964 AQGEPVAGHES(ph)PKIPYEK ddPTM_HeLa_Romidepsin_16h_R1 4 AQGEPVAGHESPKIPYEK 18 1 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;D6RHZ5;H7BXG7;O94979-7;O94979-6;O94979-10;O94979-4;H0YAB3 D6REX3 SEC31A Protein transport protein Sec31A 1 0 AQGEPVAGHES(0.944)PKIPY(0.056)EK;AQGEPVAGHES(1)PKIPYEK;AQGEPVAGHES(0.999)PKIPY(0.001)EK;AQGEPVAGHES(0.996)PKIPY(0.004)EK ;;; 119.43 0.00057305 1052780000 19680.6 17862.3 16756.2 21272.4 21846.1 23918 21518.7 23238.7 19819.1 18643.6 TRUE FALSE FALSE 19440.72528 18113.76593 17047.83463 23732.01498 20731.212 22389.71699 23346.49784 23911.07512 18046.43006 18159.23658 1.070569525 0.997496004 0.938796879 1.306883958 1.141634556 1.232965763 1.285654148 1.316744512 0.993787926 1 14.14841593 -9.256889929 24.99904564 1.024468774 1.250661298 0.831698322 0.057170777 135.113271 742440.8984 0.009081117 0.014734124 5.53E-10 9.256889929 0.226192524 AQGPAASAEEPKPVEAPAANS(ph)DQTVTVKE ddPTM_HeLa_Romidepsin_16h_R1 1 AQGPAASAEEPKPVEAPAANSDQTVTVKE 29 2 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 AQGPAAS(0.221)AEEPKPVEAPAANS(0.72)DQT(0.044)VT(0.014)VKE 69.444 0.00010394 7882400 1811.2 2179 1956.2 1744.9 1858.1 2488.7 1833 2453.5 2310.9 1884.1 TRUE FALSE FALSE 1789.124398 2209.676019 1990.24684 1946.653548 1763.274223 2329.680102 1988.694974 2524.488152 2104.207316 1835.15081 0.974919548 1.204084158 1.084514051 1.060759441 0.960833417 1.269476104 1.083668417 1.375629805 1.146612749 1 10.84168291 -4 0.336759903 0.994069118 4.494417508 0.311286205 0.105687139 29.83835936 0.377318915 0.028133794 66.34900403 1.00E-04 4 3.50034839 AQHEDQVEQYK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AQHEDQVEQYKK 12 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 1 ; AQHEDQVEQYK(1)K;AQHEDQVEQYK(1)K 196.02 1.70E-10 15532900 4732.3 5090 5047.5 3896.1 14242.1 11455.3 11446 9684.2 13209.8 10461.4 FALSE TRUE FALSE 4674.620907 5161.657154 5135.34962 4346.585414 13515.27249 10723.3433 12418.22295 9964.397048 12028.2824 10189.61132 0.458763417 0.50656075 0.503978951 0.426570286 1.326377628 1.052380014 1.218714097 0.977897658 1.180445654 1 13.3148114 -8.756275261 24.99999888 0.678741897 1.14265732 0.462398763 0.245339943 94.35049151 456754.6734 0.037418278 0.073060969 1.75E-09 8.756275261 0.463915423 AQIHDLVLVGGS(ph)TR ddPTM_HeLa_Romidepsin_16h_R1 2 AQIHDLVLVGGSTR 14 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 1 0 AQIHDLVLVGGS(0.834)T(0.166)R;AQIHDLVLVGGS(0.728)T(0.272)R ; 68.82 0.025236 5668000 3101.1 3597 3712.5 2822.3 3234.3 4170.4 4156.5 3611.2 4005.4 3989.8 TRUE FALSE FALSE 3063.3026 3647.63866 3777.114505 3148.627605 3069.241602 3903.924899 4509.553006 3715.684374 3647.146992 3886.144421 0.788262676 0.938626635 0.971943936 0.810218886 0.789790926 1.004575352 1.160418275 0.956136461 0.938500117 1 11.9241238 -8.011476673 23.54297034 0.893252307 1.064332258 0.405704587 0.084412155 206.8112883 424254.7799 0.013935909 0.038057255 9.74E-09 8.011476673 0.171079952 AQIS(ph)SPNLR ddPTM_HeLa_Romidepsin_16h_R1 1 AQISSPNLR 9 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 0 AQIS(0.5)S(0.5)PNLR 134.57 0.0068923 27826000 4272.7 3844.2 3486.4 2307.1 3085.4 2689.7 2575.8 1958.2 4039.3 4082 TRUE FALSE FALSE 4220.622689 3898.318749 3547.07933 2573.857757 2927.940525 2517.836851 2794.588388 2014.857427 3678.014891 3975.949052 1.061538424 0.980475026 0.892134 0.647356826 0.736412989 0.63326688 0.702873289 0.50676138 0.925065901 1 11.95708355 -9.434757688 1.755964728 1.029094876 0.643365042 0.854624928 0.067663307 0.072058291 0.438947848 0.009395651 0.015604149 3.67E-10 9.434757688 -0.385729834 AQLDYVDLYLIHSPMSLKPGEELS(ph)PTDENGK ddPTM_HeLa_Romidepsin_16h_R1 2 AQLDYVDLYLIHSPMSLKPGEELSPTDENGK 31 1 S4R3Z2;A0A0A0MSS8;P42330;S4R3D5 S4R3Z2 AKR1C3 Aldo-keto reductase family 1 member C3 1 0 AQLDYVDLYLIHS(0.014)PMS(0.066)LKPGEELS(0.717)PT(0.203)DENGK;AQLDYVDLYLIHS(0.065)PMS(0.329)LKPGEELS(0.448)PT(0.158)DENGK ; 93.596 1.31E-11 83015000 3537.3 3094.9 3455 2628.2 4750.1 4124.2 3755.4 4940.9 4008.6 2851.44 TRUE FALSE FALSE 3494.186027 3138.470083 3515.132826 2932.08485 4507.684672 3860.67693 4074.383582 5083.857146 3650.060776 2777.359178 1.25809656 1.130019519 1.265638544 1.055709637 1.623011063 1.39005317 1.466999161 1.830464416 1.314219927 1 11.43949805 -4 0.233601852 1.0501143 5.071284257 0.607884714 0.15239324 19.01573189 0.232533085 0.085895327 29.70041178 1.00E-04 4 4.021169956 AQLEPVAS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 3 AQLEPVASPAK 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 AQLEPVAS(1)PAK;AQLEPVAS(1)PAK;AQLEPVAS(1)PAK ;; 141.54 0.0028791 1780240000 21405.8 17889.3 24659.2 18977.7 19058.6 22275.6 18206 19186 20898.3 18627.7 TRUE FALSE FALSE 21144.89788 18141.14603 25088.38303 21171.99097 18085.96852 20852.26105 19752.41719 19741.11664 19029.10371 18143.74967 1.165409481 0.9998565 1.382756238 1.166902727 0.996815369 1.149280685 1.088662352 1.088039518 1.048796641 1 14.14718502 -12.36791606 0.969750841 0.996001883 1.132630823 0.136272321 0.103471285 0.805396314 1.289875457 0.080006981 0.018403983 4.29E-13 12.36791606 0.136628941 AQLEPVAS(ph)PAKKPK ddPTM_HeLa_Romidepsin_16h_R1 1 AQLEPVASPAKKPK 14 2 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 AQLEPVAS(1)PAKKPK 150.59 0.0001464 0 2469.8 2818 2683.1 3634.7 2700.1 3438.3 2601.8 2571.6 2846 2495.7 TRUE FALSE FALSE 2439.697128 2857.671878 2729.79823 4054.961116 2562.303822 3218.603727 2822.796827 2646.005189 2591.446632 2430.861354 1.003634832 1.175579954 1.1229757 1.668116986 1.054072383 1.324058948 1.161233166 1.088505185 1.06606106 1 11.2472519 -10.06551849 2.068036843 1.000268526 1.248879553 0.248746259 0.164797986 0.267904572 2.238397515 0.027217443 0.034723153 8.60E-11 10.06551849 0.248611027 AQLGGPEAAKS(ph)DETAAK ddPTM_HeLa_Romidepsin_16h_R1 3 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 0 AQLGGPEAAKS(0.913)DET(0.087)AAK;AQLGGPEAAKS(0.985)DET(0.015)AAK;AQLGGPEAAKS(0.986)DET(0.014)AAK ;; 85.969 0.0047004 107227100 6483.4 6366.8 5882.6 5861.5 5863.7 5643.2 5225.61 5736.47 7431.6 6390.7 TRUE FALSE FALSE 6404.377827 6456.431978 5984.984185 6539.234209 5564.453509 5282.617733 5669.473183 5902.445709 6766.899083 6224.668693 1.028870474 1.037233031 0.961494415 1.050535303 0.893935691 0.848658458 0.910807219 0.948234517 1.08710992 1 12.60378134 -8.751266777 24.99289982 1.013878838 0.897455206 0.707442059 0.039450901 74.54655135 183150.9098 0.004570171 0.009057385 1.77E-09 8.751266777 -0.116423632 AQLGGPEAAKSDET(ph)AAK ddPTM_HeLa_Romidepsin_16h_R1 1 AQLGGPEAAKSDETAAK 17 1 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 0 AQLGGPEAAKS(0.236)DET(0.764)AAK 147.49 0.00056507 11151000 2423.4 2444.6 2268.1 2330.8 2021.8 2290.4 1886.8 2100.8 2604.5 2346.1 TRUE FALSE FALSE 2393.862669 2479.015143 2307.575329 2600.298063 1918.620002 2144.050832 2047.064745 2161.583333 2371.546997 2285.147984 1.047574462 1.084837901 1.009814395 1.137912328 0.839604269 0.938254698 0.89581277 0.945927069 1.037808936 1 11.15807188 -8.751214947 24.99978509 1.034347638 0.906633142 0.692910705 0.047325909 101.9183678 249199.1287 0.006815198 0.013508573 1.77E-09 8.751214947 -0.127714496 AQLGINEDHS(ph)EGDEK ddPTM_HeLa_Romidepsin_16h_R1 1 AQLGINEDHSEGDEK 15 0 F8WAN1;Q69YQ0-2;Q69YQ0;C9J8U1;A0A494C1J1;C9JLY8 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 AQLGINEDHS(1)EGDEK 81.788 0.011989 5403000 2182 2390 2445.2 1215.2 2283 2527.9 1697.2 2099.3 2407 2573.9 TRUE FALSE FALSE 2155.404945 2423.646483 2487.75768 1355.707142 2166.489991 2366.375348 1841.360126 2160.039933 2191.711892 2507.029707 0.859744477 0.966740233 0.992312805 0.540762296 0.864166063 0.943896014 0.734478782 0.861593274 0.874226534 1 11.29176338 AQLS(ph)PGIYDDTSAR ddPTM_HeLa_Romidepsin_16h_R1 2 AQLSPGIYDDTSAR 14 0 E7EVK1;A0A088AWL3;O75376;O75376-2 E7EVK1 NCOR1 Nuclear receptor corepressor 1 1 0 AQLS(0.672)PGIYDDT(0.324)S(0.003)AR;AQLS(1)PGIYDDTSAR ; 183.73 1.57E-07 260030000 6073.9 6920 6819.6 5068.1 7114.6 6050.9 5728.1 6300.9 7621.5 6854.1 TRUE FALSE FALSE 5999.868971 7017.419942 6938.292277 5654.097568 6751.515414 5664.267018 6214.644671 6483.2066 6939.813952 6676.029494 0.898718164 1.051136749 1.039284246 0.846925193 1.011307008 0.848448471 0.930889337 0.97111713 1.039512177 1 12.70477461 -9.263746984 24.99880368 0.965893787 0.923150349 0.176341225 0.067283681 432.5151425 4685555.272 0.010403142 0.016374871 5.45E-10 9.263746984 -0.042743438 AQLSVQTS(ph)PVPTPDPK ddPTM_HeLa_Romidepsin_16h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 AQLSVQT(0.103)S(0.897)PVPTPDPK 180.56 2.21E-08 6390600 3531.2 4135.4 3306.9 3549 5418.7 6317.1 5065.9 6386.4 4169.9 3821.3 TRUE FALSE FALSE 3488.160376 4193.61827 3364.455207 3959.352079 5142.163519 5913.457698 5496.19742 6571.180408 3796.9337 3722.022075 0.937168105 1.126704298 0.903932094 1.063763728 1.381551054 1.588775558 1.476669753 1.765486683 1.020126593 1 11.8618709 -8.6293714 1.925669092 0.977303061 1.60753037 0.909304035 0.086578174 0.06139339 0.458195221 0.012109677 0.029395061 2.35E-09 8.6293714 0.630227309 AQLSVQTSPVPT(ph)PDPK ddPTM_HeLa_Romidepsin_16h_R1 1 AQLSVQTSPVPTPDPK 16 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 AQLSVQT(0.002)S(0.001)PVPT(0.997)PDPK 91.093 0.024252 7644400 4273 5016.8 4103.5 4175.7 6379.5 7765.4 6353.9 7542.5 5117.3 4630.1 TRUE FALSE FALSE 4220.919032 5087.426642 4174.919696 4658.514081 6053.93031 7269.216002 6893.600107 7760.730337 4659.595871 4509.809335 0.935941793 1.128080206 0.925741952 1.032973622 1.342391631 1.6118677 1.528579059 1.720855531 1.033213497 1 12.13885073 -8.569692771 2.008909887 0.978571359 1.622086802 0.937687868 0.070967695 0.049186668 0.396285038 0.010010803 0.024869975 2.69E-09 8.569692771 0.643515443 AQLYLPST(ph)SPPHEGLDGFAQELSR ddPTM_HeLa_Romidepsin_16h_R1 2 AQLYLPSTSPPHEGLDGFAQELSR 24 0 I3L465;I3L1Z8;I3L1A6;Q8N137-4;Q8N137-5;Q8N137;Q8N137-3;Q8N137-2 I3L465 CNTROB Centrobin 1 0 AQLYLPS(0.003)T(0.54)S(0.457)PPHEGLDGFAQELSR;AQLY(0.069)LPS(0.124)T(0.461)S(0.346)PPHEGLDGFAQELSR ; 102.94 1.25E-05 14306400 2534.1 2692.4 2490.9 2919.6 2932 2538 2455.9 2791.2 3434.5 2891.2 TRUE FALSE FALSE 2503.213414 2730.303678 2534.25307 3257.177889 2782.369099 2375.829991 2664.504085 2871.958968 3127.309718 2816.086207 0.888898006 0.969538387 0.899920273 1.156632876 0.988026962 0.8436638 0.946172769 1.019840572 1.110516329 1 11.45947578 -7.25639441 22.03203803 0.954496859 1.019840716 0 0.093945286 270.5007165 1181074.952 0.011447152 0.121121211 5.54E-08 7.25639441 0.065343857 AQPFGFIDS(ph)DTDAEEER ddPTM_HeLa_Romidepsin_16h_R1 2 AQPFGFIDSDTDAEEER 17 0 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 AQPFGFIDS(0.886)DT(0.114)DAEEER;AQPFGFIDS(0.999)DT(0.001)DAEEER ; 235.11 2.16E-46 11710800 2408.04 1845.14 1834.81 1121.71 1656.06 1689.7 1725.35 1595.67 2590.2 2247.32 TRUE FALSE FALSE 2378.689882 1871.115929 1866.744098 1251.407388 1571.545079 1581.733623 1871.901186 1641.838194 2358.526025 2188.934302 1.086688568 0.854806801 0.85280956 0.571697098 0.717949861 0.72260443 0.855165541 0.750062801 1.077476844 1 11.09601294 -9.936547171 2.094907805 1.040519768 0.734333146 0.762833857 0.077219395 0.110903356 0.980749376 0.01379037 0.018461105 1.16E-10 9.936547171 -0.306186621 AQPGS(ph)PESSGQPK ddPTM_HeLa_Romidepsin_16h_R1 2 AQPGSPESSGQPK 13 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 0 AQPGS(0.923)PES(0.038)S(0.038)GQPK;AQPGS(0.986)PES(0.013)S(0.001)GQPK ; 125.47 0.0036395 40726000 10643.6 9420.2 9792.3 9066.2 7697.5 6026.9 5537.6 5418.5 11039.2 9387.8 TRUE FALSE FALSE 10513.87171 9552.817823 9962.730874 10114.4767 7304.667852 5641.800541 6007.963606 5575.275749 10051.8263 9143.903603 1.149823113 1.044719874 1.089548983 1.106144284 0.798856612 0.617001314 0.657045816 0.609725998 1.099292681 1 13.15859448 -8.587230379 3.058633619 1.074317773 0.63413167 0.959996891 0.042055761 0.048246481 0.912999142 0.008808546 0.019386824 2.59E-09 8.587230379 -0.440186103 AQPGSPES(ph)SGQPK ddPTM_HeLa_Romidepsin_16h_R1 2 AQPGSPESSGQPK 13 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 0 AQPGS(0.315)PES(0.437)S(0.249)GQPK;AQPGS(0.26)PES(0.717)S(0.023)GQPK ; 173.33 4.61E-05 39446000 14813.7 14971.5 14563.3 12537.1 11685.2 9512 8078.5 7768.8 15218 15008.2 TRUE FALSE FALSE 14633.14493 15182.26917 14816.76813 13986.69849 11088.86064 8904.213899 8764.687588 7993.577971 13856.86397 14618.2848 1.001016544 1.038580749 1.013577744 0.956794773 0.758560993 0.609114819 0.599570176 0.546820511 0.947913121 1 13.83548643 -8.571296914 1.785036324 1.005674456 0.575250396 0.981863351 0.025179033 0.022500465 0.142596874 0.002820851 0.007338716 2.68E-09 8.571296914 -0.43042406 AQPSSS(ph)EDELDNVFFK ddPTM_HeLa_Romidepsin_16h_R1 2 AQPSSSEDELDNVFFK 16 0 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 AQPS(0.017)S(0.064)S(0.919)EDELDNVFFK;AQPSS(0.052)S(0.948)EDELDNVFFK ; 231.86 1.38E-45 14866200 7198.8 6429.4 6600.3 4418.1 5408.9 4960 4283 5145.5 7117 6043.9 TRUE FALSE FALSE 7111.058257 6519.913262 6715.175453 4928.94151 5132.86365 4643.072008 4646.797913 5294.376924 6480.437695 5886.878607 1.207950551 1.107533159 1.140702213 0.837275887 0.871916 0.788715433 0.78934835 0.899352149 1.100827472 1 12.52328716 -9.256177081 24.3705468 1.104439756 0.833877939 0.851391602 0.057208028 125.527804 581338.1353 0.012603912 0.02049035 5.54E-10 9.256177081 -0.270561817 AQQELEEQTRR ddPTM_HeLa_Romidepsin_16h_R1 2 AQQELEEQTRR 11 1 P26038 P26038 MSN Moesin 0 0 ; ; 96.64 0.0026161 0 4435.8 4187.1 3896.8 3998.7 4641.5 5074.1 3870.6 4126.7 4842.7 4268.2 FALSE FALSE TRUE 4381.734763 4246.046104 3964.622169 4461.048508 4404.626935 4749.881386 4199.368667 4246.099554 4409.556783 4157.311549 1.053982775 1.021344216 0.953650484 1.073060909 1.05948926 1.142536789 1.010116422 1.021357073 1.060675086 1 12.02143515 AQQELVPPQQQAS(ph)PPQLPK ddPTM_HeLa_Romidepsin_16h_R1 2 AQQELVPPQQQASPPQLPK 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 AQQELVPPQQQAS(1)PPQLPK;AQQELVPPQQQAS(1)PPQLPK ; 85.387 0.0025279 63872000 8367.7 7350.5 7225.1 7356.4 7816.6 8452 7990.2 8176.6 8925.2 7964.1 TRUE FALSE FALSE 8265.711254 7453.980532 7350.849835 8206.981581 7417.689734 7911.944478 8668.887389 8413.17702 8126.907758 7757.191534 1.065554617 0.960912271 0.947617421 1.05798362 0.956233928 1.01994961 1.117529115 1.084564818 1.047661093 1 12.92131871 -7.770096784 23.98848678 1.016621791 1.101046968 0.435139829 0.041726719 81.25145921 225141.6084 0.006323942 0.019439376 1.70E-08 7.770096784 0.084425177 AQS(ph)LEPYGTGLR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSLEPYGTGLR 12 0 K7ERU2;Q63ZY3-3;Q63ZY3;Q63ZY3-2 K7ERU2 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 0 AQS(1)LEPYGTGLR 95.854 0.020595 4513100 733.27 1069.8 491.7 435.19 913.95 954.58 822.19 851.17 670.28 735.03 TRUE FALSE FALSE 724.3326232 1084.860672 500.2578322 485.5087154 867.3077211 893.5854188 892.0267981 875.797261 610.3284781 715.9338146 1.011731264 1.515308609 0.698748714 0.678147484 1.211435615 1.248139703 1.245962657 1.223293611 0.852492878 1 9.483682412 -8.5588321 24.99871629 0.99982831 1.238144455 0.260000877 0.219562846 197.1699592 137093.4771 0.030914656 0.061829459 2.76E-09 8.5588321 0.238316145 AQS(ph)PGAVEEILDR ddPTM_HeLa_Romidepsin_16h_R1 2 AQSPGAVEEILDR 13 0 H7BXT7;E9PHY4;A0A0C4DH16;B8ZZS0;Q9NYM9 H7BXT7 BET1L BET1-like protein 1 0 AQS(1)PGAVEEILDR;AQS(1)PGAVEEILDR ; 185.63 1.41E-07 17442600 2727.4 2583 2797.8 1875.31 3758.8 4783.2 3255.7 4982.2 2554.3 2656.8 TRUE FALSE FALSE 2694.1574 2619.363542 2846.494535 2092.142166 3566.97441 4477.568957 3532.239077 5126.352096 2325.837011 2587.775953 1.041109218 1.012206462 1.099977196 0.808471137 1.378393831 1.730276901 1.364970979 1.980987608 0.898778354 1 11.337497 -8.543192193 4.362028831 1.013342146 1.650007979 0.796038464 0.162507541 0.061038208 2.770151582 0.020302628 0.043351223 2.86E-09 8.543192193 0.636665832 ADQEQQDPLEYLQS(ph)DEEDDEKR ddPTM_HeLa_Romidepsin_16h_R1 1 ADQEQQDPLEYLQSDEEDDEKR 22 1 Q7RTV3 Q7RTV3 ZNF367 Zinc finger protein 367 1 0 ADQEQQDPLEY(0.124)LQS(0.876)DEEDDEKR 109.98 3.63E-05 10345000 2290.5 2426.7 2444.4 1351.9 821.58 918.66 737.34 885.96 2870.5 2670.7 TRUE FALSE FALSE 2262.582505 2460.863146 2486.943757 1508.213039 779.6517069 859.9605908 799.9696412 911.5938548 2613.755291 2601.314829 0.869784188 0.946007426 0.95603336 0.579788737 0.299714474 0.330586894 0.307525115 0.350435804 1.004782375 1 11.3450253 -9.057579071 2.639778923 0.939767653 0.321122028 0.979732465 0.043005784 0.033579349 0.462906617 0.008312611 0.015188563 8.76E-10 9.057579071 -0.618645625 down AQS(ph)SPASATFPVSVQEPPTKPR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSSPASATFPVSVQEPPTKPR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 0 AQS(0.722)S(0.231)PAS(0.047)AT(0.001)FPVSVQEPPTKPR 136.74 3.19E-05 51637000 2197.8 2092.5 2272.9 1764.1 1926 2082.1 1492.3 2095.6 2721.5 2325 TRUE FALSE FALSE 2171.012368 2121.95827 2312.458871 1968.073542 1827.709033 1949.06053 1619.055925 2156.23288 2478.082224 2264.596165 0.958675283 0.937013982 1.021135206 0.869061589 0.807079453 0.860665826 0.714942448 0.952148958 1.094271139 1 11.14503809 -9.104101419 4.42565725 0.978604356 0.828011399 0.569380618 0.069046269 0.108433971 3.553486595 0.008058297 0.013712426 7.87E-10 9.104101419 -0.150592957 ASAS(ph)PGENDSGTGGEEPQR ddPTM_HeLa_Romidepsin_16h_R1 2 ASASPGENDSGTGGEEPQR 19 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 AS(0.26)AS(0.738)PGENDS(0.002)GTGGEEPQR;AS(0.115)AS(0.885)PGENDSGTGGEEPQR ; 171.04 1.23E-07 7365000 2468.76 1879.01 1724.19 1743.18 876.55 809.48 1030.02 845.2 2219.09 2195.02 TRUE FALSE FALSE 2438.669804 1905.462752 1754.198804 1944.734674 831.8163826 757.7568405 1117.509873 869.6545285 2020.609033 2137.993064 1.14063504 0.891238977 0.820488538 0.909607569 0.389064117 0.354424368 0.522691066 0.406762091 0.945096159 1 11.06204146 -9.048518276 1.139942336 1.057128543 0.401804548 0.831870722 0.112916008 0.121097232 0.31084234 0.019147489 0.044178241 8.94E-10 9.048518276 -0.655323995 down AQSNGSGNGSDSEMDT(ph)SSLER ddPTM_HeLa_Romidepsin_16h_R1 2 AQSNGSGNGSDSEMDTSSLER 21 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 0 AQSNGSGNGS(0.005)DS(0.094)EMDT(0.691)S(0.168)S(0.042)LER;AQS(0.003)NGS(0.06)GNGS(0.293)DS(0.174)EMDT(0.436)S(0.027)S(0.007)LER ; 77.42 0.009341 23070600 3643.2 3442.2 3364 2559 3357.7 3299.9 2658.3 3146.6 3978.5 3425.8 TRUE FALSE FALSE 3598.795277 3490.659382 3422.549009 2854.88362 3186.34404 3089.04704 2884.095936 3237.641906 3622.652996 3336.797222 1.078517823 1.046110731 1.025698831 0.855576 0.9549109 0.925752101 0.864330597 0.970284285 1.085667709 1 11.7042483 -9.359079091 6.626181049 1.038533504 0.914545631 0.729538249 0.040368529 0.108313881 6.287480912 0.006409844 0.009818687 4.37E-10 9.359079091 -0.123987874 NKES(ph)SLLVSELEDTTEK ddPTM_HeLa_Romidepsin_16h_R1 1 NKESSLLVSELEDTTEK 17 1 Q15058 Q15058 KIF14 Kinesin-like protein KIF14 1 0 NKES(0.499)S(0.499)LLVS(0.002)ELEDTTEK 69.581 0.0041853 0 1472.1 1397.3 1041.9 1080 1028 770.23 753.26 672.82 1831.8 1617.4 TRUE FALSE FALSE 1454.157479 1416.971226 1060.033832 1204.874682 975.537324 721.0147888 817.2418856 692.2869852 1667.95922 1575.379715 0.923052052 0.899447424 0.672875131 0.764815409 0.619239485 0.457676827 0.51875867 0.439441348 1.05876647 1 10.62148389 -9.034273724 0.529293756 0.987718726 0.399544982 0.930272282 0.057041065 0.171124938 0.084791081 0.012789554 0.045773277 9.24E-10 9.034273724 -0.588173744 down AQSSPAAPAS(ph)LSAPEPASQAR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;Q8WUI4-10;H0YI15 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 0 AQS(0.006)S(0.079)PAAPAS(0.716)LS(0.2)APEPASQAR 158.45 3.42E-16 0 865.63 958.23 865.43 1051.2 1546 1090.7 888.79 1417.3 904.49 977.51 TRUE FALSE FALSE 855.0793686 971.7199871 880.4924461 1172.74469 1467.101851 1021.00779 964.2838004 1458.307339 823.5901491 952.1141493 0.898084929 1.020591898 0.924776138 1.231726985 1.540888613 1.072358594 1.012781714 1.531651788 0.865011984 1 9.894990739 -9.225016359 6.016704769 0.954958444 1.268131905 0.513534444 0.163343635 0.132808387 14.24064102 0.023646235 0.039034121 5.96E-10 9.225016359 0.313173461 AQSTDS(ph)LGTSGSLQSK ddPTM_HeLa_Romidepsin_16h_R1 3 AQSTDSLGTSGSLQSK 16 0 I3L456;Q15276-2;Q15276 I3L456 RABEP1 Rab GTPase-binding effector protein 1 1 0 AQS(0.312)T(0.31)DS(0.372)LGT(0.004)S(0.001)GSLQS(0.001)K;AQST(0.001)DS(0.892)LGT(0.081)S(0.025)GS(0.001)LQSK;AQST(0.003)DS(0.454)LGT(0.138)S(0.311)GS(0.093)LQSK ;; 168.55 1.54E-05 108840700 6728.9 6776.9 6247.4 4979.71 6191.4 6904.5 5261.4 6168.2 7175.2 6807.2 TRUE FALSE FALSE 6646.885579 6872.305376 6356.133376 5555.4875 5875.429755 6463.324733 5708.303185 6346.667135 6533.432141 6630.347963 1.00249423 1.036492416 0.958642504 0.837887775 0.886141993 0.974809281 0.860935688 0.95721479 0.985382996 1 12.69486887 -9.514368224 10.24176708 1.003577095 0.903448884 0.597641509 0.039770348 0.109944896 120.0221349 0.005700344 0.00836107 3.06E-10 9.514368224 -0.100128211 AQSTDSLGTSGS(ph)LQSK ddPTM_HeLa_Romidepsin_16h_R1 1 AQSTDSLGTSGSLQSK 16 0 I3L456;Q15276-2;Q15276 I3L456 RABEP1 Rab GTPase-binding effector protein 1 1 0 AQSTDS(0.004)LGT(0.034)S(0.09)GS(0.872)LQSK 137.4 0.0011143 12571000 1238.5 1072.2 1224.5 996.65 1079.7 922.7 863.99 1221.4 1233.6 1118.3 TRUE FALSE FALSE 1223.404686 1087.29446 1245.811909 1111.887362 1024.59888 863.7424479 937.377289 1256.739282 1123.263726 1089.246405 1.123166145 0.998207986 1.143737453 1.020785892 0.940649311 0.792972503 0.860574141 1.153769502 1.031230144 1 10.08911464 -8.813628332 3.745300591 1.060622903 0.919754239 0.255265478 0.096978664 0.213198815 6.124948428 0.014543163 0.028124407 1.54E-09 8.813628332 -0.140868664 AQT(ph)PPGPSLSGSK ddPTM_HeLa_Romidepsin_16h_R1 2 AQTPPGPSLSGSK 13 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AQT(0.989)PPGPS(0.01)LS(0.002)GSK;AQT(0.474)PPGPS(0.474)LS(0.045)GS(0.007)K ; 134.37 0.0036218 466030000 18078.1 16867.1 16590.1 10678.8 16086.9 17367.9 15137.3 16843.2 17519.6 16822.5 TRUE FALSE FALSE 17857.75716 17104.55548 16878.84373 11913.5331 15265.92546 16258.14724 16423.06188 17330.53142 15952.6031 16385.44902 1.08985461 1.043886893 1.03011176 0.72708005 0.931675747 0.992230803 1.002295504 1.05767815 0.973583517 1 14.00012759 -9.48978905 24.9969479 1.043405811 0.940813738 0.186043496 0.086465915 718.8543349 543045.1413 0.013623636 0.020801599 3.24E-10 9.48978905 -0.102592072 AQT(ph)PPISSLPTSPSDEVGR ddPTM_HeLa_Romidepsin_16h_R1 1 AQTPPISSLPTSPSDEVGR 19 0 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 AQT(0.915)PPIS(0.056)S(0.016)LPT(0.01)S(0.001)PSDEVGR 94.973 0.0053593 6787000 2323.3 2023 2144.3 1891.5 2244.9 2227.3 1795.6 2401.3 2125.8 2247.9 TRUE FALSE FALSE 2294.982726 2051.479847 2181.620642 2110.20413 2130.334376 2084.982718 1948.118219 2470.777827 1935.663124 2189.499234 1.048176994 0.936963035 0.996401647 0.963783909 0.972977904 0.952264648 0.88975515 1.128467089 0.884066591 1 11.09638523 -10.26899227 24.7962819 1.022750247 0.972962438 0 0.073389644 755.8399789 2481431.376 0.009348821 0.010796805 5.38E-11 10.26899227 -0.049787808 AQTLPT(ph)SVVTITSESSPGKR ddPTM_HeLa_Romidepsin_16h_R1 1 AQTLPTSVVTITSESSPGKR 20 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 AQT(0.013)LPT(0.744)S(0.243)VVTITSESSPGKR 158.11 3.38E-08 56225000 1456.7 2172.1 1465 1989.1 1697.8 1176.4 1139.8 1494.4 1725.2 1516.7 TRUE FALSE FALSE 1438.94518 2202.678881 1490.49771 2219.089101 1611.154931 1101.231837 1236.614584 1537.638106 1570.893791 1477.295915 0.97403991 1.491020762 1.008936459 1.502129044 1.090610834 0.745437542 0.83707981 1.04084638 1.063357568 1 10.52874312 -8.283274068 23.64222277 1.073324935 0.870717095 0.218571306 0.205886204 558.7102781 604960.9822 0.031439594 0.07037459 5.21E-09 8.283274068 -0.20260784 AQTLPTSVVTITSES(ph)SPGKR ddPTM_HeLa_Romidepsin_16h_R1 2 AQTLPTSVVTITSESSPGKR 20 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 AQTLPTSVVTIT(0.001)S(0.044)ES(0.718)S(0.238)PGKR;AQTLPTSVVTITS(0.008)ES(0.496)S(0.496)PGKR ; 183.75 6.84E-14 2013940000 5933.7 5904.4 5259.8 5687.3 5899.6 5379.1 4143.3 4305.4 6270.5 5764.5 TRUE FALSE FALSE 5861.377782 5987.522298 5351.344613 6344.892386 5598.521398 5035.39287 4495.231799 4429.969956 5709.650775 5614.737459 1.043927312 1.066393993 0.953089018 1.130042577 0.997111875 0.896817154 0.800613 0.788989688 1.01690432 1 12.45500285 -8.052836095 2.198151307 1.027200471 0.791148474 0.826872834 0.043896611 0.090759342 0.845934534 0.006195051 0.022540432 8.85E-09 8.052836095 -0.236051997 AQTLPTSVVTITSESS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 AQTLPTSVVTITSESSPGK 19 0 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 AQTLPTSVVTITSES(0.226)S(0.774)PGK;AQTLPTSVVTITSES(0.23)S(0.769)PGK ; 319.09 1.03E-166 36654000 9534.1 9215.7 10035 6775.8 8788.7 8195.6 7176 7301.4 10200.3 10473.2 TRUE FALSE FALSE 9417.894722 9345.438866 10209.65497 7559.249877 8340.179844 7671.92761 7785.529261 7512.654489 9287.959621 10201.10475 0.923223018 0.916120272 1.000838165 0.74102267 0.81757614 0.75206831 0.76320452 0.736454989 0.910485663 1 13.31643778 -9.258568955 24.99121392 0.961022954 0.764657153 0.867426845 0.036631313 66.24347804 576744.5517 0.00595042 0.009586007 5.51E-10 9.258568955 -0.196365801 AQTPPGPSLS(ph)GSKSPCPQEK ddPTM_HeLa_Romidepsin_16h_R1 1 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AQTPPGPS(0.004)LS(0.753)GS(0.201)KS(0.042)PCPQEK 73.574 0.0027425 57650000 5588.7 4994.9 4664.3 159.68 2967.1 2751.2 3013.7 3590.1 5517.5 5555.1 TRUE FALSE FALSE 5520.582775 5065.218333 4745.480185 178.1429529 2815.677815 2575.407199 3269.683603 3693.973879 5024.000981 5410.777701 1.020293769 0.936134991 0.877042164 0.032923724 0.5203832 0.47597727 0.604290877 0.682706643 0.928517352 1 12.40162025 -9.490511518 15.98929461 0.999690405 0.472962851 0.692856593 0.163297647 3.374708741 1666.771637 0.024278391 0.036977727 3.23E-10 9.490511518 -0.526727554 AQTPPGPSLSGSKS(ph)PCPQEK ddPTM_HeLa_Romidepsin_16h_R1 1 AQTPPGPSLSGSKSPCPQEK 20 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 AQTPPGPS(0.047)LS(0.173)GS(0.173)KS(0.607)PCPQEK 55.881 0.012886 30428000 2953.7 3127.4 2493.9 156.13 1977 1810 1793 2033.6 3406.8 3422.4 TRUE FALSE FALSE 2917.699168 3171.427619 2537.305283 174.1824852 1876.106313 1694.346842 1945.297375 2092.439008 3102.087276 3333.485555 0.87526978 0.951384839 0.761156826 0.052252359 0.562806193 0.508280841 0.583562563 0.627703037 0.930583686 1 11.70281576 -9.51032063 17.15066487 0.936229525 0.473592429 0.685261955 0.151847842 4.151708345 5669.5495 0.023469203 0.034713607 3.09E-10 9.51032063 -0.462637096 AQTSTDAPTSAPSAPPS(ph)TPTPSAGKR ddPTM_HeLa_Romidepsin_16h_R1 1 AQTSTDAPTSAPSAPPSTPTPSAGKR 26 1 Q8IWZ8;B4DVK3;V9GZ08;Q8IWZ8-2 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 0 AQTSTDAPTSAPSAPPS(0.475)T(0.475)PT(0.037)PS(0.012)AGKR 67.655 0.00017377 3565200 818.15 835.82 751.31 956.41 1047.3 1402.3 1221.9 1187.3 948.67 641.06 TRUE FALSE FALSE 808.1780731 847.5866959 764.3862354 1066.994624 993.852373 1312.697556 1325.688156 1221.652652 863.8185792 624.4051688 1.294316757 1.357430621 1.224183068 1.708817732 1.591678645 2.102316927 2.123121687 1.956506309 1.383426375 1 9.28633867 -8.694300614 0.429496786 1.067822769 2.330506684 0.802163229 0.1639541 0.420746066 0.113829619 0.042132816 0.228020174 2.02E-09 8.694300614 1.262683916 AQYDELAR ddPTM_HeLa_Romidepsin_16h_R1 2 AQYDELAR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 0 ; ; 195.06 1.43E-16 49131000 10450.7 9874.8 9999.1 6167.4 11231.3 11134.1 9310.3 9537.2 10617.4 8655.6 FALSE FALSE TRUE 10323.32285 10013.81769 10173.13014 6880.503806 10658.12485 10422.66694 10101.11665 9813.143835 9667.753152 8430.726264 1.224487965 1.1877764 1.206673046 0.816122312 1.264200084 1.23627154 1.198131256 1.163973723 1.14672839 1 13.0414412 -12.43381752 1.141933993 0.999206772 1.16586689 0.023338635 0.127657702 0.636914528 1.474417862 0.084560338 0.020782552 3.68E-13 12.43381752 0.166660117 ARDDLITDLLNEAK ddPTM_HeLa_Romidepsin_16h_R1 2 ARDDLITDLLNEAK 14 1 C9J8H1;P36543-2;P36543 C9J8H1 ATP6V1E1 V-type proton ATPase subunit E 1 0 0 ; ; 184 1.65E-07 7462000 5226.9 4711 4248.6 4620.8 6518.7 7328.3 6614.8 7626 5577.8 4912.7 FALSE FALSE TRUE 5163.192532 4777.321582 4322.545101 5155.078638 6186.026414 6860.045281 7176.660947 7846.646278 5078.907598 4785.067346 1.079021915 0.998381263 0.903340494 1.077326245 1.292777294 1.433636099 1.499803541 1.639819403 1.061407757 1 12.22432351 -8.399245477 1.421038566 1.023387003 1.573488003 0.939892519 0.058226565 0.079479407 0.303704784 0.009842281 0.033593153 3.99E-09 8.399245477 0.550101 AREES(ph)WGPPR ddPTM_HeLa_Romidepsin_16h_R1 2 AREESWGPPR 10 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 0 AREES(1)WGPPR;AREES(1)WGPPR ; 80.318 0.022368 33817000 2894.2 2580.08 2792.5 2916.9 2995.4 2875.4 2371.8 2422.97 2760.6 2993.9 TRUE FALSE FALSE 2858.924377 2616.402434 2841.102291 3254.165702 2842.533561 2691.67122 2573.260633 2493.074814 2513.685022 2916.118046 0.980387053 0.897221029 0.974275474 1.115923859 0.974766287 0.923032325 0.882426771 0.854929319 0.861997005 1 11.50983341 -8.011737207 2.298646488 0.990726446 0.866131509 0.263712483 0.064723863 0.201371793 2.071500667 0.007437852 0.02756643 9.73E-09 8.011737207 -0.124594937 AREETDKEEPASK(ac)QQK ddPTM_HeLa_Romidepsin_16h_R1 2 AREETDKEEPASKQQK 16 3 P05455 P05455 SSB Lupus La protein 0 1 ; AREETDKEEPASK(1)QQK;AREETDKEEPASK(1)QQK 181.75 1.68E-12 9331970 4689.06 4536.33 4348.92 3801.09 3485.91 3257.29 3372.52 3687.11 4665.67 4303.02 FALSE TRUE FALSE 4631.907933 4600.192573 4424.611128 4240.58991 3308.011005 3049.159681 3658.981765 3793.790711 4248.36079 4191.22692 1.105143678 1.097576595 1.055683983 1.011777695 0.789270318 0.727510044 0.873009702 0.905174256 1.013631777 1 12.03315692 -8.841944971 4.752481343 1.054653804 0.820479242 0.805680147 0.053995178 0.074882476 3.057307916 0.009277938 0.017313572 1.44E-09 8.841944971 -0.234174562 ARFEELCSDLFR ddPTM_HeLa_Romidepsin_16h_R1 2 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 0 ; ; 138.89 0.0024962 53498000 3564.8 3247.8 4936.5 1398.12 6794.3 6764.6 5363.4 4125.2 3478.8 3124.6 FALSE FALSE TRUE 3521.350846 3293.522614 5022.417712 1559.777213 6447.561518 6332.363892 5818.967062 4244.556154 3167.647415 3043.422442 1.157036499 1.082177278 1.650253229 0.512507627 2.118523354 2.080672011 1.911981387 1.394665458 1.040817526 1 11.57147889 -8.745129278 24.99999771 1.089456255 1.893584407 0.607521652 0.315786392 118.3314183 181376.5446 0.042630324 0.085058666 1.80E-09 8.745129278 0.804128152 ARFEELNADLFR ddPTM_HeLa_Romidepsin_16h_R1 3 ARFEELNADLFR 12 1 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;A8K7Q2;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 0 ;; ;; 155.88 0.0014206 433315040 7153.76 6693.98 9314.63 9209.85 11478.94 10165.16 8132.97 6480.95 6496.73 5355.46 FALSE FALSE TRUE 7066.567222 6788.218026 9476.747228 10274.73619 10893.12686 9515.639083 8823.784269 6668.466063 5915.646197 5216.324377 1.354702413 1.301341239 1.816748067 1.969727235 2.088276355 1.824203864 1.691571235 1.278384084 1.134064098 1 12.34881787 -10.25676129 0.992895337 1.112905077 1.796802804 0.602650981 0.225644594 0.247956035 0.482370204 0.054125752 0.06452172 5.54E-11 10.25676129 0.683897726 ARGS(ph)PPTSSNIVQGQIK ddPTM_HeLa_Romidepsin_16h_R1 2 ARGSPPTSSNIVQGQIK 17 1 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 0 ARGS(0.957)PPT(0.02)S(0.02)S(0.003)NIVQGQIK;ARGS(0.994)PPT(0.002)S(0.002)S(0.003)NIVQGQIK ; 112.44 0.00074586 54885000 8618.2 8193.6 9478.3 9982 10218.4 10317.5 8609.9 9069.1 8252.8 7213.9 TRUE FALSE FALSE 8513.158064 8308.949716 9643.265836 11136.16581 9696.916918 9658.245048 9341.224691 9331.5001 7514.648898 7026.481838 1.211581878 1.182519205 1.372417386 1.58488502 1.38005294 1.374549208 1.329431272 1.328047281 1.069475318 1 12.7785868 -10.70820127 0.621984597 1.029267069 1.398298993 0.718465305 0.0858838 0.262536412 0.231844122 0.034735889 0.029284493 1.96E-11 10.70820127 0.369031925 ARHDS(ph)PDLAPNVTYSLPR ddPTM_HeLa_Romidepsin_16h_R1 1 ARHDSPDLAPNVTYSLPR 18 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 0 ARHDS(1)PDLAPNVTYSLPR 60.334 0.017871 8993500 1243.4 1053.5 1015.2 1174.7 904.15 1021.5 993.36 994.3 1453.5 1137.6 TRUE FALSE FALSE 1228.244963 1068.331201 1032.86913 1310.524341 858.0078517 956.2294467 1077.735974 1023.068502 1323.49532 1108.044988 1.108479327 0.964158687 0.932154508 1.182735679 0.774343877 0.862987927 0.972646404 0.923309534 1.194441863 1 10.11380074 -8.755709144 24.99990757 1.04346016 0.888249848 0.459127123 0.094314303 101.4810535 442737.7806 0.012336964 0.024147888 1.76E-09 8.755709144 -0.155210312 ARLEIEPEWAYGK ddPTM_HeLa_Romidepsin_16h_R1 1 ARLEIEPEWAYGK 13 1 Q00688 Q00688 FKBP3 Peptidyl-prolyl cis-trans isomerase FKBP3 0 0 90.793 0.02484 6991300 5884.9 5943.2 5847.2 6054.9 6245.5 5289.4 5239.2 5762.5 6468.7 6127.5 FALSE FALSE TRUE 5813.172575 6026.868526 5948.968063 6754.996027 5926.76883 4951.424411 5684.217517 5929.228846 5890.123271 5968.306667 0.974007017 1.00981214 0.996759784 1.131811149 0.993040264 0.829619637 0.952400377 0.993452444 0.986900238 1 12.54310595 -8.486711226 24.90700981 1.001573985 0.925123118 0.321110462 0.057065188 582.1415412 400895.6774 0.008250814 0.018442543 3.26E-09 8.486711226 -0.076450867 ARPATDS(ph)FDDYPPR ddPTM_HeLa_Romidepsin_16h_R1 3 ARPATDSFDDYPPR 14 1 E7EX17;P23588-2;P23588;F8VP89;F8W0K0;F8VSC7 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 ARPAT(0.052)DS(0.944)FDDY(0.004)PPR;ARPAT(0.227)DS(0.77)FDDY(0.003)PPR;ARPAT(0.084)DS(0.916)FDDYPPR ;; 108.96 0.0022334 12628300 4413.93 4586.56 3707.21 3672.63 4190.3 4326.77 4678.16 4385.36 4852.5 3661.1 TRUE FALSE FALSE 4360.131323 4651.129712 3771.732435 4097.276761 3976.453355 4050.303361 5075.522794 4512.243473 4418.480247 3565.984094 1.222700721 1.304304671 1.057697493 1.148989074 1.115106868 1.135816441 1.423316162 1.265357151 1.239063364 1 11.80008455 -16.41362254 0.210992237 3.57E-15 1.245370075 0 0.1242502 38.76876694 0.502813884 16.010618 0.09515358 3.86E-17 16.41362254 1.245370075 ARPFPDGLAEDIDKGEVSAR ddPTM_HeLa_Romidepsin_16h_R1 3 ARPFPDGLAEDIDKGEVSAR 20 2 P13639 P13639 EEF2 Elongation factor 2 0 0 ;; ;; 106.19 0.00015877 53047600 5523 5608 4776.4 5308.1 6419.7 6046.6 5005.7 5707.5 5885.9 5149.8 FALSE FALSE TRUE 5455.683552 5686.949571 4859.531238 5921.847497 6092.078754 5660.241775 5430.884033 5872.637508 5359.450362 5016.007454 1.087654594 1.133760192 0.968804629 1.180589852 1.214527452 1.128435679 1.082710519 1.170779263 1.068469378 1 12.29232378 -9.244027482 24.9922881 1.045891756 1.153155668 0.484085775 0.053316554 586.2490137 841476.8892 0.008830108 0.014622549 5.70E-10 9.244027482 0.107263911 ARPSQFPEQSSSAQQNGSVSDIS(ph)PVQAAK ddPTM_HeLa_Romidepsin_16h_R1 2 ARPSQFPEQSSSAQQNGSVSDISPVQAAK 29 1 O00139-1;O00139-5;O00139;O00139-4 O00139-1 KIF2A Kinesin-like protein KIF2A 1 0 ARPSQFPEQS(0.001)S(0.002)S(0.001)AQQNGS(0.081)VS(0.303)DIS(0.612)PVQAAK;ARPSQFPEQSSSAQQNGS(0.002)VS(0.203)DIS(0.794)PVQAAK ; 128.62 1.22E-10 8320900 1631.07 1436.61 1808.9 1331.25 1565.34 1694.68 1356.85 1390.96 1981.61 1691.06 TRUE FALSE FALSE 1611.189891 1456.834633 1840.383146 1485.175389 1485.454859 1586.395417 1472.100805 1431.205233 1804.369839 1647.126017 0.978182528 0.884470659 1.117329898 0.901676844 0.901846515 0.963129354 0.893739028 0.868910586 1.095465568 1 10.68573522 -4 0.258198511 0.997646561 0.119359505 0.328428011 0.068670379 41.71041858 0.524490593 0.029027784 16.28228159 1.00E-04 4 -0.878287056 ARQPLSEASNQQPLS(ph)GGEEK ddPTM_HeLa_Romidepsin_16h_R1 4 ARQPLSEASNQQPLSGGEEK 20 1 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 0 ARQPLSEAS(0.001)NQQPLS(0.999)GGEEK;ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEASNQQPLS(1)GGEEK;ARQPLSEASNQQPLS(1)GGEEK ;;; 118.24 8.47E-05 63644000 9968.9 10106.6 9186 11276.3 12887.6 11279.3 8357.2 9565 10603.5 11334.8 TRUE FALSE FALSE 9847.395212 10248.88098 9345.878477 12580.11886 12229.89768 10558.58913 9067.060359 9841.748184 9655.096403 11040.32026 0.891948329 0.928313739 0.846522406 1.139470465 1.107748452 0.9563662 0.821267875 0.891436838 0.874530464 1 13.4304944 -8.389392732 0.004659492 1.881813839 1.79E-06 0 0.102397385 97425.37486 110.0011601 21742.86102 22687.77729 4.08E-09 8.389392732 -1.881812051 ARS(ph)RTPS(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 ARSRTPSRR 9 3 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 2 0 ARS(0.996)RT(0.005)PS(0.999)RR 70.563 0.0032592 0 66.473 0 203.39 62.8 213.3 146.65 169.72 183.4 0 127.77 TRUE FALSE FALSE 65.66280151 0 206.9299176 70.06123148 202.4145051 137.2795383 184.1360126 188.7063896 0 124.450517 0.527621766 0 1.662748558 0.562964568 1.626465763 1.10308532 1.479592187 1.516316639 0 1 6.959428413 -8.762012973 24.99997995 0.76743915 1.411361263 0.385411853 0.478527648 12.92615759 563426.0474 0.060489708 0.114649492 1.73E-09 8.762012973 0.643922113 ARTDEVPAGGS(ph)RSEAEDEDDEDYVPYVPLR ddPTM_HeLa_Romidepsin_16h_R1 1 ARTDEVPAGGSRSEAEDEDDEDYVPYVPLR 30 2 D6RD33;D6RGI7;A0A499FJW5;Q9UJV9 D6RD33 DDX41 Probable ATP-dependent RNA helicase DDX41 1 0 ART(0.003)DEVPAGGS(0.498)RS(0.498)EAEDEDDEDY(0.002)VPYVPLR 51.766 0.0050207 6717200 1396.7 1189.9 1170.7 1057.5 1645 1210.9 1280.4 1220 1397 1477.2 TRUE FALSE FALSE 1379.676483 1206.651443 1191.075542 1179.773126 1561.049512 1133.527398 1389.157144 1255.298775 1272.048821 1438.822131 0.958893009 0.838638368 0.827812915 0.819957589 1.084949611 0.78781621 0.965482191 0.872448893 0.884090392 1 10.49067254 -10.4521294 4.637474455 0.98255929 0.887650872 0.060840213 0.087101968 0.237865605 9.273010436 0.013570818 0.015221778 3.53E-11 10.4521294 -0.094908418 ARTSS(ph)TDEVLSLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ARTSSTDEVLSLEEK 15 1 K7ENH8;A0A0A0MRB7;P15923-2;K7EMM4 K7ENH8 TCF3 Transcription factor E2-alpha 1 0 ART(0.009)S(0.031)S(0.741)T(0.21)DEVLS(0.009)LEEK 119 0.024014 3280400 1375.1 1397.3 857.62 1549.3 1346.6 1232.4 778.16 716.86 1457.5 1637.9 TRUE FALSE FALSE 1358.339752 1416.971226 872.5465163 1728.437356 1277.877977 1153.653617 844.256891 737.6012131 1327.13755 1595.347122 0.85143837 0.888189916 0.546932078 1.083423997 0.801003092 0.723136427 0.529199495 0.462345281 0.831880117 1 10.63965465 -6.931554044 0.390333289 0.938460056 5.18E-43 0.48968315 0.139454338 3.9338558 0.33952097 0.037519302 1.816416028 1.17E-07 6.931554044 -0.938460056 ARVDHGAEIIT(ph)QSPGR ddPTM_HeLa_Romidepsin_16h_R1 1 ARVDHGAEIITQSPGR 16 1 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 ARVDHGAEIIT(0.619)QS(0.381)PGR 103.73 0.0025164 33321000 1111.6 1249.1 953.85 1600.9 1633.4 1658.2 1482.8 1433.6 1221.6 1250.1 TRUE FALSE FALSE 1098.051392 1266.684863 970.4513591 1786.00359 1550.041503 1552.246372 1608.748995 1475.078954 1112.337036 1217.622222 0.901799731 1.040293812 0.797005296 1.466796153 1.273006911 1.274817709 1.321221777 1.211442209 0.913532142 1 10.24985088 -9.262218221 24.999999 0.949649688 1.30616115 0.826941703 0.086446342 21.27047965 682760.4032 0.01256314 0.01991355 5.47E-10 9.262218221 0.356511462 ARVDHGAEIITQS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 ARVDHGAEIITQSPGR 16 1 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 ARVDHGAEIIT(0.132)QS(0.868)PGR 80.382 0.0090459 38473000 1342.4 1412.1 1149.6 1535.1 1740.2 1831.9 1489.9 1333.6 1422.8 1267.1 TRUE FALSE FALSE 1326.038312 1431.979581 1169.608306 1712.595485 1651.3911 1714.847502 1616.452069 1372.185612 1295.541205 1234.180559 1.074428132 1.160267491 0.947680059 1.38763771 1.338046599 1.389462416 1.309737102 1.111819176 1.049717721 1 10.26933776 -9.258898901 24.99976882 1.041450374 1.313741956 0.684333016 0.088520142 97.27519718 957242.3455 0.013422884 0.021603069 5.51E-10 9.258898901 0.272291582 ARVS(ph)SGYVPPPVATPFSSK ddPTM_HeLa_Romidepsin_16h_R1 1 ARVSSGYVPPPVATPFSSK 19 1 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 0 ARVS(0.89)S(0.108)GY(0.002)VPPPVATPFSSK 97.621 0.01231 12054000 1472.8 1858 2059 1370 1808.1 2234.1 2150.9 2112.3 1955.3 1687 TRUE FALSE FALSE 1454.848947 1884.156973 2094.836031 1528.405846 1715.82591 2091.34822 2333.597392 2173.416068 1780.413071 1643.171497 0.885390813 1.146658749 1.274873642 0.930156012 1.044215965 1.272751033 1.420178841 1.322695818 1.083522368 1 10.68226735 -7.817477175 0.472426808 0.954342523 1.583163863 0.451282608 0.12582419 1.545798013 0.323116828 0.030714629 0.491014976 1.52E-08 7.817477175 0.62882134 AS(ph)AELIEEEVAK ddPTM_HeLa_Romidepsin_16h_R1 2 ASAELIEEEVAK 12 0 A0A2R8YFR1;D6RF05;A0A2R8YCI2;E7ETE2;B4E1C5;B4DDD8;P12081-3;P12081-2;P12081-4;P12081 A0A2R8YFR1 HARS "Histidine--tRNA ligase, cytoplasmic" 1 0 AS(1)AELIEEEVAK;AS(1)AELIEEEVAK ; 186.51 2.95E-08 0 1417.15 1502.9 1312.69 1012.93 1680.95 2104.85 2320.23 2017.27 2024.64 1677.61 TRUE FALSE FALSE 1399.877231 1524.057866 1335.536819 1130.049733 1595.164849 1970.356878 2517.310278 2075.636525 1843.551128 1634.02545 0.856704668 0.932701425 0.817329264 0.691574132 0.976217873 1.205829981 1.540557571 1.270259606 1.128226691 1 10.67421474 -8.136216057 2.850183607 0.904722257 1.402460508 0.716655106 0.12603124 0.091440063 1.419753431 0.016119517 0.048392784 7.31E-09 8.136216057 0.497738251 AS(ph)DLEDEESAAR ddPTM_HeLa_Romidepsin_16h_R1 2 ASDLEDEESAAR 12 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 AS(1)DLEDEESAAR;AS(1)DLEDEESAAR ; 243.37 4.21E-50 77872000 3527.1 3176.6 3529.9 1946.63 2744.7 3265 2779.9 3306.1 3079.8 3532.8 TRUE FALSE FALSE 3484.110349 3221.320258 3591.336429 2171.70852 2604.627717 3056.377037 3016.024637 3401.756787 2804.334974 3441.017347 1.012523332 0.936153449 1.043684488 0.631123967 0.756935364 0.888219015 0.876492134 0.988590421 0.814972635 1 11.74861945 -9.316092552 24.99960769 1.002297464 0.830317566 0.23544519 0.108114039 204.5699904 93574.48 0.013980992 0.021356325 4.83E-10 9.316092552 -0.171979897 AS(ph)DPGLPAEEPK ddPTM_HeLa_Romidepsin_16h_R1 4 ASDPGLPAEEPK 12 0 P27708;F8VPD4 P27708 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 0 AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK;AS(1)DPGLPAEEPK ;;; 167.73 0.00021568 157239200 28224.9 28277.4 32701.3 13420.2 23244.7 25008.6 16422.2 21527.9 29886.4 29963.8 TRUE FALSE FALSE 27880.88406 28675.48998 33270.45241 14971.90667 22058.43622 23410.63117 17817.10126 22150.77582 27213.28553 29185.33616 0.955304538 0.982530742 1.139971533 0.512994148 0.755805453 0.802136766 0.610481276 0.758969357 0.932430087 1 14.83295606 -9.26504296 24.99973925 0.989670891 0.693865806 0.739085216 0.093097099 119.3735768 828150.9894 0.01323736 0.020725785 5.43E-10 9.26504296 -0.295805086 AS(ph)DPGLPAEEPKEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASDPGLPAEEPKEK 14 1 P27708;F8VPD4 P27708 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 0 AS(1)DPGLPAEEPKEK 81.346 0.012378 40886000 7749.8 7141.8 7039.3 6214.6 5716 6389.9 3926.1 4858.3 7064.8 6503.4 TRUE FALSE FALSE 7655.342457 7242.342448 7161.816064 6933.161293 5424.291191 5981.606012 4259.582836 4998.867245 6432.906594 6334.44073 1.208526969 1.143327842 1.130615372 1.094518299 0.856317301 0.944298994 0.672448132 0.789156842 1.015544524 1 12.62900153 -8.419866205 1.266583955 1.108921478 0.744336075 0.737197245 0.083238566 0.20363193 0.610351856 0.015062621 0.05488673 3.80E-09 8.419866205 -0.364585403 AS(ph)GEMASAQYITAALR ddPTM_HeLa_Romidepsin_16h_R1 1 ASGEMASAQYITAALR 16 0 A6NJA2;P54578-2;P54578-3;P54578 A6NJA2 USP14 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 14 1 0 AS(0.876)GEMAS(0.121)AQY(0.003)ITAALR 85.973 0.023401 11058000 1702.7 1756.1 1780.9 1402 1819.2 2596.7 1886.4 2448.5 2481 2442.1 TRUE FALSE FALSE 1681.946837 1780.822422 1811.895817 1564.105837 1726.359436 2430.77925 2046.630769 2519.343484 2259.093146 2378.65389 0.707100282 0.748668156 0.761731593 0.657559237 0.725771598 1.021913806 0.860415539 1.059146728 0.949735964 1 11.21592965 -8.251922883 24.72321401 0.818787612 0.968484378 0.349407618 0.113150965 781.216333 2029541.32 0.020243172 0.050856403 5.60E-09 8.251922883 0.149696767 AS(ph)GEWDSGTENR ddPTM_HeLa_Romidepsin_16h_R1 1 ASGEWDSGTENR 12 0 A0A0U1RQE4;A0A0U1RQN2;A0A494C1M0;Q5HYK7-3;Q5HYK7-2;Q5HYK7 A0A0U1RQE4 SH3D19 SH3 domain-containing protein 19 1 0 AS(0.995)GEWDS(0.002)GT(0.003)ENR 96.23 0.020092 6973600 1311.9 1170.9 1676.5 1326.4 1592.3 1478 1589.4 985.65 1448.6 1398 TRUE FALSE FALSE 1295.910058 1187.383961 1705.678779 1479.764609 1511.038989 1383.56057 1724.403596 1014.168228 1319.033588 1361.679758 0.951699583 0.871999421 1.252628431 1.086719987 1.109687487 1.016068985 1.266379694 0.744792027 0.968681204 1 10.41117173 -9.784803309 24.99917919 0.968664789 1.086713119 0.169466214 0.138870598 312.0400902 333878.4746 0.020218579 0.02658073 1.64E-10 9.784803309 0.118048329 AS(ph)GQAFELILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 0 AS(1)GQAFELILS(1)PR;AS(1)GQAFELILS(1)PR ; 143.99 0.0078474 24617000 4970.1 4185.3 4957.4 4344.5 6050.3 7667.7 5778.3 5526.5 4731.8 5012 TRUE FALSE FALSE 4909.52251 4244.220763 5043.681467 4846.831531 5741.530614 7177.758716 6269.108658 5686.400558 4308.575957 4881.787517 1.005681319 0.869398913 1.033162842 0.992839511 1.176112355 1.470313628 1.284183024 1.164819349 0.882581624 1 12.25319379 -8.606563488 3.726443304 0.993631971 1.307504783 0.750981034 0.088550396 0.07872997 2.138780727 0.011478572 0.024222563 2.47E-09 8.606563488 0.313872812 AS(ph)GQAFELILSPR ddPTM_HeLa_Romidepsin_16h_R1 2 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 AS(0.997)GQAFELILS(0.003)PR;AS(1)GQAFELILSPR ; 139.49 0.0011902 119643000 2207.5 1780.5 2291 3420.2 2977.2 2477.9 1970.64 1961.94 2495.9 1846.74 TRUE FALSE FALSE 2180.594141 1805.565926 2330.873894 3815.659617 2825.262375 2319.570187 2138.026112 2018.705638 2272.660453 1798.761429 1.21227535 1.003782879 1.29582159 2.121270534 1.570670979 1.289537428 1.188610162 1.122275365 1.26345852 1 10.81278814 -9.525547622 23.06940546 1.098378689 1.46715011 0.258310684 0.269352927 31.3983887 271399.9106 0.044528064 0.063241361 2.98E-10 9.525547622 0.368771421 AS(ph)GVAVSDGVIK ddPTM_HeLa_Romidepsin_16h_R1 2 ASGVAVSDGVIK 12 0 E9PP50;P23528;E9PS23 E9PP50 CFL1 Cofilin-1 1 0 AS(1)GVAVSDGVIK;AS(1)GVAVSDGVIK ; 150.22 0.0014561 39868000 8551.2 8692 7773.3 5155.7 7996.2 6395.3 5363.49 7092.1 8779.3 8471.8 TRUE FALSE FALSE 8446.974685 8814.366204 7908.591026 5751.826292 7588.124076 5986.66097 5819.064707 7297.298724 7994.05742 8251.701415 1.023664607 1.06818773 0.958419437 0.697047312 0.919582968 0.725506252 0.705195743 0.884338678 0.968776864 1 13.0104759 -9.42181759 5.167160017 1.015723473 0.786738107 0.701808476 0.0715529 0.085208461 3.495510167 0.010013709 0.015353434 3.79E-10 9.42181759 -0.228985366 AS(ph)ISEPSDTDPEPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASISEPSDTDPEPR 14 0 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 0 AS(0.873)IS(0.076)EPS(0.014)DT(0.037)DPEPR 107.46 0.0067477 3139400 1203.2 1072.2 927.99 1165.4 938.13 966.15 768.97 829.56 1140.1 1080.5 TRUE FALSE FALSE 1188.534936 1087.29446 944.1412767 1300.149031 890.2537255 904.4161331 834.2862926 853.5620098 1038.126601 1052.428454 1.129326113 1.033129098 0.897107326 1.235379969 0.845904272 0.859361156 0.792724949 0.811040415 0.986410617 1 10.03950644 -8.631884054 9.16010922 1.057304328 0.8240114 0.609912615 0.085957909 0.132000489 10.27080483 0.012310062 0.024644058 2.33E-09 8.631884054 -0.233292928 AS(ph)LEDAPVDDLTR ddPTM_HeLa_Romidepsin_16h_R1 2 ASLEDAPVDDLTR 13 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 AS(1)LEDAPVDDLTR;AS(1)LEDAPVDDLTR ; 182.72 3.89E-07 153641000 5224.5 4790.9 5112.9 3042.1 5223.9 5235.4 4878.1 4913.6 4971.8 5513.1 TRUE FALSE FALSE 5160.821784 4858.346416 5201.88788 3393.841916 4957.30489 4900.874836 5292.445692 5055.767264 4527.109756 5369.868867 0.961070356 0.904742096 0.96871786 0.63201579 0.923170568 0.912661921 0.985581924 0.941506653 0.843057786 1 12.39067114 -10.32945349 1.473919069 0.986211899 0.889705208 0 0.103257425 0.505992091 2.107143758 0.018402824 0.021247317 4.68E-11 10.32945349 -0.096506692 AS(ph)LEDAPVDDLTRK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLEDAPVDDLTRK 14 1 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 AS(1)LEDAPVDDLTRK;AS(1)LEDAPVDDLTRK ; 126.07 0.00091327 10014000 4884.4 4320.3 5299.1 3640 5104.4 5070.1 4576.7 4682.2 5456.6 5695.1 TRUE FALSE FALSE 4824.867054 4381.121297 5391.328613 4060.873927 4843.903421 4746.136973 4965.444784 4817.67207 4968.54803 5547.140481 0.869793558 0.789798151 0.971911317 0.732066177 0.873225302 0.855600645 0.895135935 0.868496496 0.895695367 1 12.43752855 -11.92730131 0.689187231 1.004462356 0.855072915 0.161834793 0.067269124 0.511054239 0.436563953 0.041937139 0.012273606 1.18E-12 11.92730131 -0.149389441 AS(ph)LSSAPVVLVGDHA ddPTM_HeLa_Romidepsin_16h_R1 2 ASLSSAPVVLVGDHA 15 0 Q9HBH9 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 0 AS(0.977)LS(0.009)S(0.014)APVVLVGDHA;AS(0.966)LS(0.017)S(0.017)APVVLVGDHA ; 174.39 6.82E-06 7276100 2957.51 2931.13 3085.48 3028.8 4826.5 5254.7 4100.9 5114.4 2972.1 2590.55 TRUE FALSE FALSE 2921.462731 2972.394525 3139.181485 3379.004107 4580.185695 4918.941629 4449.230344 5262.377095 2706.267932 2523.247138 1.157818704 1.178003724 1.244103853 1.33914909 1.815195042 1.949449008 1.763295508 2.085557541 1.072533836 1 11.3010658 -8.889501878 1.091619052 1.07758779 1.967235165 0.937846721 0.094697186 0.085018782 0.199160962 0.016727213 0.044364882 1.29E-09 8.889501878 0.889647375 AS(ph)LTLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASLTLEEK 8 0 A0A0U1RQQ9;Q6P3W7 A0A0U1RQQ9 SCYL2 SCY1-like protein 2 1 0 AS(1)LTLEEK 120.45 0.018633 3810600 1394.4 1279 1325.2 1709.9 1675.2 1881.3 1556 1777.7 1388.8 1353.7 TRUE FALSE FALSE 1377.404516 1297.005796 1348.26455 1907.606683 1589.708293 1761.091002 1688.166601 1829.134945 1264.58225 1318.530679 1.044651094 0.983675099 1.022550762 1.446767007 1.205666518 1.335646587 1.280339266 1.387252473 0.959084434 1 10.36471542 -9.277421094 24.77497702 1.018319815 1.321592658 0.867555396 0.064089002 170.1108525 263706.6194 0.008598534 0.013160918 5.28E-10 9.277421094 0.303272843 AS(ph)PAPGSGHPEGPGAHLDMNSLDR ddPTM_HeLa_Romidepsin_16h_R1 2 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 0 AS(0.752)PAPGS(0.248)GHPEGPGAHLDMNSLDR;AS(0.999)PAPGS(0.001)GHPEGPGAHLDMNSLDR ; 88.186 1.94E-05 32606000 2168.23 2178 2760.7 3173.67 2815.4 3761.8 2401.1 2609.9 3216.2 2741 TRUE FALSE FALSE 2141.802779 2208.661941 2808.748825 3540.624658 2671.719632 3521.433121 2605.049374 2685.413339 2928.535017 2669.788425 0.802236896 0.827279765 1.052049218 1.32618174 1.000723356 1.318993328 0.975751243 1.005852491 1.096916516 1 11.3825097 -9.59244632 5.799412133 0.898779437 1.127395454 0.289282209 0.139378934 0.153025028 9.365893091 0.020840213 0.029648537 2.56E-10 9.59244632 0.228616017 AS(ph)PEPEGEAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPEPEGEAAGK 12 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 AS(1)PEPEGEAAGK;AS(1)PEPEGEAAGK ; 196.7 1.01E-10 59248000 6022.6 5673.2 5412.7 5974.7 5600.6 6606.6 6032.5 6003.3 6597.4 6220.5 TRUE FALSE FALSE 5949.194235 5753.067459 5506.905773 6665.522926 5314.780483 6184.459582 6544.900399 6176.996014 6007.312021 6058.890513 0.981894989 0.949524908 0.90889673 1.100122689 0.877187081 1.020724763 1.080214337 1.019492925 0.991487139 1 12.56483792 -8.00478716 24.92789311 0.982180745 1.05000763 0.22003396 0.057981662 226.3717848 1178799.926 0.007315466 0.021169013 9.89E-09 8.00478716 0.067826885 AS(ph)PEPPDSAEGALK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPEPPDSAEGALK 14 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 AS(1)PEPPDSAEGALK;AS(1)PEPPDSAEGALK ; 210.07 8.46E-24 40422000 6125.2 5583.8 5734.3 4729.1 4202.6 3328 3103 3642.7 6667.3 6520 TRUE FALSE FALSE 6050.543706 5662.408883 5834.103086 5275.900793 3988.12564 3115.351541 3366.568743 3748.095777 6070.959989 6350.60946 0.952750086 0.891632357 0.91866822 0.830770783 0.627991009 0.490559459 0.530117426 0.590194658 0.95596494 1 12.63267934 -8.861352371 1.48910948 0.969620478 0.528230259 0.958463536 0.038063633 0.054582976 0.243316509 0.006703745 0.015498495 1.38E-09 8.861352371 -0.441390219 AS(ph)PEPPGPESSSR ddPTM_HeLa_Romidepsin_16h_R1 3 ASPEPPGPESSSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 AS(0.999)PEPPGPESSSR;AS(1)PEPPGPESSSR;AS(0.997)PEPPGPES(0.001)S(0.001)S(0.001)R ;; 136.33 0.0015393 506719000 2852.63 2807.14 2860.36 3670.24 3287.04 3144.13 2634.1 3039.5 2782.09 3049.2 TRUE FALSE FALSE 2817.861048 2846.658991 2910.143366 4094.610418 3119.290083 2943.23024 2857.840388 3127.443137 2533.252903 2969.981344 0.948780723 0.958477061 0.979852406 1.378665366 1.050272618 0.990992838 0.962241865 1.053017772 0.852952463 1 11.53623815 -9.474104214 24.99999077 0.973614246 1.083379781 0.259396395 0.113367794 495.85461 254156.7707 0.016772247 0.025619713 3.36E-10 9.474104214 0.109765535 AS(ph)PFEEDQNR ddPTM_HeLa_Romidepsin_16h_R1 2 ASPFEEDQNR 10 0 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;A0A0A0MR59;Q8TB72-4;A0A0C4DG68 C9JW01 PUM2 Pumilio homolog 2 1 0 AS(1)PFEEDQNR;AS(1)PFEEDQNR ; 152.96 0.0035512 13215500 2666.4 2507.6 2527.2 2067.21 2628.8 2848.3 1915.62 2634 2801.7 2762.3 TRUE FALSE FALSE 2633.900891 2542.902059 2571.184856 2306.230547 2494.642527 2666.302822 2078.332715 2710.210634 2551.108935 2690.535048 0.978950597 0.945128762 0.955640722 0.857164284 0.927191983 0.990993529 0.772460748 1.00731289 0.948179039 1 11.39367738 -10.00105067 1.128342864 0.992804541 0.909161408 0.130556134 0.064367205 0.43479618 1.084630971 0.011277469 0.015180464 9.98E-11 10.00105067 -0.083643133 AS(ph)PGGVSTSSSDGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPGGVSTSSSDGK 14 0 P54259 P54259 ATN1 Atrophin-1 1 0 AS(1)PGGVSTSSSDGK 160.65 0.00014544 0 791.3 816.76 905.06 553.76 696.84 609.81 476.79 458.73 994.23 817.92 TRUE FALSE FALSE 781.6553312 828.2583687 920.8121896 617.7883367 661.2776545 570.8451091 517.2885307 472.0026288 905.3035787 796.6703205 0.98115282 1.039650088 1.155825899 0.775462975 0.830051826 0.716538692 0.649313169 0.592469202 1.136359113 1 9.637839019 -8.578749451 1.169018264 1.004049311 0.624354601 0.79960791 0.085800088 0.153482033 0.400815492 0.011893284 0.039429397 2.64E-09 8.578749451 -0.379694711 AS(ph)PGLLPVANGNSLNK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPGLLPVANGNSLNK 16 0 Q14814-6;Q14814-3;Q14814-5;Q14814-4;Q14814-2;Q14814 Q14814-6 MEF2D Myocyte-specific enhancer factor 2D 1 0 AS(1)PGLLPVANGNSLNK;AS(1)PGLLPVANGNSLNK ; 226.74 3.78E-35 88766000 5313.2 4970.9 4485.2 4558.7 2540.6 2345.92 2112.05 2148.3 4817 4493.5 TRUE FALSE FALSE 5248.440675 5040.880461 4563.263025 5085.798343 2410.943702 2196.023283 2291.447474 2210.457671 4386.155456 4376.758222 1.199161664 1.151738388 1.042612544 1.162001208 0.55085147 0.501746537 0.523549019 0.505044501 1.002147076 1 12.09564697 -8.754920745 21.40015288 1.101006675 0.519203931 0.95064463 0.063905858 4.723333875 15505.13406 0.011655214 0.022796864 1.76E-09 8.754920745 -0.581802744 AS(ph)PLYASYK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPLYASYK 9 0 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 AS(0.999)PLYASYK 103.91 0.024781 16868000 1728.7 1385.1 2979.2 1074.2 939.82 761.94 403.61 310.33 1264 986.17 TRUE FALSE FALSE 1707.629939 1404.599474 3031.051726 1198.404058 891.8574784 713.254493 437.8926233 319.3089089 1150.944674 960.5491612 1.777764229 1.462287961 3.155540444 1.247623866 0.928487072 0.742548661 0.455877368 0.332423286 1.198215272 1 9.907715643 -8.529672929 2.139133941 1.524515499 0.488776318 0.447239855 0.568620473 0.278524108 2.530026218 0.093970021 0.234353662 2.95E-09 8.529672929 -1.03573918 AS(ph)PNGSISSAGNSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPNGSISSAGNSSR 15 0 E9PKU9;B7Z503;Q9BSF8;Q9BSF8-2 E9PKU9 BTBD10 BTB/POZ domain-containing protein 10 1 0 AS(0.994)PNGS(0.001)IS(0.004)S(0.001)AGNSSR 111.7 0.0041148 1755700 114.75 0 177.47 168.49 210.58 196.73 60.477 165.15 209.11 58.005 TRUE FALSE FALSE 113.3513829 0 180.5587909 187.9716066 199.8333168 184.1595879 65.61391487 169.9283547 190.4066779 56.49802174 2.006289413 0 3.19584271 3.327047581 3.536996707 3.259575862 1.161348891 3.007686808 3.370147698 1 5.820128448 -9.730588475 24.99931375 1.377829756 2.897748909 0.280640341 1.01219337 142.1268845 115169.0274 0.131642655 0.186159448 1.86E-10 9.730588475 1.519919153 AS(ph)PNLIGATGANSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPNLIGATGANSLGK 16 0 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 0 AS(0.879)PNLIGAT(0.12)GANS(0.001)LGK 106.38 0.0039849 14465000 1289.4 1476.4 1136.7 1401.9 1045.5 892.86 694.23 841.44 1263.3 1241.6 TRUE FALSE FALSE 1273.684297 1497.184798 1156.483787 1563.994274 992.1442337 835.8091276 753.1978789 865.7857388 1150.307284 1209.343053 1.053203468 1.238014965 0.956290925 1.293259402 0.820399333 0.691126579 0.622815732 0.715914096 0.951183604 1 10.24000784 -8.551898765 7.575932297 1.054896107 0.684568828 0.740195349 0.108980232 0.070110377 14.38704699 0.014787595 0.029926772 2.81E-09 8.551898765 -0.370327279 AS(ph)PNSDDTVLSPQELQK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPNSDDTVLSPQELQK 17 0 Q9UH62 Q9UH62 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 0 AS(0.969)PNS(0.03)DDT(0.001)VLSPQELQK 175.16 5.76E-07 3029300 545.78 684.78 568.12 523.86 755.52 585.81 667.88 646.28 557.65 571.92 TRUE FALSE FALSE 539.1278234 694.4203508 578.0078903 584.431158 716.9629952 548.3786316 724.6097105 664.9790921 507.7723873 557.061436 0.96780676 1.246577677 1.037601695 1.049132322 1.287044747 0.984413202 1.300771627 1.193726669 0.911519546 1 9.121692635 -9.442477555 0.498769919 0.978255667 1.213534763 0.364803134 0.10938272 0.779160775 0.389541882 0.031125466 0.076104193 3.61E-10 9.442477555 0.235279096 AS(ph)PPGDLQNPK ddPTM_HeLa_Romidepsin_16h_R1 3 ASPPGDLQNPK 11 0 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 0 AS(1)PPGDLQNPK;AS(1)PPGDLQNPK;AS(1)PPGDLQNPK ;; 140.63 0.0030458 227034000 6557.5 5904.7 5882.4 3517.75 6525.2 7418.3 5875.7 6673.7 6176.4 7063.9 TRUE FALSE FALSE 6477.574668 5987.826522 5984.780704 3924.488807 6192.194695 6944.294571 6374.781811 6866.79298 5623.967315 6880.37886 0.941456103 0.870275699 0.869833017 0.570388475 0.89997874 1.009289563 0.926516103 0.998025417 0.817392099 1 12.74827229 -10.58753795 1.66900507 0.980345541 0.873532581 0 0.125326354 0.518729859 2.938777794 0.024408532 0.025437609 2.59E-11 10.58753795 -0.106812959 AS(ph)PPPQGPLPGPPGALHR ddPTM_HeLa_Romidepsin_16h_R1 3 ASPPPQGPLPGPPGALHR 18 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 0 AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR;AS(1)PPPQGPLPGPPGALHR ;; 103.73 0.00018106 180670000 4579.4 4729.53 4610.5 4115.74 4968.54 4466.64 4528.5 5163.75 5172.4 5482.8 TRUE FALSE FALSE 4523.584511 4796.112447 4690.743818 4591.621224 4714.976864 4181.236119 4913.150677 5313.154959 4709.767589 5340.356066 0.847056724 0.898088515 0.878357877 0.859796831 0.882895598 0.782950812 0.920004325 0.994906499 0.881920144 1 12.38272022 -12.36873359 0.995366663 1.002897548 0.878050273 0 0.062453248 0.431096375 0.73558711 0.039558105 0.009329837 4.28E-13 12.36873359 -0.124847275 AS(ph)PS(ph)PQPSSQPLQIHR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 2 0 AS(1)PS(0.992)PQPS(0.008)S(0.001)QPLQIHR 85.054 0.0011837 0 713.88 596.07 571.17 540.94 628.35 629.69 691.27 666.8 737.21 704.21 TRUE FALSE FALSE 705.178956 604.4614891 581.1109743 603.486028 596.2829548 589.4548412 749.9864565 686.092806 671.2720912 685.9145227 1.028085764 0.881249003 0.84720611 0.879826871 0.869325455 0.859370697 1.09341096 1.000259921 0.978652688 1 9.421884992 -10.26930848 24.3341505 1.013262724 0.91696489 0.21304004 0.07264469 428.3485735 1324608.523 0.013169061 0.015212236 5.38E-11 10.26930848 -0.096297835 AS(ph)PSPQPSSQPLQIHR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 AS(0.589)PS(0.181)PQPS(0.115)S(0.115)QPLQIHR 125.33 0.0024841 15554000 489.21 340.69 342.76 427.01 438.32 577.96 339.28 662.57 509.78 435.13 TRUE FALSE FALSE 483.2473204 345.4862428 348.725594 476.3829053 415.9508948 541.0302213 368.0984347 681.7404176 464.184 423.8252599 1.14020415 0.815161991 0.82280512 1.124007817 0.981420727 1.276540765 0.86851462 1.60854126 1.095224952 1 8.727325764 -7.250858368 24.90180086 1.036816071 1.608541599 0.602554312 0.143823405 772.1688529 1817219.013 0.019472915 0.369877779 5.61E-08 7.250858368 0.571725528 AS(ph)PSTAGETPSGVK ddPTM_HeLa_Romidepsin_16h_R1 2 ASPSTAGETPSGVK 14 0 A0A087WW69;F8W8L6;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WW69 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 0 AS(0.993)PS(0.007)T(0.001)AGETPSGVK;AS(0.939)PS(0.054)T(0.007)AGETPSGVK ; 238.88 2.57E-43 22313000 4470.4 4423.5 4937.1 2375.7 3986 4402.4 3835.2 3781.5 4714.9 5104.1 TRUE FALSE FALSE 4415.913045 4485.774149 5023.028154 2650.389612 3782.579546 4121.100848 4160.961792 3890.911736 4293.187535 4971.494746 0.888246548 0.902298882 1.010365777 0.533117251 0.760853574 0.828946033 0.836963932 0.782644242 0.863560711 1 12.27946397 -9.306312549 24.99992695 0.946107526 0.758574011 0.506025699 0.090347777 271.9112982 151487.6807 0.014048844 0.021460011 4.94E-10 9.306312549 -0.187533514 AS(ph)PSYSALDK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSYSALDK 10 0 Q9NYD6;D6RAG4 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 0 AS(1)PSYSALDK 128.88 0.0078332 9579200 1149.4 1200.6 1221.4 865.78 940.1 849.41 1000.1 770.89 1290.8 1006.8 TRUE FALSE FALSE 1135.390671 1217.502078 1242.657955 965.8855572 892.123189 795.1354423 1085.048469 793.1944859 1175.347615 980.6431909 1.157802023 1.241534219 1.267186645 0.984951067 0.909732711 0.810830534 1.106466123 0.808851265 1.198547674 1 9.937584494 -9.014228953 18.89630227 1.105658164 0.919975636 0.519150891 0.112343109 22.83208823 30323.56894 0.018129714 0.030957726 9.68E-10 9.014228953 -0.185682528 AS(ph)PTLDFTER ddPTM_HeLa_Romidepsin_16h_R1 1 ASPTLDFTER 10 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 AS(0.857)PT(0.143)LDFTER 126.03 0.00034749 0 1409.1 1353.1 1598.2 1469.4 1794.1 1821.3 1727.1 1916.7 1508 1352.8 TRUE FALSE FALSE 1391.925347 1372.148977 1626.016001 1639.298942 1702.540382 1704.924808 1873.799831 1972.15669 1373.120703 1317.654061 1.056366302 1.041357529 1.234023443 1.244104193 1.292099674 1.293909273 1.422072672 1.496718106 1.042094996 1 10.36375594 -8.221345334 0.366263012 0.995309126 1.648705196 0.933846443 0.042026378 0.512556134 0.078162537 0.015057635 0.134025711 6.01E-09 8.221345334 0.653396069 AS(ph)PVAVGSSGAGADPSFQPVLSAR ddPTM_HeLa_Romidepsin_16h_R1 3 ASPVAVGSSGAGADPSFQPVLSAR 24 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 0 AS(0.957)PVAVGS(0.034)S(0.009)GAGADPSFQPVLSAR;AS(0.996)PVAVGS(0.004)SGAGADPSFQPVLSAR;AS(1)PVAVGSSGAGADPSFQPVLSAR ;; 261.94 3.09E-97 11001800 2637.24 2469.57 2636.9 2286.82 3306.28 3137.22 3043.27 3341.65 2740.25 2574.7 TRUE FALSE FALSE 2605.096304 2504.336671 2682.794138 2551.232888 3137.548194 2936.761767 3301.765278 3438.33537 2495.155177 2507.808923 1.038793778 0.998615424 1.069776136 1.0173155 1.251111345 1.171046861 1.31659364 1.371051574 0.994954262 1 11.29221171 -8.033481283 0.665535126 1.013221623 1.437853845 0.881973248 0.046831069 0.315824209 0.167887517 0.007824663 0.083571676 9.26E-09 8.033481283 0.424632222 AS(ph)PVPAPSSGLHAAVR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPVPAPSSGLHAAVR 16 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 AS(0.998)PVPAPS(0.001)S(0.001)GLHAAVR 93.237 0.010172 5644800 562.69 881.3 539.01 599.55 592.93 604.61 438.65 804.58 1244 1847.8 TRUE FALSE FALSE 555.8317178 893.7069645 548.3912429 668.872792 562.6705696 565.9773723 475.9089201 827.8592529 1132.733524 1799.79389 0.308830762 0.496560728 0.304696691 0.37163855 0.312630559 0.314467882 0.264424123 0.459974477 0.629368469 1 10.81361598 -12.32296298 0.618728193 1.10590583 0.336676239 0.609465631 0.133398316 0.211648193 0.114440176 0.092623414 0.015056281 4.75E-13 12.32296298 -0.769229591 AS(ph)SASVPAVGASAEGTR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSASVPAVGASAEGTR 17 0 A0A2R8YFI4;V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23 A0A2R8YFI4 PANK2 "Pantothenate kinase 2, mitochondrial" 1 0 AS(0.583)S(0.417)ASVPAVGASAEGTR 108.06 0.0004062 0 689.62 777.39 756.32 663.94 705.53 842.53 670.62 607.48 718.35 818.48 TRUE FALSE FALSE 681.2146462 788.3341168 769.4834323 740.7078667 669.5241714 788.6950521 727.5824461 625.0564754 654.0989769 797.2157716 0.854492184 0.988859158 0.965213509 0.929118431 0.839828056 0.989311903 0.912654355 0.78404931 0.820479223 1 9.638826442 AS(ph)SLEDLVLK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 0 AS(0.613)S(0.387)LEDLVLK 147.91 0.0038878 4114600 3853.6 3676.3 3804.5 3271.5 2878.4 3434.4 3128.3 3902.8 3438.7 3958.4 TRUE FALSE FALSE 3806.630841 3728.055048 3870.715727 3649.766223 2731.504507 3214.952924 3394.017724 4015.72136 3131.13406 3855.560197 0.987309404 0.96692954 1.003930824 0.946624105 0.708458529 0.833848458 0.880291722 1.041540309 0.812108721 1 11.91272478 -8.988532933 24.99839787 0.991339895 0.860102479 0.109190818 0.094858793 170.0258303 370656.6468 0.010995028 0.019918623 1.03E-09 8.988532933 -0.131237415 AS(ph)SLGEIDESSELR ddPTM_HeLa_Romidepsin_16h_R1 3 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 AS(0.618)S(0.382)LGEIDESSELR;AS(0.5)S(0.5)LGEIDESSELR;AS(0.5)S(0.5)LGEIDESSELR ;; 323.24 5.76E-174 470788000 14308.1 13538.96 12741.64 13514.77 13721 15043.26 13861.84 15884.35 15317.99 13364.29 TRUE FALSE FALSE 14133.70737 13729.56183 12963.4029 15077.4113 13020.76617 14082.04424 15039.26434 16343.93861 13947.91061 13017.08382 1.085781391 1.054734073 0.995876118 1.158278729 1.000282886 1.081812519 1.155348199 1.255576044 1.071508089 1 13.66811866 -4.000000007 0.625175917 1.041395823 17.7744892 0.638249729 0.047686175 81.77608979 0.534779705 0.008511104 1887.173819 1.00E-04 4.000000007 16.73309338 AS(ph)SLNVLNVGGK ddPTM_HeLa_Romidepsin_16h_R1 2 ASSLNVLNVGGK 12 0 Q07866-6;H0YG16;G3V5R9;Q07866-7;Q07866-4;Q07866-9;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 0 AS(0.5)S(0.5)LNVLNVGGK;AS(0.5)S(0.5)LNVLNVGGK ; 214.61 3.49E-21 524760000 14779.8 14351.2 14123.4 12553.3 13939.5 12347.3 11583.9 11852.7 14953.7 13712.8 TRUE FALSE FALSE 14599.65811 14553.23657 14369.21185 14004.77161 13228.1153 11558.34738 12567.83618 12195.63917 13616.20362 13356.53948 1.093071909 1.089596343 1.075818469 1.04853294 0.990384921 0.865369911 0.940950026 0.913083751 1.019440974 1 13.70525865 -8.519076496 3.464256661 1.05149815 0.910297087 0.803116328 0.032696573 0.099913397 2.531092561 0.006202689 0.013906326 3.03E-09 8.519076496 -0.141201062 AS(ph)SNPVY(ph)MEMEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSNPVYMEMEK 12 0 F5GWM5 F5GWM5 HPS5 2 0 AS(0.719)S(0.319)NPVY(0.962)MEMEK 69.451 0.0034459 0 314.65 460.51 539.17 1040.3 381.52 360.84 358.82 409.75 424.92 527.8 TRUE FALSE FALSE 310.8149248 466.9930719 548.5540277 1160.584381 362.0496108 337.7834886 389.2981618 421.6054698 386.914091 514.0876799 0.604595163 0.908391876 1.067043715 2.257561163 0.70425654 0.657054238 0.757260244 0.820104208 0.752622765 1 9.005870628 -6.223919747 17.05129262 0.90233276 0.781808483 0 0.459522948 0 0 0.062149569 0 5.97E-07 6.223919747 -0.120524277 AS(ph)SPGYIDSPTYSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPGYIDSPTYSR 14 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 AS(0.651)S(0.349)PGYIDSPTYSR 228.93 2.86E-33 31259000 1926.7 1878.5 1939.7 1923.8 2524.3 2460.4 1817.2 1934.3 1683 1513.3 TRUE FALSE FALSE 1903.216639 1904.945572 1973.459665 2146.238808 2395.475552 2303.188381 1971.552923 1990.265919 1532.468265 1473.984248 1.291205549 1.292378514 1.338860756 1.456079881 1.625170388 1.562559698 1.337567159 1.350262679 1.039677505 1 10.52550539 -11.17852775 0.425960808 0.976414651 1.476174732 0.762839665 0.091595208 0.422783778 0.18018314 0.088473177 0.043244299 6.63E-12 11.17852775 0.49976008 AS(ph)SPIKQSHEPVPDTSVEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPIKQSHEPVPDTSVEK 19 1 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 AS(0.426)S(0.426)PIKQS(0.149)HEPVPDTSVEK 54.103 0.018122 5532900 2192.4 2171 2362 1845.3 2561.3 3297.2 3500.4 2911.5 2283.5 2173.8 TRUE FALSE FALSE 2165.678186 2201.563395 2403.109619 2058.662268 2430.587303 3086.519561 3797.723889 2995.739659 2079.258041 2117.324363 1.02283723 1.039785606 1.134974717 0.972294234 1.147952268 1.457745264 1.793642937 1.414870443 0.982021497 1 11.04802658 -8.25381012 2.594790293 1.022179319 1.609160903 0.856994891 0.097756867 0.061809943 0.816139457 0.012458488 0.035260936 5.57E-09 8.25381012 0.586981583 AS(ph)TPDWVSEGPQPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 AS(0.5)T(0.5)PDWVSEGPQPGLR 263.98 1.78E-73 128070000 3812.5 3635 3952.2 2585.7 2761.7 2235.9 1680.2 1581.8 3640.4 3492.3 TRUE FALSE FALSE 3766.031784 3686.173625 4020.986383 2884.6708 2620.760144 2093.033206 1822.916146 1627.566887 3314.793506 3401.569543 1.107145315 1.083668459 1.182097362 0.848041107 0.770456141 0.615313954 0.535904418 0.478475265 0.974489413 1 11.73198487 -8.592950052 1.307413677 1.063221284 0.511563504 0.915813368 0.069040447 0.089179203 0.297139088 0.011243172 0.034047612 2.55E-09 8.592950052 -0.551657779 AS(ph)VALTPTAPSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 AS(0.869)VALT(0.114)PT(0.017)APSR 96.034 0.020354 88552000 4282.9 4627.2 4330.8 3476.4 3462.2 3439.6 2761.8 2985.4 4535 4410.4 TRUE FALSE FALSE 4230.698367 4692.341843 4406.175757 3878.357725 3285.511015 3219.820661 2996.387223 3071.777839 4129.378242 4295.817172 0.984841346 1.092304829 1.025689777 0.902821878 0.764816305 0.749524603 0.697512744 0.715062517 0.961255583 1 12.06871688 -8.847147343 2.185544442 1.00384277 0.720730215 0.933951631 0.035306296 0.055050195 0.535093154 0.005542795 0.011491577 1.42E-09 8.847147343 -0.283112555 AS(ph)VPMPSEYTY(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 ASVPMPSEYTYVK 13 0 Q9UNP4-3 Q9UNP4-3 2 0 AS(0.912)VPMPS(0.039)EY(0.06)T(0.08)Y(0.908)VK 66.962 0.003988 0 504.8 488.56 598.56 3931.7 559.67 516.74 529.75 623.74 466.53 549.1 TRUE FALSE FALSE 498.6473034 495.4379605 608.9776857 4386.301653 531.1079515 483.7219817 574.7469518 641.7869328 424.8023884 534.8343028 0.932339793 0.926339163 1.138628698 8.201234719 0.993032699 0.904433353 1.074626195 1.199973392 0.794269152 1 9.062948189 -9.487245513 24.99940259 0.967286252 2.471592118 0.123310515 2.026656357 1040.70938 730137.4387 0.310560495 0.474269586 3.26E-10 9.487245513 1.504305866 AS(ph)VSGPNS(ph)PSETRR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETRR 14 1 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 2 0 AS(0.985)VS(0.009)GPNS(0.731)PS(0.208)ET(0.068)RR 93.716 0.014713 5138500 1613.2 1935.9 1757.2 1881.7 1701.8 1826.9 1596.9 1567 1793.7 1971.7 TRUE FALSE FALSE 1593.537698 1963.153651 1787.783329 2099.271008 1614.950796 1710.166986 1732.540646 1612.338673 1633.26698 1920.47495 0.829762293 1.022222993 0.930906872 1.093099917 0.84091219 0.890491691 0.902141757 0.839552046 0.85044951 1 10.90724743 AS(ph)VSGPNSPSET(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETR 13 0 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 2 0 AS(0.988)VS(0.013)GPNS(0.012)PS(0.136)ET(0.852)R 111.7 0.026793 5380900 3276.1 2717.5 3288.9 2205.7 3321.5 3207.3 2519.8 2265 3678.5 3833.4 TRUE FALSE FALSE 3236.169633 2755.757036 3346.141925 2460.733412 3151.991461 3002.363881 2733.831749 2330.534201 3349.485747 3733.807715 0.86672102 0.738055424 0.896174142 0.659041279 0.84417616 0.804102436 0.732183325 0.624170921 0.897069695 1 11.86643192 -14.30323148 0.040850619 2.080873553 1.69E-07 0.520539073 0.077085003 158.1668646 0.814692793 29.67652747 14.25205872 4.97E-15 14.30323148 -2.080873385 AS(ph)VSPMDEPVPDSESPIEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSPMDEPVPDSESPIEK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 AS(0.536)VS(0.464)PMDEPVPDSESPIEK 61.736 0.0097845 36861000 4562.7 4224.5 4534 4709.1 4546.2 5052 4192.3 4075.7 5267.5 5056.4 TRUE FALSE FALSE 4507.088057 4283.972622 4612.912368 5253.588299 4314.19045 4729.193505 4548.393857 4193.623949 4796.361607 4925.033999 0.915138466 0.869836152 0.936625487 1.066711072 0.875971709 0.960235707 0.923525372 0.85149137 0.973873806 1 12.26591797 AS(ph)WESLDEEWR ddPTM_HeLa_Romidepsin_16h_R1 1 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 AS(0.756)WES(0.244)LDEEWR 111.94 0.01369 1114600 160.45 117.69 152.48 0 182.39 0 57.224 0 173.96 251.58 TRUE FALSE FALSE 158.4943737 119.3468429 155.1338504 0 173.0819577 0 62.08460513 0 158.4005819 245.0439153 0.646799875 0.48704267 0.633085911 0 0.706330363 0 0.253361138 0 0.64641712 1 7.936896514 -10.00680631 0.291203003 1.063457658 3.69E-22 0.538317877 0.227898033 0.646001081 0.169101005 0.184650354 0.263993226 9.84E-11 10.00680631 -1.063457658 ASAETVDPASLWEY ddPTM_HeLa_Romidepsin_16h_R1 1 ASAETVDPASLWEY 14 0 Q16658 Q16658 FSCN1 Fascin 0 0 129.38 0.024461 2820800 1920.7 1709.6 1699.1 1899.1 1740.7 2071.9 1904.7 2286.8 1604.5 2047 FALSE FALSE TRUE 1897.28977 1733.667794 1728.672123 2118.682878 1651.865584 1939.512277 2066.48517 2352.96495 1460.989501 1993.818645 0.95158593 0.869521307 0.867015727 1.062625672 0.828493398 0.972762634 1.036445905 1.180129876 0.732759474 1 10.96131847 -7.361895362 2.182921599 0.956425391 1.212287863 0.370303149 0.097658967 0.325450892 2.045779004 0.00963644 0.147779951 4.35E-08 7.361895362 0.255862472 ASAGRLT(ph)PESQSK ddPTM_HeLa_Romidepsin_16h_R1 2 ASAGRLTPESQSK 13 1 A0A0D9SGJ6;J3KQV8;O43426;H7BZ56;H7BZC2;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 ASAGRLT(0.557)PES(0.439)QS(0.004)K;ASAGRLT(0.99)PES(0.009)QS(0.001)K ; 161.49 0.0015944 17873500 4002.2 3694.1 3173.4 3042.1 3867.2 4236.5 3587.2 4032 3970.6 3531.9 TRUE FALSE FALSE 3953.419647 3746.105637 3228.631696 3393.841916 3669.842353 3965.801323 3891.896678 4148.659559 3615.459591 3440.140729 1.149202884 1.088939649 0.938517331 0.986541593 1.066770997 1.152802061 1.131319032 1.20595635 1.050962701 1 11.74825187 -8.257445589 4.148260481 1.056264524 1.162215439 0.467092329 0.058743294 0.216057127 9.093737185 0.010902289 0.027577425 5.53E-09 8.257445589 0.105950915 ASAGRLTPES(ph)QSK ddPTM_HeLa_Romidepsin_16h_R1 1 ASAGRLTPESQSK 13 1 A0A0D9SGJ6;J3KQV8;O43426;H7BZ56;H7BZC2;J3KPK1;C9JFZ1;O43426-4;O43426-2 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 ASAGRLT(0.236)PES(0.701)QS(0.063)K 139.86 0.0075974 3786600 1460.4 1444.5 1152.9 1581 1743.6 1910.3 1585 2016.2 1999.8 1442.9 TRUE FALSE FALSE 1442.600083 1464.835709 1172.965741 1763.802659 1654.617586 1788.237995 1719.62986 2074.535566 1820.932879 1405.41325 1.026459714 1.042281129 0.83460558 1.255006425 1.17731748 1.27239301 1.223575956 1.476103606 1.295656548 1 10.45677869 -8.104924367 0.640966828 1.002893507 1.467959842 0.425629912 0.132897036 0.60321039 0.305044364 0.017032829 0.167882166 7.85E-09 8.104924367 0.465066334 SNVSSPATPTASSSSST(ph)TPTRK ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSS(0.002)PAT(0.014)PT(0.043)AS(0.128)S(0.031)S(0.091)S(0.091)S(0.091)T(0.27)T(0.192)PT(0.047)RK 76.152 0.001024 2528300 1606.7 1326.3 1173.9 1277.1 980.91 860.25 763.72 788.62 1660.1 1684.9 TRUE FALSE FALSE 1587.116922 1344.971686 1194.331237 1424.764311 930.8505024 805.2828013 828.5903577 811.4374755 1511.616498 1641.126055 0.967090199 0.819541974 0.727751067 0.868162629 0.567202318 0.490689182 0.504891355 0.494439457 0.921084943 1 10.68047034 -9.027906248 0.573237324 0.998535582 0.428314698 0.873238869 0.069613966 0.198598253 0.11700487 0.015252889 0.053091381 9.38E-10 9.027906248 -0.570220884 down ASAISIK(ac)LGSSKPK ddPTM_HeLa_Romidepsin_16h_R1 2 ASAISIKLGSSKPK 14 2 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 1 ; ASAISIK(1)LGSSKPK;ASAISIK(1)LGSSKPK 127.57 0.0005793 8724000 4157.7 4218 3760.6 3422.8 3338.6 3163 3538.1 3443.8 4858.2 4010.7 FALSE TRUE FALSE 4107.024353 4277.381115 3826.051666 3818.560241 3168.218784 2960.894508 3838.626126 3543.44092 4423.670424 3906.501436 1.051330563 1.094939087 0.979406184 0.977488503 0.811011806 0.757940207 0.982625039 0.90706249 1.13238674 1 11.93166143 -8.96616798 3.480206838 1.027329481 0.865993055 0.596976974 0.07069352 0.129830713 3.310509446 0.009815768 0.018126163 1.08E-09 8.96616798 -0.161336426 ASAS(ph)PDRIPSLPQETVDQEPK ddPTM_HeLa_Romidepsin_16h_R1 4 ASASPDRIPSLPQETVDQEPK 21 1 A0A494C1R1;A0A2R8Y5U1;Q76L82;Q8IXJ9 A0A494C1R1 ASXH1;ASXL1 Putative Polycomb group protein ASXL1 1 0 AS(0.246)AS(0.731)PDRIPS(0.005)LPQET(0.018)VDQEPK;AS(0.198)AS(0.716)PDRIPS(0.035)LPQET(0.051)VDQEPK;AS(0.231)AS(0.765)PDRIPS(0.004)LPQET(0.001)VDQEPK;AS(0.12)AS(0.878)PDRIPS(0.002)LPQETVDQEPK ;;; 77.062 0.00144 37058000 6964.18 6828 6965.16 5260.02 4490.92 4156.03 3659.51 4055.69 8142.4 7296.4 TRUE FALSE FALSE 6879.297895 6924.124763 7086.385688 5868.208262 4261.731594 3890.473096 3970.348688 4173.034991 7414.123351 7106.838476 0.967982869 0.974290437 0.997122098 0.825712908 0.599666309 0.547426695 0.558665953 0.58718585 1.043237915 1 12.79499219 -8.900837218 2.310336868 0.984593892 0.561901245 0.985361437 0.024309981 0.018274748 0.197800706 0.002854495 0.005705349 1.26E-09 8.900837218 -0.422692647 AQSLVISPPAPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 AQSLVISPPAPSPR 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 AQSLVISPPAPS(1)PR;AQSLVISPPAPS(1)PR ; 140.77 0.00089443 41755000 5488.8 5794.6 6743.5 3248.2 2010.17 1642.59 1863.76 1624.6 7964.6 7090.1 TRUE FALSE FALSE 5421.900394 5876.176531 6860.867789 3623.772167 1907.583524 1537.6338 2022.067728 1671.605238 7252.226228 6905.89818 0.785111546 0.850892437 0.99347943 0.524735823 0.276225261 0.222655151 0.292803003 0.242054718 1.050149602 1 12.75361335 -9.026966117 2.860422566 0.898041543 0.258262223 0.939159735 0.081224482 0.051894176 0.854100748 0.013898843 0.025462826 9.40E-10 9.026966117 -0.639779319 down ASAS(ph)PSTSSTSSRPK ddPTM_HeLa_Romidepsin_16h_R1 2 ASASPSTSSTSSRPK 15 1 J3KP75;F6TH74;O75167-5;O75167-2;O75167;O75167-4;F5H858 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 0 AS(0.448)AS(0.533)PS(0.016)T(0.003)SSTSSRPK;AS(0.01)AS(0.974)PS(0.013)T(0.002)SSTSSRPK ; 115.87 0.0014187 35430000 7643.2 7589.2 7828.5 6848.3 7411.1 8174.5 6955.5 6065.6 8279.5 8142.3 TRUE FALSE FALSE 7550.041739 7696.040957 7964.751759 7640.132668 7032.883912 7652.175832 7546.299996 6241.098566 7538.960784 7930.761872 0.951994507 0.970403737 1.004285829 0.963354189 0.886785409 0.964872727 0.951522706 0.786948173 0.950597295 1 12.95324375 -6.483121943 1.233584958 0.972101792 7.56E-26 0.715531612 0.032166296 3.481544513 1.075886179 0.005096617 6.882962763 3.29E-07 6.483121943 -0.972101792 ASASGSGAQVGGPISSGS(ph)SASSVTVTR ddPTM_HeLa_Romidepsin_16h_R1 1 ASASGSGAQVGGPISSGSSASSVTVTR 27 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 ASASGSGAQVGGPIS(0.008)S(0.337)GS(0.366)S(0.243)AS(0.038)S(0.006)VT(0.002)VTR 106.27 8.36E-09 14582000 1220.6 1354.5 1272.5 1187.3 1613.4 1417.4 1171.1 1564.2 1543 1489.3 TRUE FALSE FALSE 1205.722858 1373.568687 1294.647329 1324.581212 1531.062178 1326.832714 1270.573205 1609.457659 1404.990215 1450.607771 0.831184612 0.946891857 0.892486139 0.913121547 1.05546255 0.914673657 0.875890251 1.109505747 0.968552798 1 10.50244177 ASAVSELS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 6 ASAVSELSPR 10 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 ASAVSELS(1)PR;ASAVS(0.001)ELS(0.999)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR;ASAVSELS(1)PR ;;;;; 142.19 0.0044186 4845060400 18138.1 23056 15622.1 13219.1 17272.2 17162.4 16605.8 18257.2 19046.6 17331.6 TRUE FALSE FALSE 17917.02586 23380.58297 15893.9961 14747.55454 16390.73518 16065.77803 18016.29624 18785.44328 17343.02439 16881.32253 1.061352025 1.384997113 0.94151368 0.873601847 0.970939045 0.951689537 1.067232511 1.112794524 1.027349863 1 14.04314031 ASDPAS(ph)PHIGR ddPTM_HeLa_Romidepsin_16h_R1 1 ASDPASPHIGR 11 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 ASDPAS(1)PHIGR 85.163 0.018558 11885000 8948.1 8738.2 7591.6 6732.7 8828.1 7789.5 7846.8 8292.4 9630.6 8614.2 TRUE FALSE FALSE 8839.037115 8861.216609 7723.728613 7511.166452 8377.569115 7291.776089 8513.306996 8532.327511 8769.215016 8390.401842 1.053470058 1.056113494 0.920543349 0.895209383 0.998470547 0.869061605 1.014648304 1.016915241 1.045148395 1 13.03452419 -9.762613442 24.99985127 1.028270039 0.950997049 0.42118358 0.048885493 25.98243125 553262.54 0.00799458 0.010840207 1.73E-10 9.762613442 -0.07727299 ASDPQS(ph)PPQVSR ddPTM_HeLa_Romidepsin_16h_R1 2 ASDPQSPPQVSR 12 0 Q7L7X3-2;Q7L7X3-3;Q7L7X3 Q7L7X3-2 TAOK1 Serine/threonine-protein kinase TAO1 1 0 ASDPQS(0.999)PPQVS(0.001)R;ASDPQS(0.971)PPQVS(0.029)R ; 143.56 0.0015299 11499700 5076.4 5249.4 4398.1 3922.4 4562.9 4911.6 4163.9 4267 5508.9 4418.1 TRUE FALSE FALSE 5014.526884 5323.301191 4474.647086 4375.926343 4330.038186 4597.764611 4517.581562 4390.458913 5016.170187 4303.317125 1.165270125 1.237022752 1.039813464 1.016872849 1.00620941 1.068423376 1.049790529 1.020249911 1.165651994 1 12.07123345 -9.55974758 24.99975554 1.094351574 1.033287056 0.313255691 0.064845966 284.9642351 193225.3822 0.012840559 0.018159309 2.76E-10 9.55974758 -0.061064518 ASDPQSPPQVS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 ASDPQSPPQVSR 12 0 Q7L7X3-2;Q7L7X3-3;Q7L7X3 Q7L7X3-2 TAOK1 Serine/threonine-protein kinase TAO1 1 0 ASDPQS(0.459)PPQVS(0.541)R 127.78 0.0047997 26691000 4694.6 4442.8 3421.7 3042.3 4113.7 4416.6 3623.2 3322.4 4178.4 4052.3 TRUE FALSE FALSE 4637.380409 4505.345855 3481.253253 3394.06504 3903.762539 4134.393514 3930.954518 3418.528402 3804.673439 3947.020662 1.174906545 1.141454844 0.881995194 0.859905567 0.98904031 1.047471971 0.995929552 0.866103498 0.963935526 1 11.94654836 -9.764343199 24.99888823 1.089317061 0.94607662 0.369611567 0.081413636 61.74280754 531542.7543 0.01452073 0.019559553 1.72E-10 9.764343199 -0.143240441 ASDSGPSSSSS(ph)SSSSPPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASDSGPSSSSSSSSSPPR 18 0 Q16643-3 Q16643-3 DBN1 Drebrin 1 0 ASDSGPS(0.003)S(0.006)S(0.006)S(0.077)S(0.338)S(0.338)S(0.077)S(0.077)S(0.077)PPR 69.216 0.024528 1449800 624.79 615.06 556.16 465.72 696.73 647.73 490.34 608.76 705.04 414.39 TRUE FALSE FALSE 617.1748192 623.7188308 565.8397315 519.5687377 661.1732682 606.3421435 531.9894674 626.3735101 641.9794566 403.6240881 1.529083217 1.545296352 1.401897826 1.287258994 1.638091699 1.502244691 1.318032008 1.55187346 1.590538017 1 8.656868466 -12.25871078 0.844532533 0.980126666 1.470612115 0 0.208824986 0.268810173 0.322551978 0.086818389 0.020337571 5.51E-13 12.25871078 0.490485449 ASDSGPSSSSSSSS(ph)SPPR ddPTM_HeLa_Romidepsin_16h_R1 2 ASDSGPSSSSSSSSSPPR 18 0 Q16643-3 Q16643-3 DBN1 Drebrin 1 0 ASDSGPSSSSSS(0.002)S(0.017)S(0.605)S(0.376)PPR;ASDS(0.003)GPS(0.001)S(0.004)S(0.008)S(0.031)S(0.127)S(0.127)S(0.031)S(0.334)S(0.334)PPR ; 195.6 5.74E-15 5866900 2031.84 2140.01 2023.48 1341.32 1894.6 2289.39 2303.59 2331.16 2454.96 2238.63 TRUE FALSE FALSE 2007.075153 2170.137117 2058.697821 1496.40973 1797.911492 2143.105368 2499.256877 2398.608437 2235.382229 2180.47007 0.920478194 0.995261135 0.944153212 0.6862785 0.824552245 0.982863923 1.146200955 1.100041899 1.025183634 1 11.09042347 -7.868046596 4.631614837 0.932668432 1.122249604 0.418776473 0.095500897 0.168293129 6.03665784 0.014356962 0.04641222 1.36E-08 7.868046596 0.189581173 ASDSGPSSSSSSSSS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASDSGPSSSSSSSSSPPR 18 0 Q16643-3 Q16643-3 DBN1 Drebrin 1 0 ASDSGPSSSS(0.001)S(0.006)S(0.021)S(0.131)S(0.131)S(0.71)PPR 213 9.93E-29 3696300 1522.3 1372.4 1153.4 874.37 1497.9 1574 1349.6 1558.7 1491.5 1318.8 TRUE FALSE FALSE 1503.745622 1391.720683 1173.474443 975.4687734 1421.456574 1473.42648 1464.23499 1603.798525 1358.096504 1284.537386 1.170651503 1.083441166 0.913538567 0.759393058 1.106590271 1.147048343 1.139892857 1.248541726 1.057265066 1 10.32703316 -8.329850874 3.854784532 1.045369938 1.176593088 0.291320316 0.112888781 0.330019031 9.622833354 0.019195602 0.046210433 4.68E-09 8.329850874 0.13122315 ASDSSSPSCSS(ph)GPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASDSSSPSCSSGPR 14 0 H0YM74;Q92610 H0YM74 ZNF592 Zinc finger protein 592 1 0 AS(0.015)DS(0.002)S(0.029)S(0.354)PS(0.006)CS(0.232)S(0.363)GPR 117.07 0.0045641 2736900 1391.2 1106.1 1423.6 154.24 897.42 808.87 670.25 318.63 1597.4 1601.2 TRUE FALSE FALSE 1374.243519 1121.671705 1448.377161 172.0739545 851.6213087 757.1858175 727.1810183 327.8490563 1454.524543 1559.600593 0.881150934 0.719204462 0.928684669 0.110332065 0.546050901 0.485499827 0.466261055 0.210213472 0.932626308 1 10.60696089 -9.281011895 24.47505135 0.92099068 0.386271329 0.77784165 0.140589829 209.7883911 262335.6665 0.021795188 0.033324523 5.24E-10 9.281011895 -0.534719351 ASEAAS(ph)PLPDSPGDK ddPTM_HeLa_Romidepsin_16h_R1 2 ASEAASPLPDSPGDK 15 0 Q68CZ2;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 0 ASEAAS(1)PLPDSPGDK;AS(0.047)EAAS(0.953)PLPDSPGDK ; 204.67 2.25E-18 22979000 9904.2 9743.2 9004.9 7630.2 7955.5 7796.5 5630.5 6457 9590 10313.8 TRUE FALSE FALSE 9783.483801 9880.365025 9161.626507 8512.439625 7549.501149 7298.328812 6108.754529 6643.823108 8732.246381 10045.84599 0.973883515 0.983527424 0.911981581 0.847359161 0.751504767 0.72650216 0.608087615 0.661350285 0.869239524 1 13.29431144 -8.769104915 0.817979667 0.991485311 0.622096197 0.887055567 0.044608365 0.064706962 0.079244685 0.003758286 0.013580142 1.70E-09 8.769104915 -0.369389115 ASEAASPLPDS(ph)PGDKLVIVK ddPTM_HeLa_Romidepsin_16h_R1 2 ASEAASPLPDSPGDKLVIVK 20 1 Q68CZ2;Q68CZ2-2 Q68CZ2 TNS3 Tensin-3 1 0 ASEAASPLPDS(1)PGDKLVIVK;ASEAAS(0.001)PLPDS(0.999)PGDKLVIVK ; 92.096 0.00053961 35597000 6972.7 5678.5 6153.5 6684 6321.2 6498.6 4475.5 5231.1 6331.7 6269.3 TRUE FALSE FALSE 6887.71405 5758.442072 6260.599086 7456.835529 5998.605576 6083.360433 4855.648858 5382.453625 5765.376894 6106.422682 1.127945838 0.943013999 1.025248236 1.221146311 0.982343655 0.99622328 0.795170775 0.881441378 0.944149659 1 12.57611174 -7.963105151 2.439013265 1.057960263 0.836817571 0.425274411 0.085744155 0.172718549 2.022717679 0.011710194 0.044318704 1.09E-08 7.963105151 -0.221142692 ASEDS(ph)EEEPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDSEEEPSGK 12 0 Q8IY33-4;Q8IY33-2;Q8IY33 Q8IY33-4 MICALL2 MICAL-like protein 2 1 0 ASEDS(0.999)EEEPS(0.001)GK 135.81 0.0026525 3355400 1128 1049 1152.3 1180.8 1164 1582.5 1963 957.61 1352.7 1317.2 TRUE FALSE FALSE 1114.251502 1063.76785 1172.355298 1317.329652 1104.596737 1481.383357 2129.737171 985.3169345 1231.711124 1282.978954 0.868487748 0.829138971 0.913775939 1.026774171 0.860962476 1.154643537 1.659993848 0.767991502 0.960040007 1 10.32528179 -8.115303259 5.166655239 0.929440074 1.256750106 0.256942576 0.209155189 0.18075624 6.950960055 0.026302326 0.069520137 7.67E-09 8.115303259 0.327310031 ASEDT(ph)TSGSPPKK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDTTSGSPPKK 13 1 H0YER7;G3V1C3;Q9BZZ5-1;Q9BZZ5-5;Q9BZZ5-2;Q9BZZ5-6;Q9BZZ5 H0YER7 API5 Apoptosis inhibitor 5 1 0 ASEDT(0.698)T(0.237)S(0.038)GS(0.027)PPKK 119.25 0.012386 98298000 4889.1 4330.6 6171.7 5442.4 5065.6 5565.4 6806.8 1713.9 7598.1 6072.6 TRUE FALSE FALSE 4829.509769 4391.5663 6279.11585 6071.675895 4807.08353 5209.788902 7384.969422 1763.488992 6918.506906 5914.832977 0.816508224 0.742466663 1.061588024 1.02651688 0.812716699 0.880800679 1.248550796 0.298146879 1.16968762 1 12.53012171 -16.52287517 0.01594803 2.02172094 1.09E-06 0.092448264 0.2425089 13784.91892 17.75164671 1408.042719 896.6942138 3.00E-17 16.52287517 -2.021719852 ASEDTTS(ph)GSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDTTSGSPPK 12 0 H0YER7;G3V1C3;Q9BZZ5-1;Q9BZZ5-5;Q9BZZ5-2;Q9BZZ5-6;Q9BZZ5 H0YER7 API5 Apoptosis inhibitor 5 1 0 ASEDT(0.049)T(0.295)S(0.576)GS(0.081)PPK 166.62 0.00024328 70244000 5280.2 4833.8 4826.5 4206.7 4082.6 4338.3 4440.4 3040.9 5073.4 4661.5 TRUE FALSE FALSE 5215.842891 4901.850363 4910.503208 4693.098447 3874.249688 4061.096631 4817.567465 3128.883644 4619.622397 4540.393558 1.14876449 1.079609135 1.081514883 1.033632523 0.853284994 0.894437141 1.06104623 0.689121682 1.017449774 1 12.14860164 -8.867365804 4.695724101 1.072994934 0.889611222 0.489543594 0.092493918 0.145915439 5.43312474 0.013875562 0.025787198 1.36E-09 8.867365804 -0.183383712 ASEDTTSGS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 3 ASEDTTSGSPPK 12 0 H0YER7;G3V1C3;Q9BZZ5-1;Q9BZZ5-5;Q9BZZ5-2;Q9BZZ5-6;Q9BZZ5 H0YER7 API5 Apoptosis inhibitor 5 1 0 ASEDT(0.003)T(0.003)S(0.027)GS(0.967)PPK;ASEDTT(0.001)S(0.027)GS(0.972)PPK;ASEDT(0.002)T(0.01)S(0.185)GS(0.804)PPK ;; 163.71 0.00043974 119368000 11480 11552.8 12235.9 10691.1 10488.8 11120.1 10633.4 7675.3 12792.6 12404.5 TRUE FALSE FALSE 11340.07734 11715.44062 12448.86071 11927.25529 9953.517397 10409.5615 11536.60073 7897.372696 11648.39782 12082.2293 0.938574915 0.969642301 1.030344682 0.987173392 0.823814641 0.861559671 0.954840406 0.653635393 0.964093424 1 13.56059905 -6.269998958 0.617228663 0.973055545 3.91E-20 0.64366833 0.063355626 4.802436376 0.512609561 0.011172709 4.408325567 5.37E-07 6.269998958 -0.973055545 ASEDTTSGS(ph)PPKK ddPTM_HeLa_Romidepsin_16h_R1 3 ASEDTTSGSPPKK 13 1 H0YER7;G3V1C3;Q9BZZ5-1;Q9BZZ5-5;Q9BZZ5-2;Q9BZZ5-6;Q9BZZ5 H0YER7 API5 Apoptosis inhibitor 5 1 0 AS(0.002)EDT(0.024)T(0.019)S(0.257)GS(0.698)PPKK;AS(0.001)EDT(0.041)T(0.109)S(0.061)GS(0.788)PPKK;ASEDT(0.02)T(0.01)S(0.114)GS(0.856)PPKK ;; 69.379 0.019641 696333000 9789.4 14572.5 14363.1 12934.3 11118.4 12028 17019.2 4291.3 17053.2 14415.6 TRUE FALSE FALSE 9670.083027 14777.65204 14613.08373 14429.82462 10550.98656 11259.44962 18464.81042 4415.461995 15527.91908 14041.08063 0.688699344 1.052458313 1.040737826 1.027686187 0.751436932 0.801893381 1.31505622 0.314467391 1.105892024 1 13.77736635 -7.229791412 24.18146305 0.900643449 0.314465766 0.488090093 0.189600948 6530.798188 4989906.994 0.026289628 4.888478603 5.89E-08 7.229791412 -0.586177683 ASEDTTSGSPPKK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEDTTSGSPPKK 13 1 H0YER7;G3V1C3;Q9BZZ5-1;Q9BZZ5-5;Q9BZZ5-2;Q9BZZ5-6;Q9BZZ5 H0YER7 API5 Apoptosis inhibitor 5 0 0 91.307 0.013745 3318900 2171.5 1880.5 2547.7 2027.7 2118.4 1833.2 2737.1 1022.8 2887.7 2094.3 FALSE FALSE TRUE 2145.032923 1906.973728 2592.04165 2262.152215 2010.290143 1716.064436 2969.589206 1052.393104 2629.41688 2039.889784 1.051543539 0.93484155 1.270677303 1.108958059 0.985489588 0.841253508 1.455759634 0.515906846 1.288999484 1 10.99427549 -7.22481462 24.04957257 1.047665703 0.515904755 0.454176242 0.184326291 7945.259224 5217086.608 0.020710937 6.547563875 5.96E-08 7.22481462 -0.531760948 ASEENLLSSSSVPSADRDS(ph)SPTTNSK ddPTM_HeLa_Romidepsin_16h_R1 3 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 ASEENLLSSSSVPS(0.006)ADRDS(0.34)S(0.34)PT(0.267)T(0.023)NS(0.023)K;ASEENLLSSSSVPS(0.004)ADRDS(0.433)S(0.433)PT(0.123)T(0.006)NS(0.001)K;ASEENLLS(0.001)S(0.001)S(0.001)S(0.001)VPS(0.007)ADRDS(0.421)S(0.421)PT(0.107)T(0.035)NS(0.005)K ;; 122.47 1.06E-07 147663000 5644.1 5443.5 5494.6 5177.8 5059.2 4950.6 4114.5 4152.4 6147.2 6009.5 TRUE FALSE FALSE 5575.307538 5520.133736 5590.231208 5776.481598 4801.010146 4634.272637 4463.985527 4272.543143 5597.379036 5853.372324 0.952494943 0.943068958 0.955044528 0.986863859 0.820212671 0.791726953 0.762634816 0.729928476 0.956265675 1 12.51505233 -8.621377197 2.63848986 0.973453695 0.762214073 0.939089589 0.023825989 0.051443169 0.722474473 0.004152891 0.009256865 2.39E-09 8.621377197 -0.211239622 ASEENLLSSSSVPSADRDSSPT(ph)TNSK ddPTM_HeLa_Romidepsin_16h_R1 1 ASEENLLSSSSVPSADRDSSPTTNSK 26 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 ASEENLLS(0.001)SS(0.001)S(0.002)VPS(0.179)ADRDS(0.194)S(0.194)PT(0.361)T(0.056)NS(0.012)K 58.581 0.002554 24523000 2301.7 2618.5 2366.1 2047.5 2402.3 2036.3 2089.5 1648.7 2450.2 2259.1 TRUE FALSE FALSE 2273.645995 2655.363312 2407.280978 2284.241584 2279.701667 1906.187002 2266.982078 1696.402533 2231.047975 2200.408256 1.033283705 1.206759384 1.094015609 1.038098988 1.036035772 0.866287879 1.030255213 0.770948995 1.013924561 1 11.10355551 -8.27293133 23.20254439 1.039667508 0.903273155 0.459394905 0.082563954 223.4462891 451144.8259 0.011918715 0.026906213 5.33E-09 8.27293133 -0.136394352 ASEIGEK(ac)YR ddPTM_HeLa_Romidepsin_16h_R1 2 ASEIGEKYR 9 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 0 1 ; ASEIGEK(1)YR;ASEIGEK(1)YR 123.21 0.0061524 15486300 3451.7 3635.4 3546.2 2816.9 4903.8 6392 5048.4 5615.7 3769.9 3152.7 FALSE TRUE FALSE 3409.629353 3686.579257 3607.920123 3142.603232 4653.540787 5983.571829 5477.21097 5778.181419 3432.710702 3070.7924 1.110341863 1.200530279 1.174915023 1.023385115 1.515420185 1.948543259 1.78364743 1.881658109 1.117858277 1 11.58439527 -8.561587931 3.019054988 1.073629601 1.859192464 0.952232521 0.077063168 0.039678072 0.736486435 0.012753099 0.028537541 2.74E-09 8.561587931 0.785562863 ASEIMVDDEELAQHPATTEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEIMVDDEELAQHPATTEDIR 22 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 0 73.346 0.013353 3107800 790.87 993.8 879.16 757.34 1060.7 942.11 702.89 1036 1092 890.2 FALSE FALSE TRUE 781.2305722 1007.790742 894.461411 844.9072142 1006.568521 881.9122115 762.5934591 1065.975025 994.328785 867.0724757 0.900998007 1.16229124 1.031587827 0.974436668 1.160881644 1.017114758 0.87950371 1.22939553 1.146765481 1 9.760008778 -10.28250085 24.99827735 0.95324906 1.054967654 0 0.116093903 971.5094436 1153100.428 0.01636292 0.018722442 5.22E-11 10.28250085 0.101718594 ASEK(ac)ILQVR ddPTM_HeLa_Romidepsin_16h_R1 1 ASEKILQVR 9 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 0 1 ASEK(1)ILQVR 109.66 0.011036 3600700 1991.9 1393.8 2792.7 1762.7 2256.8 2182.2 1909.9 1330 1740.1 1362.3 FALSE TRUE FALSE 1967.621957 1413.421953 2841.305772 1966.511668 2141.627075 2042.764463 2072.126858 1368.481452 1584.461098 1326.90725 1.48286322 1.065200264 2.141299456 1.48202647 1.613999076 1.53949303 1.561621477 1.031331656 1.194100867 1 10.37385181 -12.01540196 0.605047829 0.958321343 1.520408774 0.212807237 0.294750793 0.927254873 0.563210959 0.276515738 0.065603678 9.65E-13 12.01540196 0.562087431 ASELAET(ph)PKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASELAETPKEEK 12 1 Q9H6E5;F5H0R1;H3BRB1 Q9H6E5 TUT1 Speckle targeted PIP5K1A-regulated poly(A) polymerase 1 0 ASELAET(1)PKEEK 107.17 0.0027573 0 907.29 623.35 684.86 647.58 656.8 627.76 718.23 1113.7 715.44 870.17 TRUE FALSE FALSE 896.2316005 632.1255377 696.779701 722.4562466 623.2810451 587.648162 779.2364383 1145.923152 651.4492545 847.562858 1.057421986 0.745815525 0.822097965 0.852392527 0.735380319 0.693338738 0.919384835 1.352021436 0.76861468 1 9.727176557 -10.28130482 24.61749699 1.027115944 0.860918781 0 0.192807737 897.5641585 1112268.749 0.029703863 0.033994 5.23E-11 10.28130482 -0.166197163 ASEPLLS(ph)PPPFGESR ddPTM_HeLa_Romidepsin_16h_R1 3 ASEPLLSPPPFGESR 15 0 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 AS(0.013)EPLLS(0.987)PPPFGESR;AS(0.001)EPLLS(0.999)PPPFGESR;ASEPLLS(1)PPPFGESR ;; 141.06 0.00019585 28745000 5405.2 5394.8 4691.4 3893.61 4027.83 3923.36 3071.99 3283.67 5382.2 4999.5 TRUE FALSE FALSE 5339.319343 5470.748136 4773.051849 4343.807508 3822.274805 3672.669958 3332.924754 3378.677811 4900.802552 4869.612269 1.096456771 1.123446351 0.98017082 0.89202328 0.784923849 0.754201722 0.684433292 0.693828918 1.006405085 1 12.24959119 -8.915685889 1.336472602 1.052577183 0.703539361 0.932074054 0.040358053 0.087856521 0.313048387 0.008005803 0.018722745 1.21E-09 8.915685889 -0.349037821 ASES(ph)PARGPSGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASESPARGPSGSPR 14 1 J3KRZ2;O43237-2;O43237 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 AS(0.055)ES(0.941)PARGPS(0.005)GSPR 65.495 0.025497 17506000 1097.5 1073.8 862.07 1558.1 859.36 984.77 796.17 829.7 1140.6 1031.9 TRUE FALSE FALSE 1084.123248 1088.916985 877.0739667 1738.254853 815.5036525 921.8463752 863.7966599 853.7060604 1038.581879 1005.091089 1.078631837 1.083401292 0.872631323 1.729450068 0.811372881 0.917176946 0.85942127 0.849381782 1.033321149 1 9.97311054 ASES(ph)SSEEKDDYEIFVK ddPTM_HeLa_Romidepsin_16h_R1 2 ASESSSEEKDDYEIFVK 17 1 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 AS(0.029)ES(0.799)S(0.054)S(0.114)EEKDDY(0.003)EIFVK;AS(0.024)ES(0.445)S(0.265)S(0.265)EEKDDY(0.001)EIFVK ; 64.2 0.016763 51774000 3773.1 3259 3481.9 2943 3194.34 2812.1 2586.78 3114.5 3701.5 3798.81 TRUE FALSE FALSE 3727.112006 3304.880288 3542.501009 3283.283507 3031.32091 2632.415886 2806.501029 3204.613144 3370.428569 3700.116369 1.007295889 0.893182797 0.957402594 0.887346013 0.819250155 0.711441377 0.758489936 0.866084421 0.910897992 1 11.85335493 -9.195995511 0.938226823 1.001638712 0.771792641 0.641476898 0.05514707 0.167830043 0.291351967 0.008508421 0.019494095 6.37E-10 9.195995511 -0.229846072 ASESSKPWPDATYGTGS(ph)ASR ddPTM_HeLa_Romidepsin_16h_R1 2 ASESSKPWPDATYGTGSASR 20 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 ASESSKPWPDATYGT(0.019)GS(0.926)AS(0.055)R;ASESSKPWPDAT(0.004)YGT(0.028)GS(0.893)AS(0.075)R ; 150.48 5.71E-06 104251000 5097.4 4757.7 4699.6 4284.5 6144.4 6575.5 5512.1 6398.5 5339.6 4613.2 TRUE FALSE FALSE 5035.270928 4824.679025 4781.394567 4779.894049 5830.82834 6155.346771 5980.297636 6583.630502 4862.012803 4493.348399 1.1206055 1.073738023 1.064105015 1.063771073 1.297657743 1.369879703 1.330922311 1.465194754 1.082046699 1 12.13357521 -8.663236794 2.872441134 1.059520285 1.380507325 0.92226335 0.042950305 0.06168614 1.024787432 0.008026917 0.017237006 2.17E-09 8.663236794 0.32098704 ASFAEK(ac)TAQLER ddPTM_HeLa_Romidepsin_16h_R1 2 ASFAEKTAQLER 12 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 1 ; ASFAEK(1)TAQLER;ASFAEK(1)TAQLER 158.01 0.00095605 2047610 398.49 253.58 561.3 212.69 344 419.93 474.37 338.55 457.18 330.21 FALSE TRUE FALSE 393.6330506 257.1499059 571.069191 237.2822185 326.4443964 393.0978283 514.662976 348.3454101 416.2886758 321.6310966 1.223865027 0.79951817 1.775540976 0.737746508 1.014965281 1.222200939 1.600165473 1.083058864 1.294304811 1 8.329263089 -16.52276531 0.034085669 5.35E-06 1.85544216 0 0.31122831 2132.727354 5.824597139 254.6084453 97.48868268 3.00E-17 16.52276531 1.855436806 ASFGATGGPPAHLLTPS(ph)PLSGPGGSSLLEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASFGATGGPPAHLLTPSPLSGPGGSSLLEK 30 0 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 ASFGATGGPPAHLLT(0.136)PS(0.793)PLS(0.019)GPGGS(0.025)S(0.027)LLEK 50.492 0.0073894 10411000 1080.2 884.39 971.03 487.52 967.97 1101.1 904.82 766.26 1372.6 1262.5 TRUE FALSE FALSE 1067.034107 896.8404656 987.9303698 543.8893563 918.5708789 1030.743264 981.6753882 788.4305241 1249.831218 1229.700068 0.867718995 0.729316432 0.803391327 0.442294321 0.746987743 0.838207048 0.798304736 0.64115677 1.016370781 1 10.26409076 -10.62242109 0.977286631 0.967540066 0.709462986 0.537032245 0.108123405 0.285093522 0.564647049 0.026981031 0.026480538 2.39E-11 10.62242109 -0.25807708 ASGDPGASGMS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ASGDPGASGMSPR 13 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 ASGDPGASGMS(1)PR;ASGDPGASGMS(1)PR ; 103.14 0.015029 241896000 13652.2 14206.1 12974.7 8756.6 12606.9 11996.5 11174 12006.3 14845.1 13520.5 TRUE FALSE FALSE 13485.80174 14406.09385 13200.51921 9769.079293 11963.52285 11229.96237 12123.11928 12353.68335 13517.31708 13169.23546 1.024038318 1.093920288 1.002375518 0.741810663 0.908444753 0.852742166 0.920563636 0.938071415 1.026431422 1 13.68488397 -9.487328102 24.60231721 1.019303488 0.875541694 0.661277563 0.056068598 243.2115281 168311.3444 0.008370131 0.012782024 3.26E-10 9.487328102 -0.143761794 ASGGQDGAASSAGAAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ASGGQDGAASSAGAAKR 17 1 O60287 O60287 URB1 Nucleolar pre-ribosomal-associated protein 1 0 1 ; ASGGQDGAASSAGAAK(1)R;ASGGQDGAASSAGAAK(1)R 174.62 7.69E-12 550300 0 200.036 156.62 199.819 233.75 238.88 236.334 189.88 0 0 FALSE TRUE FALSE 0 202.8521121 159.3459054 222.923013 221.8208653 223.6163389 256.4082041 195.3738782 0 0 0 ASGQAFELILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 7 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 ASGQAFELILS(1)PR;AS(0.104)GQAFELILS(0.896)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR;ASGQAFELILS(1)PR ;;;;;; 162.64 0.00031398 2349520800 15738.8 14650.73 15951.14 14634.29 21616.81 22241.42 18024.44 19306.48 16106.61 15607.03 TRUE FALSE FALSE 15546.96945 14856.98336 16228.7629 16326.37547 20513.62352 20820.26504 19555.43548 19865.08254 14665.99446 15201.55711 1.022722168 0.977332996 1.067572406 1.073993628 1.349442256 1.369613974 1.286410026 1.306779456 0.964769224 1 13.89193149 -8.842305174 3.847483105 1.013801322 1.329298749 0.950267673 0.034972252 0.032527664 0.935214518 0.004989864 0.009511515 1.44E-09 8.842305174 0.315497427 ASGQAFELILSPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASGQAFELILSPR 13 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 0 0 150.14 0.00044291 395890 68.696 0 137.24 134.47 245.35 127.69 0 0 215.83 171.86 FALSE FALSE TRUE 67.85870673 0 139.6286046 150.0180541 232.828874 119.5310211 0 0 196.5256242 167.3950524 0.4053806 0 0.834126234 0.896191685 1.390894597 0.714065436 0 0 1.174022896 1 7.387113078 -12.37101179 1.142849581 0.995340203 0.541959534 0.197412475 0.436249682 0.868360684 2.060941853 0.304148438 0.081981941 4.26E-13 12.37101179 -0.45338067 ASGS(ph)ENEGDYNPGR ddPTM_HeLa_Romidepsin_16h_R1 2 ASGSENEGDYNPGR 14 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 AS(0.003)GS(0.997)ENEGDYNPGR;AS(0.004)GS(0.996)ENEGDYNPGR ; 163.9 0.00016707 30091000 3242.8 3178 3264.3 1910.79 2605.9 2925.7 2321.7 2567.3 3738 3873 TRUE FALSE FALSE 3203.275506 3222.739967 3321.113772 2131.72453 2472.911199 2738.757212 2518.90514 2641.580775 3403.663918 3772.378902 0.849139387 0.854299118 0.88037651 0.565087597 0.65553097 0.726002685 0.66772326 0.700242697 0.902259292 1 11.88125887 -10.16965492 0.455732999 0.984526051 0.65000902 0.678177395 0.073373354 0.349438714 0.179394975 0.03244265 0.041410034 6.77E-11 10.16965492 -0.334517031 ASGS(ph)ENEGDYNPGRK ddPTM_HeLa_Romidepsin_16h_R1 2 ASGSENEGDYNPGRK 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 AS(0.001)GS(0.999)ENEGDYNPGRK;ASGS(1)ENEGDYNPGRK ; 216 1.31E-28 4225800 3374.4 2765.7 2942.5 2815.4 2300.11 2293.6 1684.02 2452.8 3282.8 3671.2 TRUE FALSE FALSE 3333.271515 2804.635597 2993.712978 3140.929795 2182.726804 2147.046362 1827.060617 2523.767898 2989.178146 3575.821695 0.932169386 0.784333179 0.837209803 0.87837987 0.610412652 0.600434402 0.510948468 0.705786841 0.83594161 1 11.80405908 -9.169678442 0.542460173 0.984847963 0.549562494 0.650090299 0.08882153 0.30227786 0.165185876 0.019014698 0.058817739 6.77E-10 9.169678442 -0.435285469 ASHGYGGK(ac)FGVEQDR ddPTM_HeLa_Romidepsin_16h_R1 2 ASHGYGGKFGVEQDR 15 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 1 ; ASHGYGGK(1)FGVEQDR;ASHGYGGK(1)FGVEQDR 142.19 2.93E-06 12563100 3528.8 3327.8 3551 2345.5 3628.5 3064.5 4404.3 3412.5 5434.2 4143.8 FALSE TRUE FALSE 3485.789628 3374.648856 3612.803665 2616.697746 3443.324105 2868.68834 4778.401132 3511.235303 4948.151542 4036.143479 0.863643636 0.836107258 0.895112794 0.648316335 0.853122324 0.710749842 1.183902693 0.869948088 1.225960268 1 11.97876175 -11.95771421 0.801277922 0.999161302 0.857205097 0.245663082 0.151379121 1.007831307 1.199160841 0.083383295 0.026955289 1.10E-12 11.95771421 -0.141956204 ASIANSDGPTAGS(ph)QTPPFK ddPTM_HeLa_Romidepsin_16h_R1 1 ASIANSDGPTAGSQTPPFK 19 0 J3KP75;F6TH74;O75167-5;O75167-2;O75167;O75167-4;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 0 ASIANSDGPTAGS(0.909)QT(0.091)PPFK 255.22 8.75E-76 20121000 5341.7 5416 5421.4 4473 4212.9 3377.5 3317 3820.7 5747.3 5219.9 TRUE FALSE FALSE 5276.593306 5492.24659 5515.757193 4990.189306 3997.899993 3161.68865 3598.745897 3931.245926 5233.247094 5084.286246 1.037823807 1.080239452 1.084863622 0.981492596 0.786324727 0.621854966 0.707817326 0.773214909 1.029298281 1 12.31182954 -8.716855451 3.067468561 1.028726399 0.701580698 0.926860113 0.043712567 0.049376432 0.948267711 0.006881971 0.01428398 1.92E-09 8.716855451 -0.3271457 ASIANSDGPTAGSQT(ph)PPFKR ddPTM_HeLa_Romidepsin_16h_R1 1 ASIANSDGPTAGSQTPPFKR 20 1 J3KP75;F6TH74;O75167-5;O75167-2;O75167;O75167-4;H9KVA6 J3KP75 PHACTR2 Phosphatase and actin regulator;Phosphatase and actin regulator 2 1 0 ASIANSDGPT(0.133)AGS(0.387)QT(0.48)PPFKR 74.277 0.002923 17471000 2051.3 1994 1960.5 1761.7 1438.7 1831.1 1323.7 1367.7 2292.7 2432.7 TRUE FALSE FALSE 2026.297967 2022.071584 1994.62168 1965.396043 1365.27777 1714.09862 1436.135045 1407.272242 2087.63517 2369.498103 0.855159143 0.853375481 0.84179079 0.829456685 0.57618859 0.723401558 0.606092507 0.593911529 0.881045301 1 11.21036579 -6.533456942 0.161500571 1.05977243 1.08E-11 0.770685072 0.065197476 6.963273861 0.152104954 0.12332394 1.573315387 2.93E-07 6.533456942 -1.05977243 ASIDSS(ph)LENLSTASSR ddPTM_HeLa_Romidepsin_16h_R1 2 ASIDSSLENLSTASSR 16 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 ASIDS(0.062)S(0.938)LENLSTASSR;ASIDS(0.058)S(0.942)LENLSTASSR ; 147.75 0.0002994 28527000 3167.9 2874.8 3209.3 3176.7 3990.1 4991.9 4800.9 4894.7 4049.7 3215.4 TRUE FALSE FALSE 3129.288416 2915.27151 3265.15652 3544.005001 3786.470308 4672.933701 5208.688326 5036.320422 3687.484689 3131.863444 0.999177797 0.930842472 1.042560309 1.131596273 1.209015136 1.492061766 1.663127534 1.608090682 1.177409154 1 11.61280559 -8.348130235 1.20355525 0.996269871 1.671070823 0.926361747 0.068795535 0.046648302 0.122580315 0.005782674 0.023700553 4.49E-09 8.348130235 0.674800952 ASIGQS(ph)PGLPSTTFK ddPTM_HeLa_Romidepsin_16h_R1 2 ASIGQSPGLPSTTFK 15 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 AS(0.001)IGQS(0.986)PGLPS(0.011)T(0.001)T(0.002)FK;AS(0.015)IGQS(0.975)PGLPS(0.007)T(0.002)T(0.001)FK ; 176.49 6.42E-08 91283000 8898.7 8464.4 7690.6 6807.2 7631.8 8094.1 6033.5 7076 9032.2 8105.9 TRUE FALSE FALSE 8790.239222 8583.562045 7824.451667 7594.280493 7242.320768 7576.913133 6545.985339 7280.732896 8224.33741 7895.307549 1.113349818 1.087172601 0.99102557 0.961872662 0.91729432 0.959672956 0.829098208 0.922159504 1.041674103 1 12.94677975 -9.173273697 1.471163579 1.056903133 0.901176105 0.719044738 0.042513248 0.19282093 0.818931223 0.008780286 0.017090984 6.71E-10 9.173273697 -0.155727028 ASKAAS(ph)MS(ph)NRSDK ddPTM_HeLa_Romidepsin_16h_R1 1 ASKAASMSNRSDK 13 2 Q5JQC9-2;Q5JQC9 Q5JQC9-2 AKAP4 A-kinase anchor protein 4 2 0 ASKAAS(0.997)MS(0.95)NRS(0.053)DK 58.781 0.030525 8541100 2124.4 2089.3 2091.3 143.77 1611.5 1304.7 1106.5 1224.3 2298.9 2084 TRUE FALSE FALSE 2098.506996 2118.71322 2127.698199 160.3933639 1529.259142 1221.333881 1200.486082 1259.723189 2093.280626 2029.85738 1.033819921 1.043774426 1.048200835 0.079017061 0.753382556 0.601684578 0.591414005 0.620596896 1.031245174 1 10.98716265 -9.32144259 24.99992159 1.02110151 0.549152827 0.695952433 0.165633894 99.90031517 41622.51463 0.023210513 0.035454649 4.77E-10 9.32144259 -0.471948684 ASKPLPPAPAPDEYLVS(ph)PITGEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASKPLPPAPAPDEYLVSPITGEK 23 1 Q15459;Q15459-2;H7C1L2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 0 ASKPLPPAPAPDEY(0.051)LVS(0.925)PIT(0.023)GEK 79.407 0.00018203 13286000 2369.7 2712.1 2320.6 2036.8 1987.2 2379 2371.8 2153 2480.1 2748.4 TRUE FALSE FALSE 2340.817185 2750.281015 2360.98907 2272.304399 1885.785769 2226.989578 2573.260633 2215.293658 2258.273644 2676.996172 0.874419325 1.027375774 0.881954593 0.848826167 0.704440966 0.831898679 0.961249276 0.827529632 0.843584936 1 11.38639936 -9.529580367 23.65150261 0.945976335 0.837510178 0.278161352 0.0764374 81.14534239 286378.0869 0.012341178 0.017482836 2.95E-10 9.529580367 -0.108466157 ASLGS(ph)LEGEAEAEAS(ph)SPKGK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 AS(0.02)LGS(0.98)LEGEAEAEAS(0.675)S(0.325)PKGK;AS(0.008)LGS(0.992)LEGEAEAEAS(0.813)S(0.187)PKGK ; 94.019 0.0024031 28488000 3610 3089.51 2937.8 4672.8 3964.9 3329.9 2912.22 2617.48 3752.1 3505.3 TRUE FALSE FALSE 3565.999931 3133.004203 2988.931177 5213.091122 3762.556358 3117.130137 3159.583894 2693.212654 3416.502779 3414.231801 1.044451619 0.917630784 0.875432997 1.526870882 1.102021356 0.912981402 0.925415753 0.788819509 1.000665151 1 11.73734529 -8.081264208 4.032205913 1.045577027 0.867622445 0.20301439 0.171518313 0.318984022 9.58561031 0.024498652 0.068689283 8.29E-09 8.081264208 -0.177954582 ASLGS(ph)LEGEAEAEASS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 ASLGS(1)LEGEAEAEAS(0.033)S(0.967)PK;AS(0.001)LGS(0.904)LEGEAEAEAS(0.329)S(0.766)PK ; 211.26 1.26E-27 187048000 11285.9 10570.7 11112.6 7502.3 11622.1 11634.4 10145.1 9366.5 11674.5 11605.1 TRUE FALSE FALSE 11148.34311 10719.51459 11306.01014 8369.751225 11028.98087 10890.99939 11006.82454 9637.5049 10630.30348 11303.59783 0.986265017 0.94832767 1.000213411 0.740450196 0.975705349 0.963498485 0.973745236 0.852605077 0.940435394 1 13.46449442 ASLGS(ph)LEGEAEAEASSPK ddPTM_HeLa_Romidepsin_16h_R1 6 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 AS(0.001)LGS(0.999)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;ASLGS(1)LEGEAEAEASSPK;AS(0.09)LGS(0.91)LEGEAEAEASSPK;AS(0.026)LGS(0.974)LEGEAEAEASSPK;AS(0.001)LGS(0.999)LEGEAEAEASSPK ;;;;; 271.73 2.04E-90 1077585200 41201.9 39446.8 39593.7 36130.1 37436.9 33551.3 30747 30512.4 41593.4 38820.5 TRUE FALSE FALSE 40699.71539 40002.13309 40282.81174 40307.63216 35526.3553 31407.48021 33358.64941 31395.22815 37873.18213 37811.93781 1.076372113 1.057923381 1.065346398 1.066002815 0.939553944 0.830623396 0.882225333 0.83029937 1.001619709 1 15.20655417 -8.541353379 3.336677958 1.042905735 0.852524847 0.905234956 0.028643389 0.061468277 1.427508846 0.005071411 0.01127674 2.88E-09 8.541353379 -0.190380888 ASLGSLEGEAEAEAS(ph)S(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 ASLGS(0.001)LEGEAEAEAS(0.999)S(1)PK 125.23 0.016187 134640000 2010.7 1891 2033.4 1493.9 2190.6 1928.1 1941.2 1902.5 1914.3 2094.5 TRUE FALSE FALSE 1986.192815 1917.621548 2068.790474 1666.631747 2078.805508 1804.900633 2106.08548 1957.545836 1743.080214 2040.084588 0.97358356 0.939971587 1.014070929 0.816942472 1.018980056 0.884718527 1.032352037 0.959541505 0.854415657 1 10.99441326 -10.88762733 0.897484588 0.994818639 0.951794817 0 0.07589157 0.930979959 1.607410899 0.016083648 0.013266141 1.30E-11 10.88762733 -0.043023822 ASLGSLEGEAEAEAS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ASLGSLEGEAEAEAS(0.887)S(0.113)PK;ASLGSLEGEAEAEAS(0.591)S(0.409)PK ; 165.24 5.72E-07 140432000 12679.8 12150.1 13107.6 9131.6 12477.7 12521.9 10538.8 10783.8 13471.8 13023 TRUE FALSE FALSE 12525.25372 12321.14943 13335.73228 10187.43856 11840.91641 11721.791 11433.96541 11095.81224 12266.84847 12684.66058 0.9874331 0.971342461 1.051327483 0.80313056 0.93348311 0.924091814 0.901400974 0.874742542 0.967061624 1 13.6307973 -9.273371629 24.9998209 0.995753365 0.892751269 0.649628938 0.039581784 334.3118814 700431.5743 0.005514241 0.008463843 5.33E-10 9.273371629 -0.103002096 ASLGSLEGEAEAEAS(ph)SPKGK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ASLGSLEGEAEAEAS(0.648)S(0.352)PKGK;ASLGSLEGEAEAEAS(0.5)S(0.5)PKGK ; 120.25 7.36E-05 623634000 4582.5 3520.1 3879.6 7728.5 5106.3 4187 3862 3791.5 4612.5 4351.6 TRUE FALSE FALSE 4526.646727 3569.65606 3947.122811 8622.105534 4845.706457 3919.464213 4190.038184 3901.201071 4199.946448 4238.544805 1.067971895 0.842189059 0.9312448 2.034213611 1.143247666 0.924719307 0.988555831 0.920410483 0.990893489 1 12.04935332 -5.952530267 14.89779935 1.069396978 1.13859829 0 0.326753606 0 0 0.04231525 0 1.12E-06 5.952530267 0.069201312 ASLGSLEGEAEAEASS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 6 ASLGSLEGEAEAEASSPK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ASLGSLEGEAEAEAS(0.241)S(0.759)PK;ASLGSLEGEAEAEAS(0.023)S(0.977)PK;ASLGSLEGEAEAEAS(0.065)S(0.935)PK;ASLGSLEGEAEAEAS(0.212)S(0.788)PK;ASLGSLEGEAEAEAS(0.062)S(0.938)PK;ASLGSLEGEAEAEAS(0.058)S(0.942)PK ;;;;; 360.92 6.73E-264 2404868200 32075.7 31730.4 31054.1 23412.8 31791.4 30669.2 25904.87 26745 32077 31611.6 TRUE FALSE FALSE 31684.74903 32177.1014 31594.58358 26119.8981 30168.96623 28709.5371 28105.22901 27518.82438 29207.95278 30790.32607 1.02904883 1.045039319 1.026120461 0.848315085 0.979819641 0.932420691 0.912794134 0.89374904 0.948608102 1 14.91018953 -9.286461955 24.98742085 1.017759041 0.918129455 0.594323405 0.039427985 313.2168744 312775.8157 0.004973969 0.007599663 5.17E-10 9.286461955 -0.099629586 ASLGSLEGEAEAEASS(ph)PKGK ddPTM_HeLa_Romidepsin_16h_R1 3 ASLGSLEGEAEAEASSPKGK 20 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ASLGSLEGEAEAEAS(0.112)S(0.888)PKGK;ASLGSLEGEAEAEAS(0.133)S(0.867)PKGK;ASLGSLEGEAEAEAS(0.116)S(0.884)PKGK ;; 158.52 2.85E-08 603833000 5350.26 5504.12 5040.21 9193.28 6585.12 5906.17 4899.7 5303.18 5996.56 5332.22 TRUE FALSE FALSE 5285.048973 5581.607146 5127.932741 10256.25029 6249.056754 5528.784798 5315.880396 5456.619146 5460.212655 5193.688156 1.01759074 1.074690466 0.98733936 1.974752812 1.20320215 1.064519977 1.023527065 1.050625102 1.051317001 1 12.34254368 ASLLT(ph)DEEDVDMALDQR ddPTM_HeLa_Romidepsin_16h_R1 2 ASLLTDEEDVDMALDQR 17 0 P52948-6;P52948-2;P52948-5;P52948;A0A3B3ITD8;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 0 ASLLT(1)DEEDVDMALDQR;AS(0.002)LLT(0.998)DEEDVDMALDQR ; 121.95 0.0022899 4830300 1622.95 1402.84 1698.6 2367.86 1909.33 1631.72 1661.08 1770.49 1863.56 1627.64 TRUE FALSE FALSE 1603.168861 1422.589218 1728.16342 2641.643114 1811.889765 1527.458358 1802.172094 1821.716335 1696.878526 1585.353678 1.011237356 0.897332398 1.090080683 1.666279992 1.142893091 0.963481133 1.136763436 1.149091436 1.070346983 1 10.63058901 -9.51862314 24.98601815 0.997182909 1.208751268 0.260701668 0.17265497 193.607404 1136733.001 0.027157202 0.038953383 3.03E-10 9.51862314 0.21156836 ASLPQAATFGELS(ph)GPLKPGSPYRPPVPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASLPQAATFGELSGPLKPGSPYRPPVPR 28 2 Q14687-2;Q14687-3;Q14687;H0Y613 Q14687-2 GSE1 Genetic suppressor element 1 1 0 ASLPQAAT(0.044)FGELS(0.869)GPLKPGS(0.046)PY(0.041)RPPVPR 43.516 0.020897 20162000 1670.5 1354.4 1629.3 1653.5 738.57 567.26 587.56 876.97 1668 1573 TRUE FALSE FALSE 1650.139303 1373.467279 1657.657283 1844.68545 700.8780169 531.0139167 637.4673317 902.3437433 1518.809902 1532.133233 1.077020763 0.896441151 1.081927633 1.203998066 0.457452395 0.346584687 0.416065208 0.588946003 0.991304065 1 10.58132604 -8.750673864 24.9999717 1.039830061 0.442128007 0.906282559 0.092847352 43.35803629 100686.5564 0.013215336 0.026218958 1.78E-09 8.750673864 -0.597702053 ASLQSGQEGAGDS(ph)PGSQFSK ddPTM_HeLa_Romidepsin_16h_R1 2 ASLQSGQEGAGDSPGSQFSK 20 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 0 ASLQSGQEGAGDS(0.999)PGS(0.001)QFSK;ASLQSGQEGAGDS(0.973)PGS(0.027)QFSK ; 211.11 6.27E-32 14793500 3280.1 2914.3 3467.5 4067.6 6374.6 6350.6 5116.9 5414.9 3527.6 3344.9 TRUE FALSE FALSE 3240.12088 2955.327592 3527.850383 4537.915051 6049.280375 5944.817156 5551.529358 5571.571588 3212.082621 3257.999016 0.994512541 0.907098982 1.082827332 1.392853414 1.856747146 1.824683533 1.70396901 1.710120709 0.985906566 1 11.66977045 -9.064365319 2.382038322 0.991887146 1.773027604 0.971931788 0.062411087 0.032921093 0.36890842 0.009738564 0.018005273 8.62E-10 9.064365319 0.781140459 ASLSDLSS(ph)LDDVEGMSVR ddPTM_HeLa_Romidepsin_16h_R1 1 ASLSDLSSLDDVEGMSVR 18 0 H7BYJ1;A0A087WTM5;Q969K3;Q969K3-2 H7BYJ1 RNF34 E3 ubiquitin-protein ligase RNF34 1 0 AS(0.001)LS(0.001)DLS(0.428)S(0.569)LDDVEGMS(0.001)VR 85.28 0.013185 3503500 900.97 831.51 898.89 687.95 1086 1184.5 1155.4 1335.8 1055.1 1136 TRUE FALSE FALSE 889.9886311 843.2160196 914.5348034 767.4940159 1030.577368 1108.814273 1253.539647 1374.449265 960.7292135 1106.486556 0.804337501 0.762066213 0.826521387 0.693631578 0.931396194 1.002103701 1.132900929 1.242174392 0.868270119 1 10.11177021 -7.813056642 1.658384212 0.872897108 1.238698077 0.730483516 0.084187117 0.246093491 1.178582764 0.016147016 0.102709339 1.54E-08 7.813056642 0.36580097 ASLSLETS(ph)ESSQEAKSPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASLSLETSESSQEAKSPK 18 1 C9JNA8;Q92551 C9JNA8 IP6K1 Inositol hexakisphosphate kinase 1 1 0 ASLS(0.002)LET(0.144)S(0.535)ES(0.128)S(0.022)QEAKS(0.169)PK 52.569 0.029465 11149000 1474.3 1361 1126.3 1291.3 1555.1 1916.5 1541.8 1984.1 1544.8 1780.3 TRUE FALSE FALSE 1456.330665 1380.160194 1145.902779 1440.606182 1475.737444 1794.041835 1672.760454 2041.506803 1406.629219 1734.047549 0.839844712 0.795918309 0.660825466 0.830776631 0.851036319 1.034597832 0.964656623 1.17730728 0.811182611 1 10.75992774 -7.214867339 1.122936926 0.884037862 1.319623468 0.501176505 0.098831922 1.581585085 1.489382448 0.017896521 0.830914113 6.10E-08 7.214867339 0.435585606 ASLVALPEQTAS(ph)EEETPPPLLTK ddPTM_HeLa_Romidepsin_16h_R1 1 ASLVALPEQTASEEETPPPLLTK 23 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 AS(0.001)LVALPEQT(0.24)AS(0.735)EEET(0.024)PPPLLTK 69.439 0.00080323 16280000 5792.1 5504.2 5637.4 5449.7 5313 5534.8 4902.3 4901.3 5995.8 6096.2 TRUE FALSE FALSE 5721.503657 5581.688272 5735.516582 6079.819956 5041.857784 5181.144143 5318.70124 5043.111383 5459.520631 5937.819845 0.963569762 0.940023176 0.965929707 1.02391452 0.849109255 0.872566746 0.895733009 0.849320376 0.919448682 1 12.53571761 -8.753843202 24.99999872 0.97999606 0.869177692 0.717018118 0.030942254 54.97857284 180940.039 0.00384421 0.00757174 1.76E-09 8.753843202 -0.110818368 ASLVS(ph)EEEEDEEEDKATPR ddPTM_HeLa_Romidepsin_16h_R1 3 ASLVSEEEEDEEEDKATPR 19 1 Q96GN5-5;Q96GN5-2;Q96GN5;C9IZR6;Q96GN5-4;C9J8L0 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 0 AS(0.003)LVS(0.997)EEEEDEEEDKATPR;AS(0.003)LVS(0.997)EEEEDEEEDKATPR;AS(0.001)LVS(0.999)EEEEDEEEDKATPR ;; 116.27 0.00030761 100777200 5360.3 5112.8 4762.9 3875.5 4634.8 5198.1 4762.7 4724.5 6030.3 5335.4 TRUE FALSE FALSE 5294.966602 5184.778133 4845.796277 4323.603545 4398.268861 4865.958186 5167.243619 4861.195953 5490.934865 5196.785539 1.018892652 0.997689455 0.932460314 0.831976519 0.846344116 0.936340003 0.994315348 0.935423622 1.056602168 1 12.34340381 -9.727795289 3.891931116 1.00878115 0.909350847 0.558693578 0.046014465 0.140918474 4.561113237 0.007714564 0.010816988 1.87E-10 9.727795289 -0.099430303 ASMS(ph)EFLES(ph)EDGEVEQQR ddPTM_HeLa_Romidepsin_16h_R1 1 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 2 0 AS(0.004)MS(0.996)EFLES(1)EDGEVEQQR 116.04 7.15E-06 0 338.55 296.66 268.27 354.28 426.64 413.88 503.94 392.82 343.38 372.72 TRUE FALSE FALSE 334.4236224 300.8363873 272.9391268 395.2435205 404.8669688 387.4344037 546.744651 404.1856269 312.6672328 363.0366807 0.921184112 0.828666642 0.75182245 1.088715112 1.11522331 1.067204567 1.506031429 1.113346525 0.86125521 1 8.503971513 -8.398298755 1.354359156 0.938926708 1.290562417 0.553985014 0.134328571 0.264353578 0.911368529 0.019958311 0.070605877 4.00E-09 8.398298755 0.351635709 ASMSEFLES(ph)EDGEVEQQR ddPTM_HeLa_Romidepsin_16h_R1 3 ASMSEFLESEDGEVEQQR 18 0 J3QQW9;Q15022 J3QQW9 SUZ12 Polycomb protein SUZ12 1 0 ASMS(0.001)EFLES(0.999)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR;ASMSEFLES(1)EDGEVEQQR ;; 130.4 0.0018159 103570000 5341.5 5249.1 5204.3 5330.1 5310.3 6077.9 5447.7 6291.3 5420.9 4608.92 TRUE FALSE FALSE 5276.395743 5322.996968 5294.878658 5946.391241 5039.295576 5689.541806 5910.427502 6473.328839 4936.041127 4489.179594 1.175358578 1.185739366 1.179475792 1.324605335 1.122542654 1.267390107 1.31659413 1.441984822 1.099541915 1 12.1322361 -4 0.055420008 0.573579417 2.493766365 0.69405362 0.067349515 120.0393238 0.504663695 3.861530282 19.16055113 1.00E-04 4 1.920186949 ASNAAVK(ac)LAESK ddPTM_HeLa_Romidepsin_16h_R1 2 ASNAAVKLAESK 12 1 F8VXG7;Q99590-2;Q99590;A0A087WTB7 F8VXG7 SCAF11 Protein SCAF11 0 1 ; ASNAAVK(1)LAESK;ASNAAVK(1)LAESK 185.57 4.52E-06 2508200 2282.66 2488.4 2187.41 1747.82 1767.58 1188.24 1707.37 1178.09 2666.9 2148.61 FALSE TRUE FALSE 2254.838062 2523.431761 2225.480953 1949.911172 1677.373797 1112.315299 1852.393965 1212.176175 2428.365785 2092.788802 1.077432209 1.205774686 1.063404463 0.931728596 0.801501707 0.531499068 0.885131822 0.579215721 1.160349187 1 11.03121101 -8.795459122 2.253398365 1.053636205 0.685393011 0.751432359 0.108490078 0.114677223 1.187815209 0.015190931 0.032094562 1.60E-09 8.795459122 -0.368243194 ASNGDAWVEAHGK ddPTM_HeLa_Romidepsin_16h_R1 2 ASNGDAWVEAHGK 13 0 P38646;D6RJI2;A0A3B3ITI4 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 0 ; ; 100.11 0.0059289 30821000 12368.4 12719.3 12021.3 9348.7 12399 13335.5 12031.2 11658 12945.5 11033.7 FALSE FALSE TRUE 12217.64918 12898.36264 12230.52568 10429.64068 11766.23276 12483.40459 13053.12983 11995.30584 11787.62206 10747.04288 1.136838228 1.200177833 1.138036371 0.97046609 1.094834448 1.161566463 1.214578742 1.116149434 1.096824697 1 13.39165213 -12.15496368 0.843496227 0.99741724 1.129101222 0.117967469 0.06975065 0.595991435 0.744967392 0.049829792 0.013367882 7.00E-13 12.15496368 0.131683982 ASNIFGT(ph)PEENQASWAK ddPTM_HeLa_Romidepsin_16h_R1 1 ASNIFGTPEENQASWAK 17 0 Q9UK76-3;J3KSH8 Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 AS(0.013)NIFGT(0.981)PEENQAS(0.005)WAK 130.27 9.63E-06 0 930.35 711.07 578.38 1072.9 1677.6 1072.9 2142.6 1596.3 1705.1 993.55 TRUE FALSE FALSE 919.0105364 721.0804621 588.4464613 1196.953746 1591.985812 1004.345153 2324.592391 1642.486422 1552.591585 967.7374278 0.949648644 0.745119948 0.608064176 1.236857966 1.645059668 1.037828159 2.402089992 1.697243875 1.604352111 1 9.91847185 -8.213406551 1.005900933 0.937078252 2.042571113 0.435808556 0.387081209 0.33542749 0.55276828 0.048541562 0.277190761 6.12E-09 8.213406551 1.105492861 ASPAPGS(ph)GHPEGPGAHLDMNSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPAPGSGHPEGPGAHLDMNSLDR 24 0 O94826 O94826 TOMM70A Mitochondrial import receptor subunit TOM70 1 0 AS(0.138)PAPGS(0.862)GHPEGPGAHLDMNSLDR 76.156 0.00010311 19235000 824 538.74 630.61 387.85 904.85 1022.2 741.2 798.21 860.22 759.21 TRUE FALSE FALSE 813.9567711 546.3243959 641.5855025 432.6950419 858.672128 956.884719 804.1575095 821.304947 783.2797687 739.4856148 1.1007067 0.738789755 0.867610525 0.585129762 1.161174891 1.293986928 1.087455244 1.110643575 1.059222456 1 9.530378273 -8.579495668 24.99999998 0.974800329 1.168251989 0.335580863 0.163800016 99.86831826 44097.74997 0.02649885 0.052997706 2.63E-09 8.579495668 0.19345166 ASPAPSDSSPGEPFVGGPVS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPAPSDSSPGEPFVGGPVSSPR 23 0 O60346 O60346 PHLPP1 PH domain leucine-rich repeat-containing protein phosphatase 1 1 0 ASPAPSDSSPGEPFVGGPVS(0.5)S(0.5)PR 231.41 1.26E-51 0 953.12 930.64 630.18 687.15 917.15 882.28 502.65 895.35 869.74 775.41 TRUE FALSE FALSE 941.5030068 943.7415743 641.1480186 766.6015161 870.3444131 825.9051554 545.3450785 921.2555396 791.9482761 755.2647364 1.246586742 1.249550692 0.84890501 1.015010339 1.152369985 1.093530673 0.722058177 1.219778304 1.048570439 1 9.560838618 -9.772338691 24.99970751 1.129680319 1.006269377 0.143668634 0.152182074 353.488562 810793.816 0.025931831 0.034265559 1.69E-10 9.772338691 -0.123410943 ASPDQNASTHTPQSS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPDQNASTHTPQSSVK 17 0 Q14677-2;Q14677;Q14677-3;H0YD52 Q14677-2 CLINT1 Clathrin interactor 1 1 0 ASPDQNAS(0.005)T(0.004)HT(0.092)PQS(0.12)S(0.779)VK 58.159 0.028792 5470300 1233.5 1336.6 1156.7 1484.5 2559.9 2929.2 2466.6 2277.5 1956.5 1732.4 TRUE FALSE FALSE 1218.465628 1355.41669 1176.831878 1656.144875 2429.258751 2742.033574 2676.112942 2343.395869 1781.50574 1687.391998 0.72209992 0.8032613 0.69742649 0.981482001 1.43965288 1.625012787 1.585946209 1.388767916 1.055774676 1 10.72057945 -8.778775259 3.28184064 0.847361322 1.538399703 0.874299031 0.118679257 0.061972155 1.387038906 0.01923056 0.038433015 1.66E-09 8.778775259 0.691038381 ASPEAAS(ph)TPRDPIDVDLPEEAER ddPTM_HeLa_Romidepsin_16h_R1 2 ASPEAASTPRDPIDVDLPEEAER 23 1 P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;H3BVD2;H3BT29;P29590-2 P29590-5;P29590-2 PML Protein PML 1 0 AS(0.002)PEAAS(0.548)T(0.45)PRDPIDVDLPEEAER;ASPEAAS(0.879)T(0.12)PRDPIDVDLPEEAER ; 91.276 4.45E-05 13453800 736.21 790.18 660.79 1023.04 1156.48 943.84 1057.94 1180.93 712.83 1014.57 TRUE FALSE FALSE 727.2367893 801.3041748 672.2907728 1141.328698 1097.46051 883.5316701 1147.801397 1215.098346 649.0726995 988.2113251 0.735912219 0.810863177 0.680310735 1.154943957 1.110552452 0.894071589 1.161493871 1.229593626 0.656815686 1 9.948675779 -9.243303804 24.96450373 0.852972835 1.101004701 0.591676252 0.130919527 604.6764355 832367.1372 0.021217589 0.035139825 5.71E-10 9.243303804 0.248031866 ASPGTPLS(ph)PGSLR ddPTM_HeLa_Romidepsin_16h_R1 2 ASPGTPLSPGSLR 13 0 E1P5H9;Q96BD0-2;Q96BD0-3;Q96BD0-4;Q96BD0 E1P5H9 SLCO4A1 Solute carrier organic anion transporter family member 4A1 1 0 ASPGT(0.051)PLS(0.947)PGS(0.002)LR;ASPGT(0.001)PLS(0.998)PGS(0.001)LR ; 122.52 0.0028367 6460500 1782.27 2471.6 1688.51 1298.82 2458.2 3016.1 1810.64 2882.1 2188.4 2152.5 TRUE FALSE FALSE 1760.547008 2506.39525 1717.897808 1448.99568 2332.748881 2823.380944 1964.435716 2965.489016 1992.664023 2096.57774 0.839724173 1.195469742 0.819381879 0.691124232 1.112646022 1.3466617 0.936972514 1.41444267 0.950436507 1 11.03382061 -8.535196488 24.7752327 0.921031667 1.207542596 0.417322708 0.169584153 149.2869319 300266.8887 0.02351133 0.047047949 2.92E-09 8.535196488 0.286510929 ASPITNDGEDEFVPSDGLDKDEYTFS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPITNDGEDEFVPSDGLDKDEYTFSPGK 29 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 ASPITNDGEDEFVPS(0.011)DGLDKDEY(0.097)T(0.44)FS(0.452)PGK 55.779 0.00092503 4311900 1907.4 1939.4 1665.7 1685.2 1142.4 1380.6 1168.4 1157.1 1950.5 1787.2 TRUE FALSE FALSE 1884.151875 1966.702924 1694.69081 1880.050753 1084.099065 1292.384116 1267.643867 1190.578863 1776.042395 1740.768286 1.082367992 1.129790185 0.973530379 1.080012066 0.622770459 0.74242168 0.728209422 0.683938737 1.020263529 1 10.76550846 -8.765689072 24.99999996 1.044498815 0.700189408 0.918971538 0.051381358 21.95583604 129162.2801 0.007948122 0.01478393 1.72E-09 8.765689072 -0.344309406 ASPNLIGAT(ph)GANSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPNLIGATGANSLGK 16 0 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078 Q02078-8 MEF2A Myocyte-specific enhancer factor 2A 1 0 AS(0.149)PNLIGAT(0.843)GANS(0.009)LGK 92.19 0.022582 13524000 1369.6 1277.9 1237.7 1482.7 1081.3 762.63 840.59 566.48 1485.7 1383.4 TRUE FALSE FALSE 1352.906788 1295.89031 1259.241649 1654.13675 1026.117226 713.9004043 911.9896936 582.870205 1352.815271 1347.459069 1.004042958 0.961728887 0.934530539 1.22759703 0.761520146 0.529812312 0.676821816 0.432569878 1.003975039 1 10.39602573 -8.533234493 5.347204326 1.007423198 0.569948806 0.837729725 0.094181373 0.046063963 4.113535013 0.012438975 0.026203166 2.93E-09 8.533234493 -0.437474392 QLSPEDSSS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 QLSPEDSSSPVK 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 0 QLSPEDSS(0.097)S(0.903)PVK;QLSPEDS(0.001)S(0.423)S(0.577)PVK ; 147.73 0.0014837 29321000 8105.1 7429 8368.4 4668.5 5129.2 4159.3 3455.4 3522.1 8538.8 8392.1 TRUE FALSE FALSE 8006.311924 7533.585657 8514.048492 5208.293936 4867.437784 3893.534154 3748.90159 3624.006407 7775.068342 8174.072032 0.979476556 0.921644148 1.041592056 0.637172503 0.595472827 0.47632736 0.458633295 0.443353862 0.951186668 1 12.99683924 -9.026171813 1.776245612 0.989863683 0.472109404 0.947780065 0.054103626 0.046182819 0.289368295 0.00765761 0.015249341 9.42E-10 9.026171813 -0.517754279 down ASPS(ph)PQPSSQPLQIHR ddPTM_HeLa_Romidepsin_16h_R1 3 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 AS(0.028)PS(0.662)PQPS(0.155)S(0.155)QPLQIHR;AS(0.17)PS(0.826)PQPS(0.003)SQPLQIHR;AS(0.065)PS(0.935)PQPSSQPLQIHR ;; 115.83 0.0012409 123673000 3613.55 3814.99 3315.51 3636.46 4303.85 4185.17 3373.57 4122.77 4252.39 3872.81 TRUE FALSE FALSE 3569.506663 3868.697529 3373.215061 4056.924615 4084.208475 3917.751144 3660.120952 4242.055845 3872.045588 3772.193838 0.946268091 1.025582909 0.894231634 1.075481481 1.08271437 1.038586911 0.970289733 1.124559349 1.026470472 1 11.8811881 -9.230684876 24.99638531 0.973132995 1.053693703 0.369135764 0.051757274 525.0225207 426723.848 0.007130732 0.011824142 5.88E-10 9.230684876 0.080560708 ASPSENNAGGGS(ph)PSSGSGGNPTNTSGTTR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSENNAGGGSPSSGSGGNPTNTSGTTR 29 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 0 ASPSENNAGGGS(0.985)PS(0.009)S(0.004)GS(0.001)GGNPTNTSGTTR 81.02 1.23E-06 3567900 441.5 396.6 405.07 347.75 420.26 418.63 299.36 216.84 420.11 404.15 TRUE FALSE FALSE 436.1188282 402.1833452 412.1200734 387.9584912 398.812564 391.8808941 324.7876309 223.1139233 382.5343094 393.6501247 1.10788439 1.021677169 1.046919707 0.98554139 1.013114283 0.995505576 0.825066755 0.5667823 0.971762195 1 8.620770125 -6.935934755 0.990442863 1.046019449 4.90E-12 0.92490409 0.03990935 0.623066745 0.306161636 0.006755894 0.806426051 1.16E-07 6.935934755 -1.046019449 ASPSPQPS(ph)SQPLQIHR ddPTM_HeLa_Romidepsin_16h_R1 1 ASPSPQPSSQPLQIHR 16 0 B5MBZ0;Q9HC35 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 AS(0.016)PS(0.267)PQPS(0.596)S(0.121)QPLQIHR 89.669 0.0053677 84511000 980.75 1147.2 1222.4 1159.2 1694.4 1230.3 1098.6 1412.8 1430.4 1189.1 TRUE FALSE FALSE 968.7962418 1163.350312 1243.675359 1293.232158 1607.928445 1151.687801 1191.915057 1453.677139 1302.461441 1158.207011 0.836462077 1.004440744 1.073793672 1.116581187 1.388291066 0.994371291 1.029103645 1.255109946 1.124549782 1 10.17767742 -9.725535077 2.179854321 0.92321591 1.150450187 0.221116978 0.128002081 0.215713799 2.10199024 0.019781734 0.028554953 1.88E-10 9.725535077 0.227234277 ASPTPLAS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 ASPTPLASPGK 11 0 A0A1B0GTL5 A0A1B0GTL5 1 0 ASPT(0.003)PLAS(0.996)PGK 109.15 0.014963 14583000 4713.2 3885.7 4774.2 3875.1 3329.2 3698.7 3241.2 3213.5 4189.4 3932.7 TRUE FALSE FALSE 4655.753706 3940.402987 4857.292948 4323.157295 3159.298501 3462.365007 3516.507447 3306.477552 3814.689571 3830.527887 1.215433967 1.028684062 1.268047927 1.128606141 0.824768438 0.903887169 0.918021628 0.863191093 0.995865239 1 11.90332751 -8.767886867 24.99523731 1.113553301 0.882250976 0.628723918 0.085928857 82.68696973 320557.1187 0.014365692 0.026494994 1.71E-09 8.767886867 -0.231302325 ASQEPS(ph)PKPGTEVIPAAPR ddPTM_HeLa_Romidepsin_16h_R1 1 ASQEPSPKPGTEVIPAAPR 19 1 I3L4I0;I3L1Y9;Q96CP2 I3L4I0 FLYWCH2 FLYWCH family member 2 1 0 AS(0.065)QEPS(0.592)PKPGT(0.343)EVIPAAPR 64.89 0.0086037 62433000 1627.1 1725.4 1634.6 1719 2279.4 2039.9 1934.9 2085.4 1993.1 1736.3 TRUE FALSE FALSE 1607.268279 1749.690226 1663.049527 1917.758868 2163.073712 1909.556973 2099.250358 2145.737759 1814.832144 1691.190676 0.950376739 1.034590748 0.983360156 1.133969632 1.279024148 1.129119857 1.241285437 1.268773409 1.073109124 1 10.72382361 -9.119231175 2.871723806 0.980998141 1.223376894 0.790259884 0.052739586 0.066702227 1.061700023 0.00674104 0.011899343 7.60E-10 9.119231175 0.242378753 ASQGLLSS(ph)IENSESDSSEAKEEGSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASQGLLSSIENSESDSSEAKEEGSR 25 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 ASQGLLS(0.07)S(0.588)IENS(0.12)ES(0.193)DS(0.014)S(0.014)EAKEEGSR 59.547 0.0021339 12379000 2400.6 2551.7 2807 2033.1 1879.8 1378.7 1176.9 1711.9 2546.8 2253.7 TRUE FALSE FALSE 2371.340564 2587.6229 2855.854658 2268.176588 1783.866791 1290.60552 1276.865857 1761.431126 2319.007829 2195.148549 1.080264279 1.178791704 1.300984691 1.033267926 0.812640581 0.587935391 0.581676287 0.802420012 1.0564241 1 11.10010286 -8.628771297 3.00655907 1.073032179 0.653317344 0.803487405 0.101110168 0.096375665 1.744354861 0.01672148 0.036179926 2.35E-09 8.628771297 -0.419714835 ASQGLLSSIENS(ph)ESDSSEAKEEGSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASQGLLSSIENSESDSSEAKEEGSR 25 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 ASQGLLS(0.087)S(0.22)IENS(0.532)ES(0.157)DS(0.002)S(0.002)EAKEEGSR 54.261 0.0054573 11469000 1304.4 1249.4 1264.4 847.88 882.17 648.92 741.8 799.25 1641 1148 TRUE FALSE FALSE 1288.501471 1266.989086 1286.406352 945.915875 837.1495731 607.4561063 804.8084735 822.3750377 1494.22485 1118.174795 1.152325627 1.133086788 1.150451931 0.84594634 0.748675053 0.543256841 0.719751936 0.735461971 1.33630704 1 10.12693001 -8.990510791 2.523853857 1.084453476 0.675508038 0.807189523 0.105785724 0.080258601 1.029157055 0.012818779 0.024261725 1.02E-09 8.990510791 -0.408945438 ASQLVGIEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ASQLVGIEKK 10 1 Q9NPD8 Q9NPD8 UBE2T Ubiquitin-conjugating enzyme E2 T 0 1 ; ASQLVGIEK(1)K;ASQLVGIEK(1)K 125.74 0.0026747 5286300 5541.6 5665 4479.2 4499.7 4430.8 4545.7 4234.9 3868.2 6010.9 4994.5 FALSE TRUE FALSE 5474.056848 5744.752019 4557.158597 5019.976486 4204.679742 4255.244441 4594.6123 3980.120264 5473.270049 4864.74217 1.125251176 1.180895476 0.936772893 1.031910081 0.864317079 0.874711196 0.944471904 0.818156466 1.125089441 1 12.24814763 -9.017037598 1.534232593 1.066461214 0.878094421 0.638679057 0.070706088 0.219895915 1.028129576 0.012117093 0.025277955 9.62E-10 9.017037598 -0.188366792 ASQPDLVDT(ph)PTSSKPQPK ddPTM_HeLa_Romidepsin_16h_R1 2 ASQPDLVDTPTSSKPQPK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 AS(0.001)QPDLVDT(0.951)PT(0.009)S(0.023)S(0.016)KPQPK;AS(0.002)QPDLVDT(0.758)PT(0.21)S(0.025)S(0.004)KPQPK ; 83.905 0.005787 35454000 7305.9 6572.6 8192.2 5153.6 5958.7 6493.5 6885.9 6505.4 7919.3 7658.3 TRUE FALSE FALSE 7216.852881 6665.129235 8334.781805 5749.48348 5654.605304 6078.586307 7470.788174 6693.623485 7210.977974 7459.336262 0.967492633 0.893528459 1.117362391 0.77077682 0.758057434 0.814896405 1.001535245 0.897348403 0.966705042 1 12.86483155 -9.247014385 24.9944471 0.985024285 0.85012956 0.420347621 0.082414146 651.0435504 1128075.493 0.012560959 0.02076661 5.66E-10 9.247014385 -0.134894725 ASQS(ph)RPNSSALET(ph)LGGEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 2 0 AS(0.228)QS(0.823)RPNS(0.013)S(0.239)ALET(0.696)LGGEK 88.57 0.024658 6975800 2358.4 2222.8 2087.2 2414.6 2199.8 2267 1875.4 1716.2 2562.6 2341.8 TRUE FALSE FALSE 2329.654914 2254.092637 2123.52684 2693.787413 2087.535997 2122.146016 2034.696429 1765.855539 2333.394638 2280.959698 1.021348565 0.988221159 0.930979553 1.180988605 0.915200737 0.930374183 0.892035239 0.774172179 1.022988104 1 11.15542524 -7.473061674 1.000933091 1.011047179 0.710565069 0.560449594 0.066802054 0.744265932 0.719867775 0.009560635 0.220096182 3.36E-08 7.473061674 -0.30048211 ASQSRPNS(ph)SALETLGGEK ddPTM_HeLa_Romidepsin_16h_R1 1 ASQSRPNSSALETLGGEK 18 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 0 AS(0.001)QS(0.037)RPNS(0.948)S(0.013)ALET(0.001)LGGEK 119.68 0.010301 6193100 1940.7 1551.3 1790.1 2291.1 2413.4 2360.3 1745 2184.8 2508.6 2044.2 TRUE FALSE FALSE 1917.046002 1573.139242 1821.25594 2556.007762 2290.235192 2209.484448 1893.220256 2248.013741 2284.224533 1991.091389 0.962811658 0.790088918 0.914702333 1.283721971 1.150241121 1.1096851 0.950845484 1.129035941 1.147222345 1 10.95934373 -9.298585869 24.99949733 0.959888005 1.115631242 0.342972344 0.111537846 466.4070887 313889.6273 0.015506674 0.023687178 5.03E-10 9.298585869 0.155743237 ASS(ph)FADMMGILK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSFADMMGILK 12 0 E9PPF9;E9PLD2;Q9H019-3;Q9H019 E9PPF9 MTFR1L Mitochondrial fission regulator 1-like 1 0 AS(0.005)S(0.995)FADMMGILK 95.477 0.015975 165790000 4431.9 3379.9 5054.4 3724.8 5804.1 4691.3 4301.6 4535.5 3600.7 2864.8 TRUE FALSE FALSE 4377.882298 3427.482321 5142.369712 4155.478902 5507.895119 4391.54107 4666.977797 4666.727537 3278.644374 2790.372083 1.568924204 1.228324474 1.842897491 1.489220354 1.973892712 1.573819168 1.672528845 1.672439158 1.174984653 1 11.4462418 -12.83557744 0.273261916 0.52228643 1.740610093 0.598535813 0.183368118 2.723562536 0.208489142 1.095098053 0.110927888 1.46E-13 12.83557744 1.218323663 ASS(ph)FLDTSK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSFLDTSK 9 0 F5H269;Q9Y485 F5H269 DMXL1 DmX-like protein 1 1 0 AS(0.002)S(0.998)FLDTSK 132.25 0.0071197 6408100 2325.3 3221.6 2763.5 3521.2 3280.6 3178.7 2291.1 2764.1 2583.4 2882.9 TRUE FALSE FALSE 2296.958349 3266.953769 2811.597558 3928.337712 3113.17874 2975.591329 2485.705977 2844.074872 2352.334234 2808.001842 0.818004573 1.163444311 1.001280525 1.398979749 1.10868116 1.059682826 0.885222345 1.012846512 0.837725317 1 11.45532817 -10.25691749 24.97810518 0.914057715 1.090163804 0.321813399 0.134286053 405.5324822 2240091.017 0.024224448 0.029141839 5.53E-11 10.25691749 0.176106088 ASS(ph)FSGISILTR ddPTM_HeLa_Romidepsin_16h_R1 2 ASSFSGISILTR 12 0 H7C0E9;A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5-2;Q9Y2K5;H0YIX9;Q9Y2K5-3 H7C0E9 R3HDM2 R3H domain-containing protein 2 1 0 AS(0.002)S(0.998)FS(0.001)GISILTR;AS(0.021)S(0.978)FS(0.001)GISILTR ; 150.14 0.00048009 8497600 2630.52 2702.14 3138.16 2987.74 2862.78 3190.46 2661.55 2671.14 3149.69 2827.55 TRUE FALSE FALSE 2598.45821 2740.180798 3192.778358 3333.196557 2716.681654 2986.599903 2887.621991 2748.425222 2867.973838 2754.089843 0.94349072 0.994949676 1.159286203 1.21027154 0.986417223 1.084423556 1.048485037 0.997943196 1.041350864 1 11.42735991 -9.934029996 9.097847958 0.973098825 1.081254544 0.262682941 0.067834266 0.255428314 32.74917041 0.010829742 0.01424098 1.16E-10 9.934029996 0.10815572 ASS(ph)FSGISVLTR ddPTM_HeLa_Romidepsin_16h_R1 2 ASSFSGISVLTR 12 0 H7C1X4;H7BZ47;H7C207;Q15032-2;Q15032-4;Q15032;Q15032-3 H7C1X4 R3HDM1 R3H domain-containing protein 1 1 0 AS(0.037)S(0.962)FSGISVLTR;AS(0.114)S(0.751)FS(0.05)GIS(0.086)VLTR ; 166.45 0.00024771 57939000 4143.9 3381.2 4216.9 3306.6 4109.4 3730.4 3255.6 3492.7 3647.6 3369.1 TRUE FALSE FALSE 4093.392553 3428.800622 4290.293376 3688.92465 3899.681984 3492.039479 3532.130583 3593.755764 3321.34952 3281.570296 1.247388349 1.044865815 1.307390361 1.124133972 1.188358509 1.064136728 1.076353777 1.095132951 1.012122009 1 11.68017062 -8.22710202 24.51088856 1.133146672 1.078322405 0.064389474 0.093379774 1354.345017 966764.708 0.015193593 0.038734475 5.93E-09 8.22710202 -0.054824267 ASS(ph)HS(ph)SQTQGGGS(ph)VTK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 3 0 AS(0.057)S(0.843)HS(0.943)S(0.157)QT(0.119)QGGGS(0.744)VT(0.137)K 83.964 0.0015993 0 988.4 704.93 870.94 795.85 945.35 579.48 763.88 361.43 1175.1 1112.4 TRUE FALSE FALSE 976.3530006 714.854023 886.0983454 887.8699216 897.1052619 542.4530982 828.7639481 371.8874068 1069.996113 1083.499688 0.901110551 0.65976394 0.817811353 0.819446403 0.827970024 0.500649058 0.76489542 0.343227978 0.987537076 1 10.08148302 -6.981315167 0.224979188 1.020389966 6.80E-16 0.651428442 0.116857957 5.87085973 0.225578554 0.09852766 1.715763865 1.04E-07 6.981315167 -1.020389966 ASS(ph)HSSQT(ph)QGGGSVTK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSHSSQTQGGGSVTK 16 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 2 0 AS(0.079)S(0.895)HS(0.092)S(0.423)QT(0.51)QGGGSVTK 102.78 0.020148 74054000 1621.2 1376 1949.2 1690 2629.4 2891 2480.4 874.22 3519.8 2326.3 TRUE FALSE FALSE 1601.440191 1395.371364 1983.125008 1885.405752 2495.211906 2706.27443 2691.085114 899.5141764 3204.980272 2265.862391 0.706768512 0.615823525 0.875218644 0.832091904 1.101219525 1.194368397 1.187664849 0.396985351 1.414463776 1 11.14584453 -8.785012089 24.12394488 0.837130742 1.001624818 0 0.295728947 287.2052943 293920.6943 0.035382651 0.06416787 1.64E-09 8.785012089 0.164494077 ASS(ph)LDDLR ddPTM_HeLa_Romidepsin_16h_R1 2 ASSLDDLR 8 0 Q96P11-5;Q96P11;Q96P11-2;Q96P11-4;Q96P11-3 Q96P11-5 NSUN5 Probable 28S rRNA (cytosine-C(5))-methyltransferase 1 0 AS(0.004)S(0.996)LDDLR;AS(0.291)S(0.709)LDDLR ; 125.71 0.014819 5592100 7413.7 6455.5 6018 5904.3 5793.9 6086.1 5740.1 6055.2 8046.3 7634.7 TRUE FALSE FALSE 7323.338973 6546.380698 6122.740766 6586.982947 5498.215663 5697.217852 6227.663951 6230.397658 7326.618776 7436.349393 0.984802971 0.880321829 0.823353025 0.885781799 0.739370271 0.766131007 0.837462526 0.837830141 0.985244021 1 12.86037884 -10.04962949 1.463338481 0.996190304 0.808015873 0.808125375 0.038105653 0.108259593 0.450522154 0.007131784 0.009238941 8.92E-11 10.04962949 -0.188174432 ASS(ph)LEDLVLK ddPTM_HeLa_Romidepsin_16h_R1 6 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 1 0 ASS(1)LEDLVLK;AS(0.003)S(0.997)LEDLVLK;AS(0.001)S(0.999)LEDLVLK;AS(0.06)S(0.94)LEDLVLK;ASS(1)LEDLVLK;AS(0.156)S(0.844)LEDLVLK ;;;;; 213.35 1.47E-18 1493482700 51805.89 51423.08 53792.53 45927.58 50765.62 54611.7 46019.55 55736.39 54331.47 47670.68 TRUE FALSE FALSE 51174.45989 52147.01547 54728.76642 51237.9429 48174.86098 51122.18862 49928.44943 57349.03451 49471.92725 46432.18886 1.102133264 1.123078984 1.178681595 1.103500484 1.037531552 1.10100751 1.075298207 1.235113741 1.065466188 1 15.50283767 -11.87399396 0.663813432 0.996239039 1.117705397 0.255919642 0.055000176 0.597758194 0.479319711 0.038818586 0.011685852 1.34E-12 11.87399396 0.121466358 ASS(ph)LGEIDESSELR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSLGEIDESSELR 14 0 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 AS(0.061)S(0.898)LGEIDES(0.041)SELR 92.906 0.016534 1795800 392.56 611.67 548.23 465.44 436.22 764.82 400.8 542.55 507.86 624.88 TRUE FALSE FALSE 387.7753277 620.2811063 557.7717132 519.2563628 413.9580656 715.9504703 434.843942 558.2478282 462.4357296 608.6455275 0.637111932 1.019117168 0.916414708 0.853134278 0.680129972 1.17630121 0.714445309 0.917196961 0.759778408 1 9.249458443 ASS(ph)LNFLNK ddPTM_HeLa_Romidepsin_16h_R1 2 ASSLNFLNK 9 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 0 ASS(1)LNFLNK;AS(0.069)S(0.931)LNFLNK ; 172.21 0.0010746 978680000 12294.1 10648.3 11322.4 10348.2 11680.2 10153.2 8962.9 9570.2 12228.9 10731.4 TRUE FALSE FALSE 12144.25478 10798.20705 11519.46162 11544.70757 11084.11581 9504.443288 9724.208502 9847.098638 11135.11656 10452.59668 1.161840943 1.033064546 1.102066977 1.104482257 1.06041744 0.909290158 0.930315098 0.942071998 1.065296681 1 13.35157377 -8.309755298 5.398884178 1.078401541 0.92737433 0.727007446 0.041614109 0.111946165 7.808310183 0.00875441 0.020244011 4.90E-09 8.309755298 -0.15102721 ASS(ph)PAESSPEDSGY(ph)MR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPAESSPEDSGYMR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 2 0 AS(0.109)S(0.815)PAES(0.045)S(0.054)PEDS(0.056)GY(0.921)MR 71.933 0.014596 14545000 2041.2 2093 1594.1 2370.9 1859.6 1920.8 1583.8 1405.1 1839.1 2023.7 TRUE FALSE FALSE 2016.321069 2122.465309 1621.844642 2645.034613 1764.697673 1798.067079 1718.327932 1445.754352 1674.60629 1971.123982 1.022929601 1.076779202 0.822801943 1.341891549 0.895274822 0.912203948 0.871750305 0.733466979 0.849569233 1 10.94480281 -7.700489899 1.261433222 1.020190468 0.724732969 0.267002475 0.138341727 0.598725832 1.317643076 0.017327904 0.186046115 1.99E-08 7.700489899 -0.295457499 ASS(ph)PAESSPEDSGYMR ddPTM_HeLa_Romidepsin_16h_R1 2 ASSPAESSPEDSGYMR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 AS(0.104)S(0.547)PAES(0.28)S(0.067)PEDSGY(0.002)MR;AS(0.018)S(0.64)PAES(0.332)S(0.009)PEDSGY(0.002)MR ; 84.759 0.025645 29390000 3324.2 3018.9 2538.4 2881.7 3312.6 3289.3 3326.8 3284.7 3513.3 3213.9 TRUE FALSE FALSE 3283.683372 3061.400153 2582.579787 3214.895713 3143.545661 3079.124346 3609.378309 3379.737612 3199.061649 3130.402415 1.048965256 0.977957383 0.824999296 1.026991194 1.00419858 0.983619336 1.153007771 1.079649567 1.021933038 1 11.61213241 -7.766780563 24.99969197 1.003014611 1.116328679 0.392632462 0.061999157 103.8622482 486142.9143 0.009188697 0.028791872 1.71E-08 7.766780563 0.113314068 ASS(ph)PEKAEEDR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPEKAEEDR 11 1 Q8N3D4;H0YDZ9 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 AS(0.015)S(0.985)PEKAEEDR 145.81 0.016378 11319000 1700 2094.3 2429 1982.9 1870.9 2427.9 2820.2 972.34 2374.5 2117.3 TRUE FALSE FALSE 1679.279746 2123.78361 2471.275726 2212.172228 1775.420992 2272.765026 3059.747718 1000.473124 2162.118773 2062.292241 0.814278264 1.029817001 1.198315 1.072676405 0.860896897 1.102057691 1.483663497 0.485126746 1.048405619 1 11.01003307 -10.08063183 8.448356908 0.912574677 1.05638805 0.007930425 0.246044591 0.708016346 68.83953166 0.037745043 0.046295069 8.31E-11 10.08063183 0.143813373 ASS(ph)PELPVSVENIK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPELPVSVENIK 14 0 Q969R5 Q969R5 L3MBTL2 Lethal(3)malignant brain tumor-like protein 2 1 0 AS(0.007)S(0.987)PELPVS(0.006)VENIK 111.66 0.0052351 5130600 1567.3 1787.1 1866.3 1146.3 1473.5 1764.4 1512.7 1343.5 1620.1 1636.4 TRUE FALSE FALSE 1548.197145 1812.258841 1898.782169 1278.8406 1398.301797 1651.660534 1641.1887 1382.372053 1475.194198 1593.886092 0.971334873 1.137006496 1.191291008 0.802341275 0.87729092 1.036247535 1.029677534 0.86729664 0.925533014 1 10.63833281 -9.238223093 24.99097498 1.013771085 0.932321011 0.241515306 0.100452463 1315.858234 1416446.271 0.015598698 0.025856691 5.78E-10 9.238223093 -0.081450073 ASS(ph)PGYIDS(ph)PTYSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPGYIDSPTYSR 14 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 2 0 AS(0.096)S(0.904)PGYIDS(0.855)PT(0.141)YS(0.004)R 121.95 0.00068801 0 765.31 806.76 782.2 835.19 984.5 1040.9 890 959.96 807.95 707.41 TRUE FALSE FALSE 755.9821074 818.1175885 795.8138629 931.7585975 934.2572913 974.3898494 965.5965778 987.734928 735.6849285 689.0313862 1.097166432 1.187344444 1.154974764 1.352273084 1.35589947 1.414144361 1.401382574 1.433512243 1.067708878 1 9.428425891 -9.469333578 0.549953895 1.018940708 1.454863544 0.948480762 0.034952349 0.111326535 0.067707905 0.008787768 0.020380473 3.39E-10 9.469333578 0.435922836 ASS(ph)PGYIDSPTYSR ddPTM_HeLa_Romidepsin_16h_R1 3 ASSPGYIDSPTYSR 14 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 AS(0.07)S(0.93)PGYIDSPTYSR;AS(0.073)S(0.927)PGYIDSPTYSR;AS(0.022)S(0.975)PGY(0.001)IDS(0.002)PTYSR ;; 228.93 2.86E-33 78420000 7992.5 7280.8 7958.7 7585.5 9131 9596.9 7396.5 8834.3 7625.1 7666.5 TRUE FALSE FALSE 7895.084336 7383.299294 8097.217835 8462.571201 8665.010998 8983.689063 8024.758525 9089.906532 6943.091959 7467.323225 1.057284397 0.988747784 1.084353468 1.13328042 1.160390509 1.203066854 1.074649949 1.217291158 0.929796629 1 12.86637546 -9.378750986 2.264604212 1.024919183 1.158699879 0.688110401 0.050234004 0.124763271 1.251774256 0.00637408 0.01043607 4.18E-10 9.378750986 0.133780697 ASS(ph)PPDRIDIFGR ddPTM_HeLa_Romidepsin_16h_R1 3 ASSPPDRIDIFGR 13 1 Q9NWB6-2;Q9NWB6 Q9NWB6-2 ARGLU1 Arginine and glutamate-rich protein 1 1 0 AS(0.201)S(0.799)PPDRIDIFGR;AS(0.048)S(0.952)PPDRIDIFGR;AS(0.002)S(0.998)PPDRIDIFGR ;; 101.72 0.0043341 1090020000 10143.5 9965.9 8984.2 11616.1 10381.9 10657.7 9808.8 11329.2 10750.7 9809.6 TRUE FALSE FALSE 10019.86712 10106.2002 9140.566232 12959.20814 9852.072903 9976.707366 10641.95923 11656.99253 9789.130466 9554.745178 1.048679681 1.057715304 0.956652016 1.356311225 1.031118331 1.044162579 1.113787864 1.220021289 1.024530773 1 13.22200168 ASS(ph)PSLIER ddPTM_HeLa_Romidepsin_16h_R1 2 ASSPSLIER 9 0 A1L170;A1L170-2 A1L170 C1orf226 Uncharacterized protein C1orf226 1 0 AS(0.004)S(0.958)PS(0.037)LIER;AS(0.328)S(0.656)PS(0.016)LIER ; 113.44 0.017179 13653900 2981.1 2969.2 3634.2 4489.7 8873.3 10131.6 8290.4 8763.3 3594.2 3433.1 TRUE FALSE FALSE 2944.765207 3011.000476 3697.451727 5008.820239 8420.46239 9484.223458 8994.586369 9016.852259 3272.72575 3343.907567 0.880635947 0.900443692 1.105727851 1.497894346 2.518150464 2.836269624 2.689843002 2.696501646 0.978712983 1 11.70731925 -8.864403597 2.008139058 0.945268649 2.75422533 0.992641612 0.069937109 0.020293502 0.166131526 0.012427896 0.026048969 1.37E-09 8.864403597 1.808956681 up ASS(ph)PSPLT(ph)IGTPESQR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPSPLTIGTPESQR 16 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 0 AS(0.092)S(0.907)PSPLT(0.999)IGT(0.001)PESQR 191.89 6.51E-16 0 721.81 705.37 926.89 823.98 723.52 1070.8 708.89 1077.3 923.53 746.05 TRUE FALSE FALSE 713.0123021 715.3002174 943.0221316 919.2524445 686.5960746 1002.379336 769.1030989 1108.469976 840.9271638 726.6675135 0.981208447 0.98435695 1.297735366 1.265024826 0.944855882 1.379419497 1.058397527 1.52541562 1.157237868 1 9.5051516 -4 0.233850896 0.965801346 3.437399298 0.28848905 0.159310929 32.70147857 0.400031369 0.090469411 31.43862836 1.00E-04 4 2.471597951 ASS(ph)PSPLTIGTPESQRK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPSPLTIGTPESQRK 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 0 AS(0.167)S(0.467)PS(0.366)PLTIGTPESQRK 74.89 0.0074009 8183400 1261.7 1233.8 1099.8 990.73 1332.6 1312.5 1252.4 1280.6 1506.1 1496.7 TRUE FALSE FALSE 1246.321915 1251.169469 1118.941558 1105.282864 1264.592449 1228.635486 1358.778825 1317.652141 1371.390644 1457.815518 0.854924302 0.85824952 0.767546746 0.758177458 0.867457119 0.842792158 0.932065003 0.903853831 0.940716179 1 10.50959245 -11.94414988 0.771156784 1.000211215 0.845818994 0.445612635 0.053144645 0.416436972 0.456427793 0.036867774 0.011690783 1.14E-12 11.94414988 -0.154392222 ASS(ph)RPFR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSRPFR 7 1 Q8IU68-2;Q8IU68 Q8IU68-2 TMC8 Transmembrane channel-like protein 8 1 0 AS(0.012)S(0.988)RPFR 87.308 0.0099307 1365300 2697 3160.2 4542.3 3800.3 2439 3405.9 5914.5 879.81 4613 3725.6 TRUE FALSE FALSE 2664.127927 3204.689379 4621.356826 4239.708567 2314.528729 3188.273982 6416.877482 905.2659142 4200.401727 3628.808375 0.734160543 0.883124444 1.273519114 1.168347328 0.637820598 0.878600811 1.768315331 0.249466442 1.157515441 1 11.82528016 -9.95760316 24.99899741 0.870999946 1.022414054 0 0.390412415 427.551221 252101.7747 0.057477899 0.07554073 1.10E-10 9.95760316 0.151414109 ASSDGEGT(ph)MSRPASVDGSPVSPSTNR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSDGEGTMSRPASVDGSPVSPSTNR 26 1 P35568 P35568 IRS1 Insulin receptor substrate 1 1 0 ASS(0.002)DGEGT(0.456)MS(0.456)RPAS(0.007)VDGS(0.004)PVS(0.049)PS(0.018)T(0.008)NR 47.546 0.024834 6029500 627.38 749.36 650.16 963.37 564.81 401.07 381.38 479.15 817.61 701.87 TRUE FALSE FALSE 619.7332512 759.9095097 661.4757621 1074.759372 535.9856381 375.4429214 413.7744077 493.0134493 744.4809139 683.6353162 0.906526092 1.111571465 0.967585709 1.572123831 0.784022746 0.549185966 0.605256045 0.721164395 1.089003005 1 9.417083118 -8.52990228 24.99988134 1.014132324 0.630440247 0.551144318 0.188644457 112.509418 400470.3984 0.027641766 0.055380021 2.95E-09 8.52990228 -0.383692077 ASSEDAGPS(ph)PQTR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSEDAGPSPQTR 13 0 Q5T5P2;Q5T5P2-2;Q5T5P2-7;Q5T5P2-10;Q5T5P2-3;Q5T5P2-9;Q5T5P2-4;Q5T5P2-8;Q5T5P2-6 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 ASSEDAGPS(0.948)PQT(0.052)R 90.229 0.022393 5453700 1762 1539.2 1586.6 1791.5 1680.2 1946.7 1537.9 1783.7 2167.8 1706 TRUE FALSE FALSE 1740.524066 1560.868898 1614.214107 1998.641659 1594.453124 1822.312153 1668.529188 1835.308545 1973.906539 1661.677874 1.047449745 0.939333021 0.971436241 1.202785263 0.959544054 1.096669927 1.00412313 1.104491174 1.187899634 1 10.69842502 ASSEDVASS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 ASSEDVASSPER 12 0 M0R2H0;A0A087WWI0;Q9H2I8 M0R2H0 C10orf11 Leucine-rich repeat-containing protein C10orf11 1 0 ASSEDVAS(0.002)S(0.998)PER;ASSEDVAS(0.002)S(0.998)PER ; 212.68 4.69E-21 84027000 15434.2 15121.8 14400.7 13508.9 16821 15875.5 12895.6 12905.4 16134.3 13922 TRUE FALSE FALSE 15246.08203 15334.6851 14651.33814 15070.86258 15962.5616 14861.10679 13990.95194 13278.79739 14691.2078 13560.30443 1.124317091 1.130851094 1.080457907 1.111395592 1.177153631 1.095927223 1.031757953 0.979240359 1.083398081 1 13.72710195 -4.478527252 20.8432737 1.073213535 0.218070844 0 0.058971974 0 0 0.009271917 0 3.32E-05 4.478527252 -0.855142691 ASSK(ac)RPATADSPKPSAK ddPTM_HeLa_Romidepsin_16h_R1 2 ASSKRPATADSPKPSAK 17 3 Q03111 Q03111 MLLT1 Protein ENL 0 1 ; ASSK(0.929)RPATADSPK(0.071)PSAK;ASSK(0.998)RPATADSPK(0.002)PSAK 71.316 0.0066214 10238400 5223.7 5514.7 3861.1 4702.7 7412.6 9110.8 7198.9 8272 5346.2 4535.2 FALSE TRUE FALSE 5160.031535 5592.336091 3928.300826 5246.448301 7034.307362 8528.649284 7810.374386 8511.337269 4868.022482 4417.37485 1.168121726 1.265986311 0.889284011 1.18768465 1.592418031 1.930705356 1.76810315 1.926786283 1.102017068 1 12.10897355 -8.655972291 2.552520612 1.083383668 1.861623186 0.92021568 0.103984614 0.056097433 0.739533526 0.016484252 0.036360699 2.21E-09 8.655972291 0.778239517 ASSLEDLVLK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSLEDLVLK 10 0 Q15477 Q15477 SKIV2L Helicase SKI2W 0 0 114.86 0.0032381 0 2084.5 1787.7 1954.8 1590.8 1849.4 2224.1 1621.7 2017.1 1970 1766.3 FALSE FALSE TRUE 2059.093312 1812.867288 1988.822474 1774.735781 1755.018217 2081.987188 1759.447158 2075.461606 1793.798266 1720.411271 1.196861092 1.053740648 1.15601572 1.031576467 1.020115507 1.210168303 1.022689857 1.206375267 1.042656658 1 10.74853777 -12.62275659 1.447511552 1.000223728 1.119440283 0.180631675 0.074689574 0.447412166 1.688750564 0.051001105 0.011762345 2.38E-13 12.62275659 0.119216556 ASSLNFLNKS(ph)VEEPTQPGGTGLSDSR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSLNFLNKSVEEPTQPGGTGLSDSR 26 1 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 0 AS(0.007)S(0.023)LNFLNKS(0.912)VEEPT(0.05)QPGGT(0.005)GLS(0.002)DS(0.001)R 53.998 0.0039745 0 244.77 292.51 367.97 399.74 426.86 398.97 263.38 266.04 366.89 395.41 TRUE FALSE FALSE 241.7866491 296.6279635 374.3743635 445.9598196 405.0757414 373.4771046 285.7514906 273.7374477 334.0744395 385.1371912 0.627793562 0.770187793 0.972054561 1.157924578 1.051769994 0.969724849 0.741947278 0.710753087 0.867416721 1 8.589228635 -7.630404508 7.360855429 0.875188096 0.718861034 0.166016165 0.147456009 0.414822343 25.02064353 0.027216459 0.103214846 2.34E-08 7.630404508 -0.156327061 ASSLSESS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSLSESSPPK 11 0 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3;F8VRN8 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 ASSLS(0.001)ES(0.077)S(0.922)PPK 156.01 0.001977 771730000 2885.2 2948.5 2851.6 2644.5 2915.8 3197.4 2936.6 3035 3063.2 2914.7 TRUE FALSE FALSE 2850.034073 2990.00906 2901.230902 2950.269533 2766.995846 2993.096459 3186.034731 3122.812937 2789.21972 2838.975674 1.003895207 1.053199958 1.021928764 1.039202118 0.974645845 1.054287462 1.122247985 1.099978758 0.982473977 1 11.47115477 -7.962405752 3.999555073 1.008703628 1.109845732 0.747586193 0.023197968 0.07099058 2.470085654 0.003145989 0.009984147 1.09E-08 7.962405752 0.101142104 ASSPS(ph)PLTIGTPESQRK ddPTM_HeLa_Romidepsin_16h_R1 1 ASSPSPLTIGTPESQRK 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 0 AS(0.159)S(0.159)PS(0.676)PLT(0.005)IGTPESQRK 58.159 0.020391 18622000 2644.8 2332.9 2631.8 2293.6 2825.7 3170.5 2701.5 3156.6 3392.5 2691.9 TRUE FALSE FALSE 2612.56416 2365.742627 2677.605375 2558.796824 2681.493985 2967.915282 2930.965343 3247.931241 3089.066303 2621.96405 0.996414943 0.902278819 1.021221239 0.975908432 1.022704329 1.131943545 1.117851079 1.238739807 1.178149755 1 11.35643219 -7.834520299 1.029575723 0.989607871 1.242598068 0.490099089 0.070289359 0.25683615 0.365872789 0.005633224 0.057018423 1.46E-08 7.834520299 0.252990197 ASSSGPRS(ph)PLDQR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSSGPRSPLDQR 13 1 O14646-2;O14646 O14646-2 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 0 ASSS(0.005)GPRS(0.995)PLDQR 142.95 0.0053403 30248000 3604.6 3139.4 3103.2 2915 2803.3 3249.9 2560.7 2813.6 3527.5 3448.9 TRUE FALSE FALSE 3560.665749 3183.596556 3157.209894 3252.046015 2660.23714 3042.241879 2778.205794 2895.007077 3211.991565 3359.297081 1.059943692 0.947697235 0.939842419 0.968073361 0.791902912 0.905618588 0.827019977 0.861789537 0.956149899 1 11.71394367 -9.358900483 1.015573687 1.026827666 0.8489465 0.597250258 0.048777724 0.184675253 0.378204531 0.008058109 0.015976518 4.38E-10 9.358900483 -0.177881166 ASST(ph)PSSETQEEFVDDFR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSTPSSETQEEFVDDFR 18 0 J3KP58;P30622-2;P30622-1;P30622;F5H1T5;F5H6A0;F5H367;F5H270 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 0 AS(0.002)S(0.205)T(0.556)PS(0.205)S(0.002)ET(0.029)QEEFVDDFR 273.82 9.77E-99 0 1345 1112.8 1310.8 1059.3 1115.3 946.44 832.57 730.58 1703.5 1510.2 TRUE FALSE FALSE 1328.606623 1128.466028 1333.613924 1181.78125 1058.382079 885.9655385 903.288475 751.7181796 1551.134694 1470.964786 0.903221229 0.767160464 0.906625323 0.803405534 0.719515579 0.602302344 0.614078925 0.511037509 1.054501582 1 10.52254699 -6.930713571 0.245335679 1.011699656 2.83E-12 0.914604847 0.049774055 2.169631395 0.091841214 0.031810532 0.68446198 1.17E-07 6.930713571 -1.011699656 ASSTPS(ph)SETQEEFVDDFR ddPTM_HeLa_Romidepsin_16h_R1 1 ASSTPSSETQEEFVDDFR 18 0 J3KP58;P30622-2;P30622-1;P30622;F5H1T5;F5H6A0;F5H367;F5H270 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 0 ASST(0.042)PS(0.871)S(0.082)ET(0.004)QEEFVDDFR 287.31 1.09E-123 8158200 1350.6 1440.4 1441.9 1123.9 865.16 1031.3 769.34 862.25 1695.4 1487.7 TRUE FALSE FALSE 1334.138368 1460.677989 1466.995665 1253.850606 821.0076568 965.4032584 834.6877204 887.1978433 1543.759178 1449.04934 0.920699062 1.00802502 1.012384896 0.865291865 0.566583645 0.666232151 0.576024361 0.612261998 1.065359982 1 10.500891 -8.886768948 3.857732647 0.968354746 0.607418864 0.935184585 0.048761534 0.036985075 1.037194997 0.006449727 0.012134467 1.30E-09 8.886768948 -0.360935882 ASSTST(ph)PEPTR ddPTM_HeLa_Romidepsin_16h_R1 3 ASSTSTPEPTR 11 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6 ENAH Protein enabled homolog 1 0 ASST(0.002)S(0.02)T(0.978)PEPTR;ASST(0.021)S(0.217)T(0.751)PEPT(0.01)R;AS(0.001)S(0.003)T(0.019)S(0.2)T(0.777)PEPTR ;; 152.64 0.0046986 535616000 21259.5 23473.3 25446.6 20136.1 26339.4 27211.1 31371.2 11142.1 26152 25277.9 TRUE FALSE FALSE 21000.38104 23803.75773 25889.4874 22464.33063 24995.20213 25472.39853 34035.86894 11464.47908 23812.89962 24621.17651 0.852939786 0.966800174 1.051513009 0.912398748 1.015191216 1.03457276 1.382381907 0.465634901 0.967171476 1 14.58761208 -10.00334094 23.95098148 0.929466221 0.99783064 0 0.213353405 303.2103581 2173727.951 0.031863453 0.041378251 9.92E-11 10.00334094 0.068364419 AST(ph)PDWVSEGPQPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 ASTPDWVSEGPQPGLR 16 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 AS(0.059)T(0.941)PDWVSEGPQPGLR 321.34 2.40E-179 121510000 3159.6 3575.4 3185.6 2845.7 2210 2256.7 1608.9 1444.5 3288.4 3090.2 TRUE FALSE FALSE 3121.08958 3625.734575 3241.044032 3174.733223 2097.215453 2112.504153 1745.559926 1486.294328 2994.277268 3009.916159 1.03693572 1.204596535 1.076788808 1.054758025 0.696768728 0.701848172 0.579936395 0.493799246 0.994804211 1 11.55550759 -8.639099402 2.57550862 1.042113498 0.59300603 0.89191572 0.07577063 0.071829696 0.96254409 0.012199288 0.027088865 2.30E-09 8.639099402 -0.449107468 AST(ph)PDWVSEGPQPGLRR ddPTM_HeLa_Romidepsin_16h_R1 2 ASTPDWVSEGPQPGLRR 17 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 AS(0.077)T(0.923)PDWVSEGPQPGLRR;AS(0.211)T(0.789)PDWVSEGPQPGLRR ; 101.28 0.0012699 32995000 4425 4179.3 3297.8 5060.2 3037.1 2893.1 2687.1 2650.9 4569.6 3877.2 TRUE FALSE FALSE 4371.066398 4238.136295 3355.196826 5645.284133 2882.105454 2708.240247 2915.342207 2727.599609 4160.883531 3776.469785 1.157447735 1.122248167 0.888447947 1.494857487 0.763174504 0.71713542 0.771975515 0.722261732 1.101791824 1 11.88282253 -8.569373352 24.99991624 1.092389137 0.740532214 0.612642131 0.148051015 62.04872065 33363.05411 0.020362659 0.040725332 2.70E-09 8.569373352 -0.351856923 AST(ph)PYIEK ddPTM_HeLa_Romidepsin_16h_R1 2 ASTPYIEK 8 0 C9J618;C9J5A2;C9J347;C9J7P5;C9IZN7;Q969Z0-2;Q969Z0 C9J618 TBRG4 Protein TBRG4 1 0 AS(0.072)T(0.928)PYIEK;AS(0.006)T(0.994)PYIEK ; 140.17 0.018509 38346000 20748.8 21335 20912 20392.7 18512.3 16829.8 13616 14972.3 20279 19427.3 TRUE FALSE FALSE 20495.90564 21635.35469 21275.96459 22750.59992 17567.54825 15754.4301 14772.5427 15405.49988 18465.19545 18922.57595 1.083145641 1.143362022 1.124369359 1.202299306 0.92839095 0.832573226 0.780683494 0.814133336 0.975828846 1 14.20782088 -8.481038632 3.70698267 1.066404496 0.809661461 0.780118428 0.066135541 0.092660341 2.626974906 0.010580614 0.024084677 3.30E-09 8.481038632 -0.256743035 ASTSDYQVISDRQT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ASTSDYQVISDRQTPK 16 1 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 AS(0.001)T(0.005)S(0.004)DY(0.009)QVIS(0.122)DRQT(0.859)PK 70.02 0.022399 106680000 4412.2 4128.8 4784.8 3477.6 4706 5691 5153.1 5456.9 5252.4 4430.7 TRUE FALSE FALSE 4358.422409 4186.925355 4868.077437 3879.696475 4465.835259 5327.363467 5590.804185 5614.786792 4782.612189 4315.589775 1.009925094 0.970186133 1.128021358 0.898995659 1.034814589 1.234446216 1.295490182 1.301047385 1.108217518 1 12.07534202 -8.214847341 3.154327724 1.004103789 1.292458256 0.780906066 0.062299043 0.062074971 1.237095385 0.006879612 0.018983265 6.10E-09 8.214847341 0.288354468 ASTSSSSSSSSNQQTEKET(ph)NTPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASTSSSSSSSSNQQTEKETNTPK 23 1 C9J2P0;P51965-3;P51965 C9J2P0 UBE2E1 Ubiquitin-conjugating enzyme E2 E1 1 0 ASTSSSSSSSSNQQTEKET(0.5)NT(0.5)PK 103.16 1.54E-05 5432500 584.75 422.13 491.95 713.56 391.85 376.75 224.44 236.7 523.65 437.31 TRUE FALSE FALSE 577.6228421 428.0727572 500.5121834 796.0651646 371.8524323 352.6768909 243.503928 243.548541 476.8134325 425.9486232 1.356085712 1.004986832 1.175052943 1.868922967 0.87299832 0.827979882 0.57167441 0.571779148 1.119415363 1 8.734535617 -8.317839245 2.697983224 1.204642052 0.620386372 0.524380496 0.251103363 0.183163311 2.604196119 0.038267092 0.101723539 4.81E-09 8.317839245 -0.584255681 LEPAS(ph)PPEDTSAEVSR ddPTM_HeLa_Romidepsin_16h_R1 2 LEPASPPEDTSAEVSR 16 0 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 0 LEPAS(0.921)PPEDT(0.063)S(0.016)AEVSR;LEPAS(0.713)PPEDT(0.219)S(0.067)AEVSR ; 211.49 8.11E-26 46515000 5057.8 4637.9 4358.72 2487.53 1650.71 1376.31 1189.09 879.38 5019.8 4477.1 TRUE FALSE FALSE 4996.153588 4703.192478 4434.581693 2775.149923 1566.468109 1288.368233 1290.091275 904.8234729 4570.816516 4360.784297 1.145700692 1.078519862 1.016922964 0.6363878 0.359217059 0.295444155 0.295839277 0.207490995 1.048163863 1 12.09037191 -9.02145498 1.777044037 1.073512219 0.270034256 0.986501326 0.042572131 0.037283824 0.233972454 0.009591258 0.019142461 9.52E-10 9.02145498 -0.803477963 down ASTVS(ph)PGGYMVPK ddPTM_HeLa_Romidepsin_16h_R1 3 ASTVSPGGYMVPK 13 0 Q5TGY3 Q5TGY3 AHDC1 AT-hook DNA-binding motif-containing protein 1 1 0 AS(0.006)T(0.026)VS(0.968)PGGYMVPK;AST(0.015)VS(0.983)PGGY(0.001)MVPK;AST(0.003)VS(0.997)PGGYMVPK ;; 132.14 0.0027921 52716900 9577 8180.3 8499.9 7602 8532 8870.7 9000.9 8792.6 9090.2 8477.2 TRUE FALSE FALSE 9460.27184 8295.462478 8647.837194 8480.979008 8096.580203 8303.890899 9765.436221 9047.000009 8277.149745 8256.961122 1.145732879 1.004662897 1.047338975 1.027130791 0.980576278 1.005683662 1.182691317 1.095681556 1.002445043 1 13.0113952 -7.760559038 24.99998966 1.051412117 1.139186436 0.357340645 0.0525578 25.54107149 725192.6285 0.009201674 0.030849634 1.74E-08 7.760559038 0.087774318 ASVALT(ph)PTAPSR ddPTM_HeLa_Romidepsin_16h_R1 2 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 AS(0.001)VALT(0.941)PT(0.058)APSR;AS(0.023)VALT(0.906)PT(0.069)APS(0.001)R ; 142.76 0.0033327 123224000 7374.2 7164.4 6727.9 5909.9 5772.3 5435.4 4160.1 4735.3 7246.9 7070.9 TRUE FALSE FALSE 7284.320414 7265.260611 6844.996277 6593.230445 5477.717992 5088.095482 4513.45879 4872.308434 6598.719114 6887.196999 1.057661109 1.054893684 0.993872584 0.957316953 0.795347947 0.738775947 0.655340451 0.707444325 0.958113891 1 12.74970123 -8.678203342 1.431171447 1.029813231 0.683555452 0.947855698 0.032897243 0.050826008 0.207423041 0.004497884 0.012042467 2.10E-09 8.678203342 -0.346257779 ASVALTPTAPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 3 ASVALTPTAPSR 12 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 ASVALTPTAPS(1)R;ASVALTPTAPS(1)R;ASVALTPTAPS(1)R ;; 117.27 0.0014108 23512900 8542.5 9160.3 9186.4 5546.2 7086.8 7053 5652.5 6525.7 8469.4 8043 TRUE FALSE FALSE 8438.380724 9289.258944 9346.285438 6187.47774 6725.134152 6602.336063 6132.623209 6714.510834 7711.875652 7834.041701 1.077142687 1.185755616 1.193034936 0.789819352 0.858450135 0.8427752 0.782817279 0.857094089 0.984405744 1 12.93554109 -9.246536937 24.90155574 1.06160672 0.826495031 0.777153065 0.069396265 329.358622 550349.1272 0.011581325 0.019153235 5.67E-10 9.246536937 -0.235111689 ASVITQVFHVPLEER ddPTM_HeLa_Romidepsin_16h_R1 2 ASVITQVFHVPLEER 15 0 A0A024R4E5;Q00341-2;Q00341;C9JT62;C9JHS7;C9JK79;C9JHZ8;C9JES8;C9JZI8;C9J5E5;C9JIZ1 A0A024R4E5 HDLBP Vigilin 0 0 ; ; 118.71 0.0017092 12055800 3300.9 2756.4 2994.6 3276.6 3102.2 2669.7 2345.1 2721.5 3435.6 2945 FALSE FALSE TRUE 3260.667361 2795.204672 3046.719757 3655.455909 2943.883158 2499.114786 2544.292735 2800.242309 3128.311331 2868.488475 1.136719701 0.974452118 1.062134216 1.27434917 1.026283767 0.871230548 0.886980288 0.976208318 1.090578316 1 11.48607501 -8.405321719 5.315584959 1.074195575 0.910817894 0.480640885 0.081646416 0.171720614 6.825249228 0.012773016 0.028985875 3.93E-09 8.405321719 -0.163377681 ASVLDT(ph)SMSAGSGSPSKT(ph)VTPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASVLDTSMSAGSGSPSKTVTPK 22 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 2 0 ASVLDT(0.274)S(0.251)MS(0.273)AGS(0.234)GS(0.084)PS(0.276)KT(0.333)VT(0.275)PK 44.382 0.028731 18959000 3536.1 3579.5 3336.8 4551.4 4142.5 4616.8 4250.6 4299.3 3875.3 3634.6 TRUE FALSE FALSE 3493.000653 3629.892295 3394.875604 5077.654283 3931.092767 4321.80138 4611.645858 4423.693462 3528.683462 3540.172568 0.98667525 1.02534332 0.958957661 1.434295698 1.110424052 1.220788336 1.302661316 1.249570007 0.996754648 1 11.78960397 -9.283113596 24.9867189 0.994054554 1.254838448 0.755550328 0.076708874 271.5753567 313079.7612 0.010751458 0.016431897 5.21E-10 9.283113596 0.260783894 ASVLDTSMS(ph)AGSGSPSK ddPTM_HeLa_Romidepsin_16h_R1 6 ASVLDTSMSAGSGSPSK 17 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 ASVLDT(0.002)S(0.011)MS(0.987)AGS(0.001)GSPSK;ASVLDT(0.002)S(0.011)MS(0.987)AGS(0.001)GSPSK;ASVLDT(0.032)S(0.158)MS(0.798)AGS(0.007)GS(0.004)PSK;ASVLDTS(0.002)MS(0.996)AGS(0.002)GSPSK;ASVLDT(0.009)S(0.025)MS(0.914)AGS(0.052)GSPSK;ASVLDT(0.001)S(0.009)MS(0.99)AGS(0.001)GSPSK ;;;;; 175.74 3.90E-07 975215000 46129.6 44183.8 45007.2 34181.2 30634.2 24382.9 21484.8 20748.6 45141.7 42803.6 TRUE FALSE FALSE 45567.35469 44805.8207 45790.53144 38133.39117 29070.82246 22824.91138 23309.71838 21348.92801 41104.11329 41691.5563 1.092963629 1.074697725 1.098316674 0.914655018 0.697283216 0.547470841 0.559099262 0.512068387 0.985909785 1 15.34746761 -8.722631683 1.877157044 1.051828517 0.53840018 0.972100883 0.038452167 0.041173128 0.294502165 0.006671311 0.015422137 1.89E-09 8.722631683 -0.513428336 ASVLDTSMS(ph)AGSGSPSKTVTPK ddPTM_HeLa_Romidepsin_16h_R1 1 ASVLDTSMSAGSGSPSKTVTPK 22 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 ASVLDT(0.097)S(0.392)MS(0.468)AGS(0.013)GS(0.024)PS(0.003)KT(0.003)VTPK 64.26 0.0089186 45645000 2699.9 1939.2 1478.1 5470.9 1580 1269.4 1100.3 1033.9 2525.4 1796.2 TRUE FALSE FALSE 2666.99258 1966.500109 1503.82571 6103.471199 1499.366704 1188.289437 1193.759455 1063.814265 2299.521899 1749.534465 1.524401281 1.124013358 0.859557637 3.488625872 0.857008955 0.679203217 0.682329773 0.608055621 1.31436216 1 10.77275537 -8.541554023 24.99996488 1.383700245 0.677274399 0.24123791 0.703528649 308.9451753 413573.2138 0.102263991 0.204552926 2.87E-09 8.541554023 -0.706425846 ASVS(ph)GPNS(ph)PSETRR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETRR 14 1 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 2 0 AS(0.038)VS(0.897)GPNS(0.608)PS(0.244)ET(0.213)RR 105.19 0.0072828 13955000 4535.9 3649.7 4026.2 3903.5 4626.5 4504.5 3719.3 3853.8 4770.6 4065 TRUE FALSE FALSE 4480.614706 3701.080572 4096.274322 4354.841037 4390.392441 4216.676988 4035.217249 3965.303623 4343.905588 3959.390714 1.131642475 0.934760128 1.034571887 1.09987656 1.108855569 1.064981279 1.019151062 1.001493389 1.097114658 1 11.95106272 -7.646653885 4.281729499 1.058483508 1.005565907 0.113378786 0.055209312 0.417122088 13.09956555 0.008931102 0.037309806 2.26E-08 7.646653885 -0.052917601 ASVS(ph)PMDEPVPDSES(ph)PIEK ddPTM_HeLa_Romidepsin_16h_R1 3 ASVSPMDEPVPDSESPIEK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 AS(0.172)VS(0.828)PMDEPVPDS(0.002)ES(0.998)PIEK;AS(0.193)VS(0.807)PMDEPVPDS(0.012)ES(0.988)PIEK;AS(0.186)VS(0.814)PMDEPVPDS(0.345)ES(0.655)PIEK ;; 129.4 0.0012278 34474000 13629.2 13733 12139.1 11780.7 12113.7 13368.4 11767 12495.3 13717.3 13872.7 TRUE FALSE FALSE 13463.08207 13926.33353 12350.37594 13142.83996 11495.49269 12514.20238 12766.48869 12856.83179 12490.39033 13512.28525 0.996358633 1.030642358 0.914010895 0.972658563 0.850743784 0.926135154 0.944806037 0.951492035 0.924372902 1 13.72198407 -9.752929488 24.99866497 1.000659562 0.92608558 0.346317848 0.039654426 97.74056793 287121.8213 0.004773089 0.006688997 1.77E-10 9.752929488 -0.074573982 ASVS(ph)PMDEPVPDSESPIEK ddPTM_HeLa_Romidepsin_16h_R1 3 ASVSPMDEPVPDSESPIEK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 AS(0.019)VS(0.981)PMDEPVPDSESPIEK;AS(0.016)VS(0.984)PMDEPVPDSESPIEK;AS(0.007)VS(0.993)PMDEPVPDSESPIEK ;; 159.64 2.80E-06 205907000 21039.3 19296.3 19557.2 20155.6 19512.3 18124.5 16463.3 17629.3 20869.3 18832.8 TRUE FALSE FALSE 20782.86492 19567.95382 19897.58486 22486.08531 18516.51452 16966.40294 17861.69229 18139.37598 19002.69754 18343.52114 1.132981218 1.066750144 1.084720033 1.225832551 1.009430762 0.92492618 0.973733023 0.988870994 1.035935107 1 14.16298298 -8.530177627 24.99987289 1.078246072 0.964223359 0.487544459 0.059250862 142.5511543 488260.2836 0.010154799 0.020342864 2.95E-09 8.530177627 -0.114022713 ASVS(ph)QTSPQSASSPR ddPTM_HeLa_Romidepsin_16h_R1 2 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 0 AS(0.001)VS(0.909)QT(0.049)S(0.03)PQS(0.01)ASSPR;AS(0.006)VS(0.994)QTSPQSASSPR ; 191.15 2.01E-12 9152600 1598.09 1605.19 1467.67 1514.49 2030.78 2905.36 2352.7 3139 1504.31 1746.12 TRUE FALSE FALSE 1578.611864 1627.787907 1493.214181 1689.60246 1927.141719 2719.716873 2552.538279 3229.822012 1369.760746 1700.755551 0.928182691 0.957096925 0.877971076 0.993442273 1.133109175 1.599122738 1.500826076 1.899051284 0.805383669 1 10.73196008 -8.21217879 1.406414629 0.954704271 1.758243963 0.914521025 0.101640105 0.07886968 0.283689961 0.012769094 0.053406713 6.14E-09 8.21217879 0.803539691 ASVSGPNS(ph)PSESR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSESR 13 0 A6PVI4;Q9UJV3-2;Q9UJV3 A6PVI4 MID2 Probable E3 ubiquitin-protein ligase MID2 1 0 ASVS(0.001)GPNS(0.858)PS(0.133)ES(0.007)R 97.223 0.0032742 0 1053.7 714.2 917.93 593.27 812.51 757.02 616.83 759.87 1067.1 1148.7 TRUE FALSE FALSE 1040.857099 724.2545263 933.9061866 661.8666688 771.0445828 708.6488652 669.2235248 781.8556396 971.6559034 1118.856608 0.930286411 0.647316663 0.834696939 0.591556294 0.689136192 0.633368798 0.598131628 0.698798786 0.868436488 1 10.12780944 -10.22063998 0.974041036 0.984845134 0.645273035 0.678629034 0.079129856 0.13258464 0.248323528 0.014106242 0.017138197 6.02E-11 10.22063998 -0.339572099 ASVSGPNS(ph)PSETR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETR 13 0 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 1 0 AS(0.002)VS(0.001)GPNS(0.482)PS(0.399)ET(0.116)R 176.43 9.27E-07 18142000 1383.9 1500 1514.9 986.18 1386.3 2000.3 1485.9 1970.4 1435.6 1676.6 TRUE FALSE FALSE 1367.032494 1521.117039 1541.266199 1100.206772 1315.551938 1872.487286 1612.112309 2027.410415 1307.19634 1633.04169 0.837108142 0.931462466 0.943800889 0.673716279 0.805583805 1.146625525 0.987183805 1.24149336 0.800467219 1 10.67334591 -8.251945732 24.92927109 0.897704163 1.111309202 0.539084111 0.109139768 489.6214891 1285689.108 0.016292252 0.040936768 5.60E-09 8.251945732 0.213605039 ASVSGPNS(ph)PSETRR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETRR 14 1 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 1 0 ASVSGPNS(0.577)PS(0.305)ET(0.118)RR 88.781 0.006045 62461000 3313.1 3550.2 3777.1 3756.3 3283.1 4077.5 3458.4 4051.2 4135.3 3309.2 TRUE FALSE FALSE 3272.718663 3600.179809 3842.838841 4190.62108 3115.551156 3816.96091 3752.15641 4168.41508 3765.428411 3223.226507 1.015354849 1.116949057 1.192233569 1.300132358 0.966593924 1.184204989 1.164099514 1.293242988 1.168217127 1 11.65428986 -10.12944517 2.697279786 1.006302295 1.177513597 0.174213895 0.099928045 0.180739409 2.534262276 0.014308982 0.017787768 7.42E-11 10.12944517 0.171211302 ASVSGPNSPS(ph)ET(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 ASVSGPNSPSETRR 14 1 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 2 0 AS(0.01)VS(0.045)GPNS(0.037)PS(0.959)ET(0.948)RR 122.1 0.0031515 12433000 4999.9 4824.3 3835 4128.5 4244.3 4826 3400.1 3991.4 4900.8 4672.7 TRUE FALSE FALSE 4938.959296 4892.216622 3901.746566 4605.856595 4027.697533 4517.634175 3688.904409 4106.884862 4462.460174 4551.30258 1.085174894 1.074904719 0.857281294 1.011986462 0.884954903 0.992602468 0.810516186 0.90235373 0.980479785 1 12.15206379 -9.767987383 24.99986615 1.043946561 0.912688414 0.486996501 0.062648993 92.31462542 352451.2432 0.009856894 0.013126404 1.71E-10 9.767987383 -0.131258148 ASVSGPNSPS(ph)ETR ddPTM_HeLa_Romidepsin_16h_R1 2 ASVSGPNSPSETR 13 0 A0A087X0X0;C9J453;A0A087X255;O15344-2;O15344 A0A087X0X0 MID1 E3 ubiquitin-protein ligase Midline-1 1 0 ASVSGPNS(0.182)PS(0.636)ET(0.182)R;ASVS(0.029)GPNS(0.302)PS(0.668)ET(0.001)R ; 115.12 0.0010997 0 1286.88 1304.65 1211.49 1054.08 1596.45 1291.35 1415.13 1251.8 1703.07 1482.81 TRUE FALSE FALSE 1271.195012 1323.016897 1232.575475 1175.957689 1514.977199 1208.836903 1535.331107 1288.018858 1550.743154 1444.286382 0.880154398 0.916035014 0.85341487 0.814213651 1.048945152 0.836978675 1.063037861 0.891802951 1.073708907 1 10.49614112 -6.243994765 14.64154471 0.932010764 0.921733981 0 0.094439504 0 0 0.01087432 0 5.70E-07 6.243994765 -0.010276783 ASVSPMDEPVPDS(ph)ESPIEK ddPTM_HeLa_Romidepsin_16h_R1 3 ASVSPMDEPVPDSESPIEK 19 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 ASVSPMDEPVPDS(0.943)ES(0.057)PIEK;ASVSPMDEPVPDS(0.614)ES(0.386)PIEK;ASVS(0.001)PMDEPVPDS(0.997)ES(0.002)PIEK ;; 222.11 2.79E-38 133563000 15874 16160 14899.5 14235.9 16365.1 16787.8 15851.3 16127.9 16420.1 15320.4 TRUE FALSE FALSE 15680.52158 16387.5009 15158.81955 15881.92174 15529.92788 15715.11376 17197.70903 16594.53534 14951.44513 14922.3738 1.050806111 1.098183246 1.015845049 1.064302634 1.040714305 1.053124253 1.152478102 1.112057342 1.001948171 1 13.86518943 -4 0.142451991 0.991577358 1.449589561 0.564584507 0.031056182 41.49244199 0.38850056 0.082082653 3.899339982 1.00E-04 4 0.458012203 ASVSQT(ph)SPQSASSPR ddPTM_HeLa_Romidepsin_16h_R1 2 ASVSQTSPQSASSPR 15 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 0 ASVS(0.002)QT(0.551)S(0.223)PQS(0.007)AS(0.167)S(0.05)PR;ASVSQT(0.574)S(0.299)PQS(0.087)AS(0.014)S(0.026)PR ; 185.74 1.89E-08 38385000 5054.4 4219.9 3943.7 4254.4 5436.8 5585.5 5412.7 6358.4 4946.4 4608.2 TRUE FALSE FALSE 4992.795029 4279.307863 4012.338444 4746.313746 5159.339809 5228.604576 5872.454603 6542.370272 4503.981596 4488.4783 1.112358063 0.953398363 0.893919537 1.057443844 1.149463017 1.164894699 1.308339756 1.457592047 1.00345402 1 12.1320107 -7.588317117 0.975127396 1.03460976 1.558307309 0.845057899 0.063734031 0.432976661 0.438339092 0.011799268 0.209760109 2.58E-08 7.588317117 0.523697549 ASVVGTDGT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ASVVGTDGTPK 11 0 O43166-3;O43166-2;O43166;G3V4Z3 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 ASVVGT(0.286)DGT(0.714)PK 128.36 0.013046 3495100 3460.9 3568.5 3973.4 3203.7 4250 4337.7 3380.9 3379.5 3492.4 3477.9 TRUE FALSE FALSE 3418.71722 3618.737437 4042.55536 3574.126868 4033.106641 4060.534969 3668.073562 3477.280501 3180.030997 3387.543657 1.009202409 1.068248207 1.193358897 1.055079205 1.190569643 1.198666462 1.082812189 1.02649024 0.93874244 1 11.72602382 -10.07382147 3.59196717 1.004521165 1.126306037 0.519842989 0.059615782 0.145050189 3.620752074 0.009260903 0.011633237 8.44E-11 10.07382147 0.121784872 ASWES(ph)LDEEWR ddPTM_HeLa_Romidepsin_16h_R1 2 ASWESLDEEWR 11 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 AS(0.003)WES(0.997)LDEEWR;AS(0.04)WES(0.96)LDEEWR ; 229 9.75E-28 17891300 2018 1910.55 1780.03 1249.09 1614.11 1582.64 1583.51 1355.16 1954.08 1906.66 TRUE FALSE FALSE 1993.40384 1937.446773 1811.010675 1393.515663 1531.735944 1481.514412 1718.0133 1394.369417 1779.302191 1857.124698 1.073381794 1.043250771 0.97516913 0.750361925 0.824788957 0.79774633 0.92509313 0.750821643 0.958095163 1 10.85885497 -9.427636786 4.355738249 1.035445698 0.817058674 0.768545256 0.054857988 0.071157576 2.340491059 0.007890243 0.012127767 3.74E-10 9.427636786 -0.218387025 ASYDDPYK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ASYDDPYKK 9 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 1 ; ASYDDPYK(1)K;ASYDDPYK(1)K 142.92 0.0041127 2858700 2304.2 2014.46 1929.25 1484.95 3480 2985.1 3098.7 3001 3957.1 2907.9 FALSE TRUE FALSE 2276.115524 2042.819621 1962.827787 1656.646906 3302.402614 2794.361744 3361.903501 3087.8292 3603.167065 2832.352339 0.803613129 0.721244879 0.693002689 0.58490142 1.165957557 0.986586911 1.186965144 1.090199534 1.272146483 1 11.46778503 -8.722133901 24.99999104 0.851598316 1.104477291 0.325975288 0.184158798 129.1608519 82151.36513 0.022513884 0.04502722 1.90E-09 8.722133901 0.252878975 ASYDVSDSGQLEHVQPWS(ph)V ddPTM_HeLa_Romidepsin_16h_R1 1 ASYDVSDSGQLEHVQPWSV 19 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 0 ASYDVSDSGQLEHVQPWS(1)V 152.59 1.47E-05 7214300 1185.3 953.35 969.08 1041.2 1444.4 1518.6 1167.8 1425.6 1280.4 1051.5 TRUE FALSE FALSE 1170.853108 966.7712863 985.9464309 1161.588443 1370.686878 1421.566361 1266.992903 1466.847487 1165.877817 1024.181878 1.143208186 0.943944925 0.962667327 1.134162269 1.338323697 1.388001869 1.237078032 1.432213865 1.138350367 1 10.00025622 -8.850284634 3.619004901 1.050839011 1.345603323 0.782991538 0.0772613 0.088717307 2.270332004 0.012317925 0.023582335 1.41E-09 8.850284634 0.294764312 AT(ph)DDDMQS(ph)LAS(ph)LMS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 ATDDDMQSLASLMSVK 16 0 Q8N3D4;E9PIH6;A0A0U1RQH4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 4 0 AT(1)DDDMQS(1)LAS(1)LMS(1)VK 62.438 0.013063 12690000 1679.1 449.68 895.47 601.44 702.24 522.58 1285.9 737.69 1647.4 1330.1 TRUE FALSE FALSE 1658.634483 456.0106068 911.0552797 670.9813227 666.4020724 489.1888245 1395.124314 759.0338963 1500.052418 1295.54381 1.280261208 0.351983934 0.703222286 0.517914807 0.514380191 0.377593425 1.076863864 0.585880532 1.157855416 1 10.33934209 -10.26796941 24.99972086 1.132345576 0.598980448 0.616738871 0.200799432 265.3450735 1015850.754 0.035701843 0.041338099 5.40E-11 10.26796941 -0.533365128 AT(ph)ISDEEIER ddPTM_HeLa_Romidepsin_16h_R1 1 ATISDEEIER 10 0 Q9UQN3-2;Q9UQN3;C9J0A7 Q9UQN3-2 CHMP2B Charged multivesicular body protein 2b 1 0 AT(0.983)IS(0.017)DEEIER 182.92 5.16E-05 334510000 2557.4 2288.5 2692.7 2267.1 2658.1 3115.5 2651.4 2807.4 2241.5 2472.1 TRUE FALSE FALSE 2526.229425 2320.717563 2739.565314 2529.232769 2522.447238 2916.429605 2876.60985 2888.62769 2041.014626 2407.874486 1.049153284 0.963803378 1.137752541 1.050400585 1.047582527 1.211204995 1.19466769 1.199658748 0.847641618 1 11.23354448 -8.289102405 0.732492171 1.021092685 1.239906394 0.580804238 0.072046329 0.417456635 0.325704875 0.008203144 0.056848303 5.14E-09 8.289102405 0.218813709 AT(ph)LNAEEMADFY(ph)KEFLSK ddPTM_HeLa_Romidepsin_16h_R1 1 ATLNAEEMADFYKEFLSK 18 1 E7EVH7;Q96IL0 E7EVH7 APOPT1 "Apoptogenic protein 1, mitochondrial" 2 0 AT(1)LNAEEMADFY(0.997)KEFLS(0.003)K 40.81 0.024582 14978000 3109.6 2958.4 2838.7 3229.9 3465.4 3267.6 3008.2 3201.5 3078 3237.8 TRUE FALSE FALSE 3071.698999 3000.048433 2888.106383 3603.356235 3288.547707 3058.810906 3263.716433 3294.130351 2802.695971 3153.681489 0.974004195 0.951284536 0.915788862 1.142587242 1.042764692 0.969917513 1.03489095 1.044534891 0.888706098 1 11.62282125 -9.285422455 24.99794192 0.97919501 1.041758863 0.407581489 0.053694327 736.0803069 767225.8483 0.007200057 0.011001618 5.18E-10 9.285422455 0.062563853 AT(ph)PPPS(ph)PLLSELLK ddPTM_HeLa_Romidepsin_16h_R1 1 ATPPPSPLLSELLK 14 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 2 0 AT(1)PPPS(0.999)PLLS(0.001)ELLK 119.56 0.017714 9141400 1614.6 1318.6 1255 1077.3 1199.2 1159.8 1124 1393 1625.6 1510.6 TRUE FALSE FALSE 1594.920634 1337.163285 1276.842749 1201.862495 1138.000349 1085.692523 1219.472532 1433.304257 1480.202265 1471.354394 1.08398129 0.908797561 0.867800955 0.816840932 0.773437286 0.737886486 0.828809522 0.97413938 1.006013419 1 10.52292906 -9.978940396 2.453411792 1.039464686 0.823230713 0.655761115 0.063186281 0.120852821 1.464838527 0.011497998 0.015088103 1.05E-10 9.978940396 -0.216233974 AT(ph)PPPS(ph)PLLSELLKK ddPTM_HeLa_Romidepsin_16h_R1 1 ATPPPSPLLSELLKK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 2 0 AT(1)PPPS(1)PLLSELLKK 97.776 0.0051217 15326000 4329 3950.8 3706.9 3698 3274.3 3360 3134.6 3811.9 4488.3 4433.4 TRUE FALSE FALSE 4276.236483 4006.419466 3771.41704 4125.58016 3107.200253 3145.306844 3400.852846 3922.191312 4086.855207 4318.219629 0.990277672 0.927794279 0.873373141 0.955389145 0.719555863 0.72838047 0.787559026 0.908288982 0.94642134 1 12.07622091 -9.444056393 0.982648315 0.99644494 0.789530944 0.551768253 0.065912342 0.230630003 0.443628919 0.011800195 0.022417594 3.60E-10 9.444056393 -0.206913996 AT(ph)PPPSPLLSELLKK ddPTM_HeLa_Romidepsin_16h_R1 3 ATPPPSPLLSELLKK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 1 0 AT(0.993)PPPS(0.007)PLLSELLKK;AT(0.997)PPPS(0.003)PLLSELLKK;AT(1)PPPSPLLSELLKK ;; 115.68 0.0094926 44552700 5410.94 5317.69 4936.45 4721.45 3576.39 4261.24 3807.31 3834.45 4927.13 5171.72 TRUE FALSE FALSE 5344.989382 5392.552579 5022.366842 5267.366264 3393.873473 3988.960517 4130.702816 3945.393761 4486.435153 5037.357969 1.061069992 1.070512084 0.99702401 1.045660502 0.673740777 0.791875531 0.820013754 0.7832268 0.890632586 1 12.29845154 -8.773256998 24.99990404 1.031383057 0.772747136 0.79021005 0.060913489 47.98322588 101507.4229 0.006490217 0.011832439 1.69E-09 8.773256998 -0.258635922 AT(ph)PSENLVPSSAR ddPTM_HeLa_Romidepsin_16h_R1 2 ATPSENLVPSSAR 13 0 F5H669;Q8N684-2;Q8N684;Q8N684-3;F5H6M0;F5H047 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 0 AT(0.999)PS(0.001)ENLVPSSAR;AT(0.598)PS(0.389)ENLVPS(0.006)S(0.006)AR ; 137.93 0.0028102 33176000 1312.18 1417.57 1248.49 661.34 1028.68 1320.5 1154.64 1051.82 1463.87 1483.69 TRUE FALSE FALSE 1296.186645 1437.526588 1270.219445 737.8072425 976.1826211 1236.124312 1252.715093 1082.252752 1332.937801 1445.14352 0.896925895 0.99472929 0.878957299 0.510542539 0.675491816 0.855364394 0.866844764 0.748889461 0.922356695 1 10.49699706 -9.511295936 24.44097265 0.952441456 0.73792998 0.542185162 0.097041585 267.795865 565078.5021 0.016227302 0.023937485 3.08E-10 9.511295936 -0.214511476 AT(ph)S(ph)QS(ph)SERK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSQSSERK 9 1 Q9NQZ5 Q9NQZ5 STARD7 "StAR-related lipid transfer protein 7, mitochondrial" 3 0 AT(0.999)S(0.667)QS(0.667)S(0.667)ERK 51.193 0.028738 5436000 265.08 199.15 243.2 251.21 183.49 165.1 173.83 223.86 280.19 259.83 TRUE FALSE FALSE 261.849103 201.9536389 247.432794 280.2560822 174.1258206 154.5506428 188.5951159 230.3370359 255.1291047 253.0795791 1.03465125 0.797984727 0.977687709 1.107383232 0.688027936 0.610680022 0.745200844 0.910136791 1.008098344 1 7.983447292 -8.753007791 24.99981109 1.001011709 0.729858356 0.589062625 0.10146466 93.79874866 278112.7438 0.014917467 0.029454397 1.77E-09 8.753007791 -0.271153353 AT(ph)SNVFAMFDQSQIQEFK ddPTM_HeLa_Romidepsin_16h_R1 2 ATSNVFAMFDQSQIQEFK 18 0 J3QRS3;P19105;O14950;J3KTJ1;P24844;P24844-2 J3QRS3 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 1 0 AT(0.557)S(0.443)NVFAMFDQSQIQEFK;AT(0.5)S(0.5)NVFAMFDQSQIQEFK ; 129.29 0.00060093 738590000 17743 21255.5 17462.9 18978.8 20466.2 18852.7 15757.2 16170.1 17952.8 16158.1 TRUE FALSE FALSE 17526.74149 21554.73549 17766.83445 21173.21815 19421.73344 17648.07331 17095.61617 16637.95633 16347.0566 15738.31023 1.113635532 1.36957114 1.128890852 1.345329825 1.234041848 1.121344862 1.086242165 1.057162814 1.038679271 1 13.94199303 -11.02369725 1.37440255 1.028129499 1.18920635 0.299603545 0.100284856 0.325655492 1.270869064 0.024977321 0.021085621 9.47E-12 11.02369725 0.161076851 AT(ph)VTPSPVK ddPTM_HeLa_Romidepsin_16h_R1 1 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 AT(0.685)VT(0.267)PS(0.048)PVK 121.6 0.025957 1026900000 12762 10764 21722 7901.2 9729.7 9483.3 9198.9 6622 12454 9991.5 TRUE FALSE FALSE 12606.45184 10915.53587 22100.0623 8814.77392 9233.157102 8877.347736 9980.254336 6813.597122 11340.08305 9731.91939 1.295371584 1.121622101 2.270884233 0.905759036 0.948749854 0.912188786 1.025517571 0.700128808 1.165246299 1 13.24850866 ATAGDTHLGGEDFDNR ddPTM_HeLa_Romidepsin_16h_R1 2 ATAGDTHLGGEDFDNR 16 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066;P48741 A0A0G2JIW1;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 0 ; ; 134.81 0.00068312 114629000 12362.3 11866.9 9882.5 10570.2 16503.9 17311.3 15986.8 17841.4 12570.8 11996.8 FALSE FALSE TRUE 12211.62353 12033.96253 10054.50077 11792.37626 15661.6444 16205.1638 17344.71839 18357.61276 11446.43616 11685.12141 1.04505748 1.029853444 0.860453257 1.009178754 1.340306519 1.386820319 1.484342164 1.571024564 0.979573576 1 13.5123851 -8.596650469 2.331793779 1.007090397 1.483717921 0.921936545 0.065984129 0.062233306 0.680938221 0.010430113 0.024303244 2.53E-09 8.596650469 0.476627524 ATAPQTQHVS(ph)PMR ddPTM_HeLa_Romidepsin_16h_R1 8 ATAPQTQHVSPMR 13 0 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;E9PL12;E9PPR1;E9PK06 P29692-2 EEF1D Elongation factor 1-delta 1 0 ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQT(0.006)QHVS(0.994)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR;ATAPQTQHVS(1)PMR ;;;;;;; 102.03 0.00351 8391053700 23150.88 23286.22 21003.29 20317.58 22950.56 22105.8 19662.63 20541.02 25820.44 23753.1 TRUE FALSE FALSE 22868.70817 23614.04402 21368.84345 22666.7942 21779.30728 20693.31072 21332.7733 21135.34201 23510.99518 23135.99104 0.988447313 1.02066274 0.92361911 0.979720046 0.941360465 0.894420762 0.922060061 0.913526547 1.016208691 1 14.49785128 -8.982435914 0.782703768 0.996543402 0.906942329 0.70716578 0.023716806 0.263072721 0.305260966 0.00406027 0.012320355 1.04E-09 8.982435914 -0.089601073 ATAPQTQHVS(ph)PMRQVEPPAK ddPTM_HeLa_Romidepsin_16h_R1 1 ATAPQTQHVSPMRQVEPPAK 20 1 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;E9PL12;E9PPR1;E9PK06 P29692-2 EEF1D Elongation factor 1-delta 1 0 AT(0.001)APQT(0.151)QHVS(0.849)PMRQVEPPAK 61.111 0.025148 17807000 1350.8 1007.6 1118.5 4049.3 1126.9 1049 1046 1090.1 1347.1 1004.7 TRUE FALSE FALSE 1334.33593 1021.785019 1137.967023 4517.499119 1069.390088 981.9722855 1134.847214 1121.640324 1226.612002 978.5977492 1.363518291 1.04413179 1.162854732 4.616298293 1.092777997 1.003448339 1.159666691 1.146170962 1.253438405 1 9.934572154 ATATISAK(ac)PQITNPK ddPTM_HeLa_Romidepsin_16h_R1 2 ATATISAKPQITNPK 15 1 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 1 ; ATATISAK(1)PQITNPK;ATATISAK(1)PQITNPK 176.99 3.22E-08 2396900 1085.27 1256.35 1056.26 1140.75 1497.46 1458.83 1018.92 1218.68 1305.84 1211.7 FALSE TRUE FALSE 1072.042312 1274.036928 1074.643762 1272.648882 1421.039028 1365.615471 1105.467039 1253.940583 1189.0424 1180.219859 0.90834119 1.07949118 0.910545399 1.078315089 1.204046023 1.157085657 0.936661954 1.062463551 1.007475336 1 10.20483992 -9.187368182 7.285143636 0.963691287 1.090297161 0.294362707 0.080252965 0.242056514 20.93663925 0.012577836 0.020911518 6.50E-10 9.187368182 0.126605874 ATAVVDGAFK ddPTM_HeLa_Romidepsin_16h_R1 2 ATAVVDGAFK 10 0 P32119;A6NIW5;P32119-2 P32119 PRDX2 Peroxiredoxin-2 0 0 ; ; 140.45 0.017739 1192530 1996.48 1430.56 2106.1 2161.51 2854.8 2302.2 1878.24 1833.06 1681.17 1467.62 FALSE FALSE TRUE 1972.146134 1450.699461 2142.755787 2411.433956 2709.108903 2155.09685 2037.777659 1886.096699 1530.801945 1429.491021 1.379614216 1.014836358 1.498964146 1.686917876 1.895156293 1.507597333 1.425526729 1.31941836 1.070872025 1 10.48128584 -11.17562738 0.411975094 0.979284248 1.561277322 0.462185244 0.203375223 0.838678577 0.336808791 0.203306766 0.098989217 6.67E-12 11.17562738 0.581993074 ATCAPQHGAPGPGPADASK ddPTM_HeLa_Romidepsin_16h_R1 1 ATCAPQHGAPGPGPADASK 19 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 69.763 0.0052229 411390 314.43 143.23 199.8 185.86 229.91 303.29 339.29 211.6 377.04 257.49 FALSE FALSE TRUE 310.5976062 145.2463957 203.2774352 207.3500077 218.1768348 283.9107478 368.1092841 217.7223122 343.3165981 250.8003727 1.238425617 0.579131499 0.810514885 0.826753188 0.869922291 1.132018843 1.467738186 0.868110002 1.368883923 1 7.970395682 ATDDDMQSLAS(ph)LMSVKPSDVGNLDDFAESDEDEAHGPGAPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATDDDMQSLASLMSVKPSDVGNLDDFAESDEDEAHGPGAPEAR 43 1 Q8N3D4;E9PIH6;A0A0U1RQH4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 ATDDDMQS(0.001)LAS(0.39)LMS(0.165)VKPS(0.39)DVGNLDDFAES(0.054)DEDEAHGPGAPEAR 75.627 2.42E-07 35757000 859.39 1158.3 985.65 1055.9 878.03 1262.9 1025.9 1272.4 1285.1 1190.9 TRUE FALSE FALSE 848.9154241 1174.606578 1002.804825 1177.988126 833.2208527 1182.204766 1113.03992 1309.214886 1170.157437 1159.960246 0.731848722 1.012626581 0.864516545 1.015541808 0.718318456 1.019176967 0.959550057 1.128672203 1.008790983 1 10.17985965 -7.083135856 1.052233505 0.883612677 1.31575435 0.201507341 0.112811451 2.577019949 1.754013297 0.018530559 1.355974516 8.26E-08 7.083135856 0.432141673 ATDDDMQSLASLMSVKPSDVGNLDDFAES(ph)DEDEAHGPGAPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATDDDMQSLASLMSVKPSDVGNLDDFAESDEDEAHGPGAPEAR 43 1 Q8N3D4;E9PIH6;A0A0U1RQH4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 ATDDDMQS(0.005)LAS(0.075)LMS(0.186)VKPS(0.186)DVGNLDDFAES(0.548)DEDEAHGPGAPEAR 50.084 0.0010459 51007000 1226 996.81 1253 1183.4 1165.6 1336.4 1190.5 1291 1596.1 1233.3 TRUE FALSE FALSE 1211.05704 1010.843117 1274.807939 1320.230276 1106.115083 1251.008353 1291.62104 1328.353048 1453.340818 1201.258688 1.008156738 0.841486623 1.061226821 1.099039107 0.920796739 1.041414614 1.075223058 1.105800991 1.209848331 1 10.23033115 ATDIPASAS(ph)PPPVAGVPFFK ddPTM_HeLa_Romidepsin_16h_R1 2 ATDIPASASPPPVAGVPFFK 20 0 F8WCX2;Q8N1G0-2;Q8N1G0 F8WCX2 ZNF687 Zinc finger protein 687 1 0 ATDIPAS(0.025)AS(0.975)PPPVAGVPFFK;ATDIPAS(0.004)AS(0.996)PPPVAGVPFFK ; 140.8 0.00012661 102576000 14099.3 14531.9 13978.4 9210.7 12657.5 14543.3 12336.6 13762.1 14782.8 14092.7 TRUE FALSE FALSE 13927.45231 14736.48047 14221.68819 10275.68447 12011.54054 13614.03007 13384.4705 14160.28465 13460.58934 13726.56962 1.014634588 1.073573433 1.036070087 0.748598139 0.875057707 0.991801334 0.975077595 1.031596753 0.980622961 1 13.74468351 ATDS(ph)FSGR ddPTM_HeLa_Romidepsin_16h_R1 2 ATDSFSGR 8 0 Q9HBH9;K7EK27;Q9HBH9-2 Q9HBH9 MKNK2 MAP kinase-interacting serine/threonine-protein kinase 2 1 0 ATDS(0.98)FS(0.02)GR;ATDS(0.986)FS(0.014)GR ; 132.88 0.0095023 28640000 3104.6 3322.4 2841.9 3164.8 6200.7 6562.2 7000 2778.3 4161.6 3489.2 TRUE FALSE FALSE 3066.759941 3369.172834 2891.362077 3530.729067 5884.255141 6142.896599 7594.579825 2858.685727 3789.376073 3398.550081 0.902373032 0.991355947 0.850763416 1.038892758 1.731401627 1.807505098 2.234652909 0.841148625 1.114997862 1 11.73070367 -8.79366057 5.218646699 0.949802334 1.708997687 0.49513723 0.329590062 0.095792174 6.545892605 0.043302825 0.081697413 1.61E-09 8.79366057 0.759195353 ATDSDLSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ATDSDLSSPR 10 0 Q9BRD0;Q9BRD0-2 Q9BRD0 BUD13 BUD13 homolog 1 0 ATDSDLS(0.001)S(0.999)PR;ATDSDLS(0.001)S(0.999)PR ; 195.51 2.33E-08 67858000 17794.1 17607.1 16080.1 11502.6 13117.3 13976.5 12643.3 12058.8 17965.6 17286.8 TRUE FALSE FALSE 17577.21866 17854.97322 16359.9674 12832.58473 12447.87523 13083.44676 13717.22159 12407.70235 16358.71174 16837.68644 1.043921249 1.060417254 0.971627988 0.762134678 0.739286557 0.777033519 0.814673776 0.736900666 0.971553414 1 14.0394063 -9.333675201 3.781545972 1.023921598 0.766840724 0.939600493 0.030993099 0.035989748 1.004835121 0.004549763 0.007181716 4.64E-10 9.333675201 -0.257080874 ATEDGEEDEEMIES(ph)IENLEDLKGHSVR ddPTM_HeLa_Romidepsin_16h_R1 1 ATEDGEEDEEMIESIENLEDLKGHSVR 27 1 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 1 0 ATEDGEEDEEMIES(1)IENLEDLKGHSVR 79.025 2.75E-06 2721200 1048.2 976.47 1039.4 1042.6 982.35 1192 780.33 862.75 1101.6 867.54 TRUE FALSE FALSE 1035.424135 990.2167703 1057.490321 1163.150318 932.2170138 1115.835047 846.6112107 887.7123101 1003.070137 845.0011857 1.225352287 1.171852522 1.251466079 1.37650732 1.103213853 1.320512996 1.001905352 1.050545638 1.187063585 1 9.722809556 -12.27573086 0.936998782 0.996685032 1.192572571 0 0.123202684 0.599490649 0.918680616 0.081172327 0.020568606 5.30E-13 12.27573086 0.195887539 ATEDGEEDEEMIESIENLEDLK ddPTM_HeLa_Romidepsin_16h_R1 1 ATEDGEEDEEMIESIENLEDLK 22 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 0 156.08 1.44E-07 2505500 1403.4 1262.6 1394.3 860.31 1200.8 1163.8 972.75 1293.2 1557.2 1681.8 FALSE FALSE TRUE 1386.294821 1280.374916 1418.567207 959.7830901 1139.518695 1089.436936 1055.375361 1330.616702 1417.920132 1638.106594 0.846278763 0.781618804 0.865979792 0.585910034 0.695631591 0.665058636 0.644265376 0.812289449 0.865584778 1 10.67781352 -10.55827821 0.486446499 0.99047013 0.674447504 0.548719364 0.080847684 0.313018437 0.184749923 0.033740143 0.03059772 2.77E-11 10.55827821 -0.316022626 ATEK(ac)DKVEIYK ddPTM_HeLa_Romidepsin_16h_R1 1 ATEKDKVEIYK 11 2 B1AMU3;Q9Y3B2 B1AMU3 EXOSC1 Exosome complex component CSL4 0 1 ATEK(0.981)DK(0.019)VEIYK 99.539 0.016077 804640 533.18 643.03 723.71 782.94 807.72 809.36 659.18 720.32 1059 866.57 FALSE TRUE FALSE 526.6813971 652.0825932 736.305869 873.4672066 766.4990344 757.6445081 715.1707327 741.1613227 964.2803877 844.0563865 0.623988404 0.772558094 0.872342039 1.034844615 0.908113542 0.897623097 0.847302081 0.878094562 1.142435983 1 9.72119557 -9.531446407 18.29426618 0.814151201 0.912907857 0 0.141719376 14.61609257 31206.80243 0.023323071 0.033082012 2.94E-10 9.531446407 0.098756657 ATENDIANFFS(ph)PLNPIR ddPTM_HeLa_Romidepsin_16h_R1 2 ATENDIANFFSPLNPIR 17 0 P31942-4;P31942-3;P31942;P31942-5;P31942-2;P31942-6 P31942-4 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 1 0 ATENDIANFFS(1)PLNPIR;ATENDIANFFS(1)PLNPIR ; 182.09 4.27E-09 72571900 5030.5 4952.9 4937.7 4204.9 4801.4 5333 4418.9 4684.7 5313.7 5305.4 TRUE FALSE FALSE 4969.186331 5022.627056 5023.638597 4691.090323 4556.366642 4992.238511 4794.241256 4820.244403 4838.429364 5167.564943 0.961610814 0.971952382 0.97214813 0.907795136 0.881724118 0.966071751 0.927756363 0.932788355 0.936307413 1 12.3352689 -9.354809022 5.247123481 0.980191243 0.923673054 0.399964613 0.02582146 0.129626826 5.6847687 0.003806674 0.005864607 4.42E-10 9.354809022 -0.05651819 ATENDIYNFFS(ph)PLNPMR ddPTM_HeLa_Romidepsin_16h_R1 2 ATENDIYNFFSPLNPMR 17 0 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 1 0 ATENDIYNFFS(1)PLNPMR;ATENDIY(0.001)NFFS(0.999)PLNPMR ; 83.891 0.020432 30077000 7348.9 6469.7 5889.8 5251.5 6548.6 7142.7 6698.3 6888.7 6642.8 6165.3 TRUE FALSE FALSE 7259.32878 6560.780606 5992.309498 5858.703139 6214.400506 6686.304522 7267.253435 7088.013666 6048.651331 6005.124617 1.208855643 1.092530301 0.99786597 0.975617246 1.03484955 1.113433101 1.210175292 1.18032749 1.007248262 1 12.55197847 -12.70906512 1.614701158 1.000146352 1.114618981 0.184284325 0.078849989 0.558034673 2.630780748 0.066859019 0.014784527 1.95E-13 12.70906512 0.114472629 ATENDIYNFFS(ph)PLNPVR ddPTM_HeLa_Romidepsin_16h_R1 2 ATENDIYNFFSPLNPVR 17 0 P31943;E9PCY7;G8JLB6;H0YB39;H0YBD7;H0YBG7;P52597 P31943 HNRNPH1;HNRNPF "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed" 1 0 ATENDIYNFFS(1)PLNPVR;ATENDIYNFFS(1)PLNPVR ; 181.86 4.46E-09 139140000 4582.24 4634.65 4141.45 3839.92 4585.44 5115.23 4077.18 4795.55 5279.69 4459.99 TRUE FALSE FALSE 4526.389896 4699.896724 4213.5302 4283.909618 4351.427886 4788.383312 4423.495567 4934.301673 4807.461303 4344.118817 1.041958125 1.081898752 0.969938986 0.986140066 1.001682521 1.102268035 1.018272233 1.135857899 1.106659718 1 12.08484785 -4.000000149 0.847674428 1.019502418 39.12193093 0.247085224 0.047857043 496.8510217 1.320454523 0.006216785 36518.53184 1.00E-04 4.000000149 38.10242851 ATEPPS(ph)PDAGELSLASR ddPTM_HeLa_Romidepsin_16h_R1 2 ATEPPSPDAGELSLASR 17 0 Q8IYB8 Q8IYB8 SUPV3L1 "ATP-dependent RNA helicase SUPV3L1, mitochondrial" 1 0 ATEPPS(1)PDAGELSLASR;ATEPPS(1)PDAGELSLASR ; 194.32 1.45E-13 33016000 3655 3653.7 3428.5 3428 3577 4050.1 3592.7 3574.1 4095.3 3797 TRUE FALSE FALSE 3610.451454 3705.136885 3488.171604 3824.361489 3394.452342 3791.311681 3897.863848 3677.510945 3729.006111 3698.353393 0.976232142 1.001834192 0.94316882 1.034071405 0.917828012 1.025135048 1.053945752 0.994364398 1.008288207 1 11.85266737 -8.04588173 24.99991084 0.984905985 1.028001596 0.234341328 0.034058188 375.2404209 204459.2325 0.004167864 0.010626297 9.00E-09 8.04588173 0.043095611 ATEVSKT(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATEVSKTPEAR 11 1 Q5H909;Q9UNF1-2;Q9UNF1 Q5H909 MAGED2 Melanoma-associated antigen D2 1 0 AT(0.002)EVS(0.001)KT(0.998)PEAR 153.49 0.0095301 29977000 3875.7 3679.4 3390.4 3682.1 3064.5 3712.4 4332.9 2480.2 3555.8 3918.4 TRUE FALSE FALSE 3828.461478 3731.19869 3449.40849 4107.841727 2908.10713 3475.189621 4700.936418 2551.960674 3237.760342 3816.599403 1.003108022 0.977623873 0.903791078 1.076309377 0.761962895 0.910546079 1.231708105 0.668647768 0.848336438 1 11.89807205 -9.877696808 1.208379058 1.002558018 0.933820884 0 0.153193688 1.187689745 3.441216528 0.02530331 0.035985795 1.33E-10 9.877696808 -0.068737134 ATFSDSLLIQPTS(ph)AGSTDRLPYSK ddPTM_HeLa_Romidepsin_16h_R1 1 ATFSDSLLIQPTSAGSTDRLPYSK 24 1 P11137-4;H7BZB9 P11137-4 MAP2 Microtubule-associated protein 2 1 0 ATFSDSLLIQPT(0.034)S(0.323)AGS(0.262)T(0.262)DRLPY(0.074)S(0.044)K 59.996 0.0026092 7454300 945.33 1299.9 934.77 1232 1251.2 1426.2 1202.7 1158.2 1156.8 1103.4 TRUE FALSE FALSE 933.8079543 1318.200026 951.0392797 1374.449637 1187.346595 1335.070423 1304.857308 1191.71069 1053.332911 1074.733509 0.868873955 1.226536639 0.884907069 1.278874833 1.104782335 1.242233923 1.214121731 1.108842964 0.980087531 1 10.06976326 -9.618803365 1.11774595 0.94379992 1.188417241 0.356962226 0.114702835 0.299150341 0.748230009 0.020419816 0.033750703 2.41E-10 9.618803365 0.244617321 ATFSGS(ph)AGR ddPTM_HeLa_Romidepsin_16h_R1 1 ATFSGSAGR 9 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 ATFSGS(1)AGR 107.45 0.021559 9347900 2081.2 2378.1 2116.1 1587.3 2029.4 1951.2 1990.4 1072.5 2311.1 1830.2 TRUE FALSE FALSE 2055.833534 2411.578954 2152.929833 1770.831094 1925.832145 1826.524617 2159.464526 1103.531095 2104.389428 1782.65114 1.153245011 1.352804764 1.20771237 0.993369401 1.080319139 1.024611365 1.211378086 0.61903929 1.180483035 1 10.79980868 -7.253154137 24.5945033 1.100463544 0.619038987 0.647477729 0.111530666 454.3105589 1348569.505 0.016629552 0.249111865 5.58E-08 7.253154137 -0.481424557 ATGAALT(ph)PTEER ddPTM_HeLa_Romidepsin_16h_R1 3 ATGAALTPTEER 12 0 M0R300;M0R0P8;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 1 0 AT(0.004)GAALT(0.659)PT(0.337)EER;ATGAALT(0.983)PT(0.017)EER;ATGAALT(0.978)PT(0.021)EER ;; 179.59 3.03E-06 24779000 5591.5 6247.3 5722 6717.1 7982.6 9192.8 7169 9130.4 5634.4 5487.35 TRUE FALSE FALSE 5523.348647 6335.249653 5821.58901 7493.762707 7575.218135 8605.409748 7777.934681 9394.573719 5130.445152 5344.787856 1.033408396 1.185313585 1.089208621 1.402069251 1.417309412 1.610056373 1.455237306 1.757707503 0.959896873 1 12.38391697 -8.945630784 0.664437497 1.004835338 1.670438972 0.902548202 0.081848224 0.154080273 0.123212082 0.014785836 0.051612348 1.13E-09 8.945630784 0.665603634 ATGDGS(ph)SPELPSLER ddPTM_HeLa_Romidepsin_16h_R1 1 ATGDGSSPELPSLER 15 0 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BS99 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 AT(0.022)GDGS(0.563)S(0.414)PELPSLER 106.52 0.0055762 30892000 1902.6 1686.6 1791.2 1469 2006.7 1959.7 1884.2 1972.7 1639.1 2079.3 TRUE FALSE FALSE 1879.410379 1710.343999 1822.375085 1638.852692 1904.290611 1834.481495 2044.243901 2029.776962 1492.494791 2025.279486 0.927975814 0.844497765 0.899814123 0.809198287 0.940260652 0.905791772 1.009363851 1.002220669 0.736932755 1 10.9839053 -4.229063751 1.00858532 0.936994452 53.83017584 0 0.086462186 1830.066602 3.856838828 0.01073771 223208.3858 5.90E-05 4.229063751 52.89318138 ATGDGSS(ph)PELPSLER ddPTM_HeLa_Romidepsin_16h_R1 1 ATGDGSSPELPSLER 15 0 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BS99 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 ATGDGS(0.027)S(0.973)PELPSLER 204.17 2.50E-18 29795000 2919.4 2666.5 2683.9 1725.7 3086 3359.8 2694.8 2963.1 2956 2743.7 TRUE FALSE FALSE 2883.81723 2704.039057 2730.612154 1925.233554 2928.509905 3145.119623 2923.696245 3048.832624 2691.607957 2672.418278 1.079103991 1.011832271 1.021775736 0.720408766 1.095827673 1.176881497 1.094026436 1.140851583 1.007180642 1 11.38393012 -8.537036298 24.99976231 1.010715345 1.133501277 0.347835414 0.09628081 249.0494403 439776.497 0.014620118 0.029250434 2.90E-09 8.537036298 0.122785932 ATGEGGASDLPEDPDEDAIPIT ddPTM_HeLa_Romidepsin_16h_R1 2 ATGEGGASDLPEDPDEDAIPIT 22 0 O15541 O15541 RNF113A RING finger protein 113A 0 0 ; ; 183.79 7.05E-21 2159300 3256 3134.8 3142.6 3258.3 3846.7 3269.5 2730 3741.9 3179.1 3993 FALSE FALSE TRUE 3216.31462 3178.931797 3197.295635 3635.039977 3650.388545 3060.589502 2961.886132 3850.165973 2894.753334 3889.261284 0.826973141 0.817361335 0.822083013 0.934635066 0.938581463 0.786933373 0.761554937 0.989947882 0.74429387 1 11.92528044 -12.29575404 0.978435865 1.001588351 0.855164303 0 0.105004033 0.475840876 0.802705939 0.049344881 0.012692693 5.06E-13 12.29575404 -0.146424048 ATGEPGTFVCTSHLPAAAS(ph)ASPK ddPTM_HeLa_Romidepsin_16h_R1 2 ATGEPGTFVCTSHLPAAASASPK 23 0 Q8IY33-4;Q8IY33-2;Q8IY33 Q8IY33-4 MICALL2 MICAL-like protein 2 1 0 ATGEPGTFVCTSHLPAAAS(0.603)AS(0.397)PK;ATGEPGTFVCTSHLPAAAS(0.625)AS(0.375)PK ; 125.98 2.04E-06 36770000 4952.8 5010.2 3757.4 881.62 5642.7 7267.3 6640.8 7922.8 5368.8 4707.9 TRUE FALSE FALSE 4892.433369 5080.733727 3822.795971 983.5570525 5354.731963 6802.942984 7204.869386 8152.033718 4888.601082 4585.588079 1.066915145 1.107978658 0.833654464 0.214488749 1.167730697 1.483548646 1.57119856 1.777750983 1.06607942 1 12.16289105 -8.256169206 3.110730063 0.963835716 1.636043537 0.605377314 0.25840521 0.149738967 2.959337932 0.039013695 0.104500641 5.54E-09 8.256169206 0.672207821 ATGPEAAGGGGAGGGGGGY(ph)RPIIQSPGYK ddPTM_HeLa_Romidepsin_16h_R1 1 ATGPEAAGGGGAGGGGGGYRPIIQSPGYK 29 1 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 0 ATGPEAAGGGGAGGGGGGY(0.977)RPIIQS(0.022)PGY(0.001)K 54.465 0.012009 5537700 2363.3 2212.8 1784.5 1758.6 1841.4 1088.6 1054.8 1353.8 2322.8 1838.5 TRUE FALSE FALSE 2334.495191 2243.951856 1815.558474 1961.937606 1747.426487 1019.041973 1144.394686 1392.970067 2115.04295 1790.735505 1.303651591 1.253089499 1.013861885 1.095604349 0.975814955 0.569063366 0.639064051 0.777875942 1.181102929 1 10.80633655 -8.473971661 2.853212872 1.142148728 0.659873338 0.811700592 0.1027474 0.108094559 1.737085407 0.019950356 0.047539217 3.36E-09 8.473971661 -0.48227539 ATIAGGGVIPHIHK ddPTM_HeLa_Romidepsin_16h_R1 2 ATIAGGGVIPHIHK 14 0 P0C0S5;Q71UI9-4;Q71UI9;Q71UI9-3 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V 0 0 ; ; 67.879 0.018251 4493000 3127.6 2918.4 2891.9 2907.7 4031 4047 3268.5 3778.4 2835.1 2004.28 FALSE FALSE TRUE 3089.479608 2959.485312 2942.232306 3243.901955 3825.283028 3788.409761 3546.126308 3887.722043 2581.521555 1952.208517 1.582556157 1.515967832 1.507130146 1.661657516 1.959464368 1.940576393 1.816469029 1.991448152 1.32235954 1 10.93089144 -12.61078339 0.124828347 5.61E-14 2.353420149 0.804628188 0.132109297 5.033081059 0.148231135 2.344465953 0.711761028 2.45E-13 12.61078339 2.353420149 ATIGADFLTK ddPTM_HeLa_Romidepsin_16h_R1 1 ATIGADFLTK 10 0 C9J7D1;C9J4S4;C9IZZ0;C9J4V0;C9J592;C9J8S3;P51149 C9J7D1 RAB7A Ras-related protein Rab-7a 0 0 96.89 0.006177 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 ATIS(ph)DEEIER ddPTM_HeLa_Romidepsin_16h_R1 2 ATISDEEIER 10 0 Q9UQN3-2;Q9UQN3;C9J0A7 Q9UQN3-2 CHMP2B Charged multivesicular body protein 2b 1 0 AT(0.232)IS(0.768)DEEIER;AT(0.007)IS(0.993)DEEIER ; 171.49 0.00072559 291237600 3692.27 3581.3 2991.05 3110.92 4174.6 4279.1 3379.42 3923.4 3615.98 3362.48 TRUE FALSE FALSE 3647.267193 3631.717635 3043.107971 3470.619208 3961.554584 4005.67932 3666.46785 4036.917389 3292.557692 3275.122285 1.11362779 1.108880011 0.92915858 1.059691488 1.209589823 1.223062522 1.119490368 1.232600507 1.00532359 1 11.67733306 -8.781391553 8.851471465 1.049429107 1.192667149 0.634614694 0.058965107 0.125355158 48.47965887 0.009569055 0.017670296 1.65E-09 8.781391553 0.143238042 ATIS(ph)SPLELEGTVSR ddPTM_HeLa_Romidepsin_16h_R1 1 ATISSPLELEGTVSR 15 0 Q96GS4 Q96GS4 C17orf59 Uncharacterized protein C17orf59 1 0 AT(0.008)IS(0.74)S(0.252)PLELEGTVSR 177.93 5.56E-08 5203600 1602.3 1328.8 1574.4 1216 2090.7 2542.2 2572.4 2430.3 1401.3 1496.3 TRUE FALSE FALSE 1582.770551 1347.506881 1601.801772 1356.599641 1984.003778 2379.761625 2790.899592 2500.616896 1275.964218 1457.42591 1.086004126 0.924580023 1.09906223 0.93081894 1.361306783 1.632852557 1.914951266 1.715776341 0.875491652 1 10.50920683 -8.374447658 2.039072812 1.029544942 1.80771855 0.9263148 0.097045406 0.049251547 0.395305881 0.011504765 0.032603891 4.22E-09 8.374447658 0.778173608 ATISS(ph)PLELEGTVSR ddPTM_HeLa_Romidepsin_16h_R1 1 ATISSPLELEGTVSR 15 0 Q96GS4 Q96GS4 C17orf59 Uncharacterized protein C17orf59 1 0 ATIS(0.013)S(0.987)PLELEGTVSR 217.2 5.45E-26 4725100 1350.9 1308.7 1091.8 1228.8 1745.5 2684.3 2126.9 2697.6 1413.3 1427.9 TRUE FALSE FALSE 1334.434711 1327.123913 1110.802321 1370.879638 1656.420622 2512.781893 2307.558833 2775.6508 1286.890908 1390.802952 0.959470721 0.95421419 0.798676994 0.985674955 1.190981526 1.806713086 1.659155835 1.995718226 0.925286293 1 10.44170232 -8.360893672 2.464186245 0.963224542 1.828160633 0.944673692 0.095408502 0.045399885 0.53314247 0.013355251 0.035486025 4.36E-09 8.360893672 0.864936091 ATLLEDQQDPSPS(ph)S ddPTM_HeLa_Romidepsin_16h_R1 2 ATLLEDQQDPSPSS 14 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 1 0 ATLLEDQQDPS(0.155)PS(0.618)S(0.227);ATLLEDQQDPS(0.009)PS(0.603)S(0.388) ; 136.93 0.0013095 9711100 4279 4028.7 3684.5 3915.9 4119.2 4577.2 4113.2 4930.6 4019.1 4061.9 TRUE FALSE FALSE 4226.845902 4085.416144 3748.627177 4368.674783 3908.981853 4284.731692 4462.575105 5073.259132 3659.62163 3956.371252 1.068364325 1.032616983 0.947491258 1.104212548 0.988022004 1.082995356 1.1279465 1.28230108 0.924994495 1 11.94996209 -7.132213103 1.19156084 1.029038364 1.456789322 0.708851419 0.053097378 0.686229474 0.657367935 0.006286677 0.389036193 7.38E-08 7.132213103 0.427750959 ATLPS(ph)PDKLPGFK ddPTM_HeLa_Romidepsin_16h_R1 1 ATLPSPDKLPGFK 13 1 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 0 AT(0.04)LPS(0.96)PDKLPGFK 64.842 0.029227 56991000 6369.5 6315.4 6195.3 5708.7 6198.1 6672.2 5859.7 7681.6 6785.3 6156.6 TRUE FALSE FALSE 6291.866084 6404.308367 6303.126598 6368.766754 5881.787829 6245.867954 6357.422772 7903.854976 6178.405774 5996.650644 1.049230055 1.067980902 1.051107855 1.062053992 0.980845505 1.041559418 1.060162272 1.31804493 1.030309441 1 12.54994121 -7.248281178 3.303119541 1.029902403 1.362033181 0.912819018 0.026003631 0.079163009 1.357060142 0.004182774 0.067711804 5.65E-08 7.248281178 0.332130778 ATLSSTS(ph)GLDLMSESGEGEISPQR ddPTM_HeLa_Romidepsin_16h_R1 1 ATLSSTSGLDLMSESGEGEISPQR 24 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6 E9PMS6 LMO7 LIM domain only protein 7 1 0 AT(0.002)LS(0.02)S(0.02)T(0.023)S(0.338)GLDLMS(0.243)ES(0.177)GEGEIS(0.178)PQR 72.568 0.00029971 22212000 1478.4 1457.3 1754.4 1271.2 1696 1786.9 1238 971.59 1648.2 1602.1 TRUE FALSE FALSE 1460.380692 1477.815908 1784.934596 1418.182125 1609.446791 1672.722857 1343.155689 999.7014237 1500.780864 1560.477211 0.935855187 0.947028189 1.143838938 0.908813096 1.031381157 1.071930333 0.860733934 0.640638272 0.961744813 1 10.60777157 -7.386851863 3.057009662 0.98529919 0.627080249 0.71991654 0.068448655 0.119346214 1.773933614 0.009353832 0.086346291 4.10E-08 7.386851863 -0.358218941 ATLSSTSGLDLMS(ph)ESGEGEISPQREVSR ddPTM_HeLa_Romidepsin_16h_R1 1 ATLSSTSGLDLMSESGEGEISPQREVSR 28 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6 E9PMS6 LMO7 LIM domain only protein 7 1 0 ATLSST(0.001)S(0.003)GLDLMS(0.555)ES(0.137)GEGEIS(0.295)PQREVS(0.008)R 58.361 0.0031442 41581000 1042.1 825.95 747.31 1368.5 802.49 991.8 682.58 791.5 1076.8 915.69 TRUE FALSE FALSE 1029.398484 837.5777458 760.3166171 1526.732409 761.5359408 928.4271809 740.5583282 814.4008037 980.4883111 891.9002418 1.154163253 0.939093529 0.852468226 1.711774857 0.853835334 1.040954063 0.830315201 0.913107504 1.099325087 1 9.800738545 ATLSSTSGLDLMSESGEGEIS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 3 ATLSSTSGLDLMSESGEGEISPQR 24 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6 E9PMS6 LMO7 LIM domain only protein 7 1 0 ATLSSTSGLDLMS(0.004)ES(0.004)GEGEIS(0.991)PQR;ATLSSTSGLDLMSES(0.006)GEGEIS(0.994)PQR;ATLSSTSGLDLMSESGEGEIS(1)PQR ;; 138.95 4.86E-07 46945000 5267.7 5392.1 5204.1 4118.72 5450.8 4900.5 4091.7 4822.8 6109.4 6022 TRUE FALSE FALSE 5203.495246 5468.010125 5294.675177 4594.945786 5172.625336 4587.373866 4439.248896 4962.340109 5562.959963 5865.547572 0.887128641 0.932225007 0.90267364 0.783378829 0.881865721 0.782087914 0.756834523 0.846014809 0.948412726 1 12.51805008 -10.53363185 0.110977351 1.162449668 0.635555966 0.655648705 0.044300887 2.993757353 0.288309535 0.667565511 0.61861341 2.93E-11 10.53363185 -0.526893702 ATLSSTSGLDLMSESGEGEIS(ph)PQREVSR ddPTM_HeLa_Romidepsin_16h_R1 3 ATLSSTSGLDLMSESGEGEISPQREVSR 28 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6 E9PMS6 LMO7 LIM domain only protein 7 1 0 ATLSSTSGLDLMS(0.029)ES(0.091)GEGEIS(0.868)PQREVS(0.012)R;ATLSSTSGLDLMS(0.01)ES(0.009)GEGEIS(0.951)PQREVS(0.03)R;ATLSSTS(0.001)GLDLMS(0.237)ES(0.28)GEGEIS(0.479)PQREVS(0.002)R ;; 67.478 0.00022985 120056000 6365.1 5187.5 4815.73 8503.7 5499.4 5126.6 4615.21 5035.22 6832.5 6062.3 TRUE FALSE FALSE 6287.519713 5260.529761 4899.545761 9486.937805 5218.745097 4799.026805 5007.225822 5180.906146 6221.384088 5904.800572 1.064814914 0.890890335 0.829756348 1.606648301 0.883813947 0.812733088 0.847992368 0.877405779 1.053614599 1 12.52767262 -8.548564983 24.99909115 1.0471932 0.846577059 0.222706039 0.197326168 268.7168261 261527.1792 0.027498638 0.05499866 2.83E-09 8.548564983 -0.200616141 ATLYVTAIEDR ddPTM_HeLa_Romidepsin_16h_R1 2 ATLYVTAIEDR 11 0 E9PNR9;E9PQ98;E9PIX6;H0YDE4;E9PKG1;Q99873-2;Q99873-3;Q99873 E9PNR9 PRMT1 Protein arginine N-methyltransferase 1 0 0 ; ; 140.83 4.77E-05 337410 439.13 306.03 321.63 369.37 237.28 256.69 260.283 127.25 142.4 194.489 FALSE FALSE TRUE 433.7777147 310.3382984 327.2278352 412.0782973 225.1707162 240.2883374 282.3914315 130.931778 129.6633874 189.4361477 2.28983602 1.638221121 1.727378006 2.175288625 1.188636482 1.268439737 1.490694542 0.691165754 0.684470144 1 7.565567838 -7.013998322 0.887940036 1.650451872 5.00E-13 0.158495548 0.485327515 3.990530712 1.745881345 0.082067704 7.068756931 9.68E-08 7.013998322 -1.650451872 ATMAQNENVVVQPVVAENIPVIPLS(ph)DSPPPSR ddPTM_HeLa_Romidepsin_16h_R1 1 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 0 AT(0.001)MAQNENVVVQPVVAENIPVIPLS(0.395)DS(0.318)PPPS(0.286)R 40.295 0.020318 16896000 1149.2 1322.1 1711.8 1753.9 1785.5 1480.2 1392.4 1578.6 1825.6 1919.5 TRUE FALSE FALSE 1135.193108 1340.712559 1741.593161 1956.69417 1694.379272 1385.619997 1510.670421 1624.2743 1662.313764 1869.631113 0.607174913 0.717100047 0.931516997 1.046566971 0.906263947 0.741119458 0.808004537 0.86876726 0.889113233 1 10.86853793 -9.744841904 24.96938349 0.802011202 0.882212372 0.094925553 0.121480074 655.9255755 986778.1032 0.026901411 0.03798334 1.80E-10 9.744841904 0.08020117 ATMAQNENVVVQPVVAENIPVIPLSDSPPPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 ATMAQNENVVVQPVVAENIPVIPLSDSPPPSR 32 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 0 ATMAQNENVVVQPVVAENIPVIPLS(0.074)DS(0.188)PPPS(0.738)R 96.316 5.12E-12 17945000 1071.2 1188.8 874.02 1057.8 1214.3 1164.5 968.67 1022.4 1217.4 1273.7 TRUE FALSE FALSE 1058.143802 1205.535958 889.2319515 1180.107813 1152.32974 1090.092208 1050.948806 1051.981531 1108.512695 1240.60909 0.852922819 0.971729102 0.716770462 0.951232602 0.928841928 0.878675013 0.847123251 0.847955685 0.893522951 1 10.27683289 -12.35742424 0.790755048 1.011043474 0.873645859 0.057668525 0.074661754 0.722840263 0.701365513 0.065405101 0.012492975 4.39E-13 12.35742424 -0.137397616 ATNES(ph)EDEIPQLVPIGK ddPTM_HeLa_Romidepsin_16h_R1 9 ATNESEDEIPQLVPIGK 17 0 J3QSV6;O76021-2;O76021 J3QSV6 RSL1D1 Ribosomal L1 domain-containing protein 1 1 0 AT(0.111)NES(0.889)EDEIPQLVPIGK;AT(0.024)NES(0.976)EDEIPQLVPIGK;AT(0.272)NES(0.728)EDEIPQLVPIGK;AT(0.183)NES(0.817)EDEIPQLVPIGK;AT(0.007)NES(0.993)EDEIPQLVPIGK;AT(0.018)NES(0.982)EDEIPQLVPIGK;AT(0.005)NES(0.995)EDEIPQLVPIGK;AT(0.01)NES(0.99)EDEIPQLVPIGK;AT(0.011)NES(0.989)EDEIPQLVPIGK ;;;;;;;; 182.49 1.76E-11 1974225200 40839.8 48174.2 39853.1 40155.3 41926.9 44283.7 35294.9 40867.1 47060.7 47447.7 TRUE FALSE FALSE 40342.02881 48852.39765 40546.72649 44798.24472 39787.21384 41454.11449 38292.84793 42049.52506 42851.47313 46215.00191 0.872920635 1.057067957 0.877349882 0.969344214 0.860915551 0.89698394 0.828580468 0.909867431 0.927219979 1 15.49607362 -8.755221673 24.9741989 0.944964072 0.872471888 0.313736128 0.055069676 165.8378181 666101.2476 0.008946784 0.017539496 1.76E-09 8.755221673 -0.072492184 ATNES(ph)EDEIPQLVPIGKK ddPTM_HeLa_Romidepsin_16h_R1 1 ATNESEDEIPQLVPIGKK 18 1 J3QSV6;O76021-2;O76021 J3QSV6 RSL1D1 Ribosomal L1 domain-containing protein 1 1 0 AT(0.09)NES(0.91)EDEIPQLVPIGKK 78.354 0.0043949 143490000 2164.3 2292.6 1375 4169.6 1813.4 1604.6 1532.1 2012.6 2088.8 1641.9 TRUE FALSE FALSE 2137.920679 2324.875283 1398.931298 4651.708771 1720.855431 1502.071239 1662.236536 2070.831406 1901.972497 1599.243201 1.336832745 1.453734667 0.874745815 2.908693791 1.076043612 0.939238783 1.039389465 1.294882107 1.189295346 1 10.64317363 -11.86344918 0.799067407 1.007708579 1.368581975 0.033728844 0.551085338 1.555085788 1.892080653 0.316456764 0.112991175 1.37E-12 11.86344918 0.360873396 ATPAQTPRS(ph)EDAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATPAQTPRSEDAR 13 1 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;E5RG53 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 ATPAQT(0.005)PRS(0.994)EDAR 64.534 0.029618 3269200 1458.9 1090.3 1429.6 2024.7 1152.5 1106.2 1094.9 1182.1 1532.5 1615.2 TRUE FALSE FALSE 1441.118366 1105.649272 1454.481588 2258.80534 1093.683624 1035.51739 1187.900779 1216.302198 1395.429362 1573.236871 0.916021225 0.70278627 0.924515319 1.435769389 0.695180519 0.658208188 0.755067975 0.773120832 0.886979823 1 10.61952019 ATPATAPGTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ATPATAPGTSPR 12 0 Q96P47-5;Q96P47;Q96P47-2;Q96P47-4;H0Y873 Q96P47-5 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 0 ATPATAPGT(0.305)S(0.695)PR 164.13 0.00039691 40307000 6300.9 5876.3 5438.4 4910 4433.5 4734 3886.4 4323.9 6722.3 5658.1 TRUE FALSE FALSE 6224.102207 5959.026706 5533.053071 5477.717302 4207.241951 4431.512678 4216.510719 4449.005225 6121.040652 5511.101746 1.129375303 1.081276844 1.00398311 0.993942328 0.763412135 0.804106489 0.765093971 0.807280546 1.110674586 1 12.42812505 -8.886087009 2.754782361 1.060051197 0.782475438 0.906898142 0.042396335 0.072996469 1.121209251 0.008266654 0.016165172 1.30E-09 8.886087009 -0.277575758 ATPELGSSENSASS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 3 ATPELGSSENSASSPPR 17 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 0 ATPELGSSENSAS(0.04)S(0.96)PPR;ATPELGSSENS(0.001)AS(0.36)S(0.639)PPR;ATPELGSSENS(0.001)AS(0.231)S(0.768)PPR ;; 273.54 1.09E-87 52351000 5382.9 5918 5736.1 4792.78 4751.84 4500.56 4206.1 3992.99 6387.3 5347.77 TRUE FALSE FALSE 5317.291144 6001.313759 5835.934414 5346.943774 4509.335873 4212.988741 4563.366029 4108.520866 5816.003891 5208.834164 1.020821738 1.152141452 1.120391671 1.026514495 0.865709241 0.808816063 0.876082034 0.788760159 1.116565379 1 12.34674479 -8.71859918 4.21212514 1.032592567 0.831385206 0.785643367 0.058910753 0.087676294 3.312307524 0.008965552 0.018051144 1.91E-09 8.71859918 -0.201207361 ATPGAPALTSMT(ph)PTAVER ddPTM_HeLa_Romidepsin_16h_R1 2 ATPGAPALTSMTPTAVER 18 0 P54198-2;P54198 P54198-2 HIRA Protein HIRA 1 0 ATPGAPALT(0.014)S(0.055)MT(0.909)PT(0.022)AVER;ATPGAPALT(0.018)S(0.054)MT(0.914)PT(0.013)AVER ; 106.87 0.0038129 20070700 4274.3 3997.2 4478.9 3618 3346.2 3287 1893.66 2199.67 4454.4 3780.2 TRUE FALSE FALSE 4222.203188 4053.472687 4556.853376 4036.330183 3175.430928 3076.971308 2054.507433 2263.313981 4055.987308 3681.989859 1.146717767 1.100891866 1.237606172 1.096236095 0.862422508 0.835681636 0.557988346 0.614698592 1.101574818 1 11.84626994 -8.199262679 1.398693966 1.088317998 0.575563752 0.876159931 0.076905844 0.133556073 0.473314737 0.013605101 0.05802846 6.32E-09 8.199262679 -0.512754246 ATPPPS(ph)PLLSELLKK ddPTM_HeLa_Romidepsin_16h_R1 1 ATPPPSPLLSELLKK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 1 0 ATPPPS(0.999)PLLS(0.001)ELLKK 75.97 0.011549 2980700 1160.6 1126.9 1142.7 957.01 999.87 1079.5 749.77 1040.1 1213.1 1005.2 TRUE FALSE FALSE 1146.454161 1142.764528 1162.588214 1067.663999 948.8429029 1010.523434 813.4554451 1070.193652 1104.597298 979.0847591 1.170944752 1.167176301 1.187423462 1.090471473 0.969112116 1.032110269 0.830832507 1.093055165 1.128193742 1 9.935289949 -8.777618595 6.809410544 1.099485942 0.973911488 0.404962821 0.081409402 0.152878224 29.77961852 0.01390995 0.026099424 1.67E-09 8.777618595 -0.125574454 ATPPPSPLLSELLKK ddPTM_HeLa_Romidepsin_16h_R1 1 ATPPPSPLLSELLKK 15 1 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 0 0 146.96 0.00030934 9266500 1628.1 1327.7 1159.9 1290 998.91 1021.8 872.34 925.58 1391.5 1198.8 FALSE FALSE TRUE 1608.256091 1346.391395 1180.087573 1439.15587 947.9318953 956.5102777 946.4365378 952.360197 1267.040755 1167.655003 1.377338415 1.153072947 1.010647468 1.232518052 0.811825319 0.819171994 0.810544669 0.815617793 1.085115682 1 10.18939836 -8.755484222 24.99317021 1.169677656 0.814371061 0.701492728 0.104223424 79.74382734 334673.0837 0.02160078 0.042309839 1.76E-09 8.755484222 -0.355306596 ATPS(ph)ENLVPSSAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATPSENLVPSSAR 13 0 F5H669;Q8N684-2;Q8N684;Q8N684-3;F5H6M0;F5H047 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 0 AT(0.242)PS(0.533)ENLVPS(0.112)S(0.112)AR 108.23 0.002038 0 1037.8 904.19 775.56 604.6 927.62 811.85 1105.2 847.76 1180.2 1047.3 TRUE FALSE FALSE 1025.150894 916.9192106 789.0582965 674.5066967 880.28009 759.9754051 1199.07566 872.2885981 1074.639956 1020.090995 1.004960243 0.898860214 0.773517559 0.661222087 0.862942712 0.745007464 1.175459509 0.855108615 1.053474603 1 9.994482135 -10.13959932 3.763042868 1.002405755 0.847715892 0.268189502 0.127110091 0.265652385 6.728746657 0.021650029 0.026752008 7.25E-11 10.13959932 -0.154689863 ATRPASTSQPDPS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 ATRPASTSQPDPSPDR 16 1 P20749;H7C0A2 P20749 BCL3 B-cell lymphoma 3 protein 1 0 ATRPASTSQPDPS(1)PDR 120.77 0.019084 3276900 1886.7 2126.9 1550.9 792.49 699.8 1276.7 1585.3 784.57 2530.1 2456.1 TRUE FALSE FALSE 1863.704175 2156.842554 1577.892764 884.1214226 664.0865947 1195.12299 1719.955342 807.2702951 2303.801519 2392.290168 0.779046037 0.901580662 0.659574154 0.369571148 0.277594501 0.499572755 0.718957661 0.337446647 0.963010905 1 11.22417667 -9.561830973 3.078745439 0.893567905 0.451624164 0.758145624 0.124695721 0.108088153 2.104135166 0.022454648 0.033404805 2.74E-10 9.561830973 -0.441943741 ATS(ph)DEEDSVLSIAR ddPTM_HeLa_Romidepsin_16h_R1 1 ATSDEEDSVLSIAR 14 0 A6QL64 A6QL64 ANKRD36 Ankyrin repeat domain-containing protein 36A 1 0 AT(0.176)S(0.824)DEEDSVLSIAR 98 0.0028582 0 400.79 240.6 453.23 384.54 323.63 457.74 337.25 410.43 494.66 506.48 TRUE FALSE FALSE 395.9050173 243.9871731 461.118278 429.0023241 307.1139535 428.4918913 365.8960066 422.3051445 450.4163707 493.3215766 0.802529296 0.494580381 0.934721488 0.86962003 0.62254312 0.868585344 0.74169877 0.856044342 0.913027915 1 8.946384578 -11.77568852 0.900693842 0.987928836 0.773622474 0.239479626 0.12659453 0.471643165 0.756147167 0.056638535 0.024343892 1.68E-12 11.77568852 -0.214306362 ATS(ph)FEESER ddPTM_HeLa_Romidepsin_16h_R1 2 ATSFEESER 9 0 F8VWZ8;Q52LW3 F8VWZ8 ARHGAP29 Rho GTPase-activating protein 29 1 0 AT(0.017)S(0.971)FEES(0.012)ER;AT(0.094)S(0.773)FEES(0.134)ER ; 160.91 0.0034441 61802000 3812.1 4668 3316.1 3982.4 4834.5 6158.1 5778.6 6743.5 4116 3622.9 TRUE FALSE FALSE 3765.636659 4733.716227 3373.815329 4442.863826 4587.777425 5764.617284 6269.43414 6938.612533 3747.854651 3528.776536 1.067122449 1.341461036 0.956086421 1.259038021 1.300104265 1.633602249 1.776659439 1.966294114 1.062083307 1 11.78495236 -7.725026068 0.573895323 1.031971343 2.344632549 0.900953025 0.103990862 0.451630284 0.138064182 0.019314583 0.35413831 1.88E-08 7.725026068 1.312661206 ATS(ph)PEAGGGGGALK ddPTM_HeLa_Romidepsin_16h_R1 2 ATSPEAGGGGGALK 14 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 0 AT(0.03)S(0.97)PEAGGGGGALK;AT(0.001)S(0.999)PEAGGGGGALK ; 171.62 7.39E-06 0 4435.5 4010 4019.4 4146.5 4857.4 5013.9 3670.8 4869.2 4535.7 4362.2 TRUE FALSE FALSE 4381.43842 4066.452885 4089.355971 4625.93784 4609.508753 4693.527972 3982.59766 5010.08262 4130.015632 4248.869415 1.031201007 0.957067043 0.962457438 1.08874559 1.084878894 1.104653383 0.937331151 1.179156649 0.972026963 1 12.05286329 -9.245651823 24.62383849 1.006301331 1.072842249 0.346192967 0.061038097 741.1068509 1155904.252 0.008492712 0.014054443 5.68E-10 9.245651823 0.066540918 ATS(ph)PLVSLYPALECR ddPTM_HeLa_Romidepsin_16h_R1 1 ATSPLVSLYPALECR 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3;Q96G74-4 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 0 AT(0.001)S(0.998)PLVSLYPALECR 118.52 0.0036657 66593000 1283.2 1358.8 1178.3 243.46 1057.1 1052.6 658.73 840.42 1265.3 1134.1 TRUE FALSE FALSE 1267.559865 1377.929222 1198.807817 271.6099907 1003.152242 985.3422571 714.6825098 864.7362267 1152.128399 1104.635919 1.147491082 1.247405773 1.085251527 0.245881911 0.908129299 0.892006353 0.646984674 0.78282465 1.042993786 1 10.10935523 -9.442626036 24.99999993 1.088809094 0.710285869 0.553877838 0.183217605 63.44452991 19763.50735 0.027534524 0.042059676 3.61E-10 9.442626036 -0.378523225 ATS(ph)TATSGFAGAIGQK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSTATSGFAGAIGQK 16 0 A0A2R8YD50;P51659-3;P51659;P51659-2;E7EPL9;E7ER27;A0A2R8Y7L2;E7ET17 A0A2R8YD50 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 1 0 ATS(0.401)T(0.103)AT(0.394)S(0.102)GFAGAIGQK 258.09 4.97E-72 17674000 2009.4 1758 1651.5 2071.1 2135.1 1972.2 2041.2 2103.1 1938.3 2001.5 TRUE FALSE FALSE 1984.90866 1782.74917 1680.243665 2310.570327 2026.13788 1846.182785 2214.579477 2163.94988 1764.933593 1949.500741 1.018162557 0.914464474 0.861884086 1.18521131 1.039311161 0.947002864 1.135972626 1.110002081 0.905325941 1 10.92888899 -9.253426558 24.99618233 0.990237185 1.076377034 0.372894673 0.08058525 730.034114 2277355.418 0.011861553 0.019455549 5.58E-10 9.253426558 0.086139849 AGFNYESPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AGFNYESPSK 10 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;H0YC29;E5RJ97;E7EVN4;F8W8T0 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 0 AGFNYES(0.151)PS(0.849)K 129.82 0.0074404 8143800 3237.3 3209.7 3368 1940.5 1830 1719.2 1393.6 1116.8 3533.6 3346.5 TRUE FALSE FALSE 3197.842542 3254.886241 3426.618627 2164.86974 1736.608271 1609.348668 1511.972349 1149.112846 3217.545966 3259.557448 0.981066477 0.99856692 1.051252718 0.664160634 0.532774249 0.493732261 0.463858169 0.352536461 0.987111293 1 11.67046039 -9.014519721 2.167020065 0.996645537 0.453699865 0.963657186 0.049882784 0.039071116 0.36575936 0.007611453 0.014609389 9.67E-10 9.014519721 -0.542945672 down S(ph)LSGSPLK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSGSPLK 8 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 S(0.907)LS(0.078)GS(0.015)PLK 112.11 0.021682 130710000 8899.5 7766.9 7530.1 4858.5 4084 3318.8 3009.6 2993.7 8247.2 7566.9 TRUE FALSE FALSE 8791.029471 7876.242622 7661.158232 5420.26263 3875.57824 3106.739391 3265.235349 3080.317986 7509.549777 7370.310847 1.192762375 1.068644564 1.039462024 0.735418457 0.52583647 0.421520809 0.443025459 0.417935966 1.018891867 1 12.84750975 -9.013461688 1.671378693 1.093257971 0.428942131 0.969392006 0.051478875 0.056610295 0.314455877 0.01159424 0.023614852 9.69E-10 9.013461688 -0.664315841 down ATSS(ph)SNPSS(ph)PAPDWYK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSSSNPSSPAPDWYK 16 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 2 0 AT(0.003)S(0.05)S(0.741)S(0.205)NPS(0.226)S(0.775)PAPDWYK 187 9.15E-09 5526900 2298.6 2110.1 2008.3 1996.2 2297.5 2506.2 1989.1 2196.7 2326.3 2592.2 TRUE FALSE FALSE 2270.583779 2139.806043 2043.253619 2227.010036 2180.250002 2346.061908 2158.054104 2260.258049 2118.229902 2524.85427 0.899293003 0.847496851 0.80925606 0.882035079 0.863515185 0.929187057 0.854724223 0.895203369 0.838951351 1 11.30198441 -11.57078975 0.768154696 0.994129451 0.869929105 0 0.057140353 0.252757369 0.304200291 0.015891778 0.007296523 2.69E-12 11.57078975 -0.124200347 ATSS(ph)TQSLAR ddPTM_HeLa_Romidepsin_16h_R1 2 ATSSTQSLAR 10 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 ATS(0.017)S(0.972)T(0.011)QSLAR;ATS(0.074)S(0.86)T(0.065)QSLAR ; 160.72 0.0023638 39523000 4148.5 2933.2 5551.2 2652.8 6747.2 7735 6544.5 3606.7 3791.3 3544.4 TRUE FALSE FALSE 4097.936486 2974.493667 5647.816307 2959.529218 6402.865207 7240.758464 7100.389667 3711.054174 3452.196633 3452.315977 1.18701084 0.861593691 1.635949996 0.85725908 1.854657931 2.097362614 2.056703301 1.074946268 0.999965431 1 11.7533488 -8.751123017 24.99953476 1.102669731 1.814648488 0.496625294 0.334396892 121.6246846 294729.8885 0.045123957 0.089454557 1.77E-09 8.751123017 0.711978757 ATSSS(ph)NPSS(ph)PAPDWYK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSSSNPSSPAPDWYK 16 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 2 0 AT(0.001)S(0.039)S(0.375)S(0.55)NPS(0.036)S(1)PAPDWYK 138.98 3.18E-07 0 2003.1 1639.6 2285.4 1381 2103.3 2070 1258.2 1778.6 2045.4 2027.6 TRUE FALSE FALSE 1978.685447 1662.682332 2325.176428 1540.677718 1995.960753 1937.733681 1365.071477 1830.060985 1862.454301 1974.92266 1.001905283 0.84189744 1.177350625 0.780120533 1.010652616 0.9811694 0.691202498 0.926649444 0.943051766 1 10.94758044 -7.821961015 12.3717784 0.986075153 0.809018935 0.221382947 0.114206309 0.602097765 121.8344314 0.013856568 0.041612345 1.51E-08 7.821961015 -0.177056218 ATSSS(ph)SGSLSATGR ddPTM_HeLa_Romidepsin_16h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 0 ATSS(0.002)S(0.997)S(0.001)GSLSATGR;ATSS(0.061)S(0.926)S(0.004)GS(0.009)LSATGR ; 260.5 5.22E-68 66122000 4465.1 5020.3 5467.8 3703 6175.3 8241.4 6144 6605.9 5368.4 4575.2 TRUE FALSE FALSE 4410.677644 5090.975915 5562.964765 4131.158283 5860.151398 7714.801138 6665.871207 6797.031294 4888.236859 4456.335644 0.989754362 1.142413032 1.248327148 0.927030326 1.315015714 1.7311984 1.495818928 1.525251201 1.096918466 1 12.12164218 -8.542584129 4.12964456 1.025022816 1.572627471 0.819070076 0.107728987 0.05770496 2.260137876 0.015855797 0.034114768 2.87E-09 8.542584129 0.547604654 ATSSSNPS(ph)SPAPDWYKDFVTDADAEVLEHSGK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSSSNPSSPAPDWYKDFVTDADAEVLEHSGK 32 1 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 AT(0.018)S(0.006)S(0.006)S(0.035)NPS(0.311)S(0.258)PAPDWY(0.235)KDFVT(0.125)DADAEVLEHS(0.006)GK 44.721 0.0089821 9399800 1150.6 1252.6 1477.4 1214.2 1134 972.61 851.89 989.97 1507.4 1678 TRUE FALSE FALSE 1136.576045 1270.234136 1503.113527 1354.591517 1076.127748 910.46336 924.2495153 1018.61322 1372.574369 1634.405318 0.695406477 0.777184289 0.919669993 0.828797791 0.65842159 0.557060938 0.565495906 0.623231709 0.839800479 1 10.67455009 -16.52287875 0.048032757 2.303892048 7.82E-10 0.556699146 0.095301956 245.5811164 0.936032239 43.44949735 11.31686737 3.00E-17 16.52287875 -2.303892047 ATSSSSGS(ph)LSATGR ddPTM_HeLa_Romidepsin_16h_R1 2 ATSSSSGSLSATGR 14 0 Q03252 Q03252 LMNB2 Lamin-B2 1 0 ATS(0.005)S(0.005)S(0.028)S(0.028)GS(0.923)LS(0.011)ATGR;ATSS(0.005)S(0.028)S(0.097)GS(0.576)LS(0.293)ATGR ; 180.3 3.08E-07 29682000 3334.7 3155.5 3435.9 2810.2 3750.8 4489.2 3100.5 3659.5 3776.9 3328.9 TRUE FALSE FALSE 3294.055394 3199.923212 3495.700398 3135.128546 3559.38268 4202.354608 3363.856393 3765.381859 3439.084605 3242.414698 1.015926617 0.986895111 1.07811638 0.96691165 1.097756768 1.296057105 1.037454091 1.161289412 1.060655383 1 11.66285291 -8.554046201 6.640983287 1.009921246 1.159492692 0.500692321 0.065823908 0.091555828 12.81898654 0.008405603 0.017106133 2.79E-09 8.554046201 0.149571446 ATST(ph)ATSGFAGAIGQK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSTATSGFAGAIGQK 16 0 A0A2R8YD50;P51659-3;P51659;P51659-2;E7EPL9;E7ER27;A0A2R8Y7L2;E7ET17 A0A2R8YD50 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 1 0 ATS(0.166)T(0.833)AT(0.001)SGFAGAIGQK 314.45 1.45E-157 15044000 2148.7 1995.9 2227.5 1767.2 1932.7 2137.8 1644 2142.2 2272.7 1684.7 TRUE FALSE FALSE 2122.510818 2023.998333 2266.268703 1971.531979 1834.067107 2001.201479 1783.641319 2204.181177 2069.42402 1640.931251 1.293479429 1.23344493 1.381086929 1.201471407 1.117698932 1.219552299 1.08696895 1.343250167 1.261127801 1 10.68029908 -12.35314907 1.046210968 0.998359997 1.233228466 0 0.116767037 0.351067074 0.680064624 0.061329654 0.015548962 4.43E-13 12.35314907 0.234868469 ATST(ph)STSGAGDVGK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSTSTSGAGDVGK 14 0 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 AT(0.007)S(0.263)T(0.666)S(0.029)T(0.029)S(0.005)GAGDVGK 159.12 0.00080425 2998300 1301.8 1215.5 1485.7 846.05 1418.1 1311.4 1054 1186.7 1231.6 1361.9 TRUE FALSE FALSE 1285.933161 1232.611841 1511.557985 943.8742818 1345.729065 1227.605772 1143.526734 1221.035292 1121.442611 1326.517642 0.969405246 0.929208781 1.139493315 0.711542954 1.014482599 0.925434939 0.862051659 0.920481759 0.845403466 1 10.37342815 -9.274394826 24.99852092 0.9905593 0.894663929 0.161778295 0.099054968 824.7443507 1591404.519 0.012288895 0.018843239 5.32E-10 9.274394826 -0.095895371 ATSTS(ph)TSGAGDVGK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSTSTSGAGDVGK 14 0 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 ATS(0.002)T(0.026)S(0.884)T(0.083)S(0.005)GAGDVGK 190.57 4.70E-11 4931500 2729.3 2343.2 2785.7 2220.2 2757.7 3028.4 2360.7 2024.1 2349.2 2660.1 TRUE FALSE FALSE 2696.034242 2376.187631 2834.18394 2476.90997 2616.964279 2834.895014 2561.217799 2082.66414 2139.081668 2590.990219 1.040542038 0.917096334 1.093861304 0.955970406 1.010024762 1.094135745 0.988509251 0.803810113 0.825584617 1 11.33928785 -7.277761588 4.188909103 1.017097417 0.789695981 0.296889242 0.079528967 0.094914436 3.675363408 0.006483073 0.062635359 5.28E-08 7.277761588 -0.227401435 ATSVALPGWS(ph)PSETR ddPTM_HeLa_Romidepsin_16h_R1 2 ATSVALPGWSPSETR 15 0 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4;B1AL79 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 ATSVALPGWS(0.902)PS(0.089)ET(0.009)R;ATS(0.014)VALPGWS(0.906)PS(0.08)ETR ; 211.7 1.53E-25 118055000 10057.1 10161.4 10554.5 8998.3 12243.4 14088.2 11594.5 12635.1 10671.5 9813.1 TRUE FALSE FALSE 9934.520197 10304.45246 10738.19665 10038.72578 11618.57361 13188.00949 12579.33654 13000.67668 9717.014313 9558.154247 1.039376426 1.078079741 1.123459234 1.050278697 1.215566658 1.379765292 1.316084279 1.360166027 1.016620371 1 13.22251633 -8.608415004 1.820830122 1.031077866 1.354456208 0.921372341 0.039313256 0.068916408 0.457594258 0.006665537 0.016760634 2.46E-09 8.608415004 0.323378342 ATT(ph)PADGEEPAPEAEALAAAR ddPTM_HeLa_Romidepsin_16h_R1 3 ATTPADGEEPAPEAEALAAAR 21 0 Q5JZ02;Q96S44 Q5JZ02 TP53RK TP53-regulating kinase 1 0 AT(0.17)T(0.83)PADGEEPAPEAEALAAAR;ATT(1)PADGEEPAPEAEALAAAR;AT(0.029)T(0.971)PADGEEPAPEAEALAAAR ;; 189.44 2.07E-17 59662000 4676.12 5131.69 4587.37 4520.58 3503.91 3048.74 2809.78 3681.45 5869.55 4941.36 TRUE FALSE FALSE 4619.125651 5203.934067 4667.211251 5043.27073 3325.092398 2853.935353 3048.442643 3787.966947 5344.562747 4812.982755 0.959722045 1.081228488 0.969712855 1.047847247 0.690858989 0.592966046 0.633379091 0.787031066 1.110447101 1 12.23271554 -8.735562554 8.909777354 0.992134947 0.666372806 0.857057651 0.069474461 0.059777742 18.42301107 0.008295088 0.016422546 1.84E-09 8.735562554 -0.325762142 ATT(ph)PPNQGRPDS(ph)PVYANLQELK ddPTM_HeLa_Romidepsin_16h_R1 2 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-2;Q8IWW6-4;Q8IWW6 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 2 0 AT(0.183)T(0.807)PPNQGRPDS(0.973)PVY(0.038)ANLQELK;AT(0.06)T(0.938)PPNQGRPDS(0.981)PVY(0.021)ANLQELK ; 66.972 0.0046291 45923000 4046.6 4463.2 3954.3 4121.7 5365.1 6051.5 5448.5 6692.2 5369.6 4540.2 TRUE FALSE FALSE 3997.278483 4526.033047 4023.122933 4598.270347 5091.298927 5664.82868 5911.295454 6885.828248 4889.329528 4422.244949 0.903902549 1.02346955 0.909746741 1.039804534 1.151292835 1.280984827 1.336718233 1.557088838 1.105621598 1 12.11056322 -7.880675307 0.758258404 0.952704637 1.634347546 0.883275834 0.067035495 0.228441553 0.152529954 0.008899246 0.110080383 1.32E-08 7.880675307 0.681642909 ATT(ph)PPNQGRPDSPVYANLQELK ddPTM_HeLa_Romidepsin_16h_R1 1 ATTPPNQGRPDSPVYANLQELK 22 1 Q1RLN5;Q8IWW6-3;Q8IWW6-2;Q8IWW6-4;Q8IWW6 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 0 AT(0.087)T(0.617)PPNQGRPDS(0.294)PVY(0.002)ANLQELK 73.21 0.0017952 14453000 1012.8 671.03 902.77 793.73 1273.7 1242.9 1274.7 1574.3 1049.7 1158.6 TRUE FALSE FALSE 1000.455604 680.476778 918.4823332 885.5047972 1208.698336 1163.482701 1382.972986 1619.849887 955.812203 1128.499405 0.886536226 0.602992589 0.813897047 0.784674581 1.071066879 1.030999836 1.225497311 1.435401631 0.846976258 1 10.14018994 -7.557204718 1.126260575 0.900007487 1.544947172 0.721137507 0.119515457 0.52530864 0.74993561 0.020771068 0.351445862 2.77E-08 7.557204718 0.644939686 ATT(ph)PQLTDVSEDLDQQSLPSEPEETLSR ddPTM_HeLa_Romidepsin_16h_R1 2 ATTPQLTDVSEDLDQQSLPSEPEETLSR 28 0 Q8NC44;H7C3D5;C9JIF3 Q8NC44 FAM134A Protein FAM134A 1 0 AT(0.236)T(0.764)PQLTDVSEDLDQQSLPSEPEETLSR;AT(0.259)T(0.74)PQLTDVSEDLDQQSLPSEPEETLSR ; 120.18 4.33E-10 7631900 986.35 1188.3 1117.14 850.97 844.87 1343.86 784.32 1211.97 1055.39 931 TRUE FALSE FALSE 974.3279868 1205.028919 1136.583353 949.3631553 801.7531313 1257.991683 850.9401212 1247.03644 960.9932751 906.8124858 1.074453652 1.328862292 1.253382999 1.046923339 0.884144345 1.387267713 0.938385978 1.375186667 1.059748614 1 9.824660445 -10.49425762 10.62399426 1.032749675 1.16271135 0.113908558 0.165689723 0.813664159 296.6243789 0.027173543 0.029940884 3.20E-11 10.49425762 0.129961675 ATVPVAAATAAEGEGS(ph)PPAVAAVAGPPAAAEVGGGVGGSSR ddPTM_HeLa_Romidepsin_16h_R1 4 ATVPVAAATAAEGEGSPPAVAAVAGPPAAAEVGGGVGGSSR 41 0 O75179-4;O75179-6;O75179-2;O75179;H0YLQ3;A0A1W2PQ15;O75179-5;O75179-3 O75179-4 ANKRD17 Ankyrin repeat domain-containing protein 17 1 0 ATVPVAAAT(0.002)AAEGEGS(0.998)PPAVAAVAGPPAAAEVGGGVGGSSR;ATVPVAAAT(0.013)AAEGEGS(0.987)PPAVAAVAGPPAAAEVGGGVGGSSR;ATVPVAAATAAEGEGS(1)PPAVAAVAGPPAAAEVGGGVGGSSR;ATVPVAAATAAEGEGS(1)PPAVAAVAGPPAAAEVGGGVGGSSR ;;; 122.81 9.09E-31 24537800 4045.67 3784.78 3590.93 3716.89 3472.54 2755.66 3280.66 2778.14 4402.29 3542.08 TRUE FALSE FALSE 3996.359818 3838.062232 3653.42863 4146.65431 3295.323326 2579.582219 3559.319179 2858.521098 4008.538157 3450.056251 1.158346278 1.112463668 1.058947555 1.201909189 0.955150608 0.7476928 1.031669897 0.828543331 1.161876174 1 11.75240417 -8.545260352 10.81655207 1.086014577 0.879847019 0.61348234 0.087405259 0.261738586 124.2867414 0.01302212 0.026168731 2.85E-09 8.545260352 -0.206167559 ATVT(ph)PS(ph)PVKGK ddPTM_HeLa_Romidepsin_16h_R1 1 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 0 AT(0.022)VT(0.978)PS(0.999)PVKGK 64.82 0.0037208 0 10749 9840.5 10377 9895.6 11086 10696 8351.2 9455.2 11598 11466 TRUE FALSE FALSE 10617.98705 9979.034817 10557.60733 11039.77583 10520.24005 10012.56012 9060.55072 9728.771294 10560.64583 11168.11167 0.950741483 0.893529284 0.945335044 0.988508726 0.941989153 0.896531161 0.811287619 0.871120525 0.945607113 1 13.44709765 -4 0.202620829 0.996029695 0.21702325 0.5073713 0.037848777 25.40961471 0.293293794 0.034805647 6.359744083 1.00E-04 4 -0.779006445 ATVTPS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 ATVTPSPVK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 ATVT(0.414)PS(0.586)PVK 101.3 0.027157 966530000 8012.5 6355.1 13182 5237 7272 6273 5186.6 4214 8054.5 5442.2 TRUE FALSE FALSE 7914.840568 6444.567265 13411.42718 5842.526581 6900.882704 5872.175545 5627.149675 4335.925441 7334.085347 5300.810859 1.493137706 1.215770084 2.530070877 1.102194878 1.301854167 1.107788167 1.061563943 0.817973996 1.383578011 1 12.37199735 -7.757437781 1.348857728 1.331505067 0.825497315 0.181436768 0.406603406 1.056662857 2.898461235 0.064442287 0.569232997 1.75E-08 7.757437781 -0.506007752 AVTK(ac)YTSSK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTKYTSSK 9 1 P23527;Q96A08;A0A2R8Y619;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99879;Q99880 P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 1 AVTK(1)YTSSK 159.34 0.0090587 4866900 2198.5 1619.9 2679.7 2550.2 3801.2 4070.6 4123.4 3084.8 1804.2 1330.8 FALSE TRUE FALSE 2171.703836 1642.704995 2726.339054 2845.066123 3607.21058 3810.501797 4473.641493 3174.053821 1642.827833 1296.225624 1.675405729 1.267298659 2.10329051 2.194884957 2.782857022 2.939690225 3.451283025 2.448689304 1.267393425 1 10.34010114 -9.257954713 0.630896593 1.222234712 3.142412672 0.841191917 0.306180522 0.223460335 0.171680467 0.073441031 0.195499186 5.52E-10 9.257954713 1.920177961 AVAGVMITAS(ph)HNR ddPTM_HeLa_Romidepsin_16h_R1 1 AVAGVMITASHNR 13 0 Q6PCE3 Q6PCE3 PGM2L1 "Glucose 1,6-bisphosphate synthase" 1 0 AVAGVMIT(0.011)AS(0.989)HNR 116.58 0.0016785 7341300 1437.7 1725.9 1604.2 1484.4 2364.6 2340.9 1801.1 2285.4 1639.1 1335.7 TRUE FALSE FALSE 1420.176759 1750.197266 1632.120428 1656.033312 2243.925638 2191.324045 1954.085389 2351.524443 1492.494791 1300.998321 1.091605374 1.345272501 1.254513862 1.272894273 1.724772124 1.684340409 1.50198917 1.807476923 1.147191942 1 10.34540339 -9.232987556 0.55420479 1.014257415 1.750777175 0.799441897 0.120101696 0.248371397 0.144639822 0.028154627 0.081195372 5.85E-10 9.232987556 0.736519759 AVAISLPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVAISLPK 8 0 P50454;E9PPV6;E9PKH2 P50454 SERPINH1 Serpin H1 0 0 112.17 0.01828 680180 754.44 633.38 1733.1 892.62 1381.9 1847.1 1300.3 693.96 613.39 479.48 FALSE FALSE TRUE 745.2445951 642.2967403 1763.263878 995.8289243 1311.376486 1729.076271 1410.74745 714.0386377 558.5268621 467.0230405 1.595734108 1.375299899 3.775539375 2.132290782 2.807948158 3.702336119 3.020723449 1.528915226 1.195929994 1 8.867349917 -9.8376087 9.342620143 1.293807803 2.842915662 0.582234595 0.637532023 0.166850906 18.9782024 0.101526147 0.133563134 1.45E-10 9.8376087 1.549107859 AVAS(ph)PEATVSQTDENK ddPTM_HeLa_Romidepsin_16h_R1 2 AVASPEATVSQTDENK 16 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 AVAS(1)PEATVSQTDENK;AVAS(0.996)PEAT(0.004)VSQTDENK ; 246.66 2.39E-58 102859000 8311.9 6908.2 7700.9 5730.1 9264.4 9904.7 8534.6 9478.5 8684 7966.8 TRUE FALSE FALSE 8210.591366 7005.453821 7834.930934 6392.641123 8791.603098 9271.821636 9259.528711 9752.745443 7907.281291 7759.821388 1.058090252 0.902785447 1.009679288 0.823812921 1.132964621 1.194849878 1.193265701 1.256826022 1.019003002 1 12.92180773 -8.533289791 24.9824432 1.002473984 1.204658775 0.713462882 0.069447414 99.0735328 237737.3074 0.010561996 0.02114094 2.93E-09 8.533289791 0.20218479 AVAS(ph)PEATVSQTDENKAR ddPTM_HeLa_Romidepsin_16h_R1 4 AVASPEATVSQTDENKAR 18 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 AVAS(0.99)PEAT(0.01)VSQTDENKAR;AVAS(1)PEATVSQTDENKAR;AVAS(1)PEATVSQTDENKAR;AVAS(0.993)PEAT(0.007)VSQTDENKAR ;;; 124.82 0.00052217 44358900 6650.3 7152.1 5249.4 8446.8 7071.7 7550 6041.9 7098.8 6999.8 6283.7 TRUE FALSE FALSE 6569.243586 7252.787452 5340.763605 9423.458759 6710.804761 7067.579367 6555.098835 7304.192578 6373.720357 6120.448568 1.073327145 1.185009133 0.872609833 1.539667992 1.09645636 1.154748592 1.07101608 1.193408048 1.041381246 1 12.57942168 -10.41407073 0.75444074 1.016593365 1.171807869 0.126497831 0.15464454 0.800775542 0.960037592 0.039422122 0.042530286 3.85E-11 10.41407073 0.155214504 AVAVVVDPIQSVK ddPTM_HeLa_Romidepsin_16h_R1 1 AVAVVVDPIQSVK 13 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 0 158.41 1.03E-24 0 106.43 0 173.27 132.31 0 0 56.889 146.91 166.87 139.62 FALSE FALSE TRUE 105.1327902 0 176.2856917 147.6083047 0 0 61.72115024 151.1606091 151.9447293 135.9926523 0.77307699 0 1.296288356 1.085413824 0 0 0.453856508 1.11153512 1.117301021 1 7.087384894 -8.771879038 24.99894543 0.861599596 0.367859347 0.229077066 0.436447701 233.9569386 560236.7964 0.063820091 0.116584175 1.69E-09 8.771879038 -0.493740249 AVDS(ph)SSEEIEVEVPVVDRR ddPTM_HeLa_Romidepsin_16h_R1 1 AVDSSSEEIEVEVPVVDRR 19 1 D6RB01;Q9Y6X4 D6RB01 FAM169A Soluble lamin-associated protein of 75 kDa 1 0 AVDS(0.443)S(0.114)S(0.443)EEIEVEVPVVDRR 97.689 0.00054734 6940400 1069.2 1052.4 1066.8 1149.5 1167.3 1082 889.27 1196 1446.3 1486 TRUE FALSE FALSE 1056.168179 1067.215715 1085.367206 1282.410599 1107.728325 1012.863692 964.8045716 1230.604373 1316.939306 1447.393506 0.72970355 0.73733626 0.749877074 0.886013785 0.765326306 0.699784604 0.666580697 0.850221013 0.909869569 1 10.49924149 -12.26090035 0.807078657 1.01362411 0.756556348 0.556633986 0.067385222 0.337928748 0.362551981 0.056097883 0.01253776 5.48E-13 12.26090035 -0.257067761 AVEFS(ph)SGAKSPSK ddPTM_HeLa_Romidepsin_16h_R1 1 AVEFSSGAKSPSK 13 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 AVEFS(0.426)S(0.281)GAKS(0.281)PS(0.012)K 153.81 0.0050819 25468000 4065.1 3785.4 3836.6 3890.6 4099.8 3876.6 3351.7 3558.4 3630.4 3502.4 TRUE FALSE FALSE 4015.552998 3838.690961 3903.374414 4340.449478 3890.571908 3628.897771 3636.393314 3661.35669 3305.687931 3411.407143 1.177095793 1.125251487 1.144212417 1.272334053 1.140459565 1.063753935 1.065951134 1.073268753 0.969010087 1 11.73615123 -6.097639953 19.37296214 1.103990327 1.12492461 0 0.083742041 0 0 0.011945397 0 7.99E-07 6.097639953 0.020934283 AVEHINK(ac)TIAPALVSK ddPTM_HeLa_Romidepsin_16h_R1 2 AVEHINKTIAPALVSK 16 1 P06733;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 1 ; AVEHINK(1)TIAPALVSK;AVEHINK(1)TIAPALVSK 128.74 1.89E-05 2179800 2618.7 2354 2644.9 1849.37 3158.6 3103.1 2619.2 2576.6 2841.6 2496.9 FALSE TRUE FALSE 2586.782277 2387.139674 2690.933375 2063.202861 2997.404856 2904.821925 2841.674783 2651.149856 2587.440179 2432.030178 1.06363083 0.981541962 1.106455586 0.848345913 1.232470256 1.194402089 1.168437303 1.090097434 1.063901346 1 11.24794542 -8.727436584 24.99999785 1.021716183 1.172790072 0.532584875 0.073311645 110.344821 81128.80415 0.009795491 0.0195902 1.87E-09 8.727436584 0.151073888 AVELAANTK ddPTM_HeLa_Romidepsin_16h_R1 2 AVELAANTK 9 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 ; ; 191.17 7.46E-08 9546800 9417.3 6470.1 11230.3 8164.9 12832.1 11425.3 9992.4 5833.5 6801.2 6053.6 FALSE FALSE TRUE 9302.518325 6561.186238 11425.75866 9108.964155 12177.23005 10695.2602 10841.15421 6002.283119 6192.883638 5896.326599 1.577680301 1.112758279 1.937775744 1.544854072 2.065223126 1.81388531 1.838628513 1.01796992 1.050295219 1 12.52560072 -12.03250584 0.409005092 0.851031792 1.699375038 0.36705625 0.314906081 1.539006466 0.387508572 0.561975019 0.109798661 9.28E-13 12.03250584 0.848343246 AVFPS(ph)IVGR ddPTM_HeLa_Romidepsin_16h_R1 1 AVFPSIVGR 9 0 P0CG38;F8WCH0;P60709;A0A2R8Y793;P63267-2;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q6S8J3;A5A3E0;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P0CG38;P60709;P63261;P63267 POTEI;ACTG2;ACTB;POTEE;POTEF;ACTG1;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 0 AVFPS(1)IVGR 102.95 0.025649 15546000 1222.5 1305.8 1560.4 719.91 1507.6 1680.1 1291.6 1517.9 1710.5 1631.7 TRUE FALSE FALSE 1207.5997 1324.183087 1587.558107 803.1493815 1430.661546 1572.747032 1401.308472 1561.818042 1557.508596 1589.308199 0.759827264 0.833182065 0.998898835 0.50534527 0.900178799 0.989579638 0.88170971 0.982703067 0.979991544 1 10.6341832 -5.556377789 15.98176763 0.875946524 1.027987443 0 0.147959296 0 0 0.019807525 0 2.78E-06 5.556377789 0.152040919 AVFPS(ph)IVGRPR ddPTM_HeLa_Romidepsin_16h_R1 2 AVFPSIVGRPR 11 1 P0CG38;F8WCH0;P60709;A0A2R8Y793;P63267-2;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q6S8J3;A5A3E0;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P0CG38;P60709;P63261;P63267 POTEI;ACTG2;ACTB;POTEE;POTEF;ACTG1;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 0 AVFPS(1)IVGRPR;AVFPS(1)IVGRPR ; 154.67 0.00080333 241830000 6529.6 6627.2 5818.9 4132.2 7999.2 7639.9 7046.2 7169 6328 5140.9 TRUE FALSE FALSE 6450.014724 6720.497896 5920.175514 4609.984407 7590.970975 7151.735047 7644.704052 7376.423704 5762.007831 5007.338677 1.288112337 1.342129688 1.182299799 0.920645617 1.515969153 1.428250715 1.526700019 1.473122587 1.150712625 1 12.28982832 -4 0.072589981 0.678433908 2.817723411 0.435575094 0.15276375 143.6881456 0.775249897 3.932714233 31.39935294 1.00E-04 4 2.139289503 AVFPSIVGR ddPTM_HeLa_Romidepsin_16h_R1 1 AVFPSIVGR 9 0 P0CG38;F8WCH0;P60709;A0A2R8Y793;P63267-2;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q6S8J3;A5A3E0;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P0CG38;P60709;P63261;P63267 POTEI;ACTG2;ACTB;POTEE;POTEF;ACTG1;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 132.57 0.023685 951200 389.43 345.34 342.11 225.48 446.22 403.26 484.3 471.67 413.1 281.79 FALSE FALSE TRUE 384.6834774 350.2017056 348.064281 251.5510585 423.4477283 377.4929875 525.4364299 485.3170273 376.1513014 274.4690552 1.401555003 1.275924185 1.268136697 0.916500617 1.542788596 1.375357186 1.914374025 1.768203075 1.37046889 1 8.100499693 -4.000000001 0.315222685 1.144076808 8.449398047 0.529713057 0.199441427 27.19354268 0.347184148 0.07157995 115.5267205 1.00E-04 4.000000001 7.305321239 AVFPSIVGRPR ddPTM_HeLa_Romidepsin_16h_R1 4 AVFPSIVGRPR 11 1 P0CG38;F8WCH0;P60709;A0A2R8Y793;P63267-2;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q6S8J3;A5A3E0;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P0CG38;P60709;P63261;P63267 POTEI;ACTG2;ACTB;POTEE;POTEF;ACTG1;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ;;; ;;; 203.02 4.02E-13 197850300 7932.77 7263.17 9762.99 9611.54 12002.79 10983.25 9176.3 7461.52 6531.59 5302.93 FALSE FALSE TRUE 7836.082348 7365.421098 9932.910746 10722.87148 11390.24284 10281.45577 9955.734693 7677.407309 5947.388232 5165.159114 1.517103767 1.425981453 1.923059973 2.076000224 2.205206575 1.99053999 1.9274788 1.486383505 1.151443373 1 12.33459708 -10.70970108 0.582940477 1.062157069 1.965199702 0.700573328 0.213253197 0.279702878 0.221443494 0.090809383 0.075145643 1.95E-11 10.70970108 0.903042634 AVFVDLEPTVIDEVR ddPTM_HeLa_Romidepsin_16h_R1 3 AVFVDLEPTVIDEVR 15 0 Q9BQE3;F5H5D3;F8VVB9;A0A1W2PQM2;F8VQQ4;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A Tubulin alpha-1C chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 0 0 ;; ;; 299.42 1.84E-133 124403000 9431.5 9018.3 9127 8742.2 9006.7 9237.9 7266.11 8568 9345.3 8870.2 FALSE FALSE TRUE 9316.54525 9145.259864 9285.851606 9753.014297 8547.05449 8647.628004 7883.293202 8815.901562 8509.432962 8639.750925 1.078334935 1.058509666 1.074782327 1.128853642 0.989270937 1.000911725 0.912444499 1.020388393 0.984916468 1 13.07677401 -8.548132952 24.99842209 1.048957655 0.975321715 0.378350396 0.045980509 185.3489758 183471.0326 0.00689985 0.013800065 2.83E-09 8.548132952 -0.073635941 AVFVDLEPTVIDEVRTGTY(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 AVFVDLEPTVIDEVRTGTYR 20 1 Q9BQE3;F5H5D3;F8VVB9;A0A1W2PQM2;F8VQQ4;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A Tubulin alpha-1C chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 1 0 AVFVDLEPT(0.004)VIDEVRT(0.101)GT(0.041)Y(0.854)R 77.506 0.010193 5759900 1669.5 1722.2 1572.3 1661.6 1867.3 1912.9 1805.8 1730.5 1977.3 1567.3 TRUE FALSE FALSE 1649.151492 1746.445177 1599.665222 1853.72201 1772.004713 1790.671864 1959.184607 1780.569287 1800.445336 1526.58132 1.080290627 1.144023678 1.047874228 1.214296275 1.160766669 1.172994743 1.28338044 1.166376965 1.179396939 1 10.57608873 -9.582982684 0.279062579 0.985712813 1.271528644 0.167719494 0.071410063 0.787668251 0.15437627 0.040073809 0.083243879 2.61E-10 9.582982684 0.285815831 AVGAQASVGSRSEGEGEAAS(ph)ADDGSLNTSGAGPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVGAQASVGSRSEGEGEAASADDGSLNTSGAGPK 34 1 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 AVGAQAS(0.002)VGS(0.008)RS(0.1)EGEGEAAS(0.879)ADDGS(0.011)LNTSGAGPK 100.58 1.17E-14 0 679.08 543.11 831.36 1220.2 739.18 875.63 760.72 700.92 799.17 905.36 TRUE FALSE FALSE 670.8031118 550.7559168 845.8294721 1361.285265 701.4568863 819.680069 825.3355378 721.2000143 727.6902336 881.8386167 0.760686932 0.624554092 0.959165834 1.543689786 0.795448139 0.929512559 0.935925828 0.817836734 0.825196606 1 9.784370845 -9.533843561 24.9935178 0.860708263 1.011549079 0.144227223 0.215935873 421.3228356 960372.063 0.035725032 0.050547359 2.93E-10 9.533843561 0.150840816 AVGHPFVIQLGR ddPTM_HeLa_Romidepsin_16h_R1 1 AVGHPFVIQLGR 12 0 O14980 O14980 XPO1 Exportin-1 0 0 72.096 0.018551 851950 883.12 657.42 960.08 667.15 1069.4 756.74 774.22 556.51 643.15 323.78 FALSE FALSE TRUE 872.3561938 666.675176 976.7897897 744.289022 1014.824528 708.3867563 839.9822275 572.6117388 585.6250532 315.3681489 2.766151866 2.11395849 3.09730007 2.360064022 3.217904316 2.246221626 2.663497345 1.815692995 1.856956878 1 8.30089315 -12.28489497 0.800513101 0.899820128 2.570127606 0.414351936 0.483259689 0.323248191 0.335923194 0.349956809 0.075059059 5.19E-13 12.28489497 1.670307478 AVGK(ac)LTPEHLIK ddPTM_HeLa_Romidepsin_16h_R1 1 AVGKLTPEHLIK 12 1 A0A0A0MR70;Q96L91-4;Q96L91-3;Q96L91-5;Q96L91-2;Q96L91 A0A0A0MR70 EP400 E1A-binding protein p400 0 1 AVGK(1)LTPEHLIK 137.16 4.32E-14 0 1553.3 1513.3 1315.4 1373.8 1380.8 1281.6 1198.7 1120.3 1624.3 1172.4 FALSE TRUE FALSE 1534.367782 1534.604277 1338.293985 1532.64522 1310.332624 1199.709896 1300.517548 1152.714113 1479.01854 1141.940879 1.343649054 1.343856153 1.171946823 1.342140603 1.147461001 1.050588448 1.138865919 1.009434143 1.295179608 1 10.15727225 -8.516265971 24.68185158 1.195298362 1.077798387 0.290764921 0.111106386 440.2900723 1643357.615 0.021779444 0.044873392 3.05E-09 8.516265971 -0.117499976 AVGPTAEADK(ac)SAAEK ddPTM_HeLa_Romidepsin_16h_R1 2 AVGPTAEADKSAAEK 15 1 Q13123;D6REL4;E7EQZ7 Q13123 IK Protein Red 0 1 ; AVGPTAEADK(1)SAAEK;AVGPTAEADK(1)SAAEK 224.42 3.75E-33 3153100 1432.76 1424.06 1158.57 1064.58 1646.51 1657.21 1775.22 1681.95 1951.42 1332.49 FALSE TRUE FALSE 1415.29697 1444.107954 1178.734425 1187.671749 1562.482451 1551.319629 1926.007142 1730.61457 1776.880108 1297.871718 1.090475238 1.112673876 0.908205648 0.915091786 1.203880499 1.195279632 1.483973428 1.33342498 1.369072215 1 10.34193208 -8.166143221 1.778159022 1.032619048 1.405010507 0.439512327 0.137629929 0.140094893 0.833782263 0.013045547 0.048085332 6.82E-09 8.166143221 0.37239146 AVIVSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 AVIVSSPK 8 0 Q14966-3;Q14966;Q14966-5 Q14966-3 ZNF638 Zinc finger protein 638 1 0 AVIVS(0.044)S(0.956)PK;AVIVS(0.202)S(0.798)PK;AVIVS(0.36)S(0.64)PK ;; 123.86 0.016298 309098000 44753 39926 48700 37234.3 28015.1 26689.3 24746.7 22331 43788 35810.9 TRUE FALSE FALSE 44207.53322 40488.07928 49547.60307 41539.50496 26585.38491 24983.93987 26848.68408 22977.11225 39871.49161 34880.52766 1.267398637 1.16076453 1.420494654 1.190908159 0.762184138 0.716271844 0.769732739 0.658737519 1.143087398 1 15.09013424 -8.738654165 6.799481177 1.160814428 0.72664338 0.821955607 0.106481229 0.072151238 12.26358259 0.020182545 0.03973593 1.83E-09 8.738654165 -0.434171048 AVLFCLSEDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AVLFCLSEDKK 11 1 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;E9PS23;E9PLJ3 E9PP50 CFL1 Cofilin-1 0 1 ; AVLFCLSEDK(1)K;AVLFCLSEDK(1)K 150.61 1.68E-14 282290 0 162.52 154.8 0 209.13 179.75 162.62 154.3 213.98 180.27 FALSE TRUE FALSE 0 164.8079608 157.4942291 0 198.4573157 168.2645551 176.4329387 158.7644271 194.8410929 175.5865594 0 0.938613761 0.896960619 0 1.130253457 0.958299745 1.004820297 0.904194647 1.109658356 1 7.456038605 -8.70467177 24.99999654 0.548793727 0.996845322 0.128434256 0.377043745 106.4140076 46863.09386 0.062164744 0.124329447 1.97E-09 8.70467177 0.448051595 AVLFCLSEDKK ddPTM_HeLa_Romidepsin_16h_R1 1 AVLFCLSEDKK 11 1 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;E9PS23;E9PLJ3 E9PP50 CFL1 Cofilin-1 0 0 157.75 0.0012928 2076500 451.7 398.18 360.84 260.97 335.84 665.13 429.6 502.53 474.48 270.25 FALSE FALSE TRUE 446.1945067 403.7855885 367.1202688 291.1445793 318.7008316 622.6303396 466.0902133 517.0699127 432.0413204 263.228866 1.695081977 1.533971538 1.394680889 1.106051109 1.210736635 2.365357375 1.770665278 1.964335905 1.64131437 1 8.040173895 -4 0.050353227 8.75E-14 4.540193878 0.190700809 0.354212892 378.6678655 1.453836421 31.1794965 134.1229094 1.00E-04 4 4.540193878 AVLIDK(ac)DQSPK ddPTM_HeLa_Romidepsin_16h_R1 2 AVLIDKDQSPK 11 1 B9A058;Q6NVY1 B9A058 HIBCH "3-hydroxyisobutyryl-CoA hydrolase, mitochondrial" 0 1 ; AVLIDK(1)DQSPK;AVLIDK(1)DQSPK 212.28 6.39E-20 3873100 2758.9 2777.1 2647.6 2342.5 3318.1 3620.9 3053.6 3616.1 3031.6 2483.2 FALSE TRUE FALSE 2725.273466 2816.196087 2693.680367 2613.350872 3148.764975 3389.536176 3312.972708 3720.726148 2760.446103 2418.686106 1.126757812 1.164349553 1.113695721 1.080483683 1.301849367 1.401395645 1.369740662 1.538325349 1.141299855 1 11.24000784 -4 0.237439529 1.012546349 4.176544987 0.83828352 0.064888426 10.94798756 0.134591634 0.036834832 13.75228606 1.00E-04 4 3.163998638 AVLS(ph)DSPQLSEGK ddPTM_HeLa_Romidepsin_16h_R1 1 AVLSDSPQLSEGK 13 0 Q5VY60;Q7Z4H7-3;Q7Z4H7;Q5SYF9;Q7Z4H7-2 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 AVLS(0.853)DS(0.147)PQLSEGK 206.45 1.08E-16 63515000 6331.8 6203.5 6029.5 4876.4 6486.5 6661.9 6734.3 7102 6511.5 5925.7 TRUE FALSE FALSE 6254.625586 6290.833036 6134.440918 5440.232312 6155.469701 6236.22609 7306.311274 7307.485165 5929.095132 5771.74946 1.083662004 1.089935223 1.062839086 0.942562104 1.066482484 1.08047415 1.265874641 1.266078026 1.027261348 1 12.49479296 -7.811413747 3.404177068 1.0409043 1.27281365 0.823561159 0.041393024 0.07568216 1.757136231 0.006704555 0.025302945 1.54E-08 7.811413747 0.231909349 AVLSAEQLRDEEVHAGLGELLR ddPTM_HeLa_Romidepsin_16h_R1 2 AVLSAEQLRDEEVHAGLGELLR 22 1 P50454;E9PPV6;E9PR70;E9PK86;E9PMI5;E9PQ34;E9PJH8;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 0 ; ; 97.08 0.00013749 45360000 9093.5 8169.4 8257.5 8435.4 8067.4 7871.2 6662 7045.8 9057.3 7772.5 FALSE FALSE TRUE 8982.664924 8284.409028 8401.218324 9410.740638 7655.690474 7368.255723 7227.870114 7249.659107 8247.192404 7570.56933 1.186524359 1.094291415 1.109720809 1.243069078 1.011243691 0.973276302 0.954732702 0.95761082 1.089375454 1 12.88618608 -8.535321748 24.99707678 1.103140154 0.966342657 0.57621512 0.061433789 177.2769248 356135.432 0.011940074 0.023892187 2.92E-09 8.535321748 -0.136797497 AVLSDS(ph)PQLSEGK ddPTM_HeLa_Romidepsin_16h_R1 1 AVLSDSPQLSEGK 13 0 Q5VY60;Q7Z4H7-3;Q7Z4H7;Q5SYF9;Q7Z4H7-2 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 AVLS(0.039)DS(0.961)PQLSEGK 194.77 4.37E-11 63245000 5799.6 5488.4 4517.2 4158.7 5412.9 5555.3 5259 5318.5 5193.6 4902.5 TRUE FALSE FALSE 5728.912244 5565.665839 4595.819971 4639.548461 5136.659515 5200.334259 5705.699329 5472.382406 4729.071408 4775.132343 1.199738946 1.165552165 0.962448712 0.971606257 1.075710398 1.089045054 1.194877737 1.146016909 0.990353998 1 12.221325 -12.68496376 1.573031964 1.000307961 1.112696485 0.206838762 0.079314902 0.562505197 2.518843648 0.064568622 0.014529409 2.07E-13 12.68496376 0.112388524 AVLVDLEPGTMDSVR ddPTM_HeLa_Romidepsin_16h_R1 1 AVLVDLEPGTMDSVR 15 0 P04350;M0R0X0;M0QY85;M0QY37;M0QX14;M0QZL7;M0R278;A0A075B724;P68371;Q3ZCM7 P04350;P68371 TUBB4A;TUBB8;TUBB4B Tubulin beta-4A chain;Tubulin beta-4B chain;Tubulin beta-8 chain 0 0 161.93 7.31E-07 1081000 422.35 362.35 270.04 336.9 334.05 338.17 283.32 469 244.72 205.31 FALSE FALSE TRUE 417.2022357 367.4511728 274.7399329 375.8539632 317.002182 316.5620284 307.3851937 482.569775 222.8316303 199.9760166 2.086261357 1.837476209 1.373864414 1.879495199 1.585201002 1.582999971 1.537110294 2.413138251 1.114291774 1 7.643683176 -12.45432537 1.163324045 0.995809765 1.78792186 0.509296683 0.285996488 0.317606196 0.762395425 0.203767046 0.049457746 3.51E-13 12.45432537 0.792112094 AVNTQALS(ph)GAGILR ddPTM_HeLa_Romidepsin_16h_R1 2 AVNTQALSGAGILR 14 0 O60749-2;O60749 O60749-2 SNX2 Sorting nexin-2 1 0 AVNTQALS(1)GAGILR;AVNT(0.001)QALS(0.999)GAGILR ; 147.7 0.00061725 24391000 2990.2 2650.1 3131.6 3402.7 4180.3 4218.5 3533.6 4105.2 3040.4 2588.2 TRUE FALSE FALSE 2953.754292 2687.408177 3186.104184 3796.136184 3966.963692 3948.951465 3833.743896 4223.977485 2768.459009 2520.958191 1.171679206 1.066026476 1.263846499 1.505830679 1.573593607 1.566448614 1.520748702 1.675544442 1.09817728 1 11.29975648 -9.377962977 1.762198954 1.07938394 1.582182653 0.947001633 0.054561161 0.069718029 0.424949105 0.011735727 0.019955277 4.19E-10 9.377962977 0.502798713 AVPETEDVQASVSDTAQQPSEEQSKS(ph)LEKPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVPETEDVQASVSDTAQQPSEEQSKSLEKPK 31 2 Q6FIF0-2;Q6FIF0;H0YME2;H0YK21;H0YK54 Q6FIF0-2 ZFAND6 AN1-type zinc finger protein 6 1 0 AVPETEDVQASVS(0.001)DT(0.002)AQQPS(0.027)EEQS(0.194)KS(0.777)LEKPK 85.407 9.09E-09 17080000 2415.9 1895.7 1920.4 2185.6 2910.6 2569.5 2699.7 3138.2 2328.5 1767.2 TRUE FALSE FALSE 2386.454082 1922.387714 1953.823756 2438.309356 2762.061221 2405.317243 2929.012451 3228.998866 2120.233128 1721.287889 1.386435178 1.116831023 1.135094117 1.416561036 1.60464803 1.397393927 1.701640074 1.875920284 1.231771362 1 10.7492727 -4 0.199242746 1.056867219 4.787288353 0.758821643 0.129626516 21.00449692 0.240508914 0.144762689 24.6224783 1.00E-04 4 3.730421134 AVPIAVADEGES(ph)ESEDDDLKPR ddPTM_HeLa_Romidepsin_16h_R1 2 AVPIAVADEGESESEDDDLKPR 22 1 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 0 AVPIAVADEGES(0.697)ES(0.303)EDDDLKPR;AVPIAVADEGES(0.969)ES(0.031)EDDDLKPR ; 100.92 8.64E-05 69985200 1764.82 1569.59 1626.86 1583.56 1926.35 2775.6 2457.1 2579.8 1846.08 1900.63 TRUE FALSE FALSE 1743.309695 1591.686729 1655.174816 1766.658658 1828.041171 2598.248118 2665.806013 2654.442443 1680.961981 1851.251359 0.941692595 0.859789635 0.894084322 0.954305124 0.987462433 1.403509094 1.440002191 1.433863873 0.908013908 1 10.85428508 -8.262157439 4.285218341 0.955191696 1.434619492 0.966864453 0.041587596 0.030017448 1.396762617 0.007058109 0.01767706 5.47E-09 8.262157439 0.479427796 AVPMAPAPAS(ph)PGSSNDSSAR ddPTM_HeLa_Romidepsin_16h_R1 6 AVPMAPAPASPGSSNDSSAR 20 0 Q66K74-2;Q66K74 Q66K74-2 MAP1S Microtubule-associated protein 1S;MAP1S heavy chain;MAP1S light chain 1 0 AVPMAPAPAS(0.965)PGS(0.023)S(0.011)NDSSAR;AVPMAPAPAS(0.945)PGS(0.042)S(0.013)NDSSAR;AVPMAPAPAS(0.622)PGS(0.29)S(0.086)NDS(0.001)SAR;AVPMAPAPAS(0.958)PGS(0.032)S(0.01)NDSSAR;AVPMAPAPAS(0.973)PGS(0.021)S(0.005)NDSSAR;AVPMAPAPAS(0.959)PGS(0.031)S(0.007)NDS(0.001)S(0.003)AR ;;;;; 144.17 2.58E-09 252621600 7185.24 6688.3 6538.64 6532.33 7761.6 8360.04 6743.02 8093.3 7529.73 6741.5 TRUE FALSE FALSE 7097.663531 6782.458063 6652.442286 7287.62873 7365.496589 7825.860425 7315.77195 8327.466866 6856.25209 6566.354858 1.080913792 1.03291068 1.013110383 1.109843876 1.121702489 1.191811986 1.11412985 1.268202381 1.044148883 1 12.680877 -4 0.243133155 1.015806438 2.377703192 0.762385838 0.038681321 17.75986443 0.219916911 0.023716637 9.913593165 1.00E-04 4 1.361896754 AVPPVS(ph)PELR ddPTM_HeLa_Romidepsin_16h_R1 2 AVPPVSPELR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 AVPPVS(1)PELR;AVPPVS(1)PELR ; 131.42 0.0067711 338320000 17614.9 18116 15991.3 13726.7 14584.5 13449.1 11848.1 12558.6 18707.8 17277.9 TRUE FALSE FALSE 17400.20282 18371.03752 16269.62187 15313.84564 13840.19854 12589.74591 12854.47732 12921.96328 17034.52751 16829.01767 1.033940493 1.091628631 0.966760044 0.909966698 0.822400856 0.748097492 0.763828143 0.767838238 1.012211636 1 14.03866335 -8.917353771 1.518361982 1.021728783 0.759312205 0.946230518 0.027975594 0.064823397 0.299643045 0.004855837 0.010762886 1.21E-09 8.917353771 -0.262416577 AVPS(ph)SPAGSAAR ddPTM_HeLa_Romidepsin_16h_R1 1 AVPSSPAGSAAR 12 0 F8WBN8;B0QYH1;Q8IWD4-4;Q8IWD4-3;Q8IWD4 F8WBN8 CCDC117 Coiled-coil domain-containing protein 117 1 0 AVPS(0.5)S(0.5)PAGSAAR 142.76 0.0016153 34282000 2417.2 2381.4 2004.5 2245.4 3070.7 2532 1979.2 2099.9 2391.9 2572.3 TRUE FALSE FALSE 2387.738237 2414.925412 2039.387482 2505.023713 2913.990721 2370.213372 2147.313199 2160.657293 2177.962473 2505.471275 0.953009624 0.963860746 0.813973603 0.999821366 1.16305094 0.946014985 0.857049618 0.8623756 0.869282556 1 11.29086628 -7.837165217 4.822013414 0.978519139 0.859485943 0.177875983 0.086691263 0.202587216 8.519177908 0.011340754 0.036842603 1.45E-08 7.837165217 -0.119033196 AVPSS(ph)PAGSAAR ddPTM_HeLa_Romidepsin_16h_R1 1 AVPSSPAGSAAR 12 0 F8WBN8;B0QYH1;Q8IWD4-4;Q8IWD4-3;Q8IWD4 F8WBN8 CCDC117 Coiled-coil domain-containing protein 117 1 0 AVPS(0.015)S(0.985)PAGS(0.001)AAR 143.55 0.0015301 42227000 2060 2307.9 1862.4 1844.8 2501.8 2197.2 1629.1 1706.2 2294.9 1975 TRUE FALSE FALSE 2034.891928 2340.390677 1894.814291 2058.104456 2374.12381 2056.806011 1767.475713 1755.566205 2089.638396 1923.689215 1.057807005 1.216615791 0.984989818 1.069873678 1.234151438 1.069198702 0.918794834 0.912603861 1.086266108 1 10.90966003 -7.757908378 24.01250102 1.058404382 0.915699229 0.381804084 0.081094087 49.53953699 336864.8044 0.012015243 0.041557846 1.75E-08 7.757908378 -0.142705153 AVPVES(ph)PVQKV ddPTM_HeLa_Romidepsin_16h_R1 3 AVPVESPVQKV 11 1 Q8TB61-5;Q8TB61-4;Q8TB61-3;Q8TB61-2;Q8TB61 Q8TB61-5 SLC35B2 Adenosine 3-phospho 5-phosphosulfate transporter 1 1 0 AVPVES(1)PVQKV;AVPVES(1)PVQKV;AVPVES(1)PVQKV ;; 167.2 0.00078032 79125000 11244.9 12668.7 10617.1 9566.7 12333.7 14824.7 11204.3 14583.9 12213.1 11934.3 TRUE FALSE FALSE 11107.84283 12847.05029 10801.88617 10672.84687 11704.26527 13877.44951 12155.99296 15005.86214 11120.72975 11624.24517 0.955575409 1.105194368 0.929254848 0.918153972 1.006883896 1.193836616 1.045744716 1.290910672 0.956684033 1 13.50484942 -8.32729931 5.164687152 0.980627208 1.163714214 0.592109263 0.074145848 0.108872397 5.743158388 0.009787825 0.022553875 4.71E-09 8.32729931 0.183087006 AVQQHQHGYDS(ph)DEEVDSELGTWEHQLR ddPTM_HeLa_Romidepsin_16h_R1 1 AVQQHQHGYDSDEEVDSELGTWEHQLR 27 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 0 AVQQHQHGY(0.054)DS(0.913)DEEVDS(0.033)ELGTWEHQLR 101.92 1.18E-08 4286600 473.38 515.49 348.15 436.42 588 675.1 592.27 646.64 623.24 605.75 TRUE FALSE FALSE 467.6102625 522.7470818 354.2094047 486.8809338 557.9921659 631.9632888 642.577399 665.3495082 567.4958535 590.0125277 0.792542939 0.88599319 0.600342176 0.8252044 0.945729353 1.071101475 1.089091111 1.127687086 0.961836956 1 9.204601777 -8.339785523 2.678005635 0.868851689 1.10233941 0.534025377 0.103738136 0.216290813 3.009573369 0.018038641 0.047320407 4.57E-09 8.339785523 0.233487721 AVQTRPVLQPQPGS(ph)LNSSIWDGSEVLR ddPTM_HeLa_Romidepsin_16h_R1 1 AVQTRPVLQPQPGSLNSSIWDGSEVLR 27 1 Q86TB9;Q86TB9-4 Q86TB9 PATL1 Protein PAT1 homolog 1 1 0 AVQTRPVLQPQPGS(0.797)LNS(0.164)S(0.031)IWDGS(0.008)EVLR 74.63 3.15E-05 6791100 395.01 360.86 398.93 435.89 243.65 382.51 130.26 213.1 295.7 187.22 TRUE FALSE FALSE 390.1954662 365.9401966 405.8732093 486.2896527 231.2156313 358.0688455 141.3242811 219.2657123 269.2518514 182.3559974 2.139745727 2.006735187 2.225719006 2.666705015 1.267935437 1.963570437 0.774991134 1.202404722 1.476517665 1 7.510613838 -5.807373843 10.14681043 1.636640429 1.238900888 0 0.583344562 0 0 0.088055493 0 1.56E-06 5.807373843 -0.397739541 AVS(ph)PAVPFSR ddPTM_HeLa_Romidepsin_16h_R1 1 AVSPAVPFSR 10 0 I3L2J0 I3L2J0 CIC 1 0 AVS(0.989)PAVPFS(0.011)R 96.756 0.028744 49813000 4305.7 4489.5 3713.7 2341.9 2852.4 2650 2212.8 2237.4 4569.1 4122.9 TRUE FALSE FALSE 4253.220472 4552.703299 3778.335391 2612.681497 2706.831384 2480.673552 2400.755177 2302.135639 4160.428252 4015.786464 1.059125158 1.13370154 0.940870593 0.650602695 0.674047639 0.617730443 0.597829391 0.573271428 1.036018297 1 11.97146684 -9.311765099 3.038395991 1.036985906 0.618091299 0.960688707 0.042046314 0.03996224 0.735894072 0.007392923 0.012013076 4.88E-10 9.311765099 -0.418894606 AVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_HeLa_Romidepsin_16h_R1 1 AVSPLLLTTTNSSEGLSMGNYIGLINR 27 0 C9JZT2;P19525-2;P19525 C9JZT2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 0 AVS(0.949)PLLLT(0.006)T(0.006)T(0.016)NS(0.016)S(0.006)EGLS(0.001)MGNYIGLINR 58.838 0.0010139 6828500 865.21 706.87 801.05 661.57 703.65 588.89 463.65 503.25 912.75 663.58 TRUE FALSE FALSE 854.6644877 716.8213344 814.9919392 738.0638362 667.7401148 551.2618296 503.0324194 517.8107448 831.111354 646.3400959 1.322313892 1.109046675 1.260933593 1.141912502 1.033109533 0.852897465 0.77827822 0.801142847 1.285873117 1 9.336149682 -8.361821661 1.956559433 1.160977059 0.788692173 0.776369501 0.090084431 0.16880896 1.244073465 0.018232124 0.053192711 4.35E-09 8.361821661 -0.372284886 AVS(ph)PPHLDGPPSPR ddPTM_HeLa_Romidepsin_16h_R1 2 AVSPPHLDGPPSPR 14 0 P29590-12;P29590-11;H3BT57;P29590-13;H3BUJ5;H3BRN3;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;H3BVD2;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 AVS(1)PPHLDGPPSPR;AVS(1)PPHLDGPPSPR ; 86.411 0.010187 10406300 3318.6 2671.7 2409.17 2087.88 3530 3748.9 3972 3602.3 3759.1 2707.6 TRUE FALSE FALSE 3278.151627 2709.312263 2451.100593 2329.290509 3349.850928 3509.357389 4309.381581 3706.526867 3422.876681 2637.256162 1.243016008 1.027322375 0.929413164 0.883224976 1.270203091 1.330685066 1.634039819 1.405448178 1.29789314 1 11.36482199 -8.253433481 2.219097555 1.081606741 1.508314317 0.61438889 0.139874894 0.159744692 1.517005796 0.020998191 0.063178415 5.58E-09 8.253433481 0.426707577 AVS(ph)VY(ph)RT(ph)S(ph)NQAYGSRAPTVHEMPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSVYRTSNQAYGSRAPTVHEMPK 24 2 Q5BN46 Q5BN46 C9orf116 UPF0691 protein C9orf116 4 0 AVS(0.988)VY(0.987)RT(0.988)S(0.99)NQAY(0.029)GS(0.011)RAPT(0.007)VHEMPK 47.392 0.0043451 0 280.57 367.46 333.1 422.46 373.13 379.84 290.35 335.21 375.34 362.86 TRUE FALSE FALSE 277.1503049 372.6331115 338.8974658 471.3068129 354.0877838 355.5694499 315.0123218 344.9087725 341.7686503 353.4328449 0.784166805 1.054325077 0.958873717 1.333511641 1.001853079 1.006045293 0.891293286 0.975882059 0.966997423 1 8.465292307 -10.23200403 24.80487964 0.89807876 1.032958838 0.150654242 0.122233207 826.4041395 696404.1392 0.022539381 0.027602782 5.86E-11 10.23200403 0.134880077 AVSEDVSNGSSGS(ph)PSPGDTLPWNLGK ddPTM_HeLa_Romidepsin_16h_R1 2 AVSEDVSNGSSGSPSPGDTLPWNLGK 26 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 0 AVSEDVSNGS(0.001)S(0.019)GS(0.604)PS(0.373)PGDT(0.003)LPWNLGK;AVSEDVSNGS(0.012)S(0.123)GS(0.776)PS(0.067)PGDT(0.022)LPWNLGK ; 140.45 1.08E-07 13326500 6399.5 6445 5935.6 6094.1 7601.6 8243 6952.6 8034 6605.4 6141.7 TRUE FALSE FALSE 6321.500433 6535.732879 6038.906628 6798.728516 7213.661987 7716.298903 7543.15367 8266.451114 6014.59648 5982.137749 1.056729333 1.092541355 1.009489731 1.136504842 1.205866914 1.289889873 1.260946168 1.381855695 1.005425942 1 12.54644542 -8.321295802 0.57817745 1.020367511 1.410996603 0.922904389 0.035527062 0.280067014 0.124323214 0.007551558 0.058795506 4.77E-09 8.321295802 0.390629092 AVSLDS(ph)PVSVGSSPPVK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 AVS(0.098)LDS(0.602)PVS(0.023)VGS(0.191)S(0.086)PPVK 103.66 0.0027765 14805000 4134 4994.5 3820.1 3066 7163.8 6210.6 4423.5 6655 4119.3 4461.6 TRUE FALSE FALSE 4083.613218 5064.812702 3886.587238 3420.505346 6798.204554 5813.762704 4799.23198 6847.551925 3750.859491 4345.686989 0.939693362 1.165480329 0.894355081 0.787103479 1.564356699 1.337823621 1.104366696 1.575712181 0.863122333 1 12.08536855 -8.762456621 24.99998399 0.969065261 1.370640568 0.668401286 0.155522832 12.78224449 314152.7546 0.021127696 0.039942661 1.73E-09 8.762456621 0.401575307 AVSLDSPVS(ph)VGSSPPVK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 AVSLDS(0.115)PVS(0.658)VGS(0.225)S(0.001)PPVK 186.42 9.58E-12 0 1834 2263.7 1946.4 1986.1 3182.3 3728.8 2720.2 3304.9 2047.3 2010.6 TRUE FALSE FALSE 1811.646503 2295.568428 1980.276276 2215.742227 3019.895356 3490.541714 2951.25372 3400.522067 1864.18436 1958.364322 0.925081448 1.172186606 1.011188906 1.131424936 1.542049823 1.782376075 1.506999329 1.736409323 0.951908866 1 10.93543346 -8.78909493 2.462577831 0.986231503 1.664523035 0.914524768 0.0923925 0.054171079 0.670675212 0.013931737 0.028987714 1.63E-09 8.78909493 0.678291531 AVSLDSPVSVGS(ph)SPPVK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 AVSLDSPVSVGS(0.966)S(0.033)PPVK 192.54 2.08E-16 0 2025.3 1481.4 2259.4 2111.2 3372.9 3626 3546.3 3136.8 1741.5 1919.1 TRUE FALSE FALSE 2000.614865 1502.255188 2298.723909 2355.306877 3200.768327 3394.310302 3847.522633 3227.558359 1585.735878 1869.241505 1.07028164 0.803670999 1.229762929 1.260033479 1.712335361 1.81587574 2.05833362 1.726667394 0.848331194 1 10.86823726 -8.821341171 1.493694729 1.020676671 1.901628926 0.903271854 0.130673625 0.071584255 0.321480937 0.017411966 0.041257502 1.51E-09 8.821341171 0.880952255 AVSLDSPVSVGSS(ph)PPVK ddPTM_HeLa_Romidepsin_16h_R1 2 AVSLDSPVSVGSSPPVK 17 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 AVSLDS(0.032)PVS(0.058)VGS(0.194)S(0.717)PPVK;AVSLDSPVS(0.022)VGS(0.211)S(0.767)PPVK ; 136.57 0.00125 63083000 5960.8 4340.1 5845 5277.7 7845.9 9287.2 8945.3 8547.8 6370.6 5330.2 TRUE FALSE FALSE 5888.147477 4401.200042 5946.729773 5887.932506 7445.494446 8693.777893 9705.113559 8795.117107 5800.797581 5191.720636 1.134141817 0.847734374 1.145425609 1.134100411 1.434109223 1.674546553 1.869344335 1.694065942 1.117316972 1 12.34199704 -8.526725454 1.572367567 1.05036625 1.789030707 0.921629027 0.090466823 0.072334749 0.35047854 0.013896832 0.039804595 2.97E-09 8.526725454 0.738664456 AVSPPHLDGPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 AVSPPHLDGPPSPR 14 0 P29590-12;P29590-11;H3BT57;P29590-13;H3BUJ5;H3BRN3;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;H3BVD2;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR;AVSPPHLDGPPS(1)PR ;;; 122.5 0.0015922 74370000 13699.7 12363.3 12706.8 11351.8 16355.9 16985.7 15952 16640.1 16424.6 14693.6 TRUE FALSE FALSE 13532.72279 12537.35086 12927.95652 12664.34853 15521.19739 15900.36859 17306.96248 17121.55504 14955.54264 14311.85815 0.945560153 0.876011397 0.903303847 0.884884995 1.084499107 1.110992606 1.209274316 1.196319503 1.044975605 1 13.80492337 -8.353017949 1.967921556 0.95466615 1.192213953 0.774467344 0.055831557 0.120402349 0.897057121 0.00830998 0.024348409 4.44E-09 8.353017949 0.237547804 AVSPT(ph)EPTPR ddPTM_HeLa_Romidepsin_16h_R1 1 AVSPTEPTPR 10 0 H3BMH3;Q6PJI9-3;Q6PJI9;Q6PJI9-2 H3BMH3 WDR59 WD repeat-containing protein 59 1 0 AVS(0.334)PT(0.665)EPTPR 123.62 0.020705 14943000 2021.9 2144.6 1797.1 2274.7 2247.3 2694.4 1796.1 2200.1 2440.6 2377.7 TRUE FALSE FALSE 1997.256305 2174.791735 1828.377772 2537.711517 2132.611895 2522.236536 1948.660689 2263.756422 2222.306623 2315.927011 0.862400367 0.939058841 0.789479877 1.095764894 0.920845901 1.089082913 0.841417143 0.977473129 0.959575415 1 11.17737407 -9.249890041 24.98456804 0.923815488 0.979172091 0.143074425 0.087857056 1588.662756 3436738.607 0.013618297 0.02246674 5.62E-10 9.249890041 0.055356602 AVSTVVVTT(ph)APSPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSTVVVTTAPSPK 14 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 0 AVS(0.008)T(0.037)VVVT(0.058)T(0.865)APS(0.032)PK 106.55 0.014805 38160000 5577.7 6175.9 6315.6 6237.8 4745.3 5267.6 4157.8 4572.4 6493.7 5851.6 TRUE FALSE FALSE 5509.716847 6262.844482 6425.520369 6959.043786 4503.129634 4931.01736 4510.963428 4704.69518 5912.887208 5699.574588 0.966689138 1.098826655 1.127368415 1.220976001 0.790081709 0.865155335 0.791456162 0.825446725 1.03742606 1 12.47663853 -8.717285773 24.9999972 1.020169221 0.81950196 0.682651324 0.080832293 82.03161078 46446.33859 0.013350745 0.026701381 1.92E-09 8.717285773 -0.200667262 AVSTVVVTTAPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 AVSTVVVTTAPSPK 14 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 0 AVSTVVVT(0.003)T(0.311)APS(0.686)PK 189.09 5.61E-11 44142000 4920.4 4864.7 4458 4269.1 3327.9 3359 3241.9 3704 4837.8 4650.3 TRUE FALSE FALSE 4860.428272 4933.185374 4535.58962 4762.713429 3158.064845 3144.370741 3517.266905 3811.169396 4405.095052 4529.484536 1.073064326 1.089127325 1.001347854 1.051491266 0.697223894 0.694200569 0.776526971 0.841413491 0.972537828 1 12.14513116 -8.766213246 24.99999614 1.038156941 0.749915863 0.877294946 0.051060434 27.7352803 145246.2562 0.007621609 0.014143665 1.71E-09 8.766213246 -0.288241079 AVT(ph)PPVKDDNEDVFSAR ddPTM_HeLa_Romidepsin_16h_R1 1 AVTPPVKDDNEDVFSAR 17 1 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 0 AVT(1)PPVKDDNEDVFSAR 80.508 0.009957 17484000 2334.4 2272.6 2203 2036.2 2709.3 2718.2 2222.6 2655.7 2542.4 2114.7 TRUE FALSE FALSE 2305.947435 2304.593722 2241.342291 2271.635025 2571.034311 2544.515793 2411.387589 2732.538489 2315.001376 2059.759789 1.119522503 1.118865284 1.088157125 1.102864051 1.24822046 1.235345891 1.170713013 1.326629689 1.123918133 1 11.00826038 -4 0.112207548 0.930598038 2.007503493 0.611401336 0.055605036 33.96987831 0.266025664 0.251733592 5.699189246 1.00E-04 4 1.076905455 AVT(ph)PSSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTPSSEAK 9 0 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4;F8W0B5 Q99700 ATXN2 Ataxin-2 1 0 AVT(0.899)PS(0.097)S(0.004)EAK 123.11 0.024361 41177000 6918.9 7100.1 10618 7720.6 6700.8 7334.2 10420 1665.8 10636 8703.2 TRUE FALSE FALSE 6834.569786 7200.055394 10802.80184 8613.292099 6358.833172 6865.56829 11305.07454 1713.997295 9684.689522 8477.089609 0.806240125 0.84935464 1.274352677 1.016067129 0.750119848 0.809896864 1.333603284 0.202191716 1.142454541 1 13.04935332 -7.240486134 24.84146327 0.938538274 0.202190923 0.575029143 0.199430308 2776.034227 3291123.032 0.025690803 1.554916031 5.75E-08 7.240486134 -0.736347352 AVT(ph)PSSEAKDSR ddPTM_HeLa_Romidepsin_16h_R1 1 AVTPSSEAKDSR 12 1 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4;F8W0B5 Q99700 ATXN2 Ataxin-2 1 0 AVT(0.986)PS(0.014)SEAKDSR 126.32 0.022515 3748900 1327.6 1428.8 695.68 3695.9 1204.8 841.73 925.42 837.81 1528.8 1116.1 TRUE FALSE FALSE 1311.418701 1448.914684 707.7880186 4123.237348 1143.31456 787.9461696 1004.025152 862.0507105 1392.060299 1087.103561 1.206342015 1.33282121 0.651076902 3.792865275 1.051707124 0.724812426 0.923578201 0.792979382 1.280522251 1 10.08627367 -5.750960326 11.97398967 1.203133422 1.081677195 0 0.870267618 0 0 0.109485553 0 1.77E-06 5.750960326 -0.121456226 AVT(ph)PVPTKTEEVSNLK ddPTM_HeLa_Romidepsin_16h_R1 4 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 0 AVT(0.899)PVPT(0.048)KT(0.048)EEVS(0.006)NLK;AVT(1)PVPTKTEEVSNLK;AVT(0.983)PVPT(0.014)KT(0.003)EEVSNLK;AVT(0.632)PVPT(0.361)KT(0.007)EEVSNLK ;;; 143.28 0.0013875 1035394000 23090.6 21950.3 18481.3 26233.4 15440.5 12572.8 12298 13240.2 22022.6 19868.2 TRUE FALSE FALSE 22809.16289 22259.3169 18802.95927 29266.62914 14652.51367 11769.43866 13342.59181 13623.2843 20052.8435 19352.0213 1.178644987 1.150232141 0.971627665 1.512329316 0.757156756 0.608176194 0.689467607 0.703972163 1.036214419 1 14.24019664 -8.547600615 24.90691919 1.110190532 0.671637283 0.699812931 0.144986139 89.52825619 90198.05311 0.020518802 0.041038885 2.83E-09 8.547600615 -0.438553249 AVT(ph)PVSQGSNSSSADPK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTPVSQGSNSSSADPK 17 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 AVT(0.959)PVS(0.041)QGSNSSSADPK 212.69 3.30E-26 21969000 19003 18608 18301 19154 19511 17811 14882 15955 17610 18196 TRUE FALSE FALSE 18771.38413 18869.96391 18619.52123 21368.6756 18515.28086 16672.93458 16146.07671 16416.63275 16034.91749 17723.2653 1.059138021 1.064700189 1.050569459 1.205685027 1.044687903 0.940737178 0.91101027 0.926275857 0.904738333 1 14.11335681 -8.224931412 4.63683428 1.047864196 0.921807743 0.39083311 0.069515803 0.140303255 7.334357418 0.008543551 0.02205862 5.96E-09 8.224931412 -0.126056453 AVTELNEPLSNEDR ddPTM_HeLa_Romidepsin_16h_R1 1 AVTELNEPLSNEDR 14 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 0 230.81 5.33E-33 3865700 1437.2 1144 1172.2 958.1 838.98 1210.7 1031.3 1071.4 1334.4 1554.2 FALSE FALSE TRUE 1419.682854 1160.105262 1192.601649 1068.88003 796.1637199 1133.340177 1118.898596 1102.399269 1215.047922 1513.82166 0.937813807 0.766342095 0.787808552 0.70608055 0.525929666 0.748661621 0.739121804 0.728222682 0.802636106 1 10.56397954 -10.13513791 1.180794367 0.981190404 0.690399765 0.510188778 0.085453979 0.13874851 0.374626204 0.01319619 0.016608383 7.33E-11 10.13513791 -0.290790639 AVTEQGAELSNEER ddPTM_HeLa_Romidepsin_16h_R1 2 AVTEQGAELSNEER 14 0 E9PG15;P27348 E9PG15 YWHAQ 14-3-3 protein theta 0 0 ; ; 305.3 4.90E-131 35041000 2919.6 2941 2526.9 2699.5 2979.3 3007.3 2924.1 2708.7 3464.5 3224.9 FALSE FALSE TRUE 2884.014792 2982.403475 2570.879635 3011.628892 2827.255204 2815.143236 3172.472981 2787.071961 3154.626443 3141.116633 0.91814954 0.949472377 0.818460419 0.958776525 0.900079664 0.896223721 1.009982548 0.887287002 1.004300958 1 11.6170618 -12.07059598 0.752019282 1.002583607 0.917816982 0.33210749 0.04785221 0.700746327 0.690773408 0.035106003 0.009387347 8.50E-13 12.07059598 -0.084766625 AVTEQGHELSNEER ddPTM_HeLa_Romidepsin_16h_R1 2 AVTEQGHELSNEER 14 0 P31946-2;P31946;Q4VY20;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 0 ; ; 216.54 1.44E-24 83945000 8959.9 7559.1 7156.2 8010.1 9373.5 10909.9 8554.2 9332 9414.6 8816.5 FALSE FALSE TRUE 8850.693292 7665.517208 7280.750659 8936.265451 8895.135318 10212.7926 9280.793534 9602.006697 8572.534597 8587.446059 1.030654892 0.892642254 0.847836552 1.040619689 1.035830124 1.189270073 1.08073966 1.11814463 0.998263574 1 13.06801342 -8.545379571 2.885549288 0.992313611 1.12413899 0.534984627 0.064469586 0.199435481 3.366549805 0.010407508 0.023724126 2.85E-09 8.545379571 0.131825379 AVTGQTTQVS(ph)PPVIAGR ddPTM_HeLa_Romidepsin_16h_R1 2 AVTGQTTQVSPPVIAGR 17 0 Q6MZP7;Q6MZP7-3 Q6MZP7 LIN54 Protein lin-54 homolog 1 0 AVTGQT(0.003)T(0.004)QVS(0.994)PPVIAGR;AVTGQTTQVS(1)PPVIAGR ; 186.17 1.01E-11 9530700 1520.65 1548.56 1622.11 1653.86 1786.57 2157.61 1995.03 1704.6 1221.4 1440.11 TRUE FALSE FALSE 1502.115733 1570.360668 1650.342144 1845.087075 1695.394666 2019.745684 2164.487798 1753.919912 1112.154925 1402.695735 1.070877808 1.119530508 1.17655034 1.31538653 1.208668868 1.43990292 1.543091452 1.250392276 0.792869685 1 10.45398639 -9.263625472 0.630736956 1.018626878 1.43260789 0.712922996 0.109800494 0.25303176 0.194512019 0.01799068 0.047649306 5.45E-10 9.263625472 0.413981012 AVTIANS(ph)PSKPSEK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTIANSPSKPSEK 14 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 0 AVT(0.002)IANS(0.528)PS(0.338)KPS(0.132)EK 63.46 0.028249 155690000 6352.5 5792 6160 3350.7 3937.4 3207.9 3069.4 2938.1 6213.1 5802.2 TRUE FALSE FALSE 6275.073287 5873.539928 6267.212216 3738.1237 3736.459786 3002.925543 3330.114759 3023.109288 5657.384775 5651.458008 1.11034591 1.039296394 1.108954929 0.661444125 0.661149703 0.531354128 0.589248784 0.534925551 1.001048715 1 12.4644074 -9.178152452 3.933213858 1.056460437 0.584775275 0.953204141 0.050692033 0.038609852 1.124648956 0.008770935 0.014826088 6.64E-10 9.178152452 -0.471685162 AVTIANS(ph)PSKPSEKDSVVSLESQK ddPTM_HeLa_Romidepsin_16h_R1 2 AVTIANSPSKPSEKDSVVSLESQK 24 2 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 1 0 AVT(0.007)IANS(0.801)PS(0.186)KPS(0.006)EKDSVVSLESQK;AVT(0.006)IANS(0.355)PS(0.355)KPS(0.28)EKDS(0.003)VVSLESQK ; 70.959 0.00043873 302590000 7692.9 7251.3 6960.4 7708.9 5218.9 4504.8 4363.7 4212 7547.4 6998.8 TRUE FALSE FALSE 7599.135976 7353.383992 7081.542842 8600.239289 4952.560059 4216.957819 4734.352569 4333.867575 6872.341641 6816.970167 1.114738042 1.078688011 1.038810889 1.261592625 0.726504582 0.618597077 0.694495128 0.635746889 1.008122593 1 12.73491495 -8.640372006 6.396452769 1.068706772 0.657681391 0.886918189 0.072744353 0.051831463 2.710867482 0.010826744 0.021783266 2.29E-09 8.640372006 -0.411025381 AVTK(ac)AQK ddPTM_HeLa_Romidepsin_16h_R1 2 AVTKAQK 7 1 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 1 ; AVTK(1)AQK;AVTK(1)AQK 121.62 0.01679 22952000 1009.87 818.97 9119.9 2865.7 13627.5 17803.9 30631 3509 1423.27 597.44 FALSE TRUE FALSE 997.561316 830.4994812 9278.628034 3197.045718 12932.03782 16666.28825 33232.79638 3610.527379 1295.969167 581.9184227 1.714263163 1.427175097 15.9448948 5.493975776 22.22311121 28.64024853 57.10902951 6.204524961 2.227063307 1 9.18467311 -8.722968611 1.275895411 1.915898357 33.81722477 0.478748396 12.28099099 0.234258308 0.754640192 1.767470577 4.874403798 1.89E-09 8.722968611 31.90132641 AVTK(ac)AQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AVTKAQKK 8 2 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 2 ; AVTK(1)AQK(1)K;AVTK(1)AQK(1)K 138.4 0.0046544 200602000 2437.3 1922.47 17542.8 4297 20972.8 46113 39323 5025.2 2544.1 730.81 FALSE TRUE FALSE 2407.59325 1949.534583 17848.12508 4793.839358 19902.47976 43166.52812 42663.09464 5170.596234 2316.549324 711.8234508 3.382289874 2.738789486 25.07380876 6.734590371 27.95985399 60.64218321 59.93493834 7.263874529 3.254387477 1 9.475375653 -8.636825889 2.942860417 4.233574098 44.50228612 0.516671084 15.37199916 0.132508187 2.301427842 2.181985265 4.721919166 2.31E-09 8.636825889 40.26871202 AVTK(ac)VQK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTKVQK 7 1 Q5QNW6;Q5QNW6-2 Q5QNW6 HIST2H2BF Histone H2B type 2-F 0 1 AVTK(1)VQK 107.66 0.030429 29794000 656.27 351.98 2279.2 1961.9 4517.9 5083.2 9694.3 870.33 1053.2 627.06 FALSE TRUE FALSE 648.2711288 356.9351837 2318.86852 2188.744109 4287.334704 4758.399925 10517.7336 895.5116254 958.9991542 610.7688908 1.061401683 0.584403019 3.796638229 3.583588067 7.019569544 7.790835448 17.22048022 1.466203729 1.570150623 1 9.254482771 -8.835096369 1.227553757 1.05205734 9.711183905 0.442473858 3.638974074 0.2546805 0.761556035 0.526611353 1.360803734 1.46E-09 8.835096369 8.659126565 AVTK(ac)VQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AVTKVQKK 8 2 Q5QNW6;Q5QNW6-2 Q5QNW6 HIST2H2BF Histone H2B type 2-F 0 2 ; AVTK(1)VQK(1)K;AVTK(1)VQK(1)K 120.12 0.0029128 6326400 1558.73 1504.42 5204.7 2609.8 8810.1 14299.1 11266.3 5659.3 1708.28 708.36 FALSE TRUE FALSE 1539.731599 1525.599264 5295.28562 2911.557355 8360.487722 13385.43366 12223.25924 5823.042917 1555.487158 689.9567051 2.231635098 2.211152168 7.674808551 4.219913125 12.11740919 19.40039652 17.71598008 8.439722194 2.254470675 1 9.430362025 -8.887063979 1.347073132 1.817597377 15.64859093 0.735449336 3.269060039 0.14228444 0.515808148 0.512862962 1.218075017 1.30E-09 8.887063979 13.83099355 AVTK(ac)YTSAK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTKYTSAK 9 1 P06899 P06899 HIST1H2BJ Histone H2B type 1-J 0 1 AVTK(1)YTSAK 121.6 0.0057021 1048000 947.66 751.07 1262.9 1189.5 1515 1447.6 1518.4 915.51 912.2 562.77 FALSE TRUE FALSE 936.1095554 761.6435832 1284.880245 1327.035587 1437.683897 1355.103032 1647.372858 941.9988374 830.6105474 548.1491543 1.707764298 1.389482365 2.344033982 2.420938857 2.622796889 2.472142885 3.00533686 1.718508238 1.515300244 1 9.098424701 -10.21328831 0.530714096 1.113454794 2.57982744 0.59658013 0.385590829 0.312398195 0.20376698 0.128867909 0.15882699 6.12E-11 10.21328831 1.466372646 VNASASSLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VNASASSLKK 10 1 Q16658 Q16658 FSCN1 Fascin 0 1 VNASASSLK(1)K 110.84 0.0037499 1718700 496.95 549.5 762.3 641.28 1576.8 1648.8 1199.3 974.73 476.72 306.02 FALSE TRUE FALSE 490.8929823 557.2358754 775.5675117 715.4278109 1496.330012 1543.447001 1301.168512 1002.932275 434.0809692 298.0695563 1.646907482 1.869482688 2.601968216 2.400204234 5.020069915 5.178143721 4.365318378 3.364759176 1.45630763 1 8.219505221 -9.237064605 1.148861794 1.313987892 4.51897489 0.804041494 0.63707761 0.139309177 0.363028385 0.113984295 0.232638343 5.79E-10 9.237064605 3.204986998 AVTPVPT(ph)KTEEVSNLK ddPTM_HeLa_Romidepsin_16h_R1 1 AVTPVPTKTEEVSNLK 16 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 0 AVT(0.12)PVPT(0.703)KT(0.176)EEVS(0.001)NLK 74.296 0.018423 871930000 6948.4 6104.4 5749 7950.1 4625.9 4095.8 3274.2 3670.3 7170.3 5890 TRUE FALSE FALSE 6863.710228 6190.337903 5849.058933 8869.327968 4389.823061 3834.091599 3552.310466 3776.49434 6528.97041 5736.976951 1.196398432 1.079024364 1.019536767 1.545993307 0.76518053 0.668312185 0.619195527 0.658272531 1.138050661 1 12.48607501 -8.54350579 24.96199631 1.117571455 0.657502326 0.722094467 0.147201548 97.5884762 118097.1386 0.021676419 0.043356241 2.86E-09 8.54350579 -0.460069129 GQDGIGSK(ac)AEK ddPTM_HeLa_Romidepsin_16h_R1 2 GQDGIGSKAEK 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 1 ; GQDGIGSK(1)AEK;GQDGIGSK(1)AEK 128.85 0.01096 4310300 2473.6 2795.4 2717.3 3714.7 4733 5189.4 4463 4819.8 2932.5 2197.36 FALSE TRUE FALSE 2443.450812 2834.753715 2764.593467 4144.211092 4491.457349 4857.814088 4842.087109 4959.253309 2670.209855 2140.27227 1.141654193 1.324482756 1.291701764 1.936300885 2.098544849 2.269717809 2.262369688 2.317113284 1.247602883 1 11.06357862 -9.203175345 1.015327674 1.060529623 2.31674123 0.964699852 0.094862583 0.04668572 0.09507097 0.013689419 0.030058727 6.26E-10 9.203175345 1.256211607 up AVTTVTQSTPVPGPSVPPPEELQVS(ph)PGPR ddPTM_HeLa_Romidepsin_16h_R1 2 AVTTVTQSTPVPGPSVPPPEELQVSPGPR 29 0 P51610-2;P51610;H7C1C4 P51610-2 HCFC1 Host cell factor 1;HCF N-terminal chain 1;HCF N-terminal chain 2;HCF N-terminal chain 3;HCF N-terminal chain 4;HCF N-terminal chain 5;HCF N-terminal chain 6;HCF C-terminal chain 1;HCF C-terminal chain 2;HCF C-terminal chain 3;HCF C-terminal chain 4;HCF C-terminal chain 5;HCF C-terminal chain 6 1 0 AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR;AVTTVTQSTPVPGPSVPPPEELQVS(1)PGPR ; 158.99 4.56E-14 124591000 4514.96 4330.74 3898.4 3926 3983.99 3687.1 3363.43 3553.73 4611.7 4740.3 TRUE FALSE FALSE 4459.929931 4391.708271 3966.250017 4379.942592 3780.672124 3451.50621 3649.11966 3656.551571 4199.218002 4617.146323 0.965949446 0.951173726 0.859026277 0.948625468 0.818833076 0.747541007 0.790340917 0.79195055 0.909483414 1 12.17278574 -9.038587909 0.604036729 0.990609342 0.754877549 0.724824892 0.043863923 0.236469612 0.156905728 0.007910663 0.026543492 9.15E-10 9.038587909 -0.235731793 AVVGVVAGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 AVVGVVAGGGR 11 0 E9PKZ0;E9PKU4;P62917;E9PP36 E9PKZ0 RPL8 60S ribosomal protein L8 0 0 ; ; 157.21 0.0092754 8911600 3748.3 4164.4 3635.8 4096.3 4491.1 4498.5 3193.9 4124.2 4394.7 3485 FALSE FALSE TRUE 3702.614278 4223.026533 3699.079574 4569.93348 4261.902408 4211.060368 3465.189786 4243.52722 4001.627025 3394.459198 1.090781789 1.244094062 1.089740474 1.346292064 1.255546807 1.240568857 1.020837071 1.250133518 1.178870268 1 11.72896603 -10.64676779 1.005906599 1.02182106 1.208171703 0.136038408 0.101483422 0.307129968 0.645006737 0.021377025 0.020783737 2.26E-11 10.64676779 0.186350643 EIVEK(ac)SK ddPTM_HeLa_Romidepsin_16h_R1 1 EIVEKSK 7 1 A0A0D9SFT8;F6M2K2;Q14686 A0A0D9SFT8 NCOA6 Nuclear receptor coactivator 6 0 1 EIVEK(1)SK 111.74 0.019504 2431900 1560 1545.3 1659.8 3153 4220.9 4188.2 4109.2 3660.4 1742.5 1586.6 FALSE TRUE FALSE 1540.98612 1567.054774 1688.688123 3517.564695 4005.491723 3920.587537 4458.235345 3766.307899 1586.646436 1545.379903 0.997156826 1.014025594 1.092733327 2.276181208 2.591913946 2.53697329 2.884879851 2.437140467 1.026703164 1 10.59374583 -9.195626225 2.763099764 0.9972405 2.621590976 0.980121775 0.109013939 0.023405954 0.351255658 0.015676832 0.027012725 6.37E-10 9.195626225 1.624350476 up AVVQS(ph)PQVTEVL ddPTM_HeLa_Romidepsin_16h_R1 2 AVVQSPQVTEVL 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 AVVQS(1)PQVTEVL;AVVQS(0.672)PQVT(0.328)EVL ; 108.32 0.011515 11164400 5249.2 5261.8 4698.2 4422.1 7181.8 8923.2 7343.2 8300.8 4937.8 5318.6 TRUE FALSE FALSE 5185.220731 5335.875759 4779.9702 4933.404009 6815.285947 8353.036318 7966.931225 8540.970552 4496.150801 5180.422005 1.00092632 1.030007932 0.922698999 0.952317013 1.315585089 1.612423913 1.537892322 1.648701697 0.867912073 1 12.33885391 -8.532561997 2.814244107 0.993233264 1.592779469 0.959464581 0.058862824 0.027774857 0.443907975 0.006462411 0.014921752 2.93E-09 8.532561997 0.599546205 AVVS(ph)PPKFVFGSESVK ddPTM_HeLa_Romidepsin_16h_R1 1 AVVSPPKFVFGSESVK 16 1 P49792;J3KNE0;A6NKT7;F8VYC4;A0A286YES2;A0A1W2PNU4;P0DJD0;P0DJD1;Q7Z3J3 P49792;Q7Z3J3 RANBP2;RGPD3;RGPD1;RGPD2;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2;RanBP2-like and GRIP domain-containing protein 4 1 0 AVVS(1)PPKFVFGSESVK 136.26 0.0083679 47339000 2191.8 2076.9 1830.6 1962.3 2188.5 1808.3 1963 1742.8 2522.2 2064.7 TRUE FALSE FALSE 2165.085499 2106.138653 1862.460825 2189.190359 2076.812679 1692.755466 2129.737171 1793.225168 2296.608115 2011.058796 1.076589855 1.047278506 0.926109584 1.088576009 1.032696151 0.841723509 1.059012882 0.891682119 1.141989543 1 10.97373955 -8.433779708 25 1.033185162 0.942556684 0.316847121 0.074748353 66.00927612 18519.41464 0.009064674 0.020269227 3.68E-09 8.433779708 -0.090628477 AVY(ph)RLCVTTGPY(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 AVYRLCVTTGPYLR 14 1 Q9BYJ1 Q9BYJ1 ALOXE3 Hydroperoxide isomerase ALOXE3 2 0 AVY(0.869)RLCVT(0.131)T(0.003)GPY(0.997)LR 87.149 0.0075627 2204700 0 0 0 103.5 136.07 191.34 112.71 0 149.3 0 TRUE FALSE FALSE 0 0 0 115.467157 129.1258402 179.1139915 122.2835846 0 135.9462341 0 0 AVY(ph)SLIS(ph)T(ph)PFSSENAS(ph)LEENTKPPEE ddPTM_HeLa_Romidepsin_16h_R1 1 AVYSLISTPFSSENASLEENTKPPEE 26 1 A0A1W2PR53 A0A1W2PR53 4 0 AVY(0.827)S(0.377)LIS(0.708)T(0.71)PFS(0.278)S(0.107)ENAS(0.732)LEENT(0.262)KPPEE 42.746 0.0040901 0 537.47 464.79 475.1 521.77 478.13 432.29 326.62 473.32 658.23 524.93 TRUE FALSE FALSE 530.9191089 471.3333258 483.3689162 582.0995024 453.729242 404.6680642 354.3630946 487.0147674 599.3562602 511.2922429 1.038386786 0.921847206 0.945386759 1.138486864 0.887416635 0.79146138 0.693073481 0.952517419 1.172238125 1 8.998004328 -8.546226413 7.318640962 1.012212877 0.806443991 0.531472889 0.094584916 0.083484019 18.23053059 0.010897661 0.022165044 2.84E-09 8.546226413 -0.205768885 AVYDEQGTVDEDSPVLTQDRDWEAYWR ddPTM_HeLa_Romidepsin_16h_R1 2 AVYDEQGTVDEDSPVLTQDRDWEAYWR 27 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 0 0 ; ; 100.92 4.53E-08 19775400 1175.72 1253.5 1308.2 1208.09 1074.12 1079.18 1223.26 1272.97 1355.87 989.67 FALSE FALSE TRUE 1161.389872 1271.146806 1330.968672 1347.77505 1019.303648 1010.223881 1327.163674 1309.801379 1234.597591 963.9582307 1.204813482 1.318674156 1.380732722 1.39816748 1.057414747 1.047995493 1.376785458 1.358773997 1.28075839 1 9.912826824 -11.53599812 0.779465486 1.013753139 1.269079303 0 0.147348758 0.478118738 0.596824263 0.061198769 0.029286275 2.91E-12 11.53599812 0.255326164 AWGPGLHGGIVGR ddPTM_HeLa_Romidepsin_16h_R1 1 AWGPGLHGGIVGR 13 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 111.5 0.0030294 12664000 2047.7 2037.4 1893.6 1352.4 2396 2646 1799.1 2043.7 2101.1 1632.6 FALSE FALSE TRUE 2022.741845 2066.082571 1926.557314 1508.770851 2273.723179 2476.92914 1951.915509 2102.831235 1913.172354 1590.184817 1.272016827 1.299271977 1.211530442 0.948802199 1.429848377 1.557636014 1.227477139 1.322381658 1.203113207 1 10.63497873 -16.18745427 0.160862814 6.45E-13 1.377486888 0.15322461 0.157369583 46.79669199 0.553118488 14.89378443 0.29557013 6.49E-17 16.18745427 1.377486888 AWLDEDS(ph)NLSPSPLRDLSGGLGGQEEEEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 AWLDEDSNLSPSPLRDLSGGLGGQEEEEEQR 31 1 B8ZZ93;B8ZZH7;F8WCL7;J3KQ70;Q9C086 B8ZZ93 INO80B;INO80B-WBP1 INO80 complex subunit B 1 0 AWLDEDS(0.343)NLS(0.341)PS(0.262)PLRDLS(0.054)GGLGGQEEEEEQR 66.501 1.43E-05 3833200 544 490.93 474.09 407.35 417.28 544.24 409.47 500.03 508.02 355.18 TRUE FALSE FALSE 537.3695188 497.8413254 482.3413376 454.4497236 395.9846445 509.4648205 444.2503716 514.4975791 462.5814188 345.9523724 1.55330491 1.439045849 1.394242029 1.31361933 1.14462185 1.47264439 1.284137376 1.487191938 1.337124575 1 8.434429624 -12.46660884 1.201114052 0.999776659 1.394840762 0.118943394 0.149901961 0.258822516 0.667396878 0.084247312 0.020723208 3.42E-13 12.46660884 0.395064103 AWLDEDSNLS(ph)PSPLR ddPTM_HeLa_Romidepsin_16h_R1 1 AWLDEDSNLSPSPLR 15 0 B8ZZ93;B8ZZH7;F8WCL7;J3KQ70;Q9C086 B8ZZ93 INO80B;INO80B-WBP1 INO80 complex subunit B 1 0 AWLDEDS(0.003)NLS(0.996)PS(0.001)PLR 81.992 0.028257 8667000 2006.9 1890.5 1845.1 1438.8 2794 3419.8 3006.4 3708.4 1845 1798.8 TRUE FALSE FALSE 1982.439131 1917.114509 1877.213192 1605.160826 2651.411754 3201.285817 3261.763541 3815.696703 1679.978579 1752.066917 1.131485968 1.094201649 1.071427794 0.916152694 1.513305074 1.827148145 1.861666076 2.177825896 0.95885526 1 10.77484216 -8.398670244 1.884846346 1.056778922 1.999580012 0.934767789 0.11002239 0.058566789 0.401913412 0.015769365 0.045498157 3.99E-09 8.398670244 0.94280109 AWNDIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AWNDIKK 7 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 1 ; AWNDIK(1)K;AWNDIK(1)K 119.27 0.0036889 2195400 1296.32 1334.26 1611.4 1425.68 3352.1 2924.3 2755.4 1909.98 2944.7 2400.4 FALSE TRUE FALSE 1280.519953 1353.043747 1639.445741 1590.52383 3181.029829 2737.446668 2989.443607 1965.242258 2681.318657 2338.037262 0.547690139 0.578709232 0.701205993 0.680281643 1.360555659 1.170831069 1.278612474 0.840552155 1.146824604 1 11.19108221 -8.771526441 24.99943068 0.750394318 1.171506981 0.438749802 0.213096869 135.67287 336247.424 0.032111278 0.058694974 1.69E-09 8.771526441 0.421112663 AWT(ph)IT(ph)DT(ph)TEHSTQLHYT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 AWTITDTTEHSTQLHYTK 18 0 Q8WXI7 Q8WXI7 MUC16 Mucin-16 4 0 AWT(0.626)IT(0.626)DT(0.626)T(0.452)EHS(0.406)T(0.268)QLHY(0.639)T(0.357)K 47.548 0.0040885 0 331.77 320.84 373.65 270.54 282.77 432.65 206.76 283.56 322.45 329.43 TRUE FALSE FALSE 327.7262596 325.3567939 380.1532215 301.8211077 268.3391917 405.0050613 224.3221892 291.7643612 293.6092644 320.8713611 1.021363385 1.013978913 1.184752731 0.940629624 0.836282773 1.262203831 0.699103181 0.909287635 0.915037302 1 8.32585122 -7.735003025 24.99998616 1.019173799 0.804195435 0.321933604 0.126266037 174.8986673 165393.3114 0.015020166 0.056166496 1.84E-08 7.735003025 -0.214978363 AWY(ph)MQY(ph)LEK ddPTM_HeLa_Romidepsin_16h_R1 1 AWYMQYLEK 9 0 Q9HAP2-3;Q9HAP2 Q9HAP2-3 MLXIP MLX-interacting protein 2 0 AWY(1)MQY(1)LEK 44.753 0.0043313 0 1934.9 2328.4 2091.8 2439.8 2635.8 2469.4 1615.1 2057.3 2262.3 2291.5 TRUE FALSE FALSE 1911.316695 2361.179276 2128.206902 2721.901156 2501.28529 2311.61331 1752.286554 2116.82473 2059.954222 2231.9665 0.856337537 1.057891898 0.953512027 1.219508069 1.120664352 1.03568459 0.785086404 0.948412411 0.922932411 1 11.12409966 -13.16353882 3.466131849 1.001175505 0.964025767 0 0.123910112 1.634500478 36.34406554 0.125858603 0.019412588 6.86E-14 13.16353882 -0.037149739 AY(ph)MRNPSSSVPPPS(ph)AGS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 AYMRNPSSSVPPPSAGSVK 19 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 3 0 AY(0.704)MRNPS(0.149)S(0.15)S(0.045)VPPPS(0.975)AGS(0.978)VK 48.883 0.020861 5399300 423.93 381.64 447.12 547.97 412.86 445.41 378.82 389.62 597.99 434.64 TRUE FALSE FALSE 418.7629781 387.0127379 454.901936 611.3288697 391.7902136 416.9497385 410.9969613 400.89304 544.5042767 423.3479901 0.989169638 0.914171667 1.0745343 1.444033948 0.925456652 0.984886543 0.970825352 0.946958647 1.286186044 1 8.72570023 AYEEAQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AYEEAQKR 8 1 A2AB15;A0A140T947;O60231 A2AB15 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 0 1 ; AYEEAQK(1)R;AYEEAQK(1)R 124.98 0.0015896 3812600 1717.93 1684.55 2086.72 1534.6 2357.71 2174.66 1844.29 1713.37 1933.08 1544.6 FALSE TRUE FALSE 1696.991208 1708.265139 2123.038486 1712.037673 2237.387261 2035.706244 2000.943947 1762.943658 1760.180483 1504.471069 1.127965331 1.135458949 1.41115275 1.137966497 1.487158714 1.353104281 1.329998288 1.171802964 1.169966322 1 10.55504065 -10.28182537 0.787164202 1.031404568 1.326778491 0.393774772 0.113299967 0.281732408 0.359077519 0.025152882 0.02957152 5.23E-11 10.28182537 0.295373923 AYFETEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AYFETEKK 8 1 H3BR35;P15170;P15170-2;P15170-3;H3BSV8 H3BR35 GSPT1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A 0 1 ; AYFETEK(1)K;AYFETEK(1)K 134.91 0.0028853 2302630 889.35 802.03 1210.95 735.84 2464.7 1855.03 1916.48 1248.95 2277.2 1620.84 FALSE TRUE FALSE 878.5102601 813.3209994 1232.026077 820.921283 2338.917162 1736.49957 2079.265763 1285.086398 2073.521529 1578.730343 0.556466317 0.51517411 0.780390446 0.519988285 1.481517836 1.099934246 1.317049344 0.813999936 1.313410829 1 10.62454906 -8.767378906 24.99997489 0.744971187 1.18246341 0.322665648 0.279016085 103.2075519 434411.3411 0.035984972 0.066486289 1.71E-09 8.767378906 0.437492223 AYFHLLNQIAPK ddPTM_HeLa_Romidepsin_16h_R1 1 AYFHLLNQIAPK 12 0 P13797;A0A0A0MSQ0;P13797-3;P13797-2;H7C4N2;C9JAM8;Q14651 P13797 PLS3;PLS1 Plastin-3;Plastin-1 0 0 88.134 0.0084675 415730 1034.5 817.11 1015.1 764.06 1184.3 1163.8 889.32 861.55 904.01 742.58 FALSE FALSE TRUE 1021.891116 828.613296 1032.76739 852.4042122 1123.860752 1089.436936 964.8588186 886.4775899 823.1530815 723.2876646 1.412841897 1.145620666 1.427879169 1.17851341 1.553822645 1.506229111 1.333990424 1.225622437 1.138071506 1 9.498425737 -12.5475814 0.610887823 0.910935649 1.362437063 0.389112254 0.134684551 0.900208399 0.409868673 0.239385673 0.027867988 2.83E-13 12.5475814 0.451501414 AYLGYQAVPSGSSGSLST(ph)SSSSSPPGTPSPADAK ddPTM_HeLa_Romidepsin_16h_R1 2 AYLGYQAVPSGSSGSLSTSSSSSPPGTPSPADAK 34 0 P17676-3;P17676-2;P17676 P17676-3 CEBPB CCAAT/enhancer-binding protein beta 1 0 AYLGYQAVPSGSSGS(0.001)LS(0.043)T(0.159)S(0.159)S(0.159)S(0.159)S(0.159)S(0.159)PPGTPSPADAK;AYLGYQAVPSGSSGSLS(0.009)T(0.165)S(0.165)S(0.165)S(0.165)S(0.165)S(0.165)PPGTPSPADAK ; 127.64 8.95E-16 31445000 11634.5 11457.6 12192.8 15219 20409.6 17662.1 15760.1 16094.5 14497.5 12701.1 TRUE FALSE FALSE 11492.69424 11618.90039 12405.01057 16978.69239 19368.02195 16533.54881 17098.7625 16560.16896 13200.80729 12371.12359 0.928993568 0.93919524 1.0027392 1.372445458 1.565583094 1.336462989 1.382151134 1.338614787 1.067066156 1 13.59468892 -9.265359377 4.42080565 0.964024449 1.407226589 0.895372441 0.070274269 0.039443333 2.016168739 0.009859448 0.015920197 5.43E-10 9.265359377 0.44320214 AYLPVNESFGFTADLR ddPTM_HeLa_Romidepsin_16h_R1 1 AYLPVNESFGFTADLR 16 0 P13639 P13639 EEF2 Elongation factor 2 0 0 147.73 0.0030469 7543000 912.3 1351.1 1111.3 985.33 1034.9 1152.3 970.95 1001 990.48 1037.7 FALSE FALSE TRUE 901.1805367 1370.120821 1130.64171 1099.258491 982.0851913 1078.671749 1053.422469 1029.962356 901.8889881 1010.740404 0.891604345 1.355561542 1.118627202 1.087577469 0.971649285 1.067209487 1.042228513 1.019017694 0.892305269 1 9.981196792 AYPLADAHLTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 AYPLADAHLTKK 12 1 A0A3B3IUA2;B1AHD1;P55769 A0A3B3IUA2 NHP2L1 "NHP2-like protein 1;NHP2-like protein 1, N-terminally processed" 0 1 AYPLADAHLTK(1)K 71.888 0.024743 385300 329.57 458.15 458.7 365.06 1473.1 985.31 856.02 1061.4 1084.8 854.05 FALSE TRUE FALSE 325.5530741 464.5998477 466.6834811 407.2699549 1397.92221 922.3518709 928.7303174 1092.109934 987.7727711 831.8616579 0.391354826 0.558506145 0.561010929 0.489588564 1.680474388 1.108780363 1.11644804 1.312850429 1.187424329 1 9.700199812 -8.774961201 24.99995348 0.666483746 1.277206344 0.544811045 0.270275897 135.4034294 250341.8298 0.041316985 0.075190316 1.68E-09 8.774961201 0.610722597 AYQDQIS(ph)PVPGAPK ddPTM_HeLa_Romidepsin_16h_R1 3 AYQDQISPVPGAPK 14 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 1 0 AYQDQIS(1)PVPGAPK;AYQDQIS(1)PVPGAPK;AYQDQIS(1)PVPGAPK ;; 133.87 0.0016409 32274700 8599.2 8705.6 8144.3 8636.7 14430.9 16367.8 14524.1 16965.8 9624.9 8782.1 TRUE FALSE FALSE 8494.389643 8828.157665 8286.048125 9635.315891 13694.43732 15321.9504 15757.77669 17456.67866 8764.024838 8553.939776 0.99303828 1.032057496 0.968682074 1.126418486 1.60095087 1.791215604 1.842165961 2.040776427 1.024560035 1 13.06237333 -8.612992706 1.582862517 0.994045402 1.922422371 0.979946319 0.05715048 0.032675905 0.162942752 0.008195059 0.021880186 2.44E-09 8.612992706 0.928376969 AYQHGGVTGLS(ph)QY ddPTM_HeLa_Romidepsin_16h_R1 1 AYQHGGVTGLSQY 13 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 0 AYQHGGVTGLS(0.998)QY(0.002) 94.688 0.017862 11654000 2474.1 2514.2 2845.3 1722.2 2771.1 2223.8 1611.4 2008 2551.7 2253.5 TRUE FALSE FALSE 2443.944718 2549.594974 2894.821253 1921.328867 2629.680427 2081.706357 1748.272276 2066.098312 2323.469561 2194.953745 1.113437913 1.161571163 1.318852964 0.875339114 1.198057331 0.94840557 0.796496181 0.941294693 1.058550581 1 11.09997482 -8.026739553 8.0493925 1.07798144 0.869402246 0.395352661 0.117769209 0.182302519 49.28364086 0.016417271 0.043577838 9.40E-09 8.026739553 -0.208579193 AYS(ph)NSIVR ddPTM_HeLa_Romidepsin_16h_R1 1 AYSNSIVR 8 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 0 AYS(0.998)NS(0.002)IVR 114.89 0.020664 27471000 1885.4 1900.3 1695.5 1314.5 1893.5 1713.7 1436 1537.9 2193.1 1798.2 TRUE FALSE FALSE 1862.42002 1927.052473 1725.009466 1466.488675 1796.867629 1604.200101 1557.973804 1582.39671 1996.943643 1751.482505 1.063339208 1.100240778 0.984885354 0.837284227 1.025912405 0.915909863 0.889517195 0.903461328 1.140144785 1 10.77436086 -9.518385391 24.65620102 1.036332248 0.9184882 0.588338639 0.060097063 93.13351378 511048.6105 0.008112331 0.011644038 3.03E-10 9.518385391 -0.117844048 AYS(ph)SPSTTPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 AYSSPSTTPEAR 12 0 G3V2R1;Q9UPU9-2;Q9UPU9-3;Q9UPU9 G3V2R1 SAMD4A Protein Smaug homolog 1 1 0 AYS(0.468)S(0.468)PS(0.028)T(0.028)T(0.008)PEAR 139.76 0.0020636 32968000 2743.7 2474.1 2533.7 2843.2 3010.8 3052.5 2164.6 2338 3135.3 2903.2 TRUE FALSE FALSE 2710.258729 2508.930445 2577.797986 3171.944162 2857.147641 2857.455101 2348.46107 2405.646341 2854.870915 2827.774445 0.95844233 0.887245604 0.911599576 1.121710456 1.01038739 1.010496119 0.830498017 0.85072073 1.00958226 1 11.46545133 -7.756972128 24.99742489 0.982271831 0.840609314 0.485100236 0.060734882 73.69087278 412336.3199 0.008645849 0.030267187 1.75E-08 7.756972128 -0.141662516 AYSGS(ph)DLPSSSSGGANGTAGGGGGAR ddPTM_HeLa_Romidepsin_16h_R1 3 AYSGSDLPSSSSGGANGTAGGGGGAR 26 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 0 AYS(0.196)GS(0.802)DLPS(0.002)SSSGGANGTAGGGGGAR;AYS(0.034)GS(0.966)DLPSSSSGGANGTAGGGGGAR;AYS(0.036)GS(0.963)DLPS(0.001)SSSGGANGTAGGGGGAR ;; 220.72 3.80E-47 49732000 8359.6 9800.8 8297.4 7546.2 8115.2 7024.1 5499.4 6362.6 9944.4 8403.4 TRUE FALSE FALSE 8257.70998 9938.77592 8441.812766 8418.72715 7701.051062 6575.282679 5966.518899 6546.691792 9054.947958 8185.078457 1.00887365 1.214255425 1.031366139 1.028545688 0.94086466 0.803325553 0.728950728 0.799832503 1.106275035 1 12.99878053 -8.355987338 2.234332751 1.025590491 0.76264033 0.773514286 0.067870302 0.118878837 1.146621391 0.009950594 0.02751196 4.41E-09 8.355987338 -0.262950161 AYSS(ph)PSTTPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 AYSSPSTTPEAR 12 0 G3V2R1;Q9UPU9-2;Q9UPU9-3;Q9UPU9 G3V2R1 SAMD4A Protein Smaug homolog 1 1 0 AYS(0.029)S(0.955)PS(0.007)T(0.007)T(0.002)PEAR 126.66 0.0051997 29567000 3030.2 2978.4 3072.6 2834.4 3294.1 3399.5 2642.7 2942.3 3205.1 2893.1 TRUE FALSE FALSE 2993.266757 3020.329993 3126.077314 3162.126664 3125.989785 3182.282921 2867.170872 3027.430808 2918.427829 2817.936845 1.062219248 1.071823167 1.109349672 1.122142489 1.10931861 1.129295331 1.017471657 1.07434303 1.035661191 1 11.46042356 -11.27058505 0.677694695 1.004713926 1.092508961 0.437474302 0.031953037 0.378596627 0.377854645 0.014978059 0.008237065 5.36E-12 11.27058505 0.087795035 AYT(ph)HQVVTR ddPTM_HeLa_Romidepsin_16h_R1 3 AYTHQVVTR 9 0 D6REC6;D6R9G1;D6RAD4;P50613 D6REC6 CDK7 Cyclin-dependent kinase 7 1 0 AYT(1)HQVVTR;AYT(1)HQVVTR;AYT(1)HQVVTR ;; 129.74 0.017343 45655000 11447.4 15396 5353.57 11167.8 18540.8 11031.1 9835.9 22629.4 13282.6 15273.5 TRUE FALSE FALSE 11307.87469 15612.74529 5446.74664 12459.07358 17594.59379 10326.24831 10671.3611 23284.14599 12094.57099 14876.69227 0.760106782 1.049476927 0.366126189 0.837489501 1.182695284 0.6941226 0.71732082 1.565142679 0.812987912 1 13.86076617 -7.254367634 24.30975647 0.855892107 1.565143172 0.512257618 0.21485782 368.2572155 1265868.774 0.029240895 0.387531617 5.57E-08 7.254367634 0.709251065 AYT(ph)PPPPLGPHPNLGK ddPTM_HeLa_Romidepsin_16h_R1 2 AYTPPPPLGPHPNLGK 16 0 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 0 AY(0.014)T(0.986)PPPPLGPHPNLGK;AY(0.022)T(0.978)PPPPLGPHPNLGK ; 89.468 0.009733 134570000 12786.1 12702.5 12268.9 12919.7 13995.4 13841.7 12092.7 13605 14036.7 13224.5 TRUE FALSE FALSE 12630.2581 12881.32613 12482.43506 14413.5365 13281.16251 12957.26004 13119.85364 13998.63921 12781.2224 12880.92558 0.980539637 1.000031096 0.969063518 1.118982981 1.031072063 1.005926163 1.018548982 1.086772773 0.992259626 1 13.65294864 -9.314055778 24.99999782 0.98993246 1.046636736 0.494237714 0.032040471 231.1752418 109839.2795 0.004813574 0.00735286 4.85E-10 9.314055778 0.056704276 AYT(ph)PVVVTQWYR ddPTM_HeLa_Romidepsin_16h_R1 1 AYTPVVVTQWYR 12 0 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;Q9UQ88-5;Q9UQ88-10 Q9UQ88-2 CDK11A Cyclin-dependent kinase 11A 1 0 AY(0.002)T(0.995)PVVVT(0.003)QWYR 150.14 0.0030058 53725000 1455.4 1049.4 1660.5 1472.2 1749.6 1763.8 1373.3 1156.9 1082.6 980.11 TRUE FALSE FALSE 1437.661025 1064.173481 1689.400306 1642.422691 1660.311383 1651.098872 1489.948068 1190.373076 985.7695446 954.6466009 1.505961498 1.114730288 1.769660421 1.720450991 1.739189541 1.729539361 1.560732596 1.246925381 1.032601534 1 9.898822953 -11.99919813 0.422040011 0.881000114 1.613161469 0.538912972 0.201687468 1.097138758 0.300793785 0.351658882 0.071580779 1.00E-12 11.99919813 0.732161355 SLITGPSK(ac)LSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLITGPSKLSR 11 1 E7EVK1;A0A088AWL3;O75376;O75376-2 E7EVK1 NCOR1 Nuclear receptor corepressor 1 0 1 ; SLITGPSK(1)LSR;SLITGPSK(1)LSR 132.25 0.0067003 6057300 452.32 575.7 989.07 1913 3153.3 3429.9 3164.1 2336.5 654.76 363.3 FALSE TRUE FALSE 446.8069499 583.8047197 1006.284348 2134.190061 2992.375334 3210.740459 3432.858575 2404.102941 596.1966257 353.8614136 1.26266084 1.649811755 2.843724435 6.031146598 8.456348218 9.073440437 9.701138476 6.793910973 1.684830848 1 8.467040643 -9.19172643 1.573369418 1.139459855 8.738871642 0.951529302 0.735240162 0.046819202 0.226891161 0.108478571 0.205485118 6.43E-10 9.19172643 7.599411787 up AYTTGS(ph)PGSR ddPTM_HeLa_Romidepsin_16h_R1 1 AYTTGSPGSR 10 0 H3BMG9;H3BSV5;A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4 H3BMG9 FAM65A Protein FAM65A 1 0 AYT(0.002)T(0.172)GS(0.823)PGS(0.003)R 119.74 0.011988 17736000 2824.5 2668.2 2972.5 2202.9 2957.8 3600.1 3134.6 1707.4 3347.3 2670.3 TRUE FALSE FALSE 2790.073908 2705.76299 3024.235116 2457.609663 2806.852429 3370.065229 3400.852846 1756.800925 3047.909105 2600.925221 1.072723616 1.040307875 1.162753581 0.94489824 1.079174598 1.295717847 1.307555026 0.675452301 1.171855723 1 11.34480921 -11.77088608 0.449967285 0.988763639 1.093291543 0 0.178556169 4.392271734 1.569309894 0.205513075 0.05483748 1.69E-12 11.77088608 0.104527904 CALSSPSLAFT(ph)PPIK ddPTM_HeLa_Romidepsin_16h_R1 2 CALSSPSLAFTPPIK 15 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 CALSSPS(0.006)LAFT(0.994)PPIK;CALSSPS(0.001)LAFT(0.999)PPIK ; 138.77 0.0019919 15643200 6899.4 5528.8 6031.8 667.6 6087.1 5864.6 5027.9 5139.4 6743.6 6835.6 TRUE FALSE FALSE 6815.307459 5606.634592 6136.780949 744.7910532 5776.452573 5489.870987 5454.969701 5288.10043 6140.435526 6658.010127 1.023625277 0.842088625 0.92171397 0.111863911 0.867594441 0.824551312 0.819309313 0.794246378 0.92226287 1 12.70087535 -9.834116559 2.280009647 1.008275948 0.704317513 0.232426581 0.214429684 0.274200993 2.916646109 0.034957354 0.048398302 1.47E-10 9.834116559 -0.303958435 CCSGAIIVLTK ddPTM_HeLa_Romidepsin_16h_R1 1 CCSGAIIVLTK 11 0 P14618;B4DNK4;P14618-3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 155.11 0.015436 653230 593.85 533.86 406.09 196.31 473.93 738.45 518.82 669.24 540.65 514.74 FALSE FALSE TRUE 586.6119278 541.3756951 413.1578261 219.0082859 449.7435836 691.2654282 562.8885579 688.6034035 492.2929099 501.3669806 1.170025052 1.079799261 0.824062697 0.436822316 0.897034709 1.378761376 1.122707676 1.373451843 0.98190134 1 8.969723175 -8.261292917 24.99999967 1.002197926 1.27474704 0.356902085 0.209934122 16.094569 2746832.333 0.034415961 0.082066521 5.48E-09 8.261292917 0.272549115 CDGDASPPS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 CDGDASPPSPAR 12 0 E7EUV9;F8W8D3;Q14493 E7EUV9 SLBP Histone RNA hairpin-binding protein 1 0 CDGDAS(0.001)PPS(0.999)PAR 133.88 4.86E-05 0 2072.6 1888 1884.5 208.3 2418.7 2033.7 1623.7 2125.2 2498.3 2271.8 TRUE FALSE FALSE 2047.338354 1914.579314 1917.298932 232.3846261 2295.264714 1903.753133 1761.617037 2186.689309 2274.845791 2212.778308 0.925234284 0.865237745 0.866466796 0.105019389 1.037277302 0.860345172 0.796110948 0.988209845 1.028049571 1 11.1116432 -10.0229237 2.172108666 0.965960121 0.763859539 0.131032421 0.241733999 0.488954553 4.565595234 0.041131035 0.053264473 9.49E-11 10.0229237 -0.202100582 CKAFS(ph)TCSSHLTAVLMFYGSLMSMYLK ddPTM_HeLa_Romidepsin_16h_R1 1 CKAFSTCSSHLTAVLMFYGSLMSMYLK 27 1 Q8NGM9 Q8NGM9 OR8D4 Olfactory receptor 8D4 1 0 CKAFS(0.323)T(0.323)CS(0.323)S(0.023)HLT(0.007)AVLMFYGSLMSMYLK 41.904 0.014834 8591800 754 588.7 545.85 561.61 844.4 759.23 578.23 729.45 845.47 838.25 TRUE FALSE FALSE 744.809958 596.9877341 555.3502903 626.5459907 801.3071171 710.7176533 627.3448418 750.5554849 769.8490457 816.4721442 0.912229478 0.731179549 0.680182777 0.767381956 0.981426155 0.870473853 0.768360374 0.919266493 0.94289689 1 9.673259856 -10.60874222 2.540610262 0.967416666 0.816760062 0.336630469 0.086733152 0.215504457 2.905964777 0.017631347 0.018455011 2.46E-11 10.60874222 -0.150656604 CQEVISWLDANTLAEKDEFEHK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 104.81 7.45E-05 11641000 1468.9 1388.7 1155.1 465.29 1607.8 2036.7 1845.7 1971.1 1605.4 1478 FALSE FALSE TRUE 1450.996482 1408.250155 1175.204031 519.0890191 1525.747966 1906.561443 2002.473712 2028.130669 1461.809003 1439.601347 1.007915479 0.97822231 0.816339908 0.360578309 1.059840608 1.324367643 1.39099183 1.408814095 1.015426254 1 10.49145364 -8.295456536 3.946821891 0.938731925 1.383595583 0.566041598 0.193075347 0.146507008 5.045300117 0.029942441 0.073537483 5.06E-09 8.295456536 0.444863658 CSATPSAQVKPIVS(ph)ASPPSR ddPTM_HeLa_Romidepsin_16h_R1 1 CSATPSAQVKPIVSASPPSR 20 1 Q96EV2;H0Y3K4 Q96EV2 RBM33 RNA-binding protein 33 1 0 CSATPSAQVKPIVS(0.475)AS(0.475)PPS(0.051)R 90.762 0.00059019 13069000 4093.9 3045.4 3167.4 589.57 3412.7 3804.6 2822.2 2938.3 3759.1 3532.8 TRUE FALSE FALSE 4044.001972 3088.273221 3222.527268 657.7388574 3238.537184 3561.498339 3061.917598 3023.315075 3422.876681 3441.017347 1.175234404 0.89748842 0.936504221 0.191146626 0.94115689 1.035013189 0.889829167 0.878610821 0.99472811 1 11.74861945 -9.972913894 2.798203108 1.081831224 0.803479549 0.186778517 0.224300474 0.295487804 4.712288804 0.038641059 0.05065652 1.06E-10 9.972913894 -0.278351675 CSK(ac)LPSSTK(ac)SGWPR ddPTM_HeLa_Romidepsin_16h_R1 1 CSKLPSSTKSGWPR 14 2 B5MBX1;A0A0C4DFT8;G3XAA4;Q9NQC1-3;Q9NQC1-2;Q9NQC1;D6R9B8;C9J929 B5MBX1 JADE2 Protein Jade-2 0 2 CSK(1)LPSSTK(1)SGWPR 145.6 1.91E-06 947330 264.4 246.05 302.45 0 229.21 151.06 230.81 215.5 187.53 249.44 FALSE TRUE FALSE 261.1773911 249.5138984 307.7140154 0 217.5125584 141.4077535 250.4149956 221.7351525 170.7568471 242.9595128 1.074983186 1.026977275 1.266523841 0 0.895262572 0.582021885 1.030686112 0.912642398 0.702820174 1 7.924572111 CSPTVAFVEFPS(ph)SPQLK ddPTM_HeLa_Romidepsin_16h_R1 2 CSPTVAFVEFPSSPQLK 17 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 CSPT(0.001)VAFVEFPS(0.735)S(0.264)PQLK;CSPTVAFVEFPS(0.991)S(0.009)PQLK ; 212.35 1.67E-26 22847000 5997.9 4591 5677.1 495.02 5088.8 5074.8 3704.3 4119.9 5763.8 5283.5 TRUE FALSE FALSE 5924.795288 4655.632219 5775.907544 552.2565415 4829.099547 4750.536658 4018.94315 4239.102806 5248.271292 5146.233908 1.1512876 0.904667821 1.122356202 0.107312756 0.938375448 0.923109354 0.780948402 0.823729135 1.019827584 1 12.32930132 CT(ph)APQYVDFVMSSVQK ddPTM_HeLa_Romidepsin_16h_R1 1 CTAPQYVDFVMSSVQK 16 0 A0A087WVS8;Q70IA6-2;Q70IA6;Q70IA6-3 A0A087WVS8 MOB2 MOB kinase activator 2 1 0 CT(1)APQYVDFVMSSVQK 79.875 0.0022809 0 417.09 271.82 332.83 424.44 276.45 428.67 261.63 398.9 377.88 407.55 TRUE FALSE FALSE 412.0063467 275.6466891 338.6227665 473.5157499 262.3417249 401.2793705 283.8528457 410.4415421 344.0814664 396.9617922 1.03789925 0.694390983 0.853036169 1.192849688 0.660873994 1.010876559 0.715063392 1.033957298 0.866787366 1 8.632856344 CT(ph)REFGLLLLFLAVAITLFSPLVY(ph)VAEK ddPTM_HeLa_Romidepsin_16h_R1 1 CTREFGLLLLFLAVAITLFSPLVYVAEK 28 1 Q8TDN1 Q8TDN1 KCNG4 Potassium voltage-gated channel subfamily G member 4 2 0 CT(0.999)REFGLLLLFLAVAIT(0.002)LFS(0.013)PLVY(0.985)VAEK 53.545 0.0022222 0 1957.5 1587 1838.6 985.11 1362.2 1028.1 1191.7 1192.3 2274.8 2011.7 TRUE FALSE FALSE 1933.641237 1609.341828 1870.600062 1099.013053 1292.681851 962.407728 1292.922968 1226.797319 2071.336191 1959.435744 0.986835747 0.821329218 0.95466262 0.560882416 0.659721481 0.491165751 0.659844535 0.626097244 1.057108505 1 10.93622255 -9.40602082 1.527511931 0.987974599 0.591350315 0.827645627 0.081372896 0.09718798 0.447566727 0.012024689 0.020745282 3.93E-10 9.40602082 -0.396624284 CTELNQAWSS(ph)LGK ddPTM_HeLa_Romidepsin_16h_R1 1 CTELNQAWSSLGK 13 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 0 CTELNQAWS(0.233)S(0.767)LGK 111.72 0.0015364 0 1823.2 1711.2 1897.8 512.89 1861.8 2222.7 2161.7 1945.8 1686.9 2158.7 TRUE FALSE FALSE 1800.978137 1735.290319 1930.830413 572.192755 1766.785399 2080.676643 2345.314744 2002.098653 1536.019439 2102.616663 0.856541361 0.825300374 0.918298826 0.272133654 0.840279367 0.989565374 1.11542669 0.952193849 0.730527569 1 11.03797013 -11.83574778 0.868653093 0.993152742 0.843373099 0 0.225059286 1.331672006 1.954828532 0.113552213 0.044757786 1.46E-12 11.83574778 -0.149779644 CVPAPGAGASGGT(ph)SPSATQPNPAVFIFEHK ddPTM_HeLa_Romidepsin_16h_R1 1 CVPAPGAGASGGTSPSATQPNPAVFIFEHK 30 0 O60343-2;O60343-3;O60343 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 CVPAPGAGAS(0.092)GGT(0.304)S(0.27)PS(0.27)AT(0.066)QPNPAVFIFEHK 59.372 0.0010903 14411000 3117.7 2825.1 2826.7 568.88 3441.1 3278.8 3069.2 3757.2 3389.4 2894.6 TRUE FALSE FALSE 3079.700273 2864.871832 2875.897528 634.6565823 3265.487826 3069.295262 3329.897771 3865.908654 3086.243575 2819.397875 1.092325528 1.016128961 1.020039617 0.22510359 1.15822171 1.08863502 1.181066994 1.371182368 1.094646344 1 11.46117137 -7.592175959 1.594599534 0.987709585 1.387786763 0.219713589 0.252322866 0.775106642 2.861519254 0.036723174 0.394891169 2.56E-08 7.592175959 0.400077178 DAAGSGDK(ac)PGADTGR ddPTM_HeLa_Romidepsin_16h_R1 2 DAAGSGDKPGADTGR 15 1 Q96EL3 Q96EL3 MRPL53 "39S ribosomal protein L53, mitochondrial" 0 1 ; DAAGSGDK(1)PGADTGR;DAAGSGDK(1)PGADTGR 131.35 0.00016438 459850 69.947 0 0 0 0 245.1 170.6 0 0 0 FALSE TRUE FALSE 69.09445906 0 0 0 0 229.438901 185.0907597 0 0 0 0 DAALATALGDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DAALATALGDKK 12 1 P20700;E9PBF6;A0A0D9SFE5;A0A0D9SFY5 P20700 LMNB1 Lamin-B1 0 1 ; DAALATALGDK(1)K;DAALATALGDK(1)K 157.68 0.00039827 1637990 682.82 896.35 1135.98 660.64 1618.82 1688.34 1630.48 1761.28 1880.15 1647.1 FALSE TRUE FALSE 674.4975272 908.9688388 1155.751255 737.0263052 1536.205575 1580.460523 1768.972931 1812.239858 1711.984675 1604.308105 0.420428922 0.566579971 0.720404798 0.459404464 0.957550218 0.985135286 1.102639154 1.129608367 1.067117139 1 10.64773552 -8.580304077 6.941409655 0.689460423 1.059017571 0.417684705 0.19823805 0.178057539 17.24672265 0.034168578 0.068842922 2.63E-09 8.580304077 0.369557148 DAAS(ph)PHQDGAPGPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 DAASPHQDGAPGPGPR 16 0 A0A1B0GUL3 A0A1B0GUL3 1 0 DAAS(1)PHQDGAPGPGPR 94.339 0.002464 0 760.1 831.6 907.53 279.31 653.74 599.3 924.69 329.31 874.82 745.57 TRUE FALSE FALSE 750.8356088 843.3072866 923.325179 311.6051364 620.3772084 561.0066642 1003.233146 338.8380653 796.5739082 726.1999839 1.033924023 1.161260404 1.271447534 0.42908998 0.854278742 0.772523653 1.381483293 0.466590571 1.096907086 1 9.504223088 -9.292739462 24.99336834 1.047045811 0.817787766 0.271194831 0.257649268 896.4569205 715825.5923 0.037323296 0.057015631 5.10E-10 9.292739462 -0.229258045 DADAEIEGAPAAPLDVK ddPTM_HeLa_Romidepsin_16h_R1 1 DADAEIEGAPAAPLDVK 17 0 A8MX12;P52179-2;P52179 A8MX12 MYOM1 Myomesin-1 0 0 51.727 0.025477 1129600 67.117 0 114.44 192.59 0 128.41 0 0 174.48 119.89 FALSE FALSE TRUE 66.29895219 0 116.4317802 214.858162 0 120.2050154 0 0 158.8740718 116.7752405 0.567748368 0 0.997058792 1.83992909 0 1.029370737 0 0 1.360511621 1 6.867590606 -7.749711525 24.59902034 0.779563107 7.12E-07 0.279107577 0.536701115 177.5473537 372394.3486 0.068057362 0.250286121 1.78E-08 7.749711525 -0.779562395 DADAGDEDEESEEPR ddPTM_HeLa_Romidepsin_16h_R1 2 DADAGDEDEESEEPR 15 0 Q9NZT2-2;Q9NZT2;A0A087X028 Q9NZT2-2 OGFR Opioid growth factor receptor 0 0 ; ; 369.42 2.31E-281 19898100 3920.9 4063.5 4439.2 3803.8 4327.8 3951.9 3711.9 4603.3 4236 3818.1 FALSE FALSE TRUE 3873.110563 4120.70606 4516.462414 4243.613253 4106.936217 3699.386344 4027.188693 4736.489223 3857.121551 3718.905212 1.041465255 1.108042777 1.214460213 1.141092072 1.104340117 0.994751448 1.0828963 1.273624616 1.037165868 1 11.86066226 -10.33278248 2.682529489 1.017089579 1.127599706 0.320592494 0.070791805 0.244051519 3.324860093 0.013009873 0.015006739 4.65E-11 10.33278248 0.110510127 DADDAVYELDGK ddPTM_HeLa_Romidepsin_16h_R1 5 DADDAVYELDGK 12 0 G3V5K8;B4DJK0;B4DUA4;Q13243-2;Q13243;Q13243-3 G3V5K8 SRSF5 Serine/arginine-rich splicing factor 5 0 0 ;;;; ;;;; 180.97 1.22E-05 28938600 20883.3 20552.7 22462.9 12383.3 18045.9 18899.6 16653.8 17893.9 22044.9 22296.9 FALSE FALSE TRUE 20628.76631 20842.04145 22853.85735 13815.11541 17124.95038 17691.97656 18068.37336 18411.63176 20073.14893 21717.62332 0.949862975 0.959683347 1.052318525 0.636124644 0.78852783 0.814636864 0.831968263 0.847773787 0.924279265 1 14.40657861 -9.276821708 24.99747822 0.979391422 0.788457055 0.703613128 0.062724031 326.8849986 531212.4008 0.009300112 0.014237922 5.29E-10 9.276821708 -0.190934367 DADETKEWIEEK ddPTM_HeLa_Romidepsin_16h_R1 1 DADETKEWIEEK 12 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 128.68 0.0050983 9536200 2314.1 2378.7 2214.3 2339.1 2434.9 2562.1 1980.4 2307.8 2490.9 2475.5 FALSE FALSE TRUE 2285.894859 2412.187401 2252.838963 2609.557748 2310.637967 2398.390079 2148.615127 2374.572552 2268.107665 2411.186153 0.948037486 1.000415251 0.934328094 1.082271373 0.958299285 0.994693038 0.891102963 0.984815108 0.940660539 1 11.23552732 -7.797041889 24.99888938 0.981250181 0.937958759 0.13027242 0.045798328 219.88895 154398.2479 0.005857249 0.017572526 1.60E-08 7.797041889 -0.043291422 DADLS(ph)PVNASIIK ddPTM_HeLa_Romidepsin_16h_R1 4 DADLSPVNASIIK 13 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 DADLS(1)PVNASIIK;DADLS(0.999)PVNAS(0.001)IIK;DADLS(1)PVNASIIK;DADLS(0.999)PVNAS(0.001)IIK ;;; 180.85 5.49E-07 45174800 11698 11237.2 13074.9 6261.1 13375.8 15949.6 13200.1 13089.1 12092.5 13323 TRUE FALSE FALSE 11555.42028 11395.3976 13302.46315 6985.037841 12693.18301 14930.47203 14321.31616 13467.81246 11010.91651 12976.86654 0.890463059 0.878131679 1.025090542 0.53826845 0.978139289 1.150545241 1.103603564 1.037832393 0.848503487 1 13.66365444 -8.512402287 24.86662033 0.915448754 1.092352675 0.350991848 0.132067843 482.0980964 1144292.956 0.019144552 0.040366018 3.07E-09 8.512402287 0.176903921 DAEDALHNLDR ddPTM_HeLa_Romidepsin_16h_R1 1 DAEDALHNLDR 11 0 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 0 124.39 0.0037812 8161800 5922.4 6656.8 7836.8 3122 6296.5 7178.8 6150.5 6371 6677.8 6829.9 FALSE FALSE TRUE 5850.215511 6750.514605 7973.196217 3482.980329 5975.16611 6720.097849 6672.923316 6555.334833 6080.520843 6652.458213 0.879406578 1.014739873 1.198533829 0.523562902 0.898189198 1.010167615 1.003076322 0.985400377 0.914026161 1 12.69967183 -12.66562826 1.511903385 1.000042086 0.930139244 0 0.164229928 1.644531735 6.758713204 0.114513611 0.025608125 2.16E-13 12.66562826 -0.069902842 DAEDDGEEEDD ddPTM_HeLa_Romidepsin_16h_R1 4 DAEDDGEEEDD 11 0 Q5TB25;Q5TB19;Q9BTT0-2;Q9BTT0;H0YCE2;Q9BTT0-3 Q5TB25 ANP32E Acidic leucine-rich nuclear phosphoprotein 32 family member E 0 0 ;;; ;;; 194.44 7.03E-08 149442700 26151.2 26376 32836.7 23816.2 21882.6 22296 27851.2 12799.2 33038.9 32587.8 FALSE FALSE TRUE 25832.45912 26747.32202 33408.20899 26569.9411 20765.84927 20871.35756 30216.88023 13169.52466 30083.81804 31741.16426 0.813847246 0.842669847 1.052519962 0.837081491 0.654224561 0.657548582 0.95197769 0.414903642 0.947785588 1 14.95406743 -8.912469157 4.680882609 0.914346509 0.690326792 0.4393734 0.137850567 0.173662083 6.800112073 0.020245271 0.037377685 1.22E-09 8.912469157 -0.224019717 DAEFYEHR ddPTM_HeLa_Romidepsin_16h_R1 2 DAEFYEHR 8 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 0 ; ; 180.87 5.16E-05 12556300 13954.3 12780.9 13184.4 13614.7 13593.9 14467 10083.4 11786 15037.9 13667.8 FALSE FALSE TRUE 13784.21962 12960.82985 13413.86895 15188.89567 12900.15256 13542.60539 10939.88374 12127.00931 13692.87256 13312.70859 1.035418115 0.973568208 1.007598782 1.140932033 0.969010361 1.017268973 0.821762429 0.910934784 1.028556471 1 13.70051651 -7.772295911 24.99090541 1.018817343 0.866348613 0.613223095 0.049263435 84.95184455 195554.275 0.006495878 0.019766685 1.69E-08 7.772295911 -0.15246873 DAEGTELS(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 DAEGTELSRR 10 1 Q5T0Z8 Q5T0Z8 C6orf132 Uncharacterized protein C6orf132 1 0 DAEGT(0.124)ELS(0.876)RR 78.556 0.019234 104680000 9142 8220.9 8526.7 4942.6 9875.5 10222 8141.8 8879.6 8715.8 8261.7 TRUE FALSE FALSE 9030.573788 8336.634046 8675.103637 5514.086668 9371.516384 9568.84719 8833.364289 9136.517216 7936.237019 8047.059843 1.122220285 1.035985094 1.078046368 0.685229982 1.164588877 1.189110977 1.097713259 1.135385768 0.98622816 1 12.97424605 DAEPPS(ph)PTPAGPPR ddPTM_HeLa_Romidepsin_16h_R1 1 DAEPPSPTPAGPPR 14 0 O43306-2;O43306 O43306-2 ADCY6 Adenylate cyclase type 6 1 0 DAEPPS(0.952)PT(0.048)PAGPPR 175.6 3.93E-06 0 1253.6 2834.3 1821.4 1299.3 2531.4 3833.5 1589.9 3278.5 2017.3 1924.4 TRUE FALSE FALSE 1238.320641 2874.20135 1853.100703 1449.531179 2402.213212 3588.551722 1724.946066 3373.358225 1836.867636 1874.403811 0.66064774 1.533394957 0.988634729 0.773329189 1.281587883 1.914503002 0.92026385 1.799696632 0.979974339 1 10.87221608 -8.590627962 5.086739242 0.903533068 1.500443677 0.344010097 0.33098957 0.149481714 7.390624442 0.047707563 0.097660115 2.57E-09 8.590627962 0.596910609 DAEYIYPSLES(ph)DDDDPALK ddPTM_HeLa_Romidepsin_16h_R1 2 DAEYIYPSLESDDDDPALK 19 0 H0Y589;H0Y3N9;Q9UPP1-5;Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1 H0Y589 PHF8 Histone lysine demethylase PHF8 1 0 DAEYIYPSLES(1)DDDDPALK;DAEYIYPSLES(1)DDDDPALK ; 139.28 0.00016555 13934300 12570.8 12240.6 12687 10770.7 10801.1 9954.3 9289.4 9432.8 14390.1 13279.8 TRUE FALSE FALSE 12417.58225 12412.92349 12907.81191 12016.05901 10249.87956 9318.252356 10078.4414 9705.723186 13103.01342 12934.78888 0.960014297 0.959654124 0.997914387 0.928972179 0.792427279 0.720402354 0.779173243 0.750358067 1.013005588 1 13.65896889 -8.78402075 2.724883038 0.979635895 0.752347368 0.961731426 0.021448611 0.034816137 0.528722324 0.003183997 0.006521553 1.64E-09 8.78402075 -0.227288527 DAGDPS(ph)PPNK ddPTM_HeLa_Romidepsin_16h_R1 2 DAGDPSPPNK 10 0 A0A0A0MRT2;Q9BTA9-5;Q9BTA9-2;Q9BTA9;E9PMZ7;C9JMU2;A0A494C0B7;A0A494C0C1;A0A494C0S5;C9JVK6;C9JD58;J3QTA0;Q9BTA9-3 A0A0A0MRT2 WAC WW domain-containing adapter protein with coiled-coil 1 0 DAGDPS(1)PPNK;DAGDPS(1)PPNK ; 100.25 0.024329 78657700 15498.9 14477 14939.2 12672.4 13343.6 12489.2 11210.4 10299.7 16079.1 15690.8 TRUE FALSE FALSE 15309.99345 14680.80759 15199.21051 14137.64251 12662.6263 11691.18043 12162.6111 10597.70557 14640.94503 15283.15075 1.001756358 0.960587762 0.994507661 0.925047638 0.828535065 0.764971871 0.795818303 0.693424134 0.957979494 1 13.89965438 -8.681785391 1.094186209 0.99993061 0.735741373 0.930704066 0.028009476 0.068934802 0.158849311 0.003675744 0.011615598 2.08E-09 8.681785391 -0.264189238 DAGEGGLS(ph)LAIEGPSK ddPTM_HeLa_Romidepsin_16h_R1 1 DAGEGGLSLAIEGPSK 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 DAGEGGLS(0.999)LAIEGPS(0.001)K 172.91 6.74E-06 2380900 1268.8 1208 1427.8 805.61 1085.3 1049.6 1082 1269.8 1274 1303.9 TRUE FALSE FALSE 1253.335378 1225.006256 1452.65026 898.7584187 1029.913091 982.5339474 1173.905053 1306.53966 1160.050249 1270.02449 0.98685922 0.964553255 1.143797046 0.707670148 0.810939552 0.773633859 0.924316863 1.028751548 0.913407779 1 10.3106406 -9.260690148 24.99991221 1.001206137 0.846934793 0.380800656 0.097313981 52.79852589 1761743.538 0.014056485 0.022431116 5.49E-10 9.260690148 -0.154271345 DAGEGGLSLAIEGPSK ddPTM_HeLa_Romidepsin_16h_R1 1 DAGEGGLSLAIEGPSK 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 164.53 0.00039472 2619800 1827.9 1471 1723.5 1081.9 1582.8 1764.2 1624.7 1642.5 1816.9 1622.6 FALSE FALSE TRUE 1805.620852 1491.708777 1753.496795 1206.994368 1502.02381 1651.473314 1762.701977 1690.023146 1654.391913 1580.444618 1.14247651 0.943853875 1.109495881 0.763705577 0.95038054 1.044942224 1.115320308 1.069333988 1.046788919 1 10.62611477 -10.25082682 24.72768326 1.067280576 0.999036223 0.074756316 0.102061972 1290.658288 3007290.627 0.018459789 0.022467058 5.61E-11 10.25082682 -0.068244353 DAGT(ph)IAGLNVLR ddPTM_HeLa_Romidepsin_16h_R1 1 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 1 0 DAGT(1)IAGLNVLR 120.9 0.014936 2439400 1016 841.22 746.59 848.53 1081.5 912.92 577.28 593.38 778.31 898.62 TRUE FALSE FALSE 1003.616601 853.0627172 759.5840858 946.6410311 1026.307019 854.5873583 626.3141488 610.5485141 708.6960043 875.2737229 1.146631705 0.974623932 0.86782462 1.081537131 1.172555502 0.976365834 0.715563752 0.697551518 0.809685 1 9.773590449 -7.815338652 3.74202972 1.055418643 0.698068736 0.494222478 0.113365296 0.090177943 2.534942872 0.013240119 0.047742978 1.53E-08 7.815338652 -0.357349907 DAGTIAGLNVLR ddPTM_HeLa_Romidepsin_16h_R1 2 DAGTIAGLNVLR 12 0 P11142;E9PKE3;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 ; ; 161.51 0.0029778 1705360 476.22 468.6 674.14 445.87 593.13 659.29 580.52 367.389 370.02 371.138 FALSE FALSE TRUE 470.4156475 475.1969631 685.8731239 497.4235873 562.8603628 617.1634968 629.8293543 378.0188211 336.9244845 361.4957813 1.301303284 1.314529761 1.897319857 1.376014917 1.557031623 1.707249514 1.742286873 1.045707421 0.932028815 1 8.497835 -10.82659789 0.734806051 1.048038155 1.559391228 0.462139668 0.232391875 0.36876925 0.438848486 0.071733569 0.058058586 1.49E-11 10.82659789 0.511353073 DAGVIAGLNVLR ddPTM_HeLa_Romidepsin_16h_R1 1 DAGVIAGLNVLR 12 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931 A0A0G2JIW1 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 0 123.75 0.027034 848180 68.138 110.63 241.84 146.82 272.57 267.05 133.58 0 138.97 0 FALSE FALSE TRUE 67.30750785 112.187452 246.0491238 163.7960192 258.6597358 249.9863669 144.9262819 0 126.5401751 0 0 DAHDVS(ph)PTSTDTEAQLTVER ddPTM_HeLa_Romidepsin_16h_R1 5 DAHDVSPTSTDTEAQLTVER 20 0 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 DAHDVS(0.97)PT(0.025)S(0.005)TDTEAQLTVER;DAHDVS(1)PTSTDTEAQLTVER;DAHDVS(0.993)PT(0.003)S(0.003)TDTEAQLTVER;DAHDVS(0.771)PT(0.123)S(0.038)T(0.065)DT(0.003)EAQLTVER;DAHDVS(0.94)PT(0.03)S(0.007)T(0.002)DT(0.021)EAQLTVER ;;;; 167.95 2.46E-10 973917000 13677.4 13885.4 13611.9 13563.5 14232.1 12073.4 9449.27 9695.51 15939.3 14075.3 TRUE FALSE FALSE 13510.69459 14080.87903 13848.80941 15131.77569 13505.78283 11301.94871 10251.89076 9976.034285 14513.64909 13709.62168 0.985489965 1.027080058 1.010152558 1.103734008 0.985131694 0.824380787 0.747788013 0.727666636 1.058646944 1 13.74290114 -8.131832377 2.626612641 1.005689206 0.740242448 0.911646252 0.037126207 0.059432415 0.788243663 0.005300329 0.016456493 7.38E-09 8.131832377 -0.265446758 DAIDREVEAVDSEYQLAR ddPTM_HeLa_Romidepsin_16h_R1 2 DAIDREVEAVDSEYQLAR 18 1 F5H7V1;O43847;O43847-2;G3V1R5 F5H7V1 NRD1 Nardilysin 0 0 ; ; 201.4 1.05E-20 3269100 654.51 524.16 543.96 822.27 542.19 966.57 689.17 572.59 673.11 662.66 FALSE FALSE TRUE 646.5325804 531.5391382 553.4273956 917.3447263 514.5200211 904.8092965 747.7080826 589.1569883 612.9053558 645.4439977 1.001686564 0.823524799 0.857436738 1.421261534 0.797156722 1.401840128 1.158439904 0.912793349 0.949587196 1 9.334148114 DALDGPAAEAEPEHSFDGLR ddPTM_HeLa_Romidepsin_16h_R1 2 DALDGPAAEAEPEHSFDGLR 20 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 171.79 9.40E-11 26105000 8751.8 7867.6 9110.2 6131.6 9127.7 9859 8119.8 8842.8 9584.6 9300.2 FALSE FALSE TRUE 8645.129695 7978.360279 9268.759209 6840.564442 8661.879409 9229.041718 8809.495609 9098.652466 8727.329371 9058.579463 0.954358211 0.880751812 1.023202285 0.755147589 0.956207256 1.018817769 0.97250299 1.004423762 0.963432446 1 13.14506911 -8.289791346 20.39346665 0.95545144 0.995973606 0.093154922 0.073134132 176.4509915 126920.6358 0.010730891 0.024008985 5.13E-09 8.289791346 0.040522166 DALDGPAAEAEPEHSFDGLRR ddPTM_HeLa_Romidepsin_16h_R1 4 DALDGPAAEAEPEHSFDGLRR 21 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;;; ;;; 120.99 2.60E-05 16567900 7721.8 7405.1 6476.1 8730.7 7068.9 8086.2 6615.5 8118.5 7854.6 7286.3 FALSE FALSE TRUE 7627.683731 7509.349192 6588.813804 9740.184613 6708.147655 7569.517917 7177.420405 8353.395989 7152.064904 7097.000876 1.07477565 1.058101771 0.928394109 1.372436721 0.945208796 1.06657982 1.011331481 1.177031839 1.007758774 1 12.79299377 -13.17177815 0.298262821 0.931381737 1.086346692 0.06587428 0.118608343 16.43208393 1.224408791 0.917320834 0.058676904 6.73E-14 13.17177815 0.154964955 DALGDSLQVPVS(ph)PSSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 3 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 DALGDSLQVPVS(0.943)PS(0.03)S(0.004)T(0.01)T(0.01)S(0.003)S(0.001)R;DALGDSLQVPVS(0.986)PS(0.006)S(0.006)T(0.001)T(0.001)SSR;DALGDSLQVPVS(0.977)PS(0.014)S(0.006)T(0.002)T(0.001)SSR ;; 214.3 4.08E-32 615273700 10704.5 11065 10283 9818.8 12140 10679.6 9784.6 11214.8 11045.2 10647.6 TRUE FALSE FALSE 10574.02944 11220.77336 10461.9713 10954.09585 11520.4505 9997.208027 10615.70368 11539.28254 10057.28965 10370.97382 1.019579224 1.081940188 1.008774247 1.056226353 1.110835945 0.963960396 1.023597578 1.112651786 0.969753644 1 13.34026375 -10.47636237 6.838881357 1.008505811 1.047876349 0.226370164 0.044864945 0.314271698 35.61781188 0.007226041 0.008100958 3.34E-11 10.47636237 0.039370538 DALGDSLQVPVSPS(ph)STTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 DALGDSLQVPVS(0.061)PS(0.47)S(0.086)T(0.086)T(0.086)S(0.124)S(0.086)R 94.856 0.0011775 5585700 996.36 817.36 1072.2 742.01 888.15 1014.7 782.24 768.5 932.98 836.68 TRUE FALSE FALSE 984.2159811 828.8668155 1090.861191 827.8046875 842.8243914 949.8639448 848.6834461 790.735335 849.5319321 814.942933 1.207711536 1.017085715 1.338573717 1.015782399 1.034212774 1.165558846 1.041402302 0.970295346 1.042443462 1 9.670555227 -7.514203882 4.891117245 1.104741707 0.983120399 0.141323533 0.10230779 0.273508606 18.15000301 0.015002056 0.074027399 3.06E-08 7.514203882 -0.121621307 DALGDSLQVPVSPSS(ph)TTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 DALGDSLQVPVSPSSTTSSR 20 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 DALGDSLQVPVS(0.141)PS(0.175)S(0.592)T(0.066)T(0.026)S(0.001)SR 253.52 6.73E-80 253910000 6532.1 6137.3 5657 5604 6455.5 6847.7 5787.1 6283.6 6704.8 6185.5 TRUE FALSE FALSE 6452.484253 6223.70107 5755.457712 6251.960848 6126.051746 6410.15407 6278.65613 6465.406052 6105.105896 6024.799818 1.070987327 1.033013753 0.955294431 1.037704328 1.016805858 1.063961337 1.042135228 1.073132095 1.013329252 1 12.55669759 -16.5228157 0.006110974 0.335805414 1.673771681 0.135341422 0.031993867 62823.55223 31.05565941 3706.377579 3117.218158 3.00E-17 16.5228157 1.337966267 DALNIETAIK ddPTM_HeLa_Romidepsin_16h_R1 2 DALNIETAIK 10 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YNB8;H0YMW4;H0YKN4 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 ; ; 180.07 0.0004315 7504500 2365.76 2674.96 2117.88 1709.41 2530.51 2555.6 1943.16 2441.63 2620.84 2413.65 FALSE FALSE TRUE 2336.925207 2712.618157 2154.740813 1907.060027 2401.368632 2392.305408 2108.211962 2512.274712 2386.425506 2350.943025 0.994037364 1.153842576 0.916543187 0.811189385 1.021449098 1.017593954 0.896751618 1.068624244 1.015092872 1 11.19902386 DALQDS(ph)LAR ddPTM_HeLa_Romidepsin_16h_R1 2 DALQDSLAR 9 0 Q96A99-2;Q96A99 Q96A99-2 PTX4 Pentraxin-4 1 0 DALQDS(1)LAR;DALQDS(1)LAR ; 118.74 0.014185 10049300 3691.7 3412.7 3413.5 3709.5 4101.1 4416.5 3797.5 3013.8 3623.3 3292.6 TRUE FALSE FALSE 3646.70414 3460.74408 3472.910536 4138.409844 3891.805564 4134.299904 4120.059555 3100.999548 3299.222973 3207.057777 1.137087135 1.079102505 1.082896155 1.290407012 1.213512769 1.289125482 1.284685167 0.966929742 1.02873824 1 11.64703463 -9.358616855 6.712501039 1.068383284 1.217575426 0.364805624 0.094312415 0.211147431 12.51272714 0.014900511 0.022821098 4.38E-10 9.358616855 0.149192142 DANGNSFATR ddPTM_HeLa_Romidepsin_16h_R1 1 DANGNSFATR 10 0 P62701;C9JEH7;Q8TD47;P22090 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2;40S ribosomal protein S4, Y isoform 1" 0 0 199.33 2.72E-11 9040600 1606.4 1084.7 1483 1258.9 1533 1721.9 1633 1158.4 1468 1324.9 FALSE FALSE TRUE 1586.820579 1099.970435 1508.810993 1404.459941 1454.76529 1611.876147 1771.706979 1191.916476 1336.698403 1290.478907 1.229636975 0.85237382 1.169186869 1.088324601 1.127306523 1.249052688 1.372906577 0.923623369 1.03581577 1 10.33369085 -8.461550493 5.1349884 1.093830862 1.200422858 0.097914597 0.14262032 0.407169308 21.76874557 0.020863539 0.04691895 3.46E-09 8.461550493 0.106591996 DANSSFFDNSS(ph)SPHLLDQLK ddPTM_HeLa_Romidepsin_16h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 0 DANSSFFDNS(0.013)S(0.493)S(0.493)PHLLDQLK 130.3 0.0001521 14676000 1425.2 1421.6 1380.9 1384 1974.4 2266.9 1853.3 2161.7 1716.4 1802.2 TRUE FALSE FALSE 1407.829114 1441.613322 1404.933985 1544.024592 1873.639 2122.052406 2010.719256 2224.245379 1562.880885 1755.378584 0.802008824 0.821254933 0.800359534 0.879596348 1.06737032 1.208885892 1.145461881 1.267102948 0.890338357 1 10.7775665 -8.561566459 2.766178909 0.88643057 1.200234985 0.854822759 0.063394102 0.109702865 1.695563739 0.01333959 0.030398386 2.74E-09 8.561566459 0.313804415 DANSSFFDNSSS(ph)PHLLDQLK ddPTM_HeLa_Romidepsin_16h_R1 1 DANSSFFDNSSSPHLLDQLK 20 0 P49454 P49454 CENPF Centromere protein F 1 0 DANSSFFDNS(0.04)S(0.145)S(0.815)PHLLDQLK 108.79 0.00016758 19109000 2300.6 2101.6 2168.2 2021.8 3683.7 3881.9 3557 3773.5 3160.3 2676.1 TRUE FALSE FALSE 2272.559402 2131.18638 2205.936611 2255.570029 3495.707043 3633.859118 3859.131491 3882.680269 2877.634853 2606.574536 0.871856673 0.817619581 0.846297154 0.86533878 1.341111484 1.394112874 1.480537555 1.489571932 1.103991009 1 11.3479394 -8.677264137 4.172226262 0.915250199 1.444314304 0.899552347 0.083734318 0.044976065 1.470351514 0.011642843 0.023785603 2.10E-09 8.677264137 0.529064105 DAPAGS(ph)PPASPGPQGPSTK ddPTM_HeLa_Romidepsin_16h_R1 2 DAPAGSPPASPGPQGPSTK 19 0 A0A0A0MRX4;Q3MIN7;Q3MIN7-2 A0A0A0MRX4 RGL3 Ral guanine nucleotide dissociation stimulator-like 3 1 0 DAPAGS(1)PPASPGPQGPSTK;DAPAGS(0.997)PPAS(0.003)PGPQGPSTK ; 135.79 0.00067265 9682800 3943.5 3754.4 4158.9 4677.7 5126.2 5671.4 5114.5 5848.6 4122.6 3820.1 TRUE FALSE FALSE 3895.435105 3807.254542 4231.28391 5218.557683 4864.590886 5309.015844 5548.925502 6017.820013 3753.864331 3720.853251 1.046919844 1.023220827 1.137181078 1.402516394 1.307385849 1.426827527 1.491304582 1.617322589 1.008871911 1 11.86141778 -8.799700543 0.608890569 1.006177957 1.603426053 0.928351244 0.058452637 0.180414505 0.112690687 0.012674815 0.054323918 1.59E-09 8.799700543 0.597248097 DAPIS(ph)PASIASSSSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 2 DAPISPASIASSSSTPSSK 19 0 Q04727-4;Q04727;Q04727-3;H7C4E4;H0Y5S0 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 0 DAPIS(0.885)PAS(0.113)IASS(0.001)SSTPSSK;DAPIS(0.881)PAS(0.113)IAS(0.004)S(0.002)SSTPSSK ; 123.63 0.0008828 51176000 2982.1 3280.8 3289.9 4184.1 6407.9 6276.9 6226.3 6505.4 3573.3 4368.6 TRUE FALSE FALSE 2945.753018 3326.987189 3347.159329 4667.885329 6080.880952 5875.826348 6755.161767 6693.623485 3253.695099 4255.103142 0.692287101 0.781881679 0.786622373 1.097008738 1.429079566 1.380889288 1.587543601 1.573081371 0.764657163 1 12.05497839 -8.865051387 2.022800365 0.838975523 1.517053072 0.922091667 0.094073571 0.087601488 0.727718363 0.020201298 0.042253024 1.36E-09 8.865051387 0.67807755 DAPQDFHPDR ddPTM_HeLa_Romidepsin_16h_R1 4 DAPQDFHPDR 10 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ;;; ;;; 120.86 0.0052833 241298000 30812.7 28091.3 28355.5 18967.9 32823 36366.5 26768.2 30919 27612.9 27289.5 FALSE FALSE TRUE 30437.14296 28486.77006 28849.01558 21161.05784 31147.91983 34042.79802 29041.89024 31813.59248 25143.13307 26580.51486 1.145092303 1.071716263 1.085344499 0.796111661 1.171832826 1.280742612 1.092600741 1.196876458 0.945923478 1 14.69808143 -8.557695133 24.99996265 1.051923682 1.187986979 0.375315213 0.10360606 173.9401811 124897.4107 0.015060681 0.03012145 2.77E-09 8.557695133 0.136063297 DAPSLEEVEGHVADGS(ph)ATEMGTTK ddPTM_HeLa_Romidepsin_16h_R1 1 DAPSLEEVEGHVADGSATEMGTTK 24 0 Q15003;E9PHA2;C9J470;Q15003-2 Q15003 NCAPH Condensin complex subunit 2 1 0 DAPSLEEVEGHVADGS(0.39)AT(0.381)EMGT(0.186)T(0.044)K 89.756 2.62E-05 6462500 1237.3 1398.9 1508.8 1367.5 2044.4 2861.1 1905 2282.9 1602.7 1342.1 TRUE FALSE FALSE 1222.219312 1418.593751 1535.060031 1525.616784 1940.066639 2678.284944 2066.810652 2348.95211 1459.350498 1307.232049 0.934967371 1.085188932 1.174282739 1.167058891 1.48410272 2.04882136 1.581058738 1.796889934 1.11636683 1 10.35229954 -8.758611816 1.612015048 0.98880189 1.796456559 0.849029528 0.136932645 0.085955317 0.45127882 0.019909352 0.047612995 1.74E-09 8.758611816 0.807654669 DAPT(ph)SPASVASSSSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 DAPTSPASVASSSSTPSSK 19 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 DAPT(0.873)S(0.127)PASVASSSSTPSSK 147.49 9.77E-05 169200000 4148.7 3815.5 4445 4199.4 4173.2 3697.3 2968.4 3469.7 4557.6 4263.9 TRUE FALSE FALSE 4098.134049 3869.214709 4522.36336 4684.954387 3960.226032 3461.054462 3220.535822 3570.090295 4149.956841 4153.123263 0.986759552 0.931639748 1.088906607 1.128055704 0.953553695 0.833361844 0.77544913 0.85961578 0.999237581 1 12.01998098 -8.320874225 3.675613004 1.005666877 0.815633422 0.706978487 0.056656238 0.102806991 2.788493629 0.00847401 0.020718679 4.78E-09 8.320874225 -0.190033455 DAPTIQQSS(ph)PGSSLR ddPTM_HeLa_Romidepsin_16h_R1 1 DAPTIQQSSPGSSLR 15 0 Q9UQ49;Q9UQ49-2 Q9UQ49 NEU3 Sialidase-3 1 0 DAPT(0.001)IQQS(0.242)S(0.727)PGS(0.027)S(0.003)LR 83.292 0.0040301 0 1782.3 1843.7 2470 2399.9 2173.9 2079.9 1991.7 1987.6 2215.9 2320 TRUE FALSE FALSE 1760.576642 1869.655657 2512.989314 2677.38773 2062.957771 1947.001103 2160.874948 2045.10807 2017.704354 2259.726066 0.779110649 0.827381551 1.112076969 1.184828449 0.912923828 0.861609348 0.956255265 0.905024773 0.892897765 1 11.14193218 -9.788535461 24.98882467 0.887653418 0.986989794 0.214355742 0.105697394 358.3233283 330455.0854 0.020970398 0.027564219 1.63E-10 9.788535461 0.099336376 DAPTS(ph)PASVASS(ph)SSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 DAPTSPASVASSSSTPSSK 19 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 2 0 DAPT(0.122)S(0.686)PAS(0.191)VAS(0.007)S(0.438)S(0.318)S(0.233)T(0.005)PSSK 108.25 0.0092607 15536000 2510.3 2677.4 2931 2617.8 2345.2 2084.1 1467.6 1685.5 2929.5 2847.3 TRUE FALSE FALSE 2479.703498 2715.092507 2982.012826 2920.482353 2225.515693 1950.932736 1592.257907 1734.267283 2667.478183 2773.326736 0.894125985 0.979002031 1.075247567 1.053061046 0.80247151 0.703462997 0.574132823 0.625338248 0.961833364 1 11.43740188 -8.360745525 2.198321163 0.967493746 0.611183493 0.879904451 0.059322314 0.092429268 0.86287815 0.010380713 0.028787394 4.36E-09 8.360745525 -0.356310253 DAPTS(ph)PASVASSSS(ph)TPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 DAPTSPASVASSSSTPSSK 19 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 2 0 DAPT(0.022)S(0.977)PASVASSSS(0.716)T(0.284)PSSK 217.67 1.73E-28 15637000 2665.6 2232.5 2095.8 2294.1 1911.7 1554.9 1300.4 1243.3 2324.8 2288.3 TRUE FALSE FALSE 2633.110642 2263.929194 2132.27652 2559.354636 1814.138815 1455.546908 1410.855944 1279.272924 2116.864065 2228.849636 1.181376527 1.015738862 0.956671318 1.148285014 0.813935039 0.653048498 0.632997364 0.573961071 0.949756337 1 11.12208358 -8.514954006 2.506468332 1.075494977 0.617126491 0.846935623 0.07973258 0.077115763 0.964327425 0.012690095 0.03044241 3.06E-09 8.514954006 -0.458368486 DAPTS(ph)PASVASSSSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 3 DAPTSPASVASSSSTPSSK 19 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 DAPT(0.007)S(0.985)PAS(0.008)VASSSSTPSSK;DAPT(0.022)S(0.977)PAS(0.001)VASSSSTPSSK;DAPT(0.002)S(0.998)PASVASSSSTPSSK ;; 292.19 2.62E-124 454130000 11462.2 9894.3 9786.4 10471.7 10762.8 10116.8 8423.6 9178.1 11303.3 10369 TRUE FALSE FALSE 11322.4943 10033.59222 9956.728187 11682.48722 10213.53415 9470.36913 9139.100374 9443.653843 10292.30454 10099.61189 1.121082119 0.993463148 0.985852556 1.156726353 1.011279866 0.937696343 0.904896196 0.935051163 1.019079214 1 13.30201223 -8.330276116 3.500151179 1.054251919 0.921813986 0.4961704 0.053438261 0.15788985 3.790947578 0.008785673 0.021584478 4.67E-09 8.330276116 -0.132437933 DAPVHGSPT(ph)GPGAWTASK ddPTM_HeLa_Romidepsin_16h_R1 1 DAPVHGSPTGPGAWTASK 18 0 Q9BRP1 Q9BRP1 PDCD2L Programmed cell death protein 2-like 1 0 DAPVHGS(0.459)PT(0.54)GPGAWT(0.001)ASK 77.51 0.011603 6436800 2241.8 2225.9 2049 1968 2573 2542.1 1909.9 2462.7 2373.3 2292.8 TRUE FALSE FALSE 2214.476079 2257.236279 2084.661985 2195.54942 2441.690209 2379.668014 2072.126858 2533.954339 2161.026104 2233.232725 0.991601123 1.010748344 0.933472791 0.983126118 1.093343377 1.065570994 0.927859795 1.134657535 0.96766722 1 11.12491789 -8.790685698 24.99771062 0.991147555 1.046980449 0.300240496 0.05364415 232.2823353 198537.9036 0.007273999 0.013186807 1.62E-09 8.790685698 0.055832893 DAQHYGGWEHR ddPTM_HeLa_Romidepsin_16h_R1 2 DAQHYGGWEHR 11 0 F5H6X6;Q14697;Q14697-2;E9PKU7 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 ; ; 115.92 0.0045239 12609300 8779.6 7042.8 8149.3 9007.5 8372.9 8183.6 6663.1 8501.1 8292.8 6579.4 FALSE FALSE TRUE 8672.590858 7141.948723 8291.135148 10048.98953 7945.599669 7660.694371 7229.063548 8747.065916 7551.071198 6408.46624 1.353302106 1.114455231 1.293778392 1.568080279 1.2398598 1.195402158 1.12804894 1.36492346 1.178296166 1 12.6457634 -12.39097583 0.926584192 0.98602089 1.283524804 0.203612377 0.135496504 0.520100798 0.736244763 0.111315716 0.023630625 4.06E-13 12.39097583 0.297503914 DAS(ph)DDLDDLNFFNQK ddPTM_HeLa_Romidepsin_16h_R1 1 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 0 DAS(1)DDLDDLNFFNQK 152.11 3.88E-05 0 783.02 494.17 406.44 288.66 620.9 650.48 328.49 552.18 591.65 666.04 TRUE FALSE FALSE 773.4762511 501.1269382 413.5139177 322.0362274 589.2131561 608.9164273 356.3919324 568.1564571 538.7313422 648.7361848 1.192281653 0.772466451 0.637414603 0.496405527 0.908247713 0.938619491 0.549363425 0.875789682 0.830432084 1 9.341488101 -10.19366236 6.264888836 1.090587352 0.731395766 0.317573996 0.167194632 0.131138525 9.71179627 0.025596573 0.031354887 6.40E-11 10.19366236 -0.359191586 DAS(ph)DGEDEKPPLPPR ddPTM_HeLa_Romidepsin_16h_R1 1 DASDGEDEKPPLPPR 15 1 O15357 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 1 0 DAS(1)DGEDEKPPLPPR 121.42 0.00016382 0 825.55 909.29 756.17 644.27 711.51 648.82 547.95 807.56 937.35 935.37 TRUE FALSE FALSE 815.4878791 922.0910085 769.3308217 718.7635288 675.1989897 607.362496 594.4928593 830.9254745 853.5110684 911.0689526 0.895089089 1.012097938 0.84442656 0.788923305 0.741106354 0.66664822 0.652522356 0.912033576 0.936823789 1 9.831416436 -9.374494807 1.920278514 0.953896473 0.733873777 0.63165135 0.074375621 0.159775072 1.154659108 0.01230836 0.020663565 4.22E-10 9.374494807 -0.220022696 DAS(ph)PTPS(ph)TDAEYPANGSGADR ddPTM_HeLa_Romidepsin_16h_R1 1 DASPTPSTDAEYPANGSGADR 21 0 E9PEE2;E7EPF5;O43639 E9PEE2 NCK2 Cytoplasmic protein NCK2 2 0 DAS(0.984)PT(0.465)PS(0.468)T(0.083)DAEYPANGSGADR 119.5 0.0014166 6390400 611.17 638.65 640.28 608.08 479.67 688.19 545.29 514.31 578.09 572.23 TRUE FALSE FALSE 603.720825 647.6409315 651.4238048 678.3890707 455.19065 644.21688 591.606919 529.1907484 526.3841825 557.3633821 1.083172746 1.161972516 1.168759602 1.217139648 0.816685603 1.155829214 1.06143844 0.949453741 0.944418308 1 9.122474413 -6.144300544 13.2812088 1.057387043 0.966463646 0 0.120364874 0 0 0.014677602 0 7.17E-07 6.144300544 -0.090923397 DAS(ph)PTPSTDAEYPANGSGADR ddPTM_HeLa_Romidepsin_16h_R1 2 DASPTPSTDAEYPANGSGADR 21 0 E9PEE2;E7EPF5;O43639 E9PEE2 NCK2 Cytoplasmic protein NCK2 1 0 DAS(0.982)PT(0.017)PSTDAEYPANGSGADR;DAS(0.952)PT(0.048)PS(0.001)TDAEYPANGSGADR ; 195.48 3.17E-18 13016900 1941.35 2018.98 1353.72 1682.13 1769.33 1680.83 1683.85 1781.03 2148.82 2014.5 TRUE FALSE FALSE 1917.688079 2047.403253 1377.280929 1876.625785 1679.034488 1573.430388 1826.876177 1832.561293 1956.624157 1962.163 0.977333728 1.043441984 0.701919733 0.956406672 0.855705916 0.801885668 0.9310522 0.933949572 0.997177175 1 10.93822918 -9.816391189 24.99999733 0.993058355 0.867624949 0.479690149 0.071468422 59.42798409 27036.08726 0.010702249 0.014065516 1.53E-10 9.816391189 -0.125433406 DAS(ph)SPVPPPHVPPPVPPLRPR ddPTM_HeLa_Romidepsin_16h_R1 2 DASSPVPPPHVPPPVPPLRPR 21 1 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7;O94875-6 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 DAS(0.501)S(0.499)PVPPPHVPPPVPPLRPR;DAS(0.5)S(0.5)PVPPPHVPPPVPPLRPR ; 56.424 0.009691 28425000 2844.1 2298.5 2267.94 2046.25 1919.79 1864.92 1369.43 1740.46 2389.3 2591 TRUE FALSE FALSE 2809.435015 2330.858343 2307.412544 2282.847053 1821.815953 1745.757631 1485.74935 1790.817464 2175.595024 2523.685446 1.113227094 0.923593052 0.91430275 0.904568775 0.721887094 0.691749296 0.588722082 0.70960407 0.862070599 1 11.30131639 -8.999776707 0.90297675 1.049792743 0.635697996 0.721747138 0.080588363 0.139023506 0.219965029 0.01135843 0.030972925 1.00E-09 8.999776707 -0.414094747 DAS(ph)VPLIDVTNLPTPR ddPTM_HeLa_Romidepsin_16h_R1 1 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 0 DAS(0.942)VPLIDVT(0.056)NLPT(0.002)PR 101.78 0.0050766 2076400 827.62 879.21 1004.8 922.81 720.2 995.14 921.55 957.64 1106.5 1079.5 TRUE FALSE FALSE 817.5326491 891.5875415 1022.288123 1029.509634 683.4455066 931.5537657 999.826434 985.3478025 1007.531869 1051.454434 0.777525514 0.847956423 0.972260984 0.9791291 0.650000118 0.885966843 0.95089849 0.937128391 0.958226848 1 10.03817062 -12.60416481 1.422023132 0.999585034 0.862390296 0.142972747 0.096687696 0.543202146 1.980853306 0.0700546 0.016379362 2.49E-13 12.60416481 -0.137194738 DASAQQDSYEFVSPS(ph)PPADVSER ddPTM_HeLa_Romidepsin_16h_R1 2 DASAQQDSYEFVSPSPPADVSER 23 0 A0A494C142;A0A087X2H0;Q99728-3;Q99728-2;Q99728 A0A494C142 BARD1 BRCA1-associated RING domain protein 1 1 0 DASAQQDSYEFVS(0.009)PS(0.984)PPADVS(0.007)ER;DASAQQDSYEFVS(0.002)PS(0.998)PPADVSER ; 113.02 3.74E-06 6322400 2262.73 2233.96 2037.44 1870.51 1703.61 1655.26 1166.43 1440.09 2413.48 1966.46 TRUE FALSE FALSE 2235.150976 2265.409748 2072.900789 2086.787167 1616.668425 1549.494228 1265.506535 1481.756732 2197.612304 1915.371086 1.166954536 1.182752399 1.082245004 1.089494972 0.844049718 0.808978605 0.66071089 0.773613397 1.147355894 1 10.90340821 -8.59635212 2.078686451 1.092061749 0.734104985 0.877568434 0.062493678 0.101295641 0.878474673 0.011831118 0.028554131 2.53E-09 8.59635212 -0.357956764 DASDDLDDLNFFNQK ddPTM_HeLa_Romidepsin_16h_R1 2 DASDDLDDLNFFNQK 15 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 0 ; ; 262.15 3.92E-70 26804000 6753.1 5507.4 5950.8 3394.1 5795 5499.2 5170 5622.3 6580.3 6554.9 FALSE FALSE TRUE 6670.79062 5584.933322 6054.371178 3786.541812 5499.259526 5147.818868 5609.139671 5784.97238 5991.741487 6384.602753 1.044824694 0.874750323 0.94827688 0.593073987 0.861331509 0.806286478 0.878541687 0.906081804 0.938467391 1 12.64038114 -9.961572705 1.930952847 1.020919676 0.819507831 0.364273307 0.093732094 0.193461299 1.440950051 0.015256065 0.020284785 1.09E-10 9.961572705 -0.201411845 DASEET(ph)STSVMQK ddPTM_HeLa_Romidepsin_16h_R1 2 DASEETSTSVMQK 13 0 Q9H0W8-2;Q9H0W8;M0QZH1;M0QX70;M0QYR7;M0R2N0;M0QZC7 Q9H0W8-2 SMG9 Protein SMG9 1 0 DASEET(0.95)S(0.024)T(0.024)S(0.002)VMQK;DAS(0.159)EET(0.814)S(0.013)T(0.013)SVMQK ; 142.19 0.0022123 18605700 7388.9 6287.2 7024.2 6738.3 6117.9 5447.6 4588 5391.6 6917.4 7308.4 TRUE FALSE FALSE 7298.841245 6375.711367 7146.453254 7517.413951 5805.680734 5099.515941 4977.704605 5547.597439 6298.690419 7118.526714 1.025330316 0.895650409 1.003923079 1.056035083 0.815573358 0.716372382 0.699260508 0.779318202 0.884830622 1 12.79736297 -8.61143047 4.059904774 1.004425393 0.732528002 0.783521481 0.057978399 0.049739035 1.549898707 0.006540547 0.013622885 2.45E-09 8.61143047 -0.27189739 DASGDGELDLS(ph)GIDDLEIDR ddPTM_HeLa_Romidepsin_16h_R1 1 DASGDGELDLSGIDDLEIDR 20 0 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 1 0 DASGDGELDLS(1)GIDDLEIDR 149.24 2.04E-05 1152300 302.99 368.02 311.77 153.8 396.12 399.33 284.24 317.59 334.79 354.03 TRUE FALSE FALSE 299.2970413 373.2009952 317.1962261 171.5830797 375.9045183 373.8141018 308.3833385 326.7789656 304.8455439 344.8322496 0.867949682 1.08226825 0.919856616 0.497584202 1.090108361 1.084046235 0.894299587 0.947646184 0.884040122 1 8.429750895 -12.59058573 1.348879938 1.000481146 0.916362709 0 0.16661315 1.530621003 4.948775166 0.118030303 0.026740312 2.57E-13 12.59058573 -0.084118437 DASS(ph)SPASTASSASSTSLK ddPTM_HeLa_Romidepsin_16h_R1 1 DASSSPASTASSASSTSLK 19 0 A0A669KBK8;Q04724 A0A669KBK8 TLE1 Transducin-like enhancer protein 1 1 0 DAS(0.168)S(0.654)S(0.168)PAS(0.004)T(0.004)ASS(0.001)ASSTSLK 70.272 0.015967 41424000 1488.3 1596.9 1014.7 3337.8 1127.8 1524.4 975.12 1445.5 1841 1501.5 TRUE FALSE FALSE 1470.160027 1619.3812 1032.360428 3723.732141 1070.244158 1426.99576 1057.946668 1487.323262 1676.336349 1462.490814 1.00524394 1.107276152 0.705891906 2.546157628 0.731795474 0.975729725 0.723386881 1.016979559 1.146220088 1 10.51421185 DASSS(ph)PASTASSASSTSLK ddPTM_HeLa_Romidepsin_16h_R1 1 DASSSPASTASSASSTSLK 19 0 A0A669KBK8;Q04724 A0A669KBK8 TLE1 Transducin-like enhancer protein 1 1 0 DAS(0.026)S(0.141)S(0.788)PAS(0.036)T(0.003)AS(0.005)S(0.001)ASSTSLK 107.46 0.00094794 29427000 3768.3 3339.9 3650.1 4275.1 4190.5 3655.8 2693 3076.9 3645.1 3966.1 TRUE FALSE FALSE 3722.37051 3386.9192 3713.628459 4769.407177 3976.643148 3422.206179 2921.743353 3165.925247 3319.073127 3863.06015 0.963580779 0.876745137 0.961317793 1.234618927 1.029402337 0.885879599 0.756328724 0.81953817 0.859182357 1 11.91552843 -8.01689943 3.852679686 0.994256268 0.790495474 0.40723091 0.097719622 0.145970322 4.791874727 0.013031047 0.039249352 9.62E-09 8.01689943 -0.203760795 DASTS(ph)PMPTGSLK ddPTM_HeLa_Romidepsin_16h_R1 1 DASTSPMPTGSLK 13 0 K7EM46;Q86T90-3;Q86T90-2;Q86T90 K7EM46 KIAA1328 Uncharacterized protein KIAA1328 1 0 DAS(0.006)T(0.085)S(0.864)PMPT(0.044)GSLK 94.409 0.025003 3587600 2183.9 2088.7 2057.6 1779.9 3297.8 3483.7 2639 2995.7 2271 2383.9 TRUE FALSE FALSE 2157.281787 2118.104773 2093.411665 1985.700413 3129.50096 3261.102813 2863.156594 3082.375853 2067.876072 2321.965934 0.929075554 0.912203208 0.901568638 0.855180683 1.347780738 1.404457647 1.233074332 1.32748539 0.890571236 1 11.18113109 -8.754671 24.99998817 0.948833109 1.326851959 0.922232068 0.058313543 34.8740164 128811.0087 0.009052052 0.017781889 1.76E-09 8.754671 0.37801885 DASVPLIDVTNLPT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 DASVPLIDVTNLPTPR 16 0 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 0 DASVPLIDVTNLPT(1)PR;DASVPLIDVTNLPT(1)PR;DASVPLIDVT(0.01)NLPT(0.99)PR;DASVPLIDVT(0.002)NLPT(0.998)PR ;;; 224.67 1.14E-34 43265500 8480.45 8464.28 8527.56 7995.18 10109.65 11859.63 9240.32 10664.9 8171.79 8275.4 TRUE FALSE FALSE 8377.087013 8583.440356 8675.978605 8919.62033 9593.716836 11101.83792 10025.19255 10973.47206 7440.884636 8060.403915 1.039288738 1.064889607 1.076370204 1.106597191 1.190227802 1.377330223 1.243758087 1.361404735 0.923140418 1 12.97663642 -8.728463543 0.995899823 1.020738879 1.338285994 0.869525393 0.051866708 0.113114778 0.213654863 0.006769151 0.02193793 1.87E-09 8.728463543 0.317547115 DAT(ph)PPVSPINMEDQER ddPTM_HeLa_Romidepsin_16h_R1 1 DATPPVSPINMEDQER 16 0 P17275 P17275 JUNB Transcription factor jun-B 1 0 DAT(0.992)PPVS(0.008)PINMEDQER 92.269 0.02701 6847100 2247.2 1931.4 2114.9 2120.8 1573.2 1406.7 1286.5 1669.8 2232.1 1930.3 TRUE FALSE FALSE 2219.810262 1958.5903 2151.708947 2366.016875 1492.913734 1316.81641 1395.775278 1718.113028 2032.455386 1880.150528 1.180655607 1.041719943 1.144434403 1.258418855 0.794039473 0.700378183 0.742374218 0.913816741 1.081006736 1 10.87663246 -8.711641939 10.87587099 1.099375934 0.777737043 0.779029891 0.085719089 0.22907851 48.95304918 0.014293959 0.028574406 1.94E-09 8.711641939 -0.321638891 DATLTEHVIRGLLKYWPK ddPTM_HeLa_Romidepsin_16h_R1 1 DATLTEHVIRGLLKYWPK 18 2 Q15173-2;Q15173 Q15173-2 PPP2R5B Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform 0 0 46.319 0.021839 610600 275.74 370.1 345.02 316.3 436.31 258.39 369.53 420.84 326.41 218.97 FALSE FALSE TRUE 272.3791748 375.3102775 351.0249284 352.8720942 414.0434726 241.8797129 400.917869 433.0163414 297.2150721 213.2811278 1.277089903 1.759697547 1.645832109 1.654492818 1.941303841 1.134088681 1.879762514 2.030260932 1.393536667 1 7.736612504 -10.54486636 1.06359245 1.071026999 1.724205072 0.402650323 0.259390129 0.227501838 0.523311331 0.054085843 0.055852616 2.85E-11 10.54486636 0.653178073 DATNVGDEGGFAPNILENK ddPTM_HeLa_Romidepsin_16h_R1 2 DATNVGDEGGFAPNILENK 19 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 ; ; 213.71 4.36E-28 14196000 6298.4 5078.9 6015.2 3198.7 6591.9 6353.1 4883.7 5719.4 6096.3 5027.8 FALSE FALSE TRUE 6221.632678 5150.400888 6119.892033 3568.548744 6255.490745 5947.157414 5298.521356 5884.881815 5551.03166 4897.177031 1.270452883 1.051708128 1.249677517 0.728695067 1.277366676 1.214405233 1.08195422 1.201688601 1.133516641 1 12.25773463 -12.69350642 1.583216378 1.000241555 1.151213058 0 0.159874243 0.691833934 3.134068048 0.10750955 0.023974557 2.03E-13 12.69350642 0.150971503 DATNVGDEGGFAPNILENKEGLELLK ddPTM_HeLa_Romidepsin_16h_R1 2 DATNVGDEGGFAPNILENKEGLELLK 26 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 ; ; 180.31 1.41E-18 30776000 5488 5028.1 4419.5 5745.1 5494.5 5718.5 4647.9 5122.2 5385.6 4619 FALSE FALSE TRUE 5421.110145 5098.885724 4496.419544 6409.375494 5214.095162 5353.106306 5042.69251 5270.402776 4903.898448 4498.997714 1.204959524 1.133338145 0.999426946 1.424622972 1.158945946 1.189844193 1.120847982 1.171461537 1.089997986 1 12.13538792 -12.43404829 0.687494939 0.971496987 1.179152914 0.181447041 0.103339338 1.036512619 0.677942398 0.133596422 0.020094877 3.68E-13 12.43404829 0.207655926 DAVLLVFANK ddPTM_HeLa_Romidepsin_16h_R1 1 DAVLLVFANK 10 0 C9J1Z8;F5H423;P61204-2;P84085;P84077;P61204 C9J1Z8 ARF5;ARF3;ARF1 ADP-ribosylation factor 3;ADP-ribosylation factor 5;ADP-ribosylation factor 1 0 0 128.36 0.021125 342060 160.88 231.56 155.79 127.59 221.26 209.66 223.36 145.9 185.69 59.124 FALSE FALSE TRUE 158.9191327 234.8199078 158.5014596 142.3425561 209.9682766 196.2634026 242.3321928 150.1213863 169.0814213 57.58794996 2.759590032 4.07758755 2.752337246 2.471742027 3.64604534 3.408063715 4.208036456 2.60681942 2.936055572 1 5.84769506 -11.75778115 0.47747925 0.717150035 3.413752555 0.120461785 0.826123113 0.513985157 0.209890109 0.636701704 0.176085842 1.75E-12 11.75778115 2.696602521 DAVTYTEHAK ddPTM_HeLa_Romidepsin_16h_R1 2 DAVTYTEHAK 10 0 P62805 P62805 HIST1H4A Histone H4 0 0 ; ; 146.11 0.0018752 112299000 12164.7 11819.4 21824.1 22892.5 28882 25197 23223.4 17584.9 11855.4 7818.4 FALSE FALSE TRUE 12016.43196 11985.79382 22203.93931 25539.43856 27408.04377 23586.99302 25195.99502 18093.69134 10795.02333 7615.276841 1.577937639 1.573914393 2.915710061 3.353711112 3.599086985 3.097325746 3.308611826 2.375972892 1.417548378 1 12.89468077 -9.779333021 2.660106297 1.277333394 3.185597548 0.869339715 0.327411079 0.068749553 1.000046655 0.059267253 0.082918343 1.66E-10 9.779333021 1.908264155 up GVTQFGNK(ac)YIQQTK ddPTM_HeLa_Romidepsin_16h_R1 2 GVTQFGNKYIQQTK 14 1 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 1 ; GVTQFGNK(1)YIQQTK;GVTQFGNK(1)YIQQTK 337.53 2.05E-202 5796900 956.71 778.34 1275.82 1168.27 1898.07 1832.24 1579.95 1913.72 926.48 833.39 FALSE TRUE FALSE 945.0492505 789.297491 1298.025112 1303.350874 1801.204405 1715.165777 1714.150914 1969.090469 843.6133084 811.7384077 1.164228823 0.972354497 1.599068246 1.605629181 2.218946878 2.11295383 2.111703595 2.425769743 1.039267454 1 9.664871066 -9.154123041 1.055835794 1.061810726 2.258093069 0.928274336 0.142773963 0.08372743 0.184218365 0.023637135 0.052688571 7.01E-10 9.154123041 1.196282343 up DDAMLLK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 2 DDAMLLKGK 9 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 ; DDAMLLK(1)GK;DDAMLLK(1)GK 118.33 0.0014982 3873500 911.34 871.48 1349.24 656.45 1102.23 1376.28 1301.23 1331.95 958.5 976.49 FALSE TRUE FALSE 900.2322375 883.7487183 1372.722956 732.3518377 1045.97909 1288.34015 1411.756444 1370.487872 872.7693594 951.120649 0.946496366 0.929165736 1.443269009 0.769988369 1.099733342 1.354549658 1.484308479 1.44091906 0.917622134 1 9.893484547 -8.249511547 2.827124751 0.994868487 1.454420069 0.577193591 0.164055561 0.132557491 2.10806404 0.022117358 0.061129732 5.63E-09 8.249511547 0.459551582 DDATLSGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 DDATLSGKR 9 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 0 1 ; DDATLSGK(1)R;DDATLSGK(1)R 177.7 3.08E-05 77443000 8715 8506.3 7954.1 6179.2 7438.5 6187.4 9184.4 6502.8 11680.2 8085.4 FALSE TRUE FALSE 8608.778228 8626.051915 8092.537774 6893.668178 7058.885588 5792.045109 9964.522707 6690.948258 10635.49366 7875.340142 1.093130972 1.095324362 1.02757946 0.875348627 0.896327709 0.735466025 1.265281566 0.849607526 1.350480546 1 12.94312652 -9.40254502 6.0028499 1.049574914 0.931708482 0.211129253 0.160625976 0.329687378 15.02429198 0.019327398 0.029606442 3.96E-10 9.40254502 -0.117866433 DDDDIDLFGS(ph)DDEEESEEAKR ddPTM_HeLa_Romidepsin_16h_R1 4 DDDDIDLFGSDDEEESEEAKR 21 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 0 DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR;DDDDIDLFGS(1)DDEEESEEAKR ;;; 125.31 5.13E-05 208182000 9018.9 8002.31 8685.9 5069.14 7761.86 8262.4 7458.17 7342.2 8629.3 8953.7 TRUE FALSE FALSE 8908.974178 8114.96673 8837.074446 5655.257818 7365.743321 7734.459306 8091.666774 7554.634973 7857.473796 8721.081583 1.021544644 0.930500036 1.013300284 0.648458309 0.844590576 0.886869276 0.927828354 0.866249777 0.900974692 1 13.09029135 DDDKAWEYEER ddPTM_HeLa_Romidepsin_16h_R1 1 DDDKAWEYEER 11 1 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 0 0 96.113 0.02796 4928200 3334.1 3915.8 3408.1 2807.1 3039.3 2973.1 2793.9 2987.1 3931.5 3903.9 FALSE FALSE TRUE 3293.462707 3970.926735 3467.416551 3131.67011 2884.19318 2783.128505 3031.213796 3073.527026 3579.856793 3802.476115 0.86613633 1.044300244 0.911883848 0.823587056 0.758503957 0.731925309 0.797168399 0.808296208 0.941454117 1 11.89272347 -9.195122735 2.820963006 0.944187718 0.774100712 0.756791317 0.048543109 0.133793033 2.093988036 0.009482104 0.016309014 6.38E-10 9.195122735 -0.170087005 DDDTASVTS(ph)LNSSATGR ddPTM_HeLa_Romidepsin_16h_R1 1 DDDTASVTSLNSSATGR 17 0 H0Y9L7;P21675-10;P21675-11;P21675-8;P21675-6;P21675-7;P21675-3;P21675-5;P21675-9;P21675;P21675-2;P21675-12;P21675-4 H0Y9L7 TAF1 Transcription initiation factor TFIID subunit 1 1 0 DDDTAS(0.057)VT(0.176)S(0.764)LNS(0.002)SATGR 112.57 0.0020234 3185800 1337.5 1483.2 1446.1 771.76 1201.4 1335 1129.3 1156.9 1495.3 1928.8 TRUE FALSE FALSE 1321.198036 1504.080529 1471.268764 860.9945224 1140.088075 1249.697809 1225.222714 1190.373076 1361.556623 1878.689498 0.703255134 0.800600914 0.783135673 0.458295276 0.606852849 0.665196569 0.65216882 0.633618848 0.724737443 1 10.87551093 -12.56514988 0.279688358 1.21169875 0.600327972 0.234900721 0.118191335 2.156670618 0.196843012 0.442177829 0.057406568 2.72E-13 12.56514988 -0.611370778 DDDVPLDWR ddPTM_HeLa_Romidepsin_16h_R1 1 DDDVPLDWR 9 0 O95340;O95340-2 O95340 PAPSS2 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 0 180.87 0.0011167 14089000 4586.3 3572.8 3977.2 3300.1 4320.5 4672.1 3554.4 3853.8 4507.2 3498.8 FALSE FALSE TRUE 4530.400412 3623.097972 4046.421498 3681.673089 4100.008763 4373.567889 3856.310647 3965.303623 4104.064744 3407.900672 1.329381589 1.063146588 1.187364858 1.080334624 1.203089279 1.283361315 1.131579532 1.163561971 1.204279449 1 11.73466757 -12.62935089 1.456663674 1.000287353 1.198462804 0 0.100217096 0.32605859 1.245809531 0.062162454 0.014265353 2.35E-13 12.62935089 0.198175451 DDDYRGGGDRYEDR ddPTM_HeLa_Romidepsin_16h_R1 1 DDDYRGGGDRYEDR 14 2 E7EX17;P23588-2;P23588;F8VP89;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 0 68.262 0.020055 13101000 4337.3 4068.6 3999.9 5326.4 3380 3024.8 2886.8 3270.3 4495.8 4046.1 FALSE FALSE TRUE 4284.435319 4125.877858 4069.516582 5942.263429 3207.505987 2831.525042 3132.00472 3364.920971 4093.684388 3940.981739 1.087149244 1.046916259 1.03261493 1.507812983 0.813885017 0.718482152 0.794727032 0.853828105 1.038747363 1 11.94433935 -8.561509773 24.9999953 1.074639005 0.785682504 0.53767719 0.143677235 99.54700479 64421.29814 0.020527553 0.04105516 2.74E-09 8.561509773 -0.288956501 DDEENYLDLFSHK ddPTM_HeLa_Romidepsin_16h_R1 2 DDEENYLDLFSHK 13 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 0 ; ; 142.85 0.00038316 8720600 4598.8 5265 4360.2 5582.3 4796 4640.7 5252.8 4736.9 5532.7 4782.9 FALSE FALSE TRUE 4542.748057 5339.120808 4436.087452 6227.751792 4551.242224 4344.174247 5698.972701 4873.954728 5037.841455 4658.639569 0.975123314 1.14606866 0.952228089 1.336817691 0.976946629 0.932498465 1.223312647 1.046218463 1.081397558 1 12.185693 -10.27959235 24.03997846 0.988252671 1.087079826 0.045743421 0.12217765 713.8189411 945306.9232 0.018938991 0.021684983 5.25E-11 10.27959235 0.098827155 DDEKEAEEGEDDRDS(ph)ANGEDDS ddPTM_HeLa_Romidepsin_16h_R1 1 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;P07910-3;P07910-4 P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 DDEKEAEEGEDDRDS(0.615)ANGEDDS(0.385) 54.465 0.02392 76648000 3997.1 4046.2 4183.4 1780.2 3955.8 4270.4 3446.6 4150.7 3785.3 3943.7 TRUE FALSE FALSE 3948.381808 4103.16251 4256.210322 1986.0351 3753.920765 3997.535222 3739.354118 4270.793956 3446.733288 3841.242105 1.027891942 1.068186383 1.108029696 0.5170294 0.977267421 1.040688171 0.97347525 1.111826289 0.89729655 1 11.90735718 DDEKEAEEGEDDRDSANGEDDS(ph) ddPTM_HeLa_Romidepsin_16h_R1 1 DDEKEAEEGEDDRDSANGEDDS 22 2 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;P07910-3;P07910-4 P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 DDEKEAEEGEDDRDS(0.271)ANGEDDS(0.729) 62.028 0.010259 21265000 4244.8 3725.4 3533.7 1807.2 2983.1 3885.5 3484 3762.1 3454.1 3602.7 TRUE FALSE FALSE 4193.062745 3777.846279 3595.202566 2016.156967 2830.861276 3637.22909 3779.930873 3870.950428 3145.156645 3509.101335 1.194910704 1.076585119 1.024536547 0.574550797 0.806719728 1.036512982 1.077179173 1.103117311 0.8962855 1 11.77688589 -9.51431857 24.71407989 1.091411201 0.91568697 0.089477221 0.161684429 440.7899338 1272605.979 0.026223045 0.038174426 3.06E-10 9.51431857 -0.17572423 DDFNSGFRDDFLGGR ddPTM_HeLa_Romidepsin_16h_R1 1 DDFNSGFRDDFLGGR 15 1 Q15056 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 0 86.262 0.023939 2457200 1016.3 1132.4 1104.9 937.79 719.41 804.39 972.96 864.38 1383.3 1403 FALSE FALSE TRUE 1003.912945 1148.341957 1124.130321 1046.221692 682.6958232 752.992075 1055.603198 889.3894715 1259.574183 1366.549858 0.734633236 0.840322035 0.822604689 0.765593503 0.499576228 0.551016906 0.772458606 0.65082841 0.921718426 1 10.41632238 -16.52287875 0.126826508 2.073743904 0.548788905 0.579774838 0.095755778 43.0937508 0.389902525 11.67123919 0.401412237 3.00E-17 16.52287875 -1.524954999 DDFTEFGK ddPTM_HeLa_Romidepsin_16h_R1 2 DDFTEFGK 8 0 O75822;O75822-3;H0YGJ7;H0YLP3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 0 ; ; 133.55 2.43E-05 0 3245.4 3764.3 3504.3 2648.9 3651.6 3836.5 3445.5 3664.7 3995.8 4548.4 FALSE FALSE TRUE 3205.843816 3817.293914 3565.290872 2955.178281 3465.245226 3591.360032 3738.160684 3770.732313 3638.40564 4430.231912 0.723628893 0.861646521 0.804763936 0.667048213 0.782181451 0.810648314 0.843784424 0.851136552 0.821267535 1 12.11316651 -12.40922351 1.041128246 1.004698819 0.787633844 0.126423023 0.078191908 0.282314456 0.528043224 0.046648511 0.010838736 3.90E-13 12.40922351 -0.217064975 DDGELGGNFLHSFQNDNYSPSMT(ph)MSV ddPTM_HeLa_Romidepsin_16h_R1 1 DDGELGGNFLHSFQNDNYSPSMTMSV 26 0 Q9NW25;Q9BWW4-2;Q9BWW4-3;Q9BWW4 Q9NW25 SSBP3 Single-stranded DNA-binding protein 3 1 0 DDGELGGNFLHSFQNDNY(0.009)S(0.011)PS(0.13)MT(0.459)MS(0.39)V 84.025 1.87E-05 9028800 1690 1940.8 1214.8 1614.2 2210.4 1844.9 1774.7 1727.3 2135.5 1879.3 TRUE FALSE FALSE 1669.40163 1968.122633 1235.943084 1800.841399 2097.59504 1727.016844 1925.442974 1777.2767 1944.495532 1830.475515 0.912004349 1.075197465 0.675203287 0.983810701 1.145929035 0.943479894 1.051881305 0.970937161 1.062289834 1 10.83800276 -8.998064107 24.99900371 0.943510696 1.028861445 0.103777085 0.115109692 104.9570369 1355311.528 0.015553335 0.02805802 1.00E-09 8.998064107 0.085350749 DDGELGGNFLHSFQNDNYSPSMTMS(ph)V ddPTM_HeLa_Romidepsin_16h_R1 1 DDGELGGNFLHSFQNDNYSPSMTMSV 26 0 Q9NW25;Q9BWW4-2;Q9BWW4-3;Q9BWW4 Q9NW25 SSBP3 Single-stranded DNA-binding protein 3 1 0 DDGELGGNFLHS(0.001)FQNDNY(0.105)S(0.119)PS(0.105)MT(0.094)MS(0.576)V 52.054 0.006407 6811900 1829.1 1498.3 1499.1 1431 1772.6 1791.5 1584.1 1771.6 1831.1 1993.4 TRUE FALSE FALSE 1806.806226 1519.393107 1525.191207 1596.458953 1682.137608 1677.028932 1718.653414 1822.858451 1667.32183 1941.611181 0.930570571 0.782542417 0.785528649 0.822234116 0.866361723 0.86373057 0.885168684 0.938838048 0.858731061 1 10.92303861 -10.57560974 2.642082491 0.973748693 0.848597909 0.194627616 0.058621393 0.142825115 2.066965872 0.009705886 0.010294419 2.66E-11 10.57560974 -0.125150784 DDGLFSGDPNWFPK ddPTM_HeLa_Romidepsin_16h_R1 2 DDGLFSGDPNWFPK 14 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 0 ; ; 181.66 2.52E-06 63365000 11337.7 11181 11244.9 10787 11440.9 12306.2 9641.5 12070.4 10766.6 11711.6 FALSE FALSE TRUE 11199.51175 11338.40641 11440.61277 12034.24369 10857.02818 11519.87354 10460.44877 12419.63798 9803.608331 11407.33094 0.981781962 0.993957874 1.002917582 1.054957006 0.95175885 1.009865813 0.916993539 1.088741796 0.859412984 1 13.47767365 -7.225264113 24.04736683 0.991281409 1.08874217 0.240184414 0.054017388 8599.489574 5716311.163 0.004261003 1.283019451 5.95E-08 7.225264113 0.097460761 DDGLFSGDPNWFPKK ddPTM_HeLa_Romidepsin_16h_R1 1 DDGLFSGDPNWFPKK 15 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 0 82.483 0.0177 26422000 5525.4 5127 4541.3 7225.1 6004.5 5751.8 4770.2 6099.8 6455.2 5737.9 FALSE FALSE TRUE 5458.0543 5199.178041 4620.339422 8060.500057 5698.067959 5384.278543 5175.380669 6276.288089 5877.830745 5588.828531 0.976600779 0.930280471 0.826709819 1.442252167 1.019546033 0.963400203 0.926022446 1.123006021 1.051710696 1 12.4483302 DDGSSMSFYVRPS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 DDGSSMSFYVRPSPAK 16 1 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 0 DDGSS(0.003)MS(0.047)FY(0.009)VRPS(0.941)PAK 107.69 0.013486 11541000 3634.5 4255.3 3312.9 2930.6 4739.9 5707 4260.4 5520 4020 3631.6 TRUE FALSE FALSE 3590.201316 4315.206225 3370.559635 3269.449761 4498.005216 5342.341118 4622.27827 5679.712491 3660.441132 3537.250508 1.014969482 1.219932322 0.952875581 0.924291269 1.271610593 1.510308955 1.306743262 1.605685681 1.034826661 1 11.78841268 -8.557042366 3.891835105 1.015776256 1.45264982 0.79652267 0.102255616 0.066916032 2.193284796 0.014072381 0.030236913 2.77E-09 8.557042366 0.436873564 DDGSWEVIEGYR ddPTM_HeLa_Romidepsin_16h_R1 2 DDGSWEVIEGYR 12 0 P49448;P00367 P49448 GLUD2;GLUD1 "Glutamate dehydrogenase 2, mitochondrial;Glutamate dehydrogenase 1, mitochondrial" 0 0 ; ; 260.98 9.33E-63 58428000 4150.5 4302.2 5105.8 4407.1 4557.9 5055 4678 4460.6 4343.1 4110.8 FALSE FALSE TRUE 4099.91211 4362.766485 5194.664307 4916.669638 4325.293355 4732.001814 5075.349203 4589.660423 3954.642259 4004.000823 1.023953863 1.089601795 1.297368441 1.227939218 1.080242874 1.181818392 1.26756947 1.146268601 0.987672689 1 11.96722656 -9.991231386 4.732664649 1.01283318 1.198684241 0.699353304 0.058025229 0.079174738 4.735462939 0.009548931 0.012332526 1.02E-10 9.991231386 0.185851061 DDGVFVQEVTQNS(ph)PAAR ddPTM_HeLa_Romidepsin_16h_R1 4 DDGVFVQEVTQNSPAAR 17 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2;E9PQE3 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR;DDGVFVQEVTQNS(1)PAAR ;;; 268.82 4.20E-87 492608000 20341.5 19362.9 21014.7 19938.8 25159.6 31679 25461.1 28494 21931.3 20246.5 TRUE FALSE FALSE 20093.56997 19635.49141 21380.45204 22244.21787 23875.61173 29654.81414 27623.7652 29318.42893 19969.7096 19720.49301 1.018918237 0.995689682 1.084174317 1.127974735 1.21070055 1.503756226 1.400764432 1.486698579 1.012637442 1 14.267408 -8.598587313 1.248561856 1.010532116 1.478402183 0.950611288 0.043356355 0.061542379 0.186032076 0.006325044 0.019652074 2.52E-09 8.598587313 0.467870067 DDILNGSHPVSFDK ddPTM_HeLa_Romidepsin_16h_R1 1 DDILNGSHPVSFDK 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 100.11 0.0047669 8916900 3044.5 3034.1 2906.5 2739.1 3808.8 3315.5 2660.2 3088.1 3848 3142.7 FALSE FALSE TRUE 3007.392463 3076.814139 2957.086413 3055.80763 3614.422723 3103.65025 2886.157322 3177.449301 3503.825243 3061.052201 0.982470166 1.00514919 0.966035931 0.998286677 1.180777878 1.013916146 0.942864457 1.038025193 1.144647334 1 11.57981193 -8.970051772 24.99998083 0.99059754 1.04141222 0 0.073893692 296.0267964 247114.1821 0.008211347 0.014884207 1.07E-09 8.970051772 0.05081468 DDISEIQSLAS(ph)DHS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 DDISEIQSLASDHSGR 16 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0YKB1 G3V1L9 TJP1 Tight junction protein ZO-1 2 0 DDISEIQS(0.002)LAS(0.998)DHS(1)GR 74.698 0.002504 0 1672.6 1853.5 1656.5 945.3 1827.5 1645.8 1571.5 1737.8 1807.2 1924.7 TRUE FALSE FALSE 1652.213708 1879.593622 1685.330688 1054.600034 1734.235856 1540.638692 1704.983171 1788.080501 1645.559506 1874.696017 0.881323528 1.00261248 0.898988782 0.562544554 0.925075767 0.821807204 0.909471805 0.953797568 0.877774045 1 10.87244097 -11.68459264 0.489648657 1.009668865 0.854106868 0.027424192 0.117601316 1.60141884 0.716493596 0.114822532 0.034779907 2.07E-12 11.68459264 -0.155561997 DDKHGSYEDAVHS(ph)GALND ddPTM_HeLa_Romidepsin_16h_R1 1 DDKHGSYEDAVHSGALND 18 1 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 1 0 DDKHGS(0.292)YEDAVHS(0.708)GALND 97.235 0.020415 3658700 1072.2 989.19 942.72 1263.8 1184.7 994.09 1079.9 855.1 1183.8 1186 TRUE FALSE FALSE 1059.131614 1003.115843 959.1276461 1409.926502 1124.240338 930.5708573 1171.626679 879.8409694 1077.917963 1155.187549 0.91684819 0.868357561 0.830278726 1.220517399 0.973210228 0.805558247 1.014230702 0.761643397 0.933110787 1 10.17391138 -6.690343564 0.011504696 1.802020485 3.60E-08 0.031844926 0.122880316 13493.2112 20.84603584 1479.985541 1798.381478 2.04E-07 6.690343564 -1.802020449 DDNMFQIGK(ac)MR ddPTM_HeLa_Romidepsin_16h_R1 1 DDNMFQIGKMR 11 1 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 1 DDNMFQIGK(1)MR 79.659 0.010182 2627800 685.44 597.36 771.25 816.25 862.48 888.03 850.85 1014.3 778.91 794.41 FALSE TRUE FALSE 677.0855936 605.7696498 784.6732827 910.6286656 818.4644272 831.287749 923.1211778 1043.64717 709.2423388 773.7711137 0.875046356 0.782879639 1.014089656 1.176870847 1.05776038 1.07433288 1.193015818 1.348780216 0.916604828 1 9.595763061 -9.418276586 4.052557493 0.926388684 1.159094112 0.660765122 0.092027179 0.137547701 3.959541534 0.015889275 0.024514988 3.82E-10 9.418276586 0.232705427 DDQMLKR ddPTM_HeLa_Romidepsin_16h_R1 1 DDQMLKR 7 1 J3QLL0;J3KS65;P52292 J3QLL0 KPNA2 Importin subunit alpha-1 0 0 64.803 0.026151 24461000 6312.1 5773.8 5902.4 262.87 6898.2 8063.9 8883.8 3208.3 8632.7 6121.3 FALSE FALSE TRUE 6235.165697 5855.083708 6005.128796 293.2642662 6546.159113 7548.642815 9638.38975 3301.127099 7860.569691 5962.267744 1.045770832 0.982022942 1.007188716 0.049186699 1.097931088 1.266069076 1.616564395 0.553669718 1.318385894 1 12.54164545 -9.491097703 24.98975804 1.018075366 0.939360302 0.025789149 0.40301798 4313.860077 3392037.124 0.060796318 0.092814969 3.23E-10 9.491097703 -0.078715065 DDREDLVYQAK ddPTM_HeLa_Romidepsin_16h_R1 1 DDREDLVYQAK 11 1 P62258;I3L0W5;B4DJF2;I3L3T1 P62258 YWHAE 14-3-3 protein epsilon 0 0 117.14 0.0015099 0 2081.7 2689.4 1833.9 1533.8 1910.2 1718.9 2459.9 3046.4 3141.9 4105.9 FALSE FALSE TRUE 2056.32744 2727.261444 1865.81826 1711.145173 1812.715366 1609.067837 2668.843845 3134.542778 2860.880595 3999.228126 0.514181081 0.681946955 0.466544593 0.427868858 0.453266308 0.402344599 0.667339737 0.783786941 0.71535819 1 11.96550586 -12.23702489 0.68357341 1.04633884 0.535471657 0.350695021 0.146926475 0.445773316 0.322462917 0.134584924 0.026658997 5.79E-13 12.23702489 -0.510867183 DDS(ph)FDSLDSFGSR ddPTM_HeLa_Romidepsin_16h_R1 2 DDSFDSLDSFGSR 13 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 DDS(1)FDSLDSFGSR;DDS(0.994)FDS(0.006)LDSFGSR ; 123.68 0.00035098 0 2822 2168.4 2114.28 1626.15 2492.7 1982.67 1867.8 1756.08 2404.9 2830.5 TRUE FALSE FALSE 2787.604379 2198.926792 2151.078157 1814.173114 2365.488217 1855.983786 2026.450885 1806.889404 2189.799721 2756.963202 1.011114104 0.797590186 0.780234627 0.658033126 0.858005002 0.673198607 0.735030081 0.655391194 0.794279633 1 11.4288643 -10.12603756 2.406847971 1.00686616 0.727133715 0.473483496 0.088748065 0.075967682 0.850374167 0.009348881 0.011645427 7.48E-11 10.12603756 -0.279732445 DDSDSTLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DDSDSTLKK 9 1 Q92797;M0R3C7;A0A087WUE9;Q92797-2 Q92797 SYMPK Symplekin 0 1 ; DDSDSTLK(1)K;DDSDSTLK(1)K 149.82 0.0033222 8523600 5837.1 6182.6 6178.5 6184.1 5020.8 6010.7 5992.7 4146.1 7548.3 5221.2 FALSE TRUE FALSE 5765.95518 6269.638805 6286.034201 6899.134739 4764.569841 5626.635669 6501.719788 4266.060862 6873.161143 5085.552471 1.133791306 1.232833373 1.236057289 1.356614601 0.93688343 1.106396149 1.278468726 0.838858882 1.351507271 1 12.3121888 -11.80418766 0.954487625 1.009503673 1.147817649 0 0.182505866 0.806543558 1.452295009 0.06390603 0.027964104 1.57E-12 11.80418766 0.138313976 DDSFDSLDS(ph)FGSR ddPTM_HeLa_Romidepsin_16h_R1 1 DDSFDSLDSFGSR 13 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 DDSFDSLDS(0.999)FGS(0.001)R 191.01 9.09E-11 8056000 2003.3 2135.1 1736.5 1534.6 1733.5 1626.1 1358 1139.3 1575.8 2066.4 TRUE FALSE FALSE 1978.883009 2165.157994 1766.723054 1712.037673 1645.033026 1522.197458 1473.348486 1172.263848 1434.856501 2012.71463 0.983191049 1.075740178 0.877781195 0.850611233 0.817320549 0.75629075 0.732020558 0.582429238 0.712896145 1 10.97492692 -8.075603364 0.522573253 1.003081491 0.521657226 0.48572747 0.102647704 0.452768425 0.137972165 0.010196717 0.114052146 8.40E-09 8.075603364 -0.481424265 DDSLDLS(ph)PQGR ddPTM_HeLa_Romidepsin_16h_R1 2 DDSLDLSPQGR 11 0 Q14669;Q14669-2;Q14669-3;Q14669-4 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 DDS(0.403)LDLS(0.597)PQGR;DDS(0.419)LDLS(0.581)PQGR ; 115.37 0.012132 12380100 4503 4093.8 4743 3310.4 3852.5 3757.9 3029.4 3501.7 4919 4903.1 TRUE FALSE FALSE 4448.115704 4151.432624 4825.549925 3693.164024 3655.892549 3517.782318 3286.71716 3603.016165 4479.03232 4775.716755 0.931402747 0.86927949 1.0104347 0.773321412 0.765517039 0.736597771 0.688214425 0.754445113 0.937876459 1 12.22150156 -9.162411917 4.485672009 0.960682613 0.736804721 0.856649738 0.042166651 0.064128147 2.190883324 0.007090469 0.01195068 6.88E-10 9.162411917 -0.223877892 DDSLDLSPQGRLS(ph)DVLK ddPTM_HeLa_Romidepsin_16h_R1 1 DDSLDLSPQGRLSDVLK 17 1 Q14669;Q14669-2;Q14669-3;Q14669-4 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 DDSLDLSPQGRLS(1)DVLK 74.325 0.0095054 4796100 1766.8 1634.7 1565.7 1821.8 1744.3 1660.2 1186.4 1612.6 1833.9 1664.3 TRUE FALSE FALSE 1745.265562 1657.71335 1592.950352 2032.445088 1655.281862 1554.118578 1287.172786 1659.258037 1669.871391 1621.061246 1.076619138 1.022609944 0.982658956 1.253774398 1.021110008 0.958704418 0.794030941 1.02356283 1.030109994 1 10.66272288 -8.170630223 3.621937549 1.047820335 0.904125329 0.314989219 0.088546228 0.209232779 5.1420069 0.012183615 0.033564503 6.75E-09 8.170630223 -0.143695006 DDSSRPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 DDSSRPSR 8 1 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 0 DDS(0.031)S(0.031)RPS(0.937)R 48.756 0.028204 8656800 1547.3 1971.2 1279 1395.7 1378.1 1301.5 1412.8 2334.1 2528.8 3035.6 TRUE FALSE FALSE 1528.440912 1998.950605 1301.260458 1557.077401 1307.770415 1218.33835 1532.803197 2401.633501 2302.617795 2956.734674 0.516935431 0.676066954 0.440100517 0.526620604 0.442302255 0.412055353 0.518410803 0.812258713 0.778770518 1 11.52978907 -12.24862542 0.622119076 1.063919116 0.524353741 0.491972173 0.132576129 0.463486923 0.265193041 0.14071251 0.02540342 5.64E-13 12.24862542 -0.539565375 DDTIYEDEDVK ddPTM_HeLa_Romidepsin_16h_R1 1 DDTIYEDEDVK 11 0 E5RHG9;B7Z2R2;P14927;P14927-2 E5RHG9 UQCRB Cytochrome b-c1 complex subunit 7 0 0 154.24 0.022689 2368400 1292.5 1399.3 1268.5 989.97 1228.4 1435.1 1229.7 1127.4 1092 1084.1 FALSE FALSE TRUE 1276.746513 1418.999382 1290.57771 1104.434989 1165.710164 1343.401742 1334.150687 1160.01954 994.328785 1055.934926 1.209114768 1.343832226 1.2222133 1.045930921 1.103960231 1.27223914 1.263478132 1.09857105 0.941657256 1 10.04430521 -12.11921671 0.928578273 1.002294992 1.196336826 0.49008697 0.089074822 0.45024151 0.713403148 0.056546238 0.017360703 7.60E-13 12.11921671 0.194041834 DDTIYEDEDVKEAIR ddPTM_HeLa_Romidepsin_16h_R1 2 DDTIYEDEDVKEAIR 15 1 E5RHG9;B7Z2R2;P14927;P14927-2 E5RHG9 UQCRB Cytochrome b-c1 complex subunit 7 0 0 ; ; 217.2 6.20E-26 20120800 4544.6 5172.2 5365 4377.7 5612.7 5642.2 5158.4 4810.4 4623.5 4140.3 FALSE FALSE TRUE 4489.208667 5245.014367 5458.375574 4883.870272 5326.262975 5281.681629 5596.554367 4949.581334 4209.96258 4032.734409 1.113192244 1.300609918 1.353517247 1.211056761 1.320757192 1.309702324 1.38778154 1.22735118 1.043947395 1 11.97754268 -10.46721213 1.5062266 1.03717881 1.308161071 0.812787928 0.054926376 0.105457677 0.470770475 0.011436144 0.01248485 3.41E-11 10.46721213 0.270982261 DEALQNIS(ph)ADDLPDSASQAAHPQDSAFSYR ddPTM_HeLa_Romidepsin_16h_R1 1 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 DEALQNIS(0.883)ADDLPDS(0.105)AS(0.011)QAAHPQDSAFSYR 96.477 1.13E-08 15210000 1382.6 1212.6 903.8 790.9 1517 1998.3 1396.7 1677.6 1792.5 1576.2 TRUE FALSE FALSE 1365.748339 1229.671015 919.5302599 882.3475793 1439.581829 1870.615079 1515.335663 1726.138709 1632.174311 1535.250097 0.889593391 0.800958109 0.598944929 0.57472563 0.937685549 1.218443225 0.987028541 1.124337144 1.063132524 1 10.58425798 -8.506082571 24.51727546 0.876977636 1.094382052 0.369344492 0.158807427 637.4511505 930482.7238 0.025414259 0.055501868 3.12E-09 8.506082571 0.217404416 DEALQNISADDLPDS(ph)ASQAAHPQDSAFSYR ddPTM_HeLa_Romidepsin_16h_R1 1 DEALQNISADDLPDSASQAAHPQDSAFSYR 30 0 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 DEALQNIS(0.462)ADDLPDS(0.525)AS(0.013)QAAHPQDSAFSYR 118.61 1.02E-10 15687000 1234.1 1112.7 1011.4 660.97 1793.8 1939.8 1338.4 1524.1 1664.2 1530.6 TRUE FALSE FALSE 1219.058315 1128.36462 1029.002993 737.3944614 1702.255692 1815.85304 1452.083663 1568.197429 1515.349784 1490.834791 0.817701815 0.756867646 0.690219331 0.494618495 1.141813769 1.21801091 0.974007094 1.05189216 1.016443802 1 10.54190468 DEDDDEEEEEEGGSWGR ddPTM_HeLa_Romidepsin_16h_R1 2 DEDDDEEEEEEGGSWGR 17 0 Q5VYD6;O00165-4;O00165-6;O00165-3;O00165;O00165-2 Q5VYD6 HAX1 HCLS1-associated protein X-1 0 0 ; ; 392.58 0 28881000 5231.1 4494.1 4699.7 3630.9 4449.1 4441.5 3373.7 4189.29 5051.2 4797.6 FALSE FALSE TRUE 5167.341341 4557.368058 4781.496307 4050.721742 4222.045825 4157.702484 3660.261994 4310.500497 4599.408021 4672.95766 1.105796739 0.975264145 1.02322697 0.866843236 0.903506116 0.889736819 0.783285931 0.922435171 0.984260581 1 12.19012025 -9.348486457 1.595543511 1.047653913 0.864390285 0.631740819 0.05255431 0.155768806 0.778027745 0.009010545 0.01581656 4.48E-10 9.348486457 -0.183263628 DEDEGIPS(ph)ENEEEKK ddPTM_HeLa_Romidepsin_16h_R1 2 DEDEGIPSENEEEKK 15 1 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 DEDEGIPS(1)ENEEEKK;DEDEGIPS(1)ENEEEKK ; 71.637 0.014144 32380000 7081.8 8210.1 7417.6 4786.5 10267.8 13236 9230.4 12413.1 6927.6 7848.4 TRUE FALSE FALSE 6995.484298 8325.682003 7546.700216 5339.937651 9743.795852 12390.26232 10014.42995 12772.25346 6307.978106 7644.497437 0.915100614 1.089107829 0.987206848 0.698533513 1.274615622 1.620807963 1.310018092 1.670777389 0.825165834 1 12.90020594 -8.544574237 5.961134671 0.955868431 1.503269948 0.804740442 0.136200688 0.04920558 5.805714771 0.017417301 0.035953313 2.85E-09 8.544574237 0.547401516 DEDMLYS(ph)PELAQR ddPTM_HeLa_Romidepsin_16h_R1 1 DEDMLYSPELAQR 13 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 0 DEDMLYS(1)PELAQR 109.95 0.0095351 33827000 5081.7 5258.8 5142.2 3501 5077.5 5803.5 4311.4 5304.1 4808.7 4879.1 TRUE FALSE FALSE 5019.762286 5332.833524 5231.697834 3905.802093 4818.376228 5432.67508 4677.610208 5457.565765 4378.597828 4752.340279 1.056271645 1.122148923 1.100867684 0.821869198 1.013895459 1.143157847 0.984275101 1.14839541 0.921356126 1 12.21442242 -14.24359574 0.005939088 3.75E-06 2.018407036 0.071899914 0.096040334 70034.76002 53.12911812 9517.108431 8560.757728 5.71E-15 14.24359574 2.018403289 DEDVDVLPSTVEDS(ph)PFSR ddPTM_HeLa_Romidepsin_16h_R1 1 DEDVDVLPSTVEDSPFSR 18 0 Q7Z2Z1;Q7Z2Z1-2;H0YN97 Q7Z2Z1 TICRR Treslin 1 0 DEDVDVLPS(0.021)T(0.011)VEDS(0.958)PFS(0.01)R 120.08 0.0015707 2007600 2377.6 2398.6 2921.4 2008 3142.4 3752.4 2607.2 2905.1 2803.2 2640.6 TRUE FALSE FALSE 2348.620897 2432.367554 2972.245742 2240.174408 2982.031602 3512.63375 2828.655503 2989.154485 2552.474771 2571.996831 0.913150774 0.945711723 1.155617964 0.870986457 1.159422736 1.365722425 1.099789653 1.162192134 0.992409765 1 11.32867315 -8.63677183 6.130582882 0.96814808 1.208148638 0.561930913 0.094213084 0.108691495 5.45019741 0.013386188 0.026970025 2.31E-09 8.63677183 0.240000558 DEEDTS(ph)FESLSK ddPTM_HeLa_Romidepsin_16h_R1 1 DEEDTSFESLSK 12 0 H7C3L4;E7EQA9;Q92844 H7C3L4 TANK TRAF family member-associated NF-kappa-B activator 1 0 DEEDT(0.041)S(0.959)FESLSK 223.36 4.99E-29 4933900 3054.1 3003 2648.3 2311.1 3960.4 4091.5 3288.5 4116.4 3089 3084.6 TRUE FALSE FALSE 3016.875454 3045.276313 2694.392551 2578.320256 3758.28601 3830.066355 3567.825108 4235.501539 2812.712103 3004.461647 1.004131791 1.013584685 0.896797119 0.858163811 1.250901643 1.274792893 1.187508954 1.409737263 0.936178402 1 11.55289079 -8.68953114 7.731647999 0.985361961 1.275892303 0.824497756 0.073445661 0.080482979 7.483620748 0.01035178 0.020731644 2.04E-09 8.68953114 0.290530342 DEELEKDTMDNWDEK ddPTM_HeLa_Romidepsin_16h_R1 2 DEELEKDTMDNWDEK 15 1 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 0 ; ; 87.363 0.026878 19632200 4766.4 4469.5 4537.1 3698.9 4930.2 4570.5 4525.2 4513 4867.9 4875.9 FALSE FALSE TRUE 4708.305283 4532.421738 4616.066322 4126.584222 4678.593497 4278.459801 4909.570375 4643.576535 4432.502832 4749.223415 0.991384248 0.954350078 0.971962344 0.86889663 0.985128112 0.900875665 1.033762775 0.977754915 0.933311079 1 12.21347591 -10.30679693 3.223708217 0.996455159 0.955033668 0 0.047201221 0.334533078 6.83342761 0.007240411 0.008411805 4.93E-11 10.30679693 -0.04142149 DEEPSGWEEPS(ph)PQSISR ddPTM_HeLa_Romidepsin_16h_R1 3 DEEPSGWEEPSPQSISR 17 0 H0Y720;Q9UPQ9-1;Q9UPQ9 H0Y720 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 0 DEEPSGWEEPS(0.998)PQS(0.001)IS(0.002)R;DEEPSGWEEPS(0.862)PQS(0.135)IS(0.003)R;DEEPS(0.001)GWEEPS(0.993)PQS(0.005)ISR ;; 252.33 7.32E-60 17727000 2758.07 2462.29 2473.94 1407.76 2264.02 2495.26 2465.43 2613.03 2644.11 2661.24 TRUE FALSE FALSE 2724.453582 2496.954183 2516.997888 1570.531835 2148.478611 2335.820939 2674.843563 2688.6339 2407.614179 2592.100601 1.051060125 0.963293702 0.971026312 0.605891544 0.828856183 0.901130511 1.0319212 1.03724134 0.928827445 1 11.339906 -9.687767677 3.23211006 1.021440005 0.881552562 0.115375058 0.119085761 0.286443085 6.043336725 0.019711094 0.028130015 2.05E-10 9.687767677 -0.139887442 DEEQSEADAGS(ph)GPPTPGPTTLGPK ddPTM_HeLa_Romidepsin_16h_R1 1 DEEQSEADAGSGPPTPGPTTLGPK 24 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 DEEQSEADAGS(0.999)GPPTPGPTTLGPK 106.18 4.88E-06 5008000 3970.3 3863 3741.2 3010.8 3196.3 3166.5 3170.3 3335.2 4343.2 3835.3 TRUE FALSE FALSE 3921.908456 3917.383415 3806.314017 3358.922862 3033.180884 2964.170869 3439.585203 3431.69875 3954.733314 3735.658353 1.049857371 1.048646061 1.018913845 0.899151514 0.811953503 0.793480182 0.92074405 0.918632922 1.058644271 1 11.8671468 -9.196824201 3.57233074 1.026553617 0.860333756 0.805801952 0.041031885 0.0867126 2.20296993 0.006750904 0.011402521 6.36E-10 9.196824201 -0.166219861 DEEQSEADAGSGPPT(ph)PGPTTLGPK ddPTM_HeLa_Romidepsin_16h_R1 1 DEEQSEADAGSGPPTPGPTTLGPK 24 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 DEEQS(0.001)EADAGS(0.013)GPPT(0.936)PGPT(0.038)T(0.012)LGPK 67.877 0.0011893 3121600 1178.3 1007.6 1017.2 1009.4 669.69 739.77 786.8 582.83 1168.2 1119.6 TRUE FALSE FALSE 1163.938426 1021.785019 1034.903939 1126.111577 635.5132203 692.5010845 853.6307724 599.6932665 1063.713266 1090.512631 1.067331449 0.936976786 0.949006834 1.032644232 0.582765575 0.635023442 0.782779354 0.54991868 0.975424985 1 10.09079076 -8.766181083 24.99999901 1.017788214 0.647804546 0.861524944 0.06945573 28.84042917 152058.2993 0.010200368 0.018934701 1.71E-09 8.766181083 -0.369983669 DEEVHAGLGELLR ddPTM_HeLa_Romidepsin_16h_R1 2 DEEVHAGLGELLR 13 0 P50454;E9PPV6;E9PR70;E9PK86;E9PMI5;E9PQ34;E9PJH8;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 0 0 ; ; 117.03 0.0025462 28134000 14009.1 14959.4 15508.5 6711 10902.3 12527.1 10100.8 11614.6 14838.3 13952.4 FALSE FALSE TRUE 13838.3517 15169.99883 15778.41894 7486.957396 10345.91495 11726.65874 10958.7617 11950.65013 13511.12528 13589.91464 1.018280988 1.116268883 1.161038856 0.55092012 0.761293593 0.862894216 0.806389296 0.879376394 0.994202366 1 13.73024877 -9.275401105 24.99987295 1.029028405 0.778510987 0.672327175 0.098678431 404.205428 723769.1444 0.015427882 0.023639809 5.30E-10 9.275401105 -0.250517418 DEFEFLEK ddPTM_HeLa_Romidepsin_16h_R1 1 DEFEFLEK 8 0 A0A3B3IUA7;Q14258 A0A3B3IUA7 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 0 104.44 0.0035273 0 949.39 1065.5 870.96 1063.2 959.37 973.11 861.66 1052.2 911.15 1074.8 FALSE FALSE TRUE 937.8184695 1080.500137 886.1186934 1186.132187 910.409769 910.9314116 934.8493789 1082.643747 829.654462 1046.876541 0.895825279 1.032118014 0.846440491 1.133020122 0.869643872 0.870142157 0.892989137 1.034165639 0.792504588 1 10.0318756 -12.64243606 1.472799858 0.999987582 0.938072262 0 0.10928329 0.974260141 3.800002181 0.058714438 0.013318465 2.28E-13 12.64243606 -0.06191532 DEFPLLT(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DEFPLLTTK 9 0 P04818-2;P04818 P04818-2 TYMS Thymidylate synthase 2 0 DEFPLLT(1)T(1)K 61.213 0.0041731 0 2613.9 2452.6 2582 2508.4 2661.3 2300.4 2257.8 2482.7 2443.6 2685.3 TRUE FALSE FALSE 2582.040781 2487.127767 2626.938627 2798.43301 2525.48393 2153.411864 2449.577476 2554.533007 2225.038296 2615.535519 0.987193927 0.950905751 1.00435976 1.069927359 0.965570497 0.823315856 0.936549115 0.976676856 0.850700853 1 11.35289065 -8.513211204 24.98246102 0.996716654 0.911255074 0.130616968 0.064491894 320.3426516 827815.6582 0.006302369 0.013217794 3.07E-09 8.513211204 -0.08546158 DEGSDSHFTLDPPGS(ph)KKMFS(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 DEGSDSHFTLDPPGSKKMFSSR 22 2 A0A0A6YYG5;Q53S48;Q9Y6Q2;Q9Y6Q2-3;Q9Y6Q2-2 A0A0A6YYG5 STON1-GTF2A1L;ALF;STON1 Stonin-1 3 0 DEGSDSHFT(0.002)LDPPGS(0.998)KKMFS(0.999)S(1)R 50.425 0.0037019 0 652.82 652.08 725.74 690.51 868.18 944 644.01 957.15 832.18 805.55 TRUE FALSE FALSE 644.8631787 661.2599994 738.3712003 770.3500151 823.873535 883.6814466 698.7121933 984.8436251 757.7477366 784.6216949 0.821877834 0.842775574 0.941053765 0.981810751 1.050026453 1.126251609 0.890508379 1.255182761 0.965749152 1 9.615853416 -8.973430554 1.935342432 0.908295861 1.073393706 0.397921178 0.096733542 0.288657246 2.165765266 0.015971386 0.031977999 1.06E-09 8.973430554 0.165097845 DEHVQELESYIDR ddPTM_HeLa_Romidepsin_16h_R1 1 DEHVQELESYIDR 13 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 0 0 90.731 0.010238 2165100 805.84 672.41 857.68 758.53 910.94 903.26 673.69 875.3 715.93 958.43 FALSE FALSE TRUE 796.0181121 681.8762056 872.6075606 846.2348076 864.4513326 845.5446011 730.9132118 900.6254245 651.8954277 933.5298504 0.85269701 0.730427854 0.934739859 0.906489286 0.926002883 0.905749935 0.782956444 0.964752679 0.698312354 1 9.866552344 -12.22943477 1.034250384 0.997923228 0.873241846 0 0.115273481 0.472165739 0.928468784 0.04126208 0.012222392 5.90E-13 12.22943477 -0.124681382 DEILEWESR ddPTM_HeLa_Romidepsin_16h_R1 3 DEILEWESR 9 0 H0YK42;Q13596-2;Q13596;Q13596-3 H0YK42 SNX1 Sorting nexin-1 0 0 ;; ;; 196.99 3.87E-07 20536600 5015.3 5061.2 5214.3 3876.52 6163.7 6583.8 5803.4 6305.2 5624.2 5230.7 FALSE FALSE TRUE 4954.171595 5132.451706 5305.052704 4324.741482 5849.143389 6163.116428 6296.340651 6487.631014 5121.157466 5094.80566 0.972396579 1.007389104 1.041266941 0.848853081 1.148060158 1.209686265 1.235835294 1.273381449 1.005172289 1 12.3148114 -8.566333822 5.983096293 0.984231326 1.230394424 0.847275519 0.050438158 0.048532828 4.279152852 0.006945445 0.014149506 2.71E-09 8.566333822 0.246163099 DEILPT(ph)TPISEQK ddPTM_HeLa_Romidepsin_16h_R1 2 DEILPTTPISEQK 13 0 E9PPU1;E9PL09;P23396;P23396-2;H0YEU2;E9PSF4 E9PPU1 RPS3 40S ribosomal protein S3 1 0 DEILPT(0.993)T(0.007)PISEQK;DEILPT(0.924)T(0.076)PISEQK ; 225.33 3.00E-31 3247900000 30594 29089 29557 21658.5 29244 29135 25327 29165 29438 26884 TRUE FALSE FALSE 30221.10856 29498.51571 30071.42719 24162.75768 27751.56956 27273.36753 27478.27475 30008.84326 26804.99155 26185.5498 1.154113959 1.12651886 1.148397777 0.922751588 1.059804731 1.041542673 1.049367875 1.146007759 1.023655862 1 14.67648328 DEILPTT(ph)PISEQK ddPTM_HeLa_Romidepsin_16h_R1 3 DEILPTTPISEQK 13 0 E9PPU1;E9PL09;P23396;P23396-2;H0YEU2;E9PSF4 E9PPU1 RPS3 40S ribosomal protein S3 1 0 DEILPT(0.206)T(0.788)PIS(0.006)EQK;DEILPT(0.153)T(0.846)PIS(0.001)EQK;DEILPT(0.21)T(0.747)PIS(0.043)EQK ;; 145.83 0.0015842 237919000 20291.1 19133.9 19372 14494.5 19192.1 18347.8 16574.6 19548.3 19704.7 20268.5 TRUE FALSE FALSE 20043.78427 19403.26755 19709.16153 16170.42229 18212.65552 17175.43479 17982.44611 20113.89922 17942.26228 19741.92145 1.015290448 0.98284595 0.998340591 0.8190906 0.922537128 0.869998133 0.910876186 1.018842025 0.908840729 1 14.26897479 -9.421231437 11.23212228 1.004882382 0.907089266 0.247842709 0.05630565 0.35384572 37.4723851 0.006921601 0.010573456 3.79E-10 9.421231437 -0.097793116 DEILPTTPISEQK ddPTM_HeLa_Romidepsin_16h_R1 2 DEILPTTPISEQK 13 0 E9PPU1;E9PL09;P23396;P23396-2;H0YEU2;E9PSF4 E9PPU1 RPS3 40S ribosomal protein S3 0 0 ; ; 141.89 0.0013416 4854100 4233.8 4219.2 4523.1 3120.9 4444.9 4386.1 3749.8 4625.2 4727.9 4091.7 FALSE FALSE TRUE 4182.196817 4278.598008 4601.822658 3481.753142 4218.060167 4105.842365 4068.307918 4759.022865 4305.024783 3985.397044 1.049380218 1.073568822 1.154671067 0.873627672 1.058378907 1.030221662 1.020803667 1.194115119 1.080199723 1 11.96050774 DELADEIANS(ph)SGKGALALEEK ddPTM_HeLa_Romidepsin_16h_R1 2 DELADEIANSSGKGALALEEK 21 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 DELADEIANS(0.5)S(0.5)GKGALALEEK;DELADEIANS(0.559)S(0.441)GKGALALEEK ; 64.723 0.0040989 24386000 5958.8 6239.2 6573 3797.8 5589.3 5930.8 4889 5181.6 6277.3 7011.5 TRUE FALSE FALSE 5886.171854 6327.035621 6687.400308 4236.919505 5304.057164 5551.841021 5304.271538 5331.521421 5715.842566 6829.340219 0.861894658 0.92644903 0.97921616 0.620399536 0.776657334 0.812939588 0.776688724 0.780678843 0.836953847 1 12.73753049 -9.28246284 24.98502266 0.935398832 0.759354307 0.607428202 0.066709886 407.1518688 483872.3793 0.010809871 0.016522877 5.22E-10 9.28246284 -0.176044525 DELADEIANSS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 2 DELADEIANSSGK 13 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 DELADEIANS(0.074)S(0.926)GK;DELADEIANS(0.008)S(0.992)GK ; 258.09 6.25E-66 17508300 8978.8 10646.4 11000.7 3025.5 8228.6 9066.7 6897.4 8682.6 9423.8 10585.9 TRUE FALSE FALSE 8869.362932 10796.2803 11192.16257 3375.322545 7808.663837 8487.367131 7483.264984 8933.817332 8580.911726 10310.87679 0.860194832 1.047076841 1.085471468 0.327355531 0.75732297 0.823146984 0.725764175 0.86644594 0.832219403 1 13.3318794 DELAELS(ph)EAESEGDEKPK ddPTM_HeLa_Romidepsin_16h_R1 1 DELAELSEAESEGDEKPK 18 1 H3BTW3;Q3L8U1;Q3L8U1-2;Q3L8U1-3 H3BTW3 CHD9 Chromodomain-helicase-DNA-binding protein 9 1 0 DELAELS(0.999)EAES(0.001)EGDEKPK 94.911 0.00059398 0 809.38 1023 791.61 684.32 654.02 1009.8 738.15 749.16 1047.7 1020.1 TRUE FALSE FALSE 799.5149652 1037.401821 805.38764 763.4442982 620.6429189 945.277039 800.8484426 770.8357626 953.991088 993.5976549 0.804666719 1.044086422 0.810577235 0.768363627 0.624642093 0.951368025 0.806008789 0.775802719 0.960138224 1 9.956517958 -9.549189347 24.6998098 0.915974406 0.786975745 0.390038146 0.095928814 202.4997244 190101.2681 0.016822277 0.023790689 2.82E-10 9.549189347 -0.128998661 DELHIVEAEAMNY(ph)EGSPIK ddPTM_HeLa_Romidepsin_16h_R1 2 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 DELHIVEAEAMNY(0.989)EGS(0.011)PIK;DELHIVEAEAMNY(0.557)EGS(0.443)PIK ; 117.6 0.000254 280480000 9632.32 11356.53 11210.4 4526.7 10735.09 11893.29 9281.7 9947.01 10482.74 11439.76 TRUE FALSE FALSE 9514.917579 11516.40753 11405.51231 5050.098353 10187.2383 11133.34715 10070.08737 10234.81104 9545.13748 11142.55339 0.853926138 1.033551927 1.023599521 0.45322631 0.914264258 0.999173777 0.903750426 0.918533723 0.856638254 1 13.44379225 -12.68088452 0.632810637 1.034296107 0.881841497 0 0.162580435 3.679470702 1.665668528 0.347861969 0.033494174 2.09E-13 12.68088452 -0.15245461 DELHIVEAEAMNY(ph)EGSPIKVTLATLK ddPTM_HeLa_Romidepsin_16h_R1 2 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 DELHIVEAEAMNY(0.539)EGS(0.461)PIKVTLATLK;DELHIVEAEAMNY(0.752)EGS(0.248)PIKVTLATLK ; 103.92 6.61E-07 1245330000 10708.1 10002.5 10537.6 6503.1 9885 10552.9 9125.8 10437.4 10746.1 10511 TRUE FALSE FALSE 10577.58556 10143.31546 10721.00251 7255.01902 9380.531564 9878.603748 9900.945224 10739.3897 9784.941902 10237.9227 1.033176931 0.990759136 1.047185334 0.708641707 0.916253408 0.964903138 0.967085366 1.048981323 0.955754618 1 13.3216354 DELHIVEAEAMNYEGS(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 5 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 DELHIVEAEAMNY(0.01)EGS(0.99)PIK;DELHIVEAEAMNYEGS(1)PIK;DELHIVEAEAMNY(0.061)EGS(0.939)PIK;DELHIVEAEAMNY(0.013)EGS(0.987)PIK;DELHIVEAEAMNY(0.094)EGS(0.906)PIK ;;;; 139.25 0.00012078 591566400 29517 31993.65 35766.06 13943.46 29755.35 31748.12 27711.7 29698 31679.6 35449 TRUE FALSE FALSE 29157.23545 32444.05744 36388.55327 15555.66845 28236.82346 29719.51759 30065.53111 30557.26477 28846.09723 34528.02987 0.844451177 0.939644039 1.053884436 0.450522909 0.817794226 0.860735979 0.870757214 0.884998793 0.835439999 1 15.0754804 DELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_HeLa_Romidepsin_16h_R1 2 DELHIVEAEAMNYEGSPIKVTLATLK 26 1 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 DELHIVEAEAMNY(0.452)EGS(0.548)PIKVTLATLK;DELHIVEAEAMNY(0.447)EGS(0.553)PIKVT(0.001)LATLK ; 107.56 6.76E-07 81454600 4902.1 5113 5170.9 3132 4729.4 5430.2 4095.5 4970.2 5171.9 5253.3 TRUE FALSE FALSE 4842.35132 5184.980948 5260.897345 3494.136577 4488.04107 5083.227745 4443.371668 5114.004895 4709.312311 5116.818509 0.946359796 1.013321254 1.028157895 0.682872877 0.877115548 0.993435225 0.868385631 0.999450124 0.920359458 1 12.32103135 DELHIVEAEAMNYEGSPIK ddPTM_HeLa_Romidepsin_16h_R1 2 DELHIVEAEAMNYEGSPIK 19 0 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 0 0 ; ; 107.57 0.0038676 12703800 4210.4 3891.9 4478.7 2823.92 3845 4003.8 3359.7 3920.1 4063.3 4904.5 FALSE FALSE TRUE 4159.082025 3946.69027 4556.649895 3150.434917 3648.775302 3747.970102 3645.072834 4033.521909 3699.868271 4777.080383 0.870632623 0.826172045 0.953856651 0.659489618 0.763808647 0.78457338 0.763033598 0.844348762 0.774504085 1 12.22191344 -10.95702607 0.402777041 1.009923782 0.766130505 0 0.095368927 0.555739783 0.232224538 0.054467103 0.032795225 1.10E-11 10.95702607 -0.243793277 DELS(ph)DYAEK ddPTM_HeLa_Romidepsin_16h_R1 1 DELSDYAEK 9 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LP59 P46100-4 ATRX Transcriptional regulator ATRX 1 0 DELS(1)DYAEK 132.17 0.0071599 2022800 929 1071.6 1003.6 1098.5 1062.9 1101.7 704.44 983.14 968.58 1250.5 TRUE FALSE FALSE 917.6769907 1086.686013 1021.067237 1225.513739 1008.656247 1031.304926 764.275116 1011.585605 881.9477789 1218.01183 0.753422067 0.89218018 0.838306503 1.006159143 0.828116954 0.846711748 0.627477581 0.830521987 0.724088024 1 10.25031243 -12.47092782 1.146730508 1.002351869 0.82248755 0 0.124166022 0.480623255 1.106686349 0.07023782 0.016373581 3.38E-13 12.47092782 -0.179864319 DELT(ph)ESPK ddPTM_HeLa_Romidepsin_16h_R1 1 DELTESPK 8 0 Q8NC51-2;Q8NC51 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 DELT(0.99)ES(0.01)PK 130.41 0.022839 29906000 6945.2 7093.4 8559.9 2279.1 6754.6 10091 8552.8 7907.8 7367.4 7937.6 TRUE FALSE FALSE 6860.549231 7193.261071 8708.881469 2542.620265 6409.887557 9446.217667 9279.274619 8136.599717 6708.441292 7731.380008 0.887364122 0.930398074 1.126432986 0.328870171 0.829074182 1.221802273 1.200209356 1.052412339 0.867690022 1 12.91651023 -8.259370106 24.98772215 0.9038958 1.162348134 0.299838258 0.203556443 201.4248221 2432301.526 0.029328489 0.070925385 5.50E-09 8.259370106 0.258452334 DELTES(ph)PKYIQK ddPTM_HeLa_Romidepsin_16h_R1 1 DELTESPKYIQK 12 1 Q8NC51-2;Q8NC51 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 DELT(0.062)ES(0.938)PKYIQK 184.11 4.00E-06 20420000 2469 2258.4 2441.2 2635.6 3023.2 3949.7 3083.3 3719.3 2767.2 2538.4 TRUE FALSE FALSE 2438.906878 2290.193814 2483.688062 2940.340473 2868.914823 3697.326917 3345.195425 3826.912077 2519.694701 2472.452002 0.986432447 0.926284439 1.004544501 1.189240669 1.16035208 1.495408976 1.352987003 1.547820574 1.019107631 1 11.2717268 -8.56156768 1.098585852 0.986846649 1.489102533 0.89616248 0.068712623 0.104443917 0.236984048 0.009946307 0.035149432 2.74E-09 8.56156768 0.502255884 DELVAK(ac)VK ddPTM_HeLa_Romidepsin_16h_R1 1 DELVAKVK 8 1 Q9NXV6;D6RGD2 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 0 1 DELVAK(1)VK 107.47 0.016586 676070 734.27 585.7 858.51 735.41 977.47 1140.7 1072.3 1180.4 729.84 951.46 FALSE TRUE FALSE 725.3204348 593.9455 873.4520064 820.4415644 927.5860585 1067.812951 1163.381135 1214.553012 664.5612825 926.740932 0.78265717 0.640897018 0.942498573 0.885297645 1.000911934 1.152223793 1.255346662 1.310563686 0.717094993 1 9.856022283 -8.196721282 1.358852888 0.87472768 1.306621888 0.756492997 0.104417512 0.21404032 0.710550778 0.017732684 0.077771175 6.36E-09 8.196721282 0.431894208 DENYYQLEELAFR ddPTM_HeLa_Romidepsin_16h_R1 1 DENYYQLEELAFR 13 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;E9PNZ4;E9PLY5;A0A5F9ZGX0;A0A669KBB0;E9PLY0 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 0 158.34 0.0055858 1724700 599.41 360.96 380.75 283.86 467.67 524.69 449.35 295.83 516.78 610.03 FALSE FALSE TRUE 592.1041604 366.0416044 387.376794 316.6812288 443.8030548 491.1640024 487.5177778 304.3893743 470.5579025 594.1813327 0.996504144 0.616043595 0.651950461 0.53297068 0.746915176 0.826623078 0.820486527 0.512283637 0.791943261 1 9.214759471 -10.26899078 24.48722253 0.998349191 0.680798667 0.46437036 0.119596933 180.4616295 585189.0232 0.01731614 0.020008639 5.38E-11 10.26899078 -0.317550523 DEQLS(ph)PEEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 DEQLSPEEEEK 11 0 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 0 DEQLS(1)PEEEEK;DEQLS(1)PEEEEK ; 171.36 0.0002817 16269200 7298.6 6266.6 6225.5 3987 5322.2 4852 4045.5 4687.3 6909.5 7098 TRUE FALSE FALSE 7209.641856 6354.821359 6333.852216 4447.995699 5050.588274 4541.972859 4389.124669 4822.91963 6291.497015 6913.592937 1.042821283 0.919177831 0.9161448 0.643369626 0.730530177 0.656962726 0.634854367 0.697599595 0.910018434 1 12.75521995 -9.47565174 1.63614371 1.018022311 0.66640339 0.866213224 0.054748426 0.058807305 0.312924524 0.00679357 0.011216549 3.34E-10 9.47565174 -0.35161892 DESANQEEPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 DESANQEEPEAR 12 0 P50552;K7EM16 P50552 VASP Vasodilator-stimulated phosphoprotein 0 0 189.17 5.96E-09 2874100 763.97 697.55 614.69 617.55 736.7 738.1 674.21 618.57 648.32 911.19 FALSE FALSE TRUE 754.6584398 707.3701272 625.3884216 688.9540367 699.10345 690.9377921 731.4773806 636.467347 590.3326355 887.5171524 0.850302935 0.797021359 0.704649392 0.776271236 0.787706973 0.77850641 0.824183937 0.717132447 0.665150678 1 9.793631192 -11.25961573 0.607434794 0.994814498 0.765781208 0 0.107655521 0.197181707 0.15994784 0.020079319 0.010480821 5.50E-12 11.25961573 -0.22903329 DESTDSGLS(ph)MSSYSVPR ddPTM_HeLa_Romidepsin_16h_R1 1 DESTDSGLSMSSYSVPR 17 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 DEST(0.002)DS(0.01)GLS(0.843)MS(0.123)S(0.018)Y(0.002)S(0.001)VPR 88.187 0.014438 5198900 2213.2 2312.9 1935.3 1968.9 1728.5 1442.2 1186.4 1410.5 2494.3 2173.5 TRUE FALSE FALSE 2186.224667 2345.461067 1968.983085 2196.553482 1640.288195 1350.048074 1287.172786 1451.310592 2271.203561 2117.032157 1.032683731 1.107900539 0.930067632 1.037562644 0.774805517 0.637707873 0.608008141 0.685540174 1.072824309 1 11.04782747 -8.60177323 2.767963478 1.01866748 0.641645015 0.926620166 0.049578401 0.044902957 0.693772976 0.006630332 0.014776732 2.50E-09 8.60177323 -0.377022466 DESTDSGLSMS(ph)SYSVPR ddPTM_HeLa_Romidepsin_16h_R1 1 DESTDSGLSMSSYSVPR 17 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 DEST(0.004)DSGLS(0.226)MS(0.539)S(0.123)Y(0.08)S(0.028)VPR 110.84 0.0027087 4954000 1911.8 2092.9 1888.6 1588.3 1392.3 1491.8 1184.3 1197.8 2228.8 2154 TRUE FALSE FALSE 1888.498246 2122.363901 1921.470291 1771.946719 1321.245736 1396.478795 1284.894412 1232.456453 2029.450546 2098.038769 0.900125524 1.011594224 0.915841174 0.844572915 0.629752774 0.66561153 0.612426439 0.58743264 0.96730841 1 11.03482562 -8.90618697 1.981016896 0.955582498 0.617014798 0.948162157 0.036979126 0.061334899 0.486623793 0.007008406 0.014428881 1.24E-09 8.90618697 -0.3385677 DETFGEYS(ph)DNEEK ddPTM_HeLa_Romidepsin_16h_R1 2 DETFGEYSDNEEK 13 0 P32004-3;P32004-2;H3BLW5 P32004-3 L1CAM Neural cell adhesion molecule L1 1 0 DET(0.004)FGEYS(0.996)DNEEK;DET(0.269)FGEY(0.032)S(0.699)DNEEK ; 211.82 3.25E-23 16589000 3692.9 6576.2 5791.7 2417.17 5135.4 6943 2941.4 5504.2 5146.5 5581.9 TRUE FALSE FALSE 3647.889514 6668.779916 5892.502109 2696.654569 4873.321375 6499.364708 3191.242443 5663.455343 4686.18415 5436.881433 0.67095256 1.226581819 1.083801841 0.495992896 0.896344979 1.195421454 0.586961934 1.041673506 0.861925022 1 12.40856365 -9.588449977 0.003979624 1.746459616 1.78E-07 0 0.241274619 183651.1354 377.6273868 82261.9533 83450.11068 2.58E-10 9.588449977 -1.746459437 DETPTLEAS(ph)LDNANSR ddPTM_HeLa_Romidepsin_16h_R1 1 DETPTLEASLDNANSR 16 0 H0Y9X0;A0A286YEZ9;A0A2C9F2R7;O94915 H0Y9X0 FRYL Protein furry homolog-like 1 0 DET(0.119)PT(0.163)LEAS(0.719)LDNANSR 110.22 0.0030727 4996400 1234.8 1309 1295.9 757.73 1169.2 1442.8 1117.9 1449.2 1315.8 1341.3 TRUE FALSE FALSE 1219.749783 1327.428136 1318.454596 845.3423078 1109.531361 1350.609736 1212.854398 1491.130316 1198.111553 1306.452833 0.933634764 1.016055156 1.009186526 0.647051533 0.849270125 1.03379908 0.928356821 1.141357941 0.917072184 1 10.35143932 -9.312772559 0.005430499 1.896272419 1.64E-07 0 0.127291146 42006.61198 94.86679589 16342.87148 16781.26148 4.87E-10 9.312772559 -1.896272254 DEYRQDYDAGR ddPTM_HeLa_Romidepsin_16h_R1 1 DEYRQDYDAGR 11 1 C9JQX9;B3KSB0;P52298-3;P52298-2;P52298 C9JQX9 NCBP2 Nuclear cap-binding protein subunit 2 0 0 103.31 0.020091 17776000 2866.8 2151.4 2757.5 1984 2898.7 3044.2 3123.8 2784.5 3119.3 3053.8 FALSE FALSE TRUE 2831.858339 2181.687466 2805.493131 2213.399415 2750.768522 2849.685445 3389.135494 2865.065114 2840.301996 2974.461836 0.952057379 0.733473007 0.943193521 0.744134414 0.924795366 0.958050768 1.139411323 0.96322134 0.954896096 1 11.53841295 -7.939471456 9.938032792 0.934764566 1.051159382 0.220546503 0.09874794 0.538431047 84.16237864 0.014803719 0.044515582 1.15E-08 7.939471456 0.116394815 DFEEYPEHR ddPTM_HeLa_Romidepsin_16h_R1 2 DFEEYPEHR 9 0 O14980 O14980 XPO1 Exportin-1 0 0 ; ; 145.46 0.0027528 9345500 12180.1 10777.6 12943.7 8936.6 10142.7 10038.1 8880.7 10187.4 13755.3 12693.9 FALSE FALSE TRUE 12031.64426 10929.32734 13168.97967 9969.89174 9625.080171 9396.697806 9635.026436 10482.15635 12524.99152 12364.11065 0.973110367 0.883955801 1.065097203 0.80635737 0.778469268 0.759997874 0.779273715 0.847788947 1.013011924 1 13.59387085 -9.184038577 7.006400554 0.982786207 0.789571881 0.804459268 0.047463451 0.08010429 6.25849459 0.006674502 0.011103174 6.55E-10 9.184038577 -0.193214326 DFEPYDFTLDD ddPTM_HeLa_Romidepsin_16h_R1 1 DFEPYDFTLDD 11 0 Q69YN2-2;Q69YN2-3;Q69YN2 Q69YN2-2 CWF19L1 CWF19-like protein 1 0 0 143.12 0.026328 13789000 12753 11733 11912 11121 12167 13144 11476 13260 12644 11731 FALSE FALSE TRUE 12597.56153 11898.17748 12119.32336 12406.86235 11546.07259 12304.14082 12450.77115 13643.65718 11513.08897 11426.22693 1.102512808 1.041304147 1.060658382 1.085823205 1.010488647 1.076833227 1.089666014 1.194064958 1.007601988 1 13.48006147 -16.52287765 0.012218183 1.24E-05 1.95844576 0.436493812 0.041309021 6549.926553 6.46778909 615.7320148 435.6809135 3.00E-17 16.52287765 1.958433385 DFFHGLR ddPTM_HeLa_Romidepsin_16h_R1 2 DFFHGLR 7 0 Q9NTZ6 Q9NTZ6 RBM12 RNA-binding protein 12 0 0 ; ; 133.47 0.0064916 14464500 15021.1 15498.3 18617.5 18504.5 19789.7 19029.2 15853.9 14098.2 14858 12084.3 FALSE FALSE TRUE 14838.01706 15716.48547 18941.52978 20644.07736 18779.75776 17813.29553 17200.52987 14506.10917 13529.06327 11770.34814 1.260626863 1.335260885 1.609258243 1.753905416 1.595514214 1.513404303 1.46134419 1.232428217 1.149419125 1 13.52286937 -10.62207548 0.916595171 1.063019568 1.530921231 0.609643065 0.139368542 0.227055375 0.39834844 0.038316792 0.03726765 2.39E-11 10.62207548 0.467901664 DFGAQREEGR ddPTM_HeLa_Romidepsin_16h_R1 1 DFGAQREEGR 10 1 P46087;P46087-4;P46087-2;P46087-3;F5GYR3 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 0 0 102.06 0.0027932 0 865.28 837.29 603.15 1247 588.84 619.99 962.4 566.72 710.81 671.22 FALSE FALSE TRUE 854.7336345 849.0773906 613.6475727 1391.184007 558.7892975 580.3746399 1044.146232 583.1171491 647.2333733 653.7816076 1.307368737 1.298717157 0.938612475 2.127903249 0.8547033 0.887719436 1.597087192 0.891914276 0.989984065 1 9.352664981 -12.33078897 0.992964576 0.996221473 1.250831452 0.061273784 0.375611263 1.400612887 2.414213116 0.257706981 0.064045693 4.67E-13 12.33078897 0.254609978 DFNHINVELSLLGK ddPTM_HeLa_Romidepsin_16h_R1 1 DFNHINVELSLLGK 14 0 D6RAN4;A0A2R8Y5Y7;P32969;E7ESE0 D6RAN4 RPL9 60S ribosomal protein L9 0 0 74.89 0.021701 3705600 2463.9 2507 2690.1 2538.8 2517.7 2631.5 2146.9 2474.2 2711.8 2672.4 FALSE FALSE TRUE 2433.869039 2542.293612 2736.920062 2832.348001 2389.212374 2463.355643 2329.257632 2545.787073 2469.249816 2602.970663 0.93503514 0.976689307 1.051460203 1.088121369 0.917879102 0.946363199 0.894845903 0.978031412 0.948627601 1 11.34594334 DFPYEEDSRPR ddPTM_HeLa_Romidepsin_16h_R1 2 DFPYEEDSRPR 11 1 H0Y6J6;Q5W012;Q96I25;Q5W011;Q5W010 H0Y6J6 RBM17 Splicing factor 45 0 0 ; ; 193.83 9.13E-09 15074100 5428.8 5438.2 4960.8 4868.3 5455.8 5425.5 4842.1 5239.6 5807.8 5158.8 FALSE FALSE TRUE 5362.631697 5514.759122 5047.140643 5431.195752 5177.370168 5078.82806 5253.387853 5391.199559 5288.335822 5024.773632 1.067238465 1.097513943 1.004451347 1.080883667 1.030368838 1.010757585 1.045497417 1.072923868 1.05245255 1 12.29484289 -12.38739586 1.142340528 1.000328308 1.051231416 0 0.032461019 0.469316642 1.106441205 0.018603087 0.004896898 4.10E-13 12.38739586 0.050903108 DFQESS(ph)PQKGLEVER ddPTM_HeLa_Romidepsin_16h_R1 1 DFQESSPQKGLEVER 15 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 DFQES(0.272)S(0.728)PQKGLEVER 62.916 0.026479 9728200 1200.8 1220.2 1175.8 1066.7 2157 2648.9 2039.2 2292.2 1517.7 1480.3 TRUE FALSE FALSE 1186.164188 1237.378008 1196.264306 1190.036873 2046.920241 2479.643839 2212.409597 2358.521191 1381.953111 1441.841593 0.822673027 0.858192754 0.829678039 0.825358957 1.419656814 1.719775495 1.534433192 1.635769978 0.958463896 1 10.49369696 -8.646191217 3.985499041 0.896553243 1.614427708 0.956170623 0.073707029 0.038440981 1.126770401 0.013160015 0.02720134 2.26E-09 8.646191217 0.717874465 DFQEYVEPGEDFPAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 DFQEYVEPGEDFPASPQR 18 0 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 DFQEYVEPGEDFPAS(1)PQR;DFQEYVEPGEDFPAS(1)PQR ; 114.71 0.00054205 19056200 8267.1 7820.8 8076.6 5086.2 7809.3 7027.1 6132.1 6504 8925.1 8542.6 TRUE FALSE FALSE 8166.337405 7930.901428 8217.169835 5674.290375 7410.76228 6578.090989 6652.960421 6692.182978 8126.816703 8320.662021 0.981452844 0.953157502 0.987562025 0.681951792 0.890645752 0.79057303 0.799571044 0.804284919 0.976703138 1 13.0224826 -9.287004647 24.64130543 0.987306088 0.798992752 0.784929404 0.048653988 188.1535851 181352.9214 0.0067604 0.010329176 5.16E-10 9.287004647 -0.188313336 DFQEYVEPGEDFPAS(ph)PQRR ddPTM_HeLa_Romidepsin_16h_R1 4 DFQEYVEPGEDFPASPQRR 19 1 Q9Y6G9;E9PHI6;C9JGM7 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR;DFQEYVEPGEDFPAS(1)PQRR ;;; 102.29 0.0003634 651436000 12140.1 13895.2 11546.2 12458.1 11604.6 10927 9490.1 10056.3 13822.9 13279.2 TRUE FALSE FALSE 11992.13179 14090.81699 11747.15677 13898.56414 11012.37396 10228.79997 10296.18886 10347.26317 12586.5452 12934.20447 0.927164235 1.08942278 0.908224143 1.07455887 0.851414866 0.790833328 0.796043458 0.799992238 0.973120939 1 13.6589037 -8.580298849 6.531314633 0.977032057 0.799540784 0.734334577 0.054826502 0.082030253 7.116084877 0.00784717 0.015848219 2.63E-09 8.580298849 -0.177491273 DFS(ph)ASYFSGEQEVTPSR ddPTM_HeLa_Romidepsin_16h_R1 1 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 0 DFS(0.681)AS(0.318)YFSGEQEVTPSR 110.12 0.00027968 0 772.02 724.85 468.27 465.03 667.83 602.58 540.7 791.54 697.41 700.05 TRUE FALSE FALSE 762.6103233 735.0544573 476.4200429 518.7989566 633.7481431 564.0770827 586.6270445 814.4419611 635.0319029 681.8626001 1.118422279 1.078009642 0.698703878 0.760855569 0.929436727 0.827259161 0.860330284 1.194437062 0.931319452 1 9.413337246 -9.802525041 24.99992428 1.059140834 0.872315706 0.233022395 0.132464903 127.4918471 77576.08177 0.020585605 0.027054941 1.58E-10 9.802525041 -0.186825128 DFS(ph)PLQTQTFNR ddPTM_HeLa_Romidepsin_16h_R1 1 DFSPLQTQTFNR 12 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 0 DFS(1)PLQTQTFNR 147.52 0.001486 6095500 1859 1459.1 1882.3 1265.6 1753.5 1366.4 1445.7 1655.5 1760.2 1561.5 TRUE FALSE FALSE 1836.341793 1479.641248 1915.060642 1411.934627 1664.012352 1279.09145 1568.497722 1703.399281 1602.763303 1520.932005 1.207379283 0.972851675 1.259136264 0.928335141 1.094074125 0.840991869 1.031274059 1.119970699 1.053803391 1 10.57073994 -9.214662697 24.99962262 1.10003754 1.000571009 0.160267199 0.109444682 628.1263284 335700.2968 0.017387492 0.028833857 6.10E-10 9.214662697 -0.09946653 DFSASYFSGEQEVT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 DFSASYFSGEQEVTPSR 17 0 P49454 P49454 CENPF Centromere protein F 1 0 DFSASYFSGEQEVT(0.697)PS(0.303)R;DFSASYFSGEQEVT(1)PSR ; 197.1 8.91E-14 75653000 5256.1 4549.7 4731.9 4529.2 5276.4 5732 4898.4 4553.6 5107.1 5040.2 TRUE FALSE FALSE 5192.036632 4613.750796 4814.256735 5052.887415 5007.125619 5365.743699 5314.469974 4685.351232 4650.308185 4909.254877 1.057601767 0.939806735 0.980649173 1.029257503 1.019935967 1.092985358 1.082541059 0.954391521 0.947253361 1 12.26128835 -8.48241853 24.93870098 1.017112418 1.048768024 0.055102456 0.05125277 1048.837221 646478.3514 0.006932109 0.015498367 3.29E-09 8.48241853 0.031655607 DFSPEALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 DFSPEALKK 9 1 E5RGU4;A0A087WZK9;B3KS98;O15372;E5RJT0 E5RGU4 EIF3H Eukaryotic translation initiation factor 3 subunit H 0 1 DFSPEALK(1)K 101.11 0.0056859 493210 261.71 209.2 103.06 115.6 527.13 351.88 293.79 343.81 365.92 392.11 FALSE TRUE FALSE 258.5201779 212.1451231 104.8537161 128.9662159 500.2285891 329.3960036 318.7445153 353.7575999 333.1911987 381.9229257 0.676890965 0.555465799 0.274541561 0.337676026 1.309763189 0.862467219 0.834578115 0.926253901 0.87240429 1 8.577137713 -12.19079247 1.066720341 0.991202548 0.717944934 0.077268086 0.284745397 0.903601404 1.927136315 0.171536397 0.054834144 6.44E-13 12.19079247 -0.273257614 DFTNEAPPAPLPDASAS(ph)PLSPHR ddPTM_HeLa_Romidepsin_16h_R1 3 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 DFTNEAPPAPLPDAS(0.219)AS(0.726)PLS(0.055)PHR;DFTNEAPPAPLPDAS(0.103)AS(0.851)PLS(0.046)PHR;DFT(0.001)NEAPPAPLPDAS(0.139)AS(0.807)PLS(0.053)PHR ;; 117.49 2.48E-06 19876000 6353.3 6267.9 5966.3 5983.7 9059.3 9279.2 7583.5 8083.7 7664.8 7292.5 TRUE FALSE FALSE 6275.863536 6356.139661 6070.140949 6675.563548 8596.970116 8686.289067 8227.642301 8317.589106 6979.241091 7103.039799 0.88354616 0.894847817 0.854583547 0.939817844 1.210322673 1.222897423 1.158326932 1.170990075 0.982571024 1 12.79422085 -8.765197481 24.92911344 0.931687688 1.190631142 0.894573974 0.044496992 26.61479912 176549.2345 0.008387322 0.015635474 1.72E-09 8.765197481 0.258943454 DFTNEAPPAPLPDASASPLS(ph)PHR ddPTM_HeLa_Romidepsin_16h_R1 2 DFTNEAPPAPLPDASASPLSPHR 23 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 DFTNEAPPAPLPDAS(0.025)AS(0.265)PLS(0.709)PHR;DFTNEAPPAPLPDAS(0.019)AS(0.068)PLS(0.914)PHR ; 157.64 8.82E-10 50702000 6074.7 6229.6 5574.4 4962.7 7510 7204.3 5661.8 6810.9 7372 6889.3 TRUE FALSE FALSE 6000.65922 6317.300472 5671.420094 5536.510724 7126.736676 6743.968481 6142.713151 7007.962646 6712.629856 6710.314993 0.894244045 0.941431286 0.845179414 0.82507464 1.06205695 1.005015188 0.915413532 1.044356733 1.000344971 1 12.71216478 -7.251331575 23.56147599 0.942627722 1.044356862 0.152480382 0.071537627 998.0042077 2326258.173 0.010342092 0.178795893 5.61E-08 7.251331575 0.10172914 DFTNEAPPAPLPDASASPLS(ph)PHRR ddPTM_HeLa_Romidepsin_16h_R1 4 DFTNEAPPAPLPDASASPLSPHRR 24 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 DFTNEAPPAPLPDAS(0.215)AS(0.045)PLS(0.74)PHRR;DFTNEAPPAPLPDAS(0.03)AS(0.249)PLS(0.721)PHRR;DFTNEAPPAPLPDAS(0.046)AS(0.148)PLS(0.806)PHRR;DFTNEAPPAPLPDAS(0.099)AS(0.025)PLS(0.876)PHRR ;;; 155.68 8.28E-24 47539400 4914.7 4960.9 4609.96 4793.32 6070.5 5681 5074.74 4824.35 5838.5 5634.1 TRUE FALSE FALSE 4854.797746 5030.73968 4690.19442 5347.546212 5760.699733 5318.002435 5505.788289 4963.934956 5316.289937 5487.72527 0.884664867 0.916725862 0.854670048 0.97445589 1.049742735 0.969072279 1.003291531 0.90455238 0.96876022 1 12.42199254 -9.021657837 24.8700305 0.934434938 0.986033707 0.216262999 0.050905482 1088.091904 1249471.775 0.00905791 0.015112521 9.51E-10 9.021657837 0.051598769 DFVDDDDDDDLER ddPTM_HeLa_Romidepsin_16h_R1 2 DFVDDDDDDDLER 13 0 G3V4K3;Q9H9C1-2;Q9H9C1 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 0 0 ; ; 271.21 6.16E-79 93064000 5567.2 4769.6 5049.6 4215.7 6160 5904.1 5550.2 6036.5 5693.8 5398 FALSE FALSE TRUE 5499.344825 4836.746554 5137.48617 4703.139069 5845.632214 5526.847065 6021.633849 6211.156603 5184.532268 5257.759182 1.045948404 0.919925464 0.977124663 0.894513976 1.111810566 1.051179195 1.145285214 1.181331512 0.9860726 1 12.36023235 -7.874650207 1.306680004 1.004538612 1.188664246 0.604247064 0.056150787 0.353568372 0.959724793 0.008807004 0.064244344 1.33E-08 7.874650207 0.184125634 DFVT(ph)ISPVQPEER ddPTM_HeLa_Romidepsin_16h_R1 2 DFVTISPVQPEER 13 0 Q9H611-2;Q9H611;Q9H611-3;Q9H611-4 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 1 0 DFVT(0.919)IS(0.081)PVQPEER;DFVT(0.833)IS(0.167)PVQPEER ; 171.21 0.00016221 7604300 2343.21 2319.7 2445.7 2398.1 1667.04 1394.82 1281.44 1162.23 2259.08 2591.8 TRUE FALSE FALSE 2314.650055 2352.356797 2488.266383 2675.379605 1581.964728 1305.695504 1390.285482 1195.857291 2057.022227 2524.464662 0.916887485 0.931824015 0.985661008 1.059780969 0.626653544 0.517216788 0.550724873 0.473707281 0.814835025 1 11.30176177 -8.64476615 4.625918865 0.965349547 0.525622732 0.906624241 0.064845978 0.033608606 1.212471942 0.007415835 0.015139346 2.27E-09 8.64476615 -0.439726815 DGADFAK(ac)WR ddPTM_HeLa_Romidepsin_16h_R1 1 DGADFAKWR 9 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8;H3BU78;K7EKH5;C9J8F3;J3KSV6;J3QKP5;A8MVZ9;P09972 H3BQN4;K7EKH5 ALDOA;ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A;Fructose-bisphosphate aldolase C 0 1 DGADFAK(1)WR 135.71 0.014559 10250000 3393.5 2947.1 3845.5 5484.5 4789.5 3885.4 3947.9 3482.6 4170.2 3195.7 FALSE TRUE FALSE 3352.138717 2988.589351 3912.429314 6118.643695 4545.073943 3637.13548 4283.234527 3583.363536 3797.206868 3112.675253 1.076931721 0.960135288 1.256934629 1.965718617 1.460182503 1.16849179 1.376062126 1.151216637 1.219917453 1 11.60393935 -9.536231891 9.490529695 1.035072515 1.429498469 0.372401621 0.219016199 0.148775672 93.39820557 0.033677421 0.048094406 2.91E-10 9.536231891 0.394425954 DGAEQQGPEATVEEAEAAAFGSEKPQSMFEPPQVS(ph)SPVQEK ddPTM_HeLa_Romidepsin_16h_R1 2 DGAEQQGPEATVEEAEAAAFGSEKPQSMFEPPQVSSPVQEK 41 1 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 DGAEQQGPEATVEEAEAAAFGS(0.004)EKPQS(0.024)MFEPPQVS(0.79)S(0.182)PVQEK;DGAEQQGPEAT(0.001)VEEAEAAAFGS(0.013)EKPQS(0.005)MFEPPQVS(0.523)S(0.458)PVQEK ; 61.058 0.00017098 14232000 1325.62 1286 1668.4 1376.49 1727.7 1535.51 1469.48 1714.91 1616.34 1613.71 TRUE FALSE FALSE 1309.462834 1304.104342 1697.437802 1535.64625 1639.529022 1437.395867 1594.297595 1764.528215 1471.770502 1571.785582 0.833105259 0.829696084 1.079942342 0.977007467 1.04309967 0.914498697 1.014322573 1.122626544 0.936368497 1 10.61818871 -9.75453845 24.99970413 0.912124572 1.018337281 0.428736976 0.070099738 166.8534091 604450.4031 0.013471759 0.01881342 1.76E-10 9.75453845 0.106212709 DGAGLGLS(ph)GGSPGASTPVLLTR ddPTM_HeLa_Romidepsin_16h_R1 2 DGAGLGLSGGSPGASTPVLLTR 22 0 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 0 DGAGLGLS(0.997)GGS(0.003)PGASTPVLLTR;DGAGLGLS(0.996)GGS(0.004)PGASTPVLLTR ; 282.97 7.22E-112 36075000 3551.3 3273.2 3517.9 4382.7 4995.1 5843.6 4101.8 5492.8 3463.9 3103 TRUE FALSE FALSE 3508.01539 3319.280196 3579.127574 4889.448395 4740.181408 5470.212819 4450.20679 5651.725502 3154.080109 3022.383613 1.160678405 1.098232594 1.184206915 1.6177458 1.568358625 1.809900238 1.472416265 1.869956374 1.04357372 1 11.56147107 -9.288974157 2.199074421 1.078151843 1.676727342 0.869031129 0.111471309 0.07809474 0.73818647 0.017332104 0.029534047 5.14E-10 9.288974157 0.598575499 DGDGVPGGGPLS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 DGDGVPGGGPLSPAR 15 0 M0QZR4;Q92888-2;Q92888;Q92888-3 M0QZR4;Q92888-3 ARHGEF1 Rho guanine nucleotide exchange factor 1 1 0 DGDGVPGGGPLS(1)PAR;DGDGVPGGGPLS(1)PAR ; 192.4 1.65E-12 41093000 7641.1 6660.5 7349.6 5973.1 9965.7 12771.9 10485 12353.7 7583.2 7068.9 TRUE FALSE FALSE 7547.967334 6754.266694 7477.516705 6663.737926 9457.113142 11955.81681 11375.59564 12711.13482 6904.9396 6885.248959 1.096251912 0.980976394 1.086019801 0.967828174 1.373532489 1.736439289 1.652169109 1.84614019 1.00285983 1 12.74929311 -8.479849586 2.589631586 1.039339552 1.741943794 0.961177404 0.065028567 0.037059468 0.490199805 0.009426601 0.022902368 3.31E-09 8.479849586 0.702604242 DGDS(ph)YDPYDFSDT(ph)EEEMPQVHTPK ddPTM_HeLa_Romidepsin_16h_R1 1 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 0 DGDS(0.862)Y(0.003)DPY(0.111)DFS(0.094)DT(0.868)EEEMPQVHT(0.061)PK 61.033 0.0015412 0 2032.7 2026.2 2172.6 2154 1647.5 1640.9 1731 1507.1 2236.1 2571.7 TRUE FALSE FALSE 2007.924671 2054.724897 2210.413192 2403.055615 1563.421927 1536.051786 1878.031097 1550.705561 2036.097616 2504.886863 0.801602939 0.820286508 0.882440331 0.959346967 0.624148719 0.613222021 0.749746875 0.619072096 0.812850131 1 11.29052973 -6.261493287 0.083298407 1.219109416 2.73E-13 0.403965415 0.101386901 54.98093516 0.55404589 1.824846865 8.379304441 5.48E-07 6.261493287 -1.219109416 DGDSYDPYDFS(ph)DT(ph)EEEMPQVHTPK ddPTM_HeLa_Romidepsin_16h_R1 4 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 0 DGDSYDPY(0.008)DFS(0.992)DT(0.995)EEEMPQVHT(0.005)PK;DGDSYDPY(0.004)DFS(0.979)DT(0.992)EEEMPQVHT(0.025)PK;DGDSYDPYDFS(1)DT(1)EEEMPQVHTPK;DGDSYDPYDFS(1)DT(1)EEEMPQVHTPK ;;; 108.44 4.56E-06 1218860000 26047 26873.7 25374.9 24174.8 24730.4 23056.5 19647.3 21128.3 28370.7 27026.5 TRUE FALSE FALSE 25729.52915 27252.02865 25816.53949 26970.00412 23468.31541 21583.26406 21316.14117 21739.61403 25833.15354 26324.34763 0.977404246 1.035240418 0.980709564 1.02452697 0.891506059 0.819897395 0.809750026 0.825836763 0.981340692 1 14.68411016 -8.545179658 3.165834436 0.994341003 0.819038658 0.945571445 0.019667313 0.039619604 0.817206176 0.002913967 0.00652442 2.85E-09 8.545179658 -0.175302346 DGDSYDPYDFS(ph)DTEEEMPQVHTPK ddPTM_HeLa_Romidepsin_16h_R1 1 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 DGDS(0.003)Y(0.002)DPY(0.059)DFS(0.716)DT(0.219)EEEMPQVHTPK 63.125 0.0013591 100410000 3386.1 3832.1 3305.3 3070.1 2683.7 3252.5 2576.3 3161.9 3513.2 3164.1 TRUE FALSE FALSE 3344.828911 3886.048404 3362.82736 3425.079407 2546.740775 3044.675747 2795.130858 3253.384588 3198.970593 3081.896226 1.08531523 1.260927727 1.091155287 1.111354555 0.826355136 0.987922864 0.906951647 1.055643782 1.037987771 1 11.58960257 -8.786004974 24.99970423 1.068293127 0.944678109 0.406670873 0.086581943 218.7396436 222604.394 0.01381757 0.025054497 1.64E-09 8.786004974 -0.123615018 DGDSYDPYDFSDT(ph)EEEMPQVHTPK ddPTM_HeLa_Romidepsin_16h_R1 4 DGDSYDPYDFSDTEEEMPQVHTPK 24 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 DGDSYDPYDFS(0.061)DT(0.544)EEEMPQVHT(0.394)PK;DGDS(0.005)Y(0.006)DPY(0.085)DFS(0.312)DT(0.578)EEEMPQVHT(0.014)PK;DGDSYDPYDFS(0.423)DT(0.577)EEEMPQVHTPK;DGDSYDPYDFSDT(1)EEEMPQVHTPK ;;; 124.69 7.82E-07 1709745400 27313 28002.9 26174.8 24548.9 23901.9 25925.6 22953.9 24803.5 30099.2 28050 TRUE FALSE FALSE 26980.09865 28397.12556 26630.36141 27387.35932 22682.09685 24269.03783 24903.60369 25521.15014 27407.05217 27321.25696 0.987513082 1.039378445 0.974712161 1.002419448 0.830199609 0.888284088 0.911510174 0.934113324 1.003140237 1 14.73773624 -8.782415626 24.9998523 0.996642852 0.89229399 0.773991403 0.029098819 82.31099935 98099.47227 0.004182558 0.00758715 1.65E-09 8.782415626 -0.104348863 DGEDQTQDTELVETRPAGDGTFQK ddPTM_HeLa_Romidepsin_16h_R1 1 DGEDQTQDTELVETRPAGDGTFQK 24 1 A0A1W2PS56;A0A140T9X5;Q5SUL5;B0UXQ0;Q5RIP0;Q5QT33;O19617;O78179;A0A1W2PSE7;A0A0G2JIF0;A0A140T962;A0A140T921;A0A0G2JIF2;A0A140T8Y4;A0A140T9I0;Q5SPM2;A0A140T913;A0A140T912;A0A0G2JH50;A0A140T9H5;A2AEA2;A0A140T9J9;A0A0G2JPD3;A0A0G2JL56;A0A140T930;A0A140T9B3;A0A140T9U8;A0A1W2PP77;Q5SRN5;Q53Z42;A0A1W2PS24;Q9GJ45;A0A1W2PRX1;Q5SRN7;A0A0G2JI36;A0A140T8W8;A0A140T933;A0A140T941;A0A140T955;A0A140T975;A0A1W2PQS8;A0A1W2PR11;A0A1W2PR61;A0A1W2PRZ0;Q5RJ27;A0A1W2PRU9;A0A1W2PQD0;A0A140T937;A0A1W2PS39;A0A1W2PPF8;A0A1W2PPQ2;A0A140T9Z6;A0A1W2PRT9;A2BF26;P10321-2;P04439-2;P01893;P10321;P04439 A0A1W2PS56 HLA-A;HLA-Cw;HLA-C;HLA-H "HLA class I histocompatibility antigen, Cw-7 alpha chain;HLA class I histocompatibility antigen, A-3 alpha chain;Putative HLA class I histocompatibility antigen, alpha chain H" 0 0 62.193 0.0059706 2210100 344.49 567.27 420.44 458.86 509.47 432.16 335.74 666.9 642.72 591.76 FALSE FALSE TRUE 340.2912234 575.2560419 427.7575818 511.9155522 483.4698448 404.5463707 364.2577472 686.1956993 585.2335135 576.3859899 0.590387742 0.998039599 0.742137369 0.888147112 0.838795275 0.701867113 0.631968427 1.190514189 1.015349998 1 9.170891458 -12.72328246 1.641618287 0.999868851 0.778999298 0.11505308 0.172655654 0.523918304 2.552529794 0.12294268 0.026926667 1.89E-13 12.72328246 -0.220869554 DGES(ph)DGFADEEES(ph)GEEGEEDQEEGREPGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 DGESDGFADEEESGEEGEEDQEEGREPGAGR 31 1 P48681 P48681 NES Nestin 2 0 DGES(1)DGFADEEES(1)GEEGEEDQEEGREPGAGR 71.874 3.85E-05 6375200 478.78 564.76 575.1 333.07 592.34 576.94 404.2 598.63 640.48 527.22 TRUE FALSE FALSE 472.9444452 572.7107061 585.1093743 371.5811205 562.1106795 540.075396 438.5327379 615.9504146 583.1938647 513.5227484 0.920980515 1.115258687 1.139403028 0.723592327 1.094616901 1.051706858 0.853969448 1.199460815 1.135672892 1 9.004284377 -7.238252869 23.44022581 0.977297817 1.199461398 0.139509293 0.131513436 2971.986954 3004401.533 0.015700786 1.049191111 5.78E-08 7.238252869 0.22216358 DGESDGFADEEES(ph)GEEGEEDQEEGREPGAGR ddPTM_HeLa_Romidepsin_16h_R1 2 DGESDGFADEEESGEEGEEDQEEGREPGAGR 31 1 P48681 P48681 NES Nestin 1 0 DGES(0.134)DGFADEEES(0.866)GEEGEEDQEEGREPGAGR;DGESDGFADEEES(1)GEEGEEDQEEGREPGAGR ; 111.49 3.29E-14 36919000 1315.57 1166.89 1221.37 1218.38 1692.6 2031.29 1378.52 1492.03 1460.37 1363.14 TRUE FALSE FALSE 1299.535327 1183.317508 1242.627433 1359.254828 1606.220306 1901.497125 1495.611454 1535.199534 1329.75085 1327.725426 0.978768126 0.89123661 0.935906934 1.023746929 1.209753368 1.432146351 1.126446346 1.156262811 1.001525484 1 10.37474111 -8.784333534 3.944597261 0.977419495 1.24132048 0.707913331 0.082138833 0.091508191 3.104526076 0.012164151 0.023728227 1.64E-09 8.784333534 0.263900985 DGFIDKEDLHDMLASLGK ddPTM_HeLa_Romidepsin_16h_R1 2 DGFIDKEDLHDMLASLGK 18 1 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 0 ; ; 72.433 0.0056268 76674000 11993.4 10695.3 11601.7 9211 13323.8 14159.8 13137.2 13313.7 12969 11170.7 FALSE FALSE TRUE 11847.21983 10845.86871 11803.62272 10276.01916 12643.83677 13255.03448 14253.07344 13698.9109 11809.02016 10880.4836 1.088850483 0.996818626 1.084843574 0.944445076 1.162065698 1.218239461 1.309966906 1.259035113 1.08533964 1 13.40945506 -8.408429428 2.453239047 1.036839938 1.274010501 0.807513488 0.05009736 0.089711561 1.046133226 0.007297123 0.018814296 3.90E-09 8.408429428 0.237170563 DGFPS(ph)GTPALNAK ddPTM_HeLa_Romidepsin_16h_R1 2 DGFPSGTPALNAK 13 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 DGFPS(0.993)GT(0.007)PALNAK;DGFPS(0.999)GT(0.001)PALNAK ; 149.82 7.91E-05 8881300 5872.9 5423.5 5936.1 4315.6 6757.2 7143 6006 7163.6 6020 6478.9 TRUE FALSE FALSE 5801.318836 5499.852175 6039.41533 4814.589978 6412.354869 6686.585353 6516.14949 7370.867464 5481.556123 6310.577244 0.91930082 0.871529174 0.957030569 0.762939711 1.016128101 1.05958379 1.032575823 1.168017945 0.868629907 1 12.62355626 -8.527940354 24.99690163 0.938590814 1.074068392 0.535947432 0.074489109 101.9880639 503670.6943 0.011038942 0.022136725 2.97E-09 8.527940354 0.135477577 DGGAWGTEQR ddPTM_HeLa_Romidepsin_16h_R1 1 DGGAWGTEQR 10 0 P09382 P09382 LGALS1 Galectin-1 0 0 162.64 0.020717 133120000 3402 2649.5 2311 2745.8 2891.8 3066.7 2580.2 2312.4 2813.1 2861.2 FALSE FALSE TRUE 3360.535115 2686.799731 2351.221986 3063.282315 2744.220655 2870.747767 2799.362124 2379.305646 2561.48929 2786.865612 1.205847566 0.964093754 0.843679715 1.099185516 0.984697878 1.030099103 1.004484074 0.853756864 0.919129103 1 11.44442772 -10.22240694 24.61674408 1.097205809 0.973159089 0.017094914 0.102130567 472.287862 297860.268 0.016872147 0.020663922 5.99E-11 10.22240694 -0.12404672 DGGEALVS(ph)PDGTVTEAPR ddPTM_HeLa_Romidepsin_16h_R1 2 DGGEALVSPDGTVTEAPR 18 0 Q96HN2-2;Q96HN2 Q96HN2-2 AHCYL2 Putative adenosylhomocysteinase 3 1 0 DGGEALVS(0.901)PDGT(0.099)VTEAPR;DGGEALVS(0.999)PDGTVTEAPR ; 217.65 3.55E-29 18263900 3651.5 3922.7 3840.4 2562.4 6530.2 8556.3 7071.8 8414.5 3897.2 4090.8 TRUE FALSE FALSE 3606.994113 3977.923874 3907.240551 2858.676744 6196.939526 8009.580044 7672.478515 8657.960282 3548.624671 3984.520426 0.905251756 0.998344455 0.980604975 0.717445624 1.555253547 2.010174171 1.925571385 2.172898958 0.890602705 1 11.96019038 -8.529435258 3.228474435 0.945580571 2.016991874 0.956708766 0.10743447 0.033806562 0.728818363 0.015298072 0.034463094 2.96E-09 8.529435258 1.071411303 up DGGRSS(ph)PGGQDEGGFMAQGK ddPTM_HeLa_Romidepsin_16h_R1 1 DGGRSSPGGQDEGGFMAQGK 20 1 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GV30 A0A1B0GTU4 PXN Paxillin 1 0 DGGRS(0.177)S(0.823)PGGQDEGGFMAQGK 82.755 0.013611 7708600 3486.6 3941 2607.4 6038.7 3391.9 3107.7 2880.3 2953.8 3659.7 3156.5 TRUE FALSE FALSE 3444.103978 3996.481501 2652.780703 6736.922907 3218.798686 2909.128 3124.95261 3039.263543 3332.367266 3074.493675 1.120218268 1.299882818 0.862834985 2.191230043 1.046936187 0.946213688 1.016412112 0.98854116 1.083875141 1 11.58613312 -6.164723993 15.70588007 1.118493619 1.175163866 0 0.364194739 0 0 0.045813056 0 6.84E-07 6.164723993 0.056670247 DGGS(ph)GNSTIIVSR ddPTM_HeLa_Romidepsin_16h_R1 1 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 DGGS(0.956)GNS(0.044)TIIVSR 123.63 0.0040847 6294300 1834.4 1439.7 1404.3 1707.1 1621.3 1655.7 1461.2 1552.3 1778.7 1595.7 TRUE FALSE FALSE 1812.041627 1459.968134 1428.741252 1904.482934 1538.559011 1549.906114 1585.314292 1597.213351 1619.608617 1554.243484 1.165867283 0.939343256 0.919251885 1.225344004 0.989908613 0.997209337 1.019990952 1.027646806 1.042055916 1 10.60199682 -10.25706526 24.96472623 1.078326216 1.019530364 0.067581232 0.0868336 790.1636423 4509758.151 0.016199823 0.019467191 5.53E-11 10.25706526 -0.058795852 DGGSGNS(ph)TIIVSR ddPTM_HeLa_Romidepsin_16h_R1 1 DGGSGNSTIIVSR 13 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 DGGSGNS(0.918)T(0.082)IIVSR 160.63 0.00042392 8014800 1422.2 1648 1734.8 1247.6 1013.5 1345.1 963.75 1004.9 1446.9 1696.9 TRUE FALSE FALSE 1404.865679 1671.200587 1764.993466 1391.853382 961.7773131 1259.152451 1045.610901 1033.975196 1317.48564 1652.814293 0.849983985 1.011124235 1.067871614 0.842111172 0.581902829 0.761823307 0.632624551 0.625584617 0.797116558 1 10.69070892 -8.938156223 5.010510564 0.944834104 0.659094273 0.727515486 0.085003248 0.079354015 4.003863904 0.012333592 0.022600076 1.15E-09 8.938156223 -0.285739831 DGKKY(ph)AT(ph)LS(ph)LFNTY(ph)KGK ddPTM_HeLa_Romidepsin_16h_R1 1 DGKKYATLSLFNTYKGK 17 3 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3 E7EPN9 PRRC2C Protein PRRC2C 4 0 DGKKY(0.999)AT(0.999)LS(0.999)LFNT(0.43)Y(0.572)KGK 43.955 0.004227 0 727.43 860.53 565.05 844.47 890.19 735.89 674.19 641.03 771.82 894.92 TRUE FALSE FALSE 718.5638034 872.6445639 574.8844582 942.1115948 844.7602825 688.869004 731.4556818 659.5771917 702.7864861 871.6698494 0.82435317 1.001118215 0.659520871 1.080812415 0.969128717 0.790286603 0.839143034 0.756682352 0.806253063 1 9.767637998 -12.43594173 1.003091644 1.005281643 0.865883259 0 0.131696026 0.889824025 1.499827275 0.094069351 0.020197592 3.66E-13 12.43594173 -0.139398383 DGLAFNALIHR ddPTM_HeLa_Romidepsin_16h_R1 4 DGLAFNALIHR 11 0 O43707;C9JY79;M0QZQ3;Q9H254-2;Q9H254-4;Q9H254 O43707 ACTN4;SPTBN4 "Alpha-actinin-4;Spectrin beta chain, non-erythrocytic 4" 0 0 ;;; ;;; 182.28 4.62E-06 38694400 17408.4 13680.72 22937.7 15177.8 26559.2 24368.7 18075.9 15215.4 15703.3 13057.63 FALSE FALSE TRUE 17196.21972 13873.31754 23336.92105 16932.72865 25203.78492 22811.61872 19611.26649 15655.63359 14298.75752 12718.39089 1.352075107 1.090807607 1.834895723 1.331357779 1.981680319 1.793593145 1.541961296 1.230944522 1.124258378 1 13.63462853 -10.65194147 0.5358178 1.040328537 1.632693182 0.396985282 0.253043487 0.520776553 0.358579614 0.10867048 0.092491173 2.23E-11 10.65194147 0.592364646 DGLAPEKT(ph)SPDR ddPTM_HeLa_Romidepsin_16h_R1 1 DGLAPEKTSPDR 12 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 0 DGLAPEKT(0.978)S(0.022)PDR 154.1 0.0059787 7657700 3629.7 3438.1 3136.3 1548.2 3250.5 3573.5 2738.3 2786.6 3370.4 3676.7 TRUE FALSE FALSE 3585.45982 3486.501662 3190.885986 1727.210169 3084.614856 3345.164883 2970.891134 2867.225874 3068.942983 3581.178804 1.001195421 0.973562576 0.891015546 0.482302131 0.861340644 0.934096024 0.829584697 0.800637452 0.856964466 1 11.80621884 -9.607456616 4.366444556 0.998002053 0.788086056 0.299267583 0.120118766 0.151578039 5.395486549 0.017728937 0.025427162 2.47E-10 9.607456616 -0.209915997 DGLGFCALIHR ddPTM_HeLa_Romidepsin_16h_R1 1 DGLGFCALIHR 11 0 P12814-2;P12814;P12814-3;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V2X9 P12814-2 ACTN1 Alpha-actinin-1 0 0 108.7 0.0013485 0 3220.7 3029 4529.2 1018 4913 4166.5 3704.7 3376.4 3120.3 2471.4 FALSE FALSE TRUE 3181.44487 3071.642342 4608.028826 1135.70595 4662.271277 3900.274097 4019.377126 3474.090807 2841.212553 2407.192672 1.321641141 1.276026792 1.914275031 0.471796862 1.93680852 1.620258379 1.669736358 1.443212605 1.180301264 1 11.2331359 -13.03697593 0.083995212 4.38E-07 2.110095086 0.15027072 0.387199288 70.40615846 1.122010708 22.34036801 8.259536369 9.18E-14 13.03697593 2.110094648 DGLNDDDFEPYLS(ph)PQAR ddPTM_HeLa_Romidepsin_16h_R1 3 DGLNDDDFEPYLSPQAR 17 0 Q9Y5A9;S4R3J8 Q9Y5A9 YTHDF2 YTH domain-containing family protein 2 1 0 DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR;DGLNDDDFEPYLS(1)PQAR ;; 185.2 1.71E-09 60875800 5010.94 2917.95 5271.01 3412.26 4996.07 4764.05 4520.22 2817.88 2707.27 1932.09 TRUE FALSE FALSE 4949.864736 2959.028977 5362.749718 3806.801556 4741.101905 4459.64258 4904.167374 2899.410912 2465.124991 1881.894023 2.630256898 1.572367487 2.849655534 2.0228565 2.519324599 2.369762869 2.605974254 1.540687667 1.309917009 1 10.87796967 -12.39018115 0.936848334 0.939944611 2.305099294 0.513669473 0.426803871 0.33435227 0.486617476 0.329892368 0.070897236 4.07E-13 12.39018115 1.365154683 DGLNQTTIPVS(ph)PPSTTKPSR ddPTM_HeLa_Romidepsin_16h_R1 4 DGLNQTTIPVSPPSTTKPSR 20 1 X6RLN4;Q71RC2-2;Q71RC2-6;Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4 X6RLN4 LARP4 La-related protein 4 1 0 DGLNQTTIPVS(0.961)PPS(0.007)T(0.007)T(0.007)KPS(0.018)R;DGLNQTTIPVS(0.997)PPS(0.001)T(0.001)T(0.001)KPSR;DGLNQTTIPVS(0.993)PPS(0.002)T(0.002)T(0.002)KPSR;DGLNQTTIPVS(0.999)PPSTTKPSR ;;; 136.77 9.54E-05 584434000 5535.65 5276 5044.03 4263.16 5376.59 5474.89 4989.67 5057 5966.3 6145.69 TRUE FALSE FALSE 5468.179369 5350.275666 5131.819226 4756.086618 5102.202549 5125.062198 5413.492445 5203.316316 5432.659185 5986.024088 0.91349104 0.893794543 0.85730013 0.794531821 0.852352492 0.856171329 0.904355273 0.869244133 0.907557187 1 12.54738237 -11.0477044 0.640514256 0.992156476 0.85544914 0.450841147 0.037854923 0.235856596 0.218091677 0.013356382 0.008623984 8.96E-12 11.0477044 -0.136707336 DGLQNEK(ac)NIVSTPVK ddPTM_HeLa_Romidepsin_16h_R1 2 DGLQNEKNIVSTPVK 15 1 P35914-3;P35914-2;P35914 P35914-3 HMGCL "Hydroxymethylglutaryl-CoA lyase, mitochondrial" 0 1 ; DGLQNEK(1)NIVSTPVK;DGLQNEK(1)NIVSTPVK 320.48 9.14E-178 3553500 1409.78 1381.96 1313.17 1432.11 1594.15 1681.37 1490.36 1659.95 1339.15 1228.43 FALSE TRUE FALSE 1392.597059 1401.415269 1336.025173 1597.697296 1512.794577 1573.935883 1616.951141 1707.978034 1219.37307 1196.515212 1.163877438 1.171247349 1.116596898 1.335292089 1.264333761 1.315433242 1.35138369 1.42746036 1.019103692 1 10.22462302 -4 0.098155064 0.836036627 2.528112543 0.903427038 0.042781476 25.43355761 0.178568739 0.368661613 5.820662543 1.00E-04 4 1.692075915 DGMEYPFIGEGEPHVDGEPGDLR ddPTM_HeLa_Romidepsin_16h_R1 2 DGMEYPFIGEGEPHVDGEPGDLR 23 0 H7C2Y5;Q9UBS4 H7C2Y5 DNAJB11 DnaJ homolog subfamily B member 11 0 0 ; ; 98.3 0.00019869 9283900 4087.04 4115.78 3950.3 3208.92 4215.98 4372.59 3504.98 4456.02 4459.82 4342.9 FALSE FALSE TRUE 4037.225584 4173.722059 4019.053314 3579.950429 4000.822809 4093.195611 3802.692914 4584.947908 4060.922529 4230.070832 0.95441087 0.986679 0.950114897 0.846309807 0.945805157 0.967642334 0.898966723 1.083893885 0.960012891 1 12.04646611 -11.82710482 0.629997176 1.001390178 0.948233989 0.00904752 0.058637117 1.560509595 1.134725199 0.043054032 0.013087586 1.49E-12 11.82710482 -0.053156189 DGPEETDWWWAALHGQEGYVPR ddPTM_HeLa_Romidepsin_16h_R1 1 DGPEETDWWWAALHGQEGYVPR 22 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 0 0 81.017 0.00077519 2478800 911.97 803.14 633.52 690.03 643.92 805.57 528.57 576.36 832.56 909.02 FALSE FALSE TRUE 900.8545589 814.446626 644.5461499 769.8145153 611.0583596 754.0966769 573.4667226 593.0360673 758.0937484 885.4035294 1.017450833 0.919859249 0.727968806 0.869450471 0.69014674 0.851698296 0.647689673 0.669791849 0.856212702 1 9.790191314 -9.909129847 2.750257162 1.008146677 0.744986881 0.573855882 0.083459151 0.089876811 1.381630608 0.010971351 0.014699848 1.23E-10 9.909129847 -0.263159796 DGQDAIAQS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 3 DGQDAIAQSPEK 12 0 Q9NWH9;H0YL55;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 0 DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK;DGQDAIAQS(1)PEK ;; 164.7 0.00033835 183413000 19371.9 19780.7 21378.5 10220.3 16045.7 17353.9 14782.7 16693.6 21517.8 22043.4 TRUE FALSE FALSE 19135.78783 20059.17321 21750.58382 11402.01917 15226.82805 16245.0418 16038.34217 17176.60298 19593.19408 21470.70929 0.891250847 0.934257595 1.013035179 0.531049954 0.709190733 0.756614119 0.746987067 0.800001656 0.912554579 1 14.39008223 -9.280831575 24.98013686 0.950423894 0.713573461 0.724608654 0.074396049 341.923938 440449.7061 0.012074511 0.018461199 5.24E-10 9.280831575 -0.236850433 DGQDAIAQS(ph)PEKESK ddPTM_HeLa_Romidepsin_16h_R1 1 DGQDAIAQSPEKESK 15 1 Q9NWH9;H0YL55;H7BXE3 Q9NWH9 SLTM SAFB-like transcription modulator 1 0 DGQDAIAQS(1)PEKESK 174.68 3.83E-05 130230000 4079.9 4194.7 4214.6 2502.8 3748.7 3507.4 3030.3 2970.7 3905.4 4207.3 TRUE FALSE FALSE 4030.17261 4253.753097 4287.953345 2792.185512 3557.389851 3283.28846 3287.693606 3056.652518 3556.091243 4097.993739 0.983450163 1.038008686 1.046354294 0.681354265 0.868080841 0.801194113 0.802269065 0.745889992 0.867763952 1 12.00070207 -9.271377099 24.99987506 0.99984547 0.787106046 0.720884681 0.064188307 192.1578003 483402.0347 0.007099341 0.01092379 5.35E-10 9.271377099 -0.212739424 DGQSS(ph)PQPSPR ddPTM_HeLa_Romidepsin_16h_R1 2 DGQSSPQPSPR 11 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 DGQS(0.088)S(0.912)PQPSPR;DGQS(0.035)S(0.964)PQPSPR ; 154.1 0.0022343 35714000 6694.3 7850.4 8306.6 6915.3 6679.3 6467.1 7931.6 2649.2 7861.7 7531.3 TRUE FALSE FALSE 6612.707297 7960.918137 8451.172889 7714.879523 6338.430397 6053.873182 8605.309906 2725.850422 7158.529862 7335.63574 0.90144979 1.085239019 1.152070957 1.05169883 0.864060134 0.825269056 1.173083044 0.37159021 0.975856779 1 12.84070629 -7.249728934 24.8038147 0.977644954 0.371589804 0.733806277 0.11318549 666.3869673 1411441.879 0.015858169 0.340226041 5.63E-08 7.249728934 -0.606055151 DGQVINETS(ph)QHHDDLE ddPTM_HeLa_Romidepsin_16h_R1 3 DGQVINETSQHHDDLE 16 0 P08670 P08670 VIM Vimentin 1 0 DGQVINET(0.204)S(0.796)QHHDDLE;DGQVINET(0.098)S(0.902)QHHDDLE;DGQVINET(0.369)S(0.631)QHHDDLE ;; 120.74 0.0012106 600400000 33215.7 33074.1 31647.9 31042.4 33797.4 38964.8 30655.8 30505.9 34240 28396.8 TRUE FALSE FALSE 32810.85427 33539.71805 32198.71842 34631.66835 32072.59256 36475.07503 33259.70289 31388.54009 31177.48864 27659.04704 1.186261198 1.212612929 1.16412971 1.252091885 1.159569688 1.318739398 1.202489111 1.134838089 1.127207622 1 14.75546383 -12.05161733 0.514091684 0.967858551 1.215337448 0.386710465 0.062539242 0.510209137 0.209041167 0.061975521 0.012665413 8.88E-13 12.05161733 0.247478896 DGQVINETSQHHDDLE ddPTM_HeLa_Romidepsin_16h_R1 2 DGQVINETSQHHDDLE 16 0 P08670 P08670 VIM Vimentin 0 0 ; ; 120.32 0.0013543 36907000 10698.5 10622.4 9361.6 8684 11733.7 11565.3 9539.4 10260.4 12667 11414.2 FALSE FALSE TRUE 10568.10257 10771.94243 9524.534721 9688.084939 11134.8855 10826.31466 10349.6764 10557.26849 11534.03179 11117.65744 0.950569185 0.96890397 0.856703381 0.871414234 1.001549613 0.973794589 0.930922405 0.949594692 1.037451627 1 13.44056521 -11.50863338 0.778206154 0.996170532 0.936121101 0.32474438 0.044103608 0.679154854 0.849518825 0.020247856 0.009911636 3.10E-12 11.50863338 -0.06004943 DGQWFTDWDAVPHSR ddPTM_HeLa_Romidepsin_16h_R1 4 DGQWFTDWDAVPHSR 15 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 0 ;;; ;;; 147.53 0.000224 95184000 16339.7 16305.7 14826.2 14402.3 16514.1 17164.5 14196.9 16376.9 18495.8 16554.7 FALSE FALSE TRUE 16140.54545 16535.25207 15084.24379 16067.56169 15671.32385 16067.74385 15402.78433 16850.73976 16841.48932 16124.60651 1.000988486 1.025467013 0.935479808 0.996462251 0.971888762 0.996473547 0.955234742 1.045032619 1.044458934 1 13.97697633 DGRGPMT(ph)GS(ph)RSQGLWT(ph)QNR ddPTM_HeLa_Romidepsin_16h_R1 1 DGRGPMTGSRSQGLWTQNR 19 2 A0A075B7E4 A0A075B7E4 TAF15 3 0 DGRGPMT(0.88)GS(0.918)RS(0.203)QGLWT(0.999)QNR 59.182 0.0031299 0 0 0 0 0 152.09 66.625 0 0 0 127.65 TRUE FALSE FALSE 0 0 0 0 144.3282798 62.36787752 0 0 0 124.3336346 0 0 0 0 1.160814451 0.501617102 0 0 0 1 6.958072815 -12.35125 1.065565729 1.001652325 0.207650971 0 0.46695877 0.441571891 0.894328364 0.262232088 0.067880743 4.45E-13 12.35125 -0.794001354 DGS(ph)PEAPAS(ph)PEREEVALSEYK ddPTM_HeLa_Romidepsin_16h_R1 1 DGSPEAPASPEREEVALSEYK 21 1 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 2 0 DGS(0.994)PEAPAS(0.981)PEREEVALS(0.023)EY(0.001)K 66.447 0.015775 67043000 3854.7 4076 4752.4 2833.9 4421.8 4063.4 4063.9 4348.2 4322.9 4389.9 TRUE FALSE FALSE 3807.717434 4133.382035 4835.113528 3161.568852 4196.139046 3803.761854 4409.087565 4474.008307 3936.248997 4275.849765 0.890517124 0.966680838 1.130795934 0.739401295 0.981357923 0.889592026 1.031160543 1.046343663 0.920577011 1 12.06199545 -7.64976878 7.543472732 0.945975488 1.042074604 0.148541509 0.094008177 0.322863137 19.92863204 0.012501267 0.047303074 2.24E-08 7.64976878 0.096099116 SRSESETSTMAAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SRSESETSTMAAKK 14 2 A0A087WVF1;Q96B23-2;Q96B23 A0A087WVF1 C18orf25 Uncharacterized protein C18orf25 0 1 ; SRSESETSTMAAK(1)K;SRSESETSTMAAK(1)K 131.08 4.53E-05 1426700 129.37 0 0 582.15 883.18 722.91 829.08 750.88 285.29 289.08 FALSE TRUE FALSE 127.7931887 0 0 649.4609221 838.108029 676.7183841 899.5020345 772.6055281 259.7729479 281.5696599 0.453859939 0 0 2.306572811 2.976556598 2.403378206 3.194598576 2.743923221 0.922588563 1 8.137348077 -9.124179632 4.629560008 0.620438076 2.8062839 0.899517001 0.376984221 0.060497925 2.030138006 0.065241121 0.11033788 7.51E-10 9.124179632 2.185845825 up DGSPEAPAS(ph)PEREEVALSEYK ddPTM_HeLa_Romidepsin_16h_R1 2 DGSPEAPASPEREEVALSEYK 21 1 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 DGS(0.001)PEAPAS(0.8)PEREEVALS(0.181)EY(0.017)K;DGS(0.001)PEAPAS(0.958)PEREEVALS(0.033)EY(0.008)K ; 59.983 0.0072927 70161000 4806.4 4640 4788.6 4416.2 7485 7233.3 6705.7 7321.6 5166.8 4282.9 TRUE FALSE FALSE 4747.817748 4705.322042 4871.943574 4926.821823 7103.01252 6771.115474 7275.281991 7533.438944 4704.668468 4171.629641 1.138120628 1.127933793 1.167875385 1.181030496 1.702694901 1.623134376 1.743990387 1.805874345 1.127777121 1 12.02639536 -8.805340944 3.075119112 1.081272605 1.725092586 0.953083473 0.064562461 0.042594274 0.823668388 0.011865347 0.023628772 1.57E-09 8.805340944 0.643819981 DGT(ph)SPEEEIEIER ddPTM_HeLa_Romidepsin_16h_R1 1 DGTSPEEEIEIER 13 0 Q9H501 Q9H501 ESF1 ESF1 homolog 1 0 DGT(0.916)S(0.084)PEEEIEIER 187.74 2.72E-10 10315000 3338.3 2715.6 2696.6 1012 3476.8 3334.1 3066.5 3317.4 3153 2966.4 TRUE FALSE FALSE 3297.611516 2753.830288 2743.533192 1129.012202 3299.365922 3121.06177 3326.968433 3413.383735 2870.987783 2889.3325 1.141305653 0.95310259 0.949538757 0.390751913 1.141912854 1.080201662 1.151466103 1.181374499 0.993650881 1 11.49652052 -10.23571526 22.8769767 1.066727682 0.971496771 0.015853681 0.216964467 796.9543482 708747.3032 0.03736675 0.045750792 5.81E-11 10.23571526 -0.095230911 DGTAPPPQS(ph)PGSPGTGQDEEWS(ph)DEESPRK ddPTM_HeLa_Romidepsin_16h_R1 1 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 2 0 DGT(0.063)APPPQS(0.812)PGS(0.12)PGT(0.027)GQDEEWS(0.936)DEES(0.042)PRK 52.342 0.0049501 6088000 450.28 476.28 586.24 456.45 689.02 829.63 636.48 596.91 697.39 491.15 TRUE FALSE FALSE 444.7918142 482.9850823 596.4432613 509.2268967 653.8567383 776.6193205 690.5425953 614.1806491 635.0136918 478.3898522 0.929768498 1.009605618 1.246772394 1.064460072 1.366786388 1.62340258 1.443472499 1.28384966 1.327397914 1 8.902042977 -9.066207312 1.070007503 0.969713827 1.458480487 0.436696849 0.15934133 0.171487264 0.387129393 0.019419434 0.045680355 8.59E-10 9.066207312 0.48876666 DGTAPPPQSPGSPGT(ph)GQDEEWSDEESPRK ddPTM_HeLa_Romidepsin_16h_R1 1 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 DGTAPPPQS(0.045)PGS(0.191)PGT(0.657)GQDEEWS(0.105)DEES(0.002)PRK 62.582 0.00047611 14726000 2264.1 1973.1 1996.1 2091.6 2224.6 2293.3 1772.7 1899.5 2227 2184.6 TRUE FALSE FALSE 2236.504278 2000.877354 2030.841283 2333.440633 2111.070361 2146.765531 1923.273094 1954.459036 2027.811542 2127.843777 1.051066015 0.940330947 0.954412775 1.096622157 0.992117177 1.008892455 0.903860102 0.918516226 0.95298892 1 11.05517652 -7.779777669 7.191660544 1.015821248 0.910872747 0.319168099 0.047063125 0.090365506 20.93509031 0.006177467 0.019791693 1.66E-08 7.779777669 -0.1049485 DGTAPPPQSPGSPGTGQDEEWS(ph)DEESPRK ddPTM_HeLa_Romidepsin_16h_R1 3 DGTAPPPQSPGSPGTGQDEEWSDEESPRK 29 1 A0A0C4DGG1;Q9UKS6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 DGTAPPPQS(0.006)PGS(0.003)PGT(0.171)GQDEEWS(0.81)DEES(0.011)PRK;DGTAPPPQSPGS(0.001)PGT(0.037)GQDEEWS(0.962)DEESPRK;DGTAPPPQS(0.002)PGS(0.006)PGT(0.026)GQDEEWS(0.957)DEES(0.009)PRK ;; 110.89 5.92E-10 212196000 8639.4 9987.1 7904.8 9749.9 7820.4 8121.5 7335.8 8483.3 9190.1 9457.5 TRUE FALSE FALSE 8534.09967 10127.69866 8042.379728 10877.22931 7421.295806 7602.562361 7958.902669 8728.750901 8368.114439 9211.792787 0.926432006 1.099427537 0.873052609 1.180793963 0.805629911 0.825307574 0.863990632 0.947562663 0.90841323 1 13.16926624 DGTGVVEFVR ddPTM_HeLa_Romidepsin_16h_R1 2 DGTGVVEFVR 10 0 J3KTL2;Q07955;J3KSR8;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 0 ; ; 195.57 2.32E-07 19743100 6109.3 6258.4 6175.9 4755.6 5180.4 5320.2 5177.9 5968.3 6313.5 6183.6 FALSE FALSE TRUE 6034.837502 6346.505919 6283.388949 5305.464848 4916.024857 4980.25639 5617.710697 6140.983344 5748.804748 6022.949181 1.001973837 1.053720649 1.043241236 0.880874915 0.816215563 0.826880029 0.932717599 1.019597403 0.954483356 1 12.55625437 -9.253614917 24.86653681 1.00863944 0.889148312 0.489928252 0.058704153 359.3039573 1141885.089 0.008888756 0.014561981 5.58E-10 9.253614917 -0.119491129 DGVLTLANNVT(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 3 DGVLTLANNVTPAK 14 0 E7EVA0;P27816;P27816-6 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DGVLTLANNVT(1)PAK;DGVLT(0.001)LANNVT(0.999)PAK;DGVLT(0.001)LANNVT(0.999)PAK ;; 171.46 9.28E-05 38229600 10009 10260.4 11212 5326.1 11172.8 13187.7 11841.6 11221 9762.1 9601.9 TRUE FALSE FALSE 9887.006458 10404.84618 11407.14016 5941.928742 10602.61032 12345.04853 12847.42521 11545.66193 8888.953326 9352.441254 1.057157825 1.112527296 1.219696531 0.635334516 1.13367302 1.319981403 1.373697504 1.234507827 0.950442038 1 13.19112728 -8.398214596 4.53005331 1.021860558 1.313257558 0.468208717 0.147117336 0.151402786 4.905891804 0.019914949 0.04577241 4.00E-09 8.398214596 0.291397001 DGVLTLANNVT(ph)PAKDVPPLSETEATPVPIKDMEIAQTQK ddPTM_HeLa_Romidepsin_16h_R1 2 DGVLTLANNVTPAKDVPPLSETEATPVPIKDMEIAQTQK 39 2 E7EVA0;P27816;P27816-6 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DGVLT(0.012)LANNVT(0.778)PAKDVPPLS(0.126)ET(0.042)EAT(0.042)PVPIKDMEIAQTQK;DGVLT(0.006)LANNVT(0.486)PAKDVPPLS(0.167)ET(0.167)EAT(0.167)PVPIKDMEIAQT(0.007)QK ; 62.171 0.00021093 32372000 8541.2 8102.7 8707.8 9038.5 8465.4 9467.5 9358.7 8547 9467.6 9035.7 TRUE FALSE FALSE 8437.096569 8216.770023 8859.355606 10083.5739 8033.379049 8862.557305 10153.62774 8794.29396 8620.794144 8800.951211 0.95865735 0.933622949 1.006636146 1.145736825 0.912785318 1.006999936 1.153696629 0.999243576 0.979529819 1 13.10344374 -9.51931428 24.86087028 0.976118098 1.044062085 0.214778204 0.067576681 174.7050518 1218508.205 0.010302661 0.014750766 3.02E-10 9.51931428 0.067943987 DGVVEITGK(ac)HEER ddPTM_HeLa_Romidepsin_16h_R1 2 DGVVEITGKHEER 13 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 1 ; DGVVEITGK(1)HEER;DGVVEITGK(1)HEER 131.32 0.00059058 2689400 2030.8 1680.61 2137.42 1509.55 2660.5 2547.4 2216.7 2538.5 2235.1 1922.08 FALSE TRUE FALSE 2006.047828 1704.269672 2174.620898 1684.091274 2524.724757 2384.629361 2404.986443 2611.947492 2035.187058 1872.144085 1.071524273 0.910330399 1.161567059 0.89955217 1.348573958 1.273742433 1.284616105 1.395163713 1.087088902 1 10.87047576 -8.749413396 24.99171662 1.026535067 1.318903442 0.775185464 0.080104875 72.58466854 150840.4054 0.010331872 0.020536475 1.78E-09 8.749413396 0.292368375 DGWS(ph)LDRDR ddPTM_HeLa_Romidepsin_16h_R1 4 DGWSLDRDR 9 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 DGWS(1)LDRDR;DGWS(1)LDRDR;DGWS(1)LDRDR;DGWS(1)LDRDR ;;; 176.48 0.0012205 40288500 18563.3 14769.2 17541.3 13553.2 21004.6 20810.8 18050.9 20857 18452.6 18549.3 TRUE FALSE FALSE 18337.04336 14977.12119 17846.59897 15120.28475 19932.65688 19481.05704 19584.143 21460.46439 16802.15324 18067.38651 1.014925061 0.828958919 0.987779774 0.836882786 1.103239634 1.078244329 1.083949966 1.187801256 0.929971428 1 14.14110021 -8.574343524 24.99995512 0.97972744 1.10961904 0.54086249 0.074217131 74.76601918 36318.646 0.010892155 0.021784312 2.66E-09 8.574343524 0.129891599 DGWSLWYSEYR ddPTM_HeLa_Romidepsin_16h_R1 1 DGWSLWYSEYR 11 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 0 201.61 4.40E-12 26499000 1471.3 1197.7 1687.6 624.49 1687.2 1284.6 1090.4 1151.7 1414.5 991.24 FALSE FALSE TRUE 1453.36723 1214.561252 1716.97197 696.6964721 1601.095888 1202.518206 1183.018549 1185.022622 1287.983577 965.4874419 1.505319662 1.257977265 1.778347284 0.72160076 1.658329066 1.245503726 1.225307029 1.227382741 1.334024164 1 9.915113684 -12.50943432 1.266166364 1.000417353 1.34536241 0 0.291008068 0.588132104 1.690899812 0.173995469 0.042221862 3.09E-13 12.50943432 0.344945057 DGYGGSRDS(ph)YSSSR ddPTM_HeLa_Romidepsin_16h_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 0 DGYGGSRDS(1)YSSSR;DGYGGS(0.001)RDS(0.999)YSSSR ; 176.56 3.13E-06 42454000 4114.4 4484.4 3880.8 3654.3 3703.6 3997.4 3364.3 3624.7 4579.6 4332.2 TRUE FALSE FALSE 4064.25211 4547.531501 3948.343696 4076.82736 3514.591472 3741.979041 3650.063558 3729.574976 4169.989106 4219.648819 0.963173071 1.077703784 0.935704336 0.966153236 0.832910894 0.886798689 0.865015956 0.883859092 0.988231316 1 12.04290722 -8.869625637 5.085396689 0.986143723 0.86872143 0.72266445 0.036939343 0.087308181 3.58104664 0.005399448 0.009976967 1.35E-09 8.869625637 -0.117422293 DHANYEEDENGDIT(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 2 DHANYEEDENGDITPIK 17 0 H3BSB3;H3BNT4;Q99547 H3BSB3 MPHOSPH6 M-phase phosphoprotein 6 1 0 DHANYEEDENGDIT(1)PIK;DHANYEEDENGDIT(1)PIK ; 218.66 6.92E-27 50115500 9419.1 8493 8248.6 6301.2 8353.6 8450.3 6065.2 6102.2 9617.7 8576.9 TRUE FALSE FALSE 9304.296386 8612.564677 8392.163423 7029.774392 7927.28462 7910.353102 6580.377937 6278.757529 8757.468824 8354.070902 1.113744005 1.030942253 1.004559756 0.8414789 0.948912777 0.946886039 0.787685191 0.751580589 1.048287587 1 13.02826367 -7.89378059 0.517695389 1.053706453 0.660695485 0.740372168 0.057181261 1.029829487 0.276113832 0.015017575 0.216607573 1.28E-08 7.89378059 -0.393010968 DHAPSIPT(ph)SPFGDSLESSTELR ddPTM_HeLa_Romidepsin_16h_R1 1 DHAPSIPTSPFGDSLESSTELR 22 0 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;J3QL92 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 DHAPS(0.04)IPT(0.48)S(0.48)PFGDSLESSTELR 63.606 0.006825 2687000 1754.9 1901.3 1641.1 1248.3 2031.3 2582.4 1695.9 2081.3 2403.7 1943 TRUE FALSE FALSE 1733.510604 1928.066551 1669.662657 1392.634319 1927.635181 2417.392974 1839.949704 2141.519132 2188.707052 1892.52058 0.91597979 1.018782343 0.882242801 0.73586218 1.018554409 1.277340389 0.972221768 1.131569799 1.156503699 1 10.88609327 -8.518608112 24.99947459 0.941074799 1.117626049 0.289595633 0.122052832 139.5765623 817053.0615 0.014671947 0.029926428 3.03E-09 8.518608112 0.17655125 DHAPSIPTS(ph)PFGDSLESSTELRR ddPTM_HeLa_Romidepsin_16h_R1 1 DHAPSIPTSPFGDSLESSTELRR 23 1 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;J3QL92 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 DHAPS(0.001)IPT(0.456)S(0.544)PFGDSLESSTELRR 72.359 0.00036342 4163700 1080.3 1258.5 1221.7 1628.5 1329.3 1107 1262.5 1315 1618.9 1265 TRUE FALSE FALSE 1067.132888 1276.217196 1242.963176 1816.794832 1261.460861 1036.266273 1369.736718 1353.04745 1474.101529 1232.135118 0.866084306 1.035776984 1.008788045 1.474509416 1.023800753 0.841032982 1.111677363 1.098132365 1.196379771 1 10.26694476 -9.897636695 2.780450923 0.937575945 1.097701302 0 0.172600519 0.353246198 5.546009196 0.026360673 0.035435889 1.27E-10 9.897636695 0.160125357 DHFGLEGDEEST(ph)MLEDSVSPKK ddPTM_HeLa_Romidepsin_16h_R1 2 DHFGLEGDEESTMLEDSVSPKK 22 1 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 DHFGLEGDEES(0.13)T(0.67)MLEDS(0.13)VS(0.071)PKK;DHFGLEGDEES(0.182)T(0.721)MLEDS(0.049)VS(0.049)PKK ; 71.376 0.001297 29572000 4368.7 3749.1 3553.7 3807.4 4696.3 3787.2 3461.8 3593.5 4894.3 4194 TRUE FALSE FALSE 4315.452604 3801.879928 3615.550658 4247.629502 4456.630287 3545.210143 3755.845206 3697.472253 4456.54155 4085.039275 1.056404189 0.930683813 0.885071211 1.039801386 1.090963877 0.867852156 0.919414711 0.905125264 1.090942155 1 11.99613423 -7.056025879 0.431032071 1.019814072 0.767907361 0.260979054 0.070740192 6.00884716 0.663426828 0.017466491 0.803093545 8.79E-08 7.056025879 -0.251906711 DHFGLEGDEESTMLEDS(ph)VSPK ddPTM_HeLa_Romidepsin_16h_R1 3 DHFGLEGDEESTMLEDSVSPK 21 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 DHFGLEGDEESTMLEDS(0.647)VS(0.353)PK;DHFGLEGDEESTMLEDS(0.74)VS(0.26)PK;DHFGLEGDEES(0.005)T(0.127)MLEDS(0.706)VS(0.162)PK ;; 140.88 2.48E-05 198507000 14797.6 14455.1 13096.3 11415.8 14758.9 14909.3 11877.1 12660.7 15828.7 14460.9 TRUE FALSE FALSE 14617.24116 14658.59928 13324.23561 12735.74851 14005.69826 13956.64385 12885.94058 13027.01738 14412.94143 14085.20373 1.037772789 1.04070907 0.945973935 0.904193418 0.994355391 0.9908727 0.914856528 0.924872485 1.023268225 1 13.78189281 -9.751792243 24.9976231 1.020050935 0.946802324 0.63481534 0.029452274 113.6537489 294498.332 0.005076435 0.007126611 1.77E-10 9.751792243 -0.073248612 DHFGLEGDEESTMLEDSVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DHFGLEGDEESTMLEDSVSPK 21 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 DHFGLEGDEESTMLEDS(0.378)VS(0.622)PK 135.68 5.88E-05 30847000 2507.1 2990.1 2606.9 2367.8 3038 2645.7 1857.7 2742.5 2693.3 2697.4 TRUE FALSE FALSE 2476.542501 3032.194706 2652.272001 2641.576177 2882.959524 2476.648309 2015.492992 2821.849911 2452.404503 2627.321159 0.942611257 1.154101278 1.009496685 1.005425685 1.097300006 0.942651529 0.76712852 1.07404072 0.933423953 1 11.35937685 -8.006811202 24.90635658 0.99953609 0.904160983 0.141858126 0.09424997 400.518966 1464589.443 0.01241811 0.035346656 9.84E-09 8.006811202 -0.095375107 DHFGLEGDEESTMLEDSVS(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 1 DHFGLEGDEESTMLEDSVSPKK 22 1 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 DHFGLEGDEES(0.096)T(0.335)MLEDS(0.12)VS(0.449)PKK 76.799 0.0005481 19586000 2539.3 2552.5 2140.7 2426 2857.6 2415.1 1871.8 2159.9 2952.6 2797.1 TRUE FALSE FALSE 2508.350035 2588.434162 2177.957986 2706.505535 2711.766009 2260.782904 2030.790645 2222.393299 2688.512061 2724.430939 0.920687693 0.950082502 0.799417579 0.993420496 0.995351349 0.829818393 0.745399935 0.815727522 0.986816007 1 11.41173921 -4.392297148 0.224465524 0.984910384 8.75E-15 0.463199261 0.067231115 28.11431355 0.396310531 0.050237761 9.830032883 4.05E-05 4.392297148 -0.984910384 DHFLGPQESFPEENASS(ph)PFTQAR ddPTM_HeLa_Romidepsin_16h_R1 2 DHFLGPQESFPEENASSPFTQAR 23 0 A0A0U1RRL2;B1AM27;O14795;O14795-2;A0A1B0GUS7 A0A0U1RRL2 UNC13B Protein unc-13 homolog B 1 0 DHFLGPQESFPEENAS(0.229)S(0.711)PFT(0.06)QAR;DHFLGPQESFPEENAS(0.186)S(0.495)PFT(0.319)QAR ; 192.93 3.75E-20 19365100 2301.2 2225 2141.76 2527.7 3070.2 3251.2 2646 3313.1 2453.1 2513.3 TRUE FALSE FALSE 2273.152089 2256.323608 2179.036434 2819.964567 2913.516238 3043.458813 2870.751174 3408.959321 2233.688592 2448.004104 0.928573643 0.921699275 0.89012777 1.151944379 1.190159867 1.243240895 1.172690507 1.392546408 0.912452961 1 11.25739026 -9.043098461 2.831805297 0.956315692 1.243773546 0.843274232 0.06489959 0.082193692 1.31436438 0.00982548 0.017897812 9.06E-10 9.043098461 0.287457854 DHGDWDEASR ddPTM_HeLa_Romidepsin_16h_R1 1 DHGDWDEASR 10 0 A0A3B3IRL2;O75629 A0A3B3IRL2 CREG1 Protein CREG1 0 0 90.149 0.018018 1681900 855.37 654.16 964.82 728.03 1073.6 959.55 820.08 694.19 903.06 770.92 FALSE FALSE TRUE 844.9444214 663.3692817 981.6122874 812.2082541 1018.810186 898.2378518 889.7375747 714.2752924 822.2880518 750.8913873 1.125255178 0.88344239 1.30726268 1.08165877 1.356801001 1.196228732 1.184908483 0.951236496 1.095082546 1 9.552460434 -9.750632183 24.99978695 1.047623 1.184267493 0.270760928 0.121397523 238.012113 550580.8568 0.018612295 0.026169901 1.78E-10 9.750632183 0.136644492 DHGFEVAST(ph)SPEDESPGSNPEPDATPFQEGLR ddPTM_HeLa_Romidepsin_16h_R1 1 DHGFEVASTSPEDESPGSNPEPDATPFQEGLR 32 0 Q5JRU2;F8VVS7;P55211-2;P55211-4;P55211 Q5JRU2 CASP9 Caspase;Caspase-9;Caspase-9 subunit p35;Caspase-9 subunit p10 1 0 DHGFEVAS(0.093)T(0.392)S(0.392)PEDES(0.083)PGS(0.04)NPEPDATPFQEGLR 83.026 2.96E-08 19718000 1702.6 1622.2 1579.7 1875.3 2212.6 2488.7 1825 2366.1 2182.1 1939 TRUE FALSE FALSE 1681.848056 1645.037374 1607.194016 2092.13101 2099.682766 2329.680102 1980.015454 2434.55937 1986.927511 1888.6245 0.890514793 0.871024057 0.850986533 1.107753822 1.111752371 1.233532712 1.048390219 1.289064803 1.052050056 1 10.88312018 -9.097669171 4.316564187 0.933576702 1.161446549 0.653774058 0.082663558 0.105284728 3.387985808 0.011817036 0.020174024 7.99E-10 9.097669171 0.227869847 DHLMWVLLQFISGS(ph)IQK ddPTM_HeLa_Romidepsin_16h_R1 1 DHLMWVLLQFISGSIQK 17 0 Q5JWT2;Q9ULK4-6;Q9ULK4-2;Q9ULK4-4;Q9ULK4-5;Q9ULK4-3;Q9ULK4 Q5JWT2 MED23 Mediator of RNA polymerase II transcription subunit 23 1 0 DHLMWVLLQFIS(0.012)GS(0.988)IQK 73.666 0.026659 7531700 6325.6 7330.4 6505.9 6221.1 7861.7 8106.9 6347.9 7406.2 7121.8 6752.7 TRUE FALSE FALSE 6248.501154 7433.597564 6619.13246 6940.412853 7460.488113 7588.895254 6887.090468 7620.486712 6484.808371 6577.263881 0.950015275 1.130196036 1.006365653 1.055212772 1.134284445 1.153807327 1.047105695 1.158610457 0.985943166 1 12.68327184 -9.621106781 0.86633251 0.977788171 1.118418192 0.496489147 0.051741338 0.308238935 0.462945817 0.010647201 0.018736574 2.39E-10 9.621106781 0.140630021 DHLPPPS(ph)SASPSR ddPTM_HeLa_Romidepsin_16h_R1 1 DHLPPPSSASPSR 13 0 Q2YD98-2;Q2YD98 Q2YD98-2 UVSSA UV-stimulated scaffold protein A 1 0 DHLPPPS(0.457)S(0.457)AS(0.074)PS(0.013)R 100.18 0.0052946 3588600 3250.9 3184.8 2907.9 2275.9 4089.7 4184.7 3450 3802.2 3794.4 3508 TRUE FALSE FALSE 3211.27678 3229.635698 2958.51078 2539.050266 3880.987348 3917.311176 3743.042914 3912.210658 3455.019361 3416.861654 0.939832251 0.945205286 0.86585618 0.743094255 1.135833915 1.146464672 1.095462238 1.144971923 1.011167472 1 11.73845612 DHLPPPSS(ph)ASPSR ddPTM_HeLa_Romidepsin_16h_R1 1 DHLPPPSSASPSR 13 0 Q2YD98-2;Q2YD98 Q2YD98-2 UVSSA UV-stimulated scaffold protein A 1 0 DHLPPPS(0.073)S(0.732)AS(0.114)PS(0.081)R 110.22 0.0028361 3128400 2718 2592.6 2725.4 2448.4 3547.7 3634 3316.8 3535.5 3586.9 3124.4 TRUE FALSE FALSE 2684.871971 2629.098691 2772.834444 2731.495528 3366.647631 3401.799128 3598.528909 3637.794114 3266.07868 3043.227638 0.88224487 0.863917854 0.911149205 0.8975653 1.106275321 1.11782605 1.182471158 1.195373645 1.073228516 1 11.57138654 -8.639549839 3.698668953 0.930657505 1.160815427 0.744514909 0.06138442 0.080474302 2.098999178 0.008546362 0.017846955 2.29E-09 8.639549839 0.230157923 DHQYQFLEDAVR ddPTM_HeLa_Romidepsin_16h_R1 2 DHQYQFLEDAVR 12 0 Q13263-2;Q13263;M0R2I3;M0R3C0 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 0 0 ; ; 138.89 0.0010259 15683100 4791.5 6673.8 7583 1049.87 4661.5 8573.4 7176.5 7371.3 7412.3 5666.5 FALSE FALSE TRUE 4733.099355 6767.753932 7714.978934 1171.260909 4423.606261 8025.587409 7786.071731 7584.576936 6749.325324 5519.283513 0.857556845 1.226201538 1.397822546 0.212212492 0.801481977 1.454099502 1.410703348 1.374195929 1.222862589 1 12.43026528 -8.255260712 24.48444704 0.926642603 1.412770014 0.310984402 0.306418424 315.6241846 1250729.458 0.041333664 0.102457387 5.56E-09 8.255260712 0.48612741 DHS(ph)PT(ph)PSVFNSDEER ddPTM_HeLa_Romidepsin_16h_R1 1 DHSPTPSVFNSDEER 15 0 Q6UN15-5;Q6UN15;Q6UN15-3 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 0 DHS(0.999)PT(0.991)PS(0.004)VFNS(0.006)DEER 134.93 0.0014871 9395700 1811.8 1669.1 1225.6 490.27 1359.9 1807.1 1735 1742.3 1820.5 1723.5 TRUE FALSE FALSE 1789.717085 1692.597634 1246.931054 546.9573242 1290.499229 1691.632142 1882.370857 1792.710702 1657.66992 1678.723222 1.066118025 1.00826486 0.742785373 0.325817453 0.768738534 1.007689725 1.121311025 1.067901295 0.987458742 1 10.71314867 -9.853891712 7.051159128 1.031289673 0.833374028 0.142956173 0.210383468 0.337527692 22.05389043 0.037423189 0.049340033 1.40E-10 9.853891712 -0.197915645 DHS(ph)PTPSVFNS(ph)DEERYR ddPTM_HeLa_Romidepsin_16h_R1 3 DHSPTPSVFNSDEERYR 17 1 Q6UN15-5;Q6UN15;Q6UN15-3 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 2 0 DHS(0.877)PT(0.123)PSVFNS(1)DEERYR;DHS(0.968)PT(0.032)PSVFNS(1)DEERYR;DHS(0.621)PT(0.375)PS(0.004)VFNS(1)DEERYR ;; 150.01 1.25E-07 46564000 5863.77 5543.8 4262.25 3025.46 4753.4 6330.1 5262.75 5390.38 6592.3 5419.56 TRUE FALSE FALSE 5792.300116 5621.845762 4336.432673 3375.27792 4510.816261 5925.627039 5709.767854 5546.342141 6002.668177 5278.75905 1.09728443 1.064993819 0.82148714 0.639407461 0.854522098 1.122541678 1.081649645 1.050690529 1.137136232 1 12.3659831 -9.794722407 24.96461254 1.048652562 0.927682504 0.204696157 0.137611015 293.2144598 219930.1826 0.024531991 0.032242429 1.60E-10 9.794722407 -0.120970058 DHS(ph)PTPSVFNSDEER ddPTM_HeLa_Romidepsin_16h_R1 4 DHSPTPSVFNSDEER 15 0 Q6UN15-5;Q6UN15;Q6UN15-3 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 0 DHS(0.927)PT(0.073)PSVFNSDEER;DHS(0.998)PT(0.001)PS(0.001)VFNSDEER;DHS(1)PTPSVFNSDEER;DHS(0.999)PT(0.001)PSVFNSDEER ;;; 187.78 1.24E-12 270703200 9369.6 8876.4 6286.45 2917.5 6538.52 8615.3 6854.56 7442.83 9696.8 8840.9 TRUE FALSE FALSE 9255.399711 9001.362192 6395.863025 3254.835077 6204.834926 8064.810135 7436.786155 7658.176543 8829.493922 8611.212144 1.074808001 1.045307216 0.742736669 0.377976413 0.720553021 0.936547608 0.863616647 0.889326197 1.025348554 1 13.07200062 -9.761271006 24.99882557 1.037061656 0.749589216 0.475160552 0.144731407 3.160864361 469247.5089 0.024900774 0.033955205 1.73E-10 9.761271006 -0.28747244 DHS(ph)PTPSVFNSDEERYR ddPTM_HeLa_Romidepsin_16h_R1 3 DHSPTPSVFNSDEERYR 17 1 Q6UN15-5;Q6UN15;Q6UN15-3 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 0 DHS(0.981)PT(0.019)PSVFNSDEERYR;DHS(0.956)PT(0.043)PS(0.001)VFNSDEERYR;DHS(0.892)PT(0.107)PS(0.001)VFNSDEERYR ;; 86.497 0.0038512 21191700 3164.83 2977.23 2468.07 2581.73 2506.02 3329.28 2431.22 2843.78 3256.25 3239.32 TRUE FALSE FALSE 3126.255835 3019.143522 2511.025723 2880.24177 2378.128448 3116.549753 2637.727766 2926.060288 2965.002845 3155.161999 0.990838453 0.956890176 0.795846845 0.912866525 0.753726258 0.987762198 0.836003909 0.927388289 0.939730779 1 11.62349837 -9.949011556 6.823525209 0.994614917 0.869648095 0.369453618 0.064998714 0.121210018 12.6325864 0.009046961 0.011892048 1.12E-10 9.949011556 -0.124966822 DHS(ph)VSLSPSLFK ddPTM_HeLa_Romidepsin_16h_R1 1 DHSVSLSPSLFK 12 0 P47989 P47989 XDH Xanthine dehydrogenase/oxidase;Xanthine dehydrogenase;Xanthine oxidase 1 0 DHS(0.63)VS(0.313)LS(0.028)PS(0.028)LFK 95.099 0.021607 4725800 1541.8 1493.4 1001 1163.3 1038.8 1330.3 919 1207.5 1536.3 1236.5 TRUE FALSE FALSE 1523.007949 1514.424124 1018.421985 1297.806219 985.7861597 1245.298123 997.0598371 1242.437107 1398.88948 1204.375552 1.264562326 1.257435127 0.845601676 1.077576025 0.818503961 1.033978248 0.827864561 1.03160273 1.161506042 1 10.23406961 -9.756977003 25 1.138360681 0.93924111 0.504910055 0.11053413 95.13093196 532958.6997 0.020580704 0.028538505 1.75E-10 9.756977003 -0.199119571 DHTLEDEDVIQIVK ddPTM_HeLa_Romidepsin_16h_R1 1 DHTLEDEDVIQIVK 14 0 Q9Y295 Q9Y295 DRG1 Developmentally-regulated GTP-binding protein 1 0 0 136.27 0.00064594 1389000 2199.6 2004.8 1829.2 1590.8 1951.6 2105.9 1829.1 1764.2 2412 2316.2 FALSE FALSE TRUE 2172.790429 2033.023627 1861.036459 1774.735781 1852.00257 1971.339786 1984.463708 1815.244344 2196.264679 2256.02479 0.963105742 0.901153053 0.824918444 0.786665017 0.820914104 0.873811225 0.879628503 0.804620743 0.97351088 1 11.13956721 -10.11806115 1.974990873 0.9849058 0.833135415 0.847305569 0.028008367 0.090736123 0.682223549 0.00555251 0.006949349 7.62E-11 10.11806115 -0.151770386 DHYEATAMHR ddPTM_HeLa_Romidepsin_16h_R1 1 DHYEATAMHR 10 0 B1AJY5;B1AJY7;O75832;B1AJY6;O75832-2 B1AJY5 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 0 66.92 0.028338 2095100 754.8 741.39 945.5 791.6 1119 889.99 980.31 659.8 846.78 790.89 FALSE FALSE TRUE 745.6002073 751.8273079 961.9560309 883.1285166 1061.893254 833.1225113 1063.577507 678.890272 771.041876 770.3425638 0.967881359 0.975964906 1.248737998 1.146410127 1.378468884 1.081496143 1.380655253 0.881283605 1.000907794 1 9.589356331 -9.768672442 24.97790354 0.983743962 1.197190296 0.33886102 0.13631225 117.6318622 406217.2579 0.019213552 0.025543329 1.70E-10 9.768672442 0.213446334 DIAAHIK ddPTM_HeLa_Romidepsin_16h_R1 1 DIAAHIK 7 0 F8VXL2;F8VRV5;P63167 F8VXL2 DYNLL1 "Dynein light chain 1, cytoplasmic" 0 0 58.167 0.029478 1030300 1734.8 1515 1742.5 1880.6 2132.8 2349.2 2108 1550.8 1877.6 1699.9 FALSE FALSE TRUE 1713.65559 1536.32821 1772.827482 2098.04382 2023.955257 2199.093702 2287.053467 1595.669951 1709.662753 1655.736353 1.034980954 0.927882152 1.070718462 1.267136411 1.222389817 1.328166588 1.381290846 0.963722243 1.032569437 1 10.69325725 -9.368955042 4.025957803 1.009972603 1.245571509 0.516786543 0.106944473 0.131945191 3.757982768 0.015392625 0.023964913 4.28E-10 9.368955042 0.235598906 DIAWTEDSKR ddPTM_HeLa_Romidepsin_16h_R1 2 DIAWTEDSKR 10 1 D6RD66;O75083 D6RD66 WDR1 WD repeat-containing protein 1 0 0 ; ; 136.52 0.003584 21771500 3044.22 2703.8 2733.31 2286.53 2724.35 2913.03 2281.78 2513.25 3132.44 2999.13 FALSE FALSE TRUE 3007.115876 2741.864167 2780.882114 2550.909357 2585.316254 2726.896784 2475.594336 2585.966923 2852.266721 2921.21217 1.02940687 0.938604938 0.951961704 0.873236591 0.885014885 0.933481249 0.847454478 0.885237625 0.976398342 1 11.51235143 -9.786686803 1.42799947 1.013807739 0.885722226 0.735771229 0.028860471 0.112639936 0.463194369 0.004743561 0.006927456 1.63E-10 9.786686803 -0.128085513 DIDEVSS(ph)LLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 1 0 DIDEVS(0.102)S(0.898)LLR 99.343 0.0030521 0 1773.2 1893.1 1802.7 1384.5 1617.1 1782.1 1493.5 1720.3 2143 1892.8 TRUE FALSE FALSE 1751.587556 1919.751111 1834.075237 1544.582404 1534.573353 1668.229561 1620.357853 1770.074166 1951.324713 1843.624783 0.950078114 1.04129166 0.994820234 0.837796507 0.832367501 0.904863927 0.878897847 0.960105431 1.058417489 1 10.84832935 -9.27261756 24.70883817 0.982978034 0.881012384 0.626741478 0.046547822 332.5988597 735192.8364 0.006535338 0.010040694 5.34E-10 9.27261756 -0.10196565 DIDEVSSLLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIDEVSSLLR 10 0 P50990-2;P50990;P50990-3;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 0 199.46 2.68E-11 23670000 2330.7 2328.1 2492.6 1806.7 2490.6 2208.5 2098.5 2060.7 2447 2157.2 FALSE FALSE TRUE 2302.292532 2360.875053 2535.982657 2015.599155 2363.495388 2067.383978 2276.746538 2120.323103 2228.134191 2101.155633 1.095726797 1.123607893 1.206946605 0.959281227 1.124854985 0.983927104 1.083568728 1.009122347 1.060432724 1 11.03696731 -7.240795432 21.90951709 1.059470994 1.009122097 0.042123415 0.071634798 2572.237171 2729685.847 0.010058881 0.442681028 5.74E-08 7.240795432 -0.050348896 DIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_HeLa_Romidepsin_16h_R1 2 DIDHETVVEEQIIGENSPPDYSEYMTGK 28 0 P25490;A0A494C032;H0YJU4;H0YJV7 P25490 YY1 Transcriptional repressor protein YY1 1 0 DIDHETVVEEQIIGENS(0.906)PPDY(0.022)S(0.009)EY(0.041)MT(0.023)GK;DIDHETVVEEQIIGENS(0.993)PPDY(0.003)S(0.001)EY(0.001)MT(0.002)GK ; 112.34 8.62E-10 28395000 3034.4 2892.1 3262.7 1852.47 3055.5 3026.6 2598.5 2670.2 3922.2 3352.9 TRUE FALSE FALSE 2997.415566 2932.81506 3319.485925 2066.661298 2899.566433 2833.210028 2819.216525 2747.458024 3571.388609 3265.791175 0.917822177 0.89804121 1.016441575 0.632821019 0.887860331 0.8675417 0.863256826 0.841284049 1.093575314 1 11.67321683 DIDIHEVR ddPTM_HeLa_Romidepsin_16h_R1 3 DIDIHEVR 8 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQ74 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ;; ;; 153.08 0.0028864 110329000 33008 33280 31029 29486.9 25755.1 29610.3 29584.9 28800.2 38632 33479 FALSE FALSE TRUE 32605.6858 33748.51671 31569.04673 32896.31412 24440.72114 27718.29739 32097.84067 29633.48835 35176.65716 32609.21075 0.999891903 1.034938164 0.96810214 1.008804364 0.749503609 0.85001436 0.984318232 0.908745954 1.07873378 1 14.9929919 -8.858656617 24.99999998 1.000764378 0.879343663 0.552862045 0.06163056 8.186971188 2097.259216 0.008324086 0.015088694 1.38E-09 8.858656617 -0.121420715 DIDILNSAGK(ac)MDK ddPTM_HeLa_Romidepsin_16h_R1 1 DIDILNSAGKMDK 13 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 1 DIDILNSAGK(1)MDK 84.892 0.026968 684980 185.48 233.33 198.31 341.1 206.2 158.99 289.46 194.42 303.43 262.84 FALSE TRUE FALSE 183.2192984 236.6148259 201.7615024 380.5395869 195.6768446 148.8310521 314.0467252 200.045236 276.2904608 256.0113789 0.715668574 0.924235582 0.788095839 1.486416692 0.764328701 0.581345457 1.226690495 0.781391971 1.079211643 1 8.000064125 DIDISS(ph)PEFK ddPTM_HeLa_Romidepsin_16h_R1 3 DIDISSPEFK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 DIDIS(0.066)S(0.934)PEFK;DIDIS(0.041)S(0.959)PEFK;DIDIS(0.413)S(0.587)PEFK ;; 184.44 1.63E-05 2996420000 20961.8 22911.4 19121.6 17752.7 23122.2 23390.9 19648.4 20056.6 22170 20699.1 TRUE FALSE FALSE 20706.30952 23233.94729 19454.40343 19805.3507 21942.18785 21896.29698 21317.33461 20636.90608 20187.05967 20161.3344 1.027030707 1.152401266 0.9649363 0.982343247 1.088330138 1.086053956 1.057337485 1.023588304 1.001275971 1 14.29930351 -10.66129563 3.782029955 1.01051578 1.050122529 0.121393412 0.051219839 0.350599279 10.51359283 0.00949915 0.00985246 2.18E-11 10.66129563 0.03960675 DIDNNLITS(ph)TPR ddPTM_HeLa_Romidepsin_16h_R1 1 DIDNNLITSTPR 12 0 Q05D32;H0YMH7;Q05D32-2;H0YNU2;H0YNW9 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 DIDNNLIT(0.004)S(0.498)T(0.498)PR 214.61 3.49E-21 48011000 4710 4447.3 4803.5 4806.5 6244.4 6808.5 5291.3 5675.8 4981.6 4144.3 TRUE FALSE FALSE 4652.592708 4509.909206 4887.102903 5362.250145 5925.724967 6373.458823 5740.74289 5840.020318 4536.033219 4036.630489 1.152593164 1.117245985 1.210688696 1.328397573 1.467987963 1.578905684 1.422162099 1.446756233 1.123717723 1 11.97893581 -9.326739722 0.920091029 1.06340265 1.497941718 0.900471309 0.056888171 0.128251684 0.215347304 0.012732646 0.02681832 4.71E-10 9.326739722 0.434539068 DIDNNLITST(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DIDNNLITSTPR 12 0 Q05D32;H0YMH7;Q05D32-2;H0YNU2;H0YNW9 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 DIDNNLIT(0.001)S(0.004)T(0.996)PR 157.33 0.0022656 8666100 2866.3 2667 2673 2844.4 3652.2 3239.1 2852.3 3301.1 2812.4 2844.6 TRUE FALSE FALSE 2831.364433 2704.546096 2719.522444 3173.282911 3465.814606 3032.131964 3094.574291 3396.61212 2560.8519 2770.696882 1.021896134 0.976124856 0.98153012 1.145301362 1.250881909 1.094357157 1.116893844 1.225905346 0.924262743 1 11.43603317 -9.210060538 5.794150315 1.005532663 1.165800204 0.756019623 0.051909251 0.078124207 6.158868089 0.006647169 0.011037077 6.17E-10 9.210060538 0.160267541 DIDPQNDLTFLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIDPQNDLTFLR 12 0 H3BQI1;B1AKR6;Q9NP97;Q8TF09 H3BQI1 DYNLRB2;DYNLRB1 Dynein light chain roadblock-type 1;Dynein light chain roadblock-type 2 0 0 185.3 3.84E-06 3200600 1338.1 1181.8 1244.5 1110.5 1105.8 1297.7 1128.8 1247.3 1261 1227.7 FALSE FALSE TRUE 1321.790723 1198.437411 1266.16 1238.901235 1049.3669 1214.781158 1224.680244 1283.388658 1148.213002 1195.804177 1.105357171 1.002202062 1.058835573 1.03604023 0.877540754 1.015869639 1.024147822 1.073243163 0.960201531 1 10.22376544 -8.977721543 24.99994027 1.047317847 0.995375179 0 0.060465816 365.1367355 409739.3457 0.008935212 0.016195523 1.05E-09 8.977721543 -0.051942667 DIDVLNSSGK(ac)MDK ddPTM_HeLa_Romidepsin_16h_R1 2 DIDVLNSSGKMDK 13 1 A0A0A0MRP6;B7ZLQ5;P28370-2;P28370 A0A0A0MRP6 SMARCA1 Probable global transcription activator SNF2L1 0 1 ; DIDVLNSSGK(1)MDK;DIDVLNSSGK(1)MDK 105.03 0.0062158 1263370 560.7 427.88 457.34 352.98 366.64 312.29 294 354.377 472.46 517.76 FALSE TRUE FALSE 553.8659727 433.9037059 465.2998109 393.7932084 347.9289927 292.3356769 318.9723527 364.6303394 430.2019943 504.3085206 1.098268124 0.860393367 0.922649116 0.780857734 0.689912977 0.57967626 0.632494474 0.723030297 0.853053194 1 8.97816279 -9.343401762 1.045242727 1.043434548 0.638902908 0.706640479 0.084519779 0.11792964 0.255600565 0.011847786 0.023472393 4.54E-10 9.343401762 -0.40453164 DIEEHLQR ddPTM_HeLa_Romidepsin_16h_R1 3 DIEEHLQR 8 0 Q9UNE7;H3BTA3;Q9UNE7-2 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 0 0 ;; ;; 122.19 0.00041625 3962600 7126.9 7162.5 7210.1 8180.2 10309.4 10007.9 8790.4 9603.5 8721.8 7835.3 FALSE FALSE TRUE 7040.034602 7263.333863 7335.588766 9126.033213 9783.272848 9368.427489 9537.056357 9881.362121 7941.700364 7631.737776 0.922468094 0.951727388 0.961195075 1.195800155 1.281919418 1.227561502 1.249657239 1.294772228 1.040614942 1 12.89779589 -9.18781336 3.434141891 0.960502759 1.258339224 0.93660228 0.035926782 0.038315479 0.884413283 0.005224485 0.008872351 6.49E-10 9.18781336 0.297836465 DIEIS(ph)T(ph)EEEKDTGDLKDSSLLK ddPTM_HeLa_Romidepsin_16h_R1 1 DIEISTEEEKDTGDLKDSSLLK 22 2 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 2 0 DIEIS(0.986)T(0.986)EEEKDT(0.009)GDLKDS(0.009)S(0.009)LLK 55.206 0.02407 4097100 1320.4 1385.6 1236.3 1423.9 1422.1 1490.7 1159.7 1679.7 1521.7 1542.3 TRUE FALSE FALSE 1304.306457 1405.106513 1257.817283 1588.538018 1349.52493 1395.449081 1258.204889 1728.299469 1385.595341 1502.230824 0.868246368 0.935346613 0.83729961 1.057452685 0.898347251 0.928917886 0.83755763 1.150488621 0.922358481 1 10.55289079 -9.26764687 24.81581174 0.929130003 0.960173054 0.079909591 0.090974666 1739.752141 6955039.071 0.014176078 0.022015698 5.40E-10 9.26764687 0.031043051 DIEIST(ph)EEEKDTGDLK ddPTM_HeLa_Romidepsin_16h_R1 1 DIEISTEEEKDTGDLK 16 1 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 0 DIEIS(0.443)T(0.547)EEEKDT(0.01)GDLK 73.688 0.018989 10378000 2180.8 2083.6 2653.7 1354.9 2173.8 2073.9 2076.6 2357.3 2510.3 2402.5 TRUE FALSE FALSE 2154.219571 2112.932975 2699.886535 1511.559913 2062.862874 1941.384483 2252.986352 2425.504756 2285.772481 2340.082704 0.920574118 0.902930897 1.153756887 0.645942945 0.881534175 0.829622167 0.962780652 1.036503861 0.976791323 1 11.1923438 -9.278993898 24.9985476 0.969166542 0.874615988 0.20381143 0.114094351 1241.490667 1767943.09 0.017230987 0.026354996 5.26E-10 9.278993898 -0.094550554 DIEISTEEEKDT(ph)GDLK ddPTM_HeLa_Romidepsin_16h_R1 1 DIEISTEEEKDTGDLK 16 1 Q4G0J3;Q4G0J3-3 Q4G0J3 LARP7 La-related protein 7 1 0 DIEIS(0.004)T(0.005)EEEKDT(0.991)GDLK 85.45 0.0096468 11298000 2826.7 2960.3 3653.4 2237.9 2778.1 3407.3 2645.5 3443.6 3415.4 3089.9 TRUE FALSE FALSE 2792.247093 3001.975181 3716.985894 2496.656528 2636.32319 3189.584527 2870.208704 3543.235133 3109.91807 3009.623953 0.927772751 0.997458562 1.235033331 0.829557635 0.875964317 1.059795036 0.953676854 1.177301613 1.033324468 1 11.55536752 -7.257388286 23.71520688 0.975869592 1.177301779 0.207968892 0.106185135 212.4967159 1243853.563 0.013910836 0.140017383 5.53E-08 7.257388286 0.201432188 DIEVLS(ph)EDTDYEEDEVTK ddPTM_HeLa_Romidepsin_16h_R1 2 DIEVLSEDTDYEEDEVTK 18 0 H7C5R6;Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 1 0 DIEVLS(0.97)EDT(0.026)DY(0.004)EEDEVTK;DIEVLS(0.996)EDT(0.004)DYEEDEVTK ; 154.34 4.40E-11 2260300 2654.5 2480.9 1973.74 1886.55 2081.72 2525.9 2955 2330.54 2596.1 2962.9 TRUE FALSE FALSE 2622.145933 2515.826175 2008.092117 2104.681787 1975.48206 2364.503142 3205.997626 2397.970498 2363.898314 2885.923431 0.908598581 0.87175777 0.695823075 0.729292318 0.68452338 0.819322896 1.110908762 0.830919654 0.819113317 1 11.49481731 -10.63256562 1.313672928 0.972263093 0.818038873 0.050450791 0.124170331 0.432623734 1.529226265 0.02713831 0.027341489 2.33E-11 10.63256562 -0.15422422 DIEVLS(ph)EDTDYEEDEVTKK ddPTM_HeLa_Romidepsin_16h_R1 2 DIEVLSEDTDYEEDEVTKK 19 1 H7C5R6;Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 1 0 DIEVLS(0.497)EDT(0.497)DY(0.006)EEDEVTKK;DIEVLS(0.647)EDT(0.274)DY(0.079)EEDEVTKK ; 91.337 0.0010707 21496000 4591.7 4356.8 4382.6 4014.7 4490.9 4824.4 5626.7 5032.6 5648.8 4650.3 TRUE FALSE FALSE 4535.734594 4418.135145 4458.877315 4478.898504 4261.712615 4516.13641 6104.631758 5178.210341 5143.55718 4529.484536 1.001379861 0.975416763 0.984411643 0.988831835 0.940882474 0.997053059 1.347754189 1.143222877 1.135572302 1 12.14513116 -7.777099302 24.99795436 0.992395823 1.245488493 0.676450815 0.066779217 52.42405614 83684.9053 0.005940802 0.017910787 1.67E-08 7.777099302 0.25309267 DIHMTPS(ph)T(ph)DFY(ph)KK ddPTM_HeLa_Romidepsin_16h_R1 1 DIHMTPSTDFYKK 13 1 O95486 O95486 SEC24A Protein transport protein Sec24A 3 0 DIHMT(0.038)PS(0.995)T(0.983)DFY(0.983)KK 43.544 0.027459 4258200 888.71 863.2 961.97 904.66 1076.9 936.47 994.28 807.01 870.7 944.99 TRUE FALSE FALSE 877.8780607 875.3521523 978.7126843 1009.261046 1021.941775 876.6325893 1078.734118 830.3595611 792.8224113 920.4390236 0.953760149 0.951015906 1.063310724 1.096499627 1.110276453 0.952407022 1.171977818 0.902134242 0.861352454 1 9.84617834 -9.754077708 24.98924644 0.97551826 1.055499036 0.255927803 0.081954645 181.2618652 615292.8482 0.010522685 0.014711172 1.76E-10 9.754077708 0.079980777 DIIDYES(ph)DVEPETKR ddPTM_HeLa_Romidepsin_16h_R1 1 DIIDYESDVEPETKR 15 1 F5GYN7;Q5FWF4-2;Q5FWF4-3;Q5FWF4 F5GYN7 ZRANB3 DNA annealing helicase and endonuclease ZRANB3;DNA annealing helicase ZRANB3;Endonuclease ZRANB3 1 0 DIIDYES(1)DVEPETKR 99.371 0.0024175 3070600 3554.4 2872.3 3891.9 3541.7 3906.8 3724.5 2733.2 3815.8 4730 4203.5 TRUE FALSE FALSE 3511.077606 2912.736315 3959.636887 3951.208018 3707.421418 3486.51647 2965.35794 3926.204153 4306.936953 4094.292464 0.857554177 0.711413838 0.967111393 0.965052705 0.90550967 0.851555306 0.724266272 0.9589457 1.05193681 1 11.99939845 -12.11949213 0.929747956 0.998472921 0.866000005 0.322673787 0.088607811 0.630391346 1.001663341 0.054077329 0.016616579 7.59E-13 12.11949213 -0.132472916 DIIFAIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 DIIFAIKK 8 1 P11177-3;P11177-2;P11177 P11177-3 PDHB "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial" 0 1 DIIFAIK(1)K 114.93 0.001866 244330 319.97 228.29 457.12 496.73 788.01 451.23 571.21 145.7 150.07 0 FALSE TRUE FALSE 316.0700826 231.5038726 465.0759818 554.1642598 747.7949092 422.3978593 619.7285631 149.9155996 136.6473633 0 0 DIIHDPGR ddPTM_HeLa_Romidepsin_16h_R1 4 DIIHDPGR 8 0 E9PKZ0;E9PKU4;P62917;G3V1A1 E9PKZ0 RPL8 60S ribosomal protein L8 0 0 ;;; ;;; 99.802 0.014575 153325000 26854.2 31361.2 27196 29920.9 30645.8 33600.4 27143.6 30859.4 31008.9 30086.1 FALSE FALSE TRUE 26526.89068 31802.7038 27669.33497 33380.49524 29081.83047 31453.44288 29449.17671 31752.26805 28235.38632 29304.45878 0.905216878 1.085251362 0.944202218 1.139092705 0.99240292 1.073333007 1.004938427 1.083530267 0.963518437 1 14.83883257 -10.25828217 24.89816687 0.955241303 1.043162384 0.346099425 0.056496858 223.129365 1759626.89 0.009565876 0.011451656 5.52E-11 10.25828217 0.087921081 DIIHFFR ddPTM_HeLa_Romidepsin_16h_R1 2 DIIHFFR 7 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 0 ; ; 132.96 0.0065133 8739400 8616.5 7997.3 11910.9 11216 12401.3 12275.7 10906 8339 8685 6827.1 FALSE FALSE TRUE 8511.478784 8109.886199 12118.20422 12512.84669 11768.41539 11491.32239 11832.35537 8580.275808 7908.191848 6649.730958 1.279973406 1.2195811 1.822360077 1.881707211 1.769758124 1.728088318 1.779373548 1.290319242 1.189249896 1 12.69908026 -9.82728583 5.285954541 1.138765736 1.725933762 0.718497623 0.165234329 0.081303568 4.343533929 0.029263544 0.038965048 1.49E-10 9.82728583 0.587168026 DIIRQPS(ph)EEEIIK ddPTM_HeLa_Romidepsin_16h_R1 2 DIIRQPSEEEIIK 13 1 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 0 DIIRQPS(1)EEEIIK;DIIRQPS(1)EEEIIK ; 132.65 0.012862 31201400 3431.33 2891.22 2381.43 4975.7 2814.94 4031.6 4428.7 4235.5 3967.3 2670.7 TRUE FALSE FALSE 3389.50763 2931.922671 2422.87779 5551.013845 2671.283108 3773.993771 4804.873667 4358.04751 3612.454752 2601.314829 1.30299785 1.127092591 0.931405058 2.133926191 1.026897274 1.45080239 1.847094252 1.675324902 1.388703402 1 11.3450253 -4 0.153753677 0.949390185 4.03691738 0.22556179 0.331429309 54.0517047 0.532966537 0.607090326 37.60202153 1.00E-04 4 3.087527195 DIIS(ph)IAEDEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIISIAEDEDLR 12 0 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 1 0 DIIS(1)IAEDEDLR 116.9 0.0012249 0 152.61 281.94 390.92 275 277.1 357.32 194.14 231.08 357.41 323.14 TRUE FALSE FALSE 150.7499306 285.9091587 397.7237986 306.7967939 262.958553 334.4884052 210.6302468 237.7659352 325.4423545 314.7447762 0.478959278 0.908384127 1.263639077 0.97474785 0.83546598 1.062729012 0.669209667 0.755424564 1.033988104 1 8.298038624 -6.005585908 20.90929472 0.824127183 0.888727246 0 0.224242982 0 0 0.035089898 0 9.87E-07 6.005585908 0.064600063 DIISDTSGDFR ddPTM_HeLa_Romidepsin_16h_R1 2 DIISDTSGDFR 11 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33;H0YKS4;H0YNA0;H0YN52 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 ; ; 200.56 5.01E-12 40063000 7761.8 8853.2 8988.3 6200.1 9412.8 11500.9 7311.2 9034.4 8416.1 8806.7 FALSE FALSE TRUE 7667.196196 8977.835582 9144.737591 6916.984734 8932.429692 10766.02961 7932.213146 9295.79611 7663.342937 8577.900664 0.893831311 1.046623869 1.066081078 0.806372678 1.041330512 1.255089098 0.924726627 1.083691275 0.893382103 1 13.06640889 -8.534768471 24.99724703 0.956132088 1.084305623 0.26710549 0.103480237 226.2455385 475663.2298 0.014477781 0.0289725 2.92E-09 8.534768471 0.128173535 DIISDTSGDFRK ddPTM_HeLa_Romidepsin_16h_R1 3 DIISDTSGDFRK 12 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33;H0YKS4;H0YNA0;H0YN52 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 ;; ;; 117.95 0.0052647 95469600 7709.1 8546.4 7677.8 5527.3 8535.4 9459.2 6785.5 7715.7 7571.3 7862.9 FALSE FALSE TRUE 7615.138524 8666.716444 7811.428888 6166.392433 8099.806688 8854.787648 7361.860201 7938.941606 6894.103965 7658.620724 0.99432245 1.131628887 1.019952439 0.805157045 1.057606452 1.156185685 0.96125144 1.036602006 0.90017566 1 12.90286888 DIISIAEDEDLR ddPTM_HeLa_Romidepsin_16h_R1 4 DIISIAEDEDLR 12 0 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 0 ;;; ;;; 229.82 9.13E-29 78495000 11273.4 10977.7 10769.5 7488.6 9957.6 11649.4 10324.1 10467.3 12113.2 10722.7 FALSE FALSE TRUE 11135.99546 11132.24435 10956.93863 8354.467167 9449.426515 10905.04094 11201.0288 10770.15481 11029.76505 10444.12271 1.066245177 1.065886016 1.049100909 0.799920434 0.904760197 1.044131828 1.072471964 1.031216801 1.056073867 1 13.35040369 DIKEES(ph)DEEEEDDEESGR ddPTM_HeLa_Romidepsin_16h_R1 3 DIKEESDEEEEDDEESGR 18 1 Q96EV2;H7BXM6;A8MTF7;H7C0H2;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 0 DIKEES(0.999)DEEEEDDEES(0.001)GR;DIKEES(1)DEEEEDDEESGR;DIKEES(1)DEEEEDDEESGR ;; 106.47 0.00057872 127538300 4403.7 4724.9 4185.1 3883.62 4366.5 4194.1 3583.88 4114.3 4337.9 4099.7 TRUE FALSE FALSE 4350.026011 4791.417266 4257.93991 4332.662417 4143.661211 3926.110546 3888.294678 4233.340779 3949.90736 3993.189203 1.089361357 1.199897381 1.066300567 1.085013055 1.037682163 0.983201733 0.973731642 1.060140295 0.989161084 1 11.96332572 -8.485974345 5.507649745 1.061068851 1.003185241 0.192448024 0.058391416 0.302785334 24.44322754 0.009248907 0.020470958 3.27E-09 8.485974345 -0.05788361 DIKEES(ph)DEEEEDDEESGRLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIKEESDEEEEDDEESGRLR 20 2 Q96EV2;H7BXM6;A8MTF7;H7C0H2;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 0 DIKEES(0.999)DEEEEDDEES(0.001)GRLR 70.335 0.0082335 24028000 1573.7 1338.4 1258.9 2340.6 1458.3 1034 1324.1 1360.7 1554.1 1471.7 TRUE FALSE FALSE 1554.519139 1357.24203 1280.810626 2611.231185 1383.877509 967.9307371 1436.569021 1400.069708 1415.097404 1433.465022 1.084448602 0.946826054 0.893506718 1.821621836 0.965407239 0.675238476 1.002165382 0.976703084 0.98718656 1 10.48529099 -8.529166439 24.99972557 1.08266597 0.883760877 0.137614147 0.261224445 271.9112983 1081111.686 0.037243108 0.074642411 2.96E-09 8.529166439 -0.198905093 DIKFDDSDT(ph)EQIAEEGDDNLAK ddPTM_HeLa_Romidepsin_16h_R1 1 DIKFDDSDTEQIAEEGDDNLAK 22 1 E9PDH4 E9PDH4 PIKFYVE 1 0 DIKFDDS(0.024)DT(0.976)EQIAEEGDDNLAK 65.598 0.0034315 5971000 1316.1 1415 1406.7 1411.4 1977.7 1982.9 1609.4 2417.3 1471.7 1299.7 TRUE FALSE FALSE 1300.058867 1434.920407 1431.183023 1574.592709 1876.770589 1856.19909 1746.102396 2487.240762 1340.067466 1265.933607 1.026956596 1.133487886 1.130535611 1.243819345 1.482518972 1.46626891 1.379300136 1.964748189 1.058560622 1 10.30598603 -4.000000005 0.276479947 0.972871045 7.573398488 0.866457698 0.102731174 10.61851707 0.135118338 0.043005224 34.16360102 1.00E-04 4.000000005 6.600527444 DILETHLR ddPTM_HeLa_Romidepsin_16h_R1 1 DILETHLR 8 0 P78527-2;P78527 P78527-2 PRKDC DNA-dependent protein kinase catalytic subunit 0 0 101.54 0.0014295 0 1546.8 1466.8 2368.5 1218.9 2064.9 1919.6 1526.5 1533 1593.3 1419.4 FALSE FALSE TRUE 1527.947007 1487.449649 2409.722749 1359.834953 1959.520448 1796.943755 1656.160872 1577.354936 1450.791258 1382.523783 1.105186779 1.075894438 1.742988278 0.983588832 1.417350263 1.299756125 1.197925773 1.140924269 1.049378879 1 10.43308858 -9.961693258 24.99940175 1.051821993 1.294379346 0.282040515 0.187451998 148.5552308 96948.55149 0.027973032 0.036763731 1.09E-10 9.961693258 0.242557353 DILLRPELEELR ddPTM_HeLa_Romidepsin_16h_R1 2 DILLRPELEELR 12 1 P00387-2;P00387;P00387-3 P00387-2 CYB5R3 NADH-cytochrome b5 reductase 3;NADH-cytochrome b5 reductase 3 membrane-bound form;NADH-cytochrome b5 reductase 3 soluble form 0 0 ; ; 140.45 0.0022313 7618300 2252.41 2342 2833.24 1848.14 2344.37 3033.4 2337.2 2995.3 2642.97 2643.99 FALSE FALSE TRUE 2224.956761 2374.970737 2882.551354 2061.830643 2224.728051 2839.57553 2535.72171 3081.96428 2406.576144 2575.298759 0.863960639 0.922211735 1.119307554 0.800618039 0.86387183 1.10261985 0.984632055 1.196740483 0.934484256 1 11.33052409 -6.602906853 0.900207018 0.936182055 1.758054969 0.394459511 0.094144021 4.850483391 1.272245672 0.015072163 5.211870459 2.50E-07 6.602906853 0.821872914 DINESTPLAY(ph)ALY(ph)CGHTACVK ddPTM_HeLa_Romidepsin_16h_R1 1 DINESTPLAYALYCGHTACVK 21 0 D6RBD3;Q3KP44-2;Q3KP44 D6RBD3 ANKRD55 Ankyrin repeat domain-containing protein 55 2 0 DINES(0.144)T(0.144)PLAY(0.711)ALY(0.989)CGHT(0.012)ACVK 52.045 0.01203 15177000 2155 1864.5 1470.9 1211.3 2022.4 1941 1764.9 1959.9 2063.2 1794.4 TRUE FALSE FALSE 2128.734031 1890.74848 1496.500397 1351.356205 1919.189381 1816.976364 1914.810562 2016.606614 1878.662225 1747.781229 1.217963665 1.081799283 0.85622867 0.773183842 1.098071858 1.039590272 1.095566499 1.153809516 1.074884083 1 10.7713089 -9.978293094 24.93142052 1.105398582 0.99974134 0.123231789 0.118663968 391.4359529 449581.9418 0.0225036 0.02957428 1.05E-10 9.978293094 -0.105657242 DINTFVGT(ph)PVEK ddPTM_HeLa_Romidepsin_16h_R1 2 DINTFVGTPVEK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 DINT(0.08)FVGT(0.92)PVEK;DINT(0.002)FVGT(0.998)PVEK ; 168.93 0.00038334 93226000 13650.7 12412 15832.6 5786.2 8847 11634.5 10732.5 10529.7 14052 13587 TRUE FALSE FALSE 13484.32002 12586.73646 16108.15976 6455.227669 8395.504577 10891.093 11644.11828 10834.36026 12795.15393 13234.00778 1.018914318 0.951090302 1.217179257 0.48777572 0.634388669 0.822962566 0.87986334 0.818675675 0.96683893 1 13.69196241 -9.267723055 24.99825293 1.018099013 0.737122916 0.595441668 0.124177896 289.0695766 1150000.146 0.019070028 0.029569609 5.40E-10 9.267723055 -0.280976097 DIPGLTDTTVPR ddPTM_HeLa_Romidepsin_16h_R1 2 DIPGLTDTTVPR 12 0 A2A3R5;P62753 A2A3R5 RPS6 40S ribosomal protein S6 0 0 ; ; 171.33 0.0012798 3439500 1824.83 1456.85 1194.07 1120.24 1704.14 1287.95 1242.82 1546.55 1710.13 1744.83 FALSE FALSE TRUE 1802.58827 1477.359573 1214.852287 1249.76742 1617.171377 1205.654152 1348.3851 1591.296984 1557.17169 1699.499065 1.060658583 0.869291195 0.71482963 0.735373997 0.951557674 0.709417367 0.793401495 0.936332957 0.916253337 1 10.73089385 -10.12682307 4.261643559 1.028330373 0.80428158 0.457910037 0.087203989 0.107333351 3.241068561 0.013085608 0.016172791 7.47E-11 10.12682307 -0.224048793 DIPYHNR ddPTM_HeLa_Romidepsin_16h_R1 1 DIPYHNR 7 0 Q14432;Q13370-2;Q13370 Q14432 PDE3A;PDE3B "cGMP-inhibited 3,5-cyclic phosphodiesterase A;cGMP-inhibited 3,5-cyclic phosphodiesterase B" 0 0 108.24 0.01419 1537000 1740.9 2012 1763.9 2188.7 1426 1443.5 1039.3 929.58 2143.8 1853.7 FALSE FALSE TRUE 1719.681241 2040.324989 1794.59994 2441.767792 1353.225899 1351.265009 1127.578116 956.4759307 1952.053159 1805.540607 0.952446727 1.130035504 0.993940503 1.352374897 0.749485165 0.748399124 0.624509973 0.529744901 1.081146085 1 10.81821515 -8.540462641 24.97221937 1.015978631 0.652529624 0.717845422 0.126588966 106.8520289 151748.1929 0.018388929 0.036783614 2.88E-09 8.540462641 -0.363449007 DIQT(ph)ALNNAYGKTLR ddPTM_HeLa_Romidepsin_16h_R1 1 DIQTALNNAYGKTLR 15 1 A0A087X1S6;O95397;Q96JA3-2;Q96JA3 A0A087X1S6 PLEKHA8;PLEKHA8P1 Putative protein PLEKHA9;Pleckstrin homology domain-containing family A member 8 1 0 DIQT(1)ALNNAYGKTLR 72.315 0.025246 9378400 955.38 907.71 722.25 891.21 1148.8 964.46 991.7 1097.4 1271.3 971.08 TRUE FALSE FALSE 943.7354611 920.4887652 734.8204583 994.2558935 1090.172449 902.8341187 1075.934973 1129.151538 1157.591744 945.8512016 0.997763136 0.973185596 0.776888011 1.0511758 1.152583459 0.954520243 1.137530905 1.193794051 1.223862424 1 9.885469431 -7.055675777 0.752645602 0.986436147 1.392158349 0.177088407 0.116092281 2.79627493 0.913599869 0.014499053 1.024467147 8.80E-08 7.055675777 0.405722202 DIS(ph)GPSPSKK ddPTM_HeLa_Romidepsin_16h_R1 1 DISGPSPSKK 10 1 S4R3D6;Q96GX9-3;Q96GX9 S4R3D6 APIP Methylthioribulose-1-phosphate dehydratase 1 0 DIS(0.754)GPS(0.133)PS(0.112)KK 117.25 0.020867 96144000 3757.7 4133.2 4144.6 3100.4 3760.7 3650.6 3412.5 1851.6 4395.9 3670.5 TRUE FALSE FALSE 3711.899707 4191.387298 4216.735024 3458.882836 3568.777446 3417.338442 3702.357665 1905.173125 4002.719694 3575.139881 1.038253 1.172370156 1.179460151 0.967481819 0.998220368 0.955861464 1.035584002 0.532894708 1.119598065 1 11.80378397 -7.261151149 24.77776816 1.031481369 0.532894559 0.795145917 0.078413196 6.978273418 599548.4956 0.010718374 0.083981741 5.48E-08 7.261151149 -0.49858681 DIS(ph)LDSELHDLR ddPTM_HeLa_Romidepsin_16h_R1 2 DISLDSELHDLR 12 0 H0YJ97;Q15643-2;Q15643 H0YJ97 TRIP11 Thyroid receptor-interacting protein 11 1 0 DIS(0.999)LDS(0.001)ELHDLR;DIS(0.999)LDS(0.001)ELHDLR ; 111.81 0.0042209 7584600 5013.8 4850.6 5114.4 4505.6 4381.2 4178.9 3162 2647.6 6055.1 5113.6 TRUE FALSE FALSE 4952.689877 4918.886874 5203.413987 5026.558671 4157.611015 3911.881777 3430.580201 2724.204129 5513.516691 4980.747935 0.994366698 0.987579966 1.044705344 1.009197562 0.834736283 0.785400472 0.688768082 0.546946797 1.106965613 1 12.28214669 -7.915424857 0.922170027 1.002785313 0.512122147 0.922829513 0.047219687 0.138804731 0.156644732 0.005534834 0.054199806 1.21E-08 7.915424857 -0.490663166 DISEGGES(ph)PVVQS(ph)DEEEVQVDTALATSHTDR ddPTM_HeLa_Romidepsin_16h_R1 1 DISEGGESPVVQSDEEEVQVDTALATSHTDR 31 0 D6RJC6;A0A087WYP9;A6NFV8;Q96EV8-3;Q96EV8 D6RJC6 DTNBP1 Dysbindin 2 0 DISEGGES(1)PVVQS(1)DEEEVQVDTALATSHTDR 103.04 7.34E-12 6285900 842.51 584 577.95 507.83 695.88 649.75 556.66 832.28 751.99 719.89 TRUE FALSE FALSE 832.2411641 592.2215673 588.0089773 566.547694 660.3666469 608.233072 603.9426865 856.3607087 684.730131 701.187154 1.186903039 0.844598427 0.83859063 0.807983562 0.941783721 0.867433279 0.861314534 1.221301194 0.976529771 1 9.453655755 -10.25367911 24.93161667 1.088259769 0.902543143 0.202367636 0.123479528 499.1663232 1603684.718 0.020879104 0.025322733 5.58E-11 10.25367911 -0.185716626 DISEGGESPVVQS(ph)DEEEVQVDTALATSHTDR ddPTM_HeLa_Romidepsin_16h_R1 2 DISEGGESPVVQSDEEEVQVDTALATSHTDR 31 0 D6RJC6;A0A087WYP9;A6NFV8;Q96EV8-3;Q96EV8 D6RJC6 DTNBP1 Dysbindin 1 0 DISEGGES(0.004)PVVQS(0.996)DEEEVQVDTALATSHTDR;DISEGGES(0.005)PVVQS(0.995)DEEEVQVDTALATSHTDR ; 112.62 3.31E-14 17333200 2901.7 2918.8 2840.9 2076.68 3127.2 3005.6 2869.9 3114.8 2985.5 2951.9 TRUE FALSE FALSE 2866.332964 2959.890943 2890.344673 2316.795513 2967.607315 2813.55186 3113.669234 3204.921824 2718.469403 2875.209212 0.996912834 1.029452372 1.005264125 0.805783281 1.032136132 0.978555525 1.082936581 1.114674303 0.945485772 1 11.48945122 -7.676703754 4.034696624 0.988664526 1.107817527 0.372002816 0.06295474 0.17727283 5.314909131 0.008323638 0.034800651 2.11E-08 7.676703754 0.119153 DISGPS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 3 DISGPSPSK 9 0 S4R3D6;Q96GX9-3;Q96GX9 S4R3D6 APIP Methylthioribulose-1-phosphate dehydratase 1 0 DIS(0.008)GPS(0.896)PS(0.096)K;DIS(0.175)GPS(0.746)PS(0.079)K;DIS(0.022)GPS(0.757)PS(0.221)K ;; 116.84 0.015262 218951000 27351.6 26208.1 25754.5 20718.4 23857.8 25167.8 21398 19005 26424.2 26084.4 TRUE FALSE FALSE 27018.22818 26577.05832 26202.74627 23113.95889 22640.24744 23559.65881 23215.54559 19554.87969 24060.75337 25406.72353 1.063428275 1.04606398 1.031331184 0.909757563 0.891112442 0.927300161 0.913755981 0.769673416 0.947023072 1 14.63292272 -9.198611605 3.380146486 1.03270701 0.883317047 0.63963695 0.050458142 0.101589743 2.310524554 0.006929167 0.011734121 6.33E-10 9.198611605 -0.149389964 DISLS(ph)DYK ddPTM_HeLa_Romidepsin_16h_R1 1 DISLSDYK 8 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 1 0 DIS(0.017)LS(0.982)DYK 101.38 0.02983 7877400 4889.7 5243.1 4889.5 4056.9 4759.8 5530.2 4705.1 4889.5 4827.2 4495.6 TRUE FALSE FALSE 4830.102456 5316.912499 4974.599696 4525.977866 4516.889645 5176.838068 5104.751077 5030.969968 4395.443142 4378.803664 1.103064404 1.214238616 1.136063655 1.033610596 1.031535093 1.182249415 1.165786701 1.148937097 1.003800006 1 12.09632105 -11.71351809 0.748921269 1.00242973 1.126980388 0.436767757 0.056241742 0.516059333 0.569292648 0.033956782 0.013369027 1.93E-12 11.71351809 0.124550658 DISLSDYK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 1 DISLSDYKGK 10 1 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 1 DISLSDYK(1)GK 145.25 0.010807 591080 62.353 134.41 174.61 181.79 167.49 158.84 202.26 185.86 154.77 158.14 FALSE TRUE FALSE 61.59301765 136.3022275 177.6490138 202.8094151 158.9423603 148.6906366 219.4399594 191.2375659 140.9269836 154.0315 0.399872868 0.884898397 1.153329116 1.316674934 1.031882182 0.965326161 1.424643397 1.241548423 0.91492314 1 7.267081607 -9.863231294 3.708307921 0.713855633 1.189629324 0.489504542 0.193602015 0.163108406 4.32456456 0.041398333 0.055580588 1.37E-10 9.863231294 0.47577369 DISMEIDS(ph)PENMMR ddPTM_HeLa_Romidepsin_16h_R1 1 DISMEIDSPENMMR 14 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 DIS(0.009)MEIDS(0.991)PENMMR 42.469 0.02569 14328000 3517.9 1738.2 2697.1 1443.6 2817.3 2195.3 3676.4 2715.7 3569.6 3038.5 TRUE FALSE FALSE 3475.022482 1762.670425 2744.041894 1610.515824 2673.522668 2055.027415 3988.673324 2794.274495 3250.326036 2959.559332 1.174168885 0.595585433 0.927179214 0.544174197 0.903351604 0.694369392 1.347725413 0.944152214 1.098246621 1 11.53116666 -10.2957116 24.87847447 1.08224642 0.857169591 0.206076246 0.215316448 720.0625868 522696.7251 0.037208641 0.042550762 5.06E-11 10.2957116 -0.225076829 DITDPLSLNTCTDEGHVVLAS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 1 DITDPLSLNTCTDEGHVVLASPLK 24 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 0 DITDPLS(0.007)LNT(0.151)CT(0.42)DEGHVVLAS(0.422)PLK 50.802 0.01581 19312000 1699.9 1866 1644.3 225.8 1483.8 1246 1067.5 1266.1 2104.1 1871.4 TRUE FALSE FALSE 1679.180965 1892.269597 1672.918352 251.9080584 1408.076149 1166.384621 1158.173423 1302.732606 1915.904026 1822.780758 0.921219383 1.038122434 0.917783636 0.138199867 0.772487938 0.639892985 0.635388221 0.714695171 1.051088573 1 10.83192533 -9.490180615 24.9289035 0.967910095 0.590287212 0.601523102 0.165109195 326.2167465 248706.5384 0.023314018 0.035595143 3.23E-10 9.490180615 -0.377622883 DITSDTS(ph)GDFR ddPTM_HeLa_Romidepsin_16h_R1 1 DITSDTSGDFR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 1 0 DIT(0.001)S(0.006)DT(0.139)S(0.854)GDFR 101.71 0.018386 3340300 3488.9 3432.7 3981.1 3141.7 4268 4012.3 3768.1 3454.3 4533.5 3992.5 TRUE FALSE FALSE 3446.375945 3481.025641 4050.389376 3504.958136 4050.188034 3755.926979 4088.16232 3554.244721 4128.012406 3888.774274 0.886237077 0.895147261 1.041559394 0.901301513 1.041507619 0.96583826 1.051272723 0.913975579 1.06152019 1 11.92509978 -9.768461726 24.99961334 0.940942734 0.986649336 0 0.068055994 282.039709 1004062.421 0.009966061 0.013255743 1.70E-10 9.768461726 0.045706602 DITSDTSGDFR ddPTM_HeLa_Romidepsin_16h_R1 2 DITSDTSGDFR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 0 ; ; 308.58 3.52E-144 177030000 10830.1 10361.8 9996.3 11185.7 12597.9 12068.1 11193.6 11858 10972.7 10479.4 FALSE FALSE TRUE 10698.09858 10507.67369 10170.28141 12479.04326 11954.98215 11296.98736 12144.3841 12201.09252 9991.27423 10207.14368 1.048099146 1.029443106 0.996388581 1.222579368 1.171236786 1.10677264 1.189792609 1.195348366 0.978851141 1 13.31729158 -9.266813643 24.99999824 1.022107335 1.173610631 0.858062153 0.033698599 128.6917069 598647.8468 0.005136495 0.007987609 5.41E-10 9.266813643 0.151503297 DITTS(ph)ADQIAEVK ddPTM_HeLa_Romidepsin_16h_R1 2 DITTSADQIAEVK 13 0 A0A3B3IS79;F5H527;Q76I76 A0A3B3IS79 SSH2 Protein phosphatase Slingshot homolog 2 1 0 DIT(0.333)T(0.333)S(0.334)ADQIAEVK;DITT(0.027)S(0.973)ADQIAEVK ; 238.88 1.36E-41 22050000 11280.9 10020.4 9845.6 9699.6 9975.4 9993.6 7995.8 10332.5 10772.5 10454.3 TRUE FALSE FALSE 11143.40405 10161.46745 10016.95854 10821.11339 9466.318115 9355.041213 8674.963052 10631.45459 9808.98062 10182.69578 1.094347145 0.997915255 0.983723638 1.062696326 0.929647543 0.918719504 0.85193187 1.044070727 0.963298996 1 13.31383193 -8.753011999 24.81935826 1.037768608 0.928839989 0.271734327 0.058821699 119.2521012 351204.6636 0.008326592 0.016437805 1.77E-09 8.753011999 -0.108928619 DIVVLGVEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 DIVVLGVEKK 10 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 1 DIVVLGVEK(1)K 94.309 0.007817 0 0 0 0 0 0 64.833 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 60.69038054 0 0 0 0 0 DIWPTRDEIQAVER ddPTM_HeLa_Romidepsin_16h_R1 2 DIWPTRDEIQAVER 14 1 P21399 P21399 ACO1 Cytoplasmic aconitate hydratase 0 0 ; ; 126.5 0.0034024 13296700 2440.7 2258 1987.78 2674.5 3082.5 2684.6 2921.3 2928 2396.2 2068.57 FALSE FALSE TRUE 2410.95181 2289.788183 2022.376477 2983.738274 2925.188523 2513.062724 3169.435149 3012.71706 2181.877871 2014.828253 1.19660413 1.136468173 1.003746336 1.480889634 1.451830208 1.247283842 1.573054747 1.495272391 1.082910103 1 10.97644115 -9.256085925 24.99668488 1.093090591 1.445397861 0.790126244 0.094171409 180.3442422 842073.9508 0.016436714 0.026754354 5.55E-10 9.256085925 0.35230727 DIYLS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 2 DIYLSPDR 8 0 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 0 DIYLS(1)PDR;DIYLS(1)PDR ; 112.3 0.021613 44051000 7248 6170.1 6797.1 2989.2 6124.9 5851.7 5275.8 5239.6 7236.1 7090.7 TRUE FALSE FALSE 7159.658588 6256.96283 6915.400674 3334.825369 5812.323498 5477.795255 5723.92632 5391.199559 6588.885093 6906.482592 1.036657733 0.905955057 1.001291263 0.48285438 0.841575059 0.793138212 0.828775899 0.780599891 0.954014581 1 12.75373543 -9.456943929 24.99990934 1.006784938 0.75642297 0.562910459 0.101561767 95.54300606 36226.07384 0.014642015 0.02236604 3.49E-10 9.456943929 -0.250361968 DK(ac)GEYTLVVK ddPTM_HeLa_Romidepsin_16h_R1 2 DKGEYTLVVK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 1 ; DK(1)GEYTLVVK;DK(1)GEYTLVVK 163.84 0.013521 13001000 1947.69 1806.83 2233.09 1282 4289.5 3590.7 3507.8 3984.6 4322.8 3632.7 FALSE TRUE FALSE 1923.950805 1832.2666 2271.955995 1430.230872 4070.590809 3361.265858 3805.752444 4099.888114 3936.157941 3538.32193 0.543746681 0.517834905 0.642099854 0.404211629 1.150429749 0.94996044 1.075581171 1.158709749 1.112436352 1 11.7888496 -8.732396844 24.99996827 0.721662713 1.073541934 0.439851326 0.209504942 181.3902703 156140.9456 0.032988283 0.065968064 1.85E-09 8.732396844 0.351879221 DK(ac)HIEEVR ddPTM_HeLa_Romidepsin_16h_R1 2 DKHIEEVR 8 1 P16949 P16949 STMN1 Stathmin 0 1 ; DK(1)HIEEVR;DK(1)HIEEVR 100.48 0.0089339 5002800 1573.79 1279.23 1308.57 1144.44 1243.02 906.45 1100.81 1143.15 1838.78 1644.3 FALSE TRUE FALSE 1554.608042 1297.239034 1331.345112 1276.765538 1179.584051 848.5307704 1194.312774 1176.225242 1674.314911 1601.580849 0.970670974 0.809974117 0.831269375 0.797190812 0.736512335 0.529808265 0.745708701 0.734415151 1.045413919 1 10.64528091 -9.69253737 0.757440915 0.996266177 0.676545024 0.787435746 0.066921123 0.190415161 0.220282517 0.014418129 0.025107162 2.03E-10 9.69253737 -0.319721153 DK(ac)PHVNVGTIGHVDHGK ddPTM_HeLa_Romidepsin_16h_R1 1 DKPHVNVGTIGHVDHGK 17 1 P49411;H3BNU3 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 1 DK(1)PHVNVGTIGHVDHGK 48.391 0.018806 1287300 666.58 605.53 475.66 347.17 1237.4 1132.4 1252.8 1312.3 998.79 772.85 FALSE TRUE FALSE 658.4554666 614.0546672 483.9386628 387.3114289 1174.250861 1060.043295 1359.212801 1350.26933 909.4557209 752.7712456 0.874708579 0.815725456 0.642876127 0.514514112 1.559903978 1.408187814 1.805612009 1.79373128 1.208143545 1 9.556067711 -8.664347337 6.879281252 0.878188084 1.648182299 0.783911004 0.205368514 0.076598564 4.681342378 0.028991456 0.058195448 2.17E-09 8.664347337 0.769994216 DK(ac)TVVAYNWK(ac)TGNVVK ddPTM_HeLa_Romidepsin_16h_R1 1 DKTVVAYNWKTGNVVK 16 2 Q8NA23-2;Q8NA23 Q8NA23-2 WDR31 WD repeat-containing protein 31 0 2 DK(1)TVVAYNWK(1)TGNVVK 99.752 0.017228 2630800 0 0 38.926 87.168 3436.6 5083.8 2803.5 3676.9 188.27 104.49 FALSE TRUE FALSE 0 0 39.6034907 97.2467743 3261.217478 4758.961587 3041.62922 3783.2853 171.4306597 101.7753347 0 0 0.389126607 0.955504342 32.04329897 46.75947861 29.88572062 37.17290943 1.684402809 1 6.669244156 -8.727805925 4.503832377 0.412606226 37.39135809 0.953447461 3.88751489 0.026171247 1.199496328 0.515742157 1.030367402 1.87E-09 8.727805925 36.97875186 DKAIT(ph)PPLPESTVPFSNGVLK ddPTM_HeLa_Romidepsin_16h_R1 1 DKAITPPLPESTVPFSNGVLK 21 1 I3NI36;Q92667-2;Q92667 I3NI36 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 0 DKAIT(0.986)PPLPES(0.007)T(0.007)VPFSNGVLK 56.304 0.01443 31931000 2002 2590.4 1826.1 1031.2 1934.3 2278.4 1276.3 1845.5 2367.7 2424.1 TRUE FALSE FALSE 1977.598854 2626.867719 1857.882504 1150.432196 1835.585453 2132.817593 1384.70889 1898.896631 2155.926982 2361.121533 0.837567582 1.112550829 0.786864411 0.487239721 0.777420996 0.903306994 0.586462353 0.804235023 0.913094456 1 11.20525659 -9.534709221 24.75416574 0.936030599 0.710864481 0.466998048 0.126940293 146.4972254 306530.6313 0.020242154 0.028639484 2.92E-10 9.534709221 -0.225166117 DKALEEEEDDRPYDPEEEYDPER ddPTM_HeLa_Romidepsin_16h_R1 2 DKALEEEEDDRPYDPEEEYDPER 23 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 0 ; ; 86.136 7.69E-05 8542500 2287.43 2323.7 2144.01 1883.24 2056.49 1791.93 2202.31 1947.15 2040.1 2405.98 FALSE FALSE TRUE 2259.549923 2356.41311 2181.325595 2100.98907 1951.539641 1677.431456 2389.374156 2003.487713 1857.628346 2343.472293 0.964188879 1.005522069 0.930809211 0.896528231 0.832755586 0.715788901 1.019587116 0.854922723 0.792682018 1 11.19443202 -9.350087603 2.142768994 0.98416087 0.859200113 0.073063635 0.092599653 0.23771951 2.133808394 0.010968654 0.01829776 4.47E-10 9.350087603 -0.124960757 DKAPVQPQQS(ph)PAAAPGGTDEKPSGK ddPTM_HeLa_Romidepsin_16h_R1 4 DKAPVQPQQSPAAAPGGTDEKPSGK 25 2 Q13200;C9JPC0;F8WBS8 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 0 DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK;DKAPVQPQQS(1)PAAAPGGTDEKPSGK ;;; 73.459 0.00021189 226753900 12852.93 11789.24 12203.54 10369.17 12040.63 13454.69 12686.77 13406.72 13121.63 12120.16 TRUE FALSE FALSE 12696.27355 11955.20923 12415.93749 11568.10222 11426.15172 12594.97873 13764.38393 13794.62229 11947.99855 11805.2765 1.075474475 1.012700485 1.051727801 0.979909469 0.967885142 1.066894006 1.165951846 1.168513274 1.012089683 1 13.52714421 -7.844010237 3.73900584 1.027396501 1.169408964 0.77807876 0.031745484 0.094011157 2.51734583 0.005448834 0.01910834 1.43E-08 7.844010237 0.142012462 DKDAYSSFGSR ddPTM_HeLa_Romidepsin_16h_R1 1 DKDAYSSFGSR 11 1 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;O15523-2;O15523;A0A2R8YDH3;A0A087WX09;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89;C9J081;C9J8G5;O15523-3 A0A2R8Y4A4 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 0 102.95 0.020278 23579000 3087 2853.5 2708.2 3051.8 2523.3 2729.3 2467.9 2597.4 3429.7 2792.9 FALSE FALSE TRUE 3049.374457 2893.671648 2755.335085 3404.663475 2394.526585 2554.906538 2677.523364 2672.551671 3122.939042 2720.340055 1.120953408 1.063716884 1.012864211 1.251558043 0.88023061 0.939186457 0.984260537 0.982432937 1.147995831 1 11.40957129 DKDDQEWESPS(ph)PPKPTVFISGVIAR ddPTM_HeLa_Romidepsin_16h_R1 3 DKDDQEWESPSPPKPTVFISGVIAR 25 2 P51397 P51397 DAP Death-associated protein 1 1 0 DKDDQEWES(0.004)PS(0.993)PPKPT(0.001)VFIS(0.002)GVIAR;DKDDQEWES(0.113)PS(0.884)PPKPT(0.003)VFISGVIAR;DKDDQEWES(0.073)PS(0.916)PPKPT(0.009)VFIS(0.003)GVIAR ;; 76.028 0.00027588 1753350000 6540.1 7617.89 6490.61 3279.92 6992.4 6885.1 5360.75 5681.67 7329.1 7030 TRUE FALSE FALSE 6460.386746 7725.134855 6603.576344 3659.159783 6635.551736 6445.164331 5816.091971 5846.060157 6673.56694 6847.359587 0.94348583 1.128191788 0.964397482 0.534389897 0.969067222 0.941262723 0.849391929 0.853768534 0.974619027 1 12.74133206 -9.492689694 24.99874181 0.98714074 0.835107515 0.34112305 0.119298281 683.7537134 566198.8634 0.017879406 0.027287796 3.22E-10 9.492689694 -0.152033226 DKENGNNS(ph)PLPK ddPTM_HeLa_Romidepsin_16h_R1 2 DKENGNNSPLPK 12 1 Q6P1L5 Q6P1L5 FAM117B Protein FAM117B 1 0 DKENGNNS(1)PLPK;DKENGNNS(1)PLPK ; 75.998 0.021306 33892000 7588.4 7717.9 7114.1 6810.5 4729.8 4594.4 3758.3 3379.1 8056.7 7326.1 TRUE FALSE FALSE 7495.909662 7826.552799 7237.917926 7597.962054 4488.420657 4300.832668 4077.529908 3476.868927 7336.088574 7135.766866 1.05047009 1.096806124 1.014315358 1.064771621 0.629003265 0.602714852 0.571421402 0.487245308 1.028072905 1 12.80085277 -8.712723449 4.863054838 1.032629368 0.566383493 0.970534209 0.040162502 0.025692506 1.306894559 0.006442311 0.012924772 1.94E-09 8.712723449 -0.466245875 DKEPFTFSS(ph)PASGR ddPTM_HeLa_Romidepsin_16h_R1 1 DKEPFTFSSPASGR 14 1 H0YEX2;Q6P1X5 H0YEX2 TAF2 Transcription initiation factor TFIID subunit 2 1 0 DKEPFT(0.001)FS(0.166)S(0.823)PAS(0.01)GR 64.537 0.026793 6017300 2896.4 2576.3 3012.9 2303.4 2681.4 2383.9 2046.6 2361.6 3638.7 2982.3 TRUE FALSE FALSE 2861.097563 2612.569219 3065.338261 2569.729946 2544.558152 2231.576484 2220.438153 2429.92917 3313.245559 2904.819416 0.984948512 0.899391268 1.055259492 0.884643614 0.875978086 0.768232432 0.764398 0.836516431 1.140602937 1 11.50423276 -8.787435789 1.629249719 0.988605347 0.788721052 0.677047752 0.066126158 0.112432517 0.603608623 0.006542172 0.015293123 1.63E-09 8.787435789 -0.199884295 DKEVS(ph)DDEAEEK ddPTM_HeLa_Romidepsin_16h_R1 1 DKEVSDDEAEEK 12 1 P07900-2;P07900;G3V2J8 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 1 0 DKEVS(1)DDEAEEK 91.616 0.0097056 47038000 4437.9 4592.1 5198.2 2452.2 4573.5 4597.4 5249.6 3924.6 4555.8 4940.8 TRUE FALSE FALSE 4383.809168 4656.747704 5288.67249 2735.734902 4340.097229 4303.640977 5695.500893 4038.152109 4148.317838 4812.437304 0.910933253 0.967648493 1.09895925 0.568471801 0.901850134 0.894274711 1.183496123 0.839107474 0.861999352 1 12.23255203 -12.43918044 0.638724128 1.014491438 0.92098859 0 0.159206054 4.181816248 2.274901858 0.232107015 0.032732426 3.64E-13 12.43918044 -0.093502848 DKGEYTLVVK ddPTM_HeLa_Romidepsin_16h_R1 2 DKGEYTLVVK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 115.91 0.016372 43078000 5991.7 5036.9 5262.9 5150.7 6031.5 5984.8 4875.5 5980.8 6033.9 5545.7 FALSE FALSE TRUE 5918.670856 5107.80961 5354.498567 5746.248169 5723.690048 5602.390595 5289.624848 6153.845012 5494.212872 5401.621915 1.095721054 0.945606651 0.991276074 1.063800514 1.059624339 1.037168222 0.97926603 1.139258747 1.017141325 1 12.39917695 DKLGERDDTIPPEYR ddPTM_HeLa_Romidepsin_16h_R1 1 DKLGERDDTIPPEYR 15 2 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;A0A0A0MR45;H0YD33;E7EQA0;E7EQ12;A0A0C4DGD1;P20810-3 P20810-6;P20810-3 CAST Calpastatin 0 0 59.673 0.027475 19518000 2123.3 1687 1746 2211.4 2406.6 2086.2 1880.9 2101 2141.7 2004.1 FALSE FALSE TRUE 2097.420403 1710.74963 1776.388398 2467.092473 2283.782222 1952.898553 2040.663599 2161.78912 1950.140988 1952.033193 1.074479886 0.876393719 0.910019565 1.263857849 1.169950506 1.000443312 1.045404149 1.107455103 0.999030649 1 10.93076187 -9.281779814 24.99537408 1.013097086 1.109840624 0.364650716 0.087698392 1022.128962 1256042.09 0.014764775 0.022568022 5.23E-10 9.281779814 0.096743538 DKPTYDEIFYT(ph)LSPVNGK ddPTM_HeLa_Romidepsin_16h_R1 2 DKPTYDEIFYTLSPVNGK 18 1 A0A024R571;Q9H4M9 A0A024R571 EHD1 EH domain-containing protein 1 1 0 DKPTYDEIFY(0.079)T(0.582)LS(0.339)PVNGK;DKPTYDEIFY(0.016)T(0.981)LS(0.003)PVNGK ; 97.579 0.0015976 467120000 9832.6 8810.1 9581 10912.4 15435.2 21173.5 19455.5 21589.5 9985.3 10165.9 TRUE FALSE FALSE 9712.756489 8934.128819 9747.753286 12174.14303 14647.48415 19820.58168 21108.04968 22214.15812 9092.189759 9901.788452 0.980909311 0.902274257 0.984443703 1.229489308 1.479276619 2.001717344 2.131741128 2.243449073 0.918237125 1 13.27347341 -8.426768542 1.260068639 0.98047791 2.239307426 0.991610275 0.046980283 0.027636826 0.08204953 0.007047995 0.025606607 3.74E-09 8.426768542 1.258829516 up DKPVPLPAPEMTVK(ac)QER ddPTM_HeLa_Romidepsin_16h_R1 1 DKPVPLPAPEMTVKQER 17 2 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9;H0YAH7;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 0 1 DKPVPLPAPEMTVK(1)QER 87.668 0.0048492 3756300 1519.6 1615.6 1421.3 956.6 844.01 947.92 1227.9 1111.3 1697.8 1577.4 FALSE TRUE FALSE 1501.078531 1638.344459 1446.03713 1067.206593 800.9370203 887.3509713 1332.197795 1143.453712 1545.944516 1536.418921 0.976998207 1.066339679 0.941173733 0.694606516 0.521301196 0.577544939 0.86707979 0.744233032 1.006199868 1 10.58535592 -9.295770593 4.046747969 0.99460379 0.674701267 0.758364672 0.089964315 0.08715 3.201664101 0.014570887 0.023232599 5.06E-10 9.295770593 -0.319902523 DKPVYDELFYTLS(ph)PINGK ddPTM_HeLa_Romidepsin_16h_R1 2 DKPVYDELFYTLSPINGK 18 1 Q9H223 Q9H223 EHD4 EH domain-containing protein 4 1 0 DKPVYDELFYT(0.018)LS(0.981)PINGK;DKPVYDELFYT(0.002)LS(0.997)PINGK ; 92.034 0.0020393 135558000 9443 8059.9 9115.6 8660.3 16864.7 22903 21043 23231 10519.2 9852.4 TRUE FALSE FALSE 9327.905084 8173.367484 9274.253194 9661.644634 16004.03143 21439.57222 22830.39189 23903.15233 9578.336406 9596.433228 0.972017922 0.851708889 0.966427106 1.00679538 1.667706225 2.234118834 2.379049732 2.490837144 0.998114214 1 13.22828257 -8.461526513 1.798659163 0.968174387 2.431193182 0.99122554 0.05947743 0.02296057 0.144779584 0.00946719 0.026612798 3.46E-09 8.461526513 1.463018794 up DKRPLS(ph)GPDVGTPQPAGLASGAK ddPTM_HeLa_Romidepsin_16h_R1 2 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 0 DKRPLS(0.951)GPDVGT(0.049)PQPAGLASGAK;DKRPLS(0.968)GPDVGT(0.032)PQPAGLASGAK ; 101.51 2.93E-05 82206000 5100.5 5157.1 4957.9 6008 6474.7 5517.8 5616.2 6328.4 5312.8 4854.2 TRUE FALSE FALSE 5038.333144 5229.701789 5044.19017 6702.673228 6144.271899 5165.230388 6093.239888 6511.502269 4837.609862 4728.087184 1.065617648 1.106092503 1.066856421 1.417628941 1.299525931 1.092456672 1.288732557 1.377195897 1.023164268 1 12.20704092 -9.380135261 6.54404856 1.039822676 1.283234826 0.674238728 0.084092542 0.114832109 5.771089845 0.013470526 0.020625846 4.17E-10 9.380135261 0.24341215 DKRPLSGPDVGT(ph)PQPAGLASGAK ddPTM_HeLa_Romidepsin_16h_R1 1 DKRPLSGPDVGTPQPAGLASGAK 23 2 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 0 DKRPLS(0.072)GPDVGT(0.925)PQPAGLAS(0.003)GAK 52.522 0.0093352 34503000 1936.1 2078.4 2512.3 2637.4 2827.1 2633.4 2327 2497 2467.8 2206.1 TRUE FALSE FALSE 1912.502069 2107.65977 2556.025528 2942.348597 2682.822538 2465.134239 2524.655322 2569.246755 2247.073787 2148.785204 0.890038737 0.980861077 1.189521188 1.36930792 1.248529882 1.14722227 1.174922145 1.195674072 1.045741465 1 11.06930556 -9.759861096 4.204957537 0.947656271 1.226039583 0.747409905 0.068353728 0.070265303 2.87129882 0.011493314 0.015877203 1.74E-10 9.759861096 0.278383312 DKS(ph)PVREPIDNLTPEER ddPTM_HeLa_Romidepsin_16h_R1 2 DKSPVREPIDNLTPEER 17 2 Q14498-2;Q14498;G3XAC6;Q5QP22;H0Y4X3;Q14498-3;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 0 DKS(0.994)PVREPIDNLT(0.006)PEER;DKS(1)PVREPIDNLTPEER ; 139.29 0.0020033 56166000 4085.23 3127.62 3320.73 3461.79 3457.97 3086.81 3201.48 3093.27 4062.48 3707.81 TRUE FALSE FALSE 4035.437645 3171.650716 3378.525913 3862.058448 3281.496887 2889.572803 3473.413631 3182.768887 3699.121614 3611.480562 1.11739149 0.878213426 0.935496081 1.069383701 0.908629254 0.800107533 0.961769992 0.881291989 1.024267347 1 11.81837469 -9.374945536 0.777125486 1.049721627 0.890181063 0.277513474 0.077951412 0.526152848 0.63005142 0.017589736 0.038468234 4.22E-10 9.374945536 -0.159540565 DKSFDDEES(ph)VDGNRPSSAASAFK ddPTM_HeLa_Romidepsin_16h_R1 1 DKSFDDEESVDGNRPSSAASAFK 23 2 E7ERI8;E7EW49;O75122-3 E7ERI8 CLASP2 CLIP-associating protein 2 1 0 DKS(0.065)FDDEES(0.933)VDGNRPS(0.001)S(0.001)AASAFK 59.918 0.0080858 16647000 967.44 1103.9 1105.9 988.1 1077.8 979.05 860.64 1119.9 1117.2 1166 TRUE FALSE FALSE 955.6484692 1119.440733 1125.147726 1102.348771 1022.795844 916.4918647 933.7427401 1152.30254 1017.274834 1135.707152 0.841456768 0.985677277 0.990702334 0.970627656 0.900580614 0.806979038 0.822168583 1.014612383 0.895719317 1 10.14937516 -8.527071763 23.3163646 0.936696639 0.871750692 0.147259358 0.06948909 84.90022192 472109.5157 0.011744598 0.023586606 2.97E-09 8.527071763 -0.064945947 DKVTIADDYS(ph)DPFDAK ddPTM_HeLa_Romidepsin_16h_R1 1 DKVTIADDYSDPFDAK 16 1 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 0 DKVTIADDY(0.422)S(0.578)DPFDAK 97.129 0.0026962 5400800 1579.4 1551.1 1708.8 1847 1497 1278.4 1480.4 1312.7 2154.3 1837 TRUE FALSE FALSE 1560.149665 1572.936427 1738.540947 2060.55883 1420.602504 1196.714366 1606.145139 1350.680903 1961.614012 1789.274475 0.87194541 0.879091748 0.971645754 1.151616959 0.79395449 0.668826601 0.897651624 0.754876304 1.096318111 1 10.805159 -8.561473021 24.99995939 0.949967844 0.777041009 0.493596463 0.101446236 112.2043444 72681.46291 0.013831144 0.027662327 2.74E-09 8.561473021 -0.172926836 DKWLAPDGLIFPDR ddPTM_HeLa_Romidepsin_16h_R1 1 DKWLAPDGLIFPDR 14 1 E9PNR9;E9PQ98;E9PIX6;H0YDE4;E9PKG1;Q99873-2;Q99873-3;Q99873 E9PNR9 PRMT1 Protein arginine N-methyltransferase 1 0 0 101.04 0.011107 12970000 4923.5 4205.6 4592.3 4866.2 4912.4 4097.6 4204 4916.9 5342.4 4735.9 FALSE FALSE TRUE 4863.490488 4264.806547 4672.227055 5428.85294 4661.701897 3835.776584 4561.087655 5059.162744 4864.562364 4612.860635 1.054332847 0.924547019 1.012869762 1.17689507 1.010588064 0.831539664 0.988776383 1.0967517 1.054565214 1 12.17144599 -8.506969038 24.76739044 1.028916533 0.965175617 0.099843965 0.084211627 1127.918559 1755884.051 0.011961548 0.02603226 3.11E-09 8.506969038 -0.063740916 DLADELALVDVIEDK ddPTM_HeLa_Romidepsin_16h_R1 1 DLADELALVDVIEDK 15 0 P00338;P00338-3;P00338-5;P00338-2;F5GYU2;F5GXY2;P00338-4;F5GXH2;F5GZQ4;F5H5J4;F5H6W8 P00338 LDHA L-lactate dehydrogenase A chain 0 0 208.28 4.90E-18 1950900 1381.4 1482.4 1097.1 1249.2 1013.5 1302.6 883.28 1399.2 1539.9 1455.1 FALSE FALSE TRUE 1364.562965 1503.269266 1116.194565 1393.638382 961.7773131 1219.368064 958.3057812 1439.683644 1402.167487 1417.296292 0.962793012 1.060659845 0.787552025 0.983307717 0.678600035 0.860348024 0.67615063 1.015795817 0.989325588 1 10.46892568 -9.754194058 25 0.987806345 0.827439495 0.373925498 0.106570551 128.9512455 444945.0467 0.015124838 0.021137362 1.76E-10 9.754194058 -0.16036685 DLADELALVDVIEDKLK ddPTM_HeLa_Romidepsin_16h_R1 1 DLADELALVDVIEDKLK 17 1 P00338;P00338-3;P00338-5;P00338-2;F5GYU2;F5GXY2;P00338-4;F5GXH2;F5GZQ4;F5H5J4;F5H6W8 P00338 LDHA L-lactate dehydrogenase A chain 0 0 237.05 1.79E-46 80125000 3592.2 2910.2 2769 2726.5 2823.8 3103.8 2436.5 2796.2 3354.3 2468.1 FALSE FALSE TRUE 3548.416885 2951.169872 2817.193283 3041.750759 2679.690949 2905.477197 2643.456249 2877.103635 3054.283007 2403.978406 1.476060216 1.227619127 1.171887932 1.265298703 1.114690108 1.20861202 1.099617302 1.196809267 1.270511831 1 11.23120822 -8.762962181 24.99631919 1.228396004 1.154815388 0.105266415 0.113642447 128.0345981 2101699.679 0.026075873 0.049162478 1.73E-09 8.762962181 -0.073580617 DLAEDAPWK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DLAEDAPWKK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;Q14315-2;Q14315;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 Q60FE5;Q14315-2;O75369-8 FLNA;FLNC;FLNB Filamin-A;Filamin-C;Filamin-B 0 1 ; DLAEDAPWK(1)K;DLAEDAPWK(1)K 155.42 0.0032921 3695700 1386.85 1094.7 1400.68 690.72 2731.4 2510.27 2599.5 2552.6 2493.6 1952.23 FALSE TRUE FALSE 1369.946539 1110.111215 1425.058248 770.5842963 2592.006466 2349.871849 2820.301465 2626.455454 2270.566171 1901.510783 0.720451628 0.583804849 0.749434744 0.405248449 1.363130038 1.235792018 1.483189835 1.381246679 1.194085351 1 10.8929304 -8.730562834 24.91868903 0.802434045 1.364933226 0.654901035 0.209389529 91.69822153 74003.97553 0.028873279 0.057741496 1.86E-09 8.730562834 0.562499181 DLAEDAPWKK ddPTM_HeLa_Romidepsin_16h_R1 1 DLAEDAPWKK 10 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;Q14315-2;Q14315;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 Q60FE5;Q14315-2;O75369-8 FLNA;FLNC;FLNB Filamin-A;Filamin-C;Filamin-B 0 0 97.597 0.002456 0 2984.9 2937.5 2793.3 2094.7 2715.9 3088.8 2330.1 2670 2641.4 2731.6 FALSE FALSE TRUE 2948.518891 2978.854202 2841.916215 2336.89907 2577.297489 2891.435649 2528.018636 2747.252237 2405.146568 2660.632638 1.10820218 1.119603721 1.068135516 0.87832459 0.968678446 1.086747418 0.950156966 1.032556016 0.903975443 1 11.37755361 DLAEITTLDR ddPTM_HeLa_Romidepsin_16h_R1 1 DLAEITTLDR 10 0 Q9BS26 Q9BS26 ERP44 Endoplasmic reticulum resident protein 44 0 0 163.16 0.000122 0 1174.8 849.5 1010.3 961.48 1066.2 1169.6 957.94 855.39 1148.1 973.9 FALSE FALSE TRUE 1160.481086 861.4592833 1027.883848 1072.650841 1011.787835 1094.866335 1039.3074 880.1393601 1045.411061 948.5979376 1.223364546 0.908139528 1.083582208 1.130775009 1.066613995 1.154194302 1.095624773 0.92783183 1.102059175 1 9.889652922 -7.261211929 21.56367171 1.094677606 0.927831773 0.244101061 0.081321554 3.406080934 321246.4908 0.013403684 0.104243638 5.48E-08 7.261211929 -0.166845834 DLAVPAALT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DLAVPAALTPR 11 0 Q8TEM1 Q8TEM1 NUP210 Nuclear pore membrane glycoprotein 210 1 0 DLAVPAALT(1)PR 118.76 0.021866 12936000 4747.6 7150.8 5188.4 3345.6 4175.5 7328.6 3584.9 7257.5 5184.6 6778.4 TRUE FALSE FALSE 4689.734425 7251.46915 5278.701926 3732.434014 3962.408654 6860.326112 3889.401317 7467.484312 4720.876391 6602.296191 0.710318697 1.098325331 0.799525161 0.565323625 0.600156149 1.039081846 0.589098278 1.131043518 0.715035535 1 12.68875215 -12.516264 1.15763334 1.004673158 0.798374941 0 0.219149108 0.871316761 2.011090185 0.149874692 0.032800318 3.05E-13 12.516264 -0.206298217 DLDAPDDVDFF ddPTM_HeLa_Romidepsin_16h_R1 1 DLDAPDDVDFF 11 0 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;H7C3A1 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 0 0 143.85 0.0258 4869200 6586.9 6765.2 6334.6 5706.5 5970.9 5944.2 5437.9 6364 7056.8 6893.3 FALSE FALSE TRUE 6506.616329 6860.440663 6444.851056 6366.31238 5666.182693 5564.384804 5899.79509 6548.132299 6425.622134 6714.211072 0.96908129 1.021779117 0.959882105 0.948184725 0.843908932 0.828747375 0.878702654 0.975264589 0.957018191 1 12.71300218 -9.00102628 3.033305721 0.98640048 0.878093287 0.564426722 0.040932934 0.130070397 2.452904353 0.006104752 0.01123744 9.98E-10 9.00102628 -0.108307193 DLDDFQSWLSR ddPTM_HeLa_Romidepsin_16h_R1 2 DLDDFQSWLSR 11 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ; ; 257.72 3.21E-60 125870000 5914.4 5702 5577.7 5571.8 5896.7 5688.2 5227.6 5667.5 6085.1 6112.3 FALSE FALSE TRUE 5842.313018 5782.272906 5674.777529 6216.037732 5595.769395 5324.742378 5671.632214 5831.480171 5540.833416 5953.501565 0.98132384 0.971239 0.953183176 1.044097774 0.939912308 0.894388339 0.952654862 0.979504264 0.9306848 1 12.53952273 -8.590088001 24.99997016 0.98955652 0.938882141 0.197975324 0.03477868 38.56675799 14345.32034 0.00415457 0.008309142 2.57E-09 8.590088001 -0.050674379 DLDDIEDENEQLKQENK ddPTM_HeLa_Romidepsin_16h_R1 2 DLDDIEDENEQLKQENK 17 1 Q96IZ0;H0YHP5 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 0 0 ; ; 137.39 0.0012725 14836500 3867.6 3600.6 4161.3 2873.9 3894.8 3811.1 3097 3498.9 4120.5 4745.2 FALSE FALSE TRUE 3820.460204 3651.289341 4233.725681 3206.19384 3696.033822 3567.58301 3360.059103 3600.135151 3751.95216 4621.91902 0.826596093 0.789994227 0.916010355 0.69369321 0.799675158 0.771883496 0.726983551 0.778926488 0.811773669 1 12.17427627 -13.43049525 0.196206763 1.268866485 0.722181992 0.141580165 0.078034378 5.206938983 0.190187468 0.719649196 0.068940092 3.71E-14 13.43049525 -0.546684493 DLDEEIFDDDDFYHQLLR ddPTM_HeLa_Romidepsin_16h_R1 3 DLDEEIFDDDDFYHQLLR 18 0 Q9NY61;A0A087WTH8;A0A087WWS8 Q9NY61 AATF Protein AATF 0 0 ;; ;; 216 2.72E-29 43814800 6251.4 6536.1 6514.6 5239.9 6784.5 6501.6 6129.1 6671 7101 6985 FALSE FALSE TRUE 6175.205532 6628.115387 6627.98388 5845.761892 6438.261649 6086.168743 6649.705601 6864.01486 6465.868775 6803.528693 0.907647459 0.974217305 0.974197976 0.859224993 0.946312118 0.894560605 0.97739069 1.008890411 0.950369884 1 12.73206749 -12.52894571 1.26284417 1.000287727 0.937723564 0.02437029 0.045270694 0.568545895 1.611451701 0.030806849 0.007225844 2.96E-13 12.52894571 -0.062564163 DLDIIDNYDYSHTVK ddPTM_HeLa_Romidepsin_16h_R1 3 DLDIIDNYDYSHTVK 15 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 ;; ;; 136.63 0.0005578 74392200 12087.4 12698.8 11313.8 10821.4 15161.9 15653.1 14979.4 15777.6 13487.5 13567.7 FALSE FALSE TRUE 11940.07412 12877.57404 11510.71194 12072.62118 14388.13167 14652.91743 16251.74986 16234.09996 12281.14422 13215.2092 0.903510035 0.974451017 0.871020032 0.913539922 1.088755498 1.108791939 1.229776208 1.228440634 0.929318941 1 13.68991164 -8.2741842 1.509884027 0.94607686 1.228895287 0.870393352 0.045200119 0.125302071 0.532049653 0.007958902 0.029425159 5.32E-09 8.2741842 0.282818428 DLDITS(ph)PELR ddPTM_HeLa_Romidepsin_16h_R1 2 DLDITSPELR 10 0 P19474-2;P19474 P19474-2 TRIM21 E3 ubiquitin-protein ligase TRIM21 1 0 DLDIT(0.075)S(0.925)PELR;DLDIT(0.166)S(0.834)PELR ; 117.52 0.013378 6338200 5363.8 5899.8 5705.7 4409.9 5428.6 5978.4 4560.6 4712.3 6458.1 6398.3 TRUE FALSE FALSE 5298.423942 5982.857539 5805.005315 4919.793387 5151.558285 5596.399534 4947.97725 4848.642966 5880.471361 6232.071244 0.850186677 0.960011095 0.931472874 0.789431506 0.82662057 0.897999929 0.793953897 0.778014688 0.943582179 1 12.60549601 -16.52287875 0.093593075 1.489760521 0.724231296 0.548403848 0.050949272 75.6911903 0.533803498 7.469328513 0.582900944 3.00E-17 16.52287875 -0.765529225 DLDLEPLS(ph)DLEEGLEETR ddPTM_HeLa_Romidepsin_16h_R1 2 DLDLEPLSDLEEGLEETR 18 0 P29375-2;P29375 P29375-2 KDM5A Lysine-specific demethylase 5A 1 0 DLDLEPLS(1)DLEEGLEETR;DLDLEPLS(1)DLEEGLEETR ; 195.89 5.13E-15 1285300 406.22 544.76 393.35 198.82 423.78 584.48 240.42 410.7 289.69 367.83 TRUE FALSE FALSE 401.2688344 552.4291456 400.1960917 221.8085039 402.1529253 547.1336143 260.8412688 422.5829565 263.7794009 358.2737236 1.120006319 1.541919234 1.117012121 0.619103466 1.12247396 1.527138549 0.728050235 1.179497487 0.736251038 1 8.484918427 -12.0166515 1.214766227 1.009303075 1.114476623 0.067343715 0.287728649 1.663097985 4.832423595 0.115241037 0.049201628 9.62E-13 12.0166515 0.105173549 DLDLLASVPS(ph)PSSSGSR ddPTM_HeLa_Romidepsin_16h_R1 4 DLDLLASVPSPSSSGSR 17 0 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 0 DLDLLAS(0.008)VPS(0.982)PS(0.01)SSGSR;DLDLLAS(0.001)VPS(0.992)PS(0.007)SSGSR;DLDLLAS(0.005)VPS(0.985)PS(0.01)SSGSR;DLDLLASVPS(0.995)PS(0.005)SSGSR ;;; 260.07 7.65E-73 273742000 15097 14981.4 15066.9 11877.4 25449.1 30355.6 27406.7 30824.8 16221.1 15137.2 TRUE FALSE FALSE 14912.99196 15192.30854 15329.13307 13250.72087 24150.33746 28415.97513 29734.62441 31716.66695 14770.24419 14743.93336 1.011466316 1.030410825 1.039690882 0.8987236 1.637984713 1.927299482 2.016736218 2.151167275 1.001784519 1 13.84783384 -8.543219835 2.431411859 1.002253877 2.038771173 0.974066099 0.076530816 0.02949373 0.34863317 0.010865616 0.025833781 2.86E-09 8.543219835 1.036517295 up DLDLLASVPS(ph)PSSSGSRK ddPTM_HeLa_Romidepsin_16h_R1 1 DLDLLASVPSPSSSGSRK 18 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 0 DLDLLAS(0.004)VPS(0.702)PS(0.197)S(0.039)S(0.032)GS(0.026)RK 53.828 0.021763 24854000 1674.8 1459.2 1311.9 1482.5 2568 2282.2 2082.9 2569.6 1752 1555.6 TRUE FALSE FALSE 1654.386893 1479.742656 1334.733069 1653.913625 2436.945377 2136.374785 2259.821474 2643.947322 1595.296732 1515.185288 1.091871012 0.976608384 0.88090419 1.091558662 1.608348099 1.40997593 1.491448929 1.744966337 1.052872375 1 10.56527851 -8.807850661 5.711289352 1.026413468 1.548011541 0.882158604 0.098147192 0.048026248 3.605645074 0.01470224 0.027320062 1.56E-09 8.807850661 0.521598073 DLDRPESQS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DLDRPESQSPK 11 1 Q8WUA4;A0A087WZD8;Q8WUA4-2 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 0 DLDRPES(0.005)QS(0.995)PK 141.65 0.018892 13944000 1891.7 1642.5 1643.4 1363.5 1541.3 1458 1632.1 1590.2 1953.9 1800.1 TRUE FALSE FALSE 1868.643233 1665.623158 1672.002688 1521.154285 1462.64171 1364.838505 1770.730533 1636.209928 1779.13829 1753.333142 1.065766218 0.949975289 0.953613804 0.867578584 0.834206389 0.778425088 1.009922467 0.93319968 1.014717767 1 10.77588443 -9.79613716 1.836768758 1.030272655 0.885263332 0.479375495 0.061546506 0.208230072 1.433798525 0.01128282 0.016055477 1.60E-10 9.79613716 -0.145009323 DLDSLHR ddPTM_HeLa_Romidepsin_16h_R1 4 DLDSLHR 7 0 Q8NBS9-2;Q8NBS9 Q8NBS9-2 TXNDC5 Thioredoxin domain-containing protein 5 0 0 ;;; ;;; 143.11 0.0060815 28638100 24183.1 21970.9 20586.1 15444.9 32056.7 32650 26946.5 24940.9 30680.9 27146.4 FALSE FALSE TRUE 23888.34708 22280.20691 20944.39244 17230.71201 30420.72698 30563.77037 29235.33504 25662.52559 27936.72346 26441.13261 0.903454002 0.842634362 0.792114042 0.651663159 1.150507712 1.155917593 1.105676351 0.970553189 1.05656304 1 14.69049636 DLEAEHVEVEDTTLNR ddPTM_HeLa_Romidepsin_16h_R1 2 DLEAEHVEVEDTTLNR 16 0 H3BV85;H3BTW0;A0A0B4J295;A0A087WZT3;H3BVE0;Q9H3K6-2;Q9H3K6 H3BV85 BOLA2B;BOLA2 BolA-like protein 2 0 0 ; ; 188.19 7.18E-13 36625000 11589.4 11828.4 10885.1 11314.3 11913.9 13060.1 10972.3 12858.7 12635.6 12178.4 FALSE FALSE TRUE 11448.14394 11994.92053 11074.5506 12622.5126 11305.88923 12225.60176 11904.28689 13230.7462 11505.44029 11862.00341 0.965110491 1.011205284 0.93361553 1.064113048 0.953118022 1.030652356 1.003564615 1.115388838 0.969940733 1 13.53406007 -4.000000562 0.890648381 0.985730686 60.1034067 0.516374565 0.036142644 451.0883426 0.985576436 0.004983335 54194.16684 1.00E-04 4.000000562 59.11767601 DLEAHIDSANK ddPTM_HeLa_Romidepsin_16h_R1 1 DLEAHIDSANK 11 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 132.03 0.0022004 10302000 8167.5 7742 7465.3 6700.6 9928.4 11069 8521.3 9162.3 9761.4 8958.9 FALSE FALSE TRUE 8067.951368 7850.992079 7595.230415 7475.354899 9421.7167 10361.72662 9245.099009 9427.396695 8888.315936 8726.146486 0.924572076 0.899708948 0.870399142 0.856661633 1.07971104 1.187434412 1.059470985 1.080361957 1.018584314 1 13.09112898 -8.629626627 6.860057985 0.943797308 1.108720093 0.679911662 0.057935487 0.110954341 6.394902175 0.009130843 0.018346494 2.35E-09 8.629626627 0.164922785 DLEDGEVPQHAGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DLEDGEVPQHAGKK 14 1 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 0 1 ; DLEDGEVPQHAGK(1)K;DLEDGEVPQHAGK(1)K 100.55 0.0043625 7955200 3994.81 4813.84 4454.11 5031.9 5318.49 5549.14 5067.18 5021.86 4860.66 4913.49 FALSE TRUE FALSE 3946.119719 4881.609366 4531.631916 5613.711954 5047.067609 5194.567863 5497.586143 5167.159596 4425.910396 4785.836821 0.824541217 1.020011661 0.946883917 1.172984404 1.05458414 1.0854043 1.148719931 1.079677346 0.924793419 1 12.22455549 -9.481218969 2.244249495 0.921288885 1.106038304 0.620886338 0.062090565 0.174413538 1.745473632 0.012515833 0.019730459 3.30E-10 9.481218969 0.184749418 DLEDSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 DLEDSLAR 8 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 171.38 0.010675 34772000 4637.3 4677.8 5420.5 3774.7 5153.3 4660.8 4628.7 4571.8 5078.9 5020.4 FALSE FALSE TRUE 4580.778804 4743.654191 5514.841529 4211.148574 4890.307871 4362.989922 5021.861662 4704.07782 4624.630464 4889.969284 0.936770466 0.970078525 1.127786538 0.861180987 1.000069241 0.892232582 1.026972026 0.961985147 0.945738142 1 12.25560969 DLEEWNQR ddPTM_HeLa_Romidepsin_16h_R1 1 DLEEWNQR 8 0 P09497-2;P09497 P09497-2 CLTB Clathrin light chain B 0 0 166.68 0.01908 19517000 3890.2 3442.5 3343.7 3225.6 3516.5 3465 3173.1 3581.5 3735.9 3149.2 FALSE FALSE TRUE 3842.784746 3490.963605 3401.895696 3598.559049 3337.039883 3243.597683 3442.623035 3685.125052 3401.751747 3067.38333 1.252789212 1.138091732 1.109054634 1.173169005 1.08791094 1.057447777 1.122332185 1.201390454 1.109007705 1 11.58279276 -12.6186524 1.447108295 1.000460463 1.153893208 0.151038936 0.062991142 0.311804777 1.178142698 0.045622989 0.010594131 2.41E-13 12.6186524 0.153432744 DLEGENIEIVFAKPPDQK ddPTM_HeLa_Romidepsin_16h_R1 1 DLEGENIEIVFAKPPDQK 18 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 86.005 0.0028672 0 1009.2 883.24 880.23 630.79 701.74 735.43 556.58 646.03 903.31 742.31 FALSE FALSE TRUE 996.8994822 895.6742759 895.5500339 703.7249078 665.9275892 688.4383965 603.8558913 664.7218588 822.5156912 723.0246792 1.378790394 1.238787972 1.238616135 0.973306898 0.921030234 0.952164451 0.835180193 0.919362614 1.137603895 1 9.497901082 -9.138291159 3.877921335 1.192821619 0.908634914 0.691931401 0.093519671 0.165864905 4.38833312 0.022279186 0.03803048 7.27E-10 9.138291159 -0.284186705 DLEGSDIDTR ddPTM_HeLa_Romidepsin_16h_R1 2 DLEGSDIDTR 10 0 P55060-4;P55060-3;P55060 P55060-4 CSE1L Exportin-2 0 0 ; ; 177.3 0.00058061 56073000 9150.8 8670.9 8727.3 8168.6 8248.2 7644.8 6197.6 7446.3 8847.3 8233.8 FALSE FALSE TRUE 9039.26653 8792.969158 8879.194996 9113.091966 7827.263576 7156.321952 6724.023989 7661.746942 8055.97533 8019.884689 1.127106795 1.096395958 1.107147464 1.136312094 0.975982059 0.8923223 0.838419036 0.955343779 1.004500145 1 12.96936578 -8.507825743 3.769854874 1.073078927 0.892302946 0.723116759 0.051022401 0.105813961 3.274286729 0.008813832 0.01968367 3.11E-09 8.507825743 -0.18077598 DLELALS(ph)PIHNSSALPTTGR ddPTM_HeLa_Romidepsin_16h_R1 2 DLELALSPIHNSSALPTTGR 20 0 A0A087WUU7;Q96GX5-2;Q96GX5-3;Q96GX5 A0A087WUU7 MASTL Serine/threonine-protein kinase greatwall 1 0 DLELALS(1)PIHNSSALPTTGR;DLELALS(1)PIHNSSALPTTGR ; 107.75 0.00018218 14232300 2858.73 2729.97 2615.42 2331.24 3577.5 3711.6 2968.9 2998.6 3156.9 3273.5 TRUE FALSE FALSE 2823.886699 2768.402589 2660.940288 2600.788938 3394.926826 3474.440739 3221.078292 3085.35976 2874.538957 3188.453998 0.885660167 0.868258595 0.834555019 0.815689654 1.064756408 1.089694485 1.01023201 0.967666387 0.901546317 1 11.63864135 -8.733780211 24.99999694 0.920837607 1.035498208 0.541589537 0.061785497 196.2660991 177396.1212 0.011289959 0.022575744 1.85E-09 8.733780211 0.114660601 DLELPLS(ph)PSLLGGPGPER ddPTM_HeLa_Romidepsin_16h_R1 1 DLELPLSPSLLGGPGPER 18 0 P19419 P19419 ELK1 ETS domain-containing protein Elk-1 1 0 DLELPLS(0.995)PS(0.005)LLGGPGPER 89.049 0.0069149 2395000 344.86 672.26 411.91 394 414.43 611.58 576.34 708.5 436.09 592.66 TRUE FALSE FALSE 340.6567137 681.7240939 419.0791208 439.5561338 393.2800906 572.5020118 625.2943052 728.9993297 397.0850182 577.2626078 0.590124337 1.180960077 0.725976558 0.76144917 0.681284541 0.991753154 1.083205974 1.262855622 0.687875869 1 9.173083967 -7.760402173 1.976693728 0.814898285 1.235782133 0.448862581 0.166135908 0.30270234 2.156800302 0.027343833 0.161156563 1.74E-08 7.760402173 0.420883849 DLENGSHIR ddPTM_HeLa_Romidepsin_16h_R1 2 DLENGSHIR 9 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 0 ; ; 133.23 0.0032771 3333220 1689.58 1851.49 1995.1 1677.29 1845.72 1740.15 1547.15 1259.96 2002.35 1946.47 FALSE FALSE TRUE 1668.986749 1877.555325 2029.823879 1871.226162 1751.526021 1628.960031 1678.564882 1296.414955 1823.254801 1895.900429 0.880313504 0.990323804 1.070638441 0.986985463 0.923849161 0.859201257 0.885365527 0.683799072 0.961682783 1 10.88866748 -6.518346949 0.864795055 0.95732817 2.16E-19 0.724045036 0.053147903 3.570169108 0.786770304 0.010325257 4.421872757 3.03E-07 6.518346949 -0.95732817 DLEPESDR ddPTM_HeLa_Romidepsin_16h_R1 1 DLEPESDR 8 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 0 126.52 8.70E-05 0 1236.5 1384.4 1186 704.26 1011.5 1232.4 937.99 665.33 1041.5 1299.4 FALSE FALSE TRUE 1221.429062 1403.88962 1206.641832 785.6898548 959.8793806 1153.653617 1017.662847 684.5802738 948.3456315 1265.641401 0.965067247 1.109231745 0.953383661 0.62078394 0.758413386 0.911516972 0.804068867 0.540895923 0.749300419 1 10.30565298 -9.392031032 6.236119996 0.994098788 0.74418199 0.429906744 0.127550091 0.125501455 5.87556726 0.015421582 0.023619937 4.05E-10 9.392031032 -0.249916798 DLESAEERR ddPTM_HeLa_Romidepsin_16h_R1 1 DLESAEERR 9 1 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 0 98.582 0.019307 2777300 879.4 791.31 799.4 1012.9 950.53 971.66 913.95 871.88 1030.1 1070.8 FALSE FALSE TRUE 868.6815345 802.450083 813.3132217 1130.016264 902.0209072 909.5740619 991.5808902 897.1064722 937.9652761 1042.980462 0.832883804 0.769381702 0.779797179 1.08344912 0.864849286 0.87209118 0.950718567 0.860137371 0.899312413 1 10.02649642 -12.40259179 1.184857191 0.998551653 0.87502343 0.05456501 0.089687467 0.571298556 1.460069731 0.056015555 0.014950165 3.96E-13 12.40259179 -0.123528222 DLFDLNS(ph)SEEDDTEGFSER ddPTM_HeLa_Romidepsin_16h_R1 4 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 0 DLFDLNS(0.481)S(0.481)EEDDT(0.038)EGFSER;DLFDLNS(0.5)S(0.5)EEDDTEGFSER;DLFDLNS(0.5)S(0.5)EEDDTEGFSER;DLFDLNS(0.5)S(0.5)EEDDTEGFSER ;;; 332.61 4.57E-211 79733100 11983.2 12494.8 12080.7 11834.78 13931.2 15590.6 12815.8 15197.8 13594 12943 TRUE FALSE FALSE 11837.14415 12670.70212 12290.95952 13203.17295 13220.23888 14594.41098 13904.37373 15637.52436 12378.11859 12606.73899 0.938953694 1.005073725 0.974951534 1.047310724 1.048664439 1.157667418 1.102931832 1.24040994 0.981865223 1 13.62190752 -8.134053625 0.695402188 0.971009664 1.236249587 0.857597172 0.033281365 0.340702 0.214490265 0.006332182 0.05663063 7.34E-09 8.134053625 0.265239922 DLFDLNSSEEDDTEGFSER ddPTM_HeLa_Romidepsin_16h_R1 1 DLFDLNSSEEDDTEGFSER 19 0 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 0 0 249.6 2.01E-61 2886200 882.81 761.03 887.97 743.88 903.91 905.17 719.9 971.65 1072.9 728.35 FALSE FALSE TRUE 872.0499722 771.7438003 903.4247454 829.8909057 857.7800997 847.3325583 781.048288 999.7631597 976.9371369 709.427362 1.229230812 1.087840478 1.273456303 1.169803915 1.209116177 1.194389452 1.100955968 1.409253735 1.377078457 1 9.470511165 -12.83239158 0.469043004 0.896449266 1.212767741 0 0.146656793 1.814713222 0.377252354 0.291620245 0.020706665 1.47E-13 12.83239158 0.316318476 DLFDPIIEDR ddPTM_HeLa_Romidepsin_16h_R1 1 DLFDPIIEDR 10 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 0 0 163.94 0.018448 18893000 1907.8 2061 2074 1675.7 2246 2507.8 2342.7 2499.9 2393.4 1834.1 FALSE FALSE TRUE 1884.547 2090.014812 2110.0971 1869.452318 2131.378239 2347.559674 2541.68888 2572.230662 2179.32831 1786.449818 1.054911804 1.169926405 1.181167855 1.046462263 1.193080387 1.314092145 1.422759741 1.439856097 1.21992137 1 10.80287967 -4.247917477 0.248311762 0.993062182 3.829425729 0.63747146 0.086485237 9.482298368 0.131974946 0.031327408 11.06688802 5.65E-05 4.247917477 2.836363547 DLFNGLDS(ph)EEEKDGEEK ddPTM_HeLa_Romidepsin_16h_R1 1 DLFNGLDSEEEKDGEEK 17 1 Q96S90;Q96S90-2 Q96S90 LYSMD1 LysM and putative peptidoglycan-binding domain-containing protein 1 1 0 DLFNGLDS(1)EEEKDGEEK 65.598 0.014769 14307000 2833.6 3086.4 2967.3 1785.1 2568.3 2658.1 2143.4 3040.7 2851.9 3052.8 TRUE FALSE FALSE 2799.062993 3129.85042 3018.944612 1991.501661 2437.230067 2488.255989 2325.460343 3128.677857 2596.818921 2973.487816 0.941339991 1.052585588 1.015287366 0.669752757 0.819653625 0.836813918 0.782064863 1.052191248 0.873324218 1 11.53794045 -9.30181466 24.99848274 0.981825563 0.828886649 0.34782125 0.098690196 377.4914221 233724.0299 0.013663964 0.020872198 4.99E-10 9.30181466 -0.152938914 DLFPYEESK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 1 DLFPYEESKEK 11 1 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 0 1 DLFPYEESK(1)EK 111.06 0.022187 378120 167.77 0 156.65 61.568 235.64 122.24 186.28 63.939 223.44 278.27 FALSE TRUE FALSE 165.7251547 0 159.3764275 68.68678185 223.6144115 114.4292585 202.1026186 65.78897409 203.4549668 271.0405053 0.611440547 0 0.58801701 0.253418882 0.825022117 0.422185084 0.74565467 0.242727463 0.750644139 1 8.082364659 -11.42928946 0.953845845 0.950618815 0.467050184 0.30126058 0.245525898 0.335250407 0.63011739 0.080407854 0.04758793 3.72E-12 11.42928946 -0.483568631 DLFSLDSEDPSPAS(ph)PPLR ddPTM_HeLa_Romidepsin_16h_R1 6 DLFSLDSEDPSPASPPLR 18 0 H3BTX0;Q9BTK6 H3BTX0 PAGR1 PAXIP1-associated glutamate-rich protein 1 1 0 DLFSLDSEDPS(0.003)PAS(0.997)PPLR;DLFSLDSEDPS(0.002)PAS(0.998)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPSPAS(1)PPLR;DLFSLDSEDPS(0.001)PAS(0.999)PPLR;DLFSLDSEDPS(0.003)PAS(0.997)PPLR ;;;;; 333.65 8.38E-211 148169900 12648.25 12808.45 11910.25 11394.75 10876.62 9798.68 8025.41 9346.63 13425.6 12607.09 TRUE FALSE FALSE 12494.08826 12988.7677 12117.54291 12712.26461 10321.5455 9172.575972 8707.088125 9617.059993 12224.78071 12279.55598 1.017470687 1.057755485 0.986806275 1.035238133 0.840547126 0.74697945 0.709071903 0.783176526 0.995539312 1 13.58397077 -8.59051995 2.980188405 1.012745204 0.744776536 0.953038666 0.027214573 0.03521168 0.631740325 0.003854977 0.008512599 2.57E-09 8.59051995 -0.267968668 DLGGFDEDAEPR ddPTM_HeLa_Romidepsin_16h_R1 1 DLGGFDEDAEPR 12 0 H0Y3T6;G3V1E2;A0A5F9UJX7;A0A5F9UP49;Q9BRK5-4;Q9BRK5-3;Q9BRK5-6;Q9BRK5 H0Y3T6 SDF4 45 kDa calcium-binding protein 0 0 149.23 0.014924 2505300 1402.8 1873.6 1806.8 1256.6 1746.5 1760.4 1316.2 1330.1 1471.5 1611.2 FALSE FALSE TRUE 1385.702134 1899.97659 1838.246596 1401.894004 1657.369588 1647.916121 1427.997995 1368.584345 1339.885355 1569.340792 0.882983569 1.210684512 1.171349528 0.893301195 1.056092849 1.050069004 0.909934925 0.872075939 0.853788649 1 10.61594296 -5.692076664 14.31281738 0.97930717 0.589501844 0 0.122673722 0 0 0.016265161 0 2.03E-06 5.692076664 -0.389805326 DLGGFDEDAEPRR ddPTM_HeLa_Romidepsin_16h_R1 2 DLGGFDEDAEPRR 13 1 H0Y3T6;G3V1E2;A0A5F9UJX7;A0A5F9UP49;Q9BRK5-4;Q9BRK5-3;Q9BRK5-6;Q9BRK5 H0Y3T6 SDF4 45 kDa calcium-binding protein 0 0 ; ; 163.45 0.00017438 10631500 4328.8 4061.5 4297 4438 4575.1 4152.1 3537.6 4329 4550 4779.6 FALSE FALSE TRUE 4276.038921 4118.677904 4371.787482 4951.142441 4341.615575 3886.79421 3838.083656 4454.252785 4143.036604 4655.425303 0.918506612 0.88470497 0.939073704 1.063520972 0.932592683 0.834895623 0.824432443 0.95678751 0.889937296 1 12.18469726 -16.52287875 0.095738746 1.270173764 0.849178372 0 0.070538306 165.7013811 1.191643654 9.193413314 0.67941934 3.00E-17 16.52287875 -0.420995392 DLGHPVEEEDELES(ph)GDQEDEDDESEDPGKDLDHI ddPTM_HeLa_Romidepsin_16h_R1 2 DLGHPVEEEDELESGDQEDEDDESEDPGKDLDHI 34 1 O60763;O60763-2 O60763 USO1 General vesicular transport factor p115 1 0 DLGHPVEEEDELES(0.954)GDQEDEDDES(0.046)EDPGKDLDHI;DLGHPVEEEDELES(1)GDQEDEDDESEDPGKDLDHI ; 120.83 6.33E-16 81898000 6798.5 6581.6 7205.1 7234.5 8903.6 8781 7706.3 8924.4 6709.5 6658.6 TRUE FALSE FALSE 6715.637267 6674.255938 7330.501743 8070.986929 8449.216068 8219.922439 8360.87293 9182.613434 6109.385516 6485.608612 1.035467551 1.029087066 1.130271989 1.244445574 1.302763792 1.267409573 1.289142381 1.415844523 0.941991088 1 12.66302625 -9.314123238 1.139636254 1.013366153 1.325894465 0.919671861 0.042751055 0.077675978 0.199594096 0.006293758 0.012309514 4.85E-10 9.314123238 0.312528313 DLGLS(ph)VLDVS(ph)ARK ddPTM_HeLa_Romidepsin_16h_R1 1 DLGLSVLDVSARK 13 1 Q9Y5F9-2;Q9Y5F9 Q9Y5F9-2 PCDHGB6 Protocadherin gamma-B6 2 0 DLGLS(1)VLDVS(1)ARK 106.42 0.0083755 5542900 1096.5 1244 1390.9 1098 1360.8 1240.8 1285.7 1254.8 1350.5 1310 TRUE FALSE FALSE 1083.135436 1261.513065 1415.108031 1224.955926 1291.353298 1161.516884 1394.907326 1291.105658 1229.707898 1275.966011 0.848874834 0.988672938 1.109048375 0.96002238 1.012059324 0.910303938 1.09321668 1.011865243 0.963746594 1 10.31737418 -10.01462332 24.60172919 0.928116311 1.015119642 0.224531969 0.064559852 617.2693707 1038470.882 0.012324876 0.015397757 9.67E-11 10.01462332 0.08700333 DLGSTEDGDGT(ph)DDFLTDKEDEK ddPTM_HeLa_Romidepsin_16h_R1 3 DLGSTEDGDGTDDFLTDKEDEK 22 1 Q15527 Q15527 SURF2 Surfeit locus protein 2 1 0 DLGSTEDGDGT(0.999)DDFLTDKEDEK;DLGST(0.001)EDGDGT(0.999)DDFLTDKEDEK;DLGSTEDGDGT(0.967)DDFLT(0.032)DKEDEK ;; 125.35 3.45E-05 100355000 10003.8 8618 8318.8 6437.5 9026.5 10409.6 10250.7 11971.4 10488.7 10272.2 TRUE FALSE FALSE 9881.869838 8739.32443 8463.585224 7181.834039 8565.844022 9744.460155 11121.3942 12317.77357 9550.564403 10005.32676 0.98766088 0.873467168 0.845907927 0.717801048 0.856128363 0.973927228 1.111547325 1.231121568 0.954547975 1 13.28848066 -4.947279456 12.53130911 0.968537137 1.082657584 0 0.138044709 0 0 0.019241337 0 1.13E-05 4.947279456 0.114120446 DLGSTEDGDGTDDFLT(ph)DKEDEK ddPTM_HeLa_Romidepsin_16h_R1 2 DLGSTEDGDGTDDFLTDKEDEK 22 1 Q15527 Q15527 SURF2 Surfeit locus protein 2 1 0 DLGSTEDGDGT(0.204)DDFLT(0.796)DKEDEK;DLGSTEDGDGT(0.45)DDFLT(0.55)DKEDEK ; 95.834 0.00021432 132239000 6721.3 6929.8 6995 4144.1 6799.3 8404.3 7202.6 8142.6 6176.2 6867.1 TRUE FALSE FALSE 6639.37821 7027.357906 7116.745041 4623.260341 6452.306349 7867.292354 7814.388664 8378.193284 5623.785203 6688.691752 0.992627326 1.050632645 1.063996564 0.691205472 0.964658948 1.176207941 1.168298518 1.25259073 0.84079001 1 12.70750834 -8.228778409 5.821630324 0.980408956 1.198359741 0.515809749 0.109536393 0.126984041 13.13376507 0.014320598 0.036386765 5.91E-09 8.228778409 0.217950785 DLGTESQIFISR ddPTM_HeLa_Romidepsin_16h_R1 2 DLGTESQIFISR 12 0 P50395-2;P50395 P50395-2 GDI2 Rab GDP dissociation inhibitor beta 0 0 ; ; 174.57 5.78E-05 356090 1095.8 1205.3 1071.623 1235.2 1223.7 1048.3 1111.957 1152.318 1331.8 1087.833 FALSE FALSE TRUE 1082.443968 1222.268245 1090.274149 1378.019636 1161.250023 981.3170132 1206.4066 1185.658503 1212.680472 1059.570942 1.021587065 1.153550175 1.028977019 1.300544948 1.095962504 0.926145645 1.138580299 1.118998697 1.144501444 1 10.04926447 -10.37799413 6.007479549 1.009470792 1.10670982 0 0.099028359 0.278449885 12.805801 0.015180842 0.017283522 4.19E-11 10.37799413 0.097239028 DLHILPPPLIPT(ph)PPPDDPR ddPTM_HeLa_Romidepsin_16h_R1 2 DLHILPPPLIPTPPPDDPR 19 0 Q9NRS6;E9PK26;E9PMW6;Q9NRS6-2 Q9NRS6 SNX15 Sorting nexin-15 1 0 DLHILPPPLIPT(1)PPPDDPR;DLHILPPPLIPT(1)PPPDDPR ; 59.674 0.028579 16022500 3156.3 3425.9 2960.5 3057.2 2842.9 2936.5 2485.95 2695.1 3562.1 3340.9 TRUE FALSE FALSE 3117.829802 3474.12991 3012.026261 3410.687849 2697.816205 2748.867127 2697.106531 2773.078466 3243.496855 3254.102936 0.958122672 1.067615247 0.925608784 1.048119225 0.829050665 0.844738836 0.82883258 0.852179086 0.996740705 1 11.66804417 -8.748717118 24.99999044 0.986738789 0.838426737 0.796864056 0.039432425 75.97020033 149285.0141 0.005354087 0.010652261 1.78E-09 8.748717118 -0.148312052 DLHQGIEAAS(ph)DEEDLR ddPTM_HeLa_Romidepsin_16h_R1 3 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 DLHQGIEAAS(1)DEEDLR;DLHQGIEAAS(1)DEEDLR;DLHQGIEAAS(1)DEEDLR ;; 83.063 0.0087547 25495300 9011.4 8055.66 8092.33 6028.65 8024.8 9191.41 7033.4 7856.8 9426.6 8702.5 TRUE FALSE FALSE 8901.565591 8169.067793 8233.173609 6725.710879 7615.264511 8604.108565 7630.81682 8084.124112 8583.461287 8476.407795 1.05015778 0.963741716 0.971304568 0.793462401 0.898407049 1.015065435 0.900241825 0.953720527 1.012629582 1 13.04923728 -9.859544212 2.354320159 1.023049238 0.916256212 0.390511289 0.055556337 0.209696714 2.373339252 0.0095713 0.013113983 1.38E-10 9.859544212 -0.106793026 DLHQGIEAASDEEDLR ddPTM_HeLa_Romidepsin_16h_R1 2 DLHQGIEAASDEEDLR 16 0 A0A0C4DGG1;Q9UKS6;E9PIY1 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 0 0 ; ; 178.01 1.42E-08 10799900 4605 4662.1 4397.5 3730.7 4354.3 4395.5 3613.7 4023.3 4439 4590.8 FALSE FALSE TRUE 4548.872489 4727.733166 4474.036643 4162.061087 4132.083823 4114.641736 3920.647588 4139.707838 4041.964722 4471.530354 1.017296569 1.057296449 1.000560499 0.930791196 0.924087168 0.920186471 0.876802186 0.925792181 0.903933196 1 12.12655295 -9.210779182 2.937021173 1.012835158 0.911034176 0.490250925 0.039604973 0.074721548 1.281097092 0.00324666 0.00552942 6.15E-10 9.210779182 -0.101800982 DLIDNS(ph)FNR ddPTM_HeLa_Romidepsin_16h_R1 3 DLIDNSFNR 9 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 0 DLIDNS(1)FNR;DLIDNS(1)FNR;DLIDNS(1)FNR ;; 138.63 0.0065524 27277700 5810 5918.1 5916.1 5607.3 6825.3 8861.1 7325.6 7616.3 6405.5 6113 TRUE FALSE FALSE 5739.185485 6001.415167 6019.067239 6255.642409 6476.979472 8294.904308 7947.836281 7836.665624 5832.576037 5954.183379 0.963891288 1.007932538 1.010897189 1.050629786 1.087803156 1.393122076 1.334832298 1.316161281 0.979576151 1 12.53968794 -8.42848507 2.646980025 0.991103766 1.349062594 0.95570865 0.033124043 0.040432346 0.549158909 0.005225288 0.013012449 3.73E-09 8.42848507 0.357958828 DLIHDQDEDEEEEEGQR ddPTM_HeLa_Romidepsin_16h_R1 2 DLIHDQDEDEEEEEGQR 17 0 R4GNE6;F2Z2K0;Q9UNZ2-4;Q9UNZ2;Q9UNZ2-5 R4GNE6 NSFL1C NSFL1 cofactor p47 0 0 ; ; 213.51 6.68E-27 69230000 7157.8 6675.8 6881 6543.2 7764.3 7567.1 7071.8 7285.9 8387.5 6678.7 FALSE FALSE TRUE 7070.55798 6769.782088 7000.760919 7299.755571 7368.058798 7083.586732 7672.478515 7496.706021 7637.300993 6505.186411 1.086910894 1.040674573 1.076181446 1.122143949 1.13264376 1.08891372 1.179440224 1.152419861 1.174032612 1 12.66737468 -4 0.047728899 0.761179019 1.706756254 0 0.058258891 150.8841912 0.550462485 2.695768533 10.765282 1.00E-04 4 0.945577235 DLIHDVSFDFHGR ddPTM_HeLa_Romidepsin_16h_R1 1 DLIHDVSFDFHGR 13 0 K7ENI5;K7EP88;K7ELV2;Q96EE3;Q96EE3-1 K7ENI5 SEH1L Nucleoporin SEH1 0 0 114.87 0.0022252 7520100 2704.9 2852.7 3261.3 2054.3 3778.3 4079.2 2989.1 3194.3 3764 3192 FALSE FALSE TRUE 2671.931638 2892.860385 3318.061558 2291.827832 3585.479252 3818.552285 3242.994079 3286.722031 3427.338413 3109.07138 0.859398615 0.930458015 1.067219486 0.737142237 1.153231565 1.228197046 1.043074823 1.057139457 1.102367233 1 11.60226802 -8.717984824 24.9999973 0.930652132 1.122585996 0.365354422 0.108704788 92.19762149 53042.11915 0.01401145 0.028022767 1.91E-09 8.717984824 0.191933864 DLINLAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DLINLAKK 8 1 M0R0P1;M0R299;M0QXL5;M0R2Q4;P22087 M0R0P1 FBL rRNA 2-O-methyltransferase fibrillarin 0 1 ; DLINLAK(1)K;DLINLAK(1)K 100.02 0.0064926 820000 648.79 465.03 1020.2 778.67 1108.85 1217.7 980.19 513.53 394.06 330.32 FALSE TRUE FALSE 640.8822979 471.5767045 1037.956153 868.7034892 1052.261247 1139.8929 1063.447314 528.3881803 358.8142867 321.7382388 1.991936987 1.465715441 3.226088876 2.700031841 3.270550777 3.542920183 3.30531838 1.642292139 1.115236684 1 8.329743601 -10.36174645 0.597916148 1.18176536 3.057909819 0.582029898 0.60735669 0.351899052 0.282689627 0.200387187 0.220192121 4.35E-11 10.36174645 1.876144459 DLISHDEMFSDIYK ddPTM_HeLa_Romidepsin_16h_R1 1 DLISHDEMFSDIYK 14 0 A0A0B4J2C3;Q5W0H4;P13693 A0A0B4J2C3 TPT1 Translationally-controlled tumor protein 0 0 113.76 0.020421 36972000 6946.9 4243.7 5257.5 4645.7 6119.9 5330.3 5887.5 5093.8 6395.9 5972.4 FALSE FALSE TRUE 6862.228511 4303.44292 5349.004582 5182.857693 5807.578667 4989.711033 6387.584103 5241.181066 5823.834685 5817.236187 1.179637252 0.739774488 0.919509611 0.890948472 0.998339844 0.857745994 1.098044483 0.900974431 1.001134301 1 12.50611817 -10.28244886 24.97668495 1.084828699 0.922330765 0.298803521 0.099392623 663.6907495 789012.3575 0.017930839 0.020515652 5.22E-11 10.28244886 -0.162497935 DLISLDSS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 DLISLDSSPAK 11 0 Q9UN79 Q9UN79 SOX13 Transcription factor SOX-13 1 0 DLISLDS(0.016)S(0.984)PAK 202.31 3.94E-13 4552200 3888.4 4088.7 4624.3 2605.8 2613.7 2434.5 1696.9 1790.4 4142.1 4114.9 TRUE FALSE FALSE 3841.006685 4146.260826 4704.784002 2907.094857 2480.313136 2278.943307 1841.034644 1842.202399 3771.620202 4007.994305 0.958336363 1.034497684 1.173849972 0.725324099 0.618841482 0.568599437 0.459340634 0.45963199 0.941024342 1 11.96866474 -8.915807024 2.365156326 0.997512698 0.511960924 0.896874262 0.078869439 0.06626524 0.750960854 0.012066143 0.023852756 1.21E-09 8.915807024 -0.485551774 DLISNS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 DLISNSPR 8 0 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 1 0 DLIS(0.002)NS(0.998)PR;DLIS(0.019)NS(0.981)PR ; 125.68 0.014844 25867000 4194.2 4292.9 4277.1 4174.8 6500.7 8398.1 6523.5 7982.7 5282 4677.2 TRUE FALSE FALSE 4143.079477 4353.335559 4351.541131 4657.510019 6168.945022 7861.488514 7077.605927 8213.66683 4809.564691 4555.68567 0.909430496 0.955582952 0.955189064 1.022351048 1.354119987 1.725643313 1.553576441 1.802948541 1.05572795 1 12.15345249 -8.575098662 2.109144564 0.955521805 1.688303215 0.952321697 0.071555374 0.039180493 0.348755701 0.009398213 0.022875585 2.66E-09 8.575098662 0.73278141 DLIVATIAVK ddPTM_HeLa_Romidepsin_16h_R1 1 DLIVATIAVK 10 0 P31939-2;P31939;H7C1S2 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 0 133.57 0.015652 146700 158.57 170.1 322.03 150.24 226.4 358.13 139.74 151.69 65.76 156.41 FALSE FALSE TRUE 156.6372878 172.4946723 327.6347971 167.6114557 214.8459632 335.2466488 151.6095121 156.0789108 59.8782609 152.3464457 1.02816503 1.132252686 2.150590358 1.100199319 1.410245984 2.200554449 0.995162778 1.024499851 0.393040091 1 7.251212031 -9.980609268 24.99931171 1.016821575 1.484698519 0.287747738 0.441609273 253.9453894 327395.9251 0.06138522 0.080670095 1.05E-10 9.980609268 0.467876943 DLK(ac)DYFTK ddPTM_HeLa_Romidepsin_16h_R1 1 DLKDYFTK 8 1 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 1 DLK(1)DYFTK 87.258 0.021246 0 0 0 0 0 0 0 66.528 0 177.66 0 FALSE TRUE FALSE 0 0 0 0 0 0 72.17888666 0 161.7696446 0 0 DLLHNEDR ddPTM_HeLa_Romidepsin_16h_R1 2 DLLHNEDR 8 0 F5H669;Q8N684-2;Q8N684;Q8N684-3 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 0 0 ; ; 84.615 0.003502 1974900 4971.2 5193.5 4935.1 2181.1 4336.2 4487.8 4049.3 3827.5 5439.1 5481 FALSE FALSE TRUE 4910.609102 5266.614229 5020.993345 2433.289044 4114.907533 4201.044064 4393.247441 3938.242674 4952.613274 5338.60283 0.919830386 0.986515461 0.940507003 0.45579136 0.770783605 0.786918263 0.822920824 0.737691639 0.927698394 1 12.38224651 -9.483544737 24.98129622 0.962940888 0.724961855 0.606761846 0.096529104 274.7528957 174497.6871 0.014646175 0.022370023 3.28E-10 9.483544737 -0.237979033 DLLHPS(ph)PEEEK ddPTM_HeLa_Romidepsin_16h_R1 3 DLLHPSPEEEK 11 0 P42677 P42677 RPS27 40S ribosomal protein S27 1 0 DLLHPS(1)PEEEK;DLLHPS(1)PEEEK;DLLHPS(1)PEEEK ;; 151.16 0.0023209 61743000 16864 16882.7 18401.5 9563.8 15530.8 16054.5 12723.2 15586.8 17919.6 18051.1 TRUE FALSE FALSE 16658.45508 17120.37509 18721.77039 10669.61156 14738.20532 15028.66926 13803.90829 16037.77947 16316.8261 17582.12982 0.947465139 0.97373727 1.064818118 0.606844089 0.838249147 0.854769554 0.785110134 0.912163636 0.928034673 1 14.10182222 -9.287685176 24.98573331 0.980540362 0.803863202 0.559667468 0.081270907 405.5657363 386093.2697 0.011661994 0.017817503 5.16E-10 9.287685176 -0.17667716 DLLSDLQDIS(ph)DSER ddPTM_HeLa_Romidepsin_16h_R1 5 DLLSDLQDISDSER 14 0 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;E7ESP2;J3KS35;Q9UQ88-9 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 DLLSDLQDIS(0.997)DS(0.003)ER;DLLSDLQDIS(1)DSER;DLLSDLQDIS(0.976)DS(0.024)ER;DLLSDLQDIS(0.79)DS(0.21)ER;DLLSDLQDIS(0.978)DS(0.022)ER ;;;; 312.38 5.25E-152 216908100 10430.11 10753.89 10330.13 8239.8 10121.3 9978.84 9762.05 10404.84 11438.47 10961.09 TRUE FALSE FALSE 10302.98381 10905.28355 10509.92158 9192.524445 9604.772293 9341.224329 10591.23828 10705.88763 10415.3846 10676.3193 0.965031442 1.021445991 0.984414318 0.86102 0.899633293 0.87494801 0.992030866 1.002769524 0.975559488 1 13.38212674 -9.466179546 24.9818479 0.986684886 0.925162535 0.335032481 0.044452218 277.3853717 122216.9474 0.007197024 0.010993612 3.42E-10 9.466179546 -0.061522351 DLLSDLQDIS(ph)DSERK ddPTM_HeLa_Romidepsin_16h_R1 1 DLLSDLQDISDSERK 15 1 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;E7ESP2;J3KS35;Q9UQ88-9 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 DLLS(0.001)DLQDIS(0.795)DS(0.204)ERK 62.617 0.021621 7393600 1518.6 1433.9 1368.3 1161.4 1426.1 1420.7 1292.1 1760.2 1867.1 1731.7 TRUE FALSE FALSE 1500.090719 1454.086482 1392.114688 1295.686533 1353.320795 1329.921855 1401.850942 1811.12861 1700.1019 1686.710184 0.889358903 0.862084367 0.825343145 0.768173777 0.802343407 0.788470875 0.831115478 1.073763962 1.007939547 1 10.71999639 -11.33179586 0.715222058 0.990986423 0.84115483 0.34632505 0.081163149 0.518372167 0.567777647 0.035925243 0.019358659 4.66E-12 11.33179586 -0.149831593 DLLSDLQDISDS(ph)ER ddPTM_HeLa_Romidepsin_16h_R1 1 DLLSDLQDISDSER 14 0 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;E7ESP2;J3KS35;Q9UQ88-9 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 DLLSDLQDIS(0.178)DS(0.822)ER 167.29 8.35E-05 8650700 2063.1 1929.5 1809.9 1508.5 1642 1692.7 1620.5 1852.5 1580.1 2012.3 TRUE FALSE FALSE 2037.954144 1956.663552 1841.40055 1682.919868 1558.202613 1584.541933 1758.14523 1906.099165 1438.771899 1960.020156 1.03976183 0.998287464 0.939480415 0.858623756 0.794993158 0.808431448 0.897003648 0.972489573 0.734059746 1 10.93665278 -9.558226394 2.356179806 1.018484319 0.86105889 0 0.101413239 0.127853976 1.433234049 0.008174583 0.01245603 2.77E-10 9.558226394 -0.157425429 DLMVGDEASELR ddPTM_HeLa_Romidepsin_16h_R1 2 DLMVGDEASELR 12 0 P61160 P61160 ACTR2 Actin-related protein 2 0 0 ; ; 136.49 0.006309 18467100 2564 2337.93 2001.03 2124.45 2221.51 2426.01 2220.88 2087.12 2639.12 2680.8 FALSE FALSE TRUE 2532.748982 2370.84344 2035.857088 2370.088905 2108.138055 2270.995791 2409.521492 2147.507524 2403.070497 2611.15243 0.969973623 0.907968226 0.779677611 0.90767926 0.807359245 0.869729306 0.922780863 0.822436676 0.920310308 1 11.35047096 -10.16296897 2.957050275 0.986714623 0.855599716 0.51465346 0.046782944 0.10735582 1.802936758 0.006800718 0.008359255 6.87E-11 10.16296897 -0.131114906 DLNESPVKS(ph)FVSISEATDCLVDFKK ddPTM_HeLa_Romidepsin_16h_R1 1 DLNESPVKSFVSISEATDCLVDFKK 25 2 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 0 DLNES(0.037)PVKS(0.673)FVS(0.143)IS(0.143)EAT(0.005)DCLVDFKK 75.3 0.00015196 2044100 1428.6 1249.4 1021.7 504.21 1006.3 716.66 623.41 835.96 1626.9 1051.8 TRUE FALSE FALSE 1411.187674 1266.989086 1039.48226 562.5091326 954.944756 670.8677389 676.3624298 860.1471837 1481.385989 1024.474084 1.377475229 1.236721461 1.014649639 0.54907112 0.932131686 0.654841103 0.660204529 0.839598772 1.445996548 1 10.00066777 -9.482325452 4.664064603 1.186060788 0.731891971 0.721592659 0.154514726 0.102488955 5.130288985 0.02612804 0.039518907 3.29E-10 9.482325452 -0.454168817 DLPDGHAAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 DLPDGHAASPR 11 0 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 0 DLPDGHAAS(1)PR;DLPDGHAAS(1)PR ; 141.34 0.0029146 13860000 772.44 798.71 1070.34 1919.89 4780.2 6265.5 5959.8 7387.8 1085.83 1187.77 TRUE FALSE FALSE 763.0252042 809.9542603 1088.968819 2141.876715 4536.248557 5865.154771 6466.025263 7601.554337 988.7106453 1156.911564 0.659536327 0.70010041 0.941272308 1.851374627 3.920998542 5.06966561 5.58904022 6.57055783 0.854612121 1 10.17606287 -8.554523821 1.209153414 0.798646912 6.164136228 0.987598406 0.245763791 0.037489263 0.104827673 0.041906007 0.138674984 2.79E-09 8.554523821 5.365489316 up DLPEHAVLK ddPTM_HeLa_Romidepsin_16h_R1 2 DLPEHAVLK 9 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PQ74 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 104.01 0.01155 10336800 12658.1 11847.1 12941.1 13555.2 13701.1 12636.2 11334.5 9494.1 12219 10796.2 FALSE FALSE TRUE 12503.81821 12013.88378 13166.33442 15122.516 13001.88174 11828.7876 12297.25215 9768.796804 11126.10204 10515.71317 1.18906041 1.142469711 1.252062909 1.438087533 1.236424152 1.124867844 1.169416848 0.928971402 1.058045409 1 13.36025908 -12.00578542 0.764401202 0.997374532 1.194427731 0.204016986 0.120733076 0.768191828 0.807140309 0.088252314 0.025877889 9.87E-13 12.00578542 0.197053199 DLPEHAVLK(ac)MK ddPTM_HeLa_Romidepsin_16h_R1 2 DLPEHAVLKMK 11 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PQ74 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 1 ; DLPEHAVLK(1)MK;DLPEHAVLK(1)MK 120.09 0.0010721 5906700 5845.1 4761.5 5150.4 5222.4 5765.2 5809.1 5173 5630.3 6010.9 5153.9 FALSE TRUE FALSE 5773.857673 4828.532522 5240.040552 5826.23846 5470.980331 5437.917258 5612.394491 5793.203847 5473.270049 5020.000935 1.150170637 0.961858889 1.043832585 1.160605055 1.089836516 1.083250248 1.118006662 1.154024456 1.090292635 1 12.29347192 -9.279466349 24.52501929 1.060954654 1.117125684 0.304367825 0.052719837 970.7676309 1320689.405 0.010374598 0.015871932 5.25E-10 9.279466349 0.05617103 DLPETIPWNPT(ph)PSMGGPGTPDSRPPFLSR ddPTM_HeLa_Romidepsin_16h_R1 1 DLPETIPWNPTPSMGGPGTPDSRPPFLSR 29 1 Q16512;Q16512-2;Q16512-3 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 DLPETIPWNPT(0.323)PS(0.323)MGGPGT(0.323)PDS(0.028)RPPFLS(0.003)R 54.152 0.0040443 7349800 739.97 484.44 593.01 714.56 780.55 734.03 726.59 789.91 650.78 982.82 TRUE FALSE FALSE 730.950961 491.259959 603.3310903 797.1807893 740.7156209 687.127852 788.3065365 812.7647996 592.5726069 957.2861947 0.76356576 0.513179822 0.630251531 0.832750742 0.773766116 0.717787278 0.823480523 0.849030106 0.619013008 1 9.902806494 -11.81179046 0.939954529 0.984466421 0.737839662 0 0.149907207 0.346675621 0.603893248 0.048988796 0.021040198 1.54E-12 11.81179046 -0.246626759 DLPEWEPR ddPTM_HeLa_Romidepsin_16h_R1 4 DLPEWEPR 8 0 O94964-2;H0YDM2;O94964;X6R3R3;O94964-4 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 0 0 ;;; ;;; 98.299 0.0017891 13512700 14747.6 13903.4 13506.3 14467.5 12331 11484.3 9946.8 9162.4 14802.1 13935.2 FALSE FALSE TRUE 14567.85058 14099.13243 13741.37149 16140.30042 11701.70306 10750.49029 10791.68094 9427.499588 13478.1631 13573.1615 1.073283522 1.038750805 1.012392838 1.189133455 0.862120668 0.792040255 0.795074968 0.694569175 0.993001012 1 13.72846918 -8.568906046 5.965578695 1.043538213 0.773263128 0.834532155 0.058972436 0.054589988 4.616745597 0.008489106 0.017281206 2.70E-09 8.568906046 -0.270275085 DLPPFGINS(ph)PQALKK ddPTM_HeLa_Romidepsin_16h_R1 2 DLPPFGINSPQALKK 15 1 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8;H0Y8H7 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 0 DLPPFGINS(1)PQALKK;DLPPFGINS(1)PQALKK ; 101.54 0.0021861 60184000 7073.6 7043.9 6925 6776.8 6135.5 6299.7 4692.2 5441 7337.6 6909.9 TRUE FALSE FALSE 6987.384242 7143.064209 7045.52672 7560.365502 5822.38254 5897.169501 5090.755351 5598.426751 6681.306679 6730.379802 1.038185726 1.06131666 1.046824537 1.123319296 0.865089744 0.876201593 0.756384558 0.831814387 0.992708714 1 12.7164722 -8.625647109 5.777250328 1.030816934 0.823741531 0.84420991 0.044511161 0.062260137 3.005586749 0.006693142 0.01352347 2.37E-09 8.625647109 -0.207075403 DLPS(ph)PLPTK ddPTM_HeLa_Romidepsin_16h_R1 2 DLPSPLPTK 9 0 H7C4E7;Q9Y534 H7C4E7 CSDC2 Cold shock domain-containing protein C2 1 0 DLPS(0.983)PLPT(0.017)K;DLPS(0.989)PLPT(0.011)K ; 126.66 0.0099882 41858000 12733.6 12450.3 14258.3 12350.1 16716.2 14915 12664.3 13851.2 13390.3 13111.8 TRUE FALSE FALSE 12578.39799 12625.57565 14506.45973 13778.07667 15863.10994 13961.97964 13740.00533 14251.96262 12192.63803 12771.15355 0.984906958 0.988601038 1.135877012 1.078843553 1.242104707 1.093243424 1.075862511 1.115949516 0.954701389 1 13.64060122 -9.763744541 24.99851961 0.992353201 1.123440753 0.694270692 0.045827997 25.64532766 278113.5395 0.00689869 0.009311347 1.72E-10 9.763744541 0.131087552 DLPTIPGVTS(ph)PSSDEPPMEASQSHLR ddPTM_HeLa_Romidepsin_16h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLR 26 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 0 DLPTIPGVT(0.07)S(0.717)PS(0.159)S(0.053)DEPPMEASQS(0.001)HLR 63.111 0.00060974 0 1945.2 1670.2 1762.1 877.48 3101.6 2974.3 2661.1 2632.9 2531.2 2471.9 TRUE FALSE FALSE 1921.491154 1693.713119 1792.768611 978.9383663 2943.313778 2784.251829 2887.133768 2709.078807 2304.803132 2407.679682 0.798067604 0.703462812 0.744604286 0.406589952 1.222469002 1.156404588 1.199135329 1.125182402 0.957271497 1 11.23342775 DLPTIPGVTSPSSDEPPMEAS(ph)QSHLRNSPEDK ddPTM_HeLa_Romidepsin_16h_R1 1 DLPTIPGVTSPSSDEPPMEASQSHLRNSPEDK 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 0 DLPT(0.001)IPGVT(0.023)S(0.023)PS(0.055)S(0.055)DEPPMEAS(0.53)QS(0.176)HLRNS(0.138)PEDK 46.771 0.0076954 7958400 993.04 1175.3 1221 1159.4 2199.2 2236.4 1701 1787.2 1900 1720.1 TRUE FALSE FALSE 980.9364465 1191.845904 1242.250993 1293.455283 2086.966618 2093.501258 1845.482898 1838.909812 1730.059241 1675.411554 0.585489842 0.711375006 0.741460204 0.77202242 1.24564416 1.249544479 1.101510189 1.097586923 1.032617471 1 10.71029981 -8.766758288 24.99593185 0.784713003 1.173850871 0.643492925 0.132980647 71.67598406 336839.2784 0.024323284 0.045044196 1.71E-09 8.766758288 0.389137869 DLQAALTPGALTAAAAGTGT(ph)QGPR ddPTM_HeLa_Romidepsin_16h_R1 2 DLQAALTPGALTAAAAGTGTQGPR 24 0 P55042 P55042 RRAD GTP-binding protein RAD 1 0 DLQAALTPGALT(0.011)AAAAGT(0.006)GT(0.983)QGPR;DLQAALTPGALTAAAAGT(0.002)GT(0.998)QGPR ; 74.296 0.0015822 30706800 5392.6 5391.4 5721.1 5470.18 5864.2 5895.7 5761.4 5874.3 6307.5 5816.1 TRUE FALSE FALSE 5326.872917 5467.300271 5820.673346 6102.66795 5564.927992 5518.983798 6250.773172 6044.263602 5743.341403 5664.996884 0.940313477 0.965102079 1.027480414 1.077258836 0.982335579 0.97422539 1.103402756 1.066949149 1.013829578 1 12.46785945 -9.708259205 5.291147794 0.970497477 1.038528094 0.313881513 0.041885115 0.168384612 9.988878558 0.006998444 0.009859502 1.96E-10 9.708259205 0.068030617 DLQAMDRAHRIGQK ddPTM_HeLa_Romidepsin_16h_R1 1 DLQAMDRAHRIGQK 14 2 A0A0A0MTH9;O14981;O14981-2 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 0 70.808 0.0033925 0 1160.7 1086.8 769.33 1189.5 977.42 1024.6 583.28 1007.6 1052.7 1155.3 FALSE FALSE TRUE 1146.552942 1102.099999 782.7198659 1327.035587 927.5386101 959.1313667 632.8237886 1036.753316 958.5438755 1125.285139 1.018899923 0.979396208 0.695574693 1.179288289 0.824269847 0.852345182 0.562367498 0.921324987 0.8518231 1 10.1360749 -8.543193366 24.30936231 0.991630143 0.770591252 0.210303976 0.1470154 130.7994178 156519.7216 0.0188222 0.037648351 2.86E-09 8.543193366 -0.221038891 DLQELGDSDKYFIEDGR ddPTM_HeLa_Romidepsin_16h_R1 1 DLQELGDSDKYFIEDGR 17 1 P32004-3;P32004-2;P32004;H0Y5C3 P32004-3 L1CAM Neural cell adhesion molecule L1 0 0 92.8 0.0022326 0 929.03 1142.7 1130 900.32 1076.4 925.46 764.94 927 952.81 984.3 FALSE FALSE TRUE 917.706625 1158.786961 1149.667176 1004.419235 1021.467291 866.3260928 829.9139845 953.8212824 867.5882872 958.7277441 0.957212963 1.208671563 1.199159181 1.047658463 1.065440421 0.903620551 0.865640939 0.99488232 0.904937082 1 9.904977372 -8.251468705 24.151809 1.024002143 0.915807223 0.243493872 0.097565859 598.5170395 1449771.554 0.014974259 0.037633454 5.60E-09 8.251468705 -0.10819492 DLQEQDADAGS(ph)ER ddPTM_HeLa_Romidepsin_16h_R1 2 DLQEQDADAGSER 13 0 Q6P158;A0A087WW12;A0A087WZ11;Q6P158-3;Q6P158-2 Q6P158 DHX57 Putative ATP-dependent RNA helicase DHX57 1 0 DLQEQDADAGS(1)ER;DLQEQDADAGS(1)ER ; 276.75 2.36E-94 172699000 6866.1 5693.2 6498.7 4166.8 5950.5 6698.9 5424.2 6268.5 6741.7 6191.9 TRUE FALSE FALSE 6782.413332 5773.349019 6611.807147 4648.585021 5646.823781 6270.86191 5884.931413 6449.869157 6138.705467 6031.033545 1.124585576 0.957273571 1.096297525 0.77077751 0.93629454 1.039765716 0.975774943 1.069446739 1.01785298 1 12.55818954 DLQGRDEQSEEK ddPTM_HeLa_Romidepsin_16h_R1 1 DLQGRDEQSEEK 12 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 115.57 0.001492 0 1737.3 1535.1 1453.9 2822.6 1580.5 1619.2 1475.7 1106.7 1833 1662.6 FALSE FALSE TRUE 1716.125119 1556.711178 1479.20452 3148.962293 1499.841187 1515.738346 1601.045921 1138.720618 1669.051889 1619.405412 1.059725444 0.961285646 0.913424463 1.94451758 0.926167824 0.935984488 0.98866282 0.703172047 1.030657225 1 10.66124849 -7.103297354 1.32184558 1.072212699 0.450066298 0.144319731 0.289861746 3.131166572 3.606355787 0.041432762 2.876512521 7.88E-08 7.103297354 -0.622146401 DLQNVNITLR ddPTM_HeLa_Romidepsin_16h_R1 2 DLQNVNITLR 10 0 P35232;C9JZ20;E7ESE2;E9PCW0;C9JW96;P35232-2;D6RBK0 P35232 PHB Prohibitin 0 0 ; ; 126.39 0.023348 2911300 657.07 609.24 641.11 555.08 569.45 699.25 720.39 611.39 677.3 479.58 FALSE FALSE TRUE 649.0613781 617.8168967 652.2682506 619.2609613 540.3888416 654.5701817 781.5799086 629.079605 616.7205917 467.1204425 1.389494698 1.322607278 1.396359892 1.325698696 1.156851194 1.40128781 1.673187122 1.346718208 1.320260335 1 8.867650773 -14.97301573 0.243372949 3.18E-14 1.433298802 0.085240034 0.157164967 12.06311533 0.306476625 5.975038953 0.086138839 1.06E-15 14.97301573 1.433298802 DLQS(ph)PDFTTGFHSDKIEAK ddPTM_HeLa_Romidepsin_16h_R1 1 DLQSPDFTTGFHSDKIEAK 19 1 E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 0 DLQS(1)PDFTTGFHSDKIEAK 126.51 0.00028573 45465000 4585.8 4258.4 4166.4 4838 3772.8 3114.9 2892.8 3168.8 5141 4528.5 TRUE FALSE FALSE 4529.906506 4318.349867 4238.914444 5397.392323 3580.259938 2915.867943 3138.51436 3260.484228 4681.176084 4410.848917 1.02699199 0.979029196 0.961020095 1.223662933 0.811694076 0.661067291 0.71154429 0.739196533 1.06128688 1 12.10684063 -8.555288318 9.468074957 1.01918121 0.709851977 0.819817502 0.072292101 0.0916593 25.52046814 0.009577933 0.019232702 2.78E-09 8.555288318 -0.309329232 DLQSPDFTT(ph)GFHSDK ddPTM_HeLa_Romidepsin_16h_R1 1 DLQSPDFTTGFHSDK 15 0 E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 0 DLQS(0.081)PDFT(0.329)T(0.589)GFHS(0.001)DK 101.2 0.015445 4279600 1643.3 1747.5 1734.6 1065.5 1549.7 1195.2 927.77 981.94 2165.7 1994.1 TRUE FALSE FALSE 1623.270828 1772.101351 1764.789985 1188.698123 1470.613026 1118.830577 1006.574761 1010.350885 1971.994368 1942.292995 0.835749721 0.912375916 0.908611621 0.612007625 0.75715303 0.576035943 0.518240432 0.52018459 1.015291912 1 10.92354513 -7.137958525 0.246482697 0.995578167 3.16E-14 0.854072446 0.070976614 3.004642641 0.139606227 0.051947266 0.924611385 7.28E-08 7.137958525 -0.995578167 DLRS(ph)PLTATPTFVTDSESTR ddPTM_HeLa_Romidepsin_16h_R1 2 DLRSPLTATPTFVTDSESTR 20 1 A0A087WUK4;P13056-2;P13056-3;P13056 A0A087WUK4 NR2C1 Nuclear receptor subfamily 2 group C member 1 1 0 DLRS(0.918)PLT(0.07)AT(0.012)PTFVTDSESTR;DLRS(0.985)PLT(0.013)AT(0.002)PTFVTDSESTR ; 85.013 0.0010926 5044200 1327.46 1248.32 947.38 1278.06 918.27 1103.24 896.94 1356.05 1290.95 1035.43 TRUE FALSE FALSE 1311.280407 1265.893882 963.8687515 1425.835311 871.4072554 1032.746525 973.1260612 1395.285167 1175.484199 1008.529379 1.300190588 1.255187908 0.955717078 1.413776673 0.864037551 1.024012335 0.964896096 1.3834849 1.165542842 1 9.978037396 -8.732786684 24.9999867 1.156008141 1.049871748 0.091547272 0.177577496 495.2470356 432109.6655 0.026909875 0.053811999 1.85E-09 8.732786684 -0.106136393 DLS(ph)ADT(ph)EY(ph)QISVS(ph)AMK ddPTM_HeLa_Romidepsin_16h_R1 1 DLSADTEYQISVSAMK 16 0 D6RGG3;Q99715-4;Q99715 D6RGG3 COL12A1 Collagen alpha-1(XII) chain 4 0 DLS(0.984)ADT(0.984)EY(0.98)QIS(0.076)VS(0.977)AMK 53.211 0.02489 2146400 1145.6 1269.1 1067.1 1274.4 904.28 1130.4 950.09 1145.8 1049.5 1347.8 TRUE FALSE FALSE 1131.636987 1286.966423 1085.672428 1421.752124 858.1312173 1058.171088 1030.790621 1178.951915 955.6300915 1312.783962 0.862013111 0.980333749 0.82700007 1.083005404 0.653672837 0.8060512 0.785194404 0.898054783 0.727941626 1 10.3584138 -8.758626603 24.99999992 0.937387236 0.787154689 0.230175176 0.109169917 57.10058104 507500.7313 0.012820297 0.024755356 1.74E-09 8.758626603 -0.150232547 DLS(ph)LEEIQK ddPTM_HeLa_Romidepsin_16h_R1 3 DLSLEEIQK 9 0 P16949;P16949-2;A2A2D0;E5RGX5;Q93045;Q93045-2 P16949 STMN1;STMN2 Stathmin;Stathmin-2 1 0 DLS(1)LEEIQK;DLS(1)LEEIQK;DLS(1)LEEIQK ;; 138.76 0.006541 46108000 8131.3 7083.3 7627.5 7279.4 7127.2 6783 6329 6866.8 8300.1 6991.1 TRUE FALSE FALSE 8032.192588 7183.018883 7760.253438 8121.078479 6763.472389 6349.588191 6866.585102 7065.480024 7557.718268 6809.470214 1.179562042 1.054857229 1.139626607 1.192615317 0.993245021 0.932464346 1.008387567 1.037596142 1.109883446 1 12.73332684 -8.633296158 12.72692545 1.095572804 0.989132906 0.480229745 0.059447538 0.474946005 51.91889464 0.011423055 0.022848217 2.33E-09 8.633296158 -0.106439898 DLS(ph)PEPAPDEGPR ddPTM_HeLa_Romidepsin_16h_R1 2 DLSPEPAPDEGPR 13 0 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 0 DLS(1)PEPAPDEGPR;DLS(1)PEPAPDEGPR ; 161.87 0.00035619 24291000 2598.6 2485.9 2983.8 2537 4883.5 6179.4 5430.1 6379.6 3113.5 2602.9 TRUE FALSE FALSE 2566.927264 2520.896565 3035.731787 2830.339877 4634.276772 5784.556283 5891.332558 6564.183661 2835.020762 2535.276283 1.012484233 0.994328146 1.197396831 1.116383211 1.82791785 2.281627577 2.323743806 2.589139379 1.118229513 1 11.30792726 -8.528970388 1.419679294 1.009841968 2.479658876 0.97702849 0.092065718 0.033944662 0.133000182 0.011919798 0.036194866 2.96E-09 8.528970388 1.469816908 up DLS(ph)PEPAPDEGPRR ddPTM_HeLa_Romidepsin_16h_R1 1 DLSPEPAPDEGPRR 14 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 0 DLS(1)PEPAPDEGPRR 96.247 0.0039871 23427000 1821.6 1764.2 1939.6 2077.9 3274.7 3383.7 3255.6 3720.4 1995.1 1787.7 TRUE FALSE FALSE 1799.397639 1789.036454 1973.357924 2318.156575 3107.579839 3167.49249 3532.130583 3828.043904 1816.653259 1741.255296 1.03339105 1.027440639 1.133296151 1.331313438 1.784677896 1.819085632 2.028496677 2.198439202 1.043300924 1 10.76591203 -8.653726899 0.930060172 1.007418976 2.146210639 0.979620986 0.063465085 0.053541434 0.085399222 0.010216173 0.037551555 2.22E-09 8.653726899 1.138791663 up DLS(ph)PTLIDNSAAK ddPTM_HeLa_Romidepsin_16h_R1 3 DLSPTLIDNSAAK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 DLS(0.997)PT(0.003)LIDNSAAK;DLS(0.997)PT(0.003)LIDNSAAK;DLS(1)PTLIDNSAAK ;; 222.56 2.14E-31 144622000 10952.4 9988.5 10739.2 7729.3 12751.5 11094.5 10424.5 11661.6 10250.4 10911.3 TRUE FALSE FALSE 10818.90794 10129.11837 10926.11127 8622.998033 12100.74337 10385.59726 11309.95677 11999.01 9333.578551 10627.82285 1.017979702 0.953075574 1.028066747 0.811360723 1.138590993 0.977208352 1.064183787 1.12901863 0.878221126 1 13.37555847 -7.160637139 1.165082431 0.997896225 1.217031744 0.22464669 0.085471303 2.064232387 1.960576053 0.010379357 0.578885387 6.91E-08 7.160637139 0.219135519 DLS(ph)TPGLEK ddPTM_HeLa_Romidepsin_16h_R1 3 DLSTPGLEK 9 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DLS(0.5)T(0.5)PGLEK;DLS(0.713)T(0.287)PGLEK;DLS(0.5)T(0.5)PGLEK ;; 149.33 0.0053851 93091000 34739.2 36397 31742.4 29967.1 28068.1 24201.9 18517 24092.1 30926.2 30552.9 TRUE FALSE FALSE 34315.78527 36909.39792 32294.86316 33432.0371 26635.68012 22655.4767 20089.83352 24789.1669 28160.08322 29759.13125 1.153117844 1.240271351 1.085208533 1.123421138 0.895042261 0.761294962 0.675081317 0.832993635 0.946266979 1 14.86104479 -8.543859807 2.778650647 1.092445668 0.749377251 0.764309771 0.084054016 0.096552878 1.50474427 0.012801895 0.029444986 2.86E-09 8.543859807 -0.343068416 DLSELGS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 DLSELGSVR 9 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 DLSELGS(1)VR 119.27 0.013884 3483900 1717.8 1941.8 1814.1 1503.6 1735 1783.8 1853 1744.9 2459.3 1549.6 TRUE FALSE FALSE 1696.862793 1969.136711 1845.67365 1677.453307 1646.456476 1669.820937 2010.393774 1795.385929 2239.334049 1509.341169 1.124240714 1.304633275 1.222833967 1.111381139 1.090844476 1.106324383 1.331967759 1.189516304 1.483650016 1 10.55970323 -11.27564448 0.907642624 1.017083165 1.188397535 0 0.166726385 0.35544955 0.617128246 0.028364989 0.018226694 5.30E-12 11.27564448 0.17131437 DLSPPDNHLS(ph)PQNDDALETR ddPTM_HeLa_Romidepsin_16h_R1 1 DLSPPDNHLSPQNDDALETR 20 0 O94972-2;O94972-3;O94972 O94972-2 TRIM37 E3 ubiquitin-protein ligase TRIM37 1 0 DLSPPDNHLS(1)PQNDDALETR 81.65 0.0017078 3131900 623.98 656.57 593.14 555.31 982.69 1182.7 1168.2 850.47 875.11 789.7 TRUE FALSE FALSE 616.3746918 665.8132097 603.4633529 619.517555 932.5396624 1107.129287 1267.426879 875.0770076 796.8379698 769.1834802 0.801336362 0.865610387 0.78455059 0.805422335 1.212376093 1.439356559 1.64775624 1.137670049 1.035953047 1 9.587183968 -8.56621397 3.42252767 0.884533078 1.425265799 0.744695746 0.139888009 0.084355535 2.042720829 0.020210029 0.044083929 2.72E-09 8.56621397 0.540732721 DLSSS(ph)PPGPYGQEMYAFR ddPTM_HeLa_Romidepsin_16h_R1 4 DLSSSPPGPYGQEMYAFR 18 0 O43741-2;O43741 O43741-2 PRKAB2 5-AMP-activated protein kinase subunit beta-2 1 0 DLS(0.023)S(0.123)S(0.693)PPGPY(0.157)GQEMY(0.004)AFR;DLS(0.009)S(0.054)S(0.894)PPGPY(0.043)GQEMYAFR;DLS(0.018)S(0.09)S(0.479)PPGPY(0.411)GQEMY(0.002)AFR;DLS(0.026)S(0.138)S(0.772)PPGPY(0.061)GQEMY(0.002)AFR ;;; 101.35 0.002685 114172100 8081.12 7756.56 7808.57 7975.15 9157.55 9070.17 7818.66 8802.12 7815.23 7610.41 TRUE FALSE FALSE 7982.624201 7865.757055 7944.474885 8897.274367 8690.206052 8490.61541 8482.776785 9056.795455 7116.216255 7412.690451 1.07688622 1.0611204 1.071739733 1.20027599 1.17234169 1.145416157 1.144358697 1.221795988 0.960004509 1 12.85578155 -9.592640796 0.263377056 0.985932354 1.234835572 0.807103159 0.035763275 0.834911709 0.151059708 0.037641342 0.076122086 2.55E-10 9.592640796 0.248903219 DLST(ph)PGLEK ddPTM_HeLa_Romidepsin_16h_R1 2 DLSTPGLEK 9 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DLS(0.082)T(0.918)PGLEK;DLS(0.055)T(0.945)PGLEK ; 166.34 0.0048573 70517000 19224.8 21493.2 15102.4 16359 16065.6 12728.2 9806.5 14244 16628.7 17131.4 TRUE FALSE FALSE 18990.48074 21795.78183 15365.25094 18250.50455 15245.71248 11914.9091 10639.46387 14656.12767 15141.38742 16686.32376 1.138086556 1.306206337 0.920829007 1.093740288 0.913665149 0.714052374 0.637615812 0.878331733 0.907413019 1 14.02637852 -8.509799327 2.701323892 1.076980257 0.732775237 0.575471888 0.121509445 0.128545763 1.873792202 0.016608393 0.03922859 3.09E-09 8.509799327 -0.34420502 DLST(ph)SPKPS(ph)PIPSPVLGR ddPTM_HeLa_Romidepsin_16h_R1 1 DLSTSPKPSPIPSPVLGR 18 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 2 0 DLS(0.107)T(0.453)S(0.453)PKPS(0.853)PIPS(0.135)PVLGR 73.675 0.018096 17956000 1865.3 1493.2 1376.2 1525.7 1601.1 1632.5 1753.4 1853.6 1534.6 1399.5 TRUE FALSE FALSE 1842.565006 1514.221309 1400.152184 1702.108613 1519.389892 1528.188519 1902.333752 1907.230992 1397.341533 1363.140788 1.351705577 1.110832661 1.027151557 1.248666776 1.114624333 1.121079005 1.395551926 1.39914454 1.025089664 1 10.41271886 -12.56142167 1.323274897 0.999508311 1.228868277 0.312345885 0.123268586 0.463375354 1.449027356 0.095197655 0.02221058 2.75E-13 12.56142167 0.229359966 DLTDYLMK ddPTM_HeLa_Romidepsin_16h_R1 2 DLTDYLMK 8 0 P60709;A0A2R8Y793;P63267-2;Q562R1;A0A2R8YEA7;P63261;I3L3I0;I3L1U9;I3L4N8;P63267;P68133;P68032;P62736 P60709;P63261;P63267 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 0 ; ; 116.73 0.012209 2252760 1268.86 775.617 883.68 1087.48 1024.464 1255.36 1152.66 1208.11 743.12 965.36 FALSE FALSE TRUE 1253.394646 786.5361565 899.0600797 1213.219554 972.1817793 1175.146547 1250.566912 1243.064757 676.653486 940.279808 1.333001768 0.836491595 0.956162274 1.290275027 1.033928168 1.249783881 1.329994435 1.322015794 0.719629923 1 9.876946327 -8.043081745 4.739400964 1.123676506 1.320263848 0.204291108 0.192103123 0.250976783 12.95647533 0.024237049 0.067457188 9.06E-09 8.043081745 0.196587342 DLTGQVPT(ph)PVVK ddPTM_HeLa_Romidepsin_16h_R1 1 DLTGQVPTPVVK 12 0 P46821;D6RA32;D6RA40 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DLT(0.006)GQVPT(0.994)PVVK 103.13 0.028993 7642800 5296.5 5620.5 5403.3 5121.3 4204.6 4775.2 2993.2 3679.3 5060.6 4657.6 TRUE FALSE FALSE 5231.944221 5699.625547 5497.34217 5713.448802 3990.023572 4470.080131 3247.442333 3785.754741 4607.967261 4536.594881 1.153275608 1.256366437 1.211777184 1.259413492 0.87951948 0.985338177 0.715832561 0.834492574 1.015732589 1 12.14739412 -8.281980864 1.720258762 1.109882309 0.793266068 0.598312204 0.112444375 0.229396982 1.285117048 0.018474758 0.062018916 5.22E-09 8.281980864 -0.316616242 DLTNNNIPHLLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 DLTNNNIPHLLSPK 14 0 A0A1B0GTX4;A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A1B0GTX4 CDKL5 Cyclin-dependent kinase-like 5 1 0 DLTNNNIPHLLS(1)PK;DLTNNNIPHLLS(1)PK ; 103.39 0.0036275 38192000 5870.4 5711.4 4946.2 6250 11319.1 13471.9 11721.6 13736.6 5864.4 5654.8 TRUE FALSE FALSE 5798.849307 5791.805239 5032.286536 6972.654407 10741.44409 12611.08907 12717.23241 14134.04685 5339.873376 5507.887481 1.052826393 1.051547487 0.913650933 1.265939878 1.950193087 2.289641739 2.308912892 2.566146621 0.969495727 1 12.42728337 -8.657905931 1.803349785 1.017142279 2.405546389 0.984334739 0.078510397 0.027809281 0.182280221 0.011647224 0.028448107 2.20E-09 8.657905931 1.38840411 up DLTSLETTSEMEAGS(ph)PENKK ddPTM_HeLa_Romidepsin_16h_R1 1 DLTSLETTSEMEAGSPENKK 20 1 Q5VYS8-5;Q5VYS8-3;Q5VYS8-2;Q5VYS8-4;Q5VYS8-6;Q5VYS8 Q5VYS8-5 ZCCHC6 Terminal uridylyltransferase 7 1 0 DLTSLETTS(0.001)EMEAGS(0.999)PENKK 101.6 0.00056635 43733000 2971.1 3133.3 3399.4 3113.8 4175.6 3857.2 3799.7 3642.7 3253.2 3217.9 TRUE FALSE FALSE 2934.88709 3177.41068 3458.565131 3473.832207 3962.503551 3610.737369 4122.446423 3748.095777 2962.225644 3134.298494 0.93637766 1.013754971 1.103457484 1.108328455 1.264239369 1.152008137 1.315269248 1.195832428 0.945100044 1 11.61392687 -9.320871624 1.145916652 0.96959891 1.236859479 0.841559851 0.049295284 0.120379767 0.312772446 0.008383137 0.016301228 4.78E-10 9.320871624 0.267260569 DLVDEDLSHFQS(ph)GSPPAPNGFK ddPTM_HeLa_Romidepsin_16h_R1 1 DLVDEDLSHFQSGSPPAPNGFK 22 0 Q70EK8 Q70EK8 USP53 Inactive ubiquitin carboxyl-terminal hydrolase 53 1 0 DLVDEDLSHFQS(0.953)GS(0.047)PPAPNGFK 99.273 0.00010756 5895600 853.26 807.07 1102.5 905.62 1086.6 1004.1 801.1 852.18 1155.3 1225.6 TRUE FALSE FALSE 842.8601389 818.4319526 1121.68855 1010.332045 1031.146747 939.9412506 869.145414 876.8364838 1051.967074 1193.758735 0.706055683 0.68559243 0.939627512 0.846345259 0.86378153 0.787379579 0.7280746 0.734517334 0.881222515 1 10.22129557 -12.43252057 1.155587192 1.000334523 0.783241867 0.327461092 0.082362432 0.329719587 0.785690599 0.057217557 0.014258721 3.69E-13 12.43252057 -0.217092655 DLVLPTQALPAS(ph)PALK ddPTM_HeLa_Romidepsin_16h_R1 2 DLVLPTQALPASPALK 16 0 J3KSZ6;U3KQ35;H3BR06;Q15554 J3KSZ6 TERF2 Telomeric repeat-binding factor 2 1 0 DLVLPT(0.1)QALPAS(0.9)PALK;DLVLPT(0.005)QALPAS(0.995)PALK ; 121.51 0.0028622 257260000 17287.9 17668.3 17671.2 17242.1 16721.9 15253.1 14969.7 14806.8 17370.2 16568.6 TRUE FALSE FALSE 17077.18843 17917.03479 17978.75982 19235.71273 15868.51904 14278.47614 16241.22594 15235.2114 15816.56581 16138.14538 1.058187792 1.110228862 1.114053653 1.191940726 0.983292607 0.884765616 1.006387386 0.944049706 0.980073325 1 13.97818717 -8.535099339 24.99094579 1.053911318 0.948337784 0.445150006 0.064534654 191.7851971 392197.0945 0.010076282 0.020163121 2.92E-09 8.535099339 -0.105573534 DLVMGS(ph)SPQLK ddPTM_HeLa_Romidepsin_16h_R1 1 DLVMGSSPQLK 11 0 Q53LP3 Q53LP3 SOWAHC Ankyrin repeat domain-containing protein SOWAHC 1 0 DLVMGS(0.5)S(0.5)PQLK 103.21 0.024383 39920000 6100.7 6327.9 5904.7 4524.5 5311.2 4351.7 4489 4860.7 6381.1 6190.6 TRUE FALSE FALSE 6026.342322 6416.984342 6007.468827 5047.643978 5040.149645 4073.640414 4870.295548 5001.336686 5810.358434 6029.76732 0.999431985 1.064217573 0.996301931 0.837120856 0.835877966 0.675588327 0.807708704 0.829441075 0.963612379 1 12.55788662 -9.135236023 2.401364665 1.006239552 0.781063439 0.830040856 0.047381032 0.08136307 0.916701927 0.006986598 0.012532025 7.32E-10 9.135236023 -0.225176113 DLVQPDKPAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DLVQPDKPASPK 12 1 Q6PJT7;Q6PJT7-5;H0YJA2;Q6PJT7-2;Q6PJT7-9;G3V411;G3V4R5 Q6PJT7 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 0 DLVQPDKPAS(1)PK 70.451 0.026026 413340000 8575.4 8782.3 8180.5 8121 7754.2 7757.4 7267.8 8037.6 9243.9 8745.6 TRUE FALSE FALSE 8470.879726 8905.93745 8322.878171 9059.98823 7358.474239 7261.727176 7885.126751 8270.155275 8417.102432 8518.388051 0.99442285 1.045495626 0.977048489 1.063580125 0.863834119 0.852476681 0.925659491 0.970859184 0.988109767 1 13.05636474 -8.753704555 24.99998604 1.003761004 0.901187467 0.640084794 0.039498145 87.59629407 283120.5992 0.005590043 0.011014416 1.76E-09 8.753704555 -0.102573537 DLVVLVS(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 DLVVLVSRR 9 1 Q8WYK0 Q8WYK0 ACOT12 Acyl-coenzyme A thioesterase 12 1 0 DLVVLVS(1)RR 89.752 0.0037009 0 1315.8 1448.9 1785.7 1931.4 2026.3 2212.3 1459.2 1505.4 1026.4 1040.1 TRUE FALSE FALSE 1299.762523 1469.297652 1816.779359 2154.717556 1922.89035 2070.94117 1583.144412 1548.956374 934.5962133 1013.078052 1.282983597 1.450330159 1.793326147 2.126901823 1.898067327 2.044206925 1.562707245 1.528960548 0.922531301 1 9.984529615 -10.15135659 1.346723308 1.104531722 1.844821881 0.757626459 0.192837592 0.15551659 0.541948216 0.039822816 0.049535524 7.06E-11 10.15135659 0.740290159 DLYANTVLS(ph)GGTTMYPGIADR ddPTM_HeLa_Romidepsin_16h_R1 1 DLYANTVLSGGTTMYPGIADR 21 0 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 1 0 DLYANT(0.02)VLS(0.767)GGT(0.137)T(0.072)MY(0.003)PGIADR 89.26 0.0016391 6122300 1608.2 1543 1828.5 1426.1 2621.6 1879.9 1793.9 2037.2 1764.1 1582.7 TRUE FALSE FALSE 1588.59864 1564.722395 1860.324275 1590.992392 2487.809969 1759.780457 1946.273821 2096.143168 1606.314478 1541.581226 1.030499472 1.01501132 1.206763707 1.032052263 1.613804014 1.141542481 1.262517854 1.359735791 1.041991464 1 10.59019519 -9.295864975 1.424012964 1.014974959 1.313424091 0.467006831 0.136870658 0.237400902 0.945117282 0.020794316 0.038415442 5.06E-10 9.295864975 0.298449132 DLYANTVLSGGT(ph)TMYPGIADR ddPTM_HeLa_Romidepsin_16h_R1 1 DLYANTVLSGGTTMYPGIADR 21 0 P60709;A0A2R8Y793;P63261 P60709;P63261 ACTB;ACTG1 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 1 0 DLYANT(0.085)VLS(0.15)GGT(0.487)T(0.255)MY(0.023)PGIADR 113.25 0.00049866 7155200 2004.3 1616 1618.9 1607.5 3163.1 2091.6 2150 2141.5 1803 1645.6 TRUE FALSE FALSE 1979.870821 1638.75009 1647.076275 1793.366714 3001.675204 1957.95351 2332.620946 2203.460924 1641.735164 1602.847075 1.235221283 1.022399527 1.027594149 1.118863266 1.872714653 1.221547296 1.455298502 1.374716876 1.024261884 1 10.64642107 -8.950381346 24.99999903 1.098973932 1.465079197 0.587971277 0.166923709 65.18446453 32842.41156 0.024349484 0.044137184 1.12E-09 8.950381346 0.366105265 DLYANTVLSGGTTMYPGIADR ddPTM_HeLa_Romidepsin_16h_R1 4 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 0 ;;; ;;; 200.94 1.27E-90 146491750 5488.2 4643.8 5216.057 5378.72 6248.99 6139.12 5493.1 5519.29 5634.02 5435.2 FALSE FALSE TRUE 5421.307707 4709.175538 5306.840284 6000.632914 5930.080722 5746.850045 5959.683777 5678.981948 5130.099141 5293.99272 1.024048954 0.889531926 1.002426819 1.133479631 1.120152791 1.085541735 1.125744611 1.072721903 0.969041593 1 12.3701405 -9.270935457 24.18612953 0.999961117 1.108020064 0.706496162 0.040740296 211.894152 539685.6761 0.006334381 0.009756073 5.36E-10 9.270935457 0.108058947 DLYDAGVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 DLYDAGVKR 9 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33 P07355 ANXA2 Annexin A2;Annexin 0 1 ; DLYDAGVK(1)R;DLYDAGVK(1)R 98.033 0.0085499 15854500 5930.9 5750.2 5865.2 5089.9 14164.7 9681.7 12542.4 10524.6 14229.6 10069.8 FALSE TRUE FALSE 5858.61191 5831.151467 5967.281346 5678.418187 13441.8225 9063.070616 13607.75114 10829.1127 12956.86894 9808.185144 0.59731865 0.594518902 0.608398114 0.57894688 1.370469899 0.924031356 1.387387263 1.104089343 1.321026138 1 13.2597705 -8.761638812 24.99999999 0.756255088 1.190668026 0.390321023 0.251538403 3.501652509 439039.7275 0.031698519 0.060199228 1.73E-09 8.761638812 0.434412938 DLYDAGVKR ddPTM_HeLa_Romidepsin_16h_R1 2 DLYDAGVKR 9 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33 P07355 ANXA2 Annexin A2;Annexin 0 0 ; ; 88.177 0.02806 133772000 13786.6 16252.9 13825.6 16931.6 17513.7 14381.9 15912 13842.6 15591.2 13542 FALSE FALSE TRUE 13618.56362 16481.70875 14066.22877 18889.31126 16619.91054 13462.94301 17263.56488 14243.11379 14196.68402 13190.17689 1.032477709 1.249544179 1.066416993 1.432074143 1.260021808 1.020679489 1.308819816 1.079827353 1.076307327 1 13.68717629 -10.31798886 6.024373932 1.014627779 1.205328202 0.287246796 0.118529148 0.166013777 13.24208962 0.01893129 0.021664655 4.81E-11 10.31798886 0.190700423 DLYIRPNIAQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 DLYIRPNIAQKR 12 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 1 ; DLYIRPNIAQK(1)R;DLYIRPNIAQK(1)R 109.72 0.0079412 3177300 1427.14 840.35 2192.7 777.11 2463.6 2303.9 2134.6 1309.71 1764.19 1065.13 FALSE TRUE FALSE 1409.745469 852.1804694 2230.863024 866.9631146 2337.873299 2156.688225 2315.912871 1347.604392 1606.396428 1037.457769 1.358846124 0.821412201 2.150316948 0.835661114 2.253463581 2.078820256 2.232296041 1.298948673 1.548396933 1 10.0188369 -9.272319524 0.884510601 1.143731825 1.95824638 0.229974007 0.484064877 0.461239264 0.713322508 0.081962237 0.182690275 5.34E-10 9.272319524 0.814514556 DLYRPLSS(ph)DDLDSVGDSV ddPTM_HeLa_Romidepsin_16h_R1 1 DLYRPLSSDDLDSVGDSV 18 1 Q5VZY9 Q5VZY9 DCLK1 1 0 DLYRPLS(0.283)S(0.359)DDLDS(0.023)VGDS(0.335)V 117.07 0.0097798 9661200 2090.8 2616 2596.7 2432.8 3237.6 2946.6 3055.5 3359.4 2579.1 2214.5 TRUE FALSE FALSE 2065.316525 2652.828117 2641.894474 2714.091783 3072.373191 2758.32177 3315.034094 3456.598939 2348.418837 2156.966971 0.957509574 1.22988815 1.22481916 1.258290841 1.424395103 1.27879648 1.536896085 1.602527524 1.088759758 1 11.07478837 -8.910584079 0.482649537 0.962921562 1.614582374 0.813367874 0.087682613 0.340441591 0.131263417 0.023546608 0.09890572 1.23E-09 8.910584079 0.651660811 DLYRPLSSDDLDS(ph)VGDSV ddPTM_HeLa_Romidepsin_16h_R1 1 DLYRPLSSDDLDSVGDSV 18 1 Q5VZY9 Q5VZY9 DCLK1 1 0 DLYRPLS(0.294)S(0.085)DDLDS(0.376)VGDS(0.245)V 126.07 0.010427 10087000 1751.6 1743 1783.9 1960.5 2035.8 2744.6 2127.2 2605.6 2098.3 1751.1 TRUE FALSE FALSE 1730.250825 1767.538 1814.948031 2187.182234 1931.905529 2569.228918 2307.884315 2680.988925 1910.622793 1705.60617 1.014449207 1.036310745 1.064107332 1.282348923 1.132679726 1.506343588 1.353116772 1.571868684 1.120201619 1 10.73606885 -8.40391463 0.623873871 0.999518256 1.585308805 0.804125533 0.087657712 0.284446822 0.158450809 0.013745155 0.092270326 3.95E-09 8.40391463 0.585790549 DMDDEESWIK ddPTM_HeLa_Romidepsin_16h_R1 1 DMDDEESWIK 10 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 123.35 0.025085 11675000 1237.6 1120.2 1241.1 681.13 1089.5 1283.1 877.01 1251 947.89 1075.9 FALSE FALSE TRUE 1222.515655 1135.970205 1262.700825 759.8854554 1033.89875 1201.114051 951.5032075 1287.195711 863.1083444 1047.947963 1.166580497 1.08399486 1.204927028 0.725117546 0.986593596 1.146158105 0.907967992 1.228301172 0.82361756 1 10.03335136 DMDDGS(ph)DSLGVGLDQEFR ddPTM_HeLa_Romidepsin_16h_R1 2 DMDDGSDSLGVGLDQEFR 18 0 Q9NPG3-2;Q9NPG3 Q9NPG3-2 UBN1 Ubinuclein-1 1 0 DMDDGS(0.849)DS(0.151)LGVGLDQEFR;DMDDGS(0.98)DS(0.02)LGVGLDQEFR ; 110.34 0.0017608 10432800 2590 2618.2 2550.67 1830.57 2611.4 3010.1 2737.6 2841.8 2863.4 2779.7 TRUE FALSE FALSE 2558.432084 2655.059088 2595.063341 2042.229116 2478.130514 2817.764325 2970.131676 2924.022999 2607.290332 2707.482993 0.944948533 0.980637402 0.958478169 0.754290654 0.915289411 1.04073205 1.097008433 1.079978344 0.962994168 1 11.40273656 -8.067650133 4.312264568 0.952699871 1.085517503 0.47578765 0.066538535 0.175382977 6.310826102 0.010507051 0.029241874 8.56E-09 8.067650133 0.132817632 DMDEPS(ph)PVPNVEEVTLPK ddPTM_HeLa_Romidepsin_16h_R1 4 DMDEPSPVPNVEEVTLPK 18 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 0 DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK;DMDEPS(1)PVPNVEEVTLPK ;;; 112.34 0.0017829 73706600 24302.7 23485.3 25493.8 17796.5 24702 22991.3 20443.5 23368.7 26554.2 26022.6 TRUE FALSE FALSE 24006.48934 23815.92667 25937.50889 19854.21507 23441.36476 21522.23013 22179.97038 24044.83646 24179.12585 25346.5291 0.947131232 0.939612938 1.023316005 0.783311 0.924835297 0.849119422 0.875069336 0.948644146 0.953942283 1 14.62950058 -9.278991672 24.92802797 0.974471862 0.877331195 0.509910974 0.047333453 470.272661 667886.5939 0.006993144 0.010698149 5.26E-10 9.278991672 -0.097140667 DMESPT(ph)KLDVTLAK ddPTM_HeLa_Romidepsin_16h_R1 1 DMESPTKLDVTLAK 14 1 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;H7C456 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DMES(0.03)PT(0.947)KLDVT(0.022)LAK 92.151 0.023974 153100000 6107.2 5561 5948.9 5778.4 5495.9 5267.9 5105.7 5181.9 6432 6021.6 TRUE FALSE FALSE 6032.763097 5639.287904 6052.438109 6446.525796 5215.423715 4931.298191 5539.378031 5331.830101 5856.705811 5865.157964 1.028576406 0.961489518 1.031930964 1.09912228 0.889221356 0.840778411 0.944455045 0.909068457 0.998558921 1 12.51795425 -8.735496149 24.99255557 1.016363003 0.895414444 0.691430391 0.040560245 98.49308721 94883.42982 0.005791076 0.011578919 1.84E-09 8.735496149 -0.120948559 DMLLANK(ac)VPAAAR ddPTM_HeLa_Romidepsin_16h_R1 1 DMLLANKVPAAAR 13 1 F8VWS0;P05388-2;Q8NHW5;P05388;F8VQY6;F8VRK7;G3V210;F8VU65;F8VWV4;F8VPE8;F8VW21 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 0 1 DMLLANK(1)VPAAAR 77.288 0.014225 0 163.46 75.265 0 0 141.01 75.424 194.99 0 0 159.01 FALSE TRUE FALSE 161.4676866 76.32458265 0 0 133.8137335 70.60464982 211.5524457 0 0 154.8788973 1.042541557 0.492801692 0 0 0.863989452 0.455870045 1.365921694 0 0 1 7.274996776 -10.25341953 9.215024961 1.02017077 0.469838147 0 0.516034588 0.166969532 155.0835361 0.066396816 0.079439116 5.58E-11 10.25341953 -0.550332623 DMLPSPEQTLS(ph)PLSK ddPTM_HeLa_Romidepsin_16h_R1 1 DMLPSPEQTLSPLSK 15 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 0 DMLPSPEQT(0.027)LS(0.965)PLS(0.007)K 187.75 1.20E-09 0 1040.5 1240.4 1091.7 867.14 1067.4 1252.8 791.06 1056 878.66 1149 TRUE FALSE FALSE 1027.817986 1257.862384 1110.700581 967.4028068 1012.926595 1172.750123 858.2526167 1086.553694 800.070449 1119.148814 0.918392597 1.123945598 0.992451197 0.864409446 0.9050866 1.047894711 0.766879798 0.970875079 0.714891924 1 10.12818617 -9.279210393 24.25369162 0.977368245 0.910294331 0.000136806 0.118279637 888.0287143 1211969.361 0.012968277 0.01983914 5.26E-10 9.279210393 -0.067073914 DMPGGFLFEGLS(ph)DDEDDFHPNTR ddPTM_HeLa_Romidepsin_16h_R1 8 DMPGGFLFEGLSDDEDDFHPNTR 23 0 H3BUV9;Q96S82 H3BUV9 UBL7 Ubiquitin-like protein 7 1 0 DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(0.999)DDEDDFHPNT(0.001)R;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(0.999)DDEDDFHPNT(0.001)R;DMPGGFLFEGLS(1)DDEDDFHPNTR;DMPGGFLFEGLS(1)DDEDDFHPNTR ;;;;;;; 114.2 1.36E-08 256272400 24686.17 25199.15 22823.01 22606.97 25726.08 25302.62 21528.32 25271.28 27532.72 25503.39 TRUE FALSE FALSE 24385.28546 25553.9043 23220.23492 25220.89424 24413.18214 23685.86424 23356.93496 26002.46462 25070.12457 24840.80825 0.98166232 1.028706636 0.93476165 1.01530087 0.982785338 0.953506182 0.940264694 1.046764032 1.009231435 1 14.6004245 -9.781130932 24.99967737 0.993901031 0.9778184 0.088401796 0.034164007 598.9354534 760385.0797 0.005103947 0.006712784 1.66E-10 9.781130932 -0.016082631 DMS(ph)PLS(ph)ETEMALGK ddPTM_HeLa_Romidepsin_16h_R1 2 DMSPLSETEMALGK 14 0 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 2 0 DMS(1)PLS(0.832)ET(0.168)EMALGK;DMS(1)PLS(0.844)ET(0.156)EMALGK ; 66.059 0.0033008 0 3853.8 3471.9 3565.7 1940.53 3688.3 4304.9 3219.9 3338 4157.4 3878.9 TRUE FALSE FALSE 3806.828403 3520.777499 3627.759513 2164.903209 3500.072288 4029.830783 3493.398226 3434.579764 3785.551732 3778.125619 1.007597096 0.931884711 0.960200872 0.573009854 0.926404424 1.066621703 0.924637923 0.909069764 1.001965555 1 11.88345496 -9.982931699 2.35336332 1.003384577 0.889653176 0.149674148 0.11794739 0.421499956 4.685300347 0.020672133 0.027115517 1.04E-10 9.982931699 -0.113731402 DMS(ph)PLSETEMALGK ddPTM_HeLa_Romidepsin_16h_R1 1 DMSPLSETEMALGK 14 0 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DMS(0.99)PLS(0.01)ETEMALGK 92.8 0.00095722 0 2220.5 1987.1 1856.1 1433.5 1987.3 2421.8 1872.8 2283.9 2148.1 2203.5 TRUE FALSE FALSE 2193.435692 2015.074446 1888.404642 1599.248015 1885.880665 2267.054796 2031.875585 2349.981043 1955.968556 2146.252752 1.021983869 0.938880308 0.879861256 0.745134986 0.878685264 1.056285097 0.946708435 1.094922786 0.911341199 1 11.06760427 -10.2080715 5.655374808 1.010381516 0.927518583 0.005338316 0.096445249 0.322613853 23.54747897 0.015985098 0.019519648 6.19E-11 10.2080715 -0.082862933 DMSPLSETEMALGKDVT(ph)PPPETEVVLIK ddPTM_HeLa_Romidepsin_16h_R1 2 DMSPLSETEMALGKDVTPPPETEVVLIK 28 1 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DMS(0.021)PLS(0.048)ET(0.019)EMALGKDVT(0.909)PPPET(0.002)EVVLIK;DMS(0.041)PLS(0.298)ET(0.299)EMALGKDVT(0.361)PPPET(0.001)EVVLIK ; 49.745 0.0041689 58897000 6294.2 6505.8 5690.4 6941.1 6660.8 6056.2 5678.8 6445.3 6626.6 6278.3 TRUE FALSE FALSE 6217.483869 6597.388823 5789.439025 7743.662641 6320.874521 5669.228365 6161.15713 6631.784586 6033.900299 6115.188861 1.016728021 1.078852832 0.946731026 1.266299834 1.03363521 0.927073308 1.007517065 1.084477477 0.986707105 1 12.57818134 -10.4629304 7.493642568 1.007302951 1.046877695 0.058439027 0.087845652 0.790908179 86.60012751 0.014859107 0.016815089 3.44E-11 10.4629304 0.039574744 DMYMESEGGDGYLAPENGYLMEAAPE ddPTM_HeLa_Romidepsin_16h_R1 1 DMYMESEGGDGYLAPENGYLMEAAPE 26 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 0 72.99 0.00088466 3690600 864.67 955.49 874.33 760.85 745.79 804.01 831.35 585.02 905.1 964.54 FALSE FALSE TRUE 854.1310695 968.9414133 889.5473469 848.8230569 707.7295534 752.6363558 901.9648482 601.9466307 824.1455891 939.4811118 0.909151934 1.031358056 0.946849634 0.903501993 0.753319619 0.801119199 0.960067038 0.64072244 0.877234868 1 9.875720346 -8.965754232 3.780089367 0.96130735 0.802284 0.456107158 0.083784984 0.147905962 4.55438863 0.011570509 0.021248371 1.08E-09 8.965754232 -0.15902335 DNEESEQPPVPGT(ph)PTLR ddPTM_HeLa_Romidepsin_16h_R1 1 DNEESEQPPVPGTPTLR 17 0 A0A2R8YDC1;A0A2R8Y6V8;O15439-4;O15439-3;O15439-2;O15439 A0A2R8YDC1 ABCC4 Multidrug resistance-associated protein 4 1 0 DNEESEQPPVPGT(0.982)PT(0.018)LR 175.77 5.59E-07 3501200 1515.2 2935.9 1875.7 1361.8 2355.2 3483.2 1202 2370.1 2106 2318.1 TRUE FALSE FALSE 1496.73216 2977.231677 1908.345772 1519.257723 2235.005356 3260.634762 1304.09785 2438.675104 1917.634085 2257.875428 0.662894038 1.318598732 0.845195332 0.67287048 0.989870977 1.444116323 0.577577414 1.080075133 0.849309072 1 11.14075018 -8.544458112 24.67046926 0.865372424 1.026406025 0.053708754 0.260972738 427.8585188 489144.6534 0.038404552 0.076814347 2.85E-09 8.544458112 0.161033601 DNFDSFYSEVAELGR ddPTM_HeLa_Romidepsin_16h_R1 1 DNFDSFYSEVAELGR 15 0 E7EPJ7;O75962-4;O75962;O75962-2;O75962-3 E7EPJ7 TRIO Triple functional domain protein 0 0 132.23 0.01694 2342300 416.63 1089.6 510.42 504.24 699.31 432.41 493.34 963.93 1331.3 2606.6 FALSE FALSE TRUE 411.5519533 1104.939417 519.303646 562.5426013 663.6216012 404.7803965 535.2442873 991.8197937 1212.225194 2538.880156 0.162099795 0.435207394 0.204540433 0.221571152 0.261383587 0.159432652 0.210819044 0.390652466 0.477464519 1 11.30997658 -12.31854619 0.724239373 1.079383975 0.241811484 0.432499734 0.182065929 0.186243479 0.148435788 0.09700365 0.018067694 4.80E-13 12.31854619 -0.837572491 DNIQGITKPAIR ddPTM_HeLa_Romidepsin_16h_R1 2 DNIQGITKPAIR 12 1 P62805 P62805 HIST1H4A Histone H4 0 0 ; ; 142.76 0.0018389 78801000 3606.9 3643.7 5608.1 5056.6 7333.2 6413.4 5975.8 5531.9 4724.5 4109.7 FALSE FALSE TRUE 3562.937715 3694.996104 5705.706628 5641.267884 6958.95944 6003.604438 6483.384303 5691.956799 4301.928887 4002.929402 0.890082577 0.923073013 1.425382777 1.409284881 1.738466693 1.499802728 1.619659917 1.421947836 1.074695168 1 11.96684046 -9.676775667 3.340569687 0.943222755 1.543268415 0.871944984 0.102955721 0.051498034 1.148416338 0.015404136 0.022020192 2.10E-10 9.676775667 0.60004566 DNLAQQSFNMEQANYTIQS(ph)LKDTK ddPTM_HeLa_Romidepsin_16h_R1 1 DNLAQQSFNMEQANYTIQSLKDTK 24 1 Q9NZZ3-2;Q9NZZ3 Q9NZZ3-2 CHMP5 Charged multivesicular body protein 5 1 0 DNLAQQS(0.003)FNMEQANY(0.015)T(0.022)IQS(0.85)LKDT(0.111)K 57.543 0.0022595 0 790.22 734.55 967.95 989.1 864.64 920.01 714.23 796.13 854.64 752.82 TRUE FALSE FALSE 780.5884947 744.8910142 984.7967637 1103.464396 820.5141944 861.2243302 774.8966784 819.1647655 778.1988579 733.2616279 1.064542948 1.015859805 1.343036 1.504871323 1.118992408 1.174511658 1.056780621 1.117152097 1.061284033 1 9.518184234 -9.784940364 24.89712761 1.030233777 1.218235841 0.352012191 0.122083464 194.9134373 206491.943 0.021134384 0.027785216 1.64E-10 9.784940364 0.188002064 DNLSYIEHIFEISR ddPTM_HeLa_Romidepsin_16h_R1 1 DNLSYIEHIFEISR 14 0 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 0 95.428 0.0018498 0 2289.7 1859.5 1605.7 1780.6 2427.6 2084.4 1802.9 1616.6 2019.1 1847.1 FALSE FALSE TRUE 2261.792256 1885.67809 1633.646535 1986.48135 2303.710513 1951.213567 1956.038281 1663.37377 1838.506639 1799.112076 1.257171405 1.048115965 0.908029331 1.104145415 1.280470819 1.084542533 1.087224252 0.924552613 1.02189667 1 10.81306935 DNLTLWTADNAGEEGGEAPQEPQS ddPTM_HeLa_Romidepsin_16h_R1 1 DNLTLWTADNAGEEGGEAPQEPQS 24 0 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 0 115.36 1.59E-06 2276400 1488.3 1373.6 1625.4 1066.5 1561.7 1650.2 1147.5 1569.7 1726.1 1492.2 FALSE FALSE TRUE 1470.160027 1392.937577 1653.689405 1189.813748 1482.000621 1544.757546 1244.968621 1615.116793 1571.713293 1453.432429 1.011509031 0.95837794 1.137782103 0.818623367 1.019655673 1.062834099 0.85657138 1.111243124 1.081380367 1 10.50524829 DNLTLWTSDQQDDDGGEGNN ddPTM_HeLa_Romidepsin_16h_R1 5 DNLTLWTSDQQDDDGGEGNN 20 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 0 ;;;; ;;;; 230.69 1.19E-45 125922900 30897.6 28720.9 28807.9 28805.5 32794.7 32643.4 29357.7 32587.5 31504.1 28800.3 FALSE FALSE TRUE 30521.00817 29125.23358 29309.28942 32136.12744 31121.06409 30557.59209 31851.34231 33530.3679 28686.29439 28052.06405 1.088012922 1.038256348 1.044817571 1.145588695 1.109403715 1.089317065 1.135436674 1.195290579 1.022609044 1 14.77581931 -4 0.08467195 0.924923976 1.569083703 0.727225125 0.030401929 70.0676359 0.433516645 0.477606283 5.284875673 1.00E-04 4 0.644159727 DNLTLWTSDQQDEEAGEGN ddPTM_HeLa_Romidepsin_16h_R1 4 DNLTLWTSDQQDEEAGEGN 19 0 Q04917 Q04917 YWHAH 14-3-3 protein eta 0 0 ;;; ;;; 248.36 2.70E-61 50570100 23728.9 23193.8 22889.5 21769.3 23816.1 22479.7 19175.9 19325.5 26291 23816.3 FALSE FALSE TRUE 23439.68304 23520.32293 23287.88215 24286.36889 22600.67555 21043.31972 20804.70047 19884.65285 23939.46711 23197.54909 1.010437911 1.013914135 1.003894077 1.046936847 0.974269974 0.907135475 0.896849076 0.857187661 1.031982604 1 14.50168477 -8.245324946 2.22512826 1.008493225 0.878630691 0.915569604 0.01773184 0.058368506 0.557268126 0.002334215 0.007062959 5.68E-09 8.245324946 -0.129862534 DNLTLWTSDTQGDEAEAGEGGEN ddPTM_HeLa_Romidepsin_16h_R1 3 DNLTLWTSDTQGDEAEAGEGGEN 23 0 P63104;B0AZS6;P63104-2;B7Z2E6;H0YB80 P63104 YWHAZ 14-3-3 protein zeta/delta 0 0 ;; ;; 190.67 5.96E-20 16970000 9822.7 10671.9 10337.97 10490.5 9997.5 9654.5 8861.8 9231.05 10760.3 10304.4 FALSE FALSE TRUE 9702.977154 10822.13929 10517.89803 11703.46097 9487.290269 9037.608608 9614.521071 9498.135868 9797.871818 10036.6902 0.966750688 1.078257779 1.047944872 1.166067771 0.945260846 0.900457066 0.957937415 0.946341441 0.976205464 1 13.29299597 -8.554660354 24.99857146 1.010317092 0.934821603 0.360454891 0.059418942 216.0966092 169975.052 0.009540049 0.019080214 2.79E-09 8.554660354 -0.075495489 DNLTLWTSENQGDEGDAGEGEN ddPTM_HeLa_Romidepsin_16h_R1 7 DNLTLWTSENQGDEGDAGEGEN 22 0 P31946-2;P31946 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 0 ;;;;;; ;;;;;; 280.5 1.30E-110 115659000 83166.78 81732.9 79042.2 80196.4 89889 90115.66 79268 85744.54 87895.7 79997.1 FALSE FALSE TRUE 82153.1113 82883.53791 80417.89633 89469.0851 85301.62891 84357.56016 86001.02194 88225.42298 80034.08845 77918.76381 1.054343104 1.063717311 1.032073565 1.148235428 1.094750799 1.082634734 1.103726724 1.132274418 1.027147821 1 16.24968317 -10.25341857 0.183534572 0.962286507 1.158935893 0.647904347 0.026679911 1.266187696 0.210724482 0.091938888 0.100863572 5.58E-11 10.25341857 0.196649387 DNPAQDFSTLYGSS(ph)PLER ddPTM_HeLa_Romidepsin_16h_R1 2 DNPAQDFSTLYGSSPLER 18 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 DNPAQDFSTLYGS(0.007)S(0.993)PLER;DNPAQDFSTLYGS(0.027)S(0.973)PLER ; 340.48 7.31E-212 35952000 6242.3 6720.5 5475.5 5224.5 8077.7 9071.4 7876.5 8475.6 6467.8 6375.4 TRUE FALSE FALSE 6166.216447 6815.111375 5570.798781 5828.581272 7665.464827 8491.766817 8545.529713 8720.828114 5889.303769 6209.766189 0.992986895 1.097482766 0.897102823 0.938615255 1.234420845 1.367485757 1.376143554 1.404373023 0.948393803 1 12.60032323 -8.570376931 3.239781629 0.993218143 1.377610071 0.922873207 0.052953417 0.046006778 0.987988223 0.007575706 0.016645906 2.69E-09 8.570376931 0.384391928 DNPFSLGES(ph)FGSR ddPTM_HeLa_Romidepsin_16h_R1 1 DNPFSLGESFGSR 13 0 Q8N6H7;E9PQP3;A0A0D9SF70;G5E9L0;Q8N6H7-2;E9PMU9;H0YDN9;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 0 DNPFS(0.001)LGES(0.93)FGS(0.069)R 98.421 0.014067 2089700 801.27 619.84 633.92 634.55 605.77 437.15 415.2 418.79 632.56 674.44 TRUE FALSE FALSE 791.503813 628.5661238 644.9531117 707.9196566 574.8552965 409.2175258 450.4670776 430.9070279 575.9822493 656.9179516 1.20487469 0.956841143 0.981786401 1.077637862 0.875079293 0.62293552 0.685728068 0.655952584 0.876794808 1 9.35956938 -8.522732249 2.432489289 1.077768148 0.655357555 0.723143952 0.095210889 0.093997578 1.107467694 0.014024392 0.033757755 3.00E-09 8.522732249 -0.422410593 DNQES(ph)SDAELS(ph)SSEYIK ddPTM_HeLa_Romidepsin_16h_R1 1 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 0 DNQES(0.793)S(0.207)DAELS(0.752)S(0.195)S(0.052)EY(0.002)IK 103.24 0.012254 2739400 1429.5 1646.8 1298.3 859.23 1099.1 1292.8 954.3 1407.9 1576.9 1429.6 TRUE FALSE FALSE 1412.076704 1669.983694 1320.896367 958.5782154 1043.008826 1210.194252 1035.358218 1448.635365 1435.858115 1392.458786 1.014088689 1.199305653 0.948607155 0.688406885 0.749041075 0.869105976 0.74354676 1.040343441 1.031167406 1 10.44341891 -9.512529274 24.59206127 1.023795861 0.813501996 0.532266955 0.105244988 254.9263338 605747.7828 0.015651163 0.022964899 3.07E-10 9.512529274 -0.210293865 DNQES(ph)SDAELSSSEYIK ddPTM_HeLa_Romidepsin_16h_R1 1 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 DNQES(0.5)S(0.5)DAELSSSEYIK 67.668 0.01472 5398800 2141.1 2380 2155.6 1869.1 2128 2343.1 1920.3 2374 2386.3 2365.8 TRUE FALSE FALSE 2115.00345 2413.505702 2193.117314 2085.214136 2019.400219 2193.383472 2083.410234 2442.687944 2172.863351 2304.336175 0.917836326 1.047375695 0.951734967 0.904908823 0.876347922 0.95185047 0.904125994 1.060039751 0.942945467 1 11.17013549 -9.521573315 24.99979631 0.968149798 0.934039349 0.078276478 0.0563231 109.5398218 2097757.468 0.009103584 0.01297067 3.01E-10 9.521573315 -0.034110448 DNQESS(ph)DAELSSSEYIK ddPTM_HeLa_Romidepsin_16h_R1 3 DNQESSDAELSSSEYIK 17 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 DNQES(0.009)S(0.991)DAELSSSEYIK;DNQES(0.036)S(0.964)DAELSSSEYIK;DNQES(0.002)S(0.998)DAELSSSEYIK ;; 296.79 7.04E-121 94828000 13929.8 13322.9 12192.4 11091.2 12497.6 12021.5 10778.5 12733.3 14199 13825.3 TRUE FALSE FALSE 13760.01824 13510.46014 12404.60361 12373.61673 11859.80084 11253.36495 11694.02552 13101.71795 12929.00588 13466.11671 1.021825262 1.003292963 0.92117155 0.91887045 0.880714247 0.83568004 0.868403696 0.972939581 0.960113903 1 13.71704625 -9.62222821 1.965877483 1.011052289 0.888459551 0.60685088 0.03766616 0.12347955 0.969521959 0.005666534 0.008586036 2.39E-10 9.62222821 -0.122592738 DNQTTLQT(ph)LADMGGDLR ddPTM_HeLa_Romidepsin_16h_R1 1 DNQTTLQTLADMGGDLR 17 0 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 DNQT(0.175)T(0.175)LQT(0.65)LADMGGDLR 98.508 0.0079401 11062000 2379.6 2331.9 2185.7 2177.8 2911.1 3427.4 3121.2 2965 2455.3 2078 TRUE FALSE FALSE 2350.59652 2364.728549 2223.741192 2429.607483 2762.535704 3208.400201 3386.31465 3050.787597 2235.691819 2024.01326 1.161354308 1.16833649 1.098679161 1.200391089 1.36488024 1.58516758 1.673069399 1.50729625 1.104583583 1 10.98300303 -8.614609205 1.492924754 1.086401075 1.611267621 0.923461548 0.060676864 0.088334412 0.390334829 0.01196902 0.032901144 2.43E-09 8.614609205 0.524866546 DNRTAT(ph)PQNFSNY(ph)ESMKQDFK ddPTM_HeLa_Romidepsin_16h_R1 1 DNRTATPQNFSNYESMKQDFK 21 2 H3BR33;H3BT38;H3BVD5;Q53FZ2-2;Q53FZ2 H3BR33 ACSM3 "Acyl-coenzyme A synthetase ACSM3, mitochondrial" 2 0 DNRT(0.077)AT(0.493)PQNFS(0.493)NY(0.919)ES(0.018)MKQDFK 47.047 0.0041016 0 168.9 160.15 244.03 159.98 215.98 164.25 180.84 345.85 195.14 121.49 TRUE FALSE FALSE 166.8413818 162.4045959 248.2772398 178.4776403 204.9577347 153.7549551 196.2005451 355.8566241 177.6861897 118.3336723 1.409923132 1.372429274 2.098111509 1.508257429 1.732032233 1.299333927 1.658028026 3.007230463 1.501569133 1 6.886716846 -4 0.205909111 1.05558331 7.410478323 0.434766782 0.39577365 31.47349769 0.366008417 0.33520299 65.64568051 1.00E-04 4 6.354895012 DNS(ph)PEPNDPEEPQEVSSTPSDKK ddPTM_HeLa_Romidepsin_16h_R1 1 DNSPEPNDPEEPQEVSSTPSDKK 23 1 G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7;Q9HB58;Q9HB58-6 G5E9C0 SP110 Sp110 nuclear body protein 1 0 DNS(1)PEPNDPEEPQEVSSTPSDKK 132.78 2.44E-06 15508000 2006.8 2178.4 1788.6 1467.3 1671.4 1624.4 1377 1659.3 2078.2 2379.5 TRUE FALSE FALSE 1982.34035 2209.067572 1819.729833 1636.95613 1586.102221 1520.606083 1493.962346 1707.309228 1892.320587 2317.680247 0.855312269 0.953137334 0.785151375 0.706290754 0.684349027 0.656089676 0.644593812 0.736645717 0.81647181 1 11.17846583 -9.739000224 0.472346892 0.972992992 0.64008626 0.6368732 0.070122255 0.294112773 0.144707523 0.020323256 0.038181008 1.82E-10 9.739000224 -0.332906732 DNS(ph)PPPAFKPEPPK ddPTM_HeLa_Romidepsin_16h_R1 1 DNSPPPAFKPEPPK 14 1 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;A0A3B3IRI3 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 DNS(1)PPPAFKPEPPK 68.123 0.022829 38369000 6531.3 6553.1 6401.8 5070.7 6208.1 6024.8 5156.4 5436.4 7219.5 6861.3 TRUE FALSE FALSE 6451.694003 6645.354714 6513.220644 5656.998192 5891.277491 5639.834724 5594.384487 5593.693657 6573.769838 6683.042437 0.965382768 0.994360694 0.974589149 0.846470488 0.881526273 0.843902276 0.837101446 0.836998075 0.983649274 1 12.70628932 -9.278944065 5.564729021 0.983887287 0.849680251 0.954813023 0.014624254 0.030723095 3.319025004 0.002720646 0.004295447 5.26E-10 9.278944065 -0.134207036 DNWTDAEGYYR ddPTM_HeLa_Romidepsin_16h_R1 1 DNWTDAEGYYR 11 0 Q13523;H0YDJ3 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 0 0 143.79 0.025819 7955500 1424.8 1281.4 1455.2 1244.9 1354.2 1346 1085.8 1540.6 1466.8 1480.6 FALSE FALSE TRUE 1407.43399 1299.439583 1480.527146 1388.841195 1285.090121 1259.994944 1178.027825 1585.17483 1335.605734 1442.133799 0.975938565 0.901053414 1.026622597 0.963046006 0.891103254 0.873701834 0.816864445 1.099187074 0.926131636 1 10.49398931 -8.897710876 5.195924696 0.983429481 0.909936281 0.04760872 0.076459027 0.263341209 11.27568106 0.010197574 0.018765234 1.27E-09 8.897710876 -0.0734932 DNYVPEVSALDQEIIEVDPDTK ddPTM_HeLa_Romidepsin_16h_R1 2 DNYVPEVSALDQEIIEVDPDTK 22 0 H0YN88;A0A075B716;H3BNC9;P08708 H0YN88 RPS17 40S ribosomal protein S17 0 0 ; ; 102.66 9.95E-05 4958800 7335 6600 7532.7 5616.8 7660.4 7349.3 6186.5 7142.8 7884.1 7542.1 FALSE FALSE TRUE 7245.598199 6692.914973 7663.803484 6266.240844 7269.461203 6879.703449 6711.981156 7349.465649 7178.92635 7346.155155 0.986311621 0.911077269 1.043240079 0.852995984 0.989559988 0.936503968 0.913672665 1.000450643 0.977235874 1 12.84277365 -10.44686952 0.985002815 0.997183536 0.946533819 0.080923728 0.051231544 0.612754373 1.199475633 0.010606823 0.011454889 3.57E-11 10.44686952 -0.050649717 DPETYEVDS(ph)GTTK ddPTM_HeLa_Romidepsin_16h_R1 1 DPETYEVDSGTTK 13 0 Q3B726 Q3B726 TWISTNB DNA-directed RNA polymerase I subunit RPA43 1 0 DPETYEVDS(0.92)GT(0.079)TK 160.46 0.00043298 2974800 867.23 750.05 884.12 690.06 1025.3 1088.9 878.2 896.16 943.32 946.17 TRUE FALSE FALSE 856.6598672 760.6092236 899.5077377 769.847984 972.9751151 1019.322804 952.7942861 922.0889757 858.9470966 921.588367 0.929547179 0.825324245 0.976040681 0.835349069 1.055758894 1.10604999 1.033861017 1.000543202 0.932029014 1 9.847978696 DPGPPRPPAGATQDEELQGS(ph)PLSR ddPTM_HeLa_Romidepsin_16h_R1 1 DPGPPRPPAGATQDEELQGSPLSR 24 1 H3BPQ5;H3BME5;H3BQE6;H3BQP9;Q58EX7-3;Q58EX7-2;Q58EX7 H3BPQ5 PLEKHG4 Puratrophin-1 1 0 DPGPPRPPAGATQDEELQGS(0.95)PLS(0.05)R 73.603 0.00031588 5519200 310.41 341.22 341.98 368.83 339.86 335.26 249.49 288.09 303.82 346.79 TRUE FALSE FALSE 306.6266035 346.0237041 347.9320184 411.47586 322.515676 313.837968 270.6816744 296.4254296 276.6455783 337.7803458 0.907769227 1.024404494 1.030054066 1.21817585 0.954808887 0.929118499 0.801354128 0.877568613 0.819010288 1 8.399941575 -7.997971823 3.111784561 0.986024952 0.840212244 0.277628164 0.097914153 0.243146276 4.813519197 0.013242284 0.043392135 1.00E-08 7.997971823 -0.145812708 DPLEEMVPLSHLEEEQPPAPES(ph)PESR ddPTM_HeLa_Romidepsin_16h_R1 1 DPLEEMVPLSHLEEEQPPAPESPESR 26 0 O60307 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 0 DPLEEMVPLSHLEEEQPPAPES(0.889)PES(0.111)R 55.09 0.0024018 2721000 1128.9 878.23 1000.1 1118.7 1638.7 1331.4 1198.6 1278.6 1133.6 967.82 TRUE FALSE FALSE 1115.140533 890.593745 1017.506321 1248.049358 1555.071024 1246.327837 1300.409054 1315.594274 1032.207977 942.6758969 1.182952207 0.944750733 1.079380861 1.323943215 1.649634863 1.322117009 1.379486904 1.395595536 1.094976524 1 9.88061803 -9.165547955 3.925030589 1.075028676 1.429741329 0.760630141 0.100272096 0.098531044 2.765768678 0.016701538 0.028320798 6.83E-10 9.165547955 0.354712653 AAS(ph)PHQVTPQADEK ddPTM_HeLa_Romidepsin_16h_R1 3 AASPHQVTPQADEK 14 0 Q96L73-2;Q96L73-3;Q96L73 Q96L73-2 NSD1 "Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific" 1 0 AAS(0.636)PHQVT(0.364)PQADEK;AAS(1)PHQVTPQADEK;AAS(0.986)PHQVT(0.014)PQADEK ;; 171.81 4.18E-05 5392000 5793 4937.4 5097.1 3887.7 2283.76 2343.84 1795.43 1971.82 6330.9 6277.7 TRUE FALSE FALSE 5722.392688 5006.908847 5185.812887 4337.214166 2167.211205 2194.076188 1947.933779 2028.871501 5764.648448 6114.604449 0.93585656 0.818844275 0.848102756 0.709320481 0.354431954 0.358825531 0.318570693 0.331807481 0.942767189 1 12.57804346 -9.011796793 1.062589179 0.966117018 0.299756999 0.961225537 0.053675448 0.062725711 0.139475607 0.009459218 0.023221172 9.73E-10 9.011796793 -0.666360019 down DPQT(ph)PVLQTK ddPTM_HeLa_Romidepsin_16h_R1 1 DPQTPVLQTK 10 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 DPQT(1)PVLQTK 141.34 0.0094668 14098000 4876.2 3909.2 4349.5 4267.5 4798.5 5126.8 4152.9 4186.3 4298.7 4433.1 TRUE FALSE FALSE 4816.766999 3964.23382 4425.201223 4760.928429 4553.614639 4799.214026 4505.647222 4307.423986 3914.213506 4317.927423 1.11552755 0.918087182 1.024843817 1.102595751 1.054583413 1.111462411 1.043474515 0.997567482 0.906502848 1 12.07612328 -12.77668666 1.753202895 0.999883922 1.058317133 0.154598966 0.06481834 0.673284467 3.741336576 0.044335205 0.009371382 1.67E-13 12.77668666 0.058433211 K(ac)ETAQRRVLEESELAR ddPTM_HeLa_Romidepsin_16h_R1 2 KETAQRRVLEESELAR 16 3 Q96SB3 Q96SB3 PPP1R9B Neurabin-2 0 1 ; K(1)ETAQRRVLEESELAR;K(1)ETAQRRVLEESELAR 76.927 0.017894 11720900 356.83 241.281 273.21 1563.84 2771 2509.4 2033.04 2327.66 348.56 497.73 FALSE TRUE FALSE 352.4808187 244.6777603 277.9651054 1744.658539 2629.58553 2349.057439 2205.726367 2395.00717 317.3839206 484.7989028 0.72706604 0.504699493 0.573361664 3.598726253 5.424074837 4.845426475 4.549775905 4.940207487 0.654671285 1 8.921242624 -9.11966618 3.337937598 0.812323206 4.886620468 0.980622734 0.283835429 0.02538615 0.52886852 0.046207803 0.080273762 7.59E-10 9.11966618 4.074297263 up DPS(ph)ASPGDAGEQAIR ddPTM_HeLa_Romidepsin_16h_R1 2 DPSASPGDAGEQAIR 15 0 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 DPS(0.967)AS(0.033)PGDAGEQAIR;DPS(0.5)AS(0.5)PGDAGEQAIR ; 192.4 1.65E-12 33176000 889.32 1089.29 1231.43 1124.44 1408.96 1650.3 1082.63 1361.96 903.15 1313.28 TRUE FALSE FALSE 878.4806258 1104.625053 1252.862523 1254.453043 1337.055514 1544.851156 1174.588565 1401.366164 822.370002 1279.160796 0.68676325 0.863554493 0.979440995 0.980684404 1.045259922 1.207706772 0.918249346 1.095535579 0.642898066 1 10.32098191 -9.446518563 1.827940185 0.849421675 1.057679917 0.484809724 0.118469432 0.304689208 2.013579454 0.021964308 0.036068436 3.58E-10 9.446518563 0.208258242 DPSASNGGGS(ph)PARR ddPTM_HeLa_Romidepsin_16h_R1 2 DPSASNGGGSPARR 14 1 O60504-2;E5RIA0;E5RJP2;O60504 O60504-2 SORBS3 Vinexin 1 0 DPSAS(0.001)NGGGS(0.999)PARR;DPSASNGGGS(1)PARR ; 94.61 0.0044385 9783900 395.25 488.61 576.23 207.04 406.03 386.58 475.92 0 534.76 484.25 TRUE FALSE FALSE 390.432541 495.4886644 586.2590414 230.978939 385.308774 361.8787856 516.3446329 0 486.9297263 471.6691152 0.827767875 1.050500549 1.242945579 0.489705456 0.816904821 0.767230192 1.09471792 0 1.032354485 1 8.881631326 -9.247380115 24.97961208 0.950696841 0.676918241 0.301993672 0.285509456 1014.822996 1803074.064 0.040277296 0.066578838 5.66E-10 9.247380115 -0.2737786 DPSSNDINGGMEPTPSTVSTPS(ph)PSADLLGLR ddPTM_HeLa_Romidepsin_16h_R1 1 DPSSNDINGGMEPTPSTVSTPSPSADLLGLR 31 0 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 0 DPSSNDINGGMEPT(0.001)PS(0.002)T(0.007)VS(0.068)T(0.068)PS(0.786)PS(0.068)ADLLGLR 64.914 8.21E-05 4848200 311.42 457.85 423.99 463 570.78 657.92 644.96 530.41 388.3 462.16 TRUE FALSE FALSE 307.6242933 464.2956243 431.3693681 516.5342385 541.6509667 615.8810353 699.7428863 545.7565765 353.5694755 450.1530166 0.683377167 1.031417334 0.958272748 1.147463683 1.203259662 1.368159298 1.55445562 1.212380138 0.785442866 1 8.814271677 -8.985739829 1.076588476 0.857609055 1.398374954 0.76262753 0.120428716 0.202856053 0.463136219 0.024852668 0.061745574 1.03E-09 8.985739829 0.540765899 DPVQEAWAEDVDLR ddPTM_HeLa_Romidepsin_16h_R1 3 DPVQEAWAEDVDLR 14 0 P14618;B4DNK4;P14618-3;P14618-2;H3BR70 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ;; ;; 267.21 1.60E-80 106090300 5259.59 4366.97 4579.7 6016.29 4564.97 4721.36 4248.64 4470.08 4848.18 4481.34 FALSE FALSE TRUE 5195.484094 4428.448318 4659.407757 6711.921757 4332.002547 4419.680333 4609.519376 4599.414712 4414.546638 4364.914141 1.190283228 1.014555653 1.067468364 1.537698461 0.992459968 1.012546912 1.056038957 1.053723983 1.011370784 1 12.09173756 DQEPKPS(ph)PEPAAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 DQEPKPSPEPAAVSR 15 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 0 DQEPKPS(1)PEPAAVSR 257.72 8.06E-70 8013400 585.13 696.42 669.42 753.37 1046.2 614.49 551.88 561.14 721.45 520.15 TRUE FALSE FALSE 577.9982105 706.224219 681.0709743 840.4781841 992.8085101 575.2260722 598.7566734 577.3757006 656.9217051 506.636428 1.14085403 1.393946783 1.344299258 1.658937529 1.959607433 1.135382378 1.181827126 1.139625318 1.296633382 1 8.984807003 -10.38964832 1.664360772 1.049610381 1.419646465 0.151043126 0.252420673 0.333788584 1.779205757 0.049868199 0.056293885 4.08E-11 10.38964832 0.370036084 DQEWYDAEIAR ddPTM_HeLa_Romidepsin_16h_R1 2 DQEWYDAEIAR 11 0 Q8IVM0;Q8IVM0-2 Q8IVM0 CCDC50 Coiled-coil domain-containing protein 50 0 0 ; ; 147.62 0.02467 11545100 3595 3433.9 3318.2 3128 2696.5 2343.7 2258.3 2492.4 3267.1 3314.7 FALSE FALSE TRUE 3551.182757 3482.242534 3375.951879 3489.674078 2558.887543 2193.945134 2450.119946 2564.513662 2974.882393 3228.583616 1.099919711 1.078566625 1.045644865 1.080868422 0.792572796 0.679537963 0.758883844 0.794315392 0.921420272 1 11.65668568 -8.70564339 5.058677653 1.053012473 0.745528769 0.857225468 0.056188588 0.041935062 2.211980163 0.006919789 0.013902093 1.97E-09 8.70564339 -0.307483704 DQGTYEDYVEGLR ddPTM_HeLa_Romidepsin_16h_R1 3 DQGTYEDYVEGLR 13 0 F8VZU9;G3V1Y7;F8VPF3;F8W1R7;J3KND3;G8JLA2;G3V1V0;F8W180;B7Z6Z4;P60660-2;P60660;H0YI43 F8VZU9 MYL6 Myosin light polypeptide 6 0 0 ;; ;; 249.98 5.05E-52 81440000 4736.62 4803.27 4705.86 3761.03 5348.98 5842.34 4859.61 5625.77 5321.59 5298.48 FALSE FALSE TRUE 4678.888254 4870.890561 4787.763519 4195.897985 5076.001591 5469.033329 5272.385152 5788.542779 4845.613662 5160.824726 0.906616384 0.943820188 0.92771287 0.813028577 0.983564035 1.059720804 1.021616783 1.121631345 0.938922347 1 12.33338592 -8.360875751 3.997370549 0.941307947 1.063473748 0.597507791 0.051875227 0.158499218 4.505546149 0.008557711 0.020173915 4.36E-09 8.360875751 0.122165801 DQHLNNS(ph)SSSPQR ddPTM_HeLa_Romidepsin_16h_R1 1 DQHLNNSSSSPQR 13 0 A0A5H1ZRS1;A0A4W8VX11;E7EV93;E9PGW9 A0A5H1ZRS1 PCM1 1 0 DQHLNNS(0.732)S(0.134)S(0.067)S(0.067)PQR 161.84 0.00014995 12295000 1815.4 1354.7 1483.1 1394.7 2170.6 1868.5 2133.1 875.85 2148 1776.6 TRUE FALSE FALSE 1793.273207 1373.771502 1508.912733 1555.961776 2059.826182 1749.10888 2314.285461 901.1913379 1955.8775 1730.443676 1.036308336 0.793883974 0.871980264 0.89916927 1.190345696 1.010786369 1.337394272 0.520786288 1.130275159 1 10.75692627 -6.079805817 18.73338657 0.994221067 0.984299609 0 0.215656133 0 0 0.0248021 0 8.32E-07 6.079805817 -0.009921458 DQHLNNSS(ph)SSPQR ddPTM_HeLa_Romidepsin_16h_R1 1 DQHLNNSSSSPQR 13 0 A0A5H1ZRS1;A0A4W8VX11;E7EV93;E9PGW9 A0A5H1ZRS1 PCM1 1 0 DQHLNNS(0.039)S(0.461)S(0.039)S(0.461)PQR 217.2 1.18E-23 5652200 1373.7 1446.2 1105.6 1320.6 1718.9 1562.6 1597.5 732.97 2276.7 1889.4 TRUE FALSE FALSE 1356.956816 1466.559642 1124.842504 1473.293986 1631.178119 1462.754903 1733.19161 754.1773305 2073.06625 1840.313116 0.737351054 0.796907672 0.611223435 0.800567019 0.886359014 0.794840232 0.941791696 0.409809246 1.126474746 1 10.84573554 -12.22061028 0.786996228 1.012877823 0.757116851 0.404943798 0.147352533 0.709819586 0.729991627 0.114450941 0.026373164 6.02E-13 12.22061028 -0.255760972 DQKQRT(ph)QVQTIDT(ph)SRQQR ddPTM_HeLa_Romidepsin_16h_R1 1 DQKQRTQVQTIDTSRQQR 18 3 Q8NFW9-4;Q8NFW9-3;Q8NFW9-6;Q8NFW9-2;Q8NFW9 Q8NFW9-4 MYRIP Rab effector MyRIP 2 0 DQKQRT(1)QVQT(0.005)IDT(0.543)S(0.453)RQQR 61.903 0.024009 51270000 3422.8 3126.1 3158.9 3321.4 3785.6 3993.1 3136.9 3435.9 3729.2 3460.1 TRUE FALSE FALSE 3381.081597 3170.109318 3213.879329 3705.435896 3592.406706 3737.953797 3403.348208 3535.312346 3395.651012 3370.206103 1.003226952 0.94062773 0.95361507 1.099468633 1.065930865 1.109117271 1.009833851 1.048989954 1.007549956 1 11.71862111 -9.258817128 24.99997088 0.992760029 1.065827984 0.614885585 0.033249589 144.3720771 1376409.484 0.005253671 0.008463279 5.51E-10 9.258817128 0.073067955 DQMEGS(ph)PNSSESFEHIAR ddPTM_HeLa_Romidepsin_16h_R1 1 DQMEGSPNSSESFEHIAR 18 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3;Q9Y520-2 E7EPN9 PRRC2C Protein PRRC2C 1 0 DQMEGS(0.973)PNS(0.025)S(0.001)ESFEHIAR 135.95 4.54E-10 0 763.67 1158.9 824.99 826.43 1406.1 1823.5 1424.9 1129.8 1096.3 1160.9 TRUE FALSE FALSE 754.3620963 1175.215025 839.3486049 921.9857251 1334.34147 1706.984235 1545.93097 1162.48898 998.2441823 1130.739651 0.667140394 1.039332992 0.742300497 0.815382855 1.180060741 1.509617385 1.367185602 1.028078373 0.882824072 1 10.14305108 -8.654591583 4.183248429 0.845455338 1.312990765 0.643260524 0.152151119 0.110801347 3.503773727 0.025188787 0.051726974 2.22E-09 8.654591583 0.467535428 DQPAFTPSGILT(ph)PHALGSR ddPTM_HeLa_Romidepsin_16h_R1 2 DQPAFTPSGILTPHALGSR 19 0 Q9H0D6-2;Q9H0D6 Q9H0D6-2 XRN2 5-3 exoribonuclease 2 1 0 DQPAFTPS(0.012)GILT(0.988)PHALGSR;DQPAFT(0.001)PS(0.019)GILT(0.902)PHALGS(0.078)R ; 113.05 0.00060983 15933900 3991.5 4048.3 4334.1 3229.1 5119.4 5284 4511 5084.7 5418.6 4990.6 TRUE FALSE FALSE 3942.850063 4105.292074 4409.533192 3602.463735 4858.137915 4946.369453 4894.164227 5231.817772 4933.946845 4860.943493 0.811128553 0.844546348 0.90713525 0.741103809 0.999422833 1.017573946 1.006834215 1.076296768 1.01501835 1 12.24702065 -8.546601645 24.88450679 0.891417553 1.027162216 0.431574438 0.078403554 181.4452835 190329.1617 0.012796631 0.025594288 2.84E-09 8.546601645 0.135744663 DQPPFGDSDDS(ph)VEADK ddPTM_HeLa_Romidepsin_16h_R1 1 DQPPFGDSDDSVEADK 16 0 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 DQPPFGDS(0.047)DDS(0.953)VEADK 202.6 1.73E-18 1625400 564.1 576.82 540.65 237.95 571.85 574.9 432.68 583.6 678.02 489.63 TRUE FALSE FALSE 557.2245322 584.9404871 550.0597865 265.4628986 542.6663606 538.1657454 469.4318284 600.4855452 617.3761931 476.909342 1.168407668 1.226523441 1.153384381 0.556631786 1.137881591 1.128444545 0.984320891 1.259118856 1.294535751 1 8.897571233 -11.0065444 0.003016353 8.92E-05 2.139221395 0 0.203530833 234362.3882 413.5267022 147275.424 145977.281 9.85E-12 11.0065444 2.139132221 DQQEAALVDMVNDGVEDLR ddPTM_HeLa_Romidepsin_16h_R1 4 DQQEAALVDMVNDGVEDLR 19 0 P09211;A8MX94 P09211 GSTP1 Glutathione S-transferase P 0 0 ;;; ;;; 128.82 0.0020396 83883400 13541.7 13898.1 13390.8 11124.2 14882 14732.6 13631.4 14448.9 16082.7 15092.9 FALSE FALSE TRUE 13376.64855 14093.75782 13623.86126 12410.43234 14122.51601 13791.23441 14789.25078 14866.95612 14644.22303 14700.78428 0.909927545 0.958707886 0.926743839 0.844202058 0.960664121 0.93812916 1.006017808 1.011303604 0.996152501 1 13.8436055 -7.755255644 22.75049444 0.945613479 1.008660832 0.28216802 0.042301162 54.94415765 202122.9826 0.006631155 0.023480822 1.76E-08 7.755255644 0.063047354 DQQNLPYGVTPAS(ph)PSGHSQGR ddPTM_HeLa_Romidepsin_16h_R1 1 DQQNLPYGVTPASPSGHSQGR 21 0 E7ETY4;E9PC69;Q7KZI7-10;Q7KZI7-12;Q7KZI7-8;Q7KZI7-11;Q7KZI7-6;Q7KZI7-3;Q7KZI7-14;Q7KZI7-9;Q7KZI7-13;Q7KZI7-4;Q7KZI7-16;Q7KZI7-5;Q7KZI7-15;Q7KZI7-2;Q7KZI7-7;Q7KZI7 E7ETY4 MARK2 Serine/threonine-protein kinase MARK2 1 0 DQQNLPYGVT(0.002)PAS(0.861)PS(0.118)GHS(0.019)QGR 185.92 4.33E-21 0 998.24 967.36 1024.2 794.92 1452.3 1261.2 1109.2 1114.3 1502 1343.2 TRUE FALSE FALSE 986.0730669 980.9785195 1042.025771 886.8323906 1378.183712 1180.61339 1203.41542 1146.540512 1367.657358 1308.30347 0.753703624 0.749809614 0.796470998 0.677849146 1.053412869 0.902400259 0.91982896 0.8763567 1.045367064 1 10.35348151 -8.736103892 24.99880384 0.849694391 0.934158848 0.151290512 0.114547348 451.7572456 445751.8199 0.018290864 0.036570338 1.84E-09 8.736103892 0.084464457 DQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_HeLa_Romidepsin_16h_R1 1 DQQPSGSEGEDDDAEAALKK 20 1 H3BNW0;Q9NXG2 H3BNW0 THUMPD1 THUMP domain-containing protein 1 2 0 DQQPS(1)GS(1)EGEDDDAEAALKK 55.688 0.012371 3076900 1453.2 1619.7 1147.4 1167.7 1001.5 1325.4 946.01 1298.1 1236.6 1417 TRUE FALSE FALSE 1435.487839 1642.502179 1167.370016 1302.714968 950.3897179 1240.711218 1026.364066 1335.658475 1125.995399 1380.186136 1.040068294 1.190058454 0.845806218 0.943869044 0.688595323 0.898944849 0.743641774 0.967737931 0.815828655 1 10.43064713 -9.674415259 12.63111749 1.032269486 0.842555174 0.314566489 0.116384794 0.37598302 52.91749355 0.0138202 0.019544674 2.12E-10 9.674415259 -0.189714312 DQS(ph)PFSK ddPTM_HeLa_Romidepsin_16h_R1 4 DQSPFSK 7 0 Q13427;E9PG73 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 0 DQS(0.984)PFS(0.016)K;DQS(0.972)PFS(0.028)K;DQS(0.977)PFS(0.023)K;DQS(0.928)PFS(0.072)K ;;; 152.11 0.010931 788820000 36103.7 36349.8 42445.5 26652.3 34326.8 37094.1 41279.7 21548.3 43172.7 41627.3 TRUE FALSE FALSE 35663.65422 36861.53344 43184.24612 29733.96433 32574.97531 34723.90673 44785.99669 22171.76606 39311.22558 40545.81675 0.879588995 0.909132838 1.065072789 0.733342345 0.803411496 0.856411574 1.104577495 0.546832395 0.969550714 1 15.30726545 -9.254402612 24.99808436 0.946917083 0.827673698 0.232578318 0.13751802 801.9281544 2848844.4 0.019791832 0.03236342 5.57E-10 9.254402612 -0.119243385 DQT(ph)PDENDQVVVK ddPTM_HeLa_Romidepsin_16h_R1 2 DQTPDENDQVVVK 13 0 O00425-2;O00425 O00425-2 IGF2BP3 Insulin-like growth factor 2 mRNA-binding protein 3 1 0 DQT(1)PDENDQVVVK;DQT(1)PDENDQVVVK ; 201.75 5.97E-16 15518400 7905.1 6970.8 6172.3 6806.1 6564.2 6980 5646.8 7395.2 7136.9 6979.3 TRUE FALSE FALSE 7808.749601 7068.935105 6279.726292 7593.053306 6229.20438 6534.000527 6126.439051 7609.168444 6498.557789 6797.97678 1.148687301 1.039858672 0.92376401 1.116957817 0.916332106 0.961168409 0.90121506 1.119328396 0.955954691 1 12.73088972 -9.990470223 23.85534728 1.071479741 0.986483041 0.014115357 0.087094341 154.4834303 386706.308 0.013744007 0.018046936 1.02E-10 9.990470223 -0.0849967 DQTASAPAT(ph)PLVNK ddPTM_HeLa_Romidepsin_16h_R1 3 DQTASAPATPLVNK 14 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2;A0A0B4J1Z0 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 0 DQT(0.042)AS(0.032)APAT(0.926)PLVNK;DQT(0.002)AS(0.116)APAT(0.882)PLVNK;DQT(0.007)AS(0.098)APAT(0.895)PLVNK ;; 174.4 3.69E-05 34544500 8486.3 8133.3 8278.2 7829.1 7305 7134.8 5474.94 5450.49 8462 8608.8 TRUE FALSE FALSE 8382.865711 8247.800811 8422.278598 8734.337379 6932.198591 6678.909307 5939.981267 5608.191329 7705.137527 8385.142135 0.999728517 0.983620871 1.004428841 1.041644523 0.826724041 0.796517125 0.708393629 0.668824838 0.918903628 1 13.03361952 -8.359430709 1.458404876 1.002116675 0.689505431 0.890303161 0.042445313 0.06666785 0.26699807 0.004717263 0.016424129 4.37E-09 8.359430709 -0.312611244 DQTDFEHR ddPTM_HeLa_Romidepsin_16h_R1 2 DQTDFEHR 8 0 F8VZI0;A0A2R8Y891;P08237-2;P08237;P08237-3 F8VZI0 PFKM "ATP-dependent 6-phosphofructokinase, muscle type" 0 0 ; ; 167.12 0.00084105 10576100 6108.8 6493.2 8113.5 5789.4 6074.5 7233.7 6833.5 3864.7 7949.1 6852.2 FALSE FALSE TRUE 6034.343596 6584.61144 8254.712064 6458.797668 5764.495598 6771.489916 7413.937319 3976.518997 7238.112587 6674.178856 0.904132737 0.98658001 1.236813133 0.967729185 0.863701097 1.01458023 1.110838873 0.595806478 1.084494848 1 12.70437463 -7.249070035 24.52058156 0.981408674 0.595806163 0.565414347 0.106816149 901.1958975 1786460.721 0.01457007 0.333546481 5.64E-08 7.249070035 -0.385602511 DQVANS(ph)AFVER ddPTM_HeLa_Romidepsin_16h_R1 1 DQVANSAFVER 11 0 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 1 0 DQVANS(1)AFVER 113.43 0.013012 6384000 1668.6 1554.7 1797.9 1242 1639.6 1737.7 1583.7 2257.1 1505.8 1571.5 TRUE FALSE FALSE 1648.262461 1576.587107 1829.191695 1385.605884 1555.925094 1626.666578 1718.219438 2322.405627 1371.117477 1530.672203 1.076822626 1.029996562 1.195025095 0.90522705 1.016497909 1.062713868 1.122526061 1.517245575 0.895761662 1 10.57994964 -7.20405916 2.264879633 1.038308623 1.684347595 0.765098266 0.081664017 0.22737915 1.178499283 0.009375472 0.307853126 6.25E-08 7.20405916 0.646038972 DQVTAQEIFQDNHEDGPTAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 DQVTAQEIFQDNHEDGPTAKK 21 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 1 DQVTAQEIFQDNHEDGPTAK(1)K 56.684 0.028959 1050000 279.44 182.39 187.63 214.52 408.88 439.37 356.34 495.2 262.7 378.87 FALSE TRUE FALSE 276.0340778 184.9576912 190.8956214 239.3238117 388.0133279 411.295675 386.6075107 509.5278307 239.2034541 369.0269028 0.748005296 0.501203814 0.517294593 0.648526733 1.051449975 1.114541167 1.047640451 1.380733564 0.648200584 1 8.527582185 -8.587427302 5.230759696 0.802064038 1.155728144 0.579889351 0.180485275 0.165519483 8.812002444 0.031663597 0.064722204 2.59E-09 8.587427302 0.353664106 DQYS(ph)ELLK ddPTM_HeLa_Romidepsin_16h_R1 2 DQYSELLK 8 0 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 1 0 DQY(0.008)S(0.992)ELLK;DQY(0.002)S(0.998)ELLK ; 119.75 0.018891 17790700 8615.3 8241.2 5994.4 2212.48 8714.3 8418.7 8208.2 8644.3 9477.8 9684.2 TRUE FALSE FALSE 8510.29341 8357.21983 6098.730017 2468.297348 8269.576753 7880.77224 8905.404303 8894.409182 8630.08183 9432.603088 0.902221087 0.885992949 0.646558533 0.261677219 0.876701445 0.835482228 0.944108876 0.942943226 0.914920489 1 13.20344025 -9.953085539 5.131566365 0.951309089 0.747386009 0.173635961 0.188129215 0.2534983 15.13250384 0.032691041 0.042914944 1.11E-10 9.953085539 -0.20392308 DQYSVIFESGDR ddPTM_HeLa_Romidepsin_16h_R1 2 DQYSVIFESGDR 12 0 P55884;P55884-2;C9JZG1;C9JQN7 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 0 ; ; 210.95 5.86E-20 46156000 3305.3 3832.3 2879.2 3779.9 3171.7 3526.6 3328.6 2843.7 3356.1 3387.9 FALSE FALSE TRUE 3265.013732 3886.25122 2929.311268 4216.949823 3009.836314 3301.261642 3611.331201 2925.977973 3055.92201 3299.88187 0.98943352 1.177694043 0.887701858 1.277909328 0.912104261 1.000418128 1.094381964 0.886691733 0.926070123 1 11.68819866 -7.235594769 21.98311963 1.018604323 0.886690854 0.112151369 0.116986741 2337.961829 1988478.835 0.013879195 1.047523082 5.81E-08 7.235594769 -0.131913469 DRDGYS(ph)YGSR ddPTM_HeLa_Romidepsin_16h_R1 1 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJK4;A0A590UK01;A0A590UJP7;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 0 DRDGYS(1)YGSR 133.88 9.29E-05 0 1609.8 1321.1 1343.5 1317.5 1500.2 1550.3 1185.9 1294.2 1577.8 1827.8 TRUE FALSE FALSE 1590.179138 1339.69848 1366.883054 1469.835549 1423.639196 1451.240833 1286.630316 1331.645635 1436.677616 1780.313493 0.893201756 0.752507065 0.767776608 0.825604903 0.799656466 0.815160273 0.722698739 0.747983791 0.806980132 1 10.79791559 -10.80092872 0.692056108 0.98734927 0.769733632 0.242181369 0.067354828 0.170918268 0.182495161 0.013933886 0.011279318 1.58E-11 10.80092872 -0.217615638 DRDGYSYGSR ddPTM_HeLa_Romidepsin_16h_R1 3 DRDGYSYGSR 10 1 Q13247;Q13247-3;A0A590UJK4;A0A590UK01;A0A590UJP7;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 0 ;; ;; 144.77 0.0046641 6649300 1881.98 1953.94 1762.17 2035.84 1826.74 1880.04 1873.08 1166.22 2121.42 1894.15 FALSE FALSE TRUE 1859.041704 1981.447619 1792.83983 2271.2334 1733.514641 1759.911512 2032.179368 1199.962736 1931.674882 1844.93971 1.007643607 1.073990444 0.97176066 1.231061041 0.939605035 0.95391275 1.101488226 0.65040756 1.04701247 1 10.84935796 -7.253412564 24.73833684 1.018722822 0.65040735 0.655624359 0.083024795 388.0597558 1195953.413 0.010464281 0.153420035 5.58E-08 7.253412564 -0.368315472 DRDYFDYSR ddPTM_HeLa_Romidepsin_16h_R1 1 DRDYFDYSR 9 1 Q9HCG8;B7WP74 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 0 0 122.96 0.013529 7896500 2561.8 2167.3 2211 2013.2 2123.6 2163.4 1745.6 1926.8 2634.8 1989.9 FALSE FALSE TRUE 2530.575796 2197.811306 2249.481528 2245.975656 2015.224768 2025.165722 1893.87122 1982.548918 2399.136889 1938.202111 1.305630502 1.133943304 1.160602145 1.158793319 1.039739229 1.044868185 0.977127829 1.022880383 1.237815641 1 10.9205033 -8.681280992 3.84845098 1.149235261 1.015261007 0.459654316 0.075899408 0.262581869 7.543894837 0.016670592 0.034232838 2.08E-09 8.681280992 -0.133974255 DREAAEGLGSHDR ddPTM_HeLa_Romidepsin_16h_R1 2 DREAAEGLGSHDR 13 1 P17655 P17655 CAPN2 Calpain-2 catalytic subunit 0 0 ; ; 102.5 0.0045127 8184500 4209 4353.6 4687.3 4109 3790.1 3972.6 3612.4 3321.3 4500.2 4173.4 FALSE FALSE TRUE 4157.699089 4414.890095 4768.88049 4584.101913 3596.677054 3718.763681 3919.237166 3417.396575 4097.690841 4064.974466 1.022810629 1.086080646 1.173163701 1.127707431 0.884796961 0.91483076 0.96414804 0.840693245 1.008048359 1 11.98903057 -8.741644475 24.99991837 1.038139401 0.906598946 0.612086262 0.062726382 177.6690454 224385.5671 0.010466185 0.020910452 1.81E-09 8.741644475 -0.131540454 DREDYVPYTGEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DREDYVPYTGEKK 13 2 Q9NYL9 Q9NYL9 TMOD3 Tropomodulin-3 0 1 ; DREDYVPYTGEK(1)K;DREDYVPYTGEK(1)K 113.53 0.0040997 2031090 437.54 354.28 520.47 464.639 460.47 633.34 539.05 619.1 688.88 533.41 FALSE TRUE FALSE 432.2070942 359.2675631 529.528562 518.3627474 436.9704976 592.871618 584.8368935 637.0126817 627.2648475 519.5519313 0.831884299 0.691495001 1.019202374 0.997711136 0.84105259 1.141120997 1.125656279 1.226080866 1.207318864 1 9.021124149 -8.20948749 6.944011264 0.910255783 1.162431514 0.351549195 0.134315159 0.152239181 17.03943467 0.015206789 0.038940619 6.17E-09 8.20948749 0.252175732 DREEALHQFR ddPTM_HeLa_Romidepsin_16h_R1 1 DREEALHQFR 10 1 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1;O15523-2;O15523;A0A2R8YDH3 A0A2R8Y4A4 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 0 92.538 0.014 19812000 2222.6 1848.6 2197.6 2020.9 2005.3 2067.7 1589.7 1547.7 1872.6 1957.9 FALSE FALSE TRUE 2195.510096 1874.624639 2235.848306 2254.565967 1902.962058 1935.580643 1724.729078 1592.480258 1705.109966 1907.033476 1.151269825 0.983005628 1.17242216 1.182237226 0.997865052 1.014969411 0.904404196 0.835056268 0.894116431 1 10.89711445 -7.741162084 1.389117463 1.07922163 0.818575733 0.398524975 0.089125398 0.362093672 1.060046805 0.011632701 0.10295537 1.81E-08 7.741162084 -0.260645897 DREEDEEDAYER ddPTM_HeLa_Romidepsin_16h_R1 3 DREEDEEDAYER 12 1 P49756 P49756 RBM25 RNA-binding protein 25 0 0 ;; ;; 177.16 2.20E-06 33896000 7672.8 6901.4 6898.9 6985.2 7287 7411.1 6650.6 7564.3 8377.5 7205.7 FALSE FALSE TRUE 7579.280962 6998.55809 7018.972461 7792.86169 6915.117198 6937.554628 7215.501798 7783.161086 7628.195418 7018.494875 1.079901189 0.997159393 1.000068047 1.110332319 0.985270677 0.988467578 1.028069682 1.10895017 1.086870555 1 12.77694596 DREEDEEDAYERR ddPTM_HeLa_Romidepsin_16h_R1 2 DREEDEEDAYERR 13 2 P49756 P49756 RBM25 RNA-binding protein 25 0 0 ; ; 107.03 0.0028156 13875900 4224.9 4094 3733.2 4130.4 3917.8 3883.2 3700 3891.6 3830.2 3814.1 FALSE FALSE TRUE 4173.405294 4151.635439 3798.17478 4607.976282 3717.860047 3635.076052 4014.277908 4004.197306 3487.617319 3715.009132 1.123390319 1.117530346 1.022386391 1.240367417 1.000767404 0.978483746 1.080556673 1.077843193 0.938791049 1 11.85915004 DREPYFDR ddPTM_HeLa_Romidepsin_16h_R1 2 DREPYFDR 8 1 H0YIQ2;P49750-3;P49750-1;P49750;F8VU51;H0YI23 H0YIQ2 YLPM1 YLP motif-containing protein 1 0 0 ; ; 128.38 0.014445 15754800 4064.1 3997.9 3574.5 4181.3 4470.8 4993.9 3610.3 3778 3918.3 2908.3 FALSE FALSE TRUE 4014.565186 4054.182541 3636.712673 4664.76158 4242.638393 4674.805907 3916.958792 3887.310469 3567.837434 2832.741947 1.417201165 1.43118668 1.283813613 1.646730153 1.497714396 1.65027595 1.382744657 1.372278359 1.25949963 1 11.46798347 -12.12694555 0.444239078 0.891013553 1.495424014 0.460824834 0.133044222 0.692494513 0.196621641 0.190113227 0.033656409 7.47E-13 12.12694555 0.604410461 DRFGLEGDEESTMLEES(ph)VSPK ddPTM_HeLa_Romidepsin_16h_R1 1 DRFGLEGDEESTMLEESVSPK 21 1 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 1 0 DRFGLEGDEESTMLEES(0.587)VS(0.413)PK 95.153 0.00084599 5551700 1810.8 2131.9 2248.1 1741.6 2406 2275.7 1996.5 2300.4 1829 1999.3 TRUE FALSE FALSE 1788.729273 2161.912944 2287.227237 1942.971986 2283.212842 2130.290114 2166.08266 2366.958445 1665.409659 1947.357898 0.918541617 1.110177511 1.174528442 0.997747763 1.172466984 1.093938673 1.112318728 1.215471715 0.855214987 1 10.92730234 -10.22454335 8.768264619 0.961548704 1.12250188 0.640585441 0.067164749 0.181694273 41.19522273 0.00977651 0.011937577 5.96E-11 10.22454335 0.160953177 DRFGLEGDEESTMLEESVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DRFGLEGDEESTMLEESVSPK 21 1 Q9Y4G6 Q9Y4G6 TLN2 Talin-2 1 0 DRFGLEGDEEST(0.002)MLEES(0.188)VS(0.81)PK 69.981 0.0072678 13515000 1706.7 1804.3 1442.5 1575 1881.2 1914.3 1864.9 1853.6 1729.3 1851.8 TRUE FALSE FALSE 1685.898084 1829.700983 1467.606107 1757.108911 1785.195344 1791.982408 2023.304559 1907.230992 1574.627077 1803.689969 0.93469394 1.014421 0.813668719 0.974174576 0.989746229 0.993509106 1.121758503 1.057405111 0.873003179 1 10.81673566 -7.902414601 4.106009115 0.962372026 1.089028715 0.447146056 0.061796314 0.144211482 4.455806067 0.00778577 0.025546267 1.25E-08 7.902414601 0.126656689 DRFS(ph)AEDEALSNIAR ddPTM_HeLa_Romidepsin_16h_R1 1 DRFSAEDEALSNIAR 15 1 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608;C9JJC9;C9JC17;C9J321;C9J0U5 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 DRFS(1)AEDEALSNIAR 110.44 0.0015506 2963500 1660.8 1433.8 1427.9 1384.3 1667.5 1463.5 1271.4 1226.2 1612.6 1923.6 TRUE FALSE FALSE 1640.557531 1453.985074 1452.752001 1544.359279 1582.401253 1369.987073 1379.392684 1261.678162 1468.365017 1873.624595 0.875606317 0.776027961 0.775369839 0.82426292 0.844566866 0.731196141 0.736216149 0.673388984 0.783702894 1 10.8716162 -11.36322443 0.04451242 1.806250345 2.13E-10 0.175294125 0.078399535 23.28359256 0.458554576 10.18067114 8.324759973 4.33E-12 11.36322443 -1.806250345 DRNVIPDT(ph)PPS(ph)TPLVPSRASSEWDIKK ddPTM_HeLa_Romidepsin_16h_R1 1 DRNVIPDTPPSTPLVPSRASSEWDIKK 27 3 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 2 0 DRNVIPDT(0.896)PPS(0.529)T(0.529)PLVPS(0.042)RAS(0.002)S(0.002)EWDIKK 40.682 0.022893 11163000 1428.1 1724.5 1258.8 1404.7 1742 1797.4 1444.3 1883.8 1270.6 1444.4 TRUE FALSE FALSE 1410.693768 1748.777556 1280.708886 1567.118023 1653.09924 1682.551941 1566.978806 1938.304781 1156.954354 1406.87428 1.002714875 1.243023333 0.910322197 1.113900542 1.17501561 1.195950459 1.113801587 1.377738444 0.822358025 1 10.4582777 -4 0.260250061 0.989168123 3.192730664 0.528659429 0.107490478 25.56027375 0.321953955 0.043360546 25.30239324 1.00E-04 4 2.203562541 DRNVIPDT(ph)PPSTPLVPSR ddPTM_HeLa_Romidepsin_16h_R1 1 DRNVIPDTPPSTPLVPSR 18 1 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 0 DRNVIPDT(0.999)PPSTPLVPSR 121.65 0.00087652 6924600 1188.3 1078.9 1327.9 1564.5 1776.4 1610.4 1897.7 1788 1242 1357.9 TRUE FALSE FALSE 1173.816543 1094.088783 1351.011542 1745.394851 1685.743679 1507.500637 2058.890591 1839.732959 1130.912409 1322.621562 0.887492368 0.827212268 1.021464931 1.319647964 1.274547253 1.139782293 1.556673995 1.39097457 0.855053661 1 10.36918461 -9.314234405 3.366178704 0.935852724 1.33821463 0.787129124 0.109358225 0.093569855 2.139883161 0.017575322 0.028243298 4.85E-10 9.314234405 0.402361906 DRPFFPGLVK ddPTM_HeLa_Romidepsin_16h_R1 1 DRPFFPGLVK 10 1 Q32Q12;P22392-2;P22392;J3KPD9;F6XY72;O60361 Q32Q12 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 0 112.36 0.018905 9642500 5894.9 4009.5 10198 8904.6 9927.6 7050.4 5451.2 3326.5 3445.6 2573.1 FALSE FALSE TRUE 5823.050691 4065.945846 10375.49191 9934.191749 9420.957527 6599.902194 5914.224792 3422.747029 3137.416906 2506.250491 2.323411292 1.622322214 4.139846336 3.963766505 3.75898481 2.633376918 2.359789978 1.365684333 1.251836924 1 11.2913149 -11.19955425 0.6964496 1.137346131 2.93990833 0.372170609 0.879356574 0.50325407 0.53455186 0.39952972 0.236886788 6.32E-12 11.19955425 1.802562198 DRPGS(ph)PESPLLDAPFSR ddPTM_HeLa_Romidepsin_16h_R1 4 DRPGSPESPLLDAPFSR 17 1 A0A2R8Y5P9;Q8TF72 A0A2R8Y5P9 SHROOM3 Protein Shroom3 1 0 DRPGS(0.968)PES(0.032)PLLDAPFSR;DRPGS(0.998)PES(0.002)PLLDAPFSR;DRPGS(0.978)PES(0.022)PLLDAPFSR;DRPGS(0.999)PES(0.001)PLLDAPFSR ;;; 130.38 0.0031899 49108900 5499 6958.09 5548.57 5877.68 5303.09 5692.54 4193.94 4703.97 6277.33 6544.47 TRUE FALSE FALSE 5431.976073 7056.046174 5645.140533 6557.285017 5032.453529 5328.805066 4550.173159 4840.07195 5715.869883 6374.443726 0.852149035 1.106927361 0.885589516 1.02868349 0.789473363 0.835963936 0.713814939 0.759293228 0.896685284 1 12.63808373 -8.673149753 7.258190556 0.945607309 0.772680785 0.58564067 0.076419669 0.145561487 10.22474476 0.011936664 0.023935824 2.12E-09 8.673149753 -0.172926523 DRPQEADGIDSVIVVDNVPQVGPDR ddPTM_HeLa_Romidepsin_16h_R1 1 DRPQEADGIDSVIVVDNVPQVGPDR 25 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 0 0 111.65 3.28E-06 2444100 1343.2 1041 802.94 804.4 1099.8 1103.5 813.44 958.1 972.41 1104.3 FALSE FALSE TRUE 1326.828562 1055.655225 816.9148339 897.4085128 1043.673102 1032.989911 882.5335733 985.8211119 885.4352142 1075.610127 1.233559009 0.98144783 0.75948972 0.834325087 0.970307992 0.960375777 0.820495783 0.916522713 0.823193453 1 10.07093953 -10.00417199 24.38110151 1.110145007 0.879624706 0.111305948 0.120743732 77.03542533 450198.8852 0.016934906 0.02195727 9.90E-11 10.00417199 -0.230520301 DRPVGGS(ph)PGGPR ddPTM_HeLa_Romidepsin_16h_R1 1 DRPVGGSPGGPR 12 1 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 0 DRPVGGS(1)PGGPR 90.259 0.010377 27384000 898.8 804.58 622.24 811.97 642.23 526.48 432.5 642.99 771.1 542.92 TRUE FALSE FALSE 887.8450799 815.9068984 633.0698262 905.8537918 609.4546066 492.8396271 469.2365392 661.5939012 702.1308847 528.8148601 1.678933681 1.54289707 1.197148329 1.712988534 1.152491453 0.931970079 0.887336145 1.251087954 1.32774424 1 9.046618908 -8.53041812 24.83423544 1.36370868 1.015248301 0.378444711 0.222195548 184.0096412 606115.4216 0.04271439 0.085565795 2.95E-09 8.53041812 -0.348460379 DRPVS(ph)QPSLVGSK ddPTM_HeLa_Romidepsin_16h_R1 2 DRPVSQPSLVGSK 13 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 DRPVS(1)QPSLVGSK;DRPVS(1)QPSLVGSK ; 102.84 0.004093 27661000 7956.5 10233.1 7581.4 5116.2 8056.3 6523.4 4829.7 5817 7138.5 8110 TRUE FALSE FALSE 7859.523118 10377.16185 7713.351087 5707.759116 7645.156949 6106.575793 5239.934597 5985.305717 6500.014681 7899.301031 0.994964376 1.313681022 0.97645995 0.722565084 0.967827016 0.773052675 0.663341551 0.757700674 0.822859473 1 12.94750929 -9.357218821 5.468978435 1.026321308 0.781539847 0.457238053 0.133912982 0.147916015 6.764952385 0.018682843 0.028738042 4.39E-10 9.357218821 -0.24478146 DRRPS(ph)VDAPVTDVGFLR ddPTM_HeLa_Romidepsin_16h_R1 1 DRRPSVDAPVTDVGFLR 17 2 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8;G3V536;G3V3S3 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 DRRPS(1)VDAPVTDVGFLR 70.02 0.028878 9557200 2002.1 2318.6 1790.5 1784.5 928.19 995.67 952.51 910.03 2265.2 2110.1 TRUE FALSE FALSE 1977.697635 2351.241312 1821.662901 1990.832286 880.8210007 932.0499004 1033.416176 936.3602823 2062.594839 2055.279298 0.962252496 1.144000873 0.886333504 0.968643186 0.428565111 0.453490628 0.50281058 0.455587853 1.00355939 1 11.00511874 -8.764922915 24.78814281 0.986412787 0.462690212 0.945881314 0.062559743 12.04244006 85692.59284 0.00882259 0.016470283 1.72E-09 8.764922915 -0.523722575 DRRRAALTGNLSLGLPAAQPQNT(ph)FFNT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DRRRAALTGNLSLGLPAAQPQNTFFNTK 28 3 Q9C0I9-2;Q9C0I9 Q9C0I9-2 LRRC27 Leucine-rich repeat-containing protein 27 2 0 DRRRAALT(0.002)GNLS(0.02)LGLPAAQPQNT(0.983)FFNT(0.995)K 41.423 0.0041037 0 551 504.04 851.24 298.31 592.05 469.03 471.84 438.96 667.2 588.81 TRUE FALSE FALSE 544.2842001 511.1358884 866.0554751 332.8020058 561.8354793 439.0604967 511.9180778 451.660615 607.523961 573.5126313 0.949036116 0.891237369 1.510089626 0.580287142 0.979639242 0.765563778 0.892601226 0.787533858 1.059303541 1 9.163681451 DRS(ph)SPPPGYIPDELHQVAR ddPTM_HeLa_Romidepsin_16h_R1 4 DRSSPPPGYIPDELHQVAR 19 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 0 DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR;DRS(0.481)S(0.481)PPPGY(0.038)IPDELHQVAR;DRS(0.5)S(0.5)PPPGYIPDELHQVAR ;;; 149.86 1.02E-05 72109300 14705.8 13423.9 13697.5 14699.8 13136.5 13208.3 11123.6 11255 15070.4 13730.2 TRUE FALSE FALSE 14526.56005 13612.88202 13935.89924 16399.46004 12466.09539 12364.33226 12068.43831 11580.64567 13722.46568 13373.48742 1.086220788 1.017900685 1.042054238 1.226266532 0.932149931 0.924540613 0.902415198 0.865940596 1.026094783 1 13.70708811 -8.547611852 24.99954127 1.052580215 0.903149493 0.617491598 0.061579923 124.5223356 125863.2519 0.009325194 0.018650944 2.83E-09 8.547611852 -0.149430722 DRSWVIGS(ph)PEILR ddPTM_HeLa_Romidepsin_16h_R1 1 DRSWVIGSPEILR 13 1 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 DRS(0.001)WVIGS(0.999)PEILR 76.586 0.0037949 0 1442.7 1561.8 1335.9 1926 1670.8 1225.7 1180 1299.5 1713.4 1464.4 TRUE FALSE FALSE 1425.115817 1583.787061 1359.150779 2148.693182 1585.532841 1147.381726 1280.229171 1337.098982 1560.149213 1426.354677 0.999131451 1.110373939 0.952884161 1.506422783 1.111597885 0.804415441 0.897553176 0.937423913 1.09380173 1 10.47811705 -8.264659393 24.92764253 1.049959294 0.881573077 0.262807849 0.155422424 351.9658893 2724745.049 0.023237592 0.054092829 5.44E-09 8.264659393 -0.168386218 DRVTDALNATR ddPTM_HeLa_Romidepsin_16h_R1 1 DRVTDALNATR 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 109.39 0.0023918 0 1861.7 1995.2 1953.6 1672.5 1636 1922.6 1800.4 1598.9 2124.5 1680.7 FALSE FALSE TRUE 1839.008884 2023.288478 1987.601589 1865.882319 1552.508815 1799.752065 1953.325931 1645.161649 1934.479399 1637.035172 1.123377748 1.235946859 1.21414715 1.139793666 0.948366194 1.09939731 1.193209508 1.004964143 1.181696907 1 10.6768696 -12.00341937 1.001824141 1.005800863 1.121652854 0 0.100699234 0.609856734 1.177839158 0.044437031 0.016616164 9.92E-13 12.00341937 0.115851991 DRYDSFIELQEK ddPTM_HeLa_Romidepsin_16h_R1 2 DRYDSFIELQEK 12 1 Q9NSD9-2;Q9NSD9 Q9NSD9-2 FARSB Phenylalanine--tRNA ligase beta subunit 0 0 ; ; 146.67 0.0017023 15036900 7692 6522.4 6909.4 7618.9 8045.6 7670.5 6956.5 7618.9 7876.1 7680.2 FALSE FALSE TRUE 7598.246945 6614.222518 7029.655209 8499.833066 7635.00301 7180.379805 7547.384936 7839.340851 7171.64189 7480.667297 1.015717802 0.884175469 0.939709645 1.136239954 1.020631276 0.959858195 1.008918675 1.047946733 0.958690128 1 12.86895125 -7.289739844 4.596230251 1.001047771 1.049904037 0.049971926 0.0630933 0.470402818 23.95066341 0.008454274 0.068274251 5.13E-08 7.289739844 0.048856266 DS(ph)DGVDGFEAEGK ddPTM_HeLa_Romidepsin_16h_R1 1 DSDGVDGFEAEGK 13 0 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 0 DS(1)DGVDGFEAEGK 204.17 1.96E-16 11997000 4575.8 3700.1 4449.6 2532.3 3742.6 3998.3 3655 4259.4 4524.1 4529.8 TRUE FALSE FALSE 4520.02839 3752.190105 4527.043421 2825.096441 3551.601156 3742.821534 3965.455609 4382.639019 4119.453165 4412.115143 1.024458393 0.850428872 1.026048341 0.640304332 0.804965655 0.848305498 0.898765214 0.993319276 0.933668554 1 12.10725473 -10.2610649 24.99007709 1.011549799 0.861723097 0.21215224 0.102280617 28.72816981 1917142.699 0.01652233 0.019589294 5.48E-11 10.2610649 -0.149826701 DS(ph)ENLASPSEYPENGER ddPTM_HeLa_Romidepsin_16h_R1 1 DSENLASPSEYPENGER 17 0 P52948-6;P52948-2;P52948-5;P52948;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 0 DS(0.484)ENLAS(0.475)PS(0.041)EYPENGER 300.29 4.37E-138 231910000 3683 3632 3106.7 3273.3 5369.3 6128.1 5530.8 6695.3 3593.5 3327.8 TRUE FALSE FALSE 3638.110179 3683.131391 3160.77081 3651.774347 5095.284585 5736.534188 6000.586014 6889.017942 3272.08836 3241.343276 1.122408171 1.136297849 0.975142261 1.126623759 1.571966975 1.769801499 1.851265202 2.12535895 1.009485291 1 11.6623761 -8.43188139 1.275560936 1.054356011 2.008566894 0.954851421 0.085012314 0.070592666 0.215496855 0.013859351 0.049624872 3.70E-09 8.43188139 0.954210884 DS(ph)GDENEPIQER ddPTM_HeLa_Romidepsin_16h_R1 1 DSGDENEPIQER 12 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;Q8WX93-7 Q8WX93-3 PALLD Palladin 1 0 DS(1)GDENEPIQER 109.99 0.0107 1545300 620.22 816.21 604.92 611.9 618.14 670.04 480.62 665.64 730.15 693.62 TRUE FALSE FALSE 612.6605201 827.7006258 615.4483788 682.6507571 586.5940092 627.2266065 521.4438508 684.8992432 664.8435553 675.5996524 0.906839602 1.225134772 0.910966098 1.010436809 0.868256825 0.928399836 0.771823741 1.013764943 0.984079185 1 9.400024776 -8.756441748 24.9913569 0.977058891 0.889068535 0.188559778 0.101885199 186.5894665 933056.6637 0.0145279 0.028343763 1.75E-09 8.756441748 -0.087990356 DS(ph)GRGDSVSDSGSDALR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 0 DS(0.615)GRGDS(0.237)VS(0.145)DS(0.002)GSDALR 101.35 0.020233 37911000 2246.8 1786.2 1693.7 2276.5 1279.1 1094 717.98 960.15 1927.9 2015.8 TRUE FALSE FALSE 2219.415137 1811.34617 1723.178138 2539.719641 1213.822754 1024.096931 778.9652033 987.9304254 1755.463795 1963.429225 1.130376949 0.922542125 0.877637001 1.293512192 0.61821569 0.521585865 0.396737093 0.503165794 0.894080506 1 10.93915988 -8.611851244 5.567713101 1.049933818 0.481850945 0.808456585 0.122340374 0.055528703 2.73576355 0.016573349 0.033588215 2.44E-09 8.611851244 -0.568082873 DS(ph)HQPIMCS(ph)Y(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DSHQPIMCSYK 11 0 E7EU35;A0A0C4DGP0;Q9UKF7-2;Q9UKF7 E7EU35 PITPNC1 Cytoplasmic phosphatidylinositol transfer protein 1 3 0 DS(1)HQPIMCS(1)Y(1)K 57.785 0.02731 8684500 223.3 124.05 56.768 233.46 143.56 127.16 41.888 96.242 118.71 109.38 TRUE FALSE FALSE 220.5783337 125.7963792 57.75602323 260.4537437 136.2335975 119.0348864 45.44596567 99.02661043 108.0922803 106.5382918 2.070413651 1.180762118 0.542115161 2.444696073 1.278728945 1.117296742 0.42656931 0.929493131 1.014586196 1 6.735228245 -8.062153189 2.857406416 1.476385931 0.684203774 0.179219402 0.535890983 0.2944552 4.693235198 0.082431505 0.26216701 8.67E-09 8.062153189 -0.792182156 DS(ph)LGAYASQDANEQGQDLGKR ddPTM_HeLa_Romidepsin_16h_R1 1 DSLGAYASQDANEQGQDLGKR 21 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 DS(1)LGAYASQDANEQGQDLGKR 146.45 6.18E-06 30346000 1452.9 1440.6 1604.3 1093.3 1481.3 1887 1462.9 1322.6 1476.6 1539.6 TRUE FALSE FALSE 1435.191496 1460.880805 1632.222169 1219.71249 1405.703734 1766.42679 1587.158689 1360.867344 1344.529198 1499.60097 0.957048925 0.974179688 1.088437658 0.81335803 0.937385186 1.177931213 1.058387345 0.907486306 0.89659131 1 10.55036295 DS(ph)LGTYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 DSLGTYSSR 9 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 DS(0.999)LGT(0.001)YSSR 166.86 0.00224 35094000 2246.2 2120 2424.7 1914.3 2823.4 2531 1803.1 2512.6 2826.7 2617.1 TRUE FALSE FALSE 2218.82245 2149.845416 2466.900886 2135.640373 2679.311362 2369.277268 1956.255269 2585.298117 2573.872872 2549.107365 0.870431148 0.843371858 0.967750876 0.837799303 1.051078271 0.929453699 0.767427569 1.014197422 1.009715365 1 11.31577642 -12.42954756 1.177689183 0.999636649 0.904709518 0.172317792 0.081578088 0.680250605 1.697599327 0.05186512 0.013229454 3.72E-13 12.42954756 -0.09492713 DS(ph)LSPVLHPSDLILTR ddPTM_HeLa_Romidepsin_16h_R1 1 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 0 DS(0.893)LS(0.106)PVLHPSDLILTR 176.42 3.57E-08 3586900 668.96 852.77 805 617.08 1170.7 1447.3 1041.6 1247.5 995.26 999.88 TRUE FALSE FALSE 660.8064582 864.7753184 819.0106873 688.429693 1110.954811 1354.822201 1130.073478 1283.594444 906.2414529 973.9029735 0.678513647 0.887948124 0.840957169 0.706877083 1.140724323 1.391126465 1.160355301 1.317990066 0.930525399 1 9.927634239 -8.60031011 5.005428378 0.839225562 1.275916302 0.793637952 0.104705603 0.084608896 3.826005167 0.019416453 0.03970747 2.51E-09 8.60031011 0.436690741 DS(ph)MSMRS(ph)GRKK ddPTM_HeLa_Romidepsin_16h_R1 1 DSMSMRSGRKK 11 3 P54259 P54259 ATN1 Atrophin-1 2 0 DS(0.993)MS(0.21)MRS(0.797)GRKK 93.429 0.0086785 41721000 5927.4 5664.7 5363.8 41.691 5399.8 4658.6 4714.6 5280.6 4876.5 5231.5 TRUE FALSE FALSE 5855.154569 5744.447795 5457.154689 46.51150958 5124.228057 4360.930495 5115.058006 5433.38583 4440.333627 5095.584876 1.14906428 1.127338262 1.07095747 0.009127806 1.005621176 0.855825308 1.003821569 1.066292872 0.871408039 1 12.31503203 -9.458338632 24.99999951 1.077707413 0.788371231 0.158197613 0.289617007 255.7910425 99081.97551 0.042709828 0.065240312 3.48E-10 9.458338632 -0.289336182 DS(ph)RPLSPILHIVK ddPTM_HeLa_Romidepsin_16h_R1 1 DSRPLSPILHIVK 13 1 O95487-2;O95487;O95487-3 O95487-2 SEC24B Protein transport protein Sec24B 1 0 DS(0.5)RPLS(0.5)PILHIVK 67.648 0.026078 10660000 2050.1 1900.2 2321.6 2106.3 2336.2 2066.6 1587.3 1978.5 2332.9 1908.6 TRUE FALSE FALSE 2025.112593 1926.951065 2362.006474 2349.840316 2216.974996 1934.55093 1722.125222 2035.744776 2124.239581 1859.014297 1.089347509 1.036544511 1.270569289 1.264024876 1.192554033 1.040632626 0.926364701 1.095066767 1.142669846 1 10.86032215 -5.947081587 20.31274902 1.075253369 1.107378195 0 0.110998428 0 0 0.015950518 0 1.13E-06 5.947081587 0.032124827 DS(ph)Y(ph)HNLRLSIHDVPS(ph)SLWK ddPTM_HeLa_Romidepsin_16h_R1 1 DSYHNLRLSIHDVPSSLWK 19 1 H0Y8R2;Q6ZN44-3;Q6ZN44 H0Y8R2 UNC5A Netrin receptor UNC5A 3 0 DS(1)Y(1)HNLRLS(0.09)IHDVPS(0.455)S(0.455)LWK 48.372 0.024321 42901000 2447.7 1970.2 1921.4 1343.7 3410.2 3316.2 2131.1 2612.7 2931.8 2780.4 TRUE FALSE FALSE 2417.866491 1997.936527 1954.841161 1499.064916 3236.164769 3104.305523 2312.115581 2688.294352 2669.572465 2708.164807 0.892806259 0.737745547 0.721832422 0.553535336 1.194965964 1.146276443 0.85375734 0.99266276 0.985749633 1 11.40309982 DS(ph)YVGDEAQSK ddPTM_HeLa_Romidepsin_16h_R1 2 DSYVGDEAQSK 11 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 0 DS(0.995)YVGDEAQS(0.005)K;DS(0.979)YVGDEAQS(0.021)K ; 139.19 0.0033097 15451000 4236.8 3801.7 4828.6 2381.6 4057.6 4609 3830.4 4167.5 4985.6 3972.5 TRUE FALSE FALSE 4185.160252 3855.220432 4912.639757 2656.971798 3850.525531 4314.499775 4155.75408 4288.080037 4539.675449 3869.293877 1.081634113 0.996362787 1.269647619 0.686681312 0.995149413 1.115061278 1.074034233 1.108233226 1.173256825 1 11.91785459 -8.256066627 24.16367951 1.024339022 1.096602045 0.047717529 0.142429177 702.1358362 3157791.9 0.018266938 0.045141994 5.55E-09 8.256066627 0.072263022 DS(ph)YYVYTQQELK ddPTM_HeLa_Romidepsin_16h_R1 2 DSYYVYTQQELK 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 0 DS(0.999)YYVYT(0.001)QQELK;DS(1)YYVYTQQELK ; 225.21 3.81E-29 4801900 2428.57 2810.49 2868.22 2545.35 2832.19 2826.94 2182.29 2711.25 3012.39 2764.69 TRUE FALSE FALSE 2398.969655 2850.056152 2918.140166 2839.655343 2687.652776 2646.307658 2367.653658 2789.695741 2742.954294 2692.862955 0.89086214 1.058374005 1.083657139 1.054511644 0.99806519 0.982711598 0.879232882 1.035959047 1.018601518 1 11.39492509 -13.14546276 3.29875048 1.0009045 0.971309497 0 0.068900445 1.241415497 24.86613515 0.073044222 0.011449009 7.15E-14 13.14546276 -0.029595003 DSAAPSPIPGADNLS(ph)ADPVVSPPTSIPFK ddPTM_HeLa_Romidepsin_16h_R1 2 DSAAPSPIPGADNLSADPVVSPPTSIPFK 29 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 DSAAPS(0.004)PIPGADNLS(0.994)ADPVVS(0.002)PPTSIPFK;DSAAPS(0.005)PIPGADNLS(0.993)ADPVVS(0.002)PPTSIPFK ; 99.954 7.95E-09 15469300 15328.8 15676.6 14212 14418.6 13843.4 12688.5 11392.8 11726.5 16660.4 15560.7 TRUE FALSE FALSE 15141.96669 15897.29559 14459.3539 16085.74637 13136.91964 11877.7458 12360.50415 12065.78778 15170.2521 15156.43077 0.99904568 1.048881219 0.954007848 1.061314937 0.866755494 0.783676974 0.815528691 0.796083719 1.000911912 1 13.88764243 -8.595293799 4.578954409 1.003472258 0.803111394 0.914432666 0.02969138 0.037524722 1.504220851 0.003864832 0.007980427 2.54E-09 8.595293799 -0.200360864 DSAIPVES(ph)DTDDEGAPR ddPTM_HeLa_Romidepsin_16h_R1 2 DSAIPVESDTDDEGAPR 17 0 C9JA08;Q96D46 C9JA08 NMD3 60S ribosomal export protein NMD3 1 0 DSAIPVES(0.822)DT(0.178)DDEGAPR;DSAIPVES(0.855)DT(0.145)DDEGAPR ; 260.07 7.65E-73 108940000 10658 10943.2 9536.5 8891.5 10332.1 10182.9 7549.8 9798.4 10184.6 9750.5 TRUE FALSE FALSE 10528.0962 11097.25866 9702.478782 9919.577066 9804.814383 9532.245554 8191.079824 10081.90124 9273.663868 9497.180604 1.108549646 1.16847927 1.02161675 1.044475985 1.032392116 1.003692143 0.862474893 1.061567813 0.976464938 1 13.21328357 -8.241055892 2.470806091 1.058679466 0.958645829 0.202641284 0.068652803 0.301230799 3.581222424 0.009975422 0.029029102 5.74E-09 8.241055892 -0.100033637 DSALAEAPEGLS(ph)PAPPAR ddPTM_HeLa_Romidepsin_16h_R1 2 DSALAEAPEGLSPAPPAR 18 0 C9JPC9;Q9H9J4-2;Q9H9J4 C9JPC9 USP42 Ubiquitin carboxyl-terminal hydrolase 42 1 0 DSALAEAPEGLS(1)PAPPAR;DSALAEAPEGLS(1)PAPPAR ; 195.25 6.51E-15 186226000 10324.6 10537.8 10252.1 10785.5 10086.5 10001.8 8416.8 10442.4 11331 10649.7 TRUE FALSE FALSE 10198.7598 10686.15143 10430.5335 12032.57026 9571.748267 9362.717259 9131.722782 10744.53437 10317.52698 10373.01926 0.983200701 1.030187177 1.0055446 1.159987267 0.922754314 0.902602899 0.88033412 1.035815523 0.994650325 1 13.34054826 DSALQDTDDS(ph)DDDPVLIPGAR ddPTM_HeLa_Romidepsin_16h_R1 2 DSALQDTDDSDDDPVLIPGAR 21 0 Q58WW2;Q58WW2-2;Q58WW2-4;Q58WW2-3 Q58WW2 DCAF6 DDB1- and CUL4-associated factor 6 1 0 DSALQDT(0.002)DDS(0.998)DDDPVLIPGAR;DSALQDT(0.001)DDS(0.999)DDDPVLIPGAR ; 98.188 0.00056127 5867400 1627.9 1501.83 1514.13 1431.04 1507.81 1446.2 1452.46 1899.04 1445.48 1565.1 TRUE FALSE FALSE 1608.058529 1522.972802 1540.482798 1596.503578 1430.860829 1353.792487 1575.831916 1953.985726 1316.192649 1524.438476 1.054853019 0.999038548 1.010524742 1.047273211 0.938615006 0.888059773 1.03371303 1.28177408 0.863395059 1 10.57406221 -7.269861671 4.957838661 1.009815523 1.293983657 0.622731967 0.067136817 0.06803346 5.058682218 0.007436056 0.06533569 5.37E-08 7.269861671 0.284168134 DSAPSTPT(ph)SPTEFLTPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 DSAPSTPTSPTEFLTPGLR 19 0 Q9NZJ4-2;Q9NZJ4 Q9NZJ4-2 SACS Sacsin 1 0 DSAPSTPT(0.606)S(0.373)PT(0.02)EFLTPGLR 204.9 5.07E-21 16217000 1309.1 1934.7 1757.6 2065.3 2588.8 2712.4 1954.4 2363.2 1696.6 1472.6 TRUE FALSE FALSE 1293.144186 1961.936757 1788.190291 2304.099704 2456.683876 2539.086394 2120.406687 2431.575463 1544.851847 1434.34164 0.901559398 1.367830859 1.246697608 1.606381381 1.71276062 1.770210335 1.478313554 1.695255437 1.077045945 1 10.48617298 -9.708980073 1.199711942 0.952402063 1.662167831 0.837786987 0.121228032 0.100985182 0.291526324 0.021231673 0.03297474 1.95E-10 9.708980073 0.709765768 DSAPSTPTSPT(ph)EFLTPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 DSAPSTPTSPTEFLTPGLR 19 0 Q9NZJ4-2;Q9NZJ4 Q9NZJ4-2 SACS Sacsin 1 0 DSAPST(0.011)PT(0.062)S(0.347)PT(0.575)EFLT(0.004)PGLR 138.2 0.00099154 15535000 1778.9 2199.9 1952.4 2170.7 3207.5 2915 2105.2 2950.3 1975.9 1849.4 TRUE FALSE FALSE 1757.218083 2230.87025 1986.380703 2421.686547 3043.809306 2728.740908 2284.015635 3035.662276 1799.170555 1801.352321 0.975499385 1.238441932 1.102716376 1.344371403 1.689735689 1.514829096 1.267944981 1.685212959 0.998788818 1 10.81486467 -9.400023182 1.210313614 0.993473135 1.522809947 0.739095141 0.132691079 0.154091026 0.447632513 0.022380188 0.040936042 3.98E-10 9.400023182 0.529336812 DSAS(ph)PRY(ph)IFTMLSSLARLLFPPK ddPTM_HeLa_Romidepsin_16h_R1 1 DSASPRYIFTMLSSLARLLFPPK 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 2 0 DS(0.211)AS(0.779)PRY(0.571)IFT(0.41)MLS(0.015)S(0.013)LARLLFPPK 42.347 0.0041921 0 1733.1 1584.2 1894 1447.1 1635.9 1830.4 1598.7 1688 2084.5 2236.8 TRUE FALSE FALSE 1711.976311 1606.502409 1926.964276 1614.420511 1552.413919 1713.443347 1734.493538 1736.839617 1898.057099 2178.687614 0.785783285 0.737371617 0.884461023 0.741005962 0.712545437 0.786456643 0.796118511 0.797195342 0.871192863 1 11.08924364 -12.1458519 0.600216687 1.027180671 0.77467717 0.472854023 0.059164749 0.3794887 0.211154833 0.051859055 0.010413895 7.15E-13 12.1458519 -0.252503501 DSAYFS(ph)DNDSEPEKR ddPTM_HeLa_Romidepsin_16h_R1 1 DSAYFSDNDSEPEKR 15 1 Q8IWU2 Q8IWU2 LMTK2 Serine/threonine-protein kinase LMTK2 1 0 DS(0.006)AYFS(0.993)DNDS(0.001)EPEKR 62.589 0.021652 3625400 881.73 1495 892.09 816.43 1526.6 2015.7 1462.8 2226.2 1090 1314.2 TRUE FALSE FALSE 870.9831356 1516.046649 907.6164522 910.829478 1448.691905 1886.903275 1587.050195 2290.611585 992.50767 1280.056895 0.680425331 1.184358801 0.709043837 0.711553902 1.131740247 1.474077663 1.239827856 1.789460761 0.775362153 1 10.32199222 -8.442459297 2.874736876 0.853552715 1.480699528 0.700399174 0.191878855 0.121247739 1.943389375 0.028900607 0.069969659 3.61E-09 8.442459297 0.627146813 DSAYISS(ph)SPLGSHQVFDFR ddPTM_HeLa_Romidepsin_16h_R1 1 DSAYISSSPLGSHQVFDFR 19 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 0 DSAYISS(0.66)S(0.34)PLGSHQVFDFR 150.63 1.14E-05 46194000 3754.2 3674.2 4032.6 3574.5 5031.5 5214.4 3888.4 4287 5878.5 4586.6 TRUE FALSE FALSE 3708.442366 3725.925484 4102.785711 3987.800509 4774.72378 4881.216669 4218.680599 4411.037581 5352.712237 4467.439471 0.83010467 0.834018123 0.918375221 0.892636718 1.068783094 1.092620661 0.944317349 0.987374896 1.19816111 1 12.12523247 -8.770796559 24.99989179 0.908945152 1.022587574 0.051667566 0.108869859 176.3218451 471085.6578 0.011726911 0.021464387 1.70E-09 8.770796559 0.113642423 DSDAGS(ph)STPTTSTR ddPTM_HeLa_Romidepsin_16h_R1 2 DSDAGSSTPTTSTR 14 0 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8Y6N0;A0A2R8YG32;A0A2R8Y7F3;A0A2R8YF80;A0A2R8YF58;A0A2R8Y526;A0A2R8Y7Y7;A0A2R8Y6V2;A0A2R8YDA1;A0A2R8Y523;A0A2R8Y5K3;K7EQF0;A0A2R8YFK5;K7EP28 P51532 SMARCA4 Transcription activator BRG1 1 0 DSDAGS(0.882)S(0.042)T(0.075)PT(0.001)TSTR;DS(0.03)DAGS(0.847)S(0.047)T(0.074)PT(0.002)TSTR ; 206.67 4.37E-17 6985200 2624.9 2350.9 2069.2 2062.88 1864.3 1678.06 1607.69 1533.84 2068.96 2366.1 TRUE FALSE FALSE 2592.906709 2383.996032 2105.213558 2301.399892 1769.157814 1570.837382 1744.247148 1578.21924 1883.907036 2304.628381 1.125086687 1.034438373 0.913472027 0.998599128 0.767654269 0.681601162 0.756845296 0.68480422 0.817445039 1 11.17031842 -8.855138428 1.186156261 1.055880762 0.69703266 0.60682179 0.093559186 0.127362297 0.354673081 0.010689085 0.027734433 1.40E-09 8.855138428 -0.358848102 DSDAGSS(ph)TPTTSTR ddPTM_HeLa_Romidepsin_16h_R1 2 DSDAGSSTPTTSTR 14 0 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8Y6N0;A0A2R8YG32;A0A2R8Y7F3;A0A2R8YF80;A0A2R8YF58;A0A2R8Y526;A0A2R8Y7Y7;A0A2R8Y6V2;A0A2R8YDA1;A0A2R8Y523;A0A2R8Y5K3;K7EQF0;A0A2R8YFK5;K7EP28 P51532 SMARCA4 Transcription activator BRG1 1 0 DSDAGS(0.093)S(0.588)T(0.319)PTTSTR;DSDAGS(0.079)S(0.616)T(0.305)PTTSTR ; 275.82 1.82E-96 148471000 12985.9 13156.5 12410.3 12040.6 9441.7 8733.4 9079.6 7967.6 13351.6 12514.4 TRUE FALSE FALSE 12827.62286 13341.71755 12626.29607 13432.79082 8959.854817 8175.363926 9850.820997 8198.129935 12157.39946 12189.27408 1.052369712 1.094545701 1.035852995 1.102017293 0.735060575 0.67070146 0.808154852 0.672569168 0.997385027 1 13.57332459 -8.75281928 24.99960299 1.036881282 0.724165229 0.915415905 0.048396824 38.24123494 110904.5583 0.006926531 0.01368054 1.77E-09 8.75281928 -0.312716052 DSDAGSST(ph)PTTSTR ddPTM_HeLa_Romidepsin_16h_R1 1 DSDAGSSTPTTSTR 14 0 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8Y6N0;A0A2R8YG32;A0A2R8Y7F3;A0A2R8YF80;A0A2R8YF58;A0A2R8Y526;A0A2R8Y7Y7;A0A2R8Y6V2;A0A2R8YDA1;A0A2R8Y523;A0A2R8Y5K3;K7EQF0;A0A2R8YFK5;K7EP28 P51532 SMARCA4 Transcription activator BRG1 1 0 DSDAGS(0.063)S(0.348)T(0.573)PT(0.016)TSTR 146.67 0.00026667 0 241.16 399.03 575.02 369.14 313.14 256.45 346.41 281.26 411.67 326.93 TRUE FALSE FALSE 238.2206492 404.6475548 585.0279819 411.8217037 297.1592973 240.0636727 375.8340568 289.3978143 374.8492042 318.4363115 0.748095115 1.27073308 1.837189921 1.293262385 0.933182827 0.753882846 1.180248744 0.90880909 1.177155967 1 8.314861046 -10.2570841 24.91347101 0.881044915 1.174218979 0.054851162 0.297957076 490.9170697 2808191.678 0.052256674 0.062808805 5.53E-11 10.2570841 0.293174064 DSDFSLPPGSASGPTGS(ph)PVVK ddPTM_HeLa_Romidepsin_16h_R1 1 DSDFSLPPGSASGPTGSPVVK 21 0 Q5JSZ5;Q5JSZ5-5;A0A494C0D3;A0A494C065;H0Y412 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 DSDFS(0.002)LPPGS(0.001)AS(0.001)GPT(0.017)GS(0.979)PVVK 144.74 6.29E-16 0 2916.9 2803.8 2901.6 2731.7 2573.3 2817.4 2213.7 2237.2 2702.3 2541.6 TRUE FALSE FALSE 2881.347701 2843.27197 2952.101131 3047.552007 2441.974899 2637.377233 2401.731623 2301.929852 2460.59952 2475.568866 1.16391337 1.148532771 1.192494045 1.231051194 0.986429799 1.065362095 0.970173626 0.929858944 0.993953169 1 11.27354437 -7.815254008 1.358254705 1.101101407 0.922092977 0.372797463 0.080449221 0.577152255 1.673860242 0.013725582 0.107221084 1.53E-08 7.815254008 -0.17900843 DSDLSHVQNK ddPTM_HeLa_Romidepsin_16h_R1 2 DSDLSHVQNK 10 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 ; ; 107.79 0.0091245 8370100 10819.7 9960.4 11638.8 10189.8 12996.1 14158.9 14700.6 4888.6 15044.3 12438 FALSE FALSE TRUE 10687.82533 10100.62277 11841.36843 11367.99262 12332.86052 13254.19199 15949.2686 5030.043928 13698.70013 12114.85897 0.882207986 0.83373837 0.977425199 0.938351214 1.01799456 1.094044266 1.316504686 0.415196243 1.130735419 1 13.56448999 -8.779593161 20.67229612 0.9362385 0.995840515 0 0.225195254 137.6864002 156789.0512 0.029492902 0.053613292 1.66E-09 8.779593161 0.059602015 DSDQVAQS(ph)DGEES(ph)PAAEEQLLGEHIK ddPTM_HeLa_Romidepsin_16h_R1 2 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 2 0 DS(0.045)DQVAQS(0.978)DGEES(0.978)PAAEEQLLGEHIK;DS(0.001)DQVAQS(0.999)DGEES(1)PAAEEQLLGEHIK ; 75.248 0.00085524 5471200 1609.62 1741.97 2048.44 1154.12 1651.97 1908.24 1450.93 1973.72 1987.2 2035.05 TRUE FALSE FALSE 1590.001332 1766.493499 2084.092239 1287.564785 1567.663807 1786.309623 1574.171958 2030.826474 1809.459855 1982.179108 0.802148164 0.891187629 1.051414694 0.649570354 0.790878988 0.90118477 0.79416232 1.024542367 0.912863953 1 10.95287161 -12.45364583 1.097822343 1.002902386 0.854258168 0.074357685 0.114148836 0.697933388 1.456555298 0.082248032 0.01884029 3.52E-13 12.45364583 -0.148644217 DSDQVAQS(ph)DGEESPAAEEQLLGEHIK ddPTM_HeLa_Romidepsin_16h_R1 4 DSDQVAQSDGEESPAAEEQLLGEHIK 26 0 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 0 DS(0.002)DQVAQS(0.98)DGEES(0.018)PAAEEQLLGEHIK;DS(0.009)DQVAQS(0.963)DGEES(0.028)PAAEEQLLGEHIK;DS(0.001)DQVAQS(0.782)DGEES(0.217)PAAEEQLLGEHIK;DS(0.009)DQVAQS(0.98)DGEES(0.011)PAAEEQLLGEHIK ;;; 116.57 2.63E-07 34048900 12966 13358 15512 7353.01 14820.6 16067.6 12391.7 14261 13782.4 15273.1 TRUE FALSE FALSE 12807.9654 13546.05427 15781.97985 8203.199613 14064.24948 15040.93222 13444.25069 14673.61953 12549.66763 14876.30266 0.860964293 0.910579368 1.06088053 0.551427314 0.94541297 1.011066564 0.903736029 0.986375437 0.843601257 1 13.86072838 -12.45326425 1.1355993 1.001119582 0.898487648 0 0.139302894 1.122159482 2.542803214 0.092442327 0.021931639 3.52E-13 12.45326425 -0.102631934 DSDQVAQS(ph)DGEESPAAEEQLLGEHIKEEK ddPTM_HeLa_Romidepsin_16h_R1 2 DSDQVAQSDGEESPAAEEQLLGEHIKEEK 29 1 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;D6RHZ5;H0Y8V7 D6REX3 SEC31A Protein transport protein Sec31A 1 0 DS(0.084)DQVAQS(0.672)DGEES(0.245)PAAEEQLLGEHIKEEK;DS(0.022)DQVAQS(0.771)DGEES(0.207)PAAEEQLLGEHIKEEK ; 102.6 4.63E-09 50035000 9851.2 10158.9 10328.3 5632.7 11196.3 11093 8386.5 9730.3 10182 10904.8 TRUE FALSE FALSE 9731.129785 10301.91726 10508.05973 6283.979277 10624.91103 10384.1931 9098.849101 10011.83088 9271.296419 10621.49172 0.916173551 0.969912469 0.989320521 0.591628694 1.000321924 0.977658635 0.856645125 0.942601203 0.872880821 1 13.37469878 -11.72841606 0.485712196 1.008581798 0.895899302 0 0.119109072 2.26921145 0.976029646 0.118002605 0.033952707 1.87E-12 11.72841606 -0.112682496 DSEAWVPDSEER ddPTM_HeLa_Romidepsin_16h_R1 1 DSEAWVPDSEER 12 0 M0QXS4;Q96F63 M0QXS4 CCDC97 Coiled-coil domain-containing protein 97 0 0 126.03 0.00036892 0 461.41 434.57 520.18 566.04 494.23 612.69 379.48 535.54 598.88 638.18 FALSE FALSE TRUE 455.7861574 440.6878879 529.2335147 631.4882081 469.0075989 573.5410864 411.7130217 551.035005 545.3146729 621.5999916 0.733246724 0.708957358 0.85140528 1.015907684 0.754516739 0.922685158 0.662343995 0.886478463 0.877275869 1 9.279842674 -12.45976992 1.212152921 0.99936408 0.809138731 0.132065301 0.108037455 0.440397927 1.163649048 0.068985747 0.017305246 3.47E-13 12.45976992 -0.190225349 DSEGDSLGARPGLPYGLS(ph)DDESGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 DSEGDSLGARPGLPYGLSDDESGGGR 26 1 Q8N8E2-2;Q8N8E2;C9JT52 Q8N8E2-2 ZNF513 Zinc finger protein 513 1 0 DSEGDS(0.002)LGARPGLPY(0.004)GLS(0.789)DDES(0.204)GGGR;DS(0.001)EGDS(0.005)LGARPGLPY(0.005)GLS(0.829)DDES(0.16)GGGR ; 65.731 0.00036575 10443700 1108.28 1147.91 1094.11 863.9 858.06 1405.35 1435.95 1283.26 1678.22 1141.92 TRUE FALSE FALSE 1094.771857 1164.070307 1113.152526 963.7881828 814.2699963 1315.552671 1557.919557 1320.389103 1528.1158 1112.252754 0.984283341 1.04658793 1.000808963 0.866519035 0.732090789 1.18278212 1.400688424 1.187130442 1.373892575 1 10.11926896 -8.011707983 23.93989341 0.971924232 1.293365984 0.350319858 0.161357669 137.4563326 281067.3566 0.01386863 0.037798286 9.73E-09 8.011707983 0.321441752 DSEGFNS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DSEGFNSPK 9 0 I3L262;O43303-2;O43303 I3L262 CCP110 Centriolar coiled-coil protein of 110 kDa 1 0 DSEGFNS(1)PK 108.98 0.020169 8935900 6158.3 6073.7 6098.4 5713.4 7134.3 7377.3 6183 5786.2 6224.9 6371.3 TRUE FALSE FALSE 6083.240271 6159.205708 6204.540094 6374.01019 6770.210049 6905.914339 6708.183866 5953.614568 5668.129353 6205.772708 0.980255088 0.99249618 0.999801376 1.027109836 1.090953596 1.112821024 1.080958679 0.959367165 0.913363995 1 12.59939514 -9.063783565 3.027422236 0.991183234 1.065892941 0.410706125 0.045689673 0.179981254 3.252136956 0.005780881 0.010354833 8.63E-10 9.063783565 0.074709708 DSENLASPS(ph)EYPENGER ddPTM_HeLa_Romidepsin_16h_R1 2 DSENLASPSEYPENGER 17 0 P52948-6;P52948-2;P52948-5;P52948;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 0 DSENLAS(0.01)PS(0.99)EYPENGER;DSENLAS(0.206)PS(0.794)EYPENGER ; 285.06 1.74E-103 159506900 5193.1 4816.4 4364.36 5124.5 7899 8437.8 7582.9 9192.6 4826.7 4480.1 TRUE FALSE FALSE 5129.8045 4884.205406 4440.319855 5717.018801 7495.884555 7898.651812 8226.991337 9458.573377 4394.987863 4363.706356 1.175561342 1.119279119 1.017556979 1.310129128 1.717779324 1.810078673 1.885321941 2.167554965 1.007168564 1 12.09133831 -8.624494367 1.194922577 1.077057993 2.0224635 0.948930381 0.092825776 0.080573981 0.222626991 0.016259792 0.050869189 2.37E-09 8.624494367 0.945405507 IAQVS(ph)PGPR ddPTM_HeLa_Romidepsin_16h_R1 2 IAQVSPGPR 9 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 IAQVS(1)PGPR;IAQVS(1)PGPR ; 112.94 0.017466 229460000 12433.2 11641.9 11331.3 7154.2 7418.5 5968.9 4957.5 5066 12035.1 11670 TRUE FALSE FALSE 12281.65938 11805.79497 11528.51652 7981.402266 7039.906263 5587.506554 5378.589926 5212.576717 10958.65051 11366.81172 1.080484104 1.038619735 1.014226048 0.702167192 0.619338689 0.491563219 0.473183691 0.45857861 0.964091848 1 13.47254003 -8.995950478 1.475839701 1.042350337 0.477962753 0.968839576 0.043478542 0.042677393 0.184948594 0.006848744 0.014648273 1.01E-09 8.995950478 -0.564387585 down DSFS(ph)HSPGAVSSLK ddPTM_HeLa_Romidepsin_16h_R1 1 DSFSHSPGAVSSLK 14 0 Q9H6R7-3;Q9H6R7 Q9H6R7-3 C2orf44 WD repeat and coiled-coil-containing protein C2orf44 1 0 DS(0.07)FS(0.465)HS(0.465)PGAVSSLK 121.45 0.00036449 0 909.07 1062.4 881.02 946.38 2187.9 1938.7 1721.9 1589.8 1261.8 1109.6 TRUE FALSE FALSE 897.9899052 1077.356495 896.3537835 1055.804908 2076.243299 1814.823327 1868.158143 1635.798355 1148.941448 1080.772432 0.830877878 0.996839356 0.829364033 0.976898445 1.921073519 1.679190987 1.728539781 1.513545596 1.063074347 1 10.07784707 -8.792556194 10.16056362 0.920349087 1.709492338 0.910326066 0.116809357 0.073515164 23.37458636 0.016260792 0.029660008 1.61E-09 8.792556194 0.789143252 DSGLES(ph)PAAAEAPLR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGLESPAAAEAPLR 15 0 H0YM15;J3KNL7;Q8NBR6-2;Q8NBR6 H0YM15 FAM63B Protein FAM63B 1 0 DS(0.032)GLES(0.968)PAAAEAPLR 188.19 2.84E-12 4256400 1335.4 1208.4 1138.2 1246.8 1616 2273.3 1656.9 1843.4 1156 1356.2 TRUE FALSE FALSE 1319.123631 1225.411887 1158.009894 1390.960882 1533.52949 2128.043467 1797.637045 1896.735871 1052.604465 1320.965728 0.998605492 0.927663648 0.876638862 1.052987865 1.160915425 1.610975532 1.360850631 1.435870613 0.796844643 1 10.36737732 -8.505850159 3.12883604 0.986913001 1.457429529 0.851434836 0.097108568 0.056015205 1.115855481 0.010799378 0.024817001 3.12E-09 8.505850159 0.470516528 DSGNWDTS(ph)GSELS(ph)EGELEKR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGNWDTSGSELSEGELEKR 20 1 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 2 0 DSGNWDT(0.218)S(0.715)GS(0.071)ELS(0.997)EGELEKR 76.241 0.0021262 4396100 2081.8 2160.3 2202.8 1848.7 1867.3 2395.5 2106 1954.3 2506.1 2379 TRUE FALSE FALSE 2056.426221 2190.71276 2241.13881 2062.455392 1772.004713 2242.435281 2284.883587 2010.844587 2281.948139 2317.193237 0.887464277 0.945416517 0.967178211 0.890066206 0.764720302 0.967737712 0.986056558 0.867793223 0.984789746 1 11.17816264 -12.4122691 0.887058058 1.006193923 0.909471191 0.224852084 0.061332803 0.865027143 1.086079813 0.059430978 0.01169046 3.87E-13 12.4122691 -0.096722732 DSGNWDTSGSELS(ph)EGELEKR ddPTM_HeLa_Romidepsin_16h_R1 2 DSGNWDTSGSELSEGELEKR 20 1 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 0 DSGNWDTSGS(0.007)ELS(0.993)EGELEKR;DSGNWDTSGS(0.001)ELS(0.999)EGELEKR ; 85.17 0.00086243 30065000 3099.4 2990 3228.5 2778.4 3255.9 2953.9 3213.7 2902.9 3433.6 3283.5 TRUE FALSE FALSE 3061.623321 3032.093298 3284.690688 3099.651681 3089.739274 2765.155323 3486.671598 2986.890831 3126.490216 3198.194197 0.957297504 0.948064161 1.027045416 0.969188076 0.9660887 0.864598943 1.090200089 0.933930414 0.977579854 1 11.64304183 -6.963028513 18.03434806 0.977839148 0.730087493 0.054751338 0.054664591 17668582.74 211410424.6 0.006903407 145891602.6 1.09E-07 6.963028513 -0.247751655 DSGPLPT(ph)PPGVSLLGEPPKDYR ddPTM_HeLa_Romidepsin_16h_R1 2 DSGPLPTPPGVSLLGEPPKDYR 22 1 A0A087WZ13;E9PAU2;Q8IY67-2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 0 DS(0.04)GPLPT(0.96)PPGVSLLGEPPKDYR;DS(0.188)GPLPT(0.788)PPGVS(0.024)LLGEPPKDYR ; 99.378 0.000138 63472000 6642.3 6967.1 6471.4 6326.1 6850.3 7362.9 5667.55 7413.8 7470.2 6695.6 TRUE FALSE FALSE 6561.341093 7065.183017 6584.032002 7057.553447 6500.703629 6892.434453 6148.951556 7628.306606 6802.046603 6521.647347 1.00608646 1.083343309 1.009565782 1.082173425 0.996788585 1.056854823 0.942852508 1.169690141 1.042995158 1 12.67102072 -4 0.142012429 0.987956122 1.259192158 0.042251962 0.058507768 114.2666537 1.06759348 0.134767224 6.335614422 1.00E-04 4 0.271236036 DSGPPTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 DSGPPTKK 8 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 1 ; DSGPPTK(1)K;DSGPPTK(1)K 118.5 0.0016534 24627000 2577.27 2727.9 5012.9 6075.9 11254.3 14549.9 26682.7 3165.1 4787.2 3382.6 FALSE TRUE FALSE 2545.857242 2766.303448 5100.147422 6778.424146 10679.95108 13620.20835 28949.12787 3256.677175 4359.020842 3294.719564 0.772708327 0.839617271 1.547976185 2.057359971 3.241535696 4.13395073 8.786522588 0.988453527 1.323032433 1 11.68593996 -8.673655081 1.455214691 0.920736544 5.071892328 0.42800341 1.78162642 0.230317311 0.972641826 0.247207231 0.658322437 2.12E-09 8.673655081 4.151155785 DSGREDEPGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGREDEPGSPR 12 1 Q2TAM9 Q2TAM9 TUSC1 Tumor suppressor candidate gene 1 protein 1 0 DSGREDEPGS(1)PR 72.523 0.024263 32777000 2526.6 2325.6 3420.9 2248.8 2184.4 2068.5 2416.8 1230.3 3514.3 2939.9 TRUE FALSE FALSE 2495.804827 2358.339858 3480.43933 2508.816837 2072.921917 1936.329526 2622.082932 1265.896789 3199.972206 2863.520974 0.871586012 0.823580438 1.215440488 0.876130072 0.723906664 0.676205812 0.915684905 0.44207701 1.117495641 1 11.48357446 -8.824544097 4.035414046 0.94951761 0.702766611 0.461830965 0.154516295 0.166470562 5.421099719 0.020607972 0.039322247 1.50E-09 8.824544097 -0.246750999 DSGRGDS(ph)VSDSGSDALR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 0 DS(0.349)GRGDS(0.424)VS(0.138)DS(0.045)GS(0.045)DALR 113.14 0.013496 41459000 1728.7 1757.9 1624 1751.4 1334.9 1258 894.83 772.81 1727.2 1358.2 TRUE FALSE FALSE 1707.629939 1782.647762 1652.265039 1953.905109 1266.775072 1177.61786 970.8368379 795.1700381 1572.714906 1322.913768 1.290809712 1.347516222 1.248958986 1.476970877 0.957564357 0.890169782 0.733862525 0.601074732 1.188826471 1 10.36950331 -8.12576942 1.706495211 1.18649636 0.655228587 0.729577731 0.13955341 0.204173274 1.1097519 0.025606085 0.101491969 7.49E-09 8.12576942 -0.531267773 DSGRGDSVSDSGSDALR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGRGDSVSDSGSDALR 17 1 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 0 0 74.147 0.029576 3980900 1101.1 928.35 1097.5 1148.8 942.92 939.21 723.04 951.21 1314.6 1251.5 FALSE FALSE TRUE 1087.67937 941.4193357 1116.601527 1281.629661 894.7992739 879.1975122 784.4549996 978.7317606 1197.018884 1218.98585 0.892282195 0.772297181 0.916008605 1.051390106 0.734052224 0.721253255 0.64353085 0.802906581 0.98197931 1 10.25146566 -4.74824596 0.138152727 1.046643632 7.77E-17 0.459062214 0.095188155 40.02012733 0.445115134 0.294083919 8.014220274 1.79E-05 4.74824596 -1.046643632 DSGS(ph)DQDLDGAGVR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSDQDLDGAGVR 14 0 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 DS(0.018)GS(0.982)DQDLDGAGVR 147.75 0.00061723 6010400 1249.5 952.52 1098.3 852.94 814.71 1151.1 948.09 1045.2 993.96 1050.8 TRUE FALSE FALSE 1234.270613 965.9296016 1117.415451 951.560936 773.1323086 1077.548425 1028.620741 1075.441213 905.0577282 1023.500065 1.205931153 0.943751383 1.091759043 0.929712629 0.755380811 1.052807384 1.005003103 1.050748554 0.884277158 1 9.999295478 -9.779483661 1.801779324 1.093823371 0.962959305 0 0.122773001 0.422202925 2.797725944 0.020386534 0.029248529 1.66E-10 9.779483661 -0.130864066 DSGS(ph)ISLQETR ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 0 DSGS(0.586)IS(0.328)LQET(0.086)R 135.02 0.0040764 32807000 2151.8 3531.1 2177.8 1951 3102.4 2146 1441.3 1880.3 2514.1 2138.7 TRUE FALSE FALSE 2125.573034 3580.810918 2215.703695 2176.5838 2944.072951 2008.877526 1563.723986 1934.703514 2289.232599 2083.136266 1.020371576 1.718951841 1.063638386 1.04485906 1.413288703 0.964352433 0.75065852 0.928745539 1.098935599 1 11.0245415 -8.001906266 24.20245093 1.098036899 0.844152761 0.225168746 0.228138392 68.23291454 866384.8446 0.033305425 0.097664609 9.96E-09 8.001906266 -0.253884137 DSGS(ph)QEVLSELR ddPTM_HeLa_Romidepsin_16h_R1 2 DSGSQEVLSELR 12 0 Q9BVJ6-3;Q9BVJ6;X6RJY0;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 DS(0.003)GS(0.997)QEVLSELR;DS(0.44)GS(0.558)QEVLS(0.002)ELR ; 172.09 0.00010684 23506000 2067.52 2106.6 2148.5 1797.46 2084.46 1827.95 1555.37 1740.61 2528.4 2048.6 TRUE FALSE FALSE 2042.320271 2136.25677 2185.893741 2005.290783 1978.082228 1711.149894 1687.483089 1790.971804 2302.253572 1995.377077 1.023525977 1.070603043 1.095479028 1.004968337 0.991332541 0.857557158 0.845696339 0.897560579 1.153793736 1 10.96244569 -8.347666237 3.399807103 1.022381622 0.863564783 0.703734956 0.052390739 0.080320167 1.770800756 0.005250675 0.012853923 4.49E-09 8.347666237 -0.158816839 DSGSDQDLDGAGVRAS(ph)DLEDEESAAR ddPTM_HeLa_Romidepsin_16h_R1 2 DSGSDQDLDGAGVRASDLEDEESAAR 26 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 DSGS(0.001)DQDLDGAGVRAS(0.994)DLEDEES(0.005)AAR;DS(0.002)GS(0.018)DQDLDGAGVRAS(0.979)DLEDEESAAR ; 90.041 6.76E-06 52739000 4639 4971 3978.3 3706.7 5083.3 5044 4018 4962.9 5024.6 4464.4 TRUE FALSE FALSE 4582.458084 5040.981868 4047.540643 4135.286095 4823.880233 4721.704679 4359.28882 5106.493681 4575.187192 4348.414244 1.053822802 1.159269008 0.930808432 0.950987156 1.109342386 1.085845187 1.002500814 1.174334687 1.052150723 1 12.08627367 -6.006478425 1.958868537 1.031713052 13.84748481 0.253706822 0.06744621 143.3580471 7.287703373 0.009520649 7988.65829 9.85E-07 6.006478425 12.81577176 DSGSDTASAIIPSTTPS(ph)VDSDDESVVKDK ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSGSDTAS(0.001)AIIPS(0.029)T(0.029)T(0.014)PS(0.668)VDS(0.252)DDES(0.007)VVKDK 61.022 0.0005758 14745000 1183.5 1278.8 1358.1 1422.6 2739.3 3044.7 3074.4 3320.9 1502.4 1484.6 TRUE FALSE FALSE 1169.075047 1296.80298 1381.737161 1587.087706 2599.503299 2850.153496 3335.539459 3416.985002 1368.021581 1446.029878 0.808472262 0.896802341 0.955538459 1.097548349 1.797682979 1.971019783 2.306687787 2.363011342 0.946053468 1 10.49788165 -8.556292907 1.299531178 0.900860205 2.327740419 0.978443456 0.086734748 0.048939422 0.159867198 0.015600398 0.048994197 2.78E-09 8.556292907 1.426880214 up DSGSDTASAIIPSTTPS(ph)VDSDDESVVKDKK ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVKDKK 30 2 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSGSDTASAIIPS(0.09)T(0.09)T(0.09)PS(0.365)VDS(0.365)DDESVVKDKK 83.465 3.00E-07 29834000 1309.7 996.36 939.7 1780.6 2407.5 3248.3 2829.5 3291.8 1485.1 1223.5 TRUE FALSE FALSE 1293.736873 1010.386782 956.0550843 1986.48135 2284.636291 3040.744113 3069.837659 3387.043039 1352.268936 1191.713294 1.085610842 0.847843846 0.802252597 1.666912134 1.917102296 2.551573545 2.575986754 2.842162672 1.134726736 1 10.21882147 -8.638285927 1.328551978 1.007384942 2.721216946 0.955663673 0.156600113 0.059985571 0.208321615 0.02431147 0.070123215 2.30E-09 8.638285927 1.713832003 up DSGSDTASAIIPSTTPSVDS(ph)DDESVVK ddPTM_HeLa_Romidepsin_16h_R1 2 DSGSDTASAIIPSTTPSVDSDDESVVK 27 0 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSGSDTASAIIPSTTPS(0.003)VDS(0.965)DDES(0.032)VVK;DSGSDTASAIIPST(0.001)T(0.005)PS(0.151)VDS(0.822)DDES(0.02)VVK ; 152.57 9.82E-12 32358000 6483.9 6471.6 7922.6 5720.4 14119.4 18917.8 12817.7 17006.4 7716.9 7596.4 TRUE FALSE FALSE 6404.871733 6562.707355 8060.48953 6381.819563 13398.83433 17709.01363 13906.43512 17498.45335 7026.681137 7399.044433 0.865634987 0.88696688 1.089396016 0.862519427 1.810887129 2.393419014 1.879490689 2.364961247 0.949674137 1 12.85312325 -8.644043623 3.645423485 0.93804964 2.173110434 0.936944522 0.150928821 0.035834541 0.912396635 0.020286783 0.042378082 2.27E-09 8.644043623 1.235060794 up DSGSDTASAIIPSTTPSVDS(ph)DDESVVKDK ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSDTASAIIPSTTPSVDSDDESVVKDK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSGSDTASAIIPS(0.012)T(0.012)T(0.012)PS(0.181)VDS(0.781)DDES(0.002)VVKDK 77.062 3.22E-06 25443000 1676.2 1600 1921 2195.8 4357.7 4843.4 4441.7 5609.1 2275.5 2117.5 TRUE FALSE FALSE 1655.76983 1622.524842 1954.434199 2449.688728 4135.310308 4533.922371 4818.977887 5771.390459 2071.973581 2062.487045 0.802802536 0.786683653 0.947610412 1.187735328 2.005011531 2.1982792 2.336488803 2.798267496 1.004599562 1 11.01016934 -8.61383786 1.302697783 0.886733939 2.544943722 0.960245567 0.141273294 0.060200484 0.199767946 0.022956168 0.068433471 2.43E-09 8.61383786 1.658209783 up DSGSISLQET(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSISLQETR 11 0 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 0 DSGS(0.08)IS(0.368)LQET(0.552)R 147.58 0.005006 28380000 2449 2609.9 1865.3 1918.9 2551.9 1982.4 1604.9 1807.9 2267 2110.9 TRUE FALSE FALSE 2419.150646 2646.642241 1897.764764 2140.772247 2421.667021 1855.731038 1741.220166 1860.208734 2064.233842 2056.058514 1.176596206 1.28724072 0.923011068 1.041202005 1.177820088 0.90256723 0.846872866 0.904745036 1.003976214 1 11.00566561 -8.165662519 6.178828444 1.090577215 0.876812702 0.458132342 0.100930542 0.170224282 9.137052366 0.015281717 0.039570561 6.83E-09 8.165662519 -0.213764513 DSGSS(ph)SPLPK ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSSSPLPK 10 0 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 DSGSS(0.5)S(0.5)PLPK 143.4 0.0041886 27206000 7965.8 7977.2 7357.7 5553.5 6871.7 5918 5204.1 4984.5 8231.2 8955.1 TRUE FALSE FALSE 7868.709766 8089.503231 7485.757682 6195.6218 6521.011507 5539.858899 5646.136124 5128.718643 7494.980857 8722.445211 0.902122005 0.927435259 0.858217793 0.710307907 0.747612779 0.635126821 0.64731116 0.587990927 0.8592752 1 13.09051692 -8.88907021 0.44132127 0.981861763 0.536414566 0.862529084 0.049502121 0.248354417 0.07814278 0.010834513 0.047390202 1.29E-09 8.88907021 -0.445447197 DSGSSS(ph)PLPK ddPTM_HeLa_Romidepsin_16h_R1 1 DSGSSSPLPK 10 0 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 DSGSS(0.061)S(0.939)PLPK 150.1 0.0037415 27384000 5325.6 5065.1 5645.2 3491.7 3998.9 4098.2 3442.9 3287.6 5430.5 5310.4 TRUE FALSE FALSE 5260.689539 5136.406611 5743.452338 3895.426783 3794.821211 3836.338246 3735.33984 3382.721519 4944.782479 5172.435042 1.017062466 0.993034532 1.110396224 0.753112751 0.73366242 0.741689014 0.722162736 0.65399014 0.955987352 1 12.33662791 -9.181016133 5.99667422 1.013683042 0.720021921 0.919711268 0.043533491 0.040095301 2.38641153 0.005736712 0.009566446 6.59E-10 9.181016133 -0.293661121 DSGSSSVSSTSSSSSSS(ph)PGDK ddPTM_HeLa_Romidepsin_16h_R1 2 DSGSSSVSSTSSSSSSSPGDK 21 0 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 0 DSGSSSVSSTSSSSSS(0.075)S(0.925)PGDK;DSGSSSVSSTSSSSSS(0.006)S(0.994)PGDK ; 335.46 7.20E-218 6577800 2694.6 2524.87 2553.9 3070.1 4414.7 2317.9 2483.4 2485 2859 2344.1 TRUE FALSE FALSE 2661.757179 2560.415186 2598.349558 3425.079407 4189.401385 2169.793671 2694.339934 2556.899554 2603.28388 2283.199944 1.165801176 1.121415228 1.138029792 1.500122412 1.834881521 0.950330117 1.180071829 1.119875445 1.140190935 1 11.15684149 -10.58805337 0.762161334 1.03815902 1.292348372 0.113173644 0.233497952 0.795857065 0.991456057 0.069435327 0.066905248 2.58E-11 10.58805337 0.254189352 DSHS(ph)PDLQLPTPEVIPSSGSK ddPTM_HeLa_Romidepsin_16h_R1 2 DSHSPDLQLPTPEVIPSSGSK 21 0 H3BQK9;H3BPE1;H0Y4F5;H0Y6T5 H3BQK9 MACF1 1 0 DS(0.174)HS(0.826)PDLQLPTPEVIPSSGSK;DS(0.194)HS(0.806)PDLQLPTPEVIPSSGSK ; 142.45 2.00E-05 51144000 10615.6 10198.7 9980.2 8959.7 10967 8720.1 6659 7824.8 11403.6 11807.2 TRUE FALSE FALSE 10486.21298 10342.27757 10153.90119 9995.662671 10407.31307 8162.913753 7224.615294 8051.198243 10383.63346 11500.44724 0.911809147 0.89929351 0.882913593 0.869154256 0.904948551 0.709790983 0.628202986 0.700076969 0.902889534 1 13.48940235 -6.010772868 0.257370643 0.991531809 3.27E-13 0.775314558 0.053317125 4.82916085 0.148073382 0.028119987 1.705159969 9.75E-07 6.010772868 -0.991531809 DSHS(ph)S(ph)EEDEASSQTDLSQTISK ddPTM_HeLa_Romidepsin_16h_R1 1 DSHSSEEDEASSQTDLSQTISK 22 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YDU3;Q5JTV8-2 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 2 0 DS(0.056)HS(0.697)S(0.702)EEDEAS(0.315)S(0.23)QTDLSQTISK 96.55 0.0015795 3817800 1255.7 1900.6 1473.9 960.78 1250.4 1344.9 1197.1 1485.3 1695.2 1912.5 TRUE FALSE FALSE 1240.395045 1927.356697 1499.552611 1071.869904 1186.587422 1258.96523 1298.781644 1528.274812 1543.577066 1862.812974 0.665872024 1.034648525 0.804993648 0.575403929 0.636986879 0.675840918 0.697215266 0.820412373 0.828626968 1 10.86326712 -9.506445962 23.88433302 0.85545914 0.680400906 0.41828052 0.110670685 436.6812361 634697.4343 0.022290719 0.033474841 3.12E-10 9.506445962 -0.175058234 DSHS(ph)SEEDEAS(ph)SQTDLSQTISK ddPTM_HeLa_Romidepsin_16h_R1 1 DSHSSEEDEASSQTDLSQTISK 22 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YDU3;Q5JTV8-2 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 2 0 DS(0.051)HS(0.692)S(0.258)EEDEAS(0.917)S(0.08)QT(0.001)DLSQTISK 78.653 0.0085287 4261000 2113.2 2052.1 2072.6 1680.3 1812.4 2176.4 1909.7 2108.3 2497.8 2563.2 TRUE FALSE FALSE 2087.443506 2080.989518 2108.672734 1874.584192 1719.906465 2037.335064 2071.90987 2169.300334 2274.390512 2496.607694 0.836111941 0.833526838 0.844615171 0.750852525 0.688897366 0.81604133 0.829890044 0.868899162 0.910992351 1 11.28575343 -11.81038168 0.507555092 1.019776395 0.794577638 0.523105003 0.054798925 0.521164559 0.236405585 0.055690239 0.014945031 1.55E-12 11.81038168 -0.225198757 DSIS(ph)AVSSEKVSPSK ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSK 15 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DS(0.119)IS(0.54)AVS(0.064)S(0.043)EKVS(0.205)PS(0.03)K 144.88 0.0031807 13518000 3704.4 3545.8 3802.5 2200 3371.7 3138.5 2685.7 2135.3 3509.7 3376 TRUE FALSE FALSE 3659.249348 3595.717865 3868.680917 2454.374351 3199.629567 2937.959979 2913.823291 2197.081537 3195.783642 3288.291033 1.112811886 1.09349137 1.176501982 0.746398152 0.973037221 0.893461056 0.886120864 0.668153005 0.971867639 1 11.68312228 -9.26004887 24.98656447 1.066683759 0.847451669 0.608368972 0.094914207 69.53215034 1249443.562 0.01417709 0.022699513 5.49E-10 9.26004887 -0.21923209 DSISAVSS(ph)EKVSPSK ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSK 15 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DSISAVS(0.057)S(0.751)EKVS(0.185)PS(0.006)K 71.263 0.017881 32994000 3469.4 3511.8 3547.8 2306 3015.6 3197.6 2243.4 2333.8 4167 4493.2 TRUE FALSE FALSE 3427.113618 3561.239213 3609.547971 2572.63057 2861.702679 2993.28368 2433.95434 2401.324821 3794.293084 4376.466016 0.783077855 0.813724864 0.824763167 0.587832868 0.65388436 0.683949942 0.556146062 0.548690384 0.866976476 1 12.09555065 -8.713419544 0.091944669 1.346900511 1.35E-15 0.787940421 0.065393736 7.789931125 0.214398771 1.073248402 2.104762989 1.93E-09 8.713419544 -1.346900511 DSISAVSSEKVS(ph)PS(ph)KSPSLSPSPPS(ph)PLEK ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSKSPSLSPSPPSPLEK 29 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 3 0 DS(0.021)IS(0.082)AVS(0.229)S(0.233)EKVS(0.497)PS(0.45)KS(0.405)PS(0.303)LS(0.281)PS(0.227)PPS(0.272)PLEK 41.064 0.016266 26703000 1314.8 1206.6 1302.7 1262.8 1452.4 1341.7 1157.8 1267.3 1431.7 1616.4 TRUE FALSE FALSE 1298.774712 1223.586546 1325.372947 1408.810878 1378.278608 1255.9697 1256.143503 1303.967326 1303.645166 1574.405695 0.824930141 0.777173603 0.841824284 0.894820745 0.87542786 0.797742097 0.797852489 0.828228283 0.82802366 1 10.62059163 -12.1459753 0.757893902 1.008139152 0.829299063 0 0.062561641 0.293592031 0.285320659 0.031833134 0.007804689 7.15E-13 12.1459753 -0.178840089 DSISAVSSEKVS(ph)PSKSPS(ph)LSPSPPSPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSKSPSLSPSPPSPLEK 29 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 DSISAVS(0.002)S(0.002)EKVS(0.642)PS(0.181)KS(0.202)PS(0.408)LS(0.408)PS(0.114)PPS(0.04)PLEK 76.98 3.31E-06 60467000 3968.9 3741.4 3714 3322.1 3598.6 3516.6 3127.3 3078.5 4010.2 4077.5 TRUE FALSE FALSE 3920.52552 3794.071527 3778.640612 3706.216833 3414.950014 3291.900609 3392.932784 3167.57154 3651.517668 3971.565962 0.987148535 0.955308703 0.951423355 0.933187782 0.859849754 0.828867162 0.854306039 0.797562365 0.919415088 1 11.95549225 -8.851913714 0.692430444 0.99611292 0.805466949 0.810720227 0.028619038 0.108616162 0.092901148 0.002898629 0.010843221 1.41E-09 8.851913714 -0.190645971 DSISAVSSEKVS(ph)PSKSPSLSPSPPSPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSKSPSLSPSPPSPLEK 29 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DS(0.003)IS(0.008)AVS(0.1)S(0.026)EKVS(0.596)PS(0.157)KS(0.055)PS(0.02)LS(0.025)PS(0.011)PPSPLEK 60.951 0.00058093 17535000 3194.6 3085.8 2760.5 2222.3 2365.5 2246.1 1694.6 1837.9 3680 3707.3 TRUE FALSE FALSE 3155.662986 3129.241973 2808.545345 2479.252782 2244.779708 2102.581459 1838.539282 1891.076737 3350.851583 3610.983812 0.873906711 0.866589865 0.777778437 0.686586513 0.621653218 0.582273854 0.509151904 0.52370125 0.927960843 1 11.81817624 -9.034156725 0.404495132 0.985128538 0.421676881 0.97574048 0.026064259 0.156828687 0.04405857 0.00951971 0.035986974 9.24E-10 9.034156725 -0.563451657 DSISAVSSEKVSPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DSISAVSSEKVSPSK 15 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DSISAVS(0.067)S(0.143)EKVS(0.143)PS(0.646)K 65.175 0.023249 34449000 6119.1 6099.9 7007.4 3672.6 5138.6 5106.7 4300.7 4734.1 6401 6267.3 TRUE FALSE FALSE 6044.518056 6185.774552 7129.360858 4097.243292 4876.358067 4780.398351 4666.001351 4871.073714 5828.478528 6104.474643 0.990178256 1.013318085 1.167890978 0.67118688 0.798816991 0.783097421 0.764357561 0.797951339 0.954787901 1 12.57565143 -9.252014253 24.99994071 1.008639862 0.76625014 0.809530843 0.063315364 216.3108555 573759.8133 0.008918616 0.014666466 5.60E-10 9.252014253 -0.242389722 DSISS(ph)DSETSEPLSCR ddPTM_HeLa_Romidepsin_16h_R1 1 DSISSDSETSEPLSCR 16 0 O75164 O75164 KDM4A Lysine-specific demethylase 4A 1 0 DSIS(0.21)S(0.753)DS(0.014)ET(0.015)S(0.008)EPLS(0.001)CR 122.33 0.0027815 5458600 1226.8 1107.2 1030.5 405.64 1302.5 1343.9 1225.1 1124.6 1300.2 1241.6 TRUE FALSE FALSE 1211.84729 1122.787191 1048.43542 452.5420054 1236.028565 1258.029127 1329.159963 1157.138527 1183.906856 1209.343053 1.002070741 0.92842737 0.866946246 0.374204825 1.022066122 1.040258282 1.099076031 0.956832326 0.97896693 1 10.24000784 -10.13203349 3.572932926 1.00104427 0.892006557 0.052924131 0.188510722 0.591806231 13.77992298 0.033390728 0.04135339 7.38E-11 10.13203349 -0.109037713 DSITPDIATKPGQPLFLDSIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 DSITPDIATKPGQPLFLDSISPK 23 1 Q2TB10 Q2TB10 ZNF800 Zinc finger protein 800 1 0 DSITPDIAT(0.002)KPGQPLFLDS(0.371)IS(0.627)PK;DSITPDIATKPGQPLFLDS(0.39)IS(0.61)PK ; 146.2 2.90E-07 83103000 7824.6 8608.4 7544.8 6580 5557.6 4685.8 4014.9 4598.2 8416.8 9063.8 TRUE FALSE FALSE 7729.230766 8729.589281 7676.114079 7340.81056 5273.974934 4386.392503 4355.925506 4731.241662 7663.980328 8828.321169 0.87550403 0.988816459 0.869487407 0.831506967 0.597392736 0.496854659 0.493403607 0.535916351 0.868112995 1 13.1079234 -8.803975356 1.673849687 0.941206593 0.500601321 0.94345549 0.045670469 0.061588891 0.349398315 0.008079692 0.018505105 1.57E-09 8.803975356 -0.440605272 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPR ddPTM_HeLa_Romidepsin_16h_R1 3 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPR 32 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 0 DSLGDFIEHY(0.003)AQLGPS(0.499)S(0.499)PEQLAAGAEEGGGPR;DSLGDFIEHYAQLGPS(0.559)S(0.441)PEQLAAGAEEGGGPR;DSLGDFIEHY(0.003)AQLGPS(0.551)S(0.446)PEQLAAGAEEGGGPR ;; 77.791 3.27E-08 106166800 2174.07 2465.23 2481.26 2114.66 2604.93 2928.49 2541.07 2520.28 2903.24 2859.07 TRUE FALSE FALSE 2147.571599 2499.935573 2524.445289 2359.166939 2471.990702 2741.36894 2756.908422 2593.200325 2643.566943 2784.790949 0.771178748 0.897710319 0.906511597 0.847161235 0.887675501 0.984407444 0.989987569 0.931201075 0.949287394 1 11.44335331 -8.267993374 22.3688853 0.887495697 0.970677588 0.247715333 0.058495889 166.3168455 567649.1771 0.01216465 0.027894566 5.40E-09 8.267993374 0.083181892 DSLGDFIEHYAQLGPS(ph)SPEQLAAGAEEGGGPRR ddPTM_HeLa_Romidepsin_16h_R1 1 DSLGDFIEHYAQLGPSSPEQLAAGAEEGGGPRR 33 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 0 DS(0.001)LGDFIEHY(0.018)AQLGPS(0.491)S(0.491)PEQLAAGAEEGGGPRR 47.919 0.0055723 5236300 542.91 306.08 482.94 534.26 468.34 506.33 560.69 560 562.49 517.27 TRUE FALSE FALSE 536.2928041 310.3890023 491.3453681 596.033655 444.4388622 473.9771471 608.3149946 576.2027165 512.1794856 503.8312508 1.064429416 0.616057463 0.975218126 1.183002551 0.88211849 0.940745828 1.20737845 1.143642272 1.016569506 1 8.9767968 -7.757542093 24.98739238 0.992992024 1.175510414 0.245935974 0.141866724 115.5381528 740738.5267 0.019901181 0.06921576 1.75E-08 7.757542093 0.18251839 DSLIDSLT(ph) ddPTM_HeLa_Romidepsin_16h_R1 2 DSLIDSLT 8 0 P56537-2;P56537 P56537-2 EIF6 Eukaryotic translation initiation factor 6 1 0 DSLIDS(0.09)LT(0.91);DSLIDS(0.01)LT(0.99) ; 111.28 0.0045328 14264400 14866.5 14036 12278.2 10603.4 15499.4 15753.6 13931.9 15538.1 14580.9 12560.5 TRUE FALSE FALSE 14685.30138 14233.59918 12491.89692 11829.415 14708.40778 14746.9958 15115.27524 15987.67041 13276.74779 12234.1764 1.200350633 1.163429291 1.021065621 0.966915517 1.202239309 1.205393426 1.235495937 1.30680398 1.085217946 1 13.57862936 -4 0.019549303 3.51E-17 2.62667705 0.352228304 0.086673659 2755.660954 4.195088879 211.2497894 374.4530819 1.00E-04 4 2.62667705 DSLITPHVS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 DSLITPHVSR 10 0 Q99666;O14715;J3KQ37;H7BZ48;P49792;J3KNE0;A6NKT7;F8VYC4;A0A286YES2;A0A1W2PNU4;P0DJD0;P0DJD1;Q7Z3J3 Q99666;P49792;Q7Z3J3 RGPD5;RGPD8;RGPD6;RANBP2;RGPD3;RGPD1;RGPD2;RGPD4 RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 8;E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2;RanBP2-like and GRIP domain-containing protein 4 1 0 DSLITPHVS(1)R 100.73 0.010068 10138000 6168.8 5770.5 6083.1 3906.4 5533 5851.9 4255.5 4625.5 6539.5 6193.1 TRUE FALSE FALSE 6093.612293 5851.73725 6188.973804 4358.076348 5250.630364 5477.982476 4616.962064 4759.331545 5954.590742 6032.202369 1.010180349 0.970083046 1.025989087 0.722468525 0.870433391 0.908123127 0.765385805 0.78898738 0.987133782 1 12.55846911 -9.275648706 24.96114351 1.003216952 0.817229833 0.774774609 0.050488906 260.231975 457141.6633 0.007509758 0.01150588 5.30E-10 9.275648706 -0.185987119 DSLLDGHFVLATLSDT(ph)DSHSQDLGSPER ddPTM_HeLa_Romidepsin_16h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 0 DSLLDGHFVLATLS(0.145)DT(0.82)DS(0.004)HS(0.009)QDLGS(0.022)PER 116.04 1.33E-09 4088400 1918 2012.7 1632.4 1816.6 3466.2 3881.8 3148.7 3597.8 2772.1 2336 TRUE FALSE FALSE 1894.622678 2041.034843 1660.811237 2026.643839 3289.30688 3633.765508 3416.150499 3701.896667 2524.156433 2275.310383 0.832687572 0.897035788 0.729927332 0.890710935 1.445651944 1.597041676 1.501399776 1.626985353 1.109367958 1 11.15184765 -8.708093512 4.260427452 0.898324593 1.559506945 0.907077192 0.099669621 0.04042208 1.510280683 0.01351021 0.027302622 1.96E-09 8.708093512 0.661182352 DSLLDGHFVLATLSDTDS(ph)HSQDLGSPER ddPTM_HeLa_Romidepsin_16h_R1 1 DSLLDGHFVLATLSDTDSHSQDLGSPER 28 0 Q99638 Q99638 RAD9A Cell cycle checkpoint control protein RAD9A 1 0 DSLLDGHFVLAT(0.001)LS(0.001)DT(0.023)DS(0.494)HS(0.12)QDLGS(0.361)PER 114.01 9.88E-10 6146600 1821 1774.3 1616 1748.3 3311.4 3362.9 2811.6 2779.1 2530.6 2016.6 TRUE FALSE FALSE 1798.804952 1799.278642 1644.125802 1950.446672 3142.406901 3148.021543 3050.417234 2859.508874 2304.256798 1964.208441 0.915791274 0.916032435 0.837042428 0.992993733 1.599833722 1.602692198 1.553000776 1.455807242 1.173122338 1 10.93973232 -8.782250356 7.028359631 0.946554399 1.55719091 0.905537936 0.091617439 0.022346123 4.446583093 0.009403818 0.017529236 1.65E-09 8.782250356 0.610636512 DSLLQDGEFSMDLR ddPTM_HeLa_Romidepsin_16h_R1 2 DSLLQDGEFSMDLR 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 0 ; ; 121.21 0.010016 325160000 7289.2 7012 7358.4 7156.3 7711 7077.8 6282.7 6695.1 7435.4 6776.1 FALSE FALSE TRUE 7200.356427 7110.71512 7486.469865 7983.745077 7317.478896 6625.551423 6816.352381 6888.812155 6770.359202 6600.055945 1.090953847 1.077371946 1.134304001 1.209648091 1.108699526 1.003862918 1.032771909 1.04375057 1.025803305 1 12.68826254 -6.282790094 15.34477315 1.063047727 1.085095058 0 0.06308023 0 0 0.009572421 0 5.21E-07 6.282790094 0.022047331 DSLS(ph)PVLHPSDLILTR ddPTM_HeLa_Romidepsin_16h_R1 2 DSLSPVLHPSDLILTR 16 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 0 DS(0.002)LS(0.998)PVLHPSDLILTR;DS(0.003)LS(0.997)PVLHPSDLILTR ; 108.97 0.0014119 10405900 3593.59 3442.05 3240.97 3473.92 5315.3 5830.3 5224.77 5346.02 4727.73 4288.88 TRUE FALSE FALSE 3549.789943 3490.50727 3297.377723 3875.590976 5044.040407 5457.762646 5668.561833 5500.698654 4304.869988 4177.454279 0.849749562 0.835558461 0.789327064 0.927739891 1.207443594 1.306480522 1.356941681 1.316758553 1.030500803 1 12.02840832 -8.658092316 2.905861023 0.906548277 1.324788968 0.887391063 0.069290294 0.069595622 1.181289042 0.011865575 0.025487796 2.20E-09 8.658092316 0.418240691 DSLVEHDEEFVQRQDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DSLVEHDEEFVQRQDSPR 18 1 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 DSLVEHDEEFVQRQDS(1)PR 86.727 0.0031308 2644300 477.58 723.68 536.72 404.75 699.21 707.96 618.95 950.63 800.28 927.58 TRUE FALSE FALSE 471.7590713 733.867986 546.0613865 451.5490994 663.5267046 662.7236408 671.5235976 978.1349792 728.7009525 903.4813379 0.522156963 0.812266901 0.604396974 0.499787965 0.734411079 0.733522225 0.743262278 1.082628869 0.806547874 1 9.819350991 -7.261376823 6.354810427 0.735842743 1.090199553 0.370027021 0.141169356 0.148086751 33.58459653 0.02670745 0.224812834 5.48E-08 7.261376823 0.35435681 DSNAPKS(ph)PLTGYVR ddPTM_HeLa_Romidepsin_16h_R1 1 DSNAPKSPLTGYVR 14 1 H0YNS8;H0YKM5;Q9NP66 H0YNS8 HMG20A High mobility group protein 20A 1 0 DSNAPKS(0.5)PLT(0.5)GYVR 133.9 0.010823 25420000 1013.2 1419.1 1070.6 1651.4 1036.7 937.56 774.58 832.64 1284.5 949.44 TRUE FALSE FALSE 1000.850729 1439.078127 1089.233344 1842.342638 983.7933305 877.6529418 840.3728059 856.7311247 1169.611103 924.7734119 1.0822659 1.55614133 1.177838084 1.992209783 1.063820951 0.94904647 0.908733745 0.926422747 1.26475425 1 9.852956109 -6.007872826 12.68112489 1.122674243 0.592438199 0 0.331932652 0 0 0.044487446 0 9.82E-07 6.007872826 -0.530236044 DSNAPKSPLT(ph)GYVR ddPTM_HeLa_Romidepsin_16h_R1 1 DSNAPKSPLTGYVR 14 1 H0YNS8;H0YKM5;Q9NP66 H0YNS8 HMG20A High mobility group protein 20A 1 0 DS(0.001)NAPKS(0.242)PLT(0.757)GYVR 117.53 0.019073 29019000 1919.6 2231.6 1866.8 2895.7 1667.7 1587.2 1538.5 1569.1 1735.8 2099.4 TRUE FALSE FALSE 1896.203177 2263.016523 1899.290871 3230.514459 1582.591046 1485.783042 1669.180152 1614.499433 1580.545701 2044.857285 0.927303431 1.106686779 0.928813411 1.579823923 0.773937163 0.726594982 0.816281979 0.789541375 0.772936924 1 10.99778444 DSNELS(ph)DSAGEEDSADLKR ddPTM_HeLa_Romidepsin_16h_R1 1 DSNELSDSAGEEDSADLKR 19 1 Q9Y6X9-2;Q9Y6X9 Q9Y6X9-2 MORC2 MORC family CW-type zinc finger protein 2 1 0 DS(0.029)NELS(0.738)DS(0.234)AGEEDSADLKR 64.547 0.0072007 3865800 1041.8 1081.9 1221.3 1416.3 1211.4 1450.5 1277.4 1308.9 1449.8 1354.8 TRUE FALSE FALSE 1029.102141 1097.131017 1242.556214 1580.05927 1149.577738 1357.817731 1385.902324 1346.770956 1320.126257 1319.602101 0.779857913 0.83141048 0.941614304 1.197375534 0.871154825 1.028959965 1.050242587 1.020588673 1.000397208 1 10.36588726 -9.513874303 24.14058105 0.888207102 1.029715601 0.288745647 0.09685364 275.5378571 738707.3596 0.016829132 0.024554485 3.06E-10 9.513874303 0.141508499 DSNELSDS(ph)AGEEDSADLKR ddPTM_HeLa_Romidepsin_16h_R1 1 DSNELSDSAGEEDSADLKR 19 1 Q9Y6X9-2;Q9Y6X9 Q9Y6X9-2 MORC2 MORC family CW-type zinc finger protein 2 1 0 DSNELS(0.348)DS(0.652)AGEEDSADLKR 144.95 1.89E-05 5254600 989.38 905.26 1006.8 1007.8 1025.2 1298.9 1223.8 1469.2 1463 1184.7 TRUE FALSE FALSE 977.321056 918.004274 1024.322932 1124.326578 972.8802185 1215.904482 1327.749541 1511.708984 1332.145616 1153.921323 0.846956405 0.795551877 0.887688711 0.974352892 0.84310793 1.053715238 1.150641309 1.31006244 1.154450992 1 10.17232915 -7.674071001 1.5233601 0.91123939 1.327082683 0.601575827 0.099533543 0.216593241 0.765265882 0.011542008 0.106987544 2.12E-08 7.674071001 0.415843293 DSNNLCLHFNPR ddPTM_HeLa_Romidepsin_16h_R1 2 DSNNLCLHFNPR 12 0 P09382 P09382 LGALS1 Galectin-1 0 0 ; ; 107.39 0.0056021 10480000 1848.5 1241.94 1782.91 996.2 2388.68 2250.13 1860.85 1641.49 1881.74 1613.86 FALSE FALSE TRUE 1825.969771 1259.424064 1813.940801 1111.385331 2266.776746 2106.353955 2018.910553 1688.983923 1713.432461 1571.931685 1.161608859 0.801195164 1.15395651 0.70701885 1.442032608 1.339978051 1.284350059 1.074463948 1.090017129 1 10.6183228 -8.73042225 24.99999937 1.038554412 1.28905722 0.422891674 0.164595715 171.9797892 138616.1054 0.023360707 0.046717477 1.86E-09 8.73042225 0.250502808 LTTTGQVTS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 LTTTGQVTSPVK 12 0 K7ENR9;K7ERZ5;P49916-4;P49916-3;P49916-2;P49916 K7ENR9 LIG3 DNA ligase 3 1 0 LTTTGQVT(0.088)S(0.912)PVK;LTTTGQVT(0.479)S(0.521)PVK ; 196.38 1.21E-10 147090000 12185.5 11199 12163.8 6575.7 5852.2 4708.2 4225.3 4017.6 11696.3 10533.2 TRUE FALSE FALSE 12036.97844 11356.65982 12375.50584 7336.013374 5553.540396 4407.361215 4584.196877 4133.842917 10650.15363 10259.54595 1.173246701 1.106935909 1.206243035 0.715042694 0.541304696 0.429586381 0.446822589 0.402926498 1.03807261 1 13.32467926 -8.990227306 2.434013956 1.094702137 0.444825593 0.951622445 0.069157132 0.051960082 0.618592325 0.012922332 0.024592987 1.02E-09 8.990227306 -0.649876544 down DSPAFPDS(ph)PWRER ddPTM_HeLa_Romidepsin_16h_R1 2 DSPAFPDSPWRER 13 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 DSPAFPDS(1)PWRER;DSPAFPDS(1)PWRER ; 109.48 0.0026593 15522700 5767 5419.3 5284.2 6246 3244.1 3145.4 2615.7 1702.24 6470.2 5865.2 TRUE FALSE FALSE 5696.709586 5495.593048 5376.169284 6968.191908 3078.541472 2944.419091 2837.877493 1751.491629 5891.489107 5712.821258 0.997179735 0.961975318 0.941070802 1.21974618 0.538882862 0.515405429 0.49675587 0.306589608 1.031274889 1 12.47998768 -8.660207849 6.189449907 1.004076273 0.459912898 0.901117866 0.091098243 0.04461625 2.351591825 0.012374744 0.024898458 2.19E-09 8.660207849 -0.544163375 DSPSAGGPVGQLEPIPIPAPASPGTRPT(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 DSPSAGGPVGQLEPIPIPAPASPGTRPTLK 30 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 0 DS(0.001)PS(0.001)AGGPVGQLEPIPIPAPAS(0.332)PGT(0.302)RPT(0.364)LK 63.491 0.00035372 9701900 909.12 729.96 719.51 1130.1 817.87 788.94 677.03 799.86 1010.4 893.81 TRUE FALSE FALSE 898.0392958 740.236396 732.0327697 1260.767479 776.131042 738.5292802 734.5369113 823.0026871 920.0272934 870.5886873 1.031531088 0.850271094 0.840848015 1.448178109 0.89150141 0.848310219 0.843724392 0.945340434 1.056787559 1 9.765847463 -8.558185457 24.99998576 1.02032494 0.87463685 0.182431202 0.158966815 235.3744843 166663.1643 0.022128316 0.04425676 2.77E-09 8.558185457 -0.14568809 DSPSVWAAVPGK ddPTM_HeLa_Romidepsin_16h_R1 2 DSPSVWAAVPGK 12 0 P07737;CON__P02584;I3L3D5 P07737 PFN1 Profilin-1 0 0 ; ; 188.91 1.02E-08 1021290 1331.36 983.09 1147.7 848.07 1158.68 1117.65 1098.23 1078.52 1045.08 1084.92 FALSE FALSE TRUE 1315.132872 996.9299668 1167.675237 946.1278437 1099.548236 1046.235772 1191.513629 1109.725275 951.6054273 1056.733622 1.244526383 0.943407067 1.104985412 0.895332394 1.040515995 0.990065756 1.127543975 1.050146651 0.900515899 1 10.04539604 -10.24077314 24.90163125 1.115470804 1.023632135 0 0.108913808 1166.531573 1405606.187 0.017881358 0.021885132 5.74E-11 10.24077314 -0.09183867 DSQDAGGFGPEDR ddPTM_HeLa_Romidepsin_16h_R1 3 DSQDAGGFGPEDR 13 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;; ;; 190.35 1.01E-09 24443100 5592.3 5617.7 4736.4 5233 5596.9 5290.8 4458.9 5459.1 6007.1 5152.5 FALSE FALSE TRUE 5524.138897 5696.786128 4818.835055 5838.064082 5311.269308 4952.734955 4837.638855 5617.050445 5469.809931 5018.637307 1.10072487 1.135126087 0.960187947 1.163276747 1.058309055 0.986868477 0.963934741 1.119238172 1.089899428 1 12.29307997 -8.300866629 21.17693577 1.05812191 1.017405917 0.06976593 0.068514794 194.9893428 104731.1496 0.010009437 0.022383033 5.00E-09 8.300866629 -0.040715994 DSQDAS(ph)AEQSDHDDEVASLASASGGFGTK ddPTM_HeLa_Romidepsin_16h_R1 1 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 DS(0.015)QDAS(0.812)AEQS(0.172)DHDDEVAS(0.001)LASASGGFGTK 65.795 0.00013083 3683400 1402.6 1828.5 1724.5 1471.5 1635.8 2107.8 1604.1 1870.2 1839.2 1665.7 TRUE FALSE FALSE 1385.504572 1854.241671 1754.514199 1641.641754 1552.319022 1973.118383 1740.352214 1924.311286 1674.697346 1622.424874 0.853971481 1.142882916 1.081414756 1.011844542 0.956789462 1.216153928 1.072685856 1.186071119 1.032218732 1 10.66393596 -8.806460328 0.544371064 0.939399816 1.171135808 0.189538935 0.093273959 0.972725829 0.470393983 0.023957005 0.107916194 1.56E-09 8.806460328 0.231735993 DSQDASAEQS(ph)DHDDEVASLASASGGFGTK ddPTM_HeLa_Romidepsin_16h_R1 6 DSQDASAEQSDHDDEVASLASASGGFGTK 29 0 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 DS(0.001)QDAS(0.053)AEQS(0.945)DHDDEVAS(0.001)LASASGGFGTK;DS(0.001)QDAS(0.05)AEQS(0.949)DHDDEVASLASASGGFGTK;DSQDAS(0.014)AEQS(0.985)DHDDEVAS(0.001)LASASGGFGTK;DS(0.01)QDAS(0.151)AEQS(0.821)DHDDEVAS(0.014)LAS(0.003)AS(0.001)GGFGTK;DS(0.004)QDAS(0.33)AEQS(0.664)DHDDEVAS(0.002)LASASGGFGTK;DS(0.006)QDAS(0.048)AEQS(0.926)DHDDEVAS(0.016)LAS(0.002)AS(0.001)GGFGTK ;;;;; 97.639 2.08E-08 519771600 11584.77 10239.87 11160.14 10594.15 13333.7 13810.49 11989.31 13125.09 13079.16 11961.29 TRUE FALSE FALSE 11443.57037 10384.02716 11354.37756 11819.09547 12653.23153 12928.04426 13007.68169 13504.84377 11909.32717 11650.53396 0.982235699 0.891291952 0.974580014 1.014468136 1.086064517 1.109652511 1.116488028 1.159160929 1.022212991 1 13.50810846 -8.690136993 1.860775683 0.981173272 1.129009133 0.804515981 0.033998411 0.115937711 0.812693711 0.005332035 0.012611144 2.04E-09 8.690136993 0.147835861 DSQEDWTTFTHDR ddPTM_HeLa_Romidepsin_16h_R1 1 DSQEDWTTFTHDR 13 0 O15357;A0A0A0MTP6;O15357-2;F5GY16 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 0 0 154.65 0.00035104 2327900 2084.2 1900.1 1822.9 2067 2033.4 1854.3 1435 1976.7 2458.1 2557.8 FALSE FALSE TRUE 2058.796969 1926.849658 1854.62681 2305.996266 1929.62801 1735.816214 1556.888864 2033.892696 2238.24138 2491.347987 0.826378723 0.773416507 0.744427041 0.925601834 0.774531707 0.696737759 0.624918266 0.816382419 0.898405759 1 11.28271083 -16.52287874 0.110642974 1.821586625 0.620329418 0.454939678 0.077968748 47.35237244 0.38447939 8.692531026 0.442694326 3.00E-17 16.52287874 -1.201257207 DSQSPDS(ph)AWR ddPTM_HeLa_Romidepsin_16h_R1 2 DSQSPDSAWR 10 0 O94875-12;O94875-11;O94875-9;O94875-8;C9J4Z9;C9IZT7;C9JWC3;C9JN77;C9JI79;C9J372;C9JZ60;C9JDX2;C9JBB0;C9JFS9;C9JC90;C9J620;C9JM25 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 DS(0.364)QS(0.174)PDS(0.462)AWR;DS(0.18)QS(0.117)PDS(0.702)AWR ; 138.42 0.0051721 34303000 6206.8 6731 5914.1 5981.3 5598.1 4821.8 4663.8 4592.3 6886.1 6824.2 TRUE FALSE FALSE 6131.149134 6825.759195 6017.03243 6672.886049 5312.408068 4513.702542 5059.943056 4725.170955 6270.189969 6646.9063 0.922406434 1.02690769 0.90523804 1.003908547 0.799230172 0.679068177 0.761247839 0.710882739 0.943324561 1 12.6984673 -8.616713259 4.054925891 0.965346208 0.72314702 0.887192436 0.040742952 0.052584325 1.619110446 0.006144666 0.012779395 2.42E-09 8.616713259 -0.242199188 DSRTVYQY(ph)QY(ph)TNWS(ph)VEQLPAEPK ddPTM_HeLa_Romidepsin_16h_R1 1 DSRTVYQYQYTNWSVEQLPAEPK 23 1 P08575-4;P08575-9;P08575-10;P08575-8;P08575-7;P08575-5;P08575-6;P08575 P08575-4 PTPRC Receptor-type tyrosine-protein phosphatase C 3 0 DS(0.051)RT(0.051)VY(0.048)QY(0.757)QY(0.731)T(0.369)NWS(0.994)VEQLPAEPK 45.363 0.016681 2426800 722.56 327.73 702.04 862.86 417.08 311.56 515.61 368.82 891.28 588.02 TRUE FALSE FALSE 713.7531608 332.3437915 714.2587117 962.6279331 395.7948513 291.6523215 559.4059005 379.4912248 811.5616845 572.7431556 1.246201118 0.580266719 1.247083801 1.680732321 0.691051211 0.50922009 0.976713375 0.662585351 1.41697317 1 9.161744503 DSS(ph)KGEDSAEETEAK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSKGEDSAEETEAK 15 1 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 DS(0.018)S(0.612)KGEDS(0.261)AEET(0.11)EAK 169.37 0.00016365 4525600 1235.9 769.07 1221.7 1134.7 1069.7 1280.3 1346.9 464.17 1372.5 1260.6 TRUE FALSE FALSE 1220.836375 779.8969876 1242.963176 1265.899353 1015.109217 1198.492962 1461.305652 477.6000266 1249.740163 1227.84943 0.994288343 0.635173148 1.01230912 1.030989079 0.82673754 0.97609115 1.190134243 0.388972797 1.017828515 1 10.26191794 -7.247791269 24.8149585 0.973213216 0.388972367 0.609509314 0.138133277 1040.703485 1892170.354 0.018138954 0.482326026 5.65E-08 7.247791269 -0.584240849 DSS(ph)PVGLVEEAGSR ddPTM_HeLa_Romidepsin_16h_R1 2 DSSPVGLVEEAGSR 14 0 Q6ICB4 Q6ICB4 FAM109B Sesquipedalian-2 1 0 DS(0.234)S(0.764)PVGLVEEAGS(0.002)R;DS(0.001)S(0.999)PVGLVEEAGSR ; 187.63 6.50E-11 4509900 2108.61 1738.14 1954.99 1258.48 1291.78 1663.43 1158.06 1372.31 2033.76 1609.28 TRUE FALSE FALSE 2082.90945 1762.609581 1989.015781 1403.991379 1225.855646 1557.142191 1256.425587 1412.015625 1851.855412 1567.470674 1.328834718 1.12449286 1.26893333 0.895705038 0.782059701 0.993410733 0.801562421 0.90082427 1.181429065 1 10.61422274 -9.201174162 7.412744685 1.164081648 0.870922206 0.707948508 0.097995756 0.170781369 18.63708657 0.020117185 0.033408105 6.29E-10 9.201174162 -0.293159443 DSS(ph)TSPGDYVLSVSENSR ddPTM_HeLa_Romidepsin_16h_R1 4 DSSTSPGDYVLSVSENSR 18 0 P46108-2;I3L297;P46108 P46108-2 CRK Adapter molecule crk 1 0 DS(0.001)S(0.94)T(0.059)SPGDYVLSVSENSR;DS(0.007)S(0.971)T(0.022)SPGDYVLSVSENSR;DSS(0.929)T(0.066)S(0.005)PGDYVLSVSENSR;DS(0.004)S(0.992)T(0.004)SPGDYVLSVSENSR ;;; 382.24 0 93029000 5256.5 4737.97 4983.7 3478.37 6028.2 7392 6173.5 6970.1 5302 5365.5 TRUE FALSE FALSE 5192.431756 4804.671266 5070.439208 3880.555506 5720.55846 6919.675057 6697.876936 7171.768847 4827.775841 5226.103537 0.993557001 0.919360138 0.970214075 0.742533224 1.094612539 1.324060078 1.281619641 1.372297505 0.923781132 1 12.35151999 -8.386419523 3.822404415 0.970787095 1.321663851 0.825039159 0.080753436 0.077398018 1.985677895 0.011700211 0.027541156 4.11E-09 8.386419523 0.350876756 DSSDS(ph)ADGRATPSENLVPSSAR ddPTM_HeLa_Romidepsin_16h_R1 1 DSSDSADGRATPSENLVPSSAR 22 1 F5H669;Q8N684-2;Q8N684;Q8N684-3;F5H6M0;F5H047 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 0 DS(0.197)S(0.164)DS(0.494)ADGRAT(0.137)PS(0.007)ENLVPSSAR 59.618 0.0054224 143180000 3038.9 2899.2 2917.4 3068.1 2988.1 3181.4 2592.9 2930.7 3654.1 3318.3 TRUE FALSE FALSE 3001.860718 2940.015014 2968.176123 3422.848158 2835.606107 2978.118807 2813.140861 3015.495181 3327.268144 3232.090088 0.928767651 0.909632756 0.918345728 1.059020035 0.87732892 0.921421967 0.870378234 0.932986117 1.029447835 1 11.6582517 -16.52287875 0.167738629 1.298254868 0.905466573 0.334215063 0.049112929 61.70943196 0.678994387 6.025285918 0.08097129 3.00E-17 16.52287875 -0.392788296 DSSESQLAS(ph)TESDKPTTGR ddPTM_HeLa_Romidepsin_16h_R1 1 DSSESQLASTESDKPTTGR 19 1 A0A087WVF1;Q96B23-2;Q96B23;K7EQH1 A0A087WVF1 C18orf25 Uncharacterized protein C18orf25 1 0 DSSES(0.001)QLAS(0.416)T(0.291)ES(0.291)DKPTTGR 64.318 0.0092012 4466600 1000.4 1053.9 979.59 1240.4 1470.4 1519.6 1192 1401.3 1172.3 1142.1 TRUE FALSE FALSE 988.20674 1068.736832 996.639353 1383.820884 1395.360001 1422.502464 1293.24845 1441.844405 1067.446552 1112.428077 0.888333152 0.960724431 0.895913519 1.243964363 1.254337273 1.27873657 1.162545675 1.296123708 0.959564554 1 10.11949635 -9.255803486 24.98726989 0.943650794 1.244596808 0.922439219 0.044392674 105.3462302 467062.0986 0.007915277 0.012890239 5.55E-10 9.255803486 0.300946014 DSSESQLAST(ph)ESDKPTTGR ddPTM_HeLa_Romidepsin_16h_R1 1 DSSESQLASTESDKPTTGR 19 1 A0A087WVF1;Q96B23-2;Q96B23;K7EQH1 A0A087WVF1 C18orf25 Uncharacterized protein C18orf25 1 0 DSSESQLAS(0.064)T(0.897)ES(0.039)DKPTTGR 117.02 0.00045687 4371700 971.47 820.23 838.57 1135.1 1316 1181 1328.4 1444 1151.2 1044.9 TRUE FALSE FALSE 959.62935 831.7772195 853.1649591 1266.345603 1248.839609 1105.537912 1441.234263 1485.779862 1048.233789 1017.753347 0.942889898 0.817267977 0.838282636 1.244255896 1.227055271 1.08625328 1.416093857 1.459862417 1.029948751 1 9.991172251 -7.998310634 0.705348471 0.955061063 1.549296145 0.700032685 0.11672396 0.592709708 0.356224441 0.021260759 0.230069198 1.00E-08 7.998310634 0.594235082 DSSFTEVPRS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSFTEVPRSPK 12 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 DSS(0.005)FT(0.002)EVPRS(0.993)PK 145.83 0.0099437 6450200 1766.6 1568.3 1668.4 1806.2 1710.5 1372.1 1440.8 1570.4 2150.9 1873.2 TRUE FALSE FALSE 1745.068 1590.378569 1697.437802 2015.041342 1623.206802 1284.427238 1563.181516 1615.837046 1958.518117 1824.533994 0.956445868 0.871662887 0.930340464 1.10441425 0.889655555 0.703975504 0.856756586 0.885616301 1.073434709 1 10.83331232 -8.525311466 24.9952899 0.974627036 0.815786059 0.506528096 0.076942435 43.97955549 451873.3759 0.010084432 0.020270018 2.98E-09 8.525311466 -0.158840978 DSSIIDPGT(ph)EQDLPSPENSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSIIDPGTEQDLPSPENSSVK 22 0 H7C150;H7C183;Q70CQ2-3;Q70CQ2-2;Q70CQ2 H7C150 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 0 DS(0.046)S(0.246)IIDPGT(0.609)EQDLPS(0.098)PENSSVK 67.928 0.0035718 7417900 7376.9 7209.3 7474.8 5547.3 7318.8 8059.9 6701.8 8394.3 8068.8 8041.2 TRUE FALSE FALSE 7286.987505 7310.792715 7604.895758 6188.704927 6945.294326 7544.898402 7271.050725 8637.175826 7347.106319 7832.288465 0.930377825 0.933417193 0.970967271 0.790152834 0.8867516 0.963307013 0.928343071 1.102765286 0.938053591 1 12.93521819 -7.257640848 24.50912296 0.945170227 1.102765366 0.43588935 0.0566874 248.7565952 1604952.014 0.008780151 0.087210307 5.53E-08 7.257640848 0.157595139 DSSIIDPGTEQDLPS(ph)PENSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSIIDPGTEQDLPSPENSSVK 22 0 H7C150;H7C183;Q70CQ2-3;Q70CQ2-2;Q70CQ2 H7C150 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 0 DSSIIDPGTEQDLPS(0.995)PENS(0.004)S(0.001)VK 117.03 3.48E-05 11337000 5802.4 5460.9 5708.6 4391.7 5596.8 5417.9 5538.5 5907.8 6204 5435.7 TRUE FALSE FALSE 5731.678117 5537.778694 5807.955788 4899.489018 5311.174411 5071.713675 6008.940052 6078.732872 5649.098702 5294.47973 1.08257627 1.045953328 1.096983289 0.925395746 1.003153224 0.957924845 1.134944387 1.148126574 1.066979003 1 12.37027321 -4 0.005295551 3.75E-11 2.1678929 0.028330055 0.06898177 119372.3069 49.39648181 9353.902494 10926.00817 1.00E-04 4 2.1678929 S(ph)PVSPLAAQGIPLPAQLTK ddPTM_HeLa_Romidepsin_16h_R1 2 SPVSPLAAQGIPLPAQLTK 19 0 K7EIF1;K7EPF0;K7EQS3;K7EM48;K7EN63;Q96SI1-2;Q96SI1 K7EIF1 KCTD15 BTB/POZ domain-containing protein KCTD15 1 0 S(0.986)PVS(0.014)PLAAQGIPLPAQLTK;S(0.998)PVS(0.002)PLAAQGIPLPAQLTK ; 214.94 3.47E-29 32342000 6985 7134.4 6100.2 4290.6 3055.6 2976.6 2437.48 2510.3 7102.9 6472.8 TRUE FALSE FALSE 6899.864133 7234.83827 6206.371422 4786.69936 2899.66133 2786.404867 2644.51949 2582.93157 6467.598834 6304.635723 1.09441123 1.147542632 0.984413961 0.759234882 0.459925277 0.441961279 0.41945635 0.409687678 1.025848141 1 12.6221973 -8.98964892 1.932599872 1.053948119 0.41994083 0.980164193 0.041506132 0.038310925 0.285927613 0.008145534 0.016186337 1.02E-09 8.98964892 -0.63400729 down DSSPAS(ph)GTDRDSPEPLLK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSPASGTDRDSPEPLLK 18 1 A6NHT5 A6NHT5 HMX3 Homeobox protein HMX3 1 0 DS(0.007)S(0.027)PAS(0.516)GT(0.076)DRDS(0.374)PEPLLK 52.372 0.029839 5797200 3492.7 2680.9 3050.4 2161.2 1318.5 1392.9 820.56 1340.8 3352.4 3359.6 TRUE FALSE FALSE 3450.129629 2718.641781 3103.490932 2411.088113 1251.212025 1303.898185 890.2583459 1379.593933 3052.552948 3272.317108 1.054338414 0.830800222 0.948407758 0.736813711 0.382362706 0.398463273 0.27205748 0.421595428 0.932841423 1 11.67609685 -8.98296538 1.379179495 1.014342432 0.33512289 0.927991534 0.076010669 0.061558277 0.232931192 0.011336819 0.02506644 1.04E-09 8.98296538 -0.679219542 down DSSPSSS(ph)PSPK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSPSSSPSPK 11 0 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSS(0.002)PS(0.004)S(0.07)S(0.684)PS(0.241)PK 137.4 0.0036395 2215100 730.29 889.03 1224.2 973.17 1415.3 2259.4 4280 1097.2 1040.5 867.76 TRUE FALSE FALSE 721.3889446 901.5457877 1245.506687 1085.692494 1343.07196 2115.031632 4643.543093 1128.945751 947.435074 845.2154701 0.853497091 1.066646103 1.473596653 1.284515644 1.589029079 2.502357927 5.493916353 1.335689881 1.120939107 1 9.723175363 -8.228345315 2.620737373 1.023144861 3.493214319 0.457897709 0.968354065 0.145284608 1.953871737 0.123167957 0.35463598 5.91E-09 8.228345315 2.470069458 DSSPSSSPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSPSSSPSPK 11 0 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 DSSPSSS(0.001)PS(0.999)PK 120.53 0.0097956 1945900 651.21 778.34 1061.4 762.31 1149.5 1817.4 3701.7 641.06 1140.6 932.37 TRUE FALSE FALSE 643.272802 789.297491 1079.873222 850.451869 1090.836726 1701.274005 4016.122306 659.6080597 1038.581879 908.146893 0.708335631 0.86912976 1.189095322 0.936469502 1.201167712 1.873346722 4.422326759 0.726323092 1.14362763 1 9.826781862 -8.154792212 3.361330082 0.905887168 2.668047778 0.344977926 0.852559663 0.153288292 3.236386239 0.105159173 0.297051461 7.00E-09 8.154792212 1.762160609 DSSSSLTDPQVSYVKS(ph)PAAER ddPTM_HeLa_Romidepsin_16h_R1 2 DSSSSLTDPQVSYVKSPAAER 21 1 O94887-3;O94887-2;O94887;H7C3M7 O94887-3;H7C3M7 FARP2 "FERM, RhoGEF and pleckstrin domain-containing protein 2" 1 0 DSSS(0.001)S(0.006)LT(0.141)DPQVS(0.013)Y(0.005)VKS(0.833)PAAER;DSSSSLT(0.003)DPQVS(0.001)YVKS(0.995)PAAER ; 103.14 0.00014529 132378000 17095.9 6038.3 12090.5 4057.7 11835.4 12481.9 14820 14248.8 15339.2 11348.6 TRUE FALSE FALSE 16887.5286 6123.307346 12300.93008 4526.870366 11231.39537 11684.34687 16078.81043 14661.06655 13967.22353 11053.76174 1.527763037 0.553956878 1.112827504 0.40953211 1.016069972 1.057047108 1.454600779 1.326341828 1.263571974 1 13.4322498 -10.28733463 24.9843838 1.249221405 0.99389242 0.133515284 0.318798346 1336.306256 1289297.313 0.061022041 0.069793894 5.16E-11 10.28733463 -0.255328985 DSSSTDS(ph)ANEKPALIPR ddPTM_HeLa_Romidepsin_16h_R1 2 DSSSTDSANEKPALIPR 17 1 B8ZZZ7;Q9NUQ6-2;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3;F2Z2S1;C9JKE4;F8VZ02;F8VT91;C9JGM8;C9JW67;F8W6C2 B8ZZZ7 SPATS2L SPATS2-like protein 1 0 DS(0.12)S(0.029)S(0.009)T(0.148)DS(0.693)ANEKPALIPR;DSS(0.004)S(0.005)T(0.103)DS(0.888)ANEKPALIPR ; 119.04 2.09E-05 0 2087.41 1704.59 2044.25 1438.38 1911.93 1288.01 1425.47 1382.3 1929.63 1722.95 TRUE FALSE FALSE 2061.967844 1728.587263 2079.829314 1604.692263 1814.357078 1205.710318 1546.549386 1422.29467 1757.03906 1678.187511 1.228687397 1.030032253 1.239330707 0.956205581 1.081140854 0.718459833 0.921559347 0.847518326 1.046986138 1 10.71268821 -8.346520013 6.791602077 1.101854209 0.839111607 0.57940136 0.098220118 0.141402619 9.568913015 0.015821336 0.035644576 4.50E-09 8.346520013 -0.262742603 DSVDSAGTSPT(ph)AVLAAGEEVGAGGGPGGGRPGAGTPLR ddPTM_HeLa_Romidepsin_16h_R1 1 DSVDSAGTSPTAVLAAGEEVGAGGGPGGGRPGAGTPLR 38 1 Q5T0D9-2;Q5T0D9 Q5T0D9-2 TPRG1L Tumor protein p63-regulated gene 1-like protein 1 0 DSVDS(0.001)AGT(0.031)S(0.254)PT(0.713)AVLAAGEEVGAGGGPGGGRPGAGTPLR 64.508 0.00017222 6868700 327.59 259.45 339.67 261.31 886.75 1352.1 1266.5 1344.2 342.97 372.43 TRUE FALSE FALSE 323.5972071 263.1025439 345.5818139 291.5238917 841.4958386 1265.705174 1374.076478 1383.092306 312.2939042 362.7542149 0.892056367 0.725291487 0.952661057 0.80364026 2.319741037 3.489153597 3.787899415 3.812753234 0.860896694 1 8.502848567 -8.473644498 2.129609218 0.914397928 3.774928907 0.989532574 0.130608385 0.022062675 0.196330134 0.020131815 0.052191529 3.36E-09 8.473644498 2.860530979 up DSVDSAGTSPTAVLAAGEEVGAGGGPGGGRPGAGT(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 1 DSVDSAGTSPTAVLAAGEEVGAGGGPGGGRPGAGTPLR 38 1 Q5T0D9-2;Q5T0D9 Q5T0D9-2 TPRG1L Tumor protein p63-regulated gene 1-like protein 1 0 DSVDSAGTSPTAVLAAGEEVGAGGGPGGGRPGAGT(0.999)PLR 54.804 0.0013772 4402100 837.46 855.54 853.49 733.65 1231 1842.4 1600.9 1767.6 885.97 673.31 TRUE FALSE FALSE 827.2527154 867.5843146 868.3446354 818.4780649 1168.177477 1724.676586 1736.880406 1818.742717 806.7266242 655.8173091 1.261407261 1.322905484 1.324064832 1.248027543 1.781254414 2.629812544 2.64842111 2.773245982 1.230108771 1 9.357150169 -8.440376908 1.768667938 1.157641949 2.74701802 0.974372799 0.10508057 0.047275394 0.286931957 0.020748535 0.059797803 3.63E-09 8.440376908 1.589376072 up DSYESYGNSR ddPTM_HeLa_Romidepsin_16h_R1 4 DSYESYGNSR 10 0 P38159;P38159-2;H3BUY5;Q96E39 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 0 ;;; ;;; 232.72 4.92E-35 97635000 9011.5 8198.1 7538.5 7891.9 8080.4 7602 6909 7106.6 8695.4 8264.3 FALSE FALSE TRUE 8901.664372 8313.513067 7669.70443 8804.398611 7668.027036 7116.256734 7495.850288 7312.218259 7917.661646 8049.592295 1.105852824 1.03278685 0.952806571 1.093769509 0.952598188 0.884051822 0.931208689 0.908396101 0.983610269 1 12.9747 -8.590969531 5.29564203 1.044166106 0.911209462 0.567827604 0.046477075 0.104315416 5.517919631 0.007471205 0.015243288 2.56E-09 8.590969531 -0.132956645 DSYS(ph)SSRSDLYSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 DSYSSSRSDLYSSGR 15 1 P38159;P38159-2;H3BUY5 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 0 DSYS(0.982)S(0.001)S(0.006)RS(0.009)DLYSSGR 162.64 0.0009505 9446700 1530.8 1364.9 1494.5 1327.6 1344.7 1207.3 1106.5 1271.4 1609.6 1429.9 TRUE FALSE FALSE 1512.142021 1384.115098 1520.511146 1481.103359 1276.074941 1130.157426 1200.486082 1308.185953 1465.633345 1392.750992 1.085723169 0.993799399 1.09173223 1.063437303 0.916226195 0.811456917 0.861953134 0.939282011 1.05232978 1 10.44372163 -8.64883764 4.375059788 1.043149886 0.869234538 0.791717892 0.041948874 0.079839685 2.678797117 0.006853315 0.014039281 2.24E-09 8.64883764 -0.173915348 DSYVGDEAQS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 3 DSYVGDEAQSK 11 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 0 DSYVGDEAQS(1)K;DSYVGDEAQS(1)K;DSYVGDEAQS(1)K ;; 139.78 0.0032015 52292000 8613.3 9109.4 9743.1 5534 7735.4 9755.3 10211.6 9368.2 10405.4 9548.8 TRUE FALSE FALSE 8508.317787 9237.642372 9912.674568 6173.867118 7340.633673 9131.967814 11078.97305 9639.254086 9474.714963 9300.720799 0.914801978 0.993217899 1.065796381 0.663805231 0.789254277 0.981855924 1.191195101 1.036398608 1.0187076 1 13.18312681 -7.922526048 6.542864755 0.935209233 1.111023851 0.289534185 0.117924665 0.213335432 14.42753887 0.016784489 0.051245506 1.20E-08 7.922526048 0.175814618 DSYVGDEAQS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 2 DSYVGDEAQSKR 12 1 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 1 0 DSYVGDEAQS(1)KR;DSYVGDEAQS(1)KR ; 72.662 0.019401 239770000 8768.7 10526.7 9431.7 8022.6 9159 10928 11857.1 11175 12407.3 10651.2 TRUE FALSE FALSE 8661.823712 10674.89516 9595.854782 8950.210759 8691.582053 10229.73607 12864.24178 11498.33099 11297.56001 10374.48029 0.834916398 1.028957101 0.924947999 0.862714132 0.837784815 0.986048051 1.239989033 1.108328386 1.088975997 1 13.34075145 -7.897261346 5.029374921 0.919146765 1.171393365 0.526854998 0.085792815 0.095628875 3.868816426 0.010993972 0.034668805 1.27E-08 7.897261346 0.2522466 DSYVGDEAQSK ddPTM_HeLa_Romidepsin_16h_R1 2 DSYVGDEAQSK 11 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ; ; 265.67 3.58E-78 6363000 5134.6 4683.8 4762.6 4585.3 5251.2 5149.5 4900.3 4909.5 4776.3 5213.3 FALSE FALSE TRUE 5072.01752 4749.738659 4845.491055 5115.47396 4983.211669 4820.463569 5316.53136 5051.548637 4349.095766 5077.857714 0.99884987 0.935382385 0.954239234 1.007407897 0.981361028 0.949310485 1.047002823 0.994818863 0.856482401 1 12.31000425 -10.46572812 24.99947002 0.999492771 0.981504359 0 0.054311722 599.033544 262037.7174 0.00519835 0.005942555 3.42E-11 10.46572812 -0.017988412 DSYVGDEAQSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 DSYVGDEAQSKR 12 1 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 1 ; DSYVGDEAQSK(1)R;DSYVGDEAQSK(1)R 108.56 0.005234 70818000 2456.47 2356.9 2485.28 1973.31 5074.5 4551.6 5033.5 4220 4993.7 3404.13 FALSE TRUE FALSE 2426.529599 2390.0805 2528.535256 2201.473387 4815.529329 4260.76745 5461.045364 4342.099042 4547.050965 3315.690212 0.731832422 0.720839508 0.762596954 0.663956295 1.452345974 1.285031827 1.647031241 1.309561136 1.371373884 1 11.69509351 -8.752550703 24.97788877 0.835387463 1.429569693 0.609633547 0.213544476 65.3096656 183523.9999 0.022269643 0.044015555 1.77E-09 8.752550703 0.594182229 DSYVGDEAQSKR ddPTM_HeLa_Romidepsin_16h_R1 4 DSYVGDEAQSKR 12 1 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ;;; ;;; 99.5 0.0076192 66027900 14790.6 14098.7 12394.6 15142.8 13157.7 14751.7 13326.5 14777.3 14849.1 13843.8 FALSE FALSE TRUE 14610.32648 14297.18187 12610.32281 16893.68179 12486.21347 13809.11398 14458.45258 15204.85786 13520.95931 13484.13608 1.083519655 1.060296469 0.935196941 1.252856074 0.925992841 1.024100758 1.072256501 1.127610829 1.002730855 1 13.71897547 -12.47220761 1.161088974 0.999377159 1.059879467 0.066719433 0.087926616 1.205222 2.85839054 0.059550293 0.01403144 3.37E-13 12.47220761 0.060502307 DT(ph)EKMY(ph)PS(ph)T(ph)NIAVTNVGTTTS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 DTEKMYPSTNIAVTNVGTTTSEK 23 1 Q8WXI7 Q8WXI7 MUC16 Mucin-16 5 0 DT(0.973)EKMY(0.863)PS(0.884)T(0.873)NIAVT(0.137)NVGT(0.232)T(0.232)T(0.225)S(0.582)EK 40.012 0.024213 3240000 662.65 638.67 588.89 605.91 728.69 825.04 602.62 865.54 685.68 753.34 TRUE FALSE FALSE 654.5733669 647.661213 599.1393834 675.9681651 691.5022302 772.3226067 653.8065278 890.5830343 624.3510635 733.7681182 0.892071147 0.882651068 0.816524142 0.921228585 0.942398849 1.05254315 0.891026077 1.213711815 0.850883335 1 9.519180411 -7.255653444 24.86908837 0.936529033 1.213711944 0.620310737 0.068148823 330.3040982 1419666.992 0.009723049 0.116774297 5.55E-08 7.255653444 0.277182911 DT(ph)QVMASLVQT(ph)LMS(ph)ALRT ddPTM_HeLa_Romidepsin_16h_R1 1 DTQVMASLVQTLMSALRT 18 1 F6U495 F6U495 FBN1 3 0 DT(0.998)QVMAS(0.008)LVQT(0.892)LMS(0.891)ALRT(0.21) 43.162 0.029412 914250 290.79 348.14 228.99 345.99 102.94 42.14 125.96 203.96 248.23 262.28 TRUE FALSE FALSE 287.2457396 353.0411241 232.9754749 385.9949917 97.68658768 39.44739 136.6590393 209.8612608 226.0276871 255.4659278 1.124399414 1.381949942 0.911963004 1.5109451 0.382385974 0.154413508 0.534940375 0.821484347 0.88476647 1 7.996987077 -8.741538738 24.99727432 1.103076606 0.454930223 0.64482029 0.239943168 112.0854556 140790.3201 0.032596977 0.065124512 1.81E-09 8.741538738 -0.648146383 DT(ph)SPSSGSAVSSSK ddPTM_HeLa_Romidepsin_16h_R1 3 DTSPSSGSAVSSSK 14 0 F8WF16;B7Z8L1;F8W6A0;F8W0Q9;Q8NEY8-7;Q8NEY8-5;Q8NEY8-6;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-3;Q8NEY8 F8WF16 PPHLN1 Periphilin-1 1 0 DT(0.917)S(0.083)PSSGSAVSSSK;DT(0.754)S(0.243)PS(0.002)SGSAVSSSK;DT(0.949)S(0.05)PSSGSAVSSSK ;; 184.11 2.89E-07 1048414600 13227.4 7322.4 9079.2 4834.2 8399.7 7597.6 9860.5 7730.3 11811.6 9942.8 TRUE FALSE FALSE 13066.17936 7425.484939 9237.219667 5393.15295 7971.031965 7112.13788 10698.05062 7953.964034 10755.14091 9684.484623 1.349186856 0.76674033 0.953816339 0.556885901 0.823072396 0.734384756 1.104658744 0.821309997 1.110553771 1 13.24145956 -10.24784471 24.84688881 1.164893795 0.825208587 0.485344325 0.155699536 499.1638724 912319.488 0.030113929 0.036771577 5.65E-11 10.24784471 -0.339685208 DTASLSTT(ph)PSESPR ddPTM_HeLa_Romidepsin_16h_R1 1 DTASLSTTPSESPR 14 0 H0YJ30;G3V582;F5H039;Q9NQX3;Q9NQX3-2 H0YJ30 GPHN Gephyrin;Molybdopterin adenylyltransferase;Molybdopterin molybdenumtransferase 1 0 DTASLS(0.066)T(0.205)T(0.699)PS(0.03)ESPR 152 0.0012699 8542300 3980.5 3275.2 3303.3 3412.5 2672.3 2738.3 2063.3 2359.2 3300 3370 TRUE FALSE FALSE 3931.984135 3321.308352 3360.792551 3807.069306 2535.922559 2563.331467 2238.55665 2427.45973 3004.839735 3282.446914 1.197882018 1.011839167 1.023868059 1.159826619 0.772570776 0.780920921 0.681978021 0.739527491 0.915426757 1 11.68055596 -8.716350185 6.942629912 1.0871257 0.739467024 0.757943754 0.083780261 0.06731185 7.925732177 0.012290365 0.024520363 1.92E-09 8.716350185 -0.347658676 DTCYSPKPS(ph)VYLSTPSSASK ddPTM_HeLa_Romidepsin_16h_R1 1 DTCYSPKPSVYLSTPSSASK 20 1 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 0 DT(0.024)CY(0.263)S(0.263)PKPS(0.305)VY(0.111)LS(0.015)T(0.016)PS(0.002)S(0.001)ASK 50.87 0.023323 9209400 1672.7 1395 1591.8 179.23 1824.9 1528.8 1607.8 1334.6 1479.6 1665.9 TRUE FALSE FALSE 1652.312489 1414.638847 1619.504611 199.9534159 1731.768543 1431.114614 1744.366492 1373.214545 1347.26087 1622.619678 1.018299304 0.871824042 0.998080224 0.123228763 1.067267066 0.881977849 1.075031023 0.846294769 0.830299847 1 10.66410917 -9.996618204 2.242321627 1.008187929 0.824177668 0.025839597 0.260422167 0.55214988 5.539887727 0.042843676 0.055983609 1.01E-10 9.996618204 -0.184010261 DTDSEEEIR ddPTM_HeLa_Romidepsin_16h_R1 2 DTDSEEEIR 9 0 P0DP25;P0DP24;P0DP23;E7EMB3;G3V361;A0A590UJI2;Q96HY3;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 0 ; ; 215.88 4.85E-17 20011700 4948.6 6182 5969.9 2660.52 6757.4 8177.7 5284.8 6024.4 6329.7 6612 FALSE FALSE TRUE 4888.28456 6269.030358 6073.803605 2968.141841 6412.544663 7655.171362 5733.69078 6198.706509 5763.555779 6440.219287 0.759024552 0.973418773 0.943105092 0.460875897 0.995702844 1.188650731 0.89029434 0.962499293 0.894931604 1 12.6528941 -8.554951074 24.99966974 0.863354915 1.016582737 0.203961861 0.161089561 274.1739612 213711.5361 0.024768886 0.049538056 2.79E-09 8.554951074 0.153227821 DTDSEEEIREAFR ddPTM_HeLa_Romidepsin_16h_R1 4 DTDSEEEIREAFR 13 1 P0DP25;P0DP24;P0DP23;E7EMB3;G3V361;A0A590UJI2;Q96HY3;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 0 ;;; ;;; 143 0.00091414 535469500 5160.14 5103.08 5521.73 4607.41 6065.84 5986.19 5262.29 5482.06 5687.3 5902.02 FALSE FALSE TRUE 5097.246229 5174.921294 5617.833394 5140.140423 5756.27755 5603.691779 5709.268781 5640.674757 5178.613644 5748.68467 0.886680436 0.900192234 0.97723805 0.894142003 1.001320803 0.974778075 0.993143494 0.981211369 0.900834529 1 12.48901618 -8.731565603 24.98581429 0.940674878 0.987091641 0.363349081 0.03686251 279.8600261 234068.0864 0.006894717 0.013787932 1.86E-09 8.731565603 0.046416764 DTEEPLPVKESDQTLAALLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 DTEEPLPVKESDQTLAALLSPK 22 1 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK;DTEEPLPVKESDQTLAALLS(1)PK ;; 132.39 4.93E-05 268076000 7300 7342.4 5863.8 7428.7 7395.2 6947.1 7148.3 7521.9 7951.9 6905 TRUE FALSE FALSE 7211.024792 7445.7665 5965.856979 8287.641247 7017.795349 6503.202731 7755.476424 7739.534309 7240.662148 6725.607105 1.072174553 1.107077232 0.887036202 1.232251768 1.043444144 0.966931703 1.153126596 1.150756235 1.076581197 1 12.71544879 DTFEHDPSES(ph)IDEFNK ddPTM_HeLa_Romidepsin_16h_R1 2 DTFEHDPSESIDEFNK 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 DTFEHDPS(0.001)ES(0.999)IDEFNK;DTFEHDPS(0.101)ES(0.899)IDEFNK ; 134.33 0.00063858 11857300 7241.2 7268.8 7557.7 4143.8 7293.1 6438.6 4973 6860.1 8237.6 7384.2 TRUE FALSE FALSE 7152.941469 7371.130357 7689.238598 4622.925653 6920.905893 6027.19424 5395.406496 7058.58617 7500.808425 7192.35742 0.994519745 1.024855959 1.069084606 0.642755273 0.962258337 0.837999822 0.750158283 0.981400917 1.042885939 1 12.812249 -9.297686005 24.99995236 1.004728028 0.83745178 0.503484318 0.0937842 370.1349419 255287.807 0.012846014 0.019622988 5.04E-10 9.297686005 -0.167276248 DTGK(ac)TPVEPEVAIHR ddPTM_HeLa_Romidepsin_16h_R1 3 DTGKTPVEPEVAIHR 15 1 P60866;P60866-2;E5RIP1;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 1 ;; DTGK(1)TPVEPEVAIHR;DTGK(1)TPVEPEVAIHR;DTGK(1)TPVEPEVAIHR 201.72 6.33E-18 46271700 12336.23 12119.99 10240.54 8706.64 11305.54 10831.18 11478.85 12849.84 15954.29 13094.34 FALSE TRUE FALSE 12185.87128 12290.61554 10418.7723 9713.342683 10728.57611 10139.10255 12453.86323 13221.62985 14527.29834 12754.14716 0.955443836 0.9636564 0.816892903 0.761583081 0.84118334 0.794965153 0.976455978 1.036653387 1.139025461 1 13.63867881 -9.860913333 6.621624011 0.977866419 0.866467126 0.334390715 0.093437016 0.21085646 12.17361186 0.013524999 0.017843898 1.38E-10 9.860913333 -0.111399293 DTGS(ph)PPASEGPTDGSR ddPTM_HeLa_Romidepsin_16h_R1 1 DTGSPPASEGPTDGSR 16 0 Q969R8 Q969R8 ITFG2 Integrin-alpha FG-GAP repeat-containing protein 2 1 0 DT(0.001)GS(0.852)PPAS(0.068)EGPT(0.068)DGS(0.01)R 122.63 0.0030307 8685300 1963.5 1452.1 1781.3 1806.7 1676.3 1379.8 1705.3 1594.8 2090.5 1861.7 TRUE FALSE FALSE 1939.568107 1472.542702 1812.302779 2015.599155 1590.752156 1291.635233 1850.148139 1640.943022 1903.520444 1813.332766 1.0696151 0.812064244 0.999431993 1.111544 0.877253302 0.712299065 1.020302602 0.904932097 1.049735868 1 10.82442798 -8.731949511 24.03452977 1.017368506 0.876925728 0.272473505 0.101913168 131.7198939 107351.9491 0.014788337 0.029572266 1.85E-09 8.731949511 -0.140442778 DTHDQLSEPSEVR ddPTM_HeLa_Romidepsin_16h_R1 1 DTHDQLSEPSEVR 13 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 171.49 0.00075635 2155100 1282.4 1206.6 1011.9 1315.9 1354.1 1531.8 1087.4 1393.9 1282.2 1422.9 FALSE FALSE TRUE 1266.769616 1223.586546 1029.511695 1468.050549 1284.995224 1433.922924 1179.763729 1434.230297 1167.516821 1385.932853 0.914019473 0.882861348 0.742829418 1.059250848 0.9271699 1.034626548 0.851241621 1.034848329 0.84240504 1 10.43664165 -6.086324866 20.62572447 0.946075222 0.940107383 0 0.098928943 0 0 0.011830732 0 8.20E-07 6.086324866 -0.00596784 DTIIDVVGAPLT(ph)PNSR ddPTM_HeLa_Romidepsin_16h_R1 4 DTIIDVVGAPLTPNSR 16 0 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 0 DT(0.007)IIDVVGAPLT(0.988)PNS(0.004)R;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR;DTIIDVVGAPLT(1)PNSR ;;; 207.92 7.15E-19 240056000 30430.5 30779.3 31073.1 19842.8 22354.3 22951.1 20807.8 22391.6 33646.9 30503 TRUE FALSE FALSE 30059.60136 31212.61179 31613.91427 22137.1179 21213.47666 21484.59878 22575.21401 23039.46562 30637.43699 29710.52766 1.011749158 1.050557302 1.064064382 0.745093394 0.714005382 0.723130839 0.759838878 0.775464707 1.03119801 1 14.85868661 -9.254483885 24.99138395 1.013770619 0.741643024 0.967222 0.026407571 76.04430937 273230.2752 0.004338691 0.007093964 5.57E-10 9.254483885 -0.272127595 DTMSDQALEALSAS(ph)LGTR ddPTM_HeLa_Romidepsin_16h_R1 1 DTMSDQALEALSASLGTR 18 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;P20810-3 P20810-6;P20810-3 CAST Calpastatin 1 0 DTMSDQALEALS(0.106)AS(0.826)LGT(0.068)R 83.948 0.014574 5088400 1303.1 1567 1232.3 1138.7 1410.7 1319.3 1101.4 1649.7 1359.5 1386.2 TRUE FALSE FALSE 1287.217316 1589.060267 1253.747665 1270.361852 1338.706715 1235.000988 1194.952889 1697.431467 1237.902915 1350.186324 0.953362727 1.176919243 0.928573814 0.940878921 0.991497759 0.914689303 0.885028138 1.257183128 0.916838582 1 10.3989428 -7.249428768 24.68891296 0.977097495 1.257183332 0.550862034 0.078033961 892.7755614 1835143.848 0.010055186 0.221505677 5.63E-08 7.249428768 0.280085837 DTNGSQFFITTVK ddPTM_HeLa_Romidepsin_16h_R1 1 DTNGSQFFITTVK 13 0 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 0 174.39 0.00010979 453160 256.62 158.78 194.44 122.68 276.62 300.86 442.1 310.6 176.04 64.942 FALSE FALSE TRUE 253.4922167 161.015309 197.8241466 136.8648388 262.5030492 281.636017 479.651963 319.586721 160.2945415 63.25479748 4.007478118 2.54550351 3.127417279 2.163706854 4.149931067 4.452405639 7.582855089 5.052371262 2.534108841 1 5.983102998 -4 0.122318 0.4611294 18.66098941 0.587594111 1.120135855 48.36437106 0.405092506 5.178881932 150.9941896 1.00E-04 4 18.19986001 DTPDSLS(ph)PETYGNFDSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 DTPDSLSPETYGNFDSQSR 19 0 K7EMG7;K7EMR5;K7EJ48;K7ENU5;Q96ED9-2;Q96ED9 K7EMG7 HOOK2 Protein Hook homolog 2 1 0 DT(0.004)PDS(0.225)LS(0.771)PETYGNFDSQSR 245.04 4.47E-62 5243400 669.58 800.11 651.11 724.72 1714 2288.4 1383.2 1826.9 664.4 598.45 TRUE FALSE FALSE 661.4189014 811.3739696 662.4422964 808.5155363 1626.528184 2142.178625 1500.688973 1879.758469 604.9744 582.9021827 1.134699648 1.391955621 1.136455337 1.387051825 2.790396455 3.675022481 2.57451253 3.224826609 1.037866074 1 9.187109994 -8.757926052 3.3205918 1.104823645 3.122842616 0.92283797 0.269094406 0.041676179 0.959411773 0.037922342 0.076451998 1.75E-09 8.757926052 2.01801897 up DTPTS(ph)AGPNSFNK ddPTM_HeLa_Romidepsin_16h_R1 1 DTPTSAGPNSFNK 13 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 0 DTPT(0.01)S(0.969)AGPNS(0.021)FNK 169.58 0.00010358 6278700 1861.2 1973 1810.6 1663.3 1699.9 1597.4 1800.3 2002.9 2287.9 2146.7 TRUE FALSE FALSE 1838.514979 2000.775946 1842.112733 1855.618572 1613.14776 1495.331295 1953.217437 2060.850751 2083.264494 2090.928425 0.879281642 0.956883996 0.881002292 0.887461546 0.771498317 0.715151833 0.934138832 0.985615159 0.996334676 1 11.02992796 -12.23910162 0.38154987 1.041963188 0.858499201 0.299099901 0.076104477 2.662268317 0.515270554 0.20262894 0.031381122 5.77E-13 12.23910162 -0.183463986 DTPTSAGPNS(ph)FNK ddPTM_HeLa_Romidepsin_16h_R1 1 DTPTSAGPNSFNK 13 0 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 0 DTPT(0.001)S(0.005)AGPNS(0.994)FNK 177.93 5.66E-06 0 2041.8 2014.6 1864.2 1715 1866.3 2129.9 1861.5 2195.5 2308.4 2223.2 TRUE FALSE FALSE 2016.913756 2042.961592 1896.645619 1913.296369 1771.055747 1993.806264 2019.615764 2259.023329 2101.930923 2165.440944 0.931410188 0.943439071 0.875870397 0.883559709 0.817873031 0.920739155 0.932657974 1.043216318 0.970671091 1 11.08044511 -11.53892776 0.701653252 0.996794821 0.911706805 0.185876257 0.055083108 0.708318929 0.714772776 0.029758894 0.013169491 2.89E-12 11.53892776 -0.085088016 DTQSGSLLFIGR ddPTM_HeLa_Romidepsin_16h_R1 1 DTQSGSLLFIGR 12 0 P50454;E9PKH2;H0YEP8 P50454 SERPINH1 Serpin H1 0 0 129 0.015271 484940 150.51 63.053 180.83 154.53 164.87 137.17 187.87 139.79 219.69 204.6 FALSE FALSE TRUE 148.6755262 63.94066179 183.9772703 172.3974857 156.4560687 128.4052797 203.8276731 143.8346031 200.0403762 199.2844625 0.746046753 0.320851214 0.923189234 0.865082423 0.785089147 0.644331616 1.022797616 0.72175523 1.003793139 1 7.638685423 -12.06038826 1.050387433 0.988339202 0.758870323 0.232718859 0.178130645 0.599291521 1.269856267 0.089662399 0.032817305 8.70E-13 12.06038826 -0.229468879 DTS(ph)PSSGSAVSSSK ddPTM_HeLa_Romidepsin_16h_R1 4 DTSPSSGSAVSSSK 14 0 F8WF16;B7Z8L1;F8W6A0;F8W0Q9;Q8NEY8-7;Q8NEY8-5;Q8NEY8-6;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-3;Q8NEY8 F8WF16 PPHLN1 Periphilin-1 1 0 DT(0.007)S(0.993)PSSGSAVSSSK;DT(0.091)S(0.908)PS(0.001)SGSAVSSSK;DT(0.049)S(0.686)PS(0.217)S(0.036)GS(0.012)AVSSSK;DT(0.084)S(0.9)PS(0.003)S(0.012)GS(0.001)AVSSSK ;;; 185.32 8.63E-08 1117433300 14978.7 9466.3 11533.8 6820.36 11586.1 10143.2 12669.3 10200.4 14056.4 12592.5 TRUE FALSE FALSE 14796.13384 9599.56682 11734.54095 7608.962114 10994.81808 9495.082256 13745.43003 10495.53248 12799.16038 12265.34503 1.206336536 0.782657707 0.956723265 0.620362663 0.896413273 0.774139026 1.120672104 0.855706256 1.043522244 1 13.5823002 -10.25691533 24.88830358 1.097436698 0.861089737 0.37856023 0.13180551 275.47943 1515503.982 0.023217889 0.02792875 5.53E-11 10.25691533 -0.236346961 DTSATSQSVNGS(ph)PQAEQPSLESTSK ddPTM_HeLa_Romidepsin_16h_R1 4 DTSATSQSVNGSPQAEQPSLESTSK 25 0 C9J0I9;Q86WB0-2;Q86WB0;Q86WB0-3;F8WAU5 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 DTSATSQSVNGS(1)PQAEQPSLESTSK;DTSATSQS(0.001)VNGS(0.999)PQAEQPSLESTSK;DTSATSQSVNGS(1)PQAEQPSLESTSK;DTSATSQSVNGS(0.996)PQAEQPS(0.003)LESTSK ;;; 130.98 5.43E-07 37347000 11622.8 10299.6 10547.7 11070.4 12698.9 11517.6 10353.5 12067.5 12905.2 12928.5 TRUE FALSE FALSE 11481.13684 10444.59804 10731.27829 12350.41174 12050.82775 10781.66253 11232.92603 12416.65407 11750.92659 12592.61571 0.911735664 0.82942244 0.852188183 0.980766191 0.956975741 0.856189277 0.892024842 0.986026602 0.933160105 1 13.62029037 -11.90614857 0.935010107 0.995673739 0.906921053 0.113233945 0.054680598 0.504065212 0.854073391 0.026601277 0.010384445 1.24E-12 11.90614857 -0.088752686 DTSFLGSDDIGNIDVREPELEDLTR ddPTM_HeLa_Romidepsin_16h_R1 1 DTSFLGSDDIGNIDVREPELEDLTR 25 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 0 70.358 0.00039195 0 0 213.51 149.34 249.13 135.61 133.04 182.11 276.88 0 209.49 FALSE FALSE TRUE 0 216.5157994 151.9392001 277.9355828 128.6893157 124.5391734 197.5784189 284.891086 0 204.0474196 0 1.061105305 0.744626912 1.362112706 0.630683377 0.61034427 0.968296581 1.396200386 0 1 7.672760656 DTSGGIDLGEEQHPLGT(ph)PTPGR ddPTM_HeLa_Romidepsin_16h_R1 1 DTSGGIDLGEEQHPLGTPTPGR 22 0 Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8-3;Q9UIF8 Q9UIF8-4 BAZ2B Bromodomain adjacent to zinc finger domain protein 2B 1 0 DTSGGIDLGEEQHPLGT(0.953)PT(0.047)PGR 80.172 0.0013284 11097000 1167.2 1006.4 1238.5 1190.2 832.57 1018.8 588.2 773.26 1361.6 1142.3 TRUE FALSE FALSE 1152.973717 1020.568126 1260.055573 1327.816524 790.0808462 953.701968 638.1616933 795.6330581 1239.815086 1112.622881 1.036266409 0.917263291 1.132509131 1.193411125 0.710106595 0.857165518 0.573565135 0.715096796 1.114317444 1 10.11974897 -8.742073125 24.95503432 1.029835794 0.714180762 0.746294073 0.099133661 95.0129537 122431.5036 0.013685389 0.027337877 1.81E-09 8.742073125 -0.315655032 DTSLYRPALEELRR ddPTM_HeLa_Romidepsin_16h_R1 2 DTSLYRPALEELRR 14 2 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 0 ; ; 77.279 0.013355 47388000 5319 4547.1 5168 5319.7 5772.3 6314.9 5249.2 5308.2 5067.3 4352.4 FALSE FALSE TRUE 5254.169982 4611.114193 5257.946872 5934.788744 5477.717992 5911.39827 5695.066917 5461.784392 4614.067997 4239.324021 1.239388628 1.087700343 1.240279546 1.399937517 1.292120622 1.394420016 1.343390335 1.288362099 1.088397106 1 12.04961852 -12.79572972 0.171492334 0.691163069 1.424230562 0.683710396 0.073085995 5.424621917 0.21723048 0.931084805 0.175153618 1.60E-13 12.79572972 0.733067492 DTSPDKGELVS(ph)DEEEDT ddPTM_HeLa_Romidepsin_16h_R1 1 DTSPDKGELVSDEEEDT 17 1 Q9UPU7 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 0 DTSPDKGELVS(0.513)DEEEDT(0.487) 98.507 0.025434 60973000 7827.2 7229 7448.1 8469.8 9702.7 9017 8377.7 7946.5 7927.5 7267.1 TRUE FALSE FALSE 7731.799076 7330.770052 7577.731056 9449.118128 9207.535013 8440.842801 9089.301629 8176.41944 7218.444545 7078.299694 1.092324345 1.035668221 1.070558098 1.334941799 1.300811694 1.19249582 1.284108052 1.155138917 1.019799225 1 12.78918713 -9.356381852 6.030832324 1.044859993 1.253991867 0.795030052 0.053358815 0.083812929 4.39903454 0.00880479 0.013511035 4.40E-10 9.356381852 0.209131874 DTSPSSGSAVSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 DTSPSSGSAVSSSK 14 0 F8WF16;B7Z8L1;F8W6A0;F8W0Q9;Q8NEY8-7;Q8NEY8-5;Q8NEY8-6;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-3;Q8NEY8 F8WF16 PPHLN1 Periphilin-1 0 0 142.12 0.0076181 1613900 637.51 558.69 760.08 272.42 596.76 629.24 521.77 305.07 626.18 639.4 FALSE FALSE TRUE 629.7397829 566.5552525 773.3088736 303.9184822 566.3051104 589.0335948 566.0891308 313.8967191 570.1728925 622.7882958 1.011161878 0.909707611 1.241688193 0.487996458 0.909305962 0.945800682 0.908959167 0.504018334 0.91551639 1 9.282598022 -9.27101779 24.998625 1.012836557 0.779572639 0.366714512 0.17169675 585.9240718 1529196.892 0.024302484 0.037416217 5.36E-10 9.27101779 -0.233263918 DTSS(ph)SPTTGSTVQSVDLIFTR ddPTM_HeLa_Romidepsin_16h_R1 1 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 0 DTS(0.072)S(0.458)S(0.458)PT(0.011)TGSTVQSVDLIFTR 326.98 3.96E-193 12941000 4674.9 4460.2 4292 4261.4 4519.9 3834.5 4361 4678.6 4947.2 4030.3 TRUE FALSE FALSE 4617.920521 4522.990813 4366.70046 4754.123118 4289.232637 3589.487825 4731.423231 4813.967909 4504.710042 3925.592225 1.176362764 1.1521805 1.112367309 1.211058828 1.092633262 0.914381224 1.20527629 1.226303608 1.147523681 1 11.9386946 -12.39301012 1.087690637 0.999071581 1.135422489 0 0.095935127 0.589767014 1.234696343 0.061760435 0.01536249 4.05E-13 12.39301012 0.136350908 DTSSSPT(ph)TGSTVQSVDLIFTR ddPTM_HeLa_Romidepsin_16h_R1 1 DTSSSPTTGSTVQSVDLIFTR 21 0 P57060 P57060 RWDD2B RWD domain-containing protein 2B 1 0 DTSS(0.044)S(0.309)PT(0.633)T(0.002)GS(0.008)T(0.002)VQSVDLIFTR 155.24 1.55E-07 13765000 1744.9 1408.4 1931.3 1394 1657.2 1533.7 1940.9 1659.3 2163.9 1908.3 TRUE FALSE FALSE 1723.632488 1428.227492 1964.913466 1555.180839 1572.6269 1435.70152 2105.759998 1707.309228 1970.355364 1858.722091 0.927321247 0.768392165 1.057131389 0.836693579 0.846079631 0.772413222 1.132907393 0.918539267 1.060059152 1 10.86009536 -11.57912274 0.963698346 0.992308741 0.907914547 0.142325573 0.111882381 0.919213167 1.735443986 0.040742928 0.021697662 2.64E-12 11.57912274 -0.084394194 SSS(ph)PEAMDPPPPK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPEAMDPPPPK 13 0 K7ERU0;K7ENY2;Q9UK33 K7ERU0 ZNF580 Zinc finger protein 580 1 0 S(0.151)S(0.04)S(0.809)PEAMDPPPPK;S(0.001)S(0.002)S(0.997)PEAMDPPPPK ; 151.7 0.0010593 25514500 8935.4 12959.8 12729.3 5720.3 3231.2 3869.9 2855.1 3281.1 15071.9 9311 TRUE FALSE FALSE 8826.491908 13142.2484 12950.84813 6381.708001 3066.299807 3622.62588 3097.612123 3376.033452 13723.83152 9069.098878 0.973249054 1.449123952 1.428019289 0.703676086 0.338104132 0.39944717 0.34155677 0.37225677 1.513251945 1 13.14674349 -8.981565302 4.383349818 1.060283639 0.371302258 0.762018325 0.225873483 0.080268 3.733517325 0.030175995 0.054557149 1.04E-09 8.981565302 -0.688981381 down DTVIIVS(ph)EPS(ph)EDEESQGLPTMAR ddPTM_HeLa_Romidepsin_16h_R1 3 DTVIIVSEPSEDEESQGLPTMAR 23 0 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 2 0 DTVIIVS(0.984)EPS(0.998)EDEES(0.017)QGLPT(0.001)MAR;DTVIIVS(0.996)EPS(0.999)EDEES(0.004)QGLPTMAR;DTVIIVS(0.932)EPS(0.987)EDEES(0.078)QGLPT(0.002)MAR ;; 90.397 0.00017169 24968900 8223.7 8577.4 9679 6657.2 7412.6 7092.6 5223.8 6213 9004.4 9397.7 TRUE FALSE FALSE 8123.466381 8698.152862 9847.458935 7426.936787 7034.307362 6639.40575 5667.509442 6392.763353 8199.023912 9153.546399 0.887466565 0.950249497 1.075808054 0.811372605 0.76847891 0.725336985 0.619159962 0.698391975 0.895721019 1 13.16011509 -8.788426901 1.816806673 0.954166158 0.678481177 0.798137455 0.061360992 0.117562354 0.788274786 0.0101607 0.022836564 1.63E-09 8.788426901 -0.27568498 DTVIIVSEPS(ph)EDEES(ph)QGLPTMAR ddPTM_HeLa_Romidepsin_16h_R1 1 DTVIIVSEPSEDEESQGLPTMAR 23 0 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 2 0 DTVIIVS(0.297)EPS(0.957)EDEES(0.662)QGLPT(0.084)MAR 62.792 0.0079968 13589000 4216.3 4238.6 4759 2772.3 3566.9 3638.9 2650.2 3333.5 4494.9 4675.7 TRUE FALSE FALSE 4164.910114 4298.271122 4841.828399 3092.84637 3384.867783 3406.386034 2875.307922 3429.949563 4092.864886 4554.22464 0.914515739 0.943798662 1.063150982 0.679115901 0.743236896 0.747961794 0.631349604 0.753135788 0.898696312 1 12.15298974 -9.251945766 24.98844849 0.964225703 0.710386003 0.843122165 0.054581783 186.6562804 491303.9878 0.008105844 0.01332753 5.60E-10 9.251945766 -0.2538397 DTVIIVSEPS(ph)EDEESQGLPTMAR ddPTM_HeLa_Romidepsin_16h_R1 2 DTVIIVSEPSEDEESQGLPTMAR 23 0 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 0 DTVIIVS(0.002)EPS(0.996)EDEES(0.001)QGLPTMAR;DTVIIVS(0.009)EPS(0.968)EDEES(0.022)QGLPT(0.001)MAR ; 85.737 7.62E-05 4718100 2385.8 2907.6 2619 2124.8 2340.8 2300.6 1995.52 2416.5 2929.2 2765.9 TRUE FALSE FALSE 2356.720952 2948.533269 2664.582596 2370.479373 2221.340241 2153.599085 2165.019419 2486.417615 2667.205016 2694.041519 0.874790138 1.094464673 0.989065156 0.87989712 0.824538236 0.799393428 0.803632536 0.922932181 0.990038571 1 11.39555637 -9.048734443 4.069959344 0.956385225 0.833621491 0.541103181 0.063304899 0.178381174 6.177425286 0.011043448 0.01927652 8.94E-10 9.048734443 -0.122763734 DTYSDRS(ph)GSSS(ph)PDSEITELK ddPTM_HeLa_Romidepsin_16h_R1 1 DTYSDRSGSSSPDSEITELK 20 1 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 2 0 DT(0.012)Y(0.015)S(0.128)DRS(0.815)GS(0.09)S(0.284)S(0.639)PDS(0.015)EIT(0.002)ELK 72.654 0.015497 6179000 3845.1 3414.8 3233.6 2965.2 3347.8 3221.3 2474.5 2716.3 3895.3 3558 TRUE FALSE FALSE 3798.234442 3462.873644 3289.879452 3308.050376 3176.949274 3015.469326 2684.683968 2794.891855 3546.894612 3465.562647 1.095993589 0.999224079 0.949306011 0.954549293 0.91671962 0.870124027 0.774674776 0.80647564 1.023468618 1 11.75887388 -8.558600408 0.70850893 1.043416155 0.768951561 0.873529073 0.033603251 0.274360908 0.223512595 0.008464475 0.043022074 2.76E-09 8.558600408 -0.274464594 DVAEVDTVR ddPTM_HeLa_Romidepsin_16h_R1 1 DVAEVDTVR 9 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 117.81 0.0010591 0 1994.8 1961.3 1745.7 1427.5 1830.7 1682.3 1162 1478.1 1605 1637.6 FALSE FALSE TRUE 1970.48661 1988.911233 1776.083176 1592.554267 1737.272548 1574.806459 1260.700251 1520.866491 1461.44478 1595.054916 1.235372269 1.246923359 1.113493434 0.998432249 1.08916159 0.98730548 0.790380468 0.953488483 0.916234774 1 10.63939038 -8.222975844 1.292223072 1.121246249 0.86434531 0.352442254 0.107826103 0.362195439 1.079997276 0.017108915 0.076027099 5.98E-09 8.222975844 -0.25690094 DVAEVDTVRR ddPTM_HeLa_Romidepsin_16h_R1 3 DVAEVDTVRR 10 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;; ;; 147.73 0.0025167 27839200 11579.7 10609.2 9378.1 11368.4 10308 9942 9452.5 10905.5 11236.4 10715.5 FALSE FALSE TRUE 11438.56216 10758.5566 9541.321897 12682.8679 9781.944296 9306.738286 10255.39511 11221.03344 10231.38824 10437.10977 1.095951122 1.030798453 0.914172804 1.215170501 0.937227309 0.891696887 0.982589562 1.075109268 0.980289417 1 13.34943464 DVATSPISPT(ph)ENNTTPPDALTR ddPTM_HeLa_Romidepsin_16h_R1 2 DVATSPISPTENNTTPPDALTR 22 0 H0YCM0;E9PM17;B3KNX7;Q13153;Q13153-2 H0YCM0 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 0 DVATS(0.001)PIS(0.186)PT(0.798)ENNT(0.007)T(0.007)PPDALT(0.001)R;DVATSPIS(0.017)PT(0.953)ENNT(0.012)T(0.012)PPDALT(0.006)R ; 65.887 0.0044212 7008600 2225.91 2088.75 1971.51 1845.39 1951.59 1913.69 1720.55 1956.1 2381.2 1983.75 TRUE FALSE FALSE 2198.779753 2118.155477 2005.823305 2058.762675 1851.99308 1791.411385 1866.693474 2012.696667 2168.219508 1932.211889 1.137959954 1.096233539 1.038096969 1.065495294 0.958483431 0.927129884 0.966091496 1.04165422 1.122143757 1 10.9160376 -8.765996131 24.69943749 1.067022655 0.969521312 0.538952216 0.046247774 77.36944812 419377.617 0.008667528 0.016107088 1.71E-09 8.765996131 -0.097501343 DVDAS(ph)PSPLSVQDLK ddPTM_HeLa_Romidepsin_16h_R1 3 DVDASPSPLSVQDLK 15 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 0 DVDAS(0.998)PS(0.002)PLSVQDLK;DVDAS(0.984)PS(0.016)PLSVQDLK;DVDAS(0.97)PS(0.03)PLSVQDLK ;; 135.47 0.0013157 24969000 5385.1 5569.2 4780.2 5308.5 6033.6 6246.9 5621 5907.6 5653.9 5336.5 TRUE FALSE FALSE 5319.46433 5647.603344 4863.397376 5922.293747 5725.682878 5847.743251 6098.4476 6078.527085 5148.201024 5197.856961 1.023395674 1.086525348 0.935654331 1.139372205 1.101546834 1.12502966 1.173261913 1.169429465 0.990446844 1 12.34370122 -8.726960264 0.775860893 1.010385663 1.178387324 0.663547145 0.045268924 0.315282709 0.338049639 0.007625932 0.029960262 1.88E-09 8.726960264 0.168001661 DVDASPS(ph)PLSVQDLK ddPTM_HeLa_Romidepsin_16h_R1 2 DVDASPSPLSVQDLK 15 0 Q8IWZ8 Q8IWZ8 SUGP1 SURP and G-patch domain-containing protein 1 1 0 DVDAS(0.043)PS(0.957)PLSVQDLK;DVDAS(0.382)PS(0.585)PLS(0.033)VQDLK ; 249.54 1.20E-57 43473000 9756.3 9223.6 8548.4 8122.6 10685.4 12870.5 10913.8 12465 10554 9819.9 TRUE FALSE FALSE 9637.386463 9353.450083 8697.181316 9061.77323 10140.08417 12048.11659 11840.8179 12825.65511 9610.023807 9564.777582 1.007591277 0.977905655 0.909292583 0.947410763 1.060148454 1.259633743 1.237960611 1.340925599 1.004730505 1 13.22351571 -8.315395432 2.792698699 0.99017064 1.284120505 0.925736409 0.038525044 0.056231349 0.859741745 0.006041705 0.01591757 4.84E-09 8.315395432 0.293949864 DVDDFFEHER ddPTM_HeLa_Romidepsin_16h_R1 4 DVDDFFEHER 10 0 G3V5X9;Q9UNH7;A0A0A0MRI2;Q9UNH7-2 G3V5X9 SNX6 "Sorting nexin-6;Sorting nexin-6, N-terminally processed" 0 0 ;;; ;;; 166.86 0.00063857 90514000 31549.3 31600.1 31003.3 24776 33320.3 35044.7 30354.9 34087.3 32033.8 31031.9 FALSE FALSE TRUE 31164.765 32044.96704 31542.89943 27640.71769 31619.84076 32805.45677 32933.24445 35073.56224 29168.6167 30225.68676 1.03106888 1.060189874 1.043579247 0.914477739 1.046124808 1.085350253 1.089578037 1.160389258 0.965027426 1 14.8834875 -7.843546751 1.398096611 1.014786106 1.150126549 0.572322982 0.042644107 0.305339189 0.968857498 0.005968981 0.042868374 1.43E-08 7.843546751 0.135340443 DVDDGSGSPHS(ph)PHQLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 DVDDGSGSPHSPHQLSSK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 DVDDGSGSPHS(1)PHQLSSK 94.707 0.00179 5753000 1601.4 1316.2 1259.7 1364.1 2750.4 2878.5 2315.3 1820.3 2282.6 2262.8 TRUE FALSE FALSE 1581.881521 1334.729498 1281.62455 1521.82366 2610.036825 2694.57314 2511.961524 1872.967509 2078.438539 2204.01213 0.717728137 0.605590813 0.581496142 0.690478804 1.184220717 1.222576366 1.139722187 0.849799093 0.943025 1 11.10591645 -8.756468367 24.99992449 0.80706022 1.110803863 0.509875451 0.15987361 104.5453132 525766.9719 0.028101923 0.054832566 1.75E-09 8.756468367 0.303743643 DVDELPSLQPS(ph)VGSPSRPSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 0 DVDELPSLQPS(0.331)VGS(0.331)PS(0.331)RPS(0.002)S(0.002)S(0.002)R;DVDELPSLQPS(0.339)VGS(0.298)PS(0.339)RPS(0.008)S(0.008)S(0.008)R ; 82.859 0.00052248 47024000 5068 4452.3 4966.9 4920.9 6473.8 6570.6 5491.9 5531.9 5816.6 4745.9 TRUE FALSE FALSE 5006.229267 4514.979596 5053.346811 5489.877612 6143.417829 6150.759866 5958.381849 5691.956799 5296.348728 4622.600834 1.082989738 0.976718466 1.093182603 1.187616627 1.328995959 1.33058425 1.288967415 1.231332101 1.145750827 1 12.17448907 -9.147006753 2.218582528 1.035917875 1.296400055 0.812604943 0.05292885 0.074587356 0.717948639 0.007114552 0.012845795 7.13E-10 9.147006753 0.26048218 DVDELPSLQPSVGS(ph)PSRPSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 DVDELPSLQPSVGSPSRPSSSR 22 1 O43815-2;O43815 O43815-2 STRN Striatin 1 0 DVDELPSLQPS(0.076)VGS(0.457)PS(0.457)RPS(0.003)S(0.003)S(0.003)R;DVDELPSLQPS(0.118)VGS(0.441)PS(0.441)RPS(0.001)S(0.001)SR ; 124.25 2.95E-05 54476000 5580.8 5577.5 5869 5792.2 7304 7891.5 6473.7 7449.7 6202.5 6462.3 TRUE FALSE FALSE 5512.779063 5656.020191 5971.147483 6461.921417 6931.249625 7387.258619 7023.575916 7665.245316 5647.732866 6294.408514 0.87582162 0.898578505 0.948643144 1.02661297 1.101175688 1.173622367 1.115843673 1.217786437 0.897261888 1 12.6198551 -8.833131336 1.615914827 0.93591581 1.165558956 0.87735097 0.04058833 0.124443957 0.656472342 0.008361133 0.019056071 1.47E-09 8.833131336 0.229643146 DVDETGITVAS(ph)LER ddPTM_HeLa_Romidepsin_16h_R1 4 DVDETGITVASLER 14 0 Q8WU90;H7C466 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 1 0 DVDETGITVAS(1)LER;DVDETGITVAS(1)LER;DVDETGIT(0.001)VAS(0.999)LER;DVDETGIT(0.008)VAS(0.992)LER ;;; 227.92 4.11E-33 28654900 3495.72 3498.16 4048.07 3434.73 3307.7 3736.72 3428.51 3361.51 4243.38 3847.91 TRUE FALSE FALSE 3453.11282 3547.407188 4118.52496 3831.869643 3138.895726 3497.955652 3719.727554 3458.769988 3863.841465 3747.940743 0.921336023 0.946495004 1.098876755 1.022393337 0.83749876 0.933300682 0.992472349 0.92284543 1.03092384 1 11.87188243 -8.811722638 24.99999886 0.975681533 0.927435125 0.233608274 0.060976547 182.7420176 90855.52995 0.009650607 0.017493236 1.54E-09 8.811722638 -0.048246408 DVDFEGTDEPIFGK ddPTM_HeLa_Romidepsin_16h_R1 1 DVDFEGTDEPIFGK 14 0 H0Y8U3;P42285 H0Y8U3 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 0 131.82 0.019437 2184900 791.76 748.01 550.56 935.03 747.67 762.42 483.9 701.73 686.44 734.26 FALSE FALSE TRUE 782.1097246 758.5405044 560.1422659 1043.142568 709.51361 713.7038226 525.0024539 722.0334504 625.0430872 715.1838193 1.093578607 1.060623135 0.7832144 1.458565672 0.992071676 0.997930606 0.734080442 1.009577441 0.873961449 1 9.482170286 -7.962362856 9.500223392 1.052997796 0.869872973 0.114900326 0.177625703 0.443526745 105.4967856 0.02159032 0.064791413 1.09E-08 7.962362856 -0.183124822 DVDIIDHHDNTYTVK ddPTM_HeLa_Romidepsin_16h_R1 4 DVDIIDHHDNTYTVK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ;;; ;;; 87.083 0.0074763 101571800 16547.1 15577.6 15317.6 15837.3 17329.2 17678.7 15711.6 18574.2 16759.6 16618.3 FALSE FALSE TRUE 16345.41758 15796.90186 15584.1964 17668.48314 16444.82626 16549.08813 17046.14291 19111.61517 15260.5794 16186.55417 1.009814529 0.975927408 0.962786535 1.091553085 1.015955965 1.022397229 1.05310511 1.180709308 0.942793583 1 13.98250827 -4.000000059 0.807865562 1.004503754 47.04457613 0.681663861 0.037187899 189.3010655 0.599958848 0.004886427 15972.64075 1.00E-04 4.000000059 46.04007237 DVDLEFLAK ddPTM_HeLa_Romidepsin_16h_R1 1 DVDLEFLAK 9 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 131.06 0.02176 290450 164.61 180.74 149.21 322.41 212.42 206.09 133.08 233.89 68.436 221.12 FALSE FALSE TRUE 162.60367 183.2844625 151.8069375 359.6885612 201.5794148 192.9215141 144.3838119 240.6572381 62.31491276 215.3752705 0.754978367 0.851000498 0.704848505 1.670055064 0.935945033 0.895745893 0.670382498 1.117385657 0.289331791 1 7.750708798 DVDVS(ph)EDSPPPLPER ddPTM_HeLa_Romidepsin_16h_R1 1 DVDVSEDSPPPLPER 15 0 Q05209-2;Q05209-3;Q05209 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 DVDVS(0.74)EDS(0.26)PPPLPER 184.51 1.64E-08 43981000 1057 1293.9 939.33 686.58 1706.5 1199.7 1080.6 1150.5 1226.4 1192.9 TRUE FALSE FALSE 1044.116877 1312.115558 955.6786446 765.9656101 1619.410937 1123.043042 1172.386137 1183.787902 1116.707712 1161.908286 0.898622456 1.129276359 0.822507814 0.659230698 1.393751087 0.966550506 1.009017795 1.01883076 0.961097985 1 10.18228048 -8.769979182 24.99975085 0.936667392 1.081429932 0.234849117 0.159078973 256.6877244 751439.1244 0.022890904 0.041977048 1.70E-09 8.769979182 0.14476254 DVDVSEDS(ph)PPPLPER ddPTM_HeLa_Romidepsin_16h_R1 1 DVDVSEDSPPPLPER 15 0 Q05209-2;Q05209-3;Q05209 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 DVDVS(0.26)EDS(0.74)PPPLPER 130.27 0.0019917 48924000 636.6 693.24 683.3 409.91 909.46 725.07 447.47 664.84 728.05 692.8 TRUE FALSE FALSE 628.8408743 702.9994509 695.1925499 457.3057229 863.0468625 678.7403671 485.4780906 684.0760965 662.9313846 674.8009561 0.931890906 1.04178787 1.030218679 0.677689797 1.278965085 1.005837886 0.719438949 1.013745002 0.982410263 1 9.398318208 -8.544647006 0.006382462 1.903578953 7.10E-05 0.007450209 0.160066852 48876.44902 81.57823282 11840.39719 12492.96128 2.85E-09 8.544647006 -1.903507982 DVEDEETWIR ddPTM_HeLa_Romidepsin_16h_R1 2 DVEDEETWIR 10 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 ; ; 183.43 0.00022444 87874000 5375.4 5364.3 5224.3 5338.2 5704.6 5699.8 4741.5 5600.6 5775 5727 FALSE FALSE TRUE 5309.882557 5439.818756 5315.22675 5955.427801 5413.472975 5335.601175 5144.242892 5762.644525 5258.469536 5578.211714 0.951896921 0.975190444 0.952854969 1.067623121 0.970467464 0.95650747 0.922202877 1.033063071 0.942680164 1 12.44558698 DVEDEILWVGER ddPTM_HeLa_Romidepsin_16h_R1 4 DVEDEILWVGER 12 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ;;; ;;; 265.77 4.06E-76 33322400 7812.9 7779.3 8006.7 6338.8 8200.8 8013.5 7861.4 7815 9089.5 8026.4 FALSE FALSE TRUE 7717.67337 7888.81719 8146.053255 7071.721881 7782.282575 7501.463212 8529.14712 8041.114695 8276.512355 7817.872971 0.987183266 1.009074619 1.041978206 0.9045583 0.99544756 0.959527386 1.09098052 1.028555302 1.058665495 1 12.93256043 -7.761700954 24.99999999 0.990216351 1.059767914 0.269019766 0.042520668 4.852057871 464008.1877 0.004738478 0.01566329 1.73E-08 7.761700954 0.069551563 DVEDEILWVTER ddPTM_HeLa_Romidepsin_16h_R1 1 DVEDEILWVTER 12 0 O15020;O15020-2 O15020 SPTBN2 "Spectrin beta chain, non-erythrocytic 2" 0 0 158.08 0.01039 1863700 688.96 817.77 621.76 602.63 609.82 567.08 367.53 501.07 786.28 477.91 FALSE FALSE TRUE 680.5626905 829.2825875 632.581472 672.3089161 578.6986098 530.8454182 398.747989 515.5676699 715.9531475 465.4938293 1.462023012 1.781511452 1.358947063 1.44429179 1.24319287 1.140391955 0.856612835 1.107571438 1.538050781 1 8.862618233 -8.087316008 2.934841694 1.29622572 0.982767582 0.316920892 0.217247332 0.33425328 5.540164907 0.037704604 0.11619061 8.18E-09 8.087316008 -0.313458137 DVEDESTGLEK ddPTM_HeLa_Romidepsin_16h_R1 1 DVEDESTGLEK 11 0 P36952 P36952 SERPINB5 Serpin B5 0 0 172.56 0.0022047 12793000 2952.3 3532.3 2891.4 2936.7 2958.1 2992.4 2669.4 2622.2 3326.1 3056.6 FALSE FALSE TRUE 2916.316232 3582.027812 2941.723604 3276.255072 2807.137119 2801.195298 2896.138769 2698.06922 3028.605286 2977.189091 0.97955358 1.203157644 0.988087593 1.100452464 0.942881702 0.94088592 0.972776226 0.90624718 1.017270047 1 11.53973514 -8.617392406 24.99529009 1.014833324 0.942958644 0.30803749 0.068719657 19.68884247 5193.795016 0.010265394 0.020530787 2.41E-09 8.617392406 -0.07187468 DVEDMELS(ph)DVEDDGSK ddPTM_HeLa_Romidepsin_16h_R1 3 DVEDMELSDVEDDGSK 16 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK;DVEDMELS(1)DVEDDGSK ;; 100.68 0.007356 101326200 16718.5 16841.1 18116.1 9313.7 12140.5 12355.4 10036 11822.7 17929.9 18647.2 TRUE FALSE FALSE 16514.72849 17078.18945 18431.40312 10390.59382 11520.92498 11565.92982 10888.45759 12164.77117 16326.20484 18162.74306 0.909264005 0.940286905 1.014791822 0.57208285 0.634316356 0.636794221 0.599494116 0.669765086 0.898884314 1 14.14869448 -9.260844457 24.99999728 0.958460802 0.62266458 0.941739804 0.041046234 9.135204645 383879.8241 0.006628782 0.010570722 5.48E-10 9.260844457 -0.335796222 DVEDMELS(ph)DVEDDGSKIIVEDR ddPTM_HeLa_Romidepsin_16h_R1 1 DVEDMELSDVEDDGSKIIVEDR 22 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 DVEDMELS(0.999)DVEDDGS(0.001)KIIVEDR 63.706 0.0097668 2329100 1338.8 1559.1 1507.6 1315.7 1217.1 1028.5 1002.2 1021.7 1687.5 1677.8 TRUE FALSE FALSE 1322.482191 1581.049051 1533.839146 1467.827425 1154.986845 962.7821693 1087.326843 1051.261278 1536.565774 1634.210514 0.809248367 0.967469636 0.938581127 0.898187481 0.706755241 0.589142073 0.665352985 0.643283878 0.940249595 1 10.67437812 -8.692399789 3.309926036 0.915267817 0.636809268 0.877362458 0.050746778 0.088981293 1.95956353 0.010936351 0.022715246 2.03E-09 8.692399789 -0.278458549 DVES(ph)PSWR ddPTM_HeLa_Romidepsin_16h_R1 1 DVESPSWR 8 0 F5H6E2;O00159-2;O00159-3;O00159 F5H6E2 MYO1C Unconventional myosin-Ic 1 0 DVES(0.778)PS(0.222)WR 120.31 0.018687 50312000 2236 2494.5 2270.7 2312.1 3251.7 2821.1 2804.4 2931 2605 2410.9 TRUE FALSE FALSE 2208.746772 2529.617636 2310.220581 2579.435881 3085.753615 2640.840815 3042.605666 3015.803861 2372.002276 2348.26447 0.940586889 1.077228595 0.983799146 1.098443516 1.314057106 1.124592587 1.295682707 1.284269254 1.010108659 1 11.19737918 -9.005727232 3.022024289 0.981680107 1.24844668 0.789928972 0.060550655 0.078711551 1.470179725 0.009078148 0.016681855 9.87E-10 9.005727232 0.266766573 DVESPS(ph)WR ddPTM_HeLa_Romidepsin_16h_R1 1 DVESPSWR 8 0 F5H6E2;O00159-2;O00159-3;O00159 F5H6E2 MYO1C Unconventional myosin-Ic 1 0 DVES(0.154)PS(0.846)WR 123.11 0.016895 49253000 2766.1 2706.8 2704.3 2777.8 3026 3706.2 2695.4 3548.8 2719.2 3061.9 TRUE FALSE FALSE 2732.385709 2744.906401 2751.367207 3098.982306 2871.571928 3469.385781 2924.347209 3651.478929 2475.987942 2982.351397 0.916185032 0.920383294 0.92254964 1.039107031 0.962854991 1.1633055 0.980550854 1.224362405 0.830213349 1 11.54223454 -5.613325045 0.507073717 0.955518949 2.357855194 0.546565555 0.076279039 10.20247439 0.484254791 0.01275513 12.37880854 2.44E-06 5.613325045 1.402336245 DVESYIHR ddPTM_HeLa_Romidepsin_16h_R1 2 DVESYIHR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 0 ; ; 148.99 0.0033913 9960500 8165 7391.5 9505.4 5721.4 9872.2 8920.6 7942.4 6946.9 10985.5 9760.9 FALSE FALSE TRUE 8065.481839 7495.557731 9670.8375 6382.935188 9368.384796 8350.60245 8617.027258 7147.897591 10002.92937 9507.310411 0.848345272 0.78839939 1.017200142 0.671371283 0.985387496 0.878334891 0.906358043 0.751831726 1.052130301 1 13.21482155 -12.19913488 0.814496909 1.005475875 0.859126413 0.307086675 0.099547577 0.770072598 0.869157238 0.071630335 0.017551387 6.32E-13 12.19913488 -0.146349462 DVFFYQADDEHYIPR ddPTM_HeLa_Romidepsin_16h_R1 2 DVFFYQADDEHYIPR 15 0 K7EKE5;K7EIS0;Q9NRH3;P23258 K7EKE5 TUBG1;TUBG2 Tubulin gamma chain;Tubulin gamma-2 chain;Tubulin gamma-1 chain 0 0 ; ; 160.63 0.00010442 24172300 6663.3 6943.7 6286.6 6175.6 6711.9 7150.3 5722.3 7145.8 7103.4 6769.4 FALSE FALSE TRUE 6582.085137 7041.453591 6396.015636 6889.651929 6369.366697 6693.418907 6208.352019 7352.552449 6468.054113 6593.530012 0.998264226 1.067933804 0.970044214 1.044910983 0.966002534 1.015149532 0.941582431 1.115116248 0.980969845 1 12.68683534 DVFLSAISS(ph)GADSPNSK ddPTM_HeLa_Romidepsin_16h_R1 1 DVFLSAISSGADSPNSK 17 0 Q8NHU6-3;Q8NHU6-2;Q8NHU6 Q8NHU6-3 TDRD7 Tudor domain-containing protein 7 1 0 DVFLS(0.219)AIS(0.01)S(0.749)GADS(0.022)PNSK 284.24 3.00E-103 16080000 3853.7 3259.9 3817.1 3995.8 5300.4 5199.8 4624 4882.3 3740.8 3888.5 TRUE FALSE FALSE 3806.729622 3305.792958 3883.535024 4457.813197 5029.900809 4867.549562 5016.762445 5023.561648 3406.213479 3787.476209 1.005083441 0.872822105 1.025362223 1.176987775 1.328034958 1.285169673 1.324566061 1.326361242 0.899335941 1 11.88702111 -9.078661697 2.418934977 0.991275596 1.314871627 0.917202944 0.050203003 0.053321704 0.614128902 0.006590118 0.01208379 8.34E-10 9.078661697 0.323596031 DVHLELKNLTMCGRK ddPTM_HeLa_Romidepsin_16h_R1 1 DVHLELKNLTMCGRK 15 2 Q8TE04-3;Q8TE04-2;Q8TE04-4;Q8TE04 Q8TE04-3 PANK1 Pantothenate kinase 1 0 0 42.209 0.029493 1003400 805.17 755.67 396.76 544.7 1231.4 1287.8 1022.8 562.96 1015.3 850.38 FALSE FALSE TRUE 795.3562783 766.3083421 403.6654414 607.6807769 1168.557063 1205.513736 1109.676606 579.2483594 924.4890251 828.287005 0.960242372 0.925172479 0.487349722 0.733659677 1.410811779 1.455429976 1.339724757 0.699332907 1.116145756 1 9.693986944 -8.758727612 24.99999375 0.919488136 1.250789498 0.307189457 0.254484652 72.79479831 671087.4804 0.037342672 0.072072438 1.74E-09 8.758727612 0.331301361 DVHTLLDR ddPTM_HeLa_Romidepsin_16h_R1 2 DVHTLLDR 8 0 E9PI41;Q9NPD3 E9PI41 EXOSC4 Exosome complex component RRP41 0 0 ; ; 154.12 0.0027587 12228300 9055.4 8693.3 9262.8 8178.3 8795.1 8824.8 7774 8578.6 8773.9 8533.9 FALSE FALSE TRUE 8945.029302 8815.684506 9424.015148 9123.913526 8346.253228 8260.923761 8434.323366 8826.808256 7989.140409 8312.188048 1.076134136 1.060573276 1.133758656 1.09765485 1.004098221 0.993832636 1.014693522 1.061911521 0.961135668 1 13.02101258 -6.854634554 17.4953148 1.042754352 7.755893894 0.011853183 0.050884337 1036.185853 124663.3018 0.006913643 103.8914179 1.40E-07 6.854634554 6.713139541 DVIEEYFK ddPTM_HeLa_Romidepsin_16h_R1 1 DVIEEYFK 8 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 0 109.21 0.002312 0 3291.2 3135.8 3542.9 2861.4 3416.8 3485.3 2890.9 3177.9 3584.7 3343 FALSE FALSE TRUE 3251.085588 3179.945875 3604.562688 3192.248531 3242.427946 3262.600578 3136.452974 3269.847523 3264.075454 3256.148378 0.99844516 0.976597349 1.107001976 0.980375634 0.9957863 1.001981544 0.963240187 1.004207162 1.002434495 1 11.66895073 -7.960007584 24.36661592 1.003945181 0.98344541 0.059362245 0.035886064 283.9220001 172984.6178 0.004712488 0.014137437 1.10E-08 7.960007584 -0.020499771 DVIELTDDSFDK ddPTM_HeLa_Romidepsin_16h_R1 1 DVIELTDDSFDK 12 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 0 151.15 0.00097157 0 884.25 947.62 1080.5 597.64 949.7 1029.7 754.9 1078.9 883.51 931.8 FALSE FALSE TRUE 873.4724209 960.9606192 1099.305649 666.7419488 901.2332652 963.9054932 819.0211872 1110.116269 804.4866528 907.5917017 0.962406795 1.058802783 1.211233694 0.734627639 0.992994166 1.062047495 0.902411498 1.223145019 0.886397101 1 9.825899608 -7.247691632 24.02657405 0.987823 1.223145292 0.270254382 0.119570475 1332.982754 2329551.067 0.014656515 0.377398962 5.65E-08 7.247691632 0.235322293 DVLDVYIEHR ddPTM_HeLa_Romidepsin_16h_R1 2 DVLDVYIEHR 10 0 P33993-2;P33993 P33993-2 MCM7 DNA replication licensing factor MCM7 0 0 ; ; 100.82 0.011211 8301400 11164.2 11513.5 12166.9 7097.8 9480.2 9612.2 7067.6 9151.6 12249.3 11937.3 FALSE FALSE TRUE 11028.12644 11675.58736 12378.65979 7918.481032 8996.390018 8998.011442 7667.921768 9416.387107 11153.69193 11627.16723 0.948479214 1.004164396 1.064632472 0.681032695 0.773738766 0.773878217 0.659483227 0.809860813 0.959278534 1 13.50521203 -9.258163772 24.99986793 0.983708657 0.73894896 0.861380261 0.051184416 77.21487554 589313.0932 0.007554308 0.012195549 5.52E-10 9.258163772 -0.244759697 DVLLQVDDERR ddPTM_HeLa_Romidepsin_16h_R1 3 DVLLQVDDERR 11 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ;; ;; 188.27 1.17E-08 62500900 12646.9 10494.5 12328.3 9516.5 12190.2 11942.4 11680 12009.4 13930.7 12333.9 FALSE FALSE TRUE 12492.75472 10642.24185 12542.86889 10616.84251 11568.08861 11179.31918 12672.09891 12356.87304 12684.7033 12013.4635 1.039896173 0.88585959 1.044067674 0.88374535 0.96292702 0.930565876 1.054824773 1.02858539 1.055873962 1 13.55236452 DVLSLLNLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DVLSLLNLSPR 11 0 Q96AY4;A0A087WW06 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 0 DVLSLLNLS(1)PR 198.52 6.08E-13 13966000 1851.6 1769.2 2151.9 2338.3 1931.8 2103.6 1461.4 1501.3 1901.9 1788.1 TRUE FALSE FALSE 1829.031987 1794.106844 2189.352917 2608.665248 1833.213037 1969.186749 1585.53128 1544.737747 1731.789301 1741.644904 1.050175029 1.030122064 1.257060444 1.497816944 1.052575662 1.130647668 0.910364263 0.886941846 0.99434121 1 10.76623479 -5.607524282 10.85168172 1.063723816 0.826858073 0 0.171865446 0 0 0.023616524 0 2.47E-06 5.607524282 -0.236865743 DVMQET(ph)FK ddPTM_HeLa_Romidepsin_16h_R1 1 DVMQETFK 8 0 C9JU55;M0QYR3;C9JIP4;P17024;Q3KP31 C9JU55 ZNF791;ZNF20 Zinc finger protein 20;Zinc finger protein 791 1 0 DVMQET(1)FK 138.83 0.01871 3715200 1166.5 1109.8 905.04 1255.7 918.87 989.41 1086.6 1290.7 1197.7 1064.5 TRUE FALSE FALSE 1152.282249 1125.423794 920.7918416 1400.889942 871.9766351 926.1898942 1178.895777 1328.044368 1090.574712 1036.844137 1.111336033 1.085431989 0.88807161 1.35110948 0.840991046 0.893277843 1.137003852 1.280852465 1.051821266 1 10.01798332 -6.258581878 0.007991903 1.54E-07 2.201042715 0.029717551 0.156232148 46838.56173 45.07888829 5753.282507 6693.134566 5.51E-07 6.258581878 2.201042561 DVMS(ph)DETNNEET(ph)ESPSQEFVNITK ddPTM_HeLa_Romidepsin_16h_R1 1 DVMSDETNNEETESPSQEFVNITK 24 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 DVMS(0.834)DET(0.166)NNEET(0.718)ES(0.222)PS(0.06)QEFVNITK 88.834 5.12E-05 3531000 1549.5 1624.6 1570.4 1129 1856.9 1608.8 1515.4 1517.9 1754.8 1702.6 TRUE FALSE FALSE 1530.614098 1647.471161 1597.732153 1259.540292 1762.135464 1506.002872 1644.118038 1561.818042 1597.846293 1658.366207 0.92296508 0.993430254 0.963437477 0.759506728 1.062573186 0.908124434 0.99140831 0.941781155 0.963506303 1 10.69554691 -12.44151327 1.018664223 1.002132618 0.941666216 0.032542555 0.074890019 1.237731629 2.161432241 0.057265167 0.012382333 3.62E-13 12.44151327 -0.060466402 DVMS(ph)DETNNEETESPSQEFVNITK ddPTM_HeLa_Romidepsin_16h_R1 2 DVMSDETNNEETESPSQEFVNITK 24 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DVMS(0.97)DET(0.028)NNEET(0.001)ESPSQEFVNITK;DVMS(0.984)DET(0.007)NNEET(0.009)ESPSQEFVNITK ; 97.813 9.83E-06 7155800 2287.8 2518.8 2225.9 2522.6 2510.2 2352.7 2034.05 2115.73 2525.1 2791.2 TRUE FALSE FALSE 2259.915414 2554.259733 2264.640856 2814.274881 2382.095127 2202.370063 2206.822156 2176.945309 2299.248732 2718.684222 0.831253367 0.939520564 0.832991503 1.035160634 0.876194119 0.810086749 0.81172434 0.800734889 0.845721145 1 11.40869288 -16.52287875 0.266018179 1.944841532 0.851273478 0 0.083387213 40.24822735 0.539098642 20.13832877 0.037192534 3.00E-17 16.52287875 -1.093568054 DVMSDETNNEET(ph)ESPSQEFVNITK ddPTM_HeLa_Romidepsin_16h_R1 1 DVMSDETNNEETESPSQEFVNITK 24 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DVMS(0.017)DET(0.068)NNEET(0.658)ES(0.128)PS(0.128)QEFVNITK 59.429 0.0032879 52428000 2438.6 2482.8 2322.5 2439 2828.6 2966.9 2234.5 2865.2 2598.5 2711.5 TRUE FALSE FALSE 2408.877405 2517.752924 2362.922138 2721.008656 2684.245987 2777.324665 2424.298374 2948.100041 2366.083652 2641.054839 0.912089128 0.953313383 0.894688782 1.030273441 1.016353749 1.051596742 0.917928071 1.116258549 0.895885847 1 11.36689854 -9.229719391 24.43583939 0.952611908 1.021283914 0.393920564 0.055845997 526.9831958 405967.458 0.008215666 0.013623303 5.89E-10 9.229719391 0.068672006 DVMSDETNNEETES(ph)PSQEFVNITK ddPTM_HeLa_Romidepsin_16h_R1 3 DVMSDETNNEETESPSQEFVNITK 24 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 DVMSDETNNEET(0.052)ES(0.87)PS(0.078)QEFVNITK;DVMSDET(0.002)NNEET(0.061)ES(0.864)PS(0.073)QEFVNITK;DVMSDETNNEET(0.065)ES(0.929)PS(0.006)QEFVNITK ;; 103.25 4.90E-06 71293300 9277.1 9263.6 9641 9830.1 10297.8 10543.8 8833 10755.3 11068.5 10498.1 TRUE FALSE FALSE 9164.027137 9394.013204 9808.797561 10966.70241 9772.26484 9870.085209 9583.2748 11066.48764 10078.50564 10225.35785 0.896206008 0.918697746 0.959262033 1.072500599 0.955689276 0.965255725 0.937206789 1.082259203 0.985638428 1 13.31986371 -9.503690113 24.73987682 0.946803834 0.99643246 0.187823744 0.051942581 1020.681738 1315964.486 0.008866471 0.013410598 3.14E-10 9.503690113 0.049628626 DVNAAIAAIK ddPTM_HeLa_Romidepsin_16h_R1 1 DVNAAIAAIK 10 0 P68366-2;P68366 P68366-2 TUBA4A Tubulin alpha-4A chain 0 0 125.97 0.02382 301010 220.57 66.886 182.92 140.08 167.86 252.4 131.15 188.88 163.53 205.89 FALSE FALSE TRUE 217.881608 67.82762286 186.1036459 156.2767087 159.2934778 236.2724546 142.2898777 194.3449448 148.9034672 200.5409481 1.086469422 0.338223308 0.928008208 0.779275805 0.794318962 1.178175614 0.709530293 0.96910355 0.742509042 1 7.647753038 DVNAAIAT(ph)IK ddPTM_HeLa_Romidepsin_16h_R1 1 DVNAAIATIK 10 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;A0A1W2PQM2;Q6PEY2;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA3E;TUBA1A;TUBA1B Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 1 0 DVNAAIAT(1)IK 119.39 0.025194 12994000 4333.3 4001.8 3453.1 3635.7 6418.3 4418.1 3424.6 4139.5 3353.8 3369.7 TRUE FALSE FALSE 4280.484073 4058.137445 3513.199757 4056.07674 6090.750201 4135.797669 3715.485439 4259.269901 3053.827728 3282.154708 1.304168893 1.23642479 1.07039432 1.235796939 1.855716973 1.260086144 1.132026296 1.297705404 0.930433816 1 11.68042753 -8.990510337 24.99686891 1.150828528 1.382514377 0.280516106 0.204323012 252.2125353 664351.8542 0.031220897 0.056542132 1.02E-09 8.990510337 0.23168585 DVNAAIATIK ddPTM_HeLa_Romidepsin_16h_R1 2 DVNAAIATIK 10 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;A0A1W2PQM2;Q6PEY2;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA3E;TUBA1A;TUBA1B Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 0 0 ; ; 187.42 4.37E-05 4403300 4139.1 3538.8 3913.9 4088.5 3398.4 4278.8 3152.6 3277.3 3986.4 4057.4 FALSE FALSE TRUE 4088.651057 3588.619319 3982.019788 4561.231607 3224.966967 4005.398489 3420.381765 3372.123505 3629.8464 3951.988163 1.034580795 0.908054167 1.007599118 1.154161252 0.816036596 1.013514799 0.865483808 0.853272673 0.918486152 1 11.94836291 -7.761090162 0.828301744 1.012355722 0.811841552 0.192553421 0.087757147 1.147378762 0.880797265 0.012570646 0.17894014 1.73E-08 7.761090162 -0.20051417 DVNQQEFVR ddPTM_HeLa_Romidepsin_16h_R1 1 DVNQQEFVR 9 0 M0R2L9;M0QYF7;M0R140;P39019 M0R2L9 RPS19 40S ribosomal protein S19 0 0 117.53 0.0010875 0 1045.2 1098.3 1099.7 1192.5 1147.2 1090.9 1109.8 1026.1 1073.9 1138.8 FALSE FALSE TRUE 1032.4607 1113.761896 1118.839817 1330.382461 1088.654103 1021.195011 1204.066384 1055.788585 977.8476944 1109.213812 0.930804043 1.004100277 1.008678223 1.19939226 0.981464612 0.920647579 1.085513335 0.95183505 0.881568264 1 10.11532177 -9.965598059 3.551725949 0.967280468 1.028203586 0.16569954 0.079000821 0.383998751 10.2574574 0.012475203 0.016325826 1.08E-10 9.965598059 0.060923117 DVPNETLQVEEDDRPELPWWK ddPTM_HeLa_Romidepsin_16h_R1 2 DVPNETLQVEEDDRPELPWWK 21 1 O95373 O95373 IPO7 Importin-7 0 0 ; ; 105.96 0.00037503 16621500 2510.7 2278 2517.3 2380.5 2566.7 2442.4 2010.02 2882.3 2563 2672.1 FALSE FALSE TRUE 2480.098623 2310.069744 2561.112551 2655.744611 2435.711721 2286.338522 2180.751049 2965.694803 2333.758861 2602.678457 0.952902429 0.887574006 0.984029565 1.020389055 0.935848113 0.878456006 0.837887232 1.139477985 0.896675828 1 11.34578137 -11.90840935 0.846534649 0.998850799 0.949059152 0 0.086023085 1.493387431 2.037425137 0.043238227 0.015480851 1.23E-12 11.90840935 -0.049791647 DVPPDILLDS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 3 DVPPDILLDSPER 13 0 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 DVPPDILLDS(1)PER;DVPPDILLDS(1)PER;DVPPDILLDS(1)PER ;; 201.72 2.90E-16 45999500 10652.45 10754.8 11418.3 9115.56 7397.17 6883.95 6163.45 7038.82 11476.5 10420.3 TRUE FALSE FALSE 10522.61384 10906.20636 11617.03072 10169.54394 7019.664812 6444.087812 6686.973289 7242.477151 10450.0131 10149.5791 1.036753715 1.074547648 1.14458251 1.00196706 0.691621272 0.634911827 0.658842423 0.713574137 1.029600636 1 13.30913228 -8.765493822 4.841467622 1.033296564 0.667281929 0.947424253 0.043066348 0.033546545 2.064663224 0.007182585 0.013929563 1.72E-09 8.765493822 -0.366014635 DVPPDILLDS(ph)PERK ddPTM_HeLa_Romidepsin_16h_R1 7 DVPPDILLDSPERK 14 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK;DVPPDILLDS(1)PERK ;;;;;; 169.15 0.00010217 144709000 26296.5 25773.1 25137.07 22845.4 22286.7 19723 17040.8 20540.41 31080.3 27218.7 TRUE FALSE FALSE 25975.98814 26135.93438 25574.57016 25486.89264 21149.32654 18462.76395 18488.24513 21134.71436 28300.40013 26511.55425 0.979798766 0.985831843 0.964657519 0.961350376 0.797739972 0.696404435 0.697365569 0.797188809 1.067474199 1 14.69433363 -8.697532679 2.701633593 0.987643526 0.727419327 0.913493892 0.037549909 0.039457832 0.584932991 0.004046964 0.008647577 2.01E-09 8.697532679 -0.260224199 DVQGTDASLDEELDR ddPTM_HeLa_Romidepsin_16h_R1 2 DVQGTDASLDEELDR 15 0 A0A087WYB4;Q9UJZ1-2;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 0 ; ; 302.2 1.26E-133 11310000 1991.94 1670.13 1511.46 1229.23 2001.38 2002.77 1396.35 1735.24 1870.76 1688.01 FALSE FALSE TRUE 1967.661469 1693.642134 1537.766327 1371.359356 1899.24211 1874.799461 1514.955934 1785.446432 1703.43454 1644.155257 1.196761353 1.030098664 0.93529265 0.834081423 1.155147668 1.14028128 0.921419025 1.085935421 1.036054553 1 10.68313082 -10.0206432 24.01679891 1.093994819 1.009699707 0.065497551 0.105329612 840.7626127 978162.3473 0.019648629 0.024227622 9.54E-11 10.0206432 -0.084295112 DVQGTDASLDEELDRVK ddPTM_HeLa_Romidepsin_16h_R1 2 DVQGTDASLDEELDRVK 17 1 A0A087WYB4;Q9UJZ1-2;Q9UJZ1 A0A087WYB4 STOML2 "Stomatin-like protein 2, mitochondrial" 0 0 ; ; 171.29 2.88E-06 6354000 2304.88 2321.18 2085.99 2164.62 2161.68 2595.53 1664.34 2086.79 2325.7 1964.66 FALSE FALSE TRUE 2276.787236 2353.857633 2122.295781 2414.903549 2051.361403 2429.68401 1805.708998 2147.167976 2117.683567 1913.61785 1.189781563 1.230056269 1.109048905 1.261957057 1.0719807 1.269680887 0.943610031 1.122046377 1.106638699 1 10.90208704 -12.33606625 1.069901459 1.00036055 1.151666081 0.099078285 0.097981467 0.53035266 1.090559156 0.059681856 0.015845031 4.61E-13 12.33606625 0.151305531 DVS(ph)PFDHSR ddPTM_HeLa_Romidepsin_16h_R1 1 DVSPFDHSR 9 0 P18031 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1 1 0 DVS(1)PFDHSR 86.911 0.0032167 0 315.62 427.7 519.1 329.73 515.59 896.51 528.57 843.82 414.27 391.05 TRUE FALSE FALSE 311.773102 433.7211718 528.1347177 367.854934 489.2775184 839.2259044 573.4667226 868.2346004 377.2166536 380.8904646 0.81853743 1.13870315 1.386578995 0.96577617 1.284562266 2.203326106 1.505594852 2.279486312 0.990354679 1 8.573232361 -8.299684305 0.699156789 0.926047286 2.214295966 0.703358425 0.263914468 0.422626213 0.295367379 0.046421865 0.329198348 5.02E-09 8.299684305 1.28824868 DVS(ph)SPDENNGQSK ddPTM_HeLa_Romidepsin_16h_R1 1 DVSSPDENNGQSK 13 0 J3QL74;J3QLI2;O43829 J3QL74 ZBTB14 Zinc finger and BTB domain-containing protein 14 1 0 DVS(0.856)S(0.144)PDENNGQSK 150.51 0.00076854 2712100 1112.9 1392.1 1689 1180.1 1096.6 1095.6 1595.4 476.66 2097.4 1734.7 TRUE FALSE FALSE 1099.335547 1411.69802 1718.396336 1316.548715 1040.63641 1025.594696 1730.913236 490.4514051 1909.803291 1689.632244 0.650635989 0.835506084 1.017023878 0.779192466 0.615895213 0.606992853 1.024431939 0.290271097 1.130307082 1 10.72249356 -16.52287875 0.279578803 3.049043923 0.706460178 0.306565632 0.204196073 55.61252861 0.750101777 63.77479943 0.091867488 3.00E-17 16.52287875 -2.342583746 DVSGFSDPYCLLGIEQGVGVPGGS(ph)PGSR ddPTM_HeLa_Romidepsin_16h_R1 3 DVSGFSDPYCLLGIEQGVGVPGGSPGSR 28 0 K7EIH3;K7EQ37;K7EN81;Q70J99-2;Q70J99;Q70J99-3 K7EIH3 UNC13D Protein unc-13 homolog D 1 0 DVSGFSDPYCLLGIEQGVGVPGGS(0.5)PGS(0.5)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.613)PGS(0.387)R;DVSGFSDPYCLLGIEQGVGVPGGS(0.607)PGS(0.393)R ;; 150.09 3.43E-25 29501000 6424.6 5672 5822.4 444.64 4959.6 4459.1 3836.3 4610.7 6151.5 5451.1 TRUE FALSE FALSE 6346.294504 5751.850565 5923.73643 496.0513689 4706.493105 4174.177901 4162.155226 4744.10333 5601.294433 5309.479636 1.195276174 1.083317191 1.115690583 0.093427493 0.886432085 0.786174576 0.783910197 0.893515684 1.054961092 1 12.37435476 -9.407925014 20.29415419 1.095421895 0.699779068 0.457569931 0.218157248 3.668072195 637.9669945 0.032615937 0.049821662 3.91E-10 9.407925014 -0.395642827 DVSYQGGK(ac)SIK ddPTM_HeLa_Romidepsin_16h_R1 2 DVSYQGGKSIK 11 1 Q8NEZ4;Q8NEZ4-3;H0YMU7 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 1 ; DVSYQGGK(1)SIK;DVSYQGGK(1)SIK 205.52 2.04E-13 2252600 834.25 836.67 702.37 975.04 630.87 899.78 723.25 969.39 880.38 901.74 FALSE TRUE FALSE 824.0818401 848.4486622 714.5944552 1087.778713 598.6743498 842.2869619 784.6828369 997.4377702 801.6366078 878.3126648 0.938255673 0.965998438 0.81359917 1.238486881 0.681618715 0.958983054 0.893398067 1.135629498 0.912700727 1 9.778590797 -12.2795248 0.929448904 1.001073127 0.947215523 0 0.148133955 2.665608996 3.999828061 0.099074556 0.024776914 5.25E-13 12.2795248 -0.053857604 DVT(ph)PPPETEVVLIK ddPTM_HeLa_Romidepsin_16h_R1 4 DVTPPPETEVVLIK 14 0 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK;DVT(1)PPPETEVVLIK ;;; 185.2 1.89E-07 814494400 17748.6 19366.5 18200.9 9724.4 16593.3 17445.2 15264.3 16962.8 18972.6 18911.2 TRUE FALSE FALSE 17532.27324 19639.1421 18517.67903 10848.78088 15746.48198 16330.50802 16560.84926 17453.59186 17275.64314 18419.8843 0.951812343 1.066192479 1.005309194 0.588971174 0.854863241 0.886569522 0.899074554 0.947540797 0.937880111 1 14.16897638 DVT(ph)SPINER ddPTM_HeLa_Romidepsin_16h_R1 1 DVTSPINER 9 0 K7EJY2;K7ERF3;K7ELU8;D3DUE4;F6WF08;Q6ZW76-2;Q6ZW76 K7EJY2 ANKS3 Ankyrin repeat and SAM domain-containing protein 3 1 0 DVT(0.788)S(0.212)PINER 131.42 0.015569 18020000 4094.3 4123.8 4450.1 3009.9 4085.2 4120.1 3067.1 3520.7 4283.5 3879.2 TRUE FALSE FALSE 4044.397097 4181.854965 4527.552124 3357.9188 3876.717 3856.838907 3327.619397 3622.5659 3900.373032 3778.417825 1.070394351 1.106774094 1.198266664 0.88871029 1.026015962 1.020755005 0.880691218 0.958752067 1.032276792 1 11.88356653 -9.221506869 24.99912691 1.052022697 0.958457563 0.430243978 0.068685015 542.0139675 339319.7953 0.01113474 0.018464738 6.00E-10 9.221506869 -0.093565134 TSS(ph)TNEDEDLNPEQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSTNEDEDLNPEQK 15 0 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 T(0.004)S(0.003)S(0.695)T(0.299)NEDEDLNPEQK 189.52 2.47E-12 39311000 4836.9 3546.8 4181.6 2574.3 2068.7 1432.5 1218.4 1139.4 4276.5 4584.5 TRUE FALSE FALSE 4777.946002 3596.731943 4254.378994 2871.952678 1963.12652 1340.967873 1321.890866 1172.366741 3893.999129 4465.394029 1.069994265 0.805467988 0.952744364 0.643157728 0.439631196 0.30030225 0.296030061 0.26254497 0.87203931 1 12.12457177 -8.97822517 1.017318121 1.027836517 0.254344102 0.929527072 0.079817598 0.06518135 0.132286724 0.010886915 0.028096225 1.05E-09 8.97822517 -0.773492415 down DVTNFTVGGFAPMS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 DVTNFTVGGFAPMSPR 16 0 O00267-2;O00267 O00267-2 SUPT5H Transcription elongation factor SPT5 1 0 DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR;DVTNFTVGGFAPMS(1)PR ;; 120.32 0.0039886 543275000 6788.1 6456.1 6358.4 5915.8 6072.5 6354 5478.7 6442.9 5979.1 6267.1 TRUE FALSE FALSE 6705.364026 6546.989145 6469.065285 6599.812631 5762.597665 5947.999907 5944.060641 6629.315146 5444.314321 6104.279839 1.098469304 1.072524412 1.059758965 1.081177928 0.944025801 0.974398302 0.973752973 1.086011015 0.891884787 1 12.57560539 -8.77283213 24.99963405 1.053023224 0.991622533 0.033444123 0.066220389 228.2882287 500943.7716 0.007453762 0.013596883 1.69E-09 8.77283213 -0.061400691 DVTNNVHYENYR ddPTM_HeLa_Romidepsin_16h_R1 3 DVTNNVHYENYR 12 0 G3V1Q4;E7ES33;E7EPK1;Q16181-2;Q16181 G3V1Q4 Sep-07 Septin-7 0 0 ;; ;; 110.8 0.0048584 16595800 8851.7 7029 9638.1 8872.7 9801.4 10187.2 8151.8 7646.7 9333.7 7289.8 FALSE FALSE TRUE 8743.812076 7127.954447 9805.847088 9898.603321 9301.197984 9536.270798 8844.213689 7867.9452 8498.870495 7100.409945 1.231451725 1.003879283 1.381025485 1.394088989 1.30995225 1.343059186 1.245591981 1.108097316 1.196954903 1 12.79368661 -11.89122612 0.428798472 0.955026437 1.283821974 0.149278349 0.126599743 1.200563927 0.362182072 0.173562977 0.040020355 1.28E-12 11.89122612 0.328795537 DVTVLS(ph)VAEEQDLLK ddPTM_HeLa_Romidepsin_16h_R1 2 DVTVLSVAEEQDLLK 15 0 Q14966-3;Q14966;Q14966-5;A0A096LPK8 Q14966-3 ZNF638 Zinc finger protein 638 1 0 DVTVLS(1)VAEEQDLLK;DVTVLS(1)VAEEQDLLK ; 185.67 9.58E-09 2349800 2088.4 1818.74 2025.81 1347.35 1345.7 1436.62 1110.61 1416.8 1962.24 1559.19 TRUE FALSE FALSE 2062.945778 1844.344269 2061.068373 1503.136946 1277.023908 1344.824618 1204.945186 1457.792873 1786.73234 1518.682019 1.35837901 1.214437418 1.357142804 0.989764103 0.840876425 0.885520867 0.79341506 0.959906586 1.176501939 1 10.56860412 -9.034772441 5.35638955 1.190467931 0.869820541 0.71680961 0.104113375 0.11913529 9.168825667 0.022346781 0.038407761 9.23E-10 9.034772441 -0.32064739 DVTVLS(ph)VAEEQDLLKQER ddPTM_HeLa_Romidepsin_16h_R1 1 DVTVLSVAEEQDLLKQER 18 1 Q14966-3;Q14966;Q14966-5;A0A096LPK8 Q14966-3 ZNF638 Zinc finger protein 638 1 0 DVT(0.004)VLS(0.996)VAEEQDLLKQER 122.16 0.00059235 3452700 1154.3 915.62 1224.3 1101.3 1211.7 863.86 826.25 856.42 1146.2 1107.4 TRUE FALSE FALSE 1140.230948 928.5101224 1245.608428 1228.637488 1149.862428 808.662134 896.4316544 881.1991615 1043.681001 1078.629588 1.057110763 0.860823894 1.154806471 1.139072672 1.066040131 0.749712545 0.831083872 0.816961792 0.967599084 1 10.0749838 -8.264754497 24.99259426 1.035479354 0.802435844 0.636904372 0.081581205 132.6098714 999746.6355 0.011380352 0.026465622 5.44E-09 8.264754497 -0.23304351 DVVQAYPEVR ddPTM_HeLa_Romidepsin_16h_R1 3 DVVQAYPEVR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 ;; ;; 101.65 0.010963 57702000 10315.8 9960.1 9575.2 10096.8 9436.2 11983.9 10233.5 10296.2 9828.2 9297.2 FALSE FALSE TRUE 10190.06706 10100.31855 9741.852339 11264.23952 8954.635503 11218.16747 11102.73323 10594.1043 8949.141177 9055.657404 1.125270823 1.115360056 1.075775276 1.243889761 0.988844333 1.238802106 1.226054911 1.169887931 0.988237604 1 13.14460366 -16.52287875 0.079255066 0.463982493 1.320505998 0.473873913 0.070358372 118.1868177 0.719634768 11.19866181 1.264497932 3.00E-17 16.52287875 0.856523505 DVYLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DVYLSPR 7 0 P38159;P38159-2;H3BUY5;H0Y6E7;H3BT71;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 0 DVYLS(1)PR 120.87 0.027173 2381100000 4552.1 4201.2 4054.4 3030.3 4062.2 5012.5 4518.8 4337.5 4335.1 4902.5 TRUE FALSE FALSE 4496.617254 4260.344604 4124.965131 3380.677544 3854.890776 4692.217427 4902.626759 4462.998719 3947.357799 4775.132343 0.941673849 0.892194037 0.863843101 0.707975675 0.807284594 0.982636101 1.026699661 0.934633513 0.826648879 1 12.221325 -10.70711261 1.351785374 0.982812389 0.886433788 0 0.097611763 0.510670761 1.933216465 0.020882749 0.02037131 1.96E-11 10.70711261 -0.096378601 DVYVTTHT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DVYVTTHTPR 10 0 H0YAI5;D6RA71;P78317 H0YAI5 RNF4 E3 ubiquitin-protein ligase RNF4 1 0 DVYVT(0.004)T(0.024)HT(0.973)PR 107.46 0.00069097 0 2379.8 3263.9 2902.9 2469.1 3308.1 3796 3294.3 3163.2 2912.5 2889.7 TRUE FALSE FALSE 2350.794082 3309.84927 2953.423757 2754.588959 3139.275313 3553.447851 3574.11776 3254.722201 2651.998706 2814.625177 0.835206798 1.175946729 1.049313344 0.978669907 1.115344003 1.262494161 1.269837913 1.156360793 0.942220913 1 11.4587271 -8.904097248 0.731513719 0.932792175 1.250713363 0.540086313 0.091521063 0.420216946 0.412868032 0.020523773 0.070195055 1.25E-09 8.904097248 0.317921188 DWDDDQND ddPTM_HeLa_Romidepsin_16h_R1 1 DWDDDQND 8 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 0 172.03 0.00063177 6369600 6840.2 6300.1 6001.3 6957 6577.9 6780.4 5633 6055.3 6896.8 6038.4 FALSE FALSE TRUE 6756.829011 6388.792973 6105.750109 7761.401074 6242.205217 6347.154323 6111.466879 6230.500552 6279.932935 5881.521498 1.148823313 1.086248342 1.038124253 1.319624705 1.0613249 1.07916877 1.039096241 1.059334826 1.067739519 1 12.5219737 -4.012034827 23.8562642 1.083612077 0.001453309 0 0.085065258 0 0 0.01198306 0 9.73E-05 4.012034827 -1.082158769 DWEDDS(ph)DEDMSNFDR ddPTM_HeLa_Romidepsin_16h_R1 4 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 1 0 DWEDDS(0.992)DEDMS(0.008)NFDR;DWEDDS(1)DEDMSNFDR;DWEDDS(0.973)DEDMS(0.027)NFDR;DWEDDS(0.994)DEDMS(0.006)NFDR ;;; 146.84 0.00066065 5031459400 11800 12613.4 12040 5964.29 10892.7 11131.3 9005.1 10820 12275.4 11366.9 TRUE FALSE FALSE 11656.17706 12790.97178 12249.55115 6653.909273 10336.80487 10420.04585 9769.992969 11133.05963 11177.45748 11071.5863 1.052800994 1.155297121 1.106395309 0.600989695 0.933633591 0.941152024 0.882438406 1.005552351 1.009562422 1 13.43457432 DWEDDSDEDMSNFDR ddPTM_HeLa_Romidepsin_16h_R1 3 DWEDDSDEDMSNFDR 15 0 A0A087WYT3;Q15185-4;Q15185;B4DDC6;Q15185-2 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 0 ;; ;; 160.72 0.00054275 112628100 6034.15 6069.7 5762.1 2879.24 4940.35 5499.4 4722.46 5043.32 6033.87 5353.7 FALSE FALSE TRUE 5960.603459 6155.149396 5862.386933 3212.151276 4688.225505 5148.006089 5123.585635 5189.240507 5494.185555 5214.610102 1.143058319 1.180366178 1.124223445 0.61599069 0.899055809 0.987227422 0.982544339 0.995134901 1.053613875 1 12.34834367 DWELHVK(ac)GK(ac)LHAQK(ac)CLVFSENAGIR ddPTM_HeLa_Romidepsin_16h_R1 1 DWELHVKGKLHAQKCLVFSENAGIR 25 3 Q5T481 Q5T481 RBM20 RNA-binding protein 20 0 3 DWELHVK(1)GK(1)LHAQK(1)CLVFSENAGIR 44.341 0.028262 2244800 193.13 145.2 215.23 0 158.61 1620 1116.4 729.78 213.27 264.39 FALSE TRUE FALSE 190.7760573 147.2441294 218.9759879 0 150.5155398 1516.487228 1211.226988 750.8950329 194.1945971 257.5211097 0.740817161 0.571774988 0.850322477 0 0.584478453 5.88878803 4.703408546 2.915858175 0.754091955 1 8.008546888 -8.272788494 24.99868637 0.764933271 4.522757268 0.857078011 0.721044084 176.9156941 389691.9089 0.099565878 0.224477823 5.34E-09 8.272788494 3.757823997 DWEQFHQPR ddPTM_HeLa_Romidepsin_16h_R1 2 DWEQFHQPR 9 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 0 ; ; 114.97 0.0076348 22212600 10681.7 9872 9631.7 6511.8 10653.5 11174.3 9680.9 10044.9 10604.8 10368.3 FALSE FALSE TRUE 10551.50733 10010.97828 9799.335698 7264.724955 10109.81214 10460.29829 10503.1954 10335.53333 9656.280128 10098.93007 1.044814377 0.991290979 0.970334048 0.719355902 1.001077547 1.035782822 1.040030511 1.023428547 0.95616863 1 13.30191483 -7.369968735 0.005145117 1.959791805 2.07E-07 0 0.093746977 93662.38701 78.93548169 14506.63151 15574.85341 4.27E-08 7.369968735 -1.959791598 DWILPSDYDHAEAEAR ddPTM_HeLa_Romidepsin_16h_R1 4 DWILPSDYDHAEAEAR 16 0 O43852;O43852-3;O43852-15;O43852-2;O43852-4;H0Y875;O43852-5;O43852-9 O43852 CALU Calumenin 0 0 ;;; ;;; 249.36 6.56E-59 35562400 14536.7 12893.6 14894.6 8692.7 17129.9 18211.9 15675.2 16560.3 16279.4 16127.9 FALSE FALSE TRUE 14359.52111 13075.11644 15153.83427 9697.790874 16255.69728 17048.21837 17006.6511 17039.44615 14823.32969 15708.89483 0.914101295 0.832338403 0.964665842 0.61734393 1.034808461 1.085258928 1.08261283 1.084700505 0.943626515 1 13.93929407 -8.538614348 24.9999988 0.922920498 1.080033196 0.420164919 0.104799018 216.3064862 343656.8827 0.015958727 0.031925264 2.89E-09 8.538614348 0.157112699 DWQSYYYHHPQDR ddPTM_HeLa_Romidepsin_16h_R1 1 DWQSYYYHHPQDR 13 0 Q1KMD3 Q1KMD3 HNRNPUL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 0 0 147.96 0.00029241 4844800 1525.5 1439.7 1380.4 1227.9 2324.5 2518.4 1725.7 1774.9 1844 1495.9 FALSE FALSE TRUE 1506.906619 1459.968134 1404.425283 1369.875575 2205.872091 2357.482368 1872.280915 1826.253931 1679.068022 1457.036302 1.03422723 1.002012189 0.963891758 0.94017944 1.513944496 1.617998374 1.284992633 1.253403178 1.152385853 1 10.50882111 -8.763565833 24.99985906 1.006255074 1.422429106 0.759904444 0.11065058 18.36546476 215919.3568 0.015285646 0.028725499 1.72E-09 8.763565833 0.416174032 DWSHYFK ddPTM_HeLa_Romidepsin_16h_R1 2 DWSHYFK 7 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 0 ; ; 117.17 0.013028 46405000 37605 27868 37508 34966 42004 41382 28616.8 30999 27517.7 26508.1 FALSE FALSE TRUE 37146.6558 28260.32644 38160.81101 39008.93344 39860.37914 38737.82375 31047.51028 31895.90716 25056.44799 25819.41574 1.438710162 1.094537797 1.477988944 1.510837187 1.543814141 1.500336961 1.202486942 1.235345814 0.970449845 1 14.65616873 -12.43863483 0.651767754 0.930543787 1.38938876 0.540481736 0.143702911 0.815368586 0.466203782 0.224906234 0.032220863 3.64E-13 12.43863483 0.458844974 DY(ph)EKVYQT(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 DYEKVYQTEK 10 1 A0A6I8PLE7;K7ER44;A0A6I8PRZ0;A0A6I8PR89;A0A6I8PIK4;A0A6I8PS32;A0A6I8PUD4;A0A6I8PU73;Q99615-2;Q99615 A0A6I8PLE7 DNAJC7 DnaJ homolog subfamily C member 7 2 0 DY(0.997)EKVY(0.026)QT(0.977)EK 58.699 0.0041034 0 2096.4 2465.7 2236.5 1871.6 2047.5 2362.5 1320.7 1612.7 2646 2318.2 TRUE FALSE FALSE 2070.84827 2500.412189 2275.425344 2088.003198 1943.008435 2211.543875 1432.880225 1659.36093 2409.335133 2257.97283 0.917127187 1.107370362 1.007729285 0.924724678 0.860510104 0.979437771 0.634587009 0.73488968 1.067034599 1 11.14081241 -7.76590669 24.99905928 0.965141806 0.684738304 0.722221692 0.073322134 37.85117926 211820.9441 0.009644093 0.030436641 1.71E-08 7.76590669 -0.280403502 DY(ph)ETATLS(ph)EIKALLK ddPTM_HeLa_Romidepsin_16h_R1 1 DYETATLSEIKALLK 15 1 P12814-2;P12814;P12814-3;P12814-4;H9KV75;H7C5W8 P12814-2 ACTN1 Alpha-actinin-1 2 0 DY(0.97)ET(0.029)AT(0.001)LS(0.999)EIKALLK 99.941 0.0018665 0 500.39 667.18 636.53 464.33 848.02 644.22 411.08 615.76 607.46 621.22 TRUE FALSE FALSE 494.2910542 676.5725776 647.6085376 518.0180193 804.742375 603.0564211 445.9971249 633.5760441 553.1272562 605.0806148 0.816901157 1.11815279 1.070284722 0.856114056 1.32997547 0.996654671 0.737087115 1.047093608 0.914138121 1 9.240983555 -10.2627667 24.99362869 0.91353666 1.01754628 0.100557466 0.152760245 238.4226301 4489515.819 0.026887933 0.031626482 5.46E-11 10.2627667 0.10400962 DY(ph)ILNKR ddPTM_HeLa_Romidepsin_16h_R1 1 DYILNKR 7 1 A0A494C108;Q8N9T8;F8WFC1 A0A494C108 KRI1 Protein KRI1 homolog 1 0 DY(1)ILNKR 51.572 0.025965 2667700 796.47 776.46 717.65 1030.1 805.57 688.74 684.59 757.81 940.21 728.51 TRUE FALSE FALSE 786.7623173 787.3910243 730.1403972 1149.205009 764.4587569 644.7317368 742.7390575 779.7360367 856.1152628 709.5832052 1.108766825 1.109652848 1.028970798 1.619549336 1.077334908 0.908606252 1.046725813 1.098864842 1.206504405 1 9.470828053 -6.112365211 17.50703691 1.084652457 1.125785714 0 0.185774544 0 0 0.023903403 0 7.72E-07 6.112365211 0.041133257 DYAAYNVLDDPELR ddPTM_HeLa_Romidepsin_16h_R1 1 DYAAYNVLDDPELR 14 0 Q86SX6 Q86SX6 GLRX5 "Glutaredoxin-related protein 5, mitochondrial" 0 0 150.49 0.0062679 3288400 1208.3 1155.2 1078.4 1085.3 1140.2 1318.1 1056 1122.7 1101.2 1062.1 FALSE FALSE TRUE 1193.572775 1171.462936 1097.1691 1210.787492 1082.011339 1233.877664 1145.696614 1155.183553 1002.705914 1034.506489 1.153760549 1.132388195 1.060572468 1.170401061 1.045920302 1.192721048 1.107481322 1.11665182 0.969260149 1 10.01472698 -12.35978479 0.979565786 0.996785941 1.123873949 0.59870852 0.044406375 0.33250589 0.547787829 0.030747314 0.007230419 4.37E-13 12.35978479 0.127088009 DYAFIHFDER ddPTM_HeLa_Romidepsin_16h_R1 4 DYAFIHFDER 10 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 ;;; ;;; 181.87 1.45E-05 105750800 29945.2 29117.5 31476.2 20704.4 30858.8 32504.2 26869.5 29233.3 30914.3 28977.6 FALSE FALSE TRUE 29580.21638 29527.41693 32024.03006 23098.34015 29283.96029 30427.28652 29151.79466 30079.11941 28149.24758 28224.75777 1.048023746 1.046153068 1.134607791 0.818371599 1.037527426 1.078035346 1.032844813 1.065699825 0.997324682 1 14.78467358 -16.52273959 0.005259673 0.310944385 1.691099232 0.022924202 0.077680246 193557.0301 82.36850376 11640.9526 10029.59626 3.00E-17 16.52273959 1.380154846 DYAFVHFEDR ddPTM_HeLa_Romidepsin_16h_R1 4 DYAFVHFEDR 10 0 B4DT28;O43390-3;O43390;O43390-4;O43390-2;A0A286YEZ8 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 0 ;;; ;;; 144.55 0.0019238 101005000 28302.2 27593.2 30434.3 22604 33385.1 33463.9 28989 29653.6 35206.7 31318.5 FALSE FALSE TRUE 27957.2419 27981.65779 30963.99622 25217.58084 31681.33377 31325.66479 31451.32494 30511.58013 32057.72458 30504.84086 0.916485421 0.917285815 1.015051885 0.826674722 1.038567417 1.026907989 1.03102734 1.000220925 1.050906141 1 14.89675058 DYASHLS(ph)PGSIIQPQR ddPTM_HeLa_Romidepsin_16h_R1 2 DYASHLSPGSIIQPQR 16 0 C9J0Q5;Q9Y618-4;Q9Y618;C9JE98;Q9Y618-5;C9JQE8;C9J330 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 DY(0.001)AS(0.015)HLS(0.984)PGSIIQPQR;DYAS(0.001)HLS(0.998)PGS(0.002)IIQPQR ; 114.63 0.0029783 21006900 2272.02 2360.75 2003.52 2370.15 2828.7 2668.7 2215.05 2482.27 2534 2480.54 TRUE FALSE FALSE 2244.327746 2393.9847 2038.390425 2644.197895 2684.340884 2498.178683 2403.196292 2554.090566 2307.352693 2416.095213 0.928906996 0.990848658 0.843671398 1.094409641 1.111024462 1.033973607 0.994661253 1.057115031 0.954992453 1 11.23846159 -9.223086885 24.97269124 0.959425749 1.056289521 0.5507906 0.050724343 393.7639333 256394.2136 0.008072934 0.01338724 5.98E-10 9.223086885 0.096863773 DYDDMS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 DYDDMSPR 8 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 DYDDMS(1)PR 124.92 0.02129 4273600000 5848 5396.3 4524.7 5359.4 4872.6 4845.8 4860.9 5103.6 5505.7 5417 TRUE FALSE FALSE 5776.722327 5472.269253 4603.450505 5979.079045 4623.93304 4536.169019 5273.784725 5251.264614 5013.256403 5276.265559 1.094850565 1.037148186 0.872482716 1.133202826 0.87636473 0.859730991 0.999529812 0.995261621 0.950152404 1 12.36530146 -9.961462073 24.82704526 1.045906816 0.957840651 0.09483948 0.084327842 174.6748422 112529.3209 0.012933459 0.016997884 1.09E-10 9.961462073 -0.088066165 DYDDMSPR ddPTM_HeLa_Romidepsin_16h_R1 1 DYDDMSPR 8 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 98.523 0.02353 847050 689.94 708.47 575.67 602.05 623.23 528.92 553.01 581.08 555.09 543.37 FALSE FALSE TRUE 681.5307459 718.4438593 585.6892949 671.6618537 591.4242475 495.123719 599.9826556 597.892633 505.4413602 529.2531691 1.287721616 1.357467279 1.106633515 1.269074789 1.11746945 0.935513943 1.133640176 1.129691172 0.955008661 1 9.047814193 -8.521094224 24.97643933 1.164583218 1.065263284 0.102749047 0.127794506 128.6934902 1801202.969 0.020415529 0.041317621 3.01E-09 8.521094224 -0.099319934 DYDEEEQGYDS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 2 DYDEEEQGYDSEK 13 0 Q5T757;Q05519-2;Q05519 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 DYDEEEQGYDS(1)EK;DYDEEEQGYDS(1)EK ; 222.75 2.09E-31 29763000 8148.1 8405.4 8952.5 4727.4 7510.6 8253.3 6737.3 7334.5 7974.6 8229.3 TRUE FALSE FALSE 8048.787823 8523.731442 9108.314507 5274.004231 7127.306056 7725.940766 7309.566094 7546.712186 7261.331803 8015.5016 1.004152731 1.063405869 1.136337432 0.65797557 0.889190273 0.963874895 0.911928717 0.94151465 0.905911092 1 12.96857709 -9.296238606 24.99999224 1.016758737 0.881024585 0.378375194 0.095130378 500.5416411 359591.034 0.013544957 0.020690787 5.06E-10 9.296238606 -0.135734152 DYDEEEQGYDS(ph)EKEK ddPTM_HeLa_Romidepsin_16h_R1 1 DYDEEEQGYDSEKEK 15 1 Q5T757;Q05519-2;Q05519 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 DYDEEEQGYDS(1)EKEK 101.5 0.0027257 38755000 3395.4 3522.2 3614.5 2097.2 3196.3 3159.4 2689.1 3612.2 3106.4 3339 TRUE FALSE FALSE 3354.015559 3571.785624 3677.408856 2339.688132 3033.180884 2957.524536 2917.512087 3716.713308 2828.555804 3252.252299 1.031290088 1.098249858 1.130726807 0.719405482 0.932640092 0.909377338 0.897074341 1.142812109 0.869722132 1 11.66722347 -9.311195826 24.99996651 1.030645465 0.919055668 0.174026337 0.114939614 418.9847925 210516.5082 0.015368595 0.023475933 4.88E-10 9.311195826 -0.111589797 DYDEEEQGYDS(ph)EKEKKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 DYDEEEQGYDSEKEKKEEK 19 3 Q5T757;Q05519-2;Q05519 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 DYDEEEQGY(0.035)DS(0.964)EKEKKEEK 46.162 0.021654 21947000 5936.8 4730.7 4997.4 6004.7 5914.4 4765.3 4832 5790.1 6073.4 5775.4 TRUE FALSE FALSE 5864.439998 4797.298919 5084.377651 6698.991667 5612.566098 4460.812709 5242.429959 5957.627408 5530.179893 5625.354275 1.042501452 0.85279943 0.903832435 1.190856849 0.997726689 0.792983427 0.931928853 1.059067059 0.983081175 1 12.45772824 DYDGWTPLHAAAHWGK ddPTM_HeLa_Romidepsin_16h_R1 1 DYDGWTPLHAAAHWGK 16 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;F8VW28;H0YHL8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 0 0 129.77 0.00077821 8969500 4107.8 3893.7 4326.8 3269.3 4509.9 4348.1 3656.7 4235.7 4250.4 2979.7 FALSE FALSE TRUE 4057.732554 3948.515611 4402.106139 3647.311849 4279.742974 4070.270443 3967.300007 4358.253297 3870.233579 2902.286964 1.398115556 1.360484218 1.516771495 1.256702695 1.474610549 1.40243556 1.366956492 1.501661741 1.333511684 1 11.50297446 -12.19886531 0.56585364 0.935195682 1.418375181 0.219992447 0.125536698 0.347882659 0.163521932 0.088815611 0.015999612 6.33E-13 12.19886531 0.483179499 DYEDGMEVDTTPTVAGQFEDADVDH ddPTM_HeLa_Romidepsin_16h_R1 2 DYEDGMEVDTTPTVAGQFEDADVDH 25 0 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 0 0 ; ; 105.22 3.23E-05 21814100 7828.8 7713.7 7640.6 4025.3 6742 7631 6086.6 6926.4 7799.9 7615.2 FALSE FALSE TRUE 7733.379574 7822.293671 7773.581438 4490.724126 6397.930582 7143.403728 6603.595652 7126.804456 7102.257409 7417.356006 1.042605959 1.054593263 1.048025932 0.605434621 0.862562155 0.963066047 0.8902897 0.960828151 0.957518744 1 12.8566893 DYEEVGADS(ph)ADGEDEGEEY ddPTM_HeLa_Romidepsin_16h_R1 2 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 1 0 DYEEVGADS(0.947)ADGEDEGEEY(0.053);DYEEVGADS(1)ADGEDEGEEY ; 157.09 2.84E-06 21177800 12106.8 11064.3 13527.3 6976 11300.1 11581.4 8621.7 9988.8 12480.1 12412.7 TRUE FALSE FALSE 11959.23766 11220.06351 13762.73698 7782.597943 10723.41373 10841.38592 9354.026983 10277.81017 11363.8486 12090.21626 0.989166563 0.928028355 1.138336708 0.6437104 0.886949703 0.896707361 0.773685663 0.850093162 0.939921036 1 13.56155243 -9.267972713 24.99961836 0.998457308 0.817265644 0.551526217 0.085033434 282.9695232 1082773.889 0.011664781 0.01807972 5.40E-10 9.267972713 -0.181191664 DYEEVGADSADGEDEGEEY ddPTM_HeLa_Romidepsin_16h_R1 6 DYEEVGADSADGEDEGEEY 19 0 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 0 ;;;;; ;;;;; 196.48 1.87E-14 23977600 28109.8 27998.6 26903.4 18210 26793.9 31512.6 22117.2 25323.9 28313.4 26824.5 FALSE FALSE TRUE 27767.18695 28392.76503 27371.64239 20315.52588 25426.5073 29499.04656 23995.83442 26056.60709 25780.97859 26127.59562 1.062753242 1.086696435 1.047614284 0.777550532 0.973166749 1.129037933 0.918409591 0.997283006 0.986733681 1 14.67328675 DYEEVGVDSVEGEGEEEGEEY ddPTM_HeLa_Romidepsin_16h_R1 3 DYEEVGVDSVEGEGEEEGEEY 21 0 Q71U36-2;Q71U36;P68363;P68363-2 Q71U36-2 TUBA1A;TUBA1B Tubulin alpha-1A chain;Tubulin alpha-1B chain 0 0 ;; ;; 155.99 7.09E-07 39998800 47099.2 45104.1 46212.8 30197.2 45432.3 49213.7 36976.9 42969.9 46455.5 43764.4 FALSE FALSE TRUE 46525.13683 45739.0767 47017.1144 33688.74235 43113.7202 46069.1034 40117.71696 44213.16626 42300.40373 42627.39458 1.091437497 1.072997239 1.102978844 0.790307329 1.011408758 1.080739366 0.94112524 1.037200765 0.992329091 1 15.37949326 DYEIESQNPLAS(ph)PTNTLLGSAK ddPTM_HeLa_Romidepsin_16h_R1 2 DYEIESQNPLASPTNTLLGSAK 22 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 DYEIESQNPLAS(0.952)PT(0.046)NT(0.002)LLGSAK;DYEIESQNPLAS(0.738)PT(0.242)NT(0.021)LLGSAK ; 114.85 3.95E-05 223870000 20785 21343 21128 20419.1 22173 20949 19625.6 20708 22804 20572 TRUE FALSE FALSE 20531.66443 21643.46731 21495.72398 22780.05242 21041.42907 19610.42651 21292.59797 21307.15331 20764.35313 20037.53647 1.024660115 1.080146122 1.072772793 1.136868918 1.0501006 0.978684507 1.062635519 1.063361923 1.036272755 1 14.29041753 -10.47767607 3.057156739 1.009859599 1.062792176 0.207862917 0.037471064 0.247318854 4.497202854 0.007087868 0.007810677 3.33E-11 10.47767607 0.052932577 DYETATLSDIK ddPTM_HeLa_Romidepsin_16h_R1 1 DYETATLSDIK 11 0 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 0 167.09 0.0052142 7459800 2662.2 2411 2793.6 2096.4 3246.8 2969.2 2106.8 3012 2763.8 3069.1 FALSE FALSE TRUE 2629.752082 2444.942121 2842.221436 2338.795632 3081.103681 2779.477703 2285.751539 3099.147468 2516.598806 2989.36434 0.879702767 0.817880273 0.950777862 0.782372226 1.030688578 0.929788874 0.764627954 1.036724573 0.841850815 1 11.54562303 -12.22311572 0.985429924 0.999338259 0.895056653 0 0.10102737 0.736335287 1.296417359 0.052867336 0.015083731 5.98E-13 12.22311572 -0.104281606 DYFEEYGKIDTIEIITDR ddPTM_HeLa_Romidepsin_16h_R1 3 DYFEEYGKIDTIEIITDR 18 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ;; ;; 142.4 0.00025664 56597400 3044.97 2736.66 2446.84 3200.46 2969 2490.88 2249.14 2456.26 2997.77 2481.18 FALSE FALSE TRUE 3007.856734 2775.186771 2489.426224 3570.512244 2817.480851 2331.720807 2440.181895 2527.328008 2729.641943 2416.718586 1.244603634 1.148328476 1.030085273 1.477421602 1.165829099 0.964829261 1.009708747 1.045768433 1.129482745 1 11.23883377 -8.266930789 24.4223091 1.144686427 1.007062806 0.245801373 0.125993637 457.7217706 2035661.739 0.020699739 0.047569778 5.41E-09 8.266930789 -0.137623621 DYFGAHTYELLAK ddPTM_HeLa_Romidepsin_16h_R1 2 DYFGAHTYELLAK 13 0 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 ; ; 134.08 0.00083677 27477000 10994.3 9688.9 12690.3 9124.7 12399.6 11870.7 11217.8 10888 11452.3 7569.1 FALSE FALSE TRUE 10860.29724 9825.300589 12911.16935 10179.74075 11766.80214 11112.20058 12170.63965 11203.0271 10427.97761 7372.453691 1.47309128 1.33270428 1.751271678 1.380780562 1.596049651 1.507259462 1.650826192 1.519579176 1.414451422 1 12.84792914 -12.35432123 0.369765812 0.789885245 1.57942755 0.243934734 0.169902715 0.8951545 0.152256437 0.288198232 0.03939101 4.42E-13 12.35432123 0.789542305 DYGHSSSRDDYPSR ddPTM_HeLa_Romidepsin_16h_R1 2 DYGHSSSRDDYPSR 14 1 P38159;P38159-2;H3BUY5;H0Y6E7;H3BT71;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 0 ; ; 74.537 0.018887 3548200 1661.02 1811.38 1438.95 2651.9 2161.09 1955.65 1920.13 1736.17 2390.2 1915.42 FALSE FALSE TRUE 1640.774849 1836.880655 1463.994321 2958.525156 2050.801513 1830.690277 2083.225794 1786.40334 2176.414526 1865.657112 0.879462168 0.984575699 0.784707067 1.585781833 1.099238172 0.98125763 1.116617722 0.957519647 1.166567271 1 10.86546814 DYGNS(ph)PLHR ddPTM_HeLa_Romidepsin_16h_R1 3 DYGNSPLHR 9 0 A0A0U1RRM4;A0A0D9SF20;A0A087WUW5;K7ELW5;A6NLN1;P26599;P26599-2;P26599-3 A0A0U1RRM4;A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 0 DY(0.003)GNS(0.997)PLHR;DYGNS(1)PLHR;DYGNS(1)PLHR ;; 144.7 0.0059819 27398800 13896.9 9206.8 11758.7 7240.1 12318.2 13363 14140.7 11616.6 14457.3 12951.1 TRUE FALSE FALSE 13727.51924 9336.413572 11963.35524 8077.234428 11689.55629 12509.14743 15341.81071 11952.70799 13164.20288 12614.62855 1.088222232 0.740125921 0.948371582 0.640306957 0.926666706 0.99163819 1.21619203 0.947527542 1.043566429 1 13.62281011 -7.970236027 24.76541197 0.974102255 1.087373745 0.080292586 0.149581707 391.1225585 325432.9679 0.022749364 0.06824692 1.07E-08 7.970236027 0.11327149 DYIEEEVIDEK ddPTM_HeLa_Romidepsin_16h_R1 2 DYIEEEVIDEK 11 0 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 0 0 ; ; 182.28 7.04E-05 1890300 1880.3 2233.45 1859.29 1903.32 2076.94 2156.2 1904.41 1709.9 2393.24 2339.02 FALSE FALSE TRUE 1857.38218 2264.892568 1891.650163 2123.390814 1970.946002 2018.425779 2066.170538 1759.373259 2179.18262 2278.251923 0.815266372 0.994136138 0.830307721 0.932026345 0.865113283 0.885953725 0.906910477 0.77224702 0.956515212 1 11.15371157 -12.51663116 1.218305595 1.001290096 0.873174998 0.311249149 0.060263482 0.380418674 0.994166846 0.041417163 0.009551405 3.04E-13 12.51663116 -0.128115099 DYIPVDQEELR ddPTM_HeLa_Romidepsin_16h_R1 1 DYIPVDQEELR 11 0 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 144.55 0.025591 5557000 2842.4 3553.7 3292.8 2647.5 3114.9 3336.6 2846.9 3646.2 3005.9 2943.1 FALSE FALSE TRUE 2807.755736 3603.729082 3350.109803 2953.616407 2955.93503 3123.402028 3088.715615 3751.697044 2737.044776 2866.637838 0.979459525 1.257127438 1.168654707 1.030341666 1.031150497 1.089569804 1.077469771 1.308744689 0.954792663 1 11.48514394 -4 0.158667315 0.959746005 1.86058844 0.303981508 0.094294164 61.15683283 0.615461882 0.18607403 12.90986816 1.00E-04 4 0.900842435 DYLDFLDDEEDQGIYQSK ddPTM_HeLa_Romidepsin_16h_R1 3 DYLDFLDDEEDQGIYQSK 18 0 P25205;P25205-2 P25205 MCM3 DNA replication licensing factor MCM3 0 0 ;; ;; 140.68 0.00021055 9501300 6047.8 5902.4 6219.3 5414.3 5663.8 5746.2 4374.12 5243.8 6988.6 6590.3 FALSE FALSE TRUE 5974.087087 5985.494142 6327.544308 6040.326841 5374.755151 5379.036365 4745.657644 5395.52108 6363.522113 6419.083056 0.930676085 0.932453139 0.985739591 0.940995277 0.837308866 0.837975817 0.739304602 0.840543896 0.991344411 1 12.64815151 -8.684418287 2.000134286 0.965151303 0.798191194 0.828051926 0.033782718 0.103177014 0.836838496 0.005615918 0.013009809 2.07E-09 8.684418287 -0.166960108 DYLHLPPEIVPATLR ddPTM_HeLa_Romidepsin_16h_R1 2 DYLHLPPEIVPATLR 15 0 P46783;A0A2R8Y6L3;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6;S4R435 P46783 RPS10;RPS10-NUDT3 40S ribosomal protein S10 0 0 ; ; 87.083 0.009189 26357000 7691.4 7604.7 7398.8 7202.9 7216.9 8082.7 6453.3 6876.8 8294 6538.7 FALSE FALSE TRUE 7597.654258 7711.759166 7527.57301 8035.733189 6848.594663 7566.241556 7001.443141 7075.769358 7552.163867 6368.823631 1.192944678 1.210860845 1.18194088 1.261729584 1.075331185 1.188012417 1.099330669 1.11100099 1.185802011 1 12.63681121 -12.24890749 0.957054903 0.998987163 1.166765241 0 0.077576546 0.325627503 0.530370506 0.037648993 0.010098003 5.64E-13 12.24890749 0.167778078 DYLHYIR ddPTM_HeLa_Romidepsin_16h_R1 2 DYLHYIR 7 0 M0QZC5;P62280;M0R1H5 M0QZC5 RPS11 40S ribosomal protein S11 0 0 ; ; 105.2 0.015028 53393000 10525.3 8503.7 20216 22265 23694 20476.4 14911.7 7775.6 8142.8 6278.5 FALSE FALSE TRUE 10397.0136 8623.415312 20567.851 24839.38406 22484.80677 19168.02412 16178.29943 8000.574718 7414.487574 6115.383665 1.700140852 1.410118446 3.363296913 4.061786704 3.676761426 3.134394369 2.645508493 1.308270283 1.212432119 1 12.5782273 -9.76833153 24.26354159 1.345822025 3.094932122 0.58011402 0.707680315 61.93926141 218054.6655 0.122559728 0.163136691 1.70E-10 9.76833153 1.749110097 DYLLS(ph)ESEDEGDNDGERK ddPTM_HeLa_Romidepsin_16h_R1 1 DYLLSESEDEGDNDGERK 18 1 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 DYLLS(1)ESEDEGDNDGERK 163.79 4.49E-07 5306100 1267.1 982.72 1163.4 563.49 711.34 1037.6 1017.4 1114.4 1230.7 1247.3 TRUE FALSE FALSE 1251.656098 996.554758 1183.648489 628.6433651 675.0376654 971.3007087 1103.817931 1146.643406 1120.62311 1214.894966 1.030258691 0.820280589 0.974280511 0.517446679 0.555634589 0.799493566 0.908570668 0.94382102 0.922403287 1 10.24661588 -9.8984344 1.682372492 1.013615508 0.757202723 0.278084075 0.144319952 0.281790388 1.602055772 0.026268152 0.036042783 1.26E-10 9.8984344 -0.256412785 DYLLSES(ph)EDEGDNDGERK ddPTM_HeLa_Romidepsin_16h_R1 1 DYLLSESEDEGDNDGERK 18 1 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 DYLLS(0.435)ES(0.565)EDEGDNDGERK 107.09 0.00045129 5126400 1321.4 1087.3 1128.9 879.27 927.02 1324.4 1020.5 1342.8 1362.4 1222.8 TRUE FALSE FALSE 1305.294269 1102.607038 1148.548031 980.9353345 879.7107102 1239.775114 1107.181245 1381.651799 1240.543532 1191.03148 1.095935994 0.925758099 0.964330541 0.823601518 0.738612476 1.040925564 0.929598641 1.160046416 1.041570733 1 10.21799583 -10.24623985 23.45913856 1.045303107 0.932526468 0.161773341 0.108939823 457.1952799 705640.6928 0.018530547 0.022637227 5.67E-11 10.24623985 -0.112776639 DYLQAQHPPS(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 1 DYLQAQHPPSPIK 13 0 Q9P219 Q9P219 CCDC88C Protein Daple 1 0 DYLQAQHPPS(1)PIK 80.361 0.016725 11539000 5919.7 6294.6 6563 4741.1 4076.3 4222.9 3147.3 3332.6 6763.5 6351.8 TRUE FALSE FALSE 5847.548419 6383.215544 6677.226262 5289.28829 3868.2712 3953.070319 3414.631583 3429.023523 6158.555621 6186.77932 0.945168417 1.031750967 1.079273385 0.854934048 0.625247968 0.638954473 0.551923934 0.554250175 0.995438063 1 12.59497286 -8.845354484 2.748552664 0.985883077 0.584686916 0.952860085 0.043679378 0.044900427 0.68840085 0.007322805 0.014571622 1.43E-09 8.845354484 -0.40119616 DYNPYNYSDSIS(ph)PFNK ddPTM_HeLa_Romidepsin_16h_R1 2 DYNPYNYSDSISPFNK 16 0 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4X8;H7C5M8;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 0 DYNPYNYS(0.118)DS(0.017)IS(0.865)PFNK;DYNPYNYSDS(0.004)IS(0.996)PFNK ; 209.23 6.09E-21 22710000 4956.1 5379 6125.6 4953.9 7388.5 9384 7852.7 8308.1 5826.4 6148.2 TRUE FALSE FALSE 4895.693147 5454.725703 6232.213498 5526.693227 7011.437275 8784.392685 8519.708142 8548.481765 5305.272192 5988.468878 0.817520012 0.910871512 1.040702327 0.922889196 1.17082303 1.466884585 1.422685551 1.427490389 0.88591463 1 12.54797147 -8.518469299 2.345338225 0.921058866 1.441759631 0.933927324 0.060656602 0.066428842 0.725785287 0.011920965 0.029073558 3.03E-09 8.518469299 0.520700764 DYQDDTLELYNREDR ddPTM_HeLa_Romidepsin_16h_R1 2 DYQDDTLELYNREDR 15 1 H0YIQ2;P49750-3;P49750-1;P49750 H0YIQ2 YLPM1 YLP motif-containing protein 1 0 0 ; ; 180.95 4.29E-08 18546800 3786.5 3734.9 3523.5 2830.6 4284.9 4072.7 3573.7 3815.2 4063.6 3862.2 FALSE FALSE TRUE 3740.348682 3787.48002 3584.825039 3157.88729 4066.225564 3812.467614 3877.249989 3925.586793 3700.141439 3761.859487 0.994281869 1.006810603 0.952939644 0.839448496 1.080908412 1.013452955 1.030673794 1.043522972 0.983593739 1 11.87723025 DYQGPLKEHEVTIFVR ddPTM_HeLa_Romidepsin_16h_R1 1 DYQGPLKEHEVTIFVR 16 1 P53396;P53396-2;P53396-3;K7EIE7 P53396 ACLY ATP-citrate synthase 0 0 105.17 0.0017096 13935000 2508.9 2307.6 2348.3 2970.7 2534.3 2687.8 2219.3 2419.9 2699.8 2748.8 FALSE FALSE TRUE 2478.320562 2340.086453 2389.171176 3314.186312 2404.965214 2516.058254 2407.807287 2489.915989 2458.323126 2677.38578 0.925649408 0.874019154 0.892352232 1.237844145 0.898251284 0.939744386 0.899312794 0.929980284 0.918180393 1 11.38660931 -8.585142704 0.005872437 1.89366951 6.90E-08 0 0.1013752 40507.27924 63.48141328 9989.421288 10483.43595 2.60E-09 8.585142704 -1.893669441 DYS(ph)PSRNPPEVEAR ddPTM_HeLa_Romidepsin_16h_R1 2 DYSPSRNPPEVEAR 14 1 A0A3B3IRR3;Q9HCM7 A0A3B3IRR3 FBRSL1 Fibrosin-1-like protein 1 0 DY(0.006)S(0.932)PS(0.062)RNPPEVEAR;DY(0.006)S(0.897)PS(0.097)RNPPEVEAR ; 112.67 0.0018879 23535000 4672.3 4642.3 3865 3987.4 3405.3 3179.9 2906.9 3079 4409.7 4706.1 TRUE FALSE FALSE 4615.35221 4707.654421 3932.268704 4448.441949 3231.514834 2976.714653 3153.812013 3168.086007 4015.285388 4583.834844 1.006875764 1.027012225 0.857855668 0.970462964 0.704980643 0.649393958 0.688029155 0.69114314 0.875966418 1 12.16233935 -8.816295041 1.675336193 0.998481268 0.667278826 0.801704941 0.06396796 0.075444489 0.428676044 0.007464842 0.016963839 1.53E-09 8.816295041 -0.331202443 DYSEADGLS(ph)ER ddPTM_HeLa_Romidepsin_16h_R1 2 DYSEADGLSER 11 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;Q4VXN2;Q4VXN7;Q4VXN6;Q4VXN5;Q4VXN1;Q4VXN0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 DYSEADGLS(1)ER;DYSEADGLS(1)ER ; 147.33 0.0024338 18663400 6625 6165.1 6440.9 3939.6 5988.4 5218.9 4430 4510.1 5805.3 6669.5 TRUE FALSE FALSE 6544.251952 6251.89244 6553.001163 4395.115088 5682.789602 4885.429133 4806.284089 4640.592628 5286.059428 6496.225429 1.007392989 0.962388468 1.008739804 0.676564435 0.874783313 0.752041195 0.739857959 0.714352154 0.813712438 1 12.66538598 -9.27219226 24.96924474 1.000201076 0.757748869 0.625099724 0.076717924 169.798307 394287.7251 0.00704376 0.010824845 5.34E-10 9.27219226 -0.242452207 DYSEADGLS(ph)ERTTPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 DYSEADGLSERTTPSK 16 1 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;Q4VXN2;Q4VXN7;Q4VXN6;Q4VXN5;Q4VXN1;Q4VXN0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 2 0 DYS(0.007)EADGLS(0.941)ERT(0.051)T(0.029)PS(0.972)K 109.79 0.00023551 0 2085.1 1737.8 1925.4 1648.3 1892.6 1778.9 1212.4 1357.2 2195.6 2149.6 TRUE FALSE FALSE 2059.685999 1762.264794 1958.910779 1838.884201 1796.01356 1665.234031 1315.381226 1396.468441 1999.220037 2093.753082 0.983729178 0.841677469 0.935597801 0.878271759 0.857796258 0.795334486 0.628240855 0.66696902 0.954849955 1 11.0318756 -6.965778721 0.334253009 1.00588997 0.233562734 0.851596975 0.046406964 1.714165418 0.116759487 0.01534735 0.556039514 1.08E-07 6.965778721 -0.772327236 EAAAALVEEETRR ddPTM_HeLa_Romidepsin_16h_R1 1 EAAAALVEEETRR 13 1 O75934 O75934 BCAS2 Pre-mRNA-splicing factor SPF27 0 0 117.27 0.0034833 4185400 2240.3 2338.4 1954 1893.6 2144.1 1937.1 1879.9 2517.5 2404.9 2223.9 FALSE FALSE TRUE 2212.994362 2371.320057 1988.00855 2112.546942 2034.678576 1813.325562 2039.578659 2590.339891 2189.799721 2166.122757 1.02163848 1.094730226 0.917772801 0.975266491 0.939318222 0.837129639 0.941580366 1.195841686 1.010930573 1 11.08089929 -9.735731048 24.99917639 1.016842122 0.959728304 0.096542031 0.089406807 440.8040148 428643.8071 0.013698915 0.01936894 1.84E-10 9.735731048 -0.057113818 EAADLDAVPMSLS(ph)YEELVRR ddPTM_HeLa_Romidepsin_16h_R1 1 EAADLDAVPMSLSYEELVRR 20 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;H0YC55 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 0 EAADLDAVPMS(0.003)LS(0.982)Y(0.015)EELVRR 70.315 0.008026 3255700 1084.9 904.28 896.79 1544.3 1392.9 1927.6 1287.5 1592.2 1159.3 1022.4 TRUE FALSE FALSE 1071.676822 917.0104776 912.3982538 1722.859232 1321.815115 1804.432581 1396.860218 1638.267795 1055.609304 995.8379006 1.076155889 0.920843118 0.916211618 1.730059913 1.327339635 1.811974198 1.402698388 1.645114927 1.060021218 1 9.959767114 -9.264976035 24.99985273 1.018245752 1.571865195 0.810534781 0.142050549 92.70627958 655320.5447 0.019575075 0.030654024 5.43E-10 9.264976035 0.553619443 EAAENSLVAYK ddPTM_HeLa_Romidepsin_16h_R1 2 EAAENSLVAYK 11 0 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 0 ; ; 158.41 0.016527 14798400 3866.7 3639.1 3310.8 3447.3 4162.5 3607 3066.6 3367.1 3343.3 3294.5 FALSE FALSE TRUE 3819.571173 3690.331345 3368.423085 3845.893046 3950.072093 3376.524341 3327.076927 3464.521726 3044.266875 3208.908415 1.190302333 1.150027009 1.049709948 1.198505083 1.230970655 1.052234562 1.036825143 1.079657403 0.948692353 1 11.6478669 -5.564041611 13.61715221 1.102162543 0.754691285 0 0.089410773 0 0 0.012126792 0 2.73E-06 5.564041611 -0.347471258 EAAEPLSEPKEDQEAAELLS(ph)EPEEESER ddPTM_HeLa_Romidepsin_16h_R1 3 EAAEPLSEPKEDQEAAELLSEPEEESER 28 1 A0A0A0MTR7;A0A0A0MTC1;Q63HN8;Q63HN8-4 A0A0A0MTR7 RNF213 E3 ubiquitin-protein ligase RNF213 1 0 EAAEPLSEPKEDQEAAELLS(0.999)EPEEES(0.001)ER;EAAEPLSEPKEDQEAAELLS(1)EPEEESER;EAAEPLSEPKEDQEAAELLS(0.709)EPEEES(0.29)ER ;; 138.56 1.32E-10 61938000 4285.72 3894.82 4251.91 3483.48 3372.8 4031.93 2667.158 3255.15 4339.59 3624.53 TRUE FALSE FALSE 4233.483996 3949.651378 4325.91271 3886.256348 3200.67343 3774.302685 2893.706334 3349.332629 3951.446202 3530.364188 1.199163534 1.118765988 1.225344605 1.100808908 0.906612819 1.069097261 0.819662273 0.948721563 1.119274384 1 11.7856013 -8.770187278 23.12763282 1.109662806 0.937217233 0.565633431 0.081211285 55.34363087 146318.3732 0.014569329 0.026745303 1.70E-09 8.770187278 -0.172445574 EAAFS(ph)PGQQDWSR ddPTM_HeLa_Romidepsin_16h_R1 4 EAAFSPGQQDWSR 13 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR;EAAFS(1)PGQQDWSR ;;; 178.14 7.81E-07 61843000 7243.89 8237 7081.9 7203 10396.2 11815 9387.3 10630.3 8323 7608.6 TRUE FALSE FALSE 7155.598682 8352.960702 7205.157499 8035.844751 9865.64312 11060.05963 10184.65703 10937.87096 7578.570035 7410.927475 0.965546985 1.12711408 0.972234248 1.084323761 1.331229209 1.492398849 1.37427563 1.475911213 1.022620996 1 12.85543839 -8.744179209 2.374384034 0.995504884 1.441100149 0.928581507 0.053704221 0.047732727 0.54895907 0.007831114 0.016782501 1.80E-09 8.744179209 0.445595265 EAAGGNDS(ph)SGATSPINPAVALE ddPTM_HeLa_Romidepsin_16h_R1 2 EAAGGNDSSGATSPINPAVALE 22 0 P32004-3;P32004-2;P32004;H3BLW5 P32004-3 L1CAM Neural cell adhesion molecule L1 1 0 EAAGGNDS(0.678)S(0.315)GAT(0.006)S(0.001)PINPAVALE;EAAGGNDS(0.956)S(0.043)GAT(0.002)SPINPAVALE ; 123.83 7.71E-05 6034000 732.64 1255.11 1259.64 896.17 996.92 1065.8 667.23 831.89 1052.41 860.43 TRUE FALSE FALSE 723.7103019 1272.779472 1281.563506 999.789392 946.0434524 997.6988197 723.9044995 855.9594246 958.2798138 838.0759046 0.863537894 1.518692358 1.52917355 1.192958044 1.128827887 1.190463554 0.863769613 1.021338783 1.143428428 1 9.710937105 -10.31693843 24.99992697 0.935559514 1.201572652 0.152053186 0.203106196 299.8347515 135061.8199 0.036216562 0.041415219 4.82E-11 10.31693843 0.266013137 EAAGGNDSSGATS(ph)PINPAVALE ddPTM_HeLa_Romidepsin_16h_R1 1 EAAGGNDSSGATSPINPAVALE 22 0 P32004-3;P32004-2;P32004;H3BLW5 P32004-3 L1CAM Neural cell adhesion molecule L1 1 0 EAAGGNDS(0.002)S(0.007)GAT(0.106)S(0.885)PINPAVALE 67.312 0.0049247 2326500 526.97 746.65 516.34 356.47 690.24 769.73 325.43 702.79 641.01 663.78 TRUE FALSE FALSE 520.5470869 757.1613583 525.3266811 397.6867386 655.0144772 720.5467372 353.0720161 723.1241198 583.6764602 646.5348999 0.805133779 1.171106708 0.81252641 0.615104828 1.013115421 1.11447462 0.546098928 1.118461076 0.902776417 1 9.336584438 -12.63024071 1.427979918 1.000421126 0.882082509 0 0.20345726 1.213436408 4.41964357 0.137351517 0.030823821 2.34E-13 12.63024071 -0.118338617 EAALPPVS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 4 EAALPPVSPLK 11 0 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK;EAALPPVS(1)PLK ;;; 151.7 0.0023051 1703190000 61818.2 57971.7 58682.2 41038.2 61683.5 66535 50755.7 63901.9 57024.4 57437.3 TRUE FALSE FALSE 61064.736 58787.82711 59703.53907 45783.22977 58535.56082 62283.62823 55066.88789 65750.80066 51923.99484 55945.07067 1.091512358 1.05081335 1.067181404 0.818360389 1.046304172 1.113299661 0.984302768 1.175274244 0.928124573 1 15.7717234 -7.248435869 23.86700565 1.033066112 1.175274416 0.216457895 0.084905806 1334.108449 2448578.228 0.010907241 0.25307729 5.64E-08 7.248435869 0.142208304 EAALPPVS(ph)PLKAALSEEELEK ddPTM_HeLa_Romidepsin_16h_R1 2 EAALPPVSPLKAALSEEELEK 21 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 EAALPPVS(1)PLKAALSEEELEK;EAALPPVS(0.999)PLKAALS(0.001)EEELEK ; 96.561 0.00024964 59533000 6603.1 6680.5 6788.6 9107.2 7021.8 6653 8217.6 7685.7 7353.4 6500 TRUE FALSE FALSE 6522.618877 6774.548254 6906.752735 10160.21731 6663.451344 6227.894772 8915.602739 7908.073603 6695.693487 6331.129063 1.030245761 1.070037933 1.090919592 1.604803379 1.052490208 0.983694174 1.408216868 1.249077933 1.057582845 1 12.62824709 -9.5077609 24.25747274 1.021797471 1.25174859 0.294770257 0.162741651 426.1206594 683736.2247 0.024522612 0.036677313 3.11E-10 9.5077609 0.229951119 EAALPPVS(ph)PLKAALSEEELEKK ddPTM_HeLa_Romidepsin_16h_R1 1 EAALPPVSPLKAALSEEELEKK 22 2 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 EAALPPVS(1)PLKAALSEEELEKK 100.67 0.00021525 100740000 8323.5 10107 7095.5 12242 8897.7 8693.6 9269.2 9466.6 9900.4 8338.8 TRUE FALSE FALSE 8222.04998 10249.28661 7218.994201 13657.47764 8443.617167 8138.107017 10056.52562 9740.501135 9014.883428 8122.156774 1.012298852 1.261892241 0.888802618 1.681508745 1.039578206 1.001963794 1.238159506 1.199250569 1.109912512 1 12.98764716 -10.28325759 20.49501925 1.005807656 1.183979947 0.091912088 0.202187771 108.5014191 101920.4199 0.031851635 0.036462133 5.21E-11 10.28325759 0.178172291 EAALSTALSEK ddPTM_HeLa_Romidepsin_16h_R1 1 EAALSTALSEK 11 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 128.81 0.020961 357580 234.99 161.81 246.95 207.29 161.64 328.03 451.76 280.01 339.37 289.64 FALSE FALSE TRUE 232.1258515 164.0879654 251.2480612 231.2578451 153.3909076 307.0699417 490.1324831 288.1116476 309.0158972 282.115111 0.822805452 0.581634797 0.890587038 0.819728671 0.543717446 1.0884562 1.737349273 1.021255637 1.095353936 1 8.140140133 -7.995581335 24.96118883 0.856326405 1.38770269 0.491015585 0.226081648 71.68848444 404957.5748 0.028785449 0.085873972 1.01E-08 7.995581335 0.531376285 EAALSTALSEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EAALSTALSEKR 12 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 1 ; EAALSTALSEK(1)R;EAALSTALSEK(1)R 185.99 8.07E-07 7201800 1194.47 909.9 1216.08 1200.04 3245.9 2293.7 1985.39 2422.6 2582.2 2072.9 FALSE TRUE FALSE 1179.91134 922.7095961 1237.245362 1338.794271 3080.249611 2147.139973 2154.028977 2492.694109 2351.241565 2019.045759 0.584390589 0.457002815 0.612787183 0.663082679 1.525596731 1.063442947 1.066854957 1.234590201 1.164531093 1 10.97945789 -8.782163662 24.99988191 0.745571597 1.200125252 0.511076395 0.227488716 155.8623011 188017.6192 0.034445892 0.062487354 1.65E-09 8.782163662 0.454553654 EAANEAGDSS(ph)QDEAEDDVK ddPTM_HeLa_Romidepsin_16h_R1 1 EAANEAGDSSQDEAEDDVK 19 0 A0A0C4DH01;Q9NVU0-3;Q9NVU0-2;Q9NVU0-5;Q9NVU0-4;Q9NVU0 A0A0C4DH01 POLR3E DNA-directed RNA polymerase III subunit RPC5 1 0 EAANEAGDS(0.083)S(0.917)QDEAEDDVK 208.4 4.80E-22 8390000 4171 4419.4 3934.7 3215.4 3542.3 3031.3 2714.6 3047.9 4674.1 4311.7 TRUE FALSE FALSE 4120.162248 4481.616429 4003.181803 3587.179677 3361.523213 2837.609713 2945.178056 3136.086178 4256.03679 4199.681412 0.981065429 1.067132477 0.95321083 0.854155191 0.800423385 0.675672613 0.701286066 0.746743829 1.013418965 1 12.03606417 -8.923129077 1.497616254 0.996897373 0.708911018 0.936463601 0.033933734 0.065722366 0.295281197 0.00535925 0.011898748 1.19E-09 8.923129077 -0.287986355 EAARS(ph)PDKPGGS(ph)PSASR ddPTM_HeLa_Romidepsin_16h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 2 0 EAARS(1)PDKPGGS(0.928)PS(0.072)ASR 106.47 0.0024022 47341000 6261.3 6031.1 6449.7 5771 5383.6 5299.4 3971.7 4370 6240.8 6585.8 TRUE FALSE FALSE 6184.984867 6116.005984 6561.954323 6438.270173 5108.854803 4960.785443 4309.056099 4496.439055 5682.607218 6414.699967 0.964189268 0.953436017 1.022955767 1.003674405 0.796429269 0.773346449 0.6717471 0.700958592 0.885872644 1 12.64716607 -8.549136686 2.124404822 0.985412827 0.705355393 0.867733663 0.045475966 0.05514696 0.495820752 0.005038906 0.012438986 2.82E-09 8.549136686 -0.280057434 EAARS(ph)PDKPGGSPSASR ddPTM_HeLa_Romidepsin_16h_R1 1 EAARSPDKPGGSPSASR 17 2 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 0 EAARS(1)PDKPGGSPSASR 82.578 0.014671 36702000 1361.7 1580.5 1256.2 1253.6 1176 1044.5 1195 1328.7 1626.6 1592 TRUE FALSE FALSE 1345.103077 1602.75032 1278.063634 1398.54713 1115.984332 977.759821 1296.50327 1367.143838 1481.112822 1550.63961 0.867450481 1.033605945 0.824217068 0.901916294 0.719692909 0.630552589 0.836108701 0.881664462 0.95516251 1 10.59864771 -9.170834017 1.726209582 0.94087123 0.767346053 0.467799072 0.084764707 0.263626719 1.536758478 0.014653016 0.027421685 6.75E-10 9.170834017 -0.173525176 EAASS(ph)PAGEPLR ddPTM_HeLa_Romidepsin_16h_R1 3 EAASSPAGEPLR 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 EAAS(0.081)S(0.919)PAGEPLR;EAAS(0.03)S(0.97)PAGEPLR;EAAS(0.226)S(0.774)PAGEPLR ;; 145.81 0.001505 93898000 11399.5 11426.6 10539 11088.6 10045.8 10506.5 8759.1 10088.8 11377.3 11283.4 TRUE FALSE FALSE 11260.55851 11587.46397 10722.42687 12370.71611 9533.12534 9835.168558 9503.097735 10380.70351 10359.68579 10990.25564 1.024594775 1.054339804 0.975630342 1.125607675 0.867416159 0.89489898 0.864683957 0.944537038 0.942624642 1 13.42393732 -8.73502382 24.99997474 1.019571049 0.891013612 0.611162192 0.049842163 92.18418649 87243.73313 0.005792952 0.011583202 1.84E-09 8.73502382 -0.128557437 EAASS(ph)PAGEPLRK ddPTM_HeLa_Romidepsin_16h_R1 1 EAASSPAGEPLRK 13 1 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 EAAS(0.074)S(0.926)PAGEPLRK 182.23 6.64E-07 4785300 3122.5 3065.7 2472.4 1817.8 2891.4 2734.2 2395 2786.4 3081.5 3073 TRUE FALSE FALSE 3084.441769 3108.859005 2515.431085 2027.982589 2743.841069 2559.493444 2598.43124 2867.020088 2805.882922 2993.163017 1.03049575 1.03865342 0.840392278 0.677538302 0.91670285 0.85511328 0.868122192 0.957856312 0.937430707 1 11.54745514 -9.758534697 24.99736622 1.016622099 0.848393266 0.494008594 0.073187171 39.90900682 343449.8815 0.010899049 0.015028218 1.74E-10 9.758534697 -0.168228833 EAASSSSGTQPAPPAPAS(ph)PWDSKK ddPTM_HeLa_Romidepsin_16h_R1 2 EAASSSSGTQPAPPAPASPWDSKK 24 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 EAASSSSGTQPAPPAPAS(0.99)PWDS(0.01)KK;EAASSSSGTQPAPPAPAS(0.969)PWDS(0.031)KK ; 144.55 1.21E-07 102133000 6948.3 6783.4 7022.5 7314.5 6304.9 5283.9 5208.1 5378.6 7348 7060.9 TRUE FALSE FALSE 6863.611447 6878.896883 7144.723667 8160.236906 5983.137426 4946.275843 5650.475884 5534.221305 6690.776477 6877.4568 0.99798685 1.000209392 1.038861293 1.186519544 0.869963651 0.719201296 0.821593803 0.804690086 0.972856198 1 12.74765946 -8.532606857 24.99544073 1.014721772 0.787267844 0.770060941 0.062186956 71.56612593 183881.896 0.008787383 0.017591283 2.93E-09 8.532606857 -0.227453928 EAATQEDPEQLPELEAHGVS(ph)ES(ph)EGEERPVAEEEILLR ddPTM_HeLa_Romidepsin_16h_R1 1 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;X6RJY0;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 2 0 EAATQEDPEQLPELEAHGVS(1)ES(1)EGEERPVAEEEILLR 50.522 0.0028143 2564800 582.27 637.11 681.19 381.85 582.21 377.88 321.6 547.24 665.47 511.84 TRUE FALSE FALSE 575.1730693 646.0792513 693.0458262 426.0012937 552.4976512 353.7346876 348.916696 563.073526 605.9486965 498.542323 1.15370961 1.295936617 1.390144415 0.854493739 1.108226174 0.709537929 0.699873772 1.129439769 1.215440833 1 8.961572175 -8.278040962 23.84084579 1.10103368 0.831642828 0.344950317 0.181502929 386.4426968 554954.128 0.025979274 0.058269748 5.27E-09 8.278040962 -0.269390852 EAATQEDPEQLPELEAHGVS(ph)ESEGEERPVAEEEILLR ddPTM_HeLa_Romidepsin_16h_R1 2 EAATQEDPEQLPELEAHGVSESEGEERPVAEEEILLR 37 1 Q9BVJ6-3;Q9BVJ6;X6RJY0;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 EAATQEDPEQLPELEAHGVS(0.758)ES(0.242)EGEERPVAEEEILLR;EAATQEDPEQLPELEAHGVS(0.773)ES(0.227)EGEERPVAEEEILLR ; 64.045 0.00013814 60542000 2887.34 2345.9 2193.38 2301.33 2410.72 2509.47 2521.08 2147.66 2730.43 2735.78 TRUE FALSE FALSE 2852.147989 2378.925642 2231.554859 2567.420603 2287.691963 2349.122966 2735.220472 2209.799154 2486.213502 2664.704041 1.070343252 0.892754169 0.837449422 0.963491841 0.858516341 0.881569934 1.026463138 0.829285024 0.933016749 1 11.37975959 -10.25376236 24.84409657 1.033217647 0.901387699 0.303041556 0.066041555 304.2849084 984717.1727 0.009596276 0.011635108 5.57E-11 10.25376236 -0.131829948 EAATRNMEK(ac)IQVIK ddPTM_HeLa_Romidepsin_16h_R1 2 EAATRNMEKIQVIK 14 2 B1AK45;B1AK43;B1AK44;Q9UI95 B1AK45 MAD2L2 Mitotic spindle assembly checkpoint protein MAD2B 0 1 ; EAATRNMEK(1)IQVIK;EAATRNMEK(1)IQVIK 57.106 0.020832 661670 0 0 0 1589.96 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 1773.798656 0 0 0 0 0 0 0 EAAVSASDILQESAIHS(ph)PGTVEK ddPTM_HeLa_Romidepsin_16h_R1 3 EAAVSASDILQESAIHSPGTVEK 23 0 F5H3K2;F5H8B7;E7ENF1;G5EA44;F5H7W8;Q96C57 F5H3K2 C12orf43 Uncharacterized protein C12orf43 1 0 EAAVSASDILQES(0.001)AIHS(0.995)PGT(0.004)VEK;EAAVSASDILQES(0.001)AIHS(0.999)PGT(0.001)VEK;EAAVSASDILQES(0.001)AIHS(0.998)PGT(0.001)VEK ;; 191.71 4.61E-20 115638000 8387.6 8383 8074.3 7639.3 12042.4 11352.2 10030.3 9805 11742.8 9649.3 TRUE FALSE FALSE 8285.368705 8501.016094 8214.829804 8522.59181 11427.83139 10626.83106 10882.27343 10088.69221 10692.49456 9398.609795 0.881552579 0.904497184 0.874047331 0.906792813 1.215906569 1.130681163 1.157859904 1.073423881 1.137667675 1 13.19823166 -8.769221531 24.99996927 0.931302132 1.144439692 0.57494229 0.080559714 63.15232016 202875.7917 0.008812669 0.016190574 1.70E-09 8.769221531 0.21313756 EAAYHPEVAPDVR ddPTM_HeLa_Romidepsin_16h_R1 2 EAAYHPEVAPDVR 13 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 ; ; 91.307 0.0099646 15447100 9199.4 8080.3 8043.2 9553.8 9479.7 10066.5 7916.1 8075.3 9637.9 8578.5 FALSE FALSE TRUE 9087.274174 8194.054675 8183.188522 10658.45531 8995.915535 9423.283138 8588.493336 8308.946065 8775.862085 8355.629333 1.087563104 0.980662778 0.979362319 1.275601739 1.076629321 1.127776588 1.027869116 0.994412956 1.050293369 1 13.02853278 -13.08725554 0.435742192 0.949809645 1.076484824 0.024727582 0.084918077 7.577783983 1.156887775 0.476670365 0.023972946 8.18E-14 13.08725554 0.126675179 EADDDEEVDDNIPEMPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EADDDEEVDDNIPEMPSPK 19 0 P26358;P26358-3;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 0 EADDDEEVDDNIPEMPS(1)PK;EADDDEEVDDNIPEMPS(1)PK ; 108.96 0.00026377 111978000 5893.2 5021.8 4934.9 4376.5 3266 2714.3 2833.3 2942 5416.8 5595.4 TRUE FALSE FALSE 5821.371412 5092.497032 5020.789864 4882.531522 3099.323833 2540.86499 3073.960431 3027.122128 4932.307841 5450.030701 1.068135526 0.934397861 0.921240657 0.895872297 0.568680069 0.466211133 0.56402626 0.555432124 0.905005515 1 12.41204864 -8.883332288 1.767020533 1.02028828 0.519450251 0.908036679 0.063887702 0.057742538 0.364292214 0.00906214 0.019469079 1.31E-09 8.883332288 -0.500838029 EADDDEEVDDNIPEMPS(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 3 EADDDEEVDDNIPEMPSPKK 20 1 P26358;P26358-3;P26358-2 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 0 EADDDEEVDDNIPEMPS(1)PKK;EADDDEEVDDNIPEMPS(1)PKK;EADDDEEVDDNIPEMPS(1)PKK ;; 117.26 0.00021575 67131100 11581.5 9652.1 9993.4 10308.3 6408.9 5704.3 5353.1 5299.4 12445.5 10203.5 TRUE FALSE FALSE 11440.34022 9787.982517 10167.33093 11500.19415 6081.829918 5339.81364 5807.79218 5452.729778 11332.34331 9938.411599 1.151123609 0.984863871 1.023033795 1.157146093 0.611951906 0.53729045 0.584378311 0.548652038 1.140256991 1 13.27879958 -8.72353598 7.205926763 1.067137019 0.566248789 0.943170166 0.060778451 0.037571919 5.482969102 0.010015957 0.019928657 1.89E-09 8.72353598 -0.50088823 EADDIVNWLK ddPTM_HeLa_Romidepsin_16h_R1 1 EADDIVNWLK 10 0 P07237;I3L312;I3L3P5 P07237 P4HB Protein disulfide-isomerase 0 0 157.34 0.029925 16510000 3303.5 3249.6 2739.7 2453.1 3298 3646.6 3123 4009.5 3340.2 3289.7 FALSE FALSE TRUE 3263.235671 3295.347954 2787.383329 2736.738964 3129.690753 3413.594029 3388.267542 4125.508557 3041.444146 3204.23312 1.018413938 1.028435769 0.869906535 0.854101079 0.976736285 1.065338851 1.057434779 1.287518231 0.949195652 1 11.6457634 -6.947034462 1.295932551 0.988097087 1.635489683 0.694016152 0.063449128 1.373299312 1.152834445 0.010197517 1.427991698 1.13E-07 6.947034462 0.647392596 EADLVFISVNT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 EADLVFISVNTPTK 14 0 O60701;E7ER83;E7ETF4;E7EV97 O60701 UGDH UDP-glucose 6-dehydrogenase 1 0 EADLVFIS(0.023)VNT(0.976)PT(0.001)K;EADLVFIS(0.086)VNT(0.889)PT(0.025)K ; 217.79 4.22E-24 18284300 14860.4 12915.7 14531.8 8354.6 13043.6 12521 11005 12490.5 14790.3 14473.4 TRUE FALSE FALSE 14679.27573 13097.52756 14784.71988 9320.598162 12377.93642 11720.94851 11939.76443 12851.89291 13467.41853 14097.37898 1.041276946 0.929075368 1.048756645 0.661158232 0.878031046 0.831427496 0.846949241 0.911651232 0.955313647 1 13.78313934 -9.293743935 24.99941916 1.013762655 0.830225488 0.579183006 0.071091255 291.3207361 225442.5996 0.009938907 0.015182649 5.08E-10 9.293743935 -0.183537167 EADQPTTEPGMVLDS(ph)VEAGDTTPPTKR ddPTM_HeLa_Romidepsin_16h_R1 1 EADQPTTEPGMVLDSVEAGDTTPPTKR 27 1 A0A0J9YVR0;A0A0J9YWV8 A0A0J9YVR0 1 0 EADQPTT(0.001)EPGMVLDS(0.964)VEAGDT(0.015)T(0.015)PPT(0.005)KR 72.009 0.00013904 19473000 2551.8 2635.4 2675.4 2320.5 2941.3 3246.3 3102.4 3144 2781.9 2522 TRUE FALSE FALSE 2520.69768 2672.50123 2721.964215 2588.807128 2791.194485 3038.871907 3365.917779 3234.96668 2533.079897 2456.478076 1.026142958 1.087940192 1.108075924 1.053869421 1.136258659 1.237084888 1.370220972 1.316912498 1.031183596 1 11.26237565 -8.003988945 0.565597597 1.011793185 1.462558321 0.901761406 0.038283063 0.370286776 0.130288644 0.007730103 0.093490077 9.91E-09 8.003988945 0.450765136 EADQPTTEPGMVLDSVEAGDTT(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 2 EADQPTTEPGMVLDSVEAGDTTPPTK 26 0 A0A0J9YVR0;A0A0J9YWV8 A0A0J9YVR0 1 0 EADQPTTEPGMVLDS(0.046)VEAGDT(0.394)T(0.433)PPT(0.127)K;EADQPTTEPGMVLDS(0.107)VEAGDT(0.237)T(0.512)PPT(0.143)K ; 60.197 0.0016795 39562000 13038.8 13946.4 13102.5 11304.4 14734.8 15719.5 14358.7 17240.2 16536.7 16033.6 TRUE FALSE FALSE 12879.87809 14142.73779 13330.54352 12611.46792 13982.82817 14715.07468 15578.32762 17739.01799 15057.61614 15617.04476 0.824732098 0.905596289 0.853589378 0.807545096 0.895356861 0.94224451 0.997520841 1.135875465 0.96417833 1 13.93083386 -7.341464846 1.518061922 0.900565167 1.202336351 0.641381355 0.055793107 0.625531026 1.477410326 0.010847571 0.268323171 4.56E-08 7.341464846 0.301771184 EAEAAIYHLQLFEELR ddPTM_HeLa_Romidepsin_16h_R1 3 EAEAAIYHLQLFEELR 16 0 P14618;B4DNK4;P14618-3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ;; ;; 156.72 9.87E-05 25681200 4520.41 3856.45 4599.9 3395.36 4181.59 4564.89 3854.44 4740.63 4414.8 4588.53 FALSE FALSE TRUE 4465.313504 3910.741204 4679.95933 3787.947499 3968.187859 4273.208262 4181.836037 4877.79265 4019.929231 4469.319329 0.999103706 0.875019419 1.047130219 0.847544608 0.887872977 0.956120596 0.93567627 1.091394973 0.899449991 1 12.12583941 -10.44259811 24.99958039 0.999606077 0.945383671 0 0.077294025 161.4258961 50267.47316 0.011344348 0.012972709 3.61E-11 10.44259811 -0.054222406 EAEAAIYHLQLFEELRR ddPTM_HeLa_Romidepsin_16h_R1 8 EAEAAIYHLQLFEELRR 17 1 P14618;B4DNK4;P14618-3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ;;;;;;; ;;;;;;; 149.32 2.44E-05 242287420 30685.8 27315.087 24299.9 29701.3 30225.2 29659.2 23795.7 28039.4 28908.2 24903.8 FALSE FALSE TRUE 30311.78967 27699.62951 24722.82957 33135.50405 28682.69526 27764.07284 25816.90616 28850.6758 26322.57819 24256.79569 1.249620521 1.141932754 1.019212508 1.36602973 1.182460191 1.144589467 1.064316429 1.189385283 1.085163042 1 14.56610136 -12.4890668 1.203770384 0.998983603 1.175272613 0.21057172 0.093235117 0.442111038 1.13572525 0.065016062 0.015477884 3.24E-13 12.4890668 0.17628901 EAEALLQSMGLTPESPIVPPPMS(ph)PSSK ddPTM_HeLa_Romidepsin_16h_R1 2 EAEALLQSMGLTPESPIVPPPMSPSSK 27 0 E7EQL5;Q13409-2;E7EV09;Q13409-3;Q13409-6;E7EQU2;E9PGG1;E7ETL8 E7EQL5 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 0 EAEALLQSMGLTPES(0.001)PIVPPPMS(0.626)PS(0.168)S(0.204)K;EAEALLQSMGLTPESPIVPPPMS(0.657)PS(0.172)S(0.172)K ; 71.408 4.76E-05 218720000 7808.8 7017.4 7613 7167.9 8599.9 8948.6 6784 8287 7956.6 7459.8 TRUE FALSE FALSE 7713.623342 7116.191141 7745.501071 7996.686324 8161.015012 8376.81334 7360.232791 8526.77127 7244.941768 7265.993321 1.06160617 0.979383111 1.06599342 1.100563401 1.123179537 1.152879306 1.012969936 1.173517631 0.997102729 1 12.82694432 -9.424503106 3.269866199 1.026040211 1.110024917 0.518078857 0.045524114 0.180341601 3.665319218 0.006968388 0.01084547 3.76E-10 9.424503106 0.083984706 EAEDS(ph)DSDDNIKR ddPTM_HeLa_Romidepsin_16h_R1 1 EAEDSDSDDNIKR 13 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 EAEDS(1)DSDDNIKR 134.88 0.00050444 16232000 2799.5 2955.5 2592 2094.6 2511.8 2264.2 2046.2 1799.3 2647.7 2923.6 TRUE FALSE FALSE 2765.378617 2997.107607 2637.112673 2336.787507 2383.613473 2119.524927 2220.004177 1851.359907 2410.883081 2847.644451 0.971110918 1.052486593 0.926068095 0.820603677 0.837047432 0.744308134 0.779593174 0.650137311 0.84662363 1 11.47555331 -8.832576912 0.851072106 0.993414309 0.706346168 0.715266917 0.063008984 0.152555261 0.207184644 0.007476091 0.024644546 1.47E-09 8.832576912 -0.287068141 EAEEES(ph)S(ph)GGEEEDEDENIEVVYSK ddPTM_HeLa_Romidepsin_16h_R1 1 EAEEESSGGEEEDEDENIEVVYSK 24 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 2 0 EAEEES(1)S(1)GGEEEDEDENIEVVYSK 71.556 0.0048324 5859500 5195.1 5690.6 5162.1 4614.6 5922.1 5591.3 4374.7 5337.2 6113 6484.7 TRUE FALSE FALSE 5131.780123 5770.712416 5251.944185 5148.161764 5619.873139 5234.033975 4746.286909 5491.623461 5566.23797 6316.226559 0.812475625 0.913632904 0.831500285 0.815069206 0.889751672 0.828664698 0.751443423 0.869446878 0.881260024 1 12.62484721 -12.52030684 0.613287294 1.038877233 0.833544079 0.233883171 0.056558547 0.635050362 0.297148311 0.076599911 0.009314672 3.02E-13 12.52030684 -0.205333154 EAEEGEDDRDS(ph)ANGEDDS ddPTM_HeLa_Romidepsin_16h_R1 5 EAEEGEDDRDSANGEDDS 18 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;P07910-3;P07910-4 P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 EAEEGEDDRDS(0.604)ANGEDDS(0.396);EAEEGEDDRDS(0.81)ANGEDDS(0.19);EAEEGEDDRDS(0.844)ANGEDDS(0.156);EAEEGEDDRDS(0.998)ANGEDDS(0.002);EAEEGEDDRDS(0.984)ANGEDDS(0.016) ;;;; 149.24 0.00035092 226336000 9092.42 9316.1 9669.74 4404.9 8562.01 9544.88 8194.18 9024.96 8181.94 9737.89 TRUE FALSE FALSE 8981.598088 9447.2523 9838.037768 4914.215264 8125.05868 8934.992973 8890.193445 9286.082979 7450.126794 9484.898214 0.946936687 0.996030963 1.037231771 0.518109436 0.856631088 0.942023074 0.937299826 0.979038759 0.785472509 1 13.21141658 EAEEGPTGASES(ph)QDSPRK ddPTM_HeLa_Romidepsin_16h_R1 1 EAEEGPTGASESQDSPRK 18 1 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 0 EAEEGPTGAS(0.102)ES(0.496)QDS(0.402)PRK 67.214 0.007935 3072200 797.83 804.98 812.37 743.85 704.22 573.95 486.76 732.94 893.81 601.11 TRUE FALSE FALSE 788.1057411 816.3125296 826.5089591 829.8574369 668.2810256 537.2764473 528.1053823 754.1464625 813.865395 585.4930755 1.34605476 1.394230886 1.411646002 1.417365075 1.141398683 0.917647825 0.901983993 1.288053598 1.390051273 1 9.193508298 -8.516770089 24.10749665 1.225267043 1.023673861 0.283099337 0.169889051 234.4467702 925228.8843 0.029574533 0.060859323 3.04E-09 8.516770089 -0.201593182 EAEEGPTGASESQDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EAEEGPTGASESQDSPR 17 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 0 EAEEGPTGASESQDS(1)PR;EAEEGPT(0.001)GAS(0.057)ES(0.058)QDS(0.885)PR ; 311.24 2.68E-158 18332400 6257.7 5750.2 5180.4 5496.4 4395.5 4334 4136.1 4415.9 6675.7 6167.7 TRUE FALSE FALSE 6181.428745 5831.151467 5270.562689 6131.919629 4171.181233 4057.071387 4487.420231 4543.667099 6078.608672 6007.462265 1.028958398 0.970651368 0.877335963 1.020717128 0.694333322 0.675338639 0.746974352 0.756337185 1.011843005 1 12.55253997 -8.761644835 24.99999779 0.999486508 0.71723307 0.885435337 0.04681639 1.306687164 159028.785 0.007463207 0.014173476 1.73E-09 8.761644835 -0.282253438 EAEQAASEAAGGDT(ph)T(ph)PGSSPSSLYYEEPLGQPPR ddPTM_HeLa_Romidepsin_16h_R1 1 EAEQAASEAAGGDTTPGSSPSSLYYEEPLGQPPR 34 0 Q86TC9;Q86TC9-3 Q86TC9 MYPN Myopalladin 2 0 EAEQAASEAAGGDT(0.335)T(0.537)PGS(0.402)S(0.402)PS(0.213)S(0.103)LY(0.007)Y(0.001)EEPLGQPPR 86.191 3.58E-09 4480600 1363.5 1321.3 1363.3 1411.6 1086.5 960.11 857.48 938.3 1357.1 1378.4 TRUE FALSE FALSE 1346.881138 1339.901296 1387.027665 1574.815834 1031.051851 898.7620696 930.3143298 965.4482301 1235.717577 1342.588969 1.003196934 0.997998141 1.033099256 1.172969442 0.767957934 0.669424589 0.692925647 0.719094415 0.920399024 1 10.39080198 -8.61197243 6.303076843 1.014225659 0.697712969 0.863989504 0.060492803 0.046803351 2.710170447 0.007670457 0.015460569 2.44E-09 8.61197243 -0.31651269 EAEQAASEAAGGDTTPGS(ph)S(ph)PSSLYYEEPLGQPPR ddPTM_HeLa_Romidepsin_16h_R1 1 EAEQAASEAAGGDTTPGSSPSSLYYEEPLGQPPR 34 0 Q86TC9;Q86TC9-3 Q86TC9 MYPN Myopalladin 2 0 EAEQAASEAAGGDT(0.033)T(0.029)PGS(0.602)S(0.602)PS(0.294)S(0.337)LY(0.085)Y(0.018)EEPLGQPPR 111.61 1.14E-13 4624800 820 779.74 836.48 1024 668.24 476.17 310.02 496.45 906.8 707.58 TRUE FALSE FALSE 810.0055246 790.7172002 851.0385835 1142.399698 634.1372193 445.7442738 336.3530911 510.8139975 825.6935369 689.1969696 1.175288866 1.147302201 1.234826357 1.657580849 0.920110284 0.6467589 0.48803623 0.741172727 1.198051607 1 9.428772548 -8.398988588 3.955456405 1.142861913 0.61363117 0.670184242 0.184767256 0.124889374 3.368023792 0.028797376 0.067198405 3.99E-09 8.398988588 -0.529230743 EAETEPHEGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 EAETEPHEGKR 11 1 P41223;P41223-2 P41223 BUD31 Protein BUD31 homolog 0 1 EAETEPHEGK(1)R 78.548 0.019801 623270 341.69 558.5 275.29 241.94 342.34 532.96 660.35 390.45 535.09 448.31 FALSE TRUE FALSE 337.5253509 566.3625777 280.081307 269.9142412 324.8691124 498.905576 716.4401125 401.7470547 487.2302102 436.6628416 0.77296559 1.297024898 0.641413192 0.618129631 0.743981584 1.142541862 1.64071692 0.920039482 1.115804149 1 8.770375958 -8.046280315 6.138124616 0.874176768 1.307477122 0.287893928 0.257234658 0.155516784 14.91088774 0.033610128 0.089305276 8.99E-09 8.046280315 0.433300354 EAETPQAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EAETPQAKK 9 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ; EAETPQAK(1)K;EAETPQAK(1)K 131.44 0.0013669 5691500 4328.2 4105.6 4598.4 4464.3 4069.4 4830.7 5114 1828.49 4532.5 4498.7 FALSE TRUE FALSE 4275.446234 4163.398745 4678.433223 4980.483371 3861.723333 4522.03386 5548.383032 1881.394473 4127.101848 4381.823125 0.975723143 0.950152168 1.067691025 1.136623553 0.881305161 1.031998264 1.266227064 0.4293634 0.941868654 1 12.09731554 -7.245034982 24.99951719 1.010546305 0.429362951 0.741648466 0.105539132 1236.268738 1883986.932 0.013496616 0.498667547 5.69E-08 7.245034982 -0.581183355 EAETQAEIR ddPTM_HeLa_Romidepsin_16h_R1 1 EAETQAEIR 9 0 O60447-2;O60447;A0A1B0GUF4 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 0 0 116.9 0.0011493 0 876.27 785.85 693.81 1400.2 4247.1 4428 3877.5 4064.9 914.91 795.18 FALSE FALSE TRUE 865.5896842 796.9132169 705.885472 1562.097712 4030.354639 4145.065091 4206.854753 4182.511468 833.0781582 774.521109 1.117580495 1.028910907 0.911383129 2.016856215 5.203673073 5.351778076 5.43155597 5.400125858 1.0756042 1 9.597160749 -8.825090857 3.165686543 1.052845476 5.415067238 0.997887342 0.094541208 0.009134565 0.185523282 0.017529523 0.034469887 1.50E-09 8.825090857 4.362221762 up EAFDEVDMAHR ddPTM_HeLa_Romidepsin_16h_R1 1 EAFDEVDMAHR 11 0 Q9NX46 Q9NX46 ADPRHL2 Poly(ADP-ribose) glycohydrolase ARH3 0 0 109.24 0.0013376 0 3078 2734.2 3025.4 3048.7 3056.5 3258.6 2997.2 3123.5 3258.1 3331.6 FALSE FALSE TRUE 3040.484152 2772.692139 3078.055818 3401.205039 2900.5154 3050.385977 3251.782093 3213.873544 2966.687376 3245.044552 0.936962222 0.854438851 0.948540388 1.048122756 0.893829146 0.940013589 1.002076255 0.990394274 0.914220846 1 11.66402257 EAFEQPQT(ph)SSTPPRDLDSK ddPTM_HeLa_Romidepsin_16h_R1 1 EAFEQPQTSSTPPRDLDSK 19 1 P52564;A0A0A0MRF7;K7EIW3 P52564 MAP2K6 Dual specificity mitogen-activated protein kinase kinase 6 1 0 EAFEQPQT(0.299)S(0.299)S(0.201)T(0.201)PPRDLDSK 80.109 0.0048354 49276000 2938.3 3421.4 3218.7 3140.6 3710.9 4172.2 4251.5 4937.1 3461.1 3005.2 TRUE FALSE FALSE 2902.486869 3469.566559 3274.720123 3503.730949 3521.518926 3905.609885 4612.622304 5079.947199 3151.530548 2927.124471 0.991583002 1.185315689 1.118749871 1.196987345 1.203064291 1.334282134 1.575820349 1.735473585 1.076664344 1 11.51526838 -4 0.318568031 0.979449711 8.793466505 0.942221961 0.055547055 6.328028019 0.080711564 0.017025959 29.16518298 1.00E-04 4 7.814016794 EAFEQPQTSS(ph)TPPRDLDSK ddPTM_HeLa_Romidepsin_16h_R1 1 EAFEQPQTSSTPPRDLDSK 19 1 P52564;A0A0A0MRF7;K7EIW3 P52564 MAP2K6 Dual specificity mitogen-activated protein kinase kinase 6 1 0 EAFEQPQT(0.048)S(0.139)S(0.406)T(0.406)PPRDLDSK 83.082 0.0026852 47490000 4301.3 4367.9 4223 4406.2 4786.5 6041.9 5614 6587.5 4720.5 4498.4 TRUE FALSE FALSE 4248.874101 4429.391411 4296.499544 4915.665576 4542.227044 5655.842089 6090.85302 6778.098919 4298.286657 4381.53092 0.969723638 1.010923235 0.980593227 1.121905942 1.036675794 1.290836968 1.390119831 1.546970464 0.981001101 1 12.09721932 -7.746937571 0.813760949 0.986328074 1.677188443 0.958533626 0.039558199 0.164810734 0.119662081 0.005925054 0.087819427 1.79E-08 7.746937571 0.690860369 EAFSLFDKDGDGTITTK ddPTM_HeLa_Romidepsin_16h_R1 3 EAFSLFDKDGDGTITTK 17 1 P0DP25;P0DP24;P0DP23;E7EMB3;F8WBR5;M0QZ52;G3V479 P0DP25 CALM2;CALM3;CALM1 0 0 ;; ;; 115.31 0.0024073 120473500 4228.1 3947.4 4186.3 3672.1 3941.7 4431.2 3998.4 4606.2 3918.33 3453.4 FALSE FALSE TRUE 4176.566291 4002.971601 4259.160795 4096.68548 3740.54034 4148.060621 4338.023996 4739.47313 3567.864751 3363.68017 1.241665699 1.190057139 1.266220503 1.217917659 1.112038051 1.233191151 1.289666014 1.409014202 1.060702734 1 11.71582482 -16.36046819 0.18557707 5.70E-17 1.298064529 0.623726182 0.068983255 23.98748509 0.295577005 8.698841041 0.090586667 4.36E-17 16.36046819 1.298064529 EAGAGGLAIAVEGPSK ddPTM_HeLa_Romidepsin_16h_R1 2 EAGAGGLAIAVEGPSK 16 0 Q60FE5;P21333-2;P21333;H0Y5C6 Q60FE5 FLNA Filamin-A 0 0 ; ; 212.17 1.37E-27 923130 364.61 397.857 469.99 221.18 528.71 568.53 638.37 484.52 572.58 390.32 FALSE FALSE TRUE 360.1659931 403.4580413 478.1699788 246.7538723 501.7279558 532.2027678 692.5931319 498.5388218 521.3670107 380.1794301 0.947357917 1.061230591 1.25774816 0.649045826 1.319713577 1.399872601 1.821753301 1.31132508 1.371370909 1 8.570536666 -8.466740112 3.166905945 0.984571017 1.540577172 0.438167747 0.226192388 0.111287189 2.201202153 0.025035976 0.058711749 3.41E-09 8.466740112 0.556006155 EAGENAPVLS(ph)DDELVSMSVR ddPTM_HeLa_Romidepsin_16h_R1 1 EAGENAPVLSDDELVSMSVR 20 0 O60675 O60675 MAFK Transcription factor MafK 1 0 EAGENAPVLS(0.984)DDELVS(0.006)MS(0.01)VR 66.308 0.01551 7432000 2047 1769.4 1779.3 1922 2729.7 3508.4 3457.2 3598.3 1836.3 2027.6 TRUE FALSE FALSE 2022.050377 1794.30966 1810.26797 2144.230683 2590.393223 3284.224563 3750.854482 3702.411133 1672.056729 1974.92266 1.02386307 0.908546798 0.916627272 1.085728939 1.311642869 1.662963634 1.8992412 1.874711962 0.846644156 1 10.94758044 -8.32485592 1.506975281 0.995309361 1.906025733 0.971783495 0.06542671 0.037217464 0.158753015 0.007786018 0.027394359 4.73E-09 8.32485592 0.910716372 EAGENAPVLSDDELVSMS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 2 EAGENAPVLSDDELVSMSVR 20 0 O60675 O60675 MAFK Transcription factor MafK 1 0 EAGENAPVLS(0.081)DDELVS(0.109)MS(0.81)VR;EAGENAPVLS(0.076)DDELVS(0.112)MS(0.812)VR ; 83.087 0.004957 50232000 5212.1 5238.8 4629.9 5183.7 9048.4 9667.8 9431.9 11220.9 6486.1 5183.8 TRUE FALSE FALSE 5148.57292 5312.551964 4710.481467 5783.063784 8586.626384 9050.058781 10233.04535 11545.55904 5905.966971 5049.124129 1.019696246 1.052172977 0.932930415 1.145359796 1.700617011 1.792401722 2.026697124 2.28664591 1.169701283 1 12.30181743 -8.421271467 1.086393641 0.999525587 2.201540714 0.947594357 0.106965859 0.070244319 0.149625185 0.014453485 0.059704367 3.79E-09 8.421271467 1.202015126 up EAGEQGDIEPR ddPTM_HeLa_Romidepsin_16h_R1 1 EAGEQGDIEPR 11 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 0 152.64 0.023169 14034000 2352 2363.2 2461.5 2316.8 2479.6 2437.1 2111.5 2007.6 2426.1 2633.8 FALSE FALSE TRUE 2323.332919 2396.469192 2504.341375 2584.679317 2353.056759 2281.377175 2290.850757 2065.686739 2209.10354 2565.373496 0.90565094 0.934159956 0.976209265 1.00752554 0.917237495 0.889296307 0.892989173 0.80521871 0.861123553 1 11.32495317 -7.118651651 0.77572509 0.957303229 0.695594303 0.454959717 0.044257023 1.778589424 0.659136452 0.006943133 0.422725737 7.61E-08 7.118651651 -0.261708927 EAGS(ph)PAQEFK ddPTM_HeLa_Romidepsin_16h_R1 3 EAGSPAQEFK 10 0 Q5JSZ5;Q5JSZ5-5;Q5JT00 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 EAGS(1)PAQEFK;EAGS(1)PAQEFK;EAGS(1)PAQEFK ;; 151.16 0.0036709 286425000 20093.3 20078.4 13373.3 6026.1 12659.6 13342.3 12561.3 14780.8 22405 22010.3 TRUE FALSE FALSE 19848.39513 20361.06424 13606.05668 6722.866036 12013.53337 12489.77009 13628.25651 15208.45913 20401.04069 21438.46923 0.9258308 0.949744313 0.634656165 0.313588902 0.560372723 0.582586842 0.635691679 0.709400422 0.951609019 1 14.38791428 -9.720998303 4.295208884 0.963982933 0.558234149 0.793392987 0.096510996 0.068725901 2.7449984 0.01610041 0.022597995 1.90E-10 9.720998303 -0.405748784 EAGT(ph)PSLDSEAK ddPTM_HeLa_Romidepsin_16h_R1 4 EAGTPSLDSEAK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 EAGT(0.993)PS(0.007)LDSEAK;EAGT(0.998)PS(0.002)LDSEAK;EAGT(0.97)PS(0.03)LDSEAK;EAGT(0.973)PS(0.027)LDSEAK ;;; 180.61 2.62E-06 85684400 21765.2 22806.2 21317.5 18694.3 17315.7 13930 11221.2 11649.2 22765.6 22423.3 TRUE FALSE FALSE 21499.91737 23127.26628 21688.52215 20855.82293 16432.01522 13039.91796 12174.32845 11986.25122 20729.38772 21840.73943 0.984395123 1.058904913 0.99303058 0.954904617 0.752356177 0.597045626 0.557413749 0.548802446 0.949115655 1 14.41473408 -8.550835715 1.765150531 0.999230675 0.5536827 0.9815069 0.026308036 0.02717831 0.167733507 0.003473693 0.009216446 2.81E-09 8.550835715 -0.445547975 EAIEGTYIDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EAIEGTYIDKK 11 1 M0QZC5;P62280 M0QZC5 RPS11 40S ribosomal protein S11 0 1 ; EAIEGTYIDK(1)K;EAIEGTYIDK(1)K 202.56 7.04E-14 5439100 2414.7 2961.4 2772.3 2170.6 6841.2 5969.1 5639 5657.5 6879.5 5595.8 FALSE TRUE FALSE 2385.268708 3003.090667 2820.550719 2421.574985 6492.068036 5587.693774 6117.976519 5821.190836 6264.18029 5450.420309 0.437630233 0.550983318 0.517492332 0.444291421 1.191113284 1.025185849 1.122477932 1.068026043 1.149302244 1 12.41215177 -8.749512308 24.99505332 0.676752517 1.097719573 0.458595479 0.222636473 172.3981005 361285.0998 0.035447818 0.070453026 1.78E-09 8.749512308 0.420967056 EAIEGTYIDKK ddPTM_HeLa_Romidepsin_16h_R1 2 EAIEGTYIDKK 11 1 M0QZC5;P62280 M0QZC5 RPS11 40S ribosomal protein S11 0 0 ; ; 115.91 0.0076713 50432000 4686 4213.8 4112 3316.1 4380.4 4160.1 3713.5 4517 4582.9 4727.4 FALSE FALSE TRUE 4628.88523 4273.121987 4183.567635 3699.523085 4156.851842 3894.283036 4028.924597 4647.692268 4172.993946 4604.581467 1.00527817 0.928015286 0.908566319 0.803443942 0.902764317 0.845740935 0.874981717 1.009362589 0.906269978 1 12.16885431 -10.052815 2.305781751 1.002925736 0.884318374 0.217212501 0.058313667 0.162210577 1.696798626 0.008250788 0.010556115 8.85E-11 10.052815 -0.118607363 EAILAIHK ddPTM_HeLa_Romidepsin_16h_R1 1 EAILAIHK 8 0 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 84.743 0.0098739 2563500 2507.2 2751.3 5736.5 4816.2 5631.8 5349.2 4844.7 2296.6 3284.1 1906.5 FALSE FALSE TRUE 2476.641282 2790.032874 5836.341376 5373.071705 5344.388231 5007.403384 5256.208697 2363.048498 2990.361871 1856.968855 1.333701034 1.502466165 3.142939829 2.893463555 2.87801716 2.696546778 2.830531424 1.272529957 1.610345732 1 10.8587339 -9.893503771 5.087507043 1.169821858 2.652690741 0.593531515 0.50556914 0.089111371 3.692660062 0.077504064 0.102574943 1.28E-10 9.893503771 1.482868883 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAK ddPTM_HeLa_Romidepsin_16h_R1 3 HAPSPEPAVQGTGVAGVPEESGDAAAIPAK 30 0 P13051 P13051 UNG Uracil-DNA glycosylase 1 0 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK;HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAK ;; 123.91 3.45E-11 227121900 20304.4 17566.7 16139.3 11515.7 4951.44 4109.44 3768.11 3973.42 19200 18322.6 TRUE FALSE FALSE 20056.92216 17814.00446 16420.19775 12847.19942 4698.74954 3846.860047 4088.173169 4088.384639 17482.70391 17846.57621 1.123852661 0.998174902 0.920075512 0.719869137 0.263285769 0.215551711 0.229073248 0.229085097 0.979611087 1 14.12335971 -8.974188141 1.627580046 1.0536786 0.207769141 0.979211846 0.052861177 0.036729188 0.194329753 0.009370952 0.01964082 1.06E-09 8.974188141 -0.845909458 down EALAEAALES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EALAEAALESPR 12 0 O14745;J3QRP6;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 0 EALAEAALES(1)PR;EALAEAALES(1)PR ; 111.72 0.010099 6569700 1281.96 1290.81 1540.42 1198.53 1748.03 2351.31 2256.2 2225.72 1563.75 1682.74 TRUE FALSE FALSE 1266.334978 1308.982057 1567.230364 1337.109678 1658.821506 2201.06888 2447.841572 2290.117697 1423.884284 1639.022172 0.772616137 0.798635967 0.956198391 0.815797187 1.012079967 1.342915866 1.49347679 1.397246319 0.868740099 1 10.67861966 -8.282586945 2.545990459 0.882864307 1.444523727 0.922392448 0.070665323 0.072693687 0.921075794 0.013945125 0.038823779 5.22E-09 8.282586945 0.56165942 EALAEAALES(ph)PRPALVR ddPTM_HeLa_Romidepsin_16h_R1 5 EALAEAALESPRPALVR 17 1 O14745;J3QRP6;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 0 EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR;EALAEAALES(1)PRPALVR ;;;; 156.29 2.10E-05 2821914000 14066.9 14369.4 13735.7 12840 18891.9 21898.9 19761.1 20174.3 15505.8 14381 TRUE FALSE FALSE 13895.44721 14571.69279 13974.7641 14324.62121 17927.77585 20499.63097 21439.60734 20758.01154 14118.92241 14007.37955 0.992009045 1.040286853 0.997671552 1.022648181 1.279880779 1.463487935 1.530593732 1.481933967 1.00796315 1 13.77389947 -8.542156349 1.982754316 0.998898189 1.505891925 0.990475796 0.021364739 0.020133218 0.157159665 0.003171304 0.008063194 2.87E-09 8.542156349 0.506993736 EALAEAALESPRPALVR ddPTM_HeLa_Romidepsin_16h_R1 2 EALAEAALESPRPALVR 17 1 O14745;J3QRP6;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 0 ; ; 184.51 2.59E-09 11911400 3476.7 3228.5 2566.9 3069.3 4453 5772.6 4658.5 5509.3 3363.7 3177.6 FALSE FALSE TRUE 3434.324643 3273.950908 2611.575818 3424.186907 4225.746794 5403.74949 5054.192874 5668.702903 3062.842247 3095.045494 1.109620085 1.057803807 0.843792385 1.106344612 1.365326229 1.745935399 1.632994695 1.83154106 0.989595227 1 11.5957449 -8.513531567 2.195189493 1.037431449 1.735819039 0.936131803 0.084326411 0.05669975 0.540994637 0.013053831 0.032610371 3.07E-09 8.513531567 0.69838759 EALASLPSS(ph)PGLLQSLLER ddPTM_HeLa_Romidepsin_16h_R1 1 EALASLPSSPGLLQSLLER 19 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 0 EALASLPS(0.003)S(0.996)PGLLQS(0.001)LLER 204.81 2.51E-21 16287000 8364.9 8522 6287.4 6653.6 5692.7 6513.2 6374.1 7973.3 9635.4 9936.6 TRUE FALSE FALSE 8262.945381 8641.97294 6396.82956 7422.920538 5402.180277 6097.02754 6915.515895 8203.994856 8773.585692 9678.4457 0.853747145 0.892909172 0.660935625 0.766953783 0.558166099 0.629959368 0.714527529 0.847656236 0.906507715 1 13.24055966 -10.36066794 0.669761523 0.96923261 0.682983884 0.568230623 0.087525483 0.296281956 0.287405671 0.025871945 0.02868729 4.36E-11 10.36066794 -0.286248726 EALGLGPPAAQLT(ph)PPPAPVGLR ddPTM_HeLa_Romidepsin_16h_R1 2 EALGLGPPAAQLTPPPAPVGLR 22 0 A0A087WZ13;E9PAU2;Q8IY67-2;Q8IY67 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 0 EALGLGPPAAQLT(1)PPPAPVGLR;EALGLGPPAAQLT(1)PPPAPVGLR ; 172.81 1.04E-10 104919000 5512.6 5347.9 5038.4 3662.1 5258.7 5537.9 5410.6 5589.9 5519.7 5397.1 TRUE FALSE FALSE 5445.410311 5423.187877 5126.091238 4085.529233 4990.328916 5184.046063 5870.176229 5751.634937 5026.004208 5256.882564 1.035863032 1.031635729 0.975119983 0.777177193 0.94929435 0.986144545 1.116664897 1.094115166 0.956080747 1 12.35999179 -7.763183809 24.94180192 0.991729946 1.105390058 0.32657219 0.072989356 44.56946523 637306.425 0.011211863 0.036415571 1.73E-08 7.763183809 0.113660112 EALGQNEES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EALGQNEESPK 11 0 B8ZZS4;Q9H8Y5 B8ZZS4 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 0 EALGQNEES(1)PK 135.02 0.0040764 12785000 2866.1 2843.9 2926.9 1822.7 2815.8 2897.9 2863.2 3260.4 2652.6 2897.1 TRUE FALSE FALSE 2831.166871 2883.936499 2977.841467 2033.44915 2672.099219 2712.733543 3106.400137 3354.73453 2415.344812 2821.832924 1.00330776 1.022008239 1.055286244 0.72061288 0.946937431 0.961337406 1.100844813 1.188849453 0.855948909 1 11.46241686 -7.572955291 3.236340128 0.980797881 1.178964346 0.378474237 0.096685465 0.200104381 4.039973836 0.012601174 0.068389668 2.67E-08 7.572955291 0.198166464 EALKEAVILPIKFPHLFTGK ddPTM_HeLa_Romidepsin_16h_R1 1 EALKEAVILPIKFPHLFTGK 20 2 I3L4J1;Q9UN37;O75351 I3L4J1;O75351 VPS4A;VPS4B Vacuolar protein sorting-associated protein 4A;Vacuolar protein sorting-associated protein 4B 0 0 39.244 0.025939 726070 1065.6 580.3 1050.1 847.93 631.52 2720.4 1505.3 1396.3 1159.4 1076.8 FALSE FALSE TRUE 1052.612057 588.4694786 1068.37655 945.9716562 599.2911779 2546.57522 1633.160144 1436.699738 1055.70036 1048.824581 1.003611163 0.561075216 1.018641792 0.901935055 0.571393147 2.428027781 1.557133742 1.369818904 1.0065557 1 10.03455769 -8.274698838 24.99565679 0.936649782 1.762207548 0.649987349 0.305797581 357.2170027 673395.9597 0.041822486 0.094026578 5.31E-09 8.274698838 0.825557766 EALQDVEDENQ ddPTM_HeLa_Romidepsin_16h_R1 2 EALQDVEDENQ 11 0 P62258;P62258-2;I3L0W5 P62258 YWHAE 14-3-3 protein epsilon 0 0 ; ; 182.98 6.06E-05 42831000 11789.5 12566.7 12809.3 8446.5 12916.5 12789.1 10787.5 12125.7 12778.8 13134.8 FALSE FALSE TRUE 11645.80504 12743.61433 13032.24049 9423.124072 12257.32281 11971.91778 11703.78998 12476.538 11635.83212 12793.556 0.910286791 0.996096342 1.018656618 0.736552376 0.95808568 0.935777182 0.914819146 0.975220493 0.909507264 1 13.6431297 EALS(ph)GGEASLVEK ddPTM_HeLa_Romidepsin_16h_R1 2 EALSGGEASLVEK 13 0 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 EALS(1)GGEASLVEK;EALS(0.999)GGEAS(0.001)LVEK ; 154.13 0.00076865 9446700 4869.7 4641.5 4517.8 3109.6 4357.5 4899.5 3884.6 4407.5 4677.3 4734.6 TRUE FALSE FALSE 4810.346223 4706.843159 4596.430414 3469.146583 4135.120515 4586.437762 4214.557827 4535.024059 4258.950573 4611.594409 1.043098286 1.02065419 0.996711767 0.752266196 0.896679141 0.994544913 0.913904705 0.983396122 0.923531038 1 12.17104992 -9.499852677 24.76007463 1.020359479 0.908823994 0.266737371 0.069209919 500.9087797 538631.0151 0.009646369 0.014670564 3.16E-10 9.499852677 -0.111535485 EALTYDGALLGDR ddPTM_HeLa_Romidepsin_16h_R1 2 EALTYDGALLGDR 13 0 Q15056;Q15056-2 Q15056 EIF4H Eukaryotic translation initiation factor 4H 0 0 ; ; 202.65 2.59E-15 15877700 3245.5 3133 3130.3 2294.43 3196 3951 3553.4 3402.4 3740.9 3294.4 FALSE FALSE TRUE 3205.942598 3177.106456 3184.781558 2559.722792 3032.896194 3698.543851 3855.225707 3500.843076 3406.304535 3208.811013 0.999106082 0.990119531 0.992511415 0.797716906 0.945177569 1.152621278 1.201449911 1.09100943 1.061547259 1 11.64782311 -8.254014874 24.20368627 0.979631415 1.153669204 0.579071922 0.069477006 204.9037886 667977.2033 0.009682459 0.02412405 5.57E-09 8.254014874 0.174037789 EAMEDGEIDGNK ddPTM_HeLa_Romidepsin_16h_R1 3 EAMEDGEIDGNK 12 0 P19338;H7BY16 P19338 NCL Nucleolin 0 0 ;; ;; 150.35 0.0035962 14966900 6233.1 6956.3 6868.8 4660.84 6242.5 6869.5 5425.6 6117.4 7439.9 7228.9 FALSE FALSE TRUE 6157.12858 7054.230974 6988.348583 5199.748251 5923.921931 6430.56112 5886.450329 6294.397317 6774.45671 7041.092136 0.874456471 1.001866023 0.99250918 0.73848604 0.841335665 0.913290296 0.836013819 0.893951847 0.962131524 1 12.78158351 -9.288224396 24.99153992 0.948300184 0.847770683 0.52696544 0.056293077 618.3809753 576973.5407 0.010183272 0.015557788 5.15E-10 9.288224396 -0.100529502 EAMGIYISTLK ddPTM_HeLa_Romidepsin_16h_R1 1 EAMGIYISTLK 11 0 G3V438;H0YJG7;O95433-2;O95433;H0YJU2 G3V438 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 0 121.6 0.011843 443790 253.77 190.33 262.13 61.048 289.77 225.59 200.5 159.54 288.07 244.24 FALSE FALSE TRUE 250.6769536 193.0094707 266.6922627 68.106657 274.9819556 211.1755271 217.530465 164.1560382 262.3042977 237.8946096 1.053731121 0.81132343 1.121052146 0.286289198 1.155898219 0.887685212 0.914398461 0.690036813 1.102607151 1 7.894178772 -10.26244841 24.4992124 1.025373031 0.844822063 0.151674532 0.228954634 103.7066884 2517988.192 0.035312199 0.041618929 5.46E-11 10.26244841 -0.180550968 EANANGS(ph)SPEPVK ddPTM_HeLa_Romidepsin_16h_R1 3 EANANGSSPEPVK 13 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 EANANGS(0.5)S(0.5)PEPVK;EANANGS(0.738)S(0.262)PEPVK;EANANGS(0.5)S(0.5)PEPVK ;; 175.6 1.14E-05 188859000 18108.6 17079.4 17226.6 13120.1 15560.3 16325.6 14752.8 14959.6 19993.8 18719.8 TRUE FALSE FALSE 17887.88542 17319.84424 17526.42175 14637.10769 14766.19983 15282.44685 16005.90246 15392.43242 18205.50445 18233.4569 0.981047396 0.949893613 0.961223198 0.802760978 0.809840937 0.838154111 0.877831481 0.844186185 0.99846697 1 14.15430049 -9.36775999 4.339161757 0.986449172 0.836000526 0.902852373 0.023555579 0.053899916 1.71646782 0.004099231 0.006356609 4.29E-10 9.36775999 -0.150448647 EANANGSS(ph)PEPVK ddPTM_HeLa_Romidepsin_16h_R1 1 EANANGSSPEPVK 13 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 EANANGS(0.225)S(0.775)PEPVK 206.67 9.97E-17 127360000 10239 9950.6 10037 6672.4 8081.2 9066.1 7989.1 7946.1 10679 10197 TRUE FALSE FALSE 10114.20313 10090.68481 10211.68977 7443.894283 7668.786209 8486.805469 8667.693955 8176.007867 9723.843494 9932.08047 1.018336809 1.015968894 1.028152138 0.74947986 0.772122843 0.854484163 0.87269671 0.823191867 0.979033902 1 13.27788023 -9.270777495 24.99991679 1.010872607 0.81751278 0.881331199 0.035560258 161.1031247 431303.3057 0.00561308 0.008645829 5.36E-10 9.270777495 -0.193359827 EANANGSS(ph)PEPVKAVEAR ddPTM_HeLa_Romidepsin_16h_R1 3 EANANGSSPEPVKAVEAR 18 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 EANANGS(0.099)S(0.901)PEPVKAVEAR;EANANGS(0.019)S(0.981)PEPVKAVEAR;EANANGS(0.094)S(0.906)PEPVKAVEAR ;; 141.5 0.00012681 68437500 8601.9 7715.8 6568.5 11673.1 6662.5 6463.3 5985.1 6626.8 8047.2 6976.9 TRUE FALSE FALSE 8497.056734 7824.423235 6682.821987 13022.79875 6322.487764 6050.315989 6493.474245 6818.536003 7327.438277 6795.639132 1.250369034 1.151388866 0.983398597 1.916346423 0.930374265 0.890323319 0.955535472 1.003369348 1.078255943 1 12.73039353 EANNGSS(ph)PAGSLADAMSQK ddPTM_HeLa_Romidepsin_16h_R1 1 EANNGSSPAGSLADAMSQK 19 0 C9J4I3;P51692 C9J4I3 STAT5B Signal transducer and activator of transcription 5B 1 0 EANNGS(0.003)S(0.995)PAGS(0.002)LADAMSQK 158.58 3.26E-06 11325000 3702.1 3368.6 3216 3849.7 3531.1 3844 3308.1 3336 4049.1 3685.1 TRUE FALSE FALSE 3656.977381 3416.023239 3271.973131 4294.820427 3350.894791 3598.380806 3589.089931 3432.521897 3686.938355 3589.360571 1.018838121 0.951708019 0.911575493 1.196541931 0.933563158 1.002513048 0.9999246 0.956304564 1.027185283 1 11.80951114 -6.003883609 1.138833948 1.006259713 0.274490999 0.037994073 0.073530542 70.26607188 7.274100832 0.010024986 114.9120363 9.91E-07 6.003883609 -0.731768714 EANNGSSPAGS(ph)LADAMSQK ddPTM_HeLa_Romidepsin_16h_R1 1 EANNGSSPAGSLADAMSQK 19 0 C9J4I3;P51692 C9J4I3 STAT5B Signal transducer and activator of transcription 5B 1 0 EANNGS(0.074)S(0.234)PAGS(0.692)LADAMSQK 93.494 0.0041453 12331000 2809.3 3006.2 2667.4 3108.3 3160.2 2734 2668.7 2702.2 3452.4 3174.9 TRUE FALSE FALSE 2775.059171 3048.521363 2713.824978 3467.696271 2998.923202 2559.306224 2895.379311 2780.383894 3143.608697 3092.41564 0.897375869 0.985805829 0.877574458 1.121355172 0.969767182 0.82760745 0.936284008 0.899097734 1.016554391 1 11.59451852 -5.606320292 0.008315089 1.811329358 2.34E-07 0.101449936 0.075619928 29583.96382 25.6289308 2547.22583 3056.835382 2.48E-06 5.606320292 -1.811329124 EAPAEGEAAEPGS(ph)PTAAEGEAASAASSTS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 EAPAEGEAAEPGS(0.81)PT(0.132)AAEGEAAS(0.063)AAS(0.032)S(0.176)T(0.162)S(0.349)S(0.275)PK 50.464 0.0028995 0 963.09 1052.8 1013.4 681.43 1162.8 1219.8 829.23 1088 1035.1 1070.5 TRUE FALSE FALSE 951.3514886 1067.621346 1031.037802 760.2201428 1103.457977 1141.858717 899.6647755 1119.479563 942.5180635 1042.688256 0.912402613 1.023912315 0.988826522 0.729096294 1.058281774 1.095110365 0.862831983 1.073647428 0.903930833 1 10.02609217 -6.653066551 6.013239636 0.960043292 14.9364635 0.109845959 0.101301009 8546.31291 1538.293142 0.013178849 1623380.702 2.22E-07 6.653066551 13.97642021 EAPAEGEAAEPGS(ph)PTAAEGEAASAASSTSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 EAPAEGEAAEPGS(0.686)PT(0.313)AAEGEAAS(0.001)AAS(0.002)S(0.004)T(0.016)S(0.306)S(0.67)PK 102.62 5.87E-12 22519000 4520.8 4562.9 4581.3 2814.3 5965 6630.4 4914.1 5925.4 4618.3 4583.8 TRUE FALSE FALSE 4465.698751 4627.136626 4661.035605 3139.702608 5660.583792 6206.738839 5331.503531 6096.8421 4205.227681 4464.712215 1.000220963 1.036379592 1.043972238 0.703226201 1.267849644 1.390176688 1.194142707 1.36556217 0.941881017 1 12.12435147 -8.557127349 24.46320142 0.988122656 1.30848451 0.720596457 0.10585138 55.18255466 39415.75744 0.013932965 0.027866053 2.77E-09 8.557127349 0.320361854 EAPAEGEAAEPGS(ph)PTAAEGEAASAASSTSSPK ddPTM_HeLa_Romidepsin_16h_R1 2 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 EAPAEGEAAEPGS(0.735)PT(0.159)AAEGEAAS(0.096)AAS(0.007)S(0.002)TSSPK;EAPAEGEAAEPGS(0.968)PT(0.032)AAEGEAASAASSTSSPK ; 138.88 8.37E-16 54251700 7843.3 8220.4 5871 6469.4 8978.1 8586.7 6714.6 7559.6 7418 6968.2 TRUE FALSE FALSE 7747.702843 8336.127007 5973.182292 7217.422467 8519.914055 8038.037582 7284.937956 7778.325099 6754.515501 6787.165159 1.141522662 1.228219265 0.880070273 1.063392786 1.255297883 1.184299688 1.07334031 1.146034451 0.9951895 1 12.7285934 -12.3099358 0.883546102 0.994809335 1.121241069 0.197819593 0.099253502 0.97219509 1.272497686 0.084034157 0.019158356 4.90E-13 12.3099358 0.126431734 EAPAEGEAAEPGSPT(ph)AAEGEAASAASSTS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 EAPAEGEAAEPGS(0.114)PT(0.886)AAEGEAASAAS(0.008)S(0.017)T(0.012)S(0.511)S(0.451)PK 97.08 1.42E-11 21262000 2401.2 2774.2 2944 1221.7 3418.3 4348.1 3551.1 3104.5 2606.9 2855.5 TRUE FALSE FALSE 2371.933251 2813.25526 2995.239085 1362.958702 3243.851396 4070.270443 3852.730345 3194.323809 2373.732335 2781.313698 0.852810401 1.011484344 1.076915231 0.490041344 1.16630188 1.463434508 1.385219635 1.148494617 0.853457248 1 11.44155076 -8.52981131 24.98541678 0.916613044 1.33386691 0.59337917 0.168956012 86.28422365 310973.4735 0.023415279 0.046914414 2.95E-09 8.52981131 0.417253866 EAPAEGEAAEPGSPT(ph)AAEGEAASAASSTSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 EAPAEGEAAEPGS(0.27)PT(0.73)AAEGEAASAASSTSSPK 93.553 2.29E-11 39934000 5646.7 6201.3 4341 4941 6731.6 6645.3 5301.9 6746.9 5782.1 5159.3 TRUE FALSE FALSE 5577.875848 6288.602064 4416.553284 5512.301668 6388.061333 6220.686777 5752.243254 6942.110907 5264.934494 5025.260642 1.109967471 1.251398188 0.87887049 1.09691856 1.271190051 1.237883409 1.144665653 1.381442954 1.047693815 1 12.29498271 -4 0.208655411 1.014687176 2.537189153 0.428776964 0.105958001 36.79242452 0.430426864 0.090196394 18.71110941 1.00E-04 4 1.522501978 EAPAEGEAAEPGSPTAAEGEAAS(ph)AASS(ph)TSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 2 0 EAPAEGEAAEPGS(0.029)PT(0.141)AAEGEAAS(0.53)AAS(0.53)S(0.589)T(0.146)S(0.029)S(0.007)PK 85.982 7.64E-08 4546500 1992.1 1942.3 2333.1 1386.7 1695.3 1738.4 1259.8 1555.3 2442.1 2124.6 TRUE FALSE FALSE 1967.819519 1969.64375 2373.706627 1547.036779 1608.782515 1627.32185 1366.807381 1600.300152 2223.67246 2069.402586 0.950911888 0.951793413 1.147049222 0.747576518 0.777413987 0.786372773 0.66048404 0.773315044 1.074548024 1 11.01499862 -9.232254752 24.58231892 0.985562163 0.747764275 0.794537337 0.068692371 193.7204563 163171.5826 0.009172106 0.015208434 5.86E-10 9.232254752 -0.237797887 EAPAEGEAAEPGSPTAAEGEAASAASS(ph)TSSPK ddPTM_HeLa_Romidepsin_16h_R1 2 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 EAPAEGEAAEPGSPTAAEGEAASAAS(0.04)S(0.707)T(0.2)S(0.04)S(0.012)PK;EAPAEGEAAEPGSPTAAEGEAASAAS(0.06)S(0.627)T(0.23)S(0.06)S(0.023)PK ; 139.73 7.26E-16 9314600 6242.9 6710.2 6140.7 4895.2 5043.7 5026.1 3887.2 4554 6866.4 6598.3 TRUE FALSE FALSE 6166.809134 6804.666372 6247.576308 5461.206057 4786.301168 4704.948431 4217.378671 4685.762805 6252.251987 6426.875215 0.959534599 1.058783024 0.972101698 0.849745152 0.744732239 0.732074029 0.656209827 0.72908881 0.972829218 1 12.64990175 -8.951397748 1.83689298 0.987772825 0.703167506 0.943177151 0.032174513 0.05740576 0.388827445 0.005294379 0.010853963 1.12E-09 8.951397748 -0.284605319 EAPAEGEAAEPGSPTAAEGEAASAASSTSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EAPAEGEAAEPGSPTAAEGEAASAASSTSSPK 32 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 EAPAEGEAAEPGSPTAAEGEAASAASS(0.003)T(0.007)S(0.14)S(0.85)PK 106.23 3.18E-13 16290000 5742.3 6177.1 5683.6 2479.9 4965 6026 4231.1 4402.6 6035.8 5594.9 TRUE FALSE FALSE 5672.310639 6264.061376 5782.520674 2766.637706 4711.617523 5640.958048 4590.489528 4529.982285 5495.942931 5449.543691 1.040878092 1.1494653 1.06110181 0.507682453 0.864589366 1.035124841 0.842362184 0.831259008 1.008514335 1 12.41191972 EAPGLAQAAAAESDSR ddPTM_HeLa_Romidepsin_16h_R1 1 EAPGLAQAAAAESDSR 16 0 P51817 P51817 PRKX cAMP-dependent protein kinase catalytic subunit PRKX 0 0 63.212 0.027852 4141500 0 0 123.22 62.053 0 125.9 62.888 0 0 171.88 FALSE FALSE TRUE 0 0 125.3645924 69.22785983 0 117.8553963 68.22970515 0 0 167.4145328 0 0 0.748827418 0.413511651 0 0.70397351 0.407549476 0 0 1 7.38728096 -12.44898664 1.179506638 1.000428843 0.274433655 0 0.40979201 0.333630263 0.829523237 0.196574737 0.048775057 3.56E-13 12.44898664 -0.725995188 EAPGS(ph)PPLSPR ddPTM_HeLa_Romidepsin_16h_R1 1 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 EAPGS(0.995)PPLS(0.005)PR 119.25 0.010373 29565000 4482.2 3613.8 4317.6 3766.4 2217.3 2315.8 1944 1823.6 5294 4235.2 TRUE FALSE FALSE 4427.569222 3664.675171 4392.746017 4201.888889 2104.142907 2167.827854 2109.123311 1876.362989 4820.491381 4125.168893 1.073306169 0.888369729 1.064864526 1.018598025 0.510074366 0.525512509 0.511281687 0.454857252 1.168556126 1 12.01023747 -8.761033805 7.75195406 1.025057685 0.501930381 0.936366324 0.068320202 0.016643096 7.10064203 0.007820485 0.014944312 1.73E-09 8.761033805 -0.523127304 EAPGSPPLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 EAPGSPPLSPR 11 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;E9PNR0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 EAPGS(0.079)PPLS(0.921)PR 100.09 0.019134 27315000 3915 3359.6 3874.8 4146.9 3291.1 3122.1 3084 3018.4 4648.3 3879 TRUE FALSE FALSE 3867.282474 3406.896537 3942.239269 4626.38409 3123.142886 2922.607886 3345.954883 3105.732642 4232.544406 3778.223021 1.023571783 0.901719279 1.043410949 1.224486766 0.82661687 0.773540331 0.885589565 0.822008819 1.120247371 1 11.88349215 -8.626169118 24.99652645 1.018590484 0.827243491 0.609528221 0.085842717 5.453615504 1306.849558 0.011250482 0.022500968 2.36E-09 8.626169118 -0.191346993 EAPPMEK(ac)PEVVK ddPTM_HeLa_Romidepsin_16h_R1 2 EAPPMEKPEVVK 12 1 A0A0B4J2B4;S4R456;K7EM56;K7EJ78;S4R417;K7EQJ5;K7ELC2;P62841 A0A0B4J2B4 RPS15 40S ribosomal protein S15 0 1 ; EAPPMEK(1)PEVVK;EAPPMEK(1)PEVVK 132.17 0.0010003 4635600 401.57 430.59 594.74 484.08 1412.63 1165.78 1110.17 1022.7 1220.99 835 FALSE TRUE FALSE 396.6755104 436.6518573 605.0912002 540.0516073 1340.53822 1091.29042 1204.467812 1052.290211 1111.781596 813.3065796 0.487731835 0.536884698 0.743989063 0.66401972 1.648256947 1.341794654 1.480951762 1.293841999 1.366989551 1 9.667655475 -8.76880788 24.99982485 0.726973442 1.436948769 0.592084892 0.256497315 66.92770364 227072.7335 0.032273035 0.05935588 1.70E-09 8.76880788 0.709975327 EAPPPVLLT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EAPPPVLLTPK 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 0 EAPPPVLLT(1)PK;EAPPPVLLT(1)PK ; 120.84 0.01992 54611000 12388.2 11140.9 12126 11608.2 9718.1 10194.3 9102 9134 12839.2 13014.4 TRUE FALSE FALSE 12237.20785 11297.74188 12337.04794 12950.3947 9222.149094 9542.917131 9875.123653 9398.277879 11690.8298 12676.28401 0.965362392 0.891250296 0.973238524 1.021623899 0.727512028 0.752816608 0.779023541 0.741406383 0.922260008 1 13.62984427 -8.758395569 24.99999997 0.977069797 0.752436812 0.88043309 0.038054763 17.1845635 141141.09 0.005356045 0.010354591 1.74E-09 8.758395569 -0.224632986 EAPS(ph)PTLR ddPTM_HeLa_Romidepsin_16h_R1 4 EAPSPTLR 8 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 EAPS(0.99)PT(0.01)LR;EAPS(0.986)PT(0.014)LR;EAPS(0.988)PT(0.012)LR;EAPS(0.965)PT(0.035)LR ;;; 154.01 0.0059246 156242000 15301.3 13916.5 14482.1 12607.2 15889.9 15129.2 13233.7 15392.3 15559.6 14530.3 TRUE FALSE FALSE 15114.80187 14112.41685 14734.15488 14064.90378 15078.97911 14162.49295 14357.77015 15837.65192 14167.91041 14152.80071 1.067972494 0.997146582 1.04107697 0.993789432 1.065441351 1.000684828 1.014482606 1.119047193 1.001067612 1 13.78879996 -7.256339214 24.72581805 1.027658489 1.119047238 0.519074481 0.027720315 331.0542854 1604902.716 0.004157276 0.046228658 5.54E-08 7.256339214 0.091388749 EAPS(ph)PTLRR ddPTM_HeLa_Romidepsin_16h_R1 4 EAPSPTLRR 9 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 EAPS(0.977)PT(0.023)LRR;EAPS(0.969)PT(0.031)LRR;EAPS(0.968)PT(0.032)LRR;EAPS(0.783)PT(0.217)LRR ;;; 107.34 0.0064296 77458000 4374.49 4538.25 4217.75 4952.33 4864.8 5031.6 4002.53 4443.5 4566.74 4230.33 TRUE FALSE FALSE 4321.172033 4602.139603 4291.158169 5524.941696 4616.531103 4710.096999 4342.504798 4572.065662 4158.279337 4120.425417 1.048719876 1.116908847 1.04143571 1.340866813 1.120401569 1.143109393 1.053897197 1.109610101 1.009186896 1 12.00857758 -10.2912589 1.211382861 1.016056013 1.140842038 0.330164603 0.076372055 0.361694229 1.027946996 0.015605899 0.018290142 5.11E-11 10.2912589 0.124786026 EAQMAAK(ac)LER ddPTM_HeLa_Romidepsin_16h_R1 2 EAQMAAKLER 10 1 P16949;P16949-2 P16949 STMN1 Stathmin 0 1 ; EAQMAAK(1)LER;EAQMAAK(1)LER 99.283 0.011509 13323100 1197.69 835.21 1221.92 1113.15 1684.97 1311.13 1294.18 941.65 1535.29 1001.42 FALSE TRUE FALSE 1183.092094 846.9681083 1243.187005 1241.857641 1598.979693 1227.353024 1404.107617 968.8951571 1397.969817 975.402964 1.21292649 0.868326363 1.274536833 1.273173946 1.639301655 1.258303562 1.43951543 0.993328084 1.433222851 1 9.929854546 -9.543077784 24.61351551 1.085250412 1.334784999 0.150808973 0.205340373 176.1925726 214698.2949 0.027124233 0.038362064 2.86E-10 9.543077784 0.249534587 EAQQKVPDEEENEES(ph)DNEKETEK ddPTM_HeLa_Romidepsin_16h_R1 1 EAQQKVPDEEENEESDNEKETEK 23 2 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 EAQQKVPDEEENEES(0.967)DNEKET(0.033)EK 52.99 0.010464 14389000 1678.3 1396.7 1625.7 1238.1 1110 1101 1105.1 1442.9 1812.3 1695.9 TRUE FALSE FALSE 1657.844234 1416.362779 1653.994627 1381.254947 1053.352558 1030.649653 1198.967166 1484.648035 1650.203349 1651.840274 1.00363471 0.857445361 1.001304214 0.836191592 0.637684269 0.623940262 0.725837229 0.898784258 0.99900903 1 10.68985848 -9.066832237 3.333560208 0.988551302 0.715293539 0.671754958 0.081974764 0.102377798 2.232789793 0.012626624 0.022338397 8.57E-10 9.066832237 -0.273257763 EAQSSQATPVQTSQPDSSNIVKVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 EAQSSQATPVQTSQPDSSNIVKVSPR 26 1 H7C5E4;Q8IZH2-2;Q8IZH2 H7C5E4 XRN1 5-3 exoribonuclease 1 1 0 EAQSSQAT(0.033)PVQT(0.081)S(0.186)QPDS(0.015)S(0.228)NIVKVS(0.458)PR 104.9 1.08E-06 14569000 2916.8 2828 3159.4 3136.6 3048.7 3194.3 2857.4 2700.9 3456.6 3036.8 TRUE FALSE FALSE 2881.24892 2867.812658 3214.388032 3499.26845 2893.113463 2990.194539 3100.107485 2779.04628 3147.433039 2957.903498 0.974084828 0.969542333 1.086711596 1.183023196 0.97809596 1.010916868 1.048075938 0.939532436 1.064075634 1 11.53035927 -9.778820091 24.99599336 0.986053844 1.043599095 0.056137058 0.066486283 332.0643476 477555.2407 0.010074943 0.01325852 1.66E-10 9.778820091 0.057545251 EAQTLDSQIQET(ph)SI ddPTM_HeLa_Romidepsin_16h_R1 1 EAQTLDSQIQETSI 14 0 E7EVA0;P27816;P27816-2;P27816-4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 EAQTLDSQIQET(0.794)S(0.206)I 205.18 1.42E-16 51549000 10140 9893.7 8997.4 7562.3 6550.5 6227.1 6117.9 6018.7 10192 10455 TRUE FALSE FALSE 10016.40978 10032.98377 9153.995973 8436.688708 6216.203542 5829.208407 6637.554273 6192.841589 9280.401994 10183.37759 0.983603887 0.98523144 0.898915501 0.828476469 0.6104265 0.57242387 0.651802824 0.608132374 0.911328477 1 13.31392853 -9.043915227 1.569506093 0.990728172 0.603405582 0.944088809 0.039372603 0.041188379 0.200975247 0.004752878 0.009703861 9.04E-10 9.043915227 -0.38732259 EAQTLDSQIQETS(ph)I ddPTM_HeLa_Romidepsin_16h_R1 1 EAQTLDSQIQETSI 14 0 E7EVA0;P27816;P27816-2;P27816-4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 EAQTLDSQIQET(0.045)S(0.955)I 198.48 1.82E-16 57171000 11596 10567 11019 8616 7167.6 6817.9 6046.7 7030.4 12710 10889 TRUE FALSE FALSE 11454.66349 10715.7625 11210.78107 9612.222459 6801.810626 6382.258194 6560.306547 7233.813532 11573.18577 10606.10221 1.080006893 1.010339359 1.057012355 0.906291705 0.641311058 0.601753412 0.618540762 0.6820426 1.091181806 1 13.37260694 -8.881218231 2.819749096 1.037024142 0.627529266 0.969539478 0.034409815 0.033292129 0.535015909 0.005632552 0.011000255 1.31E-09 8.881218231 -0.409494876 EAS(ph)PAPLAQGEPGR ddPTM_HeLa_Romidepsin_16h_R1 2 EASPAPLAQGEPGR 14 0 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 0 EAS(1)PAPLAQGEPGR;EAS(1)PAPLAQGEPGR ; 166.52 9.05E-05 16168000 2710.1 2448.16 2363.3 1457.44 2666 2907.8 2621.8 2795.2 2638.9 2418.7 TRUE FALSE FALSE 2677.068259 2482.625261 2404.432245 1625.95607 2529.944072 2722.000964 2844.495627 2876.074702 2402.870175 2355.861825 1.136343494 1.05380767 1.020616837 0.690174633 1.073893233 1.15541622 1.20741191 1.220816379 1.01995378 1 11.20203921 -8.193185884 3.337290447 1.033054717 1.205624293 0.361446674 0.114757198 0.268493608 5.870159163 0.018209366 0.050369516 6.41E-09 8.193185884 0.172569577 EAS(ph)PAPLAQGEPGREDLPTR ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 EAS(0.965)PAPLAQGEPGREDLPT(0.035)R 68.705 0.0036554 102870000 1867.5 1797.6 1683.9 1356.8 2370.9 2829.3 1952.7 1973.5 1938.4 1944.9 TRUE FALSE FALSE 1844.738192 1822.90666 1713.207573 1513.6796 2249.904126 2648.516861 2118.562289 2030.600109 1765.024649 1894.371218 0.973799736 0.962275315 0.9043674 0.799040645 1.187678584 1.398098132 1.118345903 1.071912458 0.93172058 1 10.88750335 -8.65493146 9.02374237 0.966613256 1.205303451 0.622932587 0.098465329 0.151958107 11.86164177 0.014480447 0.02898876 2.21E-09 8.65493146 0.238690195 EAS(ph)PSTLNDK ddPTM_HeLa_Romidepsin_16h_R1 2 EASPSTLNDK 10 0 P54253 P54253 ATXN1 Ataxin-1 1 0 EAS(0.939)PS(0.061)TLNDK;EAS(0.774)PS(0.225)T(0.001)LNDK ; 159.44 0.0025824 50344000 9037.3 8476.3 7422.6 8609 6886.9 6864.2 5791.4 4935.3 9432.5 9034.2 TRUE FALSE FALSE 8927.149912 8595.629574 7551.787239 9604.413087 6535.435794 6425.599773 6283.321371 5078.095119 8588.833576 8799.490182 1.014507628 0.97683268 0.85820736 1.091473811 0.742706186 0.730224097 0.71405516 0.577089697 0.976060362 1 13.10320423 -8.344186289 0.91002523 1.003565241 0.599996075 0.776667172 0.075532427 0.221222665 0.30222224 0.011454918 0.060880555 4.53E-09 8.344186289 -0.403569166 EASAES(ph)DVGK ddPTM_HeLa_Romidepsin_16h_R1 1 EASAESDVGK 10 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 EAS(0.42)AES(0.58)DVGK 118.23 0.012932 4420100 1828.2 1600 1794.2 1307.2 1636.2 2776.1 3950.4 1094.9 2928.3 2481.7 TRUE FALSE FALSE 1805.917195 1622.524842 1825.427298 1458.344615 1552.698608 2598.716169 4285.946877 1126.579204 2666.385514 2417.225076 0.747103451 0.67123449 0.755174732 0.603313539 0.642347551 1.075082414 1.77308556 0.466063014 1.103077053 1 11.2391361 -8.013420545 24.39748769 0.818726384 1.195701581 0.150674727 0.329832507 502.6153797 913721.9259 0.041953367 0.112699558 9.70E-09 8.013420545 0.376975196 EASPAPLAQGEPGREDLPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 EAS(0.044)PAPLAQGEPGREDLPT(0.956)R 56.347 0.018454 91543000 2581.2 2884.5 2645.6 2010.7 2955.9 3730.6 3262.3 3278.1 2616.1 3053.4 TRUE FALSE FALSE 2549.739342 2925.108067 2691.645558 2243.186595 2805.049393 3492.2267 3539.399681 3372.946652 2382.109464 2974.072228 0.857322602 0.983536324 0.905037051 0.754247517 0.943167878 1.174223903 1.190085314 1.134117262 0.800958847 1 11.53822397 -8.281828378 5.781087823 0.919417573 1.169470495 0.724926754 0.076137468 0.074160506 8.979962689 0.011202905 0.026376784 5.23E-09 8.281828378 0.250052922 EASRPPEEPSAPS(ph)PTLPAQFK ddPTM_HeLa_Romidepsin_16h_R1 2 EASRPPEEPSAPSPTLPAQFK 21 1 H0Y3X6;A0A0C4DFX9;Q9H3P2;Q9H3P2-7 H0Y3X6 NELFA Negative elongation factor A 1 0 EASRPPEEPS(0.035)APS(0.79)PT(0.175)LPAQFK;EASRPPEEPS(0.028)APS(0.856)PT(0.117)LPAQFK ; 87.92 0.0005006 147446000 4859.8 4787.7 5359.1 4634.2 6286.1 6431.3 6535.2 6721.9 5363.5 5025 TRUE FALSE FALSE 4800.566888 4855.101366 5452.372887 5170.028009 5965.29686 6020.360686 7090.299725 6916.387571 4883.775127 4894.449776 0.9808185 0.991960606 1.113990977 1.056304231 1.218788042 1.230038301 1.448640818 1.413108294 0.99781903 1 12.25693097 -8.180515126 0.691053397 0.989391622 1.518173569 0.932004967 0.043527794 0.184549296 0.117461011 0.007162021 0.060259424 6.60E-09 8.180515126 0.528781948 EASRPPEEPSAPSPT(ph)LPAQFK ddPTM_HeLa_Romidepsin_16h_R1 1 EASRPPEEPSAPSPTLPAQFK 21 1 H0Y3X6;A0A0C4DFX9;Q9H3P2;Q9H3P2-7 H0Y3X6 NELFA Negative elongation factor A 1 0 EASRPPEEPS(0.001)APS(0.4)PT(0.599)LPAQFK 71.872 0.0032292 133800000 2221.7 2110.9 2199.5 2010.3 2653.4 2958.7 2890.6 3152.4 2200.4 2165.9 TRUE FALSE FALSE 2194.621066 2140.617306 2237.781375 2242.740345 2517.987097 2769.648619 3136.127492 3243.60972 2003.590713 2109.629606 1.040287385 1.014688692 1.060746099 1.063096734 1.193568335 1.31286014 1.486577304 1.537525692 0.949735777 1 11.04277401 -8.075909702 0.936237923 1.018523175 1.598242066 0.980526968 0.027833055 0.051958399 0.067032842 0.003068545 0.02287991 8.40E-09 8.075909702 0.579718892 EASSS(ph)SPEAGEGQIR ddPTM_HeLa_Romidepsin_16h_R1 1 EASSSSPEAGEGQIR 15 0 J3QSS7;Q86U28-2;Q86U28 J3QSS7 ISCA2 "Iron-sulfur cluster assembly 2 homolog, mitochondrial" 1 0 EASS(0.002)S(0.607)S(0.391)PEAGEGQIR 143.56 0.00048258 3976200 989.72 799.95 700.46 1034.8 1441.6 1375.3 1499.8 1357.8 1172.5 970.47 TRUE FALSE FALSE 977.656912 811.2117171 712.6512125 1154.448445 1368.029773 1287.422769 1627.192975 1397.085801 1067.628663 945.2570495 1.034276245 0.858191661 0.753923192 1.221306358 1.447256885 1.361981663 1.721429082 1.477995643 1.129458557 1 9.884562893 -8.87959835 2.756023224 0.984089451 1.518190103 0.795555178 0.129891715 0.087096377 1.33900372 0.018976172 0.037204811 1.32E-09 8.87959835 0.534100652 EASTTAAAPGEETS(ph)PVQVPAR ddPTM_HeLa_Romidepsin_16h_R1 2 EASTTAAAPGEETSPVQVPAR 21 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 EAS(0.002)T(0.017)T(0.178)AAAPGEET(0.355)S(0.447)PVQVPAR;EASTTAAAPGEET(0.241)S(0.758)PVQVPAR ; 246.1 2.00E-66 33602000 6626.6 6010.1 6309.1 5962.4 8181.5 9301.9 8639.8 9587.6 7072.7 6733.7 TRUE FALSE FALSE 6545.83245 6094.710346 6418.907239 6651.800742 7763.967526 8707.538611 9373.664396 9865.002079 6440.099998 6558.757503 0.998029344 0.929247703 0.978677324 1.014186107 1.183755844 1.327620149 1.42918295 1.504096176 0.981908539 1 12.67920682 -8.280185127 1.289625003 0.989579268 1.48940441 0.981639803 0.027236603 0.048174805 0.145086514 0.004585143 0.019104313 5.25E-09 8.280185127 0.499825142 EATAQKPTGSVGSTVT(ph)TPPPLVR ddPTM_HeLa_Romidepsin_16h_R1 2 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 0 EATAQKPTGSVGS(0.015)T(0.091)VT(0.447)T(0.447)PPPLVR;EATAQKPT(0.001)GS(0.001)VGS(0.008)T(0.009)VT(0.491)T(0.491)PPPLVR ; 68.168 0.001163 56278000 2701.2 2705.7 2541.9 2578.68 2173.3 2149.5 1560.89 1840.47 2817.7 3015.1 TRUE FALSE FALSE 2668.276735 2743.790916 2586.140703 2876.839115 2062.388391 2012.153887 1693.471958 1893.721096 2565.677855 2936.767267 0.908576163 0.934289532 0.880607984 0.979593837 0.702264839 0.685159464 0.576644931 0.644831859 0.87364017 1 11.52001322 -8.663395248 3.587085401 0.949406214 0.636637676 0.887959191 0.048188426 0.051816029 1.292584666 0.007392289 0.015374203 2.17E-09 8.663395248 -0.312768538 EATAQKPTGSVGSTVTT(ph)PPPLVR ddPTM_HeLa_Romidepsin_16h_R1 1 EATAQKPTGSVGSTVTTPPPLVR 23 1 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 0 EATAQKPTGSVGS(0.002)T(0.008)VT(0.266)T(0.724)PPPLVR 100.39 1.91E-05 38588000 2468 2118.9 2144.8 1854.9 1681 1864.9 1604 1530 2738.8 2368.4 TRUE FALSE FALSE 2437.919067 2148.72993 2182.129344 2069.372266 1595.212297 1745.738909 1740.24372 1574.268136 2493.834869 2306.868627 1.056808801 0.931448764 0.945927011 0.897048164 0.69150548 0.756756969 0.75437487 0.682426436 1.081047633 1 11.17172013 -9.132591057 1.127147795 1.023816919 0.715751498 0.893027927 0.046126815 0.099876563 0.25046194 0.007543865 0.016555464 7.37E-10 9.132591057 -0.308065421 EATDAIGHLDR ddPTM_HeLa_Romidepsin_16h_R1 4 EATDAIGHLDR 11 0 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 0 0 ;;; ;;; 142.89 0.0012302 33000800 23336.5 22600.6 21860.4 16183.1 21450.2 22526.4 19496.7 21837.8 25065.4 22978 FALSE FALSE TRUE 23052.06576 22918.77184 22240.87109 18054.26617 20355.51625 21087.03574 21152.74921 22469.64229 22823.48785 22381.02825 1.029982426 1.02402676 0.99373768 0.806677243 0.909498707 0.94218351 0.945119633 1.003959337 1.019769404 1 14.4499887 -9.501395953 24.88097992 1.014988777 0.920976598 0.499278799 0.046549813 479.1354246 554926.7794 0.007255741 0.011014899 3.15E-10 9.501395953 -0.094012178 EATGLS(ph)PQAAQEK ddPTM_HeLa_Romidepsin_16h_R1 4 EATGLSPQAAQEK 13 0 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 0 EAT(0.034)GLS(0.966)PQAAQEK;EAT(0.04)GLS(0.96)PQAAQEK;EAT(0.317)GLS(0.683)PQAAQEK;EAT(0.013)GLS(0.987)PQAAQEK ;;; 170.56 8.86E-05 71996000 7313.6 7809.6 9758.6 5315.63 7585.9 14836 12753.8 15273.1 9835.5 7104.4 TRUE FALSE FALSE 7224.45903 7919.543754 9928.444339 5930.248151 7198.763216 13888.02748 13837.10745 15715.00305 8955.788247 6919.826664 1.044023121 1.144471406 1.434782231 0.856993743 1.04030976 2.00699066 1.99963209 2.271011084 1.294221471 1 12.75652018 -8.238893034 4.95367648 1.049850306 2.098545822 0.868436278 0.172984071 0.040230389 2.80766147 0.022061651 0.055906996 5.77E-09 8.238893034 1.048695516 up EATGLS(ph)PQAAQEKDGIVIVK ddPTM_HeLa_Romidepsin_16h_R1 2 EATGLSPQAAQEKDGIVIVK 20 1 P17029;C9JRM9 P17029 ZKSCAN1 Zinc finger protein with KRAB and SCAN domains 1 1 0 EAT(0.044)GLS(0.956)PQAAQEKDGIVIVK;EAT(0.054)GLS(0.946)PQAAQEKDGIVIVK ; 83.423 0.0012877 21621000 2377.4 3293.3 3107.9 2254.9 3049.5 5754.1 4631.6 5539.5 3352.1 2503.3 TRUE FALSE FALSE 2348.423334 3339.663164 3161.991696 2515.622148 2893.872636 5386.431581 5025.007988 5699.776693 3052.279781 2438.263905 0.963153877 1.369688965 1.296820943 1.031726772 1.186857842 2.209125751 2.06089586 2.337637317 1.251825028 1 11.25163857 -8.297895647 4.132070219 1.046131874 2.199728476 0.894220492 0.162161299 0.044318153 1.703581482 0.024187816 0.058759189 5.04E-09 8.297895647 1.153596602 up EATNPPVIQEEK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EATNPPVIQEEKPK 14 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 1 ; EATNPPVIQEEK(1)PK;EATNPPVIQEEK(1)PK 252.14 1.73E-55 5217300 901.35 856.15 754 379.17 1822.49 1355.36 1570.68 1590.91 1903.16 1415.47 FALSE TRUE FALSE 890.3639995 868.2029022 767.1230537 423.0114194 1729.481535 1268.75687 1704.09352 1636.940471 1732.936603 1378.695885 0.645801593 0.629727637 0.556412086 0.306819962 1.254432941 0.920258691 1.236018427 1.187310768 1.256938982 1 10.42908854 -8.714908757 24.99986024 0.756029066 1.139310297 0.38763826 0.255551409 103.4870203 55600.74109 0.035005022 0.070009876 1.93E-09 8.714908757 0.383281231 EATNTTSEPSAPSQDLLDLS(ph)PSPR ddPTM_HeLa_Romidepsin_16h_R1 2 EATNTTSEPSAPSQDLLDLSPSPR 24 0 I3NI44;J3KQU4;I3L4I4;O75674-2;O75674-3;O75674 I3NI44 TOM1L1 TOM1-like protein 1 1 0 EATNTTSEPSAPSQDLLDLS(0.967)PS(0.033)PR;EATNTTSEPSAPSQDLLDLS(0.906)PS(0.094)PR ; 158.11 3.59E-10 15139100 3298.2 3109.17 3347.7 3575.1 4334.1 4417.4 3213.5 3612.6 3895.6 3722.6 TRUE FALSE FALSE 3258.00027 3152.940977 3405.965314 3988.469883 4112.914704 4135.142397 3486.45461 3717.124881 3547.167779 3625.886315 0.898539002 0.869564212 0.939346967 1.099998604 1.134319818 1.140450096 0.961545483 1.025163107 0.97828985 1 11.82411798 -9.267833423 24.62738043 0.942499992 1.073374819 0.561094517 0.059667149 287.729805 1108223.128 0.010658217 0.016534841 5.40E-10 9.267833423 0.130874827 EATNTTSEPSAPSQDLLDLSPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 EATNTTSEPSAPSQDLLDLSPSPR 24 0 I3NI44;J3KQU4;I3L4I4;O75674-2;O75674-3;O75674 I3NI44 TOM1L1 TOM1-like protein 1 1 0 EATNTTSEPSAPSQDLLDLS(0.087)PS(0.913)PR;EATNTTSEPSAPSQDLLDLS(0.17)PS(0.83)PR;EATNTTSEPSAPSQDLLDLS(0.101)PS(0.899)PR ;; 213.82 2.65E-37 50056600 5094.38 5760.9 4982.76 5642.39 4882.32 4558.67 3451.7 4125.65 6024.1 5676.66 TRUE FALSE FALSE 5032.287737 5842.002101 5069.482848 6294.78968 4633.156992 4267.385699 3744.887312 4245.019174 5485.289408 5529.179555 0.910132812 1.056576666 0.91685987 1.138467221 0.837946561 0.771793655 0.677295298 0.767748475 0.992062087 1 12.43284971 -8.540234479 7.736286275 0.973480337 0.744209682 0.74235811 0.069438226 0.066427052 20.38952137 0.010225211 0.020838663 2.88E-09 8.540234479 -0.229270655 EATQPEPIY(ph)AESTK ddPTM_HeLa_Romidepsin_16h_R1 1 EATQPEPIYAESTK 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 EATQPEPIY(0.999)AES(0.001)TK 174.23 0.00096809 9573900 2877 2148.7 2938.1 2985.9 4447.4 4038 3855.7 3569.3 2734.3 2857.6 TRUE FALSE FALSE 2841.934017 2178.949455 2989.236398 3331.143807 4220.432582 3779.984832 4183.203062 3672.572064 2489.73736 2783.35914 1.021044671 0.782848833 1.073967191 1.196807038 1.516309024 1.358065791 1.502933273 1.319474735 0.894508123 1 11.44261136 -9.06100418 2.566845431 0.992913658 1.424353158 0.836129819 0.097084977 0.079119589 1.030085236 0.013455409 0.024644499 8.69E-10 9.06100418 0.431439499 EATSDPS(ph)RTPEEEPLNLEGLVAHR ddPTM_HeLa_Romidepsin_16h_R1 1 EATSDPSRTPEEEPLNLEGLVAHR 24 1 A0A087WWW7;E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0 A0A087WWW7 TNS1 Tensin-1 1 0 EAT(0.043)S(0.043)DPS(0.457)RT(0.457)PEEEPLNLEGLVAHR 66.732 0.00054615 1737600 2277.8 1861.3 1476 1541.6 1857.2 1520.8 1453.9 1712.3 1907.5 2106.9 TRUE FALSE FALSE 2250.037297 1887.50343 1501.689161 1719.847045 1762.420154 1423.625788 1577.39423 1761.842699 1736.888423 2052.162434 1.096422613 0.919763172 0.731759405 0.838065748 0.858811235 0.693719836 0.768649793 0.858529846 0.846369855 1 11.00292921 -10.00140377 4.157974438 1.044812968 0.791972595 0.474936494 0.08330296 0.067025291 2.741156715 0.010018305 0.012888401 9.97E-11 10.00140377 -0.252840373 EATTEFSVDAR ddPTM_HeLa_Romidepsin_16h_R1 2 EATTEFSVDAR 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 189.18 1.67E-07 50246000 7173.6 7507.3 6697.7 7164.5 8315 7904.7 6519.3 7295.5 7454.5 6511.8 FALSE FALSE TRUE 7086.165404 7612.987966 6814.270659 7992.8932 7890.654522 7399.615181 7073.049179 7506.583782 6787.75085 6342.622497 1.11722957 1.200290254 1.074361695 1.260187439 1.244068132 1.166649156 1.11516162 1.183514199 1.07018049 1 12.63086376 -11.27557592 0.553097601 0.999945725 1.184386086 0.495269974 0.055638316 0.395081731 0.266611658 0.032223654 0.015768316 5.30E-12 11.27557592 0.184440362 EAVAPVQEES(ph)DLEK ddPTM_HeLa_Romidepsin_16h_R1 2 EAVAPVQEESDLEK 14 0 E7EQL5;Q13409-2;E7EV09;Q13409-3;Q13409-6;E7EQU2;E9PGG1;E7ETL8;E7ESD3;E7EMU4;Q13409;Q13409-7;Q13409-5;E7ET01;E7ERR6;E7EUM4;E7ERH4;E7EU01 E7EQL5 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 0 EAVAPVQEES(1)DLEK;EAVAPVQEES(1)DLEK ; 176.29 4.85E-07 3978700 3222.3 4187.2 3096.9 13242 3077.9 2414.3 2479.1 3175.4 3389 4662.6 TRUE FALSE FALSE 3183.025368 4246.147512 3150.800245 14773.10235 2920.823278 2260.034022 2689.674692 3267.275189 3085.879352 4541.46498 0.700880747 0.934973083 0.693784992 3.252937634 0.643145613 0.497644269 0.592248251 0.71943199 0.679489849 1 12.14894204 -8.559935311 24.99998222 1.035715088 0.596739185 0.112686076 0.728582218 356.6333024 240599.1814 0.106418106 0.212836615 2.75E-09 8.559935311 -0.438975903 EAVLLLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EAVLLLKK 8 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 1 ; EAVLLLK(1)K;EAVLLLK(1)K 130.27 0.0016069 617000 2106.08 798.02 967.91 1668.89 2905.4 1440.9 2348.3 1660.14 2413.3 2088.77 FALSE TRUE FALSE 2080.410287 809.2545465 984.7560675 1861.854914 2757.126596 1348.83114 2547.764543 1708.173532 2197.448404 2034.503454 1.022564146 0.397765138 0.48402772 0.915139716 1.355184033 0.662978054 1.252278308 0.839602178 1.080090771 1 10.99046101 -6.955528277 20.37274697 0.943794325 0.000448341 0 0.296910157 2031.866368 643692.0452 0.04014337 135296.0489 1.11E-07 6.955528277 -0.943345984 EAVLLLKK ddPTM_HeLa_Romidepsin_16h_R1 1 EAVLLLKK 8 1 P36578;H3BM89;H3BTP7 P36578 RPL4 60S ribosomal protein L4 0 0 77.282 0.020261 0 0 61.057 54.322 162.94 137.32 48.142 135.36 0 0 111.33 FALSE FALSE TRUE 0 61.91656205 55.26745162 181.7798895 130.312048 45.06588157 146.857475 0 0 108.4376306 0 0.570987781 0.50967041 1.676354311 1.201723491 0.415592644 1.354303615 0 0 1 6.760721684 EAVVDLHADDS(ph)RISEDETER ddPTM_HeLa_Romidepsin_16h_R1 2 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 EAVVDLHADDS(0.602)RIS(0.355)EDET(0.043)ER;EAVVDLHADDS(0.5)RIS(0.5)EDET(0.001)ER ; 99.092 0.00027446 55504000 6550.8 5726.2 6773.5 3932.1 6263.6 6841.6 5199.5 5504.2 6442.1 6393 TRUE FALSE FALSE 6470.95633 5806.813594 6891.389926 4386.747903 5943.945119 6404.44384 5641.1454 5663.455343 5865.902441 6226.908938 1.039192382 0.932535493 1.10671121 0.704482424 0.9545579 1.02851092 0.905930287 0.909513115 0.942024767 1 12.60430047 EAVVDLHADDS(ph)RISEDETERNGDDGTHDK ddPTM_HeLa_Romidepsin_16h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 EAVVDLHADDS(0.451)RIS(0.451)EDET(0.098)ERNGDDGT(0.001)HDK 80.082 1.21E-06 6092700 898.22 792.39 741.73 698.18 858.21 876.85 774.01 744.42 831.03 760.41 TRUE FALSE FALSE 887.2721491 803.5452872 754.6394995 778.9068566 814.4123413 820.8221149 839.7543901 765.9586182 756.7005954 740.6544386 1.197956973 1.084912539 1.018882032 1.051646782 1.099584771 1.108238974 1.133800523 1.034164623 1.021664836 1 9.532656782 -12.71452459 1.625963771 1.000124372 1.107921301 0.2338129 0.051200759 0.386742238 1.849078685 0.04389277 0.009676876 1.93E-13 12.71452459 0.107796928 EAVVDLHADDSRIS(ph)EDETER ddPTM_HeLa_Romidepsin_16h_R1 1 EAVVDLHADDSRISEDETER 20 1 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 EAVVDLHADDS(0.119)RIS(0.466)EDET(0.414)ER 60.09 0.0093628 48909000 2219.6 2410.8 2594.1 1617.3 2453.9 2508.3 2000.8 2080 2665.2 2665.1 TRUE FALSE FALSE 2192.546661 2444.739306 2639.249222 1804.299836 2328.668326 2348.027725 2170.747902 2140.181518 2426.817837 2595.860318 0.844631988 0.941783843 1.016714653 0.695068153 0.897069966 0.904527763 0.83623448 0.82445943 0.934879978 1 11.34199704 -9.288120547 24.99252695 0.93228761 0.839439478 0.401041891 0.069374948 818.7897891 766966.3693 0.012441104 0.019007323 5.15E-10 9.288120547 -0.092848132 EAVVDLHADDSRISEDET(ph)ERNGDDGTHDK ddPTM_HeLa_Romidepsin_16h_R1 1 EAVVDLHADDSRISEDETERNGDDGTHDK 29 2 Q9UKV3-5;G3V3T3 Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 EAVVDLHADDS(0.047)RIS(0.047)EDET(0.841)ERNGDDGT(0.065)HDK 48.759 0.0072177 33468000 1937.6 1854.6 1818.1 1821 1855.7 1623.9 1473.6 1843.1 1953.4 1601.2 TRUE FALSE FALSE 1913.983786 1880.709107 1849.743268 2031.552588 1760.996704 1520.138031 1598.767547 1896.427191 1778.683012 1559.600593 1.22722689 1.205891506 1.186036525 1.302610808 1.129133133 0.974697007 1.025113452 1.21596978 1.140473413 1 10.60696089 -6.914637234 15.98445989 1.122580178 3.378477974 0.051002479 0.100542356 4289266.678 10984597.47 2.967237186 336718682.7 1.22E-07 6.914637234 2.255897796 EAWPHIK ddPTM_HeLa_Romidepsin_16h_R1 1 EAWPHIK 7 0 P52209-2;P52209;K7EMN2;K7EM49;K7EPF6 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 81.635 0.027569 4770700 2159.9 2399.4 2044.9 2162.8 2437.2 2179.6 2041.7 2369.2 2466.7 2333.2 FALSE FALSE TRUE 2133.574308 2433.178816 2080.490627 2412.873112 2312.82059 2040.330594 2215.121947 2437.749064 2246.072174 2272.583128 0.93883224 1.070666585 0.915473939 1.061731508 1.017705606 0.897802404 0.974715477 1.072677621 0.988334441 1 11.15011735 EAYPGDVFYLHSR ddPTM_HeLa_Romidepsin_16h_R1 3 EAYPGDVFYLHSR 13 0 P25705-2;P25705;P25705-3 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 0 ;; ;; 137.09 0.00068086 52731470 4276.03 3754.65 4640.32 5010.97 4566.62 4918.25 4162.11 4331.72 4757.85 4143.55 FALSE FALSE TRUE 4223.912102 3807.508061 4721.082823 5590.361929 4333.568341 4603.989698 4515.63952 4457.051484 4332.29598 4035.899974 1.046584933 0.943409918 1.16977201 1.385158692 1.07375514 1.140759119 1.118868047 1.104351325 1.073439879 1 11.9786747 -9.743462647 24.82883978 1.016718967 1.168024318 0.423602207 0.085448252 160.4197563 221565.7621 0.013211489 0.018660972 1.81E-10 9.743462647 0.151305351 ECLNKRNS(ph)EVAVMDK ddPTM_HeLa_Romidepsin_16h_R1 1 ECLNKRNSEVAVMDK 15 2 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 ECLNKRNS(1)EVAVMDK 78.939 0.002762 0 691.18 676.77 780.58 571.12 795.07 629.59 519.62 739.58 715.09 703.49 TRUE FALSE FALSE 682.7556323 686.2975858 794.1656675 637.1555816 754.4946111 589.3612309 563.7565098 760.9785804 651.1305594 685.2132284 0.996413385 1.001582511 1.15900516 0.929864683 1.101109231 0.860113621 0.822746098 1.110571934 0.950259762 1 9.420409193 -8.249733743 24.76322491 1.011549579 0.920304113 0.148242644 0.094866801 861.0741386 1821595.16 0.0119357 0.030162515 5.63E-09 8.249733743 -0.091245466 EDAANNYAR ddPTM_HeLa_Romidepsin_16h_R1 1 EDAANNYAR 9 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q9NY65;C9J2C0;Q9NY65-2;F8VX09;F8VWV9;F8VRZ4;F8VS66;C9JEV8;C9JQ00;C9JJQ8;C9K0S6;C9JDL2;A6NHL2-2;A6NHL2;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA1A;TUBA8;TUBA4A;TUBAL3 Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha chain-like 3;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 112.41 0.014735 670910 439.16 324.69 449.66 415.84 296.2 362.18 388.07 318.52 513.52 406.17 FALSE FALSE TRUE 433.807349 329.2609943 457.4861437 463.9213774 281.0838087 339.0378669 421.0326561 327.7358737 467.5894851 395.6176448 1.096531853 0.832270751 1.156384579 1.172650875 0.71049361 0.856983684 1.064241349 0.828415714 1.181922726 1 8.627962963 -8.770257491 24.99994254 1.046044726 0.87868771 0.377963368 0.127574711 173.8357475 492836.9539 0.017599695 0.032250623 1.70E-09 8.770257491 -0.167357016 EDEEEDDDVVAPKPPIEPEEEK ddPTM_HeLa_Romidepsin_16h_R1 1 EDEEEDDDVVAPKPPIEPEEEK 22 1 E7EQL5;Q13409-2;E7EV09;Q13409-3;Q13409-6;E7EQU2;E7ESD3;E7EMU4;Q13409;Q13409-7;Q13409-5 E7EQL5 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 0 0 127.67 0.00011712 6131700 2111.8 1975.4 2087.5 1057.2 2376 2635.8 2102.7 2222.8 2373 2113.6 FALSE FALSE TRUE 2086.060569 2003.209733 2123.832062 1179.438438 2254.743854 2467.380887 2281.303286 2287.113211 2160.752937 2058.688367 1.013295942 0.973051466 1.0316433 0.57290771 1.095233203 1.198520828 1.108134345 1.110956494 1.049577474 1 11.00750974 -8.541178281 24.99999447 0.972899421 1.137893824 0.311115274 0.133032688 244.6955863 334291.1059 0.018893689 0.037792941 2.88E-09 8.541178281 0.164994402 EDEGEPGDEGQLEDEGS(ph)QEKQGR ddPTM_HeLa_Romidepsin_16h_R1 2 EDEGEPGDEGQLEDEGSQEKQGR 23 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 0 EDEGEPGDEGQLEDEGS(1)QEKQGR;EDEGEPGDEGQLEDEGS(1)QEKQGR ; 78.583 0.00019367 15742200 3707.8 3431.3 2951.3 1667.26 3612.6 3527.2 3084.7 3190.4 3659.4 3544.5 TRUE FALSE FALSE 3662.607907 3479.605931 3002.666138 1860.036446 3428.235542 3301.823304 3346.714341 3282.70919 3332.094099 3452.413379 1.060883361 1.007876389 0.869729609 0.538764117 0.99299683 0.956381215 0.969384014 0.950844766 0.965149225 1 11.7533895 -9.799331057 5.6920388 1.028616117 0.876766797 0.199216511 0.124210508 0.201352419 16.49722244 0.020423912 0.027325935 1.59E-10 9.799331057 -0.15184932 EDEGPPGYPEPLAPGHGS(ph)PFPSLSK ddPTM_HeLa_Romidepsin_16h_R1 2 EDEGPPGYPEPLAPGHGSPFPSLSK 25 0 B0QYS6;B0QYS7;P19484;B1AKB5;P19484-2 B0QYS6 TFEB Transcription factor EB 1 0 EDEGPPGY(0.301)PEPLAPGHGS(0.684)PFPS(0.014)LS(0.001)K;EDEGPPGY(0.001)PEPLAPGHGS(0.915)PFPS(0.079)LS(0.005)K ; 100.62 5.06E-06 45746000 9144 7821.9 8668.4 4833.3 6656 6332.4 5220.4 5300.9 9357.8 9334.2 TRUE FALSE FALSE 9032.549411 7932.016914 8819.269866 5392.148887 6316.319483 5927.780077 5663.820646 5454.273178 8520.814931 9091.696138 0.993494423 0.872446328 0.970035704 0.593085031 0.694734996 0.651999361 0.622966338 0.599918112 0.937208503 1 13.15033375 -9.267364344 24.34398622 0.98369983 0.636545117 0.920174384 0.04703905 59.32776444 243760.7128 0.00726861 0.011289641 5.40E-10 9.267364344 -0.347154713 EDEIS(ph)PPPPNPVVK ddPTM_HeLa_Romidepsin_16h_R1 5 EDEISPPPPNPVVK 14 0 K7EPB2;P10644-2;P10644;K7EMU2;K7EMZ6;K7EIE5;K7EID3;K7EJ40;K7EK41 K7EPB2 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 0 EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK;EDEIS(1)PPPPNPVVK ;;;; 181.75 2.44E-07 279036400 22410.2 21174.4 21147.9 13059 23723.4 25098.9 20510.4 23318 23252.9 22345.7 TRUE FALSE FALSE 22137.05586 21472.49376 21515.97033 14568.94302 22512.70637 23495.16129 22252.55286 23992.66954 21173.10239 21765.15549 1.017086961 0.986553658 0.988551188 0.669370041 1.034346223 1.079485111 1.022393471 1.102343126 0.972798122 1 14.40973271 -8.534873561 24.98246807 0.978396243 1.062407591 0.206784678 0.100573113 360.3098961 750442.2752 0.015169701 0.030359237 2.92E-09 8.534873561 0.084011349 EDENDAS(ph)DDEDDDEKRR ddPTM_HeLa_Romidepsin_16h_R1 1 EDENDASDDEDDDEKRR 17 2 Q9Y5B6-3;Q9Y5B6-4;Q9Y5B6-2;Q9Y5B6 Q9Y5B6-3 PAXBP1 PAX3- and PAX7-binding protein 1 1 0 EDENDAS(1)DDEDDDEKRR 71.001 0.027622 5483100 907.77 1007.9 998.34 595.11 689.52 786.61 657.81 918.74 994.82 775.72 TRUE FALSE FALSE 896.7057501 1022.089243 1015.715689 663.9194183 654.3312214 736.3481597 713.684365 945.3222924 905.8408076 755.5666826 1.186798956 1.352745252 1.344309791 0.878703937 0.866013863 0.974564094 0.944568337 1.251143432 1.198889295 1 9.561415276 -9.228307871 24.98585457 1.131961229 0.973895972 0.315669922 0.147365074 878.0859714 662202.2071 0.025007372 0.04146823 5.91E-10 9.228307871 -0.158065257 EDENSWFNLFVIHQNR ddPTM_HeLa_Romidepsin_16h_R1 2 EDENSWFNLFVIHQNR 16 0 F8W7U8;P49959-2;P49959;P49959-3;F5GXT0 F8W7U8 MRE11A Double-strand break repair protein MRE11A 0 0 ; ; 108.66 0.001611 7749500 2742.6 2841 2608.6 3091.5 2675.3 2789.5 2853.9 2996.3 3084.6 2586.6 FALSE FALSE TRUE 2709.172136 2880.995673 2654.001589 3448.953776 2538.769458 2611.259953 3096.310195 3082.993213 2808.70565 2519.399759 1.07532444 1.143524628 1.05342615 1.368958524 1.00768822 1.036461142 1.228987255 1.22370148 1.114831277 1 11.29886434 -16.52278078 0.033494785 0.09171704 1.713687791 0.083842381 0.107156529 880.1232035 2.362793412 91.1473378 35.47891258 3.00E-17 16.52278078 1.62197075 EDEVEEWQHR ddPTM_HeLa_Romidepsin_16h_R1 4 EDEVEEWQHR 10 0 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 ;;; ;;; 191.4 2.72E-08 27093400 20021.6 19815.2 19425.7 18933.9 24604.3 27757.8 21356.8 24377.7 22869.6 21011.6 FALSE FALSE TRUE 19777.56904 20094.15891 19763.79616 21123.1266 23348.65076 25984.16616 23170.84606 25083.03029 20824.0857 20465.7156 0.966375641 0.98184492 0.965702668 1.032122551 1.14086657 1.269643665 1.13217864 1.225612179 1.017510753 1 14.32092149 -8.747190725 2.574296477 0.982642158 1.202470031 0.885018731 0.035779355 0.056184585 0.760420317 0.004777369 0.010057469 1.79E-09 8.747190725 0.219827873 EDFDSTSSSSS(ph)TPPLQPR ddPTM_HeLa_Romidepsin_16h_R1 2 EDFDSTSSSSSTPPLQPR 18 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 EDFDSTSSS(0.002)S(0.007)S(0.913)T(0.077)PPLQPR;EDFDS(0.006)T(0.075)S(0.025)S(0.008)S(0.058)S(0.058)S(0.572)T(0.198)PPLQPR ; 265.43 5.76E-90 19289900 4445.7 4581.4 4666.4 2413.1 3492 3245.5 2731.9 2673.4 4445.6 4357 TRUE FALSE FALSE 4391.514098 4645.897069 4747.616735 2692.113976 3313.79021 3038.123024 2963.947518 2750.750611 4047.974402 4243.804512 1.034805936 1.094748134 1.118717114 0.634363333 0.780853642 0.715896082 0.698417542 0.64818033 0.953855059 1 12.05114249 -9.259267636 24.99998121 1.030946609 0.701572218 0.901124852 0.057059983 42.24397823 486289.7505 0.008293796 0.013326272 5.50E-10 9.259267636 -0.329374391 EDFDSTSSSSST(ph)PPLQPR ddPTM_HeLa_Romidepsin_16h_R1 1 EDFDSTSSSSSTPPLQPR 18 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 EDFDSTSS(0.001)S(0.003)S(0.025)S(0.221)T(0.749)PPLQPR 204.9 1.06E-20 3989000 624.44 735.54 836.74 378.54 584.21 495.42 434.66 756.43 803.09 649.59 TRUE FALSE FALSE 616.8290851 745.8949514 851.3031087 422.3085759 554.3955837 463.7642609 471.5800096 778.3161086 731.259619 632.7135582 0.974894685 1.178882516 1.345479479 0.667456182 0.876218909 0.732976645 0.745329389 1.230123961 1.155751461 1 9.305408701 -9.227021251 24.96818743 1.029547228 0.839491166 0.295167506 0.18591733 756.0513567 548468.2739 0.027090392 0.044923236 5.93E-10 9.227021251 -0.190056062 EDGGTVGVFS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EDGGTVGVFSPK 12 0 O43896 O43896 KIF1C Kinesin-like protein KIF1C 1 0 EDGGT(0.016)VGVFS(0.984)PK 114.7 0.009168 21992000 2532.1 2298.3 2721.5 2526.5 2954.5 3793.3 3300.8 3244.9 2417.2 2342.3 TRUE FALSE FALSE 2501.237791 2330.655528 2768.866566 2818.625818 2803.72084 3550.920372 3581.16987 3338.786062 2200.999578 2281.446708 1.096338469 1.021569129 1.213645077 1.235455471 1.228922346 1.556433626 1.569692536 1.463451261 0.964738545 1 11.15573324 -8.671019433 0.74543972 1.039090028 1.583909543 0.883734826 0.073216208 0.182862524 0.175422475 0.013117502 0.056436547 2.13E-09 8.671019433 0.544819515 EDGNEEDK(ac)ENQGDETQGQQPPQRR ddPTM_HeLa_Romidepsin_16h_R1 1 EDGNEEDKENQGDETQGQQPPQRR 24 2 H0Y449;P67809 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 0 1 EDGNEEDK(1)ENQGDETQGQQPPQRR 89.663 2.67E-07 363170 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 EDGNEEDKENQGDETQGQQPPQR ddPTM_HeLa_Romidepsin_16h_R1 1 EDGNEEDKENQGDETQGQQPPQR 23 1 H0Y449;P67809 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 0 0 79.341 0.0005638 3063700 427.31 381.05 539.18 199.25 333.12 298.85 359.72 237.06 441.63 490.59 FALSE FALSE TRUE 422.1017814 386.4144319 548.5642017 222.2882225 316.1196434 279.7544495 390.2746078 243.9189571 402.1295067 477.8444011 0.883345667 0.808661629 1.14799755 0.465189551 0.661553515 0.585450931 0.816739941 0.510456869 0.84154906 1 8.900397104 -9.256360254 24.99998736 0.944974118 0.621217602 0.633815016 0.124527206 199.5106801 982011.6942 0.017427499 0.028326725 5.54E-10 9.256360254 -0.323756516 EDGNEEDKENQGDETQGQQPPQRR ddPTM_HeLa_Romidepsin_16h_R1 1 EDGNEEDKENQGDETQGQQPPQRR 24 2 H0Y449;P67809 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 0 0 92.897 2.13E-05 5318700 783.15 820.09 695.03 860.39 534.19 673.23 737.77 774.71 928.36 815.98 FALSE FALSE TRUE 773.6046666 831.6352485 707.1267056 959.8723401 506.928291 630.2127758 800.4361654 797.1250116 845.3251565 794.780722 0.973356103 1.046370685 0.889712956 1.207719706 0.637821574 0.792939182 1.007115728 1.002949606 1.063595446 1 9.634413069 -8.766220043 24.99992206 0.997664636 0.865895244 0.283070669 0.12615849 141.3392807 739122.4127 0.017722686 0.032886575 1.71E-09 8.766220043 -0.131769392 EDGTFYEFGEDIPEAPER ddPTM_HeLa_Romidepsin_16h_R1 2 EDGTFYEFGEDIPEAPER 18 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 0 ; ; 278.93 4.40E-105 10617100 1968.29 1820.25 1642.43 1759.44 2211.14 2108.15 1551.6 1928.27 2082.86 2043.21 FALSE FALSE TRUE 1944.299724 1845.875527 1671.015805 1962.874731 2098.297275 1973.446019 1683.392865 1984.06145 1896.563785 1990.12711 0.976972634 0.927516397 0.839652803 0.986306212 1.054353395 0.991618078 0.845872034 0.996952125 0.952986257 1 10.95864486 -10.51683586 3.471888616 0.99068937 0.947969132 0.026588209 0.064231461 0.46314427 11.54257679 0.011757898 0.012795904 3.04E-11 10.51683586 -0.042720238 EDGVLGSRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 EDGVLGSRSPR 11 1 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312;D6RFZ4;P78312-3 E7EUR8 FAM193A Protein FAM193A 1 0 EDGVLGS(0.076)RS(0.924)PR 83.53 0.0029308 0 2676.8 2227.6 2347.1 1951.8 1722.8 1512.7 1404.3 1205.1 2739.3 2139.1 TRUE FALSE FALSE 2644.174132 2258.960211 2387.950291 2177.476299 1634.879087 1416.043352 1523.581207 1239.967667 2494.290147 2083.525874 1.269086295 1.0842007 1.146110217 1.045092037 0.784669443 0.679637997 0.731251398 0.595129479 1.197148631 1 11.0248113 -8.725983545 2.168251295 1.12823908 0.673247598 0.894724903 0.072914995 0.099155684 0.949251479 0.015645171 0.034588185 1.88E-09 8.725983545 -0.454991482 EDIFYTS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EDIFYTSK 8 0 S4R3Z2;A0A0A0MSS8;P42330;S4R3D5;P17516;P52895-2;P52895;S4R3P0;H0Y804;B4DK69 S4R3Z2;P52895 AKR1C3;AKR1C4;AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C3;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C2 1 0 EDIFYT(0.023)S(0.977)K 110.53 0.022257 2351300 3982 4515.7 3764.3 2621 3354.2 3354.1 3516.6 3035.2 4119.3 4175.2 TRUE FALSE FALSE 3933.465852 4579.272143 3829.816062 2924.052352 3183.022658 3139.783835 3815.299916 3123.018723 3750.859491 4066.727702 0.967231185 1.126033627 0.941743914 0.719018475 0.782698742 0.772066404 0.938174423 0.767943898 0.922328655 1 11.98965268 -9.443364396 6.040105737 0.996461138 0.80301093 0.656856803 0.071560559 0.106657224 6.449091028 0.010342614 0.015804983 3.60E-10 9.443364396 -0.193450208 EDILENEDEQNS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 EDILENEDEQNSPPK 15 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 EDILENEDEQNS(1)PPK 243.83 3.06E-57 5292300 4800.3 4726.3 5819.3 2755.3 3886.9 4054.8 3423.8 3286.8 5558.5 4948.9 TRUE FALSE FALSE 4741.792097 4792.836975 5920.582475 3073.88075 3688.536989 3795.711366 3714.617487 3381.898372 5061.333838 4820.326865 0.983707585 0.99429709 1.22825332 0.637691351 0.765204745 0.787438585 0.77061527 0.701591089 1.049998056 1 12.23491526 -9.245070177 24.99943805 1.008379206 0.739493426 0.785752608 0.081659442 312.5635817 477354.9282 0.011735849 0.019426052 5.69E-10 9.245070177 -0.26888578 EDILENEDEQNS(ph)PPKK ddPTM_HeLa_Romidepsin_16h_R1 1 EDILENEDEQNSPPKK 16 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 EDILENEDEQNS(1)PPKK 76.573 0.0088726 7477600 2089 2014 1934.8 1421.9 2037 1750.3 1417.8 1785.7 2260.6 2247 TRUE FALSE FALSE 2063.538464 2042.353145 1968.474382 1586.306768 1933.044289 1638.461479 1538.227897 1837.366412 2058.406274 2188.622616 0.942848004 0.933168254 0.899412429 0.724796846 0.883224122 0.74862677 0.702829207 0.839508099 0.940503063 1 11.0958075 -9.58959892 0.814288872 0.981172763 0.764499781 0.673461631 0.056040023 0.212099262 0.281717102 0.010814558 0.019819051 2.57E-10 9.58959892 -0.216672982 EDIYSGGGGGGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 EDIYSGGGGGGSR 13 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 1 0 EDIYSGGGGGGS(1)R 103.13 0.010907 3813000 1607.8 1496.9 1205.8 1152.8 1580 1566.5 1540.3 1593.3 1960.7 1851.8 TRUE FALSE FALSE 1588.203515 1517.973397 1226.786443 1286.09216 1499.366704 1466.405706 1671.133044 1639.399622 1785.330081 1803.689969 0.880530214 0.841593302 0.680153721 0.713033937 0.831277398 0.813003194 0.926507921 0.908914309 0.989820929 1 10.81673566 -11.14007443 0.920020002 0.9798636 0.815100542 0.470082684 0.073152726 0.349425554 0.629097524 0.025587327 0.018116711 7.24E-12 11.14007443 -0.164763058 EDKS(ph)LSEAPEDTSTR ddPTM_HeLa_Romidepsin_16h_R1 1 EDKSLSEAPEDTSTR 15 1 Q5SY38;P41214 Q5SY38 EIF2D Eukaryotic translation initiation factor 2D 1 0 EDKS(0.85)LS(0.15)EAPEDTSTR 64.346 0.024434 3806300 2050.5 1988.4 1844.6 1524.3 1922.5 2248.5 1797.1 1782.8 2268.2 1856 TRUE FALSE FALSE 2025.507717 2016.392747 1876.704489 1700.546738 1824.387651 2104.828107 1949.745629 1834.382505 2065.326511 1807.780852 1.120438749 1.115396672 1.038126102 0.940681906 1.00918629 1.164315964 1.07852986 1.014715087 1.142465088 1 10.82000408 -12.66763766 1.544730978 1.000262704 1.069285026 0 0.075704094 0.679339256 2.935604905 0.047077635 0.010728055 2.15E-13 12.66763766 0.069022322 EDKS(ph)PETGTAGGSSTASYSAGR ddPTM_HeLa_Romidepsin_16h_R1 2 EDKSPETGTAGGSSTASYSAGR 22 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 EDKS(0.999)PET(0.001)GTAGGSSTASYSAGR;EDKS(0.998)PET(0.002)GTAGGSSTASYSAGR ; 84.291 0.0004528 19624500 3568.1 3214.4 3533.5 2204.2 3590.2 3703.1 3186.3 3596.7 3180.9 3411.3 TRUE FALSE FALSE 3524.610625 3259.652408 3594.999085 2459.059975 3406.978697 3466.483861 3456.944242 3700.76484 2896.392337 3322.673934 1.060775356 0.981032889 1.081959637 0.74008465 1.025372566 1.043281384 1.040410317 1.113791155 0.871705257 1 11.69812901 -7.294244491 1.562728677 1.008991583 1.145844012 0.094957787 0.100550445 1.843680769 4.355182855 0.013051291 0.377080047 5.08E-08 7.294244491 0.136852429 EDKSPSEESAPTT(ph)SPESVSGSVPSSGSSGR ddPTM_HeLa_Romidepsin_16h_R1 2 EDKSPSEESAPTTSPESVSGSVPSSGSSGR 30 1 P54725-2;P54725-3;P54725;A0A494C0B4 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 1 0 EDKSPSEESAPT(0.002)T(0.499)S(0.499)PESVSGSVPSSGSSGR;EDKSPSEESAPT(0.004)T(0.951)S(0.045)PESVSGSVPSSGSSGR ; 161.91 1.24E-14 124795000 3131.7 3507.9 2980.5 1836.12 3748.3 3597.6 2847 3843.3 3127.3 3381 TRUE FALSE FALSE 3093.529636 3557.284308 3032.374352 2048.420834 3557.010264 3367.724971 3088.824109 3954.499822 2847.586456 3293.161133 0.939379979 1.080203538 0.92080959 0.622022656 1.080120322 1.022642025 0.937951101 1.200821843 0.864696971 1 11.68525739 -7.258060173 24.09803586 0.960431422 1.200821992 0.263563649 0.126613832 209.5026871 1493898.378 0.016400606 0.158004567 5.52E-08 7.258060173 0.240390569 EDLESS(ph)GLQR ddPTM_HeLa_Romidepsin_16h_R1 1 EDLESSGLQR 10 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 0 EDLES(0.079)S(0.921)GLQR 120.77 0.011345 7627700 2285.7 2276.3 2311.3 1385 2778.5 3214.1 2112.9 2919.9 2172.9 2247.9 TRUE FALSE FALSE 2257.841009 2308.345811 2351.527207 1545.140217 2636.702777 3008.729383 2292.369673 3004.3827 1978.550382 2189.499234 1.031213427 1.054280255 1.074002297 0.705704845 1.204249235 1.37416325 1.046983547 1.372178009 0.903654293 1 11.09638523 -8.548525071 24.99987036 1.002040783 1.250447701 0.518197864 0.133333787 135.2852294 131874.6512 0.017121965 0.03424474 2.83E-09 8.548525071 0.248406918 EDLLS(ph)PVQDADR ddPTM_HeLa_Romidepsin_16h_R1 1 EDLLSPVQDADR 12 0 O94991-2;O94991 O94991-2 SLITRK5 SLIT and NTRK-like protein 5 1 0 EDLLS(1)PVQDADR 91.845 0.025966 931890 623.43 713.56 711.35 712.96 815.96 1085 423.76 958.03 698.33 625.01 TRUE FALSE FALSE 615.8313954 723.6055164 723.7307484 795.3957898 774.3185164 1015.672002 459.7541638 985.7490865 635.8696158 608.7721501 1.011595874 1.18863111 1.188836822 1.306557453 1.271934855 1.668394327 0.7552155 1.619241429 1.044511671 1 9.24975855 -9.923431718 1.264165234 1.000957604 1.30892757 0.235874281 0.23278212 0.400045596 1.263438678 0.03939062 0.054530768 1.19E-10 9.923431718 0.307969965 EDLPAENGET(ph)KTEESPAS(ph)DEAGEKEAK ddPTM_HeLa_Romidepsin_16h_R1 1 EDLPAENGETKTEESPASDEAGEKEAK 27 2 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 2 0 EDLPAENGET(0.883)KT(0.117)EES(0.191)PAS(0.809)DEAGEKEAK 57.578 0.0018471 4797400 683.2 769.63 728.83 666.39 705.47 947.63 721.75 984.55 892.01 873.41 TRUE FALSE FALSE 674.8728956 780.4648713 741.5149804 743.4411473 669.4672334 887.0795013 783.055427 1013.036401 812.2263915 850.7186823 0.793297373 0.917418281 0.871633592 0.873897756 0.786943143 1.042741296 0.920463419 1.190800698 0.954753209 1 9.732538327 EDLPAENGETKTEES(ph)PAS(ph)DEAGEK ddPTM_HeLa_Romidepsin_16h_R1 1 EDLPAENGETKTEESPASDEAGEK 24 1 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 2 0 EDLPAENGET(0.007)KT(0.123)EES(0.949)PAS(0.921)DEAGEK 75.054 0.0013169 5869700 2471.6 2382.9 2293.2 935.67 2447.5 2960 2670.5 2542.3 2245.4 2530.2 TRUE FALSE FALSE 2441.475189 2416.446529 2333.112184 1043.856568 2322.594942 2770.865553 2897.332203 2615.857439 2044.5658 2464.465039 0.990671464 0.980515645 0.946701271 0.423563147 0.942433715 1.124327393 1.175643459 1.061430127 0.829618505 1 11.2670588 -5.682291493 14.99090596 0.974829926 1.009124511 0 0.199477851 0 0 0.026048445 0 2.08E-06 5.682291493 0.034294586 EDLPAENGETKTEES(ph)PASDEAGEK ddPTM_HeLa_Romidepsin_16h_R1 2 EDLPAENGETKTEESPASDEAGEK 24 1 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 1 0 EDLPAENGET(0.002)KT(0.022)EES(0.784)PAS(0.192)DEAGEK;EDLPAENGET(0.068)KT(0.068)EES(0.835)PAS(0.028)DEAGEK ; 72.578 0.00036402 23696000 3879.1 3624.4 4055 1931.06 4059.4 5129.2 4919.4 4630.4 4331.8 4345.2 TRUE FALSE FALSE 3831.820037 3675.424398 4125.575574 2154.338243 3852.23367 4801.460674 5337.253713 4764.373318 3944.352959 4232.311078 0.905372967 0.868420192 0.974780799 0.509021715 0.91019625 1.13447726 1.261073115 1.125714351 0.931961967 1 12.04722996 -8.1958208 4.395617299 0.912153451 1.191314247 0.493805398 0.13654766 0.164896358 6.34125618 0.020516929 0.054230713 6.37E-09 8.1958208 0.279160796 EDLRLPEGDLGK ddPTM_HeLa_Romidepsin_16h_R1 2 EDLRLPEGDLGK 12 1 I3L397;I3L504;P63241;P63241-2 I3L397 EIF5A Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1 0 0 ; ; 103.43 0.015833 134307000 12682.3 12953.3 13504.3 7912.4 12711.4 12986.8 10829.8 12113.1 13156.9 12849.6 FALSE FALSE TRUE 12527.72325 13135.6569 13739.33668 8827.268917 12062.68983 12156.98539 11749.68294 12463.57344 11980.11391 12515.76554 1.000955412 1.049528841 1.097762389 0.705291969 0.9637996 0.971333743 0.938790592 0.995829891 0.957201849 1 13.61145892 EDLSPAFDHS(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 4 EDLSPAFDHSPNK 13 0 K7EIY0;K7ENP9;K7EIE9;D3DUJ3;K7EQG9;P17706-3;P17706-2;P17706-4;P17706 K7EIY0 PTPN2 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 2 1 0 EDLS(0.045)PAFDHS(0.955)PNK;EDLS(0.041)PAFDHS(0.959)PNK;EDLSPAFDHS(1)PNK;EDLSPAFDHS(1)PNK ;;; 141 6.84E-05 26354000 14749.1 13847.4 15461.8 10813 12483.1 13134.3 10413 11167 17852.7 16759.5 TRUE FALSE FALSE 14569.3323 14042.34406 15730.90614 12063.24994 11846.04083 12295.06062 11297.47996 11490.09953 16255.9098 16324.08577 0.892505253 0.860222389 0.963662306 0.738984719 0.725678668 0.75318525 0.692074283 0.703873999 0.995823596 1 13.99471458 -8.94360557 0.293428501 1.002253108 0.593726094 0.832177908 0.048300784 0.897845059 0.131792666 0.033605344 0.12826191 1.14E-09 8.94360557 -0.408527013 EDLVGPEVGAS(ph)PQSGR ddPTM_HeLa_Romidepsin_16h_R1 2 EDLVGPEVGASPQSGR 16 0 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 0 EDLVGPEVGAS(0.997)PQS(0.003)GR;EDLVGPEVGAS(0.952)PQS(0.048)GR ; 113.14 0.0030002 17937200 4047.7 4678.6 5217.5 3134.3 4878.4 4287.2 3053.7 3491.6 4637.2 4518.1 TRUE FALSE FALSE 3998.365075 4744.465454 5308.308399 3496.702513 4629.437044 4013.261756 3313.081202 3592.623937 4222.437218 4400.719111 0.908570844 1.078111403 1.206236587 0.794575256 1.051972854 0.9119559 0.752849959 0.816372017 0.959488009 1 12.10352357 -7.917979845 4.424114003 0.977651837 0.786706255 0.389209243 0.104580385 0.172712508 6.251605136 0.01458817 0.046756652 1.21E-08 7.917979845 -0.190945582 EDLVGPEVGAS(ph)PQSGRK ddPTM_HeLa_Romidepsin_16h_R1 2 EDLVGPEVGASPQSGRK 17 1 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 0 EDLVGPEVGAS(1)PQSGRK;EDLVGPEVGAS(0.895)PQS(0.105)GRK ; 101.62 0.00089882 21419300 5937.7 5190 6165.8 5325.2 5558.5 4416.7 4004.1 4121.1 5776.6 5499.4 TRUE FALSE FALSE 5865.329029 5263.064956 6273.113163 5940.92468 5274.829003 4134.487124 4344.208154 4240.337526 5259.926428 5356.524795 1.094987749 0.98255215 1.171116237 1.109100566 0.984748359 0.771859981 0.811012423 0.791621002 0.981966224 1 12.3870816 -8.377231648 3.74003744 1.055055136 0.793091087 0.808422314 0.057601906 0.076407421 1.908255029 0.008563942 0.020294306 4.20E-09 8.377231648 -0.261964049 EDLYLK(ac)PIQR ddPTM_HeLa_Romidepsin_16h_R1 1 EDLYLKPIQR 10 1 P13639 P13639 EEF2 Elongation factor 2 0 1 EDLYLK(1)PIQR 132.01 0.0089333 3948500 972.2 931.54 965.63 544.42 1754.5 1680.3 1322.8 1176.3 1861.4 1360.9 FALSE TRUE FALSE 960.3504525 944.6542446 982.4363851 607.368402 1664.961318 1572.934253 1435.158599 1210.334385 1694.911722 1325.543622 0.724495548 0.712654211 0.74115734 0.458203255 1.256059243 1.186633338 1.082694357 0.913085292 1.278654051 1 10.37236843 -8.729114952 24.99987827 0.81730758 1.113196015 0.30217309 0.216175041 163.0509542 126103.7899 0.027055792 0.054108254 1.87E-09 8.729114952 0.295888434 EDMAALEKDYEEVGADS(ph)ADGEDEGEEY ddPTM_HeLa_Romidepsin_16h_R1 1 EDMAALEKDYEEVGADSADGEDEGEEY 27 1 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 1 0 EDMAALEKDY(0.001)EEVGADS(0.988)ADGEDEGEEY(0.011) 55.734 0.0050024 13977000 5376.1 3971.5 4785.8 4991.5 4730.5 4408.1 3559.8 4656 5271.2 4474 TRUE FALSE FALSE 5310.574025 4027.410881 4869.094841 5568.640716 4489.084933 4126.436636 3862.169323 4790.714014 4799.73067 4357.764835 1.218646308 0.924191881 1.117337678 1.277866275 1.030134737 0.94691586 0.886273002 1.099351203 1.101420304 1 12.08937263 -8.527168741 24.98135833 1.104867032 0.971745294 0.235734192 0.10530325 141.3932758 823355.2248 0.017131123 0.034374772 2.97E-09 8.527168741 -0.133121738 EDMAALEKDYEEVGADSADGEDEGEEY ddPTM_HeLa_Romidepsin_16h_R1 1 EDMAALEKDYEEVGADSADGEDEGEEY 27 1 Q9BQE3;F5H5D3 Q9BQE3 TUBA1C Tubulin alpha-1C chain 0 0 52.522 0.025462 36413000 9527.1 8607.1 9229.6 11403 10713 10667 9385.7 9938.9 11183 9049.2 FALSE FALSE TRUE 9410.980041 8728.27098 9390.237316 12721.46851 10166.27563 9985.413126 10182.92112 10226.46639 10182.76447 8814.100479 1.067718715 0.990262251 1.065365358 1.443308769 1.153410454 1.132890775 1.155298961 1.16023937 1.155281188 1 13.10559763 -9.499277652 24.99549682 1.029651207 1.204285972 0.388877204 0.09424438 486.2936399 515025.6967 0.013062528 0.019878804 3.17E-10 9.499277652 0.174634765 EDMAALEKDYEEVGVDSVEGEGEEEGEEY ddPTM_HeLa_Romidepsin_16h_R1 1 EDMAALEKDYEEVGVDSVEGEGEEEGEEY 29 1 Q71U36-2;Q71U36;P68363;P68363-2 Q71U36-2 TUBA1A;TUBA1B Tubulin alpha-1A chain;Tubulin alpha-1B chain 0 0 85.11 1.99E-06 11729000 2924.9 2676 2897.7 3792.4 3445.2 3439.8 2416 3354.2 3908.4 3326.4 FALSE FALSE TRUE 2889.250194 2713.672798 2948.133253 4230.895132 3269.378588 3220.007881 2621.21498 3451.248485 3558.822915 3239.979648 0.891749488 0.837558594 0.909923386 1.305840033 1.009073804 0.993835836 0.809022051 1.065206841 1.098409034 1 11.66176904 -12.95927721 2.281430772 1.000560851 0.958257667 0 0.137727015 1.834457362 17.32003716 0.110751622 0.020510905 1.10E-13 12.95927721 -0.042303183 EDNPEEPSKEITSHEEGGGDVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EDNPEEPSKEITSHEEGGGDVSPR 24 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 0 EDNPEEPS(0.002)KEIT(0.041)S(0.137)HEEGGGDVS(0.82)PR;EDNPEEPS(0.001)KEIT(0.005)S(0.025)HEEGGGDVS(0.97)PR ; 54.596 0.0049175 10661900 3946.4 3166 3606.3 2357.18 2877.5 2750 2547.4 3070.4 3613.9 4308 TRUE FALSE FALSE 3898.299759 3210.571031 3669.066139 2629.728242 2730.650438 2574.283875 2763.776092 3159.23718 3290.663733 4196.077539 0.929034252 0.76513625 0.874403798 0.62671107 0.650762626 0.61349769 0.658657059 0.752902479 0.784223767 1 12.03482562 -9.909189549 0.85119214 0.980473604 0.653761325 0.532639746 0.086757422 0.145974853 0.211569625 0.01284905 0.018859473 1.23E-10 9.909189549 -0.326712279 EDQPWMVIEGIR ddPTM_HeLa_Romidepsin_16h_R1 1 EDQPWMVIEGIR 12 0 M0R366;Q9BTV5 M0R366 FSD1 Fibronectin type III and SPRY domain-containing protein 1 0 0 108.47 0.028293 1634300 1362 1266.8 1172.5 966.45 1020.4 1427.4 1052.1 1174.1 1444.5 1548.2 FALSE FALSE TRUE 1345.39942 1284.634044 1192.906871 1078.195496 968.3251804 1336.193747 1141.465348 1208.070731 1315.300302 1507.977541 0.892187969 0.851892027 0.791064083 0.7149944 0.642135015 0.886083321 0.756951159 0.801119843 0.872228045 1 10.55839923 -10.49125687 0.778275092 0.976329094 0.759693462 0.483367077 0.069519214 0.242475568 0.309991721 0.017321223 0.017835049 3.23E-11 10.49125687 -0.216635632 EDQTEYLEER ddPTM_HeLa_Romidepsin_16h_R1 2 EDQTEYLEER 10 0 P08238;Q58FF7;Q58FF6;P07900-2;P07900;G3V2J8 P08238;P07900-2 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 0 ; ; 208.33 2.53E-12 592130000 7209.1 6857.2 8031.8 4334.5 7422.5 8617.5 7138.3 7557.1 7734.3 7011.3 FALSE FALSE TRUE 7121.232716 6953.735842 8171.59011 4835.675284 7043.702128 8066.869562 7744.627024 7775.752765 7042.524837 6829.145415 1.042770696 1.018243926 1.196575796 0.708093764 1.031417798 1.18124144 1.134055076 1.138612856 1.031245406 1 12.73748934 -8.322559439 6.542467136 1.010385173 1.149350456 0.259803474 0.113732637 0.2440855 21.34429727 0.015433584 0.034947514 4.76E-09 8.322559439 0.138965282 EDQTEYLEERR ddPTM_HeLa_Romidepsin_16h_R1 4 EDQTEYLEERR 11 1 P08238;Q58FF7;P07900-2;P07900;G3V2J8 P08238;P07900-2 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 204.32 1.80E-13 52829200 10425.9 10795.6 7977.9 13452.5 10759.7 9857 9627.3 9859.9 11109.2 8683.6 FALSE FALSE TRUE 10298.82512 10947.58074 8116.752003 15007.94135 10210.59236 9227.169512 10445.04262 10145.18065 10115.56533 8457.99882 1.217643244 1.294346449 0.959653953 1.774408068 1.207211372 1.090940033 1.234930726 1.199477662 1.195976205 1 13.04610064 -11.83897592 0.613264425 0.988504053 1.256463188 0.047311397 0.206375159 1.141231132 0.777338265 0.157572409 0.04630184 1.45E-12 11.83897592 0.267959135 EDS(ph)APPSSVAR ddPTM_HeLa_Romidepsin_16h_R1 1 EDSAPPSSVAR 11 0 Q9BZE4-3;Q9BZE4-2;Q9BZE4 Q9BZE4-3 GTPBP4 Nucleolar GTP-binding protein 1 1 0 EDS(0.61)APPS(0.357)S(0.033)VAR 145.23 0.0024956 6842100 2806.8 3800.4 3021.6 2497.5 2994.5 3147.5 2460.9 2885.8 3220 3172.9 TRUE FALSE FALSE 2772.589642 3853.902131 3074.18968 2786.272701 2841.679491 2946.384908 2669.928785 2969.29607 2931.995135 3090.467601 0.897142439 1.247028809 0.994732862 0.901569944 0.919498231 0.953378352 0.863923888 0.960791846 0.948722172 1 11.59360943 -9.262782511 24.06639262 0.980019948 0.918571514 0.163530281 0.092751273 153.4642679 2749795.679 0.015322865 0.024229715 5.46E-10 9.262782511 -0.061448434 EDS(ph)FESLDSLGSR ddPTM_HeLa_Romidepsin_16h_R1 1 EDSFESLDSLGSR 13 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 EDS(0.94)FES(0.06)LDSLGSR 121.92 0.0044964 23203000 1622 1357.3 1488.8 1711 1588.2 2002.8 1540.2 1835.6 2337.3 1602.7 TRUE FALSE FALSE 1602.23044 1376.408105 1514.711939 1908.83387 1507.148228 1874.827544 1671.02455 1888.71019 2128.246034 1561.061623 1.02637232 0.881712858 0.97030887 1.22277932 0.965463634 1.200995218 1.070441118 1.209888298 1.363332493 1 10.60831177 -9.283180757 24.98230768 0.998010902 1.124755715 0.02548062 0.141263416 607.0399106 697528.0691 0.011695268 0.01787487 5.21E-10 9.283180757 0.126744813 EDS(ph)GTFSLGK ddPTM_HeLa_Romidepsin_16h_R1 3 EDSGTFSLGK 10 0 G5E9Q4;O75569 G5E9Q4 PRKRA Interferon-inducible double-stranded RNA-dependent protein kinase activator A 1 0 EDS(0.93)GT(0.064)FS(0.007)LGK;EDS(0.859)GT(0.14)FS(0.001)LGK;EDS(0.974)GT(0.015)FS(0.01)LGK ;; 150.09 0.0037426 191716000 10959.4 10546.3 11011.8 5842 8571.2 9654.1 8666.3 8613.3 11003.3 10705.4 TRUE FALSE FALSE 10825.82262 10694.77109 11203.45576 6517.479527 8133.77968 9037.234167 9402.415306 8862.512246 10019.13729 10427.27216 1.038221929 1.025653778 1.074437838 0.625041662 0.78004866 0.866692077 0.901713809 0.849935832 0.960858903 1 13.34807417 -9.287992431 24.99768892 1.023043718 0.812152786 0.674281339 0.074659937 332.744936 313253.2261 0.01140033 0.017417425 5.15E-10 9.287992431 -0.210890932 EDSAPPS(ph)SVAR ddPTM_HeLa_Romidepsin_16h_R1 1 EDSAPPSSVAR 11 0 Q9BZE4-3;Q9BZE4-2;Q9BZE4 Q9BZE4-3 GTPBP4 Nucleolar GTP-binding protein 1 1 0 EDS(0.245)APPS(0.511)S(0.245)VAR 120.03 0.01002 4492500 3098.6 3219.4 3183.2 2633.3 2874.2 2744 2004 2367 2996.2 3312.9 TRUE FALSE FALSE 3060.833071 3264.722798 3238.602261 2937.774536 2727.518849 2568.667256 2174.21971 2435.48541 2728.212368 3226.83038 0.948557163 1.011742922 1.003648125 0.910421122 0.845262542 0.796034174 0.673794236 0.754760903 0.845477464 1 11.65590203 -8.499602553 1.267681906 0.980371327 0.71418741 0.768176903 0.052812548 0.092484205 0.283020491 0.00522035 0.017580733 3.17E-09 8.499602553 -0.266183917 EDSFES(ph)LDSLGSR ddPTM_HeLa_Romidepsin_16h_R1 1 EDSFESLDSLGSR 13 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 EDS(0.317)FES(0.683)LDSLGSR 234.04 3.33E-41 23087000 1859.9 2035.2 1654.2 1601.1 2131.5 2008.6 2028.7 1950 1848.8 1659.6 TRUE FALSE FALSE 1837.230823 2063.851599 1682.990657 1786.226715 2022.721601 1880.256942 2201.017727 2006.420173 1683.438698 1616.483353 1.136560312 1.276754008 1.041143204 1.105007801 1.251309887 1.163177424 1.361608657 1.241225386 1.041420374 1 10.65864293 -4.000000013 0.039603561 0.430814662 2.383996531 0.521802986 0.077792285 363.4902618 1.107946057 15.22397913 48.21710307 1.00E-04 4.000000013 1.953181869 EDSGLFS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 4 EDSGLFSPIR 10 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 0 EDSGLFS(1)PIR;EDS(0.001)GLFS(0.999)PIR;EDS(0.007)GLFS(0.993)PIR;EDSGLFS(1)PIR ;;; 150.09 0.0037422 44630500 9302.3 7863.5 10154.7 10604.2 19331.2 18996.4 16121.9 16992.4 9806.4 8367 TRUE FALSE FALSE 9188.91999 7974.202559 10331.43829 11830.3075 18344.65673 17782.59135 17491.29378 17484.04828 8929.291023 8149.624134 1.127526845 0.978474888 1.267719606 1.45163842 2.250981938 2.18201368 2.146269999 2.14538094 1.095669061 1 12.99251781 -8.964880796 2.121508363 1.063782195 2.191044542 0.967729138 0.093380622 0.036728732 0.332152311 0.014631565 0.028847998 1.08E-09 8.964880796 1.127262347 up EDSGSS(ph)SPPGVFLEK ddPTM_HeLa_Romidepsin_16h_R1 1 EDSGSSSPPGVFLEK 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 EDSGS(0.001)S(0.499)S(0.499)PPGVFLEK 130.66 3.09E-05 0 1159.6 1091.6 1386.5 1048.2 1813.7 2392.6 2068.6 2133.7 1112.8 938.52 TRUE FALSE FALSE 1145.466349 1106.967573 1410.631451 1169.397816 1721.140121 2239.720582 2244.306832 2195.435243 1013.268381 914.1371151 1.253057479 1.210942598 1.543128955 1.279236776 1.88280302 2.450092601 2.455109628 2.401647638 1.108442447 1 9.836266767 -8.601938214 1.073253967 1.136556798 2.537762213 0.933930746 0.143616125 0.098198511 0.213527835 0.026065208 0.090133248 2.50E-09 8.601938214 1.401205415 up EDSGSSS(ph)PPGVFLEK ddPTM_HeLa_Romidepsin_16h_R1 1 EDSGSSSPPGVFLEK 15 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 EDS(0.001)GS(0.003)S(0.018)S(0.979)PPGVFLEK 147.75 0.00047856 5442900 1316.6 1398.9 1361.3 1026.9 2198 2855.5 2551.6 2849.8 1351.4 1343.5 TRUE FALSE FALSE 1300.552773 1418.593751 1384.992855 1145.63501 2085.827858 2673.042766 2768.33284 2932.254467 1230.527399 1308.595676 0.99385379 1.084058106 1.058381042 0.875469047 1.593943718 2.04268042 2.115498997 2.240764294 0.940341942 1 10.35380369 -8.478036268 2.300207753 1.000529408 2.15314892 0.975003239 0.082108456 0.028891571 0.300605574 0.011189381 0.02816506 3.33E-09 8.478036268 1.152619511 up EDSGSSS(ph)PPGVFLEKDYEIYR ddPTM_HeLa_Romidepsin_16h_R1 1 EDSGSSSPPGVFLEKDYEIYR 21 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 EDS(0.004)GS(0.051)S(0.193)S(0.753)PPGVFLEKDYEIYR 88.282 0.00046992 3761500 812.46 731.43 632.44 788.63 1251.9 1040.4 1169 1211.8 789.41 857.74 TRUE FALSE FALSE 802.557425 741.7270907 643.4473529 879.8151112 1188.010872 973.9217977 1268.294831 1246.861521 718.8031925 835.4557911 0.960622254 0.887811298 0.770175226 1.053095951 1.421991306 1.165737084 1.518087305 1.492432675 0.860372506 1 9.706419679 -8.839406914 4.333931197 0.956425906 1.392541596 0.807306584 0.114296966 0.074953072 2.659109491 0.016780991 0.031609334 1.45E-09 8.839406914 0.43611569 EDSGSVPSTGPS(ph)QGTPISLK ddPTM_HeLa_Romidepsin_16h_R1 1 EDSGSVPSTGPSQGTPISLK 20 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 0 EDSGSVPS(0.005)T(0.035)GPS(0.955)QGT(0.004)PIS(0.001)LK 104.81 0.00053324 11083000 1972.4 1714.8 2912.6 2210.5 3020.1 3316.9 2614.9 2923.4 2308.9 1911.6 TRUE FALSE FALSE 1948.35963 1738.940999 2963.292581 2466.088411 2865.973027 3104.960795 2837.009541 3007.983967 2102.386201 1861.936356 1.046415804 0.933942234 1.591511209 1.324475137 1.539243282 1.667597705 1.523687709 1.615513847 1.129139669 1 10.86258805 -9.759527584 24.99999993 1.015932763 1.538231433 0.873946976 0.096006618 11.15831739 145912.7442 0.014143971 0.019429077 1.74E-10 9.759527584 0.52229867 EDTDHEEKAS(ph)NEDVTK ddPTM_HeLa_Romidepsin_16h_R1 2 EDTDHEEKASNEDVTK 16 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 EDTDHEEKAS(0.986)NEDVT(0.014)K;EDTDHEEKAS(0.967)NEDVT(0.033)K ; 77.037 0.01075 36869000 5272 5545.3 5669 3130.4 5587.2 6286.8 5961.1 6567.8 5702.1 5761.9 TRUE FALSE FALSE 5207.742836 5623.366879 5767.666567 3492.351577 5302.064335 5885.09377 6467.435685 6757.828931 5192.089895 5612.205007 0.927931683 1.001988857 1.02770062 0.622277977 0.944738178 1.048624161 1.15238764 1.204130805 0.925142593 1 12.45435199 -7.899852461 2.464306317 0.945780886 1.188941669 0.464178936 0.109175112 0.217326406 2.593545567 0.015939766 0.064510626 1.26E-08 7.899852461 0.243160783 EDTEEYNLR ddPTM_HeLa_Romidepsin_16h_R1 1 EDTEEYNLR 9 0 P51991;P51991-2 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 0 229.44 2.37E-25 15864000 2964.5 2715 3102.3 1481.7 2770.4 2838.6 2377.6 2519 2848.2 3377.3 FALSE FALSE TRUE 2928.367534 2753.221841 3156.29423 1653.021126 2629.01615 2657.222621 2579.553285 2591.883291 2593.449859 3289.557259 0.890201113 0.836958175 0.959489068 0.502505655 0.799200605 0.807775154 0.784164275 0.787912502 0.788388727 1 11.68367771 -10.40322454 0.673475379 0.977836891 0.756889171 0.12081435 0.119189307 0.438904553 0.431772847 0.03018941 0.032486829 3.95E-11 10.40322454 -0.22094772 EDVEVAES(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 2 EDVEVAESPLR 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 EDVEVAES(1)PLR;EDVEVAES(1)PLR ; 158.34 0.0016346 324960000 8227 7854.5 8251.6 6666.5 8653.2 8919.6 6905.9 7792.4 8489.7 6932.4 TRUE FALSE FALSE 8126.72616 7965.075857 8395.215637 7437.312097 8211.594914 8349.666347 7492.486974 8017.8608 7730.359969 6752.295249 1.20355018 1.179610127 1.243312878 1.101449481 1.216119055 1.236567129 1.109620758 1.18742746 1.144849223 1 12.72116227 -12.23223347 0.815149068 0.991533051 1.185262014 0.222834176 0.062790738 0.294458942 0.328079695 0.036663636 0.008602749 5.86E-13 12.23223347 0.193728964 EDVEVAES(ph)PLRVLAETPDSFEK ddPTM_HeLa_Romidepsin_16h_R1 2 EDVEVAESPLRVLAETPDSFEK 22 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 EDVEVAES(0.993)PLRVLAET(0.005)PDS(0.002)FEK;EDVEVAES(0.999)PLRVLAET(0.001)PDSFEK ; 58.107 0.0062055 17356500 3320.95 3166.86 2497.46 4764.3 3011.58 3488.7 2276.95 3025.56 3334.48 2768.62 TRUE FALSE FALSE 3280.472984 3211.443138 2540.927244 5315.170783 2857.887835 3265.783329 2470.354076 3113.099805 3036.235757 2696.690853 1.216480925 1.190882942 0.942238982 1.970997445 1.059775848 1.211033636 0.916068697 1.15441479 1.125911691 1 11.39697443 -12.12853437 0.745893993 0.990433486 1.211112143 0.034106223 0.278792624 1.709780005 1.611977971 0.226039142 0.055825575 7.44E-13 12.12853437 0.220678657 EDVEVVGGS(ph)DGEGAIGLSSDPK ddPTM_HeLa_Romidepsin_16h_R1 1 EDVEVVGGSDGEGAIGLSSDPK 22 0 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 1 0 EDVEVVGGS(1)DGEGAIGLSSDPK 77.907 0.00086614 5657800 5195 4946.6 5061.3 3671.1 4758.5 4807.2 4292.5 4333.1 5505.2 5356.4 TRUE FALSE FALSE 5131.681342 5016.238365 5149.389803 4095.569855 4515.655989 4500.035435 4657.104843 4458.471412 5012.801124 5217.239956 0.98360079 0.961473577 0.98699501 0.785006994 0.865525839 0.862531812 0.892637656 0.854565144 0.960814754 1 12.34907107 -9.282974015 24.615564 0.988902134 0.855638762 0.827808963 0.028636197 171.2368127 195734.9006 0.004171408 0.006375734 5.21E-10 9.282974015 -0.133263373 EDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_HeLa_Romidepsin_16h_R1 2 EDVSNFDDEFTSEAPILTPPREPR 24 1 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 EDVSNFDDEFTSEAPILT(1)PPREPR;EDVSNFDDEFTSEAPILT(1)PPREPR ; 137.12 1.13E-06 33403000 4271.6 4454.6 4342.7 3673.5 4169.1 4295.7 3435.5 4100.4 4700.5 4117.9 TRUE FALSE FALSE 4219.536096 4517.311976 4418.282872 4098.247354 3956.33527 4021.218634 3727.311284 4219.038605 4280.075507 4010.916364 1.052012985 1.126254343 1.101564448 1.021773326 0.986391864 1.002568558 0.929291699 1.05188895 1.067106646 1 11.96971617 -8.889737542 4.616341274 1.040481644 0.988964904 0.29673529 0.046192053 0.28906816 10.49765793 0.007662247 0.014207288 1.29E-09 8.889737542 -0.05151674 EDVTKDADLS(ph)PVNASIIK ddPTM_HeLa_Romidepsin_16h_R1 2 EDVTKDADLSPVNASIIK 18 1 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 EDVT(0.001)KDADLS(0.998)PVNAS(0.001)IIK;EDVT(0.003)KDADLS(0.997)PVNAS(0.001)IIK ; 106.63 0.00057422 33448000 8913.8 7969.5 8285.6 7783.9 11007 11433.2 9490.4 10303.7 8694.4 8890.9 TRUE FALSE FALSE 8805.155177 8081.69483 8429.807392 8683.911142 10445.27172 10702.65542 10296.51434 10601.8213 7916.751088 8659.913136 1.016771766 0.933230473 0.973428631 1.00277116 1.206163567 1.235884847 1.188985868 1.224241068 0.91418366 1 13.08013684 -8.758410977 6.467309451 0.998446912 1.214568407 0.908952107 0.036778801 0.025381971 4.576772998 0.00410639 0.007909233 1.74E-09 8.758410977 0.216121494 EEAAMLES(ph)LTSANVVLATNTGAS(ph)ADGPLK ddPTM_HeLa_Romidepsin_16h_R1 1 EEAAMLESLTSANVVLATNTGASADGPLK 29 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 2 0 EEAAMLES(0.68)LT(0.176)S(0.176)ANVVLAT(0.071)NT(0.179)GAS(0.72)ADGPLK 40.428 0.0042729 0 1069.3 769.09 606.65 1387.7 607.66 452.19 668.54 737.28 968.01 1158.4 TRUE FALSE FALSE 1056.26696 779.9172692 617.2084888 1548.152403 576.6488427 423.2965184 725.3257709 758.6120336 881.4287612 1128.304601 0.936154084 0.691229362 0.54702293 1.372105017 0.511075504 0.375161564 0.642845709 0.67234684 0.781197524 1 10.13994088 -9.089565058 0.379584573 1.005527882 0.494406355 0.130613119 0.254465873 1.794031433 0.456509786 0.101752911 0.362615923 8.14E-10 9.089565058 -0.511121528 EEAATGGGS(ph)TGEADGK ddPTM_HeLa_Romidepsin_16h_R1 1 EEAATGGGSTGEADGK 16 0 O43242 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 1 0 EEAAT(0.076)GGGS(0.462)T(0.462)GEADGK 134.88 0.0014501 5986600 863.6 934.76 1108.7 550.68 995.09 1258.3 915.09 657.82 1207.7 1067.8 TRUE FALSE FALSE 853.074111 947.9195758 1127.996458 614.3522126 944.3068441 1177.898691 992.8177218 676.8529838 1099.680287 1040.058402 0.820217508 0.91140995 1.084551075 0.590690111 0.907936364 1.132531297 0.95457882 0.650783631 1.057325517 1 10.02244883 -12.55486432 1.318860486 1.000134377 0.882335095 0.111451405 0.160243905 1.05013987 3.266734206 0.110272463 0.025919432 2.79E-13 12.55486432 -0.117799282 EEADEYIDIGALNGIFVLGR ddPTM_HeLa_Romidepsin_16h_R1 1 EEADEYIDIGALNGIFVLGR 20 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 0 139.77 0.001629 1383400 0 142.56 58.987 144.93 184.16 192.17 101.86 0 199.01 178.29 FALSE FALSE TRUE 0 144.5669634 60.01364399 161.6874885 174.761628 179.8909572 110.5119859 0 181.2100472 173.6580001 0 0.832480872 0.345585254 0.93106847 1.00635518 1.035892139 0.636377165 0 1.043488046 1 7.440105064 -9.260673451 24.9996856 0.531060894 0.750427959 0 0.405652024 192.827563 6293787.921 0.07106764 0.113448522 5.49E-10 9.260673451 0.219367065 EEAENTLQS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 EEAENTLQSFR 11 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 1 0 EEAENTLQS(1)FR 105.66 0.0025429 0 883.33 788.74 829.47 541.73 847.58 776.41 600.47 809.35 854.25 931.38 TRUE FALSE FALSE 872.5636342 799.8439024 843.9065774 604.3673715 804.3248298 726.7999067 651.4739068 832.7672653 777.8437405 907.1826133 0.961839018 0.881679047 0.930249946 0.666202551 0.886618436 0.801161636 0.71812874 0.917970928 0.857427963 1 9.82524918 -9.899985128 1.226982131 0.985596153 0.801015645 0.271741361 0.085573956 0.225420937 0.672051725 0.013054697 0.018331799 1.26E-10 9.899985128 -0.184580508 EEAENTLQS(ph)FRQDVDNASLAR ddPTM_HeLa_Romidepsin_16h_R1 2 EEAENTLQSFRQDVDNASLAR 21 1 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 1 0 EEAENT(0.078)LQS(0.922)FRQDVDNASLAR;EEAENT(0.209)LQS(0.791)FRQDVDNASLAR ; 98.292 0.00020465 15640400 1329.32 1060.07 1169.23 874.04 1134.17 1233.8 888.42 1165.78 1257.8 1006.68 TRUE FALSE FALSE 1313.117737 1074.993693 1189.579958 975.1006173 1076.289073 1154.964162 963.8823726 1199.510005 1145.299218 980.5263085 1.339196843 1.096343549 1.213205548 0.994466552 1.097664656 1.177902267 0.983025508 1.223332811 1.168045373 1 9.93741253 -9.292157757 24.80461733 1.162057587 1.093764818 0.094670738 0.10517453 1594.073343 1287185.063 0.021474723 0.032805114 5.10E-10 9.292157757 -0.068292769 EEAENTLQSFR ddPTM_HeLa_Romidepsin_16h_R1 1 EEAENTLQSFR 11 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 155.53 0.020831 101030000 2385.8 2527.9 2399.2 1941.2 2436.1 2425.2 2059.5 2187.1 2453.6 2393.6 FALSE FALSE TRUE 2356.720952 2563.487843 2440.95707 2165.650678 2311.776727 2270.237547 2234.433879 2250.380288 2234.143871 2331.413927 1.010854797 1.099542133 1.046985712 0.92890012 0.991577128 0.973759966 0.958402904 0.965242706 0.958278513 1 11.18698945 -9.265674067 24.99261566 1.016693455 0.965410471 0.387821859 0.036936623 324.878319 1917392.903 0.005433091 0.008481982 5.42E-10 9.265674067 -0.051282983 EEAIEHNYGGHDDDLSVR ddPTM_HeLa_Romidepsin_16h_R1 1 EEAIEHNYGGHDDDLSVR 18 0 Q93009;A0A669KBL1;Q93009-3;F5H2X1;H3BND8 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7;Ubiquitin carboxyl-terminal hydrolase 0 0 163.44 6.60E-07 3517800 2232.4 2299.6 2013.2 1711.1 1918.4 2029.1 1536.3 1762.3 2322.1 2357.3 FALSE FALSE TRUE 2205.19065 2331.973829 2048.238902 1908.945433 1820.496889 1899.447059 1666.793284 1813.28937 2114.40556 2296.057006 0.960425044 1.015642827 0.892067965 0.831401584 0.792879656 0.827264765 0.725937239 0.789740571 0.920885481 1 11.16494275 -9.338642414 1.571379038 0.984120092 0.781005543 0.851053975 0.035687606 0.078031231 0.377926758 0.004952113 0.008759641 4.59E-10 9.338642414 -0.203114549 EEAKES(ph)PSAAGPEDK ddPTM_HeLa_Romidepsin_16h_R1 1 EEAKESPSAAGPEDK 15 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 EEAKES(0.867)PS(0.133)AAGPEDK 65.954 0.022136 12699000 1876.5 1428 1972.1 1664.5 2594.9 3171.1 2718.9 2666.1 2184.7 2130.7 TRUE FALSE FALSE 1853.628496 1448.103421 2006.423573 1856.957322 2462.47257 2968.476944 2949.843298 2743.239397 1989.29496 2075.344107 0.89316682 0.697765453 0.966790792 0.894770807 1.186537 1.430354096 1.421375515 1.321823879 0.958537408 1 11.01913485 -8.556741498 2.993811016 0.925175861 1.391790763 0.871183947 0.084806 0.073081814 1.333629155 0.013861173 0.031154944 2.77E-09 8.556741498 0.466614902 EEAKESPS(ph)AAGPEDK ddPTM_HeLa_Romidepsin_16h_R1 1 EEAKESPSAAGPEDK 15 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 EEAKES(0.419)PS(0.581)AAGPEDK 61.276 0.028824 11116000 2248.4 2097.1 2128.3 1576.5 3035.5 3682.9 2614.9 2885.5 2234.8 2462.7 TRUE FALSE FALSE 2220.995636 2126.623029 2165.342169 1758.782348 2880.587108 3447.574576 2837.009541 2968.98739 2034.913891 2398.718699 0.925909168 0.886566245 0.902707837 0.733217425 1.200885752 1.437256723 1.182718733 1.237738878 0.848333692 1 11.22804827 -8.59313393 7.470686114 0.938376041 1.282725495 0.781461559 0.097032001 0.084825771 7.659736421 0.013921205 0.027958222 2.55E-09 8.59313393 0.344349455 EEAPAS(ph)PLRPLYPQISPLK ddPTM_HeLa_Romidepsin_16h_R1 1 EEAPASPLRPLYPQISPLK 19 1 P85037-2;P85037;U3KQ26 P85037-2;U3KQ26 FOXK1 Forkhead box protein K1 1 0 EEAPAS(0.986)PLRPLY(0.013)PQIS(0.001)PLK 64.507 0.0090029 108120000 2517.5 2255 2588.5 1667.5 2198.3 2395.1 2264 2162.2 2605.1 2640 TRUE FALSE FALSE 2486.815742 2286.745949 2633.551757 1860.304196 2086.112548 2242.06084 2456.304103 2224.759846 2372.093331 2571.412419 0.967101085 0.889295677 1.02416545 0.723456176 0.811271087 0.871918026 0.955235374 0.865189819 0.922486534 1 11.3283453 -9.28791788 24.99866366 0.97812497 0.851090859 0.42231863 0.065620822 488.7774118 461459.0803 0.010060541 0.015370501 5.15E-10 9.28791788 -0.127034111 EEAS(ph)DDDMEGDEAVVR ddPTM_HeLa_Romidepsin_16h_R1 2 EEASDDDMEGDEAVVR 16 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 1 0 EEAS(1)DDDMEGDEAVVR;EEAS(1)DDDMEGDEAVVR ; 155.37 0.00033125 206024000 2601.3 8320.1 4790.9 3990.6 4473.7 7729.2 2357.65 5129.9 3160 3836.8 TRUE FALSE FALSE 2569.594355 8437.230586 4874.283605 4452.011948 4245.390395 7235.329065 2557.908732 5278.325563 2877.361686 3737.119383 0.687586906 2.257682916 1.304288974 1.191295084 1.136006095 1.936071162 0.68446 1.412404856 0.769941067 1 11.86771094 EEASDYLELDTIK ddPTM_HeLa_Romidepsin_16h_R1 1 EEASDYLELDTIK 13 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 0 187.85 1.33E-09 4673600 1536.4 1307.6 1521 1192.2 1322.4 1804.1 1584.8 1707.7 1455.3 1294.2 FALSE FALSE TRUE 1517.673766 1326.008427 1547.472367 1330.047773 1254.912993 1688.823832 1719.412872 1757.109605 1325.134323 1260.576497 1.203952135 1.051906354 1.227591003 1.055110718 0.995507211 1.339723401 1.363989314 1.393893674 1.051212938 1 10.29986795 -8.175694625 6.139054612 1.096249141 1.37045976 0.751622293 0.074190993 0.110847433 6.452586565 0.012805446 0.033142189 6.67E-09 8.175694625 0.274210618 EEASGSSVTAEEAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EEASGSSVTAEEAKK 15 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 1 ; EEASGSSVTAEEAK(1)K;EEASGSSVTAEEAK(1)K 357.54 2.54E-257 8792200 1618.92 1633.94 1399.16 1296.09 2294.53 2359.7 1899.13 2320.04 2866.9 2629.29 FALSE TRUE FALSE 1599.18798 1656.94265 1423.511793 1445.950024 2177.431572 2208.922786 2060.442055 2387.166697 2610.477284 2560.980667 0.624443597 0.646995376 0.555846364 0.564607942 0.850233506 0.862530051 0.804551976 0.932129917 1.019327212 1 11.32248065 -8.561628158 24.99891019 0.763200349 0.859580165 0.122292055 0.156578085 400.039482 258081.2129 0.02764169 0.055283452 2.74E-09 8.561628158 0.096379816 EEATYGVWAERDS(ph)DDERPSFGGK ddPTM_HeLa_Romidepsin_16h_R1 1 EEATYGVWAERDSDDERPSFGGK 23 2 Q9UBB9;F6XM96;F6UKU9;F6SQZ1 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 EEAT(0.001)Y(0.003)GVWAERDS(0.99)DDERPS(0.005)FGGK 70.121 0.0016352 14342000 2084.7 1741.2 1538.9 1960.3 2260.1 1863.7 1920.8 2360.5 2077.3 2206.1 TRUE FALSE FALSE 2059.290875 1765.712659 1565.683909 2186.959109 2144.758663 1744.615585 2083.952704 2428.797343 1891.501085 2148.785204 0.958351198 0.821725995 0.728636769 1.017765343 0.998126132 0.811907855 0.969828301 1.130311833 0.880265315 1 11.06930556 -5.987192137 18.93895149 0.953644041 0.935717548 0 0.115429154 0 0 0.015037015 0 1.03E-06 5.987192137 -0.017926493 EEDEENDNDNES(ph)DHDEADS ddPTM_HeLa_Romidepsin_16h_R1 1 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 0 EEDEENDNDNES(1)DHDEADS 130.4 3.81E-09 0 1906.7 1249.1 1364.5 1088.6 1017.1 793.9 1151.8 1545.6 1616.7 1651.9 TRUE FALSE FALSE 1883.460407 1266.684863 1388.24855 1214.469054 965.1935917 743.1723522 1249.633863 1590.319497 1472.098303 1608.9834 1.170590329 0.787257881 0.862810984 0.754805211 0.599877905 0.461889384 0.776660507 0.98840019 0.914924482 1 10.65193373 -10.14647854 4.345335359 1.08022655 0.730772305 0.418517641 0.148068132 0.1341473 4.213811043 0.025670164 0.031633499 7.14E-11 10.14647854 -0.349454245 EEDEENDNDNESDHDEADS(ph) ddPTM_HeLa_Romidepsin_16h_R1 2 EEDEENDNDNESDHDEADS 19 0 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 0 EEDEENDNDNES(0.244)DHDEADS(0.756);EEDEENDNDNES(0.458)DHDEADS(0.542) ; 135.55 0.00054902 16986000 3307.27 2888.36 2395.81 1709.4 2573.21 2338.98 2028.83 2408.99 3214.54 2869.31 TRUE FALSE FALSE 3266.959721 2929.022408 2437.508068 1907.048871 2441.889492 2189.526727 2201.15877 2478.690325 2927.023491 2794.764913 1.168956897 1.048038923 0.872169268 0.682364682 0.873736993 0.783438606 0.787600689 0.886904767 1.047323687 1 11.44851122 -9.715851092 3.575183717 1.080953026 0.802943839 0.781556286 0.065917532 0.087264234 2.305515184 0.012681304 0.017886337 1.92E-10 9.715851092 -0.278009187 EEDEEPES(ph)PPEK ddPTM_HeLa_Romidepsin_16h_R1 1 EEDEEPESPPEK 12 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 EEDEEPES(1)PPEK 248.67 1.94E-50 33380000 5394.9 4855.6 5414.3 2002 4415.3 5480.6 4351.1 4271.9 5111.5 4910.8 TRUE FALSE FALSE 5329.144884 4923.957264 5508.53362 2233.48066 4189.970765 5130.407348 4720.682325 4395.500687 4654.314638 4783.216708 1.114134109 1.02942383 1.151637895 0.466941139 0.875973434 1.072585179 0.986926291 0.918942409 0.973051175 1 12.22376544 EEDEEPES(ph)PPEKK ddPTM_HeLa_Romidepsin_16h_R1 9 EEDEEPESPPEKK 13 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 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 ;;;;;;;; 209.56 6.35E-23 2457765100 77008.12 82467.1 77350.2 37995.59 76707.92 78138.79 65364.18 71492.5 80346.4 84360.9 TRUE FALSE FALSE 76069.51541 83628.074 78696.44778 42388.81889 72793.22861 73145.9735 70916.21182 73561.02269 73160.01675 82169.19166 0.925766871 1.017754615 0.957736667 0.51587241 0.885894423 0.890187332 0.863051107 0.895238485 0.890358239 1 16.32630995 -9.478349689 24.99998957 0.968870625 0.813173662 0.311874411 0.10964062 393.545 220948.6212 0.016203021 0.024749752 3.32E-10 9.478349689 -0.155696964 EEDEHPY(ph)ELLLTAETK ddPTM_HeLa_Romidepsin_16h_R1 3 EEDEHPYELLLTAETK 16 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 0 EEDEHPY(1)ELLLTAETK;EEDEHPY(1)ELLLTAETK;EEDEHPY(1)ELLLTAETK ;; 163.64 5.17E-05 13788800 6735.48 6914.28 6968.13 6870.42 6855.41 6083.8 5419.03 4677.01 8752.45 7020.37 TRUE FALSE FALSE 6653.385379 7011.619415 7089.40738 7664.810287 6505.552847 5695.064815 5879.322273 4812.331905 7969.608951 6837.979775 0.973004542 1.025393412 1.036769282 1.120917367 0.951385213 0.832857803 0.859803987 0.703765156 1.165491741 1 12.73935444 -8.137419681 1.918058666 1.003312045 0.775988683 0.679281039 0.074167153 0.136817983 0.955060118 0.008232754 0.02977228 7.29E-09 8.137419681 -0.227323362 EEDEPEERS(ph)GDET(ph)PGSEVPGDK ddPTM_HeLa_Romidepsin_16h_R1 1 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 2 0 EEDEPEERS(1)GDET(0.858)PGS(0.143)EVPGDK 71.524 0.0034662 14646000 2018.3 1572.3 1745.3 1108.5 1831.6 1945.3 1549.9 1763.7 1969.4 1964.2 TRUE FALSE FALSE 1993.700183 1594.434881 1775.676214 1236.669986 1738.126617 1821.001608 1681.548467 1814.729877 1793.251932 1913.169801 1.042092648 0.833399565 0.928133098 0.646398446 0.908506196 0.951824353 0.878933206 0.948546165 0.937319798 1 10.90174921 -10.2645989 24.99342933 1.019877086 0.869269937 0.275706556 0.08767007 196.1547793 1551682.369 0.01403853 0.016410602 5.44E-11 10.2645989 -0.150607149 EEDEPEERS(ph)GDETPGSEVPGDK ddPTM_HeLa_Romidepsin_16h_R1 3 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 EEDEPEERS(0.665)GDET(0.005)PGS(0.33)EVPGDK;EEDEPEERS(0.975)GDET(0.025)PGSEVPGDK;EEDEPEERS(0.999)GDET(0.001)PGSEVPGDK ;; 123.54 2.78E-05 952086000 9601.9 9326.7 10313.1 6488.8 10472.9 10860.2 9864.1 10088.2 9282.5 9447.2 TRUE FALSE FALSE 9484.86835 9458.001527 10492.59518 7239.065587 9938.428833 10166.26827 10701.95641 10380.08615 8452.249952 9201.760382 1.030766718 1.02784697 1.140281288 0.786704422 1.080057339 1.104817757 1.16303359 1.128054385 0.918547061 1 13.16769417 -8.529709921 24.99870405 1.009063785 1.127968862 0.351003582 0.088049129 146.4958118 536101.0138 0.01134152 0.022727606 2.95E-09 8.529709921 0.118905077 EEDEPEERSGDETPGS(ph)EVPGDK ddPTM_HeLa_Romidepsin_16h_R1 1 EEDEPEERSGDETPGSEVPGDK 22 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 EEDEPEERS(0.022)GDET(0.127)PGS(0.851)EVPGDK 70.114 0.0015326 6556200 2146.1 1952.2 1909.7 1566.7 2789.6 2398.4 1825.4 2273 2212.1 2279.7 TRUE FALSE FALSE 2119.942508 1979.683123 1942.937527 1747.849226 2647.236303 2245.14998 1980.44943 2338.765669 2014.244236 2220.473065 0.954725613 0.89155917 0.875010626 0.787151735 1.192194737 1.011113359 0.89190428 1.053273604 0.907123922 1 11.11665136 -7.213600535 21.22282091 0.964814884 1.053275972 0.06139085 0.104319 11813.1173 5239766.528 0.013910621 8.173846326 6.12E-08 7.213600535 0.088461088 EEDGADAS(ph)EEDLTR ddPTM_HeLa_Romidepsin_16h_R1 2 EEDGADASEEDLTR 14 0 Q86X53;E5RHA3 Q86X53 ERICH1 Glutamate-rich protein 1 1 0 EEDGADAS(0.995)EEDLT(0.005)R;EEDGADAS(1)EEDLTR ; 217.39 2.37E-24 66253000 5096.5 7023.9 6774.6 5161.4 6503.4 6924.6 5530.9 6471.8 6297.2 5598.5 TRUE FALSE FALSE 5034.381898 7122.782649 6892.509071 5758.185353 6171.50723 6482.140408 6000.694508 6659.051322 5733.96266 5453.050163 0.923223104 1.306201563 1.263973165 1.055956791 1.131753247 1.18871828 1.100428995 1.221160841 1.051514747 1 12.41284771 -10.27743767 24.99826385 0.963744239 1.17482343 0.549585725 0.077283301 374.2169041 584734.3177 0.012964746 0.014849964 5.28E-11 10.27743767 0.211079192 EEDGSLS(ph)LDGADSTGVVAK ddPTM_HeLa_Romidepsin_16h_R1 1 EEDGSLSLDGADSTGVVAK 19 0 Q13263-2;Q13263;M0R0K9 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 1 0 EEDGS(0.349)LS(0.651)LDGADSTGVVAK 199.41 6.93E-21 0 1015.8 962.8 1232.3 1031 610.9 1196.7 819.85 735.24 962.22 1032.7 TRUE FALSE FALSE 1003.419039 976.3543237 1253.747665 1150.209071 579.7234934 1120.234732 889.4880385 756.5130094 876.1566333 1005.870305 0.997563039 0.970656275 1.246430736 1.143496398 0.576340201 1.113696991 0.884296946 0.752097965 0.871043343 1 9.974228584 -8.823750831 25 1.026145139 0.855496994 0.286651493 0.157178648 70.93973302 28461.23355 0.021368758 0.038734178 1.50E-09 8.823750831 -0.170648144 EEEEEEEEDQEGDRETTIR ddPTM_HeLa_Romidepsin_16h_R1 2 EEEEEEEEDQEGDRETTIR 19 1 A0A0B4J2E5;Q15269 A0A0B4J2E5 PWP2 Periodic tryptophan protein 2 homolog 0 0 ; ; 128.82 0.0010491 8423600 1532.18 1463.3 1521.67 1155.5 1324.88 1617.49 1363.03 1539.71 1823.06 1364.25 FALSE FALSE TRUE 1513.505201 1483.900376 1548.154028 1289.104347 1257.26643 1514.137609 1478.805734 1584.25908 1660.000948 1328.806588 1.138995858 1.1167166 1.165071006 0.970121881 0.946162098 1.139471781 1.112882602 1.192242041 1.249241961 1 10.37591542 -12.4768654 1.229573665 1.000244095 1.097929851 0 0.107912653 0.669851774 1.819051416 0.054622911 0.013540534 3.34E-13 12.4768654 0.097685756 EEEEGISQES(ph)SEEEQ ddPTM_HeLa_Romidepsin_16h_R1 2 EEEEGISQESSEEEQ 15 0 P17096;P17096-2 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 0 EEEEGIS(0.001)QES(0.499)S(0.499)EEEQ;EEEEGISQES(0.817)S(0.183)EEEQ ; 192.65 1.59E-12 12933000 8717.3 9705.1 8610 3963.4 8891.9 9408.2 8062.2 9735.5 10091.7 9022.4 TRUE FALSE FALSE 8611.050195 9841.728653 8759.853438 4421.666956 8438.113163 8807.046384 8747.003067 10017.18133 9189.073077 8787.996747 0.979864973 1.119905814 0.996797529 0.503148452 0.960186195 1.002167688 0.995335264 1.139870851 1.045639108 1 13.10131862 EEEEQQEGGFAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EEEEQQEGGFASPR 14 0 A0A087WWG9;A0A087WVR3;A0A087WTW0;Q96T88;Q96T88-2 A0A087WWG9 UHRF1 E3 ubiquitin-protein ligase UHRF1 1 0 EEEEQQEGGFAS(1)PR;EEEEQQEGGFAS(1)PR ; 192.4 1.36E-13 5769000 1319.33 1315.88 1189.99 1000.13 1525.6 2134.25 1654.08 1953.8 1394.59 1360.52 TRUE FALSE FALSE 1303.249498 1334.404993 1210.701277 1115.769736 1447.742939 1997.878313 1794.577514 2010.33012 1269.854378 1325.173494 0.983455754 1.006966257 0.913617184 0.841980119 1.09249313 1.507635281 1.354220803 1.517031641 0.958255189 1 10.37196554 -8.371264853 4.118037666 0.977044805 1.448717236 0.921030703 0.066221965 0.044509675 1.294762765 0.009327998 0.021815446 4.25E-09 8.371264853 0.471672431 EEEEVGFDWSDR ddPTM_HeLa_Romidepsin_16h_R1 1 EEEEVGFDWSDR 12 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;E9PMV1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 310.49 1.20E-146 2622700 804.77 1027.6 926.8 599.21 981.32 975.99 807.85 1007.7 1282.3 975.65 FALSE FALSE TRUE 794.9611537 1042.06658 942.9305652 668.4934796 931.2395786 913.6273889 876.4687588 1036.85621 1167.607876 950.3024724 0.836534868 1.096563052 0.992242568 0.703453373 0.979940183 0.961406937 0.922305039 1.091080198 1.228669724 1 9.892242973 -7.259851597 23.69829884 0.929316118 1.091080299 0 0.137769438 92.569477 1381349.558 0.014343515 0.121283144 5.50E-08 7.259851597 0.161764181 EEELREYQER ddPTM_HeLa_Romidepsin_16h_R1 1 EEELREYQER 10 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 0 102.06 0.026373 4843600 3087.1 2783.3 2642.6 3104.5 2790.7 2702.2 2438.2 2521.9 2617.4 2961.5 FALSE FALSE TRUE 3049.473238 2822.48337 2688.593344 3463.456897 2648.280165 2529.538141 2645.300647 2594.867198 2383.293189 2884.559803 1.057171092 0.978479755 0.932063652 1.200688193 0.918088147 0.876923452 0.917055228 0.899571295 0.826224225 1 11.49413546 -8.553624535 24.99995014 1.027841899 0.899392864 0.171853662 0.091971659 125.1098009 101728.5662 0.009147618 0.018295368 2.79E-09 8.553624535 -0.128449035 EEEMEMSDDENCDSPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EEEMEMSDDENCDSPTK 17 0 Q8TC92-2;Q8TC92 Q8TC92-2 ENOX1 Ecto-NOX disulfide-thiol exchanger 1;Hydroquinone [NADH] oxidase;Protein disulfide-thiol oxidoreductase 1 0 EEEMEMSDDENCDS(0.146)PT(0.854)K 97.734 0.0089551 91058000 14539 15174 15080 12565 14848 14567 13209 14842 15775 15854 TRUE FALSE FALSE 14361.79308 15387.61997 15342.46107 14017.82442 14090.25115 13636.21571 14330.97213 15271.42985 14364.04449 15442.11079 0.9300408 0.996471284 0.993546885 0.907766082 0.912456292 0.883053871 0.928044898 0.988947046 0.930186597 1 13.91458235 -9.254754645 24.93427244 0.97061955 0.921353312 0.310081891 0.034180334 515.4672284 1922707.874 0.005679843 0.009278771 5.56E-10 9.254754645 -0.049266238 EEEMQPAEEGPS(ph)VPK ddPTM_HeLa_Romidepsin_16h_R1 4 EEEMQPAEEGPSVPK 15 0 Q6ZU67-5;Q6ZU67-4;Q6ZU67-2;Q6ZU67 Q6ZU67-5 BEND4 BEN domain-containing protein 4 1 0 EEEMQPAEEGPS(1)VPK;EEEMQPAEEGPS(1)VPK;EEEMQPAEEGPS(1)VPK;EEEMQPAEEGPS(1)VPK ;;; 100.22 0.010801 39313200 4600.19 4561.31 4069.48 4490.31 4976.64 4414.24 3863.85 3866 4612.21 4804.04 TRUE FALSE FALSE 4544.121115 4625.524242 4140.307592 5009.50077 4722.66349 4132.18431 4192.045323 3977.85661 4199.682386 4679.230348 0.971125757 0.988522449 0.884826624 1.070582211 1.009282112 0.883090595 0.895883513 0.850109166 0.897515633 1 12.19205554 -8.251649425 23.41054187 0.986227598 0.878313301 0.413482666 0.052296464 160.2426924 383182.2468 0.006013763 0.01509564 5.60E-09 8.251649425 -0.107914297 EEENADS(ph)DDEGELQDLLSQDWR ddPTM_HeLa_Romidepsin_16h_R1 1 EEENADSDDEGELQDLLSQDWR 22 0 J3QQQ3;Q96NB3 J3QQQ3 ZNF830 Zinc finger protein 830 1 0 EEENADS(1)DDEGELQDLLSQDWR 61.112 0.0052742 911230 423.83 537.87 520.6 412.54 348.49 473.68 405.55 304.03 493.98 425.93 TRUE FALSE FALSE 418.6641969 545.442148 529.6608246 460.2398159 330.7052549 443.4133767 439.9974069 312.8266284 449.7971916 414.8642772 1.009159429 1.314748408 1.276708682 1.109374418 0.797140832 1.068815517 1.060581571 0.75404571 1.084203235 1 8.696495626 -7.25928907 23.75638402 1.043562768 0.754045515 0.296395859 0.140930448 106.9911562 1181848.453 0.020538488 0.180595153 5.50E-08 7.25928907 -0.289517253 EEENS(ph)EEELAAATTSK ddPTM_HeLa_Romidepsin_16h_R1 1 EEENSEEELAAATTSK 16 0 P10244-2;P10244 P10244-2 MYBL2 Myb-related protein B 1 0 EEENS(1)EEELAAATTSK 144.08 0.00031928 4668500 2046.7 1665.9 2414.1 1070.4 1754.5 1923.9 1586.9 1769.8 2278.5 2133.3 TRUE FALSE FALSE 2021.754033 1689.352584 2456.116398 1194.164684 1664.961318 1800.968999 1721.691246 1821.006371 2074.705253 2077.876558 0.972990443 0.813018741 1.18203191 0.574704344 0.801280187 0.866735318 0.828582063 0.876378514 0.998473776 1 11.02089423 -9.265957372 24.99998627 0.984363602 0.796646606 0.441332168 0.114269036 283.9906806 1571440.856 0.016346139 0.025504296 5.42E-10 9.265957372 -0.187716996 EEENSEEELAAAT(ph)TSK ddPTM_HeLa_Romidepsin_16h_R1 1 EEENSEEELAAATTSK 16 0 P10244-2;P10244 P10244-2 MYBL2 Myb-related protein B 1 0 EEENS(0.315)EEELAAAT(0.663)T(0.021)S(0.002)K 197.73 1.69E-13 4474600 2618.5 2787.1 3157.2 1569.6 2168.2 2510.3 1979.9 2530.3 2595.9 2904.1 TRUE FALSE FALSE 2586.584715 2826.336867 3212.149742 1751.084537 2057.548663 2349.899932 2148.072657 2603.510238 2363.716202 2828.651063 0.914423397 0.999181873 1.135576524 0.619052862 0.727395715 0.830749314 0.759398246 0.920407 0.835633717 1 11.4658985 -9.259915004 24.99993074 0.974160867 0.771586265 0.510829913 0.100559817 82.06889043 1345937.044 0.01403323 0.022474751 5.50E-10 9.259915004 -0.202574602 EEEQEDLTKDMDEPS(ph)PVPNVEEVTLPK ddPTM_HeLa_Romidepsin_16h_R1 1 EEEQEDLTKDMDEPSPVPNVEEVTLPK 27 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 0 EEEQEDLT(0.006)KDMDEPS(0.957)PVPNVEEVT(0.037)LPK 53.747 0.0041011 2717000 1400.7 1547.7 1446.1 808.77 1871.6 1518.2 1232.1 1695.2 1842.3 1592.5 TRUE FALSE FALSE 1383.62773 1569.488561 1471.268764 902.2837928 1776.085268 1421.19192 1336.754543 1744.247937 1677.520074 1551.12662 0.892014689 1.011837809 0.948516223 0.581695769 1.145029197 0.916232048 0.861795888 1.124503902 1.081484936 1 10.59910074 -7.246593772 23.46129231 0.934248272 1.124504224 0.130738753 0.144327793 1616.054693 2553835.241 0.017657438 0.487513511 5.67E-08 7.246593772 0.190255952 EEEWDPEYT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 EEEWDPEYTPK 11 0 Q9Y2W1;A0A3B3ITZ9;Q9NYF8-2;Q9NYF8;Q9NYF8-4;H0YF14 Q9Y2W1;Q9NYF8-2 THRAP3;BCLAF1 Thyroid hormone receptor-associated protein 3;Bcl-2-associated transcription factor 1 1 0 EEEWDPEYT(1)PK;EEEWDPEYT(1)PK;EEEWDPEYT(1)PK;EEEWDPEYT(1)PK ;;; 179.67 2.18E-05 163913000 32496.1 32931 34637.3 28170.1 34333.3 36388.5 30297.3 27448.5 32797.9 31020.3 TRUE FALSE FALSE 32100.02503 33394.60348 35240.14768 31427.25951 32581.14359 34063.39229 32870.75191 28242.67904 29864.37368 30214.38813 1.062408575 1.105254998 1.166336631 1.040142179 1.078332066 1.127389777 1.087917179 0.93474271 0.988415637 1 14.88294811 -11.53407477 0.924322871 1.006708947 1.079883754 0.226075828 0.05823381 0.584498352 1.021991922 0.021946317 0.011794315 2.92E-12 11.53407477 0.073174806 EEFFS(ph)PDSLK ddPTM_HeLa_Romidepsin_16h_R1 2 EEFFSPDSLK 10 0 O15062 O15062 ZBTB5 Zinc finger and BTB domain-containing protein 5 1 0 EEFFS(0.981)PDS(0.019)LK;EEFFS(0.715)PDS(0.285)LK ; 150.09 0.0037422 9070500 6371 5900.3 5866.2 5062.2 7977.4 8088 7160.1 7722.9 6191.3 6163.5 TRUE FALSE FALSE 6293.347801 5983.364578 5968.29875 5647.515382 7570.28351 7571.202903 7768.278715 7946.349927 5637.534622 6003.371381 1.048302262 0.996667405 0.994157844 0.940723974 1.261005363 1.261158509 1.293986032 1.323647901 0.939061448 1 12.5515572 -8.712673344 7.458119463 1.013708279 1.285567661 0.93080432 0.039459534 0.040044138 5.076102912 0.005212327 0.010410342 1.94E-09 8.712673344 0.271859382 EEGAAPS(ph)PTHVAELATMEVESAR ddPTM_HeLa_Romidepsin_16h_R1 1 EEGAAPSPTHVAELATMEVESAR 23 0 Q9NRS6 Q9NRS6 SNX15 Sorting nexin-15 1 0 EEGAAPS(0.961)PT(0.039)HVAELATMEVESAR 55.204 0.0044482 9049900 1347 1205.8 1341.8 905.55 1265.3 1365.5 1118.4 1154.8 950.94 1410.4 TRUE FALSE FALSE 1330.582246 1222.775284 1365.153466 1010.253952 1200.72702 1278.248957 1213.396868 1188.212316 865.8855447 1373.757605 0.968571341 0.89009537 0.993736786 0.73539462 0.874045767 0.930476346 0.883268536 0.864935933 0.63030446 1 10.42391175 -10.08490694 1.087647044 0.989744941 0.870433144 0 0.128247377 0.314260066 0.725479094 0.01171741 0.015172006 8.22E-11 10.08490694 -0.119311797 EEGDLGPVYGFQWR ddPTM_HeLa_Romidepsin_16h_R1 2 EEGDLGPVYGFQWR 14 0 P04818-2;P04818 P04818-2 TYMS Thymidylate synthase 0 0 ; ; 172.61 0.00034968 18568300 3375.9 3170.4 3008.9 3075.8 2275.7 1966.29 1706.72 1784.8 3189.2 3221.2 FALSE FALSE TRUE 3334.753232 3215.032974 3061.268642 3431.438468 2159.562537 1840.650415 1851.688754 1836.440372 2903.949965 3137.51276 1.062865234 1.024707538 0.975699185 1.09368112 0.688303986 0.586659101 0.590177282 0.58531726 0.925557978 1 11.61540561 -8.662280793 4.37983487 1.029416615 0.595010144 0.946515769 0.046951914 0.02528486 0.863070568 0.005434388 0.011102248 2.18E-09 8.662280793 -0.43440647 EEGGEGT(ph)PVKQDLSAPPGYTLTENVAR ddPTM_HeLa_Romidepsin_16h_R1 1 EEGGEGTPVKQDLSAPPGYTLTENVAR 27 1 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;Q9Y4B5-4 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 EEGGEGT(0.947)PVKQDLS(0.052)APPGYTLTENVAR 86.039 1.33E-06 8393300 1658.9 1485.4 1581.3 2163.4 1069.2 1147.5 1051.4 956.86 1329.9 1633.3 TRUE FALSE FALSE 1638.680689 1506.3115 1608.821863 2413.542487 1014.634734 1074.178453 1140.70589 984.5452344 1210.950413 1590.866631 1.030055353 0.946849642 1.011286447 1.51712434 0.637787427 0.675215906 0.717034268 0.618873522 0.761189147 1 10.63559718 EEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_HeLa_Romidepsin_16h_R1 2 EEGPPPPSPDGASSDAEPEPPSGR 24 0 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;E9PD53;Q9NTJ3-2;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 0 EEGPPPPSPDGAS(0.551)S(0.446)DAEPEPPS(0.003)GR;EEGPPPPSPDGAS(0.84)S(0.16)DAEPEPPSGR ; 138.41 5.42E-09 7997300 3062.7 3161.4 3334.1 2456.7 3268 3091 2414.7 2738.3 3663.3 3367.7 TRUE FALSE FALSE 3025.370634 3205.906272 3392.128612 2740.755213 3101.221765 2893.495076 2619.804558 2817.52839 3335.645273 3280.206669 0.922310982 0.977348867 1.034120394 0.835543455 0.94543487 0.882107552 0.798670579 0.858948437 1.016900949 1 11.679571 -8.390352392 0.780355912 0.967643427 0.817190728 0.551265189 0.051568193 0.552483446 0.52940223 0.009029757 0.052039469 4.07E-09 8.390352392 -0.150452699 EEGS(ph)DIEDEDMEELLNDTR ddPTM_HeLa_Romidepsin_16h_R1 1 EEGSDIEDEDMEELLNDTR 19 0 F5H5U2;Q8NHQ9-2;Q8NHQ9 F5H5U2 DDX55 ATP-dependent RNA helicase DDX55 1 0 EEGS(0.94)DIEDEDMEELLNDT(0.06)R 120.6 0.0011862 13995000 4239.8 3996.3 4222.6 3374.8 4634.2 4800.3 3948 4674.8 5076.2 4445.3 TRUE FALSE FALSE 4188.123687 4052.560016 4296.092582 3765.010255 4397.699481 4493.576322 4283.343021 4810.057962 4622.171958 4329.810465 0.967276448 0.93596707 0.992212619 0.869555442 1.015679443 1.03782287 0.989268019 1.110916517 1.067522931 1 12.08008816 -4.000002108 0.863112523 0.975753049 51.86360489 0.341711086 0.051876873 491.3463245 1.220734863 0.006711637 49160.51384 1.00E-04 4.000002108 50.88785184 EEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_HeLa_Romidepsin_16h_R1 3 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 0 EEGS(0.077)LS(0.701)DT(0.221)EADAVSGQLPDPTTNPSAGK;EEGS(0.053)LS(0.707)DT(0.24)EADAVSGQLPDPTTNPSAGK;EEGS(0.061)LS(0.923)DT(0.016)EADAVSGQLPDPTTNPSAGK ;; 154.84 1.23E-13 65880000 12060.4 12277 13126.5 5739.6 12175 14164.3 11558.1 12244.1 12948.5 13901.9 TRUE FALSE FALSE 11913.40321 12449.83593 13354.96123 6403.239558 11553.66432 13259.24694 12539.84473 12598.36372 11790.35373 13540.72663 0.879820081 0.919436325 0.986280987 0.47288744 0.853252904 0.979212364 0.926083589 0.930405292 0.87073272 1 13.72501754 -11.81868715 0.618087513 1.004484433 0.86144236 0.005040668 0.143950583 1.540069399 1.077033694 0.113351165 0.034267675 1.52E-12 11.81868715 -0.143042072 EEGSLSDT(ph)EADAVSGQLPDPTTNPSAGK ddPTM_HeLa_Romidepsin_16h_R1 1 EEGSLSDTEADAVSGQLPDPTTNPSAGK 28 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 0 EEGS(0.022)LS(0.428)DT(0.55)EADAVSGQLPDPTTNPSAGK 177.34 1.22E-23 36332000 4375.1 4556.4 5227.6 2148.7 4364 5154.1 4186.7 4677.6 4773.4 5016.6 TRUE FALSE FALSE 4321.774598 4620.545119 5318.584185 2397.142804 4141.288796 4824.769644 4542.318193 4812.938976 4346.455149 4886.268009 0.884473506 0.945618437 1.08847574 0.490587663 0.847536154 0.987414042 0.929608893 0.984992834 0.889524508 1 12.25451728 -12.3134129 0.57308871 1.019850131 0.887969413 0 0.153405874 3.19245499 1.445554248 0.228248695 0.035667884 4.86E-13 12.3134129 -0.131880718 EEHDQSTQMSK(ac)VK ddPTM_HeLa_Romidepsin_16h_R1 1 EEHDQSTQMSKVK 13 1 H3BTW3;Q3L8U1;A0A087WU44 H3BTW3 CHD9 Chromodomain-helicase-DNA-binding protein 9 0 1 EEHDQSTQMSK(1)VK 88.092 0.0051132 321460 140.6 0 127.57 105.25 124.41 220.04 283.99 146.38 119.89 116.08 FALSE TRUE FALSE 138.8863131 0 129.7903023 117.4195002 118.0608935 205.9801541 308.1121035 150.6152744 109.1667381 113.0642249 1.22838425 0 1.147934305 1.038520366 1.044193188 1.821797783 2.725106937 1.332121407 0.965528559 1 6.820998702 -8.197730064 3.942396175 1.017303796 2.07497595 0.515377078 0.457008086 0.136402769 4.238198036 0.061838542 0.165555418 6.34E-09 8.197730064 1.057672154 EEHGGLIRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 EEHGGLIRSPR 11 1 P26368-2;P26368 P26368-2 U2AF2 Splicing factor U2AF 65 kDa subunit 1 0 EEHGGLIRS(1)PR 68.551 0.030219 303260000 2976.5 2674.5 3060.9 2101.4 2646.5 2894.6 2557.9 2311.4 3202 2947.1 TRUE FALSE FALSE 2940.221273 2712.151681 3114.173681 2344.373755 2511.43923 2709.644402 2775.167962 2378.276712 2915.6051 2870.533917 1.024276792 0.944824816 1.084876114 0.816703033 0.874903172 0.943951362 0.966777625 0.828513712 1.015701324 1 11.48710339 -9.26213614 24.9999992 1.010702497 0.893232161 0.586771465 0.053411522 36.20049859 1298896.781 0.007784168 0.012355118 5.47E-10 9.26213614 -0.117470336 EEILSVAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EEILSVAKK 9 1 B1ALG6;F6XU50;A0A0B4J1V9;Q9NRZ9-8;Q9NRZ9-7;Q9NRZ9-6;Q9NRZ9-5;Q9NRZ9-4;Q9NRZ9-3;Q9NRZ9-2;Q9NRZ9 B1ALG6 HELLS Lymphoid-specific helicase 0 1 EEILSVAK(1)K 126.07 0.0017079 468230 548.02 401.75 761.77 282.21 518.71 525.5 441.17 513.32 295.81 404.75 FALSE TRUE FALSE 541.3405215 407.405847 775.0282873 314.840448 492.2382931 491.922246 478.6429688 528.1721043 269.3520127 394.2345367 1.373143322 1.033409834 1.965906625 0.798612041 1.248592519 1.247790846 1.214107148 1.339740827 0.683227845 1 8.622910358 -12.42044518 1.088654693 0.996282658 1.281196327 0.215588191 0.298507653 0.855363161 1.774563694 0.189641397 0.045323896 3.80E-13 12.42044518 0.284913669 EEIQET(ph)QTPTHSR ddPTM_HeLa_Romidepsin_16h_R1 1 EEIQETQTPTHSR 13 0 H7BZL0;Q9BYG3 H7BZL0 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 0 EEIQET(0.536)QT(0.322)PT(0.141)HS(0.002)R 155.09 0.0014983 6759200 951.37 1012.7 931.87 1044.8 1318.2 1365.8 1210.9 1263.8 912.07 957.78 TRUE FALSE FALSE 939.7743365 1026.956817 948.0888064 1165.604692 1250.927335 1278.529788 1313.753816 1300.366059 830.4921749 932.8967375 1.007372305 1.100825821 1.016284834 1.249446638 1.340906539 1.370494436 1.408252128 1.39390139 0.890229477 1 9.865573588 -9.065478021 1.381344591 1.007129635 1.397118747 0.928417139 0.049626223 0.047176427 0.177986904 0.005077804 0.010688579 8.60E-10 9.065478021 0.389989111 EEIQETQT(ph)PTHSR ddPTM_HeLa_Romidepsin_16h_R1 1 EEIQETQTPTHSR 13 0 H7BZL0;Q9BYG3 H7BZL0 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 0 EEIQET(0.001)QT(0.999)PTHSR 119.04 0.0038061 9390500 3574.7 2036.6 2616.2 2401.6 2622.1 3038.7 3374.7 3240 3296.7 2960.9 TRUE FALSE FALSE 3531.130181 2065.271308 2661.733864 2679.284292 2488.284453 2844.536877 3661.346934 3333.744288 3001.834895 2883.975391 1.22439678 0.716119602 0.922939173 0.929024672 0.862796701 0.986324948 1.269548605 1.155954485 1.040867028 1 11.49384314 -7.763806138 24.99793225 1.030743522 1.212751566 0.240991896 0.1400489 82.0733324 866913.9593 0.02400973 0.077369769 1.72E-08 7.763806138 0.182008044 EEKS(ph)VEYEGDLK ddPTM_HeLa_Romidepsin_16h_R1 1 EEKSVEYEGDLK 12 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 EEKS(1)VEYEGDLK 66.673 0.029241 60317000 7265.9 6713.2 6385.2 6068.5 7127.3 8107.1 7437.9 7943.9 8849.8 8933.2 TRUE FALSE FALSE 7177.340416 6807.708606 6496.331728 6770.168523 6763.567285 7589.082474 8069.67504 8173.744213 8058.251723 8701.114176 0.824876018 0.782395044 0.746609181 0.778080644 0.777321978 0.872196631 0.927430083 0.939390525 0.926117226 1 13.08698443 -12.05479856 0.887675161 0.997718472 0.828745646 0.377561564 0.065327825 0.409770602 0.596986519 0.043102178 0.013696631 8.81E-13 12.05479856 -0.168972826 EELANERLMT(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 EELANERLMTLK 12 1 C9IZA8;F5H7J3;B4E3Q4;Q9NZK5 C9IZA8 CECR1 Adenosine deaminase CECR1 1 0 EELANERLMT(1)LK 96.135 0.0052455 6219700 6614.6 4615 5338.4 1019.7 4963.7 5621 6504.5 4750.1 7073 6399.4 TRUE FALSE FALSE 6533.978711 4679.970091 5431.312613 1137.602512 4710.383867 5261.836241 7056.992068 4887.536649 6440.373165 6233.142665 1.048263944 0.750820307 0.871360228 0.182508659 0.755699672 0.844170673 1.132172396 0.784120774 1.033246552 1 12.60574402 -10.25914298 24.04429759 1.022791309 0.75955652 0.232759111 0.222139296 135.4700222 1418426.309 0.038507788 0.045948966 5.51E-11 10.25914298 -0.263234788 EELDMDVMR ddPTM_HeLa_Romidepsin_16h_R1 2 EELDMDVMR 9 0 E9PN09;Q6YBV0 E9PN09 SLC36A4 Proton-coupled amino acid transporter 4 0 0 ; ; 78.149 0.019545 1661610 1080.47 1289.79 1343.17 829.65 1061.14 1295.98 1125.31 998.35 1267.88 1148.72 FALSE FALSE TRUE 1067.300816 1307.947697 1366.54731 925.5780366 1006.986066 1213.171061 1220.893803 1027.235682 1154.477637 1118.876089 0.953904393 1.16898351 1.221357149 0.827239089 0.899997843 1.08427651 1.091178742 0.918096018 1.031819027 1 10.12783456 EELDT(ph)DEY(ph)EET(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 EELDTDEYEETK 12 0 Q8WZA0;Q8WZA0-2 Q8WZA0 LZIC Protein LZIC 3 0 EELDT(1)DEY(1)EET(1)K;EELDT(1)DEY(1)EET(1)K ; 50.024 0.028141 98938000 2672.1 2651.6 2157.38 2551.1 2194.83 2110.88 2053.37 2312.88 2552.2 2782 TRUE FALSE FALSE 2639.531417 2688.929294 2194.928294 2846.070185 2082.819635 1976.001581 2227.783197 2379.799534 2323.92484 2709.723239 0.974096313 0.992326174 0.810019364 1.050317665 0.76864663 0.729226348 0.822144182 0.878244501 0.857624427 1 11.40392979 -9.122470697 0.921948885 0.98827582 0.799687017 0.258538412 0.089518108 0.343530817 0.573118649 0.013711013 0.033487049 7.54E-10 9.122470697 -0.188588804 EELEEVIKDI ddPTM_HeLa_Romidepsin_16h_R1 1 EELEEVIKDI 10 1 P28066;P28066-2 P28066 PSMA5 Proteasome subunit alpha type-5 0 0 110.14 0.0030315 0 5929.8 6020.4 5646.5 3409.7 6489.2 6157.9 5826.4 6079.8 6078.7 5326.4 FALSE FALSE TRUE 5857.525317 6105.155349 5744.774964 3803.945557 6158.031909 5764.430064 6321.294271 6255.709421 5535.005848 5188.01936 1.129048469 1.1767796 1.107315637 0.733217302 1.186971652 1.111104193 1.218440764 1.205799167 1.066882265 1 12.34096815 EELGLIEQAYDNPHEALSR ddPTM_HeLa_Romidepsin_16h_R1 2 EELGLIEQAYDNPHEALSR 19 0 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 ; ; 120.56 0.00040263 5323700 3946.4 4549.3 4077.8 3259.6 4011.5 4842.2 4038.7 4821.2 4578.8 5074.3 FALSE FALSE TRUE 3898.299759 4613.345165 4148.772398 3636.490289 3806.778186 4532.799047 4381.747077 4960.693815 4169.26066 4942.468954 0.788735305 0.933409032 0.839412941 0.735763911 0.770217926 0.917112295 0.886550248 1.0036874 0.84355829 1 12.27101619 -12.47931033 1.17647217 1.001338772 0.849814156 0 0.090629289 0.470186221 1.147651521 0.058664558 0.013854292 3.32E-13 12.47931033 -0.151524616 EELMS(ph)SDLEETAGSTSIPK ddPTM_HeLa_Romidepsin_16h_R1 1 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 0 EELMS(0.614)S(0.386)DLEETAGSTSIPK 203.06 4.81E-21 14334000 14132 14215 14885 7004 12846 13191 11451 12735 14758 15276 TRUE FALSE FALSE 13959.75375 14415.11914 15144.06718 7813.835435 12190.42068 12348.13767 12423.64765 13103.46713 13438.00752 14879.12732 0.938210518 0.968814826 1.017806143 0.525154148 0.819296752 0.829896634 0.834971527 0.880660999 0.903144871 1 13.86100229 EELMS(ph)SDLEETAGSTSIPKR ddPTM_HeLa_Romidepsin_16h_R1 1 EELMSSDLEETAGSTSIPKR 20 1 O00567 O00567 NOP56 Nucleolar protein 56 1 0 EELMS(0.61)S(0.39)DLEETAGSTSIPKR 88.768 0.0015933 7745200 1962.5 2340.1 1930.3 1679.5 1918.1 1713.9 1826.8 2082.7 2461.2 2267.4 TRUE FALSE FALSE 1938.580295 2373.043989 1963.896062 1873.691692 1820.2122 1604.387321 1981.968346 2142.959639 2241.064108 2208.492621 0.877784366 1.074508453 0.889247283 0.848402967 0.824187585 0.726462613 0.897430368 0.970326827 1.014748289 1 11.1088463 -9.530755561 24.98267187 0.952080946 0.849308083 0.382315827 0.077081818 189.5576932 601212.9626 0.012866892 0.018215553 2.95E-10 9.530755561 -0.102772863 EELMSS(ph)DLEETAGSTSIPK ddPTM_HeLa_Romidepsin_16h_R1 5 EELMSSDLEETAGSTSIPK 19 0 O00567 O00567 NOP56 Nucleolar protein 56 1 0 EELMS(0.002)S(0.998)DLEETAGSTSIPK;EELMS(0.189)S(0.811)DLEETAGSTSIPK;EELMS(0.001)S(0.999)DLEETAGSTSIPK;EELMS(0.049)S(0.951)DLEETAGSTSIPK;EELMS(0.209)S(0.791)DLEETAGSTSIPK ;;;; 210.57 8.73E-29 119093100 43567.4 42987.5 42918.4 21168.1 35660.3 40412.6 33961.6 35912.6 43270.4 43448.8 TRUE FALSE FALSE 43036.38377 43592.67915 43665.37675 23615.65532 33840.42182 37830.36529 36846.29746 36951.67442 39400.18705 42319.99391 1.016927929 1.030072907 1.031790714 0.558025962 0.799632011 0.893912352 0.870659328 0.873149332 0.931006444 1 15.3690518 EELQANGSAPAADKEEPAAAGS(ph)GAASPSAAEK ddPTM_HeLa_Romidepsin_16h_R1 2 EELQANGSAPAADKEEPAAAGSGAASPSAAEK 32 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 EELQANGSAPAADKEEPAAAGS(0.546)GAAS(0.403)PS(0.05)AAEK;EELQANGSAPAADKEEPAAAGS(0.736)GAAS(0.256)PS(0.008)AAEK ; 111.89 2.40E-14 89026000 8278.3 8662.9 8326.8 3404.7 9531.4 11854.5 9589 9988.9 7577.9 8202.4 TRUE FALSE FALSE 8177.400895 8784.856534 8471.724461 3798.367434 9044.977091 11097.03571 10403.48942 10277.91306 6900.113645 7989.300466 1.023544043 1.099577688 1.060383759 0.475431792 1.132136303 1.388987153 1.302177765 1.286459698 0.863669313 1 12.96385347 -8.519648232 24.99901277 0.981950051 1.31301464 0.509546999 0.172970944 88.95880469 688397.45 0.024243631 0.049279157 3.02E-09 8.519648232 0.33106459 EELRHT(ph)PELPLAPRPLK ddPTM_HeLa_Romidepsin_16h_R1 1 EELRHTPELPLAPRPLK 17 2 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 EELRHT(1)PELPLAPRPLK 65.528 0.011998 12625000 2733.8 2768.8 2535.1 1844.4 2410.3 1942.4 1748.9 1971.5 3047.7 2913.9 TRUE FALSE FALSE 2700.479394 2807.779239 2579.222352 2057.658206 2287.293397 1818.286909 1897.451522 2028.542242 2775.106079 2838.196458 0.951477262 0.989282906 0.908753989 0.724987941 0.805896784 0.640648713 0.66854129 0.714729326 0.977770961 1 11.47075874 -9.230930397 1.288285261 0.980369905 0.686349952 0.903468546 0.04205428 0.087147813 0.284630415 0.007003249 0.013776148 5.88E-10 9.230930397 -0.294019953 EELSSGDSLS(ph)PDPWKR ddPTM_HeLa_Romidepsin_16h_R1 1 EELSSGDSLSPDPWKR 16 1 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 EELS(0.01)S(0.008)GDS(0.029)LS(0.954)PDPWKR 76.761 0.0017198 0 1293.7 1359.6 1479.4 1044.9 2019.8 2002 1968.4 2135.8 1646.7 1533.7 TRUE FALSE FALSE 1277.931887 1378.740484 1505.148336 1165.716254 1916.722069 1874.078661 2135.595847 2197.596003 1499.415028 1493.854253 0.85545955 0.922941767 1.007560365 0.780341357 1.283071669 1.254525773 1.429587821 1.471091306 1.003722435 1 10.54482368 -8.639395192 5.093317646 0.926708059 1.371069716 0.86050062 0.085568059 0.058195499 2.365128669 0.013250812 0.026906365 2.29E-09 8.639395192 0.444361656 EEMIYRWRK ddPTM_HeLa_Romidepsin_16h_R1 1 EEMIYRWRK 9 2 A0A0A0MR73;H0YJP1;Q99928-2;Q99928 A0A0A0MR73 GABRG3 Gamma-aminobutyric acid receptor subunit gamma-3 0 0 65.252 0.026329 0 154.33 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 152.4489666 0 0 0 0 0 0 0 0 0 0 EEMVLSGK(ac)YK ddPTM_HeLa_Romidepsin_16h_R1 1 EEMVLSGKYK 10 1 F8VSD1;G3V1Y1;F8W057;Q9GZN1 F8VSD1 ACTR6 Actin-related protein 6 0 1 EEMVLSGK(1)YK 114.5 0.0037262 803390 139.75 143.03 94.724 179.14 172.29 226.44 149.22 133.13 107.6 113.3 FALSE TRUE FALSE 138.0466732 145.0435801 96.37263149 199.8530097 163.4973984 211.9712148 161.8947431 136.9819065 97.97598651 110.3564497 1.250916223 1.314319014 0.873284994 1.810977159 1.48153913 1.920786827 1.467016595 1.241267791 0.887813869 1 6.786027139 -9.259276897 24.99997474 1.122582342 1.590783614 0.571602036 0.22188415 115.1909925 1331694.405 0.03226548 0.051848128 5.50E-10 9.259276897 0.468201272 EENEGVYNGSWGGR ddPTM_HeLa_Romidepsin_16h_R1 1 EENEGVYNGSWGGR 14 0 P49419;A0A1B0GUY0;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GTJ4;A0A1B0GTY9;A0A1B0GV49;A0A0J9YWF7;H0YHM6;A0A1B0GW77;P49419-4;P49419-2;F8VVF2;F8WDY6;A0A0J9YWM6;F8WD33;A0A1B0GW65;A0A0J9YWK1 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 0 173.59 0.00025754 5121100 524.18 693.23 652.86 367.14 693.55 643.98 636.47 852.38 548.56 543.35 FALSE FALSE TRUE 517.7910925 702.9893101 664.2227544 409.5904542 658.1555555 602.8317564 690.5317459 877.0422705 499.4954197 529.2336887 0.978378935 1.328315497 1.255065142 0.773931182 1.243601021 1.139065349 1.304776625 1.657192823 0.943808813 1 9.04776109 -4 0.544586033 1.018334866 28.16722911 0.559852823 0.158013601 60.03986542 0.509639634 0.028965505 1911.274273 1.00E-04 4 27.14889425 EENISAPLISSS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 EENISAPLISSSPVK 15 0 A2A2Y4-4;A2A2Y4-3;A2A2Y4-5;A2A2Y4-2;A2A2Y4 A2A2Y4-4 FRMD3 FERM domain-containing protein 3 1 0 EENISAPLIS(0.004)S(0.085)S(0.911)PVK 160.65 0.00022239 3365600 2003.3 2685.6 2212.5 1473.9 1802.5 2260.8 1390.9 2084.2 2426.2 2668.5 TRUE FALSE FALSE 1978.883009 2723.407947 2251.007634 1644.319253 1710.511699 2116.342176 1509.043011 2144.503039 2209.194595 2599.171985 0.761351315 1.047798284 0.866047975 0.632631954 0.658098698 0.814237068 0.580586056 0.825071619 0.849960914 1 11.34383638 -9.360825989 5.857319967 0.898637939 0.699671125 0.500036088 0.101669801 0.17740571 8.673326927 0.017875288 0.027440138 4.36E-10 9.360825989 -0.198966815 EENPES(ph)DGEPVVEDGTSVK ddPTM_HeLa_Romidepsin_16h_R1 2 EENPESDGEPVVEDGTSVK 19 0 Q13439-3;Q13439-4;Q13439;Q13439-5;E7EVX2;H0Y6I0;A0A087WTW2 Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 EENPES(1)DGEPVVEDGTSVK;EENPES(1)DGEPVVEDGTSVK ; 272.51 7.56E-91 20592900 12234.8 13298 13244.9 6700.7 15800.4 16097.1 12998.8 15433.4 13927 13769.3 TRUE FALSE FALSE 12085.67755 13485.20959 13475.42193 7475.466462 14994.04663 15068.54726 14102.91775 15879.94108 12681.33424 13411.5716 0.901138055 1.005490631 1.004760839 0.557389297 1.117993258 1.12354821 1.051548481 1.184047743 0.945551693 1 13.71119069 EENTSNESTDVTK(ac)GDSK(ac)NAK ddPTM_HeLa_Romidepsin_16h_R1 2 EENTSNESTDVTKGDSKNAK 20 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 2 ; EENTSNESTDVTK(1)GDSK(1)NAK;EENTSNESTDVTK(1)GDSK(1)NAK 256.79 1.79E-80 11381800 4632.2 4535.7 4945.7 3006.2 3107 3053.7 2208.36 2767.8 4665.2 4803.2 FALSE TRUE FALSE 4575.740965 4599.553704 5031.777834 3353.790989 2948.438196 2858.578425 2395.938043 2847.881926 4247.932828 4678.412172 0.978054262 0.983144181 1.07553111 0.716865224 0.630221983 0.611014661 0.512126327 0.608728308 0.907986016 1 12.19180325 -9.069644058 3.100272763 0.994544234 0.588498297 0.932995794 0.050702897 0.037166015 0.700558753 0.006561693 0.011692947 8.52E-10 9.069644058 -0.406045937 EENTSNESTDVTK(ac)GDSK(ac)NAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EENTSNESTDVTKGDSKNAKK 21 3 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 3 ; EENTSNESTDVTK(1)GDSK(1)NAK(1)K;EENTSNESTDVTK(1)GDSK(1)NAK(1)K 209.25 2.35E-42 10297000 1448.08 1622.95 2022.22 1546.68 2044.12 2068.95 1496.99 1702.18 1639.31 1494.27 FALSE TRUE FALSE 1430.430244 1645.797933 2057.415891 1725.514419 1939.800929 1936.750772 1624.144293 1751.429893 1492.686008 1455.44865 0.98281052 1.130783922 1.413595657 1.185554996 1.332785549 1.330689868 1.115906283 1.203360828 1.025584797 1 10.50724822 -10.04176134 4.286457728 0.99315993 1.260997796 0.675325288 0.0810301 0.084049736 3.384831907 0.013099358 0.016514484 9.08E-11 10.04176134 0.267837866 EENTSNESTDVTKGDSK(ac)NAK ddPTM_HeLa_Romidepsin_16h_R1 1 EENTSNESTDVTKGDSKNAK 20 2 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 1 EENTSNESTDVTK(0.003)GDSK(0.997)NAK 166.47 7.82E-17 6955000 3351.4 2966.9 2547.4 1217.6 1094.2 809 711.37 1008.9 3242.4 3716 FALSE TRUE FALSE 3310.551848 3008.668096 2591.736428 1358.384641 1038.358891 757.3075109 771.79375 1038.09093 2952.391623 3619.457784 0.914654085 0.831248291 0.716056543 0.37530059 0.286882443 0.209232309 0.213234632 0.286808409 0.815699975 1 11.82155787 -9.382432165 1.195846778 0.96321253 0.223785522 0.963668645 0.057469926 0.033745467 0.095635961 0.006770177 0.01254604 4.15E-10 9.382432165 -0.739427007 down EENTSNESTDVTKGDSK(ac)NAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EENTSNESTDVTKGDSKNAKK 21 3 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 2 ; EENTSNESTDVTKGDSK(1)NAK(1)K;EENTSNESTDVTKGDSK(1)NAK(1)K 207.1 1.40E-41 11785200 3766 3435.1 3046 2240.2 2149.23 1962.92 1492.16 2033.11 4165 3998.2 FALSE TRUE FALSE 3720.098543 3483.459428 3099.014352 2499.222464 2039.546773 1837.495747 1618.904033 2091.93483 3792.471969 3894.326188 0.955261158 0.894496059 0.79577678 0.64175992 0.523722635 0.471839198 0.415708381 0.537175041 0.973845483 1 11.92715801 -9.293320255 1.00414715 0.983295649 0.45806023 0.980375991 0.030260319 0.042145609 0.084190022 0.005281763 0.010973438 5.09E-10 9.293320255 -0.525235419 EEPDSENIPQELLSNLGHPES(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 4 EEPDSENIPQELLSNLGHPESPPR 24 0 D6RF40;D6RAG5;D6R9R7;A0A0A0MTL5;Q13309-2;Q13309 D6RF40 SKP2 S-phase kinase-associated protein 2 1 0 EEPDSENIPQELLS(0.009)NLGHPES(0.991)PPR;EEPDSENIPQELLS(0.007)NLGHPES(0.993)PPR;EEPDSENIPQELLSNLGHPES(1)PPR;EEPDSENIPQELLS(0.002)NLGHPES(0.998)PPR ;;; 156.49 4.40E-10 32675200 5911.71 5982.14 5836.5 2558.43 5470.62 4575.78 3325.6 3341.84 6941.1 6390.25 TRUE FALSE FALSE 5839.655805 6066.356724 5938.081834 2854.247714 5191.433848 4283.402426 3608.076381 3438.530868 6320.270632 6224.230384 0.938213312 0.974635634 0.954026678 0.458570384 0.834068395 0.688181857 0.579682332 0.552442737 1.01543006 1 12.60367975 -9.319813126 9.976110428 0.969438632 0.635697166 0.780319198 0.093716237 0.207266145 34.76139335 0.013787851 0.021075845 4.79E-10 9.319813126 -0.333741465 EEPLDPEEAEGPLSLVT(ph)TANHSPDFDHDRDYEDEPVNEDME ddPTM_HeLa_Romidepsin_16h_R1 1 EEPLDPEEAEGPLSLVTTANHSPDFDHDRDYEDEPVNEDME 41 1 Q9H334-8;Q9H334-4;A0A3B3IST0;A0A3B3IUB6;A0A3B3IRS5;C9J0F0;Q9H334;Q9H334-3;Q9H334-7;Q9H334-6;A0A3B3IT66;A0A0B4J2F3;A0A3B3IRW5;H0Y882 Q9H334-8 FOXP1 Forkhead box protein P1 1 0 EEPLDPEEAEGPLS(0.194)LVT(0.204)T(0.204)ANHS(0.204)PDFDHDRDY(0.194)EDEPVNEDME 50.029 0.0015822 4043600 1706.5 1636.5 1540.4 1177.5 1616 1453.3 1242.3 1081.2 1878.8 1771.3 TRUE FALSE FALSE 1685.700522 1659.53869 1567.210016 1313.64809 1533.52949 1360.43882 1347.820931 1112.482816 1710.755422 1725.281371 0.977058322 0.961894517 0.908379377 0.761410928 0.888857618 0.788531566 0.78121804 0.644812397 0.991580534 1 10.75261595 -6.786077305 0.277429332 1.014697545 0.298488354 0.845845156 0.044841121 2.859604066 0.135110677 0.023016825 0.72939911 1.64E-07 6.786077305 -0.71620919 EEPLS(ph)EEEPCTSTAIAS(ph)PEKK ddPTM_HeLa_Romidepsin_16h_R1 1 EEPLSEEEPCTSTAIASPEKK 21 1 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 2 0 EEPLS(0.999)EEEPCT(0.001)S(0.007)T(0.017)AIAS(0.976)PEKK 78.978 0.0011935 3532400 974.53 1019.9 1032.4 366.7 1078.9 952.47 762.41 753.77 1233.6 1186.9 TRUE FALSE FALSE 962.6520535 1034.258179 1050.368489 409.0995794 1023.839707 891.610241 827.1690864 775.5791457 1123.263726 1156.064167 0.83269777 0.894637347 0.908572828 0.353872727 0.885625328 0.771246326 0.715504476 0.670878977 0.971627491 1 10.17500576 -9.464475011 24.99999794 0.916088363 0.691310173 0.452147157 0.132873959 202.499804 86680.99725 0.020384654 0.031138026 3.43E-10 9.464475011 -0.22477819 EEPPEPVPS(ph)PIIPILPSTAGK ddPTM_HeLa_Romidepsin_16h_R1 1 EEPPEPVPSPIIPILPSTAGK 21 0 Q8NEZ4;Q8NEZ4-3;H7BY37;Q8NEZ4-2;H7C2V8;H0Y765 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 1 0 EEPPEPVPS(1)PIIPILPSTAGK 106.58 0.00013217 4788400 4272 4273.2 4241.4 2493.5 3691.4 3592.8 3037 3563.1 4330.8 4636.7 TRUE FALSE FALSE 4219.931221 4333.358222 4315.219788 2781.810202 3503.014083 3363.231675 3294.962704 3666.192677 3943.442401 4516.237866 0.934390824 0.959506198 0.955489927 0.615957415 0.775648712 0.744697639 0.729581302 0.811780244 0.873169775 1 12.14090576 -9.324580173 9.414314013 0.96659623 0.738035461 0.764263623 0.057373764 0.135362105 19.56461588 0.00758832 0.011600497 4.74E-10 9.324580173 -0.228560769 EEPSQNDIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EEPSQNDISPK 11 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 EEPS(0.319)QNDIS(0.681)PK;EEPS(0.001)QNDIS(0.999)PK ; 162.67 0.0009968 239020000 25475 23548 25174 12239.1 16916.6 18557.8 14566.3 17986.9 26654 25709 TRUE FALSE FALSE 25164.5009 23879.50936 25612.14291 13654.24233 16053.28278 17372.01647 15803.56116 18507.32257 24269.99948 25041.07647 1.004928879 0.953613531 1.022805187 0.545273776 0.641077982 0.693740802 0.631105503 0.739078553 0.969207514 1 14.61200896 -9.269795114 24.99689142 0.999354314 0.650930784 0.920770128 0.049838495 105.4594156 315490.4811 0.00706801 0.010907098 5.37E-10 9.269795114 -0.348423529 EEPVAIES(ph)PGQDLLGESR ddPTM_HeLa_Romidepsin_16h_R1 2 EEPVAIESPGQDLLGESR 18 0 Q96RG2-4;Q96RG2;Q96RG2-2 Q96RG2-4 PASK PAS domain-containing serine/threonine-protein kinase 1 0 EEPVAIES(1)PGQDLLGESR;EEPVAIES(1)PGQDLLGESR ; 162.82 2.13E-06 8721600 4063.3 3492.1 3682.3 3620.8 5234.8 6978.4 5868.6 6202.9 4378.4 3994 TRUE FALSE FALSE 4013.774937 3541.261875 3746.388887 4039.453932 4967.648622 6532.502762 6367.078738 6382.371125 3986.784938 3890.235304 1.031756339 0.910295033 0.963023723 1.038357224 1.276953252 1.679205048 1.636682164 1.640613132 1.024818456 1 11.92564171 -8.482897338 2.365182195 1.002502853 1.657279349 0.980881001 0.041053627 0.029688488 0.327149953 0.006659165 0.016565073 3.29E-09 8.482897338 0.654776496 EERS(ph)PQTLAPVGEDAMK ddPTM_HeLa_Romidepsin_16h_R1 1 EERSPQTLAPVGEDAMK 17 1 Q92797 Q92797 SYMPK Symplekin 1 0 EERS(0.998)PQT(0.002)LAPVGEDAMK 76.533 0.024693 22779000 3055.8 2989.8 3247.4 1492.1 2848.5 2420.9 2052 2306.3 3109.4 2928.1 TRUE FALSE FALSE 3018.554734 3031.890483 3303.919635 1664.623623 2703.130416 2266.212303 2226.296829 2373.029152 2831.287476 2852.02754 1.058389056 1.063064939 1.158445909 0.583663236 0.947792536 0.794596921 0.780601448 0.832049873 0.992727958 1 11.4777722 -9.275722814 24.99653126 1.040422737 0.79661682 0.666365376 0.094017641 363.1191785 635470.4659 0.013379531 0.020497163 5.30E-10 9.275722814 -0.243805917 EES(ph)DEEEEDDEESGR ddPTM_HeLa_Romidepsin_16h_R1 1 EESDEEEEDDEESGR 15 0 Q96EV2;H7BXM6;A8MTF7;H7C0H2;Q96EV2-2 Q96EV2 RBM33 RNA-binding protein 33 1 0 EES(1)DEEEEDDEESGR 106.6 0.0055481 2256600 391.02 369.34 471.68 257.28 359.27 347.87 332.06 297.14 597.53 503.2 TRUE FALSE FALSE 386.2540978 374.5395782 479.8893925 287.0279241 340.9351113 325.6422297 360.2651681 305.7372771 544.0854203 490.1267915 0.78806975 0.764168751 0.979112754 0.58561974 0.695605948 0.664404059 0.735044838 0.623792215 1.110091164 1 8.9370112 -16.52287875 0.08389887 1.985123868 0.441600863 0.677340507 0.095029974 74.813022 0.479346834 13.43679784 1.344723478 3.00E-17 16.52287875 -1.543523006 EES(ph)DGEYDEFGR ddPTM_HeLa_Romidepsin_16h_R1 4 EESDGEYDEFGR 12 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 EES(1)DGEYDEFGR;EES(1)DGEYDEFGR;EES(1)DGEYDEFGR;EES(0.993)DGEY(0.007)DEFGR ;;; 166.45 0.00026797 18524200 4979.23 5766.51 5104.86 3700.8 5076.8 5638.57 4043.62 4471.66 5415.41 5645.8 TRUE FALSE FALSE 4918.54123 5847.691079 5193.707947 4128.703909 4817.711952 5278.283575 4387.084982 4601.040427 4931.042166 5499.121302 0.89442312 1.06338645 0.944461426 0.750793387 0.876087594 0.95984127 0.797779271 0.836686477 0.89669638 1 12.4249854 -9.48964562 24.09281612 0.959467221 0.849626314 0.420664476 0.067885245 341.065013 247260.0099 0.010792879 0.01647778 3.24E-10 9.48964562 -0.109840908 EES(ph)DGEYDEFGRK ddPTM_HeLa_Romidepsin_16h_R1 3 EESDGEYDEFGRK 13 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 EES(1)DGEYDEFGRK;EES(0.979)DGEY(0.021)DEFGRK;EES(1)DGEYDEFGRK ;; 116.98 0.0083967 137748000 7713.7 9267 8542.9 4278.1 8405.3 7919.5 7630.5 8286.6 8581.7 9163.4 TRUE FALSE FALSE 7619.682457 9397.461069 8691.585591 4772.754051 7976.346177 7413.469509 8278.63448 8526.359697 7814.131259 8925.333547 0.853714028 1.052897465 0.973810732 0.534742374 0.893674856 0.8306098 0.927543429 0.955298718 0.875500195 1 13.12369037 -13.05469811 0.393437024 1.08908285 0.863898882 0 0.135492248 7.53859499 0.965946004 0.768733036 0.042987219 8.82E-14 13.05469811 -0.225183967 EES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_HeLa_Romidepsin_16h_R1 2 EESEDELEEANGNNPIDIEVDQNK 24 0 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 0 EES(1)EDELEEANGNNPIDIEVDQNK;EES(1)EDELEEANGNNPIDIEVDQNK ; 147.86 1.13E-07 14886500 4539.3 4567 5023.6 3555.4 5511.4 6447.9 4966.6 5932 5108.7 5242.2 TRUE FALSE FALSE 4483.973266 4631.294346 5111.033651 3966.492077 5230.132692 6035.9 5388.46288 6103.633061 4651.765077 5106.006888 0.87817611 0.907028613 1.00098448 0.776828579 1.02430976 1.182117481 1.055318373 1.195382849 0.91103776 1 12.31797977 -8.520632753 24.98772731 0.931416925 1.13001683 0.679866271 0.070606358 43.23564688 481015.7324 0.010673668 0.021630193 3.02E-09 8.520632753 0.198599905 EES(ph)EEEEDEDDEEEEEEEKEK ddPTM_HeLa_Romidepsin_16h_R1 2 EESEEEEDEDDEEEEEEEKEK 21 1 D6R9L5;H0Y8X0;A0A494C198;B4DFG0;H0Y993;P35659;A0A494C028 D6R9L5 DEK Protein DEK 1 0 EES(1)EEEEDEDDEEEEEEEKEK;EES(1)EEEEDEDDEEEEEEEKEK ; 129.26 7.57E-05 1415830000 5856.6 5988.3 5895 2898.1 5006.5 5378.9 4382.4 5029.3 6428.8 5520.1 TRUE FALSE FALSE 5785.217507 6072.603445 5997.600002 3233.191958 4750.999623 5035.20565 4754.640947 5174.814861 5853.792027 5376.687006 1.075981827 1.129432202 1.115482451 0.601335349 0.883629569 0.936488519 0.884306812 0.962454176 1.088735874 1 12.39250177 EES(ph)EEEEDEDDEEEEEEEKEKS(ph)LIVEGK ddPTM_HeLa_Romidepsin_16h_R1 1 EESEEEEDEDDEEEEEEEKEKSLIVEGK 28 2 D6R9L5;H0Y8X0;A0A494C198;B4DFG0;H0Y993;P35659;A0A494C028 D6R9L5 DEK Protein DEK 2 0 EES(1)EEEEDEDDEEEEEEEKEKS(1)LIVEGK 77.433 2.33E-06 7261100 2279.5 1960.5 2246.3 1396.7 2200 2560.3 2087 2086.5 1951.9 2260.2 TRUE FALSE FALSE 2251.716577 1988.09997 2285.395909 1558.193026 2087.725791 2396.705093 2264.269728 2146.869586 1777.317175 2201.479678 1.022819606 0.903074414 1.038118104 0.707793509 0.948328441 1.088679181 1.028521749 0.975193915 0.80732845 1 11.10425781 -8.796150957 0.005903916 1.951069373 1.77E-07 0 0.119139357 35905.73247 63.3461743 10243.62066 10691.28166 1.60E-09 8.796150957 -1.951069195 EES(ph)EES(ph)DEDMGFGLFD ddPTM_HeLa_Romidepsin_16h_R1 1 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388-2;Q8NHW5;P05388;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 2 0 EES(1)EES(1)DEDMGFGLFD 101.2 0.011694 14187000 1205.7 1067.7 1201.4 881.06 1078.3 1287.3 833.37 1045.7 977.35 1103.9 TRUE FALSE FALSE 1191.004465 1082.731109 1222.309863 982.9323027 1023.270327 1205.045685 904.156427 1075.95568 889.9333682 1075.220519 1.107683906 1.006985162 1.136799235 0.914168104 0.951684152 1.120742828 0.840903248 1.00068373 0.827675209 1 10.07041686 -9.248831539 24.98851289 1.054014744 0.966548692 0 0.104778389 885.5799486 1755202.553 0.011606532 0.019164253 5.64E-10 9.248831539 -0.087466052 EES(ph)EES(ph)EAEPVQR ddPTM_HeLa_Romidepsin_16h_R1 2 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 2 0 EES(1)EES(1)EAEPVQR;EES(1)EES(1)EAEPVQR ; 137.09 0.014878 32483700 4853.5 4599.1 4483.6 2824.1 3897.1 3341.3 3669.6 3495.4 4126.3 4538.6 TRUE FALSE FALSE 4794.343675 4663.846251 4561.635177 3150.63573 3698.216445 3127.801714 3981.295732 3596.533884 3757.233393 4420.686518 1.08452469 1.055004971 1.031883885 0.712702816 0.836570616 0.707537551 0.900605758 0.813569085 0.849920794 1 12.11005472 -9.27618594 24.14568384 1.041752649 0.797648417 0.601663035 0.08267379 154.611769 253157.3375 0.008900979 0.013635905 5.29E-10 9.27618594 -0.244104232 EES(ph)EESEAEPVQR ddPTM_HeLa_Romidepsin_16h_R1 3 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 EES(0.695)EES(0.305)EAEPVQR;EES(0.956)EES(0.044)EAEPVQR;EES(0.961)EES(0.039)EAEPVQR ;; 260.5 3.78E-66 113462000 4656.4 4198.9 4800.2 3196.88 3414.55 3808.6 3921.2 3688.9 4897.1 4957.7 TRUE FALSE FALSE 4599.646006 4258.012224 4883.745467 3566.518307 3240.292772 3565.242752 4254.26663 3795.632501 4459.091111 4828.898239 0.95252494 0.88177717 1.011358125 0.738578063 0.671021134 0.738313912 0.881001508 0.786024537 0.923417908 1 12.23747835 -9.25871052 24.99908592 0.970605273 0.763064106 0.707308235 0.060900977 97.31384987 891490.9224 0.009620742 0.015495164 5.51E-10 9.25871052 -0.207541168 EES(ph)EPEVKEDVIEK ddPTM_HeLa_Romidepsin_16h_R1 2 EESEPEVKEDVIEK 14 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 EES(1)EPEVKEDVIEK;EES(1)EPEVKEDVIEK ; 97.904 0.0043936 13461900 5301.2 4848.6 4739.6 2818.8 7917.6 11225.5 9020.6 11661.4 4589.7 4163.8 TRUE FALSE FALSE 5236.586935 4916.858718 4822.09075 3144.722919 7513.535327 10508.22678 9786.809539 11998.80421 4179.185737 4055.623876 1.291191465 1.212355699 1.188988648 0.775398068 1.852621337 2.591025968 2.413145262 2.958559417 1.030466795 1 11.98570815 -8.4631511 2.905452049 1.129196897 2.637362799 0.927661832 0.196208039 0.050309537 0.833379412 0.029220239 0.069785709 3.44E-09 8.4631511 1.508165902 up EES(ph)REPAPASPAPAGVEIR ddPTM_HeLa_Romidepsin_16h_R1 1 EESREPAPASPAPAGVEIR 19 1 Q14195-2 Q14195-2 1 0 EES(0.994)REPAPAS(0.006)PAPAGVEIR 69.876 0.0060147 6134700 318.57 295.93 354.75 564.43 409.62 403.58 450.81 551.79 448.23 542.41 TRUE FALSE FALSE 314.6871463 300.0961103 360.9242749 629.6920523 388.7155629 377.7925405 489.1017901 567.7551731 408.1391862 528.31811 0.595639522 0.568021623 0.683157113 1.191880499 0.735760436 0.71508535 0.925771388 1.074646434 0.772525451 1 9.045263054 EES(ph)WESGR ddPTM_HeLa_Romidepsin_16h_R1 1 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 0 EES(0.653)WES(0.347)GR 114.86 0.020677 23447000 1942.7 1760.8 2112.6 1296.7 2271.8 2790.6 2494.7 2454.2 1771.4 2302 TRUE FALSE FALSE 1919.021625 1785.588589 2149.368917 1446.630555 2155.861569 2612.289666 2706.599756 2525.208405 1612.961547 2242.193708 0.855867902 0.796357862 0.958600905 0.64518536 0.961496574 1.165059761 1.207121287 1.126222233 0.719367618 1 11.13069521 -8.314553402 4.388246134 0.900293242 1.171938735 0.60396941 0.113323552 0.118708347 4.875956706 0.015497286 0.036773213 4.85E-09 8.314553402 0.271645493 EES(ph)WGPPR ddPTM_HeLa_Romidepsin_16h_R1 2 EESWGPPR 8 0 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 0 EES(1)WGPPR;EES(1)WGPPR ; 131.11 0.010517 15133100 3795.6 3447.3 3593 3950.7 3605.1 3392 2875.55 2983.5 3333.9 3757.5 TRUE FALSE FALSE 3749.337767 3495.83118 3655.534658 4407.498523 3421.118295 3175.262147 3119.799145 3069.822865 3035.707634 3659.879608 1.024442924 0.955176551 0.998812816 1.204274182 0.934762522 0.867586502 0.852432178 0.838777007 0.829455599 1 11.83758048 -8.525405812 24.99997634 1.020155787 0.860930665 0.359115228 0.087164163 40.983351 405443.5515 0.009065354 0.018216872 2.98E-09 8.525405812 -0.159225123 EESEES(ph)DEDMGFGLFD ddPTM_HeLa_Romidepsin_16h_R1 5 EESEESDEDMGFGLFD 16 0 F8VWS0;P05388-2;Q8NHW5;P05388;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 0 EES(0.001)EES(0.999)DEDMGFGLFD;EES(0.003)EES(0.997)DEDMGFGLFD;EES(0.025)EES(0.975)DEDMGFGLFD;EES(0.19)EES(0.81)DEDMGFGLFD;EES(0.007)EES(0.993)DEDMGFGLFD ;;;; 160.84 9.92E-07 59941100 9043.9 8874.24 7696.83 5459.61 5981.66 5910.37 5317.89 5779.97 8601.65 8049.48 TRUE FALSE FALSE 8933.669468 8999.171784 7830.790097 6090.875796 5676.39357 5532.716432 5769.591444 5947.204313 7832.296881 7840.353349 1.139447302 1.147801812 0.998780252 0.77686241 0.723997161 0.705671822 0.73588411 0.758537791 0.998972436 1 12.93670296 -9.290504195 2.953933227 1.073968876 0.731109685 0.917406813 0.048014224 0.063348812 1.110912995 0.009435986 0.015516303 5.12E-10 9.290504195 -0.342859191 EESEES(ph)EAEPVQR ddPTM_HeLa_Romidepsin_16h_R1 1 EESEESEAEPVQR 13 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 EES(0.245)EES(0.755)EAEPVQR 179.83 6.36E-07 73167000 2729.6 2900.6 3087 1908.6 2447.7 2496.4 2514.4 2238.2 3256.2 2800.4 TRUE FALSE FALSE 2696.330585 2941.434723 3140.72794 2129.281312 2322.784735 2336.888097 2727.973073 2302.958786 2964.957317 2727.645204 0.988519541 1.078378786 1.151442986 0.780629867 0.851571433 0.856741959 1.000120202 0.844302911 1.087002559 1 11.41344028 -9.249415972 24.99973956 1.012754453 0.872696267 0.595918659 0.074849137 523.4914509 1088472.619 0.011118849 0.018342463 5.63E-10 9.249415972 -0.140058187 EESGKPGAHVTVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EESGKPGAHVTVKK 14 2 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 1 EESGKPGAHVTVK(1)K 55.724 0.029497 14776000 5015 4346.9 4179.9 4442.8 9741.9 8542.7 8075.4 6366.5 9727.6 7558.1 FALSE TRUE FALSE 4953.875251 4408.095772 4252.649406 4956.49744 9244.734491 7996.84904 8761.324274 6550.704633 8857.539093 7361.739472 0.672921837 0.598784538 0.577669099 0.673278029 1.255781263 1.086271671 1.190116046 0.889831086 1.203185623 1 12.84583098 -8.764751502 24.99999729 0.788296698 1.110170573 0.377044572 0.20012126 66.86565013 504709.2762 0.028354289 0.052965327 1.72E-09 8.764751502 0.321873875 EESLVEELS(ph)PASEK ddPTM_HeLa_Romidepsin_16h_R1 1 EESLVEELSPASEK 14 0 A0A087WTL4;A0A087WX97;Q9BXK5-4;Q9BXK5 A0A087WTL4 BCL2L13 Bcl-2-like protein 13 1 0 EESLVEELS(0.901)PAS(0.099)EK 156.96 0.00049079 2923000 2897.2 2822.1 2192.8 1916.6 2423.4 3018.9 2493.2 3006.5 2858 2635.2 TRUE FALSE FALSE 2861.887812 2861.829598 2230.964764 2138.20631 2299.724855 2826.002033 2704.972346 3093.488334 2602.373322 2566.737124 1.114990618 1.114967938 0.869183191 0.833044526 0.895972101 1.101009529 1.0538564 1.205222111 1.013883852 1 11.32571983 -7.130570879 1.660456247 1.021669238 1.31356834 0.264363522 0.099127919 1.913017785 3.887659649 0.016539412 0.982910905 7.40E-08 7.130570879 0.291899102 EESQDTLTHS(ph)SPSFNLDTLLVPK ddPTM_HeLa_Romidepsin_16h_R1 1 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 0 EESQDT(0.001)LT(0.011)HS(0.714)S(0.234)PS(0.023)FNLDT(0.016)LLVPK 64.377 0.0017072 0 1184.1 1257.6 1016.6 1071.2 1146.2 1230.9 1086.1 1242.9 1202.6 1100.7 TRUE FALSE FALSE 1169.667734 1275.304526 1034.293497 1195.057184 1087.705137 1152.249463 1178.353307 1278.861351 1095.036444 1072.103655 1.091002468 1.189534724 0.96473274 1.114684367 1.014552214 1.074755651 1.099103898 1.192852337 1.021390458 1 10.06622868 -16.52287874 0.229290413 0.490560536 1.101179642 0.193486978 0.065819487 54.65138419 0.703220789 12.48821983 0.046496976 3.00E-17 16.52287874 0.610619106 EESQDTLTHSS(ph)PSFNLDTLLVPK ddPTM_HeLa_Romidepsin_16h_R1 1 EESQDTLTHSSPSFNLDTLLVPK 23 0 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 0 EESQDTLTHS(0.144)S(0.658)PS(0.175)FNLDT(0.022)LLVPK 86.748 8.89E-05 2905900 1010.4 819.53 1178.3 981.81 1328.3 1271.5 1068.1 1002.9 1137.4 1180.2 TRUE FALSE FALSE 998.0848562 831.0673649 1198.807817 1095.331492 1260.511894 1190.255254 1158.824387 1031.917329 1035.668095 1149.538234 0.868248508 0.722957567 1.042860326 0.952844768 1.096537599 1.035420327 1.00807816 0.897679867 0.900942713 1 10.16683874 EESQIPVDEVFFHR ddPTM_HeLa_Romidepsin_16h_R1 1 EESQIPVDEVFFHR 14 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 0 115.12 0.0004183 0 1416 1460.5 1253.1 1315.8 1437.9 1499.1 1278.7 1422.3 1603.2 1748.8 FALSE FALSE TRUE 1398.741247 1481.060957 1274.90968 1467.938987 1364.518597 1403.312348 1387.312746 1463.452006 1459.805777 1703.365924 0.821163103 0.869490775 0.748464943 0.861787222 0.801071912 0.823846672 0.814453739 0.859153037 0.857012434 1 10.73417268 -12.19127465 0.634919335 1.02013413 0.820498894 0.211096982 0.05507175 0.308434313 0.191366586 0.034641612 0.006853734 6.44E-13 12.19127465 -0.199635235 EESREPAPAS(ph)PAPAGVEIR ddPTM_HeLa_Romidepsin_16h_R1 2 EESREPAPASPAPAGVEIR 19 1 Q14195-2 Q14195-2 1 0 EES(0.041)REPAPAS(0.959)PAPAGVEIR;EES(0.02)REPAPAS(0.98)PAPAGVEIR ; 84.159 0.0024716 802640000 6900 6701.2 6206.7 7595.3 8725.4 9357 7956.5 8563.1 8064.1 6956.8 TRUE FALSE FALSE 6815.900146 6795.539669 6314.72501 8473.504323 8280.110279 8759.117898 8632.324911 8810.859788 7342.826699 6776.061333 1.005879347 1.002874581 0.931916743 1.250505848 1.221965073 1.29265623 1.273944329 1.300292213 1.083642302 1 12.72623122 -9.249783196 23.65471737 0.998024474 1.267036528 0.915672102 0.039880444 51.2776218 104061.0688 0.00436022 0.007185863 5.63E-10 9.249783196 0.269012054 EESTAASETTEGSQGDSK(ac)NAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EESTAASETTEGSQGDSKNAKK 22 2 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 0 2 ; EESTAASETTEGSQGDSK(1)NAK(1)K;EESTAASETTEGSQGDSK(1)NAK(1)K 171.39 1.46E-50 952140 500.66 390.54 718.31 311.859 554.76 808.59 627.21 960.36 632.71 450.14 FALSE TRUE FALSE 494.5577633 396.0380324 730.8118842 347.9176049 526.4485271 756.9237086 680.4852017 988.1465014 576.1188329 438.4452979 1.127980539 0.903278093 1.666825685 0.793525684 1.200716554 1.726381175 1.552041281 2.253750938 1.314003904 1 8.776253048 -4 0.454715155 1.051086165 28.88653416 0.629504004 0.258535007 30.17728226 0.322434021 0.047907432 788.7105571 1.00E-04 4 27.835448 EESWES(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 EESWESGR 8 0 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 1 0 EES(0.498)WES(0.502)GR 114.89 0.020664 19901000 2687.4 2466.3 2227.9 1661.6 2714.8 3059.7 3082.1 3382.5 2419.7 2605.7 TRUE FALSE FALSE 2654.644935 2501.020636 2266.675665 1853.72201 2576.253626 2864.195045 3343.893497 3480.367301 2203.275972 2538.003538 1.045957933 0.985428349 0.893093974 0.730385905 1.015070935 1.128522873 1.317529092 1.371301201 0.86811383 1 11.30947837 -7.89165101 2.240837033 0.98711485 1.364972088 0.730243727 0.096700038 0.141189893 1.375708256 0.01467412 0.063766561 1.28E-08 7.89165101 0.377857238 EETDKEEPASK(ac)QQK ddPTM_HeLa_Romidepsin_16h_R1 2 EETDKEEPASKQQK 14 2 P05455 P05455 SSB Lupus La protein 0 1 ; EETDKEEPASK(1)QQK;EETDKEEPASK(1)QQK 153.32 2.68E-06 2138900 1512.97 1364.31 1299.85 894.84 1133.68 1057.09 1065.27 1085.09 1494.08 1522.24 FALSE TRUE FALSE 1494.52934 1383.516792 1322.473344 998.3056111 1075.824079 989.5453606 1155.754007 1116.485367 1360.445743 1482.691985 1.007983691 0.933111398 0.891940711 0.673306136 0.725588382 0.667397794 0.779497036 0.753012344 0.917551154 1 10.53400321 -9.556844063 2.0141679 1.00158452 0.719942051 0.855297344 0.047028022 0.05876245 0.480004332 0.006182458 0.009584979 2.77E-10 9.556844063 -0.281642469 EETEELKR ddPTM_HeLa_Romidepsin_16h_R1 2 EETEELKR 8 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 0 ; ; 96.492 0.022362 5985900 2091.95 2104.9 3001.9 1970.31 2554.7 2845.3 3832.8 1669.38 3344.8 2800.4 FALSE FALSE TRUE 2066.452509 2134.532837 3054.14681 2198.126513 2424.324126 2663.494513 4158.357936 1717.680876 3045.632711 2727.645204 0.757595785 0.782555163 1.119700907 0.80586966 0.888797459 0.976481292 1.524523032 0.629730316 1.116579497 1 11.41344028 -7.991357516 24.98523707 0.888905504 1.120470488 0.041245946 0.236003374 259.544785 750324.4117 0.02885655 0.086383945 1.02E-08 7.991357516 0.231564984 EETGDEEDGS(ph)PIALHR ddPTM_HeLa_Romidepsin_16h_R1 1 EETGDEEDGSPIALHR 16 0 P79522-2 P79522-2 1 0 EETGDEEDGS(1)PIALHR 86.453 0.0017127 0 1003.4 1330.1 1161.6 639.43 932.34 889.98 661.09 870.57 1271.3 937.5 TRUE FALSE FALSE 991.1701749 1348.825183 1181.817161 713.3639052 884.7592108 833.1131503 717.2429681 895.7585694 1157.591744 913.1436149 1.08544829 1.477122723 1.294229234 0.781217646 0.968915728 0.912357199 0.785465678 0.980961324 1.267699544 1 9.834697968 -9.245527176 24.96254009 1.098392001 0.886305077 0.44575136 0.160616868 857.046736 1344507.106 0.025937657 0.042927903 5.68E-10 9.245527176 -0.212086924 EETQPPVALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EETQPPVALKK 11 1 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 ; EETQPPVALK(1)K;EETQPPVALK(1)K 190.57 6.71E-09 15989600 3405 3545 3679.8 3009.75 6514.3 6155.9 6424.1 6545.4 7306.1 5904.1 FALSE TRUE FALSE 3363.49855 3594.906603 3743.845375 3357.751456 6181.850963 5762.557857 6969.762894 6734.780822 6652.624118 5750.710631 0.584883985 0.625123891 0.651023085 0.583884614 1.074971662 1.002060133 1.211982891 1.171121493 1.156835136 1 12.48952453 -8.657414045 6.745093646 0.758321375 1.119936118 0.467160199 0.182376696 0.153335752 8.801446762 0.027561993 0.05535722 2.20E-09 8.657414045 0.361614743 EEVVGGDDS(ph)DGLR ddPTM_HeLa_Romidepsin_16h_R1 1 EEVVGGDDSDGLR 13 0 P25490 P25490 YY1 Transcriptional repressor protein YY1 1 0 EEVVGGDDS(1)DGLR 99.941 0.012774 5018500 4098.5 3367.1 4222 2324 4666.4 3993.3 4282.3 3641.7 4442.7 4118.7 TRUE FALSE FALSE 4048.545906 3414.502122 4295.482139 2592.711815 4428.256195 3738.141018 4646.038455 3747.066844 4045.333785 4011.69558 1.009185723 0.851136896 1.070739804 0.646288275 1.103836547 0.931810738 1.158123383 0.934035689 1.008385034 1 11.96999642 EEYEERLARLK ddPTM_HeLa_Romidepsin_16h_R1 1 EEYEERLARLK 11 2 Q9P2E2;Q9P2E2-3;A0A0A0MRS8 Q9P2E2 KIF17 Kinesin-like protein KIF17;Kinesin-like protein 0 0 140.14 0.02676 69328000 2156.9 2023.2 1995.3 1871.2 2532.1 2060.4 2003.8 1809.6 1955.9 2028.9 FALSE FALSE TRUE 2130.610873 2051.682663 2030.02736 2087.556948 2402.877488 1928.74709 2174.002722 1861.957921 1780.959405 1976.188886 1.07814131 1.038201701 1.027243587 1.056354969 1.215914889 0.975993289 1.100098648 0.942196333 0.901209099 1 10.94850513 -12.42999853 1.053267125 0.998553033 1.059084004 0.164398342 0.076781923 1.086247888 2.07069532 0.050745563 0.011558435 3.72E-13 12.42999853 0.060530972 GSK(ac)K(ac)AVTK(ac)VQK ddPTM_HeLa_Romidepsin_16h_R1 2 GSKKAVTKVQK 11 3 Q5QNW6;Q5QNW6-2 Q5QNW6 HIST2H2BF Histone H2B type 2-F 0 3 ; GSK(1)K(1)AVTK(1)VQK;GSK(1)K(1)AVTK(1)VQK 178.1 2.97E-05 37325000 1167.25 1170.72 1793.16 6732.8 12479.6 11685.1 10802.8 10075.5 1436.48 1415.21 FALSE TRUE FALSE 1153.023108 1187.201427 1824.369198 7511.278015 11842.71944 10938.45982 11720.38956 10367.0187 1307.997631 1378.44264 0.836467963 0.861262843 1.323500264 5.449104515 8.59137631 7.935375403 8.502631318 7.520819796 0.948895219 1 10.42882352 -9.111188448 2.443797763 0.909288307 8.155284116 0.990004392 0.340202245 0.017777071 0.207730793 0.049507435 0.089449254 7.74E-10 9.111188448 7.245995809 up EFAGEDT(ph)SDLFLEER ddPTM_HeLa_Romidepsin_16h_R1 1 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 1 0 EFAGEDT(0.771)S(0.229)DLFLEER 143.58 0.00099559 3219900 1530.6 1388.7 1379.8 1380.8 1201 1313.6 1099.2 910.78 1717.5 1436 TRUE FALSE FALSE 1511.944458 1408.250155 1403.81484 1540.454593 1139.708488 1229.665199 1192.566021 937.1319823 1563.882498 1398.692513 1.080969866 1.006833269 1.003662225 1.101353284 0.814838485 0.879153344 0.852629159 0.670005719 1.118103146 1 10.44986312 -7.678758908 0.656140402 1.039830252 0.59526289 0.757502012 0.06752352 0.733622973 0.297698763 0.011456903 0.218309429 2.10E-08 7.678758908 -0.444567362 EFAGEDTS(ph)DLFLEER ddPTM_HeLa_Romidepsin_16h_R1 1 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 1 0 EFAGEDT(0.226)S(0.774)DLFLEER 252.01 3.91E-58 3447900 1040.8 780.35 1149.5 920.63 917.67 686.75 802.79 908.34 1380.4 1035.8 TRUE FALSE FALSE 1028.114329 791.3357878 1169.506565 1027.077572 870.8378756 642.8688914 870.9789626 934.6213848 1256.933567 1008.889767 1.019055167 0.784362984 1.159201534 1.018027545 0.863164544 0.637204294 0.863304388 0.926386029 1.245858178 1 9.978552836 -8.656173993 4.645424818 1.003423545 0.805470834 0.372018489 0.133559972 0.153541078 5.627671024 0.015275556 0.031119326 2.21E-09 8.656173993 -0.197952712 EFAGEDTSDLFLEER ddPTM_HeLa_Romidepsin_16h_R1 2 EFAGEDTSDLFLEER 15 0 O14980 O14980 XPO1 Exportin-1 0 0 ; ; 174.46 6.69E-05 12221600 3496.4 3909.7 4186.4 3941.4 3602 3263.1 2928.5 3096.9 3934.6 3499.8 FALSE FALSE TRUE 3453.784532 3964.740859 4259.262536 4397.123213 3418.176499 3054.598441 3177.246717 3186.503915 3582.679522 3408.874691 1.013174389 1.163064418 1.249462923 1.28990462 1.002728703 0.896072375 0.932051485 0.934767102 1.050985984 1 11.73507985 -8.518230888 24.95703596 1.060991904 0.926627097 0.368383147 0.102702032 245.3095118 1317205.865 0.018316898 0.037414158 3.03E-09 8.518230888 -0.134364807 EFAPS(ph)DEELDSYR ddPTM_HeLa_Romidepsin_16h_R1 2 EFAPSDEELDSYR 13 0 I3L0X5;I3L4C3;O75391 I3L0X5 SPAG7 Sperm-associated antigen 7 1 0 EFAPS(1)DEELDSYR;EFAPS(1)DEELDSYR ; 261.38 2.88E-66 60329000 12214.3 11728.6 10688.2 9001.1 8994.5 8758.6 7888.2 7508.7 11629.2 11108.1 TRUE FALSE FALSE 12065.42741 11893.71554 10874.22364 10041.84953 8535.477102 8198.953727 8558.223511 7725.952388 10589.05523 10819.50996 1.115154703 1.099284125 1.005056946 0.928124247 0.788896829 0.757793445 0.79099918 0.714075999 0.978700076 1 13.40134754 -8.968864571 1.675197118 1.058729459 0.754950915 0.900273086 0.043514701 0.084002894 0.471367168 0.007830868 0.016317438 1.07E-09 8.968864571 -0.303778544 EFAPS(ph)DEELDSYRR ddPTM_HeLa_Romidepsin_16h_R1 3 EFAPSDEELDSYRR 14 1 I3L0X5;I3L4C3;O75391 I3L0X5 SPAG7 Sperm-associated antigen 7 1 0 EFAPS(0.915)DEELDS(0.046)Y(0.038)RR;EFAPS(0.999)DEELDS(0.001)YRR;EFAPS(1)DEELDSYRR ;; 101.53 0.002828 8464700 5491 4329.9 3789.7 4208.1 4273.6 3717.8 3301.56 3455.4 4974.2 4233 TRUE FALSE FALSE 5424.07358 4390.856446 3855.658139 4694.660322 4055.502245 3480.244579 3581.994424 3555.376547 4529.295094 4123.02605 1.315556466 1.064959666 0.935152505 1.138644351 0.983622756 0.844099585 0.868778024 0.862322116 1.098536618 1 12.00948786 -8.659077814 0.9160935 1.139685017 0.836589888 0.50623061 0.098484836 0.462375275 0.713464593 0.023172071 0.085738858 2.19E-09 8.659077814 -0.30309513 EFAPSDEELDSYR ddPTM_HeLa_Romidepsin_16h_R1 1 EFAPSDEELDSYR 13 0 I3L0X5;I3L4C3;O75391 I3L0X5 SPAG7 Sperm-associated antigen 7 0 0 187.31 1.40E-09 3992800 1039.9 966.49 863.58 768.7 807.09 710.34 493.88 660.82 795.7 868.3 FALSE FALSE TRUE 1027.225299 980.0962716 878.6102476 857.5807108 765.9011856 664.9515665 535.8301549 679.9397841 724.5305991 845.7414408 1.21458551 1.158860408 1.038863895 1.013998687 0.905597324 0.786235053 0.63356261 0.803957038 0.856680971 1 9.724072861 -8.578813532 1.308011237 1.105671178 0.711732586 0.623105968 0.103879493 0.161806804 0.538266007 0.014478656 0.04437768 2.64E-09 8.578813532 -0.393938592 EFASHLQQLQDALNELTEEHSK ddPTM_HeLa_Romidepsin_16h_R1 1 EFASHLQQLQDALNELTEEHSK 22 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;Q14980-4;Q14980-3;F5H6Y5;F5H4J1 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 0 0 151.64 1.38E-06 1869300 1182.2 1241.7 1170.6 1394.7 1273.9 1194.8 957.67 1041.2 1269.9 983.79 FALSE FALSE TRUE 1167.790892 1259.180685 1190.973802 1555.961776 1208.888129 1118.456136 1039.014466 1071.325479 1156.316963 958.230994 1.218694552 1.314067999 1.242887998 1.623785691 1.261583206 1.167209309 1.0843048 1.11802424 1.206720478 1 9.904229668 -11.7051779 0.816278659 1.011761632 1.259231784 0.083700899 0.152613087 0.565997082 0.749578235 0.075068838 0.03191099 1.97E-12 11.7051779 0.247470152 EFDEDS(ph)DEKEEEEDTYEK ddPTM_HeLa_Romidepsin_16h_R1 1 EFDEDSDEKEEEEDTYEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 EFDEDS(0.999)DEKEEEEDT(0.001)YEK 71.143 0.0082777 85482000 2078.7 1583 1717.1 766.39 1833.9 1792.4 2424.4 2311 1981.3 2233.9 TRUE FALSE FALSE 2053.364005 1605.285516 1746.985405 855.0036178 1740.30924 1677.871425 2630.328475 2377.865139 1804.087566 2175.862956 0.94370098 0.737769588 0.802893124 0.392949205 0.79982484 0.771129184 1.208866794 1.092837732 0.829136578 1 11.08737198 -10.4331786 5.446423794 0.975735983 0.823008042 0.025538468 0.209706427 0.4268314 19.68427116 0.037957383 0.04294961 3.69E-11 10.4331786 -0.152727941 EFDELNPS(ph)AQR ddPTM_HeLa_Romidepsin_16h_R1 2 EFDELNPSAQR 11 0 H7C5W9;P16615-5;P16615-2;P16615-3;P16615-4;P16615 H7C5W9 ATP2A2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 1 0 EFDELNPS(1)AQR;EFDELNPS(1)AQR ; 135.94 0.0039074 7719000 2693.49 5168.1 3075.3 1777.34 2296.2 3437.1 1709.05 4221.8 3477 4215.5 TRUE FALSE FALSE 2660.660708 5240.856647 3128.824306 1982.844413 2179.016346 3217.480403 1854.216664 4343.951122 3166.008412 4105.980702 0.647996399 1.27639583 0.76201632 0.482916155 0.530693275 0.783608262 0.45158923 1.057957023 0.771072404 1 12.00351113 -9.52168304 24.99913662 0.869798437 0.646555735 0.216933193 0.225269891 61.14898254 1278477.201 0.036396744 0.051869762 3.01E-10 9.52168304 -0.223242702 EFDPTITDAS(ph)LSLPSRR ddPTM_HeLa_Romidepsin_16h_R1 1 EFDPTITDASLSLPSRR 17 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 1 0 EFDPTIT(0.003)DAS(0.498)LS(0.498)LPS(0.002)RR 65.085 0.012456 4145000 2159.4 2305.4 2214.6 1466 2078.2 1910.3 1557.9 1807.9 1769.1 2135.9 TRUE FALSE FALSE 2133.080402 2337.855482 2253.144184 1635.505818 1972.141699 1788.237995 1690.227987 1860.208734 1610.867265 2080.40901 1.025317806 1.123748008 1.08302943 0.786146287 0.947958642 0.859560782 0.812449849 0.894155296 0.774303157 1 11.02265148 -9.265749244 24.9928137 1.027268202 0.862265657 0.331243352 0.096850234 164.8365602 955883.3292 0.008696538 0.013576187 5.42E-10 9.265749244 -0.165002545 EFDPTITDASLS(ph)LPSRR ddPTM_HeLa_Romidepsin_16h_R1 1 EFDPTITDASLSLPSRR 17 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 1 0 EFDPTITDAS(0.207)LS(0.79)LPS(0.002)RR 92.563 0.002264 4724500 1741.1 1708.5 1603 1349.7 1731.9 1528 1187.1 1835.9 1972.2 1616.9 TRUE FALSE FALSE 1719.878804 1732.552308 1630.899543 1505.758665 1643.51468 1430.365731 1287.932244 1889.01887 1795.801493 1574.892705 1.092060937 1.100108155 1.03556232 0.956102381 1.043572477 0.908230591 0.817790469 1.199458772 1.140269103 1 10.62103783 -9.35877586 5.262370768 1.049669273 0.974874898 0.140991777 0.099854267 0.371531933 15.9751193 0.014385132 0.022150864 4.38E-10 9.35877586 -0.074794374 EFETAETLLNSEVHMLLEHR ddPTM_HeLa_Romidepsin_16h_R1 1 EFETAETLLNSEVHMLLEHR 20 0 E9PHV4;O15514 E9PHV4 POLR2D DNA-directed RNA polymerase II subunit RPB4 0 0 79.462 0.0014632 1233300 484.23 386.65 243.61 398.74 510.27 468.33 295.33 317.85 416.54 486.57 FALSE FALSE TRUE 478.3280185 392.0932688 247.8499299 444.8441949 484.2290178 438.4052245 320.4153228 327.0464883 379.2836192 473.9288413 1.009282358 0.82732519 0.522968657 0.938630774 1.021733593 0.925044408 0.67608319 0.690075091 0.800296555 1 8.88852665 -10.23626669 5.89066775 1.004563595 0.802736194 0.098989784 0.151822038 0.170549218 20.41747961 0.02411306 0.029116154 5.80E-11 10.23626669 -0.201827401 EFEVYGPIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EFEVYGPIKR 10 1 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 1 ; EFEVYGPIK(1)R;EFEVYGPIK(1)R 128.6 0.0023166 1785040 278.93 441.99 579.89 359.45 971.11 758.03 815.21 615.08 828.07 752.33 FALSE TRUE FALSE 275.5302939 448.2123468 589.9827422 401.0113003 921.550633 709.5943294 884.4539171 632.8763694 754.0053453 732.7843581 0.376004606 0.611656542 0.80512464 0.547243259 1.257601398 0.968353543 1.206977069 0.863659769 1.028959389 1 9.517244898 -8.765012913 24.99999493 0.689102858 1.076079004 0.37854688 0.21367845 78.41523761 548588.6459 0.037275854 0.069545525 1.72E-09 8.765012913 0.386976146 EFFVGLSK ddPTM_HeLa_Romidepsin_16h_R1 1 EFFVGLSK 8 0 B4DYP1;H0Y7N1;A0A140T971;Q5SSV3;Q5SRR8;O94760-2;O95865;O94760 B4DYP1 DDAH2;DDAH1 "N(G),N(G)-dimethylarginine dimethylaminohydrolase 1;N(G),N(G)-dimethylarginine dimethylaminohydrolase 2" 0 0 109.11 0.026102 255730 271.53 147.14 180.52 140.42 227.22 322.76 176.74 126.13 253.54 199.43 FALSE FALSE TRUE 268.2204879 149.2114408 183.6618749 156.6560211 215.6241155 302.1366777 191.7522912 129.7793725 230.8627474 194.2487799 1.380809126 0.76814609 0.945498216 0.806471069 1.110041029 1.555410942 0.987147983 0.668109075 1.188490077 1 7.601761726 -10.2668744 24.75335605 1.179826523 0.997193943 0.133208433 0.244347239 763.2508821 3476153.651 0.046499532 0.053992427 5.41E-11 10.2668744 -0.182632581 EFGSLPTT(ph)PSEQR ddPTM_HeLa_Romidepsin_16h_R1 1 EFGSLPTTPSEQR 13 0 O15400-2;O15400 O15400-2 STX7 Syntaxin-7 1 0 EFGSLPT(0.141)T(0.827)PS(0.031)EQR 148.13 0.0015849 3561000 1450.7 2518.4 1688.3 1248.5 2230.2 2912.2 1728.1 3004.3 1692.7 1943.3 TRUE FALSE FALSE 1433.01831 2553.854101 1717.684153 1392.857444 2116.384572 2726.119819 1874.884771 3091.22468 1541.300673 1892.812786 0.757084019 1.349237558 0.907477045 0.73586646 1.118116164 1.440247994 0.990528374 1.633138102 0.814291135 1 10.88631601 -4.000000022 0.427518347 0.903946561 13.49085375 0.440670711 0.217640889 48.41542325 0.546034455 0.049517542 529.0523034 1.00E-04 4.000000022 12.58690718 EFGYDSPHDLDS(ph)D ddPTM_HeLa_Romidepsin_16h_R1 2 EFGYDSPHDLDSD 13 0 Q96CW6 Q96CW6 SLC7A6OS Probable RNA polymerase II nuclear localization protein SLC7A6OS 1 0 EFGYDSPHDLDS(1)D;EFGYDSPHDLDS(1)D ; 106.49 0.0089438 32178000 7343.3 7679.3 5773.1 4899.8 12859.8 15039.1 14045.4 15926.4 10020.9 7553.4 TRUE FALSE FALSE 7253.797035 7787.409387 5873.578384 5466.33793 12203.51642 14078.15005 15238.41593 16387.20526 9124.605606 7357.161579 0.985950486 1.058480136 0.798348428 0.742995498 1.658726166 1.913530088 2.071235729 2.227381454 1.240234499 1 12.84493356 -8.538829939 2.884364633 0.967153197 2.066706172 0.911221029 0.155504941 0.045676894 0.769948637 0.019833795 0.045390026 2.89E-09 8.538829939 1.099552975 up EFHLNESGDPS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 EFHLNESGDPSSK 13 0 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105-2 Q01105;Q01105-2 SET;SETSIP Protein SET;Protein SETSIP 1 0 EFHLNES(0.032)GDPS(0.936)S(0.032)K 166.79 0.00011857 0 2433 2075.2 2102.9 2005.4 2205.4 2153.9 1883.3 2046.6 2251.4 2319.1 TRUE FALSE FALSE 2403.34566 2104.41472 2139.500092 2237.273784 2092.850209 2016.272741 2043.267455 2105.815142 2050.029145 2258.849448 1.063968943 0.931631244 0.947163652 0.990448383 0.926511597 0.892610503 0.90456115 0.932251215 0.907554573 1 11.1413724 -10.24906939 24.76595157 1.030207556 0.932185707 0.094884125 0.048038299 314.7206791 630103.0369 0.005884146 0.00717487 5.64E-11 10.24906939 -0.098021849 EFITGDVEPTDAES(ph)EWHSENEEEEK ddPTM_HeLa_Romidepsin_16h_R1 3 EFITGDVEPTDAESEWHSENEEEEK 25 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;A8MXH2 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 EFITGDVEPT(0.148)DAES(0.465)EWHS(0.387)ENEEEEK;EFITGDVEPT(0.002)DAES(0.897)EWHS(0.1)ENEEEEK;EFITGDVEPT(0.401)DAES(0.584)EWHS(0.014)ENEEEEK ;; 133.46 7.62E-07 284119000 9131.3 8072 8611.7 5149.47 13954.3 13353.6 11475.9 11106.8 12012.9 11216.7 TRUE FALSE FALSE 9020.004203 8185.637828 8761.583026 5744.87595 13242.16 12500.34806 12450.66266 11428.15773 10938.43614 10925.28852 0.825607872 0.749237681 0.801954384 0.525832882 1.212065016 1.144166402 1.13961866 1.046028003 1.001203412 1 13.41538376 -8.679856549 24.99998328 0.867525563 1.136389072 0.550262995 0.136451296 21.11009447 6467.239782 0.02147427 0.042948535 2.09E-09 8.679856549 0.268863508 EFITGDVEPTDAES(ph)EWHSENEEEEKLAGDMK ddPTM_HeLa_Romidepsin_16h_R1 2 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PKT8;C9JZI7;A8MXH2 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 EFIT(0.002)GDVEPT(0.053)DAES(0.473)EWHS(0.473)ENEEEEKLAGDMK;EFITGDVEPT(0.027)DAES(0.525)EWHS(0.448)ENEEEEKLAGDMK ; 49.445 0.0059567 107373000 4464.7 3851.5 3483.7 4218.1 5114.4 5410.5 4840.3 4547.5 5015.9 4302.4 TRUE FALSE FALSE 4410.282519 3905.721518 3544.332337 4705.816569 4853.393084 5064.786512 5251.434961 4679.074738 4567.265341 4190.623028 1.052416906 0.932014522 0.845776944 1.122939605 1.158155494 1.208599886 1.253139432 1.116558256 1.089877403 1 12.03294903 -9.024433227 11.56188016 1.003851727 1.184561141 0.638541506 0.07108076 0.508296591 240.0546215 0.010733622 0.01807543 9.45E-10 9.024433227 0.180709414 EFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_HeLa_Romidepsin_16h_R1 1 EFITGDVEPTDAESEWHSENEEEEK 25 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;A8MXH2 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 EFITGDVEPT(0.041)DAES(0.263)EWHS(0.696)ENEEEEK 62.735 0.0015272 303950000 624.54 819.71 926.87 557.24 1123.2 1225.2 923.83 1142.8 1219.7 1206 TRUE FALSE FALSE 616.9278663 831.2498989 943.0017835 621.6707107 1065.878913 1146.913674 1002.300097 1175.865115 1110.606977 1174.667946 0.525193412 0.707646703 0.802781575 0.529231016 0.907387416 0.976372666 0.85326249 1.001019155 0.945464615 1 10.19803728 -8.552706153 24.91431152 0.750390092 0.935748986 0.27151106 0.147400957 258.7909074 216162.5504 0.027737132 0.055474805 2.80E-09 8.552706153 0.185358894 EFITGDVEPTDAESEWHS(ph)ENEEEEKLAGDMK ddPTM_HeLa_Romidepsin_16h_R1 2 EFITGDVEPTDAESEWHSENEEEEKLAGDMK 31 1 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PKT8;C9JZI7;A8MXH2 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 EFITGDVEPT(0.018)DAES(0.216)EWHS(0.766)ENEEEEKLAGDMK;EFITGDVEPT(0.008)DAES(0.115)EWHS(0.877)ENEEEEKLAGDMK ; 46.695 0.0084392 679760000 6721.3 5777.4 5552.7 5470.3 8689 8998.1 7042.1 7254.4 9438.6 7398.2 TRUE FALSE FALSE 6639.37821 5858.734389 5649.342414 6102.801825 8245.567907 8423.15045 7640.255798 7464.294618 8594.387977 7205.993697 0.921368862 0.813036291 0.783978262 0.846906351 1.144265212 1.168908939 1.060264013 1.035845288 1.192672147 1 12.81498167 -8.753380673 24.99752299 0.927362848 1.104073116 0.366975897 0.113224319 128.0571501 397220.7403 0.013696702 0.027013904 1.76E-09 8.753380673 0.176710268 EFLEDYDDDRDDPKYYR ddPTM_HeLa_Romidepsin_16h_R1 1 EFLEDYDDDRDDPKYYR 17 2 P49756 P49756 RBM25 RNA-binding protein 25 0 0 63.212 0.016045 8314700 3936.6 4146.3 3407.3 4951.9 3742.6 3279.1 3307.2 3956.4 4031.5 3597.1 FALSE FALSE TRUE 3888.619205 4204.67172 3466.602627 5524.461977 3551.601156 3069.576093 3588.113485 4070.872192 3670.912543 3503.646823 1.109877622 1.20008435 0.989426961 1.576774788 1.013686977 0.87610888 1.024108212 1.161895704 1.047740462 1 11.77464164 -7.229435941 20.5883039 1.077907507 1.161897197 0.006634115 0.180933028 4468.616212 2874196.509 0.024394832 2.750345371 5.90E-08 7.229435941 0.08398969 EFLHAQEEVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EFLHAQEEVKR 11 1 P43686 P43686 PSMC4 26S protease regulatory subunit 6B 0 1 ; EFLHAQEEVK(1)R;EFLHAQEEVK(1)R 92.943 0.0086087 2162400 1047.87 957.74 1263.81 758.37 2242.4 2205.7 1709.54 1938.31 2549.8 2439 FALSE TRUE FALSE 1035.098157 971.2230889 1285.806083 846.0563076 2127.96196 2064.762889 1854.748285 1994.391942 2321.739502 2375.634428 0.435714412 0.408826828 0.541247453 0.3561391 0.895744705 0.869141676 0.780738089 0.839519716 0.97731346 1 11.21409713 EFNAEVHR ddPTM_HeLa_Romidepsin_16h_R1 4 EFNAEVHR 8 0 A0A2R8Y6J3;P46777 A0A2R8Y6J3 RPL5 60S ribosomal protein L5 0 0 ;;; ;;; 168.25 1.36E-08 54157000 21835.5 19524.4 25114.2 18221.2 26139.8 26786.5 21865.2 18903.8 20449.7 18687 FALSE FALSE TRUE 21569.36053 19799.26502 25551.30212 20328.02088 24805.78846 25074.9291 23722.42954 19450.75163 18620.62761 18201.50905 1.185031443 1.087781511 1.403801303 1.116831622 1.362842411 1.377629132 1.30332213 1.068634012 1.023026584 1 14.15177045 -11.34782908 0.431717153 0.982110847 1.278936507 0.409279605 0.113502177 0.818968232 0.333163461 0.10404814 0.042986158 4.49E-12 11.34782908 0.29682566 EFNAEVHRK ddPTM_HeLa_Romidepsin_16h_R1 1 EFNAEVHRK 9 1 A0A2R8Y6J3;P46777 A0A2R8Y6J3 RPL5 60S ribosomal protein L5 0 0 61.679 0.022556 5504400 3174 3523.2 3574.1 4671.9 3774 3784.2 4689.4 1111.6 4379.4 2894.6 FALSE FALSE TRUE 3135.314067 3572.799702 3636.305711 5212.08706 3581.398697 3542.401833 5087.717519 1143.762392 3987.695496 2819.397875 1.112050944 1.267220825 1.289745496 1.848652546 1.270270766 1.256439137 1.804540453 0.405676121 1.414378414 1 11.46117137 -10.27682489 1.745507039 1.042516478 1.352382451 0 0.388252774 0.520131375 3.003182369 0.063891174 0.075341478 5.29E-11 10.27682489 0.309865973 EFPGFLENQKDPLAVDK ddPTM_HeLa_Romidepsin_16h_R1 1 EFPGFLENQKDPLAVDK 17 1 P60903 P60903 S100A10 Protein S100-A10 0 0 116.78 0.0024629 13179000 646.1 697.14 804.46 953.96 763.56 627.71 807.47 868.18 627.47 705.69 FALSE FALSE TRUE 638.2250847 706.9543552 818.4612888 1064.261344 724.592684 587.6013568 876.0564816 893.2994185 571.3475117 687.3560721 0.928521782 1.028512563 1.190738428 1.548340645 1.054173686 0.85487185 1.274530796 1.299616683 0.831224943 1 9.424913844 -9.845707413 3.942358469 0.967013749 1.200282423 0.348842959 0.172784318 0.220147178 6.588912945 0.028223254 0.037937041 1.43E-10 9.845707413 0.233268674 EFRPEDQPWLLR ddPTM_HeLa_Romidepsin_16h_R1 2 EFRPEDQPWLLR 12 1 P35269;M0QXD6;M0R0R9;M0R0Z3 P35269 GTF2F1 General transcription factor IIF subunit 1 0 0 ; ; 130.69 0.0042803 32430000 3028.8 3266.9 3036.1 1946.05 4050.7 4045.5 3231.6 3781.2 3409.9 2777.4 FALSE FALSE TRUE 2991.883821 3312.891504 3088.942047 2171.061457 3843.977664 3787.005606 3506.092023 3890.603056 3104.910004 2705.242748 1.105957616 1.224618939 1.141835441 0.8025385 1.420936316 1.399876447 1.296036012 1.438171513 1.147738038 1 11.40154234 -6.482992864 0.284955335 1.01800535 2.036335855 0.389665788 0.149908829 8.377244128 0.358407889 0.06887932 3.226049813 3.29E-07 6.482992864 1.018330505 EFS(ph)PFGSITSAK ddPTM_HeLa_Romidepsin_16h_R1 1 EFSPFGSITSAK 12 0 H0Y5F5;B1ANR0;Q13310-2;Q13310;Q13310-3;H0YEU6 H0Y5F5 PABPC4 Polyadenylate-binding protein;Polyadenylate-binding protein 4 1 0 EFS(0.849)PFGS(0.151)ITSAK 89.43 0.029201 7504600 820.46 946.83 760.34 1026.5 920.65 803.61 681.58 1079.6 1157.1 756.7 TRUE FALSE FALSE 810.4599179 960.1594976 773.5733988 1145.18876 873.6657951 752.2619145 739.4733882 1110.836523 1053.606078 737.0408249 1.099613333 1.302722271 1.049566554 1.553765709 1.18536961 1.020651623 1.003300446 1.507157385 1.429508437 1 9.525600723 -10.68647291 1.297832996 1.027970398 1.219848968 0 0.220191968 0.488899427 1.701535056 0.038841363 0.038114563 2.06E-11 10.68647291 0.19187857 EFSGPST(ph)PTGTLEFEGGEVSLEGGK ddPTM_HeLa_Romidepsin_16h_R1 2 EFSGPSTPTGTLEFEGGEVSLEGGK 25 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 EFS(0.006)GPS(0.372)T(0.598)PT(0.022)GT(0.002)LEFEGGEVSLEGGK;EFS(0.005)GPS(0.065)T(0.359)PT(0.359)GT(0.212)LEFEGGEVSLEGGK ; 168.69 2.05E-14 124530000 13827.8 15082.9 13319.6 8279 13559.8 12124.6 9949.1 10480.3 13350.4 13426.8 TRUE FALSE FALSE 13659.26145 15295.23746 13551.42205 9236.256934 12867.79281 11349.87719 10794.17631 10783.53095 12156.30679 13077.9698 1.044448157 1.169542192 1.036202274 0.70624547 0.983928928 0.867862318 0.825370946 0.824556954 0.929525528 1 13.67485098 -9.299447503 23.45326193 1.036064649 0.850058683 0.570859786 0.084094042 138.9345493 85730.4534 0.011781269 0.017996593 5.02E-10 9.299447503 -0.186005966 EFSIDVGYER ddPTM_HeLa_Romidepsin_16h_R1 1 EFSIDVGYER 10 0 P61158;B4DXW1 P61158 ACTR3 Actin-related protein 3 0 0 200.56 2.38E-11 8672000 3076.6 2664 2757.6 2240.8 2659.6 2849.6 2514.4 2605.7 2822.9 2740.5 FALSE FALSE TRUE 3039.101216 2701.503862 2805.594871 2499.891839 2523.870688 2667.519757 2727.973073 2681.091818 2570.412754 2669.301415 1.138538046 1.012063998 1.051059598 0.936534115 0.945517308 0.999332538 1.021980155 1.004417037 0.962953355 1 11.38224651 -9.534800737 2.635828755 1.063574694 0.983446731 0.043108178 0.053839791 0.278228728 3.90712582 0.009557277 0.014538753 2.92E-10 9.534800737 -0.080127962 EFVS(ph)SDESSSGENK ddPTM_HeLa_Romidepsin_16h_R1 1 EFVSSDESSSGENK 14 0 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 0 EFVS(0.958)S(0.042)DESSSGENK 115.06 0.00071055 0 1129.7 1030.6 857.1 755.94 697.33 675.92 591.19 662.52 1161.8 982.68 TRUE FALSE FALSE 1115.930782 1045.108814 872.017466 843.3453396 661.742648 632.7308934 641.4056638 681.6889709 1057.885698 957.1498319 1.165889336 1.091896774 0.911056385 0.881100651 0.691367878 0.66105731 0.670120437 0.712207168 1.105245661 1 9.902600971 -9.167882392 1.390108101 1.080606893 0.674899922 0.920141563 0.052690188 0.103292152 0.392333427 0.011836791 0.023503456 6.79E-10 9.167882392 -0.40570697 EGAAS(ph)PAPETPQPTSPETSPK ddPTM_HeLa_Romidepsin_16h_R1 1 EGAASPAPETPQPTSPETSPK 21 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 0 EGAAS(0.784)PAPET(0.214)PQPT(0.001)SPETSPK 94.838 0.00033404 8202600 2526.7 2713.9 2548 2399.2 1770 2235.6 1579.9 1759.5 2619 2659.2 TRUE FALSE FALSE 2495.903609 2752.106355 2592.346871 2676.606793 1679.670295 2092.752375 1714.096667 1810.408356 2384.750081 2590.113601 0.963627081 1.062542722 1.000862229 1.03339359 0.648492906 0.807977061 0.661784358 0.698968708 0.920712543 1 11.33879966 -8.763944513 25 0.993731012 0.708673587 0.878416491 0.053302916 14.13437704 141056.2059 0.00688189 0.012907594 1.72E-09 8.763944513 -0.285057424 EGAASPAPETPQPT(ph)SPETSPK ddPTM_HeLa_Romidepsin_16h_R1 1 EGAASPAPETPQPTSPETSPK 21 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 0 EGAAS(0.001)PAPET(0.034)PQPT(0.794)S(0.169)PET(0.001)SPK 101.92 0.00031617 8964200 3447 3412.3 3136.4 3360.8 2699.1 2419.7 1962.6 2587.1 3679.7 3480.1 TRUE FALSE FALSE 3404.986638 3460.338449 3190.987726 3749.391509 2561.354855 2265.088979 2129.303195 2661.953657 3350.578416 3389.6865 1.004513732 1.02084321 0.941381371 1.106117486 0.755631783 0.668229637 0.628171129 0.785309691 0.988462625 1 11.72693613 -8.642852589 5.380628365 1.004820921 0.691517322 0.883145936 0.053846591 0.04335601 1.876740226 0.006995277 0.014159495 2.28E-09 8.642852589 -0.313303599 EGAKDIDIS(ph)SPEFK ddPTM_HeLa_Romidepsin_16h_R1 2 EGAKDIDISSPEFK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 EGAKDIDIS(0.5)S(0.5)PEFK;EGAKDIDIS(0.873)S(0.127)PEFK ; 213.02 3.97E-23 80859000 15389 12632.4 7693.7 45051 14308.7 12414 12274.6 12597.6 16174.9 11580.8 TRUE FALSE FALSE 15201.43295 12810.23926 7827.605621 50260.00859 13578.47365 11620.78546 13317.20422 12962.09168 14728.17643 11279.92915 1.34765323 1.135666642 0.693941027 4.455702508 1.203772955 1.030217948 1.180610627 1.149128821 1.305697602 1 13.46147039 EGDELEDNGKNFY(ph)ESDDDQKEK ddPTM_HeLa_Romidepsin_16h_R1 1 EGDELEDNGKNFYESDDDQKEK 22 2 O00203-3;O00203 O00203-3 AP3B1 AP-3 complex subunit beta-1 1 0 EGDELEDNGKNFY(0.995)ES(0.005)DDDQKEK 90.896 0.00025453 24136000 1228.6 1078.6 1092.8 1182.8 1224.4 1326.6 1117.7 1300.2 1341.1 1235.6 TRUE FALSE FALSE 1213.625351 1093.784559 1111.819726 1319.560901 1161.914299 1241.834541 1212.63741 1337.819236 1221.148657 1203.498934 1.008414147 0.908837165 0.923822776 1.096437117 0.965446887 1.031853462 1.007593257 1.11160816 1.014665342 1 10.23301915 -4.000005734 0.988447182 0.995433656 105.9156883 0.328966767 0.050463927 1326.407091 1.853723311 0.007453015 315133.1057 1.00E-04 4.000005734 104.9202546 EGDGVYYNELETR ddPTM_HeLa_Romidepsin_16h_R1 1 EGDGVYYNELETR 13 0 Q8N7H5-3;Q8N7H5-2;Q8N7H5 Q8N7H5-3 PAF1 RNA polymerase II-associated factor 1 homolog 0 0 145.81 0.0078113 4448100 1549.8 1666.8 1189.6 1238.3 1167.1 1474.6 1467.2 1328.9 1363.7 1113.4 FALSE FALSE TRUE 1530.910441 1690.265254 1210.304489 1381.478072 1107.538532 1380.377819 1591.823931 1367.349625 1241.727257 1084.473707 1.411662109 1.558604181 1.116029352 1.273869586 1.021268219 1.272855035 1.46783082 1.260841656 1.145004483 1 10.08277936 -12.41847153 1.175476024 1.001823471 1.305197856 0.235796626 0.154843048 0.430405627 1.073650297 0.104223724 0.026972559 3.82E-13 12.41847153 0.303374386 EGDNVNYDWIHWDPEHSYEFK ddPTM_HeLa_Romidepsin_16h_R1 2 EGDNVNYDWIHWDPEHSYEFK 21 0 E9PGM4;Q04446 E9PGM4 GBE1 "1,4-alpha-glucan-branching enzyme" 0 0 ; ; 136.49 6.70E-05 9983900 5247.1 5087.3 5861.8 5803 5173.3 5639.7 4494 4927.2 5416.2 4812.2 FALSE FALSE TRUE 5183.146327 5158.919143 5963.82217 6473.970164 4909.287197 5279.341371 4875.720248 5069.760758 4931.761507 4687.17835 1.105813762 1.100644942 1.272369371 1.381208412 1.047386472 1.12633678 1.040225032 1.081623181 1.052181321 1 12.19450398 -11.27837825 0.880691314 1.01498385 1.150713223 0.184800086 0.100607858 0.591755632 0.970244049 0.037292841 0.023562993 5.27E-12 11.27837825 0.135729374 EGDPVSLSTPLETEFGS(ph)PSELS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EGDPVSLSTPLETEFGSPSELSPR 24 0 E9PMR3;E9PMG4;Q9BUR4 E9PMR3 WRAP53 Telomerase Cajal body protein 1 2 0 EGDPVSLSTPLET(0.002)EFGS(0.979)PS(0.124)ELS(0.896)PR;EGDPVSLSTPLET(0.001)EFGS(0.991)PS(0.06)ELS(0.948)PR ; 124.57 7.66E-06 10772200 5934.7 5657.5 5591.5 5969.5 7313.4 8401.5 7681.2 8793.4 6792.5 6711.9 TRUE FALSE FALSE 5862.365594 5737.146434 5688.817712 6659.721677 6940.169908 7864.671265 8333.640936 9047.823155 6184.961788 6537.52387 0.896725688 0.877571776 0.870179264 1.018691757 1.061589991 1.203004596 1.274739657 1.383983192 0.946071006 1 12.67452859 -8.139500149 1.10919267 0.938548496 1.376837474 0.932100752 0.044015778 0.144821517 0.293556031 0.008920156 0.051055964 7.25E-09 8.139500149 0.438288978 EGDPVSLSTPLETEFGS(ph)PSELSPR ddPTM_HeLa_Romidepsin_16h_R1 3 EGDPVSLSTPLETEFGSPSELSPR 24 0 E9PMR3;E9PMG4;Q9BUR4 E9PMR3 WRAP53 Telomerase Cajal body protein 1 1 0 EGDPVSLSTPLET(0.001)EFGS(0.482)PS(0.149)ELS(0.368)PR;EGDPVSLSTPLET(0.004)EFGS(0.983)PS(0.013)ELSPR;EGDPVSLSTPLETEFGS(0.986)PS(0.014)ELSPR ;; 170.87 1.36E-14 19309900 5391.25 5589.48 5518.88 6014.38 8328.8 9161.1 8395.13 9110.7 6070.9 6025.81 TRUE FALSE FALSE 5325.539371 5668.168846 5614.933791 6709.790914 7903.750257 8575.735276 9108.212133 9374.30373 5527.903499 5869.258588 0.907361516 0.965738476 0.956668327 1.143209285 1.346635208 1.461127525 1.551850544 1.597187037 0.941840169 1 12.51896256 -8.670215492 1.229265412 0.952378433 1.573208076 0.986198676 0.030616654 0.047646256 0.140931543 0.006622957 0.019527739 2.14E-09 8.670215492 0.620829643 EGDPVSLSTPLETEFGSPSELS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 EGDPVSLSTPLETEFGSPSELSPR 24 0 E9PMR3;E9PMG4;Q9BUR4 E9PMR3 WRAP53 Telomerase Cajal body protein 1 1 0 EGDPVSLSTPLET(0.001)EFGS(0.254)PS(0.325)ELS(0.421)PR;EGDPVSLSTPLETEFGSPS(0.186)ELS(0.814)PR;EGDPVSLSTPLETEFGSPS(0.005)ELS(0.995)PR ;; 212.66 3.13E-37 57560500 7618.41 8068.21 6649.82 7574.41 9880.93 10728.92 9322.2 10462.11 8441.61 7982.9 TRUE FALSE FALSE 7525.553889 8181.794472 6765.557328 8450.198923 9376.669271 10043.37664 10114.02744 10764.81465 7686.571259 7775.503107 0.967854271 1.052252743 0.870111842 1.086771982 1.205924445 1.291669041 1.300755372 1.384452491 0.98856256 1 12.92472031 -8.66594236 1.721303515 0.982219638 1.329446899 0.903231585 0.05036709 0.071545054 0.426817472 0.007268918 0.017992562 2.16E-09 8.66594236 0.347227261 EGDVLTLLES(ph)ER ddPTM_HeLa_Romidepsin_16h_R1 1 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 1 0 EGDVLTLLES(1)ER 123.95 0.0061693 798000 400.44 650.32 503.02 307.88 460.75 442.51 343.84 497.1 491.72 469.94 TRUE FALSE FALSE 395.5592833 659.475222 511.7748521 343.4785342 437.2362082 414.2350391 373.045761 511.4828042 447.7393317 457.7308911 0.864174324 1.440748778 1.118069289 0.750394044 0.955225476 0.904975057 0.814989262 1.117431255 0.978171542 1 8.838355849 -9.274109853 24.61261752 0.992553192 0.905790826 0.100996117 0.176919819 1746.883195 3393346.574 0.029268139 0.044904513 5.32E-10 9.274109853 -0.086762366 EGDVLTLLES(ph)EREAR ddPTM_HeLa_Romidepsin_16h_R1 2 EGDVLTLLESEREAR 15 1 P62857 P62857 RPS28 40S ribosomal protein S28 1 0 EGDVLTLLES(1)EREAR;EGDVLTLLES(1)EREAR ; 95.554 0.0042015 5149200 1670.09 1441.2 1450.01 1179.68 1372.86 1656.47 1442.73 1533.96 1970.17 1600.49 TRUE FALSE FALSE 1649.734301 1461.489251 1475.246816 1316.080152 1302.797831 1550.626913 1565.27545 1578.342712 1793.953061 1558.909039 1.058262066 0.937507715 0.946332838 0.844231523 0.835711256 0.994687229 1.004083889 1.012466201 1.150774687 1 10.60632104 -10.2478161 23.1988654 1.027512641 0.936542629 0.380361727 0.070276666 280.2795682 477283.499 0.010865545 0.013258114 5.65E-11 10.2478161 -0.090970012 EGDVLTLLESER ddPTM_HeLa_Romidepsin_16h_R1 4 EGDVLTLLESER 12 0 P62857 P62857 RPS28 40S ribosomal protein S28 0 0 ;;; ;;; 238.86 3.83E-38 109764000 9030.1 8943.1 8864.9 8716.2 8752.3 9928.6 8036 8882.2 9545.2 8735.4 FALSE FALSE TRUE 8920.037668 9069.001197 9019.189866 9724.008055 8305.637472 9294.194503 8718.577639 9139.192443 8691.453406 8508.453049 1.048373613 1.065881324 1.060026989 1.142864396 0.976163049 1.092348333 1.024695981 1.074130913 1.021508064 1 13.05468114 -11.61702606 0.718499901 1.001650578 1.061373527 0.188062714 0.041051159 0.674044803 0.699735221 0.020452996 0.008558005 2.42E-12 11.61702606 0.059722949 EGDYVLFHHEGGVDVGDVDAK ddPTM_HeLa_Romidepsin_16h_R1 2 EGDYVLFHHEGGVDVGDVDAK 21 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 0 ; ; 112.16 8.07E-05 11708000 13159 13576.3 13452.4 11957.7 14270.4 14044.7 12629.5 12988.6 14881.1 13317.5 FALSE FALSE TRUE 12998.61305 13767.42751 13686.53338 13340.30554 13542.12824 13147.289 13702.24941 13364.40465 13550.09715 12971.50943 1.002089473 1.061358941 1.055122648 1.028431241 1.043990162 1.013551204 1.056334229 1.03028909 1.044604502 1 13.66305875 -10.28421154 22.95455645 1.000986688 1.040948537 0.165617269 0.019465572 117.3239626 118263.1384 0.002247057 0.002570985 5.20E-11 10.28421154 0.039961849 EGEDGDQPT(ph)TPPKPLK ddPTM_HeLa_Romidepsin_16h_R1 1 EGEDGDQPTTPPKPLK 16 1 M0R0Q7;P18858-2;P18858-3;P18858;B4E135 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 EGEDGDQPT(0.596)T(0.404)PPKPLK 82.01 0.012165 45766000 7296.4 7201.7 7857.6 4005.6 5457.8 5807.6 4836.4 5410.8 7618.2 7677.1 TRUE FALSE FALSE 7207.46867 7303.085722 7994.358232 4468.746319 5179.2681 5436.513103 5247.203695 5567.352961 6936.809112 7477.647835 0.963868429 0.976655478 1.069100659 0.597613904 0.692633327 0.727035188 0.701718483 0.74453265 0.927672614 1 12.86836881 -9.263364767 24.99999984 0.987808084 0.695110423 0.900155868 0.049079567 34.39955881 446657.5815 0.00683883 0.01077921 5.45E-10 9.263364767 -0.292697661 EGEEEEENTEEPPQGEEEESMETQE ddPTM_HeLa_Romidepsin_16h_R1 2 EGEEEEENTEEPPQGEEEESMETQE 25 0 B4DY09;Q12905 B4DY09 ILF2 Interleukin enhancer-binding factor 2 0 0 ; ; 103.92 3.72E-05 16525400 3477.1 3823.7 3383.8 3386.2 4871 4341.3 3244.2 4177.7 3832.3 3625 FALSE FALSE TRUE 3434.719768 3877.530149 3442.69362 3777.728377 4622.414694 4063.904941 3519.762267 4298.575158 3489.52949 3530.821977 0.972781916 1.098194747 0.975040272 1.069928872 1.309161074 1.150979847 0.996867667 1.217443186 0.988305135 1 11.78578837 -8.996391775 24.98923705 0.997237896 1.159393311 0.474185591 0.079784761 70.17359964 485988.1368 0.011549497 0.0208642 1.01E-09 8.996391775 0.162155415 EGEELVMDEEAYVLYHR ddPTM_HeLa_Romidepsin_16h_R1 2 EGEELVMDEEAYVLYHR 17 0 Q9BQ67 Q9BQ67 GRWD1 Glutamate-rich WD repeat-containing protein 1 0 0 ; ; 162.7 8.33E-05 3503000 3915.7 4113.5 4376.9 2714.3 3772 4497.4 3603.2 3928.9 4176.3 4735.9 FALSE FALSE TRUE 3867.973942 4171.409961 4453.078108 3028.140137 3579.500765 4210.030655 3909.255718 4042.576523 3802.761268 4612.860635 0.838519576 0.904300019 0.96536151 0.656456021 0.775982855 0.912672415 0.847468854 0.876370834 0.824382432 1 12.17144599 -12.53744099 0.463831601 1.055539853 0.837640649 0 0.096842267 2.033233604 0.495873597 0.2147868 0.022913394 2.90E-13 12.53744099 -0.217899205 EGEEPTVYS(ph)DEEEPKDESAR ddPTM_HeLa_Romidepsin_16h_R1 4 EGEEPTVYSDEEEPKDESAR 20 1 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 EGEEPT(0.01)VY(0.047)S(0.943)DEEEPKDESAR;EGEEPT(0.001)VY(0.13)S(0.869)DEEEPKDESAR;EGEEPTVYS(1)DEEEPKDESAR;EGEEPT(0.008)VY(0.146)S(0.846)DEEEPKDESAR ;;; 185.71 3.77E-14 826566200 6934.9 9888.9 7851 4145.41 5941.1 8954.7 4740.4 7966.1 8248.3 9049.6 TRUE FALSE FALSE 6850.374771 10028.11619 7987.643362 4624.721809 5637.903498 8382.52357 5143.049458 8196.586535 7510.55139 8814.490087 0.777171987 1.137685345 0.906194605 0.524672643 0.639617657 0.95099359 0.583476685 0.929899115 0.852068732 1 13.1056614 -9.470638905 24.80672647 0.915381764 0.724546604 0.308807954 0.154984112 334.1544574 158677.3789 0.024389742 0.037255722 3.38E-10 9.470638905 -0.19083516 EGEEPTVYS(ph)DEEEPKDESARK ddPTM_HeLa_Romidepsin_16h_R1 1 EGEEPTVYSDEEEPKDESARK 21 2 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 EGEEPT(0.104)VY(0.069)S(0.826)DEEEPKDESARK 58.5 0.020382 6955900 1075.8 1335.7 1301.7 610.54 880.82 1490.7 652.36 1287.2 1492.3 1451.6 TRUE FALSE FALSE 1062.687736 1354.50402 1324.355542 681.1335075 835.8684686 1395.449081 707.7714421 1324.443101 1358.82495 1413.887223 0.751607143 0.958000043 0.93667693 0.481745288 0.591184682 0.986959256 0.5005855 0.936738857 0.961056107 1 10.46545133 -9.310324207 24.99440491 0.890249101 0.698353475 0.29662225 0.167530183 425.2903958 217446.3982 0.026073453 0.0398279 4.89E-10 9.310324207 -0.191895625 EGEETEGS(ph)EEDDKENDKTEEMPNDSVLENK ddPTM_HeLa_Romidepsin_16h_R1 1 EGEETEGSEEDDKENDKTEEMPNDSVLENK 30 2 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 EGEET(0.125)EGS(0.605)EEDDKENDKT(0.267)EEMPNDS(0.003)VLENK 54.05 0.0016492 29952000 1912 1852.8 2020.7 955.93 2017.9 2399.6 2300.6 2118.8 2041.9 2373.5 TRUE FALSE FALSE 1888.695809 1878.883767 2055.869436 1066.459124 1914.919033 2246.273304 2496.012907 2180.104135 1859.26735 2311.836128 0.816967858 0.812723594 0.889279915 0.461303944 0.828310887 0.971640367 1.079666883 0.943018456 0.804238383 1 11.17482342 -8.112999099 4.816429049 0.862682965 1.01427037 0.218588319 0.14122044 0.336878429 11.95545473 0.022618898 0.060391386 7.71E-09 8.112999099 0.151587406 EGFEK(ac)ISK ddPTM_HeLa_Romidepsin_16h_R1 1 EGFEKISK 8 1 P10809;E7EXB4;E7ESH4;P10809-2;C9JL25 P10809;C9JL25 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 EGFEK(1)ISK 116.3 0.0084321 8809700 1109.4 976.59 1173.6 1134.4 1613.4 1927.6 1730.2 1865.4 1518.8 1318.6 FALSE TRUE FALSE 1095.878206 990.3384597 1194.026016 1265.564666 1531.062178 1804.432581 1877.163145 1919.372406 1382.954724 1284.342582 0.853260043 0.771085903 0.929678757 0.985379355 1.192097964 1.404946473 1.461575106 1.494439593 1.076780248 1 10.32681436 -8.498365348 1.586969013 0.914104906 1.481539164 0.902624478 0.076860814 0.079681342 0.391372089 0.011715352 0.034158521 3.17E-09 8.498365348 0.567434258 EGFES(ph)DTDSEFTFK ddPTM_HeLa_Romidepsin_16h_R1 2 EGFESDTDSEFTFK 14 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 EGFES(0.872)DT(0.12)DS(0.008)EFTFK;EGFES(0.498)DT(0.498)DS(0.003)EFTFK ; 240.73 1.15E-43 86798000 6946.5 6666.9 7122.1 5532 7938.1 8094 5972.9 6609.4 7142.4 7105.5 TRUE FALSE FALSE 6861.833386 6760.756793 7246.057163 6171.635869 7532.989136 7576.819522 6480.237977 6800.632561 6503.565856 6920.898086 0.991465746 0.976861198 1.046982209 0.891739163 1.088440986 1.094774035 0.936329057 0.982622844 0.9396997 1 12.75674355 EGFGLSENPFAS(ph)LSPDEQKDEK ddPTM_HeLa_Romidepsin_16h_R1 1 EGFGLSENPFASLSPDEQKDEK 22 1 B4DT96;C9JYA1;O15504-2;O15504 B4DT96 NUPL2 Nucleoporin-like protein 2 1 0 EGFGLSENPFAS(0.822)LS(0.178)PDEQKDEK 83.202 0.00050576 15111000 1814.8 1815.8 1817.2 1841.5 2364.9 2878.6 2228.9 2517.7 2080.8 2287.9 TRUE FALSE FALSE 1792.68052 1841.36288 1848.827604 2054.422895 2244.210328 2694.66675 2418.22271 2590.545677 1894.688037 2228.460028 0.804448138 0.826293879 0.829643602 0.92190251 1.007067796 1.209205782 1.085154178 1.162482452 0.85022303 1 11.12183137 -8.547330401 2.802814179 0.892778146 1.145149476 0.797908792 0.062650073 0.12913969 2.050246948 0.012677969 0.029045731 2.84E-09 8.547330401 0.252371329 EGFGLSENPFASLS(ph)PDEQKDEK ddPTM_HeLa_Romidepsin_16h_R1 2 EGFGLSENPFASLSPDEQKDEK 22 1 B4DT96;C9JYA1;O15504-2;O15504 B4DT96 NUPL2 Nucleoporin-like protein 2 1 0 EGFGLSENPFAS(0.426)LS(0.574)PDEQKDEK;EGFGLSENPFAS(0.243)LS(0.757)PDEQKDEK ; 122.44 2.51E-05 31389000 2610.6 2348.57 2589.8 2469.15 3463.8 3738.6 2875.4 3652.1 3253.9 2641.2 TRUE FALSE FALSE 2578.781003 2381.63323 2634.874383 2754.644741 3287.029361 3499.715526 3119.636404 3757.767751 2962.863034 2572.581243 1.002409937 0.925775711 1.024214255 1.070770747 1.277716445 1.360390672 1.212648352 1.460699351 1.151708247 1 11.32900092 -8.795681837 2.28814889 0.996044458 1.33410322 0.778116187 0.07849341 0.068105999 0.727452288 0.008359987 0.017601429 1.60E-09 8.795681837 0.338058761 EGFLDTLVVLHR ddPTM_HeLa_Romidepsin_16h_R1 2 EGFLDTLVVLHR 12 0 P42771-2;P42771;K7ES20;K7ENC6;J3QRG6;P42771-4;P42772 P42771-2 CDKN2A;CDKN2B Cyclin-dependent kinase inhibitor 2A;Cyclin-dependent kinase 4 inhibitor B 0 0 ; ; 142.89 0.00074658 25180000 27599.5 25535 27325.3 25469 26252.5 23851.4 20048.5 20288.9 26787.9 19223 FALSE FALSE TRUE 27263.10668 25894.4824 27800.88538 28413.84562 24912.73696 22327.37252 21751.41909 20875.92731 24391.92313 18723.58369 1.456083789 1.382987511 1.484805785 1.51754312 1.330553882 1.192473241 1.161712386 1.114953615 1.302737955 1 14.19256897 -5.799337017 17.94584084 1.263041762 1.251421301 0 0.166764724 0 0 0.028948505 0 1.59E-06 5.799337017 -0.011620461 EGGDGEEQDVGDAGR ddPTM_HeLa_Romidepsin_16h_R1 1 EGGDGEEQDVGDAGR 15 0 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 0 0 153 0.0048172 5842000 1763.6 1110.4 1346.8 1266.2 1301.2 1253.3 1388.5 1774.8 1611 1476 FALSE FALSE TRUE 1742.104565 1126.03224 1370.240489 1412.604002 1234.794909 1173.218175 1506.439155 1826.151038 1466.908125 1437.653307 1.211769594 0.783243244 0.953109127 0.982576254 0.858896162 0.816064742 1.047845922 1.270230471 1.020349008 1 10.48950009 -10.27618325 24.9916556 1.100002304 0.953630376 0.12426424 0.139899263 1053.036998 1784949.826 0.025648298 0.029394722 5.29E-11 10.27618325 -0.146371928 EGGSKS(ph)DSEDITR ddPTM_HeLa_Romidepsin_16h_R1 2 EGGSKSDSEDITR 13 1 E9PDC4;F5GYS8;H0YNY8;U3KPR8;O00470;O00470-2 E9PDC4 MEIS1 Homeobox protein Meis1 1 0 EGGS(0.035)KS(0.84)DS(0.125)EDITR;EGGS(0.049)KS(0.897)DS(0.031)EDIT(0.023)R ; 161.49 0.00249 39761400 5103.4 4860.1 4562.5 4157.6 4602.5 4276.9 3526.4 3378.5 5365.7 4894.5 TRUE FALSE FALSE 5041.197798 4928.520615 4641.908399 4638.321274 4367.617251 4003.619893 3825.932328 3476.251567 4885.778353 4767.340184 1.057444529 1.033809299 0.973689357 0.97293692 0.916153889 0.839801595 0.80252975 0.729180514 1.024843658 1 12.21896886 -8.15474943 0.758321773 1.028170568 0.706263891 0.967109343 0.018961809 0.173203655 0.137075921 0.004525302 0.036654076 7.00E-09 8.15474943 -0.321906676 EGHLS(ph)PDIVAEQK ddPTM_HeLa_Romidepsin_16h_R1 2 EGHLSPDIVAEQK 13 0 B4DLR8;H3BNV2;H3BRK3;P15559-3;P15559-2;P15559 B4DLR8 NQO1 NAD(P)H dehydrogenase [quinone] 1 1 0 EGHLS(1)PDIVAEQK;EGHLS(1)PDIVAEQK ; 151.54 0.00027125 3999100 3338.7 3366.3 2842.6 3123.3 3272.9 2769 2705.7 2587.8 3472.3 3448 TRUE FALSE FALSE 3298.00664 3413.69086 2892.074261 3484.430642 3105.8717 2592.069837 2935.52209 2662.67391 3161.728791 3358.420463 0.982011239 1.016457259 0.86114121 1.037520668 0.924801327 0.771812185 0.874078193 0.792835185 0.94143328 1 11.71356715 -8.462841119 4.679307912 0.985422747 0.820570801 0.645763382 0.052411546 0.085002453 3.772389878 0.006684411 0.015083631 3.44E-09 8.462841119 -0.164851945 EGHSLEMENENLVENGADS(ph)DEDDNSFLK ddPTM_HeLa_Romidepsin_16h_R1 3 EGHSLEMENENLVENGADSDEDDNSFLK 28 0 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 EGHSLEMENENLVENGADS(0.608)DEDDNS(0.392)FLK;EGHSLEMENENLVENGADS(0.999)DEDDNS(0.001)FLK;EGHSLEMENENLVENGADS(0.994)DEDDNS(0.006)FLK ;; 103.52 6.54E-09 240296500 4240.3 3677.36 4519.9 3736.7 5429.5 6233.2 5354.5 6134.1 4507.31 4622.8 TRUE FALSE FALSE 4188.617593 3729.129971 4598.566963 4168.754836 5152.412355 5834.918637 5809.311096 6311.580505 4104.164905 4502.69899 0.930245971 0.828198816 1.021291224 0.925834671 1.144294204 1.295871354 1.290184201 1.401732721 0.911489956 1 12.13657432 -8.451602098 1.934791639 0.955505443 1.340672067 0.899098528 0.059086667 0.078018632 0.569532797 0.008904949 0.024378075 3.54E-09 8.451602098 0.385166624 EGIDPTPYYWYTDQR ddPTM_HeLa_Romidepsin_16h_R1 1 EGIDPTPYYWYTDQR 15 0 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 0 196.16 6.05E-12 13518000 1835.4 1587.7 1591.7 1291.4 1560.5 1484.3 1439.4 1704.4 1545.4 1606.1 FALSE FALSE TRUE 1813.029439 1610.051682 1619.402871 1440.717744 1480.861862 1389.45802 1561.6626 1753.714125 1407.175553 1564.37329 1.15894937 1.029199164 1.035176758 0.920955218 0.946616687 0.888188279 0.998267236 1.121033027 0.899513922 1 10.61136909 -9.620295768 2.553409279 1.074503885 0.970621393 0 0.088809143 0.303733707 4.026680502 0.01356533 0.020068358 2.40E-10 9.620295768 -0.103882492 EGIREETVSLR ddPTM_HeLa_Romidepsin_16h_R1 1 EGIREETVSLR 11 1 P20618 P20618 PSMB1 Proteasome subunit beta type-1 0 0 145.23 0.002841 10579000 1967.8 2043.3 2241.1 1602 2161.5 2004 1547 1866.7 1856.3 2034.9 FALSE FALSE TRUE 1943.815697 2072.065631 2280.105405 1787.230778 2051.190589 1875.950868 1678.402141 1920.710019 1690.267879 1982.033005 0.980718127 1.045424383 1.150387203 0.901715952 1.034892247 0.946478118 0.846808372 0.969060563 0.852795021 1 10.95276527 -8.024144542 6.675506218 1.002510722 0.904925072 0.157271705 0.08081776 0.154922145 27.72733259 0.008800126 0.02385261 9.46E-09 8.024144542 -0.09758565 EGISQEALHTQMLTAVQEISHLIEPLANAAR ddPTM_HeLa_Romidepsin_16h_R1 1 EGISQEALHTQMLTAVQEISHLIEPLANAAR 31 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 85.745 6.67E-09 2605100 256.51 309.68 215.2 280.52 308.18 305.86 220.88 313.85 187.39 248.91 FALSE FALSE TRUE 253.3835575 314.0396832 218.9454657 312.9550423 292.4524246 286.3165331 239.6415417 322.9307546 170.6293691 242.4432823 1.045125091 1.29531196 0.903079119 1.290838168 1.206271512 1.180962947 0.988443728 1.331984749 0.703790872 1 7.921503469 -10.48240392 0.819021656 1.006437744 1.170255192 0.290498322 0.161398873 0.577052128 0.807640163 0.031334682 0.032635183 3.29E-11 10.48240392 0.163817449 EGITGPPADSSKPIGPDDAIDALS(ph)SDFTCGSPTAAGKK ddPTM_HeLa_Romidepsin_16h_R1 1 EGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGKK 38 2 P20810-6;P20810-7;P20810-10;P20810-9;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PDE4 P20810-6 CAST Calpastatin 1 0 EGITGPPADSSKPIGPDDAIDALS(0.403)S(0.403)DFT(0.046)CGS(0.111)PT(0.038)AAGKK 72.009 6.75E-06 24534000 2219 1722 2263.4 182.86 2232 2489.8 2139.8 2226.5 2132.3 1859.3 TRUE FALSE FALSE 2191.953974 1746.242361 2302.793528 204.0031336 2118.092711 2330.709815 2321.554559 2290.920265 1941.581748 1810.995118 1.210358853 0.964244654 1.271562526 0.112646982 1.169573949 1.286977415 1.281922041 1.265006317 1.072107665 1 10.82256694 -8.52896335 24.99997776 1.026997049 1.270016049 0.172916025 0.306043474 262.2093214 1077344.963 0.044810065 0.089818048 2.96E-09 8.52896335 0.243019 EGITGPPADSSKPIGPDDAIDALSS(ph)DFTCGSPTAAGK ddPTM_HeLa_Romidepsin_16h_R1 1 EGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGK 37 1 P20810-6;P20810-7;P20810-10;P20810-9;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PDE4 P20810-6 CAST Calpastatin 1 0 EGITGPPADSSKPIGPDDAIDALS(0.081)S(0.302)DFT(0.302)CGS(0.302)PT(0.012)AAGK 86.492 1.92E-09 3892400 1215.8 1193.8 1094.5 296.79 1357.1 1566.7 1180.3 1236.5 1215.8 1406.2 TRUE FALSE FALSE 1200.981362 1210.606348 1113.549313 331.1062562 1287.842123 1466.592926 1280.554653 1272.276177 1107.055803 1369.666721 0.87684204 0.883869287 0.813007497 0.241742207 0.940259483 1.07076627 0.934938867 0.928894713 0.808266555 1 10.41960917 -11.3043028 0.894360946 0.982424339 0.82888195 0 0.217099723 1.064727828 1.792737809 0.076782513 0.048004113 4.96E-12 11.3043028 -0.153542389 EGITGPPADSSKPIGPDDAIDALSSDFTCGSPT(ph)AAGKK ddPTM_HeLa_Romidepsin_16h_R1 1 EGITGPPADSSKPIGPDDAIDALSSDFTCGSPTAAGKK 38 2 P20810-6;P20810-7;P20810-10;P20810-9;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PDE4 P20810-6 CAST Calpastatin 1 0 EGITGPPADSSKPIGPDDAIDALS(0.055)S(0.055)DFT(0.253)CGS(0.253)PT(0.385)AAGKK 68.733 8.79E-06 28296000 1308 1204.8 1146.5 288.02 1470.2 1313.4 1238.2 1429.6 1317.7 1207.4 TRUE FALSE FALSE 1292.057593 1221.761206 1166.454352 321.3222276 1395.170208 1229.477979 1343.372677 1470.96322 1199.841612 1176.031574 1.098658932 1.038884698 0.991856322 0.273225851 1.186337373 1.045446403 1.142293036 1.250785483 1.020246087 1 10.19971108 -7.664076292 1.701970713 0.99391662 1.252203739 0.136782542 0.238620511 0.897282249 4.181159409 0.034953739 0.293065891 2.17E-08 7.664076292 0.258287119 EGLELPEDEEEK ddPTM_HeLa_Romidepsin_16h_R1 4 EGLELPEDEEEK 12 0 P08238;Q58FF7;Q58FF6;P07900-2;P07900;Q58FG0 P08238;P07900-2 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 0 ;;; ;;; 238.86 3.83E-38 79691000 25814.3 27217.3 25964.2 15596.4 26320.3 30092.1 29445.7 28724.2 27294.7 25394.4 FALSE FALSE TRUE 25499.66538 27600.46586 26416.09601 17399.72915 24977.07688 28169.31193 31946.81702 29555.28941 24853.39367 24734.64983 1.030928902 1.115862406 1.067979381 0.703455649 1.009801111 1.138860349 1.291581536 1.194894192 1.004800709 1 14.59424585 -8.071160714 3.340851193 1.002948683 1.240841196 0.482823601 0.106227588 0.164126108 3.544622492 0.015277691 0.045569931 8.49E-09 8.071160714 0.237892513 EGLELPEDEEEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EGLELPEDEEEKK 13 1 P08238;Q58FF7;Q58FF6;P07900-2;P07900;Q58FG0 P08238;P07900-2 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 1 EGLELPEDEEEK(1)K 193.23 1.19E-10 397570 142.26 140.48 229.87 106.27 613.96 478.81 412.74 543.96 704.91 522.29 FALSE TRUE FALSE 140.5260804 142.4576811 233.8707909 118.5574374 582.6273302 448.2155863 447.7981253 559.6986244 641.8610841 508.7208305 0.276234178 0.280031154 0.459723245 0.233050094 1.145279091 0.881063954 0.880243345 1.100207797 1.26171575 1 8.990730359 -8.744834706 24.99611082 0.575632952 0.984406434 0.289184499 0.319285953 262.8471697 395679.1845 0.04813434 0.09605366 1.80E-09 8.744834706 0.408773483 EGLELPEDEEEKK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EGLELPEDEEEKKK 14 2 P08238;Q58FF7;P07900-2;P07900;Q58FG0 P08238;P07900-2 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 1 EGLELPEDEEEK(0.008)K(0.992)K 176.25 1.55E-07 13427000 528.59 619.8 706.4 474.72 1505.6 1460.7 1599.1 1329.6 1774 1215.2 FALSE TRUE FALSE 522.1473418 628.5255607 718.6945957 529.60936 1428.763614 1367.365984 1734.927514 1368.069878 1615.328997 1183.628929 0.441141078 0.531015714 0.607195869 0.447445434 1.207104337 1.155231974 1.46576978 1.155826666 1.364725851 1 10.20900115 -8.688347146 7.369011586 0.684395546 1.260380625 0.445360265 0.27807025 0.133717334 11.39918641 0.035848474 0.07182549 2.05E-09 8.688347146 0.575985079 EGLGQGQS(ph)LEQLEALVQTK ddPTM_HeLa_Romidepsin_16h_R1 2 EGLGQGQSLEQLEALVQTK 19 0 Q9NSC5-5;Q9NSC5-2;Q9NSC5;M0QYF9 Q9NSC5-5 HOMER3 Homer protein homolog 3 1 0 EGLGQGQS(1)LEQLEALVQTK;EGLGQGQS(1)LEQLEALVQTK ; 217.26 3.38E-35 0 1056.68 1182.82 1202.36 2408.59 1154.06 1239.53 1460.89 1394.37 1035.75 1015.2 TRUE FALSE FALSE 1043.800778 1199.471771 1223.286571 2687.082509 1095.164012 1160.328033 1584.97796 1434.713896 943.1099259 988.8249576 1.05559712 1.213027404 1.237111343 2.717450129 1.107540827 1.17344129 1.602890327 1.450928079 0.953768327 1 9.949571347 -9.511218823 24.59906405 1.049761102 1.599759256 0.286995944 0.416389256 442.2150924 932946.7897 0.062932128 0.092864177 3.08E-10 9.511218823 0.549998154 EGLISQDGS(ph)SLEALLR ddPTM_HeLa_Romidepsin_16h_R1 2 EGLISQDGSSLEALLR 16 0 J3KMZ8;Q92785;Q92785-2 J3KMZ8 DPF2 Zinc finger protein ubi-d4 1 0 EGLISQDGS(0.689)S(0.311)LEALLR;EGLISQDGS(0.5)S(0.5)LEALLR ; 204.81 1.15E-18 9727400 2936.7 3458.7 2590.5 3372.7 3286.7 4121 3275.3 3548.2 3439.6 2635.8 TRUE FALSE FALSE 2900.906371 3507.391669 2635.586566 3762.667443 3118.967435 3857.6814 3553.5039 3650.861569 3131.953561 2567.321536 1.129934965 1.366167665 1.026589981 1.465600389 1.21487215 1.502609372 1.384128887 1.422050771 1.219930389 1 11.32604828 -9.604312147 0.315413272 0.979911154 1.5104064 0.387752883 0.134385631 0.78573609 0.188161429 0.07508318 0.15783836 2.49E-10 9.604312147 0.530495246 EGLVFSRLS(ph)PEYYDLAR ddPTM_HeLa_Romidepsin_16h_R1 2 EGLVFSRLSPEYYDLAR 17 1 P22749-2 P22749-2 1 0 EGLVFS(0.352)RLS(0.648)PEYYDLAR;EGLVFS(0.113)RLS(0.887)PEYYDLAR ; 104.94 0.00096716 4159600 1515.14 1221.03 1213.87 1863.64 1846.58 1725.45 1297.49 1602.56 2072.01 1787.83 TRUE FALSE FALSE 1496.672891 1238.219692 1234.996898 2079.122825 1752.342132 1615.199314 1407.698768 1648.927545 1886.684236 1741.381919 0.859474234 0.711055788 0.709205077 1.193949933 1.006293974 0.92753881 0.80838026 0.946907469 1.08344081 1 10.76601693 -9.284522433 24.98999134 0.896417622 0.966190321 0.10734492 0.140261149 2078.678916 2250396.747 0.022328673 0.034121141 5.19E-10 9.284522433 0.069772698 EGMNPSYDEY(ph)ADSDEDQHDAYLER ddPTM_HeLa_Romidepsin_16h_R1 1 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 0 EGMNPS(0.027)Y(0.264)DEY(0.614)ADS(0.085)DEDQHDAY(0.01)LER 55.247 0.003705 21336000 1696.3 2012.2 1783.2 1703.5 1685.3 1696.7 1559.8 1511.6 1868.3 1763 TRUE FALSE FALSE 1675.624843 2040.527804 1814.235848 1900.466685 1599.292852 1588.286346 1692.289373 1555.335761 1701.194569 1717.197006 0.975790685 1.188289869 1.056510023 1.106726065 0.931339181 0.924929604 0.98549518 0.905741016 0.990681071 1 10.74583985 -8.659174199 24.4870952 1.01804301 0.939491628 0.358595993 0.066874815 12.22004483 2904.178638 0.010774788 0.021549575 2.19E-09 8.659174199 -0.078551382 EGMNPSYDEYADS(ph)DEDQHDAYLER ddPTM_HeLa_Romidepsin_16h_R1 6 EGMNPSYDEYADSDEDQHDAYLER 24 0 Q08945;A0A0U1RRK2 Q08945 SSRP1 FACT complex subunit SSRP1 1 0 EGMNPSY(0.001)DEY(0.207)ADS(0.793)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSY(0.002)DEY(0.015)ADS(0.983)DEDQHDAYLER;EGMNPSYDEYADS(1)DEDQHDAYLER;EGMNPSY(0.001)DEY(0.001)ADS(0.998)DEDQHDAYLER;EGMNPSY(0.003)DEY(0.346)ADS(0.65)DEDQHDAYLER ;;;;; 141.38 2.94E-07 3853729600 11420.41 13343.12 10636.15 11857.52 10649.29 11526.45 9904.85 10830.66 11385.13 11876.94 TRUE FALSE FALSE 11281.21365 13530.96479 10821.26773 13228.54225 10105.81699 10789.94704 10746.16771 11144.02806 10366.81546 11568.37539 0.975177004 1.169651255 0.9354181 1.143509076 0.873572706 0.93271066 0.928926263 0.96331833 0.896134082 1 13.49789865 EGNEAGPSSPPDPLPNEAAR ddPTM_HeLa_Romidepsin_16h_R1 1 EGNEAGPSSPPDPLPNEAAR 20 0 Q9C0A1 Q9C0A1 ZFHX2 Zinc finger homeobox protein 2 0 0 53.536 0.02206 12985000 2319.3 2038.3 1981.1 2534.7 1421.3 1838.3 1488.7 1895.7 2056.1 2275 FALSE FALSE TRUE 2291.03148 2066.995241 2015.580214 2827.77394 1348.765757 1720.838563 1615.150141 1950.549089 1872.197266 2215.895172 1.03390788 0.932803712 0.909600887 1.27613164 0.608677601 0.776588435 0.728892847 0.880253323 0.84489433 1 11.11367392 -8.744869964 24.99999962 1.016840759 0.749194157 0.492307991 0.124104438 124.1244033 187278.4312 0.014864218 0.029662409 1.80E-09 8.744869964 -0.267646602 EGNPEEDLTADK ddPTM_HeLa_Romidepsin_16h_R1 2 EGNPEEDLTADK 12 0 P40121-2;P40121;E7ENU9 P40121-2 CAPG Macrophage-capping protein 0 0 ; ; 179.6 1.49E-05 3589400 1931.05 1978.01 2102.5 1370.32 2142.82 2526.05 1755.51 2293.3 1932.02 2426.09 FALSE FALSE TRUE 1907.51362 2005.856477 2139.093131 1528.762846 2033.463899 2364.643557 1904.622976 2359.653017 1759.215292 2363.059832 0.807221888 0.848838633 0.905221739 0.646942081 0.860521546 1.000670201 0.805998625 0.998558304 0.744464981 1 11.20644044 -12.39744734 1.088121153 1.001146947 0.852446569 0 0.124280181 0.586080528 1.225981635 0.067081468 0.016584016 4.00E-13 12.39744734 -0.148700378 EGNPST(ph)T(ph)ACDSQDEGRPCSMKHK ddPTM_HeLa_Romidepsin_16h_R1 1 EGNPSTTACDSQDEGRPCSMKHK 23 2 Q86TE4-4;Q86TE4 Q86TE4-4 LUZP2 Leucine zipper protein 2 2 0 EGNPS(0.065)T(0.814)T(0.814)ACDS(0.302)QDEGRPCS(0.005)MKHK 55.206 0.0026733 0 380.06 357.95 432.38 331.52 395.13 312.42 364.21 396.09 318.27 436.92 TRUE FALSE FALSE 375.4276825 362.9892295 439.9053925 369.8519022 374.9650417 292.4573703 395.1459883 407.5502392 289.8031341 425.5687554 0.882178679 0.852950845 1.033688181 0.86907673 0.881091567 0.687215324 0.928512686 0.957660153 0.680978409 1 8.733248424 -9.033595261 24.31225523 0.941192378 0.858083433 0 0.116445434 604.3276914 437339.3801 0.013212347 0.021920991 9.26E-10 9.033595261 -0.083108945 EGNTTEDDFPS(ph)SPGNGNK ddPTM_HeLa_Romidepsin_16h_R1 2 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 0 EGNTTEDDFPS(0.986)S(0.014)PGNGNK;EGNTTEDDFPS(0.5)S(0.5)PGNGNK ; 253.36 2.21E-75 160291000 13375.5 12340.4 12612.2 12021.8 12335.6 12478.7 10721.4 12499.3 13973.1 12631.7 TRUE FALSE FALSE 13212.47426 12514.12848 12831.71005 13411.81708 11706.0683 11681.35134 11632.07545 12860.94752 12723.31094 12303.52661 1.073877001 1.017117195 1.042929434 1.090079089 0.951440076 0.949431144 0.945426122 1.045305783 1.034119025 1 13.58678428 -8.742766999 24.99996266 1.038337708 0.96926189 0.472631756 0.036001232 189.5191128 253740.9947 0.005831663 0.011646288 1.81E-09 8.742766999 -0.069075819 EGNTTEDDFPSS(ph)PGNGNK ddPTM_HeLa_Romidepsin_16h_R1 2 EGNTTEDDFPSSPGNGNK 18 0 Q15007 Q15007 WTAP Pre-mRNA-splicing regulator WTAP 1 0 EGNTTEDDFPS(0.011)S(0.989)PGNGNK;EGNTTEDDFPS(0.14)S(0.86)PGNGNK ; 186.17 7.93E-11 164317000 9747.1 9723.6 9142.5 8267 9200.2 8637 8493.5 9322.8 10757.5 10293.4 TRUE FALSE FALSE 9628.298596 9860.489096 9301.621377 9222.869437 8730.679463 8085.123575 9214.937678 9592.540509 9795.322257 10025.97598 0.960335294 0.983494187 0.92775221 0.91989742 0.870805942 0.806417608 0.919106299 0.95676875 0.976994387 1 13.29145506 -9.4725206 1.523471639 0.981890835 0.886498133 0.53446885 0.037719869 0.22399206 1.033555524 0.006754724 0.011309421 3.37E-10 9.4725206 -0.095392701 EGPEPPEEVPPPT(ph)TPPVPK ddPTM_HeLa_Romidepsin_16h_R1 2 EGPEPPEEVPPPTTPPVPK 19 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 EGPEPPEEVPPPT(0.924)T(0.076)PPVPK;EGPEPPEEVPPPT(0.997)T(0.003)PPVPK ; 161.94 2.70E-06 27399000 9901.8 8510.1 9007.4 7441.8 8395.7 8242.2 7130.3 7765 10233.4 10011.7 TRUE FALSE FALSE 9781.113053 8629.905411 9164.170019 8302.255931 7967.2361 7715.55002 7735.947504 7989.668024 9318.099074 9751.594591 1.00302704 0.884973768 0.939761178 0.851374188 0.817018799 0.791209063 0.793300771 0.819319133 0.955546192 1 13.25142243 -9.511812778 0.820664386 1.004123644 0.794767606 0.856732769 0.029899499 0.105846726 0.142431689 0.005078966 0.009810975 3.08E-10 9.511812778 -0.209356037 EGPGS(ph)EPDSQVDGGLSGASLGEK ddPTM_HeLa_Romidepsin_16h_R1 2 EGPGSEPDSQVDGGLSGASLGEK 23 0 Q5JSZ5;A0A494C0D3;A0A494C065;H0Y412 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 EGPGS(0.994)EPDS(0.006)QVDGGLSGASLGEK;EGPGS(1)EPDSQVDGGLSGASLGEK ; 139.41 1.56E-06 10356100 8359.7 7548.8 7494.4 7675.3 6144.1 5243.7 4810.1 4891.8 7883.2 8314.1 TRUE FALSE FALSE 8257.808761 7655.072205 7624.836888 8562.754299 5830.54365 4908.644493 5218.669774 5033.336515 7178.106848 8098.098483 1.019721948 0.945292555 0.941558923 1.057378385 0.719989225 0.606147789 0.644431503 0.621545481 0.886394116 1 12.98336747 -8.650570246 4.249121743 1.001476253 0.631079155 0.908822374 0.050849398 0.029571733 0.953503923 0.005353565 0.010989192 2.24E-09 8.650570246 -0.370397098 EGPGT(ph)PPTTLAR ddPTM_HeLa_Romidepsin_16h_R1 1 EGPGTPPTTLAR 12 0 O00562-2;O00562 O00562-2 PITPNM1 Membrane-associated phosphatidylinositol transfer protein 1 1 0 EGPGT(0.997)PPT(0.002)T(0.001)LAR 109.44 0.022629 9848300 4138.7 3763.3 4014 4427.7 3484.6 3481.2 2674.3 2855 3933.4 3963.2 TRUE FALSE FALSE 4088.255932 3816.279836 4083.861986 4939.651507 3306.767859 3258.762555 2901.454975 2937.604921 3581.586853 3860.235493 1.059069049 0.988613219 1.05793079 1.279624395 0.85662335 0.844187501 0.751626418 0.760991117 0.927815637 1 11.91447315 -8.541850567 24.99212191 1.044490822 0.793570984 0.655536114 0.089318878 101.6015842 133842.2459 0.012004007 0.024010824 2.87E-09 8.541850567 -0.250919838 EGPLGWSSDGSLGSVLLDSPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 EGPLGWSSDGSLGSVLLDSPSSPR 24 0 C9JRJ5;Q9UGP4 C9JRJ5 LIMD1 LIM domain-containing protein 1 1 0 EGPLGWSSDGSLGSVLLDS(0.124)PS(0.641)S(0.235)PR 90.435 3.42E-05 3917800 1594 2445.6 1829.1 13758 0 1321.5 1774.3 1737.8 1926 1647.5 TRUE FALSE FALSE 1574.571715 2480.029221 1860.934718 15348.76469 0 1237.060415 1925.008998 1788.080501 1753.733736 1604.697712 0.981226372 1.545480623 1.159679299 9.56489473 0 0.770899345 1.199608489 1.114278713 1.092874828 1 10.64808584 EGPST(ph)SPDLIDPESFSQDILHDK ddPTM_HeLa_Romidepsin_16h_R1 1 EGPSTSPDLIDPESFSQDILHDK 23 0 C9J2X2;G5E962;P43364-2;P43364 C9J2X2 MAGEA11 Melanoma-associated antigen 11 1 0 EGPS(0.104)T(0.448)S(0.448)PDLIDPESFSQDILHDK 128.19 4.93E-06 3274900 945.91 853.31 739.56 750.92 1036.5 926.08 963.41 943.02 910.85 864.75 TRUE FALSE FALSE 934.3808851 865.3229206 752.4317316 837.7449036 983.6035373 866.9064768 1045.242021 970.3047959 829.3812947 842.2836703 1.109342277 1.027353315 0.893323423 0.994611356 1.167781796 1.029233389 1.240961992 1.151992886 0.984681674 1 9.718162386 -7.994095174 1.387001937 1.03759523 1.197775361 0.405895897 0.076538041 0.448768147 1.484776961 0.012111427 0.068278771 1.01E-08 7.994095174 0.160180131 EGPSTS(ph)PDLIDPESFSQDILHDK ddPTM_HeLa_Romidepsin_16h_R1 1 EGPSTSPDLIDPESFSQDILHDK 23 0 C9J2X2;G5E962;P43364-2;P43364 C9J2X2 MAGEA11 Melanoma-associated antigen 11 1 0 EGPS(0.058)T(0.204)S(0.738)PDLIDPESFSQDILHDK 119.2 1.99E-06 3040600 2159.9 1862.1 2112.4 1610.8 2185.7 2345.9 1997 2218.8 2220.5 2186.7 TRUE FALSE FALSE 2133.574308 1888.314693 2149.165436 1797.048275 2074.155573 2196.004561 2166.62513 2282.997477 2021.892919 2129.889219 1.001730179 0.886578831 1.009050338 0.843728518 0.973832608 1.031041681 1.017247804 1.07188555 0.949294875 1 11.05656268 -8.207031422 5.07363943 0.979043831 1.039020532 0.264059333 0.05586415 0.291066609 16.46490526 0.008191852 0.021267922 6.21E-09 8.207031422 0.059976701 EGPTVETK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EGPTVETKR 9 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 0 1 ; EGPTVETK(1)R;EGPTVETK(1)R 109.66 0.0023352 11734400 2921.69 3434.69 2284.98 2196.65 2159.02 1988.37 2312.17 2018.71 3627.15 2916.57 FALSE TRUE FALSE 2886.079318 3483.043656 2324.749118 2450.637009 2048.837153 1861.319574 2508.565662 2077.118189 3302.72862 2840.797091 1.015939973 1.226079704 0.818343952 0.862658236 0.721219111 0.655210321 0.883049926 0.731174428 1.162606309 1 11.47208007 -9.584305043 10.96682165 1.0241701 0.774993844 0.696812224 0.099552969 0.238657987 41.61086324 0.013844493 0.019582137 2.60E-10 9.584305043 -0.249176256 EGPVAS(ph)PPFMDLEQAVLPAVIPK ddPTM_HeLa_Romidepsin_16h_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 0 EGPVAS(1)PPFMDLEQAVLPAVIPK 111.65 2.67E-07 0 441.66 435.69 315.2 462.66 477.85 350.16 729.79 581.92 532.91 450.58 TRUE FALSE FALSE 436.276878 441.8236553 320.6859238 516.1549261 453.4635314 327.7859061 791.7783444 598.7569371 485.2451949 438.8738666 0.994082608 1.006721267 0.730701799 1.176089454 1.033243412 0.746879527 1.804113675 1.36430301 1.105659807 1 8.777662555 -7.760636095 24.99999997 0.980734803 1.584208402 0.686563871 0.164825228 7.245111458 225440.7637 0.01968348 0.06594403 1.74E-08 7.760636095 0.603473599 EGPVLATS(ph)SGAGVFK ddPTM_HeLa_Romidepsin_16h_R1 1 EGPVLATSSGAGVFK 15 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 EGPVLAT(0.051)S(0.653)S(0.296)GAGVFK 109.99 0.004332 6658700 2162.3 2472.8 2195.6 1682.8 1855.8 1236 1088.1 1524.6 1984.2 1473 TRUE FALSE FALSE 2135.945056 2507.612143 2233.813497 1877.373254 1761.091601 1157.023589 1180.523187 1568.711896 1806.728182 1434.731248 1.488742271 1.747792242 1.556956051 1.308519109 1.227471419 0.806439248 0.822818342 1.093383794 1.259279872 1 10.4865648 -8.377847406 4.491333036 1.309778776 0.900701955 0.494968565 0.209099137 0.215253756 6.97306979 0.039922526 0.092190851 4.19E-09 8.377847406 -0.409076821 EGPYS(ph)ISVLYGDEEVPR ddPTM_HeLa_Romidepsin_16h_R1 1 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 EGPYS(0.9)IS(0.1)VLYGDEEVPR 168.47 3.95E-06 5842100 1321.3 1303.9 1209.8 837.63 1084.4 1104.7 1264.5 1334.7 1405.9 1384.8 TRUE FALSE FALSE 1305.195487 1322.256338 1230.856062 934.4807218 1029.059022 1034.113235 1371.906598 1373.317439 1280.152783 1348.822696 0.967655342 0.98030404 0.912541037 0.692812127 0.762931277 0.766678406 1.017114112 1.018160091 0.949088999 1 10.397485 -9.576478103 4.774465913 0.983319578 0.846840603 0.251024651 0.098791087 0.205385014 9.947198071 0.016638148 0.023924093 2.65E-10 9.576478103 -0.136478975 EGPYSIS(ph)VLYGDEEVPRSPFK ddPTM_HeLa_Romidepsin_16h_R1 2 EGPYSISVLYGDEEVPRSPFK 21 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 EGPY(0.008)S(0.044)IS(0.901)VLY(0.04)GDEEVPRS(0.007)PFK;EGPY(0.002)S(0.009)IS(0.951)VLY(0.038)GDEEVPRS(0.001)PFK ; 119.51 5.12E-05 247260000 3618.3 3711.8 3957.1 3625.3 4364.3 5597.7 4388.3 4299.8 4175.1 3873.3 TRUE FALSE FALSE 3574.198768 3764.054818 4025.971666 4044.474244 4141.573486 5240.025036 4761.042092 4424.207929 3801.668599 3772.671108 0.947392091 0.99771613 1.067140906 1.072045277 1.097782809 1.388942976 1.261981752 1.172699078 1.007686197 1 11.88137062 -8.765430135 1.323701527 0.980130367 1.271625718 0.74880829 0.065180269 0.143607791 0.501417527 0.010368063 0.027093367 1.72E-09 8.765430135 0.291495351 EGPYSISVLY(ph)GDEEVPRSPFK ddPTM_HeLa_Romidepsin_16h_R1 1 EGPYSISVLYGDEEVPRSPFK 21 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 EGPY(0.01)S(0.054)IS(0.054)VLY(0.875)GDEEVPRS(0.006)PFK 98.077 0.0010642 116620000 1015.4 845.43 780.77 800.92 931.09 1157.8 1177.3 1192.5 837.36 757.65 TRUE FALSE FALSE 1003.023914 857.3319857 794.3589743 893.5261388 883.5730029 1083.820317 1277.299833 1227.003106 762.4644244 737.9661438 1.359173348 1.161749754 1.076416555 1.210795572 1.197308319 1.468658591 1.730837984 1.662682111 1.033197025 1 9.52741082 -8.072197633 2.248043606 1.167963682 1.703194355 0.835459367 0.099104187 0.124242122 1.210912695 0.019697249 0.069388044 8.47E-09 8.072197633 0.535230673 EGPYSISVLYGDEEVPR ddPTM_HeLa_Romidepsin_16h_R1 2 EGPYSISVLYGDEEVPR 17 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 231.07 3.23E-36 58574000 3106.9 3248.5 3443.9 3331.5 3510.8 3665.4 2906.1 3865.6 3736.4 3223.8 FALSE FALSE TRUE 3069.031908 3294.232468 3503.839635 3716.703705 3331.630775 3431.19277 3152.944061 3977.445037 3402.207026 3140.045211 0.977384624 1.049103515 1.115856429 1.183646558 1.061013632 1.092720817 1.004107855 1.266684003 1.083489822 1 11.61656962 -9.980934762 3.062663608 0.989536326 1.114106333 0.257015193 0.072600931 0.168602722 3.259911681 0.010344863 0.013496914 1.04E-10 9.980934762 0.124570007 EGPYSISVLYGDEEVPRS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 1 EGPYSISVLYGDEEVPRSPFK 21 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 EGPYS(0.014)IS(0.014)VLYGDEEVPRS(0.972)PFK 109.5 9.21E-05 160300000 9920.9 9804 9937.6 9349.5 11125 13442 10986 12732 10612 8729.5 TRUE FALSE FALSE 9799.980255 9942.020969 10110.55976 10430.53318 10557.24974 12583.09958 11919.15057 13100.38033 9662.836142 8502.706332 1.152571884 1.169277237 1.189099019 1.226730969 1.241634055 1.479893471 1.401806684 1.540730659 1.136442418 1 13.0537064 -4 0.173521546 0.970487442 3.378053355 0.872829324 0.05705747 9.822831783 0.104431981 0.063916703 6.207774097 1.00E-04 4 2.407565913 EGQEEDDDDEEDDADEEAPKPDHFVQDPAVLR ddPTM_HeLa_Romidepsin_16h_R1 1 EGQEEDDDDEEDDADEEAPKPDHFVQDPAVLR 32 1 Q9H1I8-3;Q9H1I8 Q9H1I8-3 ASCC2 Activating signal cointegrator 1 complex subunit 2 0 0 55.484 0.00074501 6241600 891.44 926.37 1138.6 934.68 1044.6 805.68 1016 958.77 1165.3 1184.1 FALSE FALSE TRUE 880.5747864 939.4114612 1158.416855 1042.752099 991.2901641 754.1996482 1102.299015 986.5104973 1061.072649 1153.336911 0.763501781 0.814516081 1.004404562 0.904117513 0.859497476 0.653928302 0.955747626 0.855353269 0.920002333 1 10.1715983 -12.53928698 1.309196964 0.99979883 0.843104631 0.151049244 0.09544995 0.48318853 1.486398591 0.066738453 0.015971162 2.89E-13 12.53928698 -0.156694198 EGQPSPADEKGNDS(ph)DGEGESDDPEK ddPTM_HeLa_Romidepsin_16h_R1 1 EGQPSPADEKGNDSDGEGESDDPEK 25 1 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 0 EGQPS(0.031)PADEKGNDS(0.779)DGEGES(0.19)DDPEK 56.461 0.0028963 46033000 1483.4 1598 1325.3 1158.3 1644.4 1399.1 1273.1 1812.9 1454.1 1651.2 TRUE FALSE FALSE 1465.31975 1620.496686 1348.366291 1292.228096 1560.480132 1309.702025 1381.237082 1865.353401 1324.041654 1608.301586 0.911097622 1.007582595 0.838379009 0.803473744 0.970265866 0.814338577 0.858817211 1.159828118 0.823254585 1 10.65132225 -12.13165857 0.622408052 1.008689174 0.91021282 0 0.115626988 1.962172132 1.19898316 0.106305838 0.022346755 7.38E-13 12.13165857 -0.098476354 EGRGES(ph)ENAGTNQETR ddPTM_HeLa_Romidepsin_16h_R1 1 EGRGESENAGTNQETR 16 1 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 0 EGRGES(0.578)ENAGT(0.283)NQET(0.139)R 134.93 0.0095402 12407000 1684.8 1789 1736.1 1800.4 2055 1764.2 1756.5 1752.3 1826.8 1666.6 TRUE FALSE FALSE 1664.26501 1814.185589 1766.316092 2008.570719 1950.125682 1651.473314 1905.697066 1803.000036 1663.406433 1623.301492 1.025234695 1.117590046 1.088101071 1.237336828 1.201333019 1.017354646 1.173963725 1.110699426 1.024705787 1 10.66471526 -10.19068445 1.665421818 1.008835086 1.142882949 0.474359233 0.057661778 0.207119866 1.093460639 0.010564155 0.01288193 6.45E-11 10.19068445 0.134047864 PEPAK(ac)SAPAPKK(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PEPAKSAPAPKKGSK 15 3 P06899;Q16778 P06899;Q16778 HIST1H2BJ;HIST2H2BE Histone H2B type 1-J;Histone H2B type 2-E 0 2 PEPAK(1)SAPAPK(0.357)K(0.643)GSK 86.455 0.028349 8117600 784.59 782.07 667.15 5206.3 7291.1 7076.4 8477.3 7803.7 829.15 946.98 FALSE TRUE FALSE 775.0271153 793.080002 678.7614659 5808.276902 6919.00796 6624.240878 9197.36165 8029.487747 754.9887474 922.3773231 0.840249533 0.859821661 0.735882647 6.297072529 7.501277175 7.181703965 9.971365753 8.705209404 0.818524836 1 9.849213234 -9.110427871 2.26918429 0.870895175 8.435711688 0.958628509 0.743303916 0.042131089 0.425379579 0.117808716 0.215234518 7.75E-10 9.110427871 7.564816513 up EGRPSGEAFVELES(ph)EDEVK ddPTM_HeLa_Romidepsin_16h_R1 2 EGRPSGEAFVELESEDEVK 19 1 P31943;E9PCY7;G8JLB6;D6RDU3;D6RBM0;D6RIH9;D6RJ04;D6RIU0;D6RIT2;D6RFM3;D6R9T0;D6RAM1;E7EN40;D6RDL0;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 1 0 EGRPSGEAFVELES(1)EDEVK;EGRPSGEAFVELES(1)EDEVK ; 152.27 6.20E-06 62039000 7518.8 6207.5 7424.6 4604.8 6973.4 7225.9 5981.2 7547.6 7007.9 6769.4 TRUE FALSE FALSE 7427.157974 6294.889348 7553.822049 5137.228642 6617.521377 6764.188311 6489.242979 7765.977898 6381.095872 6593.530012 1.126431208 0.954707014 1.145641566 0.77913176 1.003638622 1.025882691 0.984183429 1.177817934 0.967781425 1 12.68683534 EGRPSGEAFVELES(ph)EEEVK ddPTM_HeLa_Romidepsin_16h_R1 2 EGRPSGEAFVELESEEEVK 19 1 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 1 0 EGRPSGEAFVELES(1)EEEVK;EGRPSGEAFVELES(1)EEEVK ; 150.48 1.04E-05 5604600 3014.6 2887.5 2732.47 2447.54 3704 4227.1 3187.7 3487.5 3198.5 3199.8 TRUE FALSE FALSE 2977.856896 2928.150301 2780.027494 2730.536091 3514.971058 3957.001952 3458.463158 3588.40531 2912.418149 3116.668735 0.955461472 0.939512842 0.891986839 0.876107255 1.127797452 1.269625452 1.109666587 1.151359229 0.934465096 1 11.60578911 -8.627954187 5.972120022 0.961830571 1.174462545 0.811988378 0.053872842 0.076362865 3.798526633 0.008395576 0.016938298 2.36E-09 8.627954187 0.212631974 EGRPSGEAFVELESEDEVK ddPTM_HeLa_Romidepsin_16h_R1 1 EGRPSGEAFVELESEDEVK 19 1 P31943;E9PCY7;G8JLB6;D6RDU3;D6RBM0;D6RIH9;D6RJ04;D6RIU0;D6RIT2;D6RFM3;D6R9T0;D6RAM1;E7EN40;D6RDL0;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 0 153.75 5.32E-11 0 1571.8 1466.9 1422.2 1581.8 1384.4 1460.2 1218.9 1457.2 1345.1 1554.2 FALSE FALSE TRUE 1552.642297 1487.551057 1446.952794 1764.695159 1313.748902 1366.897933 1322.433336 1499.361783 1224.790887 1513.82166 1.025644128 0.98264617 0.955827779 1.165721964 0.867835979 0.902945154 0.87357274 0.990448097 0.809072112 1 10.56397954 EGS(ph)PAPLEPEPGAAQPK ddPTM_HeLa_Romidepsin_16h_R1 1 EGSPAPLEPEPGAAQPK 17 0 Q01167-2;Q01167 Q01167-2 FOXK2 Forkhead box protein K2 1 0 EGS(1)PAPLEPEPGAAQPK 160.79 3.12E-05 85546000 8112.1 8161 7912.1 4841 6553.5 6110.5 4962.6 5689.9 8520.7 8495.9 TRUE FALSE FALSE 8013.226605 8275.890772 8049.806782 5400.739198 6219.050441 5720.058771 5384.12312 5854.528279 7758.587252 8275.175293 0.96834524 1.000086461 0.972765711 0.65264348 0.751530961 0.69123113 0.650635537 0.707480878 0.937573764 1 13.01457416 -9.2676446 24.92261407 0.985201309 0.691886863 0.95212841 0.031922502 58.95528307 236787.4695 0.004274382 0.006631002 5.40E-10 9.2676446 -0.293314446 EGS(ph)PIPHDPEFGSK ddPTM_HeLa_Romidepsin_16h_R1 4 EGSPIPHDPEFGSK 14 0 P85037-2;P85037 P85037-2 FOXK1 Forkhead box protein K1 1 0 EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK;EGS(1)PIPHDPEFGSK ;;; 209.39 9.03E-24 232056000 23177.9 24103.5 22356.1 16211.7 19594.4 19760.7 17337 19319.7 25807.3 24921.6 TRUE FALSE FALSE 22895.39884 24442.82971 22745.19854 18086.17303 18594.42465 18498.05504 18809.60435 19878.68504 23499.03045 24274.13324 0.943201498 1.006949639 0.937013829 0.745080076 0.766018068 0.762048015 0.774882636 0.818924608 0.968068776 1 14.56713216 -9.347791766 4.453332737 0.974691887 0.772474613 0.940726531 0.02492356 0.042934281 1.525692092 0.00447623 0.006956257 4.49E-10 9.347791766 -0.202217275 EGS(ph)QGELTPANSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 EGSQGELTPANSQSR 15 0 J3QQX0;C9JFE4;A0A096LP07;A0A096LPJ3;A8K070;Q13098-5;Q13098;Q13098-7 J3QQX0 GPS1 COP9 signalosome complex subunit 1 1 0 EGS(0.999)QGELT(0.001)PANSQSR 148.36 0.00047797 13222000 1109.9 992.92 1063 540.04 959.21 842.8 717.77 904.02 963.34 1092.2 TRUE FALSE FALSE 1096.372112 1006.898354 1081.501069 602.4819658 910.2579344 788.9478 778.7373659 930.1763924 877.1764577 1063.824487 1.03059492 0.946489169 1.01661607 0.56633587 0.855646722 0.741614627 0.732016771 0.874370166 0.824549979 1 10.05504443 -9.293806336 24.99210762 1.008784417 0.757735029 0.501126895 0.099590474 240.2800535 185531.2945 0.011255275 0.01719352 5.08E-10 9.293806336 -0.251049388 EGSEFS(ph)FSDGEVAEK ddPTM_HeLa_Romidepsin_16h_R1 2 EGSEFSFSDGEVAEK 15 0 Q9BVS4;Q9BVS4-2 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 1 0 EGS(0.001)EFS(0.854)FS(0.144)DGEVAEK;EGS(0.093)EFS(0.853)FS(0.054)DGEVAEK ; 136.57 0.001199 9091200 3277.7 3093.7 3391.1 2773.5 3324.9 3847 3032.6 3445.5 3485.1 3979 TRUE FALSE FALSE 3237.750132 3137.25319 3450.120673 3094.18512 3155.217946 3601.189116 3290.188968 3545.190106 3173.383927 3875.625006 0.835413676 0.809483163 0.890210138 0.798370615 0.814118482 0.929189256 0.848944096 0.914740229 0.818805721 1 11.92021327 -12.22220598 0.899085629 1.002423009 0.853274445 0 0.069552394 0.308934116 0.437942438 0.030711648 0.008031864 6.00E-13 12.22220598 -0.149148564 EGSEFSFS(ph)DGEVAEK ddPTM_HeLa_Romidepsin_16h_R1 1 EGSEFSFSDGEVAEK 15 0 Q9BVS4;Q9BVS4-2 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 1 0 EGSEFS(0.006)FS(0.994)DGEVAEK 171.08 1.87E-05 4544500 1624 1656.1 1649.5 1283.2 1869.6 1835.7 1728.3 1827.7 1691.8 1666.1 TRUE FALSE FALSE 1604.206063 1679.414619 1678.208856 1431.569622 1774.187336 1718.404694 1875.101759 1880.581616 1540.481171 1622.814482 0.988533244 1.034877762 1.034134754 0.882152358 1.093277978 1.058903968 1.155462796 1.158839557 0.949265112 1 10.66428237 -8.068999621 1.466654703 0.995273913 1.16441306 0.626822038 0.050341377 0.204227209 0.785672436 0.006659014 0.032032846 8.53E-09 8.068999621 0.169139147 EGSGPIAFAHK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EGSGPIAFAHKR 12 1 Q9UNI6 Q9UNI6 DUSP12 Dual specificity protein phosphatase 12 0 1 ; EGSGPIAFAHK(1)R;EGSGPIAFAHK(1)R 87.667 0.011593 1969700 1386.92 1049.25 1703.51 1142.44 1953.45 2271.12 2232.18 1321 1596.81 1140.45 FALSE TRUE FALSE 1370.015686 1064.021369 1733.158877 1274.534288 1853.758157 2126.002762 2421.781313 1359.221051 1453.987314 1110.820945 1.233336203 0.95786938 1.560250448 1.147380498 1.668818153 1.913902301 2.180172534 1.223618494 1.30893041 1 10.11741057 -8.848692527 1.363067013 1.116987418 1.823447335 0.449881638 0.282762791 0.228204429 0.848354518 0.041937059 0.101672754 1.42E-09 8.848692527 0.706459917 EGSIAMQS(ph)S(ph)AT(ph)HLT(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EGSIAMQSSATHLTSK 16 0 E9PKB1;Q0P6D6 E9PKB1 CCDC15 Coiled-coil domain-containing protein 15 5 0 EGS(0.439)IAMQS(0.781)S(0.781)AT(0.999)HLT(1)S(1)K 47.545 0.0043519 0 1454.4 1300.4 1464.9 777.7 1262.9 1608.2 1077.4 1187.5 1368.1 1501.9 TRUE FALSE FALSE 1436.673213 1318.707065 1490.39597 867.6213332 1198.4495 1505.44121 1168.914329 1221.858439 1245.73371 1462.880421 0.982085201 0.901445563 1.018809158 0.593091083 0.819239552 1.029093826 0.799049814 0.835241501 0.851562227 1 10.51459613 EGSIETLSNSSGSTSGS(ph)IPR ddPTM_HeLa_Romidepsin_16h_R1 2 EGSIETLSNSSGSTSGSIPR 20 0 K7ESE9;Q9H6U6-6;Q9H6U6-2;Q9H6U6;Q9H6U6-3;Q9H6U6-8 K7ESE9 BCAS3 Breast carcinoma-amplified sequence 3 1 0 EGSIETLSNSSGSTS(0.009)GS(0.99)IPR;EGSIETLSNSSGS(0.004)T(0.002)S(0.086)GS(0.909)IPR ; 203.23 5.12E-24 5599700 1810.18 1973.31 1789.16 2020.27 1974.38 2255 1823.66 2370.3 2312.3 1602.61 TRUE FALSE FALSE 1788.11683 2001.09031 1820.299579 2253.863123 1873.620021 2110.912778 1978.561635 2438.880891 2105.482097 1560.973961 1.145513554 1.281949834 1.16613065 1.443882588 1.200289094 1.352304926 1.267517386 1.562409721 1.348825893 1 10.60823076 -4 0.075791411 0.672206746 2.712692148 0.106573188 0.14410907 72.32784159 0.405693553 1.795504428 15.64141627 1.00E-04 4 2.040485402 EGSITQGT(ph)PLKYDTGASTTGSK ddPTM_HeLa_Romidepsin_16h_R1 2 EGSITQGTPLKYDTGASTTGSK 22 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 EGS(0.01)IT(0.033)QGT(0.591)PLKY(0.077)DT(0.103)GAS(0.136)T(0.038)T(0.011)GS(0.002)K;EGS(0.014)IT(0.053)QGT(0.932)PLKYDTGASTTGSK ; 96.55 0.00019885 27938000 2814.8 2712.3 2969.6 2556 2112.46 2253.27 1740.95 1823.38 2767.3 2765.5 TRUE FALSE FALSE 2780.492135 2750.483831 3021.284642 2851.536746 2004.653284 2109.293319 1888.82625 1876.136623 2519.785757 2693.651911 1.032238844 1.021098465 1.121631429 1.058613674 0.744213933 0.783060837 0.701213933 0.696502995 0.93545337 1 11.39534771 -8.756410807 24.99943213 1.027647084 0.732803491 0.897775865 0.049083223 24.93793424 123976.9335 0.006432019 0.012553601 1.75E-09 8.756410807 -0.294843593 EGSQGELT(ph)PANSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 EGSQGELTPANSQSR 15 0 J3QQX0;C9JFE4;A0A096LP07;A0A096LPJ3;A8K070;Q13098-5;Q13098;Q13098-7 J3QQX0 GPS1 COP9 signalosome complex subunit 1 1 0 EGSQGELT(0.914)PANS(0.086)QSR 156.06 0.00083197 45237000 2815 2460.9 2348.5 1994.2 1824.8 1611 945.6 1394.6 2826.7 2267.8 TRUE FALSE FALSE 2780.689697 2495.544615 2389.374657 2224.778787 1731.673647 1508.062299 1025.91924 1434.950551 2573.872872 2208.882229 1.258867341 1.129777125 1.08171211 1.007196653 0.783959246 0.682726439 0.464451761 0.649627459 1.165237711 1 11.10910079 -8.608532785 1.353245221 1.125444827 0.558266262 0.903660686 0.076942428 0.123061144 0.442261579 0.016559274 0.048415049 2.46E-09 8.608532785 -0.567178565 EGSQGELTPANS(ph)QSR ddPTM_HeLa_Romidepsin_16h_R1 1 EGSQGELTPANSQSR 15 0 J3QQX0;C9JFE4;A0A096LP07;A0A096LPJ3;A8K070;Q13098-5;Q13098;Q13098-7 J3QQX0 GPS1 COP9 signalosome complex subunit 1 1 0 EGSQGELT(0.004)PANS(0.569)QS(0.427)R 128.45 4.29E-05 0 940.69 843.1 744.37 1080 914.66 709.98 479.87 639.28 1038 1104.3 TRUE FALSE FALSE 929.2245085 854.9691839 757.3254476 1204.874682 867.9814871 664.6145694 520.6301458 657.7765582 945.1586803 1075.610127 0.863904574 0.794869035 0.704089176 1.120177889 0.806966637 0.617895418 0.484032395 0.611538086 0.878718652 1 10.07093953 -8.300378264 3.0688423 0.915815809 0.551783702 0.621346899 0.111647195 0.119754935 2.258908533 0.016908289 0.043847118 5.01E-09 8.300378264 -0.364032107 EGSSSEYSSSSSS(ph)PMGVQAR ddPTM_HeLa_Romidepsin_16h_R1 2 EGSSSEYSSSSSSPMGVQAR 20 0 H3BS18;A0A5F9XIK1;A0A590UJW6;Q8WYQ9;Q8WYQ9-2 H3BS18 ZCCHC14 Zinc finger CCHC domain-containing protein 14 1 0 EGSSS(0.001)EY(0.001)S(0.005)S(0.003)S(0.003)S(0.008)S(0.254)S(0.725)PMGVQAR;EGSSSEYSSSS(0.002)S(0.035)S(0.963)PMGVQAR ; 137.62 2.86E-11 4416800 1907.21 1868.87 1928.36 2180.6 3133.6 3738 3267.3 3466.4 2604.5 1869.61 TRUE FALSE FALSE 1883.964191 1895.180001 1961.922297 2432.731232 2973.680699 3499.153864 3544.82438 3566.694815 2371.546997 1821.037263 1.034555541 1.040714564 1.077365267 1.335904148 1.63295983 1.921516893 1.946596291 1.958606168 1.302305585 1 10.83054473 -8.749585327 1.286922592 1.015824701 1.97463536 0.941934987 0.092424636 0.014006204 0.046049054 0.003232047 0.008684164 1.78E-09 8.749585327 0.958810659 EGSTQQLQTT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 EGSTQQLQTTSPK 13 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 0 EGSTQQLQTT(0.5)S(0.5)PK 141.37 0.0020272 39847000 3300.7 3043.6 3120.3 3296 3588.7 3407.4 3504.9 3601.2 3362.4 3097 TRUE FALSE FALSE 3260.469799 3086.447881 3174.607513 3677.099028 3405.555248 3189.678137 3802.606119 3705.39504 3061.658523 3016.539494 1.080864284 1.023175028 1.052400447 1.218979243 1.128960935 1.057396445 1.260585557 1.228359532 1.014957215 1 11.55867876 -4 0.176467275 0.993510881 2.041638247 0.619188754 0.056695462 28.46674618 0.305614867 0.077175178 8.003312495 1.00E-04 4 1.048127366 EGSTQQLQTTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EGSTQQLQTTSPK 13 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 0 EGSTQQLQTT(0.37)S(0.629)PK 169.17 0.00010986 42910000 6152.9 6110.5 5819.8 6381.3 6599.6 6885.3 6180 7019.6 6184.3 5602.8 TRUE FALSE FALSE 6077.906088 6196.523779 5921.091178 7119.135931 6262.797785 6445.351551 6704.929046 7222.701051 5631.160719 5457.238448 1.113732916 1.135468761 1.084997702 1.304530854 1.147613 1.181064674 1.228630398 1.323508423 1.031870015 1 12.41395537 -4 0.071664263 0.781254808 2.078929966 0.717603192 0.053953315 78.42525965 0.418245332 1.321120596 10.28451311 1.00E-04 4 1.297675157 EGSTQQLQTTS(ph)PKPLVQQPILPVVK ddPTM_HeLa_Romidepsin_16h_R1 1 EGSTQQLQTTSPKPLVQQPILPVVK 25 1 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4 A0A087X0H9 RBM26 RNA-binding protein 26 1 0 EGST(0.001)QQLQT(0.06)T(0.207)S(0.733)PKPLVQQPILPVVK 74.516 0.00017799 37112000 2106.6 2170.6 2161 1988.8 2340.8 2046.5 2114.4 2048.1 1860.5 1883.3 TRUE FALSE FALSE 2080.923949 2201.157764 2198.611299 2218.754414 2221.340241 1915.735255 2293.997083 2107.358542 1694.09222 1834.371595 1.134406984 1.199951946 1.198563751 1.209544686 1.210954339 1.044355059 1.250562912 1.148817692 0.923527286 1 10.8410702 -11.53190241 0.671896873 1.003496663 1.181259149 0.651814406 0.060235805 0.332623835 0.307850269 0.028916473 0.012487509 2.94E-12 11.53190241 0.177762486 EGSVLDILKS(ph)PGFASPK ddPTM_HeLa_Romidepsin_16h_R1 2 EGSVLDILKSPGFASPK 17 1 P49790-3;P49790 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 EGSVLDILKS(0.999)PGFAS(0.001)PK;EGSVLDILKS(0.798)PGFAS(0.202)PK ; 94.632 0.0023318 75619000 6609.9 5965.1 6173.8 7173.5 5975.3 4963.9 4421 4955.4 6774.4 6009.8 TRUE FALSE FALSE 6529.335996 6049.076834 6281.252399 8002.933822 5670.358144 4646.72281 4796.51963 5098.776681 6168.480697 5853.66453 1.115427091 1.033382901 1.073046186 1.367166462 0.968685191 0.793814334 0.819404598 0.871040124 1.05378104 1 12.51512435 -8.519671155 24.99948432 1.078815098 0.836223408 0.612046282 0.098344517 75.209246 586168.1091 0.015152174 0.030791831 3.02E-09 8.519671155 -0.24259169 EGT(ph)APSENGETK ddPTM_HeLa_Romidepsin_16h_R1 1 EGTAPSENGETK 12 0 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 0 EGT(0.89)APS(0.11)ENGETK 190.85 9.84E-10 15635000 3965.7 4490.1 5354.3 2026.9 3248.6 3931.4 4722.1 1963.8 4542.7 4646.3 TRUE FALSE FALSE 3917.364523 4553.311746 5447.489345 2261.259715 3082.81182 3680.196228 5123.195056 2020.619455 4136.389535 4525.588456 0.865603349 1.006125897 1.203708512 0.499660925 0.681195794 0.813197281 1.132050584 0.446487672 0.914000372 1 12.14388968 -9.261031873 24.99999914 0.959465665 0.741345588 0.332396281 0.195226994 42.55780208 2610840.69 0.029150415 0.046456436 5.48E-10 9.261031873 -0.218120077 EGT(ph)PPPPPPSR ddPTM_HeLa_Romidepsin_16h_R1 4 EGTPPPPPPSR 11 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;C9JQE8 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 EGT(1)PPPPPPSR;EGT(1)PPPPPPSR;EGT(1)PPPPPPSR;EGT(1)PPPPPPSR ;;; 134.18 0.0087267 242076000 22356.1 23049.1 21144.8 22405.9 14877 13988 12483.5 14245.8 20855.6 22146 TRUE FALSE FALSE 22083.61525 23373.58583 21512.81637 24996.57558 14117.77118 13094.21194 13543.84818 14657.97975 18990.2229 21570.64373 1.023781002 1.083583139 0.997319164 1.158823812 0.654490026 0.607038534 0.627883356 0.679533719 0.88037349 1 14.39678161 -8.747325454 24.99544597 1.025586215 0.638696904 0.882193651 0.068334361 40.02064752 70875.26864 0.007140354 0.01422569 1.79E-09 8.747325454 -0.386889312 EGTAPS(ph)ENGETK ddPTM_HeLa_Romidepsin_16h_R1 2 EGTAPSENGETK 12 0 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 0 EGT(0.027)APS(0.965)ENGET(0.009)K;EGT(0.077)APS(0.923)ENGETK ; 168.89 0.00018685 26497100 11572.7 12420.4 14646 5680.2 10631 12510 12126.2 5541.7 13028.3 13606 TRUE FALSE FALSE 11431.64748 12595.25472 14900.90749 6336.97145 10088.4604 11710.65137 13156.19913 5702.040346 11863.01622 13252.51416 0.862602171 0.950404924 1.124383442 0.478171264 0.761248792 0.883655074 0.99273232 0.430261027 0.895152126 1 13.69397846 -9.275900968 24.99336515 0.947763837 0.737546738 0.353066054 0.1710789 808.9765947 1398118.058 0.025705975 0.039375011 5.30E-10 9.275900968 -0.210217098 EGTETFADHR ddPTM_HeLa_Romidepsin_16h_R1 2 EGTETFADHR 10 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 ; ; 141.88 0.0020967 25172000 21560.2 20605.3 18781.5 17766 22627.1 22736.2 19584.4 19898.4 23026.1 20591.9 FALSE FALSE TRUE 21297.41599 20895.38195 19108.38413 19820.18851 21472.35465 21283.4302 21247.89845 20474.12881 20966.58795 20056.91947 1.061848806 1.041804151 0.952707825 0.988197043 1.070570916 1.061151501 1.059379955 1.020801267 1.045354347 1 14.29181242 -16.52280505 0.006121878 0.388471118 1.618580485 0.007991058 0.036696613 74197.25195 36.75301399 4026.091276 3385.211612 3.00E-17 16.52280505 1.230109367 EGTGQQERES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 EGTGQQERESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 48 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 0 EGT(0.072)GQQERES(0.92)PRPLQLPGAEGPAIS(0.008)DGEEGGGEPGAGGGAAGAAGAGR 51.989 0.00039043 11060000 489.76 420 392.34 368.53 445.86 478.69 387.32 380.15 533.41 471.46 TRUE FALSE FALSE 483.7906167 425.912771 399.1685131 411.1411726 423.1061005 448.1032539 420.2189511 391.1490405 485.7004737 459.2114012 1.053524837 0.927487362 0.869247828 0.895320045 0.921375426 0.975810384 0.915088236 0.851784253 1.05768383 1 8.843014651 -10.17249823 5.323004909 1.025165017 0.908284229 0.738814106 0.035064599 0.095344676 4.409119683 0.006266457 0.00769155 6.72E-11 10.17249823 -0.116880788 EGTGSTATSSS(ph)STAGAAGK ddPTM_HeLa_Romidepsin_16h_R1 1 EGTGSTATSSSSTAGAAGK 19 0 E5RGU4;A0A087WZK9;B3KS98;O15372;E5RHC7;E5RH59;E5RFW7;E5RFH0 E5RGU4 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 0 EGTGSTATS(0.028)S(0.144)S(0.747)S(0.062)T(0.019)AGAAGK 161.94 1.31E-06 4272500 2395.4 2568.7 2324.3 2302.1 2406.2 2171.7 1308.9 2257.6 2392.4 2381.1 TRUE FALSE FALSE 2366.203943 2604.862226 2364.753467 2568.279634 2283.402635 2032.935379 1420.077933 2322.920094 2178.417752 2319.238679 1.020250294 1.123154012 1.019624883 1.107380477 0.984548359 0.876552895 0.612303488 1.001587338 0.9392814 1 11.17943558 -8.202050104 3.340746448 1.026235265 0.796989353 0.449634582 0.101455728 0.138963641 3.085284602 0.012583837 0.034596024 6.28E-09 8.202050104 -0.229245912 EGTGSTATSSSS(ph)TAGAAGK ddPTM_HeLa_Romidepsin_16h_R1 1 EGTGSTATSSSSTAGAAGK 19 0 E5RGU4;A0A087WZK9;B3KS98;O15372;E5RHC7;E5RH59;E5RFW7;E5RFH0 E5RGU4 EIF3H Eukaryotic translation initiation factor 3 subunit H 1 0 EGTGSTATSSS(0.019)S(0.962)T(0.019)AGAAGK 354.71 1.23E-263 4602800 1283.2 1342.3 1415.3 1252.2 1249.4 1224.2 1004.1 1158.8 1625.1 1316.9 TRUE FALSE FALSE 1267.559865 1361.196935 1439.932703 1396.985256 1185.638456 1145.977571 1089.388229 1192.32805 1479.746986 1282.686748 0.988206876 1.061207607 1.122591081 1.089108668 0.924339834 0.89341967 0.849301851 0.929555132 1.153630836 1 10.32495317 -8.585023901 6.734543146 1.016387635 0.890088125 0.56158894 0.064604021 0.124331094 10.65302812 0.008220046 0.016569195 2.60E-09 8.585023901 -0.126299509 EGVFAK(ac)EVR ddPTM_HeLa_Romidepsin_16h_R1 2 EGVFAKEVR 9 1 A0A0U1RQF0;P49327 A0A0U1RQF0 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 1 ; EGVFAK(1)EVR;EGVFAK(1)EVR 123.86 0.0065923 29515000 4323.6 3810.8 5741 5040.3 6101.6 5452.5 4218.8 4639.1 4443.7 3118.1 FALSE TRUE FALSE 4270.9023 3864.448542 5840.919697 5623.083201 5790.212584 5104.102847 4577.144767 4773.325039 4046.244343 3037.091312 1.406247577 1.272417634 1.923195286 1.851469917 1.90649934 1.680589196 1.507081709 1.571676498 1.332276157 1 11.56847457 -10.79408155 0.654665098 1.058416123 1.725228236 0.532909416 0.196184347 0.284892151 0.275754016 0.070819621 0.056635645 1.61E-11 10.79408155 0.666812113 EGVHGGLINK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVHGGLINK 10 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 0 ; ; 110.53 0.0083037 38813000 11536.7 11153 11652.5 8107.1 11351.4 11925.2 10214.9 10469.3 12003.7 11381.9 FALSE FALSE TRUE 11396.08626 11310.01223 11855.30687 9044.481047 10772.0957 11163.21821 11082.55335 10772.21268 10930.05901 11086.1966 1.027952749 1.020188676 1.069375486 0.815832641 0.971667389 1.006947523 0.999671371 0.971677941 0.985916036 1 13.43647688 EGVHGGLINK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 1 ; EGVHGGLINK(1)K;EGVHGGLINK(1)K 143.24 0.00036073 48491000 7517.1 8281.8 9459.4 7121.6 19175.5 16643.6 19556.9 8032.6 22843 15474.1 FALSE TRUE FALSE 7425.478694 8398.391398 9624.036889 7945.0329 18196.90268 15580.12767 21218.0626 8265.010608 20799.86487 15072.08065 0.492664475 0.557215131 0.638534063 0.527135774 1.207325193 1.033707823 1.407772629 0.548365604 1.380026113 1 13.87959097 -8.756345145 24.99990601 0.713174261 1.073785314 0.142215179 0.323595804 129.1680477 633883.5933 0.040338246 0.078744499 1.75E-09 8.756345145 0.360611053 EGVHGGLINKK ddPTM_HeLa_Romidepsin_16h_R1 1 EGVHGGLINKK 11 1 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 0 51.927 0.026452 13342000 5460.3 5177.2 5777.6 6482.4 5465.8 6399.3 6142 2946.8 6717.6 5619 FALSE FALSE TRUE 5393.747763 5250.084757 5878.156704 7231.925589 5186.85983 5990.405383 6663.701327 3032.061009 6116.761031 5473.01757 0.985516252 0.959266929 1.074024819 1.321378106 0.947714814 1.094534287 1.217555259 0.554001695 1.117621304 1 12.41812077 -7.247270648 24.90651888 1.032993901 0.55400135 0.610907124 0.120793971 1293.40516 2273575.997 0.016498083 0.463764779 5.66E-08 7.247270648 -0.47899255 EGVILTNESAAS(ph)TGQPDNDVTEGQR ddPTM_HeLa_Romidepsin_16h_R1 2 EGVILTNESAASTGQPDNDVTEGQR 25 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 EGVILTNES(0.015)AAS(0.844)T(0.141)GQPDNDVTEGQR;EGVILT(0.001)NES(0.008)AAS(0.835)T(0.155)GQPDNDVT(0.001)EGQR ; 71.78 0.00030326 4974700 2525.9 2241.19 2021.28 1480.24 1961.12 2287.41 1921.48 2559.35 2216.5 2100.96 TRUE FALSE FALSE 2495.113359 2272.741532 2056.459531 1651.392314 1861.036728 2141.251883 2084.690463 2633.400754 2018.250689 2046.376756 1.219283473 1.110617351 1.004927135 0.806983518 0.909430154 1.046362492 1.018722704 1.286860177 0.986255675 1 10.99885607 -9.75347347 9.184598653 1.106997406 0.999978568 0.038124213 0.129969195 0.244864546 190.1071844 0.022411415 0.030919764 1.76E-10 9.75347347 -0.107018838 EGVK(ac)FDESEK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVKFDESEK 10 1 P14625 P14625 HSP90B1 Endoplasmin 0 1 ; EGVK(1)FDESEK;EGVK(1)FDESEK 112.15 0.016374 3718200 1448.86 1393.84 1357.21 1143.69 4096.7 3510.4 3039.6 3239.1 3769.3 2424.5 FALSE TRUE FALSE 1431.200737 1413.462516 1380.831671 1275.928819 3887.630112 3286.096769 3297.783548 3332.818248 3432.164368 2361.51114 0.606052926 0.598541541 0.584723759 0.540301842 1.64624678 1.391522874 1.39647173 1.411307442 1.453376319 1 11.20549463 -8.760406718 24.99999755 0.755477476 1.451760127 0.594314212 0.267472514 10.70594667 259171.0789 0.029918119 0.057215941 1.74E-09 8.760406718 0.696282651 EGVK(ac)TENNDHINLK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVKTENNDHINLK 14 1 P61956-2;P61956 P61956-2 SUMO2 Small ubiquitin-related modifier 2 0 1 ; EGVK(1)TENNDHINLK;EGVK(1)TENNDHINLK 214.58 3.04E-24 5101900 3223.5 3753.3 2786 1855.61 2162 1979.1 1854.49 1910.02 3809.3 3171.1 FALSE TRUE FALSE 3184.210742 3806.139056 2834.489161 2070.164359 2051.665072 1852.641897 2012.010334 1965.283415 3468.586667 3088.714365 1.03091784 1.232272916 0.917692226 0.670234963 0.664245647 0.599810043 0.651407057 0.636278782 1.122987191 1 11.59279075 -9.334313239 3.374972653 1.03266455 0.6400618 0.890915822 0.073477405 0.059162891 1.320112016 0.010815985 0.017242608 4.63E-10 9.334313239 -0.39260275 EGVMVAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EGVMVAKK 8 1 Q15149;P46783;Q9NQ39;A0A2R8Y6L3;F6U211;A0A2R8Y7H1;A0A2R8YFH6;A0A1W2PQS6 Q15149;P46783 PLEC;RPS10;RPS10P5 Plectin;40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 0 1 EGVMVAK(1)K 75.38 0.021775 1249800 507.59 448.43 1041.6 227.16 581.47 755.51 656.2 450.7 706.04 411.03 FALSE TRUE FALSE 501.4032978 454.7430093 1059.728611 253.425308 551.7954161 707.2353493 711.9376116 463.7402934 642.8900141 400.3513813 1.252408063 1.135859723 2.646996265 0.633007203 1.378277788 1.766536553 1.778281891 1.158333192 1.605814402 1 8.645122974 -9.939688325 24.99999857 1.123117289 1.559301726 0.06174023 0.508961256 97.17995957 40281.86522 0.074145275 0.097445979 1.15E-10 9.939688325 0.436184437 EGVMYVGAK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 1 EGVMYVGAKTK 11 1 F8W754;O76070 F8W754 SNCG Gamma-synuclein 0 1 EGVMYVGAK(1)TK 109.39 0.0058699 2159300 577.91 602.38 780.21 394.22 499.16 580.11 372.35 416.16 488.04 536.32 FALSE TRUE FALSE 570.8662106 610.8603215 793.7892278 439.8015713 473.6860026 543.0428432 403.9773997 428.200933 444.3884801 522.3863291 1.092804652 1.169365061 1.519544413 0.841908654 0.906773352 1.039542601 0.773330727 0.819701644 0.850689337 1 9.028973332 EGVQGPLNVS(ph)LSEEGK ddPTM_HeLa_Romidepsin_16h_R1 3 EGVQGPLNVSLSEEGK 16 0 P12270 P12270 TPR Nucleoprotein TPR 1 0 EGVQGPLNVS(0.999)LS(0.001)EEGK;EGVQGPLNVS(1)LSEEGK;EGVQGPLNVS(0.993)LS(0.007)EEGK ;; 236.27 7.96E-46 49461900 7259.9 7067.3 7137.2 5137.6 6711.3 6414.3 5266.8 5276.3 7443.4 7229.5 TRUE FALSE FALSE 7171.413546 7166.793635 7261.419972 5731.633485 6368.797318 6004.446931 5714.161861 5428.961416 6777.643662 7041.676548 1.018424163 1.017768082 1.031206123 0.813958643 0.90444332 0.852701326 0.811477469 0.770975687 0.962504258 1 12.78170324 -9.261651399 24.99999973 1.01128013 0.834960632 0.852709419 0.036367154 4.845795449 571385.3611 0.005166148 0.008212502 5.47E-10 9.261651399 -0.176319498 EGVQGPLNVSLS(ph)EEGK ddPTM_HeLa_Romidepsin_16h_R1 1 EGVQGPLNVSLSEEGK 16 0 P12270 P12270 TPR Nucleoprotein TPR 1 0 EGVQGPLNVS(0.093)LS(0.907)EEGK 204.81 1.15E-18 32992000 3233.5 3514.8 4102.2 2190.7 2486 2745.4 2214.6 2396 2851.6 3399.2 TRUE FALSE FALSE 3194.088858 3564.281447 4173.59707 2443.999042 2359.130143 2569.9778 2402.708069 2465.32448 2596.545754 3310.888294 0.964722629 1.076533284 1.260567165 0.73817019 0.712536919 0.776220027 0.725698923 0.744611192 0.784244445 1 11.69300262 -9.205525031 24.62367946 1.010291868 0.739231275 0.611097263 0.110724669 106.5254603 46911.85821 0.013375006 0.022179932 6.23E-10 9.205525031 -0.271060593 EGVSSTT(ph)PAKDAASAGLGSIGVK ddPTM_HeLa_Romidepsin_16h_R1 1 EGVSSTTPAKDAASAGLGSIGVK 23 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 EGVS(0.015)S(0.051)T(0.182)T(0.747)PAKDAAS(0.003)AGLGS(0.002)IGVK 60.133 0.0047407 17140000 1131.1 1085.1 1051.7 1184.3 1056.1 1170 1069.3 1093.4 1257.1 1208 TRUE FALSE FALSE 1117.313718 1100.376066 1070.004397 1321.234338 1002.203276 1095.240776 1160.126315 1125.035804 1144.661828 1176.615986 0.949599301 0.935204076 0.909391348 1.122910409 0.851767517 0.930839619 0.985985512 0.956162263 0.972842322 1 10.20042783 -10.39755767 0.005745563 1.932120453 1.51E-07 0.017643116 0.066355959 8134.890992 40.95582562 6887.53626 6882.666905 4.00E-11 10.39755767 -1.932120302 EGVTPWAS(ph)FK ddPTM_HeLa_Romidepsin_16h_R1 1 EGVTPWASFK 10 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 EGVT(0.003)PWAS(0.997)FK 96.745 0.02876 15884000 1300.4 1765.6 1863.3 1429.6 1838.7 1616.7 1103.9 1305.9 1295.4 1299.5 TRUE FALSE FALSE 1284.550225 1790.456163 1895.729955 1594.897078 1744.864278 1513.398088 1197.665238 1343.684156 1179.53618 1265.738803 1.014862009 1.414554219 1.497726032 1.260052291 1.37853424 1.195663817 0.946218316 1.061580915 0.931895409 1 10.30576401 -10.33738472 10.09017341 1.00682714 1.251523599 0.382226773 0.155410646 0.492889573 63.63083936 0.028811137 0.032918401 4.60E-11 10.33738472 0.244696459 EGVTPWAS(ph)FKK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVTPWASFKK 11 1 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 EGVT(0.011)PWAS(0.989)FKK;EGVT(0.075)PWAS(0.925)FKK ; 128.57 0.0096024 127079000 8274.8 9711.5 9749.9 8787.3 10489.2 8957.5 6691.1 9366.5 7482.8 7587.2 TRUE FALSE FALSE 8173.943555 9848.218752 9919.59292 9803.328971 9953.896983 8385.144659 7259.441867 9637.5049 6813.519627 7390.08345 1.106069182 1.33262619 1.34228429 1.326551863 1.346926195 1.134648169 0.982322042 1.304113135 0.921981419 1 12.85137494 -10.52427554 2.862690358 1.041393145 1.247287551 0.471878822 0.117168482 0.200184717 3.324753806 0.022459284 0.024314117 2.99E-11 10.52427554 0.205894406 EGVVAAAEK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVVAAAEKTK 11 1 D6RA31;H6UYS7;E7EPV7;A0A669KB41;A0A669KBH5;P37840-2;P37840-3;P37840;G4Y816;Q16143 D6RA31;G4Y816 SNCA;SNCB Alpha-synuclein;Beta-synuclein 0 1 ; EGVVAAAEK(1)TK;EGVVAAAEK(1)TK 154.66 0.0079039 4036600 3107.7 3105.4 2993.9 2360.4 2890.6 2927.7 2734.1 2897.1 3801.5 2977.3 FALSE TRUE FALSE 3069.822157 3149.117903 3046.007574 2633.320554 2743.081896 2740.629419 2966.334386 2980.923018 3461.484319 2899.949317 1.058577865 1.085921704 1.050365796 0.90805744 0.94590684 0.945061144 1.022891803 1.027922454 1.193636144 1 11.50181197 -9.293474176 24.74665469 1.035208771 0.970187693 0.328387391 0.063936409 521.8283869 403107.2923 0.007079481 0.01081467 5.09E-10 9.293474176 -0.065021078 EGVVGAVEK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 EGVVGAVEKTK 11 1 F8W754;O76070 F8W754 SNCG Gamma-synuclein 0 1 ; EGVVGAVEK(1)TK;EGVVGAVEK(1)TK 155.97 0.0079039 5648100 5926.6 6086.4 4290.9 4263.5 3783.8 3717.7 3843.6 3867.8 6888.8 5757.1 FALSE TRUE FALSE 5854.36432 6172.084499 4365.581315 4756.46593 3590.698567 3480.150968 4170.075288 3979.708691 6272.648475 5607.529712 1.044018422 1.100677984 0.778521299 0.848228395 0.640335183 0.620621048 0.743656387 0.709707999 1.118611723 1 12.45314964 -9.437602438 1.67433005 1.026919235 0.690216002 0.82920324 0.074701509 0.099504261 0.551630235 0.011049996 0.018476555 3.65E-10 9.437602438 -0.336703233 EGWPS(ph)SAYGVTK ddPTM_HeLa_Romidepsin_16h_R1 1 EGWPSSAYGVTK 12 0 P16152 P16152 CBR1 Carbonyl reductase [NADPH] 1 1 0 EGWPS(0.958)S(0.042)AYGVTK 119.25 0.0077512 3253900 2233.9 2284.8 2462.9 1758.7 2017.2 2394.2 1780.7 2421.8 2463 1994.3 TRUE FALSE FALSE 2206.672368 2316.965474 2505.765741 1962.049169 1914.254757 2241.218347 1931.952614 2491.870962 2242.703111 1942.487799 1.136003206 1.192782511 1.289977596 1.010070267 0.985465524 1.153787606 0.994576447 1.282824512 1.154551968 1 10.92368982 -12.13625577 0.989726412 1.002981088 1.124553667 0 0.113684293 0.745120352 1.359556449 0.060163496 0.019189493 7.31E-13 12.13625577 0.121572579 EGYGGFRGQREGSRGFR ddPTM_HeLa_Romidepsin_16h_R1 1 EGYGGFRGQREGSRGFR 17 3 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 0 73.781 0.0030681 0 1085.9 1606 1251.6 1274.2 1289.5 1427.2 1150 1453.1 1427 1440 FALSE FALSE TRUE 1072.664633 1628.60931 1273.383573 1421.528999 1223.692003 1336.006526 1247.680971 1495.143156 1299.365546 1402.588592 0.764774959 1.161145413 0.907881028 1.013503893 0.872452557 0.952529155 0.88955591 1.06598839 0.926405329 1 10.45387618 -10.30182647 24.99976027 0.888921538 0.970196116 0.123573606 0.098448559 914.9096674 566329.8391 0.019434402 0.022224256 4.99E-11 10.30182647 0.081274578 EGYK(ac)FYPPK ddPTM_HeLa_Romidepsin_16h_R1 1 EGYKFYPPK 9 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 1 EGYK(1)FYPPK 109.29 0.011727 1550500 1840.3 1582.7 1376 1366.5 2231.2 1789.5 1459.8 1356.1 1879.8 1680.1 FALSE TRUE FALSE 1817.869716 1604.981292 1399.948703 1524.50116 2117.333538 1675.156725 1583.795376 1395.336614 1711.66598 1636.45076 1.110861237 0.980769683 0.85547866 0.931589998 1.293857163 1.023652386 0.967823423 0.852660311 1.04596241 1 10.67635448 -10.22374597 24.30048055 1.052351162 0.991919088 0.059291397 0.118630521 1079.577676 695991.0834 0.020952466 0.025660949 5.97E-11 10.22374597 -0.060432073 EGYVLQTEVAAS(ph)PSGAWQR ddPTM_HeLa_Romidepsin_16h_R1 2 EGYVLQTEVAASPSGAWQR 19 0 A0A494BZV2;H0Y2S9 A0A494BZV2 MPRIP 1 0 EGYVLQTEVAAS(0.81)PS(0.19)GAWQR;EGYVLQT(0.035)EVAAS(0.604)PS(0.361)GAWQR ; 173.49 1.55E-12 0 1611.4 2040.96 1813.75 2113.8 2543 3347.9 2287.79 2415.3 2077.73 1594.92 TRUE FALSE FALSE 1591.759637 2069.692688 1845.317558 2358.207502 2413.221221 3133.979995 2482.114825 2485.182895 1891.892625 1553.483748 1.024638744 1.332291175 1.187857652 1.518012341 1.553425469 2.017388336 1.597773281 1.599748241 1.217838698 1 10.60129143 -9.378221016 0.901067632 1.007547206 1.734670127 0.736297314 0.152427732 0.151094166 0.243823967 0.02525033 0.051748577 4.19E-10 9.378221016 0.727122921 EHALLAYTLGVK ddPTM_HeLa_Romidepsin_16h_R1 3 EHALLAYTLGVK 12 0 Q5VTE0;P68104;A0A087WV01;A0A2R8Y488;A0A2U3TZH3;Q05639;A0A2R8Y660 Q5VTE0;A0A2R8Y488 EEF1A1P5;EEF1A1;EEF1A2 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha;Elongation factor 1-alpha 2 0 0 ;; ;; 103.08 0.0026232 28817600 16279.7 13206.2 18542.6 12402.7 19254 18605.7 15842.7 14140.3 16203.1 12178 FALSE FALSE TRUE 16081.27675 13392.11723 18865.32617 13836.75853 18271.39653 17416.85582 17188.37854 14549.42727 14753.85415 11861.6138 1.35574105 1.129029949 1.590451897 1.166515683 1.540380326 1.468337791 1.449075887 1.226597621 1.243831944 1 13.53401269 -12.65268983 0.347154876 0.796623715 1.41091064 0.215371827 0.162975251 2.326502403 0.29621421 0.564220607 0.056236565 2.22E-13 12.65268983 0.614286925 EHEVFQR ddPTM_HeLa_Romidepsin_16h_R1 2 EHEVFQR 7 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 0 ; ; 138.24 0.0062885 4880900 3074.1 3638.9 4415.8 3204.1 3457.6 3866.1 3813.2 1709.34 3832.8 3943.9 FALSE FALSE TRUE 3036.631687 3690.12853 4492.655147 3574.573118 3281.14577 3619.068687 4137.093113 1758.797056 3489.984769 3841.436909 0.790493703 0.960611515 1.169524647 0.930530216 0.854145427 0.94211327 1.076965003 0.457848742 0.90851024 1 11.90743034 -7.250211328 24.5600816 0.931458032 0.457848387 0.666185835 0.104826105 732.141001 1601437.276 0.016664863 0.338995652 5.62E-08 7.250211328 -0.473609645 EHIEELLR ddPTM_HeLa_Romidepsin_16h_R1 2 EHIEELLR 8 0 B4DIH5;P61201;P61201-2;H0YMC2 B4DIH5 COPS2 COP9 signalosome complex subunit 2 0 0 ; ; 143.28 0.0040912 7610700 5479.7 4654.2 5328.9 4876.8 5562.3 5733.8 4917.5 4869.5 5284.5 5017.2 FALSE FALSE TRUE 5412.911309 4719.72195 5421.647269 5440.678562 5278.435075 5367.428685 5335.192327 5010.3913 4811.841085 4886.852421 1.107647795 0.965799976 1.109435441 1.113329827 1.08012983 1.098340654 1.091744106 1.025279846 0.984650378 1 12.25468982 -12.49331883 1.059542802 0.996842873 1.078008721 0.346475724 0.044087514 0.564767159 1.059430227 0.036476467 0.007559875 3.21E-13 12.49331883 0.081165848 EHIYDLR ddPTM_HeLa_Romidepsin_16h_R1 4 EHIYDLR 7 0 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 0 ;;; ;;; 139.68 0.0062274 24516700 20924.1 20002.8 23076.9 21706.1 26070.6 24010.6 21009.1 20767.1 20979.5 18697 FALSE FALSE TRUE 20669.06902 20284.39994 23478.54376 24215.86141 24740.12 22476.40015 22793.61243 21367.96327 19103.04098 18211.24924 1.134961624 1.113839016 1.289233015 1.329719949 1.358507572 1.234204192 1.251622671 1.173338687 1.048969278 1 14.15254227 -10.50958504 0.73828622 1.029011144 1.275757037 0.705245826 0.061541899 0.236430496 0.275897994 0.019249367 0.019448919 3.09E-11 10.50958504 0.246745893 EHLELFWSR ddPTM_HeLa_Romidepsin_16h_R1 2 EHLELFWSR 9 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 ; ; 174.86 0.00023281 51491000 10716.2 8068.2 16429.2 12806.5 16541.2 15145 11792.4 8891.4 9309.3 6370.9 FALSE FALSE TRUE 10585.58683 8181.784331 16715.14333 14287.24779 15697.04084 14177.28338 12794.04616 9148.658631 8476.652892 6205.3831 1.705871606 1.318497859 2.693652119 2.302395768 2.52958449 2.284674959 2.061765721 1.474310044 1.366016047 1 12.59930456 -10.85546214 0.632874553 1.091699487 2.200676055 0.469575672 0.39941113 0.370474798 0.338239259 0.157297484 0.11845715 1.39E-11 10.85546214 1.108976568 EHLLLAR ddPTM_HeLa_Romidepsin_16h_R1 1 EHLLLAR 7 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 0 85.359 0.024371 5197600 3138.7 3526.1 4323.1 4152 4039.4 5036.5 4740.6 2078.7 4178.9 3216.4 FALSE FALSE TRUE 3100.444317 3575.740528 4398.341742 4632.073776 3833.254345 4714.683905 5143.266446 2138.843905 3805.128718 3132.837464 0.989660125 1.141374415 1.403948271 1.478555408 1.223572684 1.504924516 1.641727828 0.682717801 1.214594999 1 11.61325421 -9.972556617 3.365087194 0.996172648 1.347326684 0.155054585 0.252643663 0.204505036 4.861797379 0.03720578 0.048604837 1.07E-10 9.972556617 0.351154036 EHPDAWTR ddPTM_HeLa_Romidepsin_16h_R1 2 EHPDAWTR 8 0 O14980;C9IYM2;H7BZC5;F8WF71;C9IZS4;C9JQ02;C9JV99;C9J673;C9JKM9 O14980 XPO1 Exportin-1 0 0 ; ; 130.56 0.0051236 11016800 7152.9 6937.7 7806.3 6301.6 5999.1 6747.4 5951.5 5030.6 8084.5 6920.3 FALSE FALSE TRUE 7065.717704 7035.369123 7942.165377 7030.220642 5692.943541 6316.262916 6457.020261 5176.152474 7361.402072 6740.509608 1.048246811 1.043744395 1.178273727 1.042980583 0.844586518 0.937060146 0.957942446 0.767917083 1.092113579 1 12.71864195 -8.770460427 24.9977272 1.039280362 0.886965797 0.634432524 0.068762785 111.4210749 308753.2875 0.010145416 0.018581838 1.70E-09 8.770460427 -0.152314566 EHPGQPEDS(ph)PEAEASTLDVFTER ddPTM_HeLa_Romidepsin_16h_R1 1 EHPGQPEDSPEAEASTLDVFTER 23 0 F8VW41;Q86VP3-4;Q86VP3;Q86VP3-3;Q86VP3-2 F8VW41 PACS2 Phosphofurin acidic cluster sorting protein 2 1 0 EHPGQPEDS(0.999)PEAEASTLDVFTER 61.903 0.0029004 3502000 697.4 828.32 725.85 939.14 849.05 864.85 698.84 985.53 709.68 833.25 TRUE FALSE FALSE 688.8998206 839.9811107 738.4831148 1047.727786 805.7198103 809.5888762 758.1994522 1014.044756 646.2044434 811.6020449 0.848814792 1.034966725 0.909907903 1.290937834 0.992752317 0.997519513 0.934201013 1.24943593 0.796208496 1 9.66462869 EHQALQDLVDLAR ddPTM_HeLa_Romidepsin_16h_R1 1 EHQALQDLVDLAR 13 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 0 0 61.235 0.026343 1725900 839.99 827.91 757.14 879.39 1404.9 1083.2 1045.2 1045.5 1597.2 981.87 FALSE FALSE TRUE 829.7518788 839.5653387 770.3177041 981.0692095 1333.202711 1013.987016 1133.979262 1075.749893 1454.342432 956.3608759 0.867613784 0.877875036 0.805467605 1.025835785 1.394037276 1.060255644 1.185723183 1.124836785 1.520704651 1 9.901411301 -8.992687906 24.93499867 0.921222918 1.185025701 0.06310136 0.211332214 85.6980202 292236.1537 0.014258437 0.025806947 1.02E-09 8.992687906 0.263802783 EHSLQVS(ph)PSLEK ddPTM_HeLa_Romidepsin_16h_R1 1 EHSLQVSPSLEK 12 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 0 EHSLQVS(0.995)PS(0.005)LEK 117.13 0.0035259 68440000 4806.1 3851 4446.9 4023.9 5887.6 6297.3 5867.4 5266.8 5086.8 4234.5 TRUE FALSE FALSE 4747.521405 3905.214479 4524.296429 4489.162251 5587.133802 5894.922854 6365.77681 5419.186548 4631.823868 4124.48708 1.151057407 0.946836395 1.096935532 1.088417096 1.354625119 1.429249926 1.543410535 1.31390557 1.123006032 1 12.009999 -8.700649897 2.851814285 1.063720011 1.43746244 0.833917493 0.075435625 0.078658632 1.298803142 0.011965857 0.025293087 1.99E-09 8.700649897 0.373742429 EHSNPS(ph)PSQDTDGTK ddPTM_HeLa_Romidepsin_16h_R1 2 EHSNPSPSQDTDGTK 15 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 0 EHS(0.04)NPS(0.956)PS(0.003)QDTDGTK;EHS(0.01)NPS(0.881)PS(0.11)QDTDGTK ; 114.99 0.0016339 4142400 7317.9 6283.3 7123.8 5704.5 5918.2 6882.3 6316.1 4725.9 7873.4 7381 TRUE FALSE FALSE 7228.70662 6371.756462 7247.786751 6364.08113 5616.17217 6442.543242 6852.589376 4862.63646 7169.183385 7189.240556 1.005489601 0.886290619 1.008143585 0.885223005 0.781191299 0.89613683 0.953172915 0.676376931 0.997210113 1 12.81162366 -4.744606803 0.22149666 1.02297773 5.01E-21 0.513520206 0.072768362 20.68020576 0.331645736 0.054071451 7.140566164 1.80E-05 4.744606803 -1.02297773 EHVEEISELFYDAK ddPTM_HeLa_Romidepsin_16h_R1 2 EHVEEISELFYDAK 14 0 Q9Y265;H7C4G5 Q9Y265 RUVBL1 RuvB-like 1 0 0 ; ; 161.87 0.00012253 8769900 7686.6 7528.4 8089.1 5207.1 8679.6 8509.9 7025.2 8441.4 8550.3 8356.4 FALSE FALSE TRUE 7592.912763 7634.385013 8229.887392 5809.169402 8236.647624 7966.144854 7621.920313 8685.638591 7785.539753 8139.299523 0.932870543 0.937965852 1.011129689 0.713718593 1.011960255 0.978726097 0.93643443 1.067123598 0.956536829 1 12.99068892 -7.255823706 23.52932612 0.953582916 1.067123709 0.159216856 0.082472333 400.0569963 1676088.067 0.010909555 0.124320024 5.55E-08 7.255823706 0.113540793 EHVIEALR ddPTM_HeLa_Romidepsin_16h_R1 2 EHVIEALR 8 0 F8W7C6;A0A087WV22;X1WI28;P27635;H7C123;H7C2C5 F8W7C6 RPL10 60S ribosomal protein L10 0 0 ; ; 118.5 0.0090525 21726000 9820 9619.3 10811.9 9265.5 11353.2 12605.3 8827.2 10116.4 9305.8 9472.5 FALSE FALSE TRUE 9700.310063 9754.720758 11000.07658 10336.82071 10773.80384 11799.86201 9576.982148 10409.10207 8473.465941 9226.403084 1.051364218 1.057261499 1.192238891 1.120352169 1.167714411 1.278923314 1.037997371 1.128186356 0.91839321 1 13.17155261 -9.906193858 4.437328045 1.025464983 1.153467711 0.531455334 0.067452777 0.131562338 4.685629662 0.009634224 0.012766843 1.24E-10 9.906193858 0.128002729 EHVIEALRR ddPTM_HeLa_Romidepsin_16h_R1 1 EHVIEALRR 9 1 F8W7C6;A0A087WV22;X1WI28;P27635;H7C123;H7C2C5 F8W7C6 RPL10 60S ribosomal protein L10 0 0 92.051 0.0030999 0 1889.8 1794.3 2137.5 2352.5 2456.7 2158.5 1837.9 1522.6 1915.5 1772.2 FALSE FALSE TRUE 1866.766391 1819.560202 2174.702291 2624.507119 2331.325432 2020.578816 1994.01118 1566.654029 1744.172883 1726.157989 1.081457435 1.054109887 1.259851245 1.520432739 1.350586358 1.170564241 1.155173045 0.907595967 1.010436411 1 10.7533488 -9.779727376 8.479712138 1.040554628 1.240482735 0.283482316 0.147731492 0.187930436 69.9476408 0.025093798 0.033508288 1.66E-10 9.779727376 0.199928108 EHYPVSSPS(ph)SPSPPAQPGGVSR ddPTM_HeLa_Romidepsin_16h_R1 1 EHYPVSSPSSPSPPAQPGGVSR 22 0 O75179-4;O75179-6;O75179-2;O75179;H0YM23;O75179-7 O75179-4 ANKRD17 Ankyrin repeat domain-containing protein 17 1 0 EHYPVS(0.032)S(0.013)PS(0.477)S(0.477)PSPPAQPGGVSR 234.62 1.54E-53 5574700 2027.1 2173.8 2182.8 1833.5 2262.6 2176.3 1878.3 1840 2636.4 2233.4 TRUE FALSE FALSE 2002.392925 2204.402813 2220.790718 2045.497897 2147.131079 2037.241454 2037.842755 1893.237497 2400.593781 2175.375946 0.920481321 1.01334338 1.020876747 0.940296274 0.987016099 0.936500864 0.936777277 0.870303591 1.103530535 1 11.08704903 -6.9299382 1.022289783 0.969673609 0.75608358 0.293110762 0.052439832 2.646765351 1.370524703 0.00579186 0.724083942 1.18E-07 6.9299382 -0.213590029 EHYVDLK ddPTM_HeLa_Romidepsin_16h_R1 2 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 0 ; ; 104.37 0.015259 252510000 39065 37837 37396 22500.7 36561 38732 33853 33726 38492 36854 FALSE FALSE TRUE 38588.86075 38369.67028 38046.86169 25102.3368 34695.15574 36257.1502 36728.47298 34701.8086 35049.17912 35896.52777 1.075002602 1.068896427 1.059903675 0.699297073 0.966532361 1.010046165 1.023176203 0.966717695 0.97639469 1 15.13155668 EIAEAYLGK ddPTM_HeLa_Romidepsin_16h_R1 1 EIAEAYLGK 9 0 P11142;E9PKE3;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 114.89 0.013688 287850 203.69 235.56 287.84 233.85 355.65 309.46 272.18 177.17 368.97 312.21 FALSE FALSE TRUE 201.2073479 238.8762199 292.8497345 260.8888373 337.4998534 289.6865047 295.2989624 182.2961344 335.9683991 304.0987392 0.661651372 0.785521902 0.96300871 0.857908316 1.109836411 0.952606727 0.971062765 0.599463631 1.104800368 1 8.248396025 -9.759984806 24.99562868 0.83165726 0.920594267 0 0.167992494 96.49070585 1658087.901 0.027334146 0.037479641 1.74E-10 9.759984806 0.088937007 EIDDTYIEDAADVDAR ddPTM_HeLa_Romidepsin_16h_R1 2 EIDDTYIEDAADVDAR 16 0 Q99459 Q99459 CDC5L Cell division cycle 5-like protein 0 0 ; ; 332.41 2.41E-202 20964900 5729.8 5522.6 5630.4 4148 5535.5 5591.4 5108.2 4948.3 6433.1 6216.9 FALSE FALSE TRUE 5659.962994 5600.347308 5728.39475 4627.611277 5253.002779 5234.127585 5542.09038 5091.471253 5857.707424 6055.384042 0.934699262 0.924854191 0.946000239 0.764214333 0.867492919 0.864375826 0.915233508 0.840817233 0.96735523 1 12.56400275 -10.38074287 0.597561515 0.988794389 0.857768755 0.53846409 0.044502256 0.371497103 0.298760963 0.014914396 0.016146588 4.16E-11 10.38074287 -0.131025634 EIDELIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EIDELIKK 8 1 A0A087X020;Q9Y3A5 A0A087X020 SBDS Ribosome maturation protein SBDS 0 1 EIDELIK(1)K 122.52 0.0014504 620860 420.23 323.96 302.01 246.07 652.69 592.18 441.57 597.05 752.27 542.1 FALSE TRUE FALSE 415.1080751 328.5207174 307.2663574 274.5217712 619.3807938 554.3416092 479.0769448 614.3246998 684.9850871 528.0161639 0.786165469 0.622179281 0.581926044 0.519911681 1.173033775 1.049857272 0.907314922 1.163458132 1.297280527 1 9.044438284 -8.722744139 24.99949211 0.823481548 1.059868889 0.260193664 0.222480017 182.487924 117897.5912 0.029168791 0.058336733 1.89E-09 8.722744139 0.236387341 EIDSELEAMT(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 EIDSELEAMTEK 12 0 Q8NF91;A0A0C4DG40;Q8NF91-4;Q8NF91-2;E7ENN3 Q8NF91 SYNE1 Nesprin-1 1 0 EIDSELEAMT(1)EK 108.98 0.027768 30082000 3086.3 2952.8 3176.7 1977.7 3136.7 3139.6 2644.4 3100 3062.3 3029.1 TRUE FALSE FALSE 3048.682988 2994.369596 3231.989131 2206.370979 2976.622494 2938.989693 2869.01527 3189.693609 2788.400218 2950.403545 1.033310509 1.014901707 1.095439685 0.747820068 1.008886564 0.996131427 0.972414528 1.081104181 0.945091129 1 11.52669658 EIEDFDSLEALR ddPTM_HeLa_Romidepsin_16h_R1 1 EIEDFDSLEALR 12 0 P46060;B0QYT5;B0QYT4 P46060 RANGAP1 Ran GTPase-activating protein 1 0 0 195.83 1.60E-09 5015400 2172 2097.9 2120.5 1043.7 1943.1 2296.3 1858.1 2061 2231.4 1993.8 FALSE FALSE TRUE 2145.526829 2127.434291 2157.406413 1164.377505 1843.936356 2149.573841 2015.926968 2120.631783 2031.817995 1942.000789 1.104802244 1.095485802 1.110919432 0.599576227 0.949503402 1.106886183 1.038067018 1.091982967 1.04624983 1 10.92332807 EIEELQSQAQALS(ph)QEGK ddPTM_HeLa_Romidepsin_16h_R1 1 EIEELQSQAQALSQEGK 17 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 EIEELQSQAQALS(1)QEGK 300.54 4.80E-132 0 1619.7 1431.5 1604.2 1440.2 1859.4 2367.8 2156 2336.9 1463.1 1447.1 TRUE FALSE FALSE 1599.958473 1451.652695 1632.120428 1606.7227 1764.50788 2216.505222 2339.130586 2404.514514 1332.236672 1409.504133 1.135121519 1.029903113 1.157939441 1.139920531 1.251864282 1.572542548 1.659541488 1.705929381 0.945181103 1 10.46097199 -8.304012939 1.263037072 1.067503489 1.724205761 0.951930292 0.058679914 0.071933542 0.20806221 0.008916529 0.03682327 4.97E-09 8.304012939 0.656702272 EIEIDIEPTDKVER ddPTM_HeLa_Romidepsin_16h_R1 2 EIEIDIEPTDKVER 14 1 F8VSA6;E9PS38;S4R3E9;E9PL57;Q15843 F8VSA6 NEDD8;NEDD8-MDP1 NEDD8 0 0 ; ; 145.52 0.00070367 49411000 8581.6 7928.6 8260 8533.8 9843.3 9187.5 8031.3 9642.2 9541.7 9136.5 FALSE FALSE TRUE 8477.004158 8040.219039 8403.761835 9520.518109 9340.959671 8600.448401 8713.478422 9921.181844 8688.266454 8899.132413 0.952565235 0.903483471 0.944334958 1.069825424 1.049648352 0.966436727 0.979137967 1.11484821 0.976304886 1 13.11944898 -9.270928329 24.96069628 0.968025295 1.029717394 0.410906845 0.046768261 680.4832747 1790007.257 0.007673349 0.011813191 5.36E-10 9.270928329 0.061692099 EIEMS(ph)VDDDDINSSK ddPTM_HeLa_Romidepsin_16h_R1 3 EIEMSVDDDDINSSK 15 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 0 EIEMS(1)VDDDDINSSK;EIEMS(1)VDDDDINSSK;EIEMS(1)VDDDDINSSK ;; 140.77 0.0010376 32886200 14709.9 14889.4 14589.3 13568.36 14992.6 13500.7 11913.44 12049.3 16015.2 14416.5 TRUE FALSE FALSE 14530.61008 15099.01336 14843.22065 15137.19762 14227.47168 12638.04884 12925.3673 12397.92748 14582.7604 14041.95725 1.034799481 1.075278403 1.057062088 1.0779977 1.013211436 0.900020461 0.920481886 0.882920184 1.038513374 1 13.77745642 -8.295088573 4.765317087 1.029432841 0.902288583 0.853763583 0.02646702 0.070546305 4.061276792 0.004660561 0.011081332 5.07E-09 8.295088573 -0.127144258 EIEMSVDDDDINS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 EIEMSVDDDDINSSK 15 0 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 1 0 EIEMSVDDDDINS(0.859)S(0.141)K 88.224 0.024401 3846100 2437.3 1952.2 2926.2 1708.8 3172.1 3089.8 1973.6 2296 2275.1 1911.8 TRUE FALSE FALSE 2407.59325 1979.683123 2977.129284 1906.379496 3010.2159 2892.371752 2141.237535 2362.431138 2071.609358 1862.13116 1.292923561 1.063127649 1.598775289 1.023762201 1.616543434 1.553258875 1.149885454 1.268670643 1.112493793 1 10.86273898 -12.15906219 0.375440669 0.897840992 1.36028954 0.222762659 0.201900591 2.392867042 0.469772914 0.453458055 0.077129383 6.93E-13 12.15906219 0.462448548 EIEPNY(ph)ESPSSNNQDKDSSQASK ddPTM_HeLa_Romidepsin_16h_R1 1 EIEPNYESPSSNNQDKDSSQASK 23 1 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 EIEPNY(0.525)ES(0.42)PS(0.044)S(0.011)NNQDKDSSQASK 82.189 0.00072266 8666800 1115.1 904.32 1025.3 835.84 1006.7 1212.2 1024.3 1068.1 1003.4 884.61 TRUE FALSE FALSE 1101.508732 917.0510407 1043.144916 932.4837535 955.3243425 1134.744332 1111.304016 1099.003788 913.6533909 861.6277047 1.278404497 1.064323995 1.210667799 1.08223511 1.108743762 1.316977537 1.289772846 1.275497274 1.060380703 1 9.750920829 -12.45935562 1.061468806 0.993723937 1.206219327 0.377691822 0.087846049 0.443851879 0.850628843 0.073981464 0.016224965 3.47E-13 12.45935562 0.21249539 EIES(ph)LKS(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EIESLKSSK 9 1 Q14789-4;Q14789-3;Q14789;Q14789-2;E7EU81 Q14789-4 GOLGB1 Golgin subfamily B member 1 3 0 EIES(1)LKS(1)S(1)K 109.86 0.00044082 0 927.33 1043.9 810.76 636.07 847.68 952.43 700.36 982.49 871.87 1177.4 TRUE FALSE FALSE 916.0273453 1058.596052 824.8709377 709.6154062 804.4197265 891.5727968 759.8485609 1010.916798 793.8877636 1146.810978 0.79876053 0.923078059 0.719273667 0.61877277 0.701440553 0.777436573 0.662575242 0.881502547 0.692256857 1 10.16341191 -11.63367303 0.412968722 1.033522243 0.724560143 0 0.126224546 0.821753874 0.264867655 0.1087289 0.032997366 2.32E-12 11.63367303 -0.3089621 EIES(ph)SPQYR ddPTM_HeLa_Romidepsin_16h_R1 2 EIESSPQYR 9 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 EIES(0.499)S(0.499)PQY(0.002)R;EIES(0.5)S(0.5)PQYR ; 129.88 0.0083368 343440000 12495.1 11950.3 11569.6 10520.1 12819.1 13301.4 12228.2 11750.1 11831.4 10664.3 TRUE FALSE FALSE 12342.80492 12118.53664 11770.96403 11736.48346 12164.89349 12451.48347 13266.863 12090.0706 10773.16995 10387.23995 1.188266082 1.166675334 1.133213837 1.129894324 1.1711382 1.19872878 1.27722697 1.163934853 1.03715424 1 13.34252474 -16.52287875 0.21820966 0.0325667 1.209013675 0.725560405 0.039464722 17.5603592 0.221704685 7.234366989 0.033578274 3.00E-17 16.52287875 1.176446975 EIESEIDS(ph)EEELINK ddPTM_HeLa_Romidepsin_16h_R1 3 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 EIESEIDS(1)EEELINK;EIES(0.154)EIDS(0.846)EEELINK;EIES(0.346)EIDS(0.654)EEELINK ;; 304.86 6.84E-135 79914000 10487.1 9770.5 10356.5 10023.4 10169 8991.4 8136.1 8313.8 11560.3 10014.4 TRUE FALSE FALSE 10359.27919 9908.049355 10536.75054 11182.35267 9650.037984 8416.878558 8827.180131 8554.346686 10526.31781 9754.224444 1.062030021 1.015770081 1.080224327 1.146411253 0.989318837 0.862895723 0.904959711 0.876988912 1.079154768 1 13.25181145 -8.410867879 4.454259544 1.041290778 0.885212337 0.776899683 0.042583198 0.095053661 3.065359755 0.006678463 0.015337876 3.88E-09 8.410867879 -0.156078441 EIESEIDS(ph)EEELINKK ddPTM_HeLa_Romidepsin_16h_R1 2 EIESEIDSEEELINKK 16 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 EIESEIDS(1)EEELINKK;EIES(0.004)EIDS(0.996)EEELINKK ; 103.88 0.001359 6838300 1481.71 1303.23 1338.49 1509.32 1393.49 1285.98 1305.61 1203.39 1419.33 1467.53 TRUE FALSE FALSE 1463.650349 1321.576906 1361.785857 1683.83468 1322.375005 1203.810028 1416.508481 1238.208191 1292.38157 1429.403359 1.02395894 0.924565412 0.952695297 1.177998267 0.925123757 0.842176577 0.990978839 0.866241277 0.904140572 1 10.48119737 -8.547944578 24.99780016 1.011548415 0.904705641 0.231488046 0.079618825 182.2991926 181803.669 0.009833197 0.019666925 2.83E-09 8.547944578 -0.106842774 EIESEIDSEEELINK ddPTM_HeLa_Romidepsin_16h_R1 2 EIESEIDSEEELINK 15 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 0 ; ; 273.24 4.90E-84 5164200 2061.41 2186.23 2266.45 2376.14 2157.08 2405.78 1609.26 1751.41 2602.21 2435.16 FALSE FALSE TRUE 2036.284742 2217.007803 2305.896612 2650.880487 2046.996158 2252.058422 1745.950504 1802.084285 2369.46182 2371.894192 0.858505725 0.934699284 0.972175158 1.117621729 0.8630217 0.949476764 0.736099658 0.759765883 0.998974502 1 11.21182394 -7.762528129 24.9991103 0.943778665 0.747932714 0.578537427 0.071710047 16.52588022 379505.1486 0.011005167 0.036008711 1.73E-08 7.762528129 -0.195845951 EIGSST(ph)SSSSETVVK ddPTM_HeLa_Romidepsin_16h_R1 2 EIGSSTSSSSETVVK 15 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 0 EIGSS(0.001)T(0.867)S(0.036)S(0.026)S(0.026)S(0.036)ET(0.008)VVK;EIGSS(0.102)T(0.884)S(0.006)SSS(0.006)ETVVK ; 290.34 5.85E-116 12451800 2339.8 2355.4 2301.68 3580.6 3474.4 4097.9 3042.3 3582.9 2701.2 2393.36 TRUE FALSE FALSE 2311.281618 2388.559383 2341.739775 3994.605819 3297.088403 3836.057415 3300.712886 3686.565559 2459.597907 2331.180162 0.991464176 1.024613808 1.004529728 1.71355517 1.414343025 1.645543093 1.41589781 1.581415979 1.05508701 1 11.18684479 -9.273087947 24.87273581 0.99905452 1.543780506 0.903271341 0.088082327 122.0694817 260649.814 0.011488237 0.017639054 5.33E-10 9.273087947 0.544725986 EIHQFNR ddPTM_HeLa_Romidepsin_16h_R1 1 EIHQFNR 7 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 129.4 0.0081757 2767200 1711.4 1889.2 2500.6 1601.6 1927.2 2234.5 2176.7 829.6 2222.5 1555.2 FALSE FALSE TRUE 1690.540799 1915.796207 2544.121894 1786.784528 1828.847793 2091.722662 2361.588844 853.6031671 2023.714034 1514.79568 1.116019026 1.264722519 1.679514886 1.179554808 1.207323085 1.380861254 1.559014774 0.563510431 1.335965015 1 10.5649075 -10.43184812 2.623546823 1.04634781 1.288280082 0 0.294244514 0.400533765 5.241557234 0.047970224 0.053556773 3.70E-11 10.43184812 0.241932272 EIIKQEES(ph)VDPDYWEK ddPTM_HeLa_Romidepsin_16h_R1 1 EIIKQEESVDPDYWEK 16 1 Q14839-2;A0A2R8Y8C1;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2R8YFD8;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8Y445;A0A2R8YER1;A0A2R8YDJ9;A0A2R8YD40;A0A2R8Y5Z7;Q14839;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y5M9;A0A2R8YE38 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 0 EIIKQEES(0.603)VDPDY(0.397)WEK 68.944 0.015846 9040700 2339.8 2008.1 2547.6 2077.5 2253.1 2718.4 2529.3 2387.1 2101.8 2132.2 TRUE FALSE FALSE 2311.281618 2036.370085 2591.939909 2317.710325 2138.1159 2544.703013 2744.138679 2456.166972 1913.809744 2076.805137 1.112902495 0.980530166 1.248041939 1.115997974 1.029521673 1.225296957 1.321326989 1.182666072 0.92151628 1 11.02015014 -4 0.13025656 0.964578409 1.944455407 0.497889022 0.087664541 54.56736561 0.479137593 0.278365031 9.862591696 1.00E-04 4 0.979876998 EIKLPTEMEGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EIKLPTEMEGKK 12 2 Q9NWX6 Q9NWX6 THG1L Probable tRNA(His) guanylyltransferase 0 1 ; EIKLPTEMEGK(1)K;EIKLPTEMEGK(1)K 98.368 0.0028946 13016600 2233.26 2114.2 1754.26 3254.9 2137.42 1362.94 1492.81 1408.7 2132.29 1777.38 FALSE TRUE FALSE 2206.040168 2143.963763 1784.792159 3631.246853 2028.339482 1275.852533 1619.609244 1449.458512 1941.572642 1731.203411 1.27428132 1.238423948 1.030954622 2.097527552 1.171635562 0.736974364 0.935539541 0.837254884 1.121516183 1 10.75755953 -8.313405531 7.776137509 1.210374105 0.846851508 0.295025592 0.299584108 0.339505112 46.43176986 0.044936207 0.10121148 4.86E-09 8.313405531 -0.363522597 EILS(ph)PVDIIDR ddPTM_HeLa_Romidepsin_16h_R1 2 EILSPVDIIDR 11 0 A0A286YF41;A0A286YEZ7;A0A286YES4;O14495 A0A286YF41 PPAP2B Lipid phosphate phosphohydrolase 3 1 0 EILS(1)PVDIIDR;EILS(1)PVDIIDR ; 130.1 0.0026959 1040300 834.4 1031.73 811.83 616.55 1301.78 1360.14 856.59 1330.11 1066.12 1027.64 TRUE FALSE FALSE 824.2300119 1046.254722 825.9595606 687.838412 1235.345309 1273.231444 929.3487332 1368.594634 970.7635571 1000.941765 0.823454512 1.045270323 0.825182433 0.68719124 1.234182999 1.272033487 0.928474329 1.367306953 0.969850186 1 9.967142324 -8.737611906 24.98957055 0.903449268 1.18617876 0.529143745 0.142137722 153.4622589 160946.0723 0.020379516 0.040741696 1.83E-09 8.737611906 0.282729492 EILSEVER ddPTM_HeLa_Romidepsin_16h_R1 1 EILSEVER 8 0 B4DUR8;P49368-2;P49368 B4DUR8 CCT3 T-complex protein 1 subunit gamma 0 0 176.09 0.0022767 15300000 4605.5 3912.8 4634.8 4136.7 4760.8 4543.6 3633.3 3930.2 4721.9 4532.5 FALSE FALSE TRUE 4549.366395 3967.884501 4715.46675 4615.004718 4517.838611 4253.278624 3941.912411 4043.914136 4299.561438 4414.744997 1.030493584 0.898779998 1.068117582 1.04536156 1.023352111 0.963425663 0.892896966 0.916001749 0.973909352 1 12.10811439 -7.979489567 3.277059123 1.012676475 0.90484842 0.446696058 0.044283299 0.141975769 3.160721716 0.005907698 0.019391693 1.05E-08 7.979489567 -0.107828055 IPMTPTSSFVSPPPPTAS(ph)PHSNR ddPTM_HeLa_Romidepsin_16h_R1 2 IPMTPTSSFVSPPPPTASPHSNR 23 0 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 0 IPMTPTSSFVS(0.001)PPPPT(0.243)AS(0.666)PHS(0.09)NR;IPMTPT(0.004)S(0.022)S(0.02)FVS(0.071)PPPPT(0.172)AS(0.538)PHS(0.172)NR ; 112.75 2.76E-06 113725000 1933.59 1841.97 1987.15 1265.64 987.94 767.29 959.91 911.77 2106.92 1935.81 TRUE FALSE FALSE 1910.022661 1867.901302 2021.735512 1411.979252 937.5217353 718.2626453 1041.444731 938.1506264 1918.471798 1885.517377 1.012996584 0.990657166 1.072244434 0.748855072 0.497222538 0.380936635 0.552338973 0.497556075 1.017477654 1 10.88074473 -8.973449389 2.736981827 1.009145824 0.477482554 0.965674849 0.047617281 0.03254974 0.494952373 0.007071509 0.01333757 1.06E-09 8.973449389 -0.53166327 down EIPEDVDMEEEKES(ph)EDS(ph)DEENDFTEK ddPTM_HeLa_Romidepsin_16h_R1 2 EIPEDVDMEEEKESEDSDEENDFTEK 26 1 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 2 0 EIPEDVDMEEEKES(0.899)EDS(0.899)DEENDFT(0.202)EK;EIPEDVDMEEEKES(0.975)EDS(0.975)DEENDFT(0.049)EK ; 52.79 0.0042376 5596700 3696.4 3500.5 4139.6 3338 3208.7 2985 2487.09 3354.1 3633.3 3628.5 TRUE FALSE FALSE 3651.346855 3549.780131 4211.648002 3723.955266 3044.948066 2794.268134 2698.343363 3451.145592 3308.328548 3534.231047 1.033137564 1.004399566 1.191673081 1.053681895 0.861558858 0.790629729 0.763488104 0.976491221 0.93608157 1 11.78718064 -8.713475735 5.711746847 1.032151249 0.835375357 0.568541016 0.080231772 0.099353592 7.315319209 0.010890496 0.021770784 1.93E-09 8.713475735 -0.196775892 EIPSATQS(ph)PISK ddPTM_HeLa_Romidepsin_16h_R1 4 EIPSATQSPISK 12 0 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 EIPS(0.001)AT(0.006)QS(0.981)PIS(0.012)K;EIPS(0.016)AT(0.001)QS(0.983)PISK;EIPS(0.001)AT(0.001)QS(0.996)PIS(0.002)K;EIPS(0.018)AT(0.088)QS(0.578)PIS(0.317)K ;;; 203.11 7.45E-15 1018670000 23136.6 23405.2 23076 19348.8 17163.5 14686.7 13806.7 13548.6 23131.5 20139.3 TRUE FALSE FALSE 22854.60222 23734.69902 23477.6281 21585.99929 16287.58255 13748.26727 14979.44075 13940.60736 21062.56071 19616.07808 1.165095394 1.209961488 1.196856375 1.100423806 0.830317991 0.700867279 0.763630767 0.710672506 1.073739644 1 14.25974901 -8.667764939 3.476172232 1.102752462 0.732793151 0.897036887 0.062327854 0.076695926 1.816527984 0.012757876 0.026590511 2.15E-09 8.667764939 -0.369959311 EIPSATQS(ph)PISKK ddPTM_HeLa_Romidepsin_16h_R1 1 EIPSATQSPISKK 13 1 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 EIPS(0.01)AT(0.417)QS(0.495)PIS(0.078)KK 83.404 0.010083 42095000 6468.7 6434.8 5743.7 6745.7 4246.9 3475.5 3155.8 3627.3 6247.2 6036.4 TRUE FALSE FALSE 6389.856996 6525.389283 5843.666689 7525.669573 4030.164846 3253.426767 3423.853573 3732.250203 5688.434786 5879.573458 1.086789211 1.109840591 0.993892964 1.279968628 0.685451908 0.553344012 0.582330266 0.634782477 0.967491065 1 12.52149578 -8.62592571 6.257159466 1.058132034 0.594470346 0.875018765 0.085360456 0.048490242 2.56213128 0.011552452 0.023272517 2.37E-09 8.62592571 -0.463661688 EIPYTFEDR ddPTM_HeLa_Romidepsin_16h_R1 3 EIPYTFEDR 9 0 G3V2Y4;H0YIZ0;P34897-3;P34897-2;P34897 G3V2Y4 SHMT2 "Serine hydroxymethyltransferase;Serine hydroxymethyltransferase, mitochondrial" 0 0 ;; ;; 209.19 7.11E-13 32268300 4323.6 4072.8 4253.9 3854.2 4141.1 4591.3 4265.8 4020.3 4610 4069.7 FALSE FALSE TRUE 4270.9023 4130.136985 4327.937345 4299.840739 3929.764214 4297.930748 4628.136946 4136.621038 4197.670054 3963.968607 1.077430909 1.041919701 1.091819279 1.084731279 0.991371175 1.084249441 1.167551362 1.043555448 1.058956432 1 11.95272982 -16.52287875 0.201986505 0.637371579 1.088897169 0.062385676 0.046254844 46.20343867 0.563588781 6.593217061 0.042603253 3.00E-17 16.52287875 0.45152559 EIQNGNLHES(ph)DSESVPR ddPTM_HeLa_Romidepsin_16h_R1 2 EIQNGNLHESDSESVPR 17 0 Q86UP2-2;Q86UP2-3;Q86UP2-4;Q86UP2 Q86UP2-2 KTN1 Kinectin 1 0 EIQNGNLHES(0.967)DS(0.033)ESVPR;EIQNGNLHES(0.966)DS(0.034)ESVPR ; 203.64 1.42E-19 56801000 5292.3 8192.2 6140.6 3259.36 5507.5 7691.4 4222.2 8223.7 7412.8 8017 TRUE FALSE FALSE 5227.795412 8307.530007 6247.474567 3636.222539 5226.431724 7199.944363 4580.833563 8461.639785 6749.780602 7808.717184 0.669481976 1.063878971 0.800064136 0.465661959 0.66930734 0.92203933 0.586630743 1.083614579 0.864390455 1 12.93086985 -12.49801154 1.116285486 1.006500144 0.764735221 0.06628509 0.193008562 0.742242669 1.580559695 0.146213563 0.03174653 3.18E-13 12.49801154 -0.241764923 EIQTAVR ddPTM_HeLa_Romidepsin_16h_R1 1 EIQTAVR 7 0 P06899;P23527;Q96A08;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 0 122.18 0.0031756 0 2831.4 2705.5 3071.6 3369.9 3187.6 3803 3734.8 1198.4 3146.8 2537.1 FALSE FALSE TRUE 2796.889808 2743.5881 3125.05991 3759.543694 3024.924877 3560.000574 4052.033819 1233.073813 2865.342327 2471.185776 1.131800707 1.110231423 1.264599343 1.52135211 1.224078297 1.440604186 1.639712343 0.498980621 1.159500979 1 11.27098776 -9.804718124 3.141684228 1.064407476 1.302010447 0.060517942 0.291591581 0.375074789 7.611117628 0.044069676 0.060627832 1.57E-10 9.804718124 0.237602971 EIRINMS(ph)CAVFITMNPR ddPTM_HeLa_Romidepsin_16h_R1 1 EIRINMSCAVFITMNPR 17 1 Q0VDD8-4;Q0VDD8 Q0VDD8-4 DNAH14 "Dynein heavy chain 14, axonemal" 1 0 EIRINMS(1)CAVFITMNPR 55.031 0.029949 9911100 4401.5 4680.8 4485.8 3662 4619.5 4639.7 4022.9 4815.4 4721.4 4664.2 TRUE FALSE FALSE 4347.852825 4746.696425 4563.873467 4085.41767 4383.749677 4343.238144 4364.605026 4954.726002 4299.106159 4543.023412 0.957039494 1.044832041 1.004589467 0.899272863 0.964941027 0.95602372 0.96072695 1.090623039 0.946309488 1 12.14943702 -7.597153811 0.001225203 1.446346903 0.512842519 0 0.052000366 5241730.274 1176.713361 444954.7687 451622.3523 2.53E-08 7.597153811 -0.933504384 EIS(ph)DDEAEEEK ddPTM_HeLa_Romidepsin_16h_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 0 EIS(1)DDEAEEEK;EIS(1)DDEAEEEK ; 234.3 8.34E-37 59922000 5957.8 6038.8 6326.2 2384.6 5988.5 6964.3 5853.6 5978 5541.1 6429.5 TRUE FALSE FALSE 5885.184042 6123.814385 6436.304857 2660.318672 5682.884499 6519.303706 6350.804638 6150.963998 5045.490138 6262.460663 0.93975585 0.977860735 1.027759726 0.424804053 0.907452327 1.041013119 1.014106911 0.98219603 0.805672149 1 12.61251392 EIS(ph)DDEAEEEKGEK ddPTM_HeLa_Romidepsin_16h_R1 2 EISDDEAEEEKGEK 14 1 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 0 EIS(1)DDEAEEEKGEK;EIS(1)DDEAEEEKGEK ; 206.63 2.93E-16 46533000 4284.4 5205.6 5186.5 1425.71 4536.4 5045.5 3834.4 4338.7 4546.6 5475.3 TRUE FALSE FALSE 4232.180085 5278.884573 5276.768857 1590.557298 4304.89058 4723.108834 4160.09384 4464.233439 4139.940709 5333.050917 0.793575788 0.989843273 0.989446555 0.298245286 0.807209728 0.885629803 0.780058902 0.837088096 0.776279989 1 12.38074539 -12.58900568 0.344260502 1.104782797 0.769681871 0 0.193870842 5.658346142 0.734853198 0.741545222 0.079929462 2.58E-13 12.58900568 -0.335100926 EIS(ph)PGSGPGEIR ddPTM_HeLa_Romidepsin_16h_R1 2 EISPGSGPGEIR 12 0 O43491;O43491-4;E9PHY5;E9PK52;H0Y5B0;Q6R5J7;E9PMV8;E9PMG5 O43491 EPB41L2 Band 4.1-like protein 2 1 0 EIS(1)PGSGPGEIR;EIS(0.908)PGS(0.092)GPGEIR ; 196.02 1.44E-10 82600000 4404.4 3918.7 4059.3 3451.8 5055 5585.6 5183.3 5814.3 4391.7 3996.6 TRUE FALSE FALSE 4350.717479 3973.867561 4129.950414 3850.913357 4797.024487 5228.698187 5623.569373 5982.527597 3998.895353 3892.767756 1.117641162 1.020833456 1.060929054 0.989248164 1.232291467 1.34318267 1.444619799 1.536831368 1.027262761 1 11.92658056 -8.214733482 1.392015634 1.049556526 1.511089604 0.937528163 0.047565331 0.092980176 0.327049398 0.008560015 0.036007113 6.10E-09 8.214733482 0.461533078 EIS(ph)QDSLAAR ddPTM_HeLa_Romidepsin_16h_R1 2 EISQDSLAAR 10 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0YKB1 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 EIS(0.74)QDS(0.26)LAAR;EIS(0.879)QDS(0.121)LAAR ; 106.26 0.020482 7030000 4759.1 4975.5 4649.5 3483.6 4054.7 4532.9 3840.1 4433.8 4186.6 4511.1 TRUE FALSE FALSE 4701.094259 5045.54522 4730.422597 3886.390223 3847.773529 4243.262319 4166.277998 4562.085008 3812.14001 4393.900972 1.069913566 1.148306539 1.07658835 0.884496544 0.87570784 0.965716421 0.948195698 1.038276702 0.867598072 1 12.10128664 -9.270329717 24.82308338 1.047305351 0.940377753 0.230973249 0.07980893 446.9257779 1247878.376 0.009771963 0.01506307 5.37E-10 9.270329717 -0.106927598 EISELNETFLS(ph)DSEK ddPTM_HeLa_Romidepsin_16h_R1 1 EISELNETFLSDSEK 15 0 Q8IWJ2;B8ZZW2 Q8IWJ2 GCC2 GRIP and coiled-coil domain-containing protein 2 1 0 EISELNETFLS(0.5)DS(0.5)EK 97.597 0.0096417 9639300 1336.5 1030.2 1106 1106.7 1355.9 1583.9 1102.1 1385.5 1748.9 1132.4 TRUE FALSE FALSE 1320.210224 1044.703183 1125.249466 1234.661861 1286.703363 1482.693902 1195.712346 1425.587257 1592.474004 1102.980085 1.196948378 0.947164139 1.020190193 1.119387266 1.166569897 1.344261716 1.084074285 1.292486851 1.443792164 1 10.10719103 -8.714080183 2.947504193 1.077436375 1.227526075 0.070996315 0.14658399 0.245025286 4.33720629 0.015302941 0.031984163 1.93E-09 8.714080183 0.150089701 EISLWFKPEELVDYK ddPTM_HeLa_Romidepsin_16h_R1 1 EISLWFKPEELVDYK 15 1 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 0 168 3.38E-05 2469500 2009.4 1960 1678.6 1318.7 1731.9 1835.6 1585.5 1689.1 1936.9 1420.5 FALSE FALSE TRUE 1984.90866 1987.592931 1707.815329 1471.174299 1643.51468 1718.311084 1720.17233 1737.971444 1763.658813 1383.595205 1.434602153 1.436542223 1.234331633 1.063298205 1.187858034 1.24191749 1.243262714 1.256127108 1.274692776 1 10.4342062 -12.56427782 1.370807495 1.0015236 1.279796602 0 0.133181976 0.340105627 1.155349604 0.085873335 0.020674141 2.73E-13 12.56427782 0.278273003 EISPGS(ph)GPGEIR ddPTM_HeLa_Romidepsin_16h_R1 1 EISPGSGPGEIR 12 0 O43491;O43491-4;E9PHY5;E9PK52;H0Y5B0;Q6R5J7;E9PMV8;E9PMG5 O43491 EPB41L2 Band 4.1-like protein 2 1 0 EIS(0.382)PGS(0.618)GPGEIR 133.88 0.0029415 29902000 2225.7 2230.9 1765.6 1664.1 2306 2657 2179.9 2099.3 1899.6 2115.8 TRUE FALSE FALSE 2198.572312 2262.306669 1796.329527 1856.511072 2188.316215 2487.226275 2365.060652 2160.039933 1729.695018 2060.831211 1.066837643 1.097764172 0.871652913 0.900855471 1.061860963 1.206904409 1.147624628 1.048140149 0.83931911 1 11.00901063 -8.515057567 24.90114488 1.014920576 1.135366476 0.336089585 0.093289755 317.0988315 1009581.438 0.011672316 0.024227466 3.05E-09 8.515057567 0.1204459 EISS(ph)SPTSK ddPTM_HeLa_Romidepsin_16h_R1 2 EISSSPTSK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 EIS(0.001)S(0.963)S(0.035)PTSK;EIS(0.294)S(0.543)S(0.162)PT(0.001)SK ; 157.78 0.0040613 41391000 10608.7 12294.5 21180.6 10448 7020.9 8491 18516.5 3009.3 20546.4 16198.8 TRUE FALSE FALSE 10479.39708 12467.58229 21549.23946 11656.04692 6662.597274 7948.452503 20089.29105 3096.369348 18708.67852 15777.95284 0.66417977 0.79019011 1.365781713 0.73875534 0.422272607 0.503769569 1.273250798 0.196246584 1.185748158 1 13.94562241 -9.004570028 24.90873293 0.876475616 0.632791668 0.210351974 0.326277096 322.9820885 1760418.688 0.045806082 0.081516236 9.90E-10 9.004570028 -0.243683947 EITALAPS(ph)TMK ddPTM_HeLa_Romidepsin_16h_R1 2 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P63267;P68133;P68032;P62736;A6NL76 P60709;P63261;P63267 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 0 EITALAPS(0.946)T(0.054)MK;EITALAPS(0.862)T(0.138)MK ; 105.36 0.023022 293000000 16752 15861.7 14768.7 12568.4 18287.3 18969.9 18141 19060.7 15996.6 14382.3 TRUE FALSE FALSE 16547.82018 16085.00143 15025.74303 14021.61754 17354.03084 17757.78461 19681.89609 19612.19128 14565.82403 14008.64577 1.181257664 1.148219585 1.072604966 1.000925983 1.238808599 1.267630355 1.404982067 1.400006225 1.039773885 1 13.77402988 -8.23306699 1.576286692 1.087096128 1.404164024 0.803048402 0.063792523 0.167247998 0.774126652 0.012180856 0.045537991 5.85E-09 8.23306699 0.317067896 EITALAPSTMK ddPTM_HeLa_Romidepsin_16h_R1 4 EITALAPSTMK 11 0 P60709;P63267-2;A0A2R8YFE2;P63261;P63267;P68133;P68032;P62736;A6NL76 P60709;P63261;P63267 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 0 ;;; ;;; 175.65 1.09E-06 10288600 4543.05 3472.04 4104.78 3323.55 4371.71 5127.77 4464.7 3711.49 4289.11 3730.45 FALSE FALSE TRUE 4487.677559 3520.91947 4176.221974 3707.834489 4148.605326 4800.122046 4843.931507 3818.876107 3905.481259 3633.532371 1.235072954 0.969007321 1.149355929 1.020449004 1.141755433 1.321062139 1.333119128 1.051009243 1.074844218 1 11.82715704 -12.51918473 1.176324643 0.996769648 1.162615878 0.120877944 0.116133832 0.656500975 1.57368707 0.091469783 0.020257211 3.03E-13 12.51918473 0.16584623 EITALAPSTMK(ac)IK ddPTM_HeLa_Romidepsin_16h_R1 2 EITALAPSTMKIK 13 1 P60709;P63267-2;A0A2R8YFE2;P63261;P63267;P68133;P68032;P62736;A6NL76 P60709;P63261;P63267 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 1 ; EITALAPSTMK(1)IK;EITALAPSTMK(1)IK 128.85 0.00075707 4238800 2045.32 1410.97 2365.7 2296.36 2854.6 2599.8 1864.73 2014.2 1726.18 1642.53 FALSE TRUE FALSE 2020.390853 1430.833673 2406.874016 2561.875948 2708.91911 2433.68117 2023.12012 2072.477699 1571.786138 1599.856834 1.262857282 0.894351071 1.504430875 1.601315751 1.693225952 1.521186846 1.264563226 1.295414474 0.982454245 1 10.64372709 -9.741048154 24.99762996 1.11036211 1.487304798 0.651747573 0.155478257 142.5887766 174799.4873 0.027293419 0.038572449 1.82E-10 9.741048154 0.376942688 LQANGPVAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LQANGPVAKK 10 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2;S4R3C2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ; LQANGPVAK(1)K;LQANGPVAK(1)K 162.97 0.0029998 10869800 4039.2 4515.8 4424.3 5405.7 7016.2 7548.1 6946.4 7144.3 3811.9 3659.8 FALSE TRUE FALSE 3989.968677 4579.373551 4501.303086 6030.732469 6658.137133 7065.80077 7536.427043 7351.009049 3470.954117 3564.717868 1.11929438 1.284638426 1.262737544 1.691783948 1.867787965 1.982148667 2.114172095 2.062157321 0.973696726 1 11.79957218 -9.105426813 0.790401912 1.041577298 2.128528116 0.98185868 0.058080859 0.052504479 0.063391341 0.010617968 0.02870045 7.84E-10 9.105426813 1.086950818 up EIVHLQAGQCGNQIGAK ddPTM_HeLa_Romidepsin_16h_R1 2 EIVHLQAGQCGNQIGAK 17 0 P04350;M0QYM7;M0R0X0;M0QY85;M0QY37;M0QX14;M0R042;M0R2D3;M0QZL7;M0R278;M0R2T4;P68371 P04350;P68371 TUBB4A;TUBB4B Tubulin beta-4A chain;Tubulin beta-4B chain 0 0 ; ; 204.23 1.63E-22 3472700 1494.22 1425.77 1505.77 439.67 1446.75 1652.71 1303.82 1172.01 1438.12 1548.16 FALSE FALSE TRUE 1476.007872 1445.842027 1531.977295 490.5067141 1372.916949 1547.107165 1414.566438 1205.92026 1309.490945 1507.93858 0.978824928 0.958820238 1.015941442 0.325282953 0.910459462 1.025974921 0.938079612 0.799714442 0.868398065 1 10.55836195 EIVLADVIDNDSWR ddPTM_HeLa_Romidepsin_16h_R1 2 EIVLADVIDNDSWR 14 0 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 0 ; ; 312.95 4.89E-151 28186000 4601.1 4786.3 4944.7 5034.4 5040.7 4158.8 4533.2 4310.8 5421.2 5093.5 FALSE FALSE TRUE 4545.020023 4853.681657 5030.760429 5616.501016 4783.45427 3893.066102 4918.249895 4435.526197 4936.314294 4961.170136 0.916118557 0.978334047 1.014026992 1.132091999 0.964178639 0.784707235 0.991348767 0.894048395 0.994989924 1 12.27646472 -8.496284731 24.90240745 0.979042498 0.895878978 0.306400464 0.071259044 883.664727 827456.2157 0.01088898 0.024272763 3.19E-09 8.496284731 -0.08316352 EK(ac)EELMER ddPTM_HeLa_Romidepsin_16h_R1 2 EKEELMER 8 1 P26038;A0A2R8Y7M3;A0A2R8Y5S7;P35241-4;P35241;P35241-5 P26038;A0A2R8Y7M3 MSN;RDX Moesin;Radixin 0 1 ; EK(1)EELMER;EK(1)EELMER 104.42 0.0051098 9532700 1341.21 1338.54 1415.25 1041.9 3807.5 3518.3 3028.2 1986.94 3430 2933.9 FALSE TRUE FALSE 1324.862817 1357.384001 1439.881833 1162.36938 3613.189067 3293.491985 3285.415232 2044.428974 3123.212209 2857.676855 0.463615336 0.474995624 0.50386447 0.406753261 1.264379862 1.152506792 1.149680457 0.71541643 1.092920007 1 11.48062707 -8.75381379 24.99939864 0.676682834 1.082009845 0.387590274 0.253730194 159.5985635 523216.5768 0.040702042 0.080177769 1.76E-09 8.75381379 0.405327011 EK(ac)EESMK(ac)ETLR ddPTM_HeLa_Romidepsin_16h_R1 1 EKEESMKETLR 11 2 H0YNP7;F5GWZ1;E9PFL3;A0A087WXI8;Q9BTZ2-6;Q9BTZ2-3;Q9BTZ2-2;Q9BTZ2-5;Q9BTZ2-8;Q9BTZ2-4;Q9BTZ2;P0CG22 H0YNP7 DHRS4;DHRS4L2;DHRS4L1 Dehydrogenase/reductase SDR family member 4;Putative dehydrogenase/reductase SDR family member 4-like 1 0 2 EK(1)EESMK(1)ETLR 42.095 0.028063 1006000 363.16 518.69 489.15 528.98 729.99 617.61 523.67 593.24 403.21 438.3 FALSE TRUE FALSE 358.7336662 525.9921314 497.6634506 590.1431565 692.7358863 578.1467142 568.1505167 610.4044634 367.1458877 426.9129028 0.840297081 1.232083003 1.165725953 1.382350247 1.622663269 1.354249802 1.330834728 1.429810295 0.860001854 1 8.737797956 -9.772460466 1.469142492 0.926556215 1.422083129 0.805412309 0.106971166 0.123388223 0.538359518 0.020325879 0.02979277 1.69E-10 9.772460466 0.495526914 EK(ac)EPIAASTNR ddPTM_HeLa_Romidepsin_16h_R1 2 EKEPIAASTNR 11 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 1 ; EK(1)EPIAASTNR;EK(1)EPIAASTNR 177.57 0.0001079 2724500 893.12 790.37 1277.4 808.74 2242.3 2199.12 2008.79 1440.26 1986.31 1271.94 FALSE TRUE FALSE 882.2343099 801.4968496 1299.632611 902.250324 2127.867064 2058.603329 2179.416572 1481.931651 1808.649459 1238.894815 0.712113974 0.646945035 1.049025789 0.72827032 1.717552642 1.661644963 1.759161912 1.196172292 1.45988944 1 10.27483799 -8.761178612 24.9999806 0.849723848 1.601743104 0.576505014 0.26752229 2.357804154 226001.6813 0.028196359 0.053694033 1.73E-09 8.761178612 0.752019256 EK(ac)LEMEMEAAR ddPTM_HeLa_Romidepsin_16h_R1 2 EKLEMEMEAAR 11 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; EK(1)LEMEMEAAR;EK(1)LEMEMEAAR 81.625 0.0092934 2457900 789.28 745.72 1165.34 604.48 1777.8 1259.07 1590.47 1383.35 2003.33 1315.69 FALSE TRUE FALSE 779.6599518 756.2182657 1185.622254 674.3728218 1687.072232 1178.61949 1725.564482 1423.37505 1824.147147 1281.508184 0.608392487 0.590100223 0.925177278 0.526233722 1.316474021 0.919712808 1.3465107 1.110703051 1.423437766 1 10.32362698 -8.751406236 24.99999528 0.783143242 1.167601817 0.243069716 0.270155812 145.6024162 362801.0528 0.029604206 0.058657942 1.77E-09 8.751406236 0.384458574 GSK(ac)K(ac)AVTK(ac)AQK ddPTM_HeLa_Romidepsin_16h_R1 2 GSKKAVTKAQK 11 3 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 3 ; GSK(1)K(1)AVTK(1)AQK;GSK(1)K(1)AVTK(1)AQK 167.44 0.0023105 309790000 2043.39 2029.93 2986.2 11950.1 24143 22703 20484 17713.9 2124.23 1719.39 FALSE TRUE FALSE 2018.484377 2058.507408 3038.173558 13331.82679 22910.89262 21252.35157 22223.91045 18226.42375 1934.233549 1674.72 1.205266777 1.229165119 1.814138219 7.960630308 13.68043173 12.69009242 13.27022454 10.88326631 1.154959366 1 10.70970419 -9.095559012 2.447425088 1.111060431 12.68929801 0.979716214 0.771772428 0.025219869 0.296271378 0.112257837 0.204069921 8.02E-10 9.095559012 11.57823758 up EK(ac)PDQDAEGKAEEK ddPTM_HeLa_Romidepsin_16h_R1 2 EKPDQDAEGKAEEK 14 2 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 0 1 ; EK(1)PDQDAEGKAEEK;EK(1)PDQDAEGKAEEK 115.06 0.002792 3907000 1041.23 1781.96 1288.67 855.53 3210.8 3714.03 2916.61 2517.01 3832.1 2962.02 FALSE TRUE FALSE 1028.539088 1807.04648 1311.098761 954.450404 3046.940895 3476.715469 3164.346781 2589.835713 3489.347378 2885.066293 0.35650449 0.626344872 0.454443201 0.330824427 1.056107758 1.205072992 1.096802104 0.897669395 1.209451369 1 11.49438875 -8.667772752 9.616154518 0.640404348 1.078854658 0.348817523 0.267138332 0.265645837 25.03513885 0.040508872 0.081067159 2.15E-09 8.667772752 0.43845031 EK(ac)PPITVVGDVGGR ddPTM_HeLa_Romidepsin_16h_R1 1 EKPPITVVGDVGGR 14 1 I3L0S1;E7EPA1;O60256-4;O60256-3;O60256-2;O60256;I3L4G9;C9J168;B4DP31;Q14558;Q14558-2 I3L0S1;C9J168 PRPSAP2;PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 2;Phosphoribosyl pyrophosphate synthase-associated protein 1 0 1 EK(1)PPITVVGDVGGR 158.25 7.57E-06 732250 0 132.34 146.27 0 200.24 71.044 0 154.25 181.91 205.28 FALSE TRUE FALSE 0 134.203086 148.815768 0 190.0210056 66.50451768 0 158.7129804 165.639514 199.946796 0 0.671193981 0.744276832 0 0.950357842 0.33261107 0 0.793776062 0.828417946 1 7.643472353 -12.60062926 1.404616523 0.999303442 0.377874692 0.220137293 0.342444309 0.410727059 1.456691051 0.23849204 0.055390954 2.51E-13 12.60062926 -0.62142875 EK(ac)PTTALLDK ddPTM_HeLa_Romidepsin_16h_R1 2 EKPTTALLDK 10 1 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906;K7EKJ9;K7ER69;K7EKY0 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 0 1 ; EK(1)PTTALLDK;EK(1)PTTALLDK 134.38 0.0083464 3337300 1182.88 1126.31 1540.03 1158.89 3190.7 2535.8 2190.4 2025.69 2916.5 1993.78 FALSE TRUE FALSE 1168.462604 1142.166222 1566.833576 1292.886315 3027.866673 2373.770564 2376.452521 2084.300144 2655.640935 1941.981308 0.601685814 0.588144807 0.806822172 0.665756312 1.559163654 1.222344702 1.223725744 1.073285379 1.367490472 1 10.9233136 -8.775241216 24.99994918 0.779322508 1.262973524 0.413540756 0.245621459 122.5768737 222029.4076 0.029469359 0.053616773 1.68E-09 8.775241216 0.483651016 EK(ac)TPSPKEEDEEPESPPEKK ddPTM_HeLa_Romidepsin_16h_R1 2 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 1 ; EK(0.996)TPSPK(0.004)EEDEEPESPPEKK;EK(0.995)TPSPK(0.005)EEDEEPESPPEKK 61.477 0.0087473 5195400 1732.26 1351.19 1281.45 1514.22 2614.5 3333.3 2768.8 3402.6 2093.61 1790.13 FALSE TRUE FALSE 1711.146549 1370.212088 1303.7531 1689.301241 2481.072309 3120.312888 3003.981803 3501.048863 1906.352278 1743.622165 0.981374626 0.785842321 0.747726845 0.968845932 1.422941483 1.789557939 1.722839881 2.007917159 1.093328771 1 10.76787173 -8.515445192 2.209991804 0.950295037 1.842970799 0.924043814 0.117736358 0.061106261 0.591278736 0.018072637 0.044991708 3.05E-09 8.515445192 0.892675761 EK(ac)VLATVTKPVGGDK ddPTM_HeLa_Romidepsin_16h_R1 2 EKVLATVTKPVGGDK 15 2 Q02878;F8VZA3;F8VWR1;F8VU16;F8VZ45;U3KQR5 Q02878 RPL6 60S ribosomal protein L6 0 1 ; EK(1)VLATVTKPVGGDK;EK(1)VLATVTKPVGGDK 101.2 0.017095 1394040 645.28 432.19 486.78 462.25 804.73 846.7 653.12 738.94 926.75 559.64 FALSE TRUE FALSE 637.4150792 438.2743822 495.2522017 515.69752 763.6616252 792.5986026 708.5959965 760.320063 843.8591589 545.1004721 1.169353379 0.804024954 0.908552142 0.946059573 1.400955722 1.454041306 1.299936494 1.394825545 1.548080037 1 9.09037836 -8.753859073 24.99769872 1.03618433 1.385946866 0.40105139 0.192802939 83.55552019 275540.1399 0.018469076 0.03637481 1.76E-09 8.753859073 0.349762536 EK(ac)VMYEK ddPTM_HeLa_Romidepsin_16h_R1 1 EKVMYEK 7 1 E5RJD8;E5RHG6;O75347;A0A494C144;E5RIX8;O75347-2 E5RJD8 TBCA Tubulin-specific chaperone A 0 1 EK(1)VMYEK 96.331 0.017484 10008000 2460.2 2442.1 2537.9 2790.8 2731.2 1922.9 2475.9 2052.3 3415.6 2935.7 FALSE TRUE FALSE 2430.214136 2476.479948 2582.071085 3113.485427 2591.816672 1800.032896 2686.202884 2111.680063 3110.100181 2859.430091 0.84989458 0.866074661 0.903001998 1.088848242 0.906410225 0.629507573 0.939418975 0.738496832 1.087664354 1 11.48151192 -15.53831472 0.020846974 2.049531757 1.96E-06 0.282514348 0.115331285 2645.985551 5.296362506 332.6853717 202.7966706 2.90E-16 15.53831472 -2.049529794 EK(ac)YIDQEELNK ddPTM_HeLa_Romidepsin_16h_R1 2 EKYIDQEELNK 11 1 P08238;Q58FF8;P07900-2;P07900;Q14568 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB2P;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 1 ; EK(1)YIDQEELNK;EK(1)YIDQEELNK 229.68 1.01E-28 5214200 1734.58 1630.36 1469.1 1392.56 2870.58 2203.43 2541.73 2238.4 3007.1 2257.6 FALSE TRUE FALSE 1713.438272 1653.312251 1494.669069 1553.574339 2724.083591 2062.637934 2757.624483 2303.164572 2738.137445 2198.947227 0.779208455 0.751865361 0.6797203 0.706508242 1.238812627 0.938011567 1.254065786 1.047394201 1.245203801 1 11.10259727 -8.758494981 24.9999989 0.851492074 1.116209279 0.339000592 0.176993185 57.01441828 484083.3904 0.021600343 0.041740444 1.74E-09 8.758494981 0.264717205 EKDLEDLFYK ddPTM_HeLa_Romidepsin_16h_R1 2 EKDLEDLFYK 10 1 Q13242;H0YIB4;S4R3G0 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 0 0 ; ; 117.14 0.015503 20043100 8465.1 8629.6 8545.1 8267.9 9115.5 8448.9 8434.1 8926.9 9413.9 8547.9 FALSE FALSE TRUE 8361.924105 8751.087735 8693.823881 9223.8735 8650.30202 7909.042558 9150.492243 9185.185767 8571.897206 8325.824326 1.004335881 1.051077634 1.044199774 1.107863094 1.038972441 0.949941081 1.099049402 1.103216379 1.029555377 1 13.0233774 -10.25067538 3.762841231 1.001745814 1.05522227 0.17196166 0.04386942 0.247780138 7.768076579 0.007485994 0.008911215 5.61E-11 10.25067538 0.053476456 EKDLLPS(ph)PAGPVPSKDPK ddPTM_HeLa_Romidepsin_16h_R1 1 EKDLLPSPAGPVPSKDPK 18 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 EKDLLPS(1)PAGPVPSKDPK 66.977 0.0099422 48126000 6816.3 6274.2 5754.9 6156.9 7444.4 7896 7499.5 7959.6 6566 5652.6 TRUE FALSE FALSE 6733.220314 6362.528352 5855.06162 6868.789747 7064.484489 7391.471083 8136.507343 8189.898468 5978.720515 5505.744637 1.222944535 1.155616319 1.063445911 1.247567804 1.283111542 1.342501618 1.477821417 1.487518766 1.085905887 1 12.42672198 -4 0.18548657 1.017529749 3.239962673 0.85827901 0.059530716 17.51511813 0.193334851 0.088066819 11.13760616 1.00E-04 4 2.222432924 EKDQAWK(ac)TLK ddPTM_HeLa_Romidepsin_16h_R1 1 EKDQAWKTLK 10 2 O75528 O75528 TADA3 Transcriptional adapter 3 0 1 EKDQAWK(1)TLK 144.1 0.0034563 2191500 1923.6 1441.2 2174.2 2667.9 2548.2 1863 1960.6 1368.4 1748.4 1459.1 FALSE TRUE FALSE 1900.154423 1461.489251 2212.041039 2976.375151 2418.155845 1743.960313 2127.133315 1407.992495 1592.018725 1421.192372 1.337014229 1.028354275 1.556468416 2.094280275 1.701497907 1.227110662 1.496724411 0.990712111 1.120199318 1 10.47288613 -11.12419089 0.627368091 1.033334325 1.487265958 0.208246329 0.303645301 0.75966796 0.670484462 0.146845206 0.087952499 7.51E-12 11.12419089 0.453931633 EKDSPFK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EKDSPFKPK 9 2 Q15291 Q15291 RBBP5 Retinoblastoma-binding protein 5 0 1 EKDSPFK(1)PK 112.3 0.0027109 5094000 4576.7 4619.9 4731.3 5633.4 6330.2 5201.5 5273.5 5517.2 4122.5 4231.5 FALSE TRUE FALSE 4520.91742 4684.939073 4813.646292 6284.760214 6007.146273 4869.140937 5721.430958 5676.831477 3753.773275 4121.56502 1.096893388 1.136689352 1.167917106 1.524848009 1.45749157 1.181381566 1.388169526 1.377348519 0.910764056 1 12.00897654 -9.567731405 2.600542548 1.051888277 1.377652877 0.723336439 0.101520982 0.110780358 1.519551297 0.015488147 0.023305847 2.71E-10 9.567731405 0.325764601 EKEDDEEEEDEDASGGDQDQEER ddPTM_HeLa_Romidepsin_16h_R1 1 EKEDDEEEEDEDASGGDQDQEER 23 1 O60216;E5RFZ5;E5RI01 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 0 132.6 9.49E-06 8015000 1589.4 1973 1515.8 1290.7 1172.6 1666.6 1341.7 1421.9 2218.6 2273.4 FALSE FALSE TRUE 1570.027781 2000.775946 1542.181863 1439.936807 1112.757846 1560.109639 1455.663965 1463.040433 2020.162859 2214.33674 0.709028466 0.903555412 0.696453179 0.650279057 0.502524221 0.704549408 0.65738148 0.660712712 0.912310591 1 11.11265892 -14.13979682 0.19457169 1.535071494 0.593671413 0.641986214 0.085817731 8.763884524 0.241484597 2.102813163 0.115695722 7.25E-15 14.13979682 -0.941400081 EKEIS(ph)DDEAEEEK ddPTM_HeLa_Romidepsin_16h_R1 4 EKEISDDEAEEEK 13 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 0 EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK;EKEIS(1)DDEAEEEK ;;; 206.63 6.70E-16 151013000 12763 11824.7 12861 6415.56 12227.5 12993.9 11329.9 12191.7 11857.9 12339.2 TRUE FALSE FALSE 12607.43965 11991.16844 13084.84031 7157.357233 11603.48505 12163.63173 12292.26142 12544.4476 10797.29973 12018.62581 1.048991778 0.997715432 1.088713512 0.595522096 0.96545855 1.0120651 1.022767629 1.043750576 0.898380555 1 13.55298433 EKEIS(ph)DDEAEEEKGEK ddPTM_HeLa_Romidepsin_16h_R1 1 EKEISDDEAEEEKGEK 16 2 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 0 EKEIS(1)DDEAEEEKGEK 83.065 0.018964 62842000 3802.3 4072.4 4081.2 2063.9 3653 3801.9 3272.8 3881.6 4091.1 3960.5 TRUE FALSE FALSE 3755.956105 4129.731354 4152.231574 2302.537829 3466.573779 3558.97086 3550.79155 3993.907972 3725.18177 3857.605639 0.973649579 1.070542648 1.076375338 0.596882638 0.898633532 0.922585457 0.920465149 1.035333403 0.965672004 1 11.91348995 EKELEARVRK ddPTM_HeLa_Romidepsin_16h_R1 1 EKELEARVRK 10 3 A0A140T907;A0A140T9W4;A0A140T9X0;A2AB09;A0A140T9R1;O75955-2;O75955 A0A140T907 FLOT1 Flotillin-1 0 0 90.05 0.0038682 0 1256.3 942.6 745.34 1187.6 2073.8 2061.8 1317.6 1300.8 1741.9 1693 FALSE FALSE TRUE 1240.987732 955.8699475 758.31233 1324.9159 1967.966248 1930.057634 1429.516911 1338.436596 1586.100101 1649.015616 0.752562753 0.579660943 0.45985758 0.803458674 1.193418806 1.170430174 0.86689107 0.811657927 0.961846623 1 10.68738935 -7.260834152 17.05922456 0.866235102 0.811658359 0.005244317 0.221528459 6.07564958 166049.0224 0.033724038 0.265565535 5.48E-08 7.260834152 -0.054576742 EKELS(ph)PPPGLPSK ddPTM_HeLa_Romidepsin_16h_R1 1 EKELSPPPGLPSK 13 1 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78;H0YIM6 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 EKELS(1)PPPGLPSK 74.519 0.01959 221850000 3060.4 3122 2897.3 2627.2 2834.9 2148 2499.3 2111.3 3047.5 2985.6 TRUE FALSE FALSE 3023.098668 3165.951598 2947.726291 2930.969225 2690.224475 2010.749732 2711.59048 2172.387134 2774.923967 2908.033682 1.039567969 1.088691516 1.013649295 1.007886959 0.925100865 0.691446507 0.932448099 0.747029564 0.954226901 1 11.50582826 -8.547554479 3.591730205 1.023550438 0.80338348 0.700500519 0.065934394 0.083286788 2.28720891 0.008356431 0.018287396 2.83E-09 8.547554479 -0.220166958 EKENLS(ph)Y(ph)DLVPLK ddPTM_HeLa_Romidepsin_16h_R1 1 EKENLSYDLVPLK 13 1 A0A0A0MSM0;Q92598-2;Q92598-3;Q92598;Q92598-4;R4GN69 A0A0A0MSM0 HSPH1 Heat shock protein 105 kDa 2 0 EKENLS(1)Y(1)DLVPLK 81.709 0.015414 5425000 2038.1 1714.7 2409.2 1606.3 2370.9 2623.3 2100.1 2009.6 2268.5 2220.2 TRUE FALSE FALSE 2013.258853 1738.839592 2451.131115 1792.027964 2249.904126 2455.679596 2278.482442 2067.744605 2065.599678 2162.518884 0.930978623 0.804080651 1.133461138 0.828676215 1.040409008 1.135564464 1.053624298 0.956174127 0.955182262 1 11.07849702 -8.552560329 24.99402379 0.957257913 1.055473996 0.215389098 0.094786216 236.351197 199023.7313 0.01292753 0.025855329 2.80E-09 8.552560329 0.098216083 EKEPGEQASVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 EKEPGEQASVPLSPK 15 1 P42858 P42858 HTT Huntingtin 1 0 EKEPGEQASVPLS(1)PK;EKEPGEQAS(0.004)VPLS(0.996)PK;EKEPGEQAS(0.001)VPLS(0.999)PK;EKEPGEQASVPLS(1)PK ;;; 122.64 0.0012052 129181000 28083.8 27625.5 30541.1 25769.9 23569.4 24861.9 19198.3 23965.7 28746.8 28382.2 TRUE FALSE FALSE 27741.50384 28014.41251 31072.65503 28749.53709 22366.56557 23273.30483 20829.00312 24659.10972 26175.61421 27644.82635 1.003497128 1.01336909 1.123995305 1.039960849 0.809068767 0.841868367 0.753450315 0.891997273 0.946853993 1 14.75472189 -8.75903758 24.99971664 1.015256014 0.820319457 0.770657591 0.052619499 21.06077625 219211.5609 0.007161849 0.013799786 1.74E-09 8.75903758 -0.194936557 EKEQS(ph)PTAEKDEDEENDASLANSSTTTLEDK ddPTM_HeLa_Romidepsin_16h_R1 1 EKEQSPTAEKDEDEENDASLANSSTTTLEDK 31 2 Q5JSZ5;A0A494C0D3 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 EKEQS(0.498)PT(0.262)AEKDEDEENDAS(0.22)LANS(0.005)S(0.006)T(0.006)T(0.003)T(0.001)LEDK 42.468 0.01805 7732400 2124.2 1815.4 2216.6 1361.6 1649.2 1825.6 1124.6 1564.4 2372.9 2195.6 TRUE FALSE FALSE 2098.309433 1840.957249 2255.178993 1519.034599 1565.03517 1708.950052 1220.123496 1609.663446 2160.661881 2138.557995 0.981179579 0.86084046 1.054532539 0.710307881 0.73181797 0.79911326 0.570535613 0.752686366 1.010335883 1 11.06242262 -9.252098137 24.66559368 0.983367997 0.710824987 0.780208778 0.071242791 179.6296024 474312.6582 0.010076346 0.016560692 5.60E-10 9.252098137 -0.27254301 EKET(ph)RLRDTMR ddPTM_HeLa_Romidepsin_16h_R1 1 EKETRLRDTMR 11 3 Q8IZY2-2;Q8IZY2 Q8IZY2-2 ABCA7 ATP-binding cassette sub-family A member 7 1 0 EKET(0.817)RLRDT(0.183)MR 57.785 0.030171 4351700 950.01 1003.8 981.16 1053.5 1021.6 894.82 933.65 939.34 1071.8 938.68 TRUE FALSE FALSE 938.4309127 1017.931523 998.2366782 1175.310627 969.4639399 837.6438899 1012.954208 966.5183209 975.9355236 914.2929583 1.026400678 1.113353782 1.091812716 1.285485813 1.060342783 0.916165746 1.107909887 1.057121038 1.067421022 1 9.836512698 -10.3940305 4.253103565 1.011251679 1.090580013 0.077427942 0.086387172 0.338150408 9.905975775 0.015288641 0.017319119 4.04E-11 10.3940305 0.079328334 EKEVDGLLTSEPMGS(ph)PVSSK ddPTM_HeLa_Romidepsin_16h_R1 6 EKEVDGLLTSEPMGSPVSSK 20 1 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 EKEVDGLLTSEPMGS(0.955)PVS(0.034)S(0.011)K;EKEVDGLLTSEPMGS(0.823)PVS(0.135)S(0.042)K;EKEVDGLLT(0.002)S(0.041)EPMGS(0.92)PVS(0.028)S(0.009)K;EKEVDGLLTSEPMGS(0.86)PVS(0.11)S(0.03)K;EKEVDGLLTSEPMGS(0.929)PVS(0.056)S(0.014)K;EKEVDGLLT(0.001)S(0.031)EPMGS(0.906)PVS(0.045)S(0.017)K ;;;;; 122.13 0.00021238 1481320000 31690.3 30083.4 30491.8 29807.8 29010.9 26269.2 23379.5 24995.2 32910.5 33034.6 TRUE FALSE FALSE 31304.04643 30506.91489 31022.49699 33254.31809 27530.36552 24590.6829 25365.35415 25718.39668 29966.90245 32176.35633 0.972889724 0.948115895 0.964139527 1.033501673 0.855608548 0.764246972 0.788322764 0.799294874 0.931333 1 14.97371334 -8.586030353 4.285796972 0.984384442 0.78702523 0.899579842 0.028909999 0.036623355 1.353849287 0.003637659 0.007594462 2.59E-09 8.586030353 -0.197359212 EKFPEFCSSPS(ph)PPVEVK ddPTM_HeLa_Romidepsin_16h_R1 1 EKFPEFCSSPSPPVEVK 17 1 Q68E01-4;Q68E01-3;Q68E01-2;Q68E01 Q68E01-4 INTS3 Integrator complex subunit 3 1 0 EKFPEFCS(0.004)S(0.022)PS(0.974)PPVEVK 100.58 0.00049562 0 1789.6 1650.5 1567.8 325.44 1650 1846.1 1341.1 1633.5 2164.6 1899.1 TRUE FALSE FALSE 1767.787667 1673.735782 1595.086901 363.068904 1565.794343 1728.140168 1455.013001 1680.762745 1970.992755 1849.761108 0.955684309 0.904838887 0.862320488 0.196278807 0.846484628 0.934250461 0.786595087 0.908637736 1.065539083 1 10.85312325 -9.689777767 3.692292072 0.974180741 0.737827206 0.249004989 0.198572544 0.254926751 6.923119607 0.031626032 0.044901943 2.04E-10 9.689777767 -0.236353535 EKGSETDS(ph)AQDQPVK ddPTM_HeLa_Romidepsin_16h_R1 1 EKGSETDSAQDQPVK 15 1 K7EN42;B7Z8J4;P30419 K7EN42 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 0 EKGSETDS(1)AQDQPVK 80.459 0.011398 5036700 3439.5 3064.6 3098.4 3025.9 3006.5 3001.3 2418.6 2717.4 3322.4 3638.8 TRUE FALSE FALSE 3397.578051 3107.743519 3152.326352 3375.768795 2853.067086 2809.526616 2624.035824 2796.023682 3025.236223 3544.263451 0.958613291 0.876837617 0.889416488 0.952459895 0.804981663 0.79269689 0.740361392 0.78888709 0.853558508 1 11.79127013 -8.632353491 0.364671338 0.999478439 0.686641311 0.491030694 0.057807641 0.675015829 0.126005259 0.014572463 0.082692006 2.33E-09 8.632353491 -0.312837128 EKGSFS(ph)DTGLGDGK ddPTM_HeLa_Romidepsin_16h_R1 1 EKGSFSDTGLGDGK 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 EKGS(0.136)FS(0.659)DT(0.206)GLGDGK 132.25 0.012043 14989000 2227.3 2291.1 2374.1 2545.1 2639.1 2311.7 2397.6 2601.4 2395.2 2376.8 TRUE FALSE FALSE 2200.152811 2323.354166 2415.420215 2839.376437 2504.416879 2163.989831 2601.252084 2676.667405 2180.967313 2315.050393 0.950369295 1.003586865 1.043355351 1.226485801 1.081797997 0.934748478 1.123626549 1.156202652 0.942082004 1 11.17682788 -9.674574166 3.369640961 0.97735187 1.09756691 0.420815049 0.071501333 0.194530905 4.40168402 0.011699473 0.016728204 2.12E-10 9.674574166 0.120215041 EKLLS(ph)GSESSSK ddPTM_HeLa_Romidepsin_16h_R1 1 EKLLSGSESSSK 12 1 G3XAI9;Q5BKY9-2;Q5BKY9 G3XAI9 FAM133B Protein FAM133B 1 0 EKLLS(0.894)GS(0.095)ES(0.01)S(0.001)SK 69.379 0.026938 3924400 3268.3 3080.3 3097.6 2255.7 3742.9 3117.6 2647.3 3079.9 3064.4 2953.9 TRUE FALSE FALSE 3228.464702 3123.664544 3151.512429 2516.514647 3551.885846 2918.395422 2872.161596 3169.012047 2790.312389 2877.157252 1.122102276 1.085677379 1.095356337 0.874653148 1.234512241 1.014332956 0.998263683 1.101438597 0.96981574 1 11.49042836 EKLLSGSES(ph)SSK ddPTM_HeLa_Romidepsin_16h_R1 1 EKLLSGSESSSK 12 1 G3XAI9;Q5BKY9-2;Q5BKY9 G3XAI9 FAM133B Protein FAM133B 1 0 EKLLS(0.005)GS(0.063)ES(0.506)S(0.16)S(0.266)K 68.751 0.027473 5785800 1629.1 1549.2 1523.1 1268.2 1515.4 1207.2 1117.5 1139.5 1196.6 1024.9 TRUE FALSE FALSE 1609.243903 1571.009678 1549.608917 1414.835251 1438.063483 1130.063816 1212.420422 1172.469635 1089.573099 998.2729503 1.612027955 1.573727584 1.552289798 1.417282969 1.440551387 1.132018869 1.214517955 1.174498051 1.091458101 1 9.963290525 -8.253575127 24.44410769 1.355987669 1.177762251 0.194065453 0.190411971 907.8634872 2821858.728 0.03695647 0.092316481 5.58E-09 8.253575127 -0.178225417 EKLQEEGGGSDEEET(ph)GSPSEDGMQSAR ddPTM_HeLa_Romidepsin_16h_R1 3 EKLQEEGGGSDEEETGSPSEDGMQSAR 27 1 Q13610-2;Q13610 Q13610-2 PWP1 Periodic tryptophan protein 1 homolog 1 0 EKLQEEGGGS(0.336)DEEET(0.438)GS(0.096)PS(0.096)EDGMQS(0.034)AR;EKLQEEGGGSDEEET(0.764)GS(0.103)PS(0.103)EDGMQS(0.029)AR;EKLQEEGGGS(0.084)DEEET(0.496)GS(0.19)PS(0.136)EDGMQS(0.094)AR ;; 80.981 3.58E-06 217347000 3088.3 3294.5 3267.13 2868.55 2706.54 2621.01 2751.52 2830.49 3136.82 2908.87 TRUE FALSE FALSE 3050.658612 3340.880057 3323.993027 3200.225248 2568.415164 2453.53592 2985.23404 2912.385762 2856.254963 2833.297138 1.076716794 1.179149201 1.173188997 1.129505693 0.90651105 0.865964917 1.053625474 1.027913989 1.008102865 1 11.46826619 -8.759141719 24.99999124 1.06622442 0.962974052 0.373116109 0.078170052 70.10363957 762754.068 0.01321148 0.025437927 1.74E-09 8.759141719 -0.103250368 EKLQSFDS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 EKLQSFDSPER 11 1 E9PGM9;P78332-2;P78332 E9PGM9 RBM6 RNA-binding protein 6 1 0 EKLQS(0.005)FDS(0.995)PER;EKLQS(0.028)FDS(0.972)PER ; 85.271 0.016262 44718000 8985.4 8037.2 7355.8 7892.4 8482.6 9138.3 7930.9 8337.4 9136.3 9153.3 TRUE FALSE FALSE 8875.882489 8150.347913 7483.824613 8804.956423 8049.701269 8554.392123 8604.550448 8578.629515 8319.126446 8915.495946 0.995556786 0.914177737 0.839417645 0.987601416 0.902888781 0.959497057 0.965123028 0.962215626 0.933108657 1 13.12209934 -10.27400103 22.75774367 0.997901824 0.932588148 0.112678099 0.044493427 176.7968355 320299.203 0.006647848 0.007636623 5.32E-11 10.27400103 -0.065313676 EKNT(ph)SSETTMEEELGLVGATADDTEAELIR ddPTM_HeLa_Romidepsin_16h_R1 1 EKNTSSETTMEEELGLVGATADDTEAELIR 30 1 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 1 0 EKNT(0.2)S(0.2)S(0.2)ET(0.2)T(0.2)MEEELGLVGATADDTEAELIR 79.407 7.60E-07 4888200 236.13 166.76 207.81 247.26 248.95 341.82 331.91 334.41 365.19 275.48 TRUE FALSE FALSE 233.2519567 169.1076517 211.4268459 275.8493646 236.2451525 319.9788052 360.1024271 344.0856257 332.5264918 268.3229899 0.869295459 0.630239145 0.787956507 1.028049683 0.880450656 1.192513565 1.342048355 1.282356111 1.239276932 1 8.06782686 -8.133504528 3.055453885 0.904525969 1.30955766 0.536983541 0.151929385 0.120102905 2.120801291 0.017949698 0.052760243 7.35E-09 8.133504528 0.405031692 EKNTSSET(ph)TMEEELGLVGATADDTEAELIR ddPTM_HeLa_Romidepsin_16h_R1 1 EKNTSSETTMEEELGLVGATADDTEAELIR 30 1 Q15021;E7EN77 Q15021 NCAPD2 Condensin complex subunit 1 1 0 EKNT(0.023)S(0.023)S(0.023)ET(0.465)T(0.465)MEEELGLVGATADDTEAELIR 92.449 2.88E-08 5300500 1162.6 1065.2 1017.9 999.5 1142.3 1329.6 994.12 1292.2 1209.9 943.53 TRUE FALSE FALSE 1148.429784 1080.195914 1035.616123 1115.066893 1084.004168 1244.642851 1078.560528 1329.587768 1101.683514 919.0169546 1.249628506 1.175381921 1.126873794 1.213325703 1.179525756 1.354319792 1.173602427 1.446749988 1.198762992 1 9.843947667 -16.52287875 0.148783092 0.13124805 1.326822348 0.238688365 0.100631068 36.96476277 0.375865652 9.470167999 0.194906525 3.00E-17 16.52287875 1.195574298 EKPDS(ph)DDDLDIASLVTAK ddPTM_HeLa_Romidepsin_16h_R1 2 EKPDSDDDLDIASLVTAK 18 1 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 EKPDS(1)DDDLDIASLVTAK;EKPDS(0.94)DDDLDIAS(0.06)LVTAK ; 99.964 0.00075801 472040000 28366 28260 26131 26751 32636 37888 34101 36492 29669 26758 TRUE FALSE FALSE 28020.26428 28657.84502 26585.79909 29844.07649 30970.46314 35467.07908 36997.53809 37547.83845 27015.33033 26062.8233 1.075104717 1.099567944 1.020065968 1.145082255 1.188300392 1.360830278 1.419552197 1.440666577 1.036546579 1 14.66970575 -8.372307827 0.97617967 1.037855175 1.469257942 0.963014521 0.030730268 0.096540728 0.157757236 0.006013246 0.028929003 4.24E-09 8.372307827 0.431402767 EKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_HeLa_Romidepsin_16h_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 0 EKPELSEPSHLNGPS(0.499)S(0.499)DPEAAFLS(0.002)R;EKPELSEPS(0.022)HLNGPS(0.487)S(0.487)DPEAAFLS(0.004)R;EKPELSEPSHLNGPS(0.495)S(0.495)DPEAAFLS(0.009)R ;; 122.67 7.95E-12 17296500 4165.88 3725.4 4138.3 3616.16 5890.3 6236.3 4904.2 4882.1 6231.9 5575.2 TRUE FALSE FALSE 4115.104652 3777.846279 4210.325376 4034.277434 5589.696011 5837.820557 5320.762626 5023.355861 5674.503256 5430.3555 0.757796548 0.695690416 0.775331445 0.742912215 1.029342556 1.075034693 0.979818471 0.925051014 1.044959811 1 12.40683093 -8.741071869 24.98761771 0.849024202 1.005899578 0.347955902 0.110568781 258.2383601 316814.9548 0.018326189 0.036617818 1.82E-09 8.741071869 0.156875377 EKPYFPIPEEYTFIQNVPLEDR ddPTM_HeLa_Romidepsin_16h_R1 2 EKPYFPIPEEYTFIQNVPLEDR 22 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQ74 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 143.4 1.67E-05 161163000 11318 9974.1 10104.2 10087.1 9471.2 8804 8981 8748.1 10153.2 10395.1 FALSE FALSE TRUE 11180.05186 10114.51564 10280.05936 11253.41796 8987.849322 8241.452814 9743.845916 9001.212471 9245.072363 10125.0338 1.104198967 0.998961173 1.015311115 1.111444977 0.887685858 0.813967931 0.962351939 0.889005671 0.913090518 1 13.3056391 -8.746701071 24.99669007 1.047229279 0.888239517 0.493249772 0.064769912 110.5035907 187416.9448 0.008015555 0.015977784 1.79E-09 8.746701071 -0.158989761 EKQIESSDYDSSSSK(ac)GK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EKQIESSDYDSSSSKGKK 18 3 Q9UNL4-2;Q9UNL4-6;Q9UNL4-8;Q9UNL4-3;Q9UNL4 Q9UNL4-2;Q9UNL4-8 ING4 Inhibitor of growth protein 4 0 2 ; EKQIESSDYDSSSSK(1)GK(1)K;EKQIESSDYDSSSSK(1)GK(1)K 212.41 2.60E-34 17273300 7162.4 7300.4 7751.2 10046.8 9227.4 9207.6 8232.7 9244 7595.4 7570.3 FALSE TRUE FALSE 7075.101914 7403.175223 7886.106385 11208.45829 8756.491346 8619.264076 8931.985333 9511.460555 6916.048401 7373.622515 0.959515069 1.004007895 1.06950232 1.52007487 1.187542667 1.168932103 1.211342907 1.289930497 0.937944462 1 12.84815785 -9.506319275 21.83747279 0.984685754 1.264543282 0.700445745 0.093417321 58.31377954 76899.92633 0.013899541 0.020851721 3.12E-10 9.506319275 0.279857529 EKQS(ph)DDEVYAPGLDIESSLK ddPTM_HeLa_Romidepsin_16h_R1 2 EKQSDDEVYAPGLDIESSLK 20 1 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 0 EKQS(0.836)DDEVY(0.164)APGLDIESSLK;EKQS(0.999)DDEVY(0.001)APGLDIESSLK ; 105.77 0.00018503 109726000 8661.9 8654.3 7910.8 7539.5 9867 10753.1 9058.3 9671.5 8354.5 8191.4 TRUE FALSE FALSE 8556.325431 8776.135463 8048.484156 8411.252464 9363.450171 10066.01161 9827.711776 9951.329593 7607.252596 7978.586247 1.072411222 1.09996122 1.008760688 1.054228431 1.173572596 1.261628477 1.23176105 1.24725475 0.953458716 1 12.96191742 -8.640773923 2.687861608 1.038755244 1.244523559 0.864102002 0.039044041 0.067039979 0.977224621 0.005354228 0.01177041 2.29E-09 8.640773923 0.205768315 EKT(ph)KLGSSSEIEVPAKTTHVLK ddPTM_HeLa_Romidepsin_16h_R1 1 EKTKLGSSSEIEVPAKTTHVLK 22 3 A0A087WYF7;Q6UXV4 A0A087WYF7 APOOL MICOS complex subunit MIC27 1 0 EKT(0.25)KLGS(0.25)S(0.25)S(0.25)EIEVPAKTTHVLK 48.477 0.023586 1748400 0 178.18 100.29 117.66 168.48 184.65 131.47 217.6 110 123.89 TRUE FALSE FALSE 0 180.6884227 102.0355054 131.2644028 159.8818369 172.8514609 142.6370585 223.8959127 100.1613245 120.6713199 0 1.497360125 0.845565503 1.087784594 1.324936505 1.432415432 1.182029488 1.855419438 0.830034216 1 6.91493902 -9.498226818 1.054454784 0.560021211 1.427807574 0.340348194 0.385583754 0.380716238 0.844524184 0.086366046 0.155268739 3.18E-10 9.498226818 0.867786363 EKT(ph)PATT(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 1 EKTPATTPEAR 11 1 H0Y7U4;A0A0C4DG98;Q8NI27-2;Q8NI27;H7C477 H0Y7U4 THOC2 THO complex subunit 2 2 0 EKT(0.998)PAT(0.003)T(1)PEAR 130.1 0.0073911 5146600 3653.7 3621 3688.5 3312.3 3667.4 4528.2 3607.8 3611.3 3573.7 3383.2 TRUE FALSE FALSE 3609.167299 3671.976533 3752.696795 3695.283711 3480.238893 4238.862634 3914.246442 3715.787268 3254.059322 3295.303976 1.095245636 1.114305861 1.138801404 1.121378707 1.056120746 1.28633433 1.187825606 1.12760076 0.987483809 1 11.68619584 -11.31588632 0.165239514 0.899272529 1.23910047 0.589087445 0.05311075 3.492457438 0.307491211 0.378631442 0.202865089 4.83E-12 11.31588632 0.339827941 EKT(ph)PELPEPSVK ddPTM_HeLa_Romidepsin_16h_R1 4 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 EKT(0.975)PELPEPS(0.025)VK;EKT(0.92)PELPEPS(0.08)VK;EKT(0.998)PELPEPS(0.002)VK;EKT(1)PELPEPSVK ;;; 135.86 0.0059539 3284300000 29131 28100.3 27015.7 27662.8 29541.4 28275.4 26540.8 30074.8 31340.4 29005.6 TRUE FALSE FALSE 28775.94017 28495.89676 27485.89693 30861.30309 28033.79212 26468.69319 28795.17489 30944.96689 28537.23613 28252.03033 1.018544148 1.00863182 0.972882182 1.092357 0.992275309 0.936877558 1.019224974 1.095318337 1.010095055 1 14.78606693 EKTPELPEPS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 EKT(0.088)PELPEPS(0.912)VK 155.66 0.0083973 661310000 5263.6 5828.4 5525.6 5927 5930.7 5641.4 6031.4 5841.7 5837.8 5544.4 TRUE FALSE FALSE 5199.445219 5910.452368 5621.77075 6612.307627 5628.034249 5280.932747 6543.706965 6010.720373 5315.652547 5400.355689 0.962796808 1.094456126 1.041000089 1.224420762 1.042159919 0.977886097 1.211717772 1.113023052 0.984315266 1 12.39883872 -10.25257798 21.61196868 0.982431826 1.100429887 0.367417511 0.071130161 78.38792244 191178.3683 0.011637272 0.014109375 5.59E-11 10.25257798 0.117998062 EKTPELPEPSVK ddPTM_HeLa_Romidepsin_16h_R1 1 EKTPELPEPSVK 12 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 0 0 95.183 0.024468 11051000 4969.5 4425.4 4381.2 4134 4552.1 5392 4637.3 5138.4 4922.1 4768.2 FALSE FALSE TRUE 4908.929823 4487.700897 4457.452948 4611.992531 4319.789351 5047.468602 5031.192146 5287.071497 4481.855048 4644.321477 1.056974597 0.966276973 0.959764084 0.993039038 0.930122812 1.086804311 1.083299718 1.138394817 0.965018264 1 12.18125212 -8.05780885 11.04499179 1.009409956 1.104437597 0.605190256 0.040989284 0.549356901 104.2191894 0.006406509 0.01637215 8.75E-09 8.05780885 0.095027642 EKTPSPKEEDEEPES(ph)PPEK ddPTM_HeLa_Romidepsin_16h_R1 1 EKTPSPKEEDEEPESPPEK 19 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 EKT(0.008)PS(0.002)PKEEDEEPES(0.99)PPEK 60.761 0.012879 42413000 9233.3 7655.8 7382.3 8340.5 8045.3 7410.5 7122.7 7879.2 8906.8 9055.3 TRUE FALSE FALSE 9120.760988 7763.578553 7510.785835 9304.867853 7634.71832 6936.992966 7727.70196 8107.172221 8110.153501 8820.042001 1.034094961 0.880220134 0.851558965 1.054968656 0.8656102 0.786503394 0.876152513 0.919176147 0.919514159 1 13.10656981 -10.25912423 24.75719265 1.0161004 0.889898603 0.233353078 0.071449478 123.0995888 1316376.071 0.011063641 0.013213156 5.51E-11 10.25912423 -0.126201797 EKTPSPKEEDEEPESPPEKK ddPTM_HeLa_Romidepsin_16h_R1 1 EKTPSPKEEDEEPESPPEKK 20 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 0 56.424 0.0067446 6833600 2587.2 1966.1 1642.1 2736.4 2317.9 1853.3 1818 2005 2248.1 2123.6 FALSE FALSE TRUE 2555.666211 1993.778807 1670.680062 3052.795443 2199.608914 1734.880111 1972.420875 2063.011512 2047.024306 2068.428566 1.235559329 0.963909917 0.807704984 1.475900833 1.063420294 0.838743063 0.953584236 0.997381077 0.989651922 1 11.01431942 -8.503703601 24.99999997 1.105871012 0.935406027 0.119610998 0.173501496 1084.758685 1414276.806 0.025189266 0.055485875 3.14E-09 8.503703601 -0.170464985 EKVAS(ph)DTEEADRTSSK ddPTM_HeLa_Romidepsin_16h_R1 2 EKVASDTEEADRTSSK 16 2 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 EKVAS(0.97)DT(0.024)EEADRT(0.002)S(0.001)S(0.003)K;EKVAS(0.669)DT(0.331)EEADRTSSK ; 90.718 0.010926 14817800 3778.1 3496.1 2940.2 4454.4 3844.9 4150.2 3443.5 3784.5 3663.1 3264.6 TRUE FALSE FALSE 3732.051064 3545.318188 2991.372948 4969.438687 3648.680406 3885.015614 3735.990804 3893.998537 3335.463162 3179.785221 1.173680234 1.114955238 0.940746855 1.562822122 1.147461275 1.221785543 1.17491923 1.224610552 1.048958634 1 11.63471361 -12.59347025 0.244112362 0.860266425 1.244778585 0.210580335 0.14294685 7.704336373 0.5573234 0.899820446 0.130401363 2.55E-13 12.59347025 0.384512159 EKVASDT(ph)EEADR ddPTM_HeLa_Romidepsin_16h_R1 2 EKVASDTEEADR 12 1 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 EKVAS(0.079)DT(0.921)EEADR;EKVAS(0.003)DT(0.997)EEADR ; 141 0.0079465 85741000 4095.4 4313.1 3736.6 3136.1 5004.3 5181.1 4248.8 4279.4 4124.8 4400.5 TRUE FALSE FALSE 4045.48369 4373.819935 3801.633956 3498.710638 4748.911897 4850.044431 4609.692966 4403.217687 3755.867557 4286.174376 0.943844868 1.020448435 0.886952705 0.816278185 1.107960498 1.131555557 1.075479568 1.027307174 0.876275025 1 12.06547483 -8.692915788 24.99999779 0.959740253 1.088139531 0.55241688 0.066741134 34.5387071 12600.45307 0.009424616 0.018849229 2.03E-09 8.692915788 0.128399278 EKVEPEVLSTDTQT(ph)SPEPGTR ddPTM_HeLa_Romidepsin_16h_R1 1 EKVEPEVLSTDTQTSPEPGTR 21 1 P29375-2;P29375 P29375-2 KDM5A Lysine-specific demethylase 5A 1 0 EKVEPEVLS(0.001)T(0.01)DT(0.213)QT(0.304)S(0.304)PEPGT(0.168)R 94.73 0.00043891 14149000 2386.5 2085.4 2007.5 2011.1 2458.7 2587.9 1843.5 2772.2 2366.1 2610.4 TRUE FALSE FALSE 2357.41242 2114.758316 2042.439695 2243.632845 2333.223364 2422.541542 2000.086844 2852.409233 2154.47009 2542.581432 0.927172829 0.83173671 0.80329372 0.882423201 0.917659248 0.952788183 0.786636298 1.121855606 0.847355394 1 11.31207826 -11.29079959 1.116724621 0.986977216 0.895527502 0 0.100102813 0.554716673 1.424672419 0.024688169 0.017170782 5.12E-12 11.29079959 -0.091449714 EKVIET(ph)PENDFK ddPTM_HeLa_Romidepsin_16h_R1 1 EKVIETPENDFK 12 1 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 0 EKVIET(1)PENDFK 80.488 0.026043 68748000 9264 9216.8 9024.4 7998.3 7411.6 6101.1 5980.2 5974.8 9252.8 8385.5 TRUE FALSE FALSE 9151.086805 9346.554352 9181.465896 8923.101079 7033.358396 5711.2594 6488.158039 6147.671411 8425.206394 8167.643501 1.120407227 1.144339166 1.124126671 1.092493946 0.861124557 0.699254246 0.794373314 0.752686061 1.031534541 1 12.99570418 -8.623448075 3.596323648 1.073376762 0.755473144 0.911171871 0.047970206 0.06324914 1.586437287 0.009154601 0.019293156 2.38E-09 8.623448075 -0.317903617 EKVSSIDLEIDSLSSLLDDMTK ddPTM_HeLa_Romidepsin_16h_R1 1 EKVSSIDLEIDSLSSLLDDMTK 22 1 Q15942;H7C3R3;C9IZ41 Q15942 ZYX Zyxin 0 0 65.184 0.0096367 2077600 1099.9 628 974.92 1188.7 1432.8 1027.9 1207.2 1477.1 985.83 884.53 FALSE FALSE TRUE 1086.493996 636.8410005 991.8880736 1326.143087 1359.678869 962.2205074 1309.739538 1519.837558 897.6548957 861.5497831 1.26109253 0.739180733 1.151283528 1.539252999 1.578177949 1.116848412 1.520213415 1.764073984 1.041907169 1 9.750790352 -9.3157547 5.648407429 1.092018105 1.487245977 0.573361042 0.197956099 0.146654777 10.55444545 0.032113404 0.049664411 4.83E-10 9.3157547 0.395227872 EKYIDQEELNK ddPTM_HeLa_Romidepsin_16h_R1 1 EKYIDQEELNK 11 1 P08238;Q58FF8;P07900-2;P07900;Q14568 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB2P;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 0 120.03 0.011406 9335400 2861.3 2843.4 2582.6 3243.9 2972.2 3118.1 2961.5 3446.6 3286.8 2957.9 FALSE FALSE TRUE 2826.425375 2883.42946 2627.54907 3618.974981 2820.517543 2918.863473 3213.049736 3546.321933 2992.820376 2881.053332 0.981038894 1.000824743 0.912009868 1.256129118 0.978988314 1.013123722 1.115234383 1.230911589 1.038793813 1 11.49238065 -9.288189112 24.99980045 0.986318836 1.105028257 0.373575116 0.084744147 634.7129513 593188.9238 0.012312793 0.018811896 5.15E-10 9.288189112 0.118709421 ELAAQLNEEAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 ELAAQLNEEAKR 12 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 1 ELAAQLNEEAK(1)R 102.4 0.0033094 0 154.46 0 147.41 0 141.12 275.85 221.91 146.82 248.41 145.02 FALSE TRUE FALSE 152.5773821 0 149.9756092 0 133.9181198 258.2240753 240.7590299 151.0680051 226.1915874 141.2523595 1.080175812 0 1.061756489 0 0.948077047 1.828104509 1.704460235 1.069490135 1.601329622 1 7.142131156 -8.339717909 7.132014106 0.874269819 1.549327897 0.300291856 0.498588744 0.238232163 18.81535002 0.065287081 0.146922027 4.57E-09 8.339717909 0.675058078 ELAEDGYS(ph)GVEVR ddPTM_HeLa_Romidepsin_16h_R1 2 ELAEDGYSGVEVR 13 0 E9PPU1;E9PL09;P23396;P23396-2;E9PQ96;E9PJH4;F2Z2S8;E9PK82;H0YCJ7;H0YEU2;H0YF32 E9PPU1 RPS3 40S ribosomal protein S3 1 0 ELAEDGYS(1)GVEVR;ELAEDGYS(1)GVEVR ; 151.3 0.00026468 2155400 2437.2 2237.5 2401.5 1754.83 2150.57 2286.5 2061.39 2480.6 2959.9 2315.2 TRUE FALSE FALSE 2407.494469 2268.999584 2443.2971 1957.731701 2040.818388 2140.400029 2236.484415 2552.372247 2695.159131 2255.05077 1.067601005 1.006185587 1.083477646 0.868154157 0.904998865 0.949158244 0.991766768 1.13184691 1.195165611 1 11.1389442 -9.291918989 24.99067324 1.033908937 0.965760988 0.205113708 0.08559787 908.9741632 745278.4098 0.010953931 0.01673369 5.11E-10 9.291918989 -0.068147949 ELAEDGYSGVEVR ddPTM_HeLa_Romidepsin_16h_R1 2 ELAEDGYSGVEVR 13 0 E9PPU1;E9PL09;P23396;P23396-2;E9PQ96;E9PJH4;F2Z2S8;E9PK82;H0YCJ7;H0YEU2;H0YF32 E9PPU1 RPS3 40S ribosomal protein S3 0 0 ; ; 231.07 4.12E-32 31457000 2079 1770.1 1869.95 1821.58 1768.97 1818.09 1822.78 2118.5 1944.98 2404.4 FALSE FALSE TRUE 2053.660348 1795.019514 1902.495695 2032.19965 1678.69286 1701.919917 1977.606888 2179.795455 1771.016118 2341.933341 0.876908114 0.766469089 0.812361164 0.867744446 0.716797882 0.726715781 0.844433466 0.930767506 0.756219695 1 11.1934843 -11.21294824 0.706485073 0.989366762 0.80426107 0 0.096025323 0.336034781 0.366047858 0.027559004 0.016285572 6.12E-12 11.21294824 -0.185105692 ELAHVLQS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ELAHVLQSK 9 0 Q63HR2-5;Q63HR2-6;Q63HR2;Q63HR2-4;F8VV64;Q63HR2-2 Q63HR2-5 TNS2 Tensin-2 1 0 ELAHVLQS(1)K 117.04 0.015149 13766000 3254.1 2593.9 2686.7 2045 2748.6 2718.7 2905.1 2725.8 2852.8 2580.7 TRUE FALSE FALSE 3214.437778 2630.416992 2733.460886 2281.452522 2608.328686 2544.983844 3151.859121 2804.666722 2597.638423 2513.653042 1.278791354 1.046451896 1.087445579 0.907624276 1.037664563 1.012464251 1.253895852 1.11577321 1.033411684 1 11.29556981 ELAPYDENWFYTR ddPTM_HeLa_Romidepsin_16h_R1 2 ELAPYDENWFYTR 13 0 M0R2L9;M0QYF7;M0R140;P39019 M0R2L9 RPS19 40S ribosomal protein S19 0 0 ; ; 204.32 1.93E-15 113251000 3555.8 3575.5 3235 2416.8 3533.3 3715.3 3251 3658.2 3707.6 3199.2 FALSE FALSE TRUE 3512.460542 3625.835983 3291.303818 2696.241787 3352.982516 3477.904321 3527.139859 3764.044245 3375.98297 3116.084323 1.127203303 1.163587248 1.056230665 0.86526599 1.076024321 1.116113674 1.131914125 1.207940433 1.083405525 1 11.60551856 -7.414665079 0.011034893 3.76E-06 2.232062448 0.088645772 0.086767772 7840.953182 14.37633248 1347.941476 1566.291226 3.85E-08 7.414665079 2.232058691 ELASPVS(ph)PELR ddPTM_HeLa_Romidepsin_16h_R1 2 ELASPVSPELR 11 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 ELAS(0.015)PVS(0.985)PELR;ELAS(0.047)PVS(0.953)PELR ; 132.86 0.0044724 8860700 4108.9 4506.5 4254.6 2618.7 4455.1 6101.1 4315.6 5274.4 4695.4 4597.5 TRUE FALSE FALSE 4058.819146 4569.942625 4328.649528 2921.486415 4227.739623 5711.2594 4682.166956 5427.006442 4275.431664 4478.056287 0.906379663 1.020519246 0.966635801 0.652400557 0.944101492 1.275388033 1.045580193 1.211911172 0.954751658 1 12.12865695 -8.283473233 22.70148642 0.93664152 1.164421772 0.526250375 0.110785307 157.2245321 161988.4079 0.016063121 0.035961895 5.21E-09 8.283473233 0.227780252 ELAVQIQK ddPTM_HeLa_Romidepsin_16h_R1 1 ELAVQIQK 8 0 P38919 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 0 133.55 0.024538 1332300 841.48 675.32 1048 734.02 1391.4 1289.4 1357.1 1307.5 1125 1085.4 FALSE FALSE TRUE 831.2237181 684.8271727 1066.24 818.8908461 1320.391666 1207.011501 1472.37204 1345.33045 1024.377182 1057.201152 0.78624935 0.647773767 1.008549791 0.774583763 1.248950272 1.141704679 1.392707564 1.272539713 0.968952012 1 10.04603419 -8.75030658 24.55244037 0.877115293 1.264437232 0.72639384 0.119999422 78.67092964 173500.5389 0.019016935 0.037740852 1.78E-09 8.75030658 0.387321939 ELDALDANDELTPLGR ddPTM_HeLa_Romidepsin_16h_R1 1 ELDALDANDELTPLGR 16 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 265.77 2.77E-85 8618500 1851.4 1704.1 2047.9 1615.6 1914.7 1856.9 1256.3 1708.7 1859.9 1724.3 FALSE FALSE TRUE 1828.834425 1728.090365 2083.54284 1802.403274 1816.985714 1738.250083 1363.010091 1758.138539 1693.545886 1679.502437 1.088914421 1.028929953 1.24057149 1.073176932 1.081859528 1.034979196 0.811555887 1.04682107 1.008361672 1 10.71381817 -7.975329126 24.44516295 1.06173316 0.927708062 0.316235831 0.082869044 157.9624134 156514.805 0.011352572 0.03405571 1.06E-08 7.975329126 -0.134025098 ELDEEGS(ph)DPPLPGR ddPTM_HeLa_Romidepsin_16h_R1 4 ELDEEGSDPPLPGR 14 0 C9JQV0;Q9BRJ6;H7C0T1;H7C2R9 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 0 ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR;ELDEEGS(1)DPPLPGR ;;; 150.11 0.00061627 134440000 14480.5 14888.5 14197.8 14378.8 14738.9 15607.3 15745.9 16379 15788.8 14920.8 TRUE FALSE FALSE 14304.0061 15098.10069 14444.90675 16041.34451 13986.71893 14610.0439 17083.35635 16852.90052 14376.61018 14533.15547 0.984232649 1.038872854 0.993927767 1.103775746 0.962400696 1.005290553 1.175474686 1.159617439 0.989228404 1 13.82706036 -7.763751968 24.8862628 1.002285127 1.167546108 0.73878558 0.037330916 17.47431734 188057.0145 0.0050309 0.016242735 1.72E-08 7.763751968 0.165260981 ELDFSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 ELDFSSPGR 9 0 Q4AC94;Q4AC94-2;Q4AC94-4;Q4AC94-1;Q4AC94-3;H0YG44;H7C288;H7BZB4 Q4AC94 C2CD3 C2 domain-containing protein 3 1 0 ELDFS(0.004)S(0.996)PGR 102.06 0.026461 5295500 3498.4 3806 3497.6 3814.4 4906.3 5508.6 4666.7 5116.2 3615.8 3902.4 TRUE FALSE FALSE 3455.760155 3859.580968 3558.474261 4255.438875 4655.913203 5156.618238 5063.089382 5264.229175 3292.393792 3801.015085 0.909167703 1.015407958 0.936190512 1.119553272 1.224913108 1.356642403 1.332036119 1.384953508 0.866188036 1 11.89216904 -8.7836458 1.428892437 0.957972991 1.362885475 0.940173675 0.045750268 0.061265241 0.251009036 0.006559639 0.016269404 1.65E-09 8.7836458 0.404912483 ELDLS(ph)ELDDPDSAYLQEAR ddPTM_HeLa_Romidepsin_16h_R1 2 ELDLSELDDPDSAYLQEAR 19 0 Q9UER7-3;Q9UER7-2;Q9UER7;Q9UER7-5;Q9UER7-4 Q9UER7-3 DAXX Death domain-associated protein 6 1 0 ELDLS(1)ELDDPDSAYLQEAR;ELDLS(0.566)ELDDPDS(0.433)AY(0.002)LQEAR ; 151.31 2.29E-05 8750900 2151.47 2043.86 2444.29 2186.6 2246.5 1805.79 1732.83 1943.77 2664.9 2049.07 TRUE FALSE FALSE 2125.247056 2072.633515 2486.831842 2439.42498 2131.852722 1690.405847 1880.016537 2000.009918 2426.54467 1995.834866 1.064841131 1.03847946 1.246010822 1.222257924 1.068150857 0.846966789 0.941969984 1.002091883 1.215804329 1 10.96277664 -8.287352473 23.79913823 1.065357431 0.931505602 0.360181416 0.098553799 396.7744168 364405.3614 0.014322605 0.032039373 5.16E-09 8.287352473 -0.133851829 ELDPSLVSANDS(ph)PSGMQTR ddPTM_HeLa_Romidepsin_16h_R1 3 ELDPSLVSANDSPSGMQTR 19 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 ELDPSLVS(0.002)ANDS(0.98)PS(0.017)GMQTR;ELDPS(0.001)LVS(0.006)ANDS(0.764)PS(0.225)GMQT(0.004)R;ELDPSLVSANDS(0.603)PS(0.397)GMQTR ;; 145.99 7.85E-05 73136000 13031.8 13163 13297.3 11245.4 8635.3 8608.4 5845.9 6795.9 14914 12763.6 TRUE FALSE FALSE 12872.96341 13348.30906 13528.73393 12545.64606 8194.608418 8058.351022 6342.4506 6992.528644 13580.05449 12431.99983 1.035470044 1.073705698 1.088218638 1.009141428 0.659154483 0.648194267 0.510171387 0.562462093 1.09234674 1 13.60177077 -8.704182787 3.194318257 1.029141829 0.575949167 0.960207873 0.045482201 0.035155562 0.727840542 0.006921031 0.014368111 1.98E-09 8.704182787 -0.453192662 ELDQDMVT(ph)EDEDDPGSHK ddPTM_HeLa_Romidepsin_16h_R1 2 ELDQDMVTEDEDDPGSHK 18 0 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 0 ELDQDMVT(1)EDEDDPGSHK;ELDQDMVT(1)EDEDDPGSHK ; 159.98 2.50E-10 3137400 4900.2 2371.8 3748.4 1658.76 2644.2 2505.9 2548.7 2753.9 4110.1 3723.5 TRUE FALSE FALSE 4840.474478 2405.190263 3813.63933 1850.553636 2509.256607 2345.781077 2765.186514 2833.579752 3742.482362 3626.762933 1.334654227 0.663178241 1.05152705 0.510249407 0.691872243 0.646797467 0.762439279 0.781297207 1.031907084 1 11.82446673 -10.2522834 24.85773555 1.158031163 0.73019107 0.570971431 0.15500754 318.601974 864978.742 0.028777822 0.034975951 5.59E-11 10.2522834 -0.427840093 ELDQDMVT(ph)EDEDDPGSHKR ddPTM_HeLa_Romidepsin_16h_R1 1 ELDQDMVTEDEDDPGSHKR 19 1 Q9NRL2;Q9NRL2-2;A0A087WWN7 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 0 ELDQDMVT(1)EDEDDPGSHKR 52.926 0.021822 14163000 3770.9 3847.3 4395.6 2651.3 3326.4 3567.8 2540.5 3731.2 4481.3 4000.9 TRUE FALSE FALSE 3724.93882 3901.46239 4472.103574 2957.855781 3156.641395 3339.829095 2756.290007 3839.156385 4080.481304 3896.956041 0.955858568 1.001156377 1.14758892 0.759016974 0.810027458 0.857035353 0.707293071 0.985167999 1.047094517 1 11.92813194 -9.239780373 24.99288319 0.992110155 0.818332131 0.573285404 0.085967603 478.8913299 552605.4922 0.011852294 0.019643378 5.76E-10 9.239780373 -0.173778023 ELEAENYHDIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 ELEAENYHDIKR 12 1 A0A087WUZ3;Q01082;Q01082-2;F8W6C1;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 1 ELEAENYHDIK(1)R 126.1 0.001161 1428600 258.21 287.04 366.76 268.13 658.08 572.56 548.56 707.14 614.1 593.38 FALSE TRUE FALSE 255.0628372 291.0809567 373.143304 299.1324522 624.495722 535.9752639 595.1546727 727.5999802 559.173358 577.9639021 0.441312747 0.503631724 0.645616971 0.517562518 1.080509907 0.92735076 1.029743675 1.258902118 0.967488378 1 9.174835579 -8.746164163 24.71884648 0.689443998 1.060472559 0.508919795 0.189671994 182.6205139 295520.4591 0.035036622 0.069855759 1.79E-09 8.746164163 0.371028561 ELEAIFGRPVVDGEEGEPHS(ph)ISPR ddPTM_HeLa_Romidepsin_16h_R1 2 ELEAIFGRPVVDGEEGEPHSISPR 24 1 P36507;G5E9C7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 0 ELEAIFGRPVVDGEEGEPHS(0.833)IS(0.167)PR;ELEAIFGRPVVDGEEGEPHS(0.954)IS(0.046)PR ; 115.83 1.02E-06 23699000 7547.9 6478.8 7749.5 5656.5 9362 10147.7 9920.1 9843.4 7709.3 6683 TRUE FALSE FALSE 7455.903292 6570.008716 7884.376797 6310.531145 8884.222206 9499.29472 10762.71305 10128.20325 7019.7609 6509.374697 1.145410065 1.009314876 1.21123413 0.969452741 1.364834968 1.459325229 1.653417348 1.555941042 1.07840787 1 12.66830325 -8.441813526 1.914529013 1.070138893 1.590112487 0.873097214 0.083854685 0.083223469 0.593666399 0.012684894 0.035145162 3.62E-09 8.441813526 0.519973594 ELEDATETADAMNR ddPTM_HeLa_Romidepsin_16h_R1 1 ELEDATETADAMNR 14 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 172.21 9.40E-05 23935000 1521.8 1929.2 1851.7 2053.5 1716.3 2115.3 1779.3 1808.5 1852.6 1525.8 FALSE FALSE TRUE 1503.251716 1956.359328 1883.928062 2290.935332 1628.710807 1980.139157 1930.433698 1860.826094 1686.898816 1486.159496 1.011500933 1.316385848 1.267648638 1.541513773 1.095919254 1.332386707 1.298941132 1.252103895 1.135072528 1 10.53737324 -10.26404921 23.02877997 1.005430976 1.301965677 0.512054932 0.110235239 31.78918381 280503.4241 0.016002769 0.018762437 5.44E-11 10.26404921 0.296534701 ELEDHIR ddPTM_HeLa_Romidepsin_16h_R1 1 ELEDHIR 7 0 E9PM95;J3KQL8;Q9BQE5 E9PM95 APOL2 Apolipoprotein L2 0 0 151.29 4.18E-12 0 1782.6 1606.6 1316.5 1333 1542.1 1259.2 912.16 1252.5 1713.9 1849 FALSE FALSE TRUE 1760.872986 1629.217757 1339.41313 1487.127732 1463.400883 1178.741184 989.6388476 1288.739111 1560.604491 1800.962713 0.977739835 0.904637139 0.743720634 0.825740434 0.812565897 0.654506157 0.549505462 0.71558345 0.866539035 1 10.8145526 -9.132828957 0.532022551 1.004158014 0.599946931 0.682185629 0.076000223 0.291742724 0.15119185 0.016324511 0.052768768 7.36E-10 9.132828957 -0.404211083 ELEEEEENSDEDELDS(ph)HTMVK ddPTM_HeLa_Romidepsin_16h_R1 2 ELEEEEENSDEDELDSHTMVK 21 0 E5RFQ9;A0A087WZ06;Q13188;Q13188-2 E5RFQ9 STK3 Serine/threonine-protein kinase 3;Serine/threonine-protein kinase 3 36kDa subunit;Serine/threonine-protein kinase 3 20kDa subunit 1 0 ELEEEEENSDEDELDS(0.845)HT(0.155)MVK;ELEEEEENSDEDELDS(0.849)HT(0.151)MVK ; 143.71 8.52E-06 283460000 8647.8 8500.2 8353.4 6587.2 11880.3 12682.2 11779.8 12734.6 9566.7 8616.2 TRUE FALSE FALSE 8542.397287 8619.866039 8498.787423 7348.843058 11274.00396 11871.84835 12780.37592 13103.05556 8711.030392 8392.349882 1.017879069 1.027109947 1.012682686 0.875659757 1.343366771 1.414603599 1.522860236 1.561309495 1.037972739 1 13.03485911 -8.590390703 3.749057651 1.002536092 1.490133523 0.939775529 0.058461837 0.037814436 1.067512247 0.008621142 0.018300474 2.57E-09 8.590390703 0.487597431 ELEELKEIEADLER ddPTM_HeLa_Romidepsin_16h_R1 1 ELEELKEIEADLER 14 1 K7EJH0;K7EMX1;K7EJV2;K7ESQ2;Q8NBT2 K7EJH0 SPC24 Kinetochore protein Spc24 0 0 99.732 0.011803 1710200 2037.6 1739.3 1591.8 1372.3 1765.2 1768.6 1214 1387.6 1967.1 1681.8 FALSE FALSE TRUE 2012.764947 1763.785911 1619.504611 1530.971783 1675.115257 1655.592168 1317.11713 1427.748017 1791.157649 1638.106594 1.22871427 1.076722307 0.988644217 0.934598389 1.022592342 1.010674259 0.804048488 0.871584317 1.093431683 1 10.67781352 -8.361754454 0.6530835 1.103206529 0.819250742 0.537596488 0.076556364 0.848018545 0.517187338 0.020090058 0.138086153 4.35E-09 8.361754454 -0.283955787 ELEELS(ph)LEAQGIK ddPTM_HeLa_Romidepsin_16h_R1 2 ELEELSLEAQGIK 13 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 ELEELS(1)LEAQGIK;ELEELS(1)LEAQGIK ; 176.87 8.90E-07 6223700 4286.7 4066.5 4451.1 2621.8 4297.5 5171.9 4188.3 4861.8 4452 4669.3 TRUE FALSE FALSE 4234.452052 4123.748294 4528.569528 2924.944852 4078.182539 4841.432282 4544.054097 5002.468512 4053.80197 4547.990913 0.931059919 0.906718675 0.995729678 0.643129001 0.896699799 1.064521098 0.999134384 1.099929311 0.891339065 1 12.15101366 -8.254106079 24.25993902 0.935220911 1.048988886 0.290341488 0.101358849 495.0155131 1637596.077 0.015135071 0.037725725 5.57E-09 8.254106079 0.113767975 ELEEVS(ph)PETPVVPATTQR ddPTM_HeLa_Romidepsin_16h_R1 4 ELEEVSPETPVVPATTQR 18 0 Q15149 Q15149 PLEC Plectin 1 0 ELEEVS(0.998)PET(0.002)PVVPATTQR;ELEEVS(0.983)PET(0.017)PVVPATTQR;ELEEVS(1)PETPVVPATTQR;ELEEVS(0.942)PET(0.058)PVVPATTQR ;;; 139.49 0.0006043 104279300 9604.3 9195.5 9843.2 7942.8 9355.6 9919.9 8675.9 9535 10345.9 9949.9 TRUE FALSE FALSE 9487.239097 9324.95449 10014.51677 8861.183908 8878.148821 9286.050405 9412.830729 9810.880181 9420.536792 9691.400164 0.97893379 0.962188573 1.033340549 0.914334746 0.916085258 0.958174283 0.971256018 1.012328458 0.972051162 1 13.2424894 -9.25762701 24.94623971 0.990217822 0.953447327 0.233800287 0.031512628 367.224652 2402935.939 0.004795363 0.00775681 5.53E-10 9.25762701 -0.036770494 ELEKPIQSKPQSPVIQAAAVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ELEKPIQSKPQSPVIQAAAVSPK 23 2 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 0 ELEKPIQSKPQSPVIQAAAVS(1)PK;ELEKPIQSKPQSPVIQAAAVS(1)PK ; 94.037 3.39E-05 210374000 7882.8 7544 7733.8 8264 5816 5577.4 4388.8 5751.7 7166.6 7507.2 TRUE FALSE FALSE 7786.721402 7650.20463 7868.403545 9219.522563 5519.187818 5221.02214 4761.584562 5918.116365 6525.601347 7312.161862 1.064900032 1.046230209 1.076070756 1.260847713 0.75479563 0.714018951 0.651186975 0.809352484 0.892431195 1 12.83608229 -8.647454801 7.972564071 1.050611142 0.720742553 0.746969234 0.092528869 0.076558423 5.069391505 0.011489787 0.023025246 2.25E-09 8.647454801 -0.32986859 ELEQHIQT(ph)SDPENFQSEER ddPTM_HeLa_Romidepsin_16h_R1 1 ELEQHIQTSDPENFQSEER 19 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 0 ELEQHIQT(0.813)S(0.187)DPENFQSEER 105.51 0.0007907 7982400 4968.7 4850.7 4647.3 4420.5 5174.7 5419.3 4095.3 4556.7 5026.7 5343.4 TRUE FALSE FALSE 4908.139573 4918.988282 4728.184307 4931.619009 4910.61575 5073.02422 4443.15468 4688.540925 4577.099362 5204.577698 0.943042809 0.945127264 0.908466466 0.947554114 0.943518578 0.974723506 0.853701287 0.900849444 0.879437224 1 12.34556539 ELEQHIQTS(ph)DPENFQSEER ddPTM_HeLa_Romidepsin_16h_R1 1 ELEQHIQTSDPENFQSEER 19 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 0 ELEQHIQT(0.072)S(0.927)DPENFQSEER 102.16 0.00051595 11437000 3712.1 3968.7 3736.2 2842.2 3494.9 3863.1 2968.2 3369 3997.6 3629.5 TRUE FALSE FALSE 3666.855497 4024.571463 3801.226994 3170.828537 3316.542212 3616.260378 3220.318834 3466.4767 3640.044644 3535.205067 1.037239829 1.138426594 1.075249362 0.896929167 0.938147052 1.022928037 0.910928439 0.980558874 1.029655869 1 11.78757819 -9.266533445 24.99623475 1.032949349 0.95113768 0.507363871 0.049772707 371.1774039 1821339.466 0.008324723 0.012970743 5.41E-10 9.266533445 -0.081811669 ELESPLT(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 ELESPLTPGK 10 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 ELES(0.109)PLT(0.891)PGK;ELES(0.009)PLT(0.991)PGK ; 167.11 0.0027443 73281000 15955.9 15403.5 16186.8 12941.7 9363.1 8234.8 6986.7 7488 16098.9 15197.6 TRUE FALSE FALSE 15761.42335 15620.35088 16468.52446 14438.08025 8885.266068 7708.622857 7580.150124 7704.653466 14658.97406 14802.76416 1.064762174 1.05523203 1.112530355 0.975363796 0.600243709 0.520755635 0.512076666 0.520487483 0.990286267 1 13.85357898 -8.749121904 3.343739487 1.039824722 0.521870513 0.982699484 0.03239024 0.023037329 0.537606333 0.005392107 0.010908354 1.78E-09 8.749121904 -0.517954209 ELESQISELQEDLESER ddPTM_HeLa_Romidepsin_16h_R1 2 ELESQISELQEDLESER 17 0 P35579 P35579 MYH9 Myosin-9 0 0 ; ; 325.24 1.50E-179 33011000 3889.4 3700.1 3749.8 3004.23 4002.3 4317.4 3637 3724.6 3564.2 3545 FALSE FALSE TRUE 3841.994497 3752.190105 3815.063696 3351.593208 3798.047696 4041.532074 3945.926689 3832.365425 3245.409025 3452.900389 1.112686166 1.086677773 1.104886694 0.970660265 1.099958663 1.170474563 1.142786135 1.109897475 0.939908095 1 11.753593 -16.52287875 0.210868347 0.491377059 1.11914528 0.491824267 0.051773791 41.32143626 0.514153129 8.678879433 0.046731813 3.00E-17 16.52287875 0.627768221 AGGDLSLS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 4 AGGDLSLSPGR 11 0 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 AGGDLSLS(1)PGR;AGGDLSLS(1)PGR;AGGDLS(0.002)LS(0.998)PGR;AGGDLSLS(1)PGR ;;; 158.34 0.0016346 77483000 18894.2 17967.8 15420.1 11117.9 6372.3 4945.5 4473.02 5110.9 17778 16963.1 TRUE FALSE FALSE 18663.91022 18220.75116 15688.48037 12403.40391 6047.097753 4629.498511 4852.958207 5258.775828 16187.89115 16522.39622 1.129612798 1.10279108 0.949528154 0.750702486 0.365993992 0.280195345 0.293719999 0.318281668 0.979754446 1 14.01213531 -8.955062375 1.721237306 1.064436368 0.287442113 0.978925645 0.04977374 0.037505672 0.222668987 0.00907762 0.018905206 1.11E-09 8.955062375 -0.776994255 down ELFDDPSYVNVQNLDK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFDDPSYVNVQNLDK 16 0 Q5T188;H0Y539;X6R6D0;P29353-5;P29353-3;P29353-2;P29353-7;P29353;P29353-6 Q5T188 SHC1 SHC-transforming protein 1 0 0 142.1 4.51E-07 0 583.92 505.57 592.62 805.82 680.59 472.41 240.69 462.16 870.65 745.73 FALSE FALSE TRUE 576.8029584 512.6874277 602.9343025 898.9926999 645.8569527 442.2245256 261.1342026 475.5318704 792.7768834 726.3558271 0.794105226 0.705835086 0.830081181 1.237675346 0.889174326 0.608826293 0.35951278 0.654681704 1.09144424 1 9.504532658 -8.181568893 3.841982042 0.905262664 0.504986866 0.558520205 0.160433767 0.135920638 3.810810919 0.022752745 0.061675147 6.58E-09 8.181568893 -0.400275798 ELFQT(ph)PDHTEESTTDDK ddPTM_HeLa_Romidepsin_16h_R1 3 ELFQTPDHTEESTTDDK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.996)PDHT(0.004)EESTTDDK;ELFQT(1)PDHTEESTTDDK;ELFQT(0.997)PDHT(0.003)EESTTDDK ;; 119.04 0.0016821 21822100 6999.2 5607.65 7204.9 3677.7 4828.29 6572.8 6222.8 5670.2 8071 7551 TRUE FALSE FALSE 6913.891058 5686.594644 7330.298262 4102.932978 4581.884344 6152.819293 6751.364477 5834.258291 7349.109546 7354.823931 0.94004848 0.773178895 0.996665363 0.557856043 0.622976755 0.836569216 0.917950523 0.793256011 0.999223042 1 12.84447509 -10.21108245 1.118827833 0.981538774 0.770129546 0.363087352 0.119658542 0.367632977 0.894237592 0.025463105 0.030984067 6.15E-11 10.21108245 -0.211409228 ELFQT(ph)PGHTEEAVAAGK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFQTPGHTEEAVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.975)PGHT(0.025)EEAVAAGK 105.38 0.0019262 12582000 5223.1 4768.5 4513.8 3388.8 3279.5 3836.2 3607.1 3815.3 4576.7 4337.9 TRUE FALSE FALSE 5159.438848 4835.631068 4592.360796 3780.629001 3112.134877 3591.079201 3913.486984 3925.689686 4167.348489 4225.200733 1.221110942 1.144473689 1.086897661 0.89478092 0.736564976 0.849919194 0.926225103 0.929113179 0.986307812 1 12.04480417 -9.250164007 4.10175652 1.110442615 0.859514359 0.645999072 0.081126437 0.113482014 4.579499231 0.015069265 0.024669908 5.62E-10 9.250164007 -0.250928257 ELFQT(ph)PGHTEELVAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 ELFQTPGHTEELVAAGK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.989)PGHT(0.011)EELVAAGK;ELFQT(0.971)PGHT(0.029)EELVAAGK ; 117.53 0.0045151 11513500 4710.9 4084.7 5634.7 3586.1 3370.9 3772.3 3327 3399.4 4814.7 4769.2 TRUE FALSE FALSE 4653.481739 4142.204514 5732.76959 4000.741755 3198.870394 3531.262205 3609.595297 3497.756276 4384.061173 4645.295496 1.001762265 0.89169882 1.234102243 0.861245912 0.688625814 0.760180317 0.777043204 0.752967444 0.94376368 1 12.18155466 -9.005827391 21.9424996 1.008612421 0.751471392 0.687996444 0.085745248 20.79360939 78299.76027 0.01124537 0.019868131 9.87E-10 9.005827391 -0.257141029 ELFQT(ph)PGPSEESMTDEK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFQTPGPSEESMTDEK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.597)PGPS(0.134)EES(0.235)MT(0.034)DEK 100.69 0.007799 6556100 4250.1 3844.2 4154.6 2752.9 2837.4 3303.2 2767.6 3027.2 4270.3 3852.7 TRUE FALSE FALSE 4198.298146 3898.318749 4226.90907 3071.203251 2692.59689 3092.136181 3002.679875 3114.787256 3888.353673 3752.606299 1.118768614 1.038829666 1.126392894 0.818418722 0.717527147 0.82399696 0.800158513 0.830033051 1.036174158 1 11.87367722 -9.2138981 7.070710757 1.060688006 0.794065143 0.893694939 0.045866248 0.069031379 8.697399736 0.008322536 0.013794118 6.11E-10 9.2138981 -0.266622863 ELFQTPDHT(ph)EESTTDDKTTK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFQTPDHTEESTTDDKTTK 20 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.042)PDHT(0.936)EES(0.009)T(0.009)T(0.003)DDKTTK 108.34 0.00022633 11209000 933.82 878.23 1056.7 767.8 855.93 811.79 852.51 873.8 1105.8 959.07 TRUE FALSE FALSE 922.4382427 890.593745 1075.09142 856.5766486 812.2486982 759.9192389 924.9221781 899.0820244 1006.894478 934.1532231 0.987459252 0.953370093 1.150872677 0.916955193 0.869502645 0.813484576 0.990118275 0.962456696 1.077868655 1 9.867515395 -9.035754888 24.99357945 1.00235202 0.906046634 0.395842196 0.07109222 509.5194705 356166.2115 0.009861069 0.016356883 9.21E-10 9.035754888 -0.096305387 ELFQTPDHTEES(ph)TTDDKTTK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFQTPDHTEESTTDDKTTK 20 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQTPDHT(0.006)EES(0.787)T(0.144)T(0.046)DDKT(0.005)T(0.013)K 96.153 0.00038587 11446000 1826.4 1414.5 1680.4 980.3 1408.6 1450.8 1851.3 1519.7 1887.4 1604.7 TRUE FALSE FALSE 1804.139134 1434.413368 1709.646657 1093.646898 1336.713886 1358.098562 2008.549376 1563.670122 1718.586217 1563.009663 1.154272541 0.917725208 1.093817075 0.699705782 0.855217928 0.868899659 1.285052437 1.000422556 1.099536527 1 10.61011098 -10.24871531 24.61117697 1.072850923 0.96020057 0.124141586 0.150554869 1147.903595 2220302.885 0.026531637 0.032375129 5.64E-11 10.24871531 -0.112650353 ELFQTPGPS(ph)EESMTDEK ddPTM_HeLa_Romidepsin_16h_R1 1 ELFQTPGPSEESMTDEK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 ELFQT(0.017)PGPS(0.568)EES(0.218)MT(0.197)DEK 84.41 0.019708 6538200 4170.4 3831.5 4275.4 2349 2812.4 3838.3 3065.5 3056.3 3956.1 3867 TRUE FALSE FALSE 4119.569561 3885.439958 4349.811544 2620.602432 2668.872733 3593.045018 3325.883493 3144.729218 3602.256508 3766.534783 1.093729329 1.031568851 1.15485766 0.69575952 0.708575093 0.953939158 0.883008836 0.834913097 0.956384772 1 11.87902214 -9.264749277 24.99964561 1.051772189 0.820783899 0.643045067 0.086370222 140.4168101 1060568.517 0.013282222 0.020807622 5.44E-10 9.264749277 -0.230988289 ELGITALHIK ddPTM_HeLa_Romidepsin_16h_R1 2 ELGITALHIK 10 0 P62263;A0A2R8Y811;E5RH77 P62263 RPS14 40S ribosomal protein S14 0 0 ; ; 108.43 0.00049121 889600 1431.79 1336.78 2276.75 1600.89 2115.52 1735.03 1636.25 1305.32 1479.03 1103.95 FALSE FALSE TRUE 1414.338793 1355.599224 2316.375879 1785.992434 2007.55712 1624.167183 1775.233034 1343.087375 1346.741853 1075.26922 1.315334585 1.260706806 2.154228761 1.660972342 1.867027423 1.510474914 1.650966104 1.249070791 1.252469454 1 10.0704822 -10.41839795 1.254800509 1.104771945 1.666585965 0.416912226 0.250540107 0.253211994 0.782989811 0.052094232 0.057726621 3.82E-11 10.41839795 0.56181402 LTPVS(ph)PESS(ph)STEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTPVSPESSSTEEK 14 0 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 LT(0.001)PVS(0.999)PES(0.004)S(0.917)S(0.068)T(0.011)EEK 144.8 0.0063226 11241000 8904.4 8549.4 8239.6 5478.4 3885.1 3209.3 3092.9 3233.4 9009.3 8317.6 TRUE FALSE FALSE 8795.869748 8669.758678 8383.006782 6111.838385 3686.82885 3004.236088 3355.610849 3326.953328 8203.485644 8101.507553 1.085707776 1.070141405 1.034746524 0.75440754 0.455079357 0.370824327 0.414195855 0.410658548 1.012587545 1 12.98397468 -8.954338307 2.112443589 1.045248981 0.397510584 0.990874474 0.028422284 0.026202709 0.235280804 0.005978374 0.011855776 1.11E-09 8.954338307 -0.647738398 down ELGSPT(ph)DEDSGQDQQLLR ddPTM_HeLa_Romidepsin_16h_R1 1 ELGSPTDEDSGQDQQLLR 18 0 H0Y713;Q86YN6-6;Q86YN6-5;Q86YN6-4;Q86YN6-2;Q86YN6-3;Q86YN6 H0Y713 PPARGC1B Peroxisome proliferator-activated receptor gamma coactivator 1-beta 1 0 ELGS(0.242)PT(0.758)DEDSGQDQQLLR 81.01 0.026401 2222100 346.86 352.39 334.46 323.12 343.58 296.27 280.99 298.03 427.82 487.6 TRUE FALSE FALSE 342.6323369 357.3509557 340.281136 360.4806547 326.0458305 277.3393032 304.8572836 306.6530278 389.5547077 474.9320817 0.721434391 0.752425388 0.716483786 0.75901517 0.686510436 0.583955715 0.64189659 0.645677645 0.820232456 1 8.891577403 -16.52287875 0.152266833 2.217002085 0.577668193 0.62143191 0.067585276 12.82491188 0.132493238 4.634028114 0.08808466 3.00E-17 16.52287875 -1.639333893 ELGTGEQPLS(ph)PTTATSPYGGGHALAGQTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ELGTGEQPLSPTTATSPYGGGHALAGQTSPK 31 0 A0A087WXB3;A0A087X223;A0A087WYW1;Q96NU1-4;Q96NU1-5;H7C3J6;H7BY14;A0A087WYU3;A0A087X1J5;Q96NU1-1;Q96NU1-2;Q96NU1-6;Q96NU1 A0A087WXB3 SAMD11 Sterile alpha motif domain-containing protein 11 2 0 ELGT(0.003)GEQPLS(0.722)PT(0.13)T(0.087)AT(0.07)S(0.059)PY(0.098)GGGHALAGQT(0.102)S(0.731)PK 59.525 0.0048263 9762200 2158.6 2082.2 2356.4 1274.1 1950.5 1507.9 1269.6 1524 2504.5 2432.1 TRUE FALSE FALSE 2132.290153 2111.513266 2397.412154 1421.417437 1850.958707 1411.550057 1377.439792 1568.094536 2280.491247 2368.913691 0.900113061 0.891342422 1.012030182 0.600029221 0.781353375 0.59586386 0.581464744 0.661946673 0.962673843 1 11.21000992 -9.259567579 24.99957667 0.950079441 0.64559197 0.85715661 0.063083323 48.75352977 651145.5596 0.01026703 0.016475118 5.50E-10 9.259567579 -0.304487471 ELGTGEQPLS(ph)PTTATSPYGGGHALAGQTSPK ddPTM_HeLa_Romidepsin_16h_R1 1 ELGTGEQPLSPTTATSPYGGGHALAGQTSPK 31 0 A0A087WXB3;A0A087X223;A0A087WYW1;Q96NU1-4;Q96NU1-5;H7C3J6;H7BY14;A0A087WYU3;A0A087X1J5;Q96NU1-1;Q96NU1-2;Q96NU1-6;Q96NU1 A0A087WXB3 SAMD11 Sterile alpha motif domain-containing protein 11 1 0 ELGT(0.001)GEQPLS(0.379)PT(0.162)T(0.162)AT(0.162)S(0.128)PY(0.006)GGGHALAGQTSPK 80.465 2.76E-08 10327000 2727.8 2701.3 2755.8 2050.3 2915.2 2716.5 1745 1658.6 4501 3857.6 TRUE FALSE FALSE 2694.552524 2739.328972 2803.763543 2287.365333 2766.426466 2542.924417 1893.220256 1706.588974 4098.419287 3757.378996 0.717136208 0.729053145 0.746201952 0.6087662 0.736264952 0.676781453 0.503867259 0.454196656 1.090765475 1 11.87551093 -16.52287875 0.058170726 2.452491274 4.92E-11 0.860632451 0.069653536 86.89276891 0.397529373 18.51306674 3.659685453 3.00E-17 16.52287875 -2.452491274 ELGTGEQPLSPT(ph)TATSPYGGGHALAGQTSPK ddPTM_HeLa_Romidepsin_16h_R1 1 ELGTGEQPLSPTTATSPYGGGHALAGQTSPK 31 0 A0A087WXB3;A0A087X223;A0A087WYW1;Q96NU1-4;Q96NU1-5;H7C3J6;H7BY14;A0A087WYU3;A0A087X1J5;Q96NU1-1;Q96NU1-2;Q96NU1-6;Q96NU1 A0A087WXB3 SAMD11 Sterile alpha motif domain-containing protein 11 1 0 ELGTGEQPLS(0.134)PT(0.409)T(0.409)AT(0.045)S(0.003)PYGGGHALAGQTSPK 135.78 2.94E-15 14522000 3645.9 3854.8 2920.4 2342.4 3182.8 3106.1 2461.4 2278.8 5300.9 4695.5 TRUE FALSE FALSE 3601.462368 3909.067976 2971.228337 2613.239309 3020.369839 2907.630234 2670.471255 2344.733483 4826.774228 4573.510233 0.787461312 0.854719412 0.649660367 0.571385911 0.660405178 0.635754614 0.5838997 0.512676995 1.055376282 1 12.15908616 -10.33069902 0.190542598 1.138168941 0.402954027 0.898119184 0.056337017 0.668856239 0.11792441 0.188298464 0.195759044 4.67E-11 10.33069902 -0.735214914 ELHINLIPNK ddPTM_HeLa_Romidepsin_16h_R1 2 ELHINLIPNK 10 0 P07900-2;P07900;G3V2J8;Q14568 P07900-2 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 0 ; ; 107.79 0.0019506 4327000 6124.4 4680.3 10116.1 4407.5 9108.1 10508.6 9097.8 6980.8 4971 4401.5 FALSE FALSE TRUE 6049.753457 4746.189386 10292.16648 4917.115888 8643.27967 9837.134375 9870.566905 7182.778434 4526.38131 4287.148395 1.411136937 1.107073735 2.400702175 1.146943244 2.016090621 2.294563534 2.302361849 1.675420996 1.05580234 1 12.06580264 -9.767338845 0.411925597 1.035185021 2.1913117 0.485001602 0.387715855 0.677394175 0.267573852 0.163672378 0.302438811 1.71E-10 9.767338845 1.156126679 ELHIQGNR ddPTM_HeLa_Romidepsin_16h_R1 1 ELHIQGNR 8 0 Q15404-2;Q15404 Q15404-2 RSU1 Ras suppressor protein 1 0 0 84.916 0.023539 1688600 1167 1091.3 1252.3 1360.1 1278.5 1667.1 1667.2 488.46 1268.1 1213.2 FALSE FALSE TRUE 1152.776155 1106.66335 1274.095756 1517.361161 1213.253374 1560.57769 1808.811926 502.5928194 1154.67796 1181.680889 0.975539307 0.936516246 1.078206281 1.284070154 1.026718284 1.320642235 1.530710992 0.425320257 0.977148713 1 10.20662478 -9.544874123 6.870273414 0.985003328 1.150125603 0.053329584 0.271144679 0.32360981 60.25969831 0.038818817 0.055617291 2.85E-10 9.544874123 0.165122275 ELHPQLLS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 ELHPQLLSPTK 11 0 E9PK89;Q8TBN0 E9PK89 RAB3IL1 Guanine nucleotide exchange factor for Rab-3A 1 0 ELHPQLLS(0.972)PT(0.028)K 121.92 0.0038436 12105000 6987.4 7075.6 9755.1 9214.6 9095 9200.7 7541.8 7125.1 8102.1 6796.1 TRUE FALSE FALSE 6902.234881 7175.210483 9924.883423 10280.03541 8630.848212 8612.804964 8182.400304 7331.253527 7377.427884 6619.536342 1.042706698 1.083944571 1.499332115 1.552984209 1.303844826 1.301119069 1.236098706 1.107517679 1.114493146 1 12.69251445 -9.903607764 6.454085782 1.022372217 1.335485179 0.544417402 0.121630306 0.112861792 6.45345127 0.020440277 0.026945008 1.25E-10 9.903607764 0.313112962 ELILGSETPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ELILGSETPSSPR 13 0 R4GNJ5;A0A590TQL1;Q96AP0-2;Q96AP0 R4GNJ5 ACD Adrenocortical dysplasia protein homolog 1 0 ELILGSETPS(0.078)S(0.922)PR;ELILGSETPS(0.049)S(0.951)PR ; 222.56 2.14E-31 58463000 11120.8 11271.5 10944.6 10455 10154.7 12587.1 11747.7 12084.7 11223.3 10238.8 TRUE FALSE FALSE 10985.25541 11430.18047 11135.08617 11663.85629 9636.467767 11782.82493 12745.54934 12434.35173 10219.45994 9972.7945 1.101522288 1.146136168 1.116546237 1.169567496 0.966275578 1.181496814 1.278031884 1.246827229 1.024733834 1 13.28378211 -4 0.142699957 0.981616602 1.926458701 0.522463726 0.06747621 44.44604761 0.416659981 0.180698781 8.634788373 1.00E-04 4 0.944842099 ELIPQES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ELIPQESPR 9 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 0 ELIPQES(1)PR 121.68 0.012543 12464000 4518.7 3921.8 4019.6 3521.3 4861.4 4625.6 4034.4 3918.9 4498.5 3967 TRUE FALSE FALSE 4463.624346 3977.011203 4089.559452 3928.449274 4613.304618 4330.039088 4377.081835 4032.287188 4096.142893 3863.936768 1.155201188 1.029264049 1.058391919 1.016696056 1.193938953 1.120628869 1.132803692 1.043569662 1.060095736 1 11.91585577 -8.774780354 24.99975111 1.066548619 1.123304025 0.275152241 0.052645859 353.3714108 662185.05 0.01001457 0.018229811 1.68E-09 8.774780354 0.056755406 ELIPTEEALR ddPTM_HeLa_Romidepsin_16h_R1 1 ELIPTEEALR 10 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 159.28 0.026565 3743800 2124.8 2099.7 2502.7 1966.5 2063.4 2880.4 2123.7 1731.3 2412.5 1874.9 FALSE FALSE TRUE 2098.90212 2129.259632 2546.258444 2193.875983 1958.096998 2696.351736 2304.087025 1781.392434 2196.719958 1826.189828 1.149334033 1.165957448 1.394301077 1.2013406 1.07223081 1.476490393 1.261690866 0.975469476 1.202897927 1 10.83462102 -11.18565083 0.697480435 1.013980861 1.233371197 0.033898048 0.148244376 0.582336407 0.621356381 0.055989919 0.033607227 6.52E-12 11.18565083 0.219390336 ELIQEYGAQS(ph)GGLEK ddPTM_HeLa_Romidepsin_16h_R1 2 ELIQEYGAQSGGLEK 15 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 ELIQEYGAQS(1)GGLEK;ELIQEY(0.002)GAQS(0.998)GGLEK ; 149.97 0.00047643 7857500 2809 2998.2 2673.8 2694 4118.4 4965.1 4270.3 5311.2 3328.5 3150.6 TRUE FALSE FALSE 2774.762828 3040.408738 2720.336367 3005.492956 3908.22268 4647.846134 4633.019175 5464.871192 3030.790624 3068.746958 0.904200596 0.99076554 0.886464868 0.979387677 1.273556515 1.51457458 1.509742979 1.780815189 0.987631325 1 11.58343397 -8.376040378 1.380934592 0.948076531 1.665061548 0.946930066 0.069034578 0.068815661 0.246130861 0.010676387 0.038054842 4.21E-09 8.376040378 0.716985017 ELIS(ph)NASDALDK ddPTM_HeLa_Romidepsin_16h_R1 2 ELISNASDALDK 12 0 P14625;Q96GW1;A0A1W2PRR1;F8W026;P08238 P14625;P08238 HSP90B1;HSP90AB1 Endoplasmin;Heat shock protein HSP 90-beta 1 0 ELIS(1)NASDALDK;ELIS(1)NASDALDK ; 169.17 0.00017974 9057300 4827 4806.8 5051.1 2892.4 4752.4 4392.7 4155 5211.4 5861.2 5809.7 TRUE FALSE FALSE 4768.166667 4874.470257 5139.012277 3226.832897 4509.867294 4112.020647 4507.925596 5362.183637 5336.959592 5658.763156 0.842616405 0.861402063 0.908151152 0.570236429 0.796970499 0.726664208 0.796627367 0.947589339 0.94313182 1 12.46627104 -11.49624541 0.488386632 1.010431198 0.782013538 0.324196111 0.098053297 0.815998595 0.396885613 0.083922252 0.031013884 3.19E-12 11.49624541 -0.22841766 ELISNASDALDK ddPTM_HeLa_Romidepsin_16h_R1 1 ELISNASDALDK 12 0 P14625;Q96GW1;A0A1W2PRR1;F8W026;P08238 P14625;P08238 HSP90B1;HSP90AB1 Endoplasmin;Heat shock protein HSP 90-beta 0 0 167.11 0.0020557 496510 255.53 274.56 183.6 219.67 513.7 287.32 325.58 312.53 444.17 361.57 FALSE FALSE TRUE 252.4155021 278.4252629 186.795481 245.069279 487.4839721 268.9611793 353.2347571 321.5725625 404.4423228 352.1763593 0.716730398 0.790584761 0.530403237 0.695870897 1.384204133 0.763711624 1.003005306 0.913100934 1.148408495 1 8.460154258 -7.745455351 24.9197132 0.853509531 0.958053108 0.008895001 0.235389547 782.1443185 1219372.265 0.031259198 0.116205552 1.80E-08 7.745455351 0.104543577 ELISNSSDALDK ddPTM_HeLa_Romidepsin_16h_R1 1 ELISNSSDALDK 12 0 P07900-2;P07900;G3V2J8;Q14568 P07900-2 HSP90AA1;HSP90AA2P Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 0 246.08 3.10E-49 34435000 2295.6 2174.7 2956.9 1674 2312.3 2582.3 2133.8 2573 2604.5 2300.7 FALSE FALSE TRUE 2267.620344 2205.315484 3008.363604 1867.555756 2194.294703 2417.299364 2315.044919 2647.445695 2371.546997 2240.927482 1.011911524 0.984108366 1.342463613 0.833385181 0.979190411 1.078704859 1.033074447 1.181406233 1.058288149 1 11.12988025 -6.520824653 1.27648224 1.017131685 1.853896998 0.100412511 0.121540442 11.74052949 4.061704153 0.016504167 20.43017737 3.01E-07 6.520824653 0.836765312 ELISNSSDALDKIR ddPTM_HeLa_Romidepsin_16h_R1 3 ELISNSSDALDKIR 14 1 P07900-2;P07900;G3V2J8 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;; ;; 143.58 0.00070457 55471400 5990.3 5183.4 4965.71 7221.9 6171.8 5874.1 5146.8 4765.6 5181.03 4129.12 FALSE FALSE TRUE 5917.287919 5256.372041 5052.1361 8056.930058 5856.830016 5498.763968 5583.969064 4903.485117 4717.625701 4021.844867 1.471286963 1.306955443 1.256173788 2.003292102 1.456254582 1.367224284 1.388409859 1.219212893 1.173000416 1 11.97364172 -12.2726369 0.657933766 0.945353288 1.448663271 0.284465244 0.213014306 0.846048907 0.546730285 0.248478129 0.045407533 5.34E-13 12.2726369 0.503309983 ELKTDSS(ph)PNQAR ddPTM_HeLa_Romidepsin_16h_R1 1 ELKTDSSPNQAR 12 1 A6NLN1;P26599;P26599-2;P26599-3;K7ES59;A0A087WU68 A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 1 0 ELKTDS(0.03)S(0.969)PNQAR 159.58 0.0057282 22636000 2931.5 2472.4 2113.5 4393.6 2853.2 2590.4 2524.3 2182.4 2513 2558.2 TRUE FALSE FALSE 2895.76975 2507.206512 2150.284581 4901.608705 2707.590557 2424.8818 2738.713979 2245.544301 2288.230986 2491.737595 1.162148758 1.006208084 0.862965902 1.967144821 1.086627485 0.973169007 1.099118135 0.901196139 0.918327432 1 11.28293643 -5.612972001 8.592135308 1.10317582 0.886698825 0 0.303286307 0 0 0.037476846 0 2.44E-06 5.612972001 -0.216476995 ELLDT(ph)SFEDLSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 0 ELLDT(0.979)S(0.021)FEDLSKPK 122.96 0.002022 51233000 5013.5 4646.5 4728.2 2343.9 3365 3855.1 3448.5 3695.8 5243.7 5625.7 TRUE FALSE FALSE 4952.393534 4711.913549 4810.492338 2614.912746 3193.271493 3608.771552 3741.415504 3802.732142 4774.690339 5479.543503 0.903796736 0.859909871 0.8779002 0.477213612 0.582762322 0.658589817 0.682796934 0.693987034 0.871366444 1 12.41983999 -9.418272315 5.035670706 0.943181198 0.623574955 0.795633847 0.070981831 0.073320585 2.862398015 0.012015791 0.018436784 3.82E-10 9.418272315 -0.319606243 ELLDTS(ph)FEDLSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 ELLDTSFEDLSKPK 14 1 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 0 ELLDT(0.408)S(0.592)FEDLSKPK 64.275 0.027147 58014000 4130.4 3860.3 3830.9 1837.4 2611.7 3045.9 2812.6 2714.5 4056.4 3774.6 TRUE FALSE FALSE 4080.057096 3914.645405 3897.575208 2049.848833 2478.415203 2851.27682 3051.502174 2793.039775 3693.585425 3676.535348 1.109755982 1.064764795 1.060121783 0.557549062 0.674117061 0.775533634 0.829993971 0.759693437 1.004637539 1 11.84413114 -9.280505415 24.83381828 1.05488711 0.726128125 0.83256341 0.073588649 235.7219041 307030.8247 0.012483553 0.019088243 5.24E-10 9.280505415 -0.328758985 ELLEIVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 ELLEIVKK 8 1 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 1 ELLEIVK(1)K 105.57 0.0042128 310430 0 0 0 0 77.341 127 151.75 64.046 0 121.31 FALSE TRUE FALSE 0 0 0 0 73.39400017 118.8851099 164.6396412 65.89906996 0 118.1583487 0 0 0 0 0.621149508 1.006150739 1.393381365 0.557718271 0 1 6.884577759 -8.385123377 3.817330108 0.393676184 1.025811634 0.41045252 0.388076043 0.263196162 6.743140452 0.071657977 0.168782121 4.12E-09 8.385123377 0.63213545 ELLIHER ddPTM_HeLa_Romidepsin_16h_R1 2 ELLIHER 7 0 Q96BN8 Q96BN8 OTULIN Ubiquitin thioesterase otulin 0 0 ; ; 83.265 0.026169 6064700 5058 4624 5268.9 4617.8 5493.6 5852.7 4325.5 5458.3 5321.6 4826.4 FALSE FALSE TRUE 4996.35115 4689.096793 5360.602994 5151.731763 5213.241093 5478.731359 4692.907862 5616.227299 4845.622768 4701.009432 1.06282517 0.99746594 1.140308921 1.095877776 1.108962058 1.165437219 0.998276632 1.194685393 1.030762188 1 12.19875486 -10.52184382 0.278017529 0.985568255 1.135106221 0.330655238 0.056556343 1.305227489 0.35677503 0.074146119 0.066315191 3.01E-11 10.52184382 0.149537967 ELLKPNASVALHK ddPTM_HeLa_Romidepsin_16h_R1 1 ELLKPNASVALHK 13 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 0 49.448 0.029341 531480 862.04 754.47 574.12 491.59 1031.9 1250.5 1027.8 779.01 864.62 891.51 FALSE FALSE TRUE 851.5331249 765.0914485 584.1123178 548.4299488 979.2382925 1170.597086 1115.101306 801.5494253 787.2862217 868.3484417 0.980635289 0.881088065 0.672670428 0.631578203 1.127702021 1.348072997 1.284163422 0.923073488 0.90664782 1 9.762130258 -8.539812031 24.9929515 0.930409663 1.20215575 0.438333163 0.164923145 204.9288337 302467.1022 0.026108115 0.052225604 2.89E-09 8.539812031 0.271746086 ELLPVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 ELLPVKK 7 1 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 1 ELLPVK(1)K 105.39 0.0078625 780970 935.88 1148 1195.8 1006.3 2603.9 1988.9 1863.3 2139.3 2541.7 1934 FALSE TRUE FALSE 924.4731346 1164.161574 1216.612397 1122.653141 2471.013267 1861.815709 2021.568655 2201.19727 2314.363986 1883.754401 0.490760969 0.618000719 0.645844488 0.595965769 1.311749167 0.988353741 1.073159354 1.16851606 1.22859115 1 10.87939517 -8.767145116 24.99997552 0.722436983 1.120489157 0.402149685 0.218692131 96.42473276 422491.8887 0.031551146 0.058345762 1.71E-09 8.767145116 0.398052174 ELLQFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ELLQFKK 7 1 Q8IYH5-2;Q8IYH5;Q8IYH5-3 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 0 1 ; ELLQFK(1)K;ELLQFK(1)K 124.08 0.0035311 2452400 2167.2 2302.7 3555.5 2957.4 2921.6 2674.7 2248.1 1677.11 1882.02 1354.03 FALSE TRUE FALSE 2140.785333 2335.117471 3617.381986 3299.348503 2772.49985 2503.795302 2439.053558 1725.634532 1713.687418 1318.852105 1.623218649 1.770568103 2.742826107 2.501681947 2.102206789 1.898465561 1.849376096 1.308436727 1.299378005 1 10.36506708 -10.96007409 0.932857027 1.123524445 2.05349577 0.443118828 0.384021845 0.305468934 0.568050019 0.118317093 0.094347489 1.10E-11 10.96007409 0.929971325 ELLSPLS(ph)EPDDRYPLIVK ddPTM_HeLa_Romidepsin_16h_R1 2 ELLSPLSEPDDRYPLIVK 18 1 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 ELLS(0.181)PLS(0.819)EPDDRYPLIVK;ELLSPLS(0.999)EPDDRYPLIVK ; 109.37 0.00049866 153581000 8218.8 7887.2 7918.8 6817.9 8896 9185.9 7875 9307.3 8696.2 8077.4 TRUE FALSE FALSE 8118.626104 7998.236209 8056.623392 7606.217677 8442.003924 8598.950636 8543.902303 9576.592041 7918.390092 7867.547984 1.031913135 1.016611049 1.024032317 0.966783767 1.07301588 1.092964498 1.085967613 1.217227027 1.006462256 1 12.94169836 -4 0.553260821 1.012743036 10.23025495 0.849458799 0.026041625 33.11481172 0.273923709 0.004845754 364.7433975 1.00E-04 4 9.217511919 ELLT(ph)SDSPPHNDIMTPVDPGVAQPNSR ddPTM_HeLa_Romidepsin_16h_R1 1 ELLTSDSPPHNDIMTPVDPGVAQPNSR 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 0 ELLT(0.331)S(0.331)DS(0.331)PPHNDIMT(0.006)PVDPGVAQPNSR 43.494 0.027674 2826100 778.76 931.75 779.06 519.95 935.6 879.86 781.05 948.18 1038.2 960.42 TRUE FALSE FALSE 769.2681736 944.867201 792.6192125 580.0690654 887.8528408 823.6397856 847.3923675 975.6140923 945.3407918 935.4681499 0.822334971 1.01004743 0.847296845 0.620084249 0.949100021 0.880457326 0.905848443 1.042915349 1.010553691 1 9.869544724 -7.263158855 4.570803547 0.895440646 1.052129073 0.139291886 0.111314118 0.31788294 17.24298085 0.01580341 0.15902632 5.46E-08 7.263158855 0.156688427 ELLTLDEK(ac)DPR ddPTM_HeLa_Romidepsin_16h_R1 2 ELLTLDEKDPR 11 1 P46781;B5MCT8;C9JM19;F2Z3C0;A8MXK4 P46781 RPS9 40S ribosomal protein S9 0 1 ; ELLTLDEK(1)DPR;ELLTLDEK(1)DPR 147.3 0.004681 3058700 809.04 1312.95 1056.53 809.21 2270 2182.3 2106.9 2152.99 2561.3 2245.4 FALSE TRUE FALSE 799.1791093 1331.433745 1074.918461 902.7746676 2154.153429 2042.858073 2285.860033 2215.283369 2332.210913 2187.064184 0.365411822 0.608776713 0.491489216 0.412779229 0.984952086 0.93406407 1.045172817 1.012902769 1.066366012 1 11.09477984 -8.695350238 12.0096619 0.650378768 0.994038831 0.368244381 0.215999636 0.706916714 126.2800382 0.037611172 0.075226366 2.02E-09 8.695350238 0.343660062 ELLTSDSPPHNDIMT(ph)PVDPGVAQPNSR ddPTM_HeLa_Romidepsin_16h_R1 2 ELLTSDSPPHNDIMTPVDPGVAQPNSR 27 0 Q12778 Q12778 FOXO1 Forkhead box protein O1 1 0 ELLT(0.008)S(0.023)DS(0.191)PPHNDIMT(0.777)PVDPGVAQPNSR;ELLT(0.004)S(0.007)DS(0.037)PPHNDIMT(0.948)PVDPGVAQPNS(0.003)R ; 67.218 0.00012609 14282800 1511.31 1748.24 1492.01 1967.29 2552.3 2952.4 2040.35 2283.7 1745.47 1820.8 TRUE FALSE FALSE 1492.889572 1772.851769 1517.977808 2194.757326 2422.046607 2763.751168 2213.657278 2349.775256 1589.350792 1773.495354 0.841778113 0.999637109 0.855924322 1.237532042 1.36569098 1.558363918 1.248188936 1.324940182 0.896168568 1 10.79237984 -9.096455694 3.326913926 0.925437542 1.374881948 0.85693392 0.088645679 0.073373129 1.540849029 0.014757656 0.025834829 8.01E-10 9.096455694 0.449444405 ELLTT(ph)MGDRFTDEEVDELYR ddPTM_HeLa_Romidepsin_16h_R1 1 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 1 0 ELLT(0.453)T(0.54)MGDRFT(0.008)DEEVDELYR 61.096 0.012344 13280000 958.97 803.75 872.65 884.91 866.11 961.8 989.98 837.99 1023.8 889.24 TRUE FALSE FALSE 947.2817048 815.0652136 887.8381072 987.2274578 821.9091748 900.3440841 1074.068876 862.2359185 932.2287638 866.1374166 1.093685236 0.941034526 1.025054559 1.139804653 0.94893623 1.039493349 1.240067518 0.995495521 1.076305845 1 9.758452123 -12.21156662 0.007990042 6.27E-05 2.063209757 0.009710037 0.086227983 12620.40504 26.17238263 3494.212631 3265.441611 6.14E-13 12.21156662 2.063147059 ELLTTMGDRFTDEEVDELYR ddPTM_HeLa_Romidepsin_16h_R1 1 ELLTTMGDRFTDEEVDELYR 20 1 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 0 79.88 0.0065383 7935600 798.7 605.32 553.29 764.72 430.05 415.43 535.11 602.13 645.53 548.43 FALSE FALSE TRUE 788.9651372 613.8417108 562.9197804 853.1405245 408.1029438 388.8853637 580.56223 619.5516815 587.79218 534.1817095 1.476960224 1.149125288 1.053798306 1.597097971 0.763977756 0.72800202 1.086825362 1.15981448 1.100359989 1 9.061186769 -8.734361789 24.99890193 1.233089158 0.930763351 0.317262481 0.211865093 235.8400185 217734.0445 0.035332847 0.070650806 1.84E-09 8.734361789 -0.302325807 ELMHQKAEKEMKNNPVHLIT(ph)EEDLK ddPTM_HeLa_Romidepsin_16h_R1 1 ELMHQKAEKEMKNNPVHLITEEDLK 25 3 O94874;O94874-3;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 0 ELMHQKAEKEMKNNPVHLIT(1)EEDLK 46.178 0.01167 788950 358.71 251.57 224.12 330.81 391.57 245.18 352.07 223.91 271.37 263.57 TRUE FALSE FALSE 354.3379045 255.1116091 228.0207146 369.0598087 371.5867218 229.5137893 381.974817 230.3884826 247.0979875 256.7224134 1.38023751 0.993725502 0.888199482 1.437583123 1.447426101 0.894015393 1.48789041 0.897422549 0.962510379 1 8.004065447 -9.233558705 24.98136044 1.147358471 1.240130196 0.057661239 0.241137072 2508.497183 2247641.737 0.037131016 0.061563458 5.84E-10 9.233558705 0.092771724 ELNITAAK ddPTM_HeLa_Romidepsin_16h_R1 2 ELNITAAK 8 0 A0A2R8Y623;P62081;B5MCP9 A0A2R8Y623 RPS7 40S ribosomal protein S7 0 0 ; ; 128.36 0.019138 14089600 7759.1 6986.8 7698.1 7315.8 7657 7205.6 6931.4 6886.5 7304.6 6885.1 FALSE FALSE TRUE 7664.529105 7085.160354 7832.082201 8161.687218 7266.234718 6745.185415 7520.152943 7085.750012 6651.258281 6706.224109 1.142897848 1.056505157 1.167882563 1.217031684 1.083506098 1.005809723 1.121369167 1.056593084 0.991803759 1 12.71128498 -6.067963742 20.3598044 1.083599345 1.098007767 0 0.072650306 0 0 0.010308267 0 8.55E-07 6.067963742 0.014408422 ELNRKLS(ph)SNAVS(ph)QITRMCLLK ddPTM_HeLa_Romidepsin_16h_R1 1 ELNRKLSSNAVSQITRMCLLK 21 3 A0A087WVC1;Q9BQ39 A0A087WVC1 DDX50 ATP-dependent RNA helicase DDX50 2 0 ELNRKLS(0.807)S(0.228)NAVS(0.928)QIT(0.037)RMCLLK 42.64 0.0042107 0 493.31 427.28 524.31 663.65 623.54 354.29 558.18 611.08 579.34 483.58 TRUE FALSE FALSE 487.297348 433.2952591 533.4353956 740.3843356 591.7184271 331.6520124 605.5917953 628.7606357 527.5223794 471.0165219 1.034565297 0.919915202 1.132519499 1.571886125 1.256258325 0.704119701 1.285712426 1.334901445 1.119965765 1 8.879633856 -9.529034008 23.19922964 1.010341748 1.220456476 0.187382505 0.207275745 83.39221019 314303.3618 0.032510542 0.046071205 2.96E-10 9.529034008 0.210114728 ELNSNHDGADET(ph)SEKEQQEAIEHIDEVQNEIDR ddPTM_HeLa_Romidepsin_16h_R1 1 ELNSNHDGADETSEKEQQEAIEHIDEVQNEIDR 33 1 Q01105-2 Q01105-2 SET Protein SET 1 0 ELNS(0.002)NHDGADET(0.499)S(0.499)EKEQQEAIEHIDEVQNEIDR 70.424 6.14E-06 4544000 533.76 737.31 555.68 648.32 744.67 839.95 744.85 879.08 1345.9 1259.9 TRUE FALSE FALSE 527.2543278 747.6898695 565.3513773 723.2818088 706.6667112 786.2799058 808.1175404 904.5147928 1225.519333 1227.167616 0.429651435 0.609280965 0.460696135 0.589391212 0.575851825 0.640727392 0.658522544 0.737075181 0.998656839 1 10.2611166 -12.42334613 1.124051138 1.00256669 0.574146071 0.781231313 0.086627691 0.203455879 0.455390393 0.068705914 0.016884401 3.77E-13 12.42334613 -0.428420619 ELPDGPS(ph)PLLK ddPTM_HeLa_Romidepsin_16h_R1 1 ELPDGPSPLLK 11 0 O14613 O14613 CDC42EP2 Cdc42 effector protein 2 1 0 ELPDGPS(1)PLLK 101.72 0.018382 3502300 2635.7 2096 2102.8 2300.7 2820.1 3197.1 2701.7 2637 2577.3 2915.4 TRUE FALSE FALSE 2603.575075 2125.507543 2139.398352 2566.717759 2676.179774 2992.815628 2931.182331 2713.297435 2346.779833 2839.657488 0.916862363 0.748508421 0.753400141 0.90388287 0.942430482 1.053935427 1.032230944 0.955501657 0.826430597 1 11.47150121 -8.413783305 5.363803308 0.921370273 1.015080314 0.243398598 0.088893413 0.346696203 14.31680197 0.014776445 0.033489375 3.86E-09 8.413783305 0.093710041 ELPDSS(ph)SPVPANNIR ddPTM_HeLa_Romidepsin_16h_R1 1 ELPDSSSPVPANNIR 15 0 A0A0C4DH56;Q9BWT3-2;Q9BWT3 A0A0C4DH56 PAPOLG Poly(A) polymerase gamma 1 0 ELPDS(0.001)S(0.499)S(0.499)PVPANNIR 181.75 3.29E-08 15505000 1999.2 2174.2 1942.2 2386.8 2326.5 3013 2393.4 2553.6 2079.8 1890.5 TRUE FALSE FALSE 1974.832981 2204.808445 1976.003176 2662.773046 2207.770024 2820.479024 2596.695336 2627.484387 1893.777479 1841.384537 1.072471796 1.197364483 1.073107293 1.446071145 1.198972827 1.53171647 1.410186348 1.426906946 1.028453015 1 10.84657522 -9.281023784 0.603801553 1.016826011 1.471817555 0.751192343 0.093745277 0.25918516 0.182587308 0.019883096 0.052863775 5.24E-10 9.281023784 0.454991545 ELPESGIQLGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ELPESGIQLGTPR 13 0 A0A087WW69;F8W8L6;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WW69 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 0 ELPESGIQLGT(1)PR;ELPESGIQLGT(1)PR ; 137.39 0.0029333 58453000 2183.4 2067.9 1971.04 1801.45 2265.1 2877.2 2239.54 2292.53 2310.5 1972.63 TRUE FALSE FALSE 2156.787881 2097.01195 2005.345124 2009.742125 2149.503495 2693.356206 2429.766472 2358.860739 2103.843093 1921.380788 1.122519749 1.091408826 1.043699998 1.045988457 1.118728525 1.401781584 1.264593925 1.227690395 1.094964156 1 10.90792775 -8.433720707 5.37363525 1.060775894 1.293353619 0.797453063 0.052211701 0.082055088 3.796402826 0.008743276 0.01976713 3.68E-09 8.433720707 0.232577725 ELPPLS(ph)PSLSR ddPTM_HeLa_Romidepsin_16h_R1 2 ELPPLSPSLSR 11 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 ELPPLS(0.975)PS(0.025)LSR;ELPPLS(0.996)PS(0.004)LSR ; 140.45 9.70E-05 6295400 3706.1 3665.4 2588.7 2967 3327.8 2631.9 1876.46 2069.7 4200.1 3855.4 TRUE FALSE FALSE 3660.928628 3717.001597 2633.755238 3310.0585 3157.969948 2463.730084 2035.846466 2129.583504 3824.432537 3755.236152 0.974886393 0.989818335 0.701355422 0.88145149 0.840951093 0.656078602 0.542135403 0.567097093 1.01842664 1 11.87468792 -7.929552901 0.41514821 1.003776631 0.327015119 0.826314689 0.073478476 0.887036396 0.149877398 0.020352315 0.270394869 1.18E-08 7.929552901 -0.676761512 ELPPS(ph)PEKK ddPTM_HeLa_Romidepsin_16h_R1 3 ELPPSPEKK 9 1 E7EVA0;P27816;P27816-6;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4;P27816-3 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 ELPPS(1)PEKK;ELPPS(1)PEKK;ELPPS(1)PEKK ;; 71.153 0.024533 1647665000 30689.8 33778.9 31779.7 20525.3 24065.1 24723.6 20423.6 21750.1 36211.9 37061.9 TRUE FALSE FALSE 30315.74091 34254.44024 32332.81235 22898.53176 22836.96815 23143.84175 22158.38007 22379.40483 32973.01697 36099.0265 0.839793863 0.94890205 0.895669925 0.634325465 0.632620056 0.641120939 0.613822095 0.61994483 0.913404603 1 15.13967231 -9.279128087 4.470155526 0.923886628 0.626754024 0.937533634 0.037637646 0.054605232 2.811852817 0.009182056 0.014676639 5.26E-10 9.279128087 -0.297132604 ELPSGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ELPSGKK 7 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 1 ; ELPSGK(1)K;ELPSGK(1)K 109.86 0.0050619 48596000 20383.3 19977.3 21572 19985.1 16177.7 14402.3 22630 9746.6 28064 19190.4 FALSE TRUE FALSE 20134.8605 20258.54095 21947.45161 22295.87129 15352.0916 13482.03951 24552.19164 10028.60249 25553.88555 18691.83064 1.077201098 1.083817917 1.174173468 1.19281368 0.821326273 0.721279781 1.313525256 0.536523291 1.367115188 1 14.19012025 -8.746008804 24.99637515 1.062500556 0.872340604 0.270046438 0.214396444 297.2886275 481582.744 0.025584182 0.051022605 1.79E-09 8.746008804 -0.190159952 ELPSLS(ph)PAPDTGLSPSKR ddPTM_HeLa_Romidepsin_16h_R1 2 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 ELPS(0.315)LS(0.685)PAPDTGLSPSKR;ELPS(0.168)LS(0.831)PAPDTGLSPSKR ; 84.113 0.0031022 20576700 2802.5 2745.5 2596.24 2471.4 2582.93 2626.17 2536.38 2785.7 2887.6 2761.9 TRUE FALSE FALSE 2768.342052 2784.151221 2641.426468 2757.154896 2451.113444 2458.366213 2751.820054 2866.299834 2629.325824 2690.14544 1.029067801 1.034944498 0.981889837 1.024909232 0.911145326 0.913841377 1.022926126 1.065481365 0.9773917 1 11.39346846 ELPSLSPAPDTGLS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 3 ELPSLSPAPDTGLSPSKR 18 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8;A0A0A0MSL0 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 ELPSLSPAPDT(0.003)GLS(0.498)PS(0.498)KR;ELPSLSPAPDT(0.014)GLS(0.781)PS(0.206)KR;ELPSLS(0.001)PAPDT(0.042)GLS(0.953)PS(0.004)KR ;; 173.03 5.63E-11 5982400 4047.64 4260.4 4187 3329.59 3495.13 3753.1 2656.42 2918.81 4336.1 4026.1 TRUE FALSE FALSE 3998.305807 4320.378023 4259.872979 3714.572862 3316.760474 3513.289023 2882.056248 3003.261162 3948.268356 3921.501342 1.019585475 1.101715299 1.086286248 0.947232332 0.845788433 0.895904073 0.734936953 0.765844737 1.006825706 1 11.93719038 -8.507969886 1.22993998 1.022606496 0.765006484 0.824715689 0.050449753 0.158923334 0.456399823 0.008461965 0.028907349 3.10E-09 8.507969886 -0.257600012 VNNGNTAPEDS(ph)SPAK ddPTM_HeLa_Romidepsin_16h_R1 1 VNNGNTAPEDSSPAK 15 0 E9PJ27;G3V167;Q9UGN5-2;Q9UGN5 E9PJ27 PARP2 Poly [ADP-ribose] polymerase 2 1 0 VNNGNTAPEDS(0.855)S(0.145)PAK 135.02 0.0013625 3960900 3278.7 2886.3 3180 1931.8 1409.7 1097.7 1158 996.78 2919.6 3021.5 TRUE FALSE FALSE 3238.737943 2926.933407 3235.346566 2155.163805 1337.757749 1027.560513 1256.360491 1025.620257 2658.463664 2943.000994 1.100488226 0.994540407 1.099335873 0.732301419 0.454555656 0.349153981 0.426897746 0.348494703 0.903317284 1 11.52307231 -8.947618532 2.219116377 1.048247024 0.381326355 0.954563504 0.064080135 0.031946559 0.317212676 0.007718687 0.015210013 1.13E-09 8.947618532 -0.666920669 down ELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_HeLa_Romidepsin_16h_R1 1 ELQAEATVSGSPEAPGTNVVSEPR 24 0 K7EJ02;Q9BZV1-2;Q9BZV1 K7EJ02 UBXN6 UBX domain-containing protein 6 1 0 ELQAEAT(0.001)VS(0.247)GS(0.752)PEAPGTNVVSEPR 79.236 0.00013736 4802400 1111.3 854.83 1258.3 531.69 819.3 1249.1 835.43 1137.4 1176.6 1109 TRUE FALSE FALSE 1097.755048 866.8643192 1280.200184 593.1664995 777.4880638 1169.286541 906.3914033 1170.308874 1071.361949 1080.18802 1.016262935 0.802512436 1.185164212 0.54913264 0.719771048 1.082484271 0.839105217 1.083430711 0.991829135 1 10.07706674 -10.29214521 23.53904909 1.007679738 0.890786875 0.071415132 0.178140073 617.4962525 473369.6485 0.029142956 0.033329147 5.10E-11 10.29214521 -0.116892863 ELQAHGADELLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ELQAHGADELLKR 13 1 C9JTV5;G5E9J0;O15144 C9JTV5 ARPC2 Actin-related protein 2/3 complex subunit 2 0 1 ; ELQAHGADELLK(1)R;ELQAHGADELLK(1)R 109.95 0.0016194 1758910 800.81 801.46 678.7 649.14 2036.57 1646 1791.71 1545.8 1638.48 1284.15 FALSE TRUE FALSE 791.0494197 812.7429749 690.5124888 724.1966211 1932.636233 1540.825912 1943.897803 1590.525284 1491.930245 1250.787598 0.632441048 0.649784965 0.552062149 0.578992486 1.54513543 1.231884546 1.554139013 1.271619008 1.192792643 1 10.2886211 -8.758965071 24.99999979 0.769339673 1.399597028 0.686794563 0.209419125 27.77397024 280617.7563 0.029621517 0.057103136 1.74E-09 8.758965071 0.630257355 ELQEAAAVPT(ph)TPRR ddPTM_HeLa_Romidepsin_16h_R1 1 ELQEAAAVPTTPRR 14 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 ELQEAAAVPT(0.812)T(0.188)PRR 71.637 0.022249 2549800 1940.2 1847.5 1870.6 2836.1 2001.5 1982.2 1942.3 1636.9 2363.9 2018.2 TRUE FALSE FALSE 1916.552096 1873.509153 1903.157008 3164.023226 1899.355986 1855.543817 2107.278914 1684.261119 2152.466864 1965.766873 0.974964083 0.953067823 0.968149903 1.609561779 0.966216296 0.943928725 1.071988211 0.856795962 1.094975652 1 10.94087652 -6.090950834 11.22384515 1.018303005 1.066640893 0 0.200414831 0 0 0.025226973 0 8.11E-07 6.090950834 0.048337888 ELQELVQYPVEHPDK ddPTM_HeLa_Romidepsin_16h_R1 2 ELQELVQYPVEHPDK 15 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 ; ; 207.66 3.68E-19 23332000 8328.4 8385.6 8297.7 6101.2 8576.2 9257.5 7775 8246 8642.5 8298.2 FALSE FALSE TRUE 8226.890257 8503.652697 8442.117988 6806.649451 8138.524512 8665.975627 8435.408306 8484.585 7869.493154 8082.611568 1.017850504 1.052092214 1.044478993 0.842134921 1.006917683 1.072175194 1.043648855 1.049733113 0.973632481 1 12.9806058 -8.314302933 8.311844154 1.001820432 1.053983312 0.199698086 0.05601698 0.488931992 72.42625501 0.007970355 0.017913438 4.85E-09 8.314302933 0.05216288 ELQGDGPPS(ph)SPTNDPTVK ddPTM_HeLa_Romidepsin_16h_R1 3 ELQGDGPPSSPTNDPTVK 18 0 Q12873-2;Q12873;Q12873-3;A0A5F9ZHX5 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 ELQGDGPPS(0.565)S(0.406)PT(0.029)NDPTVK;ELQGDGPPS(0.737)S(0.255)PT(0.008)NDPTVK;ELQGDGPPS(0.494)S(0.494)PT(0.013)NDPTVK ;; 295.79 1.52E-124 55951500 22636.5 21232.6 21271.3 19860.5 20892.2 20605.3 19315.5 20153.5 22631.6 22080.1 TRUE FALSE FALSE 22360.59763 21531.5131 21641.51805 22156.86446 19825.99307 19288.68783 20956.15809 20736.60973 20607.37301 21506.45582 1.039715601 1.001165105 1.006280079 1.030242484 0.921862405 0.896878965 0.97441244 0.964203953 0.958194748 1 14.39248217 -8.763258326 24.99989366 1.01740394 0.938811758 0.527750306 0.029692627 20.87981438 286981.7197 0.003797239 0.007150894 1.72E-09 8.763258326 -0.078592182 ELQGDGPPSS(ph)PTNDPTVK ddPTM_HeLa_Romidepsin_16h_R1 1 ELQGDGPPSSPTNDPTVK 18 0 Q12873-2;Q12873;Q12873-3;A0A5F9ZHX5 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 ELQGDGPPS(0.003)S(0.986)PT(0.011)NDPTVK 224.36 3.19E-38 25176000 6401.9 5857 5625.7 5873.8 6051.1 5285.4 4876.4 5390.4 6730.3 5905.4 TRUE FALSE FALSE 6323.87118 5939.455 5723.612949 6552.956393 5742.289787 4947.679998 5290.601294 5546.362719 6128.325112 5751.976857 1.0994257 1.032593689 0.995068842 1.139252914 0.998315871 0.860170359 0.919788349 0.964253309 1.065429376 1 12.48984216 -8.514524757 24.08952127 1.049112807 0.917575861 0.641332352 0.046912287 130.8586942 377342.4378 0.007536839 0.015697075 3.06E-09 8.514524757 -0.131536945 ELQGDGPPSS(ph)PTNDPTVKYETQPR ddPTM_HeLa_Romidepsin_16h_R1 1 ELQGDGPPSSPTNDPTVKYETQPR 24 1 Q12873-2;Q12873;Q12873-3;A0A5F9ZHX5 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 ELQGDGPPS(0.268)S(0.448)PT(0.284)NDPTVKYETQPR 85.7 1.53E-05 0 1160.6 1059.5 973.66 1854.7 1297.9 750.92 704.97 1081.8 1012.3 926.54 TRUE FALSE FALSE 1146.454161 1074.415669 990.6061439 2069.149141 1231.66332 702.9386355 764.8501342 1113.100176 921.7573526 902.4683572 1.27035386 1.190530017 1.097663022 2.292766416 1.364771751 0.778906684 0.847509088 1.23339524 1.021373597 1 9.817732538 -6.921348828 20.00951714 1.183683133 3.098443755 0 0.401840492 5944.449508 1705218.105 0.055519401 65151.11327 1.20E-07 6.921348828 1.914760622 ELQLST(ph)AMET(ph)PAEEAPT(ph)EFQSPLPK ddPTM_HeLa_Romidepsin_16h_R1 1 ELQLSTAMETPAEEAPTEFQSPLPK 25 0 Q5H9T9 Q5H9T9 FSCB Fibrous sheath CABYR-binding protein 3 0 ELQLS(0.21)T(0.831)AMET(0.963)PAEEAPT(0.982)EFQS(0.014)PLPK 40.756 0.0040596 0 0 0 0 66.627 0 0 0 0 139.32 0 TRUE FALSE FALSE 0 0 0 74.33072723 0 0 0 0 126.8588703 0 0 ELS(ph)LDDPEVEQVSGR ddPTM_HeLa_Romidepsin_16h_R1 2 ELSLDDPEVEQVSGR 15 0 L7N2F4;C9J5N1;Q9BTE6;Q9BTE6-2;Q9BTE6-3 L7N2F4 AARSD1;PTGES3L-AARSD1 Alanyl-tRNA editing protein Aarsd1 1 0 ELS(1)LDDPEVEQVSGR;ELS(1)LDDPEVEQVSGR ; 190.18 2.28E-12 6687800 2620.2 2456.8 2273.16 2299 2546.6 3045.1 2572.3 3117.8 2814.1 2178.06 TRUE FALSE FALSE 2588.263995 2491.386895 2312.723396 2564.821197 2416.637499 2850.527938 2790.791098 3208.008624 2562.399848 2121.473687 1.220031156 1.174366154 1.090149461 1.208980914 1.139131498 1.343654628 1.315496447 1.512160459 1.207839561 1 11.05085107 -4 0.22215328 1.054729253 3.227389871 0.666596942 0.078303877 20.62120503 0.247625365 0.059324675 16.26896396 1.00E-04 4 2.172660617 ELS(ph)LTPITGAK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSLTPITGAK 11 0 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785;O95785-2 B9EGQ5 WIZ Protein Wiz 1 0 ELS(0.821)LT(0.179)PITGAK 105.03 0.0025969 0 1556.2 1658.3 1948.5 1348.6 1826.8 2087.7 1648.8 1998.2 1933.5 1644.9 TRUE FALSE FALSE 1537.232436 1681.645591 1982.412825 1504.531477 1733.571579 1954.302708 1788.849031 2056.014764 1760.562917 1602.165261 0.959471831 1.049608072 1.237333547 0.939061353 1.082017955 1.219788467 1.116519672 1.28327259 1.098864743 1 10.64580725 -6.111398347 0.288393987 0.972928961 1.743055884 0.319683022 0.092425162 9.028709818 0.330660666 0.037701652 2.78530017 7.74E-07 6.111398347 0.770126922 ELS(ph)NS(ph)PLRENSFGSPLEFR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 ELS(0.844)NS(0.984)PLRENS(0.055)FGS(0.118)PLEFR 86.262 0.00093397 0 1131.3 1373.4 1223.3 1131.1 1205.8 978.63 803.85 1126.1 1519.9 1263 TRUE FALSE FALSE 1117.51128 1392.734761 1244.591023 1261.883104 1144.263527 916.0987014 872.1289989 1158.681927 1383.956337 1230.187078 0.908407591 1.132132491 1.011708744 1.025765208 0.930154077 0.744682429 0.70894014 0.941874571 1.124996647 1 10.26466201 -8.404113585 4.574003364 0.979214783 0.790846209 0.52142152 0.092353089 0.141915216 4.684358867 0.012083447 0.027719687 3.94E-09 8.404113585 -0.188368574 ELS(ph)PAALEK ddPTM_HeLa_Romidepsin_16h_R1 3 ELSPAALEK 9 0 O75683 O75683 SURF6 Surfeit locus protein 6 1 0 ELS(1)PAALEK;ELS(1)PAALEK;ELS(1)PAALEK ;; 136.5 0.0067303 530920000 23029.1 21778.2 21398.1 19509.4 20585.6 20173 18382.7 17890 22401 22564.2 TRUE FALSE FALSE 22748.41247 22084.79407 21770.52495 21765.16862 19535.04002 18884.01041 19944.12608 18407.61892 20397.39846 21977.97883 1.035054799 1.004860103 0.99056083 0.990317116 0.888846066 0.85922416 0.907459518 0.837548305 0.928083452 1 14.4237711 -8.789484595 2.524992018 1.013959969 0.870492256 0.735008636 0.033595854 0.058237177 0.758194806 0.003215733 0.00665808 1.62E-09 8.789484595 -0.143467713 ELS(ph)PAGSISK ddPTM_HeLa_Romidepsin_16h_R1 2 ELSPAGSISK 10 0 O95453;O95453-3;O95453-2;A0A494C0W0;A0A494C0K5;A0A494C0Q6;O95453-4 O95453 PARN Poly(A)-specific ribonuclease PARN 1 0 ELS(1)PAGSISK;ELS(0.98)PAGS(0.013)IS(0.008)K ; 150.09 0.0037426 628500000 12907.3 12358.7 13038.3 12885.6 12280.4 12464.8 11603.4 10446.8 13215.9 12466.5 TRUE FALSE FALSE 12749.98086 12532.6861 13265.22614 14375.4937 11653.68536 11668.33951 12588.99251 10749.06168 12033.8368 12142.61853 1.050019057 1.032123843 1.092451855 1.183887451 0.959734124 0.96094096 1.036760932 0.885234239 0.991041329 1 13.56779195 -6.156095972 0.955129187 1.036042149 2.55E-15 0.331050079 0.063328257 13.35066593 1.834136415 0.009883788 23.38217252 6.98E-07 6.156095972 -1.036042149 ELS(ph)PPPGLPSK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSPPPGLPSK 11 0 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78;H0YIM6 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 ELS(1)PPPGLPSK 95.618 0.025338 7415700 2809.4 2611 2564.3 2504.9 2245.1 2803.6 1798.1 2399.8 3187.6 3380.8 TRUE FALSE FALSE 2775.157952 2647.757727 2608.930566 2794.528324 2130.524169 2624.459008 1950.830569 2469.234427 2902.493073 3292.966329 0.842753213 0.804064622 0.792273684 0.84863556 0.646992394 0.796989324 0.592423479 0.749851101 0.881422032 1 11.68517204 -11.01650729 0.123903597 1.242886673 0.496664975 0.562646849 0.072361202 2.957178519 0.230783295 0.761639146 0.542941356 9.63E-12 11.01650729 -0.746221697 ELS(ph)SPISPK ddPTM_HeLa_Romidepsin_16h_R1 2 ELSSPISPK 9 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 ELS(0.497)S(0.497)PIS(0.007)PK;ELS(0.804)S(0.073)PIS(0.123)PK ; 139.38 0.0064891 253130000 8062.3 7387.9 8456.8 8923.9 16308.3 20516.4 20626.7 23402.1 8375 7860.6 TRUE FALSE FALSE 7964.033587 7491.90705 8603.987057 9955.723306 15476.0266 19205.46825 22378.73138 24079.20284 7625.919024 7656.380479 1.040182578 0.978518122 1.123766913 1.30031721 2.021324128 2.508426574 2.922886532 3.144985141 0.996021429 1 12.90244681 -8.390056294 1.070420923 1.008808836 3.156769313 0.99493043 0.058598719 0.025676347 0.052354862 0.009071734 0.039313502 4.07E-09 8.390056294 2.147960477 up ELS(ph)TTLNADEAVTR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSTTLNADEAVTR 14 0 A0A087WYC1;P34932;A0A087WTS8 A0A087WYC1 HSPA4 Heat shock 70 kDa protein 4 1 0 ELS(0.993)T(0.005)T(0.002)LNADEAVTR 140.96 2.55E-05 0 682.88 493.68 663.06 619.74 564.59 424.81 390.72 793.29 838.2 688.37 TRUE FALSE FALSE 674.5567959 500.63004 674.6002812 691.3972548 535.7768655 397.666012 423.907747 816.2425945 763.2292927 670.4860482 1.006071338 0.746667349 1.006136195 1.031188131 0.79908727 0.593101099 0.632239475 1.21738938 1.138322408 1 9.389063502 -8.723557905 8.272149474 0.983604686 0.781463914 0.178891297 0.182120458 0.277727908 53.2980921 0.024286073 0.048366353 1.89E-09 8.723557905 -0.202140772 ELSDEIEDYTHR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSDEIEDYTHR 12 0 Q3SXZ0;Q8N9R8;Q8N9R8-2 Q3SXZ0 C9orf126;SCAI Protein SCAI 0 0 148.13 0.00069209 1224900 1039 966.08 1112.7 1045 1163.5 1354.9 913.54 1453.2 871.64 984.47 FALSE FALSE TRUE 1026.336268 979.6804996 1132.066077 1165.827817 1104.122253 1268.326263 991.1360648 1495.246049 793.6783353 958.8933275 1.070334143 1.021678295 1.180596469 1.215805537 1.151454726 1.322697975 1.033624947 1.559345556 0.827702428 1 9.905226521 -4 0.224319649 0.997680164 3.129742523 0.559048792 0.12669553 26.27142455 0.316646897 0.07188756 20.60510546 1.00E-04 4 2.13206236 ELSDFISYLQR ddPTM_HeLa_Romidepsin_16h_R1 2 ELSDFISYLQR 11 0 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 0 ; ; 214.71 2.49E-18 106400000 4047 3160.3 5455.1 4505 5964.8 4723.3 4425.4 3257.4 3232.3 2032.98 FALSE FALSE TRUE 3997.673607 3204.790786 5550.043727 5025.889297 5660.393998 4421.496374 4801.293366 3351.64773 2943.194993 1980.162887 2.018860991 1.618448062 2.802821811 2.538119127 2.858549686 2.232895285 2.424696169 1.692612134 1.486339842 1 10.95140339 -11.50103961 0.510217018 0.946201903 2.406586086 0.525649051 0.399508283 0.464429184 0.246555454 0.309440283 0.116103236 3.15E-12 11.50103961 1.460384183 ELSDIAHR ddPTM_HeLa_Romidepsin_16h_R1 5 ELSDIAHR 8 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ;;;; ;;;; 145.16 0.0038635 249194300 34859.93 33651.19 30322.55 29719.23 42041.02 42378.4 39515.07 39778.72 41314.92 38123.72 FALSE FALSE TRUE 34435.04376 34124.93234 30850.30126 33155.50721 39895.50987 39670.55701 42871.47906 40929.6545 37619.61008 37133.26026 0.927336935 0.918985624 0.830799694 0.892878971 1.074387479 1.06832949 1.154530433 1.10223703 1.013097418 1 15.18042437 -8.639957606 5.190290655 0.945385784 1.106493 0.705192643 0.05337139 0.106781073 4.435952437 0.008835976 0.017922259 2.29E-09 8.639957606 0.161107216 ELSDQATAS(ph)PIVAR ddPTM_HeLa_Romidepsin_16h_R1 2 ELSDQATASPIVAR 14 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 ELSDQATAS(1)PIVAR;ELSDQAT(0.001)AS(0.999)PIVAR ; 173.19 2.90E-05 272840000 5833.2 6156.9 6281.3 5198.8 8394.1 8147.6 8266.5 8065.7 6474.2 6422.1 TRUE FALSE FALSE 5762.102715 6243.577 6390.623392 5799.909717 7965.717754 7626.994655 8968.656304 8299.068304 5895.131337 6255.252916 0.921162228 0.998133422 1.021641087 0.927206269 1.273444553 1.219294369 1.433779964 1.326735851 0.942428934 1 12.6108525 -8.698760124 4.685055319 0.967344323 1.322812056 0.895037176 0.0579472 0.048354921 2.098222253 0.008924554 0.018013347 2.00E-09 8.698760124 0.355467734 ELSEPMEFQYLPDTDDR ddPTM_HeLa_Romidepsin_16h_R1 2 ELSEPMEFQYLPDTDDR 17 0 Q2TAM5;E9PKH5;A0A087X0W8;Q04206-2;Q04206-3;Q04206-4;Q04206 Q2TAM5 RELA Transcription factor p65 0 0 ; ; 177.42 1.28E-08 9787000 3676.3 4043.8 3414 2447.13 3939.3 4578.2 4278 4563.3 4158.8 3836.8 FALSE FALSE TRUE 3631.491842 4100.728723 3473.419238 2730.078685 3738.262821 4285.667795 4641.373213 4695.331886 3786.826512 3737.119383 0.971735572 1.097296688 0.929437591 0.730530231 1.000305968 1.146783754 1.241965465 1.256404039 1.013300921 1 11.86771094 -8.108400256 2.767221035 0.971316453 1.245019757 0.639231502 0.08885323 0.139388726 2.048938851 0.013226207 0.040989766 7.79E-09 8.108400256 0.273703304 ELSESVQQQSTPVPLIS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSESVQQQSTPVPLISPKR 20 1 Q9ULU4-9;A0A087WV57;A0A087WYS3;Q9ULU4-11;Q9ULU4-23;Q9ULU4;Q9ULU4-21;H7C4X9;A0A087WVZ6;Q9ULU4-10;Q9ULU4-13;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-19;Q9ULU4-16;Q9ULU4-22;Q9ULU4-14;Q9ULU4-8;Q9ULU4-17;Q9ULU4-6;Q9ULU4-3;Q9ULU4-4;Q9ULU4-18;Q9ULU4-15;Q9ULU4-2 Q9ULU4-9 ZMYND8 Protein kinase C-binding protein 1 1 0 ELSESVQQQS(0.002)T(0.001)PVPLIS(0.996)PKR 52.227 0.016325 9766800 1215.8 1055.5 1114.8 1348.9 1305.2 732.62 652.74 715.62 1344.9 1290.6 TRUE FALSE FALSE 1200.981362 1070.359357 1134.202626 1504.866165 1238.590774 685.8079464 708.1837193 736.3253356 1224.608776 1257.070026 0.955381432 0.851471545 0.902258906 1.197121985 0.985299743 0.545560655 0.563360596 0.58574727 0.974177055 1 10.2958493 -8.262595058 24.99487547 0.979926443 0.564736596 0.835386519 0.084608042 29.32716655 634293.0944 0.012335759 0.029109612 5.46E-09 8.262595058 -0.415189847 ELSKEDLSPAFDHS(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSKEDLSPAFDHSPNK 17 1 K7EIY0;K7ENP9;K7EIE9;D3DUJ3;K7EQG9;P17706-3;P17706-2;P17706-4;P17706 K7EIY0 PTPN2 Protein-tyrosine-phosphatase;Tyrosine-protein phosphatase non-receptor type;Tyrosine-protein phosphatase non-receptor type 2 1 0 ELSKEDLSPAFDHS(1)PNK 79.462 0.0071343 11094000 763.67 809.76 840.13 572.89 662.45 602.61 605.27 723.94 957.12 812.69 TRUE FALSE FALSE 754.3620963 821.1598225 854.7521102 639.1302373 628.6427046 564.1051658 656.6816187 744.8860617 871.51279 791.5761966 0.952987343 1.037373062 1.079810275 0.807414675 0.794165751 0.712635332 0.829587375 0.941016247 1.100984079 1 9.62858442 -9.242482067 24.32728364 0.989606709 0.810602564 0.676741466 0.071776245 277.9779916 356719.9033 0.009832927 0.016286472 5.72E-10 9.242482067 -0.179004145 ELSLT(ph)PITGAKPSATGYLGSVAAK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSLTPITGAKPSATGYLGSVAAK 24 1 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785;O95785-2 B9EGQ5 WIZ Protein Wiz 1 0 ELS(0.02)LT(0.921)PIT(0.059)GAKPSATGYLGSVAAK 89.47 4.80E-05 18802000 1853.1 1604.8 1480.5 2017 2479.1 2231.8 2074.4 2254.6 2080 1689.4 TRUE FALSE FALSE 1830.513704 1627.392417 1506.267481 2250.21503 2352.582276 2089.195183 2250.599484 2319.833294 1893.959591 1645.509144 1.11242998 0.988990199 0.915380803 1.367488621 1.429698695 1.269634502 1.367722259 1.409796659 1.150986974 1 10.68431833 -9.247638938 24.86452085 1.039223702 1.366671007 0.842532345 0.072456425 212.057671 382068.4983 0.01078526 0.017825179 5.65E-10 9.247638938 0.327447305 ELSLTPIT(ph)GAKPSATGYLGSVAAK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSLTPITGAKPSATGYLGSVAAK 24 1 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785;O95785-2 B9EGQ5 WIZ Protein Wiz 1 0 ELS(0.004)LT(0.199)PIT(0.797)GAKPSATGYLGSVAAK 87.729 6.09E-05 18957000 1646.3 1690.8 1382.3 1921.6 2125.7 2319.4 1917 1715.5 1917 1542.1 TRUE FALSE FALSE 1626.234262 1714.603127 1406.358352 2143.784433 2017.217597 2171.197826 2079.829932 1765.135286 1745.538719 1502.03602 1.082686594 1.141519314 0.936301349 1.427252346 1.34298883 1.445503168 1.384673806 1.175161756 1.162115086 1 10.55270369 -9.257067352 24.99985639 1.042348635 1.36110587 0.708425097 0.092629688 128.3223968 733764.3526 0.012619102 0.020462753 5.53E-10 9.257067352 0.318757235 ELSNS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 2 ELSNSPLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 ELSNS(1)PLR;ELSNS(1)PLR ; 141.91 0.0088443 731980000 12446.7 12523.6 12637.6 5984.3 9698.7 11148.2 9573.5 9159.4 12171 12496 TRUE FALSE FALSE 12294.99483 12699.90757 12857.55213 6676.232923 9203.739148 10435.866 10386.67285 9424.412788 11082.39528 12171.35212 1.010158503 1.04342619 1.056378289 0.548520235 0.756180501 0.857412217 0.853370501 0.774311079 0.910531153 1 13.57120183 -9.293148679 24.99978704 1.011947573 0.768685887 0.6613619 0.087807209 284.2263947 224084.8552 0.012642411 0.019312649 5.09E-10 9.293148679 -0.243261686 ELSNS(ph)PLRENSFGS(ph)PLEFR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 ELS(0.003)NS(0.945)PLRENS(0.215)FGS(0.837)PLEFR 173.03 1.16E-06 19398000 5472.3 4826.1 4303.2 3737 4220.3 4139.4 3613.3 4378.8 4795.1 4346.9 TRUE FALSE FALSE 5405.601503 4894.041962 4378.095391 4169.089523 4004.922343 3874.905699 3920.213612 4505.493669 4366.214246 4233.966911 1.276722661 1.155899908 1.034041003 0.984676926 0.94590308 0.915195083 0.925896138 1.064130581 1.031234853 1 12.04779428 -9.51858578 2.793038226 1.135937969 0.960952707 0.420051001 0.080535301 0.229302499 3.619846907 0.017663251 0.026903055 3.03E-10 9.51858578 -0.174985262 ELSNS(ph)PLRENSFGSPLEFR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 ELS(0.041)NS(0.838)PLRENS(0.107)FGS(0.014)PLEFR 98.76 0.00057139 759940000 2592.1 2786.4 2019.6 2029.1 1960 1787.4 1972 2664.5 2410.5 2507.7 TRUE FALSE FALSE 2560.506488 2825.627012 2054.750291 2263.714089 1859.973886 1673.190909 2139.501631 2741.593104 2194.898843 2442.549592 1.048292528 1.156835063 0.841231759 0.926783266 0.761488689 0.685018193 0.875929659 1.122430886 0.898609735 1 11.25417214 -9.737023885 24.99755101 1.033494276 0.858539361 0.281298579 0.122136831 195.4935446 200153.7466 0.018215129 0.025753242 1.83E-10 9.737023885 -0.174954915 ELSNSPLRENSFGS(ph)PLEFR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSNSPLRENSFGSPLEFR 19 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 ELS(0.002)NS(0.026)PLRENS(0.233)FGS(0.739)PLEFR 88.071 0.0016959 821250000 2616.9 2890.1 1995.9 2748.6 2314.9 2615.9 2249.7 2367.1 2882.5 2816.4 TRUE FALSE FALSE 2585.004216 2930.786904 2030.637802 3066.406065 2196.762015 2448.752432 2440.789462 2435.588304 2624.681981 2743.229522 0.942321521 1.068371013 0.740236202 1.117808787 0.8007941 0.892653135 0.889750363 0.887854364 0.956785409 1 11.42165962 -8.62536125 0.196822826 1.013276296 0.808487115 0.106422338 0.102546718 11.32498216 0.749484281 0.168124514 0.633229211 2.37E-09 8.62536125 -0.20478918 ELSNSVSTYRPFGLGSES(ph)PYK ddPTM_HeLa_Romidepsin_16h_R1 2 ELSNSVSTYRPFGLGSESPYK 21 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 ELS(0.001)NS(0.006)VS(0.061)T(0.071)Y(0.061)RPFGLGS(0.175)ES(0.618)PY(0.007)K;ELSNSVS(0.002)T(0.01)Y(0.012)RPFGLGS(0.203)ES(0.763)PY(0.009)K ; 76.152 0.001571 38109000 1596.34 1621.75 2043.42 1111.23 1371.11 1537.42 1246.4 1250.41 1828.38 1747.42 TRUE FALSE FALSE 1576.883194 1644.581039 2078.984868 1239.715641 1301.13714 1439.183824 1352.269185 1286.588641 1664.845114 1702.021776 0.926476509 0.966251467 1.221479594 0.728378249 0.764465625 0.845573096 0.79450757 0.755917849 0.978157352 1 10.73303378 -9.203900717 24.99992345 0.981955572 0.781726222 0.666550768 0.083118166 149.7135907 65048.90488 0.012590903 0.020879648 6.25E-10 9.203900717 -0.20022935 ELSSEPQT(ph)PPAQK ddPTM_HeLa_Romidepsin_16h_R1 4 ELSSEPQTPPAQK 13 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 ELSS(0.001)EPQT(0.999)PPAQK;ELSSEPQT(1)PPAQK;ELS(0.006)S(0.267)EPQT(0.727)PPAQK;ELSSEPQT(1)PPAQK ;;; 232.13 8.47E-41 41518900 8411.3 7679.74 6623.77 9862.4 19270.7 23579.4 22763.5 25655.9 8077.96 6783.21 TRUE FALSE FALSE 8308.77984 7787.855581 6739.053938 11002.73709 18287.24427 22072.75244 24697.03112 26398.21299 7355.447026 6606.981226 1.257575821 1.178731302 1.019989872 1.665319866 2.767866843 3.340822636 3.738020478 3.995502951 1.113284081 1 12.68977553 -8.579557287 1.319019659 1.10976635 3.870783366 0.988387701 0.124548467 0.036130753 0.122370682 0.022839947 0.069576613 2.63E-09 8.579557287 2.761017016 up ELSSPIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ELSSPISPK 9 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 ELS(0.001)S(0.262)PIS(0.737)PK 102.53 0.026034 6058100 2187.2 2184.1 2038 1968 4164.7 5219.9 4414.7 5355.5 2255.8 2062.6 TRUE FALSE FALSE 2160.541565 2214.847817 2073.470535 2195.54942 3952.159818 4886.365236 4789.684508 5510.452943 2054.035598 2009.013355 1.075424193 1.102455497 1.032083998 1.092849589 1.967214309 2.432221381 2.384097894 2.742865263 1.022410127 1 10.97227144 -8.585984208 2.08888266 1.037144695 2.527871441 0.97955168 0.096375074 0.028778033 0.25164821 0.013999672 0.033952439 2.59E-09 8.585984208 1.490726747 up ELSVSECY(ph)RITDDGIQVRSLR ddPTM_HeLa_Romidepsin_16h_R1 1 ELSVSECYRITDDGIQVRSLR 21 2 A0A0A0MRW5 A0A0A0MRW5 FBXL13 1 0 ELS(0.025)VS(0.104)ECY(0.745)RIT(0.127)DDGIQVRSLR 45.369 0.0040738 0 665.14 890.97 725.21 697.35 807.66 1206.2 850.01 880.28 1102.8 907.37 TRUE FALSE FALSE 657.0330178 903.513099 737.8319758 777.9808881 766.4420964 1129.127713 922.2098282 905.7495129 1004.162806 883.7963966 0.743421245 1.0223091 0.834843838 0.880271623 0.867215684 1.277588048 1.043464119 1.024839563 1.136192465 1 9.787570239 -8.290469762 24.93319021 0.883325521 1.108113947 0.280341055 0.126055267 454.4504805 390310.7533 0.016630912 0.037194064 5.12E-09 8.290469762 0.224788425 ELT(ph)DEEAER ddPTM_HeLa_Romidepsin_16h_R1 2 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 0 ELT(1)DEEAER;ELT(1)DEEAER ; 156.58 0.0088647 51827000 3161.6 3574.2 3411.1 1962.9 3254.6 3411.6 2841.1 3150.8 3417.4 3868 TRUE FALSE FALSE 3123.065203 3624.517681 3470.468765 2189.859734 3088.505617 3193.60977 3082.422963 3241.963427 3111.739185 3767.508802 0.828947022 0.962046241 0.92115744 0.581248737 0.819773962 0.847671482 0.818159459 0.860505867 0.825940787 1 11.87939517 -9.42786431 21.48223942 0.921251302 0.788502938 0.315054454 0.088863943 14.71797065 3324.556572 0.014614754 0.022324392 3.73E-10 9.42786431 -0.132748364 ELTDEEAER ddPTM_HeLa_Romidepsin_16h_R1 1 ELTDEEAER 9 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 0 168.26 0.019697 35141000 3836.1 3671.9 3441.4 2747.3 3731 3900.3 2846.8 3434.3 4004.6 3805.7 FALSE FALSE TRUE 3789.344138 3723.593105 3501.296123 3064.955752 3540.593148 3651.083418 3088.607121 3533.666052 3646.418546 3706.827365 1.022260754 1.004522935 0.944553328 0.826840705 0.955154583 0.984961817 0.833221193 0.953285844 0.983703363 1 11.85596921 -9.669648721 3.89453015 1.010524217 0.91088884 0.43914368 0.048487036 0.136947028 3.967536218 0.007269528 0.010354531 2.14E-10 9.669648721 -0.099635376 ELTDT(ph)ELILY(ph)TRK ddPTM_HeLa_Romidepsin_16h_R1 1 ELTDTELILYTRK 13 1 F8VZ12 F8VZ12 FRS2 2 0 ELT(0.022)DT(0.929)ELILY(0.815)T(0.234)RK 67.456 0.026177 6156300 2777.4 2642.9 2617.4 2082.3 2790.3 2648.2 2518.5 2332.6 2944 3012.9 TRUE FALSE FALSE 2743.547981 2680.106816 2662.954749 2323.065324 2647.900579 2478.988567 2732.421327 2400.090101 2680.681267 2934.624424 0.934888962 0.913270807 0.907426084 0.791605667 0.902296239 0.844737932 0.931097453 0.817852561 0.913466556 1 11.51896016 -10.58733526 0.575980785 0.99255716 0.860840311 0.361055216 0.046585568 0.322993493 0.249267775 0.014449556 0.013190052 2.59E-11 10.58733526 -0.131716849 ELTIGSK ddPTM_HeLa_Romidepsin_16h_R1 2 ELTIGSK 7 0 R4GN98;P06703 R4GN98 S100A6 Protein S100;Protein S100-A6 0 0 ; ; 183.9 4.29E-07 29992000 11396.1 11642.3 12249.1 11659.1 11431.9 11366.2 11992.1 7339.3 12621.6 11067.9 FALSE FALSE TRUE 11257.19995 11806.2006 12462.29045 13007.18 10848.48748 10639.9365 13010.70867 7551.651066 11492.69248 10780.35436 1.044232831 1.095158861 1.156018627 1.206563306 1.006320119 0.986974653 1.206890631 0.700501191 1.066077431 1 13.39611698 -7.245094542 24.68731483 1.053683417 0.700500867 0.643474529 0.08297928 1481.598286 2237772.54 0.012069611 0.427864777 5.69E-08 7.245094542 -0.35318255 ELVEFAQDDDRLR ddPTM_HeLa_Romidepsin_16h_R1 2 ELVEFAQDDDRLR 13 1 Q14677-2;Q14677;Q14677-3 Q14677-2 CLINT1 Clathrin interactor 1 0 0 ; ; 212.1 3.58E-23 26623000 4216.2 4512.9 3778.6 3189.1 4331.9 4692.1 3712.8 4650.4 4811.6 4024.1 FALSE FALSE TRUE 4164.811333 4576.432725 3844.364948 3557.838747 4110.826978 4392.289953 4028.165139 4784.951987 4381.238445 3919.553302 1.062572955 1.167590379 0.980817112 0.907715363 1.048799866 1.120609828 1.027710259 1.22079013 1.117790245 1 11.93647353 -4.296342972 1.122566979 1.031950653 199.9949167 0.304426618 0.073837838 1402.182139 2.067447085 0.010442055 718021.8142 5.05E-05 4.296342972 198.9629661 ELVEPLT(ph)PSGEAPNQALLR ddPTM_HeLa_Romidepsin_16h_R1 1 ELVEPLTPSGEAPNQALLR 19 0 P00533;E9PFD7;Q504U8 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 0 ELVEPLT(0.999)PS(0.001)GEAPNQALLR 268.93 3.65E-90 13413000 2065.5 3604.4 2118.3 1762.7 3139.7 4313.8 1729.8 3977.3 2292.9 2561.2 TRUE FALSE FALSE 2040.324892 3655.142838 2155.168123 1966.511668 2979.469393 4038.162102 1876.729169 4092.3769 2087.817281 2494.659655 0.817877055 1.465186977 0.863912686 0.78828856 1.19433903 1.618722656 0.752298681 1.640454999 0.836914678 1 11.28462729 -8.585888004 6.779935109 0.946720505 1.299335412 0.251606895 0.291575279 0.214291541 18.34940031 0.039316226 0.079222386 2.59E-09 8.585888004 0.352614907 ELVGPPLAET(ph)VFTPKT(ph)SPENVQDR ddPTM_HeLa_Romidepsin_16h_R1 1 ELVGPPLAETVFTPKTSPENVQDR 24 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 2 0 ELVGPPLAET(0.458)VFT(0.477)PKT(0.548)S(0.517)PENVQDR 58.945 0.0068959 47444000 3116.2 2758.4 2906.8 2630.7 2658.5 2539 2004.3 2474.3 3346.2 3019.9 TRUE FALSE FALSE 3078.218556 2797.232828 2957.391635 2934.873912 2522.826825 2376.766094 2174.545192 2545.889967 3046.907491 2941.442563 1.046499631 0.950973126 1.005422194 0.997766861 0.857683525 0.808027369 0.739278482 0.865524284 1.035854832 1 11.52230815 -8.674552463 2.386641601 1.0152168 0.798107245 0.860435161 0.037550653 0.071489436 0.826194147 0.005649174 0.012532782 2.12E-09 8.674552463 -0.217109555 ELVGPPLAETVFT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ELVGPPLAETVFTPK 15 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 ELVGPPLAETVFT(1)PK;ELVGPPLAET(0.014)VFT(0.986)PK ; 189.52 5.10E-12 93514000 11767.6 11741.9 12020 5406.9 9378.8 9445.7 7566.5 8750 10962.4 11907.8 TRUE FALSE FALSE 11624.17196 11907.20278 12229.20306 6032.071218 8900.164839 8842.150255 8209.198321 9003.167445 9981.895488 11598.43364 1.002219121 1.026621624 1.054384018 0.520076366 0.767359207 0.762357274 0.707785083 0.776239941 0.860624443 1 13.50164236 -9.280390014 24.96332324 1.007035979 0.713275281 0.735592739 0.084136282 229.3503728 302118.2928 0.010091194 0.015429846 5.24E-10 9.280390014 -0.293760697 ELVNDDEDIDWVQTEK ddPTM_HeLa_Romidepsin_16h_R1 1 ELVNDDEDIDWVQTEK 16 0 P41743 P41743 PRKCI Protein kinase C iota type 0 0 198.59 3.01E-16 0 760.96 620.64 807.82 790.57 853.89 906.59 826.41 766.99 898.21 858.79 FALSE FALSE TRUE 751.6851268 629.3773862 821.8797682 881.9794231 810.312807 848.6618249 896.6052448 789.1816455 817.871848 836.478512 0.898630528 0.752413095 0.982547377 1.054395792 0.968719214 1.014565004 1.071880786 0.943457165 0.977755957 1 9.70818467 -9.531741706 24.99896615 0.932560705 1.012558124 0.291449579 0.072225672 253.5119483 715056.2384 0.012478932 0.017663375 2.94E-10 9.531741706 0.079997419 ELVSSSS(ph)SGSDSDSEVDK ddPTM_HeLa_Romidepsin_16h_R1 1 ELVSSSSSGSDSDSEVDK 18 0 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 ELVSSS(0.001)S(0.494)S(0.494)GS(0.009)DS(0.001)DSEVDK 230.96 1.29E-39 9489900 2628.1 2555.8 2616.7 2350 2497 2654 2429 2731.3 2916.4 2762.5 TRUE FALSE FALSE 2596.067706 2591.780619 2662.242566 2621.718057 2369.568772 2484.417965 2635.319199 2810.325856 2655.54988 2690.729852 0.964819157 0.963225876 0.989412803 0.974352017 0.880641649 0.923324935 0.979406832 1.044447422 0.986925491 1 11.39378184 -8.980786098 24.99776172 0.981557654 0.952574259 0.069230251 0.040295604 469.7245937 611119.874 0.006225837 0.01128422 1.05E-09 8.980786098 -0.028983395 ELVSSSSS(ph)GSDSDSEVDKK ddPTM_HeLa_Romidepsin_16h_R1 2 ELVSSSSSGSDSDSEVDKK 19 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 ELVSS(0.002)S(0.003)S(0.046)S(0.503)GS(0.223)DS(0.223)DSEVDKK;ELVS(0.002)S(0.023)S(0.097)S(0.097)S(0.417)GS(0.363)DS(0.002)DSEVDKK ; 105.68 0.00030964 60340000 6399.3 6034.6 5790.3 5673.1 5580 6240 5502 5518.2 6292.3 5646.9 TRUE FALSE FALSE 6321.30287 6119.555257 5891.077743 6329.050515 5295.231778 5841.284139 5969.339743 5677.860411 5729.500929 5500.192724 1.149287523 1.112607424 1.071067513 1.150696136 0.962735679 1.062014448 1.085296469 1.032302084 1.04169094 1 12.42526646 -7.24902648 21.82592896 1.072992492 1.032301937 0.037937353 0.056716839 1109.123325 1949977.046 0.00928626 0.181754929 5.64E-08 7.24902648 -0.040690556 ELVSSSSSGS(ph)DSDSEVDKK ddPTM_HeLa_Romidepsin_16h_R1 1 ELVSSSSSGSDSDSEVDKK 19 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 ELVS(0.014)S(0.056)S(0.077)S(0.062)S(0.062)GS(0.378)DS(0.319)DS(0.031)EVDKK 53.718 0.017664 36188000 1825.1 1993.1 1666.7 1792.7 1777.9 2115.7 1458.9 1880 1857.7 2129.8 TRUE FALSE FALSE 1802.854979 2021.158914 1695.708214 1999.980409 1687.167129 1980.513598 1582.81893 1934.394834 1691.542659 2074.467489 0.869068804 0.974302526 0.817418554 0.964093397 0.813301311 0.954709393 0.763000114 0.932477778 0.815410542 1 11.01852533 -16.52287874 0.241791144 1.721796035 0.868157978 0 0.090036564 38.74865946 0.507348018 13.29660333 0.038805527 3.00E-17 16.52287874 -0.853638057 ELVSSSSSGSDS(ph)DSEVDK ddPTM_HeLa_Romidepsin_16h_R1 1 ELVSSSSSGSDSDSEVDK 18 0 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 ELVSSSS(0.001)S(0.013)GS(0.323)DS(0.662)DS(0.001)EVDK 203.92 6.29E-21 8908700 1992.2 2030.7 2009.5 1850.6 2447.5 2170.4 1926 2423.7 2552.7 2332.4 TRUE FALSE FALSE 1967.9183 2059.288248 2044.474505 2064.575079 2322.594942 2031.718445 2089.594392 2493.825936 2324.380119 2271.803912 0.866235985 0.906455103 0.899934406 0.908782254 1.022357137 0.894319459 0.919795226 1.097729396 1.023142934 1 11.1496226 -7.258954281 24.23573276 0.931317112 1.097729487 0.435621645 0.05411613 110.9796303 1082213.097 0.007942359 0.07134589 5.51E-08 7.258954281 0.166412375 ELVSSSSSGSDS(ph)DSEVDKK ddPTM_HeLa_Romidepsin_16h_R1 1 ELVSSSSSGSDSDSEVDKK 19 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 ELVS(0.025)S(0.096)S(0.315)S(0.05)S(0.059)GS(0.031)DS(0.424)DS(0.001)EVDKK 73.675 0.0039384 27127000 2672.1 2272.3 2181.5 2040.6 2228.5 2504.2 1936.9 2120.6 2806.3 2395 TRUE FALSE FALSE 2639.531417 2304.289499 2219.468092 2276.543773 2114.771329 2344.189702 2101.420238 2181.956215 2555.297499 2332.777555 1.131497263 0.987787924 0.951427232 0.975894066 0.906546501 1.004892085 0.900823241 0.935346883 1.095388411 1 11.18783303 -10.03742591 5.575467764 1.062240634 0.947523926 0.648641293 0.04234564 0.122821005 10.26872396 0.009071142 0.011338937 9.17E-11 10.03742591 -0.114716708 EMCVLRMT(ph)RARR ddPTM_HeLa_Romidepsin_16h_R1 1 EMCVLRMTRARR 12 3 Q6PL18;A0A0B4J211 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 0 EMCVLRMT(1)RARR 49.31 0.026077 8264600 2301.4 2441.5 2018.1 2803.4 1356.1 1389.7 1326.9 1774.2 1915.3 1840.7 TRUE FALSE FALSE 2273.349652 2475.871501 2053.224184 3127.542298 1286.893157 1300.902655 1439.606853 1825.533678 1743.990771 1792.878349 1.267988792 1.38094785 1.145211099 1.744425271 0.717780522 0.725594492 0.802958468 1.018213912 0.972732351 1 10.80806189 EMDEEDK(ac)AFK ddPTM_HeLa_Romidepsin_16h_R1 1 EMDEEDKAFK 10 1 Q9Y2S6 Q9Y2S6 TMA7 Translation machinery-associated protein 7 0 1 EMDEEDK(1)AFK 100.25 0.01042 2312300 524.73 728.66 365.96 463.07 1218 939.88 1086.9 1055.3 1388.4 785.7 FALSE TRUE FALSE 518.3343889 738.9180946 372.3293803 516.6123322 1155.840915 879.8247013 1179.221259 1085.833441 1264.218027 765.2874007 0.677306837 0.965543264 0.486522292 0.675056628 1.510335743 1.149665734 1.540886806 1.418857072 1.651951967 1 9.579857838 -8.760006813 24.99998398 0.813019887 1.396413532 0.347520628 0.316437016 16.81390869 293412.3509 0.028402073 0.054442166 1.74E-09 8.760006813 0.583393645 EMEAELEDERK ddPTM_HeLa_Romidepsin_16h_R1 3 EMEAELEDERK 11 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ;; ;; 102.95 0.0048142 37110000 5169.1 5468 5176.5 4988 6168.7 6590.9 5904 6367.5 7224 6649.5 FALSE FALSE TRUE 5106.097021 5544.978648 5266.594811 5564.736029 5853.88822 6169.762761 6405.485613 6551.733566 6577.867347 6476.745031 0.788373943 0.856136627 0.813154568 0.859187138 0.903831816 0.952602385 0.98899765 1.011578121 1.015613138 1 12.66105324 -8.053963925 1.898984002 0.884306775 1.004555109 0.29990779 0.068242544 0.406097518 2.774485866 0.012383868 0.04936351 8.83E-09 8.053963925 0.120248334 EMEENFAVEAANYQDTIGR ddPTM_HeLa_Romidepsin_16h_R1 2 EMEENFAVEAANYQDTIGR 19 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 ; ; 188 2.62E-14 56354000 4022.5 3423.2 2838.6 3011.6 2897.9 3373.8 2480.9 3184.7 3240.8 3385.2 FALSE FALSE TRUE 3973.472223 3471.391899 2888.004642 3359.815362 2750.009349 3158.225068 2691.627584 3276.84427 2950.934731 3297.252016 1.205085994 1.052813641 0.875882289 1.01897439 0.834030683 0.957835511 0.816324494 0.993810681 0.894967906 1 11.68704844 -9.875731538 5.031397886 1.098275371 0.914859581 0.18797068 0.099726662 0.139552079 5.635792117 0.014975291 0.019853697 1.33E-10 9.875731538 -0.18341579 EMFEDTVEER ddPTM_HeLa_Romidepsin_16h_R1 1 EMFEDTVEER 10 0 E9PC52;Q16576 E9PC52 RBBP7 Histone-binding protein RBBP7 0 0 120.27 0.02882 20456000 1490.4 1490.5 1659.4 1370.6 1423 1431.8 1426.7 1678.1 1634.8 1849.1 FALSE FALSE TRUE 1472.234432 1511.483298 1688.281161 1529.075221 1350.379 1340.312601 1547.883862 1726.653176 1488.579394 1801.060115 0.817426592 0.839218683 0.937381904 0.848986221 0.749768977 0.744179825 0.859429316 0.958687143 0.826501781 1 10.81463062 -12.34016045 0.757950004 1.015579148 0.83886595 0 0.084108367 0.644441324 0.568063212 0.072984276 0.013738597 4.57E-13 12.34016045 -0.176713198 EMGVDVHFPK ddPTM_HeLa_Romidepsin_16h_R1 1 EMGVDVHFPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 72.643 0.016752 922520 1034.3 992.69 1047.5 814.33 972.54 1071.4 782.39 905.2 973.62 1180.7 FALSE FALSE TRUE 1021.693554 1006.665116 1065.731298 908.4866661 922.9076548 1002.940998 848.8461871 931.3905338 886.5369887 1150.025244 0.888409676 0.875341756 0.926702526 0.789971065 0.802510779 0.872103463 0.738110917 0.809887034 0.770884808 1 10.16744981 -16.52287418 0.035696246 1.984716859 0.227847725 0 0.082290759 258.4470034 0.738465808 29.82992118 10.92118932 3.00E-17 16.52287418 -1.756869134 EMLAS(ph)DDEEDVSSK ddPTM_HeLa_Romidepsin_16h_R1 4 EMLASDDEEDVSSK 14 0 E7ETM8;E7EUA0;Q0ZGT2-4;Q0ZGT2-2;Q0ZGT2;Q0ZGT2-3 E7ETM8 NEXN Nexilin 1 0 EMLAS(1)DDEEDVSSK;EMLAS(1)DDEEDVSSK;EMLAS(1)DDEEDVSSK;EMLAS(1)DDEEDVSSK ;;; 170.26 7.72E-05 440428200 24950.8 25742.8 27967 14747.8 25156.5 25095.3 20350.1 22664.4 26152.4 27602.3 TRUE FALSE FALSE 24646.69005 26105.20781 28453.7539 16453.01003 23872.66993 23491.79132 22078.63699 23320.15866 23813.26384 26885.18827 0.916738607 0.97098847 1.058343115 0.611973026 0.887948773 0.873781916 0.821219356 0.867398005 0.885739152 1 14.71452395 -9.299692401 24.99950381 0.967279043 0.820550502 0.451063113 0.084649901 376.6335119 246140.3924 0.012202644 0.018640072 5.02E-10 9.299692401 -0.146728542 EMLAS(ph)DDEEDVSSKVEK ddPTM_HeLa_Romidepsin_16h_R1 2 EMLASDDEEDVSSKVEK 17 1 E7ETM8;E7EUA0;Q0ZGT2-4;Q0ZGT2-2;Q0ZGT2;Q0ZGT2-3 E7ETM8 NEXN Nexilin 1 0 EMLAS(0.999)DDEEDVS(0.001)SKVEK;EMLAS(1)DDEEDVSSKVEK ; 91.547 0.0090329 292780000 13335 13367.8 12882.1 14306.6 14359.9 13398.8 13024.9 13290.5 15494.7 14108.9 TRUE FALSE FALSE 13172.46789 13555.99224 13106.30755 15960.79641 13627.06072 12542.65992 14131.23468 13675.03965 14108.81522 13742.34874 0.958531044 0.986439254 0.953716704 1.161431478 0.991610748 0.912701326 1.02829836 0.995102068 1.026666947 1 13.74634098 EMLMEDVGS(ph)EEEQEEEDEAPFQEK ddPTM_HeLa_Romidepsin_16h_R1 3 EMLMEDVGSEEEQEEEDEAPFQEK 24 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK;EMLMEDVGS(1)EEEQEEEDEAPFQEK ;; 80.067 8.40E-05 67393900 14869.6 13290.3 14666.8 8785.6 13676.6 13747.9 12419.9 12518 15794.5 15930.4 TRUE FALSE FALSE 14688.3636 13477.40119 14922.0695 9801.432409 12978.63207 12869.45356 13474.846 12880.18858 14381.80036 15516.52591 0.946627079 0.868583681 0.96168882 0.631676992 0.8364393 0.829403027 0.868419005 0.830094871 0.92686987 1 13.92151796 -10.04316393 1.137303422 0.980876895 0.813664384 0.396923851 0.075923113 0.27296075 0.68914675 0.014355145 0.018914321 9.05E-11 10.04316393 -0.167212511 EMLQQSK(ac)ILK ddPTM_HeLa_Romidepsin_16h_R1 2 EMLQQSKILK 10 1 P08238;Q58FF7;P07900-2;P07900 P08238;P07900-2 HSP90AB1;HSP90AB3P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Heat shock protein HSP 90-alpha 0 1 ; EMLQQSK(1)ILK;EMLQQSK(1)ILK 157.78 0.0042206 3208100 510.19 478.35 367.88 132.89 479.65 427.58 376.22 467.68 557.49 442.18 FALSE TRUE FALSE 503.971608 485.0842239 374.2827971 148.2553671 455.1716707 400.259018 408.1761174 481.2115829 507.6266981 430.6920999 1.170143609 1.126290043 0.869026382 0.34422588 1.056837752 0.929339122 0.947721394 1.117298374 1.178630159 1 8.75051305 -9.75414776 23.33558562 1.086036381 0.866884953 0.24884967 0.201760098 88.92028817 284570.9785 0.032482418 0.045348445 1.76E-10 9.75414776 -0.219151429 EMLWGSSTQLAS(ph)DGSPK ddPTM_HeLa_Romidepsin_16h_R1 2 EMLWGSSTQLASDGSPK 17 0 A0A0J9YW64;A6NIW2;Q5JSL3 A0A0J9YW64 DOCK11 Dedicator of cytokinesis protein 11 1 0 EMLWGSS(0.002)T(0.006)QLAS(0.832)DGS(0.16)PK;EMLWGSS(0.001)T(0.002)QLAS(0.865)DGS(0.132)PK ; 128.94 0.0028188 30655000 5312.5 5499.8 5660.8 5081.7 5767.3 6181.2 5399.6 6069.1 6134.7 5142.1 TRUE FALSE FALSE 5247.749207 5577.226329 5759.323849 5669.270064 5472.97316 5786.241269 5858.241889 6244.699833 5585.997067 5008.507501 1.047767066 1.113550559 1.149908201 1.131928037 1.092735343 1.15528254 1.169658204 1.246818505 1.115301727 1 12.29016504 -4 0.116609295 0.931389343 1.845433225 0.476711999 0.046433559 25.10701703 0.202671725 0.147491808 3.730344147 1.00E-04 4 0.914043882 EMPQDLRS(ph)PART(ph)PPSEEDSAEAER ddPTM_HeLa_Romidepsin_16h_R1 1 EMPQDLRSPARTPPSEEDSAEAER 24 2 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 2 0 EMPQDLRS(1)PART(1)PPSEEDSAEAER 72.058 0.00083772 11196000 905.12 732.41 855.47 809.92 1199 878.2 897.34 1151.1 935.44 891.82 TRUE FALSE FALSE 894.0880493 742.7208872 870.3590965 903.5667612 1137.810556 822.0858543 973.5600372 1184.405262 851.7719035 868.6503878 1.029284119 0.855028556 1.001967084 1.040196118 1.309860183 0.94639439 1.120773157 1.363500528 0.980569301 1 9.762631831 -8.979947148 24.46847518 0.999897662 1.164925617 0.418253007 0.115052971 167.0145915 203789.7507 0.016235581 0.029426831 1.05E-09 8.979947148 0.165027955 EMS(ph)PS(ph)PPAAQDPGGTALVSAR ddPTM_HeLa_Romidepsin_16h_R1 1 EMSPSPPAAQDPGGTALVSAR 21 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 2 0 EMS(1)PS(0.999)PPAAQDPGGT(0.001)ALVSAR 81.574 0.001326 0 442.85 283.38 339.91 404.63 519 528.95 417.26 424.15 480.68 445.31 TRUE FALSE FALSE 437.4523739 287.3694311 345.825991 451.4152244 492.5134933 495.1518021 452.702054 436.4221111 437.6867769 433.740782 1.008557166 0.662537264 0.797310295 1.04074886 1.135501926 1.141584611 1.043715677 1.00618187 1.009097588 1 8.760689287 -9.011900056 24.07732753 0.957264523 1.083906481 0.315818345 0.115429072 481.3058261 973828.5153 0.019568482 0.033679538 9.73E-10 9.011900056 0.126641958 EMS(ph)PSPPAAQDPGGTALVSAR ddPTM_HeLa_Romidepsin_16h_R1 1 EMSPSPPAAQDPGGTALVSAR 21 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 EMS(0.5)PS(0.5)PPAAQDPGGTALVSAR 108.47 0.00037569 6519800 731.5 517.67 436.28 664.77 783.63 644.51 619 684.73 713.21 535.61 TRUE FALSE FALSE 722.5841966 524.9577718 443.8732704 741.6338352 743.638437 603.3278911 671.5778445 704.5415822 649.4187113 521.694775 1.385070795 1.006254609 0.850829435 1.421585706 1.425428186 1.156476775 1.287300308 1.350486177 1.244825025 1 9.027062174 EMSPS(ph)PPAAQDPGGTALVSAR ddPTM_HeLa_Romidepsin_16h_R1 1 EMSPSPPAAQDPGGTALVSAR 21 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 EMS(0.401)PS(0.599)PPAAQDPGGTALVSAR 82.925 0.0034473 5892100 839.81 780.95 515.31 775.63 860.06 959.96 877.82 917.81 822.14 815.59 TRUE FALSE FALSE 829.5740727 791.9442346 524.2787544 865.31199 816.1679289 898.6216541 952.3820089 944.3653843 748.6057393 794.4008542 1.044276411 0.996907582 0.659967511 1.08926367 1.027400618 1.131194219 1.198868309 1.188776899 0.942352636 1 9.633723364 -8.205035682 1.791606535 0.994353795 1.196927689 0.413525883 0.112093796 0.324745997 1.968364441 0.016824373 0.059310426 6.24E-09 8.205035682 0.202573894 ENAEVDGDDDAEEMEAK ddPTM_HeLa_Romidepsin_16h_R1 2 ENAEVDGDDDAEEMEAK 17 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 0 ; ; 147.53 0.00054646 16985100 8457.5 8701.5 8657.8 4418.1 8010.3 9628 7745.5 8285.9 9080.4 8614.7 FALSE FALSE TRUE 8354.416737 8823.999945 8808.485377 4928.94151 7601.5045 9012.801873 8403.402577 8525.639444 8268.226282 8390.888852 0.995653367 1.051616831 1.049767853 0.587415898 0.905923632 1.074117657 1.001491347 1.016059156 0.985381457 1 13.03460793 ENAEVDGDDDAEEMEAKAED ddPTM_HeLa_Romidepsin_16h_R1 2 ENAEVDGDDDAEEMEAKAED 20 1 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 0 ; ; 126.25 0.00039483 25087000 11011 9431.8 8627.1 19325.9 12113.5 10915.6 10080.7 10207.7 12379.9 9435.4 FALSE FALSE TRUE 10876.7937 9564.581128 8777.251057 21560.45149 11495.30289 10218.12839 10936.95441 10503.04369 11272.61074 9190.266948 1.18351227 1.040729413 0.955059424 2.346009274 1.25081273 1.111842392 1.190058403 1.142844245 1.226581426 1 13.16589105 ENALSSGTLQEEQRT(ph)PPPGQDTQQFHEK ddPTM_HeLa_Romidepsin_16h_R1 1 ENALSSGTLQEEQRTPPPGQDTQQFHEK 28 1 Q12802-4;Q12802;Q12802-2;H0YMW2 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 ENALS(0.032)S(0.083)GT(0.083)LQEEQRT(0.797)PPPGQDT(0.004)QQFHEK 51.621 0.0050605 9011600 1445.5 1326.7 1234.2 1012.2 1602.7 1640.9 1698.5 1654.8 1749.2 1196.6 TRUE FALSE FALSE 1427.88169 1345.377317 1255.680733 1129.235327 1520.908239 1536.051786 1842.770548 1702.679027 1592.747171 1165.512159 1.225110934 1.15432285 1.077363907 0.968874771 1.304926959 1.31792 1.581082216 1.460884825 1.366564182 1 10.18674834 -8.233884696 1.740045225 1.103280868 1.515037635 0.581115399 0.122155144 0.154144953 0.880398749 0.015998566 0.055844619 5.84E-09 8.233884696 0.411756767 ENARS(ph)PSSVTGNALWK ddPTM_HeLa_Romidepsin_16h_R1 2 ENARSPSSVTGNALWK 16 1 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 0 ENARS(0.846)PS(0.123)S(0.03)VTGNALWK;ENARS(0.775)PS(0.167)S(0.057)VTGNALWK ; 74.744 0.012194 30106000 3551.9 3570.7 3458.2 4920.2 4536 5180.9 4854.6 6007.2 4162.3 4150.5 TRUE FALSE FALSE 3508.608077 3620.968408 3518.38852 5489.096674 4304.510994 4849.857211 5266.949603 6181.008854 3790.013463 4042.669412 0.867893889 0.895687488 0.870313192 1.357790142 1.064769477 1.199667031 1.302839551 1.528942445 0.937502694 1 11.98109252 -7.533258826 0.523900382 0.929618733 1.768017472 0.718044303 0.117238079 1.307444942 0.287511273 0.025447847 0.632450137 2.93E-08 7.533258826 0.838398739 ENAS(ph)PAPGTTAEEAMSR ddPTM_HeLa_Romidepsin_16h_R1 2 ENASPAPGTTAEEAMSR 17 0 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3;H0Y710;A0A0G2JL47;P46379-5 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 ENAS(0.715)PAPGT(0.03)T(0.254)AEEAMSR;ENAS(0.869)PAPGT(0.022)T(0.106)AEEAMS(0.003)R ; 95.365 0.0080559 72345000 8117.6 8130.3 8594.4 4677.5 6390.7 7549.9 6656.7 7348.6 8741.6 8432.9 TRUE FALSE FALSE 8018.659569 8244.758577 8743.981927 5218.334558 6064.558732 7067.485756 7222.119932 7561.220147 7959.729402 8213.812042 0.976240938 1.003767621 1.064546143 0.635312146 0.738336682 0.860439187 0.879265303 0.920549449 0.969066417 1 13.00383622 -9.283847889 24.99963638 0.995023769 0.809986059 0.609882199 0.078214572 441.6567326 492724.7034 0.012395367 0.018943114 5.20E-10 9.283847889 -0.18503771 ENCDSRY(ph)DT(ph)MRRLMSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ENCDSRYDTMRRLMSSR 17 3 C9JYG8;Q6P988 C9JYG8 NOTUM Palmitoleoyl-protein carboxylesterase NOTUM 2 0 ENCDS(0.308)RY(0.692)DT(0.928)MRRLMS(0.036)S(0.036)R 60.08 0.0036558 0 2779 2760.1 2327.3 2026.3 2845.9 3152.6 2375.4 3213.7 3032.1 2761.7 TRUE FALSE FALSE 2745.128479 2798.95676 2367.80568 2260.59034 2700.663103 2951.159035 2577.166417 3306.683339 2760.901382 2689.950636 1.020512586 1.040523466 0.880241313 0.840383578 1.003982403 1.097105276 0.958072012 1.22927287 1.026376226 1 11.39336398 ENDEEMK(ac)AAK ddPTM_HeLa_Romidepsin_16h_R1 1 ENDEEMKAAK 10 1 O95696-2;O95696;J3KQ61 O95696-2 BRD1 Bromodomain-containing protein 1 0 1 ENDEEMK(1)AAK 100.82 0.010038 467200 478.14 470.07 695.29 219.85 624.31 650.69 584.97 312.64 1028.9 617.34 FALSE TRUE FALSE 472.3122458 476.6876578 707.3912308 245.2700914 592.4491311 609.113009 634.6573372 321.6857451 936.8726071 601.3014178 0.78548334 0.79275991 1.176433665 0.407898741 0.985278121 1.01299114 1.055472877 0.534982516 1.558074835 1 9.23194455 -12.48102349 1.212085533 1.000308994 0.848765162 0.14507047 0.285607633 1.158901113 3.036532221 0.146233536 0.035501389 3.30E-13 12.48102349 -0.151543832 ENDEEMKAAK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 2 ENDEEMKAAKEK 12 2 O95696-2;O95696;J3KQ61 O95696-2 BRD1 Bromodomain-containing protein 1 0 1 ; ENDEEMK(0.271)AAK(0.729)EK;ENDEEMK(0.065)AAK(0.935)EK 61.48 0.02107 8578100 2992.6 2433.5 2012.77 3299.1 1709.35 1168.04 1683.42 1468.5 2535.4 1831.88 FALSE TRUE FALSE 2956.12504 2467.758877 2047.801418 3680.557465 1622.115491 1093.406014 1826.409653 1510.988731 2308.627474 1784.287494 1.656753775 1.383050033 1.147685799 2.062760333 0.909111058 0.612796995 1.023607271 0.84683031 1.293865188 1 10.80113237 -8.553863345 24.98702557 1.36209334 0.832934112 0.479360092 0.290679404 159.2245737 128403.4777 0.048562393 0.097125498 2.79E-09 8.553863345 -0.529159228 ENDPLRT(ph)PEALPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ENDPLRTPEALPEEK 15 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 ENDPLRT(1)PEALPEEK 77.031 0.020057 16569000 2985.9 2704.9 2708.3 2420.5 2293.2 2810.3 3251.3 3352.7 3562.1 2982.6 TRUE FALSE FALSE 2949.506702 2742.979653 2755.436825 2700.369599 2176.169447 2630.7309 3527.465341 3449.705085 3243.496855 2905.111622 1.015281712 0.944190795 0.948478814 0.929523526 0.749082903 0.905552434 1.214227128 1.187460426 1.116479253 1 11.50437788 -7.753772832 24.99950609 0.969229146 1.200843897 0.547670828 0.089588873 102.5575731 334416.8433 0.012442298 0.044814442 1.76E-08 7.753772832 0.231614751 ENDTVTIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ENDTVTISPK 10 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 ENDT(0.001)VT(0.034)IS(0.965)PK;ENDTVT(0.031)IS(0.969)PK ; 120.59 0.011459 15765100 6238 7116.2 6476.5 3269.2 5010.5 5775.7 4922.2 5601.7 7094.5 6611.3 TRUE FALSE FALSE 6161.968857 7216.38205 6589.220766 3647.200286 4754.795488 5406.65141 5340.291545 5763.776351 6459.950151 6439.537473 0.956896187 1.120636704 1.023244417 0.566376126 0.738375312 0.839602446 0.829297379 0.895060612 1.003169898 1 12.65274135 -9.305014881 24.99953521 0.994918467 0.778522688 0.637878113 0.092008126 255.5112908 146587.7712 0.014563814 0.022246672 4.95E-10 9.305014881 -0.21639578 ENGDLS(ph)PFSGTSLR ddPTM_HeLa_Romidepsin_16h_R1 1 ENGDLSPFSGTSLR 14 0 P19174;V9GY71;V9GYH5 P19174 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 0 ENGDLS(1)PFSGTSLR 187 1.21E-08 5064100 1615.6 1371.4 1550.5 1215 1526.5 1449.2 1139.2 1437 1658.5 1812.2 TRUE FALSE FALSE 1595.908446 1390.706605 1577.485802 1355.484017 1448.597009 1356.600797 1235.96362 1478.577328 1510.159606 1765.118783 0.904136572 0.78788273 0.893699516 0.767927932 0.820679618 0.768560626 0.70021555 0.837664492 0.85555693 1 10.78554956 -10.4724951 0.40298976 1.006704528 0.75369269 0.379761968 0.063673119 0.317028094 0.141673696 0.0272176 0.026046934 3.37E-11 10.4724951 -0.253011838 ENIPEDSS(ph)MVS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 ENIPEDSSMVSKR 13 1 O94768 O94768 STK17B Serine/threonine-protein kinase 17B 2 0 ENIPEDS(0.135)S(0.869)MVS(0.996)KR 67.685 0.021763 1761100 66.538 0 116.1 269.28 0 0 138.06 0 215.37 124.77 TRUE FALSE FALSE 65.72700926 0 118.1206718 300.4154206 0 0 149.786813 0 196.1067678 121.5284574 0.540836366 0 0.971958949 2.471975922 0 0 1.232524597 0 1.613669522 1 6.925150368 ENPDMANPSAMSTT(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 ENPDMANPSAMSTTAK 16 0 C9JKF1;Q5K651 C9JKF1 SAMD9 Sterile alpha motif domain-containing protein 9 1 0 ENPDMANPS(0.158)AMS(0.102)T(0.102)T(0.639)AK 67.234 0.0029383 0 714.03 906.21 765.3 784.89 684.08 789.7 881.8 490.21 880.87 937.98 TRUE FALSE FALSE 705.3271277 918.9676482 778.6197255 875.6426748 649.1688449 739.2407186 956.70007 504.3934529 802.082781 913.6111444 0.772021152 1.005863002 0.85224412 0.958441324 0.710552678 0.809141529 1.04716331 0.552087675 0.877925785 1 9.835436439 -12.51093661 1.176465658 1.002774883 0.841405158 0.047871183 0.142552234 0.716916041 1.725608192 0.096792981 0.021730334 3.08E-13 12.51093661 -0.161369726 ENPEDVLSPT(ph)SVATYLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 ENPEDVLSPTSVATYLSSK 19 0 A0A0A0MRG9;Q96SN8-4;Q96SN8-3;Q96SN8-2;Q96SN8;Q5JTU8;B1AMJ5 A0A0A0MRG9 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 0 ENPEDVLS(0.341)PT(0.503)S(0.156)VATYLSSK 171.3 2.42E-07 11349000 7844.1 7584.7 7430.8 7305.6 6984.6 6995.9 5999 5651.8 8621.7 8282.5 TRUE FALSE FALSE 7748.493092 7691.477606 7560.129957 8150.307846 6628.149799 6548.884568 6508.55491 5815.325916 7850.553559 8067.319456 0.960479269 0.953411805 0.937130356 1.010286984 0.821604975 0.811779502 0.806780362 0.720849837 0.973130369 1 12.97787367 -8.672380278 4.699592936 0.976662512 0.787886632 0.890610216 0.031396345 0.050662151 1.964932245 0.004848868 0.009844727 2.13E-09 8.672380278 -0.18877588 ENPPVEDS(ph)SDEDDKR ddPTM_HeLa_Romidepsin_16h_R1 1 ENPPVEDSSDEDDKR 15 1 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 1 0 ENPPVEDS(0.878)S(0.122)DEDDKR 126.4 0.00078259 5890100 2491.5 4280.1 3236.5 1826.2 2452.8 4078.7 2173.6 3711.6 3211 3823.6 TRUE FALSE FALSE 2461.13264 4340.35536 3292.829925 2037.353837 2327.624463 3818.084233 2358.22553 3818.98929 2923.800118 3724.262321 0.660837618 1.165426865 0.884156281 0.547048962 0.624989397 1.02519208 0.633206076 1.025435096 0.785068254 1 11.86273898 -12.63324466 1.443001126 1.000391533 0.795823916 0 0.206811168 0.710891173 2.651373458 0.139828953 0.03155758 2.33E-13 12.63324466 -0.204567617 ENPVLDVVS(ph)NPEQTAGEER ddPTM_HeLa_Romidepsin_16h_R1 1 ENPVLDVVSNPEQTAGEER 19 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 ENPVLDVVS(1)NPEQTAGEER 321.88 4.32E-187 7130800 1718.7 1656 1790.9 1120.9 1994.5 1890 1446.2 1900.6 2036.9 1855.1 TRUE FALSE FALSE 1697.751823 1679.313211 1822.069863 1250.503732 1892.713222 1769.2351 1569.040192 1955.590862 1854.714562 1806.904235 0.93959148 0.929386948 1.008393156 0.692069733 1.047489505 0.979152667 0.868358246 1.082288051 1.026459802 1 10.81930433 -12.01895839 0.806837466 1.000164062 0.938850952 0.062586115 0.102830567 1.75049627 2.07312239 0.064006973 0.019421543 9.57E-13 12.01895839 -0.06131311 ENPVVVGEK(ac)IQK ddPTM_HeLa_Romidepsin_16h_R1 2 ENPVVVGEKIQK 12 1 Q6FIF0-2;Q6FIF0 Q6FIF0-2 ZFAND6 AN1-type zinc finger protein 6 0 1 ; ENPVVVGEK(1)IQK;ENPVVVGEK(1)IQK 185.25 5.07E-06 2552200 1714.99 1504.08 1294.21 945.36 1695.28 2123.1 2190.1 2217.65 2138.9 1740.24 FALSE TRUE FALSE 1694.087042 1525.254478 1316.735182 1054.666971 1608.763536 1987.440762 2376.127039 2281.814204 1947.591427 1695.028314 0.999444687 0.899840118 0.776821939 0.622212008 0.949107176 1.172511837 1.401821444 1.346180583 1.149002297 1 10.72709366 -8.033611258 2.916164454 0.943337269 1.371762827 0.650767045 0.135840059 0.132733945 2.243199436 0.020355434 0.065940637 9.26E-09 8.033611258 0.428425558 ENPYYDSR ddPTM_HeLa_Romidepsin_16h_R1 2 ENPYYDSR 8 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 ; ; 177.7 0.0016736 93487000 9042.5 9362.3 9965.8 9286.9 10249.9 10601.2 9159.8 9558 9856.4 8740.2 FALSE FALSE TRUE 8932.286532 9494.102705 10139.25057 10360.69507 9726.809355 9923.817534 9937.833183 9834.54565 8974.818898 8513.128344 1.049236681 1.115230773 1.191013475 1.217025593 1.142565807 1.165707497 1.167353854 1.155221119 1.054232773 1 13.05547367 -10.21772115 1.740747528 1.018869882 1.173345005 0.866521193 0.024223965 0.077547309 0.446010136 0.004670737 0.005633963 6.06E-11 10.21772115 0.154475123 ENQEPLRS(ph)PEVGDEEALRPLTK ddPTM_HeLa_Romidepsin_16h_R1 1 ENQEPLRSPEVGDEEALRPLTK 22 2 P48681 P48681 NES Nestin 1 0 ENQEPLRS(1)PEVGDEEALRPLTK 69.081 0.0016335 43890000 1768.9 1871.8 1940 1446.7 2685 2844.6 2740.2 3030.9 1950.8 2037.6 TRUE FALSE FALSE 1747.339966 1898.15125 1973.764886 1613.974261 2547.974431 2662.839241 2972.95252 3118.59431 1776.315562 1984.662858 0.880421558 0.956409922 0.994508905 0.813223392 1.283832375 1.341708608 1.497963499 1.571347142 0.895021315 1 10.95467824 -8.407399544 1.715168908 0.939023767 1.515522548 0.901767666 0.081819089 0.079750028 0.4518972 0.012242422 0.036840542 3.91E-09 8.407399544 0.576498781 MDSNFGLAGLPGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 MDSNFGLAGLPGSPK 15 0 O43463;O43463-2 O43463 SUV39H1 Histone-lysine N-methyltransferase SUV39H1 1 0 MDSNFGLAGLPGS(1)PK;MDS(0.025)NFGLAGLPGS(0.975)PK ; 122.97 0.0044203 84480000 14543.1 14491.2 12308 8861.1 4942.8 3505.4 3522.1 3110.1 14616.9 14448.3 TRUE FALSE FALSE 14365.8431 14695.20749 12522.21558 9885.662075 4690.550472 3281.416253 3821.267086 3200.085837 13309.52786 14072.93108 1.02081386 1.044217968 0.889808634 0.702459354 0.333303023 0.233172197 0.271533134 0.227392987 0.945753786 1 13.78063522 -8.946283015 1.594954788 1.011813244 0.235317795 0.988530327 0.03641566 0.020333783 0.103587415 0.004680362 0.010026787 1.13E-09 8.946283015 -0.776495449 down ENQPENSQT(ph)PTKK ddPTM_HeLa_Romidepsin_16h_R1 3 ENQPENSQTPTKK 13 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 0 ENQPENS(0.014)QT(0.905)PT(0.081)KK;ENQPENS(0.002)QT(0.77)PT(0.228)KK;ENQPENS(0.005)QT(0.954)PT(0.041)KK ;; 103.67 0.0043819 65720000 9790.6 9981.1 15225.3 13079.4 7039.3 5726.4 8566.5 1089.58 14754.4 11521.1 TRUE FALSE FALSE 9671.268401 10121.61419 15490.28996 14591.70177 6680.058254 5360.501521 9294.138296 1121.105278 13434.72951 11221.78016 0.861830143 0.901961546 1.380377243 1.300301874 0.595276165 0.477687269 0.828223166 0.099904406 1.197201274 1 13.45401393 -8.6114418 7.623529504 0.990111689 0.509873264 0.579416409 0.242181967 0.153231936 11.38086879 0.034500208 0.069214087 2.45E-09 8.6114418 -0.480238425 ENQSEGKGSDS(ph)DSEGDNPEK ddPTM_HeLa_Romidepsin_16h_R1 2 ENQSEGKGSDSDSEGDNPEK 20 1 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 0 ENQS(0.002)EGKGS(0.248)DS(0.742)DS(0.007)EGDNPEK;ENQS(0.045)EGKGS(0.13)DS(0.73)DS(0.096)EGDNPEK ; 80.362 0.0016633 31117000 4355.2 3811.2 4066.9 3120.6 4558.8 4687 4543.5 3741.5 4135.4 4384.5 TRUE FALSE FALSE 4302.117147 3864.854174 4137.682689 3481.418455 4326.147425 4387.515827 4929.424777 3849.754399 3765.519467 4270.590058 1.007382373 0.904993015 0.968878453 0.81520783 1.013009295 1.027379301 1.154272527 0.901457257 0.881732832 1 12.0602197 -8.529422742 24.99932485 0.978044191 1.03699906 0.088223857 0.086470814 297.7457238 1137445.387 0.011748217 0.023548987 2.96E-09 8.529422742 0.058954868 ENS(ph)PNSFPR ddPTM_HeLa_Romidepsin_16h_R1 2 ENSPNSFPR 9 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 0 ENS(0.992)PNS(0.008)FPR;ENS(0.969)PNS(0.031)FPR ; 150.09 0.0052879 33466000 5476.7 5663.9 6089.4 5267 6095 7823.7 5912.8 6618 6452.5 5731.9 TRUE FALSE FALSE 5409.947874 5743.636533 6195.383453 5875.995322 5783.949406 7323.79082 6415.033084 6809.481389 5875.372239 5582.984412 0.969006444 1.028775313 1.109690265 1.052482846 1.03599598 1.311805708 1.149032956 1.219684829 1.052371242 1 12.44682081 -8.709621223 0.708707826 0.986438759 1.236038531 0.589990158 0.064679658 0.356865531 0.307958062 0.011423449 0.048916395 1.95E-09 8.709621223 0.249599772 ENS(ph)SSQDPQTEGTR ddPTM_HeLa_Romidepsin_16h_R1 1 ENSSSQDPQTEGTR 14 0 A0A0C4DG49;P15151-3;P15151-2;P15151 A0A0C4DG49 PVR Poliovirus receptor 1 0 ENS(0.944)S(0.05)S(0.005)QDPQTEGTR 97.129 0.0029502 0 925.18 999.96 1097.6 792.99 622.57 635.27 718.21 744.4 1166.3 1247.7 TRUE FALSE FALSE 913.9035503 1014.037463 1116.703268 884.6792349 590.7979298 594.6782972 779.2147395 765.9380395 1061.983207 1215.284574 0.752007859 0.834403303 0.918882121 0.727960557 0.486139578 0.489332548 0.641178828 0.630254062 0.87385558 1 10.24707846 -8.999754691 3.914102629 0.877151993 0.563389388 0.792181902 0.075679324 0.101047844 3.505837293 0.0160805 0.028947328 1.00E-09 8.999754691 -0.313762606 ENSFGS(ph)PLEFR ddPTM_HeLa_Romidepsin_16h_R1 2 ENSFGSPLEFR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 ENS(0.03)FGS(0.97)PLEFR;ENS(0.026)FGS(0.974)PLEFR ; 136.33 0.0038351 220320000 13314.8 13894.6 13087.2 6028.8 10518.1 11085 9389.3 10404.9 13494.8 14803.1 TRUE FALSE FALSE 13152.5141 14090.20854 13314.97723 6725.878222 9981.322109 10376.70428 10186.82691 10705.94937 12287.79129 14418.51333 0.912196271 0.97723033 0.923463947 0.466475154 0.69225737 0.71967921 0.706510212 0.742514094 0.852223181 1 13.8156348 -9.411247424 7.800267788 0.958369661 0.672675181 0.725878762 0.081667442 0.098359707 6.22988789 0.011686405 0.017863754 3.88E-10 9.411247424 -0.28569448 ENSPAVS(ph)PT(ph)TNSTAPFGLKPR ddPTM_HeLa_Romidepsin_16h_R1 1 ENSPAVSPTTNSTAPFGLKPR 21 1 Q9Y2L9-2;Q9Y2L9;Q9Y2L9-3 Q9Y2L9-2 LRCH1 Leucine-rich repeat and calponin homology domain-containing protein 1 2 0 ENS(0.056)PAVS(0.935)PT(0.797)T(0.204)NS(0.004)T(0.004)APFGLKPR 56.9 0.023394 9147700 1603.9 1333.9 1376.5 849.8 1411.1 1398.5 1215.7 1229.4 1177.9 1570.8 TRUE FALSE FALSE 1584.35105 1352.678679 1400.457405 948.0578744 1339.086301 1309.140363 1318.961528 1264.970749 1072.545674 1529.99039 1.035530067 0.884109265 0.915337387 0.619649562 0.875225302 0.855652671 0.862071773 0.826783461 0.701014648 1 10.57930688 -9.982607202 2.052069909 1.016844888 0.818985136 0 0.124595099 0.15775469 1.324461781 0.012605258 0.016594913 1.04E-10 9.982607202 -0.197859752 ENSPVQS(ph)IR ddPTM_HeLa_Romidepsin_16h_R1 1 ENSPVQSIR 9 0 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 ENS(0.344)PVQS(0.656)IR 111.5 0.018281 6231000 2055.2 2142.2 2103.6 1161.8 2084.9 2307.7 1663.7 1819.2 2235.8 2042.3 TRUE FALSE FALSE 2030.150432 2172.357948 2140.212276 1296.132782 1978.499773 2160.245418 1805.014636 1871.835682 2035.824448 1989.240752 1.020565475 1.092053813 1.075894043 0.651571602 0.994600463 1.085964791 0.907388729 0.940979959 1.023417827 1 10.95800218 ENSTAK(ac)FIPR ddPTM_HeLa_Romidepsin_16h_R1 2 ENSTAKFIPR 10 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 1 ; ENSTAK(1)FIPR;ENSTAK(1)FIPR 118.03 0.015388 2948500 957.95 850.37 862.2 666.97 1129.48 1078.28 1161.33 1242.09 1179.34 883.33 FALSE TRUE FALSE 946.2741369 862.3415312 877.2062293 744.0882096 1071.838421 1009.381388 1259.973341 1278.027914 1073.856877 860.3809593 1.099831565 1.002278725 1.019555605 0.864835747 1.245771898 1.173179598 1.46443657 1.485420965 1.248117901 1 9.748831787 -7.928301075 1.351098325 1.034212767 1.52554138 0.687779136 0.108178461 0.169442013 0.513228205 0.012634973 0.081141233 1.18E-08 7.928301075 0.491328613 ENVATTDTLESTTVGT(ph)SV ddPTM_HeLa_Romidepsin_16h_R1 1 ENVATTDTLESTTVGTSV 18 0 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 1 0 ENVATTDTLES(0.005)T(0.004)T(0.003)VGT(0.575)S(0.412)V 152.99 3.87E-10 0 688.77 721.05 675.76 476.56 614.92 701.9 466.08 555.86 708.45 513.03 TRUE FALSE FALSE 680.3750063 731.2009608 687.5213193 531.6621095 583.5383378 657.0508553 505.6688236 571.9429321 645.0844577 499.7014066 1.36156312 1.463275771 1.375864287 1.063959602 1.167774055 1.314886944 1.011941965 1.144569386 1.290939847 1 8.964922469 ENVEY(ph)IEREESDGEYDEFGRK ddPTM_HeLa_Romidepsin_16h_R1 1 ENVEYIEREESDGEYDEFGRK 21 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 ENVEY(0.776)IEREES(0.121)DGEY(0.103)DEFGRK 49.089 0.028728 168460000 1019.4 1150.8 1176.8 1056.1 1183.3 1030.9 945.47 1188.5 1298.7 1494.4 TRUE FALSE FALSE 1006.975161 1167.000993 1197.28171 1178.211251 1122.911785 965.0288171 1025.778198 1222.887372 1182.541019 1455.575273 0.691805625 0.801745547 0.822548811 0.809447147 0.771455662 0.662987916 0.704723567 0.840140249 0.812421756 1 10.50737373 -12.39317669 0.98796317 1.007810384 0.757240688 0.220985999 0.079950098 0.266107907 0.440957986 0.049360883 0.011142463 4.04E-13 12.39317669 -0.250569695 ENVEYIEREES(ph)DGEYDEFGR ddPTM_HeLa_Romidepsin_16h_R1 4 ENVEYIEREESDGEYDEFGR 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 ENVEYIEREES(0.992)DGEY(0.008)DEFGR;ENVEYIEREES(0.997)DGEY(0.003)DEFGR;ENVEY(0.001)IEREES(0.999)DGEYDEFGR;ENVEY(0.011)IEREES(0.988)DGEY(0.001)DEFGR ;;; 91.481 0.00056294 772451000 5473.94 5164.05 5061.44 5259.96 5562 5354.24 4652.32 5398.24 5593.33 5553 TRUE FALSE FALSE 5407.221514 5236.749631 5149.53224 5868.141324 5278.150385 5012.121344 5047.487945 5554.429557 5093.048556 5408.732259 0.999720684 0.968202784 0.952077491 1.0849384 0.975857212 0.926672112 0.933210908 1.026937421 0.941634437 1 12.40107477 -8.528013957 24.99987283 0.999834082 0.958016786 0.054927213 0.045010098 170.568281 830379.0532 0.005627697 0.011286862 2.96E-09 8.528013957 -0.041817297 EPAITSQNS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 4 EPAITSQNSPEAR 13 0 E5RIS7;A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193 E5RIS7 TCEA1 Transcription elongation factor A protein 1 1 0 EPAITS(0.002)QNS(0.998)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR;EPAITSQNS(1)PEAR ;;; 204.17 1.96E-16 403385400 4529.14 4650.45 4673.27 2832.52 4931.38 5323.81 4593.36 5540.16 4793.71 5206.52 TRUE FALSE FALSE 4473.9371 4715.919157 4754.606304 3160.02929 4679.713277 4983.635723 4983.519884 5700.455789 4364.948572 5071.25386 0.882215173 0.929931588 0.937560303 0.623125834 0.922792155 0.982722589 0.982699747 1.12407226 0.860723737 1 12.30812678 -7.272198648 1.474478488 0.917915214 1.198262498 0.320216493 0.100706345 1.266783096 2.496310237 0.015621314 0.515409922 5.34E-08 7.272198648 0.280347284 EPALPLEPDSGGNT(ph)SPGVTANGEAR ddPTM_HeLa_Romidepsin_16h_R1 2 EPALPLEPDSGGNTSPGVTANGEAR 25 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;Q5VY93 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 EPALPLEPDSGGNT(0.922)S(0.078)PGVTANGEAR;EPALPLEPDS(0.006)GGNT(0.484)S(0.484)PGVT(0.027)ANGEAR ; 215.03 2.31E-37 46354000 6456.8 5814.6 5845.7 6212.8 6303.2 5309.6 4687.3 5747 6141.3 5782 TRUE FALSE FALSE 6378.102038 5896.458091 5947.441956 6931.153168 5981.524184 4970.333696 5085.439145 5913.280378 5592.006747 5631.782806 1.132519179 1.046996714 1.056049596 1.230720965 1.062101361 0.882550671 0.902989217 1.049983741 0.992937217 1 12.45937598 -8.33917947 7.343342279 1.075378776 0.941272917 0.377615665 0.0760882 0.217679138 18.07087795 0.011435921 0.025713956 4.58E-09 8.33917947 -0.134105859 EPAPAS(ph)PAPAGVEIR ddPTM_HeLa_Romidepsin_16h_R1 4 EPAPASPAPAGVEIR 15 0 Q14195-2 Q14195-2 1 0 EPAPAS(1)PAPAGVEIR;EPAPAS(1)PAPAGVEIR;EPAPAS(1)PAPAGVEIR;EPAPAS(1)PAPAGVEIR ;;; 161.94 0.00017138 70961000 4224.58 4510.4 4167.61 3410.11 5058.3 5597.4 4346.9 5371.2 4654.6 4149.03 TRUE FALSE FALSE 4173.089194 4573.89753 4240.145504 3804.402963 4800.156076 5239.744205 4716.125578 5526.607198 4238.280918 4041.237602 1.032626538 1.131806139 1.049219551 0.941395517 1.187793579 1.2965692 1.167000321 1.367553146 1.048758162 1 11.98058146 -8.591457161 5.025447141 1.023986355 1.263026382 0.742997613 0.064797164 0.070853808 3.409987467 0.009016864 0.018473214 2.56E-09 8.591457161 0.239040027 EPAPLLSAQYETLS(ph)DSDD ddPTM_HeLa_Romidepsin_16h_R1 2 EPAPLLSAQYETLSDSDD 18 0 E7EVK1;A0A088AWL3;O75376;O75376-2 E7EVK1 NCOR1 Nuclear receptor corepressor 1 1 0 EPAPLLSAQYETLS(0.5)DS(0.5)DD;EPAPLLSAQYETLS(0.5)DS(0.5)DD ; 138.81 0.00069289 10326800 5226.5 5197.3 5001.7 3701.6 4150.3 4067.7 3586 3802.3 5706.1 5315.3 TRUE FALSE FALSE 5162.797408 5270.467726 5088.75249 4129.596409 3938.494704 3807.787098 3890.59475 3912.313551 5195.732125 5177.20774 0.997216582 1.018013568 0.982914487 0.797649354 0.760737236 0.735490498 0.751485153 0.755680233 1.003578065 1 12.33795849 -9.211714894 2.971103981 1.000654466 0.751348854 0.994798003 0.008741978 0.014139307 0.24853097 0.001513942 0.002574897 6.14E-10 9.211714894 -0.249305612 EPDATPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EPDATPPSPR 10 0 A0A494C0S2;A0A090HNM7;A0A1W2PS85;R4GMW8;P28715 A0A494C0S2 ERCC5-201;BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 1 0 EPDATPPS(1)PR;EPDATPPS(1)PR ; 150.09 0.0037426 26424000 6836.7 6765.9 6651.2 4226.78 6482.7 6834.4 6050.8 6451.4 6742.9 7664.8 TRUE FALSE FALSE 6753.371671 6861.150518 6766.961346 4715.500191 6151.863629 6397.703897 6564.754801 6638.06108 6139.798136 7465.667391 0.904590483 0.919027082 0.906410772 0.631624735 0.824020587 0.85695003 0.879325914 0.889145033 0.822404457 1 12.86605552 -10.71001532 0.67574678 0.983591523 0.829284503 0.021683979 0.09022492 0.479181207 0.488198808 0.026559213 0.022860696 1.95E-11 10.71001532 -0.15430702 EPDPDS(ph)DWEPEER ddPTM_HeLa_Romidepsin_16h_R1 1 EPDPDSDWEPEER 13 0 Q9NPE2-3;Q9NPE2 Q9NPE2-3 NGRN Neugrin 1 0 EPDPDS(1)DWEPEER 123.76 0.0040527 14714000 1691 1380 1713.6 999.16 1318.5 1614.7 1283.7 1338.1 1639.1 1762.4 TRUE FALSE FALSE 1670.389442 1399.427676 1743.424489 1114.68758 1251.212025 1511.525881 1392.737446 1376.815812 1492.494791 1716.612594 0.973073044 0.815226267 1.015619072 0.649353025 0.728884333 0.880528249 0.811328922 0.802053892 0.869441828 1 10.74534877 -9.913190356 1.091395871 0.991123161 0.790069289 0.285789081 0.094905219 0.273802867 0.64428658 0.016450298 0.023241013 1.22E-10 9.913190356 -0.201053872 EPEDEEEEEEEEEEDEDEDLEELEVLER ddPTM_HeLa_Romidepsin_16h_R1 2 EPEDEEEEEEEEEEDEDEDLEELEVLER 28 0 Q9NQC3-5;Q9NQC3;Q9NQC3-2;Q9NQC3-4;F8W914 Q9NQC3-5 RTN4 Reticulon-4;Reticulon 0 0 ; ; 133.98 1.59E-10 12027100 3909 5605.1 5345 3178.25 5130 6094.2 3997.8 5496.1 5271.4 4822 FALSE FALSE TRUE 3861.355604 5684.008745 5438.027483 3545.734219 4868.196957 5704.800288 4337.373032 5655.120982 4799.912782 4696.723745 0.822138115 1.210207169 1.157834222 0.754937785 1.036509112 1.214633987 0.923489068 1.204056549 1.021970429 1 12.19743902 -8.229865408 0.43623585 0.931388964 1.165359144 0.00812965 0.155635448 3.954922808 0.872971825 0.045150784 0.418226895 5.89E-09 8.229865408 0.23397018 EPEMPGPREES(ph)EEEEDEDDEEEEEEEKEK ddPTM_HeLa_Romidepsin_16h_R1 1 EPEMPGPREESEEEEDEDDEEEEEEEKEK 29 2 D6R9L5;H0Y8X0;A0A494C198;B4DFG0;H0Y993;P35659;A0A494C028 D6R9L5 DEK Protein DEK 1 0 EPEMPGPREES(1)EEEEDEDDEEEEEEEKEK 54.3 0.001792 9527300 454.79 462.84 450.43 354.49 559.12 549.58 304.04 554.87 418.1 546.5 TRUE FALSE FALSE 449.2468446 469.3558737 458.2695452 395.4778017 530.58602 514.4636117 329.86515 570.924288 380.7040888 532.3018512 0.843970096 0.881747589 0.860920442 0.74295778 0.996776582 0.966488489 0.619695666 1.072557397 0.715203391 1 9.056100773 -12.29278874 0.891423601 1.004672945 0.86607521 0 0.149854571 0.94396571 1.272598141 0.089226719 0.02102352 5.10E-13 12.29278874 -0.138597735 EPEPAAGPQAEESATVSAPAPMS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 EPEPAAGPQAEESATVSAPAPMSPTR 26 0 Q9BWG6-2;Q9BWG6 Q9BWG6-2 SCNM1 Sodium channel modifier 1 1 0 EPEPAAGPQAEESAT(0.002)VS(0.048)APAPMS(0.783)PT(0.167)R;EPEPAAGPQAEES(0.025)AT(0.167)VS(0.144)APAPMS(0.466)PT(0.199)R ; 84.942 1.27E-05 30208000 8555.6 8437.2 7519.6 5059.9 6397.4 7299.3 6524.6 7883.6 8556.7 7878.2 TRUE FALSE FALSE 8451.321056 8555.979123 7650.475484 5644.949446 6070.916806 6832.898287 7078.799361 8111.699528 7791.367321 7673.523228 1.10136124 1.115000094 0.996996459 0.735639846 0.79115116 0.890451242 0.922496636 1.057102362 1.015357234 1 12.90567341 -9.509128664 23.49796969 1.05432142 0.876362931 0.498799964 0.085100672 197.6843025 337829.3551 0.014172887 0.021087698 3.10E-10 9.509128664 -0.177958488 EPES(ph)PPASAPIPLFGADTIGQR ddPTM_HeLa_Romidepsin_16h_R1 3 EPESPPASAPIPLFGADTIGQR 22 0 Q96AY4 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 0 EPES(0.894)PPAS(0.106)APIPLFGADTIGQR;EPES(0.691)PPAS(0.309)APIPLFGADTIGQR;EPES(0.99)PPAS(0.01)APIPLFGADTIGQR ;; 120.92 2.62E-05 10530900 4876.11 5025.62 4504.11 4748.41 4884.57 5307.93 4208.13 4409.01 4952.9 5010.01 TRUE FALSE FALSE 4816.678096 5096.37081 4582.502145 5297.443506 4635.292166 4968.770404 4565.568457 4536.577748 4509.900219 4879.849218 0.987054698 1.04437055 0.93906634 1.085575244 0.949884302 1.018222117 0.935596215 0.929655312 0.924188437 1 12.25262086 -7.748111081 23.91584031 0.998164939 0.93262566 0.210590614 0.046495645 112.1839465 201292.3612 0.004769378 0.017610536 1.79E-08 7.748111081 -0.065539279 EPFPPS(ph)SPLQK ddPTM_HeLa_Romidepsin_16h_R1 1 EPFPPSSPLQK 11 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 EPFPPS(0.665)S(0.335)PLQK 96.604 0.023791 7673900 2371.8 2186 2254.6 1862.6 2289.8 2565.7 2033.7 2426 2283.7 2810.6 TRUE FALSE FALSE 2342.891589 2216.774565 2293.840367 2077.962576 2172.942962 2401.76005 2206.442427 2496.192482 2079.440152 2737.580207 0.855825734 0.809756938 0.837908004 0.759050847 0.793745862 0.877329564 0.805982751 0.911824419 0.759590586 1 11.41868552 -11.74405666 0.663536551 1.001647116 0.824855017 0 0.08405095 0.303836771 0.255935764 0.027781473 0.009618918 1.80E-12 11.74405666 -0.176792099 EPFPPSS(ph)PLQK ddPTM_HeLa_Romidepsin_16h_R1 3 EPFPPSSPLQK 11 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 EPFPPS(0.184)S(0.816)PLQK;EPFPPS(0.037)S(0.963)PLQK;EPFPPS(0.03)S(0.97)PLQK ;; 160.22 0.00055447 9415500 8530.5 8131.4 9035.1 7356.9 8135.5 8617.1 6930.2 7984.8 8946.3 9192.5 TRUE FALSE FALSE 8426.526985 8245.874063 9192.352125 8207.539393 7720.315077 8066.49512 7518.851015 8215.82759 8146.120522 8953.677525 0.94112469 0.920948296 1.0266566 0.916666852 0.862250741 0.900914188 0.839750035 0.917592527 0.909807227 1 13.12826464 -9.021717909 6.858507937 0.970669413 0.87981375 0.476789307 0.0385173 0.090532663 18.19861289 0.005312471 0.009110492 9.51E-10 9.021717909 -0.090855664 EPGEQASVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EPGEQASVPLSPK 13 0 P42858 P42858 HTT Huntingtin 1 0 EPGEQASVPLS(1)PK;EPGEQAS(0.004)VPLS(0.996)PK ; 157.07 0.00061843 39956000 8728 8883.5 9179.9 6185.6 6712.6 7539 5590.9 6541.1 8881 8760.6 TRUE FALSE FALSE 8621.619779 9008.562146 9339.672309 6900.808176 6370.030974 7057.282231 6065.790906 6730.356408 8086.661117 8532.998349 1.010385732 1.05573232 1.094535816 0.808720205 0.74651731 0.827057728 0.710862777 0.788744605 0.947692802 1 13.05883705 -9.157455332 5.372891978 1.015510915 0.770007949 0.878541952 0.04569408 0.050416698 2.152665464 0.006135749 0.01027706 6.96E-10 9.157455332 -0.245502966 T(ph)QQSPISNGSPELGIK ddPTM_HeLa_Romidepsin_16h_R1 1 TQQSPISNGSPELGIK 16 0 Q15723-2;Q15723-3;Q15723-1;Q15723 Q15723-2 ELF2 ETS-related transcription factor Elf-2 1 0 T(0.896)QQS(0.103)PIS(0.001)NGSPELGIK 207.92 7.15E-19 5939300 3005 2257.9 1987.7 1667.1 1361.1 825.65 718 893.97 2258 2281.3 TRUE FALSE FALSE 2968.373904 2289.686775 2022.295085 1859.857946 1291.637988 772.8936297 778.9869021 919.8356115 2056.038825 2222.031497 1.335882911 1.030447488 0.9101109 0.837007913 0.581286984 0.347831986 0.350574194 0.413961554 0.925296886 1 11.11766355 -8.944890914 1.074014797 1.153557224 0.347189189 0.860434588 0.118468686 0.13008613 0.295195813 0.023374081 0.05996222 1.14E-09 8.944890914 -0.806368034 down EPGGRS(ph)PAFVQLAPLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 EPGGRSPAFVQLAPLSSK 18 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 0 EPGGRS(0.999)PAFVQLAPLS(0.001)SK 61.524 0.016365 21012000 2547.6 2300.8 1919 2559.8 2140.9 1414.7 1335.1 1313.7 2441.9 2327 TRUE FALSE FALSE 2516.548871 2333.190723 1952.39939 2855.77612 2031.641884 1324.305236 1448.503361 1351.709837 2223.490348 2266.544205 1.110302136 1.029404464 0.861399211 1.259969302 0.896361024 0.584283877 0.639080128 0.596374796 0.981004625 1 11.14627858 -8.404541163 3.840359185 1.049483031 0.611002286 0.79528756 0.097920458 0.070874975 1.835522402 0.013404797 0.03135416 3.94E-09 8.404541163 -0.438480745 EPGSGGPQNLS(ph)GPGGR ddPTM_HeLa_Romidepsin_16h_R1 2 EPGSGGPQNLSGPGGR 16 0 Q9H0W8-2;Q9H0W8;M0QZH1;M0QX70;M0QYR7;M0R2N0;M0QZC7 Q9H0W8-2 SMG9 Protein SMG9 1 0 EPGSGGPQNLS(1)GPGGR;EPGSGGPQNLS(1)GPGGR ; 107.62 0.00067244 0 1186.04 1370.01 1193.19 964.44 1325.24 1193.32 1167.65 1113.36 1515.85 1403.78 TRUE FALSE FALSE 1171.584088 1389.297037 1213.956971 1075.953091 1257.608058 1117.070703 1266.830162 1145.573315 1380.268579 1367.309593 0.856853557 1.016080808 0.887843527 0.786912559 0.919768327 0.81698447 0.926513036 0.837830233 1.009477726 1 10.41712423 -9.53305234 24.86397639 0.937512642 0.860102384 0.393794347 0.06119219 219.0516519 535354.2187 0.010459233 0.014800602 2.93E-10 9.53305234 -0.077410257 EPHS(ph)PADQPEQQAESTLTSAETR ddPTM_HeLa_Romidepsin_16h_R1 1 EPHSPADQPEQQAESTLTSAETR 23 0 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BS99 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 EPHS(1)PADQPEQQAESTLTSAETR 98.98 1.74E-05 3305700 678.12 804.2 676.08 354.25 642.36 684.29 544.8 595.48 571.5 808.8 TRUE FALSE FALSE 669.8548126 815.5215487 687.8468888 395.2100518 609.5779722 640.5660774 591.0752984 612.7092743 520.3836087 787.7872594 0.850299119 1.035205303 0.873137869 0.501671038 0.77378501 0.813120636 0.750298118 0.777759816 0.660563626 1 9.621662275 -9.508308275 24.83769269 0.936174845 0.728095818 0.253451121 0.12679165 385.5200902 657181.1568 0.015199644 0.022696503 3.10E-10 9.508308275 -0.208079027 EPLIPAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EPLIPASPK 9 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 0 EPLIPAS(1)PK;EPLIPAS(1)PK ; 107.85 0.021203 103332000 10820.7 11182.2 10170.1 9542.8 10389.8 11075.7 9853.2 11986 10900.2 9827.6 TRUE FALSE FALSE 10688.81315 11339.62331 10347.10632 10646.18344 9859.569736 10367.99852 10690.13056 12332.796 9925.258812 9572.277535 1.116642628 1.184631689 1.080945082 1.112189173 1.030012941 1.083127655 1.116780257 1.288386798 1.03687537 1 13.22464651 -16.52287875 0.192809696 0.438488597 1.146219193 0.300701425 0.06618674 45.94752338 0.547563222 9.668379193 0.075667368 3.00E-17 16.52287875 0.707730596 EPPADVWT(ph)PPAR ddPTM_HeLa_Romidepsin_16h_R1 2 EPPADVWTPPAR 12 0 A0A3B3IUA7;Q14258 A0A3B3IUA7 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 1 0 EPPADVWT(1)PPAR;EPPADVWT(1)PPAR ; 154.23 0.0029121 14985200 1709.68 1606.45 1727.75 1669.48 2501.59 2653.9 2361.7 2857.3 2184.7 1622.23 TRUE FALSE FALSE 1688.841763 1629.065645 1757.820764 1862.513133 2373.924528 2484.324355 2562.302739 2939.971467 1989.29496 1580.084231 1.068830212 1.030999243 1.11248548 1.178742941 1.502403784 1.572273368 1.621624145 1.860642243 1.258980326 1 10.62578575 -8.469023337 0.805282982 1.024721207 1.823417893 0.891769763 0.092813406 0.09995221 0.106959567 0.009731055 0.049564223 3.40E-09 8.469023337 0.798696687 EPPGLIFNKVEVS(ph)EDEPASK ddPTM_HeLa_Romidepsin_16h_R1 1 EPPGLIFNKVEVSEDEPASK 20 1 O75683 O75683 SURF6 Surfeit locus protein 6 1 0 EPPGLIFNKVEVS(0.908)EDEPAS(0.092)K 79.445 0.0017757 11549000 1108.7 1076.5 967.37 1458.6 1301.3 991.6 862.02 921.88 1083.6 1278.2 TRUE FALSE FALSE 1095.186738 1091.654995 984.2066691 1627.250195 1234.889805 928.2399602 935.2399573 948.5531433 986.6801021 1244.99218 0.879673588 0.876836829 0.790532411 1.307036479 0.991885592 0.745578948 0.751201471 0.761894861 0.792519116 1 10.28192096 -8.256299481 24.13347272 0.955911621 0.752722707 0.292845897 0.138843983 241.5545391 1134166.609 0.018812424 0.04636118 5.54E-09 8.256299481 -0.203188914 EPPPLLEVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EPPPLLEVSPR 11 0 Q9ULI4 Q9ULI4 KIF26A Kinesin-like protein KIF26A 1 0 EPPPLLEVS(1)PR;EPPPLLEVS(1)PR ; 102.33 0.0181 9382600 950.47 1036.48 1106.51 928.77 1085.16 1220.31 865.24 1026.42 1126.77 1081.74 TRUE FALSE FALSE 938.8853061 1051.071593 1125.768342 1036.158757 1029.780236 1142.336129 938.733464 1056.117843 1025.988869 1053.636239 0.89109056 0.997565909 1.068460158 0.983412224 0.977358407 1.084184548 0.890946448 1.002355276 0.973760043 1 10.04116116 -10.04699895 24.81716891 0.948347252 1.000919977 0.120620424 0.055717785 557.342837 294296.0758 0.010183376 0.012472285 8.97E-11 10.04699895 0.052572725 EPPS(ph)SPLQPQK ddPTM_HeLa_Romidepsin_16h_R1 1 EPPSSPLQPQK 11 0 Q92615;A0A087X183;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 0 EPPS(0.624)S(0.376)PLQPQK 97.214 0.022834 4212300 3578.7 3525.5 3618.5 2371.9 3108 3489.7 2744.4 2974 3920.1 3621.8 TRUE FALSE FALSE 3535.081428 3575.132082 3681.478475 2646.150238 2949.387162 3266.719432 2977.509267 3060.047998 3569.476438 3527.705114 1.002090967 1.013444142 1.043590197 0.750105282 0.836063976 0.926018283 0.84403576 0.867433048 1.011840934 1 11.78451425 -9.275515807 24.99938823 1.005049651 0.848727057 0.799597975 0.042271375 269.4085603 478462.0162 0.00640475 0.009812494 5.30E-10 9.275515807 -0.156322595 EPPSS(ph)PLQPQK ddPTM_HeLa_Romidepsin_16h_R1 1 EPPSSPLQPQK 11 0 Q92615;A0A087X183;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 0 EPPS(0.167)S(0.833)PLQPQK 127.56 0.0066788 24871000 2190.9 2055.3 2036.8 1114.2 2345.8 2197.6 2273.5 2337.1 2328 2204.3 TRUE FALSE FALSE 2164.196468 2084.234567 2072.24965 1243.029046 2226.085073 2057.180452 2466.611033 2404.720301 2119.777849 2147.031968 1.007994525 0.97075153 0.965169443 0.578952277 1.036819715 0.958150825 1.148846906 1.120020725 0.987306142 1 11.06812796 -7.762330854 24.97117452 0.968305812 1.134433857 0.253903822 0.126398372 25.65566832 718756.6899 0.017890531 0.058686466 1.73E-08 7.762330854 0.166128045 EPQNPPANAAPGS(ph)QRARK ddPTM_HeLa_Romidepsin_16h_R1 1 EPQNPPANAAPGSQRARK 18 2 E7EVG6;Q5VV67-2;Q5VV67 E7EVG6 PPRC1 Peroxisome proliferator-activated receptor gamma coactivator-related protein 1 1 0 EPQNPPANAAPGS(1)QRARK 68.173 0.023314 6740700 1548.5 1899.6 617.09 2845.7 1110.7 1218.2 999.94 1882.2 2184.6 2024.3 TRUE FALSE FALSE 1529.626286 1926.342619 627.8301926 3174.733223 1054.016834 1140.360952 1084.874879 1936.658487 1989.203905 1971.708394 0.775787277 0.976991641 0.318419394 1.610143383 0.534570344 0.578361869 0.550220754 0.982223585 1.008873275 1 10.94523048 -16.52287874 0.157392223 1.843095894 0.707400584 0.062769605 0.336436451 147.0678456 1.553438548 38.3443268 0.649026454 3.00E-17 16.52287874 -1.13569531 EPS(ph)PALGPNLDGSGLLPR ddPTM_HeLa_Romidepsin_16h_R1 1 EPSPALGPNLDGSGLLPR 18 0 Q9BRZ2 Q9BRZ2 TRIM56 E3 ubiquitin-protein ligase TRIM56 1 0 EPS(1)PALGPNLDGSGLLPR 211.26 1.23E-28 30074000 989.32 983.14 910.06 534.45 707.49 859.6 629.52 665.93 1015.8 1245.5 TRUE FALSE FALSE 977.2617873 996.9806707 925.8992125 596.2456237 671.3841453 804.6743342 682.9914131 685.1976339 924.9443039 1213.14173 0.805562749 0.821817143 0.763224271 0.491488841 0.553425975 0.663297877 0.562993916 0.564812517 0.762437134 1 10.24453239 -10.1909304 0.418450349 0.990722998 0.532744414 0.604826392 0.094758476 0.28872354 0.131404828 0.037706744 0.047037166 6.44E-11 10.1909304 -0.457978584 EPS(ph)PGSHSALPGKK ddPTM_HeLa_Romidepsin_16h_R1 1 EPSPGSHSALPGKK 14 1 Q9P209 Q9P209 CEP72 Centrosomal protein of 72 kDa 1 0 EPS(0.999)PGS(0.001)HSALPGKK 68.173 0.01831 6538400 1971.7 2501.5 2479.3 1957.1 2503.5 2227 2326.2 2667.1 2191.4 2309.3 TRUE FALSE FALSE 1947.668162 2536.716183 2522.451176 2183.38911 2375.737053 2084.701887 2523.78737 2744.268331 1995.395696 2249.304053 0.865898125 1.127778247 1.121436283 0.970695406 1.056209831 0.926820847 1.12203033 1.220052188 0.887116925 1 11.13526298 -10.25792722 24.98053856 0.936674115 1.070471619 0.417351351 0.085547451 273.1832736 1943039.875 0.015563315 0.018657604 5.52E-11 10.25792722 0.133797504 EPS(ph)PPIDEVINTPR ddPTM_HeLa_Romidepsin_16h_R1 2 EPSPPIDEVINTPR 14 0 S4R3E5;O60684;Q5TFJ7 S4R3E5 KPNA6 Importin subunit alpha-7 1 0 EPS(1)PPIDEVINTPR;EPS(1)PPIDEVINTPR ; 140.03 2.10E-05 0 4854.56 7077.2 3284.01 1335.55 1891.22 2538.12 2803.24 4768.56 6138.75 7049.1 TRUE FALSE FALSE 4795.390755 7176.833007 3341.166816 1489.972575 1794.703986 2375.942323 3041.347136 4906.53076 5589.684825 6865.963366 0.698429412 1.045276915 0.486627533 0.217008524 0.261391431 0.346046461 0.44296 0.714616507 0.814115154 1 12.74524644 -9.636616194 5.768751024 0.866920445 0.385603613 0.697217436 0.15468164 0.100306741 4.737443303 0.027720688 0.039323159 2.31E-10 9.636616194 -0.481316832 EPS(ph)YFEIPTK ddPTM_HeLa_Romidepsin_16h_R1 2 EPSYFEIPTK 10 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2;J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 H0Y2V6;J3KQR7 CEP170;CEP170B Centrosomal protein of 170 kDa;Centrosomal protein of 170 kDa protein B 1 0 EPS(1)YFEIPTK;EPS(1)YFEIPTK ; 113.77 0.0018878 0 3669.6 2944.8 4308.5 3456 3700.1 3163.2 2202 2434.7 3264.6 3413.5 TRUE FALSE FALSE 3624.873504 2986.256972 4383.487635 3855.598981 3511.27009 2961.081729 2389.037825 2505.144203 2972.606 3324.816778 1.090247597 0.898171891 1.318414796 1.159642542 1.056079274 0.890599972 0.718547212 0.753468347 0.894066109 1 11.69905912 -8.03189492 2.660360388 1.063531122 0.73535736 0.554931912 0.11686137 0.140739661 1.960862377 0.015452263 0.052111772 9.29E-09 8.03189492 -0.328173762 EPSAPSIPTPAY(ph)QSSPAGGHAPTPPTPAPR ddPTM_HeLa_Romidepsin_16h_R1 2 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 0 EPS(0.001)APS(0.008)IPT(0.074)PAY(0.768)QS(0.074)S(0.074)PAGGHAPTPPTPAPR;EPS(0.001)APS(0.008)IPT(0.1)PAY(0.368)QS(0.291)S(0.232)PAGGHAPTPPTPAPR ; 58.858 0.0013745 48357000 2845.5 2379.1 2810.1 3010.4 4843.7 5835.5 4490.4 4886.7 3250.9 3417.6 TRUE FALSE FALSE 2810.817952 2412.593032 2859.008612 3358.476612 4596.507915 5462.630383 4871.814464 5028.088955 2960.131362 3328.810259 0.844391159 0.724761354 0.858868001 1.008911999 1.380826048 1.641015846 1.463530236 1.510476285 0.889246046 1 11.70079092 -8.735466449 2.804992228 0.902348672 1.530686338 0.933445887 0.081124006 0.057922177 0.931759233 0.014780885 0.030825985 1.84E-09 8.735466449 0.628337666 EPSAPSIPTPAYQS(ph)SPAGGHAPTPPTPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 0 EPSAPSIPT(0.005)PAY(0.068)QS(0.54)S(0.388)PAGGHAPTPPTPAPR 89.111 3.19E-08 25275000 1204.5 1353.4 1212.4 1479.4 1802.8 2130 1709.9 2024.5 1411.1 1362.1 TRUE FALSE FALSE 1189.819091 1372.453201 1233.501313 1650.455189 1710.796389 1993.899874 1855.138863 2083.075713 1284.887682 1326.712446 0.896817615 1.034476766 0.929742777 1.244018773 1.28950052 1.502887744 1.398297626 1.570103394 0.968474884 1 10.37364 -8.861302524 1.242673115 0.95148389 1.492299222 0.922814042 0.065815634 0.080580174 0.24731158 0.010601196 0.026688262 1.38E-09 8.861302524 0.540815332 EPSAPSIPTPAYQSS(ph)PAGGHAPTPPTPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 EPSAPSIPTPAYQSSPAGGHAPTPPTPAPR 30 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 1 0 EPSAPSIPT(0.001)PAY(0.039)QS(0.118)S(0.842)PAGGHAPTPPTPAPR 101.72 2.62E-09 21283000 2073.9 1805.4 2392.1 2100.7 3110.9 4008.9 2963.9 2954.4 2106.7 1975.7 TRUE FALSE FALSE 2048.622509 1830.816469 2433.733497 2343.592818 2952.139165 3752.744228 3215.653592 3039.880903 1918.271476 1924.371029 1.06456732 0.951384344 1.264690364 1.217848732 1.534080029 1.950114698 1.671015383 1.579675051 0.996830365 1 10.91017127 -8.864096001 1.519967644 1.033412232 1.735942415 0.869665578 0.117255063 0.091239227 0.424113993 0.018104324 0.041439685 1.37E-09 8.864096001 0.702530182 EPSLATWEATWS(ph)EGSK ddPTM_HeLa_Romidepsin_16h_R1 1 EPSLATWEATWSEGSK 16 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDQ3 E9PMS6 LMO7 LIM domain only protein 7 1 0 EPSLATWEAT(0.139)WS(0.844)EGS(0.016)K 93.106 0.0026557 0 620.61 898.2 540.5 731.6 851.69 701.87 366.92 696.17 851.42 750.65 TRUE FALSE FALSE 613.0457666 910.8448832 549.9071758 816.1910343 808.2250812 657.0227722 398.0861756 716.3125806 775.2668628 731.1480048 0.838470135 1.245773602 0.752114718 1.116314384 1.105419253 0.89861802 0.544467294 0.97970941 1.060341898 1 9.514019667 -7.985009669 24.97796087 0.960547568 0.751951841 0.219586265 0.170701757 266.8216883 444591.6005 0.022162934 0.0664544 1.04E-08 7.985009669 -0.208595727 EPST(ph)ASGGGQLNR ddPTM_HeLa_Romidepsin_16h_R1 2 EPSTASGGGQLNR 13 0 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 0 EPS(0.005)T(0.949)AS(0.046)GGGQLNR;EPS(0.052)T(0.934)AS(0.014)GGGQLNR ; 149.32 0.0015852 18129900 1415.91 1434.93 1645.15 1226.53 1314.26 1618.21 1153.41 1457.56 1759.25 1453.46 TRUE FALSE FALSE 1398.652344 1455.130982 1673.783146 1368.34717 1247.188408 1514.811604 1251.380617 1499.732199 1601.898274 1415.6989 0.987958912 1.027853439 1.18230165 0.9665524 0.880970105 1.070009734 0.883931334 1.059358172 1.131524701 1 10.46729874 EPTPS(ph)IASDISLPIATQELR ddPTM_HeLa_Romidepsin_16h_R1 2 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-5;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 0 EPT(0.005)PS(0.604)IAS(0.364)DIS(0.027)LPIATQELR;EPT(0.412)PS(0.587)IASDISLPIATQELR ; 174.87 4.80E-13 8385600 893.5 1216.74 1226.14 868.83 811.26 1481.89 935.97 1463.45 999.96 875.448 TRUE FALSE FALSE 882.6096783 1233.869298 1247.480452 969.2882126 769.858375 1387.202012 1015.471268 1505.792617 910.5210732 852.7037348 1.035071904 1.447008202 1.462970551 1.136723311 0.902843911 1.626827648 1.19088404 1.765903626 1.06780472 1 9.735900765 -4 0.178712992 0.942629836 3.60042592 0.318695537 0.228924409 44.27990173 0.478821591 0.294400871 32.08700473 1.00E-04 4 2.657796084 EPTPSIAS(ph)DISLPIATQELR ddPTM_HeLa_Romidepsin_16h_R1 3 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-5;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 0 EPT(0.001)PS(0.001)IAS(0.925)DIS(0.072)LPIAT(0.001)QELR;EPTPS(0.001)IAS(0.782)DIS(0.217)LPIATQELR;EPTPS(0.002)IAS(0.995)DIS(0.003)LPIATQELR ;; 171.85 1.98E-10 15229000 1646.66 1650.71 1540.76 4448.34 1308.22 2598.34 1424.24 2120.19 1421.71 1981.76 TRUE FALSE FALSE 1626.589875 1673.948739 1567.576281 4962.678001 1241.456652 2432.31446 1545.21491 2181.534353 1294.548697 1930.27359 0.842673227 0.867208021 0.81210057 2.570971301 0.643150618 1.260087934 0.800516009 1.130168472 0.670655551 1 10.91458963 EPTPSIASDIS(ph)LPIATQELR ddPTM_HeLa_Romidepsin_16h_R1 1 EPTPSIASDISLPIATQELR 20 0 A0A499FIX8;H7BXI1;A0A087WXU3;A0FGR8-5;A0FGR8-2;A0FGR8;A0FGR8-6 A0A499FIX8 ESYT2 Extended synaptotagmin-2 1 0 EPTPS(0.002)IAS(0.428)DIS(0.57)LPIATQELR 208.4 7.22E-25 2737000 205.88 310.31 334.16 287.52 246.66 443.26 249.73 310.42 209.82 252.08 TRUE FALSE FALSE 203.3706554 314.6785523 339.9759146 320.7644152 234.0720198 414.9371166 270.94206 319.4015129 191.0531737 245.5309253 0.82828937 1.28162492 1.384656186 1.306411463 0.953330093 1.689958673 1.10349464 1.300860625 0.778122648 1 7.939760937 -10.25171591 24.12088418 0.918914425 1.288417752 0.50732417 0.187646502 258.429653 641083.0482 0.029029339 0.035301928 5.60E-11 10.25171591 0.369503327 EPVAES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 EPVAESPK 8 0 A0A0G2JNN3;C9JMY0;A0A087WUE4;Q96PV6-1;Q96PV6 A0A0G2JNN3 LENG8 Leukocyte receptor cluster member 8 1 0 EPVAES(1)PK;EPVAES(1)PK ; 123.01 0.016978 40877300 12142.4 12638.1 16884.9 8512.2 7482.5 8349 9738.1 3621.4 14083.8 14963.7 TRUE FALSE FALSE 11994.40376 12816.0195 17178.7746 9496.420615 7100.640104 7815.525845 10565.25397 3726.179495 12824.10965 14574.94092 0.82294699 0.879318796 1.178651406 0.651558087 0.487181399 0.536230362 0.724891719 0.255656576 0.879873869 1 13.83120241 -9.048838367 6.634084688 0.928820134 0.524796777 0.697635882 0.140613762 0.102345394 11.10023047 0.020918327 0.03521009 8.94E-10 9.048838367 -0.404023356 EPYGHLGPAELLEAS(ph)PAAR ddPTM_HeLa_Romidepsin_16h_R1 2 EPYGHLGPAELLEASPAAR 19 0 Q9H6W3 Q9H6W3 NO66 Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66 1 0 EPY(0.004)GHLGPAELLEAS(0.996)PAAR;EPYGHLGPAELLEAS(1)PAAR ; 129.07 0.00036761 6498200 2389 2088.98 2757.5 2342.6 2728.2 2949 2873.2 2776.9 2771.6 2315.7 TRUE FALSE FALSE 2359.881949 2118.388715 2805.493131 2613.462434 2588.969774 2760.568417 3117.249536 2857.24522 2523.701154 2255.53778 1.046261326 0.939194517 1.243824491 1.158687058 1.147828157 1.223906973 1.382042706 1.266768948 1.118891103 1 11.13925574 -8.688811016 0.507272954 1.007690432 1.365703965 0.601947203 0.079909116 0.542942778 0.212186911 0.017327063 0.091459602 2.05E-09 8.688811016 0.358013533 EQAEAEVASLNRR ddPTM_HeLa_Romidepsin_16h_R1 1 EQAEAEVASLNRR 13 1 P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8;D6R904;A0A494C0G0 P06753-4 TPM3 Tropomyosin alpha-3 chain 0 0 126.09 0.0022524 6217100 1396.6 1408.1 1133.9 1654.8 1377.3 1422.9 1067 1433.5 1032.1 1215.8 FALSE FALSE TRUE 1379.577702 1427.923269 1153.635054 1846.135762 1307.011242 1331.981282 1157.630953 1474.976061 939.7863911 1184.213341 1.164973957 1.205799006 0.974178397 1.558955383 1.103695759 1.124781521 0.977552704 1.24553238 0.793595511 1 10.2097133 -12.0636766 0.727851027 0.993300795 1.168160974 0.247815963 0.169142596 1.181071412 1.081250597 0.120226658 0.031464654 8.64E-13 12.0636766 0.174860179 EQDLPLAEAVRPKT(ph)PPVVIK ddPTM_HeLa_Romidepsin_16h_R1 1 EQDLPLAEAVRPKTPPVVIK 20 2 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 0 EQDLPLAEAVRPKT(1)PPVVIK 60.564 0.007234 789750000 5791.1 5318.3 5251.4 6805.7 6513.2 6649.1 6614.6 7235.9 6621.1 5328.3 TRUE FALSE FALSE 5720.515846 5393.171167 5342.798414 7592.607056 6180.8071 6224.243969 7176.443959 7445.25935 6028.892233 5189.869998 1.102246462 1.03917269 1.029466714 1.462966714 1.190936787 1.199306336 1.382779137 1.434575308 1.161665366 1 12.34148269 -9.278376585 24.94453626 1.047398337 1.321373061 0.669058319 0.09340729 332.7831047 490110.4077 0.013875621 0.021230116 5.27E-10 9.278376585 0.273974723 EQDNSESPNGRT(ph)SPLVSQNNEQGSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 EQDNSESPNGRTSPLVSQNNEQGSTLR 27 1 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 0 EQDNS(0.002)ES(0.031)PNGRT(0.938)S(0.028)PLVSQNNEQGSTLR 76.351 2.13E-05 0 406.57 512.72 411.7 399.32 337.89 416.12 274.77 310.12 569.5 557.17 TRUE FALSE FALSE 401.6145685 519.9380856 418.8654658 445.4912573 320.6462125 389.531275 298.1089569 319.0928329 518.5624937 542.6946431 0.740037834 0.958067474 0.771825319 0.820887516 0.590840939 0.717772471 0.549312511 0.587978593 0.95553273 1 9.083996858 -7.285045035 0.09422587 1.214659188 6.79E-15 0.721858497 0.082184547 25.9238364 0.401607429 1.302045674 4.694545876 5.19E-08 7.285045035 -1.214659188 EQDNSESPNGRTS(ph)PLVSQNNEQGSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 EQDNSESPNGRTSPLVSQNNEQGSTLR 27 1 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 0 EQDNS(0.004)ES(0.01)PNGRT(0.2)S(0.596)PLVS(0.188)QNNEQGS(0.001)T(0.001)LR 53.123 0.00567 5510200 470.04 322.6 507.04 411.86 337.92 281.47 318.21 148.87 488.23 386.53 TRUE FALSE FALSE 464.3109717 327.1415713 515.8648185 459.4811911 320.6746814 263.4849754 345.2387495 153.1773186 444.561486 376.4878949 1.233269324 0.868929853 1.370202935 1.220440809 0.851752967 0.699849793 0.916998273 0.406858549 1.180812164 1 8.556459669 -8.578936082 4.025876054 1.120704478 0.7063534 0.599173221 0.173893041 0.125287828 4.18779195 0.025368248 0.053579226 2.64E-09 8.578936082 -0.414351078 EQDVVTGVS(ph)PLLFR ddPTM_HeLa_Romidepsin_16h_R1 3 EQDVVTGVSPLLFR 14 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 EQDVVT(0.002)GVS(0.998)PLLFR;EQDVVTGVS(1)PLLFR;EQDVVT(0.001)GVS(0.999)PLLFR ;; 189.04 5.64E-11 54111000 7330.4 8125 7460.4 7056.9 6760.9 5572.3 4506.3 4972.4 7692.7 7425.5 TRUE FALSE FALSE 7241.054265 8239.383963 7590.245133 7872.851982 6415.866045 5216.248014 4889.06501 5116.268549 7004.645645 7232.58444 1.001171065 1.139203286 1.049451299 1.088525415 0.887077932 0.721214948 0.675977591 0.707391471 0.968484461 1 12.82029555 -8.411424892 2.740236054 1.021458901 0.694334633 0.900698185 0.050197297 0.06481748 0.937459242 0.007778034 0.019382557 3.88E-09 8.411424892 -0.327124268 EQEVNILK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EQEVNILKK 9 1 P35579 P35579 MYH9 Myosin-9 0 1 ; EQEVNILK(1)K;EQEVNILK(1)K 156.83 0.0021841 5319700 2354.1 2230.7 2207.6 2400.54 5458.1 4443.3 3952.9 4381.9 5328 3776.1 FALSE TRUE FALSE 2325.407324 2262.103853 2246.022352 2678.10173 5179.55279 4159.38747 4288.659227 4508.683363 4851.450336 3677.996378 0.6322484 0.615036999 0.610664645 0.728141481 1.408253913 1.130884058 1.16603139 1.225853128 1.319047067 1 11.84470434 -8.772460284 24.99844947 0.780577101 1.22071307 0.465335073 0.21572633 112.9770299 256263.1574 0.026799278 0.048909883 1.69E-09 8.772460284 0.440135969 EQFDT(ph)LTPEPPVDPNQEVPPGPPR ddPTM_HeLa_Romidepsin_16h_R1 1 EQFDTLTPEPPVDPNQEVPPGPPR 24 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 0 EQFDT(0.5)LT(0.5)PEPPVDPNQEVPPGPPR 61.256 0.0045229 11647000 1320.8 1735.7 1277 1373.8 1151.2 958.09 596.75 837.31 1396.8 1385.6 TRUE FALSE FALSE 1304.701582 1760.13523 1299.225649 1532.64522 1092.449968 896.8711411 647.4379301 861.5362438 1271.86671 1349.601912 0.966730685 1.304188453 0.962673243 1.135627629 0.809460892 0.664544954 0.479725113 0.638363236 0.942401384 1 10.39831821 -8.391302386 2.373000201 1.017891363 0.568551913 0.760615832 0.114415912 0.108840211 1.186419001 0.016351346 0.043113032 4.06E-09 8.391302386 -0.449339449 EQFLDGDGWTSR ddPTM_HeLa_Romidepsin_16h_R1 3 EQFLDGDGWTSR 12 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 0 ;; ;; 285.32 6.23E-92 431746000 10138.3 8973.5 8856.7 7129.8 9740.8 10904.4 10139.7 10464.3 9308.2 8956.9 FALSE FALSE TRUE 10014.7305 9099.829169 9010.847148 7954.181023 9243.690628 10207.64403 11000.96586 10767.06801 8475.651279 8724.198447 1.147925573 1.043056187 1.032856738 0.911737745 1.059546122 1.170038038 1.26097153 1.23416129 0.971510601 1 13.09080687 -8.083488017 2.99088599 1.053716083 1.245325715 0.666627756 0.063150026 0.153063918 2.636895112 0.010684839 0.032796664 8.25E-09 8.083488017 0.191609632 EQGK(ac)TISNDDDVQK ddPTM_HeLa_Romidepsin_16h_R1 1 EQGKTISNDDDVQK 14 1 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 0 1 EQGK(1)TISNDDDVQK 272.59 1.33E-82 747750 131.17 212.5 172.68 186.83 285.02 269.06 355.96 427.57 497.12 260.57 FALSE TRUE FALSE 129.5712496 215.4915806 175.685423 208.4321637 270.4743658 251.8679344 386.1952335 439.9410634 452.6563421 253.8003538 0.510524306 0.849059417 0.692218984 0.821244575 1.065697355 0.992386065 1.521649705 1.733413909 1.78351344 1 7.98755027 -7.584434946 0.919553623 0.766361948 2.042000248 0.292105878 0.349272731 0.50224844 0.435966196 0.030283476 0.568577204 2.60E-08 7.584434946 1.2756383 EQGTES(ph)RS(ph)STPLPTISSSAENTR ddPTM_HeLa_Romidepsin_16h_R1 1 EQGTESRSSTPLPTISSSAENTR 23 1 G5E972;P42167;H0YJH7;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 2 0 EQGT(0.196)ES(0.425)RS(0.849)S(0.434)T(0.092)PLPT(0.002)IS(0.001)S(0.001)SAENTR 55.621 0.025927 3514500 958.09 657.22 696.17 1029.5 1141.8 785.17 620.92 566.35 825.79 899.24 TRUE FALSE FALSE 946.4124306 666.4723604 708.2865468 1148.535634 1083.529685 735.000171 673.6609293 582.7364437 751.9292742 875.8776152 1.080530446 0.760919504 0.808659263 1.311296937 1.237078864 0.839158529 0.769126779 0.665317201 0.858486689 1 9.774585488 -8.034358432 5.824954907 1.032974597 0.735181367 0.324481432 0.16839232 0.145057837 14.45925628 0.0234273 0.063534947 9.24E-09 8.034358432 -0.297793229 EQGTES(ph)RSST(ph)PLPTISSSAENTR ddPTM_HeLa_Romidepsin_16h_R1 1 EQGTESRSSTPLPTISSSAENTR 23 1 G5E972;P42167;H0YJH7;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 2 0 EQGT(0.421)ES(0.554)RS(0.03)S(0.11)T(0.868)PLPT(0.01)IS(0.002)S(0.003)S(0.001)AENTR 62.049 0.0062476 3458700 838.27 923.84 674.56 1229.3 629.81 766.59 378.36 706.61 879.62 806.7 TRUE FALSE FALSE 828.0528428 936.8458438 686.3004338 1371.43745 597.6684456 717.6073731 410.497889 727.0546455 800.9445842 785.7418177 1.053848509 1.192307476 0.873442673 1.745404685 0.760642277 0.913286473 0.522433552 0.925309853 1.019348297 1 9.617911533 EQIDIMVS(ph)NKK ddPTM_HeLa_Romidepsin_16h_R1 1 EQIDIMVSNKK 11 1 E9PIY2 E9PIY2 CCDC67 1 0 EQIDIMVS(1)NKK 66.56 0.020554 25184000 2296.5 2309 2105.3 2046.1 1902.4 1852.6 1976.8 1632.7 1989.1 1797.3 TRUE FALSE FALSE 2268.509375 2341.506163 2141.941863 2282.679709 1805.313429 1734.224839 2144.709343 1679.939599 1811.189914 1750.605887 1.295842423 1.337540437 1.223543163 1.303936955 1.031250633 0.990642641 1.225124032 0.95963324 1.034607462 1 10.77363861 -7.248594309 23.23841695 1.159136516 0.959632893 0.179500516 0.12867133 1235.878212 2235757.301 0.02070667 0.462209582 5.64E-08 7.248594309 -0.199503623 EQIS(ph)DIDDAVR ddPTM_HeLa_Romidepsin_16h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 1 0 EQIS(1)DIDDAVR;EQIS(1)DIDDAVR ; 163.62 0.00085691 63848000 4530.1 4661.4 4278 3206.9 5291.9 4546 4411.8 4648.2 4737.2 4740.8 TRUE FALSE FALSE 4474.885399 4727.023312 4352.456795 3577.696867 5021.834596 4255.525272 4786.538182 4782.688333 4313.492967 4617.633333 0.969086343 1.02368962 0.942573063 0.77479016 1.087534292 0.921581461 1.036578229 1.035744501 0.934135012 1 12.1729379 -7.718444433 23.70532224 0.973618699 1.03616184 0.113588369 0.078079562 149.0093364 82152.85433 0.010070938 0.037681096 1.91E-08 7.718444433 0.062543141 EQISDIDDAVR ddPTM_HeLa_Romidepsin_16h_R1 2 EQISDIDDAVR 11 0 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 0 ; ; 206.36 1.67E-12 113207000 7999.3 8081.7 7300 6123.2 8703 8478.2 7716.5 8530.5 8473.8 8170 FALSE FALSE TRUE 7901.801455 8195.474385 7427.053438 6831.193195 8258.853435 7936.470382 8371.939317 8777.316559 7715.882105 7957.742222 0.992970271 1.029874323 0.933311639 0.858433586 1.037838774 0.9973269 1.052049574 1.102990812 0.969606942 1 12.95814345 -7.51471185 1.575452408 0.98634585 1.118531634 0.411900215 0.049130214 0.562362246 1.848109851 0.007274741 0.098088678 3.06E-08 7.51471185 0.132185784 EQIVVDLSHPGVSEDDQVSR ddPTM_HeLa_Romidepsin_16h_R1 1 EQIVVDLSHPGVSEDDQVSR 20 0 O60701;O60701-3;O60701-2 O60701 UGDH UDP-glucose 6-dehydrogenase 0 0 95.307 0.00024622 0 1970.1 1523.1 1651.7 1643.9 1542.8 1366.4 1237.7 1460.9 1822.7 1530.3 FALSE FALSE TRUE 1946.087663 1544.542242 1680.447146 1833.975453 1464.065159 1279.09145 1342.830207 1503.168837 1659.673147 1490.542585 1.305623658 1.036228188 1.12740633 1.230407954 0.982236384 0.858138145 0.900900263 1.008470909 1.113469124 1 10.54162188 -8.601725599 5.643087278 1.142298491 0.920164302 0.54858529 0.089023459 0.150701888 8.107025164 0.017806095 0.03610584 2.50E-09 8.601725599 -0.222134189 EQIYK(ac)LAK ddPTM_HeLa_Romidepsin_16h_R1 2 EQIYKLAK 8 1 P62277;J3KMX5;E9PS50 P62277 RPS13 40S ribosomal protein S13 0 1 ; EQIYK(1)LAK;EQIYK(1)LAK 126.41 0.0068548 1453010 1046.99 1083.52 1144.83 985.91 1266.64 1395.21 1173.33 1239.17 1175.39 1019.9 FALSE TRUE FALSE 1034.228883 1098.773823 1164.755286 1099.905553 1201.998634 1306.060584 1272.992621 1275.023429 1070.260175 993.402851 1.041097156 1.106070736 1.17249038 1.107209982 1.20998106 1.31473408 1.281446515 1.283490809 1.07736773 1 9.956235077 -9.056808811 0.483067811 1.003902946 1.336873168 0.852231129 0.040106285 0.237781919 0.09754452 0.009613224 0.034640775 8.77E-10 9.056808811 0.332970222 EQLAALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EQLAALKK 8 1 Q9UII2 Q9UII2 ATPIF1 "ATPase inhibitor, mitochondrial" 0 1 ; EQLAALK(1)K;EQLAALK(1)K 130.96 0.0024268 9750200 3981.8 3629.3 5263 5237.1 11582.8 9970.6 9884 5641.5 7027.8 5090.6 FALSE TRUE FALSE 3933.26829 3680.393381 5354.600307 5842.638143 10991.68649 9333.510839 10723.54671 5804.727902 6399.215967 4958.345478 0.79326225 0.742262393 1.079916745 1.178344302 2.216805292 1.88238413 2.162726813 1.170698558 1.290595017 1 12.27564308 -8.925413496 4.516760951 0.904940449 1.878661912 0.645523984 0.305631288 0.078468089 3.060707447 0.039728566 0.073300472 1.19E-09 8.925413496 0.973721463 EQLEEEEEAKHNLEK ddPTM_HeLa_Romidepsin_16h_R1 1 EQLEEEEEAKHNLEK 15 1 P35579 P35579 MYH9 Myosin-9 0 0 84.62 0.0095296 4868700 2112.4 2323.8 2078.7 1983.3 1783.5 2103.2 1706.3 1796.9 2259.3 2188 FALSE FALSE TRUE 2086.653256 2356.514517 2114.878902 2212.618478 1692.48134 1968.812308 1851.233079 1848.890466 2057.222549 2131.155445 0.979118281 1.105745019 0.992362574 1.03822482 0.794161376 0.923823888 0.8686523 0.867553078 0.965308539 1 11.05742011 -8.771687442 24.99999329 1.002734044 0.868217717 0.702416211 0.047456633 89.46049669 218237.7671 0.006694706 0.012234274 1.69E-09 8.771687442 -0.134516327 EQLICSLRTLRY(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 EQLICSLRTLRYR 13 2 P43115-11 P43115-11 1 0 EQLICSLRT(0.005)LRY(0.995)R 110.84 0.029079 16420000 815.97 940.45 915.3 796.91 994.8 947.82 759.72 694.72 933.45 716.03 TRUE FALSE FALSE 806.0246438 953.6896798 931.2304125 889.0524838 944.0316439 887.2573609 824.2505978 714.8206271 849.9598941 697.4274374 1.155711119 1.36743929 1.335236274 1.274759833 1.353591203 1.272185913 1.181844237 1.024939067 1.218707278 1 9.445899312 -11.03771267 1.119715318 1.033457575 1.260149931 0.134180187 0.114190062 0.271699464 0.713987452 0.027589519 0.022135863 9.17E-12 11.03771267 0.226692356 EQLQLLEEQHR ddPTM_HeLa_Romidepsin_16h_R1 3 EQLQLLEEQHR 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;; ;; 207.47 1.52E-19 2449000 12592.5 11778.4 12369.3 10442.3 12784.2 13963.4 11908 14326.5 14300.4 13622.5 FALSE FALSE TRUE 12439.01777 11944.21662 12584.58248 11649.68786 12131.77457 13071.1838 12919.46522 14741.01467 13021.33641 13268.58549 0.937478813 0.900187638 0.94844944 0.877990187 0.914323127 0.985122628 0.973688208 1.110971074 0.98136583 1 13.69572696 -7.056477628 1.809639402 0.953189438 1.236818956 0.631726876 0.037708085 1.036601873 2.165073276 0.006444345 0.593652136 8.78E-08 7.056477628 0.283629518 EQLRQEQALLEEIER ddPTM_HeLa_Romidepsin_16h_R1 2 EQLRQEQALLEEIER 15 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 155.56 0.00048164 14997600 1302.54 1223.64 1436.02 1521.92 1389.28 1569.32 1238.4 1331.9 1374.89 1437.14 FALSE FALSE TRUE 1286.664141 1240.866436 1461.013326 1697.891551 1318.379857 1469.045517 1343.589665 1370.436425 1251.916395 1399.802896 0.919175225 0.886457972 1.043727892 1.212950449 0.941832498 1.049465979 0.959842039 0.979020996 0.894351911 1 10.45100798 -9.728094892 24.96221551 0.955113175 1.032936879 0.276998851 0.078138451 241.7989879 181014.2298 0.012454398 0.017612541 1.87E-10 9.728094892 0.077823704 EQLSAQELMES(ph)GLQIQKSPEPEVLSTQEDLFDQSNK ddPTM_HeLa_Romidepsin_16h_R1 1 EQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNK 36 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 EQLSAQELMES(0.816)GLQIQKS(0.11)PEPEVLS(0.037)T(0.037)QEDLFDQSNK 66.66 1.83E-05 6967300 1272.2 1036 1239.2 1218.8 1178.8 913.35 1145.3 1395.1 1060.2 1352.1 TRUE FALSE FALSE 1256.693937 1050.584835 1260.767756 1359.723391 1118.641437 854.9898827 1242.581753 1435.465017 965.3730567 1316.972247 0.954229628 0.797727391 0.95732295 1.032461689 0.849403957 0.649208732 0.943514001 1.089973627 0.733024602 1 10.36300923 -10.49265984 10.57598899 0.979868741 0.897951239 0 0.140064026 1.018253964 350.2861383 0.020675307 0.022840795 3.22E-11 10.49265984 -0.081917503 EQMDNAVYTFETLLHQELGK ddPTM_HeLa_Romidepsin_16h_R1 1 EQMDNAVYTFETLLHQELGK 20 0 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 0 0 121 0.00077119 3276500 1400.5 1364.3 1088.1 1054.2 1188 1585.3 1062 1111.8 1739.2 1533.8 FALSE FALSE TRUE 1383.430167 1383.506651 1107.037924 1176.091564 1127.371927 1484.004446 1152.206253 1143.968179 1583.641596 1493.951655 0.926020707 0.926071902 0.741013218 0.787235357 0.754624103 0.99334168 0.771247349 0.765733064 1.060035371 1 10.54491775 -9.911884555 5.315747655 0.963259316 0.806982417 0.564184358 0.07580898 0.125567054 5.889337777 0.011669315 0.01541069 1.22E-10 9.911884555 -0.156276898 EQMMNSSISSGSGS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 3 EQMMNSSISSGSGSLR 16 0 A0A590UJ18;A0A590UJ08;A0A590UJR4;A0A590UJ68;A0A590UJR5;A0A590UJS9;A0A590UJX2;C9JUA9;A0A590UJ81;A0A590UJC5;A0A590UKA8;Q12959-2;A0A0C4DFT3;Q12959-7;A0A590UJD9;Q12959;Q12959-4;Q12959-3;Q12959-6;Q12959-8;Q12959-5;Q12959-9;A0A590UK48;A0A590UJ29;A0A590UK81;A0A590UJ64;A0A590UJ25;A0A590UJL2;A0A590UK02;A0A590UK70;E7EQD7 A0A590UJ18 DLG1 Disks large homolog 1 1 0 EQMMNSSISSGS(0.034)GS(0.966)LR;EQMMNSSISSGS(0.004)GS(0.996)LR;EQMMNSSISSGS(0.022)GS(0.978)LR ;; 121.92 0.0021363 81501000 12824.9 12649.8 11517.2 11824.4 16636.4 18451 14773.1 15388.2 13318.4 12232.5 TRUE FALSE FALSE 12668.58519 12827.88422 11717.65203 13191.59276 15787.38243 17272.04065 16027.92675 15833.43329 12127.16895 11914.69789 1.063273723 1.076643683 0.983461951 1.107169723 1.325034221 1.449641511 1.345223093 1.328899267 1.017832686 1 13.54045475 -8.793053276 3.110920384 1.032015427 1.374451029 0.941796681 0.039575244 0.042188281 0.839145796 0.006289913 0.012575597 1.61E-09 8.793053276 0.342435602 EQNS(ph)LSLLEAR ddPTM_HeLa_Romidepsin_16h_R1 1 EQNSLSLLEAR 11 0 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 0 EQNS(0.5)LS(0.5)LLEAR 142.1 0.0027747 1840800 1551.1 1848 1802.1 1704.6 1785.4 1850.3 1455.2 1407.7 1702.2 1821.2 TRUE FALSE FALSE 1532.194597 1874.016193 1833.464795 1901.693872 1694.284376 1732.071802 1578.804652 1448.429579 1549.950969 1773.884961 0.863750824 1.056447421 1.033587202 1.072050282 0.95512641 0.976428483 0.890026516 0.8165296 0.873760702 1 10.79269674 -7.495620314 2.652116425 0.96335926 0.815128453 0.362844156 0.067239931 0.339206005 4.109296473 0.010993253 0.086897555 3.19E-08 7.495620314 -0.148230807 EQPEMEDANS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 EQPEMEDANSEK 12 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 0 EQPEMEDANS(1)EK 103.83 0.018894 3108500 2494.2 2196.9 2262.8 1376.6 1950.8 2187.3 2121.3 2240.4 2401.2 2562.8 TRUE FALSE FALSE 2463.799731 2227.828016 2302.183085 1535.768969 1851.243397 2047.538589 2301.483169 2305.222439 2186.430658 2496.218087 0.987013012 0.892481321 0.92226841 0.615238299 0.741619255 0.820256291 0.921988019 0.923485993 0.87589729 1 11.28552827 -9.898020823 1.864039043 0.993920039 0.81082167 0.260523222 0.095481984 0.23005126 1.613695898 0.016091785 0.021967106 1.26E-10 9.898020823 -0.18309837 EQPGEEYS(ph)EEEESVLK ddPTM_HeLa_Romidepsin_16h_R1 1 EQPGEEYSEEEESVLK 16 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 0 EQPGEEYS(0.987)EEEES(0.013)VLK 212.69 7.00E-26 18853000 1482.3 1253.3 1236.2 1565.7 2116.7 2724 2208.1 2286.1 1797.3 1420.7 TRUE FALSE FALSE 1464.233157 1270.94399 1257.715542 1746.733601 2008.676901 2549.945191 2395.655959 2352.244697 1636.544987 1383.790009 1.058132482 0.918451486 0.908891909 1.262282275 1.451576386 1.84272554 1.731227963 1.699856684 1.182654142 1 10.43440931 -8.716042698 1.873270872 1.011460076 1.754400085 0.922694128 0.09326947 0.050208773 0.357479227 0.011736321 0.02725789 1.92E-09 8.716042698 0.742940009 EQPGEEYSEEEES(ph)VLK ddPTM_HeLa_Romidepsin_16h_R1 1 EQPGEEYSEEEESVLK 16 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 0 EQPGEEYS(0.497)EEEES(0.503)VLK 209.31 1.01E-25 18957000 2350.6 2089.4 2008.7 2304 3383.9 3580.8 3552.3 3618.7 2454.7 2253.7 TRUE FALSE FALSE 2321.949983 2118.814628 2043.660581 2570.399321 3211.206956 3351.998437 3854.032273 3723.401375 2235.145484 2195.148549 1.057764398 0.96522608 0.930989651 1.170945502 1.462865444 1.527003008 1.75570454 1.69619563 1.018220605 1 11.10010286 -8.608233531 1.460973363 1.014132101 1.701707914 0.961315888 0.05960619 0.056449985 0.238221174 0.009821396 0.027457938 2.46E-09 8.608233531 0.687575813 EQQEAIEHIDEVQNEIDR ddPTM_HeLa_Romidepsin_16h_R1 2 EQQEAIEHIDEVQNEIDR 18 0 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105-2 Q01105;Q01105-2 SET;SETSIP Protein SET;Protein SETSIP 0 0 ; ; 187.04 8.02E-12 14351700 6303.7 5817 7058.8 3805.7 6104.3 6529.7 4985.7 5765.1 7041.9 7349.6 FALSE FALSE TRUE 6226.86808 5898.891879 7181.655453 4245.73294 5792.774793 6112.473244 5409.185234 5931.904073 6412.054827 7158.656332 0.869837549 0.824022219 1.003212771 0.593090762 0.809198615 0.853857618 0.755614599 0.828633726 0.895706475 1 12.80547311 -11.21896996 0.364372095 1.023343998 0.778715095 0.240551266 0.097717514 1.061805333 0.335394482 0.106062502 0.048790265 6.04E-12 11.21896996 -0.244628902 EQQSNIAVFQGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EQQSNIAVFQGKK 13 1 Q8NEF9 Q8NEF9 SRFBP1 Serum response factor-binding protein 1 0 1 ; EQQSNIAVFQGK(1)K;EQQSNIAVFQGK(1)K 247.13 2.03E-53 4712700 2311.54 2870.1 2060.66 1737.34 2173.89 2026.41 2769.4 2346.47 3123.3 2563.5 FALSE TRUE FALSE 2283.366061 2910.505343 2096.524923 1938.219425 2062.948281 1896.928941 3004.632767 2414.361407 2843.944226 2496.8999 0.914480417 1.165647587 0.83965117 0.776250351 0.826203838 0.759713652 1.203345303 0.966943612 1.138990083 1 11.28592227 -12.63767279 0.454618664 1.027724038 0.923662252 0.085784882 0.149208309 8.934480304 1.962706487 0.449371817 0.041893721 2.30E-13 12.63767279 -0.104061786 EQS(ph)DLDFFSPR ddPTM_HeLa_Romidepsin_16h_R1 1 EQSDLDFFSPR 11 0 J3KSS7;Q9NZ52-3;Q9NZ52-4;Q9NZ52-2;Q9NZ52 J3KSS7 GGA3 ADP-ribosylation factor-binding protein GGA3 1 0 EQS(0.996)DLDFFS(0.004)PR 108.66 0.0022849 0 1028.8 997.89 1345.5 932.53 1078.9 1272.6 1028.3 997.36 1392.5 1599.9 TRUE FALSE FALSE 1016.26059 1011.938322 1368.917863 1040.353506 1023.839707 1191.284967 1115.643776 1026.217038 1267.951312 1558.334367 0.6521454 0.649371754 0.878449383 0.667606085 0.657009002 0.764460434 0.715920665 0.658534561 0.813658056 1 10.60578911 -12.3128705 0.903213755 1.010779348 0.705348982 0.398577943 0.087650967 0.263306344 0.363258741 0.055562906 0.012892638 4.87E-13 12.3128705 -0.305430366 EQS(ph)TPPKSPQ ddPTM_HeLa_Romidepsin_16h_R1 1 EQSTPPKSPQ 10 1 Q92615;A0A087X183;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 0 EQS(0.927)T(0.073)PPKSPQ 151.79 0.023983 45127000 5417.2 4859.6 5200.5 5872 5165.5 4989.6 4115.4 3844.4 5937.9 5016.9 TRUE FALSE FALSE 5351.173083 4928.013576 5291.012521 6550.948269 4901.88526 4670.780663 4464.961973 3955.631649 5406.799352 4886.560215 1.095079739 1.008483137 1.082768305 1.340605248 1.003136162 0.95584224 0.913722901 0.809492051 1.106463261 1 12.25460355 -7.882815451 1.745062665 1.065711633 0.835089179 0.484991954 0.096026089 0.31000225 1.71959078 0.014767896 0.079460219 1.31E-08 7.882815451 -0.230622454 EQSDDET(ph)EESVK ddPTM_HeLa_Romidepsin_16h_R1 2 EQSDDETEESVK 12 0 A0A1B0GVI0;A0A1B0GWB9;O94885 A0A1B0GVI0 SASH1 SAM and SH3 domain-containing protein 1 1 0 EQS(0.019)DDET(0.981)EESVK;EQS(0.007)DDET(0.789)EES(0.204)VK ; 191.19 9.39E-10 15280700 3237.19 3609.3 3644.6 3078.8 4721.1 6117.9 5672.2 5987.2 3344.2 3663.9 TRUE FALSE FALSE 3197.733883 3660.11182 3708.032734 3434.785342 4480.16465 5726.985935 6153.996526 6160.430186 3045.086376 3568.71135 0.89604722 1.025611618 1.03903969 0.962472166 1.255401239 1.604777011 1.724431013 1.726233809 0.853273375 1 11.8011875 -8.382697227 1.731846809 0.960665564 1.735211963 0.972118519 0.054961912 0.038839315 0.223596335 0.007998342 0.024441983 4.14E-09 8.382697227 0.774546398 EQSEVSVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 EQSEVSVSPR 10 0 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 0 EQSEVSVS(1)PR;EQSEVSVS(1)PR ; 171.26 0.00075769 713190000 5510.1 5225.2 5269.5 4459.3 5519.4 5149.6 4773.3 5021.6 5745.2 5031.1 TRUE FALSE FALSE 5442.940782 5298.760503 5361.213437 4974.905248 5237.724422 4820.55718 5178.743983 5166.892073 5231.334923 4900.391297 1.110715543 1.081293346 1.094037825 1.015205714 1.068837998 0.983708624 1.056802135 1.054383571 1.067534123 1 12.25868124 -9.236218838 24.65322911 1.059094702 1.035897942 0.154880082 0.03599662 1786.288479 1746110.306 0.007313441 0.012121106 5.80E-10 9.236218838 -0.02319676 EQSSDLTPSGDVS(ph)PVKPLSR ddPTM_HeLa_Romidepsin_16h_R1 2 EQSSDLTPSGDVSPVKPLSR 20 1 Q8WYQ5-3;Q8WYQ5 Q8WYQ5-3 DGCR8 Microprocessor complex subunit DGCR8 1 0 EQSSDLT(0.001)PS(0.004)GDVS(0.985)PVKPLS(0.009)R;EQSSDLTPS(0.001)GDVS(0.743)PVKPLS(0.256)R ; 70.771 0.0032681 149274000 4530.2 5084.9 4664.6 3109.4 4236.8 4416.7 3464.6 3978.3 5117.5 4934.3 TRUE FALSE FALSE 4474.98418 5156.485356 4745.785406 3468.923458 4020.580286 4134.487124 3758.883038 4093.405834 4659.777983 4806.106175 0.931103895 1.072902921 0.987449139 0.721774204 0.836556693 0.860257134 0.782105701 0.851709406 0.969553691 1 12.2306528 -9.28036212 24.93502265 0.977587034 0.813118275 0.761749051 0.050473923 324.6661384 427820.5221 0.008154201 0.012468174 5.24E-10 9.28036212 -0.164468759 EQT(ph)LSPTITSGLHNIAR ddPTM_HeLa_Romidepsin_16h_R1 1 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;H7BXG7;O94979-7;O94979-6;O94979-10;O94979-4;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 0 EQT(0.598)LS(0.366)PT(0.034)IT(0.001)SGLHNIAR 113.47 0.0015428 41279000 2686.2 2600.7 2374.2 2576.8 4422.9 4852.1 3699.3 3883.4 4008.6 3575.4 TRUE FALSE FALSE 2653.459561 2637.312723 2415.521955 2874.74174 4197.182909 4542.066469 4013.51845 3995.760052 3650.060776 3482.510593 0.761938691 0.75730214 0.693615106 0.825479683 1.205217557 1.304250583 1.152478461 1.147379152 1.048111895 1 11.76591203 -8.758524656 24.96144752 0.854062583 1.20605052 0.716437976 0.109233188 34.84085937 298368.4283 0.018078544 0.034931336 1.74E-09 8.758524656 0.351987937 EQTLS(ph)PTITSGLHNIAR ddPTM_HeLa_Romidepsin_16h_R1 1 EQTLSPTITSGLHNIAR 17 0 D6REX3;O94979-3;O94979-9;O94979-2;O94979;O94979-8;H7BXG7;O94979-7;O94979-6;O94979-10;O94979-4;H0Y8W8 D6REX3 SEC31A Protein transport protein Sec31A 1 0 EQT(0.064)LS(0.722)PT(0.212)IT(0.001)SGLHNIAR 141.79 0.00017454 28328000 2034.1 1962 1876.8 1813.5 3662.2 3164.3 2901.1 3206.6 3186.7 2924.3 TRUE FALSE FALSE 2009.307607 1989.621087 1909.464917 2023.185403 3475.304268 2962.111442 3147.519362 3299.377912 2901.673571 2848.326264 0.705434497 0.698522888 0.670381389 0.710306761 1.220121554 1.039948084 1.105041723 1.158356735 1.018729352 1 11.4758987 -8.760187153 24.99979328 0.818840795 1.122528167 0.630880489 0.123233457 21.46072578 428430.9161 0.021610508 0.041376935 1.74E-09 8.760187153 0.303687372 EQVANS(ph)AFVER ddPTM_HeLa_Romidepsin_16h_R1 2 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 1 0 EQVANS(1)AFVER;EQVANS(1)AFVER ; 106.55 0.0024664 13997000 3759.2 3656.5 3734 2887 3517.7 3868.3 2957.2 3593 4015.3 3910.7 TRUE FALSE FALSE 3713.381424 3707.976303 3798.988704 3220.808524 3338.178643 3621.128114 3208.384494 3696.957786 3656.161511 3809.09945 0.974871219 0.973452217 0.997345633 0.845556428 0.876369516 0.950652027 0.842294757 0.970559534 0.959849319 1 11.89523424 -9.277837106 24.96890957 0.987125632 0.895867393 0.52631014 0.039639614 400.4085903 609703.2355 0.005474643 0.008376875 5.27E-10 9.277837106 -0.091258239 EQVANSAFVER ddPTM_HeLa_Romidepsin_16h_R1 2 EQVANSAFVER 11 0 P08238;Q58FF7 P08238 HSP90AB1;HSP90AB3P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3 0 0 ; ; 182.92 6.15E-05 24908000 3541.3 3293.4 2940.2 3442.2 3432.3 3425.6 2827.9 3298.4 3504.5 3544 FALSE FALSE TRUE 3498.137273 3339.764572 2991.372948 3840.20336 3257.136923 3206.715216 3068.101755 3393.834 3191.048743 3451.926369 1.01338699 0.967507477 0.866580752 1.112481249 0.943570799 0.928963968 0.888808575 0.983171029 0.924425495 1 11.75318598 -8.67330328 0.457987819 1.006213689 0.918305287 0 0.06823089 2.423764222 0.746901189 0.017251295 0.094982361 2.12E-09 8.67330328 -0.087908402 EQVEPTPEDEDDDIELR ddPTM_HeLa_Romidepsin_16h_R1 2 EQVEPTPEDEDDDIELR 17 0 A0A087WZG9;B4DSP0;Q86TG7-2;A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7 A0A087WZG9 PEG10 Retrotransposon-derived protein PEG10 0 0 ; ; 222.75 1.65E-34 37749000 3755.2 4439.7 4128.6 3775.7 5725 7283.3 6800.4 7535.8 4718 4149.9 FALSE FALSE TRUE 3709.430178 4502.202213 4200.456551 4212.264199 5432.831887 6817.920636 7378.025806 7753.836483 4296.010264 4042.085 0.917702171 1.113831652 1.039180658 1.042101836 1.34406671 1.686733613 1.825301993 1.918276455 1.062820367 1 11.98088394 -8.348598685 1.211175807 0.973512114 1.924756701 0.972236344 0.059404904 0.052031629 0.138691039 0.009161312 0.037326594 4.48E-09 8.348598685 0.951244587 EQYVPPRS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EQYVPPRSPK 10 1 X6RLN4;Q71RC2-2;Q71RC2-6;Q71RC2-5;Q71RC2-3;Q71RC2;Q71RC2-4 X6RLN4 LARP4 La-related protein 4 1 0 EQYVPPRS(1)PK 79.659 0.022956 72139000 2593.2 2676.5 2395.7 2486.1 2780.6 3096.2 2553.9 3164.9 3030.4 2635.9 TRUE FALSE FALSE 2561.593081 2714.179837 2437.396154 2773.554579 2638.695606 2898.362813 2770.828202 3256.471388 2759.353434 2567.418938 0.997730851 1.057162817 0.949356615 1.080289055 1.027761994 1.128901392 1.079227142 1.268383332 1.074757763 1 11.32610301 -4 0.467860246 0.999511983 7.40519557 0.685636955 0.046753105 23.57277356 0.244679016 0.007260155 146.9522389 1.00E-04 4 6.405683587 ERDDLMSALVSVR ddPTM_HeLa_Romidepsin_16h_R1 1 ERDDLMSALVSVR 13 1 A0A0G2JR20;A0A0C4DG71;A0A0G2JQM2;A0A0G2JR50;Q86SQ7-2;Q86SQ7-3;Q86SQ7-4;Q86SQ7 A0A0G2JR20 SDCCAG8 Serologically defined colon cancer antigen 8 0 0 88.596 0.0016719 0 1343.9 1292.3 1360.1 1574.1 1465.7 1310.6 1092.9 1274.6 1321.1 1064.4 FALSE FALSE TRUE 1327.52003 1310.493033 1383.77197 1756.104848 1390.89986 1226.85689 1185.730899 1311.47854 1202.937507 1036.746735 1.280467047 1.26404356 1.334725178 1.693860988 1.341600425 1.183371839 1.143703529 1.264994136 1.160300262 1 10.01784779 -11.82830718 0.697548257 0.997865905 1.320238405 0.266881334 0.147664427 0.600395864 0.547462412 0.103924343 0.034280444 1.48E-12 11.82830718 0.3223725 ERDFTSLENTVEER ddPTM_HeLa_Romidepsin_16h_R1 1 ERDFTSLENTVEER 14 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 0 127.07 0.0032707 1948700 599.63 702.11 796.92 621.33 537.3 529.55 466.47 488.05 706.86 860.43 FALSE FALSE TRUE 592.3214789 711.994323 810.7900583 693.171098 509.8795761 495.713464 506.0919502 502.1709567 643.6366712 838.0759046 0.706763523 0.849558279 0.967442273 0.827098231 0.608393074 0.591489937 0.603873644 0.599195078 0.76799329 1 9.710937105 -8.788012772 4.491980133 0.865283953 0.598095746 0.706544468 0.079809901 0.114337417 5.348764166 0.016739625 0.032147893 1.63E-09 8.788012772 -0.267188206 ERDHS(ph)PTPSVFNSDEER ddPTM_HeLa_Romidepsin_16h_R1 4 ERDHSPTPSVFNSDEER 17 1 Q6UN15-5;Q6UN15;Q6UN15-3 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 1 0 ERDHS(0.996)PT(0.003)PSVFNSDEER;ERDHS(0.457)PT(0.457)PS(0.085)VFNSDEER;ERDHS(0.997)PT(0.003)PSVFNSDEER;ERDHS(0.955)PT(0.045)PSVFNSDEER ;;; 100.01 0.0010199 66044100 6909.53 6955.27 6938.31 5413.3 7181.14 7497.99 6175.88 6670.04 8228.3 7644.34 TRUE FALSE FALSE 6825.313991 7053.186474 7059.068375 6039.211216 6814.659629 7018.892638 6700.459093 6863.027084 7492.34024 7445.738945 0.916673824 0.947278239 0.948068208 0.811096288 0.91524289 0.942672405 0.899905186 0.921738881 1.006258787 1 12.86219932 -12.27647872 0.434025415 1.025346346 0.906163533 0.495066366 0.03692345 1.483446507 0.366882731 0.079946849 0.011787569 5.29E-13 12.27647872 -0.119182813 EREAANEAGDS(ph)SQDEAEDDVK ddPTM_HeLa_Romidepsin_16h_R1 1 EREAANEAGDSSQDEAEDDVK 21 1 A0A0C4DH01;Q9NVU0-3;Q9NVU0-2;Q9NVU0-5;Q9NVU0-4;Q9NVU0 A0A0C4DH01 POLR3E DNA-directed RNA polymerase III subunit RPC5 1 0 EREAANEAGDS(0.63)S(0.37)QDEAEDDVK 60.51 0.0069373 5275500 908.35 803.39 800.43 1013.2 1086.3 1262.6 1032.3 1230.3 1182.1 917.14 TRUE FALSE FALSE 897.2786808 814.7001455 814.3611484 1130.350951 1030.862057 1181.923935 1119.983536 1265.896789 1076.370015 893.3125706 1.004439779 0.911998971 0.911619488 1.265347638 1.153976885 1.323079932 1.253742053 1.417081581 1.204919813 1 9.803021253 -9.250287031 24.24230834 0.987790237 1.276137983 0.660909743 0.098350308 156.5000754 340190.2161 0.010605879 0.01747367 5.62E-10 9.250287031 0.288347746 EREDES(ph)EDESDILEESPCGR ddPTM_HeLa_Romidepsin_16h_R1 1 EREDESEDESDILEESPCGR 20 1 Q9NSY0 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 0 EREDES(0.983)EDES(0.017)DILEESPCGR 61.488 0.0038941 0 744.57 783.51 792.08 469.26 886.17 1106.1 602.35 729.83 686.91 706.77 TRUE FALSE FALSE 735.4948944 794.5402743 805.8658201 523.5180491 840.9454381 1035.42378 653.513594 750.9464796 625.4710492 688.4080135 1.06839967 1.154170577 1.17062237 0.760476402 1.221579967 1.504084437 0.949311427 1.090845058 0.908576073 1 9.427120081 EREDS(ph)GDAEAHAFK ddPTM_HeLa_Romidepsin_16h_R1 1 EREDSGDAEAHAFK 14 1 Q9NPI1;Q9NPI1-2 Q9NPI1 BRD7 Bromodomain-containing protein 7 1 0 EREDS(1)GDAEAHAFK 62.658 0.029332 2927900 2207.2 1791.4 1875.4 1882.8 1166.9 1291.7 1072.7 1156 1821.1 1892.4 TRUE FALSE FALSE 2180.297797 1816.619376 1908.04055 2100.498195 1107.348739 1209.164539 1163.815111 1189.447036 1658.216255 1843.235175 1.182864686 0.98556028 1.035158495 1.139571457 0.600763676 0.656001228 0.631398059 0.645304003 0.899622727 1 10.84802444 -8.759366575 24.9999998 1.07902405 0.634842802 0.856262989 0.080788998 12.5613806 151498.4374 0.011222679 0.021587313 1.74E-09 8.759366575 -0.444181248 EREES(ph)EDELEEANGNNPIDIEVDQNK ddPTM_HeLa_Romidepsin_16h_R1 4 EREESEDELEEANGNNPIDIEVDQNK 26 1 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 0 EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK;EREES(1)EDELEEANGNNPIDIEVDQNK ;;; 107.61 7.51E-07 311744600 4057.93 4189.03 4108.69 3537.3 4689.83 5203.26 4116.02 5026.25 4275.94 4090.75 TRUE FALSE FALSE 4008.470388 4248.003274 4180.200026 3946.299269 4450.490475 4870.788479 4465.634636 5171.676614 3893.489217 3984.471725 1.006023048 1.066139646 1.049122773 0.990419695 1.116958729 1.222442726 1.120759524 1.297957915 0.977165729 1 11.96017274 -7.008247893 0.418957445 0.998655694 1.528921056 0.790058366 0.04632512 1.909002123 0.194664787 0.011041119 0.527012789 9.81E-08 7.008247893 0.530265362 EREES(ph)EDELEEANGNNPIDIEVDQNKESK ddPTM_HeLa_Romidepsin_16h_R1 3 EREESEDELEEANGNNPIDIEVDQNKESK 29 2 Q9UKL0 Q9UKL0 RCOR1 REST corepressor 1 1 0 EREES(1)EDELEEANGNNPIDIEVDQNKESK;EREES(1)EDELEEANGNNPIDIEVDQNKESK;EREES(1)EDELEEANGNNPIDIEVDQNKESK ;; 120.23 1.26E-10 61689000 7006.7 6826.76 6863.78 7768.08 8952.7 9191.16 8694.13 8714.04 8505.33 7914.32 TRUE FALSE FALSE 6921.299645 6922.867306 6983.241212 8666.26196 8495.810312 8603.874539 9432.609185 8966.166999 7744.591983 7708.704825 0.897855062 0.898058424 0.905890337 1.124217642 1.102106061 1.116124529 1.223630869 1.163122366 1.004655407 1 12.91227277 -9.197200153 5.18513128 0.942558738 1.148438844 0.827169005 0.046792046 0.077734423 4.211682417 0.008347258 0.01392374 6.35E-10 9.197200153 0.205880106 ERES(ph)PPPSALQPVQLPR ddPTM_HeLa_Romidepsin_16h_R1 1 ERESPPPSALQPVQLPR 17 1 Q86VE0 Q86VE0 MYPOP "Myb-related transcription factor, partner of profilin" 1 0 ERES(1)PPPSALQPVQLPR 104.42 0.00029741 0 1048.1 1080.2 986.09 1093.2 1104.3 1017.4 922.43 1031.8 1066.5 1182 TRUE FALSE FALSE 1035.325354 1095.407084 1003.252483 1219.600928 1047.94345 952.3914235 1000.781181 1061.653505 971.1095689 1151.29147 0.899273018 0.951459394 0.87141485 1.059332897 0.910232967 0.827237453 0.869268302 0.92214138 0.843495843 1 10.16903741 -16.52287875 0.207293427 1.43299375 0.89501864 0 0.075850621 54.95385749 0.678538308 9.669271917 0.056009705 3.00E-17 16.52287875 -0.53797511 ERESSANNSVS(ph)PSESLR ddPTM_HeLa_Romidepsin_16h_R1 3 ERESSANNSVSPSESLR 17 1 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 ERESSANNS(0.363)VS(0.606)PS(0.029)ES(0.003)LR;ERESSANNSVS(0.412)PS(0.176)ES(0.412)LR;ERESSANNS(0.112)VS(0.884)PS(0.004)ESLR ;; 174.18 7.07E-06 19311100 3955.6 4210 4115.8 4632.8 3577.13 3212.15 2940.68 2654.89 3982.4 4281.4 TRUE FALSE FALSE 3907.387626 4269.268491 4187.433773 5168.466134 3394.575708 3006.903982 3190.461286 2731.705053 3626.20417 4170.168611 0.936985525 1.023763998 1.004140159 1.239390206 0.814014018 0.721050936 0.765067695 0.655058658 0.869558166 1 12.02589 -8.535598204 24.99013646 0.994978635 0.726972007 0.681293882 0.092965653 95.11914705 186881.7623 0.012524628 0.02506128 2.91E-09 8.535598204 -0.268006628 EREVDEDS(ph)EPER ddPTM_HeLa_Romidepsin_16h_R1 2 EREVDEDSEPER 12 1 F8WC91;B9A018;Q53GS9-3;Q53GS9 F8WC91 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 0 EREVDEDS(1)EPER;EREVDEDS(1)EPER ; 99.069 0.0060171 18486800 3261.2 3151.7 3504.6 2111.7 2856.4 3669.3 3459 3340.65 3133.1 3236.5 TRUE FALSE FALSE 3221.45124 3196.069715 3565.596093 2355.86469 2710.627249 3434.843572 3752.807374 3437.306437 2852.867689 3152.415263 1.021899392 1.013847938 1.131068021 0.747320544 0.859857291 1.089591087 1.190454639 1.090372349 0.90497839 1 11.62224188 -8.012258482 23.68878056 0.990595464 1.14031589 0.323722157 0.104859568 279.988212 541067.6948 0.014485442 0.039284039 9.72E-09 8.012258482 0.149720426 EREVDEDS(ph)EPEREVR ddPTM_HeLa_Romidepsin_16h_R1 1 EREVDEDSEPEREVR 15 2 F8WC91;B9A018;Q53GS9-3;Q53GS9 F8WC91 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 0 EREVDEDS(1)EPEREVR 99.915 0.0072178 27923000 851.81 1088.6 961.48 1010.4 918.95 1203.1 995.48 907.25 1151.3 1210.3 TRUE FALSE FALSE 841.4278121 1103.925339 978.2141561 1127.227202 872.0525524 1126.225793 1080.036046 933.4998473 1048.324845 1178.856232 0.713766267 0.936437633 0.829799368 0.956204134 0.739744618 0.955354659 0.916172827 0.791869121 0.889272853 1 10.20317207 -12.68229777 1.56013149 0.999731469 0.837805658 0.068504879 0.09030531 0.38909753 1.710603121 0.064074817 0.014364551 2.08E-13 12.68229777 -0.161925811 EREY(ph)NKLK ddPTM_HeLa_Romidepsin_16h_R1 1 EREYNKLK 8 2 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 0 EREY(1)NKLK 53.968 0.0041192 0 1407.7 1116 1198.9 1328.6 1253.3 1336.8 833.91 955.56 1412.5 1350.8 TRUE FALSE FALSE 1390.542411 1131.711077 1219.766352 1482.218983 1189.339424 1251.382794 904.7422946 983.207621 1286.162462 1315.706021 1.056879264 0.860154973 0.927081226 1.126557878 0.903955295 0.951111247 0.687647757 0.747285188 0.977545471 1 10.36162146 -7.890663438 2.16602056 1.008127637 0.706606107 0.608616431 0.079045183 0.141084444 1.277023035 0.011305552 0.050381668 1.29E-08 7.890663438 -0.30152153 ERLDGENIY(ph)IR ddPTM_HeLa_Romidepsin_16h_R1 3 ERLDGENIYIR 11 1 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A2R8Y5G2;A0A2R8Y420;A0A2R8YCW8;A0A2R8Y5Z6;P11171-7;A0A2R8Y5C8 P11171 EPB41 Protein 4.1 1 0 ERLDGENIY(1)IR;ERLDGENIY(1)IR;ERLDGENIY(1)IR ;; 158.08 0.0026587 16320900 3051.91 2791.09 2941.16 3921.79 3401.92 2518.78 1967.4 2255.73 3908.77 3533.94 TRUE FALSE FALSE 3014.712147 2830.383038 2992.349656 4375.245812 3228.307328 2357.838087 2134.510907 2320.995989 3559.159822 3442.127729 0.875828088 0.822277167 0.869331382 1.271087582 0.937881329 0.684994362 0.6201138 0.67429107 1.033999927 1 11.74908492 -8.243670572 5.000330545 0.950952629 0.651606233 0.58796197 0.119357971 0.109236567 8.101229234 0.017502169 0.044074667 5.71E-09 8.243670572 -0.299346395 ERLEQEQLER ddPTM_HeLa_Romidepsin_16h_R1 2 ERLEQEQLER 10 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7;A0A075B6E5;A0A0U1RQP7 A0A0U1RRM6 ENAH Protein enabled homolog 0 0 ; ; 139.31 0.0056867 8053700 5424.3 5108.7 6060.3 4120.9 6196 6423.1 5252.2 5237.5 5994.9 5961.5 FALSE FALSE TRUE 5358.186545 5180.620413 6165.776979 4597.377847 5879.795 6012.68464 5698.321737 5389.038799 5458.701129 5806.619371 0.922772134 0.892192183 1.061853134 0.791747754 1.012602105 1.035487993 0.98134928 0.928085424 0.940082478 1 12.50348275 -7.234680785 20.6786661 0.962157978 0.928084976 0.015117013 0.074588726 3063.117016 2366725.99 0.009746812 0.683172966 5.83E-08 7.234680785 -0.034073001 ERLGS(ph)FGSITR ddPTM_HeLa_Romidepsin_16h_R1 1 ERLGSFGSITR 11 1 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 1 0 ERLGS(0.997)FGS(0.003)ITR 72.321 0.027195 1957800 1256.2 1212.2 1105.7 1167.1 956.69 1044.8 987.95 994.89 1257.6 1117.1 TRUE FALSE FALSE 1240.888951 1229.265383 1124.944245 1302.045593 907.8665394 978.0406519 1071.866448 1023.675572 1145.117106 1088.077581 1.140441613 1.129758948 1.033882385 1.196647754 0.834376661 0.898870328 0.985101124 0.940811198 1.052422296 1 10.08756571 -8.753993632 24.99999402 1.078592869 0.918674964 0.641029293 0.064530538 106.7222133 358329.6818 0.010917229 0.021497242 1.76E-09 8.753993632 -0.159917905 ERLNS(ph)SENGEDR ddPTM_HeLa_Romidepsin_16h_R1 1 ERLNSSENGEDR 12 1 Q7L4I2;H0YGP9;E1B6W4;Q7L4I2-2 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 0 ERLNS(0.747)S(0.253)ENGEDR 73.758 0.023213 2521100 530.14 581.15 624.62 558.12 517.76 462.41 727.98 416.1 527.51 598.93 TRUE FALSE FALSE 523.6784498 589.331445 635.4912491 622.6524604 491.3367752 432.8634934 789.814603 428.139197 480.3281844 583.3697123 0.897678503 1.010219476 1.089345634 1.067337655 0.842239089 0.742005429 1.353883457 0.73390714 0.823368396 1 9.188266675 -6.100426837 17.50927124 0.965313397 0.692029684 0 0.179801225 0 0 0.020675271 0 7.94E-07 6.100426837 -0.273283713 ERPDLEAPAPGS(ph)PFR ddPTM_HeLa_Romidepsin_16h_R1 2 ERPDLEAPAPGSPFR 15 1 H0YBA8;Q9NQT8-2;Q9NQT8 H0YBA8 KIF13B Kinesin-like protein KIF13B 1 0 ERPDLEAPAPGS(1)PFR;ERPDLEAPAPGS(1)PFR ; 100.39 0.0028736 32533000 3578.8 3436.9 2979 4396.5 4257.6 4695.8 3992.4 3973.5 3660.5 3419.8 TRUE FALSE FALSE 3535.180209 3485.284768 3030.848245 4904.844016 4040.318785 4395.753535 4331.514356 4088.466953 3333.095712 3330.953103 1.061311913 1.046332584 0.909904208 1.472504675 1.212961774 1.319668395 1.30038287 1.227416546 1.000643242 1 11.70171933 -9.268713291 24.99833118 1.023151304 1.301767547 0.794707855 0.076648034 186.8985944 642315.7748 0.01096269 0.016955383 5.39E-10 9.268713291 0.278616243 ERPSGPES(ph)PVQGPR ddPTM_HeLa_Romidepsin_16h_R1 1 ERPSGPESPVQGPR 14 1 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 0 ERPS(0.006)GPES(0.994)PVQGPR 85.496 0.0095927 11774000 2595.1 3361.1 2821.5 2187.9 2021.8 2130.6 1928.6 1966.9 3140.5 3203.4 TRUE FALSE FALSE 2563.469923 3408.417654 2870.607024 2440.875292 1918.620002 1994.461536 2092.415236 2023.809148 2859.605814 3120.175206 0.821578839 1.092380212 0.92001469 0.782287894 0.614907778 0.639214597 0.67060825 0.648620354 0.916488859 1 11.60741133 -9.035756968 2.887902053 0.929781387 0.645612081 0.818910836 0.067671415 0.108287482 1.810198265 0.012941808 0.023591185 9.21E-10 9.035756968 -0.284169306 ERPSS(ph)AIYPSDSFR ddPTM_HeLa_Romidepsin_16h_R1 1 ERPSSAIYPSDSFR 14 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF5;V9GYG5;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 ERPS(0.139)S(0.861)AIYPS(0.001)DSFR 117.48 0.029823 15513000 2142.3 1570.7 1911.5 2004.1 2119.9 2466.8 1700.8 1582.9 2063.4 1989.2 TRUE FALSE FALSE 2116.188824 1592.812356 1944.768856 2235.823472 2011.713593 2309.179441 1845.26591 1628.698714 1878.844336 1937.520297 1.092215048 0.822088088 1.003741152 1.153961316 1.038292913 1.191822065 0.952385331 0.840609885 0.96971595 1 10.91999571 -7.524091753 24.97231555 1.042273767 0.868553688 0.269809883 0.097543755 30.09148067 619525.1703 0.013181603 0.050149137 2.99E-08 7.524091753 -0.173720079 ERQAQAQES(ph)EEEEESR ddPTM_HeLa_Romidepsin_16h_R1 2 ERQAQAQESEEEEESR 16 1 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 0 ERQAQAQES(0.985)EEEEES(0.015)R;ERQAQAQES(0.961)EEEEES(0.039)R ; 79.383 0.0095412 5956600 1390.66 1835.29 1852.55 1527.48 1247.14 1518.25 1114.13 990.81 1706.53 1494.46 TRUE FALSE FALSE 1373.710101 1861.127261 1884.792856 1704.094425 1183.493792 1421.238725 1208.764174 1019.477524 1553.893683 1455.633714 0.943719624 1.278568395 1.294826327 1.170689033 0.81304368 0.976371124 0.83040408 0.700366799 1.067503224 1 10.50743166 -7.583681972 1.136890341 1.029111517 0.64448299 0.426667215 0.14263806 0.974032823 1.46341682 0.024641463 0.386983013 2.61E-08 7.583681972 -0.384628528 ERS(ph)GGEQAQDWDALPPK ddPTM_HeLa_Romidepsin_16h_R1 1 ERSGGEQAQDWDALPPK 17 1 V9GYP5;A0A087WWQ2;Q92979 V9GYP5 EMG1 Ribosomal RNA small subunit methyltransferase NEP1 1 0 ERS(1)GGEQAQDWDALPPK 98.443 0.001437 5817300 2109.8 1818 1994.9 1587.8 1904.8 2400.3 2103.4 2156.4 2235.2 2246 TRUE FALSE FALSE 2084.084946 1843.593852 2029.620398 1771.388907 1807.590948 2246.928577 2282.062743 2218.792032 2035.278114 2187.648596 0.952659833 0.842728514 0.927763445 0.809722782 0.826271162 1.027097579 1.043157821 1.014236032 0.930349654 1 11.0951653 -8.057184068 24.99911028 0.940757727 1.030305371 0.340131982 0.066512369 320.68641 140193.7772 0.011392617 0.029045689 8.77E-09 8.057184068 0.089547644 ERS(ph)PALKSPLQSVVVR ddPTM_HeLa_Romidepsin_16h_R1 1 ERSPALKSPLQSVVVR 16 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 ERS(1)PALKSPLQSVVVR 77.137 0.026269 350550000 5537.6 6573.4 4096.5 8285.9 5133.7 5162.2 4790.4 6126.9 4833.5 4531.6 TRUE FALSE FALSE 5470.105601 6665.940498 4167.797864 9243.954744 4871.708133 4832.35208 5197.296456 6304.172185 4401.179654 4413.868379 1.239299665 1.510226388 0.9442506 2.094297779 1.10372755 1.094811097 1.177492397 1.428264652 0.99712526 1 12.10782789 -11.46036667 0.794317548 1.019963295 1.326543199 0.15559707 0.302309194 0.826420254 1.085648991 0.124015492 0.064129588 3.46E-12 11.46036667 0.306579904 ERS(ph)PFGNPENVR ddPTM_HeLa_Romidepsin_16h_R1 1 ERSPFGNPENVR 12 1 K7ESB7;Q96HP0 K7ESB7 DOCK6 Dedicator of cytokinesis protein 6 1 0 ERS(1)PFGNPENVR 69.045 0.027223 4385200 811.36 705.58 829.53 1047 967.15 1014.5 715.33 852.39 1022.1 878.36 TRUE FALSE FALSE 801.4708322 715.5131738 843.9676217 1168.059066 917.7927266 949.6767241 776.0901123 877.0525598 930.6808161 855.5400806 0.936801034 0.836329226 0.986473505 1.365288539 1.072764149 1.110031833 0.907134721 1.025144911 1.087828422 1 9.740691634 -9.500370165 24.99983332 0.957004963 1.094139255 0.213431765 0.121612705 863.8234912 959433.145 0.018097885 0.027512949 3.16E-10 9.500370165 0.137134292 ERS(ph)YELVR ddPTM_HeLa_Romidepsin_16h_R1 1 ERSYELVR 8 1 A0A3B3ISE6;A0A3B3ITA8;A0A3B3ITJ7;A0A3B3ITE7;A0A3B3IT25;A0A3B3IS40;Q9UGL1;Q9UGL1-2 A0A3B3ISE6 KDM5B Lysine-specific demethylase 5B 1 0 ERS(0.998)Y(0.002)ELVR 75.652 0.0041658 0 403.48 294.99 432.92 469.02 447.07 505.73 391.31 584.05 327.04 413.3 TRUE FALSE FALSE 398.5622306 299.142877 440.454791 523.2502992 424.2543497 473.4154852 424.5478616 600.9485653 297.7887233 402.5624064 0.990063216 0.743096902 1.094127976 1.299799213 1.053884672 1.176005205 1.054613781 1.492808458 0.739733066 1 8.653068641 -9.525899681 24.99953052 0.973515555 1.195488256 0.472655415 0.157568753 70.62852907 584478.558 0.020475684 0.029045348 2.98E-10 9.525899681 0.221972701 ERSDS(ph)GGSSSEPFDR ddPTM_HeLa_Romidepsin_16h_R1 2 ERSDSGGSSSEPFDR 15 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 ERS(0.345)DS(0.589)GGS(0.057)S(0.008)SEPFDR;ERS(0.198)DS(0.786)GGS(0.012)S(0.003)SEPFDR ; 135.57 0.0086225 37982000 2089.78 1832.66 1961.81 2247.89 1645.8 1516.77 1717.19 1443.54 2348.81 2190.66 TRUE FALSE FALSE 2064.308958 1858.460236 1995.95448 2507.801618 1561.808685 1419.853292 1863.048076 1485.306552 2138.726551 2133.746337 0.967457528 0.870984617 0.935422569 1.175304475 0.731956117 0.665427407 0.87313475 0.696102684 1.002334023 1 11.05917296 -8.727204258 24.99951115 0.982620391 0.745601556 0.657301311 0.088355497 86.65782085 63279.7856 0.012141318 0.024281669 1.87E-09 8.727204258 -0.237018834 ERTDVIQGDDVADATSEVEVSSTSETT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ERTDVIQGDDVADATSEVEVSSTSETTPK 29 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 ERTDVIQGDDVADATSEVEVS(0.034)S(0.034)T(0.024)S(0.017)ET(0.199)T(0.693)PK 120.32 1.79E-10 6454500 918.39 715.62 677.7 803.28 855.33 1051.6 1005 1157.2 706.64 912.04 TRUE FALSE FALSE 907.1963094 725.6945171 689.4950842 896.1590131 811.6793184 984.4061539 1090.364675 1190.681756 643.4363486 888.3450693 1.021220628 0.816906113 0.77615682 1.008796068 0.913698231 1.108134877 1.227411186 1.34033699 0.724309022 1 9.794976377 -7.802037389 1.934489509 0.971705704 1.32762654 0.610041007 0.116233304 0.181831035 1.252061535 0.014112544 0.078898424 1.58E-08 7.802037389 0.355920836 ERVDDSTGTVIS(ph)DVEEDAGELSR ddPTM_HeLa_Romidepsin_16h_R1 3 ERVDDSTGTVISDVEEDAGELSR 23 1 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 0 ERVDDSTGTVIS(1)DVEEDAGELSR;ERVDDS(0.001)T(0.001)GT(0.027)VIS(0.971)DVEEDAGELSR;ERVDDSTGTVIS(1)DVEEDAGELSR ;; 124.97 1.86E-06 30980100 2298.29 2514.96 2620.39 2983.98 2772.19 2584.01 1963.72 2321.08 3207.39 2602.54 TRUE FALSE FALSE 2270.277557 2550.365673 2665.996789 3329.001808 2630.7148 2418.900101 2130.518328 2388.236788 2920.513005 2534.925636 0.895599273 1.006090923 1.051706114 1.313254228 1.037787761 0.954229215 0.84046581 0.942132879 1.152109933 1 11.30772771 -7.974715189 7.544868818 0.994657972 0.892154044 0.103410305 0.121060167 0.343104048 75.81557939 0.017795028 0.0530677 1.06E-08 7.974715189 -0.102503928 ES(ph)AWSPPPIEIR ddPTM_HeLa_Romidepsin_16h_R1 2 ESAWSPPPIEIR 12 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 ES(0.669)AWS(0.331)PPPIEIR;ES(0.771)AWS(0.229)PPPIEIR ; 104.94 0.013172 10313500 6085.1 5671.4 5414.3 4416.9 6071.1 6980.5 6476.8 6898.8 6465.3 5400.5 TRUE FALSE FALSE 6010.932461 5751.242118 5508.53362 4927.60276 5761.269113 6534.468579 7026.93923 7098.405893 5887.027375 5260.194231 1.142720629 1.093351664 1.047211068 0.936772017 1.095257867 1.242248535 1.335870677 1.349456994 1.119165399 1 12.36090036 -8.122419353 2.46444891 1.05992271 1.341136751 0.813526563 0.055750545 0.109717937 1.283001624 0.00990706 0.03183856 7.54E-09 8.122419353 0.281214041 ES(ph)ELRFMMDDIQLCKDIMDLK ddPTM_HeLa_Romidepsin_16h_R1 1 ESELRFMMDDIQLCKDIMDLK 21 2 H3BU79;H3BUY6;H3BRF6;Q96MC5-2;Q96MC5 H3BU79 C16orf45 Uncharacterized protein C16orf45 1 0 ES(1)ELRFMMDDIQLCKDIMDLK 62.064 0.0017644 0 3360.9 3177.9 3331.2 2195.8 2910.2 3234.2 2850.5 3161.6 3189.3 3235.3 TRUE FALSE FALSE 3319.936058 3222.63856 3389.178139 2449.688728 2761.681635 3027.545058 3092.621399 3253.075908 2904.04102 3151.24644 1.053531078 1.022655201 1.075503996 0.777371359 0.87637755 0.960745253 0.981396237 1.032314029 0.92155313 1 11.62170687 ES(ph)HSPFGLDSFNSTAK ddPTM_HeLa_Romidepsin_16h_R1 1 ESHSPFGLDSFNSTAK 16 0 Q7LBC6;Q7LBC6-3;Q7LBC6-2 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 0 ES(0.696)HS(0.304)PFGLDSFNSTAK 122.12 0.0011746 7623000 4655 4418 4668.5 3123.3 5202.9 5723.7 4685.3 4889.7 5102.5 5146.6 TRUE FALSE FALSE 4598.26307 4480.19672 4749.753284 3484.430642 4937.376598 5357.974042 5083.269265 5031.175755 4646.119621 5012.89059 0.917287738 0.893735189 0.94750787 0.695094094 0.984936038 1.068839215 1.014039539 1.003647629 0.926834436 1 12.29142703 -8.526481419 24.99901336 0.932829288 1.027282858 0.30562517 0.080939579 130.8618112 908051.4832 0.012783387 0.025664902 2.98E-09 8.526481419 0.094453571 ES(ph)HTPVSIQEEIVGDFK ddPTM_HeLa_Romidepsin_16h_R1 2 ESHTPVSIQEEIVGDFK 17 0 E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-4;Q12830;A0A0A0MR81;F5H176 E7ETD6 BPTF Nucleosome-remodeling factor subunit BPTF 1 0 ES(0.578)HT(0.422)PVSIQEEIVGDFK;ES(0.779)HT(0.216)PVS(0.006)IQEEIVGDFK ; 134.04 0.00069261 6870800 10565.7 9085.9 9870.8 5498.5 6947.5 6368.1 5536.8 6620.8 10792.3 10072.9 TRUE FALSE FALSE 10436.92118 9213.811539 10042.59713 6134.262441 6592.94315 5961.198962 6007.095654 6812.362402 9827.009658 9811.204606 1.063775714 0.93911114 1.023584518 0.625230304 0.671981007 0.607590933 0.612268921 0.694345157 1.001610919 1 13.26021456 -9.262685952 24.98598409 1.022162755 0.640338314 0.954817729 0.039435178 16.05175205 321737.7251 0.006425998 0.010161193 5.46E-10 9.262685952 -0.381824441 ES(ph)NRLSAPSYLAR ddPTM_HeLa_Romidepsin_16h_R1 1 ESNRLSAPSYLAR 13 1 H0YJH0;Q9H4B6 H0YJH0 SAV1 Protein salvador homolog 1 1 0 ES(0.622)NRLS(0.378)APSYLAR 71.545 0.022398 6639500 1944.7 1323.5 1294 1884.4 2145.9 2288.8 2050.9 2091.1 1904.5 1853.1 TRUE FALSE FALSE 1920.997248 1342.132268 1316.521527 2102.283194 2036.386716 2142.553067 2225.103395 2151.602679 1734.15675 1804.956195 1.064290233 0.743581629 0.729392509 1.164728097 1.128219467 1.187038817 1.232774181 1.192052575 0.960774979 1 10.81774811 -9.039893112 24.82689904 0.98290974 1.183313632 0.548645279 0.115985215 404.726601 251874.9153 0.02002496 0.033211122 9.12E-10 9.039893112 0.200403892 ES(ph)PEGSYTDDANQEVR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPEGSYTDDANQEVR 16 0 A0A075B6Q2;S4R347;Q5T0N5-3;Q5T0N5-4;Q5T0N5-2;Q5T0N5-5;Q5T0N5 A0A075B6Q2 FNBP1L Formin-binding protein 1-like 1 0 ES(1)PEGSYTDDANQEVR 254.72 7.72E-72 16629000 806.65 933.29 790.52 590.36 944.75 1103.4 702.76 952.88 945.41 788.34 TRUE FALSE FALSE 796.8182395 946.4288811 804.278669 658.6202009 896.5358822 1032.896301 762.4524169 980.4500794 860.8501618 767.8588132 1.03771452 1.232555862 1.047430407 0.85773607 1.167579074 1.34516435 0.992959127 1.276862442 1.121104749 1 9.584697256 -4.000000001 0.181830795 0.987323476 1.971170091 0.098054242 0.134354719 67.3461582 0.735333608 0.158247983 18.47397343 1.00E-04 4.000000001 0.983846614 ES(ph)PGAAATSSSGPQAQQHR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPGAAATSSSGPQAQQHR 19 0 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 0 ES(1)PGAAATSSSGPQAQQHR 115.85 0.00034784 6121600 1537.3 1420.3 1324.5 1029.6 1477.1 1653 1278.7 1310.3 1682.3 2105.6 TRUE FALSE FALSE 1518.562796 1440.295021 1347.552367 1148.647196 1401.718075 1547.378635 1387.312746 1348.211463 1531.830875 2050.896208 0.740438638 0.70227592 0.65705537 0.560070857 0.683466121 0.754489003 0.676442201 0.65737674 0.746908044 1 11.00203877 -11.69059633 0.557038141 1.016654756 0.663283163 0.325716524 0.089083102 0.253098923 0.148971102 0.043273057 0.013974852 2.04E-12 11.69059633 -0.353371593 ES(ph)PGSSEFFQEAVSHGK ddPTM_HeLa_Romidepsin_16h_R1 1 ESPGSSEFFQEAVSHGK 17 0 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 0 ES(0.948)PGS(0.041)S(0.011)EFFQEAVSHGK 100.47 0.0013291 4233800 4452.8 4552.4 5133.4 2883.8 5012.3 4758.7 3864.1 4217.2 4744.8 5407 TRUE FALSE FALSE 4398.527561 4616.488807 5222.744674 3217.238525 4756.503628 4454.634428 4192.316558 4339.218028 4320.413204 5266.525361 0.835185869 0.876572026 0.991686988 0.610884465 0.903157832 0.845839358 0.796030831 0.823924263 0.820353631 1 12.36263573 -14.85249803 0.228077283 1.398591889 0.806025579 0 0.106659869 18.99939344 0.475572037 3.564944256 0.07018411 1.40E-15 14.85249803 -0.59256631 ES(ph)PRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 40 1 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 0 ES(0.718)PRPLQLPGAEGPAIS(0.282)DGEEGGGEPGAGGGAAGAAGAGR 69.447 5.12E-06 5495800 512.95 350.1 358.64 275.99 393.05 337.01 237.73 263.91 447.83 343.5 TRUE FALSE FALSE 506.6979681 355.028717 364.8819788 307.9012624 372.9911918 315.4761486 257.9227803 271.5458195 407.7749632 334.5758205 1.514448855 1.061130827 1.090580838 0.920273503 1.114818134 0.942913771 0.77089486 0.811612205 1.218781927 1 8.386189377 -8.734109133 0.78183746 1.230868983 0.798725216 0.488822767 0.145719856 0.615933706 0.673650273 0.038856802 0.150631927 1.84E-09 8.734109133 -0.432143767 ES(ph)PSAAGPEDK ddPTM_HeLa_Romidepsin_16h_R1 1 ESPSAAGPEDK 11 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 ES(0.916)PS(0.084)AAGPEDK 99.732 0.019297 3798300 1576.1 1490.1 1552.9 784.52 1957.4 2524.3 2046.7 1349.1 1580.4 1839.6 TRUE FALSE FALSE 1556.889887 1511.077667 1579.927573 875.2298937 1857.506574 2363.005377 2220.546647 1388.13408 1439.045066 1791.806927 0.868893776 0.843326167 0.881751013 0.488462167 1.0366667 1.318783481 1.239277856 0.774711862 0.803125071 1 10.80719948 -8.530151791 24.99976251 0.890618248 1.132754026 0.299708856 0.189284055 181.081643 622434.2169 0.027542583 0.055175914 2.95E-09 8.530151791 0.242135779 ES(ph)PSLASR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPSLASR 8 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 ES(1)PSLASR 162.64 0.0030209 19535000 3678 3128.8 3828.1 2041.3 2482.4 2865.7 2353.5 2162.3 3540.8 3418.2 TRUE FALSE FALSE 3633.171121 3172.847329 3894.726475 2277.324711 2355.713865 2682.591019 2553.406231 2224.862739 3224.10198 3329.394671 1.091240745 0.952980239 1.169800177 0.684005633 0.7075502 0.805729354 0.766928071 0.668248423 0.968374824 1 11.70104418 -9.252689268 24.99971531 1.044628521 0.73208847 0.834131741 0.06904551 175.7210069 502047.8396 0.00980144 0.016094437 5.59E-10 9.252689268 -0.312540051 ES(ph)PSPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPSPAPKPR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 ES(0.956)PS(0.044)PAPKPR 97.965 0.0099581 14164000 3250.4 3912.5 3406.9 4119.4 3479.3 3676.3 3997.2 2366.9 4331.6 3899.6 TRUE FALSE FALSE 3210.782875 3967.580278 3466.195665 4595.70441 3301.738338 3441.396295 4336.722068 2435.382517 3944.170847 3798.28783 0.84532374 1.044570726 0.912567931 1.209941062 0.869270178 0.906038839 1.141757092 0.641179033 1.038407573 1 11.89113352 -7.237452449 24.30586942 0.956844223 0.641178493 0.416949627 0.117944623 3928.848839 3981004.272 0.015914692 1.283296222 5.79E-08 7.237452449 -0.31566573 FIQELSGS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 FIQELSGSSPK 11 0 I3L254;Q01664 I3L254 TFAP4 Transcription factor AP-4 1 0 FIQELS(0.001)GS(0.5)S(0.5)PK 177.81 1.31E-05 180890000 4963.6 4515.7 4063.3 2996.6 1678.7 1383.4 1214.2 1301 4521.4 4445.6 TRUE FALSE FALSE 4903.101734 4579.272143 4134.020032 3343.080991 1593.029675 1295.005205 1317.334118 1338.642382 4116.99466 4330.102671 1.132329209 1.057543548 0.9547164 0.772055825 0.367896513 0.299070323 0.304226994 0.309147954 0.950784536 1 12.08018552 -8.937623419 1.70219226 1.061912192 0.292510525 0.974748057 0.053085143 0.036947164 0.214914327 0.008771826 0.018500041 1.15E-09 8.937623419 -0.769401667 down ES(ph)SPFLSPLEASR ddPTM_HeLa_Romidepsin_16h_R1 2 ESSPFLSPLEASR 13 0 Q9UP95-3;Q9UP95-5;Q9UP95-2;Q9UP95-6;Q9UP95;Q9UP95-4 Q9UP95-3 SLC12A4 Solute carrier family 12 member 4 1 0 ES(0.922)S(0.078)PFLSPLEASR;ES(0.788)S(0.212)PFLSPLEASR ; 201.09 3.15E-16 14503700 3616.5 4277.7 4474.6 3829.1 4929.6 6168.4 3911.4 5341.3 4055.7 3668 TRUE FALSE FALSE 3572.420707 4337.921573 4552.478536 4271.838558 4678.024117 5774.259148 4243.634218 5495.842088 3692.948034 3572.704831 0.999920474 1.214184148 1.274238637 1.195687514 1.309378843 1.616215002 1.18779312 1.538286074 1.03365607 1 11.80280101 -9.567754052 0.703273877 0.988437095 1.42604996 0.642000112 0.119602706 0.265454574 0.264263641 0.025148667 0.049229447 2.71E-10 9.567754052 0.437612865 ES(ph)SPIPS(ph)PTSDRK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPIPSPTSDRK 13 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 0 ES(0.609)S(0.391)PIPS(0.637)PT(0.312)S(0.051)DRK 98.253 0.013273 5693800 2057.2 1786.1 2563 1120.9 1748.7 1474.1 1806.6 1756.6 2150.3 2332.4 TRUE FALSE FALSE 2032.126055 1811.244763 2607.60794 1250.503732 1659.457314 1379.909767 1960.052559 1807.42445 1957.971782 2271.803912 0.89449888 0.79727161 1.147813826 0.550445276 0.730457988 0.607407074 0.862773653 0.795589989 0.861857739 1 11.1496226 -9.256016775 24.99927553 0.948488813 0.713370043 0.482075349 0.119505899 288.5881041 1330446.864 0.017305568 0.028164896 5.55E-10 9.256016775 -0.23511877 ES(ph)SPIPSPTSDR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPIPSPTSDR 12 0 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 ES(0.499)S(0.499)PIPS(0.002)PTSDR 146.5 0.0014973 8319800 1717 1779.5 1777.1 1780.4 1542.1 1871.6 1763.6 1837.3 1967.9 1933.6 TRUE FALSE FALSE 1696.072544 1804.551848 1808.02968 1986.258225 1463.400883 1752.0108 1913.40014 1890.459377 1791.886095 1883.364793 0.900554449 0.958153117 0.959999723 1.054632768 0.777014038 0.930255682 1.015947705 1.003766973 0.951428051 1 10.87909675 ES(ph)SPLSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLSSR 8 0 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 1 0 ES(0.5)S(0.5)PLSSR 143.37 0.0087271 4850300 2667.5 2610.6 3702.6 2547.7 3570.1 4048.2 4848.4 2058.4 3994.3 3837.1 TRUE FALSE FALSE 2634.987484 2647.352095 3767.0422 2842.277061 3387.904475 3789.533085 5260.222975 2117.956556 3637.039804 3737.411589 0.705030051 0.708338387 1.00792811 0.760493457 0.906484179 1.013945881 1.407450812 0.566690745 0.973144038 1 11.86782374 -8.338783606 3.875728939 0.850596901 1.037726959 0.062307274 0.217088704 0.366687231 10.50786332 0.030324229 0.072569574 4.58E-09 8.338783606 0.187130059 ES(ph)SPLYSPTFS(ph)DSTSAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLYSPTFSDSTSAVK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 ES(0.432)S(0.559)PLY(0.05)S(0.217)PT(0.082)FS(0.553)DS(0.104)T(0.003)SAVK 90.884 0.026248 27631000 3155 3472.4 3068.9 3135.9 4358.5 4464.7 4246.4 4350.4 3940.3 3874.5 TRUE FALSE FALSE 3116.545646 3521.284538 3122.312917 3498.487513 4136.069481 4179.420079 4607.08911 4476.27196 3587.869699 3773.839931 0.825828785 0.933077344 0.827357009 0.92703654 1.095984344 1.107471476 1.220796111 1.186131908 0.950721219 1 11.88181752 -8.565260843 1.891802837 0.909009738 1.184169197 0.823028505 0.055805905 0.134160078 0.956012926 0.01118481 0.028516959 2.72E-09 8.565260843 0.275159459 ES(ph)SPLYSPTFSDSTSAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLYSPTFSDSTSAVK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 ES(0.914)S(0.086)PLYSPTFSDSTSAVK 174.04 4.65E-08 26589000 3534.6 3317.2 3210.7 3142.5 3145.5 3052 2461.5 3057.1 3814.4 3653.2 TRUE FALSE FALSE 3491.518936 3363.899629 3266.580887 3505.850636 2984.973398 2856.98705 2670.579749 3145.552365 3473.230511 3558.289337 0.981235252 0.945369898 0.918020031 0.985262946 0.838878774 0.802910269 0.750523495 0.884006911 0.976095585 1 11.79696811 -8.701555517 3.776792275 0.9810796 0.807962296 0.776653127 0.038720132 0.070726686 2.035039019 0.005809051 0.011864313 1.99E-09 8.701555517 -0.173117304 ES(ph)VSPEDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 ESVSPEDSEK 10 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 0 ES(0.674)VS(0.324)PEDS(0.002)EK 152.67 0.0035703 28519000 3518.9 2944.8 3761.3 1961.6 2498.3 2871.5 2586.3 1922.5 3746.8 3411.7 TRUE FALSE FALSE 3476.010293 2986.256972 3826.763849 2188.409422 2370.802429 2688.020417 2805.980257 1978.124504 3411.676824 3323.063542 1.046025828 0.898645763 1.151577091 0.658551783 0.713438789 0.80889829 0.844395607 0.595271345 1.026666141 1 11.69829816 -9.254616278 24.99988173 1.019949529 0.734911112 0.746492616 0.087415989 204.0464285 747626.9295 0.012356472 0.020195562 5.56E-10 9.254616278 -0.285038416 ES(ph)YSVYVYK ddPTM_HeLa_Romidepsin_16h_R1 1 ESYSVYVYK 9 0 P58876;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P58876;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BD;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-D;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 1 0 ES(0.569)YS(0.431)VYVYK 131.09 0.007716 19054000 2494.3 2178.4 1972.6 1964 3419.8 2566.7 2550.7 2175.8 2484.9 2318.8 TRUE FALSE FALSE 2463.898512 2209.067572 2006.932276 2191.086921 3245.274845 2402.696154 2767.356394 2238.75334 2262.64432 2258.557242 1.09091701 0.978087928 0.888590397 0.970126805 1.436879608 1.063819021 1.225276182 0.991231614 1.001809597 1 11.14118576 ESAAPAAAPTAEAPPPS(ph)VVTRPEPQALPSPAIR ddPTM_HeLa_Romidepsin_16h_R1 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 0 ESAAPAAAPT(0.006)AEAPPPS(0.347)VVT(0.347)RPEPQALPS(0.299)PAIR 69.092 1.41E-05 68984000 2639.6 2674.9 2264.9 2124.4 2471 2844.8 1958.7 2537.9 2342.6 2097.8 TRUE FALSE FALSE 2607.42754 2712.557312 2304.319634 2370.033124 2344.895649 2663.026461 2125.071929 2611.330132 2133.071989 2043.298854 1.276087213 1.327538215 1.127744789 1.159905277 1.14760288 1.303297585 1.040020125 1.27799716 1.043935392 1 10.99668451 -12.4011227 1.136366932 1.000411379 1.208698648 0.42103346 0.086615121 0.352997151 0.817888384 0.057543847 0.014773298 3.97E-13 12.4011227 0.208287269 ESAAPAAAPTAEAPPPSVVTRPEPQALPS(ph)PAIR ddPTM_HeLa_Romidepsin_16h_R1 1 ESAAPAAAPTAEAPPPSVVTRPEPQALPSPAIR 33 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 1 0 ESAAPAAAPT(0.016)AEAPPPS(0.096)VVT(0.096)RPEPQALPS(0.791)PAIR 59.636 0.00045845 85355000 2370.9 2654.7 2231.9 2720.8 3181.7 2730.6 2642.8 2868.1 2451.1 2713.8 TRUE FALSE FALSE 2342.002559 2692.072936 2270.745283 3035.391698 3019.325976 2556.123473 2867.279366 2951.083948 2231.867477 2643.295085 0.886016311 1.018453426 0.859058565 1.1483363 1.142258386 0.967021612 1.084736768 1.116441356 0.844350481 1 11.36812177 -9.255174551 24.99130738 0.94543825 1.087244446 0.573799121 0.071826452 322.7811153 1287619.362 0.01048804 0.017114711 5.56E-10 9.255174551 0.141806197 ESADPLGAWLQDAR ddPTM_HeLa_Romidepsin_16h_R1 1 ESADPLGAWLQDAR 14 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 215.77 3.79E-23 5564000 1038.5 1258.7 1215.6 1046.1 1218.9 1263.6 1073.5 1316.5 1352.8 1133.2 FALSE FALSE TRUE 1025.842363 1276.420012 1236.757008 1167.055004 1156.694985 1182.860038 1164.683063 1354.59085 1231.80218 1103.759301 0.929407672 1.156429677 1.120495209 1.057345567 1.047959445 1.071664843 1.055196602 1.227252037 1.116006161 1 10.10820988 -10.26692463 24.99891688 0.966664733 1.098526609 0.156656746 0.072152463 253.8757732 1157032.42 0.009637166 0.011179239 5.41E-11 10.26692463 0.131861876 ESAS(ph)PTIPNLDLLEAHTK ddPTM_HeLa_Romidepsin_16h_R1 2 ESASPTIPNLDLLEAHTK 18 0 O75151 O75151 PHF2 Lysine-specific demethylase PHF2 1 0 ES(0.205)AS(0.763)PT(0.032)IPNLDLLEAHTK;ES(0.039)AS(0.96)PT(0.001)IPNLDLLEAHTK ; 177.29 2.99E-10 75298000 15120.5 14249.2 14359.4 11567.2 11452.8 11383.5 10357.8 11841.7 17027.7 15359.3 TRUE FALSE FALSE 14936.20553 14449.80061 14609.31933 12904.65409 10868.32088 10656.13109 11237.59127 12184.32091 15504.69987 14960.26317 0.998391897 0.965878771 0.9765416 0.862595393 0.726479257 0.712295697 0.751162673 0.814445626 1.036392187 1 13.86884793 -9.074852954 2.305844241 0.99593686 0.747929838 0.932489204 0.030991341 0.048126309 0.504380454 0.004442768 0.008218655 8.42E-10 9.074852954 -0.248007022 ESASSSSSVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ESASSSSSVKK 11 1 Q9NPF5 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 0 1 ; ESASSSSSVK(1)K;ESASSSSSVK(1)K 232.88 1.53E-39 3012500 1171.07 1238.71 1456.96 1071.74 661.15 671.98 1845.85 104.08 2602.2 1718.2 FALSE TRUE FALSE 1156.796548 1256.148592 1482.317778 1195.659621 627.4090484 629.0426467 2002.636453 107.0913906 2369.452715 1673.560916 0.691218669 0.750584326 0.885726814 0.714440454 0.374894659 0.37587078 1.196631944 0.063990136 1.415815039 1 10.70870535 -16.52287875 0.058699156 2.441599567 3.76E-13 0.343992458 0.311551554 338.716916 1.56289257 72.2995954 14.08982324 3.00E-17 16.52287875 -2.441599567 ESDQTLAALLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 7 ESDQTLAALLSPK 13 0 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQT(0.002)LAALLS(0.998)PK;ESDQT(0.033)LAALLS(0.966)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK;ESDQTLAALLS(1)PK ;;;;;; 212.03 3.17E-23 1229942900 19280.44 18088.12 18695.43 17843.02 18061.05 19687.66 17723.5 19079.21 20011.33 19886.36 TRUE FALSE FALSE 19045.44258 18342.76503 19020.81612 19906.11393 17139.32722 18429.68207 19228.93365 19631.23684 18221.46653 19369.7095 0.983259072 0.946981937 0.981987681 1.027692952 0.884852053 0.951469203 0.992732165 1.013501872 0.940719659 1 14.2415147 -11.06608272 0.928670972 0.997207988 0.970478223 0 0.041603041 0.981587384 1.805710512 0.011366185 0.008469847 8.59E-12 11.06608272 -0.026729765 ESDSAEGDEAES(ph)PEQQVR ddPTM_HeLa_Romidepsin_16h_R1 2 ESDSAEGDEAESPEQQVR 18 0 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 0 ESDSAEGDEAES(1)PEQQVR;ESDSAEGDEAES(1)PEQQVR ; 232.73 4.62E-49 8200400 2390.68 1948.06 2373.6 2590.4 2795.2 2262.1 1887.43 2116.36 2766.13 2243.44 TRUE FALSE FALSE 2361.541473 1975.48484 2414.911512 2889.914236 2652.550514 2117.559111 2047.748257 2177.593538 2518.720405 2185.155105 1.080720296 0.90404788 1.10514421 1.32252133 1.213895758 0.969065814 0.937118034 0.996539574 1.152650628 1 11.09351997 -8.049449399 24.99300387 1.066749414 0.963394026 0.186140733 0.113505953 565.145715 285638.4359 0.017218148 0.043898758 8.92E-09 8.049449399 -0.103355388 ESEAVEWQQK ddPTM_HeLa_Romidepsin_16h_R1 2 ESEAVEWQQK 10 0 P26038 P26038 MSN Moesin 0 0 ; ; 192.91 3.89E-13 0 4679.4 4393.3 4422.8 4046.8 5511.8 5108.1 4915.7 5104.9 4833.1 4667.7 FALSE FALSE TRUE 4622.365673 4455.148993 4499.776979 4514.710057 5230.512279 4781.708896 5333.239435 5252.602227 4400.815431 4546.432481 1.016701709 0.979921952 0.989737997 0.993022568 1.150465183 1.051749677 1.173060297 1.155323927 0.96797114 1 12.15051921 -8.764311849 24.9999808 1.003298708 1.129757669 0.806246781 0.033641241 23.94211054 208378.4745 0.004562348 0.008541522 1.72E-09 8.764311849 0.126458961 ESEDDLNKES(ph)EEEVGPTK ddPTM_HeLa_Romidepsin_16h_R1 2 ESEDDLNKESEEEVGPTK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 ESEDDLNKES(1)EEEVGPTK;ESEDDLNKES(1)EEEVGPTK ; 82.01 0.0044482 19284400 5280.9 4483.1 5220.9 2828.3 5392.1 6780.6 5111.9 6622.8 4354.8 5598.4 TRUE FALSE FALSE 5216.53436 4546.213199 5311.767574 3155.321354 5116.921016 6347.341543 5546.104658 6814.420269 3965.295781 5452.952761 0.956643967 0.83371586 0.974108489 0.578644542 0.938376186 1.164019169 1.017082836 1.24967528 0.727183226 1 12.41282194 -8.268640509 23.08694667 0.93424221 1.130941471 0.377998906 0.14629308 178.7915156 573212.6792 0.01945592 0.044468197 5.39E-09 8.268640509 0.196699261 ESEDDPES(ph)EPDDHEK ddPTM_HeLa_Romidepsin_16h_R1 2 ESEDDPESEPDDHEK 15 0 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 1 0 ESEDDPES(1)EPDDHEK;ESEDDPES(1)EPDDHEK ; 158.92 0.00012174 34038000 10605.7 9104.2 9259.1 9185.9 10073.5 9513.4 9349.7 10083.7 10893.4 9043.6 TRUE FALSE FALSE 10476.43365 9232.369167 9420.250751 10248.01698 9559.411706 8905.524443 10143.86328 10375.45595 9919.067021 8808.645968 1.189335306 1.048103102 1.069432327 1.163404343 1.08523055 1.010998112 1.151580313 1.17787183 1.126060357 1 13.10470456 -12.59517535 1.392074457 1.000065592 1.118552838 0 0.067965319 0.388940299 1.353359231 0.042797816 0.009940367 2.54E-13 12.59517535 0.118487246 ESEDKPEIEDVGS(ph)DEEEEK ddPTM_HeLa_Romidepsin_16h_R1 5 ESEDKPEIEDVGSDEEEEK 19 1 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 1 0 ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK;ESEDKPEIEDVGS(1)DEEEEK ;;;; 149.64 1.24E-05 600614500 11283.11 11503.24 12667 5976.79 12715.64 16252.06 12603.46 13653.86 12210.09 13615.82 TRUE FALSE FALSE 11145.58712 11665.18291 12887.46382 6667.854581 12066.71344 15213.60582 13673.99758 14048.9129 11117.98897 13262.07903 0.840410247 0.879589308 0.971752905 0.502775965 0.909865897 1.147150894 1.031059877 1.059329601 0.838329265 1 13.69501934 -8.33245688 7.456529399 0.889574645 1.073989698 0.354950914 0.134680345 0.290030736 27.06180971 0.020482649 0.04606085 4.65E-09 8.33245688 0.184415053 ESEDKPEIEDVGS(ph)DEEEEKK ddPTM_HeLa_Romidepsin_16h_R1 4 ESEDKPEIEDVGSDEEEEKK 20 2 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 1 0 ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK;ESEDKPEIEDVGS(1)DEEEEKK ;;; 119.69 0.00018848 463742000 6985.7 7052.2 7848.3 4266.02 8703 10194.9 8258.5 9271 7906 8851.5 TRUE FALSE FALSE 6900.555601 7151.481057 7984.896369 4759.277305 8258.853435 9543.478793 8959.976784 9539.241758 7198.867559 8621.536754 0.800385801 0.829490294 0.926156971 0.552021924 0.957932869 1.106934769 1.039255186 1.106443321 0.834986588 1 13.07372933 -8.518001472 24.99929649 0.871911088 1.071835253 0.480186801 0.11551988 184.5324129 945850.2711 0.018834976 0.038525798 3.03E-09 8.518001472 0.199924165 ESEITDEDIDGILER ddPTM_HeLa_Romidepsin_16h_R1 4 ESEITDEDIDGILER 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 0 ;;; ;;; 264.3 2.73E-83 15040100 4722.94 4205.66 4395.99 3881.09 3466.66 3809.25 3098.71 3326.89 4436.2 4057.43 FALSE FALSE TRUE 4665.374991 4264.867392 4472.500362 4329.839887 3289.743404 3565.851219 3361.91435 3423.148313 4039.415161 3952.017384 1.180504673 1.079162103 1.131700579 1.09560244 0.832421289 0.902286319 0.850683088 0.866177443 1.022114725 1 11.94837358 -8.765765602 24.99999838 1.091236309 0.864833829 0.822105759 0.05052547 43.34032651 250453.1186 0.010154531 0.018883176 1.71E-09 8.765765602 -0.22640248 ESEKQQDS(ph)QPEEVMDVLEMVENVK ddPTM_HeLa_Romidepsin_16h_R1 3 ESEKQQDSQPEEVMDVLEMVENVK 24 1 Q9H307 Q9H307 PNN Pinin 1 0 ES(0.046)EKQQDS(0.954)QPEEVMDVLEMVENVK;ES(0.029)EKQQDS(0.971)QPEEVMDVLEMVENVK;ES(0.034)EKQQDS(0.966)QPEEVMDVLEMVENVK ;; 63.726 0.0017925 46380000 3819.2 3199.21 3558.19 3627.5 3088.08 3157.38 3098.37 3223.4 3552.9 3509.6 TRUE FALSE FALSE 3772.650121 3244.248562 3620.118804 4046.928618 2930.483754 2955.633608 3361.54547 3316.663993 3235.119726 3418.420086 1.103623904 0.949049116 1.059003491 1.183859361 0.857262619 0.864619776 0.983362309 0.970233005 0.946378632 1 11.73911398 -8.740623204 24.99961307 1.051021248 0.919601091 0.374532904 0.076135711 179.1088852 215103.4351 0.010628373 0.021238749 1.82E-09 8.740623204 -0.131420157 ESENSGDSGYPS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 ESENSGDSGYPSEK 14 0 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 0 ES(0.006)ENSGDS(0.009)GYPS(0.984)EK 115.58 0.0047487 8246100 1996.2 1812.6 2699.1 1193.3 2099.2 3087.1 2266.1 2672.9 2789.1 2763.3 TRUE FALSE FALSE 1971.869547 1838.11783 2746.076703 1331.274961 1992.069991 2889.844273 2458.582477 2750.236144 2539.635911 2691.509068 0.732626009 0.682932059 1.020273993 0.494620277 0.740131257 1.073689221 0.913458738 1.021819387 0.943573232 1 11.39419957 -8.259079272 24.74759182 0.830749371 0.994036074 0.244427356 0.156069345 263.9494618 2767692.468 0.024327896 0.058899305 5.51E-09 8.259079272 0.163286704 ESEQES(ph)EEEILAQKK ddPTM_HeLa_Romidepsin_16h_R1 2 ESEQESEEEILAQKK 15 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 ESEQES(1)EEEILAQKK;ESEQES(1)EEEILAQKK ; 202.41 5.18E-18 23765000 7685.4 7514.5 6812.8 5379.4 5940.7 6873.5 6340.8 5802.3 7290.2 7374.2 TRUE FALSE FALSE 7591.727389 7620.289328 6931.373926 6001.391539 5637.523911 6434.305533 6879.387394 5970.180396 6638.146253 7182.617221 1.05695837 1.060934906 0.965020648 0.835543835 0.784884359 0.895816293 0.957782822 0.831198463 0.924196021 1 12.81029392 -9.464787317 3.906995913 1.029916746 0.864917157 0.605334682 0.056571544 0.093787509 2.873912067 0.007852633 0.011990082 3.43E-10 9.464787317 -0.164999589 ESES(ph)ESDETPPAAPQLIK ddPTM_HeLa_Romidepsin_16h_R1 1 ESESESDETPPAAPQLIK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 ES(0.002)ES(0.996)ES(0.001)DETPPAAPQLIK 242.01 1.02E-50 7924900 2600.5 2661.1 2226.5 1411.4 1552.7 1772.5 1174.9 1551.2 3018.4 2835.6 TRUE FALSE FALSE 2568.804106 2698.563036 2265.251299 1574.592709 1473.459925 1659.24297 1274.695977 1596.081525 2748.426744 2761.930703 0.930075509 0.97705675 0.820169491 0.570105798 0.5334891 0.600754743 0.461523519 0.577886159 0.995110681 1 11.43146141 -9.39519173 2.278564757 0.96738565 0.539390475 0.96348699 0.039426535 0.039773806 0.404416271 0.006541064 0.010633834 4.03E-10 9.39519173 -0.427995175 ESESES(ph)DETPPAAPQLIK ddPTM_HeLa_Romidepsin_16h_R1 1 ESESESDETPPAAPQLIK 18 0 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 ESES(0.005)ES(0.993)DET(0.002)PPAAPQLIK 155.37 6.93E-06 9537100 3365.8 2956.7 2932.3 2192.5 2314 2419.9 1820.3 1850.6 3538 3325 TRUE FALSE FALSE 3324.776335 2998.3245 2983.335451 2446.007166 2195.907945 2265.2762 1974.916237 1904.144191 3221.552419 3238.616021 1.026604054 0.925804257 0.921176031 0.755263097 0.678038993 0.699458097 0.609802528 0.58794997 0.994731206 1 11.66116171 -9.162682022 0.952915683 1.014211898 0.614596161 0.96671473 0.02964068 0.06113526 0.109361497 0.005380858 0.012533367 6.88E-10 9.162682022 -0.399615737 ESFESQFLADTER ddPTM_HeLa_Romidepsin_16h_R1 1 ESFESQFLADTER 13 0 A0A590UJ56;A0A590UJC4;A0A590UJR3;A0A590UJ21;A0A0C4DGX4;A0A590UJ50;Q13616 A0A590UJ56 CUL1 Cullin-1 0 0 150.51 0.0078184 1753300 554.53 606.77 496.2 345.31 496.51 439.2 263.74 454.39 588.91 442.83 FALSE FALSE TRUE 547.7711751 615.312124 504.8361529 385.2363669 471.171242 411.1365375 286.142069 467.5370577 536.2364146 431.3252128 1.269972538 1.426561921 1.170430427 0.89314595 1.092380478 0.953193844 0.66340214 1.083954853 1.243229931 1 8.75263224 -9.2659599 24.23054931 1.160841929 0.931511566 0.4357003 0.154340186 249.8072591 1338998.706 0.026939696 0.042042564 5.42E-10 9.2659599 -0.229330363 ESGADGASTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 ESGADGASTSPR 12 0 O75528;O75528-2 O75528 TADA3 Transcriptional adapter 3 1 0 ESGADGAST(0.081)S(0.918)PR;ESGADGAST(0.241)S(0.759)PR ; 157.03 0.00113 41646000 10374.1 11628 18709.4 11296.2 8526.2 9325.1 16125.5 2946.9 18647.9 17014.2 TRUE FALSE FALSE 10247.65648 11791.69929 19035.02926 12602.31979 8091.076198 8729.256205 17495.19957 3032.163902 16979.98512 16572.16863 0.618365448 0.711536284 1.148614263 0.760450854 0.488232794 0.526741937 1.055697655 0.182967237 1.024608517 1 14.01647479 -8.95185193 8.020283875 0.833199608 0.598473329 0.265115499 0.249788194 0.357028512 52.22233802 0.037058206 0.067255658 1.12E-09 8.95185193 -0.234726278 ESGS(ph)PYSVLVDTK ddPTM_HeLa_Romidepsin_16h_R1 2 ESGSPYSVLVDTK 13 0 Q9Y2D9;D6RF85 Q9Y2D9 ZNF652 Zinc finger protein 652 1 0 ES(0.026)GS(0.686)PY(0.001)S(0.276)VLVDT(0.011)K;ES(0.155)GS(0.8)PYS(0.045)VLVDTK ; 205.62 1.40E-16 15470800 5208.7 4810.6 5390.2 3738.6 3125.6 3480.5 2882.6 3153 5747.2 5478.4 TRUE FALSE FALSE 5145.214361 4878.323753 5484.01417 4170.874523 2966.088969 3258.107283 3127.447972 3244.22708 5233.156038 5336.070378 0.964232852 0.914216532 1.027725232 0.78163784 0.555856418 0.610581767 0.586095713 0.607980564 0.980713459 1 12.38156198 -9.006386059 3.141558346 0.97913849 0.59189689 0.967816859 0.033219808 0.02984526 0.607010096 0.005109696 0.009347251 9.85E-10 9.006386059 -0.3872416 ESGVAGDPWKEETDT(ph)DLEVVLEK ddPTM_HeLa_Romidepsin_16h_R1 1 ESGVAGDPWKEETDTDLEVVLEK 23 1 Q1ED39 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 0 ESGVAGDPWKEET(0.063)DT(0.937)DLEVVLEK 102.46 3.40E-06 0 848.52 846.49 1149 3116.4 1133.3 1036.4 723.72 884.18 859.95 1064.6 TRUE FALSE FALSE 838.1779119 858.4069084 1168.997863 3476.732831 1075.463472 970.1773848 785.1927587 909.7623533 783.0339182 1036.941539 0.808317423 0.827825752 1.127351755 3.35287256 1.037149571 0.935614351 0.757219891 0.877351634 0.75513796 1 10.01811884 -9.519087642 24.98558345 0.90448491 1.404541526 0.116441528 0.699597763 295.7529788 1949188.328 0.112067705 0.160551316 3.03E-10 9.519087642 0.500056616 ESGVVAVS(ph)PEKSES(ph)PQKEDGLSSQLK ddPTM_HeLa_Romidepsin_16h_R1 2 ESGVVAVSPEKSESPQKEDGLSSQLK 26 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 2 0 ESGVVAVS(0.972)PEKS(0.245)ES(0.783)PQKEDGLSSQLK;ESGVVAVS(0.94)PEKS(0.323)ES(0.722)PQKEDGLS(0.012)S(0.003)QLK ; 116.52 6.24E-07 28048000 9763.7 8395.4 9123.1 8549.6 8133.7 8422.3 7208.6 7420.7 10040.7 9923 TRUE FALSE FALSE 9644.696269 8513.590662 9281.883729 9538.144979 7718.606938 7884.142212 7820.898304 7635.406247 9142.634645 9665.19903 0.997878703 0.88085001 0.960340672 0.986854482 0.798597827 0.815724765 0.809181299 0.789989552 0.945933407 1 13.23858373 -8.778957935 0.640326431 0.999013003 0.768089015 0.688863958 0.046985847 0.32046494 0.223361135 0.009004773 0.038296166 1.66E-09 8.778957935 -0.230923988 ESGVVAVS(ph)PEKSESPQKEDGLSSQLK ddPTM_HeLa_Romidepsin_16h_R1 1 ESGVVAVSPEKSESPQKEDGLSSQLK 26 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 ES(0.002)GVVAVS(0.697)PEKS(0.133)ES(0.133)PQKEDGLS(0.016)S(0.018)QLK 42.806 0.027663 12164000 1626.3 1569.5 1601.5 1610.2 1337.3 1310.7 1160.8 1102.7 2101.7 2021 TRUE FALSE FALSE 1606.47803 1591.595462 1629.373436 1796.3789 1269.052591 1226.9505 1259.398323 1134.604885 1913.718688 1968.494129 0.816094906 0.808534523 0.82772583 0.912565028 0.644681928 0.62329396 0.639777536 0.576382153 0.972173938 1 10.94287669 -6.402988491 0.142170117 1.068892125 6.13E-15 0.822745117 0.061191583 11.7240081 0.21371231 0.222112858 2.382551414 3.95E-07 6.402988491 -1.068892125 ESIES(ph)EIRR ddPTM_HeLa_Romidepsin_16h_R1 2 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 0 ES(0.012)IES(0.988)EIRR;ESIES(1)EIRR ; 83.045 0.016226 3616200 1235.91 1305.2 1436.06 1160.98 1301.22 1255.34 1161.3 1151.01 1522.72 1363.51 TRUE FALSE FALSE 1220.846254 1323.57464 1461.054022 1295.21797 1234.813888 1175.127825 1259.940793 1184.312658 1386.524109 1328.085814 0.919252537 0.996603251 1.100120193 0.975251717 0.929769654 0.884828234 0.948689294 0.891744077 1.044001897 1 10.37513265 -8.671918126 4.263037605 0.976229003 0.911988814 0.365034194 0.051678197 0.257702736 8.613519586 0.008144418 0.016635356 2.13E-09 8.671918126 -0.064240189 ESIESEIRR ddPTM_HeLa_Romidepsin_16h_R1 4 ESIESEIRR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 ;;; ;;; 182.76 5.00E-05 84622900 13812.6 12232.1 11863.5 13512.3 13100.2 13957.4 11786.8 12824.1 14231.3 12785.5 FALSE FALSE TRUE 13644.24672 12404.30382 12069.97924 15074.6557 12431.64791 13065.56719 12787.9705 13195.1451 12958.41689 12453.33087 1.095630307 0.996063138 0.96921694 1.210491865 0.998258863 1.049162455 1.026871496 1.059567536 1.040558307 1 13.60424405 -12.6540906 1.497646242 1.000037279 1.056067669 0.014524617 0.065001563 0.795223822 3.21148033 0.043923119 0.009930147 2.22E-13 12.6540906 0.05603039 ESLESEAELEGLQDAPAGPQVSEE ddPTM_HeLa_Romidepsin_16h_R1 1 ESLESEAELEGLQDAPAGPQVSEE 24 0 Q8IV38 Q8IV38 ANKMY2 Ankyrin repeat and MYND domain-containing protein 2 0 0 106.89 4.94E-06 937840 216.06 170.97 364.17 172.03 378.52 354.08 144.42 307.43 183.41 266.77 FALSE FALSE TRUE 213.4265776 173.3769201 370.5082261 191.920918 359.2027119 331.4554307 156.6870312 316.325002 167.0053502 259.8392769 0.821379201 0.667246777 1.425913089 0.738613963 1.382403446 1.275617122 0.603015191 1.21738717 0.642725581 1 8.021475713 -9.784156195 24.99967236 0.894664212 1.087659337 0.212471292 0.272363402 383.3919927 421917.9509 0.04027842 0.052956266 1.64E-10 9.784156195 0.192995125 ESLPPAAEPS(ph)PVSK ddPTM_HeLa_Romidepsin_16h_R1 3 ESLPPAAEPSPVSK 14 0 Q9NWT1 Q9NWT1 PAK1IP1 p21-activated protein kinase-interacting protein 1 1 0 ES(0.002)LPPAAEPS(0.926)PVS(0.072)K;ESLPPAAEPS(0.963)PVS(0.037)K;ES(0.022)LPPAAEPS(0.97)PVS(0.008)K ;; 184.99 4.64E-09 142071000 18553.6 17876.9 17823.5 14429.7 16921.7 18401.5 15322.9 16465.5 19462.1 18717 TRUE FALSE FALSE 18327.46159 18128.57147 18133.71054 16098.12981 16058.12251 17225.70354 16624.42674 16941.90326 17721.36103 18230.72964 1.005305983 0.994396375 0.994678266 0.883021696 0.880827198 0.944871866 0.911890367 0.929304729 0.972059889 1 14.15408468 -9.304048333 8.418394969 1.00136762 0.91043552 0.804379985 0.02034711 0.090692044 16.93807583 0.002807162 0.004305399 4.97E-10 9.304048333 -0.090932101 ESLPPAAEPS(ph)PVSKEQSK ddPTM_HeLa_Romidepsin_16h_R1 2 ESLPPAAEPSPVSKEQSK 18 1 Q9NWT1 Q9NWT1 PAK1IP1 p21-activated protein kinase-interacting protein 1 1 0 ESLPPAAEPS(0.993)PVS(0.006)KEQS(0.001)K;ESLPPAAEPS(0.751)PVS(0.21)KEQS(0.038)K ; 95.662 0.001413 21646500 5582.5 5048.5 3976.9 7880.2 4837.7 4890.4 4923.3 4549.1 5559.3 4983.4 TRUE FALSE FALSE 5514.458343 5119.572916 4046.116276 8791.345801 4590.814117 4577.919223 5341.484979 4680.721031 5062.062284 4853.93055 1.136081014 1.05472727 0.83357523 1.811180797 0.94579312 0.943136532 1.100445283 0.964315617 1.04287901 1 12.24493775 ESLS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 ESLSPGK 7 0 E7ETM8;E7EUA0;Q0ZGT2-4;Q0ZGT2-2;Q0ZGT2;H7BXY5 E7ETM8 NEXN Nexilin 1 0 ES(0.005)LS(0.995)PGK 120.31 0.027275 13835000 4885.2 5695.5 9613.1 4344.8 5140.4 6633 10905 2184.5 10302 9926.1 TRUE FALSE FALSE 4825.657303 5775.681398 9780.411973 4847.166219 4878.066207 6209.172707 11831.27043 2247.705061 9380.563318 9668.218491 0.499125801 0.597388382 1.011604359 0.501350505 0.504546542 0.642225112 1.223728078 0.232483892 0.970247345 1 13.23903436 -12.49507833 1.234430299 1.000426559 0.651930521 0.201509069 0.265310944 0.600911732 1.635503336 0.176741253 0.042757545 3.20E-13 12.49507833 -0.348496038 ESLT(ph)PGREENPSSVLAQER ddPTM_HeLa_Romidepsin_16h_R1 3 ESLTPGREENPSSVLAQER 19 1 A0A494C0P1;P04150-7;P04150-5;P04150-2;P04150-6;P04150-10;P04150;P04150-3;D6RDA9;Q3MSN4 A0A494C0P1 NR3C1 Glucocorticoid receptor 1 0 ES(0.02)LT(0.98)PGREENPSSVLAQER;ES(0.015)LT(0.984)PGREENPSSVLAQER;ES(0.027)LT(0.966)PGREENPS(0.005)S(0.002)VLAQER ;; 82.709 0.0026826 23349100 3498.92 3000.31 3103.73 2892.45 3065.07 3475.01 2940.98 2890.65 3889.92 3612.2 TRUE FALSE FALSE 3456.273817 3042.548443 3157.749119 3226.888678 2908.648041 3252.968076 3190.786768 2974.286397 3541.995813 3518.354523 0.982355187 0.8647646 0.897507371 0.917158478 0.826706923 0.924570862 0.906897456 0.845362904 1.006719417 1 11.78068515 -10.30836035 6.258635085 0.991984427 0.885465822 0.748716359 0.029977365 0.074532417 7.43579701 0.004827486 0.005534793 4.92E-11 10.30836035 -0.106518605 ESNYFGLS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 3 ESNYFGLSPEER 12 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 0 ESNYFGLS(1)PEER;ESNYFGLS(1)PEER;ESNYFGLS(1)PEER ;; 196.67 1.02E-10 80920700 8858.6 8451.9 7951.1 7030.69 7712.97 7108.7 5684.2 6684.87 9252.2 8626.3 TRUE FALSE FALSE 8750.627976 8570.88607 8089.48556 7843.611458 7319.34836 6654.477012 6167.015806 6878.286166 8424.660059 8402.187482 1.041470212 1.020077937 0.962783272 0.933520167 0.871124142 0.791993398 0.73397741 0.818630408 1.00267461 1 13.03654926 -8.763108083 1.094985374 1.019722693 0.766868043 0.936526389 0.025645585 0.083815235 0.195664242 0.004454232 0.013086082 1.73E-09 8.763108083 -0.25285465 ESNYFGLS(ph)PEERR ddPTM_HeLa_Romidepsin_16h_R1 2 ESNYFGLSPEERR 13 1 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 0 ESNYFGLS(1)PEERR;ESNYFGLS(1)PEERR ; 101.08 0.0035948 9664900 6548.1 7493.7 5399 7963.5 5683.7 5211.4 4512.6 4937.5 7289.5 6168.6 TRUE FALSE FALSE 6468.289239 7599.196505 5492.96733 8884.277339 5393.63958 4878.408359 4895.900131 5080.358772 6637.508863 6008.338883 1.076552 1.264774949 0.914223954 1.478657831 0.897692305 0.811939615 0.814850864 0.845551303 1.104716127 1 12.55275047 -8.539518244 24.99990858 1.078125103 0.828458869 0.456999289 0.151555772 181.2573089 272328.1065 0.0211649 0.04233806 2.89E-09 8.539518244 -0.249666235 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGR ddPTM_HeLa_Romidepsin_16h_R1 4 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGR 40 1 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 0 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ES(0.191)PRPLQLPGAEGPAIS(0.809)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGR ;;; 130.43 3.50E-23 575696600 4551.3 4460.88 3996.94 3201.96 3900.44 3399.36 2666.23 3366.11 4656.8 4587.2 TRUE FALSE FALSE 4495.827005 4523.680386 4066.505064 3572.185681 3701.385992 3182.151867 2892.69951 3463.503082 4240.284145 4468.023883 1.006222689 1.012456626 0.910135033 0.799500131 0.828416788 0.712205653 0.647422571 0.775175597 0.949028979 1 12.12542118 -9.116717011 1.039781302 1.006306746 0.708666848 0.874094257 0.043945406 0.097536518 0.207929332 0.006697298 0.015428577 7.64E-10 9.116717011 -0.297639899 ESPRPLQLPGAEGPAIS(ph)DGEEGGGEPGAGGGAAGAAGAGRR ddPTM_HeLa_Romidepsin_16h_R1 2 ESPRPLQLPGAEGPAISDGEEGGGEPGAGGGAAGAAGAGRR 41 2 Q6PKG0;A0A0B4J210 Q6PKG0 LARP1 La-related protein 1 1 0 ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR;ESPRPLQLPGAEGPAIS(1)DGEEGGGEPGAGGGAAGAAGAGRR ; 84.183 1.14E-09 88135000 1913.8 2014.64 1547.96 2281.78 1436.29 1486.38 1147.75 1222.15 1787.64 1941.22 TRUE FALSE FALSE 1890.473869 2043.002155 1574.901594 2545.61014 1362.990762 1391.405115 1245.239856 1257.510982 1627.749001 1890.786825 0.999834484 1.080503697 0.832934509 1.346323185 0.720859033 0.735886826 0.658582893 0.66507285 0.860884464 1 10.884771 -8.562720867 24.99913868 1.015138629 0.691162706 0.591996402 0.132345857 65.6058013 41164.45198 0.015777245 0.031554521 2.74E-09 8.562720867 -0.323975923 ESPSSTT(ph)PPIEISSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ESPSSTTPPIEISSSR 16 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 0 ES(0.004)PS(0.001)S(0.002)T(0.014)T(0.322)PPIEIS(0.014)S(0.322)S(0.322)R 128.85 0.0044069 9115700 1802.7 1787.1 1615.5 1567.7 1847.3 1680.6 1698.8 1940.3 1987.1 1678.8 TRUE FALSE FALSE 1780.727999 1812.258841 1643.6171 1748.96485 1753.025388 1573.215084 1843.09603 1996.439519 1809.368799 1635.184534 1.089007364 1.108290106 1.005156951 1.069582554 1.072065783 0.962102473 1.127148644 1.220926127 1.106522696 1 10.67523774 -7.515843762 5.108947569 1.044595517 1.203154208 0.555280717 0.046959978 0.087434675 6.780500625 0.006582289 0.031755521 3.05E-08 7.515843762 0.158558691 ESPSVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ESPSVKR 7 1 Q02078-8;Q02078-7;Q02078-4;Q02078-6;Q02078-3;Q02078-5;Q02078-2;Q02078;A0A0D9SGF3;D8L7E9;A0A0D9SFD0;A0A0R4J2G5;A0A1B0GV32;A0A0D9SGI5;Q06413-4;Q06413-3;Q06413-6;Q06413-2;Q06413;Q06413-5 Q02078-8;A0A0D9SGF3 MEF2A;MEF2C Myocyte-specific enhancer factor 2A;Myocyte-specific enhancer factor 2C 0 1 ; ESPSVK(1)R;ESPSVK(1)R 116.9 0.0038267 17305600 4649.5 5056.3 4292 4095.7 5476.7 6276 7706.9 2056.92 6124.3 4805 FALSE TRUE FALSE 4592.830106 5127.482724 4366.70046 4569.264105 5197.203563 5874.983855 8361.523894 2116.433735 5576.527269 4680.165407 0.98133927 1.095577245 0.933022678 0.976303978 1.110474334 1.255294064 1.78658726 0.452213448 1.191523543 1 12.1923438 -8.533838482 3.638060728 0.994306954 1.223733079 0.019543928 0.310950564 0.376828353 10.76120873 0.039560812 0.087188907 2.93E-09 8.533838482 0.229426124 ESQLAHIKDEPPPLS(ph)PAPLTPATPSSLDPFFSR ddPTM_HeLa_Romidepsin_16h_R1 1 ESQLAHIKDEPPPLSPAPLTPATPSSLDPFFSR 33 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 ESQLAHIKDEPPPLS(0.669)PAPLT(0.286)PAT(0.034)PS(0.006)S(0.003)LDPFFS(0.001)R 57.67 0.00050162 48648000 1497.5 1613 1129.9 1739.2 2049.1 2033.7 1974.5 2148.6 2035.1 1889.6 TRUE FALSE FALSE 1479.247894 1635.707856 1149.565436 1940.294487 1944.526781 1903.753133 2142.213981 2210.766351 1853.075559 1840.50792 0.803717212 0.888726334 0.624591409 1.054216864 1.056516389 1.034362913 1.163925435 1.201171876 1.006828354 1 10.84588824 -9.021495231 24.74222954 0.882052117 1.104809511 0.537422248 0.110464056 465.506777 535824.4039 0.017957748 0.029975466 9.52E-10 9.021495231 0.222757394 ESRPGLVTVTSSQST(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 2 ESRPGLVTVTSSQSTPAK 18 1 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 0 ESRPGLVTVTSSQS(0.01)T(0.99)PAK;ESRPGLVTVTSSQS(0.06)T(0.94)PAK ; 122.3 0.00083028 18737400 7341.9 6532.6 8519.5 4361.6 4683.5 4875.7 4329.7 4078.1 7067.7 6756.2 TRUE FALSE FALSE 7252.414099 6624.566114 8667.778324 4865.908714 4444.483518 4564.158506 4697.46461 4196.093389 6435.547211 6580.67295 1.102077881 1.006670011 1.31715683 0.739424182 0.675384349 0.693570177 0.713827392 0.63763895 0.977946672 1 12.68401941 -9.110708474 7.223529148 1.063713308 0.686429134 0.818748034 0.091587413 0.078875385 4.592410825 0.013071527 0.021768608 7.75E-10 9.110708474 -0.377284174 ESS(ph)IDDLMKS(ph)LDK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSIDDLMKSLDK 13 1 P33763;P33763-2 P33763 S100A5 Protein S100-A5 2 0 ES(0.192)S(0.808)IDDLMKS(1)LDK 75.589 0.0042621 0 2250.2 2253.5 2005.8 878.77 2272.7 2241.7 1798.9 2197.4 2514.6 2389.4 TRUE FALSE FALSE 2222.773697 2285.224832 2040.710108 980.3775221 2156.715638 2098.462605 1951.698521 2260.978302 2289.687878 2327.323044 0.955077424 0.981911316 0.876848667 0.421246859 0.926693715 0.901663656 0.838602327 0.97149311 0.983828989 1 11.18445576 -9.623542432 5.199295303 0.97784446 0.8090943 0.234849943 0.142146125 0.22936472 9.893858979 0.022269635 0.03167784 2.38E-10 9.623542432 -0.16875016 ESS(ph)PIPS(ph)PTSDRK ddPTM_HeLa_Romidepsin_16h_R1 3 ESSPIPSPTSDRK 13 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 0 ES(0.083)S(0.917)PIPS(0.958)PT(0.024)S(0.017)DRK;ES(0.224)S(0.776)PIPS(0.794)PT(0.082)S(0.125)DRK;ES(0.42)S(0.58)PIPS(0.537)PT(0.265)S(0.198)DRK ;; 143.94 0.00071556 40814000 8697.6 8857.5 8441.3 7440.5 8492.9 8316.3 7004.1 7197 10227.8 9710.6 TRUE FALSE FALSE 8591.590306 8982.196117 8588.217286 8300.805619 8059.475622 7784.91527 7599.028079 7405.23384 9312.999952 9458.317212 0.908363519 0.94966112 0.908006899 0.877619711 0.852104602 0.823076145 0.80342284 0.782933547 0.984636034 1 13.20736781 -4 0.124842926 1.041325754 0.165642882 0.951704237 0.015585131 15.39455729 0.130958228 0.076283303 2.367170601 1.00E-04 4 -0.875682872 ESS(ph)PIPSPTSDRK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPIPSPTSDRK 13 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 ES(0.177)S(0.823)PIPSPTSDRK 95.822 0.0049598 10191000 2821.8 2843.6 2861.6 2175.7 2848.6 2619 2780.5 2655.2 2871.2 2687.3 TRUE FALSE FALSE 2787.406816 2883.632275 2911.404948 2427.264671 2703.225312 2451.654352 3016.675601 2732.024023 2614.392681 2617.483559 1.064918558 1.101681142 1.112291589 0.927327571 1.032757323 0.93664556 1.152509857 1.043759765 0.998819142 1 11.35396476 -12.42067312 1.226531146 1.000733808 1.047590435 0.071484679 0.067426815 1.119498297 3.083289585 0.042471692 0.011420366 3.80E-13 12.42067312 0.046856627 ESS(ph)PLSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLSSR 8 0 A0A0A0MS66;Q14693-6;Q14693;Q14693-2;Q14693-4;Q14693-3;Q14693-5;Q14693-7 A0A0A0MS66 LPIN1 Phosphatidate phosphatase LPIN1 1 0 ES(0.028)S(0.972)PLS(0.001)SR 128.6 0.012514 4709600 1995 1992.1 1992.5 1455.9 2203 2916.9 2900.1 1246.8 2024.8 2150.6 TRUE FALSE FALSE 1970.684173 2020.144836 2027.178627 1624.238008 2090.572689 2730.519504 3146.434422 1282.874191 1843.696817 2094.727102 0.940783251 0.964395235 0.96775309 0.775393609 0.998016729 1.303520397 1.502073668 0.612430225 0.880160864 1 11.03254659 -8.426358811 7.089863498 0.955373247 1.173994203 0.149432798 0.219167328 0.327539372 20.92783179 0.028391356 0.063727643 3.75E-09 8.426358811 0.218620956 ESS(ph)PLY(ph)SPTFSDSTSAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLYSPTFSDSTSAVK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 ES(0.169)S(0.831)PLY(0.814)S(0.066)PT(0.092)FS(0.022)DS(0.005)TSAVK 114.54 0.003245 3860900 1177.5 1519.4 1196.8 1035.5 1253.9 1308.4 1199.8 1506.5 1413.3 1157.2 TRUE FALSE FALSE 1163.148177 1540.790153 1217.629802 1155.229382 1189.908804 1224.797463 1301.710982 1550.088201 1286.890908 1127.135777 1.031950365 1.366996048 1.080286711 1.024924774 1.055692516 1.086645893 1.154883918 1.375245318 1.141735481 1 10.1384456 -4.000011212 0.822818445 1.047798065 98.10867412 0.301892898 0.107150644 391.307877 1.159640323 0.017389917 70985.67623 1.00E-04 4.000011212 97.06087606 ESS(ph)PLYS(ph)PTFSDSTSAVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPLYSPTFSDSTSAVK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 ES(0.006)S(0.994)PLYS(0.957)PT(0.011)FS(0.018)DS(0.011)T(0.002)SAVK 235.4 3.40E-48 124970000 6097.2 6211.2 5962.6 5988 6945.9 7259.2 6364.7 7111.8 6592.9 5510 TRUE FALSE FALSE 6022.884981 6298.641437 6066.376552 6680.360734 6591.424804 6795.360548 6905.317459 7317.568712 6003.214512 5366.849406 1.122238492 1.173619932 1.130342235 1.24474533 1.228173982 1.266173137 1.286661305 1.363475693 1.118573311 1 12.38985969 -4 0.096100115 0.847689046 2.298056302 0.819082205 0.04236374 15.1318869 0.104370821 0.194147174 2.905431896 1.00E-04 4 1.450367256 ESS(ph)PLYSPTFSDSTSAVK ddPTM_HeLa_Romidepsin_16h_R1 4 ESSPLYSPTFSDSTSAVK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 ES(0.009)S(0.991)PLYSPTFSDSTSAVK;ES(0.017)S(0.983)PLYSPTFSDSTSAVK;ES(0.14)S(0.856)PLY(0.004)SPTFSDSTSAVK;ES(0.032)S(0.964)PLY(0.001)S(0.002)PTFSDSTSAVK ;;; 236.31 2.88E-49 384969300 10836.8 12145.3 9964.5 10699.3 9723.5 9434.5 7553.83 8869.1 11333.5 11159.5 TRUE FALSE FALSE 10704.71691 12316.28185 10137.92794 11936.40341 9227.273512 8831.665898 8195.452132 9125.713415 10319.80337 10869.57458 0.984833108 1.133096954 0.932688567 1.098148167 0.848908432 0.812512563 0.753980947 0.839564911 0.949421093 1 13.40800786 -8.613976991 5.821569447 1.005695607 0.802414672 0.724357056 0.061467611 0.074897196 3.862125395 0.007972106 0.016117388 2.43E-09 8.613976991 -0.203280935 ESSANNS(ph)VSPSESLR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSANNSVSPSESLR 15 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 ESSANNS(0.818)VS(0.153)PS(0.022)ES(0.007)LR 146.27 0.00047998 208900000 3275.4 2850.3 3145.4 2709.7 3089.3 2359.8 1646 2387.7 3256 3054.5 TRUE FALSE FALSE 3235.478165 2890.426598 3200.144368 3023.008264 2931.641493 2209.016396 1785.811199 2456.784332 2964.775205 2975.14365 1.087503175 0.971525055 1.075626842 1.016088169 0.985378132 0.742490668 0.600243689 0.825769987 0.996514977 1 11.53874361 -8.283059695 3.233682701 1.036744832 0.702430194 0.830909522 0.06131022 0.063311153 1.36142862 0.008481967 0.022001587 5.21E-09 8.283059695 -0.334314638 ESSANNSVS(ph)PSESLR ddPTM_HeLa_Romidepsin_16h_R1 3 ESSANNSVSPSESLR 15 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 ESSANNS(0.002)VS(0.995)PS(0.002)ES(0.001)LR;ESSANNS(0.165)VS(0.819)PS(0.009)ES(0.007)LR;ESSANNS(0.008)VS(0.769)PS(0.222)ESLR ;; 181.81 3.25E-08 286060000 5917.9 5784.5 5500.14 5858.7 5555.5 4681.27 3890.54 4527.57 6920.6 6262.7 TRUE FALSE FALSE 5845.770359 5865.934343 5595.86763 6536.11046 5271.982105 4382.151955 4221.00237 4658.568095 6301.604203 6099.994151 0.958323928 0.961629503 0.917356229 1.071494545 0.86426019 0.718386255 0.691968265 0.76370042 1.03305086 1 12.57459214 -8.454387852 3.509494576 0.978794722 0.72279702 0.874034973 0.044990406 0.05382844 1.287169164 0.005839272 0.01356644 3.51E-09 8.454387852 -0.255997703 ESSIIAPAPAEDVDT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 ESSIIAPAPAEDVDTPPR 18 0 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 0 ES(0.001)S(0.003)IIAPAPAEDVDT(0.996)PPR;ESS(0.001)IIAPAPAEDVDT(0.999)PPR ; 234.51 7.75E-49 128567000 4230.3 4328.6 4059.8 3228.7 4040.4 3657.3 3043.47 3457.9 4230.3 4791.5 TRUE FALSE FALSE 4178.739476 4389.538144 4130.459116 3602.017485 3834.203311 3423.610333 3301.982266 3557.948881 3851.931373 4667.016139 0.895377121 0.940544882 0.885032105 0.771803092 0.821553472 0.73357585 0.707514645 0.762360526 0.825352058 1 12.18828474 -8.98448256 0.297306152 0.998775562 0.642446909 0.535955447 0.061154207 0.73206134 0.112436072 0.02492262 0.092075278 1.04E-09 8.98448256 -0.356328654 ESSKELESPLT(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 ESSKELESPLTPGK 14 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 ESSKELES(0.018)PLT(0.982)PGK;ESSKELES(0.014)PLT(0.986)PGK ; 93.427 0.0087558 51316000 11864.8 11978.4 11219.6 14555.5 6983.1 6135.8 4951.9 4510.9 11497.8 11313.4 TRUE FALSE FALSE 11720.18725 12147.03223 11414.87243 16238.4754 6626.726349 5743.742182 5372.514262 4641.415774 10469.40797 11019.47624 1.063588414 1.102323919 1.035881578 1.4736159 0.601364911 0.521235498 0.487547153 0.421201124 0.950082177 1 13.42776803 -8.596305162 8.487884435 1.064751623 0.491464527 0.816046163 0.138842482 0.082087495 8.516719612 0.019199364 0.038474579 2.53E-09 8.596305162 -0.573287096 ESSPIPS(ph)PTSDR ddPTM_HeLa_Romidepsin_16h_R1 2 ESSPIPSPTSDR 12 0 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 ES(0.119)S(0.07)PIPS(0.621)PT(0.187)S(0.002)DR;ESS(0.001)PIPS(0.881)PT(0.118)S(0.001)DR ; 164.13 0.00039691 30602000 5580 5324.7 5168.3 7824.4 5019.7 4679.7 3945.1 4727.1 5575.5 5628.8 TRUE FALSE FALSE 5511.988814 5399.661266 5258.252094 8729.093943 4763.525978 4380.682273 4280.196696 4863.87118 5076.813316 5482.562965 1.00536717 0.984879025 0.959086494 1.592155712 0.868850209 0.799020878 0.780692666 0.887152817 0.925992706 1 12.42063476 -8.545152442 24.999967 1.042198851 0.820763122 0.289530054 0.183241076 240.714287 270176.4646 0.025758966 0.051520646 2.85E-09 8.545152442 -0.22143573 ESSPIPSPTS(ph)DRK ddPTM_HeLa_Romidepsin_16h_R1 1 ESSPIPSPTSDRK 13 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 ESS(0.022)PIPS(0.199)PT(0.199)S(0.579)DRK 106.29 0.013956 19014000 2087.6 2302.3 2270.1 2370.7 1728.6 2090.2 1262.6 1680.3 2342 2109.2 TRUE FALSE FALSE 2062.155528 2334.71184 2309.610138 2644.811488 1640.383092 1956.642966 1369.845212 1728.916829 2132.525654 2054.40268 1.003773772 1.136443144 1.124224652 1.28738709 0.798472037 0.952414531 0.666785157 0.841566674 1.038027099 1 11.00450327 -8.658701212 24.80846654 1.04119746 0.814053411 0.587846312 0.110234718 7.038673322 1686.748439 0.016799594 0.033599186 2.19E-09 8.658701212 -0.227144049 ESSTSEGADQKMS(ph)S(ph)PEDDSDTKR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 2 0 ESS(0.003)T(0.003)S(0.005)EGADQKMS(0.993)S(0.995)PEDDS(0.001)DTKR 91.067 8.83E-05 7677100 3360.7 3302.5 3242.4 3193.1 3351.1 3439 3516.5 3270.1 3907.7 3018.8 TRUE FALSE FALSE 3319.738496 3348.992682 3298.832612 3562.301246 3180.080862 3219.258999 3815.191422 3364.715184 3558.185525 2940.371141 1.129020228 1.138969375 1.121910281 1.211514151 1.081523627 1.094847842 1.29752036 1.14431649 1.210114422 1 11.52178255 -16.52287875 0.140227769 0.424428902 1.216783488 0 0.087675982 40.5564541 0.395466932 6.413795052 0.160827696 3.00E-17 16.52287875 0.792354587 ESSTSEGADQKMS(ph)SPEDDSDT(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 2 0 ESSTSEGADQKMS(0.572)S(0.572)PEDDS(0.175)DT(0.68)KR 54.658 0.014371 13412000 2311.2 1946.9 1752.3 2221 2189.4 2326.7 2343.5 2353.7 2186.4 2257.8 TRUE FALSE FALSE 2283.030205 1974.308509 1782.798046 2477.80247 2077.666748 2178.031379 2542.556832 2421.800596 1990.842908 2199.142031 1.038145865 0.897763074 0.810678902 1.126713253 0.944762421 0.990400506 1.156158536 1.101247924 0.905281642 1 11.10272507 -7.7672162 24.9651205 0.996026737 1.128703245 0.318573377 0.086764217 115.4738718 499042.7095 0.011506686 0.03592084 1.71E-08 7.7672162 0.132676507 ESSTSEGADQKMS(ph)SPEDDSDTKR ddPTM_HeLa_Romidepsin_16h_R1 1 ESSTSEGADQKMSSPEDDSDTKR 23 2 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 ESSTS(0.001)EGADQKMS(0.926)S(0.07)PEDDS(0.001)DTKR 82.189 0.00027588 6662100 2545.9 2815.7 2804 2826.3 2596 2343.4 2326.9 2086.1 2645.3 2779.5 TRUE FALSE FALSE 2514.869592 2855.339499 2852.802444 3153.090104 2463.516433 2193.664303 2524.546828 2146.458012 2408.697743 2707.288189 0.928925706 1.054686202 1.053749082 1.164667329 0.909957219 0.810281045 0.932500218 0.792844301 0.889708658 1 11.40263275 -8.530345842 24.9883627 0.994460609 0.854967907 0.474316952 0.079547828 133.7246419 447503.896 0.011588733 0.023214036 2.95E-09 8.530345842 -0.139492702 ESSTVFELK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ESSTVFELKR 10 1 B8ZZU8;Q15370;Q15370-2;A0A0B4J296;I3L0M9 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 1 ; ESSTVFELK(1)R;ESSTVFELK(1)R 126.31 0.0026031 1856450 417.2 388.63 520.22 353.967 1107.33 1081.71 805.26 740.42 1012.28 652.27 FALSE TRUE FALSE 412.1150059 394.1011433 529.2742109 394.89433 1050.818818 1012.592222 873.6587643 761.8428845 921.7391415 635.3239314 0.648669105 0.620315282 0.833077718 0.621563757 1.653989038 1.593820368 1.375139077 1.199140859 1.4508176 1 9.311348553 -8.762325525 24.99999997 0.799048051 1.459659145 0.5455493 0.261377208 9.199375444 259545.5328 0.028652723 0.054210637 1.73E-09 8.762325525 0.660611094 ESSVK(ac)TVR ddPTM_HeLa_Romidepsin_16h_R1 2 ESSVKTVR 8 1 O95696-2;O95696;J3KQ61 O95696-2 BRD1 Bromodomain-containing protein 1 0 1 ; ESSVK(1)TVR;ESSVK(1)TVR 106.68 0.017956 26296000 3508.2 3106.6 3467.3 3447.1 3734.7 3779.6 3556.3 2681.8 3009.1 2563.9 FALSE TRUE FALSE 3465.440709 3150.334796 3527.646902 3845.669921 3544.104323 3538.095758 3858.372033 2759.393652 2739.95856 2497.289508 1.387680802 1.261501634 1.412590286 1.539937564 1.4191804 1.416774365 1.545023923 1.10495545 1.097172975 1 11.28614737 -12.21623823 0.528895937 0.925721638 1.410924017 0.536171558 0.124290889 0.699947959 0.278385251 0.17287667 0.029272213 6.08E-13 12.21623823 0.485202379 EST(ph)PLASGPSSFQR ddPTM_HeLa_Romidepsin_16h_R1 1 ESTPLASGPSSFQR 14 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 0 EST(1)PLASGPSSFQR 186.51 7.03E-08 9619200 569.18 1101.3 752.37 607.25 1767.8 2348.2 1891.2 2562 783.6 704.5 TRUE FALSE FALSE 562.2426152 1116.80413 765.4646842 677.4631022 1677.582569 2198.157598 2051.838481 2636.127428 713.5128534 686.1969884 0.819360365 1.627527006 1.115517406 0.987272042 2.444753617 3.203391498 2.990159554 3.841648203 1.039807614 1 9.422478984 -8.568027945 1.979388232 0.979695021 3.363506561 0.918254846 0.302498655 0.061116489 0.477686153 0.045590516 0.11400515 2.70E-09 8.568027945 2.38381154 up ESTESSNT(ph)TIEDEDVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESTESSNTTIEDEDVK 16 0 D6R938;H0Y9J2;E9PBG7;E9PF82;Q13557-8;Q13557-12;Q13557-10;Q13557;Q13557-6;Q13557-11 D6R938 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 0 ESTESSNT(0.5)T(0.5)IEDEDVK 190.34 2.49E-12 19052000 4618.2 4590.6 4662.1 3285.1 5174.8 5047.6 4048.1 4796 4995.2 4628.9 TRUE FALSE FALSE 4561.911602 4655.226587 4743.241895 3664.938719 4910.710646 4725.07465 4391.945513 4934.764693 4548.416801 4508.640511 1.011815334 1.032512256 1.05203373 0.812870024 1.089177688 1.048004302 0.974117476 1.094512787 1.008822236 1 12.13847677 -7.248303947 23.28760562 1.004557008 1.094512939 0.13046697 0.070601679 1250.033763 2216062.033 0.008875764 0.204217521 5.65E-08 7.248303947 0.089955931 ESTESSNT(ph)TIEDEDVKAR ddPTM_HeLa_Romidepsin_16h_R1 1 ESTESSNTTIEDEDVKAR 18 1 D6R938;H0Y9J2;E9PBG7;E9PF82;Q13557-8;Q13557-12;Q13557-10;Q13557;Q13557-6;Q13557-11 D6R938 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 0 ESTESSNT(0.5)T(0.5)IEDEDVKAR 183.18 1.60E-10 38130000 1566 1832.7 1806.5 2515.1 2037.5 2046.3 1977.1 1920.9 2063.7 1696.8 TRUE FALSE FALSE 1546.91299 1858.500799 1837.941375 2805.907696 1933.518772 1915.548034 2145.034825 1976.478211 1879.117503 1652.716891 0.935981836 1.124512497 1.112072724 1.697754595 1.169903195 1.159029743 1.297884009 1.195896418 1.136986929 1 10.6906239 -9.810308626 2.318653727 0.972253993 1.290810556 0.325224338 0.161003395 0.184385492 2.032030051 0.024784079 0.034570716 1.55E-10 9.810308626 0.318556563 ESTESSNTT(ph)IEDEDVK ddPTM_HeLa_Romidepsin_16h_R1 1 ESTESSNTTIEDEDVK 16 0 D6R938;H0Y9J2;E9PBG7;E9PF82;Q13557-8;Q13557-12;Q13557-10;Q13557;Q13557-6;Q13557-11 D6R938 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 0 ESTESSNT(0.226)T(0.774)IEDEDVK 270.95 2.53E-86 22889000 3788.8 4024.1 3794.4 2981.5 3896.1 4489.7 3529.6 3715.5 3922.4 3734.1 TRUE FALSE FALSE 3742.620648 4080.751385 3860.43994 3326.235058 3697.267479 4202.82266 3829.404136 3823.00213 3571.57072 3637.087544 1.029015827 1.121983273 1.061409684 0.914532581 1.016546188 1.155546192 1.052876536 1.051116335 0.98198646 1 11.82856794 ESTESSNTT(ph)IEDEDVKAR ddPTM_HeLa_Romidepsin_16h_R1 1 ESTESSNTTIEDEDVKAR 18 1 D6R938;H0Y9J2;E9PBG7;E9PF82;Q13557-8;Q13557-12;Q13557-10;Q13557;Q13557-6;Q13557-11 D6R938 CAMK2D Calcium/calmodulin-dependent protein kinase type II subunit delta 1 0 ESTESSNT(0.002)T(0.998)IEDEDVKAR 196.83 1.68E-15 23016000 2976.1 3000.2 2743.4 3737.8 3574.3 3489.3 3009.6 2953.9 2990.1 3102.1 TRUE FALSE FALSE 2939.826148 3042.436894 2791.147726 4169.982023 3391.890133 3266.344991 3265.235349 3039.366436 2722.657967 3021.506995 0.972966852 1.006926974 0.923760141 1.380100073 1.122582254 1.081031749 1.080664501 1.005910773 0.901092724 1 11.56105257 ESTLHLVLR ddPTM_HeLa_Romidepsin_16h_R1 2 ESTLHLVLR 9 0 P62979;A0A2R8Y422;J3QS39;F5H388;Q96C32;Q5PY61;J3QKN0;F5GXK7;F5H747;J3QTR3;F5H265;B4DV12;M0R2S1;F5H2Z3;F5GYU3;F5H6Q2;M0R1M6;P62987;P0CG47;P0CG48 P62979 RPS27A;UBB;UBC;UBA52 Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a;Ubiquitin-60S ribosomal protein L40;Ubiquitin;60S ribosomal protein L40;Polyubiquitin-B;Ubiquitin;Polyubiquitin-C;Ubiquitin 0 0 ; ; 85.862 0.0088194 1814010 1406.83 1293.83 1362.64 995.21 3026.9 2650.7 2026.89 2213.8 2029.15 2147.87 FALSE FALSE TRUE 1389.683015 1312.044573 1386.356178 1110.280863 2872.425998 2481.328825 2199.053986 2277.85281 1847.657742 2092.068028 0.664262823 0.627151964 0.662672609 0.530709732 1.373007933 1.186065076 1.051138852 1.08880437 0.883172878 1 11.03071405 -8.756984902 24.9999998 0.785586632 1.166732316 0.658711453 0.15419003 76.04661047 426793.1888 0.028242463 0.054976212 1.75E-09 8.756984902 0.381145684 ESTQLS(ph)PADLTEGKPTDPSK ddPTM_HeLa_Romidepsin_16h_R1 2 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 ES(0.011)T(0.022)QLS(0.81)PADLT(0.144)EGKPT(0.012)DPSK;ES(0.181)T(0.156)QLS(0.658)PADLT(0.002)EGKPT(0.003)DPSK ; 93.767 0.00047627 82523000 8708.9 9059.6 8852.8 5430 9478.1 10343 7771.7 9281.3 9958.6 9513.7 TRUE FALSE FALSE 8602.752577 9187.141287 9006.87927 6057.842149 8994.397189 9682.115681 8431.828004 9549.839772 9067.877874 9266.532703 0.928368016 0.991432457 0.97197944 0.653733424 0.970632434 1.044847732 0.909922651 1.030573147 0.978562119 1 13.17781391 -8.176976347 0.006866058 1.869770742 4.45E-07 0.001024573 0.105415187 32875.13609 49.81178181 6549.612691 7019.889862 6.65E-09 8.176976347 -1.869770297 ESTQLSPADLT(ph)EGKPTDPSK ddPTM_HeLa_Romidepsin_16h_R1 1 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 ES(0.002)T(0.002)QLS(0.032)PADLT(0.916)EGKPT(0.032)DPS(0.016)K 91.589 0.00082518 59235000 4408.5 4701.6 4986.8 2793.4 4317.7 5262.8 4756.9 5015.4 5021.8 4564.5 TRUE FALSE FALSE 4354.767506 4767.789248 5073.593162 3116.386051 4097.351657 4926.524065 5160.950967 5160.512686 4572.637631 4445.913632 0.979498899 1.072398081 1.141181224 0.700955149 0.921599472 1.108101613 1.160830235 1.160731655 1.028503477 1 12.11826421 -8.089500507 4.717397457 0.982068699 1.155757457 0.331586377 0.109037389 0.19546015 7.369911059 0.015326588 0.04136373 8.14E-09 8.089500507 0.173688758 ESTQLSPADLTEGKPT(ph)DPSK ddPTM_HeLa_Romidepsin_16h_R1 1 ESTQLSPADLTEGKPTDPSK 20 1 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 ES(0.008)T(0.007)QLS(0.08)PADLT(0.115)EGKPT(0.731)DPS(0.06)K 72.359 0.0043862 60857000 2902.1 2745.4 3462.1 1726 2907.4 3412.6 2709.4 3558.8 3617.2 3084.8 TRUE FALSE FALSE 2866.728089 2784.049813 3522.356398 1925.568241 2759.024529 3194.545874 2939.536368 3661.768263 3293.668573 3004.656451 0.95409513 0.926578415 1.172299215 0.640861367 0.918249582 1.063198381 0.978326946 1.218697819 1.096188075 1 11.55298433 -6.622637053 1.39224741 0.963125127 2.07680248 0.231383594 0.134194735 6.592820839 3.138676588 0.01749564 15.98552017 2.38E-07 6.622637053 1.113677353 ESTSTESS(ph)SQDVESTFSSPEDSLPK ddPTM_HeLa_Romidepsin_16h_R1 1 ESTSTESSSQDVESTFSSPEDSLPK 25 0 G3V1N5;B4E3L3;Q96RU2-3;Q96RU2-2;Q96RU2 G3V1N5 USP28 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 28 1 0 ES(0.002)T(0.002)S(0.003)T(0.011)ES(0.071)S(0.48)S(0.43)QDVES(0.001)T(0.001)FSSPEDSLPK 88.668 2.35E-05 2071600 1172 1398.7 1313.4 1249 1384.6 1098.4 901.27 1164.1 1322.2 1343.7 TRUE FALSE FALSE 1157.715213 1418.390935 1336.259176 1393.415257 1313.938695 1028.215785 977.8238513 1197.781397 1203.93912 1308.79048 0.884568791 1.083741788 1.020987848 1.064658765 1.003933567 0.785622909 0.747120235 0.915181929 0.919886826 1 10.35401844 -8.259920096 24.96713686 0.973299858 0.809089538 0.559847772 0.071303554 91.16106522 1498073.573 0.011525256 0.027731235 5.50E-09 8.259920096 -0.164210319 ESVASMGADS(ph)GDDFASDGSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 ESVASMGADSGDDFASDGSSSR 22 0 Q5T165;Q92805 Q5T165 GOLGA1 Golgin subfamily A member 1 1 0 ES(0.001)VAS(0.27)MGADS(0.727)GDDFAS(0.001)DGSSSR 73.346 0.0044829 7488800 1732.8 1847.8 1804.8 1196.3 1534.4 1079.7 1156.5 1350.1 1796.1 1825.4 TRUE FALSE FALSE 1711.679967 1873.813377 1836.211787 1334.621835 1456.093842 1010.710655 1254.733081 1389.163013 1635.452318 1777.975845 0.962712723 1.053902606 1.032754068 0.750641151 0.818961544 0.568461409 0.705708733 0.781317146 0.919839447 1 10.79602001 -9.188158118 4.453017855 0.991911722 0.715831755 0.786359548 0.070068231 0.072882931 2.766758713 0.010155272 0.017038365 6.48E-10 9.188158118 -0.276079967 ESVNS(ph)PVFGK ddPTM_HeLa_Romidepsin_16h_R1 1 ESVNSPVFGK 10 0 Q9UPS8;E7ESJ3;Q9UPS8-2 Q9UPS8 ANKRD26 Ankyrin repeat domain-containing protein 26 1 0 ESVNS(1)PVFGK 163.71 0.001852 36938000 5702.4 5706.2 5392.3 4544.7 5028.5 4509.4 4738 4454.7 5688 6070.2 TRUE FALSE FALSE 5632.896955 5786.532033 5486.15072 5070.179597 4771.876881 4221.263893 5140.445602 4583.589716 5179.251034 5912.495329 0.952710597 0.978695409 0.927890918 0.857536339 0.807083408 0.713956402 0.869420662 0.775237774 0.875983954 1 12.52955142 -9.203592883 1.579109973 0.977748892 0.789924428 0.681730526 0.04919607 0.106027514 0.517322078 0.006095434 0.011470277 6.26E-10 9.203592883 -0.187824464 ESVPEFPLS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 5 ESVPEFPLSPPK 12 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK;ESVPEFPLS(1)PPK ;;;; 197.36 5.82E-11 2427767200 36509.7 34275.5 37421.9 19838 37434.5 37446.2 30151.2 32148.2 36758.2 38824.1 TRUE FALSE FALSE 36064.70573 34758.03139 38073.21247 22131.7629 35524.07778 35053.50867 32712.24218 33078.35745 33470.45453 37815.44429 0.953703081 0.919149095 1.006816479 0.585257249 0.939406596 0.926962762 0.865049791 0.874731424 0.885100127 1 15.20668795 ESVPSAS(ph)PTGIPK ddPTM_HeLa_Romidepsin_16h_R1 2 ESVPSASPTGIPK 13 0 H3BLS7;Q5THJ4-2;Q5THJ4;A0A2R8YD87 H3BLS7 VPS13D Vacuolar protein sorting-associated protein 13D 1 0 ESVPS(0.008)AS(0.964)PT(0.029)GIPK;ESVPS(0.001)AS(0.986)PT(0.014)GIPK ; 152.11 0.00076877 18688500 9612.2 8625.9 9146.9 5595.7 10591.3 12350.5 10974.4 11328.1 8611.5 7309.3 TRUE FALSE FALSE 9495.042809 8747.335647 9306.097958 6242.701163 10050.78644 11561.34291 11906.56526 11655.8607 7841.265872 7119.403332 1.333685193 1.228661341 1.307145771 0.876857353 1.411745616 1.623920204 1.672410553 1.637196287 1.101393685 1 12.79754062 -4 0.228999843 1.077987074 4.833563997 0.604141152 0.164170305 27.67910187 0.336150703 0.124731397 39.31261442 1.00E-04 4 3.755576923 ESVS(ph)PEDSEK ddPTM_HeLa_Romidepsin_16h_R1 2 ESVSPEDSEK 10 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 0 ESVS(0.771)PEDS(0.228)EK;ES(0.006)VS(0.993)PEDS(0.001)EK ; 177.57 5.56E-05 276990000 11210 11198.8 11636.2 6509.8 8987.1 9021.5 8539.7 7994.7 13205.6 12192.4 TRUE FALSE FALSE 11073.36821 11356.457 11838.72318 7262.493706 8528.454752 8445.055266 9265.061905 8226.014031 12024.45806 11875.63969 0.932443935 0.956281707 0.996891409 0.611545474 0.718146978 0.711124241 0.780173712 0.692679657 1.012531398 1 13.53571761 -9.270764858 24.99577916 0.968177093 0.708358617 0.904712925 0.044835668 149.6001013 400983.844 0.007000412 0.010783621 5.36E-10 9.270764858 -0.259818476 ESVSTEDLSPPS(ph)PPLPK ddPTM_HeLa_Romidepsin_16h_R1 2 ESVSTEDLSPPSPPLPK 17 0 Q13127-4;Q13127 Q13127-4 REST RE1-silencing transcription factor 1 0 ESVSTEDLSPPS(1)PPLPK;ESVSTEDLS(0.21)PPS(0.79)PPLPK ; 223.14 1.55E-35 32467000 13917.6 12846.9 12333.3 9355.3 7632 8198 7641.8 8145.9 15289.6 14001.1 TRUE FALSE FALSE 13747.96694 13027.759 12547.95591 10437.0038 7242.510561 7674.174258 8290.894301 8381.588764 13922.05988 13637.3494 1.008111366 0.955299935 0.920116919 0.765324954 0.53107905 0.562732099 0.607954967 0.614605413 1.020877259 1 13.73527564 -9.146221384 1.834059954 0.999834933 0.577966649 0.969088034 0.033896563 0.038376803 0.252795042 0.005347985 0.009990969 7.14E-10 9.146221384 -0.421868284 ESYDAPPT(ph)PSGAR ddPTM_HeLa_Romidepsin_16h_R1 2 ESYDAPPTPSGAR 13 0 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 0 ESYDAPPT(0.5)PS(0.5)GAR;ESYDAPPT(0.802)PS(0.198)GAR ; 225.72 2.80E-31 47495000 7387.5 7789 7420.7 7240.8 9534.3 8143.9 6249 7416.1 6266 6453.6 TRUE FALSE FALSE 7297.458308 7898.653746 7549.854171 8078.015365 9047.729094 7623.531073 6779.789904 7630.673153 5705.553267 6285.934542 1.160918597 1.256559974 1.201071077 1.285093777 1.43936101 1.212791992 1.078565146 1.213928192 0.907669851 1 12.61791153 -11.26483585 0.691892452 1.012603285 1.243961187 0.575904229 0.092983535 0.397857134 0.413487989 0.041470705 0.023194069 5.43E-12 11.26483585 0.231357901 ESYS(ph)VYVYK ddPTM_HeLa_Romidepsin_16h_R1 1 ESYSVYVYK 9 0 P58876;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P58876;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BD;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-D;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 1 0 ES(0.281)YS(0.719)VYVYK 145.99 0.0058159 16831000 2315.4 2522.7 2265.6 1923.8 3273.4 2839.9 2481.7 2886 2242.6 2550.3 TRUE FALSE FALSE 2287.179014 2558.214637 2305.031818 2146.238808 3106.346183 2658.439555 2692.495536 2969.501857 2042.016239 2484.042838 0.92074862 1.029859307 0.927935614 0.864010384 1.250520376 1.070206807 1.083916708 1.195431017 0.822053552 1 11.27847434 -8.764642416 24.99999983 0.958264293 1.139596302 0.652829537 0.077439654 38.63449759 301549.1406 0.009514267 0.017782332 1.72E-09 8.764642416 0.181332009 ESYSIYVYK ddPTM_HeLa_Romidepsin_16h_R1 3 ESYSIYVYK 9 0 P06899;Q6DRA6;Q6DN03;P23527;P33778;Q16778;Q8N257 P06899;P23527;P33778;Q16778;Q8N257 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BB;HIST2H2BE;HIST3H2BB Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-B;Histone H2B type 2-E;Histone H2B type 3-B 0 0 ;; ;; 186.3 0.00017294 43090600 6979.3 5652.1 6130.02 5722.9 6823.7 6248.2 5344.7 5685.73 6537 6189.44 FALSE FALSE TRUE 6894.233607 5731.670412 6236.710427 6384.608625 6475.461126 5848.960185 5798.678685 5850.237627 5952.314348 6028.637457 1.143580727 0.950740603 1.034514096 1.059046704 1.074116859 0.97019604 0.961855598 0.970407935 0.987339907 1 12.55761626 -8.252638678 22.18951312 1.057384794 0.96692338 0.187575333 0.052779117 134.9330894 340204.8101 0.008830797 0.022068343 5.59E-09 8.252638678 -0.090461414 ESYSVYVYK ddPTM_HeLa_Romidepsin_16h_R1 3 ESYSVYVYK 9 0 P58876;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P58876;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BD;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-D;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 0 ;; ;; 178.99 0.00024313 133082000 9261 8281.5 9254.8 7523.1 9190.3 9252.5 8230.6 8276.9 9895.1 7840.3 FALSE FALSE TRUE 9148.12337 8398.087174 9415.875912 8392.956219 8721.284697 8661.295111 8929.706959 8516.379043 9010.057473 7636.607876 1.197930222 1.099714338 1.232991934 1.099042449 1.142036469 1.134180942 1.169328988 1.115204444 1.179850743 1 12.89871623 -12.40234465 1.051868758 0.997309575 1.152331 0 0.068089429 0.245179564 0.471601729 0.028958508 0.006869366 3.96E-13 12.40234465 0.155021426 ESYT(ph)EEIVSEAESHVS(ph)GISR ddPTM_HeLa_Romidepsin_16h_R1 1 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 2 0 ES(0.092)Y(0.008)T(0.503)EEIVS(0.396)EAES(0.006)HVS(0.942)GIS(0.053)R 76.439 0.0064682 1647300 659.11 527.81 464.37 565 817.27 670.61 431.85 639.88 717.02 404.8 TRUE FALSE FALSE 651.0765138 535.240523 472.4521651 630.3279584 775.5616622 627.7601853 468.5313282 658.3939182 652.8879354 394.2832376 1.651291386 1.357502607 1.198255771 1.598667907 1.967016571 1.592155398 1.188311557 1.669850137 1.6558856 1 8.623088568 -12.41254785 0.850074277 0.956588274 1.531556242 0 0.300297924 0.585166934 0.660070794 0.233982343 0.044109519 3.87E-13 12.41254785 0.574967968 ESYTEEIVS(ph)EAESHVSGISR ddPTM_HeLa_Romidepsin_16h_R1 3 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR;ESYTEEIVS(1)EAESHVSGISR ;; 195.13 2.28E-18 5313900 2018.71 1793.41 1769.2 1528.56 3017.99 3051.22 2009.29 2503.03 2896.29 2391.82 TRUE FALSE FALSE 1994.105186 1818.657673 1799.992184 1705.299299 2863.970709 2856.256889 2179.959042 2575.451224 2637.238569 2329.680172 0.855956629 0.78064693 0.77263489 0.731988588 1.229340724 1.226029617 0.935733183 1.105495619 1.132017433 1 11.18591619 -8.753840581 24.99890581 0.892006506 1.117968581 0.442693634 0.1342647 132.6045788 436245.5419 0.018868908 0.037166345 1.76E-09 8.753840581 0.225962075 ESYTEEIVSEAESHVS(ph)GISR ddPTM_HeLa_Romidepsin_16h_R1 1 ESYTEEIVSEAESHVSGISR 20 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 ESYTEEIVSEAES(0.011)HVS(0.925)GIS(0.064)R 92.428 0.00059795 1450800 601.49 566.98 539.46 356.31 560.87 633.69 485.12 482.16 781.35 599.34 TRUE FALSE FALSE 594.1588085 574.9619593 548.849075 397.5082387 532.246711 593.1992541 526.3260807 496.1105389 711.4640991 583.7690604 1.017797703 0.984913382 0.94018185 0.680934064 0.911741898 1.01615398 0.901599822 0.849840412 1.218742389 1 9.18925394 -9.641440546 3.982664892 1.006941555 0.878252831 0.376364858 0.103327008 0.185509608 5.466691914 0.012758014 0.018257666 2.28E-10 9.641440546 -0.128688725 ET(ph)NS(ph)LELSQGSGTFPS(ph)GY(ph)Y(ph)YK ddPTM_HeLa_Romidepsin_16h_R1 1 ETNSLELSQGSGTFPSGYYYK 21 0 A0A087WTR2;Q969Y0 A0A087WTR2 NXPE3 NXPE family member 3 5 0 ET(0.999)NS(0.998)LELS(0.034)QGS(0.038)GT(0.352)FPS(0.676)GY(0.635)Y(0.635)Y(0.635)K 53.554 0.0029027 0 801.9 533.75 729.79 526.66 640.82 754.75 709.02 608.78 715.07 744.23 TRUE FALSE FALSE 792.1261344 541.2641465 742.4916888 587.5549072 608.1165642 706.5239108 769.2441411 626.3940888 651.1123483 724.8947973 1.092746337 0.746679585 1.024275097 0.810538177 0.838903199 0.974657169 1.061180386 0.864117236 0.898216335 1 9.501627824 -10.30643327 24.9999466 1.043796888 0.910407754 0.096041359 0.104580433 392.0296697 217822.2424 0.016003978 0.018301282 4.94E-11 10.30643327 -0.133389134 ET(ph)VNSPAIYK ddPTM_HeLa_Romidepsin_16h_R1 1 ETVNSPAIYK 10 0 Q9Y3A2 Q9Y3A2 UTP11L Probable U3 small nucleolar RNA-associated protein 11 1 0 ET(0.995)VNS(0.005)PAIYK 171.26 0.0015632 27429000 4797.5 5979.1 5359.5 4625.9 4795.9 4983.2 4458.7 4331.1 6738.3 5586.3 TRUE FALSE FALSE 4739.026225 6063.273927 5452.779849 5160.768324 4551.147327 4664.789603 4837.421867 4456.413545 6135.609572 5441.167121 0.870957668 1.114333339 1.002134235 0.94846716 0.836428514 0.857314157 0.889041222 0.819017951 1.127627481 1 12.40970042 -8.797272645 7.243554312 0.958264053 0.853692697 0.401672828 0.081958456 0.183116513 28.49609723 0.01101131 0.020266856 1.59E-09 8.797272645 -0.104571356 ET(ph)VTPGPNFQER ddPTM_HeLa_Romidepsin_16h_R1 2 ETVTPGPNFQER 12 0 S4R313;Q9NP74-2;Q9NP74;Q9NP74-3 S4R313 PALMD Palmdelphin 1 0 ET(0.912)VT(0.088)PGPNFQER;ET(0.897)VT(0.103)PGPNFQER ; 143.31 0.0031647 14264400 5099.5 5311.5 4535.7 3820.4 3945.3 3044.4 2606 2693.9 4438.2 4790.3 TRUE FALSE FALSE 5037.345333 5386.275436 4614.641956 4262.132624 3743.956619 2849.872665 2827.353575 2771.843746 4041.236276 4665.847315 1.079620697 1.154404564 0.989025496 0.913474517 0.802417303 0.61079424 0.605967873 0.594070821 0.866131273 1 12.18792338 -8.645659025 1.344352904 1.046745208 0.587271922 0.860925474 0.072187779 0.074791188 0.266589887 0.008235008 0.023440234 2.26E-09 8.645659025 -0.459473286 ETAAGGLTLKEERSPQT(ph)LAPVGEDAMK ddPTM_HeLa_Romidepsin_16h_R1 1 ETAAGGLTLKEERSPQTLAPVGEDAMK 27 2 Q92797 Q92797 SYMPK Symplekin 1 0 ET(0.005)AAGGLT(0.02)LKEERS(0.42)PQT(0.555)LAPVGEDAMK 42.042 0.027518 22960000 2744.9 2441.1 2656.2 3843.8 2263.7 2543.7 2290.9 2811 2933.7 2343.3 TRUE FALSE FALSE 2711.444103 2475.46587 2702.430047 4288.238242 2148.174942 2381.165779 2485.488989 2892.33185 2671.302524 2282.420728 1.187968576 1.084579122 1.184019236 1.878811469 0.941182717 1.043263299 1.088970565 1.267221163 1.170381294 1 11.15634904 -11.82784203 0.667709374 0.996996166 1.213070265 0.024324795 0.246233225 1.528804108 1.265204632 0.174918166 0.055667132 1.49E-12 11.82784203 0.216074099 ETAIELGYLTAEQFDEWVKPK ddPTM_HeLa_Romidepsin_16h_R1 1 ETAIELGYLTAEQFDEWVKPK 21 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 0 154.55 9.15E-08 7110400 983.39 1028.1 1071.3 1051.5 1168.4 1106.2 903.67 1139.9 1298.4 1109.8 FALSE FALSE TRUE 971.4040644 1042.573619 1089.945527 1173.079377 1108.772188 1035.51739 980.4277072 1172.881208 1182.267852 1080.967236 0.898643393 0.964482164 1.008305794 1.085212704 1.025722289 0.957954465 0.906991141 1.085029378 1.093712938 1 10.07810708 -9.823206859 4.802558141 0.951279005 1.008401293 0 0.070976818 0.294519593 13.52170548 0.010141729 0.013573522 1.50E-10 9.823206859 0.057122289 ETAPTSAYS(ph)SPAR ddPTM_HeLa_Romidepsin_16h_R1 1 ETAPTSAYSSPAR 13 0 A0A6I8PRZ9;A0A6I8PIX2;A0A6I8PIU5;A0A6I8PIW1;O43301 A0A6I8PRZ9 HSPA12A Heat shock 70 kDa protein 12A 1 0 ETAPT(0.003)S(0.003)AY(0.002)S(0.66)S(0.332)PAR 95.273 0.017266 20220000 1841.6 1720.3 1963.4 2327.7 5333.1 6198.4 5666.3 6883.8 1974.3 2165 TRUE FALSE FALSE 1819.153871 1744.518429 1997.572153 2596.839626 5060.932006 5802.342244 6147.595381 7082.971892 1797.713663 2108.752988 0.86266807 0.827274905 0.947276502 1.231457473 2.399964356 2.751551404 2.915275244 3.358843797 0.852500826 1 11.0421744 -8.638163614 1.5961202 0.915836722 3.076598947 0.979029303 0.139497225 0.036415659 0.185412468 0.021583501 0.056337445 2.30E-09 8.638163614 2.160762225 up ETAVPGPLGIEDIS(ph)PNLSPDDK ddPTM_HeLa_Romidepsin_16h_R1 2 ETAVPGPLGIEDISPNLSPDDK 22 0 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 ETAVPGPLGIEDIS(0.999)PNLS(0.001)PDDK;ETAVPGPLGIEDIS(1)PNLSPDDK ; 135.69 4.09E-05 12187600 13050.8 11894.3 12819.7 9035.9 12791.7 12172.6 11379.9 11600.1 14108.7 13651.5 TRUE FALSE FALSE 12891.73183 12061.74827 13042.8215 10080.67327 12138.89182 11394.81015 12346.50842 11935.73059 12846.78254 13296.83206 0.969534079 0.907114432 0.980896911 0.758125938 0.912916081 0.856956762 0.928530071 0.897637162 0.966153628 1 13.69879495 -10.06953436 1.136391802 0.989533728 0.880347819 0.382745193 0.05305937 0.286887272 0.721761616 0.009917072 0.012901067 8.52E-11 10.06953436 -0.109185909 ETAVPGPLGIEDIS(ph)PNLSPDDKSFSR ddPTM_HeLa_Romidepsin_16h_R1 2 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 ETAVPGPLGIEDIS(1)PNLSPDDKSFSR;ETAVPGPLGIEDIS(0.997)PNLS(0.003)PDDKSFSR ; 77.657 3.20E-05 26994000 10029.6 9481.2 7387.8 12417 8535.9 8042.6 7493.2 7778.9 9623 8369.1 TRUE FALSE FALSE 9907.355377 9614.676582 7516.38156 13852.71196 8100.281171 7528.703816 8129.672221 8003.970198 8762.294779 8151.669576 1.215377449 1.179473296 0.922066515 1.699371133 0.993695966 0.923578139 0.997301491 0.981881089 1.074907992 1 12.99287986 -8.553651004 24.99984433 1.141482607 0.96857019 0.193228304 0.198434682 292.9608901 238004.7626 0.028864059 0.057728542 2.79E-09 8.553651004 -0.172912417 ETAVPGPLGIEDISPNLS(ph)PDDK ddPTM_HeLa_Romidepsin_16h_R1 4 ETAVPGPLGIEDISPNLSPDDK 22 0 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 ETAVPGPLGIEDIS(0.037)PNLS(0.962)PDDK;ETAVPGPLGIEDISPNLS(1)PDDK;ETAVPGPLGIEDIS(0.003)PNLS(0.997)PDDK;ETAVPGPLGIEDIS(0.001)PNLS(0.999)PDDK ;;; 104.26 3.71E-06 10429800 11088.1 10691.6 11377.2 7723.2 8188.7 6964.7 5639.7 5920.14 12306.8 12209.1 TRUE FALSE FALSE 10952.95397 10842.11663 11575.21539 8616.192723 7770.800083 6519.678148 6118.735977 6091.42991 11206.04899 11891.90582 0.921042778 0.911722376 0.973369245 0.72454263 0.653452878 0.54824502 0.514529468 0.512233279 0.942325743 1 13.53769232 -8.880382609 1.177467632 0.963197994 0.510892281 0.964510069 0.035911853 0.062693476 0.172033597 0.006651153 0.017001871 1.32E-09 8.880382609 -0.452305713 ETAVPGPLGIEDISPNLS(ph)PDDKSFSR ddPTM_HeLa_Romidepsin_16h_R1 2 ETAVPGPLGIEDISPNLSPDDKSFSR 26 1 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 ETAVPGPLGIEDIS(0.011)PNLS(0.984)PDDKS(0.001)FS(0.004)R;ETAVPGPLGIEDIS(0.185)PNLS(0.807)PDDKS(0.007)FS(0.001)R ; 99.29 1.79E-06 232250000 18600 18940.5 16380.6 20612.5 14345.9 11070.6 9996.8 9198.7 18451.4 16809.1 TRUE FALSE FALSE 18373.29605 19207.14486 16665.69747 22995.81423 13613.77519 10363.22439 10845.92794 9464.849871 16801.06057 16372.39716 1.122211724 1.173141884 1.017914317 1.404547789 0.831507754 0.632969277 0.662452043 0.578097989 1.02618208 1 13.99897795 -8.528551244 24.73218994 1.088274719 0.645623873 0.795062288 0.114010697 44.96188596 196034.3831 0.016766372 0.033615971 2.96E-09 8.528551244 -0.442650846 ETCSTLAES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ETCSTLAESPR 11 0 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 ETCSTLAES(1)PR 170.4 0.00033327 26268000 3165.8 2721.9 2852 140.94 3574 4547.8 3456.9 3437.4 2697.6 3332.5 TRUE FALSE FALSE 3127.214012 2760.21898 2901.637864 157.2361459 3391.605444 4257.210257 3750.529 3536.855746 2456.3199 3245.92117 0.963428823 0.850365377 0.893933559 0.048441147 1.044882259 1.311556885 1.155459053 1.08963082 0.756740466 1 11.66441225 -8.524887999 24.99823562 0.891151264 1.181819966 0.265547898 0.278027936 84.94692692 1056873.785 0.042098106 0.084653733 2.99E-09 8.524887999 0.290668702 ETDEFFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ETDEFFKK 8 1 O14745;O14745-2;J3QRA3 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 0 1 ; ETDEFFK(1)K;ETDEFFK(1)K 114.89 0.0018683 1356240 442.47 523.47 772.54 345.29 1396.53 1338.51 1242.13 1457.95 1297.2 678.99 FALSE TRUE FALSE 437.0770054 530.8394244 785.9857346 385.2140544 1325.259863 1252.983531 1347.636491 1500.133483 1181.175183 661.3497419 0.660886333 0.802660666 1.188457007 0.582466477 2.003871445 1.894585348 2.037706233 2.268290721 1.786006871 1 9.369269604 -8.752551887 24.99609916 0.845996334 2.03897555 0.673477982 0.347113249 41.81139305 117593.7869 0.028364546 0.056063829 1.77E-09 8.752551887 1.192979216 ETDKS(ph)PTSTEPR ddPTM_HeLa_Romidepsin_16h_R1 1 ETDKSPTSTEPR 12 1 Q6IQ19-2;Q6IQ19 Q6IQ19-2 CCSAP "Centriole, cilia and spindle-associated protein" 1 0 ET(0.029)DKS(0.484)PT(0.484)S(0.002)TEPR 155.43 0.0085539 3126300 1332.1 1117.1 869.26 783.56 1225.4 1148.5 1117.7 974.28 1598.9 1399.6 TRUE FALSE FALSE 1315.863853 1132.826563 884.3891057 874.158894 1162.863265 1075.114557 1212.63741 1002.469255 1455.890379 1363.23819 0.965248672 0.830982121 0.648741439 0.641237093 0.85301547 0.788647622 0.889527171 0.73535884 1.067964784 1 10.41282194 -10.19029924 3.307339101 0.984780194 0.764225286 0.668207641 0.078471077 0.118205202 2.524311492 0.013319115 0.016235936 6.45E-11 10.19029924 -0.220554908 ETDLQELFRPFGSISR ddPTM_HeLa_Romidepsin_16h_R1 1 ETDLQELFRPFGSISR 16 1 K7ENA8;O75821;K7EP16 K7ENA8 EIF3G Eukaryotic translation initiation factor 3 subunit G 0 0 85.976 0.019327 12162000 1492.5 1714.2 1625 1281 1386.6 1407 1357.7 1786.2 2008.9 1684.4 FALSE FALSE TRUE 1474.308836 1738.332553 1653.282443 1429.115247 1315.836628 1317.097241 1473.023004 1837.880879 1829.218953 1640.639045 0.898618645 1.059546009 1.007706386 0.871072313 0.802026888 0.802795255 0.897834907 1.120222565 1.11494296 1 10.68004215 -9.248415666 23.90667805 0.964464519 0.888028487 0.15938226 0.103976589 725.8733559 1332430.692 0.014684269 0.024238217 5.64E-10 9.248415666 -0.076436032 ETDPS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 2 ETDPSPEER 9 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;H0Y482 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 ET(0.002)DPS(0.998)PEER;ETDPS(1)PEER ; 113.44 0.017179 21933000 8534.7 9296.3 9285.8 8461.9 8809.9 9338.2 8935.5 6368.1 10399.6 9499.6 TRUE FALSE FALSE 8430.675794 9427.173555 9447.415454 9440.304692 8360.297929 8741.519158 9694.481147 6552.350926 9469.43373 9252.799023 0.911148699 1.018845598 1.02103325 1.020264751 0.903542583 0.944743222 1.047734974 0.708147979 1.023412884 1 13.17567414 -7.250715006 24.95452091 0.969626652 0.708147827 0.722067661 0.050942846 675.4044505 1571567.267 0.007325198 0.142569154 5.61E-08 7.250715006 -0.261478825 FIQELSGS(ph)SPKR ddPTM_HeLa_Romidepsin_16h_R1 1 FIQELSGSSPKR 12 1 I3L254;Q01664 I3L254 TFAP4 Transcription factor AP-4 1 0 FIQELS(0.016)GS(0.699)S(0.286)PKR 119.25 0.01194 16035000 2772.1 2443.6 2282.3 1938.1 945.23 1061.2 1001 1199.1 2879.4 2645.2 TRUE FALSE FALSE 2738.312579 2478.001065 2322.022474 2162.192241 896.991386 993.3927449 1086.024915 1233.794067 2621.859252 2576.477323 1.062812607 0.961778721 0.901239244 0.839204841 0.348146432 0.385562386 0.421515418 0.478868592 1.017613945 1 11.33118418 -8.933232218 2.440394154 1.016266316 0.403503268 0.951463889 0.061634298 0.043408413 0.523295223 0.010167274 0.01983889 1.17E-09 8.933232218 -0.612763048 down ETDVS(ph)PFPPR ddPTM_HeLa_Romidepsin_16h_R1 3 ETDVSPFPPR 10 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3 Q9H8V3-2 ECT2 Protein ECT2 1 0 ET(0.024)DVS(0.976)PFPPR;ET(0.121)DVS(0.879)PFPPR;ET(0.017)DVS(0.983)PFPPR ;; 126.66 0.0087633 9626500 7239.3 6536.3 6520.5 6689.5 6377.8 6346.7 4705.9 5350.1 6954.6 6833.3 TRUE FALSE FALSE 7151.064627 6628.318203 6633.986567 7462.971465 6052.317067 5941.166353 5105.619029 5504.896702 6332.563158 6655.769881 1.074415846 0.995875507 0.996727153 1.121278469 0.909333883 0.892633979 0.767096688 0.827086393 0.951439619 1 12.70038984 -8.3287639 1.896277849 1.03442852 0.804678663 0.717339316 0.05447433 0.111246432 0.766382085 0.007162748 0.021812886 4.69E-09 8.3287639 -0.229749857 ETDYPAGEDLSES(ph)GQVDK ddPTM_HeLa_Romidepsin_16h_R1 2 ETDYPAGEDLSESGQVDK 18 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5;H0YBS5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 ETDYPAGEDLS(0.009)ES(0.991)GQVDK;ETDYPAGEDLSES(1)GQVDK ; 248.7 5.17E-62 20929000 6815.7 7175.8 6483.8 6589.6 8409.9 10144.6 8274.1 11392.9 6584.3 6921.3 TRUE FALSE FALSE 6732.627627 7276.821101 6596.647819 7351.520557 7980.711421 9496.3928 8976.901847 11722.53559 5995.383717 6741.483628 0.998686342 1.079409445 0.978515737 1.090490011 1.183821227 1.40865028 1.331591433 1.738865839 0.889327045 1 12.71885041 -6.056504692 0.450608511 0.991027507 3.569255215 0.916238812 0.070601038 1.97369505 0.120100226 0.012844666 3.466287076 8.78E-07 6.056504692 2.578227708 KAPAGQEEPGT(ph)PPS(ph)SPLSAEQLDR ddPTM_HeLa_Romidepsin_16h_R1 3 KAPAGQEEPGTPPSSPLSAEQLDR 24 1 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 0 KAPAGQEEPGT(1)PPS(0.548)S(0.443)PLS(0.009)AEQLDR;KAPAGQEEPGT(1)PPS(0.538)S(0.458)PLS(0.004)AEQLDR;KAPAGQEEPGT(1)PPS(0.947)S(0.05)PLS(0.003)AEQLDR ;; 110.07 3.09E-06 29637800 8405.5 7316 6399.2 5510.31 3286.84 2779.36 2524.07 2443.31 8142.7 7560.8 TRUE FALSE FALSE 8303.050533 7418.99484 6510.575392 6147.437969 3119.10029 2601.767866 2738.464443 2514.00332 7414.396518 7364.369326 1.127462538 1.007417541 0.884064216 0.834754165 0.423539363 0.353291334 0.371853219 0.341373879 1.00679314 1 12.84634626 -8.924587622 1.353103403 1.055960949 0.335010544 0.964240328 0.05779332 0.055796313 0.203824411 0.010619459 0.024554483 1.19E-09 8.924587622 -0.720950405 down ETEEQDSDS(ph)AEQGDPAGEGK ddPTM_HeLa_Romidepsin_16h_R1 1 ETEEQDSDSAEQGDPAGEGK 20 0 H0Y626;O95361 H0Y626 TRIM16 Tripartite motif-containing protein 16 1 0 ETEEQDS(0.336)DS(0.664)AEQGDPAGEGK 189.99 6.04E-18 18122000 6618.8 9266.8 10544 3524.6 5402.4 7352.9 6272.3 6769.2 8858.3 7350.7 TRUE FALSE FALSE 6538.12752 9397.258254 10727.5139 3932.130836 5126.695369 6883.07342 6805.069005 6965.056122 8065.991462 7159.727754 0.913181024 1.312516143 1.498313101 0.549201167 0.716046133 0.961359657 0.950464772 0.972810191 1.126577956 1 12.80568902 -9.191849259 24.99999997 1.026880997 0.837640488 0.283190256 0.217190284 268.274438 96376.04277 0.035284776 0.058513179 6.43E-10 9.191849259 -0.189240509 ETEIS(ph)LKDSTLDN ddPTM_HeLa_Romidepsin_16h_R1 2 ETEISLKDSTLDN 13 1 O75475 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 ETEIS(0.934)LKDS(0.033)T(0.033)LDN;ETEIS(0.894)LKDS(0.053)T(0.053)LDN ; 145.6 0.0050739 49599000 12082.4 10624.5 11227 7585.6 9994.9 11848.7 10459.6 10137.6 12088.8 10444.8 TRUE FALSE FALSE 11935.13506 10774.07199 11422.40123 8462.682763 9484.822957 11091.60631 11348.03816 10430.91546 11007.54745 10173.44259 1.173165814 1.059038953 1.122766568 0.831840617 0.932312034 1.090251035 1.11545704 1.025308333 1.081988457 1 13.31252033 ETES(ph)APGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 ETESAPGSPR 10 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 0 ET(0.147)ES(0.832)APGS(0.021)PR 119.03 0.012435 45033000 3605.1 2894.9 3064.1 3103.8 3004.7 3217.4 2370.4 2812.6 3601.6 3162.7 TRUE FALSE FALSE 3561.159655 2935.654478 3117.429375 3462.67596 2851.358947 3011.818524 2571.741717 2893.978143 3279.463876 3080.532598 1.156020766 0.952969782 1.011977402 1.124051069 0.925605835 0.977694093 0.834836716 0.939440844 1.06457691 1 11.58896409 -8.724284097 12.11116853 1.063333619 0.917432215 0.493955373 0.064893986 0.629556765 203.4736553 0.011241311 0.022448291 1.89E-09 8.724284097 -0.145901404 ETESAPGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 6 ETESAPGSPR 10 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1 Q6PKG0 LARP1 La-related protein 1 1 0 ETES(0.001)APGS(0.999)PR;ETES(0.39)APGS(0.61)PR;ETES(0.001)APGS(0.999)PR;ETESAPGS(1)PR;ETESAPGS(1)PR;ETESAPGS(1)PR ;;;;; 152.67 0.0035703 1117951580 20608.04 17654.8 18258.99 16788.91 15627.07 16351.25 17747.6 10271.42 22789.46 20142.95 TRUE FALSE FALSE 20356.86128 17903.34474 18576.78006 18730.12277 14829.56231 15306.4579 19255.0807 10568.60733 20751.11362 19619.63326 1.037576035 0.912521886 0.946846448 0.954662227 0.755853186 0.780160245 0.981418992 0.538675071 1.057670821 1 14.26001045 -6.045547401 0.310829654 1.026925401 8.18E-16 0.59130708 0.097233486 7.681420903 0.298053594 0.03540264 3.473175004 9.00E-07 6.045547401 -1.026925401 ETFAS(ph)DTNEALASLDESQEGHAEAK ddPTM_HeLa_Romidepsin_16h_R1 2 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 0 ET(0.002)FAS(0.922)DT(0.076)NEALASLDESQEGHAEAK;ET(0.036)FAS(0.781)DT(0.183)NEALASLDESQEGHAEAK ; 157.01 2.48E-10 9837800 2553.7 2422.77 2517.7 1533.2 2698.4 2687.2 2124.72 2290.82 2940.8 3556.3 TRUE FALSE FALSE 2522.574522 2456.87782 2561.519512 1710.475798 2560.690579 2515.496593 2305.193664 2357.101262 2677.767483 3463.906813 0.728245492 0.709279421 0.739488575 0.4937996 0.739249269 0.726202155 0.665489515 0.68047479 0.77304836 1 11.7581844 -11.911242 0.506536389 1.040009982 0.668217427 0.331775368 0.095882592 0.435020333 0.186269951 0.077546488 0.018543186 1.23E-12 11.911242 -0.371792556 ETFASDTNEALAS(ph)LDESQEGHAEAK ddPTM_HeLa_Romidepsin_16h_R1 2 ETFASDTNEALASLDESQEGHAEAK 25 0 Q9H814 Q9H814 PHAX Phosphorylated adapter RNA export protein 1 0 ETFASDTNEALAS(1)LDESQEGHAEAK;ETFASDTNEALAS(1)LDESQEGHAEAK ; 134.15 7.17E-07 8863800 2947 2238.62 2342.3 1730.94 3195.3 3457.1 2930.7 3295.5 3074.4 2909.2 TRUE FALSE FALSE 2911.08083 2270.135351 2383.066749 1931.079427 3032.231918 3236.202467 3179.633585 3390.850093 2799.417964 2833.618565 1.027336871 0.801143591 0.840997719 0.681488839 1.070091774 1.142074134 1.122110655 1.196650154 0.987930415 1 11.46842985 -8.530470281 24.9945881 0.957133523 1.143065162 0.488738612 0.111725688 165.8944827 546195.0221 0.018955014 0.037970305 2.95E-09 8.530470281 0.185931639 ETFLTSPEELYR ddPTM_HeLa_Romidepsin_16h_R1 1 ETFLTSPEELYR 12 0 G3V438;H0YJG7;O95433-2;O95433;H0YJ63 G3V438 AHSA1 Activator of 90 kDa heat shock protein ATPase homolog 1 0 0 158.47 0.009979 7542300 1470.2 1687 1538.2 1305 1510.3 1619.9 1164.9 1113.7 1611.7 1579 FALSE FALSE TRUE 1452.280637 1710.74963 1564.971726 1455.89024 1433.223755 1516.393618 1263.846577 1145.923152 1467.545515 1537.977352 0.944279599 1.112337336 1.017551867 0.946626579 0.931888726 0.985966156 0.8217589 0.745084543 0.954204893 1 10.58681854 -7.633231959 2.666386004 0.982719518 0.748651696 0.730764758 0.050139306 0.117579275 1.558770765 0.007436052 0.042265114 2.33E-08 7.633231959 -0.234067822 ETGEHLVHVK ddPTM_HeLa_Romidepsin_16h_R1 2 ETGEHLVHVK 10 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 0 ; ; 101.46 0.0089653 13850600 10285.9 10619.9 9748.7 8582.1 12165.9 12584.6 10689.6 10518.2 12506 10559.7 FALSE FALSE TRUE 10160.53149 10769.40723 9918.372034 9574.402782 11545.02873 11780.48467 11597.57436 10822.52752 11387.43204 10285.35747 0.98786372 1.047062026 0.964319622 0.930877007 1.122472287 1.145364632 1.127581067 1.052226678 1.107149855 1 13.32830432 -8.745064811 24.98399407 0.992077179 1.115420022 0.496275546 0.050940393 90.85921018 138630.5009 0.005066008 0.010108203 1.80E-09 8.745064811 0.123342843 ETGEHLVHVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ETGEHLVHVKK 11 1 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 1 ; ETGEHLVHVK(1)K;ETGEHLVHVK(1)K 107.45 0.0016791 6216600 4760 4563.9 3824.8 5299.9 7429.8 7471.4 7651.8 5485.3 8011.5 6358.6 FALSE TRUE FALSE 4701.983289 4628.150704 3891.36904 5912.699375 7050.629582 6994.001653 8301.743701 5644.008501 7294.931375 6193.402655 0.759192249 0.747271082 0.628308743 0.95467705 1.138409688 1.129266421 1.340417241 0.911293648 1.177855176 1 12.59651653 -8.87049953 3.937293413 0.851113261 1.145522837 0.348330404 0.171011818 0.160332748 4.639527825 0.023020804 0.043409805 1.35E-09 8.87049953 0.294409576 ETIEQEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ETIEQEKR 8 1 P63313 P63313 TMSB10 Thymosin beta-10 0 1 ; ETIEQEK(1)R;ETIEQEK(1)R 120.12 0.0015565 6420700 4712.3 4719.6 4175.4 3307.5 4137.2 3485.8 5429.8 3099.9 6474.7 5863.2 FALSE TRUE FALSE 4654.864675 4786.042653 4248.071086 3689.928712 3926.063246 3263.06863 5891.007076 3189.590716 5895.586616 5710.873219 0.815088078 0.838057941 0.743856661 0.646123381 0.687471617 0.57137823 1.031542262 0.558511911 1.03234416 1 12.47949564 -11.2227279 0.456893258 1.010556061 0.705890663 0.459767503 0.127046837 0.730069913 0.348275759 0.094739777 0.045135976 5.99E-12 11.2227279 -0.304665398 ETIFELEDEVEQHR ddPTM_HeLa_Romidepsin_16h_R1 1 ETIFELEDEVEQHR 14 0 F8WAN1;Q69YQ0-2;Q69YQ0;C9J8U1;A0A494C1J1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 0 0 140.31 1.32E-05 0 284.59 65.762 221.57 175.75 272.58 243.5 57.138 273.51 234.33 255.9 FALSE FALSE TRUE 281.1213076 66.68779916 225.4263329 196.0710419 258.6692255 227.9411359 61.99130029 281.4235803 213.3709379 249.2516811 1.12786123 0.267552054 0.904412487 0.786638794 1.037783273 0.9145019 0.248709658 1.129073951 0.856046134 1 7.961459425 ETIHLPAS(ph)SPHPPPFP ddPTM_HeLa_Romidepsin_16h_R1 2 ETIHLPASSPHPPPFP 16 0 Q5SZC3;Q5SZC6;Q9Y2T3-3 Q5SZC3 GDA 1 0 ETIHLPAS(0.5)S(0.5)PHPPPFP;ETIHLPAS(0.5)S(0.5)PHPPPFP ; 101.04 0.002202 3609800 1859.72 1716.77 1553.91 2049.72 2747 2609.9 2205.3 1909.56 1982.5 1975.88 TRUE FALSE FALSE 1837.053017 1740.938733 1580.955152 2286.718271 2606.81034 2443.135813 2392.618127 1964.810106 1805.180235 1924.546353 0.954538203 0.904596936 0.821468992 1.188185604 1.354506394 1.269460624 1.243211484 1.020921166 0.937977011 1 10.9103027 -9.127993701 6.345473126 0.960905298 1.231903664 0.705050217 0.092786559 0.109841814 5.238374431 0.014145548 0.02361268 7.45E-10 9.127993701 0.270998366 ETIQGTGSWGPEPPGPGIPPAYS(ph)SPRR ddPTM_HeLa_Romidepsin_16h_R1 1 ETIQGTGSWGPEPPGPGIPPAYSSPRR 27 1 Q9H4L4 Q9H4L4 SENP3 Sentrin-specific protease 3 1 0 ETIQGTGSWGPEPPGPGIPPAY(0.306)S(0.347)S(0.347)PRR 47.478 0.012382 6848500 599.91 846.7 658.71 394.5 872.16 694.3 643.65 604 1075.9 751.65 TRUE FALSE FALSE 592.5980662 858.6198648 670.1745712 440.1139462 827.6504207 649.9364708 698.3216149 621.475787 979.6688094 732.1220246 0.809425268 1.172782454 0.915386437 0.601148349 1.130481522 0.887743366 0.953832273 0.848869131 1.338122303 1 9.515940316 -12.7525909 1.696356204 1.000143374 0.90073756 0.106306401 0.186603713 0.988297718 5.135766073 0.107667529 0.023060333 1.77E-13 12.7525909 -0.099405815 ETLVYLTHLDYVDTER ddPTM_HeLa_Romidepsin_16h_R1 3 ETLVYLTHLDYVDTER 16 0 O14980 O14980 XPO1 Exportin-1 0 0 ;; ;; 212.39 3.40E-26 23586200 6825 6181.8 6238.9 5458.5 5333.1 4842.8 4976.3 5366.3 8649.5 6420 FALSE FALSE TRUE 6741.814275 6268.827543 6347.485437 6089.637453 5060.932006 4533.360709 5398.986798 5521.565424 7875.867057 6253.207474 1.078136988 1.002497929 1.015076737 0.973842221 0.809333774 0.724965664 0.863394797 0.882997317 1.259492363 1 12.61038067 -8.878489765 3.269764348 1.032374189 0.815577924 0.649234539 0.084482388 0.078686583 1.668037532 0.007624485 0.014628699 1.32E-09 8.878489765 -0.216796266 ETMQSLNDR ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 112.3 0.0021157 0 1060 1072.7 1344.3 975.86 1226.2 1234.8 982.86 1030.3 945.15 1134.6 FALSE FALSE TRUE 1047.080312 1087.801499 1367.696978 1088.693525 1163.622438 1155.900265 1066.344104 1060.110105 860.6134168 1105.122928 0.947478588 0.984326242 1.237597142 0.985133415 1.052934844 1.045947229 0.964909945 0.959268944 0.778749037 1 10.10999114 -9.96888808 24.99993669 0.974708827 1.042009263 0.189660156 0.097054619 284.046812 228245.0709 0.012063241 0.015854137 1.07E-10 9.96888808 0.067300435 ETNLDS(ph)LPLVDTHSK ddPTM_HeLa_Romidepsin_16h_R1 4 ETNLDSLPLVDTHSK 15 0 P08670 P08670 VIM Vimentin 1 0 ET(0.003)NLDS(0.992)LPLVDT(0.004)HSK;ET(0.001)NLDS(0.999)LPLVDTHSK;ETNLDS(0.999)LPLVDT(0.001)HSK;ETNLDS(1)LPLVDTHSK ;;; 185.63 9.82E-09 191376000 21842.6 20661.3 21084.2 16472.4 18991.5 17474.6 14621.2 16828.2 20355.6 19120.1 TRUE FALSE FALSE 21576.37399 20952.17032 21451.16166 18377.01639 18022.29289 16358.02946 15863.12436 17315.09742 18534.94415 18623.35705 1.158565233 1.125047985 1.15184183 0.986772489 0.967725252 0.878360943 0.851786513 0.929751675 0.99525258 1 14.18482554 -8.772792961 1.884905571 1.08588455 0.886639888 0.679083703 0.058480732 0.169468319 1.224422724 0.010809039 0.024230056 1.69E-09 8.772792961 -0.199244661 ETNLDSLPLVDTHSK ddPTM_HeLa_Romidepsin_16h_R1 2 ETNLDSLPLVDTHSK 15 0 P08670 P08670 VIM Vimentin 0 0 ; ; 127.29 4.78E-05 11879060 4488.31 4366.71 4987.64 3820.12 4695.57 5077.6 4697.33 4539.67 5266.88 5097.68 FALSE FALSE TRUE 4433.604751 4428.184658 5074.447782 4261.820249 4455.937541 4753.157747 5096.321093 4671.018189 4795.797062 4965.241539 0.892928313 0.891836706 1.021994145 0.858330902 0.897426139 0.957286309 1.026399432 0.940743396 0.96587387 1 12.27764819 -7.99225693 24.72779942 0.939043472 0.985639291 0.123844164 0.052530963 301.2030225 961880.4438 0.008165825 0.024431381 1.02E-08 7.99225693 0.04659582 ETNLDSLPLVDTHSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ETNLDSLPLVDTHSKR 16 1 P08670 P08670 VIM Vimentin 0 1 ; ETNLDSLPLVDTHSK(1)R;ETNLDSLPLVDTHSK(1)R 152.94 1.42E-10 6761400 1293.96 1379.44 901.89 1052.15 2103.49 1831.37 1767.19 1563.57 2573.3 2032.53 FALSE TRUE FALSE 1278.188718 1398.859793 917.5870171 1173.804534 1996.141056 1714.351367 1917.295074 1608.809431 2343.137603 1979.724578 0.645639667 0.706593133 0.463492259 0.592913048 1.008292304 0.86595448 0.968465561 0.812643056 1.183567467 1 10.95108402 -5.674361572 22.60197658 0.804410724 0.835138079 0 0.212152136 0 0 0.027256467 0 2.12E-06 5.674361572 0.030727355 ETNLDSLPLVDTHSKR ddPTM_HeLa_Romidepsin_16h_R1 2 ETNLDSLPLVDTHSKR 16 1 P08670 P08670 VIM Vimentin 0 0 ; ; 80.719 0.0050566 41798000 7067.2 7246.5 5444.4 9606.6 7540.8 7526 6077.5 7435.8 8023.5 6999.3 FALSE FALSE TRUE 6981.062248 7348.516417 5539.157498 10717.36029 7155.964837 7045.112889 6593.722698 7650.943141 7305.858065 6817.457177 1.023997961 1.077896968 0.812496119 1.572046588 1.049653067 1.033393053 0.967182122 1.122257602 1.071639744 1 12.73501802 ETPAAQS(ph)PTRGPSDTK ddPTM_HeLa_Romidepsin_16h_R1 1 ETPAAQSPTRGPSDTK 16 1 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 0 ETPAAQS(0.94)PT(0.041)RGPS(0.019)DTK 154.31 0.0017431 4625600 803.48 672.36 803.17 721.11 1593.2 1581.7 1454.6 1158.4 687.74 538.8 TRUE FALSE FALSE 793.6868767 681.8255017 817.1488369 804.4881311 1511.893059 1480.634475 1578.153688 1191.916476 626.2268119 524.8018983 1.512355194 1.299205479 1.557061511 1.532936778 2.880883365 2.82132073 3.007141729 2.271174095 1.193263237 1 9.035629128 -8.830240619 4.163163145 1.284881884 2.774582903 0.893860204 0.235989923 0.054320959 1.846419907 0.041077266 0.077939244 1.48E-09 8.830240619 1.48970102 up ETPAATEAPS(ph)STPK ddPTM_HeLa_Romidepsin_16h_R1 1 ETPAATEAPSSTPK 14 0 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 ETPAATEAPS(0.949)S(0.043)T(0.008)PK 116.58 0.00062865 0 555.48 826 489.32 361.01 416.84 634.98 454.73 526.49 552.89 696.28 TRUE FALSE FALSE 548.7095961 837.6284497 497.8364093 402.7516748 395.5670994 594.4068273 493.3547548 541.7231575 503.4381337 678.1905452 0.809078805 1.235093081 0.734065688 0.59386212 0.583268378 0.876459915 0.727457436 0.798777219 0.742325497 1 9.405546861 -9.5617643 24.99994345 0.934234735 0.712728957 0.368289985 0.145826061 126.726509 81473.31443 0.022042386 0.031172669 2.74E-10 9.5617643 -0.221505778 ETPAATEAPSS(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 3 ETPAATEAPSSTPK 14 0 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 ETPAATEAPS(0.002)S(0.499)T(0.499)PK;ETPAATEAPSS(0.998)T(0.001)PK;ETPAATEAPS(0.001)S(0.499)T(0.499)PK ;; 195.71 1.56E-11 40080500 5445.2 6121.7 5343.9 4256.36 6591.8 8201.1 5668.8 6519.9 5923.7 5519.1 TRUE FALSE FALSE 5378.831808 6207.881453 5436.908338 4748.50037 6255.395849 7677.076178 6150.307731 6708.54302 5393.869436 5375.712986 1.000580169 1.154801506 1.011383672 0.883324757 1.163640221 1.428103806 1.144091537 1.24793549 1.003377496 1 12.3922404 -8.545624194 8.39212269 1.007262466 1.266413104 0.646073449 0.088723871 0.08812397 27.62999989 0.012205331 0.024686867 2.85E-09 8.545624194 0.259150638 ETPAATEAPSST(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 ETPAATEAPSSTPK 14 0 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 ETPAATEAPSS(0.022)T(0.978)PK;ETPAATEAPS(0.007)S(0.075)T(0.918)PK;ETPAATEAPS(0.046)S(0.074)T(0.88)PK ;; 214.61 9.67E-24 1584529300 13541.4 16132.4 12901.5 11090.3 16934.4 19103 14093.6 17417.1 13813.2 13029.7 TRUE FALSE FALSE 13376.35221 16359.51235 13126.0452 12372.61267 16070.17438 17882.37995 15290.71003 17921.03631 12577.7128 12691.18652 1.053987521 1.289045144 1.03426462 0.974898025 1.266246805 1.409039252 1.204829037 1.412085173 0.991058857 1 13.63153933 -5.913691044 0.237127468 0.988436276 2.100663749 0.555087749 0.109773387 11.22768592 0.302000927 0.076737013 4.092131293 1.22E-06 5.913691044 1.112227474 ETPHS(ph)PGVEDAPIAK ddPTM_HeLa_Romidepsin_16h_R1 5 ETPHSPGVEDAPIAK 15 0 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 ETPHS(1)PGVEDAPIAK;ET(0.01)PHS(0.99)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK;ET(0.017)PHS(0.983)PGVEDAPIAK;ETPHS(1)PGVEDAPIAK ;;;; 163.02 5.41E-05 1785860000 34562 34766.7 33694.5 41238.6 43305.6 47150.3 43870.3 48383.3 38229.7 35344.2 TRUE FALSE FALSE 34140.74505 35256.14652 34280.93864 46006.80097 41095.55364 44137.548 47596.64219 49783.19445 34810.33988 34425.95259 0.991715333 1.024115351 0.995787656 1.336398778 1.193737589 1.282100993 1.382580251 1.4460949 1.011165626 1 15.07120895 -8.781953038 0.713366282 0.988717823 1.426672025 0.847011885 0.067707566 0.209830346 0.188242486 0.012578995 0.049599761 1.65E-09 8.781953038 0.437954202 ETPPNGNLS(ph)PAPR ddPTM_HeLa_Romidepsin_16h_R1 4 ETPPNGNLSPAPR 13 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 0 ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR;ETPPNGNLS(1)PAPR ;;; 128.85 0.0028232 66988000 4576.29 4700.01 4407.48 4319.06 3012.11 3199.98 3254.93 2787.37 4405.92 3747.43 TRUE FALSE FALSE 4520.512417 4766.176864 4484.190341 4818.450039 2858.390787 2995.511605 3531.403673 2868.018153 4011.84348 3650.071228 1.238472384 1.305776399 1.228521325 1.320097537 0.783105482 0.820672096 0.967488975 0.785743065 1.099113751 1 11.8337089 -8.749414906 24.99998555 1.153958054 0.847084942 0.724713884 0.106355808 132.3967867 275263.419 0.019715851 0.03919239 1.78E-09 8.749414906 -0.306873112 ETPQGELRPEVVEDEVPRS(ph)PVAEEPGGGGSSSSEAK ddPTM_HeLa_Romidepsin_16h_R1 2 ETPQGELRPEVVEDEVPRSPVAEEPGGGGSSSSEAK 36 2 Q7L8J4 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 0 ETPQGELRPEVVEDEVPRS(0.979)PVAEEPGGGGS(0.012)S(0.005)S(0.002)S(0.002)EAK;ETPQGELRPEVVEDEVPRS(0.996)PVAEEPGGGGS(0.001)S(0.002)S(0.001)SEAK ; 78.642 1.41E-08 24757000 1567.12 1422.09 1199.53 1172.16 2115.29 2486.5 1788.81 2182.9 1854.03 1517.23 TRUE FALSE FALSE 1548.019339 1442.11022 1220.407316 1307.690654 2007.338858 2327.620675 1940.751477 2246.058767 1688.200913 1477.812146 1.047507522 0.975841364 0.825820332 0.884882871 1.358318013 1.575045029 1.313259931 1.519854045 1.142365028 1 10.52924718 -8.655868273 5.176455909 0.994547998 1.454703534 0.8296493 0.103120938 0.059510936 2.50153374 0.014045554 0.028446273 2.21E-09 8.655868273 0.460155536 ETPS(ph)QENGPTAK ddPTM_HeLa_Romidepsin_16h_R1 1 ETPSQENGPTAK 12 0 O15355 O15355 PPM1G Protein phosphatase 1G 1 0 ETPS(1)QENGPTAK 201.08 9.92E-15 7361600 2630.7 2612.7 2468.8 2305.6 2351.8 2842.8 1770 1748.7 2332.6 2420.5 TRUE FALSE FALSE 2598.636017 2649.481659 2511.768428 2572.18432 2231.77887 2661.154255 1920.343756 1799.295876 2123.966414 2357.615061 1.102230835 1.123797393 1.0653853 1.09101115 0.946625642 1.128748411 0.814528117 0.763184756 0.900896185 1 11.20311247 -7.692586172 6.196665748 1.055846188 0.780321863 0.661258854 0.073079043 0.068347272 4.603128446 0.008128694 0.031028405 2.03E-08 7.692586172 -0.275524325 ETQS(ph)PEQVK ddPTM_HeLa_Romidepsin_16h_R1 4 ETQSPEQVK 9 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 ET(0.059)QS(0.941)PEQVK;ET(0.001)QS(0.999)PEQVK;ET(0.007)QS(0.993)PEQVK;ET(0.003)QS(0.997)PEQVK ;;; 151.26 0.0051372 1010130000 19748.9 21052.3 27544.8 16661.5 18271.9 21634 27423.5 8103.4 26405 24188.1 TRUE FALSE FALSE 19508.19281 21348.67483 28024.20569 18587.98102 17339.41676 20251.65722 29752.85141 8337.859094 24043.27067 23559.68968 0.828032673 0.906152633 1.189498082 0.788973933 0.735978147 0.859589303 1.262871108 0.353903604 1.020525779 1 14.52403292 ETQS(ph)PEQVKSEK ddPTM_HeLa_Romidepsin_16h_R1 1 ETQSPEQVKSEK 12 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 ET(0.004)QS(0.996)PEQVKSEK 169.3 0.001167 160220000 2222 2056.3 1759.6 3010.2 1878 2018.5 1837.4 1745.6 2140.1 2144.3 TRUE FALSE FALSE 2194.917409 2085.248645 1790.2251 3358.253487 1782.158652 1889.524364 1993.46871 1796.106182 1948.684096 2088.590777 1.050908313 0.998399815 0.85714498 1.607904011 0.853282832 0.904688647 0.954456341 0.859960794 0.933013838 1 11.02831413 ETQST(ph)PQSAPQVR ddPTM_HeLa_Romidepsin_16h_R1 2 ETQSTPQSAPQVR 13 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 ET(0.001)QS(0.072)T(0.651)PQS(0.276)APQVR;ETQS(0.087)T(0.91)PQS(0.002)APQVR ; 193.45 1.24E-10 7024900 2865.8 2948 3052.4 3208.8 4209 4100.9 3739.9 3641.4 2942.4 2709.7 TRUE FALSE FALSE 2830.870527 2989.502021 3105.525742 3579.816554 3994.199024 3838.865725 4057.567013 3746.758164 2679.224375 2639.301603 1.072583188 1.132686775 1.176646783 1.356349933 1.513354525 1.454500585 1.537363902 1.419602125 1.015126263 1 11.36594051 -9.362401616 1.10334811 1.031694993 1.495932979 0.957875736 0.040993904 0.062456912 0.150809064 0.007474169 0.014364864 4.34E-10 9.362401616 0.464237987 ETQSTPQS(ph)APQVR ddPTM_HeLa_Romidepsin_16h_R1 2 ETQSTPQSAPQVR 13 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 ETQST(0.204)PQS(0.795)APQVR;ETQS(0.001)T(0.225)PQS(0.774)APQVR ; 229.48 4.33E-32 30591000 3290.4 3080.6 3270.3 3842.5 3507.8 2799 2851.4 3101.6 3439.4 3204.8 TRUE FALSE FALSE 3250.295339 3123.968768 3327.2182 4286.78793 3328.783877 2620.152933 3093.597845 3191.339902 3131.77145 3121.538834 1.041247767 1.000778441 1.065890375 1.37329316 1.066391948 0.839378612 0.99104897 1.022361108 1.003278068 1 11.6080417 ETS(ph)PESSLIQDEIAVK ddPTM_HeLa_Romidepsin_16h_R1 5 ETSPESSLIQDEIAVK 16 0 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 ET(0.045)S(0.955)PESSLIQDEIAVK;ET(0.015)S(0.981)PES(0.003)SLIQDEIAVK;ET(0.102)S(0.894)PES(0.003)S(0.001)LIQDEIAVK;ET(0.089)S(0.423)PES(0.423)S(0.065)LIQDEIAVK;ET(0.003)S(0.996)PESSLIQDEIAVK ;;;; 260.25 3.22E-72 274921600 12170.32 12098.85 12135.7 10585.41 12775.8 12742.96 11466.4 12513.7 12743.75 11810.33 TRUE FALSE FALSE 12021.98346 12269.17793 12346.91677 11809.34491 12123.80325 11928.72598 12440.35573 12875.76417 11603.91708 11503.49592 1.045072171 1.06656081 1.073318655 1.026587482 1.053923375 1.03696529 1.081441312 1.119291409 1.008729621 1 13.48978474 -16.52287592 0.011036393 2.56E-06 1.93344984 0.607392784 0.021298971 4364.650396 3.894122365 398.5241747 291.5728222 3.00E-17 16.52287592 1.933447277 ETSFGSS(ph)ENITMTSLSK ddPTM_HeLa_Romidepsin_16h_R1 1 ETSFGSSENITMTSLSK 17 0 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2;A0A087WZS7 Q9UMZ2-6 SYNRG Synergin gamma 1 0 ETSFGS(0.254)S(0.498)ENIT(0.247)MT(0.001)SLSK 125.67 0.0029787 65869000 2595.3 2652.4 2797.9 2539.7 3558.2 3627.6 2606.2 3002 2763.5 2945.2 TRUE FALSE FALSE 2563.667485 2689.740557 2846.596276 2833.352064 3376.611777 3395.808068 2827.570563 3088.858134 2516.325639 2868.683279 0.893673939 0.937622001 0.992300648 0.987683821 1.177059803 1.183751476 0.985668437 1.07675119 0.87717095 1 11.48617298 -8.918818287 5.811368019 0.951877193 1.102359661 0.604684253 0.063017899 0.124194114 6.88847721 0.009970325 0.0182366 1.21E-09 8.918818287 0.150482468 ETTDTDTADQVIASFK ddPTM_HeLa_Romidepsin_16h_R1 2 ETTDTDTADQVIASFK 16 0 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 166.62 0.00019565 16038900 4925.7 4780 5212.4 5029.7 5458.2 5960.5 4866.3 5678.8 5034.6 5066.6 FALSE FALSE TRUE 4865.663674 4847.292965 5303.119636 5611.257579 5179.647687 5579.643287 5279.643401 5843.107118 4584.292767 4934.969002 0.985956279 0.982233721 1.074600394 1.137040086 1.049580592 1.130633908 1.069843275 1.184021038 0.928940539 1 12.26882531 -9.640308005 3.94169149 0.992346304 1.1089307 0.722052501 0.040393918 0.081041881 2.351509522 0.005028926 0.00720123 2.29E-10 9.640308005 0.116584396 ETTSGTSTEPVKNS(ph)SPAPPQPAPGK ddPTM_HeLa_Romidepsin_16h_R1 2 ETTSGTSTEPVKNSSPAPPQPAPGK 25 1 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 ETTSGTSTEPVKNS(0.5)S(0.5)PAPPQPAPGK;ETTSGTSTEPVKNS(0.592)S(0.408)PAPPQPAPGK ; 110.67 1.15E-06 58974000 8814.5 8274.6 7147.2 7664.8 7134.2 7282.9 7139.5 7572.6 8059.1 7478.3 TRUE FALSE FALSE 8707.065484 8391.090036 7271.594018 8551.04024 6770.115153 6817.546194 7745.928952 7791.701233 7338.273912 7284.012688 1.1953666 1.15198729 0.998295078 1.173946368 0.929448567 0.935960231 1.063415082 1.06969902 1.007449359 1 12.83051772 -8.758892712 24.99860158 1.096657652 0.999638869 0.222265711 0.079819733 85.37833389 838073.6199 0.013602216 0.026244742 1.74E-09 8.758892712 -0.097018784 ETVDQVEELRR ddPTM_HeLa_Romidepsin_16h_R1 1 ETVDQVEELRR 11 1 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2;A0A2R8Y5T0 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 140.63 0.0019657 2739300 2232.9 2486.3 2957 2485.7 2501.7 2569.9 1903.8 2718.6 2792.8 2398.2 FALSE FALSE TRUE 2205.684556 2521.302197 3008.465345 2773.10833 2374.028914 2405.691684 2065.508724 2797.258402 2543.004973 2335.894418 0.944256957 1.079373356 1.28792865 1.187171949 1.016325436 1.029880317 0.884247468 1.197510632 1.088664348 1 11.18975935 -10.20558767 6.815166337 0.973721133 1.094770717 0.084117053 0.11226092 0.296574929 30.29227892 0.018562175 0.022711004 6.23E-11 10.20558767 0.121049583 ETVFTKS(ph)PYQEFTDHLVK ddPTM_HeLa_Romidepsin_16h_R1 2 ETVFTKSPYQEFTDHLVK 18 1 E9PQD7;P15880;H0YEN5 E9PQD7 RPS2 40S ribosomal protein S2 1 0 ET(0.009)VFT(0.023)KS(0.795)PY(0.15)QEFT(0.023)DHLVK;ET(0.001)VFT(0.026)KS(0.747)PY(0.221)QEFT(0.004)DHLVK ; 59.606 0.016073 57802000 8532.6 8163.3 8206.4 9562.1 7870 8157.9 7619.2 7739.9 9230.3 8218.8 TRUE FALSE FALSE 8428.601389 8278.223152 8349.22895 10667.71499 7468.364533 7636.636518 8266.374658 7963.841795 8404.71885 8005.274391 1.05288101 1.034096116 1.042965992 1.332585802 0.932930487 0.953950626 1.03261603 0.994824338 1.04989766 1 12.96673514 ETVNS(ph)PAIYK ddPTM_HeLa_Romidepsin_16h_R1 3 ETVNSPAIYK 10 0 Q9Y3A2 Q9Y3A2 UTP11L Probable U3 small nucleolar RNA-associated protein 11 1 0 ET(0.36)VNS(0.491)PAIY(0.15)K;ET(0.022)VNS(0.968)PAIY(0.01)K;ET(0.306)VNS(0.692)PAIY(0.002)K ;; 143.55 0.0041786 40594500 8008.6 9859 8165.3 7088.8 7655.2 7967 6962.4 7229.1 9948.3 9665 TRUE FALSE FALSE 7910.988103 9997.795261 8307.413621 7908.44041 7264.526579 7457.934412 7553.786082 7438.262603 9058.499132 9413.901907 0.840351661 1.062024584 0.88246231 0.84008103 0.771680718 0.792225635 0.802407562 0.790135979 0.962247028 1 13.2005771 -9.228307895 2.610598134 0.933607073 0.792164114 0.63966347 0.057163817 0.194744342 2.620027132 0.01108753 0.018964159 5.91E-10 9.228307895 -0.141442959 ETVQTTEDQILK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 ETVQTTEDQILKR 13 1 P18206-2;P18206 P18206-2 VCL Vinculin 0 1 ; ETVQTTEDQILK(1)R;ETVQTTEDQILK(1)R 221.8 1.01E-30 1617090 365.32 241.686 481.64 115.13 718.75 500.9 447.77 620.41 532.58 349.88 FALSE TRUE FALSE 360.8673393 245.0884619 490.0227422 128.4418723 682.0695055 468.8941066 485.8035726 638.3605845 484.9447109 340.7900672 1.058913901 0.719177246 1.437902068 0.376894413 2.00143599 1.37590309 1.425521514 1.873178376 1.423001307 1 8.412739476 -8.747057581 24.99999916 0.996238508 1.63068146 0.480677244 0.33834205 137.1425268 238394.6832 0.03985764 0.079423934 1.79E-09 8.747057581 0.634442951 ETVQTTQS(ph)PTPVEK ddPTM_HeLa_Romidepsin_16h_R1 2 ETVQTTQSPTPVEK 14 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 0 ETVQT(0.001)T(0.019)QS(0.62)PT(0.36)PVEK;ETVQT(0.002)T(0.002)QS(0.987)PT(0.009)PVEK ; 228.11 3.88E-33 17983500 8321.9 7785.7 8984.2 4303.8 7326.4 7714 5624.5 5877.1 8528.7 8582.2 TRUE FALSE FALSE 8220.469482 7895.307289 9140.566232 4801.425606 6952.506469 7221.100296 6102.24489 6047.144616 7765.871711 8359.233207 0.983399946 0.944501379 1.093469461 0.57438589 0.831715816 0.863847211 0.730000556 0.72340901 0.929017234 1 13.02915489 -9.273850111 24.99983676 0.994536658 0.755313274 0.685568131 0.082914556 310.2742123 625006.7463 0.011670565 0.017904309 5.32E-10 9.273850111 -0.239223384 ETVQTTQSPT(ph)PVEK ddPTM_HeLa_Romidepsin_16h_R1 2 ETVQTTQSPTPVEK 14 0 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 0 ETVQT(0.006)T(0.108)QS(0.17)PT(0.715)PVEK;ETVQT(0.001)T(0.001)QS(0.302)PT(0.696)PVEK ; 191.63 8.36E-11 29826000 7945 7681.4 8736.7 4536.8 6334.8 7173.6 5643.2 6130.3 8144.8 8489.3 TRUE FALSE FALSE 7848.163284 7789.538951 8888.758599 5061.366162 6011.511518 6715.230112 6122.533267 6307.670558 7416.308689 8268.746762 0.949135765 0.942045896 1.074982564 0.612108014 0.727016039 0.812121873 0.740442711 0.762832717 0.896908432 1 13.01345297 -9.265408623 24.99950304 0.979035797 0.73573026 0.7821013 0.063720724 106.0148902 667713.7701 0.008869864 0.013861006 5.43E-10 9.265408623 -0.243305537 ETVSEAPPLLFS(ph)DEEEKEAQLGVK ddPTM_HeLa_Romidepsin_16h_R1 3 ETVSEAPPLLFSDEEEKEAQLGVK 24 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 ETVSEAPPLLFS(1)DEEEKEAQLGVK;ETVSEAPPLLFS(1)DEEEKEAQLGVK;ETVSEAPPLLFS(1)DEEEKEAQLGVK ;; 169.51 1.50E-14 103855300 9983.6 9614 11257.4 8393.18 12634.3 13958.3 11968.8 13057.4 11212.5 11058.3 TRUE FALSE FALSE 9861.916043 9749.346144 11453.33032 9363.638963 11989.52453 13066.40968 12985.42957 13435.19527 10209.62592 10771.00377 0.915598606 0.905147408 1.063348465 0.869337637 1.113129731 1.213109749 1.205591405 1.247348488 0.947880637 1 13.39486508 -8.544417557 3.953604413 0.957668844 1.215692164 0.846493872 0.052345618 0.062894932 2.192409944 0.007894142 0.017064817 2.85E-09 8.544417557 0.258023321 ETVVEVPQVTWEDIGGLEDVKR ddPTM_HeLa_Romidepsin_16h_R1 1 ETVVEVPQVTWEDIGGLEDVKR 22 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 148.19 5.31E-06 13150000 1921 1895.7 1802.3 2056.3 2353.8 2264.5 1868.9 2215.7 2137.6 2250.6 FALSE FALSE TRUE 1897.586113 1922.387714 1833.668275 2294.059081 2233.676803 2119.805758 2027.644319 2279.807784 1946.407702 2192.129088 0.865636118 0.876950051 0.836478237 1.046498171 1.018953133 0.967007723 0.924965747 1.03999705 0.887907429 1 11.09811704 -9.243379438 24.99553172 0.922697383 0.994621778 0.434136782 0.055610412 1052.853917 1457183.729 0.010505908 0.017399104 5.71E-10 9.243379438 0.071924395 ETYYLSDS(ph)PLLGPPVGEPR ddPTM_HeLa_Romidepsin_16h_R1 3 ETYYLSDSPLLGPPVGEPR 19 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 0 ET(0.001)YYLS(0.103)DS(0.896)PLLGPPVGEPR;ETYYLS(0.006)DS(0.994)PLLGPPVGEPR;ET(0.002)YY(0.009)LS(0.407)DS(0.582)PLLGPPVGEPR ;; 169.72 1.54E-07 28788700 7525.7 7403.64 7618.4 7037.5 8815 9811.2 7945.1 9000.6 8193.9 7555.4 TRUE FALSE FALSE 7433.973874 7507.868638 7750.995056 7851.208862 8365.137657 9184.295984 8619.956596 9261.01816 7461.017062 7359.109619 1.010173004 1.020214269 1.053251746 1.0668694 1.13670513 1.248017282 1.171331457 1.258442752 1.013847795 1 12.84531551 -8.726513399 1.010289815 1.005374378 1.235368245 0.92656236 0.025499902 0.088012726 0.171528727 0.003866 0.012420313 1.88E-09 8.726513399 0.229993867 EVAATEEDVTRLPS(ph)PT(ph)SPFSSLSQDQAATSK ddPTM_HeLa_Romidepsin_16h_R1 2 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 2 0 EVAAT(0.018)EEDVT(0.022)RLPS(0.494)PT(0.292)S(0.292)PFS(0.321)S(0.321)LS(0.221)QDQAAT(0.01)S(0.011)K;EVAATEEDVT(0.001)RLPS(0.866)PT(0.596)S(0.457)PFS(0.054)S(0.019)LS(0.006)QDQAATSK ; 103.27 3.82E-13 1360100 1469.21 1633.03 1414.25 1252.95 2011.61 2035.55 1774.46 1662.41 1695.26 1459.98 TRUE FALSE FALSE 1451.302703 1656.019839 1438.864428 1397.821974 1908.950035 1905.484924 1925.182588 1710.509211 1543.6317 1422.049509 1.02057115 1.164530369 1.011824426 0.982962946 1.342393512 1.33995681 1.353808412 1.202847861 1.085497861 1 10.47375598 -8.760132188 25 1.02134559 1.315056113 0.797652658 0.064882479 9.692193194 185355.8918 0.009043124 0.01731871 1.74E-09 8.760132188 0.293710524 EVAATEEDVTRLPS(ph)PTS(ph)PFSSLSQDQAATSK ddPTM_HeLa_Romidepsin_16h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 2 0 EVAAT(0.001)EEDVT(0.006)RLPS(0.697)PT(0.443)S(0.737)PFS(0.083)S(0.031)LS(0.001)QDQAATSK 88.633 1.41E-10 5563100 1294 1438.2 1273.7 1530.9 1767.3 1511.4 1474.1 1972.4 1824.9 1540.7 TRUE FALSE FALSE 1278.22823 1458.447017 1295.868214 1707.909861 1677.108086 1414.826418 1599.310017 2029.468282 1661.676373 1500.672392 0.851770338 0.971862363 0.863525058 1.13809641 1.117571094 0.942794993 1.065728953 1.352372638 1.107287895 1 10.55139334 -9.254538493 24.93316659 0.927497516 1.109765967 0.307700557 0.117862893 409.3182148 1478880.958 0.016381661 0.026779998 5.56E-10 9.254538493 0.182268452 EVAATEEDVTRLPS(ph)PTSPFSSLSQDQAATSK ddPTM_HeLa_Romidepsin_16h_R1 5 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 1 0 EVAATEEDVT(0.001)RLPS(0.972)PT(0.022)S(0.005)PFSSLSQDQAATSK;EVAATEEDVT(0.001)RLPS(0.362)PT(0.269)S(0.269)PFS(0.073)S(0.02)LS(0.006)QDQAATSK;EVAAT(0.002)EEDVT(0.007)RLPS(0.375)PT(0.148)S(0.148)PFS(0.148)S(0.148)LS(0.023)QDQAATSK;EVAATEEDVT(0.056)RLPS(0.283)PT(0.283)S(0.283)PFS(0.039)S(0.047)LS(0.01)QDQAATSK;EVAATEEDVT(0.002)RLPS(0.892)PT(0.068)S(0.023)PFS(0.008)S(0.004)LS(0.004)QDQAATSK ;;;; 149.16 1.41E-16 686010000 11434.34 11247.58 11439.33 11799 12021.2 11468.37 10703.94 11141.32 12662.8 11371.66 TRUE FALSE FALSE 11294.97387 11405.92373 11638.42674 13163.2559 11407.71331 10735.57817 11613.1324 11463.67652 11530.20745 11076.22263 1.019749624 1.029766564 1.050757747 1.18842464 1.029928134 0.96924543 1.048474085 1.034980687 1.040987332 1 13.43517834 -10.11331612 2.238523469 1.00872471 1.053882 0.066826938 0.052424001 0.492601836 4.777516836 0.009466335 0.011853197 7.70E-11 10.11331612 0.04515729 EVAATEEDVTRLPSPTSPFSSLS(ph)QDQAATSK ddPTM_HeLa_Romidepsin_16h_R1 1 EVAATEEDVTRLPSPTSPFSSLSQDQAATSK 31 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 1 0 EVAATEEDVT(0.039)RLPS(0.151)PT(0.151)S(0.151)PFS(0.151)S(0.151)LS(0.194)QDQAAT(0.01)S(0.003)K 52.96 0.0031169 6209200 578.37 603.49 546.65 535.72 477.93 604.71 497.08 671.88 601.49 537.7 TRUE FALSE FALSE 571.320604 611.9859481 556.1642139 597.662467 453.5394487 566.0709826 539.3019628 691.3197877 547.6912279 523.7304765 1.090867592 1.168513149 1.061928299 1.141164194 0.865978722 1.080844075 1.02973187 1.31999152 1.045750157 1 9.032680749 -16.52287369 0.013187196 1.23E-07 1.949593749 0.087520861 0.107020626 12026.03121 12.81431526 1140.539046 785.2237231 3.00E-17 16.52287369 1.949593625 EVADIFNAPS(ph)DDEEFVGFR ddPTM_HeLa_Romidepsin_16h_R1 3 EVADIFNAPSDDEEFVGFR 19 0 Q96GN5-5;Q96GN5-2;Q96GN5 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 0 EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR;EVADIFNAPS(1)DDEEFVGFR ;; 250.38 1.55E-62 40720000 4972.1 4529.29 4529.52 3114.55 5655.87 5659.01 4870.28 4889.36 5092.88 5156 TRUE FALSE FALSE 4911.498133 4593.053464 4608.354396 3474.668925 5367.229849 5297.417525 5283.961462 5030.825917 4637.360057 5022.046377 0.977987411 0.914578066 0.917624819 0.691883082 1.068733629 1.054832458 1.05215306 1.0017482 0.923400485 1 12.29405964 EVAENQQNQSSDPEEEKGSQPPPAAES(ph)QSSLRR ddPTM_HeLa_Romidepsin_16h_R1 1 EVAENQQNQSSDPEEEKGSQPPPAAESQSSLRR 33 2 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3;E9PJP4;E9PQD2;E9PIG0;E9PRG1;E9PQN0 O43491 EPB41L2 Band 4.1-like protein 2 1 0 EVAENQQNQS(0.001)S(0.001)DPEEEKGS(0.002)QPPPAAES(0.332)QS(0.332)S(0.332)LRR 47.439 0.0073107 9797700 1234.4 1310 1549.6 926.15 1334.4 1669.9 1118.8 1248.5 1276.7 1474.8 TRUE FALSE FALSE 1219.354658 1328.442214 1576.570138 1033.235821 1266.300589 1563.198779 1213.830844 1284.623378 1162.508754 1436.484483 0.848846383 0.924787027 1.097519783 0.719280878 0.881527509 1.088211392 0.845001013 0.894282808 0.80927345 1 10.48832669 -9.274482012 24.95962157 0.937975952 0.894425025 0.045533246 0.111723461 2452.816196 4693933.153 0.017019629 0.026095176 5.32E-10 9.274482012 -0.043550926 EVAENQQNQSSDPEEEKGSQPPPAAESQS(ph)SLRR ddPTM_HeLa_Romidepsin_16h_R1 1 EVAENQQNQSSDPEEEKGSQPPPAAESQSSLRR 33 2 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3;E9PJP4;E9PQD2;E9PIG0;E9PRG1;E9PQN0 O43491 EPB41L2 Band 4.1-like protein 2 1 0 EVAENQQNQSSDPEEEKGS(0.015)QPPPAAES(0.092)QS(0.446)S(0.446)LRR 48.627 0.006329 10837000 3248.9 3623.6 3638.9 3268.6 3740.6 4007 3401.5 3630.7 3391.4 3954.2 TRUE FALSE FALSE 3209.301157 3674.613136 3702.233528 3646.530911 3549.703224 3750.965632 3690.423325 3735.748576 3088.06469 3851.469314 0.833266708 0.954080855 0.961252246 0.946789553 0.921649099 0.973905106 0.958185831 0.969954132 0.80178873 1 11.91119322 -10.07093658 24.99963907 0.91981269 0.954630169 0.19568582 0.054462772 353.9656361 124744.0034 0.01036018 0.012688579 8.49E-11 10.07093658 0.034817479 EVAES(ph)PRPR ddPTM_HeLa_Romidepsin_16h_R1 2 EVAESPRPR 9 1 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 EVAES(1)PRPR;EVAES(1)PRPR ; 80.737 0.022051 18972400 5172.1 4987.2 5839.3 5509.9 3948.7 3144.3 3244.9 1750.24 6259 5763.1 TRUE FALSE FALSE 5109.060456 5057.409933 5940.930567 6146.980563 3747.183104 2943.389378 3520.521725 1800.880433 5699.179364 5613.373831 0.910158598 0.900957265 1.058352917 1.095059896 0.667545618 0.524352995 0.627166804 0.320819615 1.015285911 1 12.45465243 -8.580354089 4.118653534 0.968414204 0.513936395 0.856988943 0.093710897 0.060883734 2.122933166 0.013687096 0.028796844 2.63E-09 8.580354089 -0.454477809 EVAPVTNFSDSDDT(ph)MVAK ddPTM_HeLa_Romidepsin_16h_R1 1 EVAPVTNFSDSDDTMVAK 18 0 Q9NWQ4-4;Q9NWQ4;G3V5D0;G3V290;G3V553;Q9NWQ4-1 Q9NWQ4-4 GPATCH2L G patch domain-containing protein 2-like 1 0 EVAPVTNFS(0.018)DS(0.227)DDT(0.755)MVAK 85.522 0.023286 6913500 3224.2 3039.2 2938.7 3024.3 3776.8 4009.8 3671.9 4706 3396.4 3318.2 TRUE FALSE FALSE 3184.90221 3081.985937 2989.846841 3373.983796 3584.055803 3753.586721 3983.791094 4842.160685 3092.617478 3231.992686 0.985429894 0.953586916 0.925078468 1.043932992 1.108930666 1.161384658 1.23261142 1.498196672 0.956876385 1 11.65820822 -6.48013167 0.61238446 0.984541401 2.529307397 0.952007194 0.03646015 1.158175455 0.150078227 0.006811222 1.572848819 3.31E-07 6.48013167 1.544765996 EVDAT(ph)SPAPSTSSTVK ddPTM_HeLa_Romidepsin_16h_R1 2 EVDATSPAPSTSSTVK 16 0 H3BM18;X6RHM1;Q16666-3;Q16666-2;Q16666;Q16666-6 H3BM18 IFI16 Gamma-interferon-inducible protein 16 1 0 EVDAT(0.642)S(0.358)PAPSTSSTVK;EVDAT(0.885)S(0.11)PAPS(0.004)T(0.001)SSTVK ; 260.96 5.44E-72 103810000 10216 10448.7 10666 8102.3 9665.4 10049.8 9069.6 8827.7 11828.6 10192.9 TRUE FALSE FALSE 10091.48346 10595.79707 10851.63726 9039.126048 9172.138571 9407.650214 9839.971598 9083.115572 10770.62039 9928.086989 1.016458002 1.067254657 1.09302399 0.910459997 0.923857595 0.94757935 0.991124635 0.914890813 1.08486362 1 13.27730004 -9.239580635 24.99570968 1.019189427 0.940349929 0.61845999 0.041102939 516.9417846 591128.8996 0.005816979 0.0096413 5.76E-10 9.239580635 -0.078839498 EVDATS(ph)PAPSTSSTVK ddPTM_HeLa_Romidepsin_16h_R1 2 EVDATSPAPSTSSTVK 16 0 H3BM18;X6RHM1;Q16666-3;Q16666-2;Q16666;Q16666-6 H3BM18 IFI16 Gamma-interferon-inducible protein 16 1 0 EVDAT(0.035)S(0.947)PAPS(0.015)T(0.002)SSTVK;EVDAT(0.095)S(0.901)PAPS(0.002)T(0.002)SSTVK ; 175.66 1.29E-06 113420000 9553.7 8032.7 8992.5 7053.2 8817.1 9742 8694.3 8456.7 10069.5 9320.7 TRUE FALSE FALSE 9437.25583 8145.784561 9149.01069 7868.72417 8367.130486 9119.517641 9432.793625 8701.381272 9168.8587 9078.54687 1.039511715 0.897256431 1.007761575 0.866738288 0.921637637 1.004512922 1.039020204 0.95845529 1.009947829 1 13.14824568 -10.29003719 24.98849739 1.018658311 0.958685284 0.228112883 0.050419801 786.3173108 687073.9862 0.008896759 0.010174903 5.13E-11 10.29003719 -0.059973028 EVDDLEQWIAER ddPTM_HeLa_Romidepsin_16h_R1 4 EVDDLEQWIAER 12 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ;;; ;;; 208.33 1.14E-14 38232600 8507.1 7331.7 8127.2 7544.2 7595.14 7508.2 6382.85 7900.65 9151 7671.7 FALSE FALSE TRUE 8403.412193 7434.915865 8268.650507 8416.495901 7207.531664 7028.450252 6925.00912 8129.242843 8332.511641 7472.388128 1.12459525 0.994985236 1.106560629 1.12634619 0.964555312 0.940589559 0.926746443 1.087904255 1.115106911 1 12.86735368 -8.736961934 24.99152545 1.063082014 0.973337291 0.3652146 0.061192785 225.6813457 230419.9518 0.009596641 0.019186365 1.83E-09 8.736961934 -0.089744723 EVDDLGPEVGDIK ddPTM_HeLa_Romidepsin_16h_R1 2 EVDDLGPEVGDIK 13 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 0 ; ; 164.9 0.00194 8024900 3730.7 3799.01 3863.52 3657.7 3279.76 4099.84 2907.36 3134.13 3911.57 3459.9 FALSE FALSE TRUE 3685.228793 3852.492562 3930.762945 4080.620484 3112.381609 3837.873456 3154.311086 3224.811107 3561.709382 3370.011299 1.093536035 1.143169034 1.166394589 1.210862553 0.923552277 1.138831035 0.935994217 0.956914034 1.056883514 1 11.71853771 -8.72072342 24.99999926 1.074052239 0.995764399 0.285546202 0.083032541 238.3672938 146358.8985 0.01346832 0.026936387 1.90E-09 8.72072342 -0.07828784 EVDEDFDSK ddPTM_HeLa_Romidepsin_16h_R1 1 EVDEDFDSK 9 0 Q96C19;H0Y4Y4 Q96C19 EFHD2 EF-hand domain-containing protein D2 0 0 147.51 1.58E-05 0 1437.2 2039.6 1681 1131.6 1715.3 1969.8 1627 1522.9 1726.1 1702.5 FALSE FALSE TRUE 1419.682854 2068.313542 1710.2571 1262.440916 1627.76184 1843.936137 1765.197339 1566.962709 1571.713293 1658.268805 0.856123476 1.24727278 1.031350946 0.761300528 0.981603125 1.111964557 1.064482028 0.944938905 0.947803691 1 10.69546217 -8.510527205 24.81118623 0.95103046 1.043517195 0.036006721 0.125086509 1048.87038 2106918.978 0.018988242 0.040498323 3.09E-09 8.510527205 0.092486735 EVDEDS(ph)EPER ddPTM_HeLa_Romidepsin_16h_R1 3 EVDEDSEPER 10 0 F8WC91;B9A018;Q53GS9-3;Q53GS9 F8WC91 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 0 EVDEDS(1)EPER;EVDEDS(1)EPER;EVDEDS(1)EPER ;; 165.63 0.0015351 53881200 5818.8 4768.8 5182.8 2967.39 4759.2 5080 4878.3 4495.39 5306.5 5403.8 TRUE FALSE FALSE 5747.878227 4835.935292 5273.00446 3310.493594 4516.320265 4755.404395 5292.66268 4625.457017 4831.87335 5263.408497 1.092044866 0.918783958 1.001823146 0.628963835 0.858059994 0.903483816 1.00555803 0.87879499 0.918012226 1 12.36178165 -9.859042629 2.107062292 1.041843974 0.868854151 0.18574248 0.106969421 0.250340916 2.26592303 0.017498679 0.02410466 1.38E-10 9.859042629 -0.172989823 EVDEDS(ph)EPEREVR ddPTM_HeLa_Romidepsin_16h_R1 4 EVDEDSEPEREVR 13 1 F8WC91;B9A018;Q53GS9-3;Q53GS9 F8WC91 USP39 U4/U6.U5 tri-snRNP-associated protein 2 1 0 EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR;EVDEDS(1)EPEREVR ;;; 132.51 0.011197 170196500 15443.7 13448.6 13560.6 16313.5 15179 15831.7 13990.9 16017 16013 14423.5 TRUE FALSE FALSE 15255.46624 13637.92974 13796.61655 18199.74363 14404.35899 14820.10546 15179.2867 16480.42662 14580.75717 14048.77539 1.085892956 0.970755768 0.982051187 1.295468332 1.025310647 1.054903723 1.080470452 1.173086349 1.037866773 1 13.77815676 EVDGLLTSEPMGS(ph)PVSSK ddPTM_HeLa_Romidepsin_16h_R1 7 EVDGLLTSEPMGSPVSSK 18 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 EVDGLLTSEPMGS(0.997)PVS(0.002)S(0.001)K;EVDGLLT(0.001)S(0.014)EPMGS(0.979)PVS(0.005)S(0.001)K;EVDGLLTSEPMGS(0.934)PVS(0.053)S(0.013)K;EVDGLLT(0.001)S(0.009)EPMGS(0.806)PVS(0.14)S(0.043)K;EVDGLLTS(0.004)EPMGS(0.994)PVS(0.002)SK;EVDGLLTS(0.004)EPMGS(0.971)PVS(0.02)S(0.006)K;EVDGLLTSEPMGS(0.971)PVS(0.022)S(0.007)K ;;;;;; 178.99 8.17E-10 980422400 39644.8 36792 37124.1 30993.1 32960.5 30950.2 28216 29671.8 41560.6 37655 TRUE FALSE FALSE 39161.59393 37309.95874 37770.22939 34576.66805 31278.40269 28972.58211 30612.66634 30530.30672 37843.31585 36676.71767 1.067750781 1.017265478 1.029814874 0.942741615 0.852813574 0.789944792 0.834662104 0.832416548 1.031807595 1 15.16257691 -8.917957974 1.987745679 1.031861194 0.819494607 0.957269885 0.020167075 0.060152163 0.479884359 0.004325778 0.008846552 1.21E-09 8.917957974 -0.212366587 EVDKT(ph)PPPQPPLISSMDSISQK ddPTM_HeLa_Romidepsin_16h_R1 1 EVDKTPPPQPPLISSMDSISQK 22 1 Q92625;A0A3B3ISP1;A0A3B3ITU5 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 0 EVDKT(0.995)PPPQPPLIS(0.002)S(0.002)MDSISQK 59.537 0.0079158 24941000 2653.4 2463.1 2526.9 2714.3 2996.5 3057.3 2651.8 2869 2530.1 2575.6 TRUE FALSE FALSE 2621.05934 2497.775586 2570.879635 3028.140137 2843.577424 2861.948397 2877.043826 2952.009988 2303.801519 2508.685541 1.044793896 0.995651127 1.024791506 1.207062459 1.13349297 1.140815918 1.146833184 1.17671583 0.91833013 1 11.29271593 -9.276401832 24.34906307 1.019619747 1.157550172 0.805200631 0.039587787 133.4138296 217109.8299 0.00390522 0.005981567 5.29E-10 9.276401832 0.137930425 EVDQDDEENS(ph)EEDEMDSGTMVR ddPTM_HeLa_Romidepsin_16h_R1 2 EVDQDDEENSEEDEMDSGTMVR 22 0 F5H5B4;Q13043-2;Q13043 F5H5B4 STK4 Serine/threonine-protein kinase 4;Serine/threonine-protein kinase 4 37kDa subunit;Serine/threonine-protein kinase 4 18kDa subunit 1 0 EVDQDDEENS(0.762)EEDEMDS(0.111)GT(0.127)MVR;EVDQDDEENS(0.797)EEDEMDS(0.12)GT(0.084)MVR ; 52.99 0.0096959 9388000 1846.35 1661.8 1982.7 2091.99 3351.2 3886.1 3425.2 3470.6 2206.79 2233.14 TRUE FALSE FALSE 1823.845976 1685.194864 2017.208062 2333.875727 3180.175759 3637.790752 3716.136403 3571.016335 2009.409175 2175.122701 0.838502571 0.774758529 0.927399664 1.07298578 1.462067293 1.672453122 1.708472079 1.641753973 0.923814171 1 11.08688107 -8.723429951 1.970972856 0.908271219 1.681476132 0.972387445 0.059072655 0.048728248 0.384769382 0.012282578 0.0279394 1.89E-09 8.723429951 0.773204913 EVEDKES(ph)EGEEEDEDEDLSK ddPTM_HeLa_Romidepsin_16h_R1 10 EVEDKESEGEEEDEDEDLSK 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(0.991)EGEEEDEDEDLS(0.009)K;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(0.996)EGEEEDEDEDLS(0.004)K;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK;EVEDKES(1)EGEEEDEDEDLSK ;;;;;;;;; 85.496 0.0010334 4376098900 19956.23 22110.12 19734.02 17615.88 19847.77 19418.33 18039.69 20553.47 21073.47 21267.36 TRUE FALSE FALSE 19712.99579 22421.38685 20077.48234 19652.71093 18834.86423 18177.56138 19571.98082 21148.15223 19188.60606 20714.83092 0.951636818 1.08238329 0.969232258 0.948726591 0.909245376 0.87751435 0.944829378 1.020918409 0.926322119 1 14.33837642 -9.25859412 3.726955863 0.985880248 0.934431121 0.169093043 0.050932497 0.298129188 9.259432859 0.00763663 0.01250729 5.51E-10 9.25859412 -0.051449127 EVEDKES(ph)EGEEEDEDEDLSKYK ddPTM_HeLa_Romidepsin_16h_R1 2 EVEDKESEGEEEDEDEDLSKYK 22 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 EVEDKES(1)EGEEEDEDEDLSKYK;EVEDKES(1)EGEEEDEDEDLSKYK ; 65.085 0.0030139 133755000 6735.5 5872.5 5437 6556.4 5988.7 6179.3 5251.3 6011.6 6309.1 6187 TRUE FALSE FALSE 6653.405135 5955.173209 5531.628704 7314.481817 5683.074292 5784.462673 5697.345291 6185.536161 5744.798295 6026.260848 1.10406856 0.98820369 0.917920555 1.213767874 0.943051493 0.95987592 0.945419628 1.026430206 0.953293998 1 12.55704741 EVEDKESEGEEEDEDEDLSK ddPTM_HeLa_Romidepsin_16h_R1 2 EVEDKESEGEEEDEDEDLSK 20 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 0 ; ; 91.622 0.0011138 5465100 1816.31 1451.25 1366.64 894.47 1648.76 1385.45 1381.38 1618.43 2191.66 1899.01 FALSE FALSE TRUE 1794.172115 1471.680736 1390.425796 997.89283 1564.617625 1296.924216 1498.714383 1665.256719 1995.63244 1849.673446 0.969993984 0.795643544 0.7517142 0.539496759 0.845888569 0.701163883 0.810258906 0.900297683 1.078910682 1 10.85305487 -10.22203219 2.964173193 0.987830394 0.752721631 0.59525107 0.09510415 0.134510685 2.32786035 0.01554809 0.018711766 6.00E-11 10.22203219 -0.235108763 EVEEELATSGGQS(ph)PTGEQIPQFQQR ddPTM_HeLa_Romidepsin_16h_R1 2 EVEEELATSGGQSPTGEQIPQFQQR 25 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 EVEEELATSGGQS(0.993)PT(0.007)GEQIPQFQQR;EVEEELAT(0.02)S(0.287)GGQS(0.659)PT(0.033)GEQIPQFQQR ; 142.85 1.46E-07 13109900 3150.1 3529.9 3310.9 2989.3 4167.9 4428.7 3897.2 4299.5 3641.1 3624.2 TRUE FALSE FALSE 3111.70537 3579.594025 3368.524826 3334.936931 3955.19651 4145.720363 4228.228071 4423.899249 3315.430897 3530.042762 0.881492259 1.014037015 0.954244765 0.944729896 1.120438697 1.174410805 1.197783811 1.253214068 0.939204174 1 11.78546994 -8.556296473 1.849179416 0.94794269 1.216112474 0.893418392 0.039749942 0.097166243 0.659964125 0.007745427 0.020057752 2.78E-09 8.556296473 0.268169784 EVEELEQLTQQLMQDMEHPQR ddPTM_HeLa_Romidepsin_16h_R1 1 EVEELEQLTQQLMQDMEHPQR 21 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 0 0 49.528 0.019076 2477300 362.16 378.95 380.86 499.65 306.34 482.83 276.39 387.56 390.87 292.78 FALSE FALSE TRUE 357.7458546 384.284868 387.4887085 557.4218839 290.7063267 451.9787213 299.8665597 398.7734371 355.9096082 285.1735334 1.254484771 1.347547451 1.358782156 1.954676078 1.019401496 1.584925206 1.051523106 1.3983536 1.248045722 1 8.155696283 -11.19786691 0.76882232 1.030437647 1.388551284 0.121369322 0.257674711 0.562863451 0.720116846 0.089457952 0.05595683 6.34E-12 11.19786691 0.358113637 EVEETDEMDQVELVDFDPNQER ddPTM_HeLa_Romidepsin_16h_R1 2 EVEETDEMDQVELVDFDPNQER 22 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 0 ; ; 112.58 0.00043593 22939000 3526.8 3153.4 3403.9 3835.2 3576 3811.3 3463.8 3430.7 3908.8 3662.6 FALSE FALSE TRUE 3483.814005 3197.793648 3463.143452 4278.643869 3393.503376 3567.77023 3758.015086 3529.961892 3559.187138 3567.445124 0.976557139 0.896382015 0.970762922 1.199358006 0.951241928 1.000091131 1.053419171 0.989492976 0.997685182 1 11.80067552 SSIAPEEQSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SSIAPEEQSKK 11 1 A0A1B0GVD3;Q6ZN17-2;Q6ZN17 A0A1B0GVD3 LIN28B Protein lin-28 homolog B 0 1 ; SSIAPEEQSK(1)K;SSIAPEEQSK(1)K 98.044 0.011597 7859600 2475.6 2116.7 2747.5 3020.7 5073.3 5040.3 4818.6 4353.1 2371 1728.76 FALSE TRUE FALSE 2445.426435 2146.498958 2795.319085 3369.967547 4814.39057 4718.241097 5227.891764 4479.05008 2158.931822 1683.846566 1.452285787 1.274759234 1.660079452 2.001350726 2.85916227 2.802061181 3.104731672 2.660010817 1.282142842 1 10.71754497 -9.087481781 1.203000199 1.210207357 2.938721815 0.946619614 0.171242576 0.077646336 0.221966694 0.033980699 0.074578769 8.18E-10 9.087481781 1.728514458 up EVEKVK(ac)LDQK ddPTM_HeLa_Romidepsin_16h_R1 1 EVEKVKLDQK 10 2 M0QXN5;P37198 M0QXN5 NUP62 Nuclear pore glycoprotein p62 0 1 EVEK(0.182)VK(0.818)LDQK 101.9 0.0013935 0 185.47 63.364 135.31 517.02 2091.3 2728.2 2479.4 3026.3 262.68 105.35 FALSE TRUE FALSE 183.2094203 64.25604006 137.6650138 576.8002851 1984.573157 2553.876825 2690.000174 3113.861216 239.1852429 102.6129918 1.785440782 0.626197901 1.341594386 5.621123357 19.34036931 24.88843547 26.21500579 30.34568197 2.330945026 1 6.681069592 -8.658525568 1.684167832 1.227193565 27.73486223 0.988525428 1.247780135 0.023892082 0.136191951 0.182000627 0.456968821 2.20E-09 8.658525568 26.50766867 EVEPEPTEDKDLEADEEDTR ddPTM_HeLa_Romidepsin_16h_R1 2 EVEPEPTEDKDLEADEEDTR 20 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 0 ; ; 108.97 0.00044823 45131000 3388.8 3166.9 3399.5 2252.16 3239.1 3101.4 2586.7 2991.2 3564.5 3509.1 FALSE FALSE TRUE 3347.496002 3211.483701 3458.666871 2512.565336 3073.79664 2903.230549 2806.414233 3077.745653 3245.682193 3417.933076 0.97939191 0.939598181 1.011917669 0.735112502 0.89931446 0.849411175 0.821085191 0.900469841 0.949603787 1 11.73890843 -9.284638692 24.98301071 0.986890916 0.843666122 0.660302537 0.048095278 296.6542928 319461.8917 0.006568625 0.010037773 5.19E-10 9.284638692 -0.143224794 EVFEFRPELVNDDDEEADDTR ddPTM_HeLa_Romidepsin_16h_R1 4 EVFEFRPELVNDDDEEADDTR 21 1 Q8WU90;Q8WU90-2 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 0 ;;; ;;; 240.13 9.70E-54 73201200 4800.09 4223.95 4697.43 3284.45 4354.37 4743.5 4575.26 4571.17 5102.13 4948.6 FALSE FALSE TRUE 4741.584657 4283.414879 4779.186799 3664.213563 4132.150251 4440.405659 4963.88247 4703.429592 4645.782714 4820.034659 0.983724183 0.888668896 0.991525401 0.760204816 0.857286419 0.921239363 1.02984373 0.975808251 0.963848404 1 12.2348278 -10.35827824 5.638486082 0.992835586 0.916786694 0.141494486 0.071870311 0.29338456 13.83872193 0.012832757 0.014620345 4.38E-11 10.35827824 -0.076048893 EVGEHLVSIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EVGEHLVSIKK 11 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 1 ; EVGEHLVSIK(1)K;EVGEHLVSIK(1)K 103.34 0.0036566 3323400 2192.9 1807.37 2288.4 1073.82 6167 5589.5 4814.4 5243.2 4764.7 4395.4 FALSE TRUE FALSE 2166.172091 1832.814202 2328.228642 1197.980121 5852.274978 5232.348989 5223.335016 5394.90372 4338.533299 4281.206874 0.505972301 0.4281069 0.543825307 0.279822993 1.366968509 1.22216682 1.220061345 1.26013619 1.013390249 1 12.06380184 -8.741567092 24.99634061 0.684056208 1.260730649 0.656353161 0.224277304 148.8194803 187191.5669 0.03851134 0.0769406 1.81E-09 8.741567092 0.576674441 EVIEIEDAS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 EVIEIEDASPTK 12 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 EVIEIEDAS(0.5)PT(0.5)K 147.73 0.0014837 4315400 3181.7 2483.6 3889.5 3980.5 2371.2 2108.6 1678.1 1738.6 2942.6 3009.3 TRUE FALSE FALSE 3142.920217 2518.564186 3957.195116 4440.744139 2250.188816 1973.867265 1820.637772 1788.903648 2679.406486 2931.117952 1.072259891 0.85925037 1.350063416 1.515034267 0.767689616 0.673417889 0.621141081 0.610314452 0.914124416 1 11.51723531 -8.539519222 24.98933222 1.07931523 0.648072313 0.584813071 0.186549253 135.7959688 203926.9101 0.027524991 0.055060686 2.89E-09 8.539519222 -0.431242917 EVIEIEDASPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EVIEIEDASPTK 12 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 EVIEIEDAS(0.077)PT(0.923)K 152.4 0.0029541 8479200 4683 5084.3 4808.7 6169 3969.9 3593.3 2884.4 2484.6 4729.8 5536.1 TRUE FALSE FALSE 4625.921795 5155.876909 4892.393406 6882.288806 3767.301189 3363.699727 3129.400864 2556.487981 4306.754842 5392.271324 0.857880013 0.956160512 0.907297336 1.276324649 0.698648299 0.623800162 0.580349296 0.474102253 0.798690308 1 12.39667738 -8.535946738 24.95167207 0.953992398 0.578129362 0.690386842 0.124285409 91.71822294 175123.8733 0.017114408 0.034243959 2.91E-09 8.535946738 -0.375863036 EVLDEDT(ph)DEEKETLK ddPTM_HeLa_Romidepsin_16h_R1 2 EVLDEDTDEEKETLK 15 1 Q9Y3P9 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 0 EVLDEDT(1)DEEKETLK;EVLDEDT(1)DEEKETLK ; 136.14 0.0052663 23540000 4026 3539.7 4178.4 3846.3 4593.2 5349.7 4198.5 4726.9 4135.5 3700.8 TRUE FALSE FALSE 3976.929563 3589.53199 4251.123299 4291.027303 4358.791864 5007.871435 4555.120485 4863.665394 3765.610522 3604.652682 1.103276769 0.995805229 1.179343386 1.190413524 1.209212717 1.389279877 1.263678053 1.349274347 1.044652801 1 11.81564454 -8.993545181 0.629929048 1.035204099 1.357169684 0.832841528 0.053367984 0.263163888 0.189226655 0.012053322 0.041367061 1.01E-09 8.993545181 0.321965586 EVLEDFAEDGEK ddPTM_HeLa_Romidepsin_16h_R1 1 EVLEDFAEDGEK 12 0 H7C3G2;H7C141;A0A2R8YFD1;A0A2R8Y3X5;A0A2R8YE78;A0A2R8YDM2;C9JMB8;E5KLJ9;O60313-13;O60313;O60313-9;O60313-11;O60313-2;O60313-10 H7C3G2 OPA1 "Dynamin-like 120 kDa protein, mitochondrial;Dynamin-like 120 kDa protein, form S1" 0 0 149.96 0.00085754 0 1821.1 1863.9 1937.4 1274.5 1803.7 2056.7 1701.4 1571.2 1993.8 1867.3 FALSE FALSE TRUE 1798.903733 1890.140033 1971.119634 1421.863687 1711.650458 1925.283508 1845.916874 1616.660193 1815.469534 1818.787277 0.989067691 1.039230952 1.083754906 0.781764698 0.941094366 1.058553429 1.014916311 0.888867111 0.998175849 1 10.8287611 EVLKDMGQRGMS(ph)Y(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 EVLKDMGQRGMSYAK 15 2 Q9Y584 Q9Y584 TIMM22 Mitochondrial import inner membrane translocase subunit Tim22 2 0 EVLKDMGQRGMS(1)Y(1)AK 65.043 0.0032827 0 948.77 900.99 787.29 859.29 1082.1 1177.8 967.24 967.91 1124.4 1027.2 TRUE FALSE FALSE 937.2060263 913.6741609 800.9924522 958.6451529 1026.876399 1102.542381 1049.397341 995.9149487 1023.830848 1000.513196 0.936725303 0.913205508 0.800581597 0.958153432 1.026349681 1.101976851 1.048859071 0.995404111 1.023305692 1 9.96652448 -8.708815558 4.270740193 0.949649552 1.050342586 0.407506967 0.061232097 0.18846736 7.095790885 0.009611053 0.019414989 1.96E-09 8.708815558 0.100693034 EVLTPTS(ph)TSDNETR ddPTM_HeLa_Romidepsin_16h_R1 1 EVLTPTSTSDNETR 14 0 H7C150;H7C183;Q70CQ2-3;Q70CQ2-2;Q70CQ2 H7C150 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 0 EVLT(0.089)PT(0.064)S(0.281)T(0.281)S(0.281)DNET(0.003)R 91.712 0.017643 5894800 2834.5 2502.3 2339.2 2370.6 2798.3 2885.2 2582.6 3155.1 2734.6 2558.5 TRUE FALSE FALSE 2799.952024 2537.527445 2379.912795 2644.699926 2655.492309 2700.845032 2801.96598 3246.387841 2490.010527 2492.029801 1.123562817 1.018257263 0.955009765 1.061263362 1.065594122 1.083793232 1.124370976 1.302708274 0.999189707 1 11.28310561 -6.729403966 1.097201437 1.048916193 1.809078087 0.758686502 0.045546033 2.190396175 0.938994725 0.008403717 2.561705993 1.86E-07 6.729403966 0.760161894 EVLTPTST(ph)SDNETR ddPTM_HeLa_Romidepsin_16h_R1 1 EVLTPTSTSDNETR 14 0 H7C150;H7C183;Q70CQ2-3;Q70CQ2-2;Q70CQ2 H7C150 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 0 EVLT(0.225)PT(0.044)S(0.02)T(0.547)S(0.163)DNETR 141.59 0.00014246 0 1191.7 1413.7 1034.6 1186.6 1093.4 862.53 889.25 1297.7 1309.3 1289.5 TRUE FALSE FALSE 1177.175102 1433.602106 1052.606779 1323.800275 1037.599718 807.4171167 964.7828728 1335.246902 1192.192929 1255.998604 0.937242365 1.141404219 0.838063654 1.053982282 0.826115343 0.642848737 0.768140084 1.063095849 0.949199247 1 10.29461915 -8.67466026 7.203675708 0.977998965 0.805956017 0.289981023 0.122212524 0.203927826 14.39453034 0.016709335 0.033507575 2.12E-09 8.67466026 -0.172042949 EVLTPTSTS(ph)DNETR ddPTM_HeLa_Romidepsin_16h_R1 1 EVLTPTSTSDNETR 14 0 H7C150;H7C183;Q70CQ2-3;Q70CQ2-2;Q70CQ2 H7C150 USP34 Ubiquitin carboxyl-terminal hydrolase 34 1 0 EVLT(0.009)PT(0.027)S(0.027)T(0.176)S(0.761)DNETR 158.52 0.00041805 4161000 2269.9 2055 1817.2 1449.3 2080.9 2044.9 2073.8 2386.9 1971.5 2003.3 TRUE FALSE FALSE 2242.233586 2083.930344 1848.827604 1616.874885 1974.703908 1914.23749 2249.94852 2455.961186 1795.164102 1951.253977 1.149124415 1.067995437 0.947507411 0.828633742 1.012017877 0.981029385 1.153078249 1.258657876 0.920005352 1 10.93018586 -7.53410558 3.850933607 1.036800578 1.24424175 0.422942846 0.091821953 0.189334216 6.035219234 0.014469929 0.075829714 2.92E-08 7.53410558 0.207441172 EVLYDS(ph)EGLSGEER ddPTM_HeLa_Romidepsin_16h_R1 1 EVLYDSEGLSGEER 14 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 EVLYDS(0.925)EGLS(0.075)GEER 184.51 1.22E-07 4511500 2068.5 1812.4 1661.4 1510.8 1882.8 1187.5 1383.8 1507.9 1913.7 1873.1 TRUE FALSE FALSE 2043.288326 1837.915015 1690.31597 1685.485805 1786.71369 1111.622582 1501.339937 1551.528707 1742.533879 1824.436592 1.119955791 1.007387718 0.926486553 0.92383907 0.979323534 0.609296364 0.822906065 0.850415254 0.955107942 1 10.8332353 -8.975984595 0.983618676 1.053754501 0.77645219 0.505531883 0.091584406 0.271440557 0.513355874 0.015794711 0.041662801 1.06E-09 8.975984595 -0.277302311 EVMESAVGNSS(ph)GSGQNEESPR ddPTM_HeLa_Romidepsin_16h_R1 1 EVMESAVGNSSGSGQNEESPR 21 0 Q9NVF7 Q9NVF7 FBXO28 F-box only protein 28 1 0 EVMESAVGNS(0.084)S(0.647)GS(0.011)GQNEES(0.258)PR 180.39 4.05E-13 3717900 994.23 850.57 732.42 583.38 877.51 558.57 476.86 659.15 945.75 1070.3 TRUE FALSE FALSE 982.1119423 862.5443468 745.1674629 650.8331405 832.7273903 522.8791797 517.3644765 678.2214653 861.1597513 1042.493452 0.942079723 0.827385865 0.714793423 0.624304296 0.798784289 0.501565913 0.496275996 0.650576235 0.826057708 1 10.02582261 -9.645103535 0.660353395 0.992928412 0.558488413 0.679115466 0.092243789 0.18888855 0.167652352 0.017903395 0.033678349 2.26E-10 9.645103535 -0.434439999 EVMESAVGNSSGSGQNEES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 EVMESAVGNSSGSGQNEESPR 21 0 Q9NVF7 Q9NVF7 FBXO28 F-box only protein 28 1 0 EVMESAVGNSSGS(0.005)GQNEES(0.995)PR;EVMES(0.001)AVGNS(0.124)S(0.235)GS(0.032)GQNEES(0.609)PR;EVMESAVGNS(0.002)S(0.001)GS(0.014)GQNEES(0.984)PR ;; 154.46 1.12E-07 37737800 12119.7 11584.2 11722.7 7683.7 9004.78 9016.87 7446.3 7905.43 13566.4 13267 TRUE FALSE FALSE 11971.98043 11747.28267 11926.72868 8572.125547 8545.232475 8440.721108 8078.788536 8134.161144 12352.98721 12922.32143 0.92645741 0.909069066 0.922955581 0.663358019 0.661276886 0.653189224 0.6251809 0.629465935 0.9559418 1 13.65757765 -9.283036723 2.871808209 0.959527945 0.641048044 0.970859572 0.025671407 0.041005109 0.677713808 0.005581516 0.009234275 5.21E-10 9.283036723 -0.318479901 EVNS(ph)QEEEEEELLRK ddPTM_HeLa_Romidepsin_16h_R1 3 EVNSQEEEEEELLRK 15 1 Q96RL1-2;Q96RL1-3;Q96RL1;D6RC40;D6RCQ3;Q96RL1-5 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 0 EVNS(1)QEEEEEELLRK;EVNS(1)QEEEEEELLRK;EVNS(1)QEEEEEELLRK ;; 180.32 1.23E-08 22263700 6242.3 5814.8 5483.8 5447.4 4329.4 4133.2 3913.8 4254.5 6498.4 6070 TRUE FALSE FALSE 6166.216447 5896.660907 5579.243239 6077.254019 4108.454563 3869.101859 4246.238074 4377.597245 5917.166828 5912.300525 1.042947059 0.997354732 0.943667057 1.027900052 0.69489948 0.654415628 0.718204032 0.740421977 1.000823081 1 12.52950389 -8.760316354 24.9999748 1.012934061 0.699745878 0.953309272 0.03248529 4.51685809 100546.5385 0.00522117 0.009991349 1.74E-09 8.760316354 -0.313188183 EVPAVPETLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EVPAVPETLKK 11 1 P18124 P18124 RPL7 60S ribosomal protein L7 0 1 ; EVPAVPETLK(1)K;EVPAVPETLK(1)K 138.22 0.000948 2804500 1607.17 1474.28 1614.59 1300.53 3461.31 2886.3 2779.97 3092.56 3527.7 2922.72 FALSE TRUE FALSE 1587.581194 1495.034953 1642.691262 1450.903398 3284.666435 2701.874745 3016.100582 3182.038344 3212.173677 2846.787313 0.557674676 0.525165665 0.577033365 0.509663434 1.153815187 0.949096103 1.059475209 1.117764692 1.128350426 1 11.475119 -8.74756951 24.98243545 0.728665212 1.060644677 0.428160517 0.199840631 204.3115201 368004.2586 0.031604956 0.06295171 1.79E-09 8.74756951 0.331979465 EVPSKEEPS(ph)PVKAEVAEK ddPTM_HeLa_Romidepsin_16h_R1 4 EVPSKEEPSPVKAEVAEK 18 2 P46821;D6RA32;D6RA40 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 EVPS(0.385)KEEPS(0.615)PVKAEVAEK;EVPS(0.003)KEEPS(0.997)PVKAEVAEK;EVPS(0.001)KEEPS(0.999)PVKAEVAEK;EVPS(0.002)KEEPS(0.998)PVKAEVAEK ;;; 96.208 0.0032413 930685000 14175.4 13461.1 12943.2 14316.8 13364.3 12463.1 10584.2 11759.2 14820.6 14116.3 TRUE FALSE FALSE 14002.62477 13650.60572 13168.47097 15972.17578 12682.2699 11666.74813 11483.22168 12099.4339 13495.00842 13749.55649 1.01840556 0.992803348 0.957737871 1.161650253 0.922376653 0.848518142 0.835170334 0.879987213 0.981486816 1 13.74709746 -8.529044451 24.99652852 1.014048857 0.858090998 0.665462942 0.052708206 64.30675008 260707.008 0.0070152 0.014060195 2.96E-09 8.529044451 -0.15595786 EVPWS(ph)PSAEK ddPTM_HeLa_Romidepsin_16h_R1 2 EVPWSPSAEK 10 0 Q5JSZ5;Q5JSZ5-5;Q5JT00 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 EVPWS(0.992)PS(0.008)AEK;EVPWS(0.992)PS(0.008)AEK ; 166.11 0.0014693 203400000 12489.7 12721 11785.5 11520.5 9980.6 8958.2 7640.4 7402.4 13666.9 13241.3 TRUE FALSE FALSE 12337.47073 12900.08657 11990.62168 12852.55442 9471.252739 8385.799931 8289.375385 7616.576765 12444.49823 12897.28912 0.956594104 1.000216903 0.92970093 0.996531465 0.734359961 0.650198647 0.642722305 0.59055641 0.964892554 1 13.65478024 -8.624882529 2.814825317 0.978539247 0.631373903 0.968594586 0.028624729 0.031849225 0.50794939 0.004395804 0.009648609 2.37E-09 8.624882529 -0.347165344 EVQAEIGK(ac)LR ddPTM_HeLa_Romidepsin_16h_R1 2 EVQAEIGKLR 10 1 H3BP71;O75150-3;O75150-4;O75150 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 1 ; EVQAEIGK(1)LR;EVQAEIGK(1)LR 134.84 0.0084202 2022590 959.54 971.34 1198.94 849.06 1147.88 983.32 953.21 1020.81 940.24 1101.19 FALSE TRUE FALSE 947.8447574 985.01455 1219.807048 947.2323121 1089.2994 920.4890255 1034.175634 1050.345527 856.1425795 1072.580925 0.883704656 0.91835919 1.137263417 0.883133655 1.015587146 0.858200071 0.964193572 0.979269258 0.798207911 1 10.06687079 -7.526381503 24.97430491 0.950362958 0.975500378 0.006925179 0.091266929 431.8193291 3078870.574 0.010842319 0.041008933 2.98E-08 7.526381503 0.02513742 EVQAEQPSSS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 EVQAEQPSSSSPR 13 0 A0A1W2PP04;Q9Y388 A0A1W2PP04 RBMX2 "RNA-binding motif protein, X-linked 2" 1 0 EVQAEQPS(0.022)S(0.033)S(0.721)S(0.223)PR;EVQAEQPS(0.006)S(0.072)S(0.704)S(0.218)PR ; 130.47 0.0024301 282520000 12201.9 12366.4 12268.6 9512.9 10269.7 11055.9 10380.3 11027.3 13147.2 12303.7 TRUE FALSE FALSE 12053.17855 12540.4945 12482.12984 10612.82626 9745.598887 10349.46367 11262.00242 11346.35753 11971.2815 11984.0481 1.005768539 1.046432257 1.041562061 0.885579411 0.813214267 0.863603315 0.939749434 0.946788383 0.998934701 1 13.5488277 -9.252363922 24.6373824 1.009414748 0.886853961 0.732449656 0.038691858 241.4568312 655488.8299 0.006293539 0.010331514 5.59E-10 9.252363922 -0.122560787 EVQDKDYPLT(ph)PPPS(ph)PTVDEPK ddPTM_HeLa_Romidepsin_16h_R1 1 EVQDKDYPLTPPPSPTVDEPK 21 1 H3BLS7;Q5THJ4-2;Q5THJ4 H3BLS7 VPS13D Vacuolar protein sorting-associated protein 13D 2 0 EVQDKDY(0.001)PLT(0.996)PPPS(0.755)PT(0.248)VDEPK 65.954 0.0013061 0 1217.2 1049.9 1203 1255.7 1274.3 1384.1 1127.3 1120.2 1256.8 1003.1 TRUE FALSE FALSE 1202.364298 1064.68052 1223.93771 1400.889942 1209.267716 1295.660477 1223.052834 1152.61122 1144.38866 977.0393174 1.230620178 1.089700794 1.252700571 1.433811227 1.237685827 1.326108841 1.251794899 1.179697888 1.171282097 1 9.932272809 -12.16215787 0.382590709 0.922125642 1.280769887 0.278711708 0.096380028 1.288659446 0.262292807 0.191673394 0.032394568 6.88E-13 12.16215787 0.358644246 SK(ac)IPNEHK(ac)KPAEVFR ddPTM_HeLa_Romidepsin_16h_R1 1 SKIPNEHKKPAEVFR 15 3 F2Z2B6;F2Z3N8;Q92613 F2Z2B6 JADE3 Protein Jade-3 0 2 SK(1)IPNEHK(0.988)K(0.012)PAEVFR 81.128 0.0066126 3634500 885.74 779.69 1081.3 1317 1612.6 1887.8 1701.3 1746.1 1200.4 870.55 FALSE TRUE FALSE 874.9442602 790.6664963 1100.119573 1469.277737 1530.303005 1767.175673 1845.80838 1796.620649 1093.033218 847.9329855 1.031855436 0.932463426 1.297413347 1.732775776 1.804745222 2.084098275 2.176832852 2.118823869 1.289056136 1 9.727806439 -9.084718802 1.148379671 1.001587864 2.133615994 0.936739177 0.117546431 0.046274 0.120510949 0.012836829 0.028814504 8.23E-10 9.084718802 1.132028131 up EVS(ph)DLQEEGK ddPTM_HeLa_Romidepsin_16h_R1 1 EVSDLQEEGK 10 0 Q9HBI1 Q9HBI1 PARVB Beta-parvin 1 0 EVS(1)DLQEEGK 104.59 0.021547 2312000 1599.1 1644.9 1617.7 1655.5 1849 1882.5 1663.1 1982.1 1842.7 1577.5 TRUE FALSE FALSE 1579.609554 1668.056945 1645.85539 1846.916699 1754.63863 1762.214325 1804.363672 2039.448936 1677.884297 1536.516323 1.028046062 1.085609649 1.071160368 1.202015672 1.141958992 1.146889427 1.174321187 1.327320059 1.092005514 1 10.58544738 -4 0.192675161 0.975238435 2.409588969 0.698954889 0.049255933 14.12813377 0.159095406 0.041231222 6.093447618 1.00E-04 4 1.434350534 EVS(ph)DSEAGGGPQGER ddPTM_HeLa_Romidepsin_16h_R1 1 EVSDSEAGGGPQGER 15 0 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 EVS(0.959)DS(0.041)EAGGGPQGER 135.61 0.0012999 21854000 1680.6 963.37 1338.3 634.13 1005.4 982.09 1322.4 1067.2 1736.8 1353.8 TRUE FALSE FALSE 1660.116201 976.9323481 1361.59255 707.4510943 954.0906863 919.3376186 1434.724623 1098.077748 1581.456258 1318.628081 1.25897228 0.740870274 1.032582705 0.536505406 0.723547982 0.697192508 1.088043432 0.832742579 1.199319415 1 10.36482199 -10.25369531 24.96364052 1.122292466 0.808935636 0.4815889 0.163304823 420.7390049 1356288.545 0.029271789 0.035494592 5.58E-11 10.25369531 -0.31335683 EVS(ph)DSEAGGGPQGERK ddPTM_HeLa_Romidepsin_16h_R1 2 EVSDSEAGGGPQGERK 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 EVS(0.966)DS(0.034)EAGGGPQGERK;EVS(0.987)DS(0.013)EAGGGPQGERK ; 89.604 0.0038157 11775500 3365.3 3777.3 3566.9 2795.98 3067.5 2763.15 2745.4 2854.6 4007.2 4176.3 TRUE FALSE FALSE 3324.282429 3830.476929 3628.980398 3119.264363 2910.954029 2586.593633 2978.594207 2937.193347 3648.785996 4067.799124 0.817218925 0.94165833 0.892123797 0.766818682 0.71560909 0.635870542 0.73223729 0.722059585 0.89699267 1 11.99003272 -9.139793953 2.193837059 0.914098458 0.698492565 0.806459065 0.048717789 0.143520225 1.351552138 0.011257516 0.020422708 7.25E-10 9.139793953 -0.215605893 EVS(ph)PEVVR ddPTM_HeLa_Romidepsin_16h_R1 2 EVSPEVVR 8 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 EVS(1)PEVVR;EVS(1)PEVVR ; 109.29 0.02321 351020000 12598.2 12019.3 11714.4 11451.4 12116.9 12172.3 10563.8 11562.4 13191.1 11422.3 TRUE FALSE FALSE 12444.64829 12188.50802 11918.28422 12775.46475 11498.52938 11394.52931 11461.08891 11896.9398 12011.25498 11125.547 1.118565073 1.09554236 1.071253775 1.148299922 1.033524858 1.024176997 1.030159588 1.06933527 1.079610286 1 13.44158865 -6.86108455 17.94429083 1.06153769 3.494784744 0 0.043942188 3414.929653 426653.6664 0.007428185 11224.83139 1.38E-07 6.86108455 2.433247054 EVS(ph)PLLPKLPEEPEAESK ddPTM_HeLa_Romidepsin_16h_R1 2 EVSPLLPKLPEEPEAESK 18 1 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 EVS(1)PLLPKLPEEPEAESK;EVS(1)PLLPKLPEEPEAESK ; 63.225 0.014214 18695500 5843.7 4841.9 4178.3 7209.2 3541.6 3086.1 2564.3 2776.3 5594.3 4418.4 TRUE FALSE FALSE 5772.474737 4910.064395 4251.021559 8042.761624 3360.858936 2888.90817 2782.111578 2856.62786 5093.931797 4303.609331 1.341310117 1.140917778 0.987780542 1.868841014 0.780939597 0.671275654 0.646460067 0.663774902 1.183641777 1 12.0713314 -8.545937758 24.99881511 1.19829362 0.670266925 0.574516764 0.236186417 136.1263789 147577.2602 0.035101748 0.070206648 2.84E-09 8.545937758 -0.528026695 EVS(ph)PPGAR ddPTM_HeLa_Romidepsin_16h_R1 1 EVSPPGAR 8 0 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 EVS(1)PPGAR 120.31 0.018687 102870000 1128.1 1036.1 1120 1008.2 1113.7 1103.1 1134.6 1057.8 1159.9 1113.3 TRUE FALSE FALSE 1114.350283 1050.686243 1139.49313 1124.772828 1056.863733 1032.61547 1230.972896 1088.405774 1056.155639 1084.376306 1.027641675 0.968931392 1.050828134 1.037253232 0.974628206 0.952266722 1.135189776 1.003715932 0.973975209 1 10.08264978 -7.766857591 24.99999936 1.008587757 1.06945285 0.278799632 0.043337546 114.2151956 527007.0656 0.005417209 0.016936472 1.71E-08 7.766857591 0.060865093 EVS(ph)S(ph)RPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 0 EVS(0.497)S(0.497)RPS(0.497)T(0.497)PGLS(0.011)VVS(0.001)GISATSEDIPNKIEDLR 65.765 5.02E-05 15499000 2804.9 2579.2 2622.7 2018.7 2940.4 2733.1 2053.4 3096.3 2601.9 2602.6 TRUE FALSE FALSE 2770.7128 2615.510045 2668.346993 2252.111592 2790.340416 2558.463731 2227.815745 3185.886555 2369.179547 2534.984077 1.092990218 1.031765868 1.052608976 0.88841252 1.100732916 1.009262249 0.878828299 1.256767877 0.934593463 1 11.30776097 EVS(ph)SRPSTPGLSVVSGISATSEDIPNKIEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 EVS(0.233)S(0.233)RPS(0.233)T(0.233)PGLS(0.031)VVS(0.003)GIS(0.031)AT(0.002)S(0.001)EDIPNKIEDLR 57.009 0.00059208 67339000 1808.2 1833.6 1925.6 1136.1 2189 2114.4 2143.8 2581.7 2359.2 1842.6 TRUE FALSE FALSE 1786.160963 1859.413469 1959.11426 1267.461228 2077.287162 1979.296664 2325.894318 2656.397416 2148.187243 1794.728986 0.995226007 1.036041365 1.091593369 0.706213159 1.157437796 1.102838746 1.295958519 1.480110611 1.196942413 1 10.80955029 -7.583386806 1.246677902 0.993153368 1.559129873 0.58001576 0.125564725 0.3430489 0.656659055 0.014863805 0.213465242 2.61E-08 7.583386806 0.565976505 EVSSRPST(ph)PGLS(ph)VVSGISATSEDIPNK ddPTM_HeLa_Romidepsin_16h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNK 27 1 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 2 0 EVS(0.326)S(0.326)RPS(0.171)T(0.393)PGLS(0.775)VVS(0.007)GIS(0.001)ATSEDIPNK 68.657 0.00022996 5253100 1049.2 1318.1 1609.8 792.04 1309.3 1469.6 888.94 1177.9 1255.8 1504 TRUE FALSE FALSE 1036.411947 1336.656246 1637.817894 883.6193915 1242.481535 1375.697303 964.4465414 1211.980678 1143.478103 1464.925863 0.70748423 0.912439517 1.11802101 0.603183693 0.848153184 0.939090051 0.658358601 0.827332433 0.780570629 1 10.51661194 -9.237471254 24.98897298 0.880421336 0.78188647 0.167876409 0.137847261 1613.749035 1682483.302 0.023468382 0.038904758 5.79E-10 9.237471254 -0.098534866 EVSSRPST(ph)PGLSVVSGISATSEDIPNKIEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 EVSSRPSTPGLSVVSGISATSEDIPNKIEDLR 32 2 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 EVS(0.007)S(0.007)RPS(0.198)T(0.763)PGLS(0.024)VVSGISATSEDIPNKIEDLR 89.879 1.44E-11 52623000 1051.9 1284.2 983.16 1048.9 1301.8 1304.8 1175.6 1444.9 1287.1 1335 TRUE FALSE FALSE 1039.079038 1302.279001 1000.271487 1170.178753 1235.364288 1221.427491 1275.455435 1486.705902 1171.978552 1300.316508 0.799097014 1.001509243 0.769252318 0.899918402 0.950048916 0.939330912 0.980880753 1.143341558 0.901302526 1 10.34464711 -6.498251179 0.93360287 0.901582936 1.855007567 0.51653202 0.070427514 5.412602041 1.27814221 0.013311028 7.378776465 3.18E-07 6.498251179 0.953424631 EVSTAPAGTDMPAAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EVSTAPAGTDMPAAKK 16 1 A0A5F9ZI63;H0YEL4;E9PJK2;O75530-3;O75530;O75530-2 A0A5F9ZI63 EED Polycomb protein EED 0 1 EVSTAPAGTDMPAAK(1)K 124.21 1.13E-05 2581000 0 135.3 145.87 0 126.45 195.73 250.58 167.3 56.731 57.735 FALSE TRUE FALSE 0 137.204757 148.4088062 0 119.9967847 183.2234847 271.8642589 172.1405615 51.65683727 56.23503638 0 2.439844727 2.639080824 0 2.133843817 3.258173134 4.834428436 3.061090961 0.918588137 1 5.813397354 -8.351175208 0.703209595 0.663453293 4.510785661 0.513240095 1.023573789 0.565118953 0.411277245 0.19737876 1.302731772 4.45E-09 8.351175208 3.847332368 EVSTYIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EVSTYIKK 8 1 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 1 ; EVSTYIK(1)K;EVSTYIK(1)K 188.98 2.37E-09 55600000 8417.7 6315.1 7803.8 8769.3 13432.5 11652.7 10243.5 8677.7 10938.5 7922 FALSE TRUE FALSE 8315.101835 6404.004144 7939.621865 9783.247727 12746.9894 10908.13008 11113.58263 8928.775558 9960.133164 7716.185298 1.077618216 0.829944318 1.028956869 1.267886572 1.651980727 1.413668757 1.440294939 1.15714893 1.290810521 1 12.91367207 -9.123845594 3.72616694 1.018449665 1.421039197 0.555326762 0.155108637 0.103018979 2.561774947 0.019345116 0.033233771 7.52E-10 9.123845594 0.402589532 EVSTYIKK ddPTM_HeLa_Romidepsin_16h_R1 2 EVSTYIKK 8 1 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 0 ; ; 98.523 0.0067041 8568200 5157.3 4534.9 4400.4 5928 5012.5 4398 3948.1 3268.9 4387.1 3623.4 FALSE FALSE TRUE 5094.440844 4598.742441 4476.987116 6613.423252 4756.693421 4116.981994 4283.451515 3363.480464 3994.706788 3529.263546 1.443485526 1.303031746 1.268532955 1.873881949 1.347786403 1.16652722 1.213695566 0.953026154 1.131881124 1 11.78515145 -5.891407327 14.58572545 1.258373297 1.277672599 0 0.246907968 0 0 0.036089102 0 1.28E-06 5.891407327 0.019299302 EVTPEGLQMVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 EVTPEGLQMVKK 12 1 E9PBS1;P22234;P22234-2;D6RF62 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 0 1 EVTPEGLQMVK(1)K 68.657 0.025653 438960 75.829 138.29 0 62.761 0 0 148.82 0 0 0 FALSE TRUE FALSE 74.90476698 140.2368502 0 70.01772212 0 0 161.4607671 0 0 0 0 EVTWEVLEGEVEK ddPTM_HeLa_Romidepsin_16h_R1 1 EVTWEVLEGEVEK 13 0 P05455 P05455 SSB Lupus La protein 0 0 144.1 0.00020109 0 1072.9 1203.7 999.75 778.78 1230.6 1176.1 910.91 1168 1351.1 1239.3 FALSE FALSE TRUE 1059.823082 1220.64572 1017.150229 868.8262079 1167.79789 1100.951006 988.2826727 1201.794237 1230.254232 1207.102807 0.877989079 1.011219353 0.842637614 0.719761567 0.967438633 0.912060679 0.818722868 0.995602222 1.019179331 1 10.23733284 -12.45389481 0.554580642 1.027464093 0.885563766 0.2368448 0.083134958 1.991925707 0.76574987 0.153422427 0.019400221 3.52E-13 12.45389481 -0.141900327 EVVEEAENGR ddPTM_HeLa_Romidepsin_16h_R1 1 EVVEEAENGR 10 0 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 0 214.05 1.34E-17 85082000 5562.2 5131 4954 3887.3 5219.4 5598.7 4528.1 4792.9 5179.5 5368.8 FALSE FALSE TRUE 5494.405767 5203.234353 5040.222292 4336.767916 4953.034542 5240.961139 4912.716701 4931.575 4716.232548 5229.317802 1.050692648 0.995012074 0.963839354 0.829318102 0.947166481 1.00222655 0.939456519 0.943062783 0.901882947 1 12.35240703 -9.783632087 3.126733542 1.023618404 0.934682081 0.044470758 0.057084524 0.168276033 3.407360654 0.007376597 0.010221115 1.65E-10 9.783632087 -0.088936323 EVVEGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 EVVEGKK 7 1 O76031 O76031 CLPX "ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial" 0 1 ; EVVEGK(1)K;EVVEGK(1)K 104.45 0.0084531 4746800 3649.3 5355.2 3389 5478.2 5796.6 5348.6 5462.5 5882.1 5539.2 4414.4 FALSE TRUE FALSE 3604.820928 5430.590646 3447.984123 6111.61526 5500.777872 5006.841722 5926.484614 6052.289283 5043.760079 4299.713252 0.838386357 1.263012282 0.801910249 1.421400661 1.279335981 1.164459449 1.378344152 1.407603003 1.173045686 1 12.07002473 -9.257562649 24.99894256 0.944289415 1.320864969 0.485522478 0.153501406 160.0907318 1032337.668 0.020765191 0.033606196 5.53E-10 9.257562649 0.376575554 EVVKPVPIT(ph)SPAVSK ddPTM_HeLa_Romidepsin_16h_R1 1 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 EVVKPVPIT(0.961)S(0.039)PAVSK 157.62 0.00018651 672620000 4537.2 4204 3999 4939.3 6080.7 7188.8 6029.5 6050.8 4161.1 4063.2 TRUE FALSE FALSE 4481.898861 4263.184022 4068.600917 5510.405106 5770.379189 6729.458881 6541.64558 6225.870351 3788.920794 3957.637478 1.132468268 1.077204278 1.028037798 1.39234711 1.458036321 1.700372739 1.652916826 1.573128005 0.957369343 1 11.95042375 -8.938202501 1.607023834 1.060587462 1.636788808 0.932974884 0.070991967 0.065346347 0.338297156 0.011200671 0.024044962 1.15E-09 8.938202501 0.576201346 EVVKPVPITS(ph)PAVSK ddPTM_HeLa_Romidepsin_16h_R1 1 EVVKPVPITSPAVSK 15 1 Q96HC4;A0A0D9SFR4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 EVVKPVPIT(0.035)S(0.798)PAVS(0.168)K 139 0.0062138 152170000 4016.3 4237.8 4248.4 4528.5 5924.9 6755.7 6494.1 6917.7 3904.6 3882.1 TRUE FALSE FALSE 3967.347791 4297.45986 4322.34162 5052.106477 5622.530244 6324.032573 7045.708692 7117.852735 3555.362797 3781.242482 1.049218031 1.13652057 1.143100883 1.336096931 1.486953103 1.672474749 1.863331623 1.882411077 0.940263105 1 11.88464465 -8.482709862 0.664255614 1.014773413 2.004759377 0.989722035 0.03421693 0.047457175 0.031989616 0.004536366 0.026478512 3.29E-09 8.482709862 0.989985964 EVVSFS(ph)PDPLPVR ddPTM_HeLa_Romidepsin_16h_R1 1 EVVSFSPDPLPVR 13 0 Q8NFI3;J3QLG5;F8W925;Q8NFI3-2;Q8NFI3-3 Q8NFI3 ENGASE Cytosolic endo-beta-N-acetylglucosaminidase 1 0 EVVS(0.001)FS(0.999)PDPLPVR 131.79 0.0021105 2877400 1464.5 1200.3 1236.7 1066 1475 1314.9 1331.1 1761.5 1648.3 1246 TRUE FALSE FALSE 1446.650111 1217.197855 1258.224245 1189.255936 1399.725246 1230.882134 1444.163601 1812.466223 1500.87192 1213.62874 1.192003833 1.002940862 1.03674559 0.979917413 1.153338908 1.014216368 1.189955011 1.493427243 1.23668126 1 10.24511144 -7.312552465 2.722927648 1.07490292 1.549328126 0.685813748 0.08484385 0.165313882 1.747396794 0.011756589 0.165740998 4.87E-08 7.312552465 0.474425206 EVWFFGLQYQDTK ddPTM_HeLa_Romidepsin_16h_R1 1 EVWFFGLQYQDTK 13 0 P26038;V9GZ54 P26038 MSN Moesin 0 0 142.97 0.0082 2224800 459.59 512.79 478.62 667.77 577.89 631.12 322.87 370.19 407.55 595.47 FALSE FALSE TRUE 453.9883403 520.0090711 486.9501803 744.9807094 548.3981169 590.7934688 350.2945697 380.9008636 371.0977073 579.9996036 0.782739053 0.896567977 0.83956985 1.284450377 0.945514641 1.018610125 0.603956568 0.656726076 0.639824071 1 9.179908104 -7.75393252 24.99790564 0.928741872 0.630341181 0.353840819 0.159728956 127.0330175 423010.2412 0.020159217 0.072544337 1.76E-08 7.75393252 -0.298400691 EVWYFGLHYVDNK ddPTM_HeLa_Romidepsin_16h_R1 2 EVWYFGLHYVDNK 13 0 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 ; ; 174.21 1.53E-05 27655000 7698.5 6351.4 7194.2 6529.3 8486.5 9144 8150.2 8121.7 7164.6 5204.6 FALSE FALSE TRUE 7604.667721 6440.815176 7319.412033 7284.248387 8053.402238 8559.727911 8842.477785 8356.688576 6523.780232 5069.383742 1.500116801 1.27053218 1.443846512 1.436910038 1.588635354 1.688514492 1.744290477 1.648462417 1.286898086 1 12.30759466 -14.04719047 0.121097828 2.96E-13 1.926104798 0.703240321 0.117465996 12.78417054 0.214982262 4.136581022 0.609521573 8.97E-15 14.04719047 1.926104798 EVYELLDS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 5 EVYELLDSPGK 11 0 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 0 EVYELLDS(1)PGK;EVYELLDS(1)PGK;EVYELLDS(1)PGK;EVYELLDS(1)PGK;EVYELLDS(1)PGK ;;;; 185.57 2.37E-06 562936000 24763.9 23459.7 28121.6 17236.7 35109.5 43835.3 37047.8 38187.6 27102.7 25653.2 TRUE FALSE FALSE 24462.06806 23789.96627 28611.04465 19229.68836 33317.7312 41034.3658 40194.63921 39292.49796 24678.56663 24986.72617 0.979002527 0.952104174 1.145049754 0.769596154 1.333417231 1.642246588 1.608639681 1.572534861 0.98766707 1 14.60887427 -8.535454513 4.278075912 0.986125259 1.597307269 0.911561758 0.089353674 0.037341501 1.632061072 0.011741782 0.025285478 2.91E-09 8.535454513 0.61118201 EVYELLDS(ph)PGKVLLQSK ddPTM_HeLa_Romidepsin_16h_R1 2 EVYELLDSPGKVLLQSK 17 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 0 EVY(0.001)ELLDS(0.999)PGKVLLQSK;EVYELLDS(0.999)PGKVLLQS(0.001)K ; 90.316 0.0033452 205450000 6002.6 5112.7 5076.6 8030.8 8227.8 9728.9 8688 9907.3 6652.5 5649.5 TRUE FALSE FALSE 5929.438002 5184.676725 5164.956093 8959.358882 7807.904664 9107.254689 9425.958503 10193.95209 6057.483739 5502.725176 1.077545727 0.942201647 0.938617854 1.628167607 1.418915976 1.655044437 1.712961887 1.852527933 1.100815241 1 12.42593056 -9.255736438 24.55936945 1.022283707 1.643876475 0.893625064 0.110642546 88.79683526 382397.5337 0.017237152 0.028068761 5.55E-10 9.255736438 0.621592769 EVYQQQQYGS(ph)GGR ddPTM_HeLa_Romidepsin_16h_R1 4 EVYQQQQYGSGGR 13 0 Q99729-3;Q99729-4;D6R9P3;D6RD18;D6RBZ0;Q99729-2;Q99729 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 0 EVYQQQQYGS(1)GGR;EVYQQQQYGS(1)GGR;EVYQQQQYGS(1)GGR;EVYQQQQYGS(1)GGR ;;; 225.21 1.48E-31 45902900 5868.39 5778.08 4943.19 4984.31 6166.6 7284 6376 6584 6575.6 5601.78 TRUE FALSE FALSE 5796.863805 5859.423962 5029.224148 5560.619374 5851.895391 6818.575908 6917.577281 6774.497652 5987.461867 5456.244948 1.06242734 1.073893129 0.921737238 1.019129351 1.072513321 1.249682881 1.26782748 1.241604385 1.097359434 1 12.4136927 -8.325591482 3.205228899 1.024696817 1.258333668 0.828374145 0.045719508 0.067703946 1.368408454 0.006310976 0.01588603 4.73E-09 8.325591482 0.233636851 EWNGVVSESDS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 EWNGVVSESDSPVK 14 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135;F5GZ28;M0QY71;M0R1G7 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 EWNGVVSESDS(1)PVK;EWNGVVSES(0.002)DS(0.998)PVK ; 205.33 6.62E-17 53031000 6054.6 6432.7 7521.1 3859.9 4694.3 4406.6 3170.1 3785.3 7229.4 7239.9 TRUE FALSE FALSE 5980.804206 6523.259719 7652.001591 4306.199799 4454.732354 4125.032482 3439.368215 3894.821683 6582.784358 7051.806354 0.848123716 0.92504805 1.085112269 0.610652021 0.631715071 0.584961111 0.487728681 0.552315462 0.933489099 1 12.78377714 -9.16511248 6.014674422 0.936546333 0.568390146 0.889219882 0.067780926 0.069224646 3.58781156 0.012294484 0.020521721 6.84E-10 9.16511248 -0.368156187 EWQELDDAEK ddPTM_HeLa_Romidepsin_16h_R1 2 EWQELDDAEK 10 0 Q13200;Q13200-2;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 0 ; ; 171.62 0.0072047 29331000 6474.6 5822.2 5657.2 4439.1 6428.6 7059.1 5856.6 7007.2 6849.3 6384.7 FALSE FALSE TRUE 6395.685085 5904.165084 5755.661193 4952.369629 6100.524554 6608.046292 6354.059458 7209.942276 6236.681454 6218.824574 1.02843954 0.949402096 0.92552236 0.796351396 0.980977109 1.062587667 1.021746052 1.1593738 1.002871424 1 12.60242621 -7.032395497 1.269049924 0.986203303 1.309089151 0.400516075 0.069260849 2.244507657 2.100165926 0.011502905 1.078936961 9.28E-08 7.032395497 0.322885848 EWSLESS(ph)PAQNWTPPQPR ddPTM_HeLa_Romidepsin_16h_R1 1 EWSLESSPAQNWTPPQPR 18 0 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;E5RHT6;E5RHC5;F8W1U7;Q8N6T3-3 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 EWSLES(0.208)S(0.689)PAQNWT(0.102)PPQPR 93.181 0.0049839 13631000 1433.4 1273.8 1200.9 1507.3 1474.5 1231.4 1400.9 1149.2 1548.6 1362.2 TRUE FALSE FALSE 1415.929169 1291.73259 1221.801161 1681.581118 1399.250763 1152.717514 1519.892411 1182.450289 1410.089337 1326.809848 1.067168119 0.973562709 0.920856265 1.267386673 1.054597812 0.868788784 1.145523915 0.891198005 1.062766711 1 10.37374591 -7.219326745 22.21842428 1.033106107 0.891196112 0.145840774 0.106896519 9114.010041 4808074.366 0.013718418 5.501215333 6.03E-08 7.219326745 -0.141909995 EWSLESSPAQNWT(ph)PPQPR ddPTM_HeLa_Romidepsin_16h_R1 1 EWSLESSPAQNWTPPQPR 18 0 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;E5RHT6;E5RHC5;F8W1U7;Q8N6T3-3 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 EWSLES(0.066)S(0.037)PAQNWT(0.897)PPQPR 95.554 0.0079946 16343000 1498.3 1443 1469.1 1332.5 1939.6 2152.8 2256.1 1744.8 1678.7 1704.4 TRUE FALSE FALSE 1480.038143 1463.314592 1494.669069 1486.56992 1840.614974 2015.243028 2447.733078 1795.283035 1528.552868 1660.119442 0.891525095 0.881451391 0.900338272 0.895459617 1.108724425 1.213914479 1.474431909 1.081417993 0.92074873 1 10.69707133 -8.453212088 2.420032849 0.934806284 1.283245975 0.712680489 0.097183326 0.11606641 1.329203333 0.013925986 0.035049794 3.52E-09 8.453212088 0.348439691 EWTDGLFTHVLR ddPTM_HeLa_Romidepsin_16h_R1 2 EWTDGLFTHVLR 12 0 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 ; ; 124.38 0.0028144 18706800 9528.2 9304 10399.2 9634.8 10933 11482.6 7911.1 9740.4 9858.7 7596.5 FALSE FALSE TRUE 9412.066633 9434.981956 10580.19371 10748.82091 10375.04821 10748.89892 8583.068637 10022.22311 8976.91318 7399.141835 1.272048414 1.275145438 1.429921733 1.452711835 1.402196153 1.452722378 1.160008664 1.354511554 1.213237073 1 12.85314224 -11.52508866 0.581582418 0.99598821 1.370177933 0.440455801 0.104576467 0.343300018 0.236573526 0.060885903 0.024000746 2.98E-12 11.52508866 0.374189723 EY(ph)LFKVCARNK ddPTM_HeLa_Romidepsin_16h_R1 1 EYLFKVCARNK 11 2 A0A0A0MRA3;A0A0A0MTS7;Q8WZ42-3;Q8WZ42-10;Q8WZ42-9;Q8WZ42-5;Q8WZ42-11;Q8WZ42-4;Q8WZ42-7;Q8WZ42-2;Q8WZ42;Q8WZ42-8;Q8WZ42-13;Q8WZ42-12 A0A0A0MRA3 TTN Titin 1 0 EY(1)LFKVCARNK 83.862 0.020475 10933000 4603.9 3604.2 3948 3858.3 4268.8 4501 3454.9 3924.4 4557.9 3921.9 TRUE FALSE FALSE 4547.785896 3654.940022 4016.713284 4304.4148 4050.947207 4213.400626 3748.35912 4037.946322 4150.230009 3820.008473 1.190517228 0.95678846 1.051493292 1.126807658 1.060455032 1.102982011 0.981243667 1.057051667 1.086445237 1 11.89936012 -7.7704686 24.98709944 1.080722034 1.019147661 0.086195029 0.063813176 333.2484066 922228.1305 0.011265321 0.034541033 1.70E-08 7.7704686 -0.061574373 EY(ph)VMS(ph)VGLVS(ph)VS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 EYVMSVGLVSVSK 13 0 Q96PD6 Q96PD6 MOGAT1 2-acylglycerol O-acyltransferase 1 4 0 EY(1)VMS(1)VGLVS(1)VS(1)K 51.771 0.0042057 0 4264.2 4568.5 5043.6 4451.2 4307.4 5211.8 4529.1 5020.4 5559 5274.3 TRUE FALSE FALSE 4212.22629 4632.815463 5131.381742 4965.868688 4087.577305 4878.7828 4913.801641 5165.657353 5061.789117 5137.272926 0.819934302 0.901804426 0.998853247 0.96663517 0.795670653 0.949683396 0.956500017 1.005525194 0.985306638 1 12.32678701 -7.590202894 2.268590191 0.915052494 1.001498059 0.095598671 0.068015253 0.642939105 5.753050913 0.011492989 0.083690991 2.57E-08 7.590202894 0.086445565 EY(ph)YETKK ddPTM_HeLa_Romidepsin_16h_R1 2 EYYETKK 7 1 E5RFN6;Q4W5N1;Q8WWZ4-2;Q8WWZ4 E5RFN6 ABCA10;ABCA11P Putative ATP-binding cassette sub-family A member 11;ATP-binding cassette sub-family A member 10 1 0 EY(0.999)Y(0.001)ETKK;EY(0.5)Y(0.5)ETKK ; 86.794 0.012562 16188000 6221.6 6380.8 5778.3 6424.2 5841.7 5723.8 4250.2 4926.8 6545 5821.8 TRUE FALSE FALSE 6145.768746 6470.62907 5878.868888 7166.996231 5543.576251 5358.067653 4611.211882 5069.349185 5959.598808 5670.548797 1.083804931 1.141093976 1.036737201 1.263898167 0.97760842 0.944894021 0.813186174 0.893978584 1.050973904 1 12.46927265 -8.206326344 2.489905676 1.063278675 0.859829634 0.583305016 0.077984525 0.176592126 2.124646024 0.011843285 0.035356091 6.22E-09 8.206326344 -0.203449041 EYAENIGDGRS(ph)PEFR ddPTM_HeLa_Romidepsin_16h_R1 1 EYAENIGDGRSPEFR 15 1 A0A087WUB9;Q8WYA6-3;Q8WYA6-2;Q8WYA6-4;Q8WYA6 A0A087WUB9 CTNNBL1 Beta-catenin-like protein 1 1 0 EYAENIGDGRS(1)PEFR 63.894 0.025081 9915000 2184.3 2761.3 2289.7 1700.3 2265.3 2753.3 2021.6 2608.9 2814.7 2793.5 TRUE FALSE FALSE 2157.676911 2800.173654 2329.551268 1896.896686 2149.693288 2577.373016 2193.314654 2684.384405 2562.946182 2720.924467 0.792994049 1.029125831 0.856161682 0.697151541 0.790059891 0.947241662 0.806091709 0.986570718 0.941939482 1 11.40988119 -12.50030292 1.145049744 1.003142584 0.853915131 0.15135963 0.097166851 0.60430391 1.368250725 0.07429124 0.016500246 3.16E-13 12.50030292 -0.149227453 EYDQLY(ph)EEYTR ddPTM_HeLa_Romidepsin_16h_R1 1 EYDQLYEEYTR 11 0 A0A5F9ZHY3;E9PFP1;O00459 A0A5F9ZHY3 PIK3R2 Phosphatidylinositol 3-kinase regulatory subunit beta 1 0 EYDQLY(1)EEYTR 167.18 0.025213 1518200 695.95 470.93 621.39 661.73 703.24 538.47 471.59 621.24 778.86 443.79 TRUE FALSE FALSE 687.4674937 477.5597649 632.2050323 738.2423361 667.3510386 504.0635048 511.6468428 639.2145992 709.1968109 432.2602718 1.590401752 1.1047968 1.462556412 1.70786534 1.543863922 1.166111109 1.183654562 1.478772492 1.640670811 1 8.755756437 -12.48896118 1.177543845 0.995312617 1.416833688 0 0.271712741 0.420686868 1.024847032 0.146777937 0.034170467 3.24E-13 12.48896118 0.421521071 EYDSGDT(ph)DEIIAMK ddPTM_HeLa_Romidepsin_16h_R1 2 EYDSGDTDEIIAMK 14 0 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 EYDS(0.197)GDT(0.803)DEIIAMK;EYDS(0.09)GDT(0.91)DEIIAMK ; 133.98 1.76E-05 5658800 6899.4 8670.1 7831.3 4688.1 6977.4 7515.1 5839.1 6905.2 7300.5 7519.1 TRUE FALSE FALSE 6815.307459 8792.157895 7967.600491 5230.16018 6621.317242 7034.909364 6335.073008 7104.991067 6647.524996 7323.752698 0.930575859 1.200499014 1.087912279 0.714136645 0.904088043 0.960560747 0.865003676 0.970129845 0.907666502 1 12.83836736 -9.29501096 24.99868343 0.995820409 0.88730038 0.305378856 0.102670428 773.0766275 575660.2069 0.016156943 0.024680921 5.07E-10 9.29501096 -0.108520028 EYFSWEGAFQHVGK ddPTM_HeLa_Romidepsin_16h_R1 1 EYFSWEGAFQHVGK 14 0 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 0 148.48 0.00028865 63011000 3032 2958.5 2391.4 2595.1 2931.8 3162.2 2236.9 2764 3365.4 2607.7 FALSE FALSE TRUE 2995.044818 3000.149841 2433.021314 2895.157672 2782.179306 2960.145626 2426.90223 2843.971979 3064.390195 2539.951578 1.179173983 1.181183872 0.957900668 1.139847585 1.095367065 1.165433881 0.955491534 1.119695353 1.206475833 1 11.31058528 -7.767665937 24.99747375 1.093189817 1.037593448 0.070022151 0.087086053 321.1872474 1289481.374 0.01251827 0.038952061 1.71E-08 7.767665937 -0.055596369 EYGS(ph)TSSIDR ddPTM_HeLa_Romidepsin_16h_R1 1 EYGSTSSIDR 10 0 Q9P2F8 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 0 EYGS(0.935)T(0.042)S(0.023)SIDR 155.33 0.0032855 8981300 1448.2 1406.8 1272.7 1574.2 2049.4 1932.7 1883.4 1987.1 1864.1 1476.5 TRUE FALSE FALSE 1430.548781 1426.604967 1294.85081 1756.216411 1944.811471 1809.206708 2043.375949 2044.593603 1697.370227 1438.140317 0.994721283 0.991978982 0.900364724 1.221171808 1.352309957 1.25801821 1.420846022 1.421692709 1.180253559 1 10.48998873 -9.043744528 3.388193718 0.990623315 1.357707855 0.808046042 0.08004962 0.04814139 1.121231939 0.008103053 0.014449974 9.04E-10 9.043744528 0.367084541 EYIPGQPPLSQS(ph)SDS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 0 EYIPGQPPLS(0.113)QS(0.75)S(0.285)DS(0.603)S(0.243)PT(0.007)R 136.61 0.0062074 72133000 6934.6 6265.8 7049.3 5349.4 7304.9 6967.4 5127 6437 7508.2 7707.9 TRUE FALSE FALSE 6850.078428 6354.010097 7171.990109 5967.922798 6932.103695 6522.205626 5562.487252 6623.244439 6836.647787 7507.647647 0.912413415 0.846338347 0.955291251 0.794912478 0.923338977 0.868741573 0.740909472 0.882199692 0.910624487 1 12.87414523 -12.51929646 0.102310406 1.22825523 0.712108693 0.255977362 0.06200018 18.50422762 0.452296693 1.746950526 0.668966465 3.02E-13 12.51929646 -0.516146537 EYIPGQPPLSQS(ph)SDSS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 2 0 EYIPGQPPLS(0.223)QS(0.76)S(0.036)DS(0.329)S(0.631)PT(0.021)R 129.06 0.0094403 59214000 2793.7 2365.3 2319.1 1844.3 2529.8 2792.6 2261.2 2494.5 2688.7 2589.7 TRUE FALSE FALSE 2759.64931 2398.598755 2359.462963 2057.546644 2400.694866 2614.161873 2453.266272 2566.674422 2448.215938 2522.419221 1.094048637 0.95091202 0.935396838 0.815703681 0.951743012 1.036370898 0.972584672 1.017544745 0.970582494 1 11.30059235 -10.23891956 22.50609582 1.044411853 0.952021767 0.162673348 0.063701012 212.1462339 212016.6819 0.011257682 0.013778927 5.77E-11 10.23891956 -0.092390086 EYIPGQPPLSQSSDS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 2 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 EYIPGQPPLSQSS(0.017)DS(0.656)S(0.297)PT(0.029)R;EYIPGQPPLSQS(0.002)S(0.124)DS(0.61)S(0.25)PT(0.014)R ; 219.06 7.75E-30 2801700000 25303 23728.4 24691 19040.3 24009 26382 20753.8 23586.2 25856 24252 TRUE FALSE FALSE 24994.5973 24062.44904 25120.7365 21241.82907 22783.73114 24696.27534 22516.62725 24268.62948 23543.3746 23621.92954 1.058109891 1.018648752 1.063449811 0.899241911 0.964516091 1.045480865 0.953208637 1.027377101 0.996674491 1 14.52783919 -9.319013599 24.99989028 1.029793686 0.979592474 0.251413427 0.042482457 291.7494606 126682.6751 0.006542247 0.009993448 4.80E-10 9.319013599 -0.050201212 EYIPGQPPLSQSSDS(ph)SPTRNSEPAGLETPEAK ddPTM_HeLa_Romidepsin_16h_R1 1 EYIPGQPPLSQSSDSSPTRNSEPAGLETPEAK 32 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 EYIPGQPPLS(0.145)QS(0.145)S(0.145)DS(0.179)S(0.179)PT(0.179)RNS(0.022)EPAGLET(0.004)PEAK 44.264 0.0096507 13070000 1222.9 1134.3 973.22 1812.8 1176.3 1211.8 1198.9 1166.5 1273.6 1305.3 TRUE FALSE FALSE 1207.994824 1150.268705 990.1584859 2022.404465 1116.269022 1134.369891 1300.734536 1200.250837 1159.686026 1271.388118 0.95013852 0.90473451 0.778801117 1.59070581 0.877992334 0.892229426 1.023082187 0.944047549 0.912141627 1 10.3121888 EYIPGQPPLSQSSDSSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 EYIPGQPPLSQSSDSSPTR 19 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 0 178.67 6.25E-13 0 1955.6 1598.5 1726.2 1300.3 1838 1669.5 1651.6 1807.8 1788.5 1477.2 FALSE FALSE TRUE 1931.764395 1621.003725 1756.243787 1450.646804 1744.200001 1562.824338 1791.886863 1860.105841 1628.532081 1438.822131 1.342601252 1.126618565 1.220612158 1.008218301 1.212241572 1.086183139 1.245384557 1.29279763 1.13185087 1 10.49067254 -12.62684259 1.457291155 1.000472303 1.206826545 0.143991046 0.101445509 0.363136222 1.39036886 0.071984213 0.016599337 2.36E-13 12.62684259 0.206354243 EYPS(ph)PPPS(ph)PLRR ddPTM_HeLa_Romidepsin_16h_R1 1 EYPSPPPSPLRR 12 1 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 2 0 EY(0.096)PS(0.904)PPPS(0.999)PLRR 69.431 0.025499 4991100 3387.7 3028.5 2788.9 3199.6 3360.6 3318.1 2454.4 2896 3392.4 3190.7 TRUE FALSE FALSE 3346.409409 3071.135302 2837.439635 3569.552807 3189.096042 3106.084119 2662.876675 2979.791191 3088.975248 3107.805154 1.076775809 0.988200724 0.913004353 1.14857677 1.026157009 0.999446222 0.856835143 0.958808884 0.993941092 1 11.60168034 -7.918948793 5.472017454 1.031298752 0.908926485 0.326490315 0.06274005 0.152622798 7.687362109 0.008653668 0.026855249 1.21E-08 7.918948793 -0.122372266 EYPS(ph)PPPSPLR ddPTM_HeLa_Romidepsin_16h_R1 1 EYPSPPPSPLR 11 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 0 EYPS(0.5)PPPS(0.5)PLR 122.55 0.0088942 15048000 3106.2 3188.7 3098.1 2551.7 3300.4 3245.1 3079.7 3055.2 3441.7 3198.7 TRUE FALSE FALSE 3068.34044 3233.590602 3152.021131 2846.73956 3131.968273 3037.748583 3341.289641 3143.597392 3133.865732 3115.597313 0.984832163 1.037871804 1.011690798 0.913705872 1.005254517 0.975013225 1.072439505 1.008987066 1.005863537 1 11.60529306 -7.772542839 24.99989626 0.991537688 1.040713293 0.251404176 0.033774124 182.7409297 411452.3462 0.004434851 0.013482357 1.69E-08 7.772542839 0.049175605 EYPSPPPS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 1 EYPSPPPSPLR 11 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 0 EYPS(0.4)PPPS(0.6)PLR 94.538 0.027033 14463000 2893 2603.9 2715.3 2240.7 2968.8 3054.6 2596.5 3047.7 2919.9 2613.1 TRUE FALSE FALSE 2857.739003 2640.557773 2762.558657 2499.780277 2817.291058 2859.420918 2817.046645 3135.880391 2658.736831 2545.211285 1.122790481 1.037461129 1.085394629 0.982150398 1.106898698 1.123451296 1.10680267 1.232070755 1.044603584 1 11.31356971 EYQDLLNVK ddPTM_HeLa_Romidepsin_16h_R1 1 EYQDLLNVK 9 0 P08670;B0YJC4;B0YJC5;P17661;E7EMV2;E7ESP9;Q16352;P07197-2;P07196;P07197;P12036-2;P12036 P08670;P12036-2 VIM;DES;NEFM;INA;NEFL;NEFH Vimentin;Desmin;Alpha-internexin;Neurofilament medium polypeptide;Neurofilament light polypeptide;Neurofilament heavy polypeptide 0 0 119.68 0.011671 860230 530.32 445.65 437.52 384.17 428.51 672.59 398.67 398.07 392.45 266.42 FALSE FALSE TRUE 523.8562559 451.9238724 445.1348521 428.589543 406.6415357 629.6136697 432.5330198 409.5875274 357.3482891 259.49837 2.018726576 1.741528752 1.715366659 1.651607842 1.567029248 2.426272156 1.666804381 1.578381889 1.377073348 1 8.019581666 -12.37256015 0.990238344 0.978711023 1.811914183 0.427564216 0.267988479 0.314121677 0.528384969 0.192280223 0.044861512 4.24E-13 12.37256015 0.833203161 EYTINIHK ddPTM_HeLa_Romidepsin_16h_R1 2 EYTINIHK 8 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 0 ; ; 118.74 0.00059396 9596400 10273.4 10315.3 10356.1 7543.5 11136.4 11188.8 9657.6 9696.2 11463.7 11078.4 FALSE FALSE TRUE 10148.18385 10460.51906 10536.34358 8415.714963 10568.06795 10473.87179 10477.9163 9976.744249 10438.35796 10790.58157 0.940466812 0.969411982 0.976438898 0.779913011 0.979378904 0.970649424 0.971024243 0.924578919 0.967358237 1 13.397485 -12.11157072 0.579548343 1.007334763 0.937360952 0.081840598 0.056875987 1.784688611 0.931869143 0.065942183 0.013478831 7.73E-13 12.11157072 -0.069973811 EYTINIHK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 1 EYTINIHK(1)R 75.652 0.022409 3572400 1198.1 1299.4 1197 1126.7 2498.9 2084.1 1899.5 1795.2 2438.4 2063.9 FALSE TRUE FALSE 1183.497096 1317.692987 1217.833283 1256.974355 2371.371808 1950.932736 2060.843483 1847.14128 2220.303397 2010.27958 0.588722637 0.655477477 0.605802941 0.625273404 1.17962289 0.970478313 1.025152672 0.918847954 1.104474929 1 10.97318044 -8.764701543 24.99997224 0.760790613 1.019852603 0.353854272 0.172226287 80.15434521 614279.1674 0.027711001 0.051780999 1.72E-09 8.764701543 0.259061989 EYTINIHKR ddPTM_HeLa_Romidepsin_16h_R1 2 EYTINIHKR 9 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 0 ; ; 103.83 0.0013361 4999300 7915.2 8062.2 6531.1 10331 7547.7 8055.4 6943.2 7508 8416.9 7858.3 FALSE FALSE TRUE 7818.726498 8175.699863 6644.771056 11525.51883 7162.512705 7540.685938 7532.955235 7725.232134 7664.071383 7654.140233 1.021502907 1.068140851 0.868127687 1.505788825 0.935769725 0.985177395 0.984167392 1.009288032 1.001297487 1 12.90202462 -5.912598922 9.319598629 1.028181312 0.912147176 0 0.164185204 0 0 0.019717744 0 1.22E-06 5.912598922 -0.116034135 EYVEPELHINDLWR ddPTM_HeLa_Romidepsin_16h_R1 1 EYVEPELHINDLWR 14 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 0 102.63 0.004216 3001200 2474.6 2206 1853.3 2040.7 2297.1 2106.1 2263.1 1869.9 2128.7 1964.1 FALSE FALSE TRUE 2444.438623 2237.056126 1885.555909 2276.655336 2179.870415 1971.527007 2455.327658 1924.002606 1938.303741 1913.072399 1.277755418 1.16935257 0.985616598 1.190051844 1.139460491 1.030555356 1.283447327 1.005713431 1.013188911 1 10.90167576 EYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_HeLa_Romidepsin_16h_R1 4 EYVSNDAAQSDDEEKLQSQPTDTDGGR 27 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 EYVS(0.002)NDAAQS(0.992)DDEEKLQS(0.006)QPTDTDGGR;EYVSNDAAQS(0.878)DDEEKLQS(0.101)QPT(0.02)DT(0.002)DGGR;EYVS(0.001)NDAAQS(0.999)DDEEKLQSQPTDTDGGR;EY(0.001)VS(0.021)NDAAQS(0.837)DDEEKLQS(0.134)QPT(0.005)DT(0.001)DGGR ;;; 101.76 1.36E-08 208077600 5543.3 5672.9 5727 5208.93 6446 7107.8 5216.2 6143.7 6264.7 6126.9 TRUE FALSE FALSE 5475.736127 5752.763235 5826.676033 5811.210995 6117.036567 6653.634519 5659.263898 6321.458266 5704.369542 5967.722255 0.917558809 0.963979721 0.97636515 0.973773702 1.025020319 1.114937029 0.948312213 1.059274879 0.955870481 1 12.54296468 -8.77320989 3.753572272 0.961973265 1.037293419 0.412912381 0.042584145 0.187176902 5.695115343 0.00687937 0.013573946 1.69E-09 8.77320989 0.075320155 EYWMDPEGEMKPGRK ddPTM_HeLa_Romidepsin_16h_R1 1 EYWMDPEGEMKPGRK 15 2 P53999 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 0 53.377 0.023558 66776000 4712 5037.7 4423.4 5856.4 5433.3 5170.9 5039.6 4956.9 5281.5 4903.7 FALSE FALSE TRUE 4654.568332 5108.620873 4500.387421 6533.544523 5156.018427 4840.496178 5467.663498 5100.320081 4809.109412 4776.301167 0.974513158 1.069576791 0.942232758 1.367908826 1.079500276 1.013440319 1.144748479 1.067838878 1.006868965 1 12.22167809 EYWNDPELDEGER ddPTM_HeLa_Romidepsin_16h_R1 1 EYWNDPELDEGER 13 0 A0A494C108;Q8N9T8;F8WFC1;H0YFD2 A0A494C108 KRI1 Protein KRI1 homolog 0 0 149.41 0.0078167 4760800 633.68 941.77 824.5 618.41 965.45 881.91 660.73 784.16 791.93 875.2 FALSE FALSE TRUE 625.9564644 955.0282628 838.8500766 689.9134739 916.1794839 825.5587972 716.8523897 806.8484324 721.0977974 852.4621778 0.73429236 1.120317461 0.984032017 0.809318574 1.074745024 0.968440382 0.840919877 0.946491766 0.845900048 1 9.735492016 -10.27080774 24.99409731 0.874526955 0.958086586 0.160701502 0.10626926 1320.365862 3522630.095 0.021908665 0.025235002 5.36E-11 10.27080774 0.083559631 FAAHIS(ph)PAQGSPKPPPAASPGVR ddPTM_HeLa_Romidepsin_16h_R1 1 FAAHISPAQGSPKPPPAASPGVR 23 1 B0QYS6;B0QYS7;P19484;B1AKB1;B1AKB2;A0A1B0GXL9;B1AKB4 B0QYS6 TFEB Transcription factor EB 1 0 FAAHIS(0.999)PAQGS(0.001)PKPPPAASPGVR 74.505 0.00034136 0 876.28 1017.1 915.45 770.9 1033.7 934.68 795.27 983.79 1270.6 1106.9 TRUE FALSE FALSE 865.5995623 1031.41876 931.3830232 860.0350852 980.9464317 874.9569645 862.8202139 1012.254411 1156.954354 1078.142578 0.802861866 0.956662673 0.863877415 0.797700696 0.909848522 0.811541054 0.800283962 0.938887334 1.073099585 1 10.07433226 -12.45519224 1.07202128 1.003879069 0.85402476 0.547478142 0.061489399 0.366632505 0.721368818 0.043186518 0.009631064 3.51E-13 12.45519224 -0.149854309 FADEHVPGS(ph)PFTVK ddPTM_HeLa_Romidepsin_16h_R1 1 FADEHVPGSPFTVK 14 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-5;O75369-4;A0A0C4DGA1 O75369-8 FLNB Filamin-B 1 0 FADEHVPGS(0.953)PFT(0.047)VK 69.188 0.024885 3220500 2762.4 3088.4 3232.7 2738.9 3875.1 4507.5 3727.1 4105.8 3010.5 3178.4 TRUE FALSE FALSE 2728.730806 3131.878576 3288.963787 3055.584505 3677.339187 4219.485297 4043.679781 4224.594845 2741.23334 3095.82471 0.881422904 1.011645965 1.062386955 0.987001782 1.187838309 1.362960016 1.306172074 1.364610481 0.885461419 1 11.59610807 -8.622922676 1.405377882 0.953448324 1.357093221 0.902619239 0.055379393 0.097436057 0.38001393 0.009694352 0.027384003 2.38E-09 8.622922676 0.403644897 FADLSEAANR ddPTM_HeLa_Romidepsin_16h_R1 4 FADLSEAANR 10 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 ;;; ;;; 199.89 2.57E-11 99807000 9114.2 7587.17 9487.37 8810.36 10873.02 10147.1 9156.4 8605.56 8435.7 7895.13 FALSE FALSE TRUE 9003.112625 7693.982378 9652.493695 9829.055277 10318.12922 9498.733058 9934.144387 8854.548301 7681.189864 7690.013384 1.17075383 1.000516123 1.255198556 1.27815841 1.341756991 1.235203709 1.29182407 1.151434706 0.9988526 1 12.90877039 -9.7428887 22.99383547 1.076877956 1.263985283 0.694747205 0.068731015 51.31135155 63600.57879 0.012299657 0.017369022 1.81E-10 9.7428887 0.187107327 FADQDDIGNVS(ph)FDR ddPTM_HeLa_Romidepsin_16h_R1 2 FADQDDIGNVSFDR 14 0 H0YEN2;E9PQP7;H7BXH2;E9PKF6;Q5H9R7-3;Q5H9R7-4;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5 H0YEN2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 0 FADQDDIGNVS(1)FDR;FADQDDIGNVS(1)FDR ; 172.32 3.71E-05 24304000 6633.4 5585.3 6428.1 4787.8 5993.1 5908.4 5780.2 6563.6 6726.4 6014.3 TRUE FALSE FALSE 6552.549569 5663.93 6539.978384 5341.387963 5687.249744 5530.872308 6271.170044 6753.50741 6124.773937 5858.047619 1.11855519 0.966863086 1.116409222 0.911803439 0.970843891 0.944149428 1.070522203 1.152859767 1.045531606 1 12.51620421 -10.24914718 24.79312618 1.055984397 1.015926209 0.041801304 0.077084396 1798.326839 3627196.754 0.013887326 0.016941459 5.63E-11 10.24914718 -0.040058189 FADQDDIGNVSFDR ddPTM_HeLa_Romidepsin_16h_R1 2 FADQDDIGNVSFDR 14 0 H0YEN2;E9PQP7;H7BXH2;E9PKF6;Q5H9R7-3;Q5H9R7-4;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5 H0YEN2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 0 0 ; ; 223.36 9.95E-32 9856900 2475.8 2334.9 2440.7 2047.3 2507 2494.1 2152.6 2340.88 2692.4 2989.1 FALSE FALSE TRUE 2445.623997 2367.770783 2483.17936 2284.018459 2379.058435 2334.735059 2335.44179 2408.60967 2451.585001 2911.442751 0.840004151 0.813263727 0.852903379 0.784497122 0.817140723 0.80191687 0.802159613 0.827290754 0.842051591 1 11.50751854 -12.04707755 0.460262076 1.036659302 0.805450075 0.194385195 0.051636769 0.227873378 0.073195898 0.024299987 0.004769927 8.97E-13 12.04707755 -0.231209227 FADQHVPGS(ph)PFSVK ddPTM_HeLa_Romidepsin_16h_R1 1 FADQHVPGSPFSVK 14 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 0 FADQHVPGS(0.998)PFS(0.002)VK 77.795 0.016748 16168000 4930.3 5036.7 5076.9 4998.4 5906.9 6288 5591.4 6049.7 5832.7 5177.4 TRUE FALSE FALSE 4870.207607 5107.606795 5165.261315 5576.338526 5605.448851 5886.217094 6066.333376 6224.738525 5311.008704 5042.890402 0.965757179 1.012833194 1.024266027 1.105782217 1.111554764 1.167230819 1.202947693 1.234359272 1.053167585 1 12.30003516 -8.682587778 0.73757913 0.982457555 1.23558297 0.900947262 0.027327753 0.110409104 0.103709076 0.003669194 0.015713019 2.08E-09 8.682587778 0.253125415 FAEHVFR ddPTM_HeLa_Romidepsin_16h_R1 2 FAEHVFR 7 0 E5RK89;E5RI78;E9PC71;E5RIA5;E5RIZ1;E5RIG4;E5RFL9;E5RHC8;E5RHE8;A0A1B0GXG3;E5RI95;E5RGZ0;E5RJJ6;E5RJT1;E5RGA9;P61601;P37235;P84074 E5RK89 NCALD;HPCAL1;HPCA Neurocalcin-delta;Hippocalcin-like protein 1;Neuron-specific calcium-binding protein hippocalcin 0 0 ; ; 97.602 0.017464 14813400 9072 9565.7 9810.9 7946.2 11478.2 14044.1 10801.6 11398.4 9177 8609.4 FALSE FALSE TRUE 8961.426975 9700.366176 9981.654599 8864.977032 10892.42462 13146.72734 11719.08763 11728.19472 8356.186136 8385.726547 1.068652421 1.156771106 1.190314822 1.057150741 1.298924376 1.567750542 1.397504148 1.39859017 0.996477299 1 13.03372007 -8.62073106 3.192444661 1.057473956 1.449351186 0.837271494 0.074684817 0.071834414 1.457826524 0.012024889 0.025840881 2.39E-09 8.62073106 0.39187723 FAFSS(ph)EDEGVGPGPAGPK ddPTM_HeLa_Romidepsin_16h_R1 1 FAFSSEDEGVGPGPAGPK 18 0 O60307 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 0 FAFS(0.135)S(0.865)EDEGVGPGPAGPK 254.72 1.93E-75 11634000 1490.5 1598.9 1538.4 2070.6 3866.6 4345.1 3786.2 4090.3 1398.5 1490.6 TRUE FALSE FALSE 1472.333213 1621.409356 1565.175207 2310.012514 3669.272974 4067.462133 4107.799733 4208.646377 1273.414657 1451.873997 1.014091592 1.116770022 1.078037908 1.59105578 2.527266816 2.801525574 2.829308701 2.89876834 0.877083452 1 10.50370054 -8.834477248 1.783096945 1.0147985 2.860930462 0.994663729 0.060823651 0.012010092 0.077428889 0.006929433 0.015257558 1.46E-09 8.834477248 1.846131961 up FAGGLHFS(ph)GPK ddPTM_HeLa_Romidepsin_16h_R1 1 FAGGLHFSGPK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 FAGGLHFS(1)GPK 72.681 0.030527 10709000 7064.8 8645.1 7455 4750.5 8539 8550.8 6812.8 6162.3 7683.3 7508.5 TRUE FALSE FALSE 6978.6915 8766.805945 7584.751148 5299.775162 8103.222967 8004.431476 7391.479062 6340.596428 6996.086405 7313.428088 0.954229865 1.198727305 1.0370993 0.724663605 1.107992431 1.094484198 1.010672283 0.866980074 0.956608354 1 12.8363321 -7.371501928 0.004638442 0.883698681 1.103567111 0 0.126105303 1452641.221 1102.38631 25299.86662 26975.55888 4.25E-08 7.371501928 0.21986843 FAIQDIS(ph)VEETSAK ddPTM_HeLa_Romidepsin_16h_R1 2 FAIQDISVEETSAK 14 0 O43707;P35609-2;P35609;A0A494C1A0;G3V2E8;A0A087WSZ2;A0A494C033;A0A494C166;Q08043;P12814-2;P12814;P12814-3;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V5M4;G3V2X9 O43707;P12814-2 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-2;Alpha-actinin-3;Alpha-actinin-1 1 0 FAIQDIS(1)VEETSAK;FAIQDIS(0.842)VEET(0.121)S(0.037)AK ; 182.7 2.03E-07 97538300 9848.9 9178.3 10905 7867.2 12673.7 11830.8 9798.5 11654.8 10826.8 10760.8 TRUE FALSE FALSE 9728.857819 9307.512348 11094.79695 8776.84268 12026.9138 11074.85006 10630.78435 11992.01325 9858.423892 10481.23286 0.928216933 0.888016941 1.058539305 0.837386479 1.14747129 1.0566362 1.014268501 1.144141477 0.940578653 1 13.3555208 -8.744449606 24.99953764 0.958464345 1.082746926 0.526553534 0.067769725 169.042199 248735.2594 0.009369159 0.018700262 1.80E-09 8.744449606 0.124282581 FAIQDISVEET(ph)SAK ddPTM_HeLa_Romidepsin_16h_R1 2 FAIQDISVEETSAK 14 0 O43707;P35609-2;P35609;A0A494C1A0;G3V2E8;A0A087WSZ2;A0A494C033;A0A494C166;Q08043;P12814-2;P12814;P12814-3;P12814-4;H9KV75;G3V2N5;G3V2W4;G3V5M4;G3V2X9 O43707;P12814-2 ACTN4;ACTN2;ACTN1;ACTN3 Alpha-actinin-4;Alpha-actinin-2;Alpha-actinin-3;Alpha-actinin-1 1 0 FAIQDIS(0.002)VEET(0.925)S(0.072)AK;FAIQDIS(0.003)VEET(0.989)S(0.008)AK ; 233.62 1.36E-42 90649400 10169.9 8818.7 10099.4 8066.9 12934.8 11515.9 10259.2 10125.7 8858.2 10344.3 TRUE FALSE FALSE 10045.94535 8942.84989 10275.17582 8999.632934 12274.68889 10780.07116 11130.61619 10418.67115 8065.900406 10075.55359 0.997061378 0.887579011 1.019812532 0.893214735 1.218264463 1.069923459 1.104715099 1.034054462 0.800541661 1 13.29857149 -8.768215413 24.9999904 0.984506572 1.103965074 0.438522055 0.085045702 100.2991537 370052.1984 0.008630009 0.015899469 1.71E-09 8.768215413 0.119458502 FAMEPEEFDSDTLR ddPTM_HeLa_Romidepsin_16h_R1 2 FAMEPEEFDSDTLR 14 0 A0A499FI48;P13667 A0A499FI48 PDIA4 Protein disulfide-isomerase A4 0 0 ; ; 159.94 0.00087003 16372500 2081.04 2087.4 2259.7 2543.9 2174 2746.5 2040.44 2122 2747.6 2605.1 FALSE FALSE TRUE 2055.675484 2116.786472 2299.029131 2838.037687 2063.052668 2571.007514 2213.754923 2183.396722 2501.847775 2537.419126 0.810144238 0.834228153 0.906050209 1.118474145 0.813051595 1.013237225 0.872443539 0.860479335 0.985981286 1 11.30914613 -9.118827425 0.006617644 1.804567319 5.96E-05 0.030462184 0.096315201 23128.1832 55.65715125 7443.273224 7732.581635 7.61E-10 9.118827425 -1.804507742 FAQK(ac)IGGSER ddPTM_HeLa_Romidepsin_16h_R1 2 FAQKIGGSER 10 1 E9PP21;P21291;E9PS42;E9PND2 E9PP21 CSRP1 Cysteine and glycine-rich protein 1 0 1 ; FAQK(1)IGGSER;FAQK(1)IGGSER 167.93 0.0099592 22615000 2974.85 2858.28 2819.53 1147.81 3961.2 3476.4 3973.6 3282 3468.8 2370.54 FALSE TRUE FALSE 2938.591384 2898.518941 2868.602737 1280.525193 3759.045183 3254.26926 4311.117485 3376.959492 3158.54184 2308.953029 1.272694311 1.255339067 1.242382457 0.55459127 1.628030166 1.409413366 1.867130873 1.462550104 1.367954134 1 11.17302311 FAQSAPGS(ph)PLSSQPVLITVQR ddPTM_HeLa_Romidepsin_16h_R1 1 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167-2;Q01167 Q01167-2 FOXK2 Forkhead box protein K2 1 0 FAQS(0.003)APGS(0.934)PLS(0.061)S(0.003)QPVLITVQR 173.19 9.06E-11 71905000 4560.9 4483.8 4312.6 4497.3 3795.3 3519.2 3369 3778.3 4750.4 4467.2 TRUE FALSE FALSE 4505.309997 4546.923054 4387.658994 5017.298986 3601.611679 3294.334478 3655.162776 3887.619149 4325.512326 4351.1415 1.035431736 1.044995446 1.008392624 1.153099477 0.827739498 0.757119592 0.840046865 0.893471092 0.994109782 1 12.08717822 -8.735384974 24.99803671 1.027304616 0.825163969 0.78929545 0.052851213 75.38779065 72330.87727 0.007406586 0.014809207 1.84E-09 8.735384974 -0.202140647 FAQSAPGSPLS(ph)SQPVLITVQR ddPTM_HeLa_Romidepsin_16h_R1 1 FAQSAPGSPLSSQPVLITVQR 21 0 Q01167-2;Q01167 Q01167-2 FOXK2 Forkhead box protein K2 1 0 FAQSAPGS(0.332)PLS(0.51)S(0.158)QPVLITVQR 109.99 0.00023812 69703000 3163 3580.9 3069.3 3623.7 3449 2658.1 2412.1 2888.1 3569.2 3205.2 TRUE FALSE FALSE 3124.448139 3631.312004 3122.719879 4042.689244 3272.98466 2488.255989 2616.983714 2971.662617 3249.961813 3121.928442 1.000807096 1.163163113 1.000253509 1.294933346 1.048385548 0.797025311 0.838258712 0.951867627 1.041010988 1 11.60822175 -8.272307449 24.43208807 1.038328548 0.859971367 0.467593099 0.099369639 407.3160564 915671.6625 0.015018595 0.033913222 5.34E-09 8.272307449 -0.178357181 FARS(ph)DDEQSSADKER ddPTM_HeLa_Romidepsin_16h_R1 1 FARSDDEQSSADKER 15 2 A6NGV6;P27540-3;P27540-4;P27540 A6NGV6 ARNT Aryl hydrocarbon receptor nuclear translocator 1 0 FARS(0.999)DDEQS(0.001)SADKER 106.44 0.005092 8777800 1517.8 1892.1 1727.9 1664 1757.7 1700.5 1360.7 1447.7 1971.6 1645.9 TRUE FALSE FALSE 1499.30047 1918.737033 1757.973375 1856.399509 1667.99801 1591.843538 1476.277824 1489.586915 1795.255158 1603.139281 0.935227829 1.196862342 1.09658181 1.157977683 1.040457327 0.992953986 0.920866853 0.929168746 1.119837296 1 10.64668406 -5.969216542 10.15552616 1.003818484 0.681532872 0 0.100861115 0 0 0.013764093 0 1.07E-06 5.969216542 -0.322285613 FAS(ph)DDEHDEHDENGATGPVK ddPTM_HeLa_Romidepsin_16h_R1 4 FASDDEHDEHDENGATGPVK 20 0 P05455 P05455 SSB Lupus La protein 1 0 FAS(1)DDEHDEHDENGATGPVK;FAS(0.983)DDEHDEHDENGAT(0.017)GPVK;FAS(0.999)DDEHDEHDENGAT(0.001)GPVK;FAS(1)DDEHDEHDENGATGPVK ;;; 79.94 0.00098218 277824000 18029.5 17363.1 17784.5 11637.6 18008.1 19359 16428.4 19262.2 18384 15983.6 TRUE FALSE FALSE 17809.74952 17607.53818 18094.03176 12983.19407 17089.07946 18122.02238 17823.82789 19819.52137 16739.689 15568.34377 1.14397201 1.130983388 1.162232286 0.833948316 1.097681276 1.164030204 1.144876305 1.273065501 1.075238911 1 13.92632785 -7.523036937 1.269033202 1.067046001 1.295889539 0.324296651 0.091596614 0.928948396 1.74717048 0.014691755 0.242984116 3.00E-08 7.523036937 0.228843537 FAS(ph)DDEHDEHDENGATGPVKR ddPTM_HeLa_Romidepsin_16h_R1 4 FASDDEHDEHDENGATGPVKR 21 1 P05455 P05455 SSB Lupus La protein 1 0 FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR;FAS(1)DDEHDEHDENGATGPVKR ;;; 94.276 0.00024832 1358543500 11465 10427.8 10063.3 10583 11932.4 11797.1 10247.9 12140 12158.1 9824.4 TRUE FALSE FALSE 11325.26017 10574.60284 10238.44752 11806.65625 11323.4451 11043.30338 11118.35637 12491.25175 11070.64909 9569.160672 1.183516565 1.105071093 1.069942064 1.233823598 1.183326886 1.154051412 1.161894627 1.305365452 1.156909103 1 13.22417667 -16.52287875 0.172707518 0.286247062 1.221749154 0.161604825 0.073389407 30.38569017 0.340363563 7.332354247 0.088342722 3.00E-17 16.52287875 0.935502092 FAS(ph)ENDLPEWK ddPTM_HeLa_Romidepsin_16h_R1 2 FASENDLPEWK 11 0 C9JJ34;C9JDM3;F6WQW2;P43487-2;P43487;C9JIC6;C9JXG8;C9JGV6 C9JJ34 RANBP1 Ran-specific GTPase-activating protein 1 0 FAS(1)ENDLPEWK;FAS(1)ENDLPEWK ; 178.22 1.25E-05 68856000 11184.5 12036.5 8477.2 10087.9 9331.1 10470 10485.4 11512.3 13130.6 10415.7 TRUE FALSE FALSE 11048.17901 12205.95016 8624.74211 11254.31046 8854.899148 9801.00079 11376.02961 11845.39024 11956.16625 10145.09861 1.089016424 1.203137656 0.850138815 1.109334753 0.87282534 0.966082358 1.121332581 1.167597348 1.178516514 1 13.30849527 -10.9675097 0.003590998 0.000209377 2.077670373 0 0.121981121 80284.96661 173.7782538 50514.16843 50014.19949 1.08E-11 10.9675097 2.077460997 FDDDKVSIVTPEDILR ddPTM_HeLa_Romidepsin_16h_R1 1 FDDDKVSIVTPEDILR 16 1 A6NJA2;P54578-2;P54578-3;P54578 A6NJA2 USP14 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 14 0 0 125.33 0.0028278 6409800 1887.5 1503.5 1897.1 1737 2251.8 2088.8 1594.3 1934.1 2221.1 1660.2 FALSE FALSE TRUE 1864.494424 1524.666312 1930.11823 1937.840113 2136.882243 1955.332421 1729.719802 1990.060132 2022.439253 1617.067765 1.153009456 0.942858639 1.193591433 1.19836667 1.321454976 1.209183971 1.069664389 1.230659701 1.250683056 1 10.65916442 -9.618733087 11.4282539 1.06459024 1.204008875 0.248610456 0.096980091 0.344315025 38.656877 0.013736422 0.019427033 2.41E-10 9.618733087 0.139418635 FDGSENRPFS(ph)PSPLNNISSTVTVK ddPTM_HeLa_Romidepsin_16h_R1 2 FDGSENRPFSPSPLNNISSTVTVK 24 1 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 FDGSENRPFS(0.548)PS(0.066)PLNNIS(0.357)S(0.027)T(0.002)VTVK;FDGS(0.001)ENRPFS(0.822)PS(0.171)PLNNIS(0.005)STVTVK ; 86.856 4.95E-05 56991000 4979.3 5375.3 5281.4 4391.3 3052.1 2793.9 2333.68 2782.9 5595.2 5079.2 TRUE FALSE FALSE 4918.610376 5450.973614 5373.320552 4899.042768 2896.339948 2615.378807 2531.902721 2863.418821 5094.751299 4947.241652 0.994212679 1.101820772 1.086124538 0.990257423 0.585445416 0.528653943 0.511780685 0.578790975 1.029816544 1 12.27240866 -8.749859479 4.675416069 1.014128233 0.540665818 0.97172207 0.040316591 0.025291395 1.38178785 0.006742668 0.013263012 1.78E-09 8.749859479 -0.473462414 FDIYDPFHPTDEAYS(ph)PPPAPEQK ddPTM_HeLa_Romidepsin_16h_R1 5 FDIYDPFHPTDEAYSPPPAPEQK 23 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 FDIY(0.001)DPFHPT(0.091)DEAY(0.421)S(0.487)PPPAPEQK;FDIYDPFHPT(0.008)DEAY(0.446)S(0.546)PPPAPEQK;FDIYDPFHPTDEAY(0.451)S(0.548)PPPAPEQK;FDIYDPFHPTDEAY(0.121)S(0.879)PPPAPEQK;FDIY(0.004)DPFHPT(0.017)DEAY(0.455)S(0.523)PPPAPEQK ;;;; 118.16 1.81E-08 540204900 17279.9 18589.3 15823.9 16002.1 18361.2 19135.5 16273 17008.5 20032.2 18370.5 TRUE FALSE FALSE 17069.28593 18851.00065 16099.30834 17852.33809 17424.15945 17912.80331 17655.22821 17500.61411 18240.46986 17893.23176 0.953952095 1.053526881 0.899742906 0.997714573 0.973784931 1.001093796 0.986698683 0.978057756 1.019406114 1 14.12712636 -8.300227426 24.32029901 0.9787775 0.988424983 0 0.038994633 1849.473082 1159624.373 0.005073608 0.011345125 5.01E-09 8.300227426 0.009647483 FDLGQDVIDFTGHALALYR ddPTM_HeLa_Romidepsin_16h_R1 1 FDLGQDVIDFTGHALALYR 19 0 P50395-2;P50395;Q5SX87;P31150;Q5SX91 P50395-2 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 0 243.37 2.52E-62 19527000 1710.4 1252.5 1457.8 987.03 1721.6 1649.2 1314.4 1379.3 1614.1 1012.2 FALSE FALSE TRUE 1689.552987 1270.132728 1483.172397 1101.155053 1633.740328 1543.821443 1426.045103 1419.207869 1469.730853 985.9028981 1.71371135 1.288293939 1.504379793 1.116900107 1.657100644 1.565896039 1.446435654 1.439500657 1.490746052 1 9.945301752 -12.51373954 1.245704641 0.998095813 1.488280744 0 0.220644393 0.290110827 0.800838658 0.121592631 0.028822459 3.06E-13 12.51373954 0.490184932 FDLSHGS(ph)PQMVR ddPTM_HeLa_Romidepsin_16h_R1 1 FDLSHGSPQMVR 12 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 FDLS(0.04)HGS(0.96)PQMVR 60.08 0.029939 20048000 4685 3766.7 3358.9 3897.3 3707.2 3646.1 2975.4 3024.4 3844.8 3653.5 TRUE FALSE FALSE 4627.897418 3819.727701 3417.360246 4347.924163 3518.007751 3413.125977 3228.130402 3111.906242 3500.911459 3558.581543 1.300489356 1.073384902 0.960315284 1.221813835 0.988598324 0.959125409 0.907139646 0.874479397 0.983794081 1 11.79708658 -8.309501815 1.092163808 1.132312549 0.871368391 0.301100095 0.107598935 0.493987746 1.027410683 0.020474047 0.095684439 4.90E-09 8.309501815 -0.260944158 FDQLFDDES(ph)DPFEVLK ddPTM_HeLa_Romidepsin_16h_R1 2 FDQLFDDESDPFEVLK 16 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 FDQLFDDES(1)DPFEVLK;FDQLFDDES(1)DPFEVLK ; 177.6 3.18E-08 80364000 9198.6 9047.7 9250.7 6969.4 8665 8277.6 6921.6 8470.2 9673.6 9260.5 TRUE FALSE FALSE 9086.483925 9175.073758 9411.704553 7775.23482 8222.792716 7748.688075 7509.520531 8715.271873 8808.368988 9019.910875 1.007380677 1.017202263 1.043436535 0.862007943 0.911626825 0.859064816 0.832549305 0.966225941 0.976547231 1 13.13889746 -9.257313537 24.99900324 1.007544793 0.883203632 0.732617184 0.037010363 125.0600798 757753.9713 0.005017344 0.008128935 5.53E-10 9.257313537 -0.12434116 FDREVDIGIPDATGR ddPTM_HeLa_Romidepsin_16h_R1 2 FDREVDIGIPDATGR 15 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 ; ; 89.466 0.018821 14035700 4430.5 3743.6 4132 3881.8 4613.1 4985.7 4126.8 4189.9 4659.2 3929.9 FALSE FALSE TRUE 4376.499362 3796.302499 4203.915727 4330.63198 4377.676293 4667.129861 4477.330289 4311.128146 4242.469483 3827.800631 1.143345692 0.991771219 1.0982588 1.131362993 1.143653161 1.219271929 1.169687432 1.126267682 1.108330838 1 11.90229997 -9.132464106 1.846758768 1.063572123 1.169628468 0.484447734 0.04794363 0.27491071 1.838078421 0.009653589 0.018121553 7.37E-10 9.132464106 0.106056345 FDSSLLSS(ph)DDETK ddPTM_HeLa_Romidepsin_16h_R1 1 FDSSLLSSDDETK 13 0 A0A494C0S2;A0A090HNM7;A0A1W2PS85;R4GMW8;P28715 A0A494C0S2 ERCC5-201;BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 1 0 FDSSLLS(0.038)S(0.962)DDETK 311.54 3.73E-150 31187000 7890.9 7196.6 6906.5 6925.1 7746 7718.2 7039.9 7475.2 8422.5 8070.8 TRUE FALSE FALSE 7794.722676 7297.913924 7026.704735 7725.812646 7350.692716 7225.031929 7637.86893 7691.483118 7669.170505 7861.119453 0.991553776 0.928355556 0.893855484 0.982787845 0.935069459 0.919084359 0.97160067 0.978420843 0.975582492 1 12.94051906 -10.31600813 6.953653672 0.996135753 0.943484645 0.356291578 0.027145765 0.162904026 17.62239015 0.004517299 0.005166039 4.83E-11 10.31600813 -0.052651108 FDVPGDENAEMDAR ddPTM_HeLa_Romidepsin_16h_R1 1 FDVPGDENAEMDAR 14 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 0 99.752 0.02561 5407400 1602.5 1173.8 1266.5 1047.2 1576.5 1853.9 1392.8 1406.7 1800 1467 FALSE FALSE TRUE 1582.968114 1190.324787 1288.542901 1168.282191 1496.045322 1735.441773 1511.104397 1447.400645 1639.003492 1428.887129 1.10783286 0.833043257 0.901780746 0.817616849 1.047000349 1.21454084 1.057539372 1.012956598 1.147048958 1 10.48067624 -8.519984024 24.9974142 1.003955109 1.097849259 0.167133561 0.113182624 202.9752909 1752788.881 0.017631632 0.035799564 3.02E-09 8.519984024 0.09389415 FEDEDS(ph)DDVPR ddPTM_HeLa_Romidepsin_16h_R1 2 FEDEDSDDVPR 11 0 P49756 P49756 RBM25 RNA-binding protein 25 1 0 FEDEDS(1)DDVPR;FEDEDS(1)DDVPR ; 154.36 0.002221 18010000 2824.2 2957.7 2844.7 2200.8 2996.9 3432 2365.1 2911.1 3022.3 3147.3 TRUE FALSE FALSE 2789.777564 2999.338578 2894.21081 2455.266851 2843.95701 3212.706276 2565.991535 2995.328086 2751.977919 3065.532692 0.910046587 0.978406978 0.944113503 0.800926657 0.927720333 1.048009139 0.837045888 0.977098725 0.897716056 1 11.58192207 -12.40793962 0.801122297 1.007366028 0.925090046 0 0.073814291 1.262154949 1.229659084 0.069904895 0.012532997 3.91E-13 12.40793962 -0.082275983 FEDEGAGFEESS(ph)ETGDYEEK ddPTM_HeLa_Romidepsin_16h_R1 1 FEDEGAGFEESSETGDYEEK 20 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 FEDEGAGFEES(0.486)S(0.512)ET(0.001)GDYEEK 106.02 0.00020651 4258700 2154.4 2068.8 2071 672.58 1936.9 1710.7 1674.9 1930.2 2026.7 2324.4 TRUE FALSE FALSE 2128.141344 2097.924621 2107.044886 750.3468642 1838.052765 1601.391791 1817.165964 1986.047292 1845.426876 2264.011753 0.93998688 0.92664034 0.930668705 0.331423573 0.811856548 0.707324858 0.802630977 0.877224815 0.815113647 1 11.14466573 -9.490782622 24.99995231 0.96564276 0.708764332 0.335018831 0.147045861 444.2447293 346026.7029 0.020547033 0.031368417 3.23E-10 9.490782622 -0.256878428 FEDENFILK ddPTM_HeLa_Romidepsin_16h_R1 2 FEDENFILK 9 0 F8WE65;C9J5S7;P62937;P62937-2 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 0 ; ; 168.25 0.010705 123261010 3900.85 3211.94 4114.7 1980.29 3749.43 4301.44 3168.62 3391.88 3736.25 3741.39 FALSE FALSE TRUE 3853.30494 3257.157776 4186.314627 2209.260447 3558.082596 4026.591866 3437.762504 3490.018696 3402.070442 3644.188148 1.057383643 0.893795173 1.148764679 0.606242147 0.976371815 1.104935229 0.943354833 0.957694431 0.933560591 1 11.83138173 -10.27315824 24.45867252 1.027097832 0.948967061 0.012301878 0.140003175 1195.288856 2494704.994 0.022454819 0.025795349 5.33E-11 10.27315824 -0.07813077 FEDYLNAESR ddPTM_HeLa_Romidepsin_16h_R1 1 FEDYLNAESR 10 0 G3V1Q4;E7ES33;E7EPK1;Q16181-2;Q16181;A0A0U1RRH9;A0A0U1RRE1;A0A5F9ZGZ7 G3V1Q4 Sep-07 Septin-7 0 0 197.79 4.08E-08 14854000 3584.2 3246.2 3251.3 2918.5 3685.4 3407.8 2542.3 3134.4 3684.7 3596.7 FALSE FALSE TRUE 3540.514392 3291.900089 3307.887513 3255.950702 3497.320286 3190.052578 2758.242899 3225.088919 3355.131203 3503.257216 1.01063501 0.939668396 0.944231984 0.929406693 0.998305312 0.910596163 0.787336678 0.920597239 0.957717632 1 11.7744812 -8.235565274 0.442796059 1.006722153 0.81557117 0.383995183 0.047728174 1.27850176 0.292461003 0.012109552 0.111532901 5.81E-09 8.235565274 -0.191150983 FEEELAAR ddPTM_HeLa_Romidepsin_16h_R1 1 FEEELAAR 8 0 Q02818 Q02818 NUCB1 Nucleobindin-1 0 0 117.4 0.00076976 0 981.33 926.81 788.49 1067.1 1191.3 1177.5 980.18 1027.1 1118.9 1019.5 FALSE FALSE TRUE 969.3691725 939.8576555 802.2133377 1190.483123 1130.503516 1102.26155 1063.436465 1056.817518 1018.822782 993.013243 0.976189572 0.946470414 0.807857643 1.198859261 1.138457643 1.110016969 1.070918714 1.064253196 1.025991132 1 9.955669148 -9.239218834 24.97076 0.972292417 1.114828365 0.602772655 0.065955014 480.027373 539440.443 0.009930693 0.016460322 5.76E-10 9.239218834 0.142535948 FEEESKEPVADEEEEDS(ph)DDDVEPITEFR ddPTM_HeLa_Romidepsin_16h_R1 9 FEEESKEPVADEEEEDSDDDVEPITEFR 28 1 P54105;E9PJF4 P54105 CLNS1A Methylosome subunit pICln 1 0 FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(0.996)DDDVEPIT(0.004)EFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(0.996)DDDVEPIT(0.004)EFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR;FEEESKEPVADEEEEDS(1)DDDVEPITEFR ;;;;;;;; 141.3 7.81E-11 2101005300 31891.45 35926.74 31907.27 33975.28 35539.4 35677.75 27866.07 31583.54 35393.29 33559.11 TRUE FALSE FALSE 31502.74474 36432.51759 32462.60265 37903.66173 33725.6918 33398.05692 30233.01329 32497.3599 32227.6255 32687.23948 0.963762778 1.114579211 0.99312769 1.159585891 1.031769349 1.021746022 0.924917912 0.994191018 0.985939039 1 14.99643992 -4.123312343 21.93807858 1.004893865 0.036094284 0 0.067595069 0 0 0.009160395 0 7.53E-05 4.123312343 -0.968799581 FEEESKEPVADEEEEDSDDDVEPITEFR ddPTM_HeLa_Romidepsin_16h_R1 1 FEEESKEPVADEEEEDSDDDVEPITEFR 28 1 P54105;E9PJF4 P54105 CLNS1A Methylosome subunit pICln 0 0 97.388 1.00E-07 11278000 2808.2 3177.3 2910.8 2896.6 2561.9 3374.7 1959.1 2570.9 3257.4 2778 FALSE FALSE TRUE 2773.972578 3222.030113 2961.461253 3231.518521 2431.156683 3159.067561 2125.505905 2645.284935 2966.049986 2705.82716 1.02518469 1.190774548 1.094475396 1.194281205 0.898489275 1.167505304 0.785529075 0.977625243 1.096171267 1 11.40185397 -7.755527242 24.99999792 1.044070037 0.881577186 0.331392952 0.103208644 130.9452193 553696.2359 0.013680729 0.048605165 1.76E-08 7.755527242 -0.162492851 FEELCSDLFR ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 183.43 0.00022444 12260000 2081.4 1728.6 2501.5 501.02 4038.9 3689.5 3180.9 2478.6 2238.6 1788.2 FALSE FALSE TRUE 2056.031096 1752.935276 2545.037558 558.9502898 3832.779862 3453.752857 3451.085567 2550.31438 2038.374009 1741.742306 1.180445057 1.006426307 1.461202124 0.320914459 2.200543587 1.982929877 1.981398485 1.464231747 1.170307457 1 10.76631548 -8.740468468 24.99999972 1.064192985 1.917974362 0.642845334 0.321913577 109.8832441 130994.2271 0.042387654 0.084704848 1.82E-09 8.740468468 0.853781377 FEELNADLFR ddPTM_HeLa_Romidepsin_16h_R1 4 FEELNADLFR 10 0 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;A8K7Q2;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 0 ;;; ;;; 214.71 1.20E-17 127728700 10104.8 8274.2 11744.1 9595.5 12800.4 12143.1 10090 8635.6 8153 7912.1 FALSE FALSE TRUE 9981.638811 8390.684405 11948.50113 10704.97686 12147.14782 11367.1951 10947.04435 8885.457461 7423.77526 7706.542501 1.295216215 1.088774169 1.550436027 1.389076471 1.576212396 1.475005828 1.420487118 1.152975859 0.963308158 1 12.91186803 -11.37399381 0.448112043 0.978065732 1.426550372 0.554589221 0.143283065 0.66678021 0.288204236 0.129550898 0.052641222 4.23E-12 11.37399381 0.44848464 FEHQEWK ddPTM_HeLa_Romidepsin_16h_R1 1 FEHQEWK 7 0 Q9UHB9-4;Q9UHB9-2;Q9UHB9 Q9UHB9-4 SRP68 Signal recognition particle subunit SRP68 0 0 96.492 0.017984 5996100 3969 4257.6 4772 4144 4715.8 4837.1 4369.3 3254.3 4655.2 4054.4 FALSE FALSE TRUE 3920.624301 4317.538605 4855.054658 4623.148778 4475.135129 4528.024921 4740.428233 3348.458036 4238.827253 3949.066104 0.992797841 1.093306238 1.229418432 1.170694199 1.133213527 1.146606515 1.200392222 0.847911366 1.073374601 1 11.9472958 -10.16853266 4.174269546 0.996528851 1.130859243 0.14138517 0.101350901 0.209995246 6.568195491 0.015480057 0.019013259 6.78E-11 10.16853266 0.134330393 FEIGEGENLDLPYGLER ddPTM_HeLa_Romidepsin_16h_R1 2 FEIGEGENLDLPYGLER 17 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 0 ; ; 145.49 0.001554 22810900 3534 3391.1 3344.7 3486.3 3477.1 3213.4 2696.4 3241 4244.7 3737.2 FALSE FALSE TRUE 3490.926249 3438.839995 3402.9131 3889.40241 3299.650612 3008.074111 2925.432149 3334.773222 3865.043401 3640.107005 0.95901748 0.944708491 0.934838755 1.068485735 0.906470773 0.826369694 0.803666525 0.916119558 1.061793897 1 11.82976515 -8.526699639 24.66440594 0.979218354 0.847914515 0.622454556 0.050854507 40.34860172 260455.771 0.006187199 0.01242109 2.97E-09 8.526699639 -0.131303839 FEK(ac)EAAEMGK ddPTM_HeLa_Romidepsin_16h_R1 2 FEKEAAEMGK 10 1 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01;A6PW80;Q5JR01;A0A2R8Y488;A0A2U3TZH3;Q05639;A0A2R8Y660;A0A2R8YDN5 Q5VTE0;A0A2R8Y488 EEF1A1P5;EEF1A1;EEF1A2 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha;Elongation factor 1-alpha 2 0 1 ; FEK(1)EAAEMGK;FEK(1)EAAEMGK 94.767 0.016616 3751300 610.26 714.2 571.16 616.2 985.93 708.27 661.95 954.92 1160.52 1027.05 FALSE TRUE FALSE 602.8219164 724.2545263 581.1008002 687.4479433 935.6143131 663.0138328 718.1760165 982.5491036 1056.720185 1000.367093 0.602600706 0.723988755 0.58088756 0.687195679 0.935270982 0.662770534 0.717912476 0.982188549 1.056332412 1 9.966313791 -12.47604615 1.220662382 0.9997241 0.71940371 0.450547438 0.125791827 0.370327158 0.988726126 0.086414286 0.021292338 3.34E-13 12.47604615 -0.28032039 FELAVDAVHR ddPTM_HeLa_Romidepsin_16h_R1 2 FELAVDAVHR 10 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7;H3BSQ5;H3BUE3 Q8WWM7-6 ATXN2L Ataxin-2-like protein 0 0 ; ; 104.43 0.0026009 946330 781.75 434.2 750.05 637.67 553.23 717.23 623.45 484.57 706.96 656.56 FALSE FALSE TRUE 772.2217303 440.312679 763.1043056 711.4004057 524.9966087 671.4013178 676.4058274 498.5902684 643.727727 639.5024766 1.207535168 0.688523806 1.193278109 1.112427914 0.820945388 1.049880716 1.057706346 0.779653382 1.00660709 1 9.320806136 -5.649805625 0.454098881 1.074582433 1.52E-12 0.061247904 0.160924629 26.28122555 1.184910523 0.035421307 21.07096007 2.24E-06 5.649805625 -1.074582433 FELLPTPPLS(ph)PSRR ddPTM_HeLa_Romidepsin_16h_R1 1 FELLPTPPLSPSRR 14 1 H0YBG3;A0A0B4J1R1;H0YBT0;A0A087WUS5;P01106;P01106-2 H0YBG3 MYC Myc proto-oncogene protein 1 0 FELLPTPPLS(0.5)PS(0.5)RR 63.374 0.022792 5806500 4638.7 4828.8 4788.2 5087.3 3944.9 3779.4 3429.1 3564 4602.7 4964.3 TRUE FALSE FALSE 4582.16174 4896.779973 4871.536612 5675.517562 3743.577033 3537.908537 3720.367668 3667.118717 4191.022984 4835.32677 0.947642622 1.012709214 1.007488603 1.173760913 0.774213866 0.731679306 0.769413908 0.758401426 0.866750725 1 12.23939767 -8.638992922 9.273148569 0.99281383 0.754633332 0.730779214 0.072205699 0.095934547 7.382461009 0.009038929 0.018093685 2.30E-09 8.638992922 -0.238180498 FEPES(ph)PGFESR ddPTM_HeLa_Romidepsin_16h_R1 4 FEPESPGFESR 11 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 FEPES(0.996)PGFES(0.004)R;FEPES(1)PGFESR;FEPES(1)PGFESR;FEPES(0.982)PGFES(0.018)R ;;; 184.98 3.20E-06 171737000 12595.5 14443.1 13449.4 10623.4 11758.1 16585.6 14133.2 17318.8 14104.8 11799.7 TRUE FALSE FALSE 12441.9812 14646.43034 13683.48117 11851.72749 11158.04028 15525.83369 15333.67366 17819.89215 12843.23136 11493.14209 1.082556981 1.274362591 1.190577916 1.031199945 0.970843325 1.350878077 1.334158538 1.550480453 1.117469118 1 13.48848565 -4 0.422819981 1.047089191 10.82885205 0.628970616 0.107225887 30.18917067 0.343384774 0.025511566 252.7629312 1.00E-04 4 9.781762856 FEPYANPTK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 FEPYANPTKR 10 1 A0A087X0X3;P52272-2;P52272;M0R2T0;M0QYQ7;M0R0N3;M0R019;M0R0Y6 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 1 FEPYANPTK(1)R 131.12 0.0020021 2306100 674.3 546.82 619.68 307.01 833.28 864.11 856.7 632.46 950.48 718.13 FALSE TRUE FALSE 666.0813722 554.5181463 630.4652705 342.5079407 790.7546122 808.8961598 929.4680766 650.7592322 865.4666883 699.4728791 0.952261899 0.792765757 0.901343411 0.489665791 1.130500747 1.156436774 1.328812173 0.930356632 1.237312717 1 9.45012431 -8.560071857 24.99999156 0.920126295 1.155215315 0.256784287 0.197633061 156.6607898 105301.692 0.025133794 0.050267697 2.75E-09 8.560071857 0.235089021 FES(ph)PESQASAEQPEM ddPTM_HeLa_Romidepsin_16h_R1 1 FESPESQASAEQPEM 15 0 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 1 0 FES(0.673)PES(0.327)QASAEQPEM 146.67 0.00066087 6819600 1695.4 1816.6 1381.6 1328.3 1842.7 2456.8 1807.1 1902.7 1682.1 1601.3 TRUE FALSE FALSE 1674.735813 1842.174142 1405.646168 1481.884296 1748.660143 2299.818409 1960.595029 1957.751623 1531.648763 1559.697995 1.073756469 1.181109515 0.901229708 0.950109765 1.121153036 1.474528028 1.257035038 1.255211989 0.982016242 1 10.60705099 -8.467148282 6.360528943 1.031438126 1.32015843 0.701060779 0.091290838 0.098789623 8.750555108 0.012884082 0.028782978 3.41E-09 8.467148282 0.288720304 FES(ph)PEVAER ddPTM_HeLa_Romidepsin_16h_R1 2 FESPEVAER 9 0 A0A087X0X3;P52272-2;P52272 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 0 FES(1)PEVAER;FES(1)PEVAER ; 121.61 0.012579 52438000 5099.5 5201.6 5301.9 3432.1 5587.6 7096.6 5602.4 5740.9 6116.9 5253.1 TRUE FALSE FALSE 5037.345333 5274.828261 5394.177345 3828.935551 5302.443922 6643.150163 6078.267716 5907.003884 5569.789144 5116.623705 0.984505726 1.030919717 1.054245467 0.74833245 1.03631696 1.298346438 1.187945033 1.154472993 1.088567279 1 12.32097642 -8.409849961 5.896239863 0.982185859 1.208839531 0.55085253 0.092565379 0.11772621 5.3572724 0.011912322 0.026892527 3.89E-09 8.409849961 0.226653672 FESPATGILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 FESPATGILSPR 12 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 FESPATGILS(1)PR;FESPATGILS(1)PR ; 167.84 0.00021284 128550000 2396.68 2659.21 2948.3 2420.58 3053.1 3308.3 3000.2 3112.3 3148.7 2660.24 TRUE FALSE FALSE 2367.468342 2696.646428 2999.613925 2700.458849 2897.288914 3096.910307 3255.036913 3202.34949 2867.072386 2591.126581 0.913683013 1.04072354 1.157648548 1.042194877 1.118157999 1.195198386 1.256224585 1.235890795 1.106496459 1 11.33936378 -8.827187707 0.613832507 0.959919975 1.269358541 0.562485499 0.06834437 0.343812561 0.221006102 0.012918777 0.053497607 1.49E-09 8.827187707 0.309438565 FESPESQAS(ph)AEQPEM ddPTM_HeLa_Romidepsin_16h_R1 1 FESPESQASAEQPEM 15 0 O75436 O75436 VPS26A Vacuolar protein sorting-associated protein 26A 1 0 FES(0.046)PES(0.182)QAS(0.772)AEQPEM 248.67 2.05E-57 8673400 2037.1 1730.8 2066.1 1787.6 2290.4 2590.3 2528.2 2695.6 2223 1943.4 TRUE FALSE FALSE 2012.271042 1755.166248 2102.059604 1994.290723 2173.512341 2424.78819 2742.945245 2773.592933 2024.169312 1892.910188 1.063056797 0.927231656 1.110490935 1.053558027 1.148238493 1.280984278 1.44906254 1.465253318 1.0693425 1 10.88639025 -8.097816667 1.10727673 1.025949754 1.50889444 0.929616203 0.046148663 0.105382776 0.209093889 0.006854554 0.041672889 7.98E-09 8.097816667 0.482944687 FFDEESYSLLR ddPTM_HeLa_Romidepsin_16h_R1 1 FFDEESYSLLR 11 0 A6NLM8;P51571 A6NLM8 SSR4 Translocon-associated protein subunit delta 0 0 175.91 0.00036041 5551100 753.08 525.66 686.77 579.54 706.43 650.48 623.04 714.82 617.51 586.88 FALSE FALSE TRUE 743.9011713 533.0602553 698.7229438 646.5491416 670.378241 608.9164273 675.961002 735.5021889 562.278359 571.632773 1.301362004 0.932522207 1.222328349 1.131056812 1.172742839 1.065223087 1.182509181 1.286669036 0.983635623 1 9.158944822 -12.65773556 1.503292548 1.000079426 1.175987168 0.296646175 0.102195628 0.428733644 1.744236016 0.074608086 0.016823315 2.20E-13 12.65773556 0.175907741 FFEHFIEGGR ddPTM_HeLa_Romidepsin_16h_R1 2 FFEHFIEGGR 10 0 F5GYN4;J3KR44;F5H6Q1;F5GYJ8;Q96FW1;F5H3F0;Q96FW1-2 F5GYN4 OTUB1 Ubiquitin thioesterase OTUB1 0 0 ; ; 125.68 0.0042913 52000000 12311.8 10742 13424.1 12788.2 14273.8 13194.3 11672.8 11391 11996.5 10568.7 FALSE FALSE TRUE 12161.73905 10893.22616 13657.74083 14266.83185 13545.35472 12351.22681 12664.28734 11720.58061 10923.50299 10294.12365 1.18142539 1.058198495 1.326751193 1.38592 1.315833691 1.199832762 1.230244338 1.138570024 1.061139672 1 13.3295334 -11.35629502 0.527075879 0.998877813 1.255893186 0.471470335 0.088273153 0.559774028 0.335377736 0.064385833 0.028427376 4.40E-12 11.35629502 0.257015373 FFHLAFEEEFGR ddPTM_HeLa_Romidepsin_16h_R1 1 FFHLAFEEEFGR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 0 84.605 0.018152 4612400 4009.6 3503.6 4133.4 4228.8 4378.9 4394.5 3152.4 3931 4640.6 3978 FALSE FALSE TRUE 3960.729453 3552.923773 4205.340093 4717.753753 4155.428393 4113.705633 3420.164777 4044.737283 4225.533113 3874.650987 1.022215799 0.916966144 1.085346811 1.217594506 1.072465212 1.061697078 0.882702672 1.043897192 1.090558383 1 11.91985065 -7.794332119 24.99923981 1.031329756 0.963299475 0.108370758 0.084184471 309.0783808 234906.3004 0.011973173 0.035923188 1.61E-08 7.794332119 -0.068030281 FFIDQSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 FFIDQSKK 8 1 I3L0K7;Q12931-2;Q12931 I3L0K7 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 1 FFIDQSK(1)K 101.64 0.013042 0 150.86 150.46 123.34 125.84 185.89 200.69 167.89 169.69 165.11 125.89 FALSE TRUE FALSE 149.0212603 152.5781798 125.486681 140.3902129 176.4033396 187.8665567 182.1505724 174.5997124 150.3421481 122.6193597 1.215315923 1.244323737 1.02338392 1.144926978 1.438625517 1.532111709 1.485496034 1.423916361 1.226088185 1 6.938042965 -4 0.141375067 0.941312585 3.066656319 0.530768029 0.122936875 33.49940888 0.312001753 0.312613181 14.47534088 1.00E-04 4 2.125343733 FFPNDDPEAVS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 FFPNDDPEAVSSPR 14 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38;A0A087X1U5 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 0 FFPNDDPEAVS(0.5)S(0.5)PR;FFPNDDPEAVS(0.5)S(0.5)PR ; 123.68 0.003561 5124400 2317.21 2096.18 2137.45 2158.09 2764.5 3435.5 2679.8 3104.6 1985.64 1935.74 TRUE FALSE FALSE 2288.966953 2125.690077 2174.651421 2407.61852 2623.417249 3215.982638 2907.422145 3194.426703 1808.039385 1885.449196 1.214016776 1.12741838 1.153386379 1.276946908 1.391401718 1.70568512 1.54203155 1.694252335 0.958943571 1 10.88069256 -8.690218354 1.095992805 1.102478873 1.666588832 0.89125354 0.084207754 0.130947574 0.303252966 0.014997856 0.046975201 2.04E-09 8.690218354 0.564109959 FFQGS(ph)QEFLASASASAER ddPTM_HeLa_Romidepsin_16h_R1 1 FFQGSQEFLASASASAER 18 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 FFQGS(1)QEFLASASASAER 101.23 0.0019576 6279900 1118.8 1179.6 1312.8 947.57 956.36 1052.2 607.06 685.71 1076.2 1160.6 TRUE FALSE FALSE 1105.163635 1196.20644 1335.648733 1057.132502 907.5533805 984.9678158 658.6236612 705.549937 979.9419766 1130.447445 0.977633804 1.058170767 1.181522184 0.9351452 0.80282669 0.871307924 0.582622097 0.624133338 0.866862039 1 10.14267821 -8.084117416 1.09280167 1.007020739 0.570126467 0.723205523 0.092442426 0.227665152 0.434687895 0.012957278 0.081444176 8.24E-09 8.084117416 -0.436894272 FGAVWTGDNTAEWDHLK ddPTM_HeLa_Romidepsin_16h_R1 1 FGAVWTGDNTAEWDHLK 17 0 F5H6X6;Q14697;Q14697-2;E9PKU7 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 130.39 0.00093303 12937000 1624.9 1508.1 1731.2 1844.6 1762.7 1949.7 1539.8 1652.1 1905.1 1504.7 FALSE FALSE TRUE 1605.095094 1529.331071 1761.33081 2057.881331 1672.742841 1825.120462 1670.590574 1699.900907 1734.703085 1465.607677 1.095173776 1.043479162 1.201775098 1.404114732 1.141330567 1.245299469 1.139862052 1.15986081 1.183606713 1 10.51728325 -9.741178842 5.945079232 1.045886616 1.219382967 0.343244942 0.086254982 0.099604649 11.27654158 0.012417346 0.017268647 1.81E-10 9.741178842 0.173496351 FGESEEVEMEVES(ph)DEEDDKQEK ddPTM_HeLa_Romidepsin_16h_R1 7 FGESEEVEMEVESDEEDDKQEK 22 1 Q15459;Q15459-2;H7C1L2 Q15459 SF3A1 Splicing factor 3A subunit 1 1 0 FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGES(0.004)EEVEMEVES(0.996)DEEDDKQEK;FGES(0.003)EEVEMEVES(0.997)DEEDDKQEK;FGES(0.001)EEVEMEVES(0.999)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK;FGESEEVEMEVES(1)DEEDDKQEK ;;;;;; 94.45 0.00048887 1649460900 21728.5 23750.94 22268 16376.64 22621 22211.55 18887.94 21554.38 22314.1 23565.4 TRUE FALSE FALSE 21463.66468 24085.30636 22655.5652 18270.18417 21466.56596 20792.30364 20492.28115 22178.02198 20318.27101 22953.16751 0.935106872 1.049323861 0.987034368 0.795976597 0.935233272 0.905857705 0.892786634 0.966229256 0.885205539 1 14.48640564 FGESTTGFNFS(ph)FK ddPTM_HeLa_Romidepsin_16h_R1 1 FGESTTGFNFSFK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 FGESTTGFNFS(1)FK 87.519 0.025941 15155000 1752.9 2160.5 1748.8 1894.5 1834.7 1925.4 1678.2 1762 2213.5 1892.6 TRUE FALSE FALSE 1731.534981 2190.915576 1779.23713 2113.551004 1741.068413 1802.373154 1820.746266 1812.98069 2015.519016 1843.429979 0.939300652 1.188499482 0.965177495 1.146531752 0.944472224 0.977728026 0.987694833 0.983482264 1.09335263 1 10.8481769 -5.229213183 17.50762405 0.995279475 1.011539645 0 0.087736958 0 0 0.010576924 0 5.90E-06 5.229213183 0.01626017 FGFAIGSQTTK ddPTM_HeLa_Romidepsin_16h_R1 1 FGFAIGSQTTK 11 0 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 0 145.99 0.0078174 1154900 745.15 771.05 757.14 625.98 676.33 629.67 507.73 835.1 783.97 586.37 FALSE FALSE TRUE 736.0678252 781.9048621 770.3177041 698.3587529 641.8143564 589.4361192 550.8565735 859.2623009 713.8497597 571.1360229 1.288778497 1.3690344 1.348746486 1.222753819 1.123750439 1.032041573 0.964492785 1.50447926 1.249876966 1 9.157690571 -12.35627042 1.127927658 1.002371118 1.225084189 0 0.170422666 0.599844791 1.387261065 0.102042184 0.02772438 4.40E-13 12.35627042 0.222713071 FGFAIGSQTTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 FGFAIGSQTTKK 12 1 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 1 ; FGFAIGSQTTK(1)K;FGFAIGSQTTK(1)K 159.94 0.00035852 748090 399.65 432.14 507.07 571.57 493.47 625.8 504.81 623.18 531.31 426.14 FALSE TRUE FALSE 394.7789121 438.2236783 515.8953406 637.6576127 468.2863845 585.8133997 547.6885488 641.2107301 483.7883029 415.0688214 0.951116759 1.055785585 1.242915184 1.536269601 1.12821383 1.4113645 1.319512622 1.54482991 1.165561656 1 8.697206755 -9.715477562 2.696444363 0.97812167 1.372820143 0.608471207 0.126578873 0.094894208 1.414189648 0.016878654 0.024101778 1.93E-10 9.715477562 0.394698473 FGFAIGSQTTKK ddPTM_HeLa_Romidepsin_16h_R1 1 FGFAIGSQTTKK 12 1 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 0 86.463 0.021633 558660 204.91 61.244 229.42 264.12 232.47 222.2 169.89 132 280.56 222.39 FALSE FALSE TRUE 202.4124781 62.10619464 233.4129589 294.6587971 220.6061884 208.0021371 184.3204524 135.8192117 255.4660109 216.6122757 0.934446016 0.286715951 1.077561085 1.360305163 1.018438072 0.96025092 0.850923392 0.627015303 1.17936996 1 7.758971195 -7.333997736 2.324854782 0.958317737 0.575666829 0.1417977 0.261144506 0.783117403 5.578949995 0.035673988 0.56565262 4.63E-08 7.333997736 -0.382650908 FGGEHVPNS(ph)PFQVTALAGDQPSVQPPLR ddPTM_HeLa_Romidepsin_16h_R1 1 FGGEHVPNSPFQVTALAGDQPSVQPPLR 28 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5F3 Q60FE5 FLNA Filamin-A 1 0 FGGEHVPNS(0.962)PFQVT(0.038)ALAGDQPSVQPPLR 66.012 0.00014981 12236000 1571 1493.3 1558.6 2011.8 2397.6 2361.6 1927.1 2300.7 1682.6 1769.3 TRUE FALSE FALSE 1551.852048 1514.322717 1585.726779 2244.413782 2275.241525 2210.701382 2090.787826 2367.267125 1532.104042 1723.333331 0.90049442 0.878717245 0.920150937 1.302367767 1.320256206 1.282805446 1.213223111 1.373655974 0.889035229 1 10.75098606 -9.260016906 24.99861759 0.942823209 1.29406725 0.931711174 0.051312181 27.44322405 482287.3197 0.008688306 0.013909251 5.50E-10 9.260016906 0.351244041 FGGKYCT(ph)GER ddPTM_HeLa_Romidepsin_16h_R1 1 FGGKYCTGER 10 1 P58397-3;P58397 P58397-3 ADAMTS12 A disintegrin and metalloproteinase with thrombospondin motifs 12 1 0 FGGKYCT(1)GER 91.961 0.019546 35217000 2258.8 2000.8 1706.4 3264.9 2115.1 1856.4 1961.8 2326 2303.4 2042.2 TRUE FALSE FALSE 2231.268877 2028.967315 1736.099176 3642.4031 2007.158554 1737.782031 2128.435243 2393.29914 2097.378135 1989.14335 1.121723518 1.020020661 0.872787362 1.831141582 1.009056766 0.873633382 1.070026071 1.203180827 1.054412763 1 10.95793153 -12.07503923 0.515278173 0.982054429 1.130355642 0.023439645 0.256912775 4.740688974 1.926888872 0.346456649 0.068917393 8.41E-13 12.07503923 0.148301213 FGGS(ph)GSQVDSAR ddPTM_HeLa_Romidepsin_16h_R1 2 FGGSGSQVDSAR 12 0 Q13200;Q13200-2;Q13200-3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 1 0 FGGS(0.533)GS(0.376)QVDS(0.091)AR;FGGS(0.774)GS(0.226)QVDSAR ; 170.26 0.00015247 29811000 6421.2 5915.4 7264.7 6253.6 5948.3 5788.2 4620.6 5091.4 7512.1 6783.7 TRUE FALSE FALSE 6342.935945 5998.677156 7391.139056 6976.670656 5644.736055 5418.352701 5013.073649 5238.711626 6840.198962 6607.458496 0.959966067 0.907864523 1.118605446 1.05587809 0.854297618 0.820035828 0.758699226 0.792848208 1.035223901 1 12.68987974 -8.58596899 4.387596718 0.990483659 0.793363226 0.756004982 0.057340413 0.085984271 3.326205083 0.008629092 0.017963495 2.59E-09 8.58596899 -0.197120434 FGHEFLEFEFRPDGK ddPTM_HeLa_Romidepsin_16h_R1 2 FGHEFLEFEFRPDGK 15 1 F5H6N1;P61326;Q96A72;P61326-2 F5H6N1 MAGOHB;MAGOH Protein mago nashi homolog;Protein mago nashi homolog 2 0 0 ; ; 76.24 0.015355 45259000 12254.7 10267.5 11441.6 8914.3 12022.8 12101.2 11000 11723.4 12781.5 11807.8 FALSE FALSE TRUE 12105.335 10412.04613 11640.73625 9945.013309 11409.23165 11327.97237 11934.33973 12062.59808 11638.29063 11501.03165 1.052543404 0.905314101 1.012147136 0.864706194 0.992018107 0.984952717 1.037675583 1.048827483 1.011934492 1 13.48947566 -13.35207831 21.68586874 0.999999313 1.004706039 0 0.059623648 477.1976226 617734.1172 0.250612736 0.00876225 4.45E-14 13.35207831 0.004706726 FGLNVSSISR ddPTM_HeLa_Romidepsin_16h_R1 1 FGLNVSSISR 10 0 F8VZQ9;P82979;H0YHG0 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 0 114.89 0.030311 482980 0 200.72 251.36 148.99 176.3 185.64 0 132.58 0 0 FALSE FALSE TRUE 0 203.5457414 255.7348154 166.2169248 167.3027531 173.7782031 0 136.4159931 0 0 0 FGNPGEK(ac)LVK ddPTM_HeLa_Romidepsin_16h_R1 2 FGNPGEKLVK 10 1 P17844;J3KTA4;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3QKN9;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 1 ; FGNPGEK(1)LVK;FGNPGEK(1)LVK 146.11 0.010368 34758000 6756.9 6682.4 7070 6784.3 5974 5584.6 5705.5 5553.7 6656.4 6210.4 FALSE TRUE FALSE 6674.544304 6776.475003 7193.050384 7568.732687 5669.124488 5227.762083 6190.125028 5714.387547 6061.034913 6049.052913 1.103403194 1.120253881 1.189120097 1.251226067 0.937192081 0.864228196 1.023321356 0.94467475 1.001980806 1 12.56249357 FGQAAT(ph)MEGIGAIGGTPPAFNR ddPTM_HeLa_Romidepsin_16h_R1 2 FGQAATMEGIGAIGGTPPAFNR 22 0 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 1 0 FGQAAT(0.751)MEGIGAIGGT(0.249)PPAFNR;FGQAAT(0.636)MEGIGAIGGT(0.364)PPAFNR ; 82.705 0.0035592 787665000 3358.6 3584.8 3562.4 3261.4 4664.1 5707 4302.7 4906.7 3959.2 3835.9 TRUE FALSE FALSE 3317.664091 3635.266908 3624.402078 3638.498413 4426.073573 5342.341118 4668.171231 5048.667623 3605.079236 3736.242765 0.88796802 0.972973957 0.970066001 0.973838865 1.184632223 1.429869913 1.249429313 1.351268625 0.96489427 1 11.86737248 -8.629147857 2.886668277 0.950323053 1.33390199 0.920486942 0.050722451 0.054142292 0.906534355 0.008386464 0.018279686 2.35E-09 8.629147857 0.383578937 FGQAATMEGIGAIGGT(ph)PPAFNR ddPTM_HeLa_Romidepsin_16h_R1 5 FGQAATMEGIGAIGGTPPAFNR 22 0 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 1 0 FGQAAT(0.043)MEGIGAIGGT(0.957)PPAFNR;FGQAAT(0.384)MEGIGAIGGT(0.616)PPAFNR;FGQAATMEGIGAIGGT(1)PPAFNR;FGQAAT(0.151)MEGIGAIGGT(0.849)PPAFNR;FGQAAT(0.001)MEGIGAIGGT(0.999)PPAFNR ;;;; 136.67 6.81E-16 698712000 6182.38 7122.74 5802.45 6325.27 7351.36 8361 7034.99 7944.45 7008.56 6118.43 TRUE FALSE FALSE 6107.026775 7223.014121 5903.439208 7056.627479 6976.192667 7826.759084 7632.541875 8174.310126 6381.69684 5959.472307 1.024759653 1.212022432 0.990597641 1.184102739 1.17060577 1.313330893 1.280741227 1.371649989 1.070849316 1 12.54096887 -8.050945745 0.375066895 0.995927918 1.511978561 0.73771236 0.066140375 1.002426297 0.146790699 0.019476914 0.213244242 8.89E-09 8.050945745 0.516050644 FGS(ph)TGSTPPVS(ph)PTPSER ddPTM_HeLa_Romidepsin_16h_R1 1 FGSTGSTPPVSPTPSER 17 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 2 0 FGS(0.429)T(0.318)GS(0.116)T(0.136)PPVS(0.797)PT(0.097)PS(0.107)ER 130.47 0.020359 30095000 3071.4 2879.2 2728.3 2934.5 4097.6 4142.6 3731.5 4062.4 3296.4 2970.7 TRUE FALSE FALSE 3033.964595 2919.733453 2775.784917 3273.800697 3888.484182 3877.90123 4048.453517 4179.939135 3001.561728 2893.520786 1.048537343 1.009059091 0.959310516 1.131424634 1.34385908 1.340201615 1.399144439 1.444585833 1.03733892 1 11.49861029 -8.825721487 2.42586718 1.017756647 1.391619064 0.964222978 0.033841888 0.039210786 0.470257054 0.005534088 0.01134919 1.49E-09 8.825721487 0.373862417 FGSNINLEADES(ph) ddPTM_HeLa_Romidepsin_16h_R1 2 FGSNINLEADES 12 0 Q9NQP4 Q9NQP4 PFDN4 Prefoldin subunit 4 1 0 FGSNINLEADES(1);FGS(0.011)NINLEADES(0.989) ; 172.21 0.00010373 9097200 6789.7 6863.7 6670.5 6806.8 5909.3 5244 4991.9 5856.5 7753.5 7046.9 TRUE FALSE FALSE 6706.944525 6960.327349 6786.597254 7593.834243 5607.72637 4908.925324 5415.911861 6025.948587 7060.007541 6863.820522 0.977144508 1.01406022 0.98874923 1.106356761 0.816997815 0.715188474 0.78905208 0.877929219 1.028582772 1 12.74479611 -8.651996628 7.083828336 0.998114184 0.789549024 0.80741002 0.051912883 0.070426018 4.171890872 0.007165718 0.014381562 2.23E-09 8.651996628 -0.208565159 FGSTGST(ph)PPVSPTPSER ddPTM_HeLa_Romidepsin_16h_R1 2 FGSTGSTPPVSPTPSER 17 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 1 0 FGS(0.002)T(0.001)GS(0.032)T(0.95)PPVS(0.014)PT(0.001)PSER;FGSTGS(0.004)T(0.91)PPVS(0.083)PT(0.002)PS(0.001)ER ; 122.63 0.0046823 36971600 4796.6 4947.9 4989.1 4847.4 6416.9 7078.1 5773.8 7029.4 5493 5108.6 TRUE FALSE FALSE 4738.137194 5017.556666 5075.933193 5407.879196 6089.421648 6625.832254 6264.226428 7232.784598 5001.692323 4975.877836 0.952221367 1.008376176 1.020108082 1.086819125 1.223788415 1.33159062 1.258918855 1.453569569 1.005187926 1 12.28073535 -8.650555626 0.98545563 0.976854744 1.378539878 0.927442244 0.043717292 0.096433967 0.175176232 0.006899582 0.02430282 2.24E-09 8.650555626 0.401685133 FGT(ph)FGGLGSK ddPTM_HeLa_Romidepsin_16h_R1 1 FGTFGGLGSK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 FGT(1)FGGLGSK 121.68 0.02238 34505000 3936.1 2698.1 3659.6 2827.9 4356.5 2046.9 1601.4 3099.3 2445.1 2558.6 TRUE FALSE FALSE 3888.125299 2736.083923 3723.293803 3154.875104 4134.171549 1916.109696 1737.422876 3188.973356 2226.404132 2492.127203 1.560163259 1.097890958 1.494022375 1.265936626 1.658892669 0.768865126 0.697164605 1.279619014 0.893374997 1 11.28316199 -8.23818177 24.99699076 1.297904179 0.893411055 0.274932848 0.270952748 750.9239848 807083.2107 0.038462652 0.097994505 5.78E-09 8.23818177 -0.404493124 FGTK(ac)LGSDIK ddPTM_HeLa_Romidepsin_16h_R1 2 FGTKLGSDIK 10 1 K7EJ68;K7EME0;A0A0B4J2A4;P42765 K7EJ68 ACAA2 "3-ketoacyl-CoA thiolase, mitochondrial" 0 1 ; FGTK(1)LGSDIK;FGTK(1)LGSDIK 135.8 0.0085718 2959200 1441.97 1729.78 2467.9 1385.97 2768.7 3165.1 2393.3 1953.69 1470.8 1145.88 FALSE TRUE FALSE 1424.394715 1754.131888 2510.852764 1546.222373 2627.402908 2962.860325 2596.586842 2010.216938 1339.247964 1116.109872 1.276213705 1.571648035 2.249646586 1.385367526 2.354071918 2.654631411 2.326461674 1.801092336 1.199924844 1 10.12426334 -9.881112598 0.690892182 1.054526126 2.282314738 0.640454666 0.329080428 0.26112862 0.256510692 0.079372988 0.123440115 1.31E-10 9.881112598 1.227788612 FGVPAEGRT(ph)PPPFPGEPWK ddPTM_HeLa_Romidepsin_16h_R1 1 FGVPAEGRTPPPFPGEPWK 19 1 Q9UJY1 Q9UJY1 HSPB8 Heat shock protein beta-8 1 0 FGVPAEGRT(1)PPPFPGEPWK 98.227 0.00092438 23720000 4194.5 4037.9 3577.9 4767.9 2942.3 2702.2 2217.8 2600.3 4235.9 3821.6 TRUE FALSE FALSE 4143.375821 4094.745662 3640.171849 5319.187032 2792.143452 2529.538141 2406.179877 2675.535578 3857.030495 3722.314281 1.113118213 1.100053717 0.97793243 1.42899998 0.75010954 0.679560604 0.646420397 0.718782826 1.036191521 1 11.86198415 -8.550771717 24.89824505 1.07628372 0.684198433 0.733318821 0.120861445 76.94018926 68679.22112 0.016822262 0.033645047 2.81E-09 8.550771717 -0.392085287 FGYVDFESAEDLEK ddPTM_HeLa_Romidepsin_16h_R1 2 FGYVDFESAEDLEK 14 0 P19338 P19338 NCL Nucleolin 0 0 ; ; 253.76 1.50E-66 48264000 5602.4 5518.9 5299.9 4676.7 4887.1 4642.9 4885.7 5004.1 5643.8 5605.9 FALSE FALSE TRUE 5534.115794 5596.595219 5392.142536 5217.442059 4637.693051 4346.233674 5300.691236 5148.885738 5139.004393 5460.25791 1.013526446 1.024969024 0.987525246 0.955530333 0.849354211 0.795975895 0.970776715 0.942974823 0.941165139 1 12.41475338 -9.045570543 3.043771682 1.006922113 0.8893689 0.471704414 0.050343085 0.141423395 2.620492906 0.00718734 0.01296387 9.00E-10 9.045570543 -0.117553212 FHALSSPQS(ph)PFPSTPTSR ddPTM_HeLa_Romidepsin_16h_R1 1 FHALSSPQSPFPSTPTSR 18 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 FHALS(0.001)S(0.009)PQS(0.987)PFPS(0.001)T(0.001)PTS(0.001)R 86.761 0.0035412 7791900 1230.6 1126.3 903.19 1000.4 973.45 1019.1 777.09 953.1 1536.1 1537.6 TRUE FALSE FALSE 1215.600974 1142.156081 918.9096431 1116.070955 923.7712141 953.982799 843.0960052 980.6764448 1398.707369 1497.65293 0.811670681 0.762630686 0.613566484 0.745213348 0.616812611 0.636985232 0.562944851 0.654808885 0.933932916 1 10.54848761 -10.69586485 0.362330339 1.026108731 0.583007624 0.874078505 0.049027345 0.225104438 0.085274527 0.037948458 0.029079669 2.01E-11 10.69586485 -0.443101108 FHDLLSQLDDQYSR ddPTM_HeLa_Romidepsin_16h_R1 1 FHDLLSQLDDQYSR 14 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224;E7ENM1;D2KFR9;A0A669KB17;E7EPD2;A0A669KB75;A0A669KB52;J3KPM9;A0A669KBI6;P42224-2 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta;Signal transducer and activator of transcription 0 0 111.07 0.0024835 6068000 1154.2 855.09 1444.2 1185.7 1134.2 1344.5 1255.3 1478.3 1292.8 1100.6 FALSE FALSE TRUE 1140.132166 867.1279795 1469.335695 1322.796213 1076.317542 1258.590789 1361.925151 1521.072278 1177.16873 1072.006253 1.063549921 0.808883322 1.370640974 1.233944493 1.004021701 1.174051723 1.270445155 1.41890243 1.098098753 1 10.06609761 -4 0.284863635 1.009835183 4.011008617 0.38098495 0.139223756 34.18826918 0.436403211 0.056047497 52.06994322 1.00E-04 4 3.001173434 FHILFK ddPTM_HeLa_Romidepsin_16h_R1 2 FHILFK 6 0 P32004-3;P32004-2;P32004 P32004-3 L1CAM Neural cell adhesion molecule L1 0 0 ; ; 59.818 0.025773 991620 1549.94 2411.5 2391.1 1555.16 2174.73 2414.5 1643.17 2075.79 1925.76 1547.08 FALSE FALSE TRUE 1531.048735 2445.44916 2432.716092 1734.974916 2063.745413 2260.221242 1782.740819 2135.849709 1753.515202 1506.886639 1.016034449 1.622848791 1.614398874 1.151363926 1.369542579 1.499927854 1.183062331 1.417392426 1.163667629 1 10.55735517 -10.28651476 23.4943424 1.007571758 1.399765591 0.506179342 0.154999596 171.1835011 160389.4953 0.025032379 0.028634194 5.17E-11 10.28651476 0.392193833 FHINWEDNTEKLEDAES(ph)SNPNLQSLLSTDALPSASK ddPTM_HeLa_Romidepsin_16h_R1 1 FHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASK 36 1 Q9Y294 Q9Y294 ASF1A Histone chaperone ASF1A 1 0 FHINWEDNT(0.009)EKLEDAES(0.392)S(0.392)NPNLQS(0.159)LLS(0.033)T(0.014)DALPSASK 53.002 0.0019019 9565500 1423.9 1359.5 1169.6 1363.9 1128.3 963.84 828.69 653.1 1616 1447 TRUE FALSE FALSE 1406.544959 1378.639077 1189.956397 1521.600535 1070.718641 902.2537347 899.0789079 671.9964181 1471.460913 1409.406731 0.99796952 0.978169783 0.844295952 1.079603568 0.75969457 0.64016562 0.637913022 0.476793819 1.044028583 1 10.46087229 -8.392600449 1.498201995 0.99166392 0.551083072 0.858532491 0.074039439 0.097623801 0.416580608 0.010139815 0.03357975 4.05E-09 8.392600449 -0.440580847 FHINWEDNTEKLEDAESS(ph)NPNLQSLLSTDALPSASK ddPTM_HeLa_Romidepsin_16h_R1 2 FHINWEDNTEKLEDAESSNPNLQSLLSTDALPSASK 36 1 Q9Y294 Q9Y294 ASF1A Histone chaperone ASF1A 1 0 FHINWEDNT(0.015)EKLEDAES(0.17)S(0.513)NPNLQS(0.17)LLS(0.065)T(0.065)DALPS(0.002)AS(0.001)K;FHINWEDNT(0.016)EKLEDAES(0.219)S(0.621)NPNLQS(0.1)LLS(0.022)T(0.022)DALPS(0.001)ASK ; 49.808 0.0035524 24807000 3478.9 3512 3726.3 3079.2 2448.2 2405.8 2145.18 2359.2 4100.5 3883.9 TRUE FALSE FALSE 3436.497829 3561.442028 3791.154688 3435.231592 2323.259219 2252.077144 2327.391536 2427.45973 3733.74101 3782.995718 0.908406481 0.941434327 1.002156748 0.908071763 0.61413213 0.595315806 0.61522447 0.641676573 0.986979973 1 11.88531343 -8.797899183 4.497104423 0.95705625 0.612748818 0.969065801 0.029970122 0.030612956 1.382950218 0.005727667 0.010934202 1.59E-09 8.797899183 -0.344307432 FHLGLFTDR ddPTM_HeLa_Romidepsin_16h_R1 2 FHLGLFTDR 9 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 0 0 ; ; 74.464 0.018395 1536150 773.14 552.28 1243.97 970.49 946.35 1298.99 656.89 771.76 784.05 564.46 FALSE FALSE TRUE 763.7166723 560.0550123 1265.620776 1082.70262 898.0542282 1215.988731 712.6862202 794.089658 713.9226043 549.7952478 1.389092895 1.018661064 2.301985659 1.969283337 1.633433959 2.211711971 1.296275701 1.444337071 1.298524509 1 9.102750627 -9.782575318 24.98837441 1.176491332 1.803717758 0.496721667 0.312080546 156.1557321 184617.4582 0.052664045 0.069252246 1.65E-10 9.782575318 0.627226426 FHPEPYGLEDDQR ddPTM_HeLa_Romidepsin_16h_R1 2 FHPEPYGLEDDQR 13 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 0 0 ; ; 133.88 0.00084702 13807400 6144.9 6134.5 5839.4 5916.7 6424 6680.2 6196.5 6654.6 6668.4 5826.5 FALSE FALSE TRUE 6070.003595 6220.861652 5941.032307 6600.816693 6096.159309 6253.356779 6722.830555 6847.140352 6071.961603 5675.12669 1.06958028 1.096162604 1.046854569 1.16311354 1.074189114 1.10188849 1.1846133 1.206517621 1.069925296 1 12.47043688 -4 0.12933968 0.967972666 1.717295121 0.623532767 0.037728778 28.35994179 0.247722256 0.112203795 3.887568446 1.00E-04 4 0.749322455 FHQLDIDDLQSIR ddPTM_HeLa_Romidepsin_16h_R1 2 FHQLDIDDLQSIR 13 0 P16152;E9PQ63;A8MTM1;P16152-2;O75828 P16152;O75828 CBR1;CBR3 Carbonyl reductase [NADPH] 1;Carbonyl reductase [NADPH] 3 0 0 ; ; 151.66 0.00035965 59590000 5553.14 5199.7 5305.6 4533.74 6195.32 5912.43 5405.51 5362.94 6077.35 5041.19 FALSE FALSE TRUE 5485.456194 5272.901513 5397.941742 5057.952351 5879.149702 5534.644804 5864.653884 5518.108208 5533.776595 4910.219157 1.11715099 1.073862763 1.099328069 1.030086884 1.197329389 1.12716859 1.194377216 1.123800798 1.126991773 1 12.2615717 -16.52287875 0.109869988 0.585828505 1.203533186 0.079927632 0.057124691 55.86840266 0.451031159 5.234577398 0.271715796 3.00E-17 16.52287875 0.617704681 FHVEEEGK ddPTM_HeLa_Romidepsin_16h_R1 4 FHVEEEGK 8 0 P00558;P00558-2;P07205 P00558 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 0 ;;; ;;; 171.73 0.00046226 140940900 39388.1 38241.3 40316.8 16056.5 38717.7 42894.7 38198.4 30053.7 41831.9 40170.5 FALSE FALSE TRUE 38908.02269 38779.66203 41018.49699 17913.02808 36741.79129 40153.86711 41442.97114 30923.25639 38090.35009 39126.86462 0.994406863 0.991126235 1.048346127 0.457819154 0.939042565 1.026248014 1.05919479 0.790333105 0.973508878 1 15.25587189 FHVEEEGK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 2 FHVEEEGKGK 10 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 1 ; FHVEEEGK(1)GK;FHVEEEGK(1)GK 90.827 0.028007 2660700 4491.8 4463.3 3958.2 2812.7 6125 5792 5734 5044.9 5573.6 5251.5 FALSE TRUE FALSE 4437.052214 4526.134455 4027.090811 3137.917608 5812.418394 5421.909893 6221.045817 5190.866222 5075.083257 5115.065273 0.867447819 0.884863479 0.787299985 0.6134658 1.136333181 1.059988407 1.216220221 1.014819156 0.992183479 1 12.32053693 FIHQQPQS(ph)SSPVYGSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;F5H836 A0A1B0GTU4 PXN Paxillin 1 0 FIHQQPQS(0.724)S(0.224)S(0.051)PVY(0.001)GSSAK 71.853 0.0090638 99533000 3827.5 3182 3439.6 3601.9 4188.2 3994.5 3577.2 3552.3 4478.4 4258.2 TRUE FALSE FALSE 3780.848958 3226.79628 3499.464795 4018.368625 3974.460526 3739.264342 3881.047279 3655.080196 4077.840688 4147.57135 0.911581414 0.777996569 0.843738299 0.968848583 0.958262123 0.901555157 0.935739726 0.881257943 0.983187592 1 12.01805108 -11.75262241 1.016638867 0.992013444 0.899689685 0.327997296 0.053278139 0.449444482 0.927201974 0.023540915 0.01127636 1.77E-12 11.75262241 -0.09232376 FIHQQPQSSS(ph)PVYGSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 FIHQQPQSSSPVYGSSAK 18 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;F5H836 A0A1B0GTU4 PXN Paxillin 1 0 FIHQQPQS(0.05)S(0.234)S(0.715)PVYGS(0.001)SAK 92.805 0.0021627 75466000 2796.5 3193.8 2829.7 2663.9 3779.2 3884.9 2595.4 2870.1 3806 4035.4 TRUE FALSE FALSE 2762.415182 3238.7624 2878.949741 2971.912652 3586.333322 3636.667428 2815.853211 2953.141815 3465.581828 3930.559726 0.70280453 0.823995213 0.732452867 0.756104183 0.912423057 0.925228894 0.716400057 0.751328569 0.881701862 1 11.94051906 -12.45802555 1.170784887 1.000994407 0.78535249 0.323309061 0.08092109 0.322664752 0.785330843 0.056585816 0.013744984 3.48E-13 12.45802555 -0.215641917 FIIGSVSEDNS(ph)EDEISNLVK ddPTM_HeLa_Romidepsin_16h_R1 1 FIIGSVSEDNSEDEISNLVK 20 0 A0A087X2F8;A0A087X126;A0A0C4DGT1;Q13085;A0A087WYK6;Q13085-4 A0A087X2F8 ACACA Acetyl-CoA carboxylase 1;Biotin carboxylase 1 0 FIIGSVSEDNS(1)EDEISNLVK 145.67 1.45E-05 56264000 2299.6 2664.1 2268.5 2232.8 2653.1 2273.1 2010.5 2250.4 2473 2368.2 TRUE FALSE FALSE 2271.571591 2701.60527 2307.982291 2490.966842 2517.702407 2127.856246 2181.27182 2315.511773 2251.808686 2306.673823 0.984782317 1.171212524 1.000567253 1.07989557 1.091486097 0.92247817 0.945635139 1.00383147 0.97621461 1 11.1715983 -8.236723546 24.80781282 1.019370033 0.956146951 0.226976007 0.06263031 1028.09772 1031922.937 0.009261699 0.023603187 5.80E-09 8.236723546 -0.063223081 FIIHAPPGEFNEVFNDVR ddPTM_HeLa_Romidepsin_16h_R1 2 FIIHAPPGEFNEVFNDVR 18 0 C9JUG7;F8W9N7;P47755-2;P47755;A0A0D9SET8 C9JUG7 CAPZA2 F-actin-capping protein subunit alpha-2 0 0 ; ; 104.2 0.00081228 27479000 5478.8 5697.5 5131.8 6022.5 6681.3 6217.2 5361.1 5702.5 5865.1 5318.5 FALSE FALSE TRUE 5412.022278 5777.709555 5221.116826 6718.849787 6340.32833 5819.940985 5816.4717 5867.49284 5340.510767 5180.324603 1.044726478 1.115318054 1.007874453 1.296993973 1.223924911 1.123470329 1.122800625 1.132649648 1.030922032 1 12.33882679 FIIPNVVK ddPTM_HeLa_Romidepsin_16h_R1 1 FIIPNVVK 8 0 P00338;P00338-3;P00338-5;P00338-2;F5GYU2;F5GXY2 P00338 LDHA L-lactate dehydrogenase A chain 0 0 110.36 0.02192 421490 602.98 336.02 551.37 498.71 555.46 737.28 589.37 541.71 526.48 553.94 FALSE FALSE TRUE 595.6306478 340.7504984 560.9663636 556.3731967 527.1128035 690.1701875 639.4310731 557.3835242 479.3903102 539.5485589 1.103942616 0.631547416 1.039695787 1.031182805 0.976951555 1.279162322 1.185122381 1.033055348 0.888502624 1 9.075608997 -8.280354515 24.70080498 1.011760109 1.167714266 0.260139107 0.141991564 815.7849823 1065312.036 0.020088447 0.044992974 5.24E-09 8.280354515 0.155954157 QLVAGNS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 QLVAGNSPK 9 0 Q96EU6-2;Q96EU6 Q96EU6-2 RRP36 Ribosomal RNA processing protein 36 homolog 1 0 QLVAGNS(1)PK;QLVAGNS(1)PK;QLVAGNS(1)PK ;; 125.36 0.010655 79070000 26415.2 22839.2 22867.4 16702.9 11196.3 10590.7 9005.6 7496.8 25354.1 24197.2 TRUE FALSE FALSE 26093.24138 23160.73086 23265.3975 18634.16789 10624.91103 9913.98845 9770.535439 7713.70808 23086.3658 23568.55326 1.107121048 0.982696333 0.987137278 0.7906369 0.450808792 0.420644761 0.414558133 0.327288145 0.979541067 1 14.52457558 -8.924562563 1.619087324 1.046803062 0.378608811 0.975136546 0.045803634 0.039549713 0.208157563 0.007881239 0.017007967 1.19E-09 8.924562563 -0.668194251 down SSFASSSASDASKPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSFASSSASDASKPSSPR 18 1 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 0 SSFASSSASDASKPS(0.011)S(0.989)PR;SSFASSS(0.001)AS(0.001)DAS(0.014)KPS(0.223)S(0.76)PR ; 154.52 4.94E-05 83118000 8719.2 8228.5 8024.3 6174 3733.96 3451.8 2847.28 2518.32 9387.1 9651.2 TRUE FALSE FALSE 8612.927037 8344.341039 8163.959575 6887.86693 3543.402088 3231.24112 3089.127892 2591.183616 8547.494266 9400.460433 0.916223955 0.887652376 0.868463799 0.732715911 0.376939206 0.343732219 0.328614531 0.27564433 0.909263363 1 13.19851571 -8.908146631 1.401314936 0.954898502 0.297295338 0.978281788 0.041197868 0.041264412 0.162059318 0.007314648 0.016835465 1.24E-09 8.908146631 -0.657603164 down IVPQSQVPNPES(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 IVPQSQVPNPESPGK 15 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 IVPQSQVPNPES(1)PGK;IVPQS(0.001)QVPNPES(0.999)PGK ; 200.33 4.39E-18 44869000 8969.4 9711.2 9787 5958.5 5087.8 4308 3661.7 2959.8 9344 9787.7 TRUE FALSE FALSE 8860.077503 9847.914529 9957.33863 6647.449806 4828.150581 4032.732703 3972.724707 3045.437143 8508.249238 9533.414143 0.929370881 1.032989271 1.044467227 0.697279034 0.506445069 0.423010334 0.416715843 0.319448741 0.892466131 1 13.21877725 -8.905592186 1.994797241 0.977545871 0.396415239 0.955136816 0.057679942 0.043633423 0.351088419 0.008593146 0.017667827 1.24E-09 8.905592186 -0.581130632 down FIQENVFVAANHNGS(ph)PLSIK ddPTM_HeLa_Romidepsin_16h_R1 1 FIQENVFVAANHNGSPLSIK 20 0 E9PFD2;P11172-4;P11172-2;P11172-3;P11172 E9PFD2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 1 0 FIQENVFVAANHNGS(0.999)PLS(0.001)IK 133.27 0.00015629 71732000 2838.3 2931.3 2294 2612.9 2808.9 2660.4 2562.8 2735.1 2843.7 2522.3 TRUE FALSE FALSE 2803.705708 2972.566918 2333.926108 2915.015792 2665.551352 2490.409026 2780.484168 2814.235803 2589.35235 2456.770282 1.141216062 1.20994907 0.949997696 1.186523548 1.084981926 1.013692263 1.131764003 1.145502216 1.053966001 1 11.26254725 -12.38473564 1.124514558 1.000345779 1.108204823 0.144019869 0.075145057 0.566724438 1.288531771 0.047295359 0.012306007 4.12E-13 12.38473564 0.107859044 FIQESEEK ddPTM_HeLa_Romidepsin_16h_R1 2 FIQESEEK 8 0 Q13129 Q13129 RLF Zinc finger protein Rlf 0 0 ; ; 166.78 0.018895 23745000 3397.1 3059 3022.7 2656.1 3086.6 2817.3 3081.4 3359.5 3559.4 3077 FALSE FALSE TRUE 3355.694839 3102.064682 3075.308826 2963.210779 2929.079284 2637.283622 3343.134039 3456.701832 3241.038349 2997.059096 1.119662553 1.035036208 1.026108838 0.988706156 0.977317827 0.879957164 1.115471511 1.153364589 1.08140622 1 11.54933182 -10.0067207 20.28786754 1.057604244 1.018557226 0.05593276 0.075604364 74.12128559 223762.2712 0.013804565 0.017720117 9.85E-11 10.0067207 -0.039047018 FISDKDASIVGFFDDSFSEAHSEFLK ddPTM_HeLa_Romidepsin_16h_R1 1 FISDKDASIVGFFDDSFSEAHSEFLK 26 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 0 96.881 3.34E-06 2818200 925.9 846.99 848.08 1070.6 1402.1 1263.7 986.22 1137.7 1245.3 863.11 FALSE FALSE TRUE 914.6147747 858.9139475 862.8404766 1194.387809 1330.545605 1182.953648 1069.989502 1170.617555 1133.917249 840.6862778 1.08793827 1.021681893 1.026352516 1.420729517 1.58268981 1.407128533 1.272757187 1.392454695 1.348799521 1 9.715423714 -9.26062897 24.95989253 1.039742586 1.416103055 0.61392716 0.122018174 20.15688079 620812.0622 0.012253123 0.019563361 5.49E-10 9.26062897 0.376360469 FITHAPPGEFNEVFNDVR ddPTM_HeLa_Romidepsin_16h_R1 2 FITHAPPGEFNEVFNDVR 18 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 0 ; ; 125.41 0.00061695 34840000 6824.4 6433.2 6172 6791.1 7460.5 6667.3 5648.2 6563.4 8221.6 6787.3 FALSE FALSE TRUE 6741.221588 6523.766758 6279.421071 7576.318935 7079.762846 6241.281048 6127.957967 6753.301624 7486.239505 6610.964968 1.019703118 0.986810063 0.949849394 1.146023156 1.070912171 0.944080188 0.926938502 1.02153039 1.132397395 1 12.69064515 -8.233740892 24.63218602 1.017271603 0.960458568 0.160681789 0.06603614 836.6687647 744046.6023 0.007824313 0.019942106 5.84E-09 8.233740892 -0.056813034 FKDDDGDEEDENGVGDAELR ddPTM_HeLa_Romidepsin_16h_R1 1 FKDDDGDEEDENGVGDAELR 20 1 Q6NZY4 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 0 0 144.4 4.53E-05 6221600 2112.9 1958.4 1848.1 1674.6 2147.9 2277.6 1583.6 2024.8 2236 2288.4 FALSE FALSE TRUE 2087.147162 1985.970407 1880.265405 1868.225131 2038.284648 2132.068711 1718.110944 2083.384393 2036.00656 2228.947038 0.936382573 0.890990397 0.843566659 0.838164882 0.91446078 0.956536281 0.770817303 0.934694435 0.913438734 1 11.12214662 -10.78252249 0.893532898 0.986924923 0.874350968 0.208854727 0.056177922 0.315682115 0.537300602 0.013648718 0.012003016 1.65E-11 10.78252249 -0.112573954 FKDIFQEIYDK ddPTM_HeLa_Romidepsin_16h_R1 1 FKDIFQEIYDK 11 1 O75874 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 0 119.69 0.011584 9136400 2749.1 2190.5 2933.2 3085.4 3731.5 3361.9 2737.9 2766.7 2308.7 2207.7 FALSE FALSE TRUE 2715.592912 2221.337916 2984.251116 3442.148465 3541.067631 3147.08544 2970.457158 2846.750099 2102.20409 2150.343636 1.262864626 1.033015319 1.387801962 1.600743438 1.646745 1.463526753 1.381387192 1.323858221 0.977613092 1 11.07035151 -9.628012422 4.84439243 1.121300827 1.486374189 0.72756825 0.118829752 0.104736169 4.088365626 0.021714083 0.030931455 2.35E-10 9.628012422 0.365073361 FKGQILMPNIGYGSNKK ddPTM_HeLa_Romidepsin_16h_R1 1 FKGQILMPNIGYGSNKK 17 2 D3YTB1;F8W727;P62910 D3YTB1 RPL32 60S ribosomal protein L32 0 0 63.682 0.010223 1455800 1072.2 836.17 561.39 1172.4 1032.5 965.63 652.62 859.57 877.67 934.22 FALSE FALSE TRUE 1059.131614 847.9416232 571.1607575 1307.958404 979.8076722 903.9293594 708.0535265 884.4403018 799.168997 909.9488297 1.163946344 0.931856381 0.627684479 1.437397754 1.076772276 0.993384825 0.778124553 0.971967074 0.878257074 1 9.829641609 -7.963307056 6.231094506 1.060131905 0.875352992 0.041493395 0.203076695 0.282066072 30.23786278 0.026812115 0.081071035 1.09E-08 7.963307056 -0.184778913 FLDELDAVQMD ddPTM_HeLa_Romidepsin_16h_R1 1 FLDELDAVQMD 11 0 A0A2R8YEY5;E7EQB9;O15160 A0A2R8YEY5 POLR1C DNA-directed RNA polymerases I and III subunit RPAC1 0 0 120.87 0.023837 2618200 2824.4 3009.8 2757.3 2833 3440.4 3697.8 2579.4 2909.2 3079.8 2939.7 FALSE FALSE TRUE 2789.975126 3052.172043 2805.28965 3160.56479 3264.82355 3461.522514 2798.494172 2993.373112 2804.334974 2863.32617 0.974382575 1.065953322 0.979731083 1.103808858 1.140220623 1.208916592 0.977357802 1.045418138 0.979397668 1 11.48347631 -9.258693687 24.60396022 0.994133928 1.097425618 0.375332645 0.061180558 153.8301707 1378456.794 0.009458836 0.015230293 5.51E-10 9.258693687 0.10329169 FLEDDTS(ph)DPTYTSALGGK ddPTM_HeLa_Romidepsin_16h_R1 1 FLEDDTSDPTYTSALGGK 18 0 B1AKC9;P29323-2;P29323-3;P29323 B1AKC9 EPHB2 Receptor protein-tyrosine kinase;Ephrin type-B receptor 2 1 0 FLEDDT(0.037)S(0.804)DPT(0.15)Y(0.001)T(0.007)S(0.001)ALGGK 95.662 0.0038247 4382800 523.71 1116.8 997.02 835.08 2088.6 2830.5 1295 2891.2 874.21 985.05 TRUE FALSE FALSE 517.3268211 1132.52234 1014.372715 931.6358788 1982.010948 2649.640185 1404.997268 2974.85231 796.0184681 959.458259 0.539186375 1.180376873 1.057234857 0.97100199 2.065760474 2.761600268 1.464365182 3.100554175 0.829654089 1 9.906076233 -8.73124874 3.336159353 0.836950559 2.358388088 0.730368382 0.424246985 0.088156262 2.030420465 0.060216991 0.122887573 1.86E-09 8.73124874 1.521437529 FLEESVSMS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 2 FLEESVSMSPEER 13 0 A0A087WTB8;Q5TBK7;P15374 A0A087WTB8 UCHL3 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase isozyme L3 1 0 FLEES(0.001)VS(0.039)MS(0.96)PEER;FLEESVS(0.025)MS(0.975)PEER ; 120.53 0.0065989 26255100 5734.4 4898.4 4860.2 5232.3 5930.8 5657 5358.2 5065.8 5680.8 4796.4 TRUE FALSE FALSE 5664.506927 4967.359804 4944.789742 5837.283145 5628.129145 5295.535957 5813.325374 5212.37093 5172.69502 4671.788837 1.212492072 1.063267193 1.058436054 1.249474955 1.20470538 1.133513552 1.244346775 1.115712014 1.107219355 1 12.18975935 -9.269370175 24.88442127 1.096664415 1.190323541 0.382213994 0.0639271 668.9005777 2098802.297 0.013368059 0.020664488 5.38E-10 9.269370175 0.093659127 FLESAAADFS(ph)DEDEDDDVDGR ddPTM_HeLa_Romidepsin_16h_R1 2 FLESAAADFSDEDEDDDVDGR 21 0 O43815-2;O43815 O43815-2 STRN Striatin 1 0 FLESAAADFS(1)DEDEDDDVDGR;FLESAAADFS(1)DEDEDDDVDGR ; 180.84 1.15E-13 3690600 1968.54 1739.73 1838.85 1376.41 2339 2420.81 1741.43 2164.09 2384.02 1957.87 TRUE FALSE FALSE 1944.546677 1764.221965 1870.854413 1535.557 2219.632102 2266.128054 1889.347021 2226.70453 2170.78728 1907.004255 1.019686596 0.92512744 0.981043649 0.805219493 1.163936628 1.1883183 0.990740852 1.167645286 1.138323249 1 10.89709235 FLESAAADFS(ph)DEDEDDDVDGREK ddPTM_HeLa_Romidepsin_16h_R1 2 FLESAAADFSDEDEDDDVDGREK 23 1 O43815-2;O43815 O43815-2 STRN Striatin 1 0 FLESAAADFS(1)DEDEDDDVDGREK;FLESAAADFS(1)DEDEDDDVDGREK ; 137.41 1.76E-06 226735000 6292.9 6524 5585.7 6973.8 6978.1 7755.7 6606.2 7702.4 7180.6 6638.8 TRUE FALSE FALSE 6216.199714 6615.845043 5682.916765 7780.143569 6621.981518 7260.1358 7167.330463 7925.256792 6538.349152 6466.323019 0.961319083 1.023123191 0.878848265 1.203178923 1.024072181 1.122761078 1.108408974 1.225620305 1.011138654 1 12.65872986 -9.255796064 24.99798089 0.978017751 1.128187033 0.618883789 0.063329064 235.6664171 1043922.198 0.00878664 0.014305853 5.55E-10 9.255796064 0.150169282 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL ddPTM_HeLa_Romidepsin_16h_R1 1 FLESGGQDGAGDDDDLEDLEEAEEPDMEEDDDQKAVKDEL 40 2 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 0 119.72 4.23E-22 33690000 3826.7 3514.7 3655.6 4087.1 4107 4596.4 4065.2 4553.5 4205 3570.3 FALSE FALSE TRUE 3780.058709 3564.180039 3719.224185 4559.669732 3897.404465 4302.704874 4410.497987 4685.248338 3828.894268 3477.543091 1.086991192 1.024913264 1.069497656 1.311175624 1.12073506 1.237282979 1.268279895 1.347286925 1.101034313 1 11.76385268 -4 0.184208265 0.982283232 2.604666954 0.664767695 0.067993572 19.25163917 0.211707929 0.072013151 8.856554985 1.00E-04 4 1.622383721 FLESYAT(ph)DNEK ddPTM_HeLa_Romidepsin_16h_R1 2 FLESYATDNEK 11 0 Q9BZI7-2;Q9BZI7;A0A087WYC8 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 1 0 FLES(0.005)YAT(0.995)DNEK;FLESYAT(1)DNEK ; 173.19 0.00037703 11908000 2841.9 2462.3 3385.2 2331.5 4390.9 3429.7 2339.6 3364.6 2424.9 2844.9 TRUE FALSE FALSE 2807.26183 2496.964324 3444.117986 2601.079 4166.815988 3210.553239 2538.325566 3461.949393 2208.010871 2770.989088 1.013090179 0.901109403 1.242920083 0.938682513 1.503728761 1.158630777 0.91603593 1.249355116 0.796831312 1 11.43618531 -9.758100013 24.9997986 0.998473786 1.161142613 0.288797104 0.170810393 103.1322925 772083.8679 0.023841181 0.032931247 1.75E-10 9.758100013 0.162668827 FLET(ph)DS(ph)EEEQEEVNEK ddPTM_HeLa_Romidepsin_16h_R1 1 FLETDSEEEQEEVNEK 16 0 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101 Q76FK4-2 NOL8 Nucleolar protein 8 2 0 FLET(1)DS(1)EEEQEEVNEK 189.33 1.06E-11 0 1346.5 1134 1177 1046.1 1172.2 1456.4 1138.2 943.16 1290.1 1321.5 TRUE FALSE FALSE 1330.08834 1149.964482 1197.485191 1167.055004 1112.37826 1363.34074 1234.87868 970.4488465 1174.710225 1287.167239 1.033345395 0.893407202 0.930326033 0.906684826 0.864206473 1.059179179 0.959377027 0.753941537 0.912632165 1 10.3299838 -10.26326377 24.85029688 1.015746438 0.916197705 0.103154308 0.079585205 138.4568173 1885936.225 0.011944172 0.014036407 5.45E-11 10.26326377 -0.099548733 FLGDIEVWDQAEK ddPTM_HeLa_Romidepsin_16h_R1 2 FLGDIEVWDQAEK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 ; ; 229.29 4.86E-31 28500000 6642 6058.6 6159 5758 7083.4 6669.2 5925.8 4928.1 6381.4 6052.6 FALSE FALSE TRUE 6561.044749 6143.89313 6266.194811 6423.767052 6721.907666 6243.059644 6429.137304 5070.686798 5810.631601 5895.352579 1.112918127 1.042158725 1.062904165 1.089632378 1.140204521 1.058979859 1.090543308 0.860115952 0.985629192 1 12.52536238 -7.256982704 24.79386354 1.064661248 0.86011586 0.650003139 0.045053108 213.6041056 1188297.218 0.006794257 0.072095709 5.53E-08 7.256982704 -0.204545388 FLGSDEEDKDSLQELS(ph)TEQK ddPTM_HeLa_Romidepsin_16h_R1 2 FLGSDEEDKDSLQELSTEQK 20 1 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 FLGS(0.001)DEEDKDS(0.296)LQELS(0.352)T(0.352)EQK;FLGSDEEDKDS(0.001)LQELS(0.499)T(0.499)EQK ; 73.11 0.0028295 21972000 2294.12 2360.12 2224.33 2033.2 1642.75 1830.2 1409.77 1861.51 2391.63 2392.37 TRUE FALSE FALSE 2266.158383 2393.345831 2263.043531 2268.28815 1558.914338 1713.256127 1529.515829 1915.369855 2177.716623 2330.215883 0.972510058 1.027091888 0.971173335 0.973424037 0.668999962 0.735234937 0.656383745 0.82197099 0.934555738 1 11.1862479 -8.769658721 24.86382336 0.987885734 0.717099109 0.876822966 0.047518134 32.16345322 97295.91765 0.005886226 0.010803125 1.70E-09 8.769658721 -0.270786625 FLIATGERPR ddPTM_HeLa_Romidepsin_16h_R1 4 FLIATGERPR 10 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 0 ;;; ;;; 169.65 0.001115 49738700 10399.7 10766.3 10568.01 10441.5 10167.17 9554.83 7638.11 8733.12 9912.48 9777.11 FALSE FALSE TRUE 10272.94446 10917.86825 10751.94178 11648.79536 9648.301376 8944.3072 8286.890873 8985.799049 9025.882963 9523.099273 1.078739616 1.146461666 1.129038087 1.223214736 1.013147201 0.9392223 0.870188437 0.943579269 0.947788394 1 13.21721546 -8.311202619 3.457662995 1.067707929 0.909629731 0.489055682 0.075736664 0.171667179 4.162892058 0.011369868 0.02837843 4.88E-09 8.311202619 -0.158078199 FLIPNAS(ph)QAESK ddPTM_HeLa_Romidepsin_16h_R1 1 FLIPNASQAESK 12 0 P63104;E7EX29;E7ESK7;B0AZS6;P63104-2 P63104 YWHAZ 14-3-3 protein zeta/delta 1 0 FLIPNAS(0.997)QAES(0.003)K 96.756 0.0035056 0 2257 2271.9 2202.8 2025.3 1698.8 1738.4 1736.7 2198.3 2422.7 1869 TRUE FALSE FALSE 2229.490816 2303.883868 2241.13881 2259.474715 1612.103897 1627.32185 1884.215255 2261.904342 2206.007644 1820.443111 1.22469678 1.265562134 1.231095219 1.24116744 0.885555768 0.893915246 1.035031111 1.242502075 1.211797079 1 10.83007394 -8.76698408 24.99931017 1.140722364 1.007139927 0.28868472 0.12227976 189.5900549 854806.8445 0.021352024 0.039512722 1.71E-09 8.76698408 -0.133582437 FLIVAHDDGR ddPTM_HeLa_Romidepsin_16h_R1 2 FLIVAHDDGR 10 0 Q16658 Q16658 FSCN1 Fascin 0 0 ; ; 105.86 0.0097007 197530000 15785 14827.8 17232.8 17596.8 18901.7 19508.5 16820.8 15487.4 14874.6 10889.5 FALSE FALSE TRUE 15592.60635 15036.54616 17532.72966 19631.42481 17937.07572 18261.96981 18249.55833 15935.50348 13544.17852 10606.58922 1.470086757 1.417660838 1.653003552 1.850870662 1.691125709 1.721757054 1.720586887 1.502415447 1.276958902 1 13.37267318 -11.38580133 0.435954428 0.948262 1.716826092 0.70900298 0.129807342 0.31556214 0.128571835 0.104437285 0.041600683 4.11E-12 11.38580133 0.768564092 FLLPFS(ph)T(ph)VYLCDAAFS(ph)ALTESKQKNLLGSGPALR ddPTM_HeLa_Romidepsin_16h_R1 1 FLLPFSTVYLCDAAFSALTESKQKNLLGSGPALR 34 2 O95789-5;O95789 O95789-5 ZMYM6 Zinc finger MYM-type protein 6 3 0 FLLPFS(0.826)T(0.826)VY(0.408)LCDAAFS(0.424)ALT(0.424)ES(0.091)KQKNLLGSGPALR 41.89 0.010502 3116200 549.57 536.64 523.26 652.15 924.91 997.84 989.42 1017.7 703.14 650.75 TRUE FALSE FALSE 542.8716295 544.194832 532.3671208 727.5546515 877.7083914 934.0812444 1073.46131 1047.145544 640.2493974 633.8434212 0.856475923 0.858563509 0.839903205 1.147846025 1.384740083 1.47367822 1.693574902 1.652057131 1.010106559 1 9.307982684 -8.644303297 1.3725747 0.916472851 1.649204328 0.94523927 0.073976351 0.073408344 0.273307346 0.013111368 0.03690521 2.27E-09 8.644303297 0.732731476 FLNIYS(ph)ATYGR ddPTM_HeLa_Romidepsin_16h_R1 1 FLNIYSATYGR 11 0 C9JS02;F8WEK6;B5MC74;P58658-3;P58658 C9JS02 EVA1C Protein eva-1 homolog C 1 0 FLNIY(0.004)S(0.477)AT(0.477)Y(0.041)GR 101.25 0.018597 7843800 918.3 724.68 980.92 749.21 1014.5 1005.8 1043.6 1091.3 1011.2 1021.6 TRUE FALSE FALSE 907.1074064 734.8820641 997.9925011 835.8371853 962.7262794 941.5326261 1132.243358 1122.875044 920.7557394 995.0586847 0.911611969 0.73853138 1.002948385 0.83998783 0.967507037 0.946208139 1.137865912 1.128451076 0.925328077 1 9.958637803 -7.771513975 6.858371912 0.936284508 1.134255883 0.55088965 0.076614433 0.080940684 18.21036126 0.011191029 0.0368655 1.69E-08 7.771513975 0.197971375 FLPISST(ph)PQPER ddPTM_HeLa_Romidepsin_16h_R1 1 FLPISSTPQPER 12 0 J3KNG6;Q08AE8-4;Q08AE8-3;Q08AE8-5;Q08AE8-2;Q08AE8 J3KNG6 SPIRE1 Protein spire homolog 1 1 0 FLPIS(0.006)S(0.032)T(0.963)PQPER 141.34 0.0037702 39342000 4003 3759 3937.3 3338.5 4623 4955.4 3879.9 4402.2 3700.6 3175.8 TRUE FALSE FALSE 3954.209896 3811.919301 4005.827055 3724.513078 4387.071059 4638.765933 4209.458609 4529.570711 3369.609068 3093.292258 1.278317587 1.232317862 1.29500439 1.204061164 1.418253011 1.499620969 1.360834431 1.464320321 1.089327741 1 11.59492743 -15.27218054 0.085882323 8.01E-15 1.727008172 0.803483758 0.067332633 33.13761449 0.283544475 6.995051809 1.076061945 5.34E-16 15.27218054 1.727008172 FLPLNIRNS(ph)PFTR ddPTM_HeLa_Romidepsin_16h_R1 1 FLPLNIRNSPFTR 13 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;H3BSK8 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 FLPLNIRNS(0.971)PFT(0.029)R 69.216 0.024597 68432000 3806.6 4046 3700.7 2837.6 4819.3 4694.9 4122.6 4612.4 4668.8 4234.2 TRUE FALSE FALSE 3760.203695 4102.959694 3765.109131 3165.696663 4573.353138 4394.911042 4472.773541 4745.852517 4251.210835 4124.194874 0.911742488 0.994851073 0.912931917 0.767591435 1.108908109 1.065640974 1.084520416 1.150734304 1.030797759 1 12.00989679 FLPS(ph)PVVIK ddPTM_HeLa_Romidepsin_16h_R1 2 FLPSPVVIK 9 0 H7C399;A0A087WTG3;Q13618-3;Q13618-2;Q13618 H7C399 CUL3 Cullin-3 1 0 FLPS(1)PVVIK;FLPS(1)PVVIK ; 110.84 0.018653 40570000 12322 12484.2 12437.6 11246.5 11671.3 12028.9 10743.8 11835.2 13382.1 12298.5 TRUE FALSE FALSE 12171.81472 12659.9529 12654.07121 12546.87325 11075.67001 11260.29211 11656.3781 12177.63284 12185.17146 11978.9832 1.016097487 1.056847037 1.056356036 1.0474072 0.924591831 0.940003999 0.973069075 1.016583181 1.017212501 1 13.54821783 -8.767079959 24.99995722 1.018433096 0.962558381 0.528704266 0.030131916 107.4977815 476449.9998 0.004997429 0.009238914 1.71E-09 8.767079959 -0.055874716 FLPSELRDEH ddPTM_HeLa_Romidepsin_16h_R1 3 FLPSELRDEH 10 1 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 ;; ;; 147.75 0.0044376 27289800 6401.8 5760.9 6243.7 9144.6 7913.9 6988.6 6265.4 6195.6 7446.5 5922.7 FALSE FALSE TRUE 6323.772399 5842.002101 6352.368979 10201.94168 7510.024152 6542.051015 6797.58292 6374.859911 6780.46639 5768.8274 1.096197192 1.012684502 1.101154279 1.768460204 1.30182854 1.134034798 1.178330092 1.10505298 1.175363019 1 12.49406238 -9.501182374 24.98493039 1.044843822 1.29734638 0.270335158 0.179582361 712.9150169 820973.9512 0.027527701 0.041811737 3.15E-10 9.501182374 0.252502558 FLQDYFDGNLKR ddPTM_HeLa_Romidepsin_16h_R1 2 FLQDYFDGNLKR 12 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 0 ; ; 90.412 0.017996 48725000 6681.6 5614.9 5850.3 6739.1 6053.6 6466.3 5955.2 5998.2 6819.9 6604.2 FALSE FALSE TRUE 6600.162089 5693.94671 5952.122017 7518.30645 5744.662203 6053.124299 6461.034539 6171.748453 6209.911063 6432.621932 1.026045392 0.885167319 0.925302634 1.168777915 0.893051428 0.941004207 1.004416956 0.959445234 0.965377902 1 12.65119118 FLQS(ph)S(ph)SEVESPAVPSS(ph)S(ph)RQPPAQPPR ddPTM_HeLa_Romidepsin_16h_R1 1 FLQSSSEVESPAVPSSSRQPPAQPPR 26 1 Q5T670;Q7L590-2;Q7L590 Q5T670 MCM10 Protein MCM10 homolog 4 0 FLQS(0.95)S(0.521)S(0.521)EVES(0.211)PAVPS(0.451)S(0.674)S(0.674)RQPPAQPPR 45.423 0.012248 10860000 1201.1 1455.6 994.17 6875.1 1383 983.29 869.18 1156.4 1085.9 1161.9 TRUE FALSE FALSE 1186.460531 1476.091975 1011.473112 7670.03141 1312.420349 920.4609424 943.0081275 1189.85861 988.7743843 1131.713671 1.048375187 1.304298087 0.893753551 6.777360396 1.159675264 0.813333767 0.833256814 1.051377783 0.873696598 1 10.14429328 FLSHS(ph)TDSLNK ddPTM_HeLa_Romidepsin_16h_R1 1 FLSHSTDSLNK 11 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 FLS(0.001)HS(0.964)T(0.026)DS(0.009)LNK 89.747 0.014482 39878000 3475.4 3253.9 3122.4 3128.4 8506.3 9087.8 7567.7 7965.4 5629.2 3870.3 TRUE FALSE FALSE 3433.040488 3299.70849 3176.744062 3490.120328 8072.19177 8507.11891 8210.500249 8195.866282 5125.710253 3769.749048 0.910681439 0.875312507 0.842693777 0.925822988 2.141307463 2.256680432 2.177996504 2.174114557 1.359695351 1 11.88025277 -8.754149813 7.170901499 0.937568839 2.196011143 0.94473305 0.142139162 0.009026927 2.476771713 0.00899109 0.017382722 1.76E-09 8.754149813 1.258442304 FLSLEYS(ph)PAGK ddPTM_HeLa_Romidepsin_16h_R1 1 FLSLEYSPAGK 11 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 FLSLEYS(1)PAGK 145.23 0.00020081 0 1436 1442.3 1469.1 1307.8 2303.6 2670.8 1952.9 2244 1817.9 1524 TRUE FALSE FALSE 1418.49748 1462.604737 1494.669069 1459.013989 2186.038696 2500.1445 2118.779277 2308.9266 1655.302471 1484.40626 0.95559923 0.985312967 1.006913747 0.982893988 1.472668739 1.684272403 1.427358085 1.555454636 1.115127654 1 10.53567028 -8.730532865 4.725655058 0.980618132 1.546811072 0.924793258 0.073632178 0.026326083 1.382916062 0.008195158 0.016316286 1.86E-09 8.730532865 0.56619294 FMDGHIT(ph)FQT(ph)AATVKIPT(ph)TTPATTK ddPTM_HeLa_Romidepsin_16h_R1 1 FMDGHITFQTAATVKIPTTTPATTK 25 1 C9JDI8;C9JYP5;E7ETP9;Q9UQV4 C9JDI8 LAMP3 Lysosome-associated membrane glycoprotein 3 3 0 FMDGHIT(0.897)FQT(0.89)AAT(0.224)VKIPT(0.606)T(0.171)T(0.151)PAT(0.031)T(0.031)K 46.783 0.014526 9898500 880.17 602.48 459.89 535.94 475.81 508.12 541.2 202.63 628.09 646.26 TRUE FALSE FALSE 869.4421495 610.9617293 467.8941925 597.9079045 451.5276402 475.6527719 587.1695145 208.4927794 571.9120573 629.470072 1.381228732 0.970596946 0.743314438 0.949859145 0.717313913 0.755640011 0.932799732 0.331219527 0.908561158 1 9.297993977 -9.967377904 3.999803926 1.180578978 0.758473532 0.376985215 0.200133809 0.137733166 4.868197864 0.033206513 0.043383099 1.08E-10 9.967377904 -0.422105446 FMQASEDLLKEHYVDLK ddPTM_HeLa_Romidepsin_16h_R1 1 FMQASEDLLKEHYVDLK 17 1 Q32Q12;P22392-2;J3KPD9;E7ERL0;E5RHP0;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 0 61.186 0.015285 10615000 2168.3 1724.6 1841.6 2752.6 2159.3 2471.8 2355.5 2416 2494.4 2037.3 FALSE FALSE TRUE 2141.871926 1748.878964 1873.652275 3070.868563 2049.102864 2313.859957 2555.576111 2485.903148 2271.294617 1984.370652 1.079370894 0.881326763 0.94420479 1.547527706 1.032621028 1.166042218 1.287852201 1.252741339 1.144591921 1 10.95446581 FNADEFEDMVAEKR ddPTM_HeLa_Romidepsin_16h_R1 1 FNADEFEDMVAEKR 14 1 F8W7C6;A0A087WV22;X1WI28;P27635 F8W7C6 RPL10 60S ribosomal protein L10 0 0 54.859 0.029158 7045900 577.07 811.12 698.28 819.94 791.91 1082.9 964.73 831.07 932.78 990.67 FALSE FALSE TRUE 570.0364489 822.5389687 710.4332705 914.7453207 751.4958777 1013.706185 1046.674142 855.1156992 849.3498206 964.9322506 0.590752821 0.852431835 0.73625197 0.947989167 0.778806882 1.050546486 1.084712571 0.886192475 0.880217052 1 9.914283842 -8.262204313 24.9920254 0.809935831 1.014906723 0.322809173 0.117931506 72.80978808 2378908.43 0.022872877 0.054196064 5.47E-09 8.262204313 0.204970892 FNDEHIPDSPFVVPVASLSDDAR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDEHIPDSPFVVPVASLSDDAR 23 0 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 0 0 95.344 3.68E-05 2697100 1412.2 1601.6 1508.4 1675.2 1490.8 1444 1578.4 1355.6 1683.5 1366 FALSE FALSE TRUE 1394.987563 1624.147367 1534.653069 1868.894506 1414.718913 1351.73306 1712.469257 1394.822147 1532.923544 1330.511123 1.048459903 1.220694317 1.153431221 1.40464403 1.063289805 1.015950214 1.287076242 1.048335578 1.152131325 1 10.37776486 -10.3911644 4.473374396 1.020760241 1.173008393 0.106456823 0.118124549 0.213711093 6.716517744 0.018680976 0.021182528 4.06E-11 10.3911644 0.152248151 FNDEHIPESPYLVPVIAPSDDAR ddPTM_HeLa_Romidepsin_16h_R1 2 FNDEHIPESPYLVPVIAPSDDAR 23 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3 O75369-8 FLNB Filamin-B 0 0 ; ; 101.92 1.46E-05 39876000 7649.7 6523 7123.8 6125.5 8587 8679.8 8299.3 8689 8201.4 7773.2 FALSE FALSE TRUE 7556.462514 6614.830965 7247.786751 6833.759131 8148.773347 8125.188793 9004.242335 8940.402506 7467.846243 7571.251143 0.998046739 0.873677394 0.957277287 0.902593112 1.076278305 1.073163291 1.189267423 1.18083555 0.986342429 1 12.88631601 -8.109399422 1.59566819 0.980332078 1.189801322 0.75390908 0.049982219 0.173702331 0.813675923 0.007938989 0.033770642 7.77E-09 8.109399422 0.209469244 FNDFDHR ddPTM_HeLa_Romidepsin_16h_R1 2 FNDFDHR 7 0 Q9NWH9;H7C3F4;Q9NWH9-3;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 0 ; ; 128.61 0.0086165 16472000 17497.8 14808.5 15375.6 12449.5 14086.1 14242.4 12341.6 11662.6 17495.3 15544 FALSE FALSE TRUE 17284.53008 15016.97445 15643.20587 13888.96977 13367.23375 13332.35661 13389.8952 12000.03893 15930.47655 15140.16464 1.141634222 0.991863352 1.033225612 0.917359229 0.882898837 0.88059522 0.884395614 0.79259633 1.052199691 1 13.88609327 -9.179952912 1.297941602 1.06474628 0.854833799 0.795331951 0.044607674 0.174727779 0.57941019 0.009960933 0.020100676 6.61E-10 9.179952912 -0.209912482 FNDS(ph)EGDDTEET(ph)EDYR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 2 0 FNDS(0.993)EGDDT(0.077)EET(0.93)EDYR 114.58 0.0124 13514000 2079 2362.5 2085.8 1900.4 2015.8 1970.3 1617.3 1919.1 2158.4 2039.4 TRUE FALSE FALSE 2053.660348 2395.759337 2122.102474 2120.13319 1912.926204 1844.404189 1754.673422 1974.626131 1965.347298 1986.416094 1.033852049 1.206071248 1.068307129 1.067315753 0.963003778 0.92850848 0.883336289 0.994064706 0.989393564 1 10.95595214 -8.611236791 4.519586285 1.039638604 0.932127044 0.442077151 0.063051329 0.183386218 6.75948421 0.009954382 0.020492658 2.45E-09 8.611236791 -0.10751156 FNDS(ph)EGDDTEETEDYR ddPTM_HeLa_Romidepsin_16h_R1 2 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 FNDS(0.511)EGDDT(0.48)EET(0.009)EDYR;FNDS(0.998)EGDDT(0.002)EETEDYR ; 337.71 9.29E-204 589745000 5798.4 5986.5 5553.1 4976.9 5101.4 5540.6 4476.8 5452.1 5806.4 6469.8 TRUE FALSE FALSE 5727.726871 6070.778104 5649.749376 5552.352595 4841.056522 5186.573541 4857.05928 5609.847912 5287.061042 6301.713663 0.908915761 0.96335353 0.896541747 0.881086144 0.768212709 0.823041766 0.770752138 0.890209903 0.838987825 1 12.62152849 -9.315397941 1.349955467 0.957875845 0.810779514 0.410118545 0.055156537 0.182822833 0.655763461 0.007689953 0.014269159 4.84E-10 9.315397941 -0.147096331 FNDS(ph)EGDDTEETEDYRQFR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDSEGDDTEETEDYRQFR 19 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 FNDS(0.999)EGDDT(0.001)EETEDYRQFR 141.79 7.21E-05 103730000 1056.9 1217.8 1053.1 2046.1 1070.3 935.05 756.87 933.15 1384 881.37 TRUE FALSE FALSE 1044.018096 1234.94422 1071.428764 2282.679709 1015.678597 875.3033227 821.1585189 960.149223 1260.211574 858.4718803 1.216135461 1.438537765 1.248065066 2.659003471 1.183123898 1.019606283 0.956535138 1.118439922 1.467970708 1 9.745627069 -10.88798269 1.240904777 1.055487084 1.378286317 0 0.475125813 0.800708801 2.580493997 0.113642683 0.100605165 1.29E-11 10.88798269 0.322799233 FNDSEGDDT(ph)EET(ph)EDYR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 2 0 FNDS(0.074)EGDDT(0.926)EET(0.999)EDY(0.001)R 185.86 9.25E-08 39109000 2121.1 2068.6 1710.9 1621.3 1779.8 1836.9 1435.7 1410.4 1857.6 1846.5 TRUE FALSE FALSE 2095.247217 2097.721805 1740.677497 1808.762334 1688.970165 1719.528018 1557.648322 1451.207699 1691.451604 1798.527664 1.164979143 1.16635504 0.967834708 1.005690583 0.939084896 0.956075379 0.866068592 0.806886504 0.940464602 1 10.81260063 -8.360649218 0.774387541 1.081986482 0.813942142 0.525076333 0.074508734 0.495184714 0.459281357 0.013857949 0.083475345 4.36E-09 8.360649218 -0.26804434 FNDSEGDDT(ph)EETEDYR ddPTM_HeLa_Romidepsin_16h_R1 3 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 FNDSEGDDT(0.992)EET(0.008)EDYR;FNDS(0.026)EGDDT(0.974)EETEDYR;FNDS(0.009)EGDDT(0.991)EETEDYR ;; 270.95 2.53E-86 769335700 4746.3 4759 4207.7 4253.6 4378 4472.4 3871.41 3911.7 4905.77 4630.9 TRUE FALSE FALSE 4688.45027 4825.997327 4280.933253 4745.421246 4154.574323 4186.628074 4200.247469 4024.878868 4466.985644 4510.58855 1.039432043 1.069926302 0.949085292 1.05206254 0.921071447 0.928177782 0.931197209 0.892317892 0.990333211 1 12.13909998 -8.749216039 24.95760043 1.019625223 0.919833393 0.676146808 0.03339333 93.93900526 191803.3872 0.004612571 0.00917123 1.78E-09 8.749216039 -0.09979183 FNDSEGDDTEET(ph)EDYR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 FNDSEGDDT(0.014)EET(0.985)EDYR 253.36 1.82E-71 9735500 1230.3 1147.8 1229.2 1002.7 1232.8 1185 945.87 1185.3 1056.8 1132.7 TRUE FALSE FALSE 1215.30463 1163.958759 1250.59371 1118.636892 1169.885616 1109.282324 1026.212174 1219.594785 962.2771612 1103.272291 1.101545503 1.055005884 1.133531333 1.013926391 1.060377955 1.005447462 0.93015313 1.105434076 0.872202782 1 10.10757318 -8.256173274 21.33741974 1.054207835 1.005325679 0 0.078696456 94.62798671 383399.0128 0.008136328 0.019987925 5.54E-09 8.256173274 -0.048882156 FNDSEGDDTEET(ph)EDYRQFR ddPTM_HeLa_Romidepsin_16h_R1 1 FNDSEGDDTEETEDYRQFR 19 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 FNDS(0.001)EGDDT(0.006)EET(0.963)EDY(0.031)RQFR 104.78 0.00059525 113710000 1450.3 1194.4 985.54 2461.2 1151.6 1212.2 781.88 1069.5 1618.1 1038.6 TRUE FALSE FALSE 1432.623186 1211.214795 1002.69291 2745.775524 1092.829555 1134.744332 848.2928677 1100.444295 1473.373083 1011.617022 1.41617149 1.197305668 0.991178369 2.71424409 1.080279919 1.121713363 0.838551397 1.087807214 1.456453431 1 9.982447503 -5.936527494 10.03386695 1.242621147 1.118525162 0 0.509300807 0 0 0.065194403 0 1.16E-06 5.936527494 -0.124095984 FNDSEGDDTEETEDYR ddPTM_HeLa_Romidepsin_16h_R1 2 FNDSEGDDTEETEDYR 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 0 0 ; ; 324.48 7.61E-179 15116200 3099.71 3711.51 4412.28 3000.92 2642.18 4277.21 5381 1871.89 4867.13 3465 FALSE FALSE TRUE 3061.929542 3763.760735 4489.073883 3347.90049 2507.339695 4003.910085 5838.062006 1926.050184 4431.801703 3374.9788 0.907244082 1.115195371 1.33010432 0.991976747 0.742920132 1.186351181 1.729807015 0.570685121 1.313134679 1 11.72066272 -10.24895042 21.93353629 0.956198604 1.114703078 0 0.317937506 343.5843254 603412.2992 0.047066018 0.057346857 5.64E-11 10.24895042 0.158504474 FNEEHIPDSPFVVPVASPS(ph)GDAR ddPTM_HeLa_Romidepsin_16h_R1 4 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 1 0 FNEEHIPDS(0.001)PFVVPVAS(0.444)PS(0.556)GDAR;FNEEHIPDSPFVVPVAS(0.352)PS(0.648)GDAR;FNEEHIPDS(0.038)PFVVPVAS(0.396)PS(0.566)GDAR;FNEEHIPDS(0.447)PFVVPVAS(0.087)PS(0.466)GDAR ;;; 187.75 7.39E-20 401549000 15870.3 15537.3 14707.3 14855.4 16218.8 17868.5 14686.1 16950.8 17792.3 16394.2 TRUE FALSE FALSE 15676.86668 15756.03452 14963.27439 16573.05124 15391.09412 16726.76052 15933.53697 17441.24465 16200.91213 15968.27632 0.981750714 0.986708534 0.937062591 1.037873526 0.963854445 1.047499441 0.997824477 1.092243415 1.014568624 1 13.96292097 -4 0.760337046 0.988955159 19.53648455 0.469497059 0.030764824 219.9370883 0.854187915 0.004288464 7002.440683 1.00E-04 4 18.54752939 FNEEHIPDSPFVVPVASPSGDAR ddPTM_HeLa_Romidepsin_16h_R1 4 FNEEHIPDSPFVVPVASPSGDAR 23 0 Q60FE5;P21333-2;P21333;A0A087WWY3;H0Y5C6 Q60FE5 FLNA Filamin-A 0 0 ;;; ;;; 115.84 3.28E-06 60220000 5692.3 6282.29 5417.82 6614.91 6270.15 6698 5822.15 6846.91 7216.6 6542.3 FALSE FALSE TRUE 5622.920058 6370.732244 5512.114884 7379.757018 5950.160848 6270.019417 6316.683276 7045.014538 6571.129222 6372.330103 0.88239623 0.99974925 0.865007744 1.158093962 0.933749626 0.983944541 0.991267429 1.105563338 1.031197241 1 12.63760529 -9.291564361 24.99996876 0.94266256 1.023712202 0.191648214 0.077157402 802.5223844 665991.3905 0.011433185 0.017465419 5.11E-10 9.291564361 0.081049641 FNGEDIDTIS(ph)PTLGFNIK ddPTM_HeLa_Romidepsin_16h_R1 2 FNGEDIDTISPTLGFNIK 18 0 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 1 0 FNGEDIDT(0.406)IS(0.594)PTLGFNIK;FNGEDIDT(0.002)IS(0.996)PT(0.002)LGFNIK ; 169.6 3.28E-07 135662000 5648.7 5426.1 5477 5309.8 5423.8 5113.4 3783.6 4165 5987.7 5928.1 TRUE FALSE FALSE 5579.851472 5502.488778 5572.324888 5923.744059 5147.003247 4786.670243 4104.97889 4285.507704 5452.145116 5774.087107 0.966360806 0.952962551 0.965057295 1.025918721 0.891396883 0.828991692 0.710931237 0.74219658 0.944243655 1 12.49537716 -8.204997737 1.665647598 0.982107706 0.723403209 0.914844689 0.029893566 0.065772785 0.34150336 0.004069587 0.015062118 6.24E-09 8.204997737 -0.258704497 FNGGHS(ph)PTHSPEK ddPTM_HeLa_Romidepsin_16h_R1 1 FNGGHSPTHSPEK 13 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 0 FNGGHS(1)PTHSPEK 106.82 0.0036683 7582400 3037.2 2613.7 2981.9 2561.4 3330 2986.9 2473.8 1928.5 3444.9 2795 TRUE FALSE FALSE 3000.181438 2650.495737 3033.798719 2857.56112 3160.057674 2796.04673 2683.92451 1984.298105 3136.779516 2722.385497 1.102041368 0.973593101 1.114389833 1.049653373 1.160767892 1.027057605 0.985872322 0.728882117 1.152217245 1 11.41065566 -7.218557044 2.129587561 1.055621637 0.616776617 0.741980106 0.060410909 0.289805685 1.319631356 0.007966942 0.251712544 6.05E-08 7.218557044 -0.438845019 FNGTHIPGS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 1 FNGTHIPGSPFK 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 FNGTHIPGS(1)PFK 80.102 0.020361 6817000 3843.2 3608.1 4438 4817.5 5665.4 6800.9 5599.1 5238.2 3754.3 3332.9 TRUE FALSE FALSE 3796.3576 3658.894927 4515.241528 5374.522017 5376.273497 6366.344439 6074.687414 5389.759052 3418.506005 3246.310778 1.169437512 1.127093238 1.390883941 1.655578404 1.656117934 1.961101347 1.87125874 1.660272051 1.053043359 1 11.6645854 -9.376000993 1.054545899 1.068846766 1.833108812 0.928575533 0.089200164 0.089756864 0.198232735 0.017292868 0.033471365 4.21E-10 9.376000993 0.764262047 FNHDGEEEEEDDDYGSR ddPTM_HeLa_Romidepsin_16h_R1 2 FNHDGEEEEEDDDYGSR 17 0 Q6PJT7;Q6PJT7-5;H0YJA2;Q6PJT7-2;Q6PJT7-9;Q6PJT7-3;Q6PJT7-11;Q6PJT7-4;Q6PJT7-10;G3V256;G3V5I6 Q6PJT7 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 0 ; ; 176.21 2.14E-08 18005300 3677.4 3568.2 2948.7 3122.8 3240 3668.8 3018.5 3076.5 3636 3550.5 FALSE FALSE TRUE 3632.578434 3618.433213 3000.020887 3483.872829 3074.65071 3434.375521 3274.891315 3165.513674 3310.787053 3458.257498 1.050407159 1.046316885 0.867494942 1.007407005 0.889075123 0.993094216 0.94697729 0.915349327 0.957357009 1 11.75582958 -9.786637078 24.99995316 1.026156998 0.940670306 0.376496263 0.047235387 134.909001 133849.6939 0.006512792 0.008561402 1.63E-10 9.786637078 -0.085486691 FNHWELK ddPTM_HeLa_Romidepsin_16h_R1 2 FNHWELK 7 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 0 ; ; 146.54 0.005721 31849000 19517.7 19289.4 20083 17602.9 18975.7 19707.6 17190.7 20115.6 19377.1 17054 FALSE FALSE TRUE 19279.81077 19560.95668 20432.53619 19638.23012 18007.29922 18448.34796 18650.87763 20697.61315 17643.96365 16610.93462 1.160669836 1.177595188 1.230065415 1.18224715 1.084062976 1.110614687 1.122807238 1.246023395 1.062189699 1 14.01984563 -12.05649233 0.783734964 0.996964826 1.161718136 0.507384192 0.051031204 0.373051869 0.407434316 0.03673823 0.010382234 8.78E-13 12.05649233 0.164753311 FNLTYVSHDGDDK ddPTM_HeLa_Romidepsin_16h_R1 3 FNLTYVSHDGDDK 13 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 ;; ;; 147.7 0.00035938 54313770 3385.12 3478.94 3915.99 2307.44 3948.2 3800.7 3592.8 2851.14 3828.01 3279.7 FALSE FALSE TRUE 3343.860855 3527.916609 3984.146163 2574.23707 3746.708621 3557.847536 3897.972342 2933.633238 3485.623198 3194.492921 1.046757948 1.104374527 1.247192046 0.805835897 1.1728649 1.113744066 1.220216303 0.918340816 1.091135052 1 11.64137123 -10.78904819 1.586323187 1.014086203 1.087390121 0.000442024 0.128915865 0.742891334 3.895573561 0.025496237 0.024315425 1.63E-11 10.78904819 0.073303918 FNRDVDETISWIK ddPTM_HeLa_Romidepsin_16h_R1 1 FNRDVDETISWIK 13 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 92.939 0.0039188 0 1419 1538.7 1465.6 1097.4 1535.3 1237.1 1122.9 1510.1 1634 1376.9 FALSE FALSE TRUE 1401.704682 1560.361859 1491.108153 1224.286551 1456.947912 1158.053303 1218.279098 1553.792361 1487.850948 1341.12794 1.045168504 1.163469803 1.111831399 0.912878269 1.086360122 0.863492042 0.908398865 1.158571315 1.109402693 1 10.38923116 -9.259522182 24.99322116 1.040963783 0.980408496 0.137029693 0.096328842 347.0953019 4524826.924 0.014240712 0.022867528 5.50E-10 9.259522182 -0.060555287 FNTPALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 FNTPALKK 8 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 1 FNTPALK(1)K 85.731 0.02528 844170 644 498.26 758.37 716.28 1448.5 1249.7 1193.7 937.73 1228 889.62 FALSE TRUE FALSE 636.1506803 505.2745174 771.5691117 799.0996638 1374.57764 1169.848203 1295.092848 964.8617381 1118.164604 866.5075442 0.734154809 0.58311612 0.890435539 0.922207394 1.58634238 1.350072727 1.494612317 1.113506448 1.290426854 1 9.7590685 -8.852499454 6.227862879 0.848905416 1.389734801 0.557150155 0.20807446 0.088070398 4.955641146 0.02529065 0.046327034 1.40E-09 8.852499454 0.540829385 FNVS(ph)TGNTRAALAT(ph)LER ddPTM_HeLa_Romidepsin_16h_R1 1 FNVSTGNTRAALATLER 17 1 C9JVJ9;Q8N434-2;Q8N434 C9JVJ9 SVOPL Putative transporter SVOPL 2 0 FNVS(0.997)T(0.002)GNT(0.001)RAALAT(1)LER 95.073 0.020832 776340000 3202.7 2664.6 2962 2990 3447.7 2952.4 2530.2 3013.1 3378.5 2927.2 TRUE FALSE FALSE 3163.664261 2702.112309 3013.552368 3335.717868 3271.751004 2763.751168 2745.115125 3100.279295 3076.318498 2851.150922 1.109609539 0.947726859 1.056959961 1.169954857 1.147519403 0.969345799 0.962809476 1.087378178 1.078974275 1 11.47732869 FPEAEALS(ph)PEQAAHYLR ddPTM_HeLa_Romidepsin_16h_R1 2 FPEAEALSPEQAAHYLR 17 0 Q2NKX8 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 0 FPEAEALS(1)PEQAAHYLR;FPEAEALS(1)PEQAAHYLR ; 146.97 5.81E-05 6818300 1896.9 2032.73 2396.7 1599.75 2133.2 2225.1 2141.11 2463.2 2279.2 2135.72 TRUE FALSE FALSE 1873.779853 2061.346826 2438.413558 1784.720622 2024.334844 2082.923291 2322.97583 2534.468806 2075.342644 2080.233687 0.9007545 0.990920799 1.172182517 0.857942371 0.973128575 1.001292934 1.116689844 1.218357737 0.997648801 1 11.02252989 -7.581392605 1.81735998 0.965690302 1.233447599 0.472441778 0.078411853 0.300247478 1.537376898 0.011596871 0.110440169 2.62E-08 7.581392605 0.267757297 FPEFCSSPS(ph)PPVEVK ddPTM_HeLa_Romidepsin_16h_R1 1 FPEFCSSPSPPVEVK 15 0 Q68E01-4;Q68E01-3;Q68E01-2;Q68E01 Q68E01-4 INTS3 Integrator complex subunit 3 1 0 FPEFCS(0.003)S(0.012)PS(0.985)PPVEVK 116.87 0.00024226 0 950.49 1021.6 835.87 158 924.47 832.31 701.51 710.98 970.74 880.22 TRUE FALSE FALSE 938.9050623 1035.982112 850.4179667 176.2687034 877.2908462 779.1280772 761.0962419 731.5510846 883.9145831 857.3517575 1.095122339 1.208351301 0.991912548 0.205596713 1.023256602 0.908761276 0.887729261 0.853268309 1.030982412 1 9.74374343 -9.503476099 24.99428156 1.060417165 0.782654657 0.322018344 0.212231148 745.7216855 960631.9973 0.031836657 0.048180315 3.14E-10 9.503476099 -0.277762508 FPHS(ph)S(ph)PMVKS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 FPHSSPMVKSK 11 1 B5MCD5;B5MBY2;Q9Y6T7-2;Q9Y6T7 B5MCD5 DGKB Diacylglycerol kinase;Diacylglycerol kinase beta 3 0 FPHS(1)S(1)PMVKS(1)K 49.423 0.030441 4685600 920.84 874.26 980.05 941.89 978.57 1101.4 1052.7 1098.3 893.41 788.39 TRUE FALSE FALSE 909.6164479 886.5678552 997.1073591 1050.795754 928.6299214 1031.024095 1142.116312 1130.077578 813.501172 767.9075141 1.184539064 1.154524261 1.298473242 1.368388425 1.209299172 1.342640976 1.487309722 1.4716324 1.059373892 1 9.584788755 -4 0.094766183 0.788709223 2.790085646 0.857261265 0.058979164 31.78765304 0.216680701 0.574664108 8.30501974 1.00E-04 4 2.001376423 FPPEDFRHS(ph)PEDFR ddPTM_HeLa_Romidepsin_16h_R1 3 FPPEDFRHSPEDFR 14 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 0 FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR;FPPEDFRHS(1)PEDFR ;; 90.853 0.003866 22289000 5709 5714.2 5332.5 4476 5449.4 5764.1 4681.9 4947.8 5919.1 5796.7 TRUE FALSE FALSE 5639.416512 5794.644658 5425.309926 4993.53618 5171.296783 5395.792613 5079.580469 5090.956787 5389.680871 5646.100898 0.998816106 1.026309087 0.960894965 0.884422059 0.91590584 0.955667054 0.899661653 0.901676551 0.954584583 1 12.4630392 -9.508840603 4.985527737 1.001303915 0.913887943 0.725793495 0.024115923 0.053655633 3.764138616 0.002938899 0.004373413 3.10E-10 9.508840603 -0.087415971 FPPEITVTPPT(ph)PTLLSPK ddPTM_HeLa_Romidepsin_16h_R1 1 FPPEITVTPPTPTLLSPK 18 0 A0A087WWW8;Q9Y6J0-2;Q9Y6J0;B5MEB3 A0A087WWW8 CABIN1 Calcineurin-binding protein cabin-1 1 0 FPPEITVT(0.001)PPT(0.999)PTLLSPK 164.58 2.22E-10 0 708 699.4 823.77 812.59 712.11 743.92 636.93 681.35 594.79 880.79 TRUE FALSE FALSE 699.3706237 709.2461716 838.1073713 906.5454792 675.7683695 696.3859129 691.0308183 701.0637873 541.5904927 857.9069488 0.815205687 0.826716898 0.976921066 1.056694412 0.787694249 0.811726626 0.80548458 0.817179285 0.631292815 1 9.744677367 -12.42379078 1.091761918 1.001902032 0.86093511 0 0.141128374 0.597042861 1.245457682 0.065663685 0.01565932 3.77E-13 12.42379078 -0.140966922 FPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG ddPTM_HeLa_Romidepsin_16h_R1 2 FPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG 34 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 ; ; 78.268 2.63E-08 22160700 7783.6 7955.1 6804.3 7497 8338.5 8031.3 6928.5 7957 9064.5 8750.1 FALSE FALSE TRUE 7688.730489 8067.092107 6922.725987 8363.838414 7912.95523 7518.12585 7517.006617 8187.223241 8253.748418 8522.771141 0.902139734 0.946533935 0.812262335 0.981351989 0.928448635 0.882122226 0.881990903 0.960629249 0.96843483 1 13.05710688 -12.23730876 0.766623417 1.005823421 0.909712518 0.270614433 0.046255178 0.651290609 0.623252905 0.039182615 0.008611054 5.79E-13 12.23730876 -0.096110903 FPTDYASTS(ph)EDEFGSNR ddPTM_HeLa_Romidepsin_16h_R1 1 FPTDYASTSEDEFGSNR 17 0 H0Y2V6;Q5SW79;Q5SW79-3 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 FPTDYAS(0.057)T(0.393)S(0.548)EDEFGS(0.001)NR 107.63 0.0022848 3609500 762.5 837.07 882.02 794.93 773.41 602.25 738.81 671.47 732.73 706.44 TRUE FALSE FALSE 753.2063567 848.8542934 897.3711881 886.8435469 733.9400017 563.7681687 801.564503 690.897925 667.1927936 688.086587 1.094638918 1.233644587 1.304154455 1.288854577 1.066639018 0.819327363 1.164918076 1.004085733 0.969634936 1 9.426446311 -5.870892916 14.08183462 1.081653224 0.600755911 0 0.147280203 0 0 0.020128655 0 1.35E-06 5.870892916 -0.480897312 FPTDYASTSEDEFGS(ph)NRNSPK ddPTM_HeLa_Romidepsin_16h_R1 2 FPTDYASTSEDEFGSNRNSPK 21 1 H0Y2V6;Q5SW79;Q5SW79-3 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 FPT(0.001)DY(0.007)AS(0.038)T(0.034)S(0.007)EDEFGS(0.745)NRNS(0.166)PK;FPTDY(0.001)AS(0.003)T(0.003)S(0.003)EDEFGS(0.847)NRNS(0.144)PK ; 55.061 0.011141 11438500 1872.54 1740.38 1730.1 2030.17 1784.97 2011.68 1764.11 1634.66 2092.31 1872.97 TRUE FALSE FALSE 1849.716762 1764.881115 1760.211665 2264.907808 1693.87632 1883.14014 1913.953459 1681.956308 1905.168553 1824.309969 1.013926796 0.967423927 0.964864357 1.24151479 0.928502474 1.032247903 1.0491383 0.92196849 1.044322832 1 10.83313516 -7.247154419 22.78386328 1.015605183 0.921968263 0.117209217 0.081234594 1200.303761 1914314.333 0.010181123 0.258182421 5.66E-08 7.247154419 -0.093636919 FPVNSNSNGGNELCPK ddPTM_HeLa_Romidepsin_16h_R1 1 FPVNSNSNGGNELCPK 16 0 P20849-3;P20849 P20849-3 COL9A1 Collagen alpha-1(IX) chain 0 0 51.643 0.027604 969600 291.66 233.25 264.48 341.43 392.35 327.91 270.47 190.95 289.33 242.26 FALSE FALSE TRUE 288.1051357 236.5336996 269.0831635 380.9077431 372.3269154 306.9576093 293.443715 196.474837 263.4516002 235.9660503 1.220960114 1.00240564 1.14034694 1.614248078 1.577883407 1.30085497 1.243584468 0.832640275 1.116480951 1 7.882435496 -9.496414321 24.64022657 1.098267875 1.329227591 0.216181717 0.207854841 764.5899205 711887.4555 0.033818713 0.051548876 3.19E-10 9.496414321 0.230959716 FQDGDLTLYQSNTILR ddPTM_HeLa_Romidepsin_16h_R1 1 FQDGDLTLYQSNTILR 16 0 P09211;A8MX94;A0A087X2E9 P09211 GSTP1 Glutathione S-transferase P 0 0 132.08 0.018471 24359000 873.36 726.26 981.25 1067.7 1179 997.66 869.43 850.46 824.71 851.93 FALSE FALSE TRUE 862.7151524 736.4843073 998.3282446 1191.152498 1118.831231 933.9127458 943.2793625 875.0667183 750.9458721 829.7967358 1.039670458 0.887547848 1.203099749 1.435475034 1.348319633 1.125471704 1.136759548 1.054555508 0.904975688 1 9.696614172 -9.658673724 7.718855491 1.009624809 1.227044303 0.530120579 0.115491227 0.165242828 11.14351498 0.018462906 0.026122549 2.19E-10 9.658673724 0.217419494 FQELLAS(ph)PAYR ddPTM_HeLa_Romidepsin_16h_R1 1 FQELLASPAYR 11 0 Q9NSI2-2;Q9NSI2 Q9NSI2-2 FAM207A Protein FAM207A 1 0 FQELLAS(0.798)PAY(0.202)R 93.228 0.029088 6086000 1259 1413.9 1572.1 1394.2 1848.7 2317.4 1974.8 2311.5 1511.8 1282.8 TRUE FALSE FALSE 1243.654824 1433.804921 1599.461741 1555.403964 1754.353941 2169.325619 2142.539463 2378.379606 1376.580822 1249.472671 0.995343758 1.147528037 1.280109424 1.244848327 1.40407548 1.736192931 1.714754962 1.903506704 1.101729436 1 10.28710363 -8.3620398 0.544230467 0.986100018 2.04580006 0.948693469 0.070117824 0.187574543 0.073612117 0.013456597 0.102189916 4.34E-09 8.3620398 1.059700042 FQETEFLS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 FQETEFLSPPR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 FQETEFLS(1)PPR;FQETEFLS(1)PPR ; 124.47 0.0080445 85393000 6042.1 6419.4 6505.7 4924.9 7837.2 7923.4 6987.1 6617.1 7229.3 6446.2 TRUE FALSE FALSE 5968.456561 6509.772482 6618.928979 5494.34011 7437.238439 7417.120312 7580.5841 6808.555348 6582.693302 6278.726795 0.950583893 1.036798175 1.054183308 0.875072334 1.184513785 1.181309612 1.207344156 1.084384712 1.048412125 1 12.61625632 -8.743181526 24.99870108 0.98124277 1.168665109 0.664956501 0.058730538 91.74777416 125620.7229 0.007667146 0.015310587 1.81E-09 8.743181526 0.187422338 FQFDGDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 FQFDGDKK 8 1 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 1 ; FQFDGDK(1)K;FQFDGDK(1)K 120.12 0.0015565 5601000 2690.3 2723 3005.4 1584.77 6651.7 6277.8 5020.4 5098.9 7170.6 5029.2 FALSE TRUE FALSE 2657.509589 2761.334465 3057.707726 1768.008564 6312.238928 5876.668841 5446.832651 5246.428627 6529.243577 4898.540659 0.542510469 0.563705531 0.624207889 0.360925567 1.288595802 1.199677465 1.11192966 1.071018696 1.332895658 1 12.2581363 -8.740774968 24.98991861 0.720825352 1.166090945 0.395878609 0.260004296 166.3051319 201115.4317 0.033514374 0.066969504 1.82E-09 8.740774968 0.445265593 FQPGETLTEILETPATSEQEAEHQR ddPTM_HeLa_Romidepsin_16h_R1 1 FQPGETLTEILETPATSEQEAEHQR 25 0 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 0 170.27 1.01E-14 2758000 544.12 405.43 533.87 581.28 615.57 800.66 574.93 596.84 661.45 574.14 FALSE FALSE TRUE 537.4880562 411.1376542 543.1617834 648.4903286 584.1551659 749.50041 623.7645398 614.1086237 602.2882554 559.22376 0.961132367 0.735193466 0.971278086 1.159625851 1.044582165 1.340251369 1.115411369 1.098144728 1.077007628 1 9.127281848 -9.275010576 6.692182111 0.95785066 1.154395264 0.466535701 0.108165288 0.109298237 25.26598449 0.015845368 0.024918374 5.31E-10 9.275010576 0.196544603 FQPPQVPDQAPAEAPTEKTEVS(ph)PVPR ddPTM_HeLa_Romidepsin_16h_R1 1 FQPPQVPDQAPAEAPTEKTEVSPVPR 26 1 E9PPY3;O43159 E9PPY3 RRP8 Ribosomal RNA-processing protein 8 1 0 FQPPQVPDQAPAEAPT(0.257)EKT(0.197)EVS(0.545)PVPR 80.415 2.58E-05 15825000 1428.9 1098 1114.2 1941 1308 1107.3 1115.9 1026.3 1511.3 1262.8 TRUE FALSE FALSE 1411.484017 1113.457673 1133.592184 2165.427553 1241.247879 1036.547104 1210.684518 1055.994371 1376.125543 1229.992274 1.14755519 0.905255827 0.921625451 1.760521264 1.009150956 0.842726516 0.984302539 0.858537402 1.118808282 1 10.26443354 -8.52102406 24.99999386 1.100295063 0.907739894 0.175958372 0.230435803 113.8044699 1534007.61 0.033448976 0.067718209 3.01E-09 8.52102406 -0.192555169 FQPSSVLS(ph)PYER ddPTM_HeLa_Romidepsin_16h_R1 2 FQPSSVLSPYER 12 0 J3QLM6;Q7Z6J9 J3QLM6 TSEN54 tRNA-splicing endonuclease subunit Sen54 1 0 FQPSSVLS(1)PYER;FQPSS(0.001)VLS(0.999)PYER ; 147.7 0.0014841 13359300 2284.7 1946.61 2175.1 1775.59 2991.3 3400.7 2680.3 2988.9 2128.45 2252.16 TRUE FALSE FALSE 2256.853198 1974.014427 2212.956703 1980.89207 2838.642799 3183.406245 2907.964615 3075.379106 1938.076101 2193.648559 1.028812564 0.899877247 1.00880184 0.903012501 1.294028065 1.451192459 1.325629214 1.401947041 0.883494347 1 11.0991167 -8.642471307 4.927608107 0.997533809 1.3838465 0.90569874 0.06501967 0.039566276 1.544420982 0.007783499 0.015829507 2.28E-09 8.642471307 0.38631269 FQSPQIQATIS(ph)PPLQPK ddPTM_HeLa_Romidepsin_16h_R1 1 FQSPQIQATISPPLQPK 17 0 A0A087WYN9;Q7Z478 A0A087WYN9 DHX29 ATP-dependent RNA helicase DHX29 1 0 FQSPQIQAT(0.007)IS(0.993)PPLQPK 144.25 0.00016474 108010000 1865.6 1810.1 1601.6 1568.2 2192.8 2181.1 1982.3 2340.9 1560.6 1934.2 TRUE FALSE FALSE 1842.86135 1835.582635 1629.475176 1749.522663 2080.893234 2041.734749 2150.676513 2408.630248 1421.016027 1883.949205 0.978190571 0.974327031 0.864925218 0.928646408 1.104537865 1.083752547 1.141578821 1.278500631 0.754275128 1 10.87954435 -7.617575109 0.940915582 0.97684213 1.331178282 0.615634642 0.087506043 0.477918897 0.453096902 0.008815432 0.151096775 2.41E-08 7.617575109 0.354336152 FQSQADQDQQAS(ph)GLQSPPSR ddPTM_HeLa_Romidepsin_16h_R1 1 FQSQADQDQQASGLQSPPSR 20 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 FQSQADQDQQAS(0.891)GLQS(0.105)PPS(0.004)R 114.1 0.00029145 4712600 1003.8 944.27 945.24 653.15 988.18 1150.9 908.41 1095.3 713.39 1015.9 TRUE FALSE FALSE 991.5652995 957.5634578 961.6915057 728.6702762 937.7494872 1077.361204 985.5703227 1126.990777 649.5826117 989.5067715 1.002080358 0.967717943 0.971889767 0.736397463 0.947693855 1.088786085 0.996021807 1.138941956 0.656471113 1 9.95056577 -6.995030939 1.203730124 0.976881197 1.288758371 0.10765156 0.131868454 3.146453479 2.48187755 0.013211139 1.422328007 1.01E-07 6.995030939 0.311877174 FQSQADQDQQASGLQS(ph)PPSR ddPTM_HeLa_Romidepsin_16h_R1 2 FQSQADQDQQASGLQSPPSR 20 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 FQSQADQDQQASGLQS(1)PPSR;FQSQADQDQQASGLQS(0.998)PPS(0.002)R ; 236.66 3.46E-53 14880000 2039.24 2044.66 2277.75 1600.04 2254.84 2791.74 2271.18 2433.26 2376.44 2248.59 TRUE FALSE FALSE 2014.384959 2073.444777 2317.393283 1785.044153 2139.767101 2613.356824 2464.093973 2503.662539 2163.885254 2190.171308 0.919738539 0.946704383 1.058087683 0.815024901 0.976986181 1.193220281 1.125069059 1.143135485 0.987998175 1 11.096828 -8.309248208 6.804049317 0.956724668 1.150797699 0.682794112 0.061246543 0.097109613 11.39986714 0.00868798 0.019713265 4.91E-09 8.309248208 0.194073032 FQVVINGR ddPTM_HeLa_Romidepsin_16h_R1 2 FQVVINGR 8 0 A0A3B3ITG9;A0A3B3ISX1;A0A3B3IRQ9;P55265-5;P55265-3;P55265-2;P55265;P55265-4 A0A3B3ITG9 ADAR Double-stranded RNA-specific adenosine deaminase 0 0 ; ; 130.04 0.015749 2117000 1722.08 1732.78 2005.5 1404.21 1659.79 1859.96 1495.62 1587.16 1661.47 1879.87 FALSE FALSE TRUE 1701.090627 1757.174122 2040.404886 1566.571367 1575.084723 1741.114559 1622.657925 1633.08197 1512.863962 1831.030706 0.929034462 0.959663929 1.114347716 0.855568048 0.860217536 0.950893151 0.886199188 0.891892181 0.82623626 1 10.83844027 FRIDELEPR ddPTM_HeLa_Romidepsin_16h_R1 1 FRIDELEPR 9 1 F5H6X6;Q14697;Q14697-2 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 104.42 0.027679 14419000 4494.2 4109.9 4909.6 3563.4 4099.7 4206.6 3656.4 4175.1 4361.6 3631.6 FALSE FALSE TRUE 4439.422962 4167.75928 4995.049529 3975.417074 3890.477011 3937.811836 3966.974525 4295.899931 3971.487572 3537.250508 1.25504907 1.178248267 1.412127729 1.123872077 1.099859058 1.113240871 1.121485322 1.214474327 1.122761185 1 11.78841268 -12.40597519 1.129133553 0.999878554 1.192371373 0.186991372 0.095130571 0.423518518 0.964738641 0.063819622 0.016165949 3.93E-13 12.40597519 0.192492819 FRIGGKRK ddPTM_HeLa_Romidepsin_16h_R1 1 FRIGGKRK 8 3 E9PQ90;E9PNJ2;E9PSH1;E9PJG4;E9PNM1;P37268-5;P37268 E9PQ90 FDFT1 Squalene synthase 0 0 73.931 0.014811 0 0 0 0 131.13 129.19 235.34 122.29 69.089 145.97 172.41 FALSE FALSE TRUE 0 0 0 146.2918676 122.5969522 220.3025335 132.6773095 71.08798121 132.9140776 167.9307633 0 0 0 0.871143945 0.730044631 1.311865254 0.790071497 0.423317204 0.791481412 1 7.391722733 -12.70101337 1.608294294 0.998401579 0.446713451 0.093047429 0.419518536 0.599998476 2.812024047 0.344099104 0.076928428 1.99E-13 12.70101337 -0.551688128 FS(ph)GGFGAR ddPTM_HeLa_Romidepsin_16h_R1 1 FSGGFGAR 8 0 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1;O15523-2;O15523 A0A2R8Y4A4 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 1 0 FS(1)GGFGAR 112.11 0.021682 65320000 2957.1 2799.6 2876.8 2365.5 3102 2637.4 2599.8 2299.5 2839.9 2635.3 TRUE FALSE FALSE 2921.057728 2839.012842 2926.869497 2639.01024 2943.693365 2468.878652 2820.626947 2366.032404 2585.892231 2566.834526 1.138000014 1.106036565 1.140264192 1.028118569 1.146818517 0.961837869 1.098873698 0.921770523 1.007424594 1 11.32577458 -6.43089323 1.414554274 1.073636267 2.27E-16 0.308363289 0.064182186 11.5748358 3.460329984 0.0099149 31.02597038 3.71E-07 6.43089323 -1.073636267 FS(ph)PDSQYIDNR ddPTM_HeLa_Romidepsin_16h_R1 3 FSPDSQYIDNR 11 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;F5GZI3 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 FS(1)PDSQYIDNR;FS(1)PDSQYIDNR;FS(1)PDSQYIDNR ;; 220.37 4.74E-27 35625200 7007.5 5750.3 5766.8 3826.14 6514.3 5409.2 5666.6 5641.6 6180.7 5880.2 TRUE FALSE FALSE 6922.089895 5831.252874 5867.168735 4268.536309 6181.850963 5063.569577 6147.920863 5804.830795 5627.882712 5727.431556 1.208585354 1.018127029 1.024397878 0.745279322 1.079340871 0.884090805 1.073416732 1.013513778 0.982618938 1 12.4836726 -9.88180883 3.060574991 1.09859467 0.964508764 0.096891513 0.110348795 0.291932256 5.504265174 0.019108689 0.025724681 1.31E-10 9.88180883 -0.134085907 FS(ph)PGAPGGSGSQPNQK ddPTM_HeLa_Romidepsin_16h_R1 4 FSPGAPGGSGSQPNQK 16 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK;FS(1)PGAPGGSGSQPNQK ;;; 241.66 7.48E-47 252657000 26319.4 25910.4 26715.3 14663.4 24388.9 26037.2 22765.1 22690.3 26674.8 27389.6 TRUE FALSE FALSE 25998.60903 26275.16729 27180.26859 16358.8513 23144.24343 24373.50695 24698.76703 23346.80803 24288.93908 26678.01424 0.974533141 0.984899665 1.018826527 0.613195988 0.867539961 0.913617735 0.9258098 0.875132902 0.910447789 1 14.70336366 FS(ph)PPSPLPQAVFSTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 0 FS(0.83)PPS(0.17)PLPQAVFSTSSR 140.77 0.00057965 18313000 724.08 819.62 681.03 665.94 835.17 789.21 699.4 763.55 647.87 694.73 TRUE FALSE FALSE 715.2546345 831.1586319 692.8830415 742.9391161 792.5481585 738.7820281 758.8070185 785.6421146 589.9228846 676.6808144 1.057004453 1.228287568 1.023943677 1.097916625 1.171228948 1.091773274 1.121366237 1.161023185 0.871788991 1 9.402331675 -10.49461237 6.430640532 1.024629374 1.124262254 0.456428047 0.070874627 0.123401074 15.37200437 0.00894299 0.009872567 3.20E-11 10.49461237 0.099632881 FS(ph)PTMGR ddPTM_HeLa_Romidepsin_16h_R1 1 FSPTMGR 7 0 H0Y3P2;D3DQV9;P78344-2;P78344;H0YCH5 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 0 FS(0.994)PT(0.006)MGR 93.143 0.0077705 5666400 8358.3 8403.5 9961 5203.8 6696.1 7390 5440 5663.6 8660.1 8365.2 TRUE FALSE FALSE 8256.425825 8521.804694 10134.36703 5805.487841 6354.37303 6917.80285 5902.073464 5827.46733 7885.518966 8147.870898 1.013323103 1.045893436 1.243805548 0.712515934 0.779881408 0.849031966 0.724370027 0.715213508 0.967801167 1 12.99220741 -9.235241016 24.99987611 1.026245606 0.760906751 0.767884025 0.081166834 297.4281252 283822.1045 0.011994882 0.019887654 5.82E-10 9.235241016 -0.265338856 FS(ph)QLAEAY(ph)EVLSDEVK ddPTM_HeLa_Romidepsin_16h_R1 1 FSQLAEAYEVLSDEVK 16 0 Q96EY1-2;Q96EY1 Q96EY1-2 DNAJA3 "DnaJ homolog subfamily A member 3, mitochondrial" 2 0 FS(1)QLAEAY(1)EVLSDEVK 84.759 0.0019592 0 816.77 990.81 744.56 1050.6 911.76 967.6 701.36 746.82 1040.3 936.3 TRUE FALSE FALSE 806.8148931 1004.758649 757.5187545 1172.075315 865.229485 905.7734828 760.9335009 768.4280584 947.2529625 911.974791 0.884689907 1.101739499 0.830635629 1.285205827 0.948742765 0.993200132 0.834379972 0.842597916 1.038683275 1 9.832850135 -7.757650355 24.77326885 0.974452031 0.838488878 0.200497446 0.12138163 109.9014399 718517.6625 0.016146967 0.05608165 1.75E-08 7.757650355 -0.135963153 FS(ph)SKNQLK ddPTM_HeLa_Romidepsin_16h_R1 1 FSSKNQLK 8 1 H7C5R8;Q460N5-5;Q460N5-3;Q460N5-4;Q460N5-1;Q460N5 H7C5R8 PARP14 Poly [ADP-ribose] polymerase 14 1 0 FS(0.5)S(0.5)KNQLK 98.629 0.011939 2097800 1506.4 1540.3 1378.7 1505.2 1422.9 1608.3 1393.7 1012.3 1880.1 1682.6 TRUE FALSE FALSE 1488.039417 1561.984384 1402.695695 1679.238306 1350.284103 1505.534821 1512.080843 1041.589303 1711.939147 1638.885809 0.907957961 0.953077008 0.855883727 1.024621909 0.823903713 0.918633142 0.922627333 0.63554721 1.044575002 1 10.67849962 -6.804507422 1.601573691 0.943327748 1.57E-13 0.646868316 0.066992304 1.741579539 1.546285332 0.008768266 3.686736923 1.57E-07 6.804507422 -0.943327748 FS(ph)YKS(ph)IT(ph)T(ph)DDWK ddPTM_HeLa_Romidepsin_16h_R1 1 FSYKSITTDDWK 12 1 P09960-3;P09960-2;P09960-4;P09960 P09960-3 LTA4H Leukotriene A-4 hydrolase 4 0 FS(0.89)Y(0.499)KS(0.611)IT(1)T(1)DDWK 65.895 0.0033615 0 612.86 621.74 774.69 390.56 995.56 1017.8 758.18 912.74 745.22 847.1 TRUE FALSE FALSE 605.3902266 630.492872 788.1731545 435.7183848 944.7528583 952.7658648 822.5797903 939.1486918 678.5656568 825.0922199 0.733724318 0.764148367 0.955254619 0.528084467 1.145026987 1.154738636 0.996954971 1.138234817 0.822411896 1 9.688411567 FSADEQFFSVGQAAS(ph)S(ph)S(ph)AHS(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 FSADEQFFSVGQAASSSAHSSK 22 0 P46019 P46019 PHKA2 "Phosphorylase b kinase regulatory subunit alpha, liver isoform" 5 0 FS(0.002)ADEQFFS(0.003)VGQAAS(0.999)S(0.999)S(0.999)AHS(0.999)S(0.999)K 51.566 0.003314 0 831 786.91 865.57 725.22 622.16 1005.4 920.12 985.28 982.69 961.83 TRUE FALSE FALSE 820.8714524 797.9881396 880.6348828 809.0733487 590.4088536 941.1581848 998.2749698 1013.787522 894.7957452 936.8415179 0.87621165 0.851785627 0.940004116 0.863618161 0.630212093 1.004607681 1.065575074 1.082133427 0.955119653 1 9.871661203 -8.008967549 24.46495831 0.90590551 1.064163619 0.394751633 0.097143807 313.1029619 854208.2984 0.015088164 0.042128273 9.80E-09 8.008967549 0.158258109 FSAS(ph)SGGGGSR ddPTM_HeLa_Romidepsin_16h_R1 1 FSASSGGGGSR 11 0 H0Y3P2;D3DQV9;P78344-2;P78344;H0YCH5;H0YEC5;H0YD77;H0YD99;H0YEN8;H0YDC0;H0YCF8 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 0 FS(0.128)AS(0.436)S(0.436)GGGGSR 122.18 0.0090574 10744000 3833 4052.5 4605 3225 3090.7 2853.6 3047.7 1629.9 4852.3 4517 TRUE FALSE FALSE 3786.281922 4109.551201 4685.148093 3597.889674 2932.970046 2671.26417 3306.571562 1677.058585 4418.298135 4399.647689 0.860587526 0.934063701 1.064891651 0.817767678 0.66663748 0.607154108 0.751553714 0.3811802 1.004239077 1 12.10317229 -8.821221203 2.510388561 0.941639521 0.60181078 0.746099594 0.101504722 0.11576458 1.487012878 0.015146496 0.030930734 1.51E-09 8.821221203 -0.33982874 FSASGELGNGNIK ddPTM_HeLa_Romidepsin_16h_R1 2 FSASGELGNGNIK 13 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 0 ; ; 227.36 4.23E-30 3718900 1597.25 1405.9 1408.32 1022.86 1428.53 1360.42 1550.98 1152.9 1811.58 1384.07 FALSE FALSE TRUE 1577.782103 1425.692297 1432.831219 1141.127886 1355.626784 1273.493553 1682.720202 1186.257343 1649.547748 1348.111662 1.170364553 1.057547633 1.06284313 0.846463923 1.005574554 0.944649904 1.24820536 0.879939975 1.223598752 1 10.39672428 -9.49853464 24.76711905 1.079990386 0.994111903 0.188657955 0.117332653 1169.465525 1189788.369 0.017468904 0.02659964 3.17E-10 9.49853464 -0.085878483 FSEGVLQS(ph)PSQDQEK ddPTM_HeLa_Romidepsin_16h_R1 4 FSEGVLQSPSQDQEK 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 FSEGVLQS(0.996)PS(0.004)QDQEK;FS(0.167)EGVLQS(0.818)PS(0.016)QDQEK;FSEGVLQS(0.986)PS(0.013)QDQEK;FSEGVLQS(0.998)PS(0.002)QDQEK ;;; 185.02 1.34E-08 88793000 15743 13472.2 14042.5 16848 14760.5 13728.8 11609.1 11804.6 14719 12726.1 TRUE FALSE FALSE 15551.11826 13661.86199 14286.90382 18796.04503 14007.21661 12851.57399 12595.17666 12146.14748 13402.49578 12395.47409 1.254580353 1.102165346 1.15259035 1.516363545 1.130026694 1.03679568 1.016110927 0.979885674 1.081241079 1 13.59752583 -8.234699852 4.21036131 1.155198657 1.007446848 0.24122496 0.131950248 0.317337009 13.31477179 0.021916221 0.056634534 5.83E-09 8.234699852 -0.147751809 FSEVLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 FSEVLKR 7 1 P12277;H0YJG0;H0YJK0 P12277 CKB Creatine kinase B-type 0 1 FSEVLK(1)R 129.68 0.0036107 4433200 1019.4 1261.7 1204.8 1002.1 2931 2633.3 2714.9 2641.6 2526.3 1834.5 FALSE TRUE FALSE 1006.975161 1279.462246 1225.769039 1117.967517 2781.420133 2465.040629 2945.503538 2718.030528 2300.341401 1786.839426 0.563551009 0.716047691 0.685998429 0.62566759 1.556614485 1.379553525 1.648443333 1.521138659 1.287380034 1 10.80319428 -8.756595768 24.99989253 0.76310635 1.524660641 0.734831544 0.208630132 38.52607247 198846.6319 0.026531769 0.051736363 1.75E-09 8.756595768 0.761554291 FSFSPEPTLEDIRR ddPTM_HeLa_Romidepsin_16h_R1 1 FSFSPEPTLEDIRR 14 1 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 0 0 86.262 0.01586 10904000 3516.9 1497.7 1755.2 1880.5 2284.5 1878 2334.3 2209.5 3099.1 3109.7 FALSE FALSE TRUE 3474.03467 1518.78466 1785.74852 2097.932258 2167.91344 1758.001861 2532.575384 2273.428396 2821.908734 3028.909546 1.14695887 0.50142952 0.589568124 0.692636154 0.715740569 0.580407514 0.836134373 0.750576523 0.931658305 1 11.56458278 -10.26947188 24.9989855 1.06939725 0.669767886 0.708444084 0.104595997 204.8937399 637675.2323 0.017908036 0.020669395 5.38E-11 10.26947188 -0.399629365 FSGEEGEIEDDES(ph)GTENR ddPTM_HeLa_Romidepsin_16h_R1 2 FSGEEGEIEDDESGTENR 18 0 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 FSGEEGEIEDDES(0.991)GT(0.009)ENR;FSGEEGEIEDDES(0.999)GT(0.001)ENR ; 345.11 2.68E-236 25065000 2305.6 2363.2 2279.6 1232.55 2123.6 1877.16 1596.8 1975.79 2270.5 2405 TRUE FALSE FALSE 2277.49846 2396.469192 2319.275482 1375.06323 2015.224768 1757.215534 1732.432152 2032.956366 2067.420793 2342.517753 0.972243842 1.023031389 0.990078081 0.587002266 0.860281535 0.750139687 0.739559882 0.867850996 0.882563554 1 11.19384427 -9.299576395 24.30441119 0.990062515 0.764693576 0.630997008 0.080780856 147.1243145 93760.73467 0.010138931 0.015487725 5.02E-10 9.299576395 -0.225368938 FSGEEGEIEDDES(ph)GTENREEK ddPTM_HeLa_Romidepsin_16h_R1 2 FSGEEGEIEDDESGTENREEK 21 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 FSGEEGEIEDDES(0.568)GT(0.432)ENREEK;FSGEEGEIEDDES(0.822)GT(0.178)ENREEK ; 86.08 0.00065669 33682000 2529.56 2074.32 2383.88 1148.38 2121.45 2414.12 2358.15 1986.57 2148.53 2784.83 TRUE FALSE FALSE 2498.72875 2103.522331 2425.370431 1281.161099 2013.18449 2259.865523 2558.451202 2044.048269 1956.360096 2712.479715 0.921197211 0.775497903 0.894152468 0.472320988 0.742193381 0.833136377 0.94321487 0.753571817 0.721244139 1 11.40539663 -10.38951452 1.39294316 0.974131692 0.76777486 0 0.143029217 0.316350881 1.191387287 0.024586204 0.027668523 4.08E-11 10.38951452 -0.206356831 FSGEEGEIEDDES(ph)GTENREEKDNIQPTTE ddPTM_HeLa_Romidepsin_16h_R1 4 FSGEEGEIEDDESGTENREEKDNIQPTTE 29 2 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 FSGEEGEIEDDES(0.499)GT(0.499)ENREEKDNIQPT(0.001)T(0.001)E;FSGEEGEIEDDES(0.542)GT(0.458)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.5)GT(0.5)ENREEKDNIQPTTE;FSGEEGEIEDDES(0.5)GT(0.5)ENREEKDNIQPTTE ;;; 65.023 0.00046642 731947900 5997.9 6081.9 5619.4 4706.4 6219.2 6433.7 5380 6705 6619.4 6548.3 TRUE FALSE FALSE 5924.795288 6167.521148 5717.2033 5250.576112 5901.811017 6022.607334 5836.977066 6898.998596 6027.344285 6378.174222 0.928917129 0.966972825 0.896369886 0.823209892 0.925313548 0.944252559 0.915148577 1.081657282 0.944995241 1 12.63892779 -12.0902535 0.76586322 1.002030014 0.930064493 0.020058612 0.063281332 1.090682084 1.113250462 0.047002156 0.012478733 8.12E-13 12.0902535 -0.07196552 FSGFSAKPNNSGEAPS(ph)SPTPK ddPTM_HeLa_Romidepsin_16h_R1 1 FSGFSAKPNNSGEAPSSPTPK 21 1 K7ENR9;K7ERZ5;P49916-4;P49916-3;P49916-2;P49916 K7ENR9 LIG3 DNA ligase 3 1 0 FSGFSAKPNNS(0.002)GEAPS(0.451)S(0.451)PT(0.095)PK 64.83 0.0040266 40644000 2749.8 2174.1 2380.4 1614.8 1795.8 1317.8 1326.9 1509.8 2273.7 2081.7 TRUE FALSE FALSE 2716.28438 2204.707037 2421.829863 1801.510774 1704.153625 1233.596833 1439.606853 1553.483681 2070.334577 2027.617134 1.339643631 1.087338926 1.19442168 0.888486659 0.840471111 0.608397321 0.709999353 0.766162238 1.021067806 1 10.98556954 -8.968266214 1.769777976 1.161804452 0.704078505 0.757977385 0.105702578 0.146327198 0.917357853 0.021260576 0.043634917 1.08E-09 8.968266214 -0.457725947 FSGWYDADLS(ph)PAGHEEAK ddPTM_HeLa_Romidepsin_16h_R1 2 FSGWYDADLSPAGHEEAK 18 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 1 0 FSGWYDADLS(1)PAGHEEAK;FSGWYDADLS(1)PAGHEEAK ; 98.727 0.0010027 19194700 4046.9 3393 3842.5 3607.3 4262.2 4087.1 3206.6 3791.2 4032.7 3608.3 TRUE FALSE FALSE 3997.574826 3440.766743 3909.377101 4024.392999 4044.68403 3825.947501 3478.968524 3900.89239 3672.005212 3514.555846 1.137433861 0.979004715 1.112338876 1.145064462 1.150837889 1.088600571 0.989874305 1.109924714 1.044799222 1 11.77912666 -12.53263487 1.238940382 0.999040018 1.092869276 0.15727088 0.058312808 0.535294085 1.446640286 0.043300263 0.00989826 2.93E-13 12.53263487 0.093829258 FSLPS(ph)VDGQK ddPTM_HeLa_Romidepsin_16h_R1 2 FSLPSVDGQK 10 0 H0Y8J6;D6RDW9;A0A2R8Y437;A0A2R8Y833;A0A2R8Y4F3;A0A2R8YE73;P31785-2;P31785 H0Y8J6 IL2RG Cytokine receptor common subunit gamma 1 0 FSLPS(1)VDGQK;FSLPS(1)VDGQK ; 106.36 0.020418 153391000 8724 6352.1 12505.3 9345.8 12500.2 11255.3 9629.4 6193.6 6933.2 4434.4 TRUE FALSE FALSE 8617.668532 6441.525031 12722.9495 10426.40537 11862.26815 10536.12265 10447.321 6372.802044 6313.077227 4319.193649 1.995203094 1.49137213 2.945677026 2.413970342 2.746408037 2.439372603 2.418812826 1.475461061 1.461633291 1 12.07654629 -11.46474096 0.514160651 0.959222531 2.381324658 0.449816222 0.457236231 0.527567554 0.288808025 0.340952946 0.133299986 3.43E-12 11.46474096 1.422102127 FSLS(ph)PSLGPQASR ddPTM_HeLa_Romidepsin_16h_R1 1 FSLSPSLGPQASR 13 0 Q9NYF3 Q9NYF3 FAM53C Protein FAM53C 1 0 FS(0.079)LS(0.655)PS(0.265)LGPQASR 129.76 0.0026018 29938000 702.15 795.89 780.92 845.29 2123.6 2065.1 1670.9 1461.8 794.78 752.35 TRUE FALSE FALSE 693.5919257 807.0945603 794.511585 943.026407 2015.224768 1933.146775 1812.826204 1504.094877 723.6928862 732.8038385 0.946490574 1.101378729 1.084207728 1.286874273 2.750019394 2.638013986 2.473821927 2.052520467 0.987566997 1 9.51728325 -8.855198371 4.701987973 1.001073808 2.487739526 0.936840643 0.180053326 0.035393473 1.355873657 0.027465724 0.051151289 1.40E-09 8.855198371 1.486665718 up FSPPS(ph)PLPQAVFSTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 FSPPSPLPQAVFSTSSR 17 0 Q99594;A0A1X7SBS4 Q99594 TEAD3 Transcriptional enhancer factor TEF-5 1 0 FS(0.139)PPS(0.861)PLPQAVFSTSSR 159.64 3.77E-05 13431000 552.74 440.94 378.81 599.5 539.34 540.08 377.12 354.37 492.38 380.95 TRUE FALSE FALSE 546.0029923 447.1475649 385.4030291 668.8170107 511.8154672 505.570631 409.1525634 364.6231368 448.3402996 371.0528641 1.471496504 1.205077789 1.038674179 1.802484431 1.379359969 1.362529925 1.102679976 0.982671668 1.208292249 1 8.535480933 -5.654027491 20.03844639 1.249971518 1.284687777 0 0.242442477 0 0 0.035389845 0 2.22E-06 5.654027491 0.034716259 FSPWGLRNAS(ph)LVTYYTSSGEDILIGGLK ddPTM_HeLa_Romidepsin_16h_R1 1 FSPWGLRNASLVTYYTSSGEDILIGGLK 28 1 Q8TDY8-2;Q8TDY8 Q8TDY8-2 IGDCC4 Immunoglobulin superfamily DCC subclass member 4 1 0 FS(0.003)PWGLRNAS(0.956)LVT(0.018)Y(0.004)Y(0.004)T(0.005)S(0.005)S(0.005)GEDILIGGLK 46.783 0.012494 22960000 1586.6 1375.8 1238.7 1756.4 1440.8 1380.2 812.36 1326.8 1431.7 1224.6 TRUE FALSE FALSE 1567.261909 1395.168549 1260.259054 1959.483232 1367.2706 1292.009674 881.3618381 1365.188865 1303.645166 1192.784715 1.313952039 1.169673396 1.056568748 1.6427803 1.146284474 1.083187651 0.738911076 1.144539201 1.092942548 1 10.22011796 -7.992395026 23.84617506 1.181399124 0.934056073 0.223004203 0.192486608 126.0481325 395221.5879 0.028171137 0.08422804 1.02E-08 7.992395026 -0.247343051 FSS(ph)PIVK ddPTM_HeLa_Romidepsin_16h_R1 1 FSSPIVK 7 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 FS(0.007)S(0.993)PIVK 109.48 0.029596 104060000 10624 9387.2 9174.2 9104.7 10600 12187 11020 10970 10638 9475.9 TRUE FALSE FALSE 10494.5106 9519.353248 9333.873103 10157.42825 10059.04245 11408.29003 11956.03852 11287.39964 9686.510637 9229.714752 1.137035205 1.031381089 1.01128511 1.100513778 1.089854098 1.236039286 1.295385485 1.222941331 1.049491875 1 13.17207035 -8.279506146 2.715832965 1.061724731 1.263026325 0.818818979 0.041569702 0.114176089 1.661613072 0.008190722 0.022373108 5.25E-09 8.279506146 0.201301593 FSS(ph)PTEELDYR ddPTM_HeLa_Romidepsin_16h_R1 2 FSSPTEELDYR 11 0 E9PGB3;E7EMZ9;E9PBC6;O95359-5;O95359-3;O95359;D6RAA5;Q4VXL8;O95359-6;O95359-1;H0Y911;Q4VXL4;O95359-2 E9PGB3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 0 FS(0.047)S(0.95)PT(0.003)EELDYR;FS(0.226)S(0.774)PTEELDYR ; 222.2 3.94E-27 12852600 3689.4 3811.3 3582.3 3220.2 2648.56 3246.8 3172.6 3194.4 3932.5 3523 TRUE FALSE FALSE 3644.432174 3864.955581 3644.648429 3592.534675 2513.3941 3039.339959 3442.080565 3286.824924 3580.767351 3431.471952 1.062060895 1.126325855 1.062123916 1.04693692 0.732453634 0.885724844 1.003091563 0.957846944 1.043507684 1 11.74461185 FSSPY(ph)RIES(ph)PELDCEEGWT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 FSSPYRIESPELDCEEGWTR 20 1 A0A087X279;P09913 A0A087X279 IFIT2 Interferon-induced protein with tetratricopeptide repeats 2 3 0 FS(0.062)S(0.341)PY(0.655)RIES(0.942)PELDCEEGWT(1)R 70.091 0.002995 7466000 2098.2 1891.4 2018.6 1765.7 1763.3 1843 1739.2 2219.5 2319.1 2262.3 TRUE FALSE FALSE 2072.626331 1918.027179 2053.732886 1969.858542 1673.312221 1725.238248 1886.927605 2283.717731 2111.673888 2203.52512 0.940595736 0.870435813 0.932021545 0.893957833 0.759379689 0.78294467 0.856322257 1.036392873 0.958316231 1 11.10559763 -10.4999853 0.713415019 0.988872695 0.859699304 0.243786698 0.073211929 0.5147908 0.565163922 0.02176169 0.022026157 3.16E-11 10.4999853 -0.129173391 FSSSIENSDS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 1 FSSSIENSDSPVR 13 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 FSSSIENSDS(1)PVR 187.08 1.71E-08 62176000 1894.5 1528.1 1895.6 1860.7 1916 2008.7 1707.1 1465.5 1961.2 1595 TRUE FALSE FALSE 1871.409105 1549.612632 1928.592123 2075.842889 1818.21937 1880.350553 1852.101031 1507.90193 1785.78536 1553.56167 1.204592738 0.997458074 1.241400428 1.336183126 1.170355452 1.210348188 1.192164474 0.970609638 1.149478257 1 10.6013638 -12.442695 0.70031605 0.972939843 1.175646384 0.018101088 0.112853837 1.095996049 0.746462262 0.139737732 0.021064107 3.61E-13 12.442695 0.202706541 FSSSSTSS(ph)SPSSLPR ddPTM_HeLa_Romidepsin_16h_R1 1 FSSSSTSSSPSSLPR 15 0 Q9NX09 Q9NX09 DDIT4 DNA damage-inducible transcript 4 protein 1 0 FSS(0.001)S(0.001)S(0.027)T(0.105)S(0.124)S(0.734)S(0.008)PSSLPR 185.66 1.41E-09 0 963.62 889.46 1140.4 950.06 431.09 573.39 417.33 377.47 1200.8 1072.1 TRUE FALSE FALSE 951.8750288 901.9818412 1160.248184 1059.910407 409.0898687 536.7522295 452.7779998 388.3914989 1093.397441 1044.246687 0.911542301 0.863763182 1.111086296 1.015000019 0.391755965 0.514009033 0.433592948 0.371934624 1.047068144 1 10.02824685 -8.761001543 24.99999992 0.965670006 0.434391335 0.930353134 0.075337042 2.196272136 125391.0993 0.01104848 0.021059132 1.73E-09 8.761001543 -0.531278672 FSSVSS(ph)PQPR ddPTM_HeLa_Romidepsin_16h_R1 4 FSSVSSPQPR 10 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 FS(0.001)S(0.002)VS(0.061)S(0.936)PQPR;FSSVS(0.265)S(0.735)PQPR;FSS(0.001)VS(0.032)S(0.968)PQPR;FSSVS(0.034)S(0.965)PQPR ;;; 121.68 0.010847 185191000 14884.5 15541.5 13085.2 12378.7 15101.2 13796.7 12261.9 13123.4 15426.6 14777 TRUE FALSE FALSE 14703.08199 15760.29364 13312.94242 13809.98354 14330.52941 12915.1354 13303.42548 13503.10487 14046.80626 14393.09141 1.021537456 1.094990172 0.924953649 0.959486961 0.995653332 0.897314901 0.924292433 0.938165714 0.975940877 1 13.81308887 -9.7212463 24.9997581 1.016816202 0.940743075 0.542265359 0.037237229 92.15498002 57319.4747 0.005610939 0.007935019 1.90E-10 9.7212463 -0.076073127 FSTLTDDPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 FSTLTDDPSPR 11 0 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 FSTLTDDPS(1)PR;FSTLT(0.001)DDPS(0.999)PR ; 132.03 0.004703 56651000 8802.2 6892 8185.2 6425.8 12527.2 15269 13889.1 15758.5 8315.3 7390.3 TRUE FALSE FALSE 8694.915401 6989.025757 8327.659972 7168.78123 11887.89024 14293.36018 15068.83981 16214.44733 7571.558742 7198.298941 1.207912518 0.970927411 1.156892766 0.995899349 1.651486044 1.985658042 2.093388998 2.252538755 1.05185389 1 12.8134403 -8.468312345 1.97584527 1.085865798 2.14717448 0.958108861 0.098690288 0.050491982 0.385788452 0.016208342 0.043441157 3.40E-09 8.468312345 1.061308683 up FSTYSQS(ph)PPDTPSLR ddPTM_HeLa_Romidepsin_16h_R1 3 FSTYSQSPPDTPSLR 15 0 H3BMG9;H3BSV5;A0A0A0MTL6;Q6ZS17-2;Q6ZS17;Q6ZS17-3;Q6ZS17-4 H3BMG9 FAM65A Protein FAM65A 1 0 FS(0.017)T(0.011)YS(0.023)QS(0.948)PPDT(0.001)PSLR;FS(0.256)T(0.156)YS(0.059)QS(0.528)PPDT(0.001)PSLR;FST(0.002)YS(0.081)QS(0.91)PPDT(0.007)PSLR ;; 238.64 1.21E-45 137676000 5946.8 5339.5 5310.2 5572.8 5720.8 5066.7 4564.3 5068.4 6723.6 5723.7 TRUE FALSE FALSE 5874.318114 5414.669621 5402.621803 6217.153357 5428.846229 4742.954222 4951.991528 5215.046157 6122.224376 5574.997449 1.05368983 0.971241632 0.969080588 1.115184969 0.973784523 0.85075451 0.888250008 0.935434716 1.098157341 1 12.44475543 -8.480416294 6.309371654 1.023232142 0.893549064 0.61867227 0.049824328 0.100537325 10.71671084 0.006371228 0.014134359 3.31E-09 8.480416294 -0.129683078 FSVCVLGDQQHCDEAK ddPTM_HeLa_Romidepsin_16h_R1 1 FSVCVLGDQQHCDEAK 16 0 P62906 P62906 RPL10A 60S ribosomal protein L10a 0 0 76.151 0.010037 562400 199.54 61.058 152.03 215.7 289.94 255.43 254.37 120.53 126.45 267.39 FALSE FALSE TRUE 197.1079297 61.91757613 154.6760184 240.6402489 275.1432799 239.1088474 275.9761815 124.0173454 115.1399953 260.4431693 0.756817429 0.237739298 0.59389547 0.923964524 1.056442681 0.91808454 1.059640697 0.476178146 0.44209259 1 8.024824789 FT(ph)S(ph)VTDS(ph)SQMEHAKK ddPTM_HeLa_Romidepsin_16h_R1 1 FTSVTDSSQMEHAKK 15 1 A0A0A0MRM2;Q86VF7-4;Q86VF7-3;Q86VF7;Q86VF7-2 A0A0A0MRM2 NRAP Nebulin-related-anchoring protein 3 0 FT(0.667)S(0.667)VT(0.667)DS(0.873)S(0.127)QMEHAKK 48.229 0.027712 9430300 809.5 628.94 883.7 9535.3 0 608.22 582.29 749.69 850.62 1129.5 TRUE FALSE FALSE 799.6335026 637.7942338 899.0804278 10637.81625 0 569.3567049 631.7496981 771.3810973 774.5384168 1100.155427 0.726836848 0.579731025 0.817230371 9.669375788 0 0.51752388 0.574236769 0.701156471 0.704026356 1 10.10349164 FT(ph)SPADLDASGAGPGPK ddPTM_HeLa_Romidepsin_16h_R1 1 FTSPADLDASGAGPGPK 17 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 0 FT(0.768)S(0.232)PADLDASGAGPGPK 125.52 0.0044706 14946000 3629.4 3562 3580.9 3112.2 3322.2 3930.3 3228.3 4488.2 4195.3 3527.8 TRUE FALSE FALSE 3585.163477 3612.145929 3643.224062 3472.047207 3152.655737 3679.166514 3502.511721 4618.058986 3820.061861 3436.147247 1.043367242 1.051219773 1.060264244 1.010447736 0.917497275 1.070724346 1.019313629 1.343964229 1.111728219 1 11.74657615 -7.261222719 24.92468774 1.021319409 1.343964329 0.777408451 0.049867032 4.592399749 527947.9999 0.005642712 0.043832212 5.48E-08 7.261222719 0.32264492 FTDEEVDELYR ddPTM_HeLa_Romidepsin_16h_R1 2 FTDEEVDELYR 11 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 0 ; ; 286.53 2.74E-105 410370000 6865.6 6518.1 6765.4 5040.4 6991.8 7431.1 6620.4 6608 7041.1 6069 FALSE FALSE TRUE 6781.919426 6609.861983 6883.148949 5623.194764 6634.982356 6956.276693 7182.736611 6799.192054 6411.326381 5911.326505 1.147275391 1.118168989 1.164400062 0.951257685 1.122418522 1.176770846 1.215080338 1.150197345 1.084583363 1 12.52926619 -16.52287875 0.227151392 0.26606037 1.151356496 0.161933538 0.070638874 40.66097615 0.52142624 13.30226785 0.051663397 3.00E-17 16.52287875 0.885296126 FTDFDEVRQEIEAETDR ddPTM_HeLa_Romidepsin_16h_R1 2 FTDFDEVRQEIEAETDR 17 1 P50570-3;P50570-2;P50570-5;P50570-4;P50570 P50570-3 DNM2 Dynamin-2 0 0 ; ; 79.471 0.021974 3164300 1035.55 963.95 828.12 1061.05 1030.99 1290.38 1049.54 1161.5 1423.11 1234.15 FALSE FALSE TRUE 1022.928318 977.5205134 842.5330812 1183.733593 978.3747331 1207.928883 1138.687901 1195.10617 1295.823477 1202.086605 0.850960583 0.813186429 0.700892163 0.984732372 0.813897043 1.004860114 0.947259454 0.994193068 1.077978468 1 10.23132512 -8.228111441 24.87985111 0.899119706 0.978619743 0.134631223 0.10376525 1077.120754 804087.7801 0.014282403 0.036410145 5.91E-09 8.228111441 0.079500037 FTDKDQQPS(ph)GS(ph)EGEDDDAEAALKK ddPTM_HeLa_Romidepsin_16h_R1 1 FTDKDQQPSGSEGEDDDAEAALKK 24 2 H3BNW0;Q9NXG2 H3BNW0 THUMPD1 THUMP domain-containing protein 1 2 0 FT(0.001)DKDQQPS(0.999)GS(1)EGEDDDAEAALKK 73.383 0.00087321 10420000 1911.1 1735.2 1705.5 1730.5 1479.7 1563.8 1594 1563.9 1910.6 2033.5 TRUE FALSE FALSE 1887.806778 1759.628191 1735.183512 1930.588552 1404.185387 1463.878227 1729.39432 1609.148979 1739.711151 1980.669377 0.953115548 0.888400766 0.876059141 0.974715202 0.708944867 0.739082577 0.873136294 0.812426848 0.878345054 1 10.95177236 -9.64143441 0.622058125 0.988820582 0.791671263 0.35251516 0.0726961 0.389064318 0.308335431 0.016282448 0.031292361 2.28E-10 9.64143441 -0.197149319 FTGS(ph)FDDDPDPHRDPYGEEVDR ddPTM_HeLa_Romidepsin_16h_R1 2 FTGSFDDDPDPHRDPYGEEVDR 22 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 FT(0.027)GS(0.973)FDDDPDPHRDPYGEEVDR;FT(0.277)GS(0.722)FDDDPDPHRDPY(0.001)GEEVDR ; 68.309 0.0014688 5409500 955.21 781.68 849.09 790.41 784.1 1021.93 1111.46 1040.12 1066.64 806.13 TRUE FALSE FALSE 943.5675331 792.6845116 863.8680553 881.8009232 744.0844511 956.6319711 1205.867385 1070.214231 971.237047 785.1866264 1.201711162 1.009549176 1.100207296 1.123046284 0.947652986 1.218349802 1.53577168 1.363006189 1.236950572 1 9.61689179 -7.94255948 4.839875592 1.084437787 1.443941518 0.703163075 0.092763642 0.076550768 3.700910559 0.012899711 0.040305073 1.14E-08 7.94255948 0.35950373 FTIGDHSR ddPTM_HeLa_Romidepsin_16h_R1 2 FTIGDHSR 8 0 D6RD66;O75083 D6RD66 WDR1 WD repeat-containing protein 1 0 0 ; ; 117.89 0.0010888 3818100 6845.8 6515 7006 6594.5 8363.1 9301.4 7654.7 7165.8 8510.3 6316.3 FALSE FALSE TRUE 6762.360756 6606.718341 7127.936491 7356.987118 7936.2998 8707.070559 8304.890027 7373.131117 7749.117454 6152.201615 1.099177364 1.073878711 1.158599301 1.195829977 1.289993452 1.415277181 1.349905375 1.198454078 1.25956819 1 12.58688707 -9.311856062 0.908680734 1.041285815 1.331925757 0.455933921 0.089765191 0.178865391 0.292693276 0.011719252 0.025077969 4.88E-10 9.311856062 0.290639942 FTPFS(ph)CLSLLS(ph)SWDY(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 FTPFSCLSLLSSWDYRR 17 1 H7C2G5 H7C2G5 SPATS2L 3 0 FT(0.138)PFS(0.867)CLS(0.113)LLS(0.878)S(0.151)WDY(0.852)RR 50.608 0.02087 8603400 2488.5 2234.6 2134.7 2037.9 1922.1 1948.9 1371.4 1767.5 3135.8 2502.4 TRUE FALSE FALSE 2458.169205 2266.058757 2171.853558 2273.531587 1824.008065 1824.37158 1487.886682 1818.639824 2855.326194 2437.387287 1.008526309 0.929708122 0.891058048 0.93277404 0.748345605 0.748494747 0.610443277 0.746143148 1.171470045 1 11.25111979 -8.822838091 0.782641838 1.003593127 0.659677662 0.794400776 0.07118138 0.150483353 0.168888768 0.008054875 0.028490224 1.50E-09 8.822838091 -0.343915466 FTPPAES(ph)GSPSKETLPPPAAPPKPGK ddPTM_HeLa_Romidepsin_16h_R1 1 FTPPAESGSPSKETLPPPAAPPKPGK 26 2 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 0 FT(0.046)PPAES(0.306)GS(0.306)PS(0.306)KET(0.035)LPPPAAPPKPGK 94.201 4.51E-06 21481000 2179.2 2046.4 2283.3 2367 1703.5 1570.1 1428.1 1601.1 2211 2052.2 TRUE FALSE FALSE 2152.639072 2075.209273 2323.039879 2640.683677 1616.564038 1469.775677 1549.402778 1647.425302 2013.242622 1998.883548 1.076920701 1.038184178 1.162168692 1.321079299 0.808733475 0.735298301 0.775134089 0.824172726 1.007183547 1 10.96497871 -8.582419513 15.23439703 1.065602314 0.776914829 0.72646814 0.093358615 0.950557976 242.7642624 0.014373413 0.028747609 2.62E-09 8.582419513 -0.288687485 FTPPAESGSPSKET(ph)LPPPAAPPKPGK ddPTM_HeLa_Romidepsin_16h_R1 1 FTPPAESGSPSKETLPPPAAPPKPGK 26 2 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 0 FT(0.026)PPAES(0.122)GS(0.122)PS(0.122)KET(0.608)LPPPAAPPKPGK 51.234 0.0082225 38222000 2485.3 2490.3 2458.4 2529.1 2285.4 1822.3 1567.2 1739 2681.6 2494 TRUE FALSE FALSE 2455.008208 2525.358509 2501.187421 2821.526442 2168.76751 1705.860911 1700.317929 1789.315221 2441.75098 2429.20552 1.010621863 1.039582072 1.029631869 1.161501741 0.892788812 0.702229966 0.699948158 0.736584536 1.005164429 1 11.24626884 -8.436904989 3.759411554 1.020248688 0.713542214 0.899725315 0.048659538 0.054203193 1.423914158 0.007187384 0.016677173 3.66E-09 8.436904989 -0.306706474 FTPVASK(ac)FSPGAPGGSGSQPNQK ddPTM_HeLa_Romidepsin_16h_R1 1 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 0 1 FTPVASK(1)FSPGAPGGSGSQPNQK 152.09 6.84E-17 676120 454.36 546.38 568.36 462.63 445.91 433.43 632.18 527.08 742.03 636 FALSE TRUE FALSE 448.8220856 554.071952 578.2520674 516.1214573 423.1535488 405.7352218 685.8773534 542.3302282 675.6609784 619.4766283 0.72451819 0.894419461 0.933452597 0.833157271 0.683082346 0.654964535 1.107188427 0.875465197 1.090696481 1 9.274906043 -12.58252896 1.372714384 0.999865845 0.825190978 0.267619809 0.129583626 0.578007518 1.955539807 0.092644468 0.021668346 2.61E-13 12.58252896 -0.174674867 FTPVASKFS(ph)PGAPGGSGSQPNQK ddPTM_HeLa_Romidepsin_16h_R1 1 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 FT(0.001)PVAS(0.062)KFS(0.935)PGAPGGS(0.001)GS(0.001)QPNQK 89.816 5.00E-05 302050000 3603.7 3565.7 3110.4 3635 2916.2 3683.6 3295 2965 3781.8 3516.7 TRUE FALSE FALSE 3559.776718 3615.898018 3164.535207 4055.295803 2767.375432 3448.229848 3574.877218 3050.787597 3443.546336 3425.335627 1.039249027 1.055633203 0.923861353 1.183911956 0.807913657 1.006683789 1.0436575 0.890653626 1.005316474 1 11.74202964 -8.753132842 24.99981218 1.024504098 0.949790566 0.226905472 0.085655709 256.1666246 770966.6966 0.011349442 0.022399027 1.77E-09 8.753132842 -0.074713532 FTPVASKFSPGAPGGS(ph)GSQPNQK ddPTM_HeLa_Romidepsin_16h_R1 1 FTPVASKFSPGAPGGSGSQPNQK 23 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 FTPVAS(0.001)KFS(0.023)PGAPGGS(0.612)GS(0.363)QPNQK 99.881 1.34E-05 249860000 4184.3 4281.9 3863.9 5309.4 4455.3 4409.3 3729.5 3576.1 5127.4 3838.9 TRUE FALSE FALSE 4133.300142 4342.180701 3931.149559 5923.297809 4227.929416 4127.55996 4046.283637 3679.568811 4668.792502 3739.164825 1.105407313 1.161270205 1.051344282 1.584123217 1.130714909 1.103872162 1.082135671 0.984061678 1.248619069 1 11.86850035 -11.1303414 0.861711345 1.016716776 1.162790532 0 0.169567429 0.793235005 1.263625997 0.050798251 0.035228717 7.41E-12 11.1303414 0.146073756 FTS(ph)PADLDASGAGPGPK ddPTM_HeLa_Romidepsin_16h_R1 3 FTSPADLDASGAGPGPK 17 0 P52735-3;P52735-2;P52735 P52735-3 VAV2 Guanine nucleotide exchange factor VAV2 1 0 FT(0.021)S(0.979)PADLDASGAGPGPK;FT(0.116)S(0.884)PADLDASGAGPGPK;FT(0.206)S(0.794)PADLDASGAGPGPK ;; 221.78 1.81E-35 22959700 8264.7 8246.5 7797.4 6668.9 8555.6 10128.4 7070.6 9966.3 9273.3 8745.8 TRUE FALSE FALSE 8163.966657 8362.594443 7933.110476 7439.989596 8118.975807 9481.227928 7671.176588 10254.65917 8443.872823 8518.582855 0.958371456 0.981688455 0.931271153 0.873383487 0.953089962 1.113005307 0.900522624 1.203798723 0.991229758 1 13.05639773 -7.250102688 24.75653865 0.972700126 1.203798879 0.5676002 0.061834122 829.7210768 1811868.805 0.008209352 0.167819291 5.62E-08 7.250102688 0.231098753 FTSQQGPIKPVS(ph)PNSSPFGTDYR ddPTM_HeLa_Romidepsin_16h_R1 1 FTSQQGPIKPVSPNSSPFGTDYR 23 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 FTS(0.001)QQGPIKPVS(0.783)PNS(0.088)S(0.088)PFGT(0.036)DY(0.005)R 56.452 0.0045702 25076000 1219.5 787.79 1053.7 794.3 1084.2 951.44 1244.8 1092 1027.5 911.03 TRUE FALSE FALSE 1204.636265 798.8805283 1072.039206 886.1407033 1028.869228 890.6460546 1350.533281 1123.595297 935.5978266 887.3613093 1.357548782 0.900287763 1.208120295 0.998624454 1.159470463 1.0037017 1.52196548 1.266220744 1.0543595 1 9.79337784 -7.761093635 24.99999953 1.134160626 1.394093113 0.396484197 0.142537404 8.341989616 602925.5018 0.022759039 0.075793163 1.73E-08 7.761093635 0.259932486 FVAFSGEGQS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 2 FVAFSGEGQSLR 12 0 Q92890;Q92890-1 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 0 FVAFS(0.008)GEGQS(0.992)LR;FVAFSGEGQS(1)LR ; 156 0.0012355 19366200 2907.4 4124.5 2367.24 2200.99 2803.6 4242.6 2896.8 3527.6 2800.2 2593.7 TRUE FALSE FALSE 2871.963491 4182.564819 2408.440819 2455.47882 2660.52183 3971.511552 3142.85412 3629.66554 2549.743099 2526.3153 1.136819102 1.655598895 0.953341342 0.971960554 1.053123429 1.572056961 1.244046663 1.436742888 1.009273505 1 11.30281899 -4 0.105800961 0.888017906 2.35834842 0.203050798 0.222044997 137.1434078 1.024383419 1.533040592 29.48633041 1.00E-04 4 1.470330514 FVEEEDDDEEEEEENLDDQDEQGNLK ddPTM_HeLa_Romidepsin_16h_R1 2 FVEEEDDDEEEEEENLDDQDEQGNLK 26 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 0 ; ; 179.7 6.32E-19 16237700 8757.8 7789 8098.2 7269.8 9748.4 10586.5 8796.3 9885 9772.9 8807.3 FALSE FALSE TRUE 8651.056565 7898.653746 8239.145774 8110.368481 9250.902772 9910.056816 9543.457502 10171.00688 8898.787347 8578.485076 1.008459709 0.920751587 0.96044298 0.945431321 1.078384201 1.155222248 1.11248751 1.185641379 1.03733786 1 13.06650718 -8.537942558 3.957978839 0.989996612 1.144963943 0.817014141 0.036625637 0.071629934 2.525677933 0.005395863 0.011716269 2.90E-09 8.537942558 0.15496733 FVGQSEGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 FVGQSEGKK 9 1 Q9NWH9;H7C3F4;Q9NWH9-3;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 1 FVGQSEGK(1)K 83.647 0.028205 1016100 681.9 522.63 494.55 542.27 542.34 716.77 513.34 252.55 850.37 632.41 FALSE TRUE FALSE 673.5887405 529.9875989 503.1574353 604.9698089 514.6623661 670.9707103 556.9430868 259.8571358 774.3107774 615.979897 1.093523902 0.860397557 0.816840676 0.982125897 0.835518121 1.089273714 0.904157895 0.421859767 1.257039038 1 9.266739458 -7.275945332 3.381095529 0.998935123 0.355730481 0.637960287 0.127919264 0.12086895 2.316358031 0.015385234 0.196179058 5.30E-08 7.275945332 -0.643204642 FVHDNYVIR ddPTM_HeLa_Romidepsin_16h_R1 1 FVHDNYVIR 9 0 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 0 99.013 0.013738 7495900 3530.5 2390 4386.1 3939 4852.8 3833.8 3518 2309.2 2925.1 2091.6 FALSE FALSE TRUE 3487.468908 2423.646483 4462.438231 4394.445714 4605.143508 3588.832553 3816.818832 2376.013059 2663.47173 2037.25993 1.711842881 1.189659918 2.190411819 2.157037326 2.260459472 1.761597771 1.873506063 1.166278796 1.307379432 1 10.99241435 -11.79416696 0.510492774 0.927783916 1.865887976 0.328382849 0.363965594 0.84428121 0.391085682 0.376054486 0.103068193 1.61E-12 11.79416696 0.938104061 FVIATSTK ddPTM_HeLa_Romidepsin_16h_R1 1 FVIATSTK 8 0 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 0 126.28 0.01697 2681900 2083.2 1602.8 2988.6 2711.7 3216.2 2955.5 2072.1 1390.6 1510.9 1070.5 FALSE FALSE TRUE 2057.809157 1625.36426 3040.615329 3025.239513 3052.065313 2766.653088 2248.104122 1430.834817 1375.76132 1042.688256 1.973561269 1.558820915 2.916130792 2.901384471 2.927112007 2.653384723 2.156065449 1.372255618 1.319436862 1 10.02609217 -11.19018183 0.604047029 1.061827404 2.458556907 0.461183959 0.516683948 0.451986399 0.367836902 0.274410098 0.152108333 6.45E-12 11.19018183 1.396729503 FVINYDYPNSSEDYIHR ddPTM_HeLa_Romidepsin_16h_R1 2 FVINYDYPNSSEDYIHR 17 0 P17844;J3KTA4;P17844-2 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 0 ; ; 138.81 0.0004174 39527000 6089.7 6009.2 5717.3 5040.3 5865.7 5469.1 4494.7 4694 6932.7 6854.6 FALSE FALSE TRUE 6015.476394 6093.797675 5816.807208 5623.083201 5566.351441 5119.642161 4876.479706 4829.813484 6312.621949 6676.516504 0.900990268 0.912721128 0.871233854 0.842218123 0.833720914 0.766813376 0.730392818 0.723403212 0.945496345 1 12.70487985 -4.683374883 0.14172331 1.044718308 3.83E-11 0.949215529 0.019660093 6.605001747 0.073768092 0.044595864 1.362165937 2.07E-05 4.683374883 -1.044718308 FVINYDYPNSSEDYVHR ddPTM_HeLa_Romidepsin_16h_R1 1 FVINYDYPNSSEDYVHR 17 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 0 84.403 0.0066946 6096900 2006.4 1515.2 1726.8 1453.9 1848.3 1762.3 1532.6 1695 1907.3 1805.2 FALSE FALSE TRUE 1981.945225 1536.531025 1756.85423 1622.006759 1753.974354 1649.694718 1662.779006 1744.042151 1736.706311 1758.300644 1.127193596 0.873872754 0.99917738 0.922485449 0.997539505 0.938232448 0.945673888 0.991890754 0.987718635 1 10.77996606 -10.26580087 24.99969519 1.060063642 0.9542202 0.345303805 0.051435509 252.3167415 1446255.918 0.009508094 0.011066871 5.42E-11 10.26580087 -0.105843441 FVNVVPTFGK ddPTM_HeLa_Romidepsin_16h_R1 1 FVNVVPTFGK 10 0 E9PR30;P62861 E9PR30 FAU 40S ribosomal protein S30 0 0 147.2 0.023989 389970 223.6 116.94 179.63 220.76 256.03 256.4 180.34 273.8 298.19 0 FALSE FALSE TRUE 220.8746772 118.5862844 182.7563848 246.2853099 242.9638337 240.0168675 195.6580751 281.721971 271.5191396 0 0 SSQPLASK(ac)QEK ddPTM_HeLa_Romidepsin_16h_R1 2 SSQPLASKQEK 11 1 P17096;P17096-3;P17096-2;A0A669KAX1 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 0 1 ; SSQPLASK(1)QEK;SSQPLASK(1)QEK 196.67 9.40E-09 219130000 9588.6 8100.2 10839 11707.5 19765 20096.5 18402.8 16994.3 9357.4 6979.2 FALSE TRUE FALSE 9471.730455 8214.234828 11027.64825 13061.17624 18756.3183 18812.39851 19965.93337 17486.00326 8520.450708 6797.879378 1.393336058 1.208352542 1.622218877 1.921360399 2.759142558 2.767392221 2.93708262 2.572273247 1.253398337 1 12.73086905 -9.080851753 1.295902096 1.184942856 2.825287852 0.952876115 0.154110239 0.068678274 0.227875508 0.029925533 0.063953964 8.30E-10 9.080851753 1.640344995 up FVQETELS(ph)QR ddPTM_HeLa_Romidepsin_16h_R1 1 FVQETELSQR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;H0YC55 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 0 FVQET(0.001)ELS(0.999)QR 101.38 0.023603 2254300 446.41 592.56 527.34 623.74 906.34 886.87 732.34 1179 624.11 534.09 TRUE FALSE FALSE 440.9689832 600.9020752 536.5181315 695.8597536 860.0860878 830.2018692 794.5449413 1213.112505 568.2880385 520.2142648 0.847667996 1.155104956 1.031340676 1.337640662 1.653330456 1.595884476 1.527341703 2.331947789 1.092411487 1 9.02296215 -6.968281366 0.383979602 0.905284718 3.371137787 0.827472357 0.172687841 1.856660484 0.159118428 0.049108723 2.203145085 1.08E-07 6.968281366 2.465853068 up FVS(ph)EGDGGR ddPTM_HeLa_Romidepsin_16h_R1 3 FVSEGDGGR 9 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 1 0 FVS(1)EGDGGR;FVS(1)EGDGGR;FVS(1)EGDGGR ;; 128.35 0.0091214 495737000 11236.2 9479.5 9559 10010.9 8265 5950.8 5495.5 5665.6 10644.9 9768.9 TRUE FALSE FALSE 11099.24887 9612.95265 9725.370385 11168.40736 7843.206209 5570.563085 5962.287633 5829.525197 9692.793483 9515.10257 1.16648757 1.01028366 1.022098324 1.173755856 0.824290243 0.585444355 0.62661307 0.612660258 1.018674619 1 13.21600349 -8.527598073 3.469460688 1.075668038 0.614409035 0.917636609 0.061481006 0.053286558 1.357490715 0.010865307 0.024219044 2.97E-09 8.527598073 -0.461259003 FVS(ph)VPIIMS(ph)S(ph)S(ph)VPEK ddPTM_HeLa_Romidepsin_16h_R1 1 FVSVPIIMSSSVPEK 15 0 H0YA93;Q86UW6-2;Q86UW6 H0YA93 N4BP2 NEDD4-binding protein 2 4 0 FVS(1)VPIIMS(1)S(1)S(1)VPEK 44.188 0.025691 6156200 1137.6 667.49 744.95 789.27 1122.2 761.99 910.66 992.67 1154.7 961.61 TRUE FALSE FALSE 1123.734494 676.8869417 757.9155423 880.529111 1064.929946 713.3012982 988.0114377 1021.39134 1051.42074 936.6272336 1.199767051 0.722685523 0.809196567 0.940106244 1.136983752 0.761563696 1.05486089 1.090499298 1.122560505 1 9.871331177 -10.28821687 24.98556163 1.094334434 0.932707608 0.253703893 0.138227856 862.7153011 804979.9905 0.025358723 0.02900269 5.15E-11 10.28821687 -0.161626826 FVTPVPGPQGK(ac)EGK ddPTM_HeLa_Romidepsin_16h_R1 1 FVTPVPGPQGKEGK 14 1 O15014;E7ERY8;O15014-2 O15014 ZNF609 Zinc finger protein 609 0 1 FVTPVPGPQGK(1)EGK 114.7 0.0082435 345600 299.2 426.75 301.8 437.19 284.6 369.15 394.1 424.17 397.52 393.11 FALSE TRUE FALSE 295.5532353 432.7577977 307.0527024 487.7399648 270.0758 345.5625064 427.5748442 436.4426897 361.9648156 382.8969455 0.771887159 1.130220031 0.801919958 1.273815241 0.705348536 0.902494811 1.116683873 1.139843749 0.94533221 1 8.580812341 -10.26446549 24.9959537 0.89228005 1.000432345 0.069598069 0.170152571 549.5517844 4539343.201 0.029207842 0.034161905 5.44E-11 10.26446549 0.108152294 FWAWDPEEERR ddPTM_HeLa_Romidepsin_16h_R1 1 FWAWDPEEERR 11 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 0 0 154.84 0.0013871 8234200 3387.9 3018.4 3105.5 2858.9 2848 3012.8 2552.6 2605.4 3055.5 2907 FALSE FALSE TRUE 3346.606972 3060.893114 3159.549925 3189.45947 2702.655933 2820.291803 2769.41778 2680.783138 2782.208427 2831.475721 1.181930308 1.081023966 1.115866861 1.126430096 0.954504364 0.996050145 0.978082828 0.94677949 0.982600136 1 11.46733844 -8.756543884 24.99537196 1.092533317 0.971455943 0.480161352 0.056577857 92.68769099 473238.9797 0.01007467 0.019655229 1.75E-09 8.756543884 -0.121077374 FWEGDFHR ddPTM_HeLa_Romidepsin_16h_R1 2 FWEGDFHR 8 0 B4DKY1;P49589-2;P49589;P49589-3 B4DKY1 CARS "Cysteine--tRNA ligase, cytoplasmic" 0 0 ; ; 135.83 0.0043452 22863000 10350.2 8694.9 11508.6 7909.1 12463.4 13884.3 11802.9 11113 10272.9 8583.5 FALSE FALSE TRUE 10224.04778 8817.30703 11708.90236 8823.587355 11827.34619 12997.13804 12805.43803 11434.53712 9354.066095 8360.499433 1.222899166 1.054638793 1.400502739 1.055389983 1.414669816 1.554588711 1.531659458 1.367685892 1.118840587 1 13.02937341 -7.657527751 0.169485362 0.933784378 1.953108783 0.551081655 0.131861903 8.173830784 0.283802854 0.294003479 1.884655479 2.20E-08 7.657527751 1.019324405 FWEVISDEHGIDPTGTYHGDSDLQLDR ddPTM_HeLa_Romidepsin_16h_R1 2 FWEVISDEHGIDPTGTYHGDSDLQLDR 27 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 0 ; ; 119.52 4.09E-10 23766600 2412.23 1848.77 2082.82 2819.81 3256.06 2894.93 2057.43 2322.89 3075.58 2626.44 FALSE FALSE TRUE 2382.828813 1874.797033 2119.070608 3145.8497 3089.891108 2709.953316 2232.188053 2390.099157 2800.492422 2558.20471 0.931445714 0.732856532 0.828342861 1.229709916 1.207835751 1.059318398 0.872560372 0.934287685 1.094710056 1 11.320916 -9.281544238 24.92338494 0.935965405 1.058380635 0.212460132 0.135564096 1153.313787 1429724.787 0.021815238 0.033350288 5.23E-10 9.281544238 0.12241523 FWEVISDEHGIDPTGTYHGDSDLQLER ddPTM_HeLa_Romidepsin_16h_R1 1 FWEVISDEHGIDPTGTYHGDSDLQLER 27 0 P04350;M0QYM7;M0R0X0;M0QY85;M0QY37;M0QX14;M0R2D3;M0QZL7;M0R278;P68371 P04350;P68371 TUBB4A;TUBB4B Tubulin beta-4A chain;Tubulin beta-4B chain 0 0 68.309 9.86E-05 9920700 846.3 983.34 909.99 842.87 1888.1 1699.5 1468.8 1661.8 1174 1145.3 FALSE FALSE TRUE 835.9849701 997.1834863 925.8279942 940.3265952 1791.743212 1590.907435 1593.559835 1709.881561 1068.9945 1115.544941 0.749396048 0.893898085 0.82993339 0.842930267 1.606159596 1.426125812 1.428503485 1.53277694 0.95827112 1 10.12353292 -8.766425192 24.9999643 0.873192581 1.488237662 0.933838221 0.080731344 27.03048127 135537.6501 0.015263204 0.028302786 1.71E-09 8.766425192 0.615045081 FY(ph)SHQLK ddPTM_HeLa_Romidepsin_16h_R1 1 FYSHQLK 7 0 Q9UI47 Q9UI47 CTNNA3 Catenin alpha-3 1 0 FY(0.932)S(0.068)HQLK 111.28 0.025617 18527000 4308.1 3268.5 8189.6 669.93 8128.7 9359 7236.7 3262.7 4287.6 2330.6 TRUE FALSE FALSE 4255.59122 3314.514029 8332.136553 747.3904587 7713.862107 8760.990105 7851.385117 3357.101077 3904.106318 2270.050676 1.874667938 1.460105743 3.670462797 0.329239548 3.398101279 3.859380849 3.458682751 1.478866138 1.719832231 1 11.14850879 -10.12244957 0.375559708 1.016355306 3.078824894 0.189462174 1.075581668 1.088581632 0.418745134 0.624215769 0.824528833 7.54E-11 10.12244957 2.062469588 FYDS(ph)NTVK ddPTM_HeLa_Romidepsin_16h_R1 1 FYDSNTVK 8 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 FYDS(0.95)NT(0.05)VK 146.71 0.007848 10103000 2505 2253.7 2880 1730.2 2545.3 2069.6 1377.2 1714.5 2058.7 1858.1 TRUE FALSE FALSE 2474.468096 2285.427648 2930.125192 1930.253865 2415.403843 1937.359239 1494.179334 1764.106352 1874.564716 1809.826294 1.36724066 1.262788399 1.619009074 1.066540955 1.334605344 1.070466953 0.825592676 0.974737939 1.035770517 1 10.82163552 -7.985785366 4.874705226 1.219233592 0.905116005 0.370810949 0.177090769 0.170180203 11.09498833 0.027802551 0.083474886 1.03E-08 7.985785366 -0.314117587 FYEEFDAHGR ddPTM_HeLa_Romidepsin_16h_R1 1 FYEEFDAHGR 10 0 K7EIT8;A8MX75;P18074-2;P18074 K7EIT8 ERCC2 TFIIH basal transcription factor complex helicase XPD subunit 0 0 123.11 0.00038808 0 2073.4 1721.5 2030.3 1438.1 2075.8 2524.6 1997.4 2635.1 1947.8 1866.8 FALSE FALSE TRUE 2048.128603 1745.735322 2065.63652 1604.379888 1969.86418 2363.286208 2167.059106 2711.342461 1773.58389 1818.300267 1.126397351 0.96009188 1.136026077 0.882351456 1.083354722 1.299722742 1.191804866 1.49114121 0.975407595 1 10.82837474 -7.231535734 0.864456626 1.047269947 1.715299427 0.6924696 0.09507147 1.0650766 0.562131561 0.01485522 0.682397436 5.87E-08 7.231535734 0.66802948 FYEEVHDLER ddPTM_HeLa_Romidepsin_16h_R1 7 FYEEVHDLER 10 0 F8VRJ2;F5H4R6;H0YHC3;F8W020;F8W118;F8VXI6;F8VUX1;F8VY35;P55209;F8VV59;B7Z9C2;H0YIV4;F8W0J6;P55209-3;P55209-2;F8W543;H0YH88;F8VVB5;E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;A8MXH2;E9PNW0;E9PJJ2 F8VRJ2;E9PNJ7 NAP1L1;NAP1L4 Nucleosome assembly protein 1-like 1;Nucleosome assembly protein 1-like 4 0 0 ;;;;;; ;;;;;; 182.46 1.29E-05 483590500 42487.2 39586 42011.6 35916 43191.9 42001.2 37225.1 37436.9 42295.7 36406.2 FALSE FALSE TRUE 41969.34966 40143.29275 42742.79427 40068.77691 40987.65617 39317.45887 40386.99906 38520.07764 38512.66666 35460.36168 1.183556729 1.132061007 1.205368255 1.129959623 1.155872479 1.108772077 1.138933647 1.086285526 1.086076533 1 15.11391963 -12.36039478 1.027411485 0.998048187 1.145880704 0.434476794 0.041160885 0.221794427 0.410130428 0.024306042 0.005989646 4.36E-13 12.36039478 0.147832517 FYEEVHDLERK ddPTM_HeLa_Romidepsin_16h_R1 1 FYEEVHDLERK 11 1 F8VRJ2;F5H4R6;H0YHC3;F8W020;F8W118;F8VXI6;F8VUX1;F8VY35;P55209;F8VV59;B7Z9C2;H0YIV4;F8W0J6;P55209-3;P55209-2;F8W543;H0YH88;F8VVB5;E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;A8MXH2;E9PNW0;E9PJJ2 F8VRJ2;E9PNJ7 NAP1L1;NAP1L4 Nucleosome assembly protein 1-like 1;Nucleosome assembly protein 1-like 4 0 0 83.499 0.010141 5059000 3455 2562.4 2095.1 6881.7 3153.4 2638.8 2455.1 2446.9 3342.3 2435.7 FALSE FALSE TRUE 3412.889131 2598.473534 2131.564337 7677.394533 2992.470231 2470.189196 2663.636133 2517.697191 3043.356317 2372.420163 1.438568591 1.095283869 0.898476741 3.236102379 1.261357612 1.041210674 1.122750588 1.061235792 1.282806631 1 11.21214382 -12.24748783 0.663904814 0.955324123 1.414364983 0.016516489 0.64261134 2.731473481 1.829954856 0.731268274 0.13931087 5.66E-13 12.24748783 0.45904086 FYFHDGVR ddPTM_HeLa_Romidepsin_16h_R1 2 FYFHDGVR 8 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 0 ; ; 148.04 0.0035076 29975000 12082.4 11099.2 17340.8 10356.6 12690.9 15034.3 10645 11264.1 11276.3 8833.6 FALSE FALSE TRUE 11935.13506 11255.45483 17642.60935 11554.07882 12043.23602 14073.65675 11549.18603 11590.00896 10267.71949 8604.101799 1.387144799 1.308149891 2.050488216 1.342857057 1.399708685 1.635691567 1.3422884 1.347032989 1.193351697 1 13.07080888 -11.59204234 0.692907569 1.01179227 1.494726581 0.323327389 0.21754459 0.482030022 0.467387563 0.116559874 0.048604583 2.56E-12 11.59204234 0.482934311 FYGDEEK(ac)DK ddPTM_HeLa_Romidepsin_16h_R1 2 FYGDEEKDK 9 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 1 ; FYGDEEK(1)DK;FYGDEEK(1)DK 157.96 0.0082369 11361200 3243.2 2872.5 4131.3 2366.3 10369.6 9805.1 9518.1 7621.5 9449.8 6440 FALSE TRUE FALSE 3203.670631 2912.93913 4203.203544 2639.90274 9840.400618 9178.585755 10326.56718 7842.016078 8604.586221 6272.687872 0.510733309 0.464384517 0.670080136 0.420856704 1.568769373 1.463261993 1.646274673 1.250184329 1.371754246 1 12.61486806 -8.751851154 24.99548869 0.708200586 1.492500728 0.622957718 0.282302252 83.03684433 216466.7282 0.035405656 0.07009016 1.77E-09 8.751851154 0.784300142 FYHDWNDKEIEVLNK ddPTM_HeLa_Romidepsin_16h_R1 2 FYHDWNDKEIEVLNK 15 1 J3KQ32;Q9NTK5-3;Q9NTK5;C9JCJ9;Q9NTK5-2 J3KQ32 OLA1 Obg-like ATPase 1 0 0 ; ; 114.87 0.0015634 35179000 16964 15024.8 15916.6 16734.5 18116.6 18188.7 16458.6 17732.7 18345.2 15937.1 FALSE FALSE TRUE 16757.23624 15236.31953 16193.62175 18669.42163 17192.0423 17026.50077 17856.59307 18245.7677 16704.35937 15523.05184 1.079506556 0.981528612 1.043198329 1.202690155 1.107516903 1.096852664 1.150327478 1.175398232 1.076100211 1 13.9221246 -9.362221824 7.384282983 1.033468404 1.141659472 0.6567009 0.039880133 0.139935125 9.049750416 0.006621458 0.01012992 4.34E-10 9.362221824 0.108191069 FYQGLPWGVSS(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 2 FYQGLPWGVSSLPR 14 0 Q5JTC6 Q5JTC6 AMER1 APC membrane recruitment protein 1 1 0 FYQGLPWGVS(0.024)S(0.976)LPR;FYQGLPWGVS(0.026)S(0.974)LPR ; 177.21 4.45E-07 20535900 5713.8 5669.9 4930.3 4487.5 3921.8 4059.9 3402 3769.7 5665.9 5118.5 TRUE FALSE FALSE 5644.158008 5749.721001 5016.109803 5006.365864 3721.655912 3800.485493 3690.965795 3878.770322 5159.127713 4985.520632 1.132110049 1.153283965 1.006135602 1.004181155 0.746492932 0.762304636 0.740337082 0.778007075 1.034822257 1 12.28352846 -8.84557506 3.108164561 1.067093509 0.752801198 0.903777748 0.04789801 0.068112605 1.323722617 0.009318265 0.018215651 1.43E-09 8.84557506 -0.314292311 GAAAS(ph)PPRELTEPAAR ddPTM_HeLa_Romidepsin_16h_R1 1 GAAASPPRELTEPAAR 16 1 F8WC22;F8WD19;C9J4K5;C9JSP0;H7C1C1;F8W8A5;Q9NYP3-2;Q9NYP3-3;Q9NYP3 F8WC22 DONSON Protein downstream neighbor of Son 1 0 GAAAS(0.999)PPRELT(0.001)EPAAR 64.89 0.019596 10904000 1559.2 1499.2 1554.6 1396.2 889.57 925.38 539.27 894.53 1807.2 1561.8 TRUE FALSE FALSE 1540.195871 1520.305777 1581.657161 1557.635213 844.1719235 866.2512045 585.0755803 920.4118142 1645.559506 1521.224211 1.012471311 0.999396253 1.039726524 1.023935329 0.554929324 0.569443477 0.384608381 0.605046782 1.081733708 1 10.57101709 -8.742746318 6.019029878 1.009871368 0.517505621 0.943846994 0.059398023 0.022814195 2.738601319 0.007330372 0.014385629 1.81E-09 8.742746318 -0.492365747 GAADEVEVEPPEPPGPVAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 GAADEVEVEPPEPPGPVASR 20 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 0 GAADEVEVEPPEPPGPVAS(1)R;GAADEVEVEPPEPPGPVAS(1)R ; 143.69 4.26E-05 5302300 2452.63 2048.88 2075.46 1172.8 2649.05 2858.7 2354.71 2544.2 2152.88 2226.77 TRUE FALSE FALSE 2422.736402 2077.724186 2111.582511 1308.404654 2513.859094 2676.038296 2554.719009 2617.812413 1960.321021 2168.918194 1.117025256 0.957954151 0.973564847 0.603252192 1.159038225 1.233812461 1.17787707 1.206966874 0.903824324 1 11.08275992 -8.544618114 24.99774758 1.008091567 1.202225036 0.411255036 0.13857039 227.1779935 261227.3097 0.021181408 0.042365155 2.85E-09 8.544618114 0.194133469 GAAEEAELEDS(ph)DDEEKPVK ddPTM_HeLa_Romidepsin_16h_R1 2 GAAEEAELEDSDDEEKPVK 19 1 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 GAAEEAELEDS(1)DDEEKPVK;GAAEEAELEDS(1)DDEEKPVK ; 76.78 0.0039915 20229300 3152.26 3303.9 3857.2 2180.69 3237.2 4268.2 3801.5 3975 3673.9 3836.8 TRUE FALSE FALSE 3113.839043 3350.412391 3924.332948 2432.831638 3071.993604 3995.475795 4124.399315 4090.010353 3345.297183 3737.119383 0.833219045 0.896522708 1.050095688 0.650991148 0.822021801 1.069132502 1.103630602 1.094428605 0.895153951 1 11.86771094 -8.156717048 5.980111036 0.901221484 1.095002705 0.459499929 0.102859198 0.193685881 9.352147187 0.016023528 0.041601057 6.97E-09 8.156717048 0.19378122 GAAEEAELEDS(ph)DDEEKPVKQDDFPKDFGPR ddPTM_HeLa_Romidepsin_16h_R1 1 GAAEEAELEDSDDEEKPVKQDDFPKDFGPR 30 3 Q9UBB9;F6XM96 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 GAAEEAELEDS(1)DDEEKPVKQDDFPKDFGPR 61.583 0.0002174 10386000 1418 1304.8 975.73 1809.1 1234.9 1200 1416.7 1137 1593.2 1229.4 TRUE FALSE FALSE 1400.716871 1323.169009 992.7121714 2018.276654 1171.878445 1123.323873 1537.034463 1169.897301 1450.700202 1197.460011 1.169739998 1.104979704 0.829014884 1.685464764 0.97863681 0.93808884 1.283578949 0.976982355 1.211481126 1 10.22576176 -12.43651419 1.044107904 0.996327561 1.128154375 0 0.234608902 1.65196355 3.07310701 0.167971914 0.037540048 3.66E-13 12.43651419 0.131826814 GAAIPAK(ac)GAK ddPTM_HeLa_Romidepsin_16h_R1 2 GAAIPAKGAK 10 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; GAAIPAK(1)GAK;GAAIPAK(1)GAK 152.63 0.012893 4199500 1853.26 1849.8 5392.9 5090.7 14834.3 22263 18383.5 10702.5 2026.61 1030.01 FALSE TRUE FALSE 1830.671754 1875.841533 5486.761162 5679.310686 14077.25032 20840.46615 19944.99403 11012.15995 1845.344926 1003.250192 1.824740996 1.86976444 5.46898591 5.660911638 14.03164478 20.77295008 19.88037899 10.97648427 1.839366632 1 9.970465716 -8.844825229 1.714463278 1.627001948 17.66762007 0.858042721 2.724692141 0.084025931 0.499890021 0.411333524 0.911803018 1.43E-09 8.844825229 16.04061812 GAANASGS(ph)SPDAPAKDAR ddPTM_HeLa_Romidepsin_16h_R1 1 GAANASGSSPDAPAKDAR 18 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 GAANAS(0.037)GS(0.481)S(0.481)PDAPAKDAR 100.76 0.00073605 9236600 1779.4 1424 1632.7 2232.1 1631.1 1625.2 1432.7 1361.7 2092.1 1912.9 TRUE FALSE FALSE 1757.711988 1444.047109 1661.116459 2490.185904 1547.858881 1521.354965 1554.393502 1401.098641 1904.977336 1863.202582 0.943382113 0.775034944 0.891538298 1.336508401 0.83075179 0.816526866 0.834258989 0.751984059 1.02242094 1 10.86356883 -8.554747243 24.99956782 0.97647911 0.807486514 0.306895816 0.136034589 195.7368052 153547.0238 0.019395268 0.038790772 2.79E-09 8.554747243 -0.168992596 GAANASGSS(ph)PDAPAK ddPTM_HeLa_Romidepsin_16h_R1 4 GAANASGSSPDAPAK 15 0 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 GAANAS(0.009)GS(0.231)S(0.76)PDAPAK;GAANASGS(0.011)S(0.989)PDAPAK;GAANASGS(0.014)S(0.986)PDAPAK;GAANASGS(0.099)S(0.901)PDAPAK ;;; 223.68 1.27E-34 61112000 24451.6 22849.4 26102.5 17763.9 22211.6 23954.9 19676.8 19006.4 26396.1 25088.8 TRUE FALSE FALSE 24153.57449 23171.07445 26556.80306 19817.8457 21078.05917 22424.2592 21348.1469 19556.3202 24035.16671 24436.98936 0.988402218 0.948196773 1.086746107 0.810977384 0.862547299 0.91763592 0.873599713 0.800275349 0.983556786 1 14.57677894 -9.250258756 24.99711939 0.996460577 0.858271661 0.731534903 0.044835836 293.878683 657040.4718 0.006347967 0.010462414 5.62E-10 9.250258756 -0.138188916 GAANASGSS(ph)PDAPAKDAR ddPTM_HeLa_Romidepsin_16h_R1 1 GAANASGSSPDAPAKDAR 18 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 GAANAS(0.004)GS(0.173)S(0.823)PDAPAKDAR 102.15 0.00069783 10794000 1819 1588.1 1350.8 1785.7 1318.3 1367.1 1064.7 1055.2 1791.7 1356.6 TRUE FALSE FALSE 1796.829328 1610.457313 1374.310107 1992.171036 1251.022232 1279.746722 1155.135591 1085.730547 1631.445865 1321.355336 1.359838099 1.218792 1.040076102 1.507672449 0.946771998 0.968510655 0.874205113 0.821679466 1.234676108 1 10.36780277 -8.550977055 24.99969355 1.189800445 0.898555943 0.54835591 0.142354471 158.0785764 140645.4596 0.024650307 0.049301321 2.81E-09 8.550977055 -0.291244502 GAAPNVVYTYTGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GAAPNVVYTYTGKR 14 1 F8W084;A0A3B3ISW1;F8WJN3;Q16630-3;Q16630;Q16630-2 F8W084 CPSF6 Cleavage and polyadenylation specificity factor subunit 6 0 1 ; GAAPNVVYTYTGK(1)R;GAAPNVVYTYTGK(1)R 219.43 5.57E-25 2504100 411.02 61.305 169.26 343.37 69.831 358.82 334.75 308.22 452.46 364.75 FALSE TRUE FALSE 406.0103301 62.1680534 172.2058993 383.072055 66.26726349 335.89256 363.1836566 317.1378594 411.9908444 355.2737424 1.142809844 0.174986344 0.484713275 1.078244771 0.186524518 0.945447186 1.02226428 0.89265775 1.159643383 1 8.472787256 GAAPT(ph)PPGK ddPTM_HeLa_Romidepsin_16h_R1 1 GAAPTPPGK 9 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;H0YAB7;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 GAAPT(1)PPGK 143.4 0.012687 16661000 5158.2 5093.5 4935.7 9470.3 4925.3 5625.3 4232.1 4233.9 5416.8 5462.6 TRUE FALSE FALSE 5095.329874 5165.206427 5021.603788 10565.30065 4673.943562 5265.861485 4591.574468 4356.401217 4932.307841 5320.680865 0.957646212 0.970779221 0.943789698 1.985704633 0.878448394 0.989696924 0.862967463 0.818767622 0.927006894 1 12.37739516 -7.852042022 2.224761755 1.045493434 0.826971288 0.083972308 0.308362851 0.753713066 7.194212282 0.043921339 0.202415207 1.41E-08 7.852042022 -0.218522146 GAAS(ph)PVPPPLVR ddPTM_HeLa_Romidepsin_16h_R1 2 GAASPVPPPLVR 12 0 Q4G0W2 Q4G0W2 DUSP28 Dual specificity phosphatase 28 1 0 GAAS(1)PVPPPLVR;GAAS(1)PVPPPLVR ; 101.39 0.014905 12030100 3738 3760.6 3187.7 2900.1 3210.4 2828 2249.3 2956.2 3849.4 3109.1 TRUE FALSE FALSE 3692.439818 3813.541826 3243.180581 3235.423207 3046.561308 2647.299927 2440.355486 3041.732983 3505.100023 3028.325134 1.219300985 1.259290749 1.070948606 1.068387001 1.006021868 0.874179558 0.805843289 1.00442748 1.157438474 1 11.56430439 -8.600380889 1.890419315 1.116686961 0.885489859 0.61296915 0.083860253 0.227469149 1.628124068 0.016107321 0.04012003 2.51E-09 8.600380889 -0.231197103 GAASTLVPGVSET(ph)SASPGSPSVR ddPTM_HeLa_Romidepsin_16h_R1 1 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 GAASTLVPGVS(0.007)ET(0.973)S(0.015)AS(0.005)PGSPSVR 208.4 1.44E-26 13676000 3549 3430.8 3298.6 3321.8 3090 2898.4 2183 2998.5 3941.8 3297.2 TRUE FALSE FALSE 3505.743423 3479.098892 3356.010749 3705.882146 2932.30577 2713.201594 2368.423966 3085.256867 3589.235536 3211.538269 1.091608796 1.083312295 1.044985446 1.153927444 0.913053348 0.84482929 0.737473375 0.960678843 1.117606342 1 11.64904877 -8.571996478 5.479673275 1.054536473 0.842508502 0.717126178 0.066580118 0.079486891 5.358282744 0.009530174 0.01950173 2.68E-09 8.571996478 -0.212027971 GAASTLVPGVSETS(ph)ASPGSPSVR ddPTM_HeLa_Romidepsin_16h_R1 1 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 GAASTLVPGVS(0.155)ET(0.169)S(0.292)AS(0.292)PGS(0.079)PS(0.012)VR 85.287 0.00026807 14715000 3467.5 3780.3 3711.4 3469.3 3052.2 2775.4 2612.3 3019.7 4158.5 3727 TRUE FALSE FALSE 3425.236776 3833.519163 3775.99536 3870.43679 2896.434845 2598.060897 2834.188697 3107.070255 3786.553345 3630.172003 0.94354669 1.056015847 1.04016982 1.06618551 0.797878129 0.715685344 0.780731242 0.855901663 1.043078218 1 11.82582219 -8.70836973 8.294351191 0.990924913 0.780963939 0.823308135 0.052432779 0.096355209 13.48260029 0.008116849 0.016225259 1.96E-09 8.70836973 -0.209960973 GAASTLVPGVSETSAS(ph)PGSPSVR ddPTM_HeLa_Romidepsin_16h_R1 1 GAASTLVPGVSETSASPGSPSVR 23 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 GAASTLVPGVSET(0.016)S(0.009)AS(0.519)PGS(0.228)PS(0.228)VR 96.38 2.85E-05 4176000 3921.5 3316.9 3912.4 3330.8 2982 3724.9 3312.7 3684.2 3855.8 3356.1 TRUE FALSE FALSE 3873.70325 3363.595405 3980.493681 3715.922768 2829.817413 3486.890912 3594.080655 3790.796514 3510.927591 3268.908038 1.185014447 1.028966054 1.21768298 1.136747417 0.865676666 1.066683697 1.099474385 1.159652236 1.074036819 1 11.67459308 GADAGSSGGTGPTEGY(ph)SPPAASTR ddPTM_HeLa_Romidepsin_16h_R1 1 GADAGSSGGTGPTEGYSPPAASTR 24 0 J3KT76;J3KSI9;Q969W3;Q969W3-2 J3KT76 FAM104A Protein FAM104A 1 0 GADAGSSGGTGPT(0.007)EGY(0.734)S(0.258)PPAASTR 137.21 0.00010216 10397000 1824.6 1221.9 1136.3 562.18 1479.4 1782.8 1333.9 1547.9 1445.5 1371.5 TRUE FALSE FALSE 1802.361073 1239.10194 1156.076825 627.1818967 1403.900698 1668.884834 1447.201433 1592.686044 1316.21086 1335.868232 1.34920573 0.927562996 0.865412319 0.469493833 1.050927527 1.24928851 1.083341454 1.192247862 0.985284946 1 10.38356199 -10.22910349 24.78211922 1.164902738 0.97051103 0.054831725 0.22436872 974.7530732 747048.9194 0.041626078 0.050978885 5.90E-11 10.22910349 -0.194391708 GADAGSSGGTGPTEGYS(ph)PPAASTR ddPTM_HeLa_Romidepsin_16h_R1 3 GADAGSSGGTGPTEGYSPPAASTR 24 0 J3KT76;J3KSI9;Q969W3;Q969W3-2 J3KT76 FAM104A Protein FAM104A 1 0 GADAGSSGGTGPT(0.014)EGY(0.288)S(0.696)PPAASTR;GADAGSSGGT(0.002)GPT(0.086)EGY(0.107)S(0.786)PPAAS(0.014)T(0.005)R;GADAGSSGGTGPT(0.002)EGYS(0.998)PPAASTR ;; 220.91 1.75E-46 21772500 4730.26 4605.24 5013.18 4102.91 5187.1 5799.8 4691.97 4566.94 5405.29 4665.79 TRUE FALSE FALSE 4672.605772 4670.07269 5100.432295 4577.307759 4922.382931 5429.211498 5090.505815 4699.077203 4921.827325 4544.572103 1.028172876 1.02761549 1.122312988 1.007203243 1.083134522 1.194658457 1.120128738 1.033997722 1.083012264 1 12.14992875 -9.64940273 0.610781957 1.006551846 1.112892857 0.147826591 0.054470014 0.556142345 0.426307375 0.012514275 0.024024777 2.24E-10 9.64940273 0.106341011 GADFLVTEVENGGSLGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GADFLVTEVENGGSLGSK 18 0 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 1 0 GADFLVTEVENGGS(0.222)LGS(0.778)K 140.28 0.00050202 5561900 3455 2883.4 3402.7 2378.8 3134.5 3064.8 2941.7 3355.9 3771.7 3203.4 TRUE FALSE FALSE 3412.889131 2923.992581 3461.922566 2653.848049 2974.534769 2868.969171 3191.567925 3452.997672 3434.349706 3120.175206 1.093813298 0.937124484 1.10952826 0.85054456 0.953322994 0.919489766 1.022880997 1.106667877 1.100691301 1 11.60741133 -9.292011573 24.98896595 1.04013004 0.9696895 0.191690625 0.078842918 960.5494224 785127.0589 0.012097184 0.018480035 5.10E-10 9.292011573 -0.07044054 GADFLVTEVENGGSLGS(ph)KK ddPTM_HeLa_Romidepsin_16h_R1 1 GADFLVTEVENGGSLGSKK 19 1 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 1 0 GADFLVT(0.009)EVENGGS(0.06)LGS(0.931)KK 52.321 0.0040695 0 943.7 632.93 863.97 645.27 704.36 699.85 660.33 823.15 954.39 971.94 TRUE FALSE FALSE 932.1978214 641.8404052 879.0070354 719.8791535 668.4138809 655.1318437 716.4184137 846.9665465 869.0269681 946.6888587 0.984692925 0.677984534 0.928506792 0.7604179 0.706054449 0.692024457 0.756762274 0.894661999 0.917964715 1 9.886746533 -10.28076924 22.79333609 0.9927717 0.772807825 0.541345116 0.080739461 113.8944066 134301.2224 0.012804555 0.014659395 5.24E-11 10.28076924 -0.219963875 GADFLVTEVENGGSLGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GADFLVTEVENGGSLGSK 18 0 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 112.96 0.013795 8722800 1042.8 806.71 1063.4 645.12 971.05 905.6 984.71 753.74 990.43 1184.5 FALSE FALSE TRUE 1030.089952 818.0668846 1081.908031 719.7118098 921.493695 847.7350827 1068.351243 775.5482777 901.8434602 1153.726519 0.892837198 0.709064818 0.937750856 0.623814914 0.798710682 0.734779923 0.926000421 0.672211538 0.781678713 1 10.17208557 -10.77204096 0.76378175 0.983219252 0.769860368 0.063750554 0.115752948 0.3449984 0.43897967 0.027440816 0.023348267 1.69E-11 10.77204096 -0.213358884 GADGVMRTMNTEK ddPTM_HeLa_Romidepsin_16h_R1 1 GADGVMRTMNTEK 13 1 E9PI56;E9PKP6;E9PLJ8;Q13492-4;Q13492-3;Q13492-2;Q13492-5;Q13492 E9PI56 PICALM Phosphatidylinositol-binding clathrin assembly protein 0 0 58.699 0.0041778 0 825.03 472.49 1150.8 214.51 546.94 521.68 729.93 431.66 789.42 571.61 FALSE FALSE TRUE 814.974217 479.1417266 1170.829191 239.3126555 519.0276109 488.3463316 791.930236 444.1494011 718.8122981 556.7594898 1.463781457 0.860590139 2.102935312 0.4298313 0.932229482 0.877122601 1.422391985 0.797740154 1.291064295 1 9.120910433 GADNDGS(ph)GSES(ph)GYTTPK ddPTM_HeLa_Romidepsin_16h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 0 GADNDGS(0.933)GS(0.464)ES(0.598)GYT(0.004)TPK 148.36 0.00128 29897000 5729.2 5246.6 4792.5 4859.3 4218.4 3756.3 3155.9 3311.4 5193.8 5546.3 TRUE FALSE FALSE 5659.370307 5320.461773 4875.911452 5421.15513 4003.119307 3516.284553 3423.962067 3407.210134 4729.25352 5402.206326 1.04760351 0.984868302 0.902577791 1.003507605 0.741015627 0.650897863 0.633808089 0.630707146 0.875430007 1 12.39933303 -8.652492291 1.792716553 1.013165317 0.628968524 0.857092908 0.060126151 0.058344957 0.377603664 0.006723063 0.016517567 2.23E-09 8.652492291 -0.384196793 GADNDGS(ph)GSESGYTTPK ddPTM_HeLa_Romidepsin_16h_R1 2 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGS(0.906)GS(0.064)ES(0.03)GYTTPK;GADNDGS(0.715)GS(0.031)ES(0.252)GYT(0.001)TPK ; 113.28 0.0020469 238323900 6687 6852.1 6169.3 3736.5 5341.7 5703.4 4338.8 4687.1 7269.3 7447.6 TRUE FALSE FALSE 6605.496272 6948.564044 6276.674079 4168.531711 5069.093116 5338.971147 4707.337564 4822.713843 6619.115602 7254.110278 0.910586691 0.957879571 0.865257604 0.574644105 0.698789089 0.735992553 0.648920044 0.664824997 0.912464154 1 12.82458296 -9.453200608 4.197535472 0.955461228 0.670441472 0.893327228 0.046211456 0.054091077 1.839139422 0.007935047 0.012139192 3.52E-10 9.453200608 -0.285019755 GADNDGSGS(ph)ESGYTT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 0 GADNDGS(0.317)GS(0.52)ES(0.147)GY(0.005)T(0.02)T(0.992)PK;GADNDGS(0.002)GS(0.52)ES(0.316)GY(0.002)T(0.173)T(0.986)PK ; 102.84 0.011977 40780500 5670.2 5899.8 5305.8 5165.8 4459.8 4229.6 3286.27 2990.65 5908.7 5781.7 TRUE FALSE FALSE 5601.089421 5982.857539 5398.145223 5763.094102 4232.199764 3959.34221 3565.405692 3077.179739 5380.211073 5631.490601 0.994601575 1.062393239 0.95856419 1.023369213 0.751523897 0.703071796 0.633119354 0.546423666 0.955379571 1 12.45930112 -8.466397812 1.453809777 1.003794902 0.59487091 0.92776087 0.047345316 0.064898923 0.263911463 0.006296199 0.019891032 3.42E-09 8.466397812 -0.408923992 GADNDGSGS(ph)ESGYTTPK ddPTM_HeLa_Romidepsin_16h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGS(0.303)GS(0.688)ES(0.009)GYTTPK 213.69 1.39E-26 216280000 6640.6 6043.3 5576.1 5505.2 5285.2 5011.8 4471 4543.3 6798.2 6080.9 TRUE FALSE FALSE 6559.661813 6128.377736 5673.149681 6141.737127 5015.476522 4691.562155 4850.766628 4674.753217 6190.151966 5922.917341 1.10750521 1.034689053 0.957830298 1.036944596 0.846791578 0.792103263 0.818982665 0.789265314 1.04511875 1 12.53209224 -8.712390853 3.087999063 1.043252403 0.802403079 0.889264461 0.037829334 0.072471109 1.408018482 0.00745615 0.015492471 1.94E-09 8.712390853 -0.240849323 GADNDGSGS(ph)ESGYTTPKK ddPTM_HeLa_Romidepsin_16h_R1 2 GADNDGSGSESGYTTPKK 18 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGS(0.286)GS(0.69)ES(0.021)GY(0.002)T(0.001)TPKK;GADNDGS(0.422)GS(0.577)ES(0.001)GYTTPKK ; 96.708 0.00099013 15915000 2390.7 2558.1 2136.7 2536.8 2316 1786.91 1798.48 1988.76 2728.8 2401.7 TRUE FALSE FALSE 2361.561229 2594.112999 2173.888367 2830.116752 2197.805878 1672.732218 1951.242846 2046.301633 2484.729294 2339.303488 1.009514687 1.108925376 0.92928873 1.20981171 0.939512932 0.715055668 0.834112742 0.87474825 1.062166284 1 11.19186333 -8.515509618 24.99317976 1.022057612 0.813369254 0.630757078 0.082170237 166.8576389 565914.8176 0.010900007 0.022558367 3.05E-09 8.515509618 -0.208688357 GADNDGSGSES(ph)GYTT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 2 0 GADNDGS(0.137)GS(0.422)ES(0.408)GY(0.033)T(0.059)T(0.94)PK 106.35 0.010169 10381000 4242.9 4515.9 3926 3729.5 3213.8 3380.8 2620.4 2279.2 5125.1 4465.9 TRUE FALSE FALSE 4191.185903 4579.474959 3994.330383 4160.722338 3049.787794 3164.777791 2842.976711 2345.145056 4666.69822 4349.875274 0.963518639 1.05278305 0.918263199 0.95651532 0.701120745 0.727555985 0.653576604 0.539129264 1.072834949 1 12.08675832 -8.499679446 0.977877913 0.989312267 0.580670828 0.893718828 0.057752285 0.122163953 0.209376657 0.00796864 0.033076381 3.16E-09 8.499679446 -0.408641439 GADNDGSGSESGYT(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 1 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGSGSESGY(0.034)T(0.483)T(0.483)PK 93.427 0.014603 3367100 1792 1716.2 1780.7 1602.3 1411.5 1426.2 1292.2 1256.5 2144.8 1847.6 TRUE FALSE FALSE 1770.158415 1740.360709 1811.692337 1787.565465 1339.465888 1335.070423 1401.959436 1292.854845 1952.963716 1799.599086 0.983640428 0.967082459 1.006719969 0.993313166 0.744313497 0.741871028 0.779039869 0.718412704 1.085221554 1 10.81345982 -8.761671411 24.99999999 0.991264113 0.747987263 0.932371296 0.034176159 0.548406259 59097.35253 0.002391318 0.004540515 1.73E-09 8.761671411 -0.24327685 GADNDGSGSESGYT(ph)TPKK ddPTM_HeLa_Romidepsin_16h_R1 1 GADNDGSGSESGYTTPKK 18 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGS(0.007)GS(0.03)ES(0.304)GY(0.083)T(0.524)T(0.052)PKK 75.225 0.0074087 3932500 1763 1905.8 1549.8 1728.3 1698.2 1529.2 1295.4 1686.8 1687.2 2055.9 TRUE FALSE FALSE 1741.511878 1932.629902 1576.773619 1928.134178 1611.534517 1431.489055 1405.431244 1735.604897 1536.292606 2002.487422 0.869674316 0.965114628 0.787407502 0.962869558 0.804766362 0.714855454 0.701842732 0.866724494 0.767192138 1 10.96757747 -4.959555717 0.050774906 1.355713936 6.63E-06 0 0.102408898 205.3510849 0.946039455 6.670915735 23.26572603 1.10E-05 4.959555717 -1.355707303 GADNDGSGSESGYTT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 GADNDGSGSESGYTTPK 17 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 GADNDGSGSES(0.001)GYT(0.218)T(0.781)PK;GADNDGSGSESGYT(0.012)T(0.988)PK;GADNDGSGSESGYT(0.071)T(0.929)PK ;; 211.45 3.85E-26 54820200 11141.4 11085.3 10911 10713.7 8868.8 9115.3 7970.5 8650.7 12878.2 11816.6 TRUE FALSE FALSE 11005.60433 11241.35914 11100.90138 11952.4684 8416.192042 8532.861748 8647.514071 8900.994356 11726.34154 11509.60303 0.956210593 0.976693907 0.964490378 1.038477902 0.731232174 0.741368901 0.75133035 0.773353723 1.018831102 1 13.49055045 -8.755435086 24.99999672 0.981082534 0.748896719 0.952970095 0.026387556 21.24019938 88436.65105 0.003720227 0.007287853 1.76E-09 8.755435086 -0.232185815 GADS(ph)GEEKEEGINR ddPTM_HeLa_Romidepsin_16h_R1 2 GADSGEEKEEGINR 14 1 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 0 GADS(1)GEEKEEGINR;GADS(1)GEEKEEGINR ; 172.09 0.00025893 70655000 4945.8 4599.8 4895.4 3117.39 4599.9 4643.5 3795.6 4364.3 4593.5 4639.5 TRUE FALSE FALSE 4885.518687 4664.556105 4980.602383 3477.8373 4365.149938 4346.795336 4117.998169 4490.574135 4182.645855 4518.965121 1.081114493 1.032217771 1.102155527 0.769609237 0.965962299 0.961900617 0.911270182 0.99371737 0.925576043 1 12.14177671 -9.300867235 24.99998537 1.043077239 0.924806061 0.344985385 0.072667124 355.1283639 225175.0143 0.009636149 0.014719623 5.00E-10 9.300867235 -0.118271178 GADS(ph)GEEKEEGINREDK ddPTM_HeLa_Romidepsin_16h_R1 1 GADSGEEKEEGINREDK 17 2 Q9BVG4 Q9BVG4 PBDC1 Protein PBDC1 1 0 GADS(1)GEEKEEGINREDK 84.895 0.012541 74368000 3475.5 3066.8 3197.9 2773.5 3144.7 3014.5 2619.4 3249.5 4030.6 3959.3 TRUE FALSE FALSE 3433.139269 3109.974491 3253.558108 3094.18512 2984.214225 2821.883179 2841.891771 3343.519156 3670.093041 3856.436815 0.8902361 0.806437299 0.843669497 0.802343009 0.773826817 0.731733285 0.736921647 0.866997002 0.951679806 1 11.91305276 -10.71882829 0.47819077 0.998955626 0.766334977 0.76362883 0.040852761 0.241835396 0.138826104 0.020690719 0.016169109 1.91E-11 10.71882829 -0.232620649 GAEAFGDS(ph)EEDGEDVFEVEK ddPTM_HeLa_Romidepsin_16h_R1 2 GAEAFGDSEEDGEDVFEVEK 20 0 Q99549-2;Q99549 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 0 GAEAFGDS(1)EEDGEDVFEVEK;GAEAFGDS(1)EEDGEDVFEVEK ; 226.23 3.02E-42 20385100 9746.3 9654.5 9173.4 7072.4 7001.4 7865.1 6902.7 7506.2 10702.4 9293.1 TRUE FALSE FALSE 9627.508347 9790.416304 9333.059179 7890.144165 6644.092432 7362.545493 7489.015166 7723.380054 9745.150539 9051.663922 1.063617522 1.081615092 1.031087683 0.871678868 0.734018904 0.813391389 0.82736337 0.853255282 1.076614269 1 13.1439673 -9.169299101 3.556644088 1.035928768 0.808504434 0.904118784 0.037798449 0.059578442 1.424332699 0.006251289 0.010653459 6.77E-10 9.169299101 -0.227424334 GAEDDELEEEADWIYR ddPTM_HeLa_Romidepsin_16h_R1 2 GAEDDELEEEADWIYR 16 0 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 0 ; ; 192.15 9.48E-12 8675200 1458.11 1366.32 1388.36 1113.81 1780.82 1704.92 1521.79 1953.35 1677.8 1631.87 FALSE FALSE TRUE 1440.337994 1385.555089 1412.523823 1242.593953 1689.93811 1595.981114 1651.050805 2009.8671 1527.733366 1589.473782 0.906172855 0.87170679 0.888673874 0.781764359 1.06320603 1.004094017 1.038740508 1.264485846 0.961156694 1 10.6343335 -6.574880916 0.913537031 0.936265178 2.055363225 0.673441667 0.071697902 3.187991879 0.820171876 0.012167477 4.804298552 2.66E-07 6.574880916 1.119098047 GAEDDRGPWR ddPTM_HeLa_Romidepsin_16h_R1 1 GAEDDRGPWR 10 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 0 104.42 0.002523 0 2804.9 2721.4 2693.5 2803.5 2679.7 2539.1 2065.3 2420.4 2684.5 2946.5 FALSE FALSE TRUE 2770.7128 2759.711941 2740.379238 3127.653861 2542.94491 2376.859705 2240.72653 2490.430455 2444.391597 2869.949505 0.965422142 0.961589023 0.954852771 1.089794038 0.886059112 0.828188684 0.780754688 0.867761071 0.851719374 1 11.48680964 -8.549811687 7.863823251 0.98588995 0.826815475 0.545823932 0.058975271 0.065217989 15.45636062 0.005777578 0.011687 2.82E-09 8.549811687 -0.159074476 GAEETSWS(ph)GEER ddPTM_HeLa_Romidepsin_16h_R1 2 GAEETSWSGEER 12 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 GAEETSWS(1)GEER;GAEETSWS(1)GEER ; 202.61 8.07E-15 173812000 3301.7 3325 2950.9 2632.7 2826.6 3376.6 2823.2 2646.9 3252.2 3242.5 TRUE FALSE FALSE 3261.45761 3371.809437 3002.259177 2937.105161 2682.348055 3160.846157 3063.002538 2723.483875 2961.315087 3158.259383 1.032675666 1.067616376 0.950605638 0.929975916 0.849312146 1.000819051 0.969838815 0.862336985 0.937641507 1 11.62491395 -9.596202317 6.180058236 1.019670373 0.926746932 0.376838953 0.05206812 0.130795421 8.537690518 0.007112218 0.010100039 2.53E-10 9.596202317 -0.092923441 GAES(ph)ENEEESPR ddPTM_HeLa_Romidepsin_16h_R1 1 GAESENEEESPR 12 0 Q9UEG4 Q9UEG4 ZNF629 Zinc finger protein 629 1 0 GAES(1)ENEEESPR 183.06 8.04E-07 3599100 1114 1237 1823.8 532.06 387.08 912.59 637.08 697.45 1140.9 1442.6 TRUE FALSE FALSE 1100.42214 1254.414518 1855.542474 593.5792806 367.3258632 854.2784442 691.1935593 717.6296154 1038.855047 1405.121044 0.783151134 0.892744809 1.320557031 0.422439962 0.261419374 0.607974984 0.491910332 0.510724409 0.739334914 1 10.4564787 -9.225305152 24.942655 0.923394816 0.458039445 0.675908487 0.168648278 269.0447281 185715.8195 0.025105821 0.04163238 5.95E-10 9.225305152 -0.46535537 GAES(ph)PFEEK ddPTM_HeLa_Romidepsin_16h_R1 5 GAESPFEEK 9 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 GAES(1)PFEEK;GAES(1)PFEEK;GAES(1)PFEEK;GAES(1)PFEEK;GAES(1)PFEEK ;;;; 163.84 0.0028681 2833585000 56059.6 52539.4 49560.5 44337.3 45800.9 40418 36370 37907.7 55813 49681.2 TRUE FALSE FALSE 55376.32403 53279.05105 50423.07971 49463.78724 43463.50917 37835.42024 39459.26689 39004.49949 50820.94549 48390.47526 1.144364128 1.101023513 1.042004226 1.022180232 0.898183143 0.781877426 0.81543458 0.80603671 1.050226211 1 15.56243549 -8.681318101 1.886835487 1.071097233 0.800071902 0.911582678 0.036898585 0.101306574 0.729885917 0.008601888 0.020356488 2.08E-09 8.681318101 -0.271025331 GAEVHLVPWNHDFTK ddPTM_HeLa_Romidepsin_16h_R1 1 GAEVHLVPWNHDFTK 15 0 P31327;P31327-3;Q5R211 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 0 109.84 0.0016699 13651000 16645 15315 17278 16307 15715 16474 12584 15535 14936 14535 FALSE FALSE TRUE 16442.12434 15530.60497 17578.71634 18192.49207 14913.00491 15421.36457 13652.88465 15984.48071 13600.08675 14157.3786 1.161381976 1.09699722 1.241664635 1.285018405 1.05337332 1.089281074 0.964365299 1.129056527 0.960635943 1 13.78926654 -6.911310957 20.66735837 1.096076324 3.374215658 0.009574127 0.10390044 4714.598982 1016871.302 0.014577719 37496.78713 1.23E-07 6.911310957 2.278139334 GAFFMDEDEEVYKR ddPTM_HeLa_Romidepsin_16h_R1 1 GAFFMDEDEEVYKR 14 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 0 0 57.52 0.026538 7124800 3125.4 3112.8 2875.2 1843.1 3349.6 3229.4 2901.7 3566.1 3729.8 3332.6 FALSE FALSE TRUE 3087.306423 3156.62208 2925.24165 2056.207894 3178.657413 3023.051762 3148.170326 3669.279477 3396.197347 3246.018572 0.951105594 0.972459649 0.901178347 0.63345537 0.979248067 0.93131068 0.969855919 1.130393864 1.046265532 1 11.66445554 -7.263062378 3.317579574 0.943963574 1.155328607 0.233835425 0.106835807 0.398028313 7.100004292 0.014910104 0.213509722 5.46E-08 7.263062378 0.211365033 GAFSPFGNIIDLS(ph)MDPPR ddPTM_HeLa_Romidepsin_16h_R1 1 GAFSPFGNIIDLSMDPPR 18 0 A0A0A0MSN9;P18615-4;P18615;P18615-3 A0A0A0MSN9 NELFE Negative elongation factor E 1 0 GAFSPFGNIIDLS(1)MDPPR 112.83 0.0018631 20587000 1402.6 1592.3 1569.6 1654.9 1734 2295.7 1498.3 1524.3 1939.2 1469.4 TRUE FALSE FALSE 1385.504572 1614.716441 1596.91823 1846.247325 1645.50751 2149.012179 1625.565565 1568.403216 1765.753095 1431.224776 0.968055189 1.128206043 1.115770392 1.289977197 1.149719832 1.501519688 1.13578635 1.095846887 1.233735696 1 10.48303455 -9.834539041 1.489522655 0.984357263 1.237984304 0.130568334 0.134848536 0.219513801 0.980392513 0.018870919 0.026850553 1.46E-10 9.834539041 0.253627041 GAGAGHPGAGGAQPPDS(ph)PAGVR ddPTM_HeLa_Romidepsin_16h_R1 2 GAGAGHPGAGGAQPPDSPAGVR 22 0 A0A3B3ITC2;Q13884-2;Q13884 A0A3B3ITC2 SNTB1 Beta-1-syntrophin 1 0 GAGAGHPGAGGAQPPDS(1)PAGVR;GAGAGHPGAGGAQPPDS(1)PAGVR ; 146.04 4.66E-06 11058600 4632.4 4966.2 4705.5 5632.9 5139.7 4863.8 4059.9 4111.8 5564.1 4934.4 TRUE FALSE FALSE 4575.938527 5036.114294 4787.397254 6284.202402 4877.40193 4553.018877 4404.747805 4230.768446 5066.43296 4806.203577 0.952090034 1.047836242 0.996087073 1.307518981 1.014813845 0.94732127 0.916471334 0.880272418 1.054144478 1 12.23068204 -7.991612932 2.907603019 1.010875825 0.89843206 0.234291248 0.097851417 0.374086702 6.375473951 0.014924086 0.050484359 1.02E-08 7.991612932 -0.112443765 GAGATS(ph)GSPPAGRN ddPTM_HeLa_Romidepsin_16h_R1 1 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 0 GAGAT(0.022)S(0.571)GS(0.407)PPAGRN 127.79 0.0042001 18852000 1456.8 1470.9 1543.3 1783.9 1532.9 1409.4 1360.5 855.9 1450.7 1355.5 TRUE FALSE FALSE 1439.043961 1491.607369 1570.160489 1990.162912 1454.670393 1319.343889 1476.060836 880.6641161 1320.945759 1320.283915 1.089950385 1.129762585 1.189259728 1.507374959 1.101786045 0.999288012 1.117987442 0.667026316 1.000501289 1 10.36663249 -7.259467302 23.98765664 1.094715915 0.667026052 0.46504641 0.144229866 77.97587405 948336.788 0.021349682 0.185619345 5.50E-08 7.259467302 -0.427689863 GAGATSGS(ph)PPAGR ddPTM_HeLa_Romidepsin_16h_R1 4 GAGATSGSPPAGR 13 0 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 0 GAGATS(0.01)GS(0.99)PPAGR;GAGAT(0.004)S(0.016)GS(0.98)PPAGR;GAGAT(0.001)S(0.006)GS(0.994)PPAGR;GAGATS(0.001)GS(0.999)PPAGR ;;; 137.09 0.0014552 107838000 15618.2 14787.2 16518.8 10219.7 15679.2 15432.5 13939 10669.7 17223.1 16990.8 TRUE FALSE FALSE 15427.83937 14995.37459 16806.30278 11401.3498 14879.03192 14446.41306 15122.97831 10978.41094 15682.6228 16549.37657 0.932230849 0.906099062 1.015524828 0.688929263 0.899069029 0.872927932 0.913809548 0.663373082 0.947626198 1 14.01448925 -4 0.141540289 1.032970758 0.102926519 0.367697542 0.08911091 53.46654708 0.498376253 0.217786968 10.12419466 1.00E-04 4 -0.930044239 GAGATSGS(ph)PPAGRN ddPTM_HeLa_Romidepsin_16h_R1 2 GAGATSGSPPAGRN 14 1 B4DEE8;P16455 B4DEE8 MGMT Methylated-DNA--protein-cysteine methyltransferase 1 0 GAGAT(0.009)S(0.277)GS(0.714)PPAGRN;GAGAT(0.032)S(0.393)GS(0.575)PPAGRN ; 153.81 0.00094698 162695000 7301.8 8088.6 6887.3 8046.5 8207.1 7138.9 7130.5 4494.3 8562.5 7848.8 TRUE FALSE FALSE 7212.802853 8202.471523 7007.170567 8976.87419 7788.261062 6682.74733 7736.164492 4624.33548 7796.648555 7644.887045 0.943480631 1.072935607 0.916582616 1.174232417 1.018754236 0.874145987 1.011939672 0.604892584 1.019851374 1 12.90027947 -7.259188275 24.76902334 0.9874179 0.604892432 0.684708003 0.080489203 77.27513476 850196.8991 0.010555162 0.093748089 5.51E-08 7.259188275 -0.382525468 GAGDGS(ph)DEEVDGK ddPTM_HeLa_Romidepsin_16h_R1 4 GAGDGSDEEVDGK 13 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK;GAGDGS(1)DEEVDGK ;;; 175.15 1.83E-05 344952800 13555.5 12371.1 16218.4 11792 12957.8 14760.7 13460.6 9737 14785.7 14977.5 TRUE FALSE FALSE 13390.28035 12545.26067 16500.67445 13155.44652 12296.51511 13817.53891 14603.94303 10018.72473 13463.22996 14588.38239 0.917872866 0.859948714 1.131083214 0.901775548 0.842897779 0.947160455 1.001066646 0.686760496 0.922873393 1 13.8325323 -7.255148823 24.4039047 0.954272907 0.686760327 0.494394654 0.078715588 317.7071743 1232480.725 0.010599258 0.13105848 5.56E-08 7.255148823 -0.26751258 GAGDGS(ph)DEEVDGKADGAEAK ddPTM_HeLa_Romidepsin_16h_R1 1 GAGDGSDEEVDGKADGAEAK 20 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 GAGDGS(1)DEEVDGKADGAEAK 66.732 0.0040253 12462000 1386.1 1478.5 1474.8 1285.6 1286.9 1581.2 1400.3 1424.2 1656 1674.1 TRUE FALSE FALSE 1369.20568 1499.314362 1500.468275 1434.247121 1221.224691 1480.166423 1519.241447 1465.40698 1507.883212 1630.606641 0.839690975 0.919482556 0.920190215 0.879578854 0.748938868 0.907739725 0.931703213 0.89868822 0.924737564 1 10.67119308 -12.42301679 1.041293313 1.003142854 0.877857267 0.214716174 0.055520739 0.434495088 0.807969408 0.041693517 0.009487827 3.78E-13 12.42301679 -0.125285587 GAGDGS(ph)DEEVDGKADGAEAKPAE ddPTM_HeLa_Romidepsin_16h_R1 5 GAGDGSDEEVDGKADGAEAKPAE 23 2 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE;GAGDGS(1)DEEVDGKADGAEAKPAE ;;;; 71.882 0.0013641 1672647000 10673 11054 9829.3 12298 11077.8 11035.5 8637.4 10533.6 11540.2 10795.3 TRUE FALSE FALSE 10542.91337 11209.6185 10000.37484 13719.95262 10512.45853 10330.36717 9371.06054 10838.3731 10508.01561 10514.83655 1.00267021 1.066076344 0.951072781 1.30481844 0.999773841 0.982456277 0.891222654 1.030769527 0.999351303 1 13.3601388 -8.246287319 4.213394972 1.025852027 0.958538423 0.093260634 0.098757106 0.431438853 18.74446668 0.013825607 0.035315574 5.67E-09 8.246287319 -0.067313605 GAGGS(ph)PVGVEEGLVNVGTGQK ddPTM_HeLa_Romidepsin_16h_R1 2 GAGGSPVGVEEGLVNVGTGQK 21 0 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 0 GAGGS(1)PVGVEEGLVNVGTGQK;GAGGS(1)PVGVEEGLVNVGTGQK ; 228.19 2.87E-42 51537000 9477 10051 8431.6 7140.6 7021.3 6473.8 5901.7 5884.4 9076.1 9822 TRUE FALSE FALSE 9361.490679 10192.49824 8578.348461 7966.22977 6662.976861 6060.145073 6402.990251 6054.65583 8264.310884 9566.823024 0.978537039 1.065400522 0.896676822 0.832693335 0.696467034 0.633454289 0.669291178 0.63288051 0.86385113 1 13.22382419 -9.016565147 1.442686307 0.994861926 0.643967921 0.881126839 0.052631272 0.051344754 0.212166453 0.005066863 0.01079712 9.63E-10 9.016565147 -0.350894005 GAGHVS(ph)PGHAAT(ph)RET(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 GAGHVSPGHAATRETRR 17 2 Q08378-4 Q08378-4 GOLGA3 Golgin subfamily A member 3 3 0 GAGHVS(1)PGHAAT(1)RET(1)RR 59.618 0.0042047 0 2256.5 1835.6 1976.1 1930.2 1873.6 1901.6 1491.9 1660.3 2298.5 2097.1 TRUE FALSE FALSE 2228.99691 1861.441625 2010.493192 2153.378806 1777.983201 1780.093897 1618.621949 1708.338161 2092.916403 2042.61704 1.091245626 0.911302309 0.984273191 1.05422542 0.870443733 0.871477062 0.792425559 0.836347748 1.02462496 1 10.99620303 -8.674495299 4.195299195 1.028991696 0.835169362 0.728494082 0.049812839 0.090172021 2.95557276 0.008557965 0.017488855 2.12E-09 8.674495299 -0.193822334 GAGKPATGPTNSSS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 GAGKPATGPTNSSSAK 16 1 M0R1H1;M0R3B3;Q9BT25-3;Q9BT25 M0R1H1 HAUS8 HAUS augmin-like complex subunit 8 1 0 GAGKPAT(0.002)GPT(0.024)NS(0.042)S(0.149)S(0.783)AK 61.276 0.024755 4384700 1261.6 1094.6 1500.7 883.87 1287.3 1401.1 1980.1 564.93 1440.1 1437.6 TRUE FALSE FALSE 1246.223134 1110.009808 1526.819054 986.0672081 1221.604277 1311.574232 2148.289645 581.2753582 1311.293849 1400.250945 0.889999852 0.792722056 1.09038959 0.704207494 0.872418106 0.936670842 1.534217601 0.415122275 0.936470605 1 10.45146969 -7.010378099 23.48258745 0.954155232 0.107580346 0.377269689 0.213795172 3708.245673 17975.08082 0.02670357 61532.81568 9.76E-08 7.010378099 -0.846574886 GAGQQQS(ph)QEMMEVDR ddPTM_HeLa_Romidepsin_16h_R1 1 GAGQQQSQEMMEVDR 15 0 C9JRC4;B5MBZ8;Q15435-3;Q15435 C9JRC4 PPP1R7 Protein phosphatase 1 regulatory subunit 7 1 0 GAGQQQS(1)QEMMEVDR 85.493 0.0010678 0 1950.1 1641.3 1741.3 1827.5 1769.4 1872.8 1956.6 1732.6 1656.2 1889 TRUE FALSE FALSE 1926.331431 1664.406264 1771.606596 2038.804149 1679.100915 1753.134124 2122.793555 1782.730047 1508.065324 1839.923508 1.04696278 0.904606228 0.9628697 1.108091798 0.912592784 0.952829896 1.153740113 0.968915305 0.819634793 1 10.84543007 GAGSIAGASAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GAGSIAGASASPK 13 0 P15924-2;P15924-3;P15924 P15924-2 DSP Desmoplakin 1 0 GAGSIAGAS(0.005)AS(0.995)PK 147.39 0.00076807 6532900 3818 3614.4 3332.6 2910.4 3218.9 3279.1 2902.3 2779.1 3664.4 3507.5 TRUE FALSE FALSE 3771.464747 3665.283618 3390.602505 3246.914142 3054.627522 3069.576093 3148.82129 2859.508874 3336.646886 3416.374644 1.103937694 1.072857634 0.99245629 0.950397565 0.894113743 0.898489309 0.921685007 0.837000965 0.976663052 1 11.73825048 -9.215470812 1.693848206 1.051819968 0.890072269 0.730071675 0.040568865 0.140390335 0.786728919 0.007241484 0.01333208 6.09E-10 9.215470812 -0.161747699 GAGTDDHTLIR ddPTM_HeLa_Romidepsin_16h_R1 4 GAGTDDHTLIR 11 0 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 0 ;;; ;;; 242.97 4.01E-48 33988300 21286.3 20114.9 18852.8 15385.5 20805.4 20707.5 20577.8 22256.1 22365.1 21432.2 FALSE FALSE TRUE 21026.85439 20398.07809 19180.92508 17164.4439 19743.6228 19384.35758 22325.67782 22900.04514 20364.70944 20875.38835 1.007255723 0.977135263 0.918829616 0.822233513 0.945784695 0.928574705 1.069473652 1.096987742 0.975536795 1 14.34951542 -7.645976458 5.985429166 0.974618237 1.089656298 0.433491702 0.055804802 0.183008701 8.683863153 0.009205605 0.035567381 2.26E-08 7.645976458 0.115038062 GAGTGGLGLAVEGPSEAK ddPTM_HeLa_Romidepsin_16h_R1 2 GAGTGGLGLAVEGPSEAK 18 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 318.7 5.04E-166 2564900 1537.54 1599.45 1464.9 1397.43 1552.15 1685.64 1505.32 1933.62 1730.59 1674.31 FALSE FALSE TRUE 1518.799871 1621.967099 1490.39597 1559.007432 1472.937994 1577.933044 1633.181843 1989.566244 1575.801696 1630.811185 0.931315584 0.994576879 0.913898546 0.955970529 0.903193458 0.967575559 1.001453668 1.21998565 0.966268634 1 10.67137404 -7.239982437 2.673154804 0.959726028 1.27979842 0.873899193 0.03011733 0.148968181 1.328395244 0.004917098 0.107968216 5.75E-08 7.239982437 0.320072392 GAILSEEELAAMS(ph)PTAAAVAK ddPTM_HeLa_Romidepsin_16h_R1 3 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 GAILSEEELAAMS(0.892)PT(0.108)AAAVAK;GAILSEEELAAMS(0.784)PT(0.216)AAAVAK;GAILSEEELAAMS(0.672)PT(0.328)AAAVAK ;; 163.56 1.83E-08 28729100 14826.9 14307.2 14196.1 15753.1 20076.2 22697.9 20735.1 22377.8 15233.5 14885.7 TRUE FALSE FALSE 14646.18404 14508.61714 14443.17717 17574.54754 19051.6366 21247.57744 22496.33888 23025.26634 13870.97761 14498.96737 1.010153597 1.000665549 0.996152126 1.212124084 1.31399955 1.465454532 1.551582144 1.588062498 0.956687277 1 13.82366253 -8.606279672 1.051849448 0.99999937 1.586677925 0.984645336 0.02967324 0.039791806 0.082813309 0.0043404 0.015180426 2.48E-09 8.606279672 0.586678555 GAILSEEELAAMSPT(ph)AAAVAK ddPTM_HeLa_Romidepsin_16h_R1 1 GAILSEEELAAMSPTAAAVAK 21 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 GAILSEEELAAMS(0.053)PT(0.947)AAAVAK 133.96 0.0001006 25566000 2973.3 3429.9 3395.9 3587.5 4556.3 4867.6 4585.8 4829.5 3650.4 3126.3 TRUE FALSE FALSE 2937.060276 3478.186222 3455.004215 4002.30363 4323.775009 4556.576069 4975.317738 4969.233963 3323.899081 3045.078275 0.96452702 1.142232123 1.13461918 1.314351642 1.419922451 1.496374036 1.63388829 1.631890386 1.091564413 1 11.5722636 -8.889241084 0.702405574 0.977825287 1.666817916 0.955976597 0.05009766 0.075339738 0.067275411 0.007579397 0.027033366 1.29E-09 8.889241084 0.688992629 GAILT(ph)T(ph)MLATRNFSAKS(ph)LLKK ddPTM_HeLa_Romidepsin_16h_R1 1 GAILTTMLATRNFSAKSLLKK 21 3 D6R938;H0Y9C2 D6R938 CAMK2D 3 0 GAILT(0.976)T(0.985)MLAT(0.028)RNFS(0.029)AKS(0.982)LLKK 45.094 0.019508 7179400 877.12 756.38 661.09 960.8 609.56 751.75 653.42 702.57 976.59 676.36 TRUE FALSE FALSE 866.4293241 767.0283375 672.5959941 1071.892217 578.4518786 703.7156012 708.9214785 722.8977545 889.2413445 658.7880697 1.315186725 1.164302107 1.020959585 1.627066831 0.878054575 1.068197245 1.076099449 1.097314581 1.349813977 1 9.363670619 GAK(ac)LTPEEEEILNK ddPTM_HeLa_Romidepsin_16h_R1 1 GAKLTPEEEEILNK 14 1 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 0 1 GAK(1)LTPEEEEILNK 246.63 6.37E-55 620570 244.58 321.59 259.3 309.52 267.81 321.03 251.19 115.81 323.55 374.22 FALSE TRUE FALSE 241.5989649 326.1173525 263.8130077 345.3081587 254.1426564 300.5172191 272.5260723 119.1607796 294.6108777 364.4977105 0.662827112 0.894703432 0.723771371 0.947353437 0.697240748 0.824469429 0.747675677 0.326917773 0.808265372 1 8.509765942 -16.52287875 0.039258747 2.164472212 1.92E-12 0.284785948 0.151195974 665.376534 2.086207937 99.04271944 32.8488383 3.00E-17 16.52287875 -2.164472212 GAKLT(ph)PEEEEILNK ddPTM_HeLa_Romidepsin_16h_R1 1 GAKLTPEEEEILNK 14 1 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 1 0 GAKLT(1)PEEEEILNK 92.236 0.0093593 9427800 1778.9 1540.3 1732.6 1823.1 2077.3 1966.7 1501.7 1791.4 1721 1707.3 TRUE FALSE FALSE 1757.218083 1561.984384 1762.755176 2033.8954 1971.28763 1841.034217 1629.254361 1843.231333 1567.06945 1662.9441 1.056691011 0.939288569 1.060020704 1.223069014 1.185420261 1.107093268 0.979740907 1.108414488 0.942346438 1 10.69952396 -9.516358065 24.96899912 1.019943169 1.118327901 0.423808025 0.07012666 278.0819295 1064833.738 0.011015273 0.015917706 3.05E-10 9.516358065 0.098384731 GALHT(ph)VSHEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 GALHTVSHEDIR 12 0 A0A2R8Y7R9;Q13136-2;Q13136;H0YDW2;H0YD72 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 GALHT(0.912)VS(0.088)HEDIR 106.54 0.0093059 83083000 4441.5 4500.7 4242.8 3539.5 5205.5 5636.7 5175.6 5740.1 4743.9 4239.4 TRUE FALSE FALSE 4387.36529 4564.060973 4316.644154 3948.753644 4939.843911 5276.533062 5615.215335 5906.180737 4319.593703 4129.259777 1.062506485 1.105297612 1.045379653 0.95628608 1.196302528 1.277839939 1.359860033 1.430324333 1.046093958 1 12.01166747 -8.259057993 1.512454519 1.033037309 1.402633343 0.901813483 0.047777999 0.091869691 0.390561003 0.007581653 0.028437908 5.51E-09 8.259057993 0.369596035 GALHTVS(ph)HEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 GALHTVSHEDIR 12 0 A0A2R8Y7R9;Q13136-2;Q13136;H0YDW2;H0YD72 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 GALHT(0.259)VS(0.741)HEDIR 89.46 0.012222 90133000 3840.9 3705.7 4054.6 3021.6 4336.6 5320.4 4740 5429 4621.9 3709.5 TRUE FALSE FALSE 3794.085633 3757.868942 4125.168612 3370.971609 4115.28712 4980.443611 5142.615482 5586.079549 4208.505688 3613.126655 1.050083763 1.04006012 1.141717135 0.932979087 1.138982248 1.378430397 1.423314479 1.546051407 1.16478222 1 11.81903211 -8.222721352 1.959912151 1.02877773 1.488712942 0.862265158 0.070981622 0.063204634 0.462885676 0.008071669 0.026528145 5.99E-09 8.222721352 0.459935212 GALPPS(ph)PALPRPSR ddPTM_HeLa_Romidepsin_16h_R1 2 GALPPSPALPRPSR 14 1 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 0 GALPPS(1)PALPRPSR;GALPPS(0.97)PALPRPS(0.03)R ; 102.15 0.0011415 21239000 3456.3 4040.8 3614.3 4489.7 3078.3 2954.7 2461.7 2772.3 3997 3547.2 TRUE FALSE FALSE 3414.173286 4097.686488 3677.205375 5008.820239 2921.202864 2765.904206 2670.796737 2852.512127 3639.498309 3455.043233 0.988170931 1.186001509 1.064300829 1.449712754 0.845489526 0.800541128 0.773013985 0.82560823 1.053387198 1 11.75448805 -8.549410729 24.99801346 1.048652538 0.801377503 0.518918477 0.136893657 163.6907279 154226.1885 0.020979557 0.041959967 2.82E-09 8.549410729 -0.247275035 GALQNIIPAS(ph)TGAAK ddPTM_HeLa_Romidepsin_16h_R1 1 GALQNIIPASTGAAK 15 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 GALQNIIPAS(0.99)T(0.01)GAAK 115.04 0.0038949 215100000 2729.8 3270.9 2777.3 2334.3 2876 3396.2 2857 3554 3045.6 3383 TRUE FALSE FALSE 2696.528148 3316.947816 2825.637741 2604.202749 2729.226988 3179.193781 3099.673509 3656.829383 2773.193908 3295.109172 0.818342582 1.006627593 0.857524772 0.790323662 0.828266029 0.964821988 0.940689169 1.109774879 0.841609113 1 11.68611055 -7.049974571 1.550823217 0.902186088 1.282320048 0.442863034 0.073813311 1.717266077 2.535688656 0.01261547 1.154171935 8.91E-08 7.049974571 0.38013396 GALQNIIPAST(ph)GAAK ddPTM_HeLa_Romidepsin_16h_R1 1 GALQNIIPASTGAAK 15 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 GALQNIIPAS(0.226)T(0.774)GAAK 254.72 3.68E-70 252740000 7755.8 8575 7747.6 5530.5 7370.5 7903.6 7240.2 8290.9 8738.9 8085.9 TRUE FALSE FALSE 7661.269326 8695.719075 7882.443728 6169.962432 6994.355882 7398.585468 7855.182407 8530.784111 7957.270897 7875.827152 0.972757423 1.104102326 1.000840112 0.783405008 0.888078896 0.939404246 0.99737872 1.083160403 1.010340977 1 12.94321573 GALQNIIPASTGAAK ddPTM_HeLa_Romidepsin_16h_R1 3 GALQNIIPASTGAAK 15 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ;; ;; 200.44 4.48E-17 22250400 5223.75 4864.75 4986.63 4270.16 4935.88 4825.37 4024.01 4350.82 4733.46 4992.99 FALSE FALSE TRUE 5160.080926 4933.236078 5073.420203 4763.895991 4683.983625 4517.04443 4365.809309 4476.704112 4310.087482 4863.2714 1.061030837 1.01438634 1.043211408 0.97956614 0.963134327 0.928807804 0.897710399 0.920512911 0.886252715 1 12.24771139 -8.670528232 1.284117146 1.029442607 0.909280813 0.280149401 0.048766917 0.140935688 0.457492882 0.003941822 0.011302706 2.14E-09 8.670528232 -0.120161794 GANPVEIRR ddPTM_HeLa_Romidepsin_16h_R1 1 GANPVEIRR 9 1 P10809;E7EXB4;E7ESH4;P10809-2 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 108.57 0.01326 1776000 1200.5 859.45 854 2019.1 1340.1 1099.8 1123.7 726.01 901.32 577.25 FALSE FALSE TRUE 1185.867844 871.5493597 868.8635118 2252.557842 1271.709696 1029.526329 1219.14705 747.0159539 820.7036818 562.2529618 2.109135789 1.550101856 1.545324917 4.006306761 2.261810578 1.831073199 2.168324816 1.328611861 1.459669824 1 9.135075545 -12.17117849 0.5279074 0.806752137 2.177011688 0.183967665 0.714713329 1.487662628 0.604816561 1.030513962 0.184500211 6.74E-13 12.17117849 1.370259551 GAPSITSVT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GAPSITSVTPR 11 0 H7C3L4;E7EQA9;Q92844 H7C3L4 TANK TRAF family member-associated NF-kappa-B activator 1 0 GAPSITSVT(1)PR;GAPSITS(0.001)VT(0.999)PR ; 147.58 0.005006 19754400 2882.3 2938 2516.5 2403.6 4241 5016.6 3867.1 4472.1 2852.7 2494.7 TRUE FALSE FALSE 2847.169419 2979.361241 2560.298627 2681.515541 4024.565945 4696.05545 4195.571377 4601.493158 2597.547367 2429.887334 1.171728985 1.226131434 1.053669687 1.103555504 1.65627677 1.932622712 1.726652639 1.893706384 1.068999097 1 11.24667371 -8.684495591 3.525137559 1.092379771 1.834104014 0.950373039 0.078974122 0.040279526 0.992149768 0.013591667 0.028115188 2.07E-09 8.684495591 0.741724243 GAPSQDDESGGIEDS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 2 GAPSQDDESGGIEDSPDR 18 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 GAPSQDDESGGIEDS(1)PDR;GAPSQDDESGGIEDS(1)PDR ; 256.66 1.54E-75 9125200 1040.6 1106.85 1469.09 842.52 1516.12 1300.85 1317.03 1341.09 1249.85 1340.7 TRUE FALSE FALSE 1027.916767 1122.432263 1494.658895 939.9361266 1438.746739 1217.729883 1428.898495 1379.892323 1138.060286 1305.868421 0.787151868 0.859529372 1.144570825 0.719778587 1.101754753 0.932505805 1.094213224 1.056685575 0.871496904 1 10.35079382 -8.219351916 0.949272632 0.903018817 1.082991988 0.196097545 0.123355387 0.956769358 1.371919075 0.02085576 0.125097009 6.03E-09 8.219351916 0.179973171 GAPSS(ph)PATGVLPS(ph)PQGK ddPTM_HeLa_Romidepsin_16h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5-2;Q5SRE5 Q5SRE5-2 NUP188 Nucleoporin NUP188 homolog 2 0 GAPS(0.119)S(0.876)PAT(0.005)GVLPS(1)PQGK;GAPS(0.082)S(0.698)PAT(0.22)GVLPS(1)PQGK ; 175.8 2.59E-06 15979700 5716.7 5908.7 5807.6 5170.8 6892.3 8373.5 6588.1 8076.1 6142.4 5383.3 TRUE FALSE FALSE 5647.022662 5991.882834 5908.678842 5768.672225 6540.560212 7838.460374 7147.69305 8309.769212 5593.00836 5243.44109 1.076968839 1.142738658 1.126870454 1.100169169 1.247379364 1.494907684 1.363168371 1.584793091 1.066667531 1 12.3562982 -7.496457718 0.398573478 1.01767665 1.901155806 0.882098536 0.064354159 0.987638052 0.121363035 0.017659131 0.401560481 3.19E-08 7.496457718 0.883479156 GAPSS(ph)PATGVLPSPQGK ddPTM_HeLa_Romidepsin_16h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5-2;Q5SRE5 Q5SRE5-2 NUP188 Nucleoporin NUP188 homolog 1 0 GAPS(0.046)S(0.895)PAT(0.059)GVLPSPQGK;GAPS(0.005)S(0.995)PATGVLPSPQGK ; 316.8 7.95E-159 49494000 8792.6 9577.8 9472.4 7387.9 6995.7 8065 7580 9029.4 9572.8 8739.6 TRUE FALSE FALSE 8685.432409 9712.63652 9637.263149 8242.123759 6638.683324 7549.672529 8223.845011 9290.651443 8716.584792 8512.543932 1.020309848 1.140979312 1.132124924 0.968232743 0.779870668 0.886887937 0.966085471 1.091407165 1.023969434 1 13.05537462 -9.00583415 24.99581505 1.031004936 0.923364414 0.314748862 0.086850013 303.8087274 1301647.262 0.013670235 0.024225579 9.87E-10 9.00583415 -0.107640522 GAPSSPAT(ph)GVLPSPQGK ddPTM_HeLa_Romidepsin_16h_R1 2 GAPSSPATGVLPSPQGK 17 0 Q5SRE5-2;Q5SRE5 Q5SRE5-2 NUP188 Nucleoporin NUP188 homolog 1 0 GAPS(0.025)S(0.155)PAT(0.659)GVLPS(0.161)PQGK;GAPS(0.134)S(0.097)PAT(0.524)GVLPS(0.245)PQGK ; 99.539 0.0067784 35392000 5503.6 5648 6219.2 5798.2 4915.4 4934.2 4390.2 4759.2 6309.1 6352.7 TRUE FALSE FALSE 5436.520006 5727.512692 6327.442567 6468.615165 4664.548796 4618.920544 4763.103478 4896.899943 5744.798295 6187.655938 0.878607353 0.925635289 1.022591209 1.045406408 0.753847474 0.746473396 0.769775102 0.791398228 0.928428851 1 12.59517726 -8.745279143 24.99538003 0.953001198 0.764337869 0.80256227 0.048650342 106.1437125 164173.8654 0.008994639 0.017944719 1.80E-09 8.745279143 -0.18866333 GAPTTSLISVAVTK ddPTM_HeLa_Romidepsin_16h_R1 1 GAPTTSLISVAVTK 14 0 P49419;A0A1B0GUY0;A0A1B0GW82;A0A1B0GTG2;A0A1B0GUA1;A0A1B0GTJ4;A0A1B0GTY9;A0A1B0GV49;A0A0J9YWF7;H0YHM6;A0A1B0GW77;P49419-4;P49419-2;A0A1B0GVU0 P49419 ALDH7A1 Alpha-aminoadipic semialdehyde dehydrogenase 0 0 186.81 1.59E-08 225700 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 GAPVIVPELGK(ac)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GAPVIVPELGKPR 13 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 0 1 GAPVIVPELGK(1)PR 107.83 0.0012054 0 67.827 62.198 0 0 0 75.833 150.24 0 0 150.05 FALSE TRUE FALSE 67.00029844 63.07362508 0 0 0 70.98751604 163.0013818 0 0 146.1516794 0.458429891 0.43156278 0 0 0 0.485711258 1.115289147 0 0 1 7.191322596 -11.56396261 0.720717956 0.974830652 0.303785211 0 0.4466901 0.538171485 0.569959443 0.180537883 0.079594979 2.73E-12 11.56396261 -0.671045441 GAPVNIS(ph)SSDLTGR ddPTM_HeLa_Romidepsin_16h_R1 1 GAPVNISSSDLTGR 14 0 H7BYT1;P48730-2;P48730;J3KRM8 H7BYT1 CSNK1D Casein kinase I isoform delta 1 0 GAPVNIS(0.675)S(0.207)S(0.02)DLT(0.098)GR 133.87 0.0016409 33532000 1249.4 1195.3 944.75 1272.5 636.68 942.93 760.56 883.97 1363.6 1326.4 TRUE FALSE FALSE 1234.171832 1212.127465 961.1929774 1419.632437 604.1878438 882.6798162 825.1619474 909.5462773 1241.636201 1291.939937 0.955285766 0.938222769 0.743992 1.0988378 0.467659391 0.683220474 0.63869993 0.704015915 0.96106341 1 10.33532328 -8.764063916 24.99999867 0.962927425 0.628764819 0.711332099 0.10155439 26.08807546 248505.2211 0.014243158 0.026697826 1.72E-09 8.764063916 -0.334162606 GAPVNISSS(ph)DLTGR ddPTM_HeLa_Romidepsin_16h_R1 1 GAPVNISSSDLTGR 14 0 H7BYT1;P48730-2;P48730;J3KRM8 H7BYT1 CSNK1D Casein kinase I isoform delta 1 0 GAPVNIS(0.14)S(0.201)S(0.659)DLTGR 137.39 0.0012595 4108500 1255.9 1245.5 1164.5 910.78 1084.2 975.49 1104.3 1039 1415.4 1150.6 TRUE FALSE FALSE 1240.592608 1263.034182 1184.767634 1016.088669 1028.869228 913.1593372 1198.099214 1069.061826 1288.803079 1120.707246 1.106972951 1.126997426 1.05716068 0.906649504 0.918053517 0.814806311 1.069056365 0.953917117 1.14999085 1 10.13019375 -9.26982 23.45021237 1.059204209 0.932742479 0.518148336 0.072432516 200.7517918 561733.0923 0.011353662 0.017537188 5.37E-10 9.26982 -0.12646173 GAQASSGS(ph)PALPR ddPTM_HeLa_Romidepsin_16h_R1 4 GAQASSGSPALPR 13 0 P42684-2;P42684-3;P42684-4;P42684-10;P42684-6;P42684;P42684-7;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 GAQASS(0.004)GS(0.996)PALPR;GAQAS(0.003)S(0.009)GS(0.988)PALPR;GAQAS(0.001)S(0.01)GS(0.99)PALPR;GAQAS(0.007)S(0.036)GS(0.957)PALPR ;;; 142.95 0.00080812 107319000 9082.1 9408.9 8171.6 8253.4 7637.7 7768.8 6747.4 7272 10887.2 14090.6 TRUE FALSE FALSE 8971.403872 9541.358741 8313.82327 9207.696941 7247.919669 7272.398753 7320.523988 7482.403847 9913.421565 13724.52418 0.65367686 0.695205066 0.605764044 0.67089371 0.528099887 0.529883489 0.533390003 0.545184937 0.722314408 1 13.74446851 -15.70800353 0.157187308 2.227107154 0.451274533 0.503635707 0.096092269 6.627485345 0.088511543 2.576627632 0.076791875 1.96E-16 15.70800353 -1.775832621 GARGS(ph)T(ph)GRKVGVS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GARGSTGRKVGVSK 14 3 Q96KM6 Q96KM6 ZNF512B Zinc finger protein 512B 3 0 GARGS(1)T(1)GRKVGVS(1)K 71.263 0.016404 4616200 2121.6 2273.4 2095.4 2765.6 2642 3265.2 2992.3 2737.9 2894.3 2457.5 TRUE FALSE FALSE 2095.741123 2305.404985 2131.869558 3085.371685 2507.168881 3056.564258 3246.465887 2817.116817 2635.426559 2393.653796 0.875540618 0.963132174 0.890634043 1.288979923 1.047423352 1.276945005 1.356280467 1.176910722 1.101005736 1 11.22499879 -9.262926708 24.9999388 0.938276405 1.22890374 0.640930411 0.097413749 52.60431569 884206.4207 0.013361078 0.021104448 5.46E-10 9.262926708 0.290627335 GARPPAAGPGGDEDEDEEDTAPESALDT(ph)SLDK ddPTM_HeLa_Romidepsin_16h_R1 1 GARPPAAGPGGDEDEDEEDTAPESALDTSLDK 32 1 Q27J81-2;A0A0A0MQU1;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 0 GARPPAAGPGGDEDEDEEDT(0.003)APES(0.043)ALDT(0.528)S(0.426)LDK 82.317 2.43E-08 10439000 1270.3 1244.9 1351.3 842.49 1322.3 1533.3 1565.4 1334.8 1596.7 1593.9 TRUE FALSE FALSE 1254.817095 1262.425735 1374.81881 939.9026578 1254.818097 1435.327078 1698.365037 1373.420332 1453.887153 1552.490248 0.808260855 0.813161781 0.885557131 0.605416143 0.8082615 0.924532106 1.093961807 0.884656334 0.93648714 1 10.60036849 -7.996016048 24.75106088 0.868940992 0.994293573 0.202793712 0.111305826 156.9139883 974818.1419 0.017863255 0.053255084 1.01E-08 7.996016048 0.125352581 GAS(ph)PDMAPILEPVDRR ddPTM_HeLa_Romidepsin_16h_R1 1 GASPDMAPILEPVDRR 16 1 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 GAS(1)PDMAPILEPVDRR 89.877 0.011187 6093800 1469.7 1329.1 1260.5 1200.8 1690.7 1748.1 1081.3 1356 1413.2 1468.6 TRUE FALSE FALSE 1451.786731 1347.811105 1282.438474 1339.642146 1604.41727 1636.402052 1173.145595 1395.233721 1286.799853 1430.44556 1.014919247 0.942231667 0.89653078 0.936520888 1.121620644 1.143980657 0.820126 0.975384006 0.899579745 1 10.48224888 GAS(ph)PLGPGSAAGSGAAASGGLGLGLGGR ddPTM_HeLa_Romidepsin_16h_R1 1 GASPLGPGSAAGSGAAASGGLGLGLGGR 28 0 B4E1M0;E9PPE2;A0A6I8PS01;Q6P1R3-3;Q6P1R3 B4E1M0 MSANTD2 Myb/SANT-like DNA-binding domain-containing protein 2 1 0 GAS(0.954)PLGPGS(0.044)AAGS(0.001)GAAASGGLGLGLGGR 180.68 1.39E-36 0 1407.2 1616.9 1521.3 1388.4 1514.1 1214.4 1181.8 1056.9 1483.8 1638.1 TRUE FALSE FALSE 1390.048505 1639.662761 1547.777588 1548.933341 1436.829827 1136.803759 1282.182063 1087.479734 1351.085212 1595.541926 0.871207759 1.02765257 0.970063878 0.970788242 0.900527779 0.712487551 0.803602865 0.681573901 0.846787659 1 10.6398308 -8.37282906 3.843709635 0.949339888 0.739411984 0.726036638 0.059079508 0.095412194 2.497873995 0.008674969 0.020495303 4.24E-09 8.37282906 -0.209927905 GAS(ph)SPYGAPGTPR ddPTM_HeLa_Romidepsin_16h_R1 2 GASSPYGAPGTPR 13 0 Q5UIP0-2;Q5UIP0;H7BZN3 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 GAS(0.61)S(0.39)PYGAPGT(0.001)PR;GAS(0.761)S(0.229)PYGAPGT(0.01)PR ; 130.15 0.0025069 9757700 2717.5 2564.65 2511.4 2394.82 2546.6 3045.3 2652.5 2860.3 2538.8 2672.7 TRUE FALSE FALSE 2684.378065 2600.75521 2555.109864 2671.720356 2416.637499 2850.715158 2877.803284 2943.058268 2311.723369 2603.262869 1.031159049 0.999036725 0.981502826 1.026296802 0.928310978 1.095054669 1.10546012 1.130526734 0.888009965 1 11.34610528 -8.083704947 7.941183261 1.007195042 1.113702884 0.578974372 0.047436091 0.109895024 9.398994151 0.004047227 0.010397765 8.25E-09 8.083704947 0.106507841 GASFLFPPAES(ph)LSPEEPR ddPTM_HeLa_Romidepsin_16h_R1 1 GASFLFPPAESLSPEEPR 18 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 0 GASFLFPPAES(0.5)LS(0.5)PEEPR 85.522 0.0093859 3071000 2110 1738.4 1875.7 1516.9 1473.6 1252 1226 1196.9 2120.7 1768.5 TRUE FALSE FALSE 2084.282508 1762.873241 1908.345772 1692.291115 1398.396693 1172.001241 1330.136409 1231.530413 1931.019281 1722.554115 1.209995373 1.023406595 1.107858241 0.982431321 0.811815827 0.680385731 0.77218846 0.714944397 1.121020967 1 10.75033359 -8.809983913 2.023178602 1.095816722 0.725810267 0.890782575 0.058072806 0.100746959 0.839692593 0.012574989 0.027064062 1.55E-09 8.809983913 -0.370006455 GASQAGMTGY(ph)GMPR ddPTM_HeLa_Romidepsin_16h_R1 1 GASQAGMTGYGMPR 14 0 P37802;P37802-2;C9J5W6;Q9UI15 P37802 TAGLN2;TAGLN3 Transgelin-2;Transgelin-3 1 0 GASQAGMT(0.333)GY(0.667)GMPR 55.261 0.025783 6825500 415.43 600.39 502.71 396.38 396.09 294.53 200.82 232.72 580.34 582.75 TRUE FALSE FALSE 410.3665794 608.8423062 511.4594567 442.2113206 375.8760493 275.7104836 217.8776458 239.453386 528.4329369 567.610071 0.722972689 1.072641832 0.901075373 0.779075889 0.66220821 0.485739238 0.383850916 0.421862469 0.93097879 1 9.148756377 -8.489663798 1.432989473 0.885804055 0.39701768 0.8501992 0.090030332 0.158882753 0.629831063 0.018381241 0.057418797 3.24E-09 8.489663798 -0.488786376 GATPGK(ac)ALVATPGK ddPTM_HeLa_Romidepsin_16h_R1 2 GATPGKALVATPGK 14 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; GATPGK(1)ALVATPGK;GATPGK(1)ALVATPGK 249.98 3.55E-55 9623600 4201.4 3633.9 3574.1 3173.2 3717.2 3506.1 2969.1 3172.7 3918.8 4068.5 FALSE TRUE FALSE 4150.191721 3685.05814 3636.305711 3540.100314 3527.497413 3282.071525 3221.29528 3264.497069 3568.292713 3962.799783 1.047287763 0.929912774 0.917610253 0.893333125 0.890152823 0.828220376 0.812883682 0.823785517 0.900447388 1 11.95230436 -9.40815572 0.818677771 1.022995491 0.823555239 0.582924531 0.04630085 0.143583057 0.191380232 0.00628492 0.013107296 3.91E-10 9.40815572 -0.199440252 KTVTPAK(ac)AVTTPGKK ddPTM_HeLa_Romidepsin_16h_R1 2 KTVTPAKAVTTPGKK 15 3 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; KTVTPAK(1)AVTTPGKK;KTVTPAK(1)AVTTPGKK 103.88 0.0021158 7772900 1750.49 1540.66 2035.73 4907.4 7179.1 7143.7 7173.8 8202 1992.74 1897.64 FALSE TRUE FALSE 1729.154355 1562.349452 2071.161027 5474.816678 6812.723738 6687.240625 7783.142393 8439.311929 1814.504343 1848.339039 0.935517953 0.845272117 1.120552552 2.962019717 3.685862601 3.617972939 4.210884598 4.565889564 0.98169454 1 10.8520137 -9.069376694 1.75304243 0.94269258 4.089217369 0.972740141 0.242615683 0.039602576 0.240325438 0.039787365 0.077828805 8.52E-10 9.069376694 3.146524789 up GATQQILDEAER ddPTM_HeLa_Romidepsin_16h_R1 1 GATQQILDEAER 12 0 F8VQ14;F5GWF6;P78371;P78371-2 F8VQ14 CCT2 T-complex protein 1 subunit beta 0 0 145.09 0.015392 4704600 1380.4 1613.5 1128.7 1153.2 1149.2 1115.7 1329.8 1445.6 1532.7 1349 FALSE FALSE TRUE 1363.575154 1636.214895 1148.34455 1286.53841 1090.552036 1044.410371 1442.753179 1487.426155 1395.611473 1313.952786 1.037765716 1.24526156 0.873961806 0.979135951 0.829978099 0.794861415 1.098025131 1.132024051 1.062147353 1 10.35969772 GAVAEDGDELRTEPEAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GAVAEDGDELRTEPEAKK 18 2 G3V5D9;A0A0C4DGK8;G3V3C7;G3V5Q1;G3V3M6;P27695 G3V5D9 APEX1 "DNA-(apurinic or apyrimidinic site) lyase;DNA-(apurinic or apyrimidinic site) lyase, mitochondrial" 0 1 GAVAEDGDELRTEPEAK(1)K 132.51 2.76E-06 1348600 748.59 712.41 687.31 1281.7 1314 1245.8 967.97 1212.5 1047.5 689.48 FALSE TRUE FALSE 739.4658971 722.4393267 699.2723422 1429.896185 1246.941677 1166.197401 1050.189348 1247.581774 953.8089765 671.5672102 1.101104827 1.075751341 1.041254444 2.129192973 1.856763788 1.736531181 1.563788898 1.857716928 1.420273298 1 9.391387981 -9.276437463 24.99998861 1.051060331 1.810503614 0.792101495 0.177315475 185.6811964 309507.4358 0.021114266 0.032331965 5.29E-10 9.276437463 0.759443283 GAVIVVSHDAR ddPTM_HeLa_Romidepsin_16h_R1 1 GAVIVVSHDAR 11 0 Q8NE71;Q8NE71-2;A0A0G2JIC2;H0YGW7 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 0 0 75.566 0.017176 472960 1322.2 904.06 1206.9 1269 1639.4 1693.6 1095.2 1056 1810.8 1047.2 FALSE FALSE TRUE 1306.084518 916.7873804 1227.905588 1415.727751 1555.735301 1585.384426 1188.226261 1086.553694 1648.837513 1019.993593 1.280483061 0.898816803 1.20383657 1.387977102 1.525240267 1.55430822 1.164935024 1.065255411 1.616517519 1 9.994344375 -9.44148634 5.015705782 1.115859066 1.349927344 0.036167747 0.229841503 0.239503017 10.5370583 0.029304657 0.044839918 3.62E-10 9.44148634 0.234068278 GAVMEQGTSSSMTAES(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 GAVMEQGTSSSMTAESSPR 19 0 H0Y493;H0Y7R3;F8W9F9;H0Y7T5;Q9Y3S1-2;Q9Y3S1-4;Q9Y3S1 H0Y493 WNK2 Serine/threonine-protein kinase WNK2 1 0 GAVMEQGTSSSMTAES(0.657)S(0.343)PR 91.14 0.00032928 0 650.35 382.3 462.61 348.05 484.18 565.28 476.52 596.8 604.23 761.11 TRUE FALSE FALSE 642.4232841 387.6820294 470.661533 388.2931786 459.4704879 529.1604324 516.9955969 614.0674664 550.1861555 741.3362525 0.866574759 0.522950319 0.634882661 0.523774707 0.619786887 0.713792737 0.697383401 0.828325155 0.742154661 1 9.533984253 -10.46089244 3.722201085 0.944872785 0.646950579 0.430374766 0.108594353 0.10051156 2.629627051 0.017229017 0.01916456 3.46E-11 10.46089244 -0.297922206 GAVY(ph)SS(ph)PLY(ph)QY(ph)LQEK ddPTM_HeLa_Romidepsin_16h_R1 1 GAVYSSPLYQYLQEK 15 0 Q5QJ38 Q5QJ38 TCHHL1 Trichohyalin-like protein 1 4 0 GAVY(0.982)S(0.475)S(0.638)PLY(0.922)QY(0.982)LQEK 49.466 0.0041032 0 728.68 851.23 772.27 3194.9 846.15 557.52 622.16 676.82 631.51 772.83 TRUE FALSE FALSE 719.7985679 863.2136383 785.7110354 3564.30937 802.9678081 521.8962713 675.0062549 696.4027189 575.026164 752.7517652 0.956223022 1.14674409 1.043785045 4.735039538 1.066709964 0.693317898 0.896718262 0.925142592 0.763898792 1 9.556030376 -9.478135381 24.99950774 0.996253608 1.669317054 0.088621661 1.09285503 944.537764 527743.3705 0.169420278 0.258785867 3.33E-10 9.478135381 0.673063446 GCDTQMIY(ph)DMLLR ddPTM_HeLa_Romidepsin_16h_R1 1 GCDTQMIYDMLLR 13 0 Q9NQW8-2;Q9NQW8 Q9NQW8-2 CNGB3 Cyclic nucleotide-gated cation channel beta-3 1 0 GCDTQMIY(1)DMLLR 73.273 0.017711 2433800 1069.4 904.11 1197.4 890.81 960.73 1011.7 1031.2 955.69 1160.1 1011.9 TRUE FALSE FALSE 1056.365741 916.8380843 1218.240245 993.8096436 911.7003631 947.0556351 1118.790102 983.3413823 1056.33775 985.6106921 1.071788029 0.930223355 1.2360258 1.008318651 0.925010626 0.960882063 1.135123747 0.99769756 1.07175963 1 9.944874097 -7.762803059 24.99994009 1.028091869 1.066410624 0.030863478 0.090772803 115.6055673 2119603.868 0.012068035 0.039423805 1.73E-08 7.762803059 0.038318754 GDAAS(ph)SPAPAASVGS(ph)SQGGAR ddPTM_HeLa_Romidepsin_16h_R1 1 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 2 0 GDAAS(0.691)S(0.309)PAPAAS(0.061)VGS(0.758)S(0.181)QGGAR 139.43 0.0011525 4321400 1666.2 1850.5 1776 1903.9 1538 1300.8 948.1 1169.1 1515.4 1761.6 TRUE FALSE FALSE 1645.891714 1876.551388 1806.910535 2124.037876 1459.510121 1217.683078 1028.63159 1202.926064 1379.858829 1715.833378 0.959237496 1.093667609 1.05308042 1.237904509 0.850612967 0.709674432 0.599493869 0.701073938 0.804191623 1 10.74469375 -8.40180358 3.285854783 1.01251149 0.660870651 0.679458773 0.10836362 0.093400337 1.87810213 0.013250884 0.031837786 3.96E-09 8.40180358 -0.351640839 GDAAS(ph)SPAPAASVGSSQGGAR ddPTM_HeLa_Romidepsin_16h_R1 2 GDAASSPAPAASVGSSQGGAR 21 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 0 GDAAS(0.499)S(0.499)PAPAAS(0.001)VGSSQGGAR;GDAAS(0.43)S(0.43)PAPAAS(0.138)VGS(0.002)S(0.001)QGGAR ; 187.75 1.20E-17 80659000 7109.2 6644.2 6894.4 6158.4 5781.5 6349.3 5464 5556.5 7250.3 6451.7 TRUE FALSE FALSE 7022.550336 6737.737222 7014.39414 6870.463184 5486.448481 5943.600221 5928.112024 5717.268561 6601.815009 6284.083904 1.117513777 1.072190844 1.116215863 1.093311816 0.873070533 0.945818088 0.943353417 0.909801436 1.050561245 1 12.61748673 -8.766556204 24.9999157 1.065600219 0.921807275 0.80524704 0.037627221 58.95539051 288047.5281 0.007641544 0.014159981 1.71E-09 8.766556204 -0.143792944 GDAEKPEEELEEDDDEELDETLSER ddPTM_HeLa_Romidepsin_16h_R1 1 GDAEKPEEELEEDDDEELDETLSER 25 1 Q9NS69 Q9NS69 TOMM22 Mitochondrial import receptor subunit TOM22 homolog 0 0 176.57 6.11E-18 21986000 3322.3 3341.9 3818.7 2600.4 3178.4 3756.5 2686.4 2796.5 3425.1 3548 FALSE FALSE TRUE 3281.80653 3388.947356 3885.162872 2901.070483 3016.194388 3516.471774 2914.582749 2877.412315 3118.750478 3455.822449 0.949645585 0.980648574 1.124236829 0.839473244 0.872786271 1.017549896 0.843383244 0.832627358 0.90246259 1 11.75481338 -9.207403293 24.9998671 0.986112249 0.886176633 0.366971593 0.072073925 277.479648 128376.323 0.010139556 0.016814546 6.20E-10 9.207403293 -0.099935616 GDDDEES(ph)DEEAVK ddPTM_HeLa_Romidepsin_16h_R1 2 GDDDEESDEEAVK 13 0 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 0 GDDDEES(1)DEEAVK;GDDDEES(1)DEEAVK ; 193.06 6.52E-11 16175400 9716.8 7368.9 8815.1 4756.6 7174 8648.4 7850.5 8182.6 9125.1 9138.7 TRUE FALSE FALSE 9598.367904 7472.639568 8968.523118 5306.580472 6807.88401 8095.795151 8517.321274 8419.350621 8308.928202 8901.275257 1.078313795 0.839502133 1.007554857 0.596159575 0.764821199 0.909509584 0.956865284 0.945858922 0.933453686 1 13.11979633 -10.25684528 24.68900073 1.036981515 0.857527886 0.230681959 0.115718339 274.9501985 1477602.428 0.019310828 0.02323064 5.54E-11 10.25684528 -0.179453629 GDDDEES(ph)DEEAVKK ddPTM_HeLa_Romidepsin_16h_R1 3 GDDDEESDEEAVKK 14 1 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 0 GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK;GDDDEES(1)DEEAVKK ;; 184 2.23E-07 59060000 9632.2 8698.1 10085.9 5959.8 8560.2 9856.6 9300.2 9909 11113.5 11421.1 TRUE FALSE FALSE 9514.799041 8820.55208 10261.44086 6648.900118 8123.341051 9226.795071 10090.15876 10195.70128 10119.48073 11124.37818 0.855310642 0.792902933 0.922428265 0.59768735 0.730228775 0.829421198 0.90703126 0.916518759 0.90966709 1 13.44143707 -11.5430242 0.671075821 0.99584759 0.809268715 0.231208242 0.096269868 0.597757173 0.550144822 0.054709144 0.023356565 2.86E-12 11.5430242 -0.186578875 GDDGIFDDNFIEER ddPTM_HeLa_Romidepsin_16h_R1 4 GDDGIFDDNFIEER 14 0 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 0 ;;; ;;; 270.93 8.52E-81 100764000 13722.9 13049.3 12243.4 9242.2 12523.1 13612.8 11161.4 13513.9 14016 12847.5 FALSE FALSE TRUE 13555.64002 13233.00839 12456.49124 10310.82665 11883.99948 12742.98601 12109.44904 13904.90338 12762.37386 12513.7201 1.083262204 1.057479973 0.995426711 0.823961745 0.949677585 1.018321164 0.967693775 1.111172638 1.019870491 1 13.61122312 -9.571986806 6.998114747 1.041274972 0.968605598 0.165171755 0.069488847 0.272278554 30.7577788 0.011528055 0.01637225 2.68E-10 9.571986806 -0.072669374 GDDWNDREWDR ddPTM_HeLa_Romidepsin_16h_R1 1 GDDWNDREWDR 11 1 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;C9JUL9 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 0 0 107.11 0.018099 19414000 2279 2200.8 2139.9 2244.1 2367.3 2357.1 2207.4 2162 2441.4 2974.9 FALSE FALSE TRUE 2251.222671 2231.78292 2177.144062 2503.573401 2246.487847 2206.488917 2394.896501 2224.554059 2223.035069 2897.611669 0.776923525 0.770214637 0.751358122 0.864012741 0.775289481 0.761485378 0.82650706 0.767719872 0.76719565 1 11.50064855 -12.17668086 0.756672421 1.011646468 0.786295535 0 0.078401235 0.208381221 0.198899052 0.028706484 0.006754578 6.66E-13 12.17668086 -0.225350932 GDEASEEGQNGS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 GDEASEEGQNGSSPK 15 0 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 GDEAS(0.002)EEGQNGS(0.948)S(0.051)PK 95.195 0.011677 83177000 5049.3 5339.7 6696.1 5000.7 5649.7 6344.5 8220.1 3221.5 7290.8 6961 TRUE FALSE FALSE 4987.757189 5414.872437 6812.642812 5578.904463 5361.374727 5939.106926 8918.315089 3314.70902 6638.692588 6780.152217 0.735640887 0.798635822 1.004792016 0.822828793 0.790745481 0.875954807 1.315356176 0.48888416 0.979136216 1 12.72710195 -7.964339302 24.99920493 0.866397777 0.950503518 0 0.20621177 589.3674773 413158.5592 0.026929373 0.08078779 1.09E-08 7.964339302 0.084105741 GDEASEEGQNGSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GDEASEEGQNGSSPK 15 0 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 GDEASEEGQNGS(0.421)S(0.579)PK 183.41 2.30E-08 63873000 4044.6 3870.1 5064.9 3438.1 4083.7 4319.2 6055.4 2251 5195.6 4797.9 TRUE FALSE FALSE 3995.302859 3924.583369 5153.05246 3835.629299 3875.293551 4043.21706 6569.745525 2316.129134 4730.892523 4673.249866 0.854930289 0.83979746 1.102670006 0.820762726 0.829250235 0.865183154 1.405819443 0.49561423 1.012334598 1 12.19021046 -12.58421797 1.397558198 0.99958348 0.908467354 0.033933638 0.218922063 1.627706004 5.742653929 0.136995478 0.032544323 2.60E-13 12.58421797 -0.091116126 GDEELDS(ph)LIK ddPTM_HeLa_Romidepsin_16h_R1 2 GDEELDSLIK 10 0 P0C0S5;A0A494C189;Q71UI9-4;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V;Histone H2A 1 0 GDEELDS(1)LIK;GDEELDS(1)LIK ; 131.17 0.0068737 4846400 2017.13 2300.6 2667.2 1408.86 3269.8 3357.6 3290.5 3532.5 3030.5 2508.2 TRUE FALSE FALSE 1992.544444 2332.987907 2713.621497 1571.759022 3102.929905 3143.060196 3569.994988 3634.707314 2759.44449 2443.036602 0.815601552 0.954954136 1.11075761 0.643362863 1.270111918 1.286538316 1.461294106 1.487782586 1.129514182 1 11.25445976 -8.590219775 6.268421356 0.914241329 1.395371177 0.694749606 0.142315502 0.0732843 5.20089206 0.018837314 0.038054908 2.57E-09 8.590219775 0.481129847 GDEGIFEESFIEER ddPTM_HeLa_Romidepsin_16h_R1 3 GDEGIFEESFIEER 14 0 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 0 ;; ;; 222.72 1.07E-31 25319500 5386.09 5532.31 5276.2 3509.85 5283.6 5779.9 4328.47 5348.4 6116.2 5380.7 FALSE FALSE TRUE 5320.442263 5610.194005 5368.030048 3915.675371 5013.958176 5410.583044 4696.130134 5503.147516 5569.151754 5240.908638 1.015175541 1.070462088 1.024255605 0.747136736 0.956696352 1.032374998 0.896052661 1.050036911 1.062630955 1 12.35560124 GDET(ph)PLTNVK ddPTM_HeLa_Romidepsin_16h_R1 1 GDETPLTNVK 10 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9;H0YAH7;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 1 0 GDET(0.997)PLT(0.003)NVK 132.56 0.013086 3316400 2005.6 2325.4 2464.8 1976.8 2400.3 2689.2 2208.8 2872 2504.6 2812.6 TRUE FALSE FALSE 1981.154976 2358.137042 2507.69881 2205.366917 2277.803734 2517.368799 2396.415417 2955.096789 2280.582303 2739.528247 0.723173772 0.86078216 0.915376147 0.805017039 0.831458386 0.918905947 0.874754776 1.078688198 0.832472637 1 11.41971176 -6.544395587 1.443491102 0.863746302 2.063221239 0.456504181 0.070598729 8.678588903 3.525513204 0.014979061 24.96032187 2.85E-07 6.544395587 1.199474937 GDFCIQVGR ddPTM_HeLa_Romidepsin_16h_R1 1 GDFCIQVGR 9 0 Q32Q12;P22392-2;P22392;J3KPD9;E7ERL0;O60361;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase;Nucleoside diphosphate kinase A 0 0 134.48 0.026141 1822700 1152.9 931.25 1315.1 505.89 1460.7 1121.9 946.18 937.27 849.66 696.42 FALSE FALSE TRUE 1138.848011 944.3601619 1337.988764 564.3833821 1386.155028 1050.214211 1026.548506 964.3884287 773.6642816 678.326908 1.67890732 1.39219033 1.972483692 0.832022695 2.043491143 1.548242003 1.513353655 1.42171631 1.140547828 1 9.405836913 -12.34357407 0.933454133 0.980503922 1.559175312 0.262723975 0.318441279 0.564666349 0.832760706 0.231594073 0.053133919 4.53E-13 12.34357407 0.57867139 GDLGIEIPAEK ddPTM_HeLa_Romidepsin_16h_R1 3 GDLGIEIPAEK 11 0 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BR70;P30613-2;P30613 P14618;P30613-2 PKM;PKLR Pyruvate kinase PKM;Pyruvate kinase;Pyruvate kinase PKLR 0 0 ;; ;; 162.36 0.011338 37385400 15631.9 14729 14730.8 13865.9 15280.3 16301.9 14254 15566.8 15295.2 14282.2 FALSE FALSE TRUE 15441.37239 14936.35525 14987.18339 15469.1406 14500.48927 15260.2612 15464.7344 16017.2008 13927.159 13911.14639 1.109999993 1.073696936 1.077350707 1.111996105 1.042364797 1.096980851 1.111679367 1.151393304 1.001151064 1 13.76395369 -12.41754306 0.692542673 0.985303036 1.096899096 0.66433783 0.0273827 0.535947018 0.360629522 0.037144998 0.005761378 3.82E-13 12.41754306 0.11159606 GDLS(ph)DVEEEEEEEMDVDEATGAVK ddPTM_HeLa_Romidepsin_16h_R1 4 GDLSDVEEEEEEEMDVDEATGAVK 24 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 0 GDLS(1)DVEEEEEEEMDVDEATGAVK;GDLS(1)DVEEEEEEEMDVDEATGAVK;GDLS(0.999)DVEEEEEEEMDVDEAT(0.001)GAVK;GDLS(1)DVEEEEEEEMDVDEATGAVK ;;; 196.08 1.46E-23 18205000 7690.17 7014.83 7586.28 7232.4 8085.44 7854.91 6981.86 8367.34 8517.05 7696.36 TRUE FALSE FALSE 7596.43925 7113.584961 7718.316021 8068.644117 7672.809826 7353.006602 7574.899014 8609.435781 7755.263717 7496.407458 1.013343964 0.948932539 1.029601988 1.076334786 1.023531588 0.980870723 1.010470556 1.148474897 1.034530708 1 12.87198366 -9.537077042 24.98147631 1.001560082 1.041992872 0.190776759 0.046460946 327.0119935 575365.8026 0.006939693 0.009817005 2.90E-10 9.537077042 0.040432789 GDLS(ph)DVEEEEEEEMDVDEATGAVKK ddPTM_HeLa_Romidepsin_16h_R1 3 GDLSDVEEEEEEEMDVDEATGAVKK 25 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 0 GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(1)DVEEEEEEEMDVDEATGAVKK;GDLS(0.998)DVEEEEEEEMDVDEAT(0.002)GAVKK ;; 126.25 1.12E-06 174150500 5778.26 6449.84 5249.07 6154.6 6201.04 6419.38 5621.32 6264 6807 6848.9 TRUE FALSE FALSE 5707.832345 6540.641017 5340.427861 6866.22381 5884.57779 6009.202336 6098.79478 6445.238957 6198.164872 6670.964591 0.855623241 0.980464059 0.800548075 1.029270013 0.882117977 0.900799615 0.914229824 0.966162969 0.929125734 1 12.70367967 -12.58197402 1.370847685 0.999942828 0.908322906 0.030304097 0.065408621 0.482215096 1.626546146 0.040509362 0.009470191 2.62E-13 12.58197402 -0.091619922 GDMS(ph)DEDDENEFFDAPEIITMPENLGHK ddPTM_HeLa_Romidepsin_16h_R1 6 GDMSDEDDENEFFDAPEIITMPENLGHK 28 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(0.987)DEDDENEFFDAPEIIT(0.013)MPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK;GDMS(0.998)DEDDENEFFDAPEIIT(0.002)MPENLGHK;GDMS(1)DEDDENEFFDAPEIITMPENLGHK ;;;;; 111.24 8.64E-10 96465700 15121.96 14257.11 17186.38 15212.32 18119.2 17532.79 13989.07 18011.08 17586.12 17520.78 TRUE FALSE FALSE 14937.64774 14457.82197 17485.50173 16971.24001 17194.50961 16412.5013 15177.30126 18532.20218 16013.17338 17065.58761 0.875308139 0.847191571 1.024605899 0.994471471 1.007554501 0.961730805 0.889351226 1.085939881 0.938331205 1 14.05880247 -9.714316145 24.99998898 0.932427588 0.98836676 0.268031381 0.060730171 194.3894128 103127.7009 0.011057007 0.015636944 1.93E-10 9.714316145 0.055939172 GDMS(ph)DEDDENEFFDAPEIITMPENLGHKR ddPTM_HeLa_Romidepsin_16h_R1 2 GDMSDEDDENEFFDAPEIITMPENLGHKR 29 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 GDMS(1)DEDDENEFFDAPEIITMPENLGHKR;GDMS(0.999)DEDDENEFFDAPEIIT(0.001)MPENLGHKR ; 43.831 0.0092083 7515800 1531.29 1596.8 1416.83 1272.56 1455.69 1479.35 1225.66 1180.92 1343.87 1407.87 TRUE FALSE FALSE 1512.626048 1619.279792 1441.489332 1419.699375 1381.400707 1384.824309 1329.76753 1215.088057 1223.670901 1371.293334 1.103065267 1.180841292 1.051189629 1.035299552 1.007370686 1.009867309 0.969717781 0.886089086 0.892348027 1 10.4213215 -7.226191605 0.790823421 1.059520211 0.782169273 0.298215011 0.070579082 1.803629156 0.77553714 0.009549254 0.444974084 5.94E-08 7.226191605 -0.277350937 GDPGS(ph)SPAGPR ddPTM_HeLa_Romidepsin_16h_R1 2 GDPGSSPAGPR 11 0 H3BRW8;Q9P1Z2-4;Q9P1Z2-2;Q9P1Z2-3;Q9P1Z2 H3BRW8 CALCOCO1 Calcium-binding and coiled-coil domain-containing protein 1 1 0 GDPGS(0.5)S(0.5)PAGPR;GDPGS(0.5)S(0.5)PAGPR ; 131.42 0.0049729 31049000 4470.4 4528.1 4620 3790.4 8240.5 11997.2 10617.8 7064.4 5201.9 4822.5 TRUE FALSE FALSE 4415.913045 4591.846711 4700.409162 4228.663882 7819.956535 11230.61764 11519.67567 7268.797268 4736.629036 4697.210755 0.940113884 0.977568806 1.000680916 0.900249979 1.664808531 2.390912017 2.452450245 1.547470967 1.008391848 1 12.19758861 -8.583541994 3.407982259 0.969603209 2.15518213 0.836736166 0.231852474 0.060019916 1.416357225 0.031487178 0.068094025 2.61E-09 8.583541994 1.18557892 GDPPRLS(ph)PDPVAGSAVSQELR ddPTM_HeLa_Romidepsin_16h_R1 2 GDPPRLSPDPVAGSAVSQELR 21 1 E9PMR3;E9PMG4;Q9BUR4 E9PMR3 WRAP53 Telomerase Cajal body protein 1 1 0 GDPPRLS(0.999)PDPVAGSAVSQELR;GDPPRLS(1)PDPVAGSAVSQELR ; 96.012 0.00028072 58940000 2022.82 2097.53 2363.6 1502.24 2331.07 3236.65 2568.9 2775.37 1758.83 1990.39 TRUE FALSE FALSE 1998.165092 2127.059082 2404.737467 1675.936057 2212.106799 3029.838511 2787.102302 2855.670952 1601.51584 1938.679381 1.030683625 1.097169085 1.240399774 0.86447304 1.141037977 1.5628363 1.437629311 1.472998052 0.826085971 1 10.92085851 -8.378453431 4.432864139 1.030354826 1.48415605 0.779650961 0.113895844 0.063687168 2.0259501 0.01306232 0.030204873 4.18E-09 8.378453431 0.453801223 GDQPAASGDS(ph)DDDEPPPLPR ddPTM_HeLa_Romidepsin_16h_R1 3 GDQPAASGDSDDDEPPPLPR 20 0 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 GDQPAAS(0.036)GDS(0.964)DDDEPPPLPR;GDQPAAS(0.089)GDS(0.911)DDDEPPPLPR;GDQPAAS(0.029)GDS(0.971)DDDEPPPLPR ;; 262.91 8.16E-81 31071200 5884.4 6916.3 6861.7 4776.22 5270.77 7486.5 4737.95 5995.8 6977.7 7289.9 TRUE FALSE FALSE 5812.678669 7013.667853 6981.12501 5328.469029 5001.782939 7008.136812 5140.391355 6169.279013 6353.597036 7100.507347 0.81862864 0.987769959 0.983186788 0.750434972 0.704426134 0.986990995 0.723947051 0.868850451 0.894808881 1 12.7937064 -9.260414082 24.99686429 0.923544448 0.806628499 0.334554459 0.090665375 104.1624555 2539489.745 0.015280647 0.024426076 5.49E-10 9.260414082 -0.116915949 GDQVLNFS(ph)DAEDLIDDSK ddPTM_HeLa_Romidepsin_16h_R1 1 GDQVLNFSDAEDLIDDSK 18 0 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 0 GDQVLNFS(1)DAEDLIDDSK 83.849 0.010651 2468500 2056.3 1932.3 2204.2 1393.7 1629.2 1613.3 1344.3 1608.8 1888.2 1986.6 TRUE FALSE FALSE 2031.237025 1959.50297 2242.563176 1554.846152 1546.055845 1510.215337 1458.484808 1655.34809 1719.314663 1934.987846 1.04974149 1.012669395 1.158954658 0.80354311 0.799000287 0.780477945 0.753743654 0.855482423 0.888540291 1 10.91810879 -9.235617985 21.75561108 1.032338347 0.794997791 0.738131793 0.066411779 39.5776051 33345.55181 0.007187518 0.011913434 5.81E-10 9.235617985 -0.237340556 GDQVLNFS(ph)DAEDLIDDSKLK ddPTM_HeLa_Romidepsin_16h_R1 1 GDQVLNFSDAEDLIDDSKLK 20 1 F8W126;Q96EZ8-4;Q96EZ8-3;Q96EZ8;Q96EZ8-2 F8W126 MCRS1 Microspherule protein 1 1 0 GDQVLNFS(1)DAEDLIDDSKLK 166.57 1.60E-10 11454000 837.53 769.7 611.72 466.29 382.05 450.52 354.7 342.88 797.14 685.4 TRUE FALSE FALSE 827.3218622 780.5358568 622.36673 520.2046438 362.5525629 421.733226 384.8282091 352.8006918 725.8418019 667.5932092 1.239260452 1.169178844 0.932254435 0.779223989 0.543074072 0.631721863 0.576441168 0.528466568 1.087251626 1 9.382825469 -9.224995856 1.745456572 1.119447772 0.573040233 0.924097869 0.070992906 0.090876258 0.540396214 0.016120971 0.029364186 5.96E-10 9.224995856 -0.546407539 GDREEEVERPVS(ph)SPGDPEQK ddPTM_HeLa_Romidepsin_16h_R1 1 GDREEEVERPVSSPGDPEQK 20 2 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 0 GDREEEVERPVS(0.777)S(0.223)PGDPEQK 57.238 0.028883 7791400 2494.8 2708.6 2540.5 2244.8 2658.9 2913.8 2065.6 2977.5 2880.9 2697.6 TRUE FALSE FALSE 2464.392418 2746.731742 2584.716337 2504.354338 2523.206411 2727.617584 2241.052012 3063.649265 2623.225089 2627.515963 0.937917201 1.045372047 0.983710993 0.953126212 0.960301078 1.038097436 0.852916612 1.165986927 0.998366946 1 11.35948381 -7.235891918 24.6470114 0.972728177 1.165987227 0.548388296 0.052131835 3783.89197 3650462.609 0.006613483 0.651725399 5.81E-08 7.235891918 0.19325905 GDRS(ph)PEPGQTWTR ddPTM_HeLa_Romidepsin_16h_R1 3 GDRSPEPGQTWTR 13 1 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GDRS(0.999)PEPGQTWT(0.001)R;GDRS(1)PEPGQTWTR;GDRS(1)PEPGQTWTR ;; 159.66 0.0031526 42813100 3187.91 2989.38 3064.75 7289.4 3186.3 3077.14 2805.38 3457.53 3509.1 3636.54 TRUE FALSE FALSE 3149.054527 3031.46457 3118.090688 8132.234726 3023.691221 2880.520685 3043.668907 3557.568175 3195.237307 3542.062167 0.889045527 0.855847364 0.880303773 2.295904008 0.853652782 0.813232673 0.85929291 1.004377678 0.902083915 1 11.79037382 -6.198954686 18.74810226 1.003888847 1.085061282 0 0.425428015 0 0 0.054190032 0 6.32E-07 6.198954686 0.081172434 GDRSEDFGVNEDLADSDAR ddPTM_HeLa_Romidepsin_16h_R1 3 GDRSEDFGVNEDLADSDAR 19 1 P04083 P04083 ANXA1 Annexin A1 0 0 ;; ;; 188.1 1.19E-14 259550500 7758.2 6605.87 5966.85 9379.6 8328.11 7701.1 7553.7 7750 7976.7 7011.9 FALSE FALSE TRUE 7663.640074 6698.867611 6070.700521 10464.11348 7903.09547 7209.024564 8195.311089 7974.234023 7263.243974 6829.729827 1.122100034 0.980839328 0.888863934 1.532141644 1.157160777 1.055535833 1.199946601 1.167576789 1.063474567 1 12.73761279 GDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_HeLa_Romidepsin_16h_R1 1 GDSESEEDEDLEVPVPSR 18 0 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 0 GDS(0.996)ES(0.99)EEDEDLEVPVPS(0.014)R 98.165 0.0018512 0 611.49 687.57 648.11 526.35 640.38 699.19 641.72 797.26 633.62 840.17 TRUE FALSE FALSE 604.0369247 697.2496285 659.3900827 587.2090636 607.699019 654.5140155 696.2276808 820.3274602 576.9474403 818.3422623 0.738122608 0.852026909 0.805763203 0.717559254 0.742597623 0.799804734 0.850778107 1.002425877 0.705019729 1 9.67656055 -12.42481527 1.098996249 1.002368938 0.803560907 0 0.118928311 0.377223428 0.79923111 0.05868058 0.014065888 3.76E-13 12.42481527 -0.19880803 GDS(ph)LILEHQWELEK ddPTM_HeLa_Romidepsin_16h_R1 4 GDSLILEHQWELEK 14 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4;A0A0U1RQL3 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 0 GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK;GDS(1)LILEHQWELEK ;;; 142.4 0.00030096 33385900 20114.1 19706 19785.3 12965.5 21524.4 20839.8 17675.3 21444.1 20360.1 19267.1 TRUE FALSE FALSE 19868.94161 19983.42159 20129.65485 14464.63211 20425.92955 19508.20404 19176.63954 22064.5512 18539.04166 18766.53796 1.058743048 1.064843266 1.072635501 0.77076721 1.088422893 1.039520666 1.021852809 1.175739033 0.987877556 1 14.19587491 -7.261312219 8.473339384 1.021096619 1.176683907 0.237881622 0.086644659 0.101210133 110.5738983 0.011287582 0.089043607 5.48E-08 7.261312219 0.155587288 GDS(ph)VSDSGSDALR ddPTM_HeLa_Romidepsin_16h_R1 1 GDSVSDSGSDALR 13 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 0 GDS(0.836)VS(0.155)DS(0.009)GSDALR 150.9 0.00076859 8089300 1819.4 1596.6 1729 999.25 972.37 673.94 1209.2 697.69 1635.1 1535.2 TRUE FALSE FALSE 1797.224453 1619.076977 1759.09252 1114.787987 922.7463305 630.877409 1311.909418 717.8765594 1488.852561 1495.315283 1.201903354 1.082766287 1.176402422 0.745520359 0.617091486 0.421902602 0.877346358 0.480083744 0.995678021 1 10.54623399 -9.115834394 3.554201987 1.102037141 0.611070052 0.769709833 0.128167932 0.086766356 2.009362306 0.01953819 0.03377684 7.66E-10 9.115834394 -0.490967089 GDSES(ph)EEDEDLEVPVPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GDSESEEDEDLEVPVPSR 18 0 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 0 GDS(0.48)ES(0.521)EEDEDLEVPVPS(1)R 192.6 1.25E-13 35518000 1794.3 1374.3 1804.3 904.21 1552.3 1819.2 1369.8 1327.4 1706.1 1319.8 TRUE FALSE FALSE 1772.430381 1393.647431 1835.703085 1008.759015 1473.080339 1702.958991 1486.150778 1365.806225 1553.502143 1285.511406 1.378774528 1.084119071 1.427994397 0.784714169 1.145909972 1.324732697 1.156077473 1.062461382 1.208470136 1 10.3281267 GDSES(ph)EEDEDLEVPVPSR ddPTM_HeLa_Romidepsin_16h_R1 1 GDSESEEDEDLEVPVPSR 18 0 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 0 GDS(0.489)ES(0.511)EEDEDLEVPVPSR 164.2 4.79E-11 0 1156.6 1097.9 1239.6 1208.8 1187 1142 886.01 745.9 1215.6 979.95 TRUE FALSE FALSE 1142.502914 1113.356265 1261.174718 1348.567144 1126.422961 1069.029886 961.2676673 767.4814397 1106.873691 954.4907577 1.196976403 1.166440069 1.32130637 1.412865586 1.180129772 1.120000248 1.007100026 0.804074249 1.159648412 1 9.898587418 -7.39338606 1.964108874 1.14765515 0.753392536 0.519696387 0.112537097 0.496030068 2.475350064 0.020537772 0.31813699 4.04E-08 7.39338606 -0.394262614 GDSET(ph)DLEALFNAVMNPK ddPTM_HeLa_Romidepsin_16h_R1 1 GDSETDLEALFNAVMNPK 18 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 GDS(0.024)ET(0.976)DLEALFNAVMNPK 123.76 0.0039521 132690000 4816.3 4583 3944.3 2991.3 2050.7 2520.1 1723.4 2356.3 4698.5 4843 TRUE FALSE FALSE 4757.597083 4647.519594 4012.948887 3337.16818 1946.045127 2359.073743 1869.785553 2424.475823 4278.254392 4717.178162 1.008568453 0.985233001 0.85070963 0.707450104 0.412544335 0.500102744 0.39637798 0.513967406 0.906952048 1 12.20370838 -9.159360141 1.517168676 1.003638197 0.446960408 0.946289259 0.055505748 0.039913697 0.180276978 0.006600327 0.01282594 6.93E-10 9.159360141 -0.556677789 GDSK(ac)NAK(ac)K(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GDSKNAKKK 9 3 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 3 GDSK(1)NAK(1)K(1)K 115.7 0.016072 16477000 1810.7 1956.5 1966.7 1258 1021.4 940.04 1075.4 557.36 2074 1511.4 FALSE TRUE FALSE 1788.630492 1984.043658 2000.929589 1403.455879 969.2741466 879.9744778 1166.744449 573.4863322 1888.496246 1472.13361 1.214991954 1.347733415 1.359203794 0.953348167 0.658414522 0.597754492 0.792553367 0.389561333 1.282829379 1 10.5236929 -8.868307994 3.266911093 1.144588616 0.616828721 0.792396114 0.14807794 0.102756886 2.176241234 0.024226845 0.046655337 1.35E-09 8.868307994 -0.527759895 GDTPGHAT(ph)PGHGGATSSAR ddPTM_HeLa_Romidepsin_16h_R1 2 GDTPGHATPGHGGATSSAR 19 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 GDT(0.003)PGHAT(0.997)PGHGGATSSAR;GDT(0.246)PGHAT(0.754)PGHGGATSSAR ; 98.3 0.0012578 3162100 442.1 346.8 581.83 326.63 850.23 1137.07 619.88 656.64 719.67 650.36 TRUE FALSE FALSE 436.7115152 351.6822595 591.9565071 364.3964974 806.8395905 1064.414897 672.5325917 675.6388424 655.3009128 633.4635534 0.689402749 0.555173629 0.934476031 0.575244614 1.273695363 1.68030961 1.061675274 1.066578872 1.034472953 1 9.307117806 -8.740131822 24.18607369 0.814449653 1.28491199 0.520474803 0.221651637 106.6699416 121079.3612 0.033077339 0.066095385 1.82E-09 8.740131822 0.470462337 GDVEEDETIPDSEQDIRPR ddPTM_HeLa_Romidepsin_16h_R1 2 GDVEEDETIPDSEQDIRPR 19 1 Q92973-3;Q92973-2;Q92973 Q92973-3 TNPO1 Transportin-1 0 0 ; ; 226.74 1.14E-38 13392900 4956.7 4657.5 4963.2 4363.4 4016.8 4576.8 3518.9 4686.9 5739.1 5067.2 FALSE FALSE TRUE 4896.285834 4723.068407 5049.582414 4867.916838 3811.807707 4284.357251 3817.795278 4822.508057 5225.780522 4935.553414 0.992043936 0.956948089 1.02310359 0.98629605 0.77231617 0.868060153 0.77352932 0.977095708 1.058803357 1 12.26899614 -8.812689456 10.28955836 0.994579273 0.843970924 0.621702942 0.059037501 0.188922787 36.90221766 0.007209681 0.013092915 1.54E-09 8.812689456 -0.150608349 GDVEGSQS(ph)QDEGEGSGESER ddPTM_HeLa_Romidepsin_16h_R1 2 GDVEGSQSQDEGEGSGESER 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 0 GDVEGS(0.004)QS(0.996)QDEGEGSGESER;GDVEGS(0.001)QS(0.999)QDEGEGSGESER ; 260.98 2.03E-80 12289700 1639.47 1597.85 1740.98 1806.41 1632.58 1636.05 1166.48 1514.32 1805.53 1578.47 TRUE FALSE FALSE 1619.487509 1620.344574 1771.281027 2015.275624 1549.263351 1531.511685 1265.560782 1558.13446 1644.038875 1537.461122 1.053351845 1.0539093 1.152081832 1.310781518 1.00767644 0.99613035 0.823149779 1.013446414 1.069320617 1 10.58633421 -8.109917575 3.122075939 1.058705358 0.917932919 0.296698916 0.09879384 0.289452008 5.328698421 0.015219649 0.045130483 7.76E-09 8.109917575 -0.140772439 GDVT(ph)AEEAAGASPAK ddPTM_HeLa_Romidepsin_16h_R1 1 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 GDVT(0.808)AEEAAGAS(0.192)PAK 152.07 0.00097878 3558400 2557.9 3503.9 2406.3 2518.6 3434.4 2949.9 2194.2 2727.8 2653.6 2528.8 TRUE FALSE FALSE 2526.723331 3553.227996 2448.180642 2809.812382 3259.129752 2761.41091 2380.575293 2806.724589 2416.25537 2463.101411 1.025830004 1.442582908 0.993942284 1.140761955 1.32318131 1.121111334 0.966495038 1.139508335 0.980980872 1 11.26626031 -10.48454148 24.9997026 1.011395442 1.157023365 0.231846485 0.13227433 525.0102346 342361.6592 0.021985213 0.024680963 3.28E-11 10.48454148 0.145627923 GDVTAEEAAGAS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 8 GDVTAEEAAGASPAK 15 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK;GDVTAEEAAGAS(1)PAK ;;;;;;; 163.9 3.20E-05 680448900 25150.59 26784.02 23966.81 17404.2 24728.21 29650.33 24068.92 27419.77 27216.59 26036.93 TRUE FALSE FALSE 24844.04494 27161.08614 24383.94227 19416.55549 23466.23717 27755.76961 26113.33346 28213.11778 24782.27003 25360.48681 0.979635964 1.071000188 0.961493463 0.76562235 0.925307048 1.094449401 1.029685813 1.112483289 0.977200091 1 14.63029482 -8.251707211 24.78635745 0.973112163 1.073954138 0.334688501 0.077266344 698.2706574 1778384.55 0.011634097 0.029244852 5.60E-09 8.251707211 0.100841975 GDVTAEEAAGAS(ph)PAKANGQENGHVK ddPTM_HeLa_Romidepsin_16h_R1 4 GDVTAEEAAGASPAKANGQENGHVK 25 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK;GDVTAEEAAGAS(1)PAKANGQENGHVK ;;; 87.729 2.49E-05 111095100 10749.5 9503.6 9166.1 9962.5 9860.2 10381.1 9207.9 9162.5 10771.7 8882.6 TRUE FALSE FALSE 10618.48096 9637.39193 9325.632126 11114.41112 9356.997201 9717.781213 9990.018796 9427.602481 9808.252174 8651.828771 1.227310577 1.113913854 1.077879876 1.284631425 1.08150513 1.123205448 1.154671349 1.089665865 1.133662308 1 13.0787894 -12.52685371 1.277028161 0.999793131 1.153100163 0.031572641 0.074870839 0.337560595 0.98354931 0.044935575 0.010697132 2.97E-13 12.52685371 0.153307032 GDY(ph)T(ph)IRLQIR ddPTM_HeLa_Romidepsin_16h_R1 2 GDYTIRLQIR 10 1 A0A494C1B8;A0A494C0U1;Q5VZU9;P29144 A0A494C1B8 TPP2 Tripeptidyl-peptidase 2 2 0 GDY(1)T(1)IRLQIR;GDY(1)T(1)IRLQIR ; 101.25 0.022795 3880600 1569.01 1515.21 1325.05 1376.37 1471.24 1529.97 1024.08 1400.81 1628.68 1280.13 TRUE FALSE FALSE 1549.886303 1536.541166 1348.111939 1535.512375 1396.157133 1432.209855 1111.06533 1441.340227 1483.006782 1246.872038 1.243019536 1.232316645 1.081195101 1.231491547 1.119727679 1.148642211 0.89108208 1.155964833 1.189381698 1 10.2840977 GEAAAERPGEAAVAS(ph)SPSK ddPTM_HeLa_Romidepsin_16h_R1 1 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 GEAAAERPGEAAVAS(0.449)S(0.102)PS(0.449)K 97.825 0.00066722 167740000 2916.7 3680.4 3455.8 2360.1 4262.5 4209.2 3355.8 3206.8 4013.5 3801.2 TRUE FALSE FALSE 2881.150139 3732.212768 3515.946749 2632.985867 4044.968719 3940.245705 3640.841568 3299.583699 3654.522508 3702.444276 0.778175152 1.008040227 0.949628539 0.711148007 1.092513058 1.064228226 0.983361611 0.891190644 0.987056721 1 11.85426231 -8.712905859 24.9999984 0.895233842 1.010104893 0.185124971 0.103565615 152.3766345 78489.61538 0.016616258 0.033232463 1.94E-09 8.712905859 0.114871051 GEAAAERPGEAAVASSPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 3 GEAAAERPGEAAVASSPSK 19 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 GEAAAERPGEAAVAS(0.098)S(0.098)PS(0.805)K;GEAAAERPGEAAVAS(0.012)S(0.06)PS(0.928)K;GEAAAERPGEAAVAS(0.139)S(0.101)PS(0.76)K ;; 196.65 1.10E-14 1423560000 22362.8 22521.3 25121.2 14624 24868.4 24641 21230 21300.7 22585.6 24480 TRUE FALSE FALSE 22090.23359 22838.35545 25558.42395 16314.89569 23599.27275 23066.51963 23033.27567 21917.00215 20565.48737 23844.00607 0.926448078 0.957823756 1.071901419 0.684234673 0.989736065 0.967392793 0.965998566 0.919182879 0.862501348 1 14.54133903 ALS(ph)PGLEESGLGLLAR ddPTM_HeLa_Romidepsin_16h_R1 2 ALSPGLEESGLGLLAR 16 0 H9KVB4;O15417-2;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 0 ALS(0.99)PGLEES(0.01)GLGLLAR;ALS(1)PGLEESGLGLLAR ; 227.91 2.79E-35 66930000 6665.7 5379.7 5962.4 4409.7 2574.3 2342.42 2520.3 2492.3 6234.5 5907.9 TRUE FALSE FALSE 6584.455885 5455.435558 6066.173071 4919.570262 2442.923865 2192.746922 2734.374219 2564.410768 5676.870705 5754.411906 1.144244797 0.948043979 1.054177763 0.854921466 0.424530587 0.381054912 0.475178743 0.445642545 0.986524913 1 12.49045278 -8.897152076 2.770062757 1.057274514 0.425139668 0.956391092 0.059880878 0.041032207 0.63726948 0.010622122 0.020660585 1.27E-09 8.897152076 -0.632134846 down GEAEQS(ph)EEEADEEDKAEDAR ddPTM_HeLa_Romidepsin_16h_R1 1 GEAEQSEEEADEEDKAEDAR 20 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 GEAEQS(1)EEEADEEDKAEDAR 81.65 0.0015053 11407000 2509.6 2516.1 2541.4 1012.8 2027.7 2548.7 1778.1 2242.7 2660.2 2513.8 TRUE FALSE FALSE 2479.01203 2551.521722 2585.632001 1129.904701 1924.218903 2385.846296 1929.13177 2307.588986 2422.265049 2448.491114 1.012465194 1.042079225 1.056010368 0.461469799 0.785879472 0.974414929 0.787885959 0.942453486 0.989288887 1 11.25767724 GEAERGS(ph)GGS(ph)S(ph)GDELREDDEPVK ddPTM_HeLa_Romidepsin_16h_R1 1 GEAERGSGGSSGDELREDDEPVK 23 2 A0A087WT54;Q7Z4V5-2;Q7Z4V5;Q7Z4V5-4;Q7Z4V5-3 A0A087WT54 HDGFRP2 Hepatoma-derived growth factor-related protein 2 3 0 GEAERGS(1)GGS(1)S(1)GDELREDDEPVK 64.422 0.0031624 13174000 2160 2418.1 2483.9 1647.7 2946.5 3395.2 2621.5 2951.9 2667.3 2746 TRUE FALSE FALSE 2133.673089 2452.142075 2527.131238 1838.214827 2796.12911 3178.257678 2844.170145 3037.308569 2428.730008 2674.658524 0.797736634 0.916805661 0.944842571 0.687270846 1.045415362 1.188285401 1.06337692 1.135587419 0.908052368 1 11.385139 -8.535047035 24.99583006 0.892007007 1.121568934 0.64218367 0.086118653 127.1286801 261144.3198 0.014467979 0.028951567 2.92E-09 8.535047035 0.229561926 GEAGT(ph)PVAAGTTAAAIPR ddPTM_HeLa_Romidepsin_16h_R1 2 GEAGTPVAAGTTAAAIPR 18 0 M0QXQ4;A0A0C4DGH3;Q9Y6R0 M0QXQ4 NUMBL Numb-like protein 1 0 GEAGT(0.88)PVAAGT(0.091)T(0.029)AAAIPR;GEAGT(1)PVAAGTTAAAIPR ; 137.73 0.0017205 11108000 2449.63 2250.99 2410.8 1175.37 2747.4 3291.7 2640.22 2681.1 2229.57 2429.59 TRUE FALSE FALSE 2419.772967 2282.679496 2452.758963 1311.27181 2607.189926 3081.370993 2864.480221 2758.673398 2030.151675 2366.468902 1.022524727 0.964593067 1.036463636 0.554104814 1.101721609 1.30209655 1.210444903 1.165734059 0.857882254 1 11.20852025 -8.524026179 24.99998812 0.974556264 1.220757511 0.470298268 0.143882717 28.62238168 623619.1098 0.020103633 0.040468937 2.99E-09 8.524026179 0.246201247 GEAHLAVNDFELAR ddPTM_HeLa_Romidepsin_16h_R1 2 GEAHLAVNDFELAR 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 0 ; ; 113.53 0.0023411 9505200 6115.3 5544.6 5467.9 4383.8 5310.2 5246.3 4594.5 5184.5 5973.2 5776.5 FALSE FALSE TRUE 6040.764371 5622.657024 5563.066506 4890.675582 5039.200679 4911.078362 4984.756715 5334.505328 5438.942032 5626.425697 1.073641544 0.999330183 0.988738998 0.869233123 0.895630894 0.872859365 0.88595442 0.948116196 0.966678016 1 12.458003 -9.483850612 2.439620643 1.033461683 0.892591955 0.691295951 0.035807814 0.098634032 1.167722627 0.00563996 0.008804502 3.28E-10 9.483850612 -0.140869728 GEASS(ph)LNGESH ddPTM_HeLa_Romidepsin_16h_R1 2 GEASSLNGESH 11 0 Q8IY57-3;Q8IY57;Q8IY57-5 Q8IY57-3 YAF2 YY1-associated factor 2 1 0 GEAS(0.305)S(0.695)LNGESH;GEAS(0.083)S(0.917)LNGESH ; 139.32 0.0032855 10529300 4331.5 4345.3 4159.4 2088.9 3523.5 4247.6 3978.1 2561 4662.8 4739.6 TRUE FALSE FALSE 4278.706012 4406.473247 4231.792612 2330.428447 3343.682647 3976.192069 4315.999715 2635.098494 4245.74749 4616.464509 0.926836111 0.954512536 0.916673919 0.50480805 0.724295105 0.861306756 0.934914523 0.570804452 0.919696768 1 12.17257268 -9.498569845 24.5243661 0.962327968 0.736519225 0.469538726 0.118655324 406.8670626 410473.82 0.018116156 0.027577485 3.17E-10 9.498569845 -0.225808743 GEAVLRPGLDAEPELS(ph)PEEQR ddPTM_HeLa_Romidepsin_16h_R1 2 GEAVLRPGLDAEPELSPEEQR 21 1 C9JQV0;Q9BRJ6 C9JQV0 C7orf50 Uncharacterized protein C7orf50 1 0 GEAVLRPGLDAEPELS(1)PEEQR;GEAVLRPGLDAEPELS(1)PEEQR ; 100.92 0.00016382 71087000 2070.67 1912.49 2016.27 1817.49 2926.5 3866.8 3213.2 3189.1 2556.8 2565.1 TRUE FALSE FALSE 2045.431878 1939.414084 2051.362334 2027.636745 2777.149785 3619.72396 3486.129128 3281.371577 2328.113404 2498.458332 0.818677603 0.776244318 0.821051249 0.811555158 1.111545367 1.448783001 1.395312094 1.313358536 0.931819984 1 11.28682244 -8.490513383 3.484812351 0.887281375 1.383499377 0.91093308 0.073412357 0.0659214 1.649787592 0.014162922 0.032304636 3.23E-09 8.490513383 0.496218002 GEDEEENNLEVR ddPTM_HeLa_Romidepsin_16h_R1 1 GEDEEENNLEVR 12 0 F8WF32;P04843 F8WF32 RPN1 Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 0 0 111.5 0.0034388 0 739.62 743.92 723.05 521.2 947.93 798.55 594.69 775.39 823.33 902.55 FALSE FALSE TRUE 730.605227 754.3929253 735.6343819 581.4635963 899.5535949 747.5252322 645.2029538 797.8246863 749.6893027 879.1016209 0.831081652 0.858140751 0.836802441 0.66142933 1.02326463 0.850328579 0.733934438 0.907545462 0.852790263 1 9.779886135 -12.16932341 0.692404288 1.013109242 0.833658539 0.028274553 0.101088597 0.804180678 0.621799298 0.084458245 0.018502296 6.77E-13 12.16932341 -0.179450703 GEDLEINSQNT(ph)T(ph)YLYASFLT(ph)T(ph)VFK ddPTM_HeLa_Romidepsin_16h_R1 1 GEDLEINSQNTTYLYASFLTTVFK 24 0 Q7RTR0-2;Q7RTR0 Q7RTR0-2 NLRP9 "NACHT, LRR and PYD domains-containing protein 9" 4 0 GEDLEINS(0.106)QNT(0.437)T(0.437)Y(0.413)LY(0.402)AS(0.386)FLT(0.824)T(0.995)VFK 40.756 0.020397 3633400 423.38 460.64 292.04 482.77 538.01 624.04 377.73 452.46 432.35 455.14 TRUE FALSE FALSE 418.2196817 467.124902 297.1228337 538.5901389 510.5533421 584.165858 409.8143768 465.5512162 393.6795332 443.3153972 0.943390833 1.053707823 0.670228996 1.214914127 1.151670674 1.317720661 0.924430731 1.050158012 0.888034875 1 8.792189661 GEDLTEEEDGGIIRR ddPTM_HeLa_Romidepsin_16h_R1 2 GEDLTEEEDGGIIRR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 0 ; ; 160.84 1.27E-05 3495000 3724.4 3135.4 3686.8 2135.74 3122 3523.3 2601.4 3450.4 3580.6 3755.3 FALSE FALSE TRUE 3679.00558 3179.540243 3750.967207 2382.684308 2962.67269 3298.172501 2822.362851 3550.23188 3260.342168 3657.736765 1.005814747 0.86926437 1.02548856 0.651409454 0.809974277 0.901697611 0.771614535 0.970608906 0.891355059 1 11.83673554 -9.300458373 24.99950668 0.992231572 0.82217773 0.322808456 0.093204348 331.0654618 212113.093 0.012751595 0.019478609 5.01E-10 9.300458373 -0.170053842 GEDS(ph)AEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK ddPTM_HeLa_Romidepsin_16h_R1 1 GEDSAEETEAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 41 1 Q12906-4;Q12906-6;Q12906-7 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 GEDS(0.865)AEET(0.135)EAKPAVVAPAPVVEAVSTPSAAFPSDATAENVK 51.096 0.0019255 13240000 5524.6 5383.9 6116.4 3409.7 6423.6 6402.4 5281.8 5803.5 5990.8 5989 TRUE FALSE FALSE 5457.26405 5459.694686 6222.853376 3803.945557 6095.779722 5993.307303 5730.43596 5971.415116 5454.967844 5833.404917 0.9355195 0.935936175 1.066761774 0.65209695 1.044977986 1.027411501 0.982348396 1.023658601 0.935125869 1 12.5101225 GEDVPS(ph)EEEEEEENGFEDR ddPTM_HeLa_Romidepsin_16h_R1 4 GEDVPSEEEEEEENGFEDR 19 0 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 0 GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR;GEDVPS(1)EEEEEEENGFEDR ;;; 216.77 2.28E-29 60251000 26649.5 25638.5 28155.8 14630.3 19802.9 19927 16285.2 15657.17 28627.5 30211 TRUE FALSE FALSE 26324.68564 25999.43948 28645.83989 16321.92412 18792.28412 18653.72901 17668.46448 16110.18551 26066.9847 29426.11386 0.894602861 0.883549883 0.973483621 0.55467481 0.638626093 0.633917516 0.600434857 0.547479208 0.885845301 1 14.84480941 -9.263078061 24.9998952 0.944488684 0.599909766 0.928955693 0.045841387 29.22123773 445802.6982 0.008025603 0.012666657 5.46E-10 9.263078061 -0.344578917 GEEDWLYER ddPTM_HeLa_Romidepsin_16h_R1 1 GEEDWLYER 9 0 J3QQZ9;Q9NVS9-4;Q9NVS9-3;Q9NVS9 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 0 0 182.98 0.0007491 16523000 5730.5 5275.5 5783.9 4325.1 6309.1 5449.7 5513.3 6167.2 6522.9 5011.8 FALSE FALSE TRUE 5660.654462 5349.768627 5884.566353 4825.188412 5987.123085 5101.481758 5981.599564 6345.638202 5939.475487 4881.592714 1.159591714 1.095906386 1.205460328 0.988445513 1.226469195 1.045044529 1.225337695 1.299911438 1.216708528 1 12.25313622 -16.52287875 0.112372779 0.502360925 1.249368762 0 0.105104635 84.79132018 0.697220286 9.841087843 0.480314885 3.00E-17 16.52287875 0.747007837 GEEGS(ph)DDDETENGPKPK ddPTM_HeLa_Romidepsin_16h_R1 4 GEEGSDDDETENGPKPK 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 0 GEEGS(0.999)DDDET(0.001)ENGPKPK;GEEGS(1)DDDETENGPKPK;GEEGS(0.997)DDDET(0.003)ENGPKPK;GEEGS(1)DDDETENGPKPK ;;; 160.93 9.97E-06 57800000 6952.2 6477.58 6269.01 6941.21 7466.1 7865 6263.82 6569.87 6993.95 7045.97 TRUE FALSE FALSE 6867.463912 6568.771541 6378.119489 7743.78536 7085.077057 7362.451883 6795.868714 6759.958823 6368.393595 6862.914684 1.000662871 0.957140201 0.92936016 1.12835227 1.032371432 1.072787908 0.990230686 0.984998231 0.927942993 1 12.7446057 -9.282286223 24.99938852 0.991558481 1.040089552 0.325014877 0.048676847 952.9950137 1142822.37 0.006895879 0.010541674 5.22E-10 9.282286223 0.048531071 GEEGSDDDET(ph)ENGPKPK ddPTM_HeLa_Romidepsin_16h_R1 1 GEEGSDDDETENGPKPK 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 0 GEEGS(0.001)DDDET(0.999)ENGPKPK 122.97 0.0012315 77924000 1191.6 1148.1 1161.1 1132.5 1208 1054.1 1079.5 1218.8 897.76 1248.5 TRUE FALSE FALSE 1177.076321 1164.262982 1181.308458 1263.444979 1146.351252 986.746412 1171.192703 1254.064055 817.4620971 1216.06379 0.967939618 0.957402886 0.971419812 1.038962749 0.942673618 0.811426522 0.963101371 1.031248579 0.67221975 1 10.24800319 -8.541119842 24.87395619 0.984734576 0.927877571 0 0.112930398 279.6005828 381268.2103 0.007870022 0.015742074 2.88E-09 8.541119842 -0.056857005 GEELGGAEGDTS(ph)SPDPAGR ddPTM_HeLa_Romidepsin_16h_R1 1 GEELGGAEGDTSSPDPAGR 19 0 Q6F5E8;Q6F5E8-2;R4GMZ7 Q6F5E8 RLTPR Leucine-rich repeat-containing protein 16C 1 0 GEELGGAEGDT(0.047)S(0.516)S(0.437)PDPAGR 118.21 2.37E-06 0 758.56 702.92 735.32 878.88 1136.4 1436.9 1125.3 1261.8 859.11 728.54 TRUE FALSE FALSE 749.3143789 712.8157262 748.1179361 980.5002409 1078.405268 1345.086727 1220.882954 1298.308192 782.2690499 709.6124258 1.055948785 1.004514155 1.054262734 1.381740518 1.519710237 1.895523075 1.720492637 1.829601829 1.102389166 1 9.470887462 -8.841942444 1.398248548 1.022320779 1.812737712 0.959997102 0.068453146 0.045231039 0.177244715 0.009459691 0.022766811 1.44E-09 8.841942444 0.790416933 GEGDAPFSEPGT(ph)T(ph)STQRPSSPETATK ddPTM_HeLa_Romidepsin_16h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 GEGDAPFS(0.159)EPGT(0.389)T(0.336)S(0.336)T(0.336)QRPS(0.336)S(0.098)PET(0.009)AT(0.001)K 53.266 0.0026167 0 1406.6 1463.9 1611 1010.5 1440.6 1261.3 1106.3 1344.3 1708 1877 TRUE FALSE FALSE 1389.455818 1484.508823 1639.038779 1127.338765 1367.080806 1180.707001 1200.269094 1383.1952 1555.232202 1828.235269 0.759998366 0.811990036 0.896514145 0.616626746 0.747759782 0.645817866 0.656517853 0.756573961 0.850673996 1 10.83623602 -16.52287875 0.141897062 2.00336818 0.623114255 0.452987396 0.084196117 28.71634783 0.282407587 8.022953507 0.193523068 3.00E-17 16.52287875 -1.380253925 GEGDAPFSEPGT(ph)TSTQRPSSPETATK ddPTM_HeLa_Romidepsin_16h_R1 2 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 GEGDAPFS(0.004)EPGT(0.27)T(0.196)S(0.196)T(0.196)QRPS(0.068)S(0.068)PET(0.002)ATK;GEGDAPFS(0.004)EPGT(0.278)T(0.278)S(0.278)T(0.086)QRPS(0.037)S(0.037)PET(0.003)AT(0.001)K ; 82.177 3.21E-05 414900000 7678.6 8842.1 7201.7 6566.2 6735 6996.8 5560.4 6211.1 8203.2 7924.5 TRUE FALSE FALSE 7585.01027 8966.579316 7327.042568 7325.414939 6391.287818 6549.727061 6032.700237 6390.808379 7469.485247 7718.620348 0.982689902 1.16168161 0.949268423 0.949057553 0.828035002 0.848561889 0.781577531 0.827972888 0.967722846 1 12.91412728 -8.884932866 1.924840841 1.004391019 0.814586493 0.718710507 0.056373001 0.135721082 1.018129564 0.008519745 0.017858542 1.30E-09 8.884932866 -0.189804526 GEGDAPFSEPGTTST(ph)QRPS(ph)SPETATK ddPTM_HeLa_Romidepsin_16h_R1 1 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 GEGDAPFS(0.001)EPGT(0.042)T(0.147)S(0.147)T(0.493)QRPS(0.582)S(0.582)PET(0.005)AT(0.001)K 63.376 0.0020348 3599300 3131.1 2867.9 2845.5 2793.8 2778.1 2972.8 2144.4 2490.5 3098.5 2688.8 TRUE FALSE FALSE 3092.936949 2908.274371 2895.024734 3116.832301 2636.32319 2782.847674 2326.545282 2562.558688 2821.3624 2618.944588 1.180986021 1.110475718 1.105416566 1.19011006 1.006635727 1.06258364 0.888352237 0.978469991 1.077289841 1 11.35476982 -8.03021406 1.845538492 1.095837456 0.933812681 0.492957382 0.063306182 0.296306122 1.90196861 0.011701036 0.048966416 9.33E-09 8.03021406 -0.162024775 GEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_HeLa_Romidepsin_16h_R1 2 GEGDAPFSEPGTTSTQRPSSPETATK 26 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 GEGDAPFSEPGT(0.004)T(0.004)S(0.004)T(0.026)QRPS(0.479)S(0.479)PET(0.002)ATK;GEGDAPFS(0.021)EPGT(0.096)T(0.086)S(0.086)T(0.086)QRPS(0.291)S(0.291)PET(0.033)AT(0.011)K ; 98.002 2.48E-06 361510000 6483.9 6187.6 5643.1 4719.4 5613.8 5237.4 4936.1 5292.6 6995.5 7126.3 TRUE FALSE FALSE 6404.871733 6274.709195 5741.315788 5265.079233 5327.306838 4902.747043 5355.372211 5445.733031 6369.804959 6941.157699 0.922738254 0.903985973 0.827140952 0.758530416 0.767495434 0.706329874 0.771538761 0.78455688 0.917686247 1 12.76096059 -9.886842418 0.781981398 0.97746951 0.745735235 0.877400321 0.031337868 0.109867441 0.135661296 0.006591516 0.009965016 1.30E-10 9.886842418 -0.231734276 GEGDIHENVDTDLPGS(ph)LGQSEEKPVPAAPVPSPVAPAPVPSR ddPTM_HeLa_Romidepsin_16h_R1 2 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 GEGDIHENVDTDLPGS(0.476)LGQS(0.476)EEKPVPAAPVPS(0.047)PVAPAPVPSR;GEGDIHENVDT(0.022)DLPGS(0.763)LGQS(0.213)EEKPVPAAPVPS(0.001)PVAPAPVPSR ; 98.627 2.01E-15 145838000 5463 5786.8 6446 3734.2 10274 13497.2 12222.6 12876.5 7174.4 7527.5 TRUE FALSE FALSE 5396.414855 5868.266722 6558.189926 4165.965774 9749.679442 12634.77248 13260.78734 13249.06121 6532.703695 7331.934465 0.736015151 0.800370864 0.894469251 0.568194628 1.329755399 1.723252239 1.808634188 1.807034866 0.890993192 1 12.83997818 -8.476052214 3.083937594 0.849009289 1.781672415 0.928484379 0.119986143 0.054843635 1.035908375 0.02048405 0.048015477 3.34E-09 8.476052214 0.932663126 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(ph)PVAPAPVPSR ddPTM_HeLa_Romidepsin_16h_R1 2 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPSPVAPAPVPSR 42 1 Q9UK76;Q9UK76-3 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 GEGDIHENVDTDLPGSLGQSEEKPVPAAPVPS(0.986)PVAPAPVPS(0.013)R;GEGDIHENVDTDLPGS(0.009)LGQS(0.027)EEKPVPAAPVPS(0.952)PVAPAPVPS(0.011)R ; 86.131 4.33E-10 29485000 2348.21 2123.75 2386.33 1800.36 3962.8 4853 4324 4473.4 2512.42 2395.6 TRUE FALSE FALSE 2319.589113 2153.648208 2427.863073 2008.526094 3760.563529 4542.908962 4691.280452 4602.830771 2287.702863 2333.361967 0.994097421 0.922980763 1.040499977 0.860786334 1.611650307 1.946937092 2.010524093 1.972617552 0.980432053 1 11.18819441 -8.576764946 3.080823884 0.985702136 1.97137496 0.981485071 0.063084194 0.022730134 0.438228923 0.009315255 0.02058821 2.65E-09 8.576764946 0.985672824 GEGES(ph)PPVNGTDEAAGATGDAIEPAPPSQGAEAK ddPTM_HeLa_Romidepsin_16h_R1 1 GEGESPPVNGTDEAAGATGDAIEPAPPSQGAEAK 34 0 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 GEGES(0.714)PPVNGT(0.203)DEAAGAT(0.083)GDAIEPAPPSQGAEAK 70.111 3.85E-06 0 950.97 948.66 789.81 628.96 957.43 780.57 865.71 1063.1 1093.4 946.73 TRUE FALSE FALSE 939.3792119 962.0152604 803.5563117 701.6833145 908.5687744 730.6940962 939.2433858 1093.859121 995.6035655 922.1338181 1.018701617 1.043249083 0.871409654 0.760934368 0.985289506 0.792394858 1.018554322 1.186226012 1.079673629 1 9.848832316 -9.771770717 24.98643388 1.01165941 0.927345416 0.136592303 0.115558745 353.3967655 854691.6904 0.018243172 0.024123945 1.69E-10 9.771770717 -0.084313994 GEGPGEAGGPLT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 GEGPGEAGGPLTPR 14 0 P50548;P50548-2 P50548 ERF ETS domain-containing transcription factor ERF 1 0 GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR;GEGPGEAGGPLT(1)PR ;;; 130.66 0.0044273 46981000 6200.23 6387.97 6141.97 6168.13 5045.28 3794.98 3839.05 4577.91 6539.12 6418.71 TRUE FALSE FALSE 6124.659212 6477.900009 6248.868411 6881.318213 4787.800535 3552.493026 4165.138811 4710.364603 5954.24473 6251.950989 0.979639671 1.036140562 0.999506942 1.100667332 0.765809032 0.568221509 0.666214246 0.753423149 0.952381863 1 12.61009075 -8.604203306 5.000032538 1.001089153 0.663151564 0.889286907 0.056550016 0.043606203 1.926357077 0.007707013 0.01574963 2.49E-09 8.604203306 -0.337937589 GEIKDSSPSSSPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 GEIKDSSPSSSPSPK 15 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 GEIKDSSPS(0.001)S(0.003)S(0.059)PS(0.936)PK;GEIKDSSPSS(0.001)S(0.002)PS(0.997)PK ; 100.39 0.0028736 12268400 4384.7 3707.4 3542 6379.1 9973.8 12816.6 12388.5 15488.8 4688.9 4477.2 TRUE FALSE FALSE 4331.25759 3759.592875 3603.647024 7116.681557 9464.799769 11997.66062 13440.77888 15936.94399 4269.51304 4360.881699 0.993206853 0.862117602 0.826357437 1.631936395 2.17038673 2.751200664 3.082124169 3.654523349 0.979048123 1 12.09040414 -8.400200961 0.989730933 0.962100046 3.543521191 0.976401363 0.153199703 0.06713864 0.114488772 0.026049172 0.119736217 3.98E-09 8.400200961 2.581421144 up GELIPISPS(ph)TEVGGSGIGTPPSVLKR ddPTM_HeLa_Romidepsin_16h_R1 1 GELIPISPSTEVGGSGIGTPPSVLKR 26 1 P10244-2;P10244 P10244-2 MYBL2 Myb-related protein B 1 0 GELIPIS(0.122)PS(0.433)T(0.433)EVGGS(0.006)GIGT(0.005)PPS(0.001)VLKR 60.171 0.00074748 0 1972.6 2016.5 1425 2266.1 1415.2 1173.9 1004.4 1207.1 2037.5 2031.2 TRUE FALSE FALSE 1948.557192 2044.88834 1449.801527 2528.117144 1342.977063 1098.891579 1089.713711 1242.025534 1855.260897 1978.429131 0.984901183 1.033591908 0.732804377 1.277840639 0.67880979 0.555436412 0.550797445 0.627783687 0.93774443 1 10.95013967 -8.581568424 8.669199364 0.99212359 0.582095383 0.70416905 0.12550092 0.100314614 13.58821602 0.015881572 0.031834234 2.62E-09 8.581568424 -0.410028207 GELLEAIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GELLEAIKR 9 1 G8JLJ2;F5H3C5;F5H4R2;F5GYZ5;P04179-4;P04179-2;P04179 G8JLJ2 SOD2 "Superoxide dismutase [Mn], mitochondrial" 0 1 GELLEAIK(1)R 87.308 0.021803 491490 190.08 152.34 0 140.45 373.78 370.62 293.4 231.43 287.91 128.61 FALSE TRUE FALSE 187.7632318 154.4846465 0 156.6894898 354.7046118 346.9385781 318.3213887 238.1260619 262.1586085 125.2686937 1.49888393 1.233226291 0 1.250827204 2.831550338 2.769555329 2.541108871 1.900922369 2.092770355 1 6.9688821 -8.793453188 8.796262587 1.137815506 2.531186834 0.592276776 0.5404987 0.118359124 29.8077883 0.071072542 0.130073454 1.61E-09 8.793453188 1.393371328 GELSPS(ph)FLNPPLPPSIDDR ddPTM_HeLa_Romidepsin_16h_R1 2 GELSPSFLNPPLPPSIDDR 19 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 GELS(0.021)PS(0.976)FLNPPLPPS(0.002)IDDR;GELS(0.413)PS(0.577)FLNPPLPPS(0.011)IDDR ; 77.204 0.0039493 11342000 1200.65 1061.71 948.29 831.25 1817.55 2080.89 1752.16 2211.91 1255.99 1032.11 TRUE FALSE FALSE 1186.016016 1076.656781 964.7945897 927.3630361 1724.793641 1947.927845 1900.988427 2275.908126 1143.651109 1005.295633 1.179768395 1.070985236 0.959712305 0.922477931 1.715707881 1.937666672 1.890974519 2.26391924 1.137626655 1 9.973404111 -8.60631869 3.494383887 1.06524904 2.000754027 0.93041485 0.123250084 0.046461354 1.12410491 0.019507779 0.041568748 2.48E-09 8.60631869 0.935504988 GELSPSFLNPPLPPS(ph)IDDRDLSTEEVR ddPTM_HeLa_Romidepsin_16h_R1 3 GELSPSFLNPPLPPSIDDRDLSTEEVR 27 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 GELS(0.026)PS(0.163)FLNPPLPPS(0.794)IDDRDLS(0.009)T(0.009)EEVR;GELSPSFLNPPLPPS(0.999)IDDRDLS(0.001)T(0.001)EEVR;GELS(0.002)PS(0.004)FLNPPLPPS(0.989)IDDRDLS(0.005)T(0.001)EEVR ;; 106.58 6.94E-09 50053700 1804.68 1771.72 1654.78 1674.11 2857.28 2971.09 2576.6 3419.77 1835.83 1756.12 TRUE FALSE FALSE 1782.683866 1796.662321 1683.580752 1867.678475 2711.46234 2781.246938 2795.45634 3518.715649 1671.628767 1710.495749 1.042203038 1.050375203 0.984264797 1.091893082 1.585190925 1.625988804 1.634295988 2.057132063 0.977277358 1 10.7401988 -8.454756974 1.044394978 1.012001669 1.887113447 0.910765858 0.109279901 0.114523019 0.225225701 0.01675889 0.069042838 3.51E-09 8.454756974 0.875111777 GEPAAAAAPEAGAS(ph)PVEK ddPTM_HeLa_Romidepsin_16h_R1 2 GEPAAAAAPEAGASPVEK 18 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 GEPAAAAAPEAGAS(1)PVEK;GEPAAAAAPEAGAS(1)PVEK ; 234.38 3.82E-49 238290000 18889.6 17499.5 19425.3 9344.8 22434.5 27916.5 22305.6 25649.8 16580.1 18393.9 TRUE FALSE FALSE 18659.36629 17745.85842 19763.3892 10425.28974 21289.58375 26132.72575 24200.23711 26391.93649 15097.13433 17916.02383 1.04149037 0.990502055 1.103112465 0.581897515 1.188298473 1.458623074 1.350759373 1.47309117 0.842660988 1 14.12896287 -8.52119471 24.99948149 0.992743464 1.403758532 0.689949455 0.147159928 27.8119608 412866.0138 0.019321567 0.039101471 3.01E-09 8.52119471 0.411015068 GEQVSQNGLPAEQGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 GEQVSQNGLPAEQGSPR 17 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR;GEQVSQNGLPAEQGS(1)PR ;; 268.82 4.20E-87 139126000 5102.97 5150.89 4854.2 3037.5 4911.13 5037.15 4677.16 5043.99 5520.08 5464.52 TRUE FALSE FALSE 5040.773039 5223.404365 4938.685315 3388.710042 4660.49671 4715.292372 5074.437854 5189.929893 5026.35022 5322.550983 0.947059606 0.98137235 0.927879382 0.636670283 0.875613353 0.885908352 0.953384546 0.975083171 0.94434985 1 12.37790215 -9.516818293 24.7643203 0.973820051 0.86297176 0.239532154 0.086584489 254.9064552 1041604.806 0.013932877 0.020095932 3.04E-10 9.516818293 -0.110848291 GES(ph)ENAGTNQETR ddPTM_HeLa_Romidepsin_16h_R1 4 GESENAGTNQETR 13 0 Q08170 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 1 0 GES(1)ENAGTNQETR;GES(0.973)ENAGT(0.026)NQET(0.002)R;GES(0.998)ENAGT(0.002)NQETR;GES(1)ENAGTNQETR ;;; 188.19 1.26E-10 68093500 6559.9 5917.6 5979.42 3695.69 5983.88 6197.12 5543.92 4610.59 5962.88 6552.7 TRUE FALSE FALSE 6479.945416 6000.908128 6083.489297 4123.003067 5678.500275 5801.144032 6014.820426 4743.990147 5429.545078 6382.459909 1.015273971 0.940218695 0.953157463 0.645989654 0.889704026 0.908919776 0.942398466 0.743285538 0.850697874 1 12.63989686 -9.505916357 23.4926664 0.99973726 0.836553079 0.24775821 0.095013219 216.7731343 300227.7668 0.012475312 0.01875576 3.12E-10 9.505916357 -0.163184181 GESAADS(ph)DGWDSAPSDLR ddPTM_HeLa_Romidepsin_16h_R1 2 GESAADSDGWDSAPSDLR 18 0 I3L4Q4;Q9BUL5-4;Q9BUL5;A0A087WVQ2;I3L0Y2;Q9BUL5-2 I3L4Q4 PHF23 PHD finger protein 23 1 0 GESAADS(0.998)DGWDS(0.002)APSDLR;GESAADS(1)DGWDSAPSDLR ; 297.73 3.47E-143 10031300 3017.8 2854.6 3208.8 1752.89 2226.58 2254.7 1651.54 1761.55 2950.7 2946.4 TRUE FALSE FALSE 2981.017893 2894.787134 3264.647818 1955.567389 2112.949314 2110.631947 1791.821766 1812.51767 2686.782002 2869.852103 1.038735721 1.008688612 1.137566572 0.68141748 0.736257214 0.735449727 0.624360316 0.631571804 0.936209221 1 11.48676067 -9.249995024 24.94793561 1.026015843 0.684624249 0.897827259 0.057752436 143.0400268 311817.7731 0.007756873 0.012789587 5.62E-10 9.249995024 -0.341391595 GESDDFHMDFDS(ph)AVAPR ddPTM_HeLa_Romidepsin_16h_R1 2 GESDDFHMDFDSAVAPR 17 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 GES(0.001)DDFHMDFDS(0.999)AVAPR;GES(0.031)DDFHMDFDS(0.969)AVAPR ; 67.312 0.010822 5504100 1925.55 1277.84 1405.97 1380.84 1856.96 2370.6 1733.64 1921.52 1914.45 1547.61 TRUE FALSE FALSE 1902.080656 1295.829465 1430.440318 1540.499218 1762.192402 2219.126311 1880.895338 1977.11615 1743.216797 1507.402869 1.261826347 0.859643757 0.948943609 1.021955875 1.169025506 1.472152108 1.247772163 1.311604343 1.156437229 1 10.55784933 -8.479637552 6.580977854 1.083929388 1.333472382 0.545728387 0.119762066 0.17788183 20.61784414 0.020806392 0.046175023 3.31E-09 8.479637552 0.249542994 GESLDNLDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 GESLDNLDSPR 11 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 GESLDNLDS(1)PR;GESLDNLDS(1)PR;GESLDNLDS(1)PR;GESLDNLDS(1)PR ;;; 191.48 1.23E-08 29542900 7811.2 8446 8343.3 8640.7 9253.4 10506.9 9175.7 8715.1 8680.4 8272.6 TRUE FALSE FALSE 7715.99409 8564.90301 8488.511637 9639.77839 8781.164469 9835.542999 9955.083729 8967.257668 7904.003284 8057.676659 0.957595398 1.062949455 1.053468884 1.196347135 1.089788638 1.220642552 1.235478184 1.112883781 0.980928327 1 12.9761482 -9.564864033 1.257094834 0.980204989 1.179347321 0.748965928 0.047439254 0.140156764 0.443661751 0.008154863 0.013544904 2.72E-10 9.564864033 0.199142332 GESS(ph)SPSPSAEK ddPTM_HeLa_Romidepsin_16h_R1 1 GESSSPSPSAEK 12 0 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 GES(0.003)S(0.981)S(0.015)PS(0.001)PSAEK 147.58 0.00034506 0 1194.4 1305.4 1952.2 1297.5 1139.8 1430.5 2236.4 675.71 2151.1 1715.9 TRUE FALSE FALSE 1179.842193 1323.777455 1986.177222 1447.523055 1081.631753 1339.095667 2426.35976 695.2606028 1958.700228 1671.320671 0.705934064 0.792054738 1.188387876 0.866095346 0.647171887 0.801220071 1.451761953 0.415994737 1.171947588 1 10.70677285 GESSS(ph)PSPSAEK ddPTM_HeLa_Romidepsin_16h_R1 1 GESSSPSPSAEK 12 0 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 GES(0.027)S(0.168)S(0.554)PS(0.07)PS(0.181)AEK 90.697 0.027504 2358200 1253.4 1833.7 2534.6 1575.1 1635.2 1646.4 2424 712.94 2356 2262.7 TRUE FALSE FALSE 1238.123079 1859.514877 2578.71365 1757.220473 1551.749642 1541.200354 2629.894499 733.5677941 2145.273459 2203.914728 0.561783568 0.843732679 1.170060537 0.797317814 0.704087877 0.699301263 1.193283237 0.33284763 0.973392224 1 11.10585269 -7.226014126 23.59768878 0.825832567 0.332845339 0.373672289 0.201818828 8554.644607 5698263.825 0.030686244 7.849731719 5.94E-08 7.226014126 -0.492987228 GEVDSNGS(ph)DGGEASR ddPTM_HeLa_Romidepsin_16h_R1 1 GEVDSNGSDGGEASR 15 0 Q7LBC6 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 0 GEVDS(0.015)NGS(0.983)DGGEAS(0.002)R 131.18 0.0018392 2837800 1697.6 1478.5 1661.8 914.68 1315.3 1505.2 1176.3 1070 1702.6 1600.3 TRUE FALSE FALSE 1676.908998 1499.314362 1690.722932 1020.439605 1248.175333 1409.022578 1276.214893 1100.958762 1550.315192 1558.723975 1.07582165 0.961885738 1.084683984 0.654663444 0.800767392 0.903959008 0.818756183 0.706320541 0.994605342 1 10.60614976 -9.2734292 24.99987969 1.033326926 0.78760457 0.746889808 0.071498067 279.6729735 583142.7841 0.011012685 0.016901791 5.33E-10 9.2734292 -0.245722357 GEVDSNGSDGGEAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GEVDSNGSDGGEASR 15 0 Q7LBC6 Q7LBC6 KDM3B Lysine-specific demethylase 3B 1 0 GEVDSNGS(0.009)DGGEAS(0.991)R 140.49 0.00078324 2741500 1173 811.34 1176 899.48 816.52 929.64 867.83 746.94 1287.6 1452.2 TRUE FALSE FALSE 1158.703025 822.7620658 1196.467787 1003.48211 774.8499375 870.2390043 941.5434585 768.5515304 1172.433831 1414.471635 0.819177279 0.581674489 0.845876126 0.709439543 0.54780168 0.615239629 0.665650293 0.543348846 0.828884654 1 10.46604753 -10.6878973 0.289068532 1.063716899 0.544230142 0.565874044 0.095432162 0.542871095 0.150520435 0.110679875 0.085098018 2.05E-11 10.6878973 -0.519486756 GEVPPKET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 GEVPPKETPK 10 1 P49006 P49006 MARCKSL1 MARCKS-related protein 1 0 GEVPPKET(1)PK;GEVPPKET(1)PK;GEVPPKET(1)PK ;; 142.76 0.018214 307097800 11248.5 11770.1 10076.1 9763.3 9838.5 9631 9034.1 9470.6 10496.2 10377.7 TRUE FALSE FALSE 11111.39896 11935.79978 10251.47029 10892.17868 9336.404632 9015.610183 9801.456229 9744.616869 9557.393584 10108.08586 1.099258466 1.180817016 1.014185122 1.077570851 0.923657037 0.891920618 0.969664916 0.964041759 0.945519628 1 13.3032222 -8.759578823 24.9839414 1.058320284 0.936388449 0.448874342 0.062559283 32.2732405 433358.0369 0.008865169 0.017036633 1.74E-09 8.759578823 -0.121931835 GEVQVSDK(ac)ER ddPTM_HeLa_Romidepsin_16h_R1 1 GEVQVSDKER 10 1 A0A087X020;Q9Y3A5 A0A087X020 SBDS Ribosome maturation protein SBDS 0 1 GEVQVSDK(1)ER 117.02 0.015558 727790 1439.6 469.9 911.73 226.28 946.71 601.57 1507.8 672.87 1139.4 893.9 FALSE TRUE FALSE 1422.053601 476.5152645 927.5982782 252.4435583 898.395856 563.1316185 1635.872494 692.3384318 1037.48921 870.6763491 1.633274641 0.547293222 1.06537668 0.289939607 1.031836752 0.646774911 1.878852568 0.795173123 1.191589976 1 9.765992725 -10.26405602 24.99926489 1.299046352 0.910712355 0.144266091 0.422967671 344.5535538 3291839.68 0.075243958 0.088160123 5.44E-11 10.26405602 -0.388333997 GEYQESLRS(ph)LEEEGQELPQSADVQR ddPTM_HeLa_Romidepsin_16h_R1 2 GEYQESLRSLEEEGQELPQSADVQR 25 1 P48681 P48681 NES Nestin 1 0 GEY(0.001)QES(0.024)LRS(0.976)LEEEGQELPQSADVQR;GEYQES(0.011)LRS(0.988)LEEEGQELPQSADVQR ; 92.41 1.52E-05 8818100 651.2 767.6 607.39 447.82 903.95 828.71 603.02 708.16 778.1 753.89 TRUE FALSE FALSE 643.2629239 778.4062929 617.9613682 499.5990555 857.8180584 775.7581055 654.2405037 728.6494923 708.5047872 734.3038291 0.87601739 1.060060239 0.841560868 0.680371034 1.16820589 1.056453848 0.890967033 0.992299731 0.964865985 1 9.520233313 GFAFVTFDDHDSVDK ddPTM_HeLa_Romidepsin_16h_R1 2 GFAFVTFDDHDSVDK 15 0 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;H0YH80;F8VZ49;A0A2R8Y4L2;Q32P51 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 0 ; ; 193.51 2.41E-14 12814000 4634.3 4170.6 4371.3 3561.1 5170.4 5072.5 4137.4 4689.4 5486.7 4841.8 FALSE FALSE TRUE 4577.815369 4229.313816 4447.380643 3972.851137 4906.535195 4748.383621 4488.830653 4825.08039 4995.95581 4716.009338 0.970696842 0.896799288 0.943038981 0.842417996 1.040399805 1.006864762 0.951828194 1.023127828 1.059360882 1 12.20335086 -7.247015811 22.8078413 0.970768519 1.02312795 0.065753934 0.061585318 1668.73511 2638595.605 0.00775532 0.19785141 5.66E-08 7.247015811 0.052359432 GFAFVTFDDHDTVDK ddPTM_HeLa_Romidepsin_16h_R1 1 GFAFVTFDDHDTVDK 15 0 P51991;P51991-2 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 0 116.79 0.0017684 14281000 2896.4 2621.6 2844.9 1955.9 3506.5 3139.9 2662.1 3242.7 3619.3 3091 FALSE FALSE TRUE 2861.097563 2658.506954 2894.414291 2182.050361 3327.55022 2939.270524 2888.218708 3336.522408 3295.580743 3010.695374 0.95031121 0.883020905 0.961377334 0.724766238 1.105243077 0.976276294 0.959319476 1.108223182 1.094624442 1 11.55588103 -7.261313424 20.93169868 0.959771586 1.108223425 0.158527933 0.101216817 1.342903357 220083.6231 0.012036896 0.093064429 5.48E-08 7.261313424 0.14845184 GFAFVTFES(ph)PADAK ddPTM_HeLa_Romidepsin_16h_R1 2 GFAFVTFESPADAK 14 0 P38159;H0Y6E7;H3BT71;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 0 GFAFVT(0.087)FES(0.913)PADAK;GFAFVTFES(1)PADAK ; 171.73 4.25E-05 59760000 8187.8 7787.1 8714.4 5158.6 8986.8 9832.3 9440.9 9079.6 8864.1 8927.9 TRUE FALSE FALSE 8088.003944 7896.726998 8866.070476 5755.061604 8528.170062 9204.047762 10242.80981 9342.303901 8071.272695 8695.951871 0.930088398 0.908092307 1.019562965 0.661809275 0.980705757 1.058429014 1.177882532 1.074327922 0.928164371 1 13.08612824 -8.163878716 3.252439532 0.942865852 1.123272095 0.422165009 0.0983497 0.204286475 4.099882894 0.014134464 0.040050805 6.86E-09 8.163878716 0.180406243 GFAYVQFEDVRDAEDALHNLDR ddPTM_HeLa_Romidepsin_16h_R1 1 GFAYVQFEDVRDAEDALHNLDR 22 1 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 0 78.401 0.00080107 4243900 1267 1192.8 1180.2 1207.6 1522.4 1451 1121.6 1189 1328.4 980.44 FALSE FALSE TRUE 1251.557317 1209.59227 1200.740886 1347.228394 1444.706247 1358.285783 1216.868676 1223.401839 1209.584577 954.9680275 1.310575099 1.26663117 1.257362395 1.410757591 1.512832059 1.422336396 1.274250698 1.281091936 1.266623114 1 9.899308622 -12.15065639 0.417381792 0.907676217 1.373016604 0.255265221 0.111757816 0.820690579 0.201209672 0.167189429 0.0285436 7.07E-13 12.15065639 0.465340388 GFAYVQFEDVRDAEDALHNLDRK ddPTM_HeLa_Romidepsin_16h_R1 1 GFAYVQFEDVRDAEDALHNLDRK 23 2 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 0 0 42.395 0.021521 8061400 4917.4 4593.5 4116.6 7623.8 4689.8 4157 4077.8 3894.1 4789.2 3618 FALSE FALSE TRUE 4857.464837 4658.167414 4188.247696 8505.299627 4450.462006 3891.381116 4424.16823 4006.76964 4360.841957 3524.003838 1.378393742 1.321839483 1.188491241 2.41353302 1.262899307 1.104249965 1.255437971 1.136993551 1.237467993 1 11.78299978 -11.99719186 0.731120523 0.990783982 1.394306324 0.064061605 0.363558381 1.171408638 1.114184281 0.270495688 0.076946625 1.01E-12 11.99719186 0.403522342 GFCFLEYEDHK ddPTM_HeLa_Romidepsin_16h_R1 2 GFCFLEYEDHK 11 0 B4DT28;O43390-3;O43390;O43390-4;O43390-2;O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 B4DT28;O60506-2 HNRNPR;SYNCRIP Heterogeneous nuclear ribonucleoprotein R;Heterogeneous nuclear ribonucleoprotein Q 0 0 ; ; 152.7 0.0010647 71167000 5690.6 5344.5 5229.6 739.34 4955.3 4735.2 4210 4693 5488 5574.3 FALSE FALSE TRUE 5621.240778 5419.740011 5320.618994 824.8259695 4702.41255 4432.636002 4567.597295 4828.784551 4997.139535 5429.478882 1.035318656 0.998206297 0.979950214 0.151916231 0.866089113 0.816401739 0.841258875 0.889364275 0.920371852 1 12.40659802 -9.487651824 24.99906337 1.014488488 0.71753535 0.312386112 0.201585546 508.9635755 361190.6397 0.029622728 0.045237585 3.25E-10 9.487651824 -0.296953138 GFDQTINLILDESHER ddPTM_HeLa_Romidepsin_16h_R1 2 GFDQTINLILDESHER 16 0 F2Z2Y6;C9JIZ0;C9JNV3;O95777 F2Z2Y6 LSM8 U6 snRNA-associated Sm-like protein LSm8 0 0 ; ; 123.92 0.0012275 9080500 3829.1 4493.4 3572.2 3707.9 4579 4597.3 3577.3 3595.3 4395.2 4431.7 FALSE FALSE TRUE 3782.429456 4556.658203 3634.372643 4136.624844 4345.316543 4303.547367 3881.155773 3699.324333 4002.082304 4316.563795 0.876259366 1.055621652 0.841959673 0.958314308 1.006661027 0.996984539 0.899130873 0.857006756 0.927145409 1 12.0756676 -9.486553853 0.006401851 1.871634985 4.37E-07 0.037328972 0.067519406 12783.65298 38.90432578 5612.160038 5760.307879 3.26E-10 9.486553853 -1.871634547 GFESPSDNSSAMLLQWHEK ddPTM_HeLa_Romidepsin_16h_R1 1 GFESPSDNSSAMLLQWHEK 19 0 B1ALC0;O15511;O15511-2 B1ALC0 ARPC5 Actin-related protein 2/3 complex subunit 5 0 0 98.165 0.00035654 0 1896.2 1627.4 1448.9 1429.2 1424.1 1613.3 1397.7 1409.8 1709.7 1461.7 FALSE FALSE TRUE 1873.088385 1650.31058 1474.117497 1594.450829 1351.422863 1510.215337 1516.420603 1450.590339 1556.78015 1423.724823 1.315625291 1.159149966 1.035394953 1.11991503 0.949216338 1.060749459 1.065107933 1.018869879 1.093455789 1 10.47545461 -9.762150993 24.96947146 1.153967633 1.042852245 0.253563619 0.083474859 26.60667389 933610.4288 0.019597253 0.026623539 1.73E-10 9.762150993 -0.111115389 GFFDPNTHENLTYLQLLER ddPTM_HeLa_Romidepsin_16h_R1 1 GFFDPNTHENLTYLQLLER 19 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4;A0A075B730;P58107 Q15149;Q15149-3;Q15149-4;A0A075B730 PLEC;EPPK1 Plectin;Epiplakin 0 0 101.61 0.012822 3957300 1438.3 1321.7 1298.2 1419.2 1659.4 1803.5 1867.2 1760.4 1485.2 1449.9 FALSE FALSE TRUE 1420.769446 1340.306927 1320.794626 1583.294582 1574.714626 1688.262171 2025.799921 1811.334397 1352.359992 1412.231389 1.006045792 0.949070342 0.935253696 1.12112972 1.11505426 1.195457192 1.434467423 1.282604544 0.957605108 1 10.46376077 -8.292831324 1.170512622 0.995816644 1.3691928 0.852548187 0.05998454 0.135415748 0.328731878 0.008652941 0.038704964 5.10E-09 8.292831324 0.373376156 GFFDPNTHENLTYR ddPTM_HeLa_Romidepsin_16h_R1 2 GFFDPNTHENLTYR 14 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 142.1 0.000351 35868000 7486.9 6954.6 6695.2 3856.9 7042.7 7488.7 6191.5 6949.6 7042.2 6068.1 FALSE FALSE TRUE 7395.646783 7052.507041 6811.727147 4302.852925 6683.284739 7010.196239 6717.405855 7150.675711 6412.327994 5910.449887 1.251283223 1.193226772 1.152488775 0.728007683 1.130757365 1.186068129 1.13653038 1.209836112 1.08491369 1 12.52905223 -8.518826133 24.99750039 1.098974984 1.170888339 0.091465063 0.136192238 499.3998637 3080416.525 0.02273949 0.046333119 3.03E-09 8.518826133 0.071913355 GFFDPNTHENLTYVQLLR ddPTM_HeLa_Romidepsin_16h_R1 2 GFFDPNTHENLTYVQLLR 18 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 0 0 ; ; 193.31 5.00E-15 32122000 4721.8 4404.2 4457 4678.7 6451.4 7792.9 7216.4 7243 4919.2 3591 FALSE FALSE TRUE 4664.248885 4466.202443 4534.572215 5219.673308 6122.160985 7294.95884 7829.360836 7452.564777 4479.214432 3497.705302 1.33351683 1.276895009 1.296442045 1.492313633 1.750336422 2.085641359 2.238427815 2.130701169 1.280615159 1 11.77219303 -8.483623912 0.54465308 1.120182192 2.450902545 0.93302475 0.106311775 0.271659686 0.113622479 0.027920786 0.182423018 3.28E-09 8.483623912 1.330720353 up GFGAGRGGSGGT(ph)RGPPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GFGAGRGGSGGTRGPPSR 18 2 Q96E39;A0A1B0GUK8 Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" 2 0 GFGAGRGGS(0.001)GGT(1)RGPPS(1)R 72.289 0.0036027 0 6664.4 4335.3 4487.4 1857.9 4610.6 3797.4 5219.7 4070.6 7347.5 6113.1 TRUE FALSE FALSE 6583.171729 4396.332467 4565.501315 2072.71914 4375.303877 3554.758396 5663.061188 4188.376389 6690.321198 5954.280781 1.105619969 0.738348195 0.766759493 0.34810571 0.734816519 0.597008862 0.951090719 0.703422721 1.123615336 1 12.53971154 -10.18081546 4.455823198 1.049885014 0.684540451 0.592242887 0.146225946 0.11901229 4.35719826 0.024486973 0.030012494 6.59E-11 10.18081546 -0.365344562 GFGDGYNGYGGGPGGGNFGGS(ph)PGYGGGR ddPTM_HeLa_Romidepsin_16h_R1 3 GFGDGYNGYGGGPGGGNFGGSPGYGGGR 28 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 0 GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR;GFGDGYNGYGGGPGGGNFGGS(1)PGYGGGR ;; 117.05 6.20E-10 313721000 6864 6755.6 6443.8 5148.6 6592 6406.1 5522.6 5814.4 7000.1 6389.4 TRUE FALSE FALSE 6780.338928 6850.705514 6555.951636 5743.905357 6255.585642 5996.770885 5991.689506 5982.63049 6373.993524 6223.402467 1.089490671 1.100797442 1.053435266 0.922952579 1.005171315 0.963583975 0.962767479 0.961311842 1.024197544 1 12.60348783 -9.279163212 24.31044731 1.049416541 0.965493575 0.65404324 0.032791312 368.3433422 505227.5808 0.006502172 0.009947224 5.26E-10 9.279163212 -0.083922966 GFGFGQGAGALVHS(ph)E ddPTM_HeLa_Romidepsin_16h_R1 5 GFGFGQGAGALVHSE 15 0 E9PP21;P21291 E9PP21 CSRP1 Cysteine and glycine-rich protein 1 1 0 GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E;GFGFGQGAGALVHS(1)E ;;;; 158.86 0.00029302 1430291800 24318 23166.7 21963.51 21262.33 25631.85 24304.6 22189.73 24211.49 26461.2 23047.71 TRUE FALSE FALSE 24021.60286 23492.84141 22345.77568 23720.78064 24323.76105 22751.6145 24074.52511 24912.01126 24094.444 22448.92717 1.070055717 1.046501743 0.995405059 1.056655423 1.083515522 1.013483376 1.072413168 1.109719457 1.073300466 1 14.45435888 -16.52287875 0.272426394 0.590616336 1.061303786 0 0.038593928 43.33485046 0.58263991 9.639403275 0.015819904 3.00E-17 16.52287875 0.47068745 GFGFVDFNS(ph)EEDAK ddPTM_HeLa_Romidepsin_16h_R1 1 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 1 0 GFGFVDFNS(1)EEDAK 201.16 1.37E-16 27015000 4326.6 4868.7 4668 4468.1 4911.7 4942.1 4184.1 5196.1 4485.8 4519.7 TRUE FALSE FALSE 4273.865735 4937.241686 4749.244582 4984.722745 4661.037621 4626.31576 4539.49735 5346.440955 4084.578813 4402.277542 0.970830597 1.121519858 1.078815349 1.132305425 1.058778684 1.050891434 1.031170185 1.214471578 0.927833099 1 12.10403439 -10.26578392 24.87939311 0.986225558 1.092916102 0.557770621 0.052843803 200.8058721 1149929.358 0.00799894 0.009312769 5.42E-11 10.26578392 0.106690543 GFGFVDFNSEEDAK ddPTM_HeLa_Romidepsin_16h_R1 2 GFGFVDFNSEEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 0 ; ; 248.19 1.08E-53 61318000 4488.5 4627.4 4053.3 3721.3 3307 3376.6 3060.6 3611.1 4659.7 4292.1 FALSE FALSE TRUE 4433.792436 4692.544659 4123.845986 4151.574215 3138.23145 3160.846157 3320.567288 3715.581481 4242.924762 4180.590623 1.060566038 1.122459739 0.986426646 0.993059256 0.750667007 0.75607646 0.794281858 0.88876951 1.014910366 1 12.02949106 -8.84640561 4.884192837 1.033064469 0.794534193 0.837814694 0.050208954 0.062673389 2.61706834 0.007934245 0.014757628 1.42E-09 8.84640561 -0.238530277 GFGFVEFEDPRDADDAVYELDGK ddPTM_HeLa_Romidepsin_16h_R1 2 GFGFVEFEDPRDADDAVYELDGK 23 1 G3V5K8;B4DJK0;B4DUA4;Q13243-2;Q13243 G3V5K8 SRSF5 Serine/arginine-rich splicing factor 5 0 0 ; ; 95.622 8.64E-05 16391200 4332.1 4320.2 4675 4318.6 4369.8 3746.7 3624.6 3408.8 4497.7 4556.8 FALSE FALSE TRUE 4279.298699 4381.019889 4756.366414 4817.936852 4146.7928 3507.297962 3932.473434 3507.42825 4095.414447 4438.413679 0.964150484 0.987068851 1.071636571 1.085508743 0.934296147 0.790214301 0.886008768 0.790243655 0.92272031 1 12.11582842 -8.458960448 4.897330651 0.997335624 0.830745227 0.713385699 0.051602832 0.089600525 4.255339428 0.007116886 0.016050579 3.48E-09 8.458960448 -0.166590397 GFGFVTFDDHDPVDK ddPTM_HeLa_Romidepsin_16h_R1 2 GFGFVTFDDHDPVDK 15 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ; ; 105.14 0.0028419 502860000 12026.2 12016.1 11709.7 8910.8 12087.8 11406.3 10242.5 11351.6 12715.1 11405.9 FALSE FALSE TRUE 11879.62005 12185.26297 11913.50242 9941.108623 11470.91446 10677.47424 11112.49769 11680.04064 11577.82961 11109.57307 1.069313822 1.096825494 1.072363658 0.894823641 1.032525227 0.961105721 1.000263252 1.051349189 1.042148923 1 13.43951576 GFGFVTFDDHDPVDKIVLQK ddPTM_HeLa_Romidepsin_16h_R1 2 GFGFVTFDDHDPVDKIVLQK 20 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ; ; 89.311 0.00069899 17179400 6714.4 5816.1 4851.5 12015.2 5899.6 5066.8 5524.6 5437 6438.3 5598.6 FALSE FALSE TRUE 6632.56231 5897.979208 4935.938322 13404.45396 5598.521398 4743.047832 5993.859386 5594.311017 5862.442323 5453.147565 1.216281465 1.081573374 0.905153998 2.45811319 1.026658701 0.869781677 1.099155912 1.0258866 1.075056608 1 12.41287348 -6.334734748 14.86429474 1.152069899 1.227877472 0 0.438064202 0 0 0.055380969 0 4.63E-07 6.334734748 0.075807573 GFGFVYFQNHDAADK ddPTM_HeLa_Romidepsin_16h_R1 2 GFGFVYFQNHDAADK 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 0 ; ; 138.77 0.00045172 16304300 5205.73 4705.1 4906.46 4314.36 4371.68 4924.8 4035.57 4307.04 5085.87 4615.82 FALSE FALSE TRUE 5142.28056 4771.338521 4991.854878 4813.206603 4148.576857 4610.121174 4378.351215 4431.657407 4630.977049 4495.900331 1.143771032 1.061264301 1.110312621 1.070576803 0.922746625 1.025405555 0.973854154 0.985710777 1.03004442 1 12.13439434 -8.790634455 22.72210568 1.072623335 0.980172281 0.516022365 0.043723171 60.46276047 47057.07462 0.008542097 0.015487119 1.62E-09 8.790634455 -0.092451054 GFGGK(ac)FGVQMDR ddPTM_HeLa_Romidepsin_16h_R1 2 GFGGKFGVQMDR 12 1 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 0 1 ; GFGGK(1)FGVQMDR;GFGGK(1)FGVQMDR 97.452 0.012853 3367500 793.08 738.26 1041 451.46 869.08 825.82 947.81 823.43 950.88 610.95 FALSE TRUE FALSE 783.4136359 748.6532437 1059.118168 503.6599294 824.7276046 773.0527672 1028.316958 847.2546479 865.8309113 595.0774309 1.31649025 1.258077025 1.779798919 0.846377132 1.385916457 1.299079291 1.728038914 1.423772107 1.454988656 1 9.216933593 -15.39936617 0.119381058 1.35E-11 1.614146648 0 0.277257104 63.47472713 0.721077166 16.63432319 1.237859699 3.99E-16 15.39936617 1.614146648 GFGLEGVPEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GFGLEGVPEKR 11 1 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 0 1 ; GFGLEGVPEK(1)R;GFGLEGVPEK(1)R 147.4 0.00099987 7375900 4045 4430 2704.22 2248.09 1907.69 2121.14 2051.06 1739.2 4227.4 4410.1 FALSE TRUE FALSE 3995.697984 4492.365656 2751.285815 2508.024743 1810.333461 1985.606 2225.276985 1789.521008 3849.290756 4295.524966 0.930200154 1.045824595 0.640500483 0.583869204 0.421446383 0.462249903 0.518045408 0.416601235 0.89611649 1 12.06861874 -9.53495413 2.201529715 0.973034499 0.472808558 0.92579742 0.06474277 0.048965592 0.476584842 0.009541533 0.014769188 2.92E-10 9.53495413 -0.500225941 down GFGQSNS(ph)LPTAGSVGGGMGR ddPTM_HeLa_Romidepsin_16h_R1 1 GFGQSNSLPTAGSVGGGMGR 20 0 G3V2R1;Q9UPU9-2;Q9UPU9-3;Q9UPU9 G3V2R1 SAMD4A Protein Smaug homolog 1 1 0 GFGQS(0.003)NS(0.727)LPT(0.231)AGS(0.039)VGGGMGR 84.895 0.0017672 0 1767.1 2064.4 1720.8 2004.9 2179.5 2220.6 1819.4 1946.2 1958.2 1777.1 TRUE FALSE FALSE 1745.561906 2093.462677 1750.749802 2236.715971 2068.271982 2078.710827 1973.939791 2002.510226 1783.053688 1730.930686 1.008452805 1.209443391 1.011449977 1.29220424 1.194890124 1.200920894 1.140392164 1.156897987 1.030112703 1 10.75733224 -10.16665237 1.277439539 0.999633013 1.182494009 0.493842297 0.070463371 0.205953928 0.64686543 0.012807688 0.015849176 6.81E-11 10.16665237 0.182860996 GFGSEEGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 GFGSEEGSR 9 0 Q9Y5S9 Q9Y5S9 RBM8A RNA-binding protein 8A 1 0 GFGS(0.092)EEGS(0.908)R;GFGS(0.041)EEGS(0.959)R ; 114.4 0.016639 118686000 6973.1 6403.1 5674.9 3895.3 6927.8 7264.4 6657.4 6129.5 7492.1 5886.7 TRUE FALSE FALSE 6888.109175 6493.24301 5773.669254 4345.692914 6574.248515 6800.228285 7222.87939 6306.847412 6821.987812 5733.762685 1.201324427 1.132457579 1.006959927 0.757912936 1.146585388 1.185997513 1.259710209 1.099949153 1.189792495 1 12.48526648 -8.535145721 24.99462463 1.067194953 1.185772071 0.190360789 0.12406101 336.9724842 686598.4416 0.019804331 0.039629498 2.92E-09 8.535145721 0.118577118 GFGSSAPEGLEPDSMASAASALHLLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GFGSSAPEGLEPDSMASAASALHLLSPR 28 0 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 GFGSSAPEGLEPDS(0.061)MAS(0.044)AAS(0.019)ALHLLS(0.876)PR;GFGSSAPEGLEPDS(0.089)MAS(0.015)AAS(0.08)ALHLLS(0.816)PR ; 66.031 0.00010663 11626900 1625.13 1853.44 1211.84 1591.93 2285.4 2591.2 1997.09 2044.53 2172.2 1738.67 TRUE FALSE FALSE 1605.32229 1879.532777 1232.931567 1775.996437 2168.76751 2425.630683 2166.722775 2103.68525 1977.912992 1693.499103 0.947932177 1.109851652 0.728037922 1.048714129 1.280642846 1.432318847 1.279435443 1.242212202 1.167944517 1 10.72579151 -8.797847251 3.913318925 0.967450653 1.319594628 0.617512171 0.118751936 0.079881284 2.598211113 0.014048437 0.027230452 1.59E-09 8.797847251 0.352143975 GFIYVHK(ac)PPVHIR ddPTM_HeLa_Romidepsin_16h_R1 2 GFIYVHKPPVHIR 13 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 0 1 ; GFIYVHK(1)PPVHIR;GFIYVHK(1)PPVHIR 111.86 0.00086008 1714570 468.1 620.33 606.85 316 1037.78 831.18 891.09 718.34 878.86 785.34 FALSE TRUE FALSE 462.3946172 629.063022 617.4119697 352.5374068 984.8182141 778.0702805 966.7791624 739.1240345 800.2525605 764.9367536 0.604487384 0.822372594 0.807141201 0.460871314 1.287450511 1.017169429 1.263868101 0.966255094 1.04616827 1 9.579196658 -8.742397783 24.99997668 0.787113333 1.134661925 0.457264898 0.183320752 179.2797111 235377.7096 0.02780355 0.055535903 1.81E-09 8.742397783 0.347548592 GFKDQIYDIFQK ddPTM_HeLa_Romidepsin_16h_R1 1 GFKDQIYDIFQK 12 1 P60842;J3QR64;J3KTB5;J3QL43;J3QS69;J3KT12;P60842-2;J3KSZ0;J3KTN0 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 0 105.65 0.014598 9362900 2876.5 2471.9 3315 2637 3237.2 2964.5 2348 2553.7 2667.2 2300.7 FALSE FALSE TRUE 2841.440112 2506.699473 3372.696184 2941.902347 3071.993604 2775.078017 2547.439061 2627.58728 2428.638952 2240.927482 1.267975039 1.118599104 1.505044769 1.312805689 1.370858106 1.238361366 1.136778892 1.172544538 1.08376508 1 11.12988025 -12.08617645 0.688701502 0.983985976 1.272213776 0.385544792 0.111319658 0.609316156 0.484495297 0.100440432 0.024332926 8.20E-13 12.08617645 0.288227801 GFPTDATLDDIKEWLEDK ddPTM_HeLa_Romidepsin_16h_R1 1 GFPTDATLDDIKEWLEDK 18 1 P05455;E9PGX9;E7ERC4 P05455 SSB Lupus La protein 0 0 116.78 0.0016748 1968400 761.45 590.27 465.48 515.45 653.51 805.29 483.31 616.84 683.15 509.72 FALSE FALSE TRUE 752.1691545 598.5798366 473.5814841 575.0487543 620.1589461 753.834568 524.3623393 634.6872922 622.047353 496.4774009 1.515011868 1.205653743 0.953883265 1.158257663 1.249118177 1.518366328 1.056165574 1.278381032 1.252921788 1 8.955584239 -12.71709687 1.631137577 1.000300476 1.27989401 0 0.186387212 0.466861731 2.246457323 0.137810097 0.03033583 1.92E-13 12.71709687 0.279593533 GFPTIYFSPANKK ddPTM_HeLa_Romidepsin_16h_R1 1 GFPTIYFSPANKK 13 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 0 78.903 0.027463 0 0 0 63.14 0 0 150.53 0 0 0 0 FALSE FALSE TRUE 0 0 64.23892521 0 0 140.9116188 0 0 0 0 0 GFQEVVTPNIFNSR ddPTM_HeLa_Romidepsin_16h_R1 1 GFQEVVTPNIFNSR 14 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 126.1 0.00027135 0 680.47 708.72 725.89 599.34 603.15 560 577.95 694.36 799.67 692.02 FALSE FALSE TRUE 672.1761699 718.6973788 738.523811 668.6385108 572.3690048 524.2178073 627.0410586 714.4502111 728.1455124 674.0412206 0.997233032 1.066251376 1.095665648 0.9919846 0.84916024 0.777723663 0.930271086 1.059950325 1.080268521 1 9.396693011 -8.877628814 6.393160959 1.012694836 0.897615703 0.400864562 0.07677302 0.188531168 9.88756238 0.011314013 0.020676608 1.33E-09 8.877628814 -0.115079133 GFS(ph)DSGGGPPAK ddPTM_HeLa_Romidepsin_16h_R1 3 GFSDSGGGPPAK 12 0 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 1 0 GFS(0.84)DS(0.16)GGGPPAK;GFS(0.831)DS(0.169)GGGPPAK;GFS(0.978)DS(0.022)GGGPPAK ;; 126.1 0.0053989 51290500 6758 9462.1 4504.5 5514.2 5840.6 4649.8 3963.21 5299.4 5823.4 6135.5 TRUE FALSE FALSE 6675.630897 9595.307692 4582.898933 6151.777749 5542.532388 4352.692787 4299.844958 5452.729778 5302.540519 5976.098826 1.11705497 1.605613959 0.766871343 1.029396924 0.927449922 0.728350202 0.719507003 0.91242296 0.887291304 1 12.54498829 -8.791583759 1.39654588 1.087484574 0.782822955 0.268549935 0.21026309 0.400306417 1.564353138 0.03177046 0.079229638 1.62E-09 8.791583759 -0.30466162 GFS(ph)VVADTPELQR ddPTM_HeLa_Romidepsin_16h_R1 1 GFSVVADTPELQR 13 0 C9J9W2;Q14847;Q14847-2;Q14847-3 C9J9W2 LASP1 LIM and SH3 domain protein 1 1 0 GFS(0.562)VVADT(0.438)PELQR 169.09 0.00011109 269230000 2008.2 2226.8 2029.8 1851.5 2515.5 2480.4 1729.6 1981.3 1930.9 2121.5 TRUE FALSE FALSE 1983.723286 2258.148949 2065.127818 2065.579142 2387.124648 2321.910445 1876.512181 2038.62579 1758.195468 2066.383124 0.959997816 1.092802648 0.99939251 0.999610923 1.155218807 1.123659218 0.908114356 0.986567189 0.850856478 1 11.01289205 -10.28560659 24.83264491 0.981110079 1.037772806 0.194710065 0.080205728 1157.879399 1189757.108 0.012262225 0.014026129 5.18E-11 10.28560659 0.056662726 GFSQYGVS(ph)GSPTK ddPTM_HeLa_Romidepsin_16h_R1 1 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 0 GFSQYGVS(0.875)GS(0.034)PT(0.091)K 175.6 1.14E-05 102680000 3168.2 2657.4 2757.8 2527.7 2288.2 2194.9 2252.1 2154.5 2965.3 2520.6 TRUE FALSE FALSE 3129.58476 2694.810947 2805.798352 2819.964567 2171.424616 2054.652974 2443.393318 2216.837058 2700.076141 2455.114449 1.274720517 1.097631497 1.142838108 1.148608192 0.884449447 0.83688684 0.995225831 0.902946524 1.099776079 1 11.26157456 -8.762326166 24.99989939 1.132347349 0.90647416 0.688429055 0.073241582 14.68945203 414137.3567 0.015635057 0.029583731 1.73E-09 8.762326166 -0.22587319 GFSQYGVSGSPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GFSQYGVSGSPTK 13 0 Q9NXC5 Q9NXC5 MIOS WD repeat-containing protein mio 1 0 GFSQYGVS(0.082)GS(0.082)PT(0.836)K 196.37 4.90E-11 87966000 4848 4258.8 4581.9 4175.1 4451.6 4035 3358.6 3963.3 4896.2 4165.5 TRUE FALSE FALSE 4788.910711 4318.755498 4661.646047 4657.844706 4224.418241 3777.176522 3643.8794 4077.971832 4458.271609 4057.27971 1.180325502 1.064446084 1.148958509 1.148021591 1.041194727 0.930962811 0.898108994 1.005099999 1.098832698 1 11.98629705 -8.410522095 3.764933661 1.094708185 0.940623694 0.635954584 0.054231418 0.163557207 4.129632535 0.010799484 0.02528208 3.89E-09 8.410522095 -0.154084491 GFSVVADT(ph)PELQR ddPTM_HeLa_Romidepsin_16h_R1 3 GFSVVADTPELQR 13 0 C9J9W2;Q14847;Q14847-2;Q14847-3 C9J9W2 LASP1 LIM and SH3 domain protein 1 1 0 GFS(0.079)VVADT(0.921)PELQR;GFS(0.041)VVADT(0.959)PELQR;GFSVVADT(1)PELQR ;; 195.94 6.01E-11 718640000 16903.6 17449 17011.8 14512.9 18630.1 20713.1 16059.9 16846.7 16956 15573 TRUE FALSE FALSE 16697.57242 17694.64748 17307.88324 16190.94978 17679.33648 19389.59976 17424.02751 17334.13268 15439.41289 15168.41122 1.10081222 1.166545871 1.141047866 1.067412371 1.165536471 1.278288114 1.148704848 1.142778399 1.017866187 1 13.88878236 -11.34867559 0.297397403 0.959750173 1.191404755 0.60848695 0.048046196 1.091204358 0.224784045 0.096723002 0.039984601 4.48E-12 11.34867559 0.231654582 GFVEFAAK(ac)PPAR ddPTM_HeLa_Romidepsin_16h_R1 1 GFVEFAAKPPAR 12 1 X6RDA4;Q8WXF1-2;Q8WXF1 X6RDA4 PSPC1 Paraspeckle component 1 0 1 GFVEFAAK(1)PPAR 97.456 0.0098883 0 0 204.62 172.55 0 158.25 154.8 125.48 139.75 260.06 154.82 FALSE TRUE FALSE 0 207.5006457 175.5531604 0 150.173912 144.9087796 136.1382681 143.7934458 236.7995823 150.7977541 0 1.376019471 1.164162964 0 0.995863054 0.960947863 0.902787106 0.95355164 1.570312394 1 7.236471132 -10.2576019 24.99137813 0.527777784 0.887836797 0 0.520856155 585.7675245 3814781.872 0.082330108 0.098821448 5.53E-11 10.2576019 0.360059013 GGAAGGALPT(ph)SPGPALGAK ddPTM_HeLa_Romidepsin_16h_R1 2 GGAAGGALPTSPGPALGAK 19 0 Q9UPR0 Q9UPR0 PLCL2 Inactive phospholipase C-like protein 2 1 0 GGAAGGALPT(0.932)S(0.068)PGPALGAK;GGAAGGALPT(0.5)S(0.5)PGPALGAK ; 149 7.77E-05 21707000 6512.4 6788 5743.1 6070.3 5425.7 4814.9 3266.4 3945.6 6332.9 6597.3 TRUE FALSE FALSE 6433.024364 6883.561642 5843.056246 6772.176648 5148.806283 4507.243429 3543.847934 4059.759711 5766.469563 6425.901195 1.001108509 1.071221208 0.909297555 1.053887454 0.80125824 0.701418103 0.551494308 0.6317806 0.897379121 1 12.64968308 -8.401722751 1.76521561 1.003221058 0.595951183 0.870594122 0.062449111 0.062114076 0.373008845 0.006877349 0.020469831 3.97E-09 8.401722751 -0.407269875 GGAGAWLGGPAASLSPPKGSS(ph)ASQGGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GGAGAWLGGPAASLSPPKGSSASQGGSK 28 1 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 GGAGAWLGGPAAS(0.001)LS(0.028)PPKGS(0.11)S(0.642)AS(0.214)QGGS(0.005)K 69.398 6.32E-05 33728000 2291.3 2105.9 2131.4 1917.1 2123.4 2365.4 1985.9 2350.5 2263.3 2319.3 TRUE FALSE FALSE 2263.372754 2135.546915 2168.496123 2138.764122 2015.034975 2214.258574 2154.582296 2418.508009 2060.864779 2259.044252 1.001916077 0.945332042 0.959917506 0.946756187 0.891985614 0.980174944 0.95375834 1.070589037 0.912272868 1 11.14149682 -10.27563666 22.84619834 1.000904819 0.960697447 0 0.050510919 327.0916785 526352.7319 0.00690988 0.00792684 5.30E-11 10.27563666 -0.040207372 KQVAPEKPVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 KQVAPEKPVKK 11 3 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 1 ; KQVAPEK(0.008)PVK(0.992)K;KQVAPEK(0.013)PVK(0.987)K 50.484 0.027917 23913800 4467.5 4789.5 3758.2 8851 13088.2 13153.6 14165.8 12410.4 4480.8 4040 FALSE TRUE FALSE 4413.048392 4856.926707 3823.609895 9874.394265 12420.26032 12313.12741 15369.0427 12769.47534 4080.026026 3935.040218 1.121474787 1.234276256 0.971682545 2.509350278 3.156323602 3.129098238 3.905688849 3.245068573 1.03684481 1 11.94216267 -9.035035767 1.952259268 1.057665074 3.433157508 0.958508799 0.225216875 0.041436516 0.313393315 0.033330764 0.064678893 9.22E-10 9.035035767 2.375492434 up GGAPDPSPGATATPGAPAQPS(ph)SPDARR ddPTM_HeLa_Romidepsin_16h_R1 1 GGAPDPSPGATATPGAPAQPSSPDARR 27 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 0 GGAPDPSPGAT(0.009)AT(0.009)PGAPAQPS(0.491)S(0.491)PDARR 56.461 0.0012735 5770700 2207.5 1910.9 1908 1565.9 1681.1 2217.5 1522.4 1738.2 2470.9 2271.1 TRUE FALSE FALSE 2180.594141 1937.8017 1941.20794 1746.956726 1595.307194 2075.808907 1651.712618 1788.492075 2249.896516 2212.096495 0.985759051 0.876002338 0.877542162 0.789728988 0.721174324 0.938389854 0.746672951 0.808505451 1.017087872 1 11.1111986 -9.972450544 1.355156147 0.996270423 0.803078276 0.69337211 0.05644843 0.152549671 0.550737592 0.009823486 0.013219635 1.07E-10 9.972450544 -0.193192147 GGDDYS(ph)EDEGDSSVSR ddPTM_HeLa_Romidepsin_16h_R1 4 GGDDYSEDEGDSSVSR 16 0 A6NDA1;Q99871-3;Q99871;Q99871-2 A6NDA1 HAUS7 HAUS augmin-like complex subunit 7 1 0 GGDDYS(1)EDEGDSSVSR;GGDDYS(1)EDEGDSSVSR;GGDDYS(1)EDEGDSSVSR;GGDDYS(1)EDEGDSSVSR ;;; 257.16 5.73E-72 41522800 8528.6 8742.19 7889.75 7208.95 10219.4 10767.1 9206.9 10949.9 9638.3 8199.11 TRUE FALSE FALSE 8424.650143 8865.26278 8027.067789 8042.482718 9697.865884 10079.11706 9988.933856 11266.71808 8776.226308 7986.09594 1.054914718 1.110087187 1.005130398 1.007060619 1.214343774 1.262083142 1.250790615 1.410791727 1.098938251 1 12.96327469 GGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_HeLa_Romidepsin_16h_R1 2 GGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 31 0 P31942-4;P31942-3;P31942;P31942-5 P31942-4 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 0 ; ; 175.43 5.08E-24 14710200 4667.9 4770.3 3915.7 3526.2 3888.4 3641.3 3456.2 4247.7 4732 4755.9 FALSE FALSE TRUE 4611.005839 4837.456409 3983.851116 3933.915835 3689.960438 3408.632682 3749.769542 4370.600498 4308.758068 4632.341032 0.995394296 1.044278989 0.860008166 0.849228459 0.796564936 0.735833709 0.809476141 0.943497136 0.93014699 1 12.17752575 -9.64603673 4.663786095 1.001088295 0.822309269 0.665358824 0.055670226 0.080725748 2.962924939 0.008106172 0.011536124 2.26E-10 9.64603673 -0.178779026 GGDQQSGYGK(ac)VSR ddPTM_HeLa_Romidepsin_16h_R1 2 GGDQQSGYGKVSR 13 1 Q14103-3;H0YA96;Q14103-4 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 1 ; GGDQQSGYGK(1)VSR;GGDQQSGYGK(1)VSR 134.56 0.00074768 696610 0 142.99 0 67.131 110.8 0 0 0 167.359 0 FALSE TRUE FALSE 0 145.003017 0 74.89300208 105.1454625 0 0 0 152.3899919 0 0 GGDSIGET(ph)PTPGASK ddPTM_HeLa_Romidepsin_16h_R1 2 GGDSIGETPTPGASK 15 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 GGDSIGET(0.993)PT(0.007)PGASK;GGDS(0.001)IGET(0.996)PT(0.003)PGASK ; 197.47 4.63E-13 37435000 7380.1 7588.3 7853.3 6107.4 6577.2 7645 5531.3 7158.5 7441.1 7264.8 TRUE FALSE FALSE 7290.148503 7695.128287 7989.983392 6813.566324 6241.540941 7156.509173 6001.128484 7365.619903 6775.549379 7076.059449 1.030255406 1.087487795 1.129157188 0.962904053 0.882064514 1.011369283 0.848089043 1.040921145 0.957531438 1 12.78873045 -9.019475945 24.65106082 1.029871335 0.940734921 0.307807427 0.068084367 576.3009022 729434.5334 0.009343845 0.015651924 9.56E-10 9.019475945 -0.089136413 GGDSIGET(ph)PTPGASKR ddPTM_HeLa_Romidepsin_16h_R1 2 GGDSIGETPTPGASKR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 GGDSIGET(0.853)PT(0.146)PGAS(0.001)KR;GGDSIGET(0.98)PT(0.02)PGAS(0.001)KR ; 162.7 5.79E-07 9992200 4781.6 4520.3 4135.9 4597.8 4593.1 4716.8 3592.08 4460.6 4248.2 4596.5 TRUE FALSE FALSE 4723.32002 4583.936902 4207.883605 5129.419269 4358.696968 4415.411703 3897.191186 4589.660423 3868.230352 4477.082267 1.054999604 1.023867025 0.939871853 1.145705833 0.973557488 0.986225278 0.87047567 1.025145429 0.864006985 1 12.12834311 -8.54286138 24.99997993 1.028026584 0.956316404 0.012993636 0.07940594 243.0486743 304073.5641 0.008195431 0.016392497 2.87E-09 8.54286138 -0.07171018 GGDSIGETPTPGASK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GGDSIGETPTPGASKR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 1 ; GGDSIGETPTPGASK(1)R;GGDSIGETPTPGASK(1)R 223.36 2.84E-37 2619400 337.957 399.75 514.29 479.59 701.88 835.62 729.16 744.29 484.83 364.59 FALSE TRUE FALSE 333.8378501 405.377691 523.2410017 535.0424523 666.0604445 782.2265788 791.0948322 765.8248569 441.4655905 355.1178992 0.940076101 1.141529875 1.473428973 1.506661459 1.875603697 2.202723604 2.227696306 2.156536909 1.24315218 1 8.472154269 -9.020240204 0.832159212 0.964266936 2.26520175 0.93771261 0.119570017 0.065876486 0.08778647 0.015922209 0.044907951 9.54E-10 9.020240204 1.300934815 up GGDVS(ph)PSPYSSSSWR ddPTM_HeLa_Romidepsin_16h_R1 2 GGDVSPSPYSSSSWR 15 0 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YFE7 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 GGDVS(0.993)PS(0.007)PYSSSSWR;GGDVS(0.972)PS(0.028)PYSSSSWR ; 191.63 1.87E-12 184203000 5253 4699.4 4355.3 3471.2 4120.4 4321.7 3543.4 4459.6 5116.3 4859.8 TRUE FALSE FALSE 5188.974415 4765.558277 4431.10217 3872.556476 3910.120613 4045.557318 3844.376308 4588.63149 4658.685314 4733.541695 1.096213945 1.006763769 0.936107138 0.818109721 0.826045457 0.854657586 0.812156426 0.969386515 0.984185968 1 12.20870431 -9.637449061 2.483415614 1.045212011 0.852533725 0.689515864 0.051623345 0.105655007 1.32698971 0.00865463 0.012756924 2.30E-10 9.637449061 -0.192678286 GGEFDEFVNDDT(ph)DDDLPISK ddPTM_HeLa_Romidepsin_16h_R1 2 GGEFDEFVNDDTDDDLPISK 20 0 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 0 GGEFDEFVNDDT(0.999)DDDLPIS(0.001)K;GGEFDEFVNDDT(0.873)DDDLPIS(0.127)K ; 93.392 0.00099755 51528000 16232.2 15152.8 15601.4 15552.7 17951.3 18454 16113.2 18513.1 17467.8 15908.9 TRUE FALSE FALSE 16034.3557 15366.12152 15872.93582 17350.97635 17035.17818 17274.84896 17481.85481 19048.74734 15905.43622 15495.58448 1.034769338 0.99164517 1.024352185 1.119736811 1.099356929 1.114823966 1.128182988 1.229301635 1.026449582 1 13.91956955 -4 0.271907816 1.002089066 2.568307603 0.852224646 0.027154337 12.29029733 0.156031102 0.012587653 9.174120876 1.00E-04 4 1.566218537 GGEIQPVSVK(ac)VGDK ddPTM_HeLa_Romidepsin_16h_R1 2 GGEIQPVSVKVGDK 14 1 P61604;B8ZZL8;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 1 ; GGEIQPVSVK(1)VGDK;GGEIQPVSVK(1)VGDK 151.66 6.69E-06 4261700 1805.74 1767.6 1805.61 1705.84 2186.13 2479.41 1764.61 2163.96 1779.21 1719.53 FALSE TRUE FALSE 1783.730946 1792.484319 1837.035885 1903.077247 2074.563629 2320.983703 1914.495929 2226.570768 1620.073001 1674.856363 1.065005326 1.070231668 1.096831899 1.136262959 1.238651669 1.385780748 1.143080668 1.329409983 0.967290711 1 10.70982166 -9.097840185 1.077001005 1.031052167 1.282244833 0.750779427 0.064651936 0.175149516 0.40078852 0.010345037 0.023730117 7.98E-10 9.097840185 0.251192666 GGET(ph)PEGLATSVVHYGAGAK ddPTM_HeLa_Romidepsin_16h_R1 1 GGETPEGLATSVVHYGAGAK 20 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 0 GGET(0.985)PEGLAT(0.006)S(0.009)VVHYGAGAK 105.38 0.00038622 4701400 2734.3 2420.3 2288.5 2123.9 2344.5 2148.4 1975.9 1987.6 3594.2 2778.1 TRUE FALSE FALSE 2700.9733 2454.373047 2328.330383 2369.475311 2224.851416 2011.124174 2143.732897 2045.10807 3272.72575 2705.924562 0.998170214 0.90703676 0.860456502 0.875661999 0.822214872 0.743229949 0.792236756 0.755789019 1.209466737 1 11.4019059 -9.438813268 0.690786028 1.00514711 0.759867836 0.734283241 0.069258729 0.115097501 0.109330088 0.00568111 0.012414838 3.64E-10 9.438813268 -0.245279274 GGET(ph)PGSEQWK ddPTM_HeLa_Romidepsin_16h_R1 1 GGETPGSEQWK 11 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 GGET(0.987)PGS(0.013)EQWK 142.97 0.0053971 9699800 5759.8 6606.5 5962.1 5570.9 7696.5 8272.4 6245.7 7917.5 5752.6 5768 TRUE FALSE FALSE 5689.597342 6699.50648 6065.86785 6215.03367 7303.718885 7743.820338 6776.209602 8146.580371 5238.073048 5618.146528 1.012717862 1.192476281 1.079691998 1.106242715 1.300022854 1.378358556 1.206129026 1.450047686 0.932348956 1 12.45587854 -8.830130055 0.511343079 0.996188004 1.413906071 0.772173467 0.077365237 0.423605545 0.179454157 0.018210098 0.081938469 1.48E-09 8.830130055 0.417718067 GGFDGEYQDDSLDLLR ddPTM_HeLa_Romidepsin_16h_R1 1 GGFDGEYQDDSLDLLR 16 0 Q5F1R6;Q5F1R6-3;Q5F1R6-2 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 0 0 174.94 2.76E-05 2784400 857.28 847.19 1003.3 679.06 1017.3 819.63 1006.8 997.55 974.83 978.48 FALSE FALSE TRUE 846.8311416 859.1167631 1020.762016 757.5761123 965.3833849 767.2582882 1092.317567 1026.412535 887.6387633 953.0589485 0.888540151 0.901430876 1.071037649 0.79488904 1.012931452 0.805048092 1.146117529 1.076966474 0.931357672 1 9.89642164 -7.739074127 24.98648123 0.938036114 1.11154213 0.430413172 0.084581637 168.9910573 188794.1093 0.011051017 0.041286074 1.82E-08 7.739074127 0.173506016 GGGESLQEAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GGGESLQEASPR 12 0 P98175-5 P98175-5 RBM10 RNA-binding protein 10 1 0 GGGESLQEAS(1)PR;GGGESLQEAS(1)PR ; 174.94 3.57E-05 40127000 5710.5 5014.6 4360.1 4331.4 5649 5385.4 4692.7 5358.8 5029.7 5212.2 TRUE FALSE FALSE 5640.89823 5085.19567 4435.985712 4832.216848 5360.710451 5041.290321 5091.297821 5513.848423 4579.831035 5076.786293 1.111115951 1.001656437 0.873778303 0.951825933 1.055925962 0.993008181 1.002858408 1.086090315 0.902112236 1 12.30969982 -10.02669546 24.57872378 1.052677467 0.990396444 0 0.075868895 824.7051995 759310.783 0.011299009 0.013862909 9.40E-11 10.02669546 -0.062281022 GGGGGGQGAEGPPGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GGGGGGQGAEGPPGTPR 17 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 GGGGGGQGAEGPPGT(1)PR;GGGGGGQGAEGPPGT(1)PR ; 98.552 0.0078824 9235800 8602.1 3356.8 5192.3 5162.5 2659.11 2200.69 6199.9 5807.5 6856.7 7702.7 TRUE FALSE FALSE 8497.254296 3404.057119 5282.669803 5759.41254 2523.405694 2060.073011 6726.519351 5975.53085 6243.419579 7502.582744 1.132577219 0.453718037 0.704113501 0.767657317 0.336338269 0.274581845 0.896560502 0.796463172 0.832169373 1 12.87317161 -10.26747743 24.92234205 1.062605916 0.60259805 0.408681876 0.205941317 264.3363933 1091058.832 0.03421362 0.039659527 5.40E-11 10.26747743 -0.460007866 GGGGGQDNGLEGLGNDS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GGGGGQDNGLEGLGNDSR 18 0 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 0 GGGGGQDNGLEGLGNDS(1)R 236.66 2.71E-49 37894000 4503.1 5197.2 5069 3023.4 2816.1 2752.2 2503.6 2554.5 5242.9 5371.5 TRUE FALSE FALSE 4448.214485 5270.366318 5157.223819 3372.979734 2672.383909 2576.343302 2716.255722 2628.410427 4773.961893 5231.947656 0.850202406 1.00734309 0.985717778 0.644689121 0.510781851 0.492425282 0.51916722 0.50237705 0.912463619 1 12.35313239 -9.097283213 3.227819888 0.938391381 0.509077254 0.953710208 0.046614985 0.052154896 1.036715776 0.009881045 0.017349635 7.99E-10 9.097283213 -0.429314127 GGGGNFGPGPGS(ph)NFR ddPTM_HeLa_Romidepsin_16h_R1 1 GGGGNFGPGPGSNFR 15 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 0 GGGGNFGPGPGS(1)NFR 95.483 0.011433 18825000 1063.9 1414.7 1086.6 877.66 1080.5 938.62 879.93 1171.1 1286.8 1325.8 TRUE FALSE FALSE 1050.932778 1434.616184 1105.511817 979.1391787 1025.358053 878.6452113 954.6712322 1204.983931 1171.705385 1291.355525 0.813821413 1.110938201 0.856086334 0.75822588 0.794016855 0.680405353 0.739278389 0.933115558 0.907345315 1 10.33467053 -9.521101892 24.97853185 0.927348201 0.777156932 0.427761221 0.093826119 61.8263146 869141.8813 0.01643163 0.023438114 3.01E-10 9.521101892 -0.150191269 GGGPVTLQDY(ph)RLPDSDDDEDEETAIQR ddPTM_HeLa_Romidepsin_16h_R1 1 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 GGGPVT(0.013)LQDY(0.796)RLPDS(0.191)DDDEDEETAIQR 80.68 1.30E-05 9018800 1638.8 1376 1447.7 1623 1754 1490.4 1295.7 1660.1 1602.1 1714.9 TRUE FALSE FALSE 1618.825675 1395.371364 1472.896611 1810.658896 1664.486835 1395.16825 1405.756726 1708.132374 1458.804163 1670.346651 0.969155519 0.835378311 0.881790981 1.084001872 0.996491856 0.835256711 0.8415958 1.022621486 0.87335414 1 10.70593182 -10.49710798 15.2670161 0.986397167 0.926253109 0 0.088176584 5.972471446 3539.142613 0.014477248 0.015775665 3.18E-11 10.49710798 -0.060144058 GGGPVTLQDYRLPDS(ph)DDDEDEETAIQR ddPTM_HeLa_Romidepsin_16h_R1 1 GGGPVTLQDYRLPDSDDDEDEETAIQR 27 1 Q96K21-3 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 GGGPVT(0.004)LQDY(0.177)RLPDS(0.819)DDDEDEET(0.001)AIQR 69.913 7.94E-05 7668600 1849.1 1822.2 1949.9 2575.8 2112 2175.8 1651.5 2235 2103.6 1624 TRUE FALSE FALSE 1826.562458 1847.852979 1983.837192 2873.626116 2004.216759 2036.773402 1791.778369 2299.666199 1915.448747 1581.808246 1.154730646 1.168190256 1.254157826 1.816671599 1.267041542 1.287623457 1.132740567 1.453821097 1.210923481 1 10.627359 -9.841975829 2.354728256 1.074493125 1.373903848 0.298000301 0.178107017 0.234860093 2.663278816 0.030008076 0.041365705 1.44E-10 9.841975829 0.299410722 GGGQSVQFTDIETLKQES(ph)PNGSR ddPTM_HeLa_Romidepsin_16h_R1 2 GGGQSVQFTDIETLKQESPNGSR 23 1 Q02241;A0A2U3TZL8;Q02241-3;Q02241-2 Q02241;Q02241-3 KIF23 Kinesin-like protein KIF23 1 0 GGGQSVQFTDIET(0.124)LKQES(0.867)PNGS(0.009)R;GGGQSVQFT(0.002)DIET(0.001)LKQES(0.945)PNGS(0.052)R ; 116.83 2.35E-06 82651000 4356.3 3847.4 3828.5 3037.9 2932.8 2776 2095.26 2441.1 4151.1 4327.3 TRUE FALSE FALSE 4303.20374 3901.563798 3895.133437 3389.156292 2783.128272 2598.622559 2273.231332 2511.729377 3779.815219 4214.876122 1.02095616 0.925665117 0.924139482 0.804093927 0.660310811 0.616535927 0.539335265 0.595920095 0.89677967 1 12.04127451 -8.971330719 0.978928528 1.009362528 0.558204917 0.936741083 0.042989451 0.043626715 0.081658952 0.004105669 0.010901794 1.07E-09 8.971330719 -0.451157611 GGGSAAAAAAAAASGGGVS(ph)PDNSIEHSDYR ddPTM_HeLa_Romidepsin_16h_R1 2 GGGSAAAAAAAAASGGGVSPDNSIEHSDYR 30 0 P40425 P40425 PBX2 Pre-B-cell leukemia transcription factor 2 1 0 GGGSAAAAAAAAAS(0.001)GGGVS(0.998)PDNS(0.001)IEHSDYR;GGGSAAAAAAAAAS(0.002)GGGVS(0.987)PDNS(0.011)IEHSDYR ; 111.38 3.10E-10 13712600 2214.15 2328.7 2069.69 2403 1940.04 1849.89 1780.16 1642.21 2673.1 2266.7 TRUE FALSE FALSE 2187.163088 2361.4835 2105.712086 2680.846166 1841.03252 1731.687999 1931.366746 1689.724755 2434.011241 2207.810807 0.990647877 1.069604104 0.953755675 1.214255387 0.83387241 0.784346192 0.874788157 0.765339471 1.102454628 1 11.10840083 -8.56089689 24.99787549 1.012319964 0.813868848 0.670003783 0.079481276 71.02080025 46697.69265 0.009875006 0.019750042 2.75E-09 8.56089689 -0.198451117 GGGSGGGEES(ph)EGEEVDED ddPTM_HeLa_Romidepsin_16h_R1 2 GGGSGGGEESEGEEVDED 18 0 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 0 GGGSGGGEES(1)EGEEVDED;GGGSGGGEES(1)EGEEVDED ; 146.59 7.69E-05 28381000 12036 11490.1 11293.1 11015.6 11856 13564.1 11789.8 13621.5 12247.9 11144.1 TRUE FALSE FALSE 11889.3006 11651.85793 11489.65167 12289.2755 11250.94408 12697.39779 12791.22532 14015.61661 11152.41715 10854.57468 1.095326253 1.073451358 1.058507773 1.132174762 1.036516346 1.169773866 1.178417921 1.291217485 1.02743935 1 13.40601558 -4 0.322422817 1.035817015 3.421466173 0.818399487 0.035645258 17.36633374 0.221198334 0.013539591 24.83309297 1.00E-04 4 2.385649158 GGGSGNPTTTIES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 GGGSGNPTTTIESPK 15 0 G3V0E6;O00592-2;O00592 G3V0E6 PODXL Podocalyxin 1 0 GGGSGNPTTTIES(1)PK;GGGSGNPTTTIES(1)PK ; 118.5 0.00020669 5485300 4068.2 3725.1 3229.1 3439.7 3901.5 3680.4 3146.5 3940.4 3951.6 4200.7 TRUE FALSE FALSE 4018.615214 3777.542056 3285.301131 3837.414298 3702.391896 3445.234318 3413.763631 4054.409257 3598.158999 4091.565208 0.982170639 0.923251094 0.80294483 0.937884184 0.904884001 0.84203334 0.834341739 0.990918891 0.879408934 1 11.99843713 -10.16444875 3.428185677 0.991973911 0.883314457 0.11146619 0.062224074 0.146608274 3.25266663 0.00817605 0.010047902 6.85E-11 10.16444875 -0.108659453 GGGT(ph)PDANSLAPPGK ddPTM_HeLa_Romidepsin_16h_R1 1 GGGTPDANSLAPPGK 15 0 Q5T171;Q9BRQ0 Q5T171 PYGO2 Pygopus homolog 2 1 0 GGGT(0.645)PDANS(0.355)LAPPGK 130.95 0.0038736 114030000 4845.2 4569.1 4612 4004.4 3358.7 3348.3 2495.2 2731.5 4470.9 4681.1 TRUE FALSE FALSE 4786.144839 4633.42391 4692.269925 4467.407569 3187.293006 3134.354436 2707.142226 2810.531643 4071.011506 4559.484347 1.04971187 1.01621665 1.029122938 0.979805441 0.699046814 0.687436165 0.593738682 0.616414364 0.892866648 1 12.15465496 -8.728893125 2.586082045 1.024338395 0.631255959 0.923178166 0.04878594 0.02924901 0.398979771 0.004444177 0.009431034 1.87E-09 8.728893125 -0.393082437 GGGTPDANS(ph)LAPPGK ddPTM_HeLa_Romidepsin_16h_R1 1 GGGTPDANSLAPPGK 15 0 Q5T171;Q9BRQ0 Q5T171 PYGO2 Pygopus homolog 2 1 0 GGGT(0.106)PDANS(0.894)LAPPGK 127.78 0.0024069 127940000 11334 10739 10171 10399 8971.9 7389.1 6865.9 6997.4 11559 10511 TRUE FALSE FALSE 11195.85685 10890.18392 10348.02199 11601.38131 8514.030464 6916.960357 7449.089375 7199.858729 10525.13409 10237.9227 1.093567237 1.063710309 1.010754065 1.133177271 0.83161699 0.675621467 0.727597735 0.703253867 1.028053678 1 13.3216354 -8.579653189 4.174537559 1.049244435 0.709475908 0.940794453 0.040248339 0.040199042 1.44426008 0.00680954 0.014305382 2.63E-09 8.579653189 -0.339768527 GGGTSS(ph)GGSSTNSLTGSRPPK ddPTM_HeLa_Romidepsin_16h_R1 1 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2-2;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 0 GGGT(0.045)S(0.15)S(0.627)GGS(0.065)S(0.02)T(0.004)NS(0.085)LT(0.003)GSRPPK 81.329 0.0010595 3923400 662 804.34 554.47 968.37 1572.8 1626.3 1215.6 1507 1351 1389.5 TRUE FALSE FALSE 653.9312894 815.6635196 564.1203178 1080.337496 1492.534147 1522.384679 1318.853034 1550.602667 1230.163176 1353.40059 0.483176448 0.602677083 0.416816959 0.798239268 1.102802938 1.124858885 0.974473518 1.14570858 0.908942397 1 10.40237321 -8.839675739 4.655264328 0.708990899 1.081947826 0.553460472 0.170902634 0.171977478 6.859274164 0.033792726 0.0632127 1.45E-09 8.839675739 0.372956927 GGGTSSGGSSTNS(ph)LTGSRPPK ddPTM_HeLa_Romidepsin_16h_R1 1 GGGTSSGGSSTNSLTGSRPPK 21 1 Q5T9C2-3;Q5T9C2-2;Q5T9C2 Q5T9C2-3 FAM102A Protein FAM102A 1 0 GGGTSSGGSS(0.005)T(0.056)NS(0.881)LT(0.039)GS(0.019)RPPK 79.332 0.0012288 4686400 723.44 714.45 772.91 818.38 1136 1405.1 955.44 1055.7 795.05 704.61 TRUE FALSE FALSE 714.622435 724.5080459 786.3621743 913.0049462 1078.025681 1315.318645 1036.59505 1086.245014 723.9387368 686.3041306 1.041262034 1.05566616 1.145792571 1.330321217 1.570769624 1.916524447 1.510401881 1.582745849 1.054836631 1 9.422704228 -9.040166114 1.627753472 1.023893247 1.666653073 0.880629871 0.102185144 0.082069748 0.430930998 0.016060738 0.032506019 9.12E-10 9.040166114 0.642759826 GGHDILVR ddPTM_HeLa_Romidepsin_16h_R1 2 GGHDILVR 8 0 Q9Y678;H0Y8X7 Q9Y678 COPG1 Coatomer subunit gamma-1 0 0 ; ; 107.01 0.00093159 2569400 1843.82 1573.55 1626.17 1382.01 1555.07 1574.2 1647.31 1615.82 1805.19 1811.07 FALSE FALSE TRUE 1821.346813 1595.702478 1654.472807 1541.804499 1475.708975 1473.6137 1787.23247 1662.571202 1643.729285 1764.01814 1.032498913 0.904583939 0.937900109 0.874029843 0.836561111 0.835373326 1.013159916 0.942490989 0.93180974 1 10.78464968 -10.25600047 24.44109607 1.01534671 0.904973918 0.268492507 0.056732939 207.4230411 932107.0988 0.008946885 0.010781449 5.55E-11 10.25600047 -0.110372791 DSSPASGTDRDS(ph)PEPLLK ddPTM_HeLa_Romidepsin_16h_R1 1 DSSPASGTDRDSPEPLLK 18 1 A6NHT5 A6NHT5 HMX3 Homeobox protein HMX3 1 0 DS(0.001)S(0.004)PAS(0.029)GT(0.003)DRDS(0.963)PEPLLK 64.522 0.012574 10095000 3850.3 3461.5 3384.2 2748.4 2157.6 1409.4 1401.1 1450.4 4060.2 4240.5 TRUE FALSE FALSE 3803.371063 3510.231088 3443.100581 3066.18294 2047.489621 1319.343889 1520.109399 1492.365036 3697.045543 4130.331199 0.920839245 0.849866734 0.833613678 0.742357644 0.495720445 0.31942811 0.368035716 0.361318491 0.895096632 1 12.01204176 -8.893071218 0.938648591 0.961668771 0.313854475 0.964328017 0.047249375 0.067188857 0.114178451 0.008443058 0.024588418 1.28E-09 8.893071218 -0.647814296 down GGIDNPAIT(ph)SDQELDDKK ddPTM_HeLa_Romidepsin_16h_R1 1 GGIDNPAITSDQELDDKK 18 1 H0YK04;Q13017-2;Q13017;A0A0A0MSK6 H0YK04 ARHGAP5 Rho GTPase-activating protein 5 1 0 GGIDNPAIT(0.5)S(0.5)DQELDDKK 119.72 0.00064523 60950000 4077 4037.6 4215.3 3672 4022.6 4246.1 3495.7 4238.1 4278.7 3297.6 TRUE FALSE FALSE 4027.307956 4094.441439 4288.665528 4096.573917 3817.311712 3974.787914 3792.624671 4360.722737 3896.002356 3211.927877 1.253860021 1.274761326 1.335230956 1.275425251 1.188479897 1.237508458 1.180793846 1.357665211 1.212979402 1 11.64922378 -12.0502732 0.725922084 0.989878741 1.261533577 0.225143007 0.083216724 0.275900751 0.252467791 0.043421755 0.011522373 8.91E-13 12.0502732 0.271654836 GGIDNPAITS(ph)DQELDDKK ddPTM_HeLa_Romidepsin_16h_R1 1 GGIDNPAITSDQELDDKK 18 1 H0YK04;Q13017-2;Q13017;A0A0A0MSK6 H0YK04 ARHGAP5 Rho GTPase-activating protein 5 1 0 GGIDNPAIT(0.137)S(0.863)DQELDDKK 119.38 0.00046 86779000 5268.5 4655.4 4714 4159.4 5480.5 5081.6 4479.7 5154.1 5438.9 4780.8 TRUE FALSE FALSE 5204.285496 4720.938843 4796.045193 4640.329399 5200.809634 4756.90216 4860.205606 5303.225752 4952.431162 4656.594127 1.117616299 1.013817978 1.029947009 0.996507162 1.116869861 1.021541073 1.043725408 1.138863643 1.063530775 1 12.18505943 -12.69597165 1.585270644 1.000075022 1.065594927 0 0.050505127 0.513444947 2.330588325 0.034699431 0.007712996 2.01E-13 12.69597165 0.065519905 GGIPAS(ph)PIDPFQSR ddPTM_HeLa_Romidepsin_16h_R1 2 GGIPASPIDPFQSR 14 0 Q96LD4-2;Q96LD4 Q96LD4-2 TRIM47 Tripartite motif-containing protein 47 1 0 GGIPAS(1)PIDPFQSR;GGIPAS(1)PIDPFQSR ; 145.46 0.00061816 12665100 3465.9 3911.9 3185.6 3006.4 3293.9 3604.5 2898.8 2937 3645.1 3446.5 TRUE FALSE FALSE 3423.656278 3966.971831 3241.044032 3354.014114 3125.799992 3374.184083 3145.024 3021.977461 3319.073127 3356.959433 1.019868231 1.181715749 0.965470121 0.999122623 0.931140234 1.005131027 0.936866847 0.900212684 0.988714101 1 11.71293939 -9.054451442 2.051218608 1.02256934 0.947183603 0.316534146 0.060147603 0.356461648 2.96767404 0.009370623 0.017845674 8.82E-10 9.054451442 -0.075385737 GGITQPNINDS(ph)LEITK ddPTM_HeLa_Romidepsin_16h_R1 2 GGITQPNINDSLEITK 16 0 I3L328;G5EA36;P30260;P30260-2 I3L328 CDC27 Cell division cycle protein 27 homolog 1 0 GGITQPNINDS(1)LEITK;GGITQPNINDS(0.993)LEIT(0.007)K ; 232.73 2.25E-41 7302600 7820.5 7093.3 8716.6 6175.3 6185.5 7378.1 6188.3 6291.7 8677.8 8090.1 TRUE FALSE FALSE 7725.180738 7193.159664 8868.308767 6889.317242 5869.830854 6906.663222 6713.934048 6473.740413 7901.635834 7879.918036 0.980363083 0.912847016 1.1254316 0.874287932 0.744910141 0.876489221 0.85203095 0.821549207 1.002756094 1 12.94396491 -9.016270654 24.57162058 0.992911699 0.827041042 0.684316293 0.058413838 239.8180197 362168.8001 0.007976416 0.013477294 9.63E-10 9.016270654 -0.165870657 GGK(ac)GLGK(ac)GGAK ddPTM_HeLa_Romidepsin_16h_R1 2 GGKGLGKGGAK 11 2 P62805 P62805 HIST1H4A Histone H4 0 2 ; GGK(1)GLGK(1)GGAK;GGK(1)GLGK(1)GGAK 128.27 0.0020911 63681000 8630.8 8891.6 21087 15697.8 13037.3 8599.4 8715.2 7199 8197.3 4601.7 FALSE TRUE FALSE 8525.60449 9016.776178 21454.01039 17512.8535 12371.95793 8049.926093 9455.46887 7407.291707 7464.112957 4482.147171 1.902125068 2.011709084 4.786547512 3.907246422 2.760274811 1.795997719 2.10958465 1.65262126 1.665298499 1 12.1299743 -10.57881348 1.473982552 1.297191457 2.780972842 0.268025053 0.936693396 0.345661963 1.521139842 0.213487854 0.222017335 2.64E-11 10.57881348 1.483781385 QEPLEEDSPSSSSAGLDK(ac)AQR ddPTM_HeLa_Romidepsin_16h_R1 2 QEPLEEDSPSSSSAGLDKAQR 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 0 1 ; QEPLEEDSPSSSSAGLDK(1)AQR;QEPLEEDSPSSSSAGLDK(1)AQR 206.62 4.63E-34 1473670 131.13 72.535 114.39 617.3 992.97 1112.61 1031.06 971.11 189.356 307.99 FALSE TRUE FALSE 129.5317371 73.55614963 116.38091 688.6751305 942.2950356 1041.517812 1118.638211 999.2075357 172.4195251 299.9883754 0.431789188 0.245196666 0.387951399 2.295672723 3.141105166 3.471860569 3.728938527 3.330820851 0.574754021 1 8.228762787 -9.008750332 2.410383966 0.655911291 3.472212831 0.964742664 0.260797626 0.0478131 0.555913182 0.051274632 0.096931659 9.80E-10 9.008750332 2.81630154 up GGLGLILK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GGLGLILKR 9 1 B1AJY5;B1AJY7;O75832 B1AJY5 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 1 GGLGLILK(1)R 89.142 0.018594 477940 133.74 201.37 163.97 199.87 283.83 173.1 131.13 311.72 344.6 219.17 FALSE TRUE FALSE 132.1099254 204.2048921 166.8238291 222.9799098 269.345096 162.0394687 142.2681789 320.7391264 313.7781129 213.4759318 0.618851616 0.956571031 0.781464344 1.044520138 1.261711771 0.759052636 0.666436622 1.502460365 1.46985241 1 7.737929613 -9.257578511 24.00643014 0.825227414 1.021652543 0 0.315009327 326.4877472 2030056.145 0.038299381 0.061908082 5.53E-10 9.257578511 0.196425129 GGLGLILKR ddPTM_HeLa_Romidepsin_16h_R1 1 GGLGLILKR 9 1 B1AJY5;B1AJY7;O75832 B1AJY5 PSMD10 26S proteasome non-ATPase regulatory subunit 10 0 0 80.229 0.021064 0 246.6 207.26 127.98 324.08 254.56 254.58 153.12 271.23 218.93 189.75 FALSE FALSE TRUE 243.5943443 210.1778117 130.2074382 361.5516544 241.5688533 238.3131596 166.126009 279.0776121 199.3483525 184.8202676 1.318006664 1.1372011 0.704508439 1.9562338 1.307047416 1.289431958 0.898851685 1.509994632 1.078606557 1 7.529979163 -9.298886461 24.99996876 1.122419385 1.35444596 0.239727147 0.288168803 901.9844484 602169.7052 0.045102085 0.068895552 5.02E-10 9.298886461 0.232026575 GGLLTSEEDSGFST(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 0 GGLLTSEEDSGFS(0.001)T(0.5)S(0.5)PK;GGLLTSEEDSGFS(0.001)T(0.984)S(0.015)PK ; 260.73 1.33E-72 51095000 8599.4 9463.3 9050.5 3745.1 5557.2 7317.4 5814.2 7088.7 9533.8 8688.9 TRUE FALSE FALSE 8494.587205 9596.524586 9208.020156 4178.126083 5273.595347 6849.841756 6308.058003 7293.80035 8681.07305 8463.161125 1.003713279 1.133917273 1.088011917 0.493683864 0.62312359 0.80937154 0.745354828 0.861829314 1.02574829 1 13.04698092 -9.279495795 24.99161951 1.019694185 0.709885511 0.730942721 0.103396046 358.5887104 496316.1483 0.016444495 0.025149912 5.25E-10 9.279495795 -0.309808674 GGLLTSEEDSGFST(ph)SPKDNSLPK ddPTM_HeLa_Romidepsin_16h_R1 2 GGLLTSEEDSGFSTSPKDNSLPK 23 1 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 0 GGLLTSEEDS(0.001)GFS(0.035)T(0.742)S(0.22)PKDNS(0.002)LPK;GGLLTSEEDS(0.001)GFS(0.01)T(0.494)S(0.494)PKDNS(0.001)LPK ; 90.896 6.78E-05 103902000 5667.4 4812.3 5099.8 4935 3727.1 4054.4 3966.3 4154.3 6074.4 5219.9 TRUE FALSE FALSE 5598.323549 4880.047686 5188.55988 5505.60792 3536.892179 3795.336925 4303.197423 4274.498116 5531.09045 5084.286246 1.10110314 0.959829453 1.020509001 1.082867418 0.695651662 0.746483723 0.846371981 0.840727274 1.087879435 1 12.31182954 -8.76789878 24.9998904 1.04145444 0.784325679 0.832480577 0.057073767 47.88261067 185321.352 0.00921489 0.016995064 1.71E-09 8.76789878 -0.257128761 GGLLTSEEDSGFSTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GGLLTSEEDSGFSTSPK 17 0 Q9UQR1 Q9UQR1 ZNF148 Zinc finger protein 148 1 0 GGLLTSEEDSGFST(0.063)S(0.937)PK 272.72 1.63E-87 14169000 4426.8 4271 4454.9 2024.2 2876.2 3414.2 2726.5 3344.9 4816.5 3950 TRUE FALSE FALSE 4372.844459 4331.12725 4532.435666 2258.247528 2729.416781 3196.043639 2958.088842 3441.679404 4385.700177 3847.378431 1.136577682 1.12573466 1.178058189 0.586957475 0.709422489 0.830706856 0.768858301 0.894551827 1.139919105 1 11.90966003 -9.269689681 24.99954244 1.079443445 0.760026581 0.795169164 0.089880539 241.3371396 731283.6232 0.01499608 0.023141825 5.37E-10 9.269689681 -0.319416864 GGLRPGS(ph)LDAEIDLLSSTLAELNGGR ddPTM_HeLa_Romidepsin_16h_R1 1 GGLRPGSLDAEIDLLSSTLAELNGGR 26 1 Q15654 Q15654 TRIP6 Thyroid receptor-interacting protein 6 1 0 GGLRPGS(1)LDAEIDLLSSTLAELNGGR 86.886 1.10E-05 133610000 644.55 611.39 378.34 572.55 508.15 436.77 315.94 354.72 540.97 468.18 TRUE FALSE FALSE 636.6939767 619.9971645 384.924849 638.7509249 482.2172093 408.8618066 342.7759357 364.9832635 492.5842883 456.0166161 1.396207845 1.359593363 0.844102683 1.400718532 1.057455348 0.896594098 0.751674223 0.800372729 1.080189342 1 8.832942583 -8.258376069 2.396320337 1.191355689 0.783818203 0.476532975 0.171009135 0.214823681 2.396242024 0.028512388 0.082762995 5.52E-09 8.258376069 -0.407537486 GGLS(ph)PANDTGAK ddPTM_HeLa_Romidepsin_16h_R1 3 GGLSPANDTGAK 12 0 K7EN42;B7Z8J4;P30419 K7EN42 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 0 GGLS(1)PANDTGAK;GGLS(0.999)PANDT(0.001)GAK;GGLS(1)PANDTGAK ;; 190.57 4.95E-10 3358437800 35149 33971.8 31122.5 24238.7 31041.4 29306.7 27658.1 28923.9 35219.2 32965.3 TRUE FALSE FALSE 34720.59047 34450.05589 31664.17406 27041.29254 29457.24153 27434.09645 30007.37832 29760.76741 32069.10654 32108.85675 1.081339978 1.072914435 0.986150778 0.842175502 0.91741795 0.854409008 0.93455144 0.926870976 0.998762017 1 14.97068368 -9.480588044 4.915876648 1.041784408 0.896815893 0.770002742 0.037095028 0.078336111 4.442795679 0.006459368 0.009774475 3.31E-10 9.480588044 -0.144968516 GGLS(ph)PANDTGAKK ddPTM_HeLa_Romidepsin_16h_R1 3 GGLSPANDTGAKK 13 1 K7EN42;B7Z8J4;P30419 K7EN42 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 0 GGLS(1)PANDTGAKK;GGLS(0.999)PANDT(0.001)GAKK;GGLS(1)PANDTGAKK ;; 144.8 0.0011825 45600400 8727.1 9724.1 8024.79 8900.9 7676.4 7720.2 7256.89 6860.51 9296.2 8697.22 TRUE FALSE FALSE 8620.730748 9860.996135 8164.458104 9930.063938 7284.644663 7226.904136 7873.290055 7059.008033 8464.724589 8471.264971 1.017643856 1.164052378 0.963782638 1.172205565 0.859924071 0.853108026 0.929411379 0.833288542 0.999227933 1 13.0483617 -8.71823512 24.99998343 1.028032285 0.872122289 0.605529427 0.071020651 79.61978594 46071.3251 0.009743523 0.019486936 1.91E-09 8.71823512 -0.155909996 GGLSPANDTGAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GGLSPANDTGAKK 13 1 K7EN42;B7Z8J4;P30419 K7EN42 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 0 1 ; GGLSPANDTGAK(1)K;GGLSPANDTGAK(1)K 177.1 1.33E-06 2191200 1770.78 1708.74 1600.35 1343.67 1806.91 1415.6 2020.28 1561.91 1677.45 1452.23 FALSE TRUE FALSE 1749.197052 1732.795687 1628.20342 1499.031448 1714.69664 1325.147729 2191.882533 1607.101402 1527.414671 1414.500855 1.236617882 1.225022721 1.151079842 1.059760015 1.212227362 0.936830631 1.54958021 1.136161492 1.079825908 1 10.46607733 -12.34944256 0.983625122 0.995709488 1.191678591 0.128086603 0.149725755 0.749811496 1.253401445 0.106633677 0.025560799 4.47E-13 12.34944256 0.195969103 GGLVS(ph)DAYGEDDFSR ddPTM_HeLa_Romidepsin_16h_R1 4 GGLVSDAYGEDDFSR 15 0 J3KS14;F5H478;J3KRU5;X6R3T8;J3QLH3;J3QQJ0;Q9UHR5-2;Q9UHR5 J3KS14 SAP30BP SAP30-binding protein 1 0 GGLVS(1)DAYGEDDFSR;GGLVS(1)DAYGEDDFSR;GGLVS(1)DAYGEDDFSR;GGLVS(1)DAYGEDDFSR ;;; 266.85 2.06E-84 39222800 8328.8 9050.5 7994.5 7890.2 9630.3 7678.6 6199.1 8381 8277.4 8390.7 TRUE FALSE FALSE 8227.285382 9177.913177 8133.640919 8802.502049 9138.829855 7187.962242 6725.651399 8623.491012 7537.048613 8172.708404 1.006677955 1.122995306 0.995219763 1.077060579 1.118213131 0.879507978 0.822940336 1.055157065 0.922221648 1 12.99659855 -8.239514756 24.98502285 1.024152795 0.909575637 0.299020811 0.079458121 695.1230221 792152.6336 0.009985622 0.025437067 5.76E-09 8.239514756 -0.114577158 GGNLPPVS(ph)PNDSGAK ddPTM_HeLa_Romidepsin_16h_R1 2 GGNLPPVSPNDSGAK 15 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 0 GGNLPPVS(1)PNDSGAK;GGNLPPVS(0.998)PNDS(0.002)GAK ; 128.73 0.0022483 80794000 14918.9 15057.7 14827.2 14622.5 14560 14225.7 11039.4 13960.9 17305.3 16400 TRUE FALSE FALSE 14737.06271 15269.6827 15085.2612 16313.22225 13816.94887 13316.72368 11977.08636 14364.83661 15757.47063 15973.92564 0.922569883 0.95591297 0.944367812 1.021240653 0.864968899 0.833653792 0.749789791 0.899267778 0.986449479 1 13.96343128 -8.590871431 5.123400523 0.963844968 0.823880458 0.702867417 0.043194845 0.087886618 4.392574173 0.006585507 0.01347192 2.57E-09 8.590871431 -0.13996451 GGNVFAALIQDQS(ph)EEEEEEEKHPPKPAKPEK ddPTM_HeLa_Romidepsin_16h_R1 1 GGNVFAALIQDQSEEEEEEEKHPPKPAKPEK 31 3 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 GGNVFAALIQDQS(1)EEEEEEEKHPPKPAKPEK 91.767 3.73E-11 24858000 1989.5 1496.2 1966 1242.7 1248.4 1951.2 1496.1 1701.3 1622.9 1807.2 TRUE FALSE FALSE 1965.251209 1517.263543 2000.217405 1386.386821 1184.68949 1826.524617 1623.178697 1750.524431 1477.743759 1760.248683 1.116462252 0.861959766 1.136326602 0.787608498 0.673023932 1.03765146 0.922130328 0.994475637 0.839508516 1 10.78156355 -10.25939796 24.94514513 1.054996063 0.915241134 0 0.141853572 209.2268897 2556653.767 0.021409041 0.025536097 5.50E-11 10.25939796 -0.139754929 GGPAS(ph)PGGLQGLETR ddPTM_HeLa_Romidepsin_16h_R1 3 GGPASPGGLQGLETR 15 0 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 0 GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR;GGPAS(1)PGGLQGLETR ;; 184.87 1.43E-08 137135000 8604.3 7048.7 7575.4 6700.5 5446.8 5047 4367.8 4319.5 8172.1 7663.8 TRUE FALSE FALSE 8499.427482 7147.931784 7707.246659 7475.243337 5168.829471 4724.512988 4738.800823 4444.477917 7441.166909 7464.693371 1.138617095 0.957565358 1.032493403 1.001413315 0.692436945 0.632914542 0.634828597 0.595399931 0.996848302 1 12.86586728 -8.748355442 2.784445884 1.054852729 0.623604925 0.934208599 0.049664417 0.052826096 0.83835907 0.009234368 0.019165099 1.79E-09 8.748355442 -0.431247804 GGPASVPSS(ph)SPGTSVK ddPTM_HeLa_Romidepsin_16h_R1 4 GGPASVPSSSPGTSVK 16 0 J3KRZ2;O43237-2;O43237;J3KRI4 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 GGPASVPS(0.027)S(0.587)S(0.314)PGT(0.069)S(0.003)VK;GGPASVPS(0.208)S(0.395)S(0.395)PGT(0.001)SVK;GGPASVPS(0.019)S(0.694)S(0.276)PGT(0.008)S(0.002)VK;GGPASVPS(0.268)S(0.56)S(0.167)PGT(0.003)S(0.001)VK ;;; 238.03 5.61E-46 141929000 18202.8 17874.9 17011.8 16596 26687.7 31522 28333.1 29298.6 19195 17695.3 TRUE FALSE FALSE 17980.93727 18126.54331 17307.88324 18514.90761 25325.72708 29507.84593 30739.71281 30146.30877 17478.15113 17235.57356 1.043245658 1.051693653 1.004195375 1.07422637 1.469386963 1.712031563 1.783503909 1.749074881 1.014074238 1 14.07310169 -8.586491252 2.033625654 1.020865565 1.761833405 0.994796866 0.023603409 0.017758976 0.147091099 0.004218429 0.010321658 2.59E-09 8.586491252 0.74096784 GGPEGVAAQAVAS(ph)AASAGPADAEMEEIFDDASPGKQK ddPTM_HeLa_Romidepsin_16h_R1 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGKQK 37 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 0 GGPEGVAAQAVAS(0.514)AAS(0.449)AGPADAEMEEIFDDAS(0.037)PGKQK 47.487 0.0046403 13776000 3368.4 2868.4 2747 3152.5 2985.7 2694.7 2598.1 2748.5 3104.9 3188.6 TRUE FALSE FALSE 3327.344645 2908.78141 2794.810383 3517.006883 2833.328588 2522.517367 2818.782549 2828.023511 2827.189968 3105.759712 1.071346451 0.936576451 0.899879785 1.132414355 0.91228197 0.812206223 0.907598401 0.910573828 0.910305442 1 11.6007305 -8.544137111 23.0349295 1.021440065 0.876935155 0.28867648 0.074737464 57.8994224 62737.75201 0.009842205 0.019686833 2.86E-09 8.544137111 -0.144504911 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 GGPEGVAAQAVASAASAGPADAEMEEIFDDASPGK 35 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 1 0 GGPEGVAAQAVASAASAGPADAEMEEIFDDAS(1)PGK 140.66 4.49E-17 6251100 1809.3 1653.8 1796 917.82 1370.9 1609.6 1193.5 1479.8 1737.7 1940.3 TRUE FALSE FALSE 1787.247556 1677.08224 1827.258627 1023.942667 1300.937857 1506.751755 1294.87586 1522.615678 1582.27576 1889.890726 0.945688304 0.887396407 0.966859407 0.541799932 0.688366708 0.797269246 0.685159116 0.805663342 0.837231348 1 10.8840871 -9.288261102 24.19059672 0.965285327 0.706976125 0.627439139 0.083698045 178.6452777 161120.2308 0.011304879 0.017271925 5.15E-10 9.288261102 -0.258309202 GGPGAAPGGAS(ph)PASSSSAASS(ph)PSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 2 0 GGPGAAPGGAS(0.981)PAS(0.013)S(0.005)SSAAS(0.068)S(0.915)PS(0.015)S(0.003)GR 244.86 8.87E-71 4062300 1225.4 1025.9 1095.1 780.83 1206 1629.6 1534.8 1605.7 1130 1202.8 TRUE FALSE FALSE 1210.464353 1040.342647 1114.159756 871.1132385 1144.45332 1525.473819 1665.165874 1652.158396 1028.92997 1171.551083 1.033215172 0.888004512 0.951012527 0.743555489 0.976870182 1.302097571 1.421334416 1.410231633 0.878263001 1 10.19420415 -8.16537468 3.49169728 0.977661296 1.405851902 0.842541066 0.088524252 0.079827075 1.823293108 0.013591763 0.037835981 6.83E-09 8.16537468 0.428190606 GGPGAAPGGAS(ph)PASSSSAASSPSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 0 GGPGAAPGGAS(0.687)PAS(0.18)S(0.064)S(0.026)S(0.011)AAS(0.011)S(0.011)PS(0.005)S(0.005)GR 57.829 0.002125 2514500 732.26 495.7 648.63 473.46 784.89 774 823.83 589.94 756.25 695.41 TRUE FALSE FALSE 723.3349335 502.6784776 659.9191331 528.2036729 744.8341345 724.543898 893.8060996 607.0089831 688.6091059 677.343148 1.067900274 0.742132668 0.974275941 0.779816958 1.099640761 1.069685137 1.319576499 0.896161694 1.016632571 1 9.403743091 -8.561257148 24.99794099 0.986134948 1.112098403 0.187729718 0.141960376 230.5989349 150200.7636 0.02058335 0.041166767 2.75E-09 8.561257148 0.125963455 GGPGAAPGGASPASSSS(ph)AAS(ph)SPSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 2 0 GGPGAAPGGAS(0.468)PAS(0.061)S(0.046)S(0.224)S(0.277)AAS(0.428)S(0.332)PS(0.128)S(0.035)GR 116.39 6.56E-06 4225200 1008 1242 1292.2 775.73 1673.7 1858.1 2281.1 1861.4 1161.9 1390.2 TRUE FALSE FALSE 995.7141083 1259.484909 1314.690199 865.4235525 1588.284844 1739.373407 2474.856577 1915.256672 1057.976754 1354.082404 0.735342329 0.930139041 0.970908562 0.639121777 1.172960257 1.284540292 1.827700124 1.414431402 0.781323759 1 10.40309982 -8.238094746 1.993968841 0.87179842 1.60998588 0.778309477 0.16066059 0.112256553 0.85279556 0.023444267 0.075275767 5.78E-09 8.238094746 0.738187461 GGPGAAPGGASPASSSSAAS(ph)SPSSGR ddPTM_HeLa_Romidepsin_16h_R1 2 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 0 GGPGAAPGGAS(0.012)PAS(0.059)S(0.059)S(0.059)S(0.059)AAS(0.429)S(0.256)PS(0.05)S(0.017)GR;GGPGAAPGGASPASSSSAAS(0.696)S(0.301)PS(0.001)S(0.001)GR ; 207.38 4.37E-30 19244300 2793.3 2542.8 2489.61 2064.73 3005.9 3024.9 3039.8 3359.1 2989.8 2815.7 TRUE FALSE FALSE 2759.254185 2578.597605 2532.940618 2303.463797 2852.497706 2831.618652 3298.000536 3456.290259 2722.3848 2742.547708 1.00609159 0.940219781 0.923572126 0.839899263 1.04009046 1.032477446 1.202531692 1.260247998 0.99264811 1 11.421301 -7.749325697 1.969913234 0.98163238 1.267265321 0.790647947 0.054310743 0.143047299 1.006101708 0.008621817 0.052020939 1.78E-08 7.749325697 0.285632941 GGPGAAPGGASPASSSSAASS(ph)PSSGR ddPTM_HeLa_Romidepsin_16h_R1 3 GGPGAAPGGASPASSSSAASSPSSGR 26 0 Q9BXK1 Q9BXK1 KLF16 Krueppel-like factor 16 1 0 GGPGAAPGGASPAS(0.007)S(0.035)S(0.115)S(0.115)AAS(0.166)S(0.541)PS(0.016)S(0.005)GR;GGPGAAPGGASPASSSSAAS(0.199)S(0.561)PS(0.12)S(0.12)GR;GGPGAAPGGASPASSSSAAS(0.226)S(0.774)PSSGR ;; 356.49 2.56E-279 23862200 4626.6 4003.92 3678.57 2988.61 4432.8 4884.81 4245.49 4831.93 4829.62 4537.31 TRUE FALSE FALSE 4570.20922 4060.287291 3742.593968 3334.16715 4206.577675 4572.686406 4606.101815 4971.734271 4397.646691 4419.430032 1.034117338 0.918735507 0.84684992 0.754433745 0.951837147 1.03467786 1.042238882 1.124971826 0.995071007 1 12.1096446 -7.632851258 1.811122793 0.973381711 1.120189649 0.280707722 0.086344767 0.647360967 3.4417663 0.014998318 0.126201306 2.33E-08 7.632851258 0.146807938 GGPGSAVS(ph)PYPTFNPSSDVAALHK ddPTM_HeLa_Romidepsin_16h_R1 2 GGPGSAVSPYPTFNPSSDVAALHK 24 0 P04083;Q5T3N1;Q5T3N0 P04083 ANXA1 Annexin A1;Annexin 1 0 GGPGS(0.001)AVS(0.736)PY(0.077)PT(0.186)FNPSSDVAALHK;GGPGS(0.011)AVS(0.981)PY(0.002)PT(0.006)FNPSSDVAALHK ; 109.25 2.92E-06 111793000 4276.7 3858.4 3728.9 3680.59 4632.74 4448.5 4053.2 4150.7 3928.6 3825.3 TRUE FALSE FALSE 4224.573935 3912.718656 3793.79994 4106.157133 4396.313991 4164.255207 4397.478707 4270.793956 3577.216177 3725.918155 1.133834336 1.050135428 1.018218808 1.102052424 1.179927687 1.117645379 1.180240286 1.146239337 0.960089843 1 11.86338027 -16.52287875 0.111083413 0.619429826 1.195253444 0.607670748 0.045997751 68.52690797 0.558214336 6.055597326 0.305073779 3.00E-17 16.52287875 0.575823618 GGPGSAVSPYPT(ph)FNPSSDVAALHK ddPTM_HeLa_Romidepsin_16h_R1 1 GGPGSAVSPYPTFNPSSDVAALHK 24 0 P04083;Q5T3N1;Q5T3N0 P04083 ANXA1 Annexin A1;Annexin 1 0 GGPGS(0.004)AVS(0.067)PY(0.397)PT(0.435)FNPS(0.053)S(0.043)DVAALHK 64.27 0.00078483 0 1850.1 1654.2 1281 1932.5 1746.1 1610 1322.6 1289.4 2199.8 1477 TRUE FALSE FALSE 1827.55027 1677.487871 1303.295268 2155.944743 1656.990001 1507.126196 1434.941611 1326.706755 2003.044378 1438.627327 1.27034308 1.166033648 0.905929731 1.498612394 1.151785435 1.047614047 0.997438033 0.922203221 1.392330273 1 10.4904772 -7.903345798 2.362736004 1.145401369 0.948791399 0.215414494 0.168187593 0.405654493 4.431104341 0.023202194 0.095941844 1.25E-08 7.903345798 -0.19660997 GGPPFAFVEFEDPRDAEDAVYGR ddPTM_HeLa_Romidepsin_16h_R1 1 GGPPFAFVEFEDPRDAEDAVYGR 23 1 J3KTL2;Q07955;Q07955-3;Q07955-2 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 0 56.017 0.014577 38296000 1107.5 975.59 1140.4 538.78 970.82 950.48 957.15 912.03 1468.1 1383.3 FALSE FALSE TRUE 1094.001364 989.3243816 1160.248184 601.0762786 921.2754328 889.7473955 1038.450297 938.4181491 1336.789459 1347.361667 0.811958208 0.73426787 0.861126016 0.446113537 0.683762538 0.660362706 0.770728694 0.696485712 0.9921534 1 10.39592144 -10.97042115 0.533650619 0.992457944 0.669031185 0.609578895 0.097437026 0.389343899 0.261958744 0.050613139 0.032433346 1.07E-11 10.97042115 -0.323426759 GGPS(ph)PGDVEAIK ddPTM_HeLa_Romidepsin_16h_R1 1 GGPSPGDVEAIK 12 0 P09661;H0YLR3;H0YMA0 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 1 0 GGPS(1)PGDVEAIK 160.18 0.00080407 10880000 5169.9 4608.8 4839.9 4065 5009.9 5154.4 5385.3 5349.6 5364.9 5300.5 TRUE FALSE FALSE 5106.88727 4673.682807 4924.136429 4535.014426 4754.226108 4825.050475 5842.727248 5504.382236 4885.049907 5162.792246 0.989171562 0.905262615 0.953773887 0.878403432 0.920863339 0.934581569 1.131699082 1.066163807 0.946203077 1 12.33393583 -7.761103779 24.99999831 0.96860796 1.098931469 0.629893041 0.044569765 5.240401596 390196.9817 0.007376171 0.024574383 1.73E-08 7.761103779 0.130323508 GGQGDPAVPAQQPADPST(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 GGQGDPAVPAQQPADPSTPER 21 0 H0Y704;O15231-2;O15231-3;H7BZT5;O15231-9;O15231-5;O15231-4;O15231-7;O15231;O15231-8;O15231-6 H0Y704 ZNF185 Zinc finger protein 185 1 0 GGQGDPAVPAQQPADPS(0.089)T(0.911)PER;GGQGDPAVPAQQPADPS(0.049)T(0.951)PER ; 156.61 1.34E-07 112168000 10922.3 11206.2 10622 9525.4 10482.4 10603.7 9393.9 10062.9 11827.5 12171.7 TRUE FALSE FALSE 10789.17481 11363.96118 10806.87145 10626.77157 9947.444013 9926.157792 10191.81763 10354.05413 10769.61878 11855.47748 0.910058226 0.958540995 0.911550924 0.896359643 0.83905891 0.837263434 0.859671629 0.873356147 0.908408691 1 13.53326615 -11.91274553 0.115516306 1.146681122 0.765606388 0.431378164 0.036732026 6.571538498 0.251432174 0.5682375 0.264220869 1.22E-12 11.91274553 -0.381074734 GGQGDPAVPAQQPADPSTPERQS(ph)S(ph)PSGSEQLVR ddPTM_HeLa_Romidepsin_16h_R1 1 GGQGDPAVPAQQPADPSTPERQSSPSGSEQLVR 33 1 H0Y704;O15231-2;O15231-3;H7BZT5;O15231-9;O15231-5;O15231-4;O15231-7;O15231;O15231-8;O15231-6 H0Y704 ZNF185 Zinc finger protein 185 2 0 GGQGDPAVPAQQPADPS(0.21)T(0.21)PERQS(0.534)S(0.554)PS(0.164)GS(0.327)EQLVR 57.041 0.0033358 15323000 2466 2636.6 2186.8 2625.6 2502.3 2783.6 2090.7 2271 2857.3 2348.3 TRUE FALSE FALSE 2435.943443 2673.718124 2224.860337 2929.184226 2374.598294 2605.736944 2268.284006 2336.707802 2601.735932 2287.290827 1.064990693 1.168945414 0.972705486 1.280634798 1.038170689 1.139224148 0.991690247 1.021605025 1.137474912 1 11.1594241 -11.47177067 0.916411603 1.007370468 1.0870524 0 0.096469437 0.769557181 1.332947273 0.030709163 0.017220125 3.37E-12 11.47177067 0.079681932 GGQGDPAVPT(ph)QQPADPSTPEQQNS(ph)PSGSEQFVR ddPTM_HeLa_Romidepsin_16h_R1 1 GGQGDPAVPTQQPADPSTPEQQNSPSGSEQFVR 33 0 H0Y704;O15231-2;O15231-3;H7BZT5;O15231-9;O15231-5;O15231-4;O15231-7;O15231;O15231-8;O15231-6 H0Y704 ZNF185 Zinc finger protein 185 2 0 GGQGDPAVPT(0.879)QQPADPS(0.075)T(0.082)PEQQNS(0.708)PS(0.188)GS(0.068)EQFVR 64.767 0.00036472 10604000 2149.1 2050.7 1878.5 1634.5 1632.5 1971.8 1925.2 1641.5 2100.1 1839.1 TRUE FALSE FALSE 2122.905943 2079.569808 1911.194505 1823.488581 1549.187433 1845.808344 2088.72644 1688.994213 1912.261796 1791.319917 1.185107095 1.160914803 1.066919698 1.017958078 0.864830128 1.030418032 1.16602647 0.942876924 1.067515511 1 10.8068073 -9.342795504 3.940235004 1.095849381 1.006938604 0.229412022 0.08523736 0.357676335 10.5024454 0.015829429 0.024834401 4.54E-10 9.342795504 -0.088910778 GGQGDPAVPTQQPADPS(ph)TPEQQNS(ph)PSGSEQFVR ddPTM_HeLa_Romidepsin_16h_R1 1 GGQGDPAVPTQQPADPSTPEQQNSPSGSEQFVR 33 0 H0Y704;O15231-2;O15231-3;H7BZT5;O15231-9;O15231-5;O15231-4;O15231-7;O15231;O15231-8;O15231-6 H0Y704 ZNF185 Zinc finger protein 185 2 0 GGQGDPAVPT(0.187)QQPADPS(0.469)T(0.406)PEQQNS(0.856)PS(0.066)GS(0.015)EQFVR 113.05 1.71E-13 9850300 3970.8 3740.5 3895.9 3479.6 3845.8 4130.2 3202.5 3356.1 4244.8 3562.1 TRUE FALSE FALSE 3922.402362 3793.158857 3963.706505 3881.927724 3649.534475 3866.29355 3474.52027 3453.203458 3865.134457 3469.556128 1.130519933 1.093269201 1.142424667 1.11885428 1.051873594 1.114348178 1.001430771 0.995286812 1.114014103 1 11.76053539 -7.73963688 22.51920843 1.077108744 0.998358408 0.401546337 0.042980232 87.16129241 90021.14309 0.007958965 0.029695683 1.82E-08 7.73963688 -0.078750336 GGQNSTAASTK(ac)YDVFR ddPTM_HeLa_Romidepsin_16h_R1 2 GGQNSTAASTKYDVFR 16 1 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 0 1 ; GGQNSTAASTK(1)YDVFR;GGQNSTAASTK(1)YDVFR 191.01 1.79E-15 5472100 889.37 954.03 663.94 762.46 958.94 1082.62 908.87 896.6 944.87 771.37 FALSE TRUE FALSE 878.5300164 967.4608594 675.4955972 850.6192127 910.0017135 1013.444076 986.0693951 922.5417064 860.3584607 751.3296962 1.16930027 1.287664875 0.899066815 1.132151726 1.211188268 1.348867323 1.312432345 1.227878668 1.145114409 1 9.553302315 -4.000000018 0.055632516 0.677584576 2.178106144 0.243974366 0.115160209 281.6699616 1.188458426 7.057143941 35.22643188 1.00E-04 4.000000018 1.500521568 GGQVQIVTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GGQVQIVTKK 10 1 A0A669KB77;P11137-3;P11137;P11137-2 A0A669KB77 MAP2 Microtubule-associated protein 2 0 1 ; GGQVQIVTK(1)K;GGQVQIVTK(1)K 164.97 0.0026798 1551180 1070.45 797.26 858.71 765.62 1182.37 1285.76 1458.25 1647.5 1176.01 1191.05 FALSE TRUE FALSE 1057.402944 808.4838472 873.6554873 854.1445868 1122.029247 1203.604086 1582.113719 1695.167813 1070.82472 1160.106349 0.911470698 0.696904941 0.753082239 0.736264039 0.967177921 1.037494611 1.363766106 1.461217598 0.923040134 1 10.18004135 -7.792394716 2.060250278 0.904772604 1.46907534 0.815030055 0.103706246 0.13962785 1.107818954 0.018400168 0.098819423 1.61E-08 7.792394716 0.564302737 GGREGFES(ph)DTDSEFTFK ddPTM_HeLa_Romidepsin_16h_R1 1 GGREGFESDTDSEFTFK 17 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 GGREGFES(0.999)DT(0.001)DSEFTFK 155.79 0.00039381 5012700 1474.6 1462.2 1200.3 2010.6 1588.3 1404.5 1279.2 1273.4 1178.1 1319.8 TRUE FALSE FALSE 1456.627008 1482.78489 1221.190718 2243.075032 1507.243124 1314.756983 1387.855216 1310.24382 1072.727785 1285.511406 1.133110917 1.153459147 0.949964903 1.74488925 1.172485221 1.02275015 1.079613304 1.019239358 0.83447551 1 10.3281267 -11.54795032 0.706579866 1.006504918 1.169402121 0.140884967 0.215348615 1.364468869 1.393454274 0.11018649 0.048599072 2.83E-12 11.54795032 0.162897204 GGREGFESDTDS(ph)EFTFK ddPTM_HeLa_Romidepsin_16h_R1 1 GGREGFESDTDSEFTFK 17 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 GGREGFES(0.115)DT(0.204)DS(0.679)EFT(0.002)FK 109.48 0.013594 6522700 1202.2 1077.7 1203.8 2275.2 1243.2 1365.5 1093 1468.3 1255.3 1195.2 TRUE FALSE FALSE 1187.547124 1092.871889 1224.751634 2538.269329 1179.754865 1278.248957 1185.839393 1510.782944 1143.022824 1164.148532 1.020099319 0.938773584 1.052057878 2.180365529 1.013405792 1.098011914 1.018632383 1.297757892 0.981853082 1 10.18505943 -9.493724927 24.99923168 1.004022254 1.309349643 0.21107338 0.313143654 920.8584855 789632.2795 0.047196542 0.072014558 3.21E-10 9.493724927 0.305327389 GGRS(ph)PDEVTLTSIVPTR ddPTM_HeLa_Romidepsin_16h_R1 1 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 GGRS(1)PDEVTLTSIVPTR 95.751 0.002069 22002000 330.53 432.21 242.6 384.04 315.55 330.96 333.82 393.4 438.28 400.38 TRUE FALSE FALSE 326.5013732 438.2946637 246.8223512 428.4445118 299.446306 309.8127241 362.1746625 404.7824083 399.0791391 389.9780699 0.837230087 1.123895669 0.632913413 1.098637449 0.767854218 0.794436272 0.928705203 1.037961977 1.023337387 1 8.607249187 -12.55538779 1.266432899 1.00120533 0.892439477 0.075665801 0.146608692 1.037103251 2.925663569 0.0992093 0.022341013 2.78E-13 12.55538779 -0.108765853 GGRSPDEVT(ph)LTSIVPTR ddPTM_HeLa_Romidepsin_16h_R1 1 GGRSPDEVTLTSIVPTR 17 1 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 GGRS(0.003)PDEVT(0.465)LT(0.131)S(0.131)IVPT(0.27)R 137.91 0.0043834 20451000 1160.8 1124.5 1180.6 1044.3 1501.8 1590.3 1209.8 1635.7 1283.3 1379.3 TRUE FALSE FALSE 1146.651723 1140.330741 1201.147848 1165.04688 1425.157542 1488.684962 1312.560382 1683.026399 1168.518434 1343.465587 0.853502862 0.848797879 0.894066703 0.867195178 1.060806883 1.108093111 0.976995908 1.252749914 0.869779208 1 10.39174365 -8.65438894 5.203206237 0.915509458 1.096469226 0.634672217 0.077108469 0.13265835 5.593583585 0.012317716 0.024944775 2.22E-09 8.65438894 0.180959768 GGS(ph)DDSSKDPIDVNYEK ddPTM_HeLa_Romidepsin_16h_R1 1 GGSDDSSKDPIDVNYEK 17 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 1 0 GGS(0.615)DDS(0.192)S(0.192)KDPIDVNYEK 64.203 0.016759 7067200 2826 2014.6 2485.5 2212.1 2792.6 3002.5 3043 3089 2890.4 3137.6 TRUE FALSE FALSE 2791.555625 2042.961592 2528.759085 2467.87341 2650.083201 2810.64994 3301.472344 3178.375341 2631.875385 3056.0847 0.913441838 0.668489846 0.827450589 0.807527818 0.867149789 0.919689805 1.080294779 1.040015462 0.861191899 1 11.57746881 -7.784310415 8.492110312 0.908539521 1.06024074 0.339068239 0.093635 0.206983722 66.69656469 0.01583273 0.049307171 1.64E-08 7.784310415 0.151701218 GGS(ph)GSGPTIEEVD ddPTM_HeLa_Romidepsin_16h_R1 1 GGSGSGPTIEEVD 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 1 0 GGS(0.862)GS(0.138)GPTIEEVD 126.71 0.0033396 8254000 852.41 925.34 1017.3 1011.1 1282.1 1585.5 1398.1 1351.7 1343.6 1111.3 TRUE FALSE FALSE 842.0204991 938.3669608 1035.00568 1128.008139 1216.669653 1484.191667 1516.854579 1390.809307 1223.425051 1082.428266 0.777899585 0.866909144 0.956188703 1.042108909 1.124018738 1.371168616 1.401344206 1.284897439 1.130259704 1 10.0800557 -8.662355676 1.351164183 0.892837768 1.368431315 0.746343151 0.099707323 0.126839195 0.457989016 0.014617239 0.040922738 2.18E-09 8.662355676 0.475593547 GGS(ph)PDLWK ddPTM_HeLa_Romidepsin_16h_R1 3 GGSPDLWK 8 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 GGS(1)PDLWK;GGS(1)PDLWK;GGS(1)PDLWK ;; 134.23 0.0094038 581710000 25156.1 26093.3 24581.6 20997.5 24302.7 22449.7 21737.6 23009.5 26176.3 24982.4 TRUE FALSE FALSE 24849.48778 26460.64216 25009.43244 23425.32975 23062.44253 21015.23662 23583.9912 23675.24358 23835.02617 24333.35365 1.021210974 1.087422743 1.027784037 0.96268398 0.94777082 0.86363914 0.969204309 0.972954403 0.979520806 1 14.57064755 -9.077370317 3.209470293 1.018413494 0.936187646 0.526605975 0.038223196 0.161421617 3.230709767 0.005863333 0.010375634 8.37E-10 9.077370317 -0.082225848 GGS(ph)PQMDDIKVFQNEVLGTLQR ddPTM_HeLa_Romidepsin_16h_R1 2 GGSPQMDDIKVFQNEVLGTLQR 22 1 A0A3B3ITG6;A0A3B3IUB1;Q13144 A0A3B3ITG6 EIF2B5 Translation initiation factor eIF-2B subunit epsilon 1 0 GGS(1)PQMDDIKVFQNEVLGTLQR;GGS(1)PQMDDIKVFQNEVLGTLQR ; 71.434 0.0041304 42503000 2452.8 2857.4 2682.5 3212 2247.97 2359.9 2247.92 2692.33 2798.6 2331 TRUE FALSE FALSE 2422.90433 2897.626552 2729.187787 3583.386553 2133.247703 2209.110006 2438.858269 2770.228321 2548.286207 2270.440284 1.067151753 1.276239931 1.202052222 1.578278265 0.939574459 0.972987496 1.074178557 1.220128246 1.122375349 1 11.14875638 -10.4645454 5.513938745 1.028827326 1.17562906 0.083275341 0.17080706 0.333149874 20.20449478 0.030242747 0.033940328 3.43E-11 10.4645454 0.146801735 GGS(ph)PYNQFDIIPGDTLGGHTGPAGDSWLPAK ddPTM_HeLa_Romidepsin_16h_R1 1 GGSPYNQFDIIPGDTLGGHTGPAGDSWLPAK 31 0 H0Y720;Q9UPQ9-1;Q9UPQ9;Q9UPQ9-2 H0Y720 TNRC6B Trinucleotide repeat-containing gene 6B protein 1 0 GGS(0.78)PY(0.163)NQFDIIPGDT(0.041)LGGHT(0.015)GPAGDS(0.001)WLPAK 62.345 0.0003413 0 597.52 683.77 549.55 587.42 1005.9 883.55 771.03 658.57 681.98 610.4 TRUE FALSE FALSE 590.2371964 693.396132 559.1146872 655.3402643 954.5651695 827.0940065 836.521269 677.6246839 620.9820007 594.54172 0.99275993 1.166269933 0.940412873 1.102261191 1.605547832 1.391145446 1.407001798 1.139742866 1.0444717 1 9.21563424 -8.930521236 7.041142835 1.008611601 1.386519949 0.6715662 0.118599971 0.087597337 7.328682894 0.016491026 0.030015242 1.17E-09 8.930521236 0.377908348 GGS(ph)REYDTGGGSSSSR ddPTM_HeLa_Romidepsin_16h_R1 3 GGSREYDTGGGSSSSR 16 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 GGS(0.999)REY(0.001)DTGGGSSSSR;GGS(0.999)REYDT(0.001)GGGSSSSR;GGS(0.867)REYDT(0.132)GGGSSSSR ;; 106.82 0.024884 15290000 3965.97 3140.16 3714.84 4746.88 3886.12 4154.26 4978.42 2617.11 4670.46 4243.64 TRUE FALSE FALSE 3917.631232 3184.367255 3779.495232 5295.7366 3687.796795 3888.816193 5401.286871 2692.831949 4252.72236 4133.389621 0.947801101 0.770400941 0.914381556 1.281209149 0.892196752 0.940829815 1.306745157 0.651482729 1.028870431 1 12.01310965 GGS(ph)SKDLLDNQSQEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 GGSSKDLLDNQSQEEQR 17 1 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-4 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 0 GGS(0.771)S(0.229)KDLLDNQSQEEQR 195.45 6.88E-13 8535900 1166.9 1051.7 1286.7 880.38 1088 1055.8 807.77 1070.5 1467.4 1166.1 TRUE FALSE FALSE 1152.677374 1066.50586 1309.094474 982.1736779 1032.4753 988.3377874 876.3819636 1101.473229 1336.152069 1135.804554 1.01485539 0.938987132 1.152570193 0.864738281 0.909025498 0.870165368 0.771595747 0.969773562 1.176392597 1 10.14949889 -9.19046589 24.99997253 1.01093346 0.872593208 0.486978961 0.085900139 90.42562173 31851.64729 0.009231772 0.015309162 6.45E-10 9.19046589 -0.138340252 GGSDGT(ph)PRGS(ph)PSPASVSSGR ddPTM_HeLa_Romidepsin_16h_R1 2 GGSDGTPRGSPSPASVSSGR 20 1 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 2 0 GGS(0.014)DGT(0.986)PRGS(0.954)PS(0.03)PAS(0.01)VS(0.006)S(0.001)GR;GGS(0.01)DGT(0.981)PRGS(0.96)PS(0.044)PAS(0.004)VS(0.001)S(0.001)GR ; 91.889 0.0051186 8072800 2379.32 2226.96 2727.27 2591.46 1745.59 1608.15 1579.05 1510.25 2815.05 2406.19 TRUE FALSE FALSE 2350.319933 2258.311201 2774.73699 2891.096798 1656.506029 1505.394405 1713.174468 1553.946701 2563.264878 2343.676837 1.002834476 0.963576192 1.18392474 1.233573141 0.706797969 0.642321664 0.730977258 0.663037957 1.093693822 1 11.19455794 -8.675459464 8.651505169 1.02779939 0.683536138 0.81437551 0.09012634 0.100546737 9.089460266 0.01366431 0.027357161 2.11E-09 8.675459464 -0.344263252 GGSGS(ph)GPTIEEVD ddPTM_HeLa_Romidepsin_16h_R1 1 GGSGSGPTIEEVD 13 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 1 0 GGS(0.123)GS(0.692)GPT(0.185)IEEVD 101.35 0.011951 7526800 1723.6 1674.7 1754.1 1407.9 2250.3 2450.3 2171.9 2686.4 1729.7 1909.4 TRUE FALSE FALSE 1702.5921 1698.276471 1784.629375 1570.688022 2135.458794 2293.733738 2356.381132 2764.126746 1574.9913 1859.793513 0.915473728 0.913153239 0.959584686 0.844549683 1.148223595 1.233327099 1.267012233 1.486254644 0.84686353 1 10.86092674 -8.050383412 1.12955276 0.948162924 1.447043689 0.866153118 0.074109235 0.163413747 0.333692753 0.01077874 0.068819287 8.90E-09 8.050383412 0.498880766 GGSISVQVNSIKFDS(ph)E ddPTM_HeLa_Romidepsin_16h_R1 3 GGSISVQVNSIKFDSE 16 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 0 GGSISVQVNSIKFDS(1)E;GGSISVQVNS(0.036)IKFDS(0.964)E;GGSISVQVNS(0.022)IKFDS(0.978)E ;; 161.08 3.25E-05 832090000 16081.5 16888.13 14045.39 14176.43 14765.67 15111.8 13526.65 15899.47 17028.89 15381.8 TRUE FALSE FALSE 15885.49249 17125.88154 14289.84412 15815.57554 14012.12276 14146.20475 14675.60331 16359.49608 15505.78343 14982.17862 1.060292558 1.143083524 0.953789464 1.055625883 0.935252684 0.944202116 0.979537335 1.091930386 1.034948509 1 13.87095981 GGTLGGGTLGPPS(ph)PPGAPSPPEPGGEIELVFRPHPLLVEK ddPTM_HeLa_Romidepsin_16h_R1 1 GGTLGGGTLGPPSPPGAPSPPEPGGEIELVFRPHPLLVEK 40 1 Q06587;Q06587-2 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 0 GGT(0.004)LGGGT(0.066)LGPPS(0.783)PPGAPS(0.147)PPEPGGEIELVFRPHPLLVEK 44.84 0.004633 55892000 1071.1 799.99 901.29 646.05 805.86 866.97 867.7 961.65 1227.1 985.2 TRUE FALSE FALSE 1058.045021 811.2522802 916.9765744 720.7493408 764.7339571 811.573415 941.4024163 989.4738255 1117.345103 959.604362 1.102584631 0.845402868 0.955577747 0.751090105 0.796926304 0.845737522 0.981031823 1.031126853 1.164381017 1 9.906295905 -10.25788335 24.86669144 1.048442743 0.882732427 0.493074961 0.091194498 207.2092665 1448981.037 0.015348859 0.018408934 5.52E-11 10.25788335 -0.165710316 GGTMT(ph)DLDEQEDESMET(ph)T(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 GGTMTDLDEQEDESMETTGK 20 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 3 0 GGT(0.241)MT(0.759)DLDEQEDES(0.154)MET(0.925)T(0.92)GK 40.798 0.0042266 0 707.8 862.93 507.73 469.67 457.83 621.05 590.54 703.22 917.63 772 TRUE FALSE FALSE 699.1730614 875.0783512 516.5668277 523.9754553 434.4652267 581.3669093 640.7004529 723.5665612 835.5548746 751.9433287 0.929821483 1.163755722 0.686975744 0.696828385 0.577789855 0.77315256 0.852059495 0.962262093 1.111193946 1 9.554480125 -9.741615153 24.99991169 0.980701369 0.752137915 0.56056513 0.120739035 160.7924071 202771.5532 0.018569766 0.026241158 1.81E-10 9.741615153 -0.228563454 GGTPAFLPSS(ph)LSPQSSLPASR ddPTM_HeLa_Romidepsin_16h_R1 1 GGTPAFLPSSLSPQSSLPASR 21 0 E5RGS7;H0YBP7;B3KPU0;A0A087WVI1;Q96JY6;Q96JY6-3;Q96JY6-5 E5RGS7 PDLIM2 PDZ and LIM domain protein 2 1 0 GGTPAFLPS(0.258)S(0.564)LS(0.176)PQSS(0.001)LPASR 181.49 2.47E-13 31994000 3283.7 3302.1 3637.4 3275 4226.1 4598.4 4616.7 4584.6 4107.5 3943.3 TRUE FALSE FALSE 3243.677001 3348.58705 3700.707421 3653.670909 4010.426347 4304.577081 5008.842383 4717.248168 3740.114913 3840.852498 0.844520065 0.871834327 0.963511987 0.951265614 1.044150055 1.120734807 1.304096522 1.228177383 0.973772077 1 11.90721084 -8.231697396 1.272609611 0.92251821 1.280085694 0.866462677 0.051281914 0.156518795 0.451810113 0.01016276 0.045309382 5.87E-09 8.231697396 0.357567484 GGTPAFLPSSLS(ph)PQSSLPASR ddPTM_HeLa_Romidepsin_16h_R1 1 GGTPAFLPSSLSPQSSLPASR 21 0 E5RGS7;H0YBP7;B3KPU0;A0A087WVI1;Q96JY6;Q96JY6-3;Q96JY6-5 E5RGS7 PDLIM2 PDZ and LIM domain protein 2 1 0 GGTPAFLPS(0.01)S(0.21)LS(0.78)PQSSLPASR 240.91 5.36E-54 34916000 4167.4 3759 3643.1 3698.3 5124.9 5102.6 4197 5107.2 4068.4 4056.6 TRUE FALSE FALSE 4116.606126 3811.919301 3706.506627 4125.914847 4863.357229 4776.560328 4553.493075 5254.968774 3704.512115 3951.208947 1.041859892 0.964747588 0.938069 1.044215809 1.23085296 1.208885785 1.152430341 1.329964789 0.937564215 1 11.94807843 -8.809723359 4.673763094 1.009149291 1.224301619 0.821773985 0.054997238 0.063131474 2.948897618 0.007428738 0.01403977 1.55E-09 8.809723359 0.215152328 GGTSQVGSPTLLSPAVPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GGTSQVGSPTLLSPAVPSK 19 0 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 1 0 GGTSQVGS(0.024)PT(0.005)LLS(0.002)PAVPS(0.969)K 182.23 1.76E-15 0 2979.8 2564.3 2245.1 2281.6 1930.1 2585.4 2604.7 3003.6 3197.3 3196.3 TRUE FALSE FALSE 2943.481051 2600.400283 2284.175024 2545.409327 1831.599795 2420.201284 2825.943153 3090.504427 2911.32548 3113.259665 0.945465964 0.835266108 0.733692422 0.817602642 0.588322206 0.777384974 0.907711999 0.992690864 0.935137378 1 11.6042102 -10.28023871 2.462860434 0.977789086 0.796312537 0.326590228 0.100833944 0.226608086 2.621687526 0.018850837 0.022179498 5.25E-11 10.28023871 -0.181476549 GGTVS(ph)PPPGTSR ddPTM_HeLa_Romidepsin_16h_R1 2 GGTVSPPPGTSR 12 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 0 GGT(0.122)VS(0.878)PPPGTSR;GGT(0.443)VS(0.557)PPPGTSR ; 162.93 0.0005212 13985100 7511.9 6941.6 6582.8 4733 5875.9 5935.9 4527.6 5073.5 7689 7138.7 TRUE FALSE FALSE 7420.342073 7039.324027 6697.370873 5280.251729 5576.030897 5556.615147 4912.174231 5220.293718 7001.276583 6953.235545 1.067178298 1.012381068 0.96320207 0.759394917 0.801933267 0.799140934 0.70645877 0.750771879 1.006909163 1 12.76346875 -9.370911367 2.543359142 1.031137404 0.761225915 0.938516791 0.03170857 0.053656611 0.676774965 0.00586156 0.009492361 4.26E-10 9.370911367 -0.269911488 GGVGAPGS(ph)PSTPPTR ddPTM_HeLa_Romidepsin_16h_R1 2 GGVGAPGSPSTPPTR 15 0 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 0 GGVGAPGS(0.597)PS(0.026)T(0.377)PPTR;GGVGAPGS(0.956)PS(0.012)T(0.031)PPT(0.001)R ; 96.135 0.010881 6769400 3920.8 4330.5 4000.2 4465.9 3929.1 3785.9 3325 3198.8 4626.3 4492.2 TRUE FALSE FALSE 3873.011782 4391.464893 4069.821803 4982.268371 3728.583366 3543.993208 3607.425417 3291.352231 4212.512141 4375.491996 0.885160294 1.003650537 0.930140383 1.138676148 0.852151797 0.809964505 0.824461665 0.752224489 0.96275165 1 12.09522953 -8.537084574 24.99542982 0.961498114 0.803877457 0.622679472 0.066777548 139.2182941 244956.6921 0.010479806 0.02096666 2.90E-09 8.537084574 -0.157620657 GGVT(ph)GSPEASISGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GGVT(0.984)GS(0.015)PEAS(0.001)ISGSK 196.37 1.10E-12 934700000 10224 10228 10237 7573.1 11415 11752 10984 11135 11490 11030 TRUE FALSE FALSE 10099.38596 10371.99005 10415.17069 8448.737455 10832.44995 11001.08513 11916.98069 11457.17366 10462.30562 10743.43901 0.9400515 0.965425507 0.969444764 0.78640903 1.008285145 1.023981717 1.109233335 1.066434467 0.973832086 1 13.39116826 -8.134582676 2.520687073 0.957828873 1.08484921 0.470542466 0.059362129 0.213754228 2.613975466 0.008876437 0.02796236 7.34E-09 8.134582676 0.127020336 GGVTGS(ph)PEASISGSK ddPTM_HeLa_Romidepsin_16h_R1 3 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GGVT(0.008)GS(0.985)PEAS(0.008)ISGSK;GGVT(0.199)GS(0.768)PEAS(0.025)IS(0.007)GS(0.001)K;GGVT(0.319)GS(0.671)PEAS(0.01)ISGSK ;; 208.79 2.30E-19 1301250000 10248 10185 9248.5 7502.6 11523.2 11110.6 9053.8 10359.4 10560.4 9874.6 TRUE FALSE FALSE 10123.09343 10328.3847 9409.466263 8370.085913 10935.12811 10400.66852 9822.829546 10659.13289 9615.851375 9618.056468 1.052509254 1.073853614 0.978312645 0.870247117 1.136937399 1.081369043 1.021290484 1.108241871 0.999770734 1 13.23152968 GGVTGSPEAS(ph)ISGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GGVT(0.017)GS(0.22)PEAS(0.76)ISGS(0.003)K 225.33 9.93E-35 260970000 6888.8 6142.8 6118.6 4608 6911.1 6617.3 6262 5770 6773.4 6334.8 TRUE FALSE FALSE 6804.836656 6229.2785 6225.091666 5140.798641 6558.400778 6194.475886 6793.894124 5936.945846 6167.57014 6170.220983 1.102851369 1.009571378 1.008892823 0.833162808 1.062911814 1.003930962 1.101077926 0.96219339 0.999570381 1 12.59110644 -10.02272707 22.34458965 1.048970955 0.997335679 0.043478753 0.071532602 366.0459932 359885.4271 0.012317022 0.015164504 9.49E-11 10.02272707 -0.051635276 GGVTGSPEASISGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GGVTGSPEASISGSK 15 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GGVT(0.001)GS(0.001)PEAS(0.003)IS(0.141)GS(0.855)K 83.499 0.025706 4675200 1836.3 1867.4 1911.3 951.46 1690.9 1475.3 1566.2 1586.9 1827 1972.2 TRUE FALSE FALSE 1813.918469 1893.689306 1944.565375 1061.472282 1604.607063 1381.033091 1699.232989 1632.814448 1663.588544 1920.96196 0.944276101 0.985802606 1.012287289 0.552573296 0.835314336 0.718927871 0.884573992 0.849998325 0.866018474 1 10.90761323 -9.319886235 24.99999875 0.976751006 0.775720138 0.508153979 0.094413697 138.6281235 59296.31591 0.012878237 0.019671833 4.79E-10 9.319886235 -0.201030868 GGVTGSPEASISGS(ph)KGDLK ddPTM_HeLa_Romidepsin_16h_R1 2 GGVTGSPEASISGSKGDLK 19 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GGVTGSPEAS(0.044)IS(0.144)GS(0.812)KGDLK;GGVTGSPEAS(0.08)IS(0.251)GS(0.669)KGDLK ; 95.138 0.00094271 278280000 9350.3 9184.8 9815.4 8408.8 6340.5 6015.5 5602.3 5351.6 7765.5 8776.1 TRUE FALSE FALSE 9236.334947 9314.103855 9986.23292 9381.065021 6016.920625 5631.128964 6078.159222 5506.440103 7070.934231 8548.095657 1.080513756 1.089611561 1.168240661 1.097445021 0.703890184 0.6587583 0.711054189 0.644171559 0.827194093 1 13.06138734 -8.744407798 9.1395422 1.057804562 0.679644243 0.808765714 0.086641807 0.044743245 20.65502098 0.008533496 0.016748611 1.80E-09 8.744407798 -0.37816032 GGVVGIK(ac)VDK ddPTM_HeLa_Romidepsin_16h_R1 2 GGVVGIKVDK 10 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8;H3BU78 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 1 ; GGVVGIK(1)VDK;GGVVGIK(1)VDK 123.86 0.013751 8154500 4333.2 3614 3743.6 3229.2 3823.9 4061.8 4089.6 4512.7 4300.3 3847.7 FALSE TRUE FALSE 4280.385292 3664.877987 3808.755788 3602.575298 3628.752114 3802.264089 4436.970522 4643.267855 3915.670398 3747.736199 1.142125556 0.97789113 1.016281719 0.961267044 0.968251745 1.014549554 1.18390684 1.238952692 1.044809504 1 11.87180369 -7.658826633 4.464207618 1.041077571 1.225667302 0.660112671 0.054243039 0.134348816 4.537863738 0.010214726 0.041805089 2.19E-08 7.658826633 0.184589731 GGY(ph)IT(ph)S(ph)NNKVVCT(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 GGYITSNNKVVCTLR 15 1 Q5CZC0-2;Q5CZC0 Q5CZC0-2 FSIP2 Fibrous sheath-interacting protein 2 4 0 GGY(1)IT(1)S(1)NNKVVCT(1)LR 57.174 0.01789 2881700 735.02 894.91 840.68 2720.5 1008.8 802.04 788.98 877.77 731.8 800.28 TRUE FALSE FALSE 726.0612935 907.5085665 855.3116828 3035.05701 957.3171716 750.7922325 855.9959415 903.1668901 666.3459752 779.4886102 0.931458502 1.164235827 1.097272842 3.893651518 1.228134907 0.963185636 1.098150672 1.158665923 0.854850175 1 9.606384132 -9.494131444 24.98046579 0.988582262 1.665287899 0.148425299 0.792470639 1076.667113 935590.0022 0.122425536 0.186780331 3.21E-10 9.494131444 0.676705638 GGYFDEFGIIR ddPTM_HeLa_Romidepsin_16h_R1 2 GGYFDEFGIIR 11 0 P11413;P11413-3;P11413-2;E7EM57;E7EUI8 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 0 ; ; 163.16 0.0094016 32380000 3468.4 2480 4632.3 4034.6 5324.3 5021.2 3676 3168.6 3084.7 2545.6 FALSE FALSE TRUE 3426.125807 2514.913505 4712.923238 4501.099435 5052.581103 4700.361525 3988.239348 3260.278442 2808.796706 2479.464945 1.381800462 1.014296859 1.900782363 1.815351108 2.037770735 1.895716064 1.60850806 1.314912094 1.132823721 1 11.27581311 -9.759478962 24.99998448 1.172882459 1.776203095 0.681748066 0.20998907 26.73117678 340883.0243 0.038175016 0.052447796 1.74E-10 9.759478962 0.603320637 GGYLS(ph)DGDSPELTTK ddPTM_HeLa_Romidepsin_16h_R1 3 GGYLSDGDSPELTTK 15 0 Q5VT97-2;Q5VT97 Q5VT97-2 SYDE2 Rho GTPase-activating protein SYDE2 1 0 GGYLS(0.976)DGDS(0.024)PELTTK;GGYLS(1)DGDSPELTTK;GGYLS(0.786)DGDS(0.214)PELTTK ;; 192.54 1.62E-12 5192800 3968.71 4214.27 4110.14 4328.13 4607.86 3596.26 3128.96 3737.76 4714.3 4399.7 TRUE FALSE FALSE 3920.337836 4273.598604 4181.675263 4828.568755 4372.70371 3366.470592 3394.733784 3845.906188 4292.641201 4285.39516 0.914813615 0.997247265 0.975796888 1.126749944 1.020373512 0.7855683 0.792163536 0.897444937 1.001690869 1 12.06521253 -8.260379028 24.99993807 0.97936427 0.82176938 0.633311979 0.060614966 57.05314546 1345119.626 0.00976514 0.023422324 5.49E-09 8.260379028 -0.157594889 GHAVGDIPGVR ddPTM_HeLa_Romidepsin_16h_R1 1 GHAVGDIPGVR 11 0 D6RD47;P62266 D6RD47 RPS23 40S ribosomal protein S23 0 0 108.47 0.0071464 5029200 2204.2 1716.1 1988.9 1798.2 2176.9 2309.2 1591 2460.2 2073.9 2279.5 FALSE FALSE TRUE 2177.334363 1740.259301 2023.51597 2006.116345 2065.80467 2161.649573 1726.1395 2531.382005 1888.40519 2220.278261 0.980658326 0.783802342 0.911379445 0.903542758 0.930426022 0.973593991 0.777442868 1.140119259 0.850526361 1 11.11652478 -10.49041567 24.8308261 0.991466965 0.911491634 0 0.105242432 524.5021723 401193.059 0.014874897 0.016345436 3.23E-11 10.49041567 -0.079975331 GHDLNEDGLVSWEEYK ddPTM_HeLa_Romidepsin_16h_R1 1 GHDLNEDGLVSWEEYK 16 0 O43852;O43852-3;O43852-10;O43852-5;O43852-6;O43852-13;O43852-14;O43852-11 O43852 CALU Calumenin 0 0 135.23 0.00065641 9216700 3522.2 3510.3 4291.6 2258.1 3949.1 4698.9 4129.9 4716.5 4704.6 3946.6 FALSE FALSE TRUE 3479.270072 3559.718096 4366.293498 2519.192147 3747.562691 4398.655455 4480.693603 4852.964486 4283.808793 3844.066763 0.905101364 0.926029207 1.13585267 0.655345576 0.974895318 1.144271348 1.165612847 1.262455827 1.114395003 1 11.90841768 -8.192599618 3.261013054 0.943421721 1.202265113 0.418502207 0.126340831 0.157868191 3.290681391 0.0158515 0.044091482 6.42E-09 8.192599618 0.258843392 GHLDAELDAYMAQT(ph)DPETND ddPTM_HeLa_Romidepsin_16h_R1 1 GHLDAELDAYMAQTDPETND 20 0 X6R700;Q9Y3Y2-4;Q9Y3Y2;Q9Y3Y2-3 X6R700 CHTOP Chromatin target of PRMT1 protein 1 0 GHLDAELDAY(0.002)MAQT(0.967)DPET(0.031)ND 110.15 0.00087897 2861100 753.77 652.06 590.75 711.32 980.2 835.18 705.99 908.34 841.56 1031.6 TRUE FALSE FALSE 744.5827613 661.2397178 601.0317559 793.5661653 930.1767364 781.8146934 765.956773 934.6213848 766.2887659 1004.798883 0.741026661 0.658081661 0.59816125 0.789776122 0.925734246 0.778080775 0.762298591 0.930157667 0.762628998 1 9.972691051 -12.18487983 0.987297237 0.996650982 0.769351847 0 0.120159835 0.415614675 0.743810468 0.064023789 0.019205901 6.53E-13 12.18487983 -0.227299135 GHLLYVALSPGQHR ddPTM_HeLa_Romidepsin_16h_R1 1 GHLLYVALSPGQHR 14 0 O15067 O15067 PFAS Phosphoribosylformylglycinamidine synthase 0 0 110.64 0.0011004 890180 294.6 121.84 152.57 167.69 357.9 497.29 322.11 257.63 403.91 121.86 FALSE FALSE TRUE 291.0093019 123.5552667 155.2254168 187.0791068 339.6350275 465.5147739 349.4700154 265.0841176 367.783278 118.6940596 2.451759614 1.040955774 1.307777469 1.57614549 2.861432396 3.921971962 2.94429238 2.23333938 3.098582011 1 6.891103923 -4 0.077651004 8.75E-14 8.060991039 0.030055179 0.92273355 169.0247393 0.968843125 16.09881569 147.4944321 1.00E-04 4 8.060991039 GHLS(ph)EGLVTK ddPTM_HeLa_Romidepsin_16h_R1 1 GHLSEGLVTK 10 0 Q16659 Q16659 MAPK6 Mitogen-activated protein kinase 6 1 0 GHLS(1)EGLVTK 133.07 0.0062419 5662000 1196.1 1245.6 993.71 641.72 931.47 935.91 773.58 814.63 1301.4 1172.2 TRUE FALSE FALSE 1181.521473 1263.135589 1011.005106 715.9186858 883.9336101 876.1083715 839.2878659 838.2000338 1184.999525 1141.746075 1.034837342 1.106319187 0.885490327 0.627038447 0.774194569 0.767340822 0.735091527 0.734138748 1.037883598 1 10.15702611 -9.515440503 5.181342293 1.023112588 0.733704987 0.908738188 0.047164569 0.038188625 3.117512782 0.007251847 0.010729454 3.05E-10 9.515440503 -0.2894076 GHQQLYWSHPR ddPTM_HeLa_Romidepsin_16h_R1 1 GHQQLYWSHPR 11 0 A0A2R8Y851;P62273;P62273-2 A0A2R8Y851 RPS29 40S ribosomal protein S29 0 0 104.43 0.0065217 6240400 1967.4 1670.5 2731.9 4023.3 3053.3 3382.3 2695.2 1880.2 1848.4 1289.9 FALSE FALSE TRUE 1943.420572 1694.017343 2779.447574 4488.492876 2897.478708 3166.181946 2924.130221 1934.600621 1683.074475 1256.388212 1.546831269 1.348323175 2.21225219 3.572536604 2.306196986 2.520066581 2.327409787 1.539811184 1.339613392 1 10.2950666 -9.721789793 4.121094766 1.267900288 2.479370554 0.562407275 0.47972049 0.116762776 4.250390774 0.079986182 0.112284403 1.90E-10 9.721789793 1.211470266 GHTAS(ph)ESDEQQWPEEK ddPTM_HeLa_Romidepsin_16h_R1 3 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 GHT(0.023)AS(0.652)ES(0.325)DEQQWPEEK;GHT(0.035)AS(0.482)ES(0.482)DEQQWPEEK;GHT(0.001)AS(0.985)ES(0.014)DEQQWPEEK ;; 217.79 6.85E-31 12461900 11719.9 11311.2 11332.3 8722.37 10125.9 10053.2 7783.45 9320.2 13892.5 13284 TRUE FALSE FALSE 11577.05335 11470.43937 11529.53393 9730.891459 9609.137538 9410.832965 8444.576049 9589.865282 12649.92001 12938.87976 0.89474928 0.886509464 0.891076673 0.752065993 0.742656065 0.72732981 0.65265125 0.741166581 0.977667328 1 13.6594251 -9.340876318 0.38213863 0.989557236 0.6422808 0.903411947 0.034787667 0.323664952 0.094100518 0.015930075 0.044266396 4.56E-10 9.340876318 -0.347276436 GHTASES(ph)DEQQWPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 GHTASESDEQQWPEEK 16 0 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 GHT(0.034)AS(0.132)ES(0.834)DEQQWPEEK 79.88 0.010545 6616900 3163.4 2893 3128.7 2481.2 2406.6 2643.6 2349 2205.4 3626.5 3495.7 TRUE FALSE FALSE 3124.843264 2933.72773 3183.153711 2768.088018 2283.782222 2474.682492 2548.524001 2269.209769 3302.136757 3404.88121 0.917753975 0.861624106 0.93487952 0.812976385 0.670737709 0.726804355 0.748491311 0.666457838 0.969824365 1 11.73338875 -9.223127901 0.48145844 0.982882427 0.659040373 0.858023352 0.044237359 0.307511092 0.133407444 0.013941292 0.042508753 5.98E-10 9.223127901 -0.323842054 GHTDTEGRPPS(ph)PPPTSTPEK ddPTM_HeLa_Romidepsin_16h_R1 2 GHTDTEGRPPSPPPTSTPEK 20 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 0 GHT(0.003)DT(0.001)EGRPPS(0.994)PPPT(0.001)STPEK;GHT(0.001)DT(0.004)EGRPPS(0.992)PPPT(0.001)S(0.001)TPEK ; 69.913 0.0029327 90436000 11540.4 10601.1 9649.8 10755.4 11554.7 12441 11873 13531.1 11787.6 11055.2 TRUE FALSE FALSE 11399.74117 10750.34256 9817.750721 11998.98995 10965.02054 11646.06025 12881.49232 13922.60103 10733.28753 10767.98431 1.058669927 0.998361648 0.91175381 1.114320899 1.018298339 1.081545061 1.196277033 1.292962604 0.996777783 1 13.39446059 -7.542718938 1.255789093 1.021438193 1.349099165 0.787226077 0.048575566 0.311659966 0.582718147 0.007249113 0.11487364 2.87E-08 7.542718938 0.327660972 GHWDDVFLDSTQR ddPTM_HeLa_Romidepsin_16h_R1 1 GHWDDVFLDSTQR 13 0 Q9H6T3-3;Q9H6T3 Q9H6T3-3 RPAP3 RNA polymerase II-associated protein 3 0 0 120.59 0.0022353 4638500 3607.3 3572 2987.1 3289.5 4371.4 4157.4 3634.3 3925.3 4139.5 3357.9 FALSE FALSE TRUE 3563.33284 3622.28671 3039.089222 3669.847468 4148.311146 3891.755557 3942.997351 4038.872362 3769.252752 3270.661274 1.089483912 1.107508973 0.929197177 1.122050607 1.268340191 1.189898688 1.205565793 1.23487944 1.15244363 1 11.67536664 -8.980988595 6.096676968 1.040798655 1.218875837 0.625763523 0.060982414 0.066861891 8.821843344 0.007984467 0.01434116 1.04E-09 8.980988595 0.178077182 GHYEVT(ph)GSDDETGK ddPTM_HeLa_Romidepsin_16h_R1 3 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GHYEVT(0.782)GS(0.215)DDET(0.003)GK;GHYEVT(0.976)GS(0.023)DDET(0.001)GK;GHYEVT(0.91)GS(0.09)DDETGK ;; 228.17 7.85E-33 94283200 10520.4 11741.4 12292.1 6367.9 11083.8 11101.3 7977.5 8528 10787.6 12026.4 TRUE FALSE FALSE 10392.17332 11906.69574 12506.03884 7104.18656 10518.15233 10391.96276 8655.108651 8774.744225 9822.730038 11713.95239 0.88716199 1.016454168 1.06761906 0.606472207 0.897916602 0.887144015 0.738871762 0.749084846 0.838549595 1 13.51594032 -9.276977427 24.9998501 0.959945218 0.786800025 0.474728619 0.097508522 555.9940003 894561.327 0.014371945 0.022000455 5.28E-10 9.276977427 -0.173145192 GHYEVT(ph)GSDDETGKLQGSGVSLASK ddPTM_HeLa_Romidepsin_16h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GHY(0.1)EVT(0.428)GS(0.384)DDET(0.076)GKLQGS(0.01)GVS(0.001)LASK;GHY(0.003)EVT(0.507)GS(0.443)DDET(0.044)GKLQGS(0.002)GVSLASK ; 75.103 0.00010219 19517000 1955.64 1980.27 1920.83 1789.2 2037.73 1781.67 1503.78 1876.27 2349.54 2311.16 TRUE FALSE FALSE 1931.803907 2008.148293 1954.26124 1996.075722 1933.737034 1667.827037 1631.511036 1930.556912 2139.391258 2251.11573 0.858153973 0.892067994 0.868130063 0.886705066 0.859012715 0.740889069 0.724756624 0.857600028 0.95036929 1 11.13642451 -16.52287875 0.074942702 1.615294582 0.621271263 0.635271411 0.047522826 83.96676353 0.486019341 8.802431388 1.112783888 3.00E-17 16.52287875 -0.99402332 GHYEVTGS(ph)DDETGK ddPTM_HeLa_Romidepsin_16h_R1 1 GHYEVTGSDDETGK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GHYEVT(0.055)GS(0.941)DDET(0.004)GK 198.48 1.82E-16 78135000 3479.9 3288.3 3699.1 2373.6 3449.9 3304.1 2726 2960.4 3551.4 3883.8 TRUE FALSE FALSE 3437.48564 3334.592774 3763.481284 2648.0468 3273.83873 3092.978673 2957.546372 3046.054503 3233.753889 3782.898316 0.908690996 0.881491517 0.994867155 0.700004753 0.865431332 0.817621415 0.781820214 0.805217124 0.854835002 1 11.88527628 -9.856337721 0.265234323 1.018406663 0.744597425 0.240422329 0.076564327 1.091396785 0.2336398 0.07108451 0.114203234 1.39E-10 9.856337721 -0.273809238 GHYEVTGS(ph)DDETGKLQGSGVSLASK ddPTM_HeLa_Romidepsin_16h_R1 2 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GHY(0.008)EVT(0.188)GS(0.623)DDET(0.084)GKLQGS(0.094)GVS(0.002)LASK;GHYEVT(0.055)GS(0.942)DDET(0.003)GKLQGSGVSLASK ; 74.392 0.0001557 33697800 3639.9 4040.5 3441.2 3191.7 3531.5 3849.3 3083.1 3249.6 4061 4004 TRUE FALSE FALSE 3595.535499 4097.382265 3501.092642 3560.739371 3351.274377 3603.342153 3344.978437 3343.622049 3697.773989 3899.975503 0.92193797 1.050617436 0.897721701 0.91301583 0.85930652 0.923939689 0.857692166 0.857344372 0.948153132 1 11.92924935 -9.551847556 24.99319745 0.968930375 0.884278565 0.593254735 0.038383334 130.6620644 112729.7275 0.006610538 0.009348782 2.81E-10 9.551847556 -0.084651811 GHYEVTGSDDET(ph)GKLQGSGVSLASK ddPTM_HeLa_Romidepsin_16h_R1 4 GHYEVTGSDDETGKLQGSGVSLASK 25 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GHY(0.001)EVT(0.029)GS(0.183)DDET(0.753)GKLQGS(0.035)GVS(0.001)LASK;GHY(0.001)EVT(0.003)GS(0.038)DDET(0.959)GKLQGSGVSLASK;GHY(0.001)EVT(0.012)GS(0.042)DDET(0.941)GKLQGS(0.005)GVSLASK;GHY(0.008)EVT(0.284)GS(0.284)DDET(0.412)GKLQGS(0.011)GVS(0.001)LASK ;;; 121.91 4.02E-07 291536000 8375.12 8153.47 8327.04 6039.13 8597.52 7963.74 7126.09 6600.5 9261 8860.93 TRUE FALSE FALSE 8273.040816 8268.254765 8471.968638 6737.402626 8158.756473 7454.882716 7731.379907 6791.475054 8432.672965 8630.721761 0.958557238 0.958002702 0.981606043 0.780630266 0.945315664 0.863761215 0.895797608 0.786895377 0.977053044 1 13.0752655 -9.290164799 24.80085137 0.977974082 0.862337493 0.624380139 0.046529152 312.4481638 269759.4906 0.006778466 0.010355383 5.13E-10 9.290164799 -0.115636589 GHYTEGAELVDSVLDVVR ddPTM_HeLa_Romidepsin_16h_R1 2 GHYTEGAELVDSVLDVVR 18 0 Q5JP53;P07437;Q5ST81;P68371;A0A0B4J269;Q13509;Q13509-2;G3V2A3;Q9BVA1;Q13885 Q5JP53;P68371;A0A0B4J269;Q9BVA1 TUBB;TUBB4B;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 0 ; ; 191.93 6.39E-15 73029000 4338 3728 3638.7 3320.1 6790.9 6484.3 5069.6 5861.1 5344.9 5400.2 FALSE FALSE TRUE 4285.126787 3780.482882 3702.030047 3703.985584 6444.335033 6069.974157 5500.211697 6030.681681 4866.838757 5259.902026 0.814678062 0.718736369 0.703821103 0.704192885 1.225181572 1.154008977 1.0456871 1.146538786 0.925271751 1 12.36082021 -8.752152625 24.99934941 0.863896115 1.136710404 0.685528586 0.106500004 130.3649334 350931.5171 0.019649543 0.038873871 1.77E-09 8.752152625 0.272814289 GHYTEGAELVDSVLDVVRK ddPTM_HeLa_Romidepsin_16h_R1 2 GHYTEGAELVDSVLDVVRK 19 1 Q5JP53;P07437;Q5ST81;P68371;A0A0B4J269;Q13509;Q13509-2;G3V2A3;Q9BVA1;Q13885 Q5JP53;P68371;A0A0B4J269;Q9BVA1 TUBB;TUBB4B;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-4B chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 0 ; ; 169.15 3.53E-08 18092500 11524.4 10981.4 8417.8 15250.4 16711.5 15322.7 12925.6 14926.6 15523.2 11959.4 FALSE FALSE TRUE 11383.93618 11135.99644 8564.308278 17013.723 15858.6498 14343.62892 14023.50014 15358.47762 14134.76611 11648.69306 0.977271537 0.955986768 0.735216237 1.46056926 1.361410221 1.23135092 1.203868972 1.31847217 1.213420771 1 13.50788048 -9.253092064 24.99985113 0.96864735 1.306869151 0.643376274 0.125963077 244.8187676 733221.4938 0.015254904 0.025029618 5.58E-10 9.253092064 0.338221801 GIAIAYEDEGS(ph)G ddPTM_HeLa_Romidepsin_16h_R1 2 GIAIAYEDEGSG 12 0 H0YCR5;Q9BQC3-2;Q9BQC3-3;Q9BQC3 H0YCR5 DPH2 Diphthamide biosynthesis protein 2 1 0 GIAIAYEDEGS(1)G;GIAIAYEDEGS(1)G ; 121.61 0.0070054 7045100 8646.9 8815.9 7701.9 7375.7 7807.9 6571 5749.8 6290.8 9447.9 8819.3 TRUE FALSE FALSE 8541.508257 8940.010472 7835.948339 8228.513138 7409.433728 6151.134307 6238.187868 6472.814373 8602.856161 8590.173315 0.994334799 1.040725273 0.912199097 0.957898384 0.862547641 0.71606638 0.726200467 0.753513827 1.001476437 1 13.06847152 -8.596069591 1.45227999 0.996266416 0.722945248 0.923761768 0.032585645 0.070035323 0.291319558 0.004796665 0.013587071 2.53E-09 8.596069591 -0.273321167 GIAPAS(ph)PMLGNASNPNK ddPTM_HeLa_Romidepsin_16h_R1 2 GIAPASPMLGNASNPNK 17 0 H0YIY6;J3KNR0;P27448-8;P27448-6;P27448-3;P27448-4;P27448-2;P27448;P27448-7;H0YKP9 H0YIY6 MARK3 MAP/microtubule affinity-regulating kinase 3 1 0 GIAPAS(0.998)PMLGNAS(0.002)NPNK;GIAPAS(0.996)PMLGNAS(0.004)NPNK ; 98.898 0.0049613 29547800 9033.5 9582.7 9191.7 5676.4 9045.9 9667.2 8542.6 9167.9 9524.5 9830.5 TRUE FALSE FALSE 8923.396227 9717.605502 9351.677683 6332.732076 8584.253968 9049.497119 9268.208231 9433.158722 8672.604865 9575.102193 0.93193744 1.014882693 0.976666097 0.661374881 0.896518261 0.945107106 0.967948753 0.985175775 0.90574541 1 13.22507217 -11.30263845 0.562723104 0.996458002 0.91177561 0 0.096634909 1.552806674 1.075375324 0.058692937 0.028234941 4.98E-12 11.30263845 -0.084682392 GIAPAS(ph)PMLGNASNPNKADIPER ddPTM_HeLa_Romidepsin_16h_R1 3 GIAPASPMLGNASNPNKADIPER 23 1 H0YIY6;J3KNR0;P27448-8;P27448-6;P27448-3;P27448-4;P27448-2;P27448;P27448-7;H0YKP9 H0YIY6 MARK3 MAP/microtubule affinity-regulating kinase 3 1 0 GIAPAS(0.992)PMLGNAS(0.008)NPNKADIPER;GIAPAS(0.95)PMLGNAS(0.05)NPNKADIPER;GIAPAS(1)PMLGNASNPNKADIPER ;; 94.911 9.08E-05 83992000 8024 6961.3 6241.9 7684.5 6485.9 6968.5 6272.6 6498.3 7185.6 6404.7 TRUE FALSE FALSE 7926.200402 7059.301364 6350.537651 8573.018047 6154.900321 6523.23534 6805.394487 6686.318058 6542.901939 6238.304971 1.27056956 1.131605684 1.017990894 1.374254399 0.986630238 1.045674325 1.090904423 1.071816477 1.04882688 1 12.60693837 GIASTSDPPTANIKPTPVVST(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 GIASTSDPPTANIKPTPVVSTPSK 24 1 P12270 P12270 TPR Nucleoprotein TPR 1 0 GIASTSDPPTANIKPT(0.033)PVVS(0.215)T(0.702)PS(0.05)K;GIASTSDPPT(0.001)ANIKPT(0.023)PVVS(0.155)T(0.665)PS(0.155)K ; 79.663 0.00017285 104767000 6683.9 7163.8 8432.8 5264 8053.3 7449.6 5857.7 6678.1 7188.4 6769.4 TRUE FALSE FALSE 6602.434056 7264.652164 8579.569347 5872.648448 7642.31005 6973.594602 6355.252892 6871.320287 6545.4515 6593.530012 1.001350421 1.101784955 1.301210328 0.890668343 1.159061995 1.057642051 0.96386198 1.042130736 0.992708229 1 12.68683534 -10.27752571 22.24516112 1.000637684 1.073904836 0.101290555 0.103305245 332.1955057 459378.2915 0.016889276 0.019358866 5.28E-11 10.27752571 0.073267152 GIAYIEFK ddPTM_HeLa_Romidepsin_16h_R1 2 GIAYIEFK 8 0 P19338;H7BY16 P19338 NCL Nucleolin 0 0 ; ; 138.9 0.014682 2859900 1879.65 1404.39 6082.7 2078.78 3341.6 4975.3 3722.1 1760.64 1487.15 738.3 FALSE FALSE TRUE 1856.740103 1424.161039 6188.566842 2319.138325 3171.065683 4657.394387 4038.255081 1811.581341 1354.135579 719.1188596 2.581965524 1.9804251 8.605763511 3.224972192 4.409654455 6.476529332 5.615559969 2.519168169 1.883048346 1 9.490086436 -9.952624381 24.99916302 1.775150392 5.119497772 0.495007273 1.623574164 71.84958513 37913.42447 0.254196604 0.334079734 1.12E-10 9.952624381 3.34434738 GIDLLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GIDLLKK 7 1 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2 D6REM6 MATR3 Matrin-3 0 1 ; GIDLLK(1)K;GIDLLK(1)K 89.298 0.024395 3109100 2757.4 2655.8 2437.51 1909.54 5108.9 3778.3 3749.9 3317.7 4668.8 3371.8 FALSE TRUE FALSE 2723.791748 2693.188422 2479.933839 2130.329999 4848.173769 3536.878824 4068.416412 3413.692415 4251.210835 3284.20015 0.829362287 0.820043937 0.755110446 0.648660222 1.476211421 1.07693766 1.238784552 1.039428859 1.294443286 1 11.68132634 -8.766383451 24.99994872 0.878648332 1.200700686 0.386268032 0.195016459 75.31261529 380824.443 0.022439385 0.041617785 1.71E-09 8.766383451 0.322052354 GIEK(ac)NLGIGK ddPTM_HeLa_Romidepsin_16h_R1 1 GIEKNLGIGK 10 1 G3XAL0;P40926-2;P40926 G3XAL0 MDH2 "Malate dehydrogenase;Malate dehydrogenase, mitochondrial" 0 1 GIEK(1)NLGIGK 115.78 0.015765 854560 475.12 282.53 394.59 428.02 634.31 595.38 455.24 220.44 319.33 199.83 FALSE TRUE FALSE 469.3290547 286.5074648 401.4576734 477.5096863 601.9387938 557.3371395 493.9080742 226.8180836 290.768325 194.6383878 2.411287208 1.471998756 2.062582197 2.453317106 3.092600594 2.863449219 2.537567639 1.165330674 1.493889917 1 7.604652465 -12.93271891 0.397783021 0.179488449 2.390706668 0.317477665 0.572849803 2.842717708 0.399289029 2.831243044 0.184780283 1.17E-13 12.93271891 2.211218219 GIGLDESELDS(ph)EAELMR ddPTM_HeLa_Romidepsin_16h_R1 2 GIGLDESELDSEAELMR 17 0 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 0 GIGLDESELDS(1)EAELMR;GIGLDESELDS(1)EAELMR ; 85.909 0.017616 37349000 8869.2 8430.4 8417.1 9333.5 10925.2 10149.3 9282.1 9562.9 9647.3 9048.2 TRUE FALSE FALSE 8761.098779 8549.083392 8563.596095 10412.68319 10367.64628 9500.792485 10070.52134 9839.587424 8784.421326 8813.12646 0.994096569 0.970039796 0.97168651 1.181497081 1.176386873 1.078027477 1.142672965 1.11646956 0.996742911 1 13.10543819 -9.26683877 24.99999647 0.992930838 1.137902734 0.872172511 0.029137379 117.2898441 543069.6904 0.004504974 0.007006335 5.41E-10 9.26683877 0.144971896 GIGT(ph)PPNTTPIK ddPTM_HeLa_Romidepsin_16h_R1 1 GIGTPPNTTPIK 12 0 O96028;D6RIS1;D6R9V2;O96028-7;O96028-6;O96028-3;O96028-5 O96028;O96028-3;O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 GIGT(0.999)PPNTTPIK 111.94 0.020694 6692200 2280.3 2446.7 2725.4 1463.3 1255.7 1044.8 972.07 1207.7 2382.7 2038.5 TRUE FALSE FALSE 2252.506827 2481.144707 2772.834444 1632.493631 1191.616943 978.0406519 1054.637602 1242.642894 2169.585344 1985.539476 1.134455826 1.249607342 1.396514387 0.822191475 0.600147697 0.492581822 0.531159221 0.625846481 1.09269313 1 10.95531533 -8.952369304 3.593583791 1.10548829 0.557065265 0.857238266 0.11607142 0.077362593 2.083613924 0.020171443 0.037380718 1.12E-09 8.952369304 -0.548423025 GIGTPPNTTPIKNGS(ph)PEIK ddPTM_HeLa_Romidepsin_16h_R1 2 GIGTPPNTTPIKNGSPEIK 19 1 O96028;D6RIS1;D6R9V2;O96028-7;O96028-6;O96028-3;O96028-5 O96028;O96028-3;O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 GIGT(0.044)PPNT(0.113)T(0.113)PIKNGS(0.73)PEIK;GIGT(0.001)PPNT(0.076)T(0.328)PIKNGS(0.596)PEIK ; 80.41 0.0032149 58032000 6778.9 5900.5 5037.7 5768 3312.7 2962.1 2427.5 3097.2 6382.3 5529.6 TRUE FALSE FALSE 6696.276159 5983.567394 5125.379055 6434.923299 3143.640558 2772.83137 2633.691789 3186.812595 5811.451103 5385.940195 1.24328825 1.110960608 0.951621977 1.194763229 0.583675355 0.514827731 0.488993879 0.591691047 1.079004017 1 12.39498249 -8.730721184 7.497050185 1.108658188 0.536055793 0.911740735 0.084055875 0.049851409 9.322327929 0.015609124 0.030943638 1.86E-09 8.730721184 -0.572602395 GILAADES(ph)TGSIAK ddPTM_HeLa_Romidepsin_16h_R1 2 GILAADESTGSIAK 14 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BPS8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 GILAADES(0.775)T(0.225)GSIAK;GILAADES(0.896)T(0.091)GS(0.013)IAK ; 195.94 1.42E-11 85358000 9471.1 9126.4 8701.5 6748.5 9325 8311.7 9360.2 8480.3 9897.8 8935.4 TRUE FALSE FALSE 9355.66259 9254.881699 8852.945957 7528.793323 8849.110454 7780.609195 10155.25515 8725.664101 9012.515979 8703.25702 1.074961083 1.063381407 1.017199186 0.865054692 1.016758489 0.893988213 1.16683388 1.002574563 1.035533704 1 13.08733969 -9.51853328 24.91908515 1.03857201 0.989773203 0.097126656 0.077723058 379.4813321 2176139.394 0.012308025 0.017663658 3.03E-10 9.51853328 -0.048798808 GILAADESTGS(ph)IAK ddPTM_HeLa_Romidepsin_16h_R1 1 GILAADESTGSIAK 14 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BPS8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 GILAADES(0.075)T(0.045)GS(0.88)IAK 175.6 6.77E-06 21462000 2977.7 3153.7 2916.7 2049.9 3343.1 2904.3 3232.5 3400.4 3019.5 2693.5 TRUE FALSE FALSE 2941.406647 3198.097871 2967.46394 2286.919083 3172.489132 2718.724603 3507.068469 3498.785209 2749.428358 2623.522482 1.12116693 1.219009135 1.131099108 0.871697917 1.209247931 1.0362879 1.336778508 1.333621203 1.047991156 1 11.35728944 -7.756955927 24.99682169 1.071680081 1.335199985 0.526574858 0.096726421 62.92229948 350800.3678 0.013681799 0.047908027 1.75E-08 7.756955927 0.263519904 GILAADESTGS(ph)IAKR ddPTM_HeLa_Romidepsin_16h_R1 3 GILAADESTGSIAKR 15 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BPS8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 GILAADES(0.001)T(0.002)GS(0.997)IAKR;GILAADEST(0.006)GS(0.994)IAKR;GILAADES(0.109)T(0.35)GS(0.541)IAKR ;; 118.52 0.0011651 79838000 7743.8 8380.7 7085.9 7699.5 8364.7 7401.4 7996.7 8214.4 9342.1 8003.1 TRUE FALSE FALSE 7649.415587 8498.683715 7209.227117 8589.752417 7937.818146 6928.474427 8675.939498 8452.070704 8506.519178 7795.178308 0.981300913 1.09024879 0.924831586 1.101931486 1.01829847 0.888815387 1.112987947 1.084269066 1.091253957 1 12.92836631 -7.702150798 24.99999468 0.997697775 1.098629295 0.181866468 0.06816084 64.72793235 27292.31168 0.00769939 0.02880847 1.99E-08 7.702150798 0.10093152 GILAADESTGSIAK ddPTM_HeLa_Romidepsin_16h_R1 2 GILAADESTGSIAK 14 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BPS8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ; ; 196.88 6.94E-12 1410920 1221.32 754.305 1099.74 957.56 895.7 1071.41 961.51 1084.2 1056.04 1066.45 FALSE FALSE TRUE 1206.434082 764.9241256 1118.880513 1068.277593 849.9890867 1002.950359 1043.180635 1115.569616 961.5851375 1038.743475 1.161436015 0.736393675 1.077148054 1.028432542 0.818285849 0.96554191 1.004271661 1.073960649 0.925719545 1 10.0206237 GILAADESTGSIAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GILAADESTGSIAKR 15 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BPS8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 1 ; GILAADESTGSIAK(1)R;GILAADESTGSIAK(1)R 360.54 1.38E-257 48349000 9054.5 7984.7 7750.7 7347.9 9925.3 9788.7 8691.3 9658.7 9104.8 7886.6 FALSE TRUE FALSE 8944.140271 8097.108816 7885.597682 8197.498771 9418.774905 9163.233662 9429.538805 9938.159246 8290.443885 7681.704995 1.164343108 1.054077034 1.026542634 1.067145741 1.226130776 1.192864562 1.227532014 1.293743935 1.079245283 1 12.90721084 -4 0.220684821 1.039864744 2.389256554 0.68035114 0.053782438 27.95510372 0.334825321 0.051018828 13.57699503 1.00E-04 4 1.34939181 GILFVGSGVSGGEEGAR ddPTM_HeLa_Romidepsin_16h_R1 2 GILFVGSGVSGGEEGAR 17 0 P52209-2;P52209;K7EMN2;K7EM49;K7EPF6 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 ; ; 256.31 8.22E-73 1649370 323.52 505.02 505.17 285.488 595.67 445.48 476.21 607.19 501.47 194.352 FALSE FALSE TRUE 319.5768138 512.1296848 513.9622719 318.4974658 565.2707371 417.0152657 516.6592655 624.7580847 456.6172672 189.302707 1.688178784 2.705347921 2.715028644 1.68247708 2.986067902 2.202901756 2.729275633 3.30031247 2.412101097 1 7.564551231 -10.57066519 0.296278817 0.720043838 3.046390454 0.143362242 0.616863171 0.599387463 0.176411235 0.530586809 0.454165247 2.69E-11 10.57066519 2.326346616 GILHLS(ph)PDVYQEMEASR ddPTM_HeLa_Romidepsin_16h_R1 1 GILHLSPDVYQEMEASR 17 0 E5RJ67;H0YBY0;E5RJN7;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3 E5RJ67 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 0 GILHLS(0.998)PDVYQEMEAS(0.001)R 62.303 0.016009 16526000 2926.1 2820.7 3021.1 2760.3 4099.7 4428.7 3989.5 3635.4 3318 2949.8 TRUE FALSE FALSE 2890.435568 2860.409889 3073.680978 3079.458874 3890.477011 4145.720363 4328.36803 3740.584563 3021.22977 2873.163771 1.006011421 0.995561032 1.06978969 1.071800677 1.354074227 1.442911262 1.506481487 1.301904403 1.051534131 1 11.48842451 -8.763501401 2.446672967 1.007281216 1.427503555 0.920115497 0.053471856 0.045840269 0.560291702 0.007247103 0.015286669 1.72E-09 8.763501401 0.420222338 GILIGIQQSFRPR ddPTM_HeLa_Romidepsin_16h_R1 2 GILIGIQQSFRPR 13 1 P31327;P31327-3;P31327-2 P31327 CPS1 "Carbamoyl-phosphate synthase [ammonia], mitochondrial" 0 0 ; ; 138.63 6.85E-05 2805500 741.76 535.68 941.39 744.28 706.52 837.03 649.42 475.14 323.6 286.08 FALSE FALSE TRUE 732.7191438 543.2213171 957.7744981 830.3371555 670.463648 783.5464844 704.5817186 488.8874263 294.6564055 278.6476004 2.629554832 1.949492177 3.437225 2.979882671 2.406134656 2.811962075 2.528576301 1.754500759 1.057451796 1 8.122297919 -12.16719256 0.675796036 0.863275282 2.611842455 0.642249558 0.456468666 0.450638559 0.329010342 0.455442235 0.097945471 6.80E-13 12.16719256 1.748567173 GILSLPHQAS(ph)PVSR ddPTM_HeLa_Romidepsin_16h_R1 2 GILSLPHQASPVSR 14 0 O75925;O75925-2 O75925 PIAS1 E3 SUMO-protein ligase PIAS1 1 0 GILSLPHQAS(1)PVSR;GILSLPHQAS(0.989)PVS(0.011)R ; 130.64 0.00090095 97775000 7638.3 7578.8 7235.7 7925.7 8510.7 8592.3 7257.4 7536.7 8493.8 8007.6 TRUE FALSE FALSE 7545.201462 7685.494545 7361.634323 8842.106726 8076.367221 8043.27976 7873.843375 7754.762524 7734.093255 7799.561398 0.967387918 0.985375222 0.943852346 1.133667174 1.035489922 1.031247701 1.009523866 0.994256232 0.991606176 1 12.92917728 GIPGLDVEDDEEGGGGAP ddPTM_HeLa_Romidepsin_16h_R1 1 GIPGLDVEDDEEGGGGAP 18 0 Q9ULX6-2;Q9ULX6 Q9ULX6-2 AKAP8L A-kinase anchor protein 8-like 0 0 156.12 6.56E-05 5094200 2169.2 2247.3 1856.8 1610 2299.5 2135.5 2130 1926 2332.6 2007.3 FALSE FALSE TRUE 2142.760956 2278.937548 1889.116825 1796.155775 2182.147934 1999.048442 2310.922147 1981.725771 2123.966414 1955.150057 1.095957289 1.165607489 0.966226003 0.918679244 1.116102535 1.022452694 1.181966642 1.013592673 1.08634445 1 10.93306362 -12.51761762 1.320912086 1.00058279 1.064561319 0 0.083579378 0.94615895 2.997548256 0.052854207 0.013211815 3.04E-13 12.51761762 0.06397853 GIPHLVTHDAR ddPTM_HeLa_Romidepsin_16h_R1 2 GIPHLVTHDAR 11 0 P62701;C9JEH7;Q8TD47;P22090 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2;40S ribosomal protein S4, Y isoform 1" 0 0 ; ; 172.98 7.38E-05 23592300 8888.3 8980.9 12117.3 11276.1 12874.3 13964.4 11242.4 9117.7 9615.7 7306.7 FALSE FALSE TRUE 8779.965981 9107.333346 12328.19652 12579.89574 12217.27643 13072.11991 12197.32918 9381.506264 8755.647709 7116.870881 1.233683472 1.279682251 1.73224957 1.767616126 1.716664056 1.83677913 1.713861243 1.318206614 1.230266483 1 12.79702735 -10.02063248 1.554604219 1.095829635 1.700168662 0.710214335 0.152639717 0.131820047 0.623075255 0.028481476 0.037262417 9.54E-11 10.02063248 0.604339027 GIPLATGDTS(ph)PEPELLPGAPLPPPK ddPTM_HeLa_Romidepsin_16h_R1 2 GIPLATGDTSPEPELLPGAPLPPPK 25 0 K7ENA8;O75821;K7EL60;K7ER90;K7EL20 K7ENA8 EIF3G Eukaryotic translation initiation factor 3 subunit G 1 0 GIPLAT(0.002)GDT(0.154)S(0.844)PEPELLPGAPLPPPK;GIPLAT(0.002)GDT(0.156)S(0.842)PEPELLPGAPLPPPK ; 94.594 1.36E-05 189313000 13012.3 12236.6 13558.3 10489.4 12909.1 13534 11485.6 12994.7 14095.4 13988.4 TRUE FALSE FALSE 12853.70108 12408.86718 13794.27652 11702.23378 12250.30046 12669.22108 12461.18658 13370.68114 12834.67212 13624.97935 0.943392335 0.910743925 1.012425499 0.858880845 0.899105983 0.929852498 0.914583887 0.981335883 0.941995712 1 13.73396642 -11.69516751 0.491061177 1.006562674 0.924450921 0.060748973 0.043795702 1.037601187 0.464635406 0.039359248 0.011801332 2.02E-12 11.69516751 -0.082111753 GIQLYDTPYEPEGQSVDS(ph)DSESTVSPR ddPTM_HeLa_Romidepsin_16h_R1 1 GIQLYDTPYEPEGQSVDSDSESTVSPR 27 0 Q15464 Q15464 SHB SH2 domain-containing adapter protein B 1 0 GIQLYDTPYEPEGQS(0.027)VDS(0.318)DS(0.173)ES(0.184)T(0.226)VS(0.072)PR 72.459 6.07E-05 5639600 1625.8 1687.5 1539.8 1331.4 1444.6 1163.3 1318.3 1463.8 1716.3 1435.9 TRUE FALSE FALSE 1605.984124 1711.256669 1566.599573 1485.342732 1370.876671 1088.968884 1430.276369 1506.152744 1562.789829 1398.595111 1.148283811 1.223554019 1.12012373 1.062024828 0.980181227 0.778616253 1.022652201 1.076904053 1.117399751 1 10.44976265 -8.771993984 3.916414022 1.088968584 0.953390386 0.375499636 0.09072179 0.226145633 7.638877255 0.015381922 0.030239019 1.69E-09 8.771993984 -0.135578198 GIQLYDTPYEPEGQSVDSDS(ph)ESTVSPR ddPTM_HeLa_Romidepsin_16h_R1 1 GIQLYDTPYEPEGQSVDSDSESTVSPR 27 0 Q15464 Q15464 SHB SH2 domain-containing adapter protein B 1 0 GIQLYDT(0.001)PY(0.002)EPEGQS(0.079)VDS(0.315)DS(0.41)ES(0.074)T(0.09)VS(0.029)PR 75.755 2.28E-05 7148800 1781.2 1827.3 1686.5 1750.3 1624.6 1474.6 1347.6 1422.8 1750.2 2031.5 TRUE FALSE FALSE 1759.490049 1853.024777 1715.852825 1952.677921 1541.6906 1380.377819 1462.06511 1463.966473 1593.657729 1978.721337 0.889205577 0.936475866 0.867152334 0.98683826 0.779134773 0.697611024 0.738893892 0.739854797 0.805397758 1 10.95035274 -5.251010621 0.18809012 1.005303142 0.045972627 0.401016964 0.079264062 14.17224883 0.238580456 0.074458375 3.601525911 5.61E-06 5.251010621 -0.959330514 GIRDDIEEEDDQEAYFR ddPTM_HeLa_Romidepsin_16h_R1 2 GIRDDIEEEDDQEAYFR 17 1 J3KRE3;A0A0A0MSJ0;Q86XP3-2;Q86XP3 J3KRE3 DDX42 ATP-dependent RNA helicase DDX42 0 0 ; ; 178.47 8.25E-09 14653200 1733.38 1821.97 1496.65 1729.25 2170.73 2166.38 1647.35 1839.76 1794.48 1762.2 FALSE FALSE TRUE 1712.252898 1847.619741 1522.698565 1929.194021 2059.949548 2027.95531 1787.275868 1892.990553 1633.977214 1716.41779 0.997573497 1.076439403 0.887137487 1.123965291 1.200144604 1.181504481 1.041282535 1.102872834 0.9519694 1 10.74518504 -9.124612783 9.572835124 0.998301852 1.132702512 0.590547724 0.060659402 0.19841092 14.55663527 0.0085311 0.014161936 7.51E-10 9.124612783 0.134400661 GIRPAINVGLSVSR ddPTM_HeLa_Romidepsin_16h_R1 2 GIRPAINVGLSVSR 14 1 P25705-2;P25705;P25705-3 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 0 ; ; 118.73 0.00080828 4089600 3075.2 2249.1 2780.8 2737.1 2885.7 2796 2375.8 2396.2 2603.8 1935.08 FALSE FALSE TRUE 3037.71828 2280.762889 2829.198658 3053.57638 2738.431961 2617.344624 2577.600393 2465.530266 2370.909607 1884.806343 1.611687212 1.210078106 1.501055357 1.620100862 1.452898316 1.388654401 1.367567762 1.308108006 1.257906212 1 10.88020058 -12.45363019 1.119347162 0.993369311 1.448127315 0.374151841 0.142443562 0.262884853 0.575171877 0.095471332 0.022307803 3.52E-13 12.45363019 0.454758004 GIS(ph)PIVFDR ddPTM_HeLa_Romidepsin_16h_R1 1 GISPIVFDR 9 0 J3QR07;Q96MU7-2;Q96MU7 J3QR07 YTHDC1 YTH domain-containing protein 1 1 0 GIS(1)PIVFDR 121.61 0.012579 95992000 5806.4 6002.9 6097.4 3781.2 5180.3 5786.8 5991.8 5669.8 6347.9 6496.2 TRUE FALSE FALSE 5735.629363 6087.408984 6203.522689 4218.400135 4915.929961 5417.042156 6500.743342 5833.846718 5780.127925 6327.427788 0.906470932 0.962066923 0.980417778 0.666684833 0.776923914 0.856120739 1.027391155 0.921993409 0.913503578 1 12.62740342 -11.36184635 0.537246113 0.998697081 0.874412118 0.068023664 0.100674611 1.273334416 0.790781056 0.071153315 0.031543007 4.35E-12 11.36184635 -0.124284963 GISAGAVQTAGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GISAGAVQTAGKK 13 1 P46087;P46087-4;F5GWB7;F5H709 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 0 1 GISAGAVQTAGK(1)K 182.23 3.90E-07 1182000 852.41 859.64 546.86 433.48 923.33 838.32 1126.6 889.33 1072.4 1143.5 FALSE TRUE FALSE 842.0204991 871.7420345 556.3778689 483.6009972 876.2090247 784.7540576 1222.293376 915.0613604 976.4818581 1113.791705 0.755994586 0.782679589 0.499534937 0.434193391 0.786690205 0.704578831 1.097416483 0.821573151 0.876718558 1 10.12126374 -11.84551303 0.827094439 0.99156347 0.732542907 0.168361395 0.174138093 0.696150314 0.917505005 0.101901288 0.038175103 1.43E-12 11.84551303 -0.259020562 GISHVIVDEIHER ddPTM_HeLa_Romidepsin_16h_R1 1 GISHVIVDEIHER 13 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 155.88 0.00026 4122300 4798.8 4781.7 4774.8 4226.9 4468.8 4185.5 3954.7 4915.6 5001 4802.8 FALSE FALSE TRUE 4740.31038 4849.016898 4857.903391 4715.634066 4240.740461 3918.060058 4290.612119 5057.82513 4553.698035 4678.022564 1.013314988 1.036552696 1.038452321 1.008040043 0.906524157 0.837546208 0.917184999 1.081188699 0.9734237 1 12.1916831 -8.77216937 24.14805093 1.011746054 0.927290245 0.278444377 0.059349336 121.3090969 273009.0935 0.008452756 0.01544315 1.69E-09 8.77216937 -0.084455809 GITINAAHVEYSTAAR ddPTM_HeLa_Romidepsin_16h_R1 1 GITINAAHVEYSTAAR 16 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 0 71.685 0.010824 2757700 521.78 576.68 576.88 532.48 721.45 870.73 699.22 633.03 728.48 608.1 FALSE FALSE TRUE 515.4203447 584.7985162 586.9203544 594.047843 684.6317144 815.0931632 758.6117293 651.3457243 663.3229243 592.3014743 0.870199328 0.987332535 0.990914897 1.002948446 1.15588386 1.376145761 1.280786495 1.099686144 1.119907603 1 9.210187867 -8.724689124 2.512145514 0.946424158 1.257114027 0.598080612 0.091417317 0.102725304 1.321474454 0.012114093 0.025906859 1.88E-09 8.724689124 0.310689869 GIVEFASK(ac)PAAR ddPTM_HeLa_Romidepsin_16h_R1 2 GIVEFASKPAAR 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 1 ; GIVEFASK(1)PAAR;GIVEFASK(1)PAAR 152.7 0.0016758 6766500 1686.15 1144.55 1352.94 1290.03 2279.41 2076.1 2135.07 1800.22 2512 2121.3 FALSE TRUE FALSE 1665.598555 1160.663005 1376.487353 1439.189338 2163.083202 1943.44391 2316.422793 1852.306525 2287.320429 2066.18832 0.806121368 0.561741151 0.666196464 0.696543158 1.046895475 0.940593794 1.121109228 0.89648485 1.107024179 1 11.01275604 -8.734099981 24.99782081 0.843990891 1.005496697 0.241809976 0.160982057 308.2333894 281832.3442 0.024807632 0.049605381 1.84E-09 8.734099981 0.161505806 GIVEFSGK(ac)PAAR ddPTM_HeLa_Romidepsin_16h_R1 1 GIVEFSGKPAAR 12 1 Q15233;Q15233-2;H7C367;C9IZL7 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 GIVEFSGK(1)PAAR 163.9 0.001365 46927000 2759 2566.3 2268.2 2213.9 2381.3 2151.4 1782.6 2274.8 2227.3 2112.1 FALSE TRUE FALSE 2725.372247 2602.428439 2307.67707 2469.881535 2259.773375 2013.932483 1934.014 2340.617749 2028.08471 2057.227338 1.324779327 1.26501743 1.121741398 1.200587553 1.098455836 0.978954755 0.940107087 1.137753571 0.985834027 1 11.00648551 -8.492601349 4.120038174 1.166365001 1.012546674 0.211088919 0.109772775 0.263227311 9.939560583 0.019366837 0.043311512 3.22E-09 8.492601349 -0.153818326 GIWHNDNK ddPTM_HeLa_Romidepsin_16h_R1 2 GIWHNDNK 8 0 P12277;H0YJG0;P06732 P12277 CKB;CKM "Creatine kinase B-type;Creatine kinase M-type;Creatine kinase M-type, N-terminally processed" 0 0 ; ; 95.741 0.016595 13440400 7150.8 7135.5 10617.7 8233.6 7904.1 9891.1 16247 2591.4 10031 6463.6 FALSE FALSE TRUE 7063.643299 7235.953756 10802.49661 9185.607572 7500.724283 9259.090632 17627.01977 2666.37807 9133.802237 6295.67474 1.121983519 1.149353176 1.715860025 1.459034647 1.191409117 1.470706638 2.79986189 0.423525385 1.450805928 1 12.62014529 -9.873394753 5.516845133 1.061656684 1.549003357 0.059697637 0.562324953 0.282831575 12.74326273 0.081312196 0.107581158 1.34E-10 9.873394753 0.487346673 GIWKPET(ph)PQDSSGLAPFK ddPTM_HeLa_Romidepsin_16h_R1 1 GIWKPETPQDSSGLAPFK 18 1 A0A0A0MR88;A0A096LPC5;F8W7U3;Q641Q2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21A 1 0 GIWKPET(0.999)PQDS(0.001)SGLAPFK 64.203 0.019162 8774400 1422.4 1596.1 1591.3 1384.8 1326.3 1622.3 1392.9 1474.8 1721 1720.6 TRUE FALSE FALSE 1405.063242 1618.569938 1618.995909 1544.917092 1258.613962 1518.640266 1511.212891 1517.471011 1567.06945 1675.898564 0.838393965 0.965792305 0.96604648 0.921844033 0.751008437 0.906164787 0.901732911 0.905467099 0.935062231 1 10.71071912 -8.964991013 24.99766352 0.929136834 0.867116872 0.261979562 0.058027434 280.7618206 200472.9539 0.010872146 0.019707397 1.08E-09 8.964991013 -0.062019962 GIYAYGFEK(ac)PSAIQQR ddPTM_HeLa_Romidepsin_16h_R1 1 GIYAYGFEKPSAIQQR 16 1 P38919;I3L3H2;J3KT04;J3KS93;J3QQP0;E9PBH4;F8WE11;E7EMV8;J3KSN7;E7EQG2;Q14240;Q14240-2;P60842;J3QR64;J3KTB5;J3QL43;J3QS69;J3KT12;P60842-2;J3QKZ9;J3QLN6;J3KS25 P38919;P60842 EIF4A3;EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-I" 0 1 GIYAYGFEK(1)PSAIQQR 123.26 0.00013201 279780 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 GIYAYGFEKPSAIQQR ddPTM_HeLa_Romidepsin_16h_R1 3 GIYAYGFEKPSAIQQR 16 1 P38919;I3L3H2;J3KT04;J3KS93;J3QQP0;E9PBH4;F8WE11;E7EMV8;J3KSN7;E7EQG2;Q14240;Q14240-2;P60842;J3QR64;J3KTB5;J3QL43;J3QS69;J3KT12;P60842-2;J3QKZ9;J3QLN6;J3KS25 P38919;P60842 EIF4A3;EIF4A1;EIF4A2 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed;Eukaryotic initiation factor 4A-II;Eukaryotic initiation factor 4A-II, N-terminally processed;Eukaryotic initiation factor 4A-I" 0 0 ;; ;; 143.58 1.84E-08 8498730 1446.18 1315.346 1523.07 978.82 1818.98 1545.114 1457.3 1400.01 1535.61 1281.2 FALSE FALSE TRUE 1428.553402 1333.863476 1549.578394 1091.995774 1726.150663 1446.386202 1581.083026 1440.51708 1398.261196 1247.914239 1.144752866 1.068874313 1.241734685 0.875056746 1.383228598 1.159042951 1.266980515 1.154339806 1.120478597 1 10.28530308 -16.52287875 0.076598359 0.402978297 1.365597576 0.112914883 0.126866755 193.0460166 1.139795508 19.96307007 2.416341314 3.00E-17 16.52287875 0.962619278 GK(ac)FEDMAK ddPTM_HeLa_Romidepsin_16h_R1 1 GKFEDMAK 8 1 P23497;Q5T7C4;B2RPK0;P09429 P23497 SP100;HMGB1;HMGB1P1 Nuclear autoantigen Sp-100;Putative high mobility group protein B1-like 1;High mobility group protein B1 0 1 GK(1)FEDMAK 92.838 0.015769 9653200 2164.9 2087.9 3069 1445.2 3678.7 3982.8 3385.8 2216.8 3181.6 1813.8 FALSE TRUE FALSE 2138.513366 2117.293511 3122.414658 1612.300824 3490.962212 3728.311934 3673.389767 2280.93961 2897.029728 1766.677215 1.210472037 1.19846087 1.767393971 0.912617659 1.976004549 2.110352646 2.079264813 1.291090184 1.639818357 1 10.78682276 -9.326182584 0.686372971 1.072530005 1.888782991 0.203136109 0.382464065 0.460143873 0.425695026 0.07090362 0.170777863 4.72E-10 9.326182584 0.816252986 GATPGK(ac)ALVATPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GATPGKALVATPGKK 15 2 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 2 ; GATPGK(1)ALVATPGK(1)K;GATPGK(1)ALVATPGK(1)K 206.46 9.95E-25 3625700 1331.66 1462.25 1054.56 2562.2 3546.8 3943.8 3564.3 3892.1 1556.55 1418.93 FALSE TRUE FALSE 1315.429216 1482.835594 1072.914174 2858.45362 3365.793561 3691.803908 3867.051553 4004.711773 1417.32827 1382.065994 0.951784663 1.072912292 0.776311825 2.068246836 2.435334908 2.671221146 2.798022359 2.897627024 1.025514176 1 10.43261079 -9.008042768 2.044790626 0.967249908 2.745845916 0.969237732 0.146346275 0.034810778 0.290224993 0.021485235 0.041820556 9.82E-10 9.008042768 1.778596008 up TVTELVTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TVTELVTKK 9 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 1 ; TVTELVTK(1)K;TVTELVTK(1)K 187.22 3.01E-06 29227000 5395.9 5411 7023.9 8306.9 12451.9 14559.4 13980.6 12066.5 5140.8 4737.6 FALSE TRUE FALSE 5330.132695 5487.1762 7146.148033 9267.382863 11816.43308 13629.10133 15168.11182 12415.62514 4680.993973 4614.516469 1.155079353 1.189111847 1.548623367 2.008310714 2.560708832 2.953527508 3.287042514 2.690558203 1.014406169 1 12.17196377 -8.996637897 1.048153157 1.066388193 3.063418798 0.967429962 0.149568184 0.054539554 0.117853308 0.024256401 0.06067637 1.01E-09 8.996637897 1.997030605 up GK(ac)LEAIITPPPAK ddPTM_HeLa_Romidepsin_16h_R1 2 GKLEAIITPPPAK 13 1 O75367-2;O75367-3;O75367;D6RCF2 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 1 ; GK(1)LEAIITPPPAK;GK(1)LEAIITPPPAK 136.27 9.93E-14 0 366.69 298.67 228.179 66.032 335.98 437.526 478.63 589.24 649.69 455.38 FALSE TRUE FALSE 362.2206412 302.8746841 232.1503598 73.66693053 318.8336869 409.5695007 519.2848203 606.2887297 591.5800992 443.549162 0.816641474 0.682843549 0.523392624 0.166085153 0.718823784 0.923391443 1.170749186 1.366903112 1.333741894 1 8.792950208 -11.61637343 1.067028269 0.977488449 0.780614707 0.115314347 0.332348833 1.150895797 2.646257805 0.122790251 0.067505191 2.42E-12 11.61637343 -0.196873742 GK(ac)PASGAGAGAGAGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GKPASGAGAGAGAGKR 16 2 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 2 GK(1)PASGAGAGAGAGK(1)R 99.941 0.017765 957740 0 0 0 0 204.05 175.78 174.68 189.15 0 0 FALSE TRUE FALSE 0 0 0 0 193.6365671 164.5482253 189.5173148 194.6227568 0 0 0 GK(ac)QGGK(ac)AR ddPTM_HeLa_Romidepsin_16h_R1 2 GKQGGKAR 8 2 A0A0U1RR32;A0A0U1RRH7;Q99878;Q96KK5;Q16777;Q6FI13;P20671;P0C0S8;A0A3B3IS11;Q96QV6;Q8IUE6;Q93077;Q7L7L0;P04908 A0A0U1RR32;Q93077 HIST1H2AJ;HIST1H2AH;HIST2H2AC;HIST2H2AA3;HIST1H2AD;HIST1H2AG;HIST1H2AA;HIST2H2AB;HIST1H2AC;HIST3H2A;HIST1H2AB Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-C;Histone H2A type 2-A;Histone H2A type 1-D;Histone H2A type 1;Histone H2A type 1-A;Histone H2A type 2-B;Histone H2A type 1-C;Histone H2A type 3;Histone H2A type 1-B/E 0 2 ; GK(1)QGGK(1)AR;GK(1)QGGK(1)AR 95.909 0.010249 6744100 0 0 598.72 205.327 4902.4 8408.4 18852.6 3229.1 63.755 0 FALSE TRUE FALSE 0 0 609.1404704 229.0678738 4652.212235 7871.130377 20453.93937 3322.528914 58.05259312 0 0 GK(ac)VGRPTASK(ac)ASK ddPTM_HeLa_Romidepsin_16h_R1 2 GKVGRPTASKASK 13 3 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 2 ; GK(1)VGRPTASK(1)ASK;GK(1)VGRPTASK(1)ASK 93.716 0.01388 17543900 502.83 779.47 1412.77 3963 11117.6 18110.7 16004.9 9584.4 315.17 418.3 FALSE TRUE FALSE 496.7013146 790.4433991 1437.358669 4421.220706 10550.22739 16953.48472 17364.35581 9861.709492 286.9804058 407.4325057 1.219100851 1.940059735 3.527844856 10.85141869 25.89441745 41.61053544 42.61897508 24.20452309 0.704363058 1 8.670417275 -8.7662392 1.919237662 1.331627924 36.84560818 0.909006716 4.847790521 0.060629085 0.454339409 0.69647698 1.558453828 1.71E-09 8.7662392 35.51398026 GKAS(ph)PFEEDQNR ddPTM_HeLa_Romidepsin_16h_R1 1 GKASPFEEDQNR 12 1 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;A0A0A0MR59;Q8TB72-4;A0A0C4DG68 C9JW01 PUM2 Pumilio homolog 2 1 0 GKAS(1)PFEEDQNR 158.86 0.006219 63257000 3181.2 2969.3 3504.7 2621.6 2855.8 3051.2 2689.7 2213.7 3330.5 3424.1 TRUE FALSE FALSE 3142.426311 3011.101883 3565.697833 2924.721727 2710.05787 2856.238167 2918.163051 2277.749917 3032.611739 3335.141388 0.942216819 0.902840849 1.069129437 0.876940851 0.812576606 0.856406921 0.874974315 0.682954529 0.909290308 1 11.70353221 -5.436361276 0.303354627 0.986589211 1.19E-18 0.573588177 0.064565793 9.895861358 0.275367156 0.023027476 4.536439365 3.66E-06 5.436361276 -0.986589211 GKELSDQAT(ph)ASPIVAR ddPTM_HeLa_Romidepsin_16h_R1 1 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 GKELSDQAT(0.716)AS(0.284)PIVAR 120.4 0.0015783 38658000 6358.6 6100.9 5004.8 7490 7390.5 7741 7286.8 7564.4 5996.1 5403.2 TRUE FALSE FALSE 6281.098937 6186.78863 5091.906445 8356.029042 7013.335207 7246.375083 7905.74061 7783.263979 5459.793798 5262.824085 1.193484493 1.175564399 0.967523589 1.587746219 1.332618209 1.376898594 1.50218599 1.478913954 1.037426619 1 12.36162146 -9.262944012 24.99930467 1.092898845 1.447043985 0.807013677 0.092867932 52.12946354 866126.2486 0.015956331 0.025198365 5.46E-10 9.262944012 0.35414514 GKELSDQATAS(ph)PIVAR ddPTM_HeLa_Romidepsin_16h_R1 3 GKELSDQATASPIVAR 16 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 GKELSDQATAS(1)PIVAR;GKELSDQAT(0.016)AS(0.984)PIVAR;GKELSDQAT(0.061)AS(0.939)PIVAR ;; 169.51 4.98E-06 87296000 12897.51 13476.2 12511 16613.2 16902 16948.1 15935.5 17619.4 13633.1 12410.4 TRUE FALSE FALSE 12740.31019 13665.9183 12728.74871 18534.09635 16039.42787 15865.17111 17289.06097 18129.18954 12413.72139 12087.97602 1.053965541 1.130538171 1.053009097 1.533267134 1.326891106 1.312475396 1.430269298 1.499770475 1.026947884 1 13.56128508 -9.275622051 23.99674085 1.037558153 1.40986977 0.868780908 0.071254985 118.1549051 199914.8996 0.011353492 0.017400887 5.30E-10 9.275622051 0.372311617 GKFGHEFLEFEFRPDGK ddPTM_HeLa_Romidepsin_16h_R1 1 GKFGHEFLEFEFRPDGK 17 2 F5H6N1;P61326;Q96A72;P61326-2 F5H6N1 MAGOHB;MAGOH Protein mago nashi homolog;Protein mago nashi homolog 2 0 0 44.132 0.029171 11539000 5718.5 5206.5 4584.3 5711.4 5372 5010.7 5215.5 5164.4 6118.2 5539.8 FALSE FALSE TRUE 5648.800722 5279.797244 4664.087818 6371.778941 5097.846794 4690.532441 5658.50444 5313.823766 5570.972869 5395.875197 1.046873865 0.97848765 0.864380225 1.180861067 0.944767365 0.869281121 1.048672223 0.984793675 1.032450282 1 12.39764126 -10.2386866 22.71299946 1.022134881 0.981603528 0.053883723 0.085524599 653.0837767 651941.1383 0.0137444 0.01682377 5.77E-11 10.2386866 -0.040531353 GKGDK(ac)AQIEK ddPTM_HeLa_Romidepsin_16h_R1 1 GKGDKAQIEK 10 2 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 GKGDK(1)AQIEK 169.65 4.55E-26 0 3009.6 2505.4 4559.7 3110.8 4573.5 5497.1 4797.5 1897.2 2897.6 2219.5 FALSE TRUE FALSE 2972.917838 2540.671087 4639.059666 3470.485333 4340.097229 5145.853051 5204.99953 1952.092489 2638.431399 2161.83707 1.375181265 1.175237081 2.145887741 1.605340838 2.007596821 2.380314929 2.407674289 0.902978543 1.220458024 1 11.07804208 -9.986006592 0.907629337 1.123600841 1.976587683 0.34756475 0.438070382 0.373592328 0.611282227 0.090245073 0.125319595 1.03E-10 9.986006592 0.852986842 GKGGEIQPVSVK(ac)VGDK ddPTM_HeLa_Romidepsin_16h_R1 1 GKGGEIQPVSVKVGDK 16 2 P61604;B8ZZL8 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 1 GKGGEIQPVSVK(1)VGDK 156 3.16E-10 2940900 2356 2434.4 2320.3 2617.1 2598 2522.6 2651.7 3109.3 2367.2 2315.7 FALSE TRUE FALSE 2327.284166 2468.671547 2360.683848 2919.701416 2465.414366 2361.414001 2876.935332 3199.26269 2155.471703 2255.53778 1.031808993 1.094493548 1.046616851 1.294459105 1.093049466 1.046940566 1.275498623 1.418403504 0.95563538 1 11.13925574 -4 0.310063774 1.008662062 4.438824169 0.661815005 0.083188153 21.90357499 0.279965248 0.029040065 42.73581011 1.00E-04 4 3.430162106 GKGGVTGS(ph)PEASISGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GKGGVTGSPEASISGSK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GKGGVT(0.002)GS(0.997)PEASISGSK 204.78 1.78E-18 179970000 4348.8 4766.5 4511.8 4366 5194.3 5105.5 4397.5 5563.5 5351.7 4593.4 TRUE FALSE FALSE 4295.795153 4833.602912 4590.325986 4870.817463 4929.215488 4779.275027 4771.02354 5724.471095 4873.030548 4474.062806 0.960155308 1.080360988 1.025986041 1.08867883 1.101731402 1.068218135 1.066373841 1.279479378 1.089173478 1 12.12736979 -4 0.304564565 0.981032558 3.110277402 0.481684345 0.057716622 20.45604213 0.261646731 0.018147054 24.18631188 1.00E-04 4 2.129244844 GKGGVTGSPEASISGS(ph)KGDLK ddPTM_HeLa_Romidepsin_16h_R1 2 GKGGVTGSPEASISGSKGDLK 21 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GKGGVTGSPEASIS(0.13)GS(0.87)KGDLK;GKGGVTGSPEAS(0.001)IS(0.02)GS(0.979)KGDLK ; 135.12 0.00018662 59090000 6888.5 6306.1 6453.3 6949.6 4772.4 4159.3 4199.2 3591.8 6002.9 6627.6 TRUE FALSE FALSE 6804.540312 6394.877441 6565.616979 7753.145451 4528.84662 3893.534154 4555.879943 3695.723066 5465.985589 6455.413997 1.054082715 0.990622359 1.017071404 1.201029935 0.70155789 0.603142441 0.705745587 0.572499776 0.8467289 1 12.65629391 -8.650310651 6.256884589 1.033060504 0.638627312 0.811721457 0.088090776 0.045240679 2.332701972 0.009086422 0.018285296 2.24E-09 8.650310651 -0.394433192 GKIEVLDS(ph)PASK ddPTM_HeLa_Romidepsin_16h_R1 1 GKIEVLDSPASK 12 1 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 0 GKIEVLDS(0.853)PAS(0.147)K 66.289 0.029593 96319000 6763.6 6536.4 6127.2 5634.4 6818 6280.7 5137.4 5586.2 5870 5690.4 TRUE FALSE FALSE 6681.162642 6628.419611 6233.841346 6285.875839 6470.052019 5879.38354 5573.770628 5747.827883 5344.972498 5542.562588 1.205428452 1.195912451 1.124721868 1.134110033 1.16733946 1.060769896 1.005630616 1.037034367 0.964350409 1 12.43633744 -8.024366929 6.19686594 1.115784406 1.023590131 0.204198009 0.073744872 0.220933373 30.88340643 0.011941703 0.032621538 9.45E-09 8.024366929 -0.092194275 GKIEVLDSPAS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 GKIEVLDSPASK 12 1 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 0 GKIEVLDS(0.044)PAS(0.956)K;GKIEVLDS(0.008)PAS(0.992)K ; 182.02 6.63E-06 70493000 5289 5035.2 5018.8 4753.3 5048.3 4937.3 4462.1 4807.5 4991.2 4897.7 TRUE FALSE FALSE 5224.535634 5106.085678 5106.150109 5302.898911 4790.666413 4621.822464 4841.110663 4946.597428 4544.774571 4770.457048 1.095185552 1.070355655 1.070369161 1.111612338 1.004236358 0.968842695 1.014810659 1.036923166 0.952691645 1 12.21991178 -8.613935645 24.99992837 1.054538854 1.004111722 0.174245076 0.046035453 20.6322722 5656.595207 0.006425901 0.012851801 2.43E-09 8.613935645 -0.050427133 GKKDS(ph)SS(ph)SGS(ph)GSDNDVEVIK ddPTM_HeLa_Romidepsin_16h_R1 1 GKKDSSSSGSGSDNDVEVIK 20 2 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNX6 P46100-4 ATRX Transcriptional regulator ATRX 3 0 GKKDS(0.531)S(0.531)S(0.895)S(0.06)GS(0.558)GS(0.425)DNDVEVIK 51.265 0.0038269 0 970.94 768.54 676.22 570 936.89 983.27 801.22 804.49 750.4 1055.2 TRUE FALSE FALSE 959.1058098 779.3595263 687.9893254 635.9060819 889.0770073 920.4422204 869.2756068 827.7666489 683.2823446 1027.785752 0.933176791 0.758289872 0.669389826 0.618714631 0.865041187 0.895558455 0.845775109 0.805388329 0.664810096 1 10.00532384 -10.37709178 3.556692631 0.97188862 0.779611713 0 0.126438146 0.154773153 3.482166449 0.016181828 0.018376195 4.20E-11 10.37709178 -0.192276907 AVTTPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 AVTTPGKK 8 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; AVTTPGK(1)K;AVTTPGK(1)K 136.75 0.001966 447230000 12827.1 13622.2 15955.6 31703 53530 62222 65151 39379 13486.4 12275.5 FALSE TRUE FALSE 12670.75837 13813.97369 16233.30052 35368.65003 50798.16435 58246.21501 70684.92431 40518.36924 12280.14261 11956.58074 1.059730925 1.155344826 1.357687526 2.958090678 4.248552781 4.87147758 5.911800861 3.388792341 1.027061404 1 13.54551726 -8.993819086 1.651974004 1.031394055 4.840317616 0.891419023 0.575824048 0.07100235 0.386190182 0.082563044 0.170470297 1.01E-09 8.993819086 3.80892356 up GKLPIVNEDDELVAIIAR ddPTM_HeLa_Romidepsin_16h_R1 2 GKLPIVNEDDELVAIIAR 18 1 P12268;H0Y4R1;E7ETK5 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 0 0 ; ; 171.26 2.81E-07 14311200 3421.4 3454.7 2791.6 3319.7 3314.3 3279.1 2657.9 2994.8 3505 3325.1 FALSE FALSE TRUE 3379.698661 3503.335357 2840.186627 3703.539334 3145.158904 3069.576093 2883.66196 3081.449813 3191.504022 3238.713423 1.043531248 1.081705881 0.87694904 1.143521779 0.971113678 0.947776383 0.890372683 0.951442567 0.985423409 1 11.6612051 -8.40436437 3.661057219 1.022750504 0.925951392 0.270064094 0.066886903 0.212360554 5.108343203 0.008705655 0.020506224 3.94E-09 8.40436437 -0.096799112 GKLS(ph)AEENPDDSEVPSSSGINSTK ddPTM_HeLa_Romidepsin_16h_R1 3 GKLSAEENPDDSEVPSSSGINSTK 24 1 A0A494C1S7;Q9Y5Q9-2;Q9Y5Q9 A0A494C1S7 GTF3C3 General transcription factor 3C polypeptide 3 1 0 GKLS(0.927)AEENPDDS(0.073)EVPSSSGINSTK;GKLS(1)AEENPDDSEVPSSSGINSTK;GKLS(0.988)AEENPDDS(0.012)EVPSSSGINSTK ;; 85.366 6.35E-05 272811000 17493.1 16211.4 16805 16118.3 16407.4 16738.8 14233.3 16369.4 18672.8 15990.3 TRUE FALSE FALSE 17279.88737 16439.62451 17097.48398 17981.97368 15570.06915 15669.2447 15442.27615 16843.02276 17002.658 15574.8697 1.109472355 1.055522443 1.097760964 1.154550505 0.999691776 1.006059441 0.991486699 1.081423029 1.091672568 1 13.92693247 GKPASGAGAGAGAGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GKPASGAGAGAGAGKR 16 2 O43818 O43818 RRP9 U3 small nucleolar RNA-interacting protein 2 0 1 ; GKPASGAGAGAGAGK(1)R;GKPASGAGAGAGAGK(1)R 167.18 1.26E-10 8156900 688.42 680.07 924.42 2340.8 4009.3 5527.3 6045.1 3179.2 822.24 685.1 FALSE TRUE FALSE 680.0292722 689.6440433 940.5091423 2611.45431 3804.69046 5174.123369 6558.570643 3271.185136 748.6967951 667.3010032 1.019074254 1.033482701 1.409422641 3.913457791 5.70161058 7.753807268 9.828504095 4.902113319 1.121977625 1 9.382193863 -8.869414888 1.503174899 0.999212867 7.719925624 0.859043236 1.144469877 0.087177577 0.396023148 0.164409987 0.376732823 1.35E-09 8.869414888 6.720712757 GKSEEELEAS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GKSEEELEASK 11 1 Q7RTP6;J3QR21;A0A5F9ZHV5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 GKS(0.003)EEELEAS(0.997)K 150.49 0.015469 8414100 735.67 590.32 572.77 743.14 817.45 1022.8 978.19 1000.7 697.82 778.81 TRUE FALSE FALSE 726.7033711 598.6305405 582.7388216 829.0653434 775.7324762 957.4463809 1061.277434 1029.653676 635.4052315 758.5764039 0.957983095 0.789149962 0.768200564 1.092922663 1.022616143 1.262162092 1.399038289 1.357349992 0.837628521 1 9.567150686 -8.229865323 1.632473772 0.951968199 1.391129396 0.797230758 0.097352363 0.141887218 0.707565629 0.014784357 0.054084326 5.89E-09 8.229865323 0.439161198 GKSEVPEDLAGFIELFQT(ph)PSHTK ddPTM_HeLa_Romidepsin_16h_R1 1 GKSEVPEDLAGFIELFQTPSHTK 23 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 GKSEVPEDLAGFIELFQT(0.94)PS(0.05)HT(0.009)K 125.83 1.41E-06 3651000 1423.5 1127.7 1365.4 1084.4 1241.6 1452.7 952.04 1093.9 1020.5 1107.9 TRUE FALSE FALSE 1406.149834 1143.57579 1389.164214 1209.78343 1178.236519 1359.877158 1032.906254 1125.550271 929.2239241 1079.116598 1.303056441 1.059733297 1.28731614 1.121086852 1.091852837 1.260176297 0.957177617 1.043029338 0.861096869 1 10.07563504 -7.745210899 24.99184153 1.151348244 1.00010343 0.091222432 0.133053525 302.8774759 466423.2673 0.016874206 0.06274341 1.80E-08 7.745210899 -0.151244814 GKTPEEVLKK ddPTM_HeLa_Romidepsin_16h_R1 1 GKTPEEVLKK 10 2 Q9Y2E6-2;Q9Y2E6 Q9Y2E6-2 DTX4 E3 ubiquitin-protein ligase DTX4 0 0 51.436 0.029065 5447800 944.53 801.34 1203.6 2847.7 6552.3 5576.7 4208.3 4092.7 1264.7 832.75 FALSE FALSE TRUE 933.0177051 812.6212856 1224.548153 3176.964473 6217.911681 5220.366868 4565.752897 4211.115817 1151.582065 811.115035 1.150290236 1.001857012 1.509709598 3.916786567 7.665881426 6.436037606 5.62898319 5.191761508 1.419751841 1 9.663762726 -9.098006887 2.866683671 1.08446197 6.193503628 0.927884984 0.656931436 0.046634804 0.743707742 0.099307889 0.176701131 7.98E-10 9.098006887 5.109041658 up GKTS(ph)GTEPADFALPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 GKTSGTEPADFALPSSR 17 1 A6NNK5;Q12888;Q12888-3;Q12888-2;M0R142 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 GKT(0.088)S(0.857)GT(0.055)EPADFALPSSR 84.895 0.0036034 0 739.01 812.03 779.31 626.1 725.39 821.29 906.68 631.77 780.9 654.08 TRUE FALSE FALSE 730.0026619 823.4617797 792.8735636 698.4926279 688.3706415 768.8122196 983.6933766 650.0492682 711.0543482 637.0869073 1.145844709 1.292542305 1.244529678 1.096385155 1.080497235 1.20676192 1.54404896 1.020346299 1.116102591 1 9.315346379 -11.88235964 0.323659718 0.927515206 1.242384604 0.107846613 0.14319295 2.761284282 0.478630383 0.327996853 0.078070008 1.31E-12 11.88235964 0.314869398 GLAAEDS(ph)GGDSK ddPTM_HeLa_Romidepsin_16h_R1 2 GLAAEDSGGDSK 12 0 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 0 GLAAEDS(1)GGDSK;GLAAEDS(0.965)GGDS(0.035)K ; 165.51 0.00027119 18718800 6887.5 6864.3 9241.9 3837.4 6378.4 7715.2 8688.1 3550.7 8728 9140.3 TRUE FALSE FALSE 6803.552501 6960.935796 9402.751393 4281.098244 6052.886447 7222.22362 9426.066997 3653.433902 7947.34582 8902.833688 0.764200786 0.781878674 1.05615265 0.48086917 0.679883131 0.811227512 1.058771547 0.410367534 0.892675984 1 13.12004889 -16.52287875 0.199123628 2.137780941 0.718349625 0.134503445 0.197477631 64.47704001 0.781038067 28.38528122 0.194645625 3.00E-17 16.52287875 -1.419431315 GLAAEDS(ph)GGDSKDLSEVSETTESTDVK ddPTM_HeLa_Romidepsin_16h_R1 2 GLAAEDSGGDSKDLSEVSETTESTDVK 27 1 P41227-2;P41227 P41227-2 NAA10 N-alpha-acetyltransferase 10 1 0 GLAAEDS(0.982)GGDS(0.016)KDLS(0.002)EVSETTESTDVK;GLAAEDS(0.97)GGDS(0.029)KDLSEVSETTESTDVK ; 97.152 4.90E-08 40030000 3354.1 3031.5 3470 2510.28 3135.6 3365.5 2876.7 3153 3673.2 3464.1 TRUE FALSE FALSE 3313.218939 3074.177537 3530.393894 2800.530385 2975.578631 3150.455412 3121.046826 3244.22708 3344.659792 3374.102183 0.98195572 0.911109792 1.046320978 0.830007579 0.881887528 0.933716657 0.925000684 0.961508249 0.991274008 1 11.72028795 -9.269831311 24.99969544 0.987695568 0.907609275 0.44145049 0.04480208 444.0453384 1322817.071 0.006747086 0.010413045 5.37E-10 9.269831311 -0.080086294 GLAEVQQDGEAEEGAT(ph)SDGEK ddPTM_HeLa_Romidepsin_16h_R1 1 GLAEVQQDGEAEEGATSDGEK 21 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 GLAEVQQDGEAEEGAT(0.821)S(0.179)DGEK 115.81 0.00013183 13706000 6371 5720.5 6215.8 5075.4 8488.5 8663.5 7031.4 8308.4 6472.6 7158.9 TRUE FALSE FALSE 6293.347801 5801.033349 6323.983392 5662.241628 8055.30017 8109.93031 7628.64694 8548.790446 5893.674445 6972.910746 0.902542429 0.831938563 0.906935944 0.812034147 1.155227776 1.1630624 1.094040526 1.226000268 0.845224421 1 12.7675453 -8.741136687 24.84667871 0.929945093 1.155149826 0.788369405 0.067594857 96.64651523 118276.5522 0.010491665 0.020962432 1.81E-09 8.741136687 0.225204733 GLAEVQQDGEAEEGAT(ph)SDGEKKR ddPTM_HeLa_Romidepsin_16h_R1 1 GLAEVQQDGEAEEGATSDGEKKR 23 2 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 GLAEVQQDGEAEEGAT(0.836)S(0.164)DGEKKR 89.055 0.00064718 16280000 1943.2 2010.5 2014 2502 2375.4 2207.3 2070.4 2791.8 2621.2 2069.9 TRUE FALSE FALSE 1919.515531 2038.803872 2049.052825 2791.293012 2254.174474 2066.260654 2246.259724 2872.576328 2386.753307 2016.1237 0.952082222 1.011249395 1.016332889 1.384484996 1.118073496 1.024867995 1.11414777 1.424801627 1.183832772 1 10.97736844 -9.492174525 22.72008303 0.98092403 1.192851849 0.279070118 0.131839296 153.6576375 113701.245 0.017319685 0.026425563 3.22E-10 9.492174525 0.211927819 GLAEVQQDGEAEEGATS(ph)DGEK ddPTM_HeLa_Romidepsin_16h_R1 1 GLAEVQQDGEAEEGATSDGEK 21 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 GLAEVQQDGEAEEGAT(0.219)S(0.781)DGEK 71.882 0.0024794 11784000 3755.1 2548.3 3160.6 2145 5205.8 4586.4 4536.3 4410.5 4264.7 4143.7 TRUE FALSE FALSE 3709.331397 2584.175034 3215.608917 2393.014993 4940.1286 4293.343842 4921.613209 4538.110859 3883.254551 4036.046077 0.919050805 0.640273918 0.796722549 0.592910722 1.224002032 1.063749957 1.219414525 1.124395206 0.962143265 1 11.97872693 -8.707715669 24.99996951 0.89728252 1.155561093 0.541879889 0.142197908 77.63802185 36127.84226 0.023184564 0.046369101 1.96E-09 8.707715669 0.258278573 GLAEVQQDGEAEEGATS(ph)DGEKKR ddPTM_HeLa_Romidepsin_16h_R1 1 GLAEVQQDGEAEEGATSDGEKKR 23 2 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 GLAEVQQDGEAEEGAT(0.35)S(0.65)DGEKKR 57.902 0.009917 19097000 2433.4 2527.5 2360.7 3052.7 3320.7 3227.6 3144.8 2740.1 2667.9 2209.1 TRUE FALSE FALSE 2403.740785 2563.082211 2401.786993 3405.667537 3151.232288 3021.366777 3411.919234 2819.38047 2429.276342 2151.707264 1.117131882 1.191185369 1.116223863 1.582774569 1.464526491 1.404171854 1.585680028 1.310299276 1.128999462 1 11.0712661 -9.339102067 5.543534503 1.071390977 1.471504615 0.793137409 0.090613105 0.068264585 3.67805301 0.0143583 0.022119154 4.58E-10 9.339102067 0.400113638 GLAGPPAS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 4 GLAGPPASPGK 11 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK;GLAGPPAS(1)PGK ;;; 117.95 0.010965 618902000 29547.8 29936.6 27669.8 24966.7 26935.8 25405.5 21679.3 23045.5 28515.3 27512.2 TRUE FALSE FALSE 29187.66005 30358.04824 28151.38126 27853.46733 25561.16561 23782.17054 23520.7392 23712.28518 25964.82015 26797.42908 1.089196279 1.13287167 1.050525451 1.039408193 0.953866341 0.887479559 0.877723722 0.884871646 0.968929522 1 14.70980698 -8.57385471 2.129802294 1.052097831 0.881080091 0.756143146 0.042004149 0.119631067 1.085891672 0.006737923 0.016360222 2.67E-09 8.57385471 -0.17101774 GLAHQLAS(ph)PGLTTLPEASDVGSITLALR ddPTM_HeLa_Romidepsin_16h_R1 1 GLAHQLASPGLTTLPEASDVGSITLALR 28 0 P42345 P42345 MTOR Serine/threonine-protein kinase mTOR 1 0 GLAHQLAS(0.977)PGLT(0.021)T(0.002)LPEASDVGSITLALR 87.808 2.85E-07 6909600 552.02 604 627.24 520.92 910.56 1039.3 858.09 996.78 626.04 527.13 TRUE FALSE FALSE 545.2917679 612.5031279 638.1568491 581.1512214 864.0907254 972.8920842 930.9761432 1025.620257 570.0454145 513.4350866 1.062046171 1.192951444 1.242916321 1.131888405 1.682960024 1.894868718 1.81323047 1.99756558 1.110258004 1 9.004038078 -8.688269168 1.182685359 1.044857544 1.950159941 0.930851004 0.09657333 0.078053233 0.21306537 0.015400909 0.045855739 2.05E-09 8.688269168 0.905302398 GLALALFGGEPK ddPTM_HeLa_Romidepsin_16h_R1 1 GLALALFGGEPK 12 0 P49736;H0Y8E6 P49736 MCM2 DNA replication licensing factor MCM2 0 0 188.04 6.66E-07 436180 691.58 721.34 968.82 683.75 609.52 791.83 589.59 647.67 594.72 531.76 FALSE FALSE TRUE 683.150757 731.4950435 985.6819057 762.8083921 578.41392 741.2346185 639.6697599 666.4093096 541.5267537 517.9447985 1.318964413 1.412303098 1.903063625 1.472760021 1.116748197 1.43110737 1.235015318 1.286641572 1.045529862 1 9.016654537 -11.56250945 0.877687126 1.02972547 1.402392118 0.363619526 0.197267351 0.453751913 0.7139046 0.087036031 0.044216332 2.74E-12 11.56250945 0.372666648 GLANPEPAPEPKLS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GLANPEPAPEPKLSR 15 1 O15027-4;A0A3F2YNZ0 O15027-4 SEC16A Protein transport protein Sec16A 1 0 GLANPEPAPEPKLS(1)R 73.984 0.015854 3536000 2707.2 3075.2 2564 4125.4 2611.6 2313.4 2152.5 2889.1 2659.4 2667.5 TRUE FALSE FALSE 2674.203605 3118.492746 2608.625344 4602.398159 2478.320307 2165.581206 2335.333296 2972.69155 2421.536603 2598.197965 1.029253213 1.20025217 1.004013312 1.771380865 0.95386123 0.833493535 0.898828083 1.144135893 0.932006196 1 11.34329564 -6.929509275 18.90947522 1.053516277 3.094850743 0.004398599 0.252942383 935.5906216 283833.4798 0.033211671 10402.87798 1.18E-07 6.929509275 2.041334465 GLDDST(ph)GGTPLTPAAR ddPTM_HeLa_Romidepsin_16h_R1 1 GLDDSTGGTPLTPAAR 16 0 I3L533;I3L2R9;Q9NXR1;Q9NXR1-1;I3L2R3;I3L2T8;I3L522 I3L533 NDE1 Nuclear distribution protein nudE homolog 1 1 0 GLDDS(0.041)T(0.421)GGT(0.295)PLT(0.244)PAAR 116.58 0.0060851 4668400 848.07 772.04 788.4 796.01 949.81 1088 831.4 759.07 815.79 937.28 TRUE FALSE FALSE 837.7333966 782.9087994 802.1217713 888.0484215 901.3376515 1018.480311 902.0190952 781.0324928 742.8236992 912.9293305 0.917632251 0.857578756 0.878624166 0.972746073 0.987302764 1.11561791 0.988049201 0.855523496 0.813670538 1 9.834359376 -9.0069487 18.48302149 0.944237797 0.993950139 0.100738106 0.08168477 22.00915209 58555.66466 0.011573671 0.02030165 9.84E-10 9.0069487 0.049712342 GLDDSTGGTPLT(ph)PAAR ddPTM_HeLa_Romidepsin_16h_R1 1 GLDDSTGGTPLTPAAR 16 0 I3L533;I3L2R9;Q9NXR1;Q9NXR1-1;I3L2R3;I3L2T8;I3L522 I3L533 NDE1 Nuclear distribution protein nudE homolog 1 1 0 GLDDST(0.002)GGT(0.006)PLT(0.992)PAAR 141.06 0.001289 3418300 813.49 754.85 659.7 528.6 812.75 758.75 863.76 828.68 631.77 894.47 TRUE FALSE FALSE 803.574871 765.4767981 671.1818018 589.7192191 771.2723347 710.2683238 937.1277528 852.6565484 575.2629089 871.2315405 0.922343641 0.878614654 0.770382809 0.676880016 0.885266773 0.815246339 1.075635706 0.978679615 0.660287056 1 9.766912373 -10.89657626 1.213121681 0.980324922 0.866339994 0 0.144445759 0.544107196 1.67747211 0.02713764 0.023831383 1.27E-11 10.89657626 -0.113984928 GLDEDETNFLDEVSR ddPTM_HeLa_Romidepsin_16h_R1 2 GLDEDETNFLDEVSR 15 0 H3BU93;Q9GZU8;H3BQQ6;H3BTI2;H3BTP8;H3BSY6;H3BP64;H3BUL4;H3BMX9 H3BU93 FAM192A Protein FAM192A 0 0 ; ; 350.9 1.26E-225 10285400 2512.7 2611.2 2060.28 2034.53 2473.7 2101.4 2036.47 2351.3 2658.4 2574.9 FALSE FALSE TRUE 2482.074246 2647.960542 2096.138309 2269.771931 2347.457858 1967.127322 2209.447711 2419.331156 2420.626046 2508.003727 0.989661307 1.05580407 0.835779583 0.905011387 0.935986591 0.784339872 0.880958703 0.964644163 0.965160466 1 11.29232378 -9.758741271 24.99999784 0.999532894 0.883020791 0.559400561 0.051352552 37.97004333 351818.4653 0.007676114 0.010576602 1.74E-10 9.758741271 -0.116512103 GLDIESYDS(ph)LERPLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLDIESYDSLERPLR 15 1 Q9H792 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 GLDIES(0.002)YDS(0.998)LERPLR 113.14 0.001485 2809300 1209.8 1022.3 1395.6 1061 1219 1317.8 1233.5 1075.1 1362.8 1284.6 TRUE FALSE FALSE 1195.054492 1036.691966 1419.889833 1183.677812 1156.789881 1233.596833 1338.273459 1106.206322 1240.907755 1251.225907 0.955106896 0.828541002 1.13479894 0.946014469 0.9245252 0.985910559 1.069569813 0.884098 0.991753566 1 10.28912657 -9.317776859 0.002298249 1.943496746 2.46E-05 0.008270625 0.082669726 330430.7797 316.0714715 132891.395 134385.29 4.81E-10 9.317776859 -1.943472143 GLDNTEFQGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GLDNTEFQGKR 11 1 E9PB51;Q9BWF3;Q9BQ04 E9PB51 RBM4;RBM4B RNA-binding protein 4;RNA-binding protein 4B 0 1 GLDNTEFQGK(1)R 108.9 0.00034174 0 407.36 308.47 352.81 289.47 628.68 639.51 552.01 501.03 332.7 360.85 FALSE TRUE FALSE 402.3949396 312.8126488 358.9505101 322.9398834 596.5961137 598.6473749 598.8977156 515.5265126 302.9424787 351.475065 1.144874786 0.889999547 1.021268778 0.91881307 1.697406653 1.703242803 1.703955061 1.466751312 0.861917413 1 8.457278532 -8.757018482 24.99999494 1.041859545 1.651519061 0.893454682 0.111820965 25.49714078 144183.4277 0.015235498 0.029652242 1.75E-09 8.757018482 0.609659517 GLDS(ph)GAETEEEKDTWEEK ddPTM_HeLa_Romidepsin_16h_R1 3 GLDSGAETEEEKDTWEEK 18 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 GLDS(0.5)GAET(0.5)EEEKDTWEEK;GLDS(0.575)GAET(0.425)EEEKDTWEEK;GLDS(0.698)GAET(0.299)EEEKDT(0.002)WEEK ;; 99.344 0.00077721 47876000 3792.9 3540.8 3824.25 4244.1 8190.1 11155 10818.2 11754.8 4745.9 4470.3 TRUE FALSE FALSE 3746.670676 3590.647475 3890.809467 4734.822811 7772.128636 10442.2315 11737.09764 12094.90659 4321.414818 4354.160962 0.860480517 0.824647391 0.893584206 1.087424846 1.78498882 2.398218989 2.695604903 2.77778123 0.992479345 1 12.08817903 -8.449042392 1.496639183 0.914985438 2.753786325 0.992804743 0.064883524 0.02721647 0.117200544 0.012088493 0.038066034 3.56E-09 8.449042392 1.838800887 up GLDSGAET(ph)EEEKDTWEEK ddPTM_HeLa_Romidepsin_16h_R1 1 GLDSGAETEEEKDTWEEK 18 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 GLDS(0.011)GAET(0.989)EEEKDTWEEK 87.138 0.0044532 18114000 1197.1 933.85 1113.6 1392.3 2421.9 3125.3 3233.7 3402.1 1401.5 1155.2 TRUE FALSE FALSE 1182.509285 946.9967648 1132.981741 1553.284277 2298.301406 2925.603416 3508.370397 3500.534396 1276.14633 1125.187737 1.050943985 0.841634452 1.006926847 1.380466766 2.042593719 2.600102471 3.118031134 3.111066962 1.134163027 1 10.13595002 -8.44913828 1.226456286 1.000500752 3.16833462 0.988426777 0.092991938 0.032391098 0.091150911 0.014005725 0.050812406 3.56E-09 8.44913828 2.167833867 up GLDSSSTAPS(ph)ALGER ddPTM_HeLa_Romidepsin_16h_R1 2 GLDSSSTAPSALGER 15 0 J3KTM2;O15534-4;O15534;J3QL46 J3KTM2 PER1 Period circadian protein homolog 1 1 0 GLDSSST(0.002)APS(0.998)ALGER;GLDS(0.001)SST(0.001)APS(0.998)ALGER ; 155.37 0.00043022 11583900 1321.59 869.69 1297.34 1103.5 2262.8 1501.03 977.82 1795.95 1235.31 1179.69 TRUE FALSE FALSE 1305.481953 881.9335186 1319.919658 1231.091862 2147.320872 1405.119027 1060.876006 1847.91298 1124.82078 1149.041484 1.136148669 0.767538449 1.148713669 1.071407673 1.868793166 1.222861879 0.923270414 1.608221292 0.978920949 1 10.16621517 -8.955991598 24.99996337 1.047544747 1.372236043 0.359289373 0.250918284 131.5593702 74734.74661 0.035582231 0.064498248 1.11E-09 8.955991598 0.324691296 GLEANAPAFDRHMVLLK ddPTM_HeLa_Romidepsin_16h_R1 1 GLEANAPAFDRHMVLLK 17 1 H0YEV8;A0A1W2PR85;O15056-3;O15056-2;O15056 H0YEV8 SYNJ2 Synaptojanin-2 0 0 68.355 0.026576 3588300 0 57.626 0 489.7 669.65 807.49 565.61 471.54 0 0 FALSE FALSE TRUE 0 58.43726034 0 546.3214181 635.4752617 755.8939951 613.6528993 485.1832659 0 0 0 GLEERLS(ph)PPLPHEER ddPTM_HeLa_Romidepsin_16h_R1 1 GLEERLSPPLPHEER 15 1 Q9UPV0 Q9UPV0 CEP164 Centrosomal protein of 164 kDa 1 0 GLEERLS(1)PPLPHEER 58.688 0.027817 1868700 712.17 551.41 700.95 669.44 515.78 767.54 610.62 548.07 458.76 753.46 TRUE FALSE FALSE 703.4897981 559.1727645 713.1497407 746.8438026 489.457822 718.4966711 662.4860476 563.9275407 417.7273566 733.8850006 0.958583153 0.761935132 0.9717459 1.01765781 0.666940763 0.979031688 0.902710979 0.768414043 0.569200019 1 9.519410201 -10.29067559 0.270271276 1.027426899 0.824326371 0 0.17326848 2.009335899 0.526581412 0.139792828 0.153508095 5.12E-11 10.29067559 -0.203100528 GLEGKS(ph)PDTGPDWLK ddPTM_HeLa_Romidepsin_16h_R1 1 GLEGKSPDTGPDWLK 15 1 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 GLEGKS(0.981)PDT(0.019)GPDWLK 126.88 0.016895 9705400 657.05 837.61 664.4 607.47 616.31 616.17 528.2 586.7 917.05 792.77 TRUE FALSE FALSE 649.0416219 849.4018956 675.9636033 677.7085396 584.8574009 576.7987256 573.0652948 603.6752388 835.0267512 772.1737211 0.840538345 1.10001399 0.875403533 0.877663304 0.757416867 0.746980517 0.742145555 0.781786821 1.081397525 1 9.592781647 -8.935008696 2.088277806 0.93558561 0.752417376 0.603063208 0.081251857 0.189939659 1.67066183 0.012152937 0.024380579 1.16E-09 8.935008696 -0.183168234 GLEGNANS(ph)PAHLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLEGNANSPAHLR 13 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 GLEGNANS(1)PAHLR 103.13 0.0045722 16116000 2658.8 3026.8 2719.3 2254.1 3368 3474 3237.5 3405.4 2868 2974.7 TRUE FALSE FALSE 2626.393523 3069.41137 2766.628276 2514.729648 3196.118392 3252.022612 3512.493169 3503.929876 2611.478897 2897.416865 0.906460356 1.059361325 0.954860279 0.867921243 1.103092355 1.122386858 1.212284367 1.209328874 0.901312796 1 11.50055155 -8.419739301 2.194667167 0.95825773 1.194520059 0.762060613 0.0586622 0.115806951 1.083975321 0.008759055 0.023299015 3.80E-09 8.419739301 0.236262329 GLEVTAYSPLGSSDR ddPTM_HeLa_Romidepsin_16h_R1 1 GLEVTAYSPLGSSDR 15 0 P14550 P14550 AKR1A1 Alcohol dehydrogenase [NADP(+)] 0 0 169.89 1.60E-38 0 331.82 182.94 303.53 0 293.81 243.75 228.92 290.21 221.5 286.02 FALSE FALSE TRUE 327.7756502 185.5154341 308.8128123 0 278.8157793 228.1751617 248.3644591 298.6067685 201.6884852 278.5891592 1.176555653 0.665910456 1.10848826 0 1.000813457 0.819038194 0.891507982 1.071853511 0.723963868 1 8.121995309 -10.26488101 24.94770636 1.083373504 0.788180133 0.020909124 0.319514765 364.5647997 2642649.163 0.048461484 0.056603874 5.43E-11 10.26488101 -0.295193372 GLEYLYLNVHDEDRDDQTR ddPTM_HeLa_Romidepsin_16h_R1 2 GLEYLYLNVHDEDRDDQTR 19 1 Q9Y6G9;C9JGM7;C9JLW1 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 0 0 ; ; 83.37 0.0028473 22005000 11453.8 10391.6 10227.1 10051.3 10477.3 10382.6 9653.2 10278.2 11624.9 11136.5 FALSE FALSE TRUE 11314.19668 10537.89322 10405.09839 11213.4786 9942.604285 9719.185368 10473.14257 10575.5835 10585.13983 10847.17212 1.043054959 0.9714876 0.959245255 1.033769767 0.916607957 0.896010984 0.965518243 0.974962265 0.975843262 1 13.40503136 -9.391363583 0.982852352 1.018699746 0.94287987 0.20853308 0.038463304 0.385798173 0.74106135 0.007111439 0.013974674 4.06E-10 9.391363583 -0.075819876 GLFDDEDEESDLFTEAPQDR ddPTM_HeLa_Romidepsin_16h_R1 4 GLFDDEDEESDLFTEAPQDR 20 0 F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 F8W7U3 FAM21A WASH complex subunit FAM21A 0 0 ;;; ;;; 238.88 2.12E-52 17793600 6627.51 6662.62 6703.3 6031.94 6838.4 6154.02 5771.48 6558.27 7461.2 6973 FALSE FALSE TRUE 6546.731359 6756.416539 6819.968125 6729.381284 6489.41093 5760.797983 6261.709367 6748.023195 6793.851585 6791.840455 0.963911241 0.994784342 1.004141391 0.990803793 0.955471639 0.84819395 0.921945886 0.993548544 1.00029611 1 12.72958685 -8.516682727 15.83912652 0.985296487 0.918056284 0.453641483 0.034596166 1.648078521 4208.804143 0.004998388 0.01038662 3.04E-09 8.516682727 -0.067240203 GLFDDEDEESDLFTEASQDR ddPTM_HeLa_Romidepsin_16h_R1 2 GLFDDEDEESDLFTEASQDR 20 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 0 0 ; ; 281.6 3.23E-110 12953200 3572.2 3721.5 3518.6 3360.5 3932.4 3903.3 3442.1 3743.5 4271.7 3730.3 FALSE FALSE TRUE 3528.660652 3773.891375 3579.839757 3749.056822 3731.714954 3653.891727 3734.471888 3851.812266 3889.628453 3633.386268 0.971176856 1.038670567 0.985262643 1.031835468 1.027062547 1.005643622 1.027821325 1.060116371 1.070524345 1 11.82709903 -9.487605337 0.882353788 0.987507611 1.031680891 0 0.033427795 0.40694695 0.632197164 0.004248418 0.008135921 3.25E-10 9.487605337 0.04417328 GLFDEEMNEILTDPSDDTK ddPTM_HeLa_Romidepsin_16h_R1 1 GLFDEEMNEILTDPSDDTK 19 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 88.385 0.018168 3731900 2595.2 2616.2 2519.5 2318.6 2745.7 3027.1 2514.2 2904.1 3034.8 2704.2 FALSE FALSE TRUE 2563.568704 2653.030932 2563.350841 2586.687441 2605.576683 2833.67808 2727.756085 2988.125552 2763.359887 2633.944494 0.973281218 1.007246333 0.973198504 0.982058448 0.989229913 1.075830598 1.035616389 1.134467928 1.049133683 1 11.36300923 -7.100086483 0.747777318 0.986406606 1.238051517 0.646131413 0.029501158 1.005065142 0.338521115 0.003547522 0.223517563 7.94E-08 7.100086483 0.251644911 GLFDEYGSK ddPTM_HeLa_Romidepsin_16h_R1 1 GLFDEYGSK 9 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 0 138.1 5.35E-06 0 1890.6 1602.4 1953.9 1456.9 1836.3 2084.8 1784.4 1906.3 1820 1856.7 FALSE FALSE TRUE 1867.55664 1624.958629 1987.90681 1625.353633 1742.586759 1951.588008 1935.966891 1961.455783 1657.214642 1808.462666 1.032676358 0.89853037 1.099224688 0.89874879 0.963573532 1.079141994 1.070504206 1.084598438 0.916366521 1 10.8205481 -8.242986078 24.08908402 1.001248278 1.077323833 0.303746252 0.063539599 525.0998867 685467.7225 0.007773487 0.019766816 5.71E-09 8.242986078 0.076075555 GLFITIHDR ddPTM_HeLa_Romidepsin_16h_R1 2 GLFITIHDR 9 0 P48163;P48163-2 P48163 ME1 NADP-dependent malic enzyme 0 0 ; ; 114.89 0.00055119 2088600 1924.82 1772.13 2386.7 1877.01 2476.8 2128.4 1612.2 1536.95 2005.19 1367.34 FALSE FALSE TRUE 1901.359553 1797.078093 2428.239512 2094.038728 2350.399654 1992.402109 1749.140228 1581.419223 1825.840784 1331.81631 1.427643992 1.349343809 1.823254074 1.572317979 1.764807682 1.496003687 1.313349457 1.18741542 1.3709404 1 10.3791794 -11.723702 0.678495752 1.001354211 1.514092531 0.183745395 0.213552589 0.472270332 0.420499492 0.125322189 0.045108918 1.89E-12 11.723702 0.51273832 GLFS(ph)DEEDSEDLFSSQSASK ddPTM_HeLa_Romidepsin_16h_R1 2 GLFSDEEDSEDLFSSQSASK 20 0 F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 F8W7U3 FAM21A WASH complex subunit FAM21A 1 0 GLFS(0.999)DEEDS(0.001)EDLFSSQSASK;GLFS(1)DEEDSEDLFSSQSASK ; 181.23 1.66E-13 39768000 7755.2 7374.3 7717.7 7122.4 8184.2 8624.3 7425.6 7961.1 8474 7501.3 TRUE FALSE FALSE 7660.676639 7478.115589 7852.023331 7945.9254 7766.529735 8073.235064 8056.330279 8191.441868 7716.064216 7306.415145 1.048486363 1.023499957 1.074675224 1.087527227 1.062974055 1.104951594 1.102637904 1.12113009 1.05606704 1 12.83494801 -4 0.095779749 0.949012208 1.446947175 0.645069612 0.021452497 28.76239298 0.197828445 0.127331138 1.889639221 1.00E-04 4 0.497934966 GLFS(ph)DEEDSEDLFSSQSASNLK ddPTM_HeLa_Romidepsin_16h_R1 4 GLFSDEEDSEDLFSSQSASNLK 22 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5 A0A0A0MR88 FAM21C WASH complex subunit FAM21C 1 0 GLFS(1)DEEDSEDLFSSQSASNLK;GLFS(1)DEEDSEDLFSSQSASNLK;GLFS(1)DEEDSEDLFSSQSASNLK;GLFS(1)DEEDSEDLFSSQSASNLK ;;; 161.56 6.00E-09 56691300 16758.5 16316.2 16248.2 15382.4 19032.9 19388.5 16592 18358.6 18442.5 17841.8 TRUE FALSE FALSE 16554.24096 16545.89989 16530.99311 17160.98546 18061.58009 18149.63742 18001.32407 18889.77713 16792.95661 17378.26746 0.952582931 0.95210296 0.951245177 0.987496912 1.039319951 1.044387046 1.03585263 1.086977005 0.966319378 1 14.08499664 -8.755985395 2.903281008 0.972728491 1.052593895 0.823689062 0.019034869 0.108847876 1.883276734 0.003616788 0.007430777 1.75E-09 8.755985395 0.079865404 GLGAGAGAGEES(ph)PATSLPR ddPTM_HeLa_Romidepsin_16h_R1 2 GLGAGAGAGEESPATSLPR 19 0 O15173;O15173-2 O15173 PGRMC2 Membrane-associated progesterone receptor component 2 1 0 GLGAGAGAGEES(0.889)PAT(0.107)S(0.004)LPR;GLGAGAGAGEES(0.844)PAT(0.121)S(0.035)LPR ; 208.85 2.30E-22 6128800 1787.97 2091.67 1973.68 1704.24 1507.42 2135.5 1658.41 2088.39 2091.67 2287.6 TRUE FALSE FALSE 1766.177534 2121.116585 2008.031072 1901.292247 1430.490732 1999.048442 1799.275304 2148.81427 1904.585797 2228.167822 0.792659115 0.951955487 0.901202797 0.853298494 0.642003137 0.897171399 0.807513369 0.964386187 0.854776636 1 11.12164218 -9.159249509 4.755696917 0.903991975 0.822600915 0.116861142 0.092313414 0.395307752 14.49383075 0.015988107 0.026892162 6.93E-10 9.159249509 -0.08139106 GLGHPPSS(ph)PLLK ddPTM_HeLa_Romidepsin_16h_R1 1 GLGHPPSSPLLK 12 0 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785 B9EGQ5 WIZ Protein Wiz 1 0 GLGHPPS(0.285)S(0.715)PLLK 87.863 0.0025682 0 6511.7 6239.6 6207.2 5786.6 5005.5 5076.8 4158.3 4316.9 7380.7 6725.6 TRUE FALSE FALSE 6432.332896 6327.441253 6315.233712 6455.673919 4750.050657 4752.408865 4511.505898 4441.802691 6720.551707 6550.867942 0.981905444 0.965893574 0.964030075 0.985468487 0.72510249 0.725462474 0.688688268 0.678047967 1.025902486 1 12.67747035 -8.744585355 5.180696215 0.986950624 0.701685752 0.979021438 0.020305509 0.016255879 1.198350264 0.002783502 0.005472428 1.80E-09 8.744585355 -0.285264872 GLGHPPSS(ph)PLLKK ddPTM_HeLa_Romidepsin_16h_R1 1 GLGHPPSSPLLKK 13 1 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785 B9EGQ5 WIZ Protein Wiz 1 0 GLGHPPS(0.084)S(0.916)PLLKK 86.539 0.0082678 18082000 3967.9 4387.7 3983.9 4475.5 3244.9 2941.6 2812.2 2522.4 4733.9 4213.9 TRUE FALSE FALSE 3919.537709 4449.470156 4053.238108 4992.978368 3079.300645 2753.641254 3051.068198 2595.381664 4310.488128 4104.422271 0.95495479 1.084067346 0.987529509 1.216487495 0.750239727 0.670896188 0.743361184 0.632337877 1.050205813 1 12.00296345 -8.601120521 8.175457914 1.002428902 0.691965858 0.815968396 0.079977681 0.083884023 7.727615813 0.01126826 0.022588801 2.51E-09 8.601120521 -0.310463044 GLGK(ac)GGAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GLGKGGAKR 9 2 P62805 P62805 HIST1H4A Histone H4 0 2 ; GLGK(1)GGAK(1)R;GLGK(1)GGAK(1)R 148.99 0.0037646 5200500000 9021.1 9412.9 49283 68551 107876 82527 68776 34009 7958.5 2998.2 FALSE TRUE FALSE 8911.147363 9545.415053 50140.74994 76477.18916 102370.6852 77253.79104 74617.83172 34992.99676 7246.671828 2920.306332 3.051442674 3.268634852 17.16968847 26.18807086 35.0547763 26.45400251 25.55137141 11.98264592 2.4814766 1 11.511904 -9.627759848 2.561140411 1.964465705 25.64073625 0.801561563 5.301448122 0.084957002 1.133505885 0.867491448 1.279754259 2.36E-10 9.627759848 23.67627054 GLGKPGGQGDAIQLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GLGKPGGQGDAIQLSPK 17 1 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 0 GLGKPGGQGDAIQLS(1)PK 122.19 0.00084415 42844000 6967.4 6297.2 6618.5 6840.5 5895.7 6438.5 5528 5742.3 6501.4 6074.5 TRUE FALSE FALSE 6882.478649 6385.852147 6733.692216 7631.430796 5594.820429 6027.100629 5997.548182 5908.444391 5919.898501 5916.683614 1.163232496 1.079295863 1.138085565 1.289815595 0.945600744 1.018661977 1.013667212 0.998607459 1.00054336 1 12.53057304 GLGLGANLTEAQALT(ph)PTGPSR ddPTM_HeLa_Romidepsin_16h_R1 2 GLGLGANLTEAQALTPTGPSR 21 0 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 0 GLGLGANLT(0.009)EAQALT(0.991)PTGPSR;GLGLGANLT(0.006)EAQALT(0.982)PT(0.011)GPS(0.001)R ; 166.21 6.06E-10 34858000 3148 3265 3622.2 3699.8 3650.6 4353.3 2664.5 4114.1 3875.8 3255 TRUE FALSE FALSE 3109.630965 3310.964756 3685.242872 4127.588284 3464.29626 4075.13818 2890.822563 4233.134993 3529.138741 3170.434631 0.980821662 1.044325192 1.162377813 1.301899823 1.092688121 1.285356317 0.911806393 1.33519075 1.113140358 1 11.63046492 -9.85363817 3.2686815 0.991648577 1.176369031 0.245422205 0.120394451 0.18070739 3.862367351 0.016815513 0.022754667 1.40E-10 9.85363817 0.184720454 GLGLSK(ac)AYVGQK ddPTM_HeLa_Romidepsin_16h_R1 2 GLGLSKAYVGQK 12 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 1 ; GLGLSK(1)AYVGQK;GLGLSK(1)AYVGQK 168.3 0.00095511 1409750 486.77 383.75 512.97 373.08 745.05 904.83 450.73 424.41 318.63 488.51 FALSE TRUE FALSE 480.83706 389.1524426 521.8980277 416.217265 707.0273183 847.0142832 489.0149949 436.6896337 290.1309348 475.8184398 1.010547343 0.817859103 1.096842796 0.87473967 1.485918281 1.780120761 1.027734434 0.917765259 0.609751347 1 8.894267373 -8.767241361 24.9997173 0.989018303 1.317319393 0.331708375 0.261633821 129.8865433 559660.896 0.034605842 0.063968718 1.71E-09 8.767241361 0.32830109 GLGPPS(ph)PPAPPR ddPTM_HeLa_Romidepsin_16h_R1 2 GLGPPSPPAPPR 12 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 0 GLGPPS(1)PPAPPR;GLGPPS(1)PPAPPR ; 126.34 0.0053121 457660000 4712.9 4422.9 3800.5 3888.4 4566.7 5311.8 3794.5 4716.9 4584.7 4055.6 TRUE FALSE FALSE 4655.457362 4485.165702 3866.646108 4337.995103 4333.644258 4972.393123 4116.804735 4853.376059 4174.632949 3950.234927 1.178526707 1.135417459 0.978839532 1.098161295 1.097059881 1.258758837 1.042167064 1.228629727 1.056806247 1 11.94772274 -12.47165217 1.169720036 0.998921011 1.127822733 0.185434238 0.079974814 0.526615177 1.27177168 0.055566964 0.013203475 3.38E-13 12.47165217 0.128901722 GLGPS(ph)PAGDGPSGSGK ddPTM_HeLa_Romidepsin_16h_R1 2 GLGPSPAGDGPSGSGK 16 0 Q92934;F5GYS3;A8MXU7 Q92934 BAD Bcl2-associated agonist of cell death 1 0 GLGPS(1)PAGDGPSGSGK;GLGPS(0.992)PAGDGPS(0.008)GS(0.001)GK ; 122.31 0.0027836 31928000 7477.5 6152.8 7045.9 6735.4 9353.4 11374.6 9037 10484.8 7833 7137.5 TRUE FALSE FALSE 7386.361354 6239.41928 7168.530934 7514.178639 8876.061096 10647.79977 9804.602554 10788.16115 7132.396862 6952.066721 1.06246986 0.897491283 1.031136671 1.080855369 1.276751425 1.531602068 1.410314795 1.551791946 1.025939069 1 12.76322621 -8.594011038 2.064879904 1.018932355 1.493689722 0.937388633 0.056260656 0.05488001 0.469387531 0.008457771 0.020488388 2.55E-09 8.594011038 0.474757367 GLGSS(ph)PDLELLLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLGSSPDLELLLR 13 0 Q9NQQ7-2;Q9NQQ7;Q9NQQ7-3 Q9NQQ7-2 SLC35C2 Solute carrier family 35 member C2 1 0 GLGS(0.029)S(0.971)PDLELLLR 153.49 0.00076898 9360500 417.43 599.68 308.28 431.14 434.52 535.87 275.8 567.12 559.52 487.36 TRUE FALSE FALSE 412.3422026 608.1223108 313.6454841 480.9904354 412.344823 501.6296364 299.2264451 583.5287224 509.4751299 474.6983169 0.86864054 1.281071133 0.660725924 1.013254984 0.868646061 1.056733547 0.630350761 1.229262253 1.073260873 1 8.890867124 GLGTDEDSLIEIICSR ddPTM_HeLa_Romidepsin_16h_R1 1 GLGTDEDSLIEIICSR 16 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33;H0YKS4;H0YNA0;H0YN52;H0YMM1;H0YLE2 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 125.28 1.88E-09 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 GLGTDEDTIIDIITHR ddPTM_HeLa_Romidepsin_16h_R1 1 GLGTDEDTIIDIITHR 16 0 E5RK69;P08133-2;P08133 E5RK69 ANXA6 Annexin;Annexin A6 0 0 108.34 0.0016465 4123700 2622 2257.9 2389.1 2058.5 3324.9 3327.6 3024.2 3045 2466.4 2766.9 FALSE FALSE TRUE 2590.042055 2289.686775 2430.681283 2296.513456 3155.217946 3114.977099 3281.075473 3133.102271 2245.799007 2695.015539 0.961049025 0.849600584 0.901917354 0.85213366 1.170760576 1.155828994 1.217460688 1.162554436 0.833315791 1 11.39607788 -8.7423923 24.86218343 0.955444908 1.178078962 0.789874682 0.066343105 87.36860834 114041.7762 0.009262945 0.018501503 1.81E-09 8.7423923 0.222634054 GLGTDEDTLIEILASR ddPTM_HeLa_Romidepsin_16h_R1 2 GLGTDEDTLIEILASR 16 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 0 ; ; 231.74 1.42E-44 51805400 1654.06 1391.31 1300.17 1498.27 1590.99 1882.08 1626.54 1599.02 1734.62 1176.39 FALSE FALSE TRUE 1633.899681 1410.896899 1322.798913 1671.507027 1509.795843 1761.821162 1764.698267 1645.285121 1579.471243 1145.827218 1.425956422 1.231334774 1.154448849 1.458777554 1.317647041 1.537597584 1.540108525 1.43589286 1.378454987 1 10.1621738 -15.25136951 0.187200725 7.02E-13 1.49841096 0.112587449 0.155634683 16.40097576 0.294291703 6.397087061 0.158562117 5.61E-16 15.25136951 1.49841096 GLGVEIAK ddPTM_HeLa_Romidepsin_16h_R1 2 GLGVEIAK 8 0 P22314;P22314-2;Q5JRR9;Q5JRS1;Q5JRS3;Q5JRS2;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 ; ; 137.18 0.027239 8838600 6735.2 5723.9 5227.3 5605.5 6383.3 5843.1 5465.1 6203.7 5808.5 5242.1 FALSE FALSE TRUE 6653.108792 5804.481214 5318.278964 6253.634285 6057.536382 5469.744768 5929.305458 6383.194272 5288.973212 5105.909486 1.303021295 1.136816316 1.041592879 1.224783616 1.186377549 1.071257683 1.161263331 1.250158133 1.035853304 1 12.31795225 -12.61752084 1.439780232 1.000395192 1.184865427 0.389926618 0.075467795 0.339299561 1.267264844 0.059553101 0.013783395 2.41E-13 12.61752084 0.184470236 GLHVVEVTY(ph)DDVPIPNSPFK ddPTM_HeLa_Romidepsin_16h_R1 1 GLHVVEVTYDDVPIPNSPFK 20 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 GLHVVEVT(0.034)Y(0.954)DDVPIPNS(0.012)PFK 148.41 2.10E-05 58185000 3078.3 2800.9 3053.3 3155.4 3717.5 4480.3 3883.2 4425.2 3019.6 3136.9 TRUE FALSE FALSE 3040.780496 2840.331144 3106.441406 3520.242195 3527.782103 4194.02329 4213.038911 4553.23618 2749.519413 3055.402886 0.995214251 0.929609367 1.01670435 1.15213683 1.15460456 1.372658025 1.37888163 1.490224481 0.89988768 1 11.57714691 -8.3860303 0.936375884 0.990942464 1.483324297 0.939516017 0.048685467 0.092904494 0.138229147 0.006325197 0.031103535 4.11E-09 8.3860303 0.492381833 GLHVVEVTYDDVPIPNS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 1 GLHVVEVTYDDVPIPNSPFK 20 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 GLHVVEVT(0.01)Y(0.001)DDVPIPNS(0.989)PFK 95.996 0.00044454 54626000 1844.7 1598.6 1855 2110.1 2483.7 2669.7 2762.2 2929.7 2368.3 2033.2 TRUE FALSE FALSE 1822.216087 1621.105133 1887.285497 2354.07969 2356.947521 2499.114786 2996.821199 3014.466247 2156.473316 1980.377171 0.920135878 0.818584034 0.952992957 1.1887027 1.190150824 1.261938798 1.513257799 1.522167742 1.088920509 1 10.95155951 -8.257201356 0.843202575 0.948512946 1.581524694 0.859492207 0.084952821 0.202987006 0.221119773 0.013616603 0.086983577 5.53E-09 8.257201356 0.633011747 GLLAQGLRPES(ph)PPPAGPLLNGAPAGES(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 2 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 2 0 GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPES(1)PPPAGPLLNGAPAGES(1)PQPK ; 82.767 9.15E-08 442390000 5072.3 4784.1 4875.7 4106.9 5324.1 5488.5 4926.8 4474.4 4935.6 4519.2 TRUE FALSE FALSE 5010.476857 4851.450685 4960.559513 4581.759102 5052.39131 5137.802563 5345.282269 4603.859705 4494.147575 4401.790533 1.138281529 1.102153919 1.126941293 1.04088531 1.147803666 1.167207418 1.214342716 1.045906131 1.020981699 1 12.10387478 -12.77048973 0.470510601 0.940536822 1.131204618 0.442580056 0.049936023 1.757410901 0.382413335 0.169137668 0.013115695 1.70E-13 12.77048973 0.190667797 GLLAQGLRPESPPPAGPLLNGAPAGES(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 2 GLLAQGLRPESPPPAGPLLNGAPAGESPQPK 31 1 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 1 0 GLLAQGLRPESPPPAGPLLNGAPAGES(1)PQPK;GLLAQGLRPESPPPAGPLLNGAPAGES(1)PQPK ; 131.26 1.19E-15 1760340000 3898.1 4765.3 4799.3 4791.8 3852.1 4160.7 3400.2 3681.6 4709.9 4572.9 TRUE FALSE FALSE 3850.588458 4832.386018 4882.829803 5345.850462 3655.512963 3894.844698 3689.012903 3788.121287 4288.634748 4454.095399 0.864505161 1.084930965 1.096256224 1.20021014 0.820708278 0.874441239 0.828229432 0.850480501 0.962852019 1 12.12091674 GLLASDLNTDGDMRVT(ph)PEPGAGPTQGLLR ddPTM_HeLa_Romidepsin_16h_R1 2 GLLASDLNTDGDMRVTPEPGAGPTQGLLR 29 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9;V9GYX5;C9JVY3;V9GY85;H7C3H1 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 0 GLLAS(0.023)DLNT(0.014)DGDMRVT(0.958)PEPGAGPT(0.005)QGLLR;GLLAS(0.006)DLNT(0.015)DGDMRVT(0.977)PEPGAGPT(0.002)QGLLR ; 62.069 0.00068772 166443000 3092.6 3293.6 3520.6 2703.8 2605.8 2651.1 2516.9 2216.6 3619.2 3743.4 TRUE FALSE FALSE 3054.906202 3339.967387 3581.874566 3016.426078 2472.816302 2481.703266 2730.685423 2280.733824 3295.489688 3646.145928 0.837845292 0.9160268 0.982372795 0.827291649 0.678200037 0.680637395 0.748923789 0.625519074 0.903828248 1 11.83215659 -8.932280204 3.417989399 0.924619884 0.687780535 0.838847726 0.050426183 0.093465863 2.215810686 0.010186045 0.01909651 1.17E-09 8.932280204 -0.23683935 GLLDDLRNDLDR ddPTM_HeLa_Romidepsin_16h_R1 1 GLLDDLRNDLDR 12 1 Q07065 Q07065 CKAP4 Cytoskeleton-associated protein 4 0 0 96.756 0.02207 2196100 1627.7 1796.1 1473.7 1254.6 1206.8 1228 1177.5 1403.1 1492.4 1678.2 FALSE FALSE TRUE 1607.860966 1821.385543 1499.34913 1399.662755 1145.212493 1149.534763 1277.516821 1443.696485 1358.916006 1634.600122 0.983641776 1.114269795 0.917257444 0.856272269 0.700607125 0.703251363 0.781546999 0.883210802 0.831344613 1 10.67472203 -9.231398733 2.418069718 1.000877794 0.765943195 0.561350989 0.08308859 0.108420328 1.244354326 0.009851088 0.016977941 5.87E-10 9.231398733 -0.234934599 GLLEFEHQR ddPTM_HeLa_Romidepsin_16h_R1 2 GLLEFEHQR 9 0 F5H6X6;Q14697;Q14697-2;E9PKU7;E9PNH1 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 ; ; 131.62 0.0034831 20437800 10137.4 9102.7 15907 12055.8 18262.3 20876 15558.7 15812.2 15343.4 12762.8 FALSE FALSE TRUE 10013.84147 9230.84805 16183.85466 13449.74832 17330.30668 19542.09097 16880.25559 16269.70106 13971.04788 12431.22062 0.805539679 0.742553634 1.301871728 1.081933041 1.394095336 1.572017067 1.357892045 1.308777437 1.123867745 1 13.60168034 -9.276075896 1.380481525 0.897881536 1.408184485 0.614474551 0.156845297 0.168270124 0.629895602 0.024665063 0.046404151 5.30E-10 9.276075896 0.510302949 GLLLT(ph)ASLLNFWNPPTT(ph)AQVT(ph)IEAQPPK ddPTM_HeLa_Romidepsin_16h_R1 1 GLLLTASLLNFWNPPTTAQVTIEAQPPK 28 0 A0A087WT09;Q13046 A0A087WT09 PSG7 Putative pregnancy-specific beta-1-glycoprotein 7 3 0 GLLLT(0.819)AS(0.181)LLNFWNPPT(0.184)T(0.82)AQVT(0.996)IEAQPPK 49.106 0.0031946 0 1184.6 1267.2 1190.3 801.32 1258.8 1243.7 1218.6 1126.3 1442.1 1423 TRUE FALSE FALSE 1170.16164 1285.039675 1211.016672 893.9723887 1194.558739 1164.231584 1322.107854 1158.887713 1313.114964 1386.030255 0.844254038 0.927136814 0.87373033 0.644987644 0.861856179 0.839975592 0.953880948 0.83612007 0.947392714 1 10.43674303 -12.24268289 0.576614274 1.024504913 0.843259629 0.286037728 0.078598435 1.116651591 0.534929736 0.108871486 0.018760851 5.72E-13 12.24268289 -0.181245284 GLLLYGPPGTGK ddPTM_HeLa_Romidepsin_16h_R1 2 GLLLYGPPGTGK 12 0 K7EM02;K7EIJ8;Q8IYT4-2;Q8IYT4 K7EM02 KATNAL2 Katanin p60 ATPase-containing subunit A-like 2 0 0 ; ; 180.67 2.44E-05 2201080 1381.64 1354.54 1223.04 1156.44 1414.24 1170.83 1398.78 936.43 1350.07 1284.53 FALSE FALSE TRUE 1364.80004 1373.60925 1244.326498 1290.153034 1342.066056 1096.017742 1517.592338 963.5241246 1229.316358 1251.157725 1.090829727 1.097870574 0.994540075 1.03116738 1.072659368 0.876002857 1.21295046 0.770106043 0.982543074 1 10.28904796 -7.235752126 24.76274853 1.042712456 0.770105643 0.479757457 0.084217669 4660.262424 4492464.439 0.010326991 1.071768851 5.81E-08 7.235752126 -0.272606813 GLLPGGTQVLDGTSGFS(ph)PAPK ddPTM_HeLa_Romidepsin_16h_R1 2 GLLPGGTQVLDGTSGFSPAPK 21 0 Q96S94;Q96S94-3 Q96S94 CCNL2 Cyclin-L2 1 0 GLLPGGTQVLDGTSGFS(1)PAPK;GLLPGGTQVLDGT(0.011)S(0.005)GFS(0.985)PAPK ; 221.86 8.83E-42 105899000 19312.8 16636.6 17212.4 14823.6 14868.5 14085.9 13111.5 13938.1 18321.5 18027.3 TRUE FALSE FALSE 19077.40817 16870.81049 17511.9746 16537.57438 14109.70496 13185.85645 14225.19048 14341.37693 16682.77915 17558.94815 1.086477846 0.960809859 0.997324809 0.941831723 0.803562084 0.750947969 0.810139102 0.816756039 0.950101282 1 14.0999188 -8.993219184 1.554322284 1.035135489 0.787044263 0.810150802 0.045141206 0.097005056 0.466753734 0.007071204 0.014882866 1.02E-09 8.993219184 -0.248091226 GLLPGLLPAPADKLT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 GLLPGLLPAPADKLTPK 17 1 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 GLLPGLLPAPADKLT(1)PK;GLLPGLLPAPADKLT(1)PK ; 109.83 0.001098 126395000 9107.4 9422.5 9765.5 9913.2 13766.7 18470.9 15021 18103.8 10475 9634 TRUE FALSE FALSE 8996.395506 9555.150202 9935.464431 11059.41083 13064.13393 17290.6691 16296.88337 18627.60489 9538.089765 9383.707291 0.958725078 1.018270275 1.058799483 1.178575853 1.392214561 1.842626647 1.736721198 1.985100804 1.016452183 1 13.1959423 -8.512466404 1.161259901 0.982894674 1.919018234 0.971653028 0.062966969 0.048950361 0.124102595 0.008951417 0.031808543 3.07E-09 8.512466404 0.936123561 GLLSDS(ph)MTDVPVDTGVAAR ddPTM_HeLa_Romidepsin_16h_R1 4 GLLSDSMTDVPVDTGVAAR 19 0 O43399;O43399-5;O43399-7;A0A087WYR3;O43399-2;O43399-4;O43399-3;A0A087WZ51 O43399 TPD52L2 Tumor protein D54 1 0 GLLS(0.033)DS(0.957)MT(0.009)DVPVDTGVAAR;GLLSDS(0.619)MT(0.38)DVPVDTGVAAR;GLLS(0.033)DS(0.946)MT(0.021)DVPVDTGVAAR;GLLS(0.136)DS(0.783)MT(0.081)DVPVDTGVAAR ;;; 210.67 8.65E-29 290477000 11207.4 11549.6 9961.6 8224 14843.6 17643.8 13818.5 18824.6 10882.5 10777 TRUE FALSE FALSE 11070.7999 11712.19557 10134.97747 9174.897575 14086.0757 16516.41812 14992.24305 19369.2601 9909.141944 10497.01199 1.054662023 1.115764714 0.965510707 0.874048499 1.341912891 1.57343996 1.428239109 1.845216536 0.94399644 1 13.3576911 -8.512211435 3.150028107 1.019711498 1.594271079 0.849800604 0.117611579 0.067035482 1.360072773 0.015895315 0.036344413 3.07E-09 8.512211435 0.574559581 GLLSGQTSPT(ph)NAK ddPTM_HeLa_Romidepsin_16h_R1 1 GLLSGQTSPTNAK 13 0 G3V1P3;Q969J3 G3V1P3 LOH12CR1 Loss of heterozygosity 12 chromosomal region 1 protein 1 0 GLLS(0.002)GQT(0.227)S(0.308)PT(0.463)NAK 155.09 0.0014983 18878000 3740.7 3446.7 3047.3 2418 3416.5 3633.5 3154.5 3510 3175.7 3891.1 TRUE FALSE FALSE 3695.10691 3495.222733 3100.336978 2697.580537 3242.143256 3401.331077 3422.443151 3611.556312 2891.657438 3790.008661 0.974960017 0.92222025 0.818028996 0.711761048 0.855444815 0.897446782 0.903017238 0.952915055 0.762968557 1 11.88798543 -10.06605091 2.960731319 0.988395237 0.85425192 0 0.093341258 0.171667933 2.960047984 0.0110894 0.014049779 8.59E-11 10.06605091 -0.134143317 GLLSNHTGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GLLSNHTGSPR 11 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 0 GLLSNHT(0.099)GS(0.901)PR 77.633 0.0040994 0 2418.8 2230.2 2289.9 1395.6 1981.5 2218.9 1834.3 1909.3 2340.8 2400.2 TRUE FALSE FALSE 2389.318735 2261.596814 2329.754749 1556.965838 1880.376661 2077.119451 1990.105396 1964.542583 2131.432985 2337.842458 1.022018711 0.967386321 0.996540524 0.665984071 0.804321375 0.888477085 0.851257273 0.840322912 0.911709417 1 11.190962 -9.382103443 9.244457492 1.006223647 0.816518956 0.627017077 0.063645538 0.133207466 9.581783659 0.008697174 0.013289453 4.15E-10 9.382103443 -0.189704691 GLLT(ph)DSPAATVLAEAR ddPTM_HeLa_Romidepsin_16h_R1 1 GLLTDSPAATVLAEAR 16 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 GLLT(0.797)DS(0.202)PAAT(0.001)VLAEAR 101.72 0.010503 4814000 1654.6 1639.7 1568.6 1629.2 1871.7 1962.8 1776.2 1585.3 1890.1 1639.6 TRUE FALSE FALSE 1634.433099 1662.78374 1595.900825 1817.57577 1776.180165 1837.383415 1927.070384 1631.168154 1721.044722 1597.002956 1.023437742 1.041190145 0.999309876 1.138116722 1.112195916 1.150519733 1.206679284 1.021393322 1.077671595 1 10.64115127 -9.259438112 24.95133691 1.013285671 1.130894997 0.484533584 0.048907994 79.46584931 990757.9836 0.006247282 0.01003201 5.50E-10 9.259438112 0.117609326 GLLTDS(ph)PAATVLAEAR ddPTM_HeLa_Romidepsin_16h_R1 3 GLLTDSPAATVLAEAR 16 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 GLLT(0.228)DS(0.769)PAAT(0.003)VLAEAR;GLLT(0.018)DS(0.896)PAAT(0.086)VLAEAR;GLLT(0.014)DS(0.985)PAAT(0.001)VLAEAR ;; 215.37 4.52E-26 23593000 5254.6 4616.1 4963.9 5258.2 6090.1 6201.9 5092.2 5480.3 5302.8 4799.6 TRUE FALSE FALSE 5190.554914 4681.085577 5050.294597 5866.177825 5779.299472 5805.618606 5524.731341 5638.863834 4828.504287 4674.9057 1.110301522 1.001321925 1.08029871 1.254822707 1.236238727 1.241868602 1.181784553 1.206198412 1.032855975 1 12.19072155 -9.34785172 4.877865932 1.049554319 1.22327874 0.865109482 0.035497467 0.079829663 3.278719717 0.007255945 0.011222049 4.49E-10 9.34785172 0.173724422 GLLTILK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GLLTILKK 8 1 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 0 1 GLLTILK(1)K 105.57 0.016214 0 0 0 0 0 0 0 63.322 0 99.587 0 FALSE TRUE FALSE 0 0 0 0 0 0 68.7005691 0 90.6796893 0 0 GLLYDS(ph)DEEDEER ddPTM_HeLa_Romidepsin_16h_R1 2 GLLYDSDEEDEER 13 0 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 0 GLLYDS(1)DEEDEER;GLLY(0.001)DS(0.999)DEEDEER ; 109.6 0.007127 3776200 4368.9 4746.5 2888.29 2696.77 2743.41 3022.91 2677.29 3765.83 4627.9 4719.6 TRUE FALSE FALSE 4315.650166 4813.321352 2938.559476 3008.583236 2603.403551 2829.755807 2904.698946 3874.78835 4213.969033 4596.984112 0.938800322 1.047060689 0.639236379 0.654468922 0.566328594 0.615567889 0.631870565 0.842897921 0.916681226 1 12.16647196 -9.755016254 24.99997161 0.975989701 0.650879354 0.81074335 0.075036531 43.66565855 169954.0672 0.011385789 0.015879552 1.76E-10 9.755016254 -0.325110347 GLLYDS(ph)DEEDEERPAR ddPTM_HeLa_Romidepsin_16h_R1 11 GLLYDSDEEDEERPAR 16 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 0 GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLY(0.003)DS(0.997)DEEDEERPAR;GLLYDS(1)DEEDEERPAR;GLLYDS(1)DEEDEERPAR ;;;;;;;;;; 197.06 1.22E-12 5491606400 24002.28 23039.38 22444.44 21601.96 21232.32 20543.95 15663.23 19781.98 25187.01 23954.4 TRUE FALSE FALSE 23709.73098 23363.729 22835.07606 24099.68026 20148.75548 19231.2579 16993.66437 20354.34038 22934.22074 23332.06123 1.016186729 1.001357264 0.978699474 1.032899752 0.863565172 0.824241703 0.728339609 0.872376434 0.982948764 1 14.51002615 -8.610832768 3.219857914 1.006598964 0.803407579 0.852335305 0.03701183 0.055872677 1.156854294 0.004868243 0.010492792 2.45E-09 8.610832768 -0.203191385 GLLYDS(ph)DEEDEERPARK ddPTM_HeLa_Romidepsin_16h_R1 1 GLLYDSDEEDEERPARK 17 2 P49736 P49736 MCM2 DNA replication licensing factor MCM2 1 0 GLLYDS(1)DEEDEERPARK 75.91 0.021334 20802000 1368.8 1148.7 1079.3 1171.2 1028.8 990.3 1033.2 1391.9 1595.3 1637.9 TRUE FALSE FALSE 1352.116539 1164.871429 1098.084764 1306.619655 976.296497 927.023026 1120.959982 1432.17243 1452.612372 1595.347122 0.847537517 0.730168007 0.688304601 0.819019031 0.611964935 0.581079198 0.70264331 0.897718378 0.9105306 1 10.63965465 -10.82685479 0.66654209 0.98157452 0.69914759 0.510667059 0.091219585 0.306133275 0.306091826 0.032716551 0.025652394 1.49E-11 10.82685479 -0.28242693 GLLYDSDEEDEERPAR ddPTM_HeLa_Romidepsin_16h_R1 2 GLLYDSDEEDEERPAR 16 1 P49736 P49736 MCM2 DNA replication licensing factor MCM2 0 0 ; ; 203.29 1.76E-18 10165800 6486.7 5545.3 5475.2 5337.9 4799.4 4879.6 4050.9 4930.6 6150.9 5941.7 FALSE FALSE TRUE 6407.637605 5623.366879 5570.493559 5955.093114 4554.468709 4567.809308 4394.983345 5073.259132 5600.748099 5787.333777 1.107183005 0.971667973 0.962531932 1.028987327 0.78697184 0.789276977 0.759414182 0.876614228 0.967759648 1 12.49868314 -8.764541489 23.06840918 1.036522035 0.798965849 0.765908887 0.053501207 9.903773622 73650.8202 0.008730538 0.01634402 1.72E-09 8.764541489 -0.237556186 GLNGGITPLNSIS(ph)PLKK ddPTM_HeLa_Romidepsin_16h_R1 2 GLNGGITPLNSISPLKK 17 1 Q17RY0-2;B7ZLQ8;E5RJM0;Q17RY0;H0YBG1 Q17RY0-2 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 0 GLNGGITPLNS(0.02)IS(0.98)PLKK;GLNGGITPLNS(0.006)IS(0.994)PLKK ; 82.189 0.0049129 34631000 3584.7 3332.7 2835.4 3794.5 3998.5 4373.9 3554.5 4045.9 3692.8 3324.3 TRUE FALSE FALSE 3541.008298 3379.617838 2884.748948 4233.237944 3794.441625 4094.421906 3856.419141 4162.961733 3362.506719 3237.934207 1.093601065 1.043757415 0.890922657 1.307388499 1.171871132 1.264516709 1.191012199 1.285684473 1.038472836 1 11.66085796 -9.248038901 24.99870138 1.034832198 1.23826773 0.766353102 0.06310831 329.7591815 615168.6232 0.009795299 0.016183923 5.65E-10 9.248038901 0.203435531 GLNNDS(ph)PERR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNNDSPERR 10 1 Q7Z6B7;Q7Z6B7-2;G5EA48 Q7Z6B7 SRGAP1 SLIT-ROBO Rho GTPase-activating protein 1 1 0 GLNNDS(1)PERR 74.78 0.021947 15891000 2995.4 2311.4 2992.3 2356.8 1904.4 1605.2 2306.8 1705.6 2931.4 2588 TRUE FALSE FALSE 2958.890913 2343.93995 3044.379726 2629.304305 1807.211362 1502.632901 2502.739534 1754.948845 2669.208242 2520.763387 1.173807478 0.929853219 1.207721336 1.043058749 0.716930185 0.596102319 0.992849844 0.696197372 1.058888849 1 11.29964499 -8.802023317 6.274735996 1.080202892 0.7566565 0.630731691 0.119239631 0.091716304 9.297788091 0.01781792 0.032981316 1.58E-09 8.802023317 -0.323546392 GLNPDGTPALS(ph)TLGGFSPASKPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58-6;Q9UK58 Q9UK58-6 CCNL1 Cyclin-L1 2 0 GLNPDGT(0.003)PALS(0.766)T(0.271)LGGFS(0.05)PAS(0.084)KPS(0.264)S(0.563)PR 79.27 0.00015085 69810000 1065.2 1327.8 1108.5 1172.2 998.51 858.76 808.76 1199.1 1547.1 1369.8 TRUE FALSE FALSE 1052.216933 1346.492803 1127.792978 1307.735279 947.5523087 803.8880075 877.4560542 1233.794067 1408.723501 1334.212399 0.788642748 1.009204235 0.845287436 0.980155244 0.710196 0.602518766 0.657658447 0.924735873 1.055846507 1 10.38177264 -8.747868326 24.74659124 0.907375036 0.710393098 0.466982675 0.111625368 157.7673677 287684.2633 0.016335673 0.03252286 1.79E-09 8.747868326 -0.196981938 GLNPDGTPALSTLGGFS(ph)PASKPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58-6;Q9UK58 Q9UK58-6 CCNL1 Cyclin-L1 2 0 GLNPDGT(0.001)PALS(0.217)T(0.093)LGGFS(0.684)PAS(0.017)KPS(0.319)S(0.67)PR 79.886 0.0001434 141170000 2583.9 2774.9 2285.7 2405.6 2073 1930.9 1686.5 2124.6 2579.5 2507.2 TRUE FALSE FALSE 2552.406433 2813.965115 2325.48165 2683.746791 1967.207075 1807.521722 1829.751268 2186.071949 2348.78306 2442.062583 1.045184694 1.152290337 0.952261284 1.098967246 0.805551458 0.740161917 0.749264692 0.895174417 0.961802976 1 11.25388446 -8.747605559 22.3560505 1.03184232 0.789991323 0.742395348 0.068477234 22.80402472 36851.24251 0.009044763 0.017987077 1.79E-09 8.747605559 -0.241850997 GLNPDGTPALSTLGGFSPASKPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNPDGTPALSTLGGFSPASKPSSPR 26 1 Q9UK58-6;Q9UK58 Q9UK58-6 CCNL1 Cyclin-L1 1 0 GLNPDGTPALSTLGGFS(0.002)PAS(0.107)KPS(0.445)S(0.445)PR 79.82 2.71E-05 39759000 4731.1 4554.6 5037.2 4564.1 3591.2 3532.9 3382.8 3524.9 5252.8 4490.6 TRUE FALSE FALSE 4673.435533 4618.719778 5124.870353 5091.822717 3407.927663 3307.159092 3670.134948 3626.88742 4782.976412 4373.933565 1.068474284 1.055964776 1.171684544 1.164128957 0.779144816 0.756106384 0.839092522 0.829204963 1.093518304 1 12.09471559 -8.748916678 24.99988093 1.054906693 0.800417429 0.848108777 0.059159024 81.92220612 163545.652 0.009966107 0.019821949 1.78E-09 8.748916678 -0.254489264 GLNTS(ph)QES(ph)DDDILDESSSPEGTQK ddPTM_HeLa_Romidepsin_16h_R1 2 GLNTSQESDDDILDESSSPEGTQK 24 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 2 0 GLNT(0.467)S(0.557)QES(0.975)DDDILDESSSPEGTQK;GLNT(0.235)S(0.858)QES(0.907)DDDILDESSSPEGTQK ; 108.78 3.88E-09 3043500 2758.19 2734.36 2883.73 2889.18 2884.7 2822.74 1952.73 2513.7 3093.28 2971.97 TRUE FALSE FALSE 2724.572119 2772.854392 2933.920111 3223.240586 2737.482995 2642.376024 2118.594837 2586.429944 2816.60929 2894.757791 0.941209012 0.957888221 1.013528704 1.113475053 0.9456691 0.912814202 0.73187292 0.893487514 0.97300344 1 11.49922693 -8.041576505 3.174940792 0.982830478 0.812693557 0.578483807 0.060234267 0.133852022 2.697497885 0.008658036 0.026968449 9.09E-09 8.041576505 -0.170136921 GLNTSQES(ph)DDDILDESSSPEGTQK ddPTM_HeLa_Romidepsin_16h_R1 1 GLNTSQESDDDILDESSSPEGTQK 24 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 0 GLNT(0.029)S(0.09)QES(0.881)DDDILDESSSPEGTQK 151.03 5.79E-08 12740000 5179.6 5361.6 5310.6 4055.5 4657.5 4906.4 3493.9 4475 6264.6 5536.6 TRUE FALSE FALSE 5116.469043 5437.080746 5403.028765 4524.415992 4419.810395 4592.896875 3790.671779 4604.477065 5704.278486 5392.758334 0.94876661 1.008218876 1.001904486 0.838979927 0.819582507 0.851678601 0.702918904 0.853825961 1.057766385 1 12.39680767 -9.162486918 3.938090706 0.979941425 0.805308065 0.784083087 0.049211683 0.078191422 2.191358655 0.006523411 0.011067268 6.88E-10 9.162486918 -0.17463336 GLNVIGASDQS(ph)PLQS(ph)PSNLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 2 0 GLNVIGAS(0.02)DQS(0.982)PLQS(0.988)PS(0.01)NLR 112.74 0.0031871 4161300 921.45 1058.7 856.95 856.58 1289 1167.8 884.98 993.05 1016.5 1031 TRUE FALSE FALSE 910.219013 1073.604406 871.8648553 955.6218099 1223.21752 1093.181349 960.1501791 1021.782335 925.5816941 1004.214471 0.90639902 1.06909872 0.868205827 0.951611271 1.21808394 1.088593503 0.956120636 1.017494135 0.921697228 1 9.971851705 GLNVIGASDQS(ph)PLQSPSNLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 GLNVIGAS(0.014)DQS(0.98)PLQS(0.006)PSNLR 99.011 0.0007513 13980000 2412.5 2328.5 2404.9 2377 2654.3 2220.1 1798.5 2536.6 2567.5 2366.3 TRUE FALSE FALSE 2383.095522 2361.280684 2446.756276 2651.839924 2518.841166 2078.242775 1951.264545 2609.992519 2337.85637 2304.823185 1.033960235 1.024495371 1.061580902 1.150561111 1.092856573 0.901692932 0.846600537 1.132404662 1.014332199 1 11.17044036 -8.2572503 24.97996737 1.035315452 0.948869494 0.192738739 0.08090645 450.6971056 2687546.796 0.011336168 0.027783354 5.53E-09 8.2572503 -0.086445957 GLNVIGASDQSPLQS(ph)PSNLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLNVIGASDQSPLQSPSNLR 20 0 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 GLNVIGASDQS(0.013)PLQS(0.879)PS(0.108)NLR 89.43 0.0017342 10041000 2514.2 4397.9 1501.1 2481.4 3366.1 2323.2 1714.3 1875.7 2325.2 2706 TRUE FALSE FALSE 2483.555963 4459.813752 1527.226016 2768.311143 3194.315356 2174.755018 1859.912599 1929.97042 2117.228288 2635.69773 0.942276474 1.692080887 0.579438984 1.050314348 1.211942978 0.825115488 0.705662329 0.732242699 0.803289491 1 11.36396921 -8.038660925 7.476633489 1.017263092 0.729578158 0.191522036 0.271731434 0.285338969 48.43970751 0.034892972 0.09154802 9.15E-09 8.038660925 -0.287684934 GLPLGSAVSSPVLFS(ph)PVGR ddPTM_HeLa_Romidepsin_16h_R1 1 GLPLGSAVSSPVLFSPVGR 19 0 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 0 GLPLGSAVS(0.032)S(0.078)PVLFS(0.89)PVGR 109.13 0.00085925 21658000 5049 4524.6 4279.6 3785.8 4583.7 3699 3174.3 3350.2 4989.2 4782.1 TRUE FALSE FALSE 4987.460846 4588.297438 4354.084643 4223.532009 4349.776685 3462.645838 3443.924963 3447.132751 4542.953456 4657.860353 1.07076221 0.985065479 0.934782135 0.906753679 0.933857255 0.743398379 0.739379179 0.740067862 0.975330541 1 12.18545167 -8.561017639 0.731852686 1.031888943 0.698564268 0.865752208 0.041821978 0.207893738 0.183296901 0.008123942 0.040157766 2.75E-09 8.561017639 -0.333324676 GLPPS(ph)MER ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 GLPPS(1)MER 91.265 0.0075034 13258000 3319.1 3374.6 2630.5 1657.1 3030.9 2994.6 2645.1 3313.9 3216.4 2960.5 TRUE FALSE FALSE 3278.645533 3422.107707 2676.282749 1848.701699 2876.221863 2803.254725 2869.774728 3409.782468 2928.717128 2883.585783 1.137002947 1.186754258 0.928109288 0.641112087 0.997446263 0.972141956 0.995210458 1.182479983 1.015651119 1 11.49364823 -9.729579165 24.99045219 1.075657922 0.943427706 0.185076556 0.134398632 267.7540354 210019.9954 0.022224822 0.031429117 1.86E-10 9.729579165 -0.132230216 GLPSTAS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 3 GLPSTASGR 9 0 H7BYT1;P48730-2;P48730 H7BYT1 CSNK1D Casein kinase I isoform delta 1 0 GLPSTAS(1)GR;GLPST(0.004)AS(0.996)GR;GLPSTAS(1)GR ;; 122.7 0.016169 55804300 11428 11696.2 10118.9 19637.1 7490.5 7763.4 6088.7 7376.8 11551 11218.3 TRUE FALSE FALSE 11288.71114 11860.85941 10295.01521 21907.6339 7108.231834 7267.343795 6605.874026 7590.236069 10517.84963 10926.84695 1.033116982 1.085478681 0.942176207 2.004936465 0.650529093 0.665090655 0.604554457 0.694641016 0.962569502 1 13.41558954 GLPTGDS(ph)PLGPMTHR ddPTM_HeLa_Romidepsin_16h_R1 2 GLPTGDSPLGPMTHR 15 0 J3QQZ9;Q9NVS9-4;Q9NVS9-3;Q9NVS9 J3QQZ9 PNPO Pyridoxine-5-phosphate oxidase 1 0 GLPT(0.254)GDS(0.746)PLGPMTHR;GLPT(0.007)GDS(0.993)PLGPMTHR ; 77.795 0.010742 9082000 4665.2 4182.2 4234 4266.5 4960.6 5048.1 4852.7 4724.2 4201 4310.9 TRUE FALSE FALSE 4608.338748 4241.077121 4307.690994 4759.812804 4707.442071 4725.542702 5264.888217 4860.887273 3825.252038 4198.902197 1.097510381 1.010044274 1.025908867 1.133585061 1.121112579 1.12542338 1.253872553 1.157656703 0.911012417 1 12.03579647 -4 0.18181803 1.005203249 1.924699046 0.626038855 0.056657482 27.04025585 0.295233481 0.059393784 6.931721201 1.00E-04 4 0.919495796 GLQPGEEELPDIS(ph)PPIVIPDDSKDR ddPTM_HeLa_Romidepsin_16h_R1 2 GLQPGEEELPDISPPIVIPDDSKDR 25 1 Q92995;Q92995-2 Q92995 USP13 Ubiquitin carboxyl-terminal hydrolase 13 1 0 GLQPGEEELPDIS(1)PPIVIPDDSKDR;GLQPGEEELPDIS(1)PPIVIPDDSKDR ; 113.59 9.00E-07 16005900 4085.9 4295.4 4822.2 4361.1 3987 3618.9 3553.8 3828.1 5053.8 4624.4 TRUE FALSE FALSE 4036.099479 4355.870754 4906.128368 4865.350902 3783.528512 3387.663969 3855.659683 3938.860034 4601.775471 4504.257421 0.896063236 0.967056353 1.089220244 1.08016715 0.839989405 0.752102656 0.856003404 0.874474895 1.021650194 1 12.13707357 -8.628834553 9.072565114 0.970650197 0.824760563 0.60668846 0.066206223 0.188527717 14.77747301 0.011074789 0.022172718 2.35E-09 8.628834553 -0.145889634 GLQPST(ph)PPPKPPR ddPTM_HeLa_Romidepsin_16h_R1 1 GLQPSTPPPKPPR 13 1 A0A1B0GTL5 A0A1B0GTL5 1 0 GLQPS(0.385)T(0.615)PPPKPPR 88.78 0.013019 28348000 4410.8 3600.4 3662 3957.2 3873.8 5117.9 4045.2 4276.9 4785.5 4847 TRUE FALSE FALSE 4357.039473 3651.086526 3725.735574 4414.750083 3676.105531 4790.882707 4388.799187 4400.645354 4357.472894 4721.074241 0.922891539 0.773359269 0.789171147 0.935115581 0.7786587 1.014786564 0.929618761 0.932127971 0.922983345 1 12.20489945 -11.1604632 1.314599013 0.982839632 0.882342244 0.122968892 0.078585217 0.408300783 1.446166844 0.02003927 0.015697796 6.91E-12 11.1604632 -0.100497388 GLQVDLQS(ph)DGAAAEDIVASEQSLGQK ddPTM_HeLa_Romidepsin_16h_R1 2 GLQVDLQSDGAAAEDIVASEQSLGQK 26 0 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 GLQVDLQS(1)DGAAAEDIVASEQSLGQK;GLQVDLQS(1)DGAAAEDIVASEQSLGQK ; 122.06 1.13E-07 8856800 2896.95 2580.28 2448.5 2299.44 1988.04 1715.12 1371.57 1619.37 2953.13 2704.75 TRUE FALSE FALSE 2861.640859 2616.60525 2491.115115 2565.312072 1886.5829 1605.529367 1488.071122 1666.223916 2688.994657 2634.480205 1.086225986 0.993214997 0.945581261 0.973745055 0.716112004 0.609429277 0.564844298 0.632467806 1.020692678 1 11.36330262 -8.704323979 1.584590565 1.033635277 0.587336835 0.954763843 0.040166673 0.058622452 0.296189752 0.007294569 0.018227826 1.98E-09 8.704323979 -0.446298443 GLS(ph)APDLR ddPTM_HeLa_Romidepsin_16h_R1 1 GLSAPDLR 8 0 Q9P266 Q9P266 KIAA1462 Junctional protein associated with coronary artery disease 1 0 GLS(1)APDLR 101.46 0.029764 3811500 1068.2 789.38 788.45 1574.1 6657.9 8294 7288.3 8466.5 1087.5 1130.4 TRUE FALSE FALSE 1055.180368 800.4929124 802.1726415 1756.104848 6318.122519 7764.040168 7907.36802 8711.46482 990.2312763 1101.032045 0.958355728 0.727038705 0.7285643 1.594962523 5.738363881 7.05160236 7.181778274 7.912090169 0.899366445 1 10.10464074 -8.69067411 2.461742865 0.929808708 7.346797889 0.993242809 0.24519516 0.016747964 0.206213811 0.040010193 0.087403698 2.04E-09 8.69067411 6.41698918 up GLS(ph)DHVSLDGQELGTR ddPTM_HeLa_Romidepsin_16h_R1 1 GLSDHVSLDGQELGTR 16 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 0 GLS(0.51)DHVS(0.49)LDGQELGTR 69.431 0.017631 20097000 3315.1 3078.3 3164.9 2630.3 6372.2 6780.5 5294.4 4954.6 5523.8 4193.1 TRUE FALSE FALSE 3274.694286 3121.636388 3219.983757 2934.427662 6047.002856 6347.247933 5744.106204 5097.953534 5029.737493 4084.162658 0.801803102 0.764327146 0.788407325 0.718489421 1.480597949 1.554112425 1.40643424 1.248224902 1.231522325 1 11.99582461 -8.75501555 24.99998349 0.870809619 1.430618336 0.739474927 0.156364002 47.31898636 184152.2357 0.018928992 0.037139801 1.76E-09 8.75501555 0.559808718 GLS(ph)HSPWAVKK ddPTM_HeLa_Romidepsin_16h_R1 1 GLSHSPWAVKK 11 1 Q96KB5;Q96KB5-2;E5RFX4 Q96KB5 PBK Lymphokine-activated killer T-cell-originated protein kinase 1 0 GLS(0.977)HS(0.023)PWAVKK 74.987 0.020134 34151000 3468.8 3375.3 2869.3 3665 4223 3950 3679.5 3809.8 3429.9 3496.8 TRUE FALSE FALSE 3426.520931 3422.817562 2919.238963 4088.764544 4007.484552 3697.607748 3992.036638 3920.030552 3123.121154 3405.952632 1.006038927 1.004951604 0.857099108 1.200476045 1.176611945 1.085630996 1.172076382 1.150935135 0.916959656 1 11.73384266 -9.239436772 24.98854693 0.993177368 1.155083942 0.743214558 0.056860019 321.6638262 365316.7112 0.007484852 0.012405261 5.76E-10 9.239436772 0.161906574 GLS(ph)LEHQK ddPTM_HeLa_Romidepsin_16h_R1 1 GLSLEHQK 8 0 Q765P7;A0A087WXN9 Q765P7 MTSS1L MTSS1-like protein 1 0 GLS(1)LEHQK 103.26 0.028261 4410500 1312.7 1429.9 774.56 1003.3 1243.7 1245.8 806.25 1215.1 1213.7 1192.1 TRUE FALSE FALSE 1296.700307 1450.03017 788.0408919 1119.306267 1180.229348 1166.197401 874.7328549 1250.257001 1105.143632 1161.12907 1.116758111 1.248810496 0.678685008 0.963980918 1.016449746 1.004365002 0.753346788 1.07675971 0.951783622 1 10.18131263 -9.776672459 24.9999737 1.071201903 0.919041025 0.260362064 0.13484799 254.1730197 417138.249 0.020645173 0.02718988 1.67E-10 9.776672459 -0.152160878 GLS(ph)SSEKDNIER ddPTM_HeLa_Romidepsin_16h_R1 1 GLSSSEKDNIER 12 1 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 1 0 GLS(0.84)S(0.098)S(0.062)EKDNIER 142.39 0.01104 3838700 1587.3 1570.8 1270.8 1573 1299.2 1364.7 1086.8 1053 1426.6 1207.5 TRUE FALSE FALSE 1567.953377 1592.913764 1292.917741 1754.877661 1232.896976 1277.500074 1179.112765 1083.466894 1299.001323 1176.128976 1.333147477 1.354369968 1.099299284 1.492079268 1.048266815 1.086190461 1.002536957 0.921214353 1.104471831 1 10.19983056 -7.992289783 1.625841755 1.191950009 0.945059759 0.326175017 0.143977579 0.494111579 2.377818575 0.025225155 0.122895856 1.02E-08 7.992289783 -0.24689025 GLSAS(ph)LPDLDSENWIEVK ddPTM_HeLa_Romidepsin_16h_R1 5 GLSASLPDLDSENWIEVK 18 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 0 GLS(0.007)AS(0.849)LPDLDS(0.144)ENWIEVK;GLS(0.112)AS(0.85)LPDLDS(0.038)ENWIEVK;GLS(0.035)AS(0.963)LPDLDS(0.001)ENWIEVK;GLS(0.072)AS(0.928)LPDLDSENWIEVK;GLS(0.026)AS(0.971)LPDLDS(0.003)ENWIEVK ;;;; 174.18 2.28E-12 124005000 9427 9823.1 8248.3 11789.6 7002.94 6668.99 6001.94 6210.42 9682.26 10181.2 TRUE FALSE FALSE 9312.100098 9961.38986 8391.858202 13152.76902 6645.55384 6242.863062 6511.744634 6390.108704 8816.254416 9916.690956 0.939033004 1.004507441 0.846235729 1.326326401 0.670138242 0.629530868 0.656644909 0.644379131 0.889031881 1 13.27564308 -8.567287858 24.9999062 0.985620388 0.645664512 0.665433352 0.121636509 52.5650781 29591.07509 0.015475995 0.030952003 2.71E-09 8.567287858 -0.339955875 GLSAS(ph)LPDLDSENWIEVKK ddPTM_HeLa_Romidepsin_16h_R1 2 GLSASLPDLDSENWIEVKK 19 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YBW1;H0YC73 Q6PKG0 LARP1 La-related protein 1 1 0 GLS(0.34)AS(0.514)LPDLDS(0.145)ENWIEVKK;GLS(0.045)AS(0.815)LPDLDS(0.141)ENWIEVKK ; 70.994 0.0045698 50662000 4279.1 4086.3 3495.6 5985.9 3206.2 2890.1 2736.1 2944.8 4040 3681 TRUE FALSE FALSE 4226.944683 4143.827039 3556.439452 6678.017923 3042.57565 2705.431937 2968.504266 3030.003142 3678.652282 3585.367089 1.178943349 1.155760885 0.99193175 1.862575785 0.848609243 0.754575995 0.827949884 0.845102626 1.02601831 1 11.80790512 -8.557889448 24.99995741 1.142213224 0.809499538 0.363664987 0.241120267 162.0119682 115686.6749 0.034461673 0.068923535 2.77E-09 8.557889448 -0.332713686 GLSAS(ph)TMDLSSSS ddPTM_HeLa_Romidepsin_16h_R1 1 GLSASTMDLSSSS 13 0 Q9NSK0-5;Q9NSK0;Q9NSK0-3 Q9NSK0-5 KLC4 Kinesin light chain 4 1 0 GLS(0.027)AS(0.825)T(0.148)MDLSSSS 95.618 0.02331 7780700 3507.6 3419.3 3478.3 3158.2 3293.9 2811.8 2209.7 2774.6 3314.9 3371.8 TRUE FALSE FALSE 3464.848022 3467.436995 3538.838352 3523.365944 3125.799992 2632.135055 2397.391863 2854.878673 3018.407042 3284.20015 1.055005135 1.055793446 1.077534313 1.072823148 0.95176903 0.801453911 0.729977393 0.869276702 0.91906915 1 11.68132634 -8.393620018 3.005160876 1.035976766 0.791104108 0.781926162 0.05403991 0.065326873 1.120403364 0.006158277 0.0151439 4.04E-09 8.393620018 -0.244872658 GLSDHVS(ph)LDGQELGTR ddPTM_HeLa_Romidepsin_16h_R1 3 GLSDHVSLDGQELGTR 16 0 Q7L8J4;Q7L8J4-2 Q7L8J4 SH3BP5L SH3 domain-binding protein 5-like 1 0 GLSDHVS(1)LDGQELGTR;GLS(0.004)DHVS(0.996)LDGQELGTR;GLS(0.09)DHVS(0.91)LDGQELGTR ;; 236.75 7.31E-46 31155000 6993.8 5721.98 5561.08 5061.51 10938.5 11354.5 9568.1 10404.3 9830.3 8657.6 TRUE FALSE FALSE 6908.556876 5802.534185 5657.868265 5646.745601 10380.26753 10628.98409 10380.81418 10705.33201 8951.053348 8432.674304 0.819260489 0.688101304 0.670945902 0.669626906 1.230957956 1.260452344 1.231022781 1.269506164 1.061472675 1 13.04177452 -8.737762632 21.49399042 0.858161755 1.247665274 0.72599507 0.127937139 23.64763151 21466.70204 0.020994518 0.041949108 1.83E-09 8.737762632 0.389503519 GLSEDTTEETLKES(ph)FDGSVR ddPTM_HeLa_Romidepsin_16h_R1 1 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 1 0 GLSEDT(0.001)T(0.001)EET(0.008)LKES(0.751)FDGS(0.237)VR 57.936 0.011166 3680200 1239.7 930.96 803.01 727.28 1235.8 1196.9 1060 1474.4 1420.4 987.2 TRUE FALSE FALSE 1224.59006 944.0660793 816.9860522 811.3715356 1172.732515 1120.421953 1150.036374 1517.059438 1293.355867 961.5524017 1.273555198 0.981814488 0.849653176 0.843814164 1.219624133 1.165221938 1.196020489 1.577718942 1.345070601 1 9.909221672 -6.630098038 1.136550542 1.084768103 2.878039202 0.466669564 0.159662159 4.21377454 1.595067551 0.024997047 12.80335998 2.34E-07 6.630098038 1.793271099 GLSEDTTEETLKESFDGSVR ddPTM_HeLa_Romidepsin_16h_R1 2 GLSEDTTEETLKESFDGSVR 20 1 P19338;H7BY16 P19338 NCL Nucleolin 0 0 ; ; 124.45 0.00027939 32140000 3891.4 4321.7 3399.1 3695.1 4091.5 3773.9 3582 4503.9 4706.5 4401.1 FALSE FALSE TRUE 3843.97012 4382.541006 3458.25991 4122.344848 3882.695488 3532.75997 3886.254991 4634.213241 4285.538852 4286.758788 0.896707818 1.022343739 0.806730698 0.961646095 0.905741536 0.82410981 0.906571884 1.081052952 0.999715418 1 12.06567152 -12.43505052 0.917058375 1.005240666 0.919009778 0.121364977 0.078237066 1.110720664 1.497339871 0.069706492 0.013682331 3.67E-13 12.43505052 -0.086230888 GLSPLPSPPEMMPT(ph)SPQSPR ddPTM_HeLa_Romidepsin_16h_R1 1 GLSPLPSPPEMMPTSPQSPR 20 0 A0A075B6G3;H0Y304;A0A087WTU7;A0A5H1ZRP8;A0A5H1ZRP7;A0A087WV90;A0A5H1ZRQ1;A0A5H1ZRP9;A0A5H1ZRQ8;P11532;P11532-11;P11532-4;P11532-2;P11532-3;P11532-14;P11532-8;P11532-12;P11532-17;P11532-6;P11532-5;P11532-7;P11532-15;P11532-9;P11532-16;P11532-13;A0A5H1ZRR9 A0A075B6G3 DMD Dystrophin 1 0 GLSPLPSPPEMMPT(0.453)S(0.453)PQS(0.095)PR 91.093 0.00017458 0 1354.3 1277.4 1000.9 1080.9 1238.7 1185.4 890.02 944.17 1280.3 1291.4 TRUE FALSE FALSE 1337.793271 1295.383271 1018.320245 1205.878744 1175.484517 1109.656766 965.6182766 971.4880693 1165.786761 1257.849242 1.063556129 1.029839847 0.809572571 0.958683047 0.934519398 0.882185821 0.767674094 0.772340625 0.926809607 1 10.2967433 -8.002896311 0.457728414 1.031628481 0.668706742 0.531201637 0.068179578 1.162636519 0.252033236 0.016353587 0.202717616 9.93E-09 8.002896311 -0.36292174 GLSPLPSPPEMMPTSPQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GLSPLPSPPEMMPTSPQSPR 20 0 A0A075B6G3;H0Y304;A0A087WTU7;A0A5H1ZRP8;A0A5H1ZRP7;A0A087WV90;A0A5H1ZRQ1;A0A5H1ZRP9;A0A5H1ZRQ8;P11532;P11532-11;P11532-4;P11532-2;P11532-3;P11532-14;P11532-8;P11532-12;P11532-17;P11532-6;P11532-5;P11532-7;P11532-15;P11532-9;P11532-16;P11532-13;A0A5H1ZRR9 A0A075B6G3 DMD Dystrophin 1 0 GLSPLPSPPEMMPT(0.063)S(0.125)PQS(0.811)PR;GLSPLPS(0.001)PPEMMPT(0.096)S(0.3)PQS(0.603)PR ; 89.356 0.0013187 17106700 5203.6 5880.8 4487.2 5080.3 5401.5 4997.3 4006.8 4593.9 5703.5 5284.3 TRUE FALSE FALSE 5140.176522 5963.590057 4565.297834 5667.70819 5125.841299 4677.988658 4347.137492 4726.817249 5193.364675 5147.013124 0.998671734 1.158650641 0.886980026 1.101164511 0.99588658 0.908874437 0.844594212 0.918361219 1.009005524 1 12.32951975 -8.222720474 3.704274371 1.010950455 0.881487536 0.424034927 0.069653985 0.164322312 4.78367125 0.00905175 0.024051937 5.99E-09 8.222720474 -0.129462919 GLSQNQQIPQNSVT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GLSQNQQIPQNSVTPR 16 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 GLSQNQQIPQNS(0.014)VT(0.986)PR 138.98 0.0018612 5399800 1638.1 1548.6 1447.9 1737.9 1572 1678.9 1479.9 1405.8 1929.5 1601.9 TRUE FALSE FALSE 1618.134207 1570.401231 1473.100092 1938.844175 1491.774974 1571.623708 1605.602669 1446.474605 1756.920687 1560.282407 1.037077775 1.006485252 0.944124016 1.242623878 0.956092927 1.007268749 1.029046192 0.927059485 1.126027365 1 10.60759146 -7.259034557 22.70229173 1.023015299 0.92705937 0.112733982 0.084158706 95.69417363 903149.6985 0.009759288 0.086580131 5.51E-08 7.259034557 -0.095955928 GLT(ph)PT(ph)GMLPS(ph)GVLSGGK ddPTM_HeLa_Romidepsin_16h_R1 1 GLTPTGMLPSGVLSGGK 17 0 E7ETC2;Q08209-4;Q08209-5;Q08209-3;Q08209-2;Q08209 E7ETC2 PPP3CA Serine/threonine-protein phosphatase;Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform 3 0 GLT(1)PT(1)GMLPS(0.999)GVLS(0.002)GGK 51.286 0.0041975 0 628.51 567.31 717.35 571.89 698.79 711.96 720.36 675.54 682.59 773.09 TRUE FALSE FALSE 620.8494784 575.2966051 729.8351758 638.0146126 663.1281388 666.4680537 781.5473604 695.0856841 621.5374408 753.0050104 0.824495813 0.764001032 0.969230172 0.847291325 0.880642399 0.885077848 1.037904595 0.923082416 0.825409436 1 9.556515654 -7.782139137 24.99555746 0.89894317 0.980493536 0.196099238 0.073551955 325.8360228 393457.1111 0.01199653 0.036045739 1.65E-08 7.782139137 0.081550366 GLT(ph)SVINQK ddPTM_HeLa_Romidepsin_16h_R1 1 GLTSVINQK 9 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 1 0 GLT(0.5)S(0.5)VINQK 153.1 0.010108 13008000 4213.5 5042 4352.4 3387.1 4013.4 4227.7 3852.2 4014.7 5195.2 4686.6 TRUE FALSE FALSE 4162.144241 5112.981408 4428.151696 3778.732439 3808.581222 3957.563614 4179.405772 4130.85901 4730.5283 4564.841456 0.911782869 1.12007864 0.970055968 0.82779051 0.834329354 0.86696628 0.915564278 0.90492935 1.036296298 1 12.15634904 -9.279341519 23.00688093 0.972785788 0.870311074 0.530726945 0.060463493 231.163838 297078.8707 0.009850316 0.015072777 5.26E-10 9.279341519 -0.102474714 GLTLAPGLS(ph)PARPLFGSDFEK ddPTM_HeLa_Romidepsin_16h_R1 2 GLTLAPGLSPARPLFGSDFEK 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 GLTLAPGLS(0.997)PARPLFGS(0.003)DFEK;GLTLAPGLS(0.999)PARPLFGS(0.001)DFEK ; 96.504 0.00025111 141689000 7481.4 8871.2 8261.4 5975.8 8648.3 8199.9 6710.2 8049.5 8999.8 8782.6 TRUE FALSE FALSE 7390.213819 8996.088986 8405.186202 6666.750113 8206.94498 7675.952854 7280.164221 8282.399582 8194.835348 8554.426786 0.863905204 1.051629666 0.982553994 0.779333353 0.959379884 0.89730768 0.851040567 0.968200417 0.957964286 1 13.06245547 GLTLAPGLS(ph)PARPLFGSDFEKEK ddPTM_HeLa_Romidepsin_16h_R1 1 GLTLAPGLSPARPLFGSDFEKEK 23 2 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 GLT(0.001)LAPGLS(0.994)PARPLFGS(0.005)DFEKEK 62.684 0.0055747 20838000 1417.1 1526 1157.4 1659.8 1640.3 1193.1 1112.1 1327.9 1528.3 1251.9 TRUE FALSE FALSE 1399.82784 1547.483068 1177.544061 1851.713886 1556.58937 1116.864761 1206.561746 1366.320691 1391.60502 1219.375458 1.147987547 1.269078411 0.965694409 1.518575656 1.276546416 0.915931802 0.989491578 1.120508604 1.141244078 1 10.2519267 -6.141759371 12.2197643 1.105730477 1.134669637 0 0.176037239 0 0 0.02360918 0 7.22E-07 6.141759371 0.02893916 GLTPSQIGVILR ddPTM_HeLa_Romidepsin_16h_R1 1 GLTPSQIGVILR 12 0 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 0 138.25 0.0034069 1161500 156.19 170.75 294.48 150.7 124.14 105.4 0 129.93 161.69 184.56 FALSE FALSE TRUE 154.2862962 173.153823 299.6053009 168.1246431 117.8046726 98.66528016 0 133.6893196 147.2280414 179.7651046 0.858266105 0.963222664 1.666648828 0.935246267 0.655325586 0.548856689 0 0.743688937 0.819002341 1 7.489969187 -8.496939965 2.285730747 0.994442033 0.381519135 0.485584986 0.283583752 0.201382155 2.077891421 0.041554433 0.103547351 3.18E-09 8.496939965 -0.612922898 GLTS(ph)VINQK ddPTM_HeLa_Romidepsin_16h_R1 1 GLTSVINQK 9 0 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 1 0 GLT(0.12)S(0.88)VINQK 152.04 0.0050362 15650000 3858.3 3846.7 4187.7 2757.9 3217.4 3735 3262.9 4004.1 5173 4311.2 TRUE FALSE FALSE 3811.273556 3900.853944 4260.585162 3076.781374 3053.204072 3496.345554 3540.050645 4119.952316 4710.313924 4199.194403 0.907620174 0.92895293 1.014619652 0.732707534 0.727092813 0.832622932 0.843030902 0.981129217 1.121718471 1 12.03589686 -9.268899639 24.99487876 0.956746223 0.819583157 0.457002706 0.088623198 414.6874605 1389368.156 0.011833552 0.018294857 5.38E-10 9.268899639 -0.137163066 GLTTTGNS(ph)SLNSTSNTK ddPTM_HeLa_Romidepsin_16h_R1 1 GLTTTGNSSLNSTSNTK 17 0 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 0 GLTT(0.001)T(0.007)GNS(0.465)S(0.465)LNS(0.052)T(0.007)S(0.002)NTK 94.01 0.0019151 0 971.36 960.13 917.1 1011.5 1168.2 1271.5 903.32 1015.7 1104.7 1032 TRUE FALSE FALSE 959.5206907 973.6467353 933.0617408 1128.454389 1108.582395 1190.255254 980.0479783 1045.087677 1005.892865 1005.188491 0.954567923 0.968621054 0.928245547 1.122629635 1.102860214 1.184111501 0.974989255 1.039693238 1.000700738 1 9.973250343 -9.258924711 24.99387513 0.97366917 1.085267362 0.524813518 0.05439811 144.515394 1436367.698 0.008433288 0.01356908 5.51E-10 9.258924711 0.111598193 GLVAAYS(ph)GDS(ph)DNEEELVER ddPTM_HeLa_Romidepsin_16h_R1 2 GLVAAYSGDSDNEEELVER 19 0 P52756 P52756 RBM5 RNA-binding protein 5 2 0 GLVAAY(0.382)S(0.626)GDS(0.992)DNEEELVER;GLVAAY(0.303)S(0.923)GDS(0.775)DNEEELVER ; 163.44 7.48E-07 5217800 4475.1 4156.29 3929.7 2924.72 3942 3875.87 3088.45 3125.65 3912.63 4415.2 TRUE FALSE FALSE 4420.55576 4214.80236 3998.09478 3262.889888 3740.82503 3628.214416 3350.782866 3216.085751 3562.674573 4300.492468 1.027918498 0.98007435 0.92968301 0.758724707 0.869859687 0.843674171 0.779162594 0.747841271 0.828434092 1 12.07028616 -9.525201847 2.41623433 1.011962683 0.804554216 0.49869443 0.069034313 0.072400112 0.849048975 0.006130128 0.009432987 2.98E-10 9.525201847 -0.207408467 GLVAAYSGDS(ph)DNEEELVER ddPTM_HeLa_Romidepsin_16h_R1 4 GLVAAYSGDSDNEEELVER 19 0 P52756 P52756 RBM5 RNA-binding protein 5 1 0 GLVAAYS(0.03)GDS(0.97)DNEEELVER;GLVAAYS(0.013)GDS(0.987)DNEEELVER;GLVAAYS(0.001)GDS(0.999)DNEEELVER;GLVAAYSGDS(1)DNEEELVER ;;; 373.9 4.40E-294 315257000 21617.2 23280.1 20521.67 13917.95 17615.42 15975.72 14013.03 14282.72 23803.5 22152.4 TRUE FALSE FALSE 21353.72125 23607.83786 20878.84106 15527.20886 16716.43939 14954.92305 15203.29642 14695.96797 21674.45534 21576.87745 0.989657623 1.094126706 0.967648869 0.71962261 0.774738579 0.693099504 0.704610593 0.681097995 1.004522336 1 14.39719848 -9.287637798 4.336365436 1.003469623 0.714507398 0.940455046 0.037375412 0.036591503 1.669815797 0.005813071 0.009261349 5.16E-10 9.287637798 -0.288962225 GLVAAYSGDS(ph)DNEEELVERLESEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 GLVAAYSGDSDNEEELVERLESEEEK 26 1 P52756 P52756 RBM5 RNA-binding protein 5 1 0 GLVAAY(0.002)S(0.011)GDS(0.987)DNEEELVERLESEEEK;GLVAAY(0.051)S(0.191)GDS(0.756)DNEEELVERLES(0.002)EEEK ; 102.9 1.32E-06 7476900 1912.76 2132.98 1826.29 2328.89 1566.32 1342.73 1322.74 1690.2 2277.48 1863.11 TRUE FALSE FALSE 1889.446545 2163.008148 1858.075811 2598.16722 1486.384846 1256.933886 1435.093503 1739.10327 2073.776485 1814.706134 1.041185959 1.191933012 1.023899009 1.431728902 0.819077435 0.692637702 0.790813166 0.958338784 1.1427616 1 10.82552023 -8.569385889 24.99993029 1.063013451 0.802322376 0.517831804 0.141919868 83.14050048 44691.89162 0.020224128 0.040448268 2.70E-09 8.569385889 -0.260691075 GLVAAYSGES(ph)DS(ph)EEEQER ddPTM_HeLa_Romidepsin_16h_R1 2 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 2 0 GLVAAY(0.375)S(0.132)GES(0.894)DS(0.599)EEEQER;GLVAAY(0.089)S(0.222)GES(0.702)DS(0.988)EEEQER ; 158.65 4.93E-05 20624000 3372.69 3509.76 3273.97 2282.53 2740.94 2942.03 2520.95 3130.5 3757.4 2947.1 TRUE FALSE FALSE 3331.582357 3559.170493 3330.952074 2546.446858 2601.059604 2754.043778 2735.07943 3221.076078 3421.328733 2870.533917 1.160614176 1.239898429 1.160394606 0.887098683 0.906123975 0.959418651 0.952812093 1.122117408 1.191878874 1 11.48710339 -9.264519368 24.97750097 1.098450743 0.961170397 0.471514779 0.089790732 259.4194092 2103790.427 0.015656544 0.024570417 5.44E-10 9.264519368 -0.137280346 GLVAAYSGES(ph)DS(ph)EEEQERGGPER ddPTM_HeLa_Romidepsin_16h_R1 1 GLVAAYSGESDSEEEQERGGPER 23 1 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 2 0 GLVAAY(0.043)S(0.218)GES(0.984)DS(0.756)EEEQERGGPER 77.031 0.001236 5871400 3116.1 3373.5 2672.2 3216.8 2352.3 2513.8 2339 2930.3 3271.7 2788.2 TRUE FALSE FALSE 3078.119775 3420.992222 2718.70852 3588.741551 2232.253353 2353.176293 2537.674602 3015.083607 2979.070958 2715.762162 1.133427595 1.259680347 1.00108491 1.321449132 0.82196202 0.866488357 0.934424464 1.110216369 1.096955764 1 11.40714142 -8.727390226 24.99991242 1.091856589 0.928584819 0.369845389 0.121473299 187.9725028 138014.3524 0.018047781 0.036094118 1.87E-09 8.727390226 -0.16327177 GLVAAYSGES(ph)DSEEEQER ddPTM_HeLa_Romidepsin_16h_R1 3 GLVAAYSGESDSEEEQER 18 0 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 0 GLVAAYS(0.001)GES(0.975)DS(0.024)EEEQER;GLVAAYSGES(0.996)DS(0.004)EEEQER;GLVAAYS(0.003)GES(0.928)DS(0.069)EEEQER ;; 198.51 1.27E-20 12481200 9207.5 8586 9589.6 7696.1 7502 7328.8 6856.2 8175.4 10233.1 9791.9 TRUE FALSE FALSE 9095.275448 8706.873933 9756.502965 8585.959293 7119.144946 6860.513333 7438.565457 8411.9423 9317.825907 9537.505026 0.953632572 0.912908975 1.022961764 0.900231168 0.746436822 0.719319499 0.779927815 0.881985622 0.976966815 1 13.2193962 -8.936520127 4.11078271 0.97445289 0.778219815 0.780254886 0.047791494 0.073864137 2.531150678 0.007324687 0.013539458 1.16E-09 8.936520127 -0.196233075 GLVGEIIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GLVGEIIKR 9 1 Q32Q12;P22392-2;P22392;J3KPD9;E7ERL0;F6XY72;E5RHP0;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 1 ; GLVGEIIK(1)R;GLVGEIIK(1)R 138.1 0.001447 21534000 2570.4 2494.5 2533.8 1601.1 6841 4457.3 4790.4 4698.7 6345.6 4626.4 FALSE TRUE FALSE 2539.070976 2529.617636 2577.899726 1786.226715 6491.878243 4172.492915 5197.296456 4834.649471 5778.033643 4506.205461 0.563460987 0.561363138 0.572077716 0.396392648 1.440652962 0.925943779 1.153364289 1.072887047 1.282239279 1 12.13769738 -8.759554999 24.99960369 0.726359156 1.132703692 0.371190748 0.266816426 40.09160101 531870.6952 0.035989118 0.069160694 1.74E-09 8.759554999 0.406344535 GLVGEIIKR ddPTM_HeLa_Romidepsin_16h_R1 2 GLVGEIIKR 9 1 Q32Q12;P22392-2;P22392;J3KPD9;E7ERL0;F6XY72;E5RHP0;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 0 ; ; 112.41 0.011464 35648000 9308.8 9286.7 8760.5 7750.9 9202.1 8146.4 8046 9202.7 10223.7 8714.1 FALSE FALSE TRUE 9195.340765 9417.438406 8912.972828 8647.095527 8732.482499 7625.871331 8729.427039 9468.965605 9309.266666 8487.706426 1.083371679 1.109538659 1.050103807 1.018778819 1.028838895 0.898460779 1.028478908 1.115609463 1.09679414 1 13.05115904 -9.132932758 3.492038133 1.047431076 1.011247413 0.103700416 0.058369881 0.578076773 12.97019495 0.009516514 0.016401565 7.36E-10 9.132932758 -0.036183663 GLVGPELHDR ddPTM_HeLa_Romidepsin_16h_R1 3 GLVGPELHDR 10 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;; ;; 121.6 0.0050901 22642200 14212.6 13661.1 13393.6 13942.5 13744.3 14895.1 12866.7 13997.6 14748.3 14042.2 FALSE FALSE TRUE 14039.37136 13853.42132 13626.70999 15554.59745 13042.87708 13943.35118 13959.59718 14402.59847 13429.17511 13677.38162 1.026466304 1.012870863 0.996295224 1.137249649 0.95360921 1.019445941 1.020633742 1.053023076 0.981852776 1 13.73950445 -12.35646665 0.456290001 0.992135758 1.028289363 0.092201237 0.044441056 5.369736669 1.410327915 0.091333812 0.012281453 4.40E-13 12.35646665 0.036153605 GLVLDHGAR ddPTM_HeLa_Romidepsin_16h_R1 3 GLVLDHGAR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 0 ;; ;; 141.52 0.0029523 19988200 19297.3 17984.8 20455.2 19004.6 20382.9 20939.1 17939.5 15540.9 19087 15375.3 FALSE FALSE TRUE 19062.09709 18237.99049 20811.21418 21202.00127 19342.68455 19601.15909 19463.28068 15990.55142 17379.81092 14975.84749 1.272855984 1.217826938 1.38965185 1.41574634 1.291591983 1.308851409 1.299644691 1.067756027 1.160522697 1 13.87035003 -11.98137478 0.66029789 0.985273197 1.295219887 0.349368406 0.101818698 0.455527583 0.34450202 0.077308808 0.020492204 1.04E-12 11.98137478 0.30994669 GLVPEDDTK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 1 GLVPEDDTKEK 11 1 Q15459;Q15459-2;H7C1L2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 1 GLVPEDDTK(1)EK 143.4 0.0035225 725070 433.54 330.82 337.28 377.54 805.7 724.76 608.02 518.24 793.8 660.91 FALSE TRUE FALSE 428.2558477 335.4772926 343.1502169 421.1929512 764.5821225 678.4501751 659.6652036 533.2344568 722.8005399 643.7394629 0.665262691 0.521138305 0.533057606 0.654291022 1.187719825 1.053920435 1.02473942 0.828338928 1.122815334 1 9.330333102 -8.767295987 24.99183393 0.774049692 1.025915409 0.313704108 0.196700807 153.6598897 655714.1884 0.031293664 0.057834325 1.71E-09 8.767295987 0.251865716 GLVSDGTS(ph)PGER ddPTM_HeLa_Romidepsin_16h_R1 2 GLVSDGTSPGER 12 0 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 0 GLVS(0.024)DGT(0.171)S(0.805)PGER;GLVS(0.002)DGT(0.044)S(0.955)PGER ; 99.669 0.015748 20850800 7634 7194.2 7196.6 6057.2 6844.9 6931.6 5623.9 6249 7524.5 7144 TRUE FALSE FALSE 7540.953872 7295.480136 7321.853804 6757.561964 6495.579211 6488.693131 6101.593926 6429.804956 6851.489875 6958.39785 1.08371985 1.048442514 1.052232707 0.971137625 0.933487758 0.932498151 0.876867644 0.924035258 0.984636122 1 12.76453945 -8.94833253 1.895533392 1.042466276 0.910371707 0.765644139 0.030364867 0.123515442 0.891785791 0.005386832 0.010973997 1.13E-09 8.94833253 -0.13209457 GLVYETSVLDPDEGIR ddPTM_HeLa_Romidepsin_16h_R1 2 GLVYETSVLDPDEGIR 16 0 F8W642;F8VZK9;F8VX07;F8VRP1;F8VX68;F8VPF9;F8VPA1;F8VTT8;F8W1S4;F8W4S1;H0YH82;A0A0C4DGI3;B4DJV2;O75390 F8W642 CS "Citrate synthase;Citrate synthase, mitochondrial" 0 0 ; ; 152.67 0.0027747 8534600 3585.3 3589.2 3460.5 3556.6 3172 3724.7 3029.8 3648 3701.9 3077.8 FALSE FALSE TRUE 3541.600985 3639.728852 3520.728551 3967.830826 3010.121004 3486.703691 3287.151136 3753.549124 3370.792792 2997.838312 1.181384923 1.214117798 1.174422428 1.323563986 1.004097183 1.16307263 1.096507147 1.252085247 1.124407804 1 11.54970686 -12.12323598 0.84325837 0.997822997 1.173254951 0.154893414 0.088939336 0.499585401 0.631630185 0.055021394 0.015354914 7.53E-13 12.12323598 0.175431953 GLWSTDS(ph)AEEDKETK ddPTM_HeLa_Romidepsin_16h_R1 3 GLWSTDSAEEDKETK 15 1 Q99549-2;Q99549;A0A0A0MT47 Q99549-2 MPHOSPH8 M-phase phosphoprotein 8 1 0 GLWS(0.004)T(0.059)DS(0.933)AEEDKET(0.004)K;GLWST(0.004)DS(0.995)AEEDKETK;GLWS(0.006)T(0.262)DS(0.732)AEEDKETK ;; 209.56 1.26E-24 76838000 8036.14 7927.84 7815.43 5710.58 7166.61 7120.23 7426.34 7367.25 8892.96 7675.39 TRUE FALSE FALSE 7938.192435 8039.44834 7951.454281 6370.864129 6800.871149 6665.270282 8057.133134 7580.409755 8097.551385 7475.982261 1.061826013 1.075370173 1.063599939 0.852177534 0.909695999 0.891557798 1.077735721 1.013968398 1.083142135 1 12.86804743 -9.303228624 24.99956804 1.036480657 0.950799666 0.394167933 0.064363709 494.2787823 295691.0401 0.010507981 0.016051281 4.97E-10 9.303228624 -0.085680992 GMDGSTNETASS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 GMDGSTNETASSR 13 0 Q9Y3B9 Q9Y3B9 RRP15 RRP15-like protein 1 0 GMDGSTNET(0.001)AS(0.22)S(0.778)R;GMDGSTNETAS(0.24)S(0.76)R ; 115.04 0.0080116 14414400 8017.4 7614.2 7963.8 6032.7 10126.3 12009.5 8861.8 8447.9 7058.6 6893.5 TRUE FALSE FALSE 7919.680845 7721.392907 8102.406598 6730.229159 9609.517125 11242.13171 9614.521071 8692.326658 6427.261137 6714.405876 1.179505825 1.149974108 1.206719812 1.002356617 1.431179065 1.674330077 1.43192432 1.294578674 0.957234528 1 12.71304403 -8.702550923 6.654520448 1.097319978 1.475342982 0.71362928 0.116185821 0.088501048 7.736948879 0.017182261 0.034400984 1.98E-09 8.702550923 0.378023004 GMFTKK(ac)LGNTNK(ac)NK ddPTM_HeLa_Romidepsin_16h_R1 1 GMFTKKLGNTNKNK 14 3 A0A3B3ISZ1;Q8NB66 A0A3B3ISZ1 UNC13C Protein unc-13 homolog C 0 2 GMFTK(0.033)K(0.967)LGNTNK(1)NK 77.776 0.0094594 3580900 1926.2 1642.9 2204.2 2397 1112 1149.7 982.65 1111.5 1951.9 1516.6 FALSE TRUE FALSE 1902.722734 1666.028789 2242.563176 2674.152418 1055.250491 1076.23788 1066.116266 1143.659499 1777.317175 1477.198513 1.288061636 1.127829993 1.518119031 1.810286427 0.714359296 0.728566859 0.72171496 0.774208401 1.203167455 1 10.528648 GMGELLPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 GMGELLPTK 9 0 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;C9JE24 C9JW01 PUM2 Pumilio homolog 2 1 0 GMGELLPT(1)K;GMGELLPT(1)K ; 160.03 0.0089772 65631000 9486.4 1728.76 5380.4 3115.8 4190.6 3102.7 7356.3 4331.6 8170.4 5985 TRUE FALSE FALSE 9370.776108 1753.097529 5474.043605 3476.063456 3976.738045 2904.447484 7981.143938 4456.928012 7439.618961 5829.508837 1.607472665 0.300728171 0.939023125 0.596287535 0.682173774 0.498231938 1.36909372 0.76454606 1.276199963 1 12.50915862 -10.27005252 24.9812554 1.286862086 0.751348575 0.421322465 0.29969247 508.4503982 1474688.937 0.057369872 0.066147741 5.37E-11 10.27005252 -0.535513512 GMS(ph)Y(ph)LHSS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GMSYLHSSK 9 0 P25092 P25092 GUCY2C Heat-stable enterotoxin receptor 3 0 GMS(0.999)Y(0.995)LHS(0.354)S(0.652)K 54.549 0.0041617 0 479.71 360.31 485.47 733.23 406.66 457.53 598.55 376.05 594.27 648.32 TRUE FALSE FALSE 473.86311 365.3824536 493.9194017 818.0095026 385.9066227 428.2953096 649.3908221 386.9304134 541.1170028 631.4765529 0.750404917 0.578616026 0.782165861 1.295391727 0.611117897 0.6782442 1.028368859 0.612739161 0.856907514 1 9.302585357 -12.30728267 1.086697599 0.997538048 0.797431267 0.046091475 0.212728066 0.878843359 1.892883258 0.129699319 0.036360029 4.93E-13 12.30728267 -0.200106781 GNAEGS(ph)S(ph)DEEGKLVIDEPAK ddPTM_HeLa_Romidepsin_16h_R1 1 GNAEGSSDEEGKLVIDEPAK 20 1 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 2 0 GNAEGS(1)S(1)DEEGKLVIDEPAK 64.346 0.0038645 0 1375.5 1779.9 2084.3 1070.2 1450.7 1402 1129.2 1473.9 1616.9 1764.8 TRUE FALSE FALSE 1358.734877 1804.957479 2120.576367 1193.941559 1376.665366 1312.416725 1225.11422 1516.544971 1472.280414 1718.950242 0.790444566 1.050034745 1.233646161 0.694575986 0.800875635 0.763498962 0.712710694 0.882250652 0.856499728 1 10.74731207 GNAEGS(ph)S(ph)DEEGKLVIDEPAKEK ddPTM_HeLa_Romidepsin_16h_R1 2 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 2 0 GNAEGS(1)S(1)DEEGKLVIDEPAKEK;GNAEGS(1)S(1)DEEGKLVIDEPAKEK ; 65.149 0.0041236 42871000 8085 7335.6 6885.7 6067.3 7918.8 7853 6562.7 7571.8 7946.8 7627.8 TRUE FALSE FALSE 7986.45691 7438.870769 7005.54272 6768.829774 7514.674087 7351.218644 7120.135574 7790.878087 7236.018305 7429.628656 1.074946983 1.001243954 0.942919632 0.911058962 1.011446794 0.989446308 0.958343398 1.048622811 0.973940777 1 12.85907439 -10.00477506 24.30923762 1.03553394 0.97499886 0.098465713 0.043545637 137.622273 700621.0181 0.007114297 0.009207478 9.89E-11 10.00477506 -0.060535079 GNAEGS(ph)SDEEGKLVIDEPAK ddPTM_HeLa_Romidepsin_16h_R1 1 GNAEGSSDEEGKLVIDEPAK 20 1 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 GNAEGS(0.5)S(0.5)DEEGKLVIDEPAK 67.418 0.0038967 39527000 2309.3 2262.6 2700.7 1557.2 2541.7 2740 2749.2 2162.7 2768.4 3132.7 TRUE FALSE FALSE 2281.153363 2294.452942 2747.704551 1737.250791 2411.987565 2564.922843 2982.716979 2225.274312 2520.78737 3051.312002 0.747597545 0.751956188 0.900499375 0.569345511 0.79047556 0.840596714 0.977519499 0.729284423 0.826132289 1 11.57521399 -12.30801876 0.960955548 1.003869879 0.789383148 0.086179902 0.115313263 0.501610496 0.806304818 0.07606814 0.018897411 4.92E-13 12.30801876 -0.214486731 GNAEGS(ph)SDEEGKLVIDEPAKEK ddPTM_HeLa_Romidepsin_16h_R1 1 GNAEGSSDEEGKLVIDEPAKEK 22 2 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 GNAEGS(0.712)S(0.288)DEEGKLVIDEPAKEK 53.254 0.012444 70933000 3708.6 3325.8 3702.1 3159.8 3417.5 3416.4 3077 3325.3 3964.1 3942.2 TRUE FALSE FALSE 3663.398157 3372.6207 3766.533498 3525.150943 3243.092223 3198.103066 3338.360303 3421.512309 3609.540968 3839.781076 0.954064329 0.878336716 0.980924022 0.918060398 0.844603418 0.832886824 0.869414229 0.891069632 0.94003822 1 11.90680834 -9.792124303 0.401771615 0.998215556 0.846681864 0.495960288 0.038404436 0.51729054 0.197999331 0.016704651 0.03016015 1.61E-10 9.792124303 -0.151533692 GNDPLTSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 3 GNDPLTSSPGR 11 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 0 GNDPLT(0.002)S(0.015)S(0.982)PGR;GNDPLTS(0.004)S(0.996)PGR;GNDPLT(0.006)S(0.039)S(0.955)PGR ;; 144.51 0.0025168 2944797000 20396.1 20070.2 20786.7 15638.4 17969.8 17424.8 14345.8 15559.9 22017 20757.4 TRUE FALSE FALSE 20147.50449 20352.7488 21148.48379 17446.58539 17052.73405 16311.41152 15564.33189 16010.10116 20047.74438 20218.11976 0.996507328 1.006658831 1.046016348 0.862918293 0.843438176 0.806771931 0.769820937 0.791868945 0.991573134 1 14.30336122 -9.029991678 2.477192936 1.002325524 0.798834417 0.9389082 0.024835743 0.048270334 0.59030793 0.00379851 0.007085359 9.33E-10 9.029991678 -0.203491106 GNDPLTSS(ph)PGRS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 GNDPLTSSPGRSSR 14 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 2 0 GNDPLT(0.113)S(0.154)S(0.732)PGRS(0.722)S(0.278)R 98.654 0.0014002 0 2184.4 2332.1 1912.3 2077.2 1703.3 1650 1610.3 1223.9 2629 2446.3 TRUE FALSE FALSE 2157.775693 2364.931365 1945.582779 2317.375638 1616.374245 1544.570325 1747.078842 1259.311616 2393.855656 2382.744773 0.905584063 0.992523996 0.81653008 0.972565616 0.678366505 0.648231545 0.733221141 0.528513011 1.00466306 1 11.21840871 -8.003568678 0.448746403 0.973204409 0.434992682 0.788472195 0.075333742 0.901069898 0.187126034 0.018590396 0.229580795 9.92E-09 8.003568678 -0.538211726 GNDS(ph)DGEGESDDPEK ddPTM_HeLa_Romidepsin_16h_R1 1 GNDSDGEGESDDPEK 15 0 O75351;K7EKZ3 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 1 0 GNDS(0.991)DGEGES(0.009)DDPEK 163 0.00012995 6556000 1868.6 1917.8 2556.4 1037.2 2013.7 2046.7 1732.6 1659.1 2205.8 1883.9 TRUE FALSE FALSE 1845.824784 1944.798839 2600.89307 1157.125944 1910.933375 1915.922475 1879.767001 1707.103441 2008.507723 1834.956006 1.005923182 1.059861289 1.417414402 0.630601464 1.041405553 1.044124474 1.024420746 0.930323907 1.09458086 1 10.84152976 -9.230592917 24.99990401 1.03632527 0.951254517 0.151452444 0.166367755 1686.329062 1366707.888 0.02422926 0.040177767 5.88E-10 9.230592917 -0.085070753 GNDVAFHFNPR ddPTM_HeLa_Romidepsin_16h_R1 4 GNDVAFHFNPR 11 0 P17931;G3V3R6 P17931 LGALS3 Galectin-3;Galectin 0 0 ;;; ;;; 110.66 0.001756 23649020 22432.63 21132.5 22471.95 16604.4 25448.14 27382.19 16023.17 20374.19 20340.52 18492.9 FALSE FALSE TRUE 22159.21248 21430.00389 22863.06486 18524.27885 24149.42646 25632.55643 17384.17766 20963.68504 18521.21295 18012.45179 1.230216338 1.189732755 1.269292217 1.02841518 1.340707347 1.423046497 0.96512001 1.163844061 1.02824497 1 14.13670695 -12.26917784 0.844169146 0.990932373 1.203381537 0.255054101 0.127355315 0.751494922 0.896470852 0.105484463 0.024346567 5.38E-13 12.26917784 0.212449165 GNENANGAPAITLLIR ddPTM_HeLa_Romidepsin_16h_R1 2 GNENANGAPAITLLIR 16 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 0 ; ; 134.9 3.07E-06 639930 0 62.316 0 171.4 188.45 223.19 0 0 167.73 126.11 FALSE FALSE TRUE 0 63.19328628 0 191.2180745 178.8326933 208.9288793 0 0 152.7278087 122.833644 0 0.514462359 0 1.556723941 1.455893414 1.700909234 0 0 1.243371146 1 6.940561957 -9.270108443 24.83065659 0.478587507 0.960965699 0.075928055 0.656540347 1079.287111 3091380.459 0.107343614 0.165551952 5.37E-10 9.270108443 0.482378191 GNFNYIEFTR ddPTM_HeLa_Romidepsin_16h_R1 1 GNFNYIEFTR 10 0 J3QRS3;P19105;O14950 J3QRS3 MYL12A;MYL12B Myosin regulatory light chain 12A;Myosin regulatory light chain 12B 0 0 166.66 0.014174 26094000 2502 1937.9 2337.3 1611.5 2544.1 2964.4 2364 2291.2 2404.5 1501 FALSE FALSE TRUE 2471.504662 1965.181807 2377.979726 1797.829212 2414.265084 2774.984407 2564.798101 2357.492257 2189.435498 1462.003804 1.690491267 1.344170106 1.626520889 1.229702144 1.65133981 1.898069212 1.754303303 1.612507609 1.497558004 1 10.51373135 -14.07945596 0.305300778 2.60E-15 1.668117118 0.135721421 0.236846557 5.839504183 0.28782164 3.93386837 0.084851432 8.33E-15 14.07945596 1.668117118 GNIETTS(ph)EDGQVFSPK ddPTM_HeLa_Romidepsin_16h_R1 1 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 GNIET(0.195)T(0.195)S(0.589)EDGQVFS(0.022)PK 98.552 0.0062482 24192000 4832.5 4841.5 4533.3 4856.8 6794.6 7580.6 7263 7617.8 5792.7 5258.3 TRUE FALSE FALSE 4773.599631 4909.658764 4612.200185 5418.366068 6447.846208 7096.224125 7879.919039 7838.209024 5274.586404 5121.688608 0.932036287 0.958601575 0.90052335 1.057925712 1.25892976 1.38552432 1.538539267 1.530395466 1.029853005 1 12.32240383 -8.470397619 1.348952247 0.960300277 1.536276666 0.967882596 0.042179573 0.050968513 0.177056487 0.006513177 0.021565019 3.39E-09 8.470397619 0.575976389 GNIETTSEDGQVFS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 GNIETTSEDGQVFSPK 16 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIETTSEDGQVFS(1)PK;GNIET(0.036)T(0.106)S(0.315)EDGQVFS(0.543)PK ;;; 193.41 7.40E-13 174029400 12519.8 12094.7 10762.2 10035.7 10377.6 9271 8838 9179.4 13519.9 12574.8 TRUE FALSE FALSE 12367.20386 12264.9695 10949.51158 11196.07485 9847.992348 8678.613021 9588.699499 9444.991456 12310.64628 12248.10488 1.00972387 1.001376917 0.893975981 0.91410671 0.804042131 0.708567824 0.782872093 0.771139009 1.00510621 1 13.58027092 -9.055821951 1.069655627 1.005196221 0.750877705 0.918643812 0.031060945 0.088402219 0.199406012 0.005190014 0.012300165 8.79E-10 9.055821951 -0.254318517 GNKS(ph)PSPPDGSPAATPEIR ddPTM_HeLa_Romidepsin_16h_R1 3 GNKSPSPPDGSPAATPEIR 19 1 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 GNKS(0.735)PS(0.264)PPDGSPAATPEIR;GNKS(0.991)PS(0.009)PPDGSPAATPEIR;GNKS(0.983)PS(0.017)PPDGSPAATPEIR ;; 108.14 0.00033681 376732000 6931 6861.6 6336.2 7094.5 6892.7 6806.5 5809.1 6260.7 7820.3 7358.7 TRUE FALSE FALSE 6846.522306 6958.197785 6446.478903 7914.799471 6540.939799 6371.586617 6302.524809 6441.843477 7120.832782 7167.519913 0.955214968 0.970795738 0.899401604 1.104259153 0.912580625 0.888952761 0.879317377 0.898754877 0.993486292 1 12.80725829 -8.542026831 24.99897501 0.980085524 0.890160434 0.467572871 0.048376535 157.2469548 205294.7263 0.006641987 0.01328545 2.87E-09 8.542026831 -0.089925089 GNKSPS(ph)PPDGSPAATPEIR ddPTM_HeLa_Romidepsin_16h_R1 1 GNKSPSPPDGSPAATPEIR 19 1 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 GNKS(0.384)PS(0.608)PPDGS(0.008)PAATPEIR 89.043 0.0015677 20780000 2263.7 2516.1 2146.9 2189.8 2081.6 2458.3 1775.7 2329 2696.8 2185.5 TRUE FALSE FALSE 2236.109154 2551.521722 2184.265894 2442.994979 1975.368184 2301.222564 1926.527914 2396.38594 2455.591454 2128.720395 1.050447564 1.198617596 1.026093375 1.147635446 0.927960379 1.081035616 0.905016891 1.125740114 1.153552838 1 11.05577075 -6.933944416 20.88891688 1.035148919 3.298053791 0.013900327 0.092452977 874.1675983 302692.3081 0.010728752 8673.613294 1.16E-07 6.933944416 2.262904872 GNNLST(ph)IS(ph)DT(ph)SPMK ddPTM_HeLa_Romidepsin_16h_R1 1 GNNLSTISDTSPMK 14 0 A0A1B0GUM7;A0A384DVW2;A0A1B0GTI4;B5TYJ1;A0A1B0GU74;A0A590UJK2;A0A1B0GTW2;A0A1B0GU81;A0A1B0GTN7;A0A1C7CYY9;A0A087WW63;O00555-3;O00555-2;O00555-4;O00555 A0A1B0GUM7 CACNA1A Voltage-dependent P/Q-type calcium channel subunit alpha-1A 3 0 GNNLS(0.439)T(0.566)IS(0.989)DT(0.787)S(0.218)PMK 63.212 0.0035896 0 1455.7 1543.5 1545 1004.3 1311.8 1749.9 1242.9 1293.8 1952.8 1779.9 TRUE FALSE FALSE 1437.957368 1565.229434 1571.890077 1120.421891 1244.853951 1638.087038 1348.471895 1331.234062 1778.136677 1733.657941 0.829435458 0.902847901 0.90668986 0.646276214 0.7180505 0.944873264 0.77781889 0.767875848 1.025656004 1 10.75960356 -12.81017952 0.273318792 1.14003192 0.778471409 0.497830491 0.08373223 4.747585035 0.368185781 0.566357185 0.058841116 1.55E-13 12.81017952 -0.361560512 GNNVLYISTQK ddPTM_HeLa_Romidepsin_16h_R1 1 GNNVLYISTQK 11 0 P62312 P62312 LSM6 U6 snRNA-associated Sm-like protein LSm6 0 0 107.11 0.0011163 0 271.82 177.18 332.04 257.47 361.75 317.42 285.35 353.27 297.79 251.14 FALSE FALSE TRUE 268.5069533 179.6743447 337.8190169 287.2398928 343.2885476 297.1378864 309.5876219 363.4913101 271.1549166 244.6153466 1.097670105 0.734517875 1.381021353 1.174251317 1.403381073 1.214714819 1.265609972 1.485970995 1.108495114 1 7.934371108 -9.726450341 24.99968847 1.024040191 1.310582181 0.606518727 0.130801053 98.36169897 70279.35568 0.019208381 0.027164101 1.88E-10 9.726450341 0.286541991 GNPGEQSPS(ph)PEQFINNAGAGDSSR ddPTM_HeLa_Romidepsin_16h_R1 1 GNPGEQSPSPEQFINNAGAGDSSR 24 0 C9J6R3;C9J9X8;C9JCX6;C9JXA0;Q9BYV8-5;Q9BYV8-2;Q9BYV8 C9J6R3 CEP41 Centrosomal protein of 41 kDa 1 0 GNPGEQS(0.297)PS(0.703)PEQFINNAGAGDSSR 64.547 0.0012603 0 1292.5 1272.8 1183.2 865.6 1210.2 1154.9 997.64 1135.7 1328.5 1856.9 TRUE FALSE FALSE 1276.746513 1290.718512 1203.7931 965.6847448 1148.438978 1081.105617 1082.379517 1168.559688 1209.675633 1808.65747 0.705908407 0.713633473 0.665572735 0.53392351 0.634967647 0.597739282 0.598443616 0.646092313 0.668825166 1 10.8207035 -11.86930885 0.375632266 1.088786865 0.590569968 0.16654381 0.108922358 0.338276794 0.078741588 0.069017722 0.016163962 1.35E-12 11.86930885 -0.498216896 GNPTVEVDLFTS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 3 GNPTVEVDLFTSK 13 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y798;A0A2R8YEG5 P06733 ENO1 Alpha-enolase;Enolase 1 0 GNPTVEVDLFT(0.195)S(0.805)K;GNPTVEVDLFT(0.084)S(0.916)K;GNPTVEVDLFT(0.286)S(0.714)K ;; 128.95 0.0027978 49698000 7186.7 6259.5 7102.2 3758.02 6017.1 7376.1 6198.2 7157.7 7405.6 7442 TRUE FALSE FALSE 7099.105736 6347.621405 7225.810812 4192.539954 5710.024934 6904.791015 6724.674953 7364.796757 6743.224588 7248.655767 0.979368584 0.875696351 0.996848387 0.578388613 0.787735701 0.952561583 0.927713382 1.016022418 0.930272426 1 12.82349776 -10.15503371 1.663190382 0.992609142 0.864220087 0.103169562 0.119794573 0.463115288 2.448466388 0.022436904 0.027745512 7.00E-11 10.15503371 -0.128389054 GNRGS(ph)GGGGGGGGQGSTNYGK ddPTM_HeLa_Romidepsin_16h_R1 2 GNRGSGGGGGGGGQGSTNYGK 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 1 0 GNRGS(1)GGGGGGGGQGSTNYGK;GNRGS(0.996)GGGGGGGGQGS(0.003)T(0.001)NYGK ; 66.308 0.0030309 5452500 2373.6 2717.3 2566.5 2619 2495.5 3471.8 3747.2 1826.38 2901.4 2558.2 TRUE FALSE FALSE 2344.66965 2755.554221 2611.168856 2921.821103 2368.145323 3249.963185 4065.487074 1879.223424 2641.891517 2491.737595 0.940977756 1.105876568 1.047930914 1.172603852 0.950399162 1.304295922 1.631587163 0.754181912 1.060260728 1 11.28293643 -9.090816294 0.834682609 0.975998273 1.23408109 0.074294751 0.217509716 0.755633016 1.022039407 0.037645349 0.09978193 8.11E-10 9.090816294 0.258082818 GNS(ph)RPGT(ph)PSAEGGSTSSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 0 GNS(0.999)RPGT(0.924)PS(0.071)AEGGS(0.001)T(0.001)S(0.001)S(0.001)T(0.001)LR 70.704 0.0081908 78670000 2870.5 2986.5 2930.5 1646.2 3260.8 3529.2 3238.2 3261.5 3251.4 3302.5 TRUE FALSE FALSE 2835.513242 3028.544025 2981.504123 1836.54139 3094.389208 3303.69551 3513.252627 3355.866357 2960.586641 3216.700574 0.881497415 0.941506353 0.926882703 0.570939491 0.961976142 1.027044773 1.092191376 1.043263518 0.920379927 1 11.65136593 -8.274332913 3.984871366 0.912999888 1.061362889 0.30034703 0.113940391 0.254602342 9.441776097 0.017561 0.043922643 5.32E-09 8.274332913 0.148363001 GNS(ph)RPGTPS(ph)AEGGSTSSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 2 0 GNS(0.769)RPGT(0.288)PS(0.684)AEGGS(0.112)T(0.026)S(0.089)S(0.015)T(0.017)LR 91.64 0.022791 34643000 2581.3 2636 2759.5 1646.8 2599.9 3217.3 2409.7 2692.4 2695.4 2624.4 TRUE FALSE FALSE 2549.838123 2673.109677 2807.52794 1837.210764 2467.217401 3011.724913 2614.379858 2770.300346 2454.316673 2556.21771 0.997504287 1.045728487 1.098313312 0.718722336 0.965182814 1.178195778 1.022753206 1.083749767 0.96013601 1 11.319795 -8.291192088 24.40059319 0.986570806 1.087684991 0.232983681 0.100801184 651.0307734 533917.3122 0.014152377 0.031650771 5.11E-09 8.291192088 0.101114185 GNS(ph)RPGTPSAEGGSTSSTLR ddPTM_HeLa_Romidepsin_16h_R1 3 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 GNS(0.796)RPGT(0.151)PS(0.039)AEGGS(0.005)T(0.005)S(0.002)S(0.001)T(0.001)LR;GNS(0.999)RPGT(0.001)PSAEGGSTSSTLR;GNS(0.999)RPGT(0.001)PSAEGGSTSSTLR ;; 120.79 0.00027755 30094300 1765.75 2124.21 2094.33 1567.9 2120.61 2323.63 2635.83 2333.93 2486.51 2562.94 TRUE FALSE FALSE 1744.22836 2154.114684 2130.780935 1749.187975 2012.387359 2175.157542 2859.717334 2401.458582 2264.110318 2496.354449 0.698710217 0.862904178 0.853557048 0.700696961 0.806130459 0.871333613 1.145557409 0.961986221 0.906966684 1 11.28560708 -7.868831391 6.463345706 0.839769226 1.052033914 0.460663506 0.094020503 0.176232701 9.35837338 0.017302027 0.053092784 1.35E-08 7.868831391 0.212264688 GNSPNS(ph)EPPTPK ddPTM_HeLa_Romidepsin_16h_R1 2 GNSPNSEPPTPK 12 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 GNS(0.139)PNS(0.839)EPPT(0.022)PK;GNS(0.045)PNS(0.738)EPPT(0.217)PK ; 149.82 0.0014604 14581400 5684.8 5889.5 5340.6 6316.3 5504.3 5781.7 5344.4 4944.5 5804.3 6035.5 TRUE FALSE FALSE 5615.511471 5972.412536 5433.550903 7046.620325 5223.395032 5412.26803 5798.353203 5087.561306 5285.148871 5878.69684 0.955230661 1.015941577 0.924278127 1.198670474 0.888529409 0.920657788 0.986333087 0.865423315 0.899034091 1 12.52128067 -5.917286622 0.82979642 0.986387912 4.90E-18 0.126706567 0.084988327 25.72577127 2.248393996 0.011888676 38.55761082 1.21E-06 5.917286622 -0.986387912 GNSRPGTPS(ph)AEGGSTSSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 GNSRPGTPSAEGGSTSSTLR 20 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 GNS(0.009)RPGT(0.14)PS(0.847)AEGGS(0.001)T(0.001)SSTLR 66.609 0.0040483 72203000 1207.8 1248.4 1335 1111.5 1286.7 1052.2 940.59 1075.1 1522.8 1405.5 TRUE FALSE FALSE 1193.078869 1265.975008 1358.235115 1240.01686 1221.034898 984.9678158 1020.483691 1106.206322 1386.596954 1368.984907 0.871506225 0.92475454 0.992147618 0.905792937 0.891927216 0.71948771 0.745430929 0.808048589 1.012865041 1 10.41889083 -8.421823126 3.372381548 0.938352585 0.756738214 0.764335101 0.047575674 0.107561317 2.286758196 0.008010445 0.018991736 3.79E-09 8.421823126 -0.181614371 GNVFS(ph)SPT(ph)AAGTPNKETAGLK ddPTM_HeLa_Romidepsin_16h_R1 1 GNVFSSPTAAGTPNKETAGLK 21 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 2 0 GNVFS(0.745)S(0.258)PT(0.966)AAGT(0.03)PNKET(0.001)AGLK 96.562 0.0006232 315940000 3860 3782.7 4744.7 4187 5869.6 6904.2 6113.3 6537.3 4563 4076.2 TRUE FALSE FALSE 3812.952835 3835.95295 4827.279513 4671.12064 5570.05241 6463.043902 6632.563549 6726.446461 4154.873852 3970.299736 0.960369012 0.966162054 1.215847627 1.176515868 1.40292995 1.627847853 1.670544793 1.694191096 1.046488711 1 11.95503221 -8.686064646 0.882878379 0.978597145 1.734431183 0.961548654 0.055754699 0.073080163 0.104356054 0.008925491 0.0330819 2.06E-09 8.686064646 0.755834038 GNVFS(ph)SPTAAGTPNK ddPTM_HeLa_Romidepsin_16h_R1 3 GNVFSSPTAAGTPNK 15 0 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 1 0 GNVFS(0.49)S(0.49)PT(0.02)AAGTPNK;GNVFS(0.46)S(0.26)PT(0.26)AAGT(0.019)PNK;GNVFS(0.444)S(0.444)PT(0.111)AAGT(0.001)PNK ;; 187.08 1.18E-09 53791000 8468.9 8095.3 9196.3 7210.8 13976.6 17540.8 16056.6 16527.7 9689.7 10577.4 TRUE FALSE FALSE 8365.677789 8209.265846 9356.357744 8044.546624 13263.32195 16419.99949 17420.4472 17005.90292 8823.028964 10302.59762 0.811996944 0.796815148 0.908155213 0.780827022 1.287376488 1.593772764 1.69087912 1.65064225 0.856388776 1 13.33072051 -8.483234572 2.559556058 0.891122511 1.656994173 0.957929131 0.07395281 0.050018866 0.646846462 0.013785803 0.033526998 3.29E-09 8.483234572 0.765871662 GNVFSS(ph)PTAAGT(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 1 GNVFSSPTAAGTPNK 15 0 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 2 0 GNVFS(0.395)S(0.466)PT(0.273)AAGT(0.867)PNK 107.63 0.021551 4364400 1300 1005 1567.6 990.36 1761.8 2247.9 1866.3 1745.9 1190.9 1253.6 TRUE FALSE FALSE 1284.1551 1019.148416 1594.88342 1104.870083 1671.888772 2104.266445 2024.823475 1796.414862 1084.382921 1221.031291 1.051697126 0.834661997 1.306177353 0.904866313 1.369243183 1.723351776 1.658289587 1.471227539 0.888087741 1 10.25388446 -8.559694626 3.948342942 1.025785303 1.616405462 0.807032835 0.13702141 0.060317923 2.0337509 0.017308509 0.037050208 2.76E-09 8.559694626 0.590620159 GNVFSS(ph)PTAAGTPNKETAGLK ddPTM_HeLa_Romidepsin_16h_R1 1 GNVFSSPTAAGTPNKETAGLK 21 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 1 0 GNVFS(0.063)S(0.931)PT(0.006)AAGTPNKETAGLK 94.313 0.00030806 77849000 2226.7 2067.8 2059.1 2665.7 3335.7 3624.2 3753.5 4245.2 2471.8 2259.5 TRUE FALSE FALSE 2199.560124 2096.910543 2094.937772 2973.920776 3165.466782 3392.625317 4072.322196 4368.028164 2250.716017 2200.797864 0.999437595 0.95279561 0.951899221 1.351292104 1.438326906 1.541543352 1.850384473 1.984747548 1.022681844 1 11.10381093 -8.22345009 0.744712633 0.98517085 2.080714478 0.95646914 0.076659755 0.147255744 0.115660147 0.013797175 0.103067296 5.98E-09 8.22345009 1.095543628 GNVFSSPT(ph)AAGT(ph)PNKETAGLK ddPTM_HeLa_Romidepsin_16h_R1 1 GNVFSSPTAAGTPNKETAGLK 21 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 2 0 GNVFS(0.482)S(0.202)PT(0.579)AAGT(0.731)PNKET(0.006)AGLK 71.427 0.0052965 164430000 2932.9 2596.5 2627.4 2546.9 4177.2 4317.7 3783.3 3679.6 2783.5 2636.6 TRUE FALSE FALSE 2897.152687 2633.053595 2673.128795 2841.384562 3964.021897 4041.812905 4104.653408 3786.063421 2534.536789 2568.100752 1.128130462 1.025292171 1.040897166 1.106414754 1.543561674 1.573852935 1.598322575 1.474265921 0.986930434 1 11.32648609 -8.77831422 4.841424648 1.058387295 1.556686057 0.961707764 0.048882841 0.028230903 1.688589681 0.008189001 0.015722548 1.67E-09 8.77831422 0.498298762 GNVFSSPT(ph)AAGTPNKETAGLK ddPTM_HeLa_Romidepsin_16h_R1 1 GNVFSSPTAAGTPNKETAGLK 21 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4 E7EX44;E9PGZ1 CALD1 Caldesmon 1 0 GNVFS(0.006)S(0.024)PT(0.968)AAGT(0.002)PNKETAGLK 101.61 0.00023338 73887000 1940.5 1860.6 1718.4 2247.9 2767.8 3631.9 3674.1 3045.5 1906.9 1824.2 TRUE FALSE FALSE 1916.84844 1886.793576 1748.308031 2507.812775 2626.548838 3399.833311 3986.177962 3133.616737 1736.342088 1776.807021 1.078816336 1.061901238 0.98396056 1.41141539 1.478240916 1.913451079 2.243450141 1.763622442 0.977226039 1 10.79507128 -8.605929235 1.288479755 1.035906169 2.036474756 0.900470441 0.135402035 0.086101741 0.278748956 0.019546873 0.059087969 2.48E-09 8.605929235 1.000568587 GNVGVVLFNFGK ddPTM_HeLa_Romidepsin_16h_R1 2 GNVGVVLFNFGK 12 0 P33316;H0YKI0;A0A0C4DGL3;H0YMP1;H0YKC5;H0YNW5;H0YMM5;P33316-2;H0YNJ9 P33316;H0YNW5;P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 0 ; ; 126.31 6.68E-09 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 GNVVPS(ph)PLPTR ddPTM_HeLa_Romidepsin_16h_R1 2 GNVVPSPLPTR 11 0 H3BTK3;I3L3X8;H3BSW7;H3BUY4;H3BPY5;H3BNU9;Q9Y2V2 H3BTK3 CARHSP1 Calcium-regulated heat stable protein 1 1 0 GNVVPS(0.978)PLPT(0.022)R;GNVVPS(0.972)PLPT(0.028)R ; 103.13 0.017731 762978500 6316.2 5634.1 6841.4 3809 6505.3 7704.6 6913.7 6804.6 6327.5 7469.3 TRUE FALSE FALSE 6239.215725 5713.417008 6960.471697 4249.414502 6173.310266 7212.300925 7500.949505 7001.480365 5761.552552 7275.246509 0.857595096 0.785322807 0.956733451 0.584092167 0.848536233 0.991347979 1.031023416 0.96237019 0.791939152 1 12.82878042 -8.212805999 8.999086707 0.89014664 0.998827669 0.190605665 0.116624691 0.732478153 129.7665996 0.017899403 0.045656293 6.13E-09 8.212805999 0.108681029 GNVVPS(ph)PLPTRR ddPTM_HeLa_Romidepsin_16h_R1 3 GNVVPSPLPTRR 12 1 H3BTK3;I3L3X8;H3BSW7;H3BUY4;H3BPY5;H3BNU9;Q9Y2V2 H3BTK3 CARHSP1 Calcium-regulated heat stable protein 1 1 0 GNVVPS(0.987)PLPT(0.013)RR;GNVVPS(0.883)PLPT(0.117)RR;GNVVPS(1)PLPTRR ;; 118.73 0.011417 733545000 31906 29623.2 27099.5 24835.4 31220.3 35749.5 31415.7 35115.4 29740.6 27690 TRUE FALSE FALSE 31517.1174 30040.23619 27571.15543 27706.9858 29627.01159 33465.22233 34084.14877 36131.4087 27080.52625 26970.60981 1.168572666 1.113813755 1.022266668 1.027302905 1.098492463 1.240803325 1.263751506 1.339658575 1.004075415 1 14.71910052 -8.142122227 2.215517366 1.075438195 1.303215032 0.781107475 0.053698184 0.150134703 1.414436455 0.010200793 0.033869622 7.21E-09 8.142122227 0.227776836 GNVVPSPLPT(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 GNVVPSPLPTRR 12 1 H3BTK3;I3L3X8;H3BSW7;H3BUY4;H3BPY5;H3BNU9;Q9Y2V2 H3BTK3 CARHSP1 Calcium-regulated heat stable protein 1 1 0 GNVVPS(0.165)PLPT(0.835)RR 134.06 0.0012054 416210000 3908.8 3693.7 3062 2977.5 4347.1 5307.3 4198.1 4803.2 4446.3 3482.9 TRUE FALSE FALSE 3861.158042 3745.700006 3115.292826 3321.77256 4125.251266 4968.180659 4554.686509 4942.173014 4048.611792 3392.413756 1.138174268 1.104140083 0.918311577 0.979176716 1.216022444 1.464497262 1.342609374 1.456830849 1.193431015 1 11.72809642 -8.491124432 3.73293849 1.05281558 1.410532643 0.799509222 0.081854924 0.0732717 2.155776554 0.011816792 0.026714648 3.23E-09 8.491124432 0.357717062 GNYPGPSS(ph)PVVVR ddPTM_HeLa_Romidepsin_16h_R1 1 GNYPGPSSPVVVR 13 0 H3BV44;H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BP49;H3BU05 H3BV44 MYO9A Unconventional myosin-IXa 1 0 GNYPGPS(0.069)S(0.931)PVVVR 124.81 0.0037982 6802600 1424.8 1611.5 1398.6 1492.8 1809.7 1763.2 1626.1 1778.7 1721.4 1375.4 TRUE FALSE FALSE 1407.43399 1634.186739 1422.942046 1665.40456 1717.344256 1650.53721 1764.220893 1830.163878 1567.433673 1339.66691 1.050585022 1.219845566 1.062161076 1.243148239 1.281918844 1.232050444 1.316910107 1.366133525 1.170017458 1 10.38765862 -9.069929478 0.378031678 0.992961123 1.401513083 0.585567217 0.074286551 0.461266823 0.115325334 0.02048337 0.074426517 8.51E-10 9.069929478 0.40855196 GPAADPS(ph)SPGTSGVGPAAGAGDSR ddPTM_HeLa_Romidepsin_16h_R1 1 GPAADPSSPGTSGVGPAAGAGDSR 24 0 A0A0U1RRM4 A0A0U1RRM4 1 0 GPAADPS(0.976)S(0.024)PGTSGVGPAAGAGDSR 150.12 1.76E-07 15394000 3049.9 2851 2711.9 2871.1 2982.2 2898.2 2384.7 2454.6 3371.9 3142.2 TRUE FALSE FALSE 3012.726646 2891.136453 2759.099482 3203.070091 2830.007206 2713.014374 2587.256358 2525.619978 3070.308819 3060.565191 0.984369375 0.944641356 0.901499988 1.046561629 0.924668167 0.886442276 0.845352475 0.825213587 1.003183604 1 11.57958238 -5.614430754 0.340251136 0.996584234 0.262227197 0.681742648 0.038886047 7.232796044 0.24603779 0.012041968 2.775631577 2.43E-06 5.614430754 -0.734357037 GPAADPSS(ph)PGTSGVGPAAGAGDSR ddPTM_HeLa_Romidepsin_16h_R1 3 GPAADPSSPGTSGVGPAAGAGDSR 24 0 A0A0U1RRM4 A0A0U1RRM4 1 0 GPAADPS(0.041)S(0.948)PGT(0.009)S(0.003)GVGPAAGAGDSR;GPAADPS(0.073)S(0.899)PGT(0.01)S(0.018)GVGPAAGAGDSR;GPAADPS(0.044)S(0.939)PGT(0.013)S(0.004)GVGPAAGAGDSR ;; 164.89 4.88E-11 24753100 10927.5 10739.3 10043.7 9829.2 10084.1 9777.4 8201.9 9271.5 11914.4 10877.1 TRUE FALSE FALSE 10794.31143 10890.48815 10218.50639 10965.69835 9569.470748 9152.655695 8898.569181 9539.756224 10848.74622 10594.51137 1.018858827 1.027936803 0.964509454 1.035035781 0.903247956 0.86390541 0.839922566 0.900443247 1.023996845 1 13.37102943 -8.637320581 4.248338014 1.008568565 0.867625988 0.889195112 0.023490035 0.0461956 1.487787112 0.003183697 0.006554023 2.31E-09 8.637320581 -0.140942577 GPAFNMAS(ph)PESDFGINLK ddPTM_HeLa_Romidepsin_16h_R1 2 GPAFNMASPESDFGINLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GPAFNMAS(0.954)PES(0.046)DFGINLK;GPAFNMAS(0.801)PES(0.199)DFGINLK ; 89.356 0.009331 307780000 9034.6 9156.3 10317.8 8223 13232.3 15953.1 14249.2 15081.5 9961.8 9442.8 TRUE FALSE FALSE 8924.48282 9285.202632 10497.37698 9173.78195 12557.00635 14933.7484 15459.52669 15517.85941 9070.791658 9197.474695 0.970318823 1.009538263 1.141332521 0.997423995 1.365266747 1.623679205 1.680844711 1.687186964 0.986226324 1 13.16702209 -8.515603148 1.760042021 0.996253131 1.690034632 0.969395704 0.051696707 0.039743437 0.24222867 0.007794981 0.021253502 3.05E-09 8.515603148 0.693781501 GPAGEAGAS(ph)PPVR ddPTM_HeLa_Romidepsin_16h_R1 2 GPAGEAGASPPVR 13 0 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 0 GPAGEAGAS(1)PPVR;GPAGEAGAS(1)PPVR ; 123.95 0.0040073 113038000 4594.1 4314.2 4368.8 3239 4650.8 5651.7 4429.2 4640.6 4149.9 4454.7 TRUE FALSE FALSE 4538.105342 4374.935421 4444.837131 3613.50842 4413.452321 5290.57461 4805.416137 4774.868439 3778.72255 4338.966252 1.045895515 1.008289802 1.024400024 0.832803993 1.017166778 1.219316838 1.107502538 1.100462221 0.870880835 1 12.08313565 -8.36125445 7.992378177 1.006266268 1.138605525 0.471546286 0.077036154 0.196947681 14.08855975 0.009461626 0.021218703 4.35E-09 8.36125445 0.132339258 GPAGEAGAS(ph)PPVRR ddPTM_HeLa_Romidepsin_16h_R1 3 GPAGEAGASPPVRR 14 1 Q13425;Q13425-2;A0A140TA73 Q13425 SNTB2 Beta-2-syntrophin 1 0 GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR;GPAGEAGAS(1)PPVRR ;; 80.508 0.010398 276409000 5442.8 5988.2 5288 5539.6 6148.6 6416.8 5031.3 5704.4 5698.5 5449.8 TRUE FALSE FALSE 5376.46106 6072.502037 5380.035422 6180.114617 5834.813998 6006.787189 5458.658496 5869.447814 5188.811888 5308.21341 1.012856991 1.143982272 1.013530355 1.164255115 1.099204864 1.131602429 1.028341944 1.105729435 0.977506269 1 12.37401066 -10.35506599 7.193997061 1.005747584 1.09594207 0.508705333 0.045356645 0.156480886 10.51294845 0.007000471 0.007985475 4.42E-11 10.35506599 0.090194486 GPAS(ph)DSETEDASR ddPTM_HeLa_Romidepsin_16h_R1 2 GPASDSETEDASR 13 0 Q96ST2-3;Q96ST2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 GPAS(0.62)DS(0.19)ET(0.19)EDASR;GPAS(0.97)DS(0.029)ET(0.001)EDASR ; 195.71 3.20E-11 19231800 3624.4 2547.4 3310.8 2334.4 3000.2 3165.6 3222.1 3152.5 3721.8 3342.1 TRUE FALSE FALSE 3580.224419 2583.262364 3368.423085 2604.314312 2847.088599 2963.328377 3495.785094 3243.712614 3388.912887 3255.27176 1.099823512 0.793562736 1.03475941 0.800029768 0.874608576 0.91031674 1.073884256 0.996449099 1.041053754 1 11.66856227 -10.29125888 24.98916428 1.047138881 0.928631909 0.276385048 0.089460279 686.0677033 574932.1665 0.015783721 0.018050642 5.11E-11 10.29125888 -0.118506972 GPAS(ph)TPTYS(ph)PAPTQPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0;Q6P1N0-2;K7EJY5 Q6P1N0 CC2D1A Coiled-coil and C2 domain-containing protein 1A 2 0 GPAS(0.766)T(0.234)PT(0.311)YS(0.678)PAPT(0.01)QPAPR 144.15 0.0010098 3397600 804.91 794.69 1049.5 753.36 1386.6 1838.5 1565.5 1617.5 831.45 1038.4 TRUE FALSE FALSE 795.0994473 805.8776667 1067.766107 840.4670279 1315.836628 1721.025783 1698.473531 1664.299811 757.0830296 1011.422218 0.786120211 0.796776709 1.055707585 0.830975445 1.300976589 1.701589853 1.679292288 1.645504499 0.748533121 1 9.982169661 -8.521140807 2.730650295 0.896287534 1.676631168 0.932979409 0.097004671 0.051538907 0.770978987 0.015258303 0.035708516 3.01E-09 8.521140807 0.780343634 GPAS(ph)TPTYSPAPTQPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0;Q6P1N0-2;K7EJY5 Q6P1N0 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 0 GPAS(0.327)T(0.327)PT(0.173)YS(0.173)PAPTQPAPR 290.63 7.21E-124 20050000 1198.4 1273 1263.1 1513.8 1500.4 1605.1 1504 1578.8 1225.6 968.46 TRUE FALSE FALSE 1183.79344 1290.921327 1285.083726 1688.832679 1423.828989 1502.53929 1631.749722 1624.480087 1115.979266 943.2992696 1.254950023 1.368517255 1.362328761 1.790346641 1.509413857 1.592855352 1.729832488 1.722125882 1.18305961 1 9.88157174 -9.989729063 0.387528231 0.995561755 1.770291827 0.818364816 0.105969058 0.260023692 0.100663461 0.050395402 0.075523396 1.02E-10 9.989729063 0.774730073 GPASPT(ph)RPAAPRPAEAPLLDL ddPTM_HeLa_Romidepsin_16h_R1 1 GPASPTRPAAPRPAEAPLLDL 21 2 A0A0D9SFE4 A0A0D9SFE4 DNM1 1 0 GPAS(0.096)PT(0.904)RPAAPRPAEAPLLDL 72.676 0.025328 13602000 1704.9 1380.4 1358.7 2255.9 1565.9 1425.2 1422.9 1627.9 1705.2 1285.7 TRUE FALSE FALSE 1684.120023 1399.833307 1382.347604 2516.737772 1485.98628 1334.13432 1543.76109 1675.000718 1552.682641 1252.297329 1.344824415 1.11781226 1.103849359 2.009696671 1.186608201 1.065349489 1.232743259 1.337542355 1.239867407 1 10.29036142 -12.40145772 0.683813837 0.954726556 1.304922734 0.035872852 0.265608925 1.58704685 1.045135554 0.34127921 0.053645288 3.97E-13 12.40145772 0.350196178 GPASQFYITPSTSLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GPASQFYITPSTSLSPR 17 0 H0YIQ2;P49750-3;P49750-1;P49750 H0YIQ2 YLPM1 YLP motif-containing protein 1 1 0 GPASQFYITPSTS(0.002)LS(0.998)PR;GPASQFYITPSTS(0.001)LS(0.999)PR ; 161.75 2.57E-05 120503000 3727.5 3783.8 3284 3396.6 4663.2 4699.4 4179.3 4745.1 3544.3 3172 TRUE FALSE FALSE 3682.067796 3837.068436 3341.156642 3789.330873 4425.219503 4399.123507 4534.289638 4882.391982 3227.288931 3089.590983 1.191765453 1.241934113 1.081423613 1.226483018 1.432299462 1.423853038 1.467601913 1.580271308 1.044568342 1 11.59320014 -4 0.16643959 0.968655397 3.472510315 0.884155036 0.063984034 15.01336663 0.155682245 0.112955525 9.356464403 1.00E-04 4 2.503854918 GPASTPT(ph)YSPAPTQPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0;Q6P1N0-2;K7EJY5 Q6P1N0 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 0 GPAS(0.007)T(0.001)PT(0.727)YS(0.265)PAPT(0.001)QPAPR 206.13 7.60E-21 5125000 305.8 579.93 550.01 628.97 688.62 578.78 601.52 544.66 450.02 489.67 TRUE FALSE FALSE 302.072792 588.0942698 559.5826933 701.6944708 653.4771518 541.7978259 652.6130938 560.4188778 409.7690841 476.9483028 0.633344935 1.233035669 1.173256493 1.471217041 1.370121558 1.135967615 1.368309919 1.175009691 0.859147798 1 8.897689088 -10.1627575 6.126701264 0.827357737 1.284312373 0.715495062 0.1285602 0.111234929 5.809209284 0.027264344 0.033465713 6.87E-11 10.1627575 0.456954637 GPASTPTYS(ph)PAPTQPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPASTPTYSPAPTQPAPR 18 0 Q6P1N0;Q6P1N0-2;K7EJY5 Q6P1N0 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 0 GPASTPT(0.139)YS(0.861)PAPTQPAPR 278.88 4.35E-106 15146000 1263.2 1390.5 1236.8 1460.5 2147.7 2296 1727.8 1725 1351.4 1089.3 TRUE FALSE FALSE 1247.803633 1410.075495 1258.325985 1629.369882 2038.094855 2149.29301 1874.559289 1774.910153 1230.527399 1060.999829 1.176063934 1.329006336 1.185981327 1.535692879 1.920919117 2.025724181 1.766785665 1.672865636 1.159780959 1 10.05120871 -9.145882999 1.778112019 1.102981734 1.858045949 0.86734771 0.123471388 0.090708825 0.561802993 0.022236611 0.041821664 7.15E-10 9.145882999 0.755064215 GPDEAMEDGEEGS(ph)DDEAEWVVTK ddPTM_HeLa_Romidepsin_16h_R1 4 GPDEAMEDGEEGSDDEAEWVVTK 23 0 Q9NZN4-2;Q9NZN4 Q9NZN4-2 EHD2 EH domain-containing protein 2 1 0 GPDEAMEDGEEGS(0.996)DDEAEWVVT(0.004)K;GPDEAMEDGEEGS(0.988)DDEAEWVVT(0.012)K;GPDEAMEDGEEGS(1)DDEAEWVVTK;GPDEAMEDGEEGS(0.907)DDEAEWVVT(0.093)K ;;; 84.573 8.97E-05 377421000 14190.5 15630.7 17151 13459.4 15148.8 15392.9 12078.2 14765.4 15868.5 16090.1 TRUE FALSE FALSE 14017.54073 15850.7494 17449.50596 15015.63916 14375.70021 14409.34337 13104.12201 15192.61355 14449.18162 15672.07688 0.894427767 1.011400692 1.113413754 0.958114184 0.917281118 0.919427813 0.836144571 0.969406523 0.921969802 1 13.93590876 -8.726518223 4.022715993 0.968346949 0.904228518 0.218778233 0.063789165 0.332276367 11.54029579 0.01063545 0.021394343 1.88E-09 8.726518223 -0.064118431 GPDGPWGVGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GPDGPWGVGTPR 12 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 GPDGPWGVGT(1)PR 118.61 0.016407 7335900 1900 1775.8 1885.5 1741.4 1864.9 1399 967.6 1484.9 1582.6 1767.7 TRUE FALSE FALSE 1876.842069 1800.799759 1918.316337 1942.748862 1769.727194 1309.608415 1049.78792 1527.863239 1441.048292 1721.774899 1.090062394 1.045897324 1.114150484 1.128340797 1.027850502 0.760615349 0.60971264 0.88737688 0.836955105 1 10.74968083 -8.263310549 4.61003709 1.055808964 0.734217118 0.621552179 0.100047449 0.061399709 3.617765572 0.010299883 0.025508158 5.45E-09 8.263310549 -0.321591845 GPEEEEIGSPEPMAAPAS(ph)ASQKLSPLQK ddPTM_HeLa_Romidepsin_16h_R1 1 GPEEEEIGSPEPMAAPASASQKLSPLQK 28 1 H3BRB3;Q14807-2;Q14807 H3BRB3 KIF22 Kinesin-like protein;Kinesin-like protein KIF22 1 0 GPEEEEIGS(0.008)PEPMAAPAS(0.358)AS(0.358)QKLS(0.277)PLQK 62.945 0.0014941 7014700 1796.7 1380.8 1641.2 1878.1 1494.8 1671.9 1120.3 1034.4 2063.2 1486 TRUE FALSE FALSE 1774.801129 1400.238939 1669.764398 2095.254759 1418.514778 1565.070986 1215.458254 1064.328732 1878.662225 1447.393506 1.226204983 0.967421046 1.153635408 1.447605472 0.98004777 1.081303032 0.839756603 0.735341652 1.297962314 1 10.49924149 -7.67270397 1.837730974 1.120705745 0.716256627 0.497208945 0.144365084 0.295985364 1.683117558 0.020636726 0.156027177 2.12E-08 7.67270397 -0.404449118 GPEENYSRPEAPNEFYDGDHDNDKES(ph)DVEI ddPTM_HeLa_Romidepsin_16h_R1 2 GPEENYSRPEAPNEFYDGDHDNDKESDVEI 30 2 O15379;O15379-2 O15379 HDAC3 Histone deacetylase 3 1 0 GPEENYSRPEAPNEFY(0.003)DGDHDNDKES(0.997)DVEI;GPEENYSRPEAPNEFY(0.003)DGDHDNDKES(0.997)DVEI ; 57.145 0.00069446 29319000 3940.9 3551.8 4015.4 3027.4 4383.4 5535.2 4652.8 5573.5 3835 4120.2 TRUE FALSE FALSE 3892.866795 3601.802334 4085.286353 3377.442232 4159.698741 5181.518584 5048.008716 5734.760429 3491.987995 4013.15661 0.970026135 0.897498574 1.017973319 0.841592432 1.036515428 1.291132913 1.25786487 1.428989941 0.870134992 1 11.97052174 -8.27506139 3.143034245 0.970621996 1.330587562 0.856420342 0.071180641 0.062394823 1.260382538 0.008814636 0.023181268 5.31E-09 8.27506139 0.359965566 GPELPLVPVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GPELPLVPVKR 11 1 Q96DI7;Q96DI7-2 Q96DI7 SNRNP40 U5 small nuclear ribonucleoprotein 40 kDa protein 0 1 ; GPELPLVPVK(1)R;GPELPLVPVK(1)R 119.68 0.0041817 3105800 1719.65 1823.09 1606.47 2277.3 1598.43 1499.85 1642.45 1300.72 2120.9 1730.14 FALSE TRUE FALSE 1698.690244 1848.755509 1634.429936 2540.612141 1516.856153 1404.014426 1781.959662 1338.354281 1931.201392 1685.190713 1.008010684 1.09706011 0.969878319 1.50761105 0.900109489 0.833148684 1.057423144 0.794185649 1.14598388 1 10.71869616 -7.256403331 23.69770481 1.025794874 0.794185444 0.146919178 0.175979828 390.3202094 1836563.012 0.022545663 0.246823179 5.54E-08 7.256403331 -0.23160943 GPETEGEDAS(ph)PSALVVGPPETK ddPTM_HeLa_Romidepsin_16h_R1 1 GPETEGEDASPSALVVGPPETK 22 0 A0A1B0GTL5 A0A1B0GTL5 1 0 GPET(0.006)EGEDAS(0.989)PS(0.004)ALVVGPPETK 95.519 0.0001699 6190500 1986 1760.1 1862.6 1391.4 1978.6 2217.1 1715 2126.2 2062.7 2142.7 TRUE FALSE FALSE 1961.793868 1784.878734 1895.017772 1552.280215 1877.624659 2075.434465 1860.672057 2187.718242 1878.206946 2087.032345 0.939992077 0.855223321 0.90799636 0.743773913 0.899662462 0.994442885 0.891539636 1.048243573 0.899941465 1 11.02723724 -11.080989 1.172534227 0.986941878 0.903632737 0 0.081195964 0.525882231 1.50532451 0.02016858 0.016000027 8.30E-12 11.080989 -0.083309141 GPGDLMGPQGLS(ph)PEEMAR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGDLMGPQGLSPEEMAR 18 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 GPGDLMGPQGLS(1)PEEMAR 74.993 0.013756 26288000 2046.4 1745.4 1794.7 1505.2 1549.7 1283 1336.3 1471.9 2020 1753.4 TRUE FALSE FALSE 2021.45769 1769.971787 1825.936001 1679.238306 1470.613026 1201.020441 1449.805289 1514.487104 1839.326141 1707.846415 1.18362967 1.036376439 1.069145319 0.983249015 0.861092082 0.703236796 0.848908471 0.886781792 1.076985685 1 10.73796253 -8.897305039 2.130251775 1.083523372 0.811935122 0.780473836 0.062290776 0.130984876 1.204442016 0.012529099 0.025488855 1.27E-09 8.897305039 -0.27158825 GPGGS(ph)QGSQGPSPQGAR ddPTM_HeLa_Romidepsin_16h_R1 2 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 0 GPGGS(0.663)QGS(0.322)QGPS(0.015)PQGAR;GPGGS(0.966)QGS(0.024)QGPS(0.01)PQGAR ; 89.913 0.0093112 1545860 490.82 543.04 356.32 247.88 355.14 423.94 414.3 375.67 643.4 558.04 TRUE FALSE FALSE 484.8376971 550.6849314 362.5216001 276.5410519 337.0158806 396.8516022 449.4906317 386.5394187 585.8526926 543.5420404 0.891996683 1.013141377 0.666961473 0.508775829 0.620036456 0.730121265 0.826965714 0.711149074 1.077842465 1 9.086247815 -9.75488862 24.99868818 0.952384114 0.676269447 0.738547593 0.091364141 68.18131064 260189.254 0.014879496 0.02076015 1.76E-10 9.75488862 -0.276114667 GPGGSQGSQGPS(ph)PQGAR ddPTM_HeLa_Romidepsin_16h_R1 4 GPGGSQGSQGPSPQGAR 17 0 Q96MG7 Q96MG7 NDNL2 Melanoma-associated antigen G1 1 0 GPGGSQGS(0.001)QGPS(0.999)PQGAR;GPGGSQGS(0.007)QGPS(0.993)PQGAR;GPGGSQGSQGPS(1)PQGAR;GPGGSQGS(0.007)QGPS(0.993)PQGAR ;;; 184.2 2.53E-09 53765000 2559.36 2607.02 2632.35 2755.664 3363.07 2961.38 2771.12 2373.523 2668.41 2687.28 TRUE FALSE FALSE 2528.165536 2643.721696 2678.164948 3074.286837 3191.439989 2772.157375 3006.498864 2442.197143 2429.740726 2617.464078 0.965883565 1.010031701 1.023190717 1.17452876 1.219287025 1.059100447 1.14863042 0.933039412 0.928280448 1 11.35395402 -9.462136051 4.627132722 0.986391494 1.112690725 0.402394768 0.075037123 0.161584298 6.998819017 0.010932999 0.016662142 3.45E-10 9.462136051 0.126299231 GPGLAVQSGDK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 GPGLAVQSGDKTK 13 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 1 ; GPGLAVQSGDK(1)TK;GPGLAVQSGDK(1)TK 118.87 0.0087297 1433460 756.89 947.28 901.67 670.02 685.58 1090 855.46 865.84 916.98 751.16 FALSE TRUE FALSE 747.6647336 960.6158327 917.3631881 747.4908649 650.5922943 1020.352518 928.122751 890.8917143 834.9630122 731.6447549 1.021895843 1.312953898 1.253836896 1.021658202 0.889218832 1.394601015 1.268542889 1.217656121 1.141213692 1 9.514999518 -4 0.118140866 0.905302592 2.078949995 0.050737279 0.150691114 95.55869804 0.779259128 0.703897629 18.49808305 1.00E-04 4 1.173647403 GPGLLES(ph)PSIFNFTADR ddPTM_HeLa_Romidepsin_16h_R1 2 GPGLLESPSIFNFTADR 17 0 Q92615 Q92615 LARP4B La-related protein 4B 1 0 GPGLLES(0.651)PS(0.29)IFNFT(0.06)ADR;GPGLLES(0.843)PS(0.157)IFNFTADR ; 181.51 4.74E-09 68780000 4767.9 4443.2 4611.2 5036.8 6193.3 6898.6 5091.7 5632.6 5187.9 4298.4 TRUE FALSE FALSE 4709.787001 4505.751486 4691.456002 5619.178515 5877.232791 6457.801724 5524.188871 5795.570394 4723.881231 4186.726948 1.124932927 1.076199031 1.120554567 1.342141148 1.403777429 1.542446356 1.319452866 1.38427236 1.128299335 1 12.03160712 -9.246293507 2.173809391 1.061467433 1.41558128 0.86107868 0.062378853 0.08391267 0.774765588 0.010885071 0.018912078 5.67E-10 9.246293507 0.354113847 GPGPGQGS(ph)PGGGPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGPGQGSPGGGPGPR 16 0 H0YDS2;Q8IYL2 H0YDS2 TRMT44 Probable tRNA (uracil-O(2)-)-methyltransferase 1 0 GPGPGQGS(1)PGGGPGPR 133.9 0.0015817 4174500 706.15 711.38 663.04 694.71 712.85 816.04 531.49 836.22 598.21 747.79 TRUE FALSE FALSE 697.5431722 721.3948263 674.5799331 775.0356389 676.4706045 763.8976776 576.6347473 860.4147064 544.7045994 728.362308 0.95768708 0.990434044 0.92615986 1.064079827 0.928755644 1.04878804 0.791686694 1.181300428 0.747848417 1 9.508512456 GPGQPS(ph)SPQRLDR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGQPSSPQRLDR 13 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 0 GPGQPS(0.5)S(0.5)PQRLDR 85.522 0.011023 15739000 2309.5 2037 2146.2 3349 2497 2628.6 1754.4 1942.1 2647.1 2325.7 TRUE FALSE FALSE 2281.350926 2065.676939 2183.553711 3736.227138 2369.568772 2460.640943 1903.418692 1998.291599 2410.336746 2265.277979 1.007095353 0.911886735 0.963923073 1.649345984 1.04603885 1.08624238 0.84025833 0.882139684 1.064035747 1 11.14547238 -7.758148089 24.98058561 1.047700397 0.861198942 0.149942639 0.198493737 134.5793867 1021392.811 0.027928877 0.096489923 1.75E-08 7.758148089 -0.186501455 GPGQPSS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGQPSSPQR 10 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 0 GPGQPSS(1)PQR 119.03 0.012435 25711000 6174.3 6735.1 9598.2 7011 7071.1 7935.9 8972.3 2952.6 8380.4 7403 TRUE FALSE FALSE 6099.045257 6829.916915 9765.252645 7821.644808 6710.235381 7428.821602 9734.406938 3038.028823 7630.836035 7210.668993 0.845836255 0.947196012 1.354278314 1.084732196 0.930598172 1.030254143 1.350000527 0.421324128 1.058270189 1 12.8159174 -9.972828847 24.99408986 0.925585357 1.050442532 0.003836402 0.249657743 513.224773 472102.3885 0.037048367 0.048690514 1.06E-10 9.972828847 0.124857175 GPGQPSS(ph)PQRLDR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGQPSSPQRLDR 13 1 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 0 GPGQPS(0.218)S(0.782)PQRLDR 73.722 0.020342 19118000 1367.4 1905.6 1350.6 2441.4 1803.8 1187.2 1353 1225.4 1450.2 1388.5 TRUE FALSE FALSE 1350.733603 1932.427087 1374.106626 2723.686155 1711.745355 1111.341752 1467.923786 1260.855016 1320.49048 1352.42657 0.9987482 1.428859156 1.016030487 2.013925352 1.265684506 0.82173907 1.085399991 0.932290923 0.976386082 1 10.40133455 -10.31756014 21.74066657 0.999408447 1.226714142 0.103188687 0.312675671 125.673214 48683.94032 0.053970139 0.061716697 4.81E-11 10.31756014 0.227305695 GPGS(ph)RLPY(ph)S(ph)GRPAPAPAAAPGV ddPTM_HeLa_Romidepsin_16h_R1 1 GPGSRLPYSGRPAPAPAAAPGV 22 2 F8WEM1 F8WEM1 RADIL 3 0 GPGS(1)RLPY(1)S(1)GRPAPAPAAAPGV 73.918 0.0022682 9233600 3547.3 3080.6 3099.2 2375.9 3804.5 4274.5 4373 4322.1 3898.1 3492.4 TRUE FALSE FALSE 3504.064143 3123.968768 3153.140276 2650.612737 3610.342168 4001.373245 4744.442511 4447.153144 3549.444173 3401.666945 1.030102065 0.91836409 0.926939741 0.779209952 1.06134499 1.176297771 1.394740458 1.307345257 1.043442592 1 11.73202618 -8.087599697 2.399274184 0.983903042 1.349702712 0.788578444 0.080694563 0.108270286 1.203650635 0.012386551 0.041578371 8.17E-09 8.087599697 0.36579967 GPGSPSVDSSSVTTVPRPS(ph)TPSR ddPTM_HeLa_Romidepsin_16h_R1 1 GPGSPSVDSSSVTTVPRPSTPSR 23 1 Q8N612;E9PJK5;Q8N612-3 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 0 GPGSPS(0.003)VDS(0.01)S(0.003)S(0.003)VT(0.029)T(0.116)VPRPS(0.407)T(0.407)PS(0.023)R 44.953 0.028955 5295400 357.32 305.96 308.84 420.03 473.4 439.45 281.59 497.82 305.5 402.28 TRUE FALSE FALSE 352.9648464 310.2673129 314.2152306 468.5958449 449.2406315 411.3705633 305.5082476 512.2236363 278.1753149 391.8287076 0.900814156 0.79184426 0.801919881 1.195920145 1.146523016 1.049873466 0.77969848 1.307264185 0.709941129 1 8.614079291 -9.259670225 24.98742548 0.926995262 1.07855182 0.3333451 0.157441362 195.8702605 2766448.567 0.021745336 0.034854951 5.50E-10 9.259670225 0.151556558 GPHHLDNSS(ph)PGPGSEAR ddPTM_HeLa_Romidepsin_16h_R1 3 GPHHLDNSSPGPGSEAR 17 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 GPHHLDNS(0.158)S(0.84)PGPGS(0.002)EAR;GPHHLDNS(0.033)S(0.967)PGPGSEAR;GPHHLDNS(0.111)S(0.887)PGPGS(0.001)EAR ;; 162.76 8.38E-06 15705100 7437.2 6837.4 6470.9 5384.2 7712.7 8363.3 6592.7 7109.5 7244.6 6981.6 TRUE FALSE FALSE 7346.552546 6933.657097 6583.5233 6006.746537 7319.092139 7828.912121 7152.683773 7315.202166 6596.624832 6800.217026 1.080340895 1.019622914 0.968134293 0.883316888 1.076302728 1.151273863 1.051831691 1.075730692 0.970060927 1 12.73136507 -8.543960389 24.99766542 1.020134707 1.092993169 0.356706284 0.057749368 266.931172 316513.8426 0.009274762 0.018550871 2.86E-09 8.543960389 0.072858461 GPIAQWADGAIS(ph)PNGHRPQLR ddPTM_HeLa_Romidepsin_16h_R1 1 GPIAQWADGAISPNGHRPQLR 21 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;Q5SRD0;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21D;FAM21A WASH complex subunit FAM21C;Putative WASH complex subunit FAM21;WASH complex subunit FAM21A 1 0 GPIAQWADGAIS(1)PNGHRPQLR 57.432 0.0042102 0 629.02 580.46 546.42 548.52 753.45 595.55 510.04 768.28 701.31 765.25 TRUE FALSE FALSE 621.3532623 588.6317311 555.9302109 611.9424633 714.998635 557.496277 553.3627849 790.5089697 638.5830771 745.3686947 0.833618673 0.78971888 0.745845935 0.820992977 0.959254984 0.747946997 0.74240143 1.060561002 0.856734502 1 9.541810417 -12.01052939 0.835421801 0.998985002 0.831073679 0.040052277 0.105558976 0.58186773 0.748335674 0.058741863 0.01858107 9.76E-13 12.01052939 -0.167911323 GPKPEPPGS(ph)GSPAPPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 GPKPEPPGS(0.5)GS(0.5)PAPPR 68.42 0.016176 87816000 3112.3 2724.3 2775.2 2752.1 3056.3 3335.5 2639.6 2941.9 2898.8 3067.6 TRUE FALSE FALSE 3074.36609 2762.652767 2823.501192 3070.310751 2900.325606 3122.372315 2863.807558 3027.019235 2639.524068 2987.90331 1.02893761 0.924612506 0.94497743 1.027580357 0.970689244 1.04500447 0.95846728 1.013091429 0.883403442 1 11.54491775 GPKPEPPGSGS(ph)PAPPR ddPTM_HeLa_Romidepsin_16h_R1 2 GPKPEPPGSGSPAPPR 16 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 GPKPEPPGS(0.165)GS(0.835)PAPPR;GPKPEPPGS(0.032)GS(0.968)PAPPR ; 120.74 0.001067 77789000 6184.1 7191.9 6584.9 6041.6 6484.4 6669.7 7655.4 6354 7296.4 7066.9 TRUE FALSE FALSE 6108.725811 7293.147757 6699.507422 6740.158219 6153.476871 6243.527695 8305.649485 6537.842965 6643.79171 6883.300919 0.887470399 1.059542194 0.97329864 0.979204352 0.893971794 0.9070543 1.206637569 0.949812167 0.965204309 1 12.74888487 -7.789038009 24.99948444 0.952137459 1.078225206 0.282561327 0.07599673 165.77906 150166.4418 0.010469015 0.031417347 1.63E-08 7.789038009 0.126087747 GPLATGGIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GPLATGGIKK 10 1 Q9Y2S6;A0A024R1R8 Q9Y2S6 TMA7;hCG_2014768 Translation machinery-associated protein 7 0 1 GPLATGGIK(1)K 94.692 0.015156 3277700 1094.5 873.24 1394.9 1143.3 1828.2 1280.5 1302 885.08 1303.9 765.35 FALSE TRUE FALSE 1081.159813 885.5334956 1419.177649 1275.493725 1734.900132 1198.680183 1412.591848 910.6883934 1187.275918 745.4660967 1.450313861 1.18789238 1.903745396 1.711001655 2.327268993 1.607960695 1.894910921 1.221636232 1.592662528 1 9.541998931 -10.72304656 0.571767187 1.055839559 1.791905174 0.166661069 0.343383524 0.458531241 0.351602551 0.122211549 0.099489125 1.89E-11 10.72304656 0.736065615 GPLPVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GPLPVKR 7 1 P38159;P38159-2;H3BUY5;H0Y6E7;H3BT71;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 1 ; GPLPVK(1)R;GPLPVK(1)R 106.76 0.0070043 140002000 11814.4 12134.5 13553.2 11883.2 15176.8 17043.6 17334.9 11067.3 11716.8 6901 FALSE TRUE FALSE 11670.40155 12305.32981 13789.08776 13257.1915 14402.27126 15954.56897 18807.32597 11387.51486 10668.82006 6721.711025 1.736224825 1.830684146 2.051425256 1.972294174 2.142649574 2.373587455 2.797996805 1.694139308 1.587217901 1 12.71461281 -11.1221671 0.29303084 0.75572814 2.424196791 0.517598438 0.317986865 0.664864646 0.153205172 0.434628221 0.223245727 7.55E-12 11.1221671 1.66846865 GPPAS(ph)SPAPAPK ddPTM_HeLa_Romidepsin_16h_R1 1 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 GPPAS(0.598)S(0.402)PAPAPK 93.839 0.023294 6063100 2303 6527.3 2426.5 3350.1 2742.8 2539.9 2067.3 2460.5 2565.3 3113.2 TRUE FALSE FALSE 2274.93015 6619.191501 2468.732215 3737.454325 2602.824681 2377.608587 2242.89641 2531.690685 2335.853143 3032.318615 0.750227941 2.182881267 0.814140111 1.232540112 0.858361212 0.784089302 0.739663833 0.834902597 0.770319165 1 11.56620563 -8.536092729 24.33461412 1.00561421 0.788173383 0.093667572 0.39991078 406.514667 748627.5051 0.058837425 0.117733171 2.91E-09 8.536092729 -0.217440827 GPPASS(ph)PAPAPK ddPTM_HeLa_Romidepsin_16h_R1 5 GPPASSPAPAPK 12 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 GPPAS(0.005)S(0.995)PAPAPK;GPPAS(0.082)S(0.918)PAPAPK;GPPAS(0.118)S(0.882)PAPAPK;GPPAS(0.093)S(0.907)PAPAPK;GPPAS(0.078)S(0.922)PAPAPK ;;;; 163.45 0.00046748 1108202600 31676.6 35373 26767.3 32172.6 26691.5 25363.4 21531.7 24182.8 32040.4 32354.8 TRUE FALSE FALSE 31290.51342 35870.98202 27233.17363 35892.54739 25329.33316 23742.7606 23360.60206 24882.49116 29174.62638 31514.21763 0.992901483 1.138247582 0.864155155 1.138931888 0.803743042 0.753398383 0.741271839 0.789563982 0.92576077 1 14.94371523 -8.628949135 6.803287189 1.005974432 0.762694907 0.683647522 0.079619884 0.079370977 4.545507872 0.009668422 0.019430636 2.35E-09 8.628949135 -0.243279525 GPPASSPAPAPKFS(ph)PVTPK ddPTM_HeLa_Romidepsin_16h_R1 2 GPPASSPAPAPKFSPVTPK 19 1 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 GPPASSPAPAPKFS(0.968)PVT(0.031)PK;GPPASSPAPAPKFS(0.739)PVT(0.261)PK ; 73.597 0.0049244 333770000 10124.2 8344 6810.9 12713.6 7621.4 6728.8 6810.8 7095.6 9280.4 7798.6 TRUE FALSE FALSE 10000.80236 8461.467051 6929.440857 14183.60625 7232.451519 6298.851396 7389.309182 7300.899991 8450.337781 7595.991248 1.316589505 1.113938494 0.912249716 1.867248893 0.952140581 0.82923363 0.972790639 0.961151712 1.112473344 1 12.89102253 -8.557397842 24.9999054 1.184489932 0.920305554 0.24274977 0.247919836 218.4978196 158242.7949 0.03639258 0.072785397 2.77E-09 8.557397842 -0.264184378 GPPDFS(ph)S(ph)DEEREPTPVLGSGAAAAGR ddPTM_HeLa_Romidepsin_16h_R1 1 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 G5E972;P42167;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 2 0 GPPDFS(0.999)S(0.999)DEEREPT(0.002)PVLGSGAAAAGR 70.767 0.00083733 40992000 2539.5 2486 2502.4 1938.4 2353.2 2314.5 2102.9 1998.5 2822.9 2418.1 TRUE FALSE FALSE 2508.547597 2520.997973 2545.953222 2162.526928 2233.107423 2166.61092 2281.520274 2056.323444 2570.412754 2355.277413 1.065075215 1.070361376 1.080956837 0.918162301 0.948129257 0.919896275 0.968684309 0.873070591 1.091341826 1 11.20168128 -9.251100411 24.9765359 1.038537952 0.928918775 0.769183995 0.03613338 311.764058 753149.0908 0.005638625 0.009281972 5.61E-10 9.251100411 -0.109619177 GPPDFS(ph)SDEEREPTPVLGSGAAAAGR ddPTM_HeLa_Romidepsin_16h_R1 2 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 G5E972;P42167;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 GPPDFS(0.557)S(0.442)DEEREPTPVLGSGAAAAGR;GPPDFS(0.82)S(0.18)DEEREPTPVLGSGAAAAGR ; 93.416 4.95E-06 318796000 1208.27 1366.59 1146.81 887.79 900.91 877.45 659.32 735.23 1094.67 1238.46 TRUE FALSE FALSE 1193.54314 1385.82889 1166.769747 990.440457 854.9332009 821.3837768 715.3226243 756.50272 996.7599735 1206.284631 0.98943741 1.148840709 0.967242488 0.821066962 0.708732565 0.68092037 0.59299655 0.627134509 0.826305789 1 10.23635465 -8.934222239 1.641190159 1.008301481 0.632394042 0.809053843 0.076784571 0.07476987 0.404098755 0.008469438 0.018098454 1.16E-09 8.934222239 -0.375907439 GPPDFSSDEEREPT(ph)PVLGSGAAAAGR ddPTM_HeLa_Romidepsin_16h_R1 2 GPPDFSSDEEREPTPVLGSGAAAAGR 26 1 G5E972;P42167;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 GPPDFS(0.011)S(0.01)DEEREPT(0.971)PVLGS(0.008)GAAAAGR;GPPDFS(0.383)S(0.101)DEEREPT(0.477)PVLGS(0.04)GAAAAGR ; 85.11 2.23E-05 227830000 4595.9 5644.2 4403.9 3504.9 3243.6 4155.9 2300.48 4017.2 5668.1 5196.4 TRUE FALSE FALSE 4539.883403 5723.659196 4480.548032 3910.153029 3078.066988 3890.351403 2495.882714 4133.431344 5161.13094 5061.396779 0.896962558 1.130845781 0.885239436 0.77254426 0.60814576 0.768631975 0.49312133 0.816658232 1.019704869 1 12.30531986 -9.193677046 2.536906463 0.964231335 0.667403885 0.676672103 0.103613532 0.128610944 1.621883702 0.015061166 0.026210862 6.40E-10 9.193677046 -0.29682745 GPPGPALPATMNNS(ph)SSETR ddPTM_HeLa_Romidepsin_16h_R1 2 GPPGPALPATMNNSSSETR 19 0 Q15003;C9JZP1 Q15003 NCAPH Condensin complex subunit 2 1 0 GPPGPALPAT(0.081)MNNS(0.569)S(0.333)S(0.017)ETR;GPPGPALPAT(0.006)MNNS(0.729)S(0.247)S(0.017)ETR ; 86.411 0.0075538 14603500 2495.7 2167.8 2386.27 3131.7 5348.1 6215.4 4931.9 5124.3 2424 2382.5 TRUE FALSE FALSE 2465.281448 2198.318345 2427.802028 3493.801889 5075.1665 5818.255999 5350.815463 5272.563536 2207.191369 2320.602307 1.062345513 0.947305076 1.046194784 1.505558225 2.187003989 2.507218054 2.305787359 2.272066834 0.951128663 1 11.18028359 -8.885515195 2.173751566 1.022870671 2.364584056 0.986850569 0.07183681 0.023143339 0.22189462 0.011055325 0.022523141 1.30E-09 8.885515195 1.341713385 up GPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_HeLa_Romidepsin_16h_R1 3 GPPQEEEEEEDEEEEATKEDAEAPGIR 27 1 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 0 0 ;; ;; 145.61 2.43E-21 72031000 1001.5 823.06 883.72 673.5 1071.57 953.98 785.587 1032.61 1248.2 942.08 FALSE FALSE TRUE 989.2933328 834.6470603 899.1007759 751.3732389 1016.883784 893.0237568 852.3147402 1062.486941 1136.557866 917.6046258 1.078125922 0.909593344 0.979834616 0.818842035 1.10819383 0.973211917 0.928847475 1.157891876 1.238613924 1 9.841728854 -13.296247 5.081955472 0.999163329 1.012922196 0 0.122201485 2.397290367 117.1581199 0.099096485 0.013278557 5.06E-14 13.296247 0.013758867 GPPQS(ph)PVFEGVYNNSR ddPTM_HeLa_Romidepsin_16h_R1 4 GPPQSPVFEGVYNNSR 16 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 GPPQS(1)PVFEGVYNNSR;GPPQS(0.998)PVFEGVY(0.002)NNSR;GPPQS(0.98)PVFEGVY(0.015)NNS(0.005)R;GPPQS(0.999)PVFEGVY(0.001)NNSR ;;; 144.25 0.00031839 384032000 11185.8 9904.9 10902.1 8640.6 12028.8 12326.2 10592.5 11693.3 11423.5 11186.3 TRUE FALSE FALSE 11049.46317 10044.34144 11091.84648 9639.666827 11414.92545 11538.5956 11492.22669 12031.62719 10401.75355 10895.67831 1.014114298 0.92186472 1.018004218 0.884723883 1.047656247 1.059006633 1.054750916 1.104256829 0.954667828 1 13.41146839 -8.540401643 24.99716664 0.992001696 1.067954783 0.499972854 0.045412403 178.0017227 253926.4503 0.006310521 0.012622725 2.88E-09 8.540401643 0.075953086 GPPS(ph)PGPAAQPPAPPR ddPTM_HeLa_Romidepsin_16h_R1 2 GPPSPGPAAQPPAPPR 16 0 H9KV50;Q9NZV5-2;Q9NZV5 H9KV50 SEPN1 Selenoprotein N 1 0 GPPS(1)PGPAAQPPAPPR;GPPS(1)PGPAAQPPAPPR ; 102.15 0.0049883 21784900 1470.55 1279.66 1217.46 1407.46 1312.54 1584.72 1148.1 1417.32 1323.83 1442.44 TRUE FALSE FALSE 1452.626371 1297.675087 1238.649381 1570.197147 1245.556186 1483.461506 1245.619585 1458.327918 1205.423329 1404.965201 1.033923381 0.923635038 0.881622819 1.117605722 0.886538816 1.05587064 0.886583941 1.037981522 0.857973798 1 10.45631868 -10.28513687 24.77416928 1.016019375 0.969143741 0 0.091229043 1313.352534 1373019.725 0.011797797 0.013495556 5.19E-11 10.28513687 -0.046875633 GPPS(ph)TPVPTQTQNPESR ddPTM_HeLa_Romidepsin_16h_R1 1 GPPSTPVPTQTQNPESR 17 0 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;O75128-6 H7C1N2 COBL Protein cordon-bleu 1 0 GPPS(0.99)T(0.01)PVPTQTQNPESR 121.92 0.0022946 2682900 1219.4 1136.3 1129.4 680.31 884.26 737.3 703.02 451.96 841.38 984.58 TRUE FALSE FALSE 1204.537484 1152.296861 1149.056733 758.9706432 839.1329126 690.1889095 762.7345013 465.0367495 766.1248655 959.0004697 1.2560343 1.201560268 1.198181617 0.791418427 0.875007822 0.719696112 0.795343199 0.484918167 0.798878509 1 9.905387712 -9.177651343 4.189300534 1.136621431 0.735746837 0.561251133 0.155841542 0.104652038 3.39714233 0.020612362 0.034745798 6.64E-10 9.177651343 -0.400874594 GPQPPTVS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 2 GPQPPTVSPIR 11 0 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 GPQPPT(0.004)VS(0.996)PIR;GPQPPT(0.003)VS(0.997)PIR ; 161.87 0.0011142 428760000 4344 4520.9 4476.1 3181.5 3087 3293.9 2769.2 3100.1 4788 4493.1 TRUE FALSE FALSE 4291.053657 4584.545349 4554.004643 3549.359999 2929.458871 3083.430421 3004.415779 3189.796502 4359.749288 4376.368614 0.980505537 1.047568373 1.040589823 0.811028575 0.669381199 0.70456369 0.686508849 0.728868334 0.996202485 1 12.09551854 -9.068811697 3.451180943 0.998819835 0.698728437 0.967831009 0.027214506 0.032829758 0.764357067 0.004520762 0.007960835 8.53E-10 9.068811697 -0.300091398 GPQVSSALNLDTSK ddPTM_HeLa_Romidepsin_16h_R1 1 GPQVSSALNLDTSK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 117.92 1.47E-05 0 120.55 131.67 0 141.84 200.19 0 0 204.51 0 0 FALSE FALSE TRUE 119.0806902 133.5236537 0 158.2402082 189.9735573 0 0 210.4271742 0 0 0 GPRIS(ph)APNVDFNLEGPK ddPTM_HeLa_Romidepsin_16h_R1 1 GPRISAPNVDFNLEGPK 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GPRIS(1)APNVDFNLEGPK 124.99 0.013027 14179000 2010.1 1848.9 1972.2 3930.7 1882.1 1988.4 1474.2 1837.6 2245.6 1821.6 TRUE FALSE FALSE 1985.600128 1874.928863 2006.525314 4385.186028 1786.049414 1861.347657 1599.418511 1890.768057 2044.747912 1774.274569 1.11910533 1.056729829 1.130898987 2.471537441 1.006636427 1.049075318 0.901449268 1.065656967 1.15244165 1 10.79301357 -5.800128206 20.32354798 1.137596499 1.148876867 0 0.434902881 0 0 0.056750652 0 1.58E-06 5.800128206 0.011280368 GPS(ph)LDIDTPDVNIEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GPS(0.967)LDIDT(0.033)PDVNIEGPEGK 214.54 3.74E-29 25698000 5205.4 7232.6 3902.4 3781.5 4665.5 2917 2059 2728.8 4410.6 4495.9 TRUE FALSE FALSE 5141.954583 7334.420733 3970.319635 4218.734822 4427.402126 2730.613114 2233.891409 2807.753523 4016.104889 4379.09587 1.174204616 1.674871012 0.906652824 0.96338033 1.011031103 0.623556368 0.510126171 0.641171969 0.917108236 1 12.09641732 -8.368296395 1.470169 1.118836192 0.54692273 0.545712408 0.21098652 0.245204798 1.000656686 0.032121225 0.110256844 4.28E-09 8.368296395 -0.571913462 GPS(ph)PAPASS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 0 GPS(1)PAPAS(0.011)S(0.989)PKR 105.19 0.012163 7720100 1733.2 1862.3 1759.1 1072.6 1458.5 1813.8 1492.4 1275.9 2289.5 1701.5 TRUE FALSE FALSE 1712.075092 1888.517508 1789.716398 1196.619059 1384.067303 1697.904034 1619.164419 1312.816153 2084.721386 1657.294785 1.033054051 1.139518163 1.079902269 0.722031512 0.835136462 1.024503335 0.976992406 0.79214402 1.257906201 1 10.69461452 -9.29564645 24.99893639 1.031653467 0.882725225 0.453057763 0.114645725 493.6553037 360767.8544 0.014401149 0.021998695 5.06E-10 9.29564645 -0.148928243 GPS(ph)PGPSGPANGR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPGPSGPANGR 13 0 P28356 P28356 HOXD9 Homeobox protein Hox-D9 1 0 GPS(0.999)PGPS(0.001)GPANGR 88.224 0.024566 2845100 1940.8 2162.3 2405.9 1932.4 2935.4 3052.5 1773.7 2204.3 2382.2 2225 TRUE FALSE FALSE 1917.144783 2192.740916 2447.77368 2155.83318 2785.595585 2857.455101 1924.358034 2268.077943 2169.130066 2167.194179 0.884620677 1.011787932 1.12946671 0.994757738 1.285346561 1.318504419 0.88794906 1.046550403 1.000893269 1 11.08161271 -9.929680932 3.892095722 0.945410938 1.112223478 0.22991448 0.123008273 0.229020558 6.958377518 0.021049985 0.027823831 1.18E-10 9.929680932 0.16681254 GPS(ph)PS(ph)SPTPPAAAAPAEQAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPSSPTPPAAAAPAEQAPR 21 0 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 0 GPS(0.999)PS(0.658)S(0.262)PT(0.081)PPAAAAPAEQAPR 153.36 2.63E-05 27087000 1425.6 1886 1434.5 1609.5 1330.1 964.87 957.11 1013.6 1733.3 1264 TRUE FALSE FALSE 1408.224239 1912.551158 1459.466871 1795.597963 1262.220034 903.217921 1038.4069 1042.926917 1578.269307 1231.161098 1.143818012 1.553453208 1.185439398 1.458458983 1.025227353 0.733630979 0.843437062 0.847108407 1.281935654 1 10.26580384 -8.465473009 5.896339792 1.147799778 0.818515654 0.524663316 0.176517638 0.182837789 13.58509537 0.028401179 0.063550869 3.42E-09 8.465473009 -0.329284124 GPS(ph)PSPVGSPASVAQSR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSPSPVGSPASVAQSR 17 0 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3;A0A087WUV6 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 GPS(0.915)PS(0.082)PVGS(0.002)PASVAQSR;GPS(0.906)PS(0.093)PVGS(0.001)PASVAQSR ; 130.47 0.0019914 90010000 2592.39 2283.6 2476.97 1910.28 1491.12 1233.39 1399.47 1241.23 2798.57 2325.11 TRUE FALSE FALSE 2560.792954 2315.748581 2520.080624 2131.155562 1415.022582 1154.58036 1518.340947 1277.143032 2548.25889 2264.703307 1.130741032 1.022539497 1.112764138 0.941030799 0.624815877 0.509815284 0.670437025 0.563933928 1.125206504 1 11.14510634 -8.829474713 3.096434947 1.062537511 0.584850813 0.945141278 0.055456815 0.044106954 0.856213551 0.009153952 0.018021863 1.48E-09 8.829474713 -0.477686698 GPS(ph)SVEDIK ddPTM_HeLa_Romidepsin_16h_R1 2 GPSSVEDIK 9 0 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 GPS(0.635)S(0.365)VEDIK;GPS(0.5)S(0.5)VEDIK ; 120.63 0.013118 16353900 9302.4 10279.1 9166.7 7903.4 10506.5 10862.8 9891.6 11270 12378.6 12014.7 TRUE FALSE FALSE 9189.018771 10423.80944 9326.242568 8817.228295 9970.3141 10168.70214 10731.79226 11596.07967 11271.42701 11702.55636 0.785214656 0.890729266 0.796940624 0.753444634 0.851977448 0.868929986 0.917046834 0.990901416 0.963159387 1 13.51453609 -6.314993724 18.34255015 0.881606925 0.862244131 0 0.082387044 0 0 0.013118982 0 4.84E-07 6.314993724 -0.019362795 GPS(ph)WDPFR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSWDPFR 8 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 0 GPS(1)WDPFR;GPS(1)WDPFR ; 133.99 0.0094209 157052000 13284.2 17337.5 10229.6 9256 14159 13046 10086.3 14741.4 12197.7 10024.4 TRUE FALSE FALSE 13122.28706 17581.57778 10407.6419 10326.22227 13436.4134 12212.4027 10943.03007 15167.91915 11106.70716 9763.964643 1.343950694 1.800659714 1.065923759 1.057584972 1.376122701 1.250762692 1.120756831 1.553459041 1.137520215 1 13.25325136 -12.15319672 1.033931253 1.009338163 1.31009359 0.163241752 0.22002167 0.600199383 1.203914381 0.122244797 0.039748048 7.03E-13 12.15319672 0.300755428 GPS(ph)WDPFRDWYPHSR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 0 GPS(0.987)WDPFRDWY(0.012)PHS(0.001)R 78.848 0.012405 23716000 3287.6 4189.6 1883.8 3581.3 3351 2908.3 2650.4 4446.3 2847.7 2108.8 TRUE FALSE FALSE 3247.529467 4248.581299 1916.586749 3995.386757 3179.985966 2722.469016 2875.52491 4574.946675 2592.99458 2054.013072 1.581065628 2.068429533 0.933093745 1.945161309 1.548181951 1.325438992 1.399954532 2.22732111 1.262404127 1 11.00422965 -12.03827391 0.711993158 0.972866325 1.612062438 0.210896463 0.368304219 0.746175744 0.655860811 0.27326067 0.072294548 9.16E-13 12.03827391 0.639196112 GPSLDIDT(ph)PDVNIEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 GPSLDIDTPDVNIEGPEGK 19 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 GPSLDIDT(1)PDVNIEGPEGK 86.756 0.010927 28165000 1843.2 2580.7 1342.4 1455.2 2019.7 1240.9 939.26 1193.5 1890.9 2212.4 TRUE FALSE FALSE 1820.734369 2617.031162 1365.763909 1623.457071 1916.627172 1161.610495 1019.040721 1228.032039 1721.773168 2154.921529 0.844919105 1.214443833 0.633788233 0.753371781 0.889418546 0.539050021 0.472889944 0.569873206 0.798995762 1 11.07341962 -8.393966868 0.621242062 0.945202853 0.430471205 0.508152301 0.1523024 0.685725298 0.376187541 0.028664365 0.195369305 4.04E-09 8.393966868 -0.514731648 GPSPAAAS(ph)PEGSPLR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSPAAASPEGSPLR 15 0 Q9P107-2;Q9P107 Q9P107-2 GMIP GEM-interacting protein 1 0 GPS(0.001)PAAAS(0.982)PEGS(0.016)PLR;GPS(0.001)PAAAS(0.876)PEGS(0.123)PLR ; 116.87 0.0037739 9888600 1681.89 1660.05 1702.28 1373.03 1833.56 2091.22 1800.63 1958.15 1845.09 1692.25 TRUE FALSE FALSE 1661.390478 1683.420227 1731.907469 1531.786189 1739.986591 1957.597791 1953.575467 2014.805981 1680.060529 1648.285101 1.007950916 1.021316171 1.050732952 0.92932114 1.055634483 1.187657275 1.185216966 1.222364978 1.019277871 1 10.68675009 -8.327887225 3.309531701 1.004217936 1.20040723 0.888156819 0.030715173 0.050791736 1.093039053 0.00405285 0.010105023 4.70E-09 8.327887225 0.196189294 GPSPAPASS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 GPSPAPASSPK 11 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 GPSPAPAS(0.199)S(0.801)PK;GPSPAPAS(0.159)S(0.841)PK ; 138.42 0.003451 33904000 13318.2 13633.2 12586.2 7917 9891.9 10989.4 10326.7 7695.8 13911.2 13741 TRUE FALSE FALSE 13155.87266 13825.12855 12805.25753 8832.400791 9387.079431 10287.21281 11203.84964 7918.465831 12666.94743 13384.00684 0.982954717 1.032958868 0.956758143 0.659922017 0.701365409 0.768619811 0.837107286 0.591636415 0.94642416 1 13.70822247 -9.336988588 5.404579438 0.994393219 0.721597447 0.817300131 0.064265798 0.062999194 3.31694849 0.009108238 0.014048909 4.60E-10 9.336988588 -0.272795772 GPSPAPASS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPAPASSPKR 12 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 GPSPAPAS(0.127)S(0.873)PKR 111.66 0.0030029 12814000 3161.4 4018.6 2901.4 2665.1 2489.3 2786.9 3003.9 2210.8 4194.3 3540.3 TRUE FALSE FALSE 3122.867641 4075.173956 2951.89765 2973.251402 2362.261732 2608.826084 3259.051191 2274.76601 3819.151303 3448.322496 0.905619368 1.181784465 0.856038742 0.862231246 0.685046638 0.756549333 0.945112064 0.659673222 1.1075389 1 11.75167899 -9.324718106 2.690397371 0.971532291 0.779154923 0.506932084 0.113719195 0.202625713 2.881322122 0.016149412 0.026447511 4.73E-10 9.324718106 -0.192377368 GPSPRPPAT(ph)AYDAPASAFGSSLLGSGGSAFAPPLR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 GPS(0.232)PRPPAT(0.386)AY(0.348)DAPAS(0.028)AFGS(0.002)S(0.001)LLGS(0.002)GGS(0.002)AFAPPLR 49.744 0.00669 14923000 759.61 968.88 787.01 555.86 759.09 536.65 479.68 628.82 742.97 747.74 TRUE FALSE FALSE 750.3515811 982.5199181 800.7075789 620.1311486 720.3508047 502.359797 520.4240072 647.0139146 676.5169024 728.313607 1.030258908 1.349034137 1.09939945 0.851461709 0.989066795 0.689757533 0.714560324 0.888372685 0.928881317 1 9.508415989 -8.669198958 1.623604939 1.046390475 0.76691237 0.476300152 0.131254355 0.258387182 1.367876665 0.020272061 0.05134646 2.14E-09 8.669198958 -0.279478105 GPSPRPPATAYDAPAS(ph)AFGSSLLGSGGSAFAPPLR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLR 35 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 GPS(0.085)PRPPAT(0.012)AY(0.073)DAPAS(0.82)AFGS(0.007)S(0.003)LLGSGGSAFAPPLR 77.175 4.39E-07 13439000 985.49 1230.3 895.04 1031.8 945.14 1030.7 571.76 672.69 1089.5 952.72 TRUE FALSE FALSE 973.4784688 1247.620196 910.6177957 1151.101571 896.905979 964.8415964 620.3252801 692.1532238 992.0523913 927.9681971 1.049042922 1.34446439 0.981302806 1.240453686 0.966526635 1.039735628 0.668476875 0.745880329 1.06905861 1 9.857931553 -7.767238845 23.7782322 1.055945928 0.707178518 0.61824771 0.11724393 34.12680948 139928.1626 0.016103401 0.050385404 1.71E-08 7.767238845 -0.348767409 GPSPS(ph)PVGSPASVAQSR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSPSPVGSPASVAQSR 17 0 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3;A0A087WUV6 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 GPS(0.16)PS(0.839)PVGS(0.001)PASVAQSR;GPS(0.065)PS(0.728)PVGS(0.206)PAS(0.002)VAQSR ; 177.66 7.91E-09 95258000 2967.7 2940.7 2908.2 2147.53 1861.8 2259.58 1354.99 1371.29 2825.1 2906.39 TRUE FALSE FALSE 2931.528531 2982.099252 2958.816001 2395.837523 1766.785399 2115.20013 1470.082817 1410.966113 2572.41598 2830.881569 1.035553222 1.05341717 1.045192435 0.846322061 0.624111379 0.747187786 0.519302126 0.498419336 0.908697845 1 11.46703568 -8.834907773 1.485164218 1.024647575 0.569344617 0.872410264 0.074028112 0.081565329 0.361930436 0.010247352 0.024125019 1.46E-09 8.834907773 -0.455302958 GPSPS(ph)SPTPPAAAAPAEQAPR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSPSSPTPPAAAAPAEQAPR 21 0 Q86VQ1 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 GPSPS(0.507)S(0.491)PT(0.002)PPAAAAPAEQAPR;GPSPS(0.918)S(0.082)PTPPAAAAPAEQAPR ; 276.8 4.25E-111 44621000 4526.9 4486.3 4354.1 4440.9 5046.3 4330.7 4465.2 5008.3 4596.3 4997.9 TRUE FALSE FALSE 4471.724402 4549.458249 4429.881284 4954.377753 4788.768481 4053.982247 4844.473977 5153.207259 4185.195416 4868.053838 0.918585651 0.934553808 0.9099902 1.017732736 0.983713131 0.832772681 0.995156204 1.058576472 0.859726609 1 12.24912941 -7.520987824 24.99616011 0.952495659 1.042721446 0.273783613 0.058272336 60.29817252 797055.9392 0.007421826 0.028713664 3.01E-08 7.520987824 0.090225787 GPSQATS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 1 GPSQATSPIR 10 0 Q7RTP6;J3QR21;J3QLA3 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 GPSQAT(0.033)S(0.967)PIR 120.03 0.011806 21925000 4305.2 4565.2 5643.6 4627.3 5816.5 7193.9 6536.8 6005.7 4870.3 4259.3 TRUE FALSE FALSE 4252.726566 4629.469005 5741.824491 5162.330198 5519.662301 6734.233007 7092.035629 6179.465454 4434.68817 4148.642772 1.025088637 1.115899647 1.384024802 1.244341941 1.330474231 1.623237617 1.709483322 1.489514956 1.068949151 1 12.01842372 -9.012582774 0.5972342 0.996624317 1.668174048 0.831536975 0.098164193 0.232726618 0.14943859 0.021528153 0.074584647 9.71E-10 9.012582774 0.671549731 GPSQEEEDNHS(ph)DEEDRASEPK ddPTM_HeLa_Romidepsin_16h_R1 2 GPSQEEEDNHSDEEDRASEPK 21 1 E7ERS3;Q86VM9;H3BPD0 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 GPSQEEEDNHS(0.992)DEEDRAS(0.008)EPK;GPS(0.086)QEEEDNHS(0.914)DEEDRASEPK ; 71.794 0.0021981 21107000 3148.6 3005.2 2918.7 2787.1 3222.8 3461.6 3274.3 3522.5 2914.9 3217.2 TRUE FALSE FALSE 3110.223652 3047.507284 2969.498749 3109.357616 3058.32849 3240.414932 3552.41896 3624.41798 2654.184043 3133.61668 0.992534815 0.972520763 0.947626673 0.992258445 0.975974027 1.034081466 1.133648216 1.156624549 0.847003419 1 11.613613 -7.820224614 2.572488879 0.989359332 1.155191494 0.679806585 0.047639707 0.050964378 0.660775929 0.002551116 0.011103168 1.51E-08 7.820224614 0.165832162 GPSS(ph)VEDIK ddPTM_HeLa_Romidepsin_16h_R1 3 GPSSVEDIK 9 0 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 GPS(0.003)S(0.997)VEDIK;GPS(0.088)S(0.912)VEDIK;GPS(0.011)S(0.989)VEDIK ;; 123.62 0.011548 217636400 20256 19289.5 18419.7 15236.8 19781.4 21385.4 19183.6 20495.1 22101.7 20993.5 TRUE FALSE FALSE 20009.11208 19561.05809 18740.28715 16998.55051 18771.88134 20018.94196 20813.05451 21088.09338 20124.8686 20448.08584 0.978532281 0.956620499 0.916481244 0.831302775 0.918026337 0.979013005 1.017848549 1.031299142 0.984193276 1 14.31967818 -7.780357644 3.669397635 0.964635773 1.027226749 0.231516989 0.049226288 0.331788646 9.370422333 0.008367666 0.031810968 1.66E-08 7.780357644 0.062590976 GPSTPKS(ph)PGASNFSTLPK ddPTM_HeLa_Romidepsin_16h_R1 1 GPSTPKSPGASNFSTLPK 18 1 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 0 GPS(0.001)T(0.003)PKS(0.961)PGAS(0.031)NFS(0.003)T(0.001)LPK 81.808 0.0045047 30949000 5779.8 4863.4 3783.7 9417.3 5110.6 4605.2 4906.2 5926.6 5900.1 4462.6 TRUE FALSE FALSE 5709.353574 4931.867073 3849.553711 10506.17254 4849.787012 4310.942583 5322.932506 6098.07682 5372.380279 4346.661009 1.313503299 1.134633472 0.885634675 2.41706738 1.115749998 0.99178256 1.224602631 1.40293361 1.235978667 1 12.08569187 -12.28371482 0.502784051 0.930633471 1.32406783 0.023650566 0.40484016 3.546292848 1.207069279 0.694077334 0.105306342 5.20E-13 12.28371482 0.393434359 GPSWDPFRDWYPHSR ddPTM_HeLa_Romidepsin_16h_R1 2 GPSWDPFRDWYPHSR 15 1 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 0 ; ; 124.47 0.001184 53747000 7334.7 6803.6 6253.2 10357.9 8073.7 7277.8 4996 5966.3 5997.8 5175.7 FALSE FALSE TRUE 7245.301855 6899.381259 6362.034323 11555.52913 7661.668962 6812.772068 5420.360115 6138.925477 5461.341746 5041.234568 1.437207842 1.368589612 1.261999266 2.292202233 1.519800132 1.351409457 1.075204901 1.217742478 1.083334186 1 12.29956137 -12.02619655 0.712293608 0.983493073 1.452742396 0.207180867 0.310715715 0.970475364 0.858326932 0.260100857 0.069842116 9.41E-13 12.02619655 0.469249323 GPT(ph)PATPESFSK ddPTM_HeLa_Romidepsin_16h_R1 1 GPTPATPESFSK 12 0 P49454 P49454 CENPF Centromere protein F 1 0 GPT(0.985)PAT(0.01)PES(0.005)FSK 112.84 0.02011 13276000 3596.4 3242.9 3800.8 3254.5 3051.7 3485.9 2895.1 2750.8 3657.8 3227 TRUE FALSE FALSE 3552.565693 3288.553631 3866.95133 3630.800603 2895.960362 3263.16224 3141.009722 2830.390058 3330.637207 3143.162075 1.13025215 1.046256462 1.230274239 1.155142661 0.92135254 1.038178167 0.999315227 0.900491286 1.059645391 1 11.61800095 -7.505976737 0.911671601 1.075763368 0.864472223 0.349724109 0.078256447 1.641382168 1.297045244 0.013906724 0.314188312 3.12E-08 7.505976737 -0.211291145 GPTSTSIDNIDGT(ph)PVRDER ddPTM_HeLa_Romidepsin_16h_R1 4 GPTSTSIDNIDGTPVRDER 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 GPTSTSIDNIDGT(1)PVRDER;GPTSTS(0.001)IDNIDGT(0.998)PVRDER;GPTSTSIDNIDGT(1)PVRDER;GPTSTSIDNIDGT(1)PVRDER ;;; 243.37 2.28E-61 175754000 16176.5 16144.5 15147.8 14253.8 11930.8 10959.4 9255.1 10630.7 17383.4 16393.4 TRUE FALSE FALSE 15979.3346 16371.78269 15411.4411 15901.89142 11321.92676 10259.12971 10041.22796 10938.28253 15828.58517 15967.4971 1.000741349 1.025319284 0.965175757 0.995891298 0.70906083 0.642500803 0.628854222 0.685034258 0.991300331 1 13.96285057 -8.717070025 3.92043512 1.000157045 0.653351282 0.984654532 0.020258468 0.016739012 0.537102177 0.002836102 0.005739922 1.92E-09 8.717070025 -0.346805762 GPTTGEGALDLSDVHS(ph)PPKS(ph)PEGK ddPTM_HeLa_Romidepsin_16h_R1 2 GPTTGEGALDLSDVHSPPKSPEGK 24 1 O95684;O95684-2 O95684 FGFR1OP FGFR1 oncogene partner 2 0 GPT(0.001)T(0.001)GEGALDLS(0.043)DVHS(0.959)PPKS(0.996)PEGK;GPT(0.001)T(0.001)GEGALDLS(0.123)DVHS(0.973)PPKS(0.903)PEGK ; 63.606 0.0012211 5557800 2891.1 2489 2781.7 2649.3 2986.1 3043.1 2536.7 2858.1 3022.7 3041.2 TRUE FALSE FALSE 2855.862161 2524.040207 2830.114322 2955.624531 2833.708174 2848.655731 2752.167235 2940.794614 2752.342142 2962.189186 0.964105255 0.852086092 0.95541309 0.99778385 0.956626332 0.96167245 0.929099076 0.992777446 0.929158122 1 11.53244807 -11.35802328 1.318091621 0.993093922 0.95056738 0 0.04326725 0.484270931 1.702239291 0.010689865 0.007562866 4.39E-12 11.35802328 -0.042526541 GPVEGYEENEEFLR ddPTM_HeLa_Romidepsin_16h_R1 2 GPVEGYEENEEFLR 14 0 F5GYQ2;F5GX77;Q9UI30-2;Q9UI30 F5GYQ2 TRMT112 Multifunctional methyltransferase subunit TRM112-like protein 0 0 ; ; 269.04 1.23E-80 24681000 2980.2 2674.7 2683.5 2656.9 2514.9 2999.1 2132.6 2505.2 2959.2 2689.7 FALSE FALSE TRUE 2943.876176 2712.354497 2730.205192 2964.103279 2386.555269 2807.467189 2313.742991 2577.684009 2694.521741 2619.821206 1.123693544 1.03532046 1.042134168 1.131414339 0.910961123 1.071625492 0.883168281 0.983916003 1.0285136 1 11.35525264 -8.755341353 24.99995406 1.061053028 0.96455761 0.388841065 0.060013361 130.7719726 536118.1474 0.009395883 0.018411122 1.76E-09 8.755341353 -0.096495417 GPVS(ph)GTEPEPVYSMEAADYR ddPTM_HeLa_Romidepsin_16h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 GPVS(0.807)GT(0.193)EPEPVYSMEAADYR 139.49 0.00023327 8072800 942.66 1055.6 874.95 1077.3 1094.5 1212 1110.7 1387.6 984.02 985.52 TRUE FALSE FALSE 931.1704973 1070.460765 890.1781377 1201.862495 1038.643581 1134.557112 1205.04283 1427.748017 896.0067867 959.9160483 0.970054099 1.115160817 0.92734999 1.25204959 1.082015019 1.181933684 1.255362729 1.487367587 0.93342203 1 9.906764427 -4 0.355847305 0.982229369 6.974896944 0.784380538 0.078367389 16.02762921 0.199734306 0.020042822 65.64977452 1.00E-04 4 5.992667575 GPVS(ph)PSVSFQPLAR ddPTM_HeLa_Romidepsin_16h_R1 1 GPVSPSVSFQPLAR 14 0 Q7Z434-4;Q7Z434 Q7Z434-4 MAVS Mitochondrial antiviral-signaling protein 1 0 GPVS(0.484)PS(0.258)VS(0.258)FQPLAR 98.582 0.011264 4011300 544.77 715.65 746.51 699.06 668.19 785.85 667.25 529.06 666.82 616.89 TRUE FALSE FALSE 538.1301337 725.7249395 759.5026934 779.8886064 634.0897709 735.6367212 723.9261983 544.3675164 607.1779491 600.8631089 0.895595229 1.207804122 1.264019512 1.297947228 1.055298223 1.224300028 1.204810526 0.905975934 1.010509616 1 9.230892537 -10.25806793 24.76202784 0.950697746 1.174109321 0.394140284 0.110938155 165.406742 1214851.177 0.018327598 0.021957072 5.52E-11 10.25806793 0.223411576 GPVSGS(ph)PDSMNASR ddPTM_HeLa_Romidepsin_16h_R1 1 GPVSGSPDSMNASR 14 0 A0A499FJS7;O14920-4;O14920-2;O14920 A0A499FJS7 IKBKB Inhibitor of nuclear factor kappa-B kinase subunit beta 1 0 GPVS(0.001)GS(0.701)PDS(0.298)MNASR 117.7 0.0061813 11570000 3022 2899.1 2769 2613.6 2746.7 3223.7 2412.2 2874.9 3188.9 2827 TRUE FALSE FALSE 2985.166702 2939.913606 2817.193283 2915.796729 2606.52565 3017.715974 2617.092208 2958.080696 2903.676797 2753.554132 1.084114042 1.067679611 1.02311164 1.058921158 0.946604107 1.095934864 0.950441532 1.074277299 1.054519598 1 11.42707926 GPVSGSPDS(ph)MNASR ddPTM_HeLa_Romidepsin_16h_R1 3 GPVSGSPDSMNASR 14 0 A0A499FJS7;O14920-4;O14920-2;O14920 A0A499FJS7 IKBKB Inhibitor of nuclear factor kappa-B kinase subunit beta 1 0 GPVSGS(0.489)PDS(0.511)MNASR;GPVSGS(0.386)PDS(0.614)MNASR;GPVSGS(0.257)PDS(0.743)MNASR ;; 153.49 0.00084733 85660000 16802.3 17144.5 18262.2 13477.3 17182.8 18462.9 15155.8 17613.1 17084.3 15980.1 TRUE FALSE FALSE 16597.5071 17385.86072 18580.04593 15035.60884 16305.8976 17283.18028 16443.13327 18122.70726 15556.23742 15564.9347 1.066339656 1.116988992 1.193711782 0.965992414 1.047604626 1.110392084 1.056421604 1.164329155 0.999441226 1 13.9260119 -11.50041191 0.843926665 1.005988689 1.088567768 0.26051855 0.060435774 0.600201971 0.882178565 0.02480317 0.012915531 3.16E-12 11.50041191 0.082579079 GPVSGTEPEPVY(ph)SMEAADYR ddPTM_HeLa_Romidepsin_16h_R1 1 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 GPVSGTEPEPVY(0.777)S(0.223)MEAADYR 90.689 0.020055 5578600 1725 1783.1 1873.5 2021.6 1200.6 1359 956.01 1122.1 1916.2 1713.8 TRUE FALSE FALSE 1703.975036 1808.202529 1906.107482 2255.346904 1139.328902 1272.164286 1037.213466 1154.566193 1744.810273 1669.275229 1.020787349 1.083226119 1.141877294 1.351093495 0.682529089 0.762105771 0.621355572 0.691657177 1.045250204 1 10.70500613 -8.720879335 24.99413079 1.048497238 0.689742603 0.776460895 0.107046618 64.21144136 39568.44367 0.016577166 0.033154021 1.90E-09 8.720879335 -0.358754634 GPVSGTEPEPVYS(ph)MEAADYR ddPTM_HeLa_Romidepsin_16h_R1 5 GPVSGTEPEPVYSMEAADYR 20 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 GPVSGTEPEPVY(0.161)S(0.823)MEAADY(0.016)R;GPVSGTEPEPVY(0.051)S(0.893)MEAADY(0.056)R;GPVSGTEPEPVYS(1)MEAADYR;GPVSGTEPEPVY(0.133)S(0.866)MEAADY(0.001)R;GPVS(0.017)GT(0.437)EPEPVY(0.103)S(0.442)MEAADY(0.001)R ;;;; 122.5 0.00028421 39368000 8587.91 9524.45 7629.08 10353.8 12530.8 13667.6 10945.1 12810 9055.03 8099.5 TRUE FALSE FALSE 8483.23725 9658.535457 7761.860937 11550.95507 11891.30652 12794.28447 11874.77652 13180.63714 8245.125438 7889.073822 1.075314725 1.224292696 0.983874801 1.464171249 1.507313379 1.621772689 1.505218076 1.670745823 1.045132245 1 12.94564022 -9.152097403 3.372319813 1.049434464 1.569104108 0.90503174 0.079360974 0.053026296 1.132766415 0.012381936 0.021288148 7.05E-10 9.152097403 0.519669644 GQDAEMLSYLTNLEVKELRHPRT(ph)GCK ddPTM_HeLa_Romidepsin_16h_R1 1 GQDAEMLSYLTNLEVKELRHPRTGCK 26 3 Q8N831 Q8N831 TSPYL6 Testis-specific Y-encoded-like protein 6 1 0 GQDAEMLSYLTNLEVKELRHPRT(0.999)GCK 49.088 0.0038085 0 649.33 497.4 481.42 577.7 412.87 509.33 524.83 399.54 536.87 415.77 TRUE FALSE FALSE 641.4157162 504.4024103 489.7989132 644.4963922 391.7997033 476.7854568 569.4090471 411.1000595 488.8510026 404.9682355 1.583866733 1.245535739 1.209474893 1.591473937 0.967482555 1.177340381 1.406058543 1.015141494 1.207134189 1 8.661664941 -7.240186048 22.71008965 1.274883439 1.015140621 0.121334895 0.200551125 2948.631028 3150565.23 0.033829192 1.737803497 5.75E-08 7.240186048 -0.259742818 SSGPYGGGGQYFAK(ac)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-3;P09651-2;P09651;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 1 ; SSGPYGGGGQYFAK(1)PR;SSGPYGGGGQYFAK(1)PR 198.52 1.56E-16 35908000 613.27 652.55 945.16 844.99 1561.23 1619.95 1412.69 1496.43 1117.27 710.1 FALSE TRUE FALSE 605.7952294 661.736616 961.6101133 942.6917196 1481.554607 1516.440423 1532.683853 1539.726841 1017.338573 691.6514996 0.875867731 0.956748617 1.390310169 1.362957675 2.142053633 2.192492063 2.215977055 2.226159911 1.470883203 1 9.433901484 -8.990024241 1.204082758 0.941609694 2.260481619 0.852605158 0.204185327 0.058366669 0.167615685 0.01900447 0.044417688 1.02E-09 8.990024241 1.318871925 up GQEEISGALPVAS(ph)PASSR ddPTM_HeLa_Romidepsin_16h_R1 4 GQEEISGALPVASPASSR 18 0 H0Y9D5;H0Y8S9;Q9UBK8;Q9UBK8-1 H0Y9D5 MTRR Methionine synthase reductase 1 0 GQEEISGALPVAS(0.999)PAS(0.001)SR;GQEEISGALPVAS(0.999)PAS(0.001)SR;GQEEISGALPVAS(1)PASSR;GQEEISGALPVAS(0.959)PAS(0.037)S(0.004)R ;;; 279.5 3.98E-106 164992400 10556.8 10705 10287.5 9685 14379.1 17071.6 14056.2 16155.4 11402.9 10371.8 TRUE FALSE FALSE 10428.12966 10855.70527 10466.54962 10804.82527 13645.28087 15980.77986 15250.13328 16622.83101 10382.99606 10102.33914 1.032249018 1.074573435 1.036052094 1.069536977 1.350705087 1.581889069 1.509564574 1.645443771 1.02778138 1 13.30240176 -8.594493353 1.997847624 1.021489626 1.580282059 0.976793 0.037609015 0.031387133 0.251101572 0.005569269 0.013642454 2.54E-09 8.594493353 0.558792433 GQESFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GQESFKK 7 1 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 0 1 ; GQESFK(1)K;GQESFK(1)K 114.89 0.0039435 18515800 5339.1 5495.8 6785.2 3897.2 7778.2 7979 8280.4 3564 6577.5 6006.6 FALSE TRUE FALSE 5274.024996 5573.170017 6903.29356 4347.812601 7381.24943 7469.167651 8983.736969 3667.118717 5989.191926 5850.547666 0.901458341 0.952589456 1.179939717 0.743146257 1.261633927 1.276661276 1.535537779 0.626799221 1.023697655 1 12.51435597 -8.7347766 24.9944369 0.958037575 1.208149785 0.151295886 0.236099076 250.0791324 234430.0668 0.030814395 0.061615055 1.84E-09 8.7347766 0.25011221 GQFSTDELVAEVEKR ddPTM_HeLa_Romidepsin_16h_R1 1 GQFSTDELVAEVEKR 15 1 A0A087WVQ6;Q00610-2;Q00610;A0A087WX41;P53675-2;P53675 A0A087WVQ6 CLTC;CLTCL1 Clathrin heavy chain;Clathrin heavy chain 1;Clathrin heavy chain 2 0 0 163.9 6.09E-05 6918200 8093.8 8246.7 7954.9 8012.3 9603.1 9335.5 8310.9 10210 9355.6 8839.6 FALSE FALSE TRUE 7995.149652 8362.797259 8093.351698 8938.719825 9113.017973 8738.991679 9016.827639 10505.41024 8518.811704 8609.945918 0.928594643 0.971294981 0.940000294 1.038185363 1.058429177 1.014987987 1.047257175 1.220148226 0.98941524 1 13.07178846 -4 0.544592778 0.967658325 11.17949174 0.786871467 0.03608341 42.46135516 0.36041042 0.007703084 508.4347599 1.00E-04 4 10.21183342 GQGESDPLDHEPAVS(ph)PLLPR ddPTM_HeLa_Romidepsin_16h_R1 4 GQGESDPLDHEPAVSPLLPR 20 0 P00519;P00519-2 P00519 ABL1 Tyrosine-protein kinase ABL1 1 0 GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR;GQGESDPLDHEPAVS(1)PLLPR ;;; 143.47 1.82E-05 71026500 5129.2 5312.02 4666.38 4826.43 6947 6427.8 5362.2 5697.77 7897.8 6545.9 TRUE FALSE FALSE 5066.683338 5386.802757 4747.596386 5384.484546 6592.468667 6017.084325 5817.665134 5862.625985 7191.400988 6375.836574 0.794669574 0.844877797 0.744623287 0.844514203 1.033977046 0.943732521 0.912455184 0.919506941 1.127914887 1 12.63839894 -8.793169816 24.9798454 0.879074987 0.948943251 0.060916562 0.106567064 348.6337518 274461.3669 0.01465233 0.026561167 1.61E-09 8.793169816 0.069868264 GQGGAGAGDDEEED ddPTM_HeLa_Romidepsin_16h_R1 2 GQGGAGAGDDEEED 14 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 0 ; ; 151.83 0.0062624 17938200 11856.8 13172.3 18126 16058.4 11396.4 13489.9 19191.4 5448.7 17808.5 16691.5 FALSE FALSE TRUE 11712.28476 13357.73999 18441.47543 17915.14777 10814.79918 12627.93893 20821.51704 5606.349538 16215.66316 16257.85242 0.720407865 0.821617741 1.134311897 1.101938146 0.665204659 0.776728598 1.280705255 0.34483949 0.997404991 1 13.98884908 -7.22997218 23.69778352 0.896811016 0.344837524 0.449339666 0.192732755 5210.513107 3923883.236 0.027125784 4.630467309 5.89E-08 7.22997218 -0.551973492 GQGT(ph)PPSGPGVVR ddPTM_HeLa_Romidepsin_16h_R1 2 GQGTPPSGPGVVR 13 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 0 GQGT(0.595)PPS(0.405)GPGVVR;GQGT(0.589)PPS(0.411)GPGVVR ; 132.23 0.004138 11495500 5902.6 5646.9 5117.4 4539.2 4210.9 3906.7 3353.5 3601.6 5823.6 5733.2 TRUE FALSE FALSE 5830.656841 5726.397206 5206.4662 5064.043662 3996.00206 3657.074478 3638.346206 3705.806614 5302.722631 5584.250638 1.044125205 1.025454905 0.93234823 0.906843906 0.715584296 0.65489082 0.651537053 0.66361753 0.949585356 1 12.44714798 -8.883689061 1.358194033 1.020527491 0.646388141 0.955197482 0.032857115 0.043505335 0.160420753 0.00426374 0.010111107 1.31E-09 8.883689061 -0.37413935 GQGTPPS(ph)GPGVVR ddPTM_HeLa_Romidepsin_16h_R1 1 GQGTPPSGPGVVR 13 0 A0A669KBI7;Q9UMN6 A0A669KBI7 KMT2B Histone-lysine N-methyltransferase 2B 1 0 GQGT(0.184)PPS(0.816)GPGVVR 111.66 0.0064441 9973700 3911.2 3652.4 3449.6 3005.1 2375.1 2553.4 1977 2397.3 3999.6 3617.8 TRUE FALSE FALSE 3863.52879 3703.818583 3509.638841 3352.563801 2253.889784 2390.245981 2144.926331 2466.662093 3641.865759 3523.809034 1.096406971 1.051083798 0.995978728 0.951403373 0.63961746 0.678313143 0.608695395 0.699998799 1.033502589 1 11.78292003 -8.861445574 3.011955229 1.042682687 0.650975008 0.95860034 0.037345286 0.041637638 0.759707577 0.006979731 0.013616402 1.38E-09 8.861445574 -0.391707679 GQK(ac)YFDSGDYNMAK ddPTM_HeLa_Romidepsin_16h_R1 1 GQKYFDSGDYNMAK 14 1 O43768-2;O43768;H3BMD8;O43768-6;O43768-5;P56211;H3BTD3;P56211-2 O43768-2;P56211;H3BTD3 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 0 1 GQK(1)YFDSGDYNMAK 138.02 3.08E-05 1289300 479.92 806.74 485.23 399.3 702.06 392.32 527.42 595.49 1027.4 848.65 FALSE TRUE FALSE 474.0705504 818.0973069 493.6752246 445.4689448 666.2312585 367.2520182 572.2190416 612.7195636 935.5067708 826.6019507 0.573517338 0.989711319 0.597234526 0.538915913 0.805988007 0.444291255 0.692254647 0.74125105 1.131750016 1 9.691048958 -12.46532234 0.857823001 1.031988977 0.663354351 0.506562144 0.151429317 0.575232388 0.643946341 0.150759415 0.026391471 3.43E-13 12.46532234 -0.368634627 GQKS(ph)PGALETPSAAGSQGNTASQGK ddPTM_HeLa_Romidepsin_16h_R1 1 GQKSPGALETPSAAGSQGNTASQGK 25 1 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 GQKS(0.662)PGALET(0.336)PS(0.002)AAGSQGNTASQGK 103.18 3.59E-06 27054000 5906 5471 4930.5 8610.4 5270.6 5160.3 4461.2 5088.7 7223.8 5919 TRUE FALSE FALSE 5834.0154 5548.020882 5016.313284 9605.974961 5001.621615 4830.573484 4840.134217 5235.933506 6577.685236 5765.223527 1.011932213 0.962325373 0.870098663 1.666192979 0.867550337 0.837881387 0.839539732 0.908192628 1.140924581 1 12.49316083 -8.573979609 24.99999432 1.041535734 0.858469744 0.210046998 0.210141846 144.3058764 70597.93879 0.029226984 0.058453979 2.67E-09 8.573979609 -0.183065991 GQKSPGALET(ph)PSAAGSQGNTASQGK ddPTM_HeLa_Romidepsin_16h_R1 3 GQKSPGALETPSAAGSQGNTASQGK 25 1 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 GQKSPGALET(0.999)PS(0.001)AAGSQGNTASQGK;GQKS(0.016)PGALET(0.958)PS(0.026)AAGSQGNTASQGK;GQKS(0.385)PGALET(0.596)PS(0.019)AAGSQGNTASQGK ;; 164.19 4.30E-11 50221300 9298.8 7621.3 7326.6 11321.6 7489.1 6594.5 6607.4 6739.7 8737.4 7822 TRUE FALSE FALSE 9185.462649 7728.592861 7454.1164 12630.65666 7106.903281 6173.132733 7168.632391 6934.702586 7955.905061 7618.783312 1.205633796 1.014413003 0.978386718 1.657831197 0.932813415 0.810251779 0.940915642 0.91021129 1.044248764 1 12.89534491 -8.548540439 24.99997934 1.124734881 0.889009152 0.295986678 0.188602323 227.8176585 221942.294 0.027365544 0.054732449 2.83E-09 8.548540439 -0.235725729 GQLELEFS(ph)MAMGT(ph)LIS(ph)ELVQAMR ddPTM_HeLa_Romidepsin_16h_R1 1 GQLELEFSMAMGTLISELVQAMR 23 0 A0A669KBH4;Q14999;Q14999-2 A0A669KBH4 CUL7 Cullin-7 3 0 GQLELEFS(1)MAMGT(1)LIS(1)ELVQAMR 42.395 0.018865 9817300 1228 1276.7 1330.3 993.59 1214.6 1676.3 999.62 1178.3 1346.3 1109.2 TRUE FALSE FALSE 1213.032664 1294.673416 1353.453313 1108.473551 1152.61443 1569.18984 1084.527698 1212.392251 1225.883556 1080.382824 1.122780404 1.198346907 1.252753453 1.026000716 1.066857418 1.452438714 1.003836486 1.12218764 1.134675162 1 10.07732689 -11.59406307 0.72727366 1.004622002 1.159542732 0.033904542 0.1284647 0.799347592 0.85593746 0.062602332 0.027016307 2.55E-12 11.59406307 0.154920731 GQLQSAPS ddPTM_HeLa_Romidepsin_16h_R1 1 GQLQSAPS 8 0 G8JLQ3;P78537-2;P78537 G8JLQ3 BLOC1S1 Biogenesis of lysosome-related organelles complex 1 subunit 1 0 0 57.811 0.029176 443200 0 267.94 294.06 489.07 1254.5 2109 1712.7 1268.5 163.98 136.81 FALSE FALSE TRUE 0 271.7120664 299.1779909 545.6185745 1190.478184 1974.241706 1858.176695 1305.202046 149.3132181 133.2556565 0 2.039028388 2.245142899 4.094524683 8.933790995 14.81544393 13.94444892 9.79472152 1.120501914 1 7.058052964 -8.777359892 1.650431222 0.72036972 13.05131957 0.926493221 1.438877923 0.061915647 0.341284588 0.223700956 0.523650521 1.67E-09 8.777359892 12.33094985 GQLTNIVSPT(ph)AATTPR ddPTM_HeLa_Romidepsin_16h_R1 2 GQLTNIVSPTAATTPR 16 0 Q8NEY1-2;Q8NEY1-3;Q8NEY1;Q8NEY1-6;Q8NEY1-5;H0Y6F6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 GQLT(0.106)NIVS(0.189)PT(0.481)AAT(0.207)T(0.017)PR;GQLTNIVS(0.007)PT(0.984)AAT(0.009)TPR ; 147.49 0.0006206 23756000 8488.1 7816.1 6600.7 5260.7 8744.4 8287.8 7526.2 8109.7 8403.5 8588.3 TRUE FALSE FALSE 8384.643772 7926.135261 6715.582415 5868.966886 8298.140638 7758.236328 8165.47524 8344.341375 7651.869913 8365.174728 1.002327392 0.947515804 0.802802408 0.701595254 0.991986528 0.927444624 0.976127278 0.997509514 0.914729239 1 13.03017996 -10.00074318 24.97759951 0.99972129 0.897494528 0.098689167 0.089769424 31.68996486 1065110.739 0.01461313 0.019075492 9.98E-11 10.00074318 -0.102226762 GQMGPTEQGPYAKT(ph)Y(ph)EGRR ddPTM_HeLa_Romidepsin_16h_R1 1 GQMGPTEQGPYAKTYEGRR 19 2 Q96S66-4;Q96S66-3;Q96S66-2;Q96S66 Q96S66-4 CLCC1 Chloride channel CLIC-like protein 1 2 0 GQMGPTEQGPY(0.006)AKT(0.997)Y(0.997)EGRR 57.788 0.013731 10611000 2202.5 2200.6 2019.2 2734.2 2242.2 2303.9 2065 2225.9 2378.3 2276 TRUE FALSE FALSE 2175.655083 2231.580105 2054.343329 3050.341069 2127.772167 2156.688225 2240.401048 2290.302905 2165.578891 2216.869192 0.981408867 1.006635896 0.92668676 1.375968 0.959809526 0.972853172 1.010614905 1.033124964 0.976863632 1 11.11430793 GQPEGPLPSSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GQPEGPLPSSSPR 13 0 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4 P49815 TSC2 Tuberin 1 0 GQPEGPLPSS(0.031)S(0.969)PR;GQPEGPLPSS(0.003)S(0.997)PR ; 191.63 8.31E-11 72568000 9829.8 9887.4 9043.1 8125.3 7934.2 8804.7 6719.5 8757.2 9805.4 9810.7 TRUE FALSE FALSE 9709.990617 10026.59508 9200.491362 9064.785417 7529.288167 8242.108086 7290.254162 9010.575765 8928.380466 9555.8166 1.016134049 1.049266169 0.962815817 0.94861442 0.787927237 0.862522632 0.762912733 0.942941471 0.934339873 1 13.22216345 -9.021969428 2.433714747 1.009134518 0.835535034 0.621414894 0.055274868 0.102795443 1.21515307 0.006833314 0.012824447 9.51E-10 9.021969428 -0.173599484 GQQPPPAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GQQPPPAKR 9 1 Q9HCJ5 Q9HCJ5 ZSWIM6 Zinc finger SWIM domain-containing protein 6 0 1 GQQPPPAK(1)R 98.299 0.0082528 349100 234.93 184.59 229.65 217.04 412.28 461.33 401.53 264.24 118.33 166.55 FALSE TRUE FALSE 232.0665828 187.1886629 233.6469619 242.135186 391.2398132 431.8525019 435.6359482 271.8853675 107.7462684 162.223007 1.430540508 1.153897134 1.440282524 1.49260694 2.411740606 2.662091585 2.685414087 1.675997582 0.664186113 1 7.341834632 -8.855918859 3.013314964 1.224823492 2.41504156 0.740743891 0.339023541 0.089272393 1.63171348 0.045477724 0.088908838 1.39E-09 8.855918859 1.190218068 PEPVK(ac)SAPVPK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPVKSAPVPK 11 1 Q99879 Q99879 HIST1H2BM Histone H2B type 1-M 0 1 ; PEPVK(1)SAPVPK;PEPVK(1)SAPVPK 181.87 6.44E-05 43664000 2539.25 2029.05 2484.4 8252.9 15890 15471.7 15808.3 16297.8 1657.6 1839.71 FALSE TRUE FALSE 2508.300644 2057.615019 2527.63994 9207.139129 15079.07401 14483.1083 17151.05661 16769.35113 1509.340104 1791.914069 1.399788465 1.14827773 1.410581 5.138158848 8.415065358 8.082479262 9.571361096 9.358345592 0.842306074 1 10.80728574 -8.989624593 1.850685145 1.162896292 9.057899715 0.987631747 0.406684529 0.024769306 0.169421375 0.0639228 0.128315144 1.02E-09 8.989624593 7.895003423 up GQS(ph)ADKLGTGER ddPTM_HeLa_Romidepsin_16h_R1 1 GQSADKLGTGER 12 1 O60307 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 0 GQS(0.999)ADKLGT(0.001)GER 152 0.00066222 0 1194 1011.3 1454.2 1689.8 2359.1 3320.7 3416.6 3097.4 1601 1372.9 TRUE FALSE FALSE 1179.447069 1025.537108 1479.509741 1885.182627 2238.706324 3108.517987 3706.805919 3187.018382 1457.80255 1337.23186 0.882006407 0.766910465 1.106397316 1.409764965 1.674134749 2.324591628 2.771999404 2.383295281 1.090164386 1 10.38503392 -8.533642713 1.174223004 0.932681565 2.639095825 0.954224367 0.144984682 0.063466385 0.165707057 0.021660375 0.074739628 2.93E-09 8.533642713 1.70641426 up GQSPAGDGSPEPPT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GQSPAGDGSPEPPTPR 16 0 A0A0A0MRW6;Q9H6R4-3;Q9H6R4-2;Q9H6R4-4;Q9H6R4 A0A0A0MRW6 NOL6 Nucleolar protein 6 1 0 GQSPAGDGS(0.026)PEPPT(0.973)PR 149.86 0.00059411 5382000 1204.1 1290.2 1239.5 1029.1 1293.2 1296.1 1292.7 1519.9 1340.2 1464 TRUE FALSE FALSE 1189.423966 1308.363469 1261.072978 1148.089384 1227.203178 1213.283393 1402.501906 1563.875908 1220.329155 1425.965069 0.834118585 0.917528415 0.884364565 0.805131492 0.860612371 0.850850711 0.983545766 1.096714038 0.85579176 1 10.47772293 -7.44223804 3.222185729 0.900778526 1.095471805 0.589132324 0.055401604 0.210344784 3.756114349 0.010370404 0.079014568 3.61E-08 7.44223804 0.194693279 GQSQLS(ph)NPTDDSWK ddPTM_HeLa_Romidepsin_16h_R1 1 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 0 GQSQLS(0.975)NPT(0.025)DDSWK 213.69 5.45E-24 17795000 2518.7 2274.8 2536 2118 2158.6 1950.6 1739 2220.5 2262.7 2391.2 TRUE FALSE FALSE 2488.001116 2306.824694 2580.138016 2362.893125 2048.438587 1825.962955 1886.710617 2284.746664 2060.318445 2329.076279 1.068235136 0.990446176 1.107794553 1.014519424 0.879506869 0.783985897 0.810068195 0.980966868 0.884607543 1 11.18554217 -8.748202459 4.087437284 1.035402607 0.850755109 0.468360895 0.074529951 0.088912261 3.338345216 0.008411477 0.016706639 1.79E-09 8.748202459 -0.184647498 GQSQLSNPT(ph)DDSWK ddPTM_HeLa_Romidepsin_16h_R1 1 GQSQLSNPTDDSWK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 0 GQSQLS(0.04)NPT(0.96)DDSWK 135.91 0.0029294 17656000 3605.3 4294.2 4431.8 3749.9 3340.2 3548.6 3376.6 3538.3 4224.2 4031.6 TRUE FALSE FALSE 3561.357217 4354.65386 4508.93362 4183.481082 3169.73713 3321.855913 3663.40832 3640.675128 3846.376972 3926.858451 0.906922738 1.108940879 1.148229221 1.065350619 0.80719414 0.845932176 0.932910714 0.927121559 0.979504869 1 11.93915988 -8.760794971 24.99999807 0.99061128 0.87987991 0.427139721 0.079452058 19.89083294 771612.512 0.014140039 0.026982883 1.73E-09 8.760794971 -0.110731371 GQTPLTEGSEDLDGHS(ph)DPEESFAR ddPTM_HeLa_Romidepsin_16h_R1 2 GQTPLTEGSEDLDGHSDPEESFAR 24 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 0 GQTPLTEGS(0.016)EDLDGHS(0.969)DPEES(0.015)FAR;GQTPLT(0.001)EGS(0.003)EDLDGHS(0.955)DPEES(0.042)FAR ; 98.033 1.30E-05 28455000 633.55 585.37 602.58 740.14 973.73 975.22 830.01 928.51 787.78 718.16 TRUE FALSE FALSE 625.8280489 593.6108542 613.0676521 825.7184693 924.0369246 912.9065894 900.5110287 955.3749719 717.3189838 699.5020997 0.894676441 0.848619117 0.876434327 1.180437442 1.320992353 1.305080556 1.287360008 1.365792858 1.025470809 1 9.450184578 -9.070910814 3.354351854 0.935046752 1.313925708 0.919344511 0.054842141 0.054478762 1.196157145 0.009333563 0.016474663 8.49E-10 9.070910814 0.378878957 GQVIIISDS(ph)DDDDDER ddPTM_HeLa_Romidepsin_16h_R1 2 GQVIIISDSDDDDDER 16 0 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 0 GQVIIIS(0.002)DS(0.998)DDDDDER;GQVIIISDS(1)DDDDDER ; 227.88 2.83E-35 10190000 4796.3 4338.3 4251.5 4085.3 6188.5 7233.7 6756.8 7951.1 5704.8 4971 TRUE FALSE FALSE 4737.840851 4399.374701 4325.495574 4557.661608 5872.677753 6771.489916 7330.722423 8181.152534 5194.5484 4841.852703 0.978518171 0.908613907 0.893355465 0.941305299 1.212898886 1.39853282 1.514032515 1.689673981 1.072843128 1 12.24134348 -8.193120652 1.34775582 0.970777285 1.64017112 0.942685353 0.063963375 0.073482166 0.239269728 0.009322543 0.041358693 6.41E-09 8.193120652 0.669393835 GQVKEEGINKSEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GQVKEEGINKSEKR 14 3 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 1 GQVKEEGINK(0.073)SEK(0.926)R 44.691 0.029941 5602800 3031.6 4014.1 1861.7 5694.2 2577.6 2459.8 2302.9 2529.1 3961 2632.1 FALSE TRUE FALSE 2994.649693 4070.610605 1894.102108 6352.590196 2446.055454 2302.626719 2498.508269 2602.275518 3606.718239 2563.717663 1.168088724 1.58777648 0.738810726 2.477882135 0.954104849 0.898159244 0.974564518 1.015039821 1.406831295 1 11.32402167 -5.760696482 12.18128786 1.149935907 0.968874695 0 0.486175727 0 0 0.058997132 0 1.74E-06 5.760696482 -0.181061211 GQVSESEDS(ph)ITK ddPTM_HeLa_Romidepsin_16h_R1 1 GQVSESEDSITK 12 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 GQVSES(0.011)EDS(0.988)IT(0.001)K 133.47 0.0030024 5088100 1426.8 1193.8 1346 982.59 876.5 860.23 851.14 946.34 1216.4 1425.6 TRUE FALSE FALSE 1409.409613 1210.606348 1369.426565 1096.201679 831.7689343 805.2640793 923.4358104 973.7208548 1107.602137 1388.562706 1.015013298 0.871841323 0.986218742 0.789450612 0.599014312 0.579926334 0.665029967 0.701243703 0.797660871 1 10.43937661 -9.087230867 2.324968436 0.99564057 0.633520405 0.727401194 0.081385629 0.062020402 0.659271289 0.008400575 0.015439651 8.18E-10 9.087230867 -0.362120165 GQVSESEDSIT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 GQVSESEDSITK 12 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 GQVSES(0.018)EDS(0.23)IT(0.752)K;GQVSESEDS(0.372)IT(0.628)K ; 206.45 7.02E-15 46345000 7023.8 7124.2 8518.7 4218.2 5362.4 4645.5 3414.2 4061.3 7085.5 7241.4 TRUE FALSE FALSE 6938.191224 7224.494675 8666.9644 4705.928131 5088.736718 4348.667543 3704.202063 4178.807308 6451.755134 7053.267384 0.983684702 1.024276308 1.22878716 0.667198317 0.721472254 0.616546532 0.525175335 0.592464043 0.914718638 1 12.78407602 -9.134613723 6.385033736 1.010780791 0.618387291 0.83999605 0.088507927 0.06959002 3.346164154 0.012920092 0.021559553 7.33E-10 9.134613723 -0.392393499 GRAEGEWEDQEALDY(ph)FSDKESGK ddPTM_HeLa_Romidepsin_16h_R1 1 GRAEGEWEDQEALDYFSDKESGK 23 2 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 GRAEGEWEDQEALDY(0.721)FS(0.277)DKES(0.002)GK 76.533 0.00028773 35994000 2294.5 1907.8 1831.3 1860.2 2395.9 1865.3 1886.2 2364.3 2312.9 2783.3 TRUE FALSE FALSE 2266.533751 1934.658058 1863.173008 2075.285077 2273.628283 1746.11335 2046.413781 2432.70729 2106.028431 2710.989465 0.836054061 0.713635403 0.687266783 0.765508352 0.838671014 0.644087103 0.754858625 0.89735033 0.776848622 1 11.40460379 -11.29687755 0.769502201 0.983780797 0.754643471 0.07829517 0.095898594 0.27558064 0.349082438 0.029061075 0.016830889 5.05E-12 11.29687755 -0.229137326 GRAEGEWEDQEALDYFS(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 2 GRAEGEWEDQEALDYFSDK 19 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 GRAEGEWEDQEALDY(0.001)FS(0.999)DK;GRAEGEWEDQEALDY(0.043)FS(0.957)DK ; 99.11 0.00053541 6254600 1991.75 2576.8 2238 1652.5 2499.4 2311 1861.14 2507.9 2685.4 3113.4 TRUE FALSE FALSE 1967.473785 2613.076258 2276.951451 1843.569825 2371.846291 2163.334558 2019.225185 2580.46213 2445.211098 3032.513419 0.648793101 0.861686627 0.75084629 0.607934598 0.782138762 0.713380045 0.665858615 0.850931809 0.806331501 1 11.56629831 -12.41233597 0.990243614 1.009974431 0.726877556 0.236689533 0.097556252 0.299232524 0.494183053 0.06326959 0.013905504 3.87E-13 12.41233597 -0.283096875 GRAEGEWEDQEALDYFS(ph)DKESGK ddPTM_HeLa_Romidepsin_16h_R1 2 GRAEGEWEDQEALDYFSDKESGK 23 2 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 GRAEGEWEDQEALDY(0.45)FS(0.536)DKES(0.014)GK;GRAEGEWEDQEALDY(0.362)FS(0.618)DKES(0.021)GK ; 84.214 0.00011384 90236000 8018.9 8610.4 8366.7 9310.4 8335.9 8432.6 7136.6 7198.3 9870.5 8936.8 TRUE FALSE FALSE 7921.162562 8731.617437 8512.318904 10386.91225 7910.487917 7893.784075 7742.782626 7406.571453 8987.657759 8704.620648 0.909995149 1.003101432 0.977908084 1.193264207 0.90876883 0.906849867 0.889502592 0.850878143 1.032515732 1 13.08756571 -8.543589115 24.99995947 0.979715518 0.887234281 0.362654014 0.074783119 262.6608144 317062.7355 0.011530921 0.023063643 2.86E-09 8.543589115 -0.092481237 GRAS(ph)PGGVSTSSSDGK ddPTM_HeLa_Romidepsin_16h_R1 4 GRASPGGVSTSSSDGK 16 1 P54259 P54259 ATN1 Atrophin-1 1 0 GRAS(0.994)PGGVS(0.002)T(0.003)S(0.002)SSDGK;GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK;GRAS(1)PGGVSTSSSDGK ;;; 95.073 0.003257 64478600 13425.6 12832.1 13100.77 8835.79 9094.45 7214.26 7485.74 7727.28 13644.6 13878.2 TRUE FALSE FALSE 13261.96362 13012.75064 13328.78341 9857.425613 8630.32628 6753.292069 8121.578569 7950.856655 12424.1928 13517.64236 0.981085552 0.962649424 0.986028706 0.729226691 0.638449076 0.499590971 0.600813245 0.588183682 0.919109447 1 13.72255593 -9.052217574 1.909405141 0.990452033 0.569490528 0.954619092 0.04002632 0.035019697 0.252685392 0.004935987 0.009546706 8.87E-10 9.052217574 -0.420961505 GRDGY(ph)MGIGLS(ph)AQGVNMNR ddPTM_HeLa_Romidepsin_16h_R1 1 GRDGYMGIGLSAQGVNMNR 19 1 A0A0D9SEU5;R4GMX8;Q6VN20-3;Q6VN20;R4GN91;Q96S59 A0A0D9SEU5 RANBP10;RANBP9 Ran-binding protein 10;Ran-binding protein 9 2 0 GRDGY(1)MGIGLS(1)AQGVNMNR 48.372 0.020518 2039400 616.04 584.24 777 676.95 766.27 799.1 582.56 908.12 835.39 590.2 TRUE FALSE FALSE 608.5314675 592.4649461 790.5233591 755.2221441 727.1643826 748.040089 632.0426319 934.3950194 760.6706261 574.8665189 1.058561331 1.030613067 1.37514246 1.313734788 1.26492735 1.301241357 1.099459807 1.625412141 1.323212609 1 9.167083198 -9.769173925 24.99831253 1.028648553 1.314505323 0.2959926 0.15417729 87.16984415 281735.6047 0.018002351 0.023906024 1.70E-10 9.769173925 0.28585677 GRDIVVLGVEK ddPTM_HeLa_Romidepsin_16h_R1 2 GRDIVVLGVEK 11 1 O14818;O14818-4 O14818 PSMA7 Proteasome subunit alpha type-7 0 0 ; ; 134.99 0.00075279 941440 1189.48 778.28 1319.5 1034.44 1518.48 903.06 1020.18 924.66 896.57 942.89 FALSE FALSE TRUE 1174.98216 789.2366463 1342.465344 1154.04682 1440.986299 845.3573805 1106.834064 951.4135782 816.3785337 918.3935819 1.279388471 0.859366465 1.461753839 1.256592863 1.569029148 0.920473964 1.205184885 1.03595408 0.888920121 1 9.84296875 -12.4767844 0.979570036 0.987913002 1.209316419 0.173480117 0.212178381 1.087118392 1.690647006 0.183642201 0.036057713 3.34E-13 12.4767844 0.221403416 GRDS(ph)PYQSR ddPTM_HeLa_Romidepsin_16h_R1 1 GRDSPYQSR 9 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 0 GRDS(1)PYQSR 74.237 0.027671 24716000 302.96 547.09 902.02 360.19 454.38 474.63 957.34 149.17 661.9 417.85 TRUE FALSE FALSE 299.267407 554.7919474 917.7192797 401.8368625 431.1912931 444.3026748 1038.656436 153.4859986 602.6980062 406.9941968 0.735311239 1.363144614 2.254870676 0.987328236 1.059453173 1.091668329 2.552017803 0.377120853 1.480851597 1 8.668864413 -10.21059273 7.21644449 0.875162902 1.424652111 0.019295179 0.624337417 0.345055447 42.50754214 0.092172933 0.112720695 6.16E-11 10.21059273 0.549489209 GRDWNVDLIPK ddPTM_HeLa_Romidepsin_16h_R1 1 GRDWNVDLIPK 11 1 P50395-2;P50395;Q5SX87;P31150;V9GYJ7;V9GYF8;G5E9U5;Q5SX90;Q5SX86 P50395-2 GDI2;GDI1 Rab GDP dissociation inhibitor beta;Rab GDP dissociation inhibitor alpha 0 0 112.94 0.015068 24562000 6095.9 5919.4 5257 5379.8 6097.6 5489 5758 5500.2 5761.3 5678.4 FALSE FALSE TRUE 6021.600826 6002.733469 5348.49588 6001.837789 5786.416719 5138.270615 6247.084376 5659.339609 5245.994899 5530.874349 1.088724937 1.085313657 0.967025382 1.085151716 1.046202888 0.929015973 1.129493093 1.023226935 0.948492872 1 12.43329185 GREDVSNFDDEFTSEAPILT(ph)PPREPR ddPTM_HeLa_Romidepsin_16h_R1 5 GREDVSNFDDEFTSEAPILTPPREPR 26 2 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR;GREDVSNFDDEFTSEAPILT(0.999)PPREPR;GREDVSNFDDEFT(0.034)S(0.034)EAPILT(0.933)PPREPR;GREDVSNFDDEFTSEAPILT(1)PPREPR ;;;; 116.45 1.90E-07 364987000 9111.38 7929.97 8158.14 8779.25 8559 9197.45 7402.76 8170.05 9911.2 9126.55 TRUE FALSE FALSE 9000.326996 8041.608326 8300.129005 9794.348193 8122.202292 8609.762628 8031.55025 8406.437507 9024.717449 8889.440915 1.012473909 0.904624757 0.933706527 1.101795747 0.913691015 0.968538147 0.903493293 0.945665491 1.015217665 1 13.11787697 -6.661259072 0.268532125 1.008244548 0.81914987 0.143673676 0.055444039 15.43453829 0.65971623 0.030072359 1.017954731 2.18E-07 6.661259072 -0.189094678 GREEYEGPNK(ac)KPR ddPTM_HeLa_Romidepsin_16h_R1 2 GREEYEGPNKKPR 13 3 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 1 ; GREEYEGPNK(0.841)K(0.159)PR;GREEYEGPNK(0.967)K(0.033)PR 74.698 0.010406 33493000 1321.26 1210.5 1245.43 2272.98 2887.6 3005.6 3126.3 2076.03 1576.3 1411.67 FALSE TRUE FALSE 1305.155975 1227.541451 1267.106187 2535.792642 2740.234997 2813.55186 3391.847844 2136.096653 1435.31178 1374.99461 0.949208066 0.892760918 0.921535385 1.84422006 1.992905992 2.046227556 2.466808102 1.553530928 1.043867205 1 10.42521025 -9.188439326 3.671958545 0.962327147 2.037377187 0.854679216 0.210662144 0.057793636 1.522428668 0.029316073 0.049581792 6.48E-10 9.188439326 1.07505004 GRETIT(ph)KSK ddPTM_HeLa_Romidepsin_16h_R1 1 GRETITKSK 9 2 Q8N9C0-2 Q8N9C0-2 1 0 GRETIT(0.596)KS(0.404)K 84.188 0.0024985 0 4050.4 4221.2 4764.4 3127.9 4598.3 5266 4059.2 4419.4 4665.3 5189.6 TRUE FALSE FALSE 4001.032167 4280.626164 4847.322383 3489.562515 4363.631592 4929.519595 4403.988347 4547.268366 4248.023884 5054.773444 0.791535409 0.846848274 0.958959375 0.690349934 0.86326947 0.97522068 0.87125336 0.899598848 0.840398473 1 12.30343072 -12.49618038 1.23915235 1.000081785 0.855393342 0 0.090591552 0.443613502 1.217902016 0.05427161 0.01315752 3.19E-13 12.49618038 -0.144688443 GREVS(ph)PSDVR ddPTM_HeLa_Romidepsin_16h_R1 1 GREVSPSDVR 10 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 GREVS(0.777)PS(0.223)DVR 82.705 0.020243 7993300 3412.8 3660 3402.1 1774.5 1898.4 2419.4 2120.4 2676.7 4021.4 4272.8 TRUE FALSE FALSE 3371.203481 3711.525576 3461.312123 1979.676039 1801.517564 2264.808148 2300.506723 2754.146091 3661.715912 4161.79204 0.810036506 0.891809475 0.83168791 0.475678751 0.432870635 0.54419061 0.552768303 0.661769273 0.879841154 1 12.02298916 -9.361545782 4.149160124 0.904625462 0.529739464 0.857932015 0.071219396 0.076035948 2.303727692 0.014286652 0.022234884 4.35E-10 9.361545782 -0.374885999 GRLGS(ph)VDSFER ddPTM_HeLa_Romidepsin_16h_R1 2 GRLGSVDSFER 11 1 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 GRLGS(0.997)VDS(0.003)FER;GRLGS(0.999)VDS(0.001)FER ; 85.45 0.016106 34061900 4778.5 5014.3 4107.4 4734.3 4921.1 5128.1 3780.2 4537.9 4478.9 5013.1 TRUE FALSE FALSE 4720.257804 5084.891447 4178.887574 5281.702042 4669.957904 4800.43096 4101.290094 4669.196977 4078.295966 4882.858939 0.966699604 1.041375864 0.855828036 1.08168229 0.956398283 0.98311891 0.839936223 0.956242446 0.83522707 1 12.25351039 -7.792000646 23.90127915 0.983769453 0.898089391 0.068463214 0.077076101 100.4440968 78555.06216 0.007465391 0.022401179 1.61E-08 7.792000646 -0.085680062 GRLS(ph)PVPVPR ddPTM_HeLa_Romidepsin_16h_R1 1 GRLSPVPVPR 10 1 Q9UKM9-2;Q9UKM9;Q5QPM0;Q5QPM1;Q5QPL9 Q9UKM9-2 RALY RNA-binding protein Raly 1 0 GRLS(1)PVPVPR 71.806 0.029977 7673100 1295.9 1175.3 1134.5 891.29 1161 988.74 1385.4 1080.1 1466.6 1355.5 TRUE FALSE FALSE 1280.105072 1191.845904 1154.245497 994.3451434 1101.749838 925.562705 1503.075841 1111.350989 1335.423623 1320.283915 0.969568029 0.902719401 0.874240369 0.753129787 0.834479482 0.701033084 1.138448954 0.841751518 1.01146701 1 10.36663249 -10.15734187 1.938228497 0.987913529 0.8572031 0.244323052 0.107724765 0.363026779 2.608671975 0.019103729 0.023560991 6.96E-11 10.15734187 -0.130710428 GRLT(ph)PS(ph)PDIIVLS(ph)DNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 3 0 GRLT(1)PS(1)PDIIVLS(0.983)DNEAS(0.012)S(0.006)PR;GRLT(1)PS(1)PDIIVLS(0.991)DNEAS(0.005)S(0.005)PR ; 74.392 0.00059078 2394700 1452.27 1284.84 1350.95 1349.45 1351.72 1436.7 1162.86 1368.91 1494.74 1506.64 TRUE FALSE FALSE 1434.569175 1302.928011 1374.462718 1505.479758 1282.736684 1344.899507 1261.633299 1408.517251 1361.046711 1467.497276 0.977561729 0.887857193 0.93660325 1.025882489 0.874098171 0.916457924 0.859717643 0.959809108 0.92746115 1 10.51914211 -10.04834637 0.379110908 1.004818619 0.899717143 0.019150474 0.051356522 0.948184118 0.362005552 0.026169698 0.037076901 8.95E-11 10.04834637 -0.105101476 GRLT(ph)PS(ph)PDIIVLSDNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 3 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 0 GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR;GRLT(1)PS(1)PDIIVLSDNEASSPR ;; 96.133 0.00065104 13196300 2392.14 2223.72 2299.56 2473.9 2986.72 2823.68 2342.79 2662.12 2643 2681.28 TRUE FALSE FALSE 2362.983678 2255.025589 2339.582877 2759.943958 2834.296533 2643.255961 2541.786524 2739.144242 2406.60346 2611.619959 0.904796147 0.863458552 0.895835885 1.056793868 1.085263774 1.012113555 0.973260491 1.048829571 0.921498341 1 11.35072926 -9.252837138 24.9318058 0.941538012 1.033301202 0.60406527 0.045718043 511.7290945 1483140.659 0.008718037 0.014308819 5.59E-10 9.252837138 0.09176319 GRLT(ph)PSPDIIVLS(ph)DNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 3 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 0 GRLT(0.994)PS(0.006)PDIIVLS(0.933)DNEAS(0.036)S(0.03)PR;GRLT(1)PSPDIIVLS(0.992)DNEAS(0.006)S(0.002)PR;GRLT(0.986)PS(0.016)PDIIVLS(0.933)DNEAS(0.031)S(0.035)PR ;; 123.88 0.00014189 18008800 6449.6 6252.7 5492.2 5943.2 5606 4744.14 4670 5022.9 6413.1 6287.6 TRUE FALSE FALSE 6370.989794 6340.725675 5587.789437 6630.380748 5319.904901 4441.004765 5066.669683 5168.229687 5839.496274 6124.247246 1.040289449 1.035347761 0.912404286 1.082644198 0.86866266 0.725151123 0.827313053 0.843896316 0.953504331 1 12.58031681 -8.597357731 5.140812423 1.015556856 0.800619286 0.751565655 0.053681919 0.060755751 2.919650447 0.006928369 0.014147725 2.53E-09 8.597357731 -0.21493757 VS(ph)PDFTQESR ddPTM_HeLa_Romidepsin_16h_R1 2 VSPDFTQESR 10 0 D6RE87;E7EPB1;E7EQS8;Q6N021-2;Q6N021-3;Q6N021 D6RE87 TET2 Methylcytosine dioxygenase TET2 1 0 VS(1)PDFTQESR;VS(1)PDFTQESR ; 155.47 0.0032618 10005500 1733.72 1908.46 1675.49 1264.84 966.8 704.6 754.74 767.69 1838.09 1879.54 TRUE FALSE FALSE 1712.588754 1935.32735 1704.651201 1411.086752 917.4605884 659.578334 818.8475968 789.9018989 1673.686627 1830.70928 0.935478272 1.057146195 0.931142492 0.770786912 0.501150346 0.360285678 0.447284343 0.43147315 0.914228515 1 10.83818699 -8.888513361 1.956293037 0.975285414 0.412761247 0.971279521 0.043408293 0.03512025 0.27214576 0.006602497 0.013757647 1.29E-09 8.888513361 -0.562524167 down GRLT(ph)PSPDIIVLSDNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 3 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 0 GRLT(0.5)PS(0.5)PDIIVLSDNEASSPR;GRLT(0.881)PS(0.119)PDIIVLSDNEASSPR;GRLT(0.904)PS(0.096)PDIIVLSDNEASSPR ;; 103.59 0.00020892 59005700 6024.46 6153.78 5638.72 5760.31 5620.7 5456 4583.46 5456.53 6417.7 5912.75 TRUE FALSE FALSE 5951.031564 6240.413076 5736.859556 6426.344145 5333.854705 5107.379208 4972.778978 5614.406087 5843.684839 5759.135903 1.033320218 1.083567601 0.996131998 1.115852144 0.926155381 0.886830819 0.863459217 0.974869526 1.014680837 1 12.49163665 -8.597083343 8.95641974 1.026324782 0.904320066 0.655542628 0.044765083 0.137155655 15.13568074 0.006269806 0.012557411 2.53E-09 8.597083343 -0.122004715 GRNDS(ph)GEENVPLDLTR ddPTM_HeLa_Romidepsin_16h_R1 5 GRNDSGEENVPLDLTR 16 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR;GRNDS(1)GEENVPLDLTR ;;;; 163.96 1.90E-05 90218000 7891.9 7880.7 7734.52 6928.6 9146.8 9821.8 9361.9 10153.2 9093.7 8527.9 TRUE FALSE FALSE 7795.710487 7991.644701 7869.136076 7729.717332 8680.004665 9194.218678 10157.09955 10446.96682 8280.336696 8306.343929 0.938524886 0.962113388 0.947364586 0.930579976 1.044984982 1.106891161 1.222812303 1.257709398 0.996868992 1 13.01999789 -8.023669694 1.405587161 0.965287465 1.2651644 0.946651552 0.025894589 0.086155223 0.296842785 0.004550733 0.024247708 9.47E-09 8.023669694 0.299876936 GRPYDYNGPR ddPTM_HeLa_Romidepsin_16h_R1 1 GRPYDYNGPR 10 1 A0A499FI48;P13667 A0A499FI48 PDIA4 Protein disulfide-isomerase A4 0 0 106.4 0.023212 2056800 817.22 704.98 808.06 517.03 798.94 892.17 653.11 667.89 730.41 821.55 FALSE FALSE TRUE 807.2594083 714.9047269 822.1239453 576.8114413 758.1671105 835.1632163 708.5851471 687.2143434 665.0803003 800.2060126 1.008814475 0.893400844 1.027390363 0.720828677 0.947464901 1.043685255 0.885503403 0.858796776 0.831136345 1 9.644227659 -10.26773559 24.09489457 1.004162394 0.913695509 0 0.101172804 361.6889782 1384139.731 0.013949689 0.016164822 5.40E-11 10.26773559 -0.090466885 GRS(ph)IDQDYER ddPTM_HeLa_Romidepsin_16h_R1 2 GRSIDQDYER 10 1 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IRI3;Q9UDY2-5;A0A3B3IRV6;A0A3B3ISF1;A0A3B3ISZ5 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 GRS(1)IDQDYER;GRS(1)IDQDYER ; 171.99 0.0043363 57555000 7520.8 6286.2 6691.8 8575.9 8335.9 7454.5 6378.9 7161.5 7089.7 7352.2 TRUE FALSE FALSE 7429.133597 6374.697289 6808.267972 9567.485909 7910.487917 6978.181508 6920.723607 7368.706704 6455.579476 7161.188784 1.037416248 0.890173054 0.950717566 1.336019228 1.104633345 0.974444568 0.966421053 1.028978138 0.901467573 1 12.80598338 GRS(ph)PDELPSAGGDGGK ddPTM_HeLa_Romidepsin_16h_R1 2 GRSPDELPSAGGDGGK 16 1 A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;B4E2I7 A0A2R8Y5N1 DIAPH1 Protein diaphanous homolog 1 1 0 GRS(0.957)PDELPS(0.043)AGGDGGK;GRS(1)PDELPSAGGDGGK ; 146.67 0.0020174 14257200 4235.1 4317.4 3727.9 4351.8 4601.7 4499.5 4196.7 4543.6 4699.7 4226.6 TRUE FALSE FALSE 4183.480972 4378.180471 3792.782536 4854.975592 4366.858078 4211.996471 4553.167593 4675.061897 4279.347061 4116.792323 1.016199177 1.063493159 0.921295572 1.179310301 1.060742864 1.023125808 1.105998855 1.135607903 1.039485776 1 12.00730496 -9.261000814 24.99999983 1.007032832 1.094679148 0.441981196 0.051925537 29.00587725 1653463.966 0.007356637 0.011720569 5.48E-10 9.261000814 0.087646316 GRT(ph)SSTNEDEDLNPEQK ddPTM_HeLa_Romidepsin_16h_R1 1 GRTSSTNEDEDLNPEQK 17 1 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 GRT(0.314)S(0.059)S(0.314)T(0.314)NEDEDLNPEQK 118.84 0.0012177 21200000 6332.4 6918.6 5403.5 7363.1 3167.6 2434.4 2336.1 1606.3 6559.7 6422.6 TRUE FALSE FALSE 6255.218273 7016.000232 5497.545651 8214.456266 3005.945552 2278.849697 2534.528276 1652.775756 5972.984003 6255.739926 0.999916612 1.121530037 0.878800224 1.313107061 0.480509994 0.3642814 0.405152437 0.264201481 0.954800563 1 12.61096482 -8.636928238 6.135867045 1.018816091 0.362821354 0.887777187 0.116382785 0.044576678 2.236862181 0.015002792 0.030226057 2.31E-09 8.636928238 -0.655994737 GRTSS(ph)TNEDEDLNPEQK ddPTM_HeLa_Romidepsin_16h_R1 1 GRTSSTNEDEDLNPEQK 17 1 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 GRT(0.183)S(0.183)S(0.317)T(0.317)NEDEDLNPEQK 114.53 0.00077154 27758000 4920.5 5892.4 4437.3 6143 2469.1 1811.2 1836.7 1580.3 5990.2 4924.6 TRUE FALSE FALSE 4860.527053 5975.353362 4514.529345 6853.282564 2343.092614 1695.470165 1992.709252 1626.023487 5454.421509 4796.658182 1.013315285 1.245732578 0.941182209 1.428761922 0.488484383 0.353469041 0.415436993 0.338990903 1.137129498 1 12.22781392 -8.628988742 7.053901752 1.046732761 0.382094886 0.853647144 0.14601706 0.060304248 3.592093663 0.01976248 0.039686156 2.35E-09 8.628988742 -0.664637875 GRWPPS(ph)S(ph)RGGGPPPEAET(ph)AER ddPTM_HeLa_Romidepsin_16h_R1 1 GRWPPSSRGGGPPPEAETAER 21 2 A0A3B3ISC0;A0A3B3ISS4;E9PR03;E9PIA7;M9RSF4;Q92985-3;Q92985-2;Q92985;Q92985-4 A0A3B3ISC0 IRF7 Interferon regulatory factor 7 3 0 GRWPPS(1)S(1)RGGGPPPEAET(1)AER 50.364 0.020964 11628000 3945.7 4009.5 3807.2 3638.5 3759.1 3768.9 3662.4 4115.7 4246.3 3969.1 TRUE FALSE FALSE 3897.608291 4065.945846 3873.462719 4059.20049 3567.2591 3528.079454 3973.484165 4234.781286 3866.500293 3865.98221 1.008180607 1.051723889 1.001934957 1.049979092 0.922730345 0.912595884 1.027807152 1.095395958 1.000134011 1 11.91661928 GS(ph)DSDSEGDNPEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 0 GS(0.824)DS(0.012)DS(0.165)EGDNPEK 88.78 0.023866 11951000 2968.6 3053.2 4009.4 2372.9 2872.6 3110.2 4240.1 1281 4055.5 4308 TRUE FALSE FALSE 2932.417561 3096.18303 4079.181925 2647.265863 2726.000503 2911.468258 4600.253988 1318.063714 3692.765923 4196.077539 0.698847324 0.737875552 0.972141694 0.630890597 0.649654464 0.693854732 1.096322445 0.314118055 0.880051879 1 12.03482562 -12.46439376 0.644657777 1.052148456 0.731658277 0.145196251 0.199551171 1.472698825 0.806458039 0.283290854 0.038745204 3.43E-13 12.46439376 -0.320490179 GS(ph)GDTSSLIDPDTSLSELR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGDTSSLIDPDTSLSELR 19 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 GS(0.339)GDT(0.243)S(0.243)S(0.175)LIDPDTSLSELR 100.68 0.0013098 3380200 478.29 403.79 505.85 376.59 837.02 1057.3 897.73 937.98 630.4 687 TRUE FALSE FALSE 472.4604175 409.4745662 514.6541071 420.1331077 794.303746 989.7419423 973.9831638 965.1189714 574.0154451 669.151641 0.706058819 0.6119309 0.769114317 0.62785934 1.187031007 1.479099627 1.455549242 1.442302331 0.857825656 1 9.386189377 -8.545198379 4.016874634 0.815471331 1.448273073 0.881604658 0.114886286 0.072758979 2.637995561 0.022652375 0.048831859 2.85E-09 8.545198379 0.632801742 GS(ph)GGLFSPSTAHVPDGALGQR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 GS(0.993)GGLFS(0.005)PS(0.001)TAHVPDGALGQR 100.27 0.00045836 10446000 1400.2 1204.9 932.48 835.02 2104 2183.1 1853.4 1706.8 1333.4 1349.5 TRUE FALSE FALSE 1383.133824 1221.862614 948.7094232 931.5689413 1996.625029 2043.606956 2010.82775 1756.183565 1214.137364 1314.439795 1.052261069 0.929569097 0.72175951 0.708719368 1.518993137 1.554736065 1.529798289 1.336069991 0.923691879 1 10.36023235 -8.744314859 24.99910705 0.972336915 1.493094968 0.82302259 0.131949345 93.12815617 135951.775 0.021653982 0.043222929 1.80E-09 8.744314859 0.520758053 GS(ph)IGLLLGK ddPTM_HeLa_Romidepsin_16h_R1 1 GSIGLLLGK 9 0 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 1 0 GS(1)IGLLLGK 109.42 0.019774 2431500 1363.4 1082.6 1536.3 1161 1411.1 1369.3 1197.2 1303.5 962.88 1367.3 TRUE FALSE FALSE 1346.782356 1097.840871 1563.038657 1295.240283 1339.086301 1281.806149 1298.890138 1341.214716 876.7576012 1331.777349 1.011266904 0.824342652 1.173648627 0.972565184 1.005488119 0.962477812 0.975305774 1.007086295 0.658336472 1 10.37913719 GS(ph)LASLDSLR ddPTM_HeLa_Romidepsin_16h_R1 1 GSLASLDSLR 10 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22;O60716-25;O60716-27;O60716-29;O60716-26;O60716-28;O60716-30;O60716-31;O60716-32;E9PKY0 O60716 CTNND1 Catenin delta-1 1 0 GS(0.647)LAS(0.352)LDSLR 155.33 0.0032855 129450000 3589 3526.3 3992.3 2771.3 3516 4229.5 4322.2 3768.1 3666.9 3610.2 TRUE FALSE FALSE 3545.255888 3575.943344 4061.784307 3091.730745 3336.5654 3959.2486 4689.32756 3877.124028 3338.92328 3516.406484 1.008204229 1.016931166 1.155095216 0.879230191 0.948856572 1.125935986 1.333556738 1.102581299 0.949527108 1 11.77988613 -8.02861704 5.456238567 1.004535856 1.222006311 0.537585389 0.084597375 0.090049549 7.870319976 0.010765136 0.029725194 9.36E-09 8.02861704 0.217470455 GS(ph)LDESSLGFGYPK ddPTM_HeLa_Romidepsin_16h_R1 2 GSLDESSLGFGYPK 14 0 Q2KJU6;Q9BUZ4 Q2KJU6 TRAF4 TNF receptor-associated factor 4 1 0 GS(0.951)LDES(0.042)S(0.007)LGFGYPK;GS(1)LDESSLGFGYPK ; 201.3 1.34E-16 109507000 8719.2 9181.5 9181.2 5673.9 8297 8105.3 6808.8 7579.3 10049.5 9172 TRUE FALSE FALSE 8612.927037 9310.757398 9340.994935 6329.943015 7873.57313 7587.397489 7387.139302 7798.595087 9150.647551 8933.710118 0.964092961 1.042205005 1.045589661 0.708545826 0.881332954 0.849299719 0.826883703 0.872940244 1.024283017 1 13.12504373 -9.277709784 24.99938947 0.992255963 0.831917978 0.759889738 0.051856617 323.5816502 497180.382 0.007659396 0.011721179 5.28E-10 9.277709784 -0.160337985 GS(ph)NEYT(ph)EGPS(ph)VVKRPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 GSNEYTEGPSVVKRPAPR 18 2 D6REX7;D6RHD2;O43609 D6REX7 SPRY1 Protein sprouty homolog 1 3 0 GS(0.681)NEY(0.607)T(0.712)EGPS(1)VVKRPAPR 41.871 0.02858 8337800 1857.8 2007.8 2209.3 2183.5 2225.3 2176.3 1866.7 2244.2 2199.7 1913.9 TRUE FALSE FALSE 1835.156419 2036.065861 2247.75194 2435.966544 2111.734637 2037.241454 2025.257451 2309.132386 2002.953323 1864.176602 0.984432707 1.092206532 1.205761266 1.3067252 1.132797523 1.092837155 1.086408578 1.238687571 1.074443977 1 10.86432282 -10.05258924 3.340945549 0.992867408 1.172569543 0.510281638 0.067827756 0.12102137 2.704471342 0.011113953 0.014092405 8.86E-11 10.05258924 0.179702136 GS(ph)PDGSLQTGKPSAPK ddPTM_HeLa_Romidepsin_16h_R1 3 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 0 GS(0.988)PDGS(0.009)LQT(0.003)GKPSAPK;GS(0.87)PDGS(0.129)LQTGKPSAPK;GS(0.997)PDGS(0.002)LQT(0.001)GKPSAPK ;; 165.24 0.00015214 154223100 7701 7962.6 7641.9 4921.05 7922 7965.1 6887.7 7790.6 7703.4 7852 TRUE FALSE FALSE 7607.13725 8074.697692 7774.904064 5490.044955 7517.710779 7456.155816 7472.741066 8016.008719 7014.38861 7648.003908 0.994656559 1.055791523 1.016592585 0.717840239 0.982963773 0.974915273 0.977083845 1.048117759 0.917152854 1 12.90086755 GS(ph)PEEELPLPAFEK ddPTM_HeLa_Romidepsin_16h_R1 4 GSPEEELPLPAFEK 14 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 0 GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK;GS(1)PEEELPLPAFEK ;;; 227.91 4.12E-33 135551000 8428.73 8268.94 8061.49 6273.31 8455.56 8775.98 8004.92 8802.29 9544.64 8810.46 TRUE FALSE FALSE 8325.997397 8385.350354 8201.796852 6998.659619 8024.041221 8215.223201 8684.857705 9056.970373 8690.943493 8581.562979 0.970219227 0.977135561 0.955746275 0.81554603 0.935032609 0.957310833 1.01203682 1.055398695 1.01274599 1 13.06702472 -7.526994041 3.049385898 0.965582278 1.052585033 0.268434116 0.052218688 0.328863357 5.756397029 0.007946604 0.050631117 2.97E-08 7.526994041 0.087002754 GS(ph)PETNHLIR ddPTM_HeLa_Romidepsin_16h_R1 2 GSPETNHLIR 10 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 GS(0.999)PET(0.001)NHLIR;GS(1)PETNHLIR ; 158.34 0.0011618 39253000 3139 2350.9 2901.7 4033.8 7316.6 8764.6 7446.3 6979.8 2746.5 2333.2 TRUE FALSE FALSE 3100.740661 2383.996032 2952.202871 4500.206936 6943.2066 8204.570346 8078.788536 7181.749501 2500.846161 2272.583128 1.364412427 1.049024787 1.299051654 1.980216645 3.055204677 3.610239928 3.554892421 3.16017021 1.100442105 1 11.15011735 -8.870998776 1.888944829 1.167903637 3.465267334 0.978990287 0.151617334 0.037351907 0.270052504 0.027994873 0.059406514 1.35E-09 8.870998776 2.297363697 up GS(ph)PGGYLGAK ddPTM_HeLa_Romidepsin_16h_R1 2 GSPGGYLGAK 10 0 O60551 O60551 NMT2 Glycylpeptide N-tetradecanoyltransferase 2 1 0 GS(1)PGGYLGAK;GS(1)PGGYLGAK ; 127.87 0.0040437 15805000 5577.9 5240.1 5636.4 2893.9 5870.1 6148.4 4828.6 5469.3 5865.8 6938.3 TRUE FALSE FALSE 5509.914409 5313.870265 5734.499178 3228.506334 5570.526893 5755.537083 5238.741163 5627.545566 5341.148157 6758.041966 0.815312251 0.786303236 0.848544476 0.477728068 0.824281193 0.851657494 0.775186243 0.832718352 0.790339596 1 12.72238959 -11.65969957 0.618629846 1.003069903 0.765802563 0.043239551 0.120464373 0.60403825 0.451216569 0.071175341 0.025507622 2.19E-12 11.65969957 -0.237267339 GS(ph)PHY(ph)FSPFRPY ddPTM_HeLa_Romidepsin_16h_R1 2 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 0 GS(1)PHY(0.993)FS(0.007)PFRPY;GS(1)PHY(0.712)FS(0.287)PFRPY ; 69.456 0.030083 73026000 1761.51 1609.87 1251.93 1671.69 1937.14 1977.57 1474.77 1679.41 1711.1 1768.51 TRUE FALSE FALSE 1740.040039 1632.533792 1273.719316 1864.978663 1838.280517 1851.209659 1600.036927 1728.001079 1558.05493 1722.563855 1.010145449 0.947734847 0.739432279 1.082676069 1.067176994 1.074682749 0.928869442 1.003156471 0.904497633 1 10.75034175 -6.838793872 18.70710645 0.992710719 11.84117219 0 0.099370802 7809.142124 913031.7823 0.012733111 27430.15421 1.45E-07 6.838793872 10.84846147 GS(ph)PHYFS(ph)PFRPY ddPTM_HeLa_Romidepsin_16h_R1 1 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 2 0 GS(1)PHY(0.015)FS(0.985)PFRPY 86.539 0.0029859 0 714.43 554.1 654.06 384.87 505.57 543.27 766.62 592.13 860.51 693.73 TRUE FALSE FALSE 705.7222524 561.9006343 665.4436399 429.3704803 479.7688764 508.5568003 831.7366837 609.2623473 783.5438304 675.7067946 1.044420832 0.83157464 0.984811231 0.635439045 0.710025236 0.752629401 1.230913601 0.901666747 1.159591463 1 9.400253552 -10.26338222 24.54302235 1.020976506 0.863653777 0.237090114 0.161321676 177.2616058 2239254.644 0.027205808 0.031941668 5.45E-11 10.26338222 -0.157322729 GS(ph)PHYFSPFRPY ddPTM_HeLa_Romidepsin_16h_R1 1 GSPHYFSPFRPY 12 1 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 0 GS(0.977)PHY(0.023)FSPFRPY 68.033 0.028084 237310000 598.96 542.74 606.83 760.39 1021.3 598.62 715.91 328.54 861.77 588.2 TRUE FALSE FALSE 591.6596451 550.380708 617.3916216 848.3098695 969.17925 560.370114 776.7193775 338.0457865 784.6911329 572.9184792 1.03271175 0.960661469 1.077625603 1.480681633 1.691652975 0.978097468 1.355724079 0.590041688 1.369638371 1 9.162186062 -9.505550678 23.29920133 1.012120999 1.243618789 0.016867312 0.299700396 458.3767163 616329.9749 0.040992324 0.061689086 3.12E-10 9.505550678 0.23149779 GS(ph)PLAEGPQAFFPER ddPTM_HeLa_Romidepsin_16h_R1 1 GSPLAEGPQAFFPER 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 GS(1)PLAEGPQAFFPER 156.29 0.00039419 9044400 532.17 429.31 557.14 5373.8 541.68 590.56 503.03 439.51 399.58 489.47 TRUE FALSE FALSE 525.6837073 435.3538374 566.836788 5995.14404 514.0360483 552.8251219 545.7573556 452.2265284 363.840564 476.7534988 1.102632091 0.913163382 1.188951501 12.57493454 1.078200893 1.159561751 1.14473697 0.948554189 0.763162861 1 8.897099716 -9.476077824 24.99993277 1.040203244 3.393215442 0.118807812 3.252428248 737.1980676 393794.0659 0.497245464 0.759540012 3.34E-10 9.476077824 2.353012199 GS(ph)PNTASAEATLPR ddPTM_HeLa_Romidepsin_16h_R1 2 GSPNTASAEATLPR 14 0 Q6PJG6-3;Q6PJG6 Q6PJG6-3 BRAT1 BRCA1-associated ATM activator 1 1 0 GS(1)PNTASAEATLPR;GS(1)PNTASAEATLPR ; 216 3.53E-24 106402000 3043.6 3079 2535.1 1906.59 2834.17 2974.3 2087.5 2525.79 2858.5 2860.27 TRUE FALSE FALSE 3006.503433 3122.346243 2579.222352 2127.038907 2689.531729 2784.251829 2264.812198 2598.869749 2602.828601 2785.959773 1.079162543 1.120743477 0.925793106 0.763485147 0.965387855 0.999386946 0.812937868 0.932845396 0.934266397 1 11.44395871 -9.618595603 6.851433379 1.044402361 0.894701916 0.407893472 0.079072961 0.139454743 8.581839232 0.011562034 0.016379108 2.41E-10 9.618595603 -0.149700445 GS(ph)PPTSSNIVQGQIK ddPTM_HeLa_Romidepsin_16h_R1 1 GSPPTSSNIVQGQIK 15 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 0 GS(0.995)PPT(0.004)S(0.001)SNIVQGQIK 180.7 3.92E-08 6029800 1097 920.75 1257.7 1171.1 1330.4 1374.4 1184.2 1375.6 1085.2 1281.4 TRUE FALSE FALSE 1083.629342 933.7123427 1279.589741 1306.508092 1262.504724 1286.580276 1284.785918 1415.400816 988.1369941 1248.109043 0.868216882 0.748101576 1.025222714 1.046790021 1.011533992 1.030823615 1.029385954 1.134036183 0.791707263 1 10.28552827 -9.55183804 24.99205902 0.920131722 1.045073384 0.5283316 0.080406886 172.2753934 148674.0242 0.012858728 0.01818515 2.81E-10 9.55183804 0.124941662 GS(ph)PPVPSGPPMEEDGLR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPPVPSGPPMEEDGLR 17 0 Q9H4L4;A0A087X0R7 Q9H4L4 SENP3;SENP3-EIF4A1 Sentrin-specific protease 3 1 0 GS(0.851)PPVPS(0.149)GPPMEEDGLR 94.339 0.0089541 8878900 1450.6 1574 1879.9 812.71 1614.3 1803.4 1434.7 1793.2 1419.2 1544.3 TRUE FALSE FALSE 1432.919529 1596.158813 1912.618871 906.6793541 1531.916247 1688.16856 1556.563382 1845.083413 1292.263198 1504.178863 0.952625758 1.061149609 1.271536861 0.60277363 1.018440216 1.122319028 1.034825991 1.226638306 0.859115381 1 10.55476041 -7.013050216 1.027769618 0.983823371 1.437111979 0.175410611 0.163200018 3.784915456 2.226768086 0.022794373 2.117306344 9.70E-08 7.013050216 0.453288608 GS(ph)PQQIDHAK ddPTM_HeLa_Romidepsin_16h_R1 1 GSPQQIDHAK 10 0 A0A087WTP3;Q92945;M0R3J3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 0 GS(1)PQQIDHAK 94.547 0.0038581 0 1406 1335.2 1963.8 1208.2 1621.7 1568.1 1921 660.55 2438.9 1843.9 TRUE FALSE FALSE 1388.863131 1353.996981 1997.979115 1347.897769 1538.938598 1467.903471 2084.169692 679.6619721 2220.758676 1795.995212 0.773311155 0.753897879 1.112463497 0.750501872 0.856872327 0.81732037 1.160453924 0.378431951 1.2365059 1 10.81056779 -12.45201501 1.169275113 1.000581128 0.835478472 0.181703313 0.216748857 0.961166133 2.337781399 0.128608098 0.031487468 3.53E-13 12.45201501 -0.165102656 GS(ph)PQSAAAELSSGLLASAAASSR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPQSAAAELSSGLLASAAASSR 23 0 Q12948 Q12948 FOXC1 Forkhead box protein C1 1 0 GS(1)PQSAAAELSSGLLASAAASSR 121.47 1.46E-08 0 418.33 296.31 218.81 308.53 262.95 231.44 280.62 229.82 395.73 410.78 TRUE FALSE FALSE 413.2312331 300.48146 222.6182963 344.2036903 249.5306803 216.6517309 304.4558558 236.4694791 360.3349177 400.1078764 1.032799546 0.751001112 0.556395686 0.860277217 0.623658506 0.541483294 0.760934422 0.591014307 0.900594412 1 8.644245219 -10.16495008 3.850800803 1.015847703 0.66259605 0.676197885 0.09827045 0.076449555 2.076652729 0.014447651 0.017756584 6.84E-11 10.16495008 -0.353251653 GS(ph)PSAAFTFPDTDDFGK ddPTM_HeLa_Romidepsin_16h_R1 2 GSPSAAFTFPDTDDFGK 17 0 H7C055;Q9ULT0-3;Q9ULT0;Q9ULT0-4 H7C055 TTC7A Tetratricopeptide repeat protein 7A 1 0 GS(0.922)PS(0.078)AAFTFPDTDDFGK;GS(0.92)PS(0.08)AAFTFPDTDDFGK ; 217.79 5.22E-27 12925800 2934 2694.95 3364.9 2855.3 3168.2 4053 3321.4 4016.7 3281.9 3506.9 TRUE FALSE FALSE 2898.239279 2732.889577 3423.464673 3185.443221 3006.514932 3794.02638 3603.519633 4132.916877 2988.358644 3415.790232 0.848482806 0.800075353 1.002246754 0.932564064 0.880181372 1.110731667 1.054959288 1.20994458 0.874865973 1 11.73800366 -7.93662887 1.378877313 0.919373556 1.176797791 0.648725332 0.07226791 0.301235181 0.962951197 0.012237337 0.075916402 1.16E-08 7.93662887 0.257424235 GS(ph)PSGGS(ph)TAEASDTLSIR ddPTM_HeLa_Romidepsin_16h_R1 2 GSPSGGSTAEASDTLSIR 18 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 2 0 GS(0.983)PS(0.021)GGS(0.974)T(0.02)AEAS(0.001)DT(0.001)LSIR;GS(1)PS(0.01)GGS(0.931)T(0.054)AEAS(0.001)DT(0.003)LS(0.001)IR ; 124.45 0.015623 5877000 2332.9 2944.1 2663.3 2015.05 2616 2713.1 2222.4 2066.64 3081.7 2692.5 TRUE FALSE FALSE 2304.465717 2985.547117 2709.653619 2248.039562 2482.495758 2539.741666 2411.170601 2126.434968 2806.065034 2622.548462 0.878712348 1.13841447 1.033213936 0.857196576 0.946596715 0.968425066 0.919399826 0.810827712 1.069976427 1 11.35675372 -7.283180695 2.437636248 0.957589969 0.781263196 0.246346482 0.083341869 0.608672729 4.551280861 0.011565325 0.21908489 5.21E-08 7.283180695 -0.176326774 GS(ph)PSGGSTAEASDTLSIR ddPTM_HeLa_Romidepsin_16h_R1 3 GSPSGGSTAEASDTLSIR 18 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 GS(0.999)PS(0.001)GGSTAEASDTLSIR;GS(0.936)PS(0.058)GGS(0.001)T(0.001)AEAS(0.003)DT(0.001)LSIR;GS(0.829)PS(0.139)GGS(0.012)T(0.006)AEAS(0.01)DT(0.003)LS(0.001)IR ;; 259.22 1.01E-75 26095800 2313.45 2390.11 2353.91 2131.8 1782.14 1886.18 2092.43 1975.01 2675.13 2781.76 TRUE FALSE FALSE 2285.252782 2423.758031 2394.878816 2378.288746 1691.190746 1765.659185 2270.160952 2032.153798 2435.859673 2709.489474 0.843425599 0.894544177 0.883885632 0.877762682 0.624173211 0.651657518 0.837855608 0.750013542 0.899010569 1 11.40380533 -8.901669596 6.150433388 0.916881126 0.720763516 0.651862123 0.065618872 0.117847467 6.276859214 0.012112421 0.022140254 1.25E-09 8.901669596 -0.19611761 GS(ph)PSPAAPGPPAGPLPR ddPTM_HeLa_Romidepsin_16h_R1 2 GSPSPAAPGPPAGPLPR 17 0 Q6F5E8;Q6F5E8-2 Q6F5E8 RLTPR Leucine-rich repeat-containing protein 16C 1 0 GS(0.969)PS(0.031)PAAPGPPAGPLPR;GS(0.946)PS(0.054)PAAPGPPAGPLPR ; 174.24 1.04E-06 20641400 684.12 511.06 639.79 696.06 876.85 1242.36 790.98 876.86 751.55 545.48 TRUE FALSE FALSE 675.7816823 518.2547161 650.9252766 776.5417323 832.1010725 1162.977206 858.1658215 902.2305606 684.3294857 531.308351 1.271919933 0.975431151 1.225136543 1.46156508 1.566135881 2.188893142 1.61519355 1.698129832 1.288008149 1 9.053405579 -8.950772915 1.687974053 1.120865141 1.80982613 0.732650534 0.177636646 0.133384549 0.761671928 0.028261738 0.059330864 1.12E-09 8.950772915 0.688960989 GS(ph)PSPASVSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPSPASVSSGR 12 0 Q96II5;P10398 Q96II5 ARAF Serine/threonine-protein kinase A-Raf 1 0 GS(0.989)PS(0.011)PASVSSGR 105.25 0.013018 6369600 905.73 793.83 933.21 759.22 671.65 804.36 982.43 904.84 1051.1 946.04 TRUE FALSE FALSE 894.6906144 805.0055596 949.4521286 847.0045886 637.3731942 752.963992 1065.87758 931.0201178 957.0869835 921.4617444 0.970947106 0.873617993 1.030376068 0.919196693 0.691697944 0.817140805 1.156724721 1.010373055 1.038661658 1 9.847780462 -10.47470473 7.642389007 0.987315163 0.926971096 0.072530133 0.119816619 0.731621704 100.9523554 0.021634619 0.024335121 3.35E-11 10.47470473 -0.060344066 GS(ph)PSSQSIPEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSPSSQSIPEK 11 0 Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;A0A1B0GUA8;Q9H1H9;H0Y9Z7 Q9H1H9-3 KIF13A Kinesin-like protein KIF13A 1 0 GS(0.954)PS(0.035)S(0.011)QSIPEK 133.04 0.0044398 7229500 3654.8 3637.8 4029.9 1959.9 4114 4037.8 4173.7 4248.4 4136.9 4082.7 TRUE FALSE FALSE 3610.253892 3689.013044 4100.038719 2186.51286 3904.047229 3779.797611 4528.213974 4371.320751 3766.885303 3976.630865 0.907867492 0.92767299 1.031033269 0.549840539 0.981747454 0.950502508 1.138706138 1.099252332 0.947255461 1 11.95733093 -7.802004867 5.61203669 0.930763085 1.119663595 0.286072318 0.128212823 0.174673451 13.38155236 0.017732794 0.05721208 1.58E-08 7.802004867 0.188900509 GS(ph)PTGGAQLLK ddPTM_HeLa_Romidepsin_16h_R1 2 GSPTGGAQLLK 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 GS(1)PTGGAQLLK;GS(0.999)PT(0.001)GGAQLLK ; 153.75 0.0022446 195034000 4928.4 4587.7 5266.3 4326 6269.8 7578.1 4586 5187.3 4880.4 4775.4 TRUE FALSE FALSE 4868.330765 4652.285761 5357.957742 4826.192474 5949.82871 7093.883867 4975.534726 5337.386341 4443.884801 4651.33442 1.046652493 1.000204531 1.151918409 1.037593095 1.279165971 1.525128754 1.069700494 1.147495721 0.955399978 1 12.18342895 -8.765026346 24.26706564 1.032521144 1.261378748 0.457066421 0.119214573 42.27041424 285978.5935 0.017127029 0.03196837 1.72E-09 8.765026346 0.228857604 GS(ph)PTGGAQLLKR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPTGGAQLLKR 12 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 GS(0.891)PT(0.109)GGAQLLKR 109.16 0.017109 12968000 1182.7 1475.7 1132 1338.9 1600.3 1627.6 1486.1 1260.3 1366.1 1082.1 TRUE FALSE FALSE 1168.284797 1496.474943 1151.701985 1493.709918 1518.630719 1523.601613 1612.329297 1296.764792 1243.912595 1053.986886 1.108443391 1.419823115 1.092709976 1.417199718 1.440844037 1.445560313 1.529743224 1.230342435 1.180197411 1 10.0416412 -10.10053785 0.630113224 1.015238406 1.432360664 0.467462949 0.128266521 0.281466664 0.239608263 0.031463526 0.042187606 7.93E-11 10.10053785 0.417122258 GS(ph)PVTTREPTPR ddPTM_HeLa_Romidepsin_16h_R1 2 GSPVTTREPTPR 12 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 GS(0.981)PVT(0.017)TREPT(0.001)PR;GS(0.594)PVT(0.041)T(0.005)REPT(0.361)PR ; 149.57 0.0096697 17524700 6282.8 6496.1 5517.9 7516.1 4603.8 3807.2 3328.2 3278.5 6501.4 6396.2 TRUE FALSE FALSE 6206.222817 6587.552266 5613.936735 8385.146846 4368.850907 3563.932207 3610.897225 3373.358225 5919.898501 6230.025802 0.996179312 1.057387638 0.901109709 1.345924899 0.701257273 0.572057375 0.57959587 0.541467778 0.950220543 1 12.60502242 -8.53993966 23.88075342 1.017003564 0.577689424 0.787610455 0.113921731 42.71144744 59784.47767 0.014823663 0.029654293 2.88E-09 8.53993966 -0.43931414 GS(ph)RLS(ph)QPFES(ph)Y(ph)ITAPPGT(ph)AAAPAK ddPTM_HeLa_Romidepsin_16h_R1 1 GSRLSQPFESYITAPPGTAAAPAK 24 1 Q96GE9-2;Q96GE9 Q96GE9-2 TMEM261 Transmembrane protein 261 5 0 GS(0.998)RLS(0.998)QPFES(0.997)Y(0.915)IT(0.119)APPGT(0.973)AAAPAK 50.858 0.0090355 9180800 1315.8 1272.4 1419.9 424.78 1013.6 1068.6 1072.6 1545.7 1237.8 1151 TRUE FALSE FALSE 1299.762523 1290.312881 1444.612764 473.8950622 961.8722097 1000.319909 1163.706617 1590.422391 1127.088068 1121.096854 1.159366846 1.150937919 1.288570884 0.42270662 0.85797423 0.892268946 1.03800721 1.418630679 1.005344064 1 10.13069521 GS(ph)SANASKWSPPQNYK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSANASKWSPPQNYK 16 1 Q96K21-3;H3BRM1;H3BRF9;Q96K21-2;Q96K21 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 GS(0.455)S(0.455)ANAS(0.029)KWS(0.06)PPQNYK 58.885 0.028169 30302000 1771.6 1555.1 1283.8 2130.1 1971 1589.2 1597.3 1614.1 1748.7 1688.6 TRUE FALSE FALSE 1750.007058 1576.992739 1306.144 2376.392184 1870.412515 1487.655249 1732.974622 1660.801437 1592.291892 1644.729929 1.064008764 0.958815615 0.79413889 1.444852521 1.137215589 0.904498193 1.053652999 1.009771518 0.96811754 1 10.68363499 -14.11193964 0.303918764 0.918236234 1.055111104 0.022377861 0.161495496 64.07586274 3.089433376 3.53896583 0.074118929 7.73E-15 14.11193964 0.136874869 GS(ph)SGSPAHAESYSSGGGGQQK ddPTM_HeLa_Romidepsin_16h_R1 2 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 0 GS(0.333)S(0.333)GS(0.333)PAHAES(0.001)YS(0.001)SGGGGQQK;GS(0.333)S(0.333)GS(0.333)PAHAESYSSGGGGQQK ; 98.391 0.00022928 6363100 1977.38 1533.22 1497.03 883.11 2535.7 2082.86 1909.13 1843.72 3063.92 2706.15 TRUE FALSE FALSE 1953.278932 1554.804711 1523.085179 985.2193334 2406.293767 1949.771968 2071.291455 1897.065129 2789.875321 2635.843833 0.741045015 0.589869814 0.577835895 0.373777582 0.912912115 0.739714525 0.785817213 0.719718333 1.058437259 1 11.36404918 -11.6070573 0.842272685 0.980321361 0.677310819 0.489225628 0.139936877 0.407924149 0.587034007 0.064278855 0.030562811 2.47E-12 11.6070573 -0.303010542 GS(ph)SPLGPAGLGAEEPAAGPQLPSWLQPER ddPTM_HeLa_Romidepsin_16h_R1 1 GSSPLGPAGLGAEEPAAGPQLPSWLQPER 29 0 H0YKL4;O43482 H0YKL4 OIP5 Protein yippee-like;Protein Mis18-beta 1 0 GS(0.5)S(0.5)PLGPAGLGAEEPAAGPQLPSWLQPER 107.84 2.58E-09 7134000 1498.9 1173.7 1096.7 1161.4 1255.1 1062.4 780.49 1040 1686.7 1211.8 TRUE FALSE FALSE 1480.63083 1190.223379 1115.787603 1295.686533 1191.047564 994.5160687 846.7848011 1070.090759 1535.837328 1180.317261 1.254434616 1.008392759 0.945328549 1.097744289 1.009091032 0.842583686 0.717421348 0.906612819 1.301207208 1 10.20495898 -8.369798881 2.190111097 1.098306766 0.802347065 0.553842748 0.11193389 0.188670604 1.749039711 0.017599157 0.048552687 4.27E-09 8.369798881 -0.295959701 GS(ph)SPLPTATTPKPLIPTEASIR ddPTM_HeLa_Romidepsin_16h_R1 1 GSSPLPTATTPKPLIPTEASIR 22 1 A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-2;Q9BUK6 A0A3B3IUD2 MSTO1 Protein misato homolog 1 1 0 GS(0.465)S(0.465)PLPT(0.031)AT(0.034)T(0.006)PKPLIPTEASIR 51.966 0.015406 30190000 1010.1 1032.5 1014.6 1111.7 1611 1556 1179.1 1741.4 1181.7 1004.4 TRUE FALSE FALSE 997.7885127 1047.035562 1032.258687 1240.239985 1528.784659 1456.576622 1279.252725 1791.784662 1076.005792 978.3055432 1.019915015 1.070254144 1.055149584 1.26774298 1.562686289 1.488876999 1.307620849 1.83151846 1.099866805 1 9.934141306 -9.038378062 2.026079595 1.014860676 1.532141721 0.775065352 0.12554721 0.097619195 0.794953396 0.017468123 0.03359037 9.15E-10 9.038378062 0.517281045 GS(ph)SQPNLSTSHSEQEYGK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSQPNLSTSHSEQEYGK 18 0 F6PQP6;E9PBC1;I3L2B2;O95208-3;O95208-2;O95208 F6PQP6 EPN2 Epsin-2 1 0 GS(0.543)S(0.451)QPNLS(0.001)T(0.002)S(0.003)HSEQEYGK 80.835 0.0054192 5759500 1447.3 1790.8 2031.1 1489.5 2559.9 2861.8 2368.5 1825.2 2602.3 2419.1 TRUE FALSE FALSE 1429.659751 1816.010929 2066.450443 1661.722998 2429.258751 2678.940216 2569.680331 1878.009282 2369.54377 2356.251433 0.60675178 0.77072035 0.877007612 0.705240101 1.030984519 1.136950063 1.090579848 0.797032632 1.005641307 1 11.20227778 -8.745136696 24.68493082 0.804753425 1.028155182 0.281006389 0.14252104 210.4698884 318683.8278 0.024461423 0.048800001 1.80E-09 8.745136696 0.223401758 GS(ph)SSQGPSQTSTPTDVTAIHL ddPTM_HeLa_Romidepsin_16h_R1 1 GSSSQGPSQTSTPTDVTAIHL 21 0 Q5T8J1;P30281-4;P30281-2;P30281-3;P30281 Q5T8J1 CCND3 G1/S-specific cyclin-D3 1 0 GS(0.44)S(0.32)S(0.233)QGPS(0.003)QT(0.001)S(0.001)T(0.002)PTDVTAIHL 142.58 4.50E-05 3447000 256.42 340.48 353.85 193.73 407.69 395.62 206.17 415.29 550.32 407.87 TRUE FALSE FALSE 253.2946544 345.2732864 360.0086108 216.1299741 386.884058 370.3411588 223.6820747 427.3057609 501.0980009 397.2734786 0.637582592 0.869107315 0.906198451 0.544033231 0.97384819 0.932207104 0.563043059 1.075595991 1.261342697 1 8.633988674 -12.63808482 1.477562967 0.999515527 0.783950689 0.238799133 0.191622015 0.548533018 2.160012445 0.114889493 0.026350992 2.30E-13 12.63808482 -0.215564838 GS(ph)YGDLGGPIITTQVTIPK ddPTM_HeLa_Romidepsin_16h_R1 2 GSYGDLGGPIITTQVTIPK 19 0 P61978-3;P61978;P61978-2;Q5T6W2;S4R359 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 GS(1)YGDLGGPIITTQVTIPK;GS(1)YGDLGGPIITTQVTIPK ; 260.31 3.79E-76 179238000 10330.1 8331.8 9969.9 5209.6 6643.5 7290 6202 5461.5 8808.9 6663.7 TRUE FALSE FALSE 10204.19277 8449.095299 10143.42193 5811.958464 6304.457405 6824.192527 6728.797725 5619.519886 8021.009922 6490.576113 1.572155166 1.301748127 1.562792231 0.895445699 0.971324778 1.051400124 1.036702691 0.865796778 1.235793215 1 12.66413082 -9.239015668 24.88512435 1.299867333 0.973413193 0.559383886 0.162804113 707.5227453 785186.9587 0.035051692 0.058099277 5.77E-10 9.239015668 -0.32645414 GSALDDAVNPLHENGDDS(ph)LSPR ddPTM_HeLa_Romidepsin_16h_R1 1 GSALDDAVNPLHENGDDSLSPR 22 0 Q9BVI0 Q9BVI0 PHF20 PHD finger protein 20 1 0 GSALDDAVNPLHENGDDS(0.846)LS(0.154)PR 129.22 4.97E-12 0 1051.5 1049.5 944.2 637.95 977.14 634.36 784.1 898.04 1129.3 1156.3 TRUE FALSE FALSE 1038.683914 1064.274889 960.6334049 711.7127806 927.2728996 593.8264433 850.7014344 924.0233705 1028.29258 1126.259159 0.922242368 0.944964469 0.852941703 0.631926298 0.823321073 0.527255595 0.755333644 0.820435832 0.913015953 1 10.13732312 -9.53111506 3.004714811 0.961059592 0.710051246 0.620932022 0.085636306 0.113464072 2.099423197 0.013099892 0.019750215 2.94E-10 9.53111506 -0.251008346 GSALGTPAAAEPVT(ph)PTSK ddPTM_HeLa_Romidepsin_16h_R1 2 GSALGTPAAAEPVTPTSK 18 0 P00519;P00519-2 P00519 ABL1 Tyrosine-protein kinase ABL1 1 0 GSALGTPAAAEPVT(0.981)PT(0.017)S(0.002)K;GSALGTPAAAEPVT(0.947)PT(0.046)S(0.007)K ; 152.89 4.19E-05 8266800 5096.8 4805 4238.4 4560.5 5136 4741.4 3689.9 4165.3 5021.7 4468.1 TRUE FALSE FALSE 5034.678241 4872.644916 4312.167574 5087.806468 4873.890755 4438.439842 4003.320014 4285.816384 4572.546575 4352.018118 1.156860589 1.119628821 0.990843204 1.16906831 1.119915088 1.01985785 0.919876688 0.984788268 1.050672688 1 12.08746885 -7.994492179 4.687980444 1.082523748 0.953962611 0.459633799 0.05849749 0.154075664 9.084106023 0.010116026 0.030158844 1.01E-08 7.994492179 -0.128561137 GSAST(ph)PVQGSIPEGKPLR ddPTM_HeLa_Romidepsin_16h_R1 1 GSASTPVQGSIPEGKPLR 18 1 O95081 O95081 AGFG2 Arf-GAP domain and FG repeat-containing protein 2 1 0 GS(0.015)AS(0.436)T(0.55)PVQGSIPEGKPLR 110.38 0.00069714 5900600 1824 1472.4 1376.6 1693.6 2196.1 3141.7 2358.5 3114.7 1766.6 1645.2 TRUE FALSE FALSE 1801.768386 1493.128486 1400.559146 1889.422001 2084.024822 2940.955509 2558.830931 3204.81893 1608.590871 1602.457467 1.12437829 0.931774176 0.874007064 1.179077785 1.300518026 1.835278359 1.596816754 1.99994009 1.003827499 1 10.64607035 -8.446200595 1.85423931 1.037404736 1.816264507 0.892398215 0.122841649 0.080900345 0.541211938 0.018068765 0.050643954 3.58E-09 8.446200595 0.778859771 GSAVHQLSEELR ddPTM_HeLa_Romidepsin_16h_R1 1 GSAVHQLSEELR 12 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 0 0 83.617 0.019156 4787100 3355.4 2958.8 3304.9 3473.9 7083.1 7490.7 6479.6 6931.9 4627 3560.5 FALSE FALSE TRUE 3314.503094 3000.454064 3362.420398 3875.568663 6721.622976 7012.068445 7029.977062 7132.46359 4213.149531 3467.997697 0.955739705 0.865183407 0.969556699 1.117523425 1.938185536 2.021935727 2.027099692 2.056651767 1.214865147 1 11.75988723 -8.77889339 3.503124618 0.969488753 2.031553001 0.969829487 0.085814888 0.013435768 0.347211908 0.006668228 0.013219906 1.66E-09 8.77889339 1.062064248 up GSDALS(ph)ET(ph)SSVS(ph)HIEDLEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 3 0 GS(0.029)DALS(0.585)ET(0.585)S(0.572)S(0.572)VS(0.657)HIEDLEK 62.475 0.0028383 0 504.77 504.61 411.99 579.5 482.27 498.31 345.07 518.63 569.13 456.24 TRUE FALSE FALSE 498.6176691 511.7139128 419.1605131 646.5045166 457.6579623 466.4695992 374.3802372 533.6357408 518.2255874 444.386819 1.122035235 1.151505605 0.943233452 1.454823791 1.029863944 1.049692698 0.842464765 1.200836114 1.166158772 1 8.795672215 -6.928439497 20.34945909 1.069093654 4.967530731 0.040049001 0.155465321 960.6690699 279190.4451 0.019654997 3728.207347 1.18E-07 6.928439497 3.898437077 GSDALS(ph)ETSSVSHIEDLEK ddPTM_HeLa_Romidepsin_16h_R1 4 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 0 GS(0.033)DALS(0.644)ET(0.299)S(0.023)S(0.001)VSHIEDLEK;GS(0.012)DALS(0.84)ET(0.14)S(0.008)SVSHIEDLEK;GSDALS(0.876)ET(0.124)SSVSHIEDLEK;GSDALS(0.549)ET(0.42)S(0.024)S(0.007)VSHIEDLEK ;;; 199.91 5.28E-21 22608500 10053 9189.9 8610.4 5590.75 12966.6 14644 11394.8 11372.2 14135.8 13137.3 TRUE FALSE FALSE 9930.470169 9319.275653 8760.2604 6237.17882 12304.86602 13708.29566 12362.67403 11701.23666 12871.45864 12795.99105 0.776061044 0.728296512 0.684609763 0.487432259 0.961618836 1.071296127 0.966136501 0.914445518 1.005897753 1 13.64340427 -8.550785692 24.99793392 0.830641453 0.987890979 0.260663747 0.149930755 299.3693743 268162.0744 0.025110519 0.050221733 2.81E-09 8.550785692 0.157249526 GSDALSET(ph)S(ph)SVSHIEDLEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 2 0 GS(0.013)DALS(0.538)ET(0.606)S(0.681)S(0.156)VS(0.005)HIEDLEK 66.889 0.020207 8599300 4272.4 4409.2 4323.8 2912.3 4344.4 4145.1 3266.6 4183.4 4840.7 4822.3 TRUE FALSE FALSE 4220.326345 4471.272833 4399.053925 3249.033829 4122.689057 3880.241488 3544.064922 4304.440079 4407.735668 4697.015951 0.898512245 0.951939035 0.936563548 0.691722971 0.877725156 0.826107794 0.754535424 0.916420154 0.938411901 1 12.19752878 -9.469073863 17.57544893 0.950417712 0.814306431 0.530353994 0.062037676 7.859961828 2567.101985 0.009765599 0.014916152 3.40E-10 9.469073863 -0.136111281 GSDALSETS(ph)SVSHIEDLEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSDALSETSSVSHIEDLEK 19 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 0 GSDALS(0.003)ET(0.015)S(0.547)S(0.433)VS(0.002)HIEDLEK 110.38 4.24E-05 0 3032.4 2862.3 3210.7 2289.4 3323.2 3254 2549.2 3034.9 3298.5 3721.5 TRUE FALSE FALSE 2995.439942 2902.595535 3266.580887 2554.1112 3153.604703 3046.079902 2765.728984 3122.710043 3003.473899 3624.814894 0.826370458 0.800756899 0.901171779 0.704618381 0.870004344 0.840340815 0.762998681 0.861481244 0.828586835 1 11.82369161 -12.14014542 0.580394759 1.024091027 0.814909624 0.009116744 0.075031937 0.536083057 0.276475829 0.059540084 0.011755035 7.24E-13 12.14014542 -0.209181403 GSDASWKNDQEPPPEALDFS(ph)DDEKEK ddPTM_HeLa_Romidepsin_16h_R1 2 GSDASWKNDQEPPPEALDFSDDEKEK 26 2 Q96HR8-2;Q96HR8 Q96HR8-2 NAF1 H/ACA ribonucleoprotein complex non-core subunit NAF1 1 0 GSDASWKNDQEPPPEALDFS(1)DDEKEK;GSDASWKNDQEPPPEALDFS(1)DDEKEK ; 80.245 2.61E-05 30486000 5759.6 5754.1 4029 6392.2 4148.7 3707.7 3603.9 3718.2 5022.8 4378.2 TRUE FALSE FALSE 5689.39978 5835.106371 4099.123055 7131.29624 3936.976358 3470.789936 3910.015176 3825.780251 4573.548188 4264.453733 1.334145036 1.36831274 0.961230514 1.672264887 0.923207661 0.81388852 0.916885355 0.89713255 1.072481606 1 12.05814523 -8.554339222 24.99995026 1.198901046 0.878141061 0.420964705 0.197252517 160.3967891 127458.1193 0.029858136 0.059716648 2.79E-09 8.554339222 -0.320759985 GSDDAPYS(ph)PTAR ddPTM_HeLa_Romidepsin_16h_R1 2 GSDDAPYSPTAR 12 0 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 0 GSDDAPYS(0.936)PT(0.064)AR;GSDDAPYS(0.944)PT(0.056)AR ; 174.94 3.57E-05 19751300 6944 6635.2 5946.2 4516.2 3807.5 4010.7 3682.9 3738 6707.8 7086.1 TRUE FALSE FALSE 6859.363857 6728.61052 6049.691117 5038.384293 3613.189067 3754.429214 3995.725434 3846.153132 6107.837568 6902.0021 0.993822337 0.974878075 0.8765125 0.729988809 0.523498691 0.54396234 0.578922663 0.557251806 0.884937078 1 12.7527992 -9.199495801 1.585380344 0.996359657 0.548239073 0.949129666 0.043068071 0.028471849 0.140028663 0.003911512 0.007367805 6.32E-10 9.199495801 -0.448120584 GSDIDNPTLTVMDIS(ph)PPS(ph)RSPR ddPTM_HeLa_Romidepsin_16h_R1 1 GSDIDNPTLTVMDISPPSRSPR 22 1 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 2 0 GSDIDNPTLT(0.001)VMDIS(0.911)PPS(0.635)RS(0.453)PR 66.264 0.0094986 9584300 4908.1 5072.4 5036.7 3701.8 4760.1 4158.5 3665.2 3569.9 5736.3 5016.1 TRUE FALSE FALSE 4848.278189 5143.80938 5124.361651 4129.819533 4517.174335 3892.785271 3976.521997 3673.189424 5223.230961 4885.780999 0.992324091 1.052812105 1.04883163 0.845273158 0.924555222 0.796758036 0.813896897 0.751812131 1.069067763 1 12.25437348 -8.650749397 1.093070288 1.003837408 0.777853924 0.803629714 0.050040784 0.161133555 0.368459812 0.00722297 0.023508788 2.23E-09 8.650749397 -0.225983484 GSDIDNPTLTVMDIS(ph)PPSR ddPTM_HeLa_Romidepsin_16h_R1 4 GSDIDNPTLTVMDISPPSR 19 0 Q9Y2U5 Q9Y2U5 MAP3K2 Mitogen-activated protein kinase kinase kinase 2 1 0 GSDIDNPTLTVMDIS(0.998)PPS(0.002)R;GSDIDNPTLTVMDIS(0.999)PPS(0.001)R;GSDIDNPTLTVMDIS(0.781)PPS(0.219)R;GSDIDNPT(0.011)LT(0.143)VMDIS(0.834)PPS(0.012)R ;;; 169.58 2.17E-07 27076900 12430.6 12348.5 12440.7 10708 9734.7 8773.2 6676.7 8140.3 13148.8 12151.8 TRUE FALSE FALSE 12279.09107 12522.34251 12657.22516 11946.10934 9237.901934 8212.620834 7243.818731 8375.826737 11972.7384 11836.09448 1.037427598 1.057979262 1.069375137 1.009294861 0.780485653 0.693862392 0.612010891 0.707651223 1.011544679 1 13.5309055 -8.631223889 2.501254199 1.026728968 0.666561067 0.965861455 0.031114867 0.038502851 0.486586028 0.005141731 0.011542009 2.34E-09 8.631223889 -0.3601679 GSDS(ph)DSEGDNPEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSDSDSEGDNPEK 13 0 I3L4J1;Q9UN37 I3L4J1 VPS4A Vacuolar protein sorting-associated protein 4A 1 0 GS(0.009)DS(0.951)DS(0.04)EGDNPEK 178.68 7.35E-07 4833400 1122.6 1420.9 1870.9 1105.4 1352.8 1323.6 1884.9 605.09 1988.2 1773.8 TRUE FALSE FALSE 1108.917319 1440.903467 1903.46223 1233.211549 1283.761568 1239.026232 2045.003359 622.5973245 1810.370412 1727.71642 0.641839891 0.833993039 1.101721444 0.713781229 0.743039513 0.717146759 1.183645264 0.360358516 1.047840022 1 10.75465072 -7.229527954 24.03800448 0.842379689 0.360357048 0.410191594 0.182525162 7331.112188 5522178.953 0.025576905 4.870056845 5.89E-08 7.229527954 -0.482022641 GSDYSWSYQT(ph)PPS(ph)SPSSSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 GSDYSWSYQTPPSSPSSSSSR 21 0 Q765P7;A0A087WXN9;H3BPV0 Q765P7 MTSS1L MTSS1-like protein 2 0 GSDYS(0.002)WS(0.035)Y(0.036)QT(0.929)PPS(0.463)S(0.348)PS(0.063)S(0.069)S(0.022)S(0.019)S(0.013)R;GSDYSWS(0.018)Y(0.003)QT(0.979)PPS(0.216)S(0.178)PS(0.178)S(0.147)S(0.122)S(0.101)S(0.059)R ; 78.736 0.00052587 4141900 2367.74 2483.19 2192.45 2426.09 2101.66 2055.22 1883.61 1843.58 2934.5 2281.33 TRUE FALSE FALSE 2338.881074 2518.148414 2230.608673 2706.605941 1994.404448 1923.898075 2043.603786 1896.921079 2672.03097 2222.060718 1.052572981 1.133249147 1.003846859 1.218061198 0.897547233 0.865817059 0.919688544 0.853676528 1.202501331 1 11.11768252 -8.563617176 24.99487782 1.045289856 0.883383018 0.579695937 0.082845089 77.3558233 47461.03453 0.00958883 0.019177678 2.73E-09 8.563617176 -0.161906838 GSEEDPLLS(ph)PVETWK ddPTM_HeLa_Romidepsin_16h_R1 2 GSEEDPLLSPVETWK 15 0 H0YK04;Q13017-2;Q13017;A0A0A0MSK6 H0YK04 ARHGAP5 Rho GTPase-activating protein 5 1 0 GSEEDPLLS(0.999)PVET(0.001)WK;GSEEDPLLS(0.978)PVET(0.022)WK ; 93.738 0.012913 9320600 5305.1 4640.4 4793.8 4132.5 5799.6 7277.7 5582.1 6758.5 5227.5 5214.7 TRUE FALSE FALSE 5240.439401 4705.727673 4877.234078 4610.319094 5503.624771 6812.678458 6056.243435 6954.046534 4759.939307 5079.221342 1.031740703 0.926466353 0.960232632 0.907682257 1.083556789 1.341284027 1.192356668 1.369116655 0.937139571 1 12.31039163 -8.408574434 4.156973292 0.996552455 1.288651677 0.852784409 0.061985136 0.065934445 1.924988025 0.008525378 0.019724967 3.90E-09 8.408574434 0.292099223 GSEGSQS(ph)PGSSVDDAEDDPSR ddPTM_HeLa_Romidepsin_16h_R1 1 GSEGSQSPGSSVDDAEDDPSR 21 0 Q8IX07 Q8IX07 ZFPM1 Zinc finger protein ZFPM1 1 0 GSEGS(0.009)QS(0.991)PGSSVDDAEDDPSR 178.19 3.88E-13 3446300 616.42 873.02 584.44 656.14 1305.1 1010.9 1041.5 1216.4 805.43 629.62 TRUE FALSE FALSE 608.9068359 885.3103985 594.611933 732.005994 1238.495877 946.3067525 1129.964984 1251.594615 733.3903236 613.2623816 0.992897745 1.443607867 0.969588142 1.193626115 2.019520378 1.54306995 1.842547363 2.040879487 1.195883435 1 9.260360647 -8.862083862 5.017725916 1.037521253 1.83552283 0.771528041 0.191323567 0.064277913 2.63524397 0.027056157 0.050087411 1.37E-09 8.862083862 0.798001577 GSEGYLAATYPTVGQTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GSEGYLAATYPTVGQTSPR 19 0 J3QSG6;H0Y465;P21359-2;P21359-6;P21359 J3QSG6 NF1 Neurofibromin;Neurofibromin truncated 1 0 GSEGYLAATYPTVGQT(0.145)S(0.855)PR;GSEGYLAATYPTVGQT(0.028)S(0.972)PR ; 268.82 1.80E-90 152656000 6961.8 7438.7 6739.2 6359.4 5351.4 5566.8 4455.6 5237.6 7424.9 6320.9 TRUE FALSE FALSE 6876.946904 7543.422214 6856.492949 7094.70375 5078.298089 5211.099446 4834.058553 5389.141692 6760.798348 6156.682107 1.116989116 1.225241467 1.113666879 1.152358304 0.824843317 0.846413597 0.785172674 0.875332135 1.09812367 1 12.58793736 -8.75222543 24.99633871 1.081635675 0.830490751 0.826607275 0.062599003 81.75578654 221792.0075 0.011419378 0.022586944 1.77E-09 8.75222543 -0.251144924 GSEPVPEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GSEPVPEKK 9 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79;X6RCC3 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 0 1 GSEPVPEK(1)K 118.18 0.0016326 0 3077.8 2893.1 2323.8 2452.5 3074.4 2889.8 2822.8 3382.8 3129.3 2864 FALSE TRUE FALSE 3040.28659 2933.829138 2364.244764 2736.069589 2917.501896 2705.151106 3062.568562 3480.675981 2849.407571 2789.592867 1.089867495 1.051705133 0.847523233 0.98081323 1.045852221 0.969729719 1.09785503 1.247736192 1.021442091 1 11.44583886 -7.363627148 2.944798996 1.022037764 1.262632548 0.564184396 0.064806 0.211379297 2.83986144 0.010088611 0.104511427 4.33E-08 7.363627148 0.240594784 GSES(ph)PEMGPEVTPAPR ddPTM_HeLa_Romidepsin_16h_R1 2 GSESPEMGPEVTPAPR 16 0 A0A0A0MSQ2;H0Y4B4;F8W689;P48382-2;P48382 A0A0A0MSQ2 RFX5 DNA-binding protein RFX5 1 0 GS(0.001)ES(0.999)PEMGPEVTPAPR;GS(0.008)ES(0.991)PEMGPEVT(0.001)PAPR ; 103.13 0.0065527 65753000 7136.9 7063.4 6893.7 6427.9 7585.1 7218.6 6422.2 6976 7445.1 7394.2 TRUE FALSE FALSE 7049.912718 7162.838731 7013.681957 7171.124042 7198.004043 6757.354757 6967.701508 7177.839554 6779.191609 7202.097618 0.978869364 0.994548965 0.97383878 0.995699367 0.999431614 0.938248149 0.967454466 0.996631806 0.941280162 1 12.81420144 GSES(ph)PNSFLDQESR ddPTM_HeLa_Romidepsin_16h_R1 1 GSESPNSFLDQESR 14 0 Q5T4Y8;A0A5H1ZRR2;G9CGD6-3;G9CGD6;G9CGD6-2;Q6P9H4 Q5T4Y8 CNKSR3 Connector enhancer of kinase suppressor of ras 3 1 0 GS(0.085)ES(0.908)PNS(0.007)FLDQESR 144.15 0.00061869 8840100 1520.3 1457.7 1587.7 1532.8 1707.8 1795.8 1508.3 1861.1 1569.8 1920.8 TRUE FALSE FALSE 1501.769999 1478.221539 1615.333252 1710.029548 1620.644593 1681.054176 1636.414964 1914.947992 1429.393156 1870.897339 0.802700377 0.790113657 0.863400262 0.914015704 0.866239189 0.898528284 0.874668497 1.023545201 0.764014747 1 10.86951468 -6.39432424 15.98904506 0.896048865 0.890364764 0 0.081957912 0 0 0.011642554 0 4.03E-07 6.39432424 -0.005684102 GSET(ph)PGATPGSK ddPTM_HeLa_Romidepsin_16h_R1 4 GSETPGATPGSK 12 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 GS(0.002)ET(0.998)PGATPGSK;GS(0.005)ET(0.994)PGAT(0.001)PGSK;GS(0.078)ET(0.921)PGATPGSK;GS(0.003)ET(0.997)PGATPGSK ;;; 199.4 2.47E-14 402264000 34617.4 36239.3 40248.5 31525.1 31579.8 36787.4 35154.1 18874.5 42119.6 39734.3 TRUE FALSE FALSE 34195.46981 36749.47782 40949.00826 35170.18039 29968.16497 34436.80387 38140.08838 19420.60388 38352.31749 38701.99716 0.883558274 0.949549907 1.058059306 0.908743294 0.774331227 0.889793974 0.985481143 0.501798494 0.990964816 1 15.2401204 -7.257489388 24.9554062 0.936373389 0.501798321 0.752075697 0.075100863 154.1247963 973695.3127 0.011084387 0.112731768 5.53E-08 7.257489388 -0.434575068 GSETDS(ph)AQDQPVK ddPTM_HeLa_Romidepsin_16h_R1 2 GSETDSAQDQPVK 13 0 K7EN42;B7Z8J4;P30419 K7EN42 NMT1 Glycylpeptide N-tetradecanoyltransferase 1 1 0 GSET(0.101)DS(0.899)AQDQPVK;GSETDS(1)AQDQPVK ; 154.13 0.00076907 11851400 6647.1 6342.9 6658.4 5659 5884 6264.2 5179.2 5267.4 7107.8 6785.5 TRUE FALSE FALSE 6566.082588 6432.195513 6774.286659 6313.320206 5583.717524 5863.937837 5619.121119 5419.803908 6472.060566 6609.211732 0.993474389 0.973216743 1.024976492 0.955230436 0.844838651 0.887237098 0.850195356 0.82003787 0.979248484 1 12.6902625 -8.87283014 3.626310491 0.996493252 0.852617576 0.916291482 0.020527714 0.041503741 1.052372437 0.002807533 0.005335058 1.34E-09 8.87283014 -0.143875676 GSFS(ph)DTGLGDGK ddPTM_HeLa_Romidepsin_16h_R1 2 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 GS(0.104)FS(0.651)DT(0.245)GLGDGK;GS(0.008)FS(0.894)DT(0.098)GLGDGK ; 153.81 0.0014162 207625400 4666.4 4752.3 4500.9 3723.9 5376.7 5471.1 4953.3 6080.1 5119.9 5684.4 TRUE FALSE FALSE 4609.524122 4819.203004 4579.236276 4154.474839 5102.306936 5121.514367 5374.033178 6256.018101 4661.963321 5536.718469 0.832537206 0.870407811 0.827066845 0.750349663 0.921539891 0.925008992 0.97061702 1.129914431 0.842008375 1 12.43481545 -7.185392313 1.510011099 0.895935664 1.251458476 0.569169292 0.067245464 1.053945758 1.900967562 0.012486547 0.586208638 6.53E-08 7.185392313 0.355522812 GSFSDT(ph)GLGDGK ddPTM_HeLa_Romidepsin_16h_R1 2 GSFSDTGLGDGK 12 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 GS(0.001)FS(0.277)DT(0.723)GLGDGK;GSFS(0.272)DT(0.728)GLGDGK ; 152 0.0029631 193360200 6486.3 6311.8 6062.9 4791.4 6747.8 7625.2 6448.8 7421.3 6311.4 6920.4 TRUE FALSE FALSE 6407.242481 6400.657686 6168.422231 5345.404212 6403.434586 7137.974329 6996.560911 7636.023607 5746.892577 6740.60701 0.950543841 0.949566957 0.915113761 0.793015259 0.949978923 1.058951266 1.037971936 1.132839163 0.852577901 1 12.7186628 -8.209358092 4.470042416 0.953601247 1.07597077 0.500406624 0.066649986 0.169160488 7.303578655 0.009495612 0.024873939 6.18E-09 8.209358092 0.122369523 GSFSEQGINEFLR ddPTM_HeLa_Romidepsin_16h_R1 1 GSFSEQGINEFLR 13 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 0 0 112.43 0.0026137 0 579.55 586.4 522.35 625.43 599.27 689.2 684.32 497.91 654.64 552.22 FALSE FALSE TRUE 572.4862217 594.6553546 531.4412826 697.7451593 568.6870157 645.1623443 742.4461237 512.3162403 596.0873588 537.8732448 1.06435155 1.105567827 0.988041863 1.297229721 1.057288164 1.199469114 1.380336596 0.952485079 1.108230172 1 9.071122417 -9.684183793 0.667683053 1.019682438 1.189021928 0.110416417 0.123887166 0.705801832 0.641863427 0.026703246 0.048551382 2.07E-10 9.684183793 0.16933949 GSGDTS(ph)SLIDPDTSLSELR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGDTSSLIDPDTSLSELR 19 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 GS(0.267)GDT(0.198)S(0.506)S(0.028)LIDPDTSLSELR 178.47 3.01E-10 4173600 954.44 1072.8 941.99 872.96 2089.5 1633.3 1541.6 1839.7 820.82 1010.6 TRUE FALSE FALSE 942.8069182 1087.902907 958.3849408 973.8957426 1982.865018 1528.937401 1672.543466 1892.928817 747.4038034 984.3444663 0.957801817 1.105205488 0.973627601 0.989385094 2.014401549 1.553254428 1.699144479 1.923034955 0.759290908 1 9.943019457 -8.772478668 24.99999874 0.990081604 1.772993212 0.891288221 0.142288064 39.70491665 89917.33727 0.016716578 0.030508701 1.69E-09 8.772478668 0.782911608 GSGGGGGGGGQGSTNYGK(ac)SQR ddPTM_HeLa_Romidepsin_16h_R1 2 GSGGGGGGGGQGSTNYGKSQR 21 1 Q99729-3;Q99729-4 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 1 ; GSGGGGGGGGQGSTNYGK(1)SQR;GSGGGGGGGGQGSTNYGK(1)SQR 263.08 8.32E-87 1801190 0 0 0 59.703 0 0 0 108.43 0 0 FALSE TRUE FALSE 0 0 0 66.60614177 0 0 0 111.567251 0 0 0 GSGGGGGPQVPHQS(ph)PPKR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGGGGGPQVPHQSPPKR 18 1 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 0 GSGGGGGPQVPHQS(1)PPKR 60.454 0.012263 4195100 3391.7 3647.6 3344.5 4248.2 8928.8 8740 7534.7 7582.8 3600.6 3830.1 TRUE FALSE FALSE 3350.360656 3698.951009 3402.70962 4739.396872 8473.130018 8181.542207 8174.69723 7802.196354 3278.553318 3730.59345 0.898077129 0.991518121 0.912109471 1.270413658 2.271255266 2.193094026 2.191259203 2.091408903 0.878828895 1 11.86518943 -8.86697508 3.645096445 0.955257045 2.191686286 0.987074919 0.067725725 0.018284885 0.46841455 0.010659999 0.020281839 1.36E-09 8.86697508 1.23642924 up GSGGLFS(ph)PSTAHVPDGALGQR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGGLFSPSTAHVPDGALGQR 21 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 GSGGLFS(0.835)PS(0.01)T(0.155)AHVPDGALGQR 82.865 0.0025153 11164000 924.97 784.2 679.44 764.25 1344.8 1501.5 1018.2 1475.5 1009.9 1091.6 TRUE FALSE FALSE 913.6961099 795.2399882 691.2653682 852.6161809 1276.169838 1405.558996 1104.685883 1518.191265 919.5720147 1063.240075 0.859350707 0.747940194 0.650149844 0.801903729 1.20026499 1.321958257 1.038980668 1.427891311 0.864877121 1 10.05425167 -8.704868877 6.572591646 0.884830789 1.241284327 0.698160569 0.133542886 0.116873957 10.31458357 0.021693011 0.043416812 1.97E-09 8.704868877 0.356453537 GSGIFDEST(ph)PVQTR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGIFDESTPVQTR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BU16;H3BMV3;Q9H910-2;H3BMT0;H3BTV5 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 0 GSGIFDES(0.022)T(0.978)PVQTR 234.04 1.30E-42 50572000 4055.3 4292.3 4219.6 3589 4898.2 5611.3 4244.3 4876.6 4363.3 3500.8 TRUE FALSE FALSE 4005.872444 4352.727112 4293.040368 4003.977067 4648.226576 5252.75604 4604.810736 5017.696727 3973.03552 3409.848711 1.174794773 1.276516198 1.259011977 1.17423892 1.363176777 1.54046601 1.350444294 1.471530602 1.16516475 1 11.73549202 -8.446685918 0.148785659 0.858810254 1.845745079 0.676390819 0.086392801 4.244016676 0.177500666 0.291606257 0.956398676 3.58E-09 8.446685918 0.986934825 GSGNLEAIHIIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GSGNLEAIHIIKK 13 1 F8VQ14;F5GWF6;P78371;P78371-2 F8VQ14 CCT2 T-complex protein 1 subunit beta 0 1 ; GSGNLEAIHIIK(1)K;GSGNLEAIHIIK(1)K 95.273 0.0060071 1337890 798.36 669.24 715.5 426.96 1531.16 1255.73 1110.79 1141.81 1390.3 1124.73 FALSE TRUE FALSE 788.6292812 678.6615783 727.9529774 476.3271241 1453.019192 1175.492906 1205.140475 1174.846471 1265.948086 1095.509352 0.719874531 0.619494098 0.664488145 0.434799688 1.326341202 1.073010379 1.100073196 1.072420302 1.155579442 1 10.09738609 -8.741479943 24.99999197 0.799959719 1.134901297 0.453540944 0.200687442 194.0263997 243024.6581 0.029120425 0.058179882 1.81E-09 8.741479943 0.334941577 GSGS(ph)PTHSLSQK ddPTM_HeLa_Romidepsin_16h_R1 2 GSGSPTHSLSQK 12 0 I3L419;I3L156;Q9BSJ6-2;Q9BSJ6;I3L2R2 I3L419 FAM64A Protein FAM64A 1 0 GSGS(0.999)PT(0.001)HSLSQK;GS(0.001)GS(0.996)PT(0.001)HS(0.002)LSQK ; 191.48 4.37E-10 49429000 3288.4 3032.6 3109.7 2399.4 5950.5 7534.5 7315.8 2818.3 5099.6 3911.5 TRUE FALSE FALSE 3248.319716 3075.293022 3163.823024 2676.829918 5646.823781 7053.069766 7937.203869 2899.843064 4643.479004 3809.878666 0.852604505 0.807189229 0.83042619 0.702602406 1.48215318 1.851258369 2.083321955 0.761137904 1.218799707 1 11.89552934 -8.659702525 5.438861656 0.896657137 1.622775502 0.454321655 0.343243857 0.118825551 5.360650473 0.044447552 0.089797309 2.19E-09 8.659702525 0.726118365 GSGS(ph)QSSVPSVDQFTGVGIR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGSQSSVPSVDQFTGVGIR 20 0 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 0 GS(0.001)GS(0.538)QS(0.149)S(0.042)VPS(0.154)VDQFT(0.116)GVGIR 169.58 2.99E-10 15152000 1879.7 1599.6 1783.4 1696.8 1383.4 1247.9 1136.1 1296.7 1782.3 1850 TRUE FALSE FALSE 1856.789493 1622.119211 1814.439329 1892.992 1312.799936 1168.163217 1232.600306 1334.217969 1622.886624 1801.936733 1.030441002 0.900208748 1.006938421 1.050531889 0.728549406 0.648282038 0.684041944 0.740435524 0.900634631 1 10.81533264 -8.715401866 6.013090078 1.006866249 0.69200754 0.859904952 0.055055504 0.036478117 3.088358936 0.006422383 0.012823235 1.93E-09 8.715401866 -0.314858709 GSGSGFK(ac)PFK ddPTM_HeLa_Romidepsin_16h_R1 2 GSGSGFKPFK 10 1 Q9NWH9;H7C3F4;Q9NWH9-3;H0YKH2 Q9NWH9 SLTM SAFB-like transcription modulator 0 1 ; GSGSGFK(1)PFK;GSGSGFK(1)PFK 117.7 0.015444 2226400 1013.27 1020.8 1698.44 1002.98 1815.49 1671.16 1307.05 916.49 999.48 752.86 FALSE TRUE FALSE 1000.919875 1035.170849 1728.000636 1118.949267 1722.838771 1564.378269 1418.070794 943.0071922 910.0840056 733.3005887 1.364951687 1.411659646 2.356469724 1.525908044 2.349430503 2.133338352 1.93381925 1.28597632 1.24107906 1 9.518260887 -10.26278475 1.211910776 1.123831062 1.940710641 0.472271569 0.338957297 0.24027281 0.682147704 0.067263937 0.079843512 5.46E-11 10.26278475 0.816879579 GSGT(ph)ASDDEFENLR ddPTM_HeLa_Romidepsin_16h_R1 1 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 GS(0.006)GT(0.623)AS(0.371)DDEFENLR 184 2.99E-07 15826000 1272.6 1599.8 1089.9 1621.3 1400.4 1199.6 1200.4 1202.6 1442.9 1550.3 TRUE FALSE FALSE 1257.089062 1622.322026 1108.869252 1808.762334 1328.932362 1122.949432 1302.361946 1237.395334 1313.84341 1510.022983 0.832496642 1.074369096 0.734339321 1.197837619 0.880074262 0.743663802 0.862478228 0.819454636 0.870081731 1 10.56035479 -8.520430094 24.99938933 0.937823952 0.813583836 0.206443243 0.124306206 124.9920296 1276095.83 0.017413628 0.035309856 3.02E-09 8.520430094 -0.124240115 GSGTAEVELKK ddPTM_HeLa_Romidepsin_16h_R1 1 GSGTAEVELKK 11 1 P14618;P14618-3;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 94.465 0.013248 13445000 5262.5 5145.5 5277.7 4739.9 6211.7 5054 5051.1 5158.8 5873.4 5129.1 FALSE FALSE TRUE 5198.358626 5217.938484 5369.556155 5287.94954 5894.69377 4731.065711 5480.140308 5308.061739 5348.068394 4995.845243 1.04053636 1.044455589 1.074804341 1.058469445 1.17991921 0.947000053 1.096939565 1.06249523 1.070503215 1 12.28651307 -10.95593408 0.635379705 1.004235496 1.069834994 0.005112979 0.057307925 0.785476808 0.720317663 0.020578311 0.014294469 1.11E-11 10.95593408 0.065599498 GSGTAS(ph)DDEFENLR ddPTM_HeLa_Romidepsin_16h_R1 3 GSGTASDDEFENLR 14 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 GSGT(0.018)AS(0.982)DDEFENLR;GSGT(0.009)AS(0.991)DDEFENLR;GSGT(0.008)AS(0.991)DDEFENLR ;; 247.11 1.29E-54 640933000 4816.6 5015.5 5330.6 4595.9 4659 4360.5 4248.1 4779.2 5335.3 5268.5 TRUE FALSE FALSE 4757.893427 5086.108341 5423.376857 5127.299582 4421.233845 4081.878123 4608.933508 4917.478612 4858.097405 5131.62361 0.927171162 0.991130435 1.056853984 0.999157376 0.861566276 0.795435993 0.898143328 0.958269543 0.946697921 1 12.32519964 -8.757965343 24.99961538 0.976635225 0.873844609 0.523577776 0.050057896 64.73855647 465859.3677 0.008149704 0.01579156 1.75E-09 8.757965343 -0.102790616 GSISTPNS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 GSISTPNSPVK 11 0 Q96AY4;A0A087WW06 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 0 GSIS(0.009)T(0.373)PNS(0.618)PVK 143.56 0.0025446 14936000 4215.4 3791.3 5556.3 4462 3971.5 4724.4 3891.9 3270 5049.4 3411.8 TRUE FALSE FALSE 4164.021083 3844.674021 5653.005071 4977.917434 3768.819535 4422.526087 4222.477889 3364.612291 4597.769018 3323.160944 1.253030218 1.156932838 1.701092775 1.497946539 1.134106833 1.330819109 1.270620942 1.012473469 1.383552917 1 11.69834045 -11.63566623 0.767106703 1.013415623 1.308761451 0 0.215659575 0.625314675 0.73968997 0.095544314 0.041298149 2.31E-12 11.63566623 0.295345827 GSK(ac)K(ac)AVTK ddPTM_HeLa_Romidepsin_16h_R1 1 GSKKAVTK 8 2 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 2 GSK(1)K(1)AVTK 120.27 0.0032156 72568000 2024.6 2250.1 4776.5 35682 31421 36463 32114 12851 2002.9 1598.6 FALSE TRUE FALSE 1999.923396 2281.776967 4859.632979 39807.72073 29817.46912 34133.13198 34841.76236 13222.82341 1823.755608 1557.068142 1.284416104 1.46543167 3.12101497 25.56581801 19.14975223 21.92141183 22.3765174 8.492128929 1.171275398 1 10.60461637 -9.330551617 6.355844587 1.248332585 19.75390164 0.820558638 4.183996957 0.06441337 4.801818967 0.596999886 0.916926866 4.67E-10 9.330551617 18.50556905 EEYEGPNK(ac)KPR ddPTM_HeLa_Romidepsin_16h_R1 1 EEYEGPNKKPR 11 2 P23246 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 1 EEYEGPNK(0.878)K(0.122)PR 127.83 0.0042721 44838000 4797.3 4872.9 4461.8 5966 8797.6 9358.6 8752.3 8273.4 5288.9 3942.8 FALSE TRUE FALSE 4738.828662 4941.500814 4539.455757 6655.816991 8348.625644 8760.615663 9495.720144 8512.777776 4815.847538 3840.365488 1.233952518 1.286726701 1.182037432 1.733120718 2.17391435 2.281193207 2.472608447 2.216658233 1.254007608 1 11.9070279 -8.982526707 1.456295072 1.119709863 2.354573725 0.960404725 0.104723504 0.053501627 0.225982277 0.018575815 0.040233139 1.04E-09 8.982526707 1.234863862 up TVALK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 TVALKR 6 1 Q01658 Q01658 DR1 Protein Dr1 0 1 TVALK(1)R 100.07 0.019594 6272200 1189.7 1261.5 1545.5 1920.8 3395 4467.5 3588.8 3040 1272.7 893.25 FALSE TRUE FALSE 1175.199479 1279.25943 1572.398779 2142.891934 3221.740482 4182.041168 3893.632582 3127.957604 1158.866524 870.0432362 1.350736871 1.470340067 1.807265103 2.462971775 3.702965953 4.806704994 4.475217346 3.595174899 1.331964294 1 9.764943286 -8.96739081 1.353444172 1.190839002 4.35945769 0.938392857 0.33526261 0.066308116 0.241762241 0.056043404 0.126083722 1.08E-09 8.96739081 3.168618688 up GSKPGGVGTGLGGSS(ph)GTETLEK ddPTM_HeLa_Romidepsin_16h_R1 1 GSKPGGVGTGLGGSSGTETLEK 22 1 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 1 0 GSKPGGVGTGLGGS(0.049)S(0.317)GT(0.317)ET(0.317)LEK 48.196 0.023968 13674000 1880.4 1824.1 1502.6 1475.1 1717.9 1514.6 1710.4 1721.5 1588.6 1738.2 TRUE FALSE FALSE 1857.480962 1849.779728 1528.752123 1645.658003 1630.229153 1417.821948 1855.681333 1771.308886 1446.511637 1693.041313 1.097126778 1.092578021 0.90296209 0.972012903 0.962899806 0.837440845 1.096063822 1.04622898 0.854386497 1 10.72540146 -9.772102615 24.99985421 1.0506504 0.969147391 0 0.09424791 252.4807825 591937.7423 0.012344924 0.016316334 1.69E-10 9.772102615 -0.081503009 GSLAEAVGS(ph)PPPAATPTPTPPTR ddPTM_HeLa_Romidepsin_16h_R1 2 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 1 0 GSLAEAVGS(0.965)PPPAAT(0.03)PT(0.005)PTPPTR;GS(0.06)LAEAVGS(0.94)PPPAATPTPTPPTR ; 179.84 4.68E-15 21788900 5895.9 6440.9 5236 5805.4 7957 9036.7 7642.7 8458.4 6874.4 6793.1 TRUE FALSE FALSE 5824.038503 6531.575159 5327.130384 6476.647663 7550.924598 8459.284035 8291.870747 8703.130459 6259.536447 6616.614283 0.880214299 0.987147638 0.805114241 0.978846187 1.141206707 1.278491336 1.253189379 1.315344992 0.946033149 1 12.69187746 -8.601739971 2.328564953 0.934947033 1.279942147 0.895006504 0.054471909 0.077473341 0.845845018 0.009403477 0.021854776 2.50E-09 8.601739971 0.344995114 GSLAEAVGSPPPAAT(ph)PTPTPPTR ddPTM_HeLa_Romidepsin_16h_R1 1 GSLAEAVGSPPPAATPTPTPPTR 23 0 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 1 0 GSLAEAVGSPPPAAT(0.969)PT(0.027)PT(0.004)PPTR 202.21 4.14E-32 0 2015.4 2564.9 1877.2 1877.1 1752.4 1765.1 1239.5 1540.6 2079.7 1955.1 TRUE FALSE FALSE 1990.83553 2601.00873 1909.871879 2094.139134 1662.968489 1652.315807 1344.783099 1585.17483 1893.686423 1904.30622 1.045438758 1.365856343 1.00292267 1.099686128 0.873267372 0.867673376 0.70618007 0.832415928 0.994423273 1 10.89504977 -8.518743461 2.16213357 1.054234171 0.786433482 0.564764025 0.112226509 0.195184259 1.807868353 0.017088119 0.042763309 3.03E-09 8.518743461 -0.267800689 GSLAPQDS(ph)DSEVSQNR ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 GSLAPQDS(0.992)DS(0.008)EVSQNR 265.08 2.93E-86 10556000 2853.7 2627.6 2624.3 2752.8 3028.5 3455.4 2859.8 2948.2 2776.9 2327.2 TRUE FALSE FALSE 2818.918007 2664.591422 2669.974841 3071.091688 2873.944344 3234.611092 3102.711341 3033.501516 2528.527109 2266.739009 1.243600607 1.175517522 1.177892484 1.354850151 1.267876157 1.426988762 1.368799553 1.338266781 1.115491064 1 11.14640257 -16.17791181 0.08778566 2.95E-14 1.596830767 0.740223818 0.063624391 38.18455301 0.27335325 7.418042904 0.769181824 6.64E-17 16.17791181 1.596830767 GSLAS(ph)LDSLR ddPTM_HeLa_Romidepsin_16h_R1 4 GSLASLDSLR 10 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22;O60716-25;O60716-27;O60716-29;O60716-26;O60716-28;O60716-30;O60716-31;O60716-32;E9PKY0 O60716 CTNND1 Catenin delta-1 1 0 GS(0.001)LAS(0.998)LDSLR;GS(0.002)LAS(0.997)LDSLR;GS(0.003)LAS(0.992)LDS(0.004)LR;GS(0.004)LAS(0.996)LDSLR ;;; 166.29 0.001444 205772300 8851.3 8582.8 7557.2 4612.67 9245.1 9065.8 7183.8 8513.4 9046 8469.3 TRUE FALSE FALSE 8743.416951 8703.628884 7688.729896 5146.008609 8773.288049 8486.524639 7793.991793 8759.721797 8236.903104 8249.266365 1.059902368 1.055079143 0.932050143 0.623814092 1.063523429 1.028761136 0.944810296 1.061878888 0.99850129 1 13.01005011 -9.754218362 24.12910179 1.031087002 0.937519203 0.110172547 0.118993966 178.5038134 596468.2074 0.018936105 0.026445533 1.76E-10 9.754218362 -0.093567799 GSLAS(ph)LDSLRK ddPTM_HeLa_Romidepsin_16h_R1 1 GSLASLDSLRK 11 1 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22;O60716-25;O60716-27;O60716-29;O60716-26;O60716-28;O60716-30;O60716-31;O60716-32;E9PKY0 O60716 CTNND1 Catenin delta-1 1 0 GS(0.012)LAS(0.987)LDS(0.001)LRK 146.5 0.0037863 131720000 1682.3 1563.6 1598.7 1377.4 1498.6 2390 1631.6 1452.8 1679 1543.3 TRUE FALSE FALSE 1661.795481 1585.612402 1626.524703 1536.661469 1422.12085 2237.286713 1770.188063 1494.834476 1528.826035 1503.204844 1.10550168 1.054821243 1.08203796 1.022256864 0.946059252 1.488344535 1.17760934 0.994431652 1.017044378 1 10.55382591 -11.87052569 0.048967075 0.631665547 1.464253739 0.097582284 0.139532039 190.8005678 2.957591355 29.33605359 21.00829086 1.35E-12 11.87052569 0.832588193 GSLGIS(ph)QEEQ ddPTM_HeLa_Romidepsin_16h_R1 2 GSLGISQEEQ 10 0 H3BRR0;Q9NZD8-2;Q9NZD8 H3BRR0 SPG21 Maspardin 1 0 GS(0.001)LGIS(0.999)QEEQ;GSLGIS(1)QEEQ ; 99.343 0.0030521 19109000 16407.3 15569.6 13991 11235.7 12495.4 12062.7 9839 11084 16008.5 14606.5 TRUE FALSE FALSE 16207.32152 15788.78924 14234.50749 12534.8245 11857.71311 11291.9324 10674.72441 11404.69805 14576.65967 14227.02102 1.139192912 1.109774788 1.000526214 0.881057565 0.833464229 0.793696191 0.750313393 0.801622352 1.024575675 1 13.79634599 -9.1464674 1.665686858 1.070898499 0.786065057 0.902676164 0.041132838 0.104283419 0.56723433 0.00929511 0.017740901 7.14E-10 9.1464674 -0.284833442 GSLLPTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GSLLPTSPR 9 0 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;Q9H0E9-3 H7C128;Q9H0E9-3 BRD8 Bromodomain-containing protein 8 1 0 GSLLPT(0.003)S(0.997)PR 99.013 0.029362 28796000 6999.4 7260 6649.9 4016.9 5235 5413.5 5189.9 4887 7462.7 6657.6 TRUE FALSE FALSE 6914.088621 7362.206471 6765.63872 4481.352878 4967.838416 5067.594821 5630.729976 5028.397635 6795.217421 6484.634592 1.066226404 1.135330968 1.043333842 0.691072537 0.766093809 0.781477314 0.868318777 0.775432688 1.047895194 1 12.66280957 -9.273854821 24.91268405 1.042350023 0.781281961 0.879654331 0.051979675 206.2218019 413801.5855 0.008917095 0.013680391 5.32E-10 9.273854821 -0.261068061 GSLLTILGSPS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 GSLLTILGSPSPER 14 0 Q96A19 Q96A19 CCDC102A Coiled-coil domain-containing protein 102A 1 0 GSLLTILGS(0.001)PS(0.999)PER 130.66 0.0021459 7102100 1910.9 1707 1544.6 1278.6 1049 986.4 813.96 849.51 1960 1681 TRUE FALSE FALSE 1887.609216 1731.031191 1571.483115 1426.437748 995.4656156 923.3722235 883.0977421 874.0892315 1784.692691 1637.327378 1.152859985 1.057229736 0.959785524 0.871198862 0.607982026 0.563950885 0.539353189 0.533851228 1.090003573 1 10.6771271 -8.940198003 1.38794369 1.072139057 0.532861524 0.968942265 0.041800381 0.067790402 0.260589975 0.009861915 0.022331663 1.15E-09 8.940198003 -0.539277533 GSLPQLVSPIVS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 GSLPQLVSPIVSR 13 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 GSLPQLVS(0.359)PIVS(0.641)R;GSLPQLVS(0.296)PIVS(0.704)R ; 156.96 0.00062426 95308000 3272.3 3392.5 3386.3 3216.8 4208.2 4539.7 3734.5 3793.3 3049.4 3435.7 TRUE FALSE FALSE 3232.415949 3440.259704 3445.237131 3588.741551 3993.439851 4249.627821 4051.708337 3903.053151 2776.654027 3346.440019 0.965926755 1.028035669 1.029523049 1.07240576 1.193339737 1.269895112 1.210751818 1.166329929 0.82973369 1 11.70841144 -8.966158764 1.623159222 0.988008591 1.220444222 0.788541798 0.058291835 0.072511733 0.381901839 0.00506856 0.010678936 1.08E-09 8.966158764 0.232435631 GSLS(ph)PGGER ddPTM_HeLa_Romidepsin_16h_R1 1 GSLSPGGER 9 0 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3;H7C1F2;H0Y3R4 E7EWN3 SETD5 SET domain-containing protein 5 1 0 GSLS(1)PGGER 102.53 0.026034 11573000 2032.3 2171.7 1843.1 1049.8 2104.8 1663.6 1497.3 1294.2 2010.1 1899.1 TRUE FALSE FALSE 2007.529546 2202.27325 1875.178382 1171.182815 1997.384202 1557.301329 1624.480625 1331.645635 1830.311622 1849.761108 1.08529125 1.190571712 1.013740841 0.633153552 1.079806572 0.841893216 0.878211039 0.719901413 0.989485406 1 10.85312325 -9.498194493 24.73785182 1.055030248 0.845285108 0.47048242 0.119761629 467.3453421 468360.7446 0.017408285 0.026509013 3.18E-10 9.498194493 -0.20974514 SVSLT(ph)IY ddPTM_HeLa_Romidepsin_16h_R1 2 SVSLTIY 7 0 P30291-2;P30291 P30291-2 WEE1 Wee1-like protein kinase 1 0 S(0.005)VS(0.111)LT(0.635)IY(0.249);SVS(0.04)LT(0.885)IY(0.075) ; 105.39 0.0065995 11347500 11119.7 12738.7 9470.6 7969.6 4159 3351.9 2222.8 3027.1 12245.8 12459.9 TRUE FALSE FALSE 10984.16882 12918.03575 9635.43182 8891.08265 3946.750711 3137.724408 2411.604577 3114.684363 11150.50498 12136.19 0.905075548 1.064422669 0.793942071 0.732609052 0.325205086 0.258542789 0.198711834 0.256644331 0.918781345 1 13.56702796 -8.887291646 1.507975633 0.959754141 0.218563741 0.963392531 0.062761299 0.046816412 0.213852821 0.009797687 0.022174372 1.30E-09 8.887291646 -0.7411904 down GSNEEQVNGS(ph)PLER ddPTM_HeLa_Romidepsin_16h_R1 2 GSNEEQVNGSPLER 14 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 0 GSNEEQVNGS(1)PLER;GSNEEQVNGS(1)PLER ; 194.77 2.13E-11 9224100 1730.11 2076.19 1803.43 1613.13 1694.09 1258 973.66 1182.6 2391.93 2073.29 TRUE FALSE FALSE 1709.022754 2105.418657 1834.817943 1799.647681 1607.634266 1177.61786 1056.362656 1216.816665 2177.98979 2019.425627 0.846291505 1.042582915 0.908584064 0.891168091 0.796084909 0.583144952 0.52310055 0.60255582 1.078519437 1 10.9797293 -8.435043355 1.900749276 0.933332231 0.552669815 0.858378066 0.07080182 0.09159529 0.643125917 0.010143684 0.028341956 3.67E-09 8.435043355 -0.380662416 GSPALLPS(ph)TPTMPLFPHVLDLLAPLDSSR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPALLPSTPTMPLFPHVLDLLAPLDSSR 29 0 Q9UGR2 Q9UGR2 ZC3H7B Zinc finger CCCH domain-containing protein 7B 1 0 GSPALLPS(0.333)T(0.333)PT(0.333)MPLFPHVLDLLAPLDSSR 112.55 5.16E-10 210850000 478.63 438.06 327.19 582.28 419.66 467.7 347.31 408.59 385.64 419.03 TRUE FALSE FALSE 472.7962735 444.2270202 332.8846047 649.6059533 398.2431842 437.8154794 376.8105027 420.411907 351.1473925 408.1435402 1.158406852 1.088408798 0.815606697 1.591611503 0.975742956 1.072699764 0.923230348 1.030058951 0.86035269 1 8.672932813 -8.051458836 2.581297516 1.091320254 0.980667253 0.022079216 0.203253757 0.716800535 9.32313015 0.026027702 0.087314599 8.88E-09 8.051458836 -0.110653002 GSPATS(ph)PHLGR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPATSPHLGR 11 0 E9PNR2;Q13671-2;Q13671 E9PNR2 RIN1 Ras and Rab interactor 1 1 0 GS(0.004)PAT(0.183)S(0.813)PHLGR 81.565 0.022114 2265200 1385.7 1222.7 1360.4 739.08 1594.7 1446.9 929.32 1005.1 1862.8 1461.2 TRUE FALSE FALSE 1368.810555 1239.913203 1384.077191 824.5359071 1513.316508 1354.44776 1008.256418 1034.180983 1696.186503 1423.237813 0.961758142 0.871191863 0.972484836 0.579338112 1.063291387 0.951666508 0.708424417 0.726639619 1.191780099 1 10.47496103 -4.425844027 0.168246647 1.029771199 1.12E-12 0.334213638 0.142237912 49.81467666 0.590979451 0.199351427 12.57892199 3.75E-05 4.425844027 -1.029771199 GSPDGS(ph)LQTGKPSAPK ddPTM_HeLa_Romidepsin_16h_R1 1 GSPDGSLQTGKPSAPK 16 1 E7EV54;C9JFV4;Q8IZL8 E7EV54 PELP1 "Proline-, glutamic acid- and leucine-rich protein 1" 1 0 GS(0.058)PDGS(0.937)LQT(0.005)GKPSAPK 69.878 0.015258 26535000 3571.6 3780.7 3929.3 2234 3471.7 3530.2 3863.2 4084.1 3884.8 3538.5 TRUE FALSE FALSE 3528.067965 3833.924794 3997.687818 2492.305591 3294.526194 3304.631613 4191.340112 4202.26699 3537.333758 3446.56926 1.023646328 1.112388728 1.159903521 0.723126507 0.955885678 0.958817701 1.216090493 1.219260857 1.026334738 1 11.75094529 -7.754058735 24.73033439 1.001916154 1.217675824 0.396934329 0.109517727 113.2165013 379343.236 0.015034758 0.054007887 1.76E-08 7.754058735 0.21575967 GSPLNAAPY(ph)GIESMSQDTEVR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPLNAAPYGIESMSQDTEVR 21 0 P18031;B4DSN5 P18031 PTPN1 Tyrosine-protein phosphatase non-receptor type 1;Tyrosine-protein phosphatase non-receptor type 1 0 GSPLNAAPY(0.878)GIES(0.061)MS(0.061)QDTEVR 87.831 0.017189 3628500 357.73 498.01 596.74 550.79 618.17 1310.6 614.5 1158.9 818.24 598.58 TRUE FALSE FALSE 353.3698492 505.0209979 607.1260094 614.4749313 586.6224782 1226.85689 666.6956147 1192.430943 745.0545651 583.0288053 0.606093294 0.866202481 1.041331069 1.053935802 1.0061638 2.104281776 1.143503732 2.045235042 1.277903524 1 9.187423353 -8.407424512 5.389650751 0.854327196 1.698615705 0.56084522 0.305666756 0.10341141 4.2012656 0.039691867 0.089988213 3.91E-09 8.407424512 0.844288509 GSPS(ph)GGSTAEASDTLSIR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPSGGSTAEASDTLSIR 18 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 GS(0.107)PS(0.861)GGS(0.013)T(0.017)AEAS(0.002)DTLSIR 108.96 0.0013807 14888000 884.07 1017.4 807.89 575.64 850.29 748.63 605.93 718.22 1187.6 852.9 TRUE FALSE FALSE 873.2946148 1031.722984 821.9509866 642.1982053 806.8965284 700.7949591 657.3976791 739.0005625 1081.378082 830.741535 1.051223007 1.24193018 0.989418431 0.773042129 0.97129672 0.843577611 0.791338402 0.88956737 1.301702197 1 9.698255877 -9.464057988 7.368096117 1.044628524 0.858032859 0.530197508 0.115238247 0.164073061 18.1085615 0.012918451 0.019692414 3.44E-10 9.464057988 -0.186595666 AES(ph)PESSAIESTQS(ph)TPQK ddPTM_HeLa_Romidepsin_16h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 AES(0.711)PES(0.02)S(0.237)AIES(0.025)T(0.009)QS(0.779)T(0.219)PQK 166.67 4.82E-06 32322000 7208.3 7312 8061.2 5063.9 4205.3 3669.6 3121.3 3324.7 8840.1 7424.3 TRUE FALSE FALSE 7120.442467 7414.938528 8201.501804 5649.411944 3990.687849 3435.124403 3386.423144 3420.894949 8049.419316 7231.415616 0.984654021 1.02537856 1.134148864 0.781231815 0.551854306 0.475027932 0.468293253 0.473060204 1.113118059 1 12.82006238 -8.887187445 2.57119711 1.004925539 0.478849479 0.951181505 0.059247353 0.035885169 0.481298754 0.007410427 0.014634091 1.30E-09 8.887187445 -0.52607606 down GSPTDAEGS(ph)PGLSR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPTDAEGSPGLSR 14 0 Q8TER5;Q8TER5-4;Q8TER5-3;G3V485;G3V3N2;G3V5C1 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 GSPTDAEGS(1)PGLSR 196.37 1.16E-11 29194000 3634 3292.1 2936.9 3435.6 3215.6 2810.4 2214.3 2510.4 3445 3353.4 TRUE FALSE FALSE 3589.70741 3338.44627 2988.015513 3832.840237 3051.495933 2630.82451 2402.382587 2583.034463 3136.870572 3266.278185 1.099020722 1.022094899 0.914807418 1.173457991 0.934242511 0.805450229 0.73551071 0.790818882 0.960380713 1 11.67343195 -8.369012674 2.96315378 1.042998116 0.768163994 0.711607557 0.070687139 0.092910608 1.559644944 0.009729027 0.024333777 4.28E-09 8.369012674 -0.274834122 GSPVSEIGWETPPPES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 GSPVSEIGWETPPPESPR 18 0 A0A3B3ITC2;Q13884-2;Q13884 A0A3B3ITC2 SNTB1 Beta-1-syntrophin 1 0 GSPVSEIGWET(0.061)PPPES(0.939)PR 122.97 0.0015981 9102500 590.55 623.41 896.37 643.88 696.59 674.59 666.06 565.98 734.2 690.34 TRUE FALSE FALSE 583.3521495 632.1863823 911.9709438 718.3284351 661.040413 631.4858761 722.6351198 582.3557383 668.5313132 672.4048673 0.867560867 0.9401871 1.356282484 1.068297495 0.983098792 0.939145308 1.074702393 0.866079005 0.994239253 1 9.393186358 -9.944605473 24.99998876 0.935688377 1.051021901 0.121878492 0.125531902 125.9368992 56835.86084 0.020845353 0.02739616 1.14E-10 9.944605473 0.115333523 GSQAGAEGQPSTVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GSQAGAEGQPSTVKR 15 1 H7C4B2;A0A075B6Q3;Q5H9F3-2;Q5H9F3;Q5H9F3-3 H7C4B2 BCORL1 BCL-6 corepressor-like protein 1 0 1 GSQAGAEGQPSTVK(1)R 94.532 0.011883 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 GSQEDDPAATQRPPS(ph)NGGAK ddPTM_HeLa_Romidepsin_16h_R1 3 GSQEDDPAATQRPPSNGGAK 20 1 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 GSQEDDPAAT(0.085)QRPPS(0.915)NGGAK;GSQEDDPAAT(0.004)QRPPS(0.996)NGGAK;GSQEDDPAAT(0.002)QRPPS(0.998)NGGAK ;; 125.23 0.0017249 30556600 6436.39 6030.53 5833.75 3749.63 4442.72 3967.27 3444.55 4205.87 6626.7 5955.57 TRUE FALSE FALSE 6357.940803 6115.42796 5935.283972 4183.179863 4215.99142 3713.774251 3737.129991 4327.560213 6033.991355 5800.843433 1.096037305 1.054230825 1.023176033 0.721133041 0.726789383 0.640212806 0.644239072 0.746022585 1.040192073 1 12.50204697 -9.249703935 3.622284177 1.047468698 0.686143928 0.956131468 0.037242154 0.040797781 1.170791703 0.00718083 0.011838614 5.63E-10 9.249703935 -0.36132477 GSQPPPAAES(ph)QSSLRR ddPTM_HeLa_Romidepsin_16h_R1 2 GSQPPPAAESQSSLRR 16 1 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3;E9PJP4;E9PQD2;E9PIG0;E9PRG1;E9PQN0 O43491 EPB41L2 Band 4.1-like protein 2 1 0 GSQPPPAAES(0.333)QS(0.333)S(0.333)LRR;GSQPPPAAES(0.436)QS(0.127)S(0.436)LRR ; 110.64 0.00090152 6633700 4396.6 4963.7 4801.8 3344.9 4933.8 5705.2 4015.4 4510.6 4540.1 4588.9 TRUE FALSE FALSE 4343.012548 5033.579099 4885.373315 3731.653076 4682.009775 5340.656133 4356.467976 4641.107094 4134.022085 4469.679716 0.971660795 1.126161027 1.093002995 0.834881538 1.047504536 1.194863272 0.974671174 1.038353392 0.924903426 1 12.12595574 GSREEK(ac)QKPQAER ddPTM_HeLa_Romidepsin_16h_R1 1 GSREEKQKPQAER 13 3 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 1 GSREEK(0.994)QK(0.006)PQAER 49.243 0.028436 666580 450.63 353.91 379.28 555.16 326.33 435.65 494.34 290.63 734.4 534.78 FALSE TRUE FALSE 445.1375482 358.8923543 385.8812093 619.3502113 309.6761624 407.813371 536.3292273 299.0389205 668.7134247 520.8863385 0.854577122 0.6890032 0.740816529 1.189031398 0.594517728 0.782921994 1.029647329 0.574096302 1.283799123 1 9.024824789 -11.63066025 0.750159332 0.994656945 0.812588308 0.244713307 0.201198897 0.933545722 1.055839561 0.087434029 0.03732541 2.34E-12 11.63066025 -0.182068637 GSS(ph)GSPAHAESYSSGGGGQQK ddPTM_HeLa_Romidepsin_16h_R1 2 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 0 GS(0.12)S(0.499)GS(0.381)PAHAESYSSGGGGQQK;GS(0.126)S(0.437)GS(0.437)PAHAESYSSGGGGQQK ; 129.26 9.43E-05 8614300 3031.1 2348.7 2202.13 1483.71 4400.5 3374.5 3220.7 2805.1 4575.8 3940.8 TRUE FALSE FALSE 2994.155787 2381.76506 2240.457149 1655.263531 4175.926064 3158.880341 3494.266178 2886.261143 4166.528988 3838.417448 0.780049546 0.620507043 0.583692936 0.431235933 1.087929107 0.822964251 0.910340323 0.751940398 1.085480942 1 11.90629591 -11.76300644 0.947103691 0.983249513 0.751290937 0.296215093 0.174820784 0.60748188 1.08289094 0.079285489 0.035805289 1.73E-12 11.76300644 -0.231958575 GSS(ph)LSGTDDGAQEVVK ddPTM_HeLa_Romidepsin_16h_R1 2 GSSLSGTDDGAQEVVK 16 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 0 GS(0.289)S(0.684)LS(0.027)GT(0.001)DDGAQEVVK;GS(0.005)S(0.993)LS(0.001)GT(0.001)DDGAQEVVK ; 196.97 1.97E-13 38483000 7367.5 7798.3 8312.9 4638.3 5968.4 5932 4209 5797.3 7358.1 7187.6 TRUE FALSE FALSE 7277.702076 7908.084672 8457.582537 5174.60207 5663.810277 5552.964345 4566.512355 5965.035729 6699.973107 7000.865116 1.03954325 1.129586778 1.208076773 0.739137519 0.809015769 0.793182593 0.652278294 0.852042659 0.957020739 1 12.7733175 -9.242192841 24.98705426 1.042144454 0.766191487 0.763045057 0.082370917 316.4052412 410777.2977 0.01227853 0.020341262 5.73E-10 9.242192841 -0.275952967 GSS(ph)PGPRPVEGTPASR ddPTM_HeLa_Romidepsin_16h_R1 1 GSSPGPRPVEGTPASR 16 1 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 GS(0.001)S(0.999)PGPRPVEGTPASR 137.39 0.0073648 139170000 3492.7 3743.5 3009.6 3301.9 3362.8 2779.3 2583.5 3204.6 3572.7 3525.5 TRUE FALSE FALSE 3450.129629 3796.201091 3061.980826 3683.681214 3191.183768 2601.7117 2802.942426 3297.320045 3253.148764 3433.907002 1.004724248 1.105504922 0.891690085 1.072737617 0.929315723 0.757653512 0.816254611 0.960224037 0.947360765 1 11.74563525 -8.515827361 7.926637661 1.005959349 0.841878625 0.491439875 0.07256618 0.071232481 35.0518054 0.009197869 0.019412877 3.05E-09 8.515827361 -0.164080724 GSS(ph)PLGPAGLGAEEPAAGPQLPSWLQPER ddPTM_HeLa_Romidepsin_16h_R1 1 GSSPLGPAGLGAEEPAAGPQLPSWLQPER 29 0 H0YKL4;O43482 H0YKL4 OIP5 Protein yippee-like;Protein Mis18-beta 1 0 GS(0.456)S(0.544)PLGPAGLGAEEPAAGPQLPSWLQPER 98.667 1.33E-08 6068600 1193.5 1255.2 1231.1 1018.4 1328.8 1346.8 954.52 1061.9 1598 1578.6 TRUE FALSE FALSE 1178.953163 1272.870739 1252.526779 1136.1522 1260.986378 1260.743827 1035.596905 1092.624401 1455.070878 1537.587744 0.766755047 0.827836163 0.814605074 0.738918611 0.820106938 0.819949191 0.673520525 0.710609463 0.946333556 1 10.58645303 -16.52287875 0.202833129 2.121038848 0.728426872 0.744560197 0.048112428 17.00243509 0.207811474 7.524526327 0.047777017 3.00E-17 16.52287875 -1.392611976 GSSAAASPGS(ph)PPPGR ddPTM_HeLa_Romidepsin_16h_R1 2 GSSAAASPGSPPPGR 15 0 Q86UX6 Q86UX6 STK32C Serine/threonine-protein kinase 32C 1 0 GSSAAAS(0.004)PGS(0.996)PPPGR;GSSAAASPGS(1)PPPGR ; 188.39 2.79E-12 33987000 2946.9 3034.2 2760.93 2499.8 2748.2 3121.2 2545.7 2880.9 2818.4 2986.4 TRUE FALSE FALSE 2910.982049 3076.915547 2808.982828 2788.838638 2607.949099 2921.765393 2761.931694 2964.254296 2566.315245 2908.812897 1.000745717 1.057790809 0.965680134 0.958754907 0.896568185 1.004452846 0.949504761 1.019059802 0.88225518 1 11.50621479 -9.56952144 24.99947469 1.005006361 0.962998958 0 0.052317935 121.7615562 65260.99126 0.005233677 0.007401539 2.69E-10 9.56952144 -0.042007403 GSSANAS(ph)KWSPPQNYK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSANASKWSPPQNYK 16 1 Q96K21-3;H3BRM1;H3BRF9;Q96K21-2;Q96K21 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 GS(0.034)S(0.085)ANAS(0.785)KWS(0.095)PPQNY(0.001)K 58.817 0.028267 34525000 2408.4 2247.2 1656 3974.2 2604.3 2268.5 2694.5 2564 2372.5 2151.3 TRUE FALSE FALSE 2379.045494 2278.836141 1684.821985 4433.715703 2471.392853 2123.550171 2923.370763 2638.185295 2160.297658 2095.408916 1.135360968 1.087537675 0.804054031 2.115919079 1.17943225 1.013429959 1.395131394 1.259031244 1.030967102 1 11.0330161 GSSDAVSPDTFT(ph)AEVSSDAVPDVR ddPTM_HeLa_Romidepsin_16h_R1 1 GSSDAVSPDTFTAEVSSDAVPDVR 24 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 GS(0.018)S(0.018)DAVS(0.257)PDT(0.257)FT(0.447)AEVS(0.003)S(0.001)DAVPDVR 55.153 0.0092454 5901800 489.71 678.67 453.77 598.58 1112.5 909.52 856.26 899.22 535.77 577.16 TRUE FALSE FALSE 483.7412262 688.2243341 461.6676765 667.790636 1055.724974 851.4046073 928.990703 925.237512 487.8493893 562.1653 0.860496417 1.224238376 0.821231187 1.187890174 1.877961827 1.514509358 1.652522315 1.645846003 0.867804166 1 9.134850595 -8.935746898 4.859486538 0.952633526 1.656505752 0.863343985 0.134782393 0.050141592 2.350567246 0.018980579 0.034834437 1.16E-09 8.935746898 0.703872226 GSSDGRGS(ph)DSESDLPHR ddPTM_HeLa_Romidepsin_16h_R1 2 GSSDGRGSDSESDLPHR 17 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 GS(0.049)S(0.049)DGRGS(0.89)DS(0.012)ESDLPHR;GS(0.041)S(0.041)DGRGS(0.869)DS(0.05)ESDLPHR ; 69.878 0.010112 9392800 4442.7 3454.1 3034.7 3476.6 4211.8 3686.1 3201 3460 5614.3 4339.6 TRUE FALSE FALSE 4388.550664 3502.72691 3087.517681 3878.58085 3996.85613 3450.570106 3472.89286 3560.109641 5112.142947 4226.856566 1.038253983 0.828683646 0.730452437 0.917604084 0.945585938 0.816344262 0.821625434 0.842259392 1.209443204 1 12.04536944 -10.2604311 24.99804037 1.018064383 0.843818371 0.615009745 0.082153178 39.42278387 977405.075 0.009802585 0.011640219 5.49E-11 10.2604311 -0.174246012 GSSEQAES(ph)DNMDVPPEDDSKEGAGEQK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSEQAESDNMDVPPEDDSKEGAGEQK 27 1 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906;K7EKJ9;K7ER69;K7EM82;K7EJ09 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 GS(0.001)S(0.01)EQAES(0.989)DNMDVPPEDDSKEGAGEQK 103.53 3.29E-08 13461000 1658.7 1569.6 1582.3 1076.5 1596.8 1954.8 1412.4 1730.8 1754.7 2106 TRUE FALSE FALSE 1638.483126 1591.69687 1609.839268 1200.969995 1515.309338 1829.894589 1532.369221 1780.877967 1597.755237 2051.285816 0.798759058 0.7759508 0.784795203 0.585471798 0.738711946 0.892071975 0.747028624 0.868176416 0.778904248 1 11.00231281 -11.82536767 0.66522441 1.004697015 0.766037222 0.015901675 0.102555185 0.459935225 0.377850931 0.058016796 0.018456885 1.49E-12 11.82536767 -0.238659793 GSSGDSDS(ph)PGSSSLSLTR ddPTM_HeLa_Romidepsin_16h_R1 2 GSSGDSDSPGSSSLSLTR 18 0 H0Y507;Q5TCZ1-2;Q5TCZ1-3;Q5TCZ1 H0Y507 SH3PXD2A SH3 and PX domain-containing protein 2A 1 0 GSSGDSDS(0.987)PGS(0.007)S(0.003)S(0.003)LSLTR;GSSGDS(0.001)DS(0.971)PGS(0.013)S(0.013)S(0.002)LSLTR ; 196.71 3.36E-15 13391400 3771.2 4196.9 3332.1 3232.2 2926.3 2720.4 2645.1 2641.5 4224.4 4712.2 TRUE FALSE FALSE 3725.235164 4255.984068 3390.093803 3605.922172 2776.959991 2546.57522 2869.774728 2717.927635 3846.559084 4589.776365 0.81163762 0.927274823 0.738618515 0.785642237 0.605031655 0.554836449 0.625253716 0.592169949 0.838071134 1 12.16420815 -8.719608067 0.205273747 1.044866278 0.340517302 0.725678628 0.075248498 1.937830115 0.143180175 0.106449495 0.386582398 1.91E-09 8.719608067 -0.704348976 GSSGENNNPGS(ph)PTVSNFR ddPTM_HeLa_Romidepsin_16h_R1 2 GSSGENNNPGSPTVSNFR 18 0 D6RDZ7;D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;D6R8Z7 D6RDZ7 TSC22D3 1 0 GSSGENNNPGS(0.98)PT(0.02)VSNFR;GSSGENNNPGS(0.677)PT(0.321)VS(0.002)NFR ; 244.52 9.94E-62 26771000 4565.4 5250.7 4507.7 4798 3765.3 2544.1 2301.6 2802.8 5609.9 4461.9 TRUE FALSE FALSE 4509.755149 5324.619492 4586.154628 5352.767335 3573.142691 2381.540221 2497.097847 2883.894596 5108.136494 4345.979195 1.037684477 1.225182923 1.055263825 1.231659678 0.822172065 0.547987028 0.574576576 0.663577635 1.175370674 1 12.08546555 -8.509225272 4.409172407 1.052047555 0.600694144 0.856755712 0.09464031 0.058206246 2.773043831 0.013484848 0.029595925 3.10E-09 8.509225272 -0.451353412 GSSGS(ph)PAHAESYSSGGGGQQK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSGSPAHAESYSSGGGGQQK 21 0 P15408 P15408 FOSL2 Fos-related antigen 2 1 0 GS(0.001)S(0.028)GS(0.97)PAHAESYSSGGGGQQK 164.58 5.69E-09 1018700 199.75 180.1 220.15 167.81 364.18 193.13 327.47 0 469.64 379.82 TRUE FALSE FALSE 197.3153702 182.6354525 223.9816184 187.2129818 345.5945357 180.7896163 355.2852936 0 427.6342222 369.9522216 0.533353657 0.493673079 0.605433906 0.506046378 0.934159914 0.488683689 0.960354535 0 1.155917432 1 8.531195152 -12.23513306 0.870687835 1.011749222 0.583161286 0.374195661 0.257755546 0.618119721 0.806967033 0.175220362 0.043658906 5.82E-13 12.23513306 -0.428587936 GSSLGTEWQT(ph)PVISEPFR ddPTM_HeLa_Romidepsin_16h_R1 2 GSSLGTEWQTPVISEPFR 18 0 Q6P2H3-2;Q6P2H3 Q6P2H3-2 CEP85 Centrosomal protein of 85 kDa 1 0 GSSLGT(0.003)EWQT(0.952)PVIS(0.045)EPFR;GSSLGT(0.017)EWQT(0.753)PVIS(0.229)EPFR ; 128.82 0.0032179 13216900 1372.57 1243.9 1661.32 1329.7 2176.03 2861.12 1671.24 1950.01 1419.88 1235.82 TRUE FALSE FALSE 1355.840589 1261.411657 1690.234578 1483.44617 2064.979069 2678.303666 1813.195084 2006.430463 1292.882377 1203.713218 1.12638174 1.047933709 1.404183781 1.232391693 1.715507513 2.225034689 1.506334778 1.666867517 1.074078408 1 10.233276 -9.029019654 1.387835564 1.066480107 1.797969302 0.699357981 0.201901464 0.162266632 0.619650324 0.032625865 0.070014151 9.35E-10 9.029019654 0.731489194 GSSPLPT(ph)ATTPKPLIPTEASIR ddPTM_HeLa_Romidepsin_16h_R1 1 GSSPLPTATTPKPLIPTEASIR 22 1 A0A3B3IUD2;Q9BUK6-7;Q9BUK6-3;Q9BUK6-2;Q9BUK6 A0A3B3IUD2 MSTO1 Protein misato homolog 1 1 0 GS(0.015)S(0.141)PLPT(0.767)AT(0.069)T(0.007)PKPLIPTEASIR 63.639 0.0049307 38862000 1298.8 1190.6 1094.4 1289.9 1532.6 2289.2 1354.8 1964.8 1035.6 1217.1 TRUE FALSE FALSE 1282.969726 1207.361298 1113.447573 1439.044307 1454.385703 2142.927508 1469.876678 2021.648388 942.9733423 1185.479567 1.082236896 1.018458126 0.939238098 1.213892122 1.226833211 1.807646094 1.239900475 1.705342247 0.795436184 1 10.21125508 -8.62438786 2.14761836 1.034970789 1.549020911 0.685243526 0.172513333 0.119166633 1.108335386 0.020588364 0.04834099 2.37E-09 8.62438786 0.514050122 GSSPSIRPIQGSQGS(ph)SSPVEK ddPTM_HeLa_Romidepsin_16h_R1 2 GSSPSIRPIQGSQGSSSPVEK 21 1 Q92560;F8W6N3;H0Y8E8 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 0 GSSPS(0.001)IRPIQGS(0.175)QGS(0.641)S(0.134)S(0.048)PVEK;GSSPSIRPIQGS(0.007)QGS(0.876)S(0.059)S(0.059)PVEK ; 116.44 6.25E-05 23995000 3484.8 3176 3464.6 2256.78 3187.8 2581 2306.91 2905.9 3622.3 3488.3 TRUE FALSE FALSE 3442.325917 3220.711811 3524.89991 2517.719522 3025.114671 2416.08243 2502.858878 2989.977632 3298.312416 3397.673463 1.013142068 0.947916816 1.037445166 0.741012799 0.890348853 0.711099067 0.736639028 0.880007353 0.970756152 1 11.73033149 -9.263800209 24.99961606 1.003194547 0.7897449 0.743534052 0.05919361 69.1290725 732031.359 0.008227968 0.012948467 5.45E-10 9.263800209 -0.213449648 GSSQPNLST(ph)SHSEQEYGK ddPTM_HeLa_Romidepsin_16h_R1 1 GSSQPNLSTSHSEQEYGK 18 0 F6PQP6;E9PBC1;I3L2B2;O95208-3;O95208-2;O95208 F6PQP6 EPN2 Epsin-2 1 0 GS(0.079)S(0.257)QPNLS(0.186)T(0.292)S(0.186)HSEQEYGK 82.362 0.0088465 7869000 1253.5 1334.7 1374.2 1207.6 1714.2 1721.5 1412.1 1549 1930.2 1534.5 TRUE FALSE FALSE 1238.22186 1353.489942 1398.117375 1347.228394 1626.717977 1611.501706 1532.043739 1593.817871 1757.558078 1494.633469 0.828445158 0.905566462 0.935424908 0.901377108 1.088372508 1.078191904 1.025029729 1.066360351 1.175912432 1 10.54557602 -8.764018706 24.99997064 0.916252278 1.062648948 0.16603874 0.092294362 39.40886193 381973.6275 0.009610134 0.018018225 1.72E-09 8.764018706 0.14639667 GSSSANPVNS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 GSSSANPVNSVR 12 0 Q5JR89;Q99661-2;Q99661 Q5JR89 KIF2C Kinesin-like protein KIF2C 1 0 GSSSANPVNS(1)VR 96.707 0.019452 4636400 1212.5 1128.7 1205.5 1210 1030.6 1020.3 999.71 1219.9 1365.1 1294.7 TRUE FALSE FALSE 1197.721584 1144.589868 1226.481222 1349.905893 978.0046363 955.1061229 1084.625342 1255.195882 1243.002037 1261.063507 0.949771028 0.907638562 0.972576888 1.070450366 0.775539559 0.757381462 0.860087804 0.995347082 0.985677589 1 10.30042522 -8.753853665 24.99928752 0.975585239 0.841609788 0.4588225 0.071011146 124.1552055 409159.2315 0.010487492 0.020658734 1.76E-09 8.753853665 -0.13397545 GSSSQGPSQTST(ph)PTDVTAIHL ddPTM_HeLa_Romidepsin_16h_R1 1 GSSSQGPSQTSTPTDVTAIHL 21 0 Q5T8J1;P30281-4;P30281-2;P30281-3;P30281 Q5T8J1 CCND3 G1/S-specific cyclin-D3 1 0 GSSSQGPSQT(0.003)S(0.037)T(0.542)PT(0.134)DVT(0.285)AIHL 139.12 0.0002464 6808200 896.19 1135.4 1020.3 1067.4 1186.1 1226.7 1243.2 1043.8 1407 1224.5 TRUE FALSE FALSE 885.2668916 1151.384191 1038.057894 1190.81781 1125.568891 1148.317829 1348.797377 1074.000706 1281.154396 1192.687313 0.742245584 0.965369697 0.870352088 0.998432529 0.943725047 0.962798729 1.130889347 0.900488078 1.074174582 1 10.22000015 -9.176047569 1.461309732 0.880694585 0.999847909 0 0.105219085 0.522001743 2.187520365 0.018124191 0.035297704 6.67E-10 9.176047569 0.119153324 GSSSQGPSQTSTPT(ph)DVTAIHL ddPTM_HeLa_Romidepsin_16h_R1 1 GSSSQGPSQTSTPTDVTAIHL 21 0 Q5T8J1;P30281-4;P30281-2;P30281-3;P30281 Q5T8J1 CCND3 G1/S-specific cyclin-D3 1 0 GSSSQGPSQTS(0.002)T(0.037)PT(0.953)DVT(0.008)AIHL 125.84 0.00037089 6299700 1176.8 1097.8 1031 1107.1 1211.9 1376.1 1161.9 1395.7 1337.5 1283.9 TRUE FALSE FALSE 1162.456709 1113.254857 1048.944123 1235.108111 1150.052221 1288.171651 1260.591757 1436.082377 1217.87065 1250.544093 0.929560753 0.890216397 0.838790194 0.987656587 0.91964148 1.03008895 1.008034634 1.148366048 0.973872618 1 10.28834021 -6.920001407 1.006902363 0.949971472 1.376552925 0.612006213 0.050520483 2.047128327 1.015304743 0.008645944 1.10725931 1.20E-07 6.920001407 0.426581454 GSTAENAEY(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 GSTAENAEYLR 11 0 P00533;E9PFD7 P00533 EGFR Epidermal growth factor receptor;Receptor protein-tyrosine kinase 1 0 GSTAENAEY(1)LR 105.13 0.0021205 0 914.86 1355.5 840.29 917.25 939.57 976.39 701.31 910.32 1338.3 1141.7 TRUE FALSE FALSE 903.7093344 1374.582765 854.914895 1023.306761 891.6202369 914.0018302 760.8792539 936.658673 1218.599096 1112.038469 0.812660137 1.236092817 0.768781763 0.920208058 0.801789022 0.821915658 0.684220263 0.842289812 1.095824587 1 10.11899098 -8.752641315 1.354650678 0.929605951 0.768427429 0.284330682 0.134338744 0.49973821 1.82992548 0.020231732 0.05272178 1.77E-09 8.752641315 -0.161178522 GSTEGSESYEEDPYLVVNPNYLLED ddPTM_HeLa_Romidepsin_16h_R1 3 GSTEGSESYEEDPYLVVNPNYLLED 25 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 0 ;; ;; 120.75 3.76E-07 12780000 5406.6 4549.6 4742.9 4602 4247 4905.2 3770.6 3920.79 5635.1 4623.8 FALSE FALSE TRUE 5340.70228 4613.649388 4825.448185 5134.104893 4030.259742 4591.773551 4090.87467 4034.231873 5131.082543 4503.673009 1.185854805 1.024419264 1.071447278 1.139981718 0.894882851 1.019561931 0.908341849 0.895764827 1.139310632 1 12.13688637 -8.758252997 24.99996611 1.08643329 0.934539855 0.62713106 0.061709334 56.39430454 442455.7322 0.011386211 0.022023489 1.74E-09 8.758252997 -0.151893434 GSTIYTGYPLS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 GSTIYTGYPLSPTK 14 0 H3BLW0;Q5SQL3;J3KP92;Q86Z02-4;Q86Z02-3;Q86Z02 H3BLW0 HIPK1 Homeodomain-interacting protein kinase 1 1 0 GSTIYTGYPLS(0.869)PT(0.131)K 98.943 0.010928 11228000 1785.6 1598.2 1589.5 1761.3 1670.7 2009.1 1555.7 1517.1 1664.3 1713 TRUE FALSE FALSE 1763.83642 1620.699502 1617.164581 1964.949793 1585.437945 1880.724994 1687.841119 1560.994895 1515.44084 1668.496013 1.057141525 0.971353536 0.969234909 1.177677248 0.950219798 1.127197775 1.011594338 0.935570048 0.908267582 1 10.70433252 -12.69643468 1.575310385 0.999986578 1.031900213 0.047400576 0.07976314 1.512643949 6.762474827 0.049713797 0.010967532 2.01E-13 12.69643468 0.031913635 GSTPY(ph)SQDSAYSSSTTSTSFKPR ddPTM_HeLa_Romidepsin_16h_R1 1 GSTPYSQDSAYSSSTTSTSFKPR 23 1 O15047 O15047 SETD1A Histone-lysine N-methyltransferase SETD1A 1 0 GS(0.02)T(0.061)PY(0.738)S(0.168)QDS(0.01)AY(0.003)SSSTTSTSFKPR 67.413 0.0042263 5113800 382.83 660.93 510.02 393.29 780.1 615.58 546.84 646.68 736.59 505.26 TRUE FALSE FALSE 378.1639207 670.2345899 518.8966842 438.7640403 740.288586 576.2464247 593.288576 665.3906655 670.7075456 492.1332724 0.768417707 1.361896518 1.054382447 0.891555326 1.50424413 1.170915394 1.205544533 1.352053809 1.362857549 1 8.942905248 -9.540703481 0.833778635 0.900951123 1.273186135 0 0.235817676 0.45407939 0.631173416 0.039514265 0.074367035 2.88E-10 9.540703481 0.372235013 GSTSSSPYVAAS(ph)HTPPINGSDSILGTR ddPTM_HeLa_Romidepsin_16h_R1 1 GSTSSSPYVAASHTPPINGSDSILGTR 27 0 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2 B4DGI9 TCF12 Transcription factor 12 1 0 GSTSSSPY(0.001)VAAS(0.911)HT(0.088)PPINGSDSILGTR 64.707 0.00041323 6429500 776.97 788.7 776.69 808.06 770.08 741.31 311.15 456.02 1047 931.37 TRUE FALSE FALSE 767.4999908 799.8033393 790.2079636 901.4916992 730.779944 693.9426835 337.5790732 469.2142192 953.3536977 907.1728731 0.846034988 0.8816438 0.871066571 0.993737496 0.805557536 0.764950875 0.372122098 0.517226907 1.050906311 1 9.82523369 -7.974845539 2.141229023 0.917867687 0.435837323 0.833255733 0.083441742 0.087262865 0.773389846 0.011545051 0.046593324 1.06E-08 7.974845539 -0.482030364 EIMLTPVTVAYS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 EIMLTPVTVAYSPK 14 0 F5H1U6;H0YG46;J3KNE4;A0A0A0MTP3;Q99550-2;Q99550 F5H1U6 MPHOSPH9 M-phase phosphoprotein 9 1 0 EIMLTPVT(0.001)VAYS(0.999)PK 118.13 0.0061089 8522600 1653 1642.2 1404.3 1022.6 874.93 449.68 561.83 653.09 1714.8 1461.4 TRUE FALSE FALSE 1632.8526 1665.318935 1428.741252 1140.837823 830.2790573 420.9468993 609.5518262 671.9861287 1561.423993 1423.432617 1.147123215 1.169931695 1.00372946 0.801469497 0.583293545 0.295726608 0.428226682 0.472088472 1.096942682 1 10.47515848 -8.883157239 1.67825104 1.07843924 0.40094252 0.952745252 0.067843298 0.062310923 0.354049593 0.012794835 0.027938556 1.31E-09 8.883157239 -0.67749672 down GSVGAVPSGT(ph)SPGGVATTAAAGSR ddPTM_HeLa_Romidepsin_16h_R1 1 GSVGAVPSGTSPGGVATTAAAGSR 24 0 Q6ZNB6-2;Q6ZNB6 Q6ZNB6-2 NFXL1 NF-X1-type zinc finger protein NFXL1 1 0 GSVGAVPS(0.001)GT(0.906)S(0.093)PGGVATTAAAGSR 184.91 3.12E-27 0 1962.9 2452.8 2179.7 1357.3 1900.6 3586.5 1665.9 2499.9 2116.4 2325.2 TRUE FALSE FALSE 1938.97542 2487.330583 2217.636764 1514.237412 1803.60529 3357.334225 1807.401504 2572.230662 1927.103883 2264.790969 0.856138799 1.098260553 0.979179445 0.668599192 0.796367221 1.482403573 0.798043409 1.135747492 0.850897019 1 11.14516219 GSVIS(ph)PTELEAPILVPHTAQR ddPTM_HeLa_Romidepsin_16h_R1 1 GSVISPTELEAPILVPHTAQR 21 0 Q8N1B4-2;Q8N1B4 Q8N1B4-2 VPS52 Vacuolar protein sorting-associated protein 52 homolog 1 0 GS(0.089)VIS(0.685)PT(0.226)ELEAPILVPHTAQR 63.823 0.0053386 2349800 1292.1 1136 1466.1 1149.8 1235.2 1208.2 1086.2 1312 1408.3 1002.4 TRUE FALSE FALSE 1276.351388 1151.992638 1491.616856 1282.745286 1172.163135 1130.999919 1178.461801 1349.96065 1282.338121 976.3575035 1.307258236 1.179888139 1.527736357 1.313806962 1.200547065 1.158387082 1.206998253 1.382649947 1.313389938 1 9.931265692 -12.21231176 0.80553387 0.987652703 1.282673828 0 0.142167438 0.47892557 0.523188251 0.089763273 0.021385859 6.13E-13 12.21231176 0.295021125 GSVISPT(ph)ELEAPILVPHTAQR ddPTM_HeLa_Romidepsin_16h_R1 1 GSVISPTELEAPILVPHTAQR 21 0 Q8N1B4-2;Q8N1B4 Q8N1B4-2 VPS52 Vacuolar protein sorting-associated protein 52 homolog 1 0 GS(0.04)VIS(0.436)PT(0.525)ELEAPILVPHTAQR 86.604 0.001245 4937200 1675.6 1138.2 1211.9 1483.8 1568.5 1787.4 1187.6 1373 1916.3 1506.7 TRUE FALSE FALSE 1655.177143 1154.223609 1232.992611 1655.363937 1488.453592 1673.190909 1288.474714 1412.725589 1744.901329 1467.555717 1.127846203 0.786493893 0.840167496 1.127973486 1.01423992 1.140120875 0.877973286 0.962638469 1.188984724 1 10.51919956 GSVLPNSDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 GSVLPNSDKK 10 1 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 1 ; GSVLPNSDK(1)K;GSVLPNSDK(1)K 128.35 0.0023484 3901000 3714.9 4188.5 4170.2 3435 5353.6 4794.8 4698.2 3638.4 5091.2 4371 FALSE TRUE FALSE 3669.62137 4247.465813 4242.780582 3832.170862 5080.385815 4488.427755 5097.264991 3743.671364 4635.830321 4257.44079 0.861931275 0.997657049 0.996556568 0.90011137 1.193295706 1.054254886 1.197260336 0.879324352 1.088877227 1 12.05577075 -8.7779285 24.99997099 0.941498984 1.087422956 0.162840192 0.103465077 193.869196 293934.3751 0.013630601 0.024757377 1.67E-09 8.7779285 0.145923971 GSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_HeLa_Romidepsin_16h_R1 1 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 GS(0.003)VPLS(0.051)S(0.279)S(0.279)PPAT(0.254)HFPDET(0.056)EIT(0.08)NPVPK 55.469 0.0026358 16532000 2174.4 2055.1 2425.5 1393.2 1952.4 2020.9 1620.3 1998.2 2667.7 2360.6 TRUE FALSE FALSE 2147.897576 2084.031752 2467.71481 1554.288339 1852.761743 1891.771012 1757.928242 2056.014764 2429.094231 2299.271272 0.934164491 0.90638794 1.073259532 0.675991719 0.805803893 0.822769821 0.764558868 0.894202781 1.056462654 1 11.16696097 -9.264169953 24.99932207 0.969552072 0.793506325 0.661830819 0.070903294 113.0859492 1035339.696 0.009668706 0.01518431 5.44E-10 9.264169953 -0.176045747 GSVPLSSSPPAT(ph)HFPDETEITNPVPK ddPTM_HeLa_Romidepsin_16h_R1 2 GSVPLSSSPPATHFPDETEITNPVPK 26 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 GS(0.001)VPLS(0.02)S(0.083)S(0.083)PPAT(0.81)HFPDET(0.002)EIT(0.001)NPVPK;GS(0.001)VPLS(0.045)S(0.184)S(0.184)PPAT(0.581)HFPDET(0.004)EITNPVPK ; 83.31 3.90E-05 871400000 8835.3 8257 10007.4 5141.2 7652.8 8473 6454.9 7783.8 10731 9846.7 TRUE FALSE FALSE 8727.611965 8373.242263 10181.5746 5735.649734 7262.249059 7931.602645 7003.179045 8009.011972 9771.192484 9590.881315 0.909990613 0.873042006 1.061589052 0.598031562 0.757203517 0.82699414 0.730191399 0.835065278 1.018800271 1 13.22744768 -9.270079014 24.99317269 0.955835595 0.75315815 0.661998137 0.079261616 309.1778432 894404.3667 0.011828198 0.01824158 5.37E-10 9.270079014 -0.202677444 GSVSQPSTPS(ph)PPKPTGIFQTSANSSFEPVK ddPTM_HeLa_Romidepsin_16h_R1 1 GSVSQPSTPSPPKPTGIFQTSANSSFEPVK 30 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 GS(0.029)VS(0.288)QPS(0.22)T(0.084)PS(0.336)PPKPT(0.043)GIFQTS(0.001)ANSSFEPVK 73.371 4.23E-06 0 1641.4 1834.8 1562.7 1407.5 2181.9 2399.2 1975.9 2591.5 1894 1929.9 TRUE FALSE FALSE 1621.393985 1860.630363 1589.898138 1570.241772 2070.549501 2245.898863 2143.732897 2666.480964 1724.595896 1879.76092 0.8625533 0.989822877 0.845798059 0.835341216 1.101496195 1.194778995 1.140428484 1.418521332 0.917454916 1 10.87633347 -7.960311768 1.031690727 0.925652675 1.374564208 0.780605667 0.08252866 0.303222371 0.470090545 0.014074454 0.113918149 1.10E-08 7.960311768 0.448911534 GSWSS(ph)APTSR ddPTM_HeLa_Romidepsin_16h_R1 2 GSWSSAPTSR 10 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 0 GSWS(0.491)S(0.508)APT(0.001)SR;GSWS(0.436)S(0.558)APT(0.006)SR ; 139.31 0.0049954 58610000 11257.5 10823.6 10239.8 4669.6 9356.8 7574.3 6871.4 7772.8 11289.8 10595.8 TRUE FALSE FALSE 11120.28926 10975.97492 10418.01942 5209.521123 8879.287581 7090.326675 7455.056544 7997.693705 10280.01201 10320.51959 1.07749316 1.063509916 1.009447183 0.504773144 0.860352767 0.687012569 0.722352831 0.774931304 0.996075045 1 13.33322798 -9.384944948 7.576207874 1.039374961 0.718173315 0.77127689 0.086950036 0.087604533 5.064428613 0.012275118 0.018770633 4.12E-10 9.384944948 -0.321201646 GSYGDLGGPIITTQVTIPK ddPTM_HeLa_Romidepsin_16h_R1 1 GSYGDLGGPIITTQVTIPK 19 0 P61978-3;P61978;P61978-2;Q5T6W2;S4R359 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 90.367 0.00016056 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 GSYGS(ph)DAEEEEYR ddPTM_HeLa_Romidepsin_16h_R1 2 GSYGSDAEEEEYR 13 0 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 GS(0.225)YGS(0.775)DAEEEEYR;GSYGS(1)DAEEEEYR ; 198.37 4.20E-16 182722000 3519.1 3186.5 3221.4 2188.2 3707.7 3170.9 2435.7 2964.1 3168 3656.8 TRUE FALSE FALSE 3476.207856 3231.359631 3277.467116 2441.20998 3518.482234 2968.289724 2642.588297 3049.861557 2884.646146 3561.795809 0.975970562 0.907227647 0.920172658 0.685387403 0.9878394 0.833368863 0.741925826 0.856270747 0.809885322 1 11.7983891 -9.891440345 1.432799116 0.990580028 0.82655428 0.093613637 0.095922984 0.239163208 0.97922602 0.013197568 0.018356049 1.28E-10 9.891440345 -0.164025748 GSYGS(ph)DAEEEEYRQQLSEHSK ddPTM_HeLa_Romidepsin_16h_R1 2 GSYGSDAEEEEYRQQLSEHSK 21 1 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IS03 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 GS(0.006)YGS(0.994)DAEEEEYRQQLSEHSK;GS(0.006)YGS(0.994)DAEEEEYRQQLSEHSK ; 101.05 0.00016273 27791000 3015.6 2568.68 2417.4 2710.8 4424.6 5139 3703.6 3410 4051.4 3382.8 TRUE FALSE FALSE 2978.844707 2604.841944 2459.473833 3024.235451 4198.796152 4810.634485 4018.183692 3508.66297 3689.032637 3294.914368 0.904073482 0.790564383 0.746445448 0.917849483 1.274326335 1.46001806 1.21951081 1.064872278 1.119614116 1 11.68602526 -8.761943914 24.9833791 0.920310618 1.266836572 0.616270257 0.131836892 6.526171854 323188.1506 0.018830976 0.035705632 1.73E-09 8.761943914 0.346525954 GT(ph)LSDSEIETNSATSTIFGK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 GT(0.445)LS(0.445)DS(0.11)EIETNSATSTIFGK 88.239 0.0014171 19317000 4462.8 4561.9 3677.3 3172.5 4390.5 5624.3 4711.2 5471.4 4515.9 4322.8 TRUE FALSE FALSE 4408.405677 4626.122548 3741.301864 3539.319377 4166.436402 5264.925382 5111.36921 5629.706327 4111.986594 4210.493033 1.047004625 1.09871279 0.888566217 0.840594997 0.989536467 1.250429662 1.213959783 1.337065822 0.976604536 1 12.03977346 -8.251330386 8.566495425 1.002391387 1.262250732 0.743584348 0.07700692 0.078327423 49.70428925 0.01184033 0.029010559 5.61E-09 8.251330386 0.259859344 GT(ph)PDTDLEVQR ddPTM_HeLa_Romidepsin_16h_R1 1 GTPDTDLEVQR 11 0 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 0 GT(0.879)PDT(0.121)DLEVQR 118.76 0.021866 8246300 982.25 942.96 851.43 614.4 1016.6 1002.2 820.27 833.95 1119.9 1073.3 TRUE FALSE FALSE 970.2779592 956.2350156 866.248782 685.4398188 964.7191085 938.1626545 889.9437133 858.0790275 1019.733339 1045.415511 0.928126614 0.914693732 0.82861673 0.655662568 0.922809254 0.89740648 0.851282293 0.82080189 0.975433527 1 10.02986076 -10.30837859 1.267231459 0.975006976 0.832563615 0.44871761 0.069037823 0.292736867 0.90839314 0.014739531 0.017148479 4.92E-11 10.30837859 -0.142443361 GT(ph)PPLTPSDSPQTR ddPTM_HeLa_Romidepsin_16h_R1 1 GTPPLTPSDSPQTR 14 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 0 GT(0.974)PPLT(0.023)PS(0.002)DS(0.001)PQT(0.001)R 106.55 0.014805 9546400 554.65 507.22 364.37 517.6 684.77 355.74 372.06 447.33 525.83 529.61 TRUE FALSE FALSE 547.8897125 514.3606565 370.711707 577.4473474 649.8236317 333.0093621 403.6627671 460.2727878 478.7984478 515.8506559 1.062109171 0.997111568 0.718641535 1.119407993 1.259712718 0.645553821 0.782518666 0.89225977 0.928172607 1 9.010809641 -8.245480578 24.98995996 1.023802844 0.774351551 0.372068965 0.141550952 626.8590093 981600.1266 0.019285439 0.048984711 5.68E-09 8.245480578 -0.249451294 GT(ph)PPPVFTPPLPK ddPTM_HeLa_Romidepsin_16h_R1 1 GTPPPVFTPPLPK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 0 GT(1)PPPVFTPPLPK 176.25 3.03E-06 18917000 2092.1 2056.9 1820.6 1545.6 1460.2 1436.3 1371.4 1641 1789.3 1978 TRUE FALSE FALSE 2066.60068 2085.857092 1852.286779 1724.309544 1385.680545 1344.525065 1487.886682 1688.479746 1629.260527 1926.611275 1.07266095 1.082655915 0.961422163 0.894996083 0.719232034 0.697870444 0.772281727 0.876398767 0.845661264 1 10.9118498 -9.14369698 2.092744278 1.037600476 0.763316221 0.613589155 0.080986709 0.093246163 0.799155941 0.009076368 0.016564104 7.18E-10 9.14369698 -0.274284254 GT(ph)PSQSPVVGR ddPTM_HeLa_Romidepsin_16h_R1 2 GTPSQSPVVGR 11 0 C9J2I0;B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 C9J2I0 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 0 GT(0.967)PS(0.033)QSPVVGR;GT(0.999)PS(0.001)QSPVVGR ; 147.96 0.0049827 36872000 2119.2 1745.88 2083.9 1514.16 2343.2 2156 2000.87 2063.45 2866.1 2056.92 TRUE FALSE FALSE 2093.370375 1770.458544 2120.169405 1689.234304 2223.61776 2018.238558 2170.823848 2123.15267 2609.748838 2003.480922 1.044866638 0.883691242 1.058242872 0.843149683 1.109877182 1.007365998 1.083526089 1.059731913 1.302607282 1 10.96829306 GT(ph)RPRGCAT(ph)GSRPR ddPTM_HeLa_Romidepsin_16h_R1 1 GTRPRGCATGSRPR 14 3 X6RDH7;A3KFJ8;H0Y4Y8;Q8N539-2;Q8N539 X6RDH7 FIBCD1 Fibrinogen C domain-containing protein 1 2 0 GT(1)RPRGCAT(0.998)GS(0.002)RPR 74.812 0.0022452 0 1568.8 1745.5 1278.1 1802.3 1561.4 2069.3 1428.9 1664.4 2017.2 1933.4 TRUE FALSE FALSE 1549.678862 1770.073195 1300.344794 2010.690406 1481.715932 1937.078408 1550.27073 1712.556788 1836.77658 1883.169989 0.822909706 0.939943396 0.690508452 1.067715829 0.786820064 1.028626422 0.823224 0.909401062 0.975364195 1 10.87894752 -12.50292264 1.245169986 1.000135718 0.877910716 0.129907972 0.106506456 0.641647026 1.777265822 0.066658414 0.016068321 3.14E-13 12.50292264 -0.122225002 GT(ph)SPRPPEGGLGYSQLGDDDLK ddPTM_HeLa_Romidepsin_16h_R1 1 GTSPRPPEGGLGYSQLGDDDLK 22 1 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;Q9UQ88-5;Q9UQ88-10;P21127-12;P21127-4;Q9UQ88-8 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 GT(0.5)S(0.5)PRPPEGGLGYS(0.001)QLGDDDLK 62.374 0.0058983 41463000 1134.8 1107.4 1174.4 953.42 1149.7 1327.9 989.71 1477.1 1164.5 965.1 TRUE FALSE FALSE 1120.968621 1122.990006 1194.839939 1063.658906 1091.026519 1243.051476 1073.775943 1519.837558 1060.344203 940.0265629 1.192486112 1.194636461 1.2710704 1.131520053 1.160633712 1.322357819 1.142282554 1.616802778 1.127993873 1 9.876557714 -4 0.082129256 0.816271277 2.308466933 0.435309668 0.117869979 105.931496 0.638120048 1.740805055 17.99482951 1.00E-04 4 1.492195657 GTAT(ph)PELHTATDYR ddPTM_HeLa_Romidepsin_16h_R1 1 GTATPELHTATDYR 14 0 Q12802-4;Q12802;Q12802-2;H0YMW2 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 GT(0.082)AT(0.917)PELHT(0.001)ATDYR 127.78 0.0056319 5872600 1361.7 1565.4 1233.7 1147.8 1775.5 1998.6 1581.3 1670.5 1640.4 1599.5 TRUE FALSE FALSE 1345.103077 1587.437742 1255.172031 1280.514037 1684.88961 1870.89591 1715.615583 1718.833282 1493.678516 1557.944759 0.863383036 1.018930699 0.805658881 0.821925186 1.081482254 1.200874356 1.101204373 1.103269722 0.958749344 1 10.60542836 -8.604561236 6.323515681 0.923322378 1.13325704 0.67929739 0.071161471 0.10644859 6.588524283 0.011645014 0.023481479 2.49E-09 8.604561236 0.209934662 GTDDS(ph)PKDSQEDLQER ddPTM_HeLa_Romidepsin_16h_R1 2 GTDDSPKDSQEDLQER 16 1 Q969E4;Q5H9L2;Q6IPX3-2;Q6IPX3 Q969E4 TCEAL3;TCEAL5;TCEAL6 Transcription elongation factor A protein-like 3;Transcription elongation factor A protein-like 5;Transcription elongation factor A protein-like 6 1 0 GT(0.009)DDS(0.967)PKDS(0.024)QEDLQER;GTDDS(0.723)PKDS(0.277)QEDLQER ; 189.8 8.52E-12 37503800 3524.81 3811.62 3373.13 3482.4 3343.81 3501.47 3369.76 3615 3624.4 3627.14 TRUE FALSE FALSE 3481.84826 3865.280086 3431.837913 3885.051473 3173.162898 3277.737367 3655.98733 3719.594321 3300.224587 3532.90638 0.985547842 1.094079398 0.97139226 1.09967575 0.898173503 0.927773627 1.034838441 1.052842595 0.934138704 1 11.7866398 -7.541474923 24.97035952 0.995501339 1.048341629 0.105764727 0.062542691 335.5239434 450530.7105 0.007800659 0.029197495 2.87E-08 7.541474923 0.05284029 GTDTQTPAVLS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 GTDTQTPAVLSPSK 14 0 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 GTDT(0.014)QT(0.048)PAVLS(0.643)PS(0.295)K;GTDTQTPAVLS(0.826)PS(0.174)K ; 197.15 6.81E-12 493410000 13006.6 13690.3 14965.1 8009.5 8271.6 8996.4 6893.8 7394.4 14672.8 14839.5 TRUE FALSE FALSE 12848.07056 13883.0324 15225.56129 8935.596076 7849.469386 8421.559075 7479.3592 7608.345298 13360.42802 14453.96765 0.88889576 0.960499756 1.053382826 0.618210604 0.54306676 0.582646874 0.51746063 0.526384553 0.924343291 1 13.81917795 -9.159549853 4.814061537 0.954281034 0.548239317 0.951449764 0.046192583 0.041789667 1.559728203 0.008441504 0.014191275 6.93E-10 9.159549853 -0.406041717 GTDTQTPAVLS(ph)PSKTQATLKPK ddPTM_HeLa_Romidepsin_16h_R1 2 GTDTQTPAVLSPSKTQATLKPK 22 2 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 GTDTQT(0.006)PAVLS(0.717)PS(0.223)KT(0.048)QAT(0.005)LKPK;GTDTQT(0.002)PAVLS(0.391)PS(0.391)KT(0.108)QAT(0.108)LKPK ; 77.66 0.0019059 174867000 10293.8 11323.9 8973.1 9531.7 6224.1 6181.19 5255.95 5393.1 11661.7 11002.1 TRUE FALSE FALSE 10168.33521 11483.31816 9129.273041 10633.8 5906.460952 5786.231908 5702.390262 5549.14084 10618.64834 10716.26386 0.948869433 1.07157852 0.851908199 0.992304794 0.551167929 0.539948623 0.532124847 0.517824208 0.990890901 1 13.38751439 -8.754460304 10.07478334 0.974018468 0.535051374 0.94535172 0.051902941 0.023961992 27.13133987 0.007232181 0.013978048 1.76E-09 8.754460304 -0.438967094 GTDTQTPAVLSPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 GTDTQTPAVLSPSK 14 0 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 GTDTQTPAVLS(0.205)PS(0.795)K 131.4 0.0019962 4097000 1665.2 1857.8 1931.2 1027 1116.6 1144.8 863.83 1173.2 1768.8 2123 TRUE FALSE FALSE 1644.903902 1883.954157 1964.811726 1145.746572 1059.615735 1071.650975 937.2036986 1207.144691 1610.594098 2067.844154 0.795468023 0.911071636 0.950173988 0.554077816 0.512425336 0.518245523 0.453227433 0.583769666 0.778875959 1 11.01391174 -9.223671649 5.892042177 0.904945635 0.517020301 0.870886417 0.069681351 0.056225295 5.588647827 0.012370495 0.020434584 5.97E-10 9.223671649 -0.387925335 GTEAPAVVT(ph)EEEDDDEETAPPVIAPRPDHTK ddPTM_HeLa_Romidepsin_16h_R1 3 GTEAPAVVTEEEDDDEETAPPVIAPRPDHTK 31 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(1)EEEDDDEETAPPVIAPRPDHTK;GTEAPAVVT(0.998)EEEDDDEET(0.002)APPVIAPRPDHTK ;; 141.15 4.41E-16 91189000 15428.7 15423 14441.4 14690.6 16366.6 15557.3 12140 14257.8 14943.8 16244.9 TRUE FALSE FALSE 15240.64907 15640.1254 14692.74651 16389.19629 15531.35133 14563.23874 13171.1713 14670.32695 13607.1891 15822.85516 0.963204739 0.988451531 0.928577451 1.035792601 0.98157704 0.920392596 0.832414325 0.927160541 0.859970528 1 13.94972233 -8.102459872 3.611986416 0.982494541 0.87886736 0.271421841 0.051149388 0.107537116 2.562141632 0.004509943 0.012857161 7.90E-09 8.102459872 -0.103627181 GTEASS(ph)GTEAATGLEGEEK ddPTM_HeLa_Romidepsin_16h_R1 2 GTEASSGTEAATGLEGEEK 19 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 0 GTEAS(0.002)S(0.997)GT(0.001)EAATGLEGEEK;GTEAS(0.024)S(0.975)GT(0.001)EAATGLEGEEK ; 286.85 5.43E-124 7442600 3727.5 3980.9 3497.4 1385.74 3580.5 4876.2 4026.5 5134.8 3266 4081.4 TRUE FALSE FALSE 3682.067796 4036.943215 3558.27078 1545.965779 3397.773724 4564.626557 4368.510809 5283.367337 2973.88078 3975.36464 0.926221399 1.015490044 0.895080352 0.388886535 0.854707438 1.148228394 1.098895625 1.3290271 0.748077485 1 11.95687148 -8.165469847 4.730662042 0.912432213 1.192177955 0.393505434 0.187439384 0.22455308 8.329751178 0.027547726 0.072943139 6.83E-09 8.165469847 0.279745741 GTEPS(ph)PGGT(ph)PQPS(ph)RPVSPAGPPEGVPEEAQPPR ddPTM_HeLa_Romidepsin_16h_R1 1 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 3 0 GT(0.081)EPS(0.939)PGGT(0.928)PQPS(0.729)RPVS(0.323)PAGPPEGVPEEAQPPR 42.825 0.019315 5009400 621.6 650.35 684.96 699.67 679.09 888.76 689.28 845.49 830.27 687.3 TRUE FALSE FALSE 614.0237001 659.5056444 696.8814415 780.5691374 644.4335033 831.9711043 747.827426 869.9529192 756.0085718 669.4438469 0.917214645 0.985154539 1.040985655 1.165996433 0.962640117 1.242779522 1.117087609 1.299515894 1.129308418 1 9.386819237 -8.08543913 0.528098987 0.960131816 1.323339167 0.413942746 0.091452382 0.924815357 0.290435243 0.016055139 0.176785711 8.21E-09 8.08543913 0.363207351 GTEPSPGGTPQPSRPVS(ph)PAGPPEGVPEEAQPPR ddPTM_HeLa_Romidepsin_16h_R1 2 GTEPSPGGTPQPSRPVSPAGPPEGVPEEAQPPR 33 1 I3L1Q2;Q8WUZ0;Q8WUZ0-2 I3L1Q2 BCL7C B-cell CLL/lymphoma 7 protein family member C 1 0 GTEPS(0.011)PGGT(0.003)PQPS(0.016)RPVS(0.969)PAGPPEGVPEEAQPPR;GTEPS(0.001)PGGT(0.001)PQPS(0.004)RPVS(0.993)PAGPPEGVPEEAQPPR ; 96.748 3.78E-12 65672000 3773.9 3812.2 3182.7 3070.6 3494.3 3243.2 2834.7 3316.1 4063 3528.9 TRUE FALSE FALSE 3727.902255 3865.868252 3238.093558 3425.63722 3315.972832 3035.969987 3075.479347 3412.046122 3699.595104 3437.218669 1.084569419 1.124708267 0.942067954 0.996630575 0.964725597 0.883263557 0.89475813 0.992676478 1.076333937 1 11.74702592 -9.172406624 1.408587298 1.045153273 0.926848418 0.538274973 0.051632214 0.274054588 1.068255289 0.009238275 0.018224796 6.72E-10 9.172406624 -0.118304855 GTEVQVDDIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 GTEVQVDDIKR 11 1 Q9Y230;Q9Y230-2 Q9Y230 RUVBL2 RuvB-like 2 0 1 GTEVQVDDIK(1)R 90.614 0.02083 885000 556.13 614.98 577.65 420.57 1066 929.38 880.71 908.55 885.61 774.95 FALSE TRUE FALSE 549.3516737 623.6377046 587.7037559 469.1982822 1011.598042 869.9956174 955.5174854 934.8374608 806.3988235 754.8166873 0.727794818 0.826210807 0.778604615 0.621605603 1.340190353 1.152591923 1.26589343 1.238496017 1.068337302 1 9.559982508 -8.750452793 24.99998976 0.841341354 1.243571522 0.717858029 0.126561428 95.01066328 216195.4811 0.019297535 0.038300329 1.78E-09 8.750452793 0.402230167 GTFS(ph)DQELDAQSLDDEDDNMHHAVYPAVNR ddPTM_HeLa_Romidepsin_16h_R1 1 GTFSDQELDAQSLDDEDDNMHHAVYPAVNR 30 0 Q9P270;D6RIF6 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 0 GT(0.176)FS(0.823)DQELDAQS(0.001)LDDEDDNMHHAVYPAVNR 52.155 0.0024118 5030100 2953.4 2747.8 2569 1879.4 2891.2 3794 2712.8 2978.6 3063 2737.1 TRUE FALSE FALSE 2917.402825 2786.483601 2613.712367 2096.705071 2743.651275 3551.575645 2943.225164 3064.781092 2789.037609 2665.989747 1.094303843 1.045196668 0.980391005 0.786464041 1.029130468 1.332179033 1.103989679 1.149584725 1.046154664 1 11.38045552 -8.407676581 10.84130971 1.019522541 1.185923818 0.45913088 0.096237247 0.400526562 35.5667202 0.014718318 0.032923979 3.91E-09 8.407676581 0.166401277 GTGQS(ph)DDS(ph)DIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 1 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 0 GT(0.002)GQS(0.989)DDS(0.893)DIWDDT(0.116)ALIK 110.64 0.013146 1200400 671.67 553.89 451.68 597.24 573.92 614.98 366.38 466.82 529.7 627.09 TRUE FALSE FALSE 663.4834277 561.687678 459.5413009 666.2956989 544.6307208 575.6847628 397.5003081 480.3267002 482.3223053 610.7981114 1.086256515 0.919596291 0.75236202 1.090860771 0.891670604 0.942512349 0.650788371 0.786391921 0.78965913 1 9.254551791 -7.300772463 0.398710945 1.036636619 0.479012201 0.078784713 0.13284025 3.413019766 0.376556396 0.030412016 0.901215214 5.00E-08 7.300772463 -0.557624418 GTGQS(ph)DDSDIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 2 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 0 GT(0.009)GQS(0.929)DDS(0.062)DIWDDTALIK;GT(0.006)GQS(0.606)DDS(0.317)DIWDDT(0.071)ALIK ; 136.66 9.06E-11 0 1322.51 1159.57 1206.3 1251.29 1038.99 954.46 1223.5 1246.92 1346.92 1394.2 TRUE FALSE FALSE 1306.390739 1175.894457 1227.295145 1395.970037 985.9664633 893.4730864 1327.424059 1282.997663 1226.448102 1357.978483 0.962011369 0.865915382 0.903766268 1.027976551 0.726054555 0.657943478 0.977500068 0.944784972 0.903142514 1 10.40724491 -10.07092867 0.704739411 0.992213099 0.849907072 0.088415601 0.10809323 0.722887921 0.74497001 0.027793136 0.037692088 8.49E-11 10.07092867 -0.142306026 GTGQSDDS(ph)DIWDDT(ph)ALIK ddPTM_HeLa_Romidepsin_16h_R1 1 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 0 GTGQSDDS(1)DIWDDT(1)ALIK 104.24 0.007211 1233700 481.01 462.7 521.04 417.66 602.52 477.3 421.58 498.35 631.73 556.58 TRUE FALSE FALSE 475.1472651 469.2139027 530.1084826 465.9518143 571.7711561 446.8020704 457.3889947 512.768971 575.2264866 542.1199714 0.876461466 0.865516726 0.977843486 0.859499445 1.054694876 0.824175633 0.843704381 0.945858847 1.061068614 1 9.082468346 -12.37660934 1.062043445 1.000868924 0.903530533 0.313985666 0.069692558 0.61556198 1.224860264 0.045284582 0.011266204 4.20E-13 12.37660934 -0.097338391 GTGQSDDS(ph)DIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 5 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 0 GT(0.006)GQS(0.052)DDS(0.942)DIWDDTALIK;GTGQS(0.003)DDS(0.935)DIWDDT(0.061)ALIK;GTGQS(0.001)DDS(0.826)DIWDDT(0.173)ALIK;GT(0.001)GQS(0.048)DDS(0.916)DIWDDT(0.035)ALIK;GTGQS(0.001)DDS(0.855)DIWDDT(0.144)ALIK ;;;; 280.01 3.68E-106 88623100 9899.07 9761.12 10592.06 8934.08 10579.37 10371.07 10098.49 10567.73 12028.01 10917.95 TRUE FALSE FALSE 9778.416327 9898.537304 10776.41036 9967.080366 10039.46527 9708.392098 10956.25549 10873.49059 10952.19466 10634.30009 0.919516682 0.930812298 1.013363388 0.937257768 0.944064507 0.91293193 1.030275185 1.02249236 1.029893324 1 13.37643746 -7.738367154 24.8875517 0.95700157 1.026383861 0.309896953 0.038677294 189.2507494 204137.743 0.005219106 0.019501839 1.83E-08 7.738367154 0.069382292 GTGQSDDSDIWDDT(ph)ALIK ddPTM_HeLa_Romidepsin_16h_R1 2 GTGQSDDSDIWDDTALIK 18 0 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 0 GTGQSDDSDIWDDT(1)ALIK;GTGQSDDSDIWDDT(1)ALIK ; 185.3 2.92E-10 63217700 5876.41 6094.01 5981.75 5021.24 5858.09 5633.44 5815.54 6282.05 7191.11 7079.11 TRUE FALSE FALSE 5804.786055 6179.801633 6085.85985 5601.819394 5559.129808 5273.481365 6309.511822 6463.811205 6547.919111 6895.193702 0.841859751 0.89624772 0.882623478 0.812423789 0.80623258 0.764805398 0.915059402 0.937437219 0.949635267 1 12.75137537 -12.33444567 0.639006066 1.022445053 0.851451118 0.43106841 0.052678891 0.719987309 0.418071006 0.071562266 0.011730764 4.63E-13 12.33444567 -0.170993935 GTGS(ph)ADSIATLPK ddPTM_HeLa_Romidepsin_16h_R1 1 GTGSADSIATLPK 13 0 Q2NKX8;B5MDQ0 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 0 GT(0.273)GS(0.727)ADSIATLPK 105.65 0.0094348 3695000 1967.7 1672.8 1735.1 1295.8 2026.2 2540.5 1926.7 2403.7 1883.8 1921.8 TRUE FALSE FALSE 1943.716916 1696.349722 1765.298688 1445.626493 1922.795453 2378.170249 2090.35385 2473.247267 1715.30821 1871.871359 1.038381674 0.906231998 0.943066242 0.772289445 1.027204911 1.270477396 1.116718753 1.321269891 0.916360092 1 10.87026558 -8.34007785 5.390499104 0.984708632 1.223701065 0.665612465 0.092042989 0.118951441 6.032333207 0.013584981 0.031052524 4.57E-09 8.34007785 0.238992432 GTHDLWDSR ddPTM_HeLa_Romidepsin_16h_R1 2 GTHDLWDSR 9 0 E9PGM4;Q04446 E9PGM4 GBE1 "1,4-alpha-glucan-branching enzyme" 0 0 ; ; 78.655 0.03005 9307100 3845.9 3618.5 3459.4 2711.8 3777.6 4039 3567 2780.8 4068.2 3404 FALSE FALSE TRUE 3799.024692 3669.441338 3519.609406 3025.351075 3584.814976 3780.920935 3869.980891 2861.258061 3704.330003 3315.563589 1.145815663 1.106732306 1.06154182 0.912469628 1.081208331 1.140355428 1.167216609 0.862977887 1.117255002 1 11.69503841 -9.51589224 24.85834228 1.074122692 1.04277378 0.063544667 0.094524592 1272.45909 4527482.054 0.015806857 0.022905491 3.05E-10 9.51589224 -0.031348912 GTIQVITQGTSLK ddPTM_HeLa_Romidepsin_16h_R1 2 GTIQVITQGTSLK 13 0 A0A286YF22;A0A2C9F2M7;O43175 A0A286YF22 PHGDH D-3-phosphoglycerate dehydrogenase 0 0 ; ; 238.13 9.85E-41 1981820 1439.81 1370.51 1395.46 1294.08 1557 1193.7 1275.23 1076.75 1459.07 1272.46 FALSE FALSE TRUE 1422.261042 1389.804076 1419.747396 1443.707618 1477.54048 1117.426422 1383.548004 1107.904062 1328.567125 1239.401306 1.147538764 1.121351147 1.14551065 1.164842744 1.19214049 0.901585642 1.116303491 0.89390261 1.071942654 1 10.27542768 -7.255538831 24.23442458 1.085105516 0.89390248 0.341419947 0.082912013 433.6914691 1781154.308 0.012516657 0.147904936 5.55E-08 7.255538831 -0.191203036 GTLDEEDEEADS(ph)DTDDIDHR ddPTM_HeLa_Romidepsin_16h_R1 4 GTLDEEDEEADSDTDDIDHR 20 0 Q9HCN4-3;Q9HCN4-2;Q9HCN4-4;Q9HCN4;Q9HCN4-5 Q9HCN4-3 GPN1 GPN-loop GTPase 1 1 0 GTLDEEDEEADS(1)DTDDIDHR;GTLDEEDEEADS(0.5)DT(0.5)DDIDHR;GTLDEEDEEADS(0.898)DT(0.102)DDIDHR;GTLDEEDEEADS(0.999)DT(0.001)DDIDHR ;;; 175.34 1.80E-11 775920000 19716.33 18265.46 19338.57 15500.3 18458.51 20301.5 17794.54 18136.4 21354.7 20043.61 TRUE FALSE FALSE 19476.01979 18522.60163 19675.1497 17292.51762 17516.50336 19004.29967 19306.00778 18661.14812 19444.68215 19522.87412 0.997600029 0.948764076 1.007799854 0.885756754 0.897229744 0.973437597 0.98889168 0.9558607 0.995994853 1 14.25287784 -10.00600146 1.398105666 0.999387176 0.946413672 0.27086392 0.03514638 0.375672657 1.436746484 0.006771428 0.008959313 9.86E-11 10.00600146 -0.052973504 GTLNPGLTK(ac)PPVPR ddPTM_HeLa_Romidepsin_16h_R1 1 GTLNPGLTKPPVPR 14 1 Q92585 Q92585 MAML1 Mastermind-like protein 1 0 1 GTLNPGLTK(1)PPVPR 182.1 3.58E-08 3625700 419.77 310.79 364.97 122.68 278.84 223.85 259.1 260.94 321.61 421.77 FALSE TRUE FALSE 414.6536818 315.1653098 371.3221498 136.8648388 264.6097543 209.5467074 281.1079475 268.4898872 292.8443961 410.8123546 1.009350564 0.767175832 0.903872889 0.333156579 0.644113429 0.510078884 0.684273353 0.653558454 0.712842233 1 8.682335759 -9.739735646 1.556671845 1.002675504 0.579661219 0.417322317 0.153302749 0.13796692 0.678686153 0.019837347 0.029335261 1.82E-10 9.739735646 -0.423014285 GTMTTGHNVADLVVILK ddPTM_HeLa_Romidepsin_16h_R1 1 GTMTTGHNVADLVVILK 17 0 B4DY09;Q12905;X6R6Z1;A0A0A0MRL0 B4DY09 ILF2 Interleukin enhancer-binding factor 2 0 0 63.128 0.012241 181610 0 0 0 0 0 51.127 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 47.8601497 0 0 0 0 0 GTNS(ph)SDSEELSAGESITK ddPTM_HeLa_Romidepsin_16h_R1 1 GTNSSDSEELSAGESITK 18 0 H7C5R6;Q4LE39-2;Q4LE39 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 1 0 GT(0.005)NS(0.904)S(0.091)DS(0.001)EELSAGESITK 264.01 3.97E-77 11052000 2067.3 2358.7 1743.6 2102.5 2397.8 2478.8 2235.9 2614.7 1994.9 1870.7 TRUE FALSE FALSE 2042.102952 2391.905841 1773.946627 2345.600943 2275.431319 2320.41268 2425.81729 2690.352219 1816.471148 1822.098944 1.120742075 1.312720063 0.97357316 1.287307119 1.248796793 1.273483357 1.331331264 1.476512693 0.996911366 1 10.83138559 -4 0.155384727 0.958568672 2.767222556 0.692802295 0.089468141 25.50968241 0.253277259 0.163749254 10.53291302 1.00E-04 4 1.808653884 GTNSS(ph)DSEELSAGESITK ddPTM_HeLa_Romidepsin_16h_R1 1 GTNSSDSEELSAGESITK 18 0 H7C5R6;Q4LE39-2;Q4LE39 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 1 0 GTNS(0.001)S(0.996)DS(0.003)EELSAGESITK 254.02 2.08E-75 12834000 2954.7 2949.7 3034.1 3045 4097.3 3870.7 3452.7 3988.8 3247 3173.5 TRUE FALSE FALSE 2918.68698 2991.225954 3086.907238 3397.077227 3888.199492 3623.374762 3745.972252 4104.209635 2956.580188 3091.052013 0.944237421 0.967704827 0.998659105 1.09900358 1.25788873 1.172214103 1.211876163 1.327771134 0.956496421 1 11.59388222 -9.028695897 2.07483777 0.972706215 1.238340804 0.905759311 0.040813782 0.070311337 0.601548503 0.006544203 0.012581732 9.36E-10 9.028695897 0.265634589 GTNTS(ph)SPYDAGADYLR ddPTM_HeLa_Romidepsin_16h_R1 2 GTNTSSPYDAGADYLR 16 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 0 GT(0.017)NT(0.07)S(0.401)S(0.401)PY(0.085)DAGADY(0.026)LR;GTNT(0.005)S(0.498)S(0.498)PYDAGADYLR ; 252.37 3.08E-59 29153000 2903.5 2730.2 3264.4 2617.5 5289.1 7452.2 6662.7 6639.4 2898.3 2745.8 TRUE FALSE FALSE 2868.111025 2768.635827 3321.215513 2920.147666 5019.177491 6976.028471 7228.629572 6831.500564 2639.068789 2674.46372 1.072406032 1.035211585 1.241824852 1.091862882 1.876704273 2.608384035 2.702833288 2.554344077 0.986765597 1 11.38503392 -8.529311843 2.088419545 1.048377606 2.655034605 0.985895813 0.08344945 0.024161303 0.209034108 0.012442399 0.031299707 2.96E-09 8.529311843 1.606657 up GTPAGTT(ph)PGASQAPK ddPTM_HeLa_Romidepsin_16h_R1 1 GTPAGTTPGASQAPK 15 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 GTPAGT(0.007)T(0.99)PGAS(0.002)QAPK 136.33 0.002525 3261000 2028.3 2412.1 1867.9 1387.8 1489.3 1566.6 1592.9 1638.9 1984 1938.1 TRUE FALSE FALSE 2003.578299 2446.057607 1900.410016 1548.263966 1413.295464 1466.499316 1728.200886 1686.318986 1806.546071 1887.747883 1.06135905 1.295754391 1.006707534 0.820164589 0.748667487 0.776851257 0.91548289 0.893296717 0.956984822 1 10.88245038 -9.319219164 4.88016378 1.053646137 0.827763391 0.59612009 0.096261085 0.123589681 6.248605229 0.015303593 0.023824027 4.79E-10 9.319219164 -0.225882746 GTPGS(ph)PSGTQEPR ddPTM_HeLa_Romidepsin_16h_R1 4 GTPGSPSGTQEPR 13 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 GT(0.014)PGS(0.782)PS(0.203)GT(0.001)QEPR;GT(0.076)PGS(0.884)PS(0.039)GTQEPR;GT(0.118)PGS(0.841)PS(0.04)GTQEPR;GTPGS(0.983)PS(0.017)GTQEPR ;;; 198.48 4.15E-16 65151000 5485.1 5340.3 4835.12 4710.34 5871.7 6817.4 6348.5 7271.7 5274.42 5270.2 TRUE FALSE FALSE 5418.245491 5415.480884 4919.273235 5254.971674 5572.045239 6381.790142 6887.741432 7482.095167 4802.662665 5133.279444 1.055513449 1.054974883 0.958310041 1.023706527 1.085474753 1.243218923 1.341781897 1.457566308 0.935593458 1 12.32566508 -7.949718339 1.297429178 1.022432682 1.459541108 0.939625412 0.040488856 0.080842325 0.223305175 0.005168488 0.033422965 1.12E-08 7.949718339 0.437108426 GTPSQS(ph)PVVGR ddPTM_HeLa_Romidepsin_16h_R1 3 GTPSQSPVVGR 11 0 C9J2I0;B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 C9J2I0 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 1 0 GTPS(0.011)QS(0.989)PVVGR;GTPS(0.005)QS(0.995)PVVGR;GT(0.001)PS(0.006)QS(0.994)PVVGR ;; 139.19 0.0033097 714603000 5314.7 5290.2 5101.2 4446.1 6360.1 6825.9 6763.8 6638.6 5746.5 5388.7 TRUE FALSE FALSE 5249.922392 5364.675574 5189.984246 4960.179002 6035.520364 6389.74702 7338.317003 6830.677417 5232.518648 5248.700797 1.000232742 1.022095902 0.988813127 0.945029864 1.149907491 1.217395936 1.398120656 1.301403467 0.996916923 1 12.35774464 -8.297516291 1.754982434 0.997788278 1.34625255 0.921233048 0.041504533 0.060568753 0.354368465 0.005494275 0.017959222 5.04E-09 8.297516291 0.348464272 GTQGATAGAS(ph)SELDASK ddPTM_HeLa_Romidepsin_16h_R1 1 GTQGATAGASSELDASK 17 0 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 0 GTQGATAGAS(0.747)S(0.251)ELDAS(0.002)K 101.54 0.0030379 7184500 1301.8 1456.8 1392.4 1042.8 1474.9 1189.7 957.13 1415.6 1310.7 1566.2 TRUE FALSE FALSE 1285.933161 1477.308869 1416.634138 1163.373443 1399.630349 1113.68201 1038.428598 1456.558153 1193.467709 1525.509898 0.84295301 0.968403332 0.928629922 0.762612844 0.917483624 0.730039189 0.680709184 0.954800853 0.782340194 1 10.57507583 -16.52287875 0.110068396 1.542333521 0.734224518 0 0.111254859 88.0776187 0.712110704 10.81685798 0.558738941 3.00E-17 16.52287875 -0.808109003 GTQSIPNDS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 4 GTQSIPNDSPAR 12 0 Q9NQ92;H9KV77;J3QRX6 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 1 0 GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR;GTQSIPNDS(1)PAR ;;; 193.45 3.10E-10 164414900 20773.9 21587.2 20700.1 10183.1 17839.7 19232.6 14203.2 17111.2 20110.2 21254.4 TRUE FALSE FALSE 20520.69972 21891.10517 21060.37656 11360.51793 16929.27354 18003.69893 15409.61945 17606.28557 18311.49335 20702.20762 0.991232437 1.057428539 1.017301002 0.548758767 0.817752089 0.869651163 0.744346677 0.850454497 0.884518872 1 14.337497 -9.316118294 24.99956186 1.002813721 0.773590834 0.591471729 0.092638505 134.9414175 61695.78914 0.012310472 0.018804562 4.83E-10 9.316118294 -0.229222887 GTQSTEGS(ph)PVSK ddPTM_HeLa_Romidepsin_16h_R1 1 GTQSTEGSPVSK 12 0 A0A087WXK8;Q9H4H8-2;Q9H4H8 A0A087WXK8 FAM83D Protein FAM83D 1 0 GTQSTEGS(0.649)PVS(0.35)K 155.56 0.0012819 6240200 2580.4 2090.5 3609.2 2367.4 2251.8 2309.7 3777.9 847.63 3651 3214.7 TRUE FALSE FALSE 2548.949092 2119.930114 3672.016612 2641.129927 2136.882243 2162.117624 4098.794732 872.1548367 3324.445416 3131.181631 0.814053413 0.677038372 1.172725522 0.843493045 0.682452344 0.690511723 1.309024903 0.278538565 1.061722317 1 11.61249148 -16.52286927 0.02663661 2.132114507 8.96E-08 0.11993308 0.264246892 3212.901013 6.883412713 399.6977794 188.4427336 3.00E-17 16.52286927 -2.132114418 GTQSTEGSPVS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 GTQSTEGSPVSK 12 0 A0A087WXK8;Q9H4H8-2;Q9H4H8 A0A087WXK8 FAM83D Protein FAM83D 1 0 GTQST(0.003)EGS(0.215)PVS(0.781)K;GTQSTEGS(0.148)PVS(0.852)K ; 160.48 0.00077361 14237900 6056 5667.9 8163.7 5762.1 5026.8 5608.2 9108.4 2061.45 8597.1 7713.1 TRUE FALSE FALSE 5982.187143 5747.692845 8305.785774 6428.341113 4770.263638 5249.85412 9882.067269 2121.094803 7828.153844 7512.71255 0.79627526 0.76506226 1.105564165 0.855661796 0.634958892 0.698796085 1.315379392 0.282334082 1.04198767 1 12.87511819 -16.52287875 0.191372159 1.799595266 0.779568338 0.109856439 0.25712596 114.8660546 1.363524116 34.49711047 0.278292997 3.00E-17 16.52287875 -1.020026929 GTS(ph)PRPPEGGLGYSQLGDDDLK ddPTM_HeLa_Romidepsin_16h_R1 1 GTSPRPPEGGLGYSQLGDDDLK 22 1 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;Q9UQ88-5;Q9UQ88-10;P21127-12;P21127-4;Q9UQ88-8 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 GT(0.206)S(0.791)PRPPEGGLGY(0.002)S(0.001)QLGDDDLK 76.606 0.00086819 33940000 1514.1 1497.2 1347.3 979.27 1595.9 1387.7 1387.5 1813.2 1850.6 1747.1 TRUE FALSE FALSE 1495.645567 1518.277621 1370.749191 1092.497805 1514.455268 1299.030449 1505.354215 1865.662081 1685.077701 1701.71009 0.878907386 0.89220698 0.80551276 0.641999957 0.889960797 0.763367659 0.884612617 1.09634543 0.990226074 1 10.73276956 -11.53686088 0.734510715 0.992873442 0.844676017 0.202430101 0.10909881 0.741616073 0.821486438 0.054630706 0.025035712 2.90E-12 11.53686088 -0.148197424 GTSGS(ph)LADVFANTR ddPTM_HeLa_Romidepsin_16h_R1 1 GTSGSLADVFANTR 14 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 0 GT(0.273)S(0.043)GS(0.683)LADVFANTR 95.822 0.0030884 0 1502.6 1623.4 1275.1 1438.8 1394.5 1548.5 1384 1380 1314.9 1243.4 TRUE FALSE FALSE 1484.285733 1646.254268 1297.292581 1605.160826 1323.333461 1449.555848 1501.556925 1419.928123 1197.292051 1211.096289 1.225572027 1.359309151 1.071172121 1.325378371 1.092674029 1.196895623 1.239832819 1.172432065 0.988601866 1 10.24209786 -12.14568655 0.894597803 0.999484117 1.210445382 0.501888499 0.085321438 0.387269947 0.557977262 0.052794623 0.015154601 7.15E-13 12.14568655 0.210961264 GTSISTK(ac)PPLTK ddPTM_HeLa_Romidepsin_16h_R1 2 GTSISTKPPLTK 12 1 C9JW34;C9JGY5;F8WE44;C9JXZ7;C9JTT7;C9J8M3;C9JZI1;P35249-2;P35249 C9JW34 RFC4 Replication factor C subunit 4 0 1 ; GTSISTK(1)PPLTK;GTSISTK(1)PPLTK 196.67 1.34E-09 3542200 3454.7 3498.2 3681.8 3398.2 3670.5 3446 3363.2 3880.9 4027.7 3505.8 FALSE TRUE FALSE 3412.592788 3547.447751 3745.880185 3791.115873 3483.180688 3225.811721 3648.870124 3993.187718 3667.452424 3414.718811 0.999377394 1.038869655 1.096980569 1.110227835 1.020049053 0.944678581 1.068571184 1.169404551 1.074013009 1 11.73755107 -7.379247701 3.51527081 1.015623562 1.171895336 0.331627042 0.050489721 0.17498529 3.457629022 0.007179332 0.05788036 4.18E-08 7.379247701 0.156271774 GTSS(ph)PDYR ddPTM_HeLa_Romidepsin_16h_R1 2 GTSSPDYR 8 0 Q66K14;Q66K14-2;G3V133 Q66K14 TBC1D9B TBC1 domain family member 9B 1 0 GT(0.006)S(0.074)S(0.919)PDYR;GT(0.001)S(0.191)S(0.808)PDYR ; 124.08 0.016122 13601800 10012.1 11635 19061.2 7334.4 9204.7 11647 19860.1 2797.6 19014.6 16546 TRUE FALSE FALSE 9890.068674 11798.79784 19392.95219 8182.437837 8734.949812 10902.79429 21547.0164 2878.544142 17313.88655 16116.13253 0.613675065 0.732110996 1.203325435 0.507717209 0.542000371 0.67651431 1.336984314 0.178612588 1.074320189 1 13.97621795 GTT(ph)PPPPSWEPNSQTK ddPTM_HeLa_Romidepsin_16h_R1 2 GTTPPPPSWEPNSQTK 16 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 GT(0.053)T(0.947)PPPPSWEPNSQTK;GT(0.034)T(0.966)PPPPSWEPNSQTK ; 121.21 0.0059446 11150100 7200.4 6385.5 6489.7 3242 6735.6 6240.9 5211.9 5310.4 6745.4 7386.2 TRUE FALSE FALSE 7112.638755 6475.395237 6602.650506 3616.855294 6391.857198 5842.126632 5654.598656 5464.048046 6142.07453 7194.305459 0.988648424 0.900072324 0.917760657 0.502738633 0.888460635 0.812048733 0.785982565 0.759496254 0.853741138 1 12.8126397 -9.638966471 2.761081798 0.98959267 0.760924303 0.356547779 0.108752257 0.148078301 2.290620158 0.015225105 0.022249377 2.30E-10 9.638966471 -0.228668367 GTTATSAQANSTPTSVASVVTSAES(ph)PASR ddPTM_HeLa_Romidepsin_16h_R1 1 GTTATSAQANSTPTSVASVVTSAESPASR 29 0 Q86YP4-2;Q86YP4;Q86YP4-3 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 0 GTTATSAQANSTPTSVASVVT(0.019)S(0.047)AES(0.887)PAS(0.046)R 141.54 5.10E-11 12643000 3330.4 2578.1 2829 3045 2852.3 2603.9 2387.4 2523.3 3466 3189.6 TRUE FALSE FALSE 3289.807804 2614.394559 2878.237558 3397.077227 2706.736488 2437.519194 2590.185696 2596.307704 3155.992279 3106.733732 1.05892815 0.841525147 0.926451317 1.093456189 0.871248302 0.784592245 0.833732762 0.835703323 1.015855413 1 11.60118288 -8.602873158 0.663056934 1.019847805 0.787265398 0.439251679 0.07711802 0.63311064 0.447837106 0.015925211 0.08065904 2.50E-09 8.602873158 -0.232582407 GTTITLVLK ddPTM_HeLa_Romidepsin_16h_R1 1 GTTITLVLK 9 0 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 0 135.83 0.027883 829540 672.34 475.66 846.12 487.04 697.6 856.2 776.87 782.72 567.48 386.23 FALSE FALSE TRUE 664.1452615 482.356354 860.8463637 543.3538564 661.9988689 801.4915833 842.8573184 805.3667683 516.7231675 376.1956889 1.765424966 1.282195326 2.288294069 1.444338339 1.759719445 2.130517725 2.24047575 2.140818707 1.373548881 1 8.555339506 -12.30881399 0.128720369 7.07E-15 2.586400445 0.558605057 0.285304309 9.073572411 0.319232236 5.007265702 1.73925321 4.91E-13 12.30881399 2.586400445 GTVGEPTYDAEFQHFLR ddPTM_HeLa_Romidepsin_16h_R1 2 GTVGEPTYDAEFQHFLR 17 0 Q14204;A0A2R8Y706;A0A2R8Y5T0;A0A2R8Y542 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 ; ; 187 1.05E-10 10734700 6843.7 6922.2 7549.6 7277.3 7526.7 7314.3 6430 7645.5 7290 6538.6 FALSE FALSE TRUE 6760.286352 7019.650913 7680.997621 8118.735667 7142.584413 6846.939836 6976.16404 7866.71048 6637.964142 6368.726229 1.061481701 1.102206416 1.20604927 1.274781703 1.121509099 1.075087795 1.095378226 1.235209396 1.042275002 1 12.63678914 -10.30410968 1.678500389 1.023268153 1.162019793 0.494623604 0.06007966 0.225815597 1.20879435 0.012326426 0.014384137 4.96E-11 10.30410968 0.138751641 GTVTDFPGFDER ddPTM_HeLa_Romidepsin_16h_R1 2 GTVTDFPGFDER 12 0 P08758;D6RBE9;E9PHT9;D6RCN3 P08758 ANXA5 Annexin A5;Annexin 0 0 ; ; 233.84 9.55E-38 109894000 13711.2 13189.9 11941.6 12415.5 13655.4 14007.2 12593 13962.8 13828.4 12736.5 FALSE FALSE TRUE 13544.08262 13375.58776 12149.43854 13851.03853 12958.51398 13112.18513 13662.64911 14366.79159 12591.55327 12405.60389 1.091771327 1.078189169 0.979350836 1.116514653 1.044569381 1.056956617 1.101328821 1.158088853 1.014989143 1 13.59870435 GTYVPSS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 GTYVPSSPTR 10 0 Q9Y4P8-4;Q9Y4P8 Q9Y4P8-4 WIPI2 WD repeat domain phosphoinositide-interacting protein 2 1 0 GTYVPS(0.108)S(0.882)PT(0.01)R;GTYVPS(0.143)S(0.823)PT(0.034)R ; 115.91 0.014382 222550000 8560.9 8029.3 9673.4 6095.4 9462.9 10732.1 9564.7 9962.6 8213.7 7526.6 TRUE FALSE FALSE 8456.556458 8142.336696 9841.761469 6800.178828 8979.972902 10046.35345 10377.12538 10250.85211 7479.0461 7331.057847 1.153524721 1.110663272 1.342474944 0.927584937 1.224921845 1.370382509 1.415501773 1.398277346 1.02018648 1 12.83980567 -4 0.191766663 1.006239414 3.044715901 0.583334248 0.110350854 27.926419 0.313715083 0.117386412 17.01195074 1.00E-04 4 2.038476487 GVAGPGPIGREPDPDS(ph)DWEPEER ddPTM_HeLa_Romidepsin_16h_R1 1 GVAGPGPIGREPDPDSDWEPEER 23 1 Q9NPE2-3;Q9NPE2 Q9NPE2-3 NGRN Neugrin 1 0 GVAGPGPIGREPDPDS(1)DWEPEER 89.297 5.20E-05 6577500 1347.3 1374.5 970.85 3230.4 1151.3 1729.1 1317.2 1330.7 1542.1 1101.8 TRUE FALSE FALSE 1330.878589 1393.850247 987.747237 3603.914047 1092.544865 1618.61609 1429.082935 1369.201705 1404.170714 1073.175077 1.240131846 1.298809744 0.920397108 3.358179037 1.018049047 1.508249795 1.33164007 1.275841877 1.308426503 1 10.06766974 GVAINFVK ddPTM_HeLa_Romidepsin_16h_R1 1 GVAINFVK 8 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 0 124.37 0.014988 751410 558.85 703.07 837.54 642.96 999.86 1094.8 1052.7 806.95 684.38 463.81 FALSE FALSE TRUE 552.0385212 712.9678379 852.1170324 717.3020604 948.8334132 1024.845813 1142.116312 830.2978251 623.1673387 451.7601493 1.221972593 1.578199934 1.886215581 1.587794013 2.100303479 2.268561791 2.528147543 1.837917369 1.379420783 1 8.819413203 -9.634204726 0.587028207 1.031541126 2.283530056 0.732147169 0.234707775 0.206088488 0.146376837 0.053283243 0.104813789 2.32E-10 9.634204726 1.25198893 GVAPADS(ph)PEAPR ddPTM_HeLa_Romidepsin_16h_R1 2 GVAPADSPEAPR 12 0 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 0 GVAPADS(1)PEAPR;GVAPADS(1)PEAPR ; 133.88 0.0029415 40119900 2829.06 2425.2 2480.1 2128.14 3390.7 3118.1 2517.24 3204.9 2732.32 2731.89 TRUE FALSE FALSE 2794.578329 2459.342029 2523.2651 2374.20556 3217.659927 2918.863473 2731.054303 3297.628725 2487.934456 2660.915104 1.050232052 0.92424671 0.948269675 0.892251525 1.209230585 1.096939722 1.026359052 1.239283704 0.934992046 1 11.37770677 -8.75288716 24.99998619 1.001479103 1.131338413 0.549569697 0.075795569 145.5167247 425373.8601 0.010980655 0.021686703 1.77E-09 8.75288716 0.12985931 GVAPADS(ph)PEAPRR ddPTM_HeLa_Romidepsin_16h_R1 4 GVAPADSPEAPRR 13 1 Q9P2G1 Q9P2G1 ANKIB1 Ankyrin repeat and IBR domain-containing protein 1 1 0 GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR;GVAPADS(1)PEAPRR ;;; 120.32 0.0014333 66327000 13622.5 12571.6 10617.8 11631.3 14099.3 14902.6 11692.2 13803.5 13327.4 11963.5 TRUE FALSE FALSE 13456.46373 12748.58331 10802.59836 12976.16563 13379.76011 13950.37196 12685.33518 14202.88249 12135.36396 11652.68655 1.154794963 1.094046705 0.92704788 1.113577164 1.148212479 1.197180745 1.088618932 1.218850472 1.041421986 1 13.50837499 -16.52287875 0.232698881 0.335794013 1.137635883 0.235732187 0.074469934 52.01511011 0.672758112 15.92099502 0.055440236 3.00E-17 16.52287875 0.801841871 GVDDLDFFIGDEAIEKPTYATK ddPTM_HeLa_Romidepsin_16h_R1 1 GVDDLDFFIGDEAIEKPTYATK 22 1 P61158;B4DXW1;F8WDR7 P61158 ACTR3 Actin-related protein 3 0 0 157.22 3.50E-08 14288000 2005.8 1679.9 1582.6 2225.5 1683.9 1878.1 1497.6 1452.7 2338.5 1844 FALSE FALSE TRUE 1981.352538 1703.549676 1610.144489 2482.822781 1597.9643 1758.095471 1624.806107 1494.731583 2129.338703 1796.092614 1.103146086 0.948475409 0.896470748 1.382346746 0.889689255 0.978844553 0.904633811 0.832212978 1.18553948 1 10.81064603 -7.924011051 1.468019363 1.047510877 0.846170854 0.242999457 0.138395687 0.545666118 2.025337877 0.018721731 0.111274253 1.19E-08 7.924011051 -0.201340023 GVDEVTIVNILTNR ddPTM_HeLa_Romidepsin_16h_R1 3 GVDEVTIVNILTNR 14 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YMW4 P07355 ANXA2 Annexin A2;Annexin 0 0 ;; ;; 243.85 2.02E-53 27080630 3931.97 4176.1 4154.54 3839.458 3757.9 3867.9 4247.65 3503.7 4386.4 4544.2 FALSE FALSE TRUE 3884.045637 4234.891245 4226.848026 4283.394199 3566.12034 3620.753673 4608.445285 3605.074032 3994.069398 4426.141029 0.877524148 0.956790852 0.954973644 0.967749146 0.805695146 0.818038479 1.041188081 0.81449597 0.902381865 1 12.1118337 -8.795142618 24.99756635 0.944702924 0.878391235 0.202635224 0.070467851 264.2865936 196019.5417 0.011041595 0.020015408 1.60E-09 8.795142618 -0.066311688 GVDLLLEGVQGES(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 GVDLLLEGVQGESSPTR 17 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 0 GVDLLLEGVQGES(0.474)S(0.474)PT(0.052)R 112.3 0.0020143 2645800 464.7 373.68 453.26 339.9 608.02 866.49 484.19 493 485.2 487.63 TRUE FALSE FALSE 459.0360577 378.9406768 461.1488002 379.2008373 576.9904706 811.1240855 525.3170865 507.2641772 441.8024968 474.9613023 0.966470438 0.797834845 0.970918679 0.798382595 1.21481575 1.707768784 1.106020815 1.068011593 0.930186301 1 8.891666164 -8.603493865 6.711565994 0.956314404 1.304979803 0.497732414 0.176453698 0.141571278 9.627462623 0.025171518 0.050660015 2.49E-09 8.603493865 0.348665399 GVDLLLEGVQGES(ph)SPTRR ddPTM_HeLa_Romidepsin_16h_R1 1 GVDLLLEGVQGESSPTRR 18 1 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 0 GVDLLLEGVQGES(0.603)S(0.386)PT(0.011)RR 88.768 0.0020917 6805800 2115.5 1843.9 1950.5 2127.8 2446.5 2559.2 2220 2714.9 2334.7 2007.3 TRUE FALSE FALSE 2089.715472 1869.858473 1984.447634 2373.826248 2321.645976 2395.675379 2408.566745 2793.451348 2125.878585 1955.150057 1.068826132 0.95637594 1.014984823 1.214140183 1.187451555 1.225315352 1.231908894 1.428765705 1.087322468 1 10.93306362 -4.572450861 0.30301615 1.008562746 3.514321562 0.796004406 0.061203416 10.45693945 0.184290737 0.022472927 13.56688001 2.68E-05 4.572450861 2.505758816 GVDLLLEGVQGESS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 GVDLLLEGVQGESSPTR 17 0 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 0 GVDLLLEGVQGES(0.408)S(0.56)PT(0.033)R;GVDLLLEGVQGES(0.301)S(0.52)PT(0.178)R ; 100.77 0.0010249 2291300 2085.47 1825.79 2059.08 1442.73 2971.5 3258 2607 2904.5 2454.6 2389 TRUE FALSE FALSE 2060.051489 1851.49352 2094.917424 1609.545231 2819.853267 3049.824315 2828.438515 2988.537125 2235.054428 2326.933436 0.885307443 0.795679623 0.900291083 0.691702309 1.211832373 1.310662466 1.215521885 1.284324287 0.960514983 1 11.18421423 -8.626855235 7.567040964 0.912679613 1.263903376 0.814624645 0.088612082 0.08524256 5.542201815 0.014194368 0.028471235 2.36E-09 8.626855235 0.351223763 GVEEEEEDGEMRE ddPTM_HeLa_Romidepsin_16h_R1 4 GVEEEEEDGEMRE 13 1 P62306 P62306 SNRPF Small nuclear ribonucleoprotein F 0 0 ;;; ;;; 133.23 0.0016374 146860900 13297.6 12123.8 11586.91 11752.5 13412.4 13039.3 11098.8 11217.37 13111.8 12215 FALSE FALSE TRUE 13135.52374 12294.47917 11788.57531 13111.37935 12727.91518 12206.13081 12041.53179 11541.9269 11939.04777 11897.65254 1.104043314 1.033353356 0.990832038 1.102013973 1.069783736 1.025927659 1.012093079 0.970101191 1.003479277 1 13.53838933 -7.524469474 1.71803228 1.049457645 0.964465941 0.239053366 0.038334068 0.662636718 2.762563311 0.006547068 0.077746165 2.99E-08 7.524469474 -0.084991704 GVEFPMADLDALS(ph)PIHTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 GVEFPMADLDALSPIHTPQR 20 0 Q6ZVM7-2;Q6ZVM7-5;Q6ZVM7 Q6ZVM7-2 TOM1L2 TOM1-like protein 2 1 0 GVEFPMADLDALS(1)PIHTPQR 59.661 0.0079946 14681000 1292.6 1186.4 1193.9 1100.4 3898.6 5340.8 4698.6 5162.5 1677.6 1472.8 TRUE FALSE FALSE 1276.845294 1203.10217 1214.679329 1227.633426 3699.639894 4999.540117 5097.698967 5311.868792 1527.551254 1434.536444 0.890075187 0.838669645 0.846739958 0.855770121 2.57897937 3.485125902 3.553551385 3.702846878 1.064839629 1 10.4863689 -8.582827431 2.557618568 0.917243279 3.578282932 0.990428024 0.119056973 0.019223475 0.253253597 0.018991967 0.043545602 2.61E-09 8.582827431 2.661039653 up GVEPSPS(ph)PIKPGDIK ddPTM_HeLa_Romidepsin_16h_R1 2 GVEPSPSPIKPGDIK 15 1 Q92890;Q92890-1;C9JNP9;Q92890-3 Q92890 UFD1L Ubiquitin fusion degradation protein 1 homolog 1 0 GVEPS(0.102)PS(0.898)PIKPGDIK;GVEPS(0.046)PS(0.954)PIKPGDIK ; 131.4 0.01192 47967000 5846.5 5108.7 5479.8 3560.6 5108.2 5475.6 4106.5 4681.6 5588.1 5598.5 TRUE FALSE FALSE 5775.240609 5180.620413 5575.17362 3972.293325 4847.509493 5125.726832 4455.306008 4817.05471 5088.28634 5453.050163 1.059084446 0.95004085 1.02239544 0.728453472 0.888953769 0.939974267 0.817030079 0.883368861 0.933108295 1 12.41284771 -9.298279547 24.14365077 1.021156158 0.856627752 0.525497162 0.064343463 170.2521532 111576.3363 0.008904839 0.013602667 5.03E-10 9.298279547 -0.164528407 GVESVFDIMEMEDEER ddPTM_HeLa_Romidepsin_16h_R1 1 GVESVFDIMEMEDEER 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 0 99.215 0.025681 5126200 2167.3 2354.1 2176.2 1412.1 2219.3 2375.5 1722.7 2042.2 2420 2114.6 FALSE FALSE TRUE 2140.884114 2387.241082 2214.075848 1575.373646 2106.04084 2223.713217 1869.026095 2101.287835 2203.549139 2059.662387 1.039434486 1.15904485 1.074970278 0.764869843 1.022517502 1.079649379 0.907442941 1.02020984 1.069859387 1 11.00819216 GVGDDQLGEES(ph)EERDDHLLPM ddPTM_HeLa_Romidepsin_16h_R1 2 GVGDDQLGEESEERDDHLLPM 21 1 H0YF90;F5GX30;P20645 H0YF90 M6PR Cation-dependent mannose-6-phosphate receptor 1 0 GVGDDQLGEES(1)EERDDHLLPM;GVGDDQLGEES(1)EERDDHLLPM ; 58.373 0.024761 45560000 4642.9 5674.9 4751.7 4914.8 5224.5 5930.6 3780.6 6143.9 5222.1 5263.2 TRUE FALSE FALSE 4586.310549 5754.791391 4834.401345 5483.072301 4957.87427 5551.6538 4101.72407 6321.664053 4755.022297 5126.461305 0.894634774 1.122566045 0.943028935 1.069562799 0.967114345 1.08294074 0.800108267 1.233143815 0.927544755 1 12.32374759 -10.28997531 24.94687961 0.950244204 1.019928876 0.113236018 0.112043037 1307.727898 1143246.403 0.017531341 0.020049304 5.13E-11 10.28997531 0.069684672 GVGDDQLGEESEERDDHLLPM ddPTM_HeLa_Romidepsin_16h_R1 1 GVGDDQLGEESEERDDHLLPM 21 1 H0YF90;F5GX30;P20645 H0YF90 M6PR Cation-dependent mannose-6-phosphate receptor 0 0 77.39 0.0052896 7150000 1925.8 2447 1891.2 1864.3 2157.6 2981.1 2019.3 3335.2 2212.8 2162.9 FALSE FALSE TRUE 1902.327609 2481.44893 1924.115543 2079.859138 2047.489621 2790.617331 2190.819292 3431.69875 2014.881626 2106.707546 0.90298609 1.177880117 0.913328262 0.98725575 0.971890771 1.324634421 1.039925687 1.628939316 0.956412593 1 11.04077434 -4 0.643519669 0.968194295 52.52617474 0.683152887 0.122340226 76.78330721 0.470434238 0.01937636 5643.734554 1.00E-04 4 51.55798044 GVGISVLEMSHR ddPTM_HeLa_Romidepsin_16h_R1 1 GVGISVLEMSHR 12 0 Q9Y617-2;Q9Y617 Q9Y617-2 PSAT1 Phosphoserine aminotransferase 0 0 128.85 0.0005565 618840 473.43 402.45 816.9 517.46 636.19 447.5 454.81 401.03 449.83 264.72 FALSE FALSE TRUE 467.6596531 408.1157017 831.1178018 577.2911599 603.7228503 418.9061942 493.44155 412.6331703 409.5960782 257.8425362 1.813741285 1.582809833 3.223354121 2.238929109 2.341440086 1.624658989 1.913732145 1.600330094 1.58855123 1 8.010346474 -11.44506835 0.73224258 1.05861441 2.093019451 0.259846728 0.489804695 0.449357947 0.504512151 0.224024495 0.111166524 3.59E-12 11.44506835 1.034405041 GVGQADWT(ph)PDLGLR ddPTM_HeLa_Romidepsin_16h_R1 2 GVGQADWTPDLGLR 14 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 GVGQADWT(1)PDLGLR;GVGQADWT(1)PDLGLR ; 181.69 5.10E-07 32197000 5480.4 4995.4 5312.8 4586.7 6501.4 7381.9 5825.1 6487.8 5407.8 4602.4 TRUE FALSE FALSE 5413.602777 5065.725372 5405.267055 5117.035835 6169.609298 6910.220414 6319.883849 6675.514257 4924.112824 4482.828985 1.207630895 1.130028692 1.205771417 1.141474692 1.376275856 1.541486512 1.409798114 1.489129806 1.098438696 1 12.13019375 -4.000000012 0.141196829 0.938700072 3.055807953 0.793873956 0.078377193 23.61045591 0.219705234 0.220074695 10.1472605 1.00E-04 4.000000012 2.117107882 GVGSGPHPPDTQQPS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 4 GVGSGPHPPDTQQPSPSK 18 0 Q68CZ2;Q68CZ2-2;E9PCX8 Q68CZ2 TNS3 Tensin-3 1 0 GVGSGPHPPDTQQPS(0.651)PS(0.349)K;GVGSGPHPPDT(0.069)QQPS(0.914)PS(0.017)K;GVGSGPHPPDTQQPS(0.538)PS(0.462)K;GVGSGPHPPDT(0.005)QQPS(0.898)PS(0.098)K ;;; 259.34 9.91E-76 22027800 11141.1 11042 10366.5 10538.9 9732.4 8311.9 5768.34 6246.24 13515.7 12927.3 TRUE FALSE FALSE 11005.30799 11197.44957 10546.92458 11757.45721 9235.719311 7780.796415 6258.302656 6426.965099 12306.82194 12591.44688 0.87403045 0.88929014 0.837626103 0.933765382 0.733491504 0.617942996 0.497028079 0.51042308 0.977395375 1 13.62015645 -8.304570782 0.943229401 0.934851377 0.454741162 0.923243107 0.049232547 0.156360585 0.229124072 0.009762774 0.052723951 4.96E-09 8.304570782 -0.480110215 GVHIHQAGGS(ph)PPASSTSSSSLTNDVAK ddPTM_HeLa_Romidepsin_16h_R1 2 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 0 GVHIHQAGGS(0.987)PPASST(0.01)S(0.002)S(0.001)SSLTNDVAK;GVHIHQAGGS(0.505)PPAS(0.055)S(0.055)T(0.267)S(0.087)S(0.029)S(0.002)SLTNDVAK ; 143.48 6.02E-11 12572800 3944.3 5072.6 4568.5 4322.2 5385.8 5081.6 4260 4304.3 6014.5 4908 TRUE FALSE FALSE 3896.225354 5144.012196 4648.012826 4821.953101 5110.942529 4756.90216 4621.844294 4428.838129 5476.548056 4780.489452 0.815026451 1.076042997 0.972288062 1.008673515 1.069125365 0.995065925 0.966814034 0.92644031 1.145604046 1 12.22294262 -10.25200136 24.98237412 0.912651379 1.002127594 0 0.094518928 761.2634621 2015061.852 0.013172896 0.016018964 5.60E-11 10.25200136 0.089476215 GVHIHQAGGSPPASSTSSSS(ph)LTNDVAK ddPTM_HeLa_Romidepsin_16h_R1 1 GVHIHQAGGSPPASSTSSSSLTNDVAK 27 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 0 GVHIHQAGGS(0.007)PPAS(0.093)S(0.093)T(0.093)S(0.093)S(0.093)S(0.121)S(0.373)LT(0.032)NDVAK 56.453 0.0014036 7606300 1909.3 1626.4 1507 2157.1 2107.5 2155.8 1940.3 1751.4 2582.2 1765.2 TRUE FALSE FALSE 1886.028717 1649.296502 1533.228703 2406.514051 1999.946411 2018.051338 2105.109034 1802.073996 2351.241565 1719.33985 1.096949342 0.959261488 0.891754299 1.399673283 1.163205989 1.173736151 1.224370525 1.048119717 1.367525778 1 10.74763902 -9.275005225 24.99530867 1.028577209 1.199368326 0.167406476 0.144737972 575.9965519 1061281.347 0.015079343 0.023110021 5.31E-10 9.275005225 0.170791116 GVIST(ph)PVIR ddPTM_HeLa_Romidepsin_16h_R1 2 GVISTPVIR 9 0 A0A494C0Y9;A0A0C4DG79;Q9NZB2-4;Q9NZB2;Q9NZB2-6 A0A494C0Y9 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 0 GVIS(0.06)T(0.94)PVIR;GVIS(0.065)T(0.935)PVIR ; 152.06 0.010385 15539600 7520.6 7207.2 8092.1 5836.7 8231.8 8887.6 6056.4 6607.8 7470.4 7037 TRUE FALSE FALSE 7428.936034 7308.663151 8232.939606 6511.566716 7811.700529 8319.711043 6570.830465 6798.986268 6802.228714 6854.177726 1.08385518 1.066307797 1.201156424 0.95001428 1.13969915 1.213816066 0.958660649 0.991947764 0.992420825 1 12.74276789 -12.14607042 0.879619807 0.999555313 1.078141687 0.114862403 0.087100322 1.158564552 1.604242143 0.058503901 0.016518756 7.14E-13 12.14607042 0.078586374 GVLEGDDVLFYDES(ph)PPPRPK ddPTM_HeLa_Romidepsin_16h_R1 4 GVLEGDDVLFYDESPPPRPK 20 1 Q5T670;Q7L590-2;Q7L590 Q5T670 MCM10 Protein MCM10 homolog 1 0 GVLEGDDVLFYDES(1)PPPRPK;GVLEGDDVLFYDES(1)PPPRPK;GVLEGDDVLFYDES(1)PPPRPK;GVLEGDDVLFY(0.017)DES(0.983)PPPRPK ;;; 154.65 4.46E-08 18128900 7050.7 6832.98 7129 5609.07 6853.56 7574.7 6652.78 7095.6 8512.3 7498.8 TRUE FALSE FALSE 6964.763356 6929.174872 7253.077255 6257.617065 6503.797259 7090.701116 7217.866967 7300.899991 7750.938569 7303.980095 0.953557275 0.948684797 0.993030808 0.856740706 0.890445644 0.970799622 0.988210109 0.999578298 1.061193824 1 12.83446712 -11.85217353 0.68532409 1.000742518 0.947556028 0.263961583 0.047529878 1.135637054 0.986738876 0.032461591 0.010280438 1.41E-12 11.85217353 -0.05318649 GVNT(ph)GAVGSYIYDRDPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 GVNTGAVGSYIYDRDPEGK 19 1 H0YHD8;H0YFA4;P52943;P52943-2 H0YHD8 CRIP2 Cysteine-rich protein 2 1 0 GVNT(0.88)GAVGS(0.104)Y(0.013)IY(0.003)DRDPEGK 54.974 0.028642 8505700 1813.7 1651 1992.8 1992 1386.3 1611 1220.7 1212.3 1906.8 1913.5 TRUE FALSE FALSE 1791.593927 1674.242821 2027.483848 2222.324413 1315.551938 1508.062299 1324.386228 1247.375988 1736.251032 1863.786994 0.961265387 0.898301591 1.087830237 1.192370383 0.705848867 0.809138761 0.710588834 0.669269606 0.9315716 1 10.86402127 -8.73469336 24.99955497 0.996342001 0.72887597 0.731172438 0.085268921 93.69800524 87579.29142 0.012337195 0.024668941 1.84E-09 8.73469336 -0.26746603 GVNTFS(ph)PEGR ddPTM_HeLa_Romidepsin_16h_R1 2 GVNTFSPEGR 10 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 0 GVNTFS(1)PEGR;GVNTFS(1)PEGR ; 196.67 1.35E-08 230150000 5867.1 5550.9 5346.2 4553.1 12604.6 17758.9 15183.4 16274.5 6426.6 5805.8 TRUE FALSE FALSE 5795.589528 5629.045716 5439.248368 5079.550845 11961.34023 16624.1636 16473.07762 16745.37698 5851.7888 5654.964479 1.024867539 0.995416636 0.961853675 0.898246287 2.115192814 2.939746778 2.913029371 2.961181638 1.03480558 1 12.46530225 -8.555458936 2.686498779 0.996962366 2.93406209 0.992568493 0.076336776 0.016638683 0.241962825 0.012241996 0.028181034 2.78E-09 8.555458936 1.937099724 up GVNTGAVGS(ph)YIYDRDPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 GVNTGAVGSYIYDRDPEGK 19 1 H0YHD8;H0YFA4;P52943;P52943-2 H0YHD8 CRIP2 Cysteine-rich protein 2 1 0 GVNT(0.002)GAVGS(0.997)Y(0.001)IYDRDPEGK 73.127 0.0050621 6022900 3108.7 2467.5 2945.3 2860.2 2676.9 2492.3 2178.8 2474.5 2999.7 2662.6 TRUE FALSE FALSE 3070.809969 2502.23753 2996.561711 3190.909782 2540.287804 2333.050074 2363.867218 2546.095753 2731.399319 2593.425268 1.184074979 0.964838879 1.15544556 1.230384319 0.979510702 0.899601813 0.911484609 0.981750191 1.053201476 1 11.34064308 -8.537818914 24.79442911 1.093910722 0.930758897 0.490229813 0.078498123 156.0641503 259000.4435 0.013267471 0.026543128 2.90E-09 8.537818914 -0.163151826 GVPAGNS(ph)DTEGGQPGR ddPTM_HeLa_Romidepsin_16h_R1 1 GVPAGNSDTEGGQPGR 16 0 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 GVPAGNS(0.72)DT(0.28)EGGQPGR 174.59 3.40E-06 95096000 1198.3 952.22 802.46 678.1 1095 951.62 960.7 985.25 1273.3 1203.5 TRUE FALSE FALSE 1183.694659 965.6253782 816.4264797 756.5051126 1039.118064 890.8145532 1042.301834 1013.756654 1159.412859 1172.232897 1.009777718 0.823748746 0.696471224 0.645353935 0.886443357 0.759929666 0.889159345 0.864808228 0.989063575 1 10.19504351 -10.21590438 4.583881805 1.004969238 0.789453129 0.611980742 0.07482259 0.100010767 4.778474615 0.012964998 0.015741198 6.08E-11 10.21590438 -0.215516109 GVPAGNS(ph)DTEGGQPGRK ddPTM_HeLa_Romidepsin_16h_R1 2 GVPAGNSDTEGGQPGRK 17 1 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 GVPAGNS(0.969)DT(0.031)EGGQPGRK;GVPAGNS(0.992)DT(0.008)EGGQPGRK ; 80.752 0.0053448 41972000 6809.2 4281.7 4737.3 3213.8 5269.5 4285.1 5374.3 4629.9 6718.8 6104.4 TRUE FALSE FALSE 6726.206851 4341.977885 4819.750719 3585.394677 5000.577752 4011.29594 5830.792908 4763.858852 6117.8537 5945.806808 1.13125217 0.730258824 0.810613408 0.603012307 0.841025939 0.674642831 0.980656301 0.801213192 1.028935836 1 12.53765687 -10.25882664 24.99297448 1.061980193 0.778239195 0.615180502 0.099980818 108.0190725 1033291.2 0.017177792 0.020528777 5.51E-11 10.25882664 -0.283740998 GVPHPEDDHS(ph)QVEGPESLR ddPTM_HeLa_Romidepsin_16h_R1 1 GVPHPEDDHSQVEGPESLR 19 0 H3BND4;Q6P996-3;Q6P996-4;Q6P996-5;Q6P996 H3BND4 PDXDC1 Pyridoxal-dependent decarboxylase domain-containing protein 1 1 0 GVPHPEDDHS(1)QVEGPESLR 135.98 0.00027552 4165200 1551.2 1967.8 1636.3 1323.5 1454.7 1531.9 1215.3 1393.7 1734 1702.1 TRUE FALSE FALSE 1532.293378 1995.50274 1664.779115 1476.529297 1380.461231 1434.016534 1318.527552 1434.024511 1578.906697 1657.879197 0.924249113 1.203647856 1.004161895 0.890613321 0.83266696 0.864970462 0.795309788 0.864975273 0.952365347 1 10.69512317 -9.081179323 3.618136506 0.987517703 0.839513047 0.547014751 0.074744411 0.178102643 4.439040199 0.012303944 0.021458431 8.30E-10 9.081179323 -0.148004656 GVPVISVK(ac)TSGSK ddPTM_HeLa_Romidepsin_16h_R1 2 GVPVISVKTSGSK 13 1 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 0 1 ; GVPVISVK(1)TSGSK;GVPVISVK(1)TSGSK 133.05 0.00096974 1791480 627.02 626 555.33 466.4 457.71 411.77 404.25 345.45 824.69 599.51 FALSE TRUE FALSE 619.3776391 634.8128444 564.9952857 520.3273625 434.3513507 385.4592259 438.5869849 355.4450507 750.9276609 583.9346438 1.060696853 1.087129957 0.967565963 0.891071232 0.743835557 0.660106795 0.751089167 0.608706907 1.285978951 1 9.189663096 -8.919518452 1.533561846 1.033332491 0.6761851 0.803543972 0.090087956 0.067041831 0.316183336 0.006883669 0.015182153 1.20E-09 8.919518452 -0.35714739 GVQKPAGPST(ph)SPDGNSR ddPTM_HeLa_Romidepsin_16h_R1 1 GVQKPAGPSTSPDGNSR 17 1 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 GVQKPAGPS(0.212)T(0.736)S(0.046)PDGNS(0.006)R 64.249 0.024649 2773100 742.81 554.79 587.68 597.32 967.96 1038.7 831.74 687.8 751.98 650.52 TRUE FALSE FALSE 733.756346 562.6003482 597.9083239 666.3849489 918.5613892 972.3304223 902.3879748 707.7004078 684.7210254 633.6193966 1.15803959 0.887915287 0.943639552 1.051711725 1.449705287 1.534565431 1.424179846 1.116917209 1.080650354 1 9.30747269 -8.767283107 24.9160687 1.048459707 1.395346345 0.667791684 0.123634831 66.97402207 285560.436 0.01955957 0.036149895 1.71E-09 8.767283107 0.346886637 GVQVETIS(ph)PGDGR ddPTM_HeLa_Romidepsin_16h_R1 2 GVQVETISPGDGR 13 0 Q1JUQ3;A0A087WTS4;A0A087WV48;A0A087WZM5;P62942 Q1JUQ3 FKBP12-Exin;FKBP1A Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase FKBP1A 1 0 GVQVET(0.001)IS(0.999)PGDGR;GVQVET(0.001)IS(0.999)PGDGR ; 167.92 0.00012903 20806000 4888.9 4486.3 4233.2 4233.3 4625.1 5235 3925.4 4414.7 4930.7 5165.5 TRUE FALSE FALSE 4829.312206 4549.458249 4306.87707 4722.774064 4389.063888 4900.500395 4258.823378 4542.432379 4489.685843 5031.299565 0.95985384 0.904231241 0.856016823 0.938678765 0.87235193 0.974002906 0.846465873 0.902834808 0.892351128 1 12.29671538 -10.47641815 1.749173187 0.985888119 0.898358896 0.092089809 0.046727795 0.180211147 1.0843857 0.006735396 0.007355746 3.34E-11 10.47641815 -0.087529223 GVS(ph)PTPSKIPVR ddPTM_HeLa_Romidepsin_16h_R1 1 GVSPTPSKIPVR 12 1 F8VXV6;F8VR46;F8VVX4;F8VVT5;F8W052;F8VXF3;B7Z5Q9;F8VVS4;F8W1E3;F8W130;Q12815-3;Q12815-2;Q12815 F8VXV6 TROAP Tastin 1 0 GVS(0.771)PT(0.228)PS(0.001)KIPVR 83.045 0.015585 11884000 2607.4 2290.2 2036.2 2698.8 2381.3 2677.2 2049.7 2322.8 2481.2 1819.2 TRUE FALSE FALSE 2575.620006 2322.441496 2071.639207 3010.847954 2259.773375 2506.13556 2223.801467 2390.006553 2259.275258 1771.936922 1.453561904 1.310679555 1.169138236 1.699184614 1.275312539 1.414348067 1.255011643 1.348810177 1.275031425 1 10.79111153 -12.36377036 0.925850142 0.984292128 1.370196595 0.170684391 0.158999548 0.397852054 0.569635495 0.109281998 0.024142962 4.33E-13 12.36377036 0.385904467 GVS(ph)QEKEAQISSAIVSSVQSK ddPTM_HeLa_Romidepsin_16h_R1 1 GVSQEKEAQISSAIVSSVQSK 21 1 Q12872;Q12872-2 Q12872 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 0 GVS(0.497)QEKEAQIS(0.386)S(0.116)AIVS(0.001)SVQSK 64.733 0.0040921 22050000 2427.8 2526 1917.4 2429 2787.7 2381.9 2494.6 2691 2468.4 2441.9 TRUE FALSE FALSE 2398.20904 2561.561094 1950.771543 2709.852409 2645.433267 2229.704277 2706.491262 2768.859839 2247.620122 2378.459086 1.008303676 1.076983459 0.82018293 1.139331101 1.112246699 0.937457487 1.137917939 1.164140201 0.944990029 1 11.21581149 -4 0.506427118 1.002950857 6.77967336 0.2680051 0.090373638 95.00781997 0.897121366 0.016000362 589.2308267 1.00E-04 4 5.776722504 GVSMSLPS(ph)SPLLPR ddPTM_HeLa_Romidepsin_16h_R1 1 GVSMSLPSSPLLPR 14 0 Q9C0D5-2;Q9C0D5 Q9C0D5-2 TANC1 Protein TANC1 1 0 GVSMS(0.128)LPS(0.436)S(0.436)PLLPR 99.732 0.014287 76889000 2524 2978.7 2684.5 2556.2 2641.1 2494.9 2116.5 2532.8 2886.4 2638.6 TRUE FALSE FALSE 2493.236517 3020.634217 2731.222596 2851.759871 2506.314812 2335.483942 2296.275457 2606.082572 2628.233155 2570.048792 0.970112523 1.17532174 1.062712352 1.109613125 0.975201257 0.908731363 0.893475433 1.01402066 1.0226394 1 11.32758003 -8.52359091 24.99983441 1.016556311 0.935507525 0.295171513 0.068638564 30.38578403 1066672.144 0.011162729 0.022483674 3.00E-09 8.52359091 -0.081048785 GVSNDTSS(ph)LETER ddPTM_HeLa_Romidepsin_16h_R1 1 GVSNDTSSLETER 13 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;Q96KQ7-2;A0A0G2JRR0 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 0 GVS(0.004)NDT(0.072)S(0.224)S(0.701)LETER 98.676 0.013808 5218100 1678.3 1530.9 1577.4 1440.5 1211.3 1336.2 1067.1 986.5 1877.8 2045.6 TRUE FALSE FALSE 1657.844234 1552.45205 1604.853985 1607.057388 1149.482841 1250.821132 1157.739447 1015.042821 1709.844865 1992.455017 0.83206106 0.77916542 0.805465605 0.806571478 0.576917838 0.627778857 0.581061774 0.509443281 0.858159833 1 10.96033144 -7.174729392 0.164615605 1.073365959 7.54E-21 0.834495683 0.060044661 3.908779403 0.108901328 0.106718841 0.911595296 6.69E-08 7.174729392 -1.073365959 GVSNESVPDS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 GVSNESVPDSPAR 13 0 Q86XJ1;G3V1N3 Q86XJ1 GAS2L3 GAS2-like protein 3 1 0 GVSNESVPDS(1)PAR;GVSNESVPDS(1)PAR ; 177.39 8.45E-07 12338300 3924 4086.4 4131.7 3346.18 5851.3 6646.2 6014.6 5871.2 4828.4 4886.7 TRUE FALSE FALSE 3876.172779 4143.928446 4203.610505 3733.081076 5552.686327 6221.52927 6525.479974 6041.073909 4396.535811 4759.74283 0.81436601 0.87062024 0.883159166 0.784303104 1.166593769 1.307114584 1.370973224 1.269201746 0.923691882 1 12.21666791 -8.57428911 3.998091687 0.896762912 1.313121228 0.910054649 0.062489867 0.060567114 2.022183244 0.012297194 0.026058907 2.67E-09 8.57428911 0.416358315 GVSS(ph)PVETR ddPTM_HeLa_Romidepsin_16h_R1 2 GVSSPVETR 9 0 A8MVZ6;Q96G01-4;Q96G01-3;Q96G01 A8MVZ6 BICD1 Protein bicaudal D homolog 1 1 0 GVS(0.222)S(0.778)PVETR;GVS(0.203)S(0.797)PVETR ; 122.96 0.011885 26046000 9049.6 8244 7538 7711.7 7114.9 5957 5075.2 5339 8760.1 9162.1 TRUE FALSE FALSE 8939.299994 8360.059248 7669.195728 8603.363039 6751.800104 5576.366925 5506.287361 5493.475541 7976.574716 8924.067321 1.00170692 0.936799214 0.859383446 0.964062992 0.756583278 0.624868317 0.617015444 0.615579796 0.893827268 1 13.12348568 -8.608812325 0.880619958 0.996713101 0.574523284 0.865823136 0.055723126 0.120098004 0.166903941 0.007737717 0.031167099 2.46E-09 8.608812325 -0.422189817 GVT(ph)MVSPSTAGGPAQK ddPTM_HeLa_Romidepsin_16h_R1 1 GVTMVSPSTAGGPAQK 16 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 0 GVT(1)MVSPSTAGGPAQK 147.3 2.08E-07 0 1468.7 1511.6 1396.3 1641.6 2014.2 1944.3 1687.4 1586.4 1691 1769 TRUE FALSE FALSE 1450.798919 1532.880344 1420.602016 1831.409516 1911.407858 1820.065505 1830.727714 1632.299981 1539.752725 1723.041125 0.841999009 0.88963654 0.824473656 1.062893676 1.10932225 1.056309962 1.062497979 0.947336635 0.893625058 1 10.75074142 -9.238737083 24.42647783 0.913362483 1.052400669 0.622675338 0.059965307 427.8398683 460333.4204 0.01147237 0.019015176 5.77E-10 9.238737083 0.139038186 GVTDTREPS(ph)PGSHSALPGKK ddPTM_HeLa_Romidepsin_16h_R1 1 GVTDTREPSPGSHSALPGKK 20 2 Q9P209 Q9P209 CEP72 Centrosomal protein of 72 kDa 1 0 GVT(0.023)DT(0.068)REPS(0.819)PGS(0.08)HS(0.01)ALPGKK 50.722 0.023581 16540000 2922.8 2554.3 2224.2 3487.1 3456.2 3524.6 3209.8 3528.1 3038.7 2587 TRUE FALSE FALSE 2887.175789 2590.259502 2262.911268 3890.294909 3279.817217 3299.389435 3482.440332 3630.180007 2766.911061 2519.789367 1.145800449 1.027966677 0.898055725 1.543896867 1.301623564 1.309390967 1.382036283 1.440668039 1.098072362 1 11.29908743 -9.261644247 24.99994804 1.055237318 1.38477211 0.802777337 0.089210991 7.060252943 861574.1307 0.014606668 0.023209498 5.47E-10 9.261644247 0.329534793 GVTFNVTTVDTK ddPTM_HeLa_Romidepsin_16h_R1 2 GVTFNVTTVDTK 12 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 0 ; ; 261.22 1.12E-65 2623700 1157.42 1058.43 1066.98 1161.65 1274.22 999.11 1024.96 993.9 1225.09 1138.52 FALSE FALSE TRUE 1143.31292 1073.330605 1085.550339 1295.965439 1209.191799 935.2700955 1112.020077 1022.656928 1115.514882 1108.941086 1.030995185 0.967887851 0.978907133 1.168651297 1.090402199 0.843390246 1.002776514 0.922192298 1.005927994 1 10.11496701 -8.269650225 24.9981342 1.024825096 0.930785367 0.364912301 0.066515096 573.9913126 1747531.75 0.009584282 0.021764546 5.37E-09 8.269650225 -0.094039729 GVTFNVTTVDTKR ddPTM_HeLa_Romidepsin_16h_R1 2 GVTFNVTTVDTKR 13 1 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 0 ; ; 124.51 0.00097736 2907500 1123.4 1220.28 1070.38 660.65 1237.96 1031.12 914.94 1040.84 1410.01 1232.92 FALSE FALSE TRUE 1109.707569 1237.459134 1089.009515 737.0374615 1174.782282 965.2347598 992.6549808 1070.955063 1283.895174 1200.888561 0.924072062 1.030452928 0.906836446 0.613743428 0.978260865 0.803767137 0.826600413 0.891802202 1.069120996 1 10.22988656 -9.517561296 24.99032994 0.968141561 0.823586523 0.433039459 0.094894774 179.0221715 841348.7551 0.013191379 0.018978809 3.04E-10 9.517561296 -0.144555039 GVTIPYRPKPSSSPVIFAGGQAYTIQGQY(ph)AIPQPDLTK ddPTM_HeLa_Romidepsin_16h_R1 1 GVTIPYRPKPSSSPVIFAGGQAYTIQGQYAIPQPDLTK 38 2 Q15366-8;Q15366-5;F8VRH0;Q15366-7;Q15366-4 Q15366-8 PCBP2 Poly(rC)-binding protein 2 1 0 GVT(0.05)IPY(0.095)RPKPS(0.118)S(0.118)S(0.118)PVIFAGGQAY(0.048)T(0.05)IQGQY(0.405)AIPQPDLTK 46.01 0.0061522 15045000 2527.1 1905.3 2026.3 2263.2 2248 1890 1781.2 1797 2307 1664.4 TRUE FALSE FALSE 2496.298733 1932.122863 2061.566902 2524.881833 2133.276172 1769.2351 1932.495084 1848.99336 2100.656142 1621.158648 1.539823839 1.19181603 1.271662649 1.557455117 1.315895995 1.091339889 1.192045631 1.140538196 1.295774565 1 10.66280957 -8.267413759 24.31937867 1.283620236 1.14638168 0.188819454 0.153614995 698.9683705 2845237.488 0.031245692 0.071702418 5.40E-09 8.267413759 -0.137238556 NETSFLPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 NETSFLPAKK 10 1 F8WAJ0;Q9H8H2-3;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 1 ; NETSFLPAK(1)K;NETSFLPAK(1)K 143.5 0.0020737 3507600 1184.95 1282.72 1634.72 2139.44 3740.7 4541.5 3686.1 3807.1 1479.75 1265.86 FALSE TRUE FALSE 1170.507374 1300.778166 1663.171616 2386.812119 3549.798121 4251.312807 3999.197242 3917.252432 1347.397454 1232.972775 0.949337567 1.054993421 1.348911874 1.935818996 2.87905637 3.448018394 3.243540591 3.177079423 1.092803898 1 10.26792523 -8.940129804 1.448205901 0.981525303 3.320171157 0.98965181 0.101968364 0.024207659 0.101457764 0.015724786 0.035003407 1.15E-09 8.940129804 2.338645853 up GVTQFGNK(ac)YIQQTKPLTLER ddPTM_HeLa_Romidepsin_16h_R1 1 GVTQFGNKYIQQTKPLTLER 20 2 O43809 O43809 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 0 1 GVTQFGNK(1)YIQQTKPLTLER 147.84 2.43E-14 1492600 0 0 0 127.63 54.048 0 0 0 0 67.129 FALSE TRUE FALSE 0 0 0 142.3871811 51.28972888 0 0 0 0 65.3849789 0 0 0 2.177674192 0.784426786 0 0 0 0 1 6.030887334 -12.54824063 1.346576924 0.996359658 0.34549867 0 0.721200666 0.81229362 2.661994725 0.472603794 0.114702295 2.83E-13 12.54824063 -0.650860988 GVVDSDDLPLNVSR ddPTM_HeLa_Romidepsin_16h_R1 3 GVVDSDDLPLNVSR 14 0 P14625 P14625 HSP90B1 Endoplasmin 0 0 ;; ;; 260.57 5.21E-67 39456000 6370.88 5262.538 5656.13 5277 5926.5 5756.69 5394.89 6385.1 6164.18 5964.31 FALSE FALSE TRUE 6293.229264 5336.624148 5754.57257 5887.151569 5624.04859 5388.856088 5853.131822 6569.842794 5612.840302 5809.356366 1.083291998 0.918625715 0.99056973 1.013391363 0.96810184 0.927616718 1.007535337 1.130907175 0.966172489 1 12.50416262 -10.28569673 24.9590651 1.039332328 0.991440701 0 0.062405611 1264.914815 1301502.035 0.010530419 0.012045322 5.18E-11 10.28569673 -0.047891627 GVVDSEDLPLNISR ddPTM_HeLa_Romidepsin_16h_R1 3 GVVDSEDLPLNISR 14 0 P08238;P07900-2;P07900 P08238;P07900-2 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 0 ;; ;; 256.31 1.13E-66 137621400 7244.74 6590.96 6539.05 6489.07 7221.24 7385.2 6506.91 6985.63 7421.05 6769.05 FALSE FALSE TRUE 7156.438322 6683.747708 6652.859422 7239.366805 6852.713177 6913.309555 7059.606773 7187.748183 6757.292702 6593.189105 1.085428949 1.013735174 1.009050297 1.098006851 1.039362449 1.048553203 1.070742346 1.090177768 1.024889866 1 12.68676075 -12.52211571 1.22241055 0.99936729 1.058375764 0.249574335 0.029759835 0.437739286 1.150529361 0.022040128 0.005055145 3.01E-13 12.52211571 0.059008474 GVVEVTHDLQK ddPTM_HeLa_Romidepsin_16h_R1 2 GVVEVTHDLQK 11 0 P50454;E9PKH2 P50454 SERPINH1 Serpin H1 0 0 ; ; 121.29 0.0014869 1832460 2486.51 2314.3 2751.6 2475.3 2530.3 2216.94 1911.51 2228.4 3019.2 2046.13 FALSE FALSE TRUE 2456.20346 2346.880776 2799.490444 2761.505833 2401.169349 2075.284689 2073.873612 2292.875238 2749.15519 1992.971248 1.232432963 1.177578843 1.404681802 1.385622515 1.204818861 1.041301871 1.040593844 1.150480842 1.379425415 1 10.96070518 -5.985782743 17.75824904 1.150837138 1.165594217 0 0.151328926 0 0 0.021013139 0 1.03E-06 5.985782743 0.014757078 GVVIPTWNIS(ph)PIKK ddPTM_HeLa_Romidepsin_16h_R1 2 GVVIPTWNISPIKK 14 1 A0A087WUE6;Q3T8J9-2;Q3T8J9-3;Q3T8J9;A4PB68 A0A087WUE6 GON4L GON-4-like protein 1 0 GVVIPTWNIS(1)PIKK;GVVIPT(0.03)WNIS(0.97)PIKK ; 83.252 0.0089185 35135000 7823.3 7633.8 7828.2 7218.4 8043.5 8504.5 7396.5 7240.9 8493.9 8261.6 TRUE FALSE FALSE 7727.94661 7741.268837 7964.446537 8053.025372 7633.010181 7961.089897 8024.758525 7450.404017 7734.184311 8046.962441 0.960355745 0.962011305 0.989745708 1.000753443 0.948557948 0.989328577 0.997240708 0.92586539 0.961130907 1 12.97422858 -9.308791785 0.003201514 1.947520214 3.67E-06 0.011073743 0.024097679 36367.44798 48.30271099 14576.17734 14806.1817 4.91E-10 9.308791785 -1.947516542 GVVPLAGTDGETTTQGLDGLSER ddPTM_HeLa_Romidepsin_16h_R1 3 GVVPLAGTDGETTTQGLDGLSER 23 0 K7EKH5;C9J8F3;J3KSV6;J3QKP5;A8MVZ9;P09972 K7EKH5 ALDOC Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase C 0 0 ;; ;; 310.93 1.34E-170 39860700 6291 6293.3 5384.7 5899.4 6745.6 6948.6 5924 6016.6 6941.9 6094.8 FALSE FALSE TRUE 6214.322872 6381.897243 5478.418445 6581.516386 6401.346861 6504.606886 6427.184412 6190.680828 6320.999078 5936.456217 1.046806823 1.075034837 0.922843232 1.108660815 1.078311138 1.095705358 1.082663491 1.042824305 1.064776501 1 12.53538625 GVVPLAGTNGETTTQGLDGLSER ddPTM_HeLa_Romidepsin_16h_R1 2 GVVPLAGTNGETTTQGLDGLSER 23 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8;H3BU78 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ; ; 169.15 3.17E-11 16919100 4432.8 4254.2 3983 3718.4 4455.8 4362.5 4154 4480.7 4710.9 4849.6 FALSE FALSE TRUE 4378.771329 4314.090739 4052.322444 4148.338904 4228.403899 4083.750329 4506.840656 4610.341985 4289.545305 4723.606693 0.926997444 0.913304392 0.857887353 0.878214291 0.895164262 0.86454072 0.954110058 0.976021563 0.908108059 1 12.20567313 -11.50803367 0.745856503 0.995338131 0.903739569 0.020460576 0.044446877 0.402468794 0.462663731 0.018191644 0.008649175 3.10E-12 11.50803367 -0.091598562 GVVVLAK(ac)SYNEQR ddPTM_HeLa_Romidepsin_16h_R1 2 GVVVLAKSYNEQR 13 1 S4R3Z2;A0A0A0MSS8;P42330;P17516;P42330-2;P52895;H0Y804;B4DK69 S4R3Z2;P52895 AKR1C3;AKR1C4;AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C3;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C2 0 1 ; GVVVLAK(1)SYNEQR;GVVVLAK(1)SYNEQR 234.3 9.08E-41 3069600 775.86 783.01 813.86 771.91 812.14 840.05 596.68 702.09 852.79 865.31 FALSE TRUE FALSE 766.4035199 794.0332353 828.0248919 861.1618661 770.6934653 786.3735161 647.3619843 722.4038664 776.5143265 842.8291215 0.909322543 0.942104651 0.982435076 1.021751437 0.914412478 0.933016546 0.768082127 0.857117829 0.921318814 1 9.719096353 -7.870259663 5.235612437 0.958292227 0.813606085 0.658730264 0.040576156 0.094636301 3.943063052 0.006354048 0.020025574 1.35E-08 7.870259663 -0.144686142 GVVVVIKR ddPTM_HeLa_Romidepsin_16h_R1 1 GVVVVIKR 8 1 H0YMF4;H0YKD8;P46779-4;P46779-5;P46779;P46779-2;P46779-3 H0YMF4 RPL28 60S ribosomal protein L28 0 0 110.34 0.010909 0 1211.4 1351.9 1211.6 1914.8 1499.7 1560.9 1521.4 1548.8 1328.2 1682.7 FALSE FALSE TRUE 1196.634991 1370.932084 1232.68739 2136.198185 1423.164713 1461.163528 1650.627678 1593.612084 1209.402465 1638.983211 0.730108144 0.836452792 0.752104952 1.303367948 0.868321715 0.891506098 1.007104689 0.972317516 0.737898019 1 10.67858536 GWAFGSNS(ph)LPIAGSVGMGVAR ddPTM_HeLa_Romidepsin_16h_R1 1 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 0 GWAFGS(0.04)NS(0.78)LPIAGS(0.181)VGMGVAR 72.676 0.0077252 23225000 3280.9 3244.5 3236.4 4218.7 6062.1 5516.6 4857 5389.4 2997.3 2964.6 TRUE FALSE FALSE 3240.911129 3290.176156 3292.728184 4706.485944 5752.728416 5164.107064 5269.553459 5545.333786 2729.213981 2887.579265 1.122362655 1.139423668 1.140307463 1.629907099 1.992232209 1.788386254 1.824903483 1.9204092 0.945156386 1 11.49564483 -9.178129046 2.532373763 1.066540387 1.871481184 0.962539529 0.07644018 0.03651798 0.457843855 0.011563953 0.020254135 6.64E-10 9.178129046 0.804940797 GWAFGSNSLPIAGS(ph)VGMGVAR ddPTM_HeLa_Romidepsin_16h_R1 1 GWAFGSNSLPIAGSVGMGVAR 21 0 M0QZ22;Q5PRF9;A0A087WZT0 M0QZ22 SAMD4B Protein Smaug homolog 2 1 0 GWAFGSNS(0.007)LPIAGS(0.993)VGMGVAR 145.81 3.10E-05 23682000 1024.1 1041.3 1207 1145.1 1862.6 2098.5 1333.1 1678.3 1194.4 898.82 TRUE FALSE FALSE 1011.617875 1055.959449 1228.007329 1277.50185 1767.544572 1964.412623 1446.333481 1726.858963 1087.569873 875.4685268 1.155515983 1.206164946 1.402685866 1.459220761 2.018969863 2.243841512 1.652067934 1.972496908 1.242271811 1 9.773911504 -9.219716529 1.18259538 1.075201908 1.975682719 0.814899164 0.171505946 0.122395757 0.337665416 0.02852062 0.058175506 6.03E-10 9.219716529 0.900480811 GWDAEGS(ph)PFR ddPTM_HeLa_Romidepsin_16h_R1 1 GWDAEGSPFR 10 0 Q8IVD9 Q8IVD9 NUDCD3 NudC domain-containing protein 3 1 0 GWDAEGS(1)PFR 104.07 0.021881 3249000 2659.2 2706.5 2483.9 2280.6 3540.7 3266 2818.8 2840.9 2834.9 2711.1 TRUE FALSE FALSE 2626.788648 2744.602178 2527.131238 2544.293703 3360.004867 3057.313141 3058.228802 2923.096959 2581.339444 2640.665231 0.994745042 1.039360138 0.957005533 0.963504829 1.272408493 1.15778142 1.158128174 1.106954765 0.977533772 1 11.3666857 -8.775801233 24.99999996 0.995445571 1.171552019 0.807937166 0.044139676 71.26627158 124054.7255 0.006174434 0.01122934 1.68E-09 8.775801233 0.176106448 GWDS(ph)SHEDDLPVYLAR ddPTM_HeLa_Romidepsin_16h_R1 1 GWDSSHEDDLPVYLAR 16 0 Q14195-2 Q14195-2 1 0 GWDS(0.591)S(0.409)HEDDLPVYLAR 139.12 0.00037047 3551800 1833.8 1676.7 1691.7 924.69 1985.4 1847.6 1423.1 1586.2 1642 2038.9 TRUE FALSE FALSE 1811.44894 1700.304627 1721.143329 1031.607009 1884.077629 1729.544323 1543.978078 1632.094194 1495.135408 1985.929084 0.912141805 0.856175903 0.866669078 0.51945813 0.948713448 0.870899337 0.777458818 0.821829041 0.75286445 1 10.95559839 -10.46733671 1.026906531 0.975127651 0.798837261 0 0.127360428 0.389257189 0.826786326 0.023939553 0.025652258 3.41E-11 10.46733671 -0.176290391 GWDSS(ph)HEDDLPVYLAR ddPTM_HeLa_Romidepsin_16h_R1 3 GWDSSHEDDLPVYLAR 16 0 Q14195-2 Q14195-2 1 0 GWDS(0.413)S(0.587)HEDDLPVYLAR;GWDS(0.193)S(0.807)HEDDLPVYLAR;GWDS(0.391)S(0.609)HEDDLPVYLAR ;; 132.4 0.00074657 10408700 5405.3 5585 6713.9 3137.58 6063.2 6453.1 4868.2 5350.9 6309.3 6143.9 TRUE FALSE FALSE 5339.418125 5663.625777 6830.752613 3500.361762 5753.772279 6040.767736 5281.704786 5505.719849 5744.980406 5984.280592 0.892240603 0.946417149 1.141449253 0.584926076 0.961481032 1.009439254 0.882596447 0.920030364 0.960011871 1 12.54696211 GWLRDPSAS(ph)PGDAGEQAIR ddPTM_HeLa_Romidepsin_16h_R1 2 GWLRDPSASPGDAGEQAIR 19 1 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 GWLRDPS(0.002)AS(0.998)PGDAGEQAIR;GWLRDPS(0.028)AS(0.972)PGDAGEQAIR ; 121.65 0.00032064 22240000 3535.9 3047 3045 1919.25 3358 3508.2 3009.8 3339.7 3498.6 3239.3 TRUE FALSE FALSE 3492.803091 3089.895746 3097.996948 2141.162715 3186.62873 3284.037342 3265.452337 3436.32895 3185.676454 3155.142519 1.107019119 0.979320499 0.981888117 0.678626307 1.009979331 1.040852298 1.034961913 1.089120041 1.009677514 1 11.62348946 -10.10935675 7.247791927 1.050474697 0.96796243 0.067215559 0.108431737 0.475676568 28.13328374 0.019063257 0.023395411 7.77E-11 10.10935675 -0.082512267 GWS(ph)QEGPVK ddPTM_HeLa_Romidepsin_16h_R1 1 GWSQEGPVK 9 0 Q9C0C2;E9PKK0 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 GWS(1)QEGPVK 113.61 0.017087 15007000 3790.8 5085.6 2233.3 2689.7 3922.1 3323 2895.5 3932.5 3651 3555.7 TRUE FALSE FALSE 3744.596272 5157.19521 2272.16965 3000.695769 3721.940602 3110.671024 3141.443698 4046.280683 3324.445416 3463.322401 1.081215041 1.489088977 0.656066455 0.866421148 1.074673441 0.898175412 0.907060716 1.168323423 0.959900648 1 11.75794098 GWSGPKPGFPEPTNNT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 GWSGPKPGFPEPTNNTPK 18 1 E5RJ67;H0YBY0;E5RJN7;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3 E5RJ67 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 0 GWSGPKPGFPEPT(0.212)NNT(0.788)PK 62.589 0.022176 15770000 2775.6 2559.4 2407.5 3181.3 3696.1 3735.9 2889.2 3300.9 2409.3 2370.1 TRUE FALSE FALSE 2741.76992 2595.4313 2449.401528 3549.136874 3507.474225 3497.188047 3134.608576 3396.406334 2193.806174 2308.52446 1.187672025 1.124281482 1.061024724 1.537404925 1.519357618 1.514901881 1.357840746 1.471245547 0.950306662 1 11.1727553 -9.264035508 24.99968234 1.092234007 1.477464029 0.875445704 0.078011508 66.06297229 636160.0323 0.013047312 0.020505386 5.44E-10 9.264035508 0.385230022 GWTIIMY(ph)AAVDS(ph)VNVDK ddPTM_HeLa_Romidepsin_16h_R1 1 GWTIIMYAAVDSVNVDK 17 0 A0A2R8YDP4;Q15858-4;Q15858-3;Q15858-2;Q15858 A0A2R8YDP4 SCN9A Sodium channel protein type 9 subunit alpha 2 0 GWT(0.007)IIMY(0.999)AAVDS(0.994)VNVDK 63.894 0.00392 0 798.25 690.7 599.06 746.03 641.67 776.39 622.84 443.78 809.3 878.77 TRUE FALSE FALSE 788.520622 700.4236927 609.486388 832.2894988 608.9231855 726.7811847 675.7440141 456.6200741 736.9141811 855.9394287 0.921234138 0.818309882 0.712067195 0.972369622 0.711409201 0.849103523 0.789476441 0.533472415 0.860941974 1 9.741364896 -5.39055524 0.150268185 1.055375102 3.75E-17 0.400215088 0.102381511 23.24567569 0.332357124 0.218144487 5.01807446 4.07E-06 5.39055524 -1.055375102 GY(ph)RHDS(ph)S(ph)TAVAGSPRGHGQSRET(ph)T(ph)QER ddPTM_HeLa_Romidepsin_16h_R1 1 GYRHDSSTAVAGSPRGHGQSRETTQER 27 3 Q9H1I8-3;Q9H1I8 Q9H1I8-3 ASCC2 Activating signal cointegrator 1 complex subunit 2 5 0 GY(0.942)RHDS(0.662)S(0.663)T(0.662)AVAGS(0.049)PRGHGQS(0.048)RET(0.987)T(0.987)QER 40.937 0.0041388 0 542.28 589.85 770.87 197.5 556.05 612.35 627.76 626.39 803.37 895.92 TRUE FALSE FALSE 535.6704828 598.1539238 784.286669 220.3358793 527.6726936 573.2228113 681.0819187 644.5136064 731.5145751 872.6438692 0.613847758 0.68545021 0.898747698 0.252492325 0.604682749 0.65688058 0.780480953 0.738575757 0.838273895 1 9.769249192 -12.2979386 0.720139043 1.035441921 0.646788287 0.270883596 0.165341675 0.714319863 0.567858321 0.171205713 0.032662282 5.04E-13 12.2979386 -0.388653634 GY(ph)RVIFWSLYVDGEWGEMQNIT(ph)T(ph)TRER ddPTM_HeLa_Romidepsin_16h_R1 1 GYRVIFWSLYVDGEWGEMQNITTTRER 27 2 A0A384DVL8;Q8TD84-2;Q8TD84 A0A384DVL8 DSCAML1 Down syndrome cell adhesion molecule-like protein 1 3 0 GY(0.91)RVIFWS(0.048)LY(0.042)VDGEWGEMQNIT(0.859)T(0.571)T(0.571)RER 47.546 0.0039049 0 738.7 828.86 817.68 1063.4 904.5 866.36 734.86 678.07 975.2 912.69 TRUE FALSE FALSE 729.6964403 840.5287128 831.9113774 1186.355311 858.3399898 811.002392 797.2789901 697.6888856 887.9756696 888.9781822 0.820826039 0.945499822 0.935806293 1.334515667 0.965535496 0.912286047 0.896848771 0.784821157 0.998872287 1 9.796004202 -7.327086349 1.801079527 0.951080518 0.746511677 0.151455236 0.130441145 1.380192753 4.956042386 0.020644094 0.456063961 4.71E-08 7.327086349 -0.20456884 GY(ph)VRVQWY(ph)PEGVK ddPTM_HeLa_Romidepsin_16h_R1 1 GYVRVQWYPEGVK 13 1 Q9C0C9 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 2 0 GY(1)VRVQWY(1)PEGVK 68.44 0.019902 3283900 796.48 989.39 727.04 597.53 999.33 947.76 781.14 1028 1146.2 1072.1 TRUE FALSE FALSE 786.7721954 1003.318658 739.6938262 666.6192301 948.3304611 887.2011948 847.4900121 1057.743558 1043.681001 1044.246687 0.753435184 0.960806168 0.708351614 0.638373325 0.908147924 0.849608819 0.811580273 1.012924983 0.999458283 1 10.02824685 -12.45549926 1.122033734 1.002634631 0.819750311 0.278450518 0.10766696 0.542594501 1.193110564 0.079387569 0.018541173 3.50E-13 12.45549926 -0.18288432 GY(ph)YSPYS(ph)VSGSGSTAGSR ddPTM_HeLa_Romidepsin_16h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GY(0.718)Y(0.196)S(0.166)PYS(0.883)VS(0.016)GS(0.014)GS(0.006)TAGSR 176.17 1.52E-08 45718000 4284.5 3987 3673.3 4240.7 4976.3 6311.8 6101.5 6627.4 5210.8 4209.7 TRUE FALSE FALSE 4232.278866 4043.129091 3737.232246 4731.029687 4722.340842 5908.49635 6619.761258 6819.153363 4744.732997 4100.331387 1.032179711 0.986049348 0.911446391 1.153816421 1.151697362 1.440980202 1.614445427 1.663073717 1.157158422 1 12.0015248 -8.175021733 1.233687703 1.007882863 1.691608835 0.929874005 0.067334862 0.063299831 0.167404356 0.007252807 0.035679998 6.68E-09 8.175021733 0.683725973 GYADS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 GYADSPSK 8 0 Q01518-2;Q01518;Q5T0R8;Q5T0S3;Q5T0R7;Q5T0R6;Q5T0R5;Q5T0R4;Q5T0R3;Q5T0R2;Q5T0R1;Q5T0R9 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 1 0 GYADS(0.996)PS(0.003)K;GYADS(0.98)PS(0.02)K ; 110.53 0.022257 84514000 10541.3 13677.7 25816 8393.7 10732.6 12793.5 28496 3143.8 19246.9 14886.5 TRUE FALSE FALSE 10412.81858 13870.25502 26265.31665 9364.219088 10184.87537 11976.03664 30916.44953 3234.760893 17525.40906 14499.74658 0.71813797 0.95658603 1.811432807 0.6458195 0.702417474 0.825947996 2.132206198 0.223090857 1.208670025 1 13.82374007 -9.993738748 24.97421662 0.865343893 1.087381349 0 0.541489027 473.7450638 1889611.253 0.080755585 0.105979335 1.01E-10 9.993738748 0.222037456 GYAFIEFASFEDAK ddPTM_HeLa_Romidepsin_16h_R1 1 GYAFIEFASFEDAK 14 0 P19338;H7BY16 P19338 NCL Nucleolin 0 0 186.81 2.09E-07 21333000 861.53 681.78 576.41 742.83 780.31 738 648.16 573.91 729.14 752.15 FALSE FALSE TRUE 851.029341 691.3781167 586.4421743 828.7194997 740.487869 690.8441818 703.2146942 590.5151804 663.9238922 732.6090346 1.161641886 0.943720435 0.800484497 1.131189298 1.010754487 0.942991622 0.95987718 0.806044087 0.906245843 1 9.516899682 -10.23377816 23.45506568 1.07633089 0.947326197 0.03769229 0.110260839 356.0596592 301917.6277 0.01746294 0.021384021 5.84E-11 10.23377816 -0.129004693 GYAFIEYEHER ddPTM_HeLa_Romidepsin_16h_R1 2 GYAFIEYEHER 11 0 P08621;P08621-2;M0QYR1;P08621-3 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 0 ; ; 187.16 8.75E-08 54818000 9146 7567.3 10806.7 8224.3 11564 11558 9668.7 8468.9 8294.8 6963.7 FALSE FALSE TRUE 9034.525034 7673.832648 10994.78608 9175.232262 10973.84593 10819.4811 10489.95914 8713.93426 7552.892313 6782.78207 1.331979259 1.131369484 1.620984718 1.352724025 1.617897467 1.595139132 1.546557007 1.284713878 1.113538993 1 12.72766142 -11.25488779 0.361926722 0.944272271 1.533911266 0.56526525 0.143524629 0.699739481 0.214433798 0.168266863 0.074661525 5.56E-12 11.25488779 0.589638995 GYAFNHSADFETVR ddPTM_HeLa_Romidepsin_16h_R1 1 GYAFNHSADFETVR 14 0 P61160;F5H6T1;P61160-2 P61160 ACTR2 Actin-related protein 2 0 0 67.234 0.02986 6531300 1280.4 1001.5 1386.5 1641.2 1782.4 1816.9 1607.4 1246.5 1542.4 1204.2 FALSE FALSE TRUE 1264.793992 1015.599143 1410.631451 1830.963266 1691.437477 1700.805954 1743.932516 1282.565511 1404.443881 1172.91471 1.078334154 0.86587638 1.202671804 1.561037005 1.442080538 1.450067885 1.486836596 1.093485741 1.197396425 1 10.19588239 -9.50860074 6.094135078 1.025145533 1.413516772 0.617058984 0.137997091 0.067789446 9.820085233 0.018795971 0.027884374 3.10E-10 9.50860074 0.388371239 GYALVPIIVNSS(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 1 GYALVPIIVNSSTPK 15 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 GYALVPIIVNS(0.136)S(0.432)T(0.432)PK 94.781 0.012028 19784000 4018.2 3625.5 3500.9 3692.4 5481.1 5793.8 5076.3 4989.5 4198.4 4045 TRUE FALSE FALSE 3969.224633 3676.539884 3561.831696 4119.332661 5201.379014 5423.594879 5507.480795 5133.86331 3822.884589 3939.910317 1.007440351 0.933153191 0.904038775 1.045539703 1.320177008 1.376578257 1.397869584 1.303040653 0.970297362 1 11.94394708 -8.77222911 3.686421696 0.989784019 1.361325482 0.953163049 0.040653073 0.035694744 1.040946883 0.006396256 0.01265174 1.69E-09 8.77222911 0.371541463 GYAYVEFENPDEAEK ddPTM_HeLa_Romidepsin_16h_R1 1 GYAYVEFENPDEAEK 15 0 H3BMS0;Q15287-3;Q15287-2;H3BPG5;H3BV80;H3BMM9;H3BTC0;Q15287 H3BMS0 RNPS1 RNA-binding protein with serine-rich domain 1 0 0 190.34 2.28E-11 6319600 1630.4 1680.7 1481.2 1595.7 1489.6 1492.5 1409.2 1520.8 1457.9 1229 FALSE FALSE TRUE 1610.528058 1704.360939 1506.979665 1780.202342 1413.580154 1397.134067 1528.897413 1564.801949 1327.501773 1197.070403 1.34539126 1.423776692 1.258889754 1.487132534 1.180866347 1.167127734 1.277199243 1.307192914 1.108958813 1 10.22529229 -12.22084376 0.9356267 0.998182559 1.30516882 0.501119791 0.09821069 0.321561791 0.501448742 0.06672229 0.018167675 6.01E-13 12.22084376 0.306986262 GYDDRDYYSR ddPTM_HeLa_Romidepsin_16h_R1 3 GYDDRDYYSR 10 1 P62995;H7C2L4;P62995-3;H7BXF3 P62995 TRA2B Transformer-2 protein homolog beta 0 0 ;; ;; 118.03 0.014864 441298000 20417.9 20539 18911.6 9092.5 20097 20414.4 18787.1 19353.7 21411.1 19395.5 FALSE FALSE TRUE 20169.03878 20828.14858 19240.74846 10143.81763 19071.3751 19109.98572 20382.87581 19913.66877 19496.03759 18891.60211 1.067619287 1.102508324 1.018481564 0.536948511 1.009516026 1.011559825 1.078938445 1.05410164 1.031994929 1 14.20545744 -9.498946017 24.98888174 1.039182465 0.936431917 0.118313827 0.145303991 1434.148465 1497439.884 0.022865717 0.034801624 3.17E-10 9.498946017 -0.102750548 GYDRYEDYDYR ddPTM_HeLa_Romidepsin_16h_R1 1 GYDRYEDYDYR 11 1 Q13595;Q13595-4;Q13595-3 Q13595 TRA2A Transformer-2 protein homolog alpha 0 0 112.71 0.0028428 0 1267 1277.5 1153.4 1297.8 1271.1 1407.7 1132.3 1509.4 1429.8 1155.2 FALSE FALSE TRUE 1251.557317 1295.484679 1173.474443 1447.857742 1206.231024 1317.752513 1228.477534 1553.072108 1301.915107 1125.187737 1.112309773 1.151349802 1.042914355 1.286769927 1.072026457 1.17114013 1.091797833 1.380278202 1.157064785 1 10.13595002 -4.000000115 0.046289497 0.640791107 2.021218483 0.170236487 0.098517722 349.4364339 1.238002749 9.321430363 35.73250719 1.00E-04 4.000000115 1.380427376 GYEEWLLNEIR ddPTM_HeLa_Romidepsin_16h_R1 4 GYEEWLLNEIR 11 0 O43707;O43707-2;P35609-2;P35609;A0A494C1A0;F6THM6;A0A494C060;P12814-2;P12814;P12814-3;P12814-4;H9KV75 O43707;P12814-2 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-2;Alpha-actinin-1 0 0 ;;; ;;; 215.72 2.04E-18 112615000 9200.5 7253.8 10278.3 5555.81 11897.4 11443.7 8127.7 8790.6 8149.4 7367.9 FALSE FALSE TRUE 9088.360767 7355.919187 10457.1895 6198.198893 11290.23128 10712.4845 8818.066635 9044.942142 7420.497253 7176.480896 1.266409108 1.02500366 1.457147264 0.863682212 1.57322669 1.492721106 1.228745225 1.26035898 1.034002231 1 12.80906085 -16.45241537 0.141603308 2.07E-11 1.392121765 0.238436602 0.196541048 74.96505038 0.74997367 20.99993658 0.53296455 3.53E-17 16.45241537 1.392121765 GYEEWLLNEIRR ddPTM_HeLa_Romidepsin_16h_R1 1 GYEEWLLNEIRR 12 1 O43707;O43707-2;P35609-2;P35609;A0A494C1A0;F6THM6;A0A494C060;P12814-2;P12814;P12814-3;P12814-4;H9KV75 O43707;P12814-2 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-2;Alpha-actinin-1 0 0 84.605 0.025039 29597000 4416.7 3699.8 4277.5 3844.4 4941.8 4156.6 4114.6 4321 4181.3 2975.9 FALSE FALSE TRUE 4362.867562 3751.885882 4351.948093 4288.907616 4689.601506 3891.006675 4464.094021 4446.021318 3807.314056 2898.585689 1.505171152 1.294385015 1.501403981 1.479655279 1.617893003 1.34238111 1.54009386 1.533858852 1.313507505 1 11.50113342 -12.60876526 0.473210725 0.816007899 1.497889242 0.405464014 0.131988673 0.697815582 0.170088318 0.23607249 0.022927054 2.46E-13 12.60876526 0.681881343 GYEK(ac)GQPDEELKPK ddPTM_HeLa_Romidepsin_16h_R1 2 GYEKGQPDEELKPK 14 2 P54577 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed" 0 1 ; GYEK(1)GQPDEELKPK;GYEK(1)GQPDEELKPK 110.44 0.0046218 2313900 1475.5 1128.48 1345.14 1262.76 1450.47 1539.98 1420.62 1506.26 1479.58 1352.67 FALSE TRUE FALSE 1457.516038 1144.366771 1368.551597 1408.766253 1376.447103 1441.580248 1541.287427 1549.841257 1347.242659 1317.527438 1.106250994 0.868571491 1.038727208 1.06925003 1.044719877 1.094155769 1.169833267 1.176325602 1.022553778 1 10.36361729 -7.924776751 1.618406612 1.036468322 1.185922199 0.498702332 0.059789325 0.336482545 1.579669765 0.009789645 0.052883943 1.19E-08 7.924776751 0.149453877 GYFEYIEENK ddPTM_HeLa_Romidepsin_16h_R1 1 GYFEYIEENK 10 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1W2PP35;Q5RI18;A0A1W2PRI6 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 192.92 4.60E-07 4241200 1551.6 1545.4 1531.1 902.05 1571.1 1432.4 1207.3 1080.3 1508.7 1742 FALSE FALSE TRUE 1532.688502 1567.156182 1557.748153 1006.349265 1490.920904 1340.874263 1309.848032 1111.556776 1373.758093 1696.742589 0.903312331 0.92362636 0.918081601 0.593106622 0.878695987 0.79026381 0.771978048 0.655112203 0.809644375 1 10.728552 -7.985636912 0.173622975 1.053956659 0.468238815 0.270618071 0.102811043 7.203619635 0.295924611 0.188591123 0.992734277 1.03E-08 7.985636912 -0.585717845 GYFEYIEENKYSR ddPTM_HeLa_Romidepsin_16h_R1 2 GYFEYIEENKYSR 13 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1W2PP35;Q5RI18;A0A1W2PRI6 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 229.56 4.71E-32 191912000 6545.4 5968.3 5258.1 4856.6 5158 4909.1 4743.7 4927.5 6821.3 5606.1 FALSE FALSE TRUE 6465.622147 6052.321884 5349.615025 5418.142943 4894.768013 4595.424353 5146.62976 5070.069438 6211.185844 5460.452714 1.184081703 1.10839196 0.97970174 0.9922516 0.896403333 0.841583032 0.942528034 0.928507159 1.137485511 1 12.41480485 -9.323871529 1.66266455 1.089841627 0.904878527 0.709874253 0.056296762 0.213222118 1.153578426 0.012670335 0.022300304 4.74E-10 9.323871529 -0.1849631 GYGFVDFDS(ph)PAAAQK ddPTM_HeLa_Romidepsin_16h_R1 4 GYGFVDFDSPAAAQK 15 0 E7EPF2;C9J9B2;E7ETU5;F6Y5H0;C9JIJ9;A0A1B0GUW5;P29558-2;P29558;Q6XE24-3;Q6XE24-4;Q6XE24-5;Q6XE24-2;Q6XE24 E7EPF2 RBMS1;RBMS3 "RNA-binding motif, single-stranded-interacting protein 1;RNA-binding motif, single-stranded-interacting protein 3" 1 0 GYGFVDFDS(1)PAAAQK;GYGFVDFDS(1)PAAAQK;GYGFVDFDS(1)PAAAQK;GYGFVDFDS(1)PAAAQK ;;; 212.43 1.40E-25 63462000 14092.2 13519.2 13398.1 11798.6 13337.2 13843.6 11880.1 13171.3 15342.9 14744.1 TRUE FALSE FALSE 13920.43885 13709.52365 13631.28831 13162.80965 12656.55292 12959.03864 12889.1954 13552.39078 13970.5926 14361.04616 0.969319275 0.954632657 0.94918491 0.916563425 0.881311346 0.902374277 0.897510896 0.943691054 0.972811621 1 13.80987323 -9.883904395 0.766709296 0.990868652 0.90353899 0.757120925 0.017801311 0.181920885 0.216488744 0.004079219 0.00620251 1.31E-10 9.883904395 -0.087329662 GYGFVDFDS(ph)PSAAQK ddPTM_HeLa_Romidepsin_16h_R1 2 GYGFVDFDSPSAAQK 15 0 F8W1T6;Q15434 F8W1T6 RBMS2 "RNA-binding motif, single-stranded-interacting protein 2" 1 0 GYGFVDFDS(0.913)PS(0.087)AAQK;GYGFVDFDS(0.949)PS(0.051)AAQK ; 212.03 1.47E-25 96408000 11809.4 11293.3 11736.5 10985.9 12368.9 12036.9 11352.5 11699.7 12070.5 11570.8 TRUE FALSE FALSE 11665.46249 11452.28737 11940.76886 12256.14145 11737.66888 11267.78094 12316.78107 12038.21236 10990.88425 11270.18895 1.035072486 1.016157531 1.059500326 1.087483227 1.041479334 0.999786338 1.09286376 1.068146454 0.97521739 1 13.46022408 -16.52287875 0.068944151 0.801773586 1.123168729 0.481050129 0.027118868 173.9939559 0.932957839 5.51046505 0.816269223 3.00E-17 16.52287875 0.321395143 GYGFVHFETQEAAER ddPTM_HeLa_Romidepsin_16h_R1 2 GYGFVHFETQEAAER 15 0 A0A087WTT1;E7EQV3;P11940-2;P11940;H0YAR2;E7ERJ7;E5RGH3;H0YBN4 A0A087WTT1 PABPC1 Polyadenylate-binding protein;Polyadenylate-binding protein 1 0 0 ; ; 132.51 0.00076235 33936000 11608.5 10584.5 10641.9 9490 11648.9 11022 10452.5 10560.6 12416.9 10948.8 FALSE FALSE TRUE 11467.01114 10733.50887 10827.11781 10587.27845 11054.41316 10317.72977 11340.33509 10866.1543 11306.30137 10664.3486 1.07526597 1.006485185 1.01526293 0.992773103 1.036576502 0.967497422 1.063387509 1.018923397 1.060196154 1 13.38050822 GYGYGQGAGTLS(ph)TDKGESLGIK ddPTM_HeLa_Romidepsin_16h_R1 1 GYGYGQGAGTLSTDKGESLGIK 22 1 E9PP21;P21291;E9PS42;E9PND2 E9PP21 CSRP1 Cysteine and glycine-rich protein 1 1 0 GYGYGQGAGT(0.071)LS(0.692)T(0.22)DKGES(0.017)LGIK 65.924 0.0021551 10616000 935.23 878.39 706.24 810.97 872.03 1092 718.01 883.1 878.51 799.48 TRUE FALSE FALSE 923.831057 890.7559975 718.5318109 904.7381671 827.5270551 1022.224724 778.9977515 908.6511052 799.9338653 778.7093943 1.186361772 1.143887571 0.922721385 1.161843139 1.062690474 1.312716569 1.000370301 1.166868041 1.027255959 1 9.604941221 -12.53474231 1.294694641 0.999978072 1.124391 0.146129755 0.101621598 0.622775722 1.869054474 0.067878013 0.016179178 2.92E-13 12.53474231 0.124412928 GYIFLEYAS(ph)PAHAVDAVK ddPTM_HeLa_Romidepsin_16h_R1 2 GYIFLEYASPAHAVDAVK 18 0 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 0 GYIFLEYAS(1)PAHAVDAVK;GYIFLEY(0.077)AS(0.923)PAHAVDAVK ; 159.4 4.34E-06 16325000 4684.7 4643.6 4742 4751.2 5642.7 5619.6 5384.9 5880.3 5527.3 5470 TRUE FALSE FALSE 4627.601074 4708.972723 4824.532521 5300.556099 5354.731963 5260.525696 5842.293272 6050.437203 5032.924445 5327.888611 0.868561904 0.883834679 0.905524284 0.994869917 1.005038272 0.987356546 1.09654944 1.13561631 0.9446377 1 12.37934821 -7.691353229 0.824325775 0.931926285 1.191952899 0.747693284 0.041273575 0.750741926 0.539684245 0.009469041 0.154508789 2.04E-08 7.691353229 0.260026614 GYIWNYGAIPQTWEDPGHNDK ddPTM_HeLa_Romidepsin_16h_R1 2 GYIWNYGAIPQTWEDPGHNDK 21 0 Q5SQT6;Q15181 Q5SQT6 PPA1 Inorganic pyrophosphatase 0 0 ; ; 87.554 0.00067338 43313000 3681.8 3243.4 3234.4 2185.46 3965.9 3485.7 2952.6 3379.8 3396.4 3079.1 FALSE FALSE TRUE 3636.924805 3289.06067 3290.693375 2438.153168 3763.505324 3262.97502 3203.39377 3477.589181 3092.617478 2999.104538 1.212670235 1.096680902 1.0972253 0.812960381 1.254876339 1.087983089 1.068116743 1.159542502 1.031180287 1 11.55031609 -12.72991931 1.659218996 1.000103154 1.113751674 0.066893779 0.112376672 0.670157119 3.338728927 0.08156147 0.017837193 1.86E-13 12.72991931 0.11364852 GYMTQFPTFPS(ph)WLGKHSS(ph)T(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 GYMTQFPTFPSWLGKHSSTGK 21 1 P35251-2;P35251 P35251-2 RFC1 Replication factor C subunit 1 3 0 GY(0.03)MT(0.032)QFPT(0.099)FPS(0.838)WLGKHS(0.219)S(0.89)T(0.89)GK 47.752 0.0043024 0 1493.5 1838.4 1477.1 1130.1 600.24 760.1 903.9 1418 1385.6 2125.7 TRUE FALSE FALSE 1475.296648 1864.281043 1502.808306 1260.767479 569.607513 711.5320631 980.6772434 1459.027593 1261.668466 2070.474008 0.71254053 0.900412677 0.725828144 0.608926977 0.275109714 0.343656603 0.473648662 0.704682883 0.609362137 1 11.01574538 -9.267305534 2.120772539 0.862342352 0.445498539 0.512839267 0.15043758 0.160112517 1.406184122 0.0242008 0.041830681 5.40E-10 9.267305534 -0.416843813 GYNDDYYEESYFTTR ddPTM_HeLa_Romidepsin_16h_R1 1 GYNDDYYEESYFTTR 15 0 P50402;Q5HY57 P50402 EMD Emerin 0 0 154.23 0.0048051 3499300 450.81 720.91 723.49 611.95 535.72 879.56 497.02 796.62 688.92 688.02 FALSE FALSE TRUE 445.3153543 731.0589899 736.08204 682.7065383 508.3802094 823.3589546 539.2368664 819.6689428 627.3012698 670.1451412 0.664505832 1.090896501 1.098391967 1.018744293 0.758612095 1.228627806 0.804656832 1.223121519 0.936067773 1 9.388329781 -10.23730589 24.94869359 0.841572182 1.022237926 0.165331081 0.166041583 963.8977741 996458.946 0.029604002 0.036247496 5.79E-11 10.23730589 0.180665743 GYS(ph)FTTTAER ddPTM_HeLa_Romidepsin_16h_R1 1 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" 1 0 GYS(0.988)FT(0.007)T(0.004)T(0.001)AER 149.94 0.0037522 13665000 2149.7 2082.3 2501.8 1816.8 2350.9 2252.7 2363.2 2399.9 2295.3 2356.5 TRUE FALSE FALSE 2123.49863 2111.614674 2545.34278 2026.866964 2230.924801 2108.75974 2563.930149 2469.33732 2090.002619 2295.27779 0.925159751 0.919982184 1.108947592 0.883059546 0.971962875 0.918738355 1.117045684 1.075833753 0.910566306 1 11.16445305 -7.755118577 24.99982169 0.963301774 1.096439767 0.453258586 0.061661051 98.56562747 389831.7818 0.007996512 0.028506948 1.76E-08 7.755118577 0.133137993 GYSFSLTT(ph)FSPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 GYSFSLTTFSPSGK 14 0 A0A024RA52;P25787;H3BT36 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 1 0 GYSFSLT(0.02)T(0.913)FS(0.067)PSGK 242.4 4.72E-54 10187000 1966.3 1370.1 1507.4 1134.2 1465.1 1280.2 1198.1 1230.6 1678.9 1292.2 TRUE FALSE FALSE 1942.333979 1389.388304 1533.635665 1265.341541 1390.33048 1198.399352 1299.866584 1266.205469 1528.734979 1258.628458 1.543214733 1.103890743 1.218497528 1.005333649 1.104639317 0.952147033 1.032764337 1.006020054 1.214603857 1 10.29763675 -9.388587488 1.838065635 1.253117806 1.016578175 0.326751009 0.135955227 0.415642898 2.757390768 0.033727935 0.056688556 4.09E-10 9.388587488 -0.236539631 GYSFSLTTFS(ph)PSGK ddPTM_HeLa_Romidepsin_16h_R1 1 GYSFSLTTFSPSGK 14 0 A0A024RA52;P25787;H3BT36 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 1 0 GYSFSLTT(0.001)FS(0.976)PS(0.023)GK 206.49 4.67E-17 13740000 4791.7 4412.1 4335.4 3335.3 4476 4278.4 3443.5 4178.5 4512.7 3809.8 TRUE FALSE FALSE 4733.296917 4474.21366 4410.855818 3720.943079 4247.573018 4005.024048 3735.990804 4299.398305 4109.07281 3710.820847 1.275539055 1.205720741 1.188646933 1.002727761 1.144645132 1.079282513 1.006782854 1.158611122 1.107321797 1 11.85752264 -9.279341909 24.73687793 1.144284697 1.078158804 0.175370749 0.0817515 1589.055113 2195676.933 0.017704964 0.02708358 5.26E-10 9.279341909 -0.066125893 GYSFTTTAER ddPTM_HeLa_Romidepsin_16h_R1 5 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 0 ;;;; ;;;; 218.58 3.61E-18 772533000 10389.4 8673.7 14156.7 9036.35 15619.4 15164.2 13165.1 10897 9814.4 7705.7 FALSE FALSE TRUE 10262.77 8795.808576 14403.09143 10081.1753 14822.28373 14195.25656 14283.34327 11212.2875 8936.575483 7505.504803 1.367365722 1.171914322 1.919003692 1.343170855 1.974855006 1.891312701 1.903048981 1.493875202 1.190669478 1 12.87373339 -10.20506673 0.459954476 1.036342672 1.846395954 0.560698801 0.23014102 0.414427045 0.217030238 0.095129287 0.117654894 6.24E-11 10.20506673 0.810053282 GYSYDDIPDFDD ddPTM_HeLa_Romidepsin_16h_R1 1 GYSYDDIPDFDD 12 0 Q96A57;Q96A57-2 Q96A57 TMEM230 Transmembrane protein 230 0 0 129.42 0.0002477 0 1497.8 2185.9 1727.6 1041.3 1595.3 2135.7 1347.9 1796 1756.8 1786.2 FALSE FALSE TRUE 1479.544237 2216.673158 1757.668153 1161.700005 1513.885888 1999.235663 1462.390592 1847.964426 1599.667408 1739.794267 0.850413331 1.274100737 1.010273563 0.667722631 0.870152246 1.149121882 0.840553749 1.06217411 0.9194578 1 10.764701 GYT(ph)SDSEVYTDHGR ddPTM_HeLa_Romidepsin_16h_R1 1 GYTSDSEVYTDHGR 14 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 GYT(0.976)S(0.024)DSEVYTDHGR 158.65 0.00030936 4111700 1390.2 1363.2 1585.2 903.46 1560 1754.8 1538.9 1992.3 1485.2 1387.8 TRUE FALSE FALSE 1373.255708 1382.391165 1612.789741 1007.922296 1480.387379 1642.673943 1669.614128 2049.944057 1352.359992 1351.744756 1.015913472 1.022671743 1.193117069 0.745645427 1.095167836 1.215224943 1.235154877 1.516517115 1.000455142 1 10.40060704 -7.363324854 0.98261769 1.007522688 1.705558393 0.6728742 0.110327174 0.698628338 0.574236756 0.015890896 0.49389574 4.33E-08 7.363324854 0.698035705 GYT(ph)SDSEVYTDHGRPGK ddPTM_HeLa_Romidepsin_16h_R1 2 GYTSDSEVYTDHGRPGK 17 1 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 GYT(0.875)S(0.121)DS(0.003)EVYTDHGRPGK;GY(0.001)T(0.491)S(0.491)DS(0.014)EVY(0.001)T(0.002)DHGRPGK ; 143.67 4.42E-05 223839000 7501.5 7624.9 7514.4 7268.2 10038.5 10973.4 9295.3 11442.6 8632.5 7969.4 TRUE FALSE FALSE 7410.068833 7732.243542 7645.18498 8108.583482 9526.197886 10272.23516 10084.84255 11773.67358 7860.38758 7762.353839 0.954616214 0.996120984 0.984905499 1.044603692 1.227230565 1.323340235 1.299199026 1.516765896 1.012629383 1 12.92227848 -8.378637196 0.932403752 0.975371121 1.455793601 0.932585833 0.047337677 0.112978253 0.165922086 0.007416295 0.036940004 4.18E-09 8.378637196 0.48042248 GYTS(ph)DSEVYTDHGR ddPTM_HeLa_Romidepsin_16h_R1 1 GYTSDSEVYTDHGR 14 0 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 GYT(0.035)S(0.951)DS(0.014)EVYTDHGR 144.41 0.00025927 4409800 1988 1585.6 2147.6 1533.2 2088.2 2823.6 2240.4 3087.7 2007.6 2156.9 TRUE FALSE FALSE 1963.769491 1607.922118 2184.978077 1710.475798 1981.631362 2643.181073 2430.69952 3177.037728 1828.035228 2100.863427 0.934744004 0.765362516 1.040038133 0.814177531 0.943246161 1.258140362 1.157000255 1.512253337 0.870135205 1 11.03676666 -7.457253496 0.999627343 0.94536561 1.644907555 0.749769496 0.107347258 0.552072482 0.523577821 0.01592242 0.382018802 3.49E-08 7.457253496 0.699541945 GYTS(ph)DSEVYTDHGRPGK ddPTM_HeLa_Romidepsin_16h_R1 3 GYTSDSEVYTDHGRPGK 17 1 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 GYT(0.002)S(0.985)DS(0.013)EVYTDHGRPGK;GYT(0.406)S(0.508)DS(0.086)EVYTDHGRPGK;GYT(0.43)S(0.553)DS(0.016)EVYTDHGRPGK ;; 252.12 5.98E-59 40350000 8644.9 8936.2 9333.3 7854.3 10720.9 12679.8 9821.8 12689.7 9727 9402 TRUE FALSE FALSE 8539.532634 9062.004058 9495.742171 8762.451122 10173.77247 11869.6017 10656.06345 13056.85645 8856.992758 9157.734685 0.932493999 0.989546473 1.036909509 0.956836098 1.110948594 1.296128585 1.163613471 1.425773611 0.96715979 1 13.16077505 -8.214814166 0.933233045 0.968614535 1.364003088 0.826475798 0.064491643 0.21694141 0.297665569 0.010089542 0.061916922 6.10E-09 8.214814166 0.395388553 GYTSDS(ph)EVYTDHGRPGK ddPTM_HeLa_Romidepsin_16h_R1 1 GYTSDSEVYTDHGRPGK 17 1 A0A669KB10;A0A669KBG8;Q92538-3;Q92538-2;Q92538 A0A669KB10 GBF1 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 1 0 GYT(0.304)S(0.304)DS(0.385)EVY(0.001)T(0.005)DHGRPGK 73.953 0.0032407 0 1185.2 1215.3 1426.1 1185.8 1434.7 1548.3 1078.6 1401.9 1567.5 1517.9 TRUE FALSE FALSE 1170.754327 1232.409025 1450.920672 1322.907775 1361.481905 1449.368627 1170.216257 1442.461765 1427.298874 1478.464739 0.791871659 0.833573499 0.981369818 0.8947848 0.920875466 0.98032005 0.791507722 0.975648405 0.96539257 1 10.52988412 -9.764120158 24.99570072 0.893860267 0.919136666 0.024562757 0.076232423 332.652425 3101690.035 0.015023408 0.02024628 1.72E-10 9.764120158 0.025276399 GYVLGETSNLPS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 GYVLGETSNLPSPGK 15 0 B1AKT1;Q9H040 B1AKT1 SPRTN SprT-like domain-containing protein Spartan 1 0 GYVLGET(0.008)S(0.001)NLPS(0.991)PGK 180.27 4.17E-08 12287000 6658.2 6756.8 6566.3 6107.9 7601.2 7038.5 5597.9 5770.7 6878.4 6206.7 TRUE FALSE FALSE 6577.047297 6851.922408 6680.583697 6814.124137 7213.2824 6588.762566 6073.385486 5937.6661 6263.178677 6045.449039 1.087933627 1.133401731 1.105059964 1.12714938 1.193175619 1.089871492 1.004621071 0.982171227 1.036015462 1 12.56163379 -4.072384184 22.03604416 1.064725562 0.008793305 0 0.065842083 0 0 0.010008864 0 8.46E-05 4.072384184 -1.055932258 GYYS(ph)PGIVSTR ddPTM_HeLa_Romidepsin_16h_R1 2 GYYSPGIVSTR 11 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 GYYS(0.995)PGIVS(0.005)TR;GY(0.001)YS(0.936)PGIVS(0.063)TR ; 138.42 0.003451 41169000 5666.4 5429.6 5454.3 3937.5 5580.4 6016.2 5889.8 5483.9 5563.7 5390.3 TRUE FALSE FALSE 5597.335737 5506.038051 5549.229804 4392.772276 5295.611365 5631.784236 6390.079465 5642.567994 5066.068737 5250.259229 1.066106547 1.04871737 1.056943964 0.836677216 1.008638076 1.072667842 1.217097897 1.07472179 0.964917829 1 12.35817294 -7.981781156 6.11280816 1.019603127 1.146829473 0.386178001 0.071787131 0.132745341 17.9635855 0.009971574 0.029600888 1.04E-08 7.981781156 0.127226346 GYYS(ph)PYS(ph)VSGSGSTAGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 3 0 GY(0.064)Y(0.185)S(0.891)PY(0.107)S(0.374)VS(0.109)GS(0.261)GS(0.11)T(0.03)AGS(0.869)R 82.859 0.018438 4485500 1320.5 1426.7 1322.8 1423.2 1729.5 1777.7 1725.5 1713 1156.5 1577.3 TRUE FALSE FALSE 1304.405238 1446.78512 1345.822779 1587.75708 1641.237161 1664.110707 1872.063927 1762.562952 1053.059743 1536.321519 0.849044437 0.941720273 0.876003338 1.033479686 1.06829016 1.083178675 1.218536553 1.147261775 0.685442292 1 10.58526446 -8.59991144 1.190033356 0.924698405 1.174284775 0.630139812 0.090555094 0.199286766 0.543295819 0.010445425 0.0335166 2.51E-09 8.59991144 0.24958637 GYYS(ph)PYSVSGS(ph)GSTAGSR ddPTM_HeLa_Romidepsin_16h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GYYS(1)PYS(0.001)VS(0.065)GS(0.863)GS(0.047)T(0.025)AGSR;GYY(0.001)S(0.996)PYS(0.003)VS(0.009)GS(0.511)GS(0.007)T(0.016)AGS(0.457)R ; 126.43 0.016106 88578000 5581.4 5438.8 5715 4845.2 7167.9 8548.8 7259.1 8563.9 6555.8 6614.4 TRUE FALSE FALSE 5513.37175 5515.367569 5814.467178 5405.424821 6802.095316 8002.55927 7875.687773 8811.682935 5969.432829 6442.556934 0.85577385 0.856083637 0.902509242 0.839018557 1.055806784 1.242140248 1.222447524 1.367730705 0.926562681 1 12.65341767 -8.36788948 2.387075008 0.915745296 1.284927918 0.895739952 0.057904614 0.086675464 0.955110484 0.010678133 0.028550939 4.29E-09 8.36788948 0.369182622 GYYS(ph)PYSVSGSGS(ph)TAGSR ddPTM_HeLa_Romidepsin_16h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GY(0.002)Y(0.079)S(0.908)PY(0.001)S(0.023)VS(0.142)GS(0.371)GS(0.423)T(0.051)AGSR;GYY(0.008)S(0.877)PY(0.011)S(0.093)VS(0.017)GS(0.045)GS(0.927)T(0.02)AGS(0.001)R ; 129.42 0.014813 50535000 7422.3 7079 6528.8 6213 8919 9131.6 7619.7 9574.8 7501 6591.2 TRUE FALSE FALSE 7331.834153 7178.658348 6642.431025 6931.376293 8463.830149 8548.120231 8266.917128 9851.831731 6830.091773 6419.959674 1.142037415 1.118178106 1.034653076 1.07966041 1.318361887 1.331491266 1.287689884 1.534562868 1.063883906 1 12.64834852 -4 0.280600857 1.035602799 4.655103693 0.829049842 0.066735752 15.21179765 0.193899017 0.031904803 27.37902537 1.00E-04 4 3.619500894 GYYS(ph)PYSVSGSGSTAGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GY(0.006)Y(0.183)S(0.7)PY(0.01)S(0.028)VS(0.016)GS(0.009)GS(0.04)T(0.034)AGS(0.974)R 98.077 0.027564 29461000 3484.8 3680.6 3977.9 2298.4 5018.5 4427.2 3371.8 4615.9 3060.6 3248.1 TRUE FALSE FALSE 3442.325917 3732.415583 4047.133681 2564.151822 4762.387218 4144.316208 3658.200608 4749.453784 2786.852271 3163.713894 1.088064861 1.179757623 1.279235044 0.810487898 1.505315391 1.309952906 1.156299441 1.501227337 0.880879992 1 11.62740342 -4 0.167896456 0.964347175 2.753407268 0.405509872 0.172819545 46.64649089 0.486278808 0.245345472 21.0028853 1.00E-04 4 1.789060093 GYYS(ph)PYSVSGSGSTAGSR ddPTM_HeLa_Romidepsin_16h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 GYYS(0.999)PYS(0.001)VSGSGSTAGSR;GYYS(0.996)PYS(0.004)VSGSGSTAGSR;GYYS(1)PYSVSGSGSTAGSR;GY(0.001)Y(0.062)S(0.787)PYS(0.15)VSGSGSTAGSR ;;; 331.4 1.09E-210 1642170000 15586.8 13681.9 14314.7 12722.3 16121.5 17838.5 17333.6 18438.6 16691.9 16602 TRUE FALSE FALSE 15396.82209 13874.51415 14563.84135 14193.31219 15298.7597 16698.67742 18805.91555 18972.0918 15198.93466 16170.67765 0.952144519 0.858004497 0.900632717 0.877719073 0.946080309 1.032651679 1.162963975 1.173240368 0.939907095 1 13.98109252 -7.896142976 2.593187296 0.952582527 1.17552752 0.817122608 0.044642872 0.115192859 1.527837288 0.008081157 0.031898643 1.27E-08 7.896142976 0.222944993 GYYSPYS(ph)VSGSGSTAGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GYYS(0.311)PYS(0.471)VS(0.217)GS(0.001)GSTAGS(1)R 161.2 3.25E-05 13634000 2630.2 2668.1 2090.1 1900.9 2508.5 2798.2 2434.6 3009.2 2248.5 2113.1 TRUE FALSE FALSE 2598.142111 2705.661582 2126.477314 2120.691002 2380.481884 2619.404051 2641.394863 3096.266454 2047.388529 2058.201357 1.262336215 1.314575745 1.033172632 1.030361288 1.156583575 1.272666565 1.283351045 1.504355462 0.994746467 1 11.00716842 -7.184894928 0.964226467 1.128938601 1.733339136 0.564963831 0.106416319 1.562513167 1.00059404 0.01943611 1.014529382 6.53E-08 7.184894928 0.604400534 GYYSPYS(ph)VSGSGSTAGSR ddPTM_HeLa_Romidepsin_16h_R1 1 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 GYYS(0.003)PYS(0.855)VS(0.141)GSGSTAGSR 268.08 4.19E-90 176880000 2374.4 2232 1678.3 1691.4 2523.6 2878.6 2630.2 2830.7 2084 2202.4 TRUE FALSE FALSE 2345.4599 2263.422155 1707.510107 1886.967626 2394.811275 2694.66675 2853.609122 2912.601838 1897.601821 2145.181331 1.09336207 1.055119268 0.795974719 0.879630826 1.116367759 1.256148705 1.330241449 1.357741556 0.884588074 1 11.06688389 -8.265811236 2.514493093 1.015028061 1.334549782 0.717734985 0.097707372 0.138376586 1.70891142 0.014911347 0.042258471 5.42E-09 8.265811236 0.319521721 GYYSPYSVS(ph)GSGSTAGSR ddPTM_HeLa_Romidepsin_16h_R1 3 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 GYYS(0.001)PYS(0.159)VS(0.835)GS(0.004)GSTAGSR;GYYSPYS(0.024)VS(0.886)GS(0.018)GS(0.008)T(0.028)AGS(0.036)R;GYYS(0.001)PYS(0.167)VS(0.831)GS(0.001)GSTAGSR ;; 169.15 3.50E-07 210196100 6872.4 6902.5 6495.5 5770.2 9212 9508.3 8628.5 9601.7 7975.1 7109.3 TRUE FALSE FALSE 6788.636545 6999.673576 6608.551453 6437.377674 8741.877265 8900.750317 9361.404575 9879.510041 7261.787082 6924.599361 0.980365244 1.010841669 0.954358672 0.929639007 1.262437985 1.285381269 1.351905589 1.426726591 1.048694185 1 12.75751489 -8.645881268 3.955516708 0.985360021 1.344339054 0.932424856 0.045755996 0.037392343 1.083523362 0.0063813 0.013201142 2.26E-09 8.645881268 0.358979033 GYYSPYSVSGSGS(ph)TAGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 GY(0.002)Y(0.001)S(0.033)PYS(0.004)VS(0.003)GS(0.006)GS(0.952)TAGS(1)R;GY(0.005)Y(0.14)S(0.009)PY(0.01)S(0.219)VS(0.094)GS(0.197)GS(0.333)T(0.023)AGS(0.97)R ; 152.94 0.00020302 35494000 5718.1 6065.6 5804.7 3899.4 6351.7 6310.6 4815.4 6824.5 5238.1 5382 TRUE FALSE FALSE 5648.405598 6150.991676 5905.728369 4350.266975 6027.549048 5907.373027 5224.419956 7021.95614 4769.591217 5242.174864 1.077492786 1.173366367 1.126579811 0.829859188 1.149818387 1.126893547 0.996613064 1.339512001 0.909849698 1 12.35594976 -7.254843741 24.66567615 1.050179642 1.339512159 0.413848264 0.105447543 438.7643207 1640791.785 0.01288906 0.162982003 5.56E-08 7.254843741 0.289332518 GYYSPYSVSGSGS(ph)TAGSR ddPTM_HeLa_Romidepsin_16h_R1 2 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 GYYSPYSVS(0.002)GS(0.032)GS(0.405)T(0.243)AGS(0.318)R;GYYSPYSVS(0.274)GS(0.274)GS(0.395)T(0.055)AGS(0.002)R ; 144.15 9.88E-05 566040900 4488 4966.4 4526.5 4032.8 6212.4 7340.7 6114.1 7151.2 5373.4 4921.4 TRUE FALSE FALSE 4433.29853 5036.31711 4605.281834 4499.091311 5895.358046 6871.652961 6633.431501 7358.108689 4892.789646 4793.541319 0.924848298 1.050646438 0.960726429 0.938573596 1.229854434 1.433523256 1.383826916 1.535004749 1.020704594 1 12.22687615 -8.521769995 2.430337376 0.96819445 1.44863964 0.939972216 0.053111642 0.045384148 0.533626779 0.007694893 0.018537655 3.01E-09 8.521769995 0.48044519 GYYSPYSVSGSGSTAGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 4 GYYSPYSVSGSGSTAGSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 GYYSPYSVS(0.312)GS(0.002)GS(0.02)T(0.069)AGS(0.597)R;GYYSPYSVS(0.001)GS(0.004)GS(0.171)T(0.171)AGS(0.654)R;GYYSPYS(0.001)VS(0.053)GS(0.053)GS(0.245)T(0.039)AGS(0.609)R;GYYSPYSVSGS(0.002)GS(0.134)T(0.078)AGS(0.786)R ;;; 239.7 1.23E-49 1420430000 4891.44 4685.03 4473.56 4019.64 5952.72 6144.54 5078.44 7146.14 5496.69 4701.54 TRUE FALSE FALSE 4831.821248 4750.985975 4551.420435 4484.40969 5648.930486 5751.923725 5509.802567 7352.902286 5005.05228 4579.393313 1.055122571 1.03747061 0.993891576 0.97925847 1.233554338 1.256044924 1.203173038 1.605649872 1.092950952 1 12.16094076 -4 0.496010455 1.019071183 18.25448436 0.841349522 0.072293873 23.42666357 0.22724333 0.013473674 422.5482963 1.00E-04 4 17.23541317 HADNS(ph)SDTEMEDMIAEETLEEMDSELLK ddPTM_HeLa_Romidepsin_16h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7 E7EX82 PHC3 Polyhomeotic-like protein 3 1 0 HADNS(0.478)S(0.357)DT(0.165)EMEDMIAEETLEEMDSELLK 91.594 5.69E-08 4164000 311.11 492.17 331.61 397.74 479.5 441.73 353.01 502.76 426.99 426.56 TRUE FALSE FALSE 307.3180717 499.0987822 337.3815329 443.7285702 455.0293257 413.5048786 382.9946606 517.3065674 388.798945 415.4779097 0.739673673 1.201264304 0.812032421 1.067995578 1.095194991 0.995251177 0.921817145 1.245088019 0.935787285 1 8.698627963 -10.26788137 24.99869226 0.877068127 1.034931624 0.217718433 0.133434664 607.1489062 2356087.273 0.024346281 0.028179263 5.40E-11 10.26788137 0.157863497 HADNSS(ph)DTEMEDMIAEETLEEMDSELLK ddPTM_HeLa_Romidepsin_16h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7 E7EX82 PHC3 Polyhomeotic-like protein 3 1 0 HADNS(0.249)S(0.723)DT(0.027)EMEDMIAEET(0.001)LEEMDSELLK 71.05 3.11E-05 4862300 897.4 711.85 887.21 797.3 986.09 922.54 1051 1039.8 950.8 1041.3 TRUE FALSE FALSE 886.4621436 721.871443 902.6515179 889.4875774 935.7661477 863.5926714 1140.271914 1069.884972 865.7580667 1014.246876 0.874010228 0.711731493 0.889972194 0.876993165 0.922621671 0.851461998 1.124254795 1.054856562 0.853596976 1 9.986193143 -7.757068658 24.99998556 0.90878293 1.08955573 0.525059923 0.076586016 81.73111573 467473.3146 0.012425654 0.043453253 1.75E-08 7.757068658 0.1807728 HADNSSDT(ph)EMEDMIAEETLEEMDSELLK ddPTM_HeLa_Romidepsin_16h_R1 1 HADNSSDTEMEDMIAEETLEEMDSELLK 28 0 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7 E7EX82 PHC3 Polyhomeotic-like protein 3 1 0 HADNS(0.306)S(0.306)DT(0.387)EMEDMIAEETLEEMDSELLK 66.793 0.00063518 13628000 1503.9 1081.5 858.7 985.05 1332.7 1441.8 1205.9 1044.5 1543.3 1326.1 TRUE FALSE FALSE 1485.569888 1096.725385 873.6453133 1098.946116 1264.687346 1349.673633 1308.329116 1074.72096 1405.263383 1291.647731 1.150135484 0.849090165 0.676380481 0.850809466 0.979127138 1.044923938 1.01291481 0.832054231 1.087961794 1 10.33499694 -10.25493975 24.88631321 1.070897312 0.896156018 0.397718299 0.105321827 443.1425267 1696740.651 0.02043065 0.024701043 5.56E-11 10.25493975 -0.174741294 HAEATLGS(ph)GNLR ddPTM_HeLa_Romidepsin_16h_R1 1 HAEATLGSGNLR 12 0 Q9H8S9-2;Q9H8S9;D6RCK3;Q7L9L4;Q7L9L4-2 Q9H8S9-2 MOB1A;MOB1B MOB kinase activator 1A;MOB kinase activator 1B 1 0 HAEAT(0.045)LGS(0.955)GNLR 85.469 0.015475 4452500 2619.2 2431.4 1982.4 2427.9 2585.7 2942.7 2690.8 2963.6 2721.5 2847.5 TRUE FALSE FALSE 2587.276183 2465.629313 2016.90284 2708.625222 2453.74208 2754.670967 2919.356485 3049.34709 2478.082224 2773.52154 0.932848779 0.888988702 0.727199271 0.976601473 0.884702731 0.99320338 1.052581148 1.099449579 0.893478629 1 11.43750321 -7.799997338 2.411822367 0.938734006 1.089492666 0.410525187 0.076310495 0.282828812 3.187522049 0.011934511 0.055840785 1.58E-08 7.799997338 0.15075866 HAEELAAQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 HAEELAAQKR 10 1 O60563 O60563 CCNT1 Cyclin-T1 0 1 ; HAEELAAQK(1)R;HAEELAAQK(1)R 115.23 0.0016105 2456590 1567.8 1555.1 1192.3 1300.8 1252.5 1258.215 1348.6 1032.7 1794.8 1625.9 FALSE TRUE FALSE 1548.691051 1576.992739 1213.051481 1451.204616 1188.580251 1177.819122 1463.15005 1062.579545 1634.268593 1583.658884 0.977919593 0.995790669 0.765980284 0.91636187 0.750527947 0.743732842 0.923904804 0.670964913 1.031957456 1 10.6290459 -9.767087054 24.9873933 0.989748131 0.802224787 0.64978252 0.07384657 61.26899191 271076.4771 0.010561137 0.014095088 1.71E-10 9.767087054 -0.187523343 HALIIYDDLSK ddPTM_HeLa_Romidepsin_16h_R1 3 HALIIYDDLSK 11 0 P25705-2;P25705;P25705-3 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 0 ;; ;; 90.653 0.0155 18032240 7544.87 6968.14 6382.07 7694.84 7567.98 8709.37 6702.27 6760.59 7117.57 6362.23 FALSE FALSE TRUE 7452.910222 7066.237658 6493.147251 8584.553606 7181.757741 8152.869365 7271.560647 6956.197005 6480.956713 6196.938347 1.202676193 1.140278838 1.047799234 1.385289497 1.158920315 1.315628607 1.173411811 1.122521577 1.045832046 1 12.5973399 -12.78679357 0.391732626 0.890732431 1.210768121 0.357912525 0.091358793 2.654850169 0.394097138 0.372155904 0.029549218 1.63E-13 12.78679357 0.32003569 HALK(ac)WIRPQTSE ddPTM_HeLa_Romidepsin_16h_R1 1 HALKWIRPQTSE 12 2 Q6PJT7;Q6PJT7-5;H0YJA2;Q6PJT7-2;Q6PJT7-9;Q6PJT7-3;Q6PJT7-11;Q6PJT7-4;Q6PJT7-10;G3V256;G3V5I6;G3V411;Q6PJT7-6;Q6PJT7-8;H0YJ51 Q6PJT7 ZC3H14 Zinc finger CCCH domain-containing protein 14 0 1 HALK(1)WIRPQTSE 100.09 0.014081 3695900 1595.5 1868.1 1744.5 1567.8 1752.7 2124.7 2642.8 2060.7 2483 1299.9 FALSE TRUE FALSE 1576.053432 1894.399161 1774.862291 1749.076413 1663.253179 1988.938527 2867.279366 2120.323103 2260.914261 1266.128411 1.244781666 1.496214085 1.401802752 1.381436826 1.313652837 1.570882156 2.264603923 1.674650917 1.785691121 1 10.30620801 -4 0.16254377 0.914601561 5.098915236 0.089091884 0.312715333 25.3599368 0.259144323 0.338070411 25.63181375 1.00E-04 4 4.184313675 LSTEADTDT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LSTEADTDTPK 11 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 LSTEADT(0.017)DT(0.983)PK 138.24 0.0071907 5679300 3367 3248.5 3275.6 2510.8 1913.9 1965.4 1379.9 1467.3 3968.5 3771.5 TRUE FALSE FALSE 3325.961709 3294.232468 3332.610444 2801.11051 1816.226541 1839.817283 1497.108672 1509.75401 3613.547421 3673.515886 0.905389227 0.896751932 0.907199138 0.762514876 0.494410967 0.50083281 0.407541091 0.41098339 0.983675458 1 11.8429458 -8.882597003 1.305609644 0.952557346 0.417178017 0.973876248 0.037626894 0.053379741 0.181464256 0.007268045 0.01757391 1.31E-09 8.882597003 -0.535379329 down ELGPLPDDDDMAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ELGPLPDDDDMASPK 15 0 Q86U86-8;Q86U86;H0Y5B5;E7EVG2;Q86U86-6;Q86U86-5;Q86U86-4;Q86U86-7;Q86U86-3;Q86U86-9;Q86U86-2 Q86U86-8 PBRM1 Protein polybromo-1 1 0 ELGPLPDDDDMAS(1)PK 103.6 0.0091285 14219000 4526 4466.2 5083.8 3267.5 2714.5 2218.2 2042.9 1853.5 4814.5 5071.3 TRUE FALSE FALSE 4470.835371 4529.075281 5172.281406 3645.303724 2575.968936 2076.464179 2216.423875 1907.128098 4383.879062 4939.546895 0.905110421 0.916900958 1.047116571 0.737983423 0.521499034 0.420375436 0.448709957 0.386093733 0.887506315 1 12.27016299 -8.867796212 2.183568532 0.957027357 0.42555006 0.955557285 0.051663887 0.042057683 0.407492928 0.007964491 0.016350089 1.36E-09 8.867796212 -0.531477297 down HAPTYTIPLS(ph)PVLS(ph)PTLPAEAPTAQVPPSLPR ddPTM_HeLa_Romidepsin_16h_R1 1 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 2 0 HAPT(0.012)Y(0.001)T(0.045)IPLS(0.933)PVLS(0.972)PT(0.037)LPAEAPTAQVPPSLPR 84.889 1.11E-07 26905000 1870.3 1612.2 1485.8 1672.2 2406.3 2647.3 2023.7 2332.2 1961.7 2093 TRUE FALSE FALSE 1847.504064 1634.896594 1511.659726 1865.547632 2283.497532 2478.146074 2195.593027 2399.678527 1786.240639 2038.623558 0.906250718 0.801961003 0.741509986 0.915101576 1.120117308 1.215597683 1.076997771 1.177107229 0.876199351 1 10.99337968 -8.726794224 5.350307893 0.921298066 1.150229387 0.717474156 0.081083319 0.106912744 7.651104932 0.014128783 0.028096034 1.88E-09 8.726794224 0.22893132 HAPTYTIPLS(ph)PVLSPTLPAEAPTAQVPPSLPR ddPTM_HeLa_Romidepsin_16h_R1 2 HAPTYTIPLSPVLSPTLPAEAPTAQVPPSLPR 32 0 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 0 HAPT(0.004)Y(0.004)T(0.014)IPLS(0.718)PVLS(0.134)PT(0.122)LPAEAPT(0.003)AQVPPS(0.001)LPR;HAPT(0.009)Y(0.001)T(0.023)IPLS(0.931)PVLS(0.028)PT(0.008)LPAEAPTAQVPPSLPR ; 67.799 1.64E-05 50687000 2383.29 2814.4 2244.1 2556.4 2687.9 2885 2467.17 2758.7 3272.9 2990.1 TRUE FALSE FALSE 2354.241545 2854.021197 2283.157619 2851.982996 2550.726433 2700.657811 2676.731358 2838.518632 2980.163627 2912.416771 0.808346377 0.979949445 0.783939181 0.979249613 0.875810927 0.927290983 0.919075657 0.974626523 1.023261388 1 11.50800111 -6.544587196 1.159636235 0.906815205 1.203820793 0.0117159 0.076763718 17.99576796 5.93628969 0.011981407 9.72921854 2.85E-07 6.544587196 0.297005587 HAS(ph)APSHVQPSDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 HASAPSHVQPSDSEK 15 0 O60343-2;O60343-3;O60343;A0A3B3IRT3 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 HAS(0.993)APS(0.007)HVQPSDSEK 75.961 0.016315 22658000 4548.1 4294.1 3994.3 3934.8 5591.8 6032.4 4520.4 4611.6 5324.2 5184.7 TRUE FALSE FALSE 4492.666008 4354.552453 4063.819116 4389.76009 5306.42958 5646.949109 4904.362663 4745.02937 4847.990217 5050.000747 0.889636702 0.862287487 0.804716538 0.869259295 1.050777979 1.118207579 0.97116078 0.939609637 0.959997921 1 12.30206789 -8.752220494 24.99841248 0.922692804 1.023474031 0.398729245 0.069550703 218.2801092 591895.4207 0.012225182 0.02417879 1.77E-09 8.752220494 0.100781227 HAS(ph)PILPITEFSDIPR ddPTM_HeLa_Romidepsin_16h_R1 2 HASPILPITEFSDIPR 16 0 G5E972;P42167;H0YJH7 G5E972 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 0 HAS(1)PILPITEFSDIPR;HAS(0.998)PILPIT(0.001)EFS(0.001)DIPR ; 102.47 0.0020597 43296000 1503.76 2077.74 2006.56 1153.56 1640.92 2488.9 1582.72 2695.8 2032.19 1851.99 TRUE FALSE FALSE 1485.431595 2106.990478 2041.483335 1286.940035 1557.177729 2329.867323 1717.156197 2773.79872 1850.425837 1803.875033 0.823467018 1.168035723 1.131721044 0.713430815 0.863240358 1.291590205 0.951926362 1.537688958 1.025806003 1 10.81688368 -4.093408253 0.876150485 0.939229467 200 0.451596369 0.170323442 403.1377653 1.136027821 0.026262513 160012.919 8.06E-05 4.093408253 199.0607705 HAT(ph)IY(ph)PT(ph)EQELLAVQR ddPTM_HeLa_Romidepsin_16h_R1 1 HATIYPTEQELLAVQR 16 0 Q9UPR6 Q9UPR6 ZFR2 Zinc finger RNA-binding protein 2 3 0 HAT(1)IY(1)PT(1)EQELLAVQR 56.599 0.0040435 0 965.74 915.88 983.7 788.32 976.01 1017.2 806.41 935.46 1129.9 836.29 TRUE FALSE FALSE 953.9691894 928.7737827 1000.820886 879.4692676 926.2005677 952.2042029 874.9064453 962.5260592 1028.838914 814.5630652 1.171142211 1.140211019 1.228659791 1.079682231 1.137052006 1.168975422 1.074080673 1.18164707 1.263056181 1 9.669882589 -12.2781846 0.918012739 0.996548232 1.146985152 0 0.092162345 0.307532095 0.448110091 0.03175676 0.00786018 5.27E-13 12.2781846 0.15043692 HAYGDQYR ddPTM_HeLa_Romidepsin_16h_R1 1 HAYGDQYR 8 0 O75874;C9J4N6 O75874 IDH1 Isocitrate dehydrogenase [NADP] cytoplasmic 0 0 90.709 0.019163 804020 296.95 183.51 619.48 292.13 368.44 564.72 546.49 0 217.25 126.05 FALSE FALSE TRUE 293.3306592 186.0934586 630.2617895 325.9074451 349.637132 528.6362146 592.908847 0 197.8186159 122.7752028 2.389168598 1.515725116 5.133461603 2.654505451 2.847782972 4.305724628 4.829223111 0 1.611226138 1 6.939875396 -10.96790874 0.600407017 1.129668014 3.299844282 0.184111591 1.452861813 0.696328064 0.576850814 0.606134266 0.407404003 1.08E-11 10.96790874 2.170176268 HCAPSGT(ph)PTGPEILAAAVPPS(ph)SLK ddPTM_HeLa_Romidepsin_16h_R1 1 HCAPSGTPTGPEILAAAVPPSSLK 24 0 Q5TBH9;Q5TBI2;Q8NDD1-7;Q8NDD1-6;Q8NDD1;Q8NDD1-5 Q5TBH9 C1orf131 Uncharacterized protein C1orf131 2 0 HCAPS(0.118)GT(0.441)PT(0.441)GPEILAAAVPPS(0.771)S(0.229)LK 46.415 0.022517 8993400 5296.4 5984.8 5697.2 4965.4 3775 3326.2 3332.2 4333.7 4229 4329.9 TRUE FALSE FALSE 5231.84544 6069.054171 5796.357376 5539.522911 3582.347664 3113.666555 3615.236985 4459.088772 3850.747648 4217.408574 1.240535591 1.439048189 1.374388389 1.313489745 0.849419164 0.738289047 0.857217631 1.057305379 0.913060137 1 12.04214108 -8.747287701 24.98953061 1.177580335 0.86444278 0.483036145 0.168649938 185.4208678 327420.8664 0.026835525 0.053467289 1.79E-09 8.747287701 -0.313137556 HDADGQATLLNLLLR ddPTM_HeLa_Romidepsin_16h_R1 1 HDADGQATLLNLLLR 15 0 O43242;O43242-2 O43242 PSMD3 26S proteasome non-ATPase regulatory subunit 3 0 0 145.49 9.62E-06 0 1639.4 1407.6 1599.2 1310.7 1629.4 1602.2 1456.3 1501.3 1499.2 1369.1 FALSE FALSE TRUE 1619.418362 1427.41623 1627.033405 1462.249301 1546.245638 1499.824591 1579.998086 1544.737747 1365.107797 1333.530585 1.214384118 1.070403818 1.220094555 1.096524758 1.159512692 1.124702056 1.184823283 1.158381941 1.023679406 1 10.3810352 -12.45199575 1.113668093 0.997528951 1.157448805 0.606611368 0.045488166 0.254800983 0.551036116 0.032454366 0.007563213 3.53E-13 12.45199575 0.159919853 HDNDLLHHQK ddPTM_HeLa_Romidepsin_16h_R1 1 HDNDLLHHQK 10 0 P51786 P51786 ZNF157 Zinc finger protein 157 0 0 81.525 0.026968 33004000 4423.2 4318.7 4310.9 3567.2 4547.4 4852.2 4253.5 4846.2 4715.3 4555.2 FALSE FALSE TRUE 4369.288337 4379.498772 4385.929406 3979.656448 4315.329209 4542.16008 4614.792184 4986.417151 4293.551758 4436.855247 0.984771441 0.987072719 0.988522086 0.896954313 0.972609871 1.023734115 1.040104292 1.123862933 0.967701563 1 12.11532177 -7.373900944 1.461524147 0.984106288 1.15816221 0.702937919 0.03006828 0.447660691 1.005948921 0.004636749 0.105814261 4.23E-08 7.373900944 0.174055921 HDS(ph)PDLAPNVTYSLPR ddPTM_HeLa_Romidepsin_16h_R1 4 HDSPDLAPNVTYSLPR 16 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 0 HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR;HDS(1)PDLAPNVTYSLPR ;;; 233.84 1.12E-45 49161100 6556.82 6361.4 6426.9 4426.23 5282.77 5559.71 5400.98 5509.3 7349.9 6523.9 TRUE FALSE FALSE 6476.902956 6450.955956 6538.757499 4938.011539 5013.170534 5204.462474 5859.739106 5668.702903 6692.506536 6354.408138 1.01927714 1.015193833 1.029011256 0.777100153 0.788928005 0.819031822 0.922153406 0.892089834 1.053206906 1 12.63354204 -9.270942681 24.99575511 1.011245404 0.840445716 0.816482558 0.043303013 223.9538314 589046.6958 0.006848441 0.010546821 5.36E-10 9.270942681 -0.170799688 HDSIPAADTFEDLS(ph)DVEGGGSEPTQR ddPTM_HeLa_Romidepsin_16h_R1 1 HDSIPAADTFEDLSDVEGGGSEPTQR 26 0 O95671;O95671-2;O95671-3 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 0 HDSIPAADT(0.004)FEDLS(0.992)DVEGGGS(0.003)EPTQR 88.688 8.50E-06 5852700 1103.3 1007.5 917.47 861.43 2583.8 3263.7 2277.1 2808.7 1191 919.62 TRUE FALSE FALSE 1089.852555 1021.683611 933.4381805 961.0325898 2451.939045 3055.160103 2470.516817 2889.965303 1084.473977 895.7281398 1.216722471 1.140617969 1.042099873 1.072906552 2.737369672 3.410811794 2.758110086 3.22638664 1.210717771 1 9.80691712 -8.708290176 4.250025424 1.097760407 3.087963405 0.967715791 0.172572486 0.02373086 0.882746977 0.023852156 0.048205283 1.96E-09 8.708290176 1.990202997 up HDVVFLITK ddPTM_HeLa_Romidepsin_16h_R1 1 HDVVFLITK 9 0 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 76.827 0.015468 282830 257.78 245.08 239.08 231.8 277.65 290.49 296.31 322.41 355.63 174.17 FALSE FALSE TRUE 254.6380782 248.5302427 243.2410871 258.6018067 263.4804844 271.9286265 321.478564 331.7384247 323.8215621 169.6450383 1.501005162 1.465001542 1.433823763 1.524369998 1.55312815 1.602927084 1.895007171 1.955485572 1.90881835 1 7.406375425 -4.092899448 0.054734002 8.19E-16 4.546601194 0 0.280974556 89.7298994 0.378885656 7.102173952 33.77819398 8.07E-05 4.092899448 4.546601194 HEDEQALLDQNSQT(ph)PPPSPFSVQAFNK ddPTM_HeLa_Romidepsin_16h_R1 1 HEDEQALLDQNSQTPPPSPFSVQAFNK 27 0 A0A499FJI4;O75592-2;O75592;A0A087WY34 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 HEDEQALLDQNSQT(0.996)PPPS(0.003)PFSVQAFNK 146.04 8.26E-11 21415000 4304.8 4928.5 4021.2 2970.9 4289.7 5258.8 5096.3 5819.4 4987.9 4479.9 TRUE FALSE FALSE 4252.331442 4997.883552 4091.187299 3314.409437 4070.780602 4922.779652 5529.179595 5987.775158 4541.769732 4363.511552 0.974520496 1.145381075 0.937590574 0.759573888 0.932913905 1.128169272 1.267139901 1.372237723 1.040852001 1 12.0912739 -7.85498785 2.260384709 0.975830648 1.347686366 0.692162705 0.093637842 0.13577495 1.342013977 0.013710281 0.062201761 1.40E-08 7.85498785 0.371855718 HEDGTQS(ph)DSEDPLAK ddPTM_HeLa_Romidepsin_16h_R1 2 HEDGTQSDSEDPLAK 15 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 HEDGT(0.001)QS(0.982)DS(0.018)EDPLAK;HEDGTQS(0.932)DS(0.068)EDPLAK ; 210.91 1.67E-25 8785400 4143.5 4387.2 4150.3 3200.3 4679.7 4784.2 4560.4 5585.8 4304.6 4671.2 TRUE FALSE FALSE 4092.997428 4448.963117 4222.534231 3570.333744 4440.877447 4478.50506 4947.760262 5747.41631 3919.585795 4549.841551 0.899591202 0.977828144 0.92806182 0.784716062 0.976051011 0.984321104 1.087457708 1.26321241 0.861477428 1 12.15160059 -7.37153561 1.491318518 0.940537851 1.347863548 0.748456797 0.062118818 0.374441737 0.883201966 0.009316479 0.210360527 4.25E-08 7.37153561 0.407325697 HEEAPGHRPTTNPNASK ddPTM_HeLa_Romidepsin_16h_R1 1 HEEAPGHRPTTNPNASK 17 1 E9PP21;P21291;E9PS42;E9PND2 E9PP21 CSRP1 Cysteine and glycine-rich protein 1 0 0 46.873 0.022992 2138500 581.77 476.45 553.49 409.03 814.55 739.43 585.78 718.74 768.29 669.67 FALSE FALSE TRUE 574.6791635 483.1574756 563.1232613 456.3239731 772.980474 692.1828094 635.5361386 739.5356079 699.5722182 652.2718769 0.881042375 0.740730197 0.863325986 0.699591672 1.185058718 1.061187572 0.974342389 1.133784292 1.072516297 1 9.349329617 -8.739590599 24.99995919 0.903620004 1.078474884 0.436024532 0.115616134 211.146288 241598.1118 0.016837598 0.033652784 1.82E-09 8.739590599 0.17485488 HEEQS(ph)NEDIPIAEQSSK ddPTM_HeLa_Romidepsin_16h_R1 2 HEEQSNEDIPIAEQSSK 17 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 HEEQS(1)NEDIPIAEQSSK;HEEQS(1)NEDIPIAEQSSK ; 118.84 0.0009356 7736300 5616.2 5613.5 5477.4 3566.7 4901.2 5107.8 3902.1 4315.3 6182.5 6606.1 TRUE FALSE FALSE 5547.747594 5692.527 5572.731849 3979.098636 4651.073475 4781.428065 4233.544277 4440.156397 5629.521716 6434.47257 0.862191506 0.884692092 0.866074381 0.618403232 0.722836787 0.74309557 0.657947366 0.690057553 0.874900259 1 12.65160618 -9.901271615 0.349667346 1.001209401 0.634459732 0.684201833 0.065249137 0.429790386 0.138692467 0.037198443 0.06011612 1.26E-10 9.901271615 -0.366749669 HEK(ac)EDGAISTIVLR ddPTM_HeLa_Romidepsin_16h_R1 1 HEKEDGAISTIVLR 14 1 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 1 HEK(1)EDGAISTIVLR 101.2 0.012705 1010700 453.3 315.36 477.12 437.62 632.96 657.61 746.65 704.5 868.31 879.67 FALSE TRUE FALSE 447.7750052 319.7996464 485.4240735 488.2196835 600.6576893 615.5908433 810.0704324 724.883596 790.6461789 856.8160466 0.52260343 0.373241897 0.566544097 0.569806886 0.701034594 0.718463252 0.945442649 0.846020098 0.922772376 1 9.742841689 -7.798672514 8.696020176 0.703515204 0.895576762 0.184275994 0.178769526 0.435751574 94.00344501 0.032558659 0.099382133 1.59E-08 7.798672514 0.192061558 HELIEFR ddPTM_HeLa_Romidepsin_16h_R1 2 HELIEFR 7 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5;J3KRF5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 ; ; 197.6 1.31E-06 26627000 9977.6 8098.9 13315.5 8557.1 11213.9 11393.2 9614.1 9451.9 10618.5 8603.2 FALSE FALSE TRUE 9855.989173 8212.916527 13547.25069 9546.512164 10641.61284 10665.21129 10430.72141 9725.375814 9668.754765 8379.687624 1.176176203 0.980098173 1.616677292 1.139244396 1.269929539 1.272745688 1.244762559 1.160589302 1.153832362 1 13.03268075 -11.23798676 0.560124952 1.0058141 1.258570111 0.140000269 0.155754327 0.741982188 0.518054063 0.082203396 0.041956148 5.78E-12 11.23798676 0.25275601 HELS(ph)PPQKR ddPTM_HeLa_Romidepsin_16h_R1 1 HELSPPQKR 9 1 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;C9JUL9 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 1 0 HELS(1)PPQKR 68.786 0.026299 29121000 4597.7 4536.1 4512.4 2479.7 4179.4 4332.1 4253.6 3937 5079.9 4668.2 TRUE FALSE FALSE 4541.661464 4599.959335 4590.936429 2766.414581 3966.109623 4055.292791 4614.900678 4050.910883 4625.541021 4546.919491 0.998843607 1.011665006 1.009680606 0.608415123 0.872262997 0.891876973 1.014951043 0.890913264 1.017291164 1 12.15067374 HERTHT(ph)INI ddPTM_HeLa_Romidepsin_16h_R1 1 HERTHTINI 9 1 Q8N8L2 Q8N8L2 ZNF491 Zinc finger protein 491 1 0 HERT(0.001)HT(0.999)INI 87.639 0.024357 3731700 57.543 58.776 0 0 145.64 0 50.252 0 131.34 151.86 TRUE FALSE FALSE 56.84164378 59.60345007 0 0 138.2074473 0 54.52040363 0 119.5926215 147.9146553 0.384286761 0.402958381 0 0 0.934372913 0 0.368593656 0 0.808524491 1 7.208621191 -11.86571577 0.505540283 1.087510492 0.228852714 0.459436129 0.280224423 0.733132673 0.320251419 0.300028592 0.075496895 1.36E-12 11.86571577 -0.858657777 HFAMNAAAT(ph)AAAERDT(ph)TIINHSR ddPTM_HeLa_Romidepsin_16h_R1 1 HFAMNAAATAAAERDTTIINHSR 23 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 2 0 HFAMNAAAT(0.998)AAAERDT(0.499)T(0.499)IINHS(0.004)R 46.461 0.022439 1705000 884.82 524.5 622.06 612.43 716.11 558.41 508.68 751.87 597.33 615.27 TRUE FALSE FALSE 874.0354735 531.8839248 632.8866934 683.2420382 679.5642345 522.7294032 551.8872665 773.6241722 543.9033088 599.2851967 1.458463313 0.887530558 1.056069292 1.14009497 1.133957986 0.872254823 0.920909226 1.290911533 0.907586758 1 9.227098927 -10.24196113 24.99146069 1.216496583 1.039556607 0 0.186680091 1213.213776 1556610.161 0.033815894 0.041384733 5.73E-11 10.24196113 -0.176939976 HFDPEFTEEPVPNS(ph)IGKSPDSVLVTASVK ddPTM_HeLa_Romidepsin_16h_R1 1 HFDPEFTEEPVPNSIGKSPDSVLVTASVK 29 1 E9PR89;O00141-4;O00141;O00141-3;O00141-5;O00141-2 E9PR89 SGK1 Serine/threonine-protein kinase Sgk1 1 0 HFDPEFTEEPVPNS(0.431)IGKS(0.431)PDS(0.128)VLVT(0.009)AS(0.001)VK 80.813 9.54E-07 13332000 1217.7 1046.6 1102.4 1290.3 1043 936.31 960.77 1134.3 1551.2 1383.5 TRUE FALSE FALSE 1202.858204 1061.334062 1121.58681 1439.490557 989.771818 876.4828128 1042.37778 1167.119181 1412.456787 1347.556471 0.892621742 0.787598951 0.832311546 1.068222808 0.734493759 0.650423809 0.773531798 0.866100387 1.048161482 1 10.39613002 -10.69742498 0.210039025 1.0668092 0.72173786 0.402163953 0.101503134 2.283043877 0.418373261 0.317728696 0.248950795 2.01E-11 10.69742498 -0.34507134 HFELGGDK ddPTM_HeLa_Romidepsin_16h_R1 2 HFELGGDK 8 0 R4GN19;H0Y5B4;H7BZ11;J3KQN4;Q969Q0;P83881 R4GN19 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a-like;60S ribosomal protein L36a 0 0 ; ; 103.55 0.013108 33654000 16444.4 15476.8 22671.1 18140.4 22580.3 22691.1 19423.7 12136.9 16684.1 15439.4 FALSE FALSE TRUE 16243.96933 15694.6828 23065.68099 20237.8784 21427.94303 21241.21194 21073.54859 12488.06205 15191.83231 15038.28216 1.080174527 1.043648645 1.533797593 1.345757327 1.424893003 1.412475954 1.401326851 0.830418123 1.010210618 1 13.87635216 -9.791718784 23.32961727 1.039351972 1.337748078 0.389617106 0.178097379 70.05520349 53975.60705 0.027373797 0.035980058 1.62E-10 9.791718784 0.298396106 HFELGGDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 HFELGGDKK 9 1 R4GN19;H0Y5B4;H7BZ11;J3KQN4;Q969Q0;P83881 R4GN19 RPL36A;RPL36A-HNRNPH2;RPL36AL 60S ribosomal protein L36a-like;60S ribosomal protein L36a 0 1 HFELGGDK(1)K 96.665 0.0048365 551870 403.77 473.46 737.91 474.74 1171.9 1292.3 1708.4 366.03 1374.3 836.13 FALSE TRUE FALSE 398.8486959 480.1253823 750.753014 529.6316725 1112.09357 1209.726201 1853.511453 376.6205006 1251.379166 814.4072221 0.489741109 0.589539691 0.921839829 0.650327819 1.365525182 1.485407015 2.275902525 0.462447398 1.536552147 1 9.669606545 -8.693403269 4.91176505 0.745935115 1.481824103 0.187587999 0.499476137 0.158264248 7.273963562 0.060837381 0.122752195 2.03E-09 8.693403269 0.735888988 HFGAEYR ddPTM_HeLa_Romidepsin_16h_R1 2 HFGAEYR 7 0 P04818-2;P04818 P04818-2 TYMS Thymidylate synthase 0 0 ; ; 143.02 0.0003299 1314000 394.25 232.45 399.59 227.52 340.465 260.47 223.49 129.05 422.43 221.499 FALSE FALSE TRUE 389.4447294 235.7224372 406.5446963 253.8269329 323.0898006 243.8268076 242.473235 132.7838581 384.6468028 215.744424 1.805120717 1.092600368 1.884381013 1.17651677 1.497558058 1.130165049 1.123891086 0.61546832 1.78288178 1 7.753179463 -7.071649903 1.038022941 1.395955366 7.04E-12 0.420614786 0.299130338 2.295794227 1.494408747 0.051064624 3.876262616 8.48E-08 7.071649903 -1.395955366 HFHPLFEYFDYESR ddPTM_HeLa_Romidepsin_16h_R1 1 HFHPLFEYFDYESR 14 0 Q96QK1 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 0 0 124.48 0.0012932 7717800 3183.3 2251.1 2763.9 2076.8 3151.5 3003.1 2955.7 3067.9 2968.4 2787.4 FALSE FALSE TRUE 3144.500715 2282.791045 2812.00452 2316.929388 2990.667195 2811.211602 3206.757084 3156.664846 2702.89887 2714.982946 1.15820275 0.840812296 1.035735611 0.85338635 1.101541798 1.035443558 1.181133417 1.162683121 0.995549115 1 11.40672742 -7.762488083 24.98438725 1.040712216 1.171908306 0.261960776 0.098221763 32.0579054 763853.6663 0.014978126 0.049071052 1.73E-08 7.762488083 0.13119609 HFIDVGAGVIDEDYR ddPTM_HeLa_Romidepsin_16h_R1 3 HFIDVGAGVIDEDYR 15 0 P33316;H0YKI0;A0A0C4DGL3;H0YMP1;H0YKC5;H0YNW5;H0YMM5;P33316-2;H0YNJ9 P33316;H0YNW5;P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 0 0 ;; ;; 166.64 1.61E-05 112242600 11689.4 10686.8 11868 8170.5 11406.7 11725.6 9394.6 11010.4 12209 10649.5 FALSE FALSE TRUE 11546.9251 10837.24905 12074.55756 9115.211653 10824.57353 10976.372 10192.57709 11328.96855 11116.99646 10372.82445 1.113190062 1.044773205 1.164056869 0.878758885 1.043551212 1.058185459 0.982623116 1.092177796 1.071742466 1 13.34052116 HFSGLEEAVYR ddPTM_HeLa_Romidepsin_16h_R1 1 HFSGLEEAVYR 11 0 P50990-2;P50990;H7C4C8 P50990-2 CCT8 T-complex protein 1 subunit theta 0 0 158.56 0.00074922 4828600 2890.5 2048.1 3128.1 2408 3273.2 2710.4 2301.9 2228.4 2494.2 1795.4 FALSE FALSE TRUE 2855.269474 2076.933206 3182.543268 2686.42429 3106.15639 2537.214187 2497.423329 2292.875238 2271.112505 1748.755249 1.632743905 1.187663743 1.819890616 1.536192267 1.776209902 1.450868661 1.428114843 1.311147023 1.298702323 1 10.77211267 -12.36265647 0.842333364 0.963166584 1.530919401 0.301257308 0.204359619 0.441167103 0.499759103 0.170572996 0.034364548 4.34E-13 12.36265647 0.567752816 HFSQS(ph)EETGNEVFGALNEEQPLPR ddPTM_HeLa_Romidepsin_16h_R1 2 HFSQSEETGNEVFGALNEEQPLPR 24 0 A0A1B0GUI1;Q6GYQ0-3;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-2 A0A1B0GUI1 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 0 HFS(0.077)QS(0.912)EET(0.011)GNEVFGALNEEQPLPR;HFS(0.413)QS(0.587)EETGNEVFGALNEEQPLPR ; 223 5.86E-47 36336000 1359.53 1529.4 1488.03 1113.34 1495.22 1376.14 1585.03 2075.7 1618.97 1481.84 TRUE FALSE FALSE 1342.959525 1550.930933 1513.928538 1242.069609 1418.913344 1288.209095 1719.662409 2135.757105 1474.165268 1443.341583 0.930451628 1.074541849 1.048905232 0.860551392 0.98307522 0.892518521 1.191445205 1.479730876 1.02135578 1 10.49519706 -7.439573217 2.754041837 0.96973231 1.494615853 0.847691285 0.066234146 0.083320349 1.035426062 0.009025007 0.080552376 3.63E-08 7.439573217 0.524883542 HFVGYPTNSDFELK ddPTM_HeLa_Romidepsin_16h_R1 1 HFVGYPTNSDFELK 14 0 F6XGT7;Q5JVP2;F2Z3J9;Q14914-2;Q14914 F6XGT7 PTGR1 Prostaglandin reductase 1 0 0 93.494 0.0019707 0 1649.9 1496.5 1480.6 1997.9 1838.5 1896.7 1653.3 1684 1827.2 1601.6 FALSE FALSE TRUE 1629.790384 1517.567766 1506.369222 2228.906598 1744.674485 1775.506991 1793.731261 1732.723883 1663.770656 1559.990201 1.044743988 0.972805961 0.965627362 1.428795256 1.118388105 1.138152656 1.149834954 1.110727415 1.06652635 1 10.60732125 HGAPAAPS(ph)PPPR ddPTM_HeLa_Romidepsin_16h_R1 3 HGAPAAPSPPPR 12 0 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 HGAPAAPS(1)PPPR;HGAPAAPS(1)PPPR;HGAPAAPS(1)PPPR ;; 118.61 0.0078761 27100000 10265.5 10180.3 8696.8 9609.3 11078.6 12206.8 10934.3 11092.8 10554.9 9671.9 TRUE FALSE FALSE 10140.38014 10323.61853 8848.164156 10720.37248 10513.2177 11426.82488 11863.05917 11413.75267 9610.843309 9420.622644 1.076402327 1.0958531 0.939233476 1.13796857 1.115979071 1.21295856 1.259264872 1.211570944 1.020191942 1 13.2016067 -8.558429609 1.349035077 1.036500358 1.239564344 0.749129182 0.048710032 0.167739522 0.593529259 0.007881421 0.024100849 2.76E-09 8.558429609 0.203063987 HGAPSPSHPIS(ph)APQAAAAAALR ddPTM_HeLa_Romidepsin_16h_R1 1 HGAPSPSHPISAPQAAAAAALR 22 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 HGAPS(0.111)PS(0.414)HPIS(0.476)APQAAAAAALR 50.226 0.021963 10466000 806.55 639.58 975.77 684.97 1180 978.67 1007.4 1029.6 882.99 1057.4 TRUE FALSE FALSE 796.7194584 648.584024 992.7528675 764.1694543 1119.780197 916.1361455 1092.968531 1059.389852 804.0131629 1029.928596 0.773567665 0.629736884 0.963904558 0.741963528 1.087240612 0.889514234 1.061208064 1.028605144 0.780649422 1 10.0083286 -8.749908755 24.99989466 0.865097376 1.010744738 0.374804517 0.117235358 266.7824708 578415.5371 0.019166893 0.038070763 1.78E-09 8.749908755 0.145647362 HGEK(ac)APMTSR ddPTM_HeLa_Romidepsin_16h_R1 1 HGEKAPMTSR 10 1 P23497;E9PHV6;P23497-7;P23497-5;P23497-2;P23497-3;P23497-4;H7C1G8;H7C4B4 P23497 SP100 Nuclear autoantigen Sp-100 0 1 HGEK(1)APMTSR 60.691 0.022328 4750700 307.25 359.15 330.88 287.55 306.36 372.52 284.22 232.28 237.37 281.68 FALSE TRUE FALSE 303.5051188 364.2061231 336.6388276 320.797884 290.725306 348.7171743 308.3616397 239.0006553 216.1390327 274.361913 1.106221762 1.327466043 1.226988192 1.169250792 1.059641635 1.271011601 1.12392291 0.871114553 0.787788036 1 8.09993641 -11.27994649 1.241821656 1.02085075 1.152748066 0.255353422 0.140127517 0.499504013 1.572494977 0.032814594 0.023794085 5.25E-12 11.27994649 0.131897316 HGEPEEDIVGLQAFQER ddPTM_HeLa_Romidepsin_16h_R1 1 HGEPEEDIVGLQAFQER 17 0 E9PF10;O75694-2;O75694 E9PF10 NUP155 Nuclear pore complex protein Nup155 0 0 114.52 0.00097704 2509600 2354.9 2619.1 2737.3 2306.7 2330.7 2335.3 2192 2084.3 3130.4 2963.8 FALSE FALSE TRUE 2326.197573 2655.971759 2784.941558 2573.411507 2211.755682 2186.081867 2378.188425 2144.605932 2850.409184 2886.800049 0.805804882 0.920040084 0.964715779 0.891440856 0.766161717 0.757268197 0.823814738 0.742900754 0.987394047 1 11.49525547 -8.807565656 5.219872597 0.911396557 0.774814683 0.641764572 0.05625894 0.142444109 8.693948453 0.011189877 0.020949046 1.56E-09 8.807565656 -0.136581874 HGESAWNLENR ddPTM_HeLa_Romidepsin_16h_R1 3 HGESAWNLENR 11 0 P18669 P18669 PGAM1 Phosphoglycerate mutase 1 0 0 ;; ;; 150.09 0.0011006 43745000 10891.2 8880.2 9079.8 10033.7 12930.4 11362.3 9920.7 10000.3 12101.4 10707.5 FALSE FALSE TRUE 10758.45387 9005.215689 9237.83011 11193.8436 12270.51344 10636.2857 10763.36401 10289.6429 11019.02048 10429.31761 1.031558753 0.863452052 0.885755949 1.073305467 1.176540393 1.019844836 1.032029555 0.986607494 1.056542805 1 13.34835714 HGGPGPGGPEPELS(ph)PITEGSEAR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 HGGPGPGGPEPELS(0.975)PIT(0.025)EGS(0.001)EAR 135.17 2.76E-06 12753000 1622 1647.1 1778 1523.8 2241.6 2181.4 1762 2065.2 1900.7 1463.1 TRUE FALSE FALSE 1602.23044 1670.287917 1808.945344 1699.988926 2127.202787 2042.01558 1911.664236 2124.953304 1730.696632 1425.088451 1.124302452 1.172059121 1.269356539 1.19290064 1.492681234 1.432904448 1.341435498 1.491102747 1.21444857 1 10.47683575 -9.474627248 0.44271939 1.014278114 1.489847784 0.669272742 0.089604654 0.294702036 0.118875112 0.023334593 0.056595027 3.35E-10 9.474627248 0.47556967 HGGPGPGGPEPELSPIT(ph)EGSEAR ddPTM_HeLa_Romidepsin_16h_R1 3 HGGPGPGGPEPELSPITEGSEAR 23 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 HGGPGPGGPEPELS(0.047)PIT(0.832)EGS(0.121)EAR;HGGPGPGGPEPELS(0.128)PIT(0.749)EGS(0.123)EAR;HGGPGPGGPEPELS(0.425)PIT(0.568)EGS(0.007)EAR ;; 161.48 7.91E-10 50668200 4174.91 4144.62 3902.75 3732.92 4941.26 5531.21 4513.2 5960.65 4820.67 4411.64 TRUE FALSE FALSE 4124.024591 4202.968069 3970.675727 4164.537774 4689.089064 5177.783532 4896.551095 6133.112003 4389.497202 4297.024957 0.959739502 0.978111161 0.924052284 0.969167695 1.091240826 1.204969388 1.139521214 1.427292619 1.021520062 1 12.06912244 -6.822428699 0.623962046 0.973618026 1.934689805 0.866951301 0.052915606 1.255597127 0.229610321 0.009174618 0.977254525 1.51E-07 6.822428699 0.961071779 HGGS(ph)PQPLAT(ph)TPLSQEPVNPPSEAS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 0 HGGS(1)PQPLAT(0.499)T(0.499)PLS(0.001)QEPVNPPS(0.306)EAS(0.541)PT(0.152)R 85.009 8.59E-06 25094000 447.1 407.72 557.47 178.47 425.97 397.14 532.95 457.33 501.11 639.56 TRUE FALSE FALSE 441.6505732 413.4598929 567.1725315 199.1055411 404.2311614 371.7640357 578.2187597 470.562122 456.2894665 622.944139 0.708972997 0.663719051 0.910470933 0.319620217 0.64890435 0.59678551 0.928203226 0.755384139 0.732472525 1 9.282958989 -12.0002782 0.63199115 1.021434386 0.682737655 0.055449692 0.179954879 0.809654124 0.548248132 0.147976636 0.036992773 9.99E-13 12.0002782 -0.338696731 HGGS(ph)PQPLATT(ph)PLSQEPVNPPS(ph)EASPTR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 0 HGGS(0.995)PQPLAT(0.353)T(0.652)PLS(0.172)QEPVNPPS(0.536)EAS(0.24)PT(0.052)R 100.64 1.06E-07 27768000 908.32 672.22 877.12 479.96 936.91 970.29 838.41 695.64 894.68 801.12 TRUE FALSE FALSE 897.2490465 681.6835308 892.3859057 535.4552335 889.0959866 908.2916005 909.6245245 715.7672459 814.65758 780.3067869 1.149867029 0.873609639 1.143634684 0.68621117 1.139418497 1.164018583 1.165726788 0.91728953 1.044022164 1 9.607897638 HGGS(ph)PQPLATTPLSQEPVNPPS(ph)EASPTR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 HGGS(0.994)PQPLAT(0.004)T(0.005)PLS(0.03)QEPVNPPS(0.403)EAS(0.282)PT(0.281)R 55.677 0.016313 45184000 1126 1091.2 1274.9 686.07 899.63 897.51 792.79 890.56 1146.4 1129.2 TRUE FALSE FALSE 1112.275879 1106.561942 1297.0891 765.3966415 853.7185241 840.1620076 860.1295628 916.3269485 1043.863113 1099.863221 1.011285638 1.006090504 1.17931855 0.69590166 0.776204266 0.763878627 0.782033208 0.833128093 0.949084479 1 10.10310841 -9.248633827 24.99886493 1.0173968 0.770864087 0.802605075 0.064071306 239.8825326 468296.255 0.008765319 0.014475794 5.64E-10 9.248633827 -0.246532713 HGGS(ph)PQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 HGGS(0.989)PQPLAT(0.007)T(0.003)PLS(0.002)QEPVNPPS(0.154)EAS(0.626)PT(0.22)R;HGGS(1)PQPLATTPLSQEPVNPPS(0.144)EAS(0.513)PT(0.343)R;HGGS(0.983)PQPLAT(0.015)T(0.004)PLS(0.003)QEPVNPPS(0.19)EAS(0.46)PT(0.344)R ;; 134.8 2.42E-09 233204000 3354.47 3678.47 3568.91 2086.61 3028.86 3507.1 3045.04 2849.9 3987.09 4118.29 TRUE FALSE FALSE 3313.584429 3730.255597 3631.025381 2327.873666 2874.285972 3283.007629 3303.685622 2932.35736 3630.474685 4011.296232 0.826063257 0.929937701 0.905200008 0.580329532 0.71654792 0.818440583 0.823595524 0.731024883 0.905062721 1 11.9698528 -9.45675997 17.49108436 0.916525971 0.74268989 0.5930219 0.074112716 6.325319344 1672.815945 0.01388466 0.02120896 3.49E-10 9.45675997 -0.173836082 HGGS(ph)PQPLATTPLSQEPVNPPSEASPTR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 HGGS(0.993)PQPLAT(0.005)T(0.003)PLSQEPVNPPSEASPTR 105.49 6.83E-09 7363200 1218.7 1140.5 932.54 765.14 921.75 814.16 552.3 767.88 1398.3 1117.1 TRUE FALSE FALSE 1203.846016 1156.555989 948.7704675 853.6090869 874.709658 762.1378036 599.2123482 790.0973963 1273.232546 1088.077581 1.106397225 1.062935226 0.871969503 0.784511235 0.80390376 0.700444359 0.550707375 0.726140682 1.170167062 1 10.08756571 -9.175922948 1.058682545 1.054166507 0.658015794 0.854125007 0.072727006 0.131516156 0.29104191 0.012400853 0.027209547 6.67E-10 9.175922948 -0.396150713 HGGSPQPLATTPLSQEPVNPPSEAS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 HGGSPQPLATTPLSQEPVNPPSEASPTR 28 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 HGGSPQPLATTPLSQEPVNPPS(0.233)EAS(0.534)PT(0.233)R 71.212 5.61E-05 17485000 1996.8 1611.3 2090.2 908.81 1863.5 1993.9 1652.7 1612.7 2445.1 2858.8 TRUE FALSE FALSE 1972.462234 1633.983924 2126.579054 1013.890888 1768.398641 1866.496225 1793.080297 1659.36093 2226.404132 2784.527964 0.70836503 0.586808229 0.763712587 0.364115894 0.635080223 0.670309743 0.64394408 0.595921805 0.799562497 1 11.44321707 -11.58141483 0.534336541 1.0184872 0.597315803 0.479733977 0.112520201 0.38389297 0.216821498 0.075752208 0.026785333 2.62E-12 11.58141483 -0.421171397 HGGVCAPAAVAT(ph)SPPGAIPK ddPTM_HeLa_Romidepsin_16h_R1 1 HGGVCAPAAVATSPPGAIPK 20 0 A0A494BZT8;Q9Y6A5;E7EMT0 A0A494BZT8 TACC3 Transforming acidic coiled-coil-containing protein 3 1 0 HGGVCAPAAVAT(0.5)S(0.5)PPGAIPK 85.813 0.005554 7757600 2056.6 1781.5 2054.5 302.37 2561.5 2994.1 2903.3 3232.1 2550 1890 TRUE FALSE FALSE 2031.533368 1806.580004 2090.257711 337.3314421 2430.777097 2802.786673 3149.90623 3325.615714 2321.921613 1840.897528 1.103555922 0.981358265 1.135455765 0.183242922 1.320430421 1.522510966 1.711070922 1.806518649 1.261298676 1 10.84619361 -8.318582365 3.039087811 0.992581255 1.7067114 0.560443425 0.287949779 0.141248899 2.573013755 0.038930449 0.099868685 4.80E-09 8.318582365 0.714130145 HGGVIHIYVDK ddPTM_HeLa_Romidepsin_16h_R1 2 HGGVIHIYVDK 11 0 Q14498-2;Q14498;H0Y4X3;Q14498-3 Q14498-2 RBM39 RNA-binding protein 39 0 0 ; ; 85.533 0.01196 1543230 2823.2 1835.41 2338.3 1012.95 2691.3 2265.4 1311.34 1736.25 2152.74 2762.7 FALSE FALSE TRUE 2788.789752 1861.24895 2378.997131 1130.072045 2553.952918 2120.648251 1422.725187 1786.485654 1960.193543 2690.924656 1.036368576 0.691676352 0.884081658 0.419956777 0.949098635 0.788074184 0.528712383 0.663892856 0.72844609 1 11.39388628 -10.26085196 24.87234079 1.017174054 0.705630846 0.19596995 0.172276518 28.46740747 1205355.482 0.023292935 0.027617457 5.48E-11 10.26085196 -0.311543208 HGITQANELVNLTEFFVNHILPDLK ddPTM_HeLa_Romidepsin_16h_R1 1 HGITQANELVNLTEFFVNHILPDLK 25 0 P55060-4;P55060-3;P55060 P55060-4 CSE1L Exportin-2 0 0 79.695 1.72E-05 7802400 1883.4 1668.4 1652.8 1589.5 1270.8 4773.3 2966.2 2582.3 2122.3 2319.1 FALSE FALSE TRUE 1860.444396 1691.887779 1681.566291 1773.285469 1205.946334 4468.301535 3218.148954 2657.014776 1932.476173 2258.849448 0.823624788 0.749004225 0.744434868 0.785039247 0.533876366 1.978131628 1.424685013 1.176269086 0.855513489 1 11.1413724 -8.268887026 24.99727025 0.856553629 1.516194226 0.694470924 0.221888299 258.6887672 868263.3143 0.032384168 0.073785767 5.38E-09 8.268887026 0.659640597 HGLQSLGK(ac)VAAAR ddPTM_HeLa_Romidepsin_16h_R1 2 HGLQSLGKVAAAR 13 1 Q5JSZ5;Q5JSZ5-5;A0A1W2PQP5 Q5JSZ5 PRRC2B Protein PRRC2B 0 1 ; HGLQSLGK(1)VAAAR;HGLQSLGK(1)VAAAR 122.34 0.002098 1483690 762.54 687.9 966.57 685.88 798.36 925.91 710.64 377.93 1111.59 606.21 FALSE TRUE FALSE 753.2458692 697.5842743 983.3927454 765.1846728 757.6167101 866.7473392 771.0017439 388.8648083 1012.166606 590.4605768 1.275692059 1.181423962 1.665467237 1.295911536 1.283094486 1.467917374 1.305763287 0.658578783 1.714198451 1 9.205696928 -11.96298013 0.801805604 1.001745312 1.286700455 0 0.327090957 0.900299169 1.070989263 0.149817922 0.048176291 1.09E-12 11.96298013 0.284955142 HGRDDS(ph)FDSLDSFGSR ddPTM_HeLa_Romidepsin_16h_R1 2 HGRDDSFDSLDSFGSR 16 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 HGRDDS(0.908)FDS(0.079)LDS(0.013)FGSR;HGRDDS(0.995)FDS(0.005)LDSFGSR ; 103.71 0.0017066 8719200 2148.81 2096.3 2241.9 2228.1 1936.43 1631.7 1886.56 1789.3 3252.6 2545 TRUE FALSE FALSE 2122.619477 2125.811766 2280.919329 2485.723406 1837.606751 1527.439636 2046.804359 1841.070572 2961.67931 2478.880533 0.856281474 0.857569269 0.920140886 1.002760469 0.741305088 0.616181222 0.825697056 0.742702421 1.194764842 1 11.27547303 -8.739954819 18.92250771 0.927753732 0.729964247 0.525672634 0.10706764 7.842452855 6906.141629 0.011217548 0.022381352 1.82E-09 8.739954819 -0.197789485 HGS(ph)GADSDY(ph)ENTQSGDPLLGLEGK ddPTM_HeLa_Romidepsin_16h_R1 1 HGSGADSDYENTQSGDPLLGLEGK 24 0 J3QRU8;A0A0C4DGN6;Q9Y2X7;Q9Y2X7-3;J3QL89 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 2 0 HGS(0.968)GADS(0.121)DY(0.901)ENT(0.006)QS(0.003)GDPLLGLEGK 110.03 4.91E-06 5207900 1810.9 1719.7 1551.5 1571.4 2120.1 2637.8 2203 2134 1662.8 1760.6 TRUE FALSE FALSE 1788.828054 1743.909982 1578.503207 1753.092662 2011.903386 2469.253093 2390.122765 2195.743923 1514.075003 1714.859358 1.043133972 1.016940528 0.920485519 1.0222953 1.17321772 1.439915805 1.393771888 1.28042216 0.882914973 1 10.74387455 -8.517309189 3.075731025 1.012569175 1.372132078 0.878798328 0.064409097 0.051148811 0.986419456 0.007496445 0.017160795 3.04E-09 8.517309189 0.359562903 HGS(ph)VSADEAAR ddPTM_HeLa_Romidepsin_16h_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 0 HGS(0.951)VS(0.049)ADEAAR 96.067 0.024633 2931700 954.24 939.42 975.17 621.2 525.39 630.33 533.99 491.92 1012.9 1155 TRUE FALSE FALSE 942.6093558 952.6451794 992.1424248 693.0260668 498.5773878 590.0539473 579.3470973 506.1529291 922.3036871 1124.992933 0.837880246 0.846801034 0.881909917 0.61602704 0.443182684 0.524495692 0.514978432 0.449916541 0.819830649 1 10.13570022 -9.173886891 2.29864502 0.91545967 0.486790189 0.910952873 0.058030351 0.068652585 0.708876191 0.011006353 0.019552234 6.70E-10 9.173886891 -0.428669481 HGS(ph)YEDAVHSGALND ddPTM_HeLa_Romidepsin_16h_R1 1 HGSYEDAVHSGALND 15 0 P17987;F5H282;E7EQR6 P17987 TCP1 T-complex protein 1 subunit alpha 1 0 HGS(1)YEDAVHSGALND 135.55 0.00054771 12002000 3057.9 2942.8 2762.1 1879.7 2708.2 2941.5 2342.2 2476.6 3024 2677.3 TRUE FALSE FALSE 3020.629139 2984.228816 2810.173192 2097.039758 2569.990448 2753.547643 2541.14641 2548.256514 2753.525866 2607.74336 1.15833068 1.144372127 1.077626439 0.804158795 0.985522766 1.055912052 0.974461846 0.977188382 1.055903701 1 11.34858618 -9.471351881 24.99568199 1.083454106 0.964470632 0.439763384 0.071977285 323.7666443 157059.2247 0.013193082 0.020152653 3.38E-10 9.471351881 -0.118983474 HGTDLWIDNMSSAVPNHS(ph)PEKK ddPTM_HeLa_Romidepsin_16h_R1 1 HGTDLWIDNMSSAVPNHSPEKK 22 1 Q8N6H7;E9PIY6;H0YF45;E9PJT7;E9PK28;E9PN48 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 0 HGTDLWIDNMS(0.003)S(0.013)AVPNHS(0.984)PEKK 69.763 0.0010133 15875000 4758.2 4106.6 3720.6 3617.5 7215.5 7237 5037.8 5403.5 7584.5 5103.5 TRUE FALSE FALSE 4700.205228 4164.412823 3785.355482 4035.772371 6847.26611 6774.579056 5465.710606 5559.841747 6906.123324 4970.910334 0.945542147 0.837756576 0.761501461 0.811877926 1.377467234 1.362844751 1.099539167 1.118475565 1.389307563 1 12.27929436 -8.763331424 24.9998708 0.934425509 1.238383153 0.359472136 0.182783348 27.74755162 366639.8252 0.018865489 0.035497865 1.72E-09 8.763331424 0.303957644 HGVESTLER ddPTM_HeLa_Romidepsin_16h_R1 1 HGVESTLER 9 0 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 0 0 118.71 0.0066448 1548500 1208.7 680.46 951.35 582.85 1296.3 1236.8 886.98 750.85 1365.4 1208.2 FALSE FALSE TRUE 1193.967899 690.0395337 967.9078477 650.2418594 1230.144974 1157.772472 962.3200591 772.5746601 1243.275204 1176.81079 1.014579327 0.586364044 0.822483832 0.5525458 1.045320951 0.983822108 0.817735584 0.65649862 1.05647842 1 10.20066666 -10.31930924 24.83554808 1.006884779 0.792931442 0.353559145 0.149420121 220.5360203 94645.07202 0.025269123 0.028896344 4.79E-11 10.31930924 -0.213953337 HGYIGEFEIIDDHR ddPTM_HeLa_Romidepsin_16h_R1 2 HGYIGEFEIIDDHR 14 0 I3L3P7;I3L246;H3BN98;P62244 I3L3P7 RPS15A 40S ribosomal protein S15a 0 0 ; ; 116.51 0.0017639 41319000 19188 16509.9 17730 17669.1 19160.3 18192.4 16291 16644.6 19923.2 17021.2 FALSE FALSE TRUE 18954.12928 16742.32681 18038.58321 19712.08448 18182.47839 17029.96435 17674.75713 17126.18524 18141.21909 16578.98677 1.143262223 1.009852233 1.088038941 1.188980048 1.096718313 1.027201758 1.066093928 1.033005544 1.094229662 1 14.01706822 -8.259106656 24.84421526 1.077237689 1.044499764 0.11097009 0.053883754 524.2486294 5583324.073 0.009644032 0.023257365 5.51E-09 8.259106656 -0.032737926 HHS(ph)LGGQYGVQGFPTIK ddPTM_HeLa_Romidepsin_16h_R1 1 HHSLGGQYGVQGFPTIK 17 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 1 0 HHS(0.999)LGGQYGVQGFPTIK 69.148 0.013845 8517900 1149.4 1705 1406.4 1487.9 1356.4 1613.3 1392.8 1585.1 1410.8 1455.4 TRUE FALSE FALSE 1135.390671 1729.003035 1430.877802 1659.937999 1287.177847 1510.215337 1511.104397 1630.962368 1284.614515 1417.588498 0.800931069 1.21967908 1.009374585 1.170958992 0.908005284 1.065341133 1.065968297 1.150518906 0.90619705 1 10.46922309 -10.26933796 24.99845858 0.905995229 1.076507198 0.439798744 0.093759232 473.3192633 1498020.933 0.017848694 0.020595505 5.38E-11 10.26933796 0.170511969 HIDFSLR ddPTM_HeLa_Romidepsin_16h_R1 3 HIDFSLR 7 0 P46781 P46781 RPS9 40S ribosomal protein S9 0 0 ;; ;; 147.69 0.0015685 20115400 1212.7 781.91 2272.58 2134.21 2808.84 2581.69 1693.61 1091.68 882.58 784.59 FALSE FALSE TRUE 1197.919146 792.9177495 2312.133302 2380.977402 2665.494414 2416.728341 1837.465191 1123.266038 803.6398343 764.2062387 1.567533848 1.03757037 3.025535758 3.115621519 3.487925482 3.162403313 2.40441009 1.469846727 1.051600725 1 9.577818225 -9.760976091 24.99998293 1.25820795 2.825799622 0.677872962 0.542724988 5.930743049 320022.4157 0.092385971 0.126148254 1.73E-10 9.760976091 1.567591672 HIDLVEGDEGR ddPTM_HeLa_Romidepsin_16h_R1 2 HIDLVEGDEGR 11 0 P19367-4;P19367-2;P19367;P19367-3 P19367-4 HK1 Hexokinase-1 0 0 ; ; 134.38 0.0019619 12756200 9048.7 8947.4 8530.8 9134.8 9235 10647.2 8932.6 10949.3 10209.2 9288.7 FALSE FALSE TRUE 8938.410964 9073.361732 8679.274995 10191.00856 8763.703489 9966.878282 9691.334821 11266.10072 9296.063583 9047.378235 0.987955928 1.002871937 0.959313822 1.12640461 0.968645641 1.101631658 1.071176043 1.245233749 1.027487007 1 13.14328407 -4.000000008 0.540751732 0.995333617 10.9510348 0.668285463 0.048523084 41.95186008 0.360126919 0.007799893 485.5857127 1.00E-04 4.000000008 9.955701178 HIEIFTDLSSR ddPTM_HeLa_Romidepsin_16h_R1 1 HIEIFTDLSSR 11 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 0 97.779 0.0043231 581000 550.53 592.36 585.29 591.04 467.77 813.34 618.6 599.16 630.01 543.75 FALSE FALSE TRUE 543.8199286 600.6992596 595.4767269 659.3788257 443.8979514 761.3701989 671.1438686 616.4957493 573.6603277 529.6232966 1.02680515 1.134200975 1.124340131 1.244995887 0.838139021 1.437569314 1.267209869 1.164026872 1.083147836 1 9.048822773 -8.89495295 0.380304122 0.994173577 1.301634474 0.188189578 0.140378341 1.834820283 0.425575972 0.051626844 0.224412418 1.27E-09 8.89495295 0.307460897 HIELGVTGGGS(ph)PENGDGALLAITPPAVK ddPTM_HeLa_Romidepsin_16h_R1 1 HIELGVTGGGSPENGDGALLAITPPAVK 28 0 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 HIELGVT(0.109)GGGS(0.888)PENGDGALLAIT(0.003)PPAVK 51.975 0.0075604 14638000 1956.1 1783.7 1696.3 1602.8 2003.3 1770.8 1444.6 1548.5 1930.7 2043 TRUE FALSE FALSE 1932.258301 1808.810975 1725.82339 1788.123277 1901.064126 1657.651595 1567.304288 1593.303404 1758.013356 1989.922565 0.971021855 0.908985609 0.867281682 0.898589376 0.95534578 0.833023166 0.787620742 0.800686133 0.883458174 1 10.95849658 -4.025769778 0.170636332 1.026432515 8.60E-12 0.433980631 0.050820162 18.23023762 0.193417615 0.05373171 4.798908194 9.42E-05 4.025769778 -1.026432515 HIEPELAGRDS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 2 HIEPELAGRDSPIR 14 1 P86791;P86790 P86791 CCZ1;CCZ1B Vacuolar fusion protein CCZ1 homolog;Vacuolar fusion protein CCZ1 homolog B 1 0 HIEPELAGRDS(1)PIR;HIEPELAGRDS(1)PIR ; 135.55 0.00053898 40728000 2644.2 2647.5 2355.2 1817.15 2089.3 2969.4 2613.8 2895.9 2880.4 2949 TRUE FALSE FALSE 2611.971473 2684.771574 2396.191268 2027.257433 1982.675225 2779.664923 2835.816107 2979.688298 2622.76981 2872.384555 0.909339061 0.934683892 0.834216736 0.705775078 0.690254103 0.967720328 0.987268958 1.037357025 0.913098424 1 11.48803319 -11.29166098 0.802796754 0.988806097 0.873449752 0.055085524 0.110205822 0.854916924 1.174534894 0.045502161 0.02710196 5.11E-12 11.29166098 -0.115356345 HIGISFTPK ddPTM_HeLa_Romidepsin_16h_R1 2 HIGISFTPK 9 0 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 0 0 ; ; 88.37 0.0072296 1333810 263.05 320.84 641.53 603.24 729.32 660.3 505.27 486.72 542.86 417.88 FALSE FALSE TRUE 259.8438454 325.3567939 652.6955605 672.9894471 692.1000789 618.108961 548.1876212 500.8024753 494.305242 407.0234174 0.638400235 0.79935645 1.603582331 1.653441592 1.70039376 1.518607861 1.346820841 1.230402119 1.214439319 1 8.66896799 -9.764621669 24.99987907 0.822231795 1.517227745 0.676970137 0.197640133 29.80107649 234116.0048 0.031255513 0.042052202 1.72E-10 9.764621669 0.69499595 HIILVLSGK ddPTM_HeLa_Romidepsin_16h_R1 2 HIILVLSGK 9 0 H3BRK5;H3BMW1;H3BNF0;H3BNS4;Q9Y5Y2 H3BRK5 NUBP2 Cytosolic Fe-S cluster assembly factor NUBP2 0 0 ; ; 90.709 0.0089334 0 1360.6 1182.99 1611.21 1367.56 1804.52 1869.98 1620.26 1305.27 1172.62 661.76 FALSE FALSE TRUE 1344.016484 1199.644164 1639.252434 1525.683722 1712.428611 1750.494313 1757.884844 1343.035928 1067.73793 644.5673798 2.085145054 1.861161768 2.543182428 2.366988727 2.656710011 2.715766215 2.727232092 2.083623792 1.656518719 1 9.332187368 -11.6904926 0.337965564 0.650006503 2.64145806 0.671210703 0.301563879 0.552230868 0.11634381 0.429284095 0.123065232 2.04E-12 11.6904926 1.991451557 HIISATSLST(ph)SPTELGSR ddPTM_HeLa_Romidepsin_16h_R1 1 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;Q5JSZ5-5;A0A1W2PQP5 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 HIIS(0.001)AT(0.049)S(0.108)LS(0.073)T(0.524)S(0.237)PT(0.008)ELGSR 139 0.0013774 20508000 1956.2 1971.2 1858.6 1395.1 2286.1 2479.7 2014.8 1856.3 3018.8 2281.9 TRUE FALSE FALSE 1932.357082 1998.950605 1890.948153 1556.408026 2169.431786 2321.255173 2185.937062 1910.009112 2748.790967 2222.615909 0.869406664 0.899368441 0.850775946 0.700259554 0.976071384 1.044379806 0.983497442 0.859351858 1.236736836 1 11.11804294 -7.196971969 19.76102773 0.924720527 0.859344088 0.007013974 0.135271593 17706.90203 5424702.03 0.014061841 27.35490305 6.35E-08 7.196971969 -0.065376439 HIISATSLSTS(ph)PTELGSR ddPTM_HeLa_Romidepsin_16h_R1 2 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;Q5JSZ5-5;A0A1W2PQP5 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 HIISAT(0.01)S(0.021)LS(0.015)T(0.224)S(0.726)PT(0.003)ELGSR;HIIS(0.01)AT(0.119)S(0.036)LS(0.023)T(0.186)S(0.624)PT(0.002)ELGSR ; 155.37 6.93E-06 13141400 3432.4 2783.7 2971.3 3218.3 3812.5 4039.5 2987.2 2923.2 3976.2 3991 TRUE FALSE FALSE 3390.564589 2822.889002 3023.01423 3590.414989 3617.933899 3781.388987 3240.932693 3007.77818 3620.558713 3887.313245 0.872212856 0.726179966 0.777661598 0.923623789 0.930702949 0.972751293 0.833720488 0.773742169 0.931378174 1 11.92455765 -11.77876559 0.948180852 0.990719324 0.855765934 0.2479701 0.076296812 0.472677766 0.842651263 0.036126388 0.016098684 1.66E-12 11.77876559 -0.13495339 HIISATSLSTSPT(ph)ELGSR ddPTM_HeLa_Romidepsin_16h_R1 1 HIISATSLSTSPTELGSR 18 0 Q5JSZ5;Q5JSZ5-5;A0A1W2PQP5 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 HIISATSLST(0.05)S(0.325)PT(0.626)ELGSR 279.19 8.60E-106 33319000 1401.9 1299.3 1167.5 1309.1 1765.3 1540.5 1775.4 1507.9 2083.7 1547.5 TRUE FALSE FALSE 1384.813104 1317.59158 1187.819848 1460.464302 1675.210154 1442.067022 1926.202432 1551.528707 1897.328653 1507.295727 0.918740151 0.874142715 0.788046981 0.968930168 1.111401116 0.95672468 1.277919387 1.02934592 1.258763373 1 10.55774678 -8.824360034 5.054933092 0.938534267 1.097424095 0.148310695 0.138211418 0.163480351 8.19153635 0.014301264 0.026675183 1.50E-09 8.824360034 0.158889827 HIKEEPLS(ph)EEEPCTSTAIASPEKK ddPTM_HeLa_Romidepsin_16h_R1 2 HIKEEPLSEEEPCTSTAIASPEKK 24 2 Q9Y2X3 Q9Y2X3 NOP58 Nucleolar protein 58 1 0 HIKEEPLS(0.992)EEEPCT(0.007)S(0.001)TAIASPEKK;HIKEEPLS(0.977)EEEPCT(0.021)S(0.001)TAIASPEKK ; 86.357 5.40E-05 29849000 3700.1 3686.48 3710.29 911.6 5720.1 6527.1 6056.9 7193.8 4319.1 4080.4 TRUE FALSE FALSE 3655.001758 3738.378362 3774.866041 1017.003481 5428.181952 6110.039375 6571.372935 7401.941253 3932.788879 3974.39062 0.919638281 0.940616744 0.949797441 0.255889161 1.365789745 1.537352505 1.653429057 1.862409099 0.989532548 1 11.95651796 -8.53151279 24.9997029 0.910089811 1.643012032 0.740302059 0.224584231 77.58077858 224633.1951 0.032459429 0.064998612 2.94E-09 8.53151279 0.732922221 HISDLYEDLR ddPTM_HeLa_Romidepsin_16h_R1 2 HISDLYEDLR 10 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;E9PIA2;E9PKG0;Q15149-3;Q15149-2;H0YDN1;E9PMV1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 138.25 0.0024363 7365800 3628.9 3088.3 3657 1763.82 4196.6 4150.3 3700.5 3615.1 3859 3176.9 FALSE FALSE TRUE 3584.669571 3131.777168 3720.648551 1967.761167 3982.431842 3885.109224 4014.820378 3719.697215 3513.841375 3094.36368 1.158451282 1.01209085 1.202395366 0.635917872 1.286995407 1.255543829 1.297462352 1.202087925 1.13556186 1 11.59542705 HIVLSGGSTMYPGLPSR ddPTM_HeLa_Romidepsin_16h_R1 1 HIVLSGGSTMYPGLPSR 17 0 P61160;F5H6T1;P61160-2 P61160 ACTR2 Actin-related protein 2 0 0 106.35 0.0024871 773150 700.7 568.16 452.36 399.89 864.68 691.57 632.67 612.58 679.2 483.67 FALSE FALSE TRUE 692.1595989 576.1585714 460.233136 446.1271633 820.552153 647.3809089 686.408974 630.3040358 618.4506509 471.1041837 1.4692283 1.222996083 0.976924324 0.94698196 1.741763672 1.374177796 1.457021605 1.337929184 1.312768327 1 8.879902334 -12.50089045 1.193997016 0.996385408 1.327520145 0 0.240505526 0.622107483 1.559151421 0.172402053 0.039943634 3.16E-13 12.50089045 0.331134737 HIVSNDSSDS(ph)DDESHEPK ddPTM_HeLa_Romidepsin_16h_R1 1 HIVSNDSSDSDDESHEPK 18 0 P47712 P47712 PLA2G4A Cytosolic phospholipase A2;Phospholipase A2;Lysophospholipase 1 0 HIVSNDS(0.005)S(0.057)DS(0.938)DDESHEPK 96.181 0.0015013 28996000 3233.7 3191.8 2939.5 1668.2 3477 3750.6 3226 3236.7 3821.6 3243.7 TRUE FALSE FALSE 3194.286421 3236.734244 2990.660764 1861.085133 3299.555716 3510.948765 3500.016359 3330.348808 3479.786525 3159.428206 1.011033077 1.024468363 0.946582916 0.58905758 1.044352174 1.111260815 1.107800567 1.054098587 1.101397562 1 11.62544777 -8.531339739 24.9973829 0.96966768 1.090241202 0.194564535 0.130552833 271.9765931 803533.1201 0.018922936 0.037896064 2.94E-09 8.531339739 0.120573522 HIYYITGETK ddPTM_HeLa_Romidepsin_16h_R1 4 HIYYITGETK 10 0 P07900-2;P07900;Q58FG0 P07900-2 HSP90AA1;HSP90AA5P Heat shock protein HSP 90-alpha;Putative heat shock protein HSP 90-alpha A5 0 0 ;;; ;;; 154.85 0.0007377 98176800 20427.1 19506.1 19604 18106.2 22961 25371.1 24090.8 24624.4 23565.6 20663.9 FALSE FALSE TRUE 20178.12665 19780.70739 19945.1994 20199.72404 21789.21449 23749.96859 26137.07195 25336.86816 21457.83371 20127.0489 1.002537766 0.982792236 0.99096492 1.003610819 1.082583671 1.180002528 1.298604285 1.258846654 1.066119222 1 14.29684803 -8.227945379 1.594252347 0.998455769 1.284568372 0.942435283 0.026840653 0.033537454 0.158947612 0.002223294 0.008287996 5.92E-09 8.227945379 0.286112603 HK(ac)LDVTSVEDYK ddPTM_HeLa_Romidepsin_16h_R1 2 HKLDVTSVEDYK 12 1 E7ENZ3;B7ZAR1;E9PCA1;P48643-2;P48643 E7ENZ3 CCT5 T-complex protein 1 subunit epsilon 0 1 ; HK(1)LDVTSVEDYK;HK(1)LDVTSVEDYK 174.72 8.80E-05 3504800 3806.5 3543.3 3788.3 2870.4 7836.6 6450.5 5687.7 6395.3 8917 7631 FALSE TRUE FALSE 3760.104914 3593.18267 3854.233772 3202.289154 7436.66906 6038.333868 6170.813096 6580.337915 8119.441187 7432.74552 0.505883715 0.483426032 0.518547791 0.430835301 1.000527872 0.812396153 0.83021988 0.885317262 1.092387889 1 12.8596795 -8.725325154 24.99977515 0.695964397 0.873428423 0.183739086 0.213201895 318.4734231 220459.3183 0.035295089 0.070588387 1.88E-09 8.725325154 0.177464027 HKAEEVEDETVELDVS(ph)DEEMAR ddPTM_HeLa_Romidepsin_16h_R1 2 HKAEEVEDETVELDVSDEEMAR 22 1 H3BSB3;H3BNT4;Q99547 H3BSB3 MPHOSPH6 M-phase phosphoprotein 6 1 0 HKAEEVEDETVELDVS(1)DEEMAR;HKAEEVEDETVELDVS(1)DEEMAR ; 98.267 9.78E-05 28787000 17124.2 14619.9 12350.3 15204.3 16278.8 15897.6 12193 14458.5 16542.5 15981.6 TRUE FALSE FALSE 16915.48366 14825.71934 12565.25179 16962.2927 15448.03209 14881.79467 13228.67312 14876.83389 15062.89737 15566.39573 1.086666686 0.952418247 0.807203672 1.089673743 0.992396208 0.95602058 0.849822486 0.955701894 0.967654789 1 13.92614732 -10.17706145 7.329971783 1.040850467 0.942084623 0.144488757 0.077834627 0.281722261 21.55960584 0.012860323 0.015766838 6.65E-11 10.17706145 -0.098765844 HKELAPYDENWFYTR ddPTM_HeLa_Romidepsin_16h_R1 2 HKELAPYDENWFYTR 15 1 M0R2L9;M0QYF7;M0R140;P39019 M0R2L9 RPS19 40S ribosomal protein S19 0 0 ; ; 86.214 0.0084494 122648000 15422.1 14204.3 11977.5 16780.8 14715.3 13790.8 13683.6 13978.6 14575.7 12344.4 FALSE FALSE TRUE 15234.12951 14404.26851 12185.96336 18721.07505 13964.32333 12909.61239 14845.88464 14383.04874 13272.01289 12023.69071 1.26700943 1.197990605 1.013496077 1.557015687 1.161400744 1.073681343 1.234719439 1.196225775 1.10382188 1 13.55359218 -12.36942258 0.950154002 0.992099259 1.215607235 0.161472005 0.139135763 0.665405067 1.012845821 0.107279599 0.024122482 4.27E-13 12.36942258 0.223507976 HKLVS(ph)S(ph)FLT(ph)TAMLK ddPTM_HeLa_Romidepsin_16h_R1 1 HKLVSSFLTTAMLK 14 1 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JQF5;Q7Z3B3-4;A0A1W2PRR3;A0A1W2PPV8;A0A1W2PRA9 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 3 0 HKLVS(1)S(0.999)FLT(0.968)T(0.033)AMLK 55.33 0.024286 33624000 1788 1635.6 1612.2 1059.1 1416.8 1446.3 1077.4 1203.1 1614.8 1876.9 TRUE FALSE FALSE 1766.207168 1658.62602 1640.259665 1181.558125 1344.495409 1353.886098 1168.914329 1237.9098 1470.368244 1828.137867 0.966123617 0.907276223 0.897229741 0.646317844 0.735445304 0.740582054 0.639401628 0.677142475 0.804298335 1 10.83615916 -9.502318314 1.612149105 0.982697892 0.686272267 0.689441709 0.070657888 0.071949183 0.373044235 0.006994737 0.011442124 3.15E-10 9.502318314 -0.296425625 HLAAVEER ddPTM_HeLa_Romidepsin_16h_R1 1 HLAAVEER 8 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2;Q92922 F8VXC8;Q92922 SMARCC2;SMARCC1 SWI/SNF complex subunit SMARCC2;SWI/SNF complex subunit SMARCC1 0 0 123.98 6.55E-05 0 203.73 270.82 308.37 351.93 246.33 289.63 323.21 0 435.59 332.95 FALSE FALSE TRUE 201.2468604 274.6326111 313.7370505 392.6218025 233.7588609 271.1235777 350.6634493 0 396.6297394 324.299911 0.620557865 0.84684763 0.967428728 1.210675024 0.720810746 0.836027296 1.081293696 0 1.22303376 1 8.341184818 -7.252404236 24.95271522 0.862351339 4.88E-06 0.64486982 0.202182239 578.3590159 1597243.164 0.02701802 0.441955566 5.59E-08 7.252404236 -0.862346456 HLAESESLLT(ph)SPPK ddPTM_HeLa_Romidepsin_16h_R1 1 HLAESESLLTSPPK 14 0 Q14669;Q14669-2;Q14669-3;Q14669-4 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 HLAESESLLT(0.592)S(0.408)PPK 133.23 0.0012846 21391000 3764.4 4046.6 3996.5 3704.9 4517.5 4660.1 3849.4 3958.6 5546.9 5430.2 TRUE FALSE FALSE 3718.518045 4103.568141 4066.057406 4133.27797 4286.955118 4362.33465 4176.36794 4073.135845 5050.771372 5289.122621 0.703050073 0.775850445 0.768758393 0.781467602 0.810522921 0.824774724 0.789614505 0.770096694 0.954935579 1 12.36881271 -12.40721831 1.094039352 1.001995369 0.77439911 0.853249973 0.032915206 0.157502881 0.332486432 0.027772441 0.006804171 3.92E-13 12.40721831 -0.22759626 HLAPPPLLS(ph)PLLPSIKPTVR ddPTM_HeLa_Romidepsin_16h_R1 1 HLAPPPLLSPLLPSIKPTVR 20 1 Q14676-3;Q14676;Q14676-2;H0Y6Z8 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 HLAPPPLLS(1)PLLPSIKPTVR 77.027 0.001792 2076200 1649.4 1927 1942.8 1977.7 1857.1 2554.1 2049.3 1952.9 1921.8 2236.1 TRUE FALSE FALSE 1629.296478 1954.128357 1976.613619 2206.370979 1762.325257 2390.901253 2223.367491 2009.40408 1749.909395 2178.0058 0.748068016 0.897209896 0.90753368 1.013023464 0.809146265 1.097747882 1.020827167 0.922588948 0.8034457 1 11.08879208 -8.721305302 1.104664872 0.882206944 1.00136457 0.220059973 0.093833997 0.756918264 1.791452837 0.018737924 0.05676 1.90E-09 8.721305302 0.119157626 HLAPPPLLSPLLPSIKPTVR ddPTM_HeLa_Romidepsin_16h_R1 1 HLAPPPLLSPLLPSIKPTVR 20 1 Q14676-3;Q14676;Q14676-2;H0Y6Z8 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 0 0 61.957 0.008451 1038200 580.62 673.77 615.63 593.24 880.65 860.92 780.86 856.82 804.78 613.14 FALSE FALSE TRUE 573.5431801 683.2553517 626.3447819 661.8332001 835.7071443 805.9099905 847.1862289 881.6107349 732.7984612 597.2105344 0.960370166 1.144077863 1.048783881 1.108207511 1.399350976 1.349457091 1.418572145 1.476214306 1.22703539 1 9.222095804 -8.843307629 0.880063113 0.985091443 1.463475805 0.704358195 0.096804467 0.121876726 0.178645886 0.010357285 0.03299201 1.43E-09 8.843307629 0.478384362 HLDGEEDGS(ph)SDQSQASGTTGGR ddPTM_HeLa_Romidepsin_16h_R1 2 HLDGEEDGSSDQSQASGTTGGR 22 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 0 HLDGEEDGS(0.551)S(0.449)DQSQASGTTGGR;HLDGEEDGS(0.728)S(0.27)DQS(0.001)QASGT(0.001)TGGR ; 80.477 0.00072423 11526300 3878.4 2628.25 3387 2365.49 2998.93 2765.68 4013.6 3833.5 4667 4222 TRUE FALSE FALSE 3831.128569 2665.250572 3445.949314 2638.999084 2845.883412 2588.961974 4354.515084 3944.416274 4249.571831 4112.311831 0.931624042 0.6481149 0.837959147 0.641731267 0.692039789 0.629563632 1.058897103 0.959172465 1.033377819 1 12.00573395 -10.44119785 6.535911306 0.970265364 0.779263464 0.328669811 0.136049352 0.235195701 15.46580365 0.024219521 0.027482172 3.62E-11 10.44119785 -0.1910019 HLEFSHDQYR ddPTM_HeLa_Romidepsin_16h_R1 1 HLEFSHDQYR 10 0 Q9NR45 Q9NR45 NANS Sialic acid synthase 0 0 144.65 0.0015626 4600000 731.76 671.04 962.77 1018.4 1165.1 1089.9 800.12 791.93 778.61 485.94 FALSE FALSE TRUE 722.8410277 680.4869187 979.526608 1136.1522 1105.640599 1020.258907 868.0821728 814.8432451 708.9691715 473.3152087 1.52718741 1.437703472 2.069501655 2.400413464 2.335949868 2.155559104 1.83404665 1.721565735 1.497879549 1 8.88665747 -10.43076188 0.764721372 1.124768204 2.103102602 0.596863235 0.268705761 0.237925602 0.292709028 0.074531745 0.079637976 3.71E-11 10.43076188 0.978334399 HLEINPDHPIVETLR ddPTM_HeLa_Romidepsin_16h_R1 5 HLEINPDHPIVETLR 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 ;;;; ;;;; 124.16 0.0011455 112162600 9509.79 8310.71 8653.15 8055.37 9193.28 9042.67 7931.03 8464.8 9279.72 8891.83 FALSE FALSE TRUE 9393.881022 8427.708394 8803.754446 8986.769781 8724.112617 8464.872571 8604.69149 8709.715633 8449.718602 8660.818975 1.084641193 0.973084464 1.01650369 1.037635102 1.007308044 0.977375534 0.993519379 1.005645731 0.975625819 1 13.08028774 -8.968631657 0.909324492 1.035913019 0.991957958 0 0.034683904 0.790400618 1.265347917 0.006795276 0.018937342 1.07E-09 8.968631657 -0.043955061 HLEINPDHSIIETLR ddPTM_HeLa_Romidepsin_16h_R1 4 HLEINPDHSIIETLR 15 0 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 137.73 0.00040958 76294370 9417.93 4648.32 6387.9 2961.76 6656.35 6183.16 7942.39 7042.65 8370.05 6981.63 FALSE FALSE TRUE 9303.140647 4713.759171 6499.07872 3304.212627 6316.651621 5788.076031 8617.016408 7246.417966 7621.411765 6800.246246 1.368059378 0.693174776 0.955712262 0.485896026 0.928885719 0.851156829 1.267162408 1.065611112 1.120755262 1 12.73137127 -10.26219504 24.99992793 1.173805815 0.893523488 0.252654635 0.212882631 75.97368285 2513462.674 0.040518537 0.047793844 5.47E-11 10.26219504 -0.280282327 HLEPEPEEEIIAEDYDDDPVDYEATR ddPTM_HeLa_Romidepsin_16h_R1 3 HLEPEPEEEIIAEDYDDDPVDYEATR 26 0 O60828-5;O60828-4;O60828-2;O60828;A0A5H1ZRR1;O60828-10;O60828-9;O60828-8;O60828-7;O60828-6;O60828-3 O60828-5 PQBP1 Polyglutamine-binding protein 1 0 0 ;; ;; 131.33 2.82E-15 16411000 3240.23 3050.96 3142.91 3567.1 3047.4 3141.87 2591.84 2880.85 3198.53 3116.76 FALSE FALSE TRUE 3200.73683 3093.911495 3197.61103 3979.544886 2891.879807 2941.114647 2811.990825 2964.20285 2912.445466 3035.786126 1.054335417 1.019146727 1.053305766 1.310877882 0.952596687 0.968814839 0.92628094 0.976420185 0.959371097 1 11.56785444 HLFSS(ph)TENLAAGSWK ddPTM_HeLa_Romidepsin_16h_R1 2 HLFSSTENLAAGSWK 15 0 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 HLFS(0.018)S(0.847)T(0.135)ENLAAGS(0.001)WK;HLFS(0.155)S(0.813)T(0.033)ENLAAGSWK ; 103.88 0.0065272 61681000 3395.6 3199 3457.3 3005.4 7824 10871.3 8624.2 9129 4107.9 3658.3 TRUE FALSE FALSE 3354.213121 3244.035606 3517.472856 3352.898489 7424.712085 10176.65902 9356.739333 9393.133212 3740.479136 3563.256839 0.941333525 0.910413072 0.987151086 0.940964584 2.083687037 2.855999294 2.625895285 2.636108941 1.049736043 1 11.79898076 -8.619107077 3.023028473 0.962513551 2.687384651 0.988242485 0.086198015 0.017075106 0.312760187 0.012194411 0.026477108 2.40E-09 8.619107077 1.7248711 up HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR ddPTM_HeLa_Romidepsin_16h_R1 1 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 HLFS(0.207)S(0.595)T(0.179)ENLAAGS(0.019)WKEPAEGGGLSSDR 52.926 0.0060098 64489000 658.78 610.39 494.34 1059.5 1140.6 1507.2 1060.5 1367.6 518.74 751.26 TRUE FALSE FALSE 650.750536 618.9830864 502.9437803 1182.004375 1082.390926 1410.894784 1150.578844 1407.169348 472.3425952 731.7421569 0.889316722 0.845903274 0.687323773 1.615329066 1.479197168 1.928131065 1.572382885 1.923039878 0.645504145 1 9.515191567 -9.179735758 5.57324345 0.919892656 1.705397362 0.860339185 0.176870388 0.058444541 3.064955506 0.022956784 0.038342245 6.61E-10 9.179735758 0.785504706 HLFSST(ph)ENLAAGSWKEPAEGGGLSSDR ddPTM_HeLa_Romidepsin_16h_R1 1 HLFSSTENLAAGSWKEPAEGGGLSSDR 27 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 HLFS(0.066)S(0.213)T(0.715)ENLAAGS(0.006)WKEPAEGGGLSSDR 51.001 0.013779 44268000 817.47 863.36 668.75 797.28 1022.9 1289.6 1141.8 1095.5 725.46 669.16 TRUE FALSE FALSE 807.5063612 875.5144047 680.3893132 889.4652649 970.697596 1207.198722 1238.784464 1127.196564 660.5730407 651.7751267 1.238933994 1.343276797 1.043901931 1.364681204 1.489313655 1.852170591 1.900631694 1.729425561 1.013498389 1 9.348230486 -8.645284179 1.42049938 1.129629867 1.851933775 0.871413092 0.115537651 0.111847184 0.447544708 0.020269461 0.055901421 2.26E-09 8.645284179 0.722303909 HLILLIK ddPTM_HeLa_Romidepsin_16h_R1 1 HLILLIK 7 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 0 0 74.743 0.020249 0 142.76 424 380.41 222.26 346.48 283.86 258.05 499.93 354.98 311.19 FALSE FALSE TRUE 141.0199862 429.9690831 387.0308765 247.958747 328.7978327 265.7222621 279.9687606 514.3946858 323.2296997 303.1052389 0.465250903 1.418547184 1.276886133 0.818061568 1.084764598 0.876666675 0.923668497 1.697082794 1.066394302 1 8.243674978 -10.26241912 24.9999502 0.747479597 1.125656912 0.162570359 0.296545337 94.28898977 2405951.789 0.052587484 0.061988232 5.46E-11 10.26241912 0.378177315 HLIPAANTGESK ddPTM_HeLa_Romidepsin_16h_R1 1 HLIPAANTGESK 12 0 P62258;P62258-2 P62258 YWHAE 14-3-3 protein epsilon 0 0 92.781 0.011562 7608900 2568.8 2766.6 2864.9 2286.7 2666.2 2795.8 2585.2 3023.8 3486.1 3115.7 FALSE FALSE TRUE 2537.490478 2805.548267 2914.762383 2551.099013 2530.133865 2617.157403 2804.786823 3111.288882 3174.294485 3034.753665 0.836143805 0.924473146 0.960460948 0.840628036 0.833719684 0.862395335 0.924222238 1.025219582 1.045980938 1 11.5673637 -12.5410629 1.298417339 1.000125055 0.891232822 0.364891473 0.061124677 0.455165224 1.371865162 0.043615499 0.010319991 2.88E-13 12.5410629 -0.108892233 HLIVLINK ddPTM_HeLa_Romidepsin_16h_R1 2 HLIVLINK 8 0 H3BR35;P15170;P15170-2;P15170-3;Q8IYD1 H3BR35 GSPT1;GSPT2 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A;Eukaryotic peptide chain release factor GTP-binding subunit ERF3B 0 0 ; ; 138.07 6.73E-07 0 7555.6 7033.9 12442.7 9864 9756.6 11161.6 8927.1 7502 7611.8 4567.5 FALSE FALSE TRUE 7463.509441 7132.923429 12659.25997 11004.52209 9258.684295 10448.40978 9685.367651 7719.058534 6930.981544 4448.835692 1.677632072 1.603323639 2.845522031 2.473573504 2.081147729 2.34857174 2.177056723 1.735073864 1.557931563 1 12.1192121 -10.78147255 0.76334388 1.122186514 2.2509156 0.512517901 0.35604616 0.252509145 0.321164794 0.106687785 0.090170019 1.65E-11 10.78147255 1.128729086 HLLIGVSSDR ddPTM_HeLa_Romidepsin_16h_R1 2 HLLIGVSSDR 10 0 P36542-2;P36542 P36542-2 ATP5C1 "ATP synthase subunit gamma, mitochondrial" 0 0 ; ; 98.048 0.0042449 3619100 1565.84 1418.78 1343.43 1361.82 2365 2735.7 2021.88 2245.55 2212.91 2205.77 FALSE FALSE TRUE 1546.75494 1438.753622 1366.811836 1519.280036 2244.305225 2560.897599 2193.618437 2310.521446 2014.981787 2148.463777 0.719935312 0.669666223 0.636181001 0.707147149 1.044609292 1.191966849 1.021017184 1.075429556 0.937870961 1 11.06908974 -8.646732811 6.197789348 0.819161412 1.092769442 0.6037543 0.118649903 0.161104647 8.170692273 0.022506226 0.045309616 2.26E-09 8.646732811 0.27360803 HLLNS(ph)PTDPFNR ddPTM_HeLa_Romidepsin_16h_R1 2 HLLNSPTDPFNR 12 0 O95155-2;O95155;O95155-4;O95155-3 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 0 HLLNS(1)PTDPFNR;HLLNS(1)PTDPFNR ; 100.18 0.0028836 12309000 6279.7 6193.2 6067.6 4899.6 6448.9 7264.2 5711 7119.1 5975.7 5876.8 TRUE FALSE FALSE 6203.160601 6280.388032 6173.204033 5466.114805 6119.788569 6800.041064 6196.092197 7325.079926 5441.218426 5724.119889 1.083688099 1.097179681 1.078454706 0.954926681 1.06912306 1.187962725 1.082453254 1.279686671 0.950577299 1 12.48283817 -4 0.548105987 1.04111066 10.76184942 0.575558272 0.062057577 65.56374441 0.550768004 0.010819421 753.0957021 1.00E-04 4 9.720738758 HLLS(ph)PQLVQYQCGDSGK ddPTM_HeLa_Romidepsin_16h_R1 1 HLLSPQLVQYQCGDSGK 17 0 Q9P209 Q9P209 CEP72 Centrosomal protein of 72 kDa 1 0 HLLS(1)PQLVQYQCGDSGK 223.29 1.52E-35 12324000 1766.8 2326.5 1895 30.709 2819 2906.6 2153.1 2736.3 2305.6 2195.3 TRUE FALSE FALSE 1745.265562 2359.252528 1927.98168 34.25971907 2675.135911 2720.877641 2335.98426 2815.470523 2099.381362 2138.26579 0.816206091 1.103348583 0.901656702 0.016022199 1.251077356 1.272469332 1.092466742 1.316707463 0.98181497 1 11.06222548 HLLTDLPLPPELPGGDLS(ph)PPDSPEPK ddPTM_HeLa_Romidepsin_16h_R1 2 HLLTDLPLPPELPGGDLSPPDSPEPK 26 0 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 HLLTDLPLPPELPGGDLS(0.972)PPDS(0.028)PEPK;HLLTDLPLPPELPGGDLS(0.764)PPDS(0.236)PEPK ; 83.332 2.17E-05 192493100 3051.3 3039.1 2776.5 3074.1 3284.9 3124.1 2716.9 3577.9 3238.1 2671.3 TRUE FALSE FALSE 3014.109582 3081.88453 2824.823818 3429.541906 3117.259295 2924.480093 2947.673418 3681.420892 2948.476226 2601.899241 1.158426712 1.184474972 1.085677636 1.318091743 1.198070719 1.123978994 1.132892993 1.414897562 1.13320154 1 11.34534938 -16.52287872 0.108739831 0.311001191 1.328422048 0.266470899 0.095236823 67.1027424 0.537147782 10.24300911 0.5467404 3.00E-17 16.52287872 1.017420856 HLLVSNVGGDGEEIER ddPTM_HeLa_Romidepsin_16h_R1 1 HLLVSNVGGDGEEIER 16 0 E9PF10;O75694-2;O75694 E9PF10 NUP155 Nuclear pore complex protein Nup155 0 0 85.473 0.0082593 5168500 2639.7 2123.1 2133.8 2281.5 2755.1 2482 1989.5 2226.5 2568.6 2552.3 FALSE FALSE TRUE 2607.526321 2152.989058 2170.937894 2545.297765 2614.496966 2323.40821 2158.48808 2290.920265 2338.857983 2485.990878 1.048888129 0.866048655 0.873268648 1.023856438 1.0516921 0.934600457 0.86826066 0.921532048 0.940815191 1 11.27960529 -10.28203201 24.86619769 1.023086063 0.937286739 0.123030737 0.065378376 746.0079552 900823.5742 0.011238608 0.012859617 5.22E-11 10.28203201 -0.085799324 HLMLPDFDLLEDIESK ddPTM_HeLa_Romidepsin_16h_R1 1 HLMLPDFDLLEDIESK 16 0 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 0 159.41 0.00062166 16858000 9657.4 9136.7 8842.1 8994.9 9240.9 8734.9 7505.8 8210.2 10003 8002.7 FALSE FALSE TRUE 9539.691894 9265.326702 8995.993041 10034.93266 8769.30239 8176.768081 8143.342465 8447.749183 9108.306627 7794.7887 1.223855099 1.188656557 1.154103515 1.287389953 1.125021181 1.049004456 1.044716256 1.08376885 1.16851232 1 12.9282942 -8.291480123 7.202619379 1.133249106 1.057685598 0.228966178 0.074465678 0.391480244 76.31466151 0.014803188 0.033850823 5.11E-09 8.291480123 -0.075563507 HLNEIDLFHCIDPNDSK ddPTM_HeLa_Romidepsin_16h_R1 1 HLNEIDLFHCIDPNDSK 17 0 A0A087WYT3;Q15185-4;Q15185;Q15185-3 A0A087WYT3 PTGES3 Prostaglandin E synthase 3 0 0 91.14 0.0032476 8765500 1536.5 1271.4 1216.6 201.63 1459.6 1120.1 1235.6 1146 1034.6 1396.3 FALSE FALSE TRUE 1517.772547 1289.298803 1237.774413 224.9434093 1385.111165 1048.529225 1340.551833 1179.157702 942.0627848 1360.023925 1.115989594 0.947997149 0.910112234 0.165396656 1.018446176 0.770963809 0.985682537 0.86701247 0.692681039 1 10.40941632 -9.756364243 3.214550901 1.051803405 0.771646381 0.029525761 0.251767239 0.25610782 5.516766513 0.035803272 0.050006302 1.75E-10 9.756364243 -0.280157024 HLPS(ph)PPLTQEVDLHSIAGPPVPPR ddPTM_HeLa_Romidepsin_16h_R1 1 HLPSPPLTQEVDLHSIAGPPVPPR 24 0 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 0 HLPS(0.949)PPLT(0.051)QEVDLHSIAGPPVPPR 103.86 6.37E-06 11961000 645.82 573.43 816.84 542.96 600.98 731.86 402.07 610.04 827.3 727.2 TRUE FALSE FALSE 637.9484974 581.5027626 831.0567576 605.7395899 570.309748 685.096508 436.2218158 627.6905449 753.304216 708.3072392 0.900666352 0.82097532 1.173299822 0.855193278 0.805172835 0.967230702 0.615865251 0.886184004 1.063527484 1 9.468231477 -8.486514968 1.20248362 0.954038904 0.779769025 0.254030471 0.12615457 0.524653297 1.42704856 0.018249804 0.064767136 3.26E-09 8.486514968 -0.17426988 HLPS(ph)PPTLDSIITEYLR ddPTM_HeLa_Romidepsin_16h_R1 4 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 1 0 HLPS(0.995)PPT(0.005)LDSIITEYLR;HLPS(1)PPTLDSIITEYLR;HLPS(1)PPTLDSIITEYLR;HLPS(0.978)PPT(0.022)LDSIITEYLR ;;; 122.13 0.00095866 21855410 12255.68 11776.35 11075.82 10731.04 9670.1 8277.15 6906.254 7895.8 12588.42 11578.57 TRUE FALSE FALSE 12106.30306 11942.13776 11268.59 11971.81334 9176.598713 7748.266828 7492.871042 8124.252515 11462.48019 11277.75708 1.073467266 1.05891071 0.999187154 1.061542047 0.813690049 0.687039699 0.664393725 0.720378392 1.016379419 1 13.46119255 -8.595466478 2.966289973 1.036678239 0.690454615 0.9655736 0.029599575 0.037251407 0.661271806 0.005259455 0.011594857 2.54E-09 8.595466478 -0.346223624 HLPSPPTLDSIITEYLR ddPTM_HeLa_Romidepsin_16h_R1 2 HLPSPPTLDSIITEYLR 17 0 Q9Y4B6-3;Q9Y4B6-2;Q9Y4B6 Q9Y4B6-3 VPRBP Protein VPRBP 0 0 ; ; 81.594 0.0021237 7284300 2538.33 2112.45 2286.56 2104.63 1833.1 1885.8 1944.66 1710.05 2485.22 2680.22 FALSE FALSE TRUE 2507.391858 2142.189127 2326.356618 2347.977223 1739.550067 1765.303466 2109.839372 1759.527599 2262.935699 2610.587498 0.960470338 0.82057741 0.891123787 0.89940568 0.666344288 0.67620927 0.808185657 0.673996792 0.866830053 1 11.3501588 -9.418287252 0.585550885 0.993595007 0.694119462 0.577627489 0.074393992 0.291559185 0.198470677 0.015797921 0.037538243 3.82E-10 9.418287252 -0.299475545 HLQLAIR ddPTM_HeLa_Romidepsin_16h_R1 2 HLQLAIR 7 0 P0C0S5;A0A494C189;Q71UI9-4;P16104;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;A0A0U1RR32;A0A0U1RRH7;Q99878;Q96KK5;Q16777;Q6FI13;P20671;P0C0S8;A0A3B3IS11;Q9BTM1;Q96QV6;Q9BTM1-2;H0YFX9;Q93077;Q7L7L0;P04908 P0C0S5;Q71UI9;A0A0U1RR32;Q93077 H2AFZ;H2AFV;H2AFX;HIST1H2AJ;HIST1H2AH;HIST2H2AC;HIST2H2AA3;HIST1H2AD;HIST1H2AG;H2AFJ;HIST1H2AA;HIST1H2AC;HIST3H2A;HIST1H2AB Histone H2A.Z;Histone H2A.V;Histone H2AX;Histone H2A;Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-C;Histone H2A type 2-A;Histone H2A type 1-D;Histone H2A type 1;Histone H2A.J;Histone H2A type 1-A;Histone H2A type 1-C;Histone H2A type 3;Histone H2A type 1-B/E 0 0 ; ; 132.72 0.0013234 25670000 2567.2 2097.43 13005.7 4408.5 5995 9363.9 6004.4 2538.6 1974.33 1221.38 FALSE FALSE TRUE 2535.909979 2126.957675 13232.05875 4918.231513 5689.05278 8765.577011 6514.413586 2612.050386 1797.74098 1189.648372 2.131646661 1.787887686 11.1226637 4.134189253 4.782129674 7.368208305 5.475915188 2.195649108 1.511153231 1 10.2163195 -9.950309565 24.99973489 1.55676605 5.829473855 0.471768769 2.198379514 68.28014371 34352.22525 0.336098121 0.44171945 1.12E-10 9.950309565 4.272707805 HLQQGSES(ph)PMMIGELR ddPTM_HeLa_Romidepsin_16h_R1 1 HLQQGSESPMMIGELR 16 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 HLQQGS(0.043)ES(0.957)PMMIGELR 85.909 0.012923 3636500 1196.4 1170.8 1304.8 857.15 1259.7 1166.6 1160.4 1265.7 1358.5 1495.7 TRUE FALSE FALSE 1181.817817 1187.282553 1327.509497 956.257716 1195.412808 1092.058025 1258.964347 1302.321033 1236.992358 1456.841498 0.811219215 0.8149703 0.911224384 0.656391047 0.820551041 0.749606616 0.864173864 0.893934607 0.849091929 1 10.50862821 -12.1796867 0.629969834 1.021308018 0.809058198 0.115118837 0.083015866 0.64137754 0.39303299 0.076090513 0.015187178 6.61E-13 12.1796867 -0.21224982 HLRKY(ph)T(ph)Y(ph)NYEAES(ph)S(ph)SGVPGTADSR ddPTM_HeLa_Romidepsin_16h_R1 1 HLRKYTYNYEAESSSGVPGTADSR 24 2 A0A669KB70;A8MUN2;P04114 A0A669KB70 APOB Apolipoprotein B-100;Apolipoprotein B-48 5 0 HLRKY(0.997)T(0.997)Y(0.997)NY(0.579)EAES(0.721)S(0.603)S(0.072)GVPGT(0.024)ADS(0.011)R 40.067 0.020482 1054500000 5212 1671.4 3583.9 180.6 3409.7 2343.5 5223.2 2947.4 5088.5 4178.6 TRUE FALSE FALSE 5148.474139 1694.930013 3646.276276 201.4818217 3235.690286 2193.757913 5666.858478 3032.678369 4633.371816 4070.03937 1.264969125 0.416440692 0.895882311 0.049503654 0.795002208 0.539001644 1.392335052 0.745122613 1.138409582 1 11.99082703 -10.27354918 24.96212334 1.125124312 0.69890728 0.274248088 0.330678523 737.9541204 1521153.294 0.056514111 0.064879903 5.33E-11 10.27354918 -0.426217033 HLS(ph)LPAGQVVPK ddPTM_HeLa_Romidepsin_16h_R1 1 HLSLPAGQVVPK 12 0 Q8IXS8 Q8IXS8 FAM126B Protein FAM126B 1 0 HLS(1)LPAGQVVPK 81.619 0.01898 6739000 4361.8 4169.9 3596 4147.2 4874.5 4993.3 4501.9 4914.8 3888.8 4100.5 TRUE FALSE FALSE 4308.636704 4228.603962 3658.586872 4626.718777 4625.736076 4674.244245 4884.291274 5057.001984 3540.975988 3993.968419 1.078785872 1.058747471 0.916027992 1.15842648 1.158180434 1.17032579 1.222916849 1.266159732 0.886580868 1 11.96360721 -9.068600897 6.784274597 1.031760231 1.198107456 0.682948753 0.06787404 0.10715105 8.934596047 0.008246487 0.013793709 8.54E-10 9.068600897 0.166347226 HLS(ph)QEDNDLNK ddPTM_HeLa_Romidepsin_16h_R1 1 HLSQEDNDLNK 11 0 F5H777;A0A2R8Y4L3;A0A2R8YE98;A0A2R8Y7C3;Q8N4S0-2;Q8N4S0 F5H777 CCDC82 Coiled-coil domain-containing protein 82 1 0 HLS(1)QEDNDLNK 148.13 0.0024102 6193000 612.23 660.11 536.94 348.12 716.95 962.37 874.19 805.79 717.54 559.5 TRUE FALSE FALSE 604.7679053 669.4030459 546.2852155 388.3712724 680.3613662 900.8776629 948.4436768 829.1042623 653.3614253 544.9641093 1.109738962 1.228343361 1.002424208 0.712654771 1.248451695 1.653095401 1.740378239 1.521392415 1.198907257 1 9.090017409 -8.385848339 3.77350351 1.040736971 1.648580543 0.772481753 0.143982926 0.076103038 1.915407187 0.019832617 0.046787706 4.11E-09 8.385848339 0.607843572 HLT(ph)PEPDIVASTK ddPTM_HeLa_Romidepsin_16h_R1 3 HLTPEPDIVASTK 13 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 HLT(1)PEPDIVASTK;HLT(1)PEPDIVASTK;HLT(1)PEPDIVASTK ;; 100.43 0.0093839 60329800 13837.6 13055 12960.1 12570 14175.6 14849.8 10991.5 13620.5 14157.4 13505.6 TRUE FALSE FALSE 13668.94201 13238.78863 13185.6651 14023.40254 13452.16624 13900.94571 11925.11774 14014.58768 12891.12669 13154.72257 1.039090102 1.006390562 1.0023522 1.066035599 1.02261117 1.056726635 0.906527498 1.065365507 0.979961882 1 13.6832932 HLTGEFEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 HLTGEFEKK 9 1 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 1 HLTGEFEK(1)K 75.294 0.022997 1703800 824.48 888.92 713.33 784.44 2239.8 2192.4 2245.9 1274.4 2367.4 1737.6 FALSE TRUE FALSE 814.4309206 901.4342391 725.7452094 875.1406437 2125.494648 2052.312716 2436.66669 1311.272753 2155.653815 1692.456902 0.481212207 0.532618726 0.428811634 0.517082971 1.255863382 1.212623325 1.43972156 0.774774679 1.273683137 1 10.72490338 -8.753827879 24.99960385 0.68872479 1.192949644 0.379361604 0.290452571 126.8175271 416522.4825 0.0402821 0.079344209 1.76E-09 8.753827879 0.504224854 HMGIGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 HMGIGKR 7 1 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 0 1 HMGIGK(1)R 62.717 0.022936 17375000 0 176.62 110.66 0 119.56 140.15 55.536 0 154.21 0 FALSE TRUE FALSE 0 179.106461 112.5859909 0 113.4584071 131.1948673 60.25322645 0 140.4170714 0 0 HNDDEQYAWESSAGGSFTVR ddPTM_HeLa_Romidepsin_16h_R1 1 HNDDEQYAWESSAGGSFTVR 20 0 P08238;P07900-2;P07900;Q14568 P08238;P07900-2 HSP90AB1;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 0 82.034 0.0018468 5381400 1225.6 1748.4 1305.8 1169.2 1487 1277.7 1292.5 1890.3 1943 2773 FALSE FALSE TRUE 1210.661916 1773.014021 1328.526901 1304.388405 1411.112841 1196.059094 1402.284918 1944.992848 1769.213214 2700.95706 0.448234418 0.656439174 0.491872648 0.482935632 0.522449195 0.442827882 0.519180752 0.720112466 0.655031966 1 11.39925499 -12.32853539 0.828222988 1.031044313 0.525252064 0.320381518 0.134440547 0.232149706 0.256681872 0.07843216 0.016338871 4.69E-13 12.32853539 -0.505792248 HNGS(ph)LSPGLEAR ddPTM_HeLa_Romidepsin_16h_R1 1 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 HNGS(0.841)LS(0.159)PGLEAR 129.17 0.0043019 29676000 955.98 982.71 796.87 740.51 1683.7 1565.2 1480.9 1652.7 1291 1052 TRUE FALSE FALSE 944.3281481 996.5446172 810.7391881 826.1312504 1597.774506 1465.188771 1606.687609 1700.518267 1175.529727 1024.668888 0.921593462 0.97255282 0.791220654 0.806242153 1.559308109 1.429914373 1.568006629 1.659578315 1.147228866 1 10.00094208 -8.754511145 25 0.938802133 1.546310376 0.887339276 0.10723434 32.97901844 119001.176 0.013509801 0.026554014 1.76E-09 8.754511145 0.607508243 HNGSLS(ph)PGLEAR ddPTM_HeLa_Romidepsin_16h_R1 1 HNGSLSPGLEAR 12 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 HNGS(0.031)LS(0.969)PGLEAR 110.22 0.01059 22491000 1277.7 1565 1250.8 1346.7 2476.6 2596.9 2068.5 2174.3 1617.9 1719.7 TRUE FALSE FALSE 1262.126901 1587.032111 1272.569649 1502.41179 2350.209861 2430.966471 2244.198338 2237.20994 1473.190972 1675.021946 0.753498725 0.947469443 0.75973312 0.896950511 1.403091981 1.451304251 1.339802349 1.335630226 0.879505475 1 10.70996428 -8.769183065 9.0474977 0.876529618 1.384677277 0.91398676 0.076581158 0.035985784 27.30535552 0.01506789 0.028289846 1.70E-09 8.769183065 0.508147659 HNMSGGEFQGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 HNMSGGEFQGKR 12 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 0 1 ; HNMSGGEFQGK(1)R;HNMSGGEFQGK(1)R 184.96 3.67E-07 3105100 575.59 773.83 415.5 411.7 802.64 807.82 636.24 849.85 766.05 558.73 FALSE TRUE FALSE 568.5744877 784.7239991 422.7316032 459.3026911 761.6782857 756.2029091 690.2822097 874.4390689 697.5325694 544.2141141 1.04476248 1.441939815 0.776774421 0.843974236 1.399593039 1.389531968 1.268401888 1.606792338 1.281724511 1 9.088030563 -8.742587687 24.68698698 1.025260518 1.403635324 0.420110212 0.198695758 131.0598842 171626.718 0.025585189 0.051098236 1.81E-09 8.742587687 0.378374806 HNPT(ph)GAVLFMGQINKP ddPTM_HeLa_Romidepsin_16h_R1 2 HNPTGAVLFMGQINKP 16 1 P07093-2;P07093;P07093-3 P07093-2 SERPINE2 Glia-derived nexin 1 0 HNPT(1)GAVLFMGQINKP;HNPT(1)GAVLFMGQINKP ; 71.031 0.0038836 6885200 5471.3 5410.5 4712.9 3064.95 6479.6 6167.3 4780.3 5396.5 5878.8 5421 TRUE FALSE FALSE 5404.613691 5486.669161 4794.926048 3419.33394 6148.921833 5773.229434 5186.338563 5552.639213 5352.985404 5280.161639 1.023569743 1.039110076 0.908102133 0.6475813 1.164532879 1.093381193 0.982231022 1.051604021 1.013791958 1 12.36636638 HNS(ph)SDGFFNNGPLR ddPTM_HeLa_Romidepsin_16h_R1 2 HNSSDGFFNNGPLR 14 0 Q9HC44 Q9HC44 GPBP1L1 Vasculin-like protein 1 1 0 HNS(0.834)S(0.166)DGFFNNGPLR;HNS(0.782)S(0.218)DGFFNNGPLR ; 92.633 0.0070363 9785900 2723.7 2293.16 2586.4 2000.72 3300.5 2918.7 2307.62 2254.56 2442.96 2347.16 TRUE FALSE FALSE 2690.502497 2325.443167 2631.415207 2232.05266 3132.063169 2732.20449 2503.629185 2319.792136 2224.455539 2286.180445 1.176854829 1.017173938 1.151009411 0.976323923 1.369998233 1.195095731 1.095114426 1.014702117 0.97300086 1 11.15872356 HPDVEVDGFSELR ddPTM_HeLa_Romidepsin_16h_R1 2 HPDVEVDGFSELR 13 0 P09874;Q5VX84;Q5VX85 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 0 ; ; 145.81 0.00035925 19412400 1769.9 1800.18 1665.18 1731.62 1766.78 1570.39 1591.98 1695.33 1887.48 1738.39 FALSE FALSE TRUE 1748.327778 1825.522981 1694.161759 1931.838052 1676.614624 1470.047147 1727.202741 1744.381699 1718.659062 1693.226377 1.032542253 1.078132851 1.000552426 1.140921307 0.99018929 0.868192917 1.020066049 1.030211744 1.01502025 1 10.72555915 -8.533836143 24.99954565 1.029087521 0.969488345 0.224794345 0.057696272 272.7512544 622286.7527 0.008342648 0.016696699 2.93E-09 8.533836143 -0.059599176 HPEHYVDY(ph)TY(ph)MAT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 HPEHYVDYTYMATK 14 0 Q96JM2;Q96JM2-3;H3BLX4;Q96JM2-2 Q96JM2 ZNF462 Zinc finger protein 462 3 0 HPEHY(0.125)VDY(0.873)T(0.213)Y(0.889)MAT(0.901)K 42.789 0.028339 1129000 288.52 387.78 464.57 278.46 318.3 481.59 293.73 398.01 338.25 374.16 TRUE FALSE FALSE 285.0034073 393.239177 472.655646 310.6568554 302.0559633 450.8179533 318.6794189 409.5257914 307.9960728 364.4392693 0.782032649 1.079025259 1.296939397 0.852424208 0.828823864 1.237018047 0.874437652 1.123714775 0.845123176 1 8.509534611 -10.24103752 24.67722373 0.897070967 1.037184341 0.185733204 0.157228511 1039.631041 1257495.649 0.027183372 0.033271057 5.74E-11 10.24103752 0.140113373 HPEPVPEEGS(ph)EDELPPQVHKV ddPTM_HeLa_Romidepsin_16h_R1 4 HPEPVPEEGSEDELPPQVHKV 21 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV;HPEPVPEEGS(1)EDELPPQVHKV ;;; 83.602 0.00069645 63590500 10568.1 10791.6 10411 10063.8 9002 9758.3 7227.2 8997.7 10951 10746.9 TRUE FALSE FALSE 10439.29193 10943.52443 10592.19909 11227.42391 8542.594349 9134.776123 7841.078188 9258.034253 9971.515133 10467.69399 0.997286694 1.045457045 1.011894224 1.072578537 0.816091334 0.872663658 0.749074075 0.884438756 0.952599029 1 13.35365603 -8.751011232 24.99999626 1.008297941 0.827752897 0.796930734 0.045138491 60.15062125 144201.5566 0.005623586 0.011151615 1.77E-09 8.751011232 -0.180545044 HPNYS(ph)PPGSPIEK ddPTM_HeLa_Romidepsin_16h_R1 2 HPNYSPPGSPIEK 13 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 0 HPNY(0.018)S(0.943)PPGS(0.039)PIEK;HPNY(0.238)S(0.76)PPGS(0.002)PIEK ; 109.84 0.0018069 0 3164 3047.1 3092.7 3250.5 2583.7 2386 1898.17 2234.41 2961.8 3296.6 TRUE FALSE FALSE 3125.435951 3089.997154 3146.527146 3626.338104 2451.844148 2233.5423 2059.400512 2299.059128 2696.88919 3210.953857 0.973366822 0.962329978 0.979935336 1.129364751 0.763587475 0.695600871 0.641367209 0.716005035 0.839902817 1 11.64878622 -8.606493145 5.703069921 0.992931074 0.687535627 0.79901279 0.068593382 0.042959065 2.264569833 0.006932996 0.014041505 2.47E-09 8.606493145 -0.305395448 HPPDDDLSQDSPEQEAS(ph)KSPR ddPTM_HeLa_Romidepsin_16h_R1 1 HPPDDDLSQDSPEQEASKSPR 21 1 Q9P0K8-2;Q9P0K8 Q9P0K8-2 FOXJ2 Forkhead box protein J2 1 0 HPPDDDLSQDS(0.002)PEQEAS(0.499)KS(0.499)PR 58.324 0.0071937 9177500 1697.8 1581.2 1539.5 1641.6 1824.1 1479.6 1197 942.66 1740.6 1663.4 TRUE FALSE FALSE 1677.106561 1603.460175 1566.294352 1831.409516 1731.00937 1385.058335 1298.67315 969.9343798 1584.916377 1620.184628 1.035132991 0.98967744 0.966738188 1.130370875 1.068402539 0.854876852 0.801558741 0.598656698 0.978231955 1 10.66194251 -7.626421584 1.440847086 1.021944373 0.575421566 0.855259899 0.055510667 0.16718778 0.48936291 0.007972541 0.088080898 2.36E-08 7.626421584 -0.446522807 HPPLYQAGLTPPLS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 2 HPPLYQAGLTPPLSPPK 17 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 0 HPPLYQAGLTPPLS(1)PPK;HPPLYQAGLTPPLS(1)PPK ; 125.23 0.00091263 110452000 14220.6 13313.6 12082.7 11147.5 8827.7 8138.4 7385.4 7477.4 14659.6 14571.6 TRUE FALSE FALSE 14047.27386 13501.02921 12292.99433 12436.4264 8377.189528 7618.382505 8012.715692 7693.746772 13348.40866 14193.02773 0.9897306 0.95124377 0.866129099 0.876234912 0.590232732 0.536769367 0.564552951 0.542079316 0.940490564 1 13.79289477 -8.909226561 1.225618664 0.99145067 0.530326485 0.94978984 0.042634247 0.055173551 0.164556122 0.006216271 0.015228224 1.23E-09 8.909226561 -0.461124185 HPS(ph)PELSR ddPTM_HeLa_Romidepsin_16h_R1 1 HPSPELSR 8 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 HPS(1)PELSR 80.102 0.02506 1481900 206.46 206.74 222.04 445.05 235.42 272.27 47.85 119.72 161.04 193.58 TRUE FALSE FALSE 203.9435861 209.6504911 225.9045131 496.508775 223.4056389 254.8728257 51.91437781 123.1839093 146.6361791 188.5507637 1.08163755 1.111904757 1.198109775 2.633289653 1.184856717 1.351746451 0.275333692 0.653319599 0.777701327 1 7.558809184 -7.763069106 24.99611784 1.197095712 0.464326534 0.299732212 0.489232499 41.11611414 630676.5229 0.06927514 0.225226554 1.73E-08 7.763069106 -0.732769177 HPS(ph)SPSALR ddPTM_HeLa_Romidepsin_16h_R1 2 HPSSPSALR 9 0 O60504-2;O60504;H0YAZ3;H0YB51 O60504-2 SORBS3 Vinexin 1 0 HPS(0.969)S(0.031)PSALR;HPS(0.62)S(0.38)PSALR ; 127.83 0.0039343 7233800 378.93 308.5 434.83 332.76 379.34 310.37 196.789 296.56 445.66 439.26 TRUE FALSE FALSE 374.3114554 312.8430711 442.3980337 371.2352769 359.9808643 290.5383587 213.5042527 305.1404957 405.7990534 427.8479619 0.874870255 0.731201499 1.034007576 0.867680368 0.841375667 0.679069166 0.499018978 0.713198432 0.948465552 1 8.740954408 -8.320462282 2.008994041 0.925383835 0.600383617 0.648646015 0.092327243 0.149738628 1.160678375 0.014212716 0.042338547 4.78E-09 8.320462282 -0.325000218 HQEGEIFDTEK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 2 HQEGEIFDTEKEK 13 1 Q02878 Q02878 RPL6 60S ribosomal protein L6 0 1 ; HQEGEIFDTEK(1)EK;HQEGEIFDTEK(1)EK 164.53 7.39E-05 5230800 1889.07 1651.07 1789.03 1216.83 4821.8 4066.6 3702 3483.7 5296.1 4122.2 FALSE TRUE FALSE 1866.045288 1674.313807 1820.167317 1357.52561 4575.725553 3806.757384 4016.447788 3584.495363 4822.403552 4015.10465 0.464756327 0.417003778 0.453329982 0.338104664 1.139627968 0.948109132 1.000334521 0.892752662 1.20106547 1 11.97122188 -12.61385607 1.459042679 0.997954365 0.673533353 0.216552418 0.276716942 0.669247531 2.583417117 0.206946 0.048864423 2.43E-13 12.61385607 -0.324421011 HQGVMVGMGQK ddPTM_HeLa_Romidepsin_16h_R1 4 HQGVMVGMGQK 11 0 P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q562R1;P63261;I3L3I0;I3L1U9;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P60709;P63261;P63267 ACTB;ACTBL2;ACTG1;ACTG2;ACTA1;ACTC1;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, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ;;; ;;; 132.78 0.00032897 191648000 26194.3 24437 29344.2 29582.2 33818 36325.3 30235.9 26803.8 23123.9 18824.7 FALSE FALSE TRUE 25875.0338 24781.02473 29854.92349 33002.63315 32092.14127 34004.23056 32804.13659 27579.32566 21055.64047 18335.63158 1.411188575 1.351522832 1.628246257 1.799917991 1.750261022 1.854543729 1.789092263 1.504138297 1.148345525 1 14.16236234 -10.73747649 0.434663895 0.999003733 1.786339257 0.80755978 0.122224645 0.265565714 0.131166421 0.078480077 0.059131567 1.83E-11 10.73747649 0.787335524 HQNS(ph)LPELEAAEAGAPGSGPVDLFR ddPTM_HeLa_Romidepsin_16h_R1 2 HQNSLPELEAAEAGAPGSGPVDLFR 25 0 Q96BZ8 Q96BZ8 LENG1 Leukocyte receptor cluster member 1 1 0 HQNS(1)LPELEAAEAGAPGSGPVDLFR;HQNS(1)LPELEAAEAGAPGSGPVDLFR ; 74.44 0.00020476 7949600 3325.3 4316.7 1885.64 2319.44 3711.9 3426.7 2264.96 3956.2 3085.7 3354.5 TRUE FALSE FALSE 3284.769965 4377.470616 1918.458773 2587.624566 3522.467892 3207.744929 2457.345646 4070.666405 2809.707264 3267.349606 1.005331648 1.33976193 0.587160544 0.791964399 1.07808111 0.981757484 0.752091432 1.245861905 0.859934688 1 11.67390512 -9.763188237 24.99999239 1.027881353 0.905211178 0.104113159 0.203954546 91.84261431 1312902.949 0.030121832 0.040745612 1.73E-10 9.763188237 -0.122670175 HQPWQSPERPLS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 HQPWQSPERPLSR 13 1 J3QRS2;V9GYU5;J3QL08;V9GYS7;E7ES68;G5E9D5;Q9BQ52-2;Q9BQ52 J3QRS2 ELAC2 Zinc phosphodiesterase ELAC protein 2 1 0 HQPWQS(0.011)PERPLS(0.989)R 96.489 0.0059221 30276000 1726.7 1505.2 1298.7 1108 1615.2 1717.2 1249.2 1727.6 1237.4 1734.2 TRUE FALSE FALSE 1705.654316 1526.390245 1321.303329 1236.112173 1532.770317 1607.476462 1355.307017 1777.58538 1126.723845 1689.145234 1.009773631 0.903646539 0.782231925 0.731797449 0.90742364 0.951650829 0.802362633 1.052357929 0.667037873 1 10.72207766 -10.16639443 4.114969341 1.004687394 0.865714635 0 0.136840104 0.185314593 5.628818017 0.014060527 0.01727653 6.82E-11 10.16639443 -0.138972759 HQQQLLAS(ph)PGSSTVDNK ddPTM_HeLa_Romidepsin_16h_R1 3 HQQQLLASPGSSTVDNK 17 0 F2Z2X4;Q9C0E2 F2Z2X4 XPO4 Exportin-4 1 0 HQQQLLAS(0.94)PGS(0.05)S(0.008)T(0.002)VDNK;HQQQLLAS(0.996)PGS(0.003)S(0.001)TVDNK;HQQQLLAS(0.998)PGS(0.002)STVDNK ;; 119.62 0.00094644 51286700 9091.2 8625.7 8622.5 7882.6 8657.6 8156.7 6611.4 8294.9 9666.3 8786.9 TRUE FALSE FALSE 8980.392958 8747.132831 8772.570996 8794.023301 8215.770366 7635.513195 7172.972151 8534.899844 8801.721918 8558.615071 1.049281091 1.022026666 1.024998896 1.027505412 0.959941567 0.892143546 0.838099633 0.997229081 1.028404928 1 13.06316165 -8.548392828 2.992703812 1.024153332 0.902928338 0.652177369 0.038215402 0.11242218 2.051385192 0.005524506 0.012478484 2.83E-09 8.548392828 -0.121224994 HQS(ph)FGAAVLSR ddPTM_HeLa_Romidepsin_16h_R1 1 HQSFGAAVLSR 11 0 Q5VV41 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 0 HQS(1)FGAAVLSR 94.007 0.01168 13312000 1767.1 1737.3 1789.1 1896.6 1805.1 1814.8 865.07 1378.6 1758.9 1482.6 TRUE FALSE FALSE 1745.561906 1761.757755 1820.238535 2115.893816 1712.979011 1698.840137 938.5490242 1418.487616 1601.579579 1444.081838 1.208769378 1.219984705 1.260481565 1.465217386 1.186206326 1.176415416 0.649927864 0.982276474 1.109064276 1 10.49593679 -7.777469291 24.998395 1.157404583 0.816102184 0.532915034 0.139807018 148.8848401 232184.435 0.022675359 0.068334844 1.67E-08 7.777469291 -0.341302399 HQYYNQEWTLWDR ddPTM_HeLa_Romidepsin_16h_R1 2 HQYYNQEWTLWDR 13 0 P22314;P22314-2;Q5JRR6 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 ; ; 76.01 0.023028 46953000 3208 3053.5 3872.4 2369.4 4693.9 5293.3 4577.4 4683.6 3444.9 3400.5 FALSE FALSE TRUE 3168.899662 3096.487253 3939.797498 2643.361176 4454.352768 4955.075213 4966.204242 4819.112577 3136.779516 3312.15452 0.95674874 0.93488611 1.189496889 0.798079063 1.344850532 1.496027792 1.499387849 1.454978186 0.94705108 1 11.69355426 -8.608473811 5.223080956 0.982141114 1.475801156 0.869016578 0.091845905 0.046597318 2.143829222 0.01206897 0.024565632 2.46E-09 8.608473811 0.493660042 HRDYETATLSDIK ddPTM_HeLa_Romidepsin_16h_R1 1 HRDYETATLSDIK 13 1 O43707;O43707-2 O43707 ACTN4 Alpha-actinin-4 0 0 89.189 0.0093861 5568300 2439.3 2460.4 2441.4 3326.1 2882.4 3162.9 2982.7 2943.2 3279.6 2776.6 FALSE FALSE TRUE 2409.568873 2495.037576 2483.891543 3710.679332 2735.300372 2960.800898 3236.050464 3028.356848 2986.264362 2704.463532 0.890960017 0.922562847 0.9184415 1.372057448 1.011402202 1.094783074 1.196559105 1.119762501 1.104198421 1 11.40112673 -9.329531967 24.99990731 0.942792081 1.14924852 0.450712622 0.103794635 96.30183437 35356.5114 0.013739847 0.020987966 4.68E-10 9.329531967 0.206456439 HRPS(ph)PPAT(ph)PPPK ddPTM_HeLa_Romidepsin_16h_R1 3 HRPSPPATPPPK 12 1 A9Z1X7;Q8IYB3;E9PCT1;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 2 0 HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK;HRPS(1)PPAT(1)PPPK ;; 89.374 0.0020108 1860400 10043.5 10053.5 9991.1 10069.4 10422.6 9618.4 8812.4 9808.7 10305.8 10244.3 TRUE FALSE FALSE 9921.085959 10195.03344 10164.9909 11233.67141 9890.69583 9003.815282 9560.925036 10092.49926 9384.023437 9978.151609 0.99428094 1.021735672 1.01872484 1.125826891 0.991235273 0.902353024 0.958185986 1.011459803 0.940457091 1 13.28455687 -8.512698422 24.94055056 1.011068833 0.955647554 0.218479164 0.049692993 529.9301827 1298262.323 0.006671905 0.014033228 3.07E-09 8.512698422 -0.055421279 HRPS(ph)PPATPPPK ddPTM_HeLa_Romidepsin_16h_R1 1 HRPSPPATPPPK 12 1 A9Z1X7;Q8IYB3;E9PCT1;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 HRPS(1)PPATPPPK 108.36 0.0042481 1911300 1277.6 1100.2 1355 962.76 1525.3 1243.2 1199.8 1058.3 1233.2 1125.7 TRUE FALSE FALSE 1262.02812 1115.688644 1378.583207 1074.078841 1447.458249 1163.763532 1301.710982 1088.920241 1122.899503 1096.454152 1.151008565 1.017542451 1.257310399 0.979593027 1.320126562 1.061388231 1.187200559 0.993128841 1.024118976 1 10.09862977 -12.39754262 0.790039006 0.987345117 1.12705893 0.13872388 0.107175887 1.10494751 1.045746843 0.102826882 0.018483652 4.00E-13 12.39754262 0.139713813 HS(ph)LEEGLDMVNR ddPTM_HeLa_Romidepsin_16h_R1 3 HSLEEGLDMVNR 12 0 Q7Z309-2;Q7Z309;Q7Z309-5 Q7Z309-2 FAM122B Protein FAM122B 1 0 HS(1)LEEGLDMVNR;HS(1)LEEGLDMVNR;HS(1)LEEGLDMVNR ;; 124.81 0.0017802 18054400 2767.7 2828.67 2888.38 2209.78 5941 8986.6 8638.5 10585.1 3171.56 3022.64 TRUE FALSE FALSE 2733.966208 2868.492091 2938.651042 2465.285161 5637.808601 8412.385263 9372.253974 10891.36317 2887.88773 2944.111377 0.928621868 0.974315073 0.998145337 0.837361378 1.914944063 2.857359721 3.183389748 3.699371991 0.980903016 1 11.52361653 -8.303989996 1.525417315 0.951959914 3.501502573 0.981114615 0.143705711 0.034926094 0.152328695 0.020491243 0.072965241 4.97E-09 8.303989996 2.549542659 up HS(ph)SNPPLESHVGWVMDSR ddPTM_HeLa_Romidepsin_16h_R1 1 HSSNPPLESHVGWVMDSR 18 0 Q6PKG0;Q6PKG0-3;H0YC33;H0YBR8 Q6PKG0 LARP1 La-related protein 1 1 0 HS(0.5)S(0.5)NPPLESHVGWVMDSR 59.618 0.01544 10338000 3127.4 2474.3 2329.1 2212.3 2498.4 2460.5 2467.2 2446.8 2981.1 3086 TRUE FALSE FALSE 3089.282046 2509.13326 2369.637008 2468.096535 2370.897325 2303.281991 2676.763906 2517.594298 2714.46295 3005.825275 1.027765011 0.834756857 0.788348221 0.821104459 0.788767512 0.766272747 0.89052545 0.837571737 0.903067444 1 11.55354543 -10.23070541 5.797756144 1.01323995 0.816008232 0.682900101 0.047728601 0.042919224 4.520556027 0.005686343 0.00688673 5.88E-11 10.23070541 -0.197231718 HS(ph)SPSGTVAAR ddPTM_HeLa_Romidepsin_16h_R1 2 HSSPSGTVAAR 11 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 HS(0.661)S(0.339)PSGTVAAR;HS(0.639)S(0.361)PSGTVAAR ; 84.169 0.01954 1334920 450.246 383.6 607.19 380.482 574.7 566.05 733.47 171.79 583.53 455.467 TRUE FALSE FALSE 444.7582286 389.0003309 617.7578872 424.4751191 545.3709145 529.8812318 795.7709235 176.7604726 531.3376153 443.6339017 1.002534357 0.876849874 1.392494769 0.95681398 1.229326506 1.194411044 1.793755889 0.398437703 1.197693894 1 8.793225808 -9.779554164 24.99588758 0.991904213 1.185001296 0.035169694 0.337965428 469.4431905 647764.4629 0.047804975 0.062897687 1.66E-10 9.779554164 0.193097083 HS(ph)SVKESFRY(ph)VNLT(ph)CS(ph)S(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 HSSVKESFRYVNLTCSSGK 19 2 A0A3B3ISZ7;Q9NQ36-2;Q9NQ36 A0A3B3ISZ7 SCUBE2 "Signal peptide, CUB and EGF-like domain-containing protein 2" 5 0 HS(0.78)S(0.353)VKES(0.239)FRY(0.762)VNLT(0.927)CS(0.954)S(0.985)GK 41.86 0.0043266 0 531.17 542.25 358.96 299.9 574.32 391.06 350.84 353.19 500.27 448.23 TRUE FALSE FALSE 524.6958957 549.8838097 365.2075482 334.5758491 545.0103073 366.0725281 380.6403408 363.4089954 455.5245983 436.58492 1.201818642 1.259511688 0.836509764 0.7663477 1.248348906 0.838491004 0.871858654 0.832390169 1.04338143 1 8.770118489 -9.746978657 24.99921371 1.110281775 0.904858392 0.380293025 0.141376846 223.716013 386751.9646 0.02368571 0.033409741 1.79E-10 9.746978657 -0.205423383 HS(ph)VSPDLKY(ph)VLLAY(ph)DVK ddPTM_HeLa_Romidepsin_16h_R1 1 HSVSPDLKYVLLAYDVK 17 1 J3KQK8;J3KPP1;Q8N608-4;Q8N608-2;Q8N608;Q8N608-3 J3KQK8 DPP10 Inactive dipeptidyl peptidase 10 3 0 HS(0.81)VS(0.23)PDLKY(0.96)VLLAY(1)DVK 49.768 0.023661 5912700 1254.7 1813.7 1096.3 1527.3 1202.3 1044.3 851.5 1556.9 1964.3 2452.3 TRUE FALSE FALSE 1239.407234 1839.233316 1115.380642 1703.893612 1140.942145 977.5726003 923.8263887 1601.946445 1788.608088 2388.588892 0.518886794 0.770008318 0.466962165 0.713347373 0.477663673 0.409267833 0.386766593 0.670666455 0.748813701 1 11.22194285 -14.92047462 0.254043397 2.202945701 0.484401955 0.397477051 0.144666228 8.78985643 0.238002088 5.463006841 0.073030214 1.20E-15 14.92047462 -1.718543746 SLSGS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSGSPLK 8 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 S(0.004)LS(0.004)GS(0.992)PLK 104.05 0.027598 132870000 6940.1 6309 7246.4 4784.6 3734.5 2886.8 2840.3 2640.8 7159.4 7150.4 TRUE FALSE FALSE 6855.511392 6397.818268 7372.520552 5337.817964 3543.91453 2702.342797 3081.555011 2717.207382 6519.045333 6964.631577 0.984332239 0.918615464 1.058565765 0.766417851 0.508844508 0.38800944 0.44245772 0.390143736 0.936021563 1 12.76583132 -8.867709929 2.169514514 0.990601713 0.411847324 0.972228935 0.043713036 0.02711739 0.259350355 0.005570426 0.011451579 1.36E-09 8.867709929 -0.57875439 down HSAGS(ph)GAEESNSSSTVQK ddPTM_HeLa_Romidepsin_16h_R1 3 HSAGSGAEESNSSSTVQK 18 0 Q8IYL3 Q8IYL3 C1orf174 UPF0688 protein C1orf174 1 0 HS(0.172)AGS(0.828)GAEESNSSSTVQK;HSAGS(1)GAEESNSSSTVQK;HS(0.013)AGS(0.987)GAEESNSSSTVQK ;; 143.72 4.30E-05 12968500 6928.63 6492.11 4825.25 5186.7 7952.68 8299.94 6974.43 6514.79 9155.11 8654.93 TRUE FALSE FALSE 6844.181193 6583.506095 4909.231452 5786.410658 7546.825064 7769.600621 7566.83791 6703.28517 8336.254032 8430.073671 0.811876795 0.780954752 0.582347396 0.68640096 0.895226466 0.921652755 0.897600449 0.795163297 0.98887084 1 13.04132952 -11.87643204 0.871890734 0.992410725 0.797696825 0.393880659 0.09752033 0.515607729 0.756102856 0.0580937 0.02205039 1.33E-12 11.87643204 -0.194713901 HSGNITFDEIVNIAR ddPTM_HeLa_Romidepsin_16h_R1 2 HSGNITFDEIVNIAR 15 0 P30050;P30050-2 P30050 RPL12 60S ribosomal protein L12 0 0 ; ; 130.95 0.00087845 32315000 3928.8 3428.72 3632.5 3874.14 3696.34 3625.54 3406.51 3530.39 4111.6 3664.85 FALSE FALSE TRUE 3880.914274 3476.98961 3695.722139 4322.086295 3507.701977 3393.879695 3695.858874 3632.536265 3743.848198 3569.636669 1.087201481 0.974045802 1.035321654 1.210791657 0.982649581 0.950763344 1.035359959 1.017620728 1.048803715 1 11.80156152 HSLDS(ph)DEEEDDDDGGSSK ddPTM_HeLa_Romidepsin_16h_R1 3 HSLDSDEEEDDDDGGSSK 18 0 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 0 HS(0.004)LDS(0.996)DEEEDDDDGGSSK;HS(0.009)LDS(0.576)DEEEDDDDGGS(0.329)S(0.085)K;HS(0.047)LDS(0.951)DEEEDDDDGGS(0.001)SK ;; 131.31 5.27E-09 16306200 10486.59 9671.2 9835.98 6670.56 10785.3 11509.4 10003.21 12051.5 12217.3 10895.3 TRUE FALSE FALSE 10358.77541 9807.351407 10007.17111 7441.841533 10234.8859 10773.98648 10852.88241 12400.19114 11124.55409 10612.23854 0.97611596 0.924154821 0.942983997 0.701250873 0.964441749 1.015241643 1.022676071 1.16848025 1.048275918 1 13.37344139 -7.229653754 1.479808403 0.958517361 1.258941233 0.367308865 0.08927292 1.157606923 2.146626433 0.013283065 0.519914241 5.89E-08 7.229653754 0.300423872 HSLEEDEGSDFITENR ddPTM_HeLa_Romidepsin_16h_R1 2 HSLEEDEGSDFITENR 16 0 Q9NUQ3 Q9NUQ3 TXLNG Gamma-taxilin 0 0 ; ; 235.71 4.07E-46 4809300 2132.6 1849.75 2072.17 2370.4 2122.26 1997.21 1800.04 2076.14 2365.1 2244.01 FALSE FALSE TRUE 2106.607051 1875.790829 2108.23525 2644.476801 2013.953153 1869.594727 1952.935353 2136.209835 2153.559532 2185.710297 0.963808906 0.858206521 0.964553835 1.209893555 0.921418157 0.855371697 0.893501465 0.977352689 0.985290473 1 11.09388648 -8.546254588 24.99929676 0.988011867 0.904080529 0.183759972 0.086730255 306.9065021 328220.0276 0.012626114 0.025253273 2.84E-09 8.546254588 -0.083931338 HSLLLSS(ph)SPNRIPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 HSLLLSSSPNRIPSSR 16 1 G1UD79;Q7Z309-4;Q7Z309-3 G1UD79 SPACIA2;FAM122B Protein FAM122B 1 0 HS(0.002)LLLS(0.162)S(0.673)S(0.162)PNRIPSSR 65.022 0.019407 14930000 720.98 665.65 558.16 909.23 1207.1 1082.5 1016.1 983.7 924.11 654.84 TRUE FALSE FALSE 712.1924184 675.0210382 567.8745407 1014.359451 1145.497183 1013.331744 1102.407509 1012.161807 841.4552871 637.8271624 1.116591548 1.058313408 0.890326681 1.590335926 1.795936658 1.588724663 1.728379683 1.58689041 1.319252827 1 9.317021727 -9.187354611 5.648389581 1.045836177 1.672348331 0.855254619 0.119352925 0.039721232 2.287678646 0.01252835 0.020900919 6.50E-10 9.187354611 0.626512154 HSLS(ph)LDDIR ddPTM_HeLa_Romidepsin_16h_R1 4 HSLSLDDIR 9 0 Q96NE9-3;Q96NE9-2;Q96NE9 Q96NE9-3 FRMD6 FERM domain-containing protein 6 1 0 HS(0.079)LS(0.921)LDDIR;HS(0.077)LS(0.923)LDDIR;HSLS(1)LDDIR;HS(0.082)LS(0.918)LDDIR ;;; 149.33 0.0027066 20148400 4134.84 4260.81 4694.54 4298.52 6463.93 7128.13 5955.77 6615.34 4354.64 4087.66 TRUE FALSE FALSE 4084.44298 4320.793795 4776.246499 4795.535108 6134.051532 6672.665498 6461.652955 6806.744426 3965.150092 3981.462004 1.025865116 1.085227937 1.199621268 1.204465873 1.540653038 1.675933487 1.622934728 1.709609289 0.995903035 1 11.95908257 -8.868132795 0.978248636 1.013202665 1.708240767 0.97010861 0.048714197 0.057884557 0.1072217 0.008007644 0.023178011 1.35E-09 8.868132795 0.695038102 HSNVVILTTSNITEK ddPTM_HeLa_Romidepsin_16h_R1 1 HSNVVILTTSNITEK 15 0 Q15645 Q15645 TRIP13 Pachytene checkpoint protein 2 homolog 0 0 121.42 0.00010889 905840 365.63 439.17 546.55 274.16 403.46 464.66 567.62 434.36 557.56 535.79 FALSE FALSE TRUE 361.1735609 445.3526468 556.0624735 305.8596692 382.8699307 434.9697256 615.8336286 446.9275213 507.6904372 521.8700986 0.692075599 0.853378356 1.065518939 0.586083912 0.733649871 0.833482751 1.180051569 0.856396108 0.972829136 1 9.027546932 -7.80846731 24.85518677 0.837720132 1.018224142 0.168264443 0.156360106 135.667781 71702.7189 0.023317956 0.069954208 1.55E-08 7.80846731 0.18050401 HSPIAPSS(ph)PSPQVLAQK ddPTM_HeLa_Romidepsin_16h_R1 1 HSPIAPSSPSPQVLAQK 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 HS(0.003)PIAPS(0.124)S(0.773)PS(0.099)PQVLAQK 69.122 0.013861 16474000 3334.6 2959.8 2467.8 2857.2 2711.4 2620.2 2149.7 2665.8 3700.1 2871.7 TRUE FALSE FALSE 3293.956613 3001.468142 2510.751024 3187.562908 2573.02714 2452.777676 2332.295464 2742.930717 3369.153789 2797.09282 1.17763579 1.07306705 0.897628783 1.139598545 0.91989337 0.876902496 0.833828412 0.980636287 1.204519837 1 11.44971241 -8.661984653 6.076429115 1.072728828 0.892515341 0.487910196 0.089713998 0.146619488 7.625505767 0.013516283 0.027205623 2.18E-09 8.661984653 -0.180213487 HSPS(ph)PPPPTPTESR ddPTM_HeLa_Romidepsin_16h_R1 1 HSPSPPPPTPTESR 14 0 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 1 0 HS(0.043)PS(0.957)PPPPTPTESR 84.734 0.011464 3882800 1860.8 1675.5 1508.5 1670.6 1776.4 1430.1 1492.1 1641.9 2028.3 2174.6 TRUE FALSE FALSE 1838.119854 1699.087733 1534.75481 1863.762632 1685.743679 1338.721225 1618.838937 1689.405786 1846.883768 2118.103579 0.86781396 0.802174053 0.724589121 0.87992044 0.795874053 0.632037658 0.764286956 0.797603008 0.871951583 1 11.04855743 -10.97916874 0.394696523 1.017774645 0.737887239 0.440963468 0.070737586 0.470103174 0.188617929 0.053101511 0.031196957 1.05E-11 10.97916874 -0.279887407 HSQAVEELAEQLEQTKR ddPTM_HeLa_Romidepsin_16h_R1 1 HSQAVEELAEQLEQTKR 17 1 P35579 P35579 MYH9 Myosin-9 0 0 137.27 0.00023933 12379000 2074.5 1954.2 2004 2407.9 2370.2 2570.4 2371.3 2418.4 2575 2336.1 FALSE FALSE TRUE 2049.215196 1981.711279 2038.878779 2686.312728 2249.23985 2406.159736 2572.718163 2488.372588 2344.685551 2275.407785 0.900592505 0.870925771 0.896049839 1.180585188 0.988499672 1.057463085 1.130662459 1.093594126 1.030446308 1 11.1519094 -9.274309921 24.99547384 0.940511764 1.084946603 0.577195436 0.06434945 449.9300956 873793.2204 0.010092432 0.01547561 5.32E-10 9.274309921 0.144434839 HSQFLGYPITLYLEK ddPTM_HeLa_Romidepsin_16h_R1 1 HSQFLGYPITLYLEK 15 0 Q58FF8 Q58FF8 HSP90AB2P Putative heat shock protein HSP 90-beta 2 0 0 84.14 0.01152 3730500 3436 2779.9 8318 5695.4 7431 8189.4 5696.1 3607.5 3804.2 1915.4 FALSE FALSE TRUE 3394.12071 2819.035505 8462.771301 6353.928946 7051.768341 7666.12377 6179.926592 3711.877321 3463.942824 1865.637632 1.819281865 1.511030576 4.536128108 3.405768 3.779816734 4.109117247 3.312501038 1.989602513 1.8567072 1 10.86545308 -9.792240094 15.9554353 1.40694535 3.54569621 0.678583382 0.663124639 1.648777392 853.8796722 0.109064485 0.143453372 1.61E-10 9.792240094 2.138750861 HSQPAT(ph)PTPLQSR ddPTM_HeLa_Romidepsin_16h_R1 1 HSQPATPTPLQSR 13 0 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 1 0 HSQPAT(0.992)PT(0.008)PLQSR 96.805 0.011803 23450000 3024.7 2942.3 3302 2952.9 3431.7 4132.4 3305.4 3117.3 3256.4 3203.5 TRUE FALSE FALSE 2987.833793 2983.721777 3359.469925 3294.328192 3256.567544 3868.352977 3586.160593 3207.494157 2965.139428 3120.272608 0.95755537 0.956237532 1.076659109 1.055782172 1.043680458 1.239748401 1.149310026 1.027953182 0.950282171 1 11.60745636 -9.163588201 1.157893342 0.978510536 1.130902202 0.544957216 0.059091216 0.260105222 0.688153286 0.00997683 0.021225222 6.86E-10 9.163588201 0.152391666 HSQPSPEPHS(ph)PTEPPAWGSSIVK ddPTM_HeLa_Romidepsin_16h_R1 1 HSQPSPEPHSPTEPPAWGSSIVK 23 0 Q5VZ89-5;Q5VZ89-3;Q5VZ89;Q5VZ89-7 Q5VZ89-5 DENND4C DENN domain-containing protein 4C 1 0 HS(0.002)QPS(0.009)PEPHS(0.765)PT(0.223)EPPAWGS(0.001)S(0.001)IVK 73.809 0.00049273 6620600 1986.1 1794 1856 1451.6 1659.2 1884.8 1501.1 1710.4 1998.4 1779.3 TRUE FALSE FALSE 1961.892649 1819.255979 1888.302901 1619.440822 1574.524833 1764.367363 1628.603397 1759.887725 1819.658099 1733.073529 1.13203082 1.049728098 1.089568832 0.934432841 0.908515886 1.018056841 0.939719734 1.015472047 1.049960125 1 10.75911715 -9.26231127 24.99866442 1.064640311 0.961938027 0.56171621 0.044607726 56.97687972 1633634.145 0.008742837 0.013845225 5.47E-10 9.26231127 -0.102702284 HSS(ph)ETFSSTPSATR ddPTM_HeLa_Romidepsin_16h_R1 1 HSSETFSSTPSATR 14 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 0 HS(0.012)S(0.988)ETFSSTPSATR 89.747 0.019468 7514600 819.24 965.31 811.64 971 1095.2 1021.6 815.6 803.2 1481.2 1094 TRUE FALSE FALSE 809.2547878 978.8996595 825.7662537 1083.271589 1039.307857 956.3230571 884.8770436 826.4393248 1348.717762 1065.577722 0.759451677 0.918656274 0.774946995 1.016604952 0.975346833 0.897469079 0.830419992 0.775578644 1.265715052 1 10.05742011 -12.64465052 1.491431591 0.999642803 0.857710278 0.33423296 0.11950252 0.458007309 1.838880235 0.063610383 0.01456202 2.27E-13 12.64465052 -0.141932525 HSS(ph)TGDSADAGPPAAGSAR ddPTM_HeLa_Romidepsin_16h_R1 3 HSSTGDSADAGPPAAGSAR 19 0 F5H1N7;Q6ZU35 F5H1N7 KIAA1211 Uncharacterized protein KIAA1211 1 0 HS(0.019)S(0.977)T(0.004)GDSADAGPPAAGSAR;HS(0.116)S(0.371)T(0.371)GDS(0.142)ADAGPPAAGSAR;HS(0.237)S(0.75)T(0.013)GDSADAGPPAAGSAR ;; 191.36 2.76E-20 4337300 1172.17 1202.04 1197.34 1339.82 1489.4 1719.13 1297.15 1198.83 1976.38 1417.12 TRUE FALSE FALSE 1157.883141 1218.962351 1218.1792 1494.736292 1413.39036 1609.283141 1407.329889 1233.516255 1799.607623 1380.303018 0.838861559 0.883112139 0.882544763 1.082904459 1.023971071 1.165891199 1.019580389 0.893656131 1.303777214 1 10.4307693 -9.263454485 24.99633561 0.915445247 1.042636246 0 0.143468641 162.4594204 2015223.075 0.013417552 0.021121555 5.45E-10 9.263454485 0.127190999 HSS(ph)YPAGTEDDEGMGEEPSPFR ddPTM_HeLa_Romidepsin_16h_R1 2 HSSYPAGTEDDEGMGEEPSPFR 22 0 Q92934 Q92934 BAD Bcl2-associated agonist of cell death 1 0 HS(0.217)S(0.782)Y(0.001)PAGTEDDEGMGEEPSPFR;HS(0.216)S(0.784)YPAGTEDDEGMGEEPSPFR ; 116.92 2.54E-05 93263000 4659.2 4553.3 4397.4 5060.9 5730.1 6557.8 5279.1 6964 4864.4 4406.3 TRUE FALSE FALSE 4602.411878 4617.401477 4473.934902 5646.06507 5437.671615 6138.777744 5727.506622 7165.492353 4429.315881 4291.823691 1.072367415 1.07586001 1.042432128 1.315539844 1.266983923 1.430342481 1.334515822 1.6695682 1.032035843 1 12.0673751 -5.261968741 0.275977001 0.99378658 3.445124454 0.87919147 0.071947243 5.267168919 0.124159305 0.031352343 5.44839363 5.47E-06 5.261968741 2.451337874 HSVTAAT(ph)PPPSPT(ph)SGESGDLLSNLLQSPSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8-2;Q96QU8 Q96QU8-2 XPO6 Exportin-6 2 0 HS(0.005)VT(0.05)AAT(0.918)PPPS(0.171)PT(0.374)S(0.2)GES(0.198)GDLLS(0.084)NLLQSPSSAK 77.286 1.27E-07 40571000 7845.4 9307.6 9092 7724.8 8596 9312.8 7097.5 9637.3 9981.1 9819.5 TRUE FALSE FALSE 7749.777247 9438.632637 9250.242446 8617.977722 8157.314044 8717.742136 7700.361473 9916.14007 9088.365418 9564.387974 0.810274245 0.986851711 0.967154665 0.90104853 0.85288406 0.91147935 0.805107603 1.036777272 0.95022969 1 13.22345694 -9.015434224 23.76635813 0.919608921 0.893079025 0.022385387 0.075152501 1609.323445 2478117.853 0.013343678 0.022618345 9.65E-10 9.015434224 -0.026529897 HSVTAAT(ph)PPPSPTS(ph)GESGDLLSNLLQSPSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8-2;Q96QU8 Q96QU8-2 XPO6 Exportin-6 2 0 HSVT(0.002)AAT(0.504)PPPS(0.305)PT(0.305)S(0.431)GES(0.431)GDLLS(0.023)NLLQSPSSAK 77.917 8.34E-08 20166000 3170.7 3766.1 3553.1 2410.8 3838.2 3704.5 3076.9 3569.5 4439.6 4354.5 TRUE FALSE FALSE 3132.054289 3819.119255 3614.940215 2689.548039 3642.322332 3467.794406 3338.251809 3672.777851 4042.511057 4241.369462 0.738453539 0.900444842 0.852304957 0.634122555 0.858760918 0.817611962 0.787069327 0.865941504 0.953114576 1 12.05031445 -12.42754431 1.035660855 1.005644343 0.801021545 0.455693132 0.073488416 0.362918337 0.664561905 0.056867495 0.012780348 3.74E-13 12.42754431 -0.204622798 HSVTAATPPPSPTSGES(ph)GDLLSNLLQSPSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 HSVTAATPPPSPTSGESGDLLSNLLQSPSSAK 32 0 Q96QU8-2;Q96QU8 Q96QU8-2 XPO6 Exportin-6 1 0 HSVTAAT(0.001)PPPS(0.238)PT(0.238)S(0.205)GES(0.278)GDLLS(0.032)NLLQS(0.008)PSSAK 83.834 1.40E-08 8302400 1443.5 1783.6 2205.2 1608.6 2488.5 2705.2 1637.8 2705.9 2099.7 2535.1 TRUE FALSE FALSE 1425.906067 1808.709568 2243.580581 1794.593901 2361.502559 2532.346451 1776.914691 2784.190947 1911.897573 2469.237737 0.577468117 0.732497135 0.908612625 0.726780526 0.956369054 1.025557974 0.719620742 1.127550785 0.774286552 1 11.26985003 -8.747573807 24.74948666 0.794566808 0.945176791 0.254520272 0.142099341 336.0091638 599758.726 0.026416248 0.052611538 1.79E-09 8.747573807 0.150609983 HT(ph)ET(ph)RNT(ph)VS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 HTETRNTVSR 10 1 O15230 O15230 LAMA5 Laminin subunit alpha-5 4 0 HT(1)ET(1)RNT(1)VS(1)R 49.934 0.028993 3737200 0 0 151.07 0 148.93 0 128.7 0 0 142.77 TRUE FALSE FALSE 0 0 153.69931 0 141.3295464 0 139.6317748 0 0 139.0608148 0 0 1.105266859 0 1.016314672 0 1.004105829 0 0 1 7.119572138 -12.57326942 1.380531835 0.997055579 0.361648771 0 0.546445643 0.50271256 1.730392032 0.292019172 0.069769071 2.67E-13 12.57326942 -0.635406808 HT(ph)PPTIGGSLPYR ddPTM_HeLa_Romidepsin_16h_R1 1 HTPPTIGGSLPYR 13 0 H7C3Q7;H0Y6B5;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;E9PEZ7 H7C3Q7 ABI2 Abl interactor 2 1 0 HT(0.944)PPT(0.052)IGGS(0.004)LPYR 86.911 0.020382 53286000 1642 1651.9 1781.6 1631.5 1872.4 1780.6 1334.6 1454.9 1842.7 1813 TRUE FALSE FALSE 1621.986672 1675.155492 1812.608001 1820.141706 1776.844441 1666.825407 1447.960891 1496.995236 1677.884297 1765.897999 0.918505301 0.948613959 1.026451133 1.030717351 1.006198797 0.943896764 0.819957264 0.847724635 0.950159238 1 10.7861863 -7.842297342 4.512572498 0.972610179 0.83352207 0.725378464 0.035702246 0.100244951 3.700173606 0.006335959 0.020887619 1.44E-08 7.842297342 -0.139088109 HTDDEMTGY(ph)VATR ddPTM_HeLa_Romidepsin_16h_R1 1 HTDDEMTGYVATR 13 0 Q16539-5;Q16539-3;Q16539-4;Q16539-2;Q16539;E7EX54;B4E0K5 Q16539-5 MAPK14 Mitogen-activated protein kinase 14 1 0 HTDDEMTGY(0.999)VATR 99.669 0.0040748 94981000 4066.9 5227.2 2536.5 3354.1 3771.3 2981.5 2016.5 2846.6 4391.8 3914.9 TRUE FALSE FALSE 4017.331059 5300.788659 2580.646718 3741.916824 3578.836488 2790.991772 2187.78146 2928.96188 3998.986409 3813.190334 1.053535414 1.390119085 0.676768399 0.981308693 0.938541267 0.731930884 0.573740429 0.768113213 1.048724574 1 11.89678283 -8.456709368 0.981873073 1.037969921 0.643971194 0.452861656 0.165939996 0.426227946 0.727348885 0.026099012 0.113238919 3.49E-09 8.456709368 -0.393998727 HTGPNS(ph)PDTANDGFVR ddPTM_HeLa_Romidepsin_16h_R1 9 HTGPNSPDTANDGFVR 16 0 P31943;E9PCY7;G8JLB6;D6RDU3;D6RBM0;D6RIH9;D6RJ04;D6RIU0;D6RIT2;D6RFM3;D6R9T0;D6RAM1;E5RGH4;E5RGV0;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 0 HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(0.999)PDT(0.001)ANDGFVR;HTGPNS(0.999)PDT(0.001)ANDGFVR;HT(0.003)GPNS(0.996)PDT(0.001)ANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(1)PDTANDGFVR;HTGPNS(0.991)PDT(0.009)ANDGFVR;HT(0.228)GPNS(0.761)PDT(0.011)ANDGFVR ;;;;;;;; 192.22 3.86E-13 2002253000 19404.52 18618.87 17497.9 17721.56 20366.23 21035.84 17795.57 20605.91 19677.48 18688.57 TRUE FALSE FALSE 19168.01025 18880.98694 17802.44361 19770.61015 19326.86529 19691.71771 19307.12527 21202.1095 17917.47691 18203.03826 1.053011589 1.03724371 0.977992979 1.086115948 1.061738431 1.081781922 1.060653996 1.16475663 0.984312435 1 14.15189165 -4 0.319286746 1.018813695 2.192898028 0.644050044 0.031513894 25.98586908 0.33136164 0.010403315 18.04967767 1.00E-04 4 1.174084333 HTGPNS(ph)PDTANDGFVRL ddPTM_HeLa_Romidepsin_16h_R1 2 HTGPNSPDTANDGFVRL 17 1 E7EQJ0 E7EQJ0 HNRNPH1 1 0 HTGPNS(0.965)PDT(0.035)ANDGFVRL;HTGPNS(1)PDTANDGFVRL ; 93.738 0.010598 15658400 1429.94 1469.93 1198.83 1633.26 1326.87 1205.63 1053.94 1473.47 1836.07 2332.01 TRUE FALSE FALSE 1412.511341 1490.623713 1219.695133 1822.105206 1259.154873 1128.594134 1143.461637 1516.10253 1671.847301 2271.424044 0.621861578 0.656250741 0.53697377 0.802186281 0.554346017 0.496866332 0.503411787 0.667467853 0.73603487 1 11.14938135 -12.70171257 0.365058649 1.21945445 0.568689606 0.351688922 0.119560822 1.321636054 0.179901904 0.353974826 0.032339142 1.99E-13 12.70171257 -0.650764844 HTGPNSPDT(ph)ANDGFVR ddPTM_HeLa_Romidepsin_16h_R1 1 HTGPNSPDTANDGFVR 16 0 P31943;E9PCY7;G8JLB6;D6RDU3;D6RBM0;D6RIH9;D6RJ04;D6RIU0;D6RIT2;D6RFM3;D6R9T0;D6RAM1;E5RGH4;E5RGV0;H0YAQ2;P55795;E7EQJ0 P31943;P55795;E7EQJ0 HNRNPH1;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 1 0 HTGPNS(0.226)PDT(0.774)ANDGFVR 231.41 2.98E-45 14869000 1500.2 1091.6 1023 1208.7 1274.4 1318.6 978.59 1126.3 1357.1 1374.4 TRUE FALSE FALSE 1481.914985 1106.967573 1040.804886 1348.455581 1209.362613 1234.345716 1061.71141 1158.887713 1235.717577 1338.69289 1.106986521 0.82690181 0.77747846 1.007292704 0.90339063 0.922052941 0.793095577 0.865686015 0.923077717 1 10.38660931 -10.25935748 24.98848011 1.050521414 0.872730949 0.369294362 0.078119741 100.2515152 1203294.906 0.012410368 0.014800878 5.50E-11 10.25935748 -0.177790465 HTLGDS(ph)DNES ddPTM_HeLa_Romidepsin_16h_R1 2 HTLGDSDNES 10 0 G3V1D1;G3V192;P02794 G3V1D1 FTH1 "Ferritin;Ferritin heavy chain;Ferritin heavy chain, N-terminally processed" 1 0 HTLGDS(0.998)DNES(0.002);HTLGDS(0.996)DNES(0.004) ; 114.89 0.015021 186157000 12179.7 11100.5 18469.5 10329.8 11970.1 14285.3 18870 4458.5 16221.8 15018.2 TRUE FALSE FALSE 12031.24913 11256.77313 18790.9539 11524.18008 11359.22113 13372.51543 20472.81733 4587.499663 14770.88158 14628.025 0.822479394 0.769534721 1.284585848 0.787815175 0.776538263 0.914170945 1.399561276 0.313610324 1.009765951 1 13.83644738 HTPLSK(ac)LMK ddPTM_HeLa_Romidepsin_16h_R1 2 HTPLSKLMK 9 1 P61956-2;P61956;A8MUA9;A8MU27;P55854;P55854-2 P61956-2 SUMO2;SUMO3 Small ubiquitin-related modifier 2;Small ubiquitin-related modifier 3 0 1 ; HTPLSK(1)LMK;HTPLSK(1)LMK 82.749 0.0076705 1730750 1842.86 978.96 5478.4 3304.6 5181.5 6024.2 3968.4 1862.78 1685.13 987.92 FALSE TRUE FALSE 1820.398513 992.7418246 5573.749254 3686.693401 4917.06872 5639.273062 4305.475797 1916.6766 1534.407752 962.253696 1.891807245 1.031684086 5.79239059 3.831311239 5.109950464 5.860484699 4.474366599 1.99186203 1.594597931 1 9.910273497 -9.771061793 24.99976205 1.403689337 4.566236842 0.676716951 1.059536878 84.57701416 219737.1548 0.169213109 0.223972265 1.69E-10 9.771061793 3.162547505 HTPPTIGGS(ph)LPYR ddPTM_HeLa_Romidepsin_16h_R1 1 HTPPTIGGSLPYR 13 0 H7C3Q7;H0Y6B5;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9;E9PEZ7 H7C3Q7 ABI2 Abl interactor 2 1 0 HT(0.001)PPT(0.361)IGGS(0.638)LPYR 91.616 0.008795 53717000 1215 1101 1111.3 1074.9 1101.2 1253 1054.4 1089.2 1159.8 1074.7 TRUE FALSE FALSE 1200.191113 1116.499907 1130.64171 1199.184996 1045.001655 1172.937344 1143.96071 1120.714284 1056.064583 1046.779139 1.146556201 1.066605041 1.080114867 1.145595046 0.998301949 1.120520366 1.092838658 1.070631083 1.00887049 1 10.03174136 -12.55105437 1.321489031 1.000034388 1.096149428 0.402368561 0.041234831 0.338385501 1.05931214 0.028947969 0.006860973 2.81E-13 12.55105437 0.09611504 HTVDDGLDIR ddPTM_HeLa_Romidepsin_16h_R1 2 HTVDDGLDIR 10 0 A0A0C4DGH5;Q86VP6-2;Q86VP6 A0A0C4DGH5 CAND1 Cullin-associated NEDD8-dissociated protein 1 0 0 ; ; 157.97 0.0013262 7321200 1540.82 1555.63 1850.06 1433.89 1697.18 1348.4 1447.85 1701.04 1728.67 1824.43 FALSE FALSE TRUE 1522.039893 1577.5302 1882.259518 1599.683108 1610.566572 1262.241592 1570.830343 1750.256909 1574.053426 1777.031046 0.856507205 0.887733618 1.059215889 0.900199866 0.906324386 0.710309251 0.883963365 0.984933219 0.885777111 1 10.79525317 -8.658047916 3.521623247 0.935768336 0.856168847 0.117333512 0.084307304 0.372313577 8.973816476 0.013384062 0.027946381 2.20E-09 8.658047916 -0.079599489 HTVLYIS(ph)PPPEDLLDNSR ddPTM_HeLa_Romidepsin_16h_R1 3 HTVLYISPPPEDLLDNSR 18 0 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 1 0 HTVLY(0.002)IS(0.998)PPPEDLLDNSR;HT(0.051)VLY(0.009)IS(0.94)PPPEDLLDNSR;HTVLYIS(1)PPPEDLLDNSR ;; 136.53 0.00041458 16972800 7685.5 7181 6711.4 6023.4 10535.6 11912.1 10794.6 11716.3 7761.9 8221.2 TRUE FALSE FALSE 7591.82617 7282.094306 6828.209102 6719.853849 9997.929018 11150.95525 11711.49305 12055.29266 7067.656224 8007.612039 0.948076172 0.909396493 0.852714775 0.839183244 1.248553123 1.392544394 1.462545013 1.505479111 0.882617213 1 12.96715636 -8.515403957 2.877589127 0.950973144 1.453848645 0.933176523 0.065863576 0.054182444 0.90398143 0.010652941 0.024733229 3.05E-09 8.515403957 0.5028755 HVDSLSQRS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 HVDSLSQRSPK 11 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 1 0 HVDS(0.001)LS(0.142)QRS(0.857)PK 70.54 0.028624 9686400 1865.1 1926.5 1638.9 6512.9 4127.4 4334.8 3342.1 1784.3 4184.3 2735.6 TRUE FALSE FALSE 1842.367444 1953.621318 1667.424367 7265.952142 3916.763377 4057.82027 3625.977891 1835.925905 3810.045728 2664.528718 0.691442142 0.73319582 0.625785849 2.726918308 1.469964782 1.52290356 1.360832731 0.689024627 1.429913554 1 11.37966467 HVEEFS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 1 0 HVEEFS(1)PR 130.98 1.36E-05 0 635.57 938.48 724.26 782.48 792.14 691.72 772.3 842.34 575.22 622.52 TRUE FALSE FALSE 627.8234284 951.6919461 736.8654415 872.9540193 751.7141399 647.5213244 837.8991427 866.7117789 523.7708825 606.3468407 1.035419641 1.569550433 1.21525403 1.439694183 1.239742816 1.067905827 1.381880941 1.429399348 0.863813988 1 9.243999466 -10.39480675 9.12988865 1.015618251 1.321967153 0.585147881 0.140110837 0.180067613 12.51478043 0.02178605 0.024875557 4.03E-11 10.39480675 0.306348902 HVEEFSPR ddPTM_HeLa_Romidepsin_16h_R1 2 HVEEFSPR 8 0 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 0 ; ; 160.88 0.0016922 6205100 2120.4 1783.8 1666.33 1835.24 2137.6 2248.83 1462.27 1700.95 2031.59 1853.63 FALSE FALSE TRUE 2094.555749 1808.912383 1695.331775 2047.439084 2028.510296 2105.137021 1586.475177 1750.164305 1849.879502 1805.472425 1.160115059 1.001905295 0.938996216 1.134018474 1.123534354 1.165975725 0.878703632 0.9693664 1.024595821 1 10.81816067 -7.750430498 24.97635374 1.074532423 0.924034983 0.366191174 0.075782232 186.2187899 422474.6719 0.011823701 0.043385272 1.78E-08 7.750430498 -0.150497441 HVEVSQAPLPPAPAYLS(ph)SPLALPSQR ddPTM_HeLa_Romidepsin_16h_R1 1 HVEVSQAPLPPAPAYLSSPLALPSQR 26 0 A0A087X0G7;A0A087WUW6;A0A087X1B1;Q9Y6K9-3;Q9Y6K9;Q9Y6K9-2 A0A087X0G7 IKBKG NF-kappa-B essential modulator 1 0 HVEVSQAPLPPAPAYLS(0.591)S(0.393)PLALPS(0.016)QR 127.12 2.04E-07 24885000 1183.7 1132.3 1170.2 1043.5 1836.1 1951.4 1715 1618.6 1459.6 1165.2 TRUE FALSE FALSE 1169.272609 1148.240549 1190.56684 1164.15438 1742.396966 1826.711838 1860.672057 1665.431637 1329.04972 1134.927936 1.030261545 1.011729919 1.049024174 1.025751806 1.535248988 1.609539936 1.639462734 1.467433821 1.171043269 1 10.14838498 -8.749445078 5.406059778 1.017093215 1.576694634 0.936938788 0.065190119 0.017135448 1.488670278 0.006010561 0.011751929 1.78E-09 8.749445078 0.55960142 HVGMAVAGLLADAR ddPTM_HeLa_Romidepsin_16h_R1 1 HVGMAVAGLLADAR 14 0 P25788;P25788-2 P25788 PSMA3 Proteasome subunit alpha type-3 0 0 101.39 0.002745 405320 261.37 334.54 479.15 409.43 615.06 293.52 467.42 359.73 187.24 389.54 FALSE FALSE TRUE 258.1843219 339.2496629 487.4894048 456.770223 583.6711931 274.7650193 507.1226431 370.13822 170.4927854 379.4196946 0.680471587 0.894127711 1.284828942 1.203865349 1.538326031 0.724171737 1.33657438 0.97553771 0.449351438 1 8.567650757 -9.842860766 6.276995358 0.846501978 1.180944852 0.387247744 0.249781425 0.180065488 11.09802601 0.035626818 0.047092352 1.44E-10 9.842860766 0.334442874 HVGNQQYNVTYVVK ddPTM_HeLa_Romidepsin_16h_R1 2 HVGNQQYNVTYVVK 14 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;A0A0A0MT44 O75369-8 FLNB Filamin-B 0 0 ; ; 136.3 1.29E-05 2827600 3212.8 2766 3112.5 3572.9 4062.2 4246.7 3642.2 3743.8 2731.9 2866.4 FALSE FALSE TRUE 3173.641158 2804.939821 3166.671757 3986.015509 3854.890776 3975.349576 3951.568377 3852.120946 2487.552022 2791.930515 1.136719249 1.004659609 1.134222983 1.427691516 1.380725901 1.423871244 1.415353411 1.379733817 0.890979202 1 11.44704732 -9.344966265 3.887743517 1.062199081 1.406512249 0.884011916 0.06738867 0.05004088 1.425513782 0.008520638 0.013373396 4.52E-10 9.344966265 0.344313168 HVINFDLPSDIEEYVHR ddPTM_HeLa_Romidepsin_16h_R1 2 HVINFDLPSDIEEYVHR 17 0 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1;O15523-2;O15523 A0A2R8Y4A4 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 0 ; ; 195.6 3.74E-14 94498000 5368.2 4219.2 4685.3 4402.6 4703 4272.3 3491 4170.9 5064.2 4060.1 FALSE FALSE TRUE 5302.770314 4278.598008 4766.845681 4911.649327 4462.988361 3999.313818 3787.525453 4291.578411 4611.245268 3954.618017 1.34090582 1.081924472 1.205387135 1.242003477 1.128551062 1.011302179 0.957747483 1.085206812 1.166040626 1 11.94932263 -8.340604323 4.012450879 1.167358152 1.011416157 0.368182086 0.090046182 0.269407766 8.179943456 0.018843015 0.044764911 4.56E-09 8.340604323 -0.155941995 HVLVTLGEK ddPTM_HeLa_Romidepsin_16h_R1 2 HVLVTLGEK 9 0 F8VZU9;G3V1Y7;F8VPF3;F8W1R7;J3KND3;G8JLA2;G3V1V0;F8W180;B7Z6Z4;P60660-2;P60660;H0YI43;F8VXL3 F8VZU9 MYL6 Myosin light polypeptide 6 0 0 ; ; 114.89 0.00055119 27424000 11296.1 9708.7 18135.5 14979.5 16436.6 17957.3 14623.1 11457.1 10558.7 6816.5 FALSE FALSE TRUE 11158.41879 9845.379333 18451.14077 16711.50027 15597.77897 16809.88648 15865.18575 11788.59311 9614.303427 6639.406347 1.680635015 1.482870428 2.779034722 2.517017245 2.349273136 2.53183577 2.389548842 1.775549273 1.448066728 1 12.69683854 -10.52350934 0.733817944 1.142572795 2.392228622 0.619853727 0.346318183 0.239739234 0.277230756 0.099405803 0.099410144 3.00E-11 10.52350934 1.249655827 HVRRTVNGLDTS(ph)AQRYS(ph)PYPT(ph)QAAT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 HVRRTVNGLDTSAQRYSPYPTQAATK 26 3 J3QLP2;J3QRR9;J3QKY8;Q8WU58 J3QLP2 FAM222B Protein FAM222B 4 0 HVRRT(0.004)VNGLDT(0.17)S(0.807)AQRY(0.491)S(0.539)PY(0.495)PT(0.535)QAAT(0.958)K 51.029 0.0031943 0 1968.1 724.69 901.14 153.82 393.26 282.78 1349.5 1306.6 3156.7 2650.5 TRUE FALSE FALSE 1944.11204 734.8922048 916.8239637 171.6053921 373.1904747 264.7112706 1464.126496 1344.40441 2874.356846 2581.639628 0.753053222 0.284661034 0.355132434 0.066471474 0.144555604 0.102536104 0.56713047 0.520756032 1.113384229 1 11.33407191 -10.41844338 1.602042418 0.915730546 0.271742902 0.750943226 0.175308884 0.136895737 0.681530108 0.035448255 0.039538363 3.82E-11 10.41844338 -0.643987644 HVS(ph)PVTPPR ddPTM_HeLa_Romidepsin_16h_R1 2 HVSPVTPPR 9 0 Q13443 Q13443 ADAM9 Disintegrin and metalloproteinase domain-containing protein 9 1 0 HVS(1)PVTPPR;HVS(1)PVTPPR ; 105.13 0.0099205 15158700 3687.62 5153.2 3823.32 3276.06 3965.71 4791.5 2540.22 5509 4280.3 4579.9 TRUE FALSE FALSE 3642.673869 5225.746885 3889.863281 3654.853472 3763.325021 4485.338614 2755.986223 5668.394223 3897.459248 4460.913538 0.816575761 1.171452179 0.871988046 0.819306055 0.843622049 1.005475353 0.617807586 1.270680137 0.873690829 1 12.12312347 -12.72866951 1.642925699 1.000095688 0.901537653 0 0.182614355 1.118526868 5.446351084 0.11760239 0.025512071 1.87E-13 12.72866951 -0.098558035 HVTLPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 5 HVTLPSSPR 9 0 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6RE05;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 HVTLPS(0.227)S(0.773)PR;HVTLPS(0.209)S(0.791)PR;HVTLPS(0.004)S(0.996)PR;HVTLPS(0.076)S(0.924)PR;HVTLPS(0.444)S(0.556)PR ;;;; 144.77 0.0044659 97736000 19526.1 17351.8 18443.9 15305.5 28755.6 32630.5 23407.8 27710.5 25756.4 23386.3 TRUE FALSE FALSE 19288.10838 17596.0791 18764.90834 17075.19392 27288.09443 30545.51636 25396.05795 28512.2596 23452.68308 22778.72055 0.846759955 0.772478817 0.823791147 0.749611634 1.197964318 1.340967167 1.114902739 1.25170593 1.029587374 1 14.47539909 -8.687698117 7.571415264 0.893425269 1.229446857 0.752927932 0.099442782 0.1021655 8.988057046 0.015562538 0.03117507 2.05E-09 8.687698117 0.336021588 HWELTAEGEEIAR ddPTM_HeLa_Romidepsin_16h_R1 2 HWELTAEGEEIAR 13 0 K7ER16;K7ER00;Q9Y285;K7EK06;Q9Y285-2 K7ER16 FARSA Phenylalanine--tRNA ligase alpha subunit 0 0 ; ; 190.85 4.35E-11 12324800 3877.7 3740.4 3541.4 3502.1 3902.4 4075 3114.7 3995 4151 3771.9 FALSE FALSE TRUE 3830.437101 3793.057449 3603.036581 3907.02928 3703.245966 3814.620651 3379.26254 4110.589022 3779.724164 3673.905494 1.042606324 1.03243196 0.980710197 1.063453942 1.00798618 1.038301246 0.919801161 1.118860849 1.028802774 1 11.8430988 HWILPQDYDHAQAEAR ddPTM_HeLa_Romidepsin_16h_R1 1 HWILPQDYDHAQAEAR 16 0 Q15293-2;Q15293 Q15293-2 RCN1 Reticulocalbin-1 0 0 100.11 0.0020833 11560000 2155.7 1845.2 1775.7 2039.9 1700.3 1693.8 1563 1538.4 2094.6 1915.4 FALSE FALSE TRUE 2129.425499 1871.176774 1806.605314 2275.762836 1613.527346 1585.571646 1695.761181 1582.911177 1907.25373 1865.637632 1.141392874 1.002969034 0.968358101 1.219831117 0.864866424 0.849881895 0.908944562 0.848455858 1.022306635 1 10.86545308 -8.72566046 24.99701788 1.064372373 0.869662108 0.629846279 0.071700149 92.6077484 64700.22164 0.011161541 0.0223225 1.88E-09 8.72566046 -0.194710264 HWPFMVVNDAGRPK ddPTM_HeLa_Romidepsin_16h_R1 3 HWPFMVVNDAGRPK 14 1 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 ;; ;; 119.21 0.0011525 54030120 19296.706 19346.8 18221.67 16254.2 18846.6 18347.1 16943.19 18829.86 20699.35 18170.62 FALSE FALSE TRUE 19061.51033 19619.16476 18538.81052 18133.58708 17884.78768 17174.77952 18382.34414 19374.67229 18847.94829 17698.54467 1.077010041 1.108518532 1.04747655 1.024580688 1.010523069 0.970406315 1.038635915 1.094704262 1.064943397 1 14.11134311 -9.254745566 20.63446619 1.044606465 1.024228658 0.078478777 0.039756132 147.9604801 456095.4626 0.007159636 0.01165701 5.56E-10 9.254745566 -0.020377807 HWPFQVINDGDKPK ddPTM_HeLa_Romidepsin_16h_R1 2 HWPFQVINDGDKPK 14 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 0 ; ; 94.538 0.0060113 35924000 9099.3 8245.7 8884.2 8126.3 11520.3 12636.9 12093.2 12624.1 9351.6 9299.1 FALSE FALSE TRUE 8988.394232 8361.783181 9038.825774 9065.901041 10932.3761 11829.44287 13120.39611 12989.35842 8515.169474 9057.508041 0.992369445 0.923188049 0.997937372 1.000926635 1.206996014 1.306037248 1.44856577 1.434098469 0.940122762 1 13.14489847 -8.37998754 1.418094376 0.987965288 1.44509372 0.96661611 0.035588976 0.048096214 0.182231917 0.004892926 0.017038 4.17E-09 8.37998754 0.457128432 HYEDGYPGGSDNY(ph)GSLSR ddPTM_HeLa_Romidepsin_16h_R1 1 HYEDGYPGGSDNYGSLSR 18 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 HYEDGYPGGSDNY(0.795)GS(0.185)LS(0.02)R 111.11 0.0011517 3691300 1525.7 1193.7 1171.8 1528.7 1499.6 1511.8 967.81 868.33 2156.1 1769.6 TRUE FALSE FALSE 1507.104182 1210.50494 1192.194687 1705.455487 1423.069816 1415.200859 1050.015757 893.4537586 1963.253016 1723.625537 0.874380281 0.702301581 0.691678478 0.989458238 0.82562586 0.821060508 0.609190184 0.51835723 1.139025255 1 10.75123066 -5.906770866 0.166436223 1.028996258 1.54E-18 0.58149756 0.117793741 19.6473238 0.362617229 0.214200698 4.511918372 1.24E-06 5.906770866 -1.028996258 HYEDGYPGGSDNYGS(ph)LSR ddPTM_HeLa_Romidepsin_16h_R1 5 HYEDGYPGGSDNYGSLSR 18 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 HYEDGYPGGSDNYGS(0.882)LS(0.118)R;HYEDGYPGGSDNYGS(0.937)LS(0.063)R;HYEDGYPGGSDNYGS(0.931)LS(0.069)R;HYEDGYPGGSDNYGS(0.975)LS(0.025)R;HYEDGYPGGSDNYGS(0.923)LS(0.077)R ;;;; 302.9 1.75E-143 149055700 15319.9 15876.5 16065.7 15913.4 21889.8 19622.7 16480.1 18773.5 15344.4 14070.4 TRUE FALSE FALSE 15133.17517 16100.00978 16345.31677 17753.38218 20772.68182 18368.8728 17879.91928 19316.6816 13971.95843 13704.84898 1.104220498 1.174767399 1.192666683 1.295408815 1.515717674 1.340319242 1.304641832 1.409477889 1.019490142 1 13.74239881 -9.752164958 0.777440414 1.032074348 1.390844415 0.847457946 0.062126403 0.165550459 0.20166379 0.014569576 0.024157932 1.77E-10 9.752164958 0.358770067 HYK(ac)IHSR ddPTM_HeLa_Romidepsin_16h_R1 1 HYKIHSR 7 1 K7ELU1;Q5MCW4-2;Q5MCW4 K7ELU1 ZNF569 Zinc finger protein 569 0 1 HYK(1)IHSR 83.614 0.029912 0 177.88 146.68 0 0 168.45 237.53 183.51 226.58 116.43 0 FALSE TRUE FALSE 175.7119301 148.7449649 0 0 159.8533679 222.3525996 199.0973348 233.1357348 106.0162092 0 0 HYLHES(ph)VLFNLT(ph)T(ph)MYELESSRSMQK ddPTM_HeLa_Romidepsin_16h_R1 1 HYLHESVLFNLTTMYELESSRSMQK 25 1 Q8WVT3;H7C0K3;H7C0T3;A0A0J9YXQ9;Q53QD4 Q8WVT3 TRAPPC12;CGI-87 Trafficking protein particle complex subunit 12 3 0 HY(0.183)LHES(0.819)VLFNLT(0.823)T(0.555)MY(0.475)ELES(0.03)S(0.017)RS(0.097)MQK 43.497 0.0042558 0 418.06 540.79 437.12 318.6 481.28 602.7 396.48 364.16 656.33 558.66 TRUE FALSE FALSE 412.9645239 548.4032558 444.7278902 355.4380311 456.7184857 564.1894151 430.1570013 374.6963951 597.626201 544.1459327 0.758922376 1.007823863 0.817295258 0.653203506 0.839330882 1.036834756 0.790517719 0.688595416 1.098282952 1 9.087849805 -12.47288716 1.070048799 1.00563654 0.823457736 0.342335238 0.119769532 0.658579533 1.279058357 0.0949962 0.020559684 3.37E-13 12.47288716 -0.182178804 HYNGEAYEDDEHHPR ddPTM_HeLa_Romidepsin_16h_R1 3 HYNGEAYEDDEHHPR 15 0 P31689 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 0 ;; ;; 73.834 0.011064 14454300 3062.23 2403.21 2681.35 2147.01 2815.58 3305.8 2902.97 2430.45 3366.74 3150.15 FALSE FALSE TRUE 3024.906363 2437.042453 2728.017772 2395.257398 2671.890446 3094.570049 3149.548199 2500.771236 3065.610342 3068.308649 0.985854654 0.794262485 0.889094965 0.780644216 0.870802371 1.008558917 1.026476981 0.815032489 0.999120588 1 11.5832279 -10.43675806 12.56117865 0.993764853 0.889607803 0.301953446 0.077349432 1.04893907 151.0755234 0.013702996 0.015661661 3.66E-11 10.43675806 -0.10415705 HYYSGYSS(ph)SPEYSSESTHK ddPTM_HeLa_Romidepsin_16h_R1 1 HYYSGYSSSPEYSSESTHK 19 0 Q5R3F8 Q5R3F8 ELFN2 Protein phosphatase 1 regulatory subunit 29 1 0 HYYS(0.004)GY(0.002)S(0.011)S(0.809)S(0.171)PEY(0.001)SS(0.001)ES(0.001)T(0.001)HK 58.246 0.017636 6294500 655.24 581.51 690.52 298.57 831.36 947.81 594.42 782.11 979.01 958.99 TRUE FALSE FALSE 647.2536828 589.696513 702.5382109 333.0920682 788.932597 887.2479999 644.91002 804.7391189 891.4448936 934.0753016 0.692935229 0.631315818 0.752121601 0.356600873 0.844613486 0.949867745 0.690426156 0.861535593 0.954360845 1 9.867395049 -12.16793174 0.912301454 1.000346804 0.719157529 0.305088317 0.152757491 0.558191988 0.835613416 0.102986708 0.029291638 6.79E-13 12.16793174 -0.281189275 HYYSITINYR ddPTM_HeLa_Romidepsin_16h_R1 1 HYYSITINYR 10 0 O00487 O00487 PSMD14 26S proteasome non-ATPase regulatory subunit 14 0 0 67.726 0.023579 433830 282.47 170.57 154.92 170.17 215.72 109.29 253.52 180.41 312.33 266.68 FALSE FALSE TRUE 279.027147 172.9712889 157.6163176 189.8458561 204.7110034 102.3067217 275.0539825 185.6298787 284.3944226 259.7516152 1.074207553 0.66591035 0.606796295 0.730874593 0.788102909 0.39386366 1.058911539 0.71464379 1.094870661 1 8.02098891 -10.26194881 24.98510537 1.03504246 0.709840703 0.50564723 0.157216965 27.08773602 1328512.677 0.025030538 0.029560083 5.47E-11 10.26194881 -0.325201757 IAAPELHKGDS(ph)DSEEDEPTK ddPTM_HeLa_Romidepsin_16h_R1 1 IAAPELHKGDSDSEEDEPTK 20 1 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 0 IAAPELHKGDS(0.845)DS(0.152)EEDEPT(0.003)K 62.203 0.0037128 0 1596 1625 1713.6 1703.8 1336.9 1472.4 1565.9 1760.8 1989.9 2025.2 TRUE FALSE FALSE 1576.547338 1647.876793 1743.424489 1900.801373 1268.673004 1378.318392 1698.907507 1811.74597 1811.91836 1972.585012 0.799229097 0.835389493 0.883827302 0.963609356 0.643152511 0.698737131 0.861259462 0.918462808 0.918550201 1 10.94587176 -12.43006673 0.645483055 1.032832641 0.818724458 0.221592517 0.094396133 1.117876911 0.627547457 0.142755311 0.020561891 3.71E-13 12.43006673 -0.214108183 IAASSS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 2 IAASSSFR 8 0 Q99961-3;Q99961-2;Q99961 Q99961-3 SH3GL1 Endophilin-A2 1 0 IAAS(0.012)S(0.075)S(0.914)FR;IAASS(0.012)S(0.988)FR ; 123.11 0.020664 289867000 9699.5 11642.8 10400.5 6497.7 10184.4 9544.2 6604.9 7618.8 9655.3 8368.3 TRUE FALSE FALSE 9581.278763 11806.70764 10581.51634 7248.994647 9664.652065 8934.356422 7165.920041 7839.237958 8791.705786 8150.89036 1.175488608 1.448517539 1.298203739 0.889350037 1.185717344 1.096120304 0.879157948 0.961764619 1.078619071 1 12.99274194 -7.819311404 6.233020222 1.120834154 0.92088366 0.25878772 0.148247299 0.224398928 17.50148759 0.022782224 0.071055367 1.52E-08 7.819311404 -0.199950494 IAAYGHEVGK ddPTM_HeLa_Romidepsin_16h_R1 1 IAAYGHEVGK 10 0 B8ZZA3;A0A087WYM2;A0A087X297;Q16719-2;Q16719 B8ZZA3 KYNU Kynureninase 0 0 81.525 0.026968 6557000 3443.4 3559 3610.8 2907.2 2718.4 2808.1 2380.8 2780.8 3891.4 3466.9 FALSE FALSE TRUE 3401.430516 3609.103695 3673.644459 3243.344143 2579.669904 2628.671473 2583.025093 2861.258061 3543.343438 3376.829438 1.007285259 1.068784717 1.087897546 0.960470229 0.763932544 0.778443662 0.764926136 0.847320871 1.049310752 1 11.7214536 -8.856185581 4.388755378 1.015476253 0.786211208 0.904028742 0.038541669 0.050032353 1.731689694 0.005856946 0.010970278 1.39E-09 8.856185581 -0.229265045 IAAYK(ac)SILQER ddPTM_HeLa_Romidepsin_16h_R1 1 IAAYKSILQER 11 1 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 1 IAAYK(1)SILQER 128.81 2.79E-07 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 IACDEEFS(ph)DS(ph)EDEGEGGRR ddPTM_HeLa_Romidepsin_16h_R1 1 IACDEEFSDSEDEGEGGRR 19 1 Q92769;Q92769-3 Q92769 HDAC2 Histone deacetylase 2 2 0 IACDEEFS(1)DS(1)EDEGEGGRR 53.359 0.021543 31337000 2097.7 1973.6 2035.7 1617.6 2235.1 2474.3 1796.4 2116.7 1992.1 1885.8 TRUE FALSE FALSE 2072.132426 2001.384393 2071.130505 1804.634523 2121.034507 2316.200215 1948.986171 2177.943375 1813.921587 1836.806644 1.128116796 1.089599931 1.127571327 0.982484754 1.154740219 1.260992943 1.061073128 1.185722723 0.987540846 1 10.84298405 -16.52287875 0.172338688 0.490447037 1.157951636 0.390712534 0.067979242 50.79055577 0.568194426 8.721396831 0.105929783 3.00E-17 16.52287875 0.667504599 IACKS(ph)PPPESVDTPTSTK ddPTM_HeLa_Romidepsin_16h_R1 2 IACKSPPPESVDTPTSTK 18 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 IACKS(0.747)PPPES(0.251)VDT(0.002)PTSTK;IACKS(1)PPPESVDTPTSTK ; 103.04 0.00017905 9921800 3014.8 2573.6 2944.7 423.37 1563.28 1459.15 2071.1 2068.86 3257.5 3109.9 TRUE FALSE FALSE 2978.054458 2609.831208 2995.951268 472.3220314 1483.499988 1365.915024 2247.019182 2128.7192 2966.141041 3029.10435 0.983146869 0.861585111 0.989055154 0.15592795 0.489748723 0.45093033 0.741809764 0.702755321 0.979213886 1 11.56467556 -9.296871142 24.43174813 0.979776187 0.517000278 0.686356575 0.153297523 193.0712467 133130.5411 0.023775497 0.036318672 5.05E-10 9.296871142 -0.462775909 IAEK(ac)GSTIETEQK ddPTM_HeLa_Romidepsin_16h_R1 1 IAEKGSTIETEQK 13 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6 ENAH Protein enabled homolog 0 1 IAEK(1)GSTIETEQK 145.71 0.00010574 616440 490.22 279.8 301.66 0 352.28 499.48 522.26 549.26 403.01 636.64 FALSE TRUE FALSE 484.2450101 283.7390317 306.9102658 0 334.3018371 467.56484 566.6207514 565.1519715 366.9637762 620.100001 0.780914384 0.457569797 0.494936728 0 0.539109557 0.754015222 0.913757056 0.911388438 0.591781609 1 9.276357082 -10.75560342 1.542918891 0.933801208 0.577019658 0.047535497 0.273836769 0.366471114 1.816585324 0.059748625 0.057676722 1.76E-11 10.75560342 -0.35678155 IAELEEEQSQGSTTNS(ph)DWMK ddPTM_HeLa_Romidepsin_16h_R1 1 IAELEEEQSQGSTTNSDWMK 20 0 P46821;D6RA32;D6RA40 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 IAELEEEQSQGS(0.003)T(0.014)T(0.231)NS(0.752)DWMK 97.352 0.00027992 6721200 3351.5 3270.1 3096.3 2773.2 3195 3215.8 2831.5 2680.6 3394.9 3533.4 TRUE FALSE FALSE 3310.650629 3316.136554 3150.189803 3093.850432 3031.947228 3010.320759 3072.007539 2758.158932 3091.251641 3441.601759 0.961950528 0.963544531 0.915326648 0.898956547 0.880969804 0.874685966 0.892609824 0.801417225 0.898201436 1 11.74886445 -6.533993697 0.190052103 1.017629828 0.601168188 0.518952359 0.036780891 4.289879735 0.112881159 0.024735529 0.444276458 2.92E-07 6.533993697 -0.41646164 IAFAITAIK ddPTM_HeLa_Romidepsin_16h_R1 1 IAFAITAIK 9 0 P62269;A0A0G2JQH2;Q5GGW2 P62269 RPS18 40S ribosomal protein S18 0 0 124.98 0.013988 237950 226.83 153.91 335.57 0 331.78 356.83 437 198.31 210.15 0 FALSE FALSE TRUE 224.0653087 156.076749 341.4104551 0 314.8480286 334.0297146 474.1187691 204.047787 191.3536577 0 0 IALLEEAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 IALLEEAKK 9 1 A0A2R8Y7M3;A0A2R8Y5S7;P35241-4;P35241;P35241-5;P35241-2 A0A2R8Y7M3 RDX Radixin 0 1 IALLEEAK(1)K 96.331 0.0088892 0 0 0 0 0 147.93 125.22 127.73 0 0 0 FALSE TRUE FALSE 0 0 0 0 140.3805801 117.2188461 138.579383 0 0 0 0 IALLEEENSRPHTNET(ph)SL ddPTM_HeLa_Romidepsin_16h_R1 1 IALLEEENSRPHTNETSL 18 1 D6REY2;P23508;P23508-2 D6REY2 MCC Colorectal mutant cancer protein 1 0 IALLEEENSRPHT(0.003)NET(0.585)S(0.412)L 176.04 5.44E-08 5141500 2000.7 1938.5 2011.9 1888.1 2002.3 1592.3 1641 1677.9 2159.1 1628.1 TRUE FALSE FALSE 1976.314699 1965.790254 2046.916276 2106.411006 1900.115159 1490.557169 1780.386499 1726.447389 1965.984688 1585.801727 1.246255862 1.239619191 1.290776924 1.328294054 1.198204748 0.939939176 1.122704351 1.088690572 1.2397418 1 10.63099669 -12.38860723 1.136329893 1.000944111 1.187573341 0 0.128495059 0.539138879 1.254770254 0.078266207 0.020460247 4.09E-13 12.38860723 0.18662923 IANLQTDLSDGLR ddPTM_HeLa_Romidepsin_16h_R1 1 IANLQTDLSDGLR 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 120.96 6.38E-07 0 71.178 0 147.3 0 0 75.873 62.792 128.8 255.85 149.38 FALSE FALSE TRUE 70.31045516 0 149.8636947 0 0 71.02496017 68.12555091 132.5266248 232.9661352 145.4990861 0.483236404 0 1.029997499 0 0 0.488147122 0.468219786 0.91084163 1.60115188 1 7.184866281 -11.82105756 0.736802401 0.997740203 0.402916738 0.389788998 0.395802498 0.6417907 0.661982435 0.207801665 0.072351641 1.51E-12 11.82105756 -0.594823465 IAQLEEELEEEQGNTELINDR ddPTM_HeLa_Romidepsin_16h_R1 2 IAQLEEELEEEQGNTELINDR 21 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ; ; 186.6 1.36E-14 30048000 5178.1 5013.8 5056.4 5175.5 5085.3 5891.9 4796 4791.5 5225.1 5357.7 FALSE FALSE TRUE 5114.987326 5084.384408 5144.404521 5773.915661 4825.778165 5515.426605 5203.37212 4930.134493 4757.753969 5218.506182 0.980163125 0.974298819 0.985800216 1.106430741 0.924743211 1.05689759 0.997099925 0.944740568 0.911708026 1 12.34942117 IAQLEEQLDNETK ddPTM_HeLa_Romidepsin_16h_R1 1 IAQLEEQLDNETK 13 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 190.85 1.29E-09 0 770.48 907.24 1042.7 862.61 815.17 844.25 765.17 935.8 913.72 770.72 FALSE FALSE TRUE 761.0890934 920.0121485 1060.847756 962.3490269 773.5688331 790.3051497 830.1635207 962.8758966 831.9945947 750.6965833 1.013843822 1.225544606 1.413151171 1.281941397 1.030468035 1.052762417 1.105857598 1.282643238 1.108296765 1 9.552086107 -10.26921878 22.9825103 1.006537343 1.194664849 0.27423071 0.113790137 159.6027194 471509.9199 0.020232529 0.02338811 5.38E-11 10.26921878 0.188127506 IAQLEEQLDNETKER ddPTM_HeLa_Romidepsin_16h_R1 2 IAQLEEQLDNETKER 15 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ; ; 230.57 1.27E-35 11489500 3596.7 3480.6 2890.3 5142 4013 3658.9 3370.6 3775.7 3860.6 3179.7 FALSE FALSE TRUE 3552.862037 3529.599978 2940.604459 5736.542234 3808.201635 3425.108099 3656.89868 3884.943922 3515.298267 3097.090936 1.147161033 1.139650095 0.949473077 1.852235647 1.229606012 1.105911376 1.180752763 1.254384842 1.135032306 1 11.59669803 -10.46342131 0.738027745 1.035541003 1.271179467 0.115209262 0.22097552 0.809170577 0.938646796 0.061617939 0.064209009 3.44E-11 10.46342131 0.235638464 SVGDDEELQQNESGT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 SVGDDEELQQNESGTSPK 18 0 F5H212;P15822 F5H212 HIVEP1 Zinc finger protein 40 1 0 SVGDDEELQQNESGT(0.987)S(0.013)PK;SVGDDEELQQNES(0.073)GT(0.838)S(0.09)PK ; 235.79 6.46E-49 10846600 5995.3 6134.4 6080.6 4589.2 3418.8 3313.2 2541.47 2771.8 6869.5 6591.2 TRUE FALSE FALSE 5922.226978 6220.760244 6186.430292 5119.824897 3244.325879 3101.497213 2757.342398 2851.99766 6255.074715 6419.959674 0.922471056 0.968971857 0.963624478 0.797485523 0.505349884 0.483102289 0.429495283 0.444239186 0.974316823 1 12.64834852 -8.861692253 2.129012792 0.963682785 0.448415185 0.990480272 0.023206112 0.027568198 0.253963903 0.004981512 0.010313515 1.38E-09 8.861692253 -0.5152676 down IAS(ph)DEEIQGTK ddPTM_HeLa_Romidepsin_16h_R1 4 IASDEEIQGTK 11 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 IAS(1)DEEIQGTK;IAS(1)DEEIQGTK;IAS(0.999)DEEIQGT(0.001)K;IAS(1)DEEIQGTK ;;; 196.7 2.84E-09 919320000 13811.7 11980.7 11905.5 12143.4 18919.6 21402.3 20127.8 22554.5 12704.3 12129.5 TRUE FALSE FALSE 13643.35769 12149.36461 12112.71023 13547.47704 17954.06221 20034.7621 21837.45483 23207.07887 11567.99559 11814.37384 1.154810054 1.028354509 1.025251985 1.146694461 1.519679541 1.695795509 1.848380212 1.964308831 0.97914589 1 13.52825555 -8.449546951 1.324710888 1.063589006 1.915107364 0.969280057 0.063693926 0.062157076 0.20673998 0.011418044 0.039062087 3.55E-09 8.449546951 0.851518358 IAS(ph)DEEIQGTKDAVIQDLER ddPTM_HeLa_Romidepsin_16h_R1 2 IASDEEIQGTKDAVIQDLER 20 1 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 IAS(1)DEEIQGTKDAVIQDLER;IAS(0.711)DEEIQGT(0.289)KDAVIQDLER ; 90.978 0.00058201 26592100 1506.9 1119.66 970.56 2327.16 1784.48 1778.23 1707.24 2530.84 1287.6 1324.28 TRUE FALSE FALSE 1488.533323 1135.422603 987.4521897 2596.237189 1693.411327 1664.606842 1852.252923 2604.065862 1172.433831 1289.875015 1.154013611 0.880257847 0.765540985 2.012781982 1.312849158 1.290517936 1.435994109 2.018851309 0.908951501 1 10.33301556 -9.273101222 24.99931767 1.036134079 1.569574718 0.609692206 0.262450288 457.2449667 980187.47 0.039473784 0.060604637 5.33E-10 9.273101222 0.53344064 IAS(ph)S(ph)VHQRVRVHSNDS(ph)YK ddPTM_HeLa_Romidepsin_16h_R1 1 IASSVHQRVRVHSNDSYK 18 2 Q96FK6 Q96FK6 WDR89 WD repeat-containing protein 89 3 0 IAS(1)S(1)VHQRVRVHS(0.118)NDS(0.525)Y(0.356)K 69.331 0.017535 15586000 1278.4 1217.2 1397.3 294.2 1600.7 1929.2 1225.7 1284.5 1356.6 1393.8 TRUE FALSE FALSE 1262.818369 1234.335774 1421.61942 328.2167883 1519.010306 1805.930346 1329.810927 1321.664981 1235.262298 1357.588875 0.930192043 0.909211762 1.047164901 0.241764495 1.11890303 1.330248339 0.979538763 0.973538459 0.90989424 1 10.40683093 IASDEEIQGT(ph)KDAVIQDLER ddPTM_HeLa_Romidepsin_16h_R1 1 IASDEEIQGTKDAVIQDLER 20 1 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 IAS(0.05)DEEIQGT(0.95)KDAVIQDLER 61.757 0.011766 24570000 1559.9 1373.7 894.73 2268.1 1883.6 1814.4 1740.1 2859 1536.4 1326.6 TRUE FALSE FALSE 1540.887339 1393.038985 910.3024003 2530.348394 1787.472863 1698.465696 1887.904051 2941.720654 1398.980536 1292.134741 1.192512894 1.078091116 0.704494951 1.958269764 1.383348661 1.314464848 1.461073672 2.276636144 1.08268936 1 10.3355408 -4 0.383853727 1.070561203 16.19128903 0.543965251 0.298396478 34.21364662 0.413339491 0.074494285 390.6663911 1.00E-04 4 15.12072783 IASEASFSSSEGS(ph)PLSR ddPTM_HeLa_Romidepsin_16h_R1 2 IASEASFSSSEGSPLSR 17 0 A0A087WX12;A0A087X032;A0A087WTH3;A0A087X251;A0A087X0T6;Q2M2Z5-5;Q2M2Z5-2;Q2M2Z5-3;Q2M2Z5-4;Q2M2Z5 A0A087WX12 KIZ Centrosomal protein kizuna 1 0 IASEASFSSS(0.001)EGS(0.999)PLSR;IASEASFSSSEGS(0.995)PLS(0.004)R ; 301.75 3.55E-138 23857000 2919.7 3165.9 2774.6 3075.6 3499.3 3143.9 2532.3 3047 2996.6 2981.1 TRUE FALSE FALSE 2884.113573 3210.469623 2822.890749 3431.215343 3320.717663 2943.014936 2747.393499 3135.160138 2728.576591 2903.650592 0.993271567 1.10566665 0.97218679 1.181690164 1.14363542 1.013556846 0.946185986 1.079730511 0.939705555 1 11.50365214 -10.28946733 23.57046594 0.996822675 1.060969705 0.220493892 0.070956039 492.5044041 414176.4611 0.011900539 0.013610808 5.13E-11 10.28946733 0.064147031 IASLEVENQSLR ddPTM_HeLa_Romidepsin_16h_R1 1 IASLEVENQSLR 12 0 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;E9PL12;E9PPR1;E9PMW7;H0YCK7;E9PIZ1;E9PN91 P29692-2 EEF1D Elongation factor 1-delta 0 0 160.91 0.0074151 8693800 1595.3 1381.4 1326.6 1180.3 1671.7 1445.1 1288 1448.8 1410.8 1308.2 FALSE FALSE TRUE 1575.85587 1400.847385 1349.688917 1316.771839 1586.386911 1352.762774 1397.402688 1490.718742 1284.614515 1274.212775 1.236728983 1.099382625 1.059233546 1.03340028 1.244993726 1.061645904 1.096679232 1.169913511 1.008163267 1 10.31539049 -12.65678261 1.513372339 1.000317543 1.138128952 0.31346442 0.069624645 0.394579171 1.631664406 0.053870636 0.012253403 2.20E-13 12.65678261 0.137811408 IDAAEGPSDIPD ddPTM_HeLa_Romidepsin_16h_R1 1 IDAAEGPSDIPD 12 0 P42771-2;P42771 P42771-2 CDKN2A Cyclin-dependent kinase inhibitor 2A 0 0 134.26 0.029344 30294000 10410 10616 9659.3 9944.7 9415.1 8373.6 7243.1 7528.4 11335 9702.8 FALSE FALSE TRUE 10283.11892 10765.45233 9827.416065 11094.55301 8934.612314 7838.553985 7858.328733 7746.222376 10321.16921 9450.719857 1.088077847 1.139114532 1.039858996 1.173937348 0.945389605 0.829413431 0.831505838 0.819643635 1.092104027 1 13.20620851 -8.478925841 3.933863165 1.059119973 0.830448537 0.834942201 0.051433222 0.080785547 2.612302909 0.008458068 0.019159233 3.32E-09 8.478925841 -0.228671435 SNS(ph)FIGVPNGEVEMPLK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSFIGVPNGEVEMPLK 17 0 Q9H7E2-3;Q9H7E2-2;Q9H7E2 Q9H7E2-3 TDRD3 Tudor domain-containing protein 3 1 0 S(0.062)NS(0.938)FIGVPNGEVEMPLK 77.13 0.030003 4221100 3618.6 3644.1 2957.7 2600.8 1752.8 1661.4 1139.5 1532.7 3341.7 3407.3 TRUE FALSE FALSE 3574.495111 3695.401735 3009.177528 2901.516733 1663.348075 1555.241902 1236.289102 1577.046256 3042.809983 3318.777855 1.077051634 1.113482703 0.906712549 0.874272657 0.501192954 0.468618862 0.372513364 0.475188857 0.916846537 1 11.69643635 -8.861148243 1.625091523 1.039772945 0.420538468 0.936780275 0.067667488 0.048432218 0.25812421 0.008860792 0.019814908 1.38E-09 8.861148243 -0.619234477 down TSST(ph)NEDEDLNPEQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSTNEDEDLNPEQK 15 0 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 T(0.301)S(0.001)S(0.176)T(0.522)NEDEDLNPEQK 231.41 3.19E-38 0 3579.6 3925.9 3372.6 2515.9 1881.9 1476.9 994.69 1229.5 4364 4100.7 TRUE FALSE FALSE 3535.970458 3981.168923 3431.298688 2806.800196 1785.859621 1382.530856 1079.178944 1265.073643 3973.67291 3994.163223 0.885284417 0.996746678 0.859078234 0.702725462 0.447117336 0.346137796 0.270188994 0.316730582 0.994869936 1 11.96367757 -8.860049324 1.325263284 0.949825156 0.290655623 0.982224132 0.038691501 0.045399231 0.159222769 0.007646803 0.018644936 1.38E-09 8.860049324 -0.659169534 down IDASKNEEDEGHSNS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;D6RAF8;Q14103;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 0 IDASKNEEDEGHS(0.018)NS(0.491)S(0.491)PR;IDASKNEEDEGHS(0.209)NS(0.582)S(0.209)PR ; 61.139 0.014414 785540000 11489.03 11277.32 10879.36 11695.32 12658.44 13235.74 11957.96 12526.6 13881.34 12843 TRUE FALSE FALSE 11348.99728 11436.08241 11068.7107 13047.58793 12012.43257 12390.01893 12973.66882 12889.03741 12639.75818 12509.33701 0.907242108 0.914203718 0.884835918 1.043027933 0.960277316 0.990461678 1.037118819 1.030353359 1.010425906 1 13.61071771 -9.244809861 24.96592139 0.946401829 1.00953195 0.389956258 0.042940256 814.5351778 1222863.717 0.007290624 0.012069448 5.69E-10 9.244809861 0.063130121 IDASKNEEDEGHSNSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IDASKNEEDEGHSNSSPR 18 1 Q14103-3;D6RAF8;Q14103;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 0 IDASKNEEDEGHS(0.011)NS(0.237)S(0.753)PR;IDASKNEEDEGHS(0.001)NS(0.193)S(0.806)PR ; 186.98 1.41E-10 273926000 3091.34 3124 2647.25 2901 3665 4002.6 3161.7 3150.7 3815.9 3732.7 TRUE FALSE FALSE 3053.661559 3167.979754 2693.324276 3236.42727 3477.961374 3746.846778 3430.254719 3241.860534 3474.596347 3635.723916 0.839904687 0.871347723 0.740794499 0.890174101 0.956607667 1.030564164 0.943486029 0.891668512 0.955682122 1 11.82802694 -6.929309216 12.4590436 0.915191547 0.712976202 0.007105695 0.079554553 7230965.106 38827467.67 0.012797269 35940215.41 1.18E-07 6.929309216 -0.202215345 IDDRDS(ph)DEEGASDR ddPTM_HeLa_Romidepsin_16h_R1 2 IDDRDSDEEGASDR 14 1 Q8TDD1-2;Q8TDD1 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 0 IDDRDS(0.998)DEEGAS(0.002)DR;IDDRDS(0.997)DEEGAS(0.003)DR ; 80.459 0.012974 63371000 7786.7 8472.6 7803.2 7012.6 6790.3 6617.5 5469 6251.1 8405.6 8136 TRUE FALSE FALSE 7691.792705 8591.877485 7939.011423 7823.429807 6443.765653 6194.663107 5933.536723 6431.965716 7653.782084 7924.625547 0.970619073 1.084199807 1.001815338 0.987230218 0.813131878 0.781697895 0.748746636 0.811642857 0.965822554 1 12.95212705 -8.725985633 3.836665883 0.996051202 0.780227465 0.905213667 0.033828507 0.048822934 1.519708297 0.005117424 0.010331841 1.88E-09 8.725985633 -0.215823736 IDEDGENTQIEDTEPMS(ph)PVLNSK ddPTM_HeLa_Romidepsin_16h_R1 4 IDEDGENTQIEDTEPMSPVLNSK 23 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 IDEDGENTQIEDT(0.001)EPMS(0.999)PVLNS(0.001)K;IDEDGENTQIEDT(0.151)EPMS(0.814)PVLNS(0.035)K;IDEDGENTQIEDTEPMS(0.993)PVLNS(0.007)K;IDEDGENTQIEDTEPMS(0.98)PVLNS(0.02)K ;;; 142.93 4.03E-07 532153700 15982.2 14856.6 13663.45 12512.96 15624.56 15507.5 12600.12 15586.11 16567.49 16799.07 TRUE FALSE FALSE 15787.4028 15065.7516 13901.25662 13959.76731 14827.1804 14516.6208 13670.37388 16037.0695 15085.6522 16362.62774 0.964845198 0.920741573 0.849573604 0.853149478 0.906161323 0.887181511 0.835463233 0.980103548 0.921957796 1 13.99811683 -10.23758123 2.051673638 0.985858791 0.882648553 0.351072382 0.043543933 0.154938847 1.236892315 0.006705826 0.008021771 5.79E-11 10.23758123 -0.103210237 IDEPLEGSEDR ddPTM_HeLa_Romidepsin_16h_R1 4 IDEPLEGSEDR 11 0 P61978-3;P61978;P61978-2;S4R359 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 ;;; ;;; 233.09 9.79E-36 341935000 11372.83 11485.87 10711.54 9381.2 11751.73 11271.87 9015.77 9614.47 11920.99 10443.87 FALSE FALSE TRUE 11234.21357 11647.56838 10897.96986 10465.89848 11151.99537 10551.63389 9781.569279 9892.64952 10854.7468 10172.53675 1.104366968 1.145001356 1.071312901 1.028838601 1.096284598 1.037266725 0.961566374 0.972485995 1.067063906 1 13.31239187 -7.850127261 4.164789237 1.060713219 0.966543684 0.519121013 0.039094207 0.175990149 5.591232922 0.007192873 0.024170257 1.41E-08 7.850127261 -0.094169535 IDFDSVSSIMAS(ph)SQ ddPTM_HeLa_Romidepsin_16h_R1 2 IDFDSVSSIMASSQ 14 0 A0A087WVB9;K7ERF1;Q9UBQ5;K7EK53 A0A087WVB9 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 0 IDFDSVSSIMAS(0.5)S(0.5)Q;IDFDSVSSIMAS(0.5)S(0.5)Q ; 144.51 0.00085235 8107200 3430 3416.3 3382 3380.6 3033.3 2410.7 2291.3 2518.2 3593.2 3319.7 TRUE FALSE FALSE 3388.193841 3464.394761 3440.862291 3771.480878 2878.499382 2256.66405 2485.922965 2591.060144 3271.815193 3233.453715 1.047855989 1.071422406 1.064144594 1.166393958 0.890224396 0.697911351 0.76881353 0.801328973 1.011863933 1 11.65886024 -8.530181924 5.702599445 1.039662742 0.761678498 0.877812539 0.050957531 0.04332312 4.980837278 0.007882057 0.016566653 2.95E-09 8.530181924 -0.277984244 IDFDSVSSIMASS(ph)Q ddPTM_HeLa_Romidepsin_16h_R1 2 IDFDSVSSIMASSQ 14 0 A0A087WVB9;K7ERF1;Q9UBQ5;K7EK53 A0A087WVB9 EIF3K Eukaryotic translation initiation factor 3 subunit K 1 0 IDFDSVSSIMAS(0.101)S(0.899)Q;IDFDSVSSIMAS(0.401)S(0.599)Q ; 155.39 0.00077753 8935600 5025.3 4403.2 4593.8 5051.5 4473.7 3630.7 3488.7 3782.7 5119.5 5023.8 TRUE FALSE FALSE 4964.049711 4465.188365 4673.753162 5635.578198 4245.390395 3398.709988 3785.030091 3892.146456 4661.599098 4893.280952 1.014462435 0.912514202 0.955136892 1.151697246 0.86759588 0.694566697 0.773515792 0.795406292 0.952653065 1 12.2565864 -8.533250569 9.913188563 1.004153849 0.760400081 0.745218018 0.064092785 0.065046982 55.43936041 0.008570401 0.017418519 2.93E-09 8.533250569 -0.243753768 IDFSSIAVPGTSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IDFSSIAVPGTSSPR 15 0 Q5TDH0-2;Q5TDH0;Q5TDH0-3 Q5TDH0-2 DDI2 Protein DDI1 homolog 2 1 0 IDFSSIAVPGTS(0.026)S(0.974)PR;IDFSSIAVPGT(0.002)S(0.01)S(0.989)PR ; 225.31 9.98E-35 370560000 9115.7 8641.7 8370.5 8648.8 10324.6 11025.7 10428.1 10770.2 9367.2 7754.6 TRUE FALSE FALSE 9004.594342 8763.358079 8516.185041 9648.81495 9797.697136 10321.19335 11313.86255 11081.81874 8529.374171 7553.134374 1.192166576 1.160228012 1.127503447 1.2774584 1.297169711 1.366478185 1.497902989 1.467181463 1.129249627 1 12.88285974 -4 0.1522558 0.959868628 3.054696249 0.876770652 0.053079817 13.64033622 0.133631298 0.106330149 6.360564725 1.00E-04 4 2.094827622 IDFTPVSPAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 IDFTPVSPAPSPTR 14 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 IDFTPVSPAPS(0.707)PT(0.293)R;IDFTPVSPAPS(0.837)PT(0.163)R ; 144.88 0.0006184 12165700 1599.55 1351.51 1558.18 1600.69 2697.2 3053.4 2388.54 2905.3 1703.42 1592.03 TRUE FALSE FALSE 1580.054069 1370.536593 1585.299469 1785.769309 2559.551819 2858.297594 2591.422528 2989.360272 1551.061849 1550.668831 1.018950041 0.883835778 1.022332711 1.151612307 1.650611509 1.843267587 1.671164388 1.927787682 1.000253451 1 10.59867489 -8.765940285 2.469651974 0.999322077 1.801307668 0.966268245 0.070613527 0.032654469 0.406718893 0.009912077 0.020844294 1.71E-09 8.765940285 0.80198559 IDFYFDENPYFENK ddPTM_HeLa_Romidepsin_16h_R1 2 IDFYFDENPYFENK 14 0 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105-2 Q01105;Q01105-2 SET;SETSIP Protein SET;Protein SETSIP 0 0 ; ; 218.94 1.11E-23 150016000 7268.1 7406.7 7161 6806.2 7534.3 7186.4 6658.4 7021.8 7802.8 7573.9 FALSE FALSE TRUE 7179.513602 7510.971717 7285.634201 7593.164868 7149.796557 6727.212233 7223.96433 7224.964704 7104.898026 7377.128986 0.973212427 1.018142929 0.987597508 1.029284547 0.96918416 0.911901127 0.979237905 0.979373509 0.96309798 1 12.84884375 -8.532799752 24.99734306 0.992542157 0.955988398 0.324895879 0.02521341 178.7270357 450327.009 0.003485054 0.006975841 2.93E-09 8.532799752 -0.036553759 IDGATQS(ph)SPAEPKSEDADR ddPTM_HeLa_Romidepsin_16h_R1 1 IDGATQSSPAEPKSEDADR 19 1 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 IDGAT(0.011)QS(0.851)S(0.133)PAEPKS(0.005)EDADR 91.307 0.02389 7412400 1143.3 1303.9 921.68 3920.2 1237.1 1456.2 1254.1 1326.4 1454.7 1093 TRUE FALSE FALSE 1129.36502 1322.256338 937.7214538 4373.471969 1173.966171 1363.15352 1360.623223 1364.777291 1324.587989 1064.603702 1.060831385 1.242017415 0.880817389 4.108075107 1.102725989 1.280432819 1.278056069 1.281958055 1.244207573 1 10.05610077 IDGATQSS(ph)PAEPK ddPTM_HeLa_Romidepsin_16h_R1 5 IDGATQSSPAEPK 13 0 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 IDGAT(0.001)QS(0.079)S(0.92)PAEPK;IDGAT(0.001)QS(0.214)S(0.786)PAEPK;IDGATQS(0.205)S(0.795)PAEPK;IDGATQS(0.08)S(0.919)PAEPK;IDGAT(0.02)QS(0.328)S(0.652)PAEPK ;;;; 205.26 1.54E-16 522155400 21744 21136.8 20051.9 16943.8 21758.5 21975.7 20261 21630.4 22173.2 20628.3 TRUE FALSE FALSE 21478.97576 21434.36443 20400.89491 18902.92188 20648.08255 20571.52369 21981.96883 22256.2415 20189.97346 20092.37379 1.069011357 1.066791045 1.015355135 0.940800827 1.027657696 1.023847352 1.094045386 1.107695971 1.004857548 1 14.2943604 -7.72375278 5.041179935 1.027004065 1.103506577 0.458147623 0.034924162 0.158071064 9.370446573 0.005662982 0.02155859 1.89E-08 7.72375278 0.076502512 IDGATQSS(ph)PAEPKSEDADR ddPTM_HeLa_Romidepsin_16h_R1 1 IDGATQSSPAEPKSEDADR 19 1 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 IDGATQS(0.004)S(0.996)PAEPKSEDADR 211.45 3.81E-28 6121800 1592.2 1381.1 1038 4403.4 1393 1541.7 1336.4 1486 1622.2 1381.6 TRUE FALSE FALSE 1572.793654 1400.543162 1056.065955 4912.541827 1321.910012 1443.190346 1449.913783 1528.995065 1477.106369 1345.705833 1.168749972 1.040749864 0.784767316 3.650531719 0.98231722 1.072441176 1.077437392 1.136203045 1.097644324 1 10.39414736 IDIFPAKQENGDLS(ph)PFSGTSLR ddPTM_HeLa_Romidepsin_16h_R1 1 IDIFPAKQENGDLSPFSGTSLR 22 1 P19174-2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 0 IDIFPAKQENGDLS(0.422)PFS(0.086)GT(0.246)S(0.246)LR 60.388 0.0050234 20346000 1334.4 1488.8 1099 1930.3 1280.4 1524.9 1003 1495.4 1516.9 1550.7 TRUE FALSE FALSE 1318.13582 1509.759365 1118.127634 2153.490368 1215.05641 1427.463811 1088.194795 1538.66704 1381.224665 1510.41259 0.872699174 0.999567519 0.740279604 1.425762988 0.804453312 0.945082039 0.720461947 1.018706444 0.914468453 1 10.56072698 IDILDSALLRPGR ddPTM_HeLa_Romidepsin_16h_R1 2 IDILDSALLRPGR 13 1 P62195-2;P62195 P62195-2 PSMC5 26S protease regulatory subunit 8 0 0 ; ; 154.67 0.00085284 11702300 5787 5317.9 5368.7 6378.6 6044.7 5031.3 4721.1 5574 5729.3 4678.6 FALSE FALSE TRUE 5716.465818 5392.765536 5462.139971 7116.123744 5736.216403 4709.816168 5122.110116 5735.274896 5216.857059 4557.049298 1.254422642 1.183389773 1.198613316 1.561563916 1.258756715 1.033523199 1.123997083 1.25855011 1.144788375 1 12.15388426 -12.2181863 0.78860724 0.988023817 1.2346378 0.153716771 0.135626502 0.755472282 0.781705486 0.117475797 0.027211177 6.05E-13 12.2181863 0.246613983 IDIS(ph)PSTFR ddPTM_HeLa_Romidepsin_16h_R1 3 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 IDIS(1)PSTFR;IDIS(0.636)PS(0.363)T(0.001)FR;IDIS(0.691)PS(0.309)TFR ;; 155.53 0.004503 2151510000 7552.6 7921 8548.9 7906.2 8862.1 8920.5 8049.3 8866 8440.3 8163.6 TRUE FALSE FALSE 7460.546006 8032.512046 8697.690018 8820.352044 8409.833968 8350.50884 8733.007341 9122.523722 7685.378429 7951.508495 0.938255428 1.010187193 1.093841505 1.109267763 1.057640066 1.050179201 1.098283093 1.147269569 0.966530871 1 12.95701287 -9.886471684 3.679686862 0.97090532 1.090339164 0.793097474 0.029034274 0.089059221 2.324272913 0.005653461 0.007554112 1.30E-10 9.886471684 0.119433844 IDIS(ph)PSTLR ddPTM_HeLa_Romidepsin_16h_R1 3 IDISPSTLR 9 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 IDIS(0.926)PS(0.064)T(0.01)LR;IDIS(0.924)PS(0.075)T(0.001)LR;IDIS(0.907)PS(0.086)T(0.007)LR ;; 133.75 0.0069603 3837740000 8703.9 7845.4 8262.1 7333.5 8182.2 8280.4 7338.5 7885.9 7949.5 8430.2 TRUE FALSE FALSE 8597.813519 7955.847747 8405.898385 8181.433775 7764.631802 7751.309164 7961.832007 8114.066075 7238.47681 8211.182189 1.047085952 0.968904058 1.02371354 0.996377085 0.945616797 0.943994298 0.969632852 0.9881727 0.881538936 1 13.00337423 -8.956491034 4.283385498 1.017863706 0.961364387 0 0.048532061 0.130788372 5.255157241 0.003878146 0.007104916 1.11E-09 8.956491034 -0.056499319 IDISPS(ph)TFR ddPTM_HeLa_Romidepsin_16h_R1 1 IDISPSTFR 9 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 IDIS(0.281)PS(0.719)TFR 143.4 0.0061494 1837600000 4328.7 4066 3895.8 3390.2 3880.8 4214.8 3666.4 4381.5 4732.3 4104.4 TRUE FALSE FALSE 4275.940139 4123.241255 3963.604765 3782.190875 3682.748295 3945.487883 3977.823924 4508.27179 4309.031236 3997.767096 1.069582103 1.03138606 0.991454647 0.946075843 0.921201312 0.986922897 0.995011422 1.127697457 1.077859498 1 11.96497871 -9.759921811 6.170419711 1.033740801 0.98868672 0.149817785 0.054871805 0.253086789 37.49012713 0.009103043 0.012474282 1.74E-10 9.759921811 -0.045054081 IDLS(ph)PESSDR ddPTM_HeLa_Romidepsin_16h_R1 2 IDLSPESSDR 10 0 O15062 O15062 ZBTB5 Zinc finger and BTB domain-containing protein 5 1 0 IDLS(1)PESSDR;IDLS(0.997)PES(0.003)SDR ; 132.03 0.0065156 20816900 13148.7 13038.2 11979.6 9340.4 14093.3 15697.7 14193.7 15069.1 13887.9 13734 TRUE FALSE FALSE 12988.43859 13221.75212 12188.09991 10420.381 13374.06631 14694.66763 15399.31252 15505.10063 12645.73144 13377.1887 0.970939326 0.988380475 0.911110711 0.778966435 0.999766589 1.098486981 1.151162092 1.159070189 0.945320555 1 13.70748734 -8.192945988 3.047804154 0.964623246 1.149031863 0.659115129 0.063578007 0.146436664 2.660982192 0.010078699 0.028498458 6.41E-09 8.192945988 0.184408617 IDNSQVESGSLEDDWDFLPPKK ddPTM_HeLa_Romidepsin_16h_R1 2 IDNSQVESGSLEDDWDFLPPKK 22 1 P27797;K7EJB9 P27797 CALR Calreticulin 0 0 ; ; 123.99 5.05E-05 29281000 4528.4 4014.7 3841.6 4298.5 4474.1 5539.9 4938.1 5217.1 4963.2 4390.1 FALSE FALSE TRUE 4473.206119 4071.219052 3908.461437 4795.512795 4245.769982 5185.918269 5357.542091 5368.048557 4519.278961 4276.044569 1.046108394 0.952099303 0.914036646 1.121483352 0.992919955 1.212783961 1.252920077 1.25537713 1.056883035 1 12.06206117 -8.192046668 4.030582921 1.014353091 1.249766365 0.788781102 0.054296725 0.074365796 2.365303882 0.007531366 0.020160996 6.43E-09 8.192046668 0.235413275 IDQLEGDHQLIQEALIFDNK ddPTM_HeLa_Romidepsin_16h_R1 2 IDQLEGDHQLIQEALIFDNK 20 0 P12814-2;P12814;P12814-3;P12814-4;H9KV75;H7C5W8;H0YJ11;H0YJW3 P12814-2 ACTN1 Alpha-actinin-1 0 0 ; ; 70.615 0.0041759 16481700 4202.7 3849 4723.5 3776.5 4881.1 5228.5 3369.5 4512.2 4500.7 4657 FALSE FALSE TRUE 4151.475876 3903.186323 4805.710536 4213.156699 4631.999253 4894.415724 3655.705246 4642.753388 4098.14612 4536.010469 0.915226255 0.860488826 1.05945755 0.928824289 1.0211615 1.079013322 0.805929632 1.023532335 0.903469282 1 12.14720825 -9.745626099 24.99245311 0.951388458 0.981303807 0.08843881 0.081711098 836.7805586 1322507.429 0.012699608 0.017924798 1.80E-10 9.745626099 0.029915349 IDRPEAISEER ddPTM_HeLa_Romidepsin_16h_R1 2 IDRPEAISEER 11 1 D6RD69;Q9Y6B6;D6R9R5;Q9H029 D6RD69 SAR1B;DKFZp434B2017 GTP-binding protein SAR1b 0 0 ; ; 112.64 0.015219 13306200 5180.9 4318 4398.7 4157.8 5341.3 5283.1 4945.3 5634.1 5203.3 5042.1 FALSE FALSE TRUE 5117.753198 4378.788917 4475.257528 4638.544399 5068.71353 4945.52696 5365.353659 5797.113794 4737.903816 4911.105515 1.04207763 0.891609619 0.911252571 0.944501067 1.032092166 1.0070089 1.092494071 1.180409131 0.964732646 1 12.2618321 -7.447291032 1.644749598 0.996878604 1.211974084 0.621737503 0.050515953 0.440861552 1.490341576 0.008453693 0.133549005 3.57E-08 7.447291032 0.21509548 IDS(ph)LSAQLSQLQK ddPTM_HeLa_Romidepsin_16h_R1 1 IDSLSAQLSQLQK 13 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 IDS(1)LSAQLSQLQK 173.06 1.81E-05 0 1083.1 1114.1 1042.5 1019.2 1176.4 1347.9 1136.5 1431.1 980.98 965.6 TRUE FALSE FALSE 1069.898761 1129.784329 1060.644275 1137.044699 1116.363918 1261.77354 1233.034282 1472.506621 893.2386919 940.5135728 1.137568656 1.201241919 1.127728834 1.2089615 1.186972682 1.341579299 1.311022315 1.565641011 0.949735036 1 9.877304954 -4 0.218433875 1.015545994 3.580809887 0.877734843 0.0582982 11.14425308 0.132933655 0.039942844 10.14943404 1.00E-04 4 2.565263894 IDSFSVQS(ph)LDSR ddPTM_HeLa_Romidepsin_16h_R1 2 IDSFSVQSLDSR 12 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 IDSFSVQS(1)LDSR;IDSFSVQS(1)LDSR ; 161.87 0.00063006 14038800 3648.2 3507.5 3127.8 1582.61 3417.9 3597.7 2866.9 2849.3 3323.5 4028.3 TRUE FALSE FALSE 3603.734335 3556.878677 3182.238047 1765.598815 3243.471809 3367.818581 3110.414414 2931.74 3026.237836 3923.644185 0.918466141 0.906524269 0.811041444 0.449989533 0.826647794 0.858339447 0.792736106 0.747198232 0.771282434 1 11.9379785 -9.772695675 3.077114302 0.959092825 0.741420629 0.234936318 0.122177959 0.169722444 3.330099316 0.018033938 0.025099121 1.69E-10 9.772695675 -0.217672197 IDSVAAQPTATS(ph)PVVYTR ddPTM_HeLa_Romidepsin_16h_R1 1 IDSVAAQPTATSPVVYTR 18 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 IDSVAAQPTAT(0.024)S(0.976)PVVYTR 321.68 9.25E-187 8554800 3926.6 3175.5 3919.9 2757.9 4221.9 4852.6 4066.3 4156.7 3984 3717.7 TRUE FALSE FALSE 3878.741089 3220.204772 3988.124215 3076.781374 4006.440689 4542.534521 4411.691421 4276.967556 3627.661062 3621.113618 1.071145923 0.889285759 1.101352964 0.84967822 1.106411207 1.254457882 1.218324495 1.181119403 1.00180813 1 11.82221773 -8.52042158 24.98571529 1.01496611 1.211741599 0.6471456 0.075456841 47.62245971 484247.8002 0.010549898 0.021390295 3.02E-09 8.52042158 0.196775489 IDTIEIITDR ddPTM_HeLa_Romidepsin_16h_R1 2 IDTIEIITDR 10 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ; ; 200.56 2.38E-11 100253000 5280.3 5148.4 5543.8 3769.4 4945.2 5464 4721 4903.4 5954 5176.6 FALSE FALSE TRUE 5215.941673 5220.87931 5640.287513 4205.235764 4692.827991 5114.868034 5122.001622 5045.272143 5421.459328 5042.111186 1.034475735 1.035455014 1.118636084 0.834022815 0.930726796 1.014429838 1.01584464 1.000626911 1.075235973 1 12.29981222 -9.285128079 24.99672959 1.025415709 0.963775196 0.330746648 0.060468163 971.3520746 1024985.032 0.009322031 0.014244265 5.19E-10 9.285128079 -0.061640513 IDVDAPDIDIHGPDAK ddPTM_HeLa_Romidepsin_16h_R1 2 IDVDAPDIDIHGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 ; ; 88.73 0.0063163 17802700 6428.8 6313.9 6562.9 6606 6613.7 6523.1 5448 5973.3 7070.1 6537 FALSE FALSE TRUE 6350.443313 6402.78725 6677.124521 7369.816802 6276.17821 6106.294962 5910.752984 6146.128011 6437.732549 6367.167798 0.997373324 1.005594238 1.04868047 1.157471742 0.985709567 0.959028434 0.928317452 0.965284441 1.011082596 1 12.63643607 -8.355992238 4.270333225 1.015151103 0.948516716 0.341795001 0.048142118 0.248892815 7.953033233 0.007525518 0.017590569 4.41E-09 8.355992238 -0.066634386 IDVPQDLEDDLTATPLS(ph)HATVPQSPAR ddPTM_HeLa_Romidepsin_16h_R1 1 IDVPQDLEDDLTATPLSHATVPQSPAR 27 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 0 IDVPQDLEDDLTAT(0.003)PLS(0.787)HAT(0.074)VPQS(0.137)PAR 134.28 3.23E-16 0 784.77 714.29 668.97 580.91 951.36 1086.8 693.91 802.54 1000.5 1002 TRUE FALSE FALSE 775.2049214 724.3457934 680.6131422 648.0775475 902.8085492 1017.356987 752.8506981 825.7602287 911.0127742 975.9678956 0.794293465 0.742181988 0.69737247 0.664035723 0.925039188 1.042408251 0.771388794 0.846093639 0.933445432 1 9.930689881 -12.13892542 0.953522979 0.997145449 0.810660191 0.250076429 0.106136418 0.567674118 0.950447678 0.069630195 0.021394847 7.26E-13 12.13892542 -0.186485258 IDVPQDLEDDLTATPLSHATVPQS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 IDVPQDLEDDLTATPLSHATVPQSPAR 27 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 0 IDVPQDLEDDLT(0.001)AT(0.001)PLS(0.017)HAT(0.327)VPQS(0.654)PAR 67.351 0.00011954 2584200 539.77 642.05 759.4 544.21 793.44 804.25 736.45 792.07 973.15 805.29 TRUE FALSE FALSE 533.1910756 651.0887968 772.6170384 607.1341208 752.9477961 752.8610206 799.0040446 814.9872958 886.1090267 784.3684497 0.679771191 0.830080298 0.985017996 0.774041996 0.959941462 0.959830831 1.018659082 1.039036305 1.129710185 1 9.615387696 -8.286173723 1.254955767 0.84952935 1.035670047 0.037121399 0.126308584 0.576114138 1.634870322 0.019862568 0.084156231 5.17E-09 8.286173723 0.186140697 IDVTAPDVS(ph)IEEPEGK ddPTM_HeLa_Romidepsin_16h_R1 4 IDVTAPDVSIEEPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IDVTAPDVS(1)IEEPEGK;IDVT(0.162)APDVS(0.838)IEEPEGK;IDVT(0.004)APDVS(0.996)IEEPEGK;IDVTAPDVS(1)IEEPEGK ;;; 242.48 3.91E-58 30406800 16312.8 18453.2 14718.8 13278.7 11768.7 11297.7 9927.5 9248 18607.6 16517.1 TRUE FALSE FALSE 16113.97332 18712.98463 14974.97454 14814.04577 11168.09932 10575.81343 10770.7416 9515.576289 16943.28965 16087.98336 1.001615489 1.16316534 0.930817381 0.920814339 0.694188891 0.657373469 0.669489852 0.591471042 1.053164295 1 13.97369587 -8.823625354 1.812019634 1.011754481 0.637246872 0.903212149 0.058523672 0.07322743 0.488008059 0.00864348 0.019053377 1.50E-09 8.823625354 -0.374507609 IECEIK(ac)INHEGEVNR ddPTM_HeLa_Romidepsin_16h_R1 2 IECEIKINHEGEVNR 15 1 E9PC52;Q16576;Q16576-2;Q5JP01 E9PC52 RBBP7 Histone-binding protein RBBP7 0 1 ; IECEIK(1)INHEGEVNR;IECEIK(1)INHEGEVNR 139.64 6.32E-06 4077500 1889.27 1765.79 1837.35 140.801 2000.22 2026.91 1785.18 1981.46 1765.56 1794.93 FALSE TRUE FALSE 1866.242851 1790.648838 1869.328306 157.0810741 1898.14131 1897.396993 1936.813145 2038.790419 1607.643892 1748.29746 1.067463 1.024224355 1.069227834 0.089848025 1.085708441 1.085282703 1.107828152 1.166157628 0.919548263 1 10.77173495 IEDFLERR ddPTM_HeLa_Romidepsin_16h_R1 2 IEDFLERR 8 1 P46781;B5MCT8;C9JM19 P46781 RPS9 40S ribosomal protein S9 0 0 ; ; 134.48 0.0060572 20914700 13048 14051.3 9875.3 27270 12963 12321.2 12599.9 12352.8 14403.4 11098.9 FALSE FALSE TRUE 12888.96596 14249.11457 10047.17545 30423.08571 12301.44974 11533.91508 13670.13519 12710.20878 13115.12383 10810.54898 1.192258227 1.318075021 0.929386239 2.814203587 1.13791166 1.066912985 1.264518131 1.175722787 1.213178337 1 13.40015217 -10.38452273 1.193105582 1.06412082 1.415942546 0.055381282 0.498970953 0.831349916 2.320051289 0.103875441 0.11669389 4.13E-11 10.38452273 0.351821727 IEDS(ph)EPHIPLIDDTDAEDDAPTKR ddPTM_HeLa_Romidepsin_16h_R1 2 IEDSEPHIPLIDDTDAEDDAPTKR 24 1 E7ERY9;P20020-1;P20020-4;P20020-6;P20020;A0A0U1RQU3;H0YHH6 E7ERY9 ATP2B1 Calcium-transporting ATPase;Plasma membrane calcium-transporting ATPase 1 1 0 IEDS(1)EPHIPLIDDTDAEDDAPTKR;IEDS(1)EPHIPLIDDTDAEDDAPTKR ; 107.34 2.53E-06 9332100 2174.02 4461.6 2631.8 1892.84 2934.3 4569.3 1963.41 3954.5 3000.2 2780.5 TRUE FALSE FALSE 2147.522208 4524.410522 2677.605375 2111.699067 2784.551722 4277.336477 2130.181996 4068.917218 2731.854598 2708.262209 0.792952101 1.670595449 0.988680256 0.779724747 1.028169175 1.579365714 0.786549393 1.50240889 1.008711265 1 11.40315171 -4 0.233999758 0.911411465 3.260843474 0.056130951 0.314273366 76.20382835 0.932386225 0.199972681 69.69941997 1.00E-04 4 2.349432009 IEDSGENLETEPLESQDRELLDT(ph)SFEDLSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 IEDSGENLETEPLESQDRELLDTSFEDLSKPK 32 2 P78345 P78345 RPP38 Ribonuclease P protein subunit p38 1 0 IEDSGENLET(0.068)EPLES(0.15)QDRELLDT(0.678)S(0.068)FEDLS(0.036)KPK 55.153 0.00074171 12602000 427.88 429.75 592.69 424.53 439.8 505 426.31 273.03 594 548.27 TRUE FALSE FALSE 422.664834 435.8000318 603.0055208 473.6161561 417.3553649 472.7321298 462.5207608 280.9296923 540.8711523 534.0258664 0.791468842 0.816065399 1.129169126 0.886878681 0.781526497 0.885223281 0.866101794 0.526060084 1.012818267 1 9.060765813 -7.251018091 3.579678038 0.898880588 0.478526979 0.547154902 0.104293103 0.196088756 4.381138031 0.015444628 0.22317042 5.61E-08 7.251018091 -0.420353609 IEDVGS(ph)DEEDDSGK ddPTM_HeLa_Romidepsin_16h_R1 9 IEDVGSDEEDDSGK 14 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.771)DEEDDS(0.229)GK;IEDVGS(0.948)DEEDDS(0.052)GK;IEDVGS(0.999)DEEDDS(0.001)GK;IEDVGS(1)DEEDDSGK;IEDVGS(0.981)DEEDDS(0.019)GK;IEDVGS(1)DEEDDSGK;IEDVGS(0.997)DEEDDS(0.003)GK;IEDVGS(0.96)DEEDDS(0.04)GK;IEDVGS(1)DEEDDSGK ;;;;;;;; 230.69 6.71E-34 3526381500 22188.4 23533.51 22267.5 10823.37 19986.61 23020.5 17466.87 21245.2 22129.6 24690.5 TRUE FALSE FALSE 21917.95925 23864.81537 22655.0565 12074.81896 18966.61871 21549.56435 18950.5055 21859.89634 20150.27315 24049.03725 0.911386141 0.99233974 0.942035902 0.502091574 0.788664366 0.896067652 0.787994351 0.908971786 0.837882737 1 14.55369152 -9.484408845 24.99360305 0.959913053 0.778411136 0.326006478 0.112846497 415.3329384 269839.0648 0.016338638 0.024954292 3.28E-10 9.484408845 -0.181501918 IEDVGS(ph)DEEDDSGKDK ddPTM_HeLa_Romidepsin_16h_R1 11 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.98)DEEDDS(0.02)GKDK;IEDVGS(0.996)DEEDDS(0.004)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.991)DEEDDS(0.009)GKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK;IEDVGS(0.999)DEEDDS(0.001)GKDK;IEDVGS(1)DEEDDSGKDK ;;;;;;;;;; 284.74 6.49E-102 10671361400 45214.56 56418.41 44297.29 28846.58 43940.66 46818.18 38610.9 43501.46 48471.66 50378.12 TRUE FALSE FALSE 44663.46755 57212.66986 45068.26575 32181.95731 41698.20416 43826.6494 41890.50888 44760.10611 44136.23333 49069.28918 0.910212239 1.165956769 0.918461761 0.655847228 0.849782111 0.893158432 0.853701156 0.912181669 0.89946755 1 15.58253275 -9.515869004 24.9983324 0.975383549 0.83324812 0.38806195 0.09429591 280.6655958 1000918.035 0.014614278 0.021145511 3.05E-10 9.515869004 -0.142135429 IEDVGS(ph)DEEDDSGKDKK ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.994)DEEDDS(0.006)GKDKK 71.637 0.026807 162970000 5133.2 4878.8 5220 3388.1 4419.5 4701.8 4824.6 4511.3 5068.6 4786.6 TRUE FALSE FALSE 5070.634584 4947.483874 5310.85191 3779.848063 4193.956424 4401.370154 5234.401404 4641.827348 4615.251721 4662.243442 1.087595413 1.061180939 1.139119391 0.810735885 0.899557579 0.944045546 1.122721597 0.995620972 0.989920792 1 12.18680862 -9.28998604 24.99926218 1.050881797 0.960242677 0.266460656 0.083362698 882.0866672 772470.0674 0.013561609 0.020718249 5.13E-10 9.28998604 -0.09063912 IEDVGS(ph)DEEDDSGKDKKK ddPTM_HeLa_Romidepsin_16h_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 0 IEDVGS(0.995)DEEDDS(0.005)GKDKKK 64.83 0.017901 13895000 1816.6 1178.1 1307.2 1193.7 996.35 809.34 606.03 796.93 886.07 889.8 TRUE FALSE FALSE 1794.45858 1194.685323 1329.951268 1331.721211 945.5025416 757.625786 657.5061731 819.9879122 806.81768 866.6828677 2.070490427 1.378457296 1.534530469 1.536572673 1.090944077 0.874167258 0.758646787 0.946122212 0.930926075 1 9.759360376 -8.592089699 2.734194204 1.512273905 0.852737563 0.365466117 0.308825088 0.229240234 3.457560778 0.058638693 0.131711394 2.56E-09 8.592089699 -0.659536343 IEDVGSDEEDDS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVGSDEEDDSGK 14 0 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.083)DEEDDS(0.917)GK 181.67 2.48E-07 5575900 2581.1 2209.9 2667.9 960.81 2097.7 2033.2 1693.1 2432.3 2402.7 2922.9 TRUE FALSE FALSE 2549.64056 2241.01103 2714.33368 1071.903373 1990.646541 1903.285082 1836.911872 2502.674763 2187.796494 2846.962637 0.895565164 0.787158567 0.953413875 0.376507707 0.699217656 0.668531809 0.645218117 0.879068355 0.76846688 1 11.47520784 -9.926146973 1.14164698 0.959183408 0.668888311 0.237414397 0.151288731 0.292497316 0.752132703 0.025963321 0.036251845 1.19E-10 9.926146973 -0.290295098 IEDVGSDEEDDS(ph)GKDK ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.39)DEEDDS(0.61)GKDK 64.374 0.020332 4895900000 3234.2 3403 3438.4 2154 3561 3672.4 2969.6 3596.1 3648.2 3797.2 TRUE FALSE FALSE 3194.780326 3450.907523 3498.24391 2403.055615 3379.268882 3437.745492 3221.83775 3700.14748 3321.895855 3698.548197 0.863793077 0.933043816 0.945842456 0.649729431 0.913674421 0.929485114 0.871108764 1.000432408 0.898162111 1 11.85274336 -12.3410472 0.820599317 1.008284561 0.883487781 0.013640524 0.093756301 0.998311326 1.071753823 0.083178588 0.016863483 4.56E-13 12.3410472 -0.124796781 IEDVGSDEEDDS(ph)GKDKK ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 1 0 IEDVGS(0.005)DEEDDS(0.995)GKDKK 55.335 0.029335 5911800 1928.8 1921.7 1884.2 1968.1 2121.8 2606.2 2214.5 2285.1 2334.9 2611 TRUE FALSE FALSE 1905.291044 1948.753743 1916.993711 2195.660982 2013.516628 2439.672231 2402.599575 2351.215763 2126.060696 2543.165844 0.749180809 0.766270807 0.753782423 0.863357373 0.791736266 0.959305205 0.94472784 0.924523176 0.835989797 1 11.31240983 -8.241163978 24.22649265 0.853732802 0.943039665 0.300571409 0.074044711 946.2427696 1130635.514 0.015379896 0.039151146 5.74E-09 8.241163978 0.089306863 IEDVGSDEEDDSGKDK ddPTM_HeLa_Romidepsin_16h_R1 5 IEDVGSDEEDDSGKDK 16 1 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 0 ;;;; ;;;; 209.22 1.13E-20 58365500 13502.9 12126.2 12303.1 7305.4 13198.3 13467.6 10972.7 13001.9 13774.5 14099.7 FALSE FALSE TRUE 13338.32146 12296.91296 12517.23029 8150.084721 12524.7415 12607.06382 11904.72086 13378.08946 12542.47422 13733.38776 0.97123315 0.895402735 0.911445196 0.593450419 0.911992126 0.917986446 0.866845171 0.974128867 0.913283338 1 13.74539993 -10.15395052 1.969624721 0.988503919 0.856171846 0.152727478 0.099241187 0.322311164 2.393870573 0.017278759 0.021334662 7.02E-11 10.15395052 -0.132332073 IEDVGSDEEDDSGKDKK ddPTM_HeLa_Romidepsin_16h_R1 4 IEDVGSDEEDDSGKDKK 17 2 P08238;Q58FF8 P08238;Q58FF8 HSP90AB1;HSP90AB2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2 0 0 ;;; ;;; 115.06 0.00068711 266938000 23135.4 22788.6 22233.3 14775.7 22867.2 24632.3 19323.7 22667.3 23977.3 24547.2 FALSE FALSE TRUE 22853.41685 23109.41851 22620.26126 16484.13596 21700.20145 23058.37553 20965.0546 23323.14256 21832.71024 23909.46021 0.955831568 0.966538697 0.946079964 0.689439904 0.90759897 0.964403852 0.876851858 0.975477588 0.913141077 1 14.54529394 -9.509764206 24.92942841 0.97660008 0.881284559 0.175047935 0.076423018 611.0510322 1161547.764 0.011413082 0.016943372 3.09E-10 9.509764206 -0.095315521 IEDVTPIPSDS(ph)TR ddPTM_HeLa_Romidepsin_16h_R1 2 IEDVTPIPSDSTR 13 0 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 0 IEDVTPIPSDS(0.996)T(0.004)R;IEDVTPIPS(0.003)DS(0.769)T(0.228)R ; 214.61 2.17E-23 66871000 6186.9 8484.7 4953.9 5649.5 6607.1 6172.4 9432 7217 9051.4 6439.1 TRUE FALSE FALSE 6111.491683 8604.147829 5040.120551 6302.721772 6269.915033 5778.003561 10233.15384 7425.812508 8241.820114 6271.811254 0.974438075 1.371876079 0.803614833 1.004928483 0.99969766 0.921265537 1.631610619 1.183998084 1.314105253 1 12.61466643 -7.77433784 24.99787202 1.000431234 1.40780439 0.329228221 0.195510075 110.587382 214325.2272 0.021052854 0.063737869 1.68E-08 7.77433784 0.407373156 IEDVTPIPSDS(ph)TRR ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 0 IEDVTPIPSDS(0.871)T(0.129)RR 204.18 1.32E-16 12575000 2691.1 3691.6 1973.9 2429.1 2938.3 2853.2 3577.6 2951.8 3562.1 2680.8 TRUE FALSE FALSE 2658.299838 3743.570442 2008.254901 2709.963971 2788.347587 2670.889728 3881.481255 3037.205676 3243.496855 2611.15243 1.018056169 1.433685142 0.769106728 1.037842119 1.067860901 1.022877752 1.486501213 1.163166746 1.242170629 1 11.35047096 -7.781773047 24.95310772 1.029064675 1.324833936 0.203265461 0.182090376 159.6954886 195975.7432 0.021635046 0.065018371 1.65E-08 7.781773047 0.295769261 IEDVTPIPSDST(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 1 0 IEDVTPIPSDS(0.078)T(0.922)RR 217.2 6.25E-24 16329000 2456.9 3134.2 1982.5 2541.6 3105.8 2523 3932.6 2861.9 3839.8 2487 TRUE FALSE FALSE 2426.954358 3178.32335 2017.004581 2835.471751 2947.299437 2361.788443 4266.634946 2944.704561 3496.358671 2422.387381 1.00188532 1.312062379 0.832651539 1.170527791 1.216692037 0.974983795 1.761334698 1.215620831 1.443352412 1 11.24221388 -7.779015564 24.9974299 1.037261076 1.488477823 0.252721323 0.220831802 113.1115011 160871.3297 0.02266857 0.068221615 1.66E-08 7.779015564 0.451216748 IEDVTPIPSDSTR ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVTPIPSDSTR 13 0 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 0 177.44 1.26E-05 0 1111.5 1347.2 1213 1021.3 1134.9 1102.3 1017.1 1154.5 1383.4 1405.4 FALSE FALSE TRUE 1097.95261 1366.165917 1234.111756 1139.387511 1076.981818 1031.866588 1103.492449 1187.903636 1259.665239 1368.887505 0.802076581 0.998011825 0.90154359 0.832345614 0.786756993 0.753799405 0.806123545 0.867787624 0.920210926 1 10.41878818 -9.174437687 3.27574722 0.91238228 0.801177002 0.490230059 0.058552352 0.25129342 5.203152117 0.012461655 0.021326097 6.69E-10 9.174437687 -0.111205278 IEDVTPIPSDSTRR ddPTM_HeLa_Romidepsin_16h_R1 1 IEDVTPIPSDSTRR 14 1 P62263;A0A2R8Y811 P62263 RPS14 40S ribosomal protein S14 0 0 125.03 0.0021208 12073000 3252.3 3452.2 2491.6 3595.2 2719.7 2900.1 2859.3 2904.1 3333.8 3547.8 FALSE FALSE TRUE 3212.659717 3500.800162 2534.965253 4010.89394 2580.90356 2714.79297 3102.168871 2988.125552 3035.616578 3455.627645 0.929689205 1.01307216 0.733575927 1.160684643 0.746869694 0.785615017 0.897715029 0.864712828 0.878455925 1 11.75473206 -9.429756136 0.26309496 1.006255238 0.80551323 0.051655933 0.122236675 3.72664124 0.608430722 0.114049657 0.266177207 3.72E-10 9.429756136 -0.200742008 IEEAMDGSET(ph)PQLFTVLPEKR ddPTM_HeLa_Romidepsin_16h_R1 4 IEEAMDGSETPQLFTVLPEKR 21 1 E9PPJ0;Q13435 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 IEEAMDGS(0.177)ET(0.823)PQLFTVLPEKR;IEEAMDGS(0.213)ET(0.787)PQLFTVLPEKR;IEEAMDGS(0.054)ET(0.946)PQLFTVLPEKR;IEEAMDGS(0.247)ET(0.753)PQLFTVLPEKR ;;; 117.27 5.49E-05 192390000 13949.9 12907.2 12643.6 11538.9 13271.4 11504.7 9896 11898.8 12311.1 11217.3 TRUE FALSE FALSE 13779.87325 13088.9079 12863.65655 12873.08191 12594.11094 10769.5868 10736.56599 12243.073 11209.96438 10925.87293 1.261214856 1.197973653 1.177357328 1.178219992 1.152686931 0.985695776 0.982673518 1.12055788 1.026001717 1 13.41546093 -8.270273321 24.35315538 1.141810235 1.024945504 0.285434233 0.081308247 535.7587215 1476965.466 0.015246725 0.034586132 5.37E-09 8.270273321 -0.11686473 IEEEEEVEQELLSHS(ph)WGR ddPTM_HeLa_Romidepsin_16h_R1 3 IEEEEEVEQELLSHSWGR 18 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 IEEEEEVEQELLS(0.001)HS(0.999)WGR;IEEEEEVEQELLSHS(1)WGR;IEEEEEVEQELLS(0.346)HS(0.654)WGR ;; 219.61 3.65E-30 5729100 3464.76 2929.07 3297.81 4339.9 5356.3 6223.4 4767.5 5087.6 3744.39 3239.65 TRUE FALSE FALSE 3422.530172 2970.305524 3355.207 4841.699658 5082.948024 5825.744825 5172.451331 5234.801679 3409.48238 3155.483426 1.084629425 0.941315521 1.063294129 1.534376514 1.610830208 1.846228941 1.639194581 1.658953945 1.080494466 1 11.62364533 -9.163332193 2.578196261 1.030448435 1.693858847 0.952620641 0.070262234 0.042483243 0.550926233 0.011171293 0.019638912 6.87E-10 9.163332193 0.663410412 IEEEEQEPEPPEPFEYIDD ddPTM_HeLa_Romidepsin_16h_R1 4 IEEEEQEPEPPEPFEYIDD 19 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 0 ;;; ;;; 158.25 2.51E-05 152630000 51207.7 47559.1 47780.7 45598.9 50072 50068 44086.5 48215.9 53703.6 47639.2 FALSE FALSE TRUE 50583.56086 48228.63826 48612.30304 50871.25937 47516.639 46868.81639 47831.20621 49610.95099 48900.21551 46401.52672 1.090127081 1.039376108 1.047644474 1.096327276 1.024031801 1.010070567 1.030811044 1.069166351 1.05384928 1 15.50188465 -7.241080383 21.76018845 1.043075359 1.0691665 0.063472001 0.029424724 2342.144537 2503098.249 0.005220419 0.224837686 5.74E-08 7.241080383 0.02609114 IEEELGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 0 IEEELGS(1)K 104.22 0.027452 16367000 3209.5 3563.3 3440.3 1121 2907.6 4200.6 3930.3 3204.7 4310.9 3329.8 TRUE FALSE FALSE 3170.38138 3613.464231 3500.176978 1250.615294 2759.214322 3932.195217 4264.139584 3297.422938 3925.322307 3243.291316 0.977519769 1.114134957 1.079205239 0.385600667 0.850745139 1.212408888 1.314756884 1.016690336 1.210289772 1 11.6632429 -8.248646469 24.01567333 0.951218361 1.194632563 0.191719717 0.221255377 556.3174137 1044350.448 0.029711837 0.075153251 5.64E-09 8.248646469 0.243414202 IEEELGSK ddPTM_HeLa_Romidepsin_16h_R1 1 IEEELGSK 8 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 112.41 0.018152 1981300 1311.4 1357.1 1292.5 1259.5 1464 1818.6 1447.8 1552.2 1424 1614.7 FALSE FALSE TRUE 1295.416152 1376.205289 1314.99542 1405.129316 1389.286617 1702.397329 1570.776096 1597.110458 1296.633874 1572.749861 0.82366318 0.875031258 0.836112247 0.893421993 0.883348746 1.082433622 0.998745023 1.015489174 0.824437443 1 10.61907352 -8.271317609 24.93383634 0.901812411 1.028874849 0.598348475 0.055799255 496.975699 1254426.568 0.010496334 0.023740572 5.35E-09 8.271317609 0.127062438 IEEVLSPEGSPSKS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 3 IEEVLSPEGSPSKSPSK 17 1 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 0 IEEVLSPEGS(0.051)PS(0.062)KS(0.794)PS(0.093)K;IEEVLSPEGS(0.006)PS(0.187)KS(0.772)PS(0.034)K;IEEVLSPEGS(0.002)PS(0.015)KS(0.982)PS(0.002)K ;; 205.98 1.30E-18 183808000 13353.1 12178 13269.8 9427.2 16545.3 18041.9 15041.1 17696.1 12949.6 12010.3 TRUE FALSE FALSE 13190.34728 12349.4422 13500.7553 10517.21722 15700.9316 16889.08082 16318.69066 18208.10873 11791.35534 11698.27067 1.127546767 1.055663914 1.154081289 0.899040338 1.342158344 1.443724572 1.394966069 1.556478666 1.007957131 1 13.51400766 -8.599985005 5.355365123 1.059445508 1.448676184 0.861563998 0.07807386 0.055672448 2.802693861 0.011524944 0.023451868 2.51E-09 8.599985005 0.389230676 IEEVPELPLVVEDK ddPTM_HeLa_Romidepsin_16h_R1 1 IEEVPELPLVVEDK 14 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 0 167.11 0.00086551 2250900 1969.4 2205.3 2445 1293.9 1736.3 2547.6 1880.4 2121.4 2104.9 2438.8 FALSE FALSE TRUE 1945.396195 2236.346271 2487.554199 1443.506806 1647.690132 2384.816582 2040.121129 2182.779362 1916.632472 2375.439624 0.818962593 0.941445216 1.0471974 0.607679855 0.693635871 1.003947462 0.858839395 0.918894902 0.806853793 1 11.21397882 -12.46688755 0.844567445 1.014450923 0.85636769 0 0.139648142 1.272640292 1.368250296 0.141913255 0.024407972 3.41E-13 12.46688755 -0.158083233 IEEVPELPLVVEDKVEGYKK ddPTM_HeLa_Romidepsin_16h_R1 1 IEEVPELPLVVEDKVEGYKK 20 2 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 0 99.711 0.00022958 2914600 3096.9 3102.2 2427.8 2965.4 3050.6 2842.8 2367.2 2757.3 2792.1 3114.8 FALSE FALSE TRUE 3059.153792 3145.872853 2470.054841 3308.273501 2894.916499 2661.154255 2568.269909 2837.078125 2542.367583 3033.877047 1.008331499 1.036915077 0.814157859 1.090444158 0.95419704 0.877146375 0.84653065 0.935132862 0.837992952 1 11.5669469 -8.412109889 4.253670025 0.997168582 0.883243169 0.07340404 0.085800488 0.181964429 5.518897848 0.009238267 0.021304788 3.87E-09 8.412109889 -0.113925413 IEGPLGQGGPR ddPTM_HeLa_Romidepsin_16h_R1 1 IEGPLGQGGPR 11 0 O94913 O94913 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 0 0 86.882 0.0096795 585360 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 IEGYEDQVLITEHGDLGNSR ddPTM_HeLa_Romidepsin_16h_R1 1 IEGYEDQVLITEHGDLGNSR 20 0 P52907 P52907 CAPZA1 F-actin-capping protein subunit alpha-1 0 0 105.52 4.53E-05 0 1441.5 1239.2 1025.5 1129.7 1810.1 1626.7 1145.9 1471.3 1603.7 1813.8 FALSE FALSE TRUE 1423.930444 1256.64549 1043.348397 1260.321229 1717.723843 1522.75912 1243.232717 1513.869744 1460.261055 1766.677215 0.805993552 0.711304521 0.590571039 0.713385116 0.97229071 0.861933978 0.703712431 0.856902286 0.826557927 1 10.78682276 -11.74384392 0.863362165 0.98848567 0.775238196 0.131039726 0.112565527 0.44639069 0.659106221 0.052284323 0.022399173 1.80E-12 11.74384392 -0.213247474 IEHAPS(ph)PSSGGTLK ddPTM_HeLa_Romidepsin_16h_R1 1 IEHAPSPSSGGTLK 14 0 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7Y0;A0A2R8YCQ1;A0A2R8YD28 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 IEHAPS(0.881)PS(0.112)S(0.007)GGTLK 139.64 0.0010172 22132000 3029.2 2829.8 2839.9 1930.2 2626.9 2853.2 2051.6 2641.7 3227.7 3346 TRUE FALSE FALSE 2992.278945 2869.637999 2889.327268 2153.378806 2492.839491 2670.889728 2225.862853 2718.133422 2939.006428 3259.070438 0.918138777 0.880508125 0.8865495 0.660734049 0.764892793 0.819525009 0.682974761 0.834021072 0.901792853 1 11.67024482 -9.958562573 0.861906037 0.974087424 0.752243594 0.599867132 0.063873696 0.20964022 0.311047607 0.012803208 0.018197073 1.10E-10 9.958562573 -0.22184383 IEHSFWR ddPTM_HeLa_Romidepsin_16h_R1 2 IEHSFWR 7 0 Q16531;Q16531-2 Q16531 DDB1 DNA damage-binding protein 1 0 0 ; ; 166.05 0.0049803 16622000 6047.1 4196.9 10766.4 9061.2 11909.9 9287.3 7024.6 4090.7 4526.3 3295.3 FALSE FALSE TRUE 5973.395619 4255.984068 10953.78468 10108.89858 11302.09336 8693.871503 7621.269349 4209.05795 4121.456392 3209.687631 1.861052011 1.325980768 3.412726077 3.14949607 3.521244015 2.708634765 2.374458273 1.311360616 1.284067755 1 11.64821718 -9.776093951 24.99667443 1.411921809 2.781254195 0.544132621 0.61712388 148.8951827 253973.5646 0.109740138 0.144571324 1.67E-10 9.776093951 1.369332386 IEPGTST(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 IEPGTSTPR 9 0 H7C2H2;Q86X27-3;Q86X27;A0A0A0MR31 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 0 IEPGT(0.001)S(0.011)T(0.988)PR 117.7 0.030483 12192000 3944.2 4033.4 4626.7 4540.8 4609 4926.8 4273 4228.9 4357 4167.2 TRUE FALSE FALSE 3896.126573 4090.182311 4707.225773 5065.828661 4373.785531 4611.993381 4635.948513 4351.256549 3967.299008 4058.935543 0.959888752 1.007698267 1.159719272 1.24806827 1.077569595 1.136256866 1.142158693 1.07201913 0.977423506 1 11.98688571 -9.826426228 5.10620815 0.981437898 1.141437867 0.722644767 0.046583427 0.078128721 3.94385896 0.00762637 0.010171081 1.49E-10 9.826426228 0.159999969 IEPIPGES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 IEPIPGESPK 10 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 IEPIPGES(1)PK;IEPIPGES(1)PK;IEPIPGES(1)PK;IEPIPGES(1)PK ;;; 158.34 0.0027718 109303000 23607.9 21192.3 20315.7 20705.2 21319.6 23869.8 21482.9 24209.3 22183.7 21435 TRUE FALSE FALSE 23320.15783 21490.64576 20669.28624 23099.23264 20231.58126 22344.59682 23307.65699 24909.7579 20199.53431 20878.11561 1.116966601 1.029338383 0.989997691 1.106384938 0.969032916 1.070240113 1.116367848 1.193103744 0.967497962 1 14.34970388 -7.492125678 2.100873382 1.047792222 1.200676432 0.483267745 0.052084466 0.330430911 2.230195144 0.00767343 0.079214993 3.22E-08 7.492125678 0.15288421 IERMHWPGS(ph)GQQLPR ddPTM_HeLa_Romidepsin_16h_R1 1 IERMHWPGSGQQLPR 15 1 B7ZLU9;Q14833-3;Q14833-2;Q14833-4;Q14833-5;Q14833 B7ZLU9 GRM4 Metabotropic glutamate receptor 4 1 0 IERMHWPGS(1)GQQLPR 86.699 0.0042672 0 1409 970.23 1099.7 3052.2 615.17 673.79 670.91 648.11 1490.2 1458.1 TRUE FALSE FALSE 1391.826566 983.8889234 1118.839817 3405.109725 583.7755794 630.7369936 727.8970787 666.8620403 1356.91278 1420.218352 0.980008859 0.692772997 0.787794226 2.397595919 0.411046357 0.444112691 0.512524766 0.469548953 0.955425465 1 10.47189704 IES(ph)DEEEDFENVGK ddPTM_HeLa_Romidepsin_16h_R1 4 IESDEEEDFENVGK 14 0 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 1 0 IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK;IES(1)DEEEDFENVGK ;;; 290.64 2.20E-113 554626000 31355.6 31177 30467.3 24020.3 28559.8 25140.1 21980.6 23989.7 33840.3 30500.3 TRUE FALSE FALSE 30973.42589 31615.91062 30997.57058 26797.6401 27102.28683 23533.72875 23847.63162 24683.80412 30813.53881 29707.89781 1.042599045 1.064225777 1.043411781 0.902037575 0.912292314 0.792170786 0.802737096 0.830883568 1.037217073 1 14.8585589 -8.819081938 1.480017359 1.026043288 0.810117046 0.905560024 0.031405542 0.089923931 0.396280427 0.005322571 0.012680821 1.52E-09 8.819081938 -0.215926242 IESDVQEPT(ph)EPEDDLDIMLGNK ddPTM_HeLa_Romidepsin_16h_R1 4 IESDVQEPTEPEDDLDIMLGNK 22 0 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 0 IES(0.002)DVQEPT(0.998)EPEDDLDIMLGNK;IES(0.121)DVQEPT(0.879)EPEDDLDIMLGNK;IESDVQEPT(1)EPEDDLDIMLGNK;IES(0.001)DVQEPT(0.999)EPEDDLDIMLGNK ;;; 116.2 3.81E-05 69800000 12118.8 9682.4 11654.7 9569.7 9616.8 9744 8815.5 9500.4 11720.8 10677.7 TRUE FALSE FALSE 11971.0914 9818.709081 11857.54516 10676.19374 9126.018811 9121.389847 9564.28835 9775.279085 10672.46229 10400.29181 1.151034184 0.944080152 1.140116583 1.026528287 0.877477188 0.877032107 0.919617307 0.939904308 1.026169504 1 13.34433639 -8.867777438 4.751342411 1.066836517 0.903177722 0.571747241 0.060759523 0.122142184 4.615164021 0.010394468 0.01929966 1.36E-09 8.867777438 -0.163658795 IESDVQEPT(ph)EPEDDLDIMLGNKK ddPTM_HeLa_Romidepsin_16h_R1 2 IESDVQEPTEPEDDLDIMLGNKK 23 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 1 0 IES(0.003)DVQEPT(0.997)EPEDDLDIMLGNKK;IES(0.001)DVQEPT(0.999)EPEDDLDIMLGNKK ; 84.291 0.00010451 48181000 2465.1 2154.24 2322.76 2741.4 2140.49 2185.9 1887.48 2086.39 2911.9 2228.5 TRUE FALSE FALSE 2435.054413 2184.567447 2363.186663 3058.373567 2031.252808 2046.228045 2047.802504 2146.756403 2651.452371 2170.603249 1.121833027 1.006433326 1.088723453 1.408997047 0.935801054 0.942700167 0.943425523 0.989013724 1.221527874 1 11.08388033 IET(ph)DEEESCDNAHGDANQPAR ddPTM_HeLa_Romidepsin_16h_R1 2 IETDEEESCDNAHGDANQPAR 21 0 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 1 0 IET(0.999)DEEES(0.001)CDNAHGDANQPAR;IET(0.985)DEEES(0.015)CDNAHGDANQPAR ; 200.33 3.72E-24 21599800 2598 2460.6 2772.2 634.34 2456.31 2192.2 1918.31 2437.67 2620 2534.9 TRUE FALSE FALSE 2566.334577 2495.240391 2820.448978 707.6853755 2330.955335 2052.125495 2081.251204 2508.200135 2385.660638 2469.042933 1.039404598 1.01061037 1.142324802 0.286623358 0.944072419 0.831142087 0.842938442 1.015859264 0.966228901 1 11.26973621 IETIAAS(ph)STPTPIRK ddPTM_HeLa_Romidepsin_16h_R1 1 IETIAASSTPTPIRK 15 1 Q96P47-5;Q96P47;Q96P47-2;Q96P47-4;H7C5G0;H7C4U6;E7ESL9;Q96P47-3;Q96P47-6 Q96P47-5 AGAP3 "Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 3" 1 0 IETIAAS(0.654)S(0.172)T(0.172)PT(0.001)PIRK 162.88 0.00020733 6053700 2004 1653.6 1495.4 1667.4 1403.1 1089.2 866.95 865.84 1725.2 1364.6 TRUE FALSE FALSE 1979.574477 1676.879424 1521.42681 1860.192633 1331.494571 1019.603635 940.5887114 890.8917143 1570.893791 1329.147495 1.489356512 1.261620272 1.14466364 1.399538155 1.001765851 0.767110978 0.707663156 0.670273027 1.181880714 1 10.37628549 -8.410994111 2.644536775 1.242226065 0.704057776 0.77034321 0.129572898 0.143793813 1.942186707 0.027799791 0.06996742 3.88E-09 8.410994111 -0.538168288 IEVEK(ac)PFAIAK ddPTM_HeLa_Romidepsin_16h_R1 1 IEVEKPFAIAK 11 1 P23284 P23284 PPIB Peptidyl-prolyl cis-trans isomerase B 0 1 IEVEK(1)PFAIAK 154.24 0.0077216 206260 0 0 127.63 0 166.53 130.71 99.241 169.39 311.92 111.62 FALSE TRUE FALSE 0 0 129.8513466 0 158.0313527 122.3580528 107.6705281 174.2910324 284.021094 108.7200963 0 0 1.194363793 0 1.453561559 1.12544099 0.990346143 1.603116979 2.612406571 1 6.764474829 -8.746923226 24.94529782 0.495363629 1.259513272 0.002483566 0.787872514 198.0552552 340346.3309 0.071014749 0.141524401 1.79E-09 8.746923226 0.764149643 IEVLDS(ph)PASK ddPTM_HeLa_Romidepsin_16h_R1 4 IEVLDSPASK 10 0 Q8N5I9 Q8N5I9 C12orf45 Uncharacterized protein C12orf45 1 0 IEVLDS(0.721)PAS(0.279)K;IEVLDS(0.98)PAS(0.02)K;IEVLDS(0.931)PAS(0.069)K;IEVLDS(0.793)PAS(0.207)K ;;; 134.18 0.0060195 127500000 25637.9 24492.4 24752.1 19057.1 27290.4 25305.6 21829 23573.2 24550 23858.7 TRUE FALSE FALSE 25325.41541 24837.20465 25182.89992 21260.57157 25897.66905 23688.65383 23683.15472 24255.25335 22354.18651 23238.84753 1.089787924 1.068779534 1.083655284 0.914872028 1.114412796 1.019355792 1.019119157 1.043737359 0.961931803 1 14.5042509 IEVLPVDTGAGGYSGNSGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 IEVLPVDTGAGGYSGNSGSPK 21 0 X6RAB3;Q92738;Q92738-2 X6RAB3 USP6NL USP6 N-terminal-like protein 1 0 IEVLPVDT(0.089)GAGGY(0.03)S(0.101)GNS(0.175)GS(0.604)PK;IEVLPVDT(0.033)GAGGY(0.122)S(0.021)GNS(0.401)GS(0.423)PK ; 88.765 0.0012243 27305000 11928.5 12252.4 12207.5 11888.4 12755.3 13755.6 12106.8 11794.6 12792.6 12133.6 TRUE FALSE FALSE 11783.11085 12424.88961 12419.96642 13262.99274 12104.34944 12876.66155 13135.15129 12135.85814 11648.39782 11818.36732 0.997016807 1.051320311 1.05090374 1.122235617 1.024198107 1.089546568 1.111418433 1.026864186 0.985618191 1 13.52874312 -10.06731684 2.044052504 0.998123644 1.074388186 0.555154962 0.030595427 0.158358872 1.291530842 0.004910545 0.006261698 8.56E-11 10.06731684 0.076264541 IEVPLYSLLEQTHLK ddPTM_HeLa_Romidepsin_16h_R1 1 IEVPLYSLLEQTHLK 15 0 A0A0A0MSM0;Q92598-2;Q92598-3;Q92598;Q92598-4 A0A0A0MSM0 HSPH1 Heat shock protein 105 kDa 0 0 167.03 1.55E-05 1233800 624.26 469.69 657.36 384.09 622.6 724.97 608.78 701.74 518.66 660.96 FALSE FALSE TRUE 616.651279 476.3023081 668.8010751 428.500293 590.8263988 678.6467567 660.489758 722.0437397 472.2697506 643.7881639 0.957848115 0.73984322 1.038852704 0.665592064 0.917734174 1.05414606 1.025942686 1.121554853 0.733579424 1 9.330442243 -8.236951046 8.810569191 0.937914889 1.063336523 0.21739266 0.132235621 0.43580607 145.4133173 0.016790427 0.042210918 5.79E-09 8.236951046 0.125421633 IEWLESHQDADIEDFK ddPTM_HeLa_Romidepsin_16h_R1 3 IEWLESHQDADIEDFK 16 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 ;; ;; 151.38 0.00013089 118702900 10100.5 9138.4 10387 8441.6 11506.9 14131.5 11242 13194.6 10519.2 10382.9 FALSE FALSE TRUE 9977.391221 9267.050635 10567.78138 9417.657511 10919.65995 13228.54276 12196.8952 13576.36493 9578.336406 10113.15076 0.98657594 0.916336645 1.044954399 0.931228826 1.079748558 1.30805355 1.206043051 1.342446608 0.94711694 1 13.30394492 -8.408386287 3.539214533 0.987644609 1.277647106 0.887741161 0.049646942 0.05107815 1.166423025 0.006188582 0.014634054 3.90E-09 8.408386287 0.290002497 IEWLESHQDADIEDFKAK ddPTM_HeLa_Romidepsin_16h_R1 1 IEWLESHQDADIEDFKAK 18 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 96.489 0.0013761 14938000 2813.7 2217.6 2022.6 3260.8 2579.8 2714.3 2636.2 3009.8 2573.8 2123.3 FALSE FALSE TRUE 2779.405542 2248.819431 2057.802505 3637.829039 2448.143179 2540.86499 2860.118762 3096.883814 2343.592882 2068.13636 1.343917933 1.087365163 0.995003301 1.758988967 1.1837436 1.228577109 1.382944963 1.497427285 1.133190696 1 11.0141156 -16.02579859 0.162783959 3.10E-14 1.414691937 0.22799601 0.199977605 53.65940131 0.671138607 17.61961799 0.376908966 9.42E-17 16.02579859 1.414691937 IFDIDEAEEGVKDLK ddPTM_HeLa_Romidepsin_16h_R1 1 IFDIDEAEEGVKDLK 15 1 P20042 P20042 EIF2S2 Eukaryotic translation initiation factor 2 subunit 2 0 0 130.61 0.0022021 8944500 2298.7 2357.1 1849.5 2399.7 2040.9 1845.7 1872.4 2231.6 2855.3 2137.4 FALSE FALSE TRUE 2270.68256 2390.283316 1881.689772 2677.164605 1936.745257 1727.765727 2031.441609 2296.167825 2599.914817 2081.87004 1.090693711 1.148142425 0.903845934 1.285942232 0.930291142 0.829910462 0.97577734 1.102935237 1.248836271 1 11.0236643 IFDLGS(ph)DNEEVVAGPAPAHAK ddPTM_HeLa_Romidepsin_16h_R1 2 IFDLGSDNEEVVAGPAPAHAK 21 0 A0A096LNM2;Q969U6-2;Q969U6 A0A096LNM2 FBXW5 F-box/WD repeat-containing protein 5 1 0 IFDLGS(1)DNEEVVAGPAPAHAK;IFDLGS(1)DNEEVVAGPAPAHAK ; 150.73 4.00E-06 39213000 5964.5 5844 6118.9 4871.6 8203 8205.4 6538 8113.3 6119.8 5769.4 TRUE FALSE FALSE 5891.80238 5926.271985 6225.396888 5434.877314 7784.3703 7681.101422 7093.337557 8348.045535 5572.429761 5619.510156 1.048454797 1.054588713 1.107818424 0.967144317 1.385240009 1.366863162 1.262269728 1.485546836 0.991621975 1 12.45622866 -8.756913176 24.99979109 1.029650991 1.366349499 0.881567671 0.062222074 26.10159795 144166.2919 0.008430945 0.016418691 1.75E-09 8.756913176 0.336698508 IFQGSFGGPTLY(ph)ENPHYQSPNMHR ddPTM_HeLa_Romidepsin_16h_R1 1 IFQGSFGGPTLYENPHYQSPNMHR 24 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 1 0 IFQGSFGGPT(0.001)LY(0.669)ENPHY(0.181)QS(0.149)PNMHR 92.034 2.24E-05 16833000 585.25 578.03 497.1 510.59 563.69 597.77 511.75 636.15 473.25 598.63 TRUE FALSE FALSE 578.1167479 586.1675215 505.751817 569.6268182 534.9227959 559.5744262 555.2180322 654.5559966 430.9213347 583.0775063 0.991492111 1.005299493 0.867383515 0.976931561 0.917412848 0.959691328 0.952219947 1.122588317 0.739046405 1 9.187543858 IFQGSFGGPTLYENPHYQS(ph)PNMHR ddPTM_HeLa_Romidepsin_16h_R1 1 IFQGSFGGPTLYENPHYQSPNMHR 24 0 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 1 0 IFQGSFGGPTLY(0.003)ENPHY(0.463)QS(0.534)PNMHR 75.797 0.00017501 8942300 1546.5 2191.4 1872.8 1534.6 2227.1 2469.2 2378.6 2453.8 2268.5 1940.4 TRUE FALSE FALSE 1527.650663 2222.250587 1905.395298 1712.037673 2113.442777 2311.426089 2580.638225 2524.796832 2065.599678 1889.988128 0.808285851 1.175801347 1.008151993 0.905845728 1.118230715 1.222984449 1.365425627 1.335879731 1.092916748 1 10.88416146 -8.271691267 1.001731093 0.930373464 1.393466352 0.588354819 0.10896939 0.283745947 0.474259652 0.018031512 0.095838081 5.35E-09 8.271691267 0.463092888 IFRDGEEAGAYDGPR ddPTM_HeLa_Romidepsin_16h_R1 2 IFRDGEEAGAYDGPR 15 1 P30101;H7BZJ3 P30101;H7BZJ3 PDIA3 Protein disulfide-isomerase A3 0 0 ; ; 109.1 0.0052941 20127500 4028.9 3450.8 3176.9 4167.8 3634.1 3625.1 3347.6 4152.9 4479.6 3698.3 FALSE FALSE TRUE 3979.794217 3499.380453 3232.192612 4649.700646 3448.638316 3393.467809 3631.94506 4273.057609 4078.933357 3602.217633 1.104817816 0.971451703 0.897278549 1.290788375 0.957365342 0.942049636 1.008252535 1.186229719 1.132339512 1 11.81466963 -16.52263183 0.006902413 0.55906595 1.482255453 0 0.118817403 193098.8721 107.8213229 7948.882461 6537.336002 3.00E-17 16.52263183 0.923189503 IFREEQNGEDEDGGWR ddPTM_HeLa_Romidepsin_16h_R1 2 IFREEQNGEDEDGGWR 16 1 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JH78;C9IYH5 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 0 0 ; ; 153.41 0.00030591 4866900 1009.14 1179.45 893.84 1148.95 838.15 1142.71 1054.51 941.65 1108.52 1116.93 FALSE FALSE TRUE 996.8402135 1196.054328 909.3969103 1281.797005 795.3760779 1069.694519 1144.080053 968.8951571 1009.371195 1087.911998 0.916287545 1.099403565 0.835910361 1.178217547 0.731103324 0.983254639 1.051629227 0.890600673 0.927805923 1 10.08734614 -8.756778928 24.9998021 0.974355913 0.928903474 0.078082791 0.118814062 373.5379538 2003726.613 0.015918553 0.031018223 1.75E-09 8.756778928 -0.045452439 IFSLSGT(ph)LETVR ddPTM_HeLa_Romidepsin_16h_R1 2 IFSLSGTLETVR 12 0 B4DEM9;Q9Y2S7 B4DEM9 POLDIP2 Polymerase delta-interacting protein 2 1 0 IFSLS(0.04)GT(0.898)LET(0.062)VR;IFSLS(0.047)GT(0.952)LET(0.001)VR ; 158.86 0.0019416 29940000 2137.57 2033.32 2090.73 2115.3 2440.97 2165.8 1910.36 2155.12 2502.2 2285.41 TRUE FALSE FALSE 2111.516475 2061.945132 2127.118279 2359.880939 2316.398192 2027.41237 2072.625931 2217.474997 2278.396965 2226.034719 0.94855505 0.926286151 0.955563838 1.060127643 1.040593919 0.910773023 0.931084279 0.996154722 1.023522655 1 11.12026038 -7.173144283 0.002535603 1.92951601 4.34E-06 0.022376299 0.048738468 445938.5583 173.2032933 64673.48478 67147.26246 6.71E-08 7.173144283 -1.929511672 IFTSIGEDYDER ddPTM_HeLa_Romidepsin_16h_R1 4 IFTSIGEDYDER 12 0 P35232;C9JZ20;E7ESE2;E9PCW0;C9JW96;P35232-2;D6RBK0 P35232 PHB Prohibitin 0 0 ;;; ;;; 300.33 4.01E-126 194297000 7940.4 6856.3 6993.1 6326.93 7354.84 8200.54 6642.64 6773.05 7303.8 6490 FALSE FALSE TRUE 7843.619351 6952.823171 7114.811972 7058.479416 6979.49507 7676.55196 7206.865676 6969.017516 6650.529835 6321.388864 1.240806335 1.09988854 1.125514048 1.116602628 1.10410785 1.214377429 1.140076308 1.102450374 1.052067825 1 12.62602585 -12.57358701 1.359423276 1.000144759 1.154231553 0.458863271 0.048753563 0.267581462 0.887835907 0.037518085 0.008818861 2.67E-13 12.57358701 0.154086794 IFTTPLT(ph)PSQYYSGSK ddPTM_HeLa_Romidepsin_16h_R1 1 IFTTPLTPSQYYSGSK 16 0 P49454 P49454 CENPF Centromere protein F 1 0 IFT(0.001)T(0.004)PLT(0.992)PS(0.003)QYYSGSK 125.67 0.0050553 25667000 2113.4 1837.5 1934.9 1809.7 1548.1 1912 1212.5 1309.4 1607.6 1911.5 TRUE FALSE FALSE 2087.641068 1863.368373 1968.576123 2018.946029 1469.09468 1789.829371 1315.48972 1347.285423 1463.81223 1861.838954 1.121279079 1.000821456 1.057328894 1.084382741 0.789055722 0.961323409 0.706553978 0.723631558 0.7862185 1 10.86251257 -8.139630555 0.870132477 1.057568532 0.677456293 0.404873116 0.11445077 0.343480459 0.381143808 0.012777916 0.093263191 7.25E-09 8.139630555 -0.380112239 IFTTPLTPS(ph)QYYSGSK ddPTM_HeLa_Romidepsin_16h_R1 1 IFTTPLTPSQYYSGSK 16 0 P49454 P49454 CENPF Centromere protein F 1 0 IFTT(0.381)PLT(0.017)PS(0.601)QYYS(0.001)GSK 220.27 9.23E-35 28573000 1487 1509.7 1313.5 1383.5 1406.2 1369.7 818.28 1214.2 1686.7 1678.3 TRUE FALSE FALSE 1468.875872 1530.953596 1336.360917 1543.46678 1334.436367 1282.180591 887.7846828 1249.330961 1535.837328 1634.697524 0.898561263 0.936536316 0.817497364 0.944191055 0.816320051 0.784353418 0.543088045 0.764258184 0.93952386 1 10.674808 -7.09970425 0.285583044 0.984527938 0.335763786 0.627569928 0.076459398 3.768100253 0.213923579 0.036462094 0.869389297 7.95E-08 7.09970425 -0.648764152 IFVGGLNPEATEEK ddPTM_HeLa_Romidepsin_16h_R1 3 IFVGGLNPEATEEK 14 0 Q99729-3;D6R9P3;D6RD18;D6RBZ0;Q99729-2 Q99729-3 HNRNPAB Heterogeneous nuclear ribonucleoprotein A/B 0 0 ;; ;; 189.13 4.48E-38 15083600 2399.1 2428.503 2186.34 2192.8 2435.01 2281.6 1927.87 2117.8 2549.3 2321.8 FALSE FALSE TRUE 2369.858846 2462.691529 2224.392331 2446.341853 2310.742353 2135.813124 2091.62323 2179.075202 2321.284223 2261.479301 1.047924182 1.088973721 0.98360057 1.081744083 1.021783552 0.944431869 0.924891609 0.96356186 1.026445045 1 11.14305108 -8.273706475 5.280160429 1.029895951 0.941749951 0.627056719 0.032141108 0.093545287 8.712117713 0.004826636 0.011601564 5.32E-09 8.273706475 -0.088146 IFVGGLS(ph)PDTPEEK ddPTM_HeLa_Romidepsin_16h_R1 2 IFVGGLSPDTPEEK 14 0 Q14103-3;D6RAF8;Q14103;H0YA96;Q14103-4;D6RF44;H0Y8G5;Q14103-2 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 0 IFVGGLS(0.5)PDT(0.5)PEEK;IFVGGLS(0.862)PDT(0.138)PEEK ; 134.06 0.0016203 37335000 8336 7878.4 8922 8304.8 9644.4 10497.5 9319.6 10034.3 10113.5 8328.9 TRUE FALSE FALSE 8234.397626 7989.312322 9077.283667 9265.040051 9152.21028 9826.743629 10111.20659 10324.62664 9208.92323 8112.513977 1.015024153 0.984813381 1.11892364 1.142067684 1.12815957 1.211306835 1.246371546 1.272679057 1.135150368 1 12.98593334 -8.671258632 0.579905424 0.999801443 1.295928185 0.719533911 0.050741353 0.205583482 0.108809123 0.006057542 0.03078564 2.13E-09 8.671258632 0.296126742 IFVGGLSPDT(ph)PEEK ddPTM_HeLa_Romidepsin_16h_R1 1 IFVGGLSPDTPEEK 14 0 Q14103-3;D6RAF8;Q14103;H0YA96;Q14103-4;D6RF44;H0Y8G5;Q14103-2 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 0 IFVGGLS(0.482)PDT(0.518)PEEK 234.83 1.17E-42 25598000 3191.6 3350.3 3111.9 3023.4 4033.9 3450.7 2777.1 3525.1 3321.4 3535.1 TRUE FALSE FALSE 3152.699552 3397.465611 3166.061314 3372.979734 3828.03503 3230.211407 3012.986805 3627.093207 3024.325665 3443.257592 0.915615363 0.986700971 0.919495922 0.979589718 1.111748084 0.938126562 0.875039617 1.053390027 0.878332679 1 11.7495584 -9.012468046 24.90754697 0.95837943 0.989963538 0.097038518 0.068579539 1598.511915 3193371.968 0.009970317 0.017110754 9.72E-10 9.012468046 0.031584107 IFVGGLSPDTPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 IFVGGLSPDTPEEK 14 0 Q14103-3;D6RAF8;Q14103;H0YA96;Q14103-4;D6RF44;H0Y8G5;Q14103-2 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 0 0 180.97 5.30E-48 0 248.38 199.43 274.74 377.66 264.38 266.23 238.17 237.3 334.03 211.98 FALSE FALSE TRUE 245.352649 202.2375808 279.5217345 421.3268261 250.8877021 249.2187622 258.4001539 244.1659011 304.1535202 206.472729 1.188305352 0.979488099 1.353794933 2.0405931 1.215113024 1.207029923 1.25149774 1.18255763 1.473092944 1 7.689807433 -9.701183923 7.730637879 1.083344185 1.386091463 0.106164449 0.270292342 0.260483718 28.88763987 0.039401807 0.055673253 1.99E-10 9.701183923 0.302747278 IFYPEIEEVQALDDT(ph)ERGSGGFGSTGK ddPTM_HeLa_Romidepsin_16h_R1 1 IFYPEIEEVQALDDTERGSGGFGSTGK 27 1 P33316;A0A0C4DGL3;H0YNW5;P33316-2 P33316;H0YNW5;P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 0 IFYPEIEEVQALDDT(0.736)ERGS(0.245)GGFGS(0.011)T(0.008)GK 57.145 0.0021909 4790700 1699 1396.3 1422.8 957.85 1601.4 1452.1 1421.5 1666.7 1935.4 1621 TRUE FALSE FALSE 1678.291934 1415.957148 1447.563237 1068.601124 1519.674582 1359.315496 1542.242175 1714.923335 1762.292977 1578.886186 1.062959413 0.896807611 0.916825576 0.676806937 0.962497864 0.860933174 0.976791227 1.086160199 1.116162135 1 10.62469146 -10.25416786 24.48024211 1.029730835 0.904781631 0.292930201 0.102458262 440.9220117 1484404.671 0.016624069 0.020138423 5.57E-11 10.25416786 -0.124949204 IFYPETTDIYDRK ddPTM_HeLa_Romidepsin_16h_R1 2 IFYPETTDIYDRK 13 1 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 0 ; ; 136.01 0.0010161 41732000 6527.8 6500.3 6152.3 6600.1 6779.9 6999.7 6922.5 6334.8 7095.7 6221.2 FALSE FALSE TRUE 6448.236663 6591.811394 6259.378201 7363.234616 6433.896404 6552.44176 7510.496977 6518.087443 6461.04282 6059.572327 1.064140556 1.087834428 1.032973593 1.215140973 1.061774009 1.08133733 1.239443408 1.075667901 1.066253932 1 12.56500026 -10.31600701 0.267782006 0.98157382 1.164440736 0.22606224 0.063194105 1.240260322 0.322836779 0.079119772 0.084896453 4.83E-11 10.31600701 0.182866916 IGAEVYHNLK ddPTM_HeLa_Romidepsin_16h_R1 4 IGAEVYHNLK 10 0 P06733;A0A2R8Y6G6;P06733-2;K7EM90 P06733 ENO1 Alpha-enolase;Enolase 0 0 ;;; ;;; 132.88 0.00087769 126887000 19760 15667.08 29914.1 21477.6 33578.1 31444.5 23792.93 16713.9 18008.14 12551.96 FALSE FALSE TRUE 19519.15752 15887.64156 30434.74236 23960.94117 31864.48426 29435.29793 25813.90088 17197.49033 16397.44686 12225.85827 1.596547014 1.299511348 2.489374708 1.959857594 2.6063188 2.407626302 2.1114183 1.40664892 1.341210285 1 13.57764813 -10.48576119 0.679938348 1.120837636 2.183057543 0.48203909 0.3881988 0.34237637 0.345431476 0.117745782 0.11957801 3.27E-11 10.48576119 1.062219907 IGEEQS(ph)AEDAEDGPPELLFIHGGHTAK ddPTM_HeLa_Romidepsin_16h_R1 4 IGEEQSAEDAEDGPPELLFIHGGHTAK 27 0 E9PC52;Q16576;Q16576-2;Q5JNZ6 E9PC52 RBBP7 Histone-binding protein RBBP7 1 0 IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK;IGEEQS(1)AEDAEDGPPELLFIHGGHTAK ;;; 96.699 4.92E-08 33908900 5350.45 5425.21 5240.61 7494.6 6947.4 7304.4 5881.3 6740.9 5803.4 5801.67 TRUE FALSE FALSE 5285.236657 5501.586249 5331.820619 8361.160915 6592.848254 6837.672414 6380.857475 6935.937306 5284.329369 5650.941777 0.935284217 0.973569799 0.943527792 1.47960486 1.166681327 1.210005816 1.129167089 1.227394933 0.935123662 1 12.46427561 -9.306111546 24.99370096 0.967272201 1.230245475 0.714749549 0.089769978 182.7653731 102255.2204 0.013184548 0.020139787 4.94E-10 9.306111546 0.262973273 AESPESS(ph)AIESTQST(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 AESPESSAIESTQSTPQK 18 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 AES(0.422)PES(0.039)S(0.466)AIES(0.057)T(0.017)QS(0.444)T(0.556)PQK 156.11 2.69E-05 20197000 6679.4 6761.3 6396.6 4458.3 3890.4 3231 2419.6 2933.2 7560.9 6411.6 TRUE FALSE FALSE 6597.988904 6856.485759 6507.93014 4973.789623 3691.858371 3024.549528 2625.120764 3018.067514 6884.634167 6245.025708 1.056519094 1.097911535 1.042098215 0.796440216 0.591167842 0.484313383 0.420353876 0.483275435 1.102418867 1 12.6084918 -8.859364678 1.733919114 1.036162299 0.458651972 0.978028928 0.040097761 0.035961538 0.218725074 0.006402583 0.0140229 1.38E-09 8.859364678 -0.577510327 down IGEGTYGVVYK ddPTM_HeLa_Romidepsin_16h_R1 1 IGEGTYGVVYK 11 0 A0A087WZZ9;A0A024QZP7;P06493-2;P06493;E5RIU6;G3V317;K7ELV5;E7ESI2;P24941-2;G3V5T9;P24941;Q00526 A0A087WZZ9;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 0 0 147.75 0.024631 39326000 2819.5 2193.2 2540.4 1618.9 1092.7 1125.6 1071.1 843.48 2456.8 2359.8 FALSE FALSE TRUE 2785.13485 2224.075927 2584.614596 1806.084835 1036.935442 1053.677793 1162.079207 867.884763 2237.057655 2298.492056 1.211722635 0.967623935 1.124482719 0.785769449 0.451137275 0.458421333 0.505583304 0.377588759 0.973271867 1 11.16647196 -8.982900818 2.414906291 1.09317091 0.447133742 0.924214314 0.081410903 0.057156563 0.670452742 0.014064699 0.026887037 1.04E-09 8.982900818 -0.646037169 down IGEHMEEHGIK ddPTM_HeLa_Romidepsin_16h_R1 1 IGEHMEEHGIK 11 0 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 0 69.346 0.024403 8642300 5877.5 5203 5189.5 5713 5393.2 5202.1 3914.1 4380.8 5279.5 4312.3 FALSE FALSE TRUE 5805.862769 5276.247971 5279.821071 6373.56394 5117.964879 4869.702599 4246.563556 4507.551536 4807.288297 4200.265824 1.382260793 1.256170012 1.257020696 1.517419184 1.218485947 1.159379621 1.011022572 1.073158634 1.144520013 1 12.03626492 -7.94007945 3.591856189 1.223562035 1.04285169 0.273620533 0.131265783 0.341010281 8.92768561 0.024848946 0.082394435 1.15E-08 7.94007945 -0.180710345 IGEHTPSALAIMENANVLAR ddPTM_HeLa_Romidepsin_16h_R1 1 IGEHTPSALAIMENANVLAR 20 0 H3BQN4;J3KPS3;P04075;P04075-2;H3BR04;H3BPS8;H3BU78 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 75.608 0.026236 17966000 1970.9 2038.9 2087.8 1794.2 2881.2 2258.7 2091.4 2285 2657.8 2009.8 FALSE FALSE TRUE 1946.877913 2067.603688 2124.137283 2001.653846 2734.161613 2114.37636 2269.043464 2351.11287 2420.079711 1957.585106 0.994530407 1.056201174 1.085080427 1.022511787 1.396701274 1.080094221 1.159103355 1.201027154 1.236257726 1 10.93485931 -8.953216184 24.99981627 1.010634348 1.198074619 0.213045344 0.106675343 64.53175138 34483.48794 0.01112044 0.020157507 1.11E-09 8.953216184 0.187440271 IGEK(ac)SLFTK ddPTM_HeLa_Romidepsin_16h_R1 1 IGEKSLFTK 9 1 F5H226;A0A3F2YNY7;P08397-3;P08397;A0A3B3IU56;F5GY90;A0A1W2PNU5;A0A3B3IU34;F5H0P4;F5H345;A0A3B3IRR1;P08397-4;P08397-2 F5H226 HMBS Porphobilinogen deaminase 0 1 IGEK(1)SLFTK 125.68 0.0078132 1207500 709.21 845.35 877.25 448.02 809.04 662.38 881.53 743.73 895.32 599.79 FALSE TRUE FALSE 700.5658757 857.2508595 892.5181683 499.8221804 767.7516699 620.0560557 956.4071362 765.2486541 815.2403368 584.2073693 1.199173294 1.467374266 1.527742057 0.855556103 1.314176627 1.061362948 1.637102143 1.309892162 1.395463973 1 9.190336747 -11.27644178 0.93069589 1.028457609 1.300793646 0 0.243350191 0.55256077 1.005850692 0.070380778 0.045747377 5.29E-12 11.27644178 0.272336037 IGELGAPEVWGLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 IGELGAPEVWGLSPK 15 0 A0A494C050;Q8N5F7 A0A494C050 NKAP NF-kappa-B-activating protein 1 0 IGELGAPEVWGLS(1)PK;IGELGAPEVWGLS(1)PK ; 137.91 0.0010566 742140000 15800.9 14871.9 14602 11633.8 18212.3 20968 20643 23965 15594.3 14561.6 TRUE FALSE FALSE 15608.31255 15081.267 14856.14168 12978.95469 17282.85837 19628.21247 22396.4159 24658.38946 14199.50675 14183.28753 1.100472124 1.063312505 1.047439929 0.915087892 1.21853684 1.38389724 1.57907085 1.738552462 1.001143544 1 13.79190435 -7.992193973 1.343209668 1.041530115 1.735310688 0.944988711 0.061173154 0.088718428 0.271364185 0.009896008 0.057766671 1.02E-08 7.992193973 0.693780573 IGEVSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 IGEVSSPK 8 0 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 0 IGEVS(0.081)S(0.919)PK;IGEVS(0.087)S(0.913)PK ; 107.21 0.024955 120216000 18252.1 17941.1 19040.3 12840 19604.6 20123.6 17605.5 14593.4 19815.9 18197.2 TRUE FALSE FALSE 18029.63638 18193.67528 19371.68843 14324.62121 18604.10411 18837.76691 19100.91073 15015.637 18043.51627 17724.43412 1.017219295 1.026474253 1.09293692 0.808184968 1.049630357 1.062813446 1.077659834 0.847171588 1.018002389 1 14.11345195 IGFAEK(ac)VAAK ddPTM_HeLa_Romidepsin_16h_R1 1 IGFAEKVAAK 10 1 P07954-2;P07954 P07954-2 FH "Fumarate hydratase, mitochondrial" 0 1 IGFAEK(1)VAAK 127.76 0.011444 583950 200.93 269.53 431.8 319.44 468.71 410.63 321.19 215.97 151.05 236.86 FALSE TRUE FALSE 198.4809879 273.3244504 439.3152979 356.3751558 444.7899797 384.3920682 348.4718706 222.2187512 137.5397097 230.7063431 0.860318729 1.184728806 1.904218549 1.544713297 1.927948637 1.666153011 1.510456392 0.96321041 0.596167872 1 7.84991386 -9.963820939 5.622820693 0.937645376 1.599119538 0.605983717 0.273651836 0.092072665 7.64991721 0.040780295 0.0533908 1.09E-10 9.963820939 0.661474162 IGFPSTS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 IGFPSTSPAK 10 0 Q9UDT6-2;Q9UDT6 Q9UDT6-2 CLIP2 CAP-Gly domain-containing linker protein 2 1 0 IGFPS(0.003)T(0.127)S(0.87)PAK 117.25 0.013547 36818000 3512.8 2621.2 7429.7 5872.4 10182 16089 12038 8637.5 3959.9 2539.2 TRUE FALSE FALSE 3469.984642 2658.101322 7559.010812 6551.394518 9662.374546 15060.96482 13060.50742 8887.412435 3605.716626 2473.231218 1.403016676 1.074748411 3.056330018 2.648921165 3.906781734 6.089590296 5.28074663 3.593441798 1.457897102 1 11.27218141 -9.096070617 1.031687019 1.166590207 5.036118795 0.806762686 0.744181721 0.142793023 0.299483385 0.125882848 0.295393333 8.02E-10 9.096070617 3.869528588 IGHPAPNFK ddPTM_HeLa_Romidepsin_16h_R1 2 IGHPAPNFK 9 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 0 ; ; 98.523 0.0061987 51732460 12650.2 11481.6 12455 12492 13373.1 14588.8 12207.7 12428.1 11703.4 10198.7 FALSE FALSE TRUE 12496.0145 11643.23827 12671.77405 13936.38382 12690.62081 13656.62276 13244.62173 12787.68747 10656.61859 9933.736304 1.257937005 1.172090532 1.275630202 1.402934746 1.27752745 1.374772024 1.333297093 1.287298865 1.072770433 1 13.27812073 -12.49166891 0.280647869 0.821089889 1.354724057 0.793803092 0.055342144 1.383564793 0.132012596 0.24841949 0.034611639 3.22E-13 12.49166891 0.533634168 IGIEIIK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 IGIEIIKR 8 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 ; IGIEIIK(1)R;IGIEIIK(1)R 114.5 0.0018919 4736200 665.2 818.76 829.94 630.78 1602.76 1449.2 1287.5 1347.87 1564.41 1264.58 FALSE TRUE FALSE 657.0922865 830.2865248 844.3847576 703.7137515 1520.965176 1356.600797 1396.860218 1386.868492 1424.485251 1231.726029 0.533472762 0.674083769 0.685529686 0.571323277 1.234824255 1.101381935 1.134067304 1.125955333 1.156495209 1 10.26646568 -8.754087953 24.99925719 0.744894442 1.144581172 0.509218736 0.181197712 107.0264967 363951.1128 0.0276075 0.054334522 1.76E-09 8.754087953 0.39968673 IGK(ac)TLPSEK ddPTM_HeLa_Romidepsin_16h_R1 1 IGKTLPSEK 9 1 Q14966-3;Q14966;Q14966-5;A0A096LNS4 Q14966-3 ZNF638 Zinc finger protein 638 0 1 IGK(1)TLPSEK 119.68 0.0061276 1443200 1196.7 1595 1107.7 1353 1210 947.44 1350.4 1128.6 1907.2 1432.8 FALSE TRUE FALSE 1182.11416 1617.454452 1126.979054 1509.440226 1148.249185 886.9016417 1465.102942 1161.25426 1736.615255 1395.575649 0.847044129 1.158987299 0.807537058 1.081589684 0.822778174 0.635509542 1.049819795 0.832096964 1.244371995 1 10.44664461 IGLPHSIK(ac)LSR ddPTM_HeLa_Romidepsin_16h_R1 1 IGLPHSIKLSR 11 1 Q14498-2;Q14498;G3XAC6;Q5QP22 Q14498-2 RBM39 RNA-binding protein 39 0 1 IGLPHSIK(1)LSR 144.17 1.17E-14 0 468.41 452.57 905.68 605.05 764.35 563.44 647.67 291.72 784.29 444.2 FALSE TRUE FALSE 462.7008388 458.9412923 921.4429805 675.0087278 725.3423673 527.4380024 702.6830736 300.1604579 714.1411381 432.65962 1.06943384 1.060744454 2.129718 1.560138032 1.676473454 1.219059922 1.624101352 0.693756579 1.650584213 1 8.75708867 -9.95111747 24.99999772 1.034486723 1.49916612 0.058056531 0.394650569 100.6039847 51451.67493 0.052255748 0.068677505 1.12E-10 9.95111747 0.464679397 IGNSYFK(ac)EEK ddPTM_HeLa_Romidepsin_16h_R1 1 IGNSYFKEEK 10 1 P31948-3;P31948;P31948-2 P31948-3 STIP1 Stress-induced-phosphoprotein 1 0 1 IGNSYFK(1)EEK 101.38 0.0016563 0 439.8 260.56 291.19 408.21 1023.8 892.35 764.87 696.56 940.95 547.24 FALSE TRUE FALSE 434.4395484 264.2281705 296.2580398 455.4091609 971.5516657 835.3317149 829.8380387 716.7138646 856.7890753 533.0226259 0.815048982 0.495716613 0.555807625 0.854389924 1.822721248 1.567159956 1.556853309 1.344621841 1.607415959 1 9.058052964 -8.774621529 24.93263989 0.842503013 1.571291561 0.545288958 0.304642237 83.92781324 158740.5349 0.03180906 0.05790842 1.68E-09 8.774621529 0.728788548 IGQQVDREPGDVAT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 IGQQVDREPGDVATPPR 17 1 H3BT22;Q9Y5N6 H3BT22 ORC6 Origin recognition complex subunit 6 1 0 IGQQVDREPGDVAT(1)PPR 100.01 0.0017608 81648000 1482.4 1303.8 1221.5 1177.3 1350.7 1246.9 996.61 1080.4 1484.8 1392.2 TRUE FALSE FALSE 1464.331939 1322.154931 1242.759695 1313.424965 1281.768739 1167.227114 1081.262029 1111.659669 1351.995769 1356.030443 1.079866566 0.975018619 0.916468875 0.968580736 0.945235961 0.860767632 0.797372975 0.819789611 0.997024643 1 10.40517385 -8.442617531 0.606000716 1.035123894 0.769377951 0.786440276 0.038650507 0.428205266 0.22659354 0.009449199 0.061509341 3.61E-09 8.442617531 -0.265745942 IGQS(ph)LS(ph)S(ph)LT(ph)SPAEQGVLS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 IGQSLSSLTSPAEQGVLSEK 20 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3-5;A0A0A6YYJ5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 5 0 IGQS(0.942)LS(0.983)S(0.992)LT(0.979)S(0.131)PAEQGVLS(0.974)EK 43.326 0.027326 11679000 1525.5 1295.6 1163.3 1186.1 1245.9 1174.5 1317.5 1356.9 1427.4 1510.6 TRUE FALSE FALSE 1506.906619 1313.839491 1183.546749 1323.242463 1182.317074 1099.453241 1429.408417 1396.159761 1299.729769 1471.354394 1.024162924 0.89294564 0.80439271 0.899336331 0.803556967 0.747238901 0.971491588 0.948894275 0.883356025 1 10.52292906 -10.17703189 4.331991691 1.011460264 0.860562185 0.228512091 0.076047883 0.13164241 4.514774535 0.011075787 0.013583113 6.65E-11 10.17703189 -0.150898079 IGS(ph)DPLAYEPK ddPTM_HeLa_Romidepsin_16h_R1 2 IGSDPLAYEPK 11 0 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 0 IGS(1)DPLAYEPK;IGS(1)DPLAYEPK ; 110.15 0.014501 14903900 2679.2 3986.5 3546 2074.2 6535.3 12809.7 7383.1 14753 3546.3 3492 TRUE FALSE FALSE 2646.54488 4042.622052 3607.716643 2314.028763 6201.779254 11991.20151 8010.22033 15179.85478 3229.110046 3401.277337 0.778103229 1.188559959 1.060694641 0.6803411 1.823367706 3.525499489 2.355062389 4.462986483 0.949381578 1 11.73186093 -8.432896726 2.812771979 0.917883907 3.362272956 0.831855934 0.501478789 0.071338286 1.091498932 0.065283472 0.159683467 3.69E-09 8.432896726 2.44438905 IGTLHTS(ph)PDLK ddPTM_HeLa_Romidepsin_16h_R1 1 IGTLHTSPDLK 11 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 0 IGTLHT(0.026)S(0.974)PDLK 74.987 0.028429 25936000 6881 6437.4 5853.7 5721.8 6475.4 6715.9 5186.3 6204.7 6843.9 6359.5 TRUE FALSE FALSE 6797.131725 6528.025886 5955.581193 6383.381438 6144.936175 6286.775665 5626.824193 6384.223205 6231.764443 6194.279273 1.097324067 1.053879814 0.961464753 1.030528518 0.992034086 1.014932551 0.908390459 1.030664412 1.006051579 1 12.59672071 -9.774864781 24.92961124 1.047836822 0.989087725 0.238846464 0.042329127 230.7595423 428495.769 0.007684561 0.010131943 1.68E-10 9.774864781 -0.058749097 IGVAKPLPLS(ph)PEEGYVSAK ddPTM_HeLa_Romidepsin_16h_R1 1 IGVAKPLPLSPEEGYVSAK 19 1 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 IGVAKPLPLS(0.999)PEEGY(0.001)VSAK 96.708 0.0007817 8458900 1117.8 1068.3 899.83 859.68 1469.9 1407.2 1504.5 1504 962.51 845.91 TRUE FALSE FALSE 1104.175824 1083.339555 915.4911637 959.0802465 1394.885518 1317.284462 1632.292192 1547.515867 876.4206949 823.9331363 1.340127949 1.314839163 1.111123128 1.164026793 1.692959606 1.598775924 1.981097884 1.878205644 1.063703663 1 9.686383454 -4 0.231983645 1.055438517 6.709087751 0.800867649 0.148851108 16.55116986 0.201918671 0.107577884 36.0082549 1.00E-04 4 5.653649234 IHEDIFDIIDR ddPTM_HeLa_Romidepsin_16h_R1 2 IHEDIFDIIDR 11 0 K7EKE5;K7EIS0;Q9NRH3;P23258 K7EKE5 TUBG1;TUBG2 Tubulin gamma chain;Tubulin gamma-2 chain;Tubulin gamma-1 chain 0 0 ; ; 95.401 0.012015 10637700 5695.4 5552.5 6244.1 4484.6 6376.3 6570.5 5530.2 5635.7 5934.6 5486.9 FALSE FALSE TRUE 5625.982274 5630.668241 6352.775941 5003.130553 6050.893618 6150.666255 5999.93505 5798.760088 5403.794513 5344.349547 1.052697288 1.053574096 1.188690202 0.936153316 1.132203941 1.150872749 1.122668904 1.085026351 1.011122956 1 12.38379865 -10.56630758 0.235232774 0.973806078 1.138723287 0.258069371 0.063435997 2.015543139 0.444998075 0.13184258 0.113804646 2.71E-11 10.56630758 0.164917209 IHFPLATYAPVISAEK ddPTM_HeLa_Romidepsin_16h_R1 3 IHFPLATYAPVISAEK 16 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;Q6PEY2;C9JDS9;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA3E;TUBA4A;TUBA1A Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 ;; ;; 132.08 0.00084949 31977000 8440.1 7921.3 8327.4 7866.3 8980.8 8868.5 7428.9 8950.4 9507.2 7904.9 FALSE FALSE TRUE 8337.228815 8032.816269 8472.334904 8775.838618 8522.476264 8301.831472 8059.910581 9209.365703 8656.852221 7699.529558 1.082823145 1.043286633 1.100370463 1.139788938 1.106882726 1.078225807 1.04680559 1.196094597 1.124335215 1 12.91055458 -16.52287875 0.135974371 0.640175168 1.140003724 0 0.055425994 45.59910841 0.434758123 4.386744163 0.121495596 3.00E-17 16.52287875 0.499828555 IHFS(ph)PSEPK ddPTM_HeLa_Romidepsin_16h_R1 2 IHFSPSEPK 9 0 Q8IZT6;Q8IZT6-2 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 0 IHFS(0.998)PS(0.002)EPK;IHFS(1)PSEPK ; 107.06 0.00077881 0 10327.8 10638 11594.5 8932.8 9698.8 11101.4 7734.6 8230.4 11523.8 11227.1 TRUE FALSE FALSE 10201.9208 10787.76204 11796.29741 9965.652366 9203.834045 10392.05637 8391.576731 8468.533639 10493.08247 10935.41832 0.932924603 0.986497427 1.078723928 0.911318806 0.841653586 0.950311736 0.767375923 0.774413323 0.959550166 1 13.41672079 -7.781771939 0.75761105 0.975347101 0.706503554 0.638767613 0.056817666 0.745505871 0.46355818 0.00991122 0.145426731 1.65E-08 7.781771939 -0.268843547 IHGVGFK ddPTM_HeLa_Romidepsin_16h_R1 2 IHGVGFK 7 0 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 0 ; ; 82.263 0.02703 21468400 19018.7 18628.7 19170.1 16498.6 19192.5 21143.7 17288.3 15082.5 19862.8 17187.7 FALSE FALSE TRUE 18786.89277 18890.95533 19503.74755 18406.24576 18213.03511 19792.68581 18756.76777 15518.88834 18086.22142 16741.16108 1.122197719 1.128413689 1.165017615 1.099460526 1.087919471 1.182276768 1.120398262 0.926989966 1.080344508 1 14.03111197 -12.20068563 0.921481961 0.99941156 1.10948608 0.07170186 0.069758637 0.594483591 0.900744671 0.043642761 0.012020653 6.30E-13 12.20068563 0.11007452 IHGVGFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 IHGVGFKK 8 1 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2;B8ZZK4 H7C2W9 RPL31 60S ribosomal protein L31 0 1 ; IHGVGFK(1)K;IHGVGFK(1)K 104.75 0.0021681 4537500 4384.9 4397.5 6005.8 3970.8 5742.2 5707.4 7948.4 4401.9 6648.9 3532 FALSE TRUE FALSE 4331.455152 4459.40812 6110.32843 4429.922579 5449.154107 5342.71556 8623.536898 4529.262031 6054.205732 3440.238131 1.259056783 1.296249838 1.776135313 1.287679053 1.583946779 1.553007483 2.5066686 1.316554802 1.759821705 1 11.74829272 -9.335180844 0.314487335 0.979209107 2.021063 0.022480489 0.393470693 1.350140957 0.27759087 0.192921832 0.521818924 4.62E-10 9.335180844 1.041853893 IHIVMK ddPTM_HeLa_Romidepsin_16h_R1 1 IHIVMK 6 0 B8ZZF8;Q9Y4Y9 B8ZZF8 LSM5 U6 snRNA-associated Sm-like protein LSm5 0 0 61.325 0.022339 1622600 2870.7 2675 3673 3169.5 3225.8 3010.8 2823.8 2011.2 3270.4 2169.2 FALSE FALSE TRUE 2835.710804 2712.65872 3736.927024 3535.972503 3061.175389 2818.419597 3063.653502 2069.390899 2977.887233 2112.843871 1.342129839 1.283889812 1.768671635 1.673560716 1.448841266 1.333945984 1.450014146 0.979433893 1.409421337 1 11.04497045 -11.56905454 0.740949177 1.018681245 1.4340268 0.014215473 0.23583121 0.504472603 0.564561383 0.10540239 0.047203783 2.70E-12 11.56905454 0.415345555 IHLGS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 IHLGSSPK 8 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 0 IHLGS(0.509)S(0.491)PK 77.533 0.02718 66049000 8300.1 7694.8 7516.3 6409.3 7925.6 7806.4 7436.4 5276.9 10120 9309.2 TRUE FALSE FALSE 8198.935189 7803.127596 7647.118049 7150.373423 7521.127058 7307.596234 8068.04763 5429.578776 9214.841854 9067.345642 0.904226607 0.860574627 0.84336898 0.788585073 0.829473956 0.805924525 0.889791561 0.598805758 1.016266746 1 13.14646457 -4.165667384 0.080148664 1.175318052 1.45E-12 0.687983532 0.062181651 72.49630244 0.441232566 1.029589502 9.506739413 6.83E-05 4.165667384 -1.175318052 IHMS(ph)GPK ddPTM_HeLa_Romidepsin_16h_R1 1 IHMSGPK 7 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IHMS(1)GPK 65.465 0.028936 4583700 6664.1 6283.7 6876.9 6266.1 5482.6 5244.9 4072.2 3851.6 6434.9 6058.3 TRUE FALSE FALSE 6582.875386 6372.162094 6996.58956 6990.615965 5202.802464 4909.767817 4418.092566 3963.039969 5859.346427 5900.904493 1.11557057 1.079861927 1.185680868 1.184668549 0.881695759 0.832036482 0.748714468 0.671598731 0.99295734 1 12.52672039 -8.37747061 2.051395909 1.076113581 0.730064156 0.811664329 0.074173855 0.115318053 0.937244102 0.012041701 0.033955724 4.19E-09 8.37747061 -0.346049425 IHPMAYQLQLQAASNFKS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 IHPMAYQLQLQAASNFKSPVK 21 1 Q5SRQ6;P67870 Q5SRQ6 CSNK2B Casein kinase II subunit beta 1 0 IHPMAYQLQLQAAS(0.08)NFKS(0.92)PVK 46.878 0.026339 142240000 8181 7622.2 7151.6 1723.8 5999.3 5347.3 4676 4491 8512.2 6757.4 TRUE FALSE FALSE 8081.286825 7729.505532 7276.070598 1923.113867 5693.133335 5005.624788 5073.179323 4620.939999 7750.847513 6581.841774 1.227815421 1.174368178 1.105476377 0.292184761 0.864975721 0.760520377 0.770784151 0.702074003 1.177610733 1 12.68427563 -9.431320972 17.01521263 1.116752837 0.698224144 0.689979389 0.153239686 1.948669098 361.0188573 0.024142808 0.036878733 3.70E-10 9.431320972 -0.418528693 IHQDSES(ph)GDELSSSSTEQIR ddPTM_HeLa_Romidepsin_16h_R1 3 IHQDSESGDELSSSSTEQIR 20 0 Q1RLN5;Q8IWW6-3;Q8IWW6-2;Q8IWW6-4;Q8IWW6 Q1RLN5 ARHGAP12 Rho GTPase-activating protein 12 1 0 IHQDS(0.001)ES(0.999)GDELSSSSTEQIR;IHQDS(0.081)ES(0.919)GDELSSSSTEQIR;IHQDSES(1)GDELSSSSTEQIR ;; 251.38 7.91E-67 41697600 5091.91 4713.91 4063.53 4931.88 7657.9 9473.2 7904.2 9252.6 6436.4 5253.73 TRUE FALSE FALSE 5029.847842 4780.272549 4134.254035 5502.127171 7267.088787 8867.893093 8575.582551 9520.309383 5860.712264 5117.237337 0.982922525 0.934151034 0.807907424 1.07521438 1.420119551 1.732945437 1.675822712 1.860439287 1.145288342 1 12.32114943 -8.578774185 2.041897889 0.972142041 1.75872375 0.938133195 0.089157684 0.043901729 0.36615825 0.011074136 0.027191746 2.64E-09 8.578774185 0.786581709 IHRAS(ph)DPGLPAEEPK ddPTM_HeLa_Romidepsin_16h_R1 1 IHRASDPGLPAEEPK 15 1 P27708;F8VPD4 P27708 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 0 IHRAS(1)DPGLPAEEPK 67.168 0.020933 23110000 2449.2 2406.9 2240 1706.5 2151.2 2190.7 1507.1 2138.3 2668.2 2084.4 TRUE FALSE FALSE 2419.348208 2440.784401 2278.98626 1903.813559 2041.416237 2050.72134 1635.113036 2200.168337 2429.549509 2030.246988 1.19165216 1.202210577 1.122516755 0.9377251 1.005501424 1.010084661 0.805376413 1.083694915 1.19667682 1 10.98743953 -9.263587372 24.86040186 1.105139353 0.963783889 0.459823755 0.089820607 163.924393 1897230.985 0.015415775 0.024264681 5.45E-10 9.263587372 -0.141355464 IHS(ph)PIIR ddPTM_HeLa_Romidepsin_16h_R1 4 IHSPIIR 7 0 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 0 IHS(1)PIIR;IHS(1)PIIR;IHS(1)PIIR;IHS(1)PIIR ;;; 86.67 0.020824 107662000 10317.64 6514.14 7074.07 4903.65 8235.6 7345.9 8739.8 8255.47 9014.05 8563.24 TRUE FALSE FALSE 10191.88464 6605.846234 7197.191221 5470.633085 7815.306601 6876.520698 9482.158394 8494.328999 8207.810792 8340.76579 1.221936318 0.791995172 0.862893336 0.655890984 0.937001086 0.824447164 1.136845061 1.018411164 0.984059617 1 13.02596413 -10.2581066 24.99205996 1.104803261 0.888443444 0.251751165 0.137246856 261.5798564 1961555.254 0.025136797 0.030103629 5.52E-11 10.2581066 -0.216359817 IHVFYIDYGNR ddPTM_HeLa_Romidepsin_16h_R1 2 IHVFYIDYGNR 11 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 0 ; ; 108.47 0.0071464 27039000 7634.1 6062.3 9012 7643.5 10559.3 10508 9047 7406.1 7540.2 4335 FALSE FALSE TRUE 7541.052653 6147.645219 9168.85008 8527.277434 10020.41952 9836.572713 9815.451954 7620.383819 6865.785627 4222.376075 1.785973707 1.455968182 2.171490629 2.01954475 2.373170779 2.329629701 2.324627598 1.804761983 1.626047871 1 12.04383937 -11.34866904 0.317151176 0.782659436 2.301708961 0.520703508 0.292077238 0.647052544 0.148904482 0.384192737 0.156818593 4.48E-12 11.34866904 1.519049526 IIAPPERK ddPTM_HeLa_Romidepsin_16h_R1 1 IIAPPERK 8 1 P60709;P63267-2;A0A2R8YFE2;Q562R1;P63261;P63267;P68133;P68032;P62736;A6NL76 P60709;P63261;P63267 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 0 96.492 0.022362 68170000 3882.4 4069 3358.9 4523 4011.5 4390.3 3973.4 3939.8 4283.4 3837.8 FALSE FALSE TRUE 3835.079815 4126.283489 3417.360246 5045.970541 3806.778186 4109.773999 4310.900497 4053.791897 3900.281976 3738.093403 1.025945423 1.10384708 0.914198731 1.349878132 1.018374282 1.099430527 1.153235094 1.084454416 1.043388047 1 11.8680869 IIAPS(ph)RGSPLPVLSWANR ddPTM_HeLa_Romidepsin_16h_R1 1 IIAPSRGSPLPVLSWANR 18 1 I3L1Q9;I3L413;C9J2U0;P24864-2;P24864-3;P24864 I3L1Q9 CCNE1 G1/S-specific cyclin-E1 1 0 IIAPS(0.789)RGS(0.21)PLPVLS(0.002)WANR 93.551 0.0017774 8516400 1855.9 1793.8 2026.6 1707.6 1048.7 1091.5 1073.8 1091.8 1985.1 1294.5 TRUE FALSE FALSE 1833.279577 1819.053163 2061.872123 1905.040746 995.1809258 1021.756673 1165.008545 1123.38951 1807.547684 1260.868703 1.453981348 1.442698323 1.635279008 1.510895418 0.789281963 0.810359294 0.923972926 0.890964703 1.433573281 1 10.30020234 -8.748754541 24.99593854 1.292005416 0.855576254 0.665991821 0.182310985 171.8880282 338709.6569 0.035751307 0.071124622 1.78E-09 8.748754541 -0.436429163 IIDDSEITKEDDALWPPPDR ddPTM_HeLa_Romidepsin_16h_R1 2 IIDDSEITKEDDALWPPPDR 20 1 F5H6N1;P61326;Q96A72;F5H3U9;F5H6P7 F5H6N1 MAGOHB;MAGOH Protein mago nashi homolog;Protein mago nashi homolog 2 0 0 ; ; 93.152 0.0015395 9757900 1656.15 1480.58 1342.8 1249.71 1684.63 1587.35 1357.38 1568.95 1820.93 1671.62 FALSE FALSE TRUE 1635.964207 1501.423644 1366.170871 1394.20735 1598.657045 1485.923458 1472.675823 1614.345093 1658.06146 1628.191071 1.004774093 0.922142168 0.839072818 0.856292222 0.981860835 0.912622286 0.904485873 0.991496097 1.018345751 1 10.6690543 -10.2352235 5.617313802 1.002349774 0.911860655 0.470287005 0.044726058 0.120112767 12.15920792 0.007497006 0.009051017 5.82E-11 10.2352235 -0.090489119 IIEDGDGAGAET(ph)PVIENR ddPTM_HeLa_Romidepsin_16h_R1 2 IIEDGDGAGAETPVIENR 18 0 A0A5H1ZRS1;Q15154-5 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 IIEDGDGAGAET(1)PVIENR;IIEDGDGAGAET(1)PVIENR ; 175.7 6.11E-08 38232000 5060.8 5705.8 5479 6184.1 6186.8 5660.1 4042.2 4926.1 4859.6 4861.2 TRUE FALSE FALSE 4999.117023 5786.126402 5574.359697 6899.134739 5871.06451 5298.437877 4385.544367 5068.628931 4424.945205 4734.905323 1.055800841 1.222015227 1.177290635 1.457079766 1.23995394 1.119016647 0.926215852 1.07048158 0.934537209 1 12.20911986 -10.41279494 4.043280803 1.023547194 1.17497358 0.272021116 0.130690918 0.287225026 7.897595989 0.024668421 0.027832213 3.87E-11 10.41279494 0.151426386 IIEGLQDLDDDVR ddPTM_HeLa_Romidepsin_16h_R1 1 IIEGLQDLDDDVR 13 0 A0A0A0MTH9;O14981 A0A0A0MTH9 BTAF1 TATA-binding protein-associated factor 172 0 0 114.87 0.002044 0 537.17 298.72 422.33 213.84 505.88 540.71 386.92 509.01 623.76 399.89 FALSE FALSE TRUE 530.6227654 302.925388 429.6804765 238.5651869 480.0630559 506.1603761 419.7849751 523.7374013 567.9693434 389.5008002 1.362314956 0.777727255 1.103156852 0.612489594 1.232508523 1.299510491 1.077751252 1.344637549 1.458198143 1 8.605482482 -7.538260373 0.005482915 0.005315941 2.287611816 0 0.258181293 163167.8191 154.8286093 31087.36442 33391.76021 2.90E-08 7.538260373 2.282295875 IIEQLS(ph)PQAATSR ddPTM_HeLa_Romidepsin_16h_R1 1 IIEQLSPQAATSR 13 0 Q03468;P0DP91;D6R9X7 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 0 IIEQLS(1)PQAATSR 148.18 0.00076819 8489700 1306.2 1050.1 1121 1132.5 1336.9 1315.2 1130.2 1198 1285.1 1119.6 TRUE FALSE FALSE 1290.279532 1064.883335 1140.510535 1263.444979 1268.673004 1231.162965 1226.19916 1232.66224 1170.157437 1090.512631 1.183186234 0.976497938 1.045848074 1.15857895 1.163373049 1.128976346 1.124424537 1.130351181 1.073034282 1 10.09079076 -9.254665528 24.56446653 1.075929277 1.140771452 0.355177026 0.054232859 649.5897282 2355646.347 0.011487512 0.018769129 5.56E-10 9.254665528 0.064842176 IIESDQER ddPTM_HeLa_Romidepsin_16h_R1 1 IIESDQER 8 0 Q7Z6W7 Q7Z6W7 DNAJB7 DnaJ homolog subfamily B member 7 0 0 108.09 0.0025987 0 1504.3 1337.7 1393.3 1194.2 1580.4 1638.1 1422.6 1317.1 1246.6 1508.3 FALSE FALSE TRUE 1485.965013 1356.532176 1417.549802 1332.279023 1499.746291 1533.430697 1543.435608 1355.20821 1135.100974 1469.114149 1.011470085 0.923367444 0.964901062 0.906858752 1.020850757 1.043779136 1.050589302 0.922466244 0.772643143 1 10.52073078 -5.712431061 24.09200301 0.99398822 0.989043851 0 0.086185908 0 0 0.006628426 0 1.94E-06 5.712431061 -0.004944369 IIFVVGGPGSGK ddPTM_HeLa_Romidepsin_16h_R1 1 IIFVVGGPGSGK 12 0 Q5T9B7;P00568 Q5T9B7 AK1 Adenylate kinase isoenzyme 1 0 0 161.17 0.0030313 3156700 828.82 683.07 970.33 828.09 725.65 805.77 836.97 763 510.46 612.57 FALSE FALSE TRUE 818.718023 692.6862774 987.2181866 923.8376621 688.6173727 754.2838975 908.0622109 785.0762012 464.8031791 596.6553431 1.372179153 1.160948754 1.654587021 1.548360662 1.154129232 1.264186949 1.521920857 1.315795141 0.779014526 1 9.220753992 -12.15025871 0.59590762 0.953352435 1.386172896 0.542326091 0.171174142 0.792447695 0.432442177 0.18505233 0.036758036 7.08E-13 12.15025871 0.432820461 IIGEDS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 3 IIGEDSPSR 9 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;C9JQE8 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 IIGEDS(0.984)PS(0.016)R;IIGEDS(0.997)PS(0.003)R;IIGEDS(0.763)PS(0.237)R ;; 149.94 0.0053063 57048200 11261.8 11786.4 11971.6 8704.2 8595.2 7037.9 6170.65 6324.8 12109.9 11470.7 TRUE FALSE FALSE 11124.53685 11952.32925 12179.96068 9710.620558 8156.554871 6588.200904 6694.784857 6507.798109 11026.76021 11172.68956 0.995690142 1.069780842 1.090154757 0.869139029 0.73004399 0.589670094 0.59920978 0.582473725 0.986938745 1 13.4476889 -8.739685597 1.922027739 1.010408324 0.591915827 0.959231656 0.039640164 0.047582384 0.357353538 0.006409509 0.014556415 1.82E-09 8.739685597 -0.418492497 IIGEDSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 IIGEDSPSR 9 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;C9JQE8 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 IIGEDS(0.188)PS(0.812)R 105.25 0.023561 4752000 1761.2 2023 1852.9 1489.8 1463.4 1223.2 1121.8 1377.7 2163.2 2279.6 TRUE FALSE FALSE 1739.733817 2051.479847 1885.148947 1662.057686 1388.717237 1145.041468 1217.085664 1417.561576 1969.717974 2220.375663 0.783531294 0.923933675 0.849022523 0.748547966 0.625442469 0.51569718 0.54814403 0.638433216 0.887110234 1 11.11658807 -8.966140907 1.55643724 0.897473548 0.562464477 0.862147005 0.058239785 0.138588748 0.670587383 0.013592741 0.029031307 1.08E-09 8.966140907 -0.335009071 IIGS(ph)PETK ddPTM_HeLa_Romidepsin_16h_R1 1 IIGSPETK 8 0 E9PMS6;H0YDG6 E9PMS6 LMO7 1 0 IIGS(0.994)PET(0.006)K 101.66 0.029592 26389000 6032.6 6137 6429.9 6558.8 6839.8 6864.8 6694.2 6144.2 6193.7 6239.8 TRUE FALSE FALSE 5959.072351 6223.396847 6541.809712 7317.159316 6490.739483 6426.161435 7262.805181 6321.972733 5639.71996 6077.689096 0.980483249 1.023974203 1.076364652 1.203937747 1.06796175 1.057336322 1.194994523 1.040193507 0.927938213 1 12.56930716 -9.768669037 2.854054682 0.991374646 1.113639714 0.557580947 0.054954641 0.136142106 2.286060762 0.007797172 0.010906879 1.70E-10 9.768669037 0.122265068 IIIHLK ddPTM_HeLa_Romidepsin_16h_R1 2 IIIHLK 6 0 I3L0K7;Q12931-2;Q12931;I3L2D5;I3L239 I3L0K7 TRAP1 "Heat shock protein 75 kDa, mitochondrial" 0 0 ; ; 87.758 0.013864 7297000 12053.3 10555.2 13350.5 12859.8 11793.1 12773.3 12356.3 12270.2 11859.9 11688.9 FALSE FALSE TRUE 11906.38974 10703.79638 13582.85985 14346.71058 11191.2541 11957.12735 13405.84381 12625.21888 10799.12084 11385.22069 1.045775929 0.940148344 1.193025609 1.260117039 0.9829633 1.050232374 1.17747773 1.108912969 0.948520993 1 13.47487464 -9.758383596 24.99999901 1.016110295 1.126771701 0.423482357 0.079421582 72.67742966 594586.1946 0.012420859 0.017131345 1.74E-10 9.758383596 0.110661406 IILDLISES(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 1 IILDLISESPIK 12 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 IILDLISES(1)PIK 175.6 1.91E-05 13254000 6071.3 6021.3 5906.8 3507.4 5568.6 6092.7 5087.6 5778.3 5996 5834.7 TRUE FALSE FALSE 5997.30066 6106.068019 6009.605376 3912.942091 5284.413563 5703.396133 5519.740617 5945.485994 5459.702743 5683.113653 1.055284308 1.074423 1.057449445 0.688520823 0.92984478 1.003568903 0.9712529 1.046167006 0.960688643 1 12.47246585 IILDLISES(ph)PIKGR ddPTM_HeLa_Romidepsin_16h_R1 1 IILDLISESPIKGR 14 1 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 IILDLIS(0.009)ES(0.991)PIKGR 75.91 0.016277 163400000 1234.3 1111 1170.3 1326 1450.3 1235.4 1317.3 1390.8 1714.3 1459.8 TRUE FALSE FALSE 1219.255877 1126.640687 1190.668581 1479.318359 1376.285779 1156.461927 1429.191429 1431.040604 1560.968714 1421.874186 0.85749913 0.792363135 0.837393767 1.040400321 0.967937806 0.813336327 1.005146196 1.006446715 1.09782478 1 10.4735781 -9.265538211 24.9972961 0.911741324 0.960345688 0.056427342 0.098665143 902.8188617 5505958.542 0.014514434 0.022689462 5.43E-10 9.265538211 0.048604364 IILDLISESPIKGR ddPTM_HeLa_Romidepsin_16h_R1 2 IILDLISESPIKGR 14 1 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 ; ; 143.76 0.00070449 12912000 2463.39 2417.77 1988.22 2755.51 2110.79 2347.39 1911.46 2290.9 2769.19 2298.76 FALSE FALSE TRUE 2433.365255 2451.80743 2022.824135 3074.115031 2003.06851 2197.399355 2073.819365 2357.183577 2521.506711 2239.037884 1.086790569 1.09502722 0.903434529 1.372962491 0.894611263 0.981403383 0.926210039 1.052766277 1.126156341 1 11.12866322 IILS(ph)PFATTTK ddPTM_HeLa_Romidepsin_16h_R1 1 IILSPFATTTK 11 0 Q9P0V3 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 0 IILS(1)PFATTTK 129.71 0.0057293 9026500 1121.9 1464.1 1380.6 1298.3 1658.4 1994.3 1774 1967 1870.8 1324.4 TRUE FALSE FALSE 1108.225851 1484.711638 1404.628764 1448.415555 1573.76566 1866.870666 1924.683516 2023.912042 1703.470962 1289.991897 0.859095203 1.150946484 1.088866346 1.122809808 1.219981043 1.447195653 1.492012097 1.568933918 1.320528421 1 10.33314629 -8.428457644 0.639458813 0.938932288 1.647127481 0.593826952 0.137730801 0.259840223 0.15558828 0.016047709 0.102811042 3.73E-09 8.428457644 0.708195193 IILWDHDLNPER ddPTM_HeLa_Romidepsin_16h_R1 2 IILWDHDLNPER 12 0 B5MBZ0;Q9HC35;Q9HC35-2 B5MBZ0 EML4 Echinoderm microtubule-associated protein-like 4 0 0 ; ; 153.95 0.00066188 16616100 4889.5 4667.4 5519.3 5961.5 6229.7 6170.8 4540.2 5064.4 5115.5 4537.1 FALSE FALSE TRUE 4829.904893 4733.10778 5615.361101 6650.79668 5911.775163 5776.505795 4925.844475 5210.930424 4657.956868 4419.225488 1.092930177 1.071026539 1.270666346 1.504968845 1.337740104 1.307130811 1.114639768 1.179150156 1.054021091 1 12.10957783 -9.76855539 4.579090916 1.045984332 1.292814164 0.571973289 0.098161665 0.113880428 5.896747481 0.017552987 0.024079525 1.70E-10 9.76855539 0.246829832 IINEPTAAAIAYGLDKK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 111.73 0.0012877 9786500 2176.7 2115.6 1758.7 2106.6 1675.8 1846.3 1483.8 1637.5 1778 2253.1 FALSE FALSE TRUE 2150.169543 2145.383472 1789.309436 2350.175004 1590.277673 1728.327389 1609.833935 1684.878479 1618.971227 2194.564137 0.979770655 0.97758978 0.815337044 1.070907413 0.724643972 0.787549272 0.7335552 0.767750849 0.737718802 1 11.09971872 -8.751692788 24.99829022 0.979589612 0.754400123 0.384253212 0.098405818 70.69584621 181321.1189 0.008566189 0.016963372 1.77E-09 8.751692788 -0.225189489 IINEPTAAAIAYGLDKR ddPTM_HeLa_Romidepsin_16h_R1 1 IINEPTAAAIAYGLDKR 17 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 164.82 5.34E-06 11243000 1251.4 1124.4 1300.2 1273.5 1489.7 1365 1525.8 1549.4 1242.3 1082.8 FALSE FALSE TRUE 1236.147455 1140.229333 1322.829436 1420.748062 1413.67505 1277.780905 1655.401414 1594.229444 1131.185577 1054.6687 1.172071813 1.081125602 1.254260637 1.347103656 1.340397274 1.211547195 1.569593763 1.51159264 1.072550628 1 10.04257417 -4 0.153168281 0.946679148 3.198898765 0.790888907 0.081531168 19.68919782 0.193654338 0.162749601 9.944315826 1.00E-04 4 2.252219617 IINEPTAAAIAYGLDR ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 161.04 0.0011757 10039000 469.3 362.89 369.08 535.24 672.69 704.26 651.23 498.57 506.52 340.12 FALSE FALSE TRUE 463.5799911 367.9987749 375.5036826 597.1269672 638.3601191 659.2600589 706.5454599 512.9953363 461.2155826 331.2836334 1.399344684 1.11082691 1.133480935 1.802464435 1.926929238 1.99001699 2.132750878 1.548507939 1.392207571 1 8.371923121 -9.200284289 4.297721632 1.181884735 1.91496422 0.777500231 0.179932136 0.080133895 3.023126336 0.02982207 0.049923812 6.31E-10 9.200284289 0.733079485 LSSGLVS(ph)PAPSFYSK ddPTM_HeLa_Romidepsin_16h_R1 2 LSSGLVSPAPSFYSK 15 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 LSS(0.001)GLVS(0.981)PAPS(0.018)FYSK;LSSGLVS(0.996)PAPS(0.003)FY(0.001)SK ; 123.63 0.0030986 60101000 5569.4 4522.4 4840.2 3679.1 2827.6 2329.35 2032.04 1766.47 5317.9 5205.7 TRUE FALSE FALSE 5501.518011 4586.066466 4924.441651 4104.494853 2683.297021 2180.512053 2204.641427 1817.580022 4842.253705 5070.455164 1.085014626 0.904468399 0.971203076 0.809492387 0.529202396 0.430042665 0.434801483 0.358464864 0.954993891 1 12.30789955 -8.856287173 1.219397402 1.033758858 0.384890086 0.961287568 0.051937749 0.053289918 0.157226598 0.008272733 0.021118244 1.39E-09 8.856287173 -0.648868772 down IIPELVGSPTQSTSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 IIPELVGSPTQSTSSR 16 0 H7C409;Q9NSI6-3;Q9NSI6-2;Q9NSI6 H7C409 BRWD1 Bromodomain and WD repeat-containing protein 1 1 0 IIPELVGS(0.19)PT(0.01)QS(0.016)T(0.054)S(0.054)S(0.677)R 80.411 0.024447 14502000 732.99 807.99 850.73 738.1 604.02 418.78 534.53 629.29 906.04 777.82 TRUE FALSE FALSE 724.0560359 819.3649044 865.5365988 823.4425949 573.1946055 392.0213096 579.9329649 647.4975133 825.0015132 757.6121243 0.95570809 1.081509757 1.142453468 1.08689205 0.75658056 0.517443289 0.765474768 0.854655691 1.088949723 1 9.565315609 -8.676486513 5.902856258 1.00724036 0.70637783 0.714846439 0.10079722 0.097480564 5.338616462 0.015153134 0.030491634 2.11E-09 8.676486513 -0.300862529 IIQLLDDY(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 IIQLLDDYPK 10 0 F8VWS0;P05388-2;Q8NHW5;P05388;F8VQY6;F8VRK7;G3V210;F8VU65;F8VS58;F8VZS0 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 0 IIQLLDDY(1)PK 111.06 0.0016552 0 1551.4 1869.5 1662.6 1391.6 1479.3 1502.9 1508.8 1794.6 1987.4 1754.9 TRUE FALSE FALSE 1532.49094 1895.81887 1691.536856 1552.50334 1403.805801 1406.86954 1636.957434 1846.52392 1809.641966 1709.307445 0.89655664 1.109115201 0.989603632 0.90826454 0.821271682 0.823064069 0.95767291 1.080276064 1.058698932 1 10.7391962 -9.246423006 22.6032602 0.96689298 0.909647568 0.122893323 0.090522911 488.0865967 734684.5863 0.014064612 0.023241568 5.67E-10 9.246423006 -0.057245412 IIS(ph)NASCTTNCLAPLAK ddPTM_HeLa_Romidepsin_16h_R1 2 IISNASCTTNCLAPLAK 17 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 IIS(0.973)NAS(0.026)CTTNCLAPLAK;IIS(0.999)NAS(0.001)CTTNCLAPLAK ; 188.41 3.64E-13 27910000 4061.8 4198.9 4029.2 417.52 3969.4 4210.2 3837.5 3912.2 4936.5 3938.6 TRUE FALSE FALSE 4012.293219 4258.012224 4099.326536 465.7956269 3766.826706 3941.181808 4163.457154 4025.393335 4494.967076 3836.274604 1.045882694 1.109934158 1.06856963 0.12141874 0.981897047 1.027346114 1.08528653 1.049297496 1.171701075 1 11.90549028 IIS(ph)VTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 0 IIS(0.933)VT(0.067)PVK 150.81 0.0067679 105930000 7361.6 7963.1 8175.9 5510.3 5431.4 5118.9 3823 4226.5 7596.6 7354.4 TRUE FALSE FALSE 7271.873988 8075.204731 8318.19811 6147.426813 5154.215391 4791.81881 4147.725525 4348.787109 6917.14107 7163.331628 1.015152497 1.127297346 1.161219184 0.858179843 0.71952768 0.668937173 0.579021849 0.607090016 0.965631836 1 12.80641502 -8.816372815 2.191577186 1.028450084 0.622476347 0.896616957 0.065510795 0.073166441 0.716222967 0.010538154 0.022170436 1.53E-09 8.816372815 -0.405973737 IISIFS(ph)GTEK ddPTM_HeLa_Romidepsin_16h_R1 2 IISIFSGTEK 10 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 IISIFS(0.856)GT(0.144)EK;IIS(0.028)IFS(0.965)GT(0.006)EK ; 158.3 0.0027783 28133000 7206.1 11652.9 5324.5 5725.1 8930.1 6057.6 4663.1 7592.4 6764.8 7026.7 TRUE FALSE FALSE 7118.269281 11816.94983 5417.170689 6387.062999 8474.363674 5670.53891 5059.183598 7812.074115 6159.739345 6844.145321 1.040052329 1.726577867 0.791504335 0.933215573 1.238191663 0.828524037 0.73919874 1.141424349 0.90000125 1 12.74065468 -8.232813132 24.60986154 1.062321329 0.886664001 0.089586646 0.261330072 1171.19972 1006874.159 0.034863266 0.088861877 5.85E-09 8.232813132 -0.175657328 IISIFSGTEK ddPTM_HeLa_Romidepsin_16h_R1 1 IISIFSGTEK 10 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 0 113.22 0.0010287 0 72.915 0 190.89 133.22 0 126.06 187.53 0 182.78 65.483 FALSE FALSE TRUE 72.02628393 0 194.2123604 148.6235232 0 118.0051728 203.4587935 0 166.431699 63.78174222 1.129261783 0 3.044952264 2.330189143 0 1.850140318 3.18992217 0 2.609394056 1 5.995071601 -9.776033879 24.99887837 0.983167999 1.755266836 0.03914708 1.177108592 390.3754641 668671.1607 0.162217337 0.213708721 1.67E-10 9.776033879 0.772098837 IISIFSGTEK(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 IISIFSGTEKGSK 13 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 0 1 IISIFSGTEK(1)GSK 105.65 0.025309 327130 198.21 259.82 268.31 240.06 217.22 436.33 310.34 141.77 184.41 172.68 FALSE TRUE FALSE 195.7941403 263.4777528 272.979823 267.8168667 206.1344528 408.4499212 336.7002719 145.8718913 167.9159077 168.1937487 1.164098796 1.56651335 1.623008139 1.592311657 1.225577374 2.428448883 2.001859608 0.867284857 0.99834809 1 7.393980275 -10.26794106 1.137241997 1.045375389 1.679625905 0.294318606 0.394350316 0.377840101 0.950362364 0.080396096 0.095234629 5.40E-11 10.26794106 0.634250515 IISNASCTTNCLAPLAK ddPTM_HeLa_Romidepsin_16h_R1 1 IISNASCTTNCLAPLAK 17 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 130.27 7.15E-05 630890 0 0 143.87 0 50.893 225.01 0 0 83.637 0 FALSE FALSE TRUE 0 0 146.373997 0 48.2957403 210.6325872 0 0 76.15629725 0 0 IISPGSS(ph)TPSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 IISPGS(0.067)S(0.466)T(0.466)PSSTR 173.76 3.97E-05 17153000 2676.8 3328.1 2730.2 1896.3 1802.4 2122.5 1653.2 1499 2838.7 2802.2 TRUE FALSE FALSE 2644.174132 3374.953079 2777.717986 2115.559128 1710.416802 1986.8791 1793.622767 1542.3712 2584.799562 2729.39844 0.968775424 1.236519018 1.017703368 0.775100878 0.626664388 0.727954948 0.65714948 0.565095655 0.947021704 1 11.4143673 -9.103768176 3.197849422 1.009884478 0.653318734 0.824644738 0.085022547 0.086043331 1.674886654 0.013468987 0.023621546 7.87E-10 9.103768176 -0.356565744 IISPGSST(ph)PSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 IISPGSST(0.998)PS(0.002)STR 162.93 0.00061607 18911000 3255 2937.7 3237.1 1979.8 2162.3 1999.8 1535.7 1663.7 2711.4 3033.1 TRUE FALSE FALSE 3215.326808 2979.057018 3293.440368 2208.713791 2051.949762 1872.019234 1666.14232 1711.836535 2468.885593 2954.299625 1.088355014 1.008380123 1.114795649 0.747626873 0.694563864 0.633659233 0.563972017 0.579439039 0.835692349 1 11.52860044 -9.039221996 2.281470482 1.045365493 0.608970239 0.828875442 0.08332438 0.052694369 0.544551001 0.008500202 0.015994823 9.14E-10 9.039221996 -0.436395254 IISPGSSTPSS(ph)TR ddPTM_HeLa_Romidepsin_16h_R1 1 IISPGSSTPSSTR 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 IISPGS(0.005)S(0.005)T(0.332)PS(0.036)S(0.51)T(0.112)R 91.307 0.003889 0 1805.2 1932.3 1820.7 1614.8 1607.9 1447.8 1359.6 1622.4 2108.6 2103.3 TRUE FALSE FALSE 1783.197528 1959.50297 1852.38852 1801.510774 1525.842863 1355.290253 1475.08439 1669.341584 1920.001535 2048.655963 0.870423126 0.956482204 0.904196973 0.879362278 0.744801905 0.661550928 0.72002543 0.814847205 0.937200569 1 11.00046201 -8.865450053 2.47878021 0.936214235 0.725420642 0.800617296 0.046907314 0.112138538 1.400294898 0.00907151 0.018196641 1.36E-09 8.865450053 -0.210793592 IISPGSSTPSS(ph)TRSPPPGR ddPTM_HeLa_Romidepsin_16h_R1 1 IISPGSSTPSSTRSPPPGR 19 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 IISPGSST(0.001)PS(0.193)S(0.328)T(0.328)RS(0.148)PPPGR 79.326 0.0034299 11226000 1125 961.24 940.27 1001.6 946.5 723.55 710.54 845.56 1060.6 953.33 TRUE FALSE FALSE 1111.288067 974.772362 956.6350049 1117.409705 898.1965731 677.3174902 770.8932499 870.0249445 965.7372797 928.5623492 1.196783467 1.049765116 1.030232386 1.203376064 0.967298075 0.729425968 0.830200848 0.936959102 1.040034932 1 9.858854974 -8.518219706 6.597024652 1.093105817 0.833772826 0.678187394 0.078633843 0.070014017 15.20612656 0.013304985 0.028152169 3.03E-09 8.518219706 -0.259332992 IISVT(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 IISVTPVK 8 0 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 0 IIS(0.002)VT(0.998)PVK 125.75 0.030519 106020000 8777.8 9471.5 10377 6449.2 6682.5 5712.1 4779.2 5425.1 8705.2 8365.1 TRUE FALSE FALSE 8670.812797 9604.840026 10557.60733 7194.886848 6341.467089 5347.115245 5185.145129 5582.066709 7926.585109 8147.773496 1.064194139 1.178830024 1.295765934 0.883049443 0.778306748 0.656267046 0.636387981 0.685103324 0.972852904 1 12.99219016 -8.817927128 2.530526358 1.062842183 0.668471893 0.799681232 0.096466154 0.10181275 1.329129326 0.015526339 0.031709068 1.52E-09 8.817927128 -0.39437029 IISVT(ph)PVKNIDPVK ddPTM_HeLa_Romidepsin_16h_R1 1 IISVTPVKNIDPVK 14 1 Q29RF7 Q29RF7 PDS5A Sister chromatid cohesion protein PDS5 homolog A 1 0 IIS(0.036)VT(0.964)PVKNIDPVK 75.376 0.024699 42462000 4566.4 4695.1 4607.6 5340.9 3577 2942.3 2737.1 2808.5 5061 4161.3 TRUE FALSE FALSE 4510.74296 4761.197741 4687.793345 5958.439988 3394.452342 2754.296526 2969.589206 2889.759516 4608.331484 4053.188826 1.112887446 1.17467948 1.156569197 1.470062275 0.837476981 0.679538172 0.732655036 0.712959509 1.13696442 1 11.98484167 -8.536766573 24.99440421 1.101493921 0.718760636 0.732936458 0.125573141 108.3773453 195049.9692 0.019908142 0.039830896 2.91E-09 8.536766573 -0.382733285 IIVDELKQEVISTSSK ddPTM_HeLa_Romidepsin_16h_R1 1 IIVDELKQEVISTSSK 16 1 D6RF23;H0YAF8;D6RAC2;J3KPE3;P63244;H0Y9P0;H0YAM7;H0Y8W2;D6REE5 D6RF23 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 0 115.04 0.0033836 7194100 2062.4 1647.9 1655.4 2054.4 1823.8 1872.7 1359.4 1500.6 1926.9 1920.5 FALSE FALSE TRUE 2037.262676 1671.099179 1684.211543 2291.939394 1730.72468 1753.040514 1474.867402 1544.017493 1754.553238 1870.605133 1.08909285 0.893346837 0.900356528 1.225239551 0.925221817 0.937151557 0.788444005 0.825410701 0.937960239 1 10.86928934 -8.077234141 1.876170377 1.029705448 0.805265593 0.336722643 0.098330738 0.242371089 1.613512217 0.013776806 0.053924647 8.37E-09 8.077234141 -0.224439855 IIYDS(ph)DS(ph)ESEETLQVK ddPTM_HeLa_Romidepsin_16h_R1 1 IIYDSDSESEETLQVK 16 0 P35251-2;P35251;E0CX09;D6RAD2 P35251-2 RFC1 Replication factor C subunit 1 2 0 IIY(0.321)DS(0.682)DS(0.973)ES(0.023)EET(0.001)LQVK 105.14 0.0018482 0 995.4 804.3 859.7 688.4 754.54 962.59 797.86 847.78 1024.8 908.12 TRUE FALSE FALSE 983.2676819 815.6229565 874.6627179 767.996047 716.0330082 901.0836056 865.6302085 872.3091767 933.1393213 884.5269115 1.111631166 0.922100782 0.988848057 0.868256281 0.80950958 1.018718135 0.978636373 0.986187266 1.054958656 1 9.788762227 -10.24759937 24.85166675 1.052714717 0.937720682 0.410604255 0.064000078 601.234208 1079601.549 0.012128398 0.014809961 5.65E-11 10.24759937 -0.114994035 IIYDS(ph)DSESEETLQVK ddPTM_HeLa_Romidepsin_16h_R1 1 IIYDSDSESEETLQVK 16 0 P35251-2;P35251;E0CX09;D6RAD2 P35251-2 RFC1 Replication factor C subunit 1 1 0 IIYDS(0.896)DS(0.025)ES(0.079)EETLQVK 184 1.08E-08 3626200 1295.3 1212.6 1031.7 553.14 852.15 1018.2 1330.3 1263.8 1418.9 1379.9 TRUE FALSE FALSE 1279.512385 1229.671015 1049.656306 617.0966494 808.6616057 953.1403061 1443.295649 1300.366059 1291.99003 1344.049999 0.951982729 0.914899755 0.780965222 0.459132212 0.60166036 0.709155394 1.073840742 0.967498278 0.961266345 1 10.39237109 -9.852095709 3.249928072 0.975744855 0.754615192 0.25634994 0.161750745 0.263155513 5.568897422 0.02923414 0.039586434 1.41E-10 9.852095709 -0.221129663 IIYIVHDEVKDK ddPTM_HeLa_Romidepsin_16h_R1 1 IIYIVHDEVKDK 12 1 P25788;P25788-2;G3V4X5 P25788 PSMA3 Proteasome subunit alpha type-3 0 0 94.363 0.0090427 9986000 7871.6 7252.1 7428.2 9173.9 8234.3 8002.8 7102.8 7865.2 8121.2 7207.4 FALSE FALSE TRUE 7775.657911 7354.195254 7557.484705 10234.62948 7814.072945 7491.446908 7706.111655 8092.767153 7394.819532 7020.150709 1.107619798 1.047583671 1.076541661 1.457893129 1.113091908 1.067134769 1.097713137 1.152791085 1.053370481 1 12.77728629 -11.25050607 0.554611205 1.003718399 1.154144182 0.16215735 0.110085354 1.01098591 0.690455704 0.066822064 0.033537385 5.62E-12 11.25050607 0.150425783 IK(ac)EMKQATDLK ddPTM_HeLa_Romidepsin_16h_R1 2 IKEMKQATDLK 11 2 Q9BRR8 Q9BRR8 GPATCH1 G patch domain-containing protein 1 0 1 ; IK(0.994)EMK(0.006)QATDLK;IK(0.976)EMK(0.024)QATDLK 56.043 0.026393 18884400 8521.9 7819.9 7174.1 9047.9 9842.2 9547.1 7844.2 9062.9 9603.5 8325.1 FALSE TRUE FALSE 8418.031805 7929.988757 7298.962201 10094.06077 9339.915808 8937.071122 8510.486152 9325.120713 8744.538908 8108.812702 1.038133709 0.977946963 0.900127117 1.244825986 1.151822856 1.102142996 1.049535421 1.149998286 1.078399419 1 12.98527497 -9.262791336 24.99980266 1.006785819 1.13324877 0.554235777 0.06278179 75.97938209 1404984.844 0.009267964 0.014653956 5.46E-10 9.262791336 0.126462951 IK(ac)IIAPPERK ddPTM_HeLa_Romidepsin_16h_R1 2 IKIIAPPERK 10 2 P60709;P63267-2;A0A2R8YFE2;Q562R1;P63261;P63267;P68133;P68032;P62736;A6NL76 P60709;P63261;P63267 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 1 ; IK(1)IIAPPERK;IK(1)IIAPPERK 99.343 0.0011557 0 1937.65 1755.94 1750.09 2465.7 2226.65 2108.2 1771.3 1830.75 2128.02 1843.77 FALSE TRUE FALSE 1914.033177 1780.660169 1780.549582 2750.795835 2113.015742 1973.492824 1921.754178 1883.719863 1937.684561 1795.86859 1.065798014 0.99153144 0.991469862 1.531735591 1.176598195 1.098907145 1.070097327 1.048918542 1.0789679 1 10.81046607 IK(ac)SK(ac)IPNEHK ddPTM_HeLa_Romidepsin_16h_R1 2 IKSKIPNEHK 10 2 F2Z2B6;F2Z3N8;Q92613 F2Z2B6 JADE3 Protein Jade-3 0 2 ; IK(1)SK(1)IPNEHK;IK(1)SK(1)IPNEHK 87.641 0.0098484 14791400 5753.2 5393.3 5436.5 5845.1 10560.6 9088.7 7234.6 7763.4 6895.7 5956.5 FALSE TRUE FALSE 5683.077785 5469.227019 5531.120002 6520.937964 10021.65317 8507.961402 7849.106743 7988.02173 6278.931321 5801.749271 0.979545568 0.942685863 0.95335385 1.123960664 1.727350271 1.466447619 1.352886238 1.376829876 1.082247961 1 12.50227223 -8.939037473 6.407551576 0.98539964 1.469334591 0.840817253 0.100857235 0.054705344 4.379682684 0.014175637 0.025822435 1.15E-09 8.939037473 0.483934951 IKDAFDRNPELQNLLLDDFFK ddPTM_HeLa_Romidepsin_16h_R1 1 IKDAFDRNPELQNLLLDDFFK 21 2 P52209-2;P52209 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 89.049 0.00039282 3075500 1947.6 2085.1 2128.6 2548.9 2102.8 2195.7 1845.6 2443.3 2391.6 1971.7 FALSE FALSE TRUE 1923.861902 2114.454093 2165.64739 2843.615811 1995.486269 2055.401856 2002.365218 2513.993031 2177.689306 1920.47495 1.001763601 1.101005818 1.1276624 1.480683625 1.039058734 1.070257051 1.042640633 1.309047551 1.13393268 1 10.90724743 -10.02911191 2.444028354 1.000515919 1.174089934 0.146628554 0.133457025 0.281686539 3.342543704 0.021518359 0.027735631 9.35E-11 10.02911191 0.173574015 IKDNGDLVLSS(ph)PSNVTLPQVK ddPTM_HeLa_Romidepsin_16h_R1 1 IKDNGDLVLSSPSNVTLPQVK 21 1 A0A494C0P1;P04150-7;P04150-5;P04150-2;P04150-6;P04150-10;P04150;P04150-3;P04150-9;P04150-8;P04150-13;P04150-12;P04150-11 A0A494C0P1 NR3C1 Glucocorticoid receptor 1 0 IKDNGDLVLS(0.187)S(0.782)PS(0.031)NVTLPQVK 101.42 0.0001597 34916000 7276.9 7080.8 7011.4 6417.2 5492.4 5729.1 4965.6 5692.5 8095.1 6328.4 TRUE FALSE FALSE 7188.206344 7180.483688 7133.430476 7159.186858 5212.102333 5363.029 5387.37794 5857.203506 7371.053981 6163.987256 1.166161779 1.164908912 1.157275345 1.161453871 0.845573185 0.870058418 0.874008611 0.950229659 1.195825636 1 12.58964816 -8.757458343 24.99999862 1.099250225 0.883119733 0.780160295 0.064318726 49.92090723 313487.4263 0.011613926 0.02256331 1.75E-09 8.757458343 -0.216130493 IKDNGDLVLSSPS(ph)NVTLPQVK ddPTM_HeLa_Romidepsin_16h_R1 1 IKDNGDLVLSSPSNVTLPQVK 21 1 A0A494C0P1;P04150-7;P04150-5;P04150-2;P04150-6;P04150-10;P04150;P04150-3;P04150-9;P04150-8;P04150-13;P04150-12;P04150-11 A0A494C0P1 NR3C1 Glucocorticoid receptor 1 0 IKDNGDLVLS(0.049)S(0.265)PS(0.632)NVT(0.053)LPQVK 79.383 0.0012245 35947000 7877.6 8225.4 7920.6 7473.6 6350.4 6214.4 5302.6 6417.3 8151 6664 TRUE FALSE FALSE 7781.584781 8341.197397 8058.45472 8337.732796 6026.315391 5817.319896 5753.002712 6602.974451 7421.954145 6490.868319 1.198851124 1.285066494 1.241506425 1.284532729 0.928429772 0.896231384 0.886322512 1.017271361 1.143445496 1 12.66419577 -8.728651287 23.86079151 1.136233522 0.926236691 0.618416402 0.094098051 91.82312577 66821.42778 0.017932365 0.03586199 1.87E-09 8.728651287 -0.209996831 IKDPDASKPEDWDER ddPTM_HeLa_Romidepsin_16h_R1 2 IKDPDASKPEDWDER 15 2 P27797;K7EJB9 P27797 CALR Calreticulin 0 0 ; ; 100.11 0.0087274 73966000 7607.5 6832.1 6713.6 8368 8643.6 9940.9 8374.6 10417.5 8461.1 7534 FALSE FALSE TRUE 7514.776864 6928.282483 6830.447392 9335.547533 8202.484838 9305.708573 9085.938315 10718.91393 7704.318025 7338.265594 1.024053541 0.944130789 0.930798607 1.272173569 1.11776887 1.268107355 1.238158826 1.46068765 1.04988269 1 12.84122341 -7.763149792 0.546584532 0.998839632 1.55831974 0.745466123 0.082786023 0.875279162 0.245157275 0.0160702 0.279576372 1.73E-08 7.763149792 0.559480107 IKEEVLS(ph)ESEAENQQAGAAALAPEIVIK ddPTM_HeLa_Romidepsin_16h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 0 IKEEVLS(0.781)ES(0.219)EAENQQAGAAALAPEIVIK 61.776 0.00064794 134490000 5058.8 5263.9 4779.9 4640.6 5145.8 5091.9 4166.9 5656.1 5562.9 5402.2 TRUE FALSE FALSE 4997.1414 5338.005322 4863.092154 5177.168007 4883.190624 4766.544023 4520.836382 5819.75033 5065.340291 5261.850065 0.949692853 1.014473095 0.924217166 0.98390641 0.928036824 0.905868462 0.859172406 1.106027397 0.962653863 1 12.36135442 -9.744632034 24.99891753 0.978447271 0.945394099 0.047483279 0.063143552 564.0614819 838971.9334 0.00939709 0.013269061 1.80E-10 9.744632034 -0.033053172 IKEEVLSES(ph)EAENQQAGAAALAPEIVIK ddPTM_HeLa_Romidepsin_16h_R1 1 IKEEVLSESEAENQQAGAAALAPEIVIK 28 1 Q9UJX5;Q9UJX5-3 Q9UJX5 ANAPC4 Anaphase-promoting complex subunit 4 1 0 IKEEVLS(0.436)ES(0.564)EAENQQAGAAALAPEIVIK 67.351 7.87E-05 136590000 4603.9 4781.7 4517.5 4537.2 4890.8 4913.1 4853.6 5241 5351.9 4863.2 TRUE FALSE FALSE 4547.785896 4849.016898 4596.125192 5061.812412 4641.204226 4599.168766 5265.864663 5392.640066 4873.21266 4736.853363 0.960085852 1.023678912 0.97029079 1.068602303 0.979807452 0.970933321 1.111679898 1.138443531 1.028786894 1 12.2097133 -7.711238629 5.617158867 0.988619691 1.129491362 0.682044551 0.033405545 0.068099766 4.666405978 0.004409611 0.016803108 1.94E-08 7.711238629 0.140871671 IKGDVDVSAPK ddPTM_HeLa_Romidepsin_16h_R1 1 IKGDVDVSAPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 78.903 0.028472 555980 1454.4 1240.6 1437.5 1143.7 1137.4 1353.2 1136.5 1204.2 1237.1 1304.5 FALSE FALSE TRUE 1436.673213 1258.065199 1462.519084 1275.939975 1079.354234 1266.734887 1233.034282 1239.041627 1126.450678 1270.608902 1.130696638 0.990127802 1.151037965 1.004195684 0.849477941 0.996951057 0.970427863 0.97515579 0.886543984 1 10.31130432 -9.001509623 24.99384662 1.063508659 0.94981815 0.137527955 0.081404315 45.49974958 753339.4502 0.009749097 0.017496553 9.97E-10 9.001509623 -0.113690509 IKGS(ph)SPGIQDTLEAEDGAFETDEAPEDR ddPTM_HeLa_Romidepsin_16h_R1 2 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 0 IKGS(0.473)S(0.473)PGIQDT(0.054)LEAEDGAFETDEAPEDR;IKGS(0.497)S(0.497)PGIQDT(0.006)LEAEDGAFETDEAPEDR ; 89.055 2.15E-08 61306000 3701.18 3167.39 3992.03 3455.64 3443.68 3777.88 3039.44 3548.74 3731.36 3435.94 TRUE FALSE FALSE 3656.068595 3211.9806 4061.509608 3855.197356 3267.936159 3536.485661 3297.609958 3651.417193 3397.617816 3346.673783 1.092448452 0.959753118 1.213595908 1.151948952 0.976472872 1.056716576 0.985339525 1.091058594 1.015222288 1 11.70851222 -6.939301225 18.83026906 1.050490933 1.654901385 0.024277697 0.077747088 763.1316115 181909.1041 0.010529521 32991.81205 1.15E-07 6.939301225 0.604410452 IKGSS(ph)PGIQDTLEAEDGAFETDEAPEDR ddPTM_HeLa_Romidepsin_16h_R1 1 IKGSSPGIQDTLEAEDGAFETDEAPEDR 28 1 Q9UNX4 Q9UNX4 WDR3 WD repeat-containing protein 3 1 0 IKGS(0.223)S(0.764)PGIQDT(0.014)LEAEDGAFETDEAPEDR 65.248 0.00022505 59179000 1730.4 1612.4 1535.6 1565.5 1724.8 1691.9 1498 1512.8 1628.7 1807.1 TRUE FALSE FALSE 1709.309219 1635.09941 1562.326474 1746.510476 1636.77702 1583.79305 1625.240083 1556.570481 1483.024993 1760.151281 0.971114947 0.928953907 0.887609202 0.992250208 0.929907013 0.899805072 0.923352498 0.884339032 0.842555415 1 10.78148372 -8.397105743 0.125899682 1.048437715 0.797715221 0 0.057737008 10.74035023 0.358705921 0.194039018 0.560488831 4.01E-09 8.397105743 -0.250722495 IKIEHAPS(ph)PSSGGTLK ddPTM_HeLa_Romidepsin_16h_R1 1 IKIEHAPSPSSGGTLK 16 1 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8Y7Y0;A0A2R8YCQ1;A0A2R8YD28 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 IKIEHAPS(0.992)PS(0.007)S(0.002)GGTLK 80.411 0.0019435 0 1926.8 2096 1503 1827 1739.8 1754.8 1502.7 1627 2006 1847.9 TRUE FALSE FALSE 1903.31542 2125.507543 1529.159085 2038.246336 1651.011514 1642.673943 1630.3393 1674.074678 1826.578336 1799.891292 1.05746132 1.180908843 0.849584134 1.132427467 0.917284017 0.912651753 0.90579876 0.93009766 1.014827031 1 10.81369406 -8.668516128 12.68125566 1.032357701 0.915187944 0.34605506 0.082335092 0.51029479 66.99640586 0.011042256 0.022086399 2.15E-09 8.668516128 -0.117169757 IKNENTEGS(ph)PQEDGVELEGLK ddPTM_HeLa_Romidepsin_16h_R1 5 IKNENTEGSPQEDGVELEGLK 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 IKNENT(0.01)EGS(0.99)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK;IKNENTEGS(1)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK;IKNENT(0.001)EGS(0.999)PQEDGVELEGLK ;;;; 135.12 5.62E-05 771053400 17763.1 15647.2 18959.9 13861.4 14926.6 16555.1 14250.6 16840.3 19767.6 16993.6 TRUE FALSE FALSE 17546.5965 15867.48169 19289.88911 15464.12029 14164.8399 15497.28254 15461.04561 17327.54751 17999.53635 16552.10382 1.060082555 0.958638362 1.165404067 0.934269169 0.85577278 0.936272676 0.934083412 1.046848648 1.087447042 1 14.01472698 IKPNLSSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 IKPNLSSSPR 10 1 A0A1P0AZG4;Q96JN0-3 A0A1P0AZG4 1 0 IKPNLSS(0.143)S(0.857)PR 72.731 0.029149 22222000 3929.2 3811.8 4560.7 4395.9 4529.3 3980.6 3286.8 3555.9 4529.8 3891.5 TRUE FALSE FALSE 3881.309399 3865.46262 4640.07707 4904.174641 4298.15292 3726.252507 3565.98071 3658.784356 4124.643343 3790.398269 1.023984585 1.019803816 1.224166101 1.293841516 1.133958127 0.983076775 0.940793145 0.965277023 1.088182046 1 11.88813373 -5.758767641 9.858198941 1.042345493 0.771122739 0 0.113669014 0 0 0.016406652 0 1.74E-06 5.758767641 -0.271222754 IKT(ph)GSPGSEVVTLQQFLEESNKLTSVQIK ddPTM_HeLa_Romidepsin_16h_R1 1 IKTGSPGSEVVTLQQFLEESNKLTSVQIK 29 2 Q3V6T2;A0A2R8Y7D4;A0A2U3TZV9;A0A2R8Y7B1;H7C2C6;A0A2R8Y820;A0A2R8YCU9;A0A2R8Y885;A0A2R8YDS8;H0Y470;H0Y7U8;A0A2R8Y5D7;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H0Y7K3;A0A2R8Y4Z5;A0A2R8Y4C6 Q3V6T2 CCDC88A Girdin 1 0 IKT(0.494)GS(0.494)PGS(0.012)EVVTLQQFLEESNKLTSVQIK 78.736 1.13E-06 2826100 760.96 880.14 746.13 1441.9 725.79 715.55 822.26 560.51 920.52 508.12 TRUE FALSE FALSE 751.6851268 892.530634 759.1160797 1608.619262 688.750228 669.8286643 892.1027439 576.7274725 838.1863857 494.9189691 1.518804438 1.803387402 1.533818922 3.250267948 1.391642412 1.353410772 1.802522836 1.165296763 1.693583067 1 8.951048528 -11.23549256 0.829371644 1.068461903 1.772845578 0.029605856 0.578807566 0.609384955 0.89585419 0.194728664 0.12310015 5.81E-12 11.23549256 0.704383675 IKTELNSS(ph)AESEQPLDK ddPTM_HeLa_Romidepsin_16h_R1 1 IKTELNSSAESEQPLDK 17 1 Q9Y5B6-3;Q9Y5B6-4;Q9Y5B6-2;Q9Y5B6 Q9Y5B6-3 PAXBP1 PAX3- and PAX7-binding protein 1 1 0 IKTELNS(0.377)S(0.582)AES(0.041)EQPLDK 78.378 0.00754 6096600 3186.7 2611 2548 2196.6 2705 2577.8 2302.2 2606.4 2900.7 3396.8 TRUE FALSE FALSE 3147.859275 2647.757727 2592.346871 2450.581227 2566.953756 2413.086899 2497.748811 2681.812072 2641.254127 3308.550646 0.951431491 0.800277224 0.783529451 0.740681189 0.775854454 0.729348636 0.754937457 0.810570053 0.79831153 1 11.69198365 -10.2473253 1.921368407 0.982129224 0.761539147 0.459406918 0.062535453 0.050259898 0.351347839 0.004534677 0.005406017 5.66E-11 10.2473253 -0.220590077 IKTEPSS(ph)PLSDPSDIIR ddPTM_HeLa_Romidepsin_16h_R1 1 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 IKTEPS(0.026)S(0.952)PLS(0.018)DPS(0.004)DIIR 81.226 0.0064745 11219000 2195.2 1747.5 1520.4 2507.1 1350.2 1381.9 1073.5 1511.9 2019.9 1917.6 TRUE FALSE FALSE 2168.444058 1772.101351 1546.861924 2796.982698 1281.294256 1293.60105 1164.683063 1555.644441 1839.235085 1867.780476 1.160973726 0.948773892 0.828181869 1.497490061 0.685998313 0.692587307 0.623565284 0.832883983 0.984716946 1 10.86710919 IKTEPSSPLSDPS(ph)DIIR ddPTM_HeLa_Romidepsin_16h_R1 1 IKTEPSSPLSDPSDIIR 17 1 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 IKTEPS(0.005)S(0.062)PLS(0.101)DPS(0.832)DIIR 98.804 0.0013522 10657000 4862.6 3756.9 3876.6 5333.7 3585.2 3232.6 2784.6 2920.3 4820.2 4509.3 TRUE FALSE FALSE 4803.332761 3809.789737 3944.070597 5950.40749 3402.233866 3026.047293 3021.123854 3004.794273 4389.06924 4392.147736 1.093618214 0.867409287 0.897982225 1.354783092 0.774617356 0.688967556 0.687846593 0.684128689 0.999299091 1 12.10071087 -8.543622411 24.98621222 1.038808913 0.694521609 0.627451921 0.124621147 105.6759081 127288.576 0.017397611 0.034797887 2.86E-09 8.543622411 -0.344287305 IKVDFVIPK ddPTM_HeLa_Romidepsin_16h_R1 1 IKVDFVIPK 9 1 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 0 91.867 0.014423 0 980.64 1067.4 970.27 870.09 712.72 717.1 502.36 585.93 803.32 660.13 FALSE FALSE TRUE 968.6875825 1082.426885 987.1571423 970.6938997 676.3472389 671.2796243 545.0304459 602.8829601 731.4690472 642.9797274 1.506560069 1.683454142 1.535285018 1.509680412 1.051895122 1.044013669 0.847663499 0.937639142 1.13762381 1 9.328629441 -8.59015527 5.605115837 1.323156 0.950530176 0.504960416 0.200580631 0.194853818 11.44813771 0.039379489 0.080039202 2.57E-09 8.59015527 -0.372625824 IKVEPVALAPS(ph)PVIPR ddPTM_HeLa_Romidepsin_16h_R1 1 IKVEPVALAPSPVIPR 16 1 Q5VWG9 Q5VWG9 TAF3 Transcription initiation factor TFIID subunit 3 1 0 IKVEPVALAPS(1)PVIPR 100.59 0.0019802 19426000 4187.1 2792.5 3817.5 3847.5 3735.2 3646.3 4048.8 3937.4 3873 3735.6 TRUE FALSE FALSE 4136.066015 2831.812888 3883.941986 4292.366053 3544.578806 3413.313198 4392.704971 4051.322457 3526.58918 3638.548573 1.136735138 0.778280908 1.067442665 1.179691838 0.974173832 0.938097466 1.20726847 1.113444654 0.969229655 1 11.82914736 -7.743973184 24.99990511 1.040605025 1.160356576 0.186695191 0.111438751 355.9758576 509511.2433 0.015527869 0.057827559 1.80E-08 7.743973184 0.119751551 IKWDEQTSNTKGDDDEES(ph)DEEAVK ddPTM_HeLa_Romidepsin_16h_R1 2 IKWDEQTSNTKGDDDEESDEEAVK 24 2 O43395 O43395 PRPF3 U4/U6 small nuclear ribonucleoprotein Prp3 1 0 IKWDEQT(0.001)S(0.001)NT(0.003)KGDDDEES(0.995)DEEAVK;IKWDEQT(0.019)S(0.019)NT(0.016)KGDDDEES(0.947)DEEAVK ; 75.695 0.00053486 23734300 1840.96 1635.98 1969.08 1275.96 1847.19 1882.16 1745.76 2061.46 2175.8 2419.01 TRUE FALSE FALSE 1818.521671 1659.011369 2003.351011 1423.492499 1752.921001 1761.89605 1894.044811 2121.105093 1981.190999 2356.163771 0.771814631 0.704115473 0.850259662 0.604156857 0.743972479 0.747781658 0.803868065 0.900236698 0.840854538 1 11.20222411 -12.00429606 0.728168002 1.006869564 0.759954646 0.257270886 0.089710843 0.406494028 0.381931469 0.05746664 0.01615282 9.90E-13 12.00429606 -0.246914918 IKWGDAGAEYVVESTGVFTTMEK ddPTM_HeLa_Romidepsin_16h_R1 1 IKWGDAGAEYVVESTGVFTTMEK 23 1 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 66.711 0.0033361 16941000 4080.4 4218.1 3125 6091.2 3987.6 3827.3 3676.9 4055.3 4493.8 3087.7 FALSE FALSE TRUE 4030.666515 4277.482523 3179.389314 6795.493204 3784.097892 3582.747882 3989.215794 4172.633707 4091.863273 3007.481109 1.340213411 1.422280762 1.057160195 2.259529805 1.258228316 1.191278599 1.326430873 1.387418094 1.360561588 1 11.55433996 -11.71314672 0.61736061 0.991120536 1.420829809 0.032006384 0.322648059 1.001394164 0.729608957 0.216227837 0.073176096 1.94E-12 11.71314672 0.429709273 ILAEGGGAK(ac)FK ddPTM_HeLa_Romidepsin_16h_R1 2 ILAEGGGAKFK 11 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 1 ; ILAEGGGAK(1)FK;ILAEGGGAK(1)FK 157.66 0.0074258 1607230 1157.99 873.8 1297.05 1050.47 1573.56 1784.01 1575.57 1565.43 1241.42 1012.5 FALSE TRUE FALSE 1143.875972 886.1013793 1319.624611 1171.930284 1493.255361 1670.017519 1709.398876 1610.723247 1130.384286 986.195104 1.159888107 0.898505149 1.3380969 1.188335127 1.514158157 1.693394656 1.733327279 1.633270375 1.146207562 1 9.94572928 -8.773525911 1.158519211 1.069072911 1.718383278 0.856283461 0.107128558 0.119094649 0.3140483 0.017177444 0.048223285 1.68E-09 8.773525911 0.649310366 ILAT(ph)PPQEDAPSVDIANIR ddPTM_HeLa_Romidepsin_16h_R1 2 ILATPPQEDAPSVDIANIR 19 0 P29401;P29401-2;A0A0B4J1R6;E9PFF2 P29401 TKT Transketolase 1 0 ILAT(1)PPQEDAPSVDIANIR;ILAT(1)PPQEDAPSVDIANIR ; 148.78 8.06E-05 84214000 3770.8 2610 3779.4 2950.7 3691 3824 3449.9 3383.4 2933 3174 TRUE FALSE FALSE 3724.840039 2646.743649 3845.178872 3291.873817 3502.634497 3579.658741 3742.93442 3481.293341 2670.665134 3091.539022 1.204849757 0.856124936 1.243774975 1.064800992 1.132974377 1.157888908 1.210702628 1.126071292 0.863862663 1 11.5941095 -12.57375942 1.295484115 0.998563084 1.13277143 0.275965048 0.112106871 0.609483206 1.8012534 0.07325343 0.016374509 2.67E-13 12.57375942 0.134208346 ILATK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 ILATKK 6 1 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 0 1 ILATK(1)K 100.74 0.01868 1987900 2567.5 2016.7 3633.2 3246.6 3323.7 4156.5 4726.2 1440 3086.4 1977.7 FALSE TRUE FALSE 2536.206322 2045.091156 3696.434322 3621.987168 3154.079187 3890.913064 5127.64331 1481.664128 2810.344654 1926.319069 1.316607598 1.061657536 1.918910725 1.880263361 1.637360725 2.019869464 2.661886804 0.769168593 1.458919604 1 10.91163097 -9.760270315 24.99127112 1.147097709 1.857352761 0.292235334 0.454471863 23.3511116 499172.8008 0.065800936 0.090116214 1.74E-10 9.760270315 0.710255052 ILDAVVAQEPLHR ddPTM_HeLa_Romidepsin_16h_R1 1 ILDAVVAQEPLHR 13 0 Q15029-3;Q15029;K7EP67;Q15029-2;K7EJ74 Q15029-3 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 0 85.536 0.0029989 0 3153.5 3399 3519.1 3189.3 4024.7 3871 3390.8 3598.6 4404.4 3247.2 FALSE FALSE TRUE 3115.063929 3446.851211 3580.348459 3558.061872 3819.304541 3623.655593 3678.814467 3702.719813 4010.459433 3162.837276 0.984895414 1.089797201 1.132005268 1.124958878 1.207556446 1.145697763 1.163137445 1.170695641 1.267994235 1 11.62700362 -9.967089221 1.724793764 0.991823631 1.16244152 0 0.089915715 0.059417213 0.350881254 0.003767109 0.00501842 1.08E-10 9.967089221 0.170617889 ILDEIEEHNIK ddPTM_HeLa_Romidepsin_16h_R1 2 ILDEIEEHNIK 11 0 B5MCX3;Q15019;Q15019-3;Q15019-2;C9J2Q4;H7C2Y0 B5MCX3 Sep-02 Septin-2 0 0 ; ; 133.42 0.0020446 14247600 11591.1 11377 11136.2 10719.7 11663.6 11597.8 10263 11160.1 12227.5 11171.7 FALSE FALSE TRUE 11449.82321 11537.1657 11330.02089 11959.16215 11068.36297 10856.73801 11134.73896 11482.99989 11133.84178 10881.45762 1.052232487 1.060259214 1.041222719 1.099040456 1.017176499 0.997728281 1.023276417 1.055281405 1.023193965 1 13.40958421 -7.248142702 22.29079062 1.031195379 1.055281475 0.028877393 0.028995221 1380.159698 2313526.638 0.004566039 0.102357724 5.65E-08 7.248142702 0.024086096 ILDPNTGEPAPVLSSPPPADVSTFLAFPS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 1 ILDPNTGEPAPVLSSPPPADVSTFLAFPSPEK 32 0 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 1 0 ILDPNTGEPAPVLSSPPPADVS(0.063)T(0.063)FLAFPS(0.874)PEK 83.903 1.38E-08 36817000 12503 12544 12001 10879 8702.7 7295.6 6291.6 6006.7 13456 12599 TRUE FALSE FALSE 12350.60863 12720.59476 12209.87237 12136.88117 8258.568745 6829.434705 6826.008347 6180.494387 12252.46166 12271.67616 1.006432085 1.036581685 0.994963704 0.989015763 0.672978054 0.556520121 0.556240912 0.503638974 0.99843424 1 13.5830447 -8.656180861 2.615951074 1.006551665 0.542227039 0.991045564 0.020393443 0.017770872 0.245896991 0.003162071 0.00693739 2.21E-09 8.656180861 -0.464324625 ILDSVGIEADDDRLNK ddPTM_HeLa_Romidepsin_16h_R1 4 ILDSVGIEADDDRLNK 16 1 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 0 0 ;;; ;;; 208.79 1.38E-19 268791000 18478.7 17223.9 17016.8 15752.9 18426.4 16660.2 15317.1 17190.9 18173.5 17828.7 FALSE FALSE TRUE 18253.4745 17466.37852 17312.97027 17574.32442 17486.03205 15595.66699 16618.13409 17688.29157 16548.01664 17365.5078 1.051133932 1.005808682 0.996974604 1.012024792 1.006940439 0.898082979 0.956962173 1.018587638 0.952924431 1 14.08393698 -8.496675733 22.60466383 1.019731679 0.956906956 0.166195114 0.037248556 161.921275 139684.3977 0.004748591 0.010571418 3.19E-09 8.496675733 -0.062824723 ILEGDNGMDS(ph)DMEEEADDGSK ddPTM_HeLa_Romidepsin_16h_R1 2 ILEGDNGMDSDMEEEADDGSK 21 0 Q9H8G2;A0A3B3ISJ3;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 0 ILEGDNGMDS(1)DMEEEADDGSK;ILEGDNGMDS(0.996)DMEEEADDGS(0.004)K ; 93.776 4.92E-05 3143500 3381.3 3029.3 2614.6 3285.5 3612.5 3672.5 3897.5 3850 3357.8 3378.9 TRUE FALSE FALSE 3340.087415 3071.946565 2660.106016 3665.384969 3428.140645 3437.839102 4228.553553 3961.393676 3057.469958 3291.115691 1.014879976 0.933405828 0.808268765 1.113721094 1.041634803 1.044581663 1.284838927 1.203662845 0.929007135 1 11.68436103 -7.856746219 4.371627783 0.997898144 1.244190203 0.624480605 0.080305465 0.099438637 3.356114252 0.010843115 0.035766505 1.39E-08 7.856746219 0.246292059 ILEGPQQSLSGSPLQPIPAS(ph)PPPQIPPGLRPR ddPTM_HeLa_Romidepsin_16h_R1 1 ILEGPQQSLSGSPLQPIPASPPPQIPPGLRPR 32 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 ILEGPQQSLSGSPLQPIPAS(1)PPPQIPPGLRPR 125.53 9.53E-16 28858000 838.16 702.21 578.76 683.33 940.12 763.2 711.95 804.37 658.41 772.32 TRUE FALSE FALSE 827.9441835 712.0957308 588.833075 762.3398298 892.1421683 714.4339831 772.4230152 827.6431769 599.5201606 752.2550151 1.100616369 0.9466148 0.782757261 1.013406112 1.18595709 0.949723124 1.026810057 1.10021623 0.796963993 1 9.555078009 -6.217478276 11.45799502 1.027075284 1.018965039 0 0.127287491 0 0 0.014242834 0 6.06E-07 6.217478276 -0.008110244 ILELT(ph)PEPDRPR ddPTM_HeLa_Romidepsin_16h_R1 4 ILELTPEPDRPR 12 1 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YF61 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR;ILELT(1)PEPDRPR ;;; 120.9 0.0039494 313649000 13253.8 12974.4 11491.1 11122.8 10006.6 9396.1 8642.8 9825.1 12971.5 12272.6 TRUE FALSE FALSE 13092.25759 13157.05394 11691.09778 12408.87047 9495.925862 8795.719535 9376.919216 10109.37377 11811.29655 11953.75608 1.095242156 1.100662742 0.978027132 1.038072919 0.794388458 0.735812198 0.784432872 0.845706881 0.988082446 1 13.54517639 -8.759670729 6.075180337 1.04502336 0.784454534 0.867889389 0.046364904 0.040436464 5.634873909 0.007470734 0.014396107 1.74E-09 8.759670729 -0.260568825 ILENEKDLEEAEEYK ddPTM_HeLa_Romidepsin_16h_R1 1 ILENEKDLEEAEEYK 15 1 E5RJD8;E5RHG6;O75347;E5RIW3 E5RJD8 TBCA Tubulin-specific chaperone A 0 0 127.03 5.46E-05 0 741.37 453.46 853 495.61 754 723.64 697 906.27 817.49 974.89 FALSE FALSE TRUE 732.3338973 459.8438218 867.8461072 552.9147601 715.5205664 677.4017394 756.2031626 932.4914926 744.371647 949.5622173 0.771233189 0.484269291 0.913943385 0.582283867 0.753526787 0.713383207 0.796370316 0.982022532 0.783910347 1 9.891118722 -11.8164633 0.903085249 0.987169515 0.744883011 0.061776057 0.149796545 0.458121276 0.733170198 0.063225986 0.026204705 1.53E-12 11.8164633 -0.242286504 ILENEKDLEEAEEYKEAR ddPTM_HeLa_Romidepsin_16h_R1 3 ILENEKDLEEAEEYKEAR 18 2 E5RJD8;E5RHG6;O75347;E5RIW3 E5RJD8 TBCA Tubulin-specific chaperone A 0 0 ;; ;; 82.578 0.0037876 24398800 4701.16 4058.74 4243.3 5052 5011.4 5008.3 4573.19 5170.13 5226 5059.52 FALSE FALSE TRUE 4643.860454 4115.879048 4317.152857 5636.13601 4755.649558 4688.285794 4961.636644 5319.719554 4758.573471 4928.072941 0.942327865 0.835190367 0.876032662 1.143679503 0.965012007 0.951342614 1.006810716 1.079472568 0.965605324 1 12.26680789 -9.291197008 24.99273769 0.952971849 1.020117716 0.320582661 0.070007802 995.7369958 836292.7717 0.011699647 0.017873019 5.11E-10 9.291197008 0.067145867 ILEPDDFLDDLDDEDYEEDT(ph)PKRR ddPTM_HeLa_Romidepsin_16h_R1 1 ILEPDDFLDDLDDEDYEEDTPKRR 24 2 J3KMZ8;Q92785 J3KMZ8 DPF2 Zinc finger protein ubi-d4 1 0 ILEPDDFLDDLDDEDY(0.408)EEDT(0.592)PKRR 87.228 3.71E-05 9908300 3821.8 3631.3 3257.6 3726.7 3060.5 2603.6 1747 1945.3 3856.7 3584.8 TRUE FALSE FALSE 3775.218432 3682.421537 3314.297162 4157.598589 2904.311265 2437.238363 1895.390136 2001.584186 3511.747093 3491.666379 1.081208232 1.054631553 0.949202129 1.190720458 0.831783724 0.698015818 0.542832542 0.573246115 1.00575104 1 11.7697 -8.330703408 2.067212417 1.042451802 0.569176798 0.886585415 0.070972436 0.069611714 0.572499636 0.009857267 0.028731444 4.67E-09 8.330703408 -0.473275004 ILEQQNSSRT(ph)LEK ddPTM_HeLa_Romidepsin_16h_R1 2 ILEQQNSSRTLEK 13 1 G3V1Q4;E7ES33;E7EPK1;Q16181-2;Q16181;Q5JXL7 G3V1Q4 SEPT7;DKFZp586I031 Septin-7 1 0 ILEQQNS(0.009)S(0.088)RT(0.903)LEK;ILEQQNS(0.006)S(0.471)RT(0.523)LEK ; 138.19 0.0056464 196878800 4179.05 4145.9 3987.7 5681.6 4317.14 4446.2 4079.3 3637.82 4393.44 3840.25 TRUE FALSE FALSE 4128.114131 4204.266089 4057.104246 6338.533325 4096.820236 4162.102169 4425.79564 3743.074582 4000.479723 3740.479751 1.103632263 1.123991137 1.084648097 1.694577633 1.095265984 1.112718808 1.18321604 1.000693716 1.069509793 1 11.86900761 -10.56431768 1.029219055 1.029315446 1.200452051 0.107198914 0.179358663 0.674848919 1.462320044 0.041949956 0.042748177 2.73E-11 10.56431768 0.171136605 ILESITVSS(ph)LMATPQDPK ddPTM_HeLa_Romidepsin_16h_R1 1 ILESITVSSLMATPQDPK 18 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 ILES(0.007)IT(0.305)VS(0.139)S(0.369)LMAT(0.18)PQDPK 80.312 0.018362 23236000 3942.4 3114.5 3640.7 3577.6 2767.3 2993.8 2526.3 2748.7 3713.6 3767.5 TRUE FALSE FALSE 3894.348512 3158.346013 3704.064856 3991.258945 2626.074355 2802.505842 2740.883859 2828.229298 3381.446315 3669.619807 1.061240324 0.860673906 1.009386544 1.087649172 0.71562573 0.763704686 0.746912215 0.770714528 0.921470477 1 11.84141488 -8.756794224 24.99999784 1.017614903 0.750106271 0.758501396 0.065474406 35.18202037 189345.5518 0.008830102 0.017203216 1.75E-09 8.756794224 -0.267508631 ILESITVSSLMAT(ph)PQDPK ddPTM_HeLa_Romidepsin_16h_R1 1 ILESITVSSLMATPQDPK 18 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 ILESITVS(0.001)S(0.006)LMAT(0.993)PQDPK 145.23 0.00022111 21684000 7006.3 6292.5 7963.2 6324.7 5558.8 5354.5 4861 5220.2 7288.5 6697.1 TRUE FALSE FALSE 6920.904521 6381.08598 8101.796156 7055.991573 5275.113693 5012.364731 5273.893219 5371.238251 6636.598306 6523.108377 1.060982605 0.978227804 1.242014648 1.081691605 0.808680983 0.768401265 0.808493883 0.823416988 1.017398136 1 12.67134388 -8.755181714 24.9563415 1.046327743 0.800276686 0.767412066 0.070049407 58.62571561 233804.2502 0.010743261 0.021067239 1.76E-09 8.755181714 -0.246051057 ILEVHIDK ddPTM_HeLa_Romidepsin_16h_R1 2 ILEVHIDK 8 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 0 ; ; 79.906 0.004261 2003800 12048.5 11312.9 11132.4 10927.6 11230.5 10877.7 10110 11000.8 12937.8 12303.4 FALSE FALSE TRUE 11901.64825 11472.1633 11326.15475 12191.10053 10657.36568 10182.65008 10968.74315 11319.09079 11780.61076 11983.75589 0.993148421 0.957309495 0.945125623 1.017302141 0.889317654 0.849704397 0.915300949 0.944536161 0.983048292 1 13.54879252 -8.754256754 24.99981438 0.990381636 0.897255898 0.644246316 0.029842498 73.41660493 255531.3064 0.004494649 0.008842168 1.76E-09 8.754256754 -0.093125738 ILEVHVDK ddPTM_HeLa_Romidepsin_16h_R1 1 ILEVHVDK 8 0 O60884 O60884 DNAJA2 DnaJ homolog subfamily A member 2 0 0 78.334 0.014489 1296600 4141.6 4133.9 3840.5 4098.7 4291.7 4273.8 3669.9 3602.2 4196.1 3907.9 FALSE FALSE TRUE 4091.120586 4192.097153 3907.342291 4572.610979 4072.678534 4000.717973 3981.621214 3706.423974 3820.790307 3806.372195 1.074808342 1.101336637 1.026526596 1.20130422 1.069963295 1.051058007 1.046040957 0.973741869 1.003787888 1 11.89420092 -4.300340791 20.88045064 1.050823353 0.114677109 0 0.061227332 0 0 0.008263772 0 5.01E-05 4.300340791 -0.936146244 ILGADTS(ph)VDLEETGR ddPTM_HeLa_Romidepsin_16h_R1 1 ILGADTSVDLEETGR 15 0 P25705-2;P25705;P25705-3;K7EK77;K7EQH4;K7EJP1;K7ERX7;K7ESA0 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 1 0 ILGADT(0.021)S(0.978)VDLEET(0.001)GR 109.99 0.004332 1966100 1044.3 830.75 831.65 773.88 861.93 904.31 829.07 872.53 1142.6 911.97 TRUE FALSE FALSE 1031.57167 842.4453203 846.1245194 863.3596468 817.9424958 846.5275095 899.4911851 897.7752789 1040.402994 888.2768879 1.161317697 0.948403962 0.952545913 0.97194879 0.920819293 0.952999589 1.012624776 1.010693052 1.171259782 1 9.794865644 -10.23646031 24.78200599 1.076177805 0.966194012 0.578243953 0.053849105 523.2841056 519156.7452 0.010763514 0.013179928 5.80E-11 10.23646031 -0.109983794 ILGADTSVDLEETGR ddPTM_HeLa_Romidepsin_16h_R1 1 ILGADTSVDLEETGR 15 0 P25705-2;P25705;P25705-3;K7EK77;K7EQH4;K7EJP1;K7ERX7;K7ESA0 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 0 280.17 1.33E-98 6511500 1346.6 1345.3 1014.7 1008.5 1152.3 1245.4 1354.1 1392 1307.8 1194.2 FALSE FALSE TRUE 1330.187121 1364.239169 1032.360428 1125.107515 1093.493831 1165.822959 1469.11722 1432.275324 1190.827093 1163.174512 1.14358345 1.172858548 0.88753701 0.967273185 0.940094388 1.002276913 1.26302391 1.231350334 1.023773372 1 10.18385185 -7.756994431 24.99998305 1.043971164 1.247187206 0.521976308 0.085006253 82.11379312 461819.4683 0.013836419 0.048440302 1.75E-08 7.756994431 0.203216041 ILGQS(ph)SPEKK ddPTM_HeLa_Romidepsin_16h_R1 1 ILGQSSPEKK 10 1 H7C485;P29374-3;P29374-2;P29374 H7C485 ARID4A AT-rich interactive domain-containing protein 4A 1 0 ILGQS(0.752)S(0.248)PEKK 138.25 0.0080211 37168000 8703.6 7786.6 6954.8 7200.1 8981.1 9371.1 8398 9401.2 8228.4 7556.5 TRUE FALSE FALSE 8597.517175 7896.219959 7075.845377 8032.609439 8522.760954 8772.316954 9111.32591 9673.208889 7492.431296 7360.181041 1.168112187 1.072829583 0.961368387 1.091360307 1.157955342 1.191861573 1.23792144 1.314262358 1.017968343 1 12.84552554 -8.024603425 1.069842837 1.071764568 1.311521895 0.713175096 0.057072728 0.409014782 0.720067182 0.011599864 0.081522226 9.45E-09 8.024603425 0.239757327 ILGQSS(ph)PEKK ddPTM_HeLa_Romidepsin_16h_R1 1 ILGQSSPEKK 10 1 H7C485;P29374-3;P29374-2;P29374 H7C485 ARID4A AT-rich interactive domain-containing protein 4A 1 0 ILGQS(0.164)S(0.836)PEKK 125.97 0.013942 20332000 3206.2 3400.5 3540.5 2886.5 3864.8 3895.4 3551.5 3824.8 3290.9 3154.7 TRUE FALSE FALSE 3167.121601 3448.372328 3602.120917 3220.250711 3667.564834 3646.496512 3853.164321 3935.464553 2996.553662 3072.740439 1.030715631 1.122246541 1.172282849 1.048006096 1.193581074 1.186724549 1.253983015 1.280767 0.975205593 1 11.58531019 -7.160377872 0.240814203 0.979784528 1.561220346 0.843160721 0.040487923 2.918681961 0.132448203 0.030647359 0.512841271 6.91E-08 7.160377872 0.581435818 ILGSAS(ph)PEEEQEKPILDRPTR ddPTM_HeLa_Romidepsin_16h_R1 1 ILGSASPEEEQEKPILDRPTR 21 2 Q7Z422-2;Q7Z422-4;Q7Z422-3;Q7Z422-5;Q7Z422 Q7Z422-2 SZRD1 SUZ domain-containing protein 1 1 0 ILGS(0.252)AS(0.748)PEEEQEKPILDRPTR 62.707 0.0054413 74767000 2560.2 2669.3 2362.5 2568.5 2687.8 2560.1 2709.5 2790.7 2669.3 3228.3 TRUE FALSE FALSE 2528.995298 2706.878475 2403.618321 2865.482055 2550.631536 2396.517872 2939.644862 2871.444502 2430.551123 3144.428301 0.804278252 0.860849165 0.764405511 0.911288724 0.81115907 0.762147406 0.934874191 0.913184919 0.772970757 1 11.61858202 -12.34512074 0.996780458 1.002775272 0.841782276 0 0.090632492 0.36840401 0.637165331 0.043184384 0.010555226 4.52E-13 12.34512074 -0.160992996 VVVSPTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VVVSPTKK 8 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; VVVSPTK(1)K;VVVSPTK(1)K 113.26 0.001966 17160900 4810.4 4512.4 6792 9546.1 19358.8 22333 20497 18094.4 4250.3 3687 FALSE TRUE FALSE 4751.768995 4575.925686 6910.211911 10649.865 18370.8482 20905.99338 22238.01467 18617.93292 3870.142523 3591.211208 1.323166118 1.274201215 1.92420092 2.965535687 5.115502022 5.821432426 6.192343858 5.184304636 1.07767054 1 11.81025479 -8.933109773 1.460984152 1.167228585 5.857843131 0.980301407 0.286569423 0.034460198 0.14710791 0.04509951 0.100476643 1.17E-09 8.933109773 4.690614546 up ILIPS(ph)DIESSK ddPTM_HeLa_Romidepsin_16h_R1 2 ILIPSDIESSK 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 0 ILIPS(1)DIESSK;ILIPS(1)DIESSK ; 150.49 0.0023408 114755000 16212.5 16157.4 15053.6 13397.4 16277.2 16821.1 15392.9 16858.9 16150.3 14527.7 TRUE FALSE FALSE 16014.89581 16384.8643 15315.60159 14946.47042 15446.51375 15746.286 16700.37254 17346.68567 14705.77672 14150.26826 1.131773301 1.157918988 1.082354151 1.056267637 1.091605718 1.112790635 1.180215967 1.225890941 1.039257804 1 13.78854178 -16.52287875 0.174745578 0.470630088 1.162027189 0.499647018 0.045942935 35.96743215 0.405724354 6.511161862 0.075034612 3.00E-17 16.52287875 0.691397101 ILISLATGHR ddPTM_HeLa_Romidepsin_16h_R1 2 ILISLATGHR 10 0 E5RK69;P08133-2;P08133;E7EMC6 E5RK69 ANXA6 Annexin;Annexin A6 0 0 ; ; 139.38 0.00070127 1238710 581.27 642.77 1023.73 234.483 1127.85 1519.88 786.36 691.79 666.62 397.62 FALSE FALSE TRUE 574.1852577 651.8189329 1041.547591 261.5950277 1070.291606 1422.764573 853.1533988 711.8058522 606.9958376 387.2897751 1.482572726 1.683026444 2.689323752 0.675450385 2.76354212 3.673643522 2.202881289 1.837915427 1.567291152 1 8.597269603 -9.873013569 0.503972897 1.067567843 2.580600184 0.262158783 0.729803982 0.702265884 0.397840738 0.243804874 0.403058114 1.34E-10 9.873013569 1.513032341 ILIVTQT(ph)PHYMR ddPTM_HeLa_Romidepsin_16h_R1 1 ILIVTQTPHYMR 12 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 0 ILIVT(0.197)QT(0.803)PHYMR 77.633 0.023546 42799000 3232.2 2680.8 2986.7 2637.9 2574.2 2134.8 1653.2 2236.8 2334.8 2506.3 TRUE FALSE FALSE 3192.804703 2718.540373 3038.682261 2942.90641 2442.828968 1998.39317 1793.622767 2301.518279 2125.96964 2441.185965 1.307890816 1.113614617 1.244756567 1.205523238 1.000673035 0.818615705 0.734734179 0.942786954 0.870875743 1 11.25336649 -8.482574574 3.093646427 1.1578174 0.82350705 0.495831209 0.128463652 0.136832983 2.615892253 0.018408887 0.042969134 3.29E-09 8.482574574 -0.33431035 ILLAELEQLKGQGK ddPTM_HeLa_Romidepsin_16h_R1 1 ILLAELEQLKGQGK 14 1 P08670;B0YJC4;A0A1B0GTT5 P08670 VIM Vimentin 0 0 201.09 1.57E-16 4046700 2157.1 2353.5 1939.7 3015.4 2344.1 2297.8 1995.7 1975.8 2469.4 1986 FALSE FALSE TRUE 2130.808435 2386.632635 1973.459665 3364.054736 2224.47183 2150.977996 2165.214708 2032.966656 2248.530679 1934.403434 1.101532596 1.233782257 1.020190324 1.739065738 1.149952379 1.111959356 1.119319099 1.050952775 1.162389727 1 10.917673 -10.67041155 1.143583772 1.027532974 1.21115536 0.049382193 0.196091191 0.610241128 1.649478244 0.044008938 0.042954383 2.14E-11 10.67041155 0.183622387 ILLSQTTGVAIPLHASSLDDVSLAS(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 1 ILLSQTTGVAIPLHASSLDDVSLASTPK 28 0 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 ILLSQTTGVAIPLHAS(0.027)S(0.011)LDDVS(0.04)LAS(0.526)T(0.396)PK 90.98 1.12E-07 14343000 792.81 673.23 717.99 428.31 1287.2 1186.8 982.84 897.91 809.5 730.23 TRUE FALSE FALSE 783.1469268 682.7077496 730.4863148 477.8332175 1221.509381 1110.96731 1066.322405 923.8896092 737.0962926 711.2585193 1.101072121 0.959858801 1.027033483 0.6718137 1.717391564 1.561973994 1.499205108 1.2989505 1.036326838 1 9.474230218 -8.750937104 24.99999898 1.016298082 1.520981631 0.766008499 0.148274551 82.0877973 195403.4724 0.021384098 0.042407525 1.77E-09 8.750937104 0.504683549 ILLVDS(ph)PGMGNADDEQQEEGTSSK ddPTM_HeLa_Romidepsin_16h_R1 4 ILLVDSPGMGNADDEQQEEGTSSK 24 0 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 0 ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(1)PGMGNADDEQQEEGTSSK;ILLVDS(0.998)PGMGNADDEQQEEGT(0.001)S(0.001)SK;ILLVDS(0.999)PGMGNADDEQQEEGT(0.001)SSK ;;; 136.2 7.05E-07 84691000 9248.2 8746.63 8597.02 8433.18 8712 8857.3 7929.89 9374 9114.3 8227.51 TRUE FALSE FALSE 9135.479381 8869.765287 8746.647527 9408.263951 8267.394131 8291.347116 8603.454659 9645.2219 8299.094181 8013.758104 1.139974437 1.106817198 1.091453899 1.174013968 1.031650073 1.034639055 1.07358552 1.20358286 1.035605776 1 12.96826325 -12.41217224 1.104071679 0.999177061 1.105762956 0.304152834 0.053107495 0.454264624 0.978275674 0.037722103 0.009258263 3.87E-13 12.41217224 0.106585895 ILMVGLDAAGK ddPTM_HeLa_Romidepsin_16h_R1 1 ILMVGLDAAGK 11 0 C9J1Z8;F5H423;P61204-2;P84085;P84077;P61204;F5H1V1;F5H6T5;F8WDB3;F5H0C7;C9JPM4;P18085 C9J1Z8 ARF5;ARF3;ARF1;ARF4 ADP-ribosylation factor 3;ADP-ribosylation factor 5;ADP-ribosylation factor 1;ADP-ribosylation factor 4 0 0 113.71 0.012977 819270 415.36 375.4 317.49 162.27 475.31 482.77 385.27 368.17 347.86 277.69 FALSE FALSE TRUE 410.2974326 380.6848911 323.0157803 181.0324209 451.0531571 451.9225551 417.9948242 378.8224181 316.7465304 270.4755738 1.516948192 1.407464954 1.194251206 0.669311533 1.667629911 1.670844242 1.545406923 1.400579035 1.171072589 1 8.079354502 -12.42507922 1.066497697 0.992147752 1.391092909 0.14501072 0.279129299 0.716534287 1.411312525 0.22120199 0.051413832 3.76E-13 12.42507922 0.398945157 ILNDLSS(ph)DAPGVPR ddPTM_HeLa_Romidepsin_16h_R1 1 ILNDLSSDAPGVPR 14 0 C9JBT4;C9J896;P16220;P16220-1;C9J4L5;H7C3I0;E7EWP8;P16220-3 C9JBT4 CREB1 Cyclic AMP-responsive element-binding protein 1 1 0 ILNDLS(0.379)S(0.621)DAPGVPR 105.28 0.007772 2224500 1192.9 1172.4 944.48 1327.1 872.75 719.49 534.2 698.02 1282.5 1134.8 TRUE FALSE FALSE 1178.360476 1188.905078 960.9182782 1480.545546 828.2103108 673.516911 579.5749347 718.2161074 1167.789988 1105.317732 1.066083029 1.075622912 0.869359325 1.339475069 0.74929614 0.609342356 0.524351431 0.649782489 1.056519726 1 10.11024543 -8.55586576 8.853402838 1.041775412 0.602423697 0.781659213 0.114223716 0.085306038 21.14541392 0.015180368 0.030520302 2.78E-09 8.55586576 -0.439351715 ILNIYRY(ph)MVVQVS(ph)MDK ddPTM_HeLa_Romidepsin_16h_R1 1 ILNIYRYMVVQVSMDK 16 1 A0A1B0GUI1;Q6GYQ0-3;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-2 A0A1B0GUI1 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 2 0 ILNIYRY(1)MVVQVS(1)MDK 55.912 0.0042415 0 685.37 771.16 627.07 602.42 747.37 697.79 555.57 619.32 897.91 903.55 TRUE FALSE FALSE 677.0164468 782.0164107 637.9838903 672.0746349 709.2289201 653.203471 602.7601019 637.2390471 817.5986807 880.0756407 0.769270748 0.888578634 0.724919383 0.763655536 0.805872686 0.742212874 0.684895791 0.724073043 0.929009557 1 9.781483716 -16.52287875 0.171590927 1.998783715 0.695855738 0.740594414 0.049557033 17.18505651 0.191744132 5.728233459 0.07072389 3.00E-17 16.52287875 -1.302927977 ILNTS(ph)PDGHPYEK ddPTM_HeLa_Romidepsin_16h_R1 1 ILNTSPDGHPYEK 13 0 Q16600 Q16600 ZNF239 Zinc finger protein 239 1 0 ILNT(0.11)S(0.89)PDGHPYEK 140.03 0.0011305 5617700 3041.3 3119.6 2494.8 2224.2 2058.6 1912.7 1812.8 1545.9 3211.7 2783.4 TRUE FALSE FALSE 3004.231466 3163.517811 2538.220947 2481.372469 1953.54196 1790.484643 1966.779187 1590.628177 2924.437508 2711.086867 1.108128073 1.166881759 0.93623741 0.915268522 0.7205752 0.660430569 0.725457827 0.586712361 1.078695612 1 11.40465562 -8.929717546 1.45792798 1.059126475 0.656899335 0.901489046 0.060794999 0.096414288 0.409940011 0.010797152 0.024124243 1.18E-09 8.929717546 -0.40222714 ILPGSMIVS(ph)SDDTVDSTIDR ddPTM_HeLa_Romidepsin_16h_R1 1 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59-2;Q9UK59 Q9UK59-2 DBR1 Lariat debranching enzyme 1 0 ILPGS(0.001)MIVS(0.907)S(0.073)DDT(0.019)VDSTIDR 118.66 0.00030719 8291700 1238.6 1086.1 948.96 734 974.1 1072 1115.8 939.83 1283.9 1156.2 TRUE FALSE FALSE 1223.503467 1101.390144 965.4762507 818.8685336 924.3880421 1003.50266 1210.576024 967.0224982 1169.064768 1126.161757 1.086436703 0.978003504 0.857315785 0.727132251 0.82083061 0.891082168 1.074957497 0.858688809 1.038096668 1 10.13719835 -9.92460101 4.012591219 1.040623975 0.873413173 0.461472757 0.083421198 0.162345566 5.152951237 0.01511885 0.020000041 1.19E-10 9.92460101 -0.167210803 ILPGSMIVSS(ph)DDTVDSTIDR ddPTM_HeLa_Romidepsin_16h_R1 2 ILPGSMIVSSDDTVDSTIDR 20 0 Q9UK59-2;Q9UK59 Q9UK59-2 DBR1 Lariat debranching enzyme 1 0 ILPGSMIVS(0.301)S(0.673)DDT(0.024)VDS(0.003)TIDR;ILPGSMIVS(0.304)S(0.65)DDT(0.021)VDS(0.023)T(0.001)IDR ; 138.98 0.0002561 12636100 3121.52 3042.3 3047.52 2389.69 2789.08 2580.23 2616.49 3198.83 3523.83 3311.36 TRUE FALSE FALSE 3083.473714 3085.129579 3100.560807 2665.997202 2646.74284 2415.36163 2838.734595 3291.383099 3208.649819 3225.33039 0.95601794 0.956531334 0.96131572 0.826581119 0.820611386 0.748872623 0.880137615 1.020479362 0.99482826 1 11.65523124 -9.328380967 5.415790449 0.975958264 0.852297081 0.429234974 0.065772363 0.155762715 8.939559536 0.010379786 0.016033415 4.69E-10 9.328380967 -0.123661183 ILPPLS(ph)PPQHR ddPTM_HeLa_Romidepsin_16h_R1 1 ILPPLSPPQHR 11 0 A0A087WV20;A0A087WTU9;Q8TCU4-3;Q8TCU4-2;Q8TCU4 A0A087WV20 ALMS1 Alstrom syndrome protein 1 1 0 ILPPLS(1)PPQHR 83.877 0.0032151 0 2463.3 1828.4 1996.9 1996.1 2072.4 1824 1698.4 1848.7 2257.9 1853.5 TRUE FALSE FALSE 2433.276352 1854.140263 2031.655207 2226.898474 1966.637695 1707.452287 1842.662054 1902.189218 2055.947769 1805.345803 1.347817326 1.027027764 1.125355156 1.233502452 1.089341273 0.945775753 1.020669863 1.053642585 1.138811061 1 10.81805949 -8.514621922 8.534680672 1.157910823 1.009472161 0.291532993 0.09560628 0.181270028 116.6073767 0.019574863 0.041343721 3.06E-09 8.514621922 -0.148438663 ILQK(ac)QGFK ddPTM_HeLa_Romidepsin_16h_R1 1 ILQKQGFK 8 1 E9PEX6;P09622-2;P09622-3;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 1 ILQK(1)QGFK 124.08 0.0077085 621350 166.43 115.36 583.71 293.22 577.96 747.13 468.54 233.29 160.07 0 FALSE TRUE FALSE 164.4014871 116.9840411 593.8692277 327.123476 548.4645445 699.3908043 508.3377759 240.0398781 145.7529383 0 0 ILQSQDFSLDS(ph)SAEEEGLR ddPTM_HeLa_Romidepsin_16h_R1 1 ILQSQDFSLDSSAEEEGLR 19 0 Q5T8I3-2;Q5T8I3 Q5T8I3-2 FAM102B Protein FAM102B 1 0 ILQSQDFSLDS(0.947)S(0.053)AEEEGLR 218.14 1.38E-29 3739700 962.74 641.78 786.15 616.95 751.32 668.95 511.78 687.08 546.29 686.8 TRUE FALSE FALSE 951.0057546 650.8149957 799.832611 688.2846618 712.9773368 626.2062539 555.2505804 706.9595758 497.4284542 668.956837 1.421624987 0.972880401 1.195641582 1.028892484 1.065804694 0.93609366 0.830024524 1.056808955 0.743588266 1 9.385769317 -8.923708416 1.113976251 1.188030371 0.933482023 0 0.191229867 0.504307458 1.234076459 0.029236324 0.074635636 1.19E-09 8.923708416 -0.254548348 ILS(ph)DVTHSAVFGVPASK ddPTM_HeLa_Romidepsin_16h_R1 1 ILSDVTHSAVFGVPASK 17 0 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 ILS(0.549)DVT(0.444)HS(0.007)AVFGVPASK 68.134 0.014445 130250000 9406.7 9994.7 8899.9 9656 11695 12106 10330 12767 10722 9951.6 TRUE FALSE FALSE 9292.047522 10135.40565 9054.799026 10772.47215 11098.16051 11332.46567 11207.42994 13136.393 9762.997466 9693.055997 0.958629304 1.045635726 0.934153174 1.111359736 1.144959909 1.169132384 1.156232869 1.355237503 1.007215626 1 13.24273587 -7.438407424 0.478449719 0.976588379 1.508859588 0.822469501 0.050370222 1.06655563 0.182306704 0.011064339 0.308808914 3.64E-08 7.438407424 0.532271209 ILTEAEIDAHLVALAERD ddPTM_HeLa_Romidepsin_16h_R1 1 ILTEAEIDAHLVALAERD 18 1 P60900-3;G3V5Z7;P60900-2;P60900;H0YJC4 P60900-3 PSMA6 Proteasome subunit alpha type-6;Proteasome subunit alpha type 0 0 86.453 0.0056027 4906000 1497.4 1676.9 1564.2 1651.2 1482.3 1541.4 1501.8 1505.9 2081.6 1574.2 FALSE FALSE TRUE 1479.149113 1700.507442 1591.424245 1842.119513 1406.6527 1442.909515 1629.362855 1549.470841 1895.416483 1533.302057 0.964682142 1.109049215 1.037906548 1.201406797 0.917400908 0.941047139 1.062649624 1.010545074 1.236166399 1 10.58242622 -10.32221977 24.9975634 0.983322114 1.038478424 0 0.110272032 420.1695615 172804.7453 0.013033604 0.014904497 4.76E-11 10.32221977 0.05515631 ILTFDQLALDS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ILTFDQLALDSPK 13 0 G3V203;H0YHA7;J3QQ67;Q07020-2;Q07020;F8VUA6 G3V203 RPL18 60S ribosomal protein L18 1 0 ILTFDQLALDS(1)PK 86.497 0.027936 30139000 1583.2 1757.1 1959.4 1192.5 1951.9 2655.9 2003.3 2029.8 1510.1 1982.5 TRUE FALSE FALSE 1563.903349 1781.8365 1993.502535 1330.382461 1852.287259 2486.196562 2173.460252 2088.529061 1375.032874 1930.994364 0.809895346 0.92275593 1.032370975 0.688962374 0.959240117 1.287521397 1.125565301 1.081582163 0.712085389 1 10.91512824 -8.423009539 6.425423678 0.902488635 1.158700643 0.552273407 0.118777316 0.144376557 7.889778843 0.015840299 0.035635927 3.78E-09 8.423009539 0.256212008 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR ddPTM_HeLa_Romidepsin_16h_R1 1 ILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVNR 36 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 128.92 2.84E-22 9773500 1141.2 893.73 1079.7 846.7 1428.7 1594 1234 1211.4 1273.1 1289.4 FALSE FALSE TRUE 1127.290615 906.3119544 1098.491726 944.5994378 1355.788108 1492.148544 1338.815929 1246.449948 1159.230747 1255.901202 0.897594981 0.721642716 0.874664125 0.752128779 1.079534047 1.188109815 1.066020103 0.992474524 0.923027023 1 10.29450726 -8.62067049 12.59512066 0.912481864 1.089441564 0.524002241 0.09552103 0.431674365 52.76729807 0.015930962 0.031865257 2.40E-09 8.62067049 0.176959699 ILVATNLFGR ddPTM_HeLa_Romidepsin_16h_R1 1 ILVATNLFGR 10 0 O00148;H0Y400;A0A140T9X3;A0A0G2JJZ9;Q5STU3;Q13838;Q13838-2 O00148;Q5STU3 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 0 120.31 0.028584 2112300 189.26 238.82 616.13 442.09 522.63 619.69 441.01 233.76 230.53 126.36 FALSE FALSE TRUE 186.9532263 242.1821142 626.8534842 493.2065259 495.9582409 580.093809 478.4693784 240.5234768 209.9108194 123.077149 1.518992176 1.967726066 5.093175211 4.007295668 4.029653311 4.713253547 3.887556564 1.954249662 1.705522277 1 6.94341912 -9.917288928 5.320677197 1.267743191 3.97946887 0.689873397 0.791606028 0.077832446 3.770237075 0.126128533 0.166488342 1.21E-10 9.917288928 2.711725679 ILVPKS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 ILVPKSPVK 9 1 Q9Y232-2;Q9Y232-4;Q9Y232 Q9Y232-2 CDYL Chromodomain Y-like protein 1 0 ILVPKS(1)PVK 104.52 0.0019872 0 730.97 726.18 6660 1076.5 1723.7 3264.6 2186.6 716.11 886.69 404.42 TRUE FALSE FALSE 722.0606565 736.4031811 6775.914506 1200.969995 1635.733157 3056.002596 2372.329749 736.829513 807.3822256 393.9131101 1.833045507 1.869455883 17.20154606 3.04881956 4.152522765 7.758062673 6.022469648 1.870538182 2.04964548 1 8.621733623 -9.958951012 24.99999889 1.417462446 6.675614006 0.276810245 3.946499196 135.4359087 82484.09082 0.603899559 0.793679076 1.10E-10 9.958951012 5.25815156 ILYLTPEQEK(ac)DK ddPTM_HeLa_Romidepsin_16h_R1 2 ILYLTPEQEKDK 12 1 B7Z7P8;P62495-2;P62495 B7Z7P8 ETF1 Eukaryotic peptide chain release factor subunit 1 0 1 ; ILYLTPEQEK(1)DK;ILYLTPEQEK(1)DK 126.19 0.011319 436350 310.08 371.05 327.14 0 647.18 422.83 553.24 411.39 569.05 424.3 FALSE TRUE FALSE 306.3006257 376.2736516 332.8337345 0 614.1519896 395.8125276 600.2321918 423.2929206 518.1527428 413.2766248 0.741151585 0.910464394 0.805353399 0 1.486055472 0.957742354 1.45237392 1.024236299 1.25376736 1 8.690963956 IMATPEQVGK(ac)MK ddPTM_HeLa_Romidepsin_16h_R1 2 IMATPEQVGKMK 12 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 1 ; IMATPEQVGK(1)MK;IMATPEQVGK(1)MK 100.93 0.002078 46688000 8705 8245.8 8098 7741.9 8352.3 8052.2 7945.3 7919.1 8769.9 7465.9 FALSE TRUE FALSE 8598.900112 8361.884589 8238.942293 8637.054905 7926.050964 7537.690407 8620.173584 8148.226664 7985.498179 7271.934842 1.182477607 1.149884422 1.132978014 1.187724463 1.089950768 1.036545372 1.185403028 1.120503256 1.098125651 1 12.82812356 -12.40478688 1.104612541 0.999193179 1.138515388 0.22621794 0.053179533 0.304637426 0.658757166 0.032956696 0.008181873 3.94E-13 12.40478688 0.139322209 IMDS(ph)AQY(ph)AEFCES(ph)RQLS(ph)FSKK ddPTM_HeLa_Romidepsin_16h_R1 1 IMDSAQYAEFCESRQLSFSKK 21 2 O75486;A0A1B0GVT7;A0A6I8PRV1;O75486-4 O75486 SUPT3H Transcription initiation protein SPT3 homolog 4 0 IMDS(0.999)AQY(0.998)AEFCES(0.995)RQLS(0.504)FS(0.504)KK 40.968 0.0041721 0 0 0 122.13 0 132.16 0 0 208.74 144.04 170.72 TRUE FALSE FALSE 0 0 124.2556214 0 125.415382 0 0 214.7795626 131.1567016 166.2846698 0 0 0.747246403 0 0.754220953 0 0 1.291637785 0.788748006 1 7.377511359 -12.47666421 1.22874963 0.99831482 0.295238223 0.190183831 0.433293131 0.472107802 1.280115427 0.276992327 0.06863907 3.34E-13 12.47666421 -0.703076597 IMEET(ph)SGMEEEEEEESIAAVPGR ddPTM_HeLa_Romidepsin_16h_R1 2 IMEETSGMEEEEEEESIAAVPGR 23 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 IMEET(0.558)S(0.442)GMEEEEEEESIAAVPGR;IMEET(0.541)S(0.459)GMEEEEEEESIAAVPGR ; 118.85 1.96E-06 9411500 2297.04 1935.23 2291.38 2036.77 2058.3 2141.32 2061.31 1967.24 2791.89 2643.94 TRUE FALSE FALSE 2269.042793 1962.474219 2331.260508 2272.270931 1953.25727 2004.496563 2236.39762 2024.158986 2542.176366 2575.250058 0.881096104 0.762051908 0.905255977 0.882349628 0.758472858 0.77836968 0.868419598 0.786004831 0.987157095 1 11.33049681 -11.55601701 0.377694632 1.031954041 0.804870285 0.651570828 0.049690276 0.755156773 0.212843807 0.070719943 0.023098143 2.78E-12 11.55601701 -0.227083756 IMGPNYT(ph)PGKK ddPTM_HeLa_Romidepsin_16h_R1 1 IMGPNYTPGKK 11 1 P13639 P13639 EEF2 Elongation factor 2 1 0 IMGPNYT(1)PGKK 95.417 0.013441 13639000 3744.1 3142.1 3447.6 2403.1 3514.9 3648.8 2954 3135 3827.8 3065.6 TRUE FALSE FALSE 3698.465469 3186.334566 3507.604032 2680.957729 3335.521537 3415.653456 3204.912686 3225.706279 3485.431981 2985.95527 1.23862052 1.067107267 1.174700796 0.897855958 1.117070162 1.143906438 1.073329101 1.0802929 1.167275349 1 11.54397684 IMNT(ph)FSVMPSPK ddPTM_HeLa_Romidepsin_16h_R1 1 IMNTFSVMPSPK 12 0 Q9BVA1;Q13885 Q9BVA1 TUBB2B;TUBB2A Tubulin beta-2B chain;Tubulin beta-2A chain 1 0 IMNT(0.995)FS(0.005)VMPSPK 76.943 0.0020933 0 4720.6 4537.4 4193 4203.6 3551.4 3568.7 3229.1 3789.4 4896.5 4474.4 TRUE FALSE FALSE 4663.063511 4601.277636 4265.977406 4689.640011 3370.158806 3340.671587 3503.379673 3899.04031 4458.544776 4358.154443 1.069962887 1.055785814 0.978849525 1.076060996 0.773299535 0.766533548 0.80386772 0.894654001 1.023035056 1 12.08950161 -8.76000781 24.99999992 1.033876179 0.806104664 0.868135292 0.0428287 10.13768 177031.7638 0.006690637 0.012825014 1.74E-09 8.76000781 -0.227771515 IMNTFSVVPSPK ddPTM_HeLa_Romidepsin_16h_R1 1 IMNTFSVVPSPK 12 0 Q5JP53;P07437;Q5ST81;P04350;M0QYM7;M0R042;M0R2D3;P68371;A0A0B4J269;Q13509;Q13509-2;G3V2A3 Q5JP53;P04350;P68371;A0A0B4J269 TUBB;TUBB4A;TUBB4B;TUBB3 Tubulin beta chain;Tubulin beta-4A chain;Tubulin beta-4B chain;Tubulin beta-3 chain 0 0 111.63 5.30E-05 0 0 119.09 0 0 55.841 0 0 0 0 136.48 FALSE FALSE TRUE 0 120.7665521 0 0 52.9912254 0 0 0 0 132.9342299 0 0.908468437 0 0 0.398627392 0 0 0 0 1 7.054568829 -16.52287875 0.256287483 6.69212453 0.056813172 0 0.419830014 24.14296245 0.320970176 69.68009762 0.154314205 3.00E-17 16.52287875 -6.635311358 IMSSIDVGINNELKEMNGPR ddPTM_HeLa_Romidepsin_16h_R1 1 IMSSIDVGINNELKEMNGPR 20 1 Q7Z6G8-6 Q7Z6G8-6 0 0 57.595 0.013288 1932000 986.63 1189 1180.2 1006.5 1243 1020.4 1111.4 781.72 1073.9 902.78 FALSE FALSE TRUE 974.6045741 1205.738773 1200.740886 1122.876266 1179.565072 955.1997332 1205.802288 804.3378348 977.8476944 879.3256455 1.108354543 1.37120847 1.365524697 1.276974317 1.341442818 1.086286677 1.371280702 0.914721229 1.112042733 1 9.780253735 -10.50677133 3.543713565 1.043973598 1.254807478 0.237254852 0.141406832 0.191336698 4.926527682 0.023950234 0.026173991 3.11E-11 10.50677133 0.21083388 INAEK(ac)SSK ddPTM_HeLa_Romidepsin_16h_R1 2 INAEKSSK 8 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 1 ; INAEK(1)SSK;INAEK(1)SSK 106.88 0.017611 1789840 336.5 419.41 887.25 633.84 355.96 459.58 1201.65 151.06 1057.97 547.33 FALSE TRUE FALSE 332.3986086 425.314465 902.6922141 707.1275631 337.7940329 430.2143212 1303.718121 155.4306828 963.3425135 533.1102877 0.623508149 0.79779827 1.693256039 1.326418903 0.633628802 0.806989344 2.445494208 0.291554461 1.807022929 1 9.058290213 INEKPQVIADYESGR ddPTM_HeLa_Romidepsin_16h_R1 1 INEKPQVIADYESGR 15 1 O60869-2;O60869-3;O60869 O60869-2 EDF1 Endothelial differentiation-related factor 1 0 0 93.228 0.015191 13731000 1826.6 2128.7 1757 1804.2 2104.2 1858.3 1669.9 1988.5 1855.2 1889.2 FALSE FALSE TRUE 1804.336697 2158.667894 1787.579848 2012.810093 1996.814822 1739.560627 1811.741264 2046.03411 1689.266266 1840.118312 0.98055472 1.173113642 0.971448323 1.093848195 1.085155672 0.945352598 0.984578683 1.111903565 0.918020464 1 10.84558281 INFS(ph)DLDQR ddPTM_HeLa_Romidepsin_16h_R1 2 INFSDLDQR 9 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154;E9PGW9;E5RGQ4;Q15154-3 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 INFS(1)DLDQR;INFS(1)DLDQR ; 163.71 0.0028926 33099000 5798.5 5111.5 5224.2 4496.7 5972.4 6457.5 5898.7 6089.3 5133.7 5177.6 TRUE FALSE FALSE 5727.825652 5183.459831 5315.12501 5016.629612 5667.606142 6044.886591 6399.735431 6265.484288 4674.529014 5043.085206 1.135778084 1.027835069 1.053943131 0.994754085 1.123837078 1.198648515 1.269011958 1.242391122 0.926918508 1 12.30009089 -8.274228063 2.284872879 1.057514075 1.252289527 0.719787494 0.057675152 0.131883237 1.331684284 0.008126712 0.023734459 5.32E-09 8.274228063 0.194775453 INFVGGNK(ac)LQSTGNK ddPTM_HeLa_Romidepsin_16h_R1 2 INFVGGNKLQSTGNK 15 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 1 ; INFVGGNK(1)LQSTGNK;INFVGGNK(1)LQSTGNK 185.2 3.49E-09 7481400 1935.43 2585.3 1846.02 1832.6 2222.9 1817.13 2325.8 2033.7 2481.6 2208.9 FALSE TRUE FALSE 1911.840235 2621.695921 1878.149204 2044.493835 2109.457118 1701.021258 2523.353394 2092.541901 2259.639481 2151.51246 0.888602911 1.218536249 0.87294368 0.950258887 0.980453127 0.790616503 1.172827693 0.972591114 1.050256284 1 11.07113548 -7.740438929 24.99994066 0.954561923 1.072709269 0.100355072 0.118123248 339.3483755 403970.3139 0.014833495 0.055384901 1.82E-08 7.740438929 0.118147346 INHTVILDDPFDDPPDLLIPDRS(ph)PEPTR ddPTM_HeLa_Romidepsin_16h_R1 1 INHTVILDDPFDDPPDLLIPDRSPEPTR 28 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 1 0 INHTVILDDPFDDPPDLLIPDRS(0.864)PEPT(0.136)R 82.486 1.23E-06 5595000 574.89 699.94 560.05 714.1 660 800.84 632.98 635 795.08 608.65 TRUE FALSE FALSE 567.8830196 709.7937737 569.7974353 796.6676019 626.3177372 749.6689086 686.7453054 653.3727231 723.9660535 592.8371853 0.957907219 1.197282814 0.961136463 1.343821916 1.056475121 1.264544342 1.158404571 1.102111574 1.221188669 1 9.211492132 -9.997654135 1.333736504 0.979709644 1.170422941 0 0.128837292 0.27829419 0.969221793 0.017660384 0.023518584 1.01E-10 9.997654135 0.190713297 INMISGVLQRY(ph)CR ddPTM_HeLa_Romidepsin_16h_R1 1 INMISGVLQRYCR 13 1 Q99909-2 Q99909-2 1 0 INMISGVLQRY(1)CR 41.052 0.028758 5012900 370.46 294.97 325.76 12219 238.53 852.71 237.29 365.73 276.1 354.31 TRUE FALSE FALSE 365.944691 299.1225954 331.4297162 13631.81827 226.356924 798.224583 257.4454067 376.3118205 251.4049245 345.1049751 1.060386599 0.866758282 0.960373626 39.50049769 0.655907449 2.312990657 0.745991583 1.09042711 0.728488265 1 8.430891462 INPDEREEMK(ac)VSAK ddPTM_HeLa_Romidepsin_16h_R1 2 INPDEREEMKVSAK 14 2 P48507-2;P48507 P48507-2 GCLM Glutamate--cysteine ligase regulatory subunit 0 1 ; INPDEREEMK(1)VSAK;INPDEREEMK(1)VSAK 114.7 0.0004775 3044600 1366.47 970.81 980.15 1174.59 1209.96 1561.13 901.78 1536.42 1268.28 1237.87 FALSE TRUE FALSE 1349.814938 984.4770887 997.2090996 1310.401622 1148.211226 1461.378831 978.3771707 1580.873889 1154.84186 1205.709959 1.119518776 0.816512364 0.827072126 1.08682989 0.952311306 1.212048404 0.811453172 1.311156035 0.957810667 1 10.23566718 -7.228106294 23.26609801 1.019413238 1.311157473 0.316397108 0.134818443 5833.422679 4071486.348 0.018166543 3.527896402 5.91E-08 7.228106294 0.291744235 INPDNY(ph)GMDLNSDDS(ph)TDDEAHPR ddPTM_HeLa_Romidepsin_16h_R1 1 INPDNYGMDLNSDDSTDDEAHPR 23 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 2 0 INPDNY(0.742)GMDLNS(0.235)DDS(0.517)T(0.506)DDEAHPR 45.079 0.020721 2070500 2857.6 3706.3 1484.5 1033.4 1083.6 1444.6 1435.5 1953.9 3572.5 3846.6 TRUE FALSE FALSE 2822.770472 3758.477389 1510.3371 1152.88657 1028.299849 1352.294722 1557.431334 2010.433014 3252.966653 3746.664777 0.753408869 1.003152834 0.403115088 0.307710094 0.274457393 0.360932937 0.415684729 0.536592712 0.868229971 1 11.87139119 -9.751490652 24.72329922 0.889270451 0.375193696 0.882186775 0.093544268 52.40715953 130235.083 0.018440462 0.025896275 1.77E-10 9.751490652 -0.514076755 INPPSSGGTSS(ph)SPIK ddPTM_HeLa_Romidepsin_16h_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 0 INPPS(0.001)S(0.003)GGT(0.003)S(0.013)S(0.49)S(0.49)PIK 126.63 0.0025982 60647000 3503.5 3637.2 3299.8 3278.5 2671.8 2710.4 2517.3 2023.2 3758.5 3780.1 TRUE FALSE FALSE 3460.797994 3688.404597 3357.231635 3657.575596 2535.448076 2537.214187 2731.119399 2081.7381 3422.330347 3681.892457 0.939950864 1.001768694 0.911822296 0.993395554 0.688626326 0.689106001 0.741770552 0.565398942 0.929503071 1 11.84623177 -8.757231099 24.55359668 0.969868054 0.677541488 0.889298462 0.05032966 18.25230926 106492.8942 0.006854254 0.013322025 1.75E-09 8.757231099 -0.292326566 INS(ph)SGESGDESDEFLQSR ddPTM_HeLa_Romidepsin_16h_R1 1 INSSGESGDESDEFLQSR 18 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 INS(0.389)S(0.389)GES(0.223)GDESDEFLQSR 116.98 0.0014771 18269000 381.58 291.22 229.54 292.9 341.73 330.29 278.78 397.62 491.55 343.26 TRUE FALSE FALSE 376.9291562 295.3198028 233.5350474 326.7664761 324.2902429 309.185535 302.4595662 409.1245074 447.5845369 334.3420557 1.127375841 0.883286436 0.698491391 0.977341829 0.969935542 0.924758132 0.904641104 1.223670491 1.338702473 1 8.385181028 -10.25627393 24.92158413 1.060149703 0.931597798 0.230219583 0.152329833 531.0800047 2562291.115 0.021251123 0.025606851 5.54E-11 10.25627393 -0.128551904 INSS(ph)PNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_HeLa_Romidepsin_16h_R1 2 INSSPNVNTTASGVEDLNIIQVTIPDDDNER 31 0 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 0 INS(0.275)S(0.725)PNVNTTASGVEDLNIIQVTIPDDDNER;INS(0.14)S(0.35)PNVNT(0.252)T(0.252)AS(0.007)GVEDLNIIQVTIPDDDNER ; 141.61 6.34E-16 16195700 1717.06 1610.6 1692.49 1574.04 1624.67 1455.68 1167.86 1449.27 1708.91 1897.81 TRUE FALSE FALSE 1696.131812 1633.274069 1721.947078 1756.037911 1541.757027 1362.666746 1267.057999 1491.202341 1556.06081 1848.504623 0.917569689 0.883565044 0.931535176 0.94997756 0.834056355 0.737172485 0.685450274 0.806707391 0.841794384 1 10.85214294 -8.552423966 2.416857987 0.951198841 0.736822338 0.671175223 0.053198597 0.09422456 1.101965891 0.007172616 0.016987077 2.80E-09 8.552423966 -0.214376503 INSSGES(ph)GDESDEFLQSR ddPTM_HeLa_Romidepsin_16h_R1 1 INSSGESGDESDEFLQSR 18 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 INS(0.001)S(0.115)GES(0.442)GDES(0.442)DEFLQSR 296.01 1.28E-124 20861000 2075.9 1728.5 1778.8 1669.9 1939.5 2136.4 2204 2267.6 2094 1871 TRUE FALSE FALSE 2050.598132 1752.833868 1809.759268 1862.981695 1840.520078 1999.890935 2391.207705 2333.209428 1906.707395 1822.39115 1.12522393 0.961831859 0.993068512 1.022273234 1.009947879 1.097399389 1.312126491 1.280301119 1.046266821 1 10.83161693 -7.840865793 4.052720371 1.04253248 1.298371826 0.848648652 0.044936102 0.075739982 2.347025782 0.008324282 0.028417086 1.44E-08 7.840865793 0.255839346 INSSGESGDES(ph)DEFLQSR ddPTM_HeLa_Romidepsin_16h_R1 2 INSSGESGDESDEFLQSR 18 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 INSSGESGDES(1)DEFLQSR;INSSGES(0.008)GDES(0.992)DEFLQSR ; 189.84 1.82E-14 5300900 1240.83 758.25 802.96 929.44 852.91 1514.04 1336.25 1376.59 1450.19 1201.15 TRUE FALSE FALSE 1225.706287 768.9246634 816.935182 1036.906226 809.3828201 1417.29773 1449.751042 1416.41946 1320.481374 1169.94395 1.0476624 0.657232052 0.69826865 0.886287096 0.69181333 1.211423616 1.239162818 1.210672922 1.128670629 1 10.1922237 -8.125319304 10.49472155 0.940429498 1.224936489 0.465728757 0.159524867 0.356808226 28.56744012 0.024894152 0.063559415 7.49E-09 8.125319304 0.28450699 INVELSTK ddPTM_HeLa_Romidepsin_16h_R1 2 INVELSTK 8 0 Q96PK6;Q96PK6-2 Q96PK6 RBM14 RNA-binding protein 14 0 0 ; ; 109.71 0.024085 1895750 1090.31 780.55 1396.93 1323.39 1550.48 1594.6 1109.67 1001.27 1002.73 825.38 FALSE FALSE TRUE 1077.020882 791.5386034 1421.242981 1476.406579 1471.35322 1492.710206 1203.925342 1030.240168 913.0433174 803.9365086 1.339684006 0.984578502 1.767854756 1.836471615 1.830185847 1.856751361 1.497537839 1.281494442 1.135715703 1 9.650937758 -9.755493549 24.997835 1.151701183 1.692356157 0.673693994 0.191256429 75.15239038 315959.1172 0.034688504 0.048322924 1.76E-10 9.755493549 0.540654974 INVELSTK(ac)GQK ddPTM_HeLa_Romidepsin_16h_R1 2 INVELSTKGQK 11 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 1 ; INVELSTK(1)GQK;INVELSTK(1)GQK 185.99 2.28E-05 4230700 2385.9 2189.9 2319.9 3066.6 2689.4 3266.1 2878.2 2750.7 2202.3 1952.08 FALSE TRUE FALSE 2356.819733 2220.72947 2360.276886 3421.174721 2552.149882 3057.406751 3122.674236 2830.287165 2005.320772 1901.36468 1.239541135 1.167966089 1.241359383 1.799325903 1.342272689 1.608006493 1.642333146 1.488555664 1.054674463 1 10.89281955 -9.843454639 0.469811001 1.037052593 1.627235262 0.677264658 0.143643268 0.400167191 0.200479486 0.052735776 0.090175608 1.43E-10 9.843454639 0.590182668 INVYYNEATGGK ddPTM_HeLa_Romidepsin_16h_R1 3 INVYYNEATGGK 12 0 P68371 P68371 TUBB4B Tubulin beta-4B chain 0 0 ;; ;; 203.03 7.14E-14 15120800 2916.31 2927.35 3280.73 2738.35 3347.09 3505.16 3139.17 3553.71 3056.74 2816.13 FALSE FALSE TRUE 2880.764892 2968.56131 3337.829729 3054.970911 3176.275508 3281.191588 3405.811021 3656.530992 2783.337519 2742.966537 1.05023698 1.082244814 1.216868556 1.113747058 1.157970929 1.196220058 1.241652414 1.333057091 1.014718 1 11.42152131 -4 0.16937486 0.965047899 2.402976387 0.868826504 0.037000785 13.65032114 0.14305666 0.056441487 4.995341418 1.00E-04 4 1.437928489 INY(ph)LLGPDAPPEFS(ph)LDCRTGMLT(ph)VVK ddPTM_HeLa_Romidepsin_16h_R1 1 INYLLGPDAPPEFSLDCRTGMLTVVK 26 1 Q9BZA7-7;Q9BZA7-2;Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-3;Q9BZA7-8;Q9BZA7 Q9BZA7-7 PCDH11X Protocadherin-11 X-linked 3 0 INY(0.999)LLGPDAPPEFS(0.984)LDCRT(0.119)GMLT(0.898)VVK 42.325 0.004215 0 568.39 511.97 456.43 498.72 659.23 539.26 355.23 648.33 578.48 458.02 TRUE FALSE FALSE 561.4622441 519.1775271 464.3739727 556.3843529 625.5870332 504.8030264 385.4032273 667.0884057 526.7393 446.1205744 1.258543713 1.163760555 1.040915841 1.247161384 1.402282408 1.131539443 0.863899245 1.495309663 1.18071062 1 8.801289874 -12.42899394 1.06951651 0.996052184 1.194869401 0.017916765 0.17553899 0.78901475 1.562108594 0.121736671 0.028207272 3.72E-13 12.42899394 0.198817217 IPASQT(ph)SVPFDHLGK ddPTM_HeLa_Romidepsin_16h_R1 1 IPASQTSVPFDHLGK 15 0 H0Y5S9;H0Y682;P49674 H0Y5S9 CSNK1E Casein kinase I isoform epsilon 1 0 IPAS(0.184)QT(0.49)S(0.326)VPFDHLGK 66.068 0.0038373 0 1605.5 1704 1348 1768 1761.7 1753.2 1832.1 1708.1 1819.8 1597.8 TRUE FALSE FALSE 1585.931548 1727.988957 1371.461375 1972.424479 1671.793875 1641.176178 1987.718528 1757.521179 1657.03253 1556.288926 1.019046992 1.110326578 0.881238279 1.267389651 1.074218192 1.054544661 1.277216907 1.129302631 1.064733227 1 10.60389421 -9.257289278 24.99971475 1.009724251 1.156333101 0.41378369 0.086381595 252.6028406 1521646.975 0.01191345 0.019309695 5.53E-10 9.257289278 0.14660885 IPCKS(ph)SPELEDTATSSK ddPTM_HeLa_Romidepsin_16h_R1 2 IPCKSSPELEDTATSSK 17 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 IPCKS(0.606)S(0.388)PELEDT(0.004)AT(0.002)S(0.001)SK;IPCKS(0.5)S(0.5)PELEDTATSSK ; 74.12 0.0096122 29969000 4621.6 3838 4348.3 903.66 3268.5 3518.6 4729.1 4087.3 5333.9 4891.5 TRUE FALSE FALSE 4565.270162 3892.031465 4423.980337 1008.145421 3101.696249 3293.772816 5130.789636 4205.559577 4856.822625 4764.418125 0.958200989 0.816895445 0.928545779 0.211598855 0.651012604 0.691327404 1.07689743 0.882701616 1.019394708 1 12.21808431 -9.966940637 1.868053493 0.981144116 0.722317691 0.224434987 0.21356889 0.390895734 2.717633111 0.039022672 0.051834731 1.08E-10 9.966940637 -0.258826424 IPDEINDR ddPTM_HeLa_Romidepsin_16h_R1 1 IPDEINDR 8 0 H7C5M9;C9JSA3;C9JND6;C9J363;C9J6F3;C9J5C3;Q9BUL8 H7C5M9 PDCD10 Programmed cell death protein 10 0 0 104.06 0.0036241 0 1196.8 788.81 703.9 689.08 950.47 1068.2 750.52 842.66 1323.1 873.27 FALSE FALSE TRUE 1182.212941 799.9148879 716.1510842 768.7546718 901.9639692 999.9454675 814.2691501 867.0410376 1204.758622 850.5823195 1.389886568 0.940432066 0.84195388 0.903798085 1.060407615 1.175601049 0.957307872 1.019349941 1.41639274 1 9.732307057 -10.2223923 24.98352439 1.184113167 0.985985365 0.419663238 0.14254736 584.5046937 373985.0032 0.028061384 0.03436775 5.99E-11 10.2223923 -0.198127802 IPEISIQDMTAQVT(ph)SPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 IPEISIQDMTAQVTSPSGK 19 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 0 IPEISIQDMT(0.006)AQVT(0.871)S(0.116)PS(0.007)GK 120.9 0.0021405 9993200 6656.7 5749.9 6078.2 4449 8343.3 8237.1 6687.4 7761.6 7094.9 7329.6 TRUE FALSE FALSE 6575.56558 5830.847243 6183.988521 4963.414313 7917.510268 7710.775894 7255.427589 7986.16965 6460.314374 7139.175935 0.921053864 0.816739536 0.866204808 0.695236307 1.109022994 1.080065257 1.016283624 1.118640264 0.904910375 1 12.80154184 IPEISIQDMTAQVTS(ph)PSGK ddPTM_HeLa_Romidepsin_16h_R1 1 IPEISIQDMTAQVTSPSGK 19 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 1 0 IPEISIQDMTAQVT(0.068)S(0.931)PS(0.001)GK 89.468 0.0056849 11699000 3847.7 3598.3 4466.7 2973.9 4706.7 5251 4512.7 5147.4 4609.9 4304.3 TRUE FALSE FALSE 3800.802752 3648.956962 4544.44104 3317.756311 4466.499536 4915.478047 4896.008625 5296.331898 4197.578998 4192.473665 0.906577609 0.870358946 1.083952197 0.791360084 1.065361381 1.172452933 1.167809035 1.26329521 1.001217738 1 12.03358601 -8.412602775 3.243920218 0.947584964 1.199444559 0.67436631 0.080137848 0.108949935 2.150675466 0.011021416 0.026419417 3.87E-09 8.412602775 0.251859595 IPEPES(ph)PAKPNVPTASTAPPADSR ddPTM_HeLa_Romidepsin_16h_R1 2 IPEPESPAKPNVPTASTAPPADSR 24 1 Q9BZL4-5;Q9BZL4-4;Q9BZL4;K7EL81;Q9BZL4-2;Q9BZL4-3;K7ER83 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 0 IPEPES(0.989)PAKPNVPT(0.001)AS(0.004)T(0.005)APPADSR;IPEPES(1)PAKPNVPTASTAPPADSR ; 81.224 0.00010239 31998000 1416.38 1249.5 1497.13 992.07 1628.91 1469.77 1241.17 1252.6 1428.11 1297.27 TRUE FALSE FALSE 1399.116616 1267.090494 1523.18692 1106.777801 1545.780644 1375.85644 1346.594949 1288.842005 1300.376265 1263.566738 1.107275598 1.002788737 1.205466141 0.875915587 1.223347052 1.088867251 1.065709399 1.020003111 1.029131446 1 10.30328615 -12.46793218 1.129922593 0.998745357 1.077650762 0.055204725 0.094350742 0.999006205 2.222257443 0.063606704 0.014674342 3.40E-13 12.46793218 0.078905405 IPEPS(ph)PVTR ddPTM_HeLa_Romidepsin_16h_R1 1 IPEPSPVTR 9 0 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 IPEPS(0.909)PVT(0.091)R 98.156 0.030464 8634700 1049.7 1137.2 846.72 3297.4 738.24 644.42 570.68 786.73 873.86 1209.8 TRUE FALSE FALSE 1036.905853 1153.209531 861.4568064 3678.660903 700.564858 603.2436418 619.153545 809.4927913 795.699773 1178.369222 0.879949878 0.978648721 0.731058475 3.121823649 0.594520669 0.511930922 0.52543255 0.68696023 0.675255055 1 10.20257594 -8.573092712 24.99998902 1.095194022 0.567026473 0.167714098 0.671140492 168.3048411 83793.12294 0.095092658 0.190185345 2.67E-09 8.573092712 -0.528167549 IPEVPLHDT(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 IPEVPLHDTPER 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 0 IPEVPLHDT(1)PER 105.53 0.0096792 4877700 1019.3 1304.1 1142.9 1107.5 1164.6 1286.2 1305.6 1108.9 1247.7 1308.6 TRUE FALSE FALSE 1006.87638 1322.459154 1162.791695 1235.554361 1105.166116 1204.015971 1416.497631 1140.984272 1136.102587 1274.602383 0.789953316 1.037546431 0.912277986 0.969364546 0.867067354 0.944620838 1.111325108 0.895168789 0.891338822 1 10.31583155 -7.987315829 24.70654365 0.913126029 1.009428487 0.11663832 0.082095563 292.9674088 570639.4184 0.013250953 0.039716578 1.03E-08 7.987315829 0.096302458 IPGTPGAGGRLS(ph)PENNQVLTK ddPTM_HeLa_Romidepsin_16h_R1 2 IPGTPGAGGRLSPENNQVLTK 21 1 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 0 IPGT(0.004)PGAGGRLS(0.992)PENNQVLT(0.004)K;IPGT(0.008)PGAGGRLS(0.988)PENNQVLT(0.004)K ; 53.659 0.014288 301030000 5105.3 4972.5 4417 5062.7 4746.3 4798.1 3955.6 4422.1 4784.1 4684.9 TRUE FALSE FALSE 5043.07464 5042.502986 4493.876032 5648.073195 4504.0786 4491.516895 4291.588565 4550.046487 4356.198114 4563.185623 1.105165351 1.105040076 0.984811139 1.23774785 0.987046983 0.984294146 0.940480822 0.997120622 0.954639691 1 12.15582563 -8.552533925 24.99976114 1.063808387 0.973125455 0.242180314 0.075935135 204.1295172 172083.5359 0.010262143 0.020524498 2.80E-09 8.552533925 -0.090682932 LTTTGQVT(ph)SPVK ddPTM_HeLa_Romidepsin_16h_R1 2 LTTTGQVTSPVK 12 0 K7ENR9;K7ERZ5;P49916-4;P49916-3;P49916-2;P49916 K7ENR9 LIG3 DNA ligase 3 1 0 LTTTGQVT(0.703)S(0.297)PVK;LTTTGQVT(0.5)S(0.5)PVK ; 168.83 0.0003884 124653000 10987.6 10416.8 11814.3 7074 6648.4 5356.8 3827.9 4243.5 11883.7 11578.9 TRUE FALSE FALSE 10853.6789 10563.44798 12019.92294 7891.929164 6309.107339 5014.517768 4153.04173 4366.278977 10820.79211 11278.07851 0.962369511 0.936635436 1.065777555 0.699758311 0.55941332 0.444625187 0.368240186 0.387147418 0.959453519 1 13.46123367 -8.847737411 1.583423076 0.984948793 0.395308804 0.962090471 0.051298589 0.044721018 0.226188438 0.007633048 0.017373034 1.42E-09 8.847737411 -0.589639989 down IPNSYEVLFPES(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 IPNSYEVLFPESPAR 15 0 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 IPNSYEVLFPES(1)PAR 187.5 3.04E-12 4127900 459.21 308.17 289.37 239.61 305.03 336.95 296.33 220.34 460.87 342.96 TRUE FALSE FALSE 453.6129719 312.5084253 294.4063635 267.3148356 289.4631809 315.4199825 321.5002628 226.7151903 419.6486329 334.0498498 1.35792 0.935514342 0.88132464 0.800224385 0.8665269 0.944230278 0.962431993 0.6786867 1.256245537 1 8.3839196 -10.07818036 6.48991741 1.168823583 0.865878401 0.654096968 0.112740735 0.15449454 10.62481907 0.024620987 0.030300492 8.35E-11 10.07818036 -0.302945181 IPNY(ph)QLSPTKLPSINK ddPTM_HeLa_Romidepsin_16h_R1 1 IPNYQLSPTKLPSINK 16 1 A0A0C4DG07;O60934 A0A0C4DG07 NBN Nibrin 1 0 IPNY(0.935)QLS(0.063)PT(0.002)KLPSINK 93.51 0.018646 114040000 2990.1 3080.2 2819.7 2517 1782.6 1617.6 1451.5 1184.4 2890.7 2773.3 TRUE FALSE FALSE 2953.655511 3123.563136 2868.775696 2808.027383 1691.62727 1514.240581 1574.790374 1218.668745 2632.148552 2701.249266 1.09344056 1.156340207 1.06201813 1.039529161 0.626238863 0.560570474 0.582985952 0.451150051 0.974418979 1 11.39941106 -8.72025175 3.70430147 1.057399178 0.543906334 0.949183806 0.056848055 0.036365682 1.037818995 0.008860703 0.017987023 1.90E-09 8.72025175 -0.513492844 IPNYQLS(ph)PTKLPSINK ddPTM_HeLa_Romidepsin_16h_R1 1 IPNYQLSPTKLPSINK 16 1 A0A0C4DG07;O60934 A0A0C4DG07 NBN Nibrin 1 0 IPNY(0.41)QLS(0.557)PT(0.033)KLPSINK 69.594 0.015437 150980000 4122.5 3793.4 3888.8 3611.1 2849 2429.2 1949 2203.2 4314.2 3539.2 TRUE FALSE FALSE 4072.253384 3846.803585 3956.482933 4028.632373 2703.604899 2273.98196 2114.548011 2266.946116 3928.327147 3447.251074 1.181304552 1.115904674 1.14772114 1.168650698 0.784278499 0.659650809 0.613401219 0.657609808 1.139553535 1 11.75123066 -8.613765351 3.692936155 1.100369327 0.648521721 0.943378644 0.054094996 0.054897987 1.454147804 0.011455995 0.024139552 2.43E-09 8.613765351 -0.451847606 IPS(ph)PLQPEMQGTPDDEPSEPEPSPSTLIYR ddPTM_HeLa_Romidepsin_16h_R1 2 IPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 30 0 K7EMY4;Q96GY3 K7EMY4 LIN37 Protein lin-37 homolog 1 0 IPS(0.974)PLQPEMQGT(0.026)PDDEPSEPEPSPSTLIYR;IPS(0.994)PLQPEMQGT(0.006)PDDEPSEPEPSPSTLIYR ; 118.89 6.83E-11 12998800 1210.82 999.37 1282.59 827.35 1170.69 1254.43 960.27 1206.94 1416.52 1053.66 TRUE FALSE FALSE 1196.06206 1013.439157 1304.912941 923.0120998 1110.945321 1174.275971 1041.83531 1241.860905 1289.822903 1026.285761 1.165427901 0.98748243 1.271490836 0.899371437 1.082491215 1.144199808 1.015151285 1.210053721 1.256787293 1 10.00321678 -12.61338012 1.422748428 1.00005017 1.101562336 0 0.131042416 0.705588045 2.566237231 0.067722988 0.015593554 2.44E-13 12.61338012 0.101512165 IPSIVS(ph)SPLNSPLDR ddPTM_HeLa_Romidepsin_16h_R1 1 IPSIVSSPLNSPLDR 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 IPSIVS(0.951)S(0.049)PLNSPLDR 209.22 1.87E-20 20313000 219.57 346.44 337.35 456.21 277.76 303.66 311.19 431.72 419.51 340.97 TRUE FALSE FALSE 216.8937964 351.3171914 343.2214352 508.9591467 263.5848707 284.257106 337.6224708 444.2111371 381.9879749 332.1115502 0.653075138 1.057828887 1.033452269 1.532494568 0.793663667 0.855908522 1.016593583 1.337535948 1.150179735 1 8.375524088 -10.11771455 7.99020468 0.83631157 1.083321062 0.037361897 0.238301082 0.3552925 22.25693062 0.039230335 0.048108086 7.63E-11 10.11771455 0.247009492 RPLPVES(ph)PDTQR ddPTM_HeLa_Romidepsin_16h_R1 3 RPLPVESPDTQR 12 1 P57682 P57682 KLF3 Krueppel-like factor 3 1 0 RPLPVES(0.966)PDT(0.034)QR;RPLPVES(0.771)PDT(0.229)QR;RPLPVES(0.848)PDT(0.152)QR ;; 138.31 0.0035128 47513000 7175.7 5944.9 6537 4795.2 3173.3 2985.47 2204.3 2276.08 7648.6 6402.5 TRUE FALSE FALSE 7088.239808 6028.592458 6650.773743 5349.643586 3011.35466 2794.708102 2391.533187 2341.934784 6964.49006 6236.162127 1.136634947 0.966715158 1.06648506 0.857842288 0.482885884 0.448145517 0.383494389 0.375541036 1.116791052 1 12.60644272 -8.842652661 2.020516421 1.058960039 0.396886483 0.972421468 0.050673859 0.041229863 0.342237688 0.00924809 0.01957262 1.44E-09 8.842652661 -0.662073556 down IPTPIVGVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 IPTPIVGVKR 10 1 H0YJL4;G3XAH6;P51003 H0YJL4 PAPOLA Poly(A) polymerase alpha 0 1 IPTPIVGVK(1)R 96.034 0.013779 4789600 317.08 426.54 220.14 174.03 304.31 173.67 178.89 268.51 283.3 199.26 FALSE TRUE FALSE 313.215307 432.5448413 223.9714444 194.1521674 288.7799252 162.5730475 194.0849121 276.2789132 257.9609385 194.0831965 1.613819809 2.22865683 1.153997092 1.000355368 1.487918225 0.837646177 1.00000884 1.423507641 1.329125566 1 7.600531406 -9.56744765 24.99992445 1.383746901 1.136406053 0.176180901 0.353470096 275.4786853 154522.39 0.064734044 0.091547793 2.71E-10 9.56744765 -0.247340848 IPVEGPLS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 IPVEGPLS(0.558)PS(0.442)R 127.52 0.006696 3979200 721.6 601.42 588.48 491.33 656.28 651.32 567.42 612.82 571.14 668.72 TRUE FALSE FALSE 712.8048616 609.8868065 598.7222475 548.1398864 622.7875827 609.702754 615.6166406 630.5509798 520.055808 651.346558 1.094355766 0.936347631 0.919206896 0.841548757 0.956153948 0.936065059 0.945144536 0.968072944 0.798431805 1 9.347281543 -10.19005801 7.362717113 1.044491815 0.926752171 0 0.086828785 0.146931466 13.42052804 0.007867646 0.009641188 6.46E-11 10.19005801 -0.117739645 IPVEGPLS(ph)PSRGDFPK ddPTM_HeLa_Romidepsin_16h_R1 1 IPVEGPLSPSRGDFPK 16 1 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 IPVEGPLS(0.981)PS(0.019)RGDFPK 64.26 0.020496 24176000 1610.9 1389.5 1217.8 1980.5 1744.4 1179.2 1071.6 1512.7 1497.7 1342.5 TRUE FALSE FALSE 1591.265731 1409.061417 1238.995298 2209.494729 1655.376759 1103.852926 1162.621677 1556.467588 1363.741961 1307.621656 1.216916012 1.077575773 0.947518185 1.689704906 1.265944741 0.844168434 0.889111672 1.190304229 1.042917846 1 10.35272946 -6.921849905 20.30416963 1.112111088 4.212796106 0.010951834 0.231392655 2802.00403 747070.1667 0.031832161 10377.00514 1.20E-07 6.921849905 3.100685019 IPVEGPLSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 IPVEGPLSPSR 11 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 IPVEGPLS(0.329)PS(0.671)R 143.55 0.002545 29804000 726.7 538.93 708.25 517.99 726.86 650.87 561.34 540.87 627.83 734.79 TRUE FALSE FALSE 717.8427009 546.5170707 720.5767942 577.882441 689.7656219 609.2815076 609.0202056 556.5192201 571.6753124 715.7000499 1.002993784 0.763611894 1.00681395 0.807436637 0.963763552 0.85130846 0.850943361 0.777587231 0.798763829 1 9.48321127 -8.606175692 0.260061167 1.027614662 0.731852767 0 0.101784995 3.142998833 0.313674223 0.061320535 0.297012488 2.48E-09 8.606175692 -0.295761895 IPYPGRS(ph)PQDLASTSR ddPTM_HeLa_Romidepsin_16h_R1 1 IPYPGRSPQDLASTSR 16 1 C9JM54;C9J6K3;Q9HC52 C9JM54 CBX8 Chromobox protein homolog 8 1 0 IPY(0.001)PGRS(0.998)PQDLAS(0.001)TSR 67.252 0.016912 10825000 846.27 810.49 702.23 680.09 890.56 1043.8 1075.5 809.35 929.17 635.09 TRUE FALSE FALSE 835.9553357 821.9000995 714.4520186 758.7252057 845.1114001 977.1045487 1166.852943 832.7672653 846.0627081 618.5902702 1.351387786 1.328666387 1.154968083 1.226539185 1.366189287 1.57956663 1.886309888 1.346234018 1.367727151 1 9.272840331 -4.000000042 0.066741756 0.516687875 3.314866858 0.265582194 0.194668694 147.1949201 0.735666434 5.776815239 39.28312915 1.00E-04 4.000000042 2.798178983 IPYQS(ph)PVSSSESAPGTIMNGHGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 IPYQSPVSSSESAPGTIMNGHGGGR 25 0 Q5T6F2;H0YDN2 Q5T6F2 UBAP2 Ubiquitin-associated protein 2 1 0 IPY(0.01)QS(0.698)PVS(0.088)S(0.088)S(0.088)ES(0.023)APGT(0.005)IMNGHGGGR;IPY(0.006)QS(0.906)PVS(0.033)S(0.033)S(0.012)ES(0.008)APGT(0.001)IMNGHGGGR ; 46.43 0.017487 26823600 7675.98 7522.22 4122.81 1187.71 5975.6 6597.6 5521.2 8421.2 7476.29 7843.02 TRUE FALSE FALSE 7582.422203 7628.118011 4194.565779 1325.038619 5670.642834 6176.034653 5990.17059 8664.854136 6807.591898 7639.25721 0.99256014 0.998541848 0.549080318 0.173451238 0.742302907 0.808460101 0.784129978 1.134253488 0.891132699 1 12.89921665 -9.777652464 24.81331724 0.996542749 0.685608117 0.249979049 0.228338297 210.7026165 322468.8788 0.03783849 0.049815009 1.67E-10 9.777652464 -0.310934632 IPYQSPVS(ph)SSESAPGTIMNGHGGGR ddPTM_HeLa_Romidepsin_16h_R1 1 IPYQSPVSSSESAPGTIMNGHGGGR 25 0 Q5T6F2;H0YDN2 Q5T6F2 UBAP2 Ubiquitin-associated protein 2 1 0 IPY(0.003)QS(0.142)PVS(0.316)S(0.316)S(0.182)ES(0.041)APGT(0.001)IMNGHGGGR 52.255 0.007818 26443000 874.92 711.4 699.13 728.98 1663.7 1933.1 1669.6 1846.2 1091 1063.7 TRUE FALSE FALSE 864.2561385 721.4151079 711.2980644 813.2680976 1578.795181 1809.581149 1811.415782 1899.616884 993.4182275 1036.064921 0.834171799 0.696302996 0.686538121 0.784958627 1.523838081 1.746590501 1.748361272 1.833492136 0.958837818 1 10.01689869 -8.642289256 3.754517581 0.872755158 1.757746499 0.944219212 0.106248096 0.048355487 1.291637288 0.019884801 0.041414633 2.28E-09 8.642289256 0.884991341 IQAAASTPT(ph)NATAASDANTGDR ddPTM_HeLa_Romidepsin_16h_R1 2 IQAAASTPTNATAASDANTGDR 22 0 P49841;P49841-2 P49841 GSK3B Glycogen synthase kinase-3 beta 1 0 IQAAAS(0.1)T(0.1)PT(0.793)NAT(0.007)AASDANTGDR;IQAAAS(0.013)T(0.305)PT(0.558)NAT(0.115)AAS(0.009)DANTGDR ; 209.73 4.84E-32 6097500 6431.5 5898.8 6658.3 4338.1 5928.2 5321.6 4117.6 4783.8 6562.4 5435.6 TRUE FALSE FALSE 6353.110404 5981.843461 6774.184918 4839.691533 5625.661833 4981.566935 4467.348841 4922.211705 5975.442508 5294.382328 1.199971972 1.129847278 1.279504293 0.914118255 1.062571889 0.940915602 0.843790373 0.929704619 1.128638269 1 12.37024667 -8.492602622 1.278675503 1.108115427 0.886900218 0.513880947 0.092820926 0.357220368 1.111955237 0.01683829 0.056727508 3.22E-09 8.492602622 -0.221215209 IQDPTEDAEAEDT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IQDPTEDAEAEDTPR 15 0 O96028;H0Y9L4;O96028-3;O96028-5 O96028;O96028-3;O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 IQDPT(0.026)EDAEAEDT(0.974)PR;IQDPTEDAEAEDT(1)PR ; 136.36 0.0025186 75080000 4278.35 4574.43 4879.6 4222.64 3315.32 2928.99 1927.12 2085.84 4657 5165.7 TRUE FALSE FALSE 4226.203825 4638.828946 4964.527391 4710.881505 3146.126849 2741.836992 2090.809525 2146.190489 4240.466256 5031.494369 0.839950026 0.921958489 0.98669044 0.936278799 0.625286767 0.544934922 0.415544443 0.426551305 0.842784657 1 12.29677123 -8.529965185 1.936973226 0.930015302 0.442986471 0.923173572 0.060308302 0.072353759 0.537385167 0.010728773 0.027760305 2.95E-09 8.529965185 -0.487028831 IQEAGTEVVK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 IQEAGTEVVKAK 12 1 G3XAL0;P40926-2;P40926 G3XAL0 MDH2 "Malate dehydrogenase;Malate dehydrogenase, mitochondrial" 0 1 ; IQEAGTEVVK(1)AK;IQEAGTEVVK(1)AK 191.79 3.87E-09 4871700 1713.54 1644.97 1895.21 1735.45 2209.93 3027.7 2776.6 2739.3 1788.46 1731.5 FALSE TRUE FALSE 1692.654715 1668.127931 1928.195335 1936.110895 2097.149026 2834.239741 3012.444335 2818.557324 1628.495658 1686.51538 1.003640248 0.989097372 1.143301364 1.147994805 1.243480522 1.680530029 1.786194404 1.671231319 0.96559787 1 10.71982976 -8.427754957 1.366905488 1.01059308 1.768838329 0.957631176 0.063194222 0.056513296 0.200036595 0.009425413 0.03218596 3.73E-09 8.427754957 0.758245249 IQEIIEQLDVTTSEYEKEK ddPTM_HeLa_Romidepsin_16h_R1 2 IQEIIEQLDVTTSEYEKEK 19 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 133.24 0.00092228 48532000 1828.26 1876.39 2126.96 2535 2083.62 2139.3 1822.32 2206.7 2202.72 2234.69 FALSE FALSE TRUE 1805.976464 1902.805868 2163.978847 2828.108628 1977.285096 2002.605634 1977.107815 2270.547383 2005.703206 2176.632432 0.829711272 0.87419715 0.994186623 1.299304644 0.908414791 0.920047687 0.908333344 1.043146904 0.92147079 1 11.08788208 -9.653647755 6.896408287 0.914105729 1.012778145 0.171947286 0.113867466 0.366048648 21.27653731 0.019861531 0.028115499 2.22E-10 9.653647755 0.098672416 IQEQES(ph)SGEEDSDLS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 1 IQEQESSGEEDSDLSPEER 19 0 P41236;Q6NXS1;E7EMN6 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 2 0 IQEQES(0.968)S(0.033)GEEDS(0.087)DLS(0.913)PEER 186.7 2.02E-10 31282000 3543.2 2984.6 3131.5 2374.3 4183.8 4162.3 3733 4420.8 3707.5 3197.1 TRUE FALSE FALSE 3500.014116 3026.617277 3186.002444 2648.827737 3970.285074 3896.342463 4050.080927 4548.708873 3375.891914 3114.038881 1.123946826 0.971926618 1.023109398 0.850608434 1.274963231 1.251218309 1.300587784 1.460710366 1.084087914 1 11.60457124 -8.615657869 7.547615081 1.036909309 1.322197211 0.75576531 0.086665079 0.099572901 7.011715262 0.013446735 0.026978522 2.42E-09 8.615657869 0.285287902 IQEQES(ph)SGEEDSDLSPEER ddPTM_HeLa_Romidepsin_16h_R1 1 IQEQESSGEEDSDLSPEER 19 0 P41236;Q6NXS1;E7EMN6 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 0 IQEQES(0.5)S(0.5)GEEDSDLSPEER 297.7 1.66E-143 27528000 1216.3 1147.7 1014.2 965.12 1571.2 1827 1956.5 1992.8 1480.9 1187.3 TRUE FALSE FALSE 1201.475268 1163.857351 1031.851726 1076.711715 1491.015801 1710.260596 2122.685061 2050.458524 1348.444595 1156.453775 1.038930646 1.006401964 0.892255054 0.931046047 1.289299956 1.478883665 1.835512242 1.773057055 1.166016856 1 10.17549189 -8.201767514 1.596138384 1.002443796 1.818014679 0.928450044 0.087608709 0.05736578 0.271711018 0.010717776 0.041042513 6.28E-09 8.201767514 0.815570883 IQEQESS(ph)GEEDSDLSPEER ddPTM_HeLa_Romidepsin_16h_R1 1 IQEQESSGEEDSDLSPEER 19 0 P41236;Q6NXS1;E7EMN6 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 0 IQEQES(0.053)S(0.947)GEEDSDLSPEER 157.73 2.63E-06 20099000 1134.6 1203.8 1039.4 882.4 1472.3 1626.6 1678.1 1807.3 1299.4 1189.3 TRUE FALSE FALSE 1120.771059 1220.747128 1057.490321 984.4272398 1397.163037 1522.66551 1820.637772 1859.591374 1183.17841 1158.401815 0.967514937 1.05382011 0.912887314 0.849815002 1.206112611 1.314453664 1.571680698 1.605307719 1.021388602 1 10.17792005 -8.129714652 1.516568118 0.976841582 1.613082666 0.920705241 0.071418077 0.077497938 0.325044041 0.010291233 0.044532752 7.42E-09 8.129714652 0.636241084 IQEQESSGEEDS(ph)DLSPEEREK ddPTM_HeLa_Romidepsin_16h_R1 1 IQEQESSGEEDSDLSPEEREK 21 1 P41236;Q6NXS1;E7EMN6 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 1 0 IQEQES(0.115)S(0.087)GEEDS(0.765)DLS(0.032)PEEREK 76.704 0.0014915 7434900 1412.8 1192 922.45 2220.7 1459.8 1835.5 1455.9 1864 1574.7 1228.9 TRUE FALSE FALSE 1395.58025 1208.781007 938.5048553 2477.467783 1385.300959 1718.217474 1579.56411 1917.931899 1433.854888 1196.973001 1.165924586 1.00986489 0.784065183 2.069777498 1.157336847 1.435468864 1.319632196 1.60231843 1.197900777 1 10.2251749 -9.29483592 24.99998783 1.054052233 1.48144702 0.489471055 0.245980398 427.3715859 319920.7011 0.034960061 0.053404374 5.07E-10 9.29483592 0.427394787 IQFK(ac)PDDGTTPER ddPTM_HeLa_Romidepsin_16h_R1 2 IQFKPDDGTTPER 13 1 Q96AE4;E9PEB5;Q96AE4-2 Q96AE4 FUBP1 Far upstream element-binding protein 1 0 1 ; IQFK(1)PDDGTTPER;IQFK(1)PDDGTTPER 145.14 8.94E-05 2045960 549.65 593.89 650.16 333.38 1334.01 894.73 1004.01 943.41 1382.69 1142.42 FALSE TRUE FALSE 542.9506544 602.250799 661.4757621 371.9269642 1265.930492 837.5596406 1089.290584 970.7060799 1259.018743 1112.739764 0.487940372 0.541232388 0.594456839 0.334244337 1.137669861 0.752700378 0.978926628 0.872356782 1.131458392 1 10.11990051 -8.735107075 24.99984877 0.694341834 0.925470399 0.211714169 0.238902978 324.6687808 308238.5549 0.036638784 0.073259805 1.84E-09 8.735107075 0.231128565 IQFLEEAMT(ph)NANKEK ddPTM_HeLa_Romidepsin_16h_R1 1 IQFLEEAMTNANKEK 15 1 Q5M9N0 Q5M9N0 CCDC158 Coiled-coil domain-containing protein 158 1 0 IQFLEEAMT(1)NANKEK 96.756 0.014404 5926200 2110.4 1986 1987.5 2107.6 1743.1 2148.3 1879.9 2059.5 2602.2 2440.9 TRUE FALSE FALSE 2084.677633 2013.95896 2022.091604 2351.290629 1654.143103 2011.030563 2039.578659 2119.088383 2369.452715 2377.485066 0.876841526 0.847096366 0.850517058 0.988982291 0.695753309 0.845864646 0.857872332 0.891315118 0.996621492 1 11.21522056 -12.01700897 0.436543907 1.03110674 0.844800941 0.419468982 0.066993432 1.280324874 0.373255334 0.10654236 0.021370071 9.62E-13 12.01700897 -0.1863058 IQFVEGPVEPGKPT(ph)SPEHVVYEGETVTR ddPTM_HeLa_Romidepsin_16h_R1 3 IQFVEGPVEPGKPTSPEHVVYEGETVTR 28 1 Q9H7C4-2;Q9H7C4;C9JTN4;C9JSS1 Q9H7C4-2 SYNC Syncoilin 1 0 IQFVEGPVEPGKPT(0.499)S(0.499)PEHVVY(0.001)EGET(0.001)VT(0.001)R;IQFVEGPVEPGKPT(0.808)S(0.174)PEHVVY(0.002)EGET(0.007)VT(0.008)R;IQFVEGPVEPGKPT(0.537)S(0.459)PEHVVY(0.001)EGET(0.002)VT(0.002)R ;; 65.151 0.00034989 28475000 2895.55 3071.06 3394.7 2593.28 2927.01 3009.15 2943.84 3354.29 3653.8 3505.9 TRUE FALSE FALSE 2860.257923 3114.294463 3453.783329 2893.127235 2777.633758 2816.875027 3193.889696 3451.341089 3326.994977 3414.816213 0.837602303 0.911994752 1.01141119 0.847227802 0.813406516 0.824897989 0.935303541 1.010696001 0.974282295 1 11.73759222 IQIISTDSAVAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 1 IQIISTDSAVASPQR 15 0 C9JKS0;P49116;P49116-2;C9JMI6;C9J2Y1 C9JKS0 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 0 IQIISTDSAVAS(1)PQR 221.34 1.67E-34 34500000 2294.8 2136.6 2417 2227.6 1579.9 1329.1 1029.9 1029.5 2287.2 2412.5 TRUE FALSE FALSE 2266.830095 2166.679111 2459.066871 2485.165593 1499.271808 1244.174799 1117.37968 1059.286958 2082.627104 2349.822902 0.96468125 0.922060598 1.046490299 1.057596975 0.638036086 0.529475987 0.47551655 0.45079438 0.886291091 1 11.19833631 -8.615077195 3.536254804 0.987716317 0.49340204 0.944094124 0.055104378 0.032483807 0.796507662 0.007250237 0.015365836 2.43E-09 8.615077195 -0.494314277 IQPAGNTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IQPAGNTSPR 10 0 H0Y5S9;H0Y682;P49674 H0Y5S9 CSNK1E Casein kinase I isoform epsilon 1 0 IQPAGNT(0.053)S(0.947)PR;IQPAGNT(0.065)S(0.935)PR ; 109.16 0.018627 285660000 16445.9 15227.1 14834.1 15406.2 17325.4 16488.3 14842.1 15539.7 17392.5 15473.4 TRUE FALSE FALSE 16245.45105 15441.46751 15092.28129 17187.53733 16441.22019 15434.75084 16102.7876 15989.3167 15836.87124 15071.39884 1.077899352 1.024554368 1.001385568 1.140407571 1.0908888 1.024108711 1.068433513 1.060904623 1.050789738 1 13.87952571 -12.48296798 0.802728118 0.992323425 1.062480875 0.05072594 0.04030065 0.945390819 0.884784371 0.045705742 0.007299256 3.29E-13 12.48296798 0.070157449 IQPGSQQADFLDALIVSMDVIQHETIGKK ddPTM_HeLa_Romidepsin_16h_R1 1 IQPGSQQADFLDALIVSMDVIQHETIGKK 29 1 P13010;C9JZ81 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 0 91.481 5.43E-11 413210 0 0 0 0 152.1 228.98 0 167.53 0 0 FALSE FALSE TRUE 0 0 0 0 144.3377694 214.348917 0 172.3772162 0 0 0 IQPLEPDS(ph)PTGLSENPTPATEK ddPTM_HeLa_Romidepsin_16h_R1 2 IQPLEPDSPTGLSENPTPATEK 22 0 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 IQPLEPDS(0.935)PT(0.054)GLS(0.011)ENPTPATEK;IQPLEPDS(0.898)PT(0.025)GLS(0.077)ENPTPATEK ; 72.848 0.0014213 7792000 7909.6 6975.5 6718 6798.8 4634.9 4793.6 3250.2 4671.4 7668.8 6523.3 TRUE FALSE FALSE 7813.194753 7073.701272 6834.923972 7584.909245 4398.363758 4487.304431 3526.271907 4806.559589 6982.883321 6353.823726 1.229683902 1.113298319 1.075718224 1.193755064 0.69223887 0.706236846 0.55498422 0.756482993 1.099004886 1 12.63340935 -8.753277117 24.73794348 1.113992535 0.670789127 0.891314148 0.075433249 46.81343512 141879.4303 0.014174548 0.027955975 1.76E-09 8.753277117 -0.443203408 IQPLEPDSPT(ph)GLSENPTPATEK ddPTM_HeLa_Romidepsin_16h_R1 1 IQPLEPDSPTGLSENPTPATEK 22 0 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 IQPLEPDS(0.12)PT(0.816)GLS(0.062)ENPT(0.002)PATEK 65.901 0.0044065 5473300 2773.6 2497.9 2513.9 2808.8 1850.5 1665.5 1540.1 1706.5 3024.2 2931.8 TRUE FALSE FALSE 2739.794296 2533.065502 2557.653375 3133.566672 1756.06208 1559.079925 1670.916056 1755.874885 2753.707978 2855.631413 0.95943555 0.887042176 0.895652486 1.097328828 0.614947038 0.545966793 0.585130156 0.614881485 0.964307916 1 11.47959406 -8.717089893 8.747740057 0.972696212 0.585443784 0.911705568 0.057468713 0.05845838 10.5800686 0.008334063 0.016635887 1.92E-09 8.717089893 -0.387252427 IQPQPPDEDGDHS(ph)DKEDEQPQVVVLK ddPTM_HeLa_Romidepsin_16h_R1 7 IQPQPPDEDGDHSDKEDEQPQVVVLK 26 1 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 0 IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK;IQPQPPDEDGDHS(1)DKEDEQPQVVVLK ;;;;;; 80.702 2.51E-05 644268900 22551.6 21321.8 22203.1 19899.8 20702.6 21023.3 19883 21781.4 24907.6 22991.1 TRUE FALSE FALSE 22276.73242 21621.96886 22589.53564 22200.70851 19646.06907 19679.97898 21571.86152 22411.61044 22679.80187 22393.78791 0.994772859 0.965534234 1.008741162 0.991377993 0.877299953 0.878814208 0.963296679 1.00079587 1.012772023 1 14.45081096 -8.874201262 9.746618709 0.99551538 0.928839722 0.443586587 0.035942817 0.21142847 17.30135661 0.005364271 0.009735193 1.34E-09 8.874201262 -0.066675658 IQQFDDGGS(ph)DEEDIWEEK ddPTM_HeLa_Romidepsin_16h_R1 4 IQQFDDGGSDEEDIWEEK 18 0 H0YEN2;E9PQP7;H7BXH2;E9PKF6;Q5H9R7-3;Q5H9R7-4;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5 H0YEN2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 0 IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK;IQQFDDGGS(1)DEEDIWEEK ;;; 208.69 2.78E-22 76817100 22293.6 21020.8 20612.6 18245.99 21376.3 21449.4 19771.53 22398.4 23090.9 21200.4 TRUE FALSE FALSE 22021.87703 21316.73137 20971.35366 20355.67721 20285.38765 20078.85256 21450.92326 23046.46237 21025.59207 20649.61055 1.066454836 1.032306702 1.015581074 0.985765672 0.982361754 0.972359867 1.038805222 1.116072495 1.018207681 1 14.33382695 -9.750451422 7.090887406 1.032340592 1.014142314 0.007401005 0.041194127 0.480988382 118.719903 0.007341337 0.0101448 1.78E-10 9.750451422 -0.018198278 IQQFDDGGS(ph)DEEDIWEEKHIAFTPESQR ddPTM_HeLa_Romidepsin_16h_R1 1 IQQFDDGGSDEEDIWEEKHIAFTPESQR 28 1 H0YEN2;E9PQP7;H7BXH2;E9PKF6;Q5H9R7-3;Q5H9R7-4;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5 H0YEN2 PPP6R3 Serine/threonine-protein phosphatase 6 regulatory subunit 3 1 0 IQQFDDGGS(1)DEEDIWEEKHIAFTPESQR 88.242 1.32E-07 4421300 1482.2 1368 936.33 2644.8 1124.1 1241.3 899.67 1085.7 1617.6 1100 TRUE FALSE FALSE 1464.134376 1387.25874 952.6264309 2950.60422 1066.732982 1161.984936 976.0879473 1117.113017 1472.917805 1071.421841 1.366534002 1.294782957 0.889123587 2.75391457 0.995623704 1.084526086 0.91102114 1.042645365 1.374731919 1 10.0653109 -5.877835244 10.62834354 1.225640166 1.099989773 0 0.524588666 0 0 0.066043276 0 1.32E-06 5.877835244 -0.125650393 IQQHVGEEAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IQQHVGEEASPR 12 0 Q8TER5;Q8TER5-4;Q8TER5-3;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 IQQHVGEEAS(1)PR;IQQHVGEEAS(1)PR ; 115.24 0.0090012 18175000 4283.12 3673.24 3987.25 4110.88 3998.63 3828.66 3347.73 3371.29 4348.28 4026.12 TRUE FALSE FALSE 4230.915686 3724.951969 4056.646414 4586.199288 3794.56499 3584.020982 3632.086103 3468.832957 3959.358946 3921.520822 1.078896652 0.949874331 1.034457446 1.169495075 0.967625868 0.913936492 0.926193247 0.884563187 1.009648839 1 11.93719755 -8.528480426 24.99473001 1.040061463 0.915152848 0.542085592 0.054786222 88.85008763 396448.9471 0.008259927 0.016559174 2.96E-09 8.528480426 -0.124908615 IQSSLSS(ph)ASPSK ddPTM_HeLa_Romidepsin_16h_R1 1 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 0 IQSSLS(0.041)S(0.479)AS(0.479)PSK 188.09 6.55E-10 31946000 3022.6 2810.8 2877.9 2651.7 2080.2 1938.2 1442.6 1560.7 3192.1 2819.5 TRUE FALSE FALSE 2985.759389 2850.370516 2927.988642 2958.302031 1974.039632 1814.355275 1565.134408 1605.856392 2906.590581 2746.248984 1.087213653 1.037914091 1.066177415 1.077215521 0.718813059 0.660666708 0.569917155 0.584745375 1.058385674 1 11.42324672 -8.645913693 3.282427395 1.046797603 0.609281832 0.971794987 0.035415537 0.035254944 0.749402028 0.006708787 0.014204463 2.26E-09 8.645913693 -0.437515771 IQSSLSSAS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 3 IQSSLSSASPSK 12 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 0 IQSSLS(0.002)S(0.003)AS(0.971)PS(0.025)K;IQSSLS(0.001)S(0.007)AS(0.899)PS(0.093)K;IQSSLS(0.001)S(0.014)AS(0.493)PS(0.493)K ;; 175.01 3.40E-05 57503000 5787 5014.6 5218.4 5362.1 3575.82 3469.84 3308.92 2851.87 5465.5 4858 TRUE FALSE FALSE 5716.465818 5085.19567 5309.224063 5982.091231 3393.332562 3248.128422 3589.979582 2934.384359 4976.651991 4731.78846 1.208098347 1.074687872 1.122033267 1.264234714 0.717135305 0.686448359 0.758694014 0.620142761 1.051748622 1 12.20816986 -8.74591158 24.73690607 1.110944966 0.699457204 0.877206589 0.077761554 65.09686034 103703.3468 0.013693291 0.027306376 1.80E-09 8.74591158 -0.411487762 IQVEQTRDEDLDTDS(ph)LD ddPTM_HeLa_Romidepsin_16h_R1 1 IQVEQTRDEDLDTDSLD 17 1 V9GYT7 V9GYT7 PSIP1 1 0 IQVEQTRDEDLDT(0.03)DS(0.97)LD 121.45 0.015275 12513000 2507.2 2786.8 2508 2734.4 2721.2 2505 2590.3 2414.4 2692.6 2491.7 TRUE FALSE FALSE 2476.641282 2826.032644 2551.650688 3050.564194 2582.32701 2344.938585 2810.320017 2484.256855 2451.767112 2426.965275 1.020468363 1.164430605 1.05137503 1.256945959 1.064014816 0.966201951 1.157956418 1.023606263 1.01021928 1 11.24493775 -10.41915111 7.791889285 1.008973042 1.098035232 0.213952267 0.077197461 0.307942231 20.70776621 0.012652117 0.014423212 3.81E-11 10.41915111 0.08906219 IQVLQQQADDAEER ddPTM_HeLa_Romidepsin_16h_R1 1 IQVLQQQADDAEER 14 0 P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8;D6R904;Q5VU61 P06753-4 TPM3 Tropomyosin alpha-3 chain 0 0 171.62 0.00044306 31451000 2372.3 2439.6 2326.4 1466.5 2413.2 3011.4 3054.6 2785.8 2824.6 2574.1 FALSE FALSE TRUE 2343.385495 2473.944753 2366.890016 1636.06363 2290.045399 2818.981259 3314.057648 2866.402728 2571.960702 2507.224511 0.934653233 0.986726455 0.94402795 0.65253974 0.913378674 1.124343371 1.321803306 1.143257301 1.025819862 1 11.29187547 -8.08830836 3.904978188 0.940816691 1.23208435 0.587792867 0.106624445 0.126083077 3.512107382 0.015536166 0.043732471 8.16E-09 8.08830836 0.291267659 IQVLVEPDHFK ddPTM_HeLa_Romidepsin_16h_R1 1 IQVLVEPDHFK 11 0 P17931 P17931 LGALS3 Galectin-3 0 0 74.392 0.01806 804580 1280.2 794.9 895.27 834.95 979.78 862.37 580.57 778.08 920.56 776.8 FALSE FALSE TRUE 1264.59643 806.0906231 910.8517988 931.4908476 929.7781705 807.2673402 629.8836013 800.5925172 838.222808 756.618624 1.671378935 1.065385648 1.203845332 1.23112334 1.228859747 1.06694088 0.832498145 1.058118967 1.107853787 1 9.563422478 -8.218826058 1.952947613 1.288935893 0.940341329 0.192031668 0.187475157 0.399383866 2.902754511 0.038495968 0.127227519 6.04E-09 8.218826058 -0.348594564 IQVWHEEHR ddPTM_HeLa_Romidepsin_16h_R1 1 IQVWHEEHR 9 0 P26038 P26038 MSN Moesin 0 0 106.68 0.0084739 8611800 1362.6 1276.1 1783.8 1353.7 1700.7 1926.8 1460.5 931.35 1146.5 877.32 FALSE FALSE TRUE 1345.992107 1294.064969 1814.846291 1510.221163 1613.906933 1803.683698 1584.554834 958.2971428 1043.954169 854.5270999 1.575130979 1.514363874 2.123801914 1.767318045 1.888655062 2.110739026 1.854306123 1.121435637 1.221674735 1 9.738982435 -11.4074321 0.582716956 1.004308989 1.817512312 0.454618383 0.281034687 0.449036231 0.323071465 0.168341697 0.074635507 3.91E-12 11.4074321 0.813203322 IQYAWANSEIS(ph)QDLNK ddPTM_HeLa_Romidepsin_16h_R1 1 IQYAWANSEISQDLNK 16 0 C9JSC4 C9JSC4 FIGNL1 1 0 IQYAWANSEIS(1)QDLNK 80.871 0.02383 74336000 3762.5 3672.4 4118.3 2503.2 3541.9 3747.2 3535.8 3329.9 4311.3 4026.2 TRUE FALSE FALSE 3716.641203 3724.100144 4189.977284 2792.631762 3361.143626 3507.766014 3836.130764 3426.245403 3925.68653 3921.598744 0.947736228 0.949638244 1.068436002 0.712115631 0.857085043 0.894473464 0.978205833 0.873685868 1.001042378 1 11.93722621 -9.287834258 24.99160234 0.97870711 0.870914493 0.459407272 0.069491163 615.6337201 582902.0029 0.010768202 0.016451556 5.15E-10 9.287834258 -0.107792617 IRAEEEDLAAVPFLAS(ph)DNEEEEDEKGNSGSLIR ddPTM_HeLa_Romidepsin_16h_R1 1 IRAEEEDLAAVPFLASDNEEEEDEKGNSGSLIR 33 2 A0A3B3IRP6;A0A0J9YVP0;O95714 A0A3B3IRP6 HERC2 E3 ubiquitin-protein ligase HERC2 1 0 IRAEEEDLAAVPFLAS(0.999)DNEEEEDEKGNS(0.001)GSLIR 61.844 0.00031374 11713000 2120.4 2611.4 2634.3 2915.9 2530 2490.7 1748.9 2390.1 2942.9 2367.1 TRUE FALSE FALSE 2094.555749 2648.163358 2680.148886 3253.050078 2400.884659 2331.552308 1897.451522 2459.253773 2679.679653 2305.602401 0.908463553 1.148577637 1.162450597 1.410932812 1.041326405 1.011255153 0.8229743 1.066642614 1.162247078 1 11.17092803 -10.26305533 24.96908879 0.956774455 1.093900686 0 0.15438843 204.4597913 3159227.999 0.025785545 0.030322998 5.46E-11 10.26305533 0.13712623 IRAENGTGSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IRAENGTGSSPR 12 1 M0R102;M0R050;Q9NQT4 M0R102 EXOSC5 Exosome complex component RRP46 1 0 IRAENGTGS(0.122)S(0.878)PR;IRAENGTGS(0.347)S(0.653)PR ; 95.981 0.0075453 26754000 3324.2 3287 3370.4 4562.8 3792.7 3974.4 4412.5 1613.45 4466.1 3514.2 TRUE FALSE FALSE 3283.683372 3333.274472 3429.060398 5090.372405 3599.144366 3720.448667 4787.29764 1660.13263 4066.64083 3422.900577 0.95932771 0.973815744 1.001799591 1.487151698 1.051489602 1.086928639 1.398608441 0.485007552 1.188068639 1 11.74100367 -9.492293477 24.97284527 0.980118066 1.127676767 0.003212652 0.258307085 1340.400379 1094437.708 0.034791036 0.053102122 3.22E-10 9.492293477 0.147558701 IRDGWQVEEADDWLR ddPTM_HeLa_Romidepsin_16h_R1 1 IRDGWQVEEADDWLR 15 1 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 0 169.3 2.85E-05 2270100 1087.3 918.73 821.92 1592.1 922.14 892.74 882.96 766.52 1180.9 868.31 FALSE FALSE TRUE 1074.047569 931.6639051 836.2251728 1776.186093 875.0797548 835.6967952 957.9586004 788.6980468 1075.277346 845.751181 1.269933278 1.10158156 0.98873663 2.100128422 1.034677544 0.988111887 1.132671904 0.932541467 1.271387342 1 9.724089476 -5.891502473 9.156109325 1.156883539 0.942089914 0 0.326478201 0 0 0.041487958 0 1.28E-06 5.891502473 -0.214793624 IREEFPDR ddPTM_HeLa_Romidepsin_16h_R1 2 IREEFPDR 8 1 P04350;M0QYM7;M0R042 P04350 TUBB4A Tubulin beta-4A chain 0 0 ; ; 106.68 0.028906 59068000 7131.6 6767.6 8173 8777.5 9420.7 8645.3 7247.4 6864.7 7072.7 6098.4 FALSE FALSE TRUE 7044.677316 6862.87445 8315.247637 9792.395849 8939.926526 8092.893231 7862.993975 7063.319264 6440.099998 5939.962689 1.185980062 1.155373326 1.399882133 1.648561845 1.505047589 1.362448496 1.323744674 1.189118456 1.084198729 1 12.53623815 -10.18197881 1.208120046 1.068048569 1.41102786 0.571314564 0.123993623 0.245195169 0.690946631 0.02810762 0.034598637 6.58E-11 10.18197881 0.342979291 IREEYPDR ddPTM_HeLa_Romidepsin_16h_R1 6 IREEYPDR 8 1 Q5JP53;P07437;Q5ST81;A0A075B736;Q5SQY0;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P68371;Q3ZCM7;Q9BVA1;Q13885 Q5JP53;P68371;Q9BVA1 TUBB;TUBB8;TUBB1;TUBB4B;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4B chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 0 ;;;;; ;;;;; 146.58 0.0089719 1355719600 22656.3 20335 24465.8 24478.5 25334.8 24585.2 20179.5 19581.2 21157 18074.2 FALSE FALSE TRUE 22380.1563 20621.27666 24891.61699 27308.81934 24041.87062 23014.28507 21893.54623 20147.75113 19264.66493 17604.62968 1.271265384 1.171355322 1.413924487 1.551229412 1.36565614 1.307285952 1.243624355 1.144457537 1.09429538 1 14.10366726 -11.7581507 0.600345749 0.989192919 1.326894673 0.459703715 0.113500467 0.557061902 0.374848861 0.094595707 0.029892885 1.75E-12 11.7581507 0.337701754 IRIDS(ph)LSAQLSQLQK ddPTM_HeLa_Romidepsin_16h_R1 1 IRIDSLSAQLSQLQK 15 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 IRIDS(0.989)LS(0.011)AQLSQLQK 126.8 0.00094937 4150200 2178.6 1864.6 1755.2 2883.1 2115.2 2382.1 1996 1922.6 1971.5 1761.1 TRUE FALSE FALSE 2152.046385 1890.849888 1785.74852 3216.457587 2007.253451 2229.891498 2165.54019 1978.227398 1795.164102 1715.346368 1.254584162 1.10231375 1.041042528 1.87510677 1.170173843 1.299965732 1.262450681 1.153252448 1.046531555 1 10.7442842 -12.05388201 0.419230175 0.937464971 1.300941102 0.18161981 0.215954117 2.430586922 0.636499129 0.386127021 0.073770093 8.83E-13 12.05388201 0.363476131 IRLDETDDPDDYGDR ddPTM_HeLa_Romidepsin_16h_R1 2 IRLDETDDPDDYGDR 15 1 P07384 P07384 CAPN1 Calpain-1 catalytic subunit 0 0 ; ; 193.98 1.38E-12 32801000 6305.6 5941.7 6646.5 3454.7 6215.4 6175.9 5125.8 6256.8 7111.5 6548.8 FALSE FALSE TRUE 6228.744922 6025.347409 6762.179544 3854.148669 5898.204945 5781.279922 5561.185324 6437.830636 6475.429629 6378.661232 0.976497214 0.944610035 1.060125205 0.604225327 0.924677566 0.906346914 0.871842088 1.009276148 1.015170644 1 12.63903794 IRPLEVPTTAGPASAS(ph)TPTDGAK ddPTM_HeLa_Romidepsin_16h_R1 2 IRPLEVPTTAGPASASTPTDGAK 23 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 0 IRPLEVPTTAGPAS(0.034)AS(0.482)T(0.482)PT(0.003)DGAK;IRPLEVPTTAGPAS(0.047)AS(0.467)T(0.467)PT(0.019)DGAK ; 92.805 3.87E-05 30689000 3556.8 3049.2 3388 3043.8 2850.5 2801.5 2440.7 2428.2 3469 3005.5 TRUE FALSE FALSE 3513.448354 3092.126718 3446.966719 3395.738478 2705.028348 2622.493191 2648.012997 2498.456136 3158.723952 2927.416677 1.200187312 1.056264638 1.177477312 1.159977841 0.924032568 0.895838714 0.904556231 0.853467891 1.079014128 1 11.51541239 -8.676183596 5.625209375 1.104394711 0.891131484 0.772857117 0.057879507 0.107104536 5.47161625 0.011854279 0.023884698 2.11E-09 8.676183596 -0.213263227 IRPLSDGNSPWS(ph)TILIK ddPTM_HeLa_Romidepsin_16h_R1 1 IRPLSDGNSPWSTILIK 17 1 Q5TCX8;Q5TCX8-3 Q5TCX8 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 0 IRPLSDGNS(0.149)PWS(0.574)T(0.277)ILIK 128.88 0.013533 5653100 868.82 974.51 1142.5 1313.3 1097.2 1025 814 1058.4 1298 986.03 TRUE FALSE FALSE 858.2304877 988.2291774 1162.384733 1465.149925 1041.20579 959.505808 883.1411397 1089.023134 1181.903629 960.4127985 0.893605842 1.028962941 1.210297005 1.525541858 1.084123193 0.999055624 0.919543285 1.133911518 1.230620449 1 9.907510819 -9.969425833 5.419473607 0.950100007 1.142281597 0.007880804 0.175951479 0.208034093 16.5945402 0.027043023 0.035324235 1.07E-10 9.969425833 0.19218159 IRQEVGPPLPPLLAPLIAT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 IRQEVGPPLPPLLAPLIATPPR 22 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 IRQEVGPPLPPLLAPLIAT(1)PPR;IRQEVGPPLPPLLAPLIAT(1)PPR ; 137.42 4.30E-05 30762000 4088.2 4207.5 4060.2 3984.13 4030.3 4220.2 3314.95 4295.2 4812.5 4020.6 TRUE FALSE FALSE 4038.371446 4266.733295 4130.866078 4444.793856 3824.618752 3950.54284 3596.52177 4419.474835 4382.057947 3916.144232 1.031211111 1.089524043 1.054829912 1.134992378 0.976628675 1.008783795 0.918383378 1.128527085 1.118972563 1 11.93521819 -6.98099857 10.40094807 1.022939301 1.294921443 0.12263485 0.064109732 7510.90182 112599.4304 0.007755012 29113.94708 1.04E-07 6.98099857 0.271982142 IRQEVGPPLPPLLAPLIATPPR ddPTM_HeLa_Romidepsin_16h_R1 1 IRQEVGPPLPPLLAPLIATPPR 22 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 0 0 73.383 0.0036917 1666700 654.43 795.78 678.12 974.16 758.63 820.49 693.78 881.8 1009.2 717.63 FALSE FALSE TRUE 646.4535554 806.9830117 689.9223941 1086.796963 719.9142803 768.063337 752.7096559 907.3134917 918.9346244 698.9858691 0.924844956 1.154505473 0.987033393 1.554819648 1.029941108 1.098825271 1.076859618 1.298042681 1.314668386 1 9.44911948 -9.979610308 1.925877002 0.965345024 1.181784279 0 0.189294681 0.303199608 2.237230726 0.025713844 0.0339539 1.05E-10 9.979610308 0.216439256 IRS(ph)SVGPVR ddPTM_HeLa_Romidepsin_16h_R1 1 IRSSVGPVR 9 1 Q9NTI2 Q9NTI2 ATP8A2 Phospholipid-transporting ATPase IB 1 0 IRS(0.885)S(0.115)VGPVR 72.34 0.029431 17299000 673.06 964.21 733.28 818.59 1008.5 839.1 747.86 946 834.26 848.94 TRUE FALSE FALSE 664.8564858 977.7841737 746.0424308 913.2392274 957.0324818 785.4842181 811.3832097 973.3710175 759.6416962 826.8844164 0.804050086 1.182491959 0.902233028 1.104433956 1.157395717 0.949932303 0.981253478 1.17715487 0.91867942 1 9.69154187 -10.26683953 24.99674448 0.907468098 1.056151323 0.332947648 0.101563584 430.5550808 1992993.554 0.018854655 0.021896072 5.41E-11 10.26683953 0.148683225 IS(ph)APNVDFNLEGPK ddPTM_HeLa_Romidepsin_16h_R1 4 ISAPNVDFNLEGPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK;IS(1)APNVDFNLEGPK ;;; 218.34 1.59E-24 743107000 31182.1 26413.6 30476.2 28402.7 26493.9 25002.4 20749 21390.8 31806.4 29585.7 TRUE FALSE FALSE 30802.04057 26785.45135 31006.62548 31686.75381 25141.81742 23404.82733 22511.41954 22009.70905 28961.55592 28817.05925 1.068882161 0.929499819 1.075981599 1.099583186 0.872462981 0.812186529 0.781183789 0.763773599 1.005014276 1 14.8146355 -8.573780446 3.848393276 1.032317091 0.790566825 0.847254212 0.047171066 0.063094749 1.944324053 0.00726976 0.01549645 2.67E-09 8.573780446 -0.241750266 IS(ph)ASSATR ddPTM_HeLa_Romidepsin_16h_R1 2 ISASSATR 8 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;A0A1B0GV30;P49023-4 A0A1B0GTU4 PXN Paxillin 1 0 IS(0.986)AS(0.013)S(0.001)ATR;IS(0.956)AS(0.044)SATR ; 112.3 0.021613 181861000 3334.5 3670.7 4012.3 5276 5898.2 5777.5 4218.5 3320.2 4526 3886.3 TRUE FALSE FALSE 3293.857831 3722.376211 4082.132398 5886.035944 5597.192845 5408.336396 4576.819285 3416.264749 4121.183224 3785.333366 0.87016321 0.983368135 1.078407634 1.554958408 1.478652553 1.428760924 1.209092791 0.902500366 1.088723984 1 11.88620465 -9.490203741 4.983696193 0.943174118 1.325594538 0.434523162 0.176518702 0.123917163 7.831175754 0.027950138 0.042088275 3.23E-10 9.490203741 0.38242042 IS(ph)DAELEAELEK ddPTM_HeLa_Romidepsin_16h_R1 4 ISDAELEAELEK 12 0 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 0 IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK;IS(1)DAELEAELEK ;;; 185.66 3.10E-07 131813900 9027.1 8876.2 9176.1 6051.27 10508 9540.5 8642.3 9170.5 9895.6 9503.8 TRUE FALSE FALSE 8917.074233 9001.159377 9335.806171 6750.946309 9971.737549 8930.892841 9376.376746 9435.833949 9010.512752 9256.889906 0.963290514 0.972374034 1.008525138 0.729288819 1.077223306 0.964783305 1.012907882 1.019330903 0.973384457 1 13.17631185 IS(ph)DAHLADTMIGK ddPTM_HeLa_Romidepsin_16h_R1 1 ISDAHLADTMIGK 13 0 Q9Y657 Q9Y657 SPIN1 Spindlin-1 1 0 IS(1)DAHLADTMIGK 84.41 0.009723 22302000 6810.2 6659.6 6183.4 5394.2 5743.1 6489.4 4989.8 5566 7141.5 6575.5 TRUE FALSE FALSE 6727.194663 6753.354024 6291.019483 6017.902784 5450.008177 6074.748284 5413.633487 5727.043428 6502.746354 6404.667562 1.050358133 1.054442554 0.982255429 0.939612045 0.850943179 0.948487681 0.845263776 0.894198391 1.015313643 1 12.64490797 -9.226672342 2.123075765 1.026391951 0.88668778 0.8048251 0.031899937 0.10321203 0.908369501 0.005202965 0.009146549 5.93E-10 9.226672342 -0.13970417 IS(ph)EDETER ddPTM_HeLa_Romidepsin_16h_R1 1 ISEDETER 8 0 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5;G3V3T3 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 IS(1)EDETER 123.86 0.016295 9126000 2211.7 2217.6 2405 731.01 2586.5 2315.9 1953.8 1859.9 2312.3 2262.1 TRUE FALSE FALSE 2184.74295 2248.819431 2446.858016 815.5328157 2454.501253 2167.921464 2119.755723 1913.713272 2105.482097 2203.330316 0.991563967 1.020645618 1.110527096 0.370136429 1.113996043 0.983929395 0.962068968 0.868554868 0.955590763 1 11.10547008 IS(ph)FVEEDVHPK ddPTM_HeLa_Romidepsin_16h_R1 2 ISFVEEDVHPK 11 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 IS(1)FVEEDVHPK;IS(1)FVEEDVHPK ; 112.08 0.0057099 21153200 15803.6 15335.7 15368.6 8743.5 11568.3 13156.8 11791.4 13444.6 17058.4 15639.6 TRUE FALSE FALSE 15610.97964 15551.59639 15636.08404 9754.464609 10977.92648 12316.12294 12792.96122 13833.59829 15532.65398 15233.28094 1.024794311 1.020896053 1.026442307 0.640339048 0.720654108 0.808501005 0.839803406 0.908116797 1.019652565 1 13.89493908 -9.284341774 24.76775872 1.013845664 0.7845112 0.756620468 0.06657936 268.7335615 290620.6457 0.010605926 0.016207611 5.20E-10 9.284341774 -0.229334464 IS(ph)MPDVDLHLK ddPTM_HeLa_Romidepsin_16h_R1 1 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IS(1)MPDVDLHLK 63.185 0.028802 8571600 3287.8 3370.4 3051.5 2902.1 2970.3 2495.6 2020.1 2045.2 3651.1 3241.6 TRUE FALSE FALSE 3247.727029 3417.84858 3104.610077 3237.654457 2818.714507 2336.139214 2191.687244 2104.374635 3324.536472 3157.382765 1.028613656 1.082494216 0.983285939 1.025423491 0.892737662 0.739897373 0.694146832 0.666493356 1.05294059 1 11.62451345 -8.359011547 1.750448136 1.018957093 0.677179918 0.964684615 0.028234511 0.044393653 0.260336296 0.004033294 0.012501834 4.38E-09 8.359011547 -0.341777175 IS(ph)MSEVDLNVAAPK ddPTM_HeLa_Romidepsin_16h_R1 1 ISMSEVDLNVAAPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IS(0.997)MS(0.003)EVDLNVAAPK 123.63 0.0049211 20278000 6339.2 7749.3 6730.7 6507.5 6491.9 6541 5016.7 5940.5 7351.3 7282.7 TRUE FALSE FALSE 6261.935392 7858.394849 6847.84501 7259.927769 6160.594118 6123.05121 5442.818373 6112.378995 6693.781316 7093.494404 0.882771598 1.107831261 0.965369763 1.023462817 0.868485089 0.863192506 0.767297197 0.861687998 0.94365075 1 12.79228079 -8.585833179 4.963346537 0.963532124 0.830057553 0.559843131 0.062337819 0.144764433 7.080193129 0.010339812 0.021242185 2.60E-09 8.585833179 -0.133474571 IS(ph)PDLNIK ddPTM_HeLa_Romidepsin_16h_R1 1 ISPDLNIK 8 0 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 IS(1)PDLNIK 104.43 0.027274 19973000 2122.7 1800.2 2093.1 1801.9 4098.2 4820.9 4817.2 4395.8 2222 2143.5 TRUE FALSE FALSE 2096.827716 1825.543263 2129.529527 2010.244156 3889.053562 4512.860049 5226.372848 4522.985538 2023.258755 2087.811561 1.004318472 0.874381241 1.019981672 0.962847507 1.862741655 2.161526516 2.503278047 2.166376325 0.969081115 1 11.02777579 -8.599191336 2.426735714 0.98612177 2.301637197 0.969495656 0.106024899 0.031380879 0.372268831 0.014897647 0.03429329 2.52E-09 8.599191336 1.315515427 up IS(ph)TPQT(ph)NTVPIKPLISTPPVSSQPK ddPTM_HeLa_Romidepsin_16h_R1 1 ISTPQTNTVPIKPLISTPPVSSQPK 25 1 A0A0A0MRT2;Q9BTA9-5;Q9BTA9-2;Q9BTA9 A0A0A0MRT2 WAC WW domain-containing adapter protein with coiled-coil 2 0 IS(0.487)T(0.466)PQT(0.433)NT(0.312)VPIKPLIS(0.156)T(0.147)PPVSSQPK 53.578 0.017069 12456000 1437.4 1365.8 1168.5 772.09 969.11 1137.1 943.03 926.98 1057.5 1189.9 TRUE FALSE FALSE 1419.880416 1385.027768 1188.837252 861.3626786 919.6527005 1064.44298 1023.130945 953.8007038 962.9145514 1158.986226 1.225105513 1.195033846 1.025756152 0.743203551 0.793497523 0.91842591 0.882780935 0.822961207 0.830824845 1 10.17864771 -9.450831701 4.957293451 1.115915489 0.839018866 0.460648386 0.115348172 0.106039615 4.877534136 0.015558688 0.023768261 3.54E-10 9.450831701 -0.276896624 IS(ph)Y(ph)FKT(ph)YLET(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ISYFKTYLETK 11 1 C9JW07;A0A2Q3DP09;Q7Z3E5-2;Q7Z3E5 C9JW07 ARMC9 LisH domain-containing protein ARMC9 4 0 IS(0.994)Y(0.9)FKT(0.606)Y(0.518)LET(0.982)K 63.76 0.0036758 0 611.75 349.5 446.18 501.17 490.67 383.44 491.51 521.6 507.65 554.27 TRUE FALSE FALSE 604.2937557 354.4202702 453.9455757 559.1176335 465.629279 358.9394215 533.2588471 536.6916731 462.2445126 539.8699855 1.119332009 0.656491896 0.840842403 1.035652376 0.862484101 0.66486271 0.987754203 0.994112819 0.856214505 1 9.076468201 -10.29694315 24.99478006 1.056351234 0.866084433 0.103664861 0.138641347 507.3158779 357150.5908 0.021722553 0.024841134 5.05E-11 10.29694315 -0.190266801 IS(ph)Y(ph)VHT(ph)S(ph)NDEK ddPTM_HeLa_Romidepsin_16h_R1 1 ISYVHTSNDEK 11 0 P0C091 P0C091 FREM3 FRAS1-related extracellular matrix protein 3 4 0 IS(1)Y(1)VHT(1)S(1)NDEK 56.956 0.027842 11935000 1708.4 1989.6 1919.8 1287.7 1443.8 1532.1 1334.7 1370.5 1901.9 2196.4 TRUE FALSE FALSE 1687.577364 2017.609641 1953.213314 1436.589933 1370.117498 1434.203755 1448.069385 1410.153255 1731.789301 2139.337211 0.788831866 0.943100335 0.912999271 0.671511684 0.640440175 0.670396302 0.676877575 0.659154269 0.80949805 1 11.06294819 -9.255819654 12.07551616 0.902513582 0.663467485 0.792193597 0.058032388 0.190875003 401.5187358 0.011955248 0.0192564 5.55E-10 9.255819654 -0.239046097 ISAAASDSGVESFDEGS(ph)SH ddPTM_HeLa_Romidepsin_16h_R1 1 ISAAASDSGVESFDEGSSH 19 0 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 0 ISAAASDS(0.002)GVES(0.003)FDEGS(0.624)S(0.371)H 67.648 0.018049 2031400 287.66 163.32 178.87 157.19 147.04 204.62 226.82 330.26 356.16 354.52 TRUE FALSE FALSE 284.1538893 165.6192232 181.9831573 175.3650474 139.5360001 191.5454424 246.0860851 339.815552 324.3041576 345.3095193 0.822896194 0.47962542 0.527014597 0.507848865 0.404089642 0.554706522 0.712653638 0.984089731 0.939169468 1 8.431746296 -10.54703965 2.22420645 0.935074461 0.585953703 0.477344251 0.156196476 0.185438418 1.858012901 0.031815385 0.033994352 2.84E-11 10.54703965 -0.349120758 ISAPELLLHS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 3 ISAPELLLHSPAR 13 0 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 0 IS(0.002)APELLLHS(0.998)PAR;ISAPELLLHS(1)PAR;IS(0.013)APELLLHS(0.987)PAR ;; 95.409 0.0029507 5887500 11837.5 11410.7 11533.4 11067.3 11173.7 9292.3 7994.3 8637.8 12565.5 11905.2 TRUE FALSE FALSE 11693.22 11571.34013 11734.13399 12346.9533 10603.46439 8698.55202 8673.335642 8887.721115 11441.61021 11595.90119 1.008392518 0.997881919 1.011920833 1.064768757 0.914414863 0.750140233 0.747965639 0.766453678 0.986694352 1 13.50132732 -8.413250369 3.198529213 1.007846231 0.753205593 0.963958247 0.022135966 0.029747091 0.572939255 0.003021758 0.007261093 3.86E-09 8.413250369 -0.254640638 ISATEDT(ph)PEAEGEVPELYHQR ddPTM_HeLa_Romidepsin_16h_R1 1 ISATEDTPEAEGEVPELYHQR 21 0 A0A1B0GUH6;A0A1B0GUA3;Q96EK5 A0A1B0GUH6 KIAA1279 KIF1-binding protein 1 0 IS(0.002)AT(0.006)EDT(0.992)PEAEGEVPELYHQR 103.71 3.70E-06 0 647.28 759.45 524.78 676.97 651.45 496.59 693.31 626.76 766.25 689.51 TRUE FALSE FALSE 639.3907024 770.141557 533.9135758 755.2444566 618.2040756 464.8595017 752.1997341 644.8943117 697.7146809 671.5964308 0.95204601 1.146732653 0.794991681 1.124551028 0.920499346 0.692170894 1.120017468 0.960240826 1.038889799 1 9.391450753 -8.607591785 24.39420887 0.986448528 0.920705837 0.075639206 0.133810776 48.68572585 14011.46924 0.017862194 0.035724388 2.47E-09 8.607591785 -0.065742691 ISDAELEAELEKLS(ph)LSEGGLVPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 1 0 IS(0.014)DAELEAELEKLS(0.86)LS(0.124)EGGLVPS(0.002)S(0.001)K 47.648 0.018807 15264000 1472.5 1243.3 947.06 1573.2 1052.1 811.37 1146 1044.5 1391.1 1009.1 TRUE FALSE FALSE 1454.552604 1260.80321 963.543182 1755.100786 998.4074111 759.5260756 1243.341211 1074.72096 1266.676532 982.8834365 1.479883117 1.282759647 0.980322942 1.785665239 1.015794319 0.772752951 1.264993554 1.093436841 1.288735251 1 9.940876522 ISDAELEAELEKLSLSEGGLVPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 ISDAELEAELEKLSLSEGGLVPSSK 25 1 Q8WUX9 Q8WUX9 CHMP7 Charged multivesicular body protein 7 0 0 102.19 3.17E-07 0 1104.8 832.05 699.06 1215.3 984.16 842.14 949.3 985.74 950.02 1100.1 FALSE FALSE TRUE 1091.334273 843.7636217 711.2268461 1355.818704 933.9346428 788.3299719 1029.933518 1014.260832 865.0478318 1071.519243 1.018492462 0.787446074 0.663755551 1.26532371 0.871598572 0.735712379 0.961189941 0.946563338 0.807309656 1 10.06544204 -10.30303104 23.67189213 1.008732584 0.892013372 0 0.16605636 435.2254719 247707.1178 0.025653124 0.029335682 4.98E-11 10.30303104 -0.116719212 ISDEDWDIIHR ddPTM_HeLa_Romidepsin_16h_R1 2 ISDEDWDIIHR 11 0 A0A2R8YD50;P51659-3;P51659;P51659-2;E7ER27;A0A2R8YDT8;A0A2R8YF45 A0A2R8YD50 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 0 ; ; 157.97 0.00079002 36081000 8723.6 7707.5 8965.9 8007 9963.1 9590.1 7926.3 8648.3 8917.4 8067.1 FALSE FALSE TRUE 8617.273408 7816.006387 9121.947728 8932.807014 9454.64583 8977.323561 8599.559724 8898.524916 8119.80541 7857.515579 1.096691864 0.994717263 1.160920094 1.136848782 1.203261481 1.142514255 1.094437502 1.132485813 1.033380759 1 12.93985751 -11.25120705 0.338187533 0.982786673 1.149764985 0.493207898 0.047305849 1.016622471 0.276808758 0.068068989 0.030358493 5.61E-12 11.25120705 0.166978313 ISDS(ph)ESEDPPR ddPTM_HeLa_Romidepsin_16h_R1 1 ISDSESEDPPR 11 0 Q96ST2-3;Q96ST2;B8ZZB6 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 IS(0.441)DS(0.478)ES(0.081)EDPPR 174.57 2.43E-05 0 3346 3061.4 3093.1 2257.7 2946.6 3765.6 4201.8 3431.7 4187.1 4072.2 TRUE FALSE FALSE 3305.217665 3104.49847 3146.934108 2518.745897 2796.224007 3524.990313 4558.700787 3530.990825 3812.595289 3966.403657 0.833303403 0.78269857 0.793397339 0.635020062 0.704977165 0.888711946 1.149328505 0.890224781 0.96122221 1 11.95361579 -7.966322958 20.51609389 0.862084206 1.019589869 0.250902212 0.122680723 36.59578709 22291.23756 0.020124805 0.06037176 1.08E-08 7.966322958 0.157505664 ISDSES(ph)EDPPR ddPTM_HeLa_Romidepsin_16h_R1 1 ISDSESEDPPR 11 0 Q96ST2-3;Q96ST2;B8ZZB6 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 IS(0.301)DS(0.332)ES(0.367)EDPPR 164.33 0.0007511 11424000 4193.3 3940.7 5047.6 3100.1 4342.1 5157.8 4900.9 5044 5362.3 5152.4 TRUE FALSE FALSE 4142.190447 3996.177278 5135.451361 3458.548148 4120.506434 4828.233226 5317.182324 5189.940182 4882.682458 5018.539905 0.825377605 0.796282854 1.02329591 0.689154259 0.821056824 0.962079273 1.05950783 1.034153415 0.97292889 1 12.29305197 -7.963039746 4.320145906 0.891294646 1.043934532 0.323954029 0.097788329 0.215187939 9.039945829 0.015109175 0.047272435 1.09E-08 7.963039746 0.152639886 ISDYFEFAGGSAPGT(ph)SPGR ddPTM_HeLa_Romidepsin_16h_R1 2 ISDYFEFAGGSAPGTSPGR 19 0 Q86UE8-2;Q86UE8 Q86UE8-2 TLK2 Serine/threonine-protein kinase tousled-like 2 1 0 ISDYFEFAGGS(0.015)APGT(0.625)S(0.36)PGR;ISDYFEFAGGSAPGT(0.5)S(0.5)PGR ; 200.81 9.83E-21 23700000 2804.7 3061 3341.8 2792.5 2471.2 1797.14 1723.2 1854.32 3991.6 3109.8 TRUE FALSE FALSE 2770.515238 3104.092838 3399.962627 3115.381989 2345.085443 1682.308554 1869.568565 1907.971824 3634.581299 3029.006948 0.914661236 1.024788946 1.122467755 1.02851596 0.774209331 0.555399371 0.617221617 0.629900115 1.199925045 1 11.56462917 -8.548154009 3.528296103 0.981639573 0.605862675 0.82657821 0.090039022 0.061070028 1.607870518 0.010336554 0.022676581 2.83E-09 8.548154009 -0.375776898 IIPELVGS(ph)PTQSTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 IIPELVGSPTQSTSSR 16 0 H7C409;Q9NSI6-3;Q9NSI6-2;Q9NSI6 H7C409 BRWD1 Bromodomain and WD repeat-containing protein 1 1 0 IIPELVGS(0.945)PT(0.055)QSTSSR 231.41 1.45E-45 15294000 1884.4 2195.1 2217.5 1604.6 992.18 956.98 913.92 783.11 1894.5 2322.3 TRUE FALSE FALSE 1861.432208 2226.002675 2256.094657 1790.131402 941.5453523 895.8320665 991.548342 805.7680523 1725.051175 2261.966311 0.822926583 0.98410072 0.997404182 0.791404979 0.416250829 0.396041295 0.438356812 0.356224603 0.762633452 1 11.14336173 -8.839809849 3.324345037 0.92530408 0.398339914 0.913606559 0.074704713 0.046938593 1.038195537 0.011167947 0.021688307 1.45E-09 8.839809849 -0.526964166 down ISEEQQQLQQALAPAQASSNSS(ph)TPTR ddPTM_HeLa_Romidepsin_16h_R1 1 ISEEQQQLQQALAPAQASSNSSTPTR 26 0 Q86W71;C9J0Y3;C9JHJ5;Q13439-3;Q13439-4;Q13439;Q13439-5;E7EVX2 Q86W71;Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 ISEEQQQLQQALAPAQAS(0.066)S(0.167)NS(0.167)S(0.43)T(0.122)PT(0.049)R 61.091 0.0014192 5840700 962.45 1036.6 609.49 342.99 911.52 1035.6 861.78 1084.6 1068.9 1126.2 TRUE FALSE FALSE 950.7192892 1051.193282 620.0979178 382.6481176 865.0017331 969.4285022 934.9795717 1115.98119 973.2949069 1096.941162 0.86670035 0.958295047 0.565297337 0.348831944 0.788558004 0.883756154 0.852351616 1.017357383 0.887280869 1 10.09927043 -9.796339886 24.97609623 0.936887348 0.738270579 0.210345764 0.17550202 214.9464133 153822.6961 0.030737938 0.040398519 1.60E-10 9.796339886 -0.198616769 ISEQSDAK(ac)LK ddPTM_HeLa_Romidepsin_16h_R1 2 ISEQSDAKLK 10 1 P25705-2;P25705;P25705-3 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 1 ; ISEQSDAK(1)LK;ISEQSDAK(1)LK 197.21 2.10E-08 5221300 2732.89 2872.4 2966 2864.4 3642.1 3682.9 3166.8 3060.4 2456.7 2543.14 FALSE TRUE FALSE 2699.580486 2912.837723 3017.621986 3195.595405 3456.230046 3447.574576 3435.787913 3148.947845 2236.966599 2477.068856 1.089828601 1.175921176 1.218222892 1.290071286 1.395290259 1.39179602 1.38703771 1.271239529 0.903070011 1 11.27441826 -9.813440428 0.764191494 1.024753498 1.372687961 0.882373788 0.055599977 0.110225444 0.130134765 0.009568504 0.015272997 1.54E-10 9.813440428 0.347934462 ISES(ph)PEPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 ISESPEPGQR 10 0 H7C4B6;O14867 H7C4B6 BACH1 Transcription regulator protein BACH1 1 0 IS(0.081)ES(0.919)PEPGQR 100.09 0.024431 12490000 1890.5 2152.2 1604.1 2120 1895.7 1738.3 1652 1917.1 1783.9 1666.9 TRUE FALSE FALSE 1867.457859 2182.498728 1632.018688 2365.124375 1798.955355 1627.22824 1792.320839 1972.568264 1624.343516 1623.593698 1.150200239 1.344239468 1.0051891 1.456721825 1.108008338 1.002238579 1.103922023 1.214939591 1.000461826 1 10.66497493 -11.78557741 0.905520917 1.009289922 1.170104066 0.206148414 0.134025603 0.674028723 1.090847087 0.061034097 0.026100423 1.64E-12 11.78557741 0.160814144 NSPQSS(ph)PTSTPK ddPTM_HeLa_Romidepsin_16h_R1 2 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 0 NSPQS(0.029)S(0.897)PT(0.058)S(0.014)T(0.002)PK;NSPQS(0.374)S(0.576)PT(0.05)STPK ; 141.34 0.00015407 19580000 7425.3 6630.83 6983.1 5800.61 3976.67 4418.27 3538.33 2734.11 7806.4 7701.6 TRUE FALSE FALSE 7334.797588 6724.178999 7104.637926 6471.303821 3773.725691 4135.956806 3838.875662 2813.217159 7108.176033 7501.511322 0.97777598 0.896376571 0.947094208 0.862666674 0.503062054 0.551349805 0.511746966 0.375020051 0.947565861 1 12.87296557 -8.839779377 2.286617317 0.978657735 0.478488785 0.945014237 0.053660253 0.044834689 0.477374753 0.008186981 0.016872987 1.45E-09 8.839779377 -0.50016895 down ISGS(ph)S(ph)KRS(ph)NEET(ph)DDY(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 ISGSSKRSNEETDDYGK 17 2 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 5 0 IS(0.436)GS(0.895)S(0.895)KRS(0.773)NEET(1)DDY(1)GK 47.545 0.0042879 0 1035.9 818.29 911.24 1487.4 1262.3 929.57 770.03 1053.9 1020 881.25 TRUE FALSE FALSE 1023.274052 829.8099081 927.09975 1659.380186 1197.880121 870.173477 835.436329 1084.392934 928.7686454 858.354998 1.192133855 0.966744424 1.080088952 1.933209675 1.395553266 1.013768754 0.973299312 1.263338521 1.082033247 1 9.74543063 -11.32890552 0.565474906 1.008851447 1.249467678 0.082783202 0.268790824 1.617002474 1.122160007 0.174976477 0.08229024 4.69E-12 11.32890552 0.240616232 ISGSGSNSDMMENS(ph)KEEGTSSSEK ddPTM_HeLa_Romidepsin_16h_R1 1 ISGSGSNSDMMENSKEEGTSSSEK 24 1 P46100-4;P46100;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LPG6;A0A087WWG0 P46100-4 ATRX Transcriptional regulator ATRX 1 0 IS(0.004)GS(0.027)GS(0.022)NS(0.178)DMMENS(0.317)KEEGT(0.244)S(0.084)S(0.041)S(0.084)EK 41.166 0.0042119 0 1557.4 1393.4 1376.3 1214.9 1191.7 1356.4 1011.6 1095 1398.2 1597.4 TRUE FALSE FALSE 1538.41781 1413.016322 1400.253924 1355.372454 1130.883102 1269.730418 1097.525279 1126.682097 1273.14149 1555.899318 0.988764371 0.90816694 0.899964354 0.871118355 0.726835657 0.816074924 0.705396079 0.724135607 0.818267272 1 10.60353299 -9.16865761 0.669765134 1.000382304 0.712980032 0.566484259 0.066493963 0.135296457 0.115928101 0.006573043 0.018430493 6.78E-10 9.16865761 -0.287402272 ISGSGSNSDMMENSKEEGTSS(ph)SEK ddPTM_HeLa_Romidepsin_16h_R1 1 ISGSGSNSDMMENSKEEGTSSSEK 24 1 P46100-4;P46100;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LPG6;A0A087WWG0 P46100-4 ATRX Transcriptional regulator ATRX 1 0 ISGSGSNSDMMENS(0.001)KEEGT(0.041)S(0.258)S(0.577)S(0.123)EK 54.363 0.0076303 7942900 1984.2 2258.3 1955.5 1395.1 1960.3 1888 1523.7 1746.6 2541.2 2492 TRUE FALSE FALSE 1960.015807 2290.092407 1989.534657 1556.408026 1860.258576 1767.362893 1653.12304 1797.135115 2313.908707 2427.257481 0.807502221 0.943489689 0.819663622 0.641220818 0.766403478 0.728131608 0.681066205 0.740397395 0.95330171 1 11.24511144 -16.50689504 0.084349499 1.863306634 0.510124653 0.694475452 0.063763858 63.29695122 0.408794078 10.01656499 0.996831142 3.11E-17 16.50689504 -1.353181982 ISGTVNIR ddPTM_HeLa_Romidepsin_16h_R1 1 ISGTVNIR 8 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 110.12 0.022731 5768000 2495.8 2556 2486.9 2136 2505.6 2696.4 2684.2 2203.3 2737.3 2252.4 FALSE FALSE TRUE 2465.38023 2591.983435 2530.183451 2382.97437 2377.729882 2524.108742 2912.195881 2267.049009 2492.469032 2193.882323 1.123752265 1.181459647 1.153290413 1.086190606 1.0838001 1.150521482 1.32741663 1.033350324 1.136099692 1 11.09927043 -12.17343631 0.410385216 0.957086145 1.156817879 0 0.085875257 1.763092724 0.411686583 0.152705051 0.025370075 6.71E-13 12.17343631 0.199731734 ISHSLYSGIEGLDES(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 ISHSLYSGIEGLDESPSR 18 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;F5GZI3;B1AP52 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 ISHSLYSGIEGLDES(0.857)PS(0.143)R;ISHSLYSGIEGLDES(0.955)PS(0.045)R ; 155.54 2.86E-06 13018600 3309.06 3287.52 3773.7 3941.97 4669.2 4413 3289.5 3469.38 4924.6 4276.2 TRUE FALSE FALSE 3268.727904 3333.801793 3839.379666 4397.759119 4430.913301 4131.023542 3568.910048 3569.761037 4484.131442 4165.103708 0.784789079 0.800412673 0.921796895 1.055858252 1.063818241 0.991817691 0.856859828 0.857064142 1.076595388 1 12.0241367 -9.517867136 24.90728695 0.886896453 0.968320271 0.023043103 0.104316683 376.1531863 1869452.147 0.017488086 0.025137504 3.03E-10 9.517867136 0.081423818 ISINQT(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 3 ISINQTPGK 9 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6 E9PMS6 LMO7 LIM domain only protein 7 1 0 IS(0.007)INQT(0.993)PGK;IS(0.093)INQT(0.907)PGK;ISINQT(1)PGK ;; 131.17 0.015829 330715000 23495.3 21928.7 22163.3 18670.5 21052.1 19679.3 18786 18190.9 21997.4 19893.8 TRUE FALSE FALSE 23208.93025 22237.41281 22549.04294 20829.27106 19977.73278 18421.85624 20381.68237 18717.22499 20029.89745 19376.95621 1.197759338 1.147621565 1.163704077 1.074950618 1.031004693 0.950709495 1.051851599 0.965952794 1.033696791 1 14.24205435 -8.736553736 2.887461346 1.105719588 0.995615561 0.425113625 0.060463235 0.268680849 4.586125764 0.012223492 0.025363689 1.83E-09 8.736553736 -0.110104027 ISKPGAVST(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 ISKPGAVSTPVK 12 1 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 ISKPGAVS(0.232)T(0.768)PVK;ISKPGAVS(0.148)T(0.852)PVK ; 82.578 0.023566 208607000 12715.3 11605.8 12908.2 8579.4 10801.4 10377.7 8583.1 8529.7 12085.8 12725.7 TRUE FALSE FALSE 12560.32103 11769.18676 13132.86181 9571.390595 10250.16425 9714.598462 9312.1483 8776.493412 11004.81578 12395.08448 1.013330813 0.94950436 1.059521767 0.772192445 0.826953965 0.783746047 0.751277518 0.708062412 0.887837094 1 13.59748048 -9.253006613 24.83827534 1.004921304 0.771593024 0.801894897 0.05245727 117.5354013 346194.2849 0.005471458 0.008975499 5.58E-10 9.253006613 -0.23332828 ISLEQPPNGS(ph)DTPNPEK ddPTM_HeLa_Romidepsin_16h_R1 4 ISLEQPPNGSDTPNPEK 17 0 E9PJ60;Q9UHI6 E9PJ60 DDX20 Probable ATP-dependent RNA helicase DDX20 1 0 ISLEQPPNGS(0.651)DT(0.349)PNPEK;ISLEQPPNGS(0.999)DT(0.001)PNPEK;ISLEQPPNGS(0.989)DT(0.011)PNPEK;ISLEQPPNGS(0.913)DT(0.087)PNPEK ;;; 235.72 1.98E-46 52967000 13468 12957.8 15484.9 10053.8 13013.6 14121.4 10660.2 13565.9 14608.3 13851.9 TRUE FALSE FALSE 13303.84684 13140.22025 15754.40819 11216.26766 12349.46743 13219.08811 11565.67712 13958.40791 13301.69706 13492.02564 0.986052591 0.973924939 1.167682942 0.8313257 0.915316036 0.979770456 0.85722318 1.034567254 0.985893254 1 13.71981934 -9.209488803 24.99999773 1.003357185 0.922606599 0.284635241 0.075464062 383.4423178 184522.638 0.010442602 0.017317093 6.17E-10 9.209488803 -0.080750586 ISLGK(ac)VGVK ddPTM_HeLa_Romidepsin_16h_R1 1 ISLGKVGVK 9 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 0 1 ISLGK(1)VGVK 105.4 0.018932 399570 209.55 161.63 196.15 120.25 154.8 294.74 380.59 135.21 433.11 157.49 FALSE TRUE FALSE 206.995924 163.9054314 199.5639085 134.1538708 146.8999784 275.9070652 412.9173051 139.122088 394.3715569 153.3983871 1.349400916 1.068495142 1.300951804 0.874545511 0.957637047 1.79863081 2.691796915 0.906933187 2.570897676 1 7.261139504 -8.200962793 6.383803381 1.13750325 1.8974361 0.071748885 0.622072287 0.170788247 14.34520943 0.054884619 0.141223934 6.30E-09 8.200962793 0.75993285 WQELSPETSGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 WQELSPETSGKR 12 1 Q9NWF9-3;Q9NWF9;Q9NWF9-1 Q9NWF9-3 RNF216 E3 ubiquitin-protein ligase RNF216 0 1 ; WQELSPETSGK(1)R;WQELSPETSGK(1)R 145.09 0.00010079 3999700 386.18 304.07 425.12 1022.73 2406.12 2458.5 2172 2279.7 389.43 380.39 FALSE TRUE FALSE 381.4730896 308.3507054 432.5190353 1140.982855 2283.326718 2301.409784 2356.489626 2345.659523 354.5984055 370.507413 1.029596376 0.832238964 1.167369451 3.079514241 6.162701846 6.211508067 6.360168632 6.330938169 0.957061568 1 8.533358597 -8.932603867 2.258222755 1.000657693 6.355983183 0.996545423 0.146163721 0.012517781 0.129003397 0.024506853 0.048471964 1.17E-09 8.932603867 5.35532549 up ISMPDIDLNLT(ph)GPK ddPTM_HeLa_Romidepsin_16h_R1 2 ISMPDIDLNLTGPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ISMPDIDLNLT(1)GPK;ISMPDIDLNLT(1)GPK ; 166.79 0.00021848 76754000 9653.2 9711.5 9780.5 8032.8 5868.7 5942.4 4559.7 5157.3 9393.3 8435.4 TRUE FALSE FALSE 9535.543085 9848.218752 9950.7255 8961.590131 5569.19834 5562.699818 4947.000804 5306.518339 8553.139722 8216.247092 1.160571606 1.198627383 1.211103487 1.090715753 0.677827514 0.677036578 0.602099809 0.645856713 1.041003225 1 13.00426385 -8.750925371 5.457767532 1.100773848 0.6452095 0.925298736 0.064864436 0.043782079 3.956975296 0.01264305 0.024678634 1.77E-09 8.750925371 -0.455564347 ISMPDLDLHLKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 ISMPDLDLHLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 ISMPDLDLHLKS(1)PK 60.08 0.029299 138090000 2184 3022.2 2511.1 2536.8 2713.2 2441.3 2407.7 2870.8 2947.7 2683.3 TRUE FALSE FALSE 2157.380568 3064.746611 2554.804642 2830.116752 2574.73528 2285.308809 2612.209978 2953.862069 2684.050329 2613.587479 0.825448004 1.172620636 0.977508755 1.082847532 0.985134533 0.874395377 0.999472946 1.130194452 1.026960203 1 11.35181573 -10.28304234 24.9908596 0.917572675 1.022533938 0.097767993 0.09534371 979.0497214 1132586.056 0.017151452 0.019623267 5.21E-11 10.28304234 0.104961263 ISMPDVDLHLK ddPTM_HeLa_Romidepsin_16h_R1 1 ISMPDVDLHLK 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 66.92 0.021073 699580 533.3 239.08 330.85 432.32 431.39 362.34 360.09 399.37 467.35 471.57 FALSE FALSE TRUE 526.7999345 242.4457745 336.6083055 482.3068725 409.3745586 339.1876434 390.6760356 410.9251408 425.5490455 459.3185434 1.146916322 0.527837985 0.732842839 1.050048772 0.891265037 0.738458415 0.850555766 0.894640869 0.926479132 1 8.843351218 -10.30645921 24.99996751 1.069377171 0.820004308 0.310838026 0.139769841 312.444946 173502.959 0.023852753 0.027276721 4.94E-11 10.30645921 -0.249372863 ISMQDVDLS(ph)LGSPK ddPTM_HeLa_Romidepsin_16h_R1 3 ISMQDVDLSLGSPK 14 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 IS(0.001)MQDVDLS(0.933)LGS(0.066)PK;ISMQDVDLS(0.999)LGS(0.001)PK;ISMQDVDLS(0.999)LGS(0.001)PK ;; 130.27 0.0030658 789701000 9745.2 8486.3 9640.4 9022.4 9726.5 10428.3 9255.9 9748.7 9120.6 8401.5 TRUE FALSE FALSE 9626.421754 8605.770354 9808.187118 10065.61234 9230.12041 9761.965286 10042.09591 10030.76325 8304.830693 8183.227819 1.176359985 1.051635191 1.198571925 1.230029588 1.127931498 1.192923563 1.227155853 1.225770989 1.014860013 1 12.9984543 -16.52287875 0.161932011 0.281994208 1.236498137 0.720291405 0.045378911 24.84756473 0.267372268 5.640633347 0.086233529 3.00E-17 16.52287875 0.954503929 ISNLS(ph)PEEEQGLWK ddPTM_HeLa_Romidepsin_16h_R1 2 ISNLSPEEEQGLWK 14 0 F5GX09;Q5HYJ3-3;Q5HYJ3-2;Q5HYJ3 F5GX09 FAM76B Protein FAM76B 1 0 ISNLS(1)PEEEQGLWK;ISNLS(1)PEEEQGLWK ; 146.27 0.00061783 288570000 6916.4 6633.5 7287.5 6076.5 7518.3 8225.1 8122.1 8078.6 7674.9 6843.8 TRUE FALSE FALSE 6832.100256 6726.886587 7414.335881 6779.093521 7134.613096 7699.542655 8811.990971 8312.341545 6988.437722 6665.997089 1.024917978 1.009134342 1.112262094 1.016966169 1.070299462 1.155047407 1.321931416 1.246976474 1.048370953 1 12.70260497 -8.097553735 1.807439759 1.020544924 1.290148016 0.860021418 0.038947818 0.082901778 0.509505998 0.005510376 0.021634407 7.99E-09 8.097553735 0.269603093 ISNYGWDQSDK ddPTM_HeLa_Romidepsin_16h_R1 1 ISNYGWDQSDK 11 0 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 0 162.68 0.00075567 0 1595.7 1415.3 1204 1397 1761 1614.3 1254.2 1570.8 1668.1 1793.5 FALSE FALSE TRUE 1576.250995 1435.224631 1224.955115 1558.527713 1671.129599 1511.15144 1360.731717 1616.24862 1518.900958 1746.904611 0.902310856 0.821581568 0.701214655 0.892165321 0.956623268 0.865045195 0.778938763 0.92520714 0.869481338 1 10.77058512 -11.18722169 0.988893341 0.98318758 0.849812922 0.086914627 0.078866998 0.364018489 0.748457792 0.022232489 0.015718831 6.50E-12 11.18722169 -0.133374658 ISPDWISS(ph)MS(ph)IIR ddPTM_HeLa_Romidepsin_16h_R1 1 ISPDWISSMSIIR 13 0 Q9Y4E6-2;Q9Y4E6;K7EMB8 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 2 0 ISPDWIS(0.398)S(0.615)MS(0.987)IIR 63.037 0.017979 1085100 174.6 142.99 0 244.01 123.39 148.4 54.382 0 194.22 249.24 TRUE FALSE FALSE 172.471908 145.003017 0 272.2235843 117.0929479 138.9177189 59.00120572 0 176.8484768 242.7647089 0.710448849 0.597298584 0 1.121347438 0.482331013 0.572231934 0.243038644 0 0.728476876 1 7.9234149 -9.610430809 0.188151634 1.162115428 5.76E-16 0.307124245 0.299298959 3.42234761 0.395682454 0.781087991 1.372230218 2.45E-10 9.610430809 -1.162115428 ISPKRDKGLVEK ddPTM_HeLa_Romidepsin_16h_R1 1 ISPKRDKGLVEK 12 3 H0YFD6;P40939;A0A2R8YG21;A0A2R8Y688 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 0 70.552 0.026562 0 0 0 221.26 172.66 1512.1 2150 3114.3 1459.2 133.23 0 FALSE FALSE TRUE 0 0 225.1109375 192.6237616 1434.931895 2012.621939 3378.828564 1501.41965 121.3135751 0 0 ISPTFADAY(ph)S(ph)NMGNTLK ddPTM_HeLa_Romidepsin_16h_R1 1 ISPTFADAYSNMGNTLK 17 0 O15294-4;O15294-2;O15294-3;O15294 O15294-4 OGT UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit 2 0 ISPTFADAY(1)S(1)NMGNTLK 78.902 0.0076764 3903800 613.67 631.45 705.37 762.47 1109.4 934.62 835.85 1160.3 836.4 859.91 TRUE FALSE FALSE 606.190354 640.3395697 717.646669 850.6303689 1052.783178 874.9007983 906.8470781 1193.87145 761.5902892 837.5694142 0.723749392 0.764521195 0.856820529 1.015593877 1.256950362 1.044571093 1.082712743 1.425400008 0.909286175 1 9.71006495 -9.025951665 3.169504853 0.856214232 1.182206464 0.65206277 0.120297173 0.150143746 3.079505368 0.021705699 0.039310221 9.42E-10 9.025951665 0.325992233 ISQRDPS(ph)PESNK ddPTM_HeLa_Romidepsin_16h_R1 1 ISQRDPSPESNK 12 1 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7;Q8NDX5-3 E7EX82 PHC3 Polyhomeotic-like protein 3 1 0 ISQRDPS(0.963)PES(0.037)NK 131.08 0.023909 11059000 4101.2 4611.9 3867.9 3373 3831 3789.5 3228.5 3257.8 4119.9 3532.5 TRUE FALSE FALSE 4051.212997 4676.826449 3935.219177 3763.00213 3635.489775 3547.36318 3502.728709 3352.059303 3751.405826 3440.725141 1.177429998 1.359256046 1.143717971 1.093665427 1.056605694 1.030992897 1.018020495 0.974230479 1.090295119 1 11.74849693 -8.427645684 1.656811516 1.11446638 1.000899535 0.299515571 0.089411562 0.579288966 3.067794399 0.017167222 0.051790757 3.74E-09 8.427645684 -0.113566845 ISREPEPAAGPQAEESATVSAPAPMS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 ISREPEPAAGPQAEESATVSAPAPMSPTR 29 1 Q9BWG6-2;Q9BWG6 Q9BWG6-2 SCNM1 Sodium channel modifier 1 1 0 ISREPEPAAGPQAEESAT(0.002)VS(0.024)APAPMS(0.682)PT(0.291)R;ISREPEPAAGPQAEESAT(0.004)VS(0.011)APAPMS(0.769)PT(0.214)R;ISREPEPAAGPQAEES(0.055)AT(0.015)VS(0.141)APAPMS(0.61)PT(0.179)R ;; 78.556 4.21E-06 134924000 3835.5 3931.5 3510.15 4289.8 3623.67 3685.8 3209.34 3033.98 3963.4 3998.2 TRUE FALSE FALSE 3788.751451 3986.84776 3571.242688 4785.80686 3438.740598 3450.289275 3481.941259 3121.763424 3608.903577 3894.326188 0.972890115 1.023758044 0.917037381 1.228917823 0.883012987 0.8859785 0.894106218 0.801618374 0.926708089 1 11.92715801 -8.558021894 24.99999936 1.001477767 0.867350016 0.414410198 0.084349911 126.688844 90122.97796 0.010910902 0.021821869 2.77E-09 8.558021894 -0.134127751 ISS(ph)LLEEQFQQGK ddPTM_HeLa_Romidepsin_16h_R1 1 ISSLLEEQFQQGK 13 0 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 1 0 IS(0.126)S(0.874)LLEEQFQQGK 203.29 2.30E-16 10606000 1087.2 1175.4 1230.1 1177.7 1256.1 1348.3 930.14 1297 1250 1253.8 TRUE FALSE FALSE 1073.948788 1191.947312 1251.509374 1313.871215 1191.99653 1262.147981 1009.146068 1334.526649 1138.196869 1221.226095 0.879402096 0.976025092 1.024797439 1.075862382 0.976065394 1.033508853 0.826338442 1.092776066 0.932011586 1 10.25411461 -10.00617011 24.0449466 0.942243759 1.000026813 0.142312449 0.073633853 301.637452 1175490.018 0.012622073 0.016264423 9.86E-11 10.00617011 0.057783054 ISS(ph)PTETER ddPTM_HeLa_Romidepsin_16h_R1 1 ISSPTETER 9 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 1 0 IS(0.247)S(0.69)PT(0.063)ETER 102.06 0.026461 8542400 1377 1496.1 1289.6 1045.7 1209.1 916.69 1008.3 865.44 1343.5 1357.9 TRUE FALSE FALSE 1360.216594 1517.162135 1312.044947 1166.608754 1147.395115 858.1164675 1093.944977 890.480141 1223.333995 1322.621562 1.028424633 1.147087102 0.992003294 0.882042746 0.867515809 0.648799696 0.82710354 0.673269034 0.924931235 1 10.36918461 -8.818637802 1.510701847 1.024489658 0.728454702 0.754174911 0.073175447 0.121835599 0.560064004 0.010032666 0.02370027 1.52E-09 8.818637802 -0.296034956 ISSIQSIVPALEIANAHR ddPTM_HeLa_Romidepsin_16h_R1 3 ISSIQSIVPALEIANAHR 18 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ;; ;; 151.57 1.51E-05 18883990 5725.44 5813.5 6090.97 5282.775 6081.9 7444.6 5789.4 5655.4 6526.2 5442.4 FALSE FALSE TRUE 5655.656135 5895.342606 6196.980778 5893.594302 5771.517948 6968.914086 6281.151491 5819.030076 5942.480327 5301.005663 1.066902489 1.112117772 1.169019837 1.111787966 1.088759061 1.31464 1.184898091 1.097721913 1.121009994 1 12.37205037 -10.25706727 0.480014649 1.003646627 1.187263746 0.224510752 0.069827392 0.477495427 0.268656393 0.02548854 0.030153325 5.53E-11 10.25706727 0.183617119 ISSLPVSRPIS(ph)PSPSAILER ddPTM_HeLa_Romidepsin_16h_R1 1 ISSLPVSRPISPSPSAILER 20 1 Q5T5P2;Q5T5P2-2;Q5T5P2-7;Q5T5P2-10;Q5T5P2-3;Q5T5P2-9;Q5T5P1;Q5T5P2-4;Q5T5P2-8;Q5T5P2-6;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 ISS(0.001)LPVS(0.198)RPIS(0.769)PS(0.031)PS(0.002)AILER 126.8 0.0019332 43979000 1080.7 909.98 931.07 1062 901.88 727.13 432.94 623.67 1132.4 941.52 TRUE FALSE FALSE 1067.528013 922.7907223 947.2748828 1184.793437 855.8536982 680.6687397 469.7139128 641.7149075 1031.115308 917.0591747 1.164077567 1.006249921 1.032948482 1.291948731 0.933258967 0.7422299 0.51219586 0.699752999 1.124371618 1 9.840871019 -8.269131289 2.597874243 1.083276163 0.61299468 0.810811479 0.097594342 0.090162014 1.193598946 0.014630884 0.040886128 5.38E-09 8.269131289 -0.470281483 ISST(ph)PPSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 ISSTPPSGSR 10 0 Q3Y452 Q3Y452 TDRG1 Testis development-related protein 1 1 0 IS(0.003)S(0.221)T(0.763)PPS(0.014)GSR 118.23 0.026681 112530000 2552.1 2676.3 2213.1 2000.7 2587.3 2420.9 2079.2 2558.6 2780.4 2494.7 TRUE FALSE FALSE 2520.994024 2713.977022 2251.618077 2232.030348 2455.260426 2266.212303 2255.807196 2632.629054 2531.71406 2429.887334 1.037494203 1.116914757 0.926634764 0.918573596 1.010442086 0.932640897 0.928358761 1.083436675 1.041905945 1 11.24667371 -9.714271595 24.99999734 1.025641446 0.963194369 0.307664655 0.05617705 135.31083 71717.499 0.00860569 0.012170264 1.93E-10 9.714271595 -0.062447077 ISSTPTT(ph)ETIR ddPTM_HeLa_Romidepsin_16h_R1 1 ISSTPTTETIR 11 0 A0A075B754;Q96QE3-2;Q96QE3 A0A075B754 ATAD5 ATPase family AAA domain-containing protein 5 1 0 IS(0.043)S(0.31)T(0.31)PT(0.011)T(0.319)ET(0.007)IR 140.91 0.0061788 5458500 2567.8 2737.2 3048.4 2186.1 2268.5 2160.1 2061 2103.8 3368.3 2854.7 TRUE FALSE FALSE 2536.502666 2775.734373 3101.456123 2438.867168 2152.72998 2022.076581 2236.061289 2164.670134 3067.030812 2780.534482 0.912235645 0.998273674 1.115417249 0.877121713 0.774214452 0.72722586 0.804183981 0.778508646 1.103036424 1 11.44114651 -8.944179733 4.162416564 0.972782905 0.771839166 0.738995325 0.067922708 0.089122523 3.21276664 0.009157431 0.016874682 1.14E-09 8.944179733 -0.200943739 ISSY(ph)VQT(ph)GIS(ph)T(ph)WPK ddPTM_HeLa_Romidepsin_16h_R1 1 ISSYVQTGISTWPK 14 0 Q5SZR4;F6TB26;Q9Y2W6-3;Q9Y2W6 Q5SZR4 TDRKH Tudor and KH domain-containing protein 4 0 IS(0.061)S(0.338)Y(0.641)VQT(0.994)GIS(0.994)T(0.972)WPK 59.294 0.024173 7866400 1139.3 1685.3 1694.3 392.55 1393.6 2610.8 1040.4 2210.1 1479.8 1706.7 TRUE FALSE FALSE 1125.413773 1709.025698 1723.788581 437.938478 1322.479392 2443.978306 1128.77155 2274.045757 1347.442982 1662.359688 0.676997753 1.028072149 1.036952829 0.263443875 0.795543468 1.47018622 0.679017639 1.367962525 0.810560429 1 10.69901686 ISTPQT(ph)NTVPIKPLISTPPVSSQPK ddPTM_HeLa_Romidepsin_16h_R1 1 ISTPQTNTVPIKPLISTPPVSSQPK 25 1 A0A0A0MRT2;Q9BTA9-5;Q9BTA9-2;Q9BTA9 A0A0A0MRT2 WAC WW domain-containing adapter protein with coiled-coil 1 0 IS(0.088)T(0.081)PQT(0.428)NT(0.358)VPIKPLIS(0.022)T(0.022)PPVS(0.001)SQPK 50.029 0.020673 12175000 2061.9 2068.2 1769.8 2141.5 1894.5 2001.6 1592.4 1905.2 2198.9 1974.4 TRUE FALSE FALSE 2036.76877 2097.316174 1800.602627 2389.110306 1797.816596 1873.70422 1727.658416 1960.323956 2002.224877 1923.104803 1.059104406 1.090588599 0.936299792 1.242319348 0.934851076 0.974312069 0.898369352 1.019353679 1.041141842 1 10.90922167 ISTPQTNTVPIKPLIST(ph)PPVSSQPK ddPTM_HeLa_Romidepsin_16h_R1 1 ISTPQTNTVPIKPLISTPPVSSQPK 25 1 A0A0A0MRT2;Q9BTA9-5;Q9BTA9-2;Q9BTA9 A0A0A0MRT2 WAC WW domain-containing adapter protein with coiled-coil 1 0 ISTPQTNTVPIKPLIS(0.131)T(0.712)PPVS(0.131)S(0.025)QPK 82.62 1.48E-05 0 1519.2 1327.1 1295.6 1153.5 1434.9 1585.2 1273.3 1462.2 1457.2 1436.2 TRUE FALSE FALSE 1500.683406 1345.782949 1318.149375 1286.873097 1361.671699 1483.910836 1381.45407 1504.50645 1326.864382 1398.887317 1.072769327 0.962038137 0.94228417 0.919926203 0.973396272 1.060779391 0.987537776 1.075502245 0.948514127 1 10.45006404 -13.20947948 3.907212087 0.999360563 1.016005492 0 0.056260801 1.583787286 44.16509854 0.060613509 0.008788237 6.17E-14 13.20947948 0.016644929 ISVISTGPTLQARRR ddPTM_HeLa_Romidepsin_16h_R1 1 ISVISTGPTLQARRR 15 2 A0A3B3ITW5;E7EPB6;P13569-2;P13569 A0A3B3ITW5 CFTR Cystic fibrosis transmembrane conductance regulator 0 0 97.813 0.0078291 0 0 47.012 62.404 310.44 1368.5 2019.1 1852.3 1345.2 140.44 0 FALSE FALSE TRUE 0 47.67383617 63.49011544 346.3345335 1298.660338 1890.086026 2009.634316 1384.12124 127.8786947 0 0 ISVSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 ISVSSPGR 8 0 O75864-2;O75864 O75864-2 PPP1R37 Protein phosphatase 1 regulatory subunit 37 1 0 ISVS(0.002)S(0.998)PGR 126.24 0.014397 33612000 6932 6864.5 7187.6 6529.4 7828.9 7909.1 7229.7 6942.8 6614.9 6143.6 TRUE FALSE FALSE 6847.510118 6961.138611 7312.697163 7284.35995 7429.362019 7403.734035 7843.790538 7143.678964 6023.246777 5983.988386 1.144305382 1.163294138 1.22204401 1.217308504 1.24154018 1.237257421 1.310796417 1.193798935 1.006560573 1 12.54689166 -11.10151088 0.334186489 0.965776818 1.271997319 0.906522244 0.029191441 0.286648004 0.082780473 0.035250514 0.018217354 7.92E-12 11.10151088 0.306220501 ISVYYNEATGGK ddPTM_HeLa_Romidepsin_16h_R1 2 ISVYYNEATGGK 12 0 Q5JP53;P07437 Q5JP53 TUBB Tubulin beta chain 0 0 ; ; 229.68 1.24E-29 8457800 2537 2680.2 2795 2239.36 2623.1 2605.2 2198.97 2240.53 2545.1 2227.7 FALSE FALSE TRUE 2506.078068 2717.931926 2843.645803 2498.28534 2489.233419 2438.736128 2385.750457 2305.356201 2317.459882 2169.824033 1.154968343 1.252604766 1.310542127 1.151376933 1.147205202 1.123932674 1.099513334 1.062462285 1.068040471 1 11.08336233 -11.89240325 0.935705336 1.008084871 1.164000252 0.333942743 0.070570502 0.407956675 0.694142488 0.037616944 0.014896866 1.28E-12 11.89240325 0.155915381 ISYIPDEEVS(ph)SPSPPQR ddPTM_HeLa_Romidepsin_16h_R1 1 ISYIPDEEVSSPSPPQR 17 0 F8W930;Q9Y6M1-5;Q9Y6M1-6;Q9Y6M1-3;Q9Y6M1-4;Q9Y6M1-1;Q9Y6M1 F8W930 IGF2BP2 Insulin-like growth factor 2 mRNA-binding protein 2 1 0 ISYIPDEEVS(0.75)S(0.238)PS(0.012)PPQR 253.79 1.93E-72 16066000 3563.1 3356.9 3177.4 2343.5 2904.6 2587.5 2204.2 2617.1 3432.3 2630.8 TRUE FALSE FALSE 3519.671567 3404.158526 3232.701314 2614.466496 2756.367423 2422.167101 2391.424693 2692.821659 3125.306492 2562.451437 1.373556398 1.328477284 1.261565885 1.020298945 1.075675966 0.945253856 0.933256591 1.050877149 1.219654916 1 11.32330895 -9.18720703 5.955791348 1.200396333 0.999851412 0.544376493 0.103301388 0.238707717 15.00509069 0.023581395 0.039305621 6.50E-10 9.18720703 -0.200544921 ISYIPDEEVSS(ph)PSPPQR ddPTM_HeLa_Romidepsin_16h_R1 3 ISYIPDEEVSSPSPPQR 17 0 F8W930;Q9Y6M1-5;Q9Y6M1-6;Q9Y6M1-3;Q9Y6M1-4;Q9Y6M1-1;Q9Y6M1 F8W930 IGF2BP2 Insulin-like growth factor 2 mRNA-binding protein 2 1 0 ISYIPDEEVS(0.033)S(0.966)PS(0.001)PPQR;ISYIPDEEVS(0.034)S(0.766)PS(0.2)PPQR;ISYIPDEEVS(0.002)S(0.607)PS(0.39)PPQR ;; 296.27 1.65E-120 45164000 6227.2 6544.61 6341.5 5329.6 6689.3 6656 4781.71 5803.5 6879.3 6738.3 TRUE FALSE FALSE 6151.300491 6636.745191 6451.871147 5945.833429 6347.92006 6230.703081 5187.868328 5971.415116 6263.998178 6563.237995 0.937235629 1.011199837 0.983031722 0.905929883 0.967193337 0.949333711 0.790443426 0.909827607 0.954406679 1 12.68019203 -7.887056378 6.643329846 0.968299418 0.851098866 0.575053883 0.039109395 0.104186237 5.645885483 0.005521175 0.016880173 1.30E-08 7.887056378 -0.117200552 ISYT(ph)PPES(ph)PVPSYASSTPLHVPVPR ddPTM_HeLa_Romidepsin_16h_R1 2 ISYTPPESPVPSYASSTPLHVPVPR 25 0 P41212 P41212 ETV6 Transcription factor ETV6 2 0 IS(0.056)Y(0.03)T(0.922)PPES(0.991)PVPSY(0.001)ASSTPLHVPVPR;IS(0.187)Y(0.01)T(0.807)PPES(0.997)PVPSYASSTPLHVPVPR ; 96.505 2.67E-05 19616700 2318.69 2376.8 1772.39 2472.17 3289.7 2707.5 1998.02 2163.26 3839.2 2871.2 TRUE FALSE FALSE 2290.428914 2410.260653 1803.237704 2758.013927 3121.814333 2534.499488 2167.731769 2225.850515 3495.812337 2796.60581 0.819003131 0.861852122 0.644795093 0.986200457 1.116286865 0.906276987 0.775129538 0.795911425 1.250019693 1 11.4494612 -12.39981867 1.135118054 0.999711694 0.863091237 0.262833529 0.144670464 0.805558601 1.862494768 0.086048269 0.02210927 3.98E-13 12.39981867 -0.136620457 IT(ph)FPS(ph)LQALVQHY(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ITFPSLQALVQHYSK 15 0 P51451;E9PJX5 P51451 BLK Tyrosine-protein kinase Blk;Non-specific protein-tyrosine kinase 4 0 IT(1)FPS(1)LQALVQHY(1)S(1)K 56.039 0.024658 5537400 1753.6 1681.8 1876.3 1862.2 2052.3 2100.1 1820.4 1736.6 2264.6 2016.8 TRUE FALSE FALSE 1732.226449 1705.476425 1908.956214 2077.516326 1947.563473 1965.910388 1975.024731 1786.845781 2062.048504 1964.403245 0.881807975 0.868190596 0.97177411 1.057581396 0.991427538 1.000767227 1.005406978 0.909612517 1.049707339 1 10.9398754 -9.529589874 24.82585337 0.936120952 0.996067215 0.084299425 0.059946718 199.7770879 739014.6647 0.009390659 0.013298715 2.95E-10 9.529589874 0.059946263 IT(ph)KPGSIDSNNQLFAPGGR ddPTM_HeLa_Romidepsin_16h_R1 1 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 IT(0.561)KPGS(0.32)IDS(0.119)NNQLFAPGGR 58.024 0.023296 23585000 1132.5 679.31 783.79 746.67 1277.4 1186.7 1169.4 1254.4 1027.1 660.92 TRUE FALSE FALSE 1118.696654 688.873344 797.4315362 833.0034986 1212.209511 1110.8737 1268.728807 1290.694085 935.2336036 643.7492031 1.737783362 1.07009584 1.238730133 1.293987619 1.883046232 1.725631184 1.970843305 2.004964167 1.452791862 1 9.330354931 -4 0.093608482 0.766269718 4.148403732 0.480361923 0.256318679 98.42926 0.663989689 3.062065016 42.92963158 1.00E-04 4 3.382134013 IT(ph)VQASPNLDK ddPTM_HeLa_Romidepsin_16h_R1 1 ITVQASPNLDK 11 0 Q5TCX8;Q5TCX8-2 Q5TCX8 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 0 IT(0.974)VQAS(0.026)PNLDK 124.81 0.016285 13215000 2415.5 2303.1 2425.8 1939.2 2424.4 2513.8 1771 2155.4 2798.5 2840.6 TRUE FALSE FALSE 2386.058957 2335.523102 2468.020031 2163.419428 2300.673821 2353.176293 1921.428696 2217.763098 2548.195151 2766.800803 0.862389137 0.844124051 0.892012186 0.78192092 0.831528536 0.850504413 0.69445863 0.801562258 0.92098974 1 11.43400306 -16.52287874 0.080538393 1.667235071 0.613265787 0.624033665 0.047876076 54.75441134 0.338245861 6.474590396 0.707028222 3.00E-17 16.52287874 -1.053969284 ITADGAHFELR ddPTM_HeLa_Romidepsin_16h_R1 1 ITADGAHFELR 11 0 J3QK89;Q8IWX8 J3QK89 CHERP Calcium homeostasis endoplasmic reticulum protein 0 0 152.67 0.00027082 0 2458.1 2158.7 2388.7 1986.2 2620.9 2474.5 2075.5 2133 2637.9 2367 FALSE FALSE TRUE 2428.139732 2189.090235 2430.274321 2215.853789 2487.145693 2316.387436 2251.792918 2194.71499 2401.959617 2305.504999 1.053192135 0.949505742 1.054118001 0.961114285 1.078785643 1.004720197 0.976702683 0.951945448 1.041836656 1 11.17086708 -7.706750665 2.850925199 1.020789983 0.957133794 0.245254676 0.038982526 0.266417776 4.195863165 0.005234431 0.025069552 1.96E-08 7.706750665 -0.063656189 ITAHSS(ph)PPLTK ddPTM_HeLa_Romidepsin_16h_R1 1 ITAHSSPPLTK 11 0 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 0 ITAHS(0.142)S(0.858)PPLTK 128.36 0.0063234 23246000 5507.3 5214.9 4556.1 4343 3776.8 3297.3 3165.6 3282.3 5086.6 5349.6 TRUE FALSE FALSE 5440.174909 5288.315499 4635.397009 4845.158094 3584.055803 3086.613172 3434.485985 3377.268172 4631.641756 5210.616621 1.044055878 1.014911647 0.88960623 0.929862711 0.687837172 0.592370039 0.659132351 0.648151345 0.888885538 1 12.34723839 -8.888192518 1.367795046 1.017884257 0.623969852 0.866423691 0.059445191 0.067707016 0.253263383 0.007030645 0.016569233 1.29E-09 8.888192518 -0.393914404 ITDAYLDQYLWYEADKR ddPTM_HeLa_Romidepsin_16h_R1 1 ITDAYLDQYLWYEADKR 17 1 Q6P2Q9;I3L0J9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 98.552 0.00096684 0 581 724.35 686.12 633.67 781.18 659.31 552.87 624.73 812.37 622.24 FALSE FALSE TRUE 573.9185485 734.5474183 698.0616308 706.9379069 741.3134696 617.1822188 599.830764 642.8055769 739.7095926 606.0741151 0.946944498 1.211976225 1.151776018 1.166421547 1.223139961 1.018327963 0.9896987 1.060605561 1.220493623 1 9.243350417 -10.27988877 24.75824138 0.974946009 1.115969315 0 0.107135007 531.0246472 712608.7626 0.013854695 0.015859659 5.25E-11 10.27988877 0.141023306 ITEFCHR ddPTM_HeLa_Romidepsin_16h_R1 2 ITEFCHR 7 0 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 0 ; ; 167.82 0.0046424 9430400 7654.6 6923.7 9722.1 1050.16 10649.1 11604.8 9602.8 6750 7585.5 6598.2 FALSE FALSE TRUE 7561.302791 7021.17203 9891.309072 1171.58444 10105.63669 10863.29073 10418.46159 6945.3006 6907.033882 6426.777813 1.176530917 1.092487127 1.539077491 0.182297331 1.572426647 1.690316835 1.62110188 1.080681611 1.074727349 1 12.64987988 ITEK(ac)LEK ddPTM_HeLa_Romidepsin_16h_R1 1 ITEKLEK 7 1 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8YGP5 P51532 SMARCA4 Transcription activator BRG1 0 1 ITEK(1)LEK 109.71 0.024362 7068400 3906.6 3772.3 3889.5 2816.2 2956.8 2300.2 2324.8 2540.6 3986.7 3920.7 FALSE TRUE FALSE 3858.984857 3825.406538 3957.195116 3141.822295 2805.903463 2153.224644 2522.268454 2614.108253 3630.119567 3818.839649 1.01051241 1.001719603 1.036229714 0.822716475 0.734752888 0.563842644 0.660480325 0.684529463 0.950581826 1 11.89891863 -8.920093118 1.944353735 1.00740573 0.641748378 0.934793133 0.04235929 0.045596825 0.347806546 0.005572489 0.011443743 1.20E-09 8.920093118 -0.365657352 ITES(ph)EEVVSR ddPTM_HeLa_Romidepsin_16h_R1 3 ITESEEVVSR 10 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 IT(0.078)ES(0.922)EEVVSR;IT(0.041)ES(0.959)EEVVSR;IT(0.001)ES(0.999)EEVVSR ;; 179.94 4.20E-05 16807000 4055.4 4623.8 4359.88 3836.4 4866.8 5246.8 5083.7 5435.8 4715 4352.32 TRUE FALSE FALSE 4005.971225 4688.893978 4435.761883 4279.982619 4618.429035 4911.546413 5515.509351 5593.076297 4293.278591 4239.246099 0.944972557 1.106067888 1.046356305 1.009609378 1.089445842 1.158589593 1.301059014 1.319356359 1.012745779 1 12.04959201 -7.641525561 0.587385305 0.980281091 1.496429227 0.862086878 0.044688205 0.595508452 0.181662037 0.009100153 0.190308433 2.28E-08 7.641525561 0.516148136 ITES(ph)SLVEITEHK ddPTM_HeLa_Romidepsin_16h_R1 2 ITESSLVEITEHK 13 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 IT(0.021)ES(0.585)S(0.395)LVEITEHK;IT(0.028)ES(0.94)S(0.032)LVEITEHK ; 143.46 0.00032168 9633200 7285.9 6616.2 8478.4 3273.6 6837.7 7567 4884.3 5756.9 6961.5 7242 TRUE FALSE FALSE 7197.096648 6709.343037 8625.962995 3652.109035 6488.746654 7083.493121 5299.17232 5923.466819 6338.846005 7053.851796 1.020307324 0.951160193 1.222872729 0.517746777 0.919887012 1.004202147 0.751245202 0.839749259 0.898636119 1 12.78419555 -9.280541312 24.99675262 1.019063416 0.820768041 0.355979977 0.141952492 674.8026863 883043.3785 0.019728237 0.030165037 5.24E-10 9.280541312 -0.198295376 ITES(ph)SLVEITEHKDFTLK ddPTM_HeLa_Romidepsin_16h_R1 1 ITESSLVEITEHKDFTLK 18 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 IT(0.161)ES(0.409)S(0.409)LVEIT(0.021)EHKDFTLK 54.171 0.02261 4079200 2532.5 2380.1 2470.1 2367 2166.2 2160.9 1954.3 1890.7 2909.8 2420.2 TRUE FALSE FALSE 2501.632916 2413.60711 2513.091054 2640.683677 2055.650731 2022.825464 2120.298193 1945.404421 2649.5402 2357.322855 1.061217775 1.023876346 1.066078433 1.120204503 0.872027659 0.858102852 0.899451761 0.825260069 1.123961529 1 11.20293365 -8.741320231 24.50903331 1.03796567 0.865862854 0.823610859 0.044726311 59.35992867 72311.44616 0.005756329 0.011500054 1.81E-09 8.741320231 -0.172102816 ITESEEVVSR ddPTM_HeLa_Romidepsin_16h_R1 2 ITESEEVVSR 10 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 227.99 6.92E-26 48615000 5652.6 5626.8 5029.7 4655.4 6495.8 6426.8 6519.2 5465.8 5609.8 5457.6 FALSE FALSE TRUE 5583.703937 5706.014238 5117.239819 5193.679252 6164.295087 6016.148222 7072.940685 5623.944299 5108.045438 5315.810765 1.050395543 1.07340432 0.962645219 0.977024857 1.159615223 1.131746123 1.330547869 1.057965482 0.96091559 1 12.37607403 -8.680656993 5.727932103 1.020570292 1.181578649 0.54711186 0.07286631 0.11458848 6.199255542 0.009599765 0.019323272 2.09E-09 8.680656993 0.161008358 ITIAINNTLTPTT(ph)LPPGTIQY(ph)LT(ph)DT(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ITIAINNTLTPTTLPPGTIQYLTDTSK 27 0 P08236-2;P08236 P08236-2 GUSB Beta-glucuronidase 5 0 IT(0.072)IAINNT(0.085)LT(0.239)PT(0.239)T(0.462)LPPGT(0.361)IQY(0.868)LT(0.891)DT(0.891)S(0.891)K 43.64 0.0039617 0 2012.4 1756.5 1822.6 1620.2 2079.3 1603 1390.3 1671.4 1909.6 2093 TRUE FALSE FALSE 1987.872095 1781.228053 1854.321588 1807.535147 1973.185562 1500.573473 1508.392047 1719.759322 1738.800593 2038.623558 0.975105034 0.873740542 0.909594898 0.886644883 0.967900893 0.736071879 0.739907101 0.843588467 0.852928725 1 10.99337968 -8.677627396 0.389942719 1.001548952 0.722461948 0.276261202 0.073433991 0.984552031 0.215454847 0.020374366 0.111726558 2.10E-09 8.677627396 -0.279087004 ITITNDK ddPTM_HeLa_Romidepsin_16h_R1 1 ITITNDK 7 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PM13;E9PS65;P54652;A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931;P17066 P11142;P54652;A0A0G2JIW1;P17066 HSPA8;HSPA2;HSPA1B;HSPA1A;HSPA1L;HSPA6 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;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 0 149.4 0.030527 1333000 1384 1336.3 1807.2 1339.3 1786.3 2264 2139.1 1018.8 1718.2 1265.8 FALSE FALSE TRUE 1367.131276 1355.112466 1838.653558 1494.156168 1695.138445 2119.337707 2320.795101 1048.277371 1564.519889 1232.914334 1.108861531 1.099113239 1.491306823 1.211889688 1.374903673 1.718965908 1.882365252 0.850243478 1.268960743 1 10.26785685 -9.695222849 0.829112823 1.033127105 1.495224308 0.177151669 0.277341841 0.465975542 0.642347545 0.053193171 0.090163819 2.02E-10 9.695222849 0.462097203 ITKPGS(ph)IDSNNQLFAPGGR ddPTM_HeLa_Romidepsin_16h_R1 1 ITKPGSIDSNNQLFAPGGR 19 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 IT(0.004)KPGS(0.629)IDS(0.367)NNQLFAPGGR 86.707 0.0019663 21003000 957.1 1017.3 852.6 1033.9 1503.7 1436.6 1111 1355.3 1119.3 1041.2 TRUE FALSE FALSE 945.4344971 1031.621576 867.4391454 1153.444383 1426.960578 1344.805896 1205.368312 1394.513467 1019.187005 1014.149474 0.932243739 1.01722833 0.855336583 1.137351458 1.407051539 1.326043084 1.188550942 1.375057132 1.004967247 1 9.986054589 -8.997816704 4.792692571 0.964533998 1.312721906 0.859266603 0.068990733 0.048152309 3.038169955 0.009875565 0.017595497 1.01E-09 8.997816704 0.348187909 ITKPGSIDSNNQLFAPGGRLS(ph)WGK ddPTM_HeLa_Romidepsin_16h_R1 2 ITKPGSIDSNNQLFAPGGRLSWGK 24 2 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 ITKPGSIDSNNQLFAPGGRLS(1)WGK;ITKPGSIDSNNQLFAPGGRLS(1)WGK ; 90.712 2.94E-05 119522000 6646.5 5501.1 5729.8 8745 8966.4 8307.4 8079.8 8101.5 5990.3 6128.8 TRUE FALSE FALSE 6565.489901 5578.54463 5829.524765 9756.138046 8508.81115 7776.583951 8766.09801 8335.90412 5454.512565 5969.572892 1.099825736 0.934496442 0.976539674 1.6343109 1.425363473 1.302703575 1.468463183 1.396398749 0.913719066 1 12.543412 -9.273974903 24.99952908 1.033283357 1.43768055 0.848546573 0.09617473 221.9660287 442664.851 0.014109279 0.021644278 5.32E-10 9.273974903 0.404397193 ITLPVDFVTADKFDENAK ddPTM_HeLa_Romidepsin_16h_R1 3 ITLPVDFVTADKFDENAK 18 1 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 0 ;; ;; 163.9 8.52E-34 83729000 4670.25 3902.9 4714.266 4284.1 5015.598 5283.377 3858.8 4954.3 4692.8 4135.18 FALSE FALSE TRUE 4613.327197 3957.845129 4796.315822 4779.447799 4759.633318 4945.786261 4186.566376 5097.644854 4273.064215 4027.747427 1.145386418 0.982644816 1.190818419 1.186630464 1.18171097 1.2279286 1.039431208 1.265631707 1.060906696 1 11.9757575 -16.52287875 0.141772999 0.435786195 1.214927738 0.335700331 0.077045331 53.07024316 0.521586103 8.361051164 0.202259807 3.00E-17 16.52287875 0.779141542 ITPGNYGNT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 ITPGNYGNTPR 11 0 Q5VYS8-5;Q5VYS8-3;Q5VYS8-2;Q5VYS8-4;Q5VYS8-6;Q5VYS8 Q5VYS8-5 ZCCHC6 Terminal uridylyltransferase 7 1 0 ITPGNYGNT(1)PR 109.6 0.03044 5211400 1743 2166.6 1662.7 1302.9 2135.2 2319 1828.6 2217.8 2071 2067.5 TRUE FALSE FALSE 1721.755646 2197.101452 1691.638596 1453.547428 2026.232776 2170.823384 1983.921238 2281.968544 1885.764573 2013.786052 0.854984393 1.091030226 0.840028957 0.721798339 1.006180758 1.07798114 0.985169818 1.133173279 0.936427468 1 10.9756947 -8.532775932 24.9897708 0.9201466 1.054858741 0.341807818 0.09867836 210.0725048 530418.8385 0.015205115 0.030439593 2.93E-09 8.532775932 0.134712141 ITPHT(ph)SPAPR ddPTM_HeLa_Romidepsin_16h_R1 2 ITPHTSPAPR 10 0 A0A0C4DFZ9;Q58A45-2;Q58A45-4;Q58A45-3;Q58A45 A0A0C4DFZ9 PAN3 PAB-dependent poly(A)-specific ribonuclease subunit PAN3 1 0 ITPHT(0.5)S(0.5)PAPR;ITPHT(0.5)S(0.5)PAPR ; 112.44 0.01244 15691500 1241.78 825.1 955.04 897.19 915.71 666.42 846.28 636.93 1181.64 898.86 TRUE FALSE FALSE 1226.644708 836.7157795 971.6620706 1000.927329 868.9779017 623.8379128 918.1630021 655.3585646 1075.951159 875.5074876 1.401067067 0.955692317 1.109827254 1.143253877 0.992541942 0.712544349 1.048720902 0.74854707 1.228945696 1 9.773975707 -8.617097587 3.10088039 1.165591024 0.855704229 0.466007949 0.14328408 0.202174627 3.888892902 0.026313976 0.056926265 2.41E-09 8.617097587 -0.309886795 ITPLEIEVLEETVQTMDTS ddPTM_HeLa_Romidepsin_16h_R1 4 ITPLEIEVLEETVQTMDTS 19 0 Q99436 Q99436 PSMB7 Proteasome subunit beta type-7 0 0 ;;; ;;; 176.18 6.88E-09 81154000 15293.7 13958.5 13189.4 14225 15176.4 15274.4 13245.7 14241.8 15977.6 14121.6 FALSE FALSE TRUE 15107.2945 14155.00813 13418.95597 15869.76143 14401.89168 14298.41514 14370.78943 14653.86401 14548.52344 13754.7188 1.098335395 1.029101964 0.975589263 1.153768511 1.047050971 1.039527987 1.044789766 1.065369945 1.057711441 1 13.74763902 -12.6027834 1.403682622 1.000021658 1.061082384 0 0.047183851 0.543506744 1.922817238 0.031043639 0.007178556 2.50E-13 12.6027834 0.061060726 ITPLSLQTQGSS(ph)HETLNIVEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ITPLSLQTQGSSHETLNIVEEK 22 0 O43491;Q6R5J7;E9PMV8 O43491 EPB41L2 Band 4.1-like protein 2 1 0 ITPLSLQTQGS(0.036)S(0.964)HETLNIVEEK 127.16 4.17E-05 27456000 1759.2 1607.4 1191 1052.9 3288 3469 2485.2 2309.9 2803.5 2235.6 TRUE FALSE FALSE 1737.758194 1630.029019 1211.728855 1174.641252 3120.201091 3247.342096 2696.292826 2376.733312 2552.747939 2177.51879 0.798045097 0.748571735 0.556472284 0.539440237 1.432915806 1.491303823 1.2382409 1.091486936 1.172319592 1 11.08846945 -8.747338406 24.99998218 0.837568918 1.320813448 0.597613725 0.204172406 134.5437895 238534.8588 0.029930603 0.05962781 1.79E-09 8.747338406 0.48324453 ITPLSLQTQGSSHET(ph)LNIVEEK ddPTM_HeLa_Romidepsin_16h_R1 1 ITPLSLQTQGSSHETLNIVEEK 22 0 O43491;Q6R5J7;E9PMV8 O43491 EPB41L2 Band 4.1-like protein 2 1 0 ITPLSLQTQGS(0.035)S(0.313)HET(0.652)LNIVEEK 117.23 6.15E-05 27132000 2382.9 1769 1543.2 2051.8 4665.6 4407.4 3215.7 3129.6 4009.6 2949.7 TRUE FALSE FALSE 2353.856298 1793.904028 1570.058749 2289.03877 4427.497022 4125.781364 3488.841478 3220.150038 3650.971334 2873.066369 0.819283649 0.624386561 0.546474932 0.796723248 1.541035414 1.436020208 1.214326796 1.120806005 1.270757743 1 11.4883756 -8.773531595 24.99990656 0.850431662 1.327636595 0.551363792 0.214310491 119.5554776 247173.5708 0.02954951 0.053854863 1.68E-09 8.773531595 0.477204933 ITPS(ph)YVAFTPEGER ddPTM_HeLa_Romidepsin_16h_R1 2 ITPSYVAFTPEGER 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 1 0 IT(0.007)PS(0.993)YVAFTPEGER;IT(0.171)PS(0.583)YVAFT(0.246)PEGER ; 186.69 2.58E-08 17179400 1491.51 1680.89 1807.8 1206.05 1482.72 1687.2 1429.52 1970.29 1600.25 1377.76 TRUE FALSE FALSE 1473.330902 1704.553614 1839.264001 1345.499176 1407.051266 1579.393365 1550.943393 2027.297233 1457.119632 1341.965597 1.097890219 1.270191738 1.37057463 1.002633137 1.048500252 1.176925377 1.155725152 1.510692404 1.085809976 1 10.39013197 -4 0.084639719 0.843479452 2.058565802 0.235864439 0.138357952 159.1216726 0.984177767 2.046990685 22.63112235 1.00E-04 4 1.21508635 ITPVTVK(ac)AQTK ddPTM_HeLa_Romidepsin_16h_R1 1 ITPVTVKAQTK 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2;S4R3C2;S4R349 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ITPVTVK(1)AQTK 141.71 0.0038345 703250 147.55 160.59 754.75 274.42 640.29 894.34 459.72 330.23 186.63 228.35 FALSE TRUE FALSE 145.7516038 162.8507902 767.8861071 306.1497316 607.613612 837.1945604 498.7686053 339.784684 169.9373454 222.4174341 0.655306561 0.732185365 3.452454662 1.376464632 2.731861441 3.764068963 2.242488802 1.527689075 0.764046875 1 7.797126067 -9.780399383 24.98350194 0.824801608 2.51818028 0.59356427 0.700218127 122.622304 161578.2302 0.11026446 0.145046911 1.66E-10 9.780399383 1.693378672 ITQDLMAKVRAMLAAS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 ITQDLMAKVRAMLAASK 17 2 Q12872;Q12872-2 Q12872 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 0 IT(0.001)QDLMAKVRAMLAAS(0.999)K 50.102 0.0042423 0 1039.8 847.69 1161.5 713.99 1025 1390.7 1191.3 1142.6 1051.8 1317.2 TRUE FALSE FALSE 1027.126518 859.6238021 1181.71542 796.5448832 972.6904252 1301.838758 1292.488992 1175.659328 957.7243737 1282.978954 0.800579397 0.670021748 0.921071555 0.620855767 0.758149946 1.014700011 1.007412466 0.916351219 0.746484867 1 10.32528179 -6.326773055 19.69974296 0.87700441 1.046650303 0 0.141435782 0 0 0.019711733 0 4.71E-07 6.326773055 0.169645894 ITS(ph)PLMEPSSIEK ddPTM_HeLa_Romidepsin_16h_R1 1 ITSPLMEPSSIEK 13 0 P28066 P28066 PSMA5 Proteasome subunit alpha type-5 1 0 IT(0.081)S(0.919)PLMEPSSIEK 141.58 0.0013218 63956000 7686.7 7482.8 6472.1 6987.2 10911 11241 10398 12316 7656.5 7024.6 TRUE FALSE FALSE 7593.011544 7588.143055 6584.744186 7795.09294 10354.17096 10522.73638 11281.20586 12672.34403 6971.683464 6842.099879 1.109748714 1.109037165 0.962386446 1.139283711 1.5133031 1.537939604 1.648792923 1.852113277 1.018939154 1 12.74022345 -8.515553143 1.221331147 1.047163936 1.748080244 0.929913638 0.079812907 0.091664588 0.259707222 0.013241051 0.045139829 3.05E-09 8.515553143 0.700916308 ITSIS(ph)PTPEPPAALEDNPDAWGDGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 ITSISPTPEPPAALEDNPDAWGDGSPR 27 0 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 IT(0.063)S(0.202)IS(0.673)PT(0.063)PEPPAALEDNPDAWGDGSPR 70.264 8.60E-05 7065500 2454.3 2543.3 2042.4 1959.5 1455.4 1352.6 978.65 1301.4 2374.1 2487.5 TRUE FALSE FALSE 2424.386048 2579.104644 2077.947115 2186.06661 1381.125507 1266.173225 1061.776507 1339.053956 2161.75455 2422.874391 1.00062391 1.064481367 0.857637161 0.902261635 0.570035951 0.522591361 0.438230108 0.552671637 0.892227248 1 11.2425039 -8.814208245 1.542819949 1.00065343 0.485226218 0.911211414 0.065986562 0.054624858 0.262209658 0.007940905 0.0186491 1.53E-09 8.814208245 -0.515427212 ITSISPT(ph)PEPPAALEDNPDAWGDGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 ITSISPTPEPPAALEDNPDAWGDGSPR 27 0 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17;G3V5H0 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 IT(0.014)S(0.072)IS(0.425)PT(0.488)PEPPAALEDNPDAWGDGSPR 106.69 1.38E-08 6887100 1843.5 1783.2 1626 1638.9 1040.8 912.49 765.21 634.95 1797.2 1649.4 TRUE FALSE FALSE 1821.030713 1808.303936 1654.299848 1828.397329 987.6840922 854.1848339 830.2069183 653.3212765 1636.453931 1606.54835 1.133505078 1.125583264 1.029723038 1.138090447 0.61478641 0.531689466 0.516764353 0.406661447 1.018614803 1 10.64974869 -8.67233158 4.231222464 1.071833279 0.500465172 0.956327335 0.058617584 0.036034421 1.19146692 0.010103513 0.020645723 2.13E-09 8.67233158 -0.571368107 ITSLSS(ph)SLDTSLDFSK ddPTM_HeLa_Romidepsin_16h_R1 1 ITSLSSSLDTSLDFSK 16 0 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 0 ITS(0.002)LS(0.011)S(0.981)S(0.005)LDTSLDFSK 106.6 0.0039313 6820300 2504 2400.6 2588.1 1740.8 2451 1994.2 1748.4 2383.8 2570.3 2254.5 TRUE FALSE FALSE 2473.480285 2434.39571 2633.144795 1942.079487 2325.916324 1866.777056 1896.909052 2452.771492 2340.405931 2195.927765 1.126394194 1.108595532 1.199103557 0.884400442 1.05919528 0.85010859 0.863830351 1.11696365 1.065793679 1 11.10061488 -9.243790434 24.91486166 1.075154284 0.949812734 0.363918227 0.092929918 799.589426 1128774.265 0.014550182 0.024093396 5.70E-10 9.243790434 -0.12534155 ITSLSSS(ph)LDTSLDFSK ddPTM_HeLa_Romidepsin_16h_R1 1 ITSLSSSLDTSLDFSK 16 0 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 0 ITSLSS(0.083)S(0.916)LDTSLDFSK 202.32 1.80E-18 9173000 848.57 899.36 1155.5 748.69 773.32 809.71 781.85 758.27 715.36 1030.6 TRUE FALSE FALSE 838.2273024 912.0212137 1175.610993 835.2570605 733.8545947 757.9721442 848.2603195 780.2093461 651.3764099 1003.824863 0.835033414 0.908546149 1.171131574 0.832074489 0.731058396 0.755084051 0.845028202 0.777236523 0.648894477 1 9.97129187 -9.012794702 24.67933786 0.9387258 0.78052914 0.190502607 0.126766662 428.9834464 827455.9084 0.01486853 0.025481563 9.71E-10 9.012794702 -0.15819666 ITVNGDSS(ph)AEAEELANEI ddPTM_HeLa_Romidepsin_16h_R1 2 ITVNGDSSAEAEELANEI 18 0 A0A0B4J1W3;Q9BXJ9 A0A0B4J1W3 NAA15 "N-alpha-acetyltransferase 15, NatA auxiliary subunit" 1 0 ITVNGDS(0.057)S(0.943)AEAEELANEI;ITVNGDS(0.008)S(0.992)AEAEELANEI ; 145.99 8.23E-05 66654000 2790.5 2756.1 2859.4 2224.47 2627.83 2446.9 2288.12 2348.92 3096.1 2568.6 TRUE FALSE FALSE 2756.488313 2794.900448 2909.166658 2481.673688 2493.722029 2290.550987 2482.472856 2416.882294 2819.177062 2501.867402 1.101772344 1.11712573 1.162798099 0.991928544 0.996744283 0.915536525 0.992247972 0.96603133 1.126829128 1 11.28878961 -9.0215211 23.33683585 1.063989703 0.969258565 0.572138446 0.051223032 265.0963399 287462.8693 0.008943178 0.014941152 9.52E-10 9.0215211 -0.094731139 ITVQAS(ph)PNLDK ddPTM_HeLa_Romidepsin_16h_R1 1 ITVQASPNLDK 11 0 Q5TCX8;Q5TCX8-2 Q5TCX8 MLK4 Mitogen-activated protein kinase kinase kinase MLK4 1 0 IT(0.287)VQAS(0.713)PNLDK 139.77 0.0032033 11385000 3345.7 3418.5 3665.7 3659.2 3472.7 3217.3 2762.3 2991.8 3867.6 3440.7 TRUE FALSE FALSE 3304.921322 3466.625733 3729.499971 4082.293921 3295.475161 3011.724913 2996.929693 3078.363013 3521.672169 3351.310118 0.986158011 1.034409115 1.112848361 1.218118818 0.983339364 0.89867091 0.894256153 0.918555104 1.050834463 1 11.71050948 -8.368564882 4.724070477 1.023302669 0.903416048 0.458688223 0.070449029 0.210115857 7.437075148 0.011588894 0.026666426 4.28E-09 8.368564882 -0.119886621 ITVTSEVPFS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 2 ITVTSEVPFSKR 12 1 K7ERI7;P35268;K7EP65;K7EKS7;K7ELC4;K7EMH1 K7ERI7 RPL22 60S ribosomal protein L22 1 0 ITVTSEVPFS(1)KR;ITVTSEVPFS(1)KR ; 72.898 0.01924 17744100 3163.8 3240 3071.4 2957.3 3528.7 3032.1 3272.1 3097.8 3204 3381.7 TRUE FALSE FALSE 3125.238389 3285.612805 3124.856429 3299.236941 3348.617272 2838.358596 3550.032092 3187.429955 2917.426215 3293.842946 0.948812205 0.997501356 0.948696243 1.001637599 1.016629307 0.861716433 1.077778191 0.967693362 0.885721105 1 11.68555605 ITVTSEVPFSK ddPTM_HeLa_Romidepsin_16h_R1 2 ITVTSEVPFSK 11 0 K7ERI7;P35268;K7EP65;K7EKS7;K7ELC4;K7EMH1;K7EJT5 K7ERI7 RPL22 60S ribosomal protein L22 0 0 ; ; 233.09 1.35E-38 3375600 2593 2041.78 2273.9 1684.07 2481.5 2770.4 1977.66 1902.26 2518.4 2335.5 FALSE FALSE TRUE 2561.395519 2070.524232 2313.476276 1878.790097 2354.859795 2593.380381 2145.642391 1957.298892 2293.147997 2274.823373 1.125975559 0.910191207 1.016991606 0.825905923 1.035183576 1.14003593 0.943212742 0.860417962 1.008055405 1 11.15153882 -10.2579843 24.96134465 1.059488458 0.967582563 0.140695328 0.090994653 399.6529771 2887302.125 0.016143378 0.019353453 5.52E-11 10.2579843 -0.091905895 IVAAK(ac)YEVIHSK ddPTM_HeLa_Romidepsin_16h_R1 2 IVAAKYEVIHSK 12 1 E7EVH3;Q92576-2;Q92576;D6R9X2;E9PE34;A0A1B0GX99 E7EVH3 PHF3 PHD finger protein 3 0 1 ; IVAAK(1)YEVIHSK;IVAAK(1)YEVIHSK 109.15 0.0073544 1176080 476.66 405.3 313.09 66.009 346.3 317.097 362.69 198.07 438.59 201.8 FALSE TRUE FALSE 470.8502846 411.005824 318.5392001 73.64127116 328.6270188 296.8355251 393.4968795 203.8008429 399.3614119 196.5572069 2.395487258 2.091023934 1.62059283 0.374655665 1.671915388 1.510173703 2.001945824 1.036852559 2.031782086 1 7.618805452 -9.504707063 24.87405758 1.71674907 1.348295693 0.173228511 0.530745386 1680.499215 2300330.776 0.102642781 0.154936753 3.13E-10 9.504707063 -0.368453377 IVADK(ac)DYSVTANSK ddPTM_HeLa_Romidepsin_16h_R1 2 IVADKDYSVTANSK 14 1 A0A5F9ZHM4;P07195;F5H793;C9J7H8;A8MW50;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 1 ; IVADK(1)DYSVTANSK;IVADK(1)DYSVTANSK 212.1 1.35E-23 5634400 1741.25 1820.01 1747.72 1732.52 4094.5 3283.8 3382.2 3403.2 4109.5 3091.4 FALSE TRUE FALSE 1720.026975 1845.632149 1778.138333 1932.842114 3885.542386 3073.975778 3669.483984 3501.666223 3741.936028 3011.084982 0.571231628 0.612945885 0.59053077 0.641908855 1.290412728 1.020886423 1.218658392 1.162925073 1.242720165 1 11.55606771 -8.762802774 24.99998062 0.750454209 1.165585215 0.463365143 0.207925334 22.46165999 411882.0989 0.02871657 0.054185079 1.73E-09 8.762802774 0.415131006 IVADKDYSVTANSK ddPTM_HeLa_Romidepsin_16h_R1 3 IVADKDYSVTANSK 14 1 A0A5F9ZHM4;P07195;F5H793;C9J7H8;A8MW50;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 0 ;; ;; 161.49 9.23E-07 22893300 6527.1 5801.4 5814.9 6356.4 6842.1 6514.1 5442.1 5468.7 5829.1 5988.7 FALSE FALSE TRUE 6447.545195 5883.072261 5916.105895 7091.356876 6492.922106 6097.870033 5904.351838 5626.928206 5307.730697 5833.112711 1.105335267 1.008564818 1.014227941 1.215707158 1.11311446 1.045388686 1.012212884 0.964652748 0.909931105 1 12.51005024 -7.558465366 2.377356697 1.061608967 0.96591186 0.101020492 0.077680983 0.488033205 4.777082413 0.009805057 0.073422259 2.76E-08 7.558465366 -0.095697106 IVAHAVEVPAVQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 IVAHAVEVPAVQSPR 15 0 Q96FF9;B5MBX0;H0YCL8 Q96FF9 CDCA5 Sororin 1 0 IVAHAVEVPAVQS(1)PR;IVAHAVEVPAVQS(1)PR ; 132.87 0.00066675 100895000 5847.8 4876 5418.5 4702.9 5720.5 6111.6 5456.6 5462.5 5681.2 5618.8 TRUE FALSE FALSE 5776.524764 4944.644456 5512.80672 5246.671426 5428.561539 5721.088484 5920.083468 5620.548819 5173.059243 5472.822766 1.055492752 0.903490697 1.007305911 0.958677386 0.991912541 1.045363376 1.081723951 1.026992662 0.94522689 1 12.41806942 -8.119670546 5.41425389 1.008777833 1.056382184 0.185891754 0.046586788 0.316139515 12.71031404 0.006661922 0.017501782 7.59E-09 8.119670546 0.047604351 IVDILYATDEGFVIPDEGGPQEEQEEY ddPTM_HeLa_Romidepsin_16h_R1 1 IVDILYATDEGFVIPDEGGPQEEQEEY 27 0 Q15691 Q15691 MAPRE1 Microtubule-associated protein RP/EB family member 1 0 0 62.005 0.00096778 4513000 189.3 282.29 247.03 161.51 273.55 215.11 99.642 138.13 292.66 293.26 FALSE FALSE TRUE 186.9927388 286.264086 251.3294535 180.1845461 259.5897227 201.3651652 108.105589 142.1265736 266.4837566 285.6410629 0.654642357 1.00218114 0.879878582 0.630807575 0.908796936 0.704958745 0.378466555 0.497570525 0.93293224 1 8.158059582 -7.915251762 3.958022235 0.837181847 0.440080269 0.638790039 0.124325272 0.126046508 3.766991666 0.021049398 0.069233881 1.22E-08 7.915251762 -0.397101578 IVEGQGQSSEVIT(ph)PPEEISR ddPTM_HeLa_Romidepsin_16h_R1 2 IVEGQGQSSEVITPPEEISR 20 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 0 IVEGQGQS(0.069)S(0.037)EVIT(0.894)PPEEISR;IVEGQGQSSEVIT(0.996)PPEEIS(0.004)R ; 145.19 7.56E-05 7411700 1391.59 1557.89 1581.07 1242.18 1486.69 1797.08 1400.72 1299.42 1713.25 1283.59 TRUE FALSE FALSE 1374.628766 1579.822016 1608.58786 1385.806696 1410.818662 1682.252388 1519.697122 1337.016668 1560.012629 1250.242147 1.099490022 1.263612829 1.286621047 1.108430635 1.128436332 1.345541255 1.21552223 1.069406171 1.247768389 1 10.28799183 -10.70490583 1.586613823 1.03087701 1.204106637 0 0.107478029 0.227051207 1.186256475 0.017836096 0.017635154 1.97E-11 10.70490583 0.173229627 IVEMSTSK(ac)TGK ddPTM_HeLa_Romidepsin_16h_R1 2 IVEMSTSKTGK 11 1 I3L397;I3L504;P63241;P63241-2;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4 I3L397 EIF5A;EIF5A2 Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-2 0 1 ; IVEMSTSK(1)TGK;IVEMSTSK(1)TGK 155.26 0.00092109 81339000 8436.4 7059.2 6988 5611.7 4732.2 5279 5192.3 5060.3 7626 5909.8 FALSE TRUE FALSE 8333.573912 7158.579603 7109.623209 6260.551158 4490.698176 4941.688937 5633.333832 5206.711797 6943.91146 5756.262544 1.447740413 1.243615896 1.235111004 1.087606952 0.780141305 0.85848915 0.978644353 0.904529937 1.206322923 1 12.49091668 -8.970681505 4.229185146 1.219950301 0.886881998 0.682498458 0.111018273 0.147282255 6.03130434 0.025910059 0.047192101 1.07E-09 8.970681505 -0.333068302 IVENEK(ac)INAEK ddPTM_HeLa_Romidepsin_16h_R1 1 IVENEKINAEK 11 1 Q9C005 Q9C005 DPY30 Protein dpy-30 homolog 0 1 IVENEK(1)INAEK 233.13 7.07E-39 2134600 1046.3 912.75 713.63 596.29 529.29 602.75 590.73 699.28 934.8 674.96 FALSE TRUE FALSE 1033.547293 925.5997185 726.0504308 665.2358554 502.2783562 564.2362203 640.9065915 719.5125635 851.1891468 657.4244419 1.57211571 1.40791802 1.104386123 1.011881842 0.764009252 0.858252575 0.974874907 1.094441456 1.294733041 1 9.360681284 -9.412866465 2.753049822 1.287094778 0.925186427 0.552692904 0.158233775 0.243064334 3.577907701 0.037289647 0.059019467 3.86E-10 9.412866465 -0.361908351 IVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_HeLa_Romidepsin_16h_R1 1 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 0 IVEPEVVGES(1)DS(1)EVEGDAWR 59.55 0.0032571 0 6897.2 6684.7 5658.8 5393.2 6539.4 7021 5759.4 6163.7 7433.7 6394.5 TRUE FALSE FALSE 6813.134273 6778.807382 5757.28904 6016.78716 6205.670016 6572.380759 6248.603292 6342.036935 6768.811254 6228.369968 1.093887214 1.088375838 0.924365295 0.966029184 0.996355394 1.055232877 1.003248575 1.018249874 1.086770903 1 12.60463893 -9.785891036 24.99995465 1.048877426 0.995968563 0.397309201 0.041828463 273.3636002 279492.3516 0.008103768 0.010653241 1.64E-10 9.785891036 -0.052908863 IVEPEVVGES(ph)DSEVEGDAWR ddPTM_HeLa_Romidepsin_16h_R1 1 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 0 IVEPEVVGES(0.875)DS(0.125)EVEGDAWR 308.73 1.74E-169 75661000 2736.1 3043.2 2265.6 2685.9 3416.5 3505.2 3860.9 4070.1 3059 2758.4 TRUE FALSE FALSE 2702.751361 3086.042249 2305.031818 2996.456396 3242.143256 3281.229033 4188.84475 4187.861922 2785.395379 2686.73637 1.00596076 1.148621161 0.857930031 1.115277416 1.206721766 1.221269444 1.559082907 1.558717099 1.036720763 1 11.39163905 -7.930708967 0.92441146 1.005642517 1.675648985 0.854640092 0.083605269 0.217818327 0.249802307 0.012156827 0.11571508 1.17E-08 7.930708967 0.670006469 IVEPEVVGESDS(ph)EVEGDAWR ddPTM_HeLa_Romidepsin_16h_R1 2 IVEPEVVGESDSEVEGDAWR 20 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 0 IVEPEVVGES(0.377)DS(0.623)EVEGDAWR;IVEPEVVGES(0.094)DS(0.906)EVEGDAWR ; 241.98 1.54E-54 80980900 6473.3 5561.6 5852.4 5318.8 6283.9 6766.5 7416 7796.3 6077.9 6092.1 TRUE FALSE FALSE 6394.40093 5639.896351 5954.258567 5933.784682 5963.209135 6334.142488 8045.914855 8021.87364 5534.277402 5933.826364 1.077618477 0.95046535 1.003443344 0.999992976 1.004951741 1.067463404 1.355940394 1.35188884 0.932665882 1 12.534747 -7.792584093 4.459007511 1.024146112 1.359692722 0.910658019 0.043592633 0.035981736 1.613074006 0.00571439 0.01988234 1.61E-08 7.792584093 0.33554661 IVEYS(ph)PPSAPR ddPTM_HeLa_Romidepsin_16h_R1 1 IVEYSPPSAPR 11 0 O95696-2;O95696 O95696-2 BRD1 Bromodomain-containing protein 1 1 0 IVEYS(0.956)PPS(0.043)APR 96.604 0.023791 32185000 2358.5 2227.3 2136.8 1833.4 2014.2 1672.8 1888.9 1315.9 2085.7 2272.8 TRUE FALSE FALSE 2329.753695 2258.655988 2173.990108 2045.386334 1911.407858 1565.913479 2049.343119 1353.97349 1899.149768 2213.752328 1.052400336 1.020283958 0.982038541 0.923945424 0.863424437 0.707357123 0.92573279 0.611619228 0.857887192 1 11.11227811 -8.760512215 1.040239861 1.026072172 0.746933335 0.535304438 0.0911371 0.200991329 0.419763227 0.011223168 0.034230386 1.74E-09 8.760512215 -0.279138837 IVFSGNLFQHQEDSKK ddPTM_HeLa_Romidepsin_16h_R1 1 IVFSGNLFQHQEDSKK 16 1 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 0 0 47.506 0.026002 342280 141.89 208.82 54.789 0 206.76 117.22 269.8 128.48 160.81 109.24 FALSE FALSE TRUE 140.1605901 211.7597734 55.74257956 0 196.2082657 109.7300203 292.7168053 132.1973661 146.4267508 106.4019291 1.317274897 1.990187352 0.523886926 0 1.844029215 1.031278486 2.751047917 1.242433923 1.376166317 1 6.733380497 -7.795776105 24.99667425 1.129235487 1.996742494 0.222210094 0.644544685 164.3616203 119652.7828 0.084631246 0.25391131 1.60E-08 7.795776105 0.867507007 IVGELEQMVSEDVPLDHR ddPTM_HeLa_Romidepsin_16h_R1 1 IVGELEQMVSEDVPLDHR 18 0 A0A024R4E5;Q00341-2;Q00341 A0A024R4E5 HDLBP Vigilin 0 0 107.51 0.0061107 794810 515.16 504.65 347.99 555.19 598.79 446.24 335.04 628.66 610.43 524.32 FALSE FALSE TRUE 508.8810318 511.7544759 354.04662 619.38368 568.2315119 417.7267042 363.4982892 646.8492852 555.831612 510.6980908 0.996442009 1.002068512 0.69326012 1.212817692 1.112656425 0.817952351 0.711767472 1.266598205 1.088376131 1 8.996326855 IVIGYQSHADTATK ddPTM_HeLa_Romidepsin_16h_R1 1 IVIGYQSHADTATK 14 0 D6RBW1;P06730;P06730-3;P06730-2 D6RBW1 EIF4E Eukaryotic translation initiation factor 4E 0 0 94.781 0.0052155 1837200 1950.4 1623.1 2043.8 1320.5 1707.7 1980 1766.5 1768.4 1945.4 1706.4 FALSE FALSE TRUE 1926.627775 1645.950044 2079.371482 1473.182423 1620.549697 1853.48439 1916.546466 1819.565864 1771.398552 1662.067482 1.159175422 0.990302778 1.251075245 0.886355361 0.975020397 1.115167952 1.153109899 1.094760522 1.065780163 1 10.69876324 -8.02752459 24.16695754 1.062802604 1.126486192 0.094049079 0.09721021 990.770876 869911.7195 0.014431961 0.036920554 9.39E-09 8.02752459 0.063683589 IVITGDGDIDHDQALAQAIR ddPTM_HeLa_Romidepsin_16h_R1 2 IVITGDGDIDHDQALAQAIR 20 0 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;Q6R5J7;E9PPC9;Q6ZSX4 O43491 EPB41L2 Band 4.1-like protein 2 0 0 ; ; 218.66 5.08E-33 7987400 3040.2 3210.6 3489.9 3549.7 3957.2 4043.6 3379.5 3652.1 3904.8 3439.3 FALSE FALSE TRUE 3003.144873 3255.798911 3550.640246 3960.133016 3755.249318 3785.22701 3666.554646 3757.767751 3555.544908 3349.94649 0.896475476 0.971895796 1.059909541 1.182148141 1.120987851 1.129936559 1.094511407 1.121739634 1.061373642 1 11.70992234 -9.64862891 3.037263081 0.950621535 1.127247544 0.663925545 0.047269777 0.084111952 1.561213311 0.007026973 0.010173914 2.25E-10 9.64862891 0.176626009 IVKPNGEKPDEFESGISQALLELEMNSDLK ddPTM_HeLa_Romidepsin_16h_R1 2 IVKPNGEKPDEFESGISQALLELEMNSDLK 30 2 A0A2R8Y623;P62081;B5MCP9 A0A2R8Y623 RPS7 40S ribosomal protein S7 0 0 ; ; 58.294 0.00036126 9558400 2995.02 2945.63 2844.82 2525.76 2712.55 2955.8 2302.78 2900.27 2609.57 2848.86 FALSE FALSE TRUE 2958.515544 2987.098656 2894.332899 2817.800255 2574.118452 2766.933919 2498.378076 2984.184737 2376.163523 2774.846207 1.066190817 1.076491609 1.043060654 1.015479794 0.927661665 0.997148567 0.900366323 1.075441489 0.856322602 1 11.4381921 -8.965539748 9.177346918 1.036641954 0.97130255 0 0.074033746 0.302180915 75.2241514 0.006976616 0.01263455 1.08E-09 8.965539748 -0.065339404 IVLQK(ac)YHTINGHNAEVR ddPTM_HeLa_Romidepsin_16h_R1 1 IVLQKYHTINGHNAEVR 17 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 1 IVLQK(1)YHTINGHNAEVR 44.045 0.029915 475140 0 150.98 121.87 0 61.811 164.97 128.55 231.88 200.59 148.65 FALSE TRUE FALSE 0 153.1055004 123.9910962 0 58.65655402 154.4289494 139.4690338 238.589082 182.648728 144.7880516 0 1.057445685 0.856362765 0 0.405120128 1.066586281 0.96326342 1.64785063 1.261490337 1 7.177798741 -7.423620127 1.215291678 0.542936357 1.89750628 0.27891585 0.430341568 0.987506068 1.478186968 0.06797638 1.552021221 3.77E-08 7.423620127 1.354569923 IVNHWAS(ph)PELR ddPTM_HeLa_Romidepsin_16h_R1 1 IVNHWASPELR 11 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 IVNHWAS(1)PELR 127.3 0.0028475 48648000 5356.4 4615.4 4962.1 4703.9 7001.2 9602.8 7661.7 7457.7 4949.7 4426.6 TRUE FALSE FALSE 5291.114137 4680.375722 5048.463269 5247.787051 6643.902639 8989.212072 8312.484607 7673.476783 4506.986435 4311.596294 1.227182179 1.085531994 1.170903518 1.217133213 1.540938016 2.084891873 1.927936671 1.779729887 1.045317355 1 12.07400639 -8.598157803 2.389355031 1.115478081 1.930435046 0.932482997 0.097628785 0.057988973 0.666638049 0.016883637 0.039046837 2.52E-09 8.598157803 0.814956964 LLQDSSS(ph)PVDLAK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQDSSSPVDLAK 13 0 E7EWM1;Q15596 E7EWM1 NCOA2 Nuclear receptor coactivator 2 1 0 LLQDS(0.003)S(0.424)S(0.573)PVDLAK 183.06 3.60E-07 25882000 2086.9 2449.9 1784.9 1594.2 1354.6 968.82 804.76 942.68 2310.9 2382.9 TRUE FALSE FALSE 2061.46406 2484.389757 1815.965436 1778.528905 1285.469707 906.9155287 873.1162943 969.9549585 2104.207316 2320.991914 0.888182353 1.070400005 0.782409204 0.766279664 0.553844974 0.390744803 0.376182394 0.417905359 0.906598297 1 11.18052578 -8.836689497 1.172867117 0.954070752 0.374288173 0.93320353 0.064123979 0.081055988 0.220295937 0.010816704 0.028652189 1.46E-09 8.836689497 -0.579782579 down IVQK(ac)HPHTGDTK ddPTM_HeLa_Romidepsin_16h_R1 2 IVQKHPHTGDTK 12 1 P51397;B4DQ75 P51397 DAP Death-associated protein 1 0 1 ; IVQK(1)HPHTGDTK;IVQK(1)HPHTGDTK 92.247 0.0057235 5224400 4581.2 4630 5161.8 2993.5 4061.2 4440.1 4446.7 1914.55 5318.7 4371.9 FALSE TRUE FALSE 4525.362572 4695.181262 5251.638964 3339.622555 3853.94181 4156.39194 4824.402587 1969.944484 4842.982151 4258.317408 1.062711428 1.102590721 1.233266208 0.784258719 0.905038643 0.97606438 1.132936351 0.462611002 1.137299475 1 12.05606777 -9.241668656 24.9497125 1.050885628 0.877598154 0.321570837 0.173984321 977.8833392 1234043.242 0.024358345 0.040353696 5.73E-10 9.241668656 -0.173287474 IVRGDQPAASGDS(ph)DDDEPPPLPR ddPTM_HeLa_Romidepsin_16h_R1 2 IVRGDQPAASGDSDDDEPPPLPR 23 1 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 IVRGDQPAAS(0.003)GDS(0.997)DDDEPPPLPR;IVRGDQPAAS(0.002)GDS(0.998)DDDEPPPLPR ; 130.51 2.67E-06 40350000 1862.68 2424.3 1442.4 2022.1 1865.45 2244.22 1516.85 2366.2 2524.8 2086.5 TRUE FALSE FALSE 1839.97694 2458.429359 1467.504367 2255.904716 1770.249126 2100.821585 1645.691201 2434.662264 2298.975565 2032.292429 0.905370169 1.20968288 0.722093113 1.110029582 0.871060237 1.033720125 0.809770866 1.197988158 1.131222816 1 10.98889229 -7.234590375 23.52183969 0.958538661 1.197988888 0.161858762 0.145510054 4197.6234 3677322.249 0.016005392 1.611822732 5.83E-08 7.234590375 0.239450227 IVSAQS(ph)LAEDDVE ddPTM_HeLa_Romidepsin_16h_R1 1 IVSAQSLAEDDVE 13 0 Q15388 Q15388 TOMM20 Mitochondrial import receptor subunit TOM20 homolog 1 0 IVS(0.011)AQS(0.989)LAEDDVE 103.21 0.0027603 0 1523.5 1720.8 1583.2 1333.9 1038.7 1148.5 728.95 961.85 1769.7 1615.7 TRUE FALSE FALSE 1504.930996 1745.025468 1610.754932 1488.131794 985.6912631 1075.114557 790.8669948 989.6796122 1611.4136 1573.723881 0.95628656 1.108851107 1.023530844 0.945611751 0.626343207 0.683165941 0.502544954 0.628877546 1.023949385 1 10.61996672 -8.77744848 3.817821958 0.993522023 0.601958944 0.918845292 0.058228518 0.0455614 1.439604107 0.008802749 0.017297464 1.67E-09 8.77744848 -0.391563078 IVSAQSLAEDDVE ddPTM_HeLa_Romidepsin_16h_R1 4 IVSAQSLAEDDVE 13 0 Q15388 Q15388 TOMM20 Mitochondrial import receptor subunit TOM20 homolog 0 0 ;;; ;;; 161.17 0.0040102 32064800 13354.6 17265.9 14724.2 11997.2 13585.6 16510.9 11734.5 14948.8 15223 15434.2 FALSE FALSE TRUE 13191.829 17508.96979 14980.46852 13384.37271 12892.27614 15455.90678 12731.22814 15381.31994 13861.41675 15033.21726 0.87751203 1.164685476 0.996491188 0.890319915 0.857585965 1.028117036 0.846873155 1.023155568 0.92205258 1 13.87586617 -9.265101633 24.51077435 0.964623453 0.926151728 0.067545283 0.091525674 785.0505124 5254208.257 0.014739724 0.023087985 5.43E-10 9.265101633 -0.038471725 IVSGSPIS(ph)T(ph)PSPSPLPR ddPTM_HeLa_Romidepsin_16h_R1 1 IVSGSPISTPSPSPLPR 17 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 2 0 IVS(0.01)GS(0.307)PIS(0.685)T(0.708)PS(0.025)PS(0.266)PLPR 100.11 0.013379 4313800 1576.6 1495.5 1726.5 1674.2 1112.9 930.07 784.43 904.54 1656.8 1875.9 TRUE FALSE FALSE 1557.383793 1516.553688 1756.549008 1867.778881 1056.10456 870.6415287 851.0594646 930.7114378 1508.611658 1827.163848 0.852350376 0.830004211 0.96135276 1.022228457 0.578002111 0.476498881 0.46578169 0.50937492 0.825657568 1 10.8353903 -8.659414623 4.888623187 0.928328256 0.489621043 0.901294819 0.066416381 0.048451894 1.910723058 0.010813939 0.02195439 2.19E-09 8.659414623 -0.438707213 IVTYLGLYNNQITDVGAR ddPTM_HeLa_Romidepsin_16h_R1 1 IVTYLGLYNNQITDVGAR 18 0 Q9Y239 Q9Y239 NOD1 Nucleotide-binding oligomerization domain-containing protein 1 0 0 56.514 0.028754 13260000 836.97 813.19 837.69 959.38 807.61 934.6 994.27 1074.6 1002.5 911.08 FALSE FALSE TRUE 826.7686877 824.6381102 852.2696431 1070.30803 766.3946481 874.8820763 1078.723269 1105.691856 912.8338892 887.4100103 0.93166482 0.929263926 0.960401205 1.206103174 0.863630835 0.985882587 1.215586095 1.245976316 1.028649529 1 9.793457017 -7.753127163 5.189962406 0.973921062 1.236653675 0.557455493 0.085926192 0.081915294 6.297194803 0.011377654 0.040963905 1.77E-08 7.753127163 0.262732613 IVVAGNNEDVSFSRPADLDLIQSTPFKPLALKT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 IVVAGNNEDVSFSRPADLDLIQSTPFKPLALKTPPR 36 3 A0A0A0MS29;Q9GZY8-2;C9JHF5;Q9GZY8-4;Q9GZY8-5;Q9GZY8-3;Q9GZY8 A0A0A0MS29 MFF Mitochondrial fission factor 1 0 IVVAGNNEDVSFSRPADLDLIQS(0.04)T(0.04)PFKPLALKT(0.92)PPR 52.237 0.0014554 5342700 818.14 793.33 997.44 775 804.17 889.07 556.94 730.62 739.84 551.82 TRUE FALSE FALSE 808.168195 804.4985206 1014.800025 864.6091465 763.1302041 832.2612963 604.2464697 751.759337 673.6668574 537.4836369 1.50361451 1.496787 1.888057524 1.608624128 1.419820348 1.548440249 1.124213703 1.398664602 1.253371845 1 9.070077024 -12.04611892 0.837465665 1.00050487 1.50020333 0.343250418 0.194492519 0.418905242 0.535540032 0.127561023 0.038810314 8.99E-13 12.04611892 0.49969846 IVYLYTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 IVYLYTKK 8 1 P49207 P49207 RPL34 60S ribosomal protein L34 0 1 ; IVYLYTK(1)K;IVYLYTK(1)K 140.09 0.0034912 207590 0 0 613.19 279.44 575.57 587.4 335.39 0 0 0 FALSE TRUE FALSE 0 0 623.8623147 311.7501676 546.1965152 549.8670357 363.8780182 0 0 0 0 IWLS(ph)TETLANED ddPTM_HeLa_Romidepsin_16h_R1 1 IWLSTETLANED 12 0 Q9NXD2 Q9NXD2 MTMR10 Myotubularin-related protein 10 1 0 IWLS(0.892)T(0.106)ET(0.001)LANED 105.46 0.012916 6615800 1291.3 1114.9 1216 886.55 1104.5 1119.8 1071.8 1053.7 1221.1 1091.8 TRUE FALSE FALSE 1275.561139 1130.595591 1237.16397 989.0570823 1048.133244 1048.248394 1162.838665 1084.187147 1111.881758 1063.434879 1.199472732 1.063154514 1.16336599 0.930058908 0.985611122 0.985719403 1.093474258 1.019514376 1.045556978 1 10.05451597 -9.265612248 24.99797876 1.09848239 1.005996611 0.32777982 0.065257348 425.7358883 2550409.24 0.013008877 0.020325452 5.42E-10 9.265612248 -0.092485779 IY(ph)LS(ph)MVY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 IYLSMVYK 8 0 Q8NFI3 Q8NFI3 ENGASE Cytosolic endo-beta-N-acetylglucosaminidase 3 0 IY(1)LS(1)MVY(1)K 48.756 0.0040866 0 985.62 951.58 1025.4 785.17 1016.9 1067 999.98 1207.3 966.55 1065.7 TRUE FALSE FALSE 973.6068843 964.9763682 1043.246657 875.9550497 965.0037984 998.8221436 1084.918276 1242.231321 880.0993472 1038.01296 0.937952532 0.929638073 1.005042034 0.843876795 0.929664499 0.962244386 1.045187601 1.196739702 0.847869324 1 10.01960874 -7.352017614 2.086922797 0.956984275 1.237643801 0.673028933 0.055544845 0.234217151 1.288862368 0.006793794 0.114530074 4.45E-08 7.352017614 0.280659525 IY(ph)NEFIS(ph)VQAT(ph)KEVNLDSCT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 IYNEFISVQATKEVNLDSCTR 21 1 E9PS05;P49798-5;P49798-2;P49798;P49798-3 E9PS05 RGS4 Regulator of G-protein signaling 4 4 0 IY(1)NEFIS(1)VQAT(0.999)KEVNLDS(0.188)CT(0.814)R 40.668 0.028223 5244800 0 0 0 0 0 0 126.82 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 137.5920876 0 0 0 0 IY(ph)SGT(ph)IK ddPTM_HeLa_Romidepsin_16h_R1 1 IYSGTIK 7 0 Q969S9-5;Q969S9-4;Q969S9-3;Q969S9 Q969S9-5 GFM2 "Ribosome-releasing factor 2, mitochondrial" 2 0 IY(0.996)S(0.005)GT(0.999)IK 73.975 0.0037117 0 9602.6 9898.5 5768 1938.9 6483.7 7038.7 6955.4 7369.7 12590 13646 TRUE FALSE FALSE 9485.559818 10037.85134 5868.38962 2163.084741 6152.812595 6588.949786 7546.191502 7582.930642 11463.91887 13291.47495 0.713657427 0.75520974 0.441515305 0.162742265 0.462914208 0.49572751 0.567746735 0.570510848 0.862501634 1 13.69821359 -10.65697165 0.70748755 0.947547257 0.452709147 0.651170682 0.133862735 0.26475661 0.29110862 0.046045854 0.041673559 2.20E-11 10.65697165 -0.49483811 IYASEEDD ddPTM_HeLa_Romidepsin_16h_R1 1 IYASEEDD 8 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 0 0 132.72 3.17E-05 0 3046.8 2701.7 2675.4 2272.5 2361.2 2186.9 1578.8 1753 2807.9 2570.8 FALSE FALSE TRUE 3009.66443 2739.734604 2721.964215 2535.257142 2240.699153 2047.164148 1712.903233 1803.720289 2556.754391 2504.010245 1.201937746 1.094138735 1.087041964 1.012478742 0.894844243 0.817554222 0.684063987 0.720332631 1.02106387 1 11.29002475 -8.471788351 1.163070012 1.098349459 0.694659962 0.883032301 0.054979318 0.158648409 0.399496563 0.012234198 0.045240417 3.37E-09 8.471788351 -0.403689498 IYEDGDDDMKR ddPTM_HeLa_Romidepsin_16h_R1 1 IYEDGDDDMKR 11 1 Q9HB71;Q9HB71-3 Q9HB71 CACYBP Calcyclin-binding protein 0 0 60.167 0.02774 91690000 3090.2 3228.9 2804.9 3065.4 3060.4 2904.9 2720.6 2982.4 3510.6 3365.8 FALSE FALSE TRUE 3052.535454 3274.356539 2853.718108 3419.835971 2904.216368 2719.286265 2951.687696 3068.691039 3196.603144 3278.356031 0.931117739 0.998780031 0.870472298 1.043155758 0.885875829 0.829466428 0.900356053 0.936045692 0.97506284 1 11.67875682 IYEFPET(ph)DDEEENKLVK ddPTM_HeLa_Romidepsin_16h_R1 1 IYEFPETDDEEENKLVK 17 1 G3V1Q4;E7ES33;E7EPK1;Q16181-2;Q16181 G3V1Q4 Sep-07 Septin-7 1 0 IYEFPET(1)DDEEENKLVK 61.641 0.030141 14872000 2986.5 2965.5 2959.7 2719.4 3147.9 3250.9 2742.5 2570.6 3137.6 3518.5 TRUE FALSE FALSE 2950.099389 3007.248387 3011.212337 3033.829823 2987.250917 3043.177982 2975.447882 2644.976255 2856.965198 3427.088863 0.860817886 0.877493554 0.878650206 0.885249827 0.871658436 0.887977553 0.868214394 0.771785139 0.833641995 1 11.74276789 -16.52287875 0.219910882 1.732490339 0.844234669 0 0.061497486 17.5136584 0.221811562 5.504502103 0.024691877 3.00E-17 16.52287875 -0.88825567 IYHLPDAES(ph)DEDEDFK ddPTM_HeLa_Romidepsin_16h_R1 4 IYHLPDAESDEDEDFK 16 0 B5MCX3;Q15019;Q15019-3;Q15019-2;H7C2Y0 B5MCX3 Sep-02 Septin-2 1 0 IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK;IYHLPDAES(1)DEDEDFK ;;; 170 5.25E-06 50392600 18800.13 20194.25 20908.7 11709.87 19047.01 21463.6 16593.39 19958.5 20977.34 20849.4 TRUE FALSE FALSE 18570.98678 20478.54518 21272.60715 13063.82027 18074.97001 20092.14523 18002.83213 20535.96771 19101.07417 20307.72958 0.914478731 1.008411359 1.047512823 0.643292999 0.890053707 0.989384123 0.88650147 1.011238978 0.940581471 1 14.30974133 -12.55430688 0.406164887 1.032900241 0.913356155 0.018520062 0.10894354 6.494764997 1.186682795 0.342391556 0.035984 2.79E-13 12.55430688 -0.119544086 IYHLPDAES(ph)DEDEDFKEQTR ddPTM_HeLa_Romidepsin_16h_R1 9 IYHLPDAESDEDEDFKEQTR 20 1 B5MCX3;Q15019;Q15019-3;Q15019-2;H7C2Y0 B5MCX3 Sep-02 Septin-2 1 0 IY(0.001)HLPDAES(0.998)DEDEDFKEQT(0.001)R;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IYHLPDAES(1)DEDEDFKEQTR;IY(0.001)HLPDAES(0.997)DEDEDFKEQT(0.002)R;IY(0.02)HLPDAES(0.969)DEDEDFKEQT(0.011)R;IYHLPDAES(1)DEDEDFKEQTR ;;;;;;;; 118.84 6.96E-05 3503626400 45935.7 47238.66 42978.78 46039.5 45937.15 47450.38 40936.34 45405.8 49555.5 46108.38 TRUE FALSE FALSE 45375.81802 47903.6871 43726.80764 51362.80361 43592.80582 44418.45386 44413.4717 46719.54518 45123.13197 44910.47764 1.01036151 1.066648355 0.973643789 1.143670838 0.970660035 0.989044343 0.988933408 1.040281637 1.004735072 1 15.45476445 -7.210921435 20.10040497 1.012132954 1.040283176 0.01386979 0.049751323 10058.53895 4000857.863 0.006298865 3.904951899 6.15E-08 7.210921435 0.028150222 IYHLPDAESDEDEDFKEQTR ddPTM_HeLa_Romidepsin_16h_R1 3 IYHLPDAESDEDEDFKEQTR 20 1 B5MCX3;Q15019;Q15019-3;Q15019-2;H7C2Y0 B5MCX3 Sep-02 Septin-2 0 0 ;; ;; 114.52 0.00011411 13003900 10308.4 10210.9 9784.4 10392 10966.2 10872.5 8148.8 9938.1 12074.6 9914.9 FALSE FALSE TRUE 10182.75726 10354.64932 9954.693378 11593.57194 10406.55389 10177.78234 8840.958869 10225.64324 10994.61753 9657.309469 1.054409335 1.072208502 1.03079366 1.200497092 1.077583143 1.05389419 0.915468112 1.058850115 1.138476257 1 13.23740559 -5.83641202 15.3663022 1.039964018 0.934454206 0 0.074746428 0 0 0.009220355 0 1.46E-06 5.83641202 -0.105509812 IYISNTFS(ph)PSKAEGDSAGTAGTPGGTPAGDK ddPTM_HeLa_Romidepsin_16h_R1 1 IYISNTFSPSKAEGDSAGTAGTPGGTPAGDK 31 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 1 0 IY(0.003)IS(0.009)NT(0.104)FS(0.358)PS(0.358)KAEGDS(0.092)AGT(0.017)AGT(0.056)PGGT(0.002)PAGDK 50.322 0.0057845 12076000 1780.1 1497.1 1880.6 1407.9 2138.7 2192.9 2047.3 2027.3 1871.2 1911.9 TRUE FALSE FALSE 1758.403457 1518.176213 1913.331054 1570.688022 2029.554158 2052.780767 2221.197611 2085.956727 1703.835185 1862.228562 0.944246851 0.815246981 1.027441579 0.84344535 1.089852341 1.102324821 1.192763153 1.120140013 0.91494418 1 10.86281444 -8.585131893 7.078600991 0.956234644 1.136243004 0.669918239 0.067886677 0.106660788 9.928272991 0.009703124 0.019526025 2.60E-09 8.585131893 0.18000836 IYISNTFSPSKAEGDS(ph)AGTAGTPGGTPAGDK ddPTM_HeLa_Romidepsin_16h_R1 1 IYISNTFSPSKAEGDSAGTAGTPGGTPAGDK 31 1 J3KMX2;B9EGA3;Q92925-3;Q92925-2;Q92925 J3KMX2 SMARCD2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 1 0 IY(0.003)IS(0.021)NT(0.137)FS(0.252)PS(0.104)KAEGDS(0.281)AGT(0.136)AGT(0.066)PGGT(0.001)PAGDK 61.725 0.00028423 13038000 1722.9 1387.9 1682.6 1211.4 1623.9 2211.1 2017.2 1913.7 1793.8 1650.7 TRUE FALSE FALSE 1701.900632 1407.438893 1711.884947 1351.467768 1541.026323 2069.817846 2188.540918 1969.06989 1633.358035 1607.814576 1.058517977 0.875373886 1.064727844 0.840561958 0.958460227 1.287348602 1.361189872 1.224687174 1.015887068 1 10.65088532 -8.2548604 23.92826593 1.000987672 1.298086736 0.773676246 0.077720102 109.0009782 396442.1487 0.011252427 0.027933875 5.56E-09 8.2548604 0.297099065 IYLEENPEKSETIQDTDTQSLVGS(ph)PSTR ddPTM_HeLa_Romidepsin_16h_R1 1 IYLEENPEKSETIQDTDTQSLVGSPSTR 28 1 E9PMR6;Q9NZN5-2;Q9NZN5 E9PMR6 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 0 IYLEENPEKS(0.007)ET(0.079)IQDT(0.018)DT(0.083)QS(0.154)LVGS(0.525)PS(0.118)T(0.016)R 71.765 1.04E-05 0 922.29 903.73 839.7 1096.7 1056.8 1274.6 1353.4 1291.3 1306.3 1087.8 TRUE FALSE FALSE 911.0487747 916.4527347 854.3146263 1223.505614 1002.867553 1193.157174 1468.357762 1328.661728 1189.461256 1059.538799 0.859854094 0.864954389 0.806308015 1.154753007 0.946513288 1.12610994 1.385846147 1.25400007 1.122621708 1 10.0492207 -8.099012385 1.283210852 0.926153663 1.34591875 0.585153796 0.115108952 0.221064229 0.626822183 0.015412238 0.080704534 7.96E-09 8.099012385 0.419765087 IYNEIPDINLDVPHSYSVLER ddPTM_HeLa_Romidepsin_16h_R1 1 IYNEIPDINLDVPHSYSVLER 21 0 Q53EL6;Q53EL6-2 Q53EL6 PDCD4 Programmed cell death protein 4 0 0 58.964 0.010106 4663900 1166.4 867.93 1363.3 1171.8 1230.8 1026.5 739.73 1040.2 1321.9 1118.5 FALSE FALSE TRUE 1152.183468 880.1487413 1387.027665 1307.289029 1167.987683 960.9099629 802.5626477 1070.296546 1203.665953 1089.441209 1.05759123 0.807890076 1.273155131 1.199962897 1.072097947 0.882020944 0.736673665 0.98242708 1.104847094 1 10.08937263 -8.196998764 5.313482518 1.045674955 0.850026755 0.331143918 0.130141466 0.202565422 11.44910299 0.018083013 0.047003788 6.35E-09 8.196998764 -0.1956482 IYNISGNGS(ph)PLADSK ddPTM_HeLa_Romidepsin_16h_R1 3 IYNISGNGSPLADSK 15 0 Q53HL2 Q53HL2 CDCA8 Borealin 1 0 IYNIS(0.001)GNGS(0.996)PLADS(0.003)K;IYNIS(0.005)GNGS(0.992)PLADS(0.003)K;IYNIS(0.003)GNGS(0.972)PLADS(0.025)K ;; 211.45 1.57E-25 174222000 10397.3 9298.3 9987.9 6293.8 7671.9 8094.9 7887.7 7721.4 11109.2 10512.9 TRUE FALSE FALSE 10270.57371 9429.201711 10161.73521 7021.518769 7280.374315 7577.662015 8557.681041 7944.806527 10115.56533 10239.77334 1.003007915 0.920840862 0.99237892 0.68571037 0.710989792 0.740022436 0.835729538 0.775877186 0.987870043 1 13.32189616 -9.271370271 24.96448842 0.993514612 0.751762763 0.873403526 0.043865621 167.1911881 420288.2491 0.007169817 0.011032866 5.35E-10 9.271370271 -0.241751849 IYQY(ph)IQSR ddPTM_HeLa_Romidepsin_16h_R1 3 IYQYIQSR 8 0 A0A2R8Y443;A0A2R8YDF3;A0A2R8Y6L5;A0A2R8Y6I6;Q13627-4;Q13627-3;Q13627-5;Q9Y463-2;Q9Y463-3;Q9Y463;Q13627-2;Q13627 A0A2R8Y443 DYRK1A;DYRK1B Dual specificity tyrosine-phosphorylation-regulated kinase 1A;Dual specificity tyrosine-phosphorylation-regulated kinase 1B 1 0 IYQY(1)IQSR;IYQY(1)IQSR;IYQY(1)IQSR ;; 215.39 3.46E-16 375700000 9315.6 9048.4 7979.5 6198.4 6689.3 7095.2 5931.7 6121.6 9835.1 8450.3 TRUE FALSE FALSE 9202.057884 9175.783613 8118.37985 6915.088172 6347.92006 6641.839619 6435.53845 6298.718838 8955.424024 8230.759988 1.118008288 1.114816083 0.986346323 0.840151843 0.77124349 0.806953383 0.781888727 0.765265765 1.088043393 1 13.00680993 -9.284808601 2.471449018 1.061594825 0.784467944 0.936764005 0.035560535 0.072316425 0.868670359 0.007899786 0.013280129 5.19E-10 9.284808601 -0.277126882 IYS(ph)SDSDEGSEEDKAQR ddPTM_HeLa_Romidepsin_16h_R1 1 IYSSDSDEGSEEDKAQR 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 IY(0.001)S(0.437)S(0.437)DS(0.124)DEGSEEDKAQR 93.753 0.0025381 3731200 1059.7 1004.1 744.06 1091.3 817.09 618.25 715.32 722.6 1056.8 905.02 TRUE FALSE FALSE 1046.783969 1018.235746 757.0100522 1217.481241 775.3908483 578.7458203 776.0792629 743.5072909 962.2771612 881.5074499 1.187493048 1.155107363 0.858767617 1.381135509 0.879619166 0.656541043 0.880400118 0.84344981 1.091626805 1 9.783828952 -8.539558548 24.98722919 1.096690745 0.796477725 0.535788103 0.136886874 138.2472205 207101.0693 0.019534709 0.03907709 2.89E-09 8.539558548 -0.30021302 IYSFTDNAPS(ph)PSIGGSSR ddPTM_HeLa_Romidepsin_16h_R1 2 IYSFTDNAPSPSIGGSSR 18 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 IYSFTDNAPS(0.693)PS(0.307)IGGSSR;IYSFTDNAPS(0.984)PS(0.016)IGGSSR ; 178.22 6.48E-10 31060000 4313.7 4361.2 4475 3186.2 4185 3827.3 3237.5 3582 4542.5 5016.3 TRUE FALSE FALSE 4261.122965 4422.597088 4552.885498 3554.603436 3971.423834 3582.747882 3512.493169 3685.639519 4136.207423 4885.975803 0.87211299 0.90516148 0.931827271 0.727511469 0.81282102 0.73327172 0.71889287 0.754330285 0.84654685 1 12.254431 -8.169407389 0.14142097 1.082259329 0.462479883 0.50450636 0.06497038 5.955787036 0.205418185 0.21239185 0.782724421 6.77E-09 8.169407389 -0.619779447 IYSSDS(ph)DEGSEEDKAQR ddPTM_HeLa_Romidepsin_16h_R1 1 IYSSDSDEGSEEDKAQR 17 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 IYS(0.255)S(0.255)DS(0.489)DEGSEEDKAQR 65.374 0.015088 3301500 636.27 619.18 885.19 657.6 343.9 639.1 466.71 518.48 703.75 485.9 TRUE FALSE FALSE 628.5148965 627.8968323 900.5963606 733.6348061 326.3494997 598.2635726 506.3523358 533.4814008 640.8048374 473.276248 1.328008535 1.326702608 1.902897863 1.550119638 0.689553936 1.264089578 1.069887487 1.127209327 1.35397633 1 8.88653871 -8.775126081 24.99863797 1.259852335 1.056156878 0.203754776 0.276790626 467.6297966 854121.21 0.047396283 0.086250115 1.68E-09 8.775126081 -0.203695458 IYVDDGLISLQVK ddPTM_HeLa_Romidepsin_16h_R1 2 IYVDDGLISLQVK 13 0 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ; ; 206.97 8.96E-16 5255050 2120.34 2099.21 2101.96 2300.66 2860.42 2508.43 2114.57 2204.26 1991.47 1989.04 FALSE FALSE TRUE 2094.496481 2128.762733 2138.543732 2566.673134 2714.442094 2348.149419 2294.181523 2268.036785 1813.347935 1937.364454 1.081106075 1.09879312 1.103841731 1.324827205 1.401100391 1.21203288 1.184176533 1.170681531 0.935986996 1 10.91987966 -9.458960431 3.40582477 1.044818244 1.25912073 0.665303312 0.076934611 0.120687895 2.756575609 0.012293477 0.018897357 3.48E-10 9.458960431 0.214302486 K(ac)AITK(ac)AQK ddPTM_HeLa_Romidepsin_16h_R1 1 KAITKAQK 8 2 P33778 P33778 HIST1H2BB Histone H2B type 1-B 0 2 K(1)AITK(1)AQK 98.044 0.0097364 1088200 403.22 341.24 831.72 905.81 3173.5 5459.6 3996.3 2869.9 620.16 561.29 FALSE TRUE FALSE 398.3053995 346.0439857 846.1957377 1010.544014 3011.544453 5110.74918 4335.745622 2952.936029 564.6913364 546.7076049 0.728552879 0.63295989 1.547803122 1.848417701 5.508510264 9.348231366 7.93064809 5.40130776 1.032894606 1 9.094625634 -8.699573753 2.645498001 0.914163077 7.61090476 0.90669299 0.947708911 0.052160441 0.741906866 0.136038986 0.291546219 2.00E-09 8.699573753 6.696741683 K(ac)AVTK(ac)AQK ddPTM_HeLa_Romidepsin_16h_R1 1 KAVTKAQK 8 2 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 2 K(1)AVTK(1)AQK 99.013 0.0084615 563500000 161.17 124.24 676.77 538.56 1709.9 2514.2 1637.7 592.91 97.583 110.11 FALSE TRUE FALSE 159.205598 125.989054 688.548898 600.8308412 1622.637422 2353.550734 1776.806197 610.0649154 88.85493208 107.2493263 1.484443805 1.174730493 6.420076671 5.602187555 15.12958149 21.94466683 16.56706161 5.688286689 0.828489419 1 6.744824775 -9.012167285 1.724311933 1.400624375 15.53598198 0.681583641 4.069129963 0.141992542 0.839834024 0.630483427 1.274085429 9.72E-10 9.012167285 14.13535761 K(ac)AVTK(ac)AQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KAVTKAQKK 9 3 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 3 K(1)AVTK(1)AQK(1)K 112.85 0.012252 17807000 1077.2 920.35 5534.9 1569.3 5127.3 7072.2 5286.2 1602.5 1232 374.52 FALSE TRUE FALSE 1064.070672 933.3067115 5631.232613 1750.74985 4865.634748 6620.309244 5735.209696 1648.865809 1121.806834 364.7899164 2.916941023 2.558477275 15.43691961 4.799337293 13.33818324 18.14827918 15.72195238 4.52004218 3.075213387 1 8.510922041 -9.776369303 23.03093779 1.979505015 12.17735741 0.555358651 4.202760938 47.63084111 73475.20077 0.663242144 0.874205238 1.67E-10 9.776369303 10.19785239 RNETSFLPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 RNETSFLPAKK 11 2 F8WAJ0;Q9H8H2-3;Q9H8H2-4;Q9H8H2-2;Q9H8H2 F8WAJ0 DDX31 Probable ATP-dependent RNA helicase DDX31 0 1 RNETSFLPAK(1)K 108.68 0.0092329 1936100 1345 1212.7 1316.3 2707.7 3943.4 4931.3 4099.5 4624.5 1429.1 1316.2 FALSE TRUE FALSE 1328.606623 1229.772422 1339.209649 3020.777014 3742.153583 4616.205845 4447.711428 4758.302611 1301.277717 1282.004934 1.036350631 0.959257168 1.044621291 2.356291254 2.91898532 3.600770732 3.469340335 3.711610216 1.015033314 1 10.3241861 -8.931723443 1.517024754 0.998018082 3.582849078 0.986191248 0.135995289 0.027584151 0.127127953 0.020398649 0.044843164 1.17E-09 8.931723443 2.584830996 up ALVATPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ALVATPGKK 9 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; ALVATPGK(1)K;ALVATPGK(1)K 141.52 0.0014256 423620000 10146.5 9894.1 12433.9 20880.1 37829 39575 39660 40539 10277.4 7888.9 FALSE TRUE FALSE 10022.83056 10033.3894 12650.30681 23294.35541 35898.44497 37046.28522 43028.71941 41711.93201 9358.163604 7683.945241 1.304385995 1.305760138 1.646329642 3.03156187 4.671876731 4.821258359 5.599821194 5.428452533 1.217885254 1 12.90763152 -8.928834504 1.253137888 1.135241206 5.440398381 0.991102519 0.172706157 0.027570441 0.086049364 0.029663083 0.070882974 1.18E-09 8.928834504 4.305157175 up K(ac)EVLNMLK ddPTM_HeLa_Romidepsin_16h_R1 1 KEVLNMLK 8 1 Q92896;Q92896-3;Q92896-2 Q92896 GLG1 Golgi apparatus protein 1 0 1 K(1)EVLNMLK 61.999 0.026803 1062400 1101.2 326.21 812.77 551.5 529.92 211.24 882.04 490.83 715.21 506.13 FALSE TRUE FALSE 1087.778151 330.8023929 826.9159209 615.2670249 502.876205 197.7424457 956.9604556 505.0313916 651.2398263 492.9806696 2.206533071 0.671025079 1.677380011 1.248055071 1.020072867 0.401116023 1.941172372 1.024444614 1.321025075 1 8.945387268 -9.51348025 1.352547036 1.533650653 1.128484337 0.011624992 0.526293132 0.872219081 3.186746428 0.105911159 0.177930486 3.07E-10 9.51348025 -0.405166316 K(ac)FADIGNTVK ddPTM_HeLa_Romidepsin_16h_R1 2 KFADIGNTVK 10 1 E9PFD2;P11172-4;P11172-2;P11172-3;P11172 E9PFD2 UMPS Uridine 5-monophosphate synthase;Orotate phosphoribosyltransferase;Orotidine 5-phosphate decarboxylase 0 1 ; K(1)FADIGNTVK;K(1)FADIGNTVK 121.61 0.0031292 717970 508.88 426.62 334.96 282.91 985.47 721.56 696.36 577.45 877.94 599.33 FALSE TRUE FALSE 502.6775748 432.6259676 340.7898383 315.6213853 935.1777886 675.4546447 755.508801 594.1576047 799.4148476 583.7593202 0.861104153 0.741103315 0.583784835 0.5406704 1.601992047 1.157077277 1.294212829 1.017812623 1.369425412 1 9.189229869 -8.763005091 24.99999871 0.86294665 1.261755284 0.388565081 0.256754256 29.82257307 476194.4139 0.032042171 0.060399943 1.73E-09 8.763005091 0.398808633 K(ac)FDDFQK ddPTM_HeLa_Romidepsin_16h_R1 2 KFDDFQK 7 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 1 ; K(1)FDDFQK;K(1)FDDFQK 101.64 0.010209 2112420 1559.17 1652.41 1921.72 1186.18 4762.4 4043.5 3465.3 3411.2 4933 3156.1 FALSE TRUE FALSE 1540.166236 1675.672671 1955.16673 1323.331713 4519.356957 3785.1334 3759.642496 3509.89769 4491.780125 3074.104067 0.501013044 0.545093021 0.636011888 0.4304772 1.470137919 1.231296442 1.223004301 1.141762807 1.46116723 1 11.58595029 -8.757050226 24.99982947 0.709043456 1.260921817 0.407126812 0.293891354 62.71706131 357220.4995 0.034188162 0.066534814 1.75E-09 8.757050226 0.551878361 K(ac)FDQLLAEEK ddPTM_HeLa_Romidepsin_16h_R1 2 KFDQLLAEEK 10 1 P35579;A0A0C4DFM8;Q7Z406;Q7Z406-6;Q7Z406-2;A1L2Z2;P35749-4;P35749-3;P35749;P35749-2;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35749-4;P35579-2;P35580 MYH9;MYH14;MYH11;MYH10 Myosin-9;Myosin-14;Myosin-11;Myosin-10 0 1 ; K(1)FDQLLAEEK;K(1)FDQLLAEEK 155.97 6.82E-05 541410 437.58 494.42 664.33 603.29 1282.11 1022.62 779.11 799.78 635.42 436.4 FALSE TRUE FALSE 432.2466066 501.3804577 675.892385 673.0452284 1216.679142 957.2778824 845.287584 822.9203725 578.5864438 425.0622651 1.016901857 1.179545913 1.590102064 1.583403853 2.8623551 2.252088602 1.988620617 1.935999594 1.361180446 1 8.731530379 -9.388177205 1.492637729 1.01227739 2.218295657 0.711742044 0.301693583 0.125327972 0.550483406 0.046390765 0.081088366 4.09E-10 9.388177205 1.206018267 K(ac)FEEETVK ddPTM_HeLa_Romidepsin_16h_R1 1 KFEEETVK 8 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 1 K(1)FEEETVK 105.4 0.016076 0 1965.1 1537.5 1361.5 77.784 1975.2 1814.6 1277.5 1546.9 1861 1352.8 FALSE TRUE FALSE 1941.148605 1559.144965 1385.196336 86.77775206 1874.398174 1698.652916 1386.010818 1591.657111 1694.547499 1317.654061 1.473185309 1.183273373 1.05125949 0.065857765 1.422526769 1.28914938 1.05187762 1.207947638 1.286033679 1 10.36375594 -9.763461047 5.12213153 1.227550646 1.003098399 0.083274738 0.36032846 0.403624786 29.87195363 0.061668534 0.084574541 1.72E-10 9.763461047 -0.224452247 K(ac)FGDPVVQSDMK ddPTM_HeLa_Romidepsin_16h_R1 2 KFGDPVVQSDMK 12 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 1 ; K(1)FGDPVVQSDMK;K(1)FGDPVVQSDMK 126.34 0.0010549 8099800 2334.4 2045.19 2428 1823.82 7125.8 6236 5804.9 5724 5154.2 3428.5 FALSE TRUE FALSE 2305.947435 2073.982239 2470.258322 2034.69865 6762.143836 5837.539726 6297.968061 5889.614909 4693.195443 3339.427076 0.690521872 0.621059299 0.739725188 0.609295728 2.02494131 1.748066238 1.885942684 1.763660285 1.405389409 1 11.70538489 -8.760701926 24.99999137 0.806258698 1.850131576 0.819929689 0.2317638 4.212366317 142791.6345 0.024721633 0.047199519 1.73E-09 8.760701926 1.043872878 K(ac)FGNPGEK ddPTM_HeLa_Romidepsin_16h_R1 1 KFGNPGEK 8 1 P17844;J3KTA4;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3QKN9;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 1 K(1)FGNPGEK 96.668 0.010139 10925000 4363.5 3924.3 3031.9 2901.2 3025.7 3159.3 3960.5 3181.3 4923.9 3958.8 FALSE TRUE FALSE 4310.315984 3979.546398 3084.668948 3236.650395 2871.287239 2957.430926 4296.904771 3273.345896 4483.494052 3855.949805 1.117835086 1.032053476 0.799976427 0.839391216 0.744638126 0.766978585 1.11435703 0.848907808 1.162746996 1 11.91287056 -9.826916753 6.521176263 1.056228495 0.855120725 0.524975246 0.104473779 0.142571104 11.06260933 0.017106886 0.022625293 1.49E-10 9.826916753 -0.20110777 K(ac)FGTINIVHPK ddPTM_HeLa_Romidepsin_16h_R1 2 KFGTINIVHPK 11 1 Q9Y617-2;Q9Y617 Q9Y617-2 PSAT1 Phosphoserine aminotransferase 0 1 ; K(1)FGTINIVHPK;K(1)FGTINIVHPK 103.91 0.0035533 2012080 2223.9 1668.15 2044.74 1606.8 4267.1 2700.9 2950.5 2981 4535.2 4130.2 FALSE TRUE FALSE 2196.794251 1691.634259 2080.327842 1792.585776 4049.333964 2528.321207 3201.115396 3067.250532 4129.560353 4022.896809 0.546072732 0.420501529 0.51712185 0.445595764 1.006571671 0.628482739 0.795723964 0.762448225 1.026514114 1 11.97401902 -12.31965991 1.085629289 0.996526861 0.634751191 0.431802232 0.169649926 0.427981437 0.915989924 0.114821661 0.03162468 4.79E-13 12.31965991 -0.36177567 K(ac)FIQTFGK ddPTM_HeLa_Romidepsin_16h_R1 1 KFIQTFGK 8 1 P78527-2;P78527 P78527-2 PRKDC DNA-dependent protein kinase catalytic subunit 0 1 K(1)FIQTFGK 93.598 0.013482 397700 379.29 382.32 312.97 234.28 197.72 215.76 317.88 217.19 322.96 259 FALSE TRUE FALSE 374.6670676 387.702311 318.4171116 261.3685559 187.6296106 201.9736323 344.8807193 223.47405 294.0736487 252.2711427 1.485176083 1.536847643 1.262201884 1.036062045 0.743761687 0.800621229 1.36710333 0.885848645 1.165704669 1 7.978831375 -9.191512924 4.373479646 1.265321447 0.961694802 0.36941991 0.211535702 0.257738849 9.626168527 0.039478246 0.066219411 6.43E-10 9.191512924 -0.303626645 K(ac)FLDGIYVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 KFLDGIYVSEK 11 1 D6RAN4;A0A2R8Y5Y7;P32969;H0Y9V9;H0Y9R4 D6RAN4 RPL9 60S ribosomal protein L9 0 1 K(1)FLDGIYVSEK 153.95 0.0016065 159810 114.88 67.488 0 0 119.07 138.39 0 122.96 172.59 0 FALSE TRUE FALSE 113.4797984 68.43809784 0 0 112.9934136 129.5473256 0 126.5176536 157.1531181 0 0 TVTPAK(ac)AVTTPGK ddPTM_HeLa_Romidepsin_16h_R1 2 TVTPAKAVTTPGK 13 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; TVTPAK(1)AVTTPGK;TVTPAK(1)AVTTPGK 164.48 0.00023909 12642900 1581.78 1186.72 1775.63 3397.1 5707.9 6542.5 6488.7 6067.2 1466.78 1148.27 FALSE TRUE FALSE 1562.500657 1203.426675 1806.534095 3789.888686 5416.604564 6124.455365 7039.850016 6242.74486 1335.587523 1118.43778 1.397038517 1.075988935 1.615229857 3.388555675 4.843009295 5.475901722 6.294359993 5.581664865 1.194154514 1 10.12726928 -8.923050765 1.359561429 1.162663741 5.900996638 0.98797461 0.225530987 0.031117702 0.114793544 0.039042176 0.090174652 1.19E-09 8.923050765 4.738332897 up K(ac)FVADGIFK ddPTM_HeLa_Romidepsin_16h_R1 1 KFVADGIFK 9 1 E9PPU1;E9PL09;P23396;P23396-2;E9PQ96;E9PJH4;F2Z2S8;E9PK82;H0YCJ7;E9PQX2 E9PPU1 RPS3 40S ribosomal protein S3 0 1 K(1)FVADGIFK 83 0.029337 181080 250.83 177.72 788.6 270.75 849.1 522.93 445.1 251.33 406.92 0 FALSE TRUE FALSE 247.7727875 180.2219468 802.3252522 302.0553889 805.7672586 489.5164607 482.9067829 258.601837 370.5240561 0 0 K(ac)FYEAFSK ddPTM_HeLa_Romidepsin_16h_R1 1 KFYEAFSK 8 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 1 K(1)FYEAFSK 96.89 0.0098977 470560 252.67 200.38 270.88 264.06 349.89 426.31 347.4 227.4 294.7 323.67 FALSE TRUE FALSE 249.5903609 203.2009549 275.5945528 294.5918596 332.0338077 399.0701669 376.9081473 233.9794602 268.3412939 315.2610067 0.79169436 0.644548328 0.874179004 0.934437984 1.053202904 1.265840552 1.195543183 0.742176975 0.851171849 1 8.30040293 -8.822638596 3.129944687 0.874944268 1.091150654 0.310902306 0.154932433 0.264109121 5.252004647 0.024961613 0.049212026 1.50E-09 8.822638596 0.216206386 K(ac)GATPGKALVATPGK ddPTM_HeLa_Romidepsin_16h_R1 2 KGATPGKALVATPGK 15 2 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; K(0.949)GATPGK(0.051)ALVATPGK;K(0.809)GATPGK(0.191)ALVATPGK 119.56 0.0010164 4923600 7384.2 7816.4 7389.4 5531.5 6568 7001.7 6407.3 6576.7 7613.1 7330.5 FALSE TRUE FALSE 7294.19853 7926.439484 7518.009407 6171.078056 6232.810451 6554.313967 6951.535902 6766.986438 6932.165269 7140.052553 1.021588913 1.110137415 1.052934744 0.864290285 0.872936215 0.917964387 0.973597302 0.947750228 0.970884348 1 12.80171898 -9.268605006 24.98536155 1.022453508 0.916339619 0.616220442 0.045434085 317.6090767 1107449.562 0.007347262 0.011365539 5.39E-10 9.268605006 -0.106113889 TVTPAK(ac)AVTTPGKK ddPTM_HeLa_Romidepsin_16h_R1 1 TVTPAKAVTTPGKK 14 2 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 TVTPAK(1)AVTTPGKK 168.67 1.16E-06 23745000 3907.8 3158.8 3514.3 9522.9 14427 16492 15592 17554 3864.3 3755.1 FALSE TRUE FALSE 3860.170231 3203.269669 3575.464917 10623.9825 13690.73636 15438.21443 16916.38409 18061.89729 3518.66733 3657.541961 1.055400122 0.875798474 0.977559507 2.904678229 3.743152232 4.220926128 4.625069042 4.93826113 0.962030612 1 11.8366587 -8.9164973 1.460688848 0.98769684 4.618052303 0.980152078 0.23055185 0.037202078 0.15893826 0.037544803 0.084506806 1.21E-09 8.9164973 3.630355463 up K(ac)HEAFESDLAAHQDR ddPTM_HeLa_Romidepsin_16h_R1 1 KHEAFESDLAAHQDR 15 1 O43707;O43707-2;P35609-2;P35609;A0A494C1A0;F6THM6;A0A494C060;P12814-2;P12814;P12814-3;P12814-4;H9KV75;H7C5W8 O43707;P12814-2 ACTN4;ACTN2;ACTN1 Alpha-actinin-4;Alpha-actinin-2;Alpha-actinin-1 0 1 K(1)HEAFESDLAAHQDR 105.17 0.001962 1909700 222.72 211.44 230.42 148.15 767.02 580.15 345 547.31 466.31 572.48 FALSE TRUE FALSE 220.005403 214.4166579 234.4303634 165.2798001 727.8761073 543.0802873 374.3042914 563.1455513 424.6020657 557.6068871 0.39455288 0.384530146 0.420422288 0.29640918 1.305357097 0.973948314 0.671269133 1.009932919 0.761472061 1 9.12310457 -8.762076427 24.99999999 0.629395623 0.966195654 0.40785406 0.25068656 21.45932301 842194.7668 0.047297836 0.089610117 1.73E-09 8.762076427 0.336800031 K(ac)IQGMQKFLGLEVTGK ddPTM_HeLa_Romidepsin_16h_R1 1 KIQGMQKFLGLEVTGK 16 2 F5GYX7;P09238 F5GYX7 MMP10 Stromelysin-2 0 1 K(0.673)IQGMQK(0.327)FLGLEVTGK 55.66 0.017202 1883100 0 0 51.935 182.27 1745.9 2449 2667.2 2602.8 225.77 115.88 FALSE TRUE FALSE 0 0 52.83890689 203.344915 1656.800208 2292.516804 2893.751901 2678.107911 205.5765657 112.8694209 0 0 0.468141915 1.801594386 14.67891121 20.31123032 25.6380504 23.72748872 1.821366355 1 6.818510867 -8.548554758 1.748094252 0.37567098 24.27775511 0.985343049 1.244112997 0.025172973 0.152242763 0.1712313 0.457101223 2.83E-09 8.548554758 23.90208413 K(ac)KK(ac)MMEEK ddPTM_HeLa_Romidepsin_16h_R1 1 KKKMMEEK 8 3 G5E9U8;Q8IXQ6-3;Q8IXQ6-2;Q8IXQ6 G5E9U8 PARP9 Poly [ADP-ribose] polymerase 9 0 2 K(0.925)K(0.114)K(0.962)MMEEK 53.775 0.027699 0 67.244 0 0 0 0 141.09 0 0 0 0 FALSE TRUE FALSE 66.42440426 0 0 0 0 132.0748043 0 0 0 0 0 K(ac)LAAAEGLEPK ddPTM_HeLa_Romidepsin_16h_R1 2 KLAAAEGLEPK 11 1 P41236;Q6NXS1 P41236 PPP1R2;PPP1R2P3 Protein phosphatase inhibitor 2;Protein phosphatase inhibitor 2-like protein 3 0 1 ; K(1)LAAAEGLEPK;K(1)LAAAEGLEPK 165.63 0.0010426 1182300 1184.34 803.29 692.52 472.79 1118.92 1252.77 1276.61 1245.77 1095.14 1202.25 FALSE TRUE FALSE 1169.904809 814.5987377 704.5730201 527.4562043 1061.817337 1172.72204 1385.045222 1281.814389 997.1879356 1171.015372 0.999051624 0.695634539 0.601677004 0.450426371 0.906749273 1.001457426 1.182772878 1.094617902 0.851558365 1 10.1935443 -10.36484524 16.02214309 0.999577456 0.843966572 0.030702907 0.215372063 4.114604432 629.2812546 0.04020004 0.045966355 4.32E-11 10.36484524 -0.155610885 K(ac)LAGSELFAK ddPTM_HeLa_Romidepsin_16h_R1 1 KLAGSELFAK 10 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 0 1 K(1)LAGSELFAK 87.298 0.017525 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 K(ac)LAVNMVPFPR ddPTM_HeLa_Romidepsin_16h_R1 1 KLAVNMVPFPR 11 1 Q5JP53;P07437;Q5ST81;A0A075B736;Q5SQY0;A6NNZ2;CON__ENSEMBL:ENSBTAP00000025008;Q9H4B7;P04350;P68371;Q3ZCM7;A0A0B4J269;Q13509;Q13509-2;Q9BVA1;Q13885 Q5JP53;P04350;P68371;A0A0B4J269;Q9BVA1 TUBB;TUBB8;TUBB1;TUBB4A;TUBB4B;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-1 chain;Tubulin beta-4A chain;Tubulin beta-4B chain;Tubulin beta-8 chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 1 K(1)LAVNMVPFPR 105.52 0.0030394 503630 0 0 64.591 0 0 60.314 52.734 0 0 0 FALSE TRUE FALSE 0 0 65.71517926 0 0 56.46013005 57.21322464 0 0 0 0 K(ac)LDASILEDR ddPTM_HeLa_Romidepsin_16h_R1 1 KLDASILEDR 10 1 J3KMZ8;Q92785 J3KMZ8 DPF2 Zinc finger protein ubi-d4 0 1 K(1)LDASILEDR 110.38 0.0039941 384800 169.02 226.87 188.3 199.78 262.35 397.79 185.22 202.26 166.17 144.77 FALSE TRUE FALSE 166.9599192 230.0638818 191.5772825 222.8795036 248.9613005 372.3725028 200.9525822 208.112074 151.307339 141.0088545 1.184038547 1.631556278 1.358618813 1.58060644 1.765572108 2.640773901 1.425106124 1.475879474 1.073034311 1 7.139641948 -9.937954537 0.73717221 1.042497765 1.830882853 0.440597831 0.330462484 0.391003132 0.433541742 0.079791443 0.117805867 1.15E-10 9.937954537 0.788385088 K(ac)LDEAVAEAHLGK ddPTM_HeLa_Romidepsin_16h_R1 2 KLDEAVAEAHLGK 13 1 P23526-2;P23526 P23526-2 AHCY Adenosylhomocysteinase 0 1 ; K(1)LDEAVAEAHLGK;K(1)LDEAVAEAHLGK 113.43 0.0011975 2331000 1350.18 1187.45 1711.31 1059.85 3251.2 2735.2 2101.16 2515.6 3936.4 2762.5 FALSE TRUE FALSE 1333.723487 1204.166952 1741.094633 1182.394844 3085.279132 2560.429547 2279.632478 2588.384917 3584.318525 2690.729852 0.495673501 0.447524285 0.647071512 0.439432759 1.14663281 0.951574364 0.847217151 0.961963876 1.332098993 1 11.39378184 -8.750615053 24.9999283 0.70039175 0.965782535 0.169202431 0.266944677 260.9706273 602735.5109 0.035226549 0.069897058 1.78E-09 8.750615053 0.265390786 K(ac)LDPGSEETQTLVR ddPTM_HeLa_Romidepsin_16h_R1 2 KLDPGSEETQTLVR 14 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 1 ; K(1)LDPGSEETQTLVR;K(1)LDPGSEETQTLVR 201.48 2.25E-17 5736400 1215.59 1146.82 1533.77 959.27 3177.8 2194.4 2341 2687.9 3367.1 2857.3 FALSE TRUE FALSE 1200.773922 1162.964962 1560.464623 1070.185311 3015.625008 2054.184922 2539.844482 2765.670146 3065.938143 2783.066934 0.431457076 0.417871718 0.560699638 0.384534521 1.083561797 0.738101156 0.912606323 0.993749059 1.101640103 1 11.44245989 -8.744978257 24.99883547 0.663210725 0.916768694 0.248533885 0.239458325 343.7547027 522043.5629 0.039032454 0.077886683 1.80E-09 8.744978257 0.25355797 K(ac)LESTESR ddPTM_HeLa_Romidepsin_16h_R1 2 KLESTESR 8 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 1 ; K(1)LESTESR;K(1)LESTESR 131.62 0.0015454 2561500 1319.98 1402.54 1378.71 1524.92 2453.89 2563.7 2892.6 1071.6 1789.01 1369.58 FALSE TRUE FALSE 1303.891576 1422.284995 1402.705869 1701.238425 2328.658837 2399.887844 3138.297372 1102.605055 1628.996465 1333.998114 0.977431349 1.066182163 1.051505137 1.275292976 1.745623785 1.799018918 2.352550081 0.82654169 1.221138507 1 10.38154091 -8.942340228 2.415174636 0.999580376 1.744279867 0.388491216 0.35724077 0.17022889 2.007831887 0.048196706 0.09381843 1.14E-09 8.942340228 0.744699491 K(ac)LLEATELK ddPTM_HeLa_Romidepsin_16h_R1 2 KLLEATELK 9 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 1 ; K(1)LLEATELK;K(1)LLEATELK 106.29 0.0036557 619020 410.96 346.83 388.67 343.84 1085.88 796.42 980.74 725.53 786.25 737.22 FALSE TRUE FALSE 405.9510614 351.7126818 395.4346383 383.5963986 1030.463492 745.5313323 1064.044031 746.5220659 715.9258308 718.0669181 0.565338761 0.489804882 0.550693297 0.534207034 1.435052174 1.038247709 1.481817369 1.039627432 0.997018262 1 9.487974488 -8.760842091 24.99999978 0.727931484 1.250307104 0.609256004 0.218081514 9.9006286 414365.2452 0.035878231 0.06845124 1.73E-09 8.760842091 0.522375621 K(ac)LLEDYK(ac)VPK ddPTM_HeLa_Romidepsin_16h_R1 1 KLLEDYKVPK 10 2 B2WTI3;B2WTI4;K7EJU9;Q6NYC1-2;Q6NYC1;Q6NYC1-3 B2WTI3 JMJD6 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 0 2 K(1)LLEDYK(1)VPK 73.781 0.02255 47123000 39688 34924 36567 39325 38214 40751 34234 33213 38634 34934 FALSE TRUE FALSE 39204.26739 35415.66099 37203.4333 43871.94153 36263.79698 38147.14262 37141.83511 34173.96575 35178.47828 34026.40964 1.152171734 1.04082862 1.093369347 1.289349714 1.065754435 1.121103961 1.091559042 1.004336517 1.033858072 1 15.05436731 -12.44388553 1.078966308 0.997537498 1.113269624 0.188238951 0.073293764 0.609803814 1.225307205 0.055328989 0.012642086 3.60E-13 12.44388553 0.115732127 K(ac)LLEGEEER ddPTM_HeLa_Romidepsin_16h_R1 2 KLLEGEEER 9 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5;P20700;E9PBF6;Q03252 P02545;P20700;Q03252 LMNA;LMNB1;LMNB2 Prelamin-A/C;Lamin-A/C;Lamin-B1;Lamin-B2 0 1 ; K(1)LLEGEEER;K(1)LLEGEEER 139.43 0.0017534 7250400 2865.8 2637.3 2719.6 2040.4 5161.8 4490.5 4332.9 4777.5 4651.6 3920.9 FALSE TRUE FALSE 2830.870527 2674.427979 2766.933497 2276.320648 4898.374085 4203.571542 4700.936418 4915.729425 4235.549246 3819.034453 0.741252943 0.700289042 0.724511269 0.596046115 1.282621077 1.10068961 1.230922757 1.287165509 1.109062853 1 11.89899222 -8.745291815 24.99988308 0.829789421 1.216843612 0.64948281 0.148410177 127.4028603 197245.8598 0.022135707 0.044162307 1.80E-09 8.745291815 0.387054191 K(ac)LNKEELPVIPK ddPTM_HeLa_Romidepsin_16h_R1 1 KLNKEELPVIPK 12 2 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 0 1 K(0.974)LNK(0.026)EELPVIPK 92.247 0.029472 378490 199.52 264.38 202.7 53.912 287.05 211.15 347.75 379.63 270.38 255.53 FALSE TRUE FALSE 197.0881735 268.1019486 206.2279085 60.1455591 272.4007674 197.6581965 377.2878763 390.6139951 246.1965356 248.8912938 0.791864474 1.077184921 0.828586269 0.241653929 1.094456794 0.794154723 1.515874142 1.569416066 0.989172951 1 7.959371955 -7.756028353 24.09824528 0.867920561 1.542645731 0.587759317 0.231013804 42.48460373 189196.6771 0.031386436 0.110734601 1.75E-08 7.756028353 0.67472517 K(ac)LNVTEQEK ddPTM_HeLa_Romidepsin_16h_R1 2 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8Y879;A0A2R8YEM5;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 1 ; K(1)LNVTEQEK;K(1)LNVTEQEK 172.98 0.00047778 21547000 3541.8 3230.6 5008 1721.48 8146.2 8087.9 9532.2 2871.9 9410.4 5877.9 FALSE TRUE FALSE 3498.631179 3276.080472 5095.162139 1920.525617 7730.469016 7571.109293 10341.86483 2954.993895 8568.710255 5725.191311 0.611094196 0.572222009 0.889954914 0.33545178 1.350255144 1.322420314 1.806378908 0.516138891 1.496667935 1 12.48310819 -8.730249058 24.97127124 0.767807398 1.293884597 0.197383566 0.414891113 167.1260552 133802.0296 0.048487188 0.096966639 1.86E-09 8.730249058 0.526077199 K(ac)LTELGTVDPK ddPTM_HeLa_Romidepsin_16h_R1 2 KLTELGTVDPK 11 1 P46940;H0YLE8 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 1 ; K(1)LTELGTVDPK;K(1)LTELGTVDPK 123.67 6.22E-07 321030 418.58 246.45 353.51 225.893 709.6 634.74 678.8 712.61 800.04 784.58 FALSE TRUE FALSE 413.478186 249.9195296 359.6626933 252.0118115 673.3864641 594.1821625 736.4572551 733.228246 728.4824187 764.1964985 0.541062654 0.327035691 0.47064164 0.329773575 0.881169261 0.777525366 0.963701426 0.959476061 0.953265842 1 9.577799837 -8.034243661 1.859536215 0.688763907 0.964304559 0.220504187 0.230184203 0.609015944 3.974747844 0.041297687 0.17102953 9.24E-09 8.034243661 0.275540652 K(ac)LVESLPQEIK ddPTM_HeLa_Romidepsin_16h_R1 1 KLVESLPQEIK 11 1 B4DLN1;P52815 B4DLN1 MRPL12 "39S ribosomal protein L12, mitochondrial" 0 1 K(1)LVESLPQEIK 91.313 0.019961 409290 149.9 229.59 166.73 266.6 246.79 238.64 277.09 281.95 323.11 280.79 FALSE TRUE FALSE 148.0729611 232.822174 169.6318657 297.4255464 234.1953854 223.3916742 300.6260177 290.1077784 294.2102324 273.4950353 0.541410051 0.851284828 0.620237459 1.087498887 0.856305801 0.816803398 1.099201005 1.060742394 1.075742498 1 8.095370834 -7.792315674 0.757666307 0.78399684 1.163198863 0.11001493 0.178898663 1.761248571 1.103665111 0.033554555 0.483241393 1.61E-08 7.792315674 0.379202024 K(ac)LYGDADYLEER ddPTM_HeLa_Romidepsin_16h_R1 1 KLYGDADYLEER 12 1 B4E1E0;P17812-2;P17812;A0A3B3IRI2 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 0 1 K(1)LYGDADYLEER 88.338 0.030137 0 160.57 0 0 114.24 118.57 180.15 237.12 170.57 215.55 171.55 FALSE TRUE FALSE 158.6129111 0 0 127.4489663 112.5189305 168.6389964 257.2609669 175.5051738 196.2706681 167.0931063 0.949248683 0 0 0.762742217 0.67339062 1.009251669 1.539626455 1.050343594 1.174618586 1 7.384508403 -10.48622721 24.97718619 0.977610099 0.715725884 0.095871825 0.440996836 1085.387269 739673.5865 0.083617336 0.093344943 3.26E-11 10.48622721 -0.261884215 K(ac)LYVSNLGIGHTR ddPTM_HeLa_Romidepsin_16h_R1 2 KLYVSNLGIGHTR 13 1 D6RCC8;Q06203 D6RCC8 PPAT Amidophosphoribosyltransferase 0 1 ; K(1)LYVSNLGIGHTR;K(1)LYVSNLGIGHTR 144.8 8.11E-06 4307900 1161.58 1048.4 1004.34 1052.1 2343.6 2340.4 1862.08 1841.42 1798.45 1278.67 FALSE TRUE FALSE 1147.422216 1063.159403 1021.820116 1173.748752 2223.997347 2190.855993 2020.245029 1894.698582 1637.592128 1245.449969 0.921291296 0.853634774 0.820442524 0.942429468 1.785697862 1.759087918 1.622100509 1.521296423 1.314859824 1 10.28245135 -8.766858121 24.99962659 0.939725804 1.674695509 0.845080806 0.145632091 22.06624749 101804.239 0.013895453 0.025723209 1.71E-09 8.766858121 0.734969705 K(ac)QLATK(ac)AAR ddPTM_HeLa_Romidepsin_16h_R1 4 KQLATKAAR 9 2 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1 0 2 ;;; K(1)QLATK(1)AAR;K(1)QLATK(1)AAR;K(1)QLATK(1)AAR;K(1)QLATK(1)AAR 153.05 0.002619 1945405200 769.93 739.6 3269.159 2255.77 8763.64 21809.8 15003.13 3311.58 1215.53 775.66 FALSE TRUE FALSE 760.545797 750.0121082 3326.057341 2516.592741 8316.398749 20416.22417 16277.49549 3407.395342 1106.809952 755.5082414 1.006667771 0.992725251 4.402410403 3.330993103 11.00768766 27.0231654 21.54509322 4.510070382 1.464987265 1 9.561303683 -8.642657319 3.076093149 1.369006407 18.20937953 0.627399601 5.424249303 0.107788414 2.034768006 0.761822877 1.631706127 2.28E-09 8.642657319 16.84037313 SATDGNTSTTPPTSAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SATDGNTSTTPPTSAKK 17 1 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 0 1 ; SATDGNTSTTPPTSAK(1)K;SATDGNTSTTPPTSAK(1)K 338.78 2.18E-208 10348800 1534.39 1591.14 1666.49 3525.9 7592.2 8029.7 7167.5 8128.1 1636.56 1608.61 FALSE TRUE FALSE 1515.688264 1613.540111 1695.494559 3933.581148 7204.741704 7516.628085 7776.307271 8363.273749 1490.181975 1566.81808 0.967367101 1.029819691 1.082125986 2.51055384 4.598326886 4.797384061 4.963120715 5.337743963 0.951088064 1 10.61362197 -8.898047503 1.914246351 0.981590163 5.05160049 0.994603682 0.13638598 0.015626832 0.115777605 0.020999563 0.043781926 1.26E-09 8.898047503 4.070010327 up K(ac)RDNSMQSRSGK ddPTM_HeLa_Romidepsin_16h_R1 1 KRDNSMQSRSGK 12 3 Q9H7E2-3;Q9H7E2-2;Q9H7E2 Q9H7E2-3 TDRD3 Tudor domain-containing protein 3 0 1 K(1)RDNSMQSRSGK 58.37 0.026507 1199300 109.46 121.17 48.903 139.79 362.75 247.9 361.86 460.42 222.52 169.41 FALSE TRUE FALSE 108.1258594 122.8758344 49.7541362 155.9531775 344.2375139 232.0599901 392.5963794 473.7415263 202.6172539 165.0087038 0.655273673 0.744662746 0.301524314 0.945120918 2.086177917 1.406349997 2.379246491 2.871009319 1.227918584 1 7.366398315 -7.898949176 0.809774427 0.786373505 3.14307635 0.774402119 0.372974655 0.39405514 0.314800219 0.060088332 0.682963235 1.26E-08 7.898949176 2.356702845 K(ac)SAPATGGVK(ac)KPHR ddPTM_HeLa_Romidepsin_16h_R1 2 KSAPATGGVKKPHR 14 3 Q5TEC6;Q71DI3;P68431;Q16695 Q5TEC6 HIST2H3PS2;HIST2H3A;HIST1H3A;HIST3H3 Histone H3;Histone H3.2;Histone H3.1;Histone H3.1t 0 2 ; K(1)SAPATGGVK(0.5)K(0.5)PHR;K(1)SAPATGGVK(0.5)K(0.5)PHR 57.267 0.017805 4390100 3110.76 3088.86 5143.2 4108.4 5603.6 5242.7 4500.2 4513.5 4345.3 2894.49 FALSE TRUE FALSE 3072.844861 3132.345052 5232.715239 4583.432539 5317.627382 4907.70839 4882.446876 4644.091001 3956.645485 2819.290733 1.089935431 1.111040098 1.856039598 1.625739583 1.886157863 1.740759948 1.731799711 1.647255087 1.403418753 1 11.46111654 -9.797719217 6.911680421 1.047208853 1.747711091 0.810131392 0.137998985 0.027725046 3.820839681 0.012681865 0.01685503 1.59E-10 9.797719217 0.700502238 K(ac)GSK(ac)K(ac)AVTK ddPTM_HeLa_Romidepsin_16h_R1 4 KGSKKAVTK 9 3 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 3 ;;; K(1)GSK(1)K(1)AVTK;K(1)GSK(1)K(1)AVTK;K(1)GSK(1)K(1)AVTK;K(1)GSK(1)K(1)AVTK 121.29 0.014617 4707314200 738.1 5229.48 1324.4 11261.4 23180.5 34699.9 27072 21530.5 1086.63 1169.64 FALSE TRUE FALSE 729.1037533 5303.100757 1347.450626 12563.49605 21997.51259 32482.68838 29371.495 22153.45105 989.4390913 1139.252584 0.639984287 4.654894648 1.182749677 11.02784073 19.30872301 28.51227974 25.78137229 19.44560088 0.868498439 1 10.15387193 -8.895143775 1.777231136 1.099822949 24.7584588 0.942577964 2.526423627 0.050943413 0.324829059 0.379763243 0.809245167 1.27E-09 8.895143775 23.65863585 up K(ac)STGGK(ac)APR ddPTM_HeLa_Romidepsin_16h_R1 1 KSTGGKAPR 9 2 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431;Q16695 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A;HIST3H3 Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1;Histone H3.1t 0 2 K(1)STGGK(1)APR 95.483 0.011647 205910000 0 0 596.91 576.1 3747.2 7065.7 5488.1 1501.8 86.261 96.745 FALSE TRUE FALSE 0 0 607.2989682 642.7113926 3555.966401 6614.224574 5954.259077 1545.252214 78.54560012 94.23155095 0 0 6.444751912 6.820554115 37.73647324 70.19118869 63.18753132 16.39845888 0.833538229 1 6.558138284 -8.709098833 3.098878607 1.069356457 51.66877895 0.731284399 13.31432623 0.085948314 1.679193171 1.859850336 3.868195052 1.95E-09 8.709098833 50.59942249 K(ac)YDEELEER ddPTM_HeLa_Romidepsin_16h_R1 1 KYDEELEER 9 1 E9PJ32;Q01995 E9PJ32 TAGLN Transgelin 0 1 K(1)YDEELEER 125.75 0.000204 0 1627.6 1411.8 1379.1 1261.3 2289.1 2240.4 1727.4 2191 2613.7 2701.4 FALSE TRUE FALSE 1607.762185 1431.675357 1403.102657 1407.137441 2172.278685 2097.245671 1874.125313 2254.393128 2379.924126 2631.217239 0.611033617 0.544111424 0.533252305 0.534785733 0.825579376 0.797062911 0.712265519 0.856787154 0.90449549 1 11.36151465 -12.26352144 1.016161099 0.998135442 0.671325034 0.456112365 0.118655123 0.361049376 0.674079876 0.083503214 0.023273679 5.45E-13 12.26352144 -0.326810408 K(ac)YEEIDNAPEER ddPTM_HeLa_Romidepsin_16h_R1 2 KYEEIDNAPEER 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 1 ; K(1)YEEIDNAPEER;K(1)YEEIDNAPEER 187.85 1.40E-07 3575900 2070.59 1543.66 2003.6 1711.34 3989.4 3905.1 3404.5 3667.7 3293.9 3019.8 FALSE TRUE FALSE 2045.352853 1565.391686 2038.471818 1909.213183 3785.806031 3655.576713 3693.678145 3773.819113 2999.285334 2941.345161 0.695380087 0.532202649 0.693040669 0.649095254 1.28710023 1.242824801 1.255778545 1.283024911 1.019698529 1 11.52226038 -8.751650821 24.99173373 0.799272929 1.264627891 0.743681294 0.143608828 100.1155275 255608.9161 0.025072802 0.049655237 1.77E-09 8.751650821 0.465354962 K(ac)YVIYIER ddPTM_HeLa_Romidepsin_16h_R1 2 KYVIYIER 8 1 J3KS10;J3QRI7;J3QQQ9;J3QQV1;E5RIT6;J3QRC4;Q9UNX3;P61254 J3KS10 RPL26;RPL26L1 60S ribosomal protein L26-like 1;60S ribosomal protein L26 0 1 ; K(1)YVIYIER;K(1)YVIYIER 102.61 0.0053097 11536700 3666.4 3516.9 4034.6 3407.8 3893.6 4316.4 4030.8 3985.9 3913.6 3301 FALSE TRUE FALSE 3621.712507 3566.411011 4104.820521 3801.82587 3694.895063 4040.595971 4373.176051 4101.225728 3563.557814 3215.239544 1.12642074 1.109220934 1.276676423 1.182439385 1.149181892 1.25670138 1.360140043 1.275558375 1.108333536 1 11.65071051 -4.000000159 0.071706018 0.742985589 2.256644939 0.639952955 0.06089257 66.65944917 0.355685744 1.30895915 10.20146765 1.00E-04 4.000000159 1.51365935 KAAVLSDS(ph)EDEEKAS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 KAAVLSDSEDEEKASAK 17 2 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 2 0 KAAVLS(0.105)DS(0.914)EDEEKAS(0.981)AK 75.611 0.02365 35473000 4111.7 3586.5 3500.5 4111 3733.1 3699.3 3539.9 3947.1 4148.4 4505.2 TRUE FALSE FALSE 4061.585019 3636.990841 3561.424734 4586.333163 3542.585977 3462.926669 3840.579018 4061.303111 3777.356714 4388.154255 0.925579363 0.82882019 0.811599713 1.045162247 0.807306619 0.789153359 0.875215135 0.92551512 0.860807641 1 12.09939853 -11.05817408 0.79859777 0.990086829 0.867806709 0 0.082435796 0.471554086 0.654133112 0.024352732 0.017201366 8.75E-12 11.05817408 -0.122280119 KADGYNQPDSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 KADGYNQPDSKR 12 2 B4DT28;O43390-3;O43390;O43390-4;O43390-2;O60506-2;O60506 B4DT28;O60506-2 HNRNPR;SYNCRIP Heterogeneous nuclear ribonucleoprotein R;Heterogeneous nuclear ribonucleoprotein Q 0 1 KADGYNQPDSK(1)R 96.371 0.021375 591200 374.72 430.24 266.53 218.17 225.32 199.27 282.86 224.53 494.68 207.79 FALSE TRUE FALSE 370.1527685 436.29693 271.1688428 243.3958419 213.8210796 186.5372901 306.8861213 231.0264213 450.4345819 202.3915858 1.828894057 2.15570686 1.339822709 1.20259862 1.056472179 0.921665243 1.516298813 1.141482341 2.225559822 1 7.661005503 -9.365750238 4.504020419 1.470509404 1.167723461 0.223654723 0.39905961 0.422830962 14.26758496 0.065286983 0.101082002 4.31E-10 9.365750238 -0.302785943 KADIDLTK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 KADIDLTKR 9 2 P62269 P62269 RPS18 40S ribosomal protein S18 0 1 KADIDLTK(1)R 91.636 0.025895 1017600 230.41 215.3 324.64 184.6 513.02 538.57 511.68 408.72 537.27 287.79 FALSE TRUE FALSE 227.6016743 218.3309991 330.290223 205.9443206 486.8386751 504.1571152 555.1420864 420.5456683 489.2152256 280.3131743 0.811954967 0.778882404 1.178290046 0.734693691 1.736767015 1.798549484 1.980435232 1.500270793 1.745245213 1 8.13089574 -8.752722079 24.86305644 0.909332504 1.773361153 0.537792404 0.30915026 42.37711744 120864.9268 0.02251331 0.044472706 1.77E-09 8.752722079 0.864028649 KADTT(ph)TPTTSAITASR ddPTM_HeLa_Romidepsin_16h_R1 2 KADTTTPTTSAITASR 16 1 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 0 KADT(0.159)T(0.796)T(0.04)PT(0.003)T(0.001)S(0.001)AITASR;KADT(0.1)T(0.837)T(0.045)PT(0.006)T(0.002)S(0.009)AITAS(0.001)R ; 103.45 0.0019358 60442000 5165.7 4320.5 4597.9 4000.9 6886.9 7738.3 6994.4 7425.2 4923.8 4307.4 TRUE FALSE FALSE 5102.738461 4381.324112 4677.924521 4463.502883 6535.435794 7243.847604 7588.504161 7640.036447 4483.402996 4195.493127 1.216242837 1.044293002 1.114988007 1.063880394 1.557727685 1.726578351 1.808727587 1.821010359 1.068623606 1 12.03462468 -8.596635054 2.582274617 1.096687946 1.787049084 0.961875263 0.063772753 0.050833656 0.683330438 0.013155448 0.02986259 2.53E-09 8.596635054 0.690361138 KADTTTPTPTAILAPGS(ph)PAS(ph)PPGSLEPK ddPTM_HeLa_Romidepsin_16h_R1 2 KADTTTPTPTAILAPGSPASPPGSLEPK 28 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;H0YDJ7;U3KPW0;E9PIQ3;U3KQA6;A0A0G2JHL0;A0A140T9F7;A0A140T9V2 H0Y6K2 BRD2 Bromodomain-containing protein 2 2 0 KADTTTPTPTAILAPGS(0.993)PAS(0.994)PPGS(0.012)LEPK;KADTTTPTPTAILAPGS(1)PAS(1)PPGSLEPK ; 114.9 7.36E-10 45400000 5721.22 5458.16 5979.9 5751.1 6866.4 5879.72 5914.4 6289.67 5344.71 5514.75 TRUE FALSE FALSE 5651.48757 5535.00012 6083.977651 6416.069242 6515.981986 5504.024868 6416.768988 6471.651678 4866.665752 5371.476 1.052129353 1.030443051 1.132645413 1.194470429 1.213071042 1.024676433 1.1946007 1.204818132 0.906020198 1 12.39110286 -9.704863656 3.513835685 1.025154929 1.162836804 0.601467507 0.064044821 0.120062058 3.022299399 0.008525198 0.012070335 1.97E-10 9.704863656 0.137681874 KADTTTPTPTAILAPGS(ph)PASPPGSLEPK ddPTM_HeLa_Romidepsin_16h_R1 2 KADTTTPTPTAILAPGSPASPPGSLEPK 28 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;H0YDJ7;U3KPW0;E9PIQ3;U3KQA6;A0A0G2JHL0;A0A140T9F7;A0A140T9V2 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 0 KADTTTPTPTAILAPGS(0.966)PAS(0.033)PPGSLEPK;KADTTTPTPTAILAPGS(0.992)PAS(0.008)PPGSLEPK ; 123.68 1.00E-10 156991000 4284.5 3926.2 4689.1 5896.1 6821.9 6653.1 6534.6 7225.5 3853.4 4309.4 TRUE FALSE FALSE 4232.278866 3981.473147 4770.711819 6577.834824 6473.752987 6227.988382 7089.648761 7434.558443 3508.742253 4197.441167 1.008299747 0.948547696 1.136576221 1.567105902 1.542309405 1.48375835 1.689040651 1.771212066 0.835924106 1 12.03529439 -9.31434129 2.676486133 0.999756306 1.615128793 0.922921189 0.091148823 0.048161479 0.679520629 0.012232372 0.020127544 4.85E-10 9.31434129 0.615372487 KAEAAVVAVAEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 KAEAAVVAVAEKR 13 2 A0A087WYP2;Q8IZQ5 A0A087WYP2 C11orf31;SELH Selenoprotein H 0 1 ; KAEAAVVAVAEK(1)R;KAEAAVVAVAEK(1)R 137.19 0.00019665 38646000 9938.8 10012.9 9806.9 12363.8 16559.4 14082.4 13512.5 13664.4 10115.3 8548.6 FALSE TRUE FALSE 9817.662083 10153.86187 9977.584981 13793.36073 15714.31203 13182.58009 14660.25141 14059.75786 9210.562234 8326.50614 1.179085431 1.219462485 1.198291914 1.656560447 1.887263609 1.583206674 1.760672624 1.688554313 1.106173716 1 13.02349554 -9.298728503 2.721286006 1.098835126 1.730444205 0.912019547 0.089515827 0.062389808 0.914974071 0.0163825 0.027078836 5.03E-10 9.298728503 0.631609079 KAEAGAGS(ph)ATEFQFR ddPTM_HeLa_Romidepsin_16h_R1 1 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 0 KAEAGAGS(0.578)AT(0.422)EFQFR 122.14 0.0051549 7482300 1395.5 1422.5 1148.9 1353.2 1275.2 1023.3 1119.1 1110.1 1423.3 1189.4 TRUE FALSE FALSE 1378.491109 1442.525992 1168.896123 1509.663351 1210.121786 957.9144325 1214.156326 1142.218992 1295.996483 1158.499217 1.189893864 1.245167862 1.008974461 1.303119872 1.044559865 0.826858075 1.048042423 0.985947142 1.11868568 1 10.17804135 -8.519108812 24.99498489 1.113833963 0.958500261 0.385217035 0.104374747 155.5814195 1031515.626 0.016646811 0.033899313 3.03E-09 8.519108812 -0.155333702 KAEAGAGSAT(ph)EFQFR ddPTM_HeLa_Romidepsin_16h_R1 1 KAEAGAGSATEFQFR 15 1 P46783;Q9NQ39 P46783 RPS10;RPS10P5 40S ribosomal protein S10;Putative 40S ribosomal protein S10-like 1 0 KAEAGAGS(0.467)AT(0.533)EFQFR 120.54 0.0087038 10644000 944.63 918.91 1007 786.85 949.11 857.65 753.72 766.52 930.87 839.96 TRUE FALSE FALSE 933.1164862 931.8464391 1024.526413 877.8292992 900.6733751 802.8489329 817.740958 788.6980468 847.6106558 818.1377181 1.14053718 1.138984817 1.252266446 1.07296031 1.100882352 0.9813127 0.999515045 0.96401624 1.036024421 1 9.676199904 -8.258450956 23.48236703 1.090176205 0.983404683 0.414933025 0.065807872 117.757629 925294.7453 0.011508948 0.027951808 5.52E-09 8.258450956 -0.106771522 KAEDS(ph)DS(ph)EPEPEDNVR ddPTM_HeLa_Romidepsin_16h_R1 2 KAEDSDSEPEPEDNVR 16 1 Q9H0D6-2;Q9H0D6 Q9H0D6-2 XRN2 5-3 exoribonuclease 2 2 0 KAEDS(1)DS(1)EPEPEDNVR;KAEDS(1)DS(1)EPEPEDNVR ; 79.471 0.023966 145375000 6517 6120.9 5566.1 5648.7 6261 5484 5342.4 6294.8 6367.9 6170.5 TRUE FALSE FALSE 6437.568297 6207.070191 5662.975636 6301.829272 5941.477807 5133.590099 5796.183323 6476.930106 5798.339075 6010.18952 1.071109035 1.032757814 0.942229129 1.048524219 0.988567463 0.85414779 0.96439277 1.077658214 0.964751453 1 12.55319477 -9.792502928 20.23826189 1.034456091 0.976463363 0.053156143 0.062650409 34.03157104 22171.44854 0.009989806 0.013132082 1.61E-10 9.792502928 -0.057992728 KAEDS(ph)DSEPEPEDNVR ddPTM_HeLa_Romidepsin_16h_R1 1 KAEDSDSEPEPEDNVR 16 1 Q9H0D6-2;Q9H0D6 Q9H0D6-2 XRN2 5-3 exoribonuclease 2 1 0 KAEDS(0.999)DS(0.001)EPEPEDNVR 98.188 0.0019345 37470000 4510.9 4501.3 4404.4 4814.8 4754.1 4878.9 4085.2 4723.5 5090.3 4791.3 TRUE FALSE FALSE 4455.919416 4564.66942 4481.056734 5371.50983 4511.480537 4567.154036 4432.196786 4860.16702 4635.010819 4666.821335 0.954808229 0.978111029 0.960194619 1.150999673 0.966713789 0.978643429 0.949724977 1.041429845 0.993183687 1 12.18822452 KAEEAGGTRLEPLK(ac)PLK ddPTM_HeLa_Romidepsin_16h_R1 1 KAEEAGGTRLEPLKPLK 17 3 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 0 1 K(0.005)AEEAGGTRLEPLK(0.995)PLK 47.537 0.021502 1964100 1047.3 1139.6 734.87 1694.6 1053.7 797.58 935.02 735.79 1066.5 852.72 FALSE TRUE FALSE 1034.535105 1155.643319 747.6601041 1890.537625 999.9257571 746.6172121 1014.440575 757.0789228 971.1095689 830.5662115 1.245578125 1.391392164 0.900181218 2.276203389 1.203908542 0.898925578 1.221384354 0.911521456 1.169213912 1 9.697951372 -5.94054572 17.36311714 1.183171111 1.227184665 0 0.388880353 0 0 0.049622168 0 1.15E-06 5.94054572 0.044013555 KAEEDAALQAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 KAEEDAALQAKK 12 2 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;A0A2R8Y4M7;H0YA99;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 0 1 ; KAEEDAALQAK(1)K;KAEEDAALQAK(1)K 159.52 0.00060393 5740900 8871.7 8351.1 8958.2 10245.6 9900.3 9423.9 8627.5 8537.8 8802.3 8479.5 FALSE TRUE FALSE 8763.568308 8468.667005 9114.113713 11430.24448 9395.050748 8821.743204 9360.319635 8784.827773 8015.000242 8259.201368 1.061067277 1.025361488 1.103510292 1.383940646 1.137525328 1.068110924 1.133320187 1.063641311 0.97043284 1 13.01178657 -9.5950276 5.301132207 1.030028519 1.158366386 0.37145295 0.086515954 0.181151074 9.355026368 0.013772784 0.019639875 2.54E-10 9.5950276 0.128337866 KAEENAS(ph)QEEEEAAEDEGGEEDLASELR ddPTM_HeLa_Romidepsin_16h_R1 1 KAEENASQEEEEAAEDEGGEEDLASELR 28 1 Q9H4I2;H0Y6F5;Q9H4I2-2 Q9H4I2 ZHX3 Zinc fingers and homeoboxes protein 3 1 0 KAEENAS(1)QEEEEAAEDEGGEEDLASELR 100.23 8.98E-09 3157600 1149.4 1284.8 1080.6 972.08 836.83 1040.4 658.83 958.29 1305 1207.8 TRUE FALSE FALSE 1135.390671 1302.887448 1099.40739 1084.476463 794.1234425 973.9217977 714.7910038 986.0166092 1188.277532 1176.421182 0.965122601 1.107500841 0.934535527 0.921843707 0.675033274 0.827868295 0.60759787 0.838149316 1.01007832 1 10.20018895 -8.915846614 3.557412169 0.989614661 0.734439443 0.727760052 0.076499126 0.086710878 2.17792199 0.010350499 0.019449009 1.21E-09 8.915846614 -0.255175217 KAEGAATEEEGT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KAEGAATEEEGTPK 14 1 P80723;P80723-2;U3KQP0 P80723 BASP1 Brain acid soluble protein 1 1 0 KAEGAATEEEGT(1)PK;KAEGAAT(0.006)EEEGT(0.994)PK ; 137.91 0.0029665 15942100 6600.75 6823.12 7119.97 4172.94 6316.63 7749.4 7664.06 5127.87 7548.63 7497.03 TRUE FALSE FALSE 6520.29752 6919.176062 7243.890091 4655.434957 5994.268801 7254.23835 8315.045065 5276.236828 6873.461627 7302.25608 0.892915484 0.947539498 0.992007129 0.637533785 0.820879018 0.993424261 1.138695353 0.722548863 0.941279182 1 12.83412655 -12.24742393 0.630228332 1.013150402 0.896223454 0.042651692 0.136304622 2.515318554 1.485765494 0.166660372 0.03043979 5.66E-13 12.24742393 -0.116926948 KAEGEPQEES(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 5 KAEGEPQEESPLK 13 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK;KAEGEPQEES(1)PLK ;;;; 137.27 0.00072134 1439876500 36278 37428.5 36933 23524.7 32138.7 31687.8 27171 31416.5 34452.3 35830 TRUE FALSE FALSE 35835.82978 37955.41941 37575.80337 26244.7365 30498.54221 29663.05185 29478.90406 32325.48686 31370.8 34899.13143 1.026840162 1.087574901 1.07669738 0.752016896 0.87390548 0.849965332 0.84468876 0.926254767 0.898899162 1 15.09090351 -9.270859742 24.99546497 1.024170789 0.850502959 0.644640019 0.062516466 242.4136894 643206.2012 0.00755662 0.011635414 5.36E-10 9.270859742 -0.17366783 KAEPSEVDMNS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KAEPSEVDMNSPK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 KAEPSEVDMNS(1)PK 111.78 0.0056786 91983000 9660.9 9052.1 9330.8 8127 7234.8 7844.6 7546.4 7662.4 10141 9622.5 TRUE FALSE FALSE 9543.149235 9179.535701 9493.19866 9066.681979 6865.581159 7343.355377 8187.391028 7884.099455 9233.963561 9372.506063 1.018206782 0.979411018 1.012877303 0.967370084 0.732523523 0.783499667 0.873554092 0.841194383 0.985218201 1 13.19421914 -8.88847594 5.823272071 1.005738304 0.811489754 0.862209564 0.036529176 0.053408846 2.551506639 0.005474427 0.010031931 1.29E-09 8.88847594 -0.19424855 KAEQGS(ph)EEEGEGEEEEEEGGESK ddPTM_HeLa_Romidepsin_16h_R1 4 KAEQGSEEEGEGEEEEEEGGESK 23 1 Q8NE71;Q5STZ8 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK;KAEQGS(1)EEEGEGEEEEEEGGESK ;;; 79.304 0.00014743 379976800 13791.64 13059.88 13875.93 8488.47 12765.95 14355.94 13113.16 13096.5 15179.26 15322.4 TRUE FALSE FALSE 13623.54219 13243.73733 14117.43474 9469.946841 12114.45594 13438.64177 14226.99148 13475.42656 13821.58897 14924.32184 0.912841624 0.887392906 0.945934756 0.634531133 0.811725723 0.900452423 0.953275575 0.902917178 0.926111693 1 13.86537776 -10.99009959 0.734233783 0.987378631 0.85660314 0.168108541 0.087802081 0.602892045 0.717623859 0.03214327 0.0230535 1.02E-11 10.99009959 -0.130775491 KAES(ph)TESIGSSEK ddPTM_HeLa_Romidepsin_16h_R1 1 KAESTESIGSSEK 13 1 Q9BZI7-2;Q9BZI7;A0A1B0GVA2 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 1 0 KAES(0.759)T(0.238)ES(0.002)IGS(0.001)S(0.001)EK 87.157 0.0079099 4247300 3652.7 3351.6 3790.5 2459.5 3662.6 4714.7 4507 4085.6 4066.7 4020.1 TRUE FALSE FALSE 3608.179487 3398.783913 3856.472062 2743.878962 3475.683855 4413.445886 4889.824468 4203.81039 3702.964167 3915.657222 0.921474808 0.867998326 0.984885 0.700745445 0.887637415 1.127127743 1.248787672 1.073589988 0.94568139 1 11.93503876 -8.183343008 5.286623 0.932118316 1.165198949 0.596776298 0.091263431 0.13226743 6.537705809 0.013739554 0.035861131 6.56E-09 8.183343008 0.233080632 KAEST(ph)ESIGSSEK ddPTM_HeLa_Romidepsin_16h_R1 1 KAESTESIGSSEK 13 1 Q9BZI7-2;Q9BZI7;A0A1B0GVA2 Q9BZI7-2 UPF3B Regulator of nonsense transcripts 3B 1 0 KAES(0.015)T(0.547)ES(0.438)IGS(0.001)SEK 108.66 0.01892 2584000 887.2 1178.2 857.1 391.93 1128 1063 1125.1 981.96 1060.2 1018.1 TRUE FALSE FALSE 876.3864651 1194.786731 872.017466 437.2467907 1070.433951 995.0777307 1220.665966 1010.371463 965.3730567 991.6496152 0.883766253 1.204847672 0.879360464 0.440928715 1.079447755 1.003456983 1.230944829 1.018879499 0.973502174 1 9.953686645 -8.570643072 24.99998677 0.921755867 1.089481618 0.182489523 0.188619422 167.9329905 87895.97861 0.027506742 0.055013499 2.69E-09 8.570643072 0.167725751 KALEVEESNS(ph)EDEASFK ddPTM_HeLa_Romidepsin_16h_R1 1 KALEVEESNSEDEASFK 17 1 Q03111 Q03111 MLLT1 Protein ENL 1 0 KALEVEES(0.164)NS(0.825)EDEAS(0.011)FK 54.768 0.02443 6939300 3232.1 2742.9 2803.2 2613.3 2164.5 2373.7 1777.1 2161.7 3183.1 3367.4 TRUE FALSE FALSE 3192.705922 2781.514618 2851.98852 2915.462042 2054.037488 2222.028231 1928.04683 2224.245379 2898.395564 3279.914463 0.973411337 0.848044865 0.869531371 0.888883559 0.626247273 0.677465299 0.587834485 0.678141276 0.883680229 1 11.67944248 -9.083810267 0.687053128 0.992441493 0.602800449 0.786101064 0.064926232 0.170181663 0.151481727 0.010840464 0.032429335 8.24E-10 9.083810267 -0.389641043 KALGITLIK ddPTM_HeLa_Romidepsin_16h_R1 1 KALGITLIK 9 1 C9K0P5;C9JFA7;Q8N335 C9K0P5 GPD1L Glycerol-3-phosphate dehydrogenase 1-like protein 0 0 90.05 0.011813 0 424.86 206.13 409 500.34 225.01 282.81 273.78 422.33 301.99 382.63 FALSE FALSE TRUE 419.6816429 209.0319036 416.1184734 558.191665 213.5269001 264.7393537 297.0348664 434.5494522 274.9792581 372.6892174 1.126090113 0.560874567 1.116529414 1.497740312 0.572935545 0.710348841 0.797004186 1.16598343 0.73782456 1 8.54182927 -8.715235846 24.99991969 1.051511674 0.803298298 0.09575054 0.272759159 167.36012 90554.80706 0.036225797 0.0724514 1.93E-09 8.715235846 -0.248213376 KALVVPEPEPDS(ph)DSNQER ddPTM_HeLa_Romidepsin_16h_R1 3 KALVVPEPEPDSDSNQER 18 1 C9J0A5;C9JXC9;Q5VTR2 C9J0A5 RNF20 E3 ubiquitin-protein ligase BRE1A 1 0 KALVVPEPEPDS(0.971)DS(0.029)NQER;KALVVPEPEPDS(0.962)DS(0.038)NQER;KALVVPEPEPDS(0.821)DS(0.179)NQER ;; 133.04 0.00047732 152077000 7754.6 6944.1 7293.8 5423.3 7503.7 7374.6 6406.6 6841.8 7935 7760.7 TRUE FALSE FALSE 7660.083952 7041.859222 7420.745529 6050.367463 7120.758189 6903.38686 6950.776444 7039.756688 7225.273726 7559.075895 1.013362488 0.931576732 0.981700096 0.800410996 0.942014379 0.913258043 0.919527273 0.931298585 0.955840876 1 12.88399416 -9.949542366 1.70161648 1.006375281 0.907889999 0.335391839 0.045921576 0.19732829 1.137583704 0.007158037 0.009609984 1.12E-10 9.949542366 -0.098485282 KANNSQEPS(ph)PQLASSVASTR ddPTM_HeLa_Romidepsin_16h_R1 2 KANNSQEPSPQLASSVASTR 20 1 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 KANNSQEPS(0.989)PQLAS(0.004)S(0.004)VAS(0.002)T(0.002)R;KANNSQEPS(1)PQLASSVASTR ; 102.78 0.00017844 87157000 2897.7 3120.7 2775.1 3383.2 4829.8 4503.7 3994.5 4896.8 3604.9 3069.1 TRUE FALSE FALSE 2862.381718 3164.633297 2823.399451 3774.381502 4583.317284 4215.928105 4333.79273 5038.481182 3282.468715 2989.36434 0.957521865 1.058630845 0.944481545 1.262603374 1.533207988 1.410309225 1.449737214 1.685469086 1.098049064 1 11.54562303 -9.019101235 2.660876847 0.983691077 1.508799733 0.89011304 0.083578689 0.052220939 0.741636441 0.011031928 0.020468887 9.57E-10 9.019101235 0.525108655 KANSSVGK(ac)WQDR ddPTM_HeLa_Romidepsin_16h_R1 1 KANSSVGKWQDR 12 2 Q6UN15-5;Q6UN15;A0A0B4J203;Q6UN15-4 Q6UN15-5 FIP1L1 Pre-mRNA 3-end-processing factor FIP1 0 1 KANSSVGK(1)WQDR 164.22 0.00046742 2725000 1010 941.99 781.37 852.11 1172.6 1092.9 1721.5 988.51 1412.9 969.01 FALSE TRUE FALSE 997.6897315 955.2513599 794.9694171 950.6349675 1112.757846 1023.067217 1867.724167 1017.110977 1286.526685 943.8349805 1.057059499 1.012095737 0.842275857 1.007204635 1.178975 1.083947129 1.978867287 1.077636449 1.363084344 1 9.882390832 -7.963416357 23.71644584 1.023578189 1.52904273 0.360069188 0.240929402 53.16445451 34464.50405 0.025854426 0.077562775 1.09E-08 7.963416357 0.505464541 KAPAGPSLEETSVS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 KAPAGPSLEETSVSSPK 17 1 A0A087WXZ7;K7EIX2;Q6AI08 A0A087WXZ7 HEATR6 HEAT repeat-containing protein 6 1 0 KAPAGPSLEET(0.002)S(0.008)VS(0.495)S(0.495)PK;KAPAGPSLEET(0.026)S(0.233)VS(0.639)S(0.103)PK ; 72.644 0.0083414 23554000 7738 6652.8 7470.4 6117.8 7764.8 8373.9 8189.7 9175.6 7750.1 7371.9 TRUE FALSE FALSE 7643.68628 6746.458293 7600.419178 6825.168821 7368.533282 7838.834816 8885.332914 9441.081509 7056.911646 7180.376975 1.064524371 0.939568816 1.058498628 0.95053071 1.026204238 1.091702405 1.237446578 1.314844825 0.982805174 1 12.80984387 -7.746575341 1.947517598 1.019822593 1.316689335 0.875442628 0.040886553 0.09728859 0.665207196 0.005983065 0.036686777 1.79E-08 7.746575341 0.296866742 KAPAGPSLEETSVSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KAPAGPSLEETSVSSPK 17 1 A0A087WXZ7;K7EIX2;Q6AI08 A0A087WXZ7 HEATR6 HEAT repeat-containing protein 6 1 0 KAPAGPSLEET(0.001)S(0.013)VS(0.055)S(0.932)PK;KAPAGPSLEETS(0.001)VS(0.212)S(0.787)PK ; 131.13 0.00058425 154743000 14363.2 14957.2 14366.1 12620.5 16878.1 18275.7 15701.5 19170.7 15005.9 14923.3 TRUE FALSE FALSE 14188.13579 15167.76785 14616.13594 14079.74159 16016.74758 17107.94175 17035.18502 19725.37396 13663.73472 14535.59051 0.976096278 1.043491686 1.005541256 0.968639119 1.101898651 1.17696916 1.17196374 1.357039739 0.940019238 1 13.82730206 -7.065203387 0.584680273 0.988369604 1.65476715 0.903162598 0.038216428 0.813716649 0.161134776 0.006421714 0.384469059 8.61E-08 7.065203387 0.666397547 STS(ph)PVTDPSIPIR ddPTM_HeLa_Romidepsin_16h_R1 1 STSPVTDPSIPIR 13 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 0 ST(0.004)S(0.498)PVT(0.498)DPSIPIR 174.21 3.27E-05 34690000 6316.9 6467.6 5321.6 4655.9 3058.7 2603.6 2232.4 2571.1 6226.8 5885.6 TRUE FALSE FALSE 6239.907193 6558.651043 5414.220216 5194.237065 2902.603125 2437.238363 2422.02 2645.490722 5669.859413 5732.691264 1.088477803 1.144078887 0.944446503 0.906073051 0.50632469 0.425147326 0.422492663 0.46147448 0.989039729 1 12.48499687 -8.825426079 2.093146326 1.0462426 0.428325543 0.963718098 0.053607609 0.040677272 0.362889335 0.008681288 0.018376587 1.49E-09 8.825426079 -0.617917056 down SQQQPT(ph)PVTPK ddPTM_HeLa_Romidepsin_16h_R1 3 SQQQPTPVTPK 11 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 0 SQQQPT(0.999)PVT(0.001)PK;S(0.019)QQQPT(0.976)PVT(0.005)PK;SQQQPT(0.978)PVT(0.022)PK ;; 163.71 0.0017382 182704000 26628 24704.6 23323.2 18434.6 10737.4 7831.9 7120 7560.7 25599.9 24892.2 TRUE FALSE FALSE 26303.44769 25052.39201 23729.13051 20566.09519 10189.43041 7331.466866 7724.772622 7779.456926 23310.18083 24245.49706 1.084879705 1.033280198 0.97870258 0.848243909 0.420260735 0.30238468 0.318606486 0.320861928 0.961423095 1 14.56542921 -8.824088478 2.02247607 1.03765363 0.308026541 0.987123331 0.036516226 0.023701492 0.197307505 0.005845829 0.012489342 1.50E-09 8.824088478 -0.729627089 down KAPAPVT(ph)PPAPVQNK ddPTM_HeLa_Romidepsin_16h_R1 2 KAPAPVTPPAPVQNK 15 1 Q03468;P0DP91 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 0 KAPAPVT(1)PPAPVQNK;KAPAPVT(1)PPAPVQNK ; 99.663 0.0033249 22215000 7266.1 7258.1 6992.6 6492.9 5935.6 5370.1 4953.3 4589.7 8069.6 7859.4 TRUE FALSE FALSE 7177.537978 7360.279722 7114.30327 7243.639648 5632.684183 5026.967941 5374.033178 4722.495728 7347.834765 7655.211655 0.937601506 0.961473053 0.929341159 0.946236365 0.735797315 0.656672626 0.702009745 0.616899433 0.959847369 1 12.90222655 -8.693881292 2.660422142 0.966071394 0.663305084 0.962139801 0.027281397 0.040605206 0.583547329 0.004798036 0.010299855 2.02E-09 8.693881292 -0.30276631 KAPDFVFYAPR ddPTM_HeLa_Romidepsin_16h_R1 1 KAPDFVFYAPR 11 1 E7EQR4;P15311;P26038;A0A2R8Y7M3;A0A2R8Y5S7;P35241-4;P35241;P35241-5 E7EQR4;P26038;A0A2R8Y7M3 EZR;MSN;RDX Ezrin;Moesin;Radixin 0 0 84.821 0.029095 6648000 1433.6 962.98 1823.1 1628.6 2351.1 2454.3 1509.3 1220.8 1233 1028 FALSE FALSE TRUE 1416.126732 976.5368577 1854.830291 1816.906395 2231.114594 2297.478151 1637.499904 1256.121922 1122.717392 1001.292412 1.414298875 0.975276399 1.85243618 1.814561234 2.228234797 2.294512696 1.635386312 1.254500591 1.121268252 1 9.967647637 -9.749272195 24.80674279 1.184580235 1.873254282 0.581180284 0.296890975 124.8624962 254571.9153 0.05136876 0.072331062 1.78E-10 9.749272195 0.688674046 KAPEPPKTDK(ac)PGAAPPSTEER ddPTM_HeLa_Romidepsin_16h_R1 2 KAPEPPKTDKPGAAPPSTEER 21 3 Q7Z3Z5;Q93074-3;Q93074;Q93074-2 Q7Z3Z5 TNRC11;MED12 Mediator of RNA polymerase II transcription subunit 12 0 1 ; K(0.004)APEPPK(0.011)TDK(0.984)PGAAPPSTEER;K(0.004)APEPPK(0.014)TDK(0.983)PGAAPPSTEER 48.824 0.022646 4508200 2446 2184.56 2262.4 2458.2 2184.39 2471.7 1982.68 2303.5 2298.6 2205.1 FALSE TRUE FALSE 2416.187211 2215.314293 2301.776123 2742.42865 2072.912427 2313.766347 2151.08879 2370.148138 2093.007459 2147.811184 1.124953268 1.031428791 1.071684578 1.27684811 0.965127867 1.07726711 1.001526021 1.103517924 0.974483919 1 11.06865146 -6.921203525 19.25391342 1.065293649 2.362050592 0.017939721 0.087323971 1037.850242 287990.3869 0.011316756 7852.701133 1.20E-07 6.921203525 1.296756943 KAPLNIPGT(ph)PVLEDFPQNDDEKER ddPTM_HeLa_Romidepsin_16h_R1 1 KAPLNIPGTPVLEDFPQNDDEKER 24 2 Q15003;E9PHA2;C9JZP1;C9J470 Q15003 NCAPH Condensin complex subunit 2 1 0 KAPLNIPGT(1)PVLEDFPQNDDEKER 86.959 3.91E-05 40892000 2138.1 2043.7 2068.7 2434.7 2965.4 3577.5 2647.5 3707 2288.7 1919.8 TRUE FALSE FALSE 2112.040015 2072.471262 2104.704856 2716.21147 2814.064573 3348.909296 2872.378584 3814.256196 2083.99294 1869.923319 1.129479478 1.10831885 1.125556772 1.452579067 1.504909075 1.790934025 1.536094317 2.039792839 1.114480427 1 10.86876339 -8.465619607 0.538592742 1.034260758 2.012543533 0.872997943 0.116335147 0.330431242 0.133399418 0.024223127 0.162504773 3.42E-09 8.465619607 0.978282775 KAPPPPIS(ph)PTQLSDVSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 KAPPPPISPTQLSDVSSPR 19 1 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 0 KAPPPPIS(0.993)PT(0.007)QLSDVSSPR;KAPPPPIS(0.986)PT(0.013)QLSDVSSPR ; 138.77 0.0001294 70652000 5756.3 5909.3 5449 5914.3 5794.5 5363.8 5476.7 5662.9 6580.8 6000.2 TRUE FALSE FALSE 5686.140002 5992.491281 5543.837559 6598.139194 5498.785043 5021.070491 5941.890761 5826.747077 5992.196766 5844.313939 0.972935414 1.025354104 0.948586544 1.128984388 0.940877766 0.859137709 1.016696027 0.996994196 1.02530371 1 12.51281796 KAPPPPISPTQLSDVSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KAPPPPISPTQLSDVSSPR 19 1 Q9P0K7-3;Q9P0K7;Q9P0K7-2 Q9P0K7-3 RAI14 Ankycorbin 1 0 KAPPPPIS(0.002)PT(0.015)QLS(0.206)DVS(0.309)S(0.468)PR 109.68 2.70E-05 0 1111.3 935.73 964.09 811.95 1293.5 1164 1269.9 1342.5 1451.2 1268.1 TRUE FALSE FALSE 1097.755048 948.9032315 980.869582 905.8314793 1227.487868 1089.624157 1377.765274 1381.343119 1321.401037 1235.154579 0.888759242 0.76824654 0.794126985 0.733374992 0.993792914 0.882176349 1.115459795 1.118356473 1.069826449 1 10.27047589 -7.757022916 24.94362406 0.907185016 1.116908243 0.428727991 0.102875106 81.75060157 461698.4264 0.014721712 0.051490442 1.75E-08 7.757022916 0.209723227 KAPS(ph)SPPPPPPPLR ddPTM_HeLa_Romidepsin_16h_R1 1 KAPSSPPPPPPPLR 14 1 Q13796 Q13796 SHROOM2 Protein Shroom2 1 0 KAPS(0.5)S(0.5)PPPPPPPLR 65.234 0.0036584 0 1154.8 1134.1 969.19 1182.9 1737.2 2396.9 1923.4 2309.9 1126.5 1172.1 TRUE FALSE FALSE 1140.724853 1150.06589 986.0583454 1319.672464 1648.544202 2243.745826 2086.773548 2376.733312 1025.743019 1141.648673 0.999190802 1.007372861 0.863714353 1.155935705 1.444003081 1.965355786 1.827859654 2.081843012 0.898475199 1 10.15690303 -8.526572847 1.795487627 0.991051445 1.971582683 0.964358267 0.084130268 0.038304255 0.243658186 0.01081772 0.028986826 2.97E-09 8.526572847 0.980531238 (ac)AGGK(ac)AGK(ac)DSGK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 AGGKAGKDSGKAK 13 3 P0C0S5;A0A494C189;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;Q71UI9-5 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V;Histone H2A 0 3 ; AGGK(1)AGK(1)DSGK(1)AK;AGGK(1)AGK(1)DSGK(1)AK 67.08 4.12E-10 25741000 365.9 554.36 686.59 5402.5 14740.3 16014.2 14486.5 15813.9 587.53 240.858 FALSE TRUE FALSE 361.4402701 562.1642946 698.5398109 6027.16247 13988.04749 14990.9443 15716.98295 16271.45025 534.9798453 234.6004744 1.540662997 2.396262395 2.97757203 25.69117767 59.62497527 63.89988912 66.99467674 69.35813018 2.280386886 1 7.874062121 -8.894803601 1.927092277 1.274957316 67.18935866 0.997139464 1.593137665 0.011563061 0.086864747 0.252581924 0.526592164 1.27E-09 8.894803601 65.91440134 up KAS(ph)GS(ph)ENEGDYNPGR ddPTM_HeLa_Romidepsin_16h_R1 1 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 0 KAS(0.939)GS(0.967)ENEGDY(0.094)NPGR 99.069 0.0078251 4180600 1802.8 1623 1889.8 1467 2071.3 2128.9 1682 2117.2 2135.4 1781 TRUE FALSE FALSE 1780.82678 1645.848637 1922.691176 1636.621442 1965.593832 1992.870161 1824.869038 2178.457842 1944.404476 1734.729363 1.026573261 0.948763923 1.10835224 0.943444826 1.133083854 1.148807533 1.051961808 1.255791184 1.120869063 1 10.76049489 -4 0.381878274 1.006062104 4.147765442 0.398625235 0.072103727 31.44520042 0.380860752 0.014601144 74.10064519 1.00E-04 4 3.141703339 KAS(ph)PEAASTPR ddPTM_HeLa_Romidepsin_16h_R1 1 KASPEAASTPR 11 1 P29590-12;P29590-11;H3BT57;P29590-13;H3BUJ5;P29590-14;P29590-10;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;H3BVD2;H3BT29;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 KAS(0.992)PEAAS(0.008)TPR 106.79 0.024723 6216000 1480.7 1524.6 1752.5 1049.6 1496.8 1933.6 2175.7 744 1761.4 1666 TRUE FALSE FALSE 1462.652659 1546.063359 1783.001527 1170.959691 1420.412711 1810.0492 2360.503904 765.5264662 1603.855972 1622.71708 0.901360241 0.952762116 1.09877535 0.721604342 0.875329858 1.115443489 1.454661403 0.471755968 0.988376836 1 10.66419577 -8.258896998 24.79380206 0.94121233 1.058024396 0.012117989 0.24271895 518.936065 5060722.433 0.031071993 0.075301423 5.51E-09 8.258896998 0.116812065 KAS(ph)PEPEGEAAGK ddPTM_HeLa_Romidepsin_16h_R1 3 KASPEPEGEAAGK 13 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK;KAS(1)PEPEGEAAGK ;; 135.72 0.0024759 222425000 11287.5 10887.7 11397.4 10280.1 11298.9 12630.6 13580.3 6920.5 11964.4 10684.5 TRUE FALSE FALSE 11149.92361 11040.97733 11595.76697 11468.73353 10722.27497 11823.54542 14733.81034 7120.733749 10894.2741 10406.91515 1.071395649 1.060927006 1.114236717 1.10203008 1.030302911 1.136123938 1.415771161 0.68423098 1.046830299 1 13.34525486 -11.5653872 0.523551383 0.99597279 1.096367817 0.006571364 0.167578168 2.699264812 1.470804024 0.125850855 0.044749552 2.72E-12 11.5653872 0.100395027 KAS(ph)PEPPDSAEGALK ddPTM_HeLa_Romidepsin_16h_R1 3 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 KAS(0.969)PEPPDS(0.031)AEGALK;KAS(0.988)PEPPDS(0.012)AEGALK;KAS(1)PEPPDSAEGALK ;; 115.09 0.0011551 600627000 18121.3 16622.3 15805.3 14228.9 12925.1 11488.3 10640.5 10588.7 18882.2 18454.7 TRUE FALSE FALSE 17900.43063 16856.30918 16080.38462 15874.11237 12265.48392 10754.23471 11544.3038 10895.06733 17193.32874 17975.24423 0.995837964 0.937751329 0.894585042 0.88310969 0.682354229 0.598280311 0.642233488 0.606115121 0.956500425 1 14.13372375 -8.901943518 1.047896563 0.9956879 0.59818861 0.956897612 0.032879674 0.059858148 0.128739644 0.005108387 0.013753472 1.25E-09 8.901943518 -0.39749929 KASAISIK(ac)LGSSKPK ddPTM_HeLa_Romidepsin_16h_R1 2 KASAISIKLGSSKPK 15 3 Q8WW12;Q8WW12-2 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 0 1 ; KASAISIK(1)LGSSKPK;KASAISIK(1)LGSSKPK 144.88 2.97E-08 3921600 3769.4 3285.36 2565.81 3322.88 3383 2598.58 2880.7 2663.78 4171.1 3101 FALSE TRUE FALSE 3723.457103 3331.611384 2610.466847 3707.08702 3210.352886 2432.539125 3125.386586 2740.852272 3798.026369 3020.435573 1.232755016 1.103023489 0.864268343 1.22733524 1.062877459 0.805360375 1.03474698 0.907436098 1.257443265 1 11.5605409 -8.498572981 22.6498327 1.100619513 0.928801131 0.338373004 0.122890563 231.6646148 215880.2145 0.01793608 0.03984877 3.17E-09 8.498572981 -0.171818382 KASGS(ph)ENEGDYNPGR ddPTM_HeLa_Romidepsin_16h_R1 2 KASGSENEGDYNPGR 15 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 KAS(0.01)GS(0.99)ENEGDYNPGR;KASGS(0.999)ENEGDYNPGR ; 161.48 0.00029241 8222400 2775.7 2522.6 2381.01 1461.52 2478.8 1947.03 2254.1 2076.72 2975.3 2757.8 TRUE FALSE FALSE 2741.868701 2558.113229 2422.45048 1630.507819 2352.297586 1822.621067 2445.563198 2136.806617 2709.181716 2686.151958 1.020742215 0.952333773 0.901829278 0.607005056 0.875712775 0.678524929 0.910433674 0.795489849 1.008573513 1 11.39132521 -9.634816685 2.937294149 1.007078622 0.779927109 0.600120911 0.084700741 0.118276765 2.060973057 0.012464279 0.018160385 2.32E-10 9.634816685 -0.227151512 KASPEAAS(ph)TPRDPIDVDLDVSNTTTAQK ddPTM_HeLa_Romidepsin_16h_R1 1 KASPEAASTPRDPIDVDLDVSNTTTAQK 28 2 P29590-12;P29590-11;H3BT57;P29590-13;H3BUJ5 P29590-12 PML Protein PML 1 0 KAS(0.099)PEAAS(0.45)T(0.45)PRDPIDVDLDVSNTT(0.001)TAQK 50.055 0.0095729 11950000 1267.4 1051.2 1098.1 1139.8 1188.3 1000.5 1018.8 1244.4 972.97 1024.1 TRUE FALSE FALSE 1251.952441 1065.998821 1117.21197 1271.589039 1127.656617 936.571279 1105.336847 1280.404751 885.9451264 997.4937344 1.25509805 1.06867721 1.120019035 1.274783986 1.130489925 0.938924473 1.108114075 1.283621848 0.888171119 1 9.962163969 -6.164718131 20.41404681 1.125104145 1.130784183 0 0.132064013 0 0 0.016442001 0 6.84E-07 6.164718131 0.005680038 KASPEPPDS(ph)AEGALK ddPTM_HeLa_Romidepsin_16h_R1 1 KASPEPPDSAEGALK 15 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 KAS(0.072)PEPPDS(0.928)AEGALK 115.26 0.0059771 7519600 5966.9 5838.6 5943.5 5046.4 4199.1 4593.6 3411.1 3566.6 6642.3 6461.1 TRUE FALSE FALSE 5894.173128 5920.795964 6046.944124 5629.888512 3984.804258 4300.083785 3700.838749 3669.793944 6048.196052 6293.239691 0.936588056 0.940818443 0.96086347 0.894593054 0.633188064 0.683286192 0.588065755 0.583132715 0.961062402 1 12.61958718 -8.818388477 2.830055442 0.96571811 0.616885257 0.96389603 0.03118431 0.038645219 0.630363212 0.005563254 0.011150494 1.52E-09 8.818388477 -0.348832853 KASS(ph)PSPLTIGTPESQR ddPTM_HeLa_Romidepsin_16h_R1 3 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 0 KAS(0.137)S(0.575)PS(0.195)PLT(0.075)IGT(0.017)PESQR;KAS(0.042)S(0.607)PS(0.35)PLT(0.001)IGTPESQR;KAS(0.097)S(0.787)PS(0.097)PLT(0.018)IGTPESQR ;; 172.42 3.02E-06 101111900 7585.4 7669.7 6731.2 8376.5 5877.8 5978.4 5578.6 5853.8 8427.9 8044.7 TRUE FALSE FALSE 7492.946227 7777.674238 6848.353712 9345.030343 5577.833933 5596.399534 6052.446145 6023.170467 7674.087516 7835.697534 0.956257716 0.992595006 0.873994138 1.192622648 0.711849061 0.714218423 0.772419573 0.76868338 0.979375159 1 12.93584599 -8.728891438 24.99999603 0.984518035 0.742010485 0.724440898 0.07744125 74.39530011 57142.5473 0.010180937 0.020360718 1.87E-09 8.728891438 -0.24250755 KASSPS(ph)PLTIGTPESQR ddPTM_HeLa_Romidepsin_16h_R1 2 KASSPSPLTIGTPESQR 17 1 Q9NPI6-2;Q9NPI6 Q9NPI6-2 DCP1A mRNA-decapping enzyme 1A 1 0 KAS(0.004)S(0.01)PS(0.954)PLT(0.031)IGT(0.001)PESQR;KASS(0.025)PS(0.93)PLT(0.039)IGT(0.005)PESQR ; 107.92 0.00066782 53445100 6055.6 6511.1 5193.1 5891.2 4313.3 4267.4 3853.8 4152.9 6360.3 5401.9 TRUE FALSE FALSE 5981.792018 6602.763437 5283.483727 6572.368263 4093.176206 3994.726912 4181.141676 4273.057609 5791.418838 5261.557859 1.136886104 1.254906553 1.004167182 1.249129714 0.777939978 0.759228924 0.7946585 0.812127838 1.100704201 1 12.36127431 -8.742046874 24.99491259 1.088492369 0.784696514 0.786497943 0.085133291 99.02194913 127628.322 0.013479232 0.026926562 1.81E-09 8.742046874 -0.303795856 KASVVDPSTESSPAPQEGSEQPAS(ph)PASPLSSR ddPTM_HeLa_Romidepsin_16h_R1 2 KASVVDPSTESSPAPQEGSEQPASPASPLSSR 32 1 Q66K14;Q66K14-2 Q66K14 TBC1D9B TBC1 domain family member 9B 1 0 KASVVDPSTESS(0.01)PAPQEGS(0.042)EQPAS(0.614)PAS(0.265)PLS(0.02)S(0.049)R;KASVVDPS(0.004)T(0.003)ES(0.023)S(0.023)PAPQEGS(0.325)EQPAS(0.431)PAS(0.09)PLS(0.028)S(0.073)R ; 75.309 2.53E-06 66713000 4730.2 4386.7 3967.3 5053.5 4599.3 4631 3612.2 3642.6 4968.9 5103.3 TRUE FALSE FALSE 4672.546503 4448.456078 4036.349192 5637.809447 4364.580559 4335.094046 3919.020178 3747.992884 4524.469139 4970.71553 0.940014868 0.894932742 0.812025787 1.134204807 0.878058809 0.872126763 0.788421738 0.754014761 0.910224919 1 12.27923783 -5.777150695 0.414485513 0.971056443 1.34E-16 0.35805242 0.08377098 10.5152956 0.479463615 0.019249415 6.632690621 1.67E-06 5.777150695 -0.971056443 KAT(ph)S(ph)T(ph)STSGAGDVGK ddPTM_HeLa_Romidepsin_16h_R1 1 KATSTSTSGAGDVGK 15 1 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 3 0 KAT(1)S(0.998)T(0.393)S(0.313)T(0.251)S(0.044)GAGDVGK 80.632 0.012474 6073600 1550.6 1637.3 1148.1 1566.8 647.95 806.4 617.18 1194.4 1265.4 1772.2 TRUE FALSE FALSE 1531.700691 1660.349952 1168.082199 1747.960788 614.8826937 754.8736425 669.6032538 1228.95808 1152.219455 1726.157989 0.887346756 0.961876006 0.676694837 1.012630825 0.356214609 0.437314341 0.387915393 0.711961528 0.667505212 1 10.7533488 -8.763258165 24.99999985 0.928425379 0.464674777 0.608115157 0.150340485 16.7779284 230624.9742 0.018086484 0.034045209 1.72E-09 8.763258165 -0.463750602 KAT(ph)VLMR ddPTM_HeLa_Romidepsin_16h_R1 1 KATVLMR 7 1 Q969T7-2 Q969T7-2 1 0 KAT(1)VLMR 75.043 0.029921 38655000 3962.6 3034.8 3371.2 3532 3032.9 3351.9 2719.1 3222.6 4033.9 3750.8 TRUE FALSE FALSE 3914.302307 3077.523994 3429.874322 3940.386459 2878.119796 3137.724408 2950.060286 3315.840847 3673.097881 3653.353675 1.071427147 0.842383264 0.938828985 1.07856693 0.787802127 0.858861388 0.807493757 0.907615616 1.005404406 1 11.83500571 -9.181855097 0.698953256 1.029188445 0.835977429 0.326142699 0.082581408 0.516035168 0.48530353 0.017560015 0.047557903 6.58E-10 9.181855097 -0.193211015 KATATISAK(ac)PQITNPK ddPTM_HeLa_Romidepsin_16h_R1 1 KATATISAKPQITNPK 16 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 1 KATATISAK(1)PQITNPK 91.592 0.030375 966150 487.58 441.33 516.21 619.4 439.78 546.68 491.88 580.81 562.39 433.46 FALSE TRUE FALSE 481.6371874 447.5430553 525.1944185 691.0179424 417.3363856 511.7489123 533.6602749 597.614821 512.0884299 422.1986467 1.140783352 1.060029583 1.243950976 1.636712831 0.988483475 1.212104578 1.264002808 1.415482559 1.212908743 1 8.721778144 -10.47677799 0.542383339 1.017014326 1.293715838 0.134572879 0.17361341 0.715004304 0.497056386 0.063911112 0.06328603 3.34E-11 10.47677799 0.276701512 KAVLFCLSEDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KAVLFCLSEDKK 12 2 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;E9PS23;E9PLJ3 E9PP50 CFL1 Cofilin-1 0 1 KAVLFCLSEDK(1)K 98.337 0.017514 255210 0 174.03 135.84 0 126.38 222.89 255.53 167.16 112.26 199.39 FALSE TRUE FALSE 0 176.4799989 138.2042382 0 119.930357 208.6480483 277.2347118 171.9965109 102.2191844 194.2098191 0 0.908707911 0.71162333 0 0.617529832 1.074343457 1.427501005 0.885622116 0.526333761 1 7.601472334 -8.256691321 4.162448336 0.523589872 1.171770386 0.399945356 0.333379987 0.19774567 8.405099845 0.06116844 0.154775437 5.54E-09 8.256691321 0.648180514 KAVS(ph)PLLLTTTNSSEGLSMGNYIGLINR ddPTM_HeLa_Romidepsin_16h_R1 1 KAVSPLLLTTTNSSEGLSMGNYIGLINR 28 1 C9JZT2;P19525-2;P19525 C9JZT2 EIF2AK2 "Interferon-induced, double-stranded RNA-activated protein kinase" 1 0 KAVS(0.712)PLLLT(0.094)T(0.094)T(0.094)NS(0.002)S(0.002)EGLS(0.002)MGNYIGLINR 51.259 0.018574 18584000 3074.3 3493.9 2809.4 3662.7 2484.7 2299.7 1515.8 1443.2 3082.5 3309.4 TRUE FALSE FALSE 3036.829249 3543.087216 2858.296429 4086.198608 2357.896487 2152.756592 1644.552014 1484.956715 2806.79348 3223.421311 0.94211366 1.099169756 0.886727534 1.267658867 0.731488769 0.667848346 0.510188354 0.460677203 0.870749806 1 11.65437705 -8.325312715 2.13205259 0.993033753 0.509705629 0.742876728 0.122451159 0.106908461 0.936358767 0.01578395 0.045567498 4.73E-09 8.325312715 -0.483328124 KAVTK(ac)AQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KAVTKAQKK 9 3 P06899;Q6DRA6;Q6DN03;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P58876;Q16778;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BD;HIST2H2BE;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 2 KAVTK(1)AQK(1)K 135.8 1.13E-07 0 513.79 535.95 10051 684.51 2242.5 5983 7848.7 468.9 741.4 358.66 FALSE TRUE FALSE 507.5277299 543.4951182 10225.93344 763.6562669 2128.056857 5600.705609 8515.368382 482.4668817 675.0873271 349.3419615 1.452810672 1.55576821 29.27198724 2.185984941 6.091615356 16.03215825 24.37545248 1.381073375 1.932454161 1 8.448496133 -9.938053033 24.99998229 1.228958321 13.23034845 0.319685456 8.386536236 56.30095229 22721.0635 1.264258618 1.661567104 1.15E-10 9.938053033 12.00139013 KAVVLPGGTATS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KAVVLPGGTATSPK 14 1 F8WCX2;Q8N1G0-2;Q8N1G0;H0Y5I5 F8WCX2 ZNF687 Zinc finger protein 687 1 0 KAVVLPGGT(0.003)AT(0.229)S(0.768)PK;KAVVLPGGT(0.001)AT(0.228)S(0.771)PK ; 108.96 0.0017955 73733000 12903.6 12926.7 12693.4 12340 10612.3 9909.7 8283.8 8573.2 13145.3 12707.9 TRUE FALSE FALSE 12746.32596 13108.68242 12914.3233 13766.80886 10070.71473 9276.502152 8987.425765 8821.252016 11969.55144 12377.74693 1.029777555 1.059052387 1.043350085 1.112222519 0.813614529 0.749449977 0.726095453 0.712670252 0.967021827 1 13.59546111 -8.614309596 4.66634371 1.026390557 0.736182525 0.931611897 0.038178366 0.037514014 1.434637874 0.005541459 0.011366385 2.43E-09 8.614309596 -0.290208032 KCANRHT(ph)RPK ddPTM_HeLa_Romidepsin_16h_R1 1 KCANRHTRPK 10 3 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 KCANRHT(1)RPK 55.258 0.0043072 0 1595.3 1946.6 1342.3 1065.7 1824.9 1542.7 1450.7 1482.3 1633.8 1934.7 TRUE FALSE FALSE 1575.85587 1974.004286 1365.662168 1188.921248 1731.768543 1444.126449 1573.922422 1525.188012 1487.668836 1884.436215 0.836247923 1.047530434 0.724705966 0.630916153 0.918984962 0.766344033 0.835221914 0.80936038 0.789450353 1 10.87991725 -12.18333546 0.318153133 1.07235818 0.789771325 0 0.120813787 3.093343636 0.43599816 0.322262464 0.056513981 6.56E-13 12.18333546 -0.282586855 KCNANASSQDALMYHILTSDIHRDLENK ddPTM_HeLa_Romidepsin_16h_R1 1 KCNANASSQDALMYHILTSDIHRDLENK 28 2 H0YM09;Q6IQ32 H0YM09 ADNP2 ADNP homeobox protein 2 0 0 39.883 0.028265 9091300 2624 2141 3180.2 2423.6 2570.7 2869.8 1851.1 1876.9 2047.4 1768.7 FALSE FALSE TRUE 2592.017679 2171.141054 3235.550047 2703.828035 2439.507586 2686.429042 2008.332388 1931.20514 1864.275416 1722.748919 1.504582386 1.260277125 1.878132101 1.56948468 1.416055212 1.559385127 1.165771962 1.121002091 1.082151552 1 10.75049674 -12.24568099 0.874930508 0.987382653 1.445685494 0.354467058 0.210673902 0.550362085 0.723759784 0.167795239 0.041415308 5.68E-13 12.24568099 0.458302841 KCS(ph)LPAEEDSVLEK ddPTM_HeLa_Romidepsin_16h_R1 1 KCSLPAEEDSVLEK 14 1 E7EVA0;P27816;P27816-6 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 KCS(0.989)LPAEEDS(0.011)VLEK 58.635 0.027938 6142600 1798.3 1336.3 1387.3 491.31 1399 1426 1420 1490.5 1875.3 1879.7 TRUE FALSE FALSE 1776.381628 1355.112466 1411.445375 548.1175739 1327.60381 1334.883202 1540.614765 1533.625266 1707.568471 1830.865123 0.970241666 0.740148714 0.770917178 0.299376271 0.725123764 0.729099695 0.841468192 0.837650598 0.932656617 1 10.8383098 -10.21129804 2.596456789 0.988913183 0.69297022 0.405691754 0.144852234 0.190300208 2.474750426 0.025990006 0.031388933 6.15E-11 10.21129804 -0.295942962 KDAPT(ph)SPASVASSSSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 KDAPTSPASVASSSSTPSSK 20 1 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 KDAPT(0.495)S(0.495)PAS(0.011)VASSSSTPSSK 58.319 0.012142 11335000 2905.2 2594.4 2817.6 2800.5 3055.8 2836.2 2454.5 2501.6 3120.6 2819.6 TRUE FALSE FALSE 2869.790305 2630.924031 2866.639146 3124.306987 2899.851123 2654.975973 2662.985169 2573.979849 2841.48572 2746.346386 1.044948416 0.957972397 1.043801015 1.137623063 1.055894165 0.966730194 0.969646503 0.937237875 1.034642147 1 11.42329788 -8.162011926 5.742134161 1.029443695 0.957338876 0.406016538 0.044093218 0.217616251 10.32221042 0.006780529 0.017645333 6.89E-09 8.162011926 -0.072104819 KDAPTS(ph)PASVASSSSTPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 KDAPTSPASVASSSSTPSSK 20 1 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 KDAPT(0.252)S(0.743)PAS(0.005)VASSSSTPSSK 78.418 0.0015281 13909000 5636.5 5437 4975.3 4926 5931.3 4791.1 4655.9 5004.7 5987.1 5374.2 TRUE FALSE FALSE 5567.80017 5513.542229 5061.893009 5495.567298 5628.603628 4484.964173 5051.37203 5149.503098 5451.598781 5234.577509 1.063657986 1.053292691 0.967010805 1.049858807 1.075273719 0.856795828 0.965000904 0.983747607 1.041459176 1 12.35385738 -8.276347504 24.99791903 1.031775271 0.938163385 0.534182381 0.042913143 488.783104 819589.6032 0.006376598 0.014312502 5.29E-09 8.276347504 -0.093611887 KDDEDEEEEEEVS(ph)DS ddPTM_HeLa_Romidepsin_16h_R1 1 KDDEDEEEEEEVSDS 15 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 0 KDDEDEEEEEEVS(0.58)DS(0.42) 97.223 0.01534 21511000 8991.2 8061.6 8538.2 4793.7 10744 13968 12145 13335 8761.3 9046.9 TRUE FALSE FALSE 8881.611796 8175.091416 8686.803789 5347.970149 10195.69359 13075.48988 13176.596 13720.82719 7977.667385 8811.860234 1.007915646 0.927737299 0.985808168 0.606905921 1.157042136 1.483851256 1.495325124 1.557086338 0.905332946 1 13.1052309 -8.362900481 3.587732438 0.968895327 1.514387755 0.825847373 0.122126309 0.075999819 1.804379609 0.01747535 0.041973178 4.34E-09 8.362900481 0.545492429 KDDEENYLDLFSHK ddPTM_HeLa_Romidepsin_16h_R1 2 KDDEENYLDLFSHK 14 1 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 0 0 ; ; 111.12 0.0011157 56621200 11582.7 10735.4 11930.6 9807.9 11712.5 12045.3 10594 12308.9 12455.3 10891.5 FALSE FALSE TRUE 11441.5256 10886.53324 12138.24709 10941.93555 11114.76742 11275.6442 11493.8541 12665.0386 11341.26677 10608.53726 1.078520565 1.026204931 1.144196112 1.031427357 1.047719129 1.062883971 1.083453243 1.193853431 1.069069797 1 13.37293813 -4.000000002 0.011576088 4.93E-09 2.314369099 0.231325041 0.047871012 6488.187918 5.863707744 494.3190148 694.0555467 1.00E-04 4.000000002 2.314369094 KDDS(ph)DDDGGGWITPSNIK ddPTM_HeLa_Romidepsin_16h_R1 1 KDDSDDDGGGWITPSNIK 18 1 Q9ULX3 Q9ULX3 NOB1 RNA-binding protein NOB1 1 0 KDDS(0.992)DDDGGGWIT(0.007)PS(0.001)NIK 70.316 0.0069213 160280000 4196.6 3761.5 4309.3 2379.8 3211.2 3181.5 3011.6 2798.8 4755.9 4062.2 TRUE FALSE FALSE 4145.450225 3814.454496 4384.301559 2654.963673 3047.320481 2978.212418 3267.405229 2879.778862 4330.520393 3956.663458 1.047713628 0.964058363 1.108080484 0.67101074 0.770174293 0.752708045 0.825798116 0.727830126 1.094487929 1 11.95006864 -9.261387471 25 1.023620915 0.755069131 0.877030661 0.054667897 1.085160966 522571.431 0.007210078 0.011467185 5.48E-10 9.261387471 -0.268551784 KDEET(ph)EESEY(ph)DS(ph)EHENSEPVTNIR ddPTM_HeLa_Romidepsin_16h_R1 1 KDEETEESEYDSEHENSEPVTNIR 24 1 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 3 0 KDEET(0.894)EES(0.441)EY(0.805)DS(0.818)EHENS(0.04)EPVT(0.003)NIR 51.758 0.0079658 5152100 935 688.6 860.95 604.97 909.42 853.52 609.58 1053.6 1136.7 857.46 TRUE FALSE FALSE 923.6038604 698.2941289 875.9344736 674.9194779 863.0089039 798.9828266 661.35771 1084.084254 1035.030705 835.1830656 1.105869956 0.836097088 1.048793384 0.80810963 1.033317053 0.956655923 0.791871552 1.298019917 1.239286029 1 9.705948649 -10.29556802 24.98965095 1.049994142 0.959897675 0.121449604 0.153519363 1133.485541 829956.2725 0.022141685 0.025320575 5.06E-11 10.29556802 -0.090096468 KDELSDWSLAGEDDRDSR ddPTM_HeLa_Romidepsin_16h_R1 1 KDELSDWSLAGEDDRDSR 18 2 E7EU85;E9PFF5;B4DXZ6;P51114-3;P51114-2;P51114;H7C4S4 E7EU85 FXR1 Fragile X mental retardation syndrome-related protein 1 0 0 65.652 0.0098397 11471000 4008.9 4328.2 4176.2 3268.8 4569.3 4977.6 3884.1 4481.6 5183.1 4303.4 FALSE FALSE TRUE 3960.037985 4389.132513 4248.885009 3646.754036 4336.111571 4659.547424 4214.015357 4611.268025 4719.510555 4191.597048 0.944756364 1.04712654 1.013667335 0.870015413 1.034477198 1.111640115 1.005348393 1.100121976 1.125945672 1 12.03328432 -8.533340686 24.99994959 0.975266575 1.066899779 0.119964652 0.069897833 152.2308862 363771.2827 0.007282617 0.014578003 2.93E-09 8.533340686 0.091633204 KDGSASAAAK(ac)K(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KDGSASAAAKKK 12 3 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2;Q68E03 D6REM6 MATR3;DKFZp686L22104 Matrin-3 0 2 KDGSASAAAK(1)K(1)K 131.66 0.00069285 2645200 766.03 1009.5 1059.8 2492.8 2556.6 2479.4 3142.1 1022.6 1007.3 670.49 FALSE TRUE FALSE 756.6933317 1023.711767 1078.245374 2781.029265 2426.127162 2320.974342 3408.989896 1052.187318 917.2045652 653.0705731 1.158670078 1.567536205 1.651039595 4.258390103 3.714954037 3.553941086 5.219941053 1.611138766 1.404449386 1 9.351095093 -9.380544269 3.909684607 1.129991747 3.751576586 0.642420217 0.86043972 0.093666399 2.514936746 0.120139714 0.186947223 4.16E-10 9.380544269 2.621584839 KDGSS(ph)PPLLEK ddPTM_HeLa_Romidepsin_16h_R1 1 KDGSSPPLLEK 11 1 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;Q6W2J9-3 H7BYY2 BCOR BCL-6 corepressor 1 0 KDGS(0.29)S(0.71)PPLLEK 135.94 7.19E-06 0 4094.1 3978.2 3599.2 4788.2 1970.9 1896 1438.8 1617.5 4078.5 3433.6 TRUE FALSE FALSE 4044.199534 4034.205204 3661.842566 5341.834213 1870.317619 1774.851719 1561.011636 1664.299811 3713.708745 3344.394577 1.209247127 1.206258745 1.094919419 1.597249993 0.55923952 0.530694473 0.466754625 0.497638593 1.11042781 1 11.70752935 -8.643526896 8.776904291 1.140587418 0.504011771 0.821717088 0.155858021 0.088948988 6.461643096 0.023738868 0.047534276 2.27E-09 8.643526896 -0.636575647 KDIDHETVVEEQIIGENS(ph)PPDYSEYMTGK ddPTM_HeLa_Romidepsin_16h_R1 2 KDIDHETVVEEQIIGENSPPDYSEYMTGK 29 1 P25490;A0A494C032;H0YJU4;H0YJV7 P25490 YY1 Transcriptional repressor protein YY1 1 0 KDIDHETVVEEQIIGENS(0.798)PPDY(0.053)S(0.079)EY(0.052)MT(0.018)GK;KDIDHET(0.001)VVEEQIIGENS(0.433)PPDY(0.116)S(0.124)EY(0.133)MT(0.192)GK ; 78.128 9.59E-07 38593000 4055.1 4473.2 4271.9 2630.9 5073.1 5473.7 4403.4 5499.9 6120.4 5636.5 TRUE FALSE FALSE 4005.674881 4536.173827 4346.250628 2935.097037 4814.200777 5123.948236 4777.424686 5659.030929 5572.976095 5490.062917 0.729622764 0.826251702 0.791657708 0.534619927 0.876893553 0.933313208 0.870194888 1.030777063 1.015102409 1 12.42260697 -6.960862555 1.196550606 0.838157936 1.232565458 0.167145442 0.131383523 4.644423789 3.421101468 0.021715372 2.695111334 1.09E-07 6.960862555 0.394407523 KDKS(ph)PVREPIDNLTPEER ddPTM_HeLa_Romidepsin_16h_R1 1 KDKSPVREPIDNLTPEER 18 3 Q14498-2;Q14498;G3XAC6;Q5QP22;H0Y4X3;Q14498-3;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 0 KDKS(1)PVREPIDNLTPEER 52.52 0.017049 19035000 3282.7 3073.3 3015.9 3023.6 2542.3 2514 2404.2 2595 3195 3104.5 TRUE FALSE FALSE 3242.68919 3116.565998 3068.390474 3373.202858 2412.556944 2353.363514 2608.412688 2670.082231 2909.231198 3023.844642 1.072372947 1.030663399 1.014731521 1.115534446 0.797844211 0.778268659 0.86261465 0.883009065 0.962096781 1 11.5621683 -8.753630657 24.99999946 1.03814367 0.829006612 0.812428734 0.047533538 50.8573592 162820.9523 0.006576452 0.012961233 1.76E-09 8.753630657 -0.209137058 KDLYANTVLSGGTTMYPGIADR ddPTM_HeLa_Romidepsin_16h_R1 3 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 0 ;; ;; 65.111 0.0018848 95186000 8760.7 7881.5 8613.1 9362.7 9389 9792.3 8676.9 9379.5 9060.8 8406.3 FALSE FALSE TRUE 8653.921219 7992.455964 8763.007392 10445.25943 8909.844295 9166.603633 9413.915669 9650.881034 8250.379355 8187.903114 1.05691544 0.976129768 1.070238286 1.275694067 1.088171681 1.119530056 1.149734619 1.178675529 1.00763031 1 12.99927832 -9.511986552 24.88588241 1.023791311 1.156939334 0.672009321 0.049951513 241.3617737 551450.2184 0.007635551 0.011220386 3.08E-10 9.511986552 0.133148022 KDMEPLT(ph)T(ph)LEFS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 KDMEPLTTLEFSEK 14 1 P23468-2;P23468 P23468-2 PTPRD Receptor-type tyrosine-protein phosphatase delta 3 0 KDMEPLT(1)T(1)LEFS(1)EK 54.199 0.025527 912140 450.45 353.17 321.92 305.05 307.23 436.79 432.87 360.84 487.33 530.4 TRUE FALSE FALSE 444.9597421 358.1419365 327.5228826 340.3213163 291.5509067 408.8805287 469.637967 371.2803361 443.7419843 516.6201315 0.861289979 0.69324038 0.633972357 0.658745751 0.564342907 0.791452953 0.909058587 0.718671831 0.858932816 1 9.012960053 -10.67991453 1.335242868 0.959534668 0.710541058 0.448335416 0.097021548 0.216338554 0.796161829 0.022491691 0.022195733 2.09E-11 10.67991453 -0.248993611 KDNDFIYHDR ddPTM_HeLa_Romidepsin_16h_R1 2 KDNDFIYHDR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 0 ; ; 68.536 0.01874 14519800 12394.2 11697.5 12181.2 11980.1 12623.1 12821.9 10648.6 12286.2 13522.9 12399.8 FALSE FALSE TRUE 12243.13472 11862.17771 12393.20868 13365.29553 11978.8961 12002.62197 11553.09182 12641.68181 12313.37796 12077.65141 1.013701614 0.982159305 1.02612737 1.106613784 0.991823302 0.993787746 0.956567749 1.046700338 1.019517582 1 13.56005232 KDPELWGSVLLESNPYR ddPTM_HeLa_Romidepsin_16h_R1 1 KDPELWGSVLLESNPYR 17 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 103.66 0.0017916 5944600 1019.3 866.36 860.07 871.18 892.38 1155.4 861.54 869.39 1081.4 1060.2 FALSE FALSE TRUE 1006.87638 878.5566388 875.0391576 971.9099306 846.8385187 1081.573669 934.7191861 894.544428 984.6768756 1032.655851 0.975035757 0.850773893 0.847367646 0.941175058 0.820058801 1.047370881 0.905160403 0.866256098 0.953538272 1 10.01214382 -10.40679324 5.988013662 0.989130177 0.899976018 0.254157362 0.061302254 0.201550147 9.207727907 0.01007362 0.011451839 3.92E-11 10.40679324 -0.089154159 ETEAAPTS(ph)PPIVPLK ddPTM_HeLa_Romidepsin_16h_R1 2 ETEAAPTSPPIVPLK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A3B3IT55;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3-4;Q7Z3B3;Q7Z3B3-2 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 0 ETEAAPTS(1)PPIVPLK;ETEAAPT(0.137)S(0.863)PPIVPLK ; 135.04 0.0013607 28922000 12014.1 11931.3 10682.9 8474.4 4630.2 3568.2 3128.9 3326.8 12603.6 11306.3 TRUE FALSE FALSE 11867.66753 12099.26915 10868.83139 9454.250001 4393.903616 3340.203536 3394.668688 3423.055709 11476.30245 11012.5607 1.07764832 1.098678998 0.986948603 0.858496971 0.398990184 0.303308525 0.308254255 0.310831949 1.042110256 1 13.42686235 -8.821925522 2.243339734 1.040065416 0.303104765 0.99138567 0.031530723 0.023485571 0.240880217 0.006232825 0.013009453 1.51E-09 8.821925522 -0.736960652 down KDS(ph)AQDDQAKQVLKGMS(ph)DVAQEK ddPTM_HeLa_Romidepsin_16h_R1 1 KDSAQDDQAKQVLKGMSDVAQEK 23 3 Q13045-2;Q13045-3;Q13045;J3KS54 Q13045-2 FLII Protein flightless-1 homolog 2 0 KDS(1)AQDDQAKQVLKGMS(1)DVAQEK 43.497 0.0041231 0 1162.1 1051.9 1342.6 771.1 990.89 1026 835.21 1045.2 1295.1 1340 TRUE FALSE FALSE 1147.935878 1066.708676 1365.96739 860.2582101 940.3211858 960.4419113 906.1527166 1075.441213 1179.263012 1305.186607 0.879518585 0.817284418 1.046568654 0.659107445 0.720449613 0.735865589 0.694270621 0.82397506 0.90352062 1 10.35004037 -9.254245229 24.99493607 0.937276777 0.725088375 0.671903176 0.070690913 262.1838275 910915.7999 0.011383258 0.01862217 5.57E-10 9.254245229 -0.212188402 KDS(ph)KLCS(ph)VLT(ph)QDFCMLFNNK ddPTM_HeLa_Romidepsin_16h_R1 1 KDSKLCSVLTQDFCMLFNNK 20 2 G3V419;Q9UHC1-2;Q9UHC1 G3V419 MLH3 DNA mismatch repair protein Mlh3 3 0 KDS(1)KLCS(1)VLT(1)QDFCMLFNNK 41.86 0.025269 5917000 901.63 852.14 621.13 335.87 981.38 1171.5 790.32 1029.3 832.8 1165.5 TRUE FALSE FALSE 890.6405868 864.1364493 631.9405071 374.7048697 931.2965166 1096.644931 857.4497611 1059.081172 758.3122822 1135.220142 0.784553193 0.761206058 0.556667807 0.330072429 0.820366449 0.966019621 0.755315845 0.932930215 0.667986987 1 10.14875638 -11.56480368 0.841802454 0.981619377 0.729498712 0 0.198744005 0.62499076 0.904831385 0.080687482 0.039761739 2.72E-12 11.56480368 -0.252120665 KDS(ph)SSEVFSDAAK ddPTM_HeLa_Romidepsin_16h_R1 2 KDSSSEVFSDAAK 13 1 Q5T5U3;E7ESW5;A0A1B0GV73;Q5T5U3-3;A0A1B0GTZ9 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 KDS(0.58)S(0.268)S(0.01)EVFS(0.142)DAAK;KDS(0.47)S(0.47)S(0.06)EVFSDAAK ; 148.41 0.0011834 29009000 4902.2 4932 5180.2 4647.3 5643 6553.4 5453.7 6099.2 6190 5751.8 TRUE FALSE FALSE 4842.450101 5001.432825 5270.359208 5184.642692 5355.016653 6134.65889 5916.937142 6275.670729 5636.350897 5602.367407 0.864357824 0.892735599 0.940737875 0.925437822 0.955848887 1.095011884 1.05614943 1.120181929 1.006065916 1 12.45182088 -8.321169925 3.896803306 0.930913444 1.088282068 0.714376922 0.043262136 0.109742013 3.367425317 0.007744772 0.018702896 4.77E-09 8.321169925 0.157368624 KDS(ph)SSVVEWTQAPK ddPTM_HeLa_Romidepsin_16h_R1 1 KDSSSVVEWTQAPK 14 1 Q8TC07-2;Q8TC07-3;F8WCB5;Q8TC07 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 0 KDS(0.691)S(0.123)S(0.186)VVEWTQAPK 113.69 0.0006045 0 351.85 462 341.4 476.87 659.15 828.85 797.05 1046.5 316.37 435.81 TRUE FALSE FALSE 347.5615169 468.5040481 347.3419238 532.0079531 625.5111159 775.88916 864.7514071 1076.778826 288.0730748 424.4875934 0.818778976 1.103693148 0.818261662 1.253294469 1.473567486 1.827825294 2.037165327 2.536655589 0.678637207 1 8.729578578 -7.958793971 0.727590841 0.909740032 2.751246453 0.94890914 0.130471939 0.181233144 0.114820646 0.019987399 0.224779736 1.10E-08 7.958793971 1.841506421 up KDSEGYSES(ph)PDLEFEYADTDK ddPTM_HeLa_Romidepsin_16h_R1 1 KDSEGYSESPDLEFEYADTDK 21 1 Q5VSL9;Q5VSL9-4 Q5VSL9 STRIP1 Striatin-interacting protein 1 1 0 KDS(0.44)EGY(0.014)S(0.094)ES(0.451)PDLEFEY(0.001)ADTDK 55.171 0.008755 2982300 1088.1 1270.1 1193.8 998.82 1362.8 1298.8 1153.7 1666.1 1511.7 1215.2 TRUE FALSE FALSE 1074.837819 1287.980501 1214.577588 1114.308268 1293.251231 1215.810872 1251.695249 1714.305975 1376.489766 1183.628929 0.90808681 1.088162404 1.026147265 0.94143379 1.09261543 1.027189216 1.057506469 1.448347479 1.162940287 1 10.20900115 -4.275200882 0.96536326 0.976192256 200 0.652895262 0.084129371 223.9371852 0.62893633 0.010101077 98095.43595 5.31E-05 4.275200882 199.0238077 KDSGSSSVSSTSS(ph)SSSSSPGDK ddPTM_HeLa_Romidepsin_16h_R1 2 KDSGSSSVSSTSSSSSSSPGDK 22 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 0 KDSGSSSVSS(0.002)T(0.006)S(0.089)S(0.559)S(0.131)S(0.131)S(0.047)S(0.025)S(0.01)PGDK;KDSGSSSVSST(0.002)S(0.008)S(0.711)S(0.256)S(0.021)SSSPGDK ; 121.59 1.84E-05 5500000 2724.2 2664.7 2392.9 3115.4 4072.8 3389.1 3033 1838.15 2981.5 2654.1 TRUE FALSE FALSE 2690.996403 2702.213717 2434.547421 3475.617206 3864.949818 3172.547448 3290.622944 1891.33397 2714.827173 2585.146099 1.040945579 1.04528472 0.941744616 1.344456782 1.495060499 1.227221722 1.272896315 0.731615892 1.050163924 1 11.3360301 -9.267197744 24.88981143 1.016895298 1.233829566 0.220080758 0.185119612 476.2579096 2058563.861 0.027531228 0.042776186 5.41E-10 9.267197744 0.216934267 KDSGSSSVSSTSSS(ph)SSSSPGDK ddPTM_HeLa_Romidepsin_16h_R1 1 KDSGSSSVSSTSSSSSSSPGDK 22 1 Q9H7S9 Q9H7S9 ZNF703 Zinc finger protein 703 1 0 KDSGSSSVS(0.004)S(0.087)T(0.087)S(0.087)S(0.03)S(0.273)S(0.273)S(0.056)S(0.077)S(0.024)PGDK 63.674 0.0026684 3806200 1363.3 1222.6 1555.6 2163.2 2081.7 1816.1 1444.8 1084.6 1465.7 1389.6 TRUE FALSE FALSE 1346.683575 1239.811795 1582.674565 2413.319362 1975.463081 1700.057071 1567.521276 1115.98119 1334.604121 1353.497992 0.994965329 0.916005641 1.169321695 1.78302397 1.459524206 1.256046985 1.158126045 0.824516325 0.98604071 1 10.40247703 -9.527866781 17.14330283 0.993871876 1.313486382 0.306714548 0.226822322 2.707854997 9303.920468 0.036693835 0.052215369 2.97E-10 9.527866781 0.319614506 KDY(ph)ARYS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 KDYARYSK 8 2 Q5TB53;Q9HD45 Q5TB53 TM9SF3 Transmembrane 9 superfamily member 3 2 0 KDY(0.999)ARY(0.414)S(0.587)K 44.377 0.0043037 0 1953 1926.2 1607 1607.5 1838.1 1802 1400 1992.4 2086.1 1575.5 TRUE FALSE FALSE 1929.196085 1953.317094 1634.969161 1793.366714 1744.294898 1686.858016 1518.915965 2050.046951 1899.513991 1534.568283 1.257158842 1.272877275 1.065426139 1.168645758 1.136668155 1.099239463 0.989800182 1.335911196 1.237816533 1 10.58361713 -12.54236841 1.336394168 1.000905061 1.169362215 0 0.121575287 0.450089318 1.452052808 0.067388271 0.016384998 2.87E-13 12.54236841 0.168457154 KEDEVEEWQHR ddPTM_HeLa_Romidepsin_16h_R1 1 KEDEVEEWQHR 11 1 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 149.49 0.00049865 7033100 5093.4 4853.6 4353.5 6974.1 5266.7 6041.6 4812.2 5763.4 5282.6 5711 FALSE FALSE TRUE 5031.319682 4921.929108 4429.270841 7780.478256 4997.920646 5655.561258 5220.948148 5930.154886 4810.111025 5562.627397 0.904486194 0.884820923 0.796255173 1.39870563 0.89848201 1.016706828 0.938575924 1.066070844 0.864719256 1 12.44155076 KEDGTFYEFGEDIPEAPER ddPTM_HeLa_Romidepsin_16h_R1 1 KEDGTFYEFGEDIPEAPER 19 1 O43776 O43776 NARS "Asparagine--tRNA ligase, cytoplasmic" 0 0 143.57 4.68E-05 12478000 5679.8 4957.6 5397.2 4484.4 5573.1 5210.2 4756.7 5704.6 6186.5 5724.7 FALSE FALSE TRUE 5610.572413 5027.393223 5491.136002 5002.907428 5288.683911 4877.285035 5160.733979 5869.653601 5633.163946 5575.971469 1.006205366 0.901617458 0.984785527 0.897226153 0.948477578 0.874696914 0.925530916 1.052669231 1.010256953 1 12.44500746 -10.28158861 24.13355679 1.002930317 0.937912632 0.27813547 0.047616195 456.2829127 546507.0164 0.007622902 0.008723845 5.23E-11 10.28158861 -0.065017685 KEDLVFIFWAPES(ph)APLKSK ddPTM_HeLa_Romidepsin_16h_R1 1 KEDLVFIFWAPESAPLKSK 19 2 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;Q9Y281-3;Q9Y281 E9PP50;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 1 0 KEDLVFIFWAPES(0.747)APLKS(0.253)K 75.548 0.0043396 6931700 7009.1 6378.9 6289.2 6173.6 7240.4 6916.6 6864 7468.2 7528.1 6812.7 TRUE FALSE FALSE 6923.670393 6468.702322 6398.660888 6887.42068 6870.89537 6474.651582 7447.027989 7684.280584 6854.767882 6635.705072 1.043396341 0.974832705 0.964277468 1.037933513 1.035443151 0.975729257 1.122266271 1.15802021 1.033012741 1 12.69603405 -7.652927003 5.252018598 1.013652817 1.148774654 0.774901182 0.028541705 0.072207786 2.981138959 0.00422005 0.016632783 2.22E-08 7.652927003 0.135121837 KEDLVFIFWAPESAPLK ddPTM_HeLa_Romidepsin_16h_R1 1 KEDLVFIFWAPESAPLK 17 1 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;Q9Y281-3;Q9Y281 E9PP50;Q9Y281 CFL1;CFL2 Cofilin-1;Cofilin-2 0 0 99.813 0.0020985 5824000 2831.4 3252.1 3142.3 2526.2 3698.1 3521.4 3063.4 3650 3330.2 2573.7 FALSE FALSE TRUE 2796.889808 3297.883149 3196.990413 2818.29113 3509.372157 3296.393905 3323.60512 3755.606991 3032.338571 2506.834903 1.115705627 1.315556579 1.275309519 1.124242816 1.399921532 1.314962505 1.325817315 1.498146921 1.209628352 1 11.29165127 -5.346790576 0.10324595 0.7937219 2.385663729 0.466078265 0.102379055 27.2869522 0.270581729 0.633477386 6.159118394 4.50E-06 5.346790576 1.591941828 KEDLYLK(ac)PIQR ddPTM_HeLa_Romidepsin_16h_R1 1 KEDLYLKPIQR 11 2 P13639 P13639 EEF2 Elongation factor 2 0 1 KEDLYLK(1)PIQR 111.5 0.0075722 4159500 1051 1142 1062.8 781.83 2340.7 1806.6 1695.2 1956.7 1917.9 1445.1 FALSE TRUE FALSE 1038.190008 1158.077106 1081.297588 872.2288632 2221.245345 1691.164091 1839.190246 2013.314027 1746.358221 1407.556094 0.737583399 0.822757339 0.768209234 0.619676095 1.578086553 1.201489659 1.306655027 1.430361487 1.240702398 1 10.4589767 -8.760952303 24.99994562 0.843737408 1.361280217 0.656644491 0.181634428 5.031074984 258202.0322 0.022148453 0.042231862 1.73E-09 8.760952303 0.517542808 KEEELQAALAR ddPTM_HeLa_Romidepsin_16h_R1 2 KEEELQAALAR 11 1 P35579;A0A0C4DFM8;Q7Z406;Q7Z406-6;Q7Z406-2;Q7Z406-5;Q7Z406-4;P35749-4;P35749-3;P35749;P35749-2 P35579;P35749-4 MYH9;MYH14;MYH11 Myosin-9;Myosin-14;Myosin-11 0 0 ; ; 110.08 0.0093802 15817100 5654.5 5008.6 5777.2 4736.7 5788.5 6141.4 4958.2 5566.9 5854.7 5379.2 FALSE FALSE TRUE 5585.580779 5079.111202 5877.749743 5284.379541 5493.091245 5748.98436 5379.349384 5727.969468 5331.040969 5239.447609 1.066062913 0.969398223 1.121826227 1.0085757 1.048410377 1.09725009 1.026701627 1.093239192 1.017481492 1 12.355199 -16.52287875 0.235848018 0.68356424 1.062107935 0.167056537 0.042390929 55.21842907 0.717401015 8.124918948 0.026605466 3.00E-17 16.52287875 0.378543695 KEEENADS(ph)DDEGELQDLLSQDWR ddPTM_HeLa_Romidepsin_16h_R1 3 KEEENADSDDEGELQDLLSQDWR 23 1 J3QQQ3;Q96NB3 J3QQQ3 ZNF830 Zinc finger protein 830 1 0 KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR;KEEENADS(1)DDEGELQDLLSQDWR ;; 124.45 1.42E-06 37229000 7714.75 7686.8 7831.88 6934.09 7399.37 6994.38 6534.82 6467.96 8708.4 7294.49 TRUE FALSE FALSE 7620.71966 7795.014972 7968.190586 7735.842112 7021.752538 6547.461691 7089.887448 6655.100218 7929.498893 7104.978098 1.072588762 1.097120197 1.121494039 1.088791831 0.988286303 0.92153158 0.997876045 0.936681314 1.116048323 1 12.79461449 -8.576978059 5.826867587 1.050821096 0.956203095 0.611571094 0.043863599 0.135032981 9.806160681 0.007156091 0.014553369 2.65E-09 8.576978059 -0.094618001 KEELVPS(ph)EEDFQGITPGAQGPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 KEELVPSEEDFQGITPGAQGPSSR 24 1 H3BP71;O75150-3;O75150-4;O75150 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 1 0 KEELVPS(0.92)EEDFQGIT(0.075)PGAQGPS(0.003)S(0.003)R 44.912 0.021408 4423500 692.14 688.83 486.79 606.6 964.95 766.68 565.88 832.85 714.95 667.34 TRUE FALSE FALSE 683.7039315 698.5273668 495.2623758 676.7379461 915.7050008 717.6916223 613.9458331 856.9472007 651.0030814 650.0024106 1.051848301 1.074653502 0.761939291 1.041131441 1.4087717 1.104136863 0.944528548 1.318375419 1.001539488 1 9.344301258 -8.976059341 24.99528164 1.00697327 1.176625415 0.331770441 0.141358655 246.8668523 257740.5881 0.020257029 0.036717747 1.06E-09 8.976059341 0.169652146 KEEPSQNDIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KEEPSQNDISPK 12 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 KEEPS(0.013)QNDIS(0.987)PK 101.61 0.022797 9951500 2558 2124 2145 2276.8 1969.1 1886.2 1763.1 1812.2 2530.7 2782.8 TRUE FALSE FALSE 2526.822112 2153.901728 2182.332825 2540.054329 1868.609479 1765.677907 1912.85767 1864.633148 2304.347854 2710.502455 0.93223384 0.794650351 0.805139586 0.937115672 0.689395974 0.651420885 0.705720693 0.687928965 0.850155236 1 11.4043446 -9.285699179 0.378567922 1.003280001 0.619043493 0.565295068 0.076414647 0.535504767 0.149079122 0.02760233 0.08092158 5.18E-10 9.285699179 -0.384236509 KEESEES(ph)DDDMGFGLFD ddPTM_HeLa_Romidepsin_16h_R1 4 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 1 0 KEES(0.458)EES(0.542)DDDMGFGLFD;KEES(0.008)EES(0.992)DDDMGFGLFD;KEES(0.007)EES(0.993)DDDMGFGLFD;KEES(0.16)EES(0.84)DDDMGFGLFD ;;; 89.506 0.001117 122005000 7827.55 7937.73 7022.14 5377.13 7450.45 6960.39 6029.8 6479.3 8069.08 7933.45 TRUE FALSE FALSE 7732.14481 8049.477571 7144.357401 5998.859071 7070.225735 6515.643543 6541.971061 6666.768323 7347.361275 7727.337825 1.000622075 1.041688322 0.92455611 0.776316399 0.914962681 0.843193826 0.846600888 0.862750985 0.950826978 1 12.91575576 -9.534629447 5.501765501 1.002924425 0.85150947 0.777344035 0.037679886 0.045452004 4.456495042 0.004806917 0.006994541 2.92E-10 9.534629447 -0.151414955 KEESEESDDDMGFGLFD ddPTM_HeLa_Romidepsin_16h_R1 1 KEESEESDDDMGFGLFD 17 1 P05387;H0YDD8;P05386-2;P05386 P05387 RPLP2;RPLP1 60S acidic ribosomal protein P2;60S acidic ribosomal protein P1 0 0 74.392 0.0223 74942000 6154.2 5583.9 6073.5 5658.5 5854.1 7114.9 6285.4 7208.2 6383 5934.2 FALSE FALSE TRUE 6079.190243 5662.510291 6179.20672 6312.762394 5555.343432 6660.280852 6819.281719 7416.757894 5812.088493 5780.028629 1.051757808 0.979668208 1.069061611 1.092168015 0.961127321 1.152292018 1.179800682 1.283169751 1.005546662 1 12.49686092 -7.769580273 1.453868082 1.026024653 1.283817963 0.790757885 0.044256317 0.176299444 0.592216711 0.006301384 0.050041913 1.70E-08 7.769580273 0.25779331 KEETQPPVALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KEETQPPVALKK 12 2 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 KEETQPPVALK(1)K 128.57 0.0029792 1370500 768.01 601.81 793.98 843.7 1139.6 1270.3 1499 1312.2 1733.6 1381.8 FALSE TRUE FALSE 758.6491987 610.282297 807.7988888 941.2525637 1081.44196 1189.13193 1626.325023 1350.166437 1578.542474 1345.900637 0.563674002 0.453437854 0.60019207 0.699347736 0.803508023 0.883521337 1.208354449 1.003169476 1.172852164 1 10.39435619 -8.01671942 2.717366892 0.741387746 1.105334687 0.308353855 0.20455758 0.245154543 3.589026601 0.030248436 0.102596467 9.62E-09 8.01671942 0.363946942 KEKPELSEPSHLNGPS(ph)SDPEAAFLSR ddPTM_HeLa_Romidepsin_16h_R1 1 KEKPELSEPSHLNGPSSDPEAAFLSR 26 2 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 KEKPELS(0.001)EPSHLNGPS(0.499)S(0.499)DPEAAFLSR 51.39 0.0057323 23412000 1665.3 1412.9 1415.2 1667.8 1989.3 1855 1442.3 1687.9 1796.1 1569.4 TRUE FALSE FALSE 1645.002683 1432.790843 1439.830962 1860.638883 1887.778598 1736.471487 1564.808926 1736.736723 1635.452318 1528.626762 1.076131024 0.937305874 0.941911393 1.217196329 1.23495064 1.135968263 1.023669718 1.136141776 1.069883348 1 10.57802048 -9.258948352 24.99806715 1.021484457 1.146576043 0.517825085 0.068798879 176.2226326 1768434.875 0.011466425 0.018450564 5.51E-10 9.258948352 0.125091586 KELLEY(ph)DLQQR ddPTM_HeLa_Romidepsin_16h_R1 1 KELLEYDLQQR 11 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 KELLEY(1)DLQQR 62.166 0.0037525 0 431.47 364.86 305.85 464.99 356.46 573.32 455.1 347.89 415.64 463.98 TRUE FALSE FALSE 426.2110777 369.9965087 311.173191 518.7543316 338.2685161 536.6867023 493.7561826 357.9556483 378.4641174 451.9257327 0.943099821 0.818710867 0.688549397 1.14787518 0.748504658 1.187555086 1.092560452 0.792067418 0.837447594 1 8.819941896 -7.218172805 21.30266843 0.9603043 0.79206366 0.058935442 0.161258019 6986.011679 3439108.18 0.02031978 7.840656896 6.05E-08 7.218172805 -0.16824064 KELQAEATVSGS(ph)PEAPGTNVVSEPR ddPTM_HeLa_Romidepsin_16h_R1 2 KELQAEATVSGSPEAPGTNVVSEPR 25 1 K7EJ02;Q9BZV1-2;Q9BZV1 K7EJ02 UBXN6 UBX domain-containing protein 6 1 0 KELQAEATVS(0.102)GS(0.894)PEAPGT(0.003)NVVSEPR;KELQAEATVS(0.105)GS(0.895)PEAPGTNVVSEPR ; 141.78 1.53E-07 28454000 5857 6255.5 5629.4 5737.3 6047 5904.2 5553 5459.2 7394.7 5724.3 TRUE FALSE FALSE 5785.612631 6343.565093 5727.377346 6400.673621 5738.399026 5526.940675 6024.671681 5617.153339 6733.299512 5575.581861 1.037669749 1.137740464 1.027225048 1.147983077 1.029201825 0.991276034 1.080545821 1.007455989 1.207640688 1 12.44490666 -11.10659555 1.417995028 1.009039519 1.059337361 0 0.079789699 0.468648549 1.928750586 0.011622521 0.009494055 7.82E-12 11.10659555 0.050297843 KELQMSKGEPK ddPTM_HeLa_Romidepsin_16h_R1 1 KELQMSKGEPK 11 2 M0QZL2;Q7Z7M0-2;Q7Z7M0 M0QZL2 MEGF8 Multiple epidermal growth factor-like domains protein 8 0 0 63.216 0.0041331 0 315.08 521.01 377.79 332.11 394.26 496.07 341.02 480.8 455.48 513.2 FALSE FALSE TRUE 311.2396838 528.3447925 384.3652765 370.5101208 374.139441 464.372728 369.9862303 494.7111894 414.740728 499.86699 0.622645004 1.05697076 0.768935105 0.74121742 0.748477992 0.928992587 0.74016936 0.989685655 0.829702173 1 8.965400448 -12.70538473 1.601689956 0.999879488 0.791822921 0 0.137978211 0.439472079 2.035725252 0.095222903 0.021022929 1.97E-13 12.70538473 -0.208056567 KELS(ph)CYDT(ph)Y(ph)PPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 KELSCYDTYPPLEK 14 1 Q9BXT8-2;Q9BXT8-1;Q9BXT8-4;Q9BXT8-5;Q9BXT8 Q9BXT8-2 RNF17 RING finger protein 17 3 0 KELS(0.866)CY(0.139)DT(0.998)Y(0.997)PPLEK 53.869 0.027622 51383000 2997.4 3029.2 2810 1770.4 2898.8 2947 2068 2558.3 3162.6 3052.9 TRUE FALSE FALSE 2960.866536 3071.845157 2858.906871 1975.101978 2750.863419 2758.696211 2243.655868 2632.320374 2879.729135 2973.585218 0.995722779 1.033044265 0.961434316 0.664215697 0.925099911 0.927734034 0.754528861 0.885234551 0.968436727 1 11.53798771 -9.502143566 24.62624324 1.000395755 0.835172586 0.534170626 0.075498154 350.9893858 416854.8721 0.010703047 0.016231423 3.15E-10 9.502143566 -0.165223169 KELSDIAHR ddPTM_HeLa_Romidepsin_16h_R1 1 KELSDIAHR 9 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 47.938 0.029828 8981000 9498.2 9395.2 8704.6 9300.8 12009 13524 10898 10698 11695 9421.2 FALSE FALSE TRUE 9382.432285 9527.465872 8856.099912 10376.20226 11396.13592 12659.86005 11823.67585 11007.52975 10648.96991 9176.435866 1.022448413 1.038253415 0.965091463 1.130744268 1.241891306 1.379605354 1.288482372 1.199543037 1.160469061 1 13.1637182 -8.896531769 2.483358259 1.01048628 1.290549019 0.74079408 0.066025768 0.062736854 0.784963268 0.006766437 0.013382083 1.27E-09 8.896531769 0.28006274 KENPS(ph)PLFSIK ddPTM_HeLa_Romidepsin_16h_R1 1 KENPSPLFSIK 11 1 A0A0J9YX88;E9PJ24;B7ZM65;F8WEF5;A0A0J9YYB5;A0A0J9YWD5;Q9P1Y6-2;Q9P1Y6-3;Q9P1Y6 A0A0J9YX88 PHRF1 PHD and RING finger domain-containing protein 1 1 0 KENPS(1)PLFSIK 64.04 0.027485 19598000 5103.3 5317.2 4575.7 4103.9 5935.8 6804.8 6231 6047.5 5015.5 5146.1 TRUE FALSE FALSE 5041.099017 5392.055681 4655.338139 4578.412227 5632.873976 6369.995241 6760.260984 6222.474871 4566.901118 5012.40358 1.005724885 1.075742525 0.928763629 0.913416518 1.123786999 1.270846439 1.348706439 1.241415375 0.911119994 1 12.29128686 -8.416542189 2.97430974 0.997338898 1.2955131 0.854532237 0.057544693 0.063211657 1.068270128 0.007246093 0.017650809 3.83E-09 8.416542189 0.298174202 KEPAITSQNS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 2 KEPAITSQNSPEAR 14 1 E5RIS7;A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193 E5RIS7 TCEA1 Transcription elongation factor A protein 1 1 0 KEPAITSQNS(0.999)PEAR;KEPAIT(0.001)S(0.005)QNS(0.993)PEAR ; 125.39 0.0049511 19556200 3794.94 3552.5 3660.45 3994.97 4233.42 4143.55 3326.48 4080.26 3911.7 4693.3 TRUE FALSE FALSE 3748.685812 3602.512188 3724.158597 4456.887228 4017.37278 3878.790528 3609.031128 4198.315886 3561.827755 4571.367389 0.820035996 0.788060088 0.814670596 0.97495713 0.878812057 0.848496784 0.789486125 0.918393891 0.779160249 1 12.15841005 -12.30397206 1.019975274 1.000341825 0.851599039 0 0.08740949 0.367194946 0.681952738 0.039394976 0.010435654 4.97E-13 12.30397206 -0.148742785 KEPAVLELEGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KEPAVLELEGKK 12 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 0 1 KEPAVLELEGK(1)K 127.79 0.0032965 1606400 1201.8 1515.5 1399.4 1379.9 3228.7 2893.1 2404.4 2730.4 2969.4 2130.8 FALSE TRUE FALSE 1187.151999 1536.835249 1423.75597 1539.450531 3063.927391 2708.240247 2608.629676 2809.399816 2703.809427 2075.441509 0.571999738 0.740485936 0.686001491 0.741746045 1.476277398 1.304898372 1.25690349 1.353639601 1.302763492 1 11.01920256 -8.767944873 24.98510605 0.775566281 1.338354195 0.592624191 0.201780366 59.69199926 229254.961 0.025163463 0.046402404 1.71E-09 8.767944873 0.562787914 KEPPLTPVPLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 KEPPLTPVPLKR 12 2 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 1 KEPPLTPVPLK(1)R 164.81 4.98E-26 0 2113.8 2470.9 1968.6 2386.1 2511.4 2892.9 2761.4 2932.9 2042.2 1686 FALSE TRUE FALSE 2088.036193 2505.685395 2002.862657 2661.992109 2383.233887 2708.053026 2995.953247 3017.758834 1859.540517 1642.197477 1.2714891 1.525812474 1.219623514 1.62099391 1.451246832 1.649042252 1.82435626 1.837634558 1.132348906 1 10.68141191 -4 0.114328428 0.746077324 4.296471773 0.840465619 0.109621363 20.879809 0.165955832 0.493595229 11.78902722 1.00E-04 4 3.550394448 KEPVVGGTLS(ph)PLALANK ddPTM_HeLa_Romidepsin_16h_R1 2 KEPVVGGTLSPLALANK 17 1 J3KTM2;O15534-4;O15534;J3KRL7 J3KTM2 PER1 Period circadian protein homolog 1 1 0 KEPVVGGT(0.012)LS(0.988)PLALANK;KEPVVGGT(0.008)LS(0.992)PLALANK ; 128.4 0.00061293 59183000 10586.4 10473.4 9792.1 8698.6 20000 23084.3 20501.9 23121.2 11199.6 10819.6 TRUE FALSE FALSE 10457.36888 10620.8448 9962.527393 9704.37306 18979.32537 21609.28773 22243.33087 23790.17544 10197.87973 10538.50523 0.992300962 1.007813211 0.945345395 0.9208491 1.800950415 2.050507852 2.110672281 2.257452544 0.967678006 1 13.36338263 -8.632424579 3.108627845 0.986517738 2.122527669 0.984235084 0.06793096 0.022576654 0.434900658 0.010810053 0.023215593 2.33E-09 8.632424579 1.136009931 up KEQSEVSVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 KEQSEVSVSPR 11 1 Q7L4I2;E9PI52 Q7L4I2 RSRC2 Arginine/serine-rich coiled-coil protein 2 1 0 KEQSEVS(0.001)VS(0.999)PR;KEQSEVS(0.028)VS(0.972)PR;KEQSEVS(0.004)VS(0.996)PR ;; 133.88 0.0066019 64367900 10856.2 11482.4 10530.7 10975.3 11570.2 10642.2 9642.8 10603.1 13206.9 13164.6 TRUE FALSE FALSE 10723.88046 11644.04953 10713.98242 12244.31583 10979.72952 9962.197766 10461.85919 10909.88397 12025.64179 12822.58179 0.836327709 0.908089316 0.835555787 0.954902532 0.856280716 0.776926045 0.815893348 0.850833642 0.937848709 1 13.64639915 -16.52287875 0.232862638 1.857126177 0.832051762 0.451308567 0.049191219 24.48076559 0.316707596 9.588348223 0.033281758 3.00E-17 16.52287875 -1.025074415 KES(ph)APQVLLPEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 KESAPQVLLPEEEK 14 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 0 KES(1)APQVLLPEEEK;KES(1)APQVLLPEEEK ; 75.743 0.013191 17690700 10604.9 11027 11510 8105.1 19026.4 26243 25314 30037 12504.7 12797.6 TRUE FALSE FALSE 10475.6434 11182.2384 11710.32672 9042.249798 18055.41181 24566.157 27464.17053 30906.0732 11386.24831 12465.11651 0.84039675 0.897082541 0.939447835 0.725404355 1.448475175 1.970792409 2.203282297 2.479405081 0.913449008 1 13.60560875 -8.284909971 1.674222738 0.907431749 2.356819999 0.966080356 0.112551014 0.048451578 0.256518368 0.0174625 0.059472768 5.19E-09 8.284909971 1.449388249 up KES(ph)PS(ph)ST(ph)GS(ph)S(ph)TWK ddPTM_HeLa_Romidepsin_16h_R1 3 KESPSSTGSSTWK 13 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 5 0 KES(0.915)PS(0.544)S(0.544)T(0.994)GS(0.688)S(0.688)T(0.628)WK;KES(0.978)PS(0.541)S(0.541)T(0.907)GS(0.702)S(0.702)T(0.628)WK;KES(0.989)PS(0.626)S(0.414)T(0.976)GS(0.911)S(0.899)T(0.184)WK ;; 82.651 0.0038765 70503700 26677.5 25002.6 25849.5 21918.2 26026.9 26059.8 23775.7 24895.6 27436.5 25771.5 TRUE FALSE FALSE 26352.34437 25354.58726 26299.3997 24452.48541 24698.65017 24394.66288 25795.20736 25615.91491 24982.51072 25101.95271 1.049812525 1.010064338 1.04770334 0.974126822 0.98393342 0.971823314 1.027617559 1.020474988 0.995241725 1 14.61551198 -9.259195521 24.99788485 1.024545291 0.995405701 0.207423899 0.023774363 233.8744475 2605498.443 0.003981967 0.006381801 5.51E-10 9.259195521 -0.029139591 KES(ph)PS(ph)ST(ph)GS(ph)ST(ph)WK ddPTM_HeLa_Romidepsin_16h_R1 2 KESPSSTGSSTWK 13 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 5 0 KES(0.972)PS(0.516)S(0.516)T(0.967)GS(0.598)S(0.598)T(0.833)WK;KES(0.998)PS(0.675)S(0.501)T(0.801)GS(0.574)S(0.574)T(0.877)WK ; 56.793 0.018517 69961000 26039.77 24517.09 24145.44 21695.81 25297.53 25817.6 22190.41 24904.77 26896.3 25062.12 TRUE FALSE FALSE 25722.38727 24862.24224 24565.68125 24204.38163 24006.50265 24167.93868 24075.26287 25625.35023 24490.62756 24411.00251 1.053721053 1.018485096 1.006336436 0.991535748 0.983429609 0.990042858 0.986246381 1.049745918 1.003261851 1 14.57524392 -9.726996307 3.22057377 1.025752211 0.998125315 0.10302331 0.022615314 0.307962787 6.600555533 0.004222758 0.0059556 1.88E-10 9.726996307 -0.027626897 KES(ph)PS(ph)STGS(ph)S(ph)T(ph)WK ddPTM_HeLa_Romidepsin_16h_R1 1 KESPSSTGSSTWK 13 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 5 0 KES(0.813)PS(0.593)S(0.593)T(0.065)GS(0.946)S(0.995)T(0.995)WK 58.268 0.016906 115440 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 KES(ph)PSS(ph)T(ph)GS(ph)S(ph)TWK ddPTM_HeLa_Romidepsin_16h_R1 1 KESPSSTGSSTWK 13 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 5 0 KES(0.992)PS(0.198)S(0.814)T(0.99)GS(0.69)S(0.69)T(0.627)WK 63.682 0.013818 4821900 5810.8 5425.4 5649 5044.5 6419.6 5888.2 5608.8 5958 6347 7117.3 TRUE FALSE FALSE 5739.975735 5501.778924 5747.318475 5627.768825 6091.983857 5511.963023 6085.211332 6130.38533 5779.308424 6932.39152 0.827993589 0.793633612 0.829052782 0.811807701 0.878770889 0.795102672 0.87779395 0.884310315 0.833667344 1 12.75913742 -12.13362344 0.834896463 1.002853673 0.836106594 0 0.059712875 0.229476879 0.282281785 0.024022082 0.006555542 7.35E-13 12.13362344 -0.166747079 KES(ph)PSS(ph)T(ph)GS(ph)ST(ph)WK ddPTM_HeLa_Romidepsin_16h_R1 1 KESPSSTGSSTWK 13 1 Q6NV74;C9JFM2;C9JXD6;C9JK00 Q6NV74 KIAA1211L Uncharacterized protein KIAA1211-like 5 0 KES(0.93)PS(0.408)S(0.665)T(0.994)GS(0.568)S(0.568)T(0.867)WK 99.927 0.0022175 4411500 8273.5 8064.1 8373 7014.5 8961.4 8389.4 7046.9 8294.8 8796.4 8733.7 TRUE FALSE FALSE 8172.6594 8177.626611 8518.728553 7825.549494 8504.066318 7853.344416 7645.46351 8534.796951 8009.627953 8506.797215 0.960721079 0.96130499 1.001402565 0.919917249 0.999678975 0.923184627 0.898747592 1.003291455 0.941556234 1 13.05440035 KES(ph)VSPEDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 KESVSPEDSEK 11 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 0 KES(0.514)VS(0.486)PEDSEK 75.02 0.020113 15055000 5064 4613.4 5363.4 3997.9 4576.6 4643.9 5666.1 2708.9 6302.3 5708.6 TRUE FALSE FALSE 5002.27802 4678.347566 5456.747727 4460.156009 4343.039024 4347.169778 6147.378393 2787.277748 5738.606504 5560.289749 0.899643408 0.841385571 0.981378305 0.80214453 0.781081422 0.781824325 1.10558598 0.501282824 1.032069687 1 12.44094435 -4.000000025 0.082521784 1.128985041 0.14763262 0.282401217 0.138920817 187.5867554 1.134751961 2.014879353 21.04845847 1.00E-04 4.000000025 -0.981352421 KESPTS(ph)SSFGK ddPTM_HeLa_Romidepsin_16h_R1 1 KESPTSSSFGK 11 1 Q5VUA4 Q5VUA4 ZNF318 Zinc finger protein 318 1 0 KES(0.104)PT(0.104)S(0.725)S(0.061)S(0.006)FGK 102.62 0.0020605 0 1030.4 907.48 1029.2 706.91 991.59 1025.1 811.26 1006.9 1178.2 1188.1 TRUE FALSE FALSE 1017.841088 920.2555273 1047.112794 788.6462603 940.9854622 959.5994184 880.1684042 1036.033063 1072.818841 1157.232991 0.879547245 0.795220612 0.90484181 0.681493067 0.813133975 0.829218857 0.760580118 0.89526748 0.927055182 1 10.17646364 -11.15061335 0.581398414 0.995576027 0.800766135 0.457582671 0.064007259 0.356323956 0.271957422 0.029714293 0.016750973 7.07E-12 11.15061335 -0.194809891 KESVSPEDS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 KESVSPEDSEK 11 1 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 1 0 KES(0.002)VS(0.218)PEDS(0.78)EK 105.65 0.0018548 0 6753.2 5441 6428.4 450 5650.5 6767.4 5138.1 4286.4 6189.5 4940.2 TRUE FALSE FALSE 6670.889401 5517.598541 6540.283605 502.0311173 5362.1339 6334.984981 5574.530086 4410.420221 5635.895618 4811.852892 1.38634525 1.146668168 1.359202734 0.104332183 1.114359483 1.316537542 1.15849969 0.916574201 1.171252685 1 12.23237682 KESYS(ph)VYVYK ddPTM_HeLa_Romidepsin_16h_R1 1 KESYSVYVYK 10 1 P58876;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P58876;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BD;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-D;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 1 0 KES(0.031)YS(0.969)VYVYK 116.71 0.021385 14515000 1127.2 1004 1041.6 740.52 1661.2 1129.6 1126.1 1192 905.57 717.96 TRUE FALSE FALSE 1113.461253 1018.134338 1059.728611 826.1424067 1576.422765 1057.422206 1221.750906 1226.488639 824.5735512 699.3072957 1.592234572 1.45591837 1.515397619 1.181372498 2.25426329 1.512099491 1.747087315 1.75386221 1.179129056 1 9.449782746 -14.06309814 0.191954581 4.98E-12 1.811554629 0.446932231 0.252860074 12.49938593 0.348739684 5.679724817 0.342207035 8.65E-15 14.06309814 1.811554629 KESYSIYVYK ddPTM_HeLa_Romidepsin_16h_R1 3 KESYSIYVYK 10 1 P06899;Q6DRA6;Q6DN03;P23527;P33778;Q16778;Q8N257 P06899;P23527;P33778;Q16778;Q8N257 HIST1H2BJ;HIST2H2BD;HIST2H2BC;HIST1H2BO;HIST1H2BB;HIST2H2BE;HIST3H2BB Histone H2B type 1-J;Putative histone H2B type 2-D;Putative histone H2B type 2-C;Histone H2B type 1-O;Histone H2B type 1-B;Histone H2B type 2-E;Histone H2B type 3-B 0 0 ;; ;; 153.54 0.0015715 28481400 17216.9 16357.7 17589.6 16992.6 19004.2 20479.7 15237.8 16080.1 16539.9 13962.3 FALSE FALSE TRUE 17007.0538 16587.98413 17895.73961 18957.36436 18034.34476 19171.11327 16532.09835 16545.35232 15060.52992 13599.55743 1.250559357 1.219744408 1.315906028 1.393969212 1.326097915 1.409686555 1.215635026 1.216609614 1.107427943 1 13.73127208 -11.79445098 0.512009122 0.97169753 1.31447341 0.644542067 0.07109654 0.433532312 0.202097712 0.070650821 0.019387897 1.61E-12 11.79445098 0.342775881 KESYSVYVYK ddPTM_HeLa_Romidepsin_16h_R1 2 KESYSVYVYK 10 1 P58876;Q5QNW6;Q5QNW6-2;Q93079;U3KQK0;Q99877;Q99879;Q99880 P58876;Q5QNW6;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BD;HIST2H2BF;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-D;Histone H2B type 2-F;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 0 ; ; 142.1 0.0016731 26665000 25954 21976 26952 25318 28035 27994 23873 22708 23674 20695 FALSE FALSE TRUE 25637.66267 22285.3787 27421.08825 28245.38628 26604.26934 26205.27375 25900.77202 23365.02015 21556.53815 20157.34092 1.271877217 1.105571355 1.360352458 1.40124565 1.319830301 1.300036243 1.284929998 1.159132063 1.06941378 1 14.29901772 -12.22149928 0.487440727 0.938419913 1.294542723 0.569722588 0.083792705 0.827521497 0.272579275 0.142809894 0.023154594 6.00E-13 12.22149928 0.35612281 KET(ph)ESEAEDNLDDLEK ddPTM_HeLa_Romidepsin_16h_R1 4 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 KET(0.5)ES(0.5)EAEDNLDDLEK;KET(0.599)ES(0.401)EAEDNLDDLEK;KET(0.807)ES(0.193)EAEDNLDDLEK;KET(0.834)ES(0.166)EAEDNLDDLEK ;;; 87.062 0.0064193 69802000 14470.2 13435.4 13323.6 14017.8 13627.1 13534.2 11169.2 13575.7 14796.4 15058.6 TRUE FALSE FALSE 14293.83164 13624.54391 13555.49167 15638.60399 12931.65824 12669.4083 12117.91157 13968.49146 13472.97293 14667.3754 0.974532338 0.928901289 0.924193409 1.066216931 0.881661366 0.863781553 0.82618132 0.952351125 0.918567403 1 13.84032312 -8.646760674 9.812358561 0.982313222 0.874957489 0.397119093 0.051193476 0.166983057 13.69265978 0.006555561 0.01311894 2.26E-09 8.646760674 -0.107355732 KET(ph)SFGSSENITMTSLSK ddPTM_HeLa_Romidepsin_16h_R1 1 KETSFGSSENITMTSLSK 18 1 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 KET(0.428)S(0.428)FGS(0.069)S(0.069)ENIT(0.007)MTSLSK 52.52 0.0040677 0 1333.6 1454.7 1421.9 1385.1 1425.9 1646.4 1235.9 1720.7 1666.3 1455.3 TRUE FALSE FALSE 1317.34557 1475.179305 1446.647573 1545.251779 1353.131002 1541.200354 1340.877315 1770.48574 1517.261955 1417.491096 0.929350155 1.040697405 1.020569072 1.090131559 0.954595768 1.087273393 0.945951138 1.249027768 1.070385527 1 10.46912396 -10.16281452 6.314771385 0.966722561 1.049182814 0.036851784 0.087619887 0.286396771 15.55460602 0.012479966 0.015316027 6.87E-11 10.16281452 0.082460253 KET(ph)SPESSLIQDEIAVK ddPTM_HeLa_Romidepsin_16h_R1 1 KETSPESSLIQDEIAVK 17 1 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 KET(0.783)S(0.217)PES(0.001)SLIQDEIAVK 117.03 0.0008982 27989000 5589.5 6208.4 6094.2 4674.1 7160.3 6129.8 5702.6 5880 6470.3 5856.7 TRUE FALSE FALSE 5521.373024 6295.802018 6200.266995 5214.541434 6794.883172 5738.125563 6186.978702 6050.128523 5891.580163 5704.54209 0.967890663 1.10364722 1.086900035 0.91410342 1.191135601 1.005887146 1.084570611 1.060580924 1.03278757 1 12.47789537 -10.27276575 24.82499036 0.984837256 1.062425835 0.140939414 0.068826362 686.6413369 1504965.925 0.010549063 0.012114743 5.34E-11 10.27276575 0.077588579 KETES(ph)EAEDNLDDLEK ddPTM_HeLa_Romidepsin_16h_R1 6 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 KET(0.37)ES(0.63)EAEDNLDDLEK;KET(0.075)ES(0.925)EAEDNLDDLEK;KET(0.276)ES(0.724)EAEDNLDDLEK;KET(0.374)ES(0.626)EAEDNLDDLEK;KET(0.05)ES(0.95)EAEDNLDDLEK;KET(0.135)ES(0.865)EAEDNLDDLEK ;;;;; 112.53 0.00089324 3148589000 17689 17782.8 16002.5 17093.4 16925.7 16612.7 14547.6 16797.3 17972.7 18816.3 TRUE FALSE FALSE 17473.39966 18033.14673 16281.0168 19069.81933 16061.91837 15551.20209 15783.27278 17283.30337 16365.1767 18327.44981 0.953400492 0.983941951 0.888340547 1.040505882 0.876385888 0.848519693 0.861182158 0.943028275 0.892932561 1 14.16171843 -8.733405381 24.98069204 0.974413676 0.878360634 0.344224968 0.049974321 123.0295997 109629.3725 0.006027271 0.012052487 1.85E-09 8.733405381 -0.096053042 KETESEAEDNLDDLEK ddPTM_HeLa_Romidepsin_16h_R1 1 KETESEAEDNLDDLEK 16 1 A9Z1X7;Q8IYB3;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 0 0 119.96 2.29E-05 0 2370.8 2067.6 2101.8 1985.6 2208.6 2308.6 1927.6 2304.7 2427.1 2167.8 FALSE FALSE TRUE 2341.903778 2096.707727 2138.380947 2215.184415 2095.886901 2161.087911 2091.330296 2371.382858 2210.014097 2111.480243 1.109128908 0.993003716 1.012740211 1.049114441 0.992614971 1.023494261 0.990456957 1.123090242 1.046665771 1 11.04403903 KETQS(ph)PEQVK ddPTM_HeLa_Romidepsin_16h_R1 3 KETQSPEQVK 10 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 KET(0.037)QS(0.963)PEQVK;KET(0.002)QS(0.998)PEQVK;KET(0.134)QS(0.866)PEQVK ;; 110.51 0.02295 72748700 9480.7 11224.8 20175.2 10792.7 9397.9 10263 25878.2 3363.78 18546.5 12134.3 TRUE FALSE FALSE 9365.145582 11382.82303 20526.34089 12040.60276 8918.290095 9607.227422 28076.29366 3461.105667 16887.65459 11819.04914 0.792377244 0.963091269 1.736716774 1.018745469 0.75456917 0.812859589 2.375512052 0.292841296 1.428850527 1 13.52882635 -9.977334699 24.99503167 0.900680973 1.193134452 0 0.563200083 515.5063188 568493.4098 0.080550888 0.105861179 1.05E-10 9.977334699 0.292453479 KETTSGTSTEPVKNS(ph)SPAPPQPAPGK ddPTM_HeLa_Romidepsin_16h_R1 1 KETTSGTSTEPVKNSSPAPPQPAPGK 26 2 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 KETTSGTS(0.001)T(0.002)EPVKNS(0.498)S(0.498)PAPPQPAPGK 59.996 0.0014554 29904000 3985.5 3682.3 3091.3 3754.2 3726.7 3599 2921 3149.4 4169.4 3986.6 TRUE FALSE FALSE 3936.923193 3734.139516 3145.10278 4188.278268 3536.512593 3369.035515 3169.109667 3240.52292 3796.478422 3883.027557 1.013879797 0.961656713 0.809961488 1.078611523 0.910761652 0.867631111 0.816144006 0.834535133 0.977710914 1 11.92296623 -7.587482217 0.381641686 1.009665183 0.69160571 0.411899288 0.067711797 2.806686177 0.333338852 0.020075736 0.391221315 2.59E-08 7.587482217 -0.318059473 KEWSGLLEELAR ddPTM_HeLa_Romidepsin_16h_R1 1 KEWSGLLEELAR 12 1 Q01813;Q01813-2;V9GYV7;Q5VSR5 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 0 0 107.99 0.0075357 7202800 2202.8 1570.7 2175.7 2356.2 1987.1 2463.5 1508.3 1668.8 2526.9 1777.9 FALSE FALSE TRUE 2175.951426 1592.812356 2213.567146 2628.63493 1885.690872 2306.090301 1636.414964 1717.084095 2300.887735 1731.709902 1.256533455 0.919791678 1.278255176 1.517941849 1.088918456 1.331683961 0.944970611 0.991554124 1.328679667 1 10.75798155 -7.723638582 24.94480539 1.157719399 0.96826191 0.191219969 0.173449726 235.6809879 155523.1459 0.02452491 0.091759558 1.89E-08 7.723638582 -0.189457489 KEYEEDDILAS(ph)DDPSSIEQYENTR ddPTM_HeLa_Romidepsin_16h_R1 2 KEYEEDDILASDDPSSIEQYENTR 24 1 Q96RS0 Q96RS0 TGS1 Trimethylguanosine synthase 1 0 KEYEEDDILAS(1)DDPSSIEQYENTR;KEYEEDDILAS(0.999)DDPS(0.001)SIEQYENTR ; 92.798 1.95E-05 43527000 6028.3 6051.1 5925.8 6449.3 7161.3 6847.8 6242.6 5752.3 6280 5702.3 TRUE FALSE FALSE 5954.824761 6136.287545 6028.936063 7194.998411 6795.832139 6410.24768 6772.846288 5918.733725 5718.301071 5554.153424 1.072139047 1.104810594 1.085482449 1.295426659 1.223558591 1.154135868 1.219420094 1.065641021 1.029554036 1 12.43935131 -10.11930707 0.94906786 1.023422144 1.188244255 0.528645907 0.061997249 0.272320087 0.484417579 0.013482265 0.017304823 7.60E-11 10.11930707 0.164822111 KFDVNTSAVQVLIEHIGNLDR ddPTM_HeLa_Romidepsin_16h_R1 1 KFDVNTSAVQVLIEHIGNLDR 21 1 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 144.27 5.59E-06 1546500 3115 2962.6 2985.5 3810.8 2964.5 3129.6 2637.5 3159 3544.3 3043.9 FALSE FALSE TRUE 3077.033182 3004.307561 3037.461375 4251.422626 2813.210503 2929.62866 2861.529184 3250.400681 3227.288931 2964.819039 1.037848564 1.013319033 1.02450144 1.433956869 0.948864152 0.988130682 0.965161498 1.096323465 1.088528132 1 11.53372834 -6.297597834 14.30220594 1.038527224 1.069894531 0 0.134344293 0 0 0.016899322 0 5.04E-07 6.297597834 0.031367307 T(ph)TPTLGLEEVLSSR ddPTM_HeLa_Romidepsin_16h_R1 3 TTPTLGLEEVLSSR 14 0 O43474-4;O43474-1;O43474 O43474-4 KLF4 Krueppel-like factor 4 1 0 T(0.997)T(0.003)PTLGLEEVLSSR;T(0.983)T(0.017)PTLGLEEVLSSR;T(0.996)T(0.004)PTLGLEEVLSSR ;; 185.66 1.48E-07 16241700 5502.6 4995.4 4430.8 3962.5 2903.35 2388.71 2014.94 2032.62 6087.7 5152 TRUE FALSE FALSE 5435.532195 5065.725372 4507.916215 4420.662894 2755.181216 2236.07914 2186.088953 2091.430653 5543.200865 5018.150297 1.083174451 1.0094806 0.89832228 0.880934733 0.549043184 0.44559828 0.435636405 0.416773219 1.104630299 1 12.29293997 -8.819876665 1.288582954 1.03619568 0.41009988 0.97082021 0.0464111 0.048505278 0.16044601 0.007499668 0.01909121 1.51E-09 8.819876665 -0.626095801 down VPTTPAS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 VPTTPASPVK 10 0 Q6IE81-2;Q6IE81 Q6IE81-2 JADE1 Protein Jade-1 1 0 VPT(0.005)T(0.406)PAS(0.589)PVK 102.97 0.022585 8295700 5415.7 4187.8 7086.1 3527.3 1798.4 1543.6 1213.7 954.58 5115.7 4476.4 TRUE FALSE FALSE 5349.691365 4246.755958 7209.430598 3935.143022 1706.620937 1444.968942 1316.791648 982.1992662 4658.138979 4360.102483 1.226964592 0.974003702 1.653500262 0.902534525 0.39141762 0.331407105 0.302009334 0.225269766 1.068355388 1 12.09014633 -8.816175044 3.480992766 1.139661247 0.301040313 0.832297105 0.184410475 0.071281838 1.758974299 0.027760154 0.054113917 1.53E-09 8.816175044 -0.838620933 down KFGVVVVGVGR ddPTM_HeLa_Romidepsin_16h_R1 1 KFGVVVVGVGR 11 1 C9J1E1;P53004 C9J1E1 BLVRA Biliverdin reductase A 0 0 89.679 0.018159 431490 271.75 187.84 238.99 324.21 194.6 251.06 186 209.33 296.51 136.56 FALSE FALSE TRUE 268.4378065 190.4844165 243.1495207 361.6966857 184.6688358 235.0180763 201.7988354 215.3866333 269.989403 133.0121515 2.018144985 1.432082816 1.828024868 2.719275506 1.38836064 1.766891773 1.517145863 1.619300424 2.029810058 1 7.055414241 -12.38940494 0.989556257 0.975486831 1.802680861 0 0.480555222 0.47194176 0.786508187 0.288736906 0.065654801 4.08E-13 12.38940494 0.82719403 KFGYVDFESAEDLEK ddPTM_HeLa_Romidepsin_16h_R1 2 KFGYVDFESAEDLEK 15 1 P19338 P19338 NCL Nucleolin 0 0 ; ; 137.79 0.00069019 95558000 10236.9 10635.3 9051.4 8946.2 8878 8812.4 7976.9 8416.4 10070 9026.7 FALSE FALSE TRUE 10112.12873 10785.02403 9208.93582 9980.601737 8424.922532 8249.316081 8654.457687 8659.915255 9169.313979 8792.185033 1.150126924 1.226660266 1.047400138 1.13516739 0.958228529 0.938255513 0.984335254 0.984955983 1.042893654 1 13.10200603 -8.749501417 24.86652288 1.087583925 0.965708293 0.523249053 0.061909606 176.9269566 368532.7023 0.011217661 0.022290935 1.78E-09 8.749501417 -0.121875632 KFLPSDINS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 KFLPSDINSGK 11 1 Q9H7E2-3 Q9H7E2-3 TDRD3 Tudor domain-containing protein 3 1 0 KFLPSDINS(1)GK 62.166 0.024917 14316000 4121.2 4246.7 4173.4 4624.2 4396.1 4075.8 3444.6 3837.5 4935 4643 TRUE FALSE FALSE 4070.969229 4306.485154 4246.036276 5158.871762 4171.750613 3815.369534 3737.184238 3948.532008 4493.60124 4522.374191 0.900184075 0.952262014 0.938895389 1.140744119 0.922469136 0.843665158 0.826376607 0.873110415 0.993637645 1 12.14286465 -8.377617083 4.583179459 0.964493324 0.846223081 0.473280665 0.063051644 0.182805633 6.081726278 0.009842209 0.022679344 4.19E-09 8.377617083 -0.118270243 KFNGEDIDTIS(ph)PTLGFNIK ddPTM_HeLa_Romidepsin_16h_R1 1 KFNGEDIDTISPTLGFNIK 19 1 V9GYD0;P36404-2;P36404 V9GYD0 ARL2-SNX15;ARL2 ADP-ribosylation factor-like protein 2 1 0 KFNGEDIDT(0.041)IS(0.931)PT(0.028)LGFNIK 94.389 0.00081922 17896000 7779.2 7215.7 6310.6 8524.4 6746.5 6203.5 5513.2 5572.7 7959.2 7082 TRUE FALSE FALSE 7684.384118 7317.282814 6420.433346 9510.031237 6402.20093 5807.116371 5981.49107 5733.937282 7247.309218 6898.008619 1.114000365 1.060781918 0.930766211 1.378663287 0.928123069 0.841854032 0.867133024 0.831245306 1.05063789 1 12.75196422 -8.534256106 24.99437514 1.069219506 0.854817202 0.495311819 0.110911343 144.1669637 316712.815 0.01566665 0.031354039 2.92E-09 8.534256106 -0.214402304 KGAANASGS(ph)SPDAPAK ddPTM_HeLa_Romidepsin_16h_R1 1 KGAANASGSSPDAPAK 16 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 KGAANAS(0.113)GS(0.586)S(0.301)PDAPAK 80.975 0.0070322 33225000 10144 9312.1 12221 8544.9 9182.6 10145 9310 5158.5 12570 11211 TRUE FALSE FALSE 10020.36103 9443.195988 12433.70138 9532.901543 8713.977657 9496.767241 10100.79117 5307.753059 11445.70772 10919.7366 0.917637612 0.864782396 1.138644807 0.872997389 0.79800255 0.869688307 0.925003188 0.486069697 1.048167015 1 13.41465044 -6.983058684 1.824585 0.945311805 5.32E-24 0.659348503 0.096584851 0.975523713 1.718186624 0.013231847 2.013858088 1.04E-07 6.983058684 -0.945311805 KGAANASGSS(ph)PDAPAK ddPTM_HeLa_Romidepsin_16h_R1 3 KGAANASGSSPDAPAK 16 1 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 KGAANASGS(0.036)S(0.964)PDAPAK;KGAANAS(0.01)GS(0.203)S(0.787)PDAPAK;KGAANAS(0.003)GS(0.113)S(0.884)PDAPAK ;; 135.29 0.00041417 79075600 25654.1 23723.8 28626.3 19612.2 21633.3 23578.8 23653.9 12053.9 27612.3 27067.7 TRUE FALSE FALSE 25341.41796 24057.78428 29124.52874 21879.85484 20529.27198 22072.19078 25663.06168 12402.66058 25142.58673 26364.47725 0.96119554 0.91250754 1.104688269 0.829899058 0.778671687 0.837194327 0.97339543 0.470430741 0.953653907 1 14.68630777 -6.5117895 0.521015826 0.979786907 6.51E-29 0.536715627 0.111633213 4.593926768 0.480253184 0.02073846 3.271067638 3.08E-07 6.5117895 -0.979786907 KGAANASGSS(ph)PDAPAKDAR ddPTM_HeLa_Romidepsin_16h_R1 2 KGAANASGSSPDAPAKDAR 19 2 E7EPJ7;O75962-4;O75962;O75962-5 E7EPJ7 TRIO Triple functional domain protein 1 0 KGAANASGS(0.045)S(0.955)PDAPAKDAR;KGAANAS(0.002)GS(0.11)S(0.887)PDAPAKDAR ; 63.125 0.010417 12220700 6231.1 5858.6 4683.9 8521.1 4654.9 4810.5 4919.9 4171.8 6156.1 5675.8 TRUE FALSE FALSE 6155.152956 5941.077525 4765.421315 9506.349675 4417.343083 4503.124575 5337.796183 4292.504451 5605.482998 5528.341898 1.113381385 1.074658123 0.861998299 1.719566165 0.799035799 0.814552475 0.965532936 0.77645423 1.01395375 1 12.43263113 KGAGDGS(ph)DEEVDGK ddPTM_HeLa_Romidepsin_16h_R1 12 KGAGDGSDEEVDGK 14 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 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 ;;;;;;;;;;; 198.61 2.77E-16 2967442400 43896.5 51069.2 67922.1 36897.9 51802.2 61070.9 70705.1 20533.15 66940.9 61376.4 TRUE FALSE FALSE 43361.47257 51788.15354 69104.25566 41164.20881 49158.54043 57168.66659 76710.78943 21127.2443 60953.53825 59781.83228 0.725328598 0.866285819 1.155940744 0.68857389 0.822298992 0.956288297 1.283178961 0.353405767 1.0195997 1 15.8674195 -7.230307675 24.64997554 0.897716705 0.353404617 0.476587801 0.180039692 8715.545222 6900813.56 0.025163245 4.758688108 5.88E-08 7.230307675 -0.544312088 KGAGDGSDEEVDGK ddPTM_HeLa_Romidepsin_16h_R1 1 KGAGDGSDEEVDGK 14 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 147.51 0.00039841 4772200 4439.8 4905.7 6136.1 3530.8 4719 5440.8 6474.7 1842 6216.6 5314.6 FALSE FALSE TRUE 4385.68601 4974.762573 6242.896247 3939.047709 4478.171821 5093.150439 7024.660856 1895.295364 5660.571726 5176.525926 0.84722574 0.961023405 1.206001155 0.760944264 0.865092126 0.983893544 1.357022249 0.36613269 1.093507848 1 12.33776848 KGAILSEEELAAMSPT(ph)AAAVAK ddPTM_HeLa_Romidepsin_16h_R1 2 KGAILSEEELAAMSPTAAAVAK 22 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 KGAILSEEELAAMS(0.314)PT(0.686)AAAVAK;KGAILSEEELAAMS(0.412)PT(0.588)AAAVAK ; 98.269 0.00010119 67350000 6133 6026.4 5226 8168.6 8896.5 9261.6 7971.9 8473.6 6293.1 5652.4 TRUE FALSE FALSE 6058.248637 6111.239817 5316.956338 9113.091966 8442.478408 8669.81365 8649.032987 8718.770247 5730.229375 5505.549833 1.100389393 1.11001444 0.965744839 1.655255559 1.533448731 1.574740746 1.570966252 1.583632972 1.040809646 1 12.42667094 -9.260957619 24.99999999 1.048734117 1.579627152 0.968508448 0.04869873 5.88520583 305399.4238 0.008283454 0.013207446 5.48E-10 9.260957619 0.530893035 KGATPGK(ac)ALVATPGKK ddPTM_HeLa_Romidepsin_16h_R1 1 KGATPGKALVATPGKK 16 3 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 K(0.089)GATPGK(0.911)ALVATPGKK 55.546 0.016412 2687200 1575 1160.1 1086.4 1034 1208.8 975.33 1410.7 1345.6 1847.9 1646.4 FALSE TRUE FALSE 1555.803294 1176.431918 1105.308336 1153.555945 1147.110425 913.0095607 1530.524823 1384.532813 1682.619196 1603.626291 0.970178216 0.733607278 0.68925556 0.719342126 0.715322786 0.569340604 0.954414898 0.863376225 1.049258924 1 10.64712226 -10.28045196 6.221649015 0.986408761 0.745214014 0.584675561 0.098904358 0.092178459 14.60490022 0.016927113 0.019682107 5.24E-11 10.28045196 -0.241194748 KGDRS(ph)PEPGQTWTR ddPTM_HeLa_Romidepsin_16h_R1 2 KGDRSPEPGQTWTR 14 2 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 KGDRS(0.736)PEPGQT(0.087)WT(0.177)R;KGDRS(0.638)PEPGQT(0.235)WT(0.127)R ; 113.43 0.0013142 9496700 6695.9 6695.6 5515.2 5859.4 6008.8 5578.6 4782.2 5958.5 7312.7 5768.5 TRUE FALSE FALSE 6614.287795 6789.860833 5611.189742 6536.891397 5702.148514 5222.145464 5188.399949 6130.899797 6658.633797 5618.633538 1.177205765 1.208454117 0.998675159 1.163430815 1.01486393 0.929433363 0.923427362 1.091172748 1.185098432 1 12.45600359 -8.558953756 8.297208679 1.093837825 0.974935782 0.353905346 0.083281925 0.244749324 50.07307949 0.013259753 0.026679724 2.76E-09 8.558953756 -0.118902043 KGDVEGSQS(ph)QDEGEGSGESER ddPTM_HeLa_Romidepsin_16h_R1 3 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 0 KGDVEGS(0.006)QS(0.876)QDEGEGS(0.049)GES(0.069)ER;KGDVEGS(0.003)QS(0.997)QDEGEGSGESER;KGDVEGS(0.216)QS(0.78)QDEGEGS(0.004)GES(0.001)ER ;; 147.76 5.15E-06 21567900 3578.17 3234.41 3387.42 3524.15 3030.88 3195.92 2646.49 3036.6 3907 3693 TRUE FALSE FALSE 3534.557888 3279.944109 3446.376624 3931.628805 2876.202884 2991.711026 2871.282795 3124.45923 3557.548135 3597.055328 0.982625388 0.91184144 0.95811054 1.093013158 0.799599289 0.831711151 0.798231479 0.868615839 0.989016796 1 11.81260063 -8.742818033 24.99995062 0.988460512 0.823172513 0.753959019 0.046050158 87.51606282 117493.4567 0.006452073 0.012886347 1.81E-09 8.742818033 -0.165287999 KGDVEGSQSQDEGEGS(ph)GESER ddPTM_HeLa_Romidepsin_16h_R1 1 KGDVEGSQSQDEGEGSGESER 21 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 1 0 KGDVEGSQS(0.069)QDEGEGS(0.883)GES(0.048)ER 99.6 0.00014054 3408500 765.62 737.69 502.84 556.96 620.91 649.64 511.27 698 1070.8 865.4 TRUE FALSE FALSE 756.288329 748.0752192 511.5917193 621.3583358 589.2226458 608.1301006 554.697261 718.1955287 975.0249661 842.9167832 0.89722775 0.887484072 0.60693028 0.737152644 0.699028252 0.721459239 0.65806883 0.8520361 1.156727432 1 9.719246398 -9.921995352 5.277266224 0.948799002 0.71134789 0.679520098 0.091305656 0.075731018 3.734341361 0.010794876 0.014243808 1.20E-10 9.921995352 -0.237451112 KGDYIEAESSYSR ddPTM_HeLa_Romidepsin_16h_R1 1 KGDYIEAESSYSR 13 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 0 91.307 0.013745 6146800 1667.4 1532.8 1541.8 1770.6 2011.8 2063.3 2293.5 2318.4 2049.7 1328.7 FALSE FALSE TRUE 1647.077087 1554.378799 1568.634382 1975.325103 1909.130339 1931.461789 2488.309833 2385.479246 1866.369698 1294.180182 1.272679886 1.201052852 1.212067998 1.526313824 1.475165796 1.492421083 1.922691961 1.843235802 1.442125079 1 10.33782278 -4 0.194259993 0.989811122 5.441402269 0.670126216 0.155991847 11.51747242 0.130237662 0.101913054 15.58342112 1.00E-04 4 4.451591147 KGEQGGPPPKASPS(ph)TAGETPSGVK ddPTM_HeLa_Romidepsin_16h_R1 1 KGEQGGPPPKASPSTAGETPSGVK 24 2 A0A087WW69;F8W8L6;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WW69 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 0 KGEQGGPPPKAS(0.127)PS(0.627)T(0.23)AGET(0.015)PS(0.001)GVK 87.671 4.17E-05 38096000 5811.6 5508.2 5723.6 5345 4926.5 5707.9 5386.6 5276.5 5406.5 5852.5 TRUE FALSE FALSE 5740.765984 5585.744584 5823.216857 5963.014049 4675.082322 5343.183611 5844.13767 5429.167203 4922.929099 5700.451206 1.007072208 0.979877624 1.021536129 1.046060011 0.820124961 0.937326436 1.025206156 0.952410082 0.86360341 1 12.4768604 KGEQGGPPPKASPSTAGET(ph)PSGVK ddPTM_HeLa_Romidepsin_16h_R1 1 KGEQGGPPPKASPSTAGETPSGVK 24 2 A0A087WW69;F8W8L6;A0A087WTA5;E7ERK9;Q9UI10-3;Q9UI10;Q9UI10-2 A0A087WW69 EIF2B4 Translation initiation factor eIF-2B subunit delta 1 0 KGEQGGPPPKAS(0.033)PS(0.267)T(0.302)AGET(0.39)PS(0.008)GVK 42.325 0.027206 13578000 1028.9 1132.3 1144.4 1008.5 1187.9 1198.3 1246.8 1111.4 1459.3 1462.8 TRUE FALSE FALSE 1016.359371 1148.240549 1164.317802 1125.107515 1127.27703 1121.732497 1352.703161 1143.556606 1328.776553 1424.796245 0.713336643 0.805898074 0.81718197 0.789662044 0.791184728 0.787293272 0.949401127 0.802610625 0.932608124 1 10.4765399 -12.48997644 1.230022651 1.000150354 0.799916356 0.533372445 0.058345488 0.256533192 0.693682942 0.043183522 0.010492927 3.24E-13 12.48997644 -0.200233998 KGGEFDEFVNDDT(ph)DDDLPISK ddPTM_HeLa_Romidepsin_16h_R1 3 KGGEFDEFVNDDTDDDLPISK 21 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 0 KGGEFDEFVNDDT(0.999)DDDLPIS(0.001)K;KGGEFDEFVNDDT(0.998)DDDLPIS(0.002)K;KGGEFDEFVNDDT(0.991)DDDLPIS(0.009)K ;; 78.057 0.0014967 467265000 14507.6 14098 13883.7 14548.7 14570.7 15690.8 13862.7 15363.7 14629.7 14648.2 TRUE FALSE FALSE 14330.77579 14296.47201 14125.33997 16230.88915 13827.10281 14688.20852 15040.19739 15808.22442 13321.18299 14267.63765 1.004425269 1.002020963 0.990026542 1.137601721 0.969123491 1.02947726 1.054147698 1.107977705 0.933664235 1 13.80045886 -4 0.348932886 1.001316196 2.110434142 0.332065237 0.048109266 46.768181 0.586287671 0.011870122 34.54466357 1.00E-04 4 1.109117946 KGGEFDEFVNDDT(ph)DDDLPISKK ddPTM_HeLa_Romidepsin_16h_R1 2 KGGEFDEFVNDDTDDDLPISKK 22 2 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 1 0 KGGEFDEFVNDDT(1)DDDLPISKK;KGGEFDEFVNDDT(1)DDDLPISKK ; 88.872 0.0030214 34201000 4884.9 4634.36 4028.64 5935.7 5295.9 5301.12 4502.02 5125.14 4653.34 4160.32 TRUE FALSE FALSE 4825.36096 4699.602642 4098.756789 6622.013562 5025.630461 4962.395541 4884.421466 5273.42784 4237.133616 4052.234287 1.190790221 1.159755905 1.011480704 1.634163549 1.240212215 1.224607263 1.205365021 1.301363018 1.045628983 1 11.98450187 -11.42716523 0.362180989 0.962046935 1.291055555 0.309412128 0.144434399 1.486306951 0.415653817 0.198999235 0.074199922 3.74E-12 11.42716523 0.329008621 KGGPGSTLSFVGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 KGGPGSTLSFVGKR 14 2 Q9BQ61 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 1 ; KGGPGSTLSFVGK(1)R;KGGPGSTLSFVGK(1)R 129.01 0.00045416 4318800 2025.48 2114.6 1441.24 1800.45 1859.84 1824.82 2230.51 1755.33 2592.6 1951.71 FALSE TRUE FALSE 2000.792671 2144.369394 1466.324178 2008.6265 1764.925425 1708.219891 2419.969464 1806.117704 2360.711363 1901.004293 1.052492453 1.128019228 0.771341855 1.056613343 0.92841738 0.898588129 1.272995265 0.950086073 1.241823268 1 10.89254607 -7.781688631 24.99979153 1.003182083 1.111540978 0.075148377 0.141508048 318.9477384 393774.5879 0.015465184 0.04647785 1.65E-08 7.781688631 0.108358895 KGGS(ph)WIQEINVAEK ddPTM_HeLa_Romidepsin_16h_R1 1 KGGSWIQEINVAEK 14 1 P78527-2;P78527 P78527-2 PRKDC DNA-dependent protein kinase catalytic subunit 1 0 KGGS(1)WIQEINVAEK 89.624 0.0028297 0 1055.9 1301.6 1098.4 940.46 1098.9 1083.1 886.69 1114.5 1313.5 1371.8 TRUE FALSE FALSE 1043.030285 1319.923959 1117.517191 1049.20041 1042.819032 1013.893406 962.0054265 1146.746299 1196.01727 1336.160438 0.780617548 0.987848406 0.836364526 0.785235351 0.780459444 0.758811125 0.719977481 0.858239974 0.895115015 1 10.38387753 -16.52287875 0.209697907 1.967903781 0.771680328 0.342179609 0.073404216 28.81390515 0.357638851 11.44701019 0.063125349 3.00E-17 16.52287875 -1.196223453 KGLPLGSAVS(ph)S(ph)PVLFSPVGR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLPLGSAVSSPVLFSPVGR 20 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 2 0 KGLPLGS(0.231)AVS(0.652)S(0.503)PVLFS(0.614)PVGR 80.786 0.0015277 26389000 3027.5 2479.5 2940.3 3150.9 4526.1 5274.6 4846.5 5407.7 3198 2714.7 TRUE FALSE FALSE 2990.599666 2514.406466 2991.474688 3515.221883 4295.116228 4937.570083 5258.161589 5564.163268 2911.96287 2644.171703 1.131015683 0.950924051 1.131346609 1.3294227 1.624371149 1.867340944 1.988585531 2.104312387 1.101276013 1 11.36860015 -8.580639169 1.06647526 1.050132859 2.080937477 0.982134229 0.0552147 0.054942254 0.117225082 0.010523331 0.037348174 2.63E-09 8.580639169 1.030804618 up KGLPLGSAVSS(ph)PVLFS(ph)PVGR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLPLGSAVSSPVLFSPVGR 20 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 2 0 KGLPLGS(0.001)AVS(0.468)S(0.62)PVLFS(0.911)PVGR 49.266 0.025481 12865000 2113.3 2090.8 2187.6 2418.1 2922.1 3100.6 2866.5 3470 2173.2 2316.8 TRUE FALSE FALSE 2087.542287 2120.234337 2225.67426 2697.6921 2772.974333 2902.481667 3109.980438 3570.398975 1978.823549 2256.609202 0.925079223 0.939566468 0.986291405 1.195462687 1.228823463 1.286213698 1.378165274 1.582196409 0.876901303 1 11.13994088 -8.11688746 0.633937623 0.956514421 1.631042622 0.929567468 0.058350855 0.281014267 0.139284758 0.011515597 0.112334801 7.64E-09 8.11688746 0.674528201 KGLPLGSAVSS(ph)PVLFSPVGR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLPLGSAVSSPVLFSPVGR 20 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 0 KGLPLGSAVS(0.018)S(0.963)PVLFS(0.019)PVGR 98.973 0.00022417 28142000 3425.8 3189.7 3082.6 4023.2 3315.2 2925.4 2164.4 2682 3440.9 3249.6 TRUE FALSE FALSE 3384.045032 3234.60468 3136.25136 4488.381314 3146.012973 2738.476381 2348.244082 2759.599439 3133.137286 3165.174924 1.069149451 1.02193552 0.990861938 1.418051584 0.993946006 0.865189586 0.741900255 0.871863169 0.989878083 1 11.62806952 -8.259248634 3.74814123 1.057787826 0.81098659 0.448813071 0.124523574 0.16142201 5.090030079 0.017595635 0.045169219 5.50E-09 8.259248634 -0.246801236 KGLPLGSAVSSPVLFS(ph)PVGR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLPLGSAVSSPVLFSPVGR 20 1 Q8WUM0 Q8WUM0 NUP133 Nuclear pore complex protein Nup133 1 0 KGLPLGSAVS(0.124)S(0.124)PVLFS(0.753)PVGR 66.264 0.0033705 17542000 1679.9 1759.8 1771.1 1891.2 1423 1531.3 1001.7 1591.4 1913.4 1337.6 TRUE FALSE FALSE 1659.424733 1784.574511 1801.925253 2109.869442 1350.379 1433.454872 1086.784373 1637.444648 1742.260712 1302.848959 1.273689265 1.369747812 1.383065351 1.619427507 1.03648162 1.100246396 0.834159912 1.25681848 1.337269911 1 10.34745412 -6.930220679 21.12321976 1.170253871 3.835444615 0 0.221399716 3463.083301 1101471.823 0.031940882 22017.76337 1.17E-07 6.930220679 2.665190744 KGLTPSQIGVILR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLTPSQIGVILR 13 1 P62277;J3KMX5 P62277 RPS13 40S ribosomal protein S13 0 0 129.76 1.03E-09 0 612.34 667.5 723.21 643.65 467.8 705.77 637.58 622.94 664.02 544.39 FALSE FALSE TRUE 604.8765646 676.8970825 735.7971667 718.0718415 443.9264204 660.6735748 691.7360293 640.9637861 604.6283881 530.2466693 1.140745618 1.276570173 1.387650709 1.354222257 0.837207372 1.245974021 1.304555161 1.20880304 1.140277579 1 9.050519843 -11.10258643 1.051664607 1.027548987 1.225705687 0.133271978 0.148840176 0.468342398 1.088078119 0.041816694 0.031783893 7.90E-12 11.10258643 0.1981567 KGLVGPELHDR ddPTM_HeLa_Romidepsin_16h_R1 1 KGLVGPELHDR 11 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 60.49 0.02142 9430200 6457.2 5336.6 6649.8 6845.7 4426.2 4707.5 4582.3 4736.5 5268.8 5775.4 FALSE FALSE TRUE 6378.497163 5411.728795 6765.53698 7637.232044 4200.314498 4406.705943 4971.520448 4873.543155 4797.545332 5625.354275 1.133883637 0.962024529 1.202686382 1.357644634 0.74667555 0.783365052 0.883770195 0.866353107 0.852843234 1 12.45772824 -8.728281756 24.99999965 1.086285204 0.821973246 0.483457542 0.134082391 114.6754776 86461.92362 0.017390143 0.034778504 1.87E-09 8.728281756 -0.264311957 KGNPDSVSNT(ph)PEMEQR ddPTM_HeLa_Romidepsin_16h_R1 1 KGNPDSVSNTPEMEQR 16 1 C9J6P7;E9PH71;O15381-2;O15381 C9J6P7 NVL Nuclear valosin-containing protein-like 1 0 KGNPDSVS(0.001)NT(0.999)PEMEQR 69.255 0.0026401 0 975 1077.9 1027.9 949.63 1204.5 1428 1587.8 1369.5 1321 907.63 TRUE FALSE FALSE 963.116325 1093.074704 1045.790168 1059.430689 1143.02987 1336.755409 1722.667692 1409.124322 1202.846451 884.0496418 1.089436927 1.236440413 1.182954123 1.198383709 1.292947609 1.51208184 1.948609683 1.593942529 1.360609625 1 9.787983573 -8.262261848 0.700901599 1.049311356 1.890634029 0.662063692 0.153907329 0.303757692 0.209444082 0.020983547 0.1561264 5.47E-09 8.262261848 0.841322673 KGNS(ph)PNSEPPTPK ddPTM_HeLa_Romidepsin_16h_R1 4 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 KGNS(0.525)PNS(0.475)EPPTPK;KGNS(0.985)PNS(0.015)EPPTPK;KGNS(0.795)PNS(0.205)EPPTPK;KGNS(0.998)PNS(0.002)EPPTPK ;;; 191.01 1.40E-10 70760800 24593.8 22583.2 20929.8 21408.5 19090.5 20960.4 18965.1 19388.5 22526.5 22474.8 TRUE FALSE FALSE 24294.04131 22901.12688 21294.07439 23883.8515 18116.24055 19621.09809 20575.99512 19949.47566 20511.67342 21890.90146 1.109778021 1.046148188 0.972736296 1.091040109 0.827569417 0.896312933 0.93993366 0.911313575 0.936995375 1 14.41804374 -8.76773123 24.99973605 1.048430476 0.897259663 0.541975796 0.057405102 69.64682859 276732.4567 0.008031361 0.014819654 1.71E-09 8.76773123 -0.151170812 KGNSPNS(ph)EPPTPK ddPTM_HeLa_Romidepsin_16h_R1 1 KGNSPNSEPPTPK 13 1 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 KGNS(0.029)PNS(0.971)EPPTPK 133.87 0.0005377 50277000 17128 16266 15481 16493 15551 15107 14633 14167 17350 16135 TRUE FALSE FALSE 16919.23735 16494.99317 15750.44031 18399.99826 14757.37444 14141.71146 15875.92665 14576.89979 15798.17255 15715.81037 1.076574287 1.04957955 1.002203509 1.170795385 0.93901454 0.899839787 1.010188229 0.927530903 1.005240721 1 13.93992905 KGPAAPPPT(ph)PVKPPR ddPTM_HeLa_Romidepsin_16h_R1 1 KGPAAPPPTPVKPPR 15 2 E9PIE3;Q969G5 E9PIE3 PRKCDBP Protein kinase C delta-binding protein 1 0 KGPAAPPPT(1)PVKPPR 58.997 0.025885 11768000 1862.5 1534.8 2050.9 3063.3 1673.4 1522.4 1454 1244.4 1763.1 1768.8 TRUE FALSE FALSE 1839.799134 1556.406955 2086.595054 3417.493159 1588.000154 1425.123553 1577.502724 1280.404751 1605.40392 1722.846321 1.067883485 0.903392796 1.211132432 1.983632038 0.921730589 0.827191338 0.915637515 0.743191505 0.931832341 1 10.7505783 -8.538212318 24.99891699 1.110725187 0.843551333 0.21317666 0.296085967 352.3560899 574458.3083 0.04439561 0.08881461 2.90E-09 8.538212318 -0.267173854 KGPELPLVPVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 KGPELPLVPVKR 12 2 Q96DI7;Q96DI7-2 Q96DI7 SNRNP40 U5 small nuclear ribonucleoprotein 40 kDa protein 0 1 ; KGPELPLVPVK(1)R;KGPELPLVPVK(1)R 96.82 0.0075759 0 4096.5 4151.3 3803.5 4194.4 3788.7 3647 3604 3281.6 5342.2 3916 FALSE TRUE FALSE 4046.570282 4209.74211 3869.698322 4679.376263 3595.348501 3413.96847 3910.12367 3376.547918 4864.380252 3814.261755 1.06090524 1.103684639 1.014534023 1.226810472 0.942606652 0.895053536 1.025132495 0.885242843 1.275313695 1 11.89718814 -8.586243286 25 1.048380408 0.93991358 0.325153884 0.101144083 52.40477613 20675.49094 0.010272912 0.020545827 2.59E-09 8.586243286 -0.108466828 KGPGLAVQSGDK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 KGPGLAVQSGDKTK 14 2 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 0 1 ; KGPGLAVQSGDK(1)TK;KGPGLAVQSGDK(1)TK 98.676 0.017772 7432400 5600.3 5250.2 4843 5422.3 7388.6 8370.5 7921.5 8881.1 5790.3 5232.9 FALSE TRUE FALSE 5532.04139 5324.112453 4927.290383 6049.251839 7011.532171 7835.652065 8594.352012 9138.060616 5272.401066 5096.948504 1.085363406 1.044568618 0.966713786 1.186837935 1.375633316 1.537322196 1.686175955 1.792849312 1.03442306 1 12.31541806 -8.358666393 1.038876685 1.033394062 1.788195533 0.976986364 0.044003875 0.070300741 0.132341111 0.00821266 0.037917877 4.38E-09 8.358666393 0.754801471 KGPGQPSS(ph)PQRLDR ddPTM_HeLa_Romidepsin_16h_R1 1 KGPGQPSSPQRLDR 14 2 O95400 O95400 CD2BP2 CD2 antigen cytoplasmic tail-binding protein 2 1 0 KGPGQPS(0.248)S(0.752)PQRLDR 95.073 0.013186 15313000 3857.7 3486.6 3435.1 4518.5 3669.6 3613.5 2941.1 3631 4355.9 3422.9 TRUE FALSE FALSE 3810.680869 3535.684446 3494.886475 5040.95023 3482.326619 3382.609012 3190.916961 3736.057256 3966.297394 3333.972565 1.142985071 1.060501962 1.048264917 1.511995115 1.044497683 1.014588137 0.957091547 1.12060228 1.189661078 1 11.70302652 -6.883181784 19.15703159 1.08454986 7.357654746 0 0.15131441 3176.360682 521415.5909 0.020172278 876.0809683 1.31E-07 6.883181784 6.273104886 KGQASLYGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 KGQASLYGKR 10 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 1 ; KGQASLYGK(1)R;KGQASLYGK(1)R 99.343 0.017137 5229000 764.36 836.86 4153.4 2300.3 7040.6 13015.5 7735.4 2396.8 733.39 355.32 FALSE TRUE FALSE 755.0436863 848.641337 4225.688185 2566.271509 6681.29191 12183.85156 8392.444683 2466.147626 667.7937616 346.0887352 2.18164768 2.452091764 12.2098403 7.415068011 19.30514123 35.20441528 24.24940147 7.125766822 1.929544922 1 8.434998174 -9.105505308 1.257435055 1.702570289 22.74907543 0.583730797 7.043681801 0.210119968 0.655804715 1.158135974 2.468226526 7.84E-10 9.105505308 21.04650514 KGQTHTLEDFQR ddPTM_HeLa_Romidepsin_16h_R1 1 KGQTHTLEDFQR 12 1 Q5H928;Q99714-2;Q99714 Q5H928 HSD17B10 3-hydroxyacyl-CoA dehydrogenase type-2 0 0 69.864 0.015107 4846800 2205.8 2114.3 2182.2 2354 1953.7 1979.9 1597.9 1632 1778.3 1743.4 FALSE FALSE TRUE 2178.914861 2144.065171 2220.180276 2626.180556 1853.995399 1853.39078 1733.625586 1679.219345 1619.244394 1698.106217 1.283144034 1.262621354 1.307444878 1.546534916 1.091801785 1.09144573 1.020917048 0.988877685 0.953558958 1 10.72971099 -8.187294749 2.584427855 1.190027293 1.015750093 0.207944626 0.159886779 0.439538664 5.690016209 0.025759325 0.077016274 6.50E-09 8.187294749 -0.1742772 KGS(ph)DSDT(ph)DAS(ph)NLET(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KGSDSDTDASNLETPR 16 1 P0CG40 P0CG40 SP9 Transcription factor Sp9 4 0 KGS(0.97)DS(0.1)DT(0.968)DAS(0.968)NLET(0.994)PR 54.259 0.0040888 0 1060 1186 1108.1 1226.8 1161.8 954.38 896.3 1020.4 1242.4 1025.7 TRUE FALSE FALSE 1047.080312 1202.696539 1127.386016 1368.648388 1102.509011 893.3981981 972.4316996 1049.923664 1131.276632 999.0521661 1.048073712 1.203837577 1.128455604 1.36994687 1.103554998 0.894245795 0.973354278 1.050919761 1.132349912 1 9.964416201 -6.050137608 10.98419958 1.057994607 0.620904815 0 0.129862662 0 0 0.018057174 0 8.91E-07 6.050137608 -0.437089792 KGS(ph)GS(ph)EQEGEDEEGGER ddPTM_HeLa_Romidepsin_16h_R1 1 KGSGSEQEGEDEEGGER 17 1 Q6PD62 Q6PD62 CTR9 RNA polymerase-associated protein CTR9 homolog 2 0 KGS(1)GS(1)EQEGEDEEGGER 128.88 0.0019091 14421000 3872.5 3647.9 3611.9 3569.8 3896.3 3822 3541.8 3701.6 3928.4 3554.4 TRUE FALSE FALSE 3825.30048 3699.255232 3674.763604 3982.557072 3697.457272 3577.786535 3842.640404 3808.699956 3577.034065 3462.056176 1.104921551 1.068513925 1.061439624 1.15034444 1.067994592 1.033428215 1.109930113 1.100126561 1.033210868 1 11.75741342 -12.35010563 0.883085835 0.995421544 1.087507046 0.424578276 0.031965914 0.420030397 0.538577286 0.026820367 0.005767074 4.47E-13 12.35010563 0.092085502 KGS(ph)ITEYTAAEEK ddPTM_HeLa_Romidepsin_16h_R1 1 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 0 KGS(0.994)IT(0.006)EYTAAEEK 103.66 0.01633 93678000 2860.4 3096.4 3141.5 2691.4 3661.1 4007.8 3411.3 3558.9 3309.5 3441.5 TRUE FALSE FALSE 2825.536345 3139.9912 3196.17649 3002.592331 3474.260406 3751.714515 3701.055737 3661.871156 3013.490031 3352.089334 0.842917972 0.936726587 0.953487861 0.895737563 1.036446246 1.119216745 1.104104148 1.092414549 0.89898858 1 11.71084488 -8.579278368 3.642749202 0.925528913 1.103146952 0.817139101 0.039516491 0.10652144 2.895348583 0.008714854 0.018682092 2.63E-09 8.579278368 0.177618039 KGS(ph)MT(ph)MS(ph)IQWKT(ph)RQLQS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 KGSMTMSIQWKTRQLQSK 18 3 H0Y327;A0A087WVM4;B7ZM99;Q6UB35;Q6UB35-2 H0Y327 MTHFD1L "Monofunctional C1-tetrahydrofolate synthase, mitochondrial" 5 0 KGS(1)MT(1)MS(1)IQWKT(1)RQLQS(1)K 45.14 0.024536 3691100 431.72 557.62 273.84 295.09 495.44 451.11 295.33 458.92 495.73 478.87 TRUE FALSE FALSE 426.4580306 565.470189 278.6060703 329.2096942 470.1558481 422.2855269 320.4153228 472.1981261 451.3906672 466.4288884 0.914304498 1.212339551 0.597317356 0.705808972 1.007990414 0.905358861 0.686954284 1.012368955 0.967758813 1 8.865513335 -9.758845707 24.99999906 0.977362479 0.820614086 0.294214538 0.14824421 81.56074671 786145.7964 0.023036688 0.031729893 1.74E-10 9.758845707 -0.156748393 KGS(ph)QITQQSTNQSR ddPTM_HeLa_Romidepsin_16h_R1 1 KGSQITQQSTNQSR 14 1 P50750;P50750-2 P50750 CDK9 Cyclin-dependent kinase 9 1 0 KGS(0.998)QIT(0.002)QQSTNQSR 63.374 0.022792 3018500 720.9 834.74 650.06 643.74 736.38 870.27 543.26 697.83 854.9 825.23 TRUE FALSE FALSE 712.1133935 846.4914916 661.3740216 718.1722477 698.7997808 814.6625557 589.4044908 718.0206101 778.4356029 803.7904056 0.885944132 1.053124653 0.822819005 0.893481986 0.869380595 1.013526101 0.733281321 0.893293332 0.968455952 1 9.650675547 -16.52287874 0.091178688 1.353656735 0.795266057 0.203499818 0.081902693 159.3799218 1.098801165 11.18768427 0.928494773 3.00E-17 16.52287874 -0.558390678 KGSIT(ph)EYTAAEEK ddPTM_HeLa_Romidepsin_16h_R1 1 KGSITEYTAAEEK 13 1 J3KN59;Q12982;Q12982-2 J3KN59 BNIP2 BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 1 0 KGS(0.005)IT(0.6)EYT(0.395)AAEEK 137.73 0.0034132 74616000 2492.9 2258.8 2241.3 1915.6 2577.3 2432.1 2050.2 2421.3 2005.2 2319 TRUE FALSE FALSE 2462.515576 2290.599446 2280.308886 2137.090685 2445.770764 2276.696659 2224.343937 2491.356495 1825.84989 2258.752046 1.090210668 1.014099556 1.009543695 0.946137797 1.082797365 1.007944481 0.984766761 1.102979187 0.808344543 1 11.14131019 KGTENGVNGTLTSNVADS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 KGTENGVNGTLTSNVADSPR 20 1 G3XAN4;Q15629-2;Q15629 G3XAN4 TRAM1 Translocating chain-associated membrane protein 1 1 0 KGTENGVNGT(0.008)LT(0.006)S(0.017)NVADS(0.969)PR;KGTENGVNGTLTSNVADS(1)PR ; 152.03 2.75E-06 25489000 5517.4 8171.7 5003 2994.2 4651.3 7080.3 3763.1 7460.4 7089 8426.5 TRUE FALSE FALSE 5450.151807 8286.741407 5090.075116 3340.403492 4413.926805 6627.891681 4082.73762 7676.254903 6454.942085 8207.578315 0.664038965 1.009645122 0.620167718 0.406990145 0.537786742 0.807533163 0.49743511 0.93526429 0.786461224 1 13.0027409 -12.58062122 0.405269472 1.141232277 0.649241434 0.126472071 0.190190438 2.655163512 0.475555087 0.57639274 0.058650471 2.63E-13 12.58062122 -0.491990844 KGVAINFVK ddPTM_HeLa_Romidepsin_16h_R1 2 KGVAINFVK 9 1 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 0 0 ; ; 125.82 0.00011305 0 2611.6 2379.5 3708.6 2708.9 4235.6 5202.8 4224.7 3941.9 2278.6 1799.82 FALSE FALSE TRUE 2579.768815 2412.998663 3773.146627 3022.115764 4019.441527 4870.357871 4583.545913 4055.952657 2074.796309 1753.060417 1.471580095 1.376449231 2.152319789 1.723908506 2.292814034 2.778203092 2.614596661 2.313641115 1.183528125 1 10.77566 -9.386266785 0.461200211 1.08003997 2.745057685 0.848056349 0.23001742 0.291446235 0.123048898 0.076218507 0.199994123 4.11E-10 9.386266785 1.665017716 up KGVAINMVTEEDK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 KGVAINMVTEEDKR 14 2 P60842 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 1 ; KGVAINMVTEEDK(1)R;KGVAINMVTEEDK(1)R 65.565 0.013807 7612900 2273.5 2679.7 2386.12 1921.68 5322.8 5226.1 4183.3 4286.8 6084.8 4264.9 FALSE TRUE FALSE 2245.789708 2717.424887 2427.649418 2143.873683 5051.157654 4892.169076 4538.629398 4410.831795 5540.560248 4154.097283 0.540620393 0.654155332 0.584398788 0.516086538 1.215945923 1.177673209 1.09256695 1.06180272 1.333757943 1 12.02031929 -8.748959657 24.99999667 0.734034228 1.136729113 0.358094801 0.236559518 154.4855714 309471.2644 0.029769281 0.059210232 1.78E-09 8.748959657 0.402694885 KGVDLLLEGVQGES(ph)SPTRR ddPTM_HeLa_Romidepsin_16h_R1 1 KGVDLLLEGVQGESSPTRR 19 2 F5H7T0;F6RJM5;Q96S38-2;Q96S38 F5H7T0 RPS6KC1 Ribosomal protein S6 kinase delta-1 1 0 KGVDLLLEGVQGES(0.769)S(0.183)PT(0.048)RR 63.398 0.024979 10445000 2056.6 1598.6 1993.5 1466.2 2641.2 2525.1 2349.9 2989.1 1794.9 1743.3 TRUE FALSE FALSE 2031.533368 1621.105133 2028.196031 1635.728943 2506.409708 2363.754259 2549.500447 3075.584892 1634.359649 1698.008815 1.196420979 0.954709492 1.194455537 0.963321821 1.476087572 1.392074198 1.501464789 1.81128912 0.962515409 1 10.72962823 -6.490928705 0.459942953 1.068523201 3.022025682 0.799118871 0.124356689 2.796405484 0.23841649 0.026919042 3.473907708 3.23E-07 6.490928705 1.953502481 KGVITVK(ac)DGK ddPTM_HeLa_Romidepsin_16h_R1 2 KGVITVKDGK 10 2 P10809;E7EXB4 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 ; KGVITVK(1)DGK;KGVITVK(1)DGK 108.72 0.00080687 0 11654.8 11713.6 11670.6 12150.5 14112.5 14661.3 13315.7 14207.3 11604.8 10882.9 FALSE TRUE FALSE 11512.74681 11878.50437 11873.7219 13555.39798 13392.28646 13724.49025 14446.73523 14618.36581 10566.83762 10600.16069 1.086091726 1.120596632 1.120145462 1.278791745 1.263404099 1.294743603 1.362878889 1.379070208 0.996856362 1 13.37179851 -8.875373476 0.378424156 1.005810131 1.457598807 0.961483313 0.026605287 0.261715617 0.059519119 0.010589963 0.04694396 1.33E-09 8.875373476 0.451788676 KGVNLPGAAVDLPAVSEK ddPTM_HeLa_Romidepsin_16h_R1 2 KGVNLPGAAVDLPAVSEK 18 1 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34;H3BR70 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ; ; 142.35 0.00014986 11840430 5894.96 5624.46 5989.3 4396.41 5862.02 6016.18 5385.37 5970.85 6149.79 6056.59 FALSE FALSE TRUE 5823.10996 5703.641296 6093.541254 4904.74361 5562.859245 5631.765514 5842.803193 6143.607124 5599.73738 5899.238919 0.987095122 0.966843583 1.032936848 0.831419727 0.942979141 0.954659676 0.990433389 1.041423683 0.949230478 1 12.52631312 KHFDS(ph)Y(ph)IETALDGR ddPTM_HeLa_Romidepsin_16h_R1 1 KHFDSYIETALDGR 14 1 E9PD17;B7Z8Q8;Q6NUS8-2;Q6NUS8 E9PD17 UGT3A1 UDP-glucuronosyltransferase 3A1 2 0 KHFDS(1)Y(1)IETALDGR 81.632 0.0015119 0 693.08 407.42 719.8 661.81 996.48 1014.3 767.19 949.98 660.2 612.43 TRUE FALSE FALSE 684.6324744 413.1556695 732.3278171 738.3315861 945.6259072 949.4895035 832.3550995 977.4661725 601.1500585 596.5189803 1.147712809 0.692611104 1.227668928 1.237733602 1.585240266 1.591717171 1.395353923 1.638617051 1.007763505 1 9.220424233 -9.03217928 2.065830024 1.045332388 1.545658128 0.754989868 0.143820246 0.127118443 1.077456087 0.022234952 0.042716227 9.29E-10 9.03217928 0.50032574 KHRT(ph)SLPSPMFS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 KHRTSLPSPMFSR 13 2 J3KRT6;Q9BXW6-2;Q9BXW6-4;Q9BXW6 J3KRT6 OSBPL1A Oxysterol-binding protein-related protein 1 2 0 KHRT(0.5)S(0.5)LPS(0.003)PMFS(0.997)R 71.614 0.0032081 0 449.51 508.02 556.78 613.11 567.25 502.99 466.73 689.3 841.7 412.62 TRUE FALSE FALSE 444.0311992 515.1719189 566.4705223 684.000663 538.3011158 470.8505623 506.3740346 709.243808 766.4162439 401.9000729 1.104829855 1.28184082 1.409481014 1.70191724 1.339390441 1.171561276 1.259950094 1.764726746 1.906982097 1 8.650693029 -10.16890644 1.859263171 1.041453767 1.427690841 0 0.322950986 0.207481448 1.368592084 0.031770488 0.039025483 6.78E-11 10.16890644 0.386237074 KHS(ph)GS(ph)DSSGRS(ph)S(ph)SESPGS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 KHSGSDSSGRSSSESPGSSK 20 2 Q8TF01 Q8TF01 PNISR Arginine/serine-rich protein PNISR 5 0 KHS(0.795)GS(0.818)DS(0.341)S(0.045)GRS(0.489)S(0.489)S(0.489)ES(0.525)PGS(0.546)S(0.462)K 40.104 0.029162 282520000 1310 1182.7 1676.2 1112.1 1314.4 1419.9 1399.5 1454.8 1556 1723.2 TRUE FALSE FALSE 1294.033216 1199.350082 1705.373558 1240.686235 1247.321263 1329.172973 1518.373495 1496.892343 1416.827463 1678.431016 0.770977898 0.714566205 1.016052219 0.739194059 0.743147172 0.791913972 0.904638607 0.891840254 0.844138037 1 10.71289753 -12.35211232 1.046255986 1.001269882 0.817720428 0.059441339 0.099756295 0.455580051 0.882965738 0.062169574 0.015785911 4.45E-13 12.35211232 -0.183549453 KHS(ph)PS(ph)PPPPT(ph)PTESR ddPTM_HeLa_Romidepsin_16h_R1 1 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 3 0 KHS(1)PS(1)PPPPT(0.733)PT(0.217)ES(0.05)R 53.278 0.023414 733640 240.87 120.45 185.23 268.41 371.85 230.31 118.34 172.89 140.38 212.6 TRUE FALSE FALSE 237.9341838 122.1456983 188.4538504 299.4448271 352.8731069 215.5939343 128.3917966 177.8922994 127.8240612 207.0766214 1.149015192 0.5898575 0.910068212 1.446058107 1.704070236 1.041131215 0.620020724 0.859065105 0.617279055 1 7.694020874 -7.848921435 6.61104618 1.09785001 0.742157195 0.124621001 0.324809278 0.253733688 15.60598221 0.042316533 0.12988464 1.42E-08 7.848921435 -0.355692815 KHS(ph)PS(ph)PPPPTPTESR ddPTM_HeLa_Romidepsin_16h_R1 2 KHSPSPPPPTPTESR 15 1 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 2 0 KHS(1)PS(1)PPPPTPTESR;KHS(1)PS(1)PPPPTPTESR ; 69.975 0.017863 7898700 3095.59 3229.03 2404.18 2679.13 3111.25 2666.82 2465.96 2876.15 3333.9 3224.07 TRUE FALSE FALSE 3057.859758 3274.488369 2446.023744 2988.903616 2952.471303 2496.418809 2675.418581 2959.366862 3035.707634 3140.308197 0.973745113 1.042728345 0.778912002 0.951786713 0.940185204 0.79495981 0.851960513 0.942381027 0.966690988 1 11.61669044 -9.777123428 24.99999279 0.991389926 0.878156712 0.496107316 0.058721662 150.4475734 239809.0614 0.009038912 0.011901976 1.67E-10 9.777123428 -0.113233214 KHSDS(ph)EVASLAR ddPTM_HeLa_Romidepsin_16h_R1 1 KHSDSEVASLAR 12 1 X6R7X0;Q96MN5-2;Q96MN5 X6R7X0 TCEANC2 Transcription elongation factor A N-terminal and central domain-containing protein 2 1 0 KHS(0.383)DS(0.616)EVASLAR 64.224 0.025599 19515000 1858.2 1954.9 1653.1 1487.4 1690.6 2004.6 1314.1 1829.2 2028.3 1729.3 TRUE FALSE FALSE 1835.551544 1982.421134 1681.871512 1659.380186 1604.322374 1876.51253 1425.719621 1882.125016 1846.883768 1684.372537 1.089753902 1.176949333 0.998515159 0.985162219 0.952474787 1.114072148 0.846439603 1.117404241 1.096481763 1 10.71799554 -9.587003407 25 1.055282906 0.997160474 0.155468104 0.085865576 110.2782075 42992.68227 0.013046937 0.018451156 2.59E-10 9.587003407 -0.058122432 KIAELEEEQSQGSTTNS(ph)DWMK ddPTM_HeLa_Romidepsin_16h_R1 2 KIAELEEEQSQGSTTNSDWMK 21 1 P46821;D6RA32;D6RA40 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 KIAELEEEQSQGS(0.004)T(0.273)T(0.273)NS(0.45)DWMK;KIAELEEEQSQGS(0.014)T(0.081)T(0.081)NS(0.824)DWMK ; 102.78 0.00035495 44980000 6809.7 6539.6 6526.2 7703.6 7722.6 7313.4 5786.5 6522.5 8283.3 6631 TRUE FALSE FALSE 6726.700757 6631.66466 6639.785773 8594.326479 7328.486905 6846.097343 6278.005166 6711.218247 7542.420902 6458.725664 1.041490397 1.026776024 1.028033411 1.330653588 1.134664528 1.059976487 0.972019171 1.039093251 1.16778778 1 12.65703383 -9.480935457 24.99811132 1.020999029 1.10672839 0.023856121 0.099131687 687.3067151 409633.7967 0.014223366 0.021725274 3.30E-10 9.480935457 0.085729361 KICTLPS(ph)PPSPLASLAPVADSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7-2;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 0 KICT(0.006)LPS(0.966)PPS(0.028)PLASLAPVADSSTR 72.532 0.00029423 13223000 1239.3 1023.9 811 113.75 719.77 896.61 1050.6 887.83 1029.4 900.99 TRUE FALSE FALSE 1224.194935 1038.314491 825.1151148 126.9023102 683.0374511 839.3195147 1139.837938 913.5179603 937.3278858 877.5821499 1.394963349 1.183153613 0.940214104 0.14460448 0.778317393 0.956399939 1.298839018 1.040948657 1.068079935 1 9.777390371 -9.69679577 4.921402236 1.191675729 0.843032697 0.205496765 0.291253759 0.253241997 11.9663866 0.051975108 0.073405278 2.01E-10 9.69679577 -0.348643032 KICTLPSPPS(ph)PLASLAPVADSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 KICTLPSPPSPLASLAPVADSSTR 24 1 Q9UER7-3;Q9UER7-2;Q9UER7 Q9UER7-3 DAXX Death domain-associated protein 6 1 0 KICTLPS(0.081)PPS(0.912)PLAS(0.006)LAPVADSSTR 99.494 6.49E-06 10157000 1919.4 1899.9 1655 317.08 1581.9 1273.6 1357.8 1562.2 1980.3 1865.3 TRUE FALSE FALSE 1896.005615 1926.646842 1683.804581 353.7422815 1501.16974 1192.22107 1473.131498 1607.399792 1803.177008 1816.839237 1.043573683 1.060438812 0.92677687 0.194702027 0.826253479 0.656206144 0.81082105 0.884723183 0.992480221 1 10.82721505 -9.506079849 24.78124066 1.022687129 0.676643857 0.466921194 0.178789763 422.5377667 623316.0391 0.026242024 0.03946687 3.12E-10 9.506079849 -0.346043273 AAS(ph)ADYLRPR ddPTM_HeLa_Romidepsin_16h_R1 2 AASADYLRPR 10 1 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B0QYZ7 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 AAS(0.904)ADY(0.096)LRPR;AAS(0.94)ADY(0.06)LRPR ; 88.155 0.0025262 0 4700.1 4678.2 3373.1 3352 2558.8 2232.8 1676.38 1664.63 4202.9 4314.2 TRUE FALSE FALSE 4642.813373 4744.059822 3431.807391 3739.574012 2428.214888 2090.131286 1818.771675 1712.793443 3826.982098 4202.116462 1.104874987 1.128969143 0.816685454 0.889926313 0.577855209 0.497399657 0.432822767 0.407602564 0.91072728 1 12.03690043 -8.813735064 1.066724793 1.054199071 0.408489387 0.900584355 0.08258698 0.089762413 0.199151073 0.01217189 0.034844203 1.54E-09 8.813735064 -0.645709685 down KIEEAMDGS(ph)ETPQLFTVLPEKR ddPTM_HeLa_Romidepsin_16h_R1 1 KIEEAMDGSETPQLFTVLPEKR 22 2 E9PPJ0;Q13435 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 KIEEAMDGS(0.5)ET(0.5)PQLFTVLPEKR 60.561 0.0034085 50470000 1750 1720.1 1381.1 1642.7 1638.7 1401.4 847.82 1403.4 1307.8 1123.5 TRUE FALSE FALSE 1728.670327 1744.315613 1405.137466 1832.636703 1555.071024 1311.855063 919.8338096 1444.005165 1190.827093 1094.311308 1.579687895 1.59398482 1.284038149 1.674694111 1.421049945 1.198795126 0.84055954 1.319556103 1.08819774 1 10.0958075 -6.89378675 19.01687297 1.30332952 3.018921281 0.000230834 0.26007121 10932.65788 2163968.135 0.041003702 85835.53348 1.28E-07 6.89378675 1.715591761 KIGEK(ac)VSK ddPTM_HeLa_Romidepsin_16h_R1 1 KIGEKVSK 8 2 Q6PID6;A0A1B0GU95;A0A1B0GV67;A0A1B0GUJ4 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 0 1 KIGEK(1)VSK 87.298 0.013798 0 3513.3 3448 4127.1 3789.1 2430.9 2731.3 4067.2 891.28 5061.6 3716.3 FALSE TRUE FALSE 3470.478548 3496.541035 4198.930444 4227.21357 2306.842102 2556.778745 4412.667866 917.0677806 4608.877819 3619.74999 0.958761947 0.965962026 1.160005651 1.167819209 0.637293213 0.706341253 1.219053216 0.253351138 1.273258604 1 11.82167434 -8.753610417 24.99999452 1.00552174 0.740965059 0.337217183 0.245754583 187.8475563 599843.035 0.030688158 0.060490361 1.76E-09 8.753610417 -0.264556681 KINS(ph)SPNVNTTASGVEDLNIIQVTIPDDDNER ddPTM_HeLa_Romidepsin_16h_R1 1 KINSSPNVNTTASGVEDLNIIQVTIPDDDNER 32 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 0 KINS(0.468)S(0.468)PNVNT(0.03)T(0.03)AS(0.005)GVEDLNIIQVTIPDDDNER 45.791 0.0065886 6036600 781.42 557.33 812.26 858.44 585.02 781.75 609.21 595.51 863.17 849.05 TRUE FALSE FALSE 771.8957525 565.1761064 826.3970446 957.6968719 555.1642464 731.798698 660.9562822 612.7401423 785.9659134 826.9915586 0.933378031 0.683412183 0.999281112 1.15804915 0.67130582 0.884892585 0.799229781 0.740926719 0.9503917 1 9.691728793 -4.126385438 0.175006137 1.006903271 1.56E-11 0.181184822 0.134760648 63.62821026 0.707144963 0.184890327 16.84880069 7.48E-05 4.126385438 -1.006903271 KIPDPDS(ph)DDVSEVDAR ddPTM_HeLa_Romidepsin_16h_R1 2 KIPDPDSDDVSEVDAR 16 1 P51532;P51532-4;P51532-3;P51532-2;P51532-5;A0A0A0MT49;Q9HBD4;A0A2R8Y4P4;A0A2R8Y7S2;A0A2R8YGG3;A0A2R8Y440;A0A2R8Y4C5;A0A2R8Y6N0;A0A2R8YG32;A0A2R8Y7F3;A0A2R8YF80;A0A2R8YF58;A0A2R8Y526;A0A2R8Y7Y7;A0A2R8Y6V2;A0A2R8YDA1;A0A2R8YGP5;A0A2R8Y7R0;A0A2R8Y583 P51532 SMARCA4 Transcription activator BRG1 1 0 KIPDPDS(0.861)DDVS(0.139)EVDAR;KIPDPDS(0.898)DDVS(0.102)EVDAR ; 72.644 0.010861 10733200 6755.8 6576.6 6415 4402.1 4675.1 5079.2 4923.9 4460.7 6990.8 6887.9 TRUE FALSE FALSE 6673.457711 6669.185547 6526.650384 4911.091515 4436.512202 4754.655512 5342.135943 4589.763317 6365.525339 6708.951365 0.994709508 0.994072722 0.972827202 0.732020736 0.661282511 0.708703231 0.796269887 0.684125293 0.948810774 1 12.71187157 -9.269302984 4.366651033 0.996518514 0.715360413 0.932170349 0.035799283 0.031192095 1.527194124 0.004899499 0.007895135 5.38E-10 9.269302984 -0.281158101 KIPEFEVENS(ph)PLSDVAK ddPTM_HeLa_Romidepsin_16h_R1 2 KIPEFEVENSPLSDVAK 17 1 Q5VY60;Q7Z4H7-3;Q7Z4H7;Q5SYF9;Q7Z4H7-2 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 KIPEFEVENS(0.995)PLS(0.005)DVAK;KIPEFEVENS(0.999)PLS(0.001)DVAK ; 142.23 0.00010289 71171000 5779.1 5448.8 5918.4 5736 7794.9 8486.4 8604.7 9079.5 5478.6 5239 TRUE FALSE FALSE 5708.662106 5525.508349 6021.407269 6399.223309 7397.097166 7944.146429 9335.583003 9342.201007 4988.580295 5102.890025 1.118711569 1.082819407 1.17999942 1.25403904 1.449589768 1.55679358 1.829469763 1.830766676 0.977599021 1 12.31709883 -8.171974927 0.597943582 1.043196456 2.04419177 0.977852936 0.045457565 0.149665515 0.066392994 0.009055328 0.084517985 6.73E-09 8.171974927 1.000995314 KIPEPS(ph)PVTR ddPTM_HeLa_Romidepsin_16h_R1 1 KIPEPSPVTR 10 1 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 KIPEPS(0.989)PVT(0.011)R 115.92 0.022149 84973000 5402 4979.4 4375.4 3532.7 3373 2974.2 2993.5 2751.5 4630 4458.7 TRUE FALSE FALSE 5336.158346 5049.500124 4451.552002 3941.167396 3200.863224 2784.158219 3247.767815 2831.110311 4215.881204 4342.862331 1.228719204 1.162712455 1.025027197 0.907504566 0.737039993 0.641088298 0.74784038 0.651899622 0.97076096 1 12.0844305 -9.01836842 1.680943147 1.113972152 0.684002794 0.845852607 0.077090846 0.110536175 0.62068968 0.014712783 0.029843409 9.59E-10 9.01836842 -0.429969358 KIPNPDFFEDLEPFR ddPTM_HeLa_Romidepsin_16h_R1 2 KIPNPDFFEDLEPFR 15 1 P27824-3;P27824;P27824-2 P27824-3 CANX Calnexin 0 0 ; ; 123.76 0.0019855 13512600 2509.1 4466.1 2912.3 2423.78 2820.3 3892.1 2036.1 3969.3 3134.4 2861.2 FALSE FALSE TRUE 2478.518124 4528.973873 2962.98736 2704.028848 2676.369567 3643.407371 2209.046283 4084.145433 2854.051414 2786.865612 0.889356887 1.625113839 1.063197073 0.970276011 0.96035114 1.307349503 0.792663368 1.465497804 1.024108017 1 11.44442772 KIS(ph)GTTALQEALK ddPTM_HeLa_Romidepsin_16h_R1 1 KISGTTALQEALK 13 1 J3KP58;P30622-2;P30622-1;P30622;F5H0N7;Q9UDT6-2;Q9UDT6 J3KP58;Q9UDT6-2 CLIP1;CLIP2 CAP-Gly domain-containing linker protein 1;CAP-Gly domain-containing linker protein 2 1 0 KIS(0.661)GT(0.139)T(0.2)ALQEALK 75.97 0.01464 9990100 1306.7 1225 1714.7 1341.6 2520.4 4733.1 4642.1 4761.4 1669.6 1292.8 TRUE FALSE FALSE 1290.773438 1242.245582 1744.543634 1496.722104 2391.774583 4430.670185 5036.399858 4899.163597 1520.266794 1259.21287 1.025063727 0.986525481 1.385423923 1.188617223 1.899420377 3.518603004 3.999641347 3.890655595 1.207315166 1 10.29830648 -8.33945504 1.806586513 1.040527493 4.00329299 0.988064858 0.131690008 0.023367393 0.145869522 0.018744126 0.058053528 4.58E-09 8.33945504 2.962765497 up KIS(ph)LEDIQAFEK ddPTM_HeLa_Romidepsin_16h_R1 2 KISLEDIQAFEK 12 1 Q8WXX5 Q8WXX5 DNAJC9 DnaJ homolog subfamily C member 9 1 0 KIS(1)LEDIQAFEK;KIS(1)LEDIQAFEK ; 106.38 0.00071534 6782100 3814.4 3910.7 3210.9 4063.3 3227.1 4169.5 4390.4 3897.5 4594.6 4264.7 TRUE FALSE FALSE 3767.908626 3965.754937 3266.784368 4533.117864 3062.409045 3903.082406 4763.320466 4010.268013 4183.647469 4153.902479 0.907076814 0.954705836 0.786437425 1.091291355 0.737236625 0.939618209 1.146709748 0.965421801 1.007160734 1 12.02025163 -7.844776008 11.30527808 0.936083427 1.055932316 0.185812655 0.106202072 0.508776192 65.68627851 0.013618014 0.040912995 1.43E-08 7.844776008 0.119848888 KISENSYS(ph)LDDLEIGPGQLSSSTFDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 KISENSYSLDDLEIGPGQLSSSTFDSEK 28 1 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VRN8 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 KIS(0.272)ENS(0.223)Y(0.063)S(0.441)LDDLEIGPGQLSSSTFDSEK 82.948 1.07E-06 29446000 3926.6 4216.4 4628.6 3402.7 5544.7 6195.7 5833.5 5602.3 4412.6 4104.9 TRUE FALSE FALSE 3878.741089 4275.75859 4709.158841 3796.136184 5261.733269 5799.814766 6328.997344 5764.393712 4017.926004 3998.254106 0.970108699 1.069406415 1.17780379 0.949448455 1.31600772 1.450586834 1.582940247 1.441727704 1.004920122 1 11.96515445 -8.549762538 2.260561868 1.004604831 1.506966693 0.883889027 0.075614348 0.06673723 0.680782486 0.011395854 0.027561963 2.82E-09 8.549762538 0.502361862 KITSLSSS(ph)LDTSLDFSK ddPTM_HeLa_Romidepsin_16h_R1 1 KITSLSSSLDTSLDFSK 17 1 E9PR71;Q9P2Y5-2;Q9P2Y5 E9PR71 UVRAG UV radiation resistance-associated gene protein 1 0 KITSLSS(0.252)S(0.746)LDT(0.001)SLDFSK 90.592 0.002636 9014800 1204.1 1324 1420.4 1180.9 1251.2 969.79 940.88 1008.7 1361 1237 TRUE FALSE FALSE 1189.423966 1342.639307 1445.121466 1317.441214 1187.346595 907.8235489 1020.798324 1037.885143 1239.268751 1204.862562 0.987186426 1.11435059 1.199407727 1.093436925 0.98546227 0.753466476 0.847232171 0.861413721 1.028556111 1 10.23465287 -8.392606486 5.272043301 1.027558146 0.824651388 0.689529301 0.071444813 0.131262655 5.084283385 0.012166238 0.027654807 4.05E-09 8.392606486 -0.202906758 KIVAAK(ac)YEVIHSK ddPTM_HeLa_Romidepsin_16h_R1 1 KIVAAKYEVIHSK 13 2 E7EVH3;Q92576-2;Q92576;D6R9X2;E9PE34;A0A1B0GX99 E7EVH3 PHF3 PHD finger protein 3 0 1 K(0.03)IVAAK(0.97)YEVIHSK 61.532 0.026292 451360 1222.3 1447 759.47 1287.8 1120.7 1106.4 1256.8 950.37 1658.3 1211.8 FALSE TRUE FALSE 1207.402137 1467.370904 772.6882568 1436.701495 1063.506497 1035.704611 1363.552561 977.8674565 1509.977495 1180.317261 1.022947115 1.243200411 0.654644545 1.217216373 0.901034435 0.877479848 1.155242413 0.828478485 1.279297986 1 10.20495898 KIVEPEVVGES(ph)DS(ph)EVEGDAWR ddPTM_HeLa_Romidepsin_16h_R1 1 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 0 KIVEPEVVGES(1)DS(1)EVEGDAWR 56.292 0.0043208 0 2065.1 2015.3 1959.5 2277.9 2566.8 2250.4 2190.1 1944.2 2168.8 1895.9 TRUE FALSE FALSE 2039.929767 2043.671446 1993.604276 2541.281516 2435.806618 2106.606703 2376.127039 2000.45236 1974.817096 1846.644245 1.104668521 1.106694726 1.07958221 1.376161934 1.31904487 1.140775604 1.286727016 1.083290604 1.069408524 1 10.85069024 -10.04650115 0.897136348 1.035457189 1.234186112 0.40603316 0.091319267 0.352553636 0.563993186 0.020152528 0.027062988 8.98E-11 10.04650115 0.198728922 KIVEPEVVGES(ph)DSEVEGDAWR ddPTM_HeLa_Romidepsin_16h_R1 4 KIVEPEVVGESDSEVEGDAWR 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 0 KIVEPEVVGES(0.94)DS(0.06)EVEGDAWR;KIVEPEVVGES(0.951)DS(0.049)EVEGDAWR;KIVEPEVVGES(0.821)DS(0.179)EVEGDAWR;KIVEPEVVGES(0.925)DS(0.075)EVEGDAWR ;;; 148.58 4.51E-06 65309100 11002.2 10035.6 7714.4 12062.5 10925 12646.6 13173.6 13576.7 11859.5 10052.2 TRUE FALSE FALSE 10868.10095 10176.88144 7848.665896 13457.22301 10367.45648 11838.52308 14292.56526 13969.52039 10798.75662 9791.042395 1.110004483 1.039407351 0.801616986 1.374442318 1.058871575 1.209117742 1.459759306 1.426765387 1.102922057 1 13.25724675 -7.873420344 0.851504222 1.04354637 1.546025464 0.550157108 0.133122966 0.608876428 0.543805412 0.020642503 0.234422594 1.34E-08 7.873420344 0.502479095 KKCT(ph)T(ph)INLT(ph)QKS(ph)ETK ddPTM_HeLa_Romidepsin_16h_R1 1 KKCTTINLTQKSETK 15 3 Q17RG1 Q17RG1 KCTD19 BTB/POZ domain-containing protein KCTD19 4 0 KKCT(1)T(1)INLT(0.998)QKS(0.984)ET(0.019)K 41.227 0.030509 11736000 1771.8 1854.2 1933.2 567.45 2137.5 2243.1 1582.6 1775.6 2341.4 2000.3 TRUE FALSE FALSE 1750.20462 1880.303476 1966.846535 633.0612389 2028.415399 2099.773149 1717.026004 1826.974185 2131.97932 1948.331918 0.898309269 0.965083752 1.009502805 0.324924739 1.041103613 1.077728661 0.881280027 0.937711982 1.094258786 1 10.92802376 -11.85646429 0.650468794 1.002579268 0.887009585 0.07498278 0.20235374 2.501790416 1.930366924 0.152818098 0.046133168 1.39E-12 11.85646429 -0.115569683 KKDDSFLGK(ac)LGGTLAR ddPTM_HeLa_Romidepsin_16h_R1 1 KKDDSFLGKLGGTLAR 16 3 Q9NVD7-2;Q9NVD7 Q9NVD7-2 PARVA Alpha-parvin 0 1 KKDDSFLGK(1)LGGTLAR 56.215 0.015837 516870 299.52 344.19 169.57 404.44 319.42 505.28 295.28 452.05 235.5 158.95 FALSE TRUE FALSE 295.869335 349.0355159 172.5212947 451.2032557 303.1188055 472.9942387 320.3610758 465.1293535 214.4362902 154.8204561 1.911048078 2.254453479 1.114331394 2.914364595 1.957873095 3.055114619 2.069242553 3.00431458 1.385064323 1 7.274452294 -10.55594803 0.130622367 1.62E-15 3.643651204 0.519843163 0.49753544 3.0065397 0.341469442 4.593198293 4.160321743 2.78E-11 10.55594803 3.643651204 KKEESTAASETTEGSQGDSK(ac)NAK ddPTM_HeLa_Romidepsin_16h_R1 2 KKEESTAASETTEGSQGDSKNAK 23 3 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 0 1 ; KKEESTAASETTEGSQGDSK(1)NAK;KKEESTAASETTEGSQGDSK(1)NAK 139.43 4.83E-11 32921400 3708.8 3382 3390.1 2385.99 1924.67 1938.45 1340.1 1735.32 3600.5 3842.5 FALSE TRUE FALSE 3663.595719 3429.611885 3449.103268 2661.86939 1826.446908 1814.589301 1453.928061 1785.528746 3278.462262 3742.671296 0.978871888 0.916354019 0.921561899 0.711221793 0.48800623 0.484838009 0.388473351 0.477073354 0.875968527 1 11.86985263 -9.024576671 1.392752524 0.986978326 0.433467336 0.957583928 0.047273234 0.031712291 0.122005405 0.004831751 0.010381927 9.45E-10 9.024576671 -0.55351099 down KKEPAITSQNS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 2 KKEPAITSQNSPEAR 15 2 E5RIS7;A0A1W2PRL9;A0A1W2PPZ5;P23193-2;P23193 E5RIS7 TCEA1 Transcription elongation factor A protein 1 1 0 KKEPAITSQNS(1)PEAR;KKEPAITS(0.001)QNS(0.999)PEAR ; 99.371 0.0060265 555930000 14419.1 13929.7 13258.6 13426.6 13669.5 14047 12673.2 15181.3 14813.7 13558.7 TRUE FALSE FALSE 14243.35446 14125.80268 13489.36037 14979.04667 12971.89441 13149.44203 13749.66129 15620.54696 13488.72557 13206.44302 1.078515573 1.06961448 1.021422676 1.13422264 0.982239835 0.99568385 1.041132822 1.182797438 1.021374609 1 13.68895433 KKETVSEAPPLLFS(ph)DEEEKEAQLGVK ddPTM_HeLa_Romidepsin_16h_R1 1 KKETVSEAPPLLFSDEEEKEAQLGVK 26 3 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 KKETVSEAPPLLFS(1)DEEEKEAQLGVK 50.055 0.024355 9505100 1520.5 1787.8 1669.1 1864 2097.7 2076.1 1747.9 2119 1933.7 1687.1 TRUE FALSE FALSE 1501.967561 1812.968695 1698.149985 2079.52445 1990.646541 1943.44391 1896.366582 2180.309922 1760.745029 1643.268899 0.914012042 1.103269645 1.033397508 1.265480319 1.211394278 1.182669441 1.154020857 1.326812625 1.071489292 1 10.68235286 -9.61978276 1.472451089 0.961757152 1.221219939 0.632300376 0.072752446 0.134090936 0.586596467 0.011185747 0.017596792 2.40E-10 9.61978276 0.259462788 KKEVDAT(ph)SPAPSTSSTVK ddPTM_HeLa_Romidepsin_16h_R1 1 KKEVDATSPAPSTSSTVK 18 2 H3BM18;X6RHM1;Q16666-3;Q16666-2;Q16666;Q16666-6 H3BM18 IFI16 Gamma-interferon-inducible protein 16 1 0 KKEVDAT(0.5)S(0.5)PAPSTSSTVK 69.024 0.0073739 26184000 5609.9 5039.3 4652.4 5333 5582.2 5176.1 5152.4 5035.3 5505.1 4807.4 TRUE FALSE FALSE 5541.524381 5110.243398 4733.37307 5949.626553 5297.319504 4845.363915 5590.044727 5180.988461 5012.710068 4682.503055 1.183453447 1.091348652 1.010863851 1.270608152 1.131300811 1.034780727 1.1938155 1.106457038 1.070519337 1 12.19306422 -12.46832768 1.143452779 0.998243013 1.132386778 0.172935481 0.075087009 0.482307953 1.104135059 0.052445609 0.012240032 3.40E-13 12.46832768 0.134143765 KKLDDQS(ph)EDEALELEGPLITPGSGSIYSSPGLYSK ddPTM_HeLa_Romidepsin_16h_R1 2 KKLDDQSEDEALELEGPLITPGSGSIYSSPGLYSK 35 2 G3V3J0;Q96AC1-2;Q96AC1;Q96AC1-3 G3V3J0 FERMT2 Fermitin family homolog 2 1 0 KKLDDQS(0.995)EDEALELEGPLIT(0.005)PGSGSIYSSPGLYSK;KKLDDQS(0.711)EDEALELEGPLIT(0.072)PGS(0.088)GS(0.108)IY(0.009)S(0.005)S(0.006)PGLYSK ; 64.654 0.00014713 79486000 4353.5 4600.7 4514.6 5046.7 4976 4945.3 3930 4395.6 4646.9 4285.4 TRUE FALSE FALSE 4300.437867 4665.468775 4593.174719 5630.223199 4722.056152 4629.31129 4263.814102 4522.779751 4231.269626 4174.06469 1.030275807 1.117727951 1.10040813 1.348858635 1.131284851 1.109065535 1.021501682 1.083543281 1.013704851 1 12.02723724 -10.26550597 2.19002926 1.011773864 1.135495395 0.310542358 0.079580996 0.282289152 2.567584561 0.015159414 0.017942517 5.43E-11 10.26550597 0.123721532 KKLDDQSEDEALELEGPLITPGSGSIYS(ph)SPGLYSK ddPTM_HeLa_Romidepsin_16h_R1 1 KKLDDQSEDEALELEGPLITPGSGSIYSSPGLYSK 35 2 G3V3J0;Q96AC1-2;Q96AC1;Q96AC1-3 G3V3J0 FERMT2 Fermitin family homolog 2 1 0 KKLDDQSEDEALELEGPLIT(0.032)PGS(0.052)GS(0.052)IY(0.265)S(0.297)S(0.297)PGLY(0.002)S(0.001)K 54.517 0.00139 37717000 1808.5 1707.7 2106.8 2266 2515.7 2470.9 1958.9 1927.8 1769 1629.5 TRUE FALSE FALSE 1786.457306 1731.741045 2143.46797 2528.005582 2387.314442 2313.017464 2125.288917 1983.577851 1610.776209 1587.165355 1.125564706 1.091090503 1.35050073 1.592780219 1.504137193 1.45732608 1.339046943 1.249761309 1.014876115 1 10.63223672 -9.72041795 3.542162019 1.061383869 1.432952595 0.787292199 0.091842008 0.085082078 2.216100618 0.016476089 0.023211117 1.90E-10 9.72041795 0.371568727 KKLGAGEGGEASVS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 1 KKLGAGEGGEASVSPEK 17 2 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 KKLGAGEGGEAS(0.001)VS(0.999)PEK 80.844 0.0043379 0 1421.2 1509 1161.1 1516 1292.8 1200.5 1029.7 922.81 1667.3 1583.6 TRUE FALSE FALSE 1403.877868 1530.243742 1181.308458 1691.287053 1226.823592 1123.791924 1117.162692 949.5100514 1518.172512 1542.457844 0.910156393 0.992081403 0.765861098 1.096488348 0.795369285 0.728572213 0.724274376 0.615582497 0.984255433 1 10.59101534 -8.552047494 5.682410199 0.952424544 0.702622008 0.675531729 0.08437034 0.076573489 7.096692234 0.011712574 0.024139167 2.81E-09 8.552047494 -0.249802536 KKPEDSPS(ph)DDDVLIVYELTPTAEQK ddPTM_HeLa_Romidepsin_16h_R1 1 KKPEDSPSDDDVLIVYELTPTAEQK 25 2 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 KKPEDS(0.089)PS(0.909)DDDVLIVY(0.002)ELTPTAEQK 57.152 0.0027175 9371600 2288.3 2061.5 1821 2128.4 1803 1675.3 1770.3 1961.1 2352.8 2098.8 TRUE FALSE FALSE 2260.409319 2090.521851 1852.693741 2374.495622 1710.986182 1568.253737 1920.669238 2017.841334 2142.359675 2044.272873 1.105727787 1.022623681 0.906284951 1.161535553 0.836965654 0.767145011 0.939536626 0.987070445 1.047981267 1 10.99737207 -8.744123563 24.99991132 1.043819619 0.878488173 0.465596987 0.082843643 169.203393 244288.1714 0.012473605 0.024900777 1.80E-09 8.744123563 -0.165331446 KKPGDASSLPDAGLS(ph)PGSQVDSK ddPTM_HeLa_Romidepsin_16h_R1 1 KKPGDASSLPDAGLSPGSQVDSK 23 2 M0R300;M0R0P8;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 1 0 KKPGDAS(0.025)S(0.11)LPDAGLS(0.583)PGS(0.278)QVDS(0.004)K 78.221 0.00048858 13068000 1282.9 1284.2 1200.1 1174.2 2105.6 2500.3 1956.6 2546.4 1630.3 1286.4 TRUE FALSE FALSE 1267.263521 1302.279001 1220.987237 1309.966529 1998.143375 2340.538899 2122.793555 2620.076066 1484.481885 1252.979143 1.011400332 1.039346113 0.974467328 1.045481512 1.594713996 1.867979139 1.694197041 2.09107716 1.184761848 1 10.29114668 -8.641718884 2.531430834 1.004225931 1.864847336 0.925389202 0.108937411 0.03862732 0.500327365 0.01244796 0.027711266 2.28E-09 8.641718884 0.860621406 KKTEFLDLDNSPLSPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KKTEFLDLDNSPLSPPSPR 19 2 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 0 KKTEFLDLDNSPLS(0.002)PPS(0.998)PR 74.561 0.0046282 47429000 4710 4075.9 4011.1 4567.5 3800.1 3296.6 2857.1 3043.2 4074.5 4524.1 TRUE FALSE FALSE 4652.592708 4133.280627 4080.911513 5095.615841 3606.166717 3085.957899 3099.782003 3131.250191 3710.066515 4406.56323 1.055832508 0.937982825 0.926098481 1.156369618 0.81836264 0.700309456 0.703446618 0.710587827 0.84194106 1 12.10543819 -8.568846808 5.344837127 1.019173154 0.71194425 0.697511689 0.082376004 0.050577045 3.327402891 0.008809606 0.01808898 2.70E-09 8.568846808 -0.307228904 KKVEEEDEEEEEEEEEEEEEEDE ddPTM_HeLa_Romidepsin_16h_R1 4 KKVEEEDEEEEEEEEEEEEEEDE 23 2 O15347 O15347 HMGB3 High mobility group protein B3 0 0 ;;; ;;; 103.1 3.15E-05 111096300 11873.54 10923.72 10884.63 10023.77 9459.21 8904.3 8233.35 8652.96 12327.12 11813.24 FALSE FALSE TRUE 11728.82073 11077.50442 11074.07242 11182.76545 8976.471217 8335.343967 8932.690543 8903.319745 11224.55151 11506.33032 1.019336348 0.962731306 0.962433036 0.971879404 0.78013328 0.724413756 0.77632836 0.773775782 0.975510975 1 13.49014017 -8.774469347 3.568542074 1.000875299 0.757623331 0.952490781 0.023785568 0.033604691 0.907654244 0.003863013 0.007659445 1.68E-09 8.774469347 -0.243251967 AAT(ph)SPGVGQSAPGTR ddPTM_HeLa_Romidepsin_16h_R1 2 AATSPGVGQSAPGTR 15 0 Q6IE81-2;Q6IE81 Q6IE81-2 JADE1 Protein Jade-1 1 0 AAT(0.609)S(0.391)PGVGQSAPGTR;AAT(0.5)S(0.5)PGVGQSAPGTR ; 192.54 3.34E-12 12786300 7379.3 6997.4 7684.2 5518.9 3552.8 2867.6 2482.7 2366.5 7649.9 7937.9 TRUE FALSE FALSE 7289.358253 7095.909581 7817.940278 6157.021185 3371.487359 2684.369615 2693.580476 2434.970944 6965.673784 7731.672214 0.942791941 0.917771652 1.01115775 0.796337586 0.436061859 0.347191337 0.348382653 0.31493458 0.900927198 1 12.91656476 -8.813349425 2.312090755 0.970135016 0.33813027 0.984046184 0.035922865 0.021520333 0.234584067 0.004982068 0.010375964 1.54E-09 8.813349425 -0.632004746 down KLCY(ph)KGS(ph)TFHR ddPTM_HeLa_Romidepsin_16h_R1 1 KLCYKGSTFHR 11 2 P30414;C9JMM5;A8K7K2 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase 2 0 KLCY(0.932)KGS(0.534)T(0.534)FHR 76.943 0.027715 7893900 1164.5 951.54 1108.5 1947.8 1311.8 1043.6 955.79 1335.8 1302.9 1159.6 TRUE FALSE FALSE 1150.306626 964.9358051 1127.792978 2173.013801 1244.853951 976.9173281 1036.974779 1374.449265 1186.365361 1129.473425 1.018445057 0.854323602 0.998512185 1.9239176 1.102154264 0.864931663 0.918104628 1.216893851 1.050370318 1 10.14143461 -9.457981059 24.99986438 0.993989142 1.1942809 0.138929166 0.273757588 365.7203256 140882.3568 0.042917344 0.065557296 3.48E-10 9.457981059 0.200291759 KLDEAVAEAHLGK ddPTM_HeLa_Romidepsin_16h_R1 1 KLDEAVAEAHLGK 13 1 P23526-2;P23526 P23526-2 AHCY Adenosylhomocysteinase 0 0 62.088 0.018634 14474000 3481 3085.8 3105.6 3635.3 3292.6 3541.3 2378.9 3158.4 3282.9 3217 FALSE FALSE TRUE 3438.572233 3129.241973 3159.651665 4055.630491 3124.566336 3315.022359 2580.963707 3249.783321 2989.269202 3133.421876 1.09738566 0.998666026 1.008370973 1.294313581 0.997173843 1.057955963 0.823688545 1.037135582 0.953995127 1 11.61352331 -7.803398134 24.85480894 1.055730546 0.930412001 0.181862273 0.101895024 130.2702481 77166.96177 0.01303842 0.039115791 1.57E-08 7.803398134 -0.125318545 KLDELYGTWR ddPTM_HeLa_Romidepsin_16h_R1 1 KLDELYGTWR 10 1 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 0 89.9 0.02509 31457000 2829.4 2252.1 4290.3 4160.4 5046.6 4725.7 4156.8 3043.5 2722.9 2191.7 FALSE FALSE TRUE 2794.914185 2283.805123 4364.970872 4641.445023 4789.053171 4423.743021 4509.878488 3131.558871 2479.357004 2134.759318 1.309240888 1.069818552 2.044713348 2.174224037 2.243369138 2.07224439 2.11259342 1.466937675 1.161422266 1 11.05985771 -9.758617334 24.99283888 1.14439476 2.042939974 0.806565529 0.211843165 23.62852504 209259.4876 0.035406521 0.048809799 1.74E-10 9.758617334 0.898545213 KLDPAQSAS(ph)RENLLEEQGSIALR ddPTM_HeLa_Romidepsin_16h_R1 1 KLDPAQSASRENLLEEQGSIALR 23 2 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 0 KLDPAQS(0.21)AS(0.79)RENLLEEQGSIALR 54.626 0.0067165 7096700 1569.8 1314 1354.8 1391.1 1529.4 1467.9 1633.7 1390.6 1349.3 1342.6 TRUE FALSE FALSE 1550.666674 1332.498526 1378.379726 1551.945527 1451.349011 1374.105927 1772.466437 1430.834817 1228.615229 1307.719058 1.18577967 1.018948617 1.054033523 1.186757597 1.109832423 1.050765391 1.355387784 1.094145419 0.939510073 1 10.35283692 -16.21333216 0.303352617 3.36E-14 1.149709456 0.324570993 0.092653623 43.08714028 0.694757812 26.18948023 0.037407663 6.12E-17 16.21333216 1.149709456 KLDPEEEDDS(ph)FNNYEVQSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 KLDPEEEDDSFNNYEVQSEAK 21 1 A0A087WWW8;Q9Y6J0-2;Q9Y6J0 A0A087WWW8 CABIN1 Calcineurin-binding protein cabin-1 1 0 KLDPEEEDDS(0.925)FNNY(0.074)EVQSEAK 63.936 0.0037193 5523500 2293.4 1705.2 2006.3 2006.7 1830.6 1745 1458.8 1492.5 1740.8 1947.4 TRUE FALSE FALSE 2265.447159 1729.20585 2041.21881 2238.724096 1737.177651 1633.500132 1582.710436 1535.683133 1585.098488 1896.806267 1.194348204 0.91164073 1.076134577 1.180259753 0.915843479 0.861184487 0.834408059 0.809615172 0.835667045 1 10.88935662 -8.585540732 4.968047292 1.082913912 0.842166528 0.349794613 0.110085583 0.106101325 5.209054679 0.01367932 0.028103005 2.60E-09 8.585540732 -0.240747384 KLDVEEPDS(ph)ANSSFYSTR ddPTM_HeLa_Romidepsin_16h_R1 1 KLDVEEPDSANSSFYSTR 18 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 KLDVEEPDS(0.996)ANS(0.003)S(0.001)FYSTR 101.05 0.00058492 12244000 2540.9 2226.3 2366.1 2409.1 2469.4 3635.7 3606.6 3009.3 2988.3 2660.8 TRUE FALSE FALSE 2509.930533 2257.64191 2407.280978 2687.651477 2343.377303 3403.390504 3912.944514 3096.369348 2721.018964 2591.672032 0.968459937 0.871114046 0.928852474 1.037033793 0.904195158 1.31320262 1.509814693 1.194738111 1.04990868 1 11.33966745 -8.205312381 5.687825126 0.971047066 1.362284631 0.787372247 0.088843087 0.061391128 4.362850111 0.011042216 0.028506322 6.23E-09 8.205312381 0.391237565 KLEAAEDIAYQLSR ddPTM_HeLa_Romidepsin_16h_R1 2 KLEAAEDIAYQLSR 14 1 P35232 P35232 PHB Prohibitin 0 0 ; ; 120.21 0.0026948 24351000 9359.5 7617 8140.7 8669.6 9001.8 9442.4 7775.5 8142.5 8952.3 7541.3 FALSE FALSE TRUE 9245.422814 7724.232326 8282.385469 9672.019944 8542.404556 8839.061114 8435.950776 8378.090391 8151.583867 7345.375939 1.258672516 1.051577535 1.127564544 1.316749479 1.162963561 1.203350405 1.148470935 1.140593819 1.109757204 1 12.84262061 -12.48753277 1.158762955 0.997252606 1.183588839 0.243130613 0.076336305 0.349391164 0.819143506 0.053536469 0.012287412 3.25E-13 12.48753277 0.186336233 KLEEEGEQFVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 KLEEEGEQFVKK 12 2 H0YF61;P22307-6;P22307-2;P22307-4;P22307-7;P22307-8;P22307 H0YF61 SCP2 Non-specific lipid-transfer protein 0 1 ; KLEEEGEQFVK(1)K;KLEEEGEQFVK(1)K 149.32 0.00039967 2927900 1721.65 1842.92 1805.11 1761.45 2422.7 2259.32 2224 2537.8 2960.1 2289.07 FALSE TRUE FALSE 1700.665868 1868.864676 1836.527182 1965.117137 2299.060579 2114.956744 2412.906504 2611.227239 2695.341242 2229.599631 0.762767379 0.838206398 0.823702676 0.881376687 1.031154 0.948581402 1.082215152 1.171164187 1.208890244 1 11.12256895 -7.660687051 0.868235335 0.877440677 1.237463917 0.23355625 0.125215558 0.885034121 0.708321472 0.015854867 0.264396485 2.18E-08 7.660687051 0.36002324 KLEELK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 2 KLEELKAK 8 2 Q9Y2S6;Q9Y2C4-3;Q9Y2C4-4;Q9Y2C4 Q9Y2S6 TMA7;EXOG "Translation machinery-associated protein 7;Nuclease EXOG, mitochondrial" 0 1 ; KLEELK(1)AK;KLEELK(1)AK 96.342 0.0093669 0 1980.54 1725.82 1753.53 2611.42 2302.39 1990.74 1985.8 1907.63 1936.62 1336.6 FALSE TRUE FALSE 1956.400417 1750.116139 1784.049454 2913.364668 2184.890447 1863.538139 2154.473802 1962.824264 1763.403857 1301.874939 1.502756031 1.344304346 1.370369304 2.23782222 1.678264464 1.431426386 1.654900742 1.507690336 1.354510947 1 10.34637515 -11.80192999 0.421993257 0.900400806 1.65778056 0.282646166 0.256403545 1.046078213 0.321018235 0.344379717 0.087422909 1.58E-12 11.80192999 0.757379754 KLEESASFESLSPSSRPAS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 KLEESASFESLSPSSRPASPTR 22 2 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 KLEESASFESLSPSS(0.001)RPAS(0.931)PT(0.068)R 124.91 2.65E-09 0 737.22 612.63 699.15 1012.5 893.48 871.95 727.73 559.14 745.96 551.17 TRUE FALSE FALSE 728.2344791 621.2546212 711.3184125 1129.570014 847.8823816 816.2352091 789.543368 575.3178337 679.2394693 536.8505239 1.356493934 1.157220853 1.324984108 2.104068011 1.579363983 1.520414292 1.470694975 1.071653669 1.265230151 1 9.068376642 -11.23567611 0.529931318 1.00840035 1.513355894 0.188137818 0.269945081 0.774260384 0.486742454 0.170259741 0.084813168 5.81E-12 11.23567611 0.504955544 KLEEVVNK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KLEEVVNKK 9 2 Q8WU90 Q8WU90 ZC3H15 Zinc finger CCCH domain-containing protein 15 0 1 KLEEVVNK(1)K 78.653 0.030131 0 264 226.2 403.16 363.68 518.47 628.7 922.1 305.51 681.79 411.56 FALSE TRUE FALSE 260.7822665 229.3844495 410.1768307 405.7303928 492.0105412 588.528099 1000.423151 314.3494498 620.8089948 400.8676119 0.650544616 0.572219962 1.023222676 1.012130641 1.227364164 1.468135817 2.49564475 0.784172731 1.54866339 1 8.646982049 -8.567139219 1.617723684 0.823761353 1.681787096 0.227988276 0.468541585 0.252551809 1.307289857 0.058542385 0.160037128 2.71E-09 8.567139219 0.858025742 KLEGNSPQGS(ph)NQGVK ddPTM_HeLa_Romidepsin_16h_R1 1 KLEGNSPQGSNQGVK 15 1 P61006 P61006 RAB8A Ras-related protein Rab-8A 1 0 KLEGNS(0.004)PQGS(0.996)NQGVK 62.589 0.021652 4823000 1399.9 1341.3 1031.1 981.27 1281.9 1303.3 879.89 1312 1391.3 1469.2 TRUE FALSE FALSE 1382.83748 1360.182857 1049.045863 1094.729054 1216.47986 1220.023336 954.6278346 1349.96065 1266.858643 1431.029972 0.966323213 0.950492221 0.733070504 0.764993799 0.850072943 0.852549115 0.667091433 0.94334897 0.885277505 1 10.48283817 -9.872788592 5.6914761 0.982722643 0.798982665 0.454639871 0.077159157 0.097653126 4.560946623 0.010583512 0.013993883 1.34E-10 9.872788592 -0.183739977 KLELQVES(ph)MLSEIK ddPTM_HeLa_Romidepsin_16h_R1 1 KLELQVESMLSEIK 14 1 Q96CV9-3;Q96CV9-2;Q96CV9 Q96CV9-3 OPTN Optineurin 1 0 KLELQVES(0.998)MLS(0.002)EIK 60.628 0.0041804 0 1775 2239.9 1581.6 978.11 1841.9 1660.8 1366.7 1757.4 2022.6 1958.6 TRUE FALSE FALSE 1753.365617 2271.433371 1609.127085 1091.20368 1747.90097 1554.68024 1482.787464 1808.247596 1841.69359 1907.71529 0.919091872 1.190656375 0.843483875 0.571995038 0.916227374 0.814943534 0.777258259 0.947860305 0.965392268 1 10.89763016 -9.542902691 24.99341365 0.979756279 0.800438042 0.416358321 0.116982719 192.1795257 239872.9286 0.017791236 0.025162233 2.86E-10 9.542902691 -0.179318237 KLENS(ph)PLGEALR ddPTM_HeLa_Romidepsin_16h_R1 1 KLENSPLGEALR 12 1 D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;D6RDK6;D6RBN5;Q9NX40-3;Q9NX40-2;Q9NX40-4;Q9NX40 D6RI08 OCIAD1 OCIA domain-containing protein 1 1 0 KLENS(1)PLGEALR 121.42 0.010896 33787000 2538.5 2279 2425.4 2032.9 1898.8 1961.2 1355.3 1699.6 2335.2 2384.8 TRUE FALSE FALSE 2507.559786 2311.083822 2467.61307 2267.953463 1801.897151 1835.885649 1470.419148 1748.775244 2126.333863 2322.842552 1.079522064 0.994937784 1.062324722 0.976369862 0.775729353 0.79036164 0.63302575 0.75286 0.915401632 1 11.18167565 -8.729572092 1.955844066 1.037327091 0.713936113 0.831282395 0.058668848 0.067355102 0.523794731 0.007075305 0.016075393 1.86E-09 8.729572092 -0.323390978 KLESGGGGEGGEGT(ph)EEEDGAER ddPTM_HeLa_Romidepsin_16h_R1 4 KLESGGGGEGGEGTEEEDGAER 22 1 Q96LA8 Q96LA8 PRMT6 Protein arginine N-methyltransferase 6 1 0 KLESGGGGEGGEGT(1)EEEDGAER;KLESGGGGEGGEGT(1)EEEDGAER;KLESGGGGEGGEGT(1)EEEDGAER;KLESGGGGEGGEGT(1)EEEDGAER ;;; 96.38 0.0001089 22053100 8246.76 6565.82 7541.78 3455.21 6957.53 6728.26 6826.46 6463.74 8006.25 7263.17 TRUE FALSE FALSE 8146.245317 6658.253786 7673.041517 3854.717637 6602.461282 6298.3459 7406.299342 6650.758119 7290.150948 7074.471796 1.151498734 0.941166207 1.084609811 0.544877094 0.933279752 0.890292036 1.046904922 0.940106669 1.030486962 1 12.78840672 KLEVEANNAFDQYR ddPTM_HeLa_Romidepsin_16h_R1 1 KLEVEANNAFDQYR 14 1 A0A6I8PRV6;B1AK87;B1AK85;B1AK88;P47756-2;P47756 A0A6I8PRV6 CAPZB F-actin-capping protein subunit beta 0 0 141.59 0.00052039 12760000 2859.9 2265.5 2406.6 2575.2 2446.2 2292.7 2264.6 2048.8 2351.6 2088.5 FALSE FALSE TRUE 2825.042439 2297.393768 2448.485863 2872.956741 2321.361286 2146.203869 2456.955067 2108.078796 2141.267006 2034.240469 1.38874557 1.129361943 1.203636394 1.412299472 1.14114399 1.055039413 1.207799719 1.036297738 1.05261253 1 10.99027452 -7.257023871 23.16408144 1.189779071 1.036297588 0.08775277 0.129854111 354.66646 1860394.633 0.021918758 0.224634158 5.53E-08 7.257023871 -0.153481483 KLFVGGLK ddPTM_HeLa_Romidepsin_16h_R1 4 KLFVGGLK 8 1 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 0 0 ;;; ;;; 98.458 0.0063488 0 11261.3 9860.8 14666.2 10318.8 13184.6 13220.6 10558.7 8538 9878.2 7337.6 FALSE FALSE TRUE 11124.04294 9999.620601 14921.45906 11511.90821 12511.74066 12375.84633 11455.55571 8785.033559 8994.669052 7146.968094 1.556470212 1.399141632 2.087802669 1.610740115 1.750636144 1.73162188 1.602855304 1.229197254 1.258529342 1 12.80311563 -11.82233848 0.626012968 0.97732398 1.652831358 0.42139268 0.224964877 0.472247031 0.339251181 0.16502538 0.0501796 1.51E-12 11.82233848 0.675507378 KLGAGEGGEASVS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 3 KLGAGEGGEASVSPEK 16 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 KLGAGEGGEAS(0.035)VS(0.965)PEK;KLGAGEGGEAS(0.139)VS(0.861)PEK;KLGAGEGGEAS(0.069)VS(0.931)PEK ;; 136.85 0.00093814 111003000 14382 14592.4 14420 9794.7 12384.4 11781.1 10571.8 11349.5 15052.7 15044.3 TRUE FALSE FALSE 14206.70665 14797.83219 14670.97405 10927.2093 11752.37786 11028.32573 11469.76843 11677.87988 13706.34881 14653.44692 0.969512957 1.009853332 1.00119611 0.74570914 0.802021389 0.752609662 0.782735181 0.796937399 0.935366872 1 13.83895245 -9.264416896 25 0.988505341 0.776522471 0.94231778 0.025612844 32.36362972 271733.4112 0.003077037 0.004829941 5.44E-10 9.264416896 -0.21198287 KLGDVS(ph)PTQIDVSQFGSFKEDTK ddPTM_HeLa_Romidepsin_16h_R1 1 KLGDVSPTQIDVSQFGSFKEDTK 23 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 KLGDVS(0.498)PT(0.498)QIDVS(0.004)QFGSFKEDTK 50.873 0.015312 699940000 4933.4 4908.8 4028.8 5858.2 5917.5 4791 4511.1 5217.3 5707.1 4984.6 TRUE FALSE FALSE 4873.269823 4977.906215 4098.919574 6535.552648 5615.507894 4484.870562 4894.272721 5368.254344 5196.642682 4855.099373 1.00374255 1.025294403 0.844250397 1.346121293 1.156620588 0.923744339 1.008068496 1.10569402 1.070347336 1 12.24528511 KLGDVSPT(ph)QIDVSQFGSFK ddPTM_HeLa_Romidepsin_16h_R1 1 KLGDVSPTQIDVSQFGSFK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 KLGDVS(0.275)PT(0.725)QIDVSQFGSFK 102.27 0.00050676 610480000 8228.1 7655.9 8171.1 6406.9 9054.3 8910.1 8288 9111 8373.8 8897.1 TRUE FALSE FALSE 8127.812752 7763.679961 8313.314568 7147.695923 8592.225285 8340.773366 8991.982513 9374.61241 7624.826355 8665.952059 0.937901883 0.895883096 0.959307703 0.824802154 0.991492363 0.962476288 1.037622001 1.081775245 0.879860205 1 13.08114254 -7.619881644 2.015332565 0.953610331 1.086002378 0.444301625 0.054100243 0.317497138 2.179206734 0.007658567 0.059052229 2.40E-08 7.619881644 0.132392047 KLGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_HeLa_Romidepsin_16h_R1 1 KLGPGRPLPTFPTSECTSDVEPDTR 25 2 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 0 KLGPGRPLPT(0.043)FPT(0.256)S(0.066)ECT(0.317)S(0.317)DVEPDTR 49.106 0.0128 13202000 1051.5 910.87 849.76 319.27 776.5 744.68 572.61 725.36 1346.8 1227.7 TRUE FALSE FALSE 1038.683914 923.6932518 864.5497163 356.1854996 736.8723075 697.0973513 621.2474791 746.3471472 1226.338835 1195.804177 0.868607029 0.772445246 0.722986031 0.297862732 0.616214863 0.582952765 0.519522754 0.624138267 1.025534831 1 10.22376544 -9.952847983 1.278937258 0.948689406 0.53683842 0.773009818 0.101162253 0.141268215 0.455006796 0.018821965 0.025667894 1.11E-10 9.952847983 -0.411850986 KLLEDTLFPSSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KLLEDTLFPSSKK 13 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 0 1 KLLEDTLFPSSK(1)K 101.62 0.011897 650450 526.34 502.29 484.73 750.06 632.79 694.38 692.75 706.03 700.67 343.1 FALSE TRUE FALSE 519.9247656 509.3612518 493.1665223 836.7854663 600.496365 650.011359 751.5921677 726.4578641 638.0003203 334.1862125 1.555793585 1.524183921 1.475723725 2.503949699 1.796891501 1.94505738 2.249022071 2.173811596 1.909116224 1 8.384508403 -10.13178097 0.214522893 0.74631677 2.536713716 0.238593381 0.364918581 0.91508288 0.17368065 0.532247673 0.651441697 7.38E-11 10.13178097 1.790396946 KLLLDPSS(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 1 KLLLDPSSPPTK 12 1 F5GX19;F5H3Y3;Q6IAA8;H0YFI1;F5H479 F5GX19 LAMTOR1 Ragulator complex protein LAMTOR1 1 0 KLLLDPS(0.112)S(0.879)PPT(0.008)K 58.98 0.030224 35334000 3059.1 4122.3 3308.3 2751.3 3720.5 5924.5 3012.4 5505.6 3036.4 3429.6 TRUE FALSE FALSE 3021.814513 4180.333848 3365.879574 3069.418251 3530.629002 5545.94357 3268.273181 5664.89585 2764.816779 3340.498498 0.904599872 1.251410186 1.007597991 0.918850361 1.056916806 1.660214359 0.978378881 1.695823499 0.827665925 1 11.70584769 -4.000000008 0.360144016 0.956279896 8.770043566 0.461913692 0.215496024 35.89296044 0.445489547 0.055272618 194.7622977 1.00E-04 4.000000008 7.813763669 KLNS(ph)GGGLSEELGSAR ddPTM_HeLa_Romidepsin_16h_R1 1 KLNSGGGLSEELGSAR 16 1 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;Q96KQ7-2;A2ABF9;A0A0G2JK64;Q96KQ7 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 0 KLNS(0.963)GGGLS(0.005)EELGS(0.032)AR 114.06 5.02E-05 0 1050.5 1089.7 1095.5 1145.3 775.28 958.71 1147.4 902 775.32 861.46 TRUE FALSE FALSE 1037.696102 1105.040825 1114.566718 1277.724975 735.7145686 897.4515251 1244.860127 928.0979469 705.9734374 839.079145 1.236708251 1.316968526 1.328321321 1.522770507 0.876811887 1.069567192 1.48360275 1.106091067 0.841366922 1 9.712663087 -11.96119584 0.849625973 1.004496487 1.245621046 0.287325896 0.190696479 0.752217389 1.019869143 0.107641625 0.036530876 1.09E-12 11.96119584 0.241124558 KLNVTEQEK ddPTM_HeLa_Romidepsin_16h_R1 2 KLNVTEQEK 9 1 P06733;K7EM90;A0A2R8Y879;A0A2R8YEM5;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 0 ; ; 89.561 0.0268 37808000 5809.4 5819.3 8433.7 3889.2 7400.7 7097.9 8931.7 2768.3 8152 5791.8 FALSE FALSE TRUE 5738.592798 5901.224258 8580.485011 4338.887603 7023.014663 6644.367097 9690.358375 2848.396393 7422.864703 5641.328201 1.017241436 1.046070012 1.521004399 0.769125186 1.244922191 1.177801904 1.717744125 0.504915915 1.315800896 1 12.46181916 -9.97764424 24.92773851 1.009379279 1.178467014 0 0.335833918 502.2253747 560004.1237 0.046585835 0.061223391 1.05E-10 9.97764424 0.169087735 KLPPPPPQAPPEEENES(ph)EPEEPSGVEGAAFQSR ddPTM_HeLa_Romidepsin_16h_R1 2 KLPPPPPQAPPEEENESEPEEPSGVEGAAFQSR 33 1 R4GMQ1;O60341 R4GMQ1 KDM1A Lysine-specific histone demethylase 1A 1 0 KLPPPPPQAPPEEENES(0.996)EPEEPS(0.004)GVEGAAFQSR;KLPPPPPQAPPEEENES(0.997)EPEEPS(0.003)GVEGAAFQSR ; 58.021 0.0003901 17599600 4604.3 4428.8 4168.5 5659.4 5015.5 4910.3 3863.11 4486.7 4280.3 4146.2 TRUE FALSE FALSE 4548.181021 4491.148763 4241.050994 6313.766456 4759.54032 4596.547677 4191.242467 4616.515586 3897.459248 4038.481126 1.12621079 1.112088585 1.050159914 1.563401254 1.178547125 1.138187238 1.037826434 1.143131648 0.965080466 1 11.97959708 -11.24853725 0.641023279 1.009354671 1.182243354 0.226199567 0.139007198 0.892401952 0.804065581 0.068679896 0.037305925 5.64E-12 11.24853725 0.172888683 KLPS(ph)DSGDLEALEGK ddPTM_HeLa_Romidepsin_16h_R1 1 KLPSDSGDLEALEGK 15 1 G3V5V3;O60524-4;O60524-5;O60524-3;O60524;O60524-2 G3V5V3 NEMF Nuclear export mediator factor NEMF 1 0 KLPS(0.965)DS(0.035)GDLEALEGK 68.189 0.016208 7697400 3556.5 3355 3501.4 2436.9 3698.3 4121.4 3627.8 4192.5 3638 3672.1 TRUE FALSE FALSE 3513.15201 3402.231778 3562.340398 2718.665844 3509.561951 3858.055841 3935.945241 4313.803373 3312.608168 3576.698313 0.982233251 0.951221345 0.995985707 0.760104881 0.981229515 1.078664037 1.100440937 1.206085332 0.926163707 1 11.80441272 -7.84245777 1.795701595 0.97110134 1.181649087 0.576846083 0.072664561 0.247470292 1.451062964 0.010749891 0.060144807 1.44E-08 7.84245777 0.210547747 KLREMNT(ph)EAEK ddPTM_HeLa_Romidepsin_16h_R1 1 KLREMNTEAEK 11 2 H0Y322;Q5TKA1;Q5TKA1-2;C9J5J4;H7C4T7;Q5TKA1-3 H0Y322 LIN9 Protein lin-9 homolog 1 0 KLREMNT(1)EAEK 77.387 0.0023701 0 5049.3 5726 5371 4037.8 4498.6 4318.4 3225.7 4027 5878.5 5403.3 TRUE FALSE FALSE 4987.757189 5806.610778 5464.480002 4504.669434 4269.019655 4042.468177 3499.690877 4143.514891 5352.712237 5262.921487 0.947716435 1.103305606 1.038297838 0.855925639 0.811150169 0.768103455 0.664971136 0.787303193 1.017061009 1 12.36164816 -8.869026945 1.938213752 0.990032642 0.739564175 0.83066367 0.055455309 0.109185044 0.831755135 0.009063578 0.019122325 1.35E-09 8.869026945 -0.250468467 KLS(ph)GDQITLPTTVDYSSVPK ddPTM_HeLa_Romidepsin_16h_R1 1 KLSGDQITLPTTVDYSSVPK 20 1 E9PJ38;E9PND3;E9PN10;O00559;O00559-2 E9PJ38 EBAG9 Receptor-binding cancer antigen expressed on SiSo cells 1 0 KLS(0.996)GDQIT(0.004)LPTTVDYSSVPK 78.451 0.0015249 92073000 4015.7 4573.5 3999.4 3507.6 4066.8 4680.8 3494.9 5631.7 4000.6 4648.4 TRUE FALSE FALSE 3966.755104 4637.885853 4069.007879 3913.165216 3859.256021 4381.711987 3791.756719 5794.644354 3642.776316 4527.633898 0.876120992 1.024350899 0.898705145 0.864284813 0.852378109 0.967770824 0.837469814 1.279839423 0.804565121 1 12.14454159 -7.252113768 24.71018522 0.928542441 1.279839641 0.696859654 0.072840402 444.4057901 1177519.064 0.009327866 0.154911141 5.60E-08 7.252113768 0.3512972 KLS(ph)NPDIFSSTGK ddPTM_HeLa_Romidepsin_16h_R1 2 KLSNPDIFSSTGK 13 1 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 KLS(0.995)NPDIFS(0.003)S(0.001)TGK;KLS(0.411)NPDIFS(0.257)S(0.257)T(0.074)GK ; 155.37 0.001095 58308000 5045.9 4095.1 4372.2 3735 4183.9 3770.7 3814 3664.5 4998 4184.8 TRUE FALSE FALSE 4984.39863 4152.750925 4448.296307 4166.858274 3970.379971 3529.764439 4137.961065 3770.526526 4550.966362 4076.078293 1.22284173 1.018810393 1.09131768 1.022271403 0.974068623 0.865970716 1.015181939 0.925037807 1.116506121 1 11.99296605 -9.008759875 1.629622445 1.100963662 0.940544925 0.518094357 0.066060255 0.296567205 1.566641487 0.014432464 0.029683471 9.80E-10 9.008759875 -0.160418737 KLS(ph)SSDAPAQDTGSSAAAVETDASR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSSSDAPAQDTGSSAAAVETDASR 25 1 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YIM6 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 KLS(0.591)S(0.205)S(0.205)DAPAQDTGSSAAAVETDASR 126.1 3.69E-07 73327000 2762.5 2735.2 2200.8 2838.1 3258.4 3162.5 2847.9 2897.2 2522.1 2169.3 TRUE FALSE FALSE 2728.829587 2773.706217 2239.104001 3166.254476 3092.111689 2960.426457 3089.800555 2981.025911 2296.517059 2112.941273 1.291483877 1.312722816 1.059709529 1.498505669 1.463415822 1.401092635 1.462322022 1.41084182 1.086881632 1 11.04503695 -15.31554596 0.105363213 9.67E-15 1.655032948 0.648510236 0.104104871 33.88746103 0.349370904 8.112851888 0.828502453 4.84E-16 15.31554596 1.655032948 KLSGDQPAAR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSGDQPAAR 10 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 0 0 95.483 0.019765 3593200 1436.9 1897.3 1756.1 1786.5 2464.3 2364.4 2313.8 1126.9 2716.9 2216.6 FALSE FALSE TRUE 1419.38651 1924.010239 1786.664184 1993.063536 2338.537575 2213.322471 2510.334114 1159.505074 2473.893659 2159.012412 0.657423969 0.891152931 0.827537708 0.923136673 1.08315152 1.025155047 1.162723336 0.537053454 1.145845038 1 11.07615582 -9.10305955 4.305866167 0.838475072 0.975386069 0 0.199489442 0.428349776 13.53131265 0.028774827 0.049077483 7.89E-10 9.10305955 0.136910997 KLSS(ph)SDAPAQDTGSSAAAVETDASR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSSSDAPAQDTGSSAAAVETDASR 25 1 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YIM6 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 KLS(0.237)S(0.382)S(0.382)DAPAQDTGSSAAAVETDASR 135.37 4.51E-07 78510000 3427.8 3804.5 3526.5 3643.3 4480.4 4008.9 3726.2 4690.8 3582.1 3405.9 TRUE FALSE FALSE 3386.020655 3858.059851 3587.877253 4064.555488 4251.748469 3752.744228 4042.703335 4826.520897 3261.708004 3317.414227 1.020680694 1.162971998 1.081528265 1.225217959 1.281645335 1.131225699 1.218630855 1.454904503 0.983207939 1 11.69584345 -4 0.187363652 0.958122381 2.839029066 0.746898775 0.069811511 19.56649885 0.217146629 0.080983099 10.66910657 1.00E-04 4 1.880906685 KLSSWDQAETPGHT(ph)PSLR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSSWDQAETPGHTPSLR 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 KLSSWDQAET(0.013)PGHT(0.886)PS(0.101)LR 59.618 0.0038275 0 1029.3 920.19 792.09 1091 920.07 1135.1 933.19 1027.6 952.62 1315.9 TRUE FALSE FALSE 1016.754496 933.144459 805.8759942 1217.146553 873.1153946 1062.570773 1012.455135 1057.331985 867.4152813 1281.712728 0.793277989 0.728044934 0.628749311 0.949625081 0.681209896 0.829024125 0.789923602 0.824936791 0.676762633 1 10.32385723 -11.91639637 0.786811712 0.998540584 0.776591566 0 0.128922264 0.392097607 0.453754752 0.049751586 0.016560966 1.21E-12 11.91639637 -0.221949018 KLSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 0 KLS(0.011)VPT(0.994)S(0.994)DEEDEVPAPKPR 114.96 0.00091058 23566000 2542 2343.5 2037.8 2039.4 2332.3 2242.9 1919.8 2422.3 2977.3 2299 TRUE FALSE FALSE 2511.017126 2376.491855 2073.267054 2275.205024 2213.274028 2099.585929 2082.867764 2492.385429 2711.002831 2239.271649 1.121354405 1.061278946 0.925866701 1.016046903 0.988390144 0.93762002 0.930154126 1.113033977 1.210662776 1 11.12881384 -9.792057839 24.70146394 1.05920543 0.982070309 0.302875041 0.07515797 188.2471895 151867.7522 0.010530861 0.013841226 1.61E-10 9.792057839 -0.077135121 KLSVPT(ph)SDEEDEVPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 KLS(0.001)VPT(0.499)S(0.499)DEEDEVPAPKPR 94.639 0.00080187 91885000 5098.2 4815.6 4471 4335 3754.9 4241.8 4156.4 4645.3 6061.6 5123 TRUE FALSE FALSE 5036.061177 4883.394143 4548.81588 4836.233097 3563.273442 3970.76267 4509.444512 4779.704426 5519.435314 4989.903721 1.00925017 0.978654983 0.911603937 0.969203689 0.714096632 0.795759376 0.903713732 0.95787508 1.106120603 1 12.28479626 -9.422239367 1.48800925 1.003529767 0.851127983 0.489057536 0.075759052 0.247211059 1.082621757 0.011629468 0.02002005 3.78E-10 9.422239367 -0.152401784 KLSVPTS(ph)DEEDEVPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 KLSVPTSDEEDEVPAPKPR 19 2 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 KLSVPT(0.01)S(0.99)DEEDEVPAPKPR 116.04 0.00030614 124210000 6209 5951.9 5736.2 5287 5240.4 5681.1 5514 5462 6960.6 7294.3 TRUE FALSE FALSE 6133.32232 6035.691004 5836.036155 5898.307816 4972.962833 5318.096045 5982.359022 5620.034352 6338.026503 7104.793034 0.863265445 0.849523832 0.821422401 0.830187141 0.699944785 0.748522303 0.842017353 0.791020136 0.89207757 1 12.79457691 -11.24157206 0.383118989 1.021774988 0.770065656 0.579222695 0.04998894 0.434779027 0.148627356 0.045209247 0.020394171 5.73E-12 11.24157206 -0.251709332 KLTS(ph)DEEGEPSGK ddPTM_HeLa_Romidepsin_16h_R1 5 KLTSDEEGEPSGK 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 KLT(0.005)S(0.976)DEEGEPS(0.019)GK;KLT(0.035)S(0.965)DEEGEPSGK;KLT(0.041)S(0.898)DEEGEPS(0.06)GK;KLT(0.028)S(0.971)DEEGEPS(0.002)GK;KLT(0.018)S(0.982)DEEGEPSGK ;;;; 213.99 3.72E-23 290366000 38670.9 35455 34676.9 33885.3 38414.2 37085.6 35351.1 36871.9 38798.3 35961.3 TRUE FALSE FALSE 38199.5642 35954.13642 35280.4369 37803.27782 36453.78003 34715.94985 38353.82155 37938.73025 35328.08288 35027.02024 1.090574189 1.0264686 1.007234891 1.079260456 1.040733119 0.991119131 1.094978142 1.08312754 1.008595154 1 15.09618064 -7.716357311 24.99784094 1.039615693 1.08905302 0.317874844 0.0321635 157.5214593 87342.98618 0.005330017 0.019942964 1.92E-08 7.716357311 0.049437327 KLVIIEGDLER ddPTM_HeLa_Romidepsin_16h_R1 2 KLVIIEGDLER 11 1 J3KN67;A0A2R2Y2Q3;P06753;A0A494C0P6;P06753-7;P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8 J3KN67;P06753-4 TPM3 Tropomyosin alpha-3 chain 0 0 ; ; 88.338 0.023741 26795870 6635.4 5922.46 6041.5 4991.8 6622.82 6849.4 6065.1 6442 6372 5561.3 FALSE FALSE TRUE 6554.525193 6005.836547 6146.649773 5568.975403 6284.832782 6411.745445 6580.269443 6628.389106 5802.072361 5416.816624 1.21003269 1.108739129 1.134734697 1.028090074 1.160244701 1.183674082 1.214785343 1.223668728 1.071122167 1 12.40322954 -12.43037928 1.047920474 0.995851946 1.159068824 0.387883055 0.059206399 0.3777347 0.711024347 0.047494336 0.010755612 3.71E-13 12.43037928 0.163216877 KLVIIESDLER ddPTM_HeLa_Romidepsin_16h_R1 1 KLVIIESDLER 11 1 Q6ZN40;P09493-3;P09493-7;P09493-8;P09493-9;P09493-2;H7BYY1;F5H7S3;A0A0S2Z4G6;H0YKX5;A0A494BZZ2;B7Z596;H0YKJ4;P09493-6;H0YK48;P09493-5;P09493-10;P09493;P09493-4;A0A494C0V8;H0YL42 Q6ZN40 TPM1 Tropomyosin alpha-1 chain 0 0 89.356 0.022694 10069000 3046.5 2817.5 3087.4 2652.9 3643.6 2763.7 2290.8 2594.3 2997.1 2838.1 FALSE FALSE TRUE 3009.368086 2857.164839 3141.134902 2959.64078 3457.653496 2587.108489 2485.380495 2669.361977 2729.03187 2764.365753 1.088628769 1.033569757 1.136294971 1.070640083 1.250794506 0.935877782 0.899078023 0.965632704 0.987218087 1 11.4327328 -8.050003772 24.99974264 1.064748031 0.928635338 0.449032569 0.073317792 254.8529714 127415.2031 0.010408966 0.026538187 8.91E-09 8.050003772 -0.136112693 KMDETDASS(ph)AVK ddPTM_HeLa_Romidepsin_16h_R1 1 KMDETDASSAVK 12 1 K7EJM5;A0A087WX29;A0A0A0N0M3;K7EN94;B1AKP7;G3V162;A0A087X260;A0A087WYY0;Q13148 K7EJM5 TARDBP;TDP43 TAR DNA-binding protein 43 1 0 KMDETDAS(0.082)S(0.918)AVK 73.219 0.0040511 0 1555 1364.5 1383.4 1071.7 1228.6 1362.6 1003.6 1193.4 1598.8 1439.8 TRUE FALSE FALSE 1536.047062 1383.709467 1407.477497 1195.614997 1165.899957 1275.534258 1088.845759 1227.929146 1455.799324 1402.393788 1.095303669 0.986676837 1.003625022 0.852552975 0.831364177 0.909540721 0.776419411 0.875595112 1.038081697 1 10.4536758 -9.363315458 2.120066389 1.042399964 0.843971948 0.81034894 0.04239129 0.10593753 0.931497999 0.007736369 0.012856726 4.33E-10 9.363315458 -0.198428016 KMEES(ph)DEEAVQAK ddPTM_HeLa_Romidepsin_16h_R1 1 KMEESDEEAVQAK 13 1 I3VM54;Q9Y2K7-3;Q9Y2K7;Q9Y2K7-4;Q9Y2K7-5;Q9Y2K7-2 I3VM54 KDM2A Lysine-specific demethylase 2A 1 0 KMEES(1)DEEAVQAK 83.292 0.025168 8140400 4017.4 3567 3765.4 3375.1 3905.6 3981.6 3680.2 3835 3823.2 3541.2 TRUE FALSE FALSE 3968.434384 3617.21632 3830.935207 3765.344942 3706.282658 3727.18861 3992.796096 3945.959674 3481.243417 3449.199114 1.150537923 1.048711947 1.110673835 1.09165775 1.074534272 1.080595375 1.157600928 1.144022002 1.00929036 1 11.7520457 -12.46592627 1.127376179 0.998226051 1.109203096 0.59706197 0.03366387 0.302439922 0.669682272 0.027034321 0.006242179 3.42E-13 12.46592627 0.110977045 KMSGGS(ph)TMSSGGGNTNNSNSK ddPTM_HeLa_Romidepsin_16h_R1 3 KMSGGSTMSSGGGNTNNSNSK 21 1 A0A6E1WJ75;Q86U70-3;Q86U70-2;Q86U70 A0A6E1WJ75 LDB1 LIM domain-binding protein 1 1 0 KMS(0.013)GGS(0.39)T(0.39)MS(0.143)S(0.054)GGGNT(0.009)NNSNSK;KMS(0.036)GGS(0.339)T(0.339)MS(0.198)S(0.085)GGGNT(0.003)NNSNSK;KMS(0.082)GGS(0.39)T(0.39)MS(0.129)S(0.01)GGGNTNNSNSK ;; 82.367 0.00072154 82760900 5876.85 5709.22 4870.22 4564.66 4576.37 4079.12 4089.72 3650.35 5367.13 5242.79 TRUE FALSE FALSE 5805.220692 5789.594549 4954.984136 5092.447467 4342.820762 3818.477397 4437.100715 3755.967118 4887.080451 5106.58156 1.13681151 1.133751509 0.970313326 0.997232181 0.850435993 0.747756078 0.868898433 0.735514957 0.957016038 1 12.31814213 -8.853861833 1.491122264 1.06853248 0.786342451 0.743580089 0.067218264 0.138378099 0.618745966 0.010856334 0.025205239 1.40E-09 8.853861833 -0.282190029 KNDMDEPPPLDYGS(ph)GEDDGK ddPTM_HeLa_Romidepsin_16h_R1 1 KNDMDEPPPLDYGSGEDDGK 20 1 Q12873-2;Q12873;Q12873-3;A0A5F9ZHX5;H7C2H0 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 KNDMDEPPPLDYGS(1)GEDDGK 129.29 0.00030288 12898000 11530 11458 11545 10082 10096 10430 9038.8 9729.8 12913 12634 TRUE FALSE FALSE 11389.46793 11619.30602 11745.93588 11247.72828 9580.763447 9763.556661 9806.555446 10011.31641 11758.02894 12305.76686 0.925539063 0.94421633 0.954506616 0.914020914 0.77855883 0.793413102 0.7969073 0.813546732 0.955489331 1 13.58704694 -8.893722335 3.428252859 0.960792476 0.795190335 0.933537409 0.020222743 0.060633518 1.402241227 0.004598192 0.008731895 1.28E-09 8.893722335 -0.165602141 KNGSTAVAESVAS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 2 KNGSTAVAESVASPQK 16 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 KNGSTAVAESVAS(1)PQK;KNGSTAVAESVAS(1)PQK ; 150.65 8.42E-05 256070000 21256.4 20007.6 19459.7 17918.9 15543.6 14324 12397 13279.2 22001.6 20814.7 TRUE FALSE FALSE 20997.31882 20289.26752 19798.38792 19990.76753 14750.35209 13408.74263 13450.00087 13663.4127 20033.72179 20273.93109 1.035680684 1.00075646 0.976544106 0.98603312 0.72755264 0.661378524 0.663413563 0.673939979 0.988151814 1 14.30733823 -8.72838119 3.136953219 1.012584771 0.667773226 0.987588674 0.01744266 0.020411052 0.412384397 0.003046418 0.006271517 1.87E-09 8.72838119 -0.344811544 KNNPS(ph)PPPDSDLER ddPTM_HeLa_Romidepsin_16h_R1 1 KNNPSPPPDSDLER 14 1 E7ESD5;E9PLN6;F2Z2Y1;O95677-3;O95677-5;O95677-2;O95677-4;O95677 E7ESD5 EYA4 Eyes absent homolog;Eyes absent homolog 4 1 0 KNNPS(0.999)PPPDS(0.001)DLER 68.525 0.018072 38728000 4351.2 4158.3 3795.2 4852.6 3543.7 3172.1 2547.1 2615.3 5008.9 4253.9 TRUE FALSE FALSE 4298.165901 4216.840657 3861.253864 5413.680444 3362.851766 2969.413047 2763.45061 2690.969579 4560.891439 4143.383065 1.037356632 1.017728892 0.931908492 1.306584585 0.811619808 0.716663895 0.666955135 0.649461934 1.100765092 1 12.01659349 -8.533240506 24.98542651 1.030178562 0.691206777 0.763432453 0.097537612 72.30214656 174342.6072 0.012955602 0.025932471 2.93E-09 8.533240506 -0.338971785 KNPDLGFSDY(ph)AAAQLR ddPTM_HeLa_Romidepsin_16h_R1 2 KNPDLGFSDYAAAQLR 16 1 O95926-2;O95926 O95926-2 SYF2 Pre-mRNA-splicing factor SYF2 1 0 KNPDLGFS(0.001)DY(0.999)AAAQLR;KNPDLGFSDY(1)AAAQLR ; 78.401 0.0068944 34683800 3303.5 3329.7 3206.2 3115.1 3386.8 3690.9 2819.5 3336.4 3573.9 3590.8 TRUE FALSE FALSE 3263.235671 3376.575604 3262.002566 3475.282519 3213.958958 3455.063402 3058.98826 3432.93347 3254.241433 3497.510498 0.933016691 0.965422579 0.932664124 0.993644628 0.918927609 0.987863626 0.87461875 0.981536287 0.930445079 1 11.77211267 -12.38978667 0.95826536 1.002115989 0.94667939 0 0.04047844 0.630341774 0.970383413 0.02550251 0.005610481 4.08E-13 12.38978667 -0.055436598 KNPLPPSVGVVDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 KNPLPPSVGVVDKK 14 2 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 ; KNPLPPSVGVVDK(1)K;KNPLPPSVGVVDK(1)K 132.84 0.00012018 4867200 3216.4 3078.7 3462.3 2026.27 6485.7 5285.8 5533.9 6096.8 8096.7 5921.4 FALSE TRUE FALSE 3177.19728 3122.042019 3522.559879 2260.556871 6154.710528 4948.054439 6003.949328 6273.201289 7372.510873 5767.561174 0.550873616 0.541310603 0.610753796 0.391943285 1.067125314 0.857911046 1.040985808 1.087669658 1.278271812 1 12.49374569 -8.697047572 24.99999302 0.722908063 1.004284712 0.243043971 0.245677506 66.34418367 25757.21293 0.033278709 0.06655741 2.01E-09 8.697047572 0.281376649 KNQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_HeLa_Romidepsin_16h_R1 2 KNQKPSQVNGAPGSPTEPAGQK 22 2 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 KNQKPSQVNGAPGS(0.9)PT(0.1)EPAGQK;KNQKPSQVNGAPGS(0.652)PT(0.348)EPAGQK ; 136.26 8.30E-05 30819100 10802.9 11447.4 10657 9243.9 8935 9976.5 8222 8883.4 10508.6 10579.8 TRUE FALSE FALSE 10671.2301 11608.5568 10842.48061 10312.72321 8479.013609 9339.033848 8920.376475 9140.427163 9568.684497 10304.93527 1.035545573 1.126504582 1.052163874 1.000755749 0.822810953 0.906268075 0.865641194 0.886995107 0.928553576 1 13.33104782 -8.8687018 5.615236059 1.029380292 0.87321125 0.694074524 0.050101862 0.076559063 3.53513491 0.00634951 0.01166967 1.35E-09 8.8687018 -0.156169043 KNS(ph)LISSLEEEVSILNR ddPTM_HeLa_Romidepsin_16h_R1 1 KNSLISSLEEEVSILNR 17 1 A0A087WY61;Q14980-2;Q14980;H0YFY6;Q14980-4;Q14980-3 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 KNS(0.997)LIS(0.002)S(0.001)LEEEVSILNR 67.979 0.0027663 0 251.46 329.55 183.66 213.3 291.31 221.37 250.78 505.27 287.26 275.89 TRUE FALSE FALSE 248.3951088 334.1894136 186.8565253 237.9627496 276.4433637 207.2251714 272.0812469 519.8891903 261.5667461 268.722338 0.924356012 1.243623496 0.695351665 0.885533936 1.028732355 0.771149778 1.012499552 1.934670538 0.973371801 1 8.069972443 -7.264273075 4.988464464 0.951066199 1.981621418 0.816571781 0.140529544 0.04691575 3.603660094 0.017909182 0.165905533 5.44E-08 7.264273075 1.030555219 KNSLISSLEEEVSILNR ddPTM_HeLa_Romidepsin_16h_R1 1 KNSLISSLEEEVSILNR 17 1 A0A087WY61;Q14980-2;Q14980;H0YFY6;Q14980-4;Q14980-3 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 0 0 107.15 0.0015129 5696700 1318.8 1159.2 1122.2 1351.7 1302.3 1362.3 1717.8 1990 1293 1087.6 FALSE FALSE TRUE 1302.725958 1175.519248 1141.73142 1507.989914 1235.838771 1275.253427 1863.709889 2047.57751 1177.350842 1059.343995 1.22974781 1.109667165 1.077772117 1.423512967 1.166607615 1.203814278 1.759305662 1.932873098 1.111396154 1 10.04895543 -4.000000001 0.478962546 1.100921569 26.24399313 0.821497306 0.124610314 26.0138765 0.263139875 0.027228703 655.4572569 1.00E-04 4.000000001 25.14307156 KNSSQDDLFPT(ph)SDTPR ddPTM_HeLa_Romidepsin_16h_R1 1 KNSSQDDLFPTSDTPR 16 1 Q9H6T3-3;Q9H6T3;Q9H6T3-2 Q9H6T3-3 RPAP3 RNA polymerase II-associated protein 3 1 0 KNSS(0.001)QDDLFPT(0.957)S(0.038)DT(0.003)PR 197.73 2.02E-13 7247200 1191.9 1141.1 1096 827.14 1316.9 1534.2 1246.1 1516.7 1222.6 1131.5 TRUE FALSE FALSE 1177.372664 1157.164436 1115.07542 922.7778186 1249.693679 1436.169571 1351.943703 1560.583322 1113.247594 1102.103467 1.068295945 1.049959891 1.011770177 0.837287829 1.133916839 1.303116826 1.226693993 1.416004367 1.010111689 1 10.10604396 -8.404964659 3.680608389 1.019589558 1.30636744 0.775747649 0.075824897 0.090074871 2.185721702 0.010963811 0.025799011 3.94E-09 8.404964659 0.286777882 KNSSTDQGS(ph)DEEGSLQK ddPTM_HeLa_Romidepsin_16h_R1 2 KNSSTDQGSDEEGSLQK 17 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 KNS(0.308)S(0.023)T(0.023)DQGS(0.646)DEEGS(0.001)LQK;KNSSTDQGS(0.998)DEEGS(0.002)LQK ; 84.113 0.0043345 12112200 5607.7 5345.6 5893.8 3384.2 5306.1 6258 5090.2 6112.2 6124.6 6458 TRUE FALSE FALSE 5539.351195 5420.855497 5996.379117 3775.497127 5035.309917 5858.133997 5522.561461 6289.046864 5576.800437 6290.220229 0.880629134 0.86179105 0.953286037 0.600217002 0.800498191 0.931308251 0.877959954 0.999813462 0.8865827 1 12.61889481 -11.697446 0.675613893 0.999144397 0.854951893 0.046103449 0.107758381 0.889367615 0.791642358 0.065818653 0.02425472 2.01E-12 11.697446 -0.144192504 KNTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_HeLa_Romidepsin_16h_R1 2 KNTFTAWSDEESDYEIDDRDVNK 23 2 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 0 KNT(0.001)FT(0.005)AWS(0.981)DEES(0.013)DYEIDDRDVNK;KNT(0.029)FT(0.326)AWS(0.644)DEES(0.001)DYEIDDRDVNK ; 107.06 1.70E-05 34584000 4342.3 4202.4 3622 4213.2 3159.9 3172.8 3330.2 3069.6 4889 4145.5 TRUE FALSE FALSE 4289.374377 4261.561498 3685.039391 4700.350008 2998.638512 2970.06832 3613.067105 3158.414033 4451.715595 4037.799312 1.062304995 1.055416866 0.912635598 1.164087079 0.742641791 0.735566107 0.894810966 0.782211742 1.102510365 1 11.97935349 -8.748782189 24.99997692 1.030957524 0.792576308 0.742985075 0.07462286 86.37759754 170608.5347 0.009792987 0.01948199 1.78E-09 8.748782189 -0.238381216 KPAAATVTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KPAAATVTKK 10 2 P16403 P16403 HIST1H1C Histone H1.2 0 1 KPAAATVTK(1)K 122.18 4.61E-05 0 1312 2290.4 1693.3 3265.1 5058.8 6909.5 7566.7 1855.4 1786.3 1527.2 FALSE TRUE FALSE 1296.008839 2322.644311 1722.771176 3642.626225 4800.630559 6468.005249 8209.415309 1909.083072 1626.528854 1487.523124 0.871252903 1.561417281 1.158147493 2.448786285 3.227264492 4.348171229 5.518848869 1.28339724 1.093447778 1 10.53869638 -8.98694383 1.620866223 0.982286458 3.880095649 0.569033424 1.006020918 0.167552675 0.877840943 0.146341317 0.304998626 1.03E-09 8.98694383 2.897809191 KPALPVS(ph)PAAR ddPTM_HeLa_Romidepsin_16h_R1 1 KPALPVSPAAR 11 1 A0A087WWF4;A0A087X0M4;Q9BWU0 A0A087WWF4 SLC4A1AP Kanadaptin 1 0 KPALPVS(1)PAAR 107.34 0.024327 60638000 3364.5 3154.7 3145.3 2453.6 2665.4 2533.2 1898.2 2263 3248.4 3579.8 TRUE FALSE FALSE 3323.49218 3199.111949 3200.042627 2737.296777 2529.374692 2371.336696 2059.433061 2328.476335 2957.854968 3486.79628 0.953165001 0.917493221 0.917760136 0.785046374 0.725415106 0.680090405 0.590637621 0.667798216 0.84830163 1 11.76768636 -8.982134831 0.783057231 0.982401203 0.613763527 0.859403116 0.049490057 0.075850339 0.088096507 0.004817537 0.014617947 1.04E-09 8.982134831 -0.368637676 KPAT(ph)PAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_HeLa_Romidepsin_16h_R1 4 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 2 0 KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPAT(1)PAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR ;;; 54.049 0.002516 161993000 10194.6 10270 10022.2 6294.6 10835.6 11626.2 9249.7 9956.3 10645.5 10443.4 TRUE FALSE FALSE 10070.34429 10414.58133 10196.63219 7022.411269 10282.6189 10883.32334 10035.36929 10244.36983 9693.339818 10172.07896 0.989998636 1.02384 1.002413786 0.690361459 1.010866996 1.06992124 0.986560301 1.007106794 0.952935959 1 13.31232695 KPATPAEDDEDDDIDLFGS(ph)DNEEEDK ddPTM_HeLa_Romidepsin_16h_R1 1 KPATPAEDDEDDDIDLFGSDNEEEDK 26 1 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 1 0 KPATPAEDDEDDDIDLFGS(1)DNEEEDK 97.312 2.29E-06 4263800 1226.1 1432.7 1537 677.37 1282.6 1414.6 1046.5 1263.8 1160.2 1396.5 TRUE FALSE FALSE 1211.155822 1452.869588 1563.75084 755.6907065 1217.144136 1324.211625 1135.389684 1300.366059 1056.428806 1360.218729 0.890412546 1.068114677 1.149631899 0.55556558 0.89481501 0.973528446 0.834711109 0.955997761 0.776660977 1 10.40962295 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLR ddPTM_HeLa_Romidepsin_16h_R1 8 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 1 0 KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLR ;;;;;;; 98.747 1.80E-12 2325709700 41667.29 42536.76 43651.07 26021.38 43393.5 48252.54 39504.01 45440.28 44066.58 45652.98 TRUE FALSE FALSE 41159.43304 43135.59362 44410.79856 29030.09439 41178.96777 45169.35842 42859.47962 46755.02281 40125.15472 44466.909 0.925619387 0.970060537 0.998738153 0.652847141 0.926058696 1.015797127 0.963851111 1.051456552 0.902359881 1 15.4404445 -9.278744353 0.005661985 1.887797157 7.50E-07 0 0.107445001 32075.67948 73.74326866 12117.78968 12467.65355 5.26E-10 9.278744353 -1.887796407 KPATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_HeLa_Romidepsin_16h_R1 9 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLREER 35 3 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 1 0 KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER;KPATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER ;;;;;;;; 69.439 9.44E-06 364997200 48010.15 42307.3 39972.11 57273.7 50691.33 46013.48 45891.1 49321.35 52773.9 46143.49 TRUE FALSE FALSE 47424.98383 42902.90328 40667.80781 63895.95467 48104.36227 43073.36713 49789.08889 50748.38545 48053.67021 44944.67548 1.055185811 0.954571433 0.904841505 1.421657938 1.070301693 0.958364182 1.107786147 1.12913009 1.069173816 1 15.45586259 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR ddPTM_HeLa_Romidepsin_16h_R1 2 KPATPAEDDEDDDIDLFGSDNEEEDKEAAQLR 32 2 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 0 0 ; ; 86.604 4.26E-09 12175200 3771.51 3643.99 3873.46 2234.42 3636.84 4069.17 3237.25 3556.45 4084.33 4099.03 FALSE FALSE TRUE 3725.541385 3695.290187 3940.875946 2492.774154 3451.238484 3809.16317 3512.221934 3659.35027 3719.017295 3992.53661 0.933126418 0.925549481 0.987060691 0.624358496 0.864422502 0.954070943 0.879696864 0.916547706 0.931492347 1 11.96308992 -10.35266444 0.894511422 0.980313694 0.865659771 0.150040322 0.092721177 0.599230564 0.969295134 0.022030249 0.024914007 4.44E-11 10.35266444 -0.114653923 KPDAEVLTVES(ph)PEEEAMTK ddPTM_HeLa_Romidepsin_16h_R1 1 KPDAEVLTVESPEEEAMTK 19 1 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 KPDAEVLTVES(0.769)PEEEAMT(0.231)K 90.778 0.0033261 11224000 2364.3 2515.1 2350.5 2264.1 2906.9 2998.9 2332.6 4107.5 2128 2651.5 TRUE FALSE FALSE 2335.483002 2550.507644 2391.409467 2525.885895 2758.550046 2807.279969 2530.730986 4226.344032 1937.66635 2582.613648 0.904309866 0.987568406 0.925964853 0.978034751 1.068123391 1.086991843 0.979910792 1.636460039 0.750273411 1 11.33461612 -5.115760912 1.311672122 0.965801907 199.9999456 0.822748885 0.092741424 96.51299282 0.712085132 0.009868664 57236.07262 7.66E-06 5.115760912 199.0341437 KPDK(ac)LTILR ddPTM_HeLa_Romidepsin_16h_R1 1 KPDKLTILR 9 2 A6NGV6;P27540-3;P27540-4;P27540;A0A087WVE9;Q9HBZ2-2;Q9HBZ2;P27540-2 A6NGV6 ARNT;ARNT2 Aryl hydrocarbon receptor nuclear translocator;Aryl hydrocarbon receptor nuclear translocator 2 0 1 KPDK(1)LTILR 99.013 0.0027655 0 731.48 740.39 1099.2 1109.5 1395.7 1193.4 922.19 673.6 349.58 341.06 FALSE TRUE FALSE 722.5644404 750.8132299 1118.331115 1237.78561 1324.472221 1117.145592 1000.520796 693.0895532 318.3126893 332.199212 2.175093782 2.260129472 3.366447223 3.726034155 3.986981826 3.362878511 3.011809659 2.08636724 0.958198207 1 8.375904841 -10.66111382 0.720621812 1.215585174 3.298672992 0.714028965 0.543925759 0.247743894 0.281485717 0.181989295 0.164912512 2.18E-11 10.66111382 2.083087818 KPEDVLDDDDAGS(ph)APLK ddPTM_HeLa_Romidepsin_16h_R1 2 KPEDVLDDDDAGSAPLK 17 1 A0A087WUV8;P35613-3;P35613-4;P35613-2;P35613 A0A087WUV8 BSG Basigin 1 0 KPEDVLDDDDAGS(1)APLK;KPEDVLDDDDAGS(1)APLK ; 114.75 0.00062216 8723800 3648.9 3826.3 4431.1 2763.6 4034.4 4562.2 2900.7 4180.1 3868.9 4420 TRUE FALSE FALSE 3604.425803 3880.166752 4508.221437 3083.140435 3828.509514 4270.690144 3147.085386 4301.044598 3522.855894 4305.167763 0.837232369 0.901281196 1.047165101 0.716148732 0.889282305 0.991991574 0.7310018 0.999042276 0.818285393 1 12.07185374 -9.280617103 24.94665384 0.927654598 0.866370845 0.060428597 0.107307346 1746.36744 2271694.66 0.016168707 0.024721049 5.24E-10 9.280617103 -0.061283753 KPEDWDEEMDGEWEPPVIQNPEYK ddPTM_HeLa_Romidepsin_16h_R1 3 KPEDWDEEMDGEWEPPVIQNPEYK 24 1 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 0 ;; ;; 73.459 0.00023604 162526900 6047 5611 6272.4 5769.5 6622.2 7275.7 7087.3 8254.5 6753.3 5858.8 FALSE FALSE TRUE 5973.296838 5689.991805 6381.568491 6436.596736 6284.244423 6810.806251 7689.295085 8493.330934 6149.267934 5706.587531 1.046737092 0.99709183 1.118281014 1.127923948 1.101226326 1.193498954 1.347441889 1.488337976 1.077573576 1 12.47841257 -4.000000003 0.388244222 1.013415425 8.57829566 0.939050028 0.03670223 7.735035865 0.092904792 0.007952515 44.8487759 1.00E-04 4.000000003 7.564880236 KPEK(ac)PLFSSASPQDSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 KPEKPLFSSASPQDSSPR 18 2 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 0 1 ; K(0.002)PEK(0.998)PLFSSASPQDSSPR;K(0.003)PEK(0.997)PLFSSASPQDSSPR 155.24 1.50E-15 4289700 1940.24 1621.44 1704.5 1409.06 1847.17 1482.39 1412.96 1501.7 1832.23 1637.87 FALSE TRUE FALSE 1916.591609 1644.266675 1734.166107 1571.982147 1752.902022 1387.670063 1532.976787 1545.14932 1668.35076 1595.317901 1.201385383 1.030682771 1.08703482 0.985372349 1.098779134 0.86983921 0.960922451 0.968552612 1.045779502 1 10.63962823 -8.670892742 1.123844622 1.09132895 0.93874423 0.345187304 0.069812282 0.451950314 1.101969953 0.014205595 0.0444844 2.13E-09 8.670892742 -0.15258472 KPEKPLFSS(ph)ASPQDSSPR ddPTM_HeLa_Romidepsin_16h_R1 1 KPEKPLFSSASPQDSSPR 18 2 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 KPEKPLFS(0.056)S(0.692)AS(0.238)PQDS(0.007)S(0.007)PR 79.341 0.012766 33084000 2072.4 2458.3 1952.9 2337.3 1661.2 1211 831.59 1189.1 2210 2018.5 TRUE FALSE FALSE 2047.140792 2492.908012 1986.889405 2607.549623 1576.422765 1133.621008 902.2252338 1223.504732 2012.332065 1966.059079 1.041240731 1.267972076 1.010594965 1.326282435 0.801818614 0.576595597 0.458900367 0.62231331 1.023535908 1 10.94109096 -8.46715133 3.674822626 1.059710568 0.54848502 0.811967156 0.119448418 0.078051874 2.10392569 0.017449056 0.040059271 3.41E-09 8.46715133 -0.511225547 KPFEEHWR ddPTM_HeLa_Romidepsin_16h_R1 2 KPFEEHWR 8 1 D6RFM5;P31040-2;P31040;A0A087X1I3;P31040-3 D6RFM5 SDHA "Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial" 0 0 ; ; 118.74 0.0040517 20723800 10981 11225.7 14523.7 16088.6 18118.5 22419.3 16829.6 14684.2 12597.5 12101.8 FALSE FALSE TRUE 10847.15935 11383.7357 14776.47891 17948.83963 17193.84534 20986.77908 18259.1058 15109.06416 11470.74805 11787.39349 0.920233922 0.965755127 1.253583238 1.522714894 1.458663898 1.780442733 1.549036758 1.281798573 0.973136941 1 13.52495711 -9.514928137 2.258644999 0.959783779 1.535779856 0.833242171 0.116522694 0.083486697 0.852316222 0.018895131 0.029389064 3.06E-10 9.514928137 0.575996077 KPGLTPS(ph)PSATTPLTK ddPTM_HeLa_Romidepsin_16h_R1 1 KPGLTPSPSATTPLTK 16 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 KPGLT(0.057)PS(0.883)PS(0.057)AT(0.003)TPLTK 57.525 0.024195 11570000 2508.2 2420.3 2675.5 2114.1 3223.9 3748 2522.8 3140.9 3227.8 2899.8 TRUE FALSE FALSE 2477.629094 2454.373047 2722.065955 2358.542189 3059.372353 3508.514896 2737.086569 3231.776986 2939.097484 2824.462778 0.877203663 0.868969868 0.963746443 0.835040988 1.083169648 1.242188399 0.969064486 1.144209444 1.040586375 1 11.46376077 -8.638354543 6.945335449 0.929915293 1.112858184 0.516892057 0.085038556 0.129962412 7.422946294 0.011772339 0.023642615 2.30E-09 8.638354543 0.18294289 KPGMFFNPEESELDLTYGNR ddPTM_HeLa_Romidepsin_16h_R1 1 KPGMFFNPEESELDLTYGNR 20 1 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 0 46.099 0.024792 47374000 1219.9 1240.8 1119.8 804.66 1020.1 1209.3 953.96 958.76 980.75 1161.4 FALSE FALSE TRUE 1205.03139 1258.268015 1139.289649 897.6985752 968.0404905 1132.029633 1034.989339 986.5002079 893.0292637 1131.226661 1.065243095 1.112304067 1.007127651 0.793562074 0.855744056 1.000709824 0.914926579 0.872062375 0.789434421 1 10.14367231 -9.457652371 8.659859002 1.038818676 0.893853481 0.175701012 0.096772763 0.21331913 26.79386263 0.009345432 0.01426571 3.49E-10 9.457652371 -0.144965195 KPGPPLS(ph)PEIR ddPTM_HeLa_Romidepsin_16h_R1 1 KPGPPLSPEIR 11 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 KPGPPLS(1)PEIR 96.135 0.0072807 98784000 3317.8 3197.6 3096 2879 3184.5 3423.5 3117.7 3370.8 3185.2 2957.2 TRUE FALSE FALSE 3277.361377 3242.615897 3149.884581 3211.883526 3021.983082 3204.749399 3382.51736 3468.32878 2900.307735 2880.371518 1.137825922 1.125763075 1.093568855 1.115093489 1.04916434 1.112616681 1.174333706 1.204125495 1.006921405 1 11.49203919 -16.52287874 0.237729516 0.25092549 1.141443944 0.623250325 0.038868921 26.071188 0.339585217 9.121744924 0.028796819 3.00E-17 16.52287874 0.890518455 KPGPSGPSES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KPGPSGPSESPK 12 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 KPGPS(0.001)GPS(0.168)ES(0.831)PK;KPGPS(0.004)GPS(0.095)ES(0.901)PK ; 110.6 0.0031013 318060000 17506.8 17957.4 17821.8 15932.3 14328.9 14715.8 12914.2 10502.9 17187.5 18502.4 TRUE FALSE FALSE 17293.42039 18210.20475 18131.98095 17774.46749 13597.64276 13775.50787 14011.13183 10806.78484 15650.20695 18021.70498 0.959588474 1.010459597 1.006119064 0.986281126 0.75451478 0.764384274 0.777458728 0.599653854 0.868408787 1 14.13744789 -8.734148765 4.753492615 0.985832507 0.72686305 0.802758823 0.060042689 0.04704476 2.554327268 0.00676684 0.013441003 1.84E-09 8.734148765 -0.258969458 KPIETGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KPIETGSPK 9 1 Q5T757;Q05519-2;Q05519 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 KPIET(0.011)GS(0.989)PK 77.644 0.01972 77873000 5113.6 6378.9 11241 8045.3 4922 5391 14623 2277.3 8925.3 5583.7 TRUE FALSE FALSE 5051.273476 6468.702322 11436.64489 8975.53544 4670.811973 5046.532499 15865.07726 2343.190083 8126.998814 5438.634669 0.928776023 1.189398207 2.102852202 1.650328802 0.858820689 0.927904301 2.917106631 0.430841604 1.494308647 1 12.4090288 -9.99312825 24.90359032 0.971246461 1.512915584 0.035519628 0.674970154 241.0176473 873455.3141 0.097877206 0.128472077 1.02E-10 9.99312825 0.541669122 KPISDNSFS(ph)SDEEQSTGPIK ddPTM_HeLa_Romidepsin_16h_R1 2 KPISDNSFSSDEEQSTGPIK 20 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 KPISDNS(0.001)FS(0.949)S(0.05)DEEQSTGPIK;KPISDNS(0.004)FS(0.753)S(0.243)DEEQSTGPIK ; 92.679 0.00014865 11601000 5183.5 5381 4876.2 4834.8 4609 3949.1 3835.3 4848.9 6413.1 5898.2 TRUE FALSE FALSE 5120.321508 5456.753859 4961.068216 5393.822324 4373.785531 3696.765255 4161.070286 4989.195271 5839.496274 5744.963914 0.891271309 0.949832574 0.863550806 0.938878365 0.761325153 0.643479282 0.724298768 0.868446755 1.016454822 1 12.48808212 -8.736982431 4.919975014 0.940229675 0.737355266 0.671579892 0.066371751 0.086833412 5.266229589 0.010045259 0.019892482 1.83E-09 8.736982431 -0.202874409 KPISDNSFSS(ph)DEEQSTGPIK ddPTM_HeLa_Romidepsin_16h_R1 1 KPISDNSFSSDEEQSTGPIK 20 1 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 KPISDNS(0.008)FS(0.044)S(0.947)DEEQS(0.001)TGPIK 79.565 0.001415 14538000 2458.9 2649 2411.5 2466.1 2393.2 2066.4 2262 2491.7 2767.1 2633.3 TRUE FALSE FALSE 2428.929981 2686.292692 2453.471146 2751.242085 2271.066074 1934.363709 2454.134224 2563.793408 2519.603646 2564.886486 0.946993169 1.047333949 0.956561298 1.07265647 0.885445062 0.754171274 0.956819819 0.99957383 0.98234509 1 11.32467926 -8.714954635 24.99938451 0.984988138 0.892787044 0.322753093 0.069877503 125.0857986 67270.22341 0.010164257 0.020328465 1.93E-09 8.714954635 -0.092201094 KPLFHGDSEIDQLFR ddPTM_HeLa_Romidepsin_16h_R1 2 KPLFHGDSEIDQLFR 15 1 A0A087WZZ9;A0A024QZP7;P06493-2;P06493 A0A087WZZ9 CDK1;CDC2 Cyclin-dependent kinase 1 0 0 ; ; 145.81 0.00010108 25491000 8558.5 7661.3 8092.8 8464.5 10721.7 8942.8 8108.7 8361.3 9644.7 8115.8 FALSE FALSE TRUE 8454.18571 7769.155982 8233.651789 9443.205317 10174.53164 8371.383942 8797.452776 8603.221024 8782.053876 7904.950346 1.069479926 0.982821604 1.041581721 1.194593881 1.287108862 1.059005253 1.112904242 1.088333341 1.110956235 1 12.94854069 -9.336636939 6.830978956 1.029381875 1.148989524 0.382264789 0.067543639 0.183261879 14.17598143 0.010223286 0.015669611 4.61E-10 9.336636939 0.119607649 KPLSLAGDEETECQS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 KPLSLAGDEETECQSSPK 18 1 F5H1K3;Q86TN4-2;Q86TN4;Q86TN4-4 F5H1K3 TRPT1 tRNA 2-phosphotransferase 1 1 0 KPLSLAGDEET(0.003)ECQS(0.499)S(0.499)PK;KPLSLAGDEET(0.012)ECQS(0.494)S(0.494)PK ; 94.01 0.0013644 26223000 9041.5 8062.4 8352 1656.59 10873 11501 10212.3 11005.2 8689.9 8750.4 TRUE FALSE FALSE 8931.29872 8175.902679 8497.363057 1848.13273 10318.11024 10766.12322 11079.73251 11323.6181 7912.65358 8523.063347 1.047897728 0.959268088 0.996984618 0.216839023 1.21061053 1.263175314 1.299970686 1.328585467 0.928381411 1 13.05715634 -8.543745224 24.99950199 0.955302764 1.287413074 0.395451838 0.23681608 221.2909526 265121.1449 0.034956637 0.069918519 2.86E-09 8.543745224 0.33211031 KPLVIIAEDVDGEALSTLVLNR ddPTM_HeLa_Romidepsin_16h_R1 2 KPLVIIAEDVDGEALSTLVLNR 22 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 157.88 1.82E-08 57783000 4475.8 5094.85 4849.4 4619.9 4337.3 4721.1 3600.79 4155.26 4300.8 4093.6 FALSE FALSE TRUE 4421.247228 5166.575432 4933.801773 5154.074575 4115.951396 4419.436947 3906.641013 4275.485892 3916.125676 3987.247682 1.108846899 1.295774891 1.237395358 1.292639682 1.032278836 1.108392881 0.979783882 1.072290019 0.982162632 1 11.96117751 -6.193511146 17.76481096 1.093144536 1.10323626 0 0.118375597 0 0 0.016893472 0 6.40E-07 6.193511146 0.010091724 KPNAGGS(ph)PAPVR ddPTM_HeLa_Romidepsin_16h_R1 1 KPNAGGSPAPVR 12 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 KPNAGGS(1)PAPVR 65.038 0.024882 32903000 3484 3375.9 2570.4 5200.9 3301.3 3136 2978.8 2499.6 4211.6 5360.9 TRUE FALSE FALSE 3441.535668 3423.426009 2615.136734 5802.252529 3132.822342 2935.619721 3231.819198 2571.921982 3834.903948 5221.623045 0.65909309 0.655624885 0.500828327 1.111197128 0.599970989 0.562204452 0.618930009 0.492552212 0.734427574 1 12.3502826 -16.52287875 0.194900405 2.627027792 0.583065505 0.117774337 0.183519697 38.80172282 0.464985716 23.91530467 0.179121552 3.00E-17 16.52287875 -2.043962287 KPNEGADGQWK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KPNEGADGQWKK 12 2 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 KPNEGADGQWK(1)K 94.547 0.024956 961630 774.43 676.45 690.28 1109.8 1525.2 1366.9 945.7 990.95 764.58 675.43 FALSE TRUE FALSE 764.9909493 685.9730809 702.2940338 1238.120298 1447.363353 1279.559501 1026.027734 1019.621575 696.1940499 657.8822312 1.162808346 1.042698903 1.067507223 1.881978626 2.200034116 1.944967413 1.559591802 1.549854254 1.058235071 1 9.361685537 -9.263025806 24.89301136 1.075087886 1.839659573 0.818926364 0.178857249 45.19461179 709160.9492 0.030020616 0.047398735 5.46E-10 9.263025806 0.764571687 KPNIFYSGPAS(ph)PARPR ddPTM_HeLa_Romidepsin_16h_R1 2 KPNIFYSGPASPARPR 16 2 Q6PL18;Q6PL18-2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 1 0 KPNIFYS(0.013)GPAS(0.987)PARPR;KPNIFYS(0.001)GPAS(0.999)PARPR ; 97.083 0.0066586 113236000 7719.3 7676.7 7572.4 6788.5 5498.8 5046.9 4420.3 4717.6 7778 7279.7 TRUE FALSE FALSE 7625.214202 7784.772784 7704.194446 7573.418311 5218.175717 4724.419378 4795.760172 4854.096313 7082.3162 7090.572345 1.075401792 1.097904711 1.08654056 1.068096896 0.735931525 0.666295914 0.676357273 0.684584555 0.998835617 1 12.79168637 -8.710265607 4.725144985 1.048244765 0.680890189 0.966426506 0.033280536 0.030907806 1.453855589 0.006015119 0.012090552 1.95E-09 8.710265607 -0.367354575 KPPAPPS(ph)PVQSQSPSTNWSPAVPVK ddPTM_HeLa_Romidepsin_16h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 KPPAPPS(0.29)PVQS(0.29)QS(0.29)PS(0.058)T(0.058)NWS(0.014)PAVPVK 51.645 0.0086291 14121000 4591.3 4643.8 4053.9 3928.1 4215.8 4105.4 4112.3 4018.6 5125.4 4611.4 TRUE FALSE FALSE 4535.33947 4709.175538 4124.456429 4382.285404 4000.651995 3843.07819 4461.598659 4134.871851 4666.971387 4491.595163 1.009739147 1.048441671 0.918260947 0.975663488 0.890697369 0.855615444 0.993321637 0.920579816 1.039045421 1 12.13301219 -9.746859296 24.99993113 1.008015742 0.926259714 0.582697655 0.039942327 142.1594276 243754.9967 0.005980495 0.008437017 1.79E-10 9.746859296 -0.081756027 KPPAPPSPVQS(ph)QS(ph)PSTNWSPAVPVK ddPTM_HeLa_Romidepsin_16h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 2 0 KPPAPPS(0.346)PVQS(0.549)QS(0.756)PS(0.174)T(0.17)NWS(0.004)PAVPVK 58.688 0.0022245 22339000 4094.3 3819.2 4378.9 3741.6 4535.1 4397.6 4122.3 4071.4 4448.8 4338.3 TRUE FALSE FALSE 4044.397097 3872.966798 4455.112918 4174.221397 4303.656924 4116.607553 4472.448059 4189.199535 4050.888186 4225.590341 0.957120017 0.916550466 1.054317281 0.987843369 1.018474717 0.974208861 1.0584197 0.991387995 0.958656154 1 12.04493719 -9.745265032 24.99789057 0.974445283 1.013313732 0.370890636 0.033099047 266.4788365 411849.4433 0.005287072 0.007463903 1.80E-10 9.745265032 0.038868449 KPPAPPSPVQS(ph)QSPSTNWSPAVPVK ddPTM_HeLa_Romidepsin_16h_R1 1 KPPAPPSPVQSQSPSTNWSPAVPVK 25 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 KPPAPPS(0.341)PVQS(0.418)QS(0.162)PS(0.036)T(0.041)NWS(0.003)PAVPVK 47.281 0.015708 16643000 3560.1 3634.5 3683.4 3197.5 3780.7 3695.2 3377.2 4060.9 3889.5 3886.6 TRUE FALSE FALSE 3516.708132 3685.666586 3747.508032 3567.209995 3587.756771 3459.088646 3664.059284 4178.395734 3541.613379 3785.625572 0.92896354 0.973595121 0.98993098 0.942303967 0.947731545 0.913742942 0.967887398 1.10375304 0.935542438 1 11.88631601 -7.26409238 5.809975002 0.961412291 1.107878548 0.735782774 0.026462052 0.064231365 9.580118252 0.004405154 0.037161836 5.44E-08 7.26409238 0.146466257 KPPATTYEGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KPPATTYEGSPR 12 1 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 KPPATTYEGS(0.999)PR 67.846 0.022694 13169000 2765.6 2694 2287.4 2433.1 1224.3 1424.6 939.64 838.68 2858 2548.7 TRUE FALSE FALSE 2731.891803 2731.926203 2327.211237 2714.42647 1161.819403 1333.572658 1019.452998 862.9458826 2602.373322 2482.484407 1.100466853 1.10048071 0.93745251 1.093431428 0.468006727 0.537192763 0.410658369 0.347613818 1.048293925 1 11.27756894 -8.757410351 24.91965978 1.046675651 0.4455903 0.954692319 0.064651884 15.1965444 93989.70632 0.010149447 0.019717196 1.75E-09 8.757410351 -0.601085351 KPPEADMNIFEDIGDYVPS(ph)TTKTPR ddPTM_HeLa_Romidepsin_16h_R1 1 KPPEADMNIFEDIGDYVPSTTKTPR 25 2 Q13123 Q13123 IK Protein Red 1 0 KPPEADMNIFEDIGDY(0.043)VPS(0.659)T(0.136)T(0.136)KT(0.025)PR 43.612 0.019107 33619000 1070.5 626.43 1175 1121.4 1550.6 1524.2 1399.7 1409.7 1168.4 857.65 TRUE FALSE FALSE 1057.452334 635.248898 1195.450382 1251.061544 1471.467096 1426.808539 1518.590483 1450.487445 1063.895378 835.3681294 1.265851901 0.760441865 1.431046194 1.497617039 1.761459462 1.70799973 1.817869787 1.736345204 1.27356472 1 9.706268293 -9.249306354 1.813309804 1.103187567 1.753560974 0.780329392 0.15688241 0.116862957 0.749503546 0.025281292 0.045212469 5.63E-10 9.249306354 0.650373408 KPPEADMNIFEDIGDYVPSTTKT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KPPEADMNIFEDIGDYVPSTTKTPR 25 2 Q13123 Q13123 IK Protein Red 1 0 KPPEADMNIFEDIGDY(0.076)VPS(0.156)T(0.156)T(0.156)KT(0.456)PR 44.721 0.024523 21983000 2270.1 2262.6 2291.2 2707.1 2671.1 3477.9 3598 3066.7 2470.8 2317.9 TRUE FALSE FALSE 2242.431148 2294.452942 2331.077375 3020.107639 2534.7838 3255.673414 3903.61403 3155.430126 2249.80546 2257.680624 0.993245512 1.016287653 1.032509802 1.337703663 1.122737987 1.442043387 1.729037309 1.397642383 0.996511834 1 11.1406257 -8.528418504 0.841850833 0.995208635 1.602863476 0.772811037 0.115575876 0.224319535 0.273149828 0.018505276 0.084638689 2.96E-09 8.528418504 0.607654841 KPPLS(ph)PAQTNPVVQR ddPTM_HeLa_Romidepsin_16h_R1 1 KPPLSPAQTNPVVQR 15 1 Q8IY33-4;Q8IY33-2;Q8IY33 Q8IY33-4 MICALL2 MICAL-like protein 2 1 0 KPPLS(0.996)PAQT(0.004)NPVVQR 67.168 0.01682 32887000 1761.2 1992.6 1686.9 1856.8 2378.6 3364.7 3183.4 3631.4 2010.7 1945 TRUE FALSE FALSE 1739.733817 2020.651875 1716.259787 2071.491953 2257.211166 3149.706529 3453.797917 3736.46883 1830.857956 1894.46862 0.918322847 1.066606147 0.905932022 1.093442209 1.191474561 1.662580471 1.82309587 1.972304419 0.966422952 1 10.88757753 -8.203033076 1.297182532 0.965536888 1.969278486 0.980939192 0.052612952 0.043795462 0.131060288 0.008010364 0.03633248 6.27E-09 8.203033076 1.003741598 KPPQHLS(ph)PDTTGPPPPPLETLEAEFGSLK ddPTM_HeLa_Romidepsin_16h_R1 1 KPPQHLSPDTTGPPPPPLETLEAEFGSLK 29 1 A0A3B3IT29;A0A3B3ISF8;A0A3B3ISF0 A0A3B3IT29 1 0 KPPQHLS(0.352)PDT(0.352)T(0.295)GPPPPPLETLEAEFGSLK 57.299 0.00064705 2877000 638.94 745.45 697.83 782.02 661.31 764.23 778.01 807.71 887.23 851.76 TRUE FALSE FALSE 631.1523535 755.9444647 709.9754384 872.4408319 627.560883 715.3981694 844.09415 831.0798145 807.8739267 829.6311524 0.760762601 0.911181388 0.855772395 1.051600858 0.756433604 0.862308711 1.017433045 1.001746152 0.973774821 1 9.696326258 -7.757156328 24.96520157 0.885367961 1.009589652 0.190222959 0.091069876 134.3835422 783267.846 0.01457737 0.050937192 1.75E-08 7.757156328 0.12422169 KPS(ph)DEEFASR ddPTM_HeLa_Romidepsin_16h_R1 1 KPSDEEFASR 10 1 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;E9PDQ5;Q14155-6;Q14155-2;Q14155-3;Q14155 B1ALK7 ARHGEF7 Rho guanine nucleotide exchange factor 7 1 0 KPS(1)DEEFASR 79.744 0.018385 31409000 2114.1 1703.4 1525.8 1811.5 2464.2 3187.9 2525 2784.6 1930.1 1748.5 TRUE FALSE FALSE 2088.332536 1727.38051 1552.355909 2020.954153 2338.442679 2984.203478 2739.473437 2865.168008 1757.467022 1703.073718 1.226213824 1.014272308 0.911502475 1.186651013 1.373071908 1.752245629 1.608546599 1.682351138 1.031938315 1 10.73392517 -8.568348124 2.356333167 1.087833765 1.674388996 0.89907562 0.093133121 0.081923286 0.91211319 0.016870824 0.039855979 2.70E-09 8.568348124 0.586555231 KPS(ph)EDEVLNK ddPTM_HeLa_Romidepsin_16h_R1 1 KPSEDEVLNK 10 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 0 KPS(1)EDEVLNK 120.59 0.017651 8210600 3416.2 3193.6 3189.5 1765.3 3512.5 4306.3 3825.2 4570 3771.6 2814 TRUE FALSE FALSE 3374.56204 3238.559585 3245.01191 1969.412292 3333.244018 4031.141328 4150.112393 4702.22574 3434.25865 2740.891874 1.231191231 1.181571449 1.183925546 0.718529728 1.216116567 1.470740734 1.514146702 1.715582356 1.252971225 1 11.4204297 -8.19710406 2.540936436 1.09624102 1.600229359 0.659188138 0.153434136 0.136070144 1.704612992 0.022860783 0.068239318 6.35E-09 8.19710406 0.503988339 VNNGNTAPEDSS(ph)PAKK ddPTM_HeLa_Romidepsin_16h_R1 2 VNNGNTAPEDSSPAKK 16 1 E9PJ27;G3V167;Q9UGN5-2;Q9UGN5 E9PJ27 PARP2 Poly [ADP-ribose] polymerase 2 1 0 VNNGNTAPEDS(0.405)S(0.595)PAKK;VNNGNTAPEDS(0.132)S(0.868)PAKK ; 171.3 2.95E-06 69946000 13159.3 11121.5 11239.8 9033.4 5666.7 4868 4058.4 3532.2 12659.2 11315.9 TRUE FALSE FALSE 12998.90939 11278.06877 11435.424 10077.88421 5377.507154 4556.950511 4403.120395 3634.398634 11526.92945 11021.91129 1.179369807 1.02324075 1.037517333 0.914349966 0.487892437 0.413444673 0.399487918 0.329743049 1.045819472 1 13.4280868 -8.801380992 1.963078585 1.07987898 0.375646698 0.972736733 0.051931582 0.047765759 0.374656948 0.011116671 0.024232782 1.58E-09 8.801380992 -0.704232282 down KPS(ph)PQPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KPSPQPSSPR 10 1 G3V5E1;O75909-1;O75909;O75909-4 G3V5E1 CCNK Cyclin-K 2 0 KPS(0.999)PQPS(0.064)S(0.937)PR 101.45 0.021961 5817500 3550.7 3870.9 3721 3984.6 3747.7 3362.7 4092.6 2039.8 3893.6 3782.4 TRUE FALSE FALSE 3507.422703 3925.394632 3785.762444 4445.3182 3556.440884 3147.834323 4440.225342 2098.818395 3545.346664 3684.132703 0.952034844 1.065486764 1.027585798 1.206611857 0.96534006 0.854430222 1.20522948 0.569691312 0.962328708 1 11.84710931 -7.243887387 24.85486842 1.003835572 0.569690928 0.615877214 0.106895931 1776.616526 2515776.006 0.013931968 0.575621493 5.70E-08 7.243887387 -0.434144644 KPS(ph)VSEEVQATPNK ddPTM_HeLa_Romidepsin_16h_R1 2 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 KPS(0.982)VS(0.018)EEVQATPNK;KPS(0.933)VS(0.067)EEVQATPNK ; 141.86 2.18E-05 19050000 8910 9398.8 8372.1 8383.3 9214.9 9865 7993 9491.8 9102.4 7811.6 TRUE FALSE FALSE 8801.401493 9531.116553 8517.812889 9352.616591 8744.629267 9234.658338 8671.92522 9766.430257 8288.258547 7608.653506 1.156762032 1.252667972 1.119490181 1.229207846 1.149300499 1.213704676 1.139745057 1.283595087 1.089320014 1 12.89342545 -11.86488047 0.509517113 0.977075897 1.199662132 0.506539803 0.056282816 0.472217537 0.209970417 0.050275638 0.012714016 1.36E-12 11.86488047 0.222586235 KPSLVSDLPWEGAAPQS(ph)PSFSGSEDSGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 KPSLVSDLPWEGAAPQSPSFSGSEDSGSPK 30 1 Q13425;Q13425-2;H7BY41;H0YCS0 Q13425 SNTB2 Beta-2-syntrophin 1 0 KPSLVSDLPWEGAAPQS(0.997)PS(0.003)FSGSEDSGSPK 130.62 4.37E-11 11637000 4103.1 4050.3 3923.4 3953.6 3420.3 3839.3 2822.4 3020.1 4044.6 3911 TRUE FALSE FALSE 4053.089839 4107.32023 3991.685131 4410.733834 3245.749328 3593.981121 3062.134586 3107.481829 3682.840846 3809.391656 1.063972992 1.078208964 1.047853697 1.157857798 0.852038756 0.943452773 0.803838214 0.815742278 0.96677926 1 11.89534491 -8.73841268 24.99807222 1.044361203 0.856607541 0.732571152 0.05867572 95.10958308 103251.664 0.008257472 0.016506347 1.83E-09 8.73841268 -0.187753662 KPSPPEAAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KPSPPEAASPR 11 1 Q9ULI4;C9JFF0 Q9ULI4 KIF26A Kinesin-like protein KIF26A;Kinesin-like protein 1 0 KPSPPEAAS(1)PR 76.156 0.019381 3525500 2020.3 1915.1 1499.5 2095.6 2380.5 2151.7 1800.2 1567.2 2241.9 1798.8 TRUE FALSE FALSE 1995.675807 1942.060828 1525.598168 2337.903132 2259.014202 2014.213314 1953.108943 1612.544459 2041.378849 1752.066917 1.139040859 1.108439872 0.870741953 1.33436863 1.289342422 1.149621225 1.114745632 0.920366936 1.165126075 1 10.77484216 -9.25546328 24.99086347 1.057925474 1.16550242 0.142238779 0.128758862 772.1822488 3229115.109 0.019719258 0.03215336 5.55E-10 9.25546328 0.107576947 KPSPQPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 KPSPQPSSPR 10 1 G3V5E1;O75909-1;O75909;O75909-4 G3V5E1 CCNK Cyclin-K 1 0 KPS(0.001)PQPS(0.124)S(0.875)PR;KPSPQPS(0.014)S(0.986)PR ; 101.38 0.0070063 17859400 4032.8 4543.7 7437.4 5912 4528.8 5351.3 10865 1194.99 8447 5521 TRUE FALSE FALSE 3983.646682 4607.666328 7566.844827 6595.573257 4297.678437 5009.369201 11787.87283 1229.56515 7691.479164 5377.563624 0.740790246 0.856831578 1.407113956 1.226498414 0.799186906 0.931531368 2.192047115 0.228647253 1.430290686 1 12.39273697 -9.8013222 24.50762675 0.872617809 1.159288286 0 0.502495535 239.3167234 147056.8208 0.069996061 0.091993671 1.58E-10 9.8013222 0.286670476 KPSPS(ph)ESPEPWKPFPAVSPEPR ddPTM_HeLa_Romidepsin_16h_R1 2 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 KPS(0.005)PS(0.495)ES(0.495)PEPWKPFPAVS(0.005)PEPR;KPS(0.013)PS(0.808)ES(0.174)PEPWKPFPAVS(0.005)PEPR ; 80.016 0.0016242 97000000 2478.63 2598 2622.38 2615.72 2841.82 3485 2746.98 3085 2946.6 2630.71 TRUE FALSE FALSE 2448.419504 2634.574712 2668.021424 2918.161854 2696.791321 3262.319747 2980.308413 3174.259608 2683.048716 2562.363775 0.955531579 1.028181376 1.041234445 1.138855412 1.052462319 1.273168072 1.163109017 1.238801313 1.047099066 1 11.32325959 -8.89323808 0.778399683 0.978640136 1.229219009 0.724624602 0.052188735 0.209668602 0.236217222 0.008520306 0.028228727 1.28E-09 8.89323808 0.250578874 KPSPSES(ph)PEPWKPFPAVSPEPR ddPTM_HeLa_Romidepsin_16h_R1 1 KPSPSESPEPWKPFPAVSPEPR 22 2 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 KPS(0.027)PS(0.214)ES(0.758)PEPWKPFPAVSPEPR 54.058 0.010625 57876000 1747.9 1804.3 1766.1 1378.5 1494.1 1543.8 1221.8 1704 1777.4 1898.7 TRUE FALSE FALSE 1726.595922 1829.700983 1796.83823 1537.888656 1417.850502 1445.156162 1325.579662 1753.302552 1618.424892 1849.3715 0.933612269 0.989363674 0.971593987 0.831573676 0.766666136 0.781430968 0.716773056 0.948053191 0.875121571 1 10.85281935 -9.192311743 3.771391823 0.970244539 0.796003625 0.548806029 0.065057997 0.102661893 2.878445897 0.008559103 0.014438355 6.42E-10 9.192311743 -0.174240914 KPSVGVPPPAS(ph)PSYPR ddPTM_HeLa_Romidepsin_16h_R1 1 KPSVGVPPPASPSYPR 16 1 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 KPSVGVPPPAS(0.848)PS(0.152)YPR 81.144 0.0069651 129270000 5312.7 5154.3 3953.8 5104.5 4220.2 4333.1 3505.8 3812.5 4835 4266.7 TRUE FALSE FALSE 5247.946769 5226.862371 4022.61423 5694.706307 4004.827446 4056.228894 3803.582564 3922.808672 4402.545491 4155.850519 1.262785258 1.257711832 0.967940067 1.370286607 0.963660129 0.976028583 0.915235653 0.943924392 1.059360887 1 12.02092805 -8.563715158 24.99724548 1.14155104 0.946707002 0.414601858 0.118026123 128.1109292 78420.24149 0.019164516 0.038329058 2.73E-09 8.563715158 -0.194844038 KPSVSEEVQAT(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 2 KPSVSEEVQATPNK 14 1 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 KPS(0.217)VS(0.222)EEVQAT(0.561)PNK;KPS(0.131)VSEEVQAT(0.868)PNK ; 178.68 9.36E-07 36969000 8174.1 7763.2 6679 8002.8 7969 7998.3 7295.3 8565 7545.4 6893.9 TRUE FALSE FALSE 8074.470925 7872.490533 6795.245193 8928.12139 7562.312194 7487.234443 7914.9626 8812.814762 6870.520526 6714.795484 1.202489479 1.172409577 1.011980962 1.329619258 1.12621631 1.115035366 1.178734724 1.312447234 1.023191331 1 12.71312774 -12.50065398 0.6180965 0.9594169 1.181276535 0.375769614 0.087294421 1.117031242 0.539466801 0.14578496 0.018348519 3.16E-13 12.50065398 0.221859635 KPVAGALDVS(ph)FNK ddPTM_HeLa_Romidepsin_16h_R1 1 KPVAGALDVSFNK 13 1 H7C3S9;E9PGT6;Q99627-2;Q99627 H7C3S9 COPS8 COP9 signalosome complex subunit 8 1 0 KPVAGALDVS(1)FNK 66.335 0.0035205 0 2433.7 2454.6 2657.3 2576.7 2130.1 2849.7 2033.1 2129.1 2726 2651.3 TRUE FALSE FALSE 2404.037128 2489.155923 2703.549192 2874.630178 2021.393049 2667.613367 2205.791463 2190.702149 2482.179733 2582.418844 0.930924561 0.96388544 1.046905771 1.113154121 0.782751819 1.032990204 0.854157128 0.848314035 0.961184023 1 11.3345073 -7.475974771 1.079047787 0.975784883 0.79492158 0.236242139 0.084486962 1.423376578 1.670766259 0.012368911 0.267645457 3.34E-08 7.475974771 -0.180863302 KPVTVS(ph)PTTPTSPTEGEAS ddPTM_HeLa_Romidepsin_16h_R1 2 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 KPVT(0.006)VS(0.739)PT(0.249)T(0.005)PTSPTEGEAS;KPVT(0.024)VS(0.619)PT(0.285)T(0.069)PT(0.001)S(0.001)PTEGEAS ; 80.719 0.01315 100256000 5219.6 5315.2 5066.3 5759.3 6179.5 5505.2 4647.9 4879.6 5636.3 5939.8 TRUE FALSE FALSE 5155.981508 5390.027525 5154.476826 6425.217364 5864.137056 5153.435487 5042.69251 5020.783527 5132.175212 5785.48314 0.891192902 0.931646916 0.890932823 1.110575765 1.013595047 0.890752831 0.871611305 0.867824416 0.887078069 1 12.49822173 -8.188156938 0.008730613 1.84555291 2.42E-06 0 0.076114666 12135.14499 23.49216942 2375.463925 2593.252878 6.48E-09 8.188156938 -1.845550492 KPVTVSPT(ph)TPTSPTEGEAS ddPTM_HeLa_Romidepsin_16h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 KPVTVS(0.008)PT(0.98)T(0.012)PTSPTEGEAS 108.66 0.0021791 85278000 4791.1 4952 4534.6 4780.3 4760.1 4678.1 3956.1 4345.5 5131.4 4579.5 TRUE FALSE FALSE 4732.70423 5021.714386 4613.522811 5333.020778 4517.174335 4379.184508 4292.131035 4471.230186 4672.434732 4460.52393 1.061019805 1.125812677 1.034300652 1.195604118 1.012700393 0.981764604 0.96224818 1.002400224 1.047508052 1 12.12299746 -8.527147034 24.99936086 1.050678529 0.982995996 0.327916804 0.055145826 145.090257 849791.4068 0.008888167 0.017835876 2.97E-09 8.527147034 -0.067682532 KPVTVSPTTPT(ph)SPTEGEAS ddPTM_HeLa_Romidepsin_16h_R1 1 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 KPVTVS(0.002)PT(0.007)T(0.033)PT(0.451)S(0.451)PT(0.024)EGEAS(0.031) 74.783 0.030526 5945900 2065.7 2234.3 1943.2 1848.3 1559.7 1974.5 1822.1 1432 2103.2 1934.9 TRUE FALSE FALSE 2040.522454 2265.754534 1977.020581 2062.009143 1480.102689 1848.335822 1976.869129 1473.432661 1915.084524 1884.631019 1.082717218 1.202227126 1.049022626 1.094118223 0.785354095 0.980741484 1.048942264 0.781814926 1.016158869 1 10.88006638 -8.789118514 24.99852219 1.057838839 0.915731463 0.45448601 0.092112302 177.626967 160423.9396 0.013698305 0.024834149 1.63E-09 8.789118514 -0.142107376 KPVTVSPTTPTS(ph)PTEGEAS ddPTM_HeLa_Romidepsin_16h_R1 2 KPVTVSPTTPTSPTEGEAS 19 1 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 KPVTVSPTTPT(0.058)S(0.902)PT(0.032)EGEAS(0.008);KPVTVSPT(0.003)T(0.124)PT(0.382)S(0.466)PT(0.012)EGEAS(0.012) ; 87.831 0.00727 119894500 9246.4 9531.3 9014.2 9430.5 10950.3 9943.6 9312.2 10716.4 9661.5 8841.9 TRUE FALSE FALSE 9133.70132 9665.481892 9171.08837 10520.89878 10391.46533 9308.236051 10103.17804 11026.46213 8797.351242 8612.186163 1.06055549 1.122302945 1.06489667 1.22162928 1.206600175 1.08082151 1.173125829 1.280332533 1.021500357 1 13.07216379 -8.546714613 0.185702227 0.955927013 1.357851714 0.648110547 0.052547361 4.033600206 0.236430121 0.111908783 0.423789789 2.84E-09 8.546714613 0.401924701 KQEEDDSLSDAGT(ph)YTIETEAQDTEVEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 KQEEDDSLSDAGTYTIETEAQDTEVEEAR 29 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 KQEEDDS(0.038)LS(0.352)DAGT(0.459)Y(0.114)T(0.037)IETEAQDTEVEEAR 74.516 3.28E-06 0 701.97 717.81 871.45 780.28 881.16 783.74 776.61 843 754.62 527.21 TRUE FALSE FALSE 693.4141196 727.915348 886.6172217 870.4996449 836.1911171 733.6615434 842.575234 867.390875 687.1248972 513.5130082 1.350334088 1.417520757 1.726572078 1.695185187 1.628373778 1.428710727 1.640806018 1.689131261 1.338086643 1 9.004257013 -10.93013925 0.571057955 1.021943336 1.639975035 0.614626202 0.134766438 0.202056784 0.153681386 0.049373971 0.033631868 1.17E-11 10.93013925 0.618031699 KQEEQMETEHINPVTEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 KQEEQMETEHINPVTEKR 18 2 V9GYT7 V9GYT7 PSIP1 0 1 KQEEQMETEHINPVTEK(1)R 61.648 0.009579 4264100 1488.7 1363.9 1411.6 1736.7 2329.9 3073.2 2154.1 2312.1 1658.8 1472.2 FALSE TRUE FALSE 1470.555152 1383.10102 1436.168306 1937.505425 2210.996509 2876.832438 2337.0692 2378.996966 1510.432773 1433.952032 1.025526042 0.964537857 1.001545571 1.351164741 1.541890147 2.006226411 1.629809888 1.659049196 1.053335635 1 10.48578105 -8.90401754 1.919762367 1.006353463 1.750114501 0.90707026 0.106474375 0.063096315 0.469910154 0.015533793 0.032263412 1.25E-09 8.90401754 0.743761038 KQEGPATQVDSAVGT(ph)LPATSPQSTSVQAK ddPTM_HeLa_Romidepsin_16h_R1 1 KQEGPATQVDSAVGTLPATSPQSTSVQAK 29 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06 E7ETY2 TCOF1 Treacle protein 1 0 KQEGPATQVDS(0.002)AVGT(0.399)LPAT(0.298)S(0.298)PQS(0.001)T(0.001)SVQAK 103.33 5.58E-09 43484000 2453.3 2663 2376.6 2118.8 2377.1 2299.6 2093.6 2376.1 2702.5 2944.8 TRUE FALSE FALSE 2423.398236 2700.489784 2417.963726 2363.785625 2255.787717 2152.662982 2271.430332 2444.848705 2460.781631 2868.293671 0.844891951 0.941496964 0.842997267 0.82410865 0.786456331 0.750502992 0.791909962 0.852370428 0.857925273 1 11.48597703 -15.38871186 0.146319902 1.463646653 0.751204123 0.258730789 0.060263056 18.70538915 0.257186597 2.659326866 0.119852282 4.09E-16 15.38871186 -0.712442529 KQEGPATQVDSAVGTLPAT(ph)SPQSTSVQAK ddPTM_HeLa_Romidepsin_16h_R1 1 KQEGPATQVDSAVGTLPATSPQSTSVQAK 29 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06 E7ETY2 TCOF1 Treacle protein 1 0 KQEGPATQVDS(0.001)AVGT(0.039)LPAT(0.468)S(0.468)PQS(0.01)T(0.011)S(0.003)VQAK 90.964 6.80E-08 55526000 5156.3 5267.8 5641.3 5622.5 5178.7 4935.7 4478.8 4777 5979 5990.2 TRUE FALSE FALSE 5093.453032 5341.960227 5739.48446 6272.599905 4914.411615 4620.324699 4859.22916 4915.214958 5444.223265 5834.57374 0.872977746 0.915569922 0.983702446 1.075074236 0.842291457 0.791887275 0.832833618 0.842429143 0.933097002 1 12.51041154 -8.552059366 24.98814052 0.949065571 0.822371819 0.605925216 0.053178545 135.9374497 116406.361 0.009492027 0.018984276 2.81E-09 8.552059366 -0.126693752 KQELEEILHDLESR ddPTM_HeLa_Romidepsin_16h_R1 1 KQELEEILHDLESR 14 1 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 0 103.6 0.0018 2831800 5616.7 5506.7 5134.8 4976.1 6544.4 6353.3 5538 6420.1 5879.8 5177.6 FALSE FALSE TRUE 5548.2415 5584.223467 5224.16904 5551.460095 6210.414847 5947.344634 6008.397582 6605.855464 5353.895962 5043.085206 1.100168106 1.107303018 1.035907352 1.100806326 1.23147133 1.179306792 1.191413061 1.309883771 1.061631074 1 12.30009089 -4 0.175362551 0.995387305 2.198271702 0.780251356 0.042322339 18.86414102 0.201790916 0.059667152 6.037663968 1.00E-04 4 1.202884397 KQHY(ph)LS(ph)SEDEPDDNPDVLDS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 KQHYLSSEDEPDDNPDVLDSR 21 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 3 0 KQHY(0.834)LS(0.583)S(0.583)EDEPDDNPDVLDS(1)R 48.376 0.014508 6648600 1430.2 1861.7 1417 1115.5 1176.6 1183.8 1030.4 942.34 1639.5 2045.6 TRUE FALSE FALSE 1412.768172 1887.909061 1441.662291 1244.479359 1116.553712 1108.159001 1117.92215 969.6051211 1492.859014 1992.455017 0.709059005 0.947529076 0.723560772 0.624595962 0.560390926 0.556177676 0.561077736 0.4866384 0.749256069 1 10.96033144 -9.48012909 0.096246974 1.373886709 8.15E-16 0.585059882 0.104732746 6.279513176 0.299632862 1.68744635 2.462536975 3.31E-10 9.48012909 -1.373886709 KQIEDLNMT(ph)LEK ddPTM_HeLa_Romidepsin_16h_R1 1 KQIEDLNMTLEK 12 1 F8WAN1;Q69YQ0-2;Q69YQ0;C9J8U1;A0A494C1J1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 KQIEDLNMT(1)LEK 83.877 0.013786 42420000 3039.4 3496.7 2250.1 2298.1 3082.9 2717.8 2431.2 2998.1 2643.9 3068.3 TRUE FALSE FALSE 3002.354624 3545.926634 2289.262047 2563.817135 2925.568109 2544.141351 2637.706067 3084.845293 2407.422962 2988.585124 1.004607364 1.186490091 0.766001955 0.857869871 0.978914097 0.851286226 0.882593588 1.032209278 0.805539365 1 11.54524692 -9.748926232 24.99999887 1.016060085 0.894422256 0.172695225 0.109410769 201.4802192 402536.0978 0.013204009 0.018600245 1.78E-10 9.748926232 -0.121637829 KQISGQYSGS(ph)PQLLK ddPTM_HeLa_Romidepsin_16h_R1 1 KQISGQYSGSPQLLK 15 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 0 KQISGQYS(0.005)GS(0.995)PQLLK 94.313 0.0036882 17660000 3364.8 3313.3 3093.7 3999.8 2962.4 2901.9 2179.9 2463.8 3330.9 3261 TRUE FALSE FALSE 3323.788523 3359.944724 3147.544551 4462.275696 2811.217674 2716.477955 2365.060652 2535.086166 3032.975962 3176.27875 1.046441067 1.057824262 0.990953502 1.404875342 0.885066424 0.855239155 0.7446011 0.798130884 0.954883434 1 11.63312181 -8.535851294 24.99993061 1.050712362 0.806568253 0.517404903 0.12128737 142.1208505 273886.268 0.016847357 0.033710235 2.91E-09 8.535851294 -0.244144108 KQLATK(ac)AAR ddPTM_HeLa_Romidepsin_16h_R1 2 KQLATKAAR 9 2 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1 0 1 ; KQLATK(1)AAR;KQLATK(1)AAR 135.55 0.0050463 49529000 343.76 647.96 32585 1137.63 5178.6 19556 15127.3 766.3 882.75 528.66 FALSE TRUE FALSE 339.5701209 657.0819979 33152.12826 1269.168133 4914.316718 18306.43471 16412.21248 788.4716815 803.7946291 514.925337 0.659455064 1.276072375 64.38239852 2.464761475 9.54374618 35.55162933 31.8729946 1.531234967 1.560992578 1 9.00821945 KQNS(ph)PVAPTAQPK ddPTM_HeLa_Romidepsin_16h_R1 1 KQNSPVAPTAQPK 13 1 Q6P1N0;Q6P1N0-2 Q6P1N0 CC2D1A Coiled-coil and C2 domain-containing protein 1A 1 0 KQNS(0.995)PVAPT(0.005)AQPK 83.404 0.010083 54579000 7902.8 7271.6 7763.4 6213.9 7528.7 8056.6 6784.1 6567.7 7789.1 7317.5 TRUE FALSE FALSE 7806.477634 7373.969776 7898.51872 6932.380355 7144.482346 7541.809261 7360.341285 6757.726037 7092.423388 7127.390295 1.09527854 1.03459604 1.108192255 0.972639363 1.00239808 1.058144559 1.032683911 0.948134697 0.99509401 1 12.79915821 -9.239034312 24.94819253 1.049499429 1.007512692 0.195508986 0.043747072 1168.880704 1301556.663 0.007205728 0.011942793 5.77E-10 9.239034312 -0.041986737 KQPPVS(ph)PGTALVGSQKEPSEVPT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 2 0 KQPPVS(0.626)PGT(0.334)ALVGS(0.043)QKEPS(0.093)EVPT(0.904)PK 52.377 0.0277 72759000 2069.9 1557.3 1807.1 2172.3 2606 3277.8 2567.3 2758.9 1896.8 1944.5 TRUE FALSE FALSE 2044.671263 1579.22371 1838.551817 2423.471547 2473.006096 3068.359159 2785.366398 2838.724419 1727.145457 1893.98161 1.079562363 0.833811533 0.970733722 1.279564455 1.305718114 1.620057525 1.470640678 1.498813085 0.911912475 1 10.88720661 -8.834653195 1.741327154 1.016636481 1.516053232 0.865932536 0.09552029 0.093682267 0.575540225 0.014397142 0.031938965 1.46E-09 8.834653195 0.499416751 KQPPVS(ph)PGTALVGSQKEPSEVPTPK ddPTM_HeLa_Romidepsin_16h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 0 KQPPVS(0.799)PGT(0.2)ALVGSQKEPSEVPTPK;KQPPVS(0.838)PGT(0.162)ALVGSQKEPSEVPTPK ; 64.349 0.0018597 80423000 5360.2 5634.4 4674.3 5285.6 5737.5 5848 6562.6 6297.6 6420 5485.1 TRUE FALSE FALSE 5294.867821 5713.721231 4755.654231 5896.745941 5444.693965 5474.331674 7120.02708 6479.81112 5845.779121 5342.596311 0.991066424 1.069465275 0.890139167 1.103722909 1.01911012 1.024657555 1.33269045 1.212858083 1.094183199 1 12.3833253 -7.793200163 8.92803372 1.004177051 1.272664575 0.688943003 0.065783073 0.071395504 18.72508937 0.00738938 0.022624093 1.61E-08 7.793200163 0.268487524 KQPPVSPGT(ph)ALVGSQK ddPTM_HeLa_Romidepsin_16h_R1 1 KQPPVSPGTALVGSQK 16 1 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 0 KQPPVS(0.279)PGT(0.708)ALVGS(0.013)QK 81.574 0.0094655 280580000 6286.2 6472.4 6536.6 4727 7671.3 9617.4 9022 8366.7 6696.3 6336.4 TRUE FALSE FALSE 6209.581376 6563.518617 6650.366781 5273.557981 7279.804935 9002.879179 9788.328455 8608.777264 6097.366157 6171.779415 1.00612497 1.063472651 1.07754447 0.854463134 1.179530966 1.458716939 1.585981578 1.394861463 0.987942982 1 12.59147078 -8.378546993 3.067683357 1.005017872 1.496149001 0.895027637 0.073495781 0.050753469 0.905529824 0.009688918 0.023897983 4.18E-09 8.378546993 0.491131129 KQPPVSPGTALVGS(ph)QKEPSEVPTPK ddPTM_HeLa_Romidepsin_16h_R1 1 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 0 KQPPVS(0.02)PGT(0.08)ALVGS(0.835)QKEPS(0.061)EVPT(0.003)PK 55.302 0.0082507 31890000 4332.9 4264.9 3838.8 4672.8 4461.7 4622.8 4637.4 4998.3 4298.8 4098.3 TRUE FALSE FALSE 4280.088948 4324.941374 3905.612704 5213.091122 4234.0028 4327.417999 5031.30064 5142.917924 3914.304561 3991.825575 1.072213419 1.083449488 0.978402646 1.305941611 1.060668288 1.084069912 1.260400923 1.288362386 0.98058006 1 11.96283297 -4 0.226716486 1.007591179 2.541618361 0.524490415 0.082809812 28.53480836 0.345289758 0.054275148 16.33349741 1.00E-04 4 1.534027182 KQPPVSPGTALVGSQKEPSEVPT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KQPPVSPGTALVGSQKEPSEVPTPK 25 2 P17096;P17096-3 P17096 HMGA1 High mobility group protein HMG-I/HMG-Y 1 0 KQPPVSPGTALVGSQKEPS(0.033)EVPT(0.966)PK;KQPPVSPGTALVGS(0.004)QKEPS(0.107)EVPT(0.888)PK ; 72.566 0.00019497 690930000 9207.6 9194 8747.1 11390.5 8461.8 6387.8 5555.8 5835.7 9612.8 8903.1 TRUE FALSE FALSE 9095.37423 9323.433373 8899.339606 12707.5232 8029.962771 5979.640196 6027.709513 6004.546772 8753.007092 8671.796179 1.04884548 1.075144432 1.026239481 1.465385364 0.925986105 0.689550362 0.695093541 0.692422498 1.009364947 1 13.08211513 -8.387066726 4.289735996 1.060080268 0.694307345 0.648280523 0.132742705 0.118039954 3.563017619 0.019300075 0.044714821 4.10E-09 8.387066726 -0.365772923 KQQQEPTGEPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 KQQQEPTGEPSPK 13 1 F5H2U8;F5H2A4;F5H6H0;P52926-3;P52926-6;P52926-4;P52926-5;P52926-2;P52926 F5H2U8 HMGA2 High mobility group protein HMGI-C 1 0 KQQQEPT(0.016)GEPS(0.984)PK;KQQQEPT(0.007)GEPS(0.993)PK;KQQQEPTGEPS(1)PK;KQQQEPT(0.01)GEPS(0.99)PK ;;; 104.78 0.002952 23515000 30399.6 26591 27532.2 25518.2 23463.2 20887.1 20932.2 18154.4 32215 30229.9 TRUE FALSE FALSE 30029.07798 26965.3488 28011.38639 28468.73435 22265.78535 19552.48172 22710.18055 18679.66892 29333.60972 29444.52284 1.019852763 0.91580186 0.951327571 0.966860102 0.75619447 0.664044781 0.771287097 0.634402161 0.996233149 1 14.84571167 -8.731114569 2.814975644 0.996567165 0.69711137 0.897534557 0.044578966 0.055888145 0.904944913 0.006805252 0.014213348 1.86E-09 8.731114569 -0.299455795 KQS(ph)LGELIGTLNAAK ddPTM_HeLa_Romidepsin_16h_R1 2 KQSLGELIGTLNAAK 15 1 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 0 KQS(1)LGELIGTLNAAK;KQS(0.882)LGELIGT(0.118)LNAAK ; 112.57 0.0062497 616840000 2701.7 3915 2682.9 2861.8 4320 5729.1 6392.8 7069.3 2694.9 2547.2 TRUE FALSE FALSE 2668.770641 3970.115473 2729.594749 3192.694781 4099.53428 5363.029 6935.804272 7273.839042 2453.861394 2481.023377 1.075673315 1.600192691 1.100189049 1.286845908 1.652356168 2.161619697 2.795541685 2.931789805 0.989052105 1 11.27671961 -7.98681638 0.785847391 1.064463833 3.347807617 0.941139492 0.168820165 0.181561446 0.142275615 0.02885141 0.291601429 1.03E-08 7.98681638 2.283343784 up KQS(ph)SDYEELIQVLK ddPTM_HeLa_Romidepsin_16h_R1 1 KQSSDYEELIQVLK 14 1 A0A0A0MRG9;Q96SN8-4;Q96SN8-3;Q96SN8-2;Q96SN8;F8WCI3 A0A0A0MRG9 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 1 0 KQS(0.499)S(0.499)DY(0.002)EELIQVLK 69.935 0.0031256 0 2664.3 2870.9 2827 2189.1 2519.4 2341.8 1671.4 1821.5 2791.1 2821.7 TRUE FALSE FALSE 2631.826487 2911.316606 2876.202749 2442.214042 2390.825617 2192.166538 1813.368674 1874.202229 2541.457026 2748.391827 0.957587801 1.05928004 1.046503894 0.888597476 0.869899842 0.797617907 0.659792631 0.681926867 0.924706951 1 11.42437198 -8.272688825 1.094147059 0.989772458 0.652223718 0.878579171 0.046258271 0.135292481 0.279001315 0.007063841 0.034460294 5.34E-09 8.272688825 -0.337548739 KQSLPAT(ph)SIPTPASFK ddPTM_HeLa_Romidepsin_16h_R1 1 KQSLPATSIPTPASFK 16 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 KQS(0.064)LPAT(0.468)S(0.468)IPTPASFK 77.037 0.012036 14193000 738.55 503.71 785.72 617.37 1882.1 4155.6 5355.7 7209.3 991.6 782.05 TRUE FALSE FALSE 729.5482685 510.8012426 799.395127 688.7532242 1786.049414 3890.070572 5810.613024 7417.889721 902.9088125 761.7322283 0.957748985 0.670578484 1.049443751 0.904193362 2.344720819 5.106874079 7.628156994 9.738185475 1.185336236 1 9.573140126 -7.902439433 1.194281374 0.924040685 10.21679862 0.995144935 0.216725397 0.028573764 0.062505137 0.032274508 0.246765607 1.25E-08 7.902439433 9.29275793 up KQVAPEK(ac)PVKK ddPTM_HeLa_Romidepsin_16h_R1 2 KQVAPEKPVKK 11 3 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 1 ; KQVAPEK(0.996)PVK(0.004)K;KQVAPEK(1)PVKK 79.201 0.010415 53647000 7906.45 8010.77 8265.59 10606.31 11314.6 11867.8 11062.5 11558.7 8116.15 7985.27 FALSE TRUE FALSE 7810.083146 8123.54583 8409.449127 11832.66147 10737.17374 11109.48588 12002.14847 11893.13275 7390.221217 7777.811534 1.004149189 1.044451359 1.081210195 1.521335586 1.380487775 1.428356271 1.543126678 1.529110431 0.950167175 1 12.92514856 -9.335105248 4.004296057 1.007392375 1.476652096 0.951584501 0.052525246 0.033946517 1.053184074 0.00802122 0.012597093 4.62E-10 9.335105248 0.469259721 RADSVANK(ac)LGSFGK ddPTM_HeLa_Romidepsin_16h_R1 2 RADSVANKLGSFGK 14 2 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 0 1 ; RADSVANK(1)LGSFGK;RADSVANK(1)LGSFGK 133.87 7.61E-05 3349900 1735.62 2075.26 1586.3 2851.3 4417.9 5027.6 4684.3 4443.6 2500.3 2023.62 FALSE TRUE FALSE 1714.465596 2104.475565 1613.908886 3180.980722 4192.438078 4706.352586 5082.184325 4572.168555 2276.666906 1971.046061 0.869825231 1.067694767 0.818808306 1.613854077 2.127011723 2.387743584 2.578419869 2.319666012 1.155055151 1 10.94474578 -8.88774195 1.803140482 0.936523248 2.438224488 0.962340111 0.128110836 0.034102332 0.224073648 0.016266365 0.034656195 1.29E-09 8.88774195 1.50170124 up KRAEFTVETR ddPTM_HeLa_Romidepsin_16h_R1 1 KRAEFTVETR 10 2 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 107.83 0.0014118 4271500 5642.9 6596.5 6277.7 6745.9 7993.9 8620.2 5274.9 5934.7 5780.9 5501 FALSE FALSE TRUE 5574.122164 6689.3657 6386.960735 7525.892698 7585.941454 8069.39704 5722.949874 6106.411181 5263.841825 5358.083227 1.040320191 1.248462448 1.192023428 1.404586749 1.415793882 1.506023087 1.068096487 1.139663369 0.982411359 1 12.38750128 -10.16248429 1.627089122 1.013084992 1.303267095 0.500484072 0.12610664 0.226350927 1.144426827 0.024599947 0.030340824 6.88E-11 10.16248429 0.290182103 KRES(ph)ESESDET(ph)PPAAPQLIK ddPTM_HeLa_Romidepsin_16h_R1 1 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 0 KRES(0.727)ES(0.106)ES(0.185)DET(0.982)PPAAPQLIK 63.272 0.020036 46288000 6751.9 6788.4 6379.1 4974.6 5585.8 5067.9 4544.8 5431.5 7631.8 7278.9 TRUE FALSE FALSE 6669.605246 6883.967273 6490.12556 5549.786658 5300.735783 4744.077546 4930.835199 5588.651883 6949.192694 7089.793129 0.940733407 0.970968708 0.915418185 0.782785415 0.747657327 0.669141886 0.695483649 0.788267271 0.980168612 1 12.79152782 -9.227989625 1.668681257 0.972289952 0.715978068 0.927737805 0.032029583 0.070539548 0.383641959 0.005728712 0.010521173 5.92E-10 9.227989625 -0.256311884 KRESESES(ph)DET(ph)PPAAPQLIK ddPTM_HeLa_Romidepsin_16h_R1 2 KRESESESDETPPAAPQLIK 20 2 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 0 KRES(0.135)ES(0.135)ES(0.735)DET(0.996)PPAAPQLIK;KRES(0.306)ES(0.366)ES(0.42)DET(0.907)PPAAPQLIK ; 62.203 0.0029684 20048000 2360 2084.6 2168.29 1885.81 2032.6 1905.78 1819.63 2247.8 2237.3 2404.15 TRUE FALSE FALSE 2331.235412 2113.947054 2206.028178 2103.856225 1928.868837 1784.006809 1974.189327 2312.836547 2037.190285 2341.689836 0.995535521 0.902744258 0.942066769 0.89843505 0.823708079 0.761845903 0.843061833 0.987678432 0.869965891 1 11.19333428 -9.730548365 1.006580416 0.999622465 0.850984957 0.144387667 0.070191344 0.274425207 0.555005892 0.011164454 0.017684608 1.86E-10 9.730548365 -0.148637507 KRNEDEDSPNKLY(ph)TLVTYVPVTTFK ddPTM_HeLa_Romidepsin_16h_R1 1 KRNEDEDSPNKLYTLVTYVPVTTFK 25 3 H7C2W9;C9JU56;B7Z4E3;B7Z4C8;P62899-3;P62899;P62899-2 H7C2W9 RPL31 60S ribosomal protein L31 1 0 KRNEDEDS(0.387)PNKLY(0.418)T(0.115)LVT(0.044)Y(0.035)VPVT(0.001)T(0.001)FK 41.423 0.022579 21944000 4130.2 3752.2 3391.8 3602.2 3783.3 3538 3368.4 3721.2 3775.9 3582 TRUE FALSE FALSE 4079.859534 3805.02357 3450.832856 4018.703313 3590.224084 3311.933218 3654.511812 3828.867051 3438.174047 3488.939124 1.169369653 1.090596148 0.989077979 1.151841053 1.029030303 0.949266554 1.047456457 1.097430169 0.98544971 1 11.76857271 -8.570198444 24.99954255 1.080074917 1.025683969 0.023015134 0.069528533 216.334149 114291.1342 0.011317385 0.022634774 2.69E-09 8.570198444 -0.054390948 KRPESPPSILT(ph)PPVVPTADK ddPTM_HeLa_Romidepsin_16h_R1 1 KRPESPPSILTPPVVPTADK 20 2 Q6P2C6;P55198 Q6P2C6 MLLT6 Protein AF-17 1 0 KRPES(0.003)PPS(0.171)ILT(0.826)PPVVPTADK 88.486 0.00032111 0 1696.5 1601 1754.6 1295 1399.4 1353.6 1088.3 1038.6 1716.5 1876.9 TRUE FALSE FALSE 1675.822405 1623.53892 1785.138077 1444.733993 1327.983396 1267.109329 1180.740175 1068.650252 1562.971941 1828.137867 0.916682727 0.888083415 0.976478913 0.79027628 0.726413155 0.693114754 0.645870421 0.584556707 0.854952993 1 10.83615916 -8.368708089 0.474317894 0.976630157 0.500209905 0.842440476 0.053558619 0.364141315 0.104199987 0.010453499 0.081661469 4.28E-09 8.368708089 -0.476420252 KS(ph)FTPDHVVYAR ddPTM_HeLa_Romidepsin_16h_R1 2 KSFTPDHVVYAR 12 1 Q6NZI2-3;Q6NZI2-2;Q6NZI2 Q6NZI2-3 PTRF Polymerase I and transcript release factor 1 0 KS(0.972)FT(0.028)PDHVVYAR;KS(0.919)FT(0.081)PDHVVYAR ; 86.498 0.010296 50935000 4537.5 4516.2 4182.2 4529.5 8143.4 9396.9 8129.2 8234.5 5358.3 4580.9 TRUE FALSE FALSE 4482.195205 4579.779182 4254.989437 5053.222102 7727.811911 8796.468417 8819.694045 8472.752266 4879.040228 4461.887558 1.004551358 1.026421917 0.953629911 1.132530131 1.731960255 1.971467973 1.976673309 1.898916581 1.093492421 1 12.12343844 -8.721891472 2.645928141 1.000776771 1.947757876 0.990773761 0.041140563 0.011723687 0.167315398 0.004344288 0.009210776 1.90E-09 8.721891472 0.946981104 KS(ph)KIS(ph)T(ph)MY(ph)Y(ph)LNQDAK ddPTM_HeLa_Romidepsin_16h_R1 2 KSKISTMYYLNQDAK 15 2 B7Z739;Q8TCQ1-2 B7Z739 Mar-01 5 0 KS(1)KIS(1)T(1)MY(1)Y(1)LNQDAK;KS(1)KIS(1)T(1)MY(1)Y(1)LNQDAK ; 65.043 0.011561 56409000 4408.1 4376.8 3792.9 3745.9 3558.2 3613.2 3394 4062.3 3739.2 4986.1 TRUE FALSE FALSE 4354.372382 4438.416705 3858.913833 4179.018583 3376.611777 3382.328181 3682.286275 4179.836241 3404.756587 4856.560403 0.896595949 0.913901267 0.794577543 0.860489366 0.695268152 0.6964452 0.758208685 0.860657728 0.701063367 1 12.24571919 -10.09973942 0.541404912 0.98175355 0.748187049 0 0.104195379 0.316769159 0.209834932 0.019539764 0.026464051 7.95E-11 10.09973942 -0.233566501 KS(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_HeLa_Romidepsin_16h_R1 1 KSLPEEDVAEIQHAEEFLIKPESK 24 2 O60832;H7C2Q9;H7C0M1;C9IYT0;O60832-2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 KS(1)LPEEDVAEIQHAEEFLIKPESK 108.22 3.15E-06 8427800 3077 2694.5 2788.4 2847.2 3321.5 3433.6 3037.5 3216.4 2924.6 3038.6 TRUE FALSE FALSE 3039.49634 2732.433242 2836.930932 3176.40666 3151.991461 3214.204041 3295.505174 3309.461459 2663.016451 2959.656734 1.026975968 0.923226403 0.958533772 1.073234819 1.064985485 1.086005686 1.11347547 1.118190978 0.899772065 1 11.53121414 -9.093787156 4.846813065 1.001315645 1.093549899 0.622506722 0.045658763 0.120880137 4.690096822 0.005624303 0.009527432 8.06E-10 9.093787156 0.092234253 KS(ph)RPGLS(ph)MR ddPTM_HeLa_Romidepsin_16h_R1 1 KSRPGLSMR 9 2 J3KRC3;A0A0A0MTQ1;Q96GE4-2;Q96GE4 J3KRC3 CEP95 Centrosomal protein of 95 kDa 2 0 KS(1)RPGLS(1)MR 73.665 0.023323 5482100 1972.4 2122.1 1863.3 1740 1807.1 1559.6 1603 1835.4 2373.4 2601.4 TRUE FALSE FALSE 1948.35963 2151.97498 1895.729955 1941.186987 1714.876944 1459.946593 1739.15878 1888.504403 2161.11716 2533.815253 0.768943051 0.849302244 0.74817213 0.766112283 0.676796361 0.576185099 0.686379474 0.745320481 0.852910313 1 11.30709562 -13.85495473 0.161489009 1.443233963 0.605143029 0.578084572 0.071249166 8.005665873 0.19703244 1.433851046 0.142133133 1.40E-14 13.85495473 -0.838090935 KS(ph)SPPASSPQPEAPTSSWR ddPTM_HeLa_Romidepsin_16h_R1 1 KSSPPASSPQPEAPTSSWR 19 1 P43250-2 P43250-2 1 0 KS(0.47)S(0.47)PPAS(0.045)S(0.014)PQPEAPTSSWR 69.422 0.0049398 12660000 1739.2 1872.2 1541.3 2002.2 1945.7 2193.6 1875.1 2141.3 1694.7 1451.2 TRUE FALSE FALSE 1718.001961 1898.556881 1568.12568 2233.703785 1846.403669 2053.43604 2034.370947 2203.255137 1543.121788 1413.497615 1.215426148 1.343162423 1.109393934 1.580267106 1.306265854 1.452733997 1.439246113 1.558725755 1.091704557 1 10.46505373 -8.588196962 0.097816 0.621923491 2.155880047 0.6837084 0.107598822 10.70472403 0.295178748 1.501574055 3.231821531 2.58E-09 8.588196962 1.533956556 KS(ph)SPSTGSLDSGNESK ddPTM_HeLa_Romidepsin_16h_R1 1 KSSPSTGSLDSGNESK 16 1 A0A0U1RQT1;A0A087X1H5;Q15057 A0A0U1RQT1 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 0 KS(0.846)S(0.099)PS(0.053)T(0.002)GSLDSGNESK 113.23 0.00089018 18251000 2815.7 2726.9 2590 2241.2 2716.9 3516.8 2541.2 2911.4 2721.8 2636.8 TRUE FALSE FALSE 2781.381165 2765.28937 2635.077864 2500.338089 2578.246455 3292.08783 2757.049465 2995.636766 2478.355391 2568.295556 1.082967713 1.076702159 1.026002579 0.973539857 1.003874515 1.281818139 1.073493842 1.166390978 0.964980602 1 11.32659552 -8.289888905 24.993771 1.034808088 1.163860312 0.567697198 0.060857808 418.2692217 367461.2535 0.008395653 0.018776309 5.13E-09 8.289888905 0.129052224 KS(ph)STGSISNVLFSTQDPVEDAVFGEATNLKK ddPTM_HeLa_Romidepsin_16h_R1 1 KSSTGSISNVLFSTQDPVEDAVFGEATNLKK 31 2 Q5VZ89-5;Q5VZ89-3;Q5VZ89;Q5VZ89-7;X6RAE7 Q5VZ89-5 DENND4C DENN domain-containing protein 4C 1 0 KS(0.2)S(0.2)T(0.2)GS(0.2)IS(0.2)NVLFS(0.002)T(0.001)QDPVEDAVFGEATNLKK 54.622 0.0014321 6462500 1515.2 1371.4 1199.7 1348.6 1525.5 2223.7 1997 2321.7 1483.5 1052.9 TRUE FALSE FALSE 1496.73216 1390.706605 1220.580275 1504.531477 1447.648043 2081.612747 2166.62513 2388.874726 1350.812045 1025.545506 1.459449776 1.356065232 1.190176611 1.467054819 1.411588305 2.029761463 2.112656257 2.329369796 1.317164413 1 10.00217579 -4 0.271605008 1.120808058 10.61182536 0.863326343 0.152840668 13.12283278 0.166572688 0.081790778 59.2702814 1.00E-04 4 9.491017307 up KS(ph)VS(ph)MLSLNTPNSNR ddPTM_HeLa_Romidepsin_16h_R1 1 KSVSMLSLNTPNSNR 15 1 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;H7C3G1 Q9H8V3-2 ECT2 Protein ECT2 2 0 KS(1)VS(0.999)MLS(0.001)LNT(0.001)PNSNR 58.831 0.0040056 0 407.22 512.44 520.56 549.92 488.94 358.89 375.07 571.59 668.14 474.02 TRUE FALSE FALSE 402.256646 519.6541438 529.6201284 613.5043379 463.9875673 335.9580873 406.9284364 588.1280548 608.379885 461.7048921 0.871241897 1.125511453 1.147096636 1.328780241 1.004944014 0.7276468 0.881360461 1.273818114 1.317681262 1 8.850827209 -10.26076548 24.99410488 0.939197563 1.059896203 0 0.206596161 118.2941557 4387378.581 0.030543787 0.036232932 5.49E-11 10.26076548 0.12069864 KS(ph)Y(ph)PETVLK ddPTM_HeLa_Romidepsin_16h_R1 1 KSYPETVLK 9 1 A0A0A6YYA4;Q96M83 A0A0A6YYA4 CCDC7 Coiled-coil domain-containing protein 7 2 0 KS(0.986)Y(0.995)PET(0.019)VLK 46.129 0.0043384 0 3690.3 3034.2 4214.7 3221.8 4296.6 4610 4727.7 3487.5 4963 4356.5 TRUE FALSE FALSE 3645.321204 3076.915547 4288.055086 3594.319675 4077.328469 4315.435878 5129.27072 3588.40531 4519.09685 4243.317502 0.859073402 0.725120273 1.010543068 0.847054144 0.96088225 1.016995753 1.208787869 0.845660337 1.064991448 1 12.05097692 -8.339561239 3.381936588 0.91544405 1.043741997 0.123264201 0.122491504 0.311314898 6.875794765 0.016418983 0.040430175 4.58E-09 8.339561239 0.128297947 KSAEPSANTTLVS(ph)ET(ph)EEEGSVPAFGAAAK ddPTM_HeLa_Romidepsin_16h_R1 1 KSAEPSANTTLVSETEEEGSVPAFGAAAK 29 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 2 0 KSAEPS(0.001)ANT(0.031)T(0.1)LVS(0.879)ET(0.894)EEEGS(0.095)VPAFGAAAK 89.055 1.07E-07 8511800 3046.7 3125.6 3491.4 3081.8 3450.7 2928.2 1879.8 2408 3180.9 3351.2 TRUE FALSE FALSE 3009.565649 3169.602279 3552.166352 3438.132216 3274.597903 2741.09747 2039.470165 2477.671681 2896.392337 3264.135341 0.922010068 0.971038866 1.088241136 1.053305656 1.003205309 0.839762199 0.624811765 0.759059114 0.88733831 1 11.67248516 -8.014740173 3.587464511 0.981293853 0.693688182 0.78088808 0.06319929 0.075778086 2.08088026 0.009054764 0.027871915 9.67E-09 8.014740173 -0.287605671 KSAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_HeLa_Romidepsin_16h_R1 2 KSAEPSANTTLVSETEEEGSVPAFGAAAK 29 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 KSAEPSANTTLVS(0.712)ET(0.286)EEEGS(0.002)VPAFGAAAK;KSAEPSANTTLVS(0.784)ET(0.194)EEEGS(0.022)VPAFGAAAK ; 144.18 1.74E-11 333851000 7121.6 6309.4 7748 6364.1 8396.4 8096.2 7342.6 7565 8095.4 8613.9 TRUE FALSE FALSE 7034.7992 6398.223899 7882.85069 7099.947186 7967.900377 7578.878949 7966.280261 7783.881339 7371.327149 8390.109636 0.838463322 0.762591215 0.939540844 0.846228177 0.949677742 0.903311074 0.949484644 0.92774489 0.8785734 1 13.03447395 -5.982895474 19.39242239 0.910607957 0.90581686 0 0.066706511 0 0 0.01048711 0 1.04E-06 5.982895474 -0.004791097 KSAEPSANTTLVSET(ph)EEEGSVPAFGAAAK ddPTM_HeLa_Romidepsin_16h_R1 1 KSAEPSANTTLVSETEEEGSVPAFGAAAK 29 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 KSAEPSANTTLVS(0.038)ET(0.773)EEEGS(0.189)VPAFGAAAK 122.8 7.65E-11 322180000 5950.5 6471 6612.7 5342.8 6067.1 6039.1 6065.2 6312.7 6704.8 6537.2 TRUE FALSE FALSE 5877.973017 6562.098908 6727.79127 5960.559675 5757.473248 5653.221 6580.377937 6495.348015 6105.105896 6367.362602 0.923140927 1.030583511 1.056605645 0.936111236 0.904216331 0.887843422 1.033454249 1.020100224 0.958812349 1 12.63648021 -7.648720627 21.07881624 0.96398216 1.026813698 0.202200935 0.051228662 3.960322235 725.1808638 0.007838087 0.029327571 2.25E-08 7.648720627 0.062831538 KSDIDEIVLVGGS(ph)TR ddPTM_HeLa_Romidepsin_16h_R1 1 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 1 0 KSDIDEIVLVGGS(0.748)T(0.252)R 107.18 0.00032463 0 3562.6 3563.5 3902.6 2720 2827.6 3640.2 4067.5 4432 4289.9 4188.4 TRUE FALSE FALSE 3519.177661 3613.667047 3970.523116 3034.499198 2683.297021 3407.602968 4412.993348 4560.232927 3906.2006 4079.584764 0.862631337 0.885792858 0.973266483 0.743825505 0.657737779 0.835281815 1.081726108 1.117817913 0.957499556 1 11.9942066 -7.701338401 6.860865047 0.89428439 1.104320628 0.43710344 0.102508047 0.191448405 17.1750884 0.016637442 0.062889627 1.99E-08 7.701338401 0.210036238 KSDIDEIVLVGGSTR ddPTM_HeLa_Romidepsin_16h_R1 1 KSDIDEIVLVGGSTR 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 105.28 0.0038877 12991000 4005.7 3930.5 4026.5 3893.6 4815 4830.4 4481.8 5043.8 4388.7 4180.7 FALSE FALSE TRUE 3956.876988 3985.833682 4096.579543 4343.796352 4569.272583 4521.753029 4862.48398 5189.734395 3996.16368 4072.084811 0.971707902 0.978818926 1.00601528 1.066725413 1.122096615 1.110427027 1.194101844 1.274466185 0.98135571 1 11.99155189 -7.761518795 0.568255062 0.983072578 1.361982126 0.95258036 0.021379461 0.378350012 0.115762534 0.00486408 0.084364015 1.73E-08 7.761518795 0.378909547 KSDVEAIFSK ddPTM_HeLa_Romidepsin_16h_R1 1 KSDVEAIFSK 10 1 P07910-2;G3V4C1;P07910;G3V2Q1;B2R5W2;P07910-4;G3V4W0;G3V576;P0DMR1;B7ZW38;A0A0G2JPF8;A0A0G2JNQ3;B2RXH8;O60812;G3V555;G3V575;G3V251;G3V3K6;G3V5X6;G3V4M8;B4DSU6;G3V2H6;B4DY08 P07910-2;B4DY08 HNRNPC;HNRNPCL4;HNRNPCL3;HNRNPCL2;HNRNPCL1 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 1 0 0 95.417 0.019827 11903000 4155.6 3684.1 4347.8 3309.6 4317.1 4285.7 4142.2 3401 3894.1 3940.9 FALSE FALSE TRUE 4104.949949 3735.964857 4423.471635 3692.271524 4096.782278 4011.857601 4494.038365 3499.402569 3545.801943 3838.51485 1.069410986 0.97328394 1.152391435 0.961901066 1.067283165 1.045158807 1.170775297 0.911655342 0.923743188 1 11.90633251 -12.48607056 1.110530317 0.99872708 1.049854115 0.101049177 0.080429733 1.299567336 2.748117339 0.053723107 0.011828872 3.27E-13 12.48607056 0.051127034 KSEDGTPAEDGT(ph)PAATGGSQPPSMGR ddPTM_HeLa_Romidepsin_16h_R1 1 KSEDGTPAEDGTPAATGGSQPPSMGR 26 1 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 KSEDGTPAEDGT(0.485)PAAT(0.214)GGS(0.273)QPPS(0.028)MGR 48.232 0.014648 4140200 631.43 522.27 443.63 423.52 529.03 739.82 771.48 668.96 434.42 439.68 TRUE FALSE FALSE 623.7338883 529.6225308 451.3511941 472.4893751 502.031625 692.5478897 837.0094919 688.3153022 395.5643872 428.2570502 1.456447449 1.236693081 1.053925893 1.103284522 1.172267041 1.617131322 1.954455838 1.607248034 0.923661121 1 8.742333187 -8.149233641 3.72560116 1.198047286 1.781958724 0.721683078 0.166611346 0.114662476 2.856445169 0.027306117 0.075529474 7.09E-09 8.149233641 0.583911437 KSEEEIDFLR ddPTM_HeLa_Romidepsin_16h_R1 2 KSEEEIDFLR 10 1 B0QY90;B0QY89;Q9Y262-2;Q9Y262 B0QY90 EIF3L Eukaryotic translation initiation factor 3 subunit L 0 0 ; ; 121.6 0.0070212 22396500 8912.2 8840.4 9525.7 7363 9442.3 8802.4 7950.5 9702.1 9721 9088.5 FALSE FALSE TRUE 8803.574678 8964.855383 9691.490813 8214.344704 8960.424197 8239.955048 8625.815272 9982.814956 8851.529413 8852.37946 0.994486818 1.012705728 1.094789357 0.927925056 1.012205163 0.930818102 0.974406408 1.127698491 0.999903975 1 13.11184958 -7.255731316 24.66653768 0.995629259 1.12769856 0.449058493 0.044353725 355.1724492 1534768.456 0.005714892 0.067185172 5.55E-08 7.255731316 0.132069301 KSKLET(ph)T(ph)YR ddPTM_HeLa_Romidepsin_16h_R1 3 KSKLETTYR 9 2 Q92628 Q92628 KIAA0232 Uncharacterized protein KIAA0232 2 0 KS(0.001)KLET(0.986)T(0.902)Y(0.111)R;KSKLET(0.993)T(0.917)Y(0.09)R;KSKLET(0.991)T(0.914)Y(0.095)R ;; 76.679 0.0032858 410830000 4677.6 4993.7 4482.01 6745.5 4780 4888.77 4136.9 4316.1 5039.2 4454.3 TRUE FALSE FALSE 4620.587612 5064.00144 4560.017504 7525.446449 4536.058763 4576.393375 4488.288183 4440.979544 4588.481331 4338.576644 1.065000804 1.167203407 1.051039979 1.734542701 1.045517721 1.054814459 1.034507063 1.023602879 1.057600616 1 12.0830061 -10.4571968 1.666589731 1.022770465 1.165749982 0.067113789 0.20080809 0.668636115 3.63477564 0.039682663 0.04361956 3.49E-11 10.4571968 0.142979516 KSLDSDES(ph)EDEEDDYQQK ddPTM_HeLa_Romidepsin_16h_R1 1 KSLDSDESEDEEDDYQQK 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 0 KS(0.001)LDS(0.008)DES(0.99)EDEEDDYQQK 62.847 0.011805 3296400 826.17 823.31 892.77 658.15 956.11 899.32 1237 933.52 1153.5 867.52 TRUE FALSE FALSE 816.1003223 834.9005798 908.3082874 734.2483997 907.316139 841.8563544 1342.070749 960.5299283 1050.328071 844.9817053 0.965820108 0.988069416 1.074944323 0.868951831 1.073770158 0.99630128 1.588283794 1.13674642 1.243018712 1 9.722776296 -7.787170753 24.68067044 0.989225077 1.362514941 0.464103884 0.140011015 65.05336887 62397.02535 0.013523292 0.040591161 1.63E-08 7.787170753 0.373289864 KSLGDDISSETSGDFR ddPTM_HeLa_Romidepsin_16h_R1 1 KSLGDDISSETSGDFR 16 1 P12429;D6RFG5;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 0 81.651 0.0026831 0 2779.1 1971.9 2296.3 1829.6 2428.8 2479.7 2294.9 2368.3 3129 2441.6 FALSE FALSE TRUE 2745.22726 1999.66046 2336.266138 2041.146961 2304.849273 2321.255173 2489.828749 2436.823024 2849.134403 2378.16688 1.154345931 0.840841102 0.982381076 0.858285841 0.969170537 0.976069086 1.046952916 1.024664436 1.198038047 1 11.21563424 -10.27295181 24.98347076 1.072885576 0.958767475 0.426659398 0.080435498 690.049976 1497494.746 0.014124152 0.016227977 5.33E-11 10.27295181 -0.1141181 KSNFSNS(ph)ADDIK ddPTM_HeLa_Romidepsin_16h_R1 1 KSNFSNSADDIK 12 1 P45973 P45973 CBX5 Chromobox protein homolog 5 1 0 KS(0.001)NFS(0.055)NS(0.944)ADDIK 129.17 0.0066266 6238300 948.98 926.83 967.51 1105.8 960.89 1455.6 996.96 1362.2 977.88 1079.9 TRUE FALSE FALSE 937.4134667 939.8779371 984.3491057 1233.657799 911.8521977 1362.591858 1081.641758 1401.613108 890.4159637 1051.844042 0.891209561 0.89355256 0.935831802 1.17285239 0.866908174 1.295431455 1.028329024 1.332529397 0.846528504 1 10.0387051 -7.788396638 0.654273391 0.943814548 1.346816555 0.493825724 0.12119076 1.196624028 0.520527891 0.019810611 0.313857566 1.63E-08 7.788396638 0.403002007 KSNLDEEVNVIPPHT(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 1 KSNLDEEVNVIPPHTPVR 18 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 0 KSNLDEEVNVIPPHT(1)PVR 113.24 0.00056425 6126300 4043.7 3429.5 3736.9 3660.7 3137.4 3078.2 2306.8 2861.3 4226.7 3540.5 TRUE FALSE FALSE 3994.413829 3477.780591 3801.939177 4083.967358 2977.286771 2881.512954 2502.739534 2944.087201 3848.653366 3448.5173 1.15829891 1.00848576 1.102485169 1.184267615 0.863352714 0.835580252 0.725743651 0.853725513 1.116031335 1 11.75176049 -8.62956136 5.453379129 1.079802976 0.805282397 0.818471667 0.063633012 0.077295278 3.449070361 0.010990272 0.022257604 2.35E-09 8.62956136 -0.274520579 SLPSTSSTSSTK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SLPSTSSTSSTKR 13 1 A0A590UJA3;S4R3W2;A0A590UJU2;A0A590UK38;A0A590UK73;B1AKN7;B1AKN5;A0A590UK09;B1AKN8;Q12857-2;Q12857-3;Q12857;Q12857-4 A0A590UJA3 NFIA Nuclear factor 1;Nuclear factor 1 A-type 0 1 ; SLPSTSSTSSTK(1)R;SLPSTSSTSSTK(1)R 252.14 5.87E-54 18298000 421.56 331.943 484.4 911.05 3043.89 3125.79 2293.92 2149.03 291.82 407.53 FALSE TRUE FALSE 416.4218646 336.6161023 492.8307788 1016.389888 2888.548935 2926.062107 2488.765508 2211.208792 265.7188883 396.9423119 1.049074014 0.848022728 1.241567765 2.560548113 7.276999324 7.371504674 6.269841821 5.570604913 0.669414372 1 8.632785544 -8.887106768 3.677821498 1.045832503 6.654629731 0.962237613 0.529937025 0.03099758 0.805451964 0.082262931 0.155445618 1.30E-09 8.887106768 5.608797228 up KSPGGGGGGGSGNDNNQAATK(ac)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 KSPGGGGGGGSGNDNNQAATKSPR 24 2 Q9NS37;E9PIM0;J3KN20 Q9NS37 CREBZF CREB/ATF bZIP transcription factor 0 1 KSPGGGGGGGSGNDNNQAATK(1)SPR 83.059 6.52E-05 397430 182.53 0 0 0 71.016 0 0 0 0 179.66 FALSE TRUE FALSE 180.3052542 0 0 0 67.39178852 0 0 0 0 174.9924073 1.030360442 0 0 0 0.385112643 0 0 0 0 1 7.451148516 -10.26301345 24.99028805 1.014336892 0.059248083 0.288909313 0.340086959 21.6713648 344058.1309 0.019146757 0.022516706 5.46E-11 10.26301345 -0.95508881 KSPS(ph)DTEGLVK ddPTM_HeLa_Romidepsin_16h_R1 1 KSPSDTEGLVK 11 1 O95297-4;O95297-2;O95297 O95297-4 MPZL1 Myelin protein zero-like protein 1 1 0 KS(0.286)PS(0.636)DT(0.078)EGLVK 113.07 0.0013897 0 960.16 1159.8 1200.4 1015.8 1134.6 1503.7 867.63 1763.9 1007.5 1105.2 TRUE FALSE FALSE 948.4572006 1176.127695 1221.292458 1133.251575 1076.697128 1407.618423 941.3264705 1814.935664 917.3866767 1076.486745 0.881067236 1.092561242 1.13451695 1.052731565 1.000195435 1.307604046 0.87444316 1.685980503 0.852204341 1 10.07211484 -5.591770734 1.745110368 0.994124323 199.9992153 0.651469465 0.140788794 188.7842401 2.458530893 0.019861695 148908.0307 2.56E-06 5.591770734 199.005091 KSPVGKS(ph)PPSTGSTYGSSQK ddPTM_HeLa_Romidepsin_16h_R1 1 KSPVGKSPPSTGSTYGSSQK 20 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 KS(0.306)PVGKS(0.659)PPS(0.028)T(0.005)GS(0.001)TYGSSQK 71.735 0.0030782 14020000 3129.7 3469.3 3234.5 2948.4 4164.2 4954.4 4377 4958 3800.6 3932.6 TRUE FALSE FALSE 3091.554013 3518.140896 3290.795116 3289.307881 3951.685335 4637.82983 4748.782271 5101.451908 3460.664817 3830.430485 0.807103542 0.918471412 0.859118871 0.858730603 1.031655672 1.210785536 1.239751586 1.331822083 0.903466289 1 11.90329082 -8.317501667 1.968237708 0.900083922 1.283746712 0.906943558 0.053135874 0.103654778 0.770167092 0.011425913 0.034465832 4.81E-09 8.317501667 0.383662789 KSS(ph)PEMEDAR ddPTM_HeLa_Romidepsin_16h_R1 1 KSSPEMEDAR 10 1 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 KS(0.026)S(0.974)PEMEDAR 103.43 0.01641 8749800 2902.1 2435.2 2641.6 2708.9 2325.5 2805.4 3585.8 985.11 2822.7 2490.6 TRUE FALSE FALSE 2866.728089 2469.48281 2687.57594 3022.115764 2206.821057 2626.143994 3890.377762 1013.612604 2570.230642 2425.893853 1.181720332 1.017968204 1.107870378 1.245774113 0.90969399 1.082546951 1.603688372 0.417830567 1.059498394 1 11.24430071 -7.229124541 24.16495902 1.108957418 0.417828558 0.578964618 0.182146529 5187.807184 3879333.231 0.023738522 4.691131594 5.90E-08 7.229124541 -0.691128859 KSS(ph)PSTGSLDSGNESK ddPTM_HeLa_Romidepsin_16h_R1 1 KSSPSTGSLDSGNESK 16 1 A0A0U1RQT1;A0A087X1H5;Q15057 A0A0U1RQT1 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 0 KS(0.022)S(0.543)PS(0.237)T(0.033)GS(0.165)LDSGNESK 156.29 0.00033926 7219700 2396.8 1874.5 2086.7 2161.2 2614.9 3031.1 2473.2 2529.3 2376 2161.3 TRUE FALSE FALSE 2367.58688 1900.88926 2123.018138 2411.088113 2481.451895 2837.422492 2683.273546 2602.481305 2163.484609 2105.149114 1.124664692 0.902971313 1.008488246 1.145328897 1.178753504 1.347848698 1.274623982 1.236245588 1.027710861 1 11.03970671 -8.763787763 1.995271632 1.04383742 1.282140347 0.762910975 0.064539684 0.143453306 1.162888473 0.011333224 0.025105535 1.72E-09 8.763787763 0.238302927 KSS(ph)PSVKPAVDPAAAK ddPTM_HeLa_Romidepsin_16h_R1 1 KSSPSVKPAVDPAAAK 16 2 H3BV90;Q6FI81-3;Q6FI81;H3BPG7;H3BT65 H3BV90 CIAPIN1 Anamorsin 1 0 KS(0.174)S(0.819)PS(0.007)VKPAVDPAAAK 64.2 0.020521 73615000 3817.5 3915.3 3159.3 3872.4 3415.2 3120.3 3297.9 2897.8 4134 3708.7 TRUE FALSE FALSE 3770.970842 3970.419696 3214.286291 4320.145108 3240.9096 2920.9229 3578.023544 2981.643271 3764.244686 3612.347439 1.043911447 1.099124534 0.889805409 1.195938425 0.897175494 0.80859412 0.990498174 0.825403237 1.042049457 1 11.81872094 -8.559063993 24.99844018 1.028541138 0.880812654 0.463397229 0.085907753 113.2870275 78263.5042 0.011086682 0.022173411 2.76E-09 8.559063993 -0.147728485 KSSEGGVGVGPGGGDEPPT(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 KSSEGGVGVGPGGGDEPPTSPR 22 1 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 KSSEGGVGVGPGGGDEPPT(0.818)S(0.182)PR;KSSEGGVGVGPGGGDEPPT(0.53)S(0.47)PR ; 115.92 3.67E-05 19458700 7286.6 6588.2 6785.9 7707.4 7248.1 7650.1 6047.1 6878.4 7306.3 7576.3 TRUE FALSE FALSE 7197.788116 6680.948853 6904.005743 8598.565852 6878.202411 7161.2833 6560.740523 7077.415652 6652.806229 7379.466634 0.975380535 0.905343053 0.935569749 1.165201535 0.932073109 0.970433726 0.889053484 0.959068724 0.901529414 1 12.84930083 KSVAEGLSGS(ph)LVQEPFQLATEK ddPTM_HeLa_Romidepsin_16h_R1 2 KSVAEGLSGSLVQEPFQLATEK 22 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 KSVAEGLS(0.072)GS(0.926)LVQEPFQLAT(0.001)EK;KSVAEGLS(0.011)GS(0.989)LVQEPFQLATEK ; 87.991 0.00021922 21171800 5098.4 4409.6 4969 4987.2 5966.8 6429 5131.6 5297.7 5538.6 4758.4 TRUE FALSE FALSE 5036.25874 4471.678465 5055.483361 5563.843529 5662.291931 6018.207649 5567.477976 5450.980591 5043.213744 4634.776082 1.08662396 0.964810033 1.090771867 1.200455735 1.221696977 1.298489407 1.201239904 1.17610441 1.088124573 1 12.17828392 -9.313856408 2.902749458 1.036039005 1.226186764 0.790269925 0.045392236 0.091964197 1.536154538 0.00753569 0.012292646 4.85E-10 9.313856408 0.190147759 KSVS(ph)SPTSSNTPTPTK ddPTM_HeLa_Romidepsin_16h_R1 2 KSVSSPTSSNTPTPTK 16 1 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 0 KS(0.154)VS(0.562)S(0.222)PT(0.008)S(0.036)S(0.002)NT(0.007)PT(0.006)PT(0.002)K;KS(0.074)VS(0.633)S(0.244)PT(0.024)S(0.025)SNTPTPTK ; 101.62 0.0015182 27477000 4674.8 5443.9 8331 6638.7 5380.3 8462.1 5826.4 7109.6 5239.8 6557.7 TRUE FALSE FALSE 4617.821739 5520.539367 8475.99756 7406.29773 5105.723214 7921.39912 6321.294271 7315.305059 4771.139165 6387.330009 0.722965892 0.86429531 1.327001666 1.159529525 0.799351718 1.240173767 0.989661449 1.145283718 0.746969259 1 12.64099728 -9.836666037 24.92579641 0.86515582 1.098715158 0.43545122 0.152273844 32.60710508 10803.04073 0.0262987 0.03456327 1.46E-10 9.836666037 0.233559338 KT(ph)PELGIVPPPPIPR ddPTM_HeLa_Romidepsin_16h_R1 2 KTPELGIVPPPPIPR 15 1 Q8TEH3;Q8TEH3-7;Q8TEH3-6 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 0 KT(1)PELGIVPPPPIPR;KT(1)PELGIVPPPPIPR ; 80.459 0.01276 31945000 3182.4 3221.1 3151.1 3044.8 2875 2702.5 2664.3 2933.5 3937 3379.5 TRUE FALSE FALSE 3143.611685 3266.44673 3205.943574 3396.854102 2728.278022 2529.818972 2890.605575 3018.376194 3584.86486 3291.700103 0.95501157 0.992328167 0.973947648 1.031945194 0.828835537 0.768544792 0.878149736 0.916965732 1.089061806 1 11.68461719 -8.752713783 24.99997987 0.982315566 0.844584395 0.674300428 0.052423407 77.08223334 220849.0471 0.006095243 0.012042291 1.77E-09 8.752713783 -0.13773117 KT(ph)PPAPSPFDLPELK ddPTM_HeLa_Romidepsin_16h_R1 1 KTPPAPSPFDLPELK 15 1 O95239 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 KT(1)PPAPSPFDLPELK 78.088 0.01442 15875000 5894.3 5323.3 6078.7 4069.9 5108.3 6070.4 4879.2 4566.2 6181.1 5652.6 TRUE FALSE FALSE 5822.458004 5398.241557 6184.497224 4540.480987 4847.604389 5682.521031 5293.639126 4698.315793 5628.246935 5505.744637 1.057524166 0.98047438 1.123280797 0.824680636 0.880462991 1.032107627 0.9614756 0.853347931 1.022249906 1 12.42672198 -9.261610271 24.99999996 1.030163065 0.918348367 0.483108276 0.06488149 11.8577851 1734718.687 0.009927542 0.015778152 5.48E-10 9.261610271 -0.111814697 KT(ph)RPS(ph)S(ph)T(ph)VIK ddPTM_HeLa_Romidepsin_16h_R1 1 KTRPSSTVIK 10 2 Q5SSJ5;Q5SSJ5-3;Q5SSJ5-2 Q5SSJ5 HP1BP3 Heterochromatin protein 1-binding protein 3 4 0 KT(1)RPS(1)S(1)T(1)VIK 57.859 0.0041375 0 709.89 451.3 612.08 579.14 644.57 599.86 676.91 611.4 456.2 575.43 TRUE FALSE FALSE 701.2375876 457.6534132 622.7329956 646.1028917 611.6751877 561.530882 734.4067185 629.0898944 415.3963294 560.4802456 1.251137026 0.81653799 1.111070373 1.152766573 1.091341207 1.001874529 1.310316865 1.122412251 0.741143569 1 9.130519715 -7.762211266 24.99951499 1.093088478 1.216364535 0.068334435 0.162435274 31.37576786 1016371.094 0.018358814 0.06031464 1.73E-08 7.762211266 0.123276056 KT(ph)S(ph)QS(ph)TSVSTK ddPTM_HeLa_Romidepsin_16h_R1 1 KTSQSTSVSTK 11 1 Q8N8Z6-2;Q8N8Z6 Q8N8Z6-2 DCBLD1 "Discoidin, CUB and LCCL domain-containing protein 1" 3 0 KT(0.999)S(0.993)QS(0.993)T(0.005)S(0.005)VS(0.005)TK 86.794 0.023154 10936000 643.74 550.98 578.62 620.59 680.45 856.9 698.7 738.37 580.34 557.22 TRUE FALSE FALSE 635.8938493 558.7367109 588.6906384 692.3455358 645.7240974 802.1468555 758.0475606 759.733571 528.4329369 542.7433441 1.171629014 1.029467642 1.084657499 1.275640767 1.189741163 1.477948766 1.39669619 1.399802649 0.973633196 1 9.084126318 -8.7173674 1.054503273 1.076164114 1.432059942 0.803804111 0.076222343 0.191123926 0.408594675 0.013487632 0.042362704 1.92E-09 8.7173674 0.355895828 KT(ph)SLDVSNSAEPGFLAPGAR ddPTM_HeLa_Romidepsin_16h_R1 1 KTSLDVSNSAEPGFLAPGAR 20 1 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6;Q8NEY1-5;H0Y6F6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 KT(0.499)S(0.499)LDVS(0.002)NSAEPGFLAPGAR 70.094 0.0038009 11167000 877.88 907.09 826.68 1292.6 1889.2 2361.1 2361.6 2606.9 976.67 978.41 TRUE FALSE FALSE 867.1800609 919.8600368 841.0680186 1442.056494 1792.787074 2210.23333 2562.194245 2682.326538 889.3141891 952.9907672 0.909956414 0.965234993 0.882556314 1.513190414 1.881221871 2.319259962 2.688582443 2.814640636 0.933182377 1 9.896318427 -8.504343243 1.03954535 0.942463026 2.824761653 0.986096048 0.087144931 0.046415603 0.091651975 0.015033113 0.05893388 3.13E-09 8.504343243 1.882298627 up KT(ph)SPASLDFPESQK ddPTM_HeLa_Romidepsin_16h_R1 1 KTSPASLDFPESQK 14 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 KT(0.888)S(0.11)PAS(0.001)LDFPESQK 90.367 0.0078137 151160000 4543.8 4404.7 4336.3 4449.9 4299 3465.5 3063.6 3476 4859.3 4560.1 TRUE FALSE FALSE 4488.418418 4466.709482 4411.771483 4964.418375 4079.605988 3244.065734 3323.822108 3576.572576 4424.672038 4441.627945 1.010534532 1.005646924 0.993278036 1.117702436 0.918493408 0.73037764 0.748334203 0.80523912 0.996182502 1 12.11687283 -8.435165948 4.08865608 1.011575491 0.762080139 0.893502485 0.039862539 0.048992789 1.481038682 0.005440847 0.012519039 3.67E-09 8.435165948 -0.249495352 KTAEISSTALRS(ph)S(ph)PIMRK ddPTM_HeLa_Romidepsin_16h_R1 1 KTAEISSTALRSSPIMRK 18 3 A0A087WWN8;A0A087WZV0;O43314-2;O43314;K7ENU7;H0Y9S9 A0A087WWN8;K7ENU7 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 2 0 KTAEISS(0.001)T(0.001)ALRS(0.999)S(0.999)PIMRK 58.83 0.0035725 0 2083.6 2044.5 1531.3 1482.3 2020.1 2466.9 2443.2 2370.8 2114.5 1728.9 TRUE FALSE FALSE 2058.204282 2073.282525 1557.951634 1653.6905 1917.006759 2309.273052 2650.725347 2439.395357 1925.373824 1683.982929 1.222223959 1.231177876 0.925158805 0.98201144 1.138376599 1.371316189 1.57408089 1.44858675 1.143345215 1 10.7176618 -8.155327129 2.821180443 1.094184715 1.507900078 0.757569028 0.098779283 0.117266863 1.792246804 0.01712561 0.050885892 6.99E-09 8.155327129 0.413715363 KTAPPGSAVGK(ac)QPAPR ddPTM_HeLa_Romidepsin_16h_R1 2 KTAPPGSAVGKQPAPR 16 2 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 1 ; KTAPPGSAVGK(1)QPAPR;KTAPPGSAVGK(1)QPAPR 121.32 0.00043695 1266940 512.17 495.46 435.24 294.5 325.23 222.09 466.89 339.86 625.59 450.13 FALSE TRUE FALSE 505.927475 502.4350989 442.8151696 328.5514757 308.6322995 207.8991658 506.5476249 349.6933129 569.6356636 438.4355577 1.153938056 1.145972515 1.00998918 0.749372331 0.703939938 0.47418409 1.155352517 0.797593413 1.299246043 1 8.776220997 -9.359694911 4.083722948 1.079991118 0.776361875 0.489426121 0.175121997 0.168827555 5.015207816 0.025593328 0.039886486 4.37E-10 9.359694911 -0.303629243 KTEAPAAPAAQETKS(ph)DGAPASDSKPGSSEAAPSSK ddPTM_HeLa_Romidepsin_16h_R1 2 KTEAPAAPAAQETKSDGAPASDSKPGSSEAAPSSK 35 3 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 KTEAPAAPAAQET(0.045)KS(0.701)DGAPAS(0.158)DS(0.053)KPGS(0.02)S(0.02)EAAPS(0.001)SK;KTEAPAAPAAQET(0.178)KS(0.704)DGAPAS(0.07)DS(0.024)KPGS(0.011)S(0.013)EAAPS(0.001)SK ; 64.273 0.00027798 49607000 5613.7 6531.4 5561.1 5716 6772.2 7468.1 6103.8 8172.4 6155.6 6631.5 TRUE FALSE FALSE 5545.278065 6623.349221 5657.888613 6376.910815 6426.589363 6990.912512 6622.25662 8408.8555 5605.027719 6459.212674 0.85850681 1.025411231 0.875940908 0.987258221 0.994949336 1.082316509 1.025242077 1.301839082 0.867757109 1 12.65714261 -4 0.597273818 0.937445289 22.31499497 0.745982466 0.062181577 61.41718962 0.441801284 0.011756003 1717.38972 1.00E-04 4 21.37754968 KTEFLDLDNSPLSPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 KTEFLDLDNSPLSPPSPR 18 1 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 0 KTEFLDLDNS(0.013)PLS(0.114)PPS(0.873)PR 120.8 0.00047272 11437000 2232.3 2449.7 2208.8 1832.9 1893.1 1446.4 1505.7 1881.4 2621.1 2412.6 TRUE FALSE FALSE 2205.091869 2484.186941 2247.243237 2044.828522 1796.488043 1353.979708 1633.59412 1935.835341 2386.662251 2349.920304 0.938368789 1.057136677 0.956306149 0.870169307 0.764488923 0.576181118 0.69517001 0.823787657 1.015635401 1 11.19839611 -8.876117334 2.146709042 0.9767528 0.695940507 0.802264221 0.065265091 0.100636506 0.941618664 0.009976513 0.020472113 1.33E-09 8.876117334 -0.280812292 KTEK(ac)EESTEVLK ddPTM_HeLa_Romidepsin_16h_R1 1 KTEKEESTEVLK 12 2 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PDE4;E9PCH5;P20810-2;H0Y9H6;P20810-3 P20810-6;P20810-3 CAST Calpastatin 0 1 KTEK(1)EESTEVLK 154.1 2.45E-24 0 592.92 726.8 543.13 644.06 1513.6 1308.2 1503.7 1045.6 1590.2 1500 FALSE TRUE FALSE 585.693263 737.0319095 552.5829498 718.5292476 1436.355344 1224.610242 1631.42424 1075.852786 1447.968529 1461.029784 0.400877018 0.504460565 0.378214706 0.491796441 0.983111611 0.838182942 1.116626272 0.736366088 0.991060241 1 10.51276987 -8.747881849 24.94173816 0.650455761 0.926976478 0.283541808 0.224592884 302.2276545 556003.7433 0.039995101 0.079639519 1.79E-09 8.747881849 0.276520717 KTETQEK(ac)NPLPSK ddPTM_HeLa_Romidepsin_16h_R1 1 KTETQEKNPLPSK 13 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 1 KTETQEK(1)NPLPSK 179.65 9.20E-07 10367000 3659.2 2545 3380.5 1875.7 5766.9 4539.9 5010.9 4251.5 6123.4 4876.1 FALSE TRUE FALSE 3614.600263 2580.828577 3439.336184 2092.577259 5472.593574 4249.815042 5436.525721 4374.510445 5575.707768 4749.418219 0.761061691 0.543398888 0.724159471 0.440596545 1.152266093 0.8948075 1.14467193 0.921062379 1.173977003 1 12.21353509 KTETQEK(ac)NPLPSKETIEQEK ddPTM_HeLa_Romidepsin_16h_R1 1 KTETQEKNPLPSKETIEQEK 20 3 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 1 K(0.001)TETQEK(0.998)NPLPSK(0.002)ETIEQEK 75.017 0.0013456 2195600 616.49 391.8 448.47 558.33 1227.3 1071 799.68 908.28 1353.6 1079.8 FALSE TRUE FALSE 608.9759828 397.3157707 456.2754322 622.8867416 1164.666301 1002.566556 867.6047992 934.5596488 1232.530626 1051.74664 0.579013956 0.377767568 0.433826375 0.592240296 1.107363938 0.953239609 0.824918061 0.888578687 1.171889292 1 10.03857149 -8.768918604 24.99949348 0.717611419 0.935747046 0.207805173 0.236924688 256.7762452 858283.3545 0.037682734 0.069284886 1.70E-09 8.768918604 0.218135627 KTGSPGS(ph)PGAGGVQSTAK ddPTM_HeLa_Romidepsin_16h_R1 2 KTGSPGSPGAGGVQSTAK 18 1 J3KRZ2;O43237-2;O43237;J3KRI4 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 KT(0.002)GS(0.006)PGS(0.991)PGAGGVQSTAK;KT(0.006)GS(0.116)PGS(0.874)PGAGGVQS(0.003)T(0.001)AK ; 120.33 0.00046854 44764000 7741.6 7324 6985.5 8191.5 8034.2 8018.5 6643.4 7255.3 7143.1 6710.7 TRUE FALSE FALSE 7647.242401 7427.107464 7107.079697 9138.639772 7624.184794 7506.143729 7207.69023 7465.220659 6504.203246 6536.355047 1.169955173 1.136276627 1.08731543 1.398124751 1.166427579 1.148368422 1.102707882 1.142107582 0.995081081 1 12.67427064 -12.15863588 0.617185541 0.980635361 1.17373186 0.41639299 0.081133577 0.876057691 0.517130378 0.093143277 0.018795857 6.94E-13 12.15863588 0.193096499 KTGSYGALAEIT(ph)ASK ddPTM_HeLa_Romidepsin_16h_R1 2 KTGSYGALAEITASK 15 1 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 KT(0.032)GS(0.086)Y(0.001)GALAEIT(0.698)AS(0.183)K;KTGSYGALAEIT(0.938)AS(0.062)K ; 236.12 5.07E-45 463690000 8517.6 7821.1 7736.6 9040 9251.5 7969.6 6920 7735.4 8182.1 8243.5 TRUE FALSE FALSE 8413.784215 7931.205651 7871.252278 10085.24733 8779.361433 7460.368281 7507.784627 7959.211595 7450.272484 8029.332682 1.047880882 0.987778931 0.980312137 1.256050501 1.093411094 0.929139267 0.935044658 0.991266885 0.927881902 1 12.97106437 -8.24755518 24.50220206 1.039204913 0.950139703 0.189919111 0.085110956 784.5775942 1384583.699 0.011504905 0.029171172 5.66E-09 8.24755518 -0.08906521 KTLDELSQGTT(ph)TVK ddPTM_HeLa_Romidepsin_16h_R1 1 KTLDELSQGTTTVK 14 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 KT(0.17)LDELS(0.011)QGT(0.082)T(0.656)T(0.082)VK 127.78 0.0067264 7607800 2436.9 1918.4 2124.7 2131.8 3059.1 3010.3 3283.4 2815.5 2515.2 2011.7 TRUE FALSE FALSE 2407.198125 1945.407286 2161.679512 2378.288746 2902.982712 2817.951545 3562.291914 2896.96205 2290.234213 1959.435744 1.228515981 0.992840562 1.10321531 1.21376205 1.481540143 1.438144401 1.818019256 1.478467492 1.168823331 1 10.93622255 -8.664898053 1.448465466 1.098061451 1.62237148 0.787056661 0.113454161 0.140798422 0.588268094 0.018956404 0.050944487 2.16E-09 8.664898053 0.524310029 KTPESFLGPNAALVDLDSLVSRPGPT(ph)PPGAK ddPTM_HeLa_Romidepsin_16h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 1 0 KTPESFLGPNAALVDLDS(0.049)LVS(0.049)RPGPT(0.903)PPGAK 63.625 0.00014065 8355700 3162.7 3165.2 3322.5 3242 4382.9 5824.7 5287.1 5585.1 3561.9 3244.3 TRUE FALSE FALSE 3124.151796 3209.759769 3380.326719 3616.855294 4159.224258 5452.520468 5736.186142 5746.696057 3243.314743 3160.012618 0.988651684 1.015742706 1.069719374 1.14456989 1.316204952 1.725474271 1.815241531 1.81856744 1.026361327 1 11.6257146 -8.431249352 1.294470716 0.999637932 1.857327183 0.991864323 0.030385495 0.025721468 0.081052908 0.004606124 0.016318941 3.70E-09 8.431249352 0.857689251 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK ddPTM_HeLa_Romidepsin_16h_R1 1 KTPESFLGPNAALVDLDSLVSRPGPTPPGAK 31 2 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 0 0 87.091 3.49E-09 5034100 1571.4 1749.7 1538.8 1157.8 2012.4 2698.8 1981.3 2848.5 1875.8 1725.1 FALSE FALSE TRUE 1552.247172 1774.332323 1565.582169 1291.670284 1909.699719 2526.35539 2149.591573 2930.916853 1708.02375 1680.281653 0.923801774 1.055973157 0.931737941 0.768722482 1.136535482 1.503530902 1.279304317 1.744300932 1.016510385 1 10.71448737 -8.391164718 3.383293033 0.955540184 1.4891855 0.788948967 0.128835063 0.078197739 1.651066029 0.017058748 0.040943562 4.06E-09 8.391164718 0.533645316 KTPLALAGSPT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KTPLALAGSPTPK 13 1 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785 B9EGQ5 WIZ Protein Wiz 1 0 KTPLALAGS(0.163)PT(0.837)PK 68.123 0.028693 43401000 6040.9 6520.5 6136 4321.4 4070.8 3226.7 3071.4 3298.8 6632.1 6911.5 TRUE FALSE FALSE 5967.271187 6612.29577 6242.794506 4821.060601 3863.051886 3020.524284 3332.284639 3394.245573 6038.908366 6731.938234 0.886412053 0.982227635 0.927339837 0.71614748 0.573839473 0.44868568 0.494996318 0.504200344 0.897053442 1 12.71680622 -8.961246869 1.730280525 0.949375303 0.484544319 0.966533041 0.038201039 0.051209551 0.307027492 0.007445204 0.015431933 1.09E-09 8.961246869 -0.464830984 KTQQLHPVLQKPS(ph)VFGNDSDDDDETSVSESLQR ddPTM_HeLa_Romidepsin_16h_R1 1 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 0 KTQQLHPVLQKPS(0.973)VFGNDS(0.026)DDDDETSVSESLQR 69.913 1.26E-05 25047000 2532.6 2055.4 1920.3 2632.7 1984.6 2169.9 1698.3 1721.1 2425.4 2437.7 TRUE FALSE FALSE 2501.731697 2084.335975 1953.722016 2937.105161 1883.318456 2031.250393 1842.55356 1770.897313 2208.466149 2374.368203 1.053641004 0.877848673 0.822838688 1.237004925 0.793187196 0.855490901 0.776018462 0.745839382 0.930127917 1 11.21332796 -8.637626987 22.25296804 1.010204194 0.795854199 0.423271439 0.109053938 2.303543757 435.7047936 0.014954495 0.029908994 2.30E-09 8.637626987 -0.214349995 KTQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_HeLa_Romidepsin_16h_R1 1 KTQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 33 2 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 0 KTQQLHPVLQKPS(0.248)VFGNDS(0.591)DDDDET(0.137)S(0.02)VS(0.004)ESLQR 58.021 0.00032648 23271000 2324.6 2155.5 1521.2 2307.2 1380.7 1074.9 1580.3 1663.3 2148.9 1813.2 TRUE FALSE FALSE 2296.266881 2185.845186 1547.675848 2573.96932 1310.237727 1006.217359 1714.530643 1711.424961 1956.697002 1766.092803 1.300196047 1.237672891 0.876327589 1.457437183 0.741884982 0.569742064 0.970804388 0.969045884 1.107924226 1 10.78634544 -8.731049628 24.97772974 1.150663464 0.806783989 0.465211585 0.183700771 151.5750654 124580.8698 0.028101938 0.056198557 1.86E-09 8.731049628 -0.343879475 KTS(ph)QSEEEEAPR ddPTM_HeLa_Romidepsin_16h_R1 2 KTSQSEEEEAPR 12 1 Q7RTP6;A0A5F9ZHV5;J3KSK6;Q7RTP6-2;Q7RTP6-4;Q7RTP6-3;Q7RTP6-5 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 KT(0.018)S(0.98)QS(0.003)EEEEAPR;KT(0.231)S(0.769)QSEEEEAPR ; 120.6 0.011292 6905400 2253.6 2052.67 1935.38 2159.16 2606.6 3599.7 3626.6 2900.5 2213.3 2174.04 TRUE FALSE FALSE 2226.132256 2081.567542 1969.064477 2408.812238 2473.575475 3369.690787 3934.643313 2984.421391 2015.336905 2117.558127 1.05127327 0.983003732 0.929875054 1.13754244 1.168126364 1.5913097 1.858104041 1.409369288 0.95172684 1 11.04818586 -8.349811602 2.401646835 1.021024688 1.660229022 0.850173342 0.114703785 0.070891353 0.791074616 0.015117463 0.040851358 4.47E-09 8.349811602 0.639204334 KTSAVS(ph)SPLLDQQR ddPTM_HeLa_Romidepsin_16h_R1 2 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 KTSAVS(0.5)S(0.5)PLLDQQR;KTS(0.007)AVS(0.496)S(0.496)PLLDQQR ; 207.4 4.83E-17 16382800 2923.7 2349.98 2722.4 2944.4 2980.3 3063.1 2920.9 2859.6 2564.9 2729.9 TRUE FALSE FALSE 2888.06482 2383.06308 2769.78223 3284.845382 2828.20417 2867.377796 3169.001173 2942.338014 2335.48892 2658.976804 1.086156455 0.896233121 1.041672205 1.23537948 1.063643792 1.078376386 1.191812267 1.106567763 0.878341216 1 11.37665548 -9.489353564 24.47751251 1.028033829 1.131911183 0.422777312 0.081489858 422.3532707 308370.2815 0.010557397 0.016118952 3.24E-10 9.489353564 0.103877354 KTSAVSS(ph)PLLDQQR ddPTM_HeLa_Romidepsin_16h_R1 1 KTSAVSSPLLDQQR 14 1 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 KT(0.024)S(0.024)AVS(0.033)S(0.92)PLLDQQR 104.16 0.0024624 21586000 2245.3 2045.8 2113.4 2242.1 2635 2127.1 2272.9 2312.3 2296.2 1767.4 TRUE FALSE FALSE 2217.93342 2074.600826 2150.18284 2501.342151 2500.526117 1991.185175 2465.960069 2379.202752 2090.822121 1721.482693 1.288385546 1.205124416 1.2490296 1.453016148 1.452542118 1.156668715 1.432462887 1.38206603 1.214547279 1 10.74943596 -13.3534429 0.229707212 0.630958263 1.40065964 0.344585515 0.113855316 5.055017065 0.2350219 1.125187101 0.08841852 4.43E-14 13.3534429 0.769701377 KTSFDQDS(ph)DVDIFPSDFPTEPPSLPR ddPTM_HeLa_Romidepsin_16h_R1 2 KTSFDQDSDVDIFPSDFPTEPPSLPR 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 KT(0.023)S(0.009)FDQDS(0.968)DVDIFPSDFPTEPPSLPR;KT(0.007)S(0.003)FDQDS(0.905)DVDIFPS(0.084)DFPT(0.001)EPPSLPR ; 86.084 1.03E-05 215611000 14621.8 13800.8 13867 12584.1 11990.9 13093.8 11915.6 12970.5 16007.8 15056.4 TRUE FALSE FALSE 14443.58388 13995.08802 14108.34932 14039.13285 11378.95963 12257.14844 12927.71077 13345.78095 14576.02228 14665.23256 0.984886112 0.954303859 0.962026975 0.957307209 0.775914026 0.835796391 0.88152102 0.910028593 0.993916886 1 13.84011233 -8.916580343 6.644745535 0.985938642 0.852295506 0.754132992 0.034896546 0.079437005 5.212453401 0.005442125 0.009921925 1.21E-09 8.916580343 -0.133643136 KTVSLTPSPTTQVETPDLVDHDNTS(ph)PLFR ddPTM_HeLa_Romidepsin_16h_R1 1 KTVSLTPSPTTQVETPDLVDHDNTSPLFR 29 1 Q05209-2;Q05209-3;Q05209;H3BM04 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 KTVSLTPS(0.002)PT(0.05)T(0.05)QVET(0.054)PDLVDHDNT(0.096)S(0.747)PLFR 40.918 0.018498 16996000 803.05 673.2 831.78 1183.3 1062.9 838.87 994.52 808.86 1062.7 748.88 TRUE FALSE FALSE 793.2621177 682.6773273 846.256782 1320.118714 1008.656247 785.2689143 1078.994504 832.2630879 967.6494504 729.4239896 1.087518547 0.935912908 1.160171305 1.809809839 1.382812001 1.076560307 1.479241867 1.140986723 1.326593948 1 9.510613838 -9.513021986 24.65707781 1.035217999 1.37884138 0.293130905 0.210360553 278.7300319 697254.9409 0.028501517 0.041737442 3.07E-10 9.513021986 0.343623381 MQKPCK(ac)ENEGK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 1 MQKPCKENEGKPK 13 3 Q9BRU2 Q9BRU2 TCEAL7 Transcription elongation factor A protein-like 7 0 2 MQK(0.015)PCK(0.987)ENEGK(0.998)PK 52.555 0.028168 0 179.05 121.8 192.8 376.56 805.71 789.6 818.71 759.6 430.03 272.98 FALSE TRUE FALSE 176.8676697 123.5147036 196.1556031 420.099639 764.5916122 739.1471083 888.251207 781.5778275 391.5670398 265.8879402 0.665196284 0.46453669 0.737737872 1.579987564 2.875615989 2.779919644 3.340697612 2.939500854 1.472676946 1 8.054674533 -8.882566136 2.336988418 0.796265441 3.045507027 0.924018292 0.286229607 0.040696231 0.451360107 0.033998732 0.068384508 1.31E-09 8.882566136 2.249241587 up GGALPPAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 GGALPPAKR 9 1 E7ETY2;Q13428-6;Q13428-7;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 0 1 ; GGALPPAK(1)R;GGALPPAK(1)R 88.942 0.018944 9103500 831.68 692.53 844.86 1327.27 2586.7 2968.8 2777.9 2632 877.75 617.9 FALSE TRUE FALSE 821.5431643 702.2794555 859.5644339 1480.735202 2454.691047 2779.103261 3013.854757 2708.152767 799.2418416 601.8468689 1.365036867 1.166873987 1.428211192 2.46031886 4.078597353 4.617625188 5.007677056 4.499737238 1.327982055 1 9.233252651 -8.862245668 1.607641233 1.172892906 4.780412599 0.989998265 0.157245776 0.026212686 0.136651621 0.027742453 0.062238594 1.37E-09 8.862245668 3.607519692 up KVAS(ph)PSPSGSVLFTDEGVPK ddPTM_HeLa_Romidepsin_16h_R1 2 KVASPSPSGSVLFTDEGVPK 20 1 P56181-2 P56181-2 1 0 KVAS(0.823)PS(0.054)PS(0.061)GS(0.061)VLFTDEGVPK;KVAS(0.864)PS(0.085)PS(0.033)GS(0.018)VLFTDEGVPK ; 71.857 0.0024623 65231000 6529.9 6750.9 6368.9 7185.5 8104.8 9283.4 8120.8 8509.4 7159.5 7169.5 TRUE FALSE FALSE 6450.311067 6845.939347 6479.748033 8016.321319 7691.181813 8690.220701 8810.580549 8755.606063 6519.136389 6983.235356 0.923685189 0.980339198 0.927900565 1.147938013 1.101378003 1.244440472 1.261676014 1.253803662 0.933540981 1 12.76967988 -8.765867052 1.159674526 0.961196341 1.261656804 0.894427416 0.043666819 0.111467843 0.29435899 0.00742215 0.020955919 1.71E-09 8.765867052 0.300460464 KVDEGAGDSAAVASGGAQT(ph)LALAGSPAPSGHPK ddPTM_HeLa_Romidepsin_16h_R1 1 KVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 33 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 0 KVDEGAGDSAAVAS(0.004)GGAQT(0.724)LALAGS(0.272)PAPS(0.001)GHPK 92.865 7.60E-12 14799000 6203 6062.5 5192.7 5821.6 9298.5 10621 8556.7 8802.5 8759.5 7824.1 TRUE FALSE FALSE 6127.39545 6147.848034 5283.076765 6494.720783 8823.962848 9942.352378 9283.505884 9057.186449 7976.028381 7620.828754 0.804032691 0.806716465 0.693241764 0.852232873 1.157874443 1.304628761 1.21817537 1.188477886 1.046609055 1 12.89573218 -8.683168311 4.42594489 0.875480033 1.233644002 0.754223946 0.098430017 0.089398354 3.276497995 0.016063367 0.032645576 2.07E-09 8.683168311 0.358163969 KVDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_HeLa_Romidepsin_16h_R1 1 KVDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 33 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 0 KVDEGAGDSAAVASGGAQT(0.119)LALAGS(0.879)PAPS(0.002)GHPK 103.3 2.20E-13 7342000 1763 1551.9 1508.8 1583.9 2704.4 2898.9 2227.2 2195.5 2505.2 2287 TRUE FALSE FALSE 1741.511878 1573.747689 1535.060031 1767.03797 2566.384376 2713.669646 2416.378312 2259.023329 2281.128638 2227.58341 0.781794239 0.706482048 0.689114501 0.793253336 1.152093504 1.218212361 1.084753236 1.014113913 1.024037361 1 11.12126374 -8.757295696 24.98909723 0.854884215 1.122177516 0.59300295 0.114678122 70.19000087 423285.1872 0.019624744 0.038150358 1.75E-09 8.757295696 0.267293301 KVDLTLLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KVDLTLLSPK 10 1 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 KVDLT(0.002)LLS(0.998)PK;KVDLTLLS(1)PK ; 119.21 0.018977 217228000 13624.4 12256.3 13511.5 11730.6 14630 14404.3 14241.1 13385.3 13465.1 12033.3 TRUE FALSE FALSE 13458.34057 12428.84451 13746.66199 13086.94717 13883.37651 13483.91172 15450.73868 13772.58254 12260.74773 11720.67313 1.148256625 1.060420709 1.172856016 1.116569588 1.184520407 1.150438338 1.3182467 1.175067539 1.046078804 1 13.51676781 -16.52287857 0.046943988 0.218216723 1.586840962 0.622259776 0.051957818 204.7842295 0.763502787 21.23438467 5.69827694 3.00E-17 16.52287857 1.368624239 KVEAPETNIDKT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KVEAPETNIDKTPK 14 2 E9PBY7;E9PQ61;O75152 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 KVEAPETNIDKT(1)PK 78.486 0.011536 79079000 5717 4833.7 5072.8 5144.8 3539 3220.1 2648.7 2725.1 5008.4 5127.8 TRUE FALSE FALSE 5647.319005 4901.748955 5161.089956 5739.665983 3358.391624 3014.346002 2873.680512 2803.946469 4560.43616 4994.579017 1.130689691 0.981413837 1.033338333 1.149179133 0.672407347 0.603523539 0.575359906 0.56139796 0.913077187 1 12.28614737 -8.674479985 4.972067662 1.059374259 0.589717678 0.902502521 0.0694854 0.038240798 1.62337417 0.009228136 0.018679188 2.12E-09 8.674479985 -0.469656581 KVEEAEPEEFVVEK ddPTM_HeLa_Romidepsin_16h_R1 1 KVEEAEPEEFVVEK 14 1 S4R2Y4;Q13185;C9JMM0;B8ZZ43 S4R2Y4 CBX3 Chromobox protein homolog 3 0 0 98.676 0.0072129 8321300 3334.7 3328.3 3013.8 3200.3 2920.6 2513.8 2100.2 2832.9 3358.5 3746.5 FALSE FALSE TRUE 3294.055394 3375.155895 3066.253925 3570.333744 2771.550884 2353.176293 2278.590936 2914.865492 3058.107348 3649.16539 0.902687339 0.924911736 0.840261703 0.978397349 0.759502677 0.644853286 0.624414268 0.798775934 0.838029254 1 11.83335082 -8.631368864 3.977257276 0.942555301 0.684808517 0.683033113 0.068459007 0.077728762 2.281108556 0.009553494 0.01982946 2.34E-09 8.631368864 -0.257746785 KVEEEGS(ph)PGDPDHEASTQGR ddPTM_HeLa_Romidepsin_16h_R1 4 KVEEEGSPGDPDHEASTQGR 20 1 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 0 KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(0.994)PGDPDHEAS(0.005)T(0.001)QGR;KVEEEGS(1)PGDPDHEASTQGR;KVEEEGS(0.999)PGDPDHEASTQGR ;;; 139.79 4.74E-05 87061700 5553.2 5115.25 5485.7 5994.4 6124.5 6183.5 5391.3 5373.9 6347.9 5581.5 TRUE FALSE FALSE 5485.515462 5187.262624 5581.176307 6687.500732 5811.943911 5788.394306 5849.236887 5529.385318 5780.127925 5436.491825 1.009017513 0.954156245 1.026613575 1.230113269 1.069061464 1.064729699 1.075921215 1.017087029 1.063209163 1 12.40846026 -9.507198971 24.97524141 1.000132229 1.091858863 0.337072604 0.05690895 521.4436979 830572.9727 0.00798519 0.011970536 3.11E-10 9.507198971 0.091726634 KVEEEQEADEEDVS(ph)EEEAESK ddPTM_HeLa_Romidepsin_16h_R1 4 KVEEEQEADEEDVSEEEAESK 21 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 0 KVEEEQEADEEDVS(0.98)EEEAES(0.02)K;KVEEEQEADEEDVS(0.971)EEEAES(0.029)K;KVEEEQEADEEDVS(0.992)EEEAES(0.008)K;KVEEEQEADEEDVS(0.99)EEEAES(0.01)K ;;; 119.75 4.04E-05 99375000 13487.3 21668.2 18168.4 8833 12102 18994.1 9827.3 19907.5 18571.7 21503 TRUE FALSE FALSE 13322.9116 21973.24549 18484.61338 9854.313021 11484.38978 17780.43831 10662.03062 20483.4921 16910.60064 20944.34896 0.636110085 1.049125257 0.882558509 0.470499849 0.548328802 0.848937264 0.509064791 0.977996124 0.807406364 1 14.35427342 -9.308362975 24.99707926 0.847594524 0.665044828 0.239003121 0.178594639 561.1966389 298958.5474 0.030422254 0.046470828 4.92E-10 9.308362975 -0.182549695 KVEGNFNPFAS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 KVEGNFNPFASPQK 14 1 Q5TH58;Q9H6K1-2;Q9H6K1 Q5TH58 C6orf106 Uncharacterized protein C6orf106 1 0 KVEGNFNPFAS(1)PQK 161.08 0.0004601 15380000 2579.8 2416.1 2279.8 2234.7 2170.7 1832 1712.4 1776 2289 1903.2 TRUE FALSE FALSE 2548.356405 2450.113919 2319.478963 2493.086529 2059.921079 1714.941113 1857.851213 1827.385758 2084.266107 1853.75459 1.374699984 1.321703495 1.251233025 1.344884885 1.111215633 0.925117662 1.002209906 0.985775446 1.124348454 1 10.85623455 -8.484582714 5.317618372 1.210630858 0.978312635 0.545558755 0.106992501 0.185682732 13.40843885 0.022521939 0.049948726 3.28E-09 8.484582714 -0.232318224 KVELS(ph)ESEEDKGGK ddPTM_HeLa_Romidepsin_16h_R1 1 KVELSESEEDKGGK 14 2 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 KVELS(0.999)ES(0.001)EEDKGGK 140.3 0.00085835 256750000 5658.1 5935.4 5099.2 5196.7 5239.1 5056.5 4971.1 5104.2 5242.5 5309.9 TRUE FALSE FALSE 5589.136901 6018.958717 5187.949437 5797.566905 4971.729177 4733.405969 5393.34511 5251.881974 4773.59767 5171.948033 1.080663778 1.163770146 1.003093883 1.120963874 0.961287535 0.915207566 1.04280729 1.015455287 0.922978661 1 12.33649206 -8.731858525 24.99327457 1.051714521 0.983020546 0.168693626 0.070355303 250.7038086 211822.1484 0.009038037 0.018074039 1.85E-09 8.731858525 -0.068693975 SDLHIKDDPDGIPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SDLHIKDDPDGIPSKR 16 2 F6WR09;Q9ULJ6-2;Q9ULJ6 F6WR09 ZMIZ1 Zinc finger MIZ domain-containing protein 1 0 1 SDLHIKDDPDGIPSK(1)R 60.918 0.017851 967070 353.5 401.23 290.44 583.71 1436.4 1562.7 1206.8 1217.8 476.62 485.44 FALSE TRUE FALSE 349.191406 406.8785265 295.4949864 651.2012966 1363.095148 1462.848513 1309.305562 1253.035122 433.9899135 472.8281988 0.738516457 0.860520856 0.624952122 1.377247166 2.882855023 3.093826716 2.769093648 2.650085432 0.917859625 1 8.885172268 -8.852393837 3.542284408 0.858567042 2.873224224 0.975622321 0.151196731 0.026955013 0.663261548 0.025301089 0.048525215 1.40E-09 8.852393837 2.014657182 up KVESLQEEIAFLK ddPTM_HeLa_Romidepsin_16h_R1 1 KVESLQEEIAFLK 13 1 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 103.14 0.0070381 17065000 5747.7 4955.6 5976.3 4923 6012.5 5385.8 5658.6 5225.9 6404.1 6052.8 FALSE FALSE TRUE 5677.644822 5025.365067 6080.314995 5492.220423 5705.659689 5041.664762 6139.241343 5377.103171 5831.301257 5895.547383 0.963039469 0.852400081 1.031340196 0.931587869 0.967791338 0.855164828 1.041335256 0.912061734 0.989102602 1 12.52541005 -11.29936192 1.130030193 0.993526748 0.945512977 0.100201306 0.059677232 0.679422681 1.783645242 0.01596473 0.011095942 5.02E-12 11.29936192 -0.048013771 KVESLQEEIAFLKK ddPTM_HeLa_Romidepsin_16h_R1 3 KVESLQEEIAFLKK 14 2 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 ;; ;; 101.38 0.0031303 32043360 7706.7 6907.5 6146 8009.5 6841.262 7034.8 6330.4 6008.9 8193.14 6781.2 FALSE FALSE TRUE 7612.767776 7004.743966 6252.968552 8935.596076 6492.126872 6585.298984 6868.104018 6182.758041 7460.325038 6605.023446 1.152572408 1.060517653 0.946698918 1.352848502 0.982907468 0.997013718 1.039830377 0.936069053 1.12949259 1 12.68934797 KVIS(ph)PPPFAPSPTLPPTFHPEEFLDEDLK ddPTM_HeLa_Romidepsin_16h_R1 1 KVISPPPFAPSPTLPPTFHPEEFLDEDLK 29 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 0 KVIS(0.994)PPPFAPS(0.004)PT(0.002)LPPTFHPEEFLDEDLK 57.934 0.00060467 5854800 1169.1 1023.7 1010.1 734.72 1050.4 1154.5 1034.3 765.44 1014.2 1157.7 TRUE FALSE FALSE 1154.85056 1038.111675 1027.680367 819.6717834 996.7941684 1080.731176 1122.153416 787.5867987 923.4874119 1127.622787 1.024146171 0.920619632 0.911368925 0.726902465 0.883978383 0.958415517 0.995149645 0.698448814 0.818968384 1 10.13906882 -10.0142052 2.365748053 1.01149333 0.867065087 0.026510567 0.106016852 0.233436304 2.602360832 0.014600338 0.018933255 9.68E-11 10.0142052 -0.144428243 KVMEEEVLIK ddPTM_HeLa_Romidepsin_16h_R1 1 KVMEEEVLIK 10 1 Q8WXE1-5 Q8WXE1-5 ATRIP ATR-interacting protein 0 0 59.908 0.022917 1535500 237.29 258.44 288.28 256.04 354.55 542.43 378.92 465.81 436.29 250.67 FALSE FALSE TRUE 234.3978182 262.0783251 293.2973925 285.6445495 336.4559905 507.7704736 411.1054553 479.2874774 397.2671297 244.1575573 0.960026881 1.073398375 1.201262807 1.169918936 1.378028165 2.079683624 1.683771168 1.963025363 1.627093317 1 7.931668623 -8.59486522 1.519252032 1.002270794 1.907016237 0.616630014 0.236776091 0.081746062 0.373402098 0.019216428 0.053139045 2.54E-09 8.59486522 0.904745443 KVPS(ph)FTFTPTVTYQR ddPTM_HeLa_Romidepsin_16h_R1 3 KVPSFTFTPTVTYQR 15 1 A0A0A0MSX4;Q9Y6N7-4;Q9Y6N7-3;Q9Y6N7;Q9Y6N7-2 A0A0A0MSX4 ROBO1 Roundabout homolog 1 1 0 KVPS(0.818)FT(0.18)FT(0.001)PT(0.001)VTYQR;KVPS(0.995)FT(0.005)FTPTVTYQR;KVPS(0.999)FT(0.001)FTPTVTYQR ;; 122.16 0.0036854 81338600 4432.9 7222.4 5103.8 4994.2 6030.2 8489.4 4584.2 7562.9 5285.6 4955.3 TRUE FALSE FALSE 4378.87011 7324.077137 5192.629498 5571.652902 5722.456392 7946.954738 4973.581834 7781.720579 4812.842698 4826.560592 0.907244409 1.517452645 1.075844672 1.154373347 1.18561785 1.646504708 1.030460871 1.612270359 0.997157832 1 12.23677977 -9.554730903 0.55906749 0.949327989 1.396869265 0.293838865 0.219421463 0.668448791 0.427166967 0.05770562 0.123356685 2.79E-10 9.554730903 0.447541276 KVQAEDEANGLQT(ph)TPASR ddPTM_HeLa_Romidepsin_16h_R1 2 KVQAEDEANGLQTTPASR 18 1 J3KP58;P30622-2;P30622-1;P30622;F5H1T5;F5H6A0 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 0 KVQAEDEANGLQT(0.785)T(0.181)PAS(0.034)R;KVQAEDEANGLQT(0.495)T(0.495)PAS(0.009)R ; 105.95 0.00066404 12440800 4266.3 4351.5 3653.3 3860.6 3931.2 4275.8 3628.9 3964 4385 4485.5 TRUE FALSE FALSE 4214.300695 4412.760531 3716.884154 4306.980737 3730.576195 4002.59018 3937.138675 4078.692086 3992.794618 4368.966063 0.964599091 1.010023989 0.850746859 0.985812358 0.85388079 0.916141284 0.901160279 0.933560029 0.913899206 1 12.09307618 -9.77704966 24.99999811 0.984821393 0.908222697 0.330895963 0.043972384 138.2993116 221486.9126 0.005627187 0.00740956 1.67E-10 9.77704966 -0.076598696 KVQVAALQAS(ph)PPLDQDDR ddPTM_HeLa_Romidepsin_16h_R1 1 KVQVAALQASPPLDQDDR 18 1 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IRI3;Q9UDY2-5;A0A3B3IRV6;A0A3B3ISF1;A0A3B3ISZ5;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 KVQVAALQAS(1)PPLDQDDR 137.52 0.0013259 25994000 2098.9 1896.2 2110.1 1709 1811.1 1766.1 1428.6 1741.2 2242.2 2079.8 TRUE FALSE FALSE 2073.317799 1922.894753 2146.825405 1906.602621 1718.672809 1653.25191 1549.945248 1791.578875 2041.652016 2025.766496 1.02347324 0.949218361 1.059759557 0.941175908 0.848406177 0.816111784 0.765115452 0.88439555 1.007841733 1 10.98425217 -8.842002676 2.556467647 1.009129814 0.818171172 0.834570187 0.037701342 0.069966089 0.93032096 0.005209207 0.010503867 1.44E-09 8.842002676 -0.190958642 KVS(ph)AHS(ph)S(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 KVSAHSSPK 9 1 H7BYJ1 H7BYJ1 RNF34 3 0 KVS(1)AHS(1)S(1)PK 84.568 0.0021842 0 473.41 674.65 496.28 324.57 750.91 598.36 531.55 514.11 752.42 703.23 TRUE FALSE FALSE 467.6398968 684.1477404 504.9175452 362.0983105 712.5882607 560.1267271 576.6998437 528.9849617 685.1216707 684.9599832 0.682725865 0.998814175 0.737148969 0.528641555 1.040335608 0.817751023 0.841946767 0.772285936 1.000236054 1 9.419875895 -12.55426384 1.305047031 1.000732668 0.791727535 0.241473374 0.138786036 0.528095512 1.60231609 0.098015349 0.02281283 2.79E-13 12.55426384 -0.209005133 KVS(ph)RFGIRT(ph)GT(ph)FNCS(ph)SDPR ddPTM_HeLa_Romidepsin_16h_R1 1 KVSRFGIRTGTFNCSSDPR 19 3 O00237 O00237 RNF103 E3 ubiquitin-protein ligase RNF103 4 0 KVS(1)RFGIRT(0.998)GT(0.998)FNCS(0.502)S(0.502)DPR 50.079 0.018137 3028500 725.56 935.58 812.45 663.67 882.16 1054 873.28 974.51 978.3 850.92 TRUE FALSE FALSE 716.7165956 948.7511198 826.5903514 740.4066481 837.1400834 986.6528016 947.4563814 1002.705909 890.7983978 828.8129757 0.864750694 1.144710746 0.997318304 0.893333804 1.010047029 1.190440824 1.143148586 1.209809618 1.07478819 1 9.69490278 -8.358502303 3.757966467 0.954356257 1.178282165 0.46300963 0.083286679 0.125893491 3.254083976 0.012157007 0.028996383 4.38E-09 8.358502303 0.223925908 KVSQKQSCT(ph)S(ph)HVLAT(ph)DT(ph)EIK ddPTM_HeLa_Romidepsin_16h_R1 1 KVSQKQSCTSHVLATDTEIK 20 2 A0A3B3IU93;A0A3B3ITI0;Q8WYB5-2 A0A3B3IU93 4 0 KVS(0.022)QKQS(0.291)CT(0.941)S(0.84)HVLAT(0.953)DT(0.953)EIK 48.907 0.0042081 0 997.46 848.5 737.27 1255.3 789.68 749.77 857.81 917.13 1155.7 967.04 TRUE FALSE FALSE 985.3025739 860.4452053 750.1018751 1400.443692 749.3796829 701.8621168 930.67236 943.6657096 1052.331297 941.9161614 1.046061862 0.913505087 0.796357368 1.486802913 0.795590641 0.745142875 0.988062843 1.001857435 1.117223953 1 9.879454843 KVSVSES(ph)NVLLDEEVLTDPK ddPTM_HeLa_Romidepsin_16h_R1 2 KVSVSESNVLLDEEVLTDPK 20 1 J3QSG6;H0Y465;P21359-2;P21359-6;P21359 J3QSG6 NF1 Neurofibromin;Neurofibromin truncated 1 0 KVS(0.199)VS(0.199)ES(0.602)NVLLDEEVLT(0.001)DPK;KVS(0.05)VS(0.078)ES(0.872)NVLLDEEVLTDPK ; 114.21 8.60E-05 12505700 13097.9 12135.6 14510.9 13981.9 13418.9 13686.4 13456.6 16642.9 13734.7 12658.6 TRUE FALSE FALSE 12938.25776 12306.4453 14763.45613 15598.55306 12734.08346 12811.88321 14599.60327 17124.43605 12506.23403 12329.72775 1.0493547 0.998111682 1.197387033 1.265117396 1.032795186 1.039105118 1.184097781 1.388873818 1.014315506 1 13.58985332 -4 0.298148144 1.017586149 3.500412638 0.491832559 0.090989289 32.36099468 0.413973893 0.036549798 43.35642618 1.00E-04 4 2.482826489 KVTAEADS(ph)SSPTGILATSESK ddPTM_HeLa_Romidepsin_16h_R1 1 KVTAEADSSSPTGILATSESK 21 1 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 KVT(0.007)AEADS(0.328)S(0.328)S(0.28)PT(0.057)GILATSESK 70.799 0.0018813 31434000 2398.6 2377.2 2376.1 2556.6 2744.7 2485.6 2501.4 2779.9 2368.8 2374.2 TRUE FALSE FALSE 2369.364941 2410.666284 2417.455024 2852.206121 2604.627717 2326.778182 2713.868854 2860.332021 2156.928595 2312.517942 1.024582295 1.042442197 1.045377846 1.233376862 1.126316761 1.006166542 1.173555805 1.236890737 0.932718642 1 11.17524884 -9.447726052 6.558118589 1.015524887 1.146406006 0.546989657 0.066702551 0.15440149 11.17849504 0.009617972 0.014689046 3.57E-10 9.447726052 0.130881119 KVTAEADSS(ph)SPTGILATSESK ddPTM_HeLa_Romidepsin_16h_R1 1 KVTAEADSSSPTGILATSESK 21 1 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 KVT(0.001)AEADS(0.011)S(0.627)S(0.174)PT(0.174)GILAT(0.009)S(0.003)ES(0.002)K 53.625 0.0032718 0 999.24 874.44 826.64 707.51 1139.9 1069.7 939.28 1041.3 1042.2 856.62 TRUE FALSE FALSE 987.0608785 886.7503893 841.0273224 789.3156351 1081.726649 1001.349622 1019.06242 1071.428373 948.9830218 834.3648889 1.183008647 1.062784881 1.007985036 0.946007731 1.296467126 1.200133941 1.221363019 1.284124472 1.137371712 1 9.704534639 -8.74574467 24.99601552 1.071151212 1.24484021 0.647973206 0.069598186 160.3131695 255319.7915 0.012568542 0.025069106 1.80E-09 8.74574467 0.173688998 KVTAEADSSSPT(ph)GILATSESK ddPTM_HeLa_Romidepsin_16h_R1 3 KVTAEADSSSPTGILATSESK 21 1 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 KVTAEADS(0.006)S(0.006)S(0.008)PT(0.977)GILAT(0.001)SESK;KVTAEADS(0.009)S(0.044)S(0.119)PT(0.826)GILAT(0.001)SESK;KVTAEADSS(0.014)S(0.401)PT(0.585)GILATSESK ;; 103.4 0.0001602 73561000 13898.7 14110.2 13498 14581.8 15972.4 17063 15156.9 16455.5 15127.1 14431.2 TRUE FALSE FALSE 13729.2973 14308.84377 13732.92703 16267.81633 15157.26883 15972.72937 16444.32671 16931.61393 13774.09429 14056.27534 0.976737931 1.017968375 0.97699616 1.15733478 1.078327541 1.136341526 1.169892187 1.204559068 0.979924906 1 13.77892674 -8.857163093 0.808471899 0.986968718 1.186346028 0.82210201 0.036098632 0.193172326 0.235081403 0.006338829 0.021175268 1.39E-09 8.857163093 0.19937731 KVTGTEGSSST(ph)LVDYTSTSSTGGSPVR ddPTM_HeLa_Romidepsin_16h_R1 1 KVTGTEGSSSTLVDYTSTSSTGGSPVR 27 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 KVTGTEGSSS(0.004)T(0.352)LVDY(0.095)T(0.2)S(0.029)T(0.007)S(0.019)S(0.019)T(0.029)GGS(0.245)PVR 129.26 3.28E-10 8701100 1567.6 1583.3 1386.2 1473.4 1696.3 1736.1 1403.1 1555.3 1518.7 1244.1 TRUE FALSE FALSE 1548.493488 1605.589739 1410.32623 1643.761441 1609.731481 1625.168813 1522.279279 1600.300152 1382.863668 1211.778103 1.277868848 1.324986592 1.163848585 1.356487163 1.328404497 1.341143902 1.256236002 1.320621447 1.141185556 1 10.24290983 -12.26444791 0.470312294 0.924514882 1.310520632 0.616617076 0.067536236 0.515668948 0.152917721 0.094709055 0.014388526 5.44E-13 12.26444791 0.386005751 KVVDYSQFQES(ph)DDADEDYGR ddPTM_HeLa_Romidepsin_16h_R1 10 KVVDYSQFQESDDADEDYGR 20 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDY(0.001)S(0.002)QFQES(0.996)DDADEDY(0.001)GR;KVVDYSQFQES(1)DDADEDYGR;KVVDYSQFQES(1)DDADEDYGR;KVVDYS(0.001)QFQES(0.999)DDADEDYGR ;;;;;;;;; 138.93 5.55E-12 1423532300 39881.9 40072.6 38239.1 30493.19 36446.88 34710.26 31958.61 36046.48 41037.5 40733.2 TRUE FALSE FALSE 39395.80406 40636.74311 38904.63549 34018.9561 34586.85971 32492.38641 34673.17354 37089.42803 37367.00322 39674.94559 0.992964287 1.024241937 0.98058447 0.857441783 0.871755694 0.818964864 0.873931218 0.934832486 0.94182872 1 15.27594062 -9.313763764 4.853304713 0.998634641 0.868454111 0.751588138 0.033284085 0.058736378 3.066568685 0.004237452 0.006611446 4.86E-10 9.313763764 -0.13018053 KVVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_HeLa_Romidepsin_16h_R1 2 KVVDYSQFQESDDADEDYGRDSGPPTK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 KVVDY(0.001)S(0.003)QFQES(0.994)DDADEDY(0.001)GRDS(0.001)GPPTK;KVVDY(0.011)S(0.012)QFQES(0.955)DDADEDY(0.01)GRDS(0.004)GPPT(0.006)K ; 86.084 2.18E-06 135820000 7083.7 6863.5 6392.3 8867.9 6630.9 6074.1 6272.6 6768.2 7175.3 7610.9 TRUE FALSE FALSE 6997.36114 6960.124533 6503.5553 9893.248323 6292.50043 5685.984613 6805.394487 6964.027189 6533.523197 7413.167721 0.94390973 0.938886694 0.877297742 1.33455072 0.848827474 0.767011462 0.918014369 0.939413143 0.881340264 1 12.85587444 KVVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_HeLa_Romidepsin_16h_R1 1 KVVDYSQFQESDDADEDYGRDSGPPTKK 28 3 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 KVVDYSQFQES(0.999)DDADEDYGRDSGPPTKK 66.613 4.86E-05 116750000 2193.5 2079.4 1594.9 3356.1 1848.5 1459 1610.2 1584.3 1995.5 1673 TRUE FALSE FALSE 2166.764778 2108.673848 1622.658565 3744.148073 1754.164147 1365.774609 1746.970348 1630.139221 1817.017482 1629.535219 1.329682693 1.29403392 0.995779991 2.297678522 1.076481273 0.838137521 1.072066641 1.000370659 1.1150526 1 10.67024482 -8.532179726 24.99984509 1.247214725 0.976533918 0.156877551 0.3582062 359.3994954 966018.1191 0.053436624 0.106986652 2.94E-09 8.532179726 -0.270680807 KVVEAVNS(ph)DSDS(ph)EFGIPK ddPTM_HeLa_Romidepsin_16h_R1 1 KVVEAVNSDSDSEFGIPK 18 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 2 0 KVVEAVNS(0.681)DS(0.333)DS(0.986)EFGIPK 55.302 0.023038 21052000 2583.6 2022.1 2353 2047.4 2102.3 2167.2 2016.7 1913 2762.1 2578.1 TRUE FALSE FALSE 2552.110089 2050.567177 2393.952978 2284.130021 1995.011786 2028.722914 2187.998448 1968.349637 2515.050858 2511.12059 1.01632319 0.816594466 0.953340507 0.909605867 0.794470721 0.807895456 0.871323526 0.783853091 1.001565145 1 11.2941156 -9.711100923 0.717005482 1.011527378 0.816686688 0.637460865 0.052996103 0.268196694 0.279596383 0.012178581 0.021252405 1.94E-10 9.711100923 -0.194840689 KVYEDSGIPLPAES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KVYEDSGIPLPAESPK 16 1 F8W038;H0YIS7;Q8IXM2;Q8IXM2-3;F8W1H0;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 0 KVYEDSGIPLPAES(1)PK;KVYEDS(0.011)GIPLPAES(0.989)PK ; 119.62 0.00086226 126515000 16344.1 17443.5 17931.8 10510.6 10811.9 9840.5 9148.7 10316.6 18474.6 17377.3 TRUE FALSE FALSE 16144.89182 17689.07005 18243.89546 11725.88503 10260.1284 9211.723809 9925.79035 10615.09454 16822.18551 16925.83524 0.953860864 1.045092889 1.077872684 0.692780289 0.606181512 0.544240428 0.586428392 0.627153366 0.993876241 1 14.04693941 -9.115645015 3.975690069 0.990161137 0.59234147 0.958793328 0.041940946 0.03807159 1.04840281 0.007230178 0.01237765 7.66E-10 9.115645015 -0.397819667 KWDGS(ph)EEDEDNSK ddPTM_HeLa_Romidepsin_16h_R1 6 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 KWDGS(1)EEDEDNSK;KWDGS(0.996)EEDEDNS(0.004)K;KWDGS(0.987)EEDEDNS(0.013)K;KWDGS(0.999)EEDEDNS(0.001)K;KWDGS(0.757)EEDEDNS(0.243)K;KWDGS(0.995)EEDEDNS(0.005)K ;;;;; 136.57 0.0023311 83177400 13529.9 13225.8 12908.6 13456.5 15019.5 15583.1 14841.6 15047.3 14972.1 14658.5 TRUE FALSE FALSE 13364.99237 13411.99316 13133.26877 15012.40384 14252.99887 14587.3902 16102.24513 15482.66988 13632.95788 14277.67006 0.936076567 0.939368476 0.919846776 1.051460342 0.998272044 1.021692625 1.127792215 1.084397512 0.954844721 1 13.80147295 -8.130749181 0.98707751 0.965424016 1.117901144 0.683871218 0.036735208 0.362771794 0.549680692 0.006489639 0.0423228 7.40E-09 8.130749181 0.152477128 KWDGSEEDEDNS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 KWDGSEEDEDNSK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 KWDGS(0.123)EEDEDNS(0.877)K 176.43 1.43E-06 53774000 3346.5 3400.9 3110.3 3117.9 3160.6 3576.9 3228.2 3623.6 3369.9 3190.4 TRUE FALSE FALSE 3305.711571 3448.777959 3164.433467 3478.406268 2999.302788 3348.347634 3502.403227 3728.443149 3068.487704 3107.512948 1.063780466 1.109819337 1.018317066 1.119353749 0.965177889 1.077500783 1.127075988 1.199815805 0.987441647 1 11.60154469 -7.592907223 1.974825198 1.038796999 1.202292691 0.538938367 0.047773056 0.240841921 1.537617475 0.006636876 0.05585483 2.55E-08 7.592907223 0.163495692 KWPQGAVPQLPPS(ph)APATSEMTTTPERPR ddPTM_HeLa_Romidepsin_16h_R1 1 KWPQGAVPQLPPSAPATSEMTTTPERPR 28 2 P27708;F8VPD4;H7BZB3 P27708 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 0 KWPQGAVPQLPPS(0.467)APAT(0.107)S(0.107)EMT(0.107)T(0.107)T(0.107)PERPR 71.091 9.72E-05 21890000 2434 2784.1 2763.3 2334.5 2220.3 2143.2 1398.6 1803.4 2623.4 2447.8 TRUE FALSE FALSE 2404.333472 2823.294633 2811.394077 2604.425874 2106.989806 2006.256437 1517.397049 1855.578534 2388.756534 2384.205803 1.008442085 1.184165658 1.179174245 1.092366217 0.883728159 0.841477877 0.636437109 0.778279514 1.001908699 1 11.21929306 -8.318886139 1.957832412 1.038072478 0.716881212 0.750830675 0.083390744 0.150000354 1.102555491 0.01379272 0.041667416 4.80E-09 8.318886139 -0.321191265 KY(ph)IFS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 2 KYIFSVR 7 1 E9PIN0;Q13315 E9PIN0 ATM Serine-protein kinase ATM 2 0 KY(1)IFS(1)VR;KY(1)IFS(1)VR ; 82.305 0.011464 29575000 6200.1 5677.5 6367.1 6278.7 6161.7 6150.6 4702.8 5005.3 5793.8 5088.1 TRUE FALSE FALSE 6124.530796 5757.427994 6477.916705 7004.672836 5847.245457 5757.59651 5102.255715 5150.120458 5275.588017 4955.910429 1.235803367 1.161729631 1.307109319 1.413397788 1.179852933 1.161763634 1.029529445 1.039187559 1.064504311 1 12.2749344 -6.127923018 14.93487264 1.146493312 1.168217432 0 0.126478274 0 0 0.019543658 0 7.45E-07 6.127923018 0.02172412 KY(ph)SAIY(ph)GRFDS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 KYSAIYGRFDSK 12 2 H0Y4C5;B8ZZS2;Q13506-2;Q13506 H0Y4C5 NAB1 NGFI-A-binding protein 1 3 0 KY(0.919)S(0.559)AIY(0.668)GRFDS(0.853)K 54.982 0.004099 0 631.83 519.27 629.64 507.39 608.21 559.41 578.91 653.35 745.36 630.85 TRUE FALSE FALSE 624.1290129 526.5802967 640.5986201 566.0568191 577.1707742 523.6655064 628.082601 672.2536514 678.6931348 614.4604261 1.015735085 0.856980001 1.04253845 0.921225835 0.939313176 0.852236343 1.022169328 1.094055244 1.104535143 1 9.263176287 KYDAFLASES(ph)LIK ddPTM_HeLa_Romidepsin_16h_R1 1 KYDAFLASESLIK 13 1 P62906 P62906 RPL10A 60S ribosomal protein L10a 1 0 KYDAFLAS(0.316)ES(0.684)LIK 60.949 0.02745 6028100 3611.8 3221 2735.2 5991.3 2538.4 3175 3403.7 3317.5 3987.3 3007 TRUE FALSE FALSE 3567.777992 3266.345323 2782.805009 6684.042296 2408.855976 2972.127747 3692.810193 3413.486628 3630.665902 2928.877707 1.21813826 1.115220794 0.950126734 2.282117236 0.822450173 1.014766762 1.260827717 1.165458913 1.239609934 1 11.51613224 -11.95855838 0.603614577 0.98415048 1.238854523 0 0.383055914 2.590295088 1.609664541 0.345902183 0.087619703 1.10E-12 11.95855838 0.254704043 KYDEELEER ddPTM_HeLa_Romidepsin_16h_R1 1 KYDEELEER 9 1 E9PJ32;Q01995 E9PJ32 TAGLN Transgelin 0 0 93.442 0.023576 46804000 5545.7 5742.4 5832 4544.9 5605.5 5892.6 4719.2 5161.4 5684.3 5737 FALSE FALSE TRUE 5478.106875 5823.241658 5933.503514 5070.402722 5319.430418 5516.081877 5120.04873 5310.736966 5175.881971 5587.951913 0.980342523 1.042106616 1.061838685 0.907381238 0.951946348 0.987138394 0.916265711 0.950390599 0.926257429 1 12.44810389 -9.244651037 24.99961615 1.000002455 0.944150965 0.362481631 0.039368193 647.7199863 964524.0661 0.005065569 0.008384056 5.69E-10 9.244651037 -0.05585149 KYEEIDNAPEER ddPTM_HeLa_Romidepsin_16h_R1 2 KYEEIDNAPEER 12 1 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 0 ; ; 111.31 0.0029104 12482000 2444.1 2893 2645 2267.6 2878.5 3264.9 2226 2754.6 2847.4 2675.8 FALSE FALSE TRUE 2414.310369 2933.72773 2691.035115 2529.790581 2731.599404 3056.283427 2415.076384 2834.300005 2592.721413 2606.28233 0.926342607 1.125636964 1.032518651 0.970651012 1.048082693 1.172660149 0.926636518 1.087487711 0.994796835 1 11.34777766 -10.27928897 24.98577735 0.965217343 1.047752701 0.20787964 0.069057018 853.2801868 1194413.856 0.011607701 0.013287216 5.26E-11 10.27928897 0.082535359 KYEQGFITDPVVLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 KYEQGFITDPVVLSPK 16 1 P12268;H0Y4R1 P12268 IMPDH2 Inosine-5-monophosphate dehydrogenase 2 1 0 KYEQGFITDPVVLS(1)PK;KYEQGFITDPVVLS(0.999)PK ; 113.78 0.0008878 55837000 8006.8 7874.4 8738.8 6069.4 8359.7 9077.1 8456.5 9206 8348.4 8131.3 TRUE FALSE FALSE 7909.210042 7985.25601 8890.895148 6771.172585 7933.073315 8497.102605 9174.794899 9472.361085 7601.698195 7920.047654 0.998631623 1.008233329 1.122581017 0.854940889 1.001644644 1.072860035 1.158426729 1.195997991 0.959804603 1 12.9512934 -7.879420714 2.238412929 0.998801018 1.189038476 0.590307542 0.061612461 0.156984856 1.524044911 0.008149118 0.036015886 1.32E-08 7.879420714 0.190237458 KYES(ph)DEDS(ph)LGSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 2 0 KY(0.016)ES(0.689)DEDS(0.887)LGS(0.304)S(0.105)GR 73.758 0.0041964 0 1515.8 1453.2 1438.9 897.62 1516.7 1013.6 865.4 1161.1 1565.7 1709 TRUE FALSE FALSE 1497.324847 1473.658188 1463.943451 1001.407048 1439.297139 948.8342312 938.9070544 1194.694597 1425.659871 1664.599934 0.899510337 0.885292711 0.879456632 0.601590225 0.864650485 0.570007371 0.564043669 0.717706743 0.856457964 1 10.70095977 -9.321535629 0.520707144 0.977596182 0.594223579 0.586269549 0.09604596 0.381903975 0.200648632 0.023181429 0.062790279 4.77E-10 9.321535629 -0.383372602 KYES(ph)DEDSLGSSGR ddPTM_HeLa_Romidepsin_16h_R1 1 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 0 KY(0.123)ES(0.815)DEDS(0.034)LGS(0.008)S(0.021)GR 61.524 0.024801 25009000 1433.9 1440.9 1352.2 1273.5 1294.7 1061.4 1214.5 1434.8 1666.7 1428.2 TRUE FALSE FALSE 1416.423075 1461.185028 1375.734474 1420.748062 1228.626628 993.5799655 1317.6596 1476.313674 1517.626178 1391.095158 1.018207178 1.05038467 0.988957848 1.02131623 0.883208184 0.71424299 0.947210255 1.061260019 1.090957846 1 10.4420054 -8.760943538 24.99815788 1.011438504 0.891372668 0.336198215 0.084876892 11.78173793 593927.9913 0.011821811 0.02254258 1.73E-09 8.760943538 -0.120065835 KYESDEDS(ph)LGSSGR ddPTM_HeLa_Romidepsin_16h_R1 2 KYESDEDSLGSSGR 14 1 O00418 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 0 KYES(0.001)DEDS(0.71)LGS(0.282)S(0.007)GR;KYES(0.044)DEDS(0.899)LGS(0.014)S(0.044)GR ; 182.7 3.12E-07 33829000 1662.3 1573.15 1379.94 1485.68 1585 1402.68 1344.34 1366.76 1859.34 1669.56 TRUE FALSE FALSE 1642.039248 1595.296847 1403.957277 1657.461312 1504.111536 1313.053275 1458.528206 1406.305044 1693.035974 1626.184591 1.009749605 0.981006004 0.863344349 1.019233193 0.924932842 0.807444175 0.896901997 0.864788077 1.041109345 1 10.66727531 -8.924820167 0.598580757 1.006323616 0.8480696 0.563404 0.050247161 0.525428197 0.329757429 0.010696306 0.040507063 1.19E-09 8.924820167 -0.158254016 KYGELPPIEKPVDPPPFMFKPVK ddPTM_HeLa_Romidepsin_16h_R1 1 KYGELPPIEKPVDPPPFMFKPVK 23 3 A0A590UJ84;B1AKN3;Q9P2R6;A0A075B770 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 0 0 41.912 0.0043426 0 399.32 332.57 432.65 252.42 437.95 268.17 468.81 276.87 432.2 327.69 FALSE FALSE TRUE 394.4529342 337.2519292 440.1800918 281.6059881 415.5997773 251.0348025 508.6307097 284.8807966 393.5429495 319.1765666 1.235845534 1.056631233 1.379111557 0.882289045 1.302099906 0.786507622 1.593571593 0.892549223 1.232994495 1 8.318210925 -12.53692963 1.295629739 0.999919663 1.157089814 0 0.247140598 1.050865872 3.156444055 0.144904664 0.034442022 2.90E-13 12.53692963 0.157170152 KYGGSVGSQPPPVAPEPGPVPS(ph)SPSQEPPTKR ddPTM_HeLa_Romidepsin_16h_R1 1 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;E9PJ81;E9PRQ7;Q04323;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 0 KYGGSVGSQPPPVAPEPGPVPS(0.45)S(0.45)PS(0.067)QEPPT(0.033)KR 57.287 0.00057501 26337000 3006.5 2455 2608 3697.8 4031.7 3803 3320.5 3864 2678.6 2643.1 TRUE FALSE FALSE 2969.855622 2489.561554 2653.391146 4125.357035 3825.947305 3560.000574 3602.543187 3975.798744 2439.019307 2574.431881 1.153596506 0.967033377 1.030670559 1.602433945 1.486132662 1.382829587 1.399354636 1.544340238 0.947400988 1 11.33003838 -9.269903528 24.99858274 1.061929135 1.472977228 0.881437503 0.084207378 171.8682878 507606.6548 0.013516512 0.020853469 5.37E-10 9.269903528 0.411048093 KYGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_HeLa_Romidepsin_16h_R1 1 KYGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 32 2 A0A087WTZ5;E9PJ81;E9PRQ7;Q04323;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 0 KYGGSVGSQPPPVAPEPGPVPS(0.365)S(0.519)PS(0.085)QEPPT(0.032)KR 51.234 0.0045059 24332000 2471.6 2189 2332.4 2635.6 2781 2917.7 2888.2 3027.2 2351 2429 TRUE FALSE FALSE 2441.475189 2219.816799 2372.994444 2940.340473 2639.075193 2731.268386 3133.523636 3114.787256 2140.720672 2365.89423 1.031946043 0.93825699 1.00300107 1.242803011 1.115466262 1.154433851 1.32445635 1.316536985 0.90482518 1 11.20816986 -8.102510653 0.583314685 1.005145424 1.402021587 0.755495415 0.071495093 0.604169175 0.242553392 0.012963454 0.134778833 7.90E-09 8.102510653 0.396876163 KYIEIDS(ph)DEEPRGELLSLR ddPTM_HeLa_Romidepsin_16h_R1 1 KYIEIDSDEEPRGELLSLR 19 2 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 0 KYIEIDS(0.999)DEEPRGELLS(0.001)LR 81.224 0.0075057 19963000 1035 788.45 814.08 1302.2 782.3 1114.6 961.24 798.41 1177.8 1188.8 TRUE FALSE FALSE 1022.385022 799.5498198 828.2487209 1452.766491 742.3763118 1043.380657 1042.887702 821.5107337 1072.454618 1157.914805 0.88295358 0.690508332 0.715293317 1.254640225 0.641132067 0.90108586 0.900660133 0.709474247 0.926194754 1 10.17731339 -11.45434957 0.987451275 0.984848436 0.841594307 0.078539422 0.167306088 0.762177194 1.527414794 0.054949548 0.032547514 3.51E-12 11.45434957 -0.143254128 KYTGEDFDEDLR ddPTM_HeLa_Romidepsin_16h_R1 2 KYTGEDFDEDLR 12 1 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 ; ; 132.86 0.0019962 29220000 10426.5 10138.2 11192.3 10912.1 10967.5 11387.5 9913 11440.4 11852.7 10363.6 FALSE FALSE TRUE 10299.41781 10280.92585 11387.09729 12173.80834 10407.78755 10659.8755 10755.00997 11771.40992 10792.56483 10094.35218 1.020314888 1.018482976 1.128066179 1.206001943 1.031050568 1.056023736 1.065448261 1.166138224 1.069168644 1 13.30126071 -9.801756231 7.950349945 1.010382795 1.105277232 0.350305488 0.052546391 0.158028665 26.91002194 0.008073995 0.010676542 1.58E-10 9.801756231 0.094894437 KYTLENKEEGSLSDTEADAVS(ph)GQLPDPTTNPSAGK ddPTM_HeLa_Romidepsin_16h_R1 1 KYTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 35 2 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 0 KY(0.022)T(0.022)LENKEEGS(0.017)LS(0.115)DT(0.213)EADAVS(0.562)GQLPDPT(0.022)T(0.022)NPS(0.004)AGK 45.518 0.0072864 60097000 3773.1 3324.9 3248.5 3304.9 3749.7 3650.5 3189.7 3417.2 3593.4 3854.3 TRUE FALSE FALSE 3727.112006 3371.708029 3305.03878 3687.028088 3558.338817 3417.244831 3460.633038 3516.071291 3271.997304 3754.16473 0.992793943 0.898124689 0.880365945 0.982116756 0.947837688 0.910254365 0.921811718 0.936578851 0.871564659 1 11.87427624 -10.28252684 19.80370699 0.996597219 0.925909894 0 0.047456518 27.67944716 25994.13614 0.004575121 0.00523911 5.22E-11 10.28252684 -0.070687325 LAAAEETAVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LAAAEETAVSPR 12 0 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 0 LAAAEETAVS(1)PR;LAAAEETAVS(1)PR ; 146.67 0.0014954 246460000 5815.5 5800.6 5964 4314.4 4511.7 4280.6 3431.3 4209 6000.8 6208.6 TRUE FALSE FALSE 5744.618449 5882.260999 6067.800918 4813.251228 4281.451114 4007.083475 3722.754536 4330.780774 5464.073419 6047.299677 0.949947705 0.972708699 1.003390148 0.795933968 0.707993872 0.662623599 0.615606094 0.716151176 0.903555919 1 12.56207536 -9.005702132 2.172762159 0.977902729 0.665247419 0.925876293 0.038698499 0.044827418 0.42256967 0.005034008 0.009696271 9.87E-10 9.005702132 -0.31265531 LAAFADALEFADEEKESPVEFTGHK ddPTM_HeLa_Romidepsin_16h_R1 1 LAAFADALEFADEEKESPVEFTGHK 25 1 Q5SY16 Q5SY16 NOL9 Polynucleotide 5-hydroxyl-kinase NOL9 0 0 65.833 0.00062922 3161100 676.4 637.63 610.6 756.53 619.54 903.72 683.05 508.21 744.39 896.41 FALSE FALSE TRUE 668.1557766 646.6065719 621.2272369 844.0035582 587.922562 845.9752086 741.06825 522.9142545 677.809894 873.121139 0.7652498 0.740569141 0.711501771 0.966651156 0.673357379 0.96890932 0.848757654 0.598902296 0.776306819 1 9.770038021 -12.22079042 0.899344944 1.003404537 0.79047522 0 0.1313032 0.545176508 0.773797998 0.077340082 0.02026982 6.01E-13 12.22079042 -0.212929317 LAAGRPFNT(ph)YPR ddPTM_HeLa_Romidepsin_16h_R1 1 LAAGRPFNTYPR 12 1 O96013 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 0 LAAGRPFNT(0.999)Y(0.001)PR 126.12 0.022819 19625000 1323.6 1351.9 1410.9 1200.4 1646.3 1645.3 1124.4 1497.3 1315.2 1040.3 TRUE FALSE FALSE 1307.467454 1370.932084 1435.456123 1339.195896 1562.283168 1540.17064 1219.906508 1540.622013 1197.565218 1013.272856 1.290340945 1.352974251 1.41665309 1.321653776 1.541818828 1.519995953 1.203926959 1.520441413 1.181878317 1 9.984807003 -11.50778232 0.436967378 0.957937631 1.436915508 0.559812616 0.109702942 0.472742174 0.182464655 0.098519873 0.034590452 3.11E-12 11.50778232 0.478977877 LAAPSVSHVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LAAPSVSHVSPR 12 0 Q8WXE1-5;A0A0U1RRM7;A0A0U1RQW3;A0A0U1RQJ8;Q8WXE1-3;Q8WXE1-2;Q8WXE1 Q8WXE1-5 ATRIP ATR-interacting protein 1 0 LAAPS(0.001)VS(0.044)HVS(0.954)PR;LAAPSVS(0.008)HVS(0.992)PR ; 94.461 0.0094145 10067000 5336.8 4945.7 4702.5 4366 5043.9 5108.3 3681 3829.4 8153.5 6763.7 TRUE FALSE FALSE 5271.753029 5015.325694 4784.34504 4870.817463 4786.490962 4781.896116 3993.664048 3940.197647 7424.230539 6587.978099 0.800208038 0.761284512 0.72622358 0.739349371 0.726549313 0.725851854 0.606204816 0.598089063 1.126936129 1 12.68562004 -16.52287875 0.05805738 2.234122018 0.168734584 0.900262621 0.0492446 45.8186858 0.209232063 8.210007734 1.627940355 3.00E-17 16.52287875 -2.065387434 LAAQESS(ph)EAEDMSVPR ddPTM_HeLa_Romidepsin_16h_R1 1 LAAQESSEAEDMSVPR 16 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;Q5SRD0 A0A0A0MR88 FAM21C;FAM21D WASH complex subunit FAM21C;Putative WASH complex subunit FAM21 1 0 LAAQES(0.226)S(0.774)EAEDMSVPR 103.77 0.0063458 2790100 1454.3 1400.3 1341.1 1263.1 1654.7 1185.7 1197.4 1537.9 1473.2 1584.2 TRUE FALSE FALSE 1436.574432 1420.01346 1364.441283 1409.145565 1570.254484 1109.937597 1299.107126 1582.39671 1341.433302 1543.042256 0.931001356 0.92026868 0.884253998 0.913225519 1.01763544 0.719317694 0.841912865 1.025504457 0.869343207 1 10.59156185 -11.34220693 0.367632747 1.014395276 0.884820145 0 0.0910264 1.932025121 0.581856584 0.102508915 0.041670917 4.55E-12 11.34220693 -0.129575131 LAAQESS(ph)ETEDMSVPR ddPTM_HeLa_Romidepsin_16h_R1 2 LAAQESSETEDMSVPR 16 0 F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 F8W7U3 FAM21A WASH complex subunit FAM21A 1 0 LAAQES(0.127)S(0.804)ET(0.069)EDMSVPR;LAAQES(0.119)S(0.871)ET(0.01)EDMSVPR ; 131.61 0.0025665 19104900 6277 6437.4 6526.9 6000.2 7481.9 7990 6383.6 7272.7 6476.4 6335.5 TRUE FALSE FALSE 6200.49351 6528.025886 6640.497957 6693.971356 7100.070724 7479.464787 6925.822825 7483.1241 5897.134564 6170.902797 1.0047952 1.057872098 1.076098292 1.084763701 1.150572446 1.212053574 1.122335427 1.212646568 0.955635627 1 12.59126585 -9.222209623 0.743848379 0.999638795 1.187935984 0.866806571 0.030374056 0.143976816 0.155255241 0.005117908 0.012946137 6.00E-10 9.222209623 0.188297189 LAAQLGAPTS(ph)PIPDSAIVNTR ddPTM_HeLa_Romidepsin_16h_R1 2 LAAQLGAPTSPIPDSAIVNTR 21 0 B8ZZS4;Q9H8Y5 B8ZZS4 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 0 LAAQLGAPT(0.351)S(0.649)PIPDSAIVNTR;LAAQLGAPT(0.342)S(0.658)PIPDSAIVNTR ; 220.82 9.82E-42 21953700 4750.5 4278.2 4394.8 1631.44 6876.9 8070.9 6199.4 7496.1 5399.6 4524.4 TRUE FALSE FALSE 4692.599079 4338.428612 4471.28965 1820.074769 6525.946132 7555.195538 6725.976881 7712.987827 4916.646252 4406.855436 1.064840712 0.984472642 1.014621359 0.413009865 1.480862313 1.714418739 1.526253125 1.750224835 1.115681312 1 12.10553386 -8.542477214 24.97891634 0.985928135 1.641185438 0.747808819 0.195648666 86.06449229 109691.7803 0.026802371 0.053609912 2.87E-09 8.542477214 0.655257303 LAAVDATVNQVLAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 LAAVDATVNQVLASR 15 0 Q15084-3;Q15084;Q15084-4;Q15084-5;Q15084-2 Q15084-3 PDIA6 Protein disulfide-isomerase A6 1 0 LAAVDAT(0.011)VNQVLAS(0.989)R 81.992 0.0041465 0 392.15 338.23 326.01 245.15 516.53 453.4 404.29 550.94 418.73 500.85 TRUE FALSE FALSE 387.370325 342.9916108 331.6840673 273.4953965 490.1695467 424.4292033 438.6303825 566.8805797 381.2777401 487.8378448 0.794055502 0.703085286 0.679906389 0.560627675 1.004779666 0.870021069 0.899131519 1.162026656 0.781566547 1 8.930257872 -6.747128269 1.383169099 0.849783706 1.868073649 0.346020783 0.13735745 5.064099804 3.175892204 0.023445189 10.21919264 1.79E-07 6.747128269 1.018289943 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR ddPTM_HeLa_Romidepsin_16h_R1 1 LADDVDLEQVANETHGHVGADLAALCSEAALQAIR 35 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 45.56 0.0075015 8152200 849.63 784.2 631.97 496.24 691.15 866.75 775.49 871.33 999.76 889.41 FALSE FALSE TRUE 839.2743828 795.2399882 642.9691728 553.6176037 655.8780365 811.3674723 841.3601012 896.5405588 910.3389617 866.303 0.968800042 0.917969796 0.742198945 0.639057701 0.757100041 0.936586243 0.971207651 1.034904137 1.050832055 1 9.758727903 -10.05354138 3.935138714 0.984656979 0.842119578 0.279225915 0.112564069 0.260350344 8.233405862 0.020490835 0.025811188 8.84E-11 10.05354138 -0.142537402 LADFGVLHR ddPTM_HeLa_Romidepsin_16h_R1 2 LADFGVLHR 9 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 ; ; 159.28 0.0017621 21709000 20767.4 16760.9 27415 18335.2 30201 25881 21425 13440.6 16709.9 11967.6 FALSE FALSE TRUE 20514.27894 16996.86039 27892.14657 20455.20209 28659.73027 24227.28763 23244.83897 13829.48256 15215.32469 11656.68003 1.759873214 1.458121897 2.392803655 1.754805146 2.45865291 2.078403763 1.994121732 1.186399775 1.305288012 1 13.50886933 -11.70246914 0.525094965 0.939501092 1.968327187 0.383347122 0.372057879 0.662159436 0.341194377 0.323294492 0.099509323 1.98E-12 11.70246914 1.028826096 LADK(ac)YPVVHIGK ddPTM_HeLa_Romidepsin_16h_R1 1 LADKYPVVHIGK 12 1 C9JXZ0;E7ETU9;O00469;O00469-2 C9JXZ0 PLOD2 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2" 0 1 LADK(1)YPVVHIGK 62.338 0.026662 0 0 0 0 0 332.49 0 59.956 169.98 125.35 0 FALSE TRUE FALSE 0 0 0 0 315.5217946 0 65.04866114 174.8981031 114.1383821 0 0 LADSGDGAGPS(ph)PEEKDFLK ddPTM_HeLa_Romidepsin_16h_R1 2 LADSGDGAGPSPEEKDFLK 19 1 Q92917 Q92917 GPKOW G patch domain and KOW motifs-containing protein 1 0 LADSGDGAGPS(1)PEEKDFLK;LADS(0.006)GDGAGPS(0.994)PEEKDFLK ; 66.906 0.006885 172408000 5328.6 5322.2 5015.4 5093.4 5142.8 5237.1 4745.5 5424.7 5458.6 5411.8 TRUE FALSE FALSE 5263.652974 5397.126071 5102.690933 5682.322873 4880.343726 4902.466212 5148.582652 5581.655136 4970.369145 5271.200656 0.998568128 1.023889323 0.968032004 1.077994037 0.925850493 0.930047352 0.976738126 1.05889635 0.942929224 1 12.3639159 -8.711162144 24.99999257 1.003665104 0.970098907 0.080811402 0.047352887 175.2783622 87155.02613 0.005958858 0.011917706 1.94E-09 8.711162144 -0.033566197 LAEAFAEELHER ddPTM_HeLa_Romidepsin_16h_R1 2 LAEAFAEELHER 12 0 B1ANE3;Q99707-2;Q99707 B1ANE3 MTR Methionine synthase 0 0 ; ; 158.58 0.00038797 1288300 2061.09 2472.1 2199.36 1768.2 2687.6 2452.2 1640.23 1918.33 2911 2310.9 FALSE FALSE TRUE 2035.968642 2506.902289 2237.638938 1972.647604 2550.441743 2295.512334 1779.551095 1973.833852 2650.632869 2250.862485 0.904528222 1.113751864 0.99412512 0.876396322 1.133095318 1.019836773 0.790608537 0.876923342 1.177607645 1 11.1362622 -7.76193768 24.99999678 0.978758803 0.833765918 0.283697428 0.101819382 10.911177 547578.9346 0.011635686 0.038358354 1.73E-08 7.76193768 -0.144992884 LAEAPSPAPTPSPTPVEDLGPQTSTSPGRLS(ph)PDFAEELR ddPTM_HeLa_Romidepsin_16h_R1 1 LAEAPSPAPTPSPTPVEDLGPQTSTSPGRLSPDFAEELR 39 1 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 LAEAPSPAPT(0.005)PS(0.006)PT(0.022)PVEDLGPQT(0.095)S(0.095)T(0.095)S(0.095)PGRLS(0.588)PDFAEELR 53.408 0.001314 8020100 2009.1 2419.5 1752.5 1729.6 2938.7 2610.5 2413.4 2397.4 2263.6 2495.8 TRUE FALSE FALSE 1984.612316 2453.561785 1783.001527 1929.58449 2788.727173 2443.697475 2618.394136 2466.764987 2061.137947 2430.958756 0.816390781 1.009297989 0.733456099 0.793754516 1.147171735 1.005240204 1.07710348 1.014729263 0.847870389 1 11.2473097 -8.758393702 24.99989686 0.896819041 1.058219832 0.508037726 0.090796265 67.05701445 550415.2988 0.015001705 0.029002706 1.74E-09 8.758393702 0.16140079 LAEDEAFQRR ddPTM_HeLa_Romidepsin_16h_R1 1 LAEDEAFQRR 10 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 99.013 0.0022813 0 2766.9 2993.7 2766.9 3380.8 3094.2 3279.8 2932.2 2913.5 2903.1 2812.5 FALSE FALSE TRUE 2733.175959 3035.845387 2815.056734 3771.704003 2936.291428 3070.231365 3181.260995 2997.797526 2643.439465 2739.430845 0.997716721 1.108202966 1.027606424 1.376820302 1.071861855 1.1207552 1.161285382 1.094314 0.964959371 1 11.41966047 -9.935954125 1.708692809 0.998671141 1.153766051 0.392422291 0.08716907 0.251477024 1.46602811 0.014365275 0.019390645 1.16E-10 9.935954125 0.15509491 LAEDEGDS(ph)EPEAVGQSR ddPTM_HeLa_Romidepsin_16h_R1 2 LAEDEGDSEPEAVGQSR 17 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 LAEDEGDS(1)EPEAVGQSR;LAEDEGDS(1)EPEAVGQSR ; 174.4 9.59E-07 463120000 7895.5 7600.6 6695.1 5879.1 5194.9 4879.7 4132.2 4205.4 8599.3 8149.3 TRUE FALSE FALSE 7799.266609 7707.601446 6811.625407 6558.869204 4929.784868 4567.902919 4483.188965 4327.076614 7830.157071 7937.580011 0.982574865 0.971026615 0.858148881 0.826305901 0.621068999 0.575478031 0.564805515 0.545138015 0.986466538 1 12.95448351 -8.970848679 1.018090965 0.993275697 0.540105628 0.98282236 0.024296228 0.039194689 0.07964346 0.003826714 0.009928105 1.07E-09 8.970848679 -0.453170069 TSVSQNVIPSS(ph)AQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSVSQNVIPSSAQK 14 0 H0Y8J2;Q03188;Q03188-2 H0Y8J2 CENPC Centromere protein C 1 0 TSVSQNVIPS(0.005)S(0.995)AQK 162.46 0.00023413 9605200 3893.2 3253.5 3719.1 2727.3 2025.6 1879.8 1381.2 1458.1 3341 3429.6 TRUE FALSE FALSE 3845.748181 3299.302858 3783.829375 3042.643258 1922.226073 1759.686847 1498.519094 1500.287823 3042.172592 3340.498498 1.151249786 0.987667817 1.132713988 0.910835093 0.575430905 0.526773728 0.448591459 0.449120939 0.910694196 1 11.70584769 -8.793844353 2.203895385 1.070496539 0.473349461 0.924760993 0.072813066 0.047300025 0.468550527 0.010020918 0.021295728 1.61E-09 8.793844353 -0.597147078 down LAGES(ph)ESNLR ddPTM_HeLa_Romidepsin_16h_R1 1 LAGESESNLR 10 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 1 0 LAGES(0.924)ES(0.076)NLR 97.163 0.028142 4742400 803.02 913.24 907.17 621.19 849.88 914.08 778.02 930.87 999.7 955.73 TRUE FALSE FALSE 793.2324834 926.0966167 922.9589133 693.0149106 806.5074523 855.6732381 844.1049994 957.8032548 910.2843282 930.8999968 0.852113531 0.994840069 0.991469456 0.744456884 0.866373891 0.919189216 0.906762275 1.028900266 0.977854046 1 9.862482382 -12.56232306 1.310989562 1.000449496 0.903608102 0.120037706 0.078550754 0.661858376 2.023185842 0.057264257 0.013212432 2.74E-13 12.56232306 -0.096841394 LAGMSIS(ph)RATSNARTS(ph)TAGSGA ddPTM_HeLa_Romidepsin_16h_R1 1 LAGMSISRATSNARTSTAGSGA 22 2 M0R093 M0R093 MRPL34 2 0 LAGMS(0.003)IS(0.593)RAT(0.202)S(0.202)NART(0.141)S(0.415)T(0.415)AGS(0.029)GA 63.292 0.016967 6316000 985.83 1193.9 972.07 960.6 1182.7 1186.5 1026.2 1117.1 1269.6 1182 TRUE FALSE FALSE 973.8143248 1210.707756 988.9884706 1071.669092 1122.342406 1110.686479 1113.365402 1149.421526 1156.043796 1151.29147 0.845845166 1.051608379 0.859025274 0.930840817 0.974855139 0.964730921 0.967057806 0.998375786 1.004127822 1 10.16903741 -8.762355496 10.5992195 0.930416597 0.974792844 0 0.061586556 0.188015276 503.3389548 0.010073018 0.019128137 1.73E-09 8.762355496 0.044376247 AGGK(ac)AGK(ac)DSGK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 4 AGGKAGKDSGKAK 13 3 P0C0S5;A0A494C189;Q71UI9;C9J0D1;Q71UI9-3;Q71UI9-2;C9J386;Q71UI9-5 P0C0S5;Q71UI9 H2AFZ;H2AFV Histone H2A.Z;Histone H2A.V;Histone H2A 0 3 ;;; AGGK(1)AGK(1)DSGK(1)AK;AGGK(1)AGK(1)DSGK(1)AK;AGGK(1)AGK(1)DSGK(1)AK;AGGK(1)AGK(1)DSGK(1)AK 202.18 1.45E-33 3956750000 640.37 1074.2 1127.113 10625.62 31967.6 34780.6 33226.7 34686 235.275 927.97 FALSE TRUE FALSE 632.5649241 1089.322616 1146.729929 11854.20418 30336.17408 32558.23191 36048.97507 35689.58468 214.2314147 903.8612056 0.69984741 1.20518793 1.268701347 13.11507132 33.56286772 36.02127374 39.88330824 39.48569146 0.237018044 1 9.819957443 -8.852315552 1.951527434 0.823048884 38.8074348 0.99611393 1.07592546 0.01327216 0.102639767 0.167388516 0.355630017 1.41E-09 8.852315552 37.98438591 up LAIEAGFR ddPTM_HeLa_Romidepsin_16h_R1 1 LAIEAGFR 8 0 S4R3Z2;A0A0A0MSS8;P42330;S4R3D5;P17516 S4R3Z2 AKR1C3;AKR1C4 Aldo-keto reductase family 1 member C3;Aldo-keto reductase family 1 member C4 0 0 116.88 0.015749 7108900 1641.3 1240.4 2492.1 1274.2 2489.4 2181.5 1597.3 1041.7 1071.5 745.64 FALSE FALSE TRUE 1621.295204 1257.862384 2535.473955 1421.528999 2362.356629 2042.10919 1732.974622 1071.839946 975.6623564 726.2681653 2.23236441 1.731953077 3.491098848 1.957305947 3.252733276 2.811783977 2.38613601 1.475818433 1.34339133 1 9.504358533 -11.75764723 0.547148364 0.906971262 2.527219676 0.407947501 0.603479366 0.660599198 0.362656112 0.520245609 0.15448955 1.75E-12 11.75764723 1.620248413 LAILGIHNEVSK ddPTM_HeLa_Romidepsin_16h_R1 1 LAILGIHNEVSK 12 0 P12814-2;P12814;P12814-3;P12814-4;H9KV75;H7C5W8 P12814-2 ACTN1 Alpha-actinin-1 0 0 105.17 0.0023467 554670 667.54 509.52 913.52 504.59 1118.8 1162.4 603.41 827.61 572.89 659.19 FALSE FALSE TRUE 659.4037657 516.6930359 929.4194324 562.93307 1061.703461 1088.126391 654.6636303 851.5555896 521.6492836 642.0641488 1.027006051 0.804737403 1.447549181 0.876755183 1.653578483 1.694731583 1.0196234 1.326278054 0.812456644 1 9.326573634 -9.230667697 1.42817278 1.005767726 1.383254887 0.338850728 0.260920634 0.365080365 1.460467098 0.040011757 0.076296576 5.88E-10 9.230667697 0.377487161 LAIQGPEDS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 0 LAIQGPEDS(0.5)PS(0.5)R;LAIQGPEDS(0.5)PS(0.5)R ; 164.93 0.00031411 464247000 10646.9 11322.2 10321.4 8179.4 11404 12033.2 10440.1 11546 11347.6 10039.4 TRUE FALSE FALSE 10517.13149 11481.59423 10501.03964 9125.140713 10822.01133 11264.31736 11326.88183 11880.06529 10332.64224 9778.574941 1.075528035 1.174158228 1.073882411 0.933176947 1.106706385 1.151938542 1.15833666 1.214907629 1.056661354 1 13.25540852 -4 0.260633874 1.025360722 2.281855964 0.400967156 0.062657756 34.8738667 0.439401298 0.033552313 19.72400476 1.00E-04 4 1.256495242 LAIQGPEDSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 LAIQGPEDSPSR 12 0 Q15773 Q15773 MLF2 Myeloid leukemia factor 2 1 0 LAIQGPEDS(0.227)PS(0.773)R;LAIQGPEDS(0.088)PS(0.912)R ; 193.45 3.10E-10 455992000 10365 10003.9 8841.9 7688.1 9090.7 10116.4 9636.4 9420.7 9624.3 8681.6 TRUE FALSE FALSE 10238.66739 10144.73517 8995.78956 8577.034296 8626.767657 9469.994689 10454.91558 9693.273091 8763.478503 8456.05078 1.210809592 1.199701306 1.063828706 1.014307331 1.020188724 1.1199075 1.23638278 1.146312072 1.036355946 1 13.04576833 -12.57317917 1.379845146 1.000616081 1.134575482 0.24831238 0.073671505 0.472676007 1.625145294 0.057874364 0.013822371 2.67E-13 12.57317917 0.133959401 LALDGETLGEEEQEDEQPPWAS(ph)PSPTSR ddPTM_HeLa_Romidepsin_16h_R1 1 LALDGETLGEEEQEDEQPPWASPSPTSR 28 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 LALDGETLGEEEQEDEQPPWAS(0.821)PS(0.162)PT(0.011)S(0.007)R 163.58 2.03E-14 5370900 1219 1061.3 1075.4 811.87 1260.9 1168.8 838.07 1048.4 1131 1218.1 TRUE FALSE FALSE 1204.142359 1076.241009 1094.116886 905.7422294 1196.551568 1094.117452 909.2556449 1078.7338 1029.840527 1186.453586 1.014908946 0.907107553 0.922174199 0.763403002 1.008511063 0.922174676 0.766364277 0.909208596 0.867999001 1 10.21243995 -10.12131908 2.52611368 1.007524777 0.879221248 0.078146246 0.082016189 0.200548031 2.474636674 0.011555517 0.014412309 7.56E-11 10.12131908 -0.128303529 LALK(ac)TLSK ddPTM_HeLa_Romidepsin_16h_R1 1 LALKTLSK 8 1 I3L1Q5;Q2NL82 I3L1Q5 TSR1 Pre-rRNA-processing protein TSR1 homolog 0 1 LALK(1)TLSK 113.71 0.0091647 688380 215.28 279.13 1915.4 305.28 845.77 974.15 726.91 31.086 262.4 0 FALSE TRUE FALSE 212.6560846 283.0595995 1948.736734 340.57791 802.6072009 911.9049589 788.6537173 31.98542436 238.9302868 0 0 LALPGHAESYNPPPEYLLS(ph)EEER ddPTM_HeLa_Romidepsin_16h_R1 1 LALPGHAESYNPPPEYLLSEEER 23 0 Q14137-2;Q14137 Q14137-2 BOP1 Ribosome biogenesis protein BOP1 1 0 LALPGHAESYNPPPEY(0.008)LLS(0.992)EEER 75.512 0.00037167 4584000 1153.8 1137.3 1309.4 992.1 1345.8 1495.1 1255.9 1248.5 1476.4 1410 TRUE FALSE FALSE 1139.737042 1153.310939 1332.189558 1106.81127 1277.118804 1399.567935 1362.576115 1284.623378 1344.347086 1373.367997 0.829884666 0.839768323 0.970016457 0.805910195 0.929917405 1.019077144 0.992142032 0.935381763 0.978868802 1 10.42350254 -8.508342526 23.87756832 0.906612431 0.981744973 0.224179608 0.064892106 528.073065 867424.8187 0.01117561 0.024134621 3.10E-09 8.508342526 0.075132542 LALS(ph)PLSLGK ddPTM_HeLa_Romidepsin_16h_R1 2 LALSPLSLGK 10 0 P49454 P49454 CENPF Centromere protein F 1 0 LALS(0.797)PLS(0.203)LGK;LALS(0.794)PLS(0.206)LGK ; 155.26 0.0032978 214280000 19257.6 17493 20112.6 12474.9 17833.4 17692.9 14978.8 15249.5 19434.6 18440.9 TRUE FALSE FALSE 19022.88096 17739.26691 20462.65137 13917.30663 16923.29505 16562.38079 16251.0989 15690.72022 17696.3207 17961.80276 1.059074149 0.987610606 1.139231493 0.77482794 0.942182435 0.922089003 0.904758788 0.873560434 0.985219632 1 14.13264453 -9.263525933 24.99995414 1.032533444 0.890071448 0.618390874 0.059088121 93.42052477 1119313.919 0.008384776 0.013206644 5.45E-10 9.263525933 -0.142461996 LALS(ph)PLSLGKENLAESSKPTAGGSR ddPTM_HeLa_Romidepsin_16h_R1 1 LALSPLSLGKENLAESSKPTAGGSR 25 2 P49454 P49454 CENPF Centromere protein F 1 0 LALS(0.498)PLS(0.498)LGKENLAES(0.001)S(0.002)KPT(0.001)AGGSR 44.726 0.024633 18842000 1639 1800.7 1294.1 2358.1 1752.2 1736.8 1309.1 1767.9 1845.6 1705 TRUE FALSE FALSE 1619.023238 1826.050302 1316.623268 2630.754617 1662.778696 1625.824085 1420.294921 1819.051397 1680.524914 1660.703854 0.974901837 1.099564078 0.792810388 1.584120258 1.001249375 0.978996996 0.855236723 1.095349657 1.011935337 1 10.69757911 -6.919566905 19.64145389 1.014378928 4.175354049 0.000701554 0.202355131 1545.881244 387031.9932 0.025489287 5437.515547 1.20E-07 6.919566905 3.160975121 LAMENNIK ddPTM_HeLa_Romidepsin_16h_R1 1 LAMENNIK 8 0 Q5VVL7;P11182 Q5VVL7 DBT "Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial" 0 0 79.713 0.028332 123400000 15510 13732 14616 10261 14965 14552 13134 13133 15009 12642 FALSE FALSE TRUE 15320.95815 13925.31946 14870.38535 11447.4251 14201.28021 13622.17416 14249.60163 13512.98263 13666.55745 12313.55902 1.24423476 1.130893143 1.207643162 0.929660148 1.153304271 1.106274323 1.157228516 1.097406738 1.109878747 1 13.58796019 -12.6489751 1.503925153 1.000453032 1.143667555 0.027836457 0.086383088 0.42127002 1.722042372 0.05935277 0.013600912 2.24E-13 12.6489751 0.143214523 LAPGGHVGR ddPTM_HeLa_Romidepsin_16h_R1 2 LAPGGHVGR 9 0 P36578;H3BM89 P36578 RPL4 60S ribosomal protein L4 0 0 ; ; 145.34 0.00276 10785100 6459.3 7884.2 8801.1 7576.4 7008.8 9063.9 9444.1 3084.5 9569.2 7456.6 FALSE FALSE TRUE 6380.571567 7995.193975 8954.279454 8452.419016 6651.114783 8484.746042 10246.28162 3173.745141 8713.306785 7262.876457 0.878518533 1.100830232 1.23288335 1.163783945 0.91576868 1.16823494 1.410774599 0.436981843 1.199704668 1 12.82632532 -10.24882917 23.89374682 0.942633751 1.083816097 0 0.257498619 879.217748 1665936.72 0.03755065 0.045802389 5.64E-11 10.24882917 0.141182345 LAPLGPLNPSYKS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 LAPLGPLNPSYKSSPTR 17 1 Q96T17-2;Q96T17 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 LAPLGPLNPS(0.101)Y(0.001)KS(0.376)S(0.376)PT(0.147)R 55.031 0.029949 24692000 1727 1381.8 1096.4 2636.2 1426.5 1387.5 897.73 1552.7 1552.7 1428.3 TRUE FALSE FALSE 1705.95066 1401.253017 1115.482382 2941.009848 1353.700382 1298.843228 973.9831638 1597.624925 1413.822623 1391.19256 1.226250563 1.007231534 0.801817386 2.114020684 0.973050332 0.933618584 0.700106651 1.148385184 1.016266665 1 10.44210641 -8.542040817 24.99960331 1.15475669 0.912758254 0.10864062 0.3487024 431.9760889 563571.4608 0.049109979 0.098230789 2.87E-09 8.542040817 -0.241998435 LAPPS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 LAPPSPAR 8 0 O75145-2;O75145 O75145-2 PPFIA3 Liprin-alpha-3 1 0 LAPPS(1)PAR 109.66 0.022898 41595000 820.72 823.61 503.55 859.27 1044.9 1096.7 1216.7 1025.1 789.37 715.42 TRUE FALSE FALSE 810.716749 835.2048032 512.3140765 958.6228404 991.5748539 1026.624409 1320.046468 1054.759651 718.7667702 696.8332853 1.16343 1.198571912 0.735203222 1.37568463 1.422972862 1.473271199 1.894350479 1.513647057 1.031475943 1 9.444669728 -8.652144535 1.458873697 1.068447068 1.670115217 0.698253862 0.169856938 0.165888491 0.702394151 0.025655283 0.069359424 2.23E-09 8.652144535 0.601668149 LAPVPS(ph)PEPQKPAPVS(ph)PESVK ddPTM_HeLa_Romidepsin_16h_R1 2 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 2 0 LAPVPS(1)PEPQKPAPVS(0.966)PES(0.034)VK;LAPVPS(1)PEPQKPAPVS(0.989)PES(0.011)VK ; 89.979 0.0022366 55423000 4371.6 3924.1 4257.4 4034.4 4070.9 4471.6 3704.8 3908.4 4604.9 4580.3 TRUE FALSE FALSE 4318.317258 3979.343583 4331.498261 4500.87631 3863.146782 4185.879191 4019.48562 4021.483388 4193.026211 4461.303146 0.967949748 0.891968883 0.970904267 1.008870315 0.865923399 0.938263789 0.90096671 0.90141451 0.939865791 1 12.12324947 -4 0.088017268 1.056894012 0.607683263 0.155106663 0.041991514 102.8962233 0.658436068 0.464098381 5.613796494 1.00E-04 4 -0.44921075 LAPVPS(ph)PEPQKPAPVSPESVK ddPTM_HeLa_Romidepsin_16h_R1 2 LAPVPSPEPQKPAPVSPESVK 21 1 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 LAPVPS(1)PEPQKPAPVSPESVK;LAPVPS(0.999)PEPQKPAPVS(0.001)PESVK ; 83.666 0.00086129 256510000 6298.2 6033.4 4964.6 6344.4 6973.5 6826.6 6953.3 8109.7 6322.7 6047.2 TRUE FALSE FALSE 6221.435116 6118.338364 5051.00678 7077.969379 6617.616273 6390.402292 7543.913128 8344.341375 5757.181877 5890.092872 1.056254163 1.038750746 0.857542808 1.201673646 1.123516457 1.084940837 1.280779997 1.416673991 0.977434822 1 12.52407467 -5.332710981 0.505353419 1.018935568 4.263854011 0.727796167 0.079709402 8.96658553 0.328355092 0.014935528 26.43926426 4.65E-06 5.332710981 3.244918442 LAQANGWGVMVSHR ddPTM_HeLa_Romidepsin_16h_R1 2 LAQANGWGVMVSHR 14 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 ; ; 178.84 3.71E-09 12003800 2345.62 1618.21 3313.7 2053.81 3800.7 3941.9 3024.65 2117.32 1846.87 977.14 FALSE FALSE TRUE 2317.030681 1640.991203 3371.373558 2291.281176 3606.736097 3690.025312 3281.563696 2178.581314 1681.681322 951.7537619 2.434485446 1.724176219 3.542275001 2.407430648 3.789568522 3.877079828 3.447912503 2.289017812 1.766928999 1 9.894444557 -11.10598597 0.343979995 0.752553785 3.45461498 0.52875005 0.644971202 0.680924619 0.205917092 0.742195005 0.381596496 7.83E-12 11.10598597 2.702061196 LAQSNGWGVMVSHR ddPTM_HeLa_Romidepsin_16h_R1 1 LAQSNGWGVMVSHR 14 0 P13929-3;P13929-2;P13929 P13929-3 ENO3 Beta-enolase 0 0 113.65 0.020473 19029000 1742.5 1423.7 2787.6 2249.3 3132.3 3127 2314.5 1562.9 1526.5 1004 FALSE FALSE TRUE 1721.26174 1443.742886 2836.117009 2509.374649 2972.447043 2927.194792 2511.093572 1608.120046 1389.966017 977.9159353 1.760132623 1.47634662 2.900164428 2.566043316 3.039573174 2.993299001 2.567801057 1.644435874 1.42135532 1 9.933566642 -10.30172556 0.801331431 1.202736856 2.659399964 0.584466253 0.461522115 0.266462219 0.351273267 0.118741184 0.1379316 4.99E-11 10.30172556 1.456663108 LAQYEPED ddPTM_HeLa_Romidepsin_16h_R1 1 LAQYEPED 8 0 H7C488;Q9NQ48-2;Q9NQ48 H7C488 LZTFL1 Leucine zipper transcription factor-like protein 1 0 0 98.458 0.021943 3981900 9013.8 7778.9 7886.1 5045.3 9914.1 12909 10702 11458 8874 8166.7 FALSE FALSE TRUE 8903.936339 7888.411558 8023.354262 5628.661325 9408.146482 12084.15656 11611.02761 11789.51915 8080.287215 7954.527957 1.119354459 0.991688206 1.008652469 0.707604695 1.182741017 1.519154452 1.459675254 1.482114239 1.01580977 1 12.9575606 -8.403408332 4.212072823 1.024030262 1.481528089 0.812835826 0.108219306 0.082391974 2.435426513 0.016738207 0.038717704 3.95E-09 8.403408332 0.457497827 LAREGGT(ph)DSQPEWALDR ddPTM_HeLa_Romidepsin_16h_R1 1 LAREGGTDSQPEWALDR 17 1 V9GY20;Q9NXG6;Q9NXG6-3 V9GY20 P4HTM Transmembrane prolyl 4-hydroxylase 1 0 LAREGGT(0.5)DS(0.5)QPEWALDR 99.069 0.014775 532600000 1300 1082 852.46 1493.1 1181.3 1069.5 1135.6 1056.8 1209.7 1124.6 TRUE FALSE FALSE 1284.1551 1097.232424 867.2967087 1665.739247 1121.013853 1001.162402 1232.057836 1087.376841 1101.501402 1095.38273 1.172334623 1.001688629 0.791775044 1.520691537 1.02339924 0.913984103 1.124773837 0.99269124 1.005585876 1 10.09721932 -8.554559415 24.99999534 1.087640779 1.01304078 0.032886814 0.180763611 587.8367897 463874.6162 0.025572884 0.051146092 2.79E-09 8.554559415 -0.074599999 LAS(ph)PELER ddPTM_HeLa_Romidepsin_16h_R1 2 LASPELER 8 0 P05412;P17535 P05412 JUN;JUND Transcription factor AP-1;Transcription factor jun-D 1 0 LAS(1)PELER;LAS(1)PELER ; 109.29 0.02321 68998000 7008.9 7194.8 6627.4 7394.1 7261.3 7028.7 6506.9 7354.3 7556.2 6551.8 TRUE FALSE FALSE 6923.472831 7296.088583 6742.747117 8249.040632 6890.728765 6579.588754 7059.595924 7567.085067 6880.354547 6381.583291 1.084914592 1.143303824 1.056594705 1.292632291 1.079783566 1.031027639 1.106245206 1.185769224 1.078157917 1 12.63969869 -11.3224643 0.663664931 1.004692971 1.126808344 0.159417473 0.07322674 0.602813329 0.572404543 0.033685114 0.017485586 4.76E-12 11.3224643 0.122115372 LAS(ph)SVLR ddPTM_HeLa_Romidepsin_16h_R1 1 LASSVLR 7 0 J3QR09;J3KTE4;P84098 J3QR09 RPL19 Ribosomal protein L19;60S ribosomal protein L19 1 0 LAS(0.959)S(0.041)VLR 109.48 0.029596 4512600 1749.5 1839 1806.5 1458.6 1819 1712 1807.7 2018.2 2245.9 1665.2 TRUE FALSE FALSE 1728.176421 1864.88949 1837.941375 1627.250195 1726.169642 1602.608725 1961.245993 2076.593433 2045.021079 1621.937864 1.065501003 1.149790958 1.133176193 1.003275299 1.064263731 0.988082689 1.209199216 1.280316268 1.260850446 1 10.66350284 -7.628738846 4.772102503 1.045657183 1.264145065 0.306065562 0.085706259 0.086673413 3.176530631 0.008110775 0.032995035 2.35E-08 7.628738846 0.218487881 LAS(ph)TLVHLGEYQAAVDGAR ddPTM_HeLa_Romidepsin_16h_R1 1 LASTLVHLGEYQAAVDGAR 19 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 1 0 LAS(0.748)T(0.252)LVHLGEYQAAVDGAR 94.61 0.00085698 0 496.15 528.87 425.67 391.44 452.13 375.52 401.94 422.91 581.3 505.07 TRUE FALSE FALSE 490.102733 536.3154457 433.0786078 436.7001346 429.056119 351.5254839 436.0807736 435.1462336 529.3070721 491.9482086 0.996248638 1.090186805 0.880333743 0.887695345 0.872157092 0.71455791 0.886436348 0.884536677 1.075940643 1 8.942362629 -9.613551829 6.427537806 1.004914018 0.848692148 0.691151045 0.059393022 0.097043617 5.728479887 0.008620846 0.01222295 2.43E-10 9.613551829 -0.15622187 LAS(ph)TSDIEEKENR ddPTM_HeLa_Romidepsin_16h_R1 1 LASTSDIEEKENR 13 1 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 LAS(0.998)T(0.001)SDIEEKENR 81.703 0.013774 13899000 2107.9 2684.1 2102.4 2591.9 3129.3 3300.7 2543.2 3794.4 2327 2380.2 TRUE FALSE FALSE 2082.208104 2721.88683 2138.99139 2891.587673 2969.600144 3089.795923 2759.219345 3904.184977 2118.867292 2318.362061 0.898137586 1.174055975 0.922630432 1.247254569 1.280904391 1.332749519 1.190158945 1.684027289 0.913950124 1 11.17889018 -6.287503625 0.334311354 0.940147014 2.612860795 0.731779113 0.120198626 4.571409957 0.219911872 0.040735488 3.53373165 5.16E-07 6.287503625 1.672713781 LASDDRPS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 LASDDRPSPPR 11 1 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 0 LAS(0.007)DDRPS(0.993)PPR 73.36 0.026362 4966200 3349.5 3683.7 4515.4 3172.6 4028.3 5060.6 5487.4 2709.4 5048.2 5006.1 TRUE FALSE FALSE 3308.675006 3735.559225 4593.988643 3539.43094 3822.720819 4737.243992 5953.499619 2787.792214 4596.676349 4876.0408 0.678557695 0.766104998 0.942155497 0.725882142 0.783980483 0.971534937 1.220970017 0.57173275 0.942706703 1 12.25149448 -8.252450545 23.75628441 0.832741356 0.951368326 0.040878825 0.176426684 716.0145381 1892317.543 0.025846411 0.064743836 5.59E-09 8.252450545 0.118626971 LASDS(ph)DAESDSR ddPTM_HeLa_Romidepsin_16h_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 0 LAS(0.007)DS(0.991)DAES(0.002)DSR 212.1 5.05E-21 72084000 1612.4 1685.9 1882.7 2002.8 2304 2332.6 1988 1878.9 1882 1837.1 TRUE FALSE FALSE 1592.747449 1709.634144 1915.467604 2234.373159 2186.418283 2183.554388 2156.86067 1933.263007 1713.669206 1789.371877 0.890115391 0.955438144 1.070469268 1.248691336 1.221891498 1.220290995 1.205373069 1.080414324 0.957693159 1 10.80523753 -9.546449894 3.060974428 0.947203002 1.198075302 0.844146397 0.049428018 0.079651593 1.535384992 0.009328663 0.013963755 2.84E-10 9.546449894 0.2508723 LASLGDT(ph)ASPLVK ddPTM_HeLa_Romidepsin_16h_R1 1 LASLGDTASPLVK 13 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 0 LASLGDT(0.618)AS(0.382)PLVK 166.62 0.00030702 22254000 2084.6 2201.5 2075 1446.3 1497.2 1782.2 1325.3 1303.3 2316.2 1885.6 TRUE FALSE FALSE 2059.192093 2232.492775 2111.114505 1613.528011 1420.792297 1668.323172 1437.870949 1341.008929 2109.033271 1836.61184 1.121190688 1.215549593 1.149461448 0.878535124 0.773594216 0.908370041 0.782893215 0.730153699 1.148328256 1 10.84283104 -9.111484318 4.445301422 1.078948424 0.807292281 0.811145559 0.074174589 0.097028097 3.144500883 0.012970665 0.022035321 7.74E-10 9.111484318 -0.271656144 LASLGDTAS(ph)PLVK ddPTM_HeLa_Romidepsin_16h_R1 1 LASLGDTASPLVK 13 0 Q6P4F7-3;Q6P4F7 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 0 LASLGDT(0.004)AS(0.996)PLVK 116.9 0.0054658 20445000 2011.7 2067 2305.5 1549.7 1659.8 2055.5 1498.4 1706.7 2198.2 2136.2 TRUE FALSE FALSE 1987.180627 2096.09928 2345.62626 1728.883606 1575.094212 1924.160184 1625.674059 1756.080672 2001.587487 2080.701216 0.955053331 1.007400421 1.127324886 0.830913921 0.75700163 0.924765252 0.781310669 0.843985027 0.961977371 1 11.0228541 -9.15357438 10.53169713 0.990942847 0.82606257 0.682773213 0.061581101 0.225181182 20.7302371 0.0090261 0.014976796 7.02E-10 9.15357438 -0.164880277 LASRPQGGRLMS(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 LASRPQGGRLMSSR 14 2 Q52M75 Q52M75 LINC01554 Putative uncharacterized protein encoded by LINC01554 2 0 LASRPQGGRLMS(1)S(1)R 87.138 0.022729 21968000 5823.8 5875.8 5169.6 4467.2 4730.4 4861.7 4398 4895.3 6227.8 5853.5 TRUE FALSE FALSE 5752.817286 5958.519667 5259.574719 4983.718683 4488.990036 4551.05306 4771.56601 5036.937782 5670.76997 5701.425226 1.009013897 1.045093013 0.922501745 0.874118047 0.787345244 0.798230772 0.836907584 0.883452397 0.994623229 1 12.47710689 -9.382121096 2.206273917 1.007218098 0.827200546 0.879616685 0.030658568 0.071198478 0.678473617 0.004831993 0.007927643 4.15E-10 9.382121096 -0.180017552 LASVPAGGAVAVSAAPGS(ph)AAPAAGSAPAAAEEKKDEK ddPTM_HeLa_Romidepsin_16h_R1 1 LASVPAGGAVAVSAAPGSAAPAAGSAPAAAEEKKDEK 37 2 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 1 0 LASVPAGGAVAVS(0.002)AAPGS(0.996)AAPAAGS(0.001)APAAAEEKKDEK 115.77 1.19E-20 15126000 3081.3 3087.4 2567.9 3773.9 2901.2 3444.7 2388.6 2902.6 3145 2625.8 TRUE FALSE FALSE 3043.74393 3130.864498 2612.593222 4210.256075 2753.140938 3224.594787 2591.487624 2986.582151 2863.703323 2557.581337 1.190086855 1.22415051 1.021509339 1.64618658 1.07646271 1.260798529 1.013257169 1.167736919 1.119691984 1 11.32056441 -11.97681666 0.698694338 0.993218822 1.203474818 0.080303976 0.172913474 1.068822029 0.923079078 0.125709853 0.035172089 1.05E-12 11.97681666 0.210255996 LASVS(ph)ADAEVAR ddPTM_HeLa_Romidepsin_16h_R1 2 LASVSADAEVAR 12 0 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 LAS(0.235)VS(0.765)ADAEVAR;LAS(0.124)VS(0.876)ADAEVAR ; 174.21 5.39E-05 25633000 2623.5 2537.1 3092.6 3720.5 5058.1 5002.2 3437.4 6131.5 2440.5 2571.7 TRUE FALSE FALSE 2591.523773 2572.81736 3146.425406 4150.681715 4799.966283 4682.575564 3729.37267 6308.905279 2222.215568 2504.886863 1.034587155 1.027119188 1.256114778 1.657033608 1.91624075 1.869376071 1.488838767 2.518638814 0.887152071 1 11.29052973 -9.243467179 1.575697902 1.013418765 1.924113441 0.772824883 0.237622178 0.123551793 0.599861608 0.034617639 0.063956509 5.71E-10 9.243467179 0.910694676 LAT(ph)QSNEITIPVTFESR ddPTM_HeLa_Romidepsin_16h_R1 1 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 0 LAT(0.815)QS(0.185)NEITIPVTFESR 191.36 5.26E-13 17004000 1174.8 1229.2 918.81 887.68 1032.7 1043.4 812.43 858.48 963.13 1009.8 TRUE FALSE FALSE 1160.481086 1246.50471 934.8015026 990.3177383 979.9974655 976.7301074 881.4377839 883.3187643 876.9852406 983.5652504 1.179871986 1.267333011 0.950421441 1.006865318 0.9963726 0.993050646 0.896166049 0.898078459 0.891639106 1 9.941876955 LATAT(ph)T(ph)GPSKAKT(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 LATATTGPSKAKTSR 15 2 A4FU49-5;A4FU49;A4FU49-3;A4FU49-6 A4FU49-5 SH3D21 SH3 domain-containing protein 21 4 0 LAT(0.218)AT(0.889)T(0.889)GPS(0.02)KAKT(0.992)S(0.992)R 50.897 0.026457 15864000 1474.3 1483.6 1570.5 1313.4 1392 1758.1 1391.2 1745.1 1536.3 1666.5 TRUE FALSE FALSE 1456.330665 1504.48616 1597.833894 1465.261488 1320.961046 1645.763084 1509.368493 1795.591715 1398.88948 1623.20409 0.897195044 0.926861982 0.984370298 0.902697016 0.813798495 1.013897818 0.929869819 1.106202064 0.861807513 1 10.66462869 -7.258852614 24.3224004 0.941760376 1.106202152 0.42156525 0.060871452 128.6861089 1209876.608 0.008308521 0.075359668 5.51E-08 7.258852614 0.164441775 LATNAAVTVLR ddPTM_HeLa_Romidepsin_16h_R1 1 LATNAAVTVLR 11 0 P50990-2;P50990;P50990-3;H7C2U0 P50990-2 CCT8 T-complex protein 1 subunit theta 0 0 180.19 0.000155 4171600 671.05 786.81 707.03 767.88 819.62 564.78 530.47 602.12 1016.8 649.11 FALSE FALSE TRUE 662.8709845 797.8867318 719.3355606 856.6658986 777.791733 528.6923807 575.5281086 619.5413922 925.8548614 632.2460286 1.048438352 1.261987732 1.13774627 1.354956551 1.230204221 0.836213051 0.910291378 0.97990555 1.464390157 1 9.30434226 -8.247222769 24.95671532 1.088101256 0.908952131 0.228818217 0.168926501 886.7255399 1556610.257 0.020376414 0.05167966 5.66E-09 8.247222769 -0.179149126 LATNTS(ph)APDLK ddPTM_HeLa_Romidepsin_16h_R1 2 LATNTSAPDLK 11 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 LATNT(0.087)S(0.913)APDLK;LATNT(0.21)S(0.79)APDLK ; 171.99 0.00024739 283630000 15548.9 13682.4 14014.8 12483.4 13135.5 15394.3 14301.5 13047.3 15053.8 14442.2 TRUE FALSE FALSE 15359.38403 13875.02119 14258.72172 13926.78944 12465.14642 14410.65391 15516.26905 13424.80304 13707.35043 14066.98956 1.091874275 0.986353272 1.013629935 0.990033396 0.886127509 1.024430554 1.103026983 0.954347978 0.974433824 1 13.78002599 -10.22089939 24.81232977 1.043385092 0.995811426 0.007754478 0.059575245 780.1034965 477459.7442 0.010223054 0.012520523 6.01E-11 10.22089939 -0.047573666 LATQSNEITIPVTFES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 3 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 1 0 LATQSNEITIPVTFES(1)R;LATQSNEITIPVT(0.001)FES(0.999)R;LATQSNEITIPVT(0.038)FES(0.962)R ;; 324.29 1.43E-197 16592300 3762.78 3750.9 3537.8 3001.06 3513.33 3189.96 3070.82 3084.86 4360.01 3706.46 TRUE FALSE FALSE 3716.91779 3803.705269 3599.373925 3348.056678 3334.03166 2986.131851 3331.655374 3174.115557 3970.039786 3610.165635 1.029569877 1.053609627 0.997010744 0.927396972 0.923512104 0.827145387 0.922853883 0.879216047 1.099683557 1 11.81784931 -9.093217516 1.852925602 1.017704611 0.88425564 0.772124375 0.038091847 0.101140514 0.683552266 0.004459481 0.008517102 8.07E-10 9.093217516 -0.133448971 LATQSNEITIPVTFESR ddPTM_HeLa_Romidepsin_16h_R1 2 LATQSNEITIPVTFESR 17 0 P04792;C9J3N8 P04792 HSPB1 Heat shock protein beta-1 0 0 ; ; 153.32 6.99E-16 366530 208.18 63.797 179.26 165.72 126.97 199.28 129.35 0 108.86 0 FALSE FALSE TRUE 205.6426221 64.69513584 182.3799451 184.8813261 120.4902471 186.5466511 140.3369858 0 99.12328896 0 0 LAVEALSS(ph)LDGDLAGR ddPTM_HeLa_Romidepsin_16h_R1 2 LAVEALSSLDGDLAGR 16 0 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 1 0 LAVEALS(0.238)S(0.762)LDGDLAGR;LAVEALS(0.382)S(0.618)LDGDLAGR ; 166.79 1.89E-05 3859700 1818.58 1456.65 1312.92 1598.24 1597.49 1985.69 1559.13 1854.04 1734.22 1545.57 TRUE FALSE FALSE 1796.414447 1477.156757 1335.770822 1783.036029 1515.964124 1858.810818 1691.562463 1907.683722 1579.10702 1505.415869 1.193301124 0.981228369 0.887310178 1.184414264 1.007006872 1.234749053 1.123651277 1.267213773 1.048950694 1 10.55594637 -8.253171101 24.67836304 1.071389463 1.200049363 0.362145696 0.095366734 603.225929 1800444.449 0.015206915 0.038069342 5.58E-09 8.253171101 0.1286599 LAVEALSSLDGDLAGR ddPTM_HeLa_Romidepsin_16h_R1 1 LAVEALSSLDGDLAGR 16 0 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 0 0 183.06 1.41E-07 4621000 801.68 911.7 1293 1130.1 743.92 896.73 1199.4 877.08 1239.2 826.23 FALSE FALSE TRUE 791.9088158 924.5349365 1315.504123 1260.767479 705.9549865 839.4318471 1301.277006 902.456926 1128.362848 804.7644255 0.984025624 1.148826796 1.634644973 1.566629239 0.877219425 1.043077726 1.616966363 1.121392668 1.40210329 1 9.652422722 -9.99891394 24.97297284 0.996349671 1.311131491 0.029853319 0.269148578 36.32345275 835195.4576 0.038615265 0.050522546 1.00E-10 9.99891394 0.31478182 LAVISDSGEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 LAVISDSGEKR 11 1 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 0 1 LAVISDSGEK(1)R 122.94 0.0038838 2682700 1962.8 2507.2 1920.8 1317.1 1530.5 2005 2149.5 2201.1 2353.7 2015.3 FALSE TRUE FALSE 1938.876639 2542.496427 1954.230718 1469.389299 1452.392874 1876.886971 2332.078476 2264.785356 2143.179177 1962.942215 0.987740048 1.295247719 0.995562021 0.748564725 0.739906077 0.956160072 1.188052536 1.153770772 1.0918198 1 10.93880199 -7.760602922 24.99688247 0.977945053 1.170911715 0.211254025 0.149960418 25.73148505 768825.0601 0.021458515 0.071915013 1.74E-08 7.760602922 0.192966662 TPITSVPLGPLASS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 TPITSVPLGPLASSPTK 17 0 Q15911 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 TPITSVPLGPLAS(0.206)S(0.791)PT(0.003)K;TPITSVPLGPLAS(0.023)S(0.974)PT(0.004)K ; 247.5 4.74E-59 79213000 9032.6 8985.9 8620.5 7621.7 4193.2 5142.1 3632.1 4016.8 9594.6 9355.4 TRUE FALSE FALSE 8922.507197 9112.403736 8770.536186 8502.956815 3979.205357 4813.536405 3940.610483 4133.019771 8736.434946 9112.345359 0.979166926 1.000006406 0.96248944 0.933124951 0.436682896 0.528243412 0.432447447 0.453562679 0.958747128 1 13.15360671 -8.792962636 5.443435461 0.986635554 0.463638805 0.985365597 0.030422608 0.013477382 1.042832996 0.004293225 0.008074227 1.61E-09 8.792962636 -0.522996748 down LAVPTEVSTEVPEMDT(ph)ST ddPTM_HeLa_Romidepsin_16h_R1 1 LAVPTEVSTEVPEMDTST 18 0 O00488 O00488 ZNF593 Zinc finger protein 593 1 0 LAVPTEVSTEVPEMDT(0.333)S(0.333)T(0.333) 88.78 0.017468 13014000 5224.4 5132.8 4705.6 3617.5 4471 4300.9 3585 3626.6 5735.9 5140.7 TRUE FALSE FALSE 5160.723003 5205.059693 4787.498994 4035.772371 4242.828186 4026.086371 3889.509811 3731.529949 5222.866738 5007.143873 1.030672003 1.039526689 0.956133699 0.806002878 0.847354958 0.804068442 0.776792101 0.745241208 1.043083017 1 12.28977219 -9.341828669 2.511654328 1.016888263 0.79413287 0.94161853 0.027535225 0.050959644 0.628652066 0.004546575 0.007455163 4.55E-10 9.341828669 -0.222755393 LAVPTEVSTEVPEMDTS(ph)T ddPTM_HeLa_Romidepsin_16h_R1 1 LAVPTEVSTEVPEMDTST 18 0 O00488 O00488 ZNF593 Zinc finger protein 593 1 0 LAVPTEVSTEVPEMDT(0.268)S(0.366)T(0.366) 114.83 0.0019463 11555000 5230 4555.3 4379.2 3354.6 3688.8 4388 3750.5 3484.5 4669.3 4993.1 TRUE FALSE FALSE 5166.254748 4619.429633 4455.418139 3742.474636 3500.546771 4107.620962 4069.067376 3585.31851 4251.666114 4863.378542 1.062276914 0.949839621 0.916115844 0.769521559 0.719776744 0.844602353 0.836675028 0.737207371 0.874220684 1 12.24774317 -9.617664222 1.84604408 1.028042985 0.784795905 0.627417937 0.065295493 0.089132121 0.61614642 0.007842616 0.011988854 2.41E-10 9.617664222 -0.24324708 LCAGIMITAS(ph)HNPK ddPTM_HeLa_Romidepsin_16h_R1 1 LCAGIMITASHNPK 14 0 Q96G03-2;Q96G03 Q96G03-2 PGM2 Phosphoglucomutase-2 1 0 LCAGIMIT(0.007)AS(0.993)HNPK 81.656 0.010008 28070000 5122.4 4574.1 4434.6 500.69 5590.2 4607.9 4508.4 5124.9 4724.7 4438 TRUE FALSE FALSE 5059.966219 4638.4943 4511.782353 558.5821336 5304.911234 4313.470061 4891.343383 5273.180896 4302.110999 4322.70012 1.170556846 1.073054843 1.043741696 0.129220653 1.227221664 0.997864747 1.131548164 1.219881266 0.995236977 1 12.07771704 -9.503882442 24.98004866 1.081094914 0.932340383 0.034284065 0.296753983 1963.599006 2582126.934 0.045470503 0.068749038 3.13E-10 9.503882442 -0.148754532 LDAQSLNLSQEDFDRYMSGQT(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 LDAQSLNLSQEDFDRYMSGQTSPR 24 1 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3;A0A0A0MSJ3;Q3HKR1 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 0 LDAQSLNLSQEDFDRY(0.068)MS(0.061)GQT(0.71)S(0.161)PR 57.238 0.0050011 24208000 1368.4 1778.7 1225.4 1461 1308.2 1208.7 1189.4 1073.5 1676.3 1372.3 TRUE FALSE FALSE 1351.721414 1803.740585 1246.727573 1629.927694 1241.437672 1131.467971 1290.427606 1104.560029 1526.36753 1336.647448 1.011277444 1.349451262 0.932727306 1.21941481 0.928769717 0.846496937 0.965421068 0.826366018 1.141937264 1 10.38440328 -8.540729404 24.99205594 1.042762754 0.887961602 0.354140873 0.127098566 240.8590184 337216.9543 0.017483651 0.034972478 2.88E-09 8.540729404 -0.154801152 LDDFLDLNHK ddPTM_HeLa_Romidepsin_16h_R1 1 LDDFLDLNHK 10 0 Q8WVY7 Q8WVY7 UBLCP1 Ubiquitin-like domain-containing CTD phosphatase 1 0 0 110.53 0.0083037 4971100 4255.3 3656 4287.6 4305.4 5468.1 5332.7 4779.2 5655.4 5248.7 4035.5 FALSE FALSE TRUE 4203.434767 3707.469264 4362.223879 4803.210606 5189.042453 4991.957681 5185.145129 5819.030076 4779.243126 3930.657128 1.069397465 0.943218689 1.109795064 1.221986668 1.320146297 1.270005884 1.319154777 1.480421692 1.215889092 1 11.94055481 -9.073542095 1.341570215 1.025545931 1.356365922 0.706525946 0.084584332 0.111678814 0.397246979 0.010022527 0.021227078 8.44E-10 9.073542095 0.330819991 LDDQES(ph)PVYAAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 LDDQESPVYAAQQR 14 0 Q96ST3;H3BMA2;H3BT34;H3BQ76;H3BQ88;H3BNA0;H3BNZ3;H3BQL7;H3BP90 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 0 LDDQES(1)PVYAAQQR 110.04 0.0055403 4930700 1036.7 891.66 901.94 740.04 1434.5 1589.1 1159.6 1284.6 939.38 1096.7 TRUE FALSE FALSE 1024.064302 904.2128129 917.6378874 825.6069068 1361.292112 1487.561639 1258.096395 1321.767874 855.3595001 1068.207576 0.958675378 0.84647669 0.859044542 0.772889956 1.274370397 1.392577316 1.17776397 1.237369875 0.800742776 1 10.06097631 -8.741139079 24.86914145 0.945769 1.272613457 0.783465566 0.098000222 89.85379263 110075.9571 0.014027928 0.028028076 1.81E-09 8.741139079 0.326844458 LDDWDRER ddPTM_HeLa_Romidepsin_16h_R1 1 LDDWDRER 8 1 H0YIQ2;P49750-3;P49750-1;P49750 H0YIQ2 YLPM1 YLP motif-containing protein 1 0 0 112.41 0.00088496 0 1856.2 1409.5 1838.3 2558.9 2303.7 1997.9 1853.9 1430.6 1590.4 1530.9 FALSE FALSE TRUE 1833.57592 1429.342978 1870.29484 2854.772058 2186.133593 1870.240638 2011.37022 1471.992154 1448.150641 1491.126997 1.229657785 0.958565555 1.25428273 1.914506318 1.466094837 1.25424638 1.348892632 0.987167529 0.971178607 1 10.54218742 -9.522934844 24.99996501 1.100532958 1.40753729 0.33314546 0.229730713 1.984572438 884097.2779 0.036871817 0.052451704 3.00E-10 9.522934844 0.307004332 LDEDEDEDDADLSK ddPTM_HeLa_Romidepsin_16h_R1 2 LDEDEDEDDADLSK 14 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 0 ; ; 277.15 1.62E-95 12446000 2317.49 1819.05 2367.89 1324.47 2378.11 2242.62 1796.01 2267.11 2392.59 2476.23 FALSE FALSE TRUE 2289.24354 1844.658634 2409.102132 1477.611453 2256.746173 2099.32382 1948.563045 2332.705251 2178.590758 2411.897188 0.949146403 0.764816445 0.998841138 0.612634511 0.935672625 0.870403527 0.807896396 0.967166123 0.903268501 1 11.2359527 -10.44776854 5.972140507 0.978006211 0.849809632 0.144346317 0.107308227 0.223435409 13.51641357 0.016495392 0.018653427 3.57E-11 10.44776854 -0.128196579 LDEEEEDNEGGEWER ddPTM_HeLa_Romidepsin_16h_R1 2 LDEEEEDNEGGEWER 15 0 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 0 ; ; 314.29 4.73E-154 29639000 3069.2 2571.5 2434.2 2574.64 2495.63 2643 2243.36 3072.2 2469.8 2788.45 FALSE FALSE TRUE 3031.79141 2607.701644 2476.56623 2872.331991 2368.268689 2474.12083 2433.910942 3161.08926 2248.894902 2716.005667 1.11626844 0.960123786 0.911841334 1.057557437 0.871967506 0.910940967 0.89613618 1.163874324 0.828015541 1 11.40727077 -10.23138998 22.26002647 1.054904534 0.960221796 0 0.112192825 214.7823237 159106.3775 0.014528507 0.017791074 5.87E-11 10.23138998 -0.094682738 LDEGT(ph)PPEPK ddPTM_HeLa_Romidepsin_16h_R1 1 LDEGTPPEPK 10 0 Q9Y4G6;H0YN01;H0YMT1;A0A1B0GVU7 Q9Y4G6 TLN2 Talin-2 1 0 LDEGT(1)PPEPK 119.74 0.024732 228970000 5633 5202.6 5003.4 4361.9 5706.8 6066.5 4701 5488.8 6194.1 5761.7 TRUE FALSE FALSE 5564.342829 5275.842339 5090.482078 4866.243401 5415.560701 5678.870229 5100.302823 5647.609768 5640.084183 5612.010203 0.991506185 0.940098494 0.907069284 0.867112358 0.964994807 1.011913739 0.908819235 1.00634346 1.005002482 1 12.45430192 -10.28399068 5.468958997 0.996169322 0.941414981 0.264106726 0.041964236 0.184069088 17.7073904 0.007185325 0.008353245 5.20E-11 10.28399068 -0.054754342 LDEIYVAGLVAHSDLDER ddPTM_HeLa_Romidepsin_16h_R1 4 LDEIYVAGLVAHSDLDER 18 0 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 ;;; ;;; 133.78 7.20E-07 13294000 5928.24 5648.61 5976.95 4425.76 5114.18 4745.59 4799.33 5034.18 6331.9 6320.31 FALSE FALSE TRUE 5855.984331 5728.13128 6080.976308 4937.487195 4853.184311 4442.362115 5206.98497 5179.836056 5765.559005 6156.107435 0.95124791 0.930479421 0.987795676 0.80204695 0.788352764 0.721618679 0.845824253 0.841414175 0.936559192 1 12.58780269 -9.25745815 24.36496354 0.972903799 0.79742033 0.814393773 0.038306166 72.06913354 441059.0345 0.006038191 0.009774033 5.53E-10 9.25745815 -0.175483469 LDEK(ac)ENLSAK ddPTM_HeLa_Romidepsin_16h_R1 1 LDEKENLSAK 10 1 U3KQ93;Q9UBT2-2;Q9UBT2 U3KQ93 UBA2 SUMO-activating enzyme subunit 2 0 1 LDEK(1)ENLSAK 128.01 0.011296 525590 190.38 348.83 160.72 151.9 363.2 252.54 193.21 212.11 297.53 314.98 FALSE TRUE FALSE 188.0595753 353.7408379 163.5172642 169.4633927 344.6645487 236.403509 209.6212526 218.2470682 270.9181716 306.7967742 0.612977681 1.153013551 0.532982345 0.552363672 1.123429507 0.77055409 0.683257681 0.711373412 0.883054173 1 8.261139504 -12.58165936 1.342611037 1.001061197 0.752916432 0.090843529 0.205836192 0.636602304 2.043344927 0.143840947 0.032928067 2.62E-13 12.58165936 -0.248144764 LDGLVET(ph)PTGYIESLPR ddPTM_HeLa_Romidepsin_16h_R1 5 LDGLVETPTGYIESLPR 17 0 F8VRJ2;F5H4R6;H0YHC3;F8W020;F8W118;F8VXI6;F8VUX1;F8VY35;P55209;F8VV59;B7Z9C2;H0YIV4;F8W0J6;P55209-3;P55209-2 F8VRJ2 NAP1L1 Nucleosome assembly protein 1-like 1 1 0 LDGLVET(0.995)PT(0.005)GYIESLPR;LDGLVET(0.996)PT(0.004)GYIESLPR;LDGLVET(0.995)PT(0.005)GYIESLPR;LDGLVET(0.994)PT(0.006)GYIESLPR;LDGLVET(0.801)PT(0.058)GY(0.135)IES(0.006)LPR ;;;; 140.49 4.63E-07 442872000 6492.03 6606.26 6709.05 7330.7 7543.06 5962.64 4321.31 5558.79 6580.28 6655.49 TRUE FALSE FALSE 6412.902641 6699.263102 6825.818201 8178.310026 7158.109501 5581.646548 4688.361964 5719.624818 5991.723276 6482.57941 0.989251691 1.033425536 1.052947873 1.261582699 1.10420699 0.861022472 0.723224764 0.882306942 0.924280737 1 12.66235226 -8.103109029 5.057330217 1.028667394 0.800246805 0.556790422 0.093206246 0.133694048 5.220483993 0.013706329 0.036422918 7.89E-09 8.103109029 -0.228420589 LDGLVETPTGYIES(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 1 LDGLVETPTGYIESLPR 17 0 F8VRJ2;F5H4R6;H0YHC3;F8W020;F8W118;F8VXI6;F8VUX1;F8VY35;P55209;F8VV59;B7Z9C2;H0YIV4;F8W0J6;P55209-3;P55209-2 F8VRJ2 NAP1L1 Nucleosome assembly protein 1-like 1 1 0 LDGLVET(0.005)PT(0.003)GYIES(0.992)LPR 171.98 2.18E-06 18281000 4788.5 4694.5 4553.3 4931.1 5243.7 4315.9 3582.9 4704.7 4805.3 4964.2 TRUE FALSE FALSE 4730.13592 4760.589294 4632.548276 5501.256984 4976.094422 4040.127919 3887.231437 4840.823072 4375.501933 4835.229368 0.978265054 0.984563282 0.958082425 1.137744782 1.029133065 0.835560759 0.803939408 1.001156864 0.904921277 1 12.23936861 -8.26368338 24.99560181 1.000341003 0.872591047 0.352888432 0.073450226 135.8325247 1513028.853 0.00929905 0.021766746 5.45E-09 8.26368338 -0.127749956 LDHFNFER ddPTM_HeLa_Romidepsin_16h_R1 1 LDHFNFER 8 0 R4GMV4;R4GNE8;Q9UHL4 R4GMV4 DPP7 Dipeptidyl peptidase 2 0 0 88.37 0.020357 5207200 3838.1 4195.6 3925.1 3864.2 5380.3 4662.1 4224.3 4137.2 4344.1 3960.8 FALSE FALSE TRUE 3791.319761 4254.665767 3993.414719 4310.996986 5105.723214 4364.206856 4583.111937 4256.903355 3955.552816 3857.897845 0.982742393 1.102845627 1.035127129 1.117447159 1.32344697 1.131239611 1.187981673 1.103425629 1.025313001 1 11.91359923 -9.515621034 1.290810509 0.994195593 1.182290172 0.549301303 0.064566215 0.196338922 0.653375474 0.010803778 0.018305764 3.05E-10 9.515621034 0.188094579 LDHKFDLMYAK ddPTM_HeLa_Romidepsin_16h_R1 1 LDHKFDLMYAK 11 1 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;Q9NY65;C9J2C0;Q9NY65-2;V9GZ17;A6NHL2-2;A6NHL2;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA8;TUBAL3;TUBA1A;TUBA1B;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha chain-like 3;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 56.225 0.030263 9537800 6072.5 3924.9 10167 12804 11222 9582.9 8749.5 4988.7 5730.3 3151 FALSE FALSE TRUE 5998.486034 3980.154845 10343.95237 14284.45872 10649.29946 8970.583617 9492.682312 5133.040164 5217.767616 3069.136566 1.954453934 1.296832109 3.37031349 4.654227148 3.469803066 2.922836252 3.092948817 1.672470434 1.700076717 1 11.58361713 -9.760609102 24.98912666 1.451766603 3.258528026 0.573055142 0.721335191 12.31005762 370492.1323 0.124175417 0.169817379 1.74E-10 9.760609102 1.806761424 LDIDS(ph)PPITAR ddPTM_HeLa_Romidepsin_16h_R1 5 LDIDSPPITAR 11 0 P14618;B4DNK4;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2;H3BU13;H3BN34;H3BQZ3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 1 0 LDIDS(1)PPITAR;LDIDS(1)PPITAR;LDIDS(0.992)PPIT(0.008)AR;LDIDS(1)PPITAR;LDIDS(0.99)PPIT(0.01)AR ;;;; 186.51 1.08E-06 418190000 15198.6 15238.9 13206.8 13087.9 15684.8 15076.3 12139.8 13494.6 15143 13927.1 TRUE FALSE FALSE 15013.35362 15453.43363 13436.65881 14601.18458 14884.34613 14112.97309 13170.95431 13885.04496 13788.57215 13565.27193 1.106749182 1.139190848 0.990518943 1.076365048 1.097239053 1.040375243 0.97093183 1.023572917 1.016461168 1 13.72763035 -7.938262745 6.504050879 1.058787497 0.998214157 0.223804112 0.046751205 0.270697236 21.87856058 0.007484791 0.022809901 1.15E-08 7.938262745 -0.06057334 LDIDSPPIT(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 2 LDIDSPPITAR 11 0 P14618;B4DNK4;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2;H3BU13;H3BN34;H3BQZ3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 1 0 LDIDSPPIT(1)AR;LDIDSPPIT(1)AR ; 163.71 0.0017382 20446200 7518.8 6957 6243 5413.5 10476.8 7291.2 5865.3 6918.8 7026.4 6969.4 TRUE FALSE FALSE 7427.157974 7054.940829 6351.656796 6039.434341 9942.129802 6825.315851 6363.498436 7118.984562 6397.941186 6788.333983 1.094106152 1.039274268 0.935672407 0.889678433 1.46459055 1.005447856 0.937416817 1.048708649 0.942490632 1 12.72884183 LDIDSPPITAR ddPTM_HeLa_Romidepsin_16h_R1 2 LDIDSPPITAR 11 0 P14618;B4DNK4;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2;H3BU13;H3BN34;H3BQZ3 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ; ; 151.83 0.023412 71654000 4199.8 3982.2 3701 3540.7 3960.7 3826.3 3434.9 4330.3 3837.1 3734.8 FALSE FALSE TRUE 4148.611222 4038.261516 3765.414353 3950.092393 3758.5707 3581.811779 3726.66032 4455.590398 3493.900166 3637.769358 1.140427227 1.110092785 1.035088809 1.085855645 1.033207532 0.984617612 1.024435569 1.224813879 0.960451261 1 11.82883836 -9.671880494 21.54065106 1.071509271 1.058737072 0 0.077385018 56.38914894 13528.05367 0.012458121 0.017618432 2.13E-10 9.671880494 -0.012772199 LDIPTGTT(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 LDIPTGTTPQR 11 0 P52732 P52732 KIF11 Kinesin-like protein KIF11 1 0 LDIPT(0.045)GT(0.15)T(0.805)PQR;LDIPT(0.002)GT(0.048)T(0.95)PQR ; 120.03 0.020672 26140000 10179 9770.1 11611 6802.2 14326.1 15210 11587.4 13153.7 11739.7 11656.8 TRUE FALSE FALSE 10054.93443 9907.643724 11813.08458 7588.702369 13594.98566 14238.13009 12571.63347 13534.28156 10689.67183 11353.95466 0.885588743 0.872616108 1.040437886 0.668375258 1.197378893 1.254023864 1.107247109 1.192032377 0.941493264 1 13.47090726 -8.688494164 24.99998928 0.929121587 1.186667989 0.65393294 0.100813265 21.40643822 7335.914361 0.014194207 0.028388412 2.05E-09 8.688494164 0.257546402 LDKDNLSYIEHIFEISR ddPTM_HeLa_Romidepsin_16h_R1 1 LDKDNLSYIEHIFEISR 17 1 Q15121-2;Q15121 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 0 0 120.59 0.00091669 1743200 1713.3 1808 1676.1 1402.1 2467.2 2324.9 2121.1 2093.3 1954 1926.5 FALSE FALSE TRUE 1692.417641 1833.453071 1705.271817 1564.217399 2341.289578 2176.346393 2301.266181 2153.866333 1779.229346 1876.449252 0.901925612 0.977086414 0.908775878 0.833604957 1.247723366 1.15982161 1.226394041 1.147841504 0.94818943 1 10.87378956 -8.753422215 24.99999993 0.943310937 1.195111264 0.864916783 0.051522392 54.51733444 170000.5546 0.008344907 0.016456278 1.76E-09 8.753422215 0.251800328 LDLAGR ddPTM_HeLa_Romidepsin_16h_R1 1 LDLAGR 6 0 P0CG38;P0CG39;P60709;A0A2R8Y793;P63267-2;Q6S8J3;A5A3E0;Q562R1;A0A2R8YEA7;Q9BYX7;P63261;I3L3I0;I3L1U9;I3L4N8;P63267;P68133;P68032;P62736 P0CG38;P60709;P63261;P63267 POTEI;POTEJ;ACTB;ACTG2;POTEE;POTEF;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;POTE ankyrin domain family member J;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;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" 0 0 121.68 0.025099 4402700 4416.4 3772.4 4225 3888 4071.4 5199.8 4744.2 4446.9 4174.9 3421.1 FALSE FALSE TRUE 4362.571218 3825.507946 4298.534353 4337.548854 3863.621266 4867.549562 5147.17223 4575.564035 3801.486488 3332.219329 1.309208905 1.148036059 1.289991423 1.301699686 1.159473877 1.460753054 1.544667899 1.373128112 1.140827212 1 11.70226765 -15.4626485 0.074063011 4.42E-12 1.76822942 0.584078998 0.100327171 76.52381462 0.543541769 14.68577199 2.706334371 3.45E-16 15.4626485 1.76822942 LDLAGTLPGS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 LDLAGTLPGSKR 12 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLAGTLPGS(1)KR 67.648 0.022829 12248000 2663.6 2677.8 2939.5 2721.6 1523.6 2341.4 1885.1 1906.3 3062.5 2888.4 TRUE FALSE FALSE 2631.135019 2715.498139 2990.660764 3036.284198 1445.845007 2191.792097 2045.220347 1961.455783 2788.58233 2813.358952 0.93522905 0.965215668 1.063021398 1.07923811 0.51392127 0.779065926 0.726967437 0.697193574 0.991193224 1 11.45807792 -8.771124229 24.99999969 0.98301637 0.689819843 0.810475516 0.076782083 67.54310422 174352.6988 0.01136581 0.020789425 1.69E-09 8.771124229 -0.293196527 LDLGEDYPSGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LDLGEDYPSGKK 12 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 1 ; LDLGEDYPSGK(1)K;LDLGEDYPSGK(1)K 111.63 0.0042034 1633860 900.9 1015.55 1049.11 548.78 994.51 957.06 889.27 827.14 1447.01 1014.01 FALSE TRUE FALSE 889.9194843 1029.84694 1067.369319 612.2325257 943.7564437 895.9069548 964.8045716 851.0719909 1317.585801 987.665874 0.901032938 1.042707829 1.080698795 0.619878181 0.955542222 0.907095181 0.976853202 0.861700311 1.334040019 1 9.947879252 LDLLGNLPGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LDLLGNLPGSK 11 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLLGNLPGS(1)K 99.161 0.019779 18976000 5026.8 4443.3 5447 3020.9 2887.3 3936.3 3391.4 3175.5 5222.5 4844.9 TRUE FALSE FALSE 4965.531428 4505.852894 5541.80275 3370.190672 2739.950307 3684.783134 3679.465431 3267.378082 4755.38652 4719.0288 1.052235881 0.954826318 1.17435239 0.714170397 0.580617416 0.78083506 0.779708196 0.692383586 1.007704492 1 12.20427426 -9.243619269 24.71406921 1.029150186 0.710239111 0.829255322 0.074428575 209.0142086 289874.3806 0.010756656 0.017811567 5.71E-10 9.243619269 -0.318911075 LDLLGNLPGS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 LDLLGNLPGSKR 12 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLLGNLPGS(1)KR 59.634 0.029648 22167000 3259 2462.4 3191.3 1950 1824.5 2421.3 2222.5 2025.7 3638.2 2888.7 TRUE FALSE FALSE 3219.278054 2497.065732 3246.843238 2175.468175 1731.388957 2266.586744 2411.279095 2084.310433 3312.79028 2813.651158 1.14416389 0.887482347 1.153960835 0.773183331 0.615353098 0.80556779 0.85699291 0.74078495 1.177399078 1 11.45822776 -9.246933085 22.8212079 1.059244583 0.758531024 0.719064802 0.09802646 105.9020166 166603.7154 0.014407573 0.023801139 5.66E-10 9.246933085 -0.300713559 LDLTENLT(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 LDLTENLTGSK 11 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLT(0.055)ENLT(0.865)GS(0.081)K 115.12 0.025271 6938000 4830.3 3931.5 5349.1 3164.2 3924.4 3437.9 2566.1 3020.1 4517 3751.1 TRUE FALSE FALSE 4771.426446 3986.84776 5442.198842 3530.059692 3724.123224 3218.229285 2784.06447 3107.481829 4112.988207 3653.645881 1.30593566 1.091197092 1.489525537 0.966174557 1.019289593 0.880826821 0.761996253 0.850515329 1.125721633 1 11.8351211 -8.534807759 1.593760566 1.164448312 0.813348451 0.549246523 0.138886583 0.263660413 1.315662416 0.024416048 0.0689767 2.92E-09 8.534807759 -0.351099861 LDLTENLTGS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LDLTENLTGSK 11 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLTENLT(0.001)GS(0.999)K 124.42 0.00039797 0 1927.1 1832.6 2042.2 1241.9 1507 2029.5 1360.1 1976.4 2017.5 1851.7 TRUE FALSE FALSE 1903.611764 1858.399391 2077.743634 1385.494321 1430.092167 1899.8215 1475.62686 2033.584016 1837.049747 1803.592567 1.055455538 1.030387586 1.152002771 0.768185868 0.792913096 1.053354031 0.818159759 1.127518517 1.018550298 1 10.81665775 -9.267953271 24.99097487 1.035812687 0.908045594 0.273043632 0.11210467 557.5258111 2138983.012 0.016201328 0.025115018 5.40E-10 9.267953271 -0.127767092 LDLTENLTGS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 LDLTENLTGSKR 12 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 LDLTENLT(0.025)GS(0.975)KR 153 0.0021953 15006000 1053.9 1171.6 1100.3 854 800.63 851.43 866.08 853.07 1396.6 1243.4 TRUE FALSE FALSE 1041.054661 1188.093816 1119.45026 952.7434982 759.7708635 797.0263709 939.6448136 877.7522345 1271.684598 1211.096289 0.859596938 0.9810069 0.924328041 0.786678571 0.627341418 0.658103223 0.775863011 0.724758422 1.050027657 1 10.24209786 -9.129273066 3.189991441 0.936038249 0.699707206 0.79947122 0.062632159 0.097101309 1.868662729 0.010048769 0.017482786 7.43E-10 9.129273066 -0.236331042 LDNS(ph)PNMNITQPSK ddPTM_HeLa_Romidepsin_16h_R1 1 LDNSPNMNITQPSK 14 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 LDNS(0.995)PNMNIT(0.004)QPSK 100.18 0.013996 18223000 4349.1 4396.2 4517 3584.6 6720.4 7054.6 5787.7 6980.7 4621.9 4332.3 TRUE FALSE FALSE 4296.091496 4458.089819 4595.61649 3999.068318 6377.432911 6603.833828 6279.307094 7182.675541 4208.505688 4219.746221 1.018092385 1.056482922 1.089074141 0.947703513 1.511330913 1.564983646 1.488076952 1.702158178 0.997336206 1 12.04294052 -8.724573611 6.345905409 1.015531917 1.565515279 0.948746267 0.062491362 0.026378366 2.89364852 0.008414095 0.016728045 1.89E-09 8.724573611 0.549983362 LDNVPHT(ph)PSSYIETLPK ddPTM_HeLa_Romidepsin_16h_R1 2 LDNVPHTPSSYIETLPK 17 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;A8MXH2;E9PNW0;E9PJJ2;E9PKI2;E9PP22 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 LDNVPHT(0.999)PS(0.001)SYIETLPK;LDNVPHT(0.55)PS(0.447)S(0.003)YIETLPK ; 101.6 0.002277 157789000 11154 10343 10250.1 10477.8 20081.3 22854 17899.8 19173.6 13256 10807 TRUE FALSE FALSE 11018.05076 10488.60903 10428.49869 11689.29254 19056.47633 21393.70316 19420.20857 19728.35787 12070.35016 10526.23258 1.046723096 0.996425734 0.990715207 1.110491569 1.810379562 2.032417866 1.844934397 1.874208812 1.146692329 1 13.36170156 -8.758506963 3.890705367 1.019054298 1.912880192 0.977476788 0.06282156 0.01569195 0.523060791 0.006987857 0.013852916 1.74E-09 8.758506963 0.893825894 LDNVPHTPSS(ph)YIETLPK ddPTM_HeLa_Romidepsin_16h_R1 1 LDNVPHTPSSYIETLPK 17 0 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;A8MXH2;E9PNW0;E9PJJ2;E9PKI2;E9PP22 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 LDNVPHTPS(0.024)S(0.974)Y(0.002)IETLPK 140.2 0.00028087 16275000 4695.6 4402.8 4189 4415.4 5021.7 4444.5 3656.1 4739.4 4653.2 4205.1 TRUE FALSE FALSE 4638.368221 4464.782734 4261.907788 4925.929323 4765.42391 4160.510794 3966.649043 4876.527061 4237.006138 4095.850896 1.132455341 1.090074528 1.040542709 1.202663243 1.163475925 1.015786683 0.968455431 1.190601705 1.034462984 1 11.99994748 -12.4226204 1.096193525 0.998788187 1.099573253 0.168804232 0.072677921 0.677464976 1.427839269 0.053320262 0.012790463 3.78E-13 12.4226204 0.100785067 LDPDSIPS(ph)PIQVIENDR ddPTM_HeLa_Romidepsin_16h_R1 1 LDPDSIPSPIQVIENDR 17 0 O94855;O94855-2 O94855 SEC24D Protein transport protein Sec24D 1 0 LDPDS(0.004)IPS(0.996)PIQVIENDR 164.82 8.27E-06 1726400 572.45 659.4 537.81 582.69 619.04 606.08 634.94 643.48 690.77 608.06 TRUE FALSE FALSE 565.4727592 668.6830505 547.1703574 650.0633594 587.4480788 567.353444 688.8717878 662.0980786 628.9858011 592.2625135 0.954767094 1.129031528 0.923864579 1.097593288 0.991871114 0.957942519 1.163119009 1.117913195 1.062005085 1 9.210092965 -4.317464733 0.428319798 0.985602167 3.413620062 0.143420276 0.074248142 42.77130247 0.634800871 0.014932798 87.59240452 4.81E-05 4.317464733 2.428017895 LDQLIYIPLPDEK ddPTM_HeLa_Romidepsin_16h_R1 1 LDQLIYIPLPDEK 13 0 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 171.29 4.13E-05 0 571.53 548.38 589.68 407.03 507.77 524.01 564.26 415.87 630.76 593.85 FALSE FALSE TRUE 564.5639725 556.100108 599.943133 454.0927237 481.8566021 490.5274522 612.1882303 427.9025423 574.3432458 578.4216914 0.976042187 0.961409498 1.037207183 0.785054797 0.83305417 0.848044704 1.058377027 0.739776099 0.99294901 1 9.175977846 -9.269818803 24.99011556 0.989227703 0.862910904 0.433252522 0.079951753 467.9630614 1395613.781 0.011490552 0.017730897 5.37E-10 9.269818803 -0.126316798 LDQPVSAPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 LDQPVSAPPSPR 12 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR;LDQPVSAPPS(1)PR ;; 177.39 1.89E-06 289440000 11604.6 12527.3 11801.2 7702.3 9822.4 10432.4 9377.3 9661.4 11620.5 11773.1 TRUE FALSE FALSE 11463.15867 12703.65966 12006.59494 8592.876166 9321.126276 9765.803309 10173.80763 9940.937366 10581.13338 11467.23316 0.999644684 1.107822565 1.04703504 0.749341715 0.812848761 0.85162682 0.887206834 0.866899384 0.922727673 1 13.48522972 -9.272188986 24.99266271 1.012863632 0.836414052 0.730176415 0.05525143 265.9237865 618267.4286 0.007895749 0.012134272 5.34E-10 9.272188986 -0.17644958 LDRETEELHHDR ddPTM_HeLa_Romidepsin_16h_R1 3 LDRETEELHHDR 12 1 O60869-2;O60869-3;O60869 O60869-2 EDF1 Endothelial differentiation-related factor 1 0 0 ;; ;; 107.97 0.0046789 20253700 10599.1 9831.2 8793 9690.3 11468.8 11709.2 11393.3 12651.1 11161.3 10276 FALSE FALSE TRUE 10469.91409 9969.603892 8946.038477 10810.73808 10883.50434 10961.01991 12361.04662 13017.13962 10163.00537 10009.02804 1.046047034 0.996061141 0.893796924 1.080098691 1.087368753 1.095113318 1.234989708 1.300539829 1.015383845 1 13.28901426 -7.662644837 0.959768607 1.013244826 1.3706022 0.827187069 0.046687454 0.368207805 0.38204917 0.007667824 0.117233365 2.17E-08 7.662644837 0.357357374 LDS(ph)DAGFHSLPR ddPTM_HeLa_Romidepsin_16h_R1 1 LDSDAGFHSLPR 12 0 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 0 LDS(0.983)DAGFHS(0.017)LPR 118.73 0.0033171 5714000 4632.5 4376.8 3960 4355.3 3902.2 3172.3 2222 2214.3 4836.8 4339.2 TRUE FALSE FALSE 4576.037308 4438.416705 4028.922139 4858.880278 3703.056173 2969.600268 2410.736625 2278.367277 4404.184494 4226.466958 1.082709827 1.050148209 0.953260058 1.149631673 0.876158789 0.702620013 0.570390505 0.539071357 1.042048722 1 12.04523646 -8.242070498 1.813172323 1.040937622 0.552091268 0.929206814 0.05514658 0.064315684 0.400788596 0.008240613 0.027815606 5.73E-09 8.242070498 -0.488846354 LDS(ph)LPEHEDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSLPEHEDSEK 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 0 LDS(1)LPEHEDSEK 72.615 0.027439 3899900 3982.2 3544.2 4343.6 2837.2 6073.8 6563.4 5515.2 6385.4 4800.8 4111.7 TRUE FALSE FALSE 3933.663415 3594.095341 4419.198536 3165.250413 5763.831322 6144.019922 5983.66095 6570.151475 4371.404424 4004.877441 0.982218176 0.897429545 1.103454126 0.790348883 1.439202923 1.534134318 1.494093399 1.640537462 1.09152015 1 11.96754238 -8.651761829 5.618013063 0.980885104 1.539029646 0.895095298 0.092591497 0.038961386 1.787742127 0.011199317 0.02261244 2.23E-09 8.651761829 0.558144542 LDS(ph)PPPS(ph)PITEASEAAEAAEAGNLAVSSR ddPTM_HeLa_Romidepsin_16h_R1 2 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 2 0 LDS(0.983)PPPS(0.973)PIT(0.022)EAS(0.022)EAAEAAEAGNLAVSSR;LDS(1)PPPS(1)PIT(0.001)EASEAAEAAEAGNLAVSSR ; 101.08 7.42E-08 5264800 1144.3 1134.62 1262.24 2137.82 1322.78 1284.63 967.31 1175.19 947.12 1032.81 TRUE FALSE FALSE 1130.352831 1150.59321 1284.208758 2385.004807 1255.273601 1202.546289 1049.473287 1209.192269 862.4072151 1005.977447 1.123636354 1.143756466 1.27657808 2.370833276 1.247814853 1.195400843 1.043237391 1.202007333 0.857282852 1 9.974382247 -9.73417888 4.004969412 1.064318369 1.407946164 0.202501778 0.351453729 0.297344136 10.41197153 0.057419934 0.08028059 1.84E-10 9.73417888 0.343627795 LDS(ph)PPPSPITEASEAAEAAEAGNLAVSSR ddPTM_HeLa_Romidepsin_16h_R1 4 LDSPPPSPITEASEAAEAAEAGNLAVSSR 29 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 LDS(0.901)PPPS(0.09)PIT(0.009)EASEAAEAAEAGNLAVSSR;LDS(0.976)PPPS(0.022)PIT(0.002)EASEAAEAAEAGNLAVSSR;LDS(0.992)PPPS(0.008)PITEASEAAEAAEAGNLAVSSR;LDS(0.967)PPPS(0.03)PIT(0.003)EASEAAEAAEAGNLAVSSR ;;; 162.68 1.89E-14 65715900 3553.84 3101.22 3131.49 3533.5 4350.09 4324.37 3605.66 3539.75 3856.64 3063.87 TRUE FALSE FALSE 3510.524431 3144.879057 3185.99227 3942.059896 4128.088675 4048.056713 3911.92467 3642.167081 3511.692459 2984.270216 1.176342683 1.053818465 1.067595104 1.320946031 1.38328247 1.356464536 1.310848009 1.220454858 1.176734077 1 11.54316246 -9.258910645 23.87242877 1.081641529 1.323699059 0.750836811 0.064112028 49.42133729 466557.2466 0.011594959 0.018648804 5.51E-10 9.258910645 0.24205753 LDS(ph)SPSVSSTLAAK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSSPSVSSTLAAK 14 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LDS(0.719)S(0.278)PS(0.003)VSSTLAAK 197.19 6.58E-12 95144000 4237.7 4275.6 4219.8 2675.1 3639 4324 3636.4 3760.3 4422.3 3701.2 TRUE FALSE FALSE 4186.049282 4335.792009 4293.243849 2984.407649 3453.288251 4047.710355 3945.275725 3869.098348 4026.758412 3605.04229 1.161165097 1.202702121 1.190899719 0.827842618 0.95790506 1.122791365 1.094377099 1.073246313 1.116979521 1 11.81580047 LDS(ph)SPVSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 LDSSPVSSPR 10 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 LDS(0.928)S(0.072)PVSSPR;LDS(0.926)S(0.074)PVSSPR ; 185.3 1.14E-05 68374000 9534.9 9082.6 9293.7 7248.8 7726.1 7392.1 7421.5 8198.7 10171.9 9680.5 TRUE FALSE FALSE 9418.684971 9210.465081 9455.45295 8086.940363 7331.808287 6919.768667 8051.882025 8435.916449 9262.099788 9428.999214 0.998906115 0.976823189 1.002805572 0.857666883 0.777580751 0.733881562 0.853948743 0.894677819 0.982299349 1 13.20288894 -9.170351648 3.541548026 0.997953159 0.812404993 0.809795113 0.041128145 0.07498923 1.782208834 0.006410698 0.010924875 6.76E-10 9.170351648 -0.185548166 LDSQEPGRQT(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 LDSQEPGRQTPDR 13 1 Q8TB03-2;Q8TB03 Q8TB03-2 CXorf38 Uncharacterized protein CXorf38 1 0 LDSQEPGRQT(1)PDR 74.698 0.028678 8154300 2577.7 2557.8 2500.5 2774.7 2868.1 3134.7 2515.6 2452.6 2899.3 2747.9 TRUE FALSE FALSE 2546.282001 2593.808776 2544.020154 3095.523869 2721.730155 2934.402787 2729.275001 2523.562111 2639.979347 2676.509162 0.951344399 0.9691014 0.950499326 1.156552689 1.016895512 1.096354471 1.019714425 0.942855772 0.986351694 1 11.38613688 LDSQPQET(ph)SPELPR ddPTM_HeLa_Romidepsin_16h_R1 1 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 0 LDSQPQET(0.5)S(0.5)PELPR 116.9 0.0094598 363830000 2219.3 2381.8 2094 2533.7 4714.7 4650 4632 4881.8 2253.3 2704.1 TRUE FALSE FALSE 2192.250318 2415.331043 2130.445192 2826.658315 4474.091266 4352.880007 5025.441964 5023.047181 2051.759205 2633.847092 0.832337733 0.917035408 0.80887201 1.07320517 1.698690588 1.652669975 1.908023431 1.907114196 0.778997084 1 11.36295588 -8.767386748 2.648644463 0.909719966 1.82113007 0.957381711 0.09285689 0.040751468 0.584573595 0.014661128 0.030411336 1.71E-09 8.767386748 0.911410104 LDSQPQETS(ph)PELPR ddPTM_HeLa_Romidepsin_16h_R1 1 LDSQPQETSPELPR 14 0 O14545 O14545 TRAFD1 TRAF-type zinc finger domain-containing protein 1 1 0 LDS(0.001)QPQET(0.072)S(0.927)PELPR 127.66 0.0027527 248600000 807.05 838.05 758.4 1080.7 1220.6 1397.2 1483.9 1583.2 734.56 867.74 TRUE FALSE FALSE 797.2133642 849.8480899 771.5996339 1205.655619 1158.308227 1307.923429 1609.942429 1629.007394 668.8591139 845.1959897 0.943228995 1.005504167 0.912923917 1.426480525 1.370461102 1.547479455 1.904815509 1.927372366 0.791365697 1 9.723142112 -8.297674853 0.743914823 0.963535797 2.052792799 0.920141466 0.111301769 0.16737337 0.136298391 0.016879699 0.114182384 5.04E-09 8.297674853 1.089257002 LDSS(ph)PSVSSTLAAK ddPTM_HeLa_Romidepsin_16h_R1 3 LDSSPSVSSTLAAK 14 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LDS(0.15)S(0.845)PS(0.004)VS(0.001)STLAAK;LDS(0.199)S(0.768)PS(0.028)VS(0.002)S(0.003)TLAAK;LDS(0.046)S(0.915)PS(0.033)VS(0.004)S(0.001)TLAAK ;; 183.06 1.86E-07 538900000 12308.8 11576.9 12082.2 8237.7 11737.7 11985.5 10574.5 11806.4 12584 13276.9 TRUE FALSE FALSE 12158.77561 11739.8799 12292.48562 9190.181634 11138.68137 11219.66523 11472.69777 12147.99956 11458.45552 12931.96422 0.940211046 0.907818774 0.950550544 0.710656283 0.86132943 0.867591731 0.887158174 0.939377758 0.886056853 1 13.6586538 -10.34827705 0.919440654 0.98291397 0.861978104 0.147478324 0.068036637 0.368806137 0.627203416 0.014383923 0.016321606 4.48E-11 10.34827705 -0.120935866 LDSS(ph)PSVSSTLAAKDDPDGK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSSPSVSSTLAAKDDPDGK 20 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LDS(0.199)S(0.597)PS(0.114)VS(0.08)S(0.005)T(0.005)LAAKDDPDGK 72.21 0.0029984 37448000 2296 2759.7 2098.1 1697.3 2673.2 2595 2388.1 2283.2 2304.8 2283.4 TRUE FALSE FALSE 2268.015469 2798.551129 2134.61655 1893.549812 2536.776629 2429.187875 2590.945154 2349.26079 2098.652916 2224.076939 1.01975585 1.258297804 0.959776397 0.851386829 1.140597515 1.09222295 1.164953024 1.056285756 0.943606257 1 11.11899098 -4.000000001 0.164311825 0.990248663 1.492781469 0.105186934 0.107412525 113.9543276 1.172332569 0.177659042 14.02290441 1.00E-04 4.000000001 0.502532805 LDSSEMDHS(ph)ENEDYTMSSPLPGK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 LDS(0.045)S(0.041)EMDHS(0.305)ENEDY(0.243)T(0.271)MS(0.077)S(0.017)PLPGK 40.642 0.030324 24161000 3901.4 3193.3 3950.4 3242.5 3226.9 3022 2329.6 3218.7 5018 4180.5 TRUE FALSE FALSE 3853.848236 3238.255361 4019.155055 3617.413106 3062.219252 2828.903953 2527.476166 3311.828006 4569.177512 4071.890007 0.94645195 0.795270834 0.987049023 0.888386744 0.752038794 0.694739776 0.620713271 0.81333926 1.122126949 1 11.99148288 -8.929508764 0.709764994 0.974766016 0.676600881 0.642653124 0.087710165 0.320999687 0.296527065 0.014529921 0.049438296 1.18E-09 8.929508764 -0.298165135 LDSSEMDHSENEDYT(ph)MSSPLPGK ddPTM_HeLa_Romidepsin_16h_R1 2 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 LDS(0.014)S(0.013)EMDHS(0.031)ENEDY(0.117)T(0.662)MS(0.13)S(0.034)PLPGK;LDS(0.001)S(0.001)EMDHS(0.062)ENEDY(0.398)T(0.441)MS(0.082)S(0.016)PLPGK ; 58.366 0.0059435 34526200 7803.9 6917.9 7787.4 5608 7112.9 6268.4 5846.9 6133.1 9766.2 8284.2 TRUE FALSE FALSE 7708.783065 7015.290378 7922.93643 6256.423346 6749.902171 5867.86947 6343.53554 6310.551572 8892.686612 8068.97529 0.955360847 0.869415276 0.981901189 0.775367766 0.836525324 0.727213712 0.786163709 0.782075957 1.102083758 1 12.97816976 -9.38299344 0.655250741 0.98709906 0.755023564 0.743016438 0.058779678 0.220324072 0.186886759 0.009673843 0.022656544 4.14E-10 9.38299344 -0.232075496 LDSSEMDHSENEDYTMS(ph)SPLPGK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSSEMDHSENEDYTMSSPLPGK 23 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 LDS(0.002)S(0.002)EMDHS(0.154)ENEDY(0.174)T(0.257)MS(0.336)S(0.074)PLPGK 61.767 0.0019319 6306500 2511.4 1989.3 2583.1 1959.5 2346.9 2002.5 1860 2426.2 3031.6 2838.4 TRUE FALSE FALSE 2480.790091 2017.305418 2628.057772 2186.06661 2227.128936 1874.546713 2017.988354 2496.398269 2760.446103 2764.657959 0.897322608 0.72967631 0.950590565 0.79071865 0.805571238 0.678039288 0.729923334 0.902968218 0.998476536 1 11.43288529 -10.71506982 0.43532092 1.005602281 0.76615593 0.508992251 0.077914126 0.530989525 0.263488292 0.047309362 0.03641762 1.93E-11 10.71506982 -0.239446352 LDSSPS(ph)VSSTLAAKDDPDGK ddPTM_HeLa_Romidepsin_16h_R1 1 LDSSPSVSSTLAAKDDPDGK 20 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LDS(0.035)S(0.156)PS(0.305)VS(0.305)S(0.099)T(0.099)LAAKDDPDGK 60.938 0.0086528 33080000 3457.4 3705.2 3445.9 3074 3655.2 3555.1 3438.4 3871.2 3971.1 3623.5 TRUE FALSE FALSE 3415.259879 3757.361903 3505.874444 3429.430344 3468.661505 3327.940584 3730.45761 3983.207064 3615.91487 3529.360948 0.967670898 1.064601201 0.993345395 0.971685921 0.982801577 0.942930075 1.056978208 1.128591585 1.024523964 1 11.78519127 -7.514113153 4.000873005 0.987484992 1.118974836 0.629811309 0.032326334 0.088106234 3.117499583 0.004258384 0.023131074 3.06E-08 7.514113153 0.131489844 LDTGPQSLS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 LDTGPQSLSGK 11 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 LDTGPQS(0.067)LS(0.933)GK 98.592 0.020671 43024000 1507 1792.5 1634.2 1482.5 2386 2449.3 1971.4 2520.7 1672.4 1701.4 TRUE FALSE FALSE 1488.632104 1817.734862 1662.642565 1653.913625 2264.233517 2292.797635 2138.850667 2593.632477 1522.816355 1657.197383 0.89828292 1.096872878 1.003285778 0.998018487 1.366302856 1.383539256 1.290643281 1.565071551 0.918910669 1 10.69452973 -8.760497523 4.383660004 0.968514928 1.397674259 0.862980482 0.081103244 0.05218457 2.389313586 0.012126361 0.023774448 1.74E-09 8.760497523 0.429159331 LDTGS(ph)PEPETR ddPTM_HeLa_Romidepsin_16h_R1 1 LDTGSPEPETR 11 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 LDT(0.024)GS(0.975)PEPETR 140.63 0.0030458 79618000 3905.4 3597.4 3790.1 3095.9 3710.5 4615.7 3959 4710.8 4596.4 3823.3 TRUE FALSE FALSE 3857.799483 3648.044292 3856.065101 3453.862525 3521.139339 4320.771666 4295.277361 4847.099566 4185.286472 3723.970115 1.035937283 0.979611592 1.035471548 0.927467842 0.945533726 1.16025949 1.153413488 1.301594647 1.123877567 1 11.86262578 -7.810722579 1.687251092 1.005711804 1.273228261 0.691749679 0.061509273 0.145321785 0.725159069 0.007126261 0.044739091 1.55E-08 7.810722579 0.267516457 LDVQFSGLTK ddPTM_HeLa_Romidepsin_16h_R1 1 LDVQFSGLTK 10 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 121.9 0.028075 450530 196.64 207.85 236.49 194.28 206.9 275.07 242.71 144.48 319.91 205.62 FALSE FALSE TRUE 194.243276 210.7761178 240.6060092 216.7435677 196.3411209 257.4939147 263.3257813 148.6603008 291.2964484 200.2779628 0.969868444 1.052417924 1.201360379 1.082213763 0.98034311 1.285682714 1.314801577 0.742269887 1.454460812 1 7.645859875 -10.0152334 6.021152529 0.986771636 1.114139213 0 0.213014487 0.247153966 34.07584834 0.023714403 0.030026408 9.66E-11 10.0152334 0.127367577 LDVTILS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 LDVTILS(0.836)PS(0.164)R;LDVTILS(0.793)PS(0.207)R ; 136.81 0.0054951 135210000 2719.9 2954.6 3057 2687.3 4769.1 6817 5646.3 6143.9 3032.8 2953.3 TRUE FALSE FALSE 2686.748813 2996.194936 3110.205803 2998.01827 4525.715031 6381.415701 6125.896581 6321.664053 2761.538772 2876.57284 0.934010353 1.041584936 1.081219206 1.042218792 1.573301036 2.218409217 2.129581596 2.197637398 0.960010028 1 11.49013529 -8.526761066 2.149485054 0.982672275 2.192424074 0.988509013 0.056662013 0.023093713 0.211717134 0.009121239 0.022753018 2.97E-09 8.526761066 1.209751799 up LDVTILS(ph)PSRK ddPTM_HeLa_Romidepsin_16h_R1 1 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 LDVTILS(0.5)PS(0.5)RK 122.46 0.01376 151240000 2024.8 1511.7 1972.9 1781.9 2987.4 4098.5 3754.4 3762.1 1598.6 1719.9 TRUE FALSE FALSE 2000.120959 1532.981752 2007.237497 1987.931662 2834.94183 3836.619077 4073.298642 3870.950428 1455.617212 1675.21675 1.193947565 0.91509457 1.198195694 1.186671314 1.692283599 2.29022249 2.431505441 2.310716167 0.868912761 1 10.71013206 -8.495039955 1.808304657 1.085161412 2.39340067 0.965757849 0.108830781 0.039011963 0.250270962 0.014614048 0.039949463 3.20E-09 8.495039955 1.308239258 up LDVTILSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 LDVTILSPSR 10 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 146.69 0.023106 1370000 379.7 315.49 837.81 610.38 844.23 642.31 548.88 305.25 318.63 289.62 FALSE FALSE TRUE 375.0720704 319.9314765 852.3917316 680.9550075 801.1457928 601.268464 595.5018535 314.0819271 290.1309348 282.0956306 1.329591917 1.134124183 3.021641029 2.413915472 2.839979446 2.13143487 2.110992829 1.113388132 1.028484327 1 8.14004051 -9.786889192 24.99095156 1.15837542 2.29047169 0.571812638 0.486486914 122.4049486 120197.4469 0.079020333 0.103874439 1.63E-10 9.786889192 1.13209627 LDVTILSPSRK ddPTM_HeLa_Romidepsin_16h_R1 2 LDVTILSPSRK 11 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 ; ; 100.82 0.0070796 5810600 1553.43 1141.55 1219.11 1468.5 1777.64 1526.39 1247.58 1331.38 1194.5 1373.26 FALSE FALSE TRUE 1534.496198 1157.620771 1240.328098 1638.29488 1686.920398 1428.858605 1353.549414 1369.90138 1087.660928 1337.582507 1.147216108 0.865457469 0.927290908 1.224817812 1.261171097 1.068239602 1.011937138 1.024162152 0.813154271 1 10.38541217 -9.257547307 24.96394359 1.043036195 1.117351727 0.142419086 0.128422723 706.2193111 4529705.009 0.018520625 0.029995655 5.53E-10 9.257547307 0.074315532 LDYGQHVVAGT(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 LDYGQHVVAGTPGR 14 0 P38919;I3L3H2 P38919 EIF4A3 "Eukaryotic initiation factor 4A-III;Eukaryotic initiation factor 4A-III, N-terminally processed" 1 0 LDYGQHVVAGT(1)PGR 114.06 0.010186 5556900 975.5 789.96 733.45 752.19 966.39 935.39 1116.7 1326.9 1086.9 887.76 TRUE FALSE FALSE 963.6102308 801.0810776 746.2153896 839.161747 917.0715122 875.6215978 1211.55247 1365.291758 989.6849418 864.6958672 1.114392085 0.926431024 0.862980174 0.970470403 1.060571175 1.012635345 1.40113133 1.578927123 1.144546862 1 9.756048984 -7.646257079 3.13568095 1.023604198 1.555208869 0.851238427 0.081270587 0.071337925 1.326149364 0.012265622 0.060198318 2.26E-08 7.646257079 0.531604671 LDYVPSSAS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 LDYVPSSASR 10 0 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 LDYVPSS(0.002)AS(0.998)R;LDYVPSSAS(1)R ; 129.74 0.0074726 29993000 6813.6 6703.6 5777.3 4829.6 4021.9 3852.2 3285.6 2947.7 6486.7 6447.4 TRUE FALSE FALSE 6730.553222 6797.973457 5877.851483 5388.021076 3816.647435 3606.056852 3564.678782 3032.987049 5906.513306 6279.895619 1.071761958 1.082497842 0.935979169 0.8579794 0.607756509 0.574222419 0.567633445 0.482967749 0.940543229 1 12.61652486 -8.906471911 1.425257043 1.037770515 0.532334228 0.95027514 0.048662496 0.049328171 0.200572161 0.006798636 0.015553031 1.24E-09 8.906471911 -0.505436286 LDYWEDDLR ddPTM_HeLa_Romidepsin_16h_R1 1 LDYWEDDLR 9 0 E9PEM5;A0A494C1L5;P50851-2;P50851;H0YAC6;A0A494BZW2;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 E9PEM5 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 0 185.72 0.00027404 3122700 2047.8 2176.2 2188.5 1619.9 2216.4 2345 2004.1 2337.5 1994.9 2015.4 FALSE FALSE TRUE 2022.840626 2206.836601 2226.589924 1807.20046 2103.288837 2195.162068 2174.328204 2405.131875 1816.471148 1963.039617 1.030463475 1.124193613 1.134256234 0.920613341 1.071444926 1.118246442 1.107633379 1.225208016 0.925335959 1 10.93887357 -4 0.378621903 1.018435548 3.72702398 0.459818281 0.067532196 38.44967678 0.467602265 0.01606817 77.24432084 1.00E-04 4 2.708588432 LDYWEDDLRR ddPTM_HeLa_Romidepsin_16h_R1 1 LDYWEDDLRR 10 1 E9PEM5;A0A494C1L5;P50851-2;P50851;H0YAC6;A0A494BZW2;Q5T321;A0A0D9SF28;F5GXV7;Q8NFP9 E9PEM5 LRBA;NBEA Lipopolysaccharide-responsive and beige-like anchor protein;Neurobeachin 0 0 88.496 0.02643 3733700 2605.7 2105.9 2125.8 2053.5 2205.8 2435.9 2343 2205.3 2343.5 2154.1 FALSE FALSE TRUE 2573.940726 2135.546915 2162.798657 2290.935332 2093.229795 2280.253852 2542.014362 2269.106876 2133.891491 2098.136171 1.226774869 1.017830465 1.030819013 1.09189068 0.997661555 1.086799743 1.211558333 1.081486944 1.017041467 1 11.0348926 -12.77580478 1.756374889 0.999853038 1.114523011 0.124372234 0.073872141 0.486469126 2.716038435 0.062853773 0.013335728 1.68E-13 12.77580478 0.114669973 LEAALGEAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LEAALGEAKK 10 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 1 ; LEAALGEAK(1)K;LEAALGEAK(1)K 148.32 0.0020868 3348600 1730.37 1709.05 1662.16 1694.92 3825.4 3120.8 3220 3475.7 3596.9 3017 FALSE TRUE FALSE 1709.279585 1733.110051 1691.089198 1890.894625 3630.175563 2921.390952 3493.50672 3576.263896 3275.184255 2938.617905 0.581661053 0.589770466 0.575470936 0.64346393 1.235334324 0.994137736 1.188826459 1.216988398 1.114532192 1 11.52092207 -8.759544596 24.99992072 0.751276167 1.149201821 0.548298149 0.181337199 33.21105024 438177.5967 0.029051045 0.055829027 1.74E-09 8.759544596 0.397925654 LEADLEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LEADLEKK 8 1 P47897;P47897-2;A0A1B0GVU9;B4DDN1;A0A0U1RQT0;C9J165;A0A0U1RRJ7;A0A0U1RQE9;A0A0U1RRI9;A0A0U1RR66;A0A0U1RQJ6;A0A0U1RQL2 P47897 QARS Glutamine--tRNA ligase 0 1 LEADLEK(1)K 108.98 0.0029488 598680 339.39 335.99 350.7 324.83 958.98 715.02 759.09 372.98 957.8 669.84 FALSE TRUE FALSE 335.2533841 340.720076 356.8037864 362.388373 910.0396722 669.3325296 823.5670857 383.7715878 872.1319691 652.4374602 0.51384754 0.522226415 0.546878143 0.555437716 1.394830505 1.025895309 1.262292765 0.588212068 1.33672884 1 9.349695808 -8.777614486 24.9999755 0.712333064 1.078705807 0.198203667 0.31259612 233.6739168 361162.0648 0.041289389 0.075007441 1.67E-09 8.777614486 0.366372743 LEAES(ph)MGFFTK ddPTM_HeLa_Romidepsin_16h_R1 1 LEAESMGFFTK 11 0 Q9BTE7;J3QQL8;H0YCN4 Q9BTE7 DCUN1D5 DCN1-like protein 5;DCN1-like protein 1 0 LEAES(0.983)MGFFT(0.017)K 101.54 0.025443 21504000 2027.1 1960.4 1907.3 2181.7 2043 1731 1969.8 1938.3 1916.2 1776.2 TRUE FALSE FALSE 2002.392925 1987.998563 1940.495756 2433.958419 1938.738087 1620.394687 2137.114763 1994.381652 1744.810273 1730.054068 1.157416385 1.149096204 1.121638793 1.406868412 1.12062283 0.936615055 1.235287846 1.152785736 1.008529332 1 10.75660141 -12.05621796 0.709760137 0.992705656 1.161835087 0.243581519 0.109521415 0.941634629 0.815113774 0.09156658 0.023638696 8.79E-13 12.05621796 0.169129431 LEAIEDDSVKETDSSSAS(ph)AATPSK ddPTM_HeLa_Romidepsin_16h_R1 1 LEAIEDDSVKETDSSSASAATPSK 24 1 A6NJA2;P54578-2;P54578-3;P54578 A6NJA2 USP14 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 14 1 0 LEAIEDDS(0.016)VKET(0.066)DS(0.239)S(0.171)S(0.171)AS(0.274)AAT(0.05)PS(0.013)K 55.049 0.0047719 5266600 611.14 644.8 580 639.54 790.16 558.24 618.54 655.42 1013.3 746.83 TRUE FALSE FALSE 603.6911906 653.8775113 590.0946567 713.4866239 749.8351867 522.5702656 671.0787722 674.3835436 922.6679101 727.4272489 0.829899061 0.898890593 0.811207798 0.980835712 1.03080437 0.718381483 0.922537303 0.927080398 1.268398883 1 9.506659159 -12.51042772 1.265437942 0.999907296 0.883802299 0.277509386 0.120606627 0.577694416 1.657962935 0.057546171 0.0139341 3.09E-13 12.51042772 -0.116104997 LEAIEDDSVKETDSSSASAAT(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 LEAIEDDSVKETDSSSASAATPSK 24 1 A6NJA2;P54578-2;P54578-3;P54578 A6NJA2 USP14 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 14 1 0 LEAIEDDS(0.001)VKET(0.024)DS(0.107)S(0.107)S(0.112)AS(0.112)AAT(0.455)PS(0.082)K 79.67 5.40E-05 0 1044.1 1113 923.69 847.68 966.18 862.4 859.91 969.45 1064.6 876.62 TRUE FALSE FALSE 1031.374108 1128.668843 939.766437 945.6927501 916.8722293 807.2954233 932.9507339 997.4995062 969.3795097 853.845286 1.207916849 1.321865754 1.100628477 1.107569211 1.073815414 0.945482087 1.092646114 1.168243852 1.13531049 1 9.737830872 -8.799303396 3.66292186 1.120434258 1.062148773 0.099708781 0.09445199 0.626223685 17.54264258 0.01750814 0.034176745 1.59E-09 8.799303396 -0.058285485 LEAQDS(ph)GEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 LEAQDSGEEAR 11 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 LEAQDS(1)GEEAR 111.72 0.013789 5356400 1390.4 1206 1329.6 790.98 833.93 998.25 935.79 926.64 918.07 1353 TRUE FALSE FALSE 1373.45327 1222.9781 1352.74113 882.4368293 791.3714403 934.4650467 1015.275979 953.4508664 835.9555199 1317.848865 1.04219331 0.928010891 1.026476682 0.669603968 0.600502426 0.709083622 0.770403956 0.723490297 0.634333376 1 10.36396921 -9.262624133 24.99926054 1.012521667 0.694402371 0.36607497 0.129487625 23.41084666 493988.6113 0.008145279 0.012879459 5.46E-10 9.262624133 -0.318119297 LEAS(ph)YSDSPPGEEDLLVHVAEGSK ddPTM_HeLa_Romidepsin_16h_R1 4 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 LEAS(0.951)YS(0.048)DS(0.001)PPGEEDLLVHVAEGSK;LEAS(0.984)YS(0.015)DS(0.001)PPGEEDLLVHVAEGSK;LEAS(0.805)Y(0.001)S(0.157)DS(0.037)PPGEEDLLVHVAEGSK;LEAS(0.953)YS(0.047)DSPPGEEDLLVHVAEGSK ;;; 187.54 9.91E-23 39241300 11564 12215.1 13003.9 10980.78 14834.2 15471.4 9645.2 15350.8 11471.79 12105.6 TRUE FALSE FALSE 11423.05352 12387.0645 13230.22742 12250.42945 14077.15542 14482.82747 10464.46305 15794.95118 10445.72437 11791.09477 0.968786508 1.050544054 1.122052505 1.038956067 1.193880271 1.228285224 0.887488673 1.339566129 0.88589945 1 13.52541005 -9.847152935 1.528561389 0.984537397 1.133249362 0.323255076 0.116177125 0.354495994 1.667358019 0.018138446 0.025608248 1.42E-10 9.847152935 0.148711965 LEASYS(ph)DSPPGEEDLLVHVAEGSK ddPTM_HeLa_Romidepsin_16h_R1 1 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 LEAS(0.126)Y(0.002)S(0.468)DS(0.404)PPGEEDLLVHVAEGSK 82.6 2.41E-05 0 701.68 645.2 791.87 540.03 824.31 753.83 525.97 705.24 902.73 791.57 TRUE FALSE FALSE 693.1276543 654.2831425 805.6521652 602.4708095 782.2423848 705.6626959 570.6458787 725.6450067 821.9875679 771.0048973 0.898992544 0.848610878 1.044937805 0.781409835 1.014575118 0.915250601 0.740132625 0.941167831 1.066124963 1 9.590596214 -16.52287875 0.167956341 1.423670162 0.866106976 0.249465374 0.090701533 75.12735038 0.827299267 10.42966951 0.139487918 3.00E-17 16.52287875 -0.557563186 LEASYSDS(ph)PPGEEDLLVHVAEGSK ddPTM_HeLa_Romidepsin_16h_R1 2 LEASYSDSPPGEEDLLVHVAEGSK 24 0 Q7Z3C6;C9JS65;C9JFV2;F2Z3I6;C9JX27;C9IYZ9;C9JKV7;C9JDK4;C9JXG2;Q7Z3C6-3 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 LEAS(0.095)Y(0.001)S(0.376)DS(0.529)PPGEEDLLVHVAEGSK;LEAS(0.02)YS(0.141)DS(0.839)PPGEEDLLVHVAEGSK ; 168.26 2.02E-14 25484000 5991.52 6037 5741.5 5430.2 5803.6 6238.7 3959.21 5141.5 7475.4 5797 TRUE FALSE FALSE 5918.49305 6121.989044 5841.428399 6058.065274 5507.420636 5840.067204 4295.505199 5290.261191 6806.781502 5646.393104 1.048190046 1.084230044 1.034541572 1.072908875 0.975387391 1.034300499 0.760752062 0.936927538 1.205509672 1 12.46311386 -7.778739146 24.98827778 1.029260623 0.848839819 0.531422669 0.074618746 80.65497898 116500.7045 0.00649495 0.019551199 1.66E-08 7.778739146 -0.180420804 LEDNDSAAS(ph)DPDAETTAR ddPTM_HeLa_Romidepsin_16h_R1 2 LEDNDSAASDPDAETTAR 18 0 C9J6R3;C9J9X8;C9JCX6;C9JXA0;Q9BYV8-5;Q9BYV8-2;Q9BYV8;F8WF85 C9J6R3 CEP41 Centrosomal protein of 41 kDa 1 0 LEDNDS(0.142)AAS(0.858)DPDAETTAR;LEDNDS(0.101)AAS(0.82)DPDAET(0.04)T(0.04)AR ; 175.16 5.59E-08 14633100 3758.3 3932.7 3653.4 3336.5 3646.7 3718.2 2866.8 3196.4 4298.5 4058.8 TRUE FALSE FALSE 3712.492394 3988.064654 3716.985894 3722.281829 3460.595291 3480.61902 3110.30592 3288.882791 3914.031394 3953.351791 0.939074636 1.008780616 0.940211267 0.941550873 0.875357285 0.880422286 0.786751619 0.831922623 0.990053909 1 11.94886062 -8.443111401 0.834867542 0.974385551 0.798563769 0.853907402 0.026890245 0.231370823 0.267313834 0.005079659 0.025864858 3.60E-09 8.443111401 -0.175821782 LEDNPSSGS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 LEDNPSSGSPPR 12 0 Q05D32;H0YMH7;Q05D32-2 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 LEDNPS(0.001)S(0.005)GS(0.994)PPR;LEDNPS(0.017)S(0.064)GS(0.919)PPR ; 103.11 0.014066 31200700 2900.3 3023.5 2984.8 2663.1 3860 4428.7 3620.4 3649 3574.3 2759.7 TRUE FALSE FALSE 2864.950028 3066.064912 3036.749192 2971.020152 3663.009796 4145.720363 3927.916686 3754.578058 3254.605656 2688.002596 1.065828594 1.140648047 1.129741912 1.105289168 1.362725543 1.542305193 1.461277118 1.396791083 1.210789625 1 11.39231882 -8.731232327 2.363729244 1.049170826 1.469114423 0.821670266 0.074224411 0.061766673 0.703506169 0.009500396 0.020513911 1.86E-09 8.731232327 0.419943597 LEDTENWLYEDGEDQPK ddPTM_HeLa_Romidepsin_16h_R1 1 LEDTENWLYEDGEDQPK 17 0 A0A087WYC1;P34932 A0A087WYC1 HSPA4 Heat shock 70 kDa protein 4 0 0 103.14 0.028899 6376500 1515.7 1776.3 1740.4 1598.1 1966.6 1943.9 1505.3 1693.1 2390.4 1788.7 FALSE FALSE TRUE 1497.226065 1801.306798 1770.690932 1782.879841 1866.237064 1819.691064 1633.160144 1742.087177 2176.596637 1742.229316 0.859373707 1.033909131 1.01633632 1.023332477 1.071177626 1.044461281 0.937396776 0.999918415 1.249316962 1 10.76671881 -10.23173527 24.87432828 0.933593132 1.018165413 0 0.109652241 612.3339084 512771.6434 0.010205174 0.012497747 5.86E-11 10.23173527 0.084572281 LEDTK(ac)LIK ddPTM_HeLa_Romidepsin_16h_R1 1 LEDTKLIK 8 1 E7ENZ3;B7ZAR1;E9PCA1;P48643-2;P48643 E7ENZ3 CCT5 T-complex protein 1 subunit epsilon 0 1 LEDTK(1)LIK 107.57 0.016394 519320 745.57 650.24 467.81 739.18 464.07 753.6 595.12 522.11 718.62 1019.3 FALSE TRUE FALSE 736.4827061 659.3940958 475.9520368 824.6474695 440.3867762 705.4473921 645.6694779 537.2164291 654.3448274 992.8184391 0.74181006 0.664163829 0.47939484 0.830612564 0.443572318 0.710550252 0.650339934 0.541102389 0.659078036 1 9.9553861 -11.3902651 0.509252624 1.014743834 0.60316343 0.101046969 0.148771793 0.405387232 0.224100851 0.074663825 0.031343599 4.07E-12 11.3902651 -0.411580404 LEDVKNS(ph)PTFK ddPTM_HeLa_Romidepsin_16h_R1 1 LEDVKNSPTFK 11 1 H0YC42;P55327-2;P55327;P55327-3 H0YC42 TPD52 Tumor protein D52 1 0 LEDVKNS(0.939)PT(0.061)FK 69.314 0.029607 39560000 6759.4 6767.4 6248.3 8242 8298.4 8679.3 7591.1 8557.4 6291.8 6737 TRUE FALSE FALSE 6677.013833 6862.671635 6357.04904 9194.97882 7874.901682 8124.720741 8235.887845 8804.994868 5729.04565 6561.971769 1.01753163 1.04582462 0.968771166 1.40125242 1.200081616 1.238152346 1.255093459 1.34182151 0.873067708 1 12.67991367 -9.272518668 24.99976968 1.009208662 1.277918416 0.824051567 0.070085762 177.6378349 400828.7255 0.007909438 0.012149283 5.34E-10 9.272518668 0.268709754 LEEELDDLLVDLDHQR ddPTM_HeLa_Romidepsin_16h_R1 2 LEEELDDLLVDLDHQR 16 0 P35579-2 P35579-2 MYH9 Myosin-9 0 0 ; ; 213.83 2.78E-26 8994400 1259.39 1132.35 1007.33 909 1429.11 1507.31 1060.66 1505.5 1386.98 1407.65 FALSE FALSE TRUE 1244.04007 1148.291253 1024.862156 1014.102857 1356.177184 1410.997756 1150.752434 1549.059267 1262.925035 1371.07905 0.907343796 0.837509152 0.747485826 0.739638504 0.989131286 1.02911481 0.839304221 1.129810325 0.921117593 1 10.42109604 -7.246622713 23.93259734 0.920360323 1.129810596 0.305012737 0.099523791 1687.671157 2725927.237 0.015398432 0.437953785 5.67E-08 7.246622713 0.209450273 LEEGMVFT(ph)EY(ph)EQIPK ddPTM_HeLa_Romidepsin_16h_R1 1 LEEGMVFTEYEQIPK 15 0 Q15678 Q15678 PTPN14 Tyrosine-protein phosphatase non-receptor type 14 2 0 LEEGMVFT(1)EY(1)EQIPK 78.401 0.0022284 0 1479.7 1112 1169.7 966.27 832.9 859.48 730.82 744.78 1539.9 1322.3 TRUE FALSE FALSE 1461.664847 1127.654765 1190.058138 1077.994684 790.394005 804.5620018 792.8958326 766.3290342 1402.167487 1287.946455 1.134880135 0.875544756 0.923996594 0.836987189 0.613685454 0.624685909 0.615627947 0.595000694 1.088684612 1 10.3308569 -9.188568644 1.003266706 1.059225083 0.59304631 0.906999657 0.060212781 0.118569168 0.235622137 0.012736573 0.028403563 6.48E-10 9.188568644 -0.466178773 LEELHVIDVK ddPTM_HeLa_Romidepsin_16h_R1 1 LEELHVIDVK 10 0 Q16531;F5GY55;F5GWI0;F5H2L3 Q16531 DDB1 DNA damage-binding protein 1 0 0 89.9 0.018189 4988700 6474 6376.8 6223.8 5903.4 5790.5 6191.8 5624.2 6113.3 7258.6 6236.7 FALSE FALSE TRUE 6395.092398 6466.572758 6332.122628 6585.978884 5494.989178 5796.163963 6101.919408 6290.17869 6609.372637 6074.669635 1.052747356 1.06451431 1.042381398 1.084170709 0.904574159 0.954152952 1.004485803 1.035476671 1.088021742 1 12.56859024 -8.774154179 24.99800801 1.033948898 0.975336234 0.418456299 0.042284694 213.3406675 419439.7298 0.00634585 0.011558976 1.68E-09 8.774154179 -0.058612664 LEEPEEPKVLT(ph)PEEQLADK ddPTM_HeLa_Romidepsin_16h_R1 1 LEEPEEPKVLTPEEQLADK 19 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 LEEPEEPKVLT(1)PEEQLADK 89.201 0.002291 16185000 3120.2 2739.4 3326.9 3002 3381.1 3793.3 3483.7 3715.8 3736.9 3007 TRUE FALSE FALSE 3082.169802 2777.965345 3384.803299 3349.105365 3208.54985 3550.920372 3779.605391 3823.31081 3402.662305 2928.877707 1.052338169 0.948474338 1.15566563 1.143477366 1.095487819 1.212382601 1.290462003 1.305384244 1.161763189 1 11.51613224 -7.521834485 0.401549972 1.010550122 1.515713569 0.625510391 0.067534414 1.27651099 0.161370068 0.013456777 0.297630597 3.01E-08 7.521834485 0.505163447 LEEPEEPKVLT(ph)PEEQLADKLR ddPTM_HeLa_Romidepsin_16h_R1 1 LEEPEEPKVLTPEEQLADKLR 21 2 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 LEEPEEPKVLT(1)PEEQLADKLR 45.572 0.026166 10661000 2841.8 2864 2107.3 3767.7 2687.4 2967.8 2626.9 2775.5 2758.7 2159.1 TRUE FALSE FALSE 2807.163049 2904.319467 2143.976673 4203.339202 2550.25195 2778.167158 2850.02882 2855.804713 2511.954963 2103.006271 1.334833418 1.381032243 1.019481826 1.998728801 1.212669684 1.321045589 1.355216511 1.357963004 1.194459093 1 11.03823744 -12.00432833 0.502745545 0.943940921 1.392995514 0.160019732 0.240262519 1.329448564 0.531920132 0.288009619 0.061568507 9.90E-13 12.00432833 0.449054593 SPAGPAATPAQAQAAST(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SPAGPAATPAQAQAASTPR 19 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 SPAGPAATPAQAQAAS(0.234)T(0.766)PR;SPAGPAATPAQAQAAS(0.051)T(0.949)PR ; 200.4 1.03E-20 147615000 5371.6 5291.6 5504.7 3923 2756.4 2328.8 1972.08 1497.45 5339.7 5418.7 TRUE FALSE FALSE 5306.128873 5366.095284 5600.506994 4376.595718 2615.730622 2179.997196 2139.588426 1540.776353 4862.103858 5277.921393 1.00534443 1.016706177 1.061119819 0.829227151 0.495598632 0.413040861 0.405384671 0.291928628 0.921215664 1 12.36575415 -8.792562119 2.098708056 1.00845318 0.373460837 0.974527891 0.046193213 0.025547176 0.229347563 0.005582774 0.012012748 1.61E-09 8.792562119 -0.634992343 down LEEPTPAPSTS(ph)YSPQADSLR ddPTM_HeLa_Romidepsin_16h_R1 1 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 LEEPTPAPS(0.139)T(0.139)S(0.437)Y(0.07)S(0.216)PQADSLR 146.28 3.23E-05 23417000 2363.6 2168.1 2041.8 2192.6 2230 2039.8 2016.8 2230 2374.8 2345.1 TRUE FALSE FALSE 2334.791534 2198.622569 2077.336673 2446.118728 2116.194779 1909.463363 2188.106942 2294.521532 2162.39194 2284.173964 1.02216012 0.962546025 0.909447663 1.070898612 0.926459548 0.835953563 0.957942335 1.004530114 0.946684436 1 11.15745682 -9.686369295 0.834658232 1.010514501 0.939553417 0.007820267 0.062099341 0.712966801 0.995647062 0.012496448 0.021270202 2.06E-10 9.686369295 -0.070961084 LEEPTPAPSTSYS(ph)PQADSLR ddPTM_HeLa_Romidepsin_16h_R1 1 LEEPTPAPSTSYSPQADSLR 20 0 G3V1L9;Q07157 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 LEEPTPAPS(0.017)T(0.009)S(0.122)Y(0.002)S(0.85)PQADSLR 154.72 1.20E-07 22433000 5748.4 5392.9 5225.9 5643 6135.1 6145.2 5519.5 5392.6 6155.9 5485.6 TRUE FALSE FALSE 5678.33629 5468.821388 5316.854597 6295.470211 5822.002954 5752.541553 5988.326192 5548.626373 5605.300886 5343.083321 1.062745226 1.023532867 0.995091088 1.178246685 1.08963357 1.076633323 1.12076227 1.038468996 1.049076076 1 12.3834568 -9.287467273 24.99498756 1.027473154 1.099903557 0.489426798 0.038109872 521.1848893 500500.5901 0.006084832 0.009297195 5.16E-10 9.287467273 0.072430402 LEEVLTNK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LEEVLTNKK 9 1 Q5TA02;P78417-3;P78417 Q5TA02 GSTO1 Glutathione S-transferase omega-1 0 1 ; LEEVLTNK(1)K;LEEVLTNK(1)K 189.38 1.01E-08 3929800 2305.71 2351.16 2319.63 1566.06 3416.7 3240.8 2781.5 2895.6 2943.9 2397.1 FALSE TRUE FALSE 2277.60712 2384.259692 2360.002187 1747.135226 3242.33305 3033.723339 3017.760541 2979.379617 2680.590211 2334.822996 0.975494555 1.021173638 1.010784197 0.748294508 1.388684733 1.299337613 1.292500779 1.276062306 1.148091403 1 11.18909747 -8.744324922 24.99999988 0.977742005 1.311542545 0.737846375 0.096366571 73.32273646 107105.8768 0.010920748 0.021798724 1.80E-09 8.744324922 0.33380054 LEFQQQLGEAPSDAS(ph)P ddPTM_HeLa_Romidepsin_16h_R1 2 LEFQQQLGEAPSDASP 16 0 Q9BUW7 Q9BUW7 C9orf16 UPF0184 protein C9orf16 1 0 LEFQQQLGEAPSDAS(1)P;LEFQQQLGEAPS(0.006)DAS(0.994)P ; 173.33 5.90E-06 56239000 3804 4068.4 3605.6 2931.7 7493.1 9876 8390.9 10274.8 3985.5 4115.1 TRUE FALSE FALSE 3757.635385 4125.675042 3668.353956 3270.676948 7110.699146 9244.955473 9103.622837 10572.08513 3629.026898 4008.189109 0.937489545 1.029311475 0.915214791 0.815998662 1.774042829 2.306516789 2.271255819 2.63762134 0.905403113 1 11.96873486 -8.519998632 2.48898043 0.959111888 2.404028246 0.967771414 0.121086416 0.033154513 0.409182514 0.017151776 0.041096339 3.02E-09 8.519998632 1.444916358 up LEGDS(ph)DVDSELEDRVDGVK ddPTM_HeLa_Romidepsin_16h_R1 2 LEGDSDVDSELEDRVDGVK 19 1 Q92614;Q92614-2 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 LEGDS(0.995)DVDS(0.005)ELEDRVDGVK;LEGDS(1)DVDSELEDRVDGVK ; 155.54 1.23E-06 10097800 3508.5 3485.4 3084.9 2511 3880 4799.3 3802.9 4951.9 3696.4 3451.3 TRUE FALSE FALSE 3465.737052 3534.467553 3138.59139 2801.333635 3681.989122 4492.640219 4125.918231 5095.175414 3365.784726 3361.634728 1.030967768 1.051413327 0.933650335 0.833324814 1.095297205 1.336445088 1.227354714 1.515683834 1.001234518 1 11.71494726 -8.331848123 3.346942276 0.998918307 1.352508424 0.786023722 0.089043707 0.086682389 1.897420316 0.01254199 0.031106339 4.66E-09 8.331848123 0.353590117 LEGDSDDLLEDS(ph)DSEEHSR ddPTM_HeLa_Romidepsin_16h_R1 1 LEGDSDDLLEDSDSEEHSR 19 0 A0A3B3IUB9;Q9NR09 A0A3B3IUB9 BIRC6 Baculoviral IAP repeat-containing protein 6 1 0 LEGDSDDLLEDS(1)DSEEHSR 251.35 2.35E-70 0 821.07 988.39 1050.6 892.99 980.55 1218.6 851.66 985.58 1192.2 1123.5 TRUE FALSE FALSE 811.062483 1002.30458 1068.885252 996.2417054 930.5088746 1140.735393 923.9999791 1014.096202 1085.566646 1094.311308 0.74116248 0.915922711 0.976765244 0.910382355 0.850314593 1.042423106 0.844366655 0.926698093 0.992008981 1 10.0958075 -10.02676623 24.88751408 0.875180199 0.924709394 0 0.087152043 1911.575181 1777397.477 0.017739739 0.021762665 9.40E-11 10.02676623 0.049529196 LEGEVT(ph)PNSLSTSYK ddPTM_HeLa_Romidepsin_16h_R1 1 LEGEVTPNSLSTSYK 15 0 H0Y785;H0Y472;H0Y4P6;Q8IWZ3;Q8IWZ3-4;Q8IWZ3-6;A0A0A0MQZ8;H0Y7Y3 H0Y785 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 0 LEGEVT(0.998)PNS(0.002)LSTSYK 224.59 2.31E-34 9643200 2534.5 2686 2187.6 2417.7 3082.7 3231.8 2037.6 2432.3 2211.2 2331.8 TRUE FALSE FALSE 2503.608539 2723.813579 2225.67426 2697.24585 2925.378316 3025.29841 2210.673693 2502.674763 2013.424734 2271.2195 1.102319058 1.199273597 0.979946791 1.187576036 1.288020958 1.332014986 0.97334216 1.101907924 0.886495002 1 11.14925143 -11.24031665 0.514696818 0.998331056 1.162530074 0.306048573 0.115578352 1.046644087 0.621611775 0.074668812 0.036549841 5.75E-12 11.24031665 0.164199018 LEGEVTPNSLST(ph)SYK ddPTM_HeLa_Romidepsin_16h_R1 1 LEGEVTPNSLSTSYK 15 0 H0Y785;H0Y472;H0Y4P6;Q8IWZ3;Q8IWZ3-4;Q8IWZ3-6;A0A0A0MQZ8;H0Y7Y3 H0Y785 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 0 LEGEVTPNS(0.002)LS(0.195)T(0.712)S(0.091)YK 132.65 9.97E-05 0 2266.9 2546.8 2287.4 1899.5 2150.6 2007.8 1678.2 1779.9 2516.2 2057.3 TRUE FALSE FALSE 2239.270151 2582.653917 2327.211237 2119.129127 2040.846857 1879.50806 1820.746266 1831.398598 2291.14477 2003.851049 1.117483334 1.288845255 1.161369373 1.057528267 1.018462354 0.937947988 0.908623556 0.913939486 1.143370796 1 10.96855956 -8.414749107 1.952841327 1.085368666 0.912214133 0.566624565 0.077082391 0.274572542 2.029779794 0.01401167 0.039265059 3.85E-09 8.414749107 -0.173154533 LEGGEVDLK(ac)GPK ddPTM_HeLa_Romidepsin_16h_R1 1 LEGGEVDLKGPK 12 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 1 LEGGEVDLK(1)GPK 159.94 1.75E-24 0 248.69 162.01 157.76 123.52 377.8 260.42 362.13 245.06 302.9 289.82 FALSE TRUE FALSE 245.6588706 164.290781 160.5057466 137.8019636 358.5194562 243.7800025 392.8893132 252.1504245 275.8078654 282.2904346 0.870234484 0.581992023 0.568583724 0.488156688 1.270037565 0.863578686 1.391791095 0.893230494 0.977035817 1 8.141036434 -8.726456355 24.99945235 0.848561975 1.107948706 0.315124819 0.230631451 229.0162149 163657.8809 0.035869653 0.07173696 1.88E-09 8.726456355 0.25938673 LEGGRQDS(ph)EDEEER ddPTM_HeLa_Romidepsin_16h_R1 2 LEGGRQDSEDEEER 14 1 A0A3B3ISZ4;Q9BYE7-3;Q9BYE7 A0A3B3ISZ4 PCGF6 Polycomb group RING finger protein 6 1 0 LEGGRQDS(1)EDEEER;LEGGRQDS(1)EDEEER ; 184.48 8.18E-07 21225000 2654 2579.6 2678.7 2520.2 2491.16 2747.8 2207.5 2170.08 2633.6 2897.5 TRUE FALSE FALSE 2621.652027 2615.915677 2725.32165 2811.597382 2364.026809 2572.224448 2395.004995 2232.867841 2398.04422 2822.222532 0.928931719 0.926899154 0.965665045 0.996235183 0.837647203 0.911418011 0.848623724 0.791173558 0.849700615 1 11.46261603 -4.54816238 0.27089914 0.97990613 7.89E-15 0.350385452 0.054574168 15.69479821 0.260552068 0.018457727 6.883007121 2.83E-05 4.54816238 -0.97990613 LEGNS(ph)PQGSNQGVK ddPTM_HeLa_Romidepsin_16h_R1 2 LEGNSPQGSNQGVK 14 0 P61006 P61006 RAB8A Ras-related protein Rab-8A 1 0 LEGNS(0.952)PQGS(0.048)NQGVK;LEGNS(0.987)PQGS(0.013)NQGVK ; 170.11 5.74E-05 12162000 2085.06 3126.3 2627.2 1642.35 2660.1 3885 2200.48 2930.7 2548.6 2521.5 TRUE FALSE FALSE 2059.646487 3170.312133 2672.925314 1832.246234 2524.345171 3636.761038 2387.388716 3015.495181 2320.646833 2455.991067 0.838621327 1.290848398 1.088328598 0.746031311 1.027831577 1.480771281 0.972067345 1.22781195 0.944892213 1 11.2620896 -8.507286836 24.62046006 0.952476971 1.210218519 0.257588984 0.179185401 550.9121599 869919.0196 0.025696117 0.055815433 3.11E-09 8.507286836 0.257741548 LEGPVS(ph)PDVEPGKEETEESK ddPTM_HeLa_Romidepsin_16h_R1 2 LEGPVSPDVEPGKEETEESK 20 1 O14686-3;O14686;A0A3B3ISC8 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 1 0 LEGPVS(0.997)PDVEPGKEET(0.002)EES(0.001)K;LEGPVS(1)PDVEPGKEETEESK ; 106.93 0.00017071 77466000 5585.9 4806 4976.3 3888.3 4721 4047.4 3379.5 3883.5 5538.9 5519.7 TRUE FALSE FALSE 5517.816902 4873.658994 5062.910414 4337.883541 4480.069754 3788.784202 3666.554646 3995.862945 5043.486912 5376.297398 1.026322856 0.906508445 0.941709515 0.806853345 0.83330021 0.704719981 0.681985086 0.743236962 0.938096712 1 12.39239723 -9.102231248 0.78428838 1.013705983 0.696886085 0.862708897 0.043074482 0.116063338 0.137778931 0.00678666 0.018479085 7.90E-10 9.102231248 -0.316819898 LEGQGDVPT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LEGQGDVPTPK 11 0 Q9Y2Z0-2;Q9Y2Z0 Q9Y2Z0-2 SUGT1 Suppressor of G2 allele of SKP1 homolog 1 0 LEGQGDVPT(1)PK 116.63 0.02385 10178000 3152.4 3497.3 3146.9 2070.7 3004.1 4075.5 2653.1 3954.9 3386.6 2925.9 TRUE FALSE FALSE 3113.977336 3546.535081 3201.670474 2310.124077 2850.789567 3815.088703 2878.454248 4069.328792 3083.694014 2849.884696 1.092667833 1.244448621 1.1234386 0.810602646 1.000317511 1.338681775 1.01002481 1.427892433 1.082041676 1 11.47668783 -4.198251579 0.984477111 1.054470204 199.9999817 0.337749804 0.140095229 823.2503369 1.803937205 0.021038188 368430.3851 6.34E-05 4.198251579 198.9455115 LEGVDGGQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LEGVDGGQSPR 11 0 O00418;H3BRH4 O00418 EEF2K Eukaryotic elongation factor 2 kinase 1 0 LEGVDGGQS(1)PR;LEGVDGGQS(1)PR ; 125.82 0.0074483 35344000 10640.7 10243.1 9700.1 7870.8 9277.4 8688.2 6882 7282.5 10943.4 10246.1 TRUE FALSE FALSE 10511.00706 10387.30263 9868.926172 8780.858929 8803.939659 8133.05206 7466.556908 7493.207648 9964.594896 9979.904845 1.053217162 1.040821811 0.988879786 0.879853973 0.882166694 0.814942846 0.748159128 0.750829568 0.998465922 1 13.28481034 -8.719306373 0.907401811 1.028260828 0.745347311 0.941391278 0.026706205 0.111035197 0.170071401 0.005344682 0.018750489 1.91E-09 8.719306373 -0.282913517 LEGVLAEVAQHYQDTLIR ddPTM_HeLa_Romidepsin_16h_R1 1 LEGVLAEVAQHYQDTLIR 18 0 P46940;A0A0J9YXZ5 P46940 IQGAP1 Ras GTPase-activating-like protein IQGAP1 0 0 168.16 1.86E-07 1705600 625.73 549.76 513.15 632.38 615.95 643.16 679.77 623.86 691.68 742.48 FALSE FALSE TRUE 618.1033621 557.4995357 522.0811605 705.498751 584.5157731 602.0641517 737.5096468 641.9104048 629.8144085 723.1902626 0.854689829 0.770889162 0.72191398 0.97553685 0.808246188 0.832511419 1.0198003 0.887609303 0.870883419 1 9.498231442 -12.05068769 0.96787599 0.995317565 0.859734214 0.03315619 0.092144454 0.550452237 0.97567378 0.047502855 0.016388619 8.90E-13 12.05068769 -0.135583351 LEIS(ph)PDSSPER ddPTM_HeLa_Romidepsin_16h_R1 2 LEISPDSSPER 11 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 0 LEIS(0.556)PDS(0.444)SPER;LEIS(0.952)PDS(0.048)SPER ; 163.12 0.00093045 7495700 2116.57 2265.2 2533.4 3050.7 4928.3 6463.8 5630.2 6059.6 2777 2656.2 TRUE FALSE FALSE 2090.772431 2297.089545 2577.492764 3403.436288 4676.790461 6050.784041 6108.429047 6234.924966 2528.618165 2587.191541 0.80812433 0.887869919 0.996251234 1.315494517 1.807670745 2.338746067 2.361026986 2.409920126 0.977360247 1 11.33717115 -8.676492154 1.383153894 0.904605013 2.41962577 0.991608167 0.058160527 0.033049041 0.125562087 0.012439762 0.033978623 2.11E-09 8.676492154 1.515020757 up LEK(ac)HELIEFR ddPTM_HeLa_Romidepsin_16h_R1 1 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 1 LEK(1)HELIEFR 105.36 0.0097846 409170 651.42 653.48 662.86 529.88 919.65 968.13 663.47 813.93 984.83 752.03 FALSE TRUE FALSE 643.4802425 662.6797086 674.3968002 591.1472188 872.7168288 906.2696175 719.8251252 837.4797804 896.7443382 732.4921522 0.878480733 0.904691889 0.92068809 0.807035566 1.191435057 1.237241402 0.982706945 1.143329356 1.224237469 1 9.516669493 -8.750333898 24.99937274 0.927818326 1.134577639 0.338222111 0.12148944 117.806665 265190.9724 0.012266868 0.024351629 1.78E-09 8.750333898 0.206759313 LEKEQAAALGPASATPALS(ph)SSPPPPSTLYR ddPTM_HeLa_Romidepsin_16h_R1 1 LEKEQAAALGPASATPALSSSPPPPSTLYR 30 1 Q9P242 Q9P242 NYAP2 Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 2 1 0 LEKEQAAALGPAS(0.009)AT(0.026)PALS(0.318)S(0.318)S(0.318)PPPPS(0.002)T(0.002)LY(0.007)R 57.347 0.00068193 13191000 1621.2 1972.7 1576.9 3222.7 1395.7 1051.1 883.95 774.3 1890.3 1678.6 TRUE FALSE FALSE 1601.440191 2000.471722 1604.345283 3595.323737 1324.472221 983.9381023 959.0326909 796.7031489 1721.226834 1634.98973 0.979480275 1.223537791 0.981257101 2.198988575 0.810079841 0.601800785 0.586568021 0.487283274 1.052744737 1 10.67506586 -8.527377783 24.99935726 1.101117137 0.585450248 0.399722714 0.356642731 118.0287731 655838.2045 0.052937931 0.106204595 2.97E-09 8.527377783 -0.51566689 LEKET(ph)TMY(ph)RSRWES(ph)SNK ddPTM_HeLa_Romidepsin_16h_R1 1 LEKETTMYRSRWESSNK 17 3 P40222 P40222 TXLNA Alpha-taxilin 3 0 LEKET(0.523)T(0.523)MY(0.945)RS(0.299)RWES(0.355)S(0.355)NK 43.798 0.028466 3224700 2016.5 2361.3 1794.1 1533.5 2293.6 1800 1577.3 1518.5 2129.7 2224.2 TRUE FALSE FALSE 1991.922122 2394.542443 1825.325558 1710.810485 2176.549033 1684.985809 1711.275823 1562.435402 1939.214298 2166.414963 0.919455486 1.105301839 0.84255583 0.789696579 1.004677807 0.777776113 0.789911375 0.721207815 0.895125971 1 11.08109389 -5.404005709 0.277409643 0.985524072 3.48E-15 0.441396744 0.087038778 13.69758506 0.34655768 0.037588913 5.635532491 3.94E-06 5.404005709 -0.985524072 LEKHELIEFR ddPTM_HeLa_Romidepsin_16h_R1 2 LEKHELIEFR 10 1 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 ; ; 108.43 0.0076409 24109900 10255.8 9723.2 9736 13293.1 10706.9 9876.4 9605.8 10045.5 10769.2 9409.4 FALSE FALSE TRUE 10130.79836 9860.083465 9905.450996 14830.11077 10160.48694 9245.329915 10421.71641 10336.15069 9805.97578 9164.942432 1.105385925 1.075847834 1.08079795 1.618134634 1.108625288 1.008771193 1.13712841 1.127792212 1.069944067 1 13.1619101 -10.82973904 0.788685827 1.020625227 1.174734904 0.103752275 0.158369996 0.84195457 1.139914899 0.049796137 0.041093677 1.48E-11 10.82973904 0.154109676 LEKPAK(ac)YDDIK ddPTM_HeLa_Romidepsin_16h_R1 2 LEKPAKYDDIK 11 2 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 1 ; LEKPAK(1)YDDIK;LEK(0.011)PAK(0.989)YDDIK 134.56 0.001801 2738300 1839.91 1514.79 1492.8 1623.88 3451 2524.9 2660.1 2549.8 3632.2 2776.3 FALSE TRUE FALSE 1817.484469 1536.115253 1518.781558 1811.640646 3274.882593 2363.567039 2886.048828 2623.57444 3307.326935 2704.171326 0.672104039 0.568053969 0.561643984 0.669942998 1.211048487 0.874044857 1.067258128 0.970195348 1.223046374 1 11.40097084 -8.772784053 24.96997982 0.783885284 1.022067414 0.258384131 0.205761483 225.5398527 496420.3733 0.028967264 0.052845036 1.69E-09 8.772784053 0.23818213 LEKPAKYDDIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LEKPAKYDDIKK 12 3 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 1 LEKPAK(0.002)YDDIK(0.998)K 46.159 0.030018 33524000 964.03 937.74 947.52 1640.7 2184.3 1707.2 1280.9 1334 2267.4 1499.6 FALSE TRUE FALSE 952.2800316 950.9415283 964.0111881 1830.405454 2072.82702 1598.11543 1389.699614 1372.597185 2064.598065 1460.640176 0.651960727 0.651044346 0.659992245 1.253152887 1.419122283 1.094119863 0.95143187 0.939723012 1.413488482 1 10.5123851 -9.258823593 24.97544369 0.802714709 1.135406878 0.175640031 0.254218145 187.6239836 1791425.128 0.031511078 0.050713908 5.51E-10 9.258823593 0.33269217 LEKPETQSS(ph)PITVQSSK ddPTM_HeLa_Romidepsin_16h_R1 2 LEKPETQSSPITVQSSK 17 1 Q96CB8;A0A087WXN4;E9PGI3 Q96CB8 INTS12 Integrator complex subunit 12 1 0 LEKPET(0.004)QS(0.179)S(0.783)PIT(0.034)VQSSK;LEKPET(0.001)QS(0.073)S(0.857)PIT(0.066)VQS(0.002)S(0.001)K ; 73.675 0.009844 94136000 8468.4 7771.6 7976.9 8518.7 8534.7 9039.4 8110.1 8303.3 8330.4 7679.4 TRUE FALSE FALSE 8365.183884 7881.008789 8115.734598 9503.672176 8099.142412 8461.811513 8798.971692 8543.542885 7585.30816 7479.888081 1.118356825 1.053626565 1.085007491 1.270563419 1.082789251 1.13127515 1.176350715 1.142201968 1.014093804 1 12.86880097 -14.70106107 0.16975805 0.714783011 1.179522658 0.496603653 0.053808896 19.46293119 0.380795 2.055792172 0.101007069 1.99E-15 14.70106107 0.464739647 LEKT(ph)IDDLEETLASAK ddPTM_HeLa_Romidepsin_16h_R1 1 LEKTIDDLEETLASAK 16 1 Q5TCU3;P07951-3;P07951-2 Q5TCU3 TPM2 Tropomyosin beta chain 1 0 LEKT(0.997)IDDLEET(0.003)LASAK 105.68 0.00039516 0 3922.4 3553.5 4783.2 2233.1 2902.6 3575.5 2599.2 2489 3834 4331.3 TRUE FALSE FALSE 3874.59228 3603.526266 4866.44959 2491.301529 2754.469491 3347.037089 2819.975983 2561.015288 3491.077438 4218.772202 0.918417041 0.854164694 1.153522721 0.590527625 0.652907851 0.793367579 0.668435234 0.607052281 0.827510297 1 12.04260747 -9.247698357 24.99962312 0.963834858 0.669532346 0.683409569 0.097837827 305.4756255 555764.9266 0.012981551 0.021454153 5.65E-10 9.247698357 -0.294302513 LEKVPDS(ph)PENELK ddPTM_HeLa_Romidepsin_16h_R1 1 LEKVPDSPENELK 13 1 A0A2R8Y549;Q8NI35-4;Q8NI35-3;Q8NI35-2;Q8NI35;A0A0U1RR46;A0A0X1KG69;A0A087WUZ6 A0A2R8Y549 INADL InaD-like protein 1 0 LEKVPDS(1)PENELK 70.335 0.02354 14128000 3708.9 3429.9 3358.2 3235.7 3904.2 3882.4 3212 3329.4 3880.6 3680.6 TRUE FALSE FALSE 3663.6945 3478.186222 3416.648062 3609.826858 3704.954105 3634.32717 3484.8272 3425.730936 3533.509417 3584.977481 1.021957465 0.970211456 0.953045892 1.006931529 1.033466493 1.01376569 0.972063902 0.955579485 0.985643406 1 11.80774834 -10.27196814 24.76788219 1.010368803 0.988248725 0.047264233 0.026061033 990.4845384 2330016.92 0.004682073 0.005388073 5.35E-11 10.27196814 -0.022120078 LELQGPRGS(ph)PNAR ddPTM_HeLa_Romidepsin_16h_R1 2 LELQGPRGSPNAR 13 1 P19338;H7BY16 P19338 NCL Nucleolin 1 0 LELQGPRGS(1)PNAR;LELQGPRGS(1)PNAR ; 69.846 0.024002 1180230000 8444.6 7854.5 5894.2 17918.9 7688.5 7072.9 6312.1 7063.3 7661.4 6047.9 TRUE FALSE FALSE 8341.673967 7965.075857 5996.786079 19990.76753 7296.127155 6620.964517 6848.249616 7267.665441 6976.145196 5890.774686 1.41605721 1.35212706 1.017996172 3.393571914 1.238568362 1.123954806 1.162538033 1.233736788 1.184249198 1 12.52424166 -11.58903265 0.697728544 1.016645979 1.517421316 0.057109847 0.652406084 1.44164651 1.41921532 0.361634418 0.152018017 2.58E-12 11.58903265 0.500775337 LELQSLEAAEIEPEAQAQRS(ph)PRPTGSDLLPGAPILSLR ddPTM_HeLa_Romidepsin_16h_R1 1 LELQSLEAAEIEPEAQAQRSPRPTGSDLLPGAPILSLR 38 2 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 0 LELQS(0.008)LEAAEIEPEAQAQRS(0.82)PRPT(0.083)GS(0.083)DLLPGAPILS(0.005)LR 42.446 0.014025 2803900 515.55 432.31 373.43 462.85 449.2 350.8 278.09 278 425.53 483.91 TRUE FALSE FALSE 509.2662783 438.3960715 379.9293925 516.3668948 426.2756478 328.3850122 301.7109577 286.0434914 387.469531 471.3379484 1.080469502 0.930109856 0.806065783 1.095534311 0.904394923 0.696708197 0.64011599 0.606875581 0.822063092 1 8.88061803 -8.292423596 2.181198519 1.014872634 0.6244341 0.63063725 0.100595675 0.106538697 0.977082118 0.0127961 0.037555651 5.10E-09 8.292423596 -0.390438534 LELSSSAS(ph)PQEER ddPTM_HeLa_Romidepsin_16h_R1 2 LELSSSASPQEER 13 0 A0A075B6T1;Q9C0C7-6;Q9C0C7-4;Q9C0C7-2;Q9C0C7-3;Q9C0C7;Q9C0C7-5 A0A075B6T1 AMBRA1 Activating molecule in BECN1-regulated autophagy protein 1 1 0 LELSSSAS(1)PQEER;LELSSS(0.001)AS(0.999)PQEER ; 242.4 1.66E-52 19866900 2934.8 2929.6 2564.6 2963.3 4104.5 4235.4 3678.1 3611.2 3022.8 2493.8 TRUE FALSE FALSE 2899.029529 2970.842986 2609.235787 3305.930689 3895.032049 3964.771609 3990.517722 3715.684374 2752.433197 2429.010716 1.193502157 1.223067056 1.074196902 1.361019392 1.603546671 1.632257767 1.642857191 1.529710984 1.133149878 1 11.24615314 -9.000962805 2.389607412 1.103431029 1.611292836 0.916713458 0.067508485 0.071876984 0.822426604 0.013829969 0.026270172 9.98E-10 9.000962805 0.507861807 LEMEDY(ph)PS(ph)FMAK ddPTM_HeLa_Romidepsin_16h_R1 1 LEMEDYPSFMAK 12 0 Q9NY61 Q9NY61 AATF Protein AATF 2 0 LEMEDY(1)PS(1)FMAK 47.96 0.025064 10560000 247.84 241.2 346.77 284.65 196.63 268.62 331.16 252.44 265.92 346.87 TRUE FALSE FALSE 244.8192308 244.5956199 352.8053864 317.5625723 186.5952374 251.4560489 359.2887221 259.7439531 242.1354492 337.8582674 0.724621104 0.723959256 1.044240797 0.939928375 0.552288505 0.744264898 1.06343031 0.768795611 0.716677591 1 8.400274348 LENEGS(ph)DEDIETDVLYSPQMALK ddPTM_HeLa_Romidepsin_16h_R1 2 LENEGSDEDIETDVLYSPQMALK 23 0 O60502-3;O60502 O60502-3 MGEA5 Protein O-GlcNAcase 1 0 LENEGS(1)DEDIETDVLYSPQMALK;LENEGS(0.998)DEDIET(0.001)DVLY(0.001)SPQMALK ; 164.07 1.04E-10 37598000 4831.3 5092.5 5233.7 4979.2 5417.9 5309.4 4436.4 5716.6 5988.5 6248.3 TRUE FALSE FALSE 4772.414257 5164.192349 5324.790353 5554.918532 5141.404346 4970.146475 4813.227705 5882.000802 5452.873562 6085.968265 0.7841668 0.848540795 0.874929037 0.912741948 0.844796444 0.816656653 0.790872955 0.966485618 0.895974695 1 12.5712711 -12.47268463 1.195665496 1.000494981 0.846453701 0.200627831 0.060758595 0.297895779 0.758017796 0.037869283 0.009185953 3.37E-13 12.47268463 -0.15404128 LENLGIPEEELLR ddPTM_HeLa_Romidepsin_16h_R1 1 LENLGIPEEELLR 13 0 Q01658 Q01658 DR1 Protein Dr1 0 0 136.27 0.015723 1782000 700.61 706.68 508.37 751.36 928.78 985.53 798.58 509.28 821.85 853.15 FALSE FALSE TRUE 692.0706958 716.6286596 517.2179666 838.2357785 881.3808908 922.5578137 866.4113653 524.0152133 748.3416776 830.98504 0.832831715 0.86238455 0.622415497 1.008725474 1.060645918 1.110197861 1.042631724 0.630595243 0.900547713 1 9.698678695 LENVSQLSLDKS(ph)PTEK ddPTM_HeLa_Romidepsin_16h_R1 1 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 0 LENVS(0.047)QLS(0.216)LDKS(0.736)PT(0.001)EK 179.09 1.78E-07 26147000 4264.4 3828.1 4046.3 3156.3 3569 3391 3305.9 3889.4 4660.9 4018.3 TRUE FALSE FALSE 4212.423853 3881.992092 4116.724154 3521.246257 3386.860612 3174.326044 3586.703063 4001.933653 4244.017431 3913.903987 1.076271637 0.991846531 1.051820425 0.899676198 0.86534075 0.811038302 0.91640037 1.022491524 1.084343777 1 11.93439265 -9.255714545 23.32447867 1.033994021 0.896534473 0.594381566 0.056678592 104.0562846 423950.3746 0.008832027 0.01436722 5.55E-10 9.255714545 -0.137459548 LENVSQLSLDKSPT(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 LENVSQLSLDKSPTEK 16 1 Q86W56-3;Q86W56-2;Q86W56 Q86W56-3 PARG Poly(ADP-ribose) glycohydrolase 1 0 LENVS(0.127)QLS(0.005)LDKS(0.245)PT(0.623)EK 70.784 0.021689 173940000 4582.3 4106.9 3839 2750 4148 3908.2 3420.8 3805.2 4135.1 4284.7 TRUE FALSE FALSE 4526.449165 4164.717046 3905.816185 3067.967939 3936.312082 3658.478633 3711.362667 3915.297458 3765.246299 4173.382876 1.084599544 0.997923548 0.935887337 0.735127361 0.943194573 0.876621854 0.889293596 0.93815918 0.902204857 1 12.02700157 -9.733762138 3.114293982 1.039436456 0.878090621 0.319294938 0.072371008 0.123616392 2.477484579 0.009737733 0.013722492 1.85E-10 9.733762138 -0.161345834 GSLVGLVDYPDDEEEDEEEESS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 GSLVGLVDYPDDEEEDEEEESSPR 24 0 Q5MIZ7-5;Q5MIZ7-3;Q5MIZ7-2;Q5MIZ7 Q5MIZ7-5 SMEK2 Serine/threonine-protein phosphatase 4 regulatory subunit 3B 1 0 GSLVGLVDYPDDEEEDEEEES(0.094)S(0.906)PR;GSLVGLVDYPDDEEEDEEEES(0.242)S(0.758)PR ; 228.32 2.07E-47 11879100 7300.9 6931.1 6513.2 5071.3 4987.7 4226.6 3418.7 3198.2 7799.7 7340.8 TRUE FALSE FALSE 7211.913823 7028.676208 6626.559514 5657.667567 4733.159057 3956.533901 3709.084293 3290.734871 7102.075297 7150.084958 1.008647291 0.983019957 0.926780528 0.791272775 0.661972422 0.55335481 0.518746884 0.460237171 0.993285442 1 12.80374467 -8.790934677 0.962594701 1.006784791 0.474031502 0.996762586 0.011988021 0.020567826 0.036416277 0.0020654 0.006475224 1.62E-09 8.790934677 -0.532753289 down LEPAT(ph)EY(ph)MARVR ddPTM_HeLa_Romidepsin_16h_R1 1 LEPATEYMARVR 12 1 H0Y9E3 H0Y9E3 OSMR 2 0 LEPAT(1)EY(1)MARVR 59.116 0.0042758 0 579.5 479.47 464.45 562.69 831.16 863.06 748.71 850.51 802.51 477 TRUE FALSE FALSE 572.4368311 486.2199912 472.5335574 627.7508653 788.7428037 807.9132514 812.3054087 875.118165 730.7314957 464.6074712 1.232087012 1.046517806 1.017059748 1.351142425 1.697654154 1.738915755 1.748369234 1.883564555 1.572793252 1 8.859868544 -8.867594533 2.347765262 1.100350662 1.781586177 0.733534087 0.166661717 0.060080264 0.673200157 0.015221986 0.030803593 1.36E-09 8.867594533 0.681235515 LEPLK(ac)PLK ddPTM_HeLa_Romidepsin_16h_R1 2 LEPLKPLK 8 1 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 0 1 ; LEPLK(1)PLK;LEPLK(1)PLK 109.11 0.013704 9071700 8065.4 7310.5 9586.2 5362.1 6902.1 6928 5744.1 5494.8 7504.3 5955 FALSE TRUE FALSE 7967.095803 7413.417411 9753.04379 5982.091231 6549.860082 6485.323159 6232.003711 5653.783369 6833.096613 5800.288242 1.373568945 1.278111898 1.68147571 1.031343785 1.129230102 1.118103599 1.074430003 0.974741794 1.17806156 1 12.50190888 LEPNS(ph)PMHGGTLLEDVVGGR ddPTM_HeLa_Romidepsin_16h_R1 4 LEPNSPMHGGTLLEDVVGGR 20 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 LEPNS(1)PMHGGTLLEDVVGGR;LEPNS(1)PMHGGTLLEDVVGGR;LEPNS(0.995)PMHGGT(0.005)LLEDVVGGR;LEPNS(1)PMHGGTLLEDVVGGR ;;; 88.471 0.00055673 32990900 4592.17 4510.02 4308.3 3985.79 5078.1 4844.22 4327.75 4676.41 4780.65 4916 TRUE FALSE FALSE 4536.198866 4573.51218 4383.284154 4446.645794 4818.945608 4534.689976 4695.348977 4811.714545 4353.056691 4788.281611 0.947354236 0.955146867 0.91541904 0.928651686 1.006403967 0.947039114 0.980591652 1.004893809 0.90910624 1 12.22529229 -5.605205354 19.84005348 0.968751046 0.966946607 0 0.036006678 0 0 0.004488692 0 2.48E-06 5.605205354 -0.00180444 LEPNSPMHGGT(ph)LLEDVVGGR ddPTM_HeLa_Romidepsin_16h_R1 1 LEPNSPMHGGTLLEDVVGGR 20 0 Q5VY60;Q7Z4H7-3;Q7Z4H7 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 LEPNS(0.006)PMHGGT(0.994)LLEDVVGGR 76.759 0.014409 5998400 1307.9 1480.7 1507 1156.8 1535.6 1537.8 1340.5 1620 1408.4 1251.9 TRUE FALSE FALSE 1291.958812 1501.545333 1533.228703 1290.554659 1457.232602 1439.539543 1454.362037 1666.872144 1282.429177 1219.375458 1.059525025 1.231405245 1.257388521 1.05837349 1.19506473 1.180554795 1.192710602 1.366988431 1.051709848 1 10.2519267 -4 0.092411203 0.846706776 2.094958727 0.530603029 0.074390701 68.67301263 0.458211748 0.803401307 10.91463061 1.00E-04 4 1.248251951 LEPQELSPLS(ph)ATVFPK ddPTM_HeLa_Romidepsin_16h_R1 2 LEPQELSPLSATVFPK 16 0 A0A087WUE6;Q3T8J9-2;Q3T8J9-3;Q3T8J9;Q9H869-7;Q9H869-5;Q9H869-6;Q9H869-4;Q9H869-3;Q9H869-2;Q9H869;Q9H869-8;Q9H869-9 A0A087WUE6 GON4L;YY1AP1 GON-4-like protein;YY1-associated protein 1 1 0 LEPQELS(0.277)PLS(0.718)AT(0.004)VFPK;LEPQELS(0.236)PLS(0.762)AT(0.001)VFPK ; 168.1 1.63E-05 73340000 8665.4 8885.8 8454.3 7601.2 10081.5 11071.7 10176.2 11146.5 9941 9215.8 TRUE FALSE FALSE 8559.782772 9010.894526 8601.443545 8480.086509 9567.003436 10364.2541 11040.56617 11469.00639 9051.852062 8976.372187 0.953590448 1.003845912 0.958231607 0.944711999 1.065798436 1.154615014 1.229958601 1.277688375 1.008408728 1 13.13191678 -8.15532405 1.468603484 0.975735465 1.268258367 0.950330659 0.025375922 0.066209363 0.25951455 0.003959189 0.01706667 6.99E-09 8.15532405 0.292522902 LEPSTSTDQPVT(ph)PEPTSQATR ddPTM_HeLa_Romidepsin_16h_R1 3 LEPSTSTDQPVTPEPTSQATR 21 0 Q14676-3;Q14676;Q14676-2 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 LEPSTSTDQPVT(0.999)PEPTSQATR;LEPSTS(0.001)T(0.006)DQPVT(0.958)PEPT(0.035)S(0.001)QATR;LEPSTSTDQPVT(1)PEPTSQATR ;; 217.33 2.71E-32 31916500 4955.5 4307.9 4540.5 4249 4626.6 4705.9 4331.6 4863.6 5567.2 4045.4 TRUE FALSE FALSE 4895.10046 4368.546729 4619.525498 4740.289372 4390.487338 4405.208178 4699.525996 5004.320593 5069.255689 3940.299925 1.242316715 1.108683809 1.172379155 1.203027552 1.114252067 1.117988037 1.192682305 1.270035451 1.286515185 1 11.94408973 -12.44579169 1.106814726 0.997193314 1.178996743 0 0.101797791 0.279480618 0.597028572 0.040257611 0.009412819 3.58E-13 12.44579169 0.181803429 LEPSTSTDQPVTPEPT(ph)SQATR ddPTM_HeLa_Romidepsin_16h_R1 1 LEPSTSTDQPVTPEPTSQATR 21 0 Q14676-3;Q14676;Q14676-2 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 LEPST(0.004)S(0.003)T(0.003)DQPVT(0.267)PEPT(0.65)S(0.072)QAT(0.001)R 246.67 3.80E-66 8432500 1773.6 1439.9 1546.8 1203.7 1560 2003.7 1504.5 1392.3 1442.4 1821.5 TRUE FALSE FALSE 1751.982681 1460.17095 1573.721405 1342.877458 1480.387379 1875.670037 1632.292192 1432.584004 1313.388131 1774.177167 0.987490265 0.823013043 0.8870148 0.756901555 0.834407863 1.0572056 0.92002773 0.807463894 0.740280145 1 10.79293437 -10.3010738 11.40882703 0.994115325 0.873610307 0 0.110745391 0.929606645 266.4393991 0.013449478 0.015388197 5.00E-11 10.3010738 -0.120505018 LEPTAPALS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LEPTAPALSPR 11 0 Q96IF1 Q96IF1 AJUBA LIM domain-containing protein ajuba 1 0 LEPTAPALS(1)PR;LEPTAPALS(1)PR ; 150.51 0.00234 111952000 7609.4 6939.6 7557 6353.9 3866 3547.9 3175.5 3035.1 6738.6 6184.7 TRUE FALSE FALSE 7516.653706 7037.295871 7688.526415 7088.567814 3668.703594 3321.20064 3445.226891 3122.91583 6135.882739 6024.020602 1.247780212 1.168205811 1.276311441 1.17671706 0.609012458 0.551326242 0.571914859 0.518410549 1.018569348 1 12.55651099 -8.736668173 6.300668677 1.141325496 0.558322527 0.921479534 0.083723498 0.042887125 5.543151974 0.01584324 0.031246208 1.83E-09 8.736668173 -0.583002969 LEPTFES(ph)NNEQTIMT(ph)MLQPRYS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LEPTFESNNEQTIMTMLQPRYSK 23 1 Q8WWQ8 Q8WWQ8 STAB2 Stabilin-2;190 kDa form stabilin-2 3 0 LEPT(0.057)FES(0.477)NNEQT(0.477)IMT(0.923)MLQPRY(0.516)S(0.55)K 45.369 0.0038942 0 198.79 188.53 186.47 195.42 182.47 188.27 243.12 151.29 276.6 178.51 TRUE FALSE FALSE 196.367071 191.1841303 189.7154321 218.0153799 173.157875 176.2401546 263.7706067 155.6673375 251.8602032 173.8722845 1.129375344 1.099566448 1.091119454 1.2538823 0.995891183 1.013618445 1.517036528 0.895297016 1.448535654 1 7.441884173 -14.39027241 0.242551603 0.744493704 1.153301746 0 0.21417759 31.15230191 1.004424155 4.144054687 0.108663767 4.07E-15 14.39027241 0.408808041 LEQLESGEEELVLAEYES(ph)DEEKK ddPTM_HeLa_Romidepsin_16h_R1 1 LEQLESGEEELVLAEYESDEEKK 23 1 F5GXJ8;F6WZM0;F5H235;C9K0E8;B4DMS8;Q96FC9-4;Q96FC9-3;Q96FC9-2;Q96FC9;Q96FC9-5;A8MPP1 F5GXJ8 DDX11;DDX11L8 Probable ATP-dependent RNA helicase DDX11;Putative ATP-dependent RNA helicase DDX11-like protein 8 1 0 LEQLESGEEELVLAEY(0.396)ES(0.604)DEEKK 76.417 0.00021768 2598900 1169.6 1245.4 1464.2 513.11 985.57 970.42 660.7 866 1525.7 1272.3 TRUE FALSE FALSE 1155.344465 1262.932774 1489.683787 572.4381925 935.2726852 908.4132939 716.8198415 891.0563437 1389.237571 1239.245463 0.932296708 1.019114301 1.202089361 0.461924784 0.754711406 0.733037418 0.578432492 0.719031355 1.121035027 1 10.27524626 -9.259320051 24.99999117 0.987819682 0.65597743 0.747456557 0.114542787 78.17116254 922120.2329 0.015800924 0.025376744 5.50E-10 9.259320051 -0.331842252 LEQLESGEEELVLAEYES(ph)DEEKKVASR ddPTM_HeLa_Romidepsin_16h_R1 2 LEQLESGEEELVLAEYESDEEKKVASR 27 2 F5GXJ8;F6WZM0;F5H235;C9K0E8;B4DMS8;Q96FC9-4;Q96FC9-3;Q96FC9-2;Q96FC9;Q96FC9-5 F5GXJ8 DDX11 Probable ATP-dependent RNA helicase DDX11 1 0 LEQLESGEEELVLAEY(0.452)ES(0.516)DEEKKVAS(0.032)R;LEQLES(0.003)GEEELVLAEY(0.455)ES(0.512)DEEKKVAS(0.03)R ; 43.884 0.022198 3963900 1795.39 1321.74 1302.28 1407.33 1052.9 1121.79 882.3 1171.01 1659.36 1542.34 TRUE FALSE FALSE 1773.507096 1340.34749 1324.945637 1570.052116 999.1665841 1050.111239 957.24254 1204.891327 1510.942686 1502.269784 1.180551666 0.892214903 0.881962515 1.045119946 0.665104627 0.699016415 0.637197493 0.802047235 1.005773198 1 10.55292821 -9.098890751 0.943922379 1.076816754 0.684348305 0.61115675 0.106542428 0.245623011 0.429542695 0.020573629 0.050506492 7.96E-10 9.098890751 -0.392468448 LERENAEVDGDDDAEEMEAKAED ddPTM_HeLa_Romidepsin_16h_R1 1 LERENAEVDGDDDAEEMEAKAED 23 2 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 0 89.831 0.00010254 10592000 560.61 532.85 528.62 1587.4 704.42 810.38 481.49 709.54 621.38 492.46 FALSE FALSE TRUE 553.7770697 540.3514763 537.8204094 1770.942657 668.4708188 758.5993334 522.3877486 730.0694204 565.8022165 479.6658182 1.15450601 1.126516537 1.121239807 3.692034307 1.393617793 1.581516349 1.08906603 1.52203762 1.179575853 1 8.905885824 -9.472869855 24.99998395 1.081150204 1.835614311 0.236671057 0.662238531 411.1614021 205544.2258 0.100109351 0.152918164 3.37E-10 9.472869855 0.754464107 LES(ph)LYSDEEDESAVGADK ddPTM_HeLa_Romidepsin_16h_R1 1 LESLYSDEEDESAVGADK 18 0 Q9UP95-3;Q9UP95-5;Q9UP95-2;Q9UP95-6;Q9UP95;I3L4N6;Q9UP95-7 Q9UP95-3 SLC12A4 Solute carrier family 12 member 4 1 0 LES(0.57)LYS(0.43)DEEDESAVGADK 113.78 0.00057865 3014600 3920.2 4343.1 3990.5 3705.7 4879.6 5700.9 4170.9 6156.6 4500 4767.7 TRUE FALSE FALSE 3872.419095 4404.242276 4059.952979 4134.17047 4630.575804 5336.630889 4525.176142 6334.731507 4097.50873 4643.834467 0.833883964 0.948406389 0.874267377 0.890249319 0.997144889 1.149186287 0.974448201 1.364116562 0.882354606 1 12.18110083 -4 0.638195202 0.918800425 34.81252319 0.73176859 0.077981353 83.73896433 0.522988981 0.014892781 4007.999679 1.00E-04 4 33.89372276 LES(ph)SDLTPPHS(ph)PPPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 LESSDLTPPHSPPPSSR 17 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 2 0 LES(0.941)S(0.053)DLT(0.007)PPHS(0.969)PPPS(0.021)S(0.01)R 107.63 0.00088287 0 2180.7 2276.5 1902.9 2002.8 2139.4 2162.9 1972.2 1801.5 2731.4 2251.4 TRUE FALSE FALSE 2154.12079 2308.548627 1936.019176 2234.373159 2030.218435 2024.69767 2139.718619 1853.62356 2487.096743 2192.908303 0.982312296 1.052733771 0.882854597 1.018908614 0.925810911 0.923293358 0.975744684 0.845280925 1.134154465 1 11.09862977 -4.213383024 0.31987188 0.996410418 1.14E-14 0.350920525 0.064644789 32.25881904 0.468138067 0.01439319 18.63784216 6.12E-05 4.213383024 -0.996410418 LES(ph)SEGEIIQTVDR ddPTM_HeLa_Romidepsin_16h_R1 2 LESSEGEIIQTVDR 14 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 LES(0.639)S(0.361)EGEIIQTVDR;LES(0.618)S(0.382)EGEIIQTVDR ; 218.45 1.49E-24 9705600 2106.48 2115.06 2232.85 1542.93 1782.22 1729.98 1256.87 1213.11 2289.35 2434.27 TRUE FALSE FALSE 2080.805412 2144.83587 2271.711818 1721.330826 1691.266663 1619.439861 1363.628506 1248.209424 2084.584802 2371.027314 0.877596559 0.904601924 0.958112884 0.725985237 0.713305432 0.683011896 0.575121382 0.526442448 0.879190547 1 11.21129657 -6.891447898 0.286389692 0.985982194 5.84E-13 0.86934868 0.055747056 2.113153271 0.109600389 0.025219542 0.75790466 1.28E-07 6.891447898 -0.985982194 LESEST(ph)SPSLEMK ddPTM_HeLa_Romidepsin_16h_R1 1 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 LES(0.004)ES(0.055)T(0.429)S(0.429)PS(0.084)LEMK 103.43 0.026631 5645200 3233.3 3159.2 3023.3 2174.5 2243.9 2310 1941.2 2359.9 3391.8 2828.5 TRUE FALSE FALSE 3193.891296 3203.675301 3075.919268 2425.925921 2129.38541 2162.398455 2106.08548 2428.179983 3088.428913 2755.015162 1.159300805 1.162852148 1.116479978 0.880549027 0.77291241 0.784895301 0.764455132 0.881367194 1.121020659 1 11.42784454 -9.126983678 3.629684857 1.087844663 0.7992219 0.879192865 0.054855829 0.084548701 2.01741478 0.011270663 0.019390478 7.46E-10 9.126983678 -0.288622764 LESESTS(ph)PSLEMK ddPTM_HeLa_Romidepsin_16h_R1 1 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 LES(0.001)ES(0.047)T(0.352)S(0.542)PS(0.06)LEMK 103.43 0.014791 19262000 4646.8 4662.9 4285.9 4087 3695.9 3719.5 3154.7 2914.7 5611.9 4958.2 TRUE FALSE FALSE 4590.163014 4728.544429 4360.494292 4559.55817 3507.284432 3481.835954 3422.660139 2999.032246 5109.957609 4829.385249 0.950465282 0.979119326 0.902908769 0.944128069 0.726238279 0.720968772 0.708715491 0.620996688 1.05809691 1 12.23762384 -8.685062347 1.069903953 0.976847624 0.656942305 0.901112737 0.045281905 0.094936325 0.20839734 0.006006165 0.01923165 2.07E-09 8.685062347 -0.319905319 LESESTSPS(ph)LEMK ddPTM_HeLa_Romidepsin_16h_R1 1 LESESTSPSLEMK 13 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 LES(0.004)ES(0.025)T(0.175)S(0.25)PS(0.546)LEMK 90.614 0.030319 21707000 5407.7 5102.4 5060.4 4947.8 3619.2 3369.3 3297.5 3589.7 5218.9 4478.3 TRUE FALSE FALSE 5341.788872 5174.231721 5148.474139 5519.887916 3434.498719 3154.012604 3577.589568 3693.562306 4752.108513 4361.95312 1.224632344 1.186219012 1.180313955 1.265462458 0.787376348 0.723073476 0.820180655 0.846767997 1.089445114 1 12.09075855 -8.747412915 24.99960426 1.131372943 0.791103421 0.839693612 0.077255075 97.16235046 173173.1126 0.015242251 0.030363997 1.79E-09 8.747412915 -0.340269522 LESGGGGEGGEGT(ph)EEEDGAER ddPTM_HeLa_Romidepsin_16h_R1 3 LESGGGGEGGEGTEEEDGAER 21 0 Q96LA8 Q96LA8 PRMT6 Protein arginine N-methyltransferase 6 1 0 LESGGGGEGGEGT(1)EEEDGAER;LESGGGGEGGEGT(1)EEEDGAER;LESGGGGEGGEGT(1)EEEDGAER ;; 195.55 6.39E-18 23142900 2598.14 2312.28 2658.05 1937.65 2428.23 1950.22 2047.18 1847.7 2628.99 3193.14 TRUE FALSE FALSE 2566.47287 2344.832339 2704.312245 2161.69021 2304.308362 1825.607236 2221.067418 1901.160284 2393.84655 3110.181762 0.825184207 0.75392132 0.869502959 0.695036617 0.740891864 0.586977667 0.714127851 0.611269832 0.769680595 1 11.60278318 -9.835007196 0.064830833 1.573505466 5.19E-07 0.400535953 0.089158565 7.343538728 0.309208323 3.393036436 3.969654631 1.46E-10 9.835007196 -1.573504948 LESLSETPGPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 LESLSETPGPSSPR 14 0 A0A2R8YFR7;A0A2R8YF49;Q12774;H0Y895;C9J591;Q12774-2 A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 0 LES(0.02)LS(0.002)ET(0.05)PGPS(0.761)S(0.167)PR;LESLSET(0.023)PGPS(0.489)S(0.489)PR ; 206.45 4.74E-17 118120000 4416.7 3320 3951.8 2794.3 2985.8 2963.1 2390.77 3030.3 3675.8 3789 TRUE FALSE FALSE 4362.867562 3366.739047 4020.579421 3117.390114 2833.423484 2773.767473 2593.841944 3117.976949 3347.027242 3690.561234 1.18216913 0.912256655 1.089422222 0.844692695 0.767748672 0.751584189 0.702831298 0.844851705 0.906915515 1 11.84962451 -9.148940502 1.986107249 1.075961765 0.757103627 0.593102963 0.092480326 0.127163117 0.981531177 0.013995759 0.025716495 7.10E-10 9.148940502 -0.318858137 LESLYS(ph)DEEDESAVGADK ddPTM_HeLa_Romidepsin_16h_R1 2 LESLYSDEEDESAVGADK 18 0 Q9UP95-3;Q9UP95-5;Q9UP95-2;Q9UP95-6;Q9UP95;I3L4N6;Q9UP95-7 Q9UP95-3 SLC12A4 Solute carrier family 12 member 4 1 0 LES(0.255)LYS(0.745)DEEDESAVGADK;LESLYS(1)DEEDESAVGADK ; 168.64 3.75E-07 12710500 6642.8 7146.7 6955 5677.4 8440.5 10644.7 7575 10909 7738.2 7251.1 TRUE FALSE FALSE 6561.834999 7247.31143 7076.048858 6333.847701 8009.749789 9964.538024 8218.420311 11224.6347 7046.076011 7062.715377 0.929081047 1.026136697 1.001887869 0.896800644 1.134089279 1.410865013 1.163634647 1.589280341 0.997644056 1 12.78600724 -8.462460454 3.309078911 0.969552883 1.365109282 0.757377556 0.103915677 0.083172614 1.790179602 0.013597875 0.03173361 3.45E-09 8.462460454 0.395556398 LESPS(ph)FTGTGDTEIAHATEDLENNGSK ddPTM_HeLa_Romidepsin_16h_R1 1 LESPSFTGTGDTEIAHATEDLENNGSK 27 0 Q08J23-2;Q08J23;Q08J23-3 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 1 0 LES(0.412)PS(0.529)FT(0.054)GT(0.004)GDT(0.001)EIAHATEDLENNGSK 133.99 3.54E-10 3045500 476.39 548.23 705.62 262.27 667.25 932.97 473.41 688.03 688.39 703.07 TRUE FALSE FALSE 470.5835754 555.9479963 717.9010201 292.5948914 633.1977426 873.356228 513.6214336 707.9370625 626.8186743 684.80414 0.687179805 0.81183504 1.048330432 0.427267994 0.924640646 1.275337249 0.750026765 1.033780348 0.915325474 1 9.419547613 -8.524751809 24.9974658 0.828872233 1.010619843 0.171684082 0.201269525 90.80993477 1211928.295 0.030038083 0.060417984 2.99E-09 8.524751809 0.18174761 LESPTVSTLTPSS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 LESPTVSTLTPSSPGK 16 0 A0A087WTV6;A0A087WZR9;Q96C36 A0A087WTV6 PYCR2 Pyrroline-5-carboxylate reductase;Pyrroline-5-carboxylate reductase 2 1 0 LESPTVSTLT(0.002)PS(0.128)S(0.87)PGK;LESPTVSTLTPS(0.304)S(0.696)PGK ; 173.59 5.39E-06 11867300 2968.7 2558.7 2731.1 2368.03 2804 3319.1 2410.6 2981.1 2857.3 2793.5 TRUE FALSE FALSE 2932.516343 2594.721446 2778.63365 2641.832771 2660.901417 3107.020222 2615.356304 3067.353425 2601.735932 2720.924467 1.0777647 0.953617595 1.021209403 0.97093205 0.9779402 1.14189874 0.961201362 1.127320314 0.956195574 1 11.40988119 -7.233114409 23.02715218 1.02576268 1.127320752 0.212718629 0.060317736 4051.945724 3293931.272 0.007714295 0.863999739 5.85E-08 7.233114409 0.101558072 LESS(ph)EGEIIQTVDR ddPTM_HeLa_Romidepsin_16h_R1 2 LESSEGEIIQTVDR 14 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 LES(0.343)S(0.657)EGEIIQTVDR;LES(0.018)S(0.982)EGEIIQTVDR ; 263.56 9.13E-69 8358900 2304.6 2458.2 2207.2 1443.97 1575.06 1525.64 1215.86 1420.37 2193.3 2408 TRUE FALSE FALSE 2276.510649 2492.806604 2245.61539 1610.928605 1494.678811 1428.156528 1319.135118 1461.466165 1997.125755 2345.439813 0.970611412 1.062831197 0.957438932 0.68683434 0.637270163 0.608907771 0.562425482 0.623109643 0.851493073 1 11.19564276 -9.201027674 2.754550682 0.992991349 0.607137484 0.912561829 0.053635831 0.031289023 0.4674795 0.004974938 0.008556641 6.29E-10 9.201027674 -0.385853865 LESSDLT(ph)PPHS(ph)PPPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 LESSDLTPPHSPPPSSR 17 0 H7BXC7;Q9H7P9-3;Q9H7P9 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 2 0 LES(0.16)S(0.293)DLT(0.547)PPHS(0.842)PPPS(0.139)S(0.019)R 119.62 0.0093989 4078200 2438.5 2162 2363.8 2386.9 2151.3 2185.5 1889.5 2108.8 2907.5 2625.2 TRUE FALSE FALSE 2408.778624 2192.436693 2404.940947 2662.884609 2041.511133 2045.853603 2049.994083 2169.814801 2647.445918 2556.996926 0.942034228 0.857426409 0.940533375 1.041410954 0.798401873 0.800100142 0.801719416 0.848579355 1.035373133 1 11.32023471 -7.866513847 0.243377224 1.00408339 0.676025333 0.525326245 0.063788159 4.910640878 0.307458399 0.054191549 0.481040335 1.36E-08 7.866513847 -0.328058057 LESSNGK(ac)MASR ddPTM_HeLa_Romidepsin_16h_R1 2 LESSNGKMASR 11 1 Q9NQ29-3;Q9NQ29;B8ZZ08 Q9NQ29-3 LUC7L Putative RNA-binding protein Luc7-like 1 0 1 ; LESSNGK(1)MASR;LESSNGK(1)MASR 100.88 0.0094238 3939800 125.28 200.144 84.467 63.764 348.71 338.9 365.05 195.16 325.84 163.93 FALSE TRUE FALSE 123.7530392 202.9616325 85.9371127 71.1366937 330.9140275 317.2453837 396.0573379 200.8066467 296.6960543 159.671075 0.775049828 1.271123355 0.538213404 0.445520228 2.072473224 1.986868215 2.480457641 1.257626948 1.858170332 1 7.318959176 -8.750698514 24.99995618 0.865100096 1.989971993 0.490607942 0.473706137 84.59980751 196909.392 0.04858417 0.096388757 1.78E-09 8.750698514 1.124871897 LETLGSASTST(ph)PGRR ddPTM_HeLa_Romidepsin_16h_R1 2 LETLGSASTSTPGRR 15 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 0 LETLGSAST(0.002)S(0.036)T(0.962)PGRR;LETLGSAS(0.007)T(0.032)S(0.156)T(0.804)PGRR ; 89.46 0.0068401 38797000 3477.1 2757.3 3382.5 2429 4305 5276.6 3938 4970 4118.2 3547.3 TRUE FALSE FALSE 3434.719768 2796.117342 3441.370994 2709.852409 4085.299786 4939.442289 4272.493622 5113.799109 3749.857878 3455.140635 0.994089715 0.809262961 0.996014738 0.784295835 1.182383069 1.429592254 1.236561424 1.480055271 1.08529819 1 11.75452872 -8.531403044 5.501608584 0.967961893 1.360179074 0.777437796 0.10495596 0.055384288 5.530434205 0.01376034 0.028969117 2.94E-09 8.531403044 0.392217181 LETYENAR ddPTM_HeLa_Romidepsin_16h_R1 1 LETYENAR 8 0 O94906-2;O94906 O94906-2 PRPF6 Pre-mRNA-processing factor 6 0 0 118.74 0.00065385 0 833.36 816.96 1055.9 552.16 993.78 1134.5 925.65 1020.3 951.15 960.38 FALSE FALSE TRUE 823.2026878 828.4611843 1074.277497 616.0033372 943.0636983 1062.009111 1004.274688 1049.820771 866.0767618 935.4291892 0.880026727 0.885648207 1.148432729 0.658524819 1.008161504 1.135317482 1.073597766 1.122287804 0.925860313 1 9.869484637 -8.519370818 24.98995277 0.932381319 1.10089052 0.35682133 0.115586913 127.2853637 906759.307 0.01613178 0.032817407 3.02E-09 8.519370818 0.168509202 LEVEANNAFDQYR ddPTM_HeLa_Romidepsin_16h_R1 1 LEVEANNAFDQYR 13 0 A0A6I8PRV6;B1AK87;B1AK85;B1AK88;P47756-2;P47756 A0A6I8PRV6 CAPZB F-actin-capping protein subunit beta 0 0 118.77 0.0014225 0 1154.4 957.09 962.81 1265.2 1481.7 1674.4 1145.3 1548.1 1595.4 1412.4 FALSE FALSE TRUE 1140.329729 970.5639381 979.5673042 1411.488377 1406.08332 1567.411244 1242.581753 1592.891831 1452.703428 1375.705644 0.828905321 0.705502621 0.712047165 1.026010457 1.022081523 1.13935074 0.903232286 1.157872571 1.055969665 1 10.4259561 -9.034243403 24.10316845 0.882967489 1.047392952 0.369226617 0.122205386 394.0880292 277389.1792 0.019175735 0.031813288 9.24E-10 9.034243403 0.164425463 LEVPAERS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LEVPAERSPR 10 1 Q9UJF2-2 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 LEVPAERS(1)PR;LEVPAERS(1)PR ; 103.14 0.0083046 26680300 5266.5 5040.8 4656.4 4818.7 5145.8 5751.1 4582.7 4656.5 5733.9 5008.8 TRUE FALSE FALSE 5202.309872 5111.764515 4737.442689 5375.860767 4883.190624 5383.623271 4971.954424 4791.228481 5221.045623 4878.670654 1.066337583 1.047778151 0.971051958 1.101910981 1.000926476 1.103502092 1.019120735 0.982076639 1.070177922 1 12.25227238 -7.355057482 4.367164131 1.036239179 0.982163428 0.148962811 0.042339622 0.313152932 9.42418643 0.005635601 0.038766751 4.42E-08 7.355057482 -0.054075751 LEVS(ph)PEAQPTAR ddPTM_HeLa_Romidepsin_16h_R1 2 LEVSPEAQPTAR 12 0 Q6WKZ4 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 LEVS(0.757)PEAQPT(0.243)AR;LEVS(0.77)PEAQPT(0.23)AR ; 127.78 0.0047997 33858000 3088.9 3209.6 2853.2 3242.6 5735.5 7705.4 6094.1 6831.9 3170 3290.3 TRUE FALSE FALSE 3051.251299 3254.784833 2902.858749 3617.524669 5442.796033 7213.049808 6611.732702 7029.570248 2886.467261 3204.817532 0.952082691 1.015591309 0.905779727 1.128777109 1.69831698 2.2506897 2.063060576 2.193438527 0.900665087 1 11.6460265 -8.632257185 2.251748993 0.975167864 2.161506515 0.985297685 0.065926861 0.020724934 0.21225352 0.00853793 0.019680503 2.33E-09 8.632257185 1.186338651 up LEVSPEAQPT(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 2 LEVSPEAQPTAR 12 0 Q6WKZ4 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 LEVS(0.088)PEAQPT(0.912)AR;LEVS(0.262)PEAQPT(0.738)AR ; 151.16 0.0029824 31851000 3493.4 3170.6 2898.3 3080 5497.8 7328.1 5504.5 7363.3 3385.7 3046.9 TRUE FALSE FALSE 3450.821097 3215.23579 2948.743696 3436.124092 5217.226751 6859.85806 5972.052093 7576.345468 3082.874512 2967.741099 1.162777002 1.083394974 0.993598699 1.157824749 1.757979075 2.311474563 2.012322468 2.552899736 1.038794966 1 11.53514952 -8.578470232 2.196846864 1.071275539 2.276110944 0.945084898 0.132958139 0.047258191 0.457123627 0.019164576 0.045941715 2.64E-09 8.578470232 1.204835405 up LFAS(ph)GGFQVK ddPTM_HeLa_Romidepsin_16h_R1 1 LFASGGFQVK 10 0 Q9Y2S2-2 Q9Y2S2-2 1 0 LFAS(1)GGFQVK 157.58 0.0029016 13474000 2103.1 1940.3 1915.7 1953.4 1787.7 2050.4 1859.7 2183.9 2076.2 2141.3 TRUE FALSE FALSE 2077.466608 1967.615594 1949.041955 2179.261299 1696.466998 1919.386057 2017.662872 2247.087701 1890.499472 2085.668717 0.996067396 0.943397951 0.934492587 1.044874136 0.813392359 0.920273695 0.967393745 1.077394354 0.90642366 1 11.02629431 -10.27360225 19.3976211 0.99814298 0.953233968 0 0.073160409 71.51548495 114053.745 0.01115695 0.0128474 5.33E-11 10.27360225 -0.044909011 LFDDEAS(ph)VDEPRR ddPTM_HeLa_Romidepsin_16h_R1 2 LFDDEASVDEPRR 13 1 A0A2R8Y549;Q8NI35-4;Q8NI35-3;Q8NI35-2;Q8NI35;A0A0U1RR46;A0A0X1KG69;A0A087WUZ6;Q8NI35-5 A0A2R8Y549 INADL InaD-like protein 1 0 LFDDEAS(1)VDEPRR;LFDDEAS(1)VDEPRR ; 88.78 0.0070844 3743300 1852.97 1833.8 1724.92 1843.42 2128.32 1776.48 1353.14 1597.88 1819.48 1966.87 TRUE FALSE FALSE 1830.385289 1859.616285 1754.941509 2056.564894 2019.703889 1662.968661 1468.075678 1644.112137 1656.741152 1915.770434 0.955430388 0.970688477 0.916050002 1.073492344 1.054251518 0.868041719 0.766310854 0.85819893 0.864791064 1 10.90370898 -8.065430973 5.303355207 0.984369117 0.812663871 0.551515718 0.061155405 0.084546356 4.66018084 0.006937089 0.018563718 8.60E-09 8.065430973 -0.171705246 LFDEEEDS(ph)SEKLFDDSDER ddPTM_HeLa_Romidepsin_16h_R1 2 LFDEEEDSSEKLFDDSDER 19 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 LFDEEEDS(0.827)S(0.173)EKLFDDSDER;LFDEEEDS(0.906)S(0.073)EKLFDDS(0.021)DER ; 75.877 0.0042561 18656800 2101.89 1739.52 2463.76 1614.86 3001.49 3541.5 2871.16 3780.1 2203.6 2242.33 TRUE FALSE FALSE 2076.271356 1764.009008 2506.640709 1801.577711 2848.312765 3315.20958 3115.036259 3889.471229 2006.504497 2184.073943 0.950641512 0.807669087 1.147690405 0.824870292 1.304128358 1.517901713 1.426250365 1.780833127 0.918698061 1 11.09280599 -8.496442558 2.633271121 0.966599973 1.565932404 0.835602108 0.126203562 0.075783146 1.043204841 0.016705922 0.040017872 3.19E-09 8.496442558 0.599332432 LFDEEEDSS(ph)EKLFDDSDER ddPTM_HeLa_Romidepsin_16h_R1 2 LFDEEEDSSEKLFDDSDER 19 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 LFDEEEDS(0.242)S(0.758)EKLFDDSDER;LFDEEEDS(0.27)S(0.729)EKLFDDS(0.001)DER ; 144.74 2.40E-05 22307000 2130.12 1864.58 2156.73 963.14 3466.1 4635.9 4410.3 5564.8 2077.2 2446.3 TRUE FALSE FALSE 2104.157278 1890.829606 2194.266981 1074.502779 3289.211983 4339.680952 4784.910772 5725.808708 1891.41003 2382.744773 0.883081269 0.793551046 0.920898875 0.450951688 1.380429839 1.82129492 2.008150779 2.403030644 0.79379464 1 11.21840871 -8.234689637 1.863431621 0.898676732 2.204190976 0.895955567 0.193746283 0.080809137 0.532954388 0.028220457 0.094379615 5.83E-09 8.234689637 1.305514244 up LFEDDDS(ph)NEK ddPTM_HeLa_Romidepsin_16h_R1 2 LFEDDDSNEK 10 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 LFEDDDS(1)NEK;LFEDDDS(1)NEK ; 135.94 0.0056687 19872300 5742.8 4882 6637.4 2189.7 5559.7 6556.8 5580.9 6305.8 6085.7 6730.9 TRUE FALSE FALSE 5672.804545 4950.728924 6752.921163 2442.883417 5275.967763 6137.841641 6054.941507 6488.248374 5541.37975 6556.030248 0.865280411 0.755141257 1.030032033 0.372616252 0.804750369 0.936213136 0.923568269 0.989661141 0.845234012 1 12.6786068 -11.55492794 0.805994246 0.98988694 0.827480123 0.012408989 0.179543285 0.950386821 1.26384863 0.078266859 0.03772674 2.79E-12 11.55492794 -0.162406817 LFEDDDS(ph)NEKLFDEEEDSSEK ddPTM_HeLa_Romidepsin_16h_R1 1 LFEDDDSNEKLFDEEEDSSEK 21 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 LFEDDDS(1)NEKLFDEEEDSSEK 75.608 0.0016493 14696000 779.73 575.4 523.41 372.66 809.62 956.09 718.88 980.46 682.4 838.6 TRUE FALSE FALSE 770.2263508 583.5004963 532.5197315 415.7487026 768.3020703 894.9989346 779.9416493 1008.828063 621.3644349 816.8130511 0.942965284 0.714362357 0.651948118 0.50898881 0.940609445 1.095720659 0.954859436 1.235078286 0.760718054 1 9.673862108 -8.341756448 5.099003554 0.889311839 1.080938634 0.294998857 0.174431009 0.315543605 14.4036044 0.028867538 0.066302259 4.55E-09 8.341756448 0.191626795 LFEEPEDPSNR ddPTM_HeLa_Romidepsin_16h_R1 2 LFEEPEDPSNR 11 0 E5RFR9;A0A590UJJ1;A0A590UJY3;Q9Y2T4-3;Q9Y2T4-4;Q9Y2T4-2;Q9Y2T4;P63151;P63151-2 E5RFR9 PPP2R2A;PPP2R2C Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform;Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform 0 0 ; ; 161.51 0.00025049 2669000 2501.8 2468.8 2397.7 2139.43 2763.7 2876.8 2052.04 2691.6 2919.8 2574 FALSE FALSE TRUE 2471.307099 2503.555831 2439.430963 2386.800963 2622.658076 2692.981764 2226.340226 2769.477199 2658.645775 2507.127109 0.985712727 0.99857555 0.972998519 0.952006364 1.046081017 1.074130528 0.888004529 1.104641719 1.060435175 1 11.29181943 -8.746997978 24.99994674 0.989273839 1.021479165 0.061086988 0.059195314 494.23506 855580.4455 0.007222993 0.014395984 1.79E-09 8.746997978 0.032205326 LFEHYYQELK ddPTM_HeLa_Romidepsin_16h_R1 2 LFEHYYQELK 10 0 Q08J23-2;Q08J23;A0A140T9Y7 Q08J23-2 NSUN2 tRNA (cytosine(34)-C(5))-methyltransferase 0 0 ; ; 136.52 0.0025982 27245000 10751 9277.1 13422.5 9435.1 13043.1 13475.2 9915.4 9578.7 10302.9 8259.8 FALSE FALSE TRUE 10619.96268 9407.703257 13656.11298 10526.03066 12377.46194 12614.17821 10757.61383 9855.844572 9381.38282 8045.209205 1.320035614 1.169354708 1.697421737 1.308360092 1.538488512 1.567911771 1.337145319 1.225057586 1.166083141 1 12.97391422 -11.55300248 0.516107147 0.981165075 1.43354072 0.390139415 0.157777279 0.588925646 0.31312313 0.122949943 0.04395708 2.80E-12 11.55300248 0.452375645 LFGAGGGK(ac)AGK ddPTM_HeLa_Romidepsin_16h_R1 2 LFGAGGGKAGK 11 1 Q9H444 Q9H444 CHMP4B Charged multivesicular body protein 4b 0 1 ; LFGAGGGK(1)AGK;LFGAGGGK(1)AGK 147.19 0.0046292 3431900 3148.8 3275.4 3067.8 2645.8 2453.6 2257.2 2813.5 2658.4 3691.8 2952.6 FALSE TRUE FALSE 3110.421214 3321.511167 3121.193772 2951.719845 2328.383636 2112.972205 3052.47862 2735.31661 3361.596162 2875.891026 1.081550443 1.154950287 1.085296259 1.026367069 0.809621649 0.734719148 1.061402742 0.9511197 1.168888574 1 11.48979329 -8.886086053 6.653165783 1.053312071 0.891116948 0.486244163 0.096000091 0.168943324 9.276365056 0.014096319 0.025724311 1.30E-09 8.886086053 -0.162195123 LFIGGLNTETNEK ddPTM_HeLa_Romidepsin_16h_R1 1 LFIGGLNTETNEK 13 0 P38159;P38159-2;H0Y6E7;H3BT71;H3BR27;P38159-3;H3BNC1;Q96E39;A0A1B0GUK8 P38159;Q96E39 RBMX;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;RNA binding motif protein, X-linked-like-1" 0 0 131.12 0.0038427 457780 0 0 127.67 0 0 155.32 0 0 0 0 FALSE FALSE TRUE 0 0 129.8920428 0 0 145.3955533 0 0 0 0 0 LFIGGLS(ph)FETTDESLR ddPTM_HeLa_Romidepsin_16h_R1 1 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646;F8VZ49;Q32P51 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 1 0 LFIGGLS(0.895)FET(0.08)T(0.024)DES(0.001)LR 150.12 0.00028656 9384400 1147.6 970.49 902.83 1148 1174.5 1112 1403 1263.7 1273.1 1239.5 TRUE FALSE FALSE 1133.61261 984.1525837 918.5433774 1280.737162 1114.560882 1040.946789 1522.170785 1300.263166 1159.230747 1207.297611 0.938966995 0.815169826 0.760825971 1.060829699 0.923186522 0.862212249 1.260808247 1.077003014 0.9601864 1 10.23756564 -7.763358094 24.99999765 0.941573046 1.168905647 0.519371415 0.094955175 30.66303935 399553.9556 0.013659277 0.04425403 1.72E-08 7.763358094 0.227332601 LFIGGLS(ph)FETTEESLR ddPTM_HeLa_Romidepsin_16h_R1 2 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 0 LFIGGLS(0.87)FET(0.041)T(0.086)EES(0.003)LR;LFIGGLS(0.522)FET(0.063)T(0.381)EES(0.034)LR ; 116.58 0.0029495 25943000 3263.67 3197.8 2869 2295.59 2922.05 3086.6 3309.77 2924.86 3421.4 3592.7 TRUE FALSE FALSE 3223.891135 3242.818712 2918.933742 2561.016917 2772.926885 2889.376222 3590.901781 3009.486209 3115.381415 3499.361136 0.921279916 0.926688783 0.834133325 0.731852706 0.792409465 0.825686778 1.026159245 0.860010183 0.890271479 1 11.77287584 -10.61604122 0.931353563 0.979942351 0.849764579 0.173677243 0.078627956 0.429024341 0.774995803 0.020169627 0.019732482 2.42E-11 10.61604122 -0.130177772 LFIGGLSFET(ph)TDDSLR ddPTM_HeLa_Romidepsin_16h_R1 1 LFIGGLSFETTDDSLR 16 0 P51991;P51991-2 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 LFIGGLS(0.034)FET(0.888)T(0.05)DDS(0.028)LR 116.58 0.00023131 0 723.71 833.84 642.59 1016.4 654.45 644.06 684.51 845.65 817.49 916.5 TRUE FALSE FALSE 714.8891442 845.5788214 653.7740094 1133.92095 621.0509744 602.9066446 742.6522623 870.1175485 744.371647 892.6891979 0.800826476 0.947226452 0.732364647 1.270230393 0.695707953 0.67538248 0.831927018 0.974714997 0.833853091 1 9.802014158 -12.47988572 1.161400491 1.00175331 0.857974697 0 0.172193709 0.997325962 2.359061115 0.117565538 0.027376226 3.31E-13 12.47988572 -0.143778613 LFIGGLSFETTDDSLREHFEK ddPTM_HeLa_Romidepsin_16h_R1 2 LFIGGLSFETTDDSLREHFEK 21 1 P51991;P51991-2 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 0 ; ; 137.73 5.98E-05 21374700 11534.4 10982.4 9817.4 13027.4 12041 11158.8 9554.7 11014.7 12535.6 10881 FALSE FALSE TRUE 11393.8143 11137.01052 9988.267729 14533.68928 11426.50284 10445.78869 10366.27598 11333.39297 11414.38454 10598.31005 1.075059537 1.050828902 0.942439661 1.371321391 1.078143853 0.985608898 0.978106503 1.069358503 1.077000435 1 13.37154662 -8.263184226 24.64880086 1.058535827 1.007732823 0.051432492 0.109982876 376.4967261 5318673.364 0.015872603 0.037360648 5.46E-09 8.263184226 -0.050803004 LFIGGLSFETTDESLR ddPTM_HeLa_Romidepsin_16h_R1 2 LFIGGLSFETTDESLR 16 0 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646;F8VZ49;Q32P51 F8W6I7 HNRNPA1;HNRNPA1L2 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed;Heterogeneous nuclear ribonucleoprotein A1-like 2" 0 0 ; ; 207.47 4.72E-18 65127000 2231.63 1828.65 2151.8 1917 1870.89 1939.58 1801.74 1797.73 2064.08 2032.97 FALSE FALSE TRUE 2204.430035 1854.393783 2189.251176 2138.65256 1775.411502 1815.647098 1954.779751 1849.744481 1879.463515 1980.153146 1.113262396 0.936490082 1.105596898 1.080044018 0.896603127 0.916922563 0.987186145 0.934142132 0.949150584 1 10.9513963 -8.764682171 24.99986867 1.050983401 0.93633361 0.34422628 0.061911127 57.10746416 440266.9183 0.008765974 0.016383079 1.72E-09 8.764682171 -0.114649791 LFIGGLSFETTEESLR ddPTM_HeLa_Romidepsin_16h_R1 2 LFIGGLSFETTEESLR 16 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ; ; 340.88 6.91E-204 55832600 2329.4 2174.02 2333.6 2003.08 2657 2344.5 2360.31 2115.25 2555.44 2166.37 FALSE FALSE TRUE 2301.008377 2204.625911 2374.215329 2234.685534 2521.403375 2194.694017 2560.794672 2176.451421 2326.875046 2110.087395 1.09048013 1.044803128 1.125173931 1.059048805 1.19492841 1.040096264 1.213596498 1.031450843 1.102738707 1 11.04308704 -12.69113821 0.260714926 0.926076688 1.123939588 0 0.067188423 5.251485138 0.400928845 0.330515363 0.040679554 2.04E-13 12.69113821 0.1978629 LFLY(ph)T(ph)S(ph)IALKYYK ddPTM_HeLa_Romidepsin_16h_R1 1 LFLYTSIALKYYK 13 1 Q8NBF2 Q8NBF2 NHLRC2 NHL repeat-containing protein 2 3 0 LFLY(1)T(1)S(1)IALKYYK 73.233 0.0040223 0 2173.7 1771.5 2027.1 2217 2477.5 2138.7 1848.6 2279.5 2387.2 1917.2 TRUE FALSE FALSE 2147.206108 1796.439223 2062.380825 2473.339971 2351.06393 2002.043972 2005.620038 2345.453736 2173.682853 1867.390868 1.149842888 0.962004931 1.104418395 1.324489701 1.259010082 1.072107617 1.074022623 1.256005787 1.164021358 1 10.86680822 -16.27881871 0.166268751 0.437837277 1.196295369 0.008008411 0.110785747 60.24004185 0.709382775 11.0539109 0.183397495 5.26E-17 16.27881871 0.758458091 LFPADT(ph)SPSTATK ddPTM_HeLa_Romidepsin_16h_R1 4 LFPADTSPSTATK 13 0 Q6NZY4;Q6NZY4-2 Q6NZY4 ZCCHC8 Zinc finger CCHC domain-containing protein 8 1 0 LFPADT(0.499)S(0.499)PS(0.001)TATK;LFPADT(0.627)S(0.211)PS(0.055)T(0.093)AT(0.014)K;LFPADT(0.816)S(0.182)PS(0.002)TATK;LFPADT(0.596)S(0.398)PS(0.005)TATK ;;; 183.89 5.97E-07 145211000 14237.2 13267.4 13303.4 11337.8 12331.6 12438.3 10151.4 10756.7 13894.4 13559.6 TRUE FALSE FALSE 14063.67153 13454.17881 13534.9401 12648.72978 11702.27244 11643.53277 11013.65966 11067.92814 12651.65006 13207.31964 1.064839189 1.018691088 1.024805976 0.957706039 0.886044463 0.881596955 0.833905741 0.838014711 0.95792715 1 13.68905009 -8.830010221 1.340708362 1.031376446 0.843973571 0.856375928 0.029545565 0.087796124 0.315418826 0.004203689 0.010408741 1.48E-09 8.830010221 -0.187402876 LFPDT(ph)PLALDANK ddPTM_HeLa_Romidepsin_16h_R1 1 LFPDTPLALDANK 13 0 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 LFPDT(1)PLALDANK 102.52 0.023243 130980000 1731.3 2333 1772.4 1911.9 1993.9 2355.9 2120.5 2431.4 1949.3 1817.5 TRUE FALSE FALSE 1710.19825 2365.844035 1803.247879 2132.962874 1892.143843 2205.365593 2300.615217 2501.748723 1774.949726 1770.281088 0.966060283 1.336422815 1.018622348 1.204872429 1.068838082 1.245771425 1.299576227 1.413192933 1.00263723 1 10.78976274 -4.000000036 0.223193353 0.95898976 3.42429511 0.571168029 0.101483906 22.46730904 0.270279013 0.072250151 20.23897011 1.00E-04 4.000000036 2.465305349 LFPDT(ph)PLALDANKK ddPTM_HeLa_Romidepsin_16h_R1 2 LFPDTPLALDANKK 14 1 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 LFPDT(1)PLALDANKK;LFPDT(1)PLALDANKK ; 86.772 0.0097811 198111000 8559.8 8052.3 8184.8 7568 9845.4 11853.6 10667.8 10686.9 8836 8611.7 TRUE FALSE FALSE 8455.469865 8165.660491 8327.253011 8443.047769 9342.9525 11096.19322 11573.92267 10996.10859 8045.68603 8387.966793 1.008047608 0.973496998 0.9927618 1.006566666 1.11385187 1.322870427 1.379824569 1.310938498 0.959193834 1 13.03410543 -8.38674476 2.328273184 1.000453688 1.351228261 0.978308421 0.023133751 0.024075449 0.25260567 0.002785614 0.007417363 4.10E-09 8.38674476 0.350774574 LFPEFDDS(ph)DYDEVPEEGPGAPAR ddPTM_HeLa_Romidepsin_16h_R1 4 LFPEFDDSDYDEVPEEGPGAPAR 23 0 Q96P48-3;Q96P48 Q96P48-3 ARAP1 "Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1" 1 0 LFPEFDDS(0.989)DY(0.011)DEVPEEGPGAPAR;LFPEFDDS(0.992)DY(0.008)DEVPEEGPGAPAR;LFPEFDDS(0.998)DY(0.002)DEVPEEGPGAPAR;LFPEFDDS(0.995)DY(0.005)DEVPEEGPGAPAR ;;; 114.91 3.20E-06 15930990 3711.67 4014.69 3901.67 4257.57 4484.78 4004.51 3571.59 3894.19 4162.26 3566.77 TRUE FALSE FALSE 3666.430738 4071.208911 3969.57693 4749.850276 4255.904942 3748.634735 3874.960765 4006.862244 3789.977041 3474.104801 1.055359855 1.171872797 1.142618648 1.367215599 1.22503643 1.079021777 1.115383959 1.153350999 1.090921909 1 11.76242556 -10.35097008 1.857076486 1.020318701 1.183660192 0.364093534 0.077131597 0.220426832 1.446315668 0.014979607 0.017178239 4.46E-11 10.35097008 0.163341491 LFPY(ph)S(ph)NY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LFPYSNYK 8 0 X6RKN2;O94856-10;O94856-3;O94856-8;O94856-11;O94856-6;O94856-7;O94856-13;O94856-5;O94856 X6RKN2 NFASC Neurofascin 3 0 LFPY(1)S(1)NY(1)K 42.718 0.0042855 0 3217.3 3245.7 2786.7 2088.2 2827 2862.1 2257.9 2167.3 3496.9 3404 TRUE FALSE FALSE 3178.08631 3291.39305 2835.201345 2329.647509 2682.727641 2679.221047 2449.68597 2230.007406 3184.128506 3315.563589 0.958535774 0.992709976 0.855118977 0.702639973 0.809131711 0.808074095 0.738844514 0.672587735 0.960358147 1 11.69503841 -9.567630331 3.299360486 0.980793731 0.753241079 0.871597473 0.041761477 0.061501377 1.38311308 0.006846778 0.010112518 2.71E-10 9.567630331 -0.227552652 LFQLGPPS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 LFQLGPPSPVK 11 0 Q9NZH5-2;Q9NZH5;O95997 Q9NZH5-2 PTTG2;PTTG1 Securin-2;Securin 1 0 LFQLGPPS(1)PVK;LFQLGPPS(1)PVK ; 134.04 0.0042555 358420000 16773.3 16138.8 17896.3 12585.3 16843.5 13699.5 11459.7 10652.6 17147.1 13979.4 TRUE FALSE FALSE 16568.86057 16366.00245 18207.77759 14040.4716 15983.91334 12824.14616 12433.08663 10960.81617 15613.42043 13616.21317 1.216847912 1.201949635 1.337213024 1.031158327 1.173888301 0.941829127 0.913108988 0.80498271 1.146678613 1 13.73303791 -7.998401511 1.887597292 1.129812442 0.839049343 0.622698895 0.096003285 0.239996501 1.616983772 0.01711795 0.073282267 1.00E-08 7.998401511 -0.290763099 LFQSDTNAMLGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LFQSDTNAMLGKK 13 1 F8VTR4;F8W0J4;F8W1B9;O95619 F8VTR4 YEATS4 YEATS domain-containing protein 4 0 1 ; LFQSDTNAMLGK(1)K;LFQSDTNAMLGK(1)K 75.739 0.017149 1251330 304.44 310.77 376.98 193.99 352.924 370.16 262.213 386.65 400.25 314.33 FALSE TRUE FALSE 300.7293682 315.1450282 383.5411788 216.4200366 334.9129713 346.5079706 284.4853657 397.8371077 364.4506376 306.1636613 0.982250365 1.029335183 1.252732533 0.706876955 1.093901771 1.13177367 0.929193767 1.299426281 1.190378492 1 8.258159249 -7.25201821 24.47019974 1.005442806 1.299426491 0.203247963 0.146707786 844.3524277 2193029.1 0.016709595 0.27821074 5.60E-08 7.25201821 0.293983686 LFS(ph)DEDDR ddPTM_HeLa_Romidepsin_16h_R1 1 LFSDEDDR 8 0 H0Y322;Q5TKA1;Q5TKA1-2;B1B047 H0Y322 LIN9 Protein lin-9 homolog 1 0 LFS(1)DEDDR 104.42 0.027283 2327300 1812.5 1760.5 2168.2 1050.4 1339.2 1350.2 1060.7 1378.2 1762.5 1945.7 TRUE FALSE FALSE 1790.408553 1785.284365 2205.936611 1171.85219 1270.855627 1263.926578 1150.795832 1418.076043 1604.857586 1895.150434 0.944731627 0.942027785 1.163990242 0.61834257 0.670582981 0.666926781 0.607231917 0.748265688 0.846823322 1 10.88809666 -9.24545136 24.99541747 0.983301163 0.659932841 0.789109039 0.081985913 220.3268773 344455.7606 0.010007317 0.016561063 5.68E-10 9.24545136 -0.323368322 LTPVS(ph)PESSSTEEK ddPTM_HeLa_Romidepsin_16h_R1 4 LTPVSPESSSTEEK 14 0 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 LTPVS(0.301)PES(0.301)S(0.301)S(0.082)T(0.015)EEK;LTPVS(0.999)PES(0.001)SSTEEK;LT(0.339)PVS(0.654)PES(0.007)SSTEEK;LT(0.004)PVS(0.996)PESSSTEEK ;;; 241.41 6.25E-44 1742274600 27588.9 25569.6 24072.7 18841.3 13053.82 9651.07 7926.78 7770.24 27624 24942.4 TRUE FALSE FALSE 27252.63588 25929.5695 24491.67525 21019.81976 12387.63485 9034.397774 8600.080495 7995.059635 25153.24025 24294.39285 1.121766493 1.067306751 1.008120491 0.865212804 0.509896869 0.371871725 0.353994461 0.329090736 1.035351672 1 14.56833576 -8.785039422 1.675061492 1.059225827 0.341347789 0.990162001 0.031282212 0.034766286 0.197542877 0.00740196 0.0171473 1.64E-09 8.785039422 -0.717878038 down LFVGGIKEDTEEHHLR ddPTM_HeLa_Romidepsin_16h_R1 4 LFVGGIKEDTEEHHLR 16 1 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 ;;; ;;; 110.51 0.00058578 199481000 17784.7 16272.9 14147 20091.3 17696.4 15824.7 14576.6 15122.7 17936.2 14781.9 FALSE FALSE TRUE 17567.93324 16501.99031 14393.2226 22414.35064 16793.28667 14813.55274 15814.73604 15560.25146 16331.94135 14397.86411 1.220176347 1.146141552 0.999677625 1.556783039 1.166373467 1.028871549 1.098408481 1.080733319 1.134330844 1 13.81356719 -5.95101969 20.27185614 1.127974954 1.160902998 0 0.154915321 0 0 0.021231767 0 1.12E-06 5.95101969 0.032928044 LFVGNLPADITEDEFK ddPTM_HeLa_Romidepsin_16h_R1 1 LFVGNLPADITEDEFK 16 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 0 138.55 2.61E-07 0 551.92 491.52 538.53 406.58 579.25 524.22 487.33 529.59 531.49 560.13 FALSE FALSE TRUE 545.1929868 498.4396315 547.9028887 453.5906926 549.688711 490.7240338 528.723798 544.9128511 483.9522033 545.5777419 0.999294775 0.913599645 1.004261807 0.831395158 1.007535075 0.899457577 0.96910808 0.998781309 0.887045358 1 9.091640977 -10.28798381 22.53413267 0.999666993 0.945545145 0 0.062879552 239.1907611 203053.1572 0.007957482 0.009102191 5.15E-11 10.28798381 -0.054121848 LFVGNLPADITEDEFKR ddPTM_HeLa_Romidepsin_16h_R1 2 LFVGNLPADITEDEFKR 17 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 0 ; ; 122.46 0.0013379 47139000 4010.9 3633.6 3201.5 3316.4 3735 3542.2 2868.5 3217.8 3584.5 3439.7 FALSE FALSE TRUE 3962.013608 3684.753916 3257.220765 3699.857772 3544.389013 3315.864852 3112.150318 3310.901966 3263.893342 3350.336098 1.182571984 1.0998162 0.972207166 1.104324361 1.057920432 0.989711108 0.9289069 0.988229798 0.974198781 1 11.71009012 -8.234598082 2.6772879 1.081051927 0.958265775 0.223480207 0.065587407 0.259807554 3.661162803 0.011124649 0.031645707 5.83E-09 8.234598082 -0.122786152 LFVLLPEQS(ph)PVSYSK ddPTM_HeLa_Romidepsin_16h_R1 1 LFVLLPEQSPVSYSK 15 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 0 LFVLLPEQS(0.991)PVS(0.008)YSK 155.06 0.00044244 97466000 6482 6800.8 6448.7 5625.9 6678.1 7293.5 6477.3 6764.6 6807.3 6923.2 TRUE FALSE FALSE 6402.994891 6896.541841 6560.936918 6276.393029 6337.291638 6827.468889 7027.4817 6960.323028 6198.438039 6743.334266 0.949529511 1.022719855 0.97295146 0.93075514 0.939786074 1.01247671 1.042137528 1.03217826 0.919194837 1 12.7192464 -8.035905918 5.708164204 0.973391436 1.035292601 0.478748774 0.031081744 0.127076422 11.70640263 0.004221248 0.011458897 9.21E-09 8.035905918 0.061901165 LGADES(ph)EEEGR ddPTM_HeLa_Romidepsin_16h_R1 1 LGADESEEEGR 11 0 F5H7V1;O43847;O43847-2 F5H7V1 NRD1 Nardilysin 1 0 LGADES(1)EEEGR 166.11 0.00056558 13891000 2603 2486.8 2438 1310.8 2265.5 2694.8 2038.3 2154.5 2345.6 2386.5 TRUE FALSE FALSE 2571.273635 2521.809236 2480.432367 1462.360863 2149.883081 2522.610977 2211.433151 2216.837058 2135.803661 2324.498386 1.106162796 1.084883195 1.067082852 0.629108143 0.924880436 1.085228104 0.951359297 0.95368406 0.918823465 1 11.18270371 LGADES(ph)EEEGRR ddPTM_HeLa_Romidepsin_16h_R1 1 LGADESEEEGRR 12 1 F5H7V1;O43847;O43847-2 F5H7V1 NRD1 Nardilysin 1 0 LGADES(1)EEEGRR 101.45 0.0044158 9316100 3127.2 3189.6 3173.4 2854.2 3118.4 3491.6 2299.2 3362.6 3540.6 3470.8 TRUE FALSE FALSE 3089.084484 3234.503273 3228.631696 3184.216033 2959.256412 3268.498029 2494.493991 3459.891526 3223.919868 3380.628116 0.913760514 0.95677583 0.955039 0.941900713 0.875356978 0.966831582 0.737878851 1.023446356 0.953645227 1 11.72307561 -16.52287875 0.149947478 1.31274421 0.885138802 0.07982857 0.072506553 82.89799474 0.847471432 7.668192806 0.153672447 3.00E-17 16.52287875 -0.427605409 LGADESEEEGR ddPTM_HeLa_Romidepsin_16h_R1 2 LGADESEEEGR 11 0 F5H7V1;O43847;O43847-2 F5H7V1 NRD1 Nardilysin 0 0 ; ; 166.34 0.00037743 3126800 2076.44 2098.95 1773.85 1797.76 2189.64 1899.33 1705.06 2000.51 2192.91 2628.46 FALSE FALSE TRUE 2051.131551 2128.499073 1804.723115 2005.62547 2077.8945 1777.968943 1849.887754 2058.391601 1996.770637 2560.17223 0.801169361 0.831389017 0.704922541 0.783394744 0.811622935 0.694472396 0.722563792 0.804005128 0.779936058 1 11.32202515 -12.11757634 0.383099961 1.0703256 0.744124509 0.044542013 0.080334966 0.663360039 0.138953239 0.089731913 0.015947563 7.63E-13 12.11757634 -0.326201091 LGADESEEEGRR ddPTM_HeLa_Romidepsin_16h_R1 2 LGADESEEEGRR 12 1 F5H7V1;O43847;O43847-2 F5H7V1 NRD1 Nardilysin 0 0 ; ; 129 0.0028152 5099700 3101.1 2994.3 2539.27 2226.93 2745.6 2762.11 2078.93 2647.37 3082.2 3070.6 FALSE FALSE TRUE 3063.3026 3036.453834 2583.464929 2484.418125 2605.481787 2585.620085 2255.514262 2723.967474 2806.520312 2990.825369 1.024233187 1.015256145 0.863796648 0.830679768 0.871158114 0.864517237 0.75414442 0.910774498 0.938376524 1 11.54632796 -9.730766564 5.038496537 1.012319401 0.844251471 0.714691684 0.04445127 0.052463868 3.286842586 0.005617941 0.007851413 1.86E-10 9.730766564 -0.16806793 LGAES(ph)PSIASTSSTEK ddPTM_HeLa_Romidepsin_16h_R1 1 LGAESPSIASTSSTEK 16 0 A0A0D9SF60;Q99569-2;Q99569;H0YFB1;E7EST6 A0A0D9SF60 PKP4 Plakophilin-4 1 0 LGAES(0.683)PS(0.317)IASTSSTEK 149.6 0.00028936 7358700 2477.5 2154.6 2607.9 2353.8 2557.6 2488.9 2520.9 2310.4 2334.1 2063.4 TRUE FALSE FALSE 2447.303277 2184.932515 2653.289406 2625.957431 2427.076128 2329.867323 2735.025183 2377.247779 2125.33225 2009.792571 1.217689483 1.087143294 1.320180721 1.306581321 1.207625187 1.159257605 1.360849484 1.182832405 1.05748836 1 10.97283089 -12.46879904 0.366349122 0.897050494 1.25550867 0.52788065 0.07714021 1.649442773 0.257990693 0.240654888 0.028904338 3.40E-13 12.46879904 0.358458176 LGAESPS(ph)IASTSSTEK ddPTM_HeLa_Romidepsin_16h_R1 1 LGAESPSIASTSSTEK 16 0 A0A0D9SF60;Q99569-2;Q99569;H0YFB1;E7EST6 A0A0D9SF60 PKP4 Plakophilin-4 1 0 LGAES(0.33)PS(0.669)IASTSSTEK 156 0.00022653 7565100 2835 3013.1 3081.8 2692.9 3748.6 3273.6 2999.4 2973.4 2941.6 2867.2 TRUE FALSE FALSE 2800.44593 3055.518501 3135.437436 3004.265768 3557.294954 3064.427525 3254.168961 3059.430638 2678.495929 2792.709731 1.002770141 1.094105294 1.12272228 1.075752963 1.273778981 1.097295394 1.16523709 1.095506133 0.959102874 1 11.44744991 -10.02304766 1.479283182 0.999253317 1.146005754 0.613007355 0.053381368 0.173281586 0.740454322 0.008898805 0.011654585 9.48E-11 10.02304766 0.146752437 LGAGEGGEAS(ph)VSPEK ddPTM_HeLa_Romidepsin_16h_R1 2 LGAGEGGEASVSPEK 15 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LGAGEGGEAS(0.744)VS(0.256)PEK;LGAGEGGEAS(0.933)VS(0.067)PEK ; 193.98 1.21E-12 276920000 7922.2 7991.9 8037 5029.99 7509.6 6509.4 5805.7 5187.3 8597.3 8360.1 TRUE FALSE FALSE 7825.641179 8104.410178 8176.880614 5611.581111 7126.35709 6093.470348 6298.836013 5337.386341 7828.335956 8142.903397 0.961038195 0.995272789 1.004172617 0.689137625 0.875161689 0.748316669 0.773536871 0.655464775 0.96136913 1 12.99132757 -9.268794107 24.99896385 0.983915834 0.75677045 0.817407655 0.055709848 169.5835713 576419.6223 0.008051331 0.012452439 5.39E-10 9.268794107 -0.227145384 LGAGEGGEASVS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 5 LGAGEGGEASVSPEK 15 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LGAGEGGEAS(0.003)VS(0.997)PEK;LGAGEGGEAS(0.105)VS(0.895)PEK;LGAGEGGEAS(0.044)VS(0.956)PEK;LGAGEGGEAS(0.007)VS(0.993)PEK;LGAGEGGEAS(0.083)VS(0.917)PEK ;;;; 204.17 2.50E-18 1137304200 19120.5 20079 19578.1 12151.9 16711.5 15787.5 12833.1 15210.35 19241.5 21073.4 TRUE FALSE FALSE 18887.45199 20361.67269 19918.84862 13556.95985 15858.6498 14778.7297 13923.14319 15650.43748 17520.49205 20525.91003 0.920176107 0.991998535 0.970424629 0.660480331 0.77261616 0.720003629 0.678320385 0.762472283 0.853579307 1 14.32515857 -9.269119412 24.99593917 0.964600868 0.719589918 0.831234149 0.05117125 127.5183777 415029.2772 0.006352609 0.009816153 5.38E-10 9.269119412 -0.24501095 LGAGEGGEASVS(ph)PEKTSTTSK ddPTM_HeLa_Romidepsin_16h_R1 4 LGAGEGGEASVSPEKTSTTSK 21 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LGAGEGGEAS(0.084)VS(0.895)PEKT(0.014)S(0.005)T(0.002)T(0.001)SK;LGAGEGGEAS(0.071)VS(0.927)PEKT(0.001)STTSK;LGAGEGGEAS(0.069)VS(0.609)PEKT(0.185)S(0.069)T(0.046)T(0.016)S(0.006)K;LGAGEGGEAS(0.002)VS(0.967)PEKT(0.029)ST(0.001)TSK ;;; 108.79 9.80E-05 850489000 10738.2 9954.7 8890.7 12066.4 9038.4 8303.8 7194.4 8836.9 11632 10900 TRUE FALSE FALSE 10607.31869 10094.84253 9045.438904 13461.57394 8577.136721 7773.213979 7805.492156 9092.581759 10591.60479 10616.81643 0.999105406 0.950835177 0.851991646 1.267948262 0.807882172 0.732160533 0.735200821 0.856432041 0.997625311 1 13.3740636 -8.551478108 24.99552356 1.00149763 0.770551794 0.541706866 0.102974084 108.2377544 94598.18836 0.013559006 0.027118348 2.81E-09 8.551478108 -0.230945836 LGAGEGGEASVSPEKT(ph)STTSK ddPTM_HeLa_Romidepsin_16h_R1 1 LGAGEGGEASVSPEKTSTTSK 21 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LGAGEGGEAS(0.103)VS(0.06)PEKT(0.6)S(0.176)T(0.052)T(0.003)S(0.005)K 85.203 0.00031498 0 771.46 939.9 591.15 699.46 610.74 565.34 462.05 606.8 915.06 796.68 TRUE FALSE FALSE 762.0571488 953.1319369 601.4387178 780.3348563 579.5716588 529.2165986 501.2965155 624.3568006 833.2147418 775.9821388 0.982055012 1.228291077 0.775067734 1.005609301 0.746887886 0.68199585 0.646015534 0.804602026 1.073755052 1 9.599879635 -8.714943142 4.135512474 0.994551168 0.705422103 0.619364185 0.111347954 0.102485877 3.674770394 0.014863076 0.030004184 1.93E-09 8.714943142 -0.289129065 LGAGGGS(ph)PEKSPS(ph)AQELK ddPTM_HeLa_Romidepsin_16h_R1 2 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 2 0 LGAGGGS(1)PEKS(0.007)PS(0.993)AQELK;LGAGGGS(1)PEKS(0.018)PS(0.982)AQELK ; 176.28 7.42E-13 28888000 8454.2 7481.8 7851.8 7350.8 8849.5 8948.9 7145.8 8274.9 8002.8 7744 TRUE FALSE FALSE 8351.156959 7587.128977 7988.457285 8200.734083 8397.876993 8377.094171 7752.764074 8514.321176 7287.009525 7542.809764 1.107167915 1.00587569 1.059082429 1.087225363 1.113361898 1.110606582 1.027835027 1.128799671 0.966086877 1 12.88088632 -9.301138728 4.045181396 1.048106618 1.09225827 0.300411002 0.045420334 0.317520547 11.44148638 0.007295086 0.011600716 5.00E-10 9.301138728 0.044151652 LGAGGGS(ph)PEKSPSAQELK ddPTM_HeLa_Romidepsin_16h_R1 2 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 0 LGAGGGS(0.542)PEKS(0.161)PS(0.296)AQELK;LGAGGGS(0.958)PEKS(0.042)PSAQELK ; 195.28 4.26E-14 379871000 9837.4 9593.1 8819.4 9086 9099.2 9039.6 8590.9 9114.2 9986.3 8827.3 TRUE FALSE FALSE 9717.497985 9728.151914 8972.897957 10136.56607 8634.83387 8461.998734 9320.610832 9377.904997 9093.100317 8597.965473 1.130209003 1.131448125 1.043607117 1.178949381 1.004288037 0.984186173 1.084048414 1.090712102 1.057587443 1 13.0697796 -7.545782651 24.88206967 1.065478039 1.089046458 0.019457014 0.060498947 859.1728199 933376.9428 0.009647565 0.036101634 2.85E-08 7.545782651 0.023568418 LGAGGGSPEKSPS(ph)AQELK ddPTM_HeLa_Romidepsin_16h_R1 1 LGAGGGSPEKSPSAQELK 18 1 Q9UNE7;H3BS86 Q9UNE7 STUB1 E3 ubiquitin-protein ligase CHIP 1 0 LGAGGGS(0.041)PEKS(0.049)PS(0.91)AQELK 77.068 0.0058682 978830000 5295.1 7540.7 4309.4 5445.6 5068.1 5370.7 4793.2 5019.9 5263.3 5544.8 TRUE FALSE FALSE 5230.561284 7646.858173 4384.403299 6075.245894 4809.455945 5027.529603 5200.334288 5165.142886 4792.537266 5400.745297 0.968488791 1.415889429 0.811814492 1.124890281 0.890517083 0.93089552 0.962891972 0.956375945 0.887384426 1 12.3989428 -8.721876024 24.99840986 1.014964465 0.936844965 0.083273189 0.15362183 375.448823 237228.5444 0.020406989 0.040813426 1.90E-09 8.721876024 -0.0781195 LGAHEGLS(ph)PTPFMNSNLMGK ddPTM_HeLa_Romidepsin_16h_R1 1 LGAHEGLSPTPFMNSNLMGK 20 0 B4DGI9;Q99081;Q99081-3;H0YNQ5 B4DGI9 TCF12 Transcription factor 12 1 0 LGAHEGLS(0.934)PT(0.066)PFMNSNLMGK 73.809 0.0020001 21029000 2233.7 2348.3 2124 1915.5 1652.5 1195.3 1371.3 1506.6 2300.3 2321.1 TRUE FALSE FALSE 2206.474805 2381.359429 2160.967329 2136.979123 1568.166759 1118.924188 1487.778188 1550.191094 2094.555407 2260.797487 0.975971894 1.053327174 0.955842945 0.945232439 0.693634334 0.494924554 0.658076717 0.685683305 0.926467505 1 11.14261605 -8.735562807 3.199831723 0.990724358 0.613535542 0.901644361 0.056010708 0.045347089 0.957867223 0.007503854 0.015358362 1.84E-09 8.735562807 -0.377188816 LGAPENSGIST(ph)LER ddPTM_HeLa_Romidepsin_16h_R1 3 LGAPENSGISTLER 14 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2;M0QYB0;Q9Y4F1-3 A0A1B0GV68 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 0 LGAPENSGIS(0.001)T(0.999)LER;LGAPENSGIST(1)LER;LGAPENSGIS(0.089)T(0.911)LER ;; 215.37 8.37E-24 145460000 12739.8 17442.3 14618.4 12214.5 16465 17899.1 11510.8 15519.8 13339.6 12377 TRUE FALSE FALSE 12584.52242 17687.85316 14872.82712 13626.79796 15624.72961 16755.40528 12488.52706 15968.84093 12146.47277 12055.44376 1.043887116 1.467208799 1.23370217 1.130343954 1.29607254 1.389862175 1.035924294 1.324616601 1.007550864 1 13.55739714 -10.43456477 10.56245265 1.019321124 1.258469037 0.497424882 0.115627057 0.337681313 39.04069087 0.018801414 0.021474727 3.68E-11 10.43456477 0.239147913 LGAQT(ph)PVGVSTLEPGQTLLPR ddPTM_HeLa_Romidepsin_16h_R1 1 LGAQTPVGVSTLEPGQTLLPR 21 0 O94887-3;O94887-2;O94887;C9JWM9;C9JVQ5 O94887-3 FARP2 "FERM, RhoGEF and pleckstrin domain-containing protein 2" 1 0 LGAQT(1)PVGVSTLEPGQTLLPR 112.53 0.00042948 11890000 659.92 743.74 877.98 1056.9 954.3 1338.9 907.6 1234.4 691.12 818.59 TRUE FALSE FALSE 651.8766412 754.2103912 893.2608736 1179.103751 905.59851 1253.348611 984.6915213 1270.115416 629.3044963 797.3229138 0.817581722 0.945928404 1.120325101 1.478828377 1.135798927 1.571946058 1.234997144 1.592974935 0.789271806 1 9.63902032 -9.516854322 2.660825728 0.91314425 1.389132867 0.738309218 0.143960486 0.10543738 1.503712297 0.021515542 0.032921183 3.04E-10 9.516854322 0.475988617 LGAS(ph)NSPGQPNSVK ddPTM_HeLa_Romidepsin_16h_R1 2 LGASNSPGQPNSVK 14 0 P49756 P49756 RBM25 RNA-binding protein 25 1 0 LGAS(0.948)NS(0.052)PGQPNSVK;LGAS(0.903)NS(0.097)PGQPNSVK ; 214.89 4.46E-24 93434000 8746.7 7971.2 7767.2 6710.6 8685.2 7578.2 7649.2 8289.3 8558.1 6979.5 TRUE FALSE FALSE 8640.091856 8083.418763 7902.384858 7486.511146 8241.961835 7093.977478 8298.922857 8529.137817 7792.642102 6798.171584 1.270943481 1.189057773 1.162427979 1.101253632 1.212379201 1.043512567 1.220758075 1.254622322 1.146284998 1 12.73093106 -12.50127668 1.247875533 0.999962949 1.186949915 0.146809385 0.078025601 0.303457684 0.845455325 0.048220893 0.011679811 3.15E-13 12.50127668 0.186986966 LGASEAAAFDS(ph)DESEAVGATR ddPTM_HeLa_Romidepsin_16h_R1 2 LGASEAAAFDSDESEAVGATR 21 0 H0YBE8;H3BLZ3;Q8IX03;Q8IX03-2 H0YBE8 WWC1 Protein KIBRA 1 0 LGASEAAAFDS(0.998)DES(0.002)EAVGATR;LGAS(0.053)EAAAFDS(0.947)DESEAVGATR ; 246.1 2.00E-66 17741400 2519.42 2581.45 2023.72 2485.78 2666.31 2453.75 2446.96 2502.71 2554.6 2443.45 TRUE FALSE FALSE 2488.71234 2617.791721 2058.941998 2773.19758 2530.238251 2296.963294 2654.804721 2575.121965 2326.110178 2379.968817 1.045691155 1.099926899 0.865113015 1.165224334 1.063139245 0.965123273 1.115478784 1.081998196 0.977370023 1 11.21672696 LGASNS(ph)PGQPNSVK ddPTM_HeLa_Romidepsin_16h_R1 2 LGASNSPGQPNSVK 14 0 P49756 P49756 RBM25 RNA-binding protein 25 1 0 LGAS(0.03)NS(0.97)PGQPNSVK;LGAS(0.002)NS(0.933)PGQPNS(0.065)VK ; 193.54 2.89E-11 1896980000 25580.8 24097.1 24635.4 19805.1 24760.3 25194.2 23636.1 25379.5 25646.4 24034.4 TRUE FALSE FALSE 25269.01137 24436.33961 25064.1688 22095.05885 23496.6895 23584.37193 25643.74974 26113.81579 23352.52175 23409.98282 1.079411786 1.043842697 1.070661563 0.94383063 1.003703833 1.007449348 1.095419417 1.115499144 0.997545446 1 14.51483626 -15.4946416 0.004758824 2.38E-06 2.021777195 0.114256071 0.048104787 105879.5694 48.868816 10978.93694 9813.042824 3.20E-16 15.4946416 2.021774815 LGASNSPGQPNSVK ddPTM_HeLa_Romidepsin_16h_R1 1 LGASNSPGQPNSVK 14 0 P49756 P49756 RBM25 RNA-binding protein 25 0 0 119.76 0.00083089 0 951.54 1148.7 1162.1 1081.9 1239.7 1208.4 1317 1177 1137.8 1242.2 FALSE FALSE TRUE 939.9422645 1164.871429 1182.325863 1206.994368 1176.433483 1131.18714 1428.865947 1211.054638 1036.032318 1209.927465 0.776858359 0.962761374 0.977187391 0.997575808 0.972317364 0.93492145 1.180951742 1.000931604 0.856276387 1 10.24070485 -8.569649949 0.750476107 0.900692939 1.07838485 0.340268139 0.080625802 0.858445614 0.80668673 0.018587228 0.089175847 2.69E-09 8.569649949 0.177691911 LGDAS(ph)DTEAADGER ddPTM_HeLa_Romidepsin_16h_R1 1 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 LGDAS(0.97)DT(0.03)EAADGER 245.4 1.65E-54 24070000 1679 1488.7 1522.2 1528.7 2126.1 2320.7 1809.1 1793.5 1632.8 1547.7 TRUE FALSE FALSE 1658.535702 1509.657958 1548.693252 1705.455487 2017.597183 2172.41476 1962.764909 1845.392093 1486.758279 1507.490531 1.100196431 1.001437771 1.027331994 1.131320862 1.338381331 1.441080203 1.302008118 1.224148381 0.986247176 1 10.55793322 -8.882004998 3.379194063 1.043810183 1.333892374 0.850139927 0.059697777 0.072914132 1.639084203 0.009611794 0.018351024 1.31E-09 8.882004998 0.290082191 LGDASDT(ph)EAADGER ddPTM_HeLa_Romidepsin_16h_R1 1 LGDASDTEAADGER 14 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 LGDAS(0.225)DT(0.775)EAADGER 227.92 8.48E-33 33210000 2134.2 2114.4 2172.4 2173.8 2164.1 2296.7 2423.1 2271.7 1995.2 1694.1 TRUE FALSE FALSE 2108.18755 2144.166579 2210.209711 2425.144984 2053.657902 2149.948282 2628.918054 2337.428055 1816.744315 1650.087038 1.277622029 1.299426351 1.339450381 1.469707311 1.244575501 1.302930229 1.593199627 1.416548341 1.100999083 1 10.68832641 -15.35887826 0.118033361 1.23E-12 1.604064223 0.688791201 0.09045121 23.51950002 0.267108038 6.057399717 0.472614317 4.38E-16 15.35887826 1.604064223 LGDEDEEIDGDTNK ddPTM_HeLa_Romidepsin_16h_R1 2 LGDEDEEIDGDTNK 14 0 A0A087WU64;A6NMQ1;P09884 A0A087WU64 POLA1 DNA polymerase;DNA polymerase alpha catalytic subunit 0 0 ; ; 289.71 2.55E-112 7376100 3180.2 3566.3 3472.9 2891 2815.9 3155.2 2834.1 2801 3584.5 3049.5 FALSE FALSE TRUE 3141.438499 3616.506465 3533.344368 3225.271023 2672.194115 2953.592903 3074.828383 2882.042516 3263.893342 2970.27355 1.057625988 1.217566801 1.189568674 1.085849828 0.899645797 0.994384138 1.035200405 0.970295317 1.098852778 1 11.53638009 -8.791394988 24.9817409 1.060903323 0.980582856 0.339183279 0.075306629 286.498375 238926.9678 0.013245001 0.024010938 1.62E-09 8.791394988 -0.080320467 LGDSHDLQR ddPTM_HeLa_Romidepsin_16h_R1 2 LGDSHDLQR 9 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 ; ; 155.58 0.0021021 12543600 11298.2 10167.8 11952.2 9478.5 12991.4 12818.8 10931.3 8706 11141 9922.4 FALSE FALSE TRUE 11160.49319 10310.94256 12160.22303 10574.44877 12328.40038 11999.72005 11859.80435 8957.894374 10144.52106 9664.614618 1.154778916 1.066875707 1.258221203 1.094140758 1.275622554 1.241613921 1.22713681 0.926875486 1.049656035 1 13.23849649 -12.09717552 0.513887301 0.973517545 1.171319419 0.200936981 0.101934971 1.368855543 0.546074982 0.133570627 0.025831213 8.00E-13 12.09717552 0.197801874 LGDSS(ph)LSR ddPTM_HeLa_Romidepsin_16h_R1 2 LGDSSLSR 8 0 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 0 LGDS(0.018)S(0.982)LSR;LGDS(0.224)S(0.776)LSR ; 148.94 0.0072596 139544000 10097.7 9393.7 10222.7 7427 11394.9 10105.8 7398.2 9668.6 9191.7 9949.2 TRUE FALSE FALSE 9974.625348 9525.944755 10400.62181 8285.744685 10813.37573 9460.071995 8026.602923 9948.345686 8369.571331 9690.71835 1.029296796 0.982996762 1.07325602 0.855018626 1.115848727 0.976199251 0.828277392 1.026584958 0.863668825 1 13.2423879 -7.992190822 24.98951847 1.011333745 0.921132944 0.02516016 0.090550254 205.2643559 656836.7574 0.009362706 0.02801927 1.02E-08 7.992190822 -0.0902008 LGDVS(ph)PTQIDVSQFGSFK ddPTM_HeLa_Romidepsin_16h_R1 1 LGDVSPTQIDVSQFGSFK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 LGDVS(0.86)PT(0.139)QIDVS(0.001)QFGSFK 125.96 0.0015785 111770000 2754.7 2496.6 3386.8 1661.3 2592.8 3079.1 3042.4 2671.1 2999.8 2835 TRUE FALSE FALSE 2721.124657 2531.7472 3445.745833 1853.387323 2460.479741 2882.355447 3300.82138 2748.384064 2731.490375 2761.346291 0.985434049 0.916852482 1.247849951 0.671189748 0.891043528 1.043822521 1.195366691 0.995305831 0.989187913 1 11.43115611 -8.00292448 24.90866998 0.975729225 1.101400864 0.131279962 0.140848232 175.1399188 1491779.146 0.018389019 0.053733274 9.93E-09 8.00292448 0.125671639 LGDVS(ph)PTQIDVSQFGSFKEDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LGDVSPTQIDVSQFGSFKEDTK 22 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 LGDVS(0.441)PT(0.279)QIDVS(0.279)QFGSFKEDTK 55.986 0.0073047 85293000 710.6 666.89 521.4 715.96 872.13 671.42 616.17 669.65 671.51 686.02 TRUE FALSE FALSE 701.9389339 676.2784949 530.4747483 798.7426639 827.6219517 628.5184289 668.5074644 689.0252662 611.4484638 668.1971015 1.050496825 1.012094326 0.793889628 1.195369842 1.238589557 0.940618311 1.000464478 1.03117069 0.915072009 1 9.384129914 LGDVSPT(ph)QIDVSQFGSFK ddPTM_HeLa_Romidepsin_16h_R1 1 LGDVSPTQIDVSQFGSFK 18 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 LGDVS(0.113)PT(0.512)QIDVS(0.375)QFGSFK 137.73 0.0017205 100420000 5766.1 4535.5 5799.5 3379.6 5709.8 5640.5 5412.1 5601.9 4870 5279.1 TRUE FALSE FALSE 5695.820555 4599.350888 5900.437865 3770.365253 5418.4076 5280.090254 5871.803639 5763.982138 4434.415003 5141.948221 1.107716436 0.894476313 1.147510168 0.733256169 1.053765493 1.026865699 1.141941417 1.120972419 0.862399778 1 12.32809937 -7.766271563 22.65385968 1.023848648 1.13145696 0.121504842 0.122990096 51.42538966 241111.6519 0.015234346 0.048107063 1.71E-08 7.766271563 0.107608311 LGDVSPT(ph)QIDVSQFGSFKEDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LGDVSPTQIDVSQFGSFKEDTK 22 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 LGDVS(0.189)PT(0.809)QIDVS(0.002)QFGSFKEDTK 54.225 0.015175 70052000 643.04 607.04 578.68 936.75 688.74 838.69 656.76 839.24 784.54 859.17 TRUE FALSE FALSE 635.2023811 615.5859251 588.7516827 1045.061443 653.5910278 785.1004157 712.545178 863.5220853 714.3687775 836.8486395 0.759040944 0.735600079 0.703534253 1.248805809 0.781014627 0.938162983 0.851462432 1.03187368 0.853641559 1 9.708822897 LGDVYVNDAFGT(ph)AHR ddPTM_HeLa_Romidepsin_16h_R1 2 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 1 0 LGDVYVNDAFGT(1)AHR;LGDVYVNDAFGT(1)AHR ; 116.69 0.0028443 6278100 3770.9 3500.6 3427.9 2964.3 4136.5 3919.3 3732.6 3585.3 4087.6 3665.6 TRUE FALSE FALSE 3724.93882 3549.881539 3487.561162 3307.046313 3925.39897 3668.869379 4049.646951 3689.034999 3721.994818 3570.367184 1.043292924 0.994262314 0.976807421 0.926248238 1.099438452 1.027588814 1.134238229 1.033236866 1.042468359 1 11.80185674 -8.712229075 24.99990481 1.009214185 1.074666761 0.414154682 0.043132857 97.93226673 49751.19038 0.006241364 0.012482709 1.94E-09 8.712229075 0.065452576 LGDVYVNDAFGTAHR ddPTM_HeLa_Romidepsin_16h_R1 3 LGDVYVNDAFGTAHR 15 0 P00558;P00558-2;P07205 P00558 PGK1;PGK2 Phosphoglycerate kinase 1;Phosphoglycerate kinase 2 0 0 ;; ;; 209.56 8.93E-26 221738900 10189.91 9354.73 9316.36 7393.62 10156.26 10453.39 9624.66 9859.48 10558.91 9089 FALSE FALSE TRUE 10065.71146 9486.426134 9478.507338 8248.505132 9637.948154 9785.452116 10442.17838 10144.7485 9614.494644 8852.86647 1.137000258 1.071565483 1.070670993 0.931732695 1.088681071 1.105342789 1.179525119 1.145928105 1.086031815 1 13.11192895 -16.52287804 0.012754028 4.31E-05 1.975099438 0.145821713 0.063205276 8976.557577 9.25179376 857.3305651 597.5161212 3.00E-17 16.52287804 1.975056291 LGEAS(ph)DSELADADK ddPTM_HeLa_Romidepsin_16h_R1 4 LGEASDSELADADK 14 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 LGEAS(0.942)DS(0.058)ELADADK;LGEAS(0.643)DS(0.357)ELADADK;LGEAS(0.937)DS(0.063)ELADADK;LGEAS(0.536)DS(0.464)ELADADK ;;; 216.27 3.30E-24 145448000 13859.7 12853.7 14604 8910.73 12575.4 12209.4 11278.99 11059.6 13699.4 14167.7 TRUE FALSE FALSE 13690.77265 13034.65473 14858.17649 9941.030529 11933.63041 11429.25874 12237.02713 11379.59208 12474.09135 13799.62111 0.992112213 0.944566131 1.076709018 0.72038431 0.86477957 0.828229895 0.886765443 0.824630762 0.903944482 1 13.75234104 -9.267923414 24.99856994 0.996963896 0.830785824 0.642742557 0.058576788 186.5955225 719400.438 0.007090373 0.010991505 5.40E-10 9.267923414 -0.166178071 LGEASDSELADADKAS(ph)VASEVSTTSSTSKPPTGR ddPTM_HeLa_Romidepsin_16h_R1 1 LGEASDSELADADKASVASEVSTTSSTSKPPTGR 34 2 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 LGEAS(0.003)DS(0.19)ELADADKAS(0.539)VAS(0.264)EVS(0.004)TTSSTSKPPTGR 72.859 8.50E-06 24636000 944.8 1237 1444.3 1420.9 1130.6 1197.5 1007.4 1194.3 1260.2 1175.8 TRUE FALSE FALSE 933.2844142 1254.414518 1469.437436 1585.191144 1072.901263 1120.983615 1092.968531 1228.855186 1147.484556 1145.252546 0.814915817 1.095316943 1.283068473 1.384141121 0.93682504 0.9788091 0.954347174 1.072999305 1.001948923 1 10.16145006 -10.23494182 20.32336488 0.912599197 1.102066129 0.206971789 0.142372999 79.12054885 60683.98542 0.026426004 0.032349444 5.82E-11 10.23494182 0.189466932 LGELTMQLHPVADS(ph)SPAGAK ddPTM_HeLa_Romidepsin_16h_R1 1 LGELTMQLHPVADSSPAGAK 20 0 F8W038;H0YIS7;Q8IXM2;Q8IXM2-3 F8W038 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 0 LGELT(0.003)MQLHPVADS(0.774)S(0.223)PAGAK 63.462 0.0053783 18213000 2738.1 2534.5 2789.2 2230.8 2998 2749.9 2773.5 2824.5 3057 2855.6 TRUE FALSE FALSE 2704.726984 2570.180758 2837.744856 2488.735592 2845.000873 2574.190265 3009.081021 2906.222451 2783.574264 2781.4111 0.97242978 0.924056411 1.02025366 0.894774452 1.022862414 0.925497948 1.081854107 1.044873392 1.000777722 1 11.44160128 -7.747261389 24.99956957 0.977286028 1.063363786 0.42840199 0.042452501 162.0809096 285786.7683 0.005256948 0.019481243 1.79E-08 7.747261389 0.086077759 LGELTMQLHPVADS(ph)SPAGAQIK ddPTM_HeLa_Romidepsin_16h_R1 2 LGELTMQLHPVADSSPAGAQIK 22 0 Q8IXM2-2 Q8IXM2-2 BAP18 Chromatin complexes subunit BAP18 1 0 LGELTMQLHPVADS(0.5)S(0.5)PAGAQIK;LGELTMQLHPVADS(0.565)S(0.435)PAGAQIK ; 75.896 0.00077374 54636000 2321.1 2141.5 2178.2 1492.16 2307 2257.28 1772.8 2181.5 2402 2225.3 TRUE FALSE FALSE 2292.80954 2171.648093 2216.110657 1664.69056 2189.265181 2113.047093 1923.381588 2244.618261 2187.159104 2167.486385 1.057819581 1.001920062 1.022433484 0.768028151 1.010047951 0.974883675 0.887378855 1.035585864 1.009076283 1 11.08180722 -9.46462706 24.99988691 1.025497263 0.934527271 0.253626945 0.07071786 253.7581913 108905.3853 0.010279013 0.015701428 3.43E-10 9.46462706 -0.090969991 LGEVTGSPS(ph)PPPR ddPTM_HeLa_Romidepsin_16h_R1 2 LGEVTGSPSPPPR 13 0 O94875-12;H7BZX1;O94875-4;O94875-10;O94875-5;O94875-3;H7BXR3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 LGEVTGS(0.019)PS(0.981)PPPR;LGEVTGS(0.001)PS(0.998)PPPR ; 136.3 0.0015429 19884500 4540 5068.5 4572.6 3898.8 4012.3 3707.2 2765.4 3023.4 5203.5 5169.1 TRUE FALSE FALSE 4484.664734 5139.854476 4652.184185 4349.5976 3807.537359 3470.321884 3000.293007 3110.877309 4738.085928 5034.806037 0.890732374 1.020864446 0.924004649 0.863905693 0.756243107 0.689266252 0.595910346 0.617874311 0.941066228 1 12.29772048 -8.563181612 1.103541361 0.954166588 0.599200803 0.939028435 0.036322305 0.112159271 0.257141946 0.007591978 0.026692553 2.73E-09 8.563181612 -0.354965785 LGEYEDVSR ddPTM_HeLa_Romidepsin_16h_R1 1 LGEYEDVSR 9 0 K7EL99;K7EP07;K7EK42;A0A494C0X0;Q99426-2;Q99426 K7EL99 TBCB Tubulin-folding cofactor B 0 0 167.23 0.021978 6777500 2542.8 2304.4 2278 1445.6 2475.9 2603.8 2381.9 2317.7 2748.5 2242.7 FALSE FALSE TRUE 2511.807376 2336.841404 2317.647634 1612.747074 2349.545584 2437.425583 2584.218527 2384.758993 2502.667276 2184.434331 1.149866279 1.069769583 1.060982975 0.738290481 1.075585359 1.115815454 1.183014976 1.091705509 1.145682084 1 11.09304402 -8.274793773 4.497946787 1.045857219 1.136959481 0.131852988 0.111035069 0.361743837 19.29483207 0.016862459 0.041327056 5.31E-09 8.274793773 0.091102262 IGEGT(ph)YGVVYK ddPTM_HeLa_Romidepsin_16h_R1 2 IGEGTYGVVYK 11 0 A0A087WZZ9;A0A024QZP7;P06493-2;P06493;E5RIU6;G3V317;K7ELV5;E7ESI2;P24941-2;G3V5T9;P24941;Q00526 A0A087WZZ9;G3V5T9 CDK1;CDC2;CDK2;CDK3 Cyclin-dependent kinase 1;Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 0 IGEGT(0.692)Y(0.308)GVVYK;IGEGT(0.534)Y(0.466)GVVYK ; 160.86 0.0026067 2077657000 5899.4 6106.1 5820.9 4194.8 2820.7 2382.88 1531.17 1770.47 5986.5 5737.4 TRUE FALSE FALSE 5827.495844 6192.061836 5922.210323 4679.822513 2676.749154 2230.621658 1661.227542 1821.695756 5451.052447 5588.341521 1.042795223 1.108032108 1.059743808 0.837426005 0.478988112 0.399156288 0.297266646 0.325981465 0.975432948 1 12.44820448 -8.783748029 1.968647082 1.032133753 0.334796849 0.982937102 0.041555534 0.029458312 0.232434168 0.006778667 0.014908202 1.65E-09 8.783748029 -0.697336904 down SNVSSPATPTASS(ph)SSSTTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSSPATPT(0.007)AS(0.073)S(0.228)S(0.228)S(0.228)S(0.114)T(0.114)T(0.006)PT(0.001)R 137.85 0.00014685 5253700 2868.7 2533.9 2909.2 2248.3 1375.3 1056.9 1012.3 1014.3 2998.8 2987.4 TRUE FALSE FALSE 2833.735181 2569.572311 2959.833406 2508.259025 1305.113309 989.367501 1098.284737 1043.64717 2730.579817 2909.786917 0.973863469 0.883079203 1.017199365 0.862007802 0.448525389 0.340013729 0.377445073 0.358667902 0.938412294 1 11.50669779 -8.78073826 2.873025435 0.979486541 0.361419834 0.982159229 0.037581009 0.021181439 0.358413248 0.005432492 0.011050366 1.66E-09 8.78073826 -0.618066707 down LGGAAQGPLPEASKGDLPSDS(ph)GFSDPESEAK ddPTM_HeLa_Romidepsin_16h_R1 2 LGGAAQGPLPEASKGDLPSDSGFSDPESEAK 31 1 Q8TEK3-1;Q8TEK3 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 LGGAAQGPLPEAS(0.067)KGDLPS(0.067)DS(0.369)GFS(0.369)DPES(0.129)EAK;LGGAAQGPLPEASKGDLPS(0.004)DS(0.585)GFS(0.395)DPES(0.016)EAK ; 87.368 6.00E-09 7817200 3084.8 3232.9 3292.9 3438.6 2468.3 2146 1853.73 2035.22 3653.8 3326.6 TRUE FALSE FALSE 3047.201271 3278.412851 3350.211543 3836.187111 2342.333441 2008.877526 2011.18578 2094.10588 3326.994977 3240.174452 0.940443583 1.011801339 1.033960237 1.18394462 0.722903496 0.619990545 0.620702931 0.646294177 1.026795015 1 11.66185578 -8.598425469 6.456146564 0.992620208 0.634909604 0.887570423 0.065978728 0.054868101 3.720667299 0.010234607 0.020632391 2.52E-09 8.598425469 -0.357710604 LGGAVPFAPPEVS(ph)PEQAK ddPTM_HeLa_Romidepsin_16h_R1 2 LGGAVPFAPPEVSPEQAK 18 0 A0A096LNZ0;A0A096LP25;Q6ZSR9 A0A096LNZ0 AAK1 Uncharacterized protein FLJ45252 1 0 LGGAVPFAPPEVS(1)PEQAK;LGGAVPFAPPEVS(1)PEQAK ; 214.28 8.18E-29 221340000 18086.7 16992.2 15747.5 15344.2 15369.8 15307.2 13486.5 14460.9 17136.8 15418 TRUE FALSE FALSE 17866.25234 17231.41664 16021.57863 17118.3686 14585.42175 14329.11932 14632.04297 14879.30333 15604.04169 15017.43814 1.189700412 1.147427176 1.066864966 1.139899392 0.971232351 0.954165364 0.974336824 0.990801706 1.039061493 1 13.8743511 -8.749156394 24.41676381 1.097739044 0.971436438 0.576488533 0.052282166 134.1288848 266626.1046 0.010810792 0.021490736 1.78E-09 8.749156394 -0.126302605 LGGK(ac)LTGTANK ddPTM_HeLa_Romidepsin_16h_R1 1 LGGKLTGTANK 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 1 LGGK(1)LTGTANK 120.86 0.019488 934500 622.76 568.33 684.39 409.22 515.99 591.79 602 480.76 833.41 467.31 FALSE TRUE FALSE 615.1695616 576.3309647 696.3015209 456.5359418 489.6571049 553.9765289 653.133865 494.6700321 758.8677223 455.1692188 1.351518372 1.266190552 1.529764079 1.00300267 1.075769372 1.21707819 1.434925381 1.086782699 1.667221092 1 8.830259187 -12.43870707 1.175488924 1.000305963 1.256965608 0 0.259066263 0.518317112 1.28334495 0.107280819 0.026942971 3.64E-13 12.43870707 0.256659645 LGGKPSSPSLS(ph)PLMGFGSNK ddPTM_HeLa_Romidepsin_16h_R1 1 LGGKPSSPSLSPLMGFGSNK 20 1 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8;A0A087WYL6;Q8TEW8-6;Q8TEW8-3 R4GN62 PARD3B Partitioning defective 3 homolog B 1 0 LGGKPS(0.003)S(0.012)PS(0.187)LS(0.797)PLMGFGSNK 70.174 0.0099903 10726000 1808.5 1501.5 1605.9 1860.8 2004.2 1783.9 1375.3 1329.1 2146.4 1901.2 TRUE FALSE FALSE 1786.457306 1522.638156 1633.850016 2075.954451 1901.918195 1669.914547 1492.117948 1367.555412 1954.420608 1851.80655 0.964710545 0.822244719 0.882300592 1.121042828 1.02706095 0.901775916 0.805763403 0.738497988 1.055412947 1 10.85471768 -7.791629479 2.429858166 0.975681451 0.751986463 0.521009919 0.080266702 0.181811815 2.079123821 0.011404495 0.053726284 1.62E-08 7.791629479 -0.223694988 LGGLRPES(ph)PESLTSVSR ddPTM_HeLa_Romidepsin_16h_R1 2 LGGLRPESPESLTSVSR 17 1 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 LGGLRPES(0.782)PES(0.011)LT(0.172)S(0.035)VSR;LGGLRPES(0.559)PES(0.32)LT(0.08)S(0.041)VSR ; 119 0.014786 2750600000 5388.4 5442.2 5452.9 4349.1 4747.2 4828.9 4262 4630.4 6021.4 5699.1 TRUE FALSE FALSE 5322.724108 5518.815434 5547.805437 4851.963405 4504.93267 4520.348875 4624.014174 4764.373318 5482.830903 5551.03656 0.958870303 0.994195476 0.999417924 0.874064394 0.811548009 0.814325185 0.833000129 0.858285343 0.987712987 1 12.43854148 -9.121673623 3.620518463 0.982572861 0.829388415 0.950824836 0.017213447 0.045559986 1.08399011 0.00322164 0.005551402 7.56E-10 9.121673623 -0.153184446 LGGSLADSYLDEGFLLDKK ddPTM_HeLa_Romidepsin_16h_R1 1 LGGSLADSYLDEGFLLDKK 19 1 F8VQ14;F5GWF6;P78371;P78371-2 F8VQ14 CCT2 T-complex protein 1 subunit beta 0 0 151.39 1.45E-05 8384200 1335.2 1184.6 970.18 1158.5 1308.8 1176.1 1097.2 1300.3 1550.2 1093.7 FALSE FALSE TRUE 1318.926069 1201.27683 987.0655759 1292.451221 1242.007052 1100.951006 1190.396141 1337.922129 1411.546229 1065.285516 1.238096312 1.127657151 0.926573731 1.213243962 1.165891241 1.033479747 1.117443279 1.255928207 1.32504029 1 10.05702444 -12.62783996 1.458294935 1.000305894 1.143609453 0 0.137199978 0.495606507 1.899878211 0.068283155 0.015729712 2.36E-13 12.62783996 0.143303559 LGHDPYRLT(ph)PDPYR ddPTM_HeLa_Romidepsin_16h_R1 1 LGHDPYRLTPDPYR 14 1 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9 P18583-6 SON Protein SON 1 0 LGHDPY(0.002)RLT(0.951)PDPY(0.048)R 67.326 0.016504 5924900 1438.2 1659.6 1355.7 1215.5 1102 1426.9 1135.5 1106 1496.5 1411.2 TRUE FALSE FALSE 1420.670665 1682.963892 1379.29539 1356.041829 1045.760828 1335.725695 1231.949342 1138.000365 1362.649292 1374.536821 1.033563193 1.224386184 1.003461944 0.986544565 0.760809614 0.971764215 0.896265071 0.827915519 0.991351611 1 10.42472984 -8.957499227 8.923069496 1.032688073 0.873776532 0.536106212 0.080843989 0.20659399 40.25500173 0.011888241 0.021554706 1.10E-09 8.957499227 -0.158911541 LGHPEALSAGTGS(ph)PQPPSFTYAQQR ddPTM_HeLa_Romidepsin_16h_R1 3 LGHPEALSAGTGSPQPPSFTYAQQR 25 0 Q15942;Q15942-2;H0Y2Y8;H7C3D3 Q15942 ZYX Zyxin 1 0 LGHPEALS(0.028)AGT(0.401)GS(0.568)PQPPS(0.002)FT(0.001)YAQQR;LGHPEALS(0.019)AGT(0.115)GS(0.866)PQPPSFTYAQQR;LGHPEALS(0.026)AGT(0.236)GS(0.738)PQPPSFTYAQQR ;; 90.127 2.11E-05 318276000 2591.63 2251.82 2351.41 2052.88 3157.4 3492.28 2664.42 2885.75 3368.5 3012.42 TRUE FALSE FALSE 2560.042217 2283.521181 2392.335305 2290.243645 2996.266096 3269.134579 2890.735768 2969.244623 3067.212923 2934.156894 0.872496703 0.778254628 0.81533994 0.780545733 1.021167649 1.114164885 0.985201498 1.011958368 1.045347278 1 11.5187303 -8.557121406 24.6527815 0.904453344 1.03787573 0.398396198 0.088593578 144.9053319 104323.1202 0.014040902 0.028081925 2.77E-09 8.557121406 0.133422386 LGHVVMGNNAVS(ph)PYQQVIEK ddPTM_HeLa_Romidepsin_16h_R1 1 LGHVVMGNNAVSPYQQVIEK 20 0 P60228;H0YAW4;E5RGA2 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 1 0 LGHVVMGNNAVS(0.94)PY(0.06)QQVIEK 73.831 0.0022157 36059000 3718.8 3793.8 3831.3 3418.4 3782 4659.6 3649.9 3595.2 4001.1 3779.8 TRUE FALSE FALSE 3673.473835 3847.209216 3897.982169 3813.651492 3588.990427 4361.866598 3959.922415 3699.22144 3643.231595 3681.600251 0.997792695 1.044982875 1.058773876 1.035867892 0.974845226 1.184774636 1.075598149 1.004786285 0.989578267 1 11.84611727 -9.654722565 0.673638197 0.996894772 1.070966631 0.201009343 0.052060384 0.743200077 0.685654227 0.012172371 0.022584751 2.21E-10 9.654722565 0.07407186 LGIAVIHGEAQDAESDLVDGRHS(ph)PPMVR ddPTM_HeLa_Romidepsin_16h_R1 2 LGIAVIHGEAQDAESDLVDGRHSPPMVR 28 1 I3L0S1;E7EPA1;O60256-4;O60256-3;O60256-2;O60256;C9K0K7 I3L0S1 PRPSAP2 Phosphoribosyl pyrophosphate synthase-associated protein 2 1 0 LGIAVIHGEAQDAES(0.293)DLVDGRHS(0.707)PPMVR;LGIAVIHGEAQDAES(0.24)DLVDGRHS(0.76)PPMVR ; 64.589 0.00017433 17019700 5984.2 6238.3 5821.3 6091.9 7246.5 6895.6 5982.7 6565.1 6401.2 6284.9 TRUE FALSE FALSE 5911.262269 6326.122951 5922.617285 6796.274141 6876.684065 6454.993415 6490.870389 6755.05081 5828.66064 6121.617392 0.965637329 1.033407112 0.967492234 1.110208905 1.12334431 1.054458814 1.060319516 1.103474846 0.952143897 1 12.57969716 -9.262261606 24.9997537 0.986763114 1.088530102 0.775093191 0.028686357 26.66263752 810681.6141 0.004260195 0.006755269 5.47E-10 9.262261606 0.101766988 LGIHEDS(ph)TNR ddPTM_HeLa_Romidepsin_16h_R1 1 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 0 LGIHEDS(0.984)T(0.016)NR 147.58 0.00391 11281000 1378.1 1585.1 1420.2 1265.6 1696.6 1443.8 1246.6 1554.3 1508.5 1391.2 TRUE FALSE FALSE 1361.303187 1607.415079 1444.917985 1411.934627 1610.016171 1351.54584 1352.486173 1599.271218 1373.575982 1355.056423 1.004609966 1.186234796 1.066315734 1.041974786 1.18815434 0.997409271 0.998103215 1.180224816 1.013667002 1 10.40413721 -10.46253522 24.99975306 1.002033666 1.087787654 0.252278774 0.068717409 236.4067565 97941.45391 0.011102162 0.012693774 3.45E-11 10.46253522 0.085753988 LGIHEDSQNR ddPTM_HeLa_Romidepsin_16h_R1 4 LGIHEDSQNR 10 0 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 189.18 3.60E-08 70971000 22602 20130.1 22813.1 16402.5 35087 38066 33817.9 28052.4 28807.7 24155.4 FALSE FALSE TRUE 22326.51813 20413.49208 23210.15244 18299.03423 33296.37946 35633.70545 36690.39158 28864.05193 26231.06716 23527.83923 0.948940441 0.8676314 0.986497409 0.777760935 1.415190708 1.514533702 1.559445865 1.226804198 1.114894866 1 14.52208121 -8.741065036 19.15738265 0.954807158 1.444427079 0.804406549 0.115763935 4.48495252 4216.471761 0.014386894 0.028694034 1.82E-09 8.741065036 0.48961992 LGIHEDST(ph)NR ddPTM_HeLa_Romidepsin_16h_R1 1 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 1 0 LGIHEDS(0.4)T(0.6)NR 103.14 0.016889 8669300 5619.7 5021.2 5150.7 3962.1 5476.2 5456.8 4980.3 5191 6368.4 5273 TRUE FALSE FALSE 5551.204935 5091.888585 5240.345773 4420.216644 5196.729079 5108.128091 5403.326558 5341.193395 5798.794354 5136.0067 1.080840672 0.991410036 1.020315214 0.860632959 1.011822878 0.994571929 1.052048191 1.039950628 1.129047272 1 12.32643137 -10.20840978 24.69444477 1.038174789 0.994294083 0.191736426 0.059844472 481.8604304 224389.2855 0.009577732 0.011730272 6.19E-11 10.20840978 -0.043880706 LGIHEDSTNR ddPTM_HeLa_Romidepsin_16h_R1 5 LGIHEDSTNR 10 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 ;;;; ;;;; 223.87 7.21E-27 135318580 37640.34 32505.74 34467.67 25470.09 47309.39 45753.29 38938.15 36502.89 44088.9 37705.56 FALSE FALSE TRUE 37181.56506 32963.35666 35067.56534 28415.06165 44895.01529 42829.80243 42245.55549 37559.04353 40145.47836 36725.96412 1.012405418 0.897549117 0.954843969 0.773704989 1.222432586 1.166199539 1.150291259 1.022683664 1.093108903 1 15.16451274 -8.72692424 24.99985687 0.978207836 1.142950847 0.481661956 0.092247431 128.2803926 92914.97174 0.01259372 0.025186542 1.88E-09 8.72692424 0.164743011 LGIHEDSTNRR ddPTM_HeLa_Romidepsin_16h_R1 1 LGIHEDSTNRR 11 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 63.184 0.019948 2891300 2886.4 2262 2075.6 1960.9 3903 3504.5 2748.8 2583.9 3410.1 2984.9 FALSE FALSE TRUE 2851.219447 2293.844495 2111.724947 2187.628484 3703.815346 3280.57376 2982.283003 2658.66107 3105.092115 2907.351868 0.980692939 0.788980694 0.726339653 0.752447101 1.273948086 1.128371766 1.025772985 0.914461404 1.068013868 1 11.50548997 -7.198325764 19.26489438 0.97350233 0.914452594 0.010630474 0.164521645 20959.46366 6393480.137 0.023291203 34.34296144 6.33E-08 7.198325764 -0.059049736 LGIYDADGDGDFDVDDAK ddPTM_HeLa_Romidepsin_16h_R1 2 LGIYDADGDGDFDVDDAK 18 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797;E5RHK2;G3XAN5;E5RG29;Q12797-4;Q12797-3;Q12797-9;Q12797-5;Q12797-8;Q12797-10 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 0 0 ; ; 200.16 1.09E-19 96863000 7559.3 9438.3 8461.4 6363 6400.9 7762.9 4727.2 7820 7892.4 9040.6 FALSE FALSE TRUE 7467.164344 9571.172635 8608.667118 7098.719999 6074.238188 7266.875744 5128.72825 8046.259362 7186.483977 8805.723909 0.847989833 1.086926269 0.977621739 0.806148373 0.689805659 0.825244559 0.582431189 0.913753309 0.816115069 1 13.1042259 -9.109257046 4.220955016 0.943860074 0.74584685 0.424027244 0.107252827 0.15998063 4.845533429 0.015418051 0.026304321 7.78E-10 9.109257046 -0.198013223 LGK(ac)ELQQK ddPTM_HeLa_Romidepsin_16h_R1 1 LGKELQQK 8 1 O75116;Q14DU5;E9PF63 O75116 ROCK2 Rho-associated protein kinase 2 0 1 LGK(1)ELQQK 106.36 0.018529 1799100 2042.5 1651.8 2321.6 2357.8 5194.4 6516.3 5039.1 2660.4 1902.3 1379.6 FALSE TRUE FALSE 2017.605224 1675.054084 2362.006474 2630.41993 4929.310385 6099.92946 5467.121028 2737.374477 1732.153524 1343.757793 1.501464948 1.246544647 1.757762066 1.957510456 3.668302733 4.539456062 4.068531588 2.037104075 1.289037007 1 10.39205741 -8.900940209 2.533347749 1.281465803 3.703713369 0.731797758 0.633313205 0.101890064 1.326294948 0.096160391 0.189203542 1.26E-09 8.900940209 2.422247566 LGK(ac)TIVITK ddPTM_HeLa_Romidepsin_16h_R1 2 LGKTIVITK 9 1 R4GNG8;Q96NC0 R4GNG8 ZMAT2 Zinc finger matrin-type protein 2 0 1 ; LGK(1)TIVITK;LGK(1)TIVITK 100.88 0.00437 0 650.81 662.7 582.62 601.81 594.47 950.99 714.52 595.31 1098.53 768.18 FALSE TRUE FALSE 642.8776774 672.029508 592.7602567 671.3941038 564.1319776 890.2248082 775.211311 612.5343556 1000.274725 748.2225729 0.859206472 0.898167915 0.792224504 0.897318697 0.753962789 1.189786088 1.036070468 0.818652601 1.336867881 1 9.54732368 -6.991255183 10.06639305 0.928313296 0.684363995 0.009906403 0.175385038 8333.01632 141769.1561 0.016850352 25555.40937 1.02E-07 6.991255183 -0.243949301 LGLAVIHGEAQCT(ph)ELDMDDGRHSPPMVK ddPTM_HeLa_Romidepsin_16h_R1 2 LGLAVIHGEAQCTELDMDDGRHSPPMVK 28 1 C9J168;B4DP31;Q14558;Q14558-2;C9JUN4 C9J168 PRPSAP1 Phosphoribosyl pyrophosphate synthase-associated protein 1 1 0 LGLAVIHGEAQCT(0.776)ELDMDDGRHS(0.224)PPMVK;LGLAVIHGEAQCT(0.913)ELDMDDGRHS(0.087)PPMVK ; 53.998 0.0021339 68037000 2488.47 2484.21 2463.42 571.65 2226.21 2651.72 2204.8 2496.74 2619.31 2421.13 TRUE FALSE FALSE 2458.13957 2519.182774 2506.294792 637.7468627 2112.598197 2482.28365 2392.075657 2568.979233 2385.032353 2358.228694 1.042366916 1.068252108 1.062786997 0.270434697 0.895841104 1.052605142 1.014352706 1.089368151 1.011366014 1 11.20348792 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR ddPTM_HeLa_Romidepsin_16h_R1 4 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSR 34 0 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 156.71 2.99E-18 509023000 12646.5 12425.3 12810.3 7147.52 13600.5 16979.6 14062.2 15257.7 14025.1 13551.3 FALSE FALSE TRUE 12492.35959 12600.2237 13033.2579 7973.949892 12906.41573 15894.65836 15256.64292 15699.15748 12770.65993 13199.23527 0.94644571 0.954617706 0.987425228 0.604122112 0.977815416 1.204210549 1.155873246 1.189399018 0.96753029 1 13.68816673 -8.302892584 6.018271838 0.944767684 1.180626871 0.53447213 0.111112931 0.132183788 13.20422705 0.016417378 0.037717361 4.98E-09 8.302892584 0.235859187 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD ddPTM_HeLa_Romidepsin_16h_R1 4 LGLGIDEDDPTADDTSAAVTEEMPPLEGDDDTSRMEEVD 39 1 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 72.959 3.71E-06 83138000 10618.2 10026.5 9365.33 15146 12485.4 12684.8 13033.1 13609.2 12152.8 10553.4 FALSE FALSE TRUE 10488.78129 10167.65333 9528.32964 16897.25178 11848.22345 11874.28222 14140.13119 14002.96073 11065.82313 10279.22115 1.020386773 0.989146277 0.926950545 1.643826078 1.152638248 1.155173339 1.375603364 1.362258923 1.0765235 1 13.32744334 -9.298182975 24.9902678 1.002372679 1.319550981 0.612577761 0.132925576 283.5812882 192870.2033 0.019056882 0.029110369 5.03E-10 9.298182975 0.317178301 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR ddPTM_HeLa_Romidepsin_16h_R1 6 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASR 34 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 ;;;;; ;;;;; 173.03 5.77E-24 370487000 10862.16 9935.736 10396.74 8397.66 11004.13 10532.488 9665.37 10253.89 11503.68 11153.87 FALSE FALSE TRUE 10729.76782 10075.61155 10577.6909 9368.636961 10442.54818 9859.496009 10486.34629 10550.57013 10474.76205 10864.09085 0.987636054 0.927423352 0.973637927 0.862348915 0.961198533 0.907530703 0.965229989 0.971141559 0.964163702 1 13.40727983 -10.33229799 4.71307642 0.994604776 0.937503453 0.261171938 0.033769492 0.154359085 6.533455888 0.005278603 0.006039561 4.65E-11 10.33229799 -0.057101323 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD ddPTM_HeLa_Romidepsin_16h_R1 2 LGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD 39 1 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 ; ; 73.487 2.68E-06 13643800 4583.7 4257.7 3713.5 10936.8 5297.1 4795.2 4723.3 4946.2 5401.9 4007.6 FALSE FALSE TRUE 4527.832101 4317.640012 3778.13191 12201.36428 5026.769221 4488.802196 5124.496984 5089.310493 4918.740535 3903.481974 1.159946973 1.106099642 0.967887628 3.125764217 1.28776545 1.149948232 1.312801498 1.303787369 1.260090495 1 11.93054589 LGLGLDDESNNQQAAAT(ph)QSPGDSRR ddPTM_HeLa_Romidepsin_16h_R1 2 LGLGLDDESNNQQAAATQSPGDSRR 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 0 LGLGLDDESNNQQAAAT(0.499)QS(0.499)PGDS(0.001)RR;LGLGLDDESNNQQAAAT(0.498)QS(0.498)PGDS(0.004)RR ; 75.054 0.00017962 12291700 1809.46 1954.72 1839.69 1591.02 1641.75 1731.17 1168.85 1905.09 2181.71 2123.71 TRUE FALSE FALSE 1787.405606 1982.238599 1871.709033 1774.981218 1557.965371 1620.553824 1268.13209 1960.210773 1986.572393 2068.535708 0.864092217 0.958281064 0.90484734 0.858085849 0.753173061 0.783430432 0.613057867 0.947632069 0.960376166 1 11.01439415 -9.032739276 1.958536521 0.935384221 0.761673637 0.460101015 0.08284318 0.223660756 1.703133624 0.013177797 0.025581908 9.27E-10 9.032739276 -0.173710584 LGLK(ac)FDGK(ac)NEDLVDK(ac)IK ddPTM_HeLa_Romidepsin_16h_R1 1 LGLKFDGKNEDLVDKIK 17 3 Q96BN8 Q96BN8 OTULIN Ubiquitin thioesterase otulin 0 3 LGLK(1)FDGK(1)NEDLVDK(1)IK 75.376 0.0032826 0 491.11 433.2 524.56 1275.2 860.65 939.13 1036.9 880.75 374.5 410.08 FALSE TRUE FALSE 485.1241624 439.298601 533.6897468 1422.644624 816.727819 879.1226239 1124.97426 906.2331117 341.003782 399.4260625 1.2145531 1.099824579 1.336141521 3.561722075 2.044753449 2.2009646 2.816476855 2.268838208 0.853734431 1 8.641784661 -9.427930515 7.62911587 1.109232715 2.539343522 0.769868176 0.405504119 0.096752812 6.92152282 0.056929665 0.087008242 3.73E-10 9.427930515 1.430110807 LGNDFHTNK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 LGNDFHTNKR 10 1 H0YN88;A0A075B716;H3BNC9;P08708;H0YN73;A0A0J9YYC4 H0YN88 RPS17 40S ribosomal protein S17 0 1 ; LGNDFHTNK(1)R;LGNDFHTNK(1)R 99.752 0.0047817 5864600 4169.3 4393.7 5383.1 2744.7 8780.9 9043 10196.4 3213.7 10554.5 5958.6 FALSE TRUE FALSE 4118.482968 4455.554624 5476.790597 3062.055128 8332.777907 8465.181485 11062.48196 3306.683339 9610.479086 5803.794713 0.709618994 0.767696799 0.943656843 0.527595354 1.435746493 1.458559771 1.906077404 0.569745055 1.655895765 1 12.50278078 -8.743302316 24.99609511 0.837527968 1.391073299 0.159085794 0.420837426 181.9344559 250736.7827 0.044942634 0.089743577 1.81E-09 8.743302316 0.553545331 LGNSGAS(ph)PSSAGK ddPTM_HeLa_Romidepsin_16h_R1 2 LGNSGASPSSAGK 13 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 0 LGNS(0.001)GAS(0.936)PS(0.063)SAGK;LGNS(0.001)GAS(0.969)PS(0.029)S(0.001)AGK ; 162.64 0.00031398 20202400 4982 4754.6 4095.7 3221.2 5327.3 6170.1 5520.1 5335.7 5056.6 5691.9 TRUE FALSE FALSE 4921.277468 4821.535384 4166.98394 3593.6503 5055.428002 5775.850523 5988.977156 5490.080061 4604.325032 5544.023617 0.887672529 0.86968161 0.751617278 0.64820256 0.911869853 1.041815642 1.080258233 0.990269963 0.83050242 1 12.43671769 -5.89803336 10.20412435 0.924417483 1.072394341 0 0.129458958 0 0 0.018417613 0 1.26E-06 5.89803336 0.147976858 LGPELSPS(ph)PTSPTATSTTPSR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPELSPSPTSPTATSTTPSR 21 0 M0QY76;P26651 M0QY76 ZFP36 Tristetraprolin 1 0 LGPELS(0.001)PS(0.604)PT(0.085)S(0.179)PT(0.126)AT(0.004)S(0.001)TTPSR 222.96 7.80E-42 10158000 1652 1961.3 1670.1 1831.1 4732 5351.2 5019.4 5782.7 2026.1 1667.8 TRUE FALSE FALSE 1631.864789 1988.911233 1699.16739 2042.820398 4490.508382 5009.27559 5445.747711 5950.013301 1844.880542 1624.470316 1.004551929 1.224344461 1.045982419 1.257530149 2.764290821 3.083636273 3.352322082 3.662740552 1.135681289 1 10.66575367 -8.660554433 1.891221444 1.016221898 3.408597931 0.978040311 0.156343045 0.030148381 0.217761566 0.022501332 0.053900219 2.18E-09 8.660554433 2.392376033 up LGPELSPSPT(ph)SPTATSTTPSR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPELSPSPTSPTATSTTPSR 21 0 M0QY76;P26651 M0QY76 ZFP36 Tristetraprolin 1 0 LGPELS(0.013)PS(0.164)PT(0.364)S(0.364)PT(0.089)AT(0.006)S(0.001)TTPSR 112.44 0.00043143 9038600 1153.9 990.01 1094 1504.3 3474.1 3115.3 2832.2 3309 1461.9 1191 TRUE FALSE FALSE 1139.835823 1003.947387 1113.040611 1678.234244 3296.803713 2916.242384 3072.766997 3404.740694 1331.144003 1160.057648 0.982568258 0.865428876 0.959470086 1.446681763 2.841930932 2.513877124 2.648805429 2.934975429 1.147480907 1 10.17998079 -8.875628486 3.467756062 0.982947615 2.720055188 0.973733876 0.135588338 0.023466824 0.551614519 0.018760678 0.035791334 1.33E-09 8.875628486 1.737107573 up LGPGGLDDRY(ph)SLVSEQLEPAATSTYR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPGGLDDRYSLVSEQLEPAATSTYR 26 1 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71;E9PQ15 E9PKC4 PKP3 Plakophilin-3 1 0 LGPGGLDDRY(0.709)S(0.291)LVSEQLEPAATSTYR 114.19 1.53E-06 7406500 718.59 823.72 695.87 953.86 296.28 306.13 254.1 316.95 704.58 665.02 TRUE FALSE FALSE 709.8315487 835.3163518 707.9813254 1064.149781 281.159726 286.569281 275.6832477 326.1204482 641.5606001 647.7426845 1.095854211 1.289580526 1.092997794 1.642858818 0.434060828 0.442412223 0.425606115 0.503472221 0.990455956 1 9.339277007 -8.724306811 24.99825205 1.108005554 0.448904351 0.782821893 0.186728865 63.7828666 42939.40858 0.027084843 0.05416859 1.89E-09 8.724306811 -0.659101202 LGPGGLDDRYS(ph)LVSEQLEPAATSTYR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPGGLDDRYSLVSEQLEPAATSTYR 26 1 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71;E9PQ15 E9PKC4 PKP3 Plakophilin-3 1 0 LGPGGLDDRY(0.455)S(0.544)LVS(0.001)EQLEPAATSTYR 72.676 0.00012146 7995400 733.46 896.47 752.07 964.07 403.91 373.21 289.55 313.98 1018.3 878.18 TRUE FALSE FALSE 724.5203074 909.0905282 765.1594629 1075.540309 383.2969655 349.3630855 314.1443698 323.0645159 927.2206976 855.364757 0.847030815 1.062810363 0.894541722 1.257405453 0.448109374 0.40843755 0.367263635 0.377692105 1.084006197 1 9.740395956 -8.664409121 7.515787347 0.95476848 0.39180882 0.866713121 0.118101708 0.062823498 4.268085667 0.01649317 0.033065983 2.17E-09 8.664409121 -0.56295966 LGPGRPLPTFPTSECT(ph)SDVEPDTR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPGRPLPTFPTSECTSDVEPDTR 24 1 Q8TDD1-2;Q8TDD1;H0YHZ9 Q8TDD1-2 DDX54 ATP-dependent RNA helicase DDX54 1 0 LGPGRPLPTFPT(0.001)S(0.002)ECT(0.498)S(0.498)DVEPDTR 93.062 3.50E-05 16532000 542.63 748.78 860.53 365 480.72 636.44 469.86 629.08 676.8 895.46 TRUE FALSE FALSE 536.0162168 759.3213445 875.5071637 407.2030174 456.1870646 595.773538 509.7698967 647.2814373 616.2653129 872.1958201 0.614559488 0.870585856 1.00379656 0.466871095 0.523032849 0.683073141 0.584467255 0.742128571 0.706567606 1 9.768508266 -9.255302642 24.99672248 0.830813725 0.599405113 0.451517 0.131652332 476.6370371 1941480.343 0.025368275 0.041386227 5.56E-10 9.255302642 -0.231408612 LGPGS(ph)SGGSAR ddPTM_HeLa_Romidepsin_16h_R1 1 LGPGSSGGSAR 11 0 P17152 P17152 TMEM11 "Transmembrane protein 11, mitochondrial" 1 0 LGPGS(0.989)S(0.011)GGSAR 98.754 0.020418 6296500 1129.5 1040.8 1273.6 777.07 1106 986.76 1100.6 1101.5 1347.7 1003.8 TRUE FALSE FALSE 1115.73322 1055.45241 1295.766474 866.9184896 1049.556693 923.7092206 1194.084937 1133.370165 1227.158337 977.7211313 1.141156904 1.079502504 1.325292491 0.886672551 1.073472445 0.944757345 1.221293985 1.159195734 1.255121013 1 9.933279224 -12.42710029 1.156115586 1.000001951 1.104398098 0 0.14273875 0.952256935 2.276351984 0.079263273 0.019922387 3.74E-13 12.42710029 0.104396146 LGS(ph)ALLIR ddPTM_HeLa_Romidepsin_16h_R1 2 LGSALLIR 8 0 Q14993 Q14993 COL19A1 Collagen alpha-1(XIX) chain 1 0 LGS(1)ALLIR;LGS(1)ALLIR ; 123.21 0.016818 34497000 5119.2 4358.3 4962.9 4214.5 5510.6 6069.9 5446.9 5631.1 4904.1 4789.3 TRUE FALSE FALSE 5056.805221 4419.656262 5049.277193 4701.80032 5229.373519 5682.05298 5909.55955 5794.026994 4465.465013 4664.873296 1.0840177 0.947433292 1.082403931 1.007915976 1.121010837 1.218050871 1.266821021 1.242054527 0.957253227 1 12.18762218 -8.381086275 2.141452201 1.034283379 1.253454351 0.828777078 0.046179976 0.093263988 0.827058744 0.006363788 0.017571311 4.16E-09 8.381086275 0.219170972 LGS(ph)FGSITR ddPTM_HeLa_Romidepsin_16h_R1 4 LGSFGSITR 9 0 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 1 0 LGS(0.922)FGS(0.063)IT(0.015)R;LGS(0.987)FGS(0.013)ITR;LGS(0.998)FGS(0.001)ITR;LGS(0.869)FGS(0.13)IT(0.001)R ;;; 139.15 0.0065083 2223643000 28389.8 27705.1 27791.3 21946.4 17517 17043.2 15723.2 17395.4 25680.8 25095.9 TRUE FALSE FALSE 28043.7742 28095.13313 28274.99592 24483.94603 16623.04213 15954.19452 17058.72822 17898.70845 23383.84493 24443.9049 1.147270631 1.149371724 1.15672991 1.001638082 0.680048552 0.652686 0.697872467 0.732236053 0.956632953 1 14.57718715 -8.828640564 4.054439082 1.084202309 0.686464909 0.893498085 0.064305582 0.052002664 1.690517961 0.010377258 0.019759237 1.48E-09 8.828640564 -0.3977374 LGS(ph)LSAR ddPTM_HeLa_Romidepsin_16h_R1 1 LGSLSAR 7 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2;H0Y4T4;Q00G26 H0Y2V6;Q00G26 CEP170;PLIN5 Centrosomal protein of 170 kDa;Perilipin-5 1 0 LGS(0.997)LS(0.003)AR 117.81 0.027728 11157000 2810.2 3032.1 2941.1 2308.1 2693.4 3221.9 1979.2 2416.5 2839.7 3071.4 TRUE FALSE FALSE 2775.948201 3074.785983 2992.288612 2574.973382 2555.945748 3016.030988 2147.313199 2486.417615 2585.71012 2991.604585 0.927912805 1.027804944 1.000228649 0.860733198 0.854372854 1.008164984 0.717779752 0.83113177 0.864322154 1 11.54670378 -7.294228176 0.456954422 0.975593572 0.644366625 0.303247589 0.079560233 3.091045766 0.440653776 0.016243503 0.549121149 5.08E-08 7.294228176 -0.331226947 LGS(ph)LVDEFK ddPTM_HeLa_Romidepsin_16h_R1 2 LGSLVDEFK 9 0 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 1 0 LGS(1)LVDEFK;LGS(1)LVDEFK ; 107.03 0.021949 113884000 9318.8 8599.7 10130.8 6671.9 9036.2 10370.2 8261.7 10063.5 9248.1 8454 TRUE FALSE FALSE 9205.218881 8720.766802 10307.12232 7443.33647 8575.048995 9707.577688 8963.448592 10354.67149 8420.926774 8234.363861 1.117902856 1.059069887 1.251720533 0.903935823 1.041373583 1.17891046 1.088541719 1.257495014 1.022656627 1 13.00744148 -16.52287392 0.017844297 5.95E-07 1.92298018 0.195596448 0.095518682 4460.382604 6.423307032 444.6954989 268.4491348 3.00E-17 16.52287392 1.922979585 LGS(ph)PDYGNSALLSLPGYRPTTR ddPTM_HeLa_Romidepsin_16h_R1 1 LGSPDYGNSALLSLPGYRPTTR 22 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 LGS(0.877)PDY(0.014)GNS(0.109)ALLSLPGYRPTTR 67.368 0.0018136 181470000 1025.3 729.09 868.72 816.49 1251.9 1216.2 1160.6 1120.5 991.52 911.74 TRUE FALSE FALSE 1012.803249 739.3541482 883.8397072 910.8964155 1188.010872 1138.488745 1259.181335 1152.9199 902.8359679 888.0528634 1.140476306 0.83255646 0.995255737 1.02572319 1.337770442 1.282005601 1.417912589 1.298255934 1.016646649 1 9.794501749 -8.759948025 24.99961538 1.03993732 1.336268043 0.788959773 0.082769723 16.72240638 280308.4571 0.013817232 0.026496451 1.74E-09 8.759948025 0.296330723 LGS(ph)PGAPQQEDAMDDKELIEYFK ddPTM_HeLa_Romidepsin_16h_R1 2 LGSPGAPQQEDAMDDKELIEYFK 23 1 H0YGG4 H0YGG4 EIF2B1 1 0 LGS(0.543)PGAPQQEDAMDDKELIEY(0.457)FK;LGS(0.98)PGAPQQEDAMDDKELIEY(0.02)FK ; 85.407 0.00028768 52927000 5031.9 4242.9 4513.2 4017 4170.6 4580.2 3993.5 4370.3 5325.6 4535.9 TRUE FALSE FALSE 4970.569267 4302.631658 4591.750353 4481.464441 3957.758719 4287.540002 4332.70779 4496.747735 4849.264998 4418.056664 1.125057835 0.973874258 1.0393145 1.014351961 0.895814386 0.970458355 0.980681806 1.017811241 1.097601359 1 12.10919621 -9.441676165 1.474268855 1.055670039 0.969613076 0.362628899 0.049662396 0.378535868 1.630738361 0.010048899 0.017175105 3.62E-10 9.441676165 -0.086056964 LGS(ph)PLAVDEALR ddPTM_HeLa_Romidepsin_16h_R1 2 LGSPLAVDEALR 12 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 LGS(1)PLAVDEALR;LGS(1)PLAVDEALR ; 149.82 0.0014604 25520000 3321 3105.4 3601.9 2880.8 4867.1 5155.9 4214.5 4262 3574 3835.3 TRUE FALSE FALSE 3280.522375 3149.117903 3664.589559 3213.891651 4618.713725 4826.45463 4572.479525 4385.314246 3254.332489 3735.658353 0.878164453 0.842988733 0.980975564 0.860328046 1.236385474 1.291995727 1.224009021 1.173906667 0.871153671 1 11.8671468 -8.753355006 24.98583475 0.930912529 1.235349752 0.882424558 0.05784407 51.22561137 158318.3624 0.009477839 0.018693266 1.76E-09 8.753355006 0.304437223 LGS(ph)PLAVDEALRR ddPTM_HeLa_Romidepsin_16h_R1 2 LGSPLAVDEALRR 13 1 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 LGS(1)PLAVDEALRR;LGS(1)PLAVDEALRR ; 116.79 0.0016289 31059000 5409 5153.5 5200.6 5674.2 6652.8 6530.1 6056.5 6659.3 5432.7 5558.5 TRUE FALSE FALSE 5343.073027 5226.051108 5291.114261 6330.277702 6313.282791 6112.847685 6570.938959 6851.976339 4946.785706 5414.089369 0.98688305 0.965268719 0.977286096 1.169222979 1.166083964 1.129062945 1.2136739 1.265582423 0.913687486 1 12.40250299 -9.230866227 5.45559527 0.989791207 1.186904254 0.871448122 0.041891742 0.046325176 4.069806412 0.005421463 0.008923487 5.88E-10 9.230866227 0.197113047 LGS(ph)PVDNLEDMDRDDLTDDSVFTR ddPTM_HeLa_Romidepsin_16h_R1 2 LGSPVDNLEDMDRDDLTDDSVFTR 24 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 0 LGS(0.992)PVDNLEDMDRDDLT(0.008)DDSVFTR;LGS(0.998)PVDNLEDMDRDDLT(0.001)DDSVFTR ; 78.257 0.00038505 55398000 2182.08 2386.61 2219.27 2542.36 2643.81 2006.04 2030.42 2093.78 2404.58 2468.12 TRUE FALSE FALSE 2155.48397 2420.208758 2257.895463 2836.319625 2508.88651 1877.860518 2202.883824 2154.360221 2189.508342 2403.997887 0.896624736 1.006743297 0.939225228 1.179834492 1.043630913 0.781140669 0.916341831 0.896157286 0.910777981 1 11.23121991 -8.268494598 24.99233035 0.976410577 0.869726118 0.324572601 0.083756545 611.5282593 2166273.618 0.012922265 0.029500776 5.39E-09 8.268494598 -0.106684459 LGS(ph)SSNLQFK ddPTM_HeLa_Romidepsin_16h_R1 1 LGSSSNLQFK 10 0 Q8TDM6-4;Q8TDM6;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-2;Q8TDM6-5 Q8TDM6-4 DLG5 Disks large homolog 5 1 0 LGS(0.784)S(0.209)S(0.007)NLQFK 121.02 0.011189 20422000 1153.8 977.56 988.96 961.07 846.39 821.07 632.1 753.44 876.17 811.13 TRUE FALSE FALSE 1139.737042 991.3221153 1006.172434 1072.193435 803.19556 768.6062769 685.7905582 775.2395977 797.8031608 790.0567257 1.442601531 1.254748024 1.273544546 1.357109433 1.016630242 0.972849483 0.868026986 0.981245488 1.00980491 1 9.625812432 -8.604298139 5.466415703 1.232004666 0.94254351 0.493857761 0.131874238 0.163676966 8.246667506 0.025093587 0.050959349 2.49E-09 8.604298139 -0.289461155 LGS(ph)VDSFER ddPTM_HeLa_Romidepsin_16h_R1 3 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 LGS(0.831)VDS(0.169)FER;LGS(0.672)VDS(0.328)FER;LGS(0.822)VDS(0.178)FER ;; 128.51 0.0090364 242568000 7964.7 8185 8434.7 7891.5 9810.7 9411.1 7586.4 9831.1 8571.5 8045.7 TRUE FALSE FALSE 7867.623173 8300.228645 8581.502415 8803.952361 9310.02337 8809.761083 8230.788627 10115.54737 7804.843572 7836.671554 1.003949587 1.059152293 1.095044287 1.123430056 1.188007345 1.124171279 1.050291386 1.290796392 0.995938584 1 12.93602532 -9.726199713 1.179620808 1.000104943 1.153388258 0.592072748 0.05677577 0.214146903 0.597011213 0.009686208 0.014947564 1.88E-10 9.726199713 0.153283315 LGS(ph)YSGPTSVSR ddPTM_HeLa_Romidepsin_16h_R1 2 LGSYSGPTSVSR 12 0 A0A2R8YFI4;V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23 A0A2R8YFI4 PANK2 "Pantothenate kinase 2, mitochondrial" 1 0 LGS(0.996)YS(0.004)GPTSVSR;LGS(0.902)YS(0.098)GPTSVSR ; 118.61 0.0079526 26363000 2727.4 2263.91 2577.4 2072.47 2741.9 2090.38 2309.23 2271.01 2824.5 2684.8 TRUE FALSE FALSE 2694.1574 2295.781384 2622.258566 2312.098733 2601.970612 1956.811464 2505.375939 2336.718091 2571.869646 2615.048509 1.030251405 0.877911586 1.002757141 0.884151374 0.994998985 0.748288782 0.958060981 0.893565868 0.983488313 1 11.35262199 -9.664745756 0.814709358 1.014318975 0.888635982 0.248792102 0.070806027 0.452520698 0.602594308 0.013777969 0.023959473 2.16E-10 9.664745756 -0.125682993 LGSGGS(ph)GDGPSVSWSR ddPTM_HeLa_Romidepsin_16h_R1 1 LGSGGSGDGPSVSWSR 16 0 Q9Y6R9-2;Q9Y6R9 Q9Y6R9-2 CCDC61 Coiled-coil domain-containing protein 61 1 0 LGS(0.072)GGS(0.812)GDGPS(0.114)VS(0.001)WSR 165.89 2.07E-05 4100000 1961.3 1857.8 1876 2025.9 2099.1 1785.7 1721.4 1428.5 2122 1811.8 TRUE FALSE FALSE 1937.394921 1883.954157 1908.650993 2260.14409 1991.975094 1671.599533 1867.615673 1469.831394 1932.203005 1764.729175 1.097842632 1.067559932 1.081554621 1.280731413 1.128770988 0.947227233 1.058301579 0.832893463 1.094900585 1 10.78523108 -6.562259291 1.263325726 1.070004127 2.70E-16 0.4458782 0.083062849 5.97625869 2.240670937 0.013403315 12.81426002 2.74E-07 6.562259291 -1.070004127 LGSLLPVLS(ph)PTSLPSPLPATLETPVPAFLK ddPTM_HeLa_Romidepsin_16h_R1 1 LGSLLPVLSPTSLPSPLPATLETPVPAFLK 30 0 P48681 P48681 NES Nestin 1 0 LGS(0.009)LLPVLS(0.261)PT(0.244)S(0.244)LPS(0.223)PLPAT(0.008)LET(0.01)PVPAFLK 50.166 0.007818 583610 70.823 267.17 135.43 0 158.93 180.94 156.98 245.69 157.91 271.81 TRUE FALSE FALSE 69.95978203 270.9312263 137.7871023 0 150.8192091 169.378518 170.3138773 252.7986525 143.7861341 264.748337 0.264250128 1.023353836 0.520445582 0 0.56967009 0.639771792 0.643304805 0.954863987 0.543104957 1 8.048477812 -12.58440994 1.361965472 1.000756094 0.532933905 0 0.314511829 0.48595923 1.612292412 0.208316077 0.048175363 2.60E-13 12.58440994 -0.467822189 LGSPDYGNS(ph)ALLSLPGYRPTTR ddPTM_HeLa_Romidepsin_16h_R1 1 LGSPDYGNSALLSLPGYRPTTR 22 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 LGS(0.404)PDY(0.117)GNS(0.479)ALLSLPGYRPTTR 65.278 0.00249 172990000 419.62 493.14 548.82 452.76 651.58 968.4 714.75 650.61 592.17 695.06 TRUE FALSE FALSE 414.50551 500.0824379 558.3719819 505.1102415 618.3274412 906.5223654 775.4608472 669.4343739 539.2048321 677.002241 0.612266083 0.738671761 0.824771246 0.74609833 0.913331454 1.339024172 1.145433206 0.988821504 0.796459449 1 9.403016799 -8.465738031 5.872815148 0.803136556 1.15508747 0.65392365 0.120394015 0.141045948 10.42802055 0.023483454 0.052544878 3.42E-09 8.465738031 0.351950914 LGSQPIRAS(ph)NPDLR ddPTM_HeLa_Romidepsin_16h_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 0 LGSQPIRAS(1)NPDLR 65.809 0.025073 10130000 3134.1 2576.5 2849.2 3044.6 3682.7 3039.9 2669.9 3083.6 3055.5 2936.4 TRUE FALSE FALSE 3095.900384 2612.772035 2898.789131 3396.630977 3494.758077 2845.660201 2896.681239 3172.819101 2782.208427 2860.111905 1.082440298 0.913520912 1.013522977 1.187586742 1.221895574 0.994947154 1.01278598 1.109333903 0.972762088 1 11.48185588 LGSVDS(ph)FER ddPTM_HeLa_Romidepsin_16h_R1 2 LGSVDSFER 9 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 LGS(0.018)VDS(0.982)FER;LGS(0.001)VDS(0.999)FER ; 131.09 0.007716 32085000 6106 6659.7 5669.4 4132.6 4673.9 7943.1 7114.5 6115.2 8342.5 5924.9 TRUE FALSE FALSE 6031.577723 6753.455431 5768.073529 4610.430656 4435.373442 7435.561545 7718.805452 6292.133664 7596.325906 5770.970244 1.045158347 1.170246102 0.999498054 0.798900438 0.768566334 1.288442191 1.337523003 1.090307764 1.316299614 1 12.49459818 -8.226006066 24.99756735 0.999867816 1.248634262 0.286545382 0.161136805 447.1599286 315463.0945 0.018551278 0.047294629 5.94E-09 8.226006066 0.248766446 DPLQNS(ph)PGSEGK ddPTM_HeLa_Romidepsin_16h_R1 1 DPLQNSPGSEGK 12 0 Q6IE81-2;Q6IE81 Q6IE81-2 JADE1 Protein Jade-1 1 0 DPLQNS(0.767)PGS(0.233)EGK 120.29 0.0074292 7199300 4513.7 4526.8 3997.2 3501.6 1863.4 1393.9 1400.3 1292.5 4161.7 4387.3 TRUE FALSE FALSE 4458.685288 4590.528409 4066.769589 3906.471468 1768.303745 1304.834289 1519.241447 1329.896448 3789.467129 4273.317314 1.043378004 1.074230644 0.951665718 0.914154316 0.413801179 0.305344582 0.355518052 0.311209384 0.886774103 1 12.06114073 -8.775765945 2.867791191 1.019757872 0.325762037 0.971491983 0.053204904 0.018990073 0.320269127 0.005459535 0.011134198 1.68E-09 8.775765945 -0.693995835 down LGVIEDHSNR ddPTM_HeLa_Romidepsin_16h_R1 4 LGVIEDHSNR 10 0 P14625;Q58FF3 P14625 HSP90B1;HSP90B2P Endoplasmin;Putative endoplasmin-like protein 0 0 ;;; ;;; 160.75 0.0011034 85627000 29878.9 29665.3 28907.4 21519.7 28876.6 31473.7 28729.6 31509.3 28182.9 26584.4 FALSE FALSE TRUE 29514.72447 30082.92887 29410.52117 24007.90897 27402.91935 29462.63215 31169.89151 32420.97188 25662.15084 25893.73346 1.139840438 1.161784141 1.13581617 0.927170623 1.058283827 1.137828664 1.203761967 1.252077918 0.991056422 1 14.66031537 -4 0.015667605 8.75E-09 2.472442686 0.346951582 0.078966319 4948.81167 6.046369597 378.7305774 599.3802183 1.00E-04 4 2.472442677 LGVSVS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 4 LGVSVSPSR 9 0 E7ERS3;Q86VM9;H3BP01 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 LGVS(0.001)VS(0.991)PS(0.008)R;LGVS(0.002)VS(0.994)PS(0.005)R;LGVSVS(0.997)PS(0.002)R;LGVS(0.013)VS(0.986)PS(0.001)R ;;; 199.19 1.90E-11 1650866000 19475.2 20035.1 17970.4 10872 19370.6 19560.6 18613.8 18128.6 20990.3 18977.1 TRUE FALSE FALSE 19237.82877 20317.15466 18283.16727 12129.07179 18382.046 18310.74079 20194.85571 18653.12244 19112.875 18484.07221 1.040778707 1.099170921 0.989130916 0.656190457 0.994480318 0.990622661 1.09255447 1.009145725 1.034018629 1 14.17399501 -9.52111873 24.99511012 1.026662654 0.947597993 0.135924038 0.109539787 127.2218652 1806773.421 0.017747896 0.025316015 3.01E-10 9.52111873 -0.07906466 LGVTVLSR ddPTM_HeLa_Romidepsin_16h_R1 2 LGVTVLSR 8 0 O75828 O75828 CBR3 Carbonyl reductase [NADPH] 3 0 0 ; ; 161.68 0.0044793 10144300 4142.6 3524.5 5014.9 4950.9 5806.2 5340.7 4434 4241.5 3410.7 2703.9 FALSE FALSE TRUE 4092.108398 3574.118004 5102.182231 5523.346353 5509.887948 4999.446506 4810.623849 4364.221111 3105.63845 2633.652288 1.553777018 1.357095627 1.937302906 2.097219279 2.092109111 1.898294064 1.826597942 1.657098445 1.179213544 1 11.36284917 -10.96083065 0.496246844 1.015538914 1.935640278 0.732617104 0.187092074 0.316417954 0.187936345 0.116808055 0.073665473 1.09E-11 10.96083065 0.920101365 LGYLVS(ph)PPQQIR ddPTM_HeLa_Romidepsin_16h_R1 1 LGYLVSPPQQIR 12 0 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;H3BSK8 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 LGYLVS(1)PPQQIR 136.27 0.0025837 24955000 1634.9 1734.7 1619.2 1612 2343.8 2393.7 1769.4 1949.7 1833.2 1938 TRUE FALSE FALSE 1614.97321 1759.121152 1647.381497 1798.387025 2224.18714 2240.750295 1919.692792 2006.111493 1669.234001 1887.650481 0.855546737 0.93191042 0.872715322 0.952711873 1.178283354 1.187057836 1.016974706 1.062755798 0.884291884 1 10.88237594 -8.857203461 6.31716231 0.925652909 1.109337219 0.713036683 0.060605729 0.112000067 6.222537426 0.010851994 0.019860789 1.39E-09 8.857203461 0.18368431 LHDFGYR ddPTM_HeLa_Romidepsin_16h_R1 2 LHDFGYR 7 0 A0A0C4DFS8;P43490 A0A0C4DFS8 NAMPT Nicotinamide phosphoribosyltransferase 0 0 ; ; 143.02 0.0060852 18985600 3608.3 3635.8 5139.5 4247.4 3813.3 3416.1 2834.6 2692.5 3393.9 2683.4 FALSE FALSE TRUE 3564.320652 3686.984888 5228.950842 4738.504373 3618.693072 3197.822235 3075.370853 2770.403239 3090.341084 2613.684881 1.36371476 1.410646293 2.000604923 1.812959323 1.384517735 1.223491882 1.176641789 1.059960694 1.182369423 1 11.3518695 -11.62230691 0.900178965 1.032801029 1.441049913 0.189282138 0.273421231 0.585018399 0.959682905 0.126179784 0.062062698 2.39E-12 11.62230691 0.408248884 LHEEGIIYR ddPTM_HeLa_Romidepsin_16h_R1 2 LHEEGIIYR 9 0 A0A140T936;P26640-2;P26640 A0A140T936 VARS Valine--tRNA ligase 0 0 ; ; 132.76 0.0032955 11499800 9530.7 9100.4 8683.3 9248.1 10981.3 11059.8 10572.7 6266.4 11264.3 6349.1 FALSE FALSE TRUE 9414.536163 9228.51567 8834.429194 10317.40884 10420.88328 10353.11447 11470.74487 6447.708397 10256.7928 6184.149467 1.522365559 1.492285353 1.428560102 1.668363433 1.685095637 1.674137168 1.854862166 1.042618461 1.658561594 1 12.59435947 -12.16014312 0.474586987 0.878433021 1.594233844 0 0.28962802 0.945487757 0.304228438 0.320754414 0.055554114 6.92E-13 12.16014312 0.715800823 LHELRIARLRQEER ddPTM_HeLa_Romidepsin_16h_R1 2 LHELRIARLRQEER 14 3 Q9BYN8 Q9BYN8 MRPS26 "28S ribosomal protein S26, mitochondrial" 0 0 ; ; 81.431 0.0074819 40124000 2442.5 2251.46 2223.7 2258.76 2816.5 2932.26 2736.6 2968.6 2292.29 2098.58 FALSE FALSE TRUE 2412.729871 2283.156113 2262.402566 2519.928459 2672.763495 2744.898049 2969.046736 3054.491757 2087.261841 2044.058589 1.180362385 1.116971952 1.106818845 1.232806375 1.307576754 1.34286662 1.452525261 1.494326911 1.021136015 1 10.99722083 -4 0.190895339 1.002737066 3.39159288 0.940006383 0.03986434 11.18614412 0.125365828 0.055814055 7.938052148 1.00E-04 4 2.388855813 LHFFMPGFAPLTSR ddPTM_HeLa_Romidepsin_16h_R1 1 LHFFMPGFAPLTSR 14 0 Q5JP53;P07437;Q5ST81;A0A075B736;Q5SQY0;A6NNZ2;P04350;P68371;Q3ZCM7;Q9BVA1;Q13885 Q5JP53;P04350;P68371;Q9BVA1 TUBB;TUBB8;TUBB4A;TUBB4B;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-8 chain-like protein LOC260334;Tubulin beta-4A chain;Tubulin beta-4B chain;Tubulin beta-8 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 0 0 63.181 0.018499 2999600 165.65 123.71 792.18 132.76 378.88 682.3 566.87 275.41 0 0 FALSE FALSE TRUE 163.6309941 125.4515926 805.9675606 148.1103359 359.5443398 638.703232 615.0199237 283.3785538 0 0 0 LHGELQDR ddPTM_HeLa_Romidepsin_16h_R1 2 LHGELQDR 8 0 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 0 ; ; 107.01 0.011753 5293000 2648.7 2451.4 2565.6 2063.86 2255 2279.7 3299.2 1951.6 3449.2 3030.8 FALSE FALSE TRUE 2616.416626 2485.910874 2610.253192 2302.493204 2139.918935 2134.034527 3579.433966 2008.066467 3140.694913 2952.059379 0.886302167 0.842093791 0.884214325 0.779961684 0.724890207 0.722896884 1.212520992 0.680225635 1.063899641 1 11.52750603 -11.40208414 0.646662384 0.9954649 0.838953969 0.215711428 0.142507611 0.982654542 0.871222194 0.07193466 0.034185908 3.96E-12 11.40208414 -0.156510931 LHGLDEEAEQK ddPTM_HeLa_Romidepsin_16h_R1 1 LHGLDEEAEQK 11 0 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;A0A3B3IU45;E5RG31 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 0 0 132.25 6.31E-05 0 3515.1 3271.5 2884.2 2817.1 2672.5 2954.5 2542 2764.2 3080.3 3435.7 FALSE FALSE TRUE 3472.256609 3317.556263 2934.398291 3142.826357 2536.112353 2765.716985 2757.917417 2844.177766 2804.790253 3346.440019 1.037597145 0.991368811 0.876871623 0.939155144 0.75785382 0.826465429 0.824134723 0.849911473 0.838141499 1 11.70841144 -9.485967272 1.267924111 1.018592249 0.821801845 0.363728834 0.069863344 0.12154884 0.38943747 0.006879575 0.011882519 3.27E-10 9.485967272 -0.196790404 LHKTEDGGWEWS(ph)DDEFDEESEEGK ddPTM_HeLa_Romidepsin_16h_R1 1 LHKTEDGGWEWSDDEFDEESEEGK 24 1 C9JIG9;O95747 C9JIG9 OXSR1 Serine/threonine-protein kinase OSR1 1 0 LHKTEDGGWEWS(1)DDEFDEESEEGK 88.976 8.65E-06 0 1077.4 977.1 672.38 820.24 1044 1085.8 833.25 1062.3 1046.6 949.45 TRUE FALSE FALSE 1064.268234 990.8556394 684.0824919 915.0800081 990.7207843 1016.420884 904.0262342 1093.035974 952.9894747 924.7831521 1.150830043 1.071446465 0.739722053 0.989507655 1.071300642 1.099091048 0.977554827 1.181937595 1.030500472 1 9.852971305 -7.242423839 22.86193265 1.042197948 1.181937997 0.135247871 0.108214773 2269.570141 2728508.24 0.016352643 0.665528388 5.72E-08 7.242423839 0.139740049 LHLETPQPS(ph)PQEGGSVDIWR ddPTM_HeLa_Romidepsin_16h_R1 2 LHLETPQPSPQEGGSVDIWR 20 0 O14613 O14613 CDC42EP2 Cdc42 effector protein 2 1 0 LHLET(0.002)PQPS(0.995)PQEGGS(0.004)VDIWR;LHLET(0.063)PQPS(0.937)PQEGGSVDIWR ; 85.203 0.0012133 5213800 1385.17 1213.7 1162.75 1123.82 1508.27 1860.23 1350.87 1545.83 1211.73 1531.21 TRUE FALSE FALSE 1368.287015 1230.7865 1182.987176 1253.761356 1431.297354 1741.367307 1465.612864 1590.556152 1103.349834 1491.428943 0.917433594 0.825239785 0.793190437 0.840644378 0.959681894 1.167583152 0.982690373 1.066464587 0.739793765 1 10.54247953 -8.501801913 23.28263807 0.9261957 1.063347538 0.410963291 0.096359438 290.7912806 321223.0071 0.013003421 0.028747236 3.15E-09 8.501801913 0.137151838 LHPDGS(ph)PDVAGEK ddPTM_HeLa_Romidepsin_16h_R1 3 LHPDGSPDVAGEK 13 0 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 LHPDGS(1)PDVAGEK;LHPDGS(1)PDVAGEK;LHPDGS(1)PDVAGEK ;; 149.32 0.00076836 43692000 15911.6 14728.3 15827.8 15698.9 16679.3 16428.7 14416.1 15965.6 17145.8 15433.7 TRUE FALSE FALSE 15717.6633 14935.64539 16103.27622 17514.08068 15828.09308 15378.95909 15640.60317 16427.53945 15612.23671 15032.73025 1.045562785 0.993541768 1.07121434 1.165063192 1.052908741 1.023031667 1.040436628 1.092784822 1.038549648 1 13.87581944 -11.05044544 0.513237708 1.002213509 1.068450534 0.155795908 0.043225235 0.949762427 0.588569055 0.025963213 0.015227043 8.90E-12 11.05044544 0.066237025 LHPEELGGPPLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LHPEELGGPPLKK 13 1 Q15742;Q15742-3 Q15742 NAB2 NGFI-A-binding protein 2 0 1 LHPEELGGPPLK(1)K 71.888 0.021513 1229100 1902.6 607.41 1166.8 639.81 820.62 611.83 1534.9 837.2 1240.6 908.06 FALSE TRUE FALSE 1879.410379 615.9611339 1187.107665 713.7878426 778.7406992 572.7360376 1665.274368 861.4230611 1129.637629 884.4684703 2.124903761 0.69641955 1.342170698 0.807024633 0.880461798 0.647548281 1.882796757 0.973944341 1.27719378 1 9.788666904 -10.24229728 24.98213794 1.531204593 1.048119265 0.170716754 0.431070644 1132.52633 1478049.458 0.086752855 0.106158117 5.72E-11 10.24229728 -0.483085327 LHPTY(ph)T(ph)VDMPS(ph)YVPK ddPTM_HeLa_Romidepsin_16h_R1 1 LHPTYTVDMPSYVPK 15 0 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 3 0 LHPT(0.507)Y(0.714)T(0.779)VDMPS(0.64)Y(0.36)VPK 77.776 0.0041685 0 471.6 386.01 635.4 618.51 796.79 905.36 923.82 919.41 901.16 666.28 TRUE FALSE FALSE 465.8519578 391.4442589 646.4588705 690.0250364 756.1268331 847.5104179 1002.289248 946.0116778 820.5579926 648.9699495 0.717832864 0.603177788 0.99613067 1.063261923 1.165118406 1.305931682 1.544430907 1.457712608 1.264400598 1 9.342007866 -8.527782824 1.062480564 0.847639049 1.511301901 0.619952975 0.175754325 0.202673731 0.423167293 0.024089143 0.090487264 2.97E-09 8.527782824 0.663662852 LHPVILASIVDSYER ddPTM_HeLa_Romidepsin_16h_R1 2 LHPVILASIVDSYER 15 0 A0A1W2PP79;E9PQV8;O00303 A0A1W2PP79 EIF3F Eukaryotic translation initiation factor 3 subunit F 0 0 ; ; 144.51 0.00022536 11443700 2884.8 3151.3 3055.4 2948.8 3345.5 3057.5 2597 3258 3272.2 3072.5 FALSE FALSE TRUE 2849.638948 3195.664084 3108.577955 3289.754131 3174.766651 2862.135618 2817.589115 3352.26509 2979.526237 2992.676007 0.952204295 1.067828284 1.038728532 1.099268388 1.060845425 0.956380046 0.941494872 1.120156369 0.995606016 1 11.54722038 -10.26499739 24.98807711 0.977429806 1.036570116 0.189521795 0.054253685 378.1510992 2655767.82 0.009523105 0.011104441 5.43E-11 10.26499739 0.05914031 LHS(ph)PQTHWK ddPTM_HeLa_Romidepsin_16h_R1 1 LHSPQTHWK 9 0 B8ZZS4;Q9H8Y5 B8ZZS4 ANKZF1 Ankyrin repeat and zinc finger domain-containing protein 1 1 0 LHS(1)PQTHWK 78.548 0.027018 25913000 3367.9 3667.6 2996.8 2903.5 4341.9 5513.9 4544.6 4594.8 4093.8 3163.3 TRUE FALSE FALSE 3326.850739 3719.232569 3048.958047 3239.216331 4120.316641 5161.579585 4930.618211 4727.743289 3727.640275 3081.11701 1.079754754 1.207105266 0.989562564 1.051312339 1.337280158 1.675229979 1.600269706 1.534425104 1.209834051 1 11.58923776 -8.552414051 2.888680407 1.049066819 1.601044392 0.880213448 0.084128538 0.048370663 0.818533496 0.010599833 0.024058167 2.80E-09 8.552414051 0.551977573 LHS(ph)SNPNLSTLDFGEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LHSSNPNLSTLDFGEEK 17 0 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5;Q9H4L5-8;Q9H4L5-6;Q9H4L5-4;Q9H4L5-2 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 LHS(0.551)S(0.449)NPNLSTLDFGEEK 109.85 0.00084303 49808000 6000.8 5909.9 7035.9 5178.3 6784.5 5958.9 5098.8 5865.3 6787.3 6237.6 TRUE FALSE FALSE 5927.659941 5993.099727 7158.356888 5777.039411 6438.261649 5578.145521 5531.891945 6035.003202 6180.226889 6075.546253 0.975658763 0.986429776 1.178224408 0.950867489 1.05970087 0.918130698 0.910517625 0.993326847 1.017229831 1 12.56879841 -8.23996463 24.86995556 1.003904753 0.93764431 0.219068757 0.064673567 1008.870577 1168374.682 0.008872617 0.022594429 5.75E-09 8.23996463 -0.066260443 LHSFLGDDVFLR ddPTM_HeLa_Romidepsin_16h_R1 2 LHSFLGDDVFLR 12 0 E9PK47;P06737-2;P06737 E9PK47 PYGL "Alpha-1,4 glucan phosphorylase;Glycogen phosphorylase, liver form" 0 0 ; ; 139.76 0.00096548 12256600 5011.1 4441.2 4636.2 4273.7 5001.4 4846.3 3879.3 3694.2 5332.1 4271.8 FALSE FALSE TRUE 4950.022786 4503.72333 4716.891116 4767.845302 4746.159895 4536.637071 4208.807645 3801.085849 4855.183622 4160.81802 1.189675386 1.082412955 1.133645137 1.145891332 1.140679518 1.090323357 1.0115337 0.913542921 1.166881992 1 12.02265148 -7.477797017 2.147689993 1.102091304 0.901790679 0.604559338 0.052171167 0.338143744 2.374574181 0.010328375 0.108512827 3.33E-08 7.477797017 -0.200300625 LHSQEEDFR ddPTM_HeLa_Romidepsin_16h_R1 1 LHSQEEDFR 9 0 Q4V328-4;Q4V328;Q4V328-2;A0A087WV84;A0A087WW92;A0A087WZF5 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 0 0 167.93 0.00093901 2777600 1137.8 1223.7 1166 854.02 1340.2 1573.5 991.26 1357.2 1102.4 1114.6 FALSE FALSE TRUE 1123.932056 1240.927281 1186.293741 952.7658107 1271.804593 1472.958428 1075.4576 1396.468441 1003.798583 1085.642531 1.035268998 1.14303488 1.092711189 0.877605458 1.17147639 1.356761904 0.990618522 1.286305944 0.924612434 1 10.08433343 -5.054216247 0.212420882 0.990721719 1.806739064 0.304316061 0.121599791 33.3879631 0.582627181 0.099707877 8.482887248 8.83E-06 5.054216247 0.816017345 LHSS(ph)NPNLSTLDFGEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LHSSNPNLSTLDFGEEK 17 0 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5;Q9H4L5-8;Q9H4L5-6;Q9H4L5-4;Q9H4L5-2 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 LHS(0.239)S(0.76)NPNLS(0.001)TLDFGEEK 75.912 0.0098457 73745000 4450.8 4604 4683.1 4134.6 4871.8 4782.3 3414.6 4640.5 4364.3 4873.9 TRUE FALSE FALSE 4396.551938 4668.815233 4764.607391 4612.661906 4623.173867 4476.726464 3704.636039 4774.765546 3973.946077 4747.275375 0.926121109 0.983472595 1.00365094 0.971644057 0.973858372 0.943009645 0.780371001 1.005790726 0.837100392 1 12.21288402 -7.986340241 24.99978799 0.969327662 0.885233213 0.095744705 0.068721108 213.3000754 390371.7407 0.00719426 0.021568948 1.03E-08 7.986340241 -0.084094449 LHSYS(ph)SPSTK ddPTM_HeLa_Romidepsin_16h_R1 4 LHSYSSPSTK 10 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 LHS(0.001)YS(0.804)S(0.192)PS(0.003)TK;LHSYS(0.856)S(0.143)PSTK;LHS(0.017)YS(0.667)S(0.249)PS(0.065)T(0.003)K;LHSYS(0.956)S(0.044)PSTK ;;; 190.57 6.51E-08 123747000 24235.6 21104.6 22508.2 16333.2 28324.6 30624.4 29412.5 17526.2 29999.7 26436.7 TRUE FALSE FALSE 23940.20719 21401.71111 22899.94578 18221.72143 26879.08997 28667.59968 31910.79702 18033.29295 27316.4517 25749.87072 0.929721452 0.831138585 0.889322748 0.70764322 1.043853395 1.113310431 1.239260475 0.700325572 1.060838401 1 14.65227757 -8.588895928 24.9999186 0.92982514 1.046278928 0.105981086 0.156285675 90.83793117 34398.32519 0.021376754 0.042753511 2.58E-09 8.588895928 0.116453787 LHTDDELNWLDHGR ddPTM_HeLa_Romidepsin_16h_R1 4 LHTDDELNWLDHGR 14 0 Q9Y490 Q9Y490 TLN1 Talin-1 0 0 ;;; ;;; 174.46 6.59E-06 35228700 4900.52 3614.68 3871.43 3373.1 4323.83 4548.62 3461.59 4336.72 4912.46 4423.59 FALSE FALSE TRUE 4840.790577 3665.56756 3938.810615 3763.113693 4103.168821 4257.977862 3755.617368 4462.196151 4473.077274 4308.664494 1.123501397 0.850743325 0.914160437 0.873382854 0.952306411 0.988236115 0.871643028 1.035633236 1.038158641 1 12.07302505 -10.26389542 24.9938975 1.058320104 0.925309426 0.484200318 0.06014743 140.8109986 1432959.263 0.011286834 0.013228733 5.45E-11 10.26389542 -0.133010678 LHVAILER ddPTM_HeLa_Romidepsin_16h_R1 2 LHVAILER 8 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;E9PMV1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 94.114 0.004683 7372000 3599.2 2815.4 5648.2 3683.6 5723.5 4595.3 4039.9 3198.5 2895.5 1673.17 FALSE FALSE TRUE 3555.331566 2855.035275 5746.504552 4109.515164 5431.408438 4301.675161 4383.049005 3291.043551 2636.519228 1629.700802 2.181585455 1.751876953 3.526110157 2.521637811 3.332764168 2.639549023 2.689480793 2.019415801 1.617793416 1 10.67039141 -11.29930322 0.53178227 0.995258741 2.759778206 0.513066556 0.514051704 0.400073433 0.248483586 0.312376877 0.146518525 5.02E-12 11.29930322 1.764519465 LHVAVK ddPTM_HeLa_Romidepsin_16h_R1 2 LHVAVK 6 0 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906;Q96SI9-2;Q96SI9 Q12906-4 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 0 ; ; 74.949 0.018771 2073400 4527.6 4733.9 9662.4 5986.8 6063.7 7313.3 12106.8 1016.81 8359 4202.6 FALSE FALSE TRUE 4472.41587 4800.543968 9830.570019 6679.021985 5754.246762 6846.003733 13135.15129 1046.229793 7611.350105 4093.415846 1.092587716 1.172747688 2.401556643 1.631650005 1.405732273 1.672442769 3.208848498 0.255588446 1.859412869 1 11.99908952 -9.931988204 10.33662776 1.048375339 1.801919721 0.058184659 0.747997603 0.463914032 67.71394607 0.10229872 0.134490868 1.17E-10 9.931988204 0.753544382 LHVEVAK ddPTM_HeLa_Romidepsin_16h_R1 2 LHVEVAK 7 0 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 0 ; ; 94.407 0.0065944 2067900 5231.8 4070.7 4761.7 3007.9 6616.3 6101.4 5224.1 4447.6 5220 5135 FALSE FALSE TRUE 5168.032809 4128.007421 4844.575391 3355.687551 6278.645522 5711.540231 5667.834924 4576.284289 4753.110126 5001.59196 1.033277575 0.825338703 0.968606682 0.670923893 1.255329418 1.14194446 1.133206181 0.91496554 0.950319451 1 12.28817165 LHVGNIS(ph)PTCTNK ddPTM_HeLa_Romidepsin_16h_R1 2 LHVGNISPTCTNK 13 0 E9PB51;Q9BWF3;D6R9K7;J3QRR5;Q9BWF3-3;Q9BWF3-4;Q9BWF3-2 E9PB51 RBM4 RNA-binding protein 4 1 0 LHVGNIS(0.955)PT(0.043)CT(0.002)NK;LHVGNIS(0.808)PT(0.144)CT(0.048)NK ; 145.81 0.00076784 48863000 5800.3 4568.4 5279.9 379.701 5780 6033.7 5249.8 4931.7 5247.2 5371.3 TRUE FALSE FALSE 5729.603713 4632.714055 5371.794445 423.6038162 5485.025032 5648.166043 5695.717881 5074.390959 4777.87729 5231.752852 1.095159476 0.885499408 1.026767624 0.080967857 1.048410578 1.079593437 1.08868252 0.969921765 0.913245986 1 12.35307867 -10.2469494 21.2458768 1.04493641 0.879382671 0.030020004 0.283155171 242.6324661 355756.9336 0.046919227 0.057243144 5.66E-11 10.2469494 -0.165553739 LIDLES(ph)PTPESQK ddPTM_HeLa_Romidepsin_16h_R1 3 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 LIDLES(0.981)PT(0.019)PESQK;LIDLES(0.987)PT(0.013)PESQK;LIDLES(0.987)PT(0.013)PESQK ;; 225.33 1.45E-31 236418000 22636.1 21792.3 21168.1 19871 17259.1 15187.4 14120 15127.8 22213.2 20108.9 TRUE FALSE FALSE 22360.20251 22099.09257 21536.5219 22168.57852 16378.30372 14216.97416 15319.35245 15565.49903 20226.39576 19586.46788 1.141614846 1.128283706 1.099561291 1.131831357 0.836205069 0.725856966 0.782139615 0.79470679 1.032671939 1 14.25756963 -8.664998671 4.732205669 1.080193749 0.771385185 0.912302291 0.046424881 0.05859055 2.243645098 0.009156753 0.018607419 2.16E-09 8.664998671 -0.308808564 LIDLESPT(ph)PESQK ddPTM_HeLa_Romidepsin_16h_R1 1 LIDLESPTPESQK 13 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 LIDLES(0.229)PT(0.76)PES(0.012)QK 124.47 0.0080068 150450000 6450.8 6182.4 6007.9 6386.1 5361 4662.4 4243.3 4686.5 6659.8 5786.2 TRUE FALSE FALSE 6372.175168 6269.435989 6112.464979 7124.49093 5087.408165 4364.487687 4603.725796 4822.096483 6064.130808 5635.87369 1.13064549 1.112415986 1.08456387 1.26413247 0.902683141 0.774411906 0.816861067 0.855607622 1.075987707 1 12.46042356 -8.549206707 12.66538371 1.081996024 0.81953535 0.794922096 0.068247013 0.401745821 192.6994135 0.011420599 0.022879636 2.82E-09 8.549206707 -0.262460673 LIDLHSPS(ph)EIVK ddPTM_HeLa_Romidepsin_16h_R1 1 LIDLHSPSEIVK 12 0 P60866;P60866-2;G3XAN0 P60866 RPS20 40S ribosomal protein S20 1 0 LIDLHS(0.004)PS(0.996)EIVK 98.654 0.0070602 9853500 6153.5 6529.5 6241 4888.9 7274.4 6189.4 5939.4 6565.8 7222.8 6647.7 TRUE FALSE FALSE 6078.498775 6621.422472 6349.621987 5454.177621 6903.160223 5793.917315 6443.892488 6755.771064 6576.774678 6474.991796 0.938765479 1.022614805 0.980637843 0.842345101 1.066126482 0.894814619 0.995197012 1.043363648 1.015719384 1 12.66066265 -7.400974179 4.290745439 0.967760832 1.040782932 0.112039286 0.061836127 0.331688888 9.253613484 0.007651371 0.050485713 3.97E-08 7.400974179 0.0730221 LIEDFLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LIEDFLAR 8 0 A6NKE1;A0A087WWM0;O43617-2;O43617 A6NKE1 TRAPPC3 Trafficking protein particle complex subunit 3 0 0 138.83 7.36E-07 0 1639.5 1812.6 1724.1 1631.9 2117.4 2140.9 1778 1945.9 1768 1631.8 FALSE FALSE TRUE 1619.517143 1838.11783 1754.107237 1820.587956 2009.341177 2004.103399 1929.023276 2002.201546 1609.865652 1589.405601 1.01894516 1.156481284 1.103624674 1.145452083 1.264209196 1.260913765 1.213675902 1.259717183 1.012872769 1 10.63427162 -9.588768267 0.697682267 1.001014756 1.257142506 0.880809501 0.034819568 0.141418195 0.138835006 0.007888331 0.015232992 2.58E-10 9.588768267 0.25612775 LIEDTEDWRPR ddPTM_HeLa_Romidepsin_16h_R1 1 LIEDTEDWRPR 11 1 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4;Q96HC4-6;H0YBI4;Q96HC4-3;Q96HC4-2 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 0 0 206.73 1.63E-13 30797000 4091.3 4188.5 4049.3 4120.9 5026.8 5196.4 4323.4 4766.7 4670.7 4527.7 FALSE FALSE TRUE 4041.433662 4247.465813 4119.776368 4597.377847 4770.263638 4864.366811 4690.629488 4904.616944 4252.940894 4410.069701 0.916410383 0.963128953 0.934174888 1.042472831 1.081675339 1.103013589 1.063617994 1.112140459 0.964370448 1 12.10658574 -9.058201923 3.123046775 0.958015063 1.088502008 0.874946999 0.024083664 0.09041307 1.747149353 0.005159924 0.009229596 8.75E-10 9.058201923 0.130486945 LIEEDFPGIGDK ddPTM_HeLa_Romidepsin_16h_R1 1 LIEEDFPGIGDK 12 0 G5E971;P45452 G5E971 MMP13 Collagenase 3 0 0 134.05 0.02966 16623000 1966.8 1843.4 1929.6 1782.7 2274.8 2129.9 2007.9 2469.1 2333.3 2430.3 FALSE FALSE TRUE 1942.827885 1869.351434 1963.183879 1988.824162 2158.708468 1993.806264 2178.450976 2540.539513 2124.603804 2367.160456 0.820741949 0.789702037 0.829341278 0.840172941 0.911940068 0.842277615 0.920280233 1.073243475 0.897532653 1 11.20894179 -7.284153353 3.626373807 0.888806749 1.089777518 0.49409593 0.059664224 0.244560014 5.833856338 0.011604278 0.127837163 5.20E-08 7.284153353 0.200970768 LIEGGAHIYVCGDAR ddPTM_HeLa_Romidepsin_16h_R1 1 LIEGGAHIYVCGDAR 15 0 E7EMD0;P16435 E7EMD0 POR NADPH--cytochrome P450 reductase 0 0 128.35 0.023518 3968200 1076.6 1145.8 900.38 889.28 1095.7 938.76 1217.4 1224.7 1383.3 1095 FALSE FALSE TRUE 1063.477985 1161.930602 916.0507362 992.1027378 1039.78234 878.7762657 1320.805926 1260.134762 1259.574183 1066.551742 0.997118042 1.089427317 0.858890104 0.930196538 0.974900982 0.823941522 1.238388981 1.181503637 1.180978038 1 10.05873824 -7.739984621 24.99995826 0.979171585 1.20994652 0.463445888 0.098100414 118.0097652 137507.6826 0.010100712 0.037722185 1.82E-08 7.739984621 0.230774935 LIELQAGKK ddPTM_HeLa_Romidepsin_16h_R1 2 LIELQAGKK 9 1 K7ELL7;P14314-2;P14314;K7EPW7 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 0 ; ; 101.46 0.0021767 0 2471.7 2035.17 2610.7 2592.7 2886.7 2387.2 2239.3 2018.96 2305.1 1981.7 FALSE FALSE TRUE 2441.57397 2063.821177 2656.138138 2892.480173 2739.380927 2234.665624 2429.506086 2077.375422 2098.926083 1930.215148 1.264923225 1.069218205 1.376083977 1.498527341 1.419210148 1.157728778 1.258671132 1.076240348 1.087405248 1 10.91454595 -12.08424188 0.577336521 0.968923921 1.281082604 0.297394296 0.134739784 0.980638125 0.515108768 0.160591621 0.0338628 8.24E-13 12.08424188 0.312158683 LIES(ph)PFER ddPTM_HeLa_Romidepsin_16h_R1 3 LIESPFER 8 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 LIES(1)PFER;LIES(1)PFER;LIES(1)PFER ;; 130.66 0.010876 43544000 7579 6802.8 7033.1 7517.5 6468.6 7288 5431.4 5766.9 7205.1 7233.3 TRUE FALSE FALSE 7486.624233 6898.569997 7155.508155 8386.708721 6138.483204 6822.320321 5892.74298 5933.756153 6560.65781 7045.377823 1.062629205 0.979162533 1.015631572 1.190384523 0.871278072 0.968339881 0.836398434 0.842219722 0.931200281 1 12.78246136 -8.699297927 24.99995978 1.034951823 0.882816903 0.511129562 0.071866097 37.13163728 14937.97105 0.009167458 0.018334913 2.00E-09 8.699297927 -0.15213492 LIFAK(ac)PINSK ddPTM_HeLa_Romidepsin_16h_R1 1 LIFAKPINSK 10 1 Q6MZP7;Q6MZP7-3;D6REW4 Q6MZP7 LIN54 Protein lin-54 homolog 0 1 LIFAK(1)PINSK 132.01 0.0089333 995800 0 154.51 169.78 130.68 1225.3 1261.4 1141.9 1156.5 107.7 34.18 FALSE TRUE FALSE 0 156.6851958 172.7349497 145.7898365 1162.768369 1180.800611 1238.892957 1189.961503 98.06704226 33.29199867 0 4.706391989 5.188482415 4.379125384 34.92636114 35.46800006 37.21293425 35.74316804 2.945664008 1 5.05710358 -8.774350525 4.599928389 1.358176304 36.22750784 0.987345632 1.816536119 0.016609554 0.863009691 0.325330461 0.629186595 1.68E-09 8.774350525 34.86933154 LIFSTITSK ddPTM_HeLa_Romidepsin_16h_R1 1 LIFSTITSK 9 0 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 0 114.89 0.0042864 0 237.81 183.61 302.4 205.74 277.5 304.87 179.71 193.55 418.45 159.95 FALSE FALSE TRUE 234.9114802 186.1948664 307.6631451 229.5286268 263.3381395 285.3897909 194.9745629 199.1500639 381.022784 155.7944759 1.50782933 1.195131376 1.974801374 1.47327834 1.690291892 1.83183511 1.251485727 1.278287068 2.445675828 1 7.28350027 -12.03991594 0.581463633 0.945070166 1.551631827 0 0.510490032 0.811994769 0.444057496 0.257425663 0.057583841 9.12E-13 12.03991594 0.606561661 LIGQSCT(ph)APKIHMDCS(ph)NLT(ph)ALAT(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LIGQSCTAPKIHMDCSNLTALATSK 25 1 A0A0G2JM87;A0A0G2JR65;Q02817 A0A0G2JM87 MUC2 Mucin-2 5 0 LIGQS(0.13)CT(0.873)APKIHMDCS(0.999)NLT(1)ALAT(1)S(1)K 41.209 0.019087 4091400 287.29 176.06 297.75 199.28 139.26 194.92 162.03 296.89 192.69 364.45 TRUE FALSE FALSE 283.788399 178.5385773 302.9322138 222.3216912 132.1530425 182.4652411 175.7928242 305.4800437 175.4553238 354.9815365 0.79944552 0.502951728 0.853374564 0.626290859 0.372281454 0.514013328 0.49521681 0.860551923 0.494266055 1 8.471600178 -10.72624755 0.574738545 0.98474961 0.563316846 0 0.213294251 0.397366572 0.307360548 0.060708071 0.049357609 1.88E-11 10.72624755 -0.421432764 LIGTAVPQRT(ph)SPTGPK ddPTM_HeLa_Romidepsin_16h_R1 2 LIGTAVPQRTSPTGPK 16 1 C9JB30;Q9UPY8 C9JB30 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 0 LIGT(0.001)AVPQRT(0.479)S(0.479)PT(0.042)GPK;LIGTAVPQRT(0.497)S(0.497)PT(0.007)GPK ; 130.47 0.0083588 44451000 3396.6 3150.8 2834.8 4908.4 5315.8 4955 5091.8 5695.7 3475.3 3100.3 TRUE FALSE FALSE 3355.200933 3195.157045 2884.138505 5475.932303 5044.51489 4638.391492 5524.297365 5860.496093 3164.460464 3019.753759 1.111084281 1.058085294 0.955090625 1.813370473 1.670505376 1.536016464 1.8293867 1.94071986 1.047920035 1 11.5602152 -9.260244076 24.99998778 1.047662042 1.744772529 0.919569134 0.106924081 22.94691209 479937.1566 0.017160788 0.027455977 5.49E-10 9.260244076 0.697110487 LIHPDEDISLEER ddPTM_HeLa_Romidepsin_16h_R1 4 LIHPDEDISLEER 13 0 J3KS31;J3QRS9;X6R4W8;O43670-3;O43670-2;O43670;O43670-4 J3KS31 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 0 ;;; ;;; 229.56 1.94E-32 34862300 10752.8 10201.8 9640.8 8476.6 11421.9 11642.1 9189.8 10075.4 11370.5 10763.2 FALSE FALSE TRUE 10621.74074 10345.42121 9808.59408 9456.704376 10838.99782 10898.20738 9970.381383 10366.9158 10353.494 10483.57051 1.013179692 0.986822304 0.935615787 0.902049961 1.033903269 1.039551112 0.951048249 0.988872616 0.987592347 1 13.35584254 -10.0086986 24.25430016 1.005896233 0.975088072 0.069510083 0.039620842 489.3506612 1364457.977 0.00668958 0.008540967 9.80E-11 10.0086986 -0.03080816 LIHPDEDISLEERR ddPTM_HeLa_Romidepsin_16h_R1 1 LIHPDEDISLEERR 14 1 J3KS31;J3QRS9;X6R4W8;O43670-3;O43670-2;O43670;O43670-4 J3KS31 ZNF207 BUB3-interacting and GLEBS motif-containing protein ZNF207 0 0 110.64 0.0011282 4263500 844.95 850.64 603.89 1007.6 820.76 790.28 641.23 607.04 763 764.22 FALSE FALSE TRUE 834.6514244 862.6153322 614.4004521 1124.103453 778.8735545 739.7836585 695.6960602 624.6037446 694.755369 744.3654542 1.121292531 1.158859976 0.82540162 1.510149949 1.046359084 0.993844696 0.934616264 0.83910899 0.933352515 1 9.539867292 -7.78596006 1.947687875 1.081317338 0.856241852 0.184708954 0.16995811 0.464550873 3.230865654 0.022626328 0.129227543 1.64E-08 7.78596006 -0.225075486 LIHTLDDR ddPTM_HeLa_Romidepsin_16h_R1 2 LIHTLDDR 8 0 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;H7C3A1 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 0 0 ; ; 151.04 0.0031387 26101000 8258.9 6971.9 9159.5 6005.8 8013.7 9149.6 7229.6 8019.6 7384.2 7329.6 FALSE FALSE TRUE 8158.23735 7070.050591 9318.917255 6700.218854 7604.730986 8564.970089 7843.682044 8251.634473 6723.738658 7139.175935 1.142742163 0.990317462 1.305321138 0.938514321 1.065211315 1.199714108 1.098681713 1.155824502 0.941808791 1 12.80154184 -12.42189701 0.923956027 0.993372697 1.112614878 0.230438841 0.099546112 0.95491863 1.32100915 0.082763547 0.01670816 3.79E-13 12.42189701 0.119242181 LILEVHQFSR ddPTM_HeLa_Romidepsin_16h_R1 2 LILEVHQFSR 10 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ; ; 136.49 0.00066589 2956800 1338.93 1539.08 1224.85 912.2 1241.67 1389.27 1498.46 1198.16 1165.38 1007.03 FALSE FALSE TRUE 1322.610606 1560.747209 1246.168 1017.672856 1178.302947 1300.500131 1625.739155 1232.826869 1061.145494 980.8672154 1.348409433 1.591191126 1.270475739 1.037523571 1.20128691 1.325867671 1.657450804 1.256874376 1.081844186 1 9.937914035 -12.10422302 0.8574156 0.998039035 1.336684164 0.316499221 0.171295077 0.572962891 0.758383831 0.121689342 0.035311905 7.87E-13 12.10422302 0.338645129 LIMGIGHR ddPTM_HeLa_Romidepsin_16h_R1 2 LIMGIGHR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 0 0 ; ; 94.262 0.004093 4260300 2557.3 2624.3 4778.5 3076.7 4599.6 5591.8 3656.6 2707 2281.1 1370.64 FALSE FALSE TRUE 2526.130644 2661.244964 4861.667788 3432.44253 4364.865249 5234.502027 3967.191513 2785.322774 2077.072703 1335.030575 1.892189356 1.993396266 3.641615315 2.571059116 3.269487104 3.920885502 2.971610978 2.086336318 1.55582407 1 10.38265707 -10.38791686 0.795488924 1.210141762 3.131388206 0.612851264 0.55928215 0.236113382 0.310041028 0.14360898 0.158146073 4.09E-11 10.38791686 1.921246445 LINRPIIVFR ddPTM_HeLa_Romidepsin_16h_R1 1 LINRPIIVFR 10 1 Q16658;C9JPH9;C9JFC0;A0A0A0MSB2 Q16658 FSCN1 Fascin 0 0 126.24 0.0018301 4934300 662.38 758.96 702.7 437.77 687.02 718.1 444.8 488.65 427.92 232.36 FALSE FALSE TRUE 654.3066578 769.6446588 714.9301987 488.3870272 651.9588058 672.2157276 482.5813009 502.7883168 389.6457635 226.3232537 2.891027091 3.400643311 3.158889717 2.157918018 2.880653203 2.97015758 2.132265655 2.221549525 1.721633801 1 7.822241012 -8.807439723 22.81309761 2.161465524 2.551164422 0 0.71926239 166.2498178 82447.78622 0.145780803 0.264252005 1.56E-09 8.807439723 0.389698898 LIPGPLS(ph)PVAR ddPTM_HeLa_Romidepsin_16h_R1 2 LIPGPLSPVAR 11 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 0 LIPGPLS(1)PVAR;LIPGPLS(1)PVAR ; 144.7 0.0025112 626910000 14653.1 12713.4 12237.4 10451.5 10342.1 11008.7 9740.7 10246.3 12457.8 11530.2 TRUE FALSE FALSE 14474.50238 12892.37958 12450.38681 11659.95161 9814.304045 10305.2796 10568.07481 10542.76052 11343.54317 11230.64374 1.288839956 1.147964433 1.108608473 1.03822647 0.873886152 0.917603642 0.941003477 0.93874944 1.010052801 1 13.45515301 -9.05144188 2.546497925 1.139658466 0.919736521 0.551633134 0.079676212 0.195242289 2.509125618 0.016855128 0.03102967 8.88E-10 9.05144188 -0.219921945 LIPITGGNARS(ph)PEDQLGK ddPTM_HeLa_Romidepsin_16h_R1 1 LIPITGGNARSPEDQLGK 18 1 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 0 LIPIT(0.01)GGNARS(0.99)PEDQLGK 97.823 0.018601 23196000 1310.2 1056.8 866 1567.9 964.53 1059.8 824.08 702.08 1156 1240.2 TRUE FALSE FALSE 1294.230778 1071.677658 881.0723667 1749.187975 915.3064349 992.0822003 894.0773346 722.3935771 1052.604465 1207.979425 1.071401343 0.88716549 0.729376965 1.448027954 0.757716908 0.821274088 0.74014285 0.598018114 0.871376153 1 10.23838017 -8.564378484 24.99999778 1.026024517 0.733118258 0.340213282 0.18387327 105.0356608 63274.50523 0.024115772 0.048231578 2.73E-09 8.564378484 -0.292906259 LIPNATGTGTFS(ph)PGASPGSEAR ddPTM_HeLa_Romidepsin_16h_R1 1 LIPNATGTGTFSPGASPGSEAR 22 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 LIPNATGT(0.013)GT(0.13)FS(0.772)PGAS(0.054)PGS(0.03)EAR 104.82 0.00018598 12045000 1825.5 1588.7 1892.4 1983.6 2491.2 2265.7 1611.9 2035.1 2069.5 1798.7 TRUE FALSE FALSE 1803.250104 1611.06576 1925.336428 2212.953165 2364.064768 2120.929082 1748.814746 2093.982408 1884.398737 1751.969515 1.029270252 0.919574083 1.09895544 1.2631231 1.349375516 1.210597025 0.998199301 1.195216235 1.075588771 1 10.77476196 -9.514093106 6.180047967 1.007010619 1.19911613 0.519152231 0.089518409 0.099065956 15.86973167 0.014289044 0.021082005 3.06E-10 9.514093106 0.192105511 LIQNLDANHDGR ddPTM_HeLa_Romidepsin_16h_R1 2 LIQNLDANHDGR 12 0 Q96FQ6 Q96FQ6 S100A16 Protein S100-A16 0 0 ; ; 177.83 8.43E-07 17696900 8193.5 6850.3 7971 7225.3 8248.7 8050.1 7052.8 6957.3 7769.4 6154.7 FALSE FALSE TRUE 8093.63447 6946.738703 8109.731911 8060.723182 7827.738059 7535.724591 7651.864656 7158.598499 7074.485405 5994.800007 1.350109172 1.158794071 1.352794406 1.344619199 1.305754662 1.257043535 1.276417003 1.194134665 1.180103656 1 12.54949591 -12.36715856 0.915441694 0.986739479 1.285942867 0.398214471 0.08194292 0.251493493 0.349583781 0.053361907 0.011597804 4.29E-13 12.36715856 0.299203388 LIRPEYAWIVQPVSGAVY(ph)DRPGASPK ddPTM_HeLa_Romidepsin_16h_R1 1 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 G3V198;Q12769 G3V198 NUP160 Nuclear pore complex protein Nup160 1 0 LIRPEYAWIVQPVS(0.116)GAVY(0.504)DRPGAS(0.381)PK 52.79 0.0079184 263210000 1917.2 1989.4 1810.8 1712.3 1840 1854 1651.6 1710.5 1745.2 1622 TRUE FALSE FALSE 1893.832429 2017.406825 1842.316214 1910.284183 1746.097934 1735.535384 1791.886863 1759.990619 1589.104941 1579.860206 1.19873418 1.276952744 1.166126096 1.209147604 1.105223062 1.098537312 1.134205961 1.114016678 1.005851616 1 10.62558119 -12.28547585 1.051456396 1.001503765 1.164543867 0.595271561 0.052488341 0.316440603 0.635442669 0.037279597 0.010427204 5.18E-13 12.28547585 0.163040103 LIRPEYAWIVQPVSGAVYDRPGAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 LIRPEYAWIVQPVSGAVYDRPGASPK 26 2 G3V198;Q12769 G3V198 NUP160 Nuclear pore complex protein Nup160 1 0 LIRPEYAWIVQPVS(0.024)GAVY(0.018)DRPGAS(0.959)PK;LIRPEYAWIVQPVS(0.117)GAVY(0.285)DRPGAS(0.598)PK ; 74.062 9.50E-05 164557000 2650.5 2393.6 2205.4 2298.48 2487.7 2340.4 2151.31 2643 2663.1 2560 TRUE FALSE FALSE 2618.194687 2427.297164 2243.784062 2564.241072 2360.743386 2190.855993 2334.042218 2719.471035 2424.905666 2493.490831 1.050011756 0.973453415 0.899856552 1.028373973 0.946762409 0.878630058 0.936054061 1.090628047 0.972494318 1 11.28395118 -10.11471112 5.927398256 1.023452029 0.958688996 0.075354898 0.060555354 0.274045483 12.54622522 0.009645039 0.011862138 7.68E-11 10.11471112 -0.064763034 LIS(ph)DSVER ddPTM_HeLa_Romidepsin_16h_R1 1 LISDSVER 8 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 LIS(1)DSVER 117.01 0.019889 3386900 2265.8 2492.7 2247.5 2300 2234.5 2092.2 1810.6 2068.1 2416.3 2346.3 TRUE FALSE FALSE 2238.183558 2527.792296 2286.616795 2565.936822 2120.465127 1958.515172 1964.392319 2127.937211 2200.180076 2285.342788 0.979364483 1.106088903 1.000557469 1.122779845 0.927854298 0.856989675 0.859561344 0.931123866 0.962735257 1 11.15819486 -8.533007438 24.99559718 1.009482404 0.882285817 0.596877674 0.053826139 114.3305479 282144.5013 0.007721222 0.015456149 2.93E-09 8.533007438 -0.127196587 LIS(ph)PLAS(ph)PADGVK ddPTM_HeLa_Romidepsin_16h_R1 1 LISPLASPADGVK 13 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 2 0 LIS(1)PLAS(1)PADGVK 118.52 0.0016366 0 2736.7 2769.7 2282.4 2260.9 2611.9 3427.9 2794.7 2992.3 2790.3 2652.7 TRUE FALSE FALSE 2703.344048 2808.691909 2322.124215 2522.315896 2478.604997 3208.868253 3032.081748 3078.877479 2540.72858 2583.782472 1.046273855 1.087046584 0.898730539 0.976210623 0.959293216 1.241926628 1.173505038 1.191616366 0.983336874 1 11.3352689 -8.259782959 24.99996178 1.010745384 1.19946492 0.769682935 0.051842703 58.06762755 876390.8963 0.00765479 0.018450957 5.50E-09 8.259782959 0.188719536 LISDS(ph)VER ddPTM_HeLa_Romidepsin_16h_R1 1 LISDSVER 8 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 LIS(0.119)DS(0.881)VER 120.99 0.018437 3607100 2287.2 2688.9 2309.5 1789.1 1696.1 2047 1694.8 1855.1 2121 2375 TRUE FALSE FALSE 2259.322727 2726.754405 2349.695879 1995.96416 1609.541688 1916.203306 1838.75627 1908.774392 1931.292448 2313.297158 0.976667749 1.178730712 1.015734564 0.862822207 0.695778181 0.828342913 0.794863843 0.825131516 0.834865699 1 11.17573489 -9.123321202 3.881013579 1.007554464 0.788739366 0.588196434 0.085150933 0.100029911 2.645138493 0.01035345 0.017729225 7.53E-10 9.123321202 -0.218815098 LISS(ph)VEDFTEFV ddPTM_HeLa_Romidepsin_16h_R1 2 LISSVEDFTEFV 12 0 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4 P49815 TSC2 Tuberin 1 0 LIS(0.058)S(0.942)VEDFTEFV;LIS(0.004)S(0.996)VEDFTEFV ; 180.07 4.18E-07 641690 598.31 603.82 601.05 485.03 635.43 786.49 842.89 815.56 407.16 798.54 TRUE FALSE FALSE 591.0175676 612.3205938 611.5110231 541.1114507 603.001636 736.2358273 914.4850556 839.1569419 370.7425898 777.7938157 0.759864061 0.787253102 0.786212246 0.695700377 0.775271831 0.946569402 1.175742256 1.078893821 0.476659215 1 9.603243954 -7.928052868 4.266507572 0.847891773 1.124470424 0.440197649 0.144926978 0.137995529 4.876832843 0.016751267 0.053810685 1.18E-08 7.928052868 0.276578651 LISWYDNEFGYS(ph)NR ddPTM_HeLa_Romidepsin_16h_R1 1 LISWYDNEFGYSNR 14 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 LISWYDNEFGYS(1)NR 97.2 0.012547 9711000 689.63 955.7 865.4 566.43 748.71 908.83 811.53 937.22 826.62 694.34 TRUE FALSE FALSE 681.2245243 969.1543697 880.461924 631.9233017 710.5005349 850.7586961 880.4613379 964.336982 752.6850369 676.3009467 1.007280158 1.433022347 1.301878887 0.934381809 1.050568594 1.257958754 1.301878021 1.425899205 1.112943935 1 9.401521563 -4 0.179974348 0.959894053 2.752088077 0.212043079 0.154774474 47.11781724 0.511532147 0.207318903 23.23373379 1.00E-04 4 1.792194024 LISWYDNEFGYSNR ddPTM_HeLa_Romidepsin_16h_R1 5 LISWYDNEFGYSNR 14 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ;;;; ;;;; 362 1.51E-249 2069291570 9340.12 8791.04 8363.47 6352.53 9708.31 9302.99 8266.22 8032.8 8207.08 7852.66 FALSE FALSE TRUE 9226.279025 8914.800492 8509.032687 7087.039408 9212.858714 8708.558963 8968.35252 8265.216394 7473.01821 7648.646761 1.206262926 1.165539575 1.112488647 0.926574286 1.204508327 1.138575128 1.172541078 1.080611597 0.977037958 1 12.90098881 -12.55076607 1.337563154 1.000443738 1.134965552 0.323971588 0.077550677 0.45803722 1.475884518 0.055044259 0.013214262 2.81E-13 12.55076607 0.134521814 LITPPPPPPS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 4 LITPPPPPPSPER 13 0 J3QKY4;J3QR53;Q96HE9 J3QKY4 PRR11 Proline-rich protein 11 1 0 LITPPPPPPS(1)PER;LITPPPPPPS(1)PER;LIT(0.001)PPPPPPS(0.999)PER;LITPPPPPPS(1)PER ;;; 150.9 0.00076859 38011300 7451 7613.9 7249.7 6450 6604.1 6941.3 5890.35 6193.9 8440.5 7802 TRUE FALSE FALSE 7360.184346 7721.088684 7375.877987 7195.779348 6267.068134 6497.773332 6390.676182 6373.110724 7685.56054 7599.302915 0.968534144 1.016025913 0.970599286 0.946899923 0.82468987 0.855048602 0.840955579 0.838644122 1.011350729 1 12.89165137 -8.893118142 3.306428412 0.986025185 0.84055 0.94450627 0.017509391 0.040316903 0.874126246 0.002637924 0.005029431 1.28E-09 8.893118142 -0.145475185 LIVAYVDDLDRR ddPTM_HeLa_Romidepsin_16h_R1 2 LIVAYVDDLDRR 12 1 O14776-2;O14776 O14776-2 TCERG1 Transcription elongation regulator 1 0 0 ; ; 152.64 0.00092236 20254600 6209.4 6025.1 6230.2 6035.3 6296.4 6319.5 5141.5 5419.1 6237 5235.4 FALSE FALSE TRUE 6133.717444 6109.921516 6338.634018 6733.129783 5975.071213 5915.704345 5578.218882 5575.893109 5679.147099 5099.383553 1.202835084 1.198168652 1.243019661 1.320381123 1.171724219 1.16008225 1.09390063 1.093444541 1.113692869 1 12.31610714 -12.16097728 0.872085239 0.997925315 1.187992267 0.295363786 0.071516875 0.404427235 0.545798816 0.049515756 0.01360962 6.90E-13 12.16097728 0.190066953 LK(ac)LSEELSGGR ddPTM_HeLa_Romidepsin_16h_R1 1 LKLSEELSGGR 11 1 P61158;B4DXW1 P61158 ACTR3 Actin-related protein 3 0 1 LK(1)LSEELSGGR 136.96 0.0047139 565610 235.88 218.42 137.49 120.71 344 227.25 254.38 325.78 335.25 267.54 FALSE TRUE FALSE 233.0050038 221.4949225 139.8829558 134.6670582 326.4443964 212.7294584 275.9870309 335.2059303 305.2644004 260.5892722 0.89414657 0.849977133 0.53679476 0.516778979 1.252716175 0.816340046 1.059088229 1.286338181 1.171438861 1 8.025633883 -7.223863561 1.534391716 0.893386347 1.471634693 0.240647597 0.223231877 1.365072125 2.7382569 0.031030542 1.218460079 5.97E-08 7.223863561 0.578248345 LK(ac)RKLSLSFLNYGMNCK ddPTM_HeLa_Romidepsin_16h_R1 1 LKRKLSLSFLNYGMNCK 17 3 F2Z3I8 F2Z3I8 ARMT1 0 1 LK(0.974)RK(0.026)LSLSFLNYGMNCK 56.599 0.021051 0 0 0 0 59.433 0 238.8 283.38 270.53 161.54 70.961 FALSE TRUE FALSE 0 0 0 66.3049231 0 223.5414507 307.4502901 278.3573587 147.0914578 69.11742299 0 0 0 0.95930838 0 3.234227218 4.448231384 4.027311012 2.128138629 1 6.110977523 -8.139360281 3.653490995 0.438314354 4.17904715 0.840328046 0.668166887 0.046758222 1.120036007 0.070695233 0.197258277 7.26E-09 8.139360281 3.740732796 LKAT(ph)VTPSPVKGK ddPTM_HeLa_Romidepsin_16h_R1 1 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 LKAT(0.896)VT(0.011)PS(0.092)PVKGK 134.04 0.0024115 22957000 983.52 1577.4 829.92 1324.7 451.2 552.94 446.79 394.12 1056.4 1014.2 TRUE FALSE FALSE 971.5324799 1599.606679 844.3644095 1477.868047 428.1735803 517.6089185 484.7403314 405.5232404 961.9129382 987.8509378 0.98348085 1.619279405 0.854748806 1.496043573 0.433439463 0.52397472 0.490701899 0.410510559 0.973743003 1 9.948149552 -8.733610838 24.99550618 1.064310413 0.470753641 0.659116294 0.237786505 110.9270264 99633.82457 0.03320409 0.06639679 1.85E-09 8.733610838 -0.593556771 LKATVTPS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 LKATVTPSPVK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 LKATVT(0.003)PS(0.997)PVK 90.498 0.012329 424360000 13587 11525 24069 8329.8 9760.6 10161 7623.9 5320.6 13444 8497.1 TRUE FALSE FALSE 13421.39642 11687.24925 24487.91085 9292.930669 9262.48016 9511.744893 8271.473876 5474.543166 12241.53497 8276.344117 1.62165761 1.412127032 2.958783553 1.122830387 1.119151165 1.149268899 0.999411547 0.66146877 1.479099322 1 13.01477792 -9.018794388 24.98514499 1.45209365 1.011159948 0.250453199 0.515629696 1261.321218 1676792.054 0.08559262 0.143548183 9.58E-10 9.018794388 -0.440933701 LAGTSGSDK(ac)GLSGK ddPTM_HeLa_Romidepsin_16h_R1 2 LAGTSGSDKGLSGK 14 1 Q9P016-2;Q9P016 Q9P016-2 THYN1 Thymocyte nuclear protein 1 0 1 ; LAGTSGSDK(1)GLSGK;LAGTSGSDK(1)GLSGK 238.07 4.38E-43 3653700 953.33 769.65 752.42 974.53 2191.2 1978.28 1777.32 2157.5 738.61 749.88 FALSE TRUE FALSE 941.7104473 780.4851529 765.5155545 1087.209744 2079.374888 1851.874293 1928.285516 2219.923859 672.5468717 730.3980095 1.289311355 1.068575137 1.048080012 1.488516849 2.846906564 2.535431735 2.640047606 3.039334486 0.92079505 1 9.512539023 -8.848119079 3.876961133 1.132310107 2.746355421 0.959296216 0.165733687 0.03203182 0.924775337 0.025179935 0.047864458 1.42E-09 8.848119079 1.614045314 up LKDDEVAQLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 1 ; LKDDEVAQLK(1)K;LKDDEVAQLK(1)K 185.3 1.04E-05 26729000 6588.5 6449.4 7118.8 5311.7 15671.5 12714.1 12125.5 13251.3 15862.9 11902.9 FALSE TRUE FALSE 6508.196828 6540.194822 7242.699728 5925.863746 14871.72488 11901.71004 13155.43967 13634.70546 14444.08249 11593.66094 0.561358216 0.564118172 0.624712053 0.51112964 1.282746231 1.026570477 1.134709712 1.176048319 1.245860351 1 13.50104858 -8.753818749 24.99998679 0.737357449 1.144393196 0.444791475 0.220574655 118.9569269 390242.7596 0.030468253 0.060014912 1.76E-09 8.753818749 0.407035747 LKDDEVAQLKK ddPTM_HeLa_Romidepsin_16h_R1 1 LKDDEVAQLKK 11 2 A0A5F9ZHM4;P07195 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain 0 0 63.864 0.030352 30259000 2437.8 2431 2052.1 2783.1 2160.9 2338.8 2372.9 1960.1 2726.4 2194.8 FALSE FALSE TRUE 2408.087156 2465.223682 2087.81594 3104.895117 2050.62121 2189.358228 2574.454067 2016.812401 2482.543956 2137.77878 1.126443568 1.153170621 0.97662862 1.452393085 0.959229846 1.024127589 1.204265891 0.943414922 1.161272616 1 11.06189685 -6.068706041 20.35830806 1.081023306 1.10315421 0 0.148755604 0 0 0.017987112 0 8.54E-07 6.068706041 0.022130903 LKDIGPEVVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LKDIGPEVVKK 11 2 A0A2R8YD50;P51659-3;P51659;P51659-2;E7EPL9;A0A2R8Y7L2;E7ET17 A0A2R8YD50 HSD17B4 Peroxisomal multifunctional enzyme type 2;(3R)-hydroxyacyl-CoA dehydrogenase;Enoyl-CoA hydratase 2 0 1 LKDIGPEVVK(1)K 81.565 0.026184 0 361.63 288.17 468.84 294.17 476.65 471.1 458.01 436.78 441.1 387.76 FALSE TRUE FALSE 357.2223145 292.2268648 476.9999635 328.1833195 452.3247719 440.9982304 496.913358 449.4175402 401.6469112 377.6859393 0.94581841 0.773729796 1.262953989 0.868931791 1.197621422 1.16763211 1.315678733 1.189923938 1.063441525 1 8.561043265 -8.676428072 6.885414739 0.974721098 1.224260914 0.449939625 0.125343669 0.13407167 9.064632035 0.016383144 0.032870838 2.11E-09 8.676428072 0.249539815 LKDLEALLNSK ddPTM_HeLa_Romidepsin_16h_R1 1 LKDLEALLNSK 11 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 99.844 0.00341 0 4773.7 4126.1 4509.2 5037.1 5414.9 4969.3 4512.7 5378.4 5551.2 5003.1 FALSE FALSE TRUE 4715.516308 4184.187344 4587.680734 5619.513202 5138.557447 4651.777768 4896.008625 5534.015518 5054.686769 4873.118741 0.967658815 0.858626183 0.94142601 1.153165663 1.054469985 0.954579196 1.004697174 1.135620906 1.037259102 1 12.25062966 -9.313366381 24.99996076 0.969923663 1.051186202 0.334127601 0.069048538 366.8528932 176618.4185 0.010644881 0.016260328 4.86E-10 9.313366381 0.081262539 LKDLFDYS(ph)PPLHK ddPTM_HeLa_Romidepsin_16h_R1 2 LKDLFDYSPPLHK 13 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 LKDLFDY(0.021)S(0.979)PPLHK;LKDLFDYS(1)PPLHK ; 115.87 0.0020906 2918900000 25797.1 25055 24736.8 23411.2 24467.2 24275.2 21616.1 23616.4 25812 26282.2 TRUE FALSE FALSE 25482.67502 25407.72495 25167.33363 26118.1131 23218.54748 22724.09306 23452.17099 24299.70327 23503.31007 25599.38466 0.99544092 0.992513113 0.983122601 1.020263317 0.906996312 0.887681222 0.91612245 0.949229976 0.918120118 1 14.64382151 -8.754506584 24.96669412 0.997526446 0.913135236 0.54276898 0.030104408 40.55856214 146059.9696 0.002345754 0.004611621 1.76E-09 8.754506584 -0.08439121 LKDLFDYSPPLHK ddPTM_HeLa_Romidepsin_16h_R1 1 LKDLFDYSPPLHK 13 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 0 0 95.417 0.0068523 7903900 15680 15717 15354 15096 16488 15921 14465 15493 16900 15460 FALSE FALSE TRUE 15488.88613 15938.26434 15621.22993 16841.47055 15646.55583 14903.69948 15693.65674 15941.26551 15388.42167 15058.34697 1.028591396 1.058433862 1.037380129 1.118414297 1.039061981 0.989730115 1.042189874 1.058633165 1.021919717 1 13.87827579 -11.02542832 0.98298361 1.005559455 1.048085296 0.186438891 0.030493294 0.483249303 0.991281997 0.008871426 0.00690831 9.43E-12 11.02542832 0.042525841 LKDYAFIHFDER ddPTM_HeLa_Romidepsin_16h_R1 2 LKDYAFIHFDER 12 1 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 ; ; 97.69 0.0072589 50198000 23676 22296 24964 22427 24036 23644 20561.4 20584.7 23252 18975.6 FALSE FALSE TRUE 23387.42781 22609.88367 25398.48795 25020.11526 22809.35323 22133.22471 22307.8848 21180.28582 21172.28288 18482.61118 1.265374658 1.223305704 1.374182885 1.353711065 1.234097986 1.197516114 1.206966082 1.145957442 1.145524444 1 14.17388097 -12.13705818 0.805373962 0.993144486 1.253850001 0.40473761 0.078582431 0.34038029 0.383925619 0.055012017 0.014445481 7.29E-13 12.13705818 0.260705515 LKDYAFVHFEDR ddPTM_HeLa_Romidepsin_16h_R1 2 LKDYAFVHFEDR 12 1 B4DT28;O43390-3;O43390;O43390-4;O43390-2 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 0 ; ; 93.649 0.0094254 61861000 28889 26632 29651 26681 26947 26052 23833 23475 29208 24387 FALSE FALSE TRUE 28536.88976 27006.926 30167.06322 29765.98276 25571.79404 24387.36128 25857.37443 24154.21209 26595.56333 23753.42222 1.201380142 1.136969896 1.270009135 1.25312397 1.076551993 1.026688325 1.088574698 1.016872931 1.119651858 1 14.53584776 -8.533436854 24.77310009 1.126836129 1.049018543 0.267490926 0.078321336 339.6207921 796869.4614 0.015396693 0.030819254 2.93E-09 8.533436854 -0.077817586 LKEDILENEDEQNS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 4 LKEDILENEDEQNSPPK 17 1 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK;LKEDILENEDEQNS(1)PPK ;;; 131.09 0.00072758 196216000 26711.1 27552.3 29455.4 20993.9 19794.2 19542.6 17545.3 19200 30567.3 28004.3 TRUE FALSE FALSE 26385.53484 27940.182 29968.05888 23421.3135 18784.02811 18293.89093 19035.59734 19755.52171 27833.28413 27276.74425 0.967327134 1.024322469 1.098667004 0.858655024 0.688646267 0.670677217 0.697869114 0.724262453 1.020403457 1 14.73538383 -8.946525765 3.561980385 0.995509264 0.694457126 0.937585584 0.039379177 0.043763281 1.147420844 0.006221557 0.011563687 1.13E-09 8.946525765 -0.301052138 LKEDILENEDEQNS(ph)PPKK ddPTM_HeLa_Romidepsin_16h_R1 2 LKEDILENEDEQNSPPKK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 LKEDILENEDEQNS(1)PPKK;LKEDILENEDEQNS(1)PPKK ; 70.783 0.008399 118670000 10928.7 10910.8 11008.5 8023.8 8500.8 7060.3 6282.3 7270.4 11468.1 10815.7 TRUE FALSE FALSE 10795.4968 11064.40253 11200.09832 8951.549509 8066.972455 6609.169616 6815.918405 7480.757553 10442.36441 10534.70655 1.02475534 1.050281037 1.06316187 0.849719872 0.765751985 0.627371022 0.646996513 0.710105926 0.991234484 1 13.36286251 -8.868238462 1.917213435 1.018935284 0.664425738 0.948766294 0.037242289 0.048379039 0.3605336 0.005645161 0.011949174 1.35E-09 8.868238462 -0.354509546 LKFS(ph)DDEEEEEVVK ddPTM_HeLa_Romidepsin_16h_R1 1 LKFSDDEEEEEVVK 14 1 Q5JSZ5;Q5JSZ5-5 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 LKFS(1)DDEEEEEVVK 70.615 0.020732 26947000 4597 4950.7 4981 4070.7 4405.7 3847.9 3140.2 3014.8 5105.7 5347.1 TRUE FALSE FALSE 4540.969996 5020.396085 5067.692216 4541.373487 4180.860689 3602.031609 3406.92851 3102.028481 4649.033405 5208.181571 0.871891645 0.963944136 0.973025258 0.871969117 0.802748643 0.691610221 0.654149335 0.595606823 0.892640424 1 12.34656403 -8.385413481 1.1237232 0.943525952 0.605563653 0.920349573 0.037913152 0.136786323 0.311234319 0.0080354 0.033535801 4.12E-09 8.385413481 -0.337962298 LKLSILYPATTGR ddPTM_HeLa_Romidepsin_16h_R1 1 LKLSILYPATTGR 13 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 0 86.262 0.029186 0 1146.3 1146.9 909.39 1581.9 952.49 957.01 561.15 1072.3 1077.7 1060.6 FALSE FALSE TRUE 1132.328455 1163.046088 925.2175515 1764.806721 903.8808811 895.8601496 608.814067 1103.325309 981.3078129 1033.045459 1.096107093 1.125842119 0.895621333 1.708353399 0.874967189 0.867203027 0.589339086 1.06803171 0.949917358 1 10.01268803 -8.548419803 24.99998137 1.09048321 0.825435201 0.239883218 0.237760713 238.5731441 233518.1754 0.03214442 0.064290431 2.83E-09 8.548419803 -0.265048009 LKLSPS(ph)PSSR ddPTM_HeLa_Romidepsin_16h_R1 1 LKLSPSPSSR 10 1 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 0 LKLS(0.09)PS(0.884)PS(0.026)SR 148.13 0.025595 399110000 5027.9 4659 5071.2 4307 3627.1 3316.7 3226.1 3226 4468.3 3882.6 TRUE FALSE FALSE 4966.618021 4724.589524 5159.462109 4804.995605 3441.995552 3104.773574 3500.124853 3319.33922 4068.644057 3781.729492 1.313319218 1.249319798 1.364312841 1.27058152 0.9101644 0.820993035 0.925535489 0.877730474 1.075868611 1 11.88483046 -8.707419901 7.223965367 1.185445637 0.879882235 0.694289456 0.105976475 0.141590856 15.46374813 0.021071803 0.042133889 1.96E-09 8.707419901 -0.305563402 LKNDMAVPT(ph)PPPPPVPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 LKNDMAVPTPPPPPVPPTK 19 1 G3V1P5;Q96RN5-3;Q96RN5-2;Q96RN5 G3V1P5 MED15 Mediator of RNA polymerase II transcription subunit 15 1 0 LKNDMAVPT(1)PPPPPVPPTK 62.468 0.016128 19358000 2657.8 2378.2 2181.4 2602.8 2859.3 3423.2 2659.3 3100.7 2623 2425.7 TRUE FALSE FALSE 2625.405711 2411.680362 2219.366352 2903.747983 2713.379251 3204.468568 2885.180876 3190.413862 2388.392311 2362.679964 1.111198195 1.020739329 0.939342774 1.229006055 1.148432836 1.356285496 1.221147561 1.350336868 1.010882704 1 11.20620851 -8.812173629 1.596293141 1.044644823 1.294811241 0.72732467 0.073323607 0.160475944 0.826090878 0.011591024 0.026888234 1.54E-09 8.812173629 0.250166418 LKPGGVGAPSSS(ph)SPSPSPSAR ddPTM_HeLa_Romidepsin_16h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 0 LKPGGVGAPSS(0.005)S(0.981)S(0.013)PS(0.001)PSPSAR 143.47 1.06E-05 80312000 5898.8 6038.2 6754.9 4653.5 5186.4 5596.7 4864.8 5430.3 6545.1 6717.5 TRUE FALSE FALSE 5826.903157 6123.205938 6872.466201 5191.559565 4921.718655 5239.088933 5278.015991 5587.417163 5959.689863 6542.978382 0.890558216 0.935843828 1.050357467 0.7934551 0.752213804 0.800719279 0.806668719 0.853956232 0.910852752 1 12.67573179 -9.237153894 24.68784347 0.952829445 0.798924489 0.725785553 0.047925495 314.4529265 319663.005 0.008333604 0.013815245 5.79E-10 9.237153894 -0.153904956 LKPGGVGAPSSSSPSPS(ph)PSAR ddPTM_HeLa_Romidepsin_16h_R1 1 LKPGGVGAPSSSSPSPSPSAR 21 1 Q92797 Q92797 SYMPK Symplekin 1 0 LKPGGVGAPSS(0.001)S(0.053)S(0.018)PS(0.254)PS(0.425)PS(0.249)AR 136.22 6.72E-05 104530000 2523.6 2419.9 2554.1 2093.3 1829.8 2063.9 1516.9 1935.1 2375.7 2788 TRUE FALSE FALSE 2492.841393 2453.967416 2598.553039 2335.337195 1736.418478 1932.023451 1645.745448 1991.089065 2163.211442 2715.567358 0.917981793 0.903666561 0.956909808 0.859981318 0.639431194 0.711462172 0.606041107 0.733212918 0.796596496 1 11.40703793 -8.919401691 3.192975397 0.95414305 0.669837501 0.744500272 0.065326718 0.056416655 1.160155852 0.007105187 0.013469506 1.20E-09 8.919401691 -0.284305549 LKPTNPAAQK(ac)ALTTPTHYK ddPTM_HeLa_Romidepsin_16h_R1 1 LKPTNPAAQKALTTPTHYK 19 2 P52948-6;P52948-2;P52948-5;P52948;A0A3B3ITD8;P52948-4;P52948-3;H0YEN4;H0YCR0 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 0 1 LK(0.007)PTNPAAQK(0.993)ALTTPTHYK 59.585 0.015722 1238700 389.95 321.45 336.76 352.64 578.61 589.96 654.52 458.62 634.34 378.01 FALSE TRUE FALSE 385.1971394 325.9753815 342.6211665 393.413896 549.0813726 552.26346 710.1149125 471.8894461 577.6030417 368.1892457 1.046193347 0.885347373 0.930557235 1.068510014 1.491302038 1.49994457 1.928668262 1.281649183 1.568766737 1 8.524303678 -8.726377269 2.899571853 1.002485316 1.596143884 0.467162462 0.236742222 0.085973043 1.477021892 0.021095389 0.043951895 1.88E-09 8.726377269 0.593658567 LKS(ph)EDGVEGDLGETQSR ddPTM_HeLa_Romidepsin_16h_R1 7 LKSEDGVEGDLGETQSR 17 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 LKS(1)EDGVEGDLGETQSR;LKS(0.997)EDGVEGDLGET(0.003)QSR;LKS(0.996)EDGVEGDLGET(0.004)QSR;LKS(0.545)EDGVEGDLGET(0.455)QSR;LKS(0.996)EDGVEGDLGET(0.004)QSR;LKS(1)EDGVEGDLGETQSR;LKS(1)EDGVEGDLGETQSR ;;;;;; 195.45 6.88E-13 429972300 8781.73 9397.31 7968.56 9355.78 11631.74 12595.21 11105.51 14949.73 9488.59 9244.96 TRUE FALSE FALSE 8674.694897 9529.605577 8107.249444 10437.5393 11038.1289 11790.41673 12048.81174 15382.27685 8639.906746 9004.774606 0.963343923 1.058283632 0.900327859 1.159111667 1.225808461 1.309351677 1.33804701 1.708235633 0.959480623 1 13.13647445 -5.962334137 0.435417858 0.973528027 3.628978583 0.916900224 0.067056758 2.469959074 0.135045396 0.015061645 4.368867707 1.09E-06 5.962334137 2.655450556 LKSPVLSNTTTEPAS(ph)TMSPPPAK ddPTM_HeLa_Romidepsin_16h_R1 2 LKSPVLSNTTTEPASTMSPPPAK 23 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 0 LKSPVLSNTTTEPAS(0.435)T(0.435)MS(0.13)PPPAK;LKSPVLSNT(0.002)T(0.006)T(0.022)EPAS(0.703)T(0.133)MS(0.133)PPPAK ; 92.289 0.00012018 27541000 5169.4 5671.3 5035.5 5039.3 3925.6 3660.4 3112.7 3440 5332.3 5493.3 TRUE FALSE FALSE 5106.393364 5751.14071 5123.140765 5621.967577 3725.261984 3426.512253 3377.09266 3539.530973 4855.365733 5350.583274 0.954362002 1.074862387 0.957492016 1.050720508 0.696234745 0.640399762 0.631163461 0.661522453 0.907446064 1 12.38548045 -8.695634662 5.544378806 0.988680316 0.648681324 0.924773648 0.046669873 0.031784149 1.844555803 0.005749926 0.011556346 2.02E-09 8.695634662 -0.339998992 LKSPVLSNTTTEPAS(ph)TMSPPPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 LKSPVLSNTTTEPASTMSPPPAKK 24 2 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 0 LKS(0.005)PVLS(0.023)NT(0.054)T(0.054)T(0.054)EPAS(0.303)T(0.254)MS(0.254)PPPAKK 45.395 0.017685 19334000 2812 2464.1 2152.1 2403.9 1915.3 1504.9 1144.9 1222.7 2453.3 2517.1 TRUE FALSE FALSE 2777.726262 2498.789664 2189.556398 2681.850229 1817.555094 1408.741747 1242.147777 1258.076895 2233.870704 2451.705379 1.132977186 1.019204708 0.893074843 1.093871332 0.741343193 0.57459667 0.50664643 0.513143588 0.911149734 1 11.25956991 -8.521675157 1.967321326 1.050962925 0.514454078 0.873965728 0.080486406 0.069873815 0.534747084 0.011506442 0.029757418 3.01E-09 8.521675157 -0.536508847 LKTEEGEIDYS(ph)AEEGENRR ddPTM_HeLa_Romidepsin_16h_R1 1 LKTEEGEIDYSAEEGENRR 19 2 B7WPG3;V9GYK2;Q8WVV9-2;Q8WVV9-5;Q8WVV9;C9IYN3;Q8WVV9-3;Q8WVV9-4 B7WPG3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 0 LKTEEGEIDY(0.089)S(0.911)AEEGENRR 71.202 0.013829 4780000 631.23 510.64 491.61 631.63 626.53 805.15 565.41 547.25 620.1 698.59 TRUE FALSE FALSE 623.536326 517.8288033 500.1662658 704.6620325 594.5558362 753.7035135 613.4359113 563.0838153 564.6367029 680.4405311 0.916371523 0.761019927 0.735062423 1.035596794 0.873780748 1.107669927 0.901527589 0.827528328 0.829810508 1 9.410325269 -11.60948236 1.149776679 0.98876208 0.899078207 0 0.118192511 0.750989363 2.000803631 0.036925186 0.021218896 2.46E-12 11.60948236 -0.089683873 LKVGLQVVAVK ddPTM_HeLa_Romidepsin_16h_R1 1 LKVGLQVVAVK 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 160.53 1.21E-20 0 334.61 276.79 289.96 466.34 330.44 388.36 291.89 289.69 317.12 218.87 FALSE FALSE TRUE 330.5316446 280.6866569 295.0066322 520.260425 313.5764138 363.5450494 316.6831293 298.0717231 288.755993 213.1837258 1.550454395 1.316642046 1.383814036 2.440432181 1.470920974 1.70531333 1.485493923 1.398191733 1.354493603 1 7.735953499 -12.01057706 0.479686419 0.900827569 1.640768559 0.194346404 0.318319843 1.218315186 0.437576814 0.424263028 0.088190789 9.76E-13 12.01057706 0.739940991 LKVPEWVDTVK ddPTM_HeLa_Romidepsin_16h_R1 1 LKVPEWVDTVK 11 1 M0R2L9;M0QYF7;M0R140;P39019 M0R2L9 RPS19 40S ribosomal protein S19 0 0 125.54 0.008618 9659300 4835.7 5314.7 4359.4 4155.3 5072.2 4608.1 4004.2 4308.4 5149.3 4321.8 FALSE FALSE TRUE 4776.760628 5389.520486 4435.273528 4635.755337 4813.346707 4313.657282 4344.316648 4433.056756 4688.733711 4209.519013 1.134752121 1.280317411 1.053629527 1.101255351 1.143443394 1.024738757 1.032022099 1.053102918 1.113840725 1 12.03943968 -8.219401777 24.89052029 1.088397663 1.036161325 0.129235348 0.072306451 1073.387006 635553.224 0.012161948 0.031006585 6.03E-09 8.219401777 -0.052236338 LLAEVTLK ddPTM_HeLa_Romidepsin_16h_R1 1 LLAEVTLK 8 0 K7ER16;K7ER00;Q9Y285;K7EPH2 K7ER16 FARSA Phenylalanine--tRNA ligase alpha subunit 0 0 117.16 0.015601 214110 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 LLAS(ph)PSSR ddPTM_HeLa_Romidepsin_16h_R1 2 LLASPSSR 8 0 Q15003;E9PHA2;C9JZP1;C9J470 Q15003 NCAPH Condensin complex subunit 2 1 0 LLAS(0.788)PS(0.212)SR;LLAS(0.977)PS(0.021)S(0.002)R ; 117.81 0.019598 31088000 13284.1 13731.5 12827.2 9470.2 14045.1 16669.1 13022.4 15090.2 14642.3 13709.9 TRUE FALSE FALSE 13122.18828 13924.81242 13050.45204 10565.18908 13328.32614 15603.99831 14128.52233 15526.81113 13332.65602 13353.71482 0.982662012 1.042766946 0.977290006 0.791179775 0.998098755 1.168513669 1.05802187 1.162733467 0.998423 1 13.70495352 -8.336655087 6.531030283 0.978999308 1.122204637 0.523185188 0.069490278 0.15732304 11.29940086 0.009981021 0.022545101 4.61E-09 8.336655087 0.143205329 LLAS(ph)SPALPSSGAQAR ddPTM_HeLa_Romidepsin_16h_R1 4 LLASSPALPSSGAQAR 16 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 0 LLAS(0.5)S(0.5)PALPSSGAQAR;LLAS(0.549)S(0.451)PALPSSGAQAR;LLAS(0.897)S(0.103)PALPSSGAQAR;LLAS(0.5)S(0.5)PALPSSGAQAR ;;; 238.88 4.47E-46 95993000 12466.1 11831.8 10355.8 10427.5 12647.2 12380.6 10117.4 11431.7 11533.2 11162.5 TRUE FALSE FALSE 12314.15838 11998.36839 10536.03835 11633.17661 12001.76619 11589.51962 10976.7717 11762.4582 10501.64171 10872.49664 1.13259712 1.103552274 0.969054184 1.069963689 1.103864787 1.065948328 1.009590719 1.081854388 0.965890545 1 13.40839564 -12.67875864 1.561421997 1.000220214 1.075352526 0.309356773 0.047024584 0.464877937 2.050917237 0.035444363 0.008004769 2.10E-13 12.67875864 0.075132313 LLDEDEIR ddPTM_HeLa_Romidepsin_16h_R1 1 LLDEDEIR 8 0 O43719;Q5H919;Q5H918 O43719 HTATSF1 HIV Tat-specific factor 1 0 0 171.38 0.010675 3732800 3114.1 2500.1 2499.2 1323.8 3775.7 3196.9 2977.7 3525.8 2765.1 2944.4 FALSE FALSE TRUE 3076.144151 2535.296473 2542.697528 1476.863985 3583.01194 2992.628408 3230.625764 3627.81346 2517.782531 2867.904064 1.072610549 0.884024157 0.886604807 0.514962827 1.249348605 1.04348972 1.126476232 1.264970299 0.877917279 1 11.48578105 -7.620303808 1.270238803 0.985632342 1.284084805 0.241243176 0.180918736 1.073035568 2.238520473 0.02728853 0.350636721 2.40E-08 7.620303808 0.298452463 LLDEEEATDNDLR ddPTM_HeLa_Romidepsin_16h_R1 2 LLDEEEATDNDLR 13 0 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 0 ; ; 336.92 3.05E-194 56144000 5792.5 5301.1 5147 5557.3 5112.9 5490.5 4491.5 4923.7 5668.8 4648.9 FALSE FALSE TRUE 5721.898782 5375.729025 5236.581376 6199.861174 4851.969634 5139.67477 4873.007898 5066.159491 5161.76833 4528.120908 1.263636484 1.187187607 1.15645794 1.369190731 1.071519452 1.135056876 1.076165588 1.118821603 1.139936065 1 12.14469677 -5.755443677 13.09300376 1.141940841 0.652466826 0 0.099362479 0 0 0.016016204 0 1.76E-06 5.755443677 -0.489474015 LLDES(ph)ESAASSR ddPTM_HeLa_Romidepsin_16h_R1 2 LLDESESAASSR 12 0 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12;Q8N108-19;Q8N108-16;Q8N108-14;Q8N108-18;Q8N108-15 Q8N108-17 MIER1 Mesoderm induction early response protein 1 1 0 LLDES(0.78)ES(0.22)AASSR;LLDES(0.5)ES(0.5)AASSR ; 209.25 9.18E-18 10938000 1938.95 2245.28 2048.61 1907.34 2497 1803.88 1847.93 2114.22 2190.4 2048.96 TRUE FALSE FALSE 1915.317332 2276.889111 2084.265198 2127.875625 2369.568772 1688.61789 2004.893128 2175.39162 1994.485138 1995.727724 0.959708736 1.140881636 1.044363504 1.066215396 1.187320667 0.846116366 1.004592512 1.090024252 0.999377377 1 10.96269919 LLDEVFFSEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLDEVFFSEK 10 0 H0YLS6;H0YLC2;H0YMI6;H0YMA1;H0YMZ1;H0YL69;P25789;H0YKT8;H0YN18 H0YLS6 PSMA4 Proteasome subunit alpha type;Proteasome subunit alpha type-4;Proteasome subunit beta type 0 0 161.76 0.022233 11971000 2512.6 2361 2591.9 2301 3269.2 2535 2173.6 2040.3 2324.3 2479.5 FALSE FALSE TRUE 2481.975465 2394.23822 2637.010932 2567.052447 3102.360525 2373.021681 2358.22553 2099.332861 2116.408787 2415.082233 1.027698118 0.991369233 1.091892813 1.062925482 1.284577595 0.982584216 0.976457653 0.869259371 0.876329906 1 11.2378566 -7.437672366 2.185231125 1.0386232 0.858999023 0.224970872 0.098354072 0.482408956 3.371528126 0.012361802 0.144484791 3.65E-08 7.437672366 -0.179624176 EPGFEAGPEAS(ph)DDDLWTR ddPTM_HeLa_Romidepsin_16h_R1 2 EPGFEAGPEASDDDLWTR 18 0 H9KVB4;O15417-2;O15417;H7C177 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 0 EPGFEAGPEAS(1)DDDLWTR;EPGFEAGPEAS(1)DDDLWTR ; 174.68 7.93E-08 8503300 1357.62 1253.91 1375.65 980.86 754.12 718.36 342.942 573.59 1502.82 1461.45 TRUE FALSE FALSE 1341.072805 1271.562578 1399.592611 1094.271648 715.6344424 672.4591144 372.0714849 590.1859217 1368.404015 1423.481318 0.942107766 0.893276618 0.98321811 0.768729195 0.502735395 0.472404594 0.261381361 0.414607423 0.961308025 1 10.47520784 -8.775713479 1.398889501 0.969737262 0.352483774 0.955930851 0.055531325 0.053096564 0.208121046 0.008506503 0.02143764 1.68E-09 8.775713479 -0.617253488 down LLDLPAAAS(ph)SEDIERS ddPTM_HeLa_Romidepsin_16h_R1 4 LLDLPAAASSEDIERS 16 1 P22466 P22466 GAL Galanin peptides;Galanin;Galanin message-associated peptide 1 0 LLDLPAAAS(0.986)S(0.014)EDIERS;LLDLPAAAS(0.954)S(0.046)EDIERS;LLDLPAAAS(0.965)S(0.035)EDIERS;LLDLPAAAS(0.967)S(0.033)EDIERS ;;; 209.89 1.48E-25 40772300 7878.28 7949.25 7343.73 8698.19 5223.49 3866.68 3077.85 3783.25 7733.1 6907.53 TRUE FALSE FALSE 7782.256493 8061.15975 7471.54454 9703.915654 4956.915814 3619.611627 3339.282502 3892.71237 7041.432168 6728.071375 1.156684592 1.198138263 1.110503163 1.442302721 0.736751372 0.537986508 0.496320909 0.578577746 1.046575129 1 12.7159773 -8.56449908 6.855980197 1.112148319 0.549444545 0.851532972 0.118097547 0.059050315 7.312601481 0.018641091 0.037705532 2.73E-09 8.56449908 -0.562703775 LLDLPAAASS(ph)EDIERS ddPTM_HeLa_Romidepsin_16h_R1 1 LLDLPAAASSEDIERS 16 1 P22466 P22466 GAL Galanin peptides;Galanin;Galanin message-associated peptide 1 0 LLDLPAAAS(0.293)S(0.707)EDIERS 175.7 1.86E-06 34662000 6106.5 6130.4 6305.1 6675.9 3779.1 2302.8 2186.5 2962 6334.5 5426.1 TRUE FALSE FALSE 6032.071629 6216.703932 6414.837621 7447.798969 3586.238425 2155.658512 2372.221255 3047.700797 5767.926455 5285.12914 1.14132909 1.176263393 1.213752295 1.409199051 0.678552658 0.407872439 0.448848305 0.57665588 1.091350145 1 12.36772301 -8.580532101 5.971495721 1.110416833 0.48466413 0.881492837 0.116035275 0.05576319 4.073160554 0.019302066 0.039159318 2.63E-09 8.580532101 -0.625752703 LLDLSDSTSVAS(ph)FPSADETDGNLPESR ddPTM_HeLa_Romidepsin_16h_R1 2 LLDLSDSTSVASFPSADETDGNLPESR 27 0 Q13464 Q13464 ROCK1 Rho-associated protein kinase 1 1 0 LLDLSDSTSVAS(0.995)FPS(0.004)ADETDGNLPESR;LLDLS(0.005)DS(0.026)T(0.072)S(0.011)VAS(0.626)FPS(0.256)ADET(0.003)DGNLPESR ; 124.98 2.30E-10 6715100 1208.87 1464.46 1320.68 1401.36 1884.1 1628.73 1676.96 1851.33 1993.75 1418.07 TRUE FALSE FALSE 1194.135827 1485.076706 1343.665881 1563.391837 1787.947346 1524.659409 1819.400941 1904.895313 1815.424007 1381.228337 0.864546285 1.075185519 0.972805036 1.131885145 1.29446182 1.103843129 1.31723401 1.379131358 1.314354736 1 10.43173612 -8.957806443 0.862045014 0.938084861 1.312164649 0.240212329 0.143644124 0.228770387 0.326177116 0.015875732 0.046233695 1.10E-09 8.957806443 0.374079788 LLDPEDISVDHPDEK ddPTM_HeLa_Romidepsin_16h_R1 2 LLDPEDISVDHPDEK 15 0 A0A087WUZ3;Q01082;Q01082-2;F8W6C1;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ; ; 139.64 0.00040865 9136100 4196.8 4418.5 3477.9 3801 4605.2 4889.8 3995.2 4886.6 5642.8 5138.9 FALSE FALSE TRUE 4145.647787 4480.703759 3538.431391 4240.489504 4370.17946 4577.357561 4334.552188 5027.986061 5138.093835 5005.390637 0.828236613 0.895175638 0.706924124 0.847184528 0.873094585 0.91448558 0.865976804 1.004514218 1.026512056 1 12.28926695 -12.33636855 1.025315715 1.001113634 0.861497195 0.392914182 0.071460751 0.489757804 0.909843074 0.050119435 0.012756266 4.61E-13 12.33636855 -0.139616439 LLDPEDVDVSS(ph)PDEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLDPEDVDVSSPDEK 15 0 F6QMI7;E9PHM6;F8W9J4;Q03001-14;Q03001;Q5T0V7;E7ETB9;A0A494C1D7;Q03001-13 F6QMI7;A0A494C1D7 DST Dystonin 1 0 LLDPEDVDVS(0.025)S(0.975)PDEK 235.93 2.12E-45 7676500 4134.3 4518.4 4180.7 4200.8 4283.1 4587.3 4118 4905.1 4854.9 4574.5 TRUE FALSE FALSE 4083.909561 4582.010154 4253.46333 4686.516261 4064.517425 4294.186335 4467.782817 5047.02133 4420.665585 4455.653831 0.916567964 1.028358649 0.954621587 1.051813368 0.91221571 0.963761212 1.002722156 1.132722945 0.99214745 1 12.12142144 -7.271096486 2.652373173 0.967573404 1.163899313 0.530190363 0.042810149 0.267883192 2.484334739 0.006310966 0.114675565 5.36E-08 7.271096486 0.196325909 LLDS(ph)WFTS(ph)T(ph)QEKK ddPTM_HeLa_Romidepsin_16h_R1 1 LLDSWFTSTQEKK 13 1 Q8N5M9 Q8N5M9 JAGN1 Protein jagunal homolog 1 3 0 LLDS(0.96)WFT(0.107)S(0.938)T(0.995)QEKK 65.511 0.016473 10042000 749.61 640.38 698.1 617.2 617.7 869.21 737.61 654.72 855.13 687.79 TRUE FALSE FALSE 740.473465 649.3952864 710.2501377 688.563568 586.176464 813.6702862 800.262575 673.6632902 778.6450311 669.9211166 1.105314412 0.969360825 1.060199656 1.027827831 0.874993263 1.214576263 1.194562397 1.005585991 1.162293607 1 9.387847418 -8.223457204 24.99990008 1.033657486 1.143873614 0.238982192 0.089192705 573.0725869 377196.5652 0.011395093 0.029051294 5.98E-09 8.223457204 0.110216128 LLEAISS(ph)LDGK ddPTM_HeLa_Romidepsin_16h_R1 2 LLEAISSLDGK 11 0 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 LLEAIS(0.131)S(0.869)LDGK;LLEAIS(0.051)S(0.949)LDGK ; 207.34 1.08E-13 13737500 6538.1 5572.2 6280.8 4401.9 6031 7517.5 5971.3 6732.7 7341.7 5832.8 TRUE FALSE FALSE 6458.411122 5650.645578 6390.114689 4910.86839 5723.215565 7037.156012 6478.502073 6927.500052 6685.039964 5681.263015 1.136791433 0.994610804 1.124770086 0.864397296 1.00738437 1.238660487 1.140327786 1.219359152 1.176682007 1 12.47199598 -8.262853681 24.98957932 1.046529069 1.193537008 0.400092139 0.087354238 99.41316376 1756569.864 0.012151367 0.028608051 5.46E-09 8.262853681 0.147007939 LLEAQIATGGVIDPVHSHR ddPTM_HeLa_Romidepsin_16h_R1 2 LLEAQIATGGVIDPVHSHR 19 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4;A0A075B730;P58107 Q15149;Q15149-3;Q15149-4;A0A075B730 PLEC;EPPK1 Plectin;Epiplakin 0 0 ; ; 72.383 0.0047833 1459490 213.434 283.39 137.93 293.99 363.66 480.97 380.44 347.33 399.29 316.42 FALSE FALSE TRUE 210.8325843 287.3795719 140.3306138 327.9825071 345.1010732 450.2375693 412.7545641 357.3794456 363.5765024 308.1993628 0.684078586 0.932447002 0.455324153 1.064189439 1.119733247 1.460864699 1.339245352 1.159572305 1.179679604 1 8.267720069 -8.781480967 2.471723072 0.827153781 1.31133019 0.488244195 0.200956451 0.14962463 1.866639416 0.027499152 0.057385809 1.65E-09 8.781480967 0.484176408 LLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_HeLa_Romidepsin_16h_R1 2 LLEDGEDFNLGDALDSSNSMQTIQK 25 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 LLEDGEDFNLGDALDS(0.35)S(0.323)NS(0.323)MQT(0.004)IQK;LLEDGEDFNLGDALDS(0.332)S(0.332)NS(0.332)MQT(0.003)IQK ; 112.64 7.18E-10 28490000 10005.7 9545.8 10052.8 8961.3 8800.5 7081.2 5010.9 5546.8 9761.9 10245.7 TRUE FALSE FALSE 9883.74668 9680.186023 10227.76477 9997.44767 8351.377646 6628.734174 5436.525721 5707.287907 8888.771215 9979.515237 0.990403486 0.970005636 1.024875911 1.001796924 0.836852036 0.664234085 0.544768517 0.571900315 0.890701703 1 13.28475402 -8.329948193 1.750384049 0.996962233 0.556095336 0.950297371 0.039698536 0.026301294 0.153628278 0.003048952 0.00969411 4.68E-09 8.329948193 -0.440866897 LLEDS(ph)EESS(ph)EETVSR ddPTM_HeLa_Romidepsin_16h_R1 1 LLEDSEESSEETVSR 15 0 A2AB15;A0A140T947;O60231 A2AB15 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 2 0 LLEDS(0.977)EES(0.124)S(0.88)EET(0.018)VSR 159.41 0.002772 112180000 2319 2444.1 2480.1 2262.8 2439.1 2622.2 2376 2500.6 2273.2 2219.1 TRUE FALSE FALSE 2290.735136 2478.508104 2523.2651 2524.435583 2314.623625 2454.649883 2577.817381 2572.950916 2069.879299 2161.447462 1.059815321 1.146689035 1.16739599 1.167937517 1.070867401 1.135650959 1.192634763 1.190383278 0.957635721 1 11.07778205 -10.5109463 1.221504151 1.017414849 1.154583395 0.746723689 0.039402115 0.1590159 0.475209601 0.008205025 0.008704527 3.08E-11 10.5109463 0.137168546 LLEDS(ph)EESSEETVSR ddPTM_HeLa_Romidepsin_16h_R1 1 LLEDSEESSEETVSR 15 0 A2AB15;A0A140T947;O60231 A2AB15 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 0 LLEDS(0.886)EES(0.114)SEETVSR 275.76 3.09E-93 0 1210.8 1147.7 971.18 1201 1027.7 1378.6 1499.1 1251.8 1208.8 1184.4 TRUE FALSE FALSE 1196.042304 1163.857351 988.0829805 1339.865271 975.2526341 1290.511909 1626.433517 1288.018858 1100.681901 1153.629117 1.036765011 1.008866137 0.856499689 1.161435032 0.845377964 1.118654072 1.409840903 1.116493021 0.954103779 1 10.17196377 -7.99571887 24.54202319 1.004984064 1.263437208 0.513487252 0.108933008 52.50632773 300985.1941 0.012938969 0.038581643 1.01E-08 7.99571887 0.258453144 LLEEENQES(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 LLEEENQESLR 11 0 P48681 P48681 NES Nestin 1 0 LLEEENQES(1)LR 108.32 0.015342 2459400 389.81 374.55 420.07 550.93 369.16 391.95 324.55 295.29 474.1 396.06 TRUE FALSE FALSE 385.0588458 379.8229247 427.3811421 614.6311188 350.3203877 366.90566 352.1172689 303.8337503 431.6953086 385.7703041 0.998155746 0.984583107 1.107864285 1.593256693 0.908106155 0.951098765 0.91276406 0.787602745 1.119047537 1 8.591598281 -7.793611256 1.690623559 1.044766112 0.811758402 0.208454957 0.184150625 0.65708582 3.269031339 0.02757642 0.178276032 1.61E-08 7.793611256 -0.23300771 LLEEERR ddPTM_HeLa_Romidepsin_16h_R1 2 LLEEERR 7 1 Q8NE71;Q8NE71-2;H0YGW7;Q5JSZ5;Q5JSZ5-5;A0A494C0D3;A0A494C065;H0Y412 Q8NE71;Q5JSZ5 ABCF1;PRRC2B ATP-binding cassette sub-family F member 1;Protein PRRC2B 0 0 ; ; 108.09 0.01963 5234100 2256.4 2423.3 2599.8 2555.9 2219.3 2321 2411.7 1556.48 2602.4 2329.2 FALSE FALSE TRUE 2228.898129 2457.415281 2645.048428 2851.425184 2106.04084 2172.695591 2616.549738 1601.514293 2369.634826 2268.687048 0.982461698 1.083188306 1.165893917 1.256861402 0.928308222 0.957688542 1.153332162 0.705921204 1.044496123 1 11.1476419 -7.246880182 24.34498407 1.028534475 0.705920877 0.491164563 0.103835668 1330.232733 2224280.544 0.015069691 0.429453556 5.66E-08 7.246880182 -0.322613598 LLEENETEAVTVPTPS(ph)PTPVR ddPTM_HeLa_Romidepsin_16h_R1 1 LLEENETEAVTVPTPSPTPVR 21 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 0 LLEENETEAVTVPTPS(0.758)PT(0.241)PVR 202.44 1.59E-24 50536000 3083.9 3081.9 3129.2 3446.6 3554 3611.6 2479.4 3057.3 3569.1 2785.8 TRUE FALSE FALSE 3046.312241 3125.287069 3183.662413 3845.112109 3372.626118 3380.830416 2690.000174 3145.758152 3249.870757 2713.424514 1.122681771 1.151786996 1.173300527 1.417069864 1.24294083 1.245964425 0.991367241 1.159331367 1.197700817 1 11.40589906 -10.99529481 0.781266412 1.019264556 1.202800912 0.03702278 0.114610781 0.47702057 0.636518616 0.035973091 0.026346846 1.01E-11 10.99529481 0.183536356 LLEESNMELEERR ddPTM_HeLa_Romidepsin_16h_R1 1 LLEESNMELEERR 13 1 H7C2F6;J3KPF9;A0A087X011;E9PES4;Q9Y496 H7C2F6 KIF3A Kinesin-like protein;Kinesin-like protein KIF3A 0 0 81.709 0.024055 9626800 1921.1 1833.4 2042.2 1419.4 1806.8 1860.2 1802.2 1687.7 2026.7 2131.6 FALSE FALSE TRUE 1897.684894 1859.210653 2077.743634 1583.517706 1714.592254 1741.339224 1955.278823 1736.530937 1845.426876 2076.220725 0.914009224 0.895478323 1.000733501 0.762692371 0.825823687 0.838706214 0.941749015 0.83639033 0.888839445 1 11.01974411 -9.273868944 24.98849448 0.955369996 0.845686873 0.431163162 0.055153837 506.5877564 1018446.204 0.008778845 0.013467184 5.32E-10 9.273868944 -0.109683123 LLEGEEER ddPTM_HeLa_Romidepsin_16h_R1 1 LLEGEEER 8 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5;P20700;E9PBF6;Q03252 P02545;P20700;Q03252 LMNA;LMNB1;LMNB2 Prelamin-A/C;Lamin-A/C;Lamin-B1;Lamin-B2 0 0 176.41 0.0018985 130300000 3300.5 3010.7 2924.2 2901 3868.7 3354.6 3301 3559.8 2853.9 3036.1 FALSE FALSE TRUE 3260.272237 3053.084714 2975.094474 3236.42727 3671.265803 3140.251886 3581.386858 3662.797197 2598.640036 2957.221684 1.102478131 1.032416585 1.006043778 1.094414831 1.241457758 1.061892621 1.211064722 1.238594055 0.878743738 1 11.53002668 -4 0.214745087 1.017398273 2.164422054 0.550437434 0.074550713 28.56034374 0.338302583 0.048282125 11.3692595 1.00E-04 4 1.147023781 LLEQWEKDDDIEEGDLPEHK ddPTM_HeLa_Romidepsin_16h_R1 1 LLEQWEKDDDIEEGDLPEHK 20 1 Q14696 Q14696 MESDC2 LDLR chaperone MESD 0 0 94.387 0.00049058 3404200 1977 1669.5 2073.8 1596.8 1767.5 1609.3 1609.9 1851.8 2340.8 1987.3 FALSE FALSE TRUE 1952.903564 1693.003265 2109.893619 1781.429529 1677.29788 1506.470924 1746.644866 1905.378911 2131.432985 1935.66966 1.008903329 0.874634397 1.090007073 0.920316915 0.866520726 0.778268604 0.902346564 0.984351282 1.101134677 1 10.91861705 -9.023594502 11.63807554 0.99868425 0.878846999 0.406406657 0.075021237 0.70713725 348.183679 0.009748339 0.016432674 9.47E-10 9.023594502 -0.119837251 LLEQYK(ac)EESK ddPTM_HeLa_Romidepsin_16h_R1 1 LLEQYKEESK 10 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 1 LLEQYK(1)EESK 162.36 0.01464 592480 124.7 0 157.89 0 275.38 246.58 268.93 164.91 276.65 187.9 FALSE TRUE FALSE 123.1801084 0 160.6380092 0 261.326331 230.8243338 291.7729075 169.6814107 251.9057311 183.0183309 0.673047928 0 0.877715409 0 1.42786971 1.261208823 1.594227781 0.927127954 1.376396178 1 7.515844344 LLEQYK(ac)EESKK ddPTM_HeLa_Romidepsin_16h_R1 1 LLEQYKEESKK 11 2 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PQD4 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 1 LLEQYK(1)EESKK 111.94 0.0075362 2332300 554.15 698.71 656.18 443.33 1244.5 1041.3 1071.2 1355.8 1690.5 1277.6 FALSE TRUE FALSE 547.3958067 708.5464577 667.6005376 494.5899005 1180.988521 974.7642906 1162.187701 1395.027934 1539.297446 1244.407768 0.439884595 0.56938447 0.536480529 0.397450027 0.949036603 0.78331582 0.933928356 1.121037629 1.236971904 1 10.28124359 -7.59831634 1.152125394 0.68628414 1.182912146 0.185942595 0.253384328 1.109008626 1.750415929 0.038145815 0.570688469 2.52E-08 7.59831634 0.496628006 LLESSLSS(ph)SEGEEPVEYK ddPTM_HeLa_Romidepsin_16h_R1 2 LLESSLSSSEGEEPVEYK 18 0 P08648 P08648 ITGA5 Integrin alpha-5;Integrin alpha-5 heavy chain;Integrin alpha-5 light chain 1 0 LLESS(0.001)LS(0.104)S(0.738)S(0.157)EGEEPVEYK;LLESSLS(0.051)S(0.941)S(0.009)EGEEPVEYK ; 132.23 0.0014475 14726600 6587.5 8045.3 8190.6 6834.5 6863.5 7375.5 4197.3 5702.1 6860.9 7097.4 TRUE FALSE FALSE 6507.209016 8158.561945 8333.153957 7624.737047 6513.229984 6904.229353 4553.818557 5867.081267 6247.243921 6913.008525 0.941299145 1.180175305 1.205430881 1.102954961 0.942170107 0.998730051 0.658731801 0.848701581 0.903693941 1 12.75509799 -7.77804486 23.33861109 1.011830424 0.753716832 0.516798262 0.106771431 62.92174969 88436.07592 0.01580148 0.04764692 1.67E-08 7.77804486 -0.258113592 LLETTDRPDGHQNNLR ddPTM_HeLa_Romidepsin_16h_R1 1 LLETTDRPDGHQNNLR 16 1 Q14974;J3KTM9;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 0 75.483 0.012707 7467000 2520.2 2059.7 2232.3 2563 2316.2 2210.4 2437.9 1962 3067 2555.8 FALSE FALSE TRUE 2489.482833 2088.696511 2271.152245 2859.346119 2197.995671 2069.162574 2644.975165 2018.767374 2792.679839 2489.399948 1.000033295 0.839036135 0.912329193 1.148608572 0.882941961 0.83118929 1.062495067 0.810945375 1.121828512 1 11.28158232 -4 0.15946175 1.017427943 0.547221765 0.159616852 0.107344012 113.466162 1.145533867 0.178051065 12.58062378 1.00E-04 4 -0.470206178 LLFS(ph)NESEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLFSNESEK 9 0 Q8WYL5;Q8WYL5-4 Q8WYL5 SSH1 Protein phosphatase Slingshot homolog 1 1 0 LLFS(0.925)NES(0.075)EK 100.19 0.028164 4005900 747.29 569.91 602.89 697.56 686.19 690.29 698.69 817.79 689.69 582.36 TRUE FALSE FALSE 738.181742 577.9332079 613.3830475 778.2151693 651.1711638 646.1826968 758.0367112 841.4514634 628.002399 567.2302032 1.301379471 1.018868891 1.08136528 1.371956509 1.14798394 1.139189509 1.336382842 1.483439102 1.107138505 1 9.147790543 -16.52287874 0.042072715 1.27E-09 1.841077125 0.368776169 0.123256835 571.6834264 1.917217156 75.0164398 23.01824286 3.00E-17 16.52287874 1.841077124 LLGGLGGEEDTGRPWGPSR ddPTM_HeLa_Romidepsin_16h_R1 1 LLGGLGGEEDTGRPWGPSR 19 1 Q9HCH0;Q9HCH0-2 Q9HCH0 NCKAP5L Nck-associated protein 5-like 0 0 99.539 0.017844 17731000 4691.1 4699.8 4570.8 5144.4 4462.8 5011.1 4324.9 4945.8 5213 5028.6 FALSE FALSE TRUE 4633.923069 4765.963908 4650.352857 5739.219733 4235.046663 4690.906883 4692.256898 5088.89892 4746.736224 4897.956247 0.946093194 0.973051548 0.949447611 1.171758065 0.864655879 0.957727396 0.958003024 1.038984152 0.969125893 1 12.25796417 -5.758903803 19.84936279 0.978831312 1.016442254 0 0.075673786 0 0 0.009186669 0 1.74E-06 5.758903803 0.037610942 LLGLNELDDLLGKES(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 LLGLNELDDLLGKESPSK 18 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 LLGLNELDDLLGKES(0.726)PS(0.274)K 59.242 0.019252 1735600 829.16 714.9 672.55 672.77 960.14 885.99 759.31 902.64 905.54 885.22 TRUE FALSE FALSE 819.053879 724.964381 684.2554506 750.5588329 911.140473 829.3780984 823.8057724 928.7564643 824.5462344 862.2218568 0.949934025 0.840809561 0.793595575 0.870493861 1.056735533 0.961907996 0.955445244 1.077166459 0.956304028 1 9.751915324 -4.497203221 1.145964369 0.9489554 94.19295015 0.222919943 0.075234468 1732.673589 3.970905534 0.012755605 423699.4464 3.18E-05 4.497203221 93.24399474 LLGPSETS(ph)SLR ddPTM_HeLa_Romidepsin_16h_R1 1 LLGPSETSSLR 11 0 H7C3M7 H7C3M7 FARP2 1 0 LLGPS(0.001)ET(0.095)S(0.452)S(0.452)LR 96.604 0.003568 0 1576.2 1681.4 1583.2 1468.2 2547.7 2863.7 2731.3 3076.3 1864.8 1750.5 TRUE FALSE FALSE 1556.988668 1705.070793 1610.754932 1637.960192 2417.681362 2680.718812 2963.296554 3165.307887 1698.007618 1705.021758 0.913178182 1.00002876 0.944712245 0.960668205 1.417976839 1.572249034 1.737981665 1.856461874 0.995886187 1 10.73557443 -8.429063992 1.414810646 0.954961839 1.79860849 0.967832748 0.062565106 0.050314471 0.191689978 0.009654178 0.032135389 3.72E-09 8.429063992 0.843646651 LLGQLPISAQSYSGSPYLDLS(ph)LFSYDDKWVSVMERPK ddPTM_HeLa_Romidepsin_16h_R1 1 LLGQLPISAQSYSGSPYLDLSLFSYDDKWVSVMERPK 37 2 Q7L5Y6;Q7L5Y6-2 Q7L5Y6 DET1 DET1 homolog 1 0 LLGQLPIS(0.002)AQS(0.002)Y(0.008)S(0.008)GS(0.043)PY(0.045)LDLS(0.288)LFS(0.288)Y(0.274)DDKWVS(0.043)VMERPK 40.764 0.012088 23283000 2401.6 2024.9 2134.1 2434.6 1296.8 1570.6 1307.8 1636 2098.4 2041.2 TRUE FALSE FALSE 2372.328375 2053.406595 2171.243115 2716.099907 1230.619457 1470.243729 1418.884499 1683.335079 1910.713848 1988.16933 1.193222499 1.032812731 1.092081586 1.366131077 0.61897115 0.739496232 0.71366381 0.846675911 0.961041809 1 10.95722492 -8.746775413 24.99998889 1.105749501 0.729255764 0.710833806 0.118058635 99.04584811 168858.2446 0.017002686 0.033887332 1.79E-09 8.746775413 -0.376493737 LLGSLDEVVLLS(ph)PVPELR ddPTM_HeLa_Romidepsin_16h_R1 1 LLGSLDEVVLLSPVPELR 18 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 0 LLGSLDEVVLLS(1)PVPELR 188.58 2.09E-14 29437000 1632.1 1472.2 1547.4 1390.3 1774.4 2012.8 1410.2 1659.4 1684.9 1554.6 TRUE FALSE FALSE 1612.207337 1492.92567 1574.331848 1551.053028 1683.845747 1884.188576 1529.982353 1707.412121 1534.198324 1514.211268 1.064717567 0.985942782 1.039704222 1.02433066 1.112028277 1.24433665 1.010415379 1.127591742 1.013199648 1 10.56435079 -8.729118645 5.7315825 1.027854147 1.1251503 0.440166696 0.05631362 0.140194987 12.41397934 0.008114054 0.016097989 1.87E-09 8.729118645 0.097296153 LLGT(ph)PDIGSISNLLIK ddPTM_HeLa_Romidepsin_16h_R1 1 LLGTPDIGSISNLLIK 16 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 0 LLGT(1)PDIGSISNLLIK 124.16 6.11E-05 0 58.626 157.85 158 262.59 135.88 179.2 173.5 275.01 236.41 195.5 TRUE FALSE FALSE 57.91144376 160.0722164 160.7499237 292.9518913 128.9455366 167.7496983 188.2370857 282.9669805 215.2648975 190.4208818 0.304123388 0.840623228 0.844182225 1.538444148 0.677160694 0.880941716 0.98853174 1.48600814 1.130468967 1 7.573047885 -9.681624945 2.991951145 0.671612159 1.07561465 0.091145278 0.328317479 0.296743661 5.386782385 0.05664122 0.081279002 2.08E-10 9.681624945 0.404002492 LLHEDLDES(ph)DDDMDEK ddPTM_HeLa_Romidepsin_16h_R1 4 LLHEDLDESDDDMDEK 16 0 O43150;O43150-2 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 0 LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK;LLHEDLDES(1)DDDMDEK ;;; 148.19 9.02E-05 101533000 16574.5 14024.6 14937.2 14020.42 15780.5 17243.8 14471.1 15202.2 15787.6 15437.3 TRUE FALSE FALSE 16372.48362 14222.03869 15197.1757 15641.52693 14975.1622 16141.97683 15700.27487 15642.05167 14375.51752 15036.23672 1.08886844 0.945850943 1.010703408 1.040255432 0.995938178 1.073538355 1.044162523 1.040290331 0.956058207 1 13.87615591 -5.564352012 9.978687139 1.033785333 1.034982368 0 0.046569205 0 0 0.005928549 0 2.73E-06 5.564352012 0.001197035 LLHIEELR ddPTM_HeLa_Romidepsin_16h_R1 2 LLHIEELR 8 0 Q9Y224 Q9Y224 C14orf166 UPF0568 protein C14orf166 0 0 ; ; 190.52 1.20E-07 29259000 11588.8 11592.3 10906.4 8502.3 11722.7 12319.3 11154.2 12140.2 11759.2 10554.1 FALSE FALSE TRUE 11447.55125 11755.4967 11096.22132 9485.375931 11124.44688 11532.13649 12101.63747 12491.45753 10707.4277 10279.90296 1.113585536 1.143541602 1.07940915 0.922710649 1.082154853 1.12181375 1.177213201 1.215133799 1.041588402 1 13.32753903 LLHMDS(ph)DDEIPIR ddPTM_HeLa_Romidepsin_16h_R1 2 LLHMDSDDEIPIR 13 0 Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5 Q1MSJ5-2 CSPP1 Centrosome and spindle pole-associated protein 1 1 0 LLHMDS(1)DDEIPIR;LLHMDS(1)DDEIPIR ; 88.768 0.0013944 3714900 5488.6 5325.3 5342.1 5021.7 6574.9 6426.5 5730.2 6201.4 5729.1 5911.8 TRUE FALSE FALSE 5421.702832 5400.269713 5435.07701 5602.332582 6239.358319 6015.867391 6216.923045 6380.827725 5216.674947 5758.210584 0.94156036 0.937838176 0.943882988 0.972929437 1.083558551 1.044745985 1.079662328 1.108126845 0.90595418 1 12.49140484 -8.775834862 7.981952005 0.966451801 1.076723234 0.812001964 0.02972343 0.054412139 19.67596226 0.004373623 0.008162884 1.68E-09 8.775834862 0.110271434 LLHPS(ph)PDLVSQEATLSEAR ddPTM_HeLa_Romidepsin_16h_R1 5 LLHPSPDLVSQEATLSEAR 19 0 A0A087WU05;A0A087WY48;Q8IY22-3;Q8IY22-2;Q8IY22 A0A087WU05 CMIP C-Maf-inducing protein 1 0 LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR;LLHPS(1)PDLVSQEATLSEAR ;;;; 187.56 1.10E-14 26645600 12645.3 12083.3 11568 12314.5 10310.6 11508.1 10379.7 10634.5 14287.8 12639.8 TRUE FALSE FALSE 12491.17422 12253.40901 11769.33619 13738.36043 9784.411608 10772.76955 11261.35146 10942.19248 13009.86338 12311.41617 1.014600924 0.995288344 0.955969323 1.115904152 0.794742982 0.875022775 0.914708048 0.888784225 1.056731671 1 13.5877091 -8.753711355 24.99999607 1.008657496 0.872107504 0.692348038 0.049964757 75.6852524 244838.1007 0.006432923 0.012677327 1.76E-09 8.753711355 -0.136549992 LLIHQS(ph)LAGGIIGVK ddPTM_HeLa_Romidepsin_16h_R1 1 LLIHQSLAGGIIGVK 15 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 LLIHQS(1)LAGGIIGVK 68.129 0.022937 3483200 3480.9 3341.4 3732.8 2872.7 3030.6 3063.7 2968.5 2844 3503.9 3358 TRUE FALSE FALSE 3438.473452 3388.440317 3797.767818 3204.85509 2875.937173 2867.939458 3220.644316 2926.286653 3190.502408 3270.758676 1.051277025 1.035979922 1.161127492 0.979850673 0.879287486 0.876842269 0.984678063 0.894681309 0.975462492 1 11.6754096 -8.994316084 11.55807851 1.036765653 0.914150227 0.585616489 0.05361667 0.139637374 263.8745476 0.007768176 0.013876236 1.01E-09 8.994316084 -0.122615425 LLIQISAEYDPSK ddPTM_HeLa_Romidepsin_16h_R1 1 LLIQISAEYDPSK 13 0 A0A0G2JQE0;A0A0G2JNC7;A0A0G2JS53;Q13075-2;Q13075 A0A0G2JQE0 NAIP Baculoviral IAP repeat-containing protein 1 0 0 131.5 0.022185 13539000 3257.8 3337.3 3062.9 3663.4 3077 3525.3 2541.7 2941.9 3581.5 3308.8 FALSE FALSE TRUE 3218.092681 3384.282597 3116.20849 4086.979545 2919.969208 3300.044707 2757.591935 3027.019235 3261.16167 3222.836899 0.998527937 1.050094281 0.966914736 1.268131051 0.906024506 1.023956474 0.85564117 0.939240591 1.011891626 1 11.65411546 -7.771289168 24.99428796 1.014464839 0.897440878 0.235957411 0.091482618 192.6254232 488800.6265 0.011817798 0.036083066 1.69E-08 7.771289168 -0.11702396 LLIVSTTPYSEKDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LLIVSTTPYSEKDTK 15 1 Q9Y230;Q9Y230-2;M0R0Y3 Q9Y230 RUVBL2 RuvB-like 2 0 0 69.92 0.025163 427590 357.68 427.31 211.91 222.94 400.81 195.66 315.98 267.65 374.5 283.59 FALSE FALSE TRUE 353.3204586 433.3256814 215.5982047 248.7173718 380.3551701 183.1579575 342.8193333 275.3940305 341.003782 276.2222909 1.279116386 1.568757105 0.78052428 0.900424694 1.376989412 0.663081741 1.24109945 0.997001471 1.234526659 1 8.109685938 LLKEGEEPTVY(ph)SDEEEPKDESAR ddPTM_HeLa_Romidepsin_16h_R1 1 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 LLKEGEEPT(0.015)VY(0.918)S(0.067)DEEEPKDESAR 90.729 5.08E-05 77679000 3941.2 5949.8 4328 3644.8 3711.7 4558.3 3107.3 4725.4 4918.5 4852.3 TRUE FALSE FALSE 3893.163138 6033.561441 4403.327024 4066.228925 3522.278099 4267.039341 3371.233984 4862.121994 4478.577041 4726.236546 0.823734297 1.276610128 0.931677241 0.860352394 0.745260645 0.902840833 0.713302001 1.0287513 0.947599003 1 12.20647612 -9.245259969 4.976854453 0.948559946 0.838646955 0.178993133 0.138185228 0.330351594 24.24032451 0.021901027 0.035736272 5.69E-10 9.245259969 -0.109912991 LLKEGEEPTVYS(ph)DEEEPKDESAR ddPTM_HeLa_Romidepsin_16h_R1 4 LLKEGEEPTVYSDEEEPKDESAR 23 2 O00264-2;O00264 O00264-2 PGRMC1 Membrane-associated progesterone receptor component 1 1 0 LLKEGEEPTVY(0.121)S(0.878)DEEEPKDESAR;LLKEGEEPT(0.001)VY(0.062)S(0.937)DEEEPKDESAR;LLKEGEEPT(0.016)VY(0.442)S(0.542)DEEEPKDESAR;LLKEGEEPT(0.169)VY(0.366)S(0.465)DEEEPKDESAR ;;; 129.27 3.99E-06 230344000 6119.22 9272.1 6087.58 6106.98 5288.75 6827.79 4890.06 7327.15 8275.7 7573.8 TRUE FALSE FALSE 6044.636593 9402.632867 6193.531776 6813.097762 5018.845352 6391.516255 5305.421574 7539.149525 7535.500665 7377.031584 0.819386026 1.274582162 0.839569643 0.923555455 0.680333993 0.866407603 0.719181084 1.02197604 1.021481416 1 12.8488247 -8.964391912 24.85714916 0.937589417 0.815823291 0.181979514 0.148604095 262.7709042 183433.0283 0.021581447 0.03911961 1.09E-09 8.964391912 -0.121766126 LLLAEDS(ph)EEEVDFLSER ddPTM_HeLa_Romidepsin_16h_R1 8 LLLAEDSEEEVDFLSER 17 0 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER;LLLAEDS(1)EEEVDFLSER ;;;;;;; 185.74 1.27E-09 655095100 7346.99 6782.72 6709.11 5440.34 5226.76 5873.13 5057.07 5416.84 7949.82 7649.62 TRUE FALSE FALSE 7257.44206 6878.20731 6825.879245 6069.377708 4960.018933 5497.855948 5486.6174 5573.567719 7238.768189 7450.88177 0.974038011 0.923140042 0.916116972 0.814585159 0.665695563 0.737879907 0.736371556 0.748041358 0.971531748 1 12.86319546 -9.316731593 1.416549797 0.985636095 0.722030274 0.930107039 0.030541712 0.067114744 0.264658812 0.005198876 0.009519127 4.82E-10 9.316731593 -0.263605821 LLLAEDS(ph)EEEVDFLSERR ddPTM_HeLa_Romidepsin_16h_R1 4 LLLAEDSEEEVDFLSERR 18 1 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 LLLAEDS(1)EEEVDFLSERR;LLLAEDS(0.999)EEEVDFLS(0.001)ERR;LLLAEDS(1)EEEVDFLSERR;LLLAEDS(1)EEEVDFLSERR ;;; 70.944 0.0067163 9113900 2204.79 2179.73 1858.61 3215.11 1754.27 2282.09 1875.65 1945 2324.5 1745.49 TRUE FALSE FALSE 2177.917171 2210.416296 1890.958327 3586.856146 1664.743056 2136.271814 2034.967664 2001.275506 2116.590898 1700.141918 1.281020807 1.300136343 1.112235577 2.109739256 0.979178878 1.256525583 1.19693988 1.177122618 1.24494954 1 10.73143946 -11.89847008 0.713690787 0.996105096 1.30937496 0.031355141 0.295776115 1.119369375 1.046863963 0.193435505 0.060269562 1.26E-12 11.89847008 0.313269864 LLLDDS(ph)FETK ddPTM_HeLa_Romidepsin_16h_R1 1 LLLDDSFETK 10 0 O00443;E9PPP3;A0A0C4DGF9;O00443-2 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 0 LLLDDS(0.971)FET(0.029)K 122.34 0.00076078 0 1096.5 1032.1 1148.8 1021.3 982.8 1095.2 671.33 729.17 1203.3 1042.8 TRUE FALSE FALSE 1083.135436 1046.629931 1168.794382 1139.387511 932.6440487 1025.220255 728.3527534 750.2673835 1095.673834 1015.707906 1.066384765 1.030443817 1.150718997 1.121766903 0.918220724 1.009365241 0.71708879 0.738664511 1.078729257 1 9.98826986 -7.790044696 4.766162035 1.038801854 0.723682767 0.808356594 0.062117651 0.057575742 3.121705233 0.009068186 0.031028566 1.62E-08 7.790044696 -0.315119087 LLLDIPLQT(ph)PHK ddPTM_HeLa_Romidepsin_16h_R1 2 LLLDIPLQTPHK 12 0 Q99666;O14715;J3KQ37;P49792;J3KNE0;A6NKT7;F8VYC4;A0A286YES2;A0A1W2PNU4;P0DJD0;P0DJD1 Q99666;P49792 RGPD5;RGPD8;RANBP2;RGPD3;RGPD1;RGPD2 RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 8;E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2 1 0 LLLDIPLQT(1)PHK;LLLDIPLQT(1)PHK ; 109.99 0.0080388 17598400 8427.4 7983.1 10405.6 6745.5 11569.7 11196.7 6876.5 8630.5 7518.6 7338.9 TRUE FALSE FALSE 8324.683607 8095.486291 10586.7051 7525.446449 10979.25504 10481.26701 7460.589738 8880.209901 6846.117585 7148.23432 1.164579004 1.132515518 1.481023793 1.052769973 1.535939443 1.466273563 1.043696863 1.242294181 0.957735474 1 12.80337121 -10.82843918 0.653734832 1.021818408 1.298006215 0.340755559 0.165312411 0.56990589 0.550697807 0.059576079 0.046355055 1.48E-11 10.82843918 0.276187807 LLLEFTDTSYEEKR ddPTM_HeLa_Romidepsin_16h_R1 1 LLLEFTDTSYEEKR 14 1 A0A0A0MTN3;P21266 A0A0A0MTN3 GSTM3 Glutathione S-transferase Mu 3 0 0 165.51 6.45E-05 7963100 933.57 909.86 756.28 1084.7 828.78 779.88 938.4 996.43 927.91 792.28 FALSE FALSE TRUE 922.1912898 922.669033 769.4427362 1210.118118 786.484264 730.0481849 1018.107673 1025.26013 844.9154056 771.6964514 1.195018181 1.195637263 0.997079531 1.568127099 1.019162732 0.946030248 1.319311072 1.328579558 1.094880512 1 9.591889661 -12.59446755 0.445429087 0.921514442 1.201940715 0.091929024 0.176859237 3.805959904 0.822053997 0.505613577 0.049943164 2.54E-13 12.59446755 0.280426273 LLLETHLPSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LLLETHLPSKK 11 1 O00567;Q5JXT2;A0A494C128 O00567 NOP56 Nucleolar protein 56 0 1 LLLETHLPSK(1)K 52.693 0.030123 0 140.92 219.02 44.405 187.55 215.83 0 257.51 0 252.83 219.84 FALSE TRUE FALSE 139.2024128 222.1033693 45.1778504 209.2354134 204.8153897 0 279.382893 0 230.2162516 214.1285251 0.650088132 1.037243259 0.210984736 0.977148716 0.956506797 0 1.304743928 0 1.075131169 1 7.742333187 -16.52287875 0.111728887 2.134375801 0.437202134 0.145847895 0.420478871 175.8007612 1.438834357 46.07236713 2.284511314 3.00E-17 16.52287875 -1.697173667 LLLEYTDSSYEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLLEYTDSSYEEK 13 0 H3BQT3;E9PLF1;B9ZVX7;E9PHN7;E9PHN6;A0A0A0MR85;F6XZQ7;E7EWW9;Q03013-3;P09488-2;P28161-2;Q03013-2;Q03013;P28161;P09488 H3BQT3 GSTM1;GSTM2;GSTM4 Glutathione S-transferase Mu 4;Glutathione S-transferase Mu 1;Glutathione S-transferase Mu 2 0 0 134.38 6.98E-05 0 1065.3 956.22 886.24 1316.6 1081.9 966.47 742.98 865.29 1013.5 1034.1 FALSE FALSE TRUE 1052.315714 969.6816903 901.6646354 1468.831487 1026.686606 904.7156861 806.0887027 890.3258009 922.8500216 1007.233933 1.044758005 0.962717457 0.895188899 1.45828237 1.019312964 0.898218037 0.800299391 0.8839315 0.916222132 1 9.976183077 -8.187550448 3.893621909 1.041018383 0.846141626 0.241315867 0.149359568 0.245569572 7.189327517 0.020214602 0.0545156 6.49E-09 8.187550448 -0.194876757 LLLPGELAK(ac)HAVSEGTK(ac)AVTK ddPTM_HeLa_Romidepsin_16h_R1 1 LLLPGELAKHAVSEGTKAVTK 21 2 P06899;P23527;Q96A08;A0A2R8Y619;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99879;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 2 LLLPGELAK(1)HAVSEGTK(1)AVTK 44.788 0.017935 0 0 0 0 81.725 278.55 332.42 319.46 299.42 143.18 0 FALSE TRUE FALSE 0 0 0 91.17442903 264.3345541 311.1794348 346.5949244 308.0832453 130.3736222 0 0 LLMISRSHNNLSFEHDEFLS(ph)NNLK ddPTM_HeLa_Romidepsin_16h_R1 1 LLMISRSHNNLSFEHDEFLSNNLK 24 1 Q86VY9 Q86VY9 TMEM200A Transmembrane protein 200A 1 0 LLMISRSHNNLS(0.004)FEHDEFLS(0.996)NNLK 43.497 0.025959 613620000 1959.6 1708.3 2080.4 1667.2 2023.6 1751.1 1703.8 1713.7 2039.4 2024 TRUE FALSE FALSE 1935.715641 1732.349492 2116.608489 1859.969508 1920.328141 1639.210361 1848.520729 1763.283206 1856.990956 1971.416188 0.981890913 0.878733523 1.073648731 0.94346872 0.97408561 0.83148874 0.937661332 0.894424636 0.941957851 1 10.94501666 -8.401454528 7.087646332 0.984663392 0.893057475 0.311331405 0.053573505 0.18302557 9.893416702 0.006870325 0.015431405 3.97E-09 8.401454528 -0.091605918 LLMSEDY(ph)FT(ph)QAMEVK ddPTM_HeLa_Romidepsin_16h_R1 1 LLMSEDYFTQAMEVK 15 0 P42704 P42704 LRPPRC "Leucine-rich PPR motif-containing protein, mitochondrial" 2 0 LLMS(0.062)EDY(0.954)FT(0.984)QAMEVK 46.408 0.0042658 0 416.21 485.27 197.64 217.17 381.99 383.49 330.73 253.07 467.24 349.28 TRUE FALSE FALSE 411.1370724 492.1016438 201.0798413 242.2802172 362.4956249 358.9862267 358.8221979 260.3921812 425.4488842 340.2056552 1.208495703 1.446482844 0.591053788 0.712158112 1.065519104 1.055203584 1.054721438 0.765396392 1.250563821 1 8.410263313 -9.758716386 24.99982243 1.127309266 0.891807299 0.415046371 0.190258782 79.46245701 729539.858 0.032249966 0.044443467 1.74E-10 9.758716386 -0.235501966 LLNGNHENGDLDPTS(ph)PLENMDYIK ddPTM_HeLa_Romidepsin_16h_R1 1 LLNGNHENGDLDPTSPLENMDYIK 24 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4;F5H6X8;F5H221;F8WE35;F5H8I0;F5H592;F5H2W9;F5H2H9;F5GZ10;F5H502;F5H1K9;A8MV73 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 0 LLNGNHENGDLDPT(0.15)S(0.82)PLENMDY(0.029)IK 60.278 0.0020748 9591400 766.49 783.53 654.59 417.98 573.48 618.15 519.01 718.39 986.21 1100.9 TRUE FALSE FALSE 757.1477251 794.5605559 665.9828644 466.3088143 544.2131757 578.65221 563.0946964 739.1754812 898.0009076 1072.298459 0.706097932 0.740988247 0.621079755 0.434868492 0.507520244 0.539637267 0.5251287 0.689337446 0.837454255 1 10.0664908 -11.22933727 0.430397863 1.02505564 0.528852999 0.706804119 0.088106072 0.337647631 0.143727042 0.070742708 0.032937784 5.90E-12 11.22933727 -0.49620264 LLPDPGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LLPDPGSPR 9 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 0 LLPDPGS(1)PR;LLPDPGS(1)PR ; 102.53 0.026034 22953000 10093.5 10408.7 9301.2 8462 8211.5 7650.7 6798.3 6947.8 9187.4 8320.4 TRUE FALSE FALSE 9970.47654 10555.23395 9463.083484 9440.416255 7792.436514 7161.844962 7375.747432 7148.823631 8365.655934 8104.234809 1.23027982 1.302434369 1.167671434 1.164874473 0.961526498 0.883716369 0.910110283 0.882109638 1.032257348 1 12.98446026 -8.639560283 3.957836929 1.135801254 0.897221046 0.670626767 0.083007612 0.141890949 4.116571497 0.01609766 0.033355808 2.29E-09 8.639560283 -0.238580207 LLPEGEETLES(ph)DDEKDEHTSK ddPTM_HeLa_Romidepsin_16h_R1 3 LLPEGEETLESDDEKDEHTSK 21 1 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 1 0 LLPEGEET(0.032)LES(0.967)DDEKDEHT(0.001)SK;LLPEGEETLES(1)DDEKDEHTSK;LLPEGEET(0.003)LES(0.997)DDEKDEHTSK ;; 106.23 0.00011944 72787000 6344.74 6471.78 6762.38 5578.71 10592.7 11184.3 8830.47 9850.79 8774.9 8217.8 TRUE FALSE FALSE 6267.407868 6562.889889 6880.076387 6223.746699 10052.11499 10469.65933 9580.529901 10135.80707 7990.050967 8004.300371 0.783005082 0.819920491 0.859547502 0.777550368 1.255839302 1.308004303 1.196922836 1.266295191 0.998219781 1 12.96655959 -8.751950941 24.99961355 0.878012803 1.256150966 0.857991649 0.076462563 66.29833287 174677.8993 0.01368635 0.027087851 1.77E-09 8.751950941 0.378138163 LLPETVSPS(ph)APSWR ddPTM_HeLa_Romidepsin_16h_R1 1 LLPETVSPSAPSWR 14 0 B0QXZ6;O95503 B0QXZ6 CBX6 Chromobox protein homolog 6 1 0 LLPET(0.135)VS(0.314)PS(0.541)APS(0.009)WR 101.3 0.0096319 2774800 747.41 771.93 735.46 668.07 859.6 836.1 861.28 539.25 854.27 718.83 TRUE FALSE FALSE 738.3002794 782.7972508 748.2603728 745.3153968 815.7314044 782.6759084 934.4371017 554.852348 777.8619516 700.154693 1.054481655 1.118034712 1.068707216 1.064501037 1.165073108 1.117861404 1.334615209 0.792471083 1.110985843 1 9.451529898 -10.77056684 0.631241144 1.006057746 1.111795867 0 0.130144875 1.101833749 1.000351319 0.042967295 0.034614361 1.70E-11 10.77056684 0.105738122 LLPPVGTGRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LLPPVGTGRSPR 12 1 Q9NWZ5;Q9NWZ5-3;Q9NWZ5-2;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 0 LLPPVGTGRS(1)PR;LLPPVGT(0.005)GRS(0.995)PR ; 125.33 0.0020962 52385000 14594.2 12592.7 12019.7 12284.6 9003.3 8339.9 7866.1 7945.4 13066.3 11221.5 TRUE FALSE FALSE 14416.32028 12769.98036 12228.89784 13705.00325 8543.828005 7807.007306 8534.246338 8175.287613 11897.6174 10929.96381 1.31897237 1.168346079 1.118841567 1.25389283 0.78168859 0.714275677 0.780811948 0.747970236 1.088532186 1 13.416001 -8.7487333 21.12641208 1.159415181 0.75495073 0.847724471 0.083447596 14.28927444 23757.40664 0.017692775 0.035100865 1.78E-09 8.7487333 -0.404464452 LLPS(ph)VWSESEDGAGSPPPYR ddPTM_HeLa_Romidepsin_16h_R1 1 LLPSVWSESEDGAGSPPPYR 20 0 K7EN65;K7EMA9;K7EPZ6;A0A0A0MS90;Q9UIS9-4;Q9UIS9-11;Q9UIS9-8;Q9UIS9-7;Q9UIS9-6;Q9UIS9-5;Q9UIS9-10;Q9UIS9-2;Q9UIS9;Q9UIS9-9;Q9UIS9-12 K7EN65 MBD1 Methyl-CpG-binding domain protein 1 1 0 LLPS(0.988)VWS(0.01)ES(0.002)EDGAGSPPPYR 226.79 6.39E-42 9143800 3121.2 2512.9 2312.5 1888.2 1998.5 2642.8 2370.8 2756.9 2426.1 2782.1 TRUE FALSE FALSE 3083.157614 2548.276672 2352.748092 2106.522568 1896.509088 2473.933609 2572.175693 2836.666552 2209.10354 2709.820641 1.137771839 0.940385734 0.868230191 0.77736605 0.699865171 0.912951054 0.949205144 1.046809707 0.815221313 1 11.40398165 -10.04393547 4.303466768 1.064795251 0.869871847 0.028634142 0.122074023 0.156490843 6.303453741 0.017732079 0.022331525 9.04E-11 10.04393547 -0.194923404 LLPSAPQTLPDGPLAS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 5 LLPSAPQTLPDGPLASPAR 19 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;A0A0C4DH09;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 LLPS(0.011)APQT(0.006)LPDGPLAS(0.983)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR;LLPSAPQTLPDGPLAS(1)PAR ;;;; 157 1.93E-06 477260700 7404.45 7151.86 7066.31 8229.1 8501.59 9598.75 7677.25 9326.99 7428.55 6823.65 TRUE FALSE FALSE 7314.201715 7252.544073 7189.296161 9180.587261 8067.722138 8985.420854 8329.355423 9596.85174 6764.121883 6646.370589 1.100480573 1.091203684 1.081687526 1.381293315 1.213853791 1.351928956 1.253218627 1.443923659 1.017716631 1 12.69835102 -8.940217584 0.368965956 1.0077873 1.448507203 0.76362675 0.073253959 0.704289099 0.157402001 0.029411658 0.121512231 1.15E-09 8.940217584 0.440719903 LLPSVWS(ph)ESEDGAGSPPPYR ddPTM_HeLa_Romidepsin_16h_R1 1 LLPSVWSESEDGAGSPPPYR 20 0 K7EN65;K7EMA9;K7EPZ6;A0A0A0MS90;Q9UIS9-4;Q9UIS9-11;Q9UIS9-8;Q9UIS9-7;Q9UIS9-6;Q9UIS9-5;Q9UIS9-10;Q9UIS9-2;Q9UIS9;Q9UIS9-9;Q9UIS9-12 K7EN65 MBD1 Methyl-CpG-binding domain protein 1 1 0 LLPSVWS(0.998)ES(0.001)EDGAGSPPPYR 127.49 0.00030651 8040900 8574.5 7353.4 7610.3 6489.9 6517.4 7299.8 5518.8 6450.9 8355.1 6959.1 TRUE FALSE FALSE 8469.990696 7456.921358 7742.754079 7240.292774 6184.792758 6833.366339 5987.566734 6637.546614 7607.79893 6778.301579 1.249574189 1.100116493 1.142285274 1.068157368 0.912439892 1.008123681 0.883343219 0.979234479 1.122375398 1 12.72670811 -8.9064722 4.167628183 1.12048127 0.946200715 0.622159197 0.065129806 0.164321968 5.31167239 0.014317176 0.026647426 1.24E-09 8.9064722 -0.174280554 LLPSVWSES(ph)EDGAGSPPPYR ddPTM_HeLa_Romidepsin_16h_R1 1 LLPSVWSESEDGAGSPPPYR 20 0 K7EN65;K7EMA9;K7EPZ6;A0A0A0MS90;Q9UIS9-4;Q9UIS9-11;Q9UIS9-8;Q9UIS9-7;Q9UIS9-6;Q9UIS9-5;Q9UIS9-10;Q9UIS9-2;Q9UIS9;Q9UIS9-9;Q9UIS9-12 K7EN65 MBD1 Methyl-CpG-binding domain protein 1 1 0 LLPS(0.001)VWS(0.221)ES(0.757)EDGAGS(0.021)PPPYR 75.682 0.0026086 0 547.82 543.58 644.03 408.54 462.02 472.31 429.4 508.61 512.52 504.65 TRUE FALSE FALSE 541.1429591 551.2325335 655.239072 455.777317 438.4413954 442.1309153 465.8732253 523.3258279 466.6789276 491.5391203 1.100915343 1.121441836 1.333035449 0.927245255 0.891976604 0.89948266 0.947784634 1.064667707 0.949423776 1 8.941162431 LLPVINT(ph)MLQLSPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLPVINTMLQLSPEEK 16 0 Q99666;O14715;J3KQ37;Q7Z3J3;Q8IWJ2 Q99666;Q7Z3J3;Q8IWJ2 RGPD5;RGPD8;RGPD4;GCC2 RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 8;RanBP2-like and GRIP domain-containing protein 4;GRIP and coiled-coil domain-containing protein 2 1 0 LLPVINT(0.967)MLQLS(0.033)PEEK 98.898 0.014867 26387000 2350.4 2448.8 2425.4 1654.5 2158.7 1983.6 1706.1 1768.4 2299.7 2302.1 TRUE FALSE FALSE 2321.752421 2483.274271 2467.61307 1845.801075 2048.533484 1856.854362 1851.016091 1819.565864 2094.009072 2242.29111 1.035437553 1.107471844 1.10048738 0.823176378 0.913589442 0.828105839 0.825502132 0.811476198 0.9338703 1 11.13075788 -9.252055964 24.9947847 1.031118761 0.842930401 0.772503061 0.05289792 226.6414736 603709.133 0.007314602 0.012020337 5.60E-10 9.252055964 -0.18818836 LLPYPTLASPAS(ph)D ddPTM_HeLa_Romidepsin_16h_R1 1 LLPYPTLASPASD 13 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 0 LLPYPTLASPAS(1)D 143 0.00080302 11533000 2366.5 2069.2 2362.3 2092.3 2388.9 2284.9 2064.9 2309 1951 2392 TRUE FALSE FALSE 2337.656188 2098.330252 2403.414841 2334.221571 2266.985519 2138.902264 2240.292554 2375.807272 1776.497674 2329.855495 1.003348144 0.90062678 1.031572493 1.001873968 0.973015504 0.918040741 0.961558586 1.019723016 0.762492643 1 11.18602476 LLQAQGVEVPSKDS(ph)LPK ddPTM_HeLa_Romidepsin_16h_R1 2 LLQAQGVEVPSKDSLPK 17 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 LLQAQGVEVPS(0.07)KDS(0.93)LPK;LLQAQGVEVPS(0.224)KDS(0.776)LPK ; 59.862 0.022948 31379000 2304 2589.4 2129.09 2164.08 2534 2478.1 2050.89 2765.1 2527.84 2221.74 TRUE FALSE FALSE 2275.917962 2625.853641 2166.145918 2414.301112 2404.680524 2319.757408 2225.092545 2845.103806 2301.743659 2164.018875 1.051708924 1.213415314 1.000982914 1.115656217 1.111210513 1.071967271 1.028222337 1.314731512 1.063643061 1 11.07949737 -4 0.094342744 0.929573192 1.592151374 0.195626595 0.084447958 129.6776118 0.880602901 0.781282158 11.1664744 1.00E-04 4 0.662578182 LLQDFFNGK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQDFFNGK 9 0 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;A8K7Q2;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 0 169.44 3.42E-06 0 2010.5 1787.9 1898.8 1674.9 1946.2 1890.1 1734.7 1925.1 1995.1 2036.6 FALSE FALSE TRUE 1985.995253 1813.070103 1931.847817 1868.559819 1846.878152 1769.32871 1882.045375 1980.799731 1816.653259 1983.688838 1.00116269 0.913989164 0.973866354 0.941962158 0.931032184 0.891938633 0.948760379 0.998543568 0.915795474 1 10.95397003 -10.27974108 23.83862889 1.000549053 0.941839887 0 0.038542655 266.7846146 347495.3935 0.00466313 0.005338932 5.25E-11 10.27974108 -0.058709166 LLQDLQLGDEEDAR ddPTM_HeLa_Romidepsin_16h_R1 1 LLQDLQLGDEEDAR 14 0 Q14692 Q14692 BMS1 Ribosome biogenesis protein BMS1 homolog 0 0 198.37 1.87E-15 1661100 835.95 707.98 649.29 602.93 738.29 999.93 727.36 645.67 1044.6 802.55 FALSE FALSE TRUE 825.7611199 717.946961 660.5906201 672.6436035 700.6123064 936.0377001 789.1419402 664.3514428 951.1683598 781.6996353 1.05636626 0.918443515 0.845069628 0.860488573 0.89626792 1.19743909 1.009520671 0.849880712 1.216795194 1 9.610470554 -10.25961388 24.98265572 1.026617401 0.943850623 0.208863629 0.116115304 271.300221 3712851.762 0.017775536 0.021188426 5.50E-11 10.25961388 -0.082766778 SPVLSNTTTEPAST(ph)MSPPPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 SPVLSNTTTEPASTMSPPPAKK 22 1 Q9P275;A0A075B784 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 0 SPVLSNTTTEPAS(0.001)T(0.814)MS(0.185)PPPAKK 151.96 1.09E-06 10854000 4135.9 4072.3 3470.6 3138.6 2878.8 2682.2 1918.7 2095 4127 4461.4 TRUE FALSE FALSE 4085.49006 4129.629946 3531.004337 3501.4997 2731.884094 2510.816076 2081.67433 2155.61552 3757.870784 4345.492185 0.940167393 0.95032502 0.812567182 0.80577747 0.62867081 0.577797858 0.479042245 0.496057852 0.864774489 1 12.08530388 -8.773657315 0.682750068 0.980632081 0.441273749 0.936602314 0.046493588 0.07936331 0.064125686 0.005551825 0.022768542 1.68E-09 8.773657315 -0.539358332 down LLQDSVDFSLADAINTEFK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQDSVDFSLADAINTEFK 19 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 0 0 203.99 1.65E-26 0 528.16 722.37 621.1 350.47 466.4 581.88 449.34 472.9 487.07 733.82 FALSE FALSE TRUE 521.7225828 732.5395438 631.909985 390.9929904 442.5978676 544.6997459 487.5069284 486.5826154 443.5052393 714.7552506 0.729931795 1.024881655 0.88409282 0.547030596 0.619229963 0.762078691 0.682061346 0.680768158 0.620499449 1 9.481305503 -9.283230944 23.25500664 0.883876786 0.663159805 0.367544042 0.123410619 225.8849456 241053.901 0.018325871 0.028013781 5.21E-10 9.283230944 -0.220716981 LLQEGSPS(ph)DITTLSVEPDKK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQEGSPSDITTLSVEPDKK 20 1 B5MCN7;Q15788-2;Q15788-3;Q15788 B5MCN7 NCOA1 Nuclear receptor coactivator 1 1 0 LLQEGS(0.011)PS(0.252)DIT(0.246)T(0.246)LS(0.246)VEPDKK 74.618 0.0020465 11683000 1224.1 1083.9 1156.4 1351.1 1069.3 1091.4 964.92 1222.4 1191.2 1123.9 TRUE FALSE FALSE 1209.180198 1099.159173 1176.526657 1507.320539 1014.729631 1021.663062 1046.880281 1257.768215 1084.656089 1094.700916 1.104575853 1.00407258 1.07474712 1.376924525 0.926946909 0.93328054 0.956316255 1.148960595 0.990824135 1 10.09632105 -6.850012938 8.034519777 1.050303051 2.730989331 0.058554255 0.124970315 13759.33579 23832.51855 0.016993873 389684.342 1.41E-07 6.850012938 1.68068628 LLQLVEDRGS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 LLQLVEDRGSGR 12 1 P17844;J3KTA4;P17844-2 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 1 0 LLQLVEDRGS(1)GR 66.568 0.029331 3878200 2256.1 2392.5 1842.9 2045.4 1826.3 1950.4 1921.7 1785.4 2471.2 1987.6 TRUE FALSE FALSE 2228.601785 2426.181678 1874.974901 2281.898772 1733.097096 1825.775735 2084.92915 1837.057732 2250.169683 1935.961865 1.151159961 1.253217701 0.968497848 1.178689938 0.895212415 0.943084555 1.076947427 0.948912148 1.162300623 1 10.91883482 -8.756763608 24.99998219 1.086329402 0.972321556 0.365732102 0.092730297 133.7354052 715036.2665 0.014230992 0.027728911 1.75E-09 8.756763608 -0.114007846 LLQNGNS(ph)PAEVAK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQNGNSPAEVAK 13 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 LLQNGNS(1)PAEVAK 137.39 0.0014218 10452000 2002.9 1528.2 1384 1591.8 2921.2 3174.9 2906.5 3240.9 1712.8 1751.4 TRUE FALSE FALSE 1978.487884 1549.71404 1408.087939 1775.851406 2772.120264 2972.034137 3153.378037 3334.670328 1559.602878 1705.898376 1.159792349 0.908444525 0.825423108 1.041006564 1.625020753 1.742210544 1.848514591 1.954788384 0.914241376 1 10.73631599 -8.647323107 2.935586814 1.038415436 1.837709981 0.930263322 0.109992168 0.057019148 0.985818565 0.018646761 0.040177461 2.25E-09 8.647323107 0.799294545 LLQTTNNSPMNS(ph)KPQQIK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQTTNNSPMNSKPQQIK 18 1 O00178;B0QY59 O00178 GTPBP1 GTP-binding protein 1 1 0 LLQT(0.001)T(0.004)NNS(0.081)PMNS(0.914)KPQQIK 68.329 0.027848 31609000 1804.2 1655.3 1610 1340.1 1778.9 1799.9 1693 1656.7 1624 1861.3 TRUE FALSE FALSE 1782.209716 1678.603357 1638.021375 1495.048667 1688.116095 1684.892199 1836.803378 1704.634001 1478.745373 1812.943158 0.983047763 0.925899607 0.903515021 0.824652809 0.931146731 0.929368465 1.013161041 0.940257831 0.815660086 1 10.82411798 -10.30194807 3.575029331 0.99275463 0.922929414 0 0.070718947 0.211477983 5.518691172 0.008132215 0.0094496 4.99E-11 10.30194807 -0.069825216 LLQTTNNSPMNSKPQQIKMQS(ph)TK ddPTM_HeLa_Romidepsin_16h_R1 1 LLQTTNNSPMNSKPQQIKMQSTK 23 2 O00178;B0QY59 O00178 GTPBP1 GTP-binding protein 1 1 0 LLQTTNNSPMNS(0.003)KPQQIKMQS(0.549)T(0.447)K 41.257 0.0042692 0 338.19 261.76 279.27 278.69 189.02 206.68 188.55 321.99 328.37 303.7 TRUE FALSE FALSE 334.0680102 265.4450642 284.1305772 310.9134491 179.3736041 193.473815 204.5654323 331.3062726 298.9997648 295.8098302 1.1293337 0.897350382 0.960517698 1.051058543 0.606381485 0.654047957 0.691543726 1.119997508 1.010783734 1 8.208526186 -8.779614912 24.94554373 1.039847005 0.754393132 0.389100106 0.143790721 151.8159006 208363.8387 0.021367445 0.03878601 1.66E-09 8.779614912 -0.285453873 LLS(ph)DPELSATESPLADKK ddPTM_HeLa_Romidepsin_16h_R1 1 LLSDPELSATESPLADKK 18 1 Q9H694;Q9H694-2;A6NGY7 Q9H694 BICC1 Protein bicaudal C homolog 1 1 0 LLS(0.895)DPELS(0.094)AT(0.01)ES(0.001)PLADKK 53.718 0.021931 12531000 1751.1 2073.1 1257.1 1504.8 1570.6 1238.6 1598.5 1907.2 1795.7 2062.7 TRUE FALSE FALSE 1729.75692 2102.285156 1278.979298 1678.792056 1490.446421 1159.457457 1734.27655 1962.381823 1635.088095 2009.110757 0.860956477 1.04637594 0.636589742 0.835589601 0.741843831 0.577099821 0.863206045 0.976741484 0.813836713 1 10.97234138 -9.766853538 24.99846058 0.940908605 0.768679586 0.286574967 0.121953883 117.5650442 542825.7322 0.019170299 0.02560442 1.71E-10 9.766853538 -0.17222902 LLS(ph)DSLPPSTGTFQEAQSR ddPTM_HeLa_Romidepsin_16h_R1 3 LLSDSLPPSTGTFQEAQSR 19 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 LLS(0.983)DS(0.017)LPPSTGTFQEAQSR;LLS(0.995)DS(0.005)LPPSTGTFQEAQSR;LLS(0.997)DS(0.003)LPPSTGTFQEAQSR ;; 247.02 3.39E-62 14325700 5066.77 4540.64 4475.44 4398.92 6081.39 6744.37 5957.44 6718.26 4516.82 4516.97 TRUE FALSE FALSE 5005.014258 4604.563249 4553.333156 4907.543828 5771.033976 6313.426523 6463.464805 6912.642253 4112.824307 4399.618468 1.137601884 1.046582399 1.034938186 1.115447592 1.311712372 1.434994095 1.469096662 1.571191298 0.934813856 1 12.1031627 -8.493746206 1.402656772 1.060912434 1.522673436 0.926942569 0.057320174 0.082415586 0.312574231 0.0088528 0.02794105 3.21E-09 8.493746206 0.461761002 LLS(ph)FSPEEFPTLK ddPTM_HeLa_Romidepsin_16h_R1 1 LLSFSPEEFPTLK 13 0 Q5JSZ5;Q5JSZ5-5;A0A1W2PQP5 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 LLS(0.5)FS(0.5)PEEFPTLK 245.5 1.18E-52 112620000 4482.6 4580.5 3977.3 3855.5 4497.5 4343.8 4265 3667.9 4839.6 4064 TRUE FALSE FALSE 4427.964347 4644.984399 4046.523238 4301.291051 4267.975793 4066.245199 4627.268994 3774.0249 4406.734055 3958.416694 1.118620067 1.173445031 1.022258027 1.086619066 1.078202757 1.027240312 1.168969654 0.953417791 1.113256738 1 11.95070777 -4.000569139 24.41979211 1.065974281 0.000229134 0 0.069407465 0 0 0.009173827 0 9.99E-05 4.000569139 -1.065745147 LLS(ph)GSESSSK ddPTM_HeLa_Romidepsin_16h_R1 2 LLSGSESSSK 10 0 G3XAI9;Q5BKY9-2;Q5BKY9 G3XAI9 FAM133B Protein FAM133B 1 0 LLS(0.65)GS(0.329)ES(0.006)S(0.015)SK;LLS(0.879)GS(0.096)ES(0.007)S(0.015)S(0.003)K ; 111.94 0.016871 35700000 6836.2 6035.9 5804.9 5333.7 7205 6649.2 5143.9 6459.5 6111 6387.9 TRUE FALSE FALSE 6752.877765 6120.873559 5905.931849 5950.40749 6837.301964 6224.337579 5580.822738 6646.395441 5564.416855 6221.941437 1.085332903 0.983756215 0.949210453 0.956358646 1.098901691 1.000385112 0.896958416 1.068218901 0.894321638 1 12.6031491 -10.22569113 24.62243213 1.040296101 0.990891632 0 0.073824557 787.0767238 542118.3532 0.010115 0.012388163 5.95E-11 10.22569113 -0.049404469 LLS(ph)PLSSAR ddPTM_HeLa_Romidepsin_16h_R1 4 LLSPLSSAR 9 0 A0A087WZ13;E9PAU2;Q8IY67-2 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 0 LLS(1)PLSSAR;LLS(0.994)PLS(0.006)SAR;LLS(0.999)PLS(0.001)SAR;LLS(0.827)PLS(0.163)S(0.01)AR ;;; 169.65 0.0016327 276113000 16856.3 15957.5 17827.4 14386.3 15742.7 15554.1 13521.3 13234.9 16105.4 13278.7 TRUE FALSE FALSE 16650.84893 16182.1501 18137.67842 16049.7117 14939.29127 14560.24321 14669.79888 13617.83095 14664.89269 12933.71746 1.287398537 1.251160013 1.402356165 1.240920234 1.155065535 1.125758565 1.134229113 1.052893802 1.133849779 1 13.65884938 -5.930970489 13.57428015 1.165153337 0.422085121 0 0.11305512 0 0 0.018923422 0 1.17E-06 5.930970489 -0.743068216 LLSAEFLEQHYDR ddPTM_HeLa_Romidepsin_16h_R1 1 LLSAEFLEQHYDR 13 0 Q9Y376 Q9Y376 CAB39 Calcium-binding protein 39 0 0 94.023 0.0086729 5387100 1883.5 1497.1 2029.4 1285.5 2379.6 2190.7 1903.7 2261.5 1883.8 1992.6 FALSE FALSE TRUE 1860.543178 1518.176213 2064.720856 1434.135558 2258.160132 2050.72134 2065.40023 2326.932934 1715.30821 1940.831965 0.958631768 0.782229601 1.063832878 0.738928245 1.163501103 1.056619727 1.064182922 1.198935805 0.883800474 1 10.9224595 LLSDPELS(ph)ATESPLADK ddPTM_HeLa_Romidepsin_16h_R1 1 LLSDPELSATESPLADK 17 0 Q9H694;Q9H694-2;A6NGY7 Q9H694 BICC1 Protein bicaudal C homolog 1 1 0 LLSDPELS(0.333)AT(0.333)ES(0.333)PLADK 86.641 0.0029082 0 631.71 749.63 669.99 368.99 541.71 588.2 520.58 657.86 650.05 642.96 TRUE FALSE FALSE 624.0104755 760.1833108 681.6508949 411.65436 514.0645173 550.6159183 564.7980522 676.8941412 591.9078999 626.2558065 0.996414674 1.213854311 1.088454411 0.657326217 0.820853894 0.879218863 0.901864775 1.080858867 0.945153552 1 9.290608265 -9.320634985 24.99995374 1.024005569 0.867903957 0.358049267 0.118717898 248.4292105 104917.9949 0.018475513 0.028221817 4.78E-10 9.320634985 -0.156101612 LLSDS(ph)LPPSTGTFQEAQSR ddPTM_HeLa_Romidepsin_16h_R1 3 LLSDSLPPSTGTFQEAQSR 19 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 LLS(0.425)DS(0.574)LPPSTGTFQEAQSR;LLS(0.233)DS(0.766)LPPSTGTFQEAQSR;LLS(0.166)DS(0.833)LPPSTGTFQEAQSR ;; 140.28 0.00031584 21267800 2037.06 2044.16 2126.28 1673 2660.21 2879.79 2052.44 2731.61 1941.95 1957.5 TRUE FALSE FALSE 2012.231529 2072.937738 2163.287011 1866.440132 2524.449557 2695.780713 2226.774202 2810.644826 1768.257128 1906.643868 1.055378806 1.087218108 1.134604657 0.978913872 1.324027837 1.41388791 1.167902533 1.474132046 0.927418674 1 10.89681968 -8.752807033 24.77743485 1.037934399 1.337260201 0.741104416 0.090927075 59.00364232 169356.7086 0.011414428 0.022541262 1.77E-09 8.752807033 0.299325802 LLSGPSQES(ph)PQTLGK ddPTM_HeLa_Romidepsin_16h_R1 1 LLSGPSQESPQTLGK 15 0 E7EVL6;C9JZE3;C9JYJ8;Q9BWE0;Q9BWE0-4 E7EVL6 REPIN1 Replication initiator 1 1 0 LLS(0.054)GPS(0.004)QES(0.887)PQT(0.054)LGK 137.61 0.0010879 12573000 2411.1 2055 2064 1788.9 1778.6 2481.1 1974.3 2239.5 2498 2012.9 TRUE FALSE FALSE 2381.712586 2083.930344 2099.923054 1995.741035 1687.831405 2322.565717 2141.996993 2304.296399 2274.572624 1960.604568 1.214784779 1.062901912 1.071058942 1.017921241 0.860872933 1.18461711 1.092518618 1.175298904 1.160138388 1 10.93708287 -12.80728294 1.830149214 0.999702048 1.104060009 0 0.108407485 0.649200156 3.936822849 0.079185509 0.01645132 1.56E-13 12.80728294 0.104357961 LLSISGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 LLSISGKR 8 1 P06748;P06748-2;P06748-3;E5RI98 P06748;E5RI98 NPM1 Nucleophosmin 0 1 LLSISGK(1)R 151.04 0.0020317 24722000 2296.1 2157.1 4423.4 1806.2 2927.4 3300.8 2208.5 1595.3 2537.3 1716.3 FALSE TRUE FALSE 2268.11425 2187.46771 4500.387421 2015.041342 2778.003854 3089.889533 2396.089935 1641.457489 2310.357533 1671.710279 1.356762759 1.308520824 2.692085751 1.205377133 1.661773508 1.848340333 1.433316506 0.98190309 1.382032259 1 10.70710912 -10.8792857 1.093945053 1.086057608 1.61218426 0.100901324 0.4495411 0.49092744 1.237574246 0.108635197 0.094420382 1.32E-11 10.8792857 0.526126653 LLSPQMS(ph)GEEEDSDLAAK ddPTM_HeLa_Romidepsin_16h_R1 1 LLSPQMSGEEEDSDLAAK 18 0 P42858;A0A3B3IU44 P42858 HTT Huntingtin 1 0 LLS(0.231)PQMS(0.769)GEEEDSDLAAK 85.536 0.012919 13507000 1641.6 1636.8 1599.9 1753 1747.9 2013.4 1770.4 1968.9 1759.3 1816 TRUE FALSE FALSE 1621.591548 1659.842913 1627.745588 1955.690108 1658.698141 1884.750238 1920.777732 2025.867015 1601.943802 1768.820058 0.916764563 0.93838992 0.920243741 1.105646727 0.937742725 1.065540969 1.085909063 1.145321145 0.905656737 1 10.78857158 -7.667011 0.710224003 0.958455605 1.201162954 0.597716838 0.054476838 1.019715904 0.496710584 0.00940356 0.176528768 2.15E-08 7.667011 0.242707349 LLSPYS(ph)PQTQETDSAVQK ddPTM_HeLa_Romidepsin_16h_R1 2 LLSPYSPQTQETDSAVQK 18 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 0 LLS(0.042)PYS(0.958)PQTQETDSAVQK;LLS(0.001)PYS(0.997)PQT(0.002)QETDSAVQK ; 255.72 1.73E-75 12987700 5480.5 4981.6 6064 4426.3 7207.4 9052.9 7425.1 8712.7 5680.9 5302.7 TRUE FALSE FALSE 5413.701558 5051.731096 6169.541376 4938.089632 6839.579483 8474.448907 8055.787809 8964.788228 5172.786076 5164.93509 1.048164491 0.978082204 1.194505114 0.956079708 1.324233386 1.64076581 1.559707464 1.735702012 1.001520055 1 12.3345345 -8.482682343 2.557757308 1.02911643 1.642827069 0.928516603 0.076470093 0.046741323 0.60348952 0.010316686 0.025103135 3.29E-09 8.482682343 0.613710639 LLSRPQDALEGVVLSPS(ph)LEAR ddPTM_HeLa_Romidepsin_16h_R1 1 LLSRPQDALEGVVLSPSLEAR 21 1 Q9NVI7-3;Q9NVI7-2;Q9NVI7 Q9NVI7-3 ATAD3A ATPase family AAA domain-containing protein 3A 1 0 LLSRPQDALEGVVLS(0.234)PS(0.766)LEAR 57.316 0.0090901 6938100 1004.9 916.88 1071.6 891.35 1067 1227.5 949.85 1043.4 1123.8 772.92 TRUE FALSE FALSE 992.6518923 929.7878607 1090.250748 994.4120809 1012.547008 1149.066712 1030.530235 1073.589133 1023.284513 752.839427 1.318543977 1.235041401 1.448184977 1.320882044 1.34497075 1.526310486 1.368857951 1.426053278 1.359233426 1 9.556198375 -13.25273261 0.224902134 0.594181347 1.462549916 0.064405984 0.130569767 2.841564882 0.134048604 0.699285608 0.062230751 5.59E-14 13.25273261 0.86836857 LLSS(ph)ESEDEEEFIPLAQR ddPTM_HeLa_Romidepsin_16h_R1 3 LLSSESEDEEEFIPLAQR 18 0 Q96AY2;Q96AY2-2;D6RIT8;F8W714 Q96AY2 EME1 Crossover junction endonuclease EME1 1 0 LLS(0.018)S(0.977)ES(0.005)EDEEEFIPLAQR;LLS(0.022)S(0.969)ES(0.009)EDEEEFIPLAQR;LLS(0.12)S(0.69)ES(0.191)EDEEEFIPLAQR ;; 296.27 9.91E-125 3739200 1475.47 1288.26 1263.21 1131.93 1025.41 1258.46 1366.01 1202.14 1620.38 1290.22 TRUE FALSE FALSE 1457.486404 1306.396158 1285.19564 1262.809072 973.0795014 1178.048467 1482.038855 1236.922024 1475.449154 1256.699898 1.159772835 1.03954505 1.022675057 1.004861283 0.774313345 0.937414309 1.179310078 0.984262055 1.174066423 1 10.29542446 -9.597238847 2.296789497 1.075396484 0.97555005 0.217230396 0.103763958 0.455805216 4.878696654 0.018401011 0.027705992 2.53E-10 9.597238847 -0.099846434 LLSS(ph)NEDDANILSSPTDR ddPTM_HeLa_Romidepsin_16h_R1 1 LLSSNEDDANILSSPTDR 18 0 H0YEG1;F5GY88;A0A0B4J1W0;O75448-2;O75448 H0YEG1 MED24 Mediator of RNA polymerase II transcription subunit 24 1 0 LLS(0.11)S(0.89)NEDDANILSSPTDR 186.17 7.93E-11 5709200 975.03 1165.8 727.08 811.55 803.14 580.38 551.38 699.39 985.43 936.75 TRUE FALSE FALSE 963.1459593 1182.212163 739.7345224 905.3852295 762.1527689 543.2955911 598.2142034 719.6257462 897.2906727 912.4131 1.055602949 1.295698366 0.810745179 0.992297491 0.835315461 0.595449135 0.655639648 0.788706066 0.983425899 1 9.83354335 -8.704061543 1.596826316 1.037153102 0.67475716 0.622129285 0.120341006 0.176100298 0.903930882 0.017892785 0.044565862 1.98E-09 8.704061543 -0.362395943 LLSSNEDDANILS(ph)SPTDR ddPTM_HeLa_Romidepsin_16h_R1 1 LLSSNEDDANILSSPTDR 18 0 H0YEG1;F5GY88;A0A0B4J1W0;O75448-2;O75448 H0YEG1 MED24 Mediator of RNA polymerase II transcription subunit 24 1 0 LLS(0.15)S(0.274)NEDDANILS(0.557)S(0.017)PT(0.002)DR 118.61 0.0015263 5137300 779.33 904.64 597.84 569.05 615.09 590.17 548.75 759.78 781.44 884.8 TRUE FALSE FALSE 769.8312262 917.3755457 608.2451544 634.8462385 583.6996621 552.4600417 595.3608113 781.7630356 711.5460492 861.8127684 0.893269692 1.064471982 0.705774127 0.736640558 0.677292892 0.641044159 0.690823846 0.907114705 0.825638788 1 9.751230663 -9.746846909 24.98206764 0.956806759 0.719175965 0.591694987 0.088976231 103.6993249 177531.177 0.012779093 0.018026853 1.79E-10 9.746846909 -0.237630793 LLSSNEDDANILSS(ph)PTDR ddPTM_HeLa_Romidepsin_16h_R1 4 LLSSNEDDANILSSPTDR 18 0 H0YEG1;F5GY88;A0A0B4J1W0;O75448-2;O75448 H0YEG1 MED24 Mediator of RNA polymerase II transcription subunit 24 1 0 LLSSNEDDANILS(0.002)S(0.997)PT(0.001)DR;LLSSNEDDANILS(0.193)S(0.796)PT(0.011)DR;LLSSNEDDANILS(0.021)S(0.979)PTDR;LLSSNEDDANILS(0.473)S(0.524)PT(0.002)DR ;;; 380.03 0 59384000 8930.8 8798.8 8954.6 7814.1 8227.5 9541.7 7025.5 9671.6 10268 8877.7 TRUE FALSE FALSE 8821.947974 8922.669737 9110.451057 8717.603008 7807.619974 8932.016164 7622.245795 9951.432487 9349.604363 8647.056074 1.0202256 1.031873699 1.053589913 1.008158492 0.902922325 1.032954579 0.881484488 1.1508463 1.081247107 1 13.07799333 -8.978747112 24.99207355 1.015523358 0.98313395 0.034765309 0.073263319 608.3843609 715418.6857 0.009184652 0.016647618 1.05E-09 8.978747112 -0.032389408 LLST(ph)DAEAVSTR ddPTM_HeLa_Romidepsin_16h_R1 2 LLSTDAEAVSTR 12 0 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 0 LLS(0.224)T(0.776)DAEAVSTR;LLS(0.082)T(0.918)DAEAVSTR ; 184.98 9.06E-07 9423200 3930.5 4231.7 3167.6 3097.1 3358.1 3828.8 2874.7 3558.9 4129.7 3628 TRUE FALSE FALSE 3882.593554 4291.273984 3222.730749 3455.201274 3186.723626 3584.152037 3118.876946 3661.871156 3760.329289 3533.744037 1.098719521 1.21437035 0.911987602 0.9777735 0.901798091 1.014264757 0.882598432 1.036258178 1.064120448 1 11.78698183 LLT(ph)GRLEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 LLTGRLEDIR 10 1 O43157-2;O43157 O43157-2 PLXNB1 Plexin-B1 1 0 LLT(1)GRLEDIR 98.898 0.0035623 0 1069.4 951.06 1334.8 847.86 1225.9 1115.3 958.07 988.07 1216.6 1040.2 TRUE FALSE FALSE 1056.365741 964.4490476 1358.031634 945.8935625 1163.337749 1044.035929 1039.448442 1016.658247 1107.784249 1013.175454 1.042628636 0.951907238 1.340371629 0.93359305 1.148209566 1.030459162 1.025931331 1.003437502 1.093378491 1 9.984668315 LLT(ph)PTHSFLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LLTPTHSFLAR 11 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7;Q14244-2;Q14244-4 A0A087WZ40 MAP7 Ensconsin 1 0 LLT(1)PTHSFLAR 164.22 0.00057715 28058000 5348.2 5378.9 6114.3 5521.8 5907.3 6496.8 4520.9 4774.4 4999.3 4689.8 TRUE FALSE FALSE 5283.014081 5454.624295 6220.716827 6160.256497 5605.828438 6081.675447 4904.905133 4912.539731 4552.150087 4567.95832 1.156537278 1.194105531 1.361815584 1.348579839 1.227206565 1.331377176 1.07376311 1.075434447 0.996539322 1 12.15733377 -11.21529109 0.828604993 1.021179252 1.234692701 0.455941995 0.097722526 0.388335578 0.570992891 0.037331792 0.023940073 6.09E-12 11.21529109 0.21351345 LLT(ph)PTQSSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LLTPTQSSLAR 11 0 Q96T17-2 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 LLT(0.838)PT(0.103)QS(0.022)S(0.037)LAR 124.48 0.016582 27176000 2183.5 2052.9 2644.6 2917.8 3931.1 3692.9 3207.1 3235.7 2053.7 2268.3 TRUE FALSE FALSE 2156.886662 2081.80078 2690.628154 3255.169765 3730.481298 3456.935608 3479.510994 3329.319874 1870.011928 2209.369239 0.976245448 0.942260236 1.217826385 1.473348007 1.688482501 1.564670833 1.574888856 1.506909672 0.846400817 1 11.10941883 -9.38235635 2.20002742 0.984912012 1.581377245 0.949442431 0.067467287 0.035576928 0.337128383 0.007988683 0.013110369 4.15E-10 9.38235635 0.596465233 LLVDVDESTLS(ph)PEEQKER ddPTM_HeLa_Romidepsin_16h_R1 3 LLVDVDESTLSPEEQKER 18 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 LLVDVDES(0.046)T(0.112)LS(0.842)PEEQKER;LLVDVDES(0.004)T(0.123)LS(0.873)PEEQKER;LLVDVDES(0.001)T(0.072)LS(0.927)PEEQKER ;; 132.6 0.00055464 54600000 10258.2 9518.1 10444.5 10026.6 9268.7 10502.2 8467.9 9670.7 11019.3 10805.6 TRUE FALSE FALSE 10133.16911 9652.096062 10626.28214 11185.92267 8795.683653 9831.143314 9187.163215 9950.506447 10033.70621 10524.86895 0.9627834 0.917075177 1.009635577 1.062808736 0.835704814 0.934087005 0.872900485 0.945428061 0.953333125 1 13.36151465 -8.75459932 24.99999789 0.983861884 0.897953483 0.464475568 0.045886973 109.9443315 401836.512 0.006412643 0.012600667 1.76E-09 8.75459932 -0.085908401 LLVGVDEK ddPTM_HeLa_Romidepsin_16h_R1 1 LLVGVDEK 8 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 0 119.17 0.014519 749180 1293.9 1102.5 1192.6 1057.4 1186.7 1134 1089.1 1284.2 1167.8 1272.5 FALSE FALSE TRUE 1278.129449 1118.021024 1213.356703 1179.661563 1126.138271 1061.54106 1181.608127 1321.356301 1063.349043 1239.440267 1.031215044 0.902037036 0.978955368 0.951769597 0.908586159 0.856468108 0.953340115 1.066091151 0.857926817 1 10.27547303 -10.2733483 24.93342935 1.014740439 0.942340844 0 0.072167692 677.1488513 1417727.25 0.009035512 0.010373817 5.33E-11 10.2733483 -0.072399595 LLVHLK ddPTM_HeLa_Romidepsin_16h_R1 2 LLVHLK 6 0 E9PPJ0;Q13435 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 0 0 ; ; 74.949 0.018771 3326800 7089 7264.8 9565.7 6996.2 9825 8704.5 7094.7 5837.9 5944.5 4718.2 FALSE FALSE TRUE 7002.596541 7367.074045 9732.186996 7805.133562 9323.593588 8148.310542 7697.323641 6006.810426 5412.809032 4595.620484 1.523754315 1.603064063 2.11770903 1.698385145 2.028799728 1.773059932 1.674925871 1.307072777 1.17781898 1 12.16604395 -11.31474196 0.68901614 1.03777291 1.766153798 0.575018951 0.218761796 0.30458156 0.311388679 0.101641654 0.054333886 4.84E-12 11.31474196 0.728380888 LMELHGEGS(ph)SSGK ddPTM_HeLa_Romidepsin_16h_R1 1 LMELHGEGSSSGK 13 0 D6RAT0;P61247;D6R9B6;H0Y9Y4;D6RG13 D6RAT0 RPS3A 40S ribosomal protein S3a 1 0 LMELHGEGS(0.854)S(0.145)SGK 123.28 0.0057455 4593300 3195.4 2802.6 2636.9 2244.6 3570.9 3735.5 2524.6 3266.9 2997.2 3362.2 TRUE FALSE FALSE 3156.453236 2842.055076 2682.794138 2504.131213 3388.663648 3496.813606 2739.039461 3361.422597 2729.122925 3274.849559 0.96384679 0.867842942 0.819211414 0.764655343 1.03475399 1.067778395 0.836386347 1.02643573 0.833358258 1 11.67721292 -10.49065098 4.384342803 0.984869017 0.914207063 0 0.106588998 0.384675279 15.74686568 0.017382622 0.019178221 3.23E-11 10.49065098 -0.070661954 LMESREREMELR ddPTM_HeLa_Romidepsin_16h_R1 1 LMESREREMELR 12 2 Q86UU1-2;Q86UU1;A0A087WZL0 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 0 0 53.567 0.0042771 0 4259.2 3769 4280.8 3684.1 4472.7 4833.3 4324.6 3333.4 4334.9 4115.6 FALSE FALSE TRUE 4207.287232 3822.060081 4355.305528 4110.072976 4244.441429 4524.467729 4691.931416 3429.84667 3947.175687 4008.676119 1.049545313 0.953446965 1.086469797 1.02529435 1.058813759 1.128668816 1.170444126 0.855605833 0.984658169 1 11.96891014 LMEWLKSTDYGKY(ph)EGLT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LMEWLKSTDYGKYEGLTK 18 2 Q9NV70-2;Q9NV70 Q9NV70-2 EXOC1 Exocyst complex component 1 2 0 LMEWLKS(0.001)T(0.001)DY(0.005)GKY(0.996)EGLT(0.998)K 42.095 0.030197 3073200 638.73 860.92 789.13 633.79 842.35 830.37 947.38 1205.2 1031.9 664.3 TRUE FALSE FALSE 630.9449131 873.0400544 802.8644766 707.0717819 799.3617363 777.3120369 1027.850434 1240.070561 939.6042796 647.0413902 0.975122956 1.349280073 1.240823986 1.092776741 1.235410514 1.201332787 1.588538924 1.91652432 1.452154829 1 9.337714192 -4 0.401137734 1.005569603 15.95595871 0.54704448 0.183644611 17.96590365 0.211815659 0.030815475 214.8072195 1.00E-04 4 14.95038911 LMGS(ph)AGNATISTVS(ph)S(ph)T(ph)QRK ddPTM_HeLa_Romidepsin_16h_R1 1 LMGSAGNATISTVSSTQRK 19 1 A0A5F9ZHD9;E9PDI6;Q13936-5;F5H522;A0A0A0MSA1;A0A0A0MR67;F5GY28;F5H638;Q13936-8;Q13936-3;Q13936;Q13936-28;Q13936-10;Q13936-7;Q13936-6;Q13936-11;Q13936-18;Q13936-14;Q13936-36;Q13936-33;Q13936-9;Q13936-34;Q13936-4;Q13936-31;Q13936-20;Q13936-30;Q13936-24;Q13936-17;Q13936-19;Q13936-35;Q13936-22;Q13936-21;Q13936-23;Q13936-12;Q13936-27;Q13936-37;Q13936-26;Q13936-15;Q13936-16;Q13936-29;Q13936-25;Q13936-32;Q13936-13;Q13936-2 A0A5F9ZHD9 CACNA1C Voltage-dependent L-type calcium channel subunit alpha-1C 4 0 LMGS(0.988)AGNAT(0.158)IS(0.448)T(0.448)VS(0.652)S(0.652)T(0.652)QRK 48.216 0.016867 15084000 422.76 296.17 466.17 262.18 437.6 524.46 394.69 451.53 512.28 466.62 TRUE FALSE FALSE 417.6072385 300.339489 474.2834933 292.4944852 415.2676391 490.9486986 428.2149587 464.5943082 466.4603938 454.4971451 0.918833579 0.660817108 1.043534593 0.643556265 0.913685913 1.080201942 0.942173044 1.02221612 1.026321945 1 8.828127422 -8.29978913 22.84596017 0.916763323 1.007594663 0.131545475 0.135989818 376.7193084 224420.8533 0.019262741 0.043074539 5.01E-09 8.29978913 0.090831339 LMGS(ph)PVA ddPTM_HeLa_Romidepsin_16h_R1 1 LMGSPVA 7 0 C9J713;Q96IZ7-2;Q96IZ7 C9J713 RSRC1 Serine/Arginine-related protein 53 1 0 LMGS(1)PVA 52.786 0.02338 14285000 11382 10216 10040 5193.3 11115 11369 10170 11007 11479 11013 TRUE FALSE FALSE 11243.27181 10359.82112 10214.74199 5793.773781 10547.76007 10642.55759 11033.83955 11325.47018 10452.28949 10726.88067 1.048139916 0.965781333 0.952256513 0.540117296 0.983301707 0.992139087 1.028615856 1.055802756 0.974401581 1 13.38894299 -9.961190036 3.197084828 1.022380822 0.91888311 0.063051799 0.137259359 0.45084197 9.529978398 0.023481543 0.030824882 1.09E-10 9.961190036 -0.103497712 LMHNAS(ph)DSEVDQDDVVEWK ddPTM_HeLa_Romidepsin_16h_R1 1 LMHNASDSEVDQDDVVEWK 19 0 Q9H2P0;A0A669KBJ7;A0A2R8Y6X0 Q9H2P0 ADNP Activity-dependent neuroprotector homeobox protein 1 0 LMHNAS(0.777)DS(0.223)EVDQDDVVEWK 78.352 0.0029793 8093100 3737 3224.9 3166.4 1967.4 2643.9 2611.5 1952 2167.4 4190.7 3789.9 TRUE FALSE FALSE 3691.452007 3270.300227 3221.509864 2194.880045 2508.971917 2444.633578 2117.802831 2230.110299 3815.873296 3691.437852 1.000003835 0.885915017 0.872697847 0.594586753 0.679673346 0.662244273 0.573706755 0.604130528 1.033709208 1 11.84996715 -9.52165348 1.352332609 1.000188782 0.615385499 0.933787665 0.045425118 0.061993097 0.226584816 0.007163126 0.011985884 3.01E-10 9.52165348 -0.384803283 LMHNASDS(ph)EVDQDDVVEWK ddPTM_HeLa_Romidepsin_16h_R1 2 LMHNASDSEVDQDDVVEWK 19 0 Q9H2P0;A0A669KBJ7;A0A2R8Y6X0 Q9H2P0 ADNP Activity-dependent neuroprotector homeobox protein 1 0 LMHNAS(0.063)DS(0.937)EVDQDDVVEWK;LMHNAS(0.042)DS(0.958)EVDQDDVVEWK ; 100.47 0.00040142 25126000 6725.7 6512.2 6208.6 4390.8 5420.5 5090.6 4225.2 4456.9 8055.4 7550.9 TRUE FALSE FALSE 6643.724581 6603.878923 6316.658079 4898.484955 5143.871658 4765.327089 4584.088383 4585.85337 7334.904849 7354.726529 0.903327208 0.897909514 0.858856961 0.666032236 0.699396726 0.647927162 0.623284682 0.623524661 0.997304906 1 12.84445598 -9.378415776 0.628682056 0.972627869 0.602412939 0.949953382 0.032843867 0.124675314 0.097184408 0.008491733 0.020322388 4.18E-10 9.378415776 -0.37021493 LMIEMDGTENK ddPTM_HeLa_Romidepsin_16h_R1 1 LMIEMDGTENK 11 0 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 0 96.342 0.0044042 1805400 1294.2 1159.5 1323.6 821.06 1575.1 1874.6 1405.1 1496.2 1489.9 1182 FALSE FALSE TRUE 1278.425793 1175.823471 1346.636703 915.9948204 1494.716769 1754.81911 1524.449159 1539.490186 1356.639612 1151.29147 1.110427573 1.021308246 1.169674872 0.795623736 1.298295704 1.524217938 1.324120954 1.337185437 1.178363297 1 10.16903741 -8.555112257 13.43192582 1.044624609 1.391937606 0.671488569 0.112909366 0.535099926 222.6065519 0.014364032 0.028746935 2.79E-09 8.555112257 0.347312998 LMLPDS(ph)PLVEEGR ddPTM_HeLa_Romidepsin_16h_R1 2 LMLPDSPLVEEGR 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 0 LMLPDS(1)PLVEEGR;LMLPDS(1)PLVEEGR ; 108.23 0.010922 9549400 2457.9 2266.62 2428.3 2909 4202 4964 4377.6 4780.7 2722.7 2554.2 TRUE FALSE FALSE 2427.942169 2298.529536 2470.563543 3245.352267 3987.55626 4646.816421 4749.433235 4919.022012 2479.174893 2487.841516 0.975923166 0.923905129 0.993055035 1.304485132 1.602817637 1.867810466 1.909057794 1.977224827 0.996516409 1 11.28067887 -8.729270475 1.390112995 0.978955522 1.944954228 0.99283934 0.035259167 0.024940204 0.09623822 0.006127114 0.016028113 1.87E-09 8.729270475 0.965998705 LMMNDNDISSSTS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 LMMNDNDISSSTSR 14 0 Q9NYK1 Q9NYK1 TLR7 Toll-like receptor 7 1 0 LMMNDNDIS(0.063)S(0.063)S(0.063)T(0.018)S(0.791)R 103.11 0.012108 6376400 222.88 123.15 214.62 162.67 165.94 242.84 132.97 111.72 180.44 271.61 TRUE FALSE FALSE 220.1634528 124.8837089 218.3553711 181.4786708 157.4714626 227.3233077 144.2644685 114.9524419 164.3009945 264.553533 0.83220757 0.472054588 0.825373105 0.6859809 0.595234775 0.859271487 0.545312954 0.434514862 0.621050086 1 8.047415874 -11.23693968 0.074582205 1.691578072 3.27E-19 0 0.179251552 16.03215998 0.59670798 7.592077926 5.689064557 5.80E-12 11.23693968 -1.691578072 LMT(ph)NAFISIIDDLS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LMTNAFISIIDDLSK 15 0 Q01344-3;Q01344-2;Q01344-4;Q01344 Q01344-3 IL5RA Interleukin-5 receptor subunit alpha 2 0 LMT(0.998)NAFIS(0.002)IIDDLS(1)K 60.332 0.0042355 0 2066.6 2095.1 2186.5 1688.2 2097.2 2215.9 1857.1 1881.2 2066.3 2447.8 TRUE FALSE FALSE 2041.411484 2124.594873 2224.555115 1883.397627 1990.172058 2074.311141 2014.842028 1935.629554 1881.484953 2384.205803 0.856222849 0.891112198 0.93303821 0.78994759 0.834731656 0.870021849 0.845078904 0.811855064 0.789145363 1 11.21929306 -16.52287875 0.189618591 1.670831694 0.821948852 0 0.075684673 20.39957381 0.240975654 5.037755161 0.042175837 3.00E-17 16.52287875 -0.848882842 LNDS(ph)PTLK ddPTM_HeLa_Romidepsin_16h_R1 2 LNDSPTLK 8 0 Q9BYW2;H7C3H4;C9JG86;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 LNDS(0.997)PT(0.003)LK;LNDS(0.997)PT(0.003)LK ; 122.18 0.01764 169973000 15043.9 14318 13120.8 12417.8 11828 10591.5 9446.1 10336.2 14703.6 13186.3 TRUE FALSE FALSE 14860.53916 14519.56918 13349.16202 13853.60446 11224.37302 9914.737333 10248.4515 10635.26164 13388.47319 12843.71803 1.157027827 1.13048022 1.039353402 1.078628824 0.873919297 0.771952274 0.79793495 0.828051629 1.042414133 1 13.64877528 -8.669518189 3.277618397 1.078708466 0.800891146 0.889942211 0.044713433 0.077734999 1.657674044 0.009425948 0.019779608 2.14E-09 8.669518189 -0.27781732 LNEAAAGLNQAATELVQASRGT(ph)PQDLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LNEAAAGLNQAATELVQASRGTPQDLAR 28 1 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 LNEAAAGLNQAAT(0.049)ELVQAS(0.321)RGT(0.63)PQDLAR 70.771 7.79E-05 7635300 977.61 847.24 941.63 2085.9 898.72 1038.1 856.68 1001.7 1353.9 1034.4 TRUE FALSE FALSE 965.6945133 859.167467 958.0186752 2327.081572 852.8549648 971.7687603 929.4463778 1030.682609 1232.803793 1007.526139 0.958480853 0.852749555 0.950862353 2.309698461 0.846484207 0.964509726 0.922503488 1.022983493 1.223594848 1 9.976601553 LNELEAMT(ph)RVR ddPTM_HeLa_Romidepsin_16h_R1 1 LNELEAMTRVR 11 1 P29375-2;P29375;F5H322;F5GZR8 P29375-2 KDM5A Lysine-specific demethylase 5A 1 0 LNELEAMT(1)RVR 92.866 0.015871 13714000 2738.9 2191.7 2304.1 1991.2 2426.7 2913.3 2075.2 2282 2205.8 2705.8 TRUE FALSE FALSE 2705.517233 2222.55481 2344.201894 2221.431913 2302.856444 2727.149532 2251.467436 2348.02607 2008.507723 2635.502926 1.026565824 0.843313353 0.88947042 0.842887288 0.873782541 1.034773859 0.854283793 0.890921443 0.762096564 1 11.36386258 -10.27164904 24.85274357 1.012544975 0.891672922 0 0.094867468 354.7258735 863485.0837 0.008876864 0.010211984 5.35E-11 10.27164904 -0.120872053 LNEQAS(ph)EEILK ddPTM_HeLa_Romidepsin_16h_R1 1 LNEQASEEILK 11 0 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105-2 Q01105;Q01105-2 SET Protein SET 1 0 LNEQAS(1)EEILK 148.41 0.002402 11937000 2568.7 2598.6 2870.9 1384.3 2497.3 2744.9 2116.7 2580.6 2557.4 2440.5 TRUE FALSE FALSE 2537.391696 2635.183159 2920.86681 1544.359279 2369.853462 2569.509749 2296.492445 2655.265589 2328.659739 2377.095458 1.067433656 1.108572712 1.228754529 0.649683324 0.996953427 1.080945126 0.966091806 1.117021018 0.979623991 1 11.21498412 LNEQAS(ph)EEILKVEQK ddPTM_HeLa_Romidepsin_16h_R1 1 LNEQASEEILKVEQK 15 1 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;Q01105-2 Q01105;Q01105-2 SET Protein SET 1 0 LNEQAS(1)EEILKVEQK 62.468 0.027119 14550000 2399 2357.3 2339.5 2068.4 2830.2 3719.9 2192.7 2569.3 2701.9 3433.2 TRUE FALSE FALSE 2369.760065 2390.486131 2380.218016 2307.55814 2685.764333 3482.210395 2378.947883 2643.638642 2460.235297 3344.004969 0.708659254 0.714857231 0.711786627 0.690058227 0.803157997 1.041329312 0.711406803 0.79056062 0.735715204 1 11.70736128 -12.34924261 1.065517489 1.000366031 0.768905728 0 0.126270259 0.408629421 0.828136829 0.070674436 0.018345831 4.47E-13 12.34924261 -0.231460303 LNFSHGTHEYHAETIK ddPTM_HeLa_Romidepsin_16h_R1 1 LNFSHGTHEYHAETIK 16 0 P14618;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 58.723 0.019681 8325200 1802 1861.9 1656.7 2194 3840.2 3593.1 2327.2 2430.5 2878.4 1983.7 FALSE FALSE TRUE 1780.036531 1888.111877 1685.534169 2447.680603 3644.220264 3363.512506 2524.87231 2500.822683 2620.948695 1932.163188 0.921266145 0.97720104 0.87235601 1.266808424 1.886083063 1.740801464 1.306759349 1.294312353 1.356484127 1 10.91600123 -9.019713686 5.171619329 0.959906286 1.557042911 0.576432388 0.210729719 0.073254969 5.696706878 0.026603035 0.046367992 9.56E-10 9.019713686 0.597136625 LNGPGENVS(ph)EDEAQSSNQR ddPTM_HeLa_Romidepsin_16h_R1 4 LNGPGENVSEDEAQSSNQR 19 0 A0A3B3IT29;A0A3B3ISF8;A0A3B3ISF0;G3V0E9;H0Y9K3;D6R9W6;D6RJB0;Q659C4-3;Q659C4-9;Q659C4-2;Q659C4 A0A3B3IT29 LARP1B La-related protein 1B 1 0 LNGPGENVS(1)EDEAQSSNQR;LNGPGENVS(0.992)EDEAQS(0.007)S(0.001)NQR;LNGPGENVS(0.994)EDEAQS(0.006)SNQR;LNGPGENVS(1)EDEAQSSNQR ;;; 305.63 4.03E-144 42386500 4562.95 4259.05 3901.23 3789.28 4350.78 4137.37 3683.43 3978.57 4917.69 4733.49 TRUE FALSE FALSE 4507.33501 4319.009018 3969.129272 4227.414383 4128.743462 3873.00541 3996.300452 4093.683646 4477.83949 4610.513247 0.977621095 0.936774018 0.860886643 0.916907545 0.895506257 0.840037801 0.866779952 0.887901938 0.971223647 1 12.17071165 -10.06523102 1.752631561 0.99131456 0.877059145 0.822700151 0.021786448 0.089922952 0.536900388 0.003901048 0.00499333 8.61E-11 10.06523102 -0.114255414 LNGPQDHSHLLY(ph)STIPR ddPTM_HeLa_Romidepsin_16h_R1 1 LNGPQDHSHLLYSTIPR 17 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;O60716-13;O60716-14;O60716-12;O60716-16;O60716-15;E9PKL1 O60716 CTNND1 Catenin delta-1 1 0 LNGPQDHSHLLY(0.653)S(0.265)T(0.082)IPR 85.576 0.011625 9881300 1859 1937.3 1743 1695.5 2036 1656.4 1372.8 1281.4 2175.3 1885.4 TRUE FALSE FALSE 1836.341793 1964.57336 1773.336184 1891.541688 1932.095323 1550.561386 1489.405598 1318.475287 1980.73572 1836.417036 0.999959027 1.069786068 0.96565004 1.030017502 1.052100522 0.844340558 0.81103887 0.717960714 1.078587097 1 10.84267801 -8.031496147 2.542871143 1.008023014 0.760982688 0.863312314 0.043239926 0.06314384 0.800442973 0.0050424 0.017371278 9.30E-09 8.031496147 -0.247040325 LNGTDPEDVIR ddPTM_HeLa_Romidepsin_16h_R1 1 LNGTDPEDVIR 11 0 J3QRS3;P19105;O14950;J3KTJ1;P24844 J3QRS3 MYL12A;MYL12B;MYL9 Myosin regulatory light chain 12A;Myosin regulatory light chain 12B;Myosin regulatory light polypeptide 9 0 0 163.12 0.0094655 6980600 782.53 698.53 831.8 591.35 1225.4 884.82 829.8 869.74 909.84 546.84 FALSE FALSE TRUE 772.9922234 708.3639237 846.2771301 659.7246694 1162.863265 828.2828576 900.2831913 894.9045547 828.4616317 532.633018 1.451266064 1.329928675 1.588855932 1.238610163 2.18323541 1.55507231 1.690250437 1.680152233 1.555407952 1 9.056998054 -12.15099819 0.172984084 0.493094502 1.902602058 0.137536071 0.277310144 5.346543926 0.296002628 1.931624262 0.566337842 7.06E-13 12.15099819 1.409507557 LNHS(ph)PPQSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 LNHSPPQSSSR 11 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 0 LNHS(0.999)PPQSSSR;LNHS(1)PPQSSSR ; 101.61 0.0077261 61839200 626.22 631.21 786.78 490.66 724.44 875.36 612.49 548.65 826.79 897.76 TRUE FALSE FALSE 618.5873898 640.0961909 800.4735759 547.3924178 687.4691235 819.4273211 664.5148853 564.5243221 752.8398317 874.4360658 0.707412942 0.732010282 0.915416927 0.625994786 0.786185692 0.937092319 0.759935359 0.645586732 0.860943254 1 9.772209095 -12.35860219 0.997719808 1.004870506 0.765280221 0.256277749 0.103794021 0.407937631 0.703151917 0.071596556 0.017178497 4.38E-13 12.35860219 -0.239590286 LNHVAAGLVS(ph)PSLK ddPTM_HeLa_Romidepsin_16h_R1 4 LNHVAAGLVSPSLK 14 0 Q5T757;Q05519-2;Q05519;Q5T760 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 LNHVAAGLVS(0.985)PS(0.015)LK;LNHVAAGLVS(0.985)PS(0.015)LK;LNHVAAGLVS(0.998)PS(0.002)LK;LNHVAAGLVS(0.993)PS(0.007)LK ;;; 162.29 0.00024199 683260000 20115 17816.69 18613.7 15447.57 20966.1 23371.2 22004.5 22980.5 21428.6 18894.59 TRUE FALSE FALSE 19869.83064 18067.51383 18937.66364 17233.69073 19896.12168 21877.85575 23873.56168 23645.40451 19511.97235 18403.70583 1.079664652 0.981732375 1.029013603 0.936425027 1.081093225 1.188774476 1.297214914 1.284817565 1.060219748 1 14.16770868 -8.134579915 2.185677857 1.026543105 1.291261895 0.881744911 0.040498783 0.084752694 0.776567275 0.006609352 0.022252222 7.34E-09 8.134579915 0.26471879 LNHVAAGLVS(ph)PSLKSDTSSK ddPTM_HeLa_Romidepsin_16h_R1 1 LNHVAAGLVSPSLKSDTSSK 20 1 Q5T757;Q05519-2;Q05519;Q5T760 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 LNHVAAGLVS(0.958)PS(0.032)LKS(0.006)DT(0.001)S(0.001)S(0.002)K 51.786 0.021294 11639000 1271.7 1011.3 658.09 1684.3 1071.7 1370.5 798.97 1104.2 1217.3 931.01 TRUE FALSE FALSE 1256.200031 1025.537108 669.5437804 1879.046691 1017.00715 1282.929473 866.8344919 1136.148285 1108.421639 906.822226 1.385277065 1.13091307 0.738340726 2.072122448 1.121506642 1.414753009 0.955903447 1.252889764 1.222314151 1 9.824675941 -12.50246235 1.181528834 0.996205351 1.269320638 0.012393581 0.338374452 1.033315487 2.522955375 0.235482532 0.053836187 3.14E-13 12.50246235 0.273115287 LNLAQFLNEDLS(ph) ddPTM_HeLa_Romidepsin_16h_R1 2 LNLAQFLNEDLS 12 0 Q9BPX3 Q9BPX3 NCAPG Condensin complex subunit 3 1 0 LNLAQFLNEDLS(1);LNLAQFLNEDLS(1) ; 106.4 0.0029894 4271500 5186.9 5052.6 5090.8 4281.8 5293.2 4685.5 3886.2 3790.5 5702.3 4823.1 TRUE FALSE FALSE 5123.680068 5123.730635 5179.403239 4776.881862 5023.068252 4386.111672 4216.293731 3900.172137 5192.272006 4697.795167 1.090656337 1.090667101 1.102517895 1.016834854 1.069239521 0.933653239 0.897504804 0.830213323 1.105257216 1 12.19776809 -7.948341139 1.680280769 1.052307151 0.843296922 0.825499657 0.038507553 0.149696318 0.771415397 0.006513901 0.032823091 1.13E-08 7.948341139 -0.20901023 LNLDK(ac)MMEQK ddPTM_HeLa_Romidepsin_16h_R1 1 LNLDKMMEQK 10 1 E9PEX6;P09622-2;P09622-3;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 1 LNLDK(1)MMEQK 79.986 0.030401 0 403.87 364 428.31 209.93 455.1 489.16 468 334.67 242.05 335.93 FALSE TRUE FALSE 398.9474771 369.1244016 435.7645559 234.2030944 431.8745488 457.9042547 507.7519083 344.3531484 220.4004418 327.2024902 1.219267851 1.128122226 1.331788629 0.715774181 1.319899945 1.39945223 1.551797201 1.052416038 0.673590356 1 8.354039918 -14.59073727 0.039935495 2.38E-09 1.956042384 0.232636467 0.237850049 612.735549 2.874148541 102.5540552 47.49558075 2.57E-15 14.59073727 1.956042381 LNLGTDSDS(ph)SPQK ddPTM_HeLa_Romidepsin_16h_R1 1 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 LNLGTDSDS(0.5)S(0.5)PQK 190.57 9.64E-11 25219000 3441.3 3166.5 3759 3202.7 3110.1 2340.4 2399.9 2540.9 3545.4 2988.8 TRUE FALSE FALSE 3399.356112 3211.07807 3824.423818 3573.011243 2951.379992 2190.855993 2603.747446 2614.416933 3228.290544 2911.150545 1.167701931 1.103027144 1.313715577 1.227353649 1.013819088 0.752573925 0.894404946 0.898069987 1.108939745 1 11.50737373 -8.484154186 6.035886771 1.112306513 0.855814901 0.679132204 0.09145384 0.121535256 12.28607308 0.016036362 0.035490229 3.28E-09 8.484154186 -0.256491612 LNLGTDSDSS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 2 LNLGTDSDSSPQK 13 0 Q16512;Q16512-2;Q16512-3;K7EN76 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 LNLGTDSDS(0.005)S(0.995)PQK;LNLGTDSDS(0.058)S(0.941)PQK ; 261.41 2.86E-66 244730000 13637.3 12620.5 13451.8 12818.3 11278.8 9393.4 7536.5 8793.8 13593.7 12140.7 TRUE FALSE FALSE 13471.08334 12798.17173 13685.92294 14300.41216 10703.20075 8793.192056 8176.650122 9048.234729 12377.84543 11825.28286 1.139176415 1.082271932 1.157344234 1.209308253 0.905111605 0.743592534 0.691454929 0.765160109 1.046727217 1 13.52958707 -8.480811353 3.437179569 1.085123474 0.731977649 0.880773522 0.061306124 0.073564451 1.760544277 0.011083608 0.025471726 3.31E-09 8.480811353 -0.353145825 LNLHYAVVSK ddPTM_HeLa_Romidepsin_16h_R1 1 LNLHYAVVSK 10 0 P47897;P47897-2;A0A1B0GVU9;B4DDN1;H7C0R3;A0A0U1RQQ5;A0A1B0GTT3 P47897 QARS Glutamine--tRNA ligase 0 0 72.434 0.019126 507680 746.69 483.83 904.41 867.13 1089 1098.7 846.62 773.14 864.08 595.71 FALSE FALSE TRUE 737.5890551 490.6413714 920.1508767 967.3916506 1033.424266 1028.496616 918.5318817 795.5095861 786.7945207 580.2333683 1.271193791 0.845593167 1.585828956 1.667245807 1.781049355 1.772556823 1.583038708 1.371016611 1.355996679 1 9.180489455 -9.665057332 7.187980347 1.110959608 1.644784113 0.686231508 0.168486527 0.091432302 5.935842993 0.026179112 0.03704397 2.16E-10 9.665057332 0.533824505 LNLYELK(ac)EGR ddPTM_HeLa_Romidepsin_16h_R1 1 LNLYELKEGR 10 1 A0A087WXQ8;A0A087WY10;A0A087WUL2;P49720 A0A087WXQ8 PSMB3 Proteasome subunit beta type-3 0 1 LNLYELK(1)EGR 133.81 0.0082549 548590 125.08 162.54 235.05 156.23 292.74 290.64 212.58 286.74 256.73 140.03 FALSE TRUE FALSE 123.5554768 164.8282424 239.1409467 174.2940477 277.8003854 272.069042 230.6365399 295.0363695 233.7674258 136.3920004 0.90588507 1.208489075 1.753335576 1.277890545 2.03677917 1.994758059 1.690982896 2.163150101 1.713937952 1 7.09161522 -9.499823388 0.901825134 0.943532778 1.953089957 0.42165488 0.322725539 0.162197636 0.263284361 0.039339761 0.074158151 3.16E-10 9.499823388 1.009557179 LNNDDNVDGLLVQLPLPEHIDER ddPTM_HeLa_Romidepsin_16h_R1 2 LNNDDNVDGLLVQLPLPEHIDER 23 0 P13995-2;P13995 P13995-2 MTHFD2 "Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial;NAD-dependent methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase" 0 0 ; ; 104.57 1.16E-05 10089700 1161.24 1290.71 1273.15 1439.51 1440.73 1355.5 1086.55 1520.72 1367.12 1479.14 FALSE FALSE TRUE 1147.08636 1308.880649 1295.308642 1605.952919 1367.204172 1268.887925 1178.84153 1564.719634 1244.841363 1440.71173 0.796194226 0.908495865 0.899075516 1.114694138 0.948978303 0.88073686 0.818235533 1.086074058 0.864046108 1 10.49256598 LNNS(ph)SPNSSGGVK ddPTM_HeLa_Romidepsin_16h_R1 2 LNNSSPNSSGGVK 13 0 O00472;H0Y8G1;O00472-2 O00472 ELL2 RNA polymerase II elongation factor ELL2 1 0 LNNS(0.98)S(0.02)PNSSGGVK;LNNS(0.933)S(0.067)PNSSGGVK ; 256.13 8.26E-66 28871000 9024.4 9284.9 10648.5 8256.3 12133.9 12039.2 11728.6 7162.5 10476.4 9892.9 TRUE FALSE FALSE 8914.407142 9415.613066 10833.83268 9210.932253 11514.66181 11269.93397 12724.82699 7369.735637 9539.364545 9635.881032 0.925126318 0.977140859 1.124321963 0.955899333 1.194977581 1.169580025 1.32056705 0.76482219 0.989983637 1 13.23420087 -9.799668665 6.929933707 0.96427571 1.101442053 0.132686478 0.141431885 0.242036618 32.34541093 0.021330221 0.028326209 1.59E-10 9.799668665 0.137166343 LNPEDIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LNPEDIKK 8 1 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 1 ; LNPEDIK(1)K;LNPEDIK(1)K 127.3 0.0019682 3673500 1859.33 2055.36 2270.18 1894 5306.8 4637.8 4449.9 3966.3 4778.9 3938.7 FALSE TRUE FALSE 1836.667771 2084.295412 2309.691531 2112.993192 5035.974194 4341.459548 4827.874395 4081.058633 4351.463215 3836.372006 0.478751218 0.543298567 0.602050981 0.550779014 1.312691831 1.131657603 1.258447926 1.063780735 1.134265188 1 11.90552691 -8.759016758 24.99957366 0.705234517 1.192131458 0.559922402 0.205435939 39.01734633 402620.2383 0.032855003 0.063313902 1.74E-09 8.759016758 0.486896941 LNPYPTPS(ph)PPHPLYPGR ddPTM_HeLa_Romidepsin_16h_R1 1 LNPYPTPSPPHPLYPGR 17 0 Q5JTD0-4;Q5JTD0-2;Q5JTD0 Q5JTD0-4 TJAP1 Tight junction-associated protein 1 1 0 LNPY(0.001)PT(0.003)PS(0.996)PPHPLYPGR 74.324 0.010785 14763000 3704 2259.6 2826.7 1824.4 2355.6 2548.9 2685.9 2636.1 3400.4 2999.7 TRUE FALSE FALSE 3658.854223 2291.410708 2875.897528 2035.345712 2235.384942 2386.033516 2914.040279 2712.371394 3096.259708 2921.767362 1.252274316 0.784255016 0.984300655 0.696614569 0.765079716 0.816640485 0.99735534 0.92833243 1.059721506 1 11.5126256 -10.25280602 24.84148199 1.119129539 0.852989434 0.528012049 0.108368043 367.55861 1057607.848 0.021595806 0.026226272 5.59E-11 10.25280602 -0.266140105 LNQPGT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 4 LNQPGTPTR 9 0 P36507;G5E9C7;M0R1B6 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 0 LNQPGT(0.997)PT(0.003)R;LNQPGT(0.775)PT(0.225)R;LNQPGT(0.992)PT(0.008)R;LNQPGT(0.908)PT(0.092)R ;;; 144.7 0.012341 2433790000 20594.7 20280.8 18817.6 16117.5 22020.8 23571.4 19987.2 22668.6 20075.7 18599.1 TRUE FALSE FALSE 20343.68387 20566.31363 19145.11243 17981.08119 20896.99641 22065.26361 21684.91227 23324.48018 18280.07911 18115.8927 1.122974408 1.135263604 1.056813084 0.992558384 1.153517342 1.218005868 1.197010417 1.287514812 1.009063115 1 14.14496828 -4 0.259277969 1.037491986 2.686190184 0.693994926 0.053009488 24.44494324 0.307662478 0.031453539 18.01392695 1.00E-04 4 1.648698198 LNQS(ph)SPDNVTDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LNQSSPDNVTDTK 13 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 LNQS(0.949)S(0.051)PDNVTDTK 127.78 0.0030814 175620000 11248 10829 9894.8 8936.5 9413.1 8849.1 7865.4 7571.6 11520 10887 TRUE FALSE FALSE 11110.90505 10981.45095 10067.01484 9969.780177 8932.714382 8283.671069 8533.48688 7790.6723 10489.62235 10604.15417 1.047787958 1.035580092 0.94934633 0.940176842 0.842378773 0.781172259 0.804730556 0.734681161 0.989199344 1 13.37234193 -8.817733856 1.058362448 1.023957872 0.762228054 0.939747517 0.02626715 0.082850313 0.180809541 0.004529631 0.012990094 1.52E-09 8.817733856 -0.261729818 LNQSDSIEDPNS(ph)PAGRR ddPTM_HeLa_Romidepsin_16h_R1 2 LNQSDSIEDPNSPAGRR 17 1 Q86VS8 Q86VS8 HOOK3 Protein Hook homolog 3 1 0 LNQSDSIEDPNS(1)PAGRR;LNQSDSIEDPNS(1)PAGRR ; 122.16 0.00067866 9826600 3536.6 3222.8 3694.3 4105.8 3982.2 3917.7 3385.9 3995.8 3907.8 3405.9 TRUE FALSE FALSE 3493.494559 3268.170663 3758.597742 4580.531914 3778.973474 3667.371614 3673.498261 4111.412169 3558.276581 3317.414227 1.053077584 0.98515604 1.13299018 1.380753684 1.139132232 1.105491013 1.107337827 1.239342418 1.07260545 1 11.69584345 -9.604980261 5.511582434 1.023311005 1.188460404 0.501348552 0.078132274 0.127262075 6.498292802 0.012320778 0.017528906 2.48E-10 9.604980261 0.165149399 LNQSS(ph)PDNVTDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LNQSSPDNVTDTK 13 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 LNQS(0.372)S(0.628)PDNVTDTK 107.93 0.0081051 156080000 11622 11249 10438 9251.3 10066 9156.9 8569 7879.7 11768 10642 TRUE FALSE FALSE 11480.34659 11407.36372 10619.66901 10320.97883 9552.294459 8571.803643 9296.850646 8107.686687 10715.44061 10365.51931 1.107551513 1.100510585 1.024518762 0.995703016 0.92154519 0.826953613 0.89690158 0.782178533 1.033758203 1 13.33950478 -8.699286621 1.438363707 1.055433153 0.834833347 0.85245765 0.039912797 0.137336517 0.567589418 0.007833028 0.020585662 2.00E-09 8.699286621 -0.220599806 LNSEAS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 LNSEASPSR 9 0 Q13111;K7EJF1;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 0 LNS(0.001)EAS(0.768)PS(0.232)R 104.94 0.023848 31718000 2378.6 2538.5 4126.9 1522.7 1966.7 2697 3206.3 836.64 3868.7 3424.2 TRUE FALSE FALSE 2349.608708 2574.23707 4198.726963 1698.761739 1866.33196 2524.670404 3478.643042 860.8468584 3522.673783 3335.23879 0.704479906 0.771829914 1.258898456 0.509337365 0.559579712 0.75696841 1.042996697 0.258106514 1.056198373 1 11.70357434 LNSEASPS(ph)REAINGQR ddPTM_HeLa_Romidepsin_16h_R1 1 LNSEASPSREAINGQR 16 1 Q13111;K7EJF1;Q13111-2;Q13111-3 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 0 LNSEAS(0.08)PS(0.92)REAINGQR 191.15 7.16E-12 9719700 2627.6 2733.9 2389.1 2687.9 2569.5 2170.3 2161.6 2471.8 2536 2766.1 TRUE FALSE FALSE 2595.573801 2772.387916 2430.681283 2998.687645 2438.368827 2031.624834 2345.20625 2543.317633 2309.173808 2694.236323 0.963380153 1.029006955 0.902178203 1.113000971 0.905031532 0.754063338 0.870453059 0.943984613 0.857079161 1 11.39566069 -8.531081595 24.91160749 0.988452382 0.852920901 0.326556596 0.078098617 106.4556044 323299.3764 0.008840246 0.017704639 2.94E-09 8.531081595 -0.13553148 LNSS(ph)ETADLLK ddPTM_HeLa_Romidepsin_16h_R1 1 LNSSETADLLK 11 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 LNS(0.1)S(0.898)ET(0.001)ADLLK 132.31 0.0045786 6610800 3232.1 2796.2 2806.7 1889.1 1800.8 1851.4 1589.9 1591.8 2735.4 3061.6 TRUE FALSE FALSE 3192.705922 2835.564977 2855.549436 2107.52663 1708.898456 1733.101515 1724.946066 1637.856222 2490.738973 2982.059191 1.070638011 0.950874814 0.957576377 0.706735345 0.573059871 0.581176095 0.578441257 0.549236657 0.835241293 1 11.54209318 -9.198764202 1.659826136 1.029995968 0.564757832 0.877484065 0.068074996 0.038285362 0.206197502 0.005602906 0.010442543 6.33E-10 9.198764202 -0.465238136 LNSSSSSSSNSSNEREDFDS(ph)TSSSSSTPPLQPR ddPTM_HeLa_Romidepsin_16h_R1 2 LNSSSSSSSNSSNEREDFDSTSSSSSTPPLQPR 33 1 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 LNSSSSSSS(0.001)NS(0.003)S(0.003)NEREDFDS(0.139)T(0.139)S(0.139)S(0.139)S(0.139)S(0.139)S(0.139)T(0.019)PPLQPR;LNSSSSSSSNSSNEREDFDS(0.125)T(0.125)S(0.125)S(0.125)S(0.125)S(0.125)S(0.125)T(0.125)PPLQPR ; 64.415 0.00014729 9781000 858.83 789.48 848.59 567.52 617.1 686.74 645.73 587.07 917.07 947.17 TRUE FALSE FALSE 848.3622496 800.5943202 863.359353 633.1393327 585.6070843 642.8595304 700.5782901 604.0559442 835.0449624 922.5623869 0.919571686 0.867794234 0.935827609 0.686283488 0.6347615 0.696819575 0.759383105 0.654758911 0.905136579 1 9.849502664 -9.274923403 5.331385484 0.951332666 0.687306369 0.865766046 0.046583301 0.047440437 4.516162304 0.00813897 0.012920491 5.31E-10 9.274923403 -0.264026297 LNSSSSSSSNSSNEREDFDSTSSSS(ph)STPPLQPR ddPTM_HeLa_Romidepsin_16h_R1 2 LNSSSSSSSNSSNEREDFDSTSSSSSTPPLQPR 33 1 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 LNS(0.001)S(0.002)S(0.006)S(0.005)S(0.014)S(0.041)S(0.01)NS(0.028)S(0.028)NEREDFDS(0.1)T(0.1)S(0.1)S(0.1)S(0.1)S(0.121)S(0.121)T(0.121)PPLQPR;LNSSSSSSSNSSNEREDFDS(0.055)T(0.055)S(0.055)S(0.055)S(0.055)S(0.242)S(0.242)T(0.242)PPLQPR ; 52.92 0.0027901 17296100 902.37 840.83 794.34 1111.25 672.04 822.71 798.53 857.29 1124.02 996.02 TRUE FALSE FALSE 891.3715674 852.6672268 808.1651545 1239.737954 637.7432911 770.1414862 866.3571183 882.0943336 1023.484836 970.1432568 0.918804064 0.878908574 0.833036924 1.277891636 0.657370225 0.793843054 0.893019781 0.909241318 1.054983198 1 9.922053989 -16.52287874 0.068734759 1.412021171 0.739349717 0.117261688 0.147858831 451.8268606 2.415906924 29.87774783 4.45049602 3.00E-17 16.52287874 -0.672671454 KVEPGEPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 KVEPGEPAKK 10 2 Q8N6N3 Q8N6N3 C1orf52 UPF0690 protein C1orf52 0 1 KVEPGEPAK(1)K 96.334 0.022235 3630700 1049.2 1477 1445.4 2935.7 6328.6 7035.7 7049.6 6770.8 1298.4 1209.6 FALSE TRUE FALSE 1036.411947 1497.793245 1470.556581 3275.139447 6005.627927 6586.141477 7648.392848 6966.702415 1182.267852 1178.174418 0.879676159 1.271283116 1.248165432 2.779842609 5.097401401 5.59012433 6.491732237 5.913133328 1.003474388 1 10.20233742 -8.845265391 1.48414973 0.954365374 6.147131245 0.991003049 0.212544415 0.021598523 0.095679033 0.031012995 0.072544026 1.43E-09 8.845265391 5.192765871 up LNTS(ph)DFQK ddPTM_HeLa_Romidepsin_16h_R1 2 LNTSDFQK 8 0 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 LNT(0.088)S(0.912)DFQK;LNT(0.08)S(0.92)DFQK ; 127.83 0.01313 1354270000 19967.4 18988.5 18213 19040.4 12137 11508.5 8244.5 10869.4 18083.8 16862.9 TRUE FALSE FALSE 19724.02965 19255.8206 18529.98963 21241.94064 11517.6036 10773.14399 8944.787624 11183.88894 16466.33964 16424.79943 1.200868829 1.172362602 1.12817144 1.293284629 0.701232527 0.655907187 0.544590372 0.680914795 1.002529115 1 14.00358813 -8.665774017 6.067004882 1.118255333 0.630002091 0.876801604 0.08955052 0.059551873 3.15322946 0.014885484 0.029956179 2.16E-09 8.665774017 -0.488253242 LNTVAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LNTVASPK 8 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 LNT(0.002)VAS(0.998)PK 126.03 0.01457 32299000 8045.4 8153.4 8455.5 9049.6 8709 9545.4 8528.9 7414.9 8758.9 8105.8 TRUE FALSE FALSE 7947.33957 8268.183779 8602.664431 10095.95733 8264.547232 8935.479746 9253.344553 7629.438433 7975.482047 7895.210147 1.006602664 1.047240495 1.089605504 1.278744599 1.046779893 1.131759583 1.172020045 0.966337601 1.010167164 1 12.94676195 -9.863281253 2.657405344 1.003687464 1.12311317 0.297190032 0.07602601 0.21747124 3.129041482 0.011806425 0.016072078 1.37E-10 9.863281253 0.119425706 LNVEFALIHK ddPTM_HeLa_Romidepsin_16h_R1 1 LNVEFALIHK 10 0 P11908;P11908-2 P11908 PRPS2 Ribose-phosphate pyrophosphokinase 2 0 0 63.624 0.02812 217870 0 0 0 0 0 0 0 0 0 133.89 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 130.4115185 0 0 0 0 0 0 0 0 0 1 7.02692749 -12.15782943 0.67715094 1.083625667 2.50E-23 0 0.307667284 0.06659167 0.049088893 0.041658112 0.0090835 6.95E-13 12.15782943 -1.083625667 LNVS(ph)KALEAALVEK ddPTM_HeLa_Romidepsin_16h_R1 2 LNVSKALEAALVEK 14 1 P49454 P49454 CENPF Centromere protein F 1 0 LNVS(1)KALEAALVEK;LNVS(1)KALEAALVEK ; 89.013 0.0074437 16683800 6629.2 6516.6 7088.1 5549.6 6758.6 7077 6146.2 6930 7132.5 7394.4 TRUE FALSE FALSE 6548.400761 6608.340866 7211.465407 6191.270864 6413.683422 6624.80254 6668.258075 7130.508616 6494.551336 7202.292422 0.90921062 0.917532985 1.00127362 0.859625033 0.890505834 0.919818601 0.925852171 0.9900332 0.901733914 1 12.81424046 -12.33962923 0.894221094 1.003500625 0.924066757 0 0.050023636 0.608040368 0.80830603 0.033553938 0.007417986 4.57E-13 12.33962923 -0.079433869 LNVTEQEK(ac)IDK ddPTM_HeLa_Romidepsin_16h_R1 2 LNVTEQEKIDK 11 1 P06733;A0A2R8Y6G6;K7EM90;A0A2R8Y879;A0A2R8YEM5 P06733 ENO1 Alpha-enolase;Enolase 0 1 ; LNVTEQEK(1)IDK;LNVTEQEK(1)IDK 130.1 0.0093941 1569330 185.08 250.702 352.74 0 466.628 486.86 487.55 422.602 434.97 301.98 FALSE TRUE FALSE 182.8241738 254.2313893 358.8792917 0 442.8142319 455.7512173 528.9624848 434.8293221 396.0651938 294.1345161 0.621566541 0.86433715 1.220119612 0 1.505482042 1.54946527 1.798369304 1.478334906 1.346544428 1 8.200332281 -8.555920128 24.96308358 0.800629927 1.610985829 0.513161452 0.353180813 86.9050099 65657.26126 0.043288658 0.086577718 2.78E-09 8.555920128 0.810355902 LNYSDES(ph)PEAGK ddPTM_HeLa_Romidepsin_16h_R1 2 LNYSDESPEAGK 12 0 Q9GZR1-2;Q9GZR1 Q9GZR1-2 SENP6 Sentrin-specific protease 6 1 0 LNY(0.008)S(0.425)DES(0.568)PEAGK;LNYS(0.011)DES(0.989)PEAGK ; 141.59 0.0017912 23325900 5796.6 5321.3 5506.3 4478.3 3899.8 3334.3 2774.9 3063.4 5919 5241.8 TRUE FALSE FALSE 5725.94881 5396.213401 5602.134842 4996.102117 3700.778654 3121.248991 3010.599937 3152.034646 5389.589816 5105.61728 1.12149981 1.056916942 1.097249272 0.978550064 0.72484451 0.611336263 0.589664241 0.617366025 1.055619628 1 12.31786968 -8.715664399 2.259736146 1.061848235 0.604898229 0.97808367 0.031089341 0.044163856 0.459126174 0.007166095 0.015764291 1.92E-09 8.715664399 -0.456950006 LPDLS(ph)PVENK ddPTM_HeLa_Romidepsin_16h_R1 1 LPDLSPVENK 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3;Q9Y520-2;A0A2R8Y7F4;A0A2R8YET2;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 0 LPDLS(1)PVENK 142.12 0.0044338 85381000 3811.6 2554.7 3744.1 2287.2 3217.3 3337.8 3259.4 3286.5 3051.1 3306.5 TRUE FALSE FALSE 3765.142753 2590.665134 3809.26449 2551.656826 3053.109176 3124.525352 3536.253355 3381.589692 2778.201974 3220.596653 1.169082365 0.804405336 1.182782229 0.792293199 0.947994892 0.97016972 1.09801187 1.049988575 0.862635801 1 11.65311227 -10.31258252 24.99998764 1.079844424 0.98185272 0 0.13737888 550.9468692 269314.4382 0.020697534 0.023668539 4.87E-11 10.31258252 -0.097991704 LPDS(ph)DDDEDEETAIQR ddPTM_HeLa_Romidepsin_16h_R1 5 LPDSDDDEDEETAIQR 16 0 Q96K21-3;H3BRM1;H3BRF9;Q96K21-2;Q96K21;Q96K21-4 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR;LPDS(1)DDDEDEETAIQR ;;;; 238.83 4.54E-46 321445700 1013.299 1002.53 896.655 1013.19 1473.14 1268.51 715 1181.684 1102.979 1165.08 TRUE FALSE FALSE 1000.948522 1016.643644 912.2609041 1130.339795 1397.960169 1187.456305 775.7320822 1215.874162 1004.325796 1134.811054 0.882039806 0.89587041 0.803887926 0.996059909 1.231888044 1.046391204 0.683578187 1.071433133 0.885015873 1 10.14823639 -9.038452171 24.88742993 0.927648037 1.003611893 0.121567205 0.13653577 1228.981765 795432.1513 0.021384687 0.035467286 9.15E-10 9.038452171 0.075963856 LPDS(ph)PALAK ddPTM_HeLa_Romidepsin_16h_R1 1 LPDSPALAK 9 0 H0YDB2;E9PNJ4;G0XQ39;Q13586 H0YDB2 STIM1 Stromal interaction molecule 1 1 0 LPDS(1)PALAK 104.43 0.024305 12518000 4076 5965.1 5483.4 2741.8 3740.4 5782.7 2554 5470.4 4842.5 5615.5 TRUE FALSE FALSE 4026.320144 6049.076834 5578.836277 3058.819817 3549.513431 5413.204133 2770.936696 5628.677393 4409.374672 5469.6085 0.736125839 1.105943293 1.019969944 0.559239261 0.64895201 0.989687677 0.506606039 1.029082318 0.806159101 1 12.41722186 -9.276336457 24.97430858 0.903044271 0.741441523 0.194067418 0.185135526 1173.281305 1966951.654 0.02881351 0.044127547 5.29E-10 9.276336457 -0.161602748 LPEASQS(ph)PLVLK ddPTM_HeLa_Romidepsin_16h_R1 2 LPEASQSPLVLK 12 0 H0Y4T7;E7ESY4;Q13330-3;Q13330;F8W9Y9 H0Y4T7 MTA1 Metastasis-associated protein MTA1 1 0 LPEAS(0.104)QS(0.896)PLVLK;LPEAS(0.002)QS(0.998)PLVLK ; 195.87 1.54E-10 54897000 4846.5 3963.8 4073 3614.7 3422.5 3482 3368.1 3060.1 4663.2 3769.5 TRUE FALSE FALSE 4787.428994 4019.60248 4143.888856 4032.648622 3247.837054 3259.511438 3654.18633 3148.639165 4246.111713 3671.567847 1.303919523 1.09479183 1.128642866 1.098345119 0.884591322 0.887770994 0.995265914 0.857573466 1.156484611 1 11.84218054 -8.841653594 4.486505989 1.140552512 0.911153263 0.666154281 0.077881527 0.145182418 5.413027099 0.017296296 0.032448509 1.44E-09 8.841653594 -0.229399248 LPEGPVDS(ph)EDDEEEDEEIDRTDPLQGR ddPTM_HeLa_Romidepsin_16h_R1 2 LPEGPVDSEDDEEEDEEIDRTDPLQGR 27 1 E9PCH4;Q8TEU7;Q8TEU7-4;B7Z7Y1;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;D6RD23;D6RIH0;D6RB02;Q8TEU7-6 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 0 LPEGPVDS(0.999)EDDEEEDEEIDRT(0.001)DPLQGR;LPEGPVDS(1)EDDEEEDEEIDRTDPLQGR ; 100.86 1.48E-08 75366000 988.61 775.66 1038.41 986.83 1102.05 1472.03 735.38 1206.64 1063.91 1137 TRUE FALSE FALSE 976.5604411 786.5797618 1056.48309 1100.931928 1045.808276 1377.972034 797.8431588 1241.552225 968.751225 1107.460576 0.88180154 0.710255316 0.953969029 0.994104848 0.944330027 1.244262833 0.720425789 1.121080291 0.874750078 1 10.11303963 -9.370794034 4.797889202 0.921406256 0.998750227 0.124351122 0.145131968 0.55056959 19.91055929 0.021842718 0.033704218 4.26E-10 9.370794034 0.07734397 LPELDPRGS(ph)DEENLDSETSASTESLLEER ddPTM_HeLa_Romidepsin_16h_R1 1 LPELDPRGSDEENLDSETSASTESLLEER 29 1 M0R300;M0R0P8;Q13459-2;Q13459;M0R240;M0QXP0 M0R300 MYO9B Unconventional myosin-IXb 1 0 LPELDPRGS(0.931)DEENLDS(0.025)ET(0.009)S(0.011)AS(0.012)T(0.01)ES(0.002)LLEER 48.694 0.010114 17434000 1936.8 1877.9 2111.5 1423.2 1786.6 2108.4 1517.8 2300.8 2032.3 2064.4 TRUE FALSE FALSE 1913.193537 1904.337125 2148.249772 1587.75708 1695.423135 1973.680045 1646.721894 2367.370018 1850.525998 2010.76659 0.951474699 0.947070204 1.068373516 0.789627741 0.843172521 0.981556016 0.818952285 1.177347003 0.920308706 1 10.97352991 -9.284295323 24.99217348 0.979998764 0.915313715 0.059362475 0.108169914 1528.645212 1671515.586 0.015166731 0.023176774 5.20E-10 9.284295323 -0.064685049 LPGDAAASSSAVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LPGDAAASSSAVKK 14 1 F5H148;Q9NYV6;H3BMT1;Q9NYV6-2 F5H148 RRN3 RNA polymerase I-specific transcription initiation factor RRN3 0 1 LPGDAAASSSAVK(1)K 107.09 0.0049286 962910 478.44 422.96 346.1 366.82 249.6 212.4 411.15 337.6 666.05 484.58 FALSE TRUE FALSE 472.6085893 428.914442 352.1237253 409.2334543 236.8619806 198.8283255 446.0730707 347.3679234 606.4768198 471.9905417 1.001309449 0.908735248 0.746039791 0.867037405 0.501836286 0.421254894 0.945089003 0.735963738 1.284934265 1 8.882614139 -9.69394183 1.320153941 1.002985624 0.674400867 0.50967496 0.167971931 0.253559686 0.890141894 0.025787543 0.039772857 2.02E-10 9.69394183 -0.328584757 LPLLPPES(ph)PGPLR ddPTM_HeLa_Romidepsin_16h_R1 2 LPLLPPESPGPLR 13 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;A0A0G2JPP5;Q14160-3;A0A669KAX5 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 LPLLPPES(1)PGPLR;LPLLPPES(1)PGPLR ; 155.14 0.00072343 121070000 3135.6 4465.7 3065.6 3039.7 4049 4694.7 3240.4 3669.4 3563.2 3597 TRUE FALSE FALSE 3097.382101 4528.568242 3118.955482 3391.164416 3842.364421 4394.723821 3515.639495 3775.5683 3244.498468 3503.549421 0.884069761 1.292565823 0.89022734 0.967922529 1.096706214 1.254363302 1.003450807 1.077640942 0.926060425 1 11.77460153 -9.460106855 0.717633489 0.95425896 1.10235835 0.118198754 0.126763112 0.917292204 0.942198268 0.028243621 0.059728307 3.47E-10 9.460106855 0.14809939 LPLPDDEHDLS(ph)DR ddPTM_HeLa_Romidepsin_16h_R1 2 LPLPDDEHDLSDR 13 0 Q8NF91;A0A0C4DG40;Q8NF91-4;Q8NF91-2;E7ENN3;H0Y326;A0A5F9ZHE1;Q5JV20;F8WAI0;A0A5F9ZH87;H0Y325;Q8NF91-11;Q8NF91-8;Q8NF91-3;Q8NF91-9;A0A5F9ZHB2 Q8NF91 SYNE1 Nesprin-1 1 0 LPLPDDEHDLS(1)DR;LPLPDDEHDLS(1)DR ; 147.53 0.00032194 3568500 1386.32 1480.52 1583.28 951.85 1249.92 1445.23 1101.72 1448.86 1327.53 1245.3 TRUE FALSE FALSE 1369.422999 1501.362799 1610.836324 1061.907376 1186.131918 1352.884467 1195.300069 1490.780478 1208.792392 1212.946926 1.12900488 1.237781115 1.328035291 0.875477197 0.977892678 1.11536988 0.985451254 1.229056643 0.996574842 1 10.24430071 -12.27315102 1.146826552 1.003316205 1.105694531 0.104476636 0.129159573 1.004590342 2.473323942 0.075777389 0.023351682 5.33E-13 12.27315102 0.102378326 LPLPS(ph)PALEYTLGSR ddPTM_HeLa_Romidepsin_16h_R1 2 LPLPSPALEYTLGSR 15 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 LPLPS(1)PALEYTLGSR;LPLPS(1)PALEYTLGSR ; 158.91 0.00029087 111677000 3622.8 4026.9 3368.4 2689.99 2007.1 2142.56 1371.38 1808.94 3352.2 3323.43 TRUE FALSE FALSE 3578.64392 4083.590804 3427.025589 3001.019301 1904.670197 2005.657331 1487.864983 1861.278825 3052.370836 3237.086809 1.105513732 1.26150179 1.058675837 0.927074088 0.588390213 0.619587132 0.459630857 0.574985762 0.94293759 1 11.66048034 -8.839892743 2.419674989 1.070603883 0.543954274 0.889343728 0.085759848 0.066041265 0.787314617 0.013130223 0.026762705 1.45E-09 8.839892743 -0.526649609 LPLQES(ph)EEEEREER ddPTM_HeLa_Romidepsin_16h_R1 1 LPLQESEEEEREER 14 1 P23497;E9PHV6;P23497-7;P23497-5;P23497-2;P23497-3;P23497-4;P23497-6;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 0 LPLQES(1)EEEEREER 106.35 0.0026849 29935000 1072.2 968.87 1192.5 878.01 863.8 993.15 820 1012.3 1295.3 1297.9 TRUE FALSE FALSE 1059.131614 982.5097773 1213.254962 979.5296474 819.7170627 929.6909202 889.6507795 1041.589303 1179.445124 1264.180371 0.837801028 0.777191135 0.959716659 0.774833774 0.648417806 0.735410027 0.70373722 0.823924598 0.932972186 1 10.3039866 -11.55727809 0.230909317 1.099480937 0.69681135 0.536068472 0.074301261 2.037574168 0.243569252 0.273999408 0.103339601 2.77E-12 11.55727809 -0.402669588 LPLQLDDAVRPEAEGEEEGR ddPTM_HeLa_Romidepsin_16h_R1 2 LPLQLDDAVRPEAEGEEEGR 20 1 P14868-2;P14868;C9J7S3;C9JLC1 P14868-2 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 0 ; ; 95.205 0.0012997 16306800 924.64 838.18 1027.62 778.65 895.9 870.84 838.27 829.32 985.47 992.43 FALSE FALSE TRUE 913.370132 849.97992 1045.505295 868.6811767 850.1788799 815.1961345 909.4726329 853.3150657 897.327095 966.6465255 0.944885341 0.879307893 1.081579737 0.898654424 0.879513718 0.843323917 0.940853361 0.882758116 0.92828875 1 9.916844624 -9.033257288 24.86452173 0.972829158 0.887605763 0.342107597 0.053815467 451.8237654 337801.2273 0.007683998 0.012748536 9.26E-10 9.033257288 -0.085223395 LPLS(ph)PPLVEDSAFEPSR ddPTM_HeLa_Romidepsin_16h_R1 4 LPLSPPLVEDSAFEPSR 17 0 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 0 LPLS(1)PPLVEDSAFEPSR;LPLS(1)PPLVEDSAFEPSR;LPLS(0.999)PPLVEDS(0.001)AFEPSR;LPLS(1)PPLVEDSAFEPSR ;;; 138.98 0.0008644 41166700 1805.11 2291.06 2418.61 1896.91 2944.96 3397.99 2983.56 3201.03 2151.08 2301.3 TRUE FALSE FALSE 1783.108625 2323.313603 2460.704892 2116.239659 2794.667702 3180.869406 3236.983512 3293.646753 1958.682017 2241.511894 0.795493715 1.036493988 1.097788015 0.944112617 1.246777994 1.419073177 1.444107221 1.469386248 0.873821826 1 11.13025644 -8.572523469 1.023284552 0.915293975 1.497950938 0.873292923 0.08345941 0.163340382 0.316999224 0.016821061 0.062212287 2.68E-09 8.572523469 0.582656962 LPLS(ph)PPLVEDSAFEPSRK ddPTM_HeLa_Romidepsin_16h_R1 2 LPLSPPLVEDSAFEPSRK 18 1 O96007 O96007 MOCS2 Molybdopterin synthase catalytic subunit 1 0 LPLS(1)PPLVEDSAFEPSRK;LPLS(1)PPLVEDSAFEPSRK ; 171.49 3.63E-07 23858000 4210.2 4902.66 3603.64 4242.13 6116.7 6448.8 5487.9 6735.3 4630.1 4561.5 TRUE FALSE FALSE 4158.884463 4971.679776 3666.359843 4732.62503 5804.541974 6036.742493 5954.042089 6930.175279 4215.97226 4442.991572 0.936054997 1.118993744 0.82520072 1.065188838 1.306449017 1.358711218 1.340097543 1.55979933 0.948903952 1 12.11731569 -8.719881001 2.302450258 0.971197464 1.409726148 0.844840239 0.087576426 0.078726413 0.85002446 0.012413647 0.027124663 1.91E-09 8.719881001 0.438528684 LPLVPES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 LPLVPESPR 9 0 C9J0I9;Q86WB0-2;Q86WB0;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 LPLVPES(1)PR;LPLVPES(1)PR;LPLVPES(1)PR ;; 145.23 0.005914 64158300 4217.3 3968.2 3982 2990.06 2616.08 2759.52 2306 2517.12 4406.5 3695.99 TRUE FALSE FALSE 4165.897925 4024.064424 4051.30504 3335.784806 2482.571676 2583.195578 2501.871582 2589.948896 4012.371604 3599.967647 1.157204268 1.117805719 1.125372625 0.926615218 0.689609441 0.717560776 0.694970574 0.719436714 1.114557684 1 11.81376823 -8.942767714 3.04780656 1.083041958 0.704438903 0.949189142 0.043147187 0.059196114 1.121648379 0.009708639 0.018324656 1.14E-09 8.942767714 -0.378603056 LPLVPES(ph)PRR ddPTM_HeLa_Romidepsin_16h_R1 2 LPLVPESPRR 10 1 C9J0I9;Q86WB0-2;Q86WB0;Q86WB0-3 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 LPLVPES(1)PRR;LPLVPES(1)PRR ; 143.55 0.0012404 104618000 9090 9762.1 9713 8805.8 6673 6275 5154.3 5216.3 8655.9 7988.6 TRUE FALSE FALSE 8979.207584 9899.5311 9882.050691 9823.968029 6332.45191 5874.047752 5592.106113 5367.225411 7881.694625 7781.05502 1.153983304 1.272260776 1.270014242 1.262549616 0.813829473 0.754916619 0.718682248 0.689781192 1.012933928 1 12.92575007 -8.630371147 5.449979196 1.118863671 0.730891441 0.80947442 0.098543328 0.08839177 3.933920292 0.017753984 0.035954015 2.34E-09 8.630371147 -0.38797223 LPNGEPSPDPGGKGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 LPNGEPSPDPGGKGTPR 17 1 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 0 LPNGEPS(0.002)PDPGGKGT(0.998)PR 65.652 0.021696 5387200 1208.5 1023.6 955.06 1048.4 830.55 1056 762.94 791.82 1079.8 803.26 TRUE FALSE FALSE 1193.770337 1038.010268 971.6824187 1169.620941 788.1639343 988.5250081 827.7441046 814.7300624 983.2199836 782.3911894 1.525797265 1.32671518 1.241939367 1.494931125 1.007378336 1.263466437 1.057967058 1.041333381 1.25668591 1 9.611746314 -7.89976437 1.151732267 1.269090762 1.020569974 0.226110962 0.161244287 1.179936044 2.347075714 0.033505513 0.267570061 1.26E-08 7.89976437 -0.248520788 LPNGLGGPNGFPKPTPEEGPPELNRQS(ph)PNSSSAAASVASR ddPTM_HeLa_Romidepsin_16h_R1 2 LPNGLGGPNGFPKPTPEEGPPELNRQSPNSSSAAASVASR 40 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 LPNGLGGPNGFPKPT(0.037)PEEGPPELNRQS(0.857)PNS(0.06)S(0.016)S(0.018)AAAS(0.006)VAS(0.006)R;LPNGLGGPNGFPKPT(0.037)PEEGPPELNRQS(0.707)PNS(0.062)S(0.071)S(0.071)AAAS(0.027)VAS(0.024)R ; 55.919 0.00043928 69378000 1006.14 1126.89 787.03 763.22 676.98 673.17 413.51 427.19 1042.22 891.59 TRUE FALSE FALSE 993.8767787 1142.754387 800.727927 851.4670875 642.4311844 630.1566096 448.6335291 439.5500687 949.0012329 868.4263633 1.144457171 1.315890944 0.922044702 0.980471256 0.739764719 0.725630446 0.516605147 0.506145469 1.092782616 1 9.762259713 -8.488751901 1.02646308 1.085323677 0.500867979 0.845367476 0.09984788 0.18160604 0.34681508 0.017806675 0.071750372 3.25E-09 8.488751901 -0.584455699 LPNLSS(ph)PSAEGPPGPPSGPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 LPNLSSPSAEGPPGPPSGPAPR 22 0 O60784-3;O60784-4;O60784;O60784-2 O60784-3 TOM1 Target of Myb protein 1 1 0 LPNLS(0.019)S(0.975)PS(0.006)AEGPPGPPSGPAPR 134.58 0.00010966 8449900 902.63 924.23 801.08 682.25 1118 1299.2 1190.7 1386.7 917.1 970.83 TRUE FALSE FALSE 891.6283984 937.2413342 815.0224614 761.1349551 1060.944288 1216.185313 1291.838028 1426.821977 835.0722791 945.6076966 0.942915758 0.991152396 0.861903371 0.804916201 1.121970868 1.286141512 1.366145848 1.508894208 0.883106474 1 9.885097968 -8.202183623 1.816270012 0.954670311 1.441481721 0.886887111 0.075584185 0.090564946 0.564894012 0.011399565 0.039954577 6.28E-09 8.202183623 0.486811411 LPPKVES(ph)LESLYFTPIPAR ddPTM_HeLa_Romidepsin_16h_R1 1 LPPKVESLESLYFTPIPAR 19 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 LPPKVES(0.766)LES(0.187)LY(0.041)FT(0.006)PIPAR 62.94 0.01064 2043900 253.69 326.35 236.2 555.47 334.64 442.09 439.41 510.81 222.65 354.1 TRUE FALSE FALSE 250.5979287 330.9443639 240.3109619 619.696055 317.5620721 413.8418758 476.7334744 525.5894814 202.7356264 344.900431 0.726580503 0.959535953 0.6967546 1.796738999 0.920735504 1.199887964 1.382235079 1.523887575 0.587809142 1 8.430036121 -9.287570508 24.99654791 0.863792192 1.331850865 0.569587305 0.243430197 459.4768434 439525.5567 0.034728723 0.05305943 5.16E-10 9.287570508 0.468058674 LPPKVESLESLYFT(ph)PIPAR ddPTM_HeLa_Romidepsin_16h_R1 1 LPPKVESLESLYFTPIPAR 19 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 LPPKVESLES(0.004)LY(0.001)FT(0.995)PIPAR 65.416 0.011893 16274000 1878.4 1871.8 1810.3 2458.6 2180.7 2200.6 1576.3 1329.4 1739.4 1515.8 TRUE FALSE FALSE 1855.505338 1898.15125 1841.807512 2742.8749 2069.410742 2059.988762 1710.190883 1367.864092 1583.823708 1476.419297 1.256760421 1.28564511 1.247482687 1.857788573 1.401641624 1.395259982 1.158336853 0.926474 1.07274655 1 10.52788678 -11.47710009 0.721859085 1.016375639 1.339860718 0.202047876 0.222563779 0.717914075 0.778313575 0.112910433 0.053938995 3.33E-12 11.47710009 0.32348508 LPS(ph)GSGAAS(ph)PTGSAVDIR ddPTM_HeLa_Romidepsin_16h_R1 3 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 LPS(0.784)GS(0.215)GAAS(0.365)PT(0.27)GS(0.365)AVDIR;LPS(0.779)GS(0.221)GAAS(0.971)PT(0.029)GSAVDIR;LPS(1)GSGAAS(0.977)PT(0.009)GS(0.013)AVDIR ;; 166.21 6.14E-11 59690100 3545.86 3604.01 2997.55 2561.25 3444.6 3585.19 2455.72 3639.5 3561.66 3204.5 TRUE FALSE FALSE 3502.641694 3654.747347 3049.7211 2857.393776 3268.809208 3356.10793 2664.308796 3744.80319 3243.096209 3121.246628 1.122193185 1.170925525 0.977084308 0.915465555 1.047276809 1.075245993 0.85360406 1.199778049 1.039038755 1 11.60790664 LPS(ph)GSGAASPTGSAVDIR ddPTM_HeLa_Romidepsin_16h_R1 2 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 LPS(0.679)GS(0.305)GAAS(0.015)PTGSAVDIR;LPS(0.816)GS(0.172)GAAS(0.01)PT(0.001)GS(0.001)AVDIR ; 95.9 0.0037133 339990000 139.29 189.758 140.19 171.597 330.49 286.31 115.11 58.438 319.47 176.913 TRUE FALSE FALSE 137.5922799 192.4294181 142.6299481 191.4378525 313.6238621 268.015715 124.8874405 60.12881133 290.8958031 172.3167748 0.798484536 1.11671901 0.827719462 1.110964692 1.82004255 1.555366362 0.724754979 0.348943458 1.688145588 1 7.428919342 -9.158252545 6.529491364 0.916731598 1.157114206 0 0.458577342 0.553701288 30.25609599 0.061653021 0.102764832 6.95E-10 9.158252545 0.240382608 LPS(ph)IVVEPTEGEVESGELR ddPTM_HeLa_Romidepsin_16h_R1 2 LPSIVVEPTEGEVESGELR 19 0 B5MBX5;B5MCP4;Q53QV2 B5MBX5 LBH Protein LBH 1 0 LPS(0.986)IVVEPT(0.014)EGEVESGELR;LPS(0.989)IVVEPT(0.011)EGEVESGELR ; 212.92 4.80E-29 7145500 546.06 680.84 465.14 436.5 497.08 944.9 704.62 824.39 688.46 534.35 TRUE FALSE FALSE 539.4044107 690.4248834 473.2355666 486.9701838 471.7121527 884.5239395 764.4704052 848.242424 626.8824133 520.46751 1.036384405 1.326547518 0.909250928 0.935639928 0.906323918 1.699479646 1.468814845 1.629770173 1.204460223 1 9.023664296 -8.261385647 25 1.020377776 1.586300904 0.771484033 0.137600051 1.42644201 663435.2832 0.017317698 0.041241669 5.48E-09 8.261385647 0.565923128 S(ph)SPPSAGNSPSSLK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPPSAGNSPSSLK 14 0 P57682;P57682-2 P57682 KLF3 Krueppel-like factor 3 1 0 S(0.5)S(0.5)PPSAGNSPSSLK;S(0.852)S(0.148)PPSAGNSPSSLK ; 170.26 5.60E-05 14360800 3535.7 3255.5 3365.4 2614.86 1882.75 1686.26 912.55 1407.06 3991.3 3744.7 TRUE FALSE FALSE 3492.605528 3301.331014 3423.973375 2917.202416 1786.666242 1578.513428 990.0619742 1447.771061 3634.308132 3647.412154 0.957557134 0.905115977 0.938740463 0.799800596 0.4898449 0.43277627 0.271442308 0.396931029 0.99640731 1 11.83265752 -8.773487522 1.395122262 0.975118215 0.337584785 0.973870309 0.043995002 0.040464485 0.157708138 0.006677122 0.01687696 1.68E-09 8.773487522 -0.637533429 down LPSAQT(ph)PNGTDYVASGK ddPTM_HeLa_Romidepsin_16h_R1 2 LPSAQTPNGTDYVASGK 17 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3;Q9Y520-2;A0A2R8Y7F4;A0A2R8YET2;H7C5N8 E7EPN9 PRRC2C Protein PRRC2C 1 0 LPSAQT(0.997)PNGT(0.003)DYVASGK;LPS(0.007)AQT(0.543)PNGT(0.413)DY(0.037)VASGK ; 183.88 5.76E-09 27872000 4871.4 4983.7 4504.3 4666.3 4715.7 4533.1 3978.1 4535.6 4528.3 4587.2 TRUE FALSE FALSE 4812.025503 5053.860659 4582.695452 5205.839562 4475.040232 4243.44954 4315.999715 4666.83043 4123.277507 4468.023883 1.076991894 1.131117647 1.025664941 1.165132438 1.001570347 0.949737435 0.965975077 1.044495408 0.92284142 1 12.12542118 -8.540896422 24.99351761 1.053501691 0.983158841 0.177687549 0.067023368 255.4088784 354293.2824 0.008414111 0.016830705 2.88E-09 8.540896422 -0.07034285 LPSGSGAAS(ph)PTGS(ph)AVDIR ddPTM_HeLa_Romidepsin_16h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 LPS(0.004)GS(0.004)GAAS(0.985)PT(0.384)GS(0.623)AVDIR 112.44 0.00012805 0 2437.2 2356.8 2030.2 1083.4 2246.2 2228.4 1544.6 2317 2526.4 2575.4 TRUE FALSE FALSE 2407.494469 2389.979092 2065.534779 1208.667806 2131.568032 2086.012432 1675.798285 2384.038739 2300.432457 2508.490737 0.959738234 0.952755797 0.823417344 0.481830683 0.849741241 0.83158068 0.668050418 0.950387699 0.917058382 1 11.2926039 -9.704826882 3.869900514 0.97921315 0.752250846 0.382254289 0.118924983 0.145084724 4.429999475 0.017811009 0.025158932 1.97E-10 9.704826882 -0.226962304 LPSGSGAAS(ph)PTGSAVDIR ddPTM_HeLa_Romidepsin_16h_R1 4 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 LPSGS(0.001)GAAS(0.701)PT(0.297)GS(0.001)AVDIR;LPSGSGAAS(0.98)PT(0.015)GS(0.005)AVDIR;LPSGSGAAS(0.988)PT(0.012)GSAVDIR;LPS(0.068)GS(0.134)GAAS(0.531)PT(0.266)GSAVDIR ;;; 245.67 8.62E-62 5142800000 3002.83 3332.03 3796.73 2892.48 3728.14 3239.23 2667.31 3063.63 3201.1 3244 TRUE FALSE FALSE 2966.230353 3378.938406 3862.810493 3226.922147 3537.879104 3032.253657 2893.871245 3152.2713 2914.785599 3159.720412 0.938763551 1.069378921 1.222516549 1.021268254 1.119681061 0.95965885 0.915863072 0.997642478 0.922482124 1 11.62558119 -6.329328154 15.77058696 1.001939659 1.026446762 0 0.093253764 0 0 0.012855113 0 4.68E-07 6.329328154 0.024507103 LPSGSGAASPTGSAVDIR ddPTM_HeLa_Romidepsin_16h_R1 1 LPSGSGAASPTGSAVDIR 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 118.24 0.015415 5140800 467.92 335.71 320.29 239.78 342.9 359.56 234.41 225.94 479.48 465.43 FALSE FALSE TRUE 462.2168111 340.4361342 325.8645131 267.5044918 325.4005335 336.5852764 254.3207795 232.4772174 436.5941079 453.3380615 1.019585273 0.750954228 0.718811282 0.590077283 0.717787808 0.742459778 0.560995869 0.512812043 0.963065193 1 8.824443482 -10.0760046 2.05744351 1.011658337 0.639069168 0.829871004 0.071395055 0.083302402 0.686995215 0.012669375 0.016101059 8.39E-11 10.0760046 -0.37258917 LPSRPPLPGSGGSQSGAK(ac)MR ddPTM_HeLa_Romidepsin_16h_R1 1 LPSRPPLPGSGGSQSGAKMR 20 2 Q9Y570-4;Q9Y570 Q9Y570-4 PPME1 Protein phosphatase methylesterase 1 0 1 LPSRPPLPGSGGSQSGAK(1)MR 41.348 0.02617 2345800 426.18 0 403.49 120.56 332.77 283.2 272.8 284.63 363 423.83 FALSE TRUE FALSE 420.9855542 0 410.5125742 134.4997145 315.7875052 265.104434 295.9716252 292.86532 330.5323708 412.8188355 1.019782815 0 0.994413382 0.325808085 0.764954208 0.642181052 0.716952813 0.709428192 0.800671729 1 8.689364987 LPSS(ph)PASPSPK ddPTM_HeLa_Romidepsin_16h_R1 1 LPSSPASPSPK 11 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 LPS(0.021)S(0.978)PAS(0.001)PSPK 110.08 0.014534 8177700 2430.7 3083.9 2334.6 3420.6 2360.1 2651.5 1709.7 2269.9 2622.1 2685.2 TRUE FALSE FALSE 2401.073693 3127.315225 2375.232734 3816.105866 2239.65529 2482.077707 1854.921875 2335.575975 2387.572809 2615.438117 0.918038809 1.195713714 0.908158644 1.459069454 0.85632127 0.949010298 0.709220327 0.892996076 0.912876811 1 11.35283692 -8.126553453 2.434806006 1.007577881 0.80918317 0.202501319 0.175700527 0.385208449 4.396058484 0.024348979 0.078393101 7.47E-09 8.126553453 -0.198394711 LPSS(ph)PVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 4 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 LPS(0.001)S(0.999)PVYEDAASFK;LPS(0.033)S(0.967)PVYEDAASFK;LPS(0.004)S(0.996)PVYEDAASFK;LPS(0.009)S(0.991)PVYEDAASFK ;;; 172.85 3.21E-05 3465200000 19593.6 20821.1 20925.8 14194.3 25340.5 26762.5 25172.1 26660 20351.5 20145.4 TRUE FALSE FALSE 19354.78567 21114.21999 21290.00477 15835.51175 24047.27973 25052.46262 27310.21755 27431.36504 18531.21087 19622.0196 0.986380916 1.076047238 1.085005784 0.807027619 1.225525212 1.276752502 1.391814813 1.397988871 0.944408947 1 14.26018592 -8.560865298 5.243149631 0.996066692 1.344482284 0.819489835 0.079604562 0.055238121 3.742084884 0.01106825 0.022857933 2.75E-09 8.560865298 0.348415592 LPSSPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 1 LPSSPVYEDAASFK 14 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 0 0 156.69 0.0051219 3680400 818.85 880.45 789.55 722.95 931.99 1035 1103.3 1263.8 844.51 904.13 FALSE FALSE TRUE 808.8695412 892.8449982 803.2917865 806.5408806 884.4270726 968.8668403 1197.014274 1300.366059 768.9749105 880.6405723 0.918501335 1.013858578 0.912167588 0.915857054 1.004299711 1.100184196 1.359254061 1.476613842 0.873199504 1 9.782409502 -7.768942077 1.659251779 0.958356306 1.498472652 0.949262607 0.043388854 0.064294849 0.301575379 0.005897761 0.040734593 1.70E-08 7.768942077 0.540116346 LPSSSGLPAADVSPATAEEPLS(ph)PSTPTR ddPTM_HeLa_Romidepsin_16h_R1 2 LPSSSGLPAADVSPATAEEPLSPSTPTR 28 0 O43149 O43149 ZZEF1 Zinc finger ZZ-type and EF-hand domain-containing protein 1 1 0 LPSSSGLPAADVSPAT(0.001)AEEPLS(0.662)PS(0.163)T(0.057)PT(0.118)R;LPSSSGLPAADVSPATAEEPLS(0.823)PS(0.116)T(0.04)PT(0.021)R ; 138.02 1.62E-10 14621800 4546.3 4490.5 4405.9 4298.2 5964.6 6576.9 5239.6 7146.8 4779.9 4992.4 TRUE FALSE FALSE 4490.887947 4553.717377 4482.582841 4795.178108 5660.204205 6156.657316 5684.651493 7353.581382 4352.373773 4862.696728 0.923538563 0.936459259 0.921830641 0.986114984 1.164005185 1.266099381 1.169032702 1.512243472 0.89505351 1 12.2475409 -7.655553691 0.679370299 0.954500149 1.599824985 0.852966483 0.072339627 0.558973366 0.242459844 0.012745152 0.249428924 2.21E-08 7.655553691 0.645324836 LPTEMEGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LPTEMEGKK 9 1 Q9NWX6 Q9NWX6 THG1L Probable tRNA(His) guanylyltransferase 0 1 ; LPTEMEGK(1)K;LPTEMEGK(1)K 75.294 0.021439 18929400 2429.89 2545.42 2514.55 1865.64 2118.94 1813.06 1703.31 1656.14 2618.32 2107.77 FALSE TRUE FALSE 2400.273566 2581.25449 2558.314688 2081.354075 2010.802585 1697.211317 1847.989109 1704.057798 2384.130901 2053.009832 1.169148598 1.257302547 1.246128805 1.01380619 0.979441284 0.826694199 0.900136512 0.830029049 1.161285672 1 11.00352482 -8.651299277 2.116389146 1.108722106 0.858603349 0.708681591 0.082947187 0.187385372 1.697633978 0.015717989 0.036485782 2.23E-09 8.651299277 -0.250118757 LPVDLAEELGHR ddPTM_HeLa_Romidepsin_16h_R1 4 LPVDLAEELGHR 12 0 P42771-2;P42771;K7ES20;K7ENC6;J3QRG6;P42771-4 P42771-2 CDKN2A Cyclin-dependent kinase inhibitor 2A 0 0 ;;; ;;; 177.04 9.14E-07 32771700 15844.5 16512 15098.1 17978.8 14511.7 12584.3 11147.2 12017.6 16949.7 15991.2 FALSE FALSE TRUE 15651.38114 16744.45637 15360.8761 20057.59345 13771.1138 11780.20384 12094.04289 12365.3103 15433.67638 15575.74632 1.004855936 1.075033968 0.98620482 1.287745257 0.884138295 0.756317136 0.77646635 0.793882363 0.990878772 1 13.92701367 -8.528935917 24.99312979 1.027349631 0.783076576 0.678800254 0.08673707 71.07792492 293281.7019 0.012271885 0.02459734 2.96E-09 8.528935917 -0.244273055 LPVY(ph)T(ph)RT(ph)GS(ph)GAVR ddPTM_HeLa_Romidepsin_16h_R1 1 LPVYTRTGSGAVR 13 1 Q96MV8-3;Q96MV8 Q96MV8-3 ZDHHC15 Palmitoyltransferase ZDHHC15 4 0 LPVY(1)T(1)RT(1)GS(1)GAVR 51.276 0.023728 2137100 603.87 414.21 601.14 462.6 554.42 715.16 493.08 409.48 646.03 653.91 TRUE FALSE FALSE 596.5098002 420.0412593 611.6025895 516.0879886 526.1258786 669.4635841 534.9622029 421.3276577 588.2474588 636.9213239 0.936551781 0.659486884 0.960248254 0.810285304 0.82604532 1.051093061 0.839918814 0.661506597 0.92357947 1 9.314971364 -10.49449867 15.30309211 0.972018286 0.839620605 0.198523785 0.11296842 4.119534106 2221.863695 0.018972799 0.020785559 3.20E-11 10.49449867 -0.132397681 LQAALDDEEAGGRPAMEPGNGS(ph)LDLGGDSAGR ddPTM_HeLa_Romidepsin_16h_R1 4 LQAALDDEEAGGRPAMEPGNGSLDLGGDSAGR 32 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 0 LQAALDDEEAGGRPAMEPGNGS(0.987)LDLGGDS(0.013)AGR;LQAALDDEEAGGRPAMEPGNGS(0.997)LDLGGDS(0.003)AGR;LQAALDDEEAGGRPAMEPGNGS(0.994)LDLGGDS(0.006)AGR;LQAALDDEEAGGRPAMEPGNGS(0.978)LDLGGDS(0.022)AGR ;;; 73.373 1.79E-05 825072000 4870.68 4380.73 4464.72 4668.78 4658.33 5187.66 5060.07 4687.94 4673.09 4122.84 TRUE FALSE FALSE 4811.314279 4442.402032 4542.426579 5208.606311 4420.598037 4856.185268 5489.872219 4823.578148 4255.117126 4015.728022 1.198117565 1.106250724 1.131158921 1.297051564 1.100821075 1.209291377 1.367092639 1.201171524 1.059612878 1 11.97144585 -16.52287875 0.129917742 0.279241034 1.304662006 0.507110145 0.073515792 44.35982481 0.408790275 8.304106066 0.265337554 3.00E-17 16.52287875 1.025420972 LQAAMASVIVRPSS(ph)S(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LQAAMASVIVRPSSSTK 17 1 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 3 0 LQAAMASVIVRPS(0.017)S(0.991)S(0.996)T(0.996)K 58.93 0.030476 3498200 1289.5 1374.4 1155.9 833.88 883.8 1096.9 690.51 1355.4 1478.1 1208.2 TRUE FALSE FALSE 1273.783078 1393.748839 1176.017955 930.2971291 838.6963881 1026.81163 749.1619022 1394.616361 1345.895034 1176.81079 1.082402616 1.184344035 0.999326285 0.790523963 0.712685842 0.872537573 0.636603529 1.185081215 1.143680059 1 10.20066666 -9.361475316 4.698936557 1.05232834 0.823449365 0.403871564 0.145468515 0.173829535 6.315619903 0.020479308 0.031664238 4.35E-10 9.361475316 -0.228878975 LQADPKPIS(ph)PQQK ddPTM_HeLa_Romidepsin_16h_R1 1 LQADPKPISPQQK 13 1 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;O75128-6 H7C1N2 COBL Protein cordon-bleu 1 0 LQADPKPIS(1)PQQK 69.805 0.024041 47575000 2552.4 1948.9 2432.3 2634 2354.4 2505.1 2203.6 2612 2543.5 2347.2 TRUE FALSE FALSE 2521.290367 1976.336665 2474.633161 2938.555473 2234.246183 2345.032195 2390.773729 2687.574099 2316.00299 2286.219406 1.102820823 0.864456255 1.082412806 1.285333974 0.977266739 1.02572491 1.04573241 1.175553883 1.013027439 1 11.15874815 -12.57114048 1.09842626 0.996194813 1.070006978 0.054018016 0.105945708 1.557667428 3.064480983 0.096255025 0.018149346 2.68E-13 12.57114048 0.073812165 LQALK(ac)DTANR ddPTM_HeLa_Romidepsin_16h_R1 2 LQALKDTANR 10 1 P29401;P29401-2;E9PFF2;F8WAX4;F8W888 P29401 TKT Transketolase 0 1 ; LQALK(1)DTANR;LQALK(1)DTANR 131.09 0.0094791 1480780 906.34 647.89 1199.4 672.9 1327.81 1408.73 1013.62 1253.15 1579.43 832.2 FALSE TRUE FALSE 895.2931795 657.0110124 1220.275054 750.7038641 1260.046901 1318.716699 1099.716857 1289.407918 1438.161825 810.579324 1.104510259 0.810544993 1.505435702 0.92613251 1.554501655 1.626881738 1.356704797 1.590723918 1.774239464 1 9.662809566 -8.75332726 24.98609016 1.060906351 1.52643031 0.185899529 0.289262026 86.37983293 266055.8701 0.024379387 0.048090088 1.76E-09 8.75332726 0.465523959 SAPGGGSK(ac)VPQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SAPGGGSKVPQKK 13 2 P06748;P06748-2;P06748-3;E5RI98 P06748;E5RI98 NPM1 Nucleophosmin 0 2 ; SAPGGGSK(1)VPQK(1)K;SAPGGGSK(1)VPQK(1)K 168.82 2.61E-05 17820700 3168.1 3074.6 3261.3 4948.6 8521.9 8922.3 8508.1 9955.4 3206.5 2529.4 FALSE TRUE FALSE 3129.485979 3117.8843 3318.061558 5520.780416 8086.995643 8352.193825 9230.777802 10243.44379 2919.702609 2463.685823 1.27024556 1.265536486 1.346787617 2.240862193 3.282478458 3.390121316 3.746734959 4.157771943 1.185095348 1 11.26660258 -8.840811393 1.0948396 1.115643024 3.924982208 0.981715445 0.158111394 0.046215786 0.108629617 0.0282296 0.077707401 1.44E-09 8.840811393 2.809339184 up LQAVTDDHIR ddPTM_HeLa_Romidepsin_16h_R1 2 LQAVTDDHIR 10 0 A0A2R8YEP4;P30043 A0A2R8YEP4 BLVRB Flavin reductase (NADPH) 0 0 ; ; 158.47 0.0012862 8275000 7700.9 7228.9 8091.8 7256.9 10445.7 10445.3 9436.9 9692 8554.1 7403.9 FALSE FALSE TRUE 7607.038469 7330.668644 8232.634385 8095.976923 9912.616951 9777.879041 10238.47005 9972.422729 7788.999872 7211.545611 1.054841622 1.016518378 1.141590836 1.12264102 1.374548188 1.35586455 1.419733106 1.382841247 1.080073578 1 12.81609278 -8.919396047 1.195641066 1.025762681 1.407110981 0.9263518 0.043312908 0.068814112 0.194993403 0.006310692 0.015547036 1.20E-09 8.919396047 0.3813483 LQDEIQNMK(ac)EEMAR ddPTM_HeLa_Romidepsin_16h_R1 2 LQDEIQNMKEEMAR 14 1 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 1 ; LQDEIQNMK(1)EEMAR;LQDEIQNMK(1)EEMAR 111.88 0.0005592 635710 0 117.1 301.19 124.568 552.03 458.59 561.19 436.53 516.24 283.85 FALSE TRUE FALSE 0 118.7485369 306.4320856 138.9711383 523.8578492 429.287579 608.8574646 449.1603068 470.0662015 276.4755361 0 0.429508298 1.108351538 0.502652568 1.894771077 1.552714519 2.202210992 1.624593312 1.700209024 1 8.111008019 -8.761850182 24.99923729 0.555404051 1.826985542 0.47885223 0.490171152 4.954814192 301554.1539 0.063837326 0.121099749 1.73E-09 8.761850182 1.271581491 LQDGTPQAALS(ph)PLTPAR ddPTM_HeLa_Romidepsin_16h_R1 1 LQDGTPQAALSPLTPAR 17 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6 A0A087WVP4 SMTN Smoothelin 1 0 LQDGTPQAALS(0.897)PLT(0.103)PAR 96.805 0.004931 4259600 656.65 745.45 685.47 627.47 1401.7 1995.2 1700.3 2083.8 933.64 871.2 TRUE FALSE FALSE 648.6464972 755.9444647 697.4003178 700.0210337 1330.166019 1867.713159 1844.72344 2144.091465 850.1329001 848.5660984 0.764403031 0.890849241 0.821857389 0.824945794 1.567545558 2.201022599 2.173930166 2.526722985 1.001846411 1 9.728883232 -8.461797194 2.070948337 0.873561539 2.330968331 0.967582603 0.116402519 0.040981743 0.343900423 0.018624752 0.049199754 3.45E-09 8.461797194 1.457406792 up LQDSSDPDT(ph)GSEEEGSSRLSPPHSPR ddPTM_HeLa_Romidepsin_16h_R1 1 LQDSSDPDTGSEEEGSSRLSPPHSPR 26 1 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 LQDS(0.013)S(0.032)DPDT(0.529)GS(0.383)EEEGS(0.014)S(0.014)RLS(0.014)PPHSPR 59.07 0.0024163 5000300 2406.2 2171.7 2404.4 2231.4 2090.7 2230.7 1608.5 1913.9 2799.3 2866.1 TRUE FALSE FALSE 2376.872309 2202.27325 2446.247573 2489.404967 1984.003778 2088.165469 1745.12595 1969.275677 2548.923597 2791.638309 0.851425595 0.788882013 0.876276689 0.891736211 0.71069514 0.748007169 0.625126093 0.705419348 0.913056533 1 11.44689632 -5.591698477 0.097740725 1.152342236 4.91E-11 0.722359278 0.057422958 27.92930034 0.278755626 0.55930031 4.375679716 2.56E-06 5.591698477 -1.152342236 LQEDPNYS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 LQEDPNYSPQR 11 0 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3;H0Y710;A0A0G2JL47;P46379-5;H0Y4L1;P46379-4 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 LQEDPNYS(1)PQR;LQEDPNYS(1)PQR ; 203.88 3.04E-13 38899000 7895.6 7893.8 8236.5 5092.8 8119.2 8934.2 7377.2 7868.4 8333.4 8339.4 TRUE FALSE FALSE 7799.36539 8004.929124 8379.852827 5681.653498 7704.846927 8363.333454 8003.819184 8096.05974 7588.039833 8122.741186 0.960188834 0.985496022 1.03165331 0.69947489 0.948552558 1.029619591 0.985359376 0.996715217 0.934172302 1 12.98775096 -9.20897337 0.005609583 1.920221058 5.91E-08 0 0.09236965 28987.5925 62.82772662 10591.3758 10914.02604 6.18E-10 9.20897337 -1.920220999 LQEDPNYS(ph)PQRFPNAQR ddPTM_HeLa_Romidepsin_16h_R1 2 LQEDPNYSPQRFPNAQR 17 1 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3;H0Y710;A0A0G2JL47;P46379-5;H0Y4L1;P46379-4 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 LQEDPNY(0.002)S(0.998)PQRFPNAQR;LQEDPNYS(1)PQRFPNAQR ; 122.46 0.015037 15602100 2847.8 3154.8 2973.2 2952 3307.7 3152.1 3108.5 3199.4 3135.1 3270.9 TRUE FALSE FALSE 2813.089918 3199.213357 3024.947299 3293.32413 3138.895726 2950.690983 3372.535912 3291.969591 2854.688804 3185.921546 0.882975264 1.004172046 0.949473254 1.033711622 0.985239492 0.926165613 1.05857469 1.033286458 0.896032361 1 11.63749503 -9.645681999 1.819483327 0.946249625 1.003435521 0.267586341 0.049246193 0.464641607 3.128532787 0.009597573 0.014528815 2.26E-10 9.645681999 0.057185896 LQEEGGGS(ph)DEEETGSPSEDGMQSAR ddPTM_HeLa_Romidepsin_16h_R1 2 LQEEGGGSDEEETGSPSEDGMQSAR 25 0 Q13610-2;Q13610 Q13610-2 PWP1 Periodic tryptophan protein 1 homolog 1 0 LQEEGGGS(0.995)DEEET(0.005)GSPSEDGMQSAR;LQEEGGGS(0.965)DEEET(0.034)GS(0.001)PSEDGMQSAR ; 73.788 0.00016591 31588000 3713.6 4699.3 4061.8 3385.7 3558.1 3636.8 3192.1 4656.3 6281.3 8348 TRUE FALSE FALSE 3668.337215 4765.456869 4132.493925 3777.170564 3376.51688 3404.420217 3463.236894 4791.022694 5719.484796 8131.117757 0.451147963 0.586076479 0.508231961 0.464532759 0.415258637 0.41869031 0.42592384 0.589220675 0.703406957 1 12.98923797 -12.36131479 0.57371283 1.106808265 0.464325878 0.597283349 0.109566571 0.28027091 0.1235977 0.098451203 0.014426124 4.35E-13 12.36131479 -0.642482387 LQEES(ph)DLELAK ddPTM_HeLa_Romidepsin_16h_R1 2 LQEESDLELAK 11 0 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 LQEES(1)DLELAK;LQEES(1)DLELAK ; 168.89 0.00041539 33075000 7355.5 6958.9 7062.8 5329.2 6941.7 7063.4 5645 6466.2 6998.3 7031.3 TRUE FALSE FALSE 7265.848337 7056.867577 7185.725071 5945.387179 6587.439146 6612.071536 6124.486159 6653.289295 6372.35452 6848.625812 1.060920619 1.030406357 1.049221445 0.868113888 0.961862909 0.9654596 0.89426497 0.971477998 0.930457393 1 12.74159882 -9.279880191 24.98720998 1.031042296 0.933618085 0.418098259 0.046248291 378.9406344 513461.4827 0.00550889 0.008423964 5.25E-10 9.279880191 -0.097424211 LQEGYDHSYYFIATFITDHIR ddPTM_HeLa_Romidepsin_16h_R1 1 LQEGYDHSYYFIATFITDHIR 21 0 X6RA14;P10768 X6RA14 ESD S-formylglutathione hydrolase 0 0 109.5 9.49E-05 1218700 2406.3 1921.9 2120.6 2086.9 2219.4 2476.9 1604.2 1924 2090 1823.4 FALSE FALSE TRUE 2376.97109 1948.956559 2157.508153 2328.197197 2106.135736 2318.634084 1740.460708 1979.667904 1903.065165 1776.027805 1.338363669 1.097368269 1.214794131 1.310901322 1.185868673 1.30551677 0.979973795 1.114660423 1.071528925 1 10.79443845 -4.097136958 19.69432896 1.168940924 0.005839956 0 0.123169223 0 0 0.019337264 0 8.00E-05 4.097136958 -1.163100968 LQEK(ac)EDLQELNDR ddPTM_HeLa_Romidepsin_16h_R1 2 LQEKEDLQELNDR 13 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 1 ; LQEK(1)EDLQELNDR;LQEK(1)EDLQELNDR 142.39 0.00019791 1867880 301.03 467.49 421.47 377.45 1361.19 1295.93 1250.52 1275.43 997.92 577.17 FALSE TRUE FALSE 297.3609306 474.0713365 428.8055086 421.092545 1291.723395 1213.124255 1356.739138 1312.332555 908.6635359 562.1750402 0.528947231 0.843280656 0.762761556 0.749041695 2.297724557 2.157911982 2.413374911 2.334384241 1.616335609 1 9.134875591 -8.760829368 24.99964357 0.774840439 2.298676961 0.839018077 0.293089807 2.571330461 105370.4999 0.026607559 0.050767972 1.73E-09 8.760829368 1.523836523 LQEKEDLQELNDR ddPTM_HeLa_Romidepsin_16h_R1 2 LQEKEDLQELNDR 13 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 120.9 0.0053735 101691000 7086.2 5880.6 6596.4 5923.5 6771.7 7594.9 7107.8 7278.9 7130.3 7573.6 FALSE FALSE TRUE 6999.830669 5963.387241 6711.207575 6608.402941 6426.11488 7109.610401 7711.536355 7489.503487 6492.54811 7376.83678 0.948893256 0.808393546 0.909767665 0.895831525 0.871120654 0.963774937 1.045371693 1.015273038 0.880126307 1 12.8487866 -7.858206844 5.21935645 0.944303294 1.02975886 0.284688908 0.059293983 0.238357183 10.21426751 0.009550939 0.030215898 1.39E-08 7.858206844 0.085455565 LQELAS(ph)PPAGRPTPAPR ddPTM_HeLa_Romidepsin_16h_R1 2 LQELASPPAGRPTPAPR 17 1 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 0 LQELAS(0.846)PPAGRPT(0.154)PAPR;LQELAS(0.5)PPAGRPT(0.5)PAPR ; 121.72 1.36E-05 0 3399.5 2912.9 2454.3 2982.4 2866.9 2847.8 2388.2 2697.3 3288 2693.6 TRUE FALSE FALSE 3358.065586 2953.907883 2497.016062 3327.239121 2720.591395 2665.834771 2591.053648 2775.34212 2993.913045 2623.619884 1.279936018 1.125890187 0.951744602 1.268186425 1.036960961 1.016090321 0.987587289 1.057829351 1.141138266 1 11.357343 -8.551077375 24.99347677 1.129181896 1.018763175 0.217014782 0.0963743 299.1526033 265148.7972 0.017751627 0.035503725 2.81E-09 8.551077375 -0.110418721 LQFSLK ddPTM_HeLa_Romidepsin_16h_R1 2 LQFSLK 6 0 P20290-2;P20290 P20290-2 BTF3 Transcription factor BTF3 0 0 ; ; 128.48 0.02481 7963700 8101.2 8112.7 11301.9 3074.2 9010.8 10056.5 7777.3 6990.5 7949.4 7045.5 FALSE FALSE TRUE 8002.459458 8226.910804 11498.60483 3429.653469 8550.945252 9413.922106 8437.903668 7192.759088 7238.385754 6862.456894 1.166121636 1.198828777 1.675581356 0.499770493 1.246047208 1.371800545 1.229574742 1.04813177 1.054780506 1 12.74450947 -11.8498523 0.868423849 1.007077694 1.182406289 0.044189409 0.277964911 1.380357825 2.018914132 0.138511603 0.053823262 1.41E-12 11.8498523 0.175328595 LQGQVS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 LQGQVSAK 8 0 O95235-2;O95235 O95235-2 KIF20A Kinesin-like protein KIF20A 1 0 LQGQVS(1)AK 112.71 0.021461 24552000 2743.1 3075.5 4537.1 3304.4 4616.8 6280.2 7401.6 2027 5440.4 5287.9 TRUE FALSE FALSE 2709.666042 3118.79697 4616.066322 3686.470276 4381.187468 5878.915488 8030.291719 2085.648047 4953.796998 5150.519596 0.526095667 0.605530551 0.896233135 0.715747258 0.850630191 1.141421827 1.559122642 0.404939348 0.961805291 1 12.33050227 -8.402407444 4.270388082 0.763625083 1.085158093 0.114801942 0.297982542 0.300972978 9.056541437 0.043123926 0.099624561 3.96E-09 8.402407444 0.32153301 LQLEETMPS(ph)PYGR ddPTM_HeLa_Romidepsin_16h_R1 1 LQLEETMPSPYGR 13 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 LQLEETMPS(0.958)PY(0.041)GR 99.834 0.017688 15911000 2097.2 1902.2 2505.1 1971.9 2808.2 3367.8 2532 3168.9 2214.7 1925.5 TRUE FALSE FALSE 2071.63852 1928.979222 2548.700215 2199.900356 2664.887075 3152.608449 2747.068017 3260.587122 2016.611685 1875.475232 1.10459391 1.02852823 1.358962342 1.172982889 1.420912966 1.68096512 1.464731695 1.738539153 1.075253701 1 10.8730405 -8.637970197 0.542279468 1.027834732 1.75606155 0.837469715 0.102862793 0.335372534 0.149419592 0.021998819 0.11997829 2.30E-09 8.637970197 0.728226818 LQLEIDQK ddPTM_HeLa_Romidepsin_16h_R1 2 LQLEIDQK 8 0 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 0 0 ; ; 133.23 0.014884 1265570 1679.05 1362.82 1373.08 920.94 1435.89 1669.51 1219.62 1264.46 1363.93 1428.94 FALSE FALSE TRUE 1658.585093 1382.005816 1396.977881 1027.423416 1362.611175 1562.833699 1323.214492 1301.045155 1241.936685 1391.815933 1.191669856 0.99295157 1.003708787 0.738189147 0.979016796 1.122873839 0.950710838 0.934782484 0.892313887 1 10.44275271 -10.05553175 6.899998227 1.090822297 0.957001502 0 0.116807665 0.273344659 28.55745217 0.018910856 0.023320878 8.80E-11 10.05553175 -0.133820796 LQLERPVS(ph)PETQADLQR ddPTM_HeLa_Romidepsin_16h_R1 2 LQLERPVSPETQADLQR 17 1 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 LQLERPVS(0.936)PET(0.064)QADLQR;LQLERPVS(0.823)PET(0.177)QADLQR ; 114.1 0.00076624 38628000 3826.9 3464 3694.9 2666.5 3626.6 3627.9 2653.6 3316.4 4073.2 3385.9 TRUE FALSE FALSE 3780.256271 3512.766283 3759.208185 2974.813276 3441.521069 3396.088899 2878.996718 3412.354802 3708.88279 3297.93383 1.146249884 1.065141529 1.13986768 0.902023336 1.043538545 1.029762595 0.872969825 1.034694745 1.124608007 1 11.68734674 -9.265346882 24.90701107 1.075287887 0.977513229 0.427623632 0.066631046 319.5099615 2036609.259 0.011409808 0.017841658 5.43E-10 9.265346882 -0.097774659 LQLLEDDK(ac)ENR ddPTM_HeLa_Romidepsin_16h_R1 1 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 1 LQLLEDDK(1)ENR 89.403 0.02279 0 136.74 0 0 0 131.68 173.17 138.08 0 277.97 0 FALSE TRUE FALSE 135.0733603 0 0 0 124.9598782 162.1049959 149.8085118 0 253.107667 0 0 LQLLEDDKENR ddPTM_HeLa_Romidepsin_16h_R1 1 LQLLEDDKENR 11 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 0 119.34 0.011767 9957600 1334.2 1298.5 1337.7 1212.1 1484.4 1568.9 1236.2 1653.7 1305.6 1282.4 FALSE FALSE TRUE 1317.938257 1316.780317 1360.982107 1352.248705 1408.645529 1468.652353 1341.202797 1701.5472 1188.823866 1249.083063 1.055124592 1.05419756 1.08958495 1.0825931 1.127743679 1.175784379 1.073749886 1.362237029 0.951757254 1 10.2866537 -4 0.302239752 1.017235403 3.323960849 0.725005523 0.055595024 17.77464156 0.227380112 0.017634517 22.53436299 1.00E-04 4 2.306725447 LQLQGLDLS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 0 LQLQGLDLS(0.99)S(0.01)R 159.66 0.0014403 13648000 2927.2 2557.2 2833.4 1423.2 2123.2 1832.1 1324.2 1772.7 2613.7 2723.5 TRUE FALSE FALSE 2891.52216 2593.200329 2882.714138 1587.75708 2014.845181 1715.034723 1436.677515 1823.990278 2379.924126 2652.743077 1.090012141 0.977554272 1.086691796 0.598534059 0.759532726 0.646513693 0.541581854 0.687586481 0.897155909 1 11.37326924 -9.261671329 24.9999999 1.040693436 0.647159697 0.847613165 0.076529282 4.471896932 481995.6796 0.009731913 0.015460151 5.47E-10 9.261671329 -0.393533739 LQLQGLDLSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 LQLQGLDLSSR 11 0 P49454 P49454 CENPF Centromere protein F 1 0 LQLQGLDLS(0.025)S(0.975)R;LQLQGLDLS(0.166)S(0.834)R ; 159.66 0.0014403 23349000 6114.5 5512.2 5884.4 3020.6 3406.7 3813.6 2928.5 3056.6 5921.5 5395 TRUE FALSE FALSE 6039.974122 5589.800896 5986.815514 3369.855984 3232.843387 3569.923268 3177.246717 3145.037898 5391.866209 5254.837122 1.149412243 1.063743893 1.139296114 0.641286477 0.615212862 0.679359452 0.604632768 0.598503403 1.026076753 1 12.35943033 -9.255467579 24.75935184 1.076415554 0.628677194 0.957587431 0.047131686 77.25390535 320297.8136 0.009303308 0.015166631 5.55E-10 9.255467579 -0.44773836 LQMEAPHIIVGTPGR ddPTM_HeLa_Romidepsin_16h_R1 2 LQMEAPHIIVGTPGR 15 0 P60842;J3QR64;J3KTB5;J3QL43;J3QS69;J3KT12;P60842-2;J3QKZ9;J3QLN6;J3KS25;J3KSZ0 P60842 EIF4A1 Eukaryotic initiation factor 4A-I 0 0 ; ; 106.36 0.0019578 11546300 2981.7 2626.5 2858.6 2515.24 2514.7 2703.61 2721.3 2656.2 3292.3 2657 FALSE FALSE TRUE 2945.357894 2663.475936 2908.352734 2806.063883 2386.365475 2530.858047 2952.447154 2733.052956 2997.828442 2587.970757 1.138095508 1.029175437 1.123796599 1.084271867 0.922099088 0.97793147 1.140834821 1.056060216 1.158370292 1 11.3376056 LQPLS(ph)PVPSDIEISR ddPTM_HeLa_Romidepsin_16h_R1 2 LQPLSPVPSDIEISR 15 0 H0Y327;A0A087WVM4;B7ZM99;Q6UB35 H0Y327 MTHFD1L "Monofunctional C1-tetrahydrofolate synthase, mitochondrial" 1 0 LQPLS(1)PVPSDIEISR;LQPLS(0.757)PVPS(0.242)DIEIS(0.001)R ; 175.7 2.17E-06 11373900 3369.2 4013.9 3651.6 2971.8 3543.8 3153 2975.6 2933.4 3585.5 3338.5 TRUE FALSE FALSE 3328.134894 4070.40779 3715.154566 3315.413499 3362.946662 2951.533476 3228.34739 3018.273301 3264.8039 3251.765289 1.023485584 1.251753257 1.142503913 1.019573433 1.034191082 0.907671131 0.992798404 0.928195313 1.004009702 1 11.66700741 -8.341688635 6.827131272 1.042155427 0.948114069 0.311481785 0.078844133 0.317399664 22.91802859 0.012672476 0.028556161 4.55E-09 8.341688635 -0.094041358 LQPQEIS(ph)PPPTANLDR ddPTM_HeLa_Romidepsin_16h_R1 4 LQPQEISPPPTANLDR 16 0 H0YBP1;E7ESA6;Q05397-2;Q05397-7;Q05397;Q05397-5;B4DWJ1;E9PEI4;H0YB16;H0YBZ1;Q05397-6 H0YBP1 PTK2 Focal adhesion kinase 1 1 0 LQPQEIS(0.99)PPPT(0.01)ANLDR;LQPQEIS(0.998)PPPT(0.002)ANLDR;LQPQEIS(0.999)PPPT(0.001)ANLDR;LQPQEIS(1)PPPTANLDR ;;; 217.65 2.40E-26 48142800 3718.91 4268.36 3655.76 4544.82 4709.62 5064.93 4911.82 5709.4 4573.82 4153.78 TRUE FALSE FALSE 3673.582494 4328.450084 3719.386969 5070.313472 4469.270517 4741.297319 5329.029868 5874.592481 4164.726084 4045.864197 0.907984627 1.069845619 0.919305935 1.253209012 1.104651639 1.171887411 1.317154904 1.451999423 1.029378615 1 11.98223218 -7.252646935 0.449929341 0.954300896 1.804024229 0.766359868 0.080890523 1.467690048 0.19791284 0.018681604 0.664563338 5.59E-08 7.252646935 0.849723333 LQPSSS(ph)PENSLDPFPPR ddPTM_HeLa_Romidepsin_16h_R1 3 LQPSSSPENSLDPFPPR 17 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 LQPS(0.016)S(0.062)S(0.919)PENS(0.003)LDPFPPR;LQPS(0.062)S(0.209)S(0.725)PENS(0.003)LDPFPPR;LQPS(0.003)S(0.009)S(0.675)PENS(0.312)LDPFPPR ;; 181.81 4.49E-09 314366800 8947.8 8821.1 8379 7661.1 8322.8 8657.8 7139.1 7105.6 9601.3 9348.2 TRUE FALSE FALSE 8838.740772 8945.283677 8524.83298 8546.912429 7898.056459 8104.594522 7745.494976 7311.189325 8742.535681 9105.332416 0.970721372 0.982422527 0.936246212 0.938671104 0.867410007 0.890093206 0.850654827 0.802956882 0.960155575 1 13.15249597 -7.250770395 0.322190771 0.998800144 0.653823436 0.901123982 0.019194622 1.079018478 0.079713759 0.006011277 0.145967614 5.61E-08 7.250770395 -0.344976709 LQPSSSPENS(ph)LDPFPPR ddPTM_HeLa_Romidepsin_16h_R1 1 LQPSSSPENSLDPFPPR 17 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 LQPS(0.001)S(0.002)S(0.017)PENS(0.98)LDPFPPR 99.711 0.0032642 5469600 957.17 1147.3 1089 905.08 909.66 1043.1 1039 1124.2 1228.7 1061.4 TRUE FALSE FALSE 945.5036439 1163.45172 1107.953588 1009.729608 863.2366558 976.4492765 1127.252634 1156.726953 1118.801995 1033.824675 0.914568656 1.125385907 1.071703563 0.976693276 0.834993279 0.94450181 1.090371183 1.118881162 1.082197032 1 10.01377583 -7.699540325 5.846505221 0.97022951 1.109230242 0.179745015 0.083759681 0.185585629 12.15874672 0.011440519 0.043770915 2.00E-08 7.699540325 0.139000732 LQQELDDLLVDLDHQR ddPTM_HeLa_Romidepsin_16h_R1 3 LQQELDDLLVDLDHQR 16 0 P35579 P35579 MYH9 Myosin-9 0 0 ;; ;; 132.51 5.56E-16 14284000 2140.95 2172.62 2265.752 2105.3 2161.18 2414.05 1915.41 2134.98 2366.55 2179.259 FALSE FALSE TRUE 2114.855278 2203.206201 2305.186463 2348.724692 2050.88692 2259.799996 2078.104878 2196.752278 2154.879841 2122.641537 0.996331807 1.037954908 1.085998942 1.106510285 0.966195603 1.064616873 0.979018285 1.034914393 1.015187823 1 11.05164504 -10.25469712 11.11799974 0.998265872 1.03954247 0.132911157 0.04078183 0.410198702 650.5823146 0.006683252 0.007997695 5.56E-11 10.25469712 0.041276598 LQQELDDLTVDLDHQR ddPTM_HeLa_Romidepsin_16h_R1 2 LQQELDDLTVDLDHQR 16 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 0 0 ; ; 206.13 3.79E-19 5372700 2582.2 2343.7 2433.2 2358.5 3074.4 3229.9 2523.9 3165.4 2627.1 2607.8 FALSE FALSE TRUE 2550.727153 2376.69467 2475.548825 2631.200867 2917.501896 3023.519814 2738.280003 3256.985855 2392.125596 2540.04898 1.004203924 0.93568852 0.974606728 1.035885878 1.148600645 1.190339178 1.078042205 1.282253169 0.94176357 1 11.3106406 -8.798860605 2.890026481 0.99431253 1.173267986 0.763329663 0.052974216 0.093198156 1.591755676 0.00695746 0.01402235 1.59E-09 8.798860605 0.178955456 LQQETAELEES(ph)VESGK ddPTM_HeLa_Romidepsin_16h_R1 1 LQQETAELEESVESGK 16 0 P42566;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 0 LQQET(0.043)AELEES(0.957)VESGK 190.55 1.18E-12 2048500 770.12 760.63 812.87 716.9 589.77 780.36 433.31 624.65 805.83 1136.2 TRUE FALSE FALSE 760.7334812 771.3381691 827.0176614 799.7913511 559.6718362 730.4975145 470.1153406 642.7232622 733.7545466 1106.68136 0.687400645 0.696983067 0.747295194 0.722693433 0.505720848 0.660079351 0.424797378 0.580766321 0.663022414 1 10.11202418 -16.52287875 0.096750348 2.307479189 0.314752766 0.249973739 0.126658572 36.70308066 0.26634083 9.739096747 0.701554154 3.00E-17 16.52287875 -1.992726422 LQQGAGLES(ph)PQGQPEPGAAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 4 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 0 LQQGAGLES(1)PQGQPEPGAAS(1)PQR;LQQGAGLES(1)PQGQPEPGAAS(1)PQR;LQQGAGLES(1)PQGQPEPGAAS(1)PQR;LQQGAGLES(1)PQGQPEPGAAS(1)PQR ;;; 136.8 2.38E-05 63740000 6539.49 6703.7 6696.78 5617.96 7805.3 8137.4 6864.7 7483 7020.9 7295.4 TRUE FALSE FALSE 6459.784181 6798.074865 6813.334647 6267.534968 7406.966415 7617.446402 7447.787447 7699.508799 6392.93312 7105.864456 0.909077878 0.95668513 0.958832622 0.882022871 1.042373727 1.071994329 1.048118423 1.083542874 0.899670006 1 12.79479445 -8.608163299 7.296493907 0.951585816 1.064480653 0.750113287 0.035317263 0.106531334 7.732781984 0.005825319 0.011697157 2.47E-09 8.608163299 0.112894836 LQQGAGLESPQGQPEPGAAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 3 LQQGAGLESPQGQPEPGAASPQR 23 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 LQQGAGLESPQGQPEPGAAS(1)PQR;LQQGAGLES(0.005)PQGQPEPGAAS(0.995)PQR;LQQGAGLES(0.006)PQGQPEPGAAS(0.994)PQR ;; 111.82 4.08E-06 162700000 8421.2 8060.5 7169.6 6271.5 6311.1 7096.4 6180.7 7075.5 8640.4 8780.4 TRUE FALSE FALSE 8318.559175 8173.975931 7294.38388 6996.640338 5989.021017 6642.962943 6705.688504 7280.218429 7867.580984 8552.283942 0.97267107 0.955765265 0.852916476 0.81810197 0.700283229 0.776747239 0.784081603 0.85126014 0.919939169 1 13.06209404 -9.637107178 1.661476619 0.987874998 0.778506353 0.795233823 0.041730156 0.085630477 0.479300215 0.006162837 0.009463528 2.31E-10 9.637107178 -0.209368645 LQQGAGLESPQGQPEPGAAS(ph)PQRQQDLHLESPQR ddPTM_HeLa_Romidepsin_16h_R1 2 LQQGAGLESPQGQPEPGAASPQRQQDLHLESPQR 34 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 LQQGAGLES(0.027)PQGQPEPGAAS(0.941)PQRQQDLHLES(0.032)PQR;LQQGAGLES(0.325)PQGQPEPGAAS(0.605)PQRQQDLHLES(0.07)PQR ; 61.526 0.00030305 20679400 2880 2456.56 2205.75 3857.5 2738.9 2437.28 2415.72 2634.69 3279.8 3022.3 TRUE FALSE FALSE 2844.897452 2491.143516 2244.140153 4303.5223 2599.123713 2281.545674 2620.911197 2710.920598 2986.446474 2943.78021 0.966409599 0.846239644 0.762332781 1.461903401 0.882920438 0.775039409 0.89032163 0.920897759 1.014493699 1 11.52345425 -8.549048474 24.99927245 0.991203877 0.858920816 0.130865984 0.175514226 359.897869 343799.831 0.024493158 0.048987388 2.82E-09 8.549048474 -0.132283061 LQQQAALS(ph)PTTAPAVSSVSK ddPTM_HeLa_Romidepsin_16h_R1 1 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 0 LQQQAALS(0.963)PT(0.036)T(0.001)APAVSSVSK 168.64 3.41E-10 21527000 4536 4411.5 4244 4311.7 5157.8 5959.7 4993 5847.4 4866.6 4371.1 TRUE FALSE FALSE 4480.713487 4473.605213 4317.86504 4810.239041 4894.57822 5578.894404 5417.105295 6016.585293 4431.319107 4257.538192 1.052418859 1.050749285 1.01416942 1.129817003 1.14962638 1.310356866 1.272356242 1.413160616 1.04081723 1 12.05580376 -8.17652588 0.691772112 1.020921425 1.436261934 0.93535459 0.034314709 0.200257081 0.127501419 0.006084583 0.051440917 6.66E-09 8.17652588 0.415340509 LQQQAALSPT(ph)TAPAVSSVSK ddPTM_HeLa_Romidepsin_16h_R1 1 LQQQAALSPTTAPAVSSVSK 20 0 A0A0U1RRM1;Q8WXI9;A0A0U1RR30 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 0 LQQQAALS(0.028)PT(0.772)T(0.186)APAVS(0.012)S(0.003)VSK 121.82 0.00039709 22930000 4751.9 4563.4 4576.8 4451.2 5384.9 6166 5522.7 6200.6 4812.8 4445.4 TRUE FALSE FALSE 4693.982015 4627.643665 4656.457284 4965.868688 5110.088459 5772.0125 5991.798 6380.004578 4382.331114 4329.907867 1.084083578 1.068762617 1.075417174 1.146876294 1.180184109 1.333056655 1.383816512 1.473473518 1.012107243 1 12.08012061 -7.512781946 0.460517343 1.027744063 1.746264323 0.97887262 0.0227565 0.447204045 0.073952573 0.006817719 0.166951206 3.07E-08 7.512781946 0.718520259 LQQQHSEQPPLQPS(ph)PVMTR ddPTM_HeLa_Romidepsin_16h_R1 2 LQQQHSEQPPLQPSPVMTR 19 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YDU3;Q5JTV8-2 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 0 LQQQHSEQPPLQPS(0.926)PVMT(0.074)R;LQQQHSEQPPLQPS(0.918)PVMT(0.082)R ; 87.748 0.0014472 56255000 3717.79 4938.1 4310.09 2801.04 3287.53 4204.6 2880.66 3951.27 4598.7 4359.3 TRUE FALSE FALSE 3672.476145 5007.618701 4385.105308 3124.909424 3119.755077 3935.93963 3125.343188 4065.593763 4187.380754 4246.044758 0.864916965 1.17936079 1.032750609 0.735957721 0.734743804 0.926966119 0.736059879 0.957501391 0.986183847 1 12.05190386 -9.263707247 24.97411982 0.963277281 0.815080919 0.417320504 0.10715755 199.9585964 2201976.587 0.017431503 0.027430664 5.45E-10 9.263707247 -0.148196362 LQQTVPADAS(ph)PDSK ddPTM_HeLa_Romidepsin_16h_R1 2 LQQTVPADASPDSK 14 0 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 0 LQQT(0.008)VPADAS(0.991)PDS(0.001)K;LQQTVPADAS(0.998)PDS(0.002)K ; 125.33 0.0032257 28686200 6621.6 7321.9 7645.3 4873.2 8260.4 9291.5 8020.4 9479.5 7590.4 8107.5 TRUE FALSE FALSE 6540.893392 7424.9779 7778.363239 5436.662313 7838.840964 8697.803137 8701.652576 9753.774376 6911.495613 7896.865981 0.828289781 0.940243626 0.9849937 0.688458222 0.992652146 1.101424686 1.101912151 1.23514498 0.875220072 1 12.94706449 -8.27151895 2.795194968 0.908352398 1.153752303 0.613104049 0.091330758 0.16217868 2.515676287 0.014429405 0.039313382 5.35E-09 8.27151895 0.245399906 LQQTVPADASPDS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 LQQTVPADASPDSK 14 0 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 0 LQQT(0.001)VPADAS(0.22)PDS(0.779)K;LQQTVPADAS(0.016)PDS(0.984)K ; 124.5 0.0033946 32282100 8946.1 8308.1 8592.5 5538.1 9425.1 10888 9801.5 11263.1 9469.3 8284.7 TRUE FALSE FALSE 8837.061492 8425.06165 8742.048858 6178.44118 8944.101977 10192.29194 10634.03917 11588.98003 8622.342092 8069.4623 1.095123958 1.044067292 1.083349613 0.765657109 1.108388842 1.263069528 1.317812609 1.436152695 1.068515072 1 12.97825683 -8.138687185 2.284097076 1.029527281 1.374486549 0.714002103 0.094157814 0.132485229 1.328459743 0.013937239 0.045729755 7.27E-09 8.138687185 0.344959269 LQS(ph)IGTENTEENRR ddPTM_HeLa_Romidepsin_16h_R1 1 LQSIGTENTEENRR 14 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 LQS(0.992)IGT(0.007)ENT(0.001)EENRR 73.597 0.014643 4267100 630.87 830.22 679.99 632.89 576.67 772.96 631.25 851.67 685.02 861.32 TRUE FALSE FALSE 623.1807138 841.907859 691.8249407 706.0677196 547.240378 723.5703506 684.8683592 876.3117277 623.7500955 838.9427822 0.742816706 1.003534301 0.824639004 0.841616061 0.652297617 0.862478784 0.816346923 1.044542901 0.743495395 1 9.712428609 -12.56166094 1.313381807 1.000674719 0.832367722 0 0.133380994 0.507634191 1.55899489 0.076350456 0.017668902 2.74E-13 12.56166094 -0.168306997 LQS(ph)PIKEENTTAVEEIGR ddPTM_HeLa_Romidepsin_16h_R1 1 LQSPIKEENTTAVEEIGR 18 1 S4R3P6;S4R3N2;A0A087X1L0;Q9NS73-3;Q9NS73-2;Q9NS73-5;Q9NS73;S4R3Y0;S4R2X9 S4R3P6 MBIP MAP3K12-binding inhibitory protein 1 1 0 LQS(0.53)PIKEENT(0.362)T(0.108)AVEEIGR 53.453 0.027794 10339000 1112.3 1054.9 1416.1 850.53 1000.3 1293.6 754.56 838.5 1446.8 1183.3 TRUE FALSE FALSE 1098.74286 1069.75091 1440.746626 948.8722805 949.2509584 1210.943135 818.6523076 862.7606746 1317.394584 1152.557695 0.953308337 0.928153891 1.250042954 0.823275298 0.823603853 1.050657281 0.710291824 0.74856181 1.143018341 1 10.17062326 -7.394137535 0.76934185 0.984543253 0.581056037 0.35105532 0.132368125 1.816015272 0.857983341 0.019113044 0.6022224 4.04E-08 7.394137535 -0.403487216 LQS(ph)PLEPHSK ddPTM_HeLa_Romidepsin_16h_R1 1 LQSPLEPHSK 10 0 O15211-2;O15211 O15211-2 RGL2 Ral guanine nucleotide dissociation stimulator-like 2 1 0 LQS(1)PLEPHSK 89.26 0.016692 9761500 4022.3 3761.9 3905.3 4438.3 4529.3 4183.3 3452 3622.8 4470.8 4174.1 TRUE FALSE FALSE 3973.27466 3814.860127 3973.270108 4951.477129 4298.15292 3916.000631 3745.212794 3727.620002 4070.920451 4065.65628 0.977277563 0.938313488 0.977276443 1.217878932 1.057185513 0.963190285 0.921182839 0.916855667 1.00129479 1 11.98927254 -7.96493856 4.273387378 1.005900252 0.921068846 0.229132073 0.073444223 0.284092972 11.70502948 0.011041511 0.034546193 1.08E-08 7.96493856 -0.084831406 LQS(ph)PLPGESAAK ddPTM_HeLa_Romidepsin_16h_R1 2 LQSPLPGESAAK 12 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 0 LQS(0.971)PLPGES(0.029)AAK;LQS(0.65)PLPGES(0.35)AAK ; 121.42 0.0070733 13864600 5758.5 5232 5215.2 4010.9 3242.2 2743.62 2366.59 2529.05 6389.7 4988.5 TRUE FALSE FALSE 5688.313187 5305.656233 5305.968368 4474.65913 3076.738436 2568.311537 2567.608096 2602.224072 5818.189229 4858.898051 1.170700255 1.0919464 1.09201064 0.920920563 0.633217327 0.528579013 0.528434239 0.535558483 1.197429781 1 12.24641345 -8.815599974 2.069088988 1.084929478 0.529417611 0.960635774 0.05311993 0.051879184 0.452338857 0.009868021 0.021054532 1.53E-09 8.815599974 -0.555511867 LQSFDS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 LQSFDSPER 9 0 E9PGM9;P78332-2;P78332 E9PGM9 RBM6 RNA-binding protein 6 1 0 LQSFDS(1)PER 132.86 0.0070349 95998000 3232.3 3593.1 3224.9 1899.2 2733.4 3283.3 3023.6 2965.8 3453.3 3377.4 TRUE FALSE FALSE 3192.903484 3643.683756 3281.028032 2118.79444 2593.904398 3073.507726 3280.424509 3051.610744 3144.428199 3289.654661 0.97058926 1.107618924 0.997377649 0.644078075 0.788503556 0.934294947 0.997194188 0.92763863 0.955853584 1 11.68372043 LQSIGT(ph)ENTEENR ddPTM_HeLa_Romidepsin_16h_R1 2 LQSIGTENTEENR 13 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 LQS(0.019)IGT(0.98)ENTEENR;LQS(0.072)IGT(0.924)ENT(0.005)EENR ; 252.52 2.19E-53 32286000 2057.8 1951.3 1880.04 1546.55 2987.5 2978 2564.8 3048.1 2371.2 1731.16 TRUE FALSE FALSE 2032.718742 1978.770453 1912.761308 1725.369388 2835.036727 2787.715411 2782.654048 3136.291964 2159.113933 1686.184214 1.205514039 1.173519736 1.134372681 1.023238964 1.681332742 1.653268598 1.650266931 1.85999367 1.280473341 1 10.71954644 -8.755440115 24.99821473 1.104177893 1.702723104 0.892447206 0.097397265 31.8263678 132615.3073 0.014391161 0.028194616 1.76E-09 8.755440115 0.598545211 LQSIGT(ph)ENTEENRR ddPTM_HeLa_Romidepsin_16h_R1 1 LQSIGTENTEENRR 14 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 LQS(0.054)IGT(0.943)ENT(0.002)EENRR 101.9 0.0038689 8679200 1363.9 1031.7 1012.6 972.32 1235.7 1261.9 1143.4 1397.7 1190.5 1154.2 TRUE FALSE FALSE 1347.276262 1046.2243 1030.223878 1084.744213 1172.637618 1181.268663 1240.520367 1438.140244 1084.018698 1124.213718 1.198416494 0.930627587 0.916395043 0.964891458 1.043073572 1.050750977 1.103455996 1.279240968 0.964246105 1 10.13470061 -7.26238607 2.557647372 1.056205303 1.326601517 0.400891087 0.087036298 0.520452726 4.286377584 0.015102841 0.3025437 5.47E-08 7.26238607 0.270396214 LQSIGTENTEENR ddPTM_HeLa_Romidepsin_16h_R1 2 LQSIGTENTEENR 13 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ; ; 203.88 2.11E-15 26393000 1781.99 1987.83 1379.05 1211.25 1865.53 2194.7 1758.44 1520.16 1859.25 1926.72 FALSE FALSE TRUE 1760.27042 2015.814723 1403.051787 1351.300424 1770.325043 2054.465753 1907.80185 1564.143431 1692.954023 1876.663537 0.937978698 1.07414818 0.747630973 0.720054713 0.94333641 1.09474379 1.016592379 0.833470359 0.902108444 1 10.8739543 -11.25979764 0.761005976 0.991852195 0.919020638 0 0.121912631 1.524907523 1.900398486 0.050376936 0.02985996 5.50E-12 11.25979764 -0.072831557 LQSIGTENTEENRR ddPTM_HeLa_Romidepsin_16h_R1 2 LQSIGTENTEENRR 14 1 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ; ; 109.1 0.0038598 183605000 4029.4 4147.5 4644.4 3627.7 4262.6 4238.9 4038.3 4538.8 4111.2 4056 FALSE FALSE TRUE 3980.288123 4205.888614 4725.233834 4047.151743 4045.063616 3968.04797 4381.313101 4670.123017 3743.483975 3950.624535 1.007508582 1.064613601 1.196072619 1.024433405 1.023904848 1.004410299 1.109017843 1.182122719 0.947567642 1 11.94786502 -4 0.163091989 0.982339671 1.557856093 0.339719655 0.063122798 60.82482054 0.622857018 0.110609597 8.491629171 1.00E-04 4 0.575516421 LQSS(ph)QEPEAPPPR ddPTM_HeLa_Romidepsin_16h_R1 1 LQSSQEPEAPPPR 13 0 Q5H909;Q9UNF1-2;Q9UNF1;Q5H907 Q5H909 MAGED2 Melanoma-associated antigen D2 1 0 LQS(0.07)S(0.93)QEPEAPPPR 239.38 1.16E-41 21226000 1814.7 1844.2 1941.5 1779.6 1745.6 1668.4 1444.5 1473.5 1926 1884 TRUE FALSE FALSE 1792.581738 1870.162696 1975.290993 1985.365725 1656.515518 1561.794625 1567.195794 1516.133398 1753.733736 1835.053408 0.976855349 1.01913257 1.076421528 1.081911685 0.902706979 0.851089465 0.854032796 0.826206687 0.955685392 1 10.84160634 -8.565961505 5.697048653 1.004353404 0.849329697 0.804315484 0.039012348 0.068658606 5.41694398 0.006177729 0.01263286 2.72E-09 8.565961505 -0.155023707 LQSSGRSQSKGRR ddPTM_HeLa_Romidepsin_16h_R1 1 LQSSGRSQSKGRR 13 3 F5H4G6;F5H0W1;Q6NUT2 F5H4G6 DPY19L2 Probable C-mannosyltransferase DPY19L2 0 0 80.102 0.0028558 0 1907.7 1547.4 2057.3 1682.8 2192.5 2521.3 2032.9 1721 1901.3 1840.2 FALSE FALSE TRUE 1884.448219 1569.184338 2093.106444 1877.373254 2080.608544 2360.197067 2205.574475 1770.79442 1731.242966 1792.391339 1.051359811 0.875469717 1.16777313 1.04741259 1.160800378 1.316786695 1.230520605 0.987950779 0.965884474 1 10.80766994 -9.089991831 1.500902316 1.017267094 1.186130443 0.365873549 0.102154583 0.318861619 1.416728551 0.015719345 0.031753457 8.13E-10 9.089991831 0.168863349 LQSVQATGPSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 3 LQSVQATGPSSPGR 14 0 D6REY2;P23508;P23508-2;A0A096LNU0 D6REY2 MCC Colorectal mutant cancer protein 1 0 LQS(0.011)VQAT(0.003)GPS(0.325)S(0.661)PGR;LQSVQATGPS(0.112)S(0.888)PGR;LQSVQAT(0.001)GPS(0.109)S(0.89)PGR ;; 161.94 0.00025825 87470300 9989.2 9064.8 9064.7 9563.7 9720.8 8060.9 7996.5 8249 9740.1 9278.3 TRUE FALSE FALSE 9867.447788 9192.414492 9222.467301 10669.49999 9224.711303 7545.834505 8675.72251 8487.6718 8868.921061 9037.248428 1.091864174 1.017169614 1.020495052 1.180613776 1.020743357 0.834970352 0.959996019 0.939187615 0.981374047 1 13.14166787 -8.453716959 8.232410267 1.050906182 0.917543814 0.504631556 0.060900209 0.214329289 23.59952778 0.008626111 0.019300137 3.52E-09 8.453716959 -0.133362368 LQTLS(ph)PSHK ddPTM_HeLa_Romidepsin_16h_R1 2 LQTLSPSHK 9 0 H0YAP0;Q96GY0 H0YAP0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 0 LQT(0.045)LS(0.845)PS(0.11)HK;LQT(0.002)LS(0.942)PS(0.057)HK ; 126.12 0.00016427 0 4634.3 4512.6 4899 4266.9 6975.8 7036.4 6462 5565.1 5387.7 4999.4 TRUE FALSE FALSE 4577.815369 4576.128501 4984.26504 4760.259054 6619.798896 6586.796749 7010.882119 5726.117388 4905.810618 4869.514867 0.940096805 0.939750391 1.023565011 0.977563306 1.359437044 1.352659747 1.439749607 1.175911265 1.007453669 1 12.24956233 -8.76359525 24.99453963 0.973076939 1.341120209 0.869455352 0.066456423 12.47354161 144617.2728 0.009094793 0.01708982 1.72E-09 8.76359525 0.368043271 LQTSSVLVSGLR ddPTM_HeLa_Romidepsin_16h_R1 1 LQTSSVLVSGLR 12 0 P22314;P22314-2;Q5JRR9;Q5JRS1;Q5JRS3;Q5JRS2;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 129 0.015271 1088300 72.842 0 231.7 74.256 331.7 174.62 138.41 0 139.18 168.13 FALSE FALSE TRUE 71.95417369 0 235.7326413 82.8418281 314.7721113 163.4623456 150.1665419 0 126.7313922 163.7619584 0.439382714 0 1.439483526 0.505867351 1.922132065 0.998170437 0.916980619 0 0.773875651 1 7.35545645 -9.731330539 24.99996671 0.672721477 0.985956554 0.105684882 0.539811126 459.4884392 381521.7433 0.086077332 0.12172295 1.86E-10 9.731330539 0.313235078 LQTTDNLLPMS(ph)PEEFDEVSR ddPTM_HeLa_Romidepsin_16h_R1 3 LQTTDNLLPMSPEEFDEVSR 20 0 A0A669KB68;A0A669KB56;A0A669KBA4;A0A669KB53;P42224 A0A669KB68 STAT1 Signal transducer and activator of transcription 1-alpha/beta 1 0 LQTTDNLLPMS(1)PEEFDEVSR;LQTTDNLLPMS(1)PEEFDEVSR;LQTTDNLLPMS(1)PEEFDEVSR ;; 145.17 1.12E-05 17037900 8292 8094 8005 7560.1 11212.8 12881.2 10953.6 14491 9494 7990.8 TRUE FALSE FALSE 8190.933915 8207.947544 8144.323667 8434.234333 10640.56898 12058.13289 11883.99851 14910.27422 8644.832862 7783.197864 1.0523867 1.054572643 1.046398127 1.083646398 1.367120451 1.549251748 1.526878632 1.915700266 1.110704496 1 12.92614732 -7.817205737 0.64815292 1.015718195 2.076906512 0.934639389 0.074408546 0.270505589 0.117279447 0.012140534 0.184310217 1.52E-08 7.817205737 1.061188317 LQVVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 LQVVKR 6 1 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;F8WCC1 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 0 1 LQVVK(1)R 107.74 0.010324 4882300 2229.6 2790.8 2926.6 3244.5 2605.1 3313.9 2689.2 3336.2 2949.4 2482.4 FALSE TRUE FALSE 2202.424778 2830.088956 2977.536245 3619.644356 2472.152026 3102.152485 2917.620581 3432.727683 2685.598277 2417.90689 0.910880724 1.170470611 1.231451987 1.497015609 1.02243475 1.282990879 1.206672016 1.419710452 1.110712033 1 11.23954297 -10.0749667 3.124481212 0.95803786 1.270566727 0.447106971 0.130112783 0.12749465 2.427933337 0.019645728 0.024782343 8.41E-11 10.0749667 0.312528867 LQVYEGGGQPPPQDLPGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LQVYEGGGQPPPQDLPGSPK 20 0 A0A494BYR6;Q86Y91-6;Q86Y91 A0A494BYR6 KIF18B Kinesin-like protein KIF18B 1 0 LQVYEGGGQPPPQDLPGS(1)PK 96.533 0.00042145 7116400 1779.8 1824.3 2306.5 1944.6 1820.3 1678.8 1287.6 1485.5 2135.6 1682.6 TRUE FALSE FALSE 1758.107113 1849.982543 2346.643665 2169.443802 1727.403299 1571.530098 1396.968712 1528.480599 1944.586587 1638.885809 1.072745339 1.128805029 1.431853062 1.323730909 1.054010773 0.958901523 0.85238929 0.932633982 1.186529639 1 10.67849962 -8.193892779 3.208562169 1.096896267 0.896824651 0.353778731 0.136953946 0.300634807 6.072818998 0.023133873 0.064535359 6.40E-09 8.193892779 -0.200071616 LQWDGSSDLS(ph)PSDSGSSK ddPTM_HeLa_Romidepsin_16h_R1 3 LQWDGSSDLSPSDSGSSK 18 0 K7EKG9;Q14CW9;Q14CW9-2;K7EJK2;K7ENU1 K7EKG9 ATXN7L3 Ataxin-7-like protein 3 1 0 LQWDGS(0.001)S(0.014)DLS(0.436)PS(0.436)DS(0.113)GS(0.001)SK;LQWDGS(0.008)S(0.02)DLS(0.91)PS(0.054)DS(0.006)GS(0.001)SK;LQWDGS(0.002)S(0.073)DLS(0.803)PS(0.053)DS(0.053)GS(0.014)S(0.002)K ;; 158.92 4.65E-06 30794500 8945.4 8017.1 8292.4 6678.1 6115.8 5858.7 5438.9 5953.8 9109.6 8145.2 TRUE FALSE FALSE 8836.370024 8129.964944 8436.725744 7450.253343 5803.687905 5484.347978 5900.88003 6126.063809 8294.814561 7933.58653 1.113792607 1.024752792 1.063418885 0.939077593 0.731533952 0.691282304 0.743784669 0.772168273 1.045531492 1 12.9537575 -8.90918924 2.812403891 1.052723497 0.729694801 0.9496654 0.034157791 0.053865523 0.862610292 0.007191317 0.01389035 1.23E-09 8.90918924 -0.323028697 LQWDGSSDLSPSDS(ph)GSSK ddPTM_HeLa_Romidepsin_16h_R1 1 LQWDGSSDLSPSDSGSSK 18 0 K7EKG9;Q14CW9;Q14CW9-2;K7EJK2;K7ENU1 K7EKG9 ATXN7L3 Ataxin-7-like protein 3 1 0 LQWDGSSDLS(0.302)PS(0.017)DS(0.68)GSSK 211.89 1.14E-28 15594000 3935.6 3773.5 3952 3074.8 2654.2 2519.3 2285.4 2513.4 4389.2 3635.5 TRUE FALSE FALSE 3887.631393 3826.623432 4020.782902 3430.322843 2518.74627 2358.324861 2479.521819 2586.121264 3996.618959 3541.049186 1.09787557 1.080646789 1.135477846 0.96873064 0.711299431 0.665996075 0.70022236 0.730326276 1.128653896 1 11.78996117 -8.829851154 3.541421951 1.05652097 0.695746918 0.943654951 0.044313076 0.043362767 1.089978927 0.007316687 0.014150927 1.48E-09 8.829851154 -0.360774052 LRAETEQGEQQR ddPTM_HeLa_Romidepsin_16h_R1 1 LRAETEQGEQQR 12 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 182.71 5.78E-08 0 1251.9 1135.1 1094.4 1238.4 1181.7 1102 1431.4 651.21 1273.3 1314 FALSE FALSE TRUE 1236.641361 1151.079968 1113.447573 1381.589635 1121.393439 1031.585757 1552.98308 670.0517339 1159.412859 1279.862091 0.966230167 0.899378125 0.869974649 1.079483208 0.876183026 0.806013214 1.213398765 0.523534324 0.905888898 1 10.32177265 -7.239848988 24.744348 0.969274467 0.523533799 0.570122191 0.112596591 2468.337191 2828870.414 0.013793017 0.885138107 5.76E-08 7.239848988 -0.445740667 LRDLEDSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LRDLEDSLAR 10 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 156.16 0.0035792 74771000 3016.1 3100.5 3179.5 3552.6 4226 3935.1 3259.7 3407.2 3675.3 2864.3 FALSE FALSE TRUE 2979.338613 3144.14892 3234.837864 3963.368327 4010.331451 3683.65981 3536.578837 3505.781956 3346.571963 2789.885073 1.067907292 1.12698152 1.159487857 1.420620643 1.437453997 1.320362565 1.267643198 1.256604435 1.199537571 1 11.44598998 -9.654041904 1.835551278 1.033812167 1.33894357 0.634973466 0.082212556 0.106091699 0.727708587 0.011768415 0.017737322 2.22E-10 9.654041904 0.305131403 LREAIAELER ddPTM_HeLa_Romidepsin_16h_R1 1 LREAIAELER 10 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 113.67 0.01797 5327900 2722.5 1973.1 1964.6 2598 2470.3 2262.3 1967.3 2199.6 2253.1 1785.9 FALSE FALSE TRUE 2689.317123 2000.877354 1998.793039 2898.392984 2344.231373 2117.746331 2134.402413 2263.241956 2051.577093 1739.502061 1.546026983 1.150258686 1.149060461 1.66621992 1.347645068 1.217443991 1.227019192 1.301086102 1.179404808 1 10.76445867 -12.57631456 1.356326571 0.999878449 1.349165727 0.208629606 0.167410624 0.37910712 1.249642889 0.120598343 0.028152103 2.65E-13 12.57631456 0.349287278 LREQLQLLEEQHR ddPTM_HeLa_Romidepsin_16h_R1 1 LREQLQLLEEQHR 13 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 128.21 0.0011911 10220000 3523.7 3852.8 4184.8 4322.4 4056.2 4580.8 3821 4116.5 4350.6 3755.4 FALSE FALSE TRUE 3480.751789 3907.03982 4257.634689 4822.176226 3849.196978 4288.101664 4145.555645 4235.604433 3961.47144 3657.834167 0.951588189 1.068129292 1.163976959 1.318314611 1.05231588 1.172306198 1.133336137 1.157954199 1.083010125 1 11.83677395 -9.973176979 3.158719676 0.977530171 1.166525096 0.480638664 0.070624664 0.108661193 2.245848621 0.010279508 0.01344071 1.06E-10 9.973176979 0.188994925 LRESTPGDS(ph)PSTVNK ddPTM_HeLa_Romidepsin_16h_R1 2 LRESTPGDSPSTVNK 15 1 Q5T6F2 Q5T6F2 UBAP2 Ubiquitin-associated protein 2 1 0 LRESTPGDS(0.97)PS(0.029)TVNK;LRESTPGDS(0.999)PSTVNK ; 239.51 6.06E-45 88867000 6843.2 6466.3 6194.6 6200.9 11352.4 14848.7 12713.5 13459.2 7013.9 6479.2 TRUE FALSE FALSE 6759.792446 6557.332741 6302.414414 6917.877234 10773.04467 13899.91599 13793.38437 13848.62072 6386.559217 6310.86945 1.071134889 1.039053777 0.998660242 1.096184494 1.70706188 2.202535816 2.185655159 2.194407732 1.011993556 1 12.62362306 -8.579076079 2.263933652 1.030531928 2.200506524 0.996145002 0.03263864 0.015344635 0.15777315 0.00616292 0.014634044 2.64E-09 8.579076079 1.169974596 up LREVEDGIAT(ph)MQAK ddPTM_HeLa_Romidepsin_16h_R1 1 LREVEDGIATMQAK 14 1 Q9P2D7-6;Q9P2D7-8;Q9P2D7 Q9P2D7-6 DNAH1 "Dynein heavy chain 1, axonemal" 1 0 LREVEDGIAT(1)MQAK 46.892 0.029387 13639000 5180.9 2027.2 3258.2 1952.8 2970.7 2064.5 4821 2751.3 4469.7 3733.8 TRUE FALSE FALSE 5117.753198 2055.738975 3314.907604 2178.591924 2819.094094 1932.585113 5230.49562 2830.904525 4069.918837 3636.795338 1.407215068 0.565261111 0.911491381 0.599041662 0.775158851 0.53139782 1.438215554 0.778406334 1.119094824 1 11.82845202 -10.26412659 24.98905025 1.192296002 0.809700902 0.303073693 0.260321278 221.9904673 2064338.124 0.046731079 0.054738905 5.44E-11 10.26412659 -0.3825951 LREVIEIEDAS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 LREVIEIEDASPTK 14 1 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 LREVIEIEDAS(0.965)PT(0.035)K 165.66 3.64E-05 8846400 4307.3 3594 4342.2 5019.8 2896.8 2644.7 2034.3 1904.9 3981.1 3767.2 TRUE FALSE FALSE 4254.800971 3644.596426 4417.77417 5600.212895 2748.965487 2475.712205 2207.093391 1960.015276 3625.020445 3669.327601 1.159558762 0.993260025 1.203973766 1.526223195 0.749174177 0.674704598 0.601498048 0.534161974 0.987924993 1 11.8413 -8.541088974 24.77281241 1.110301255 0.621372492 0.724528844 0.153583153 90.17495023 122671.7159 0.022925126 0.045856911 2.88E-09 8.541088974 -0.488928763 LRLDTGPQSLS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 LRLDTGPQSLSGK 13 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 LRLDTGPQS(0.1)LS(0.9)GK 75.743 0.018434 33389000 1653.1 2151.3 2091.1 2035.9 2398.9 2854.6 2559.6 2722.8 2114.4 1848.2 TRUE FALSE FALSE 1632.951381 2181.586058 2127.494718 2271.300337 2276.475181 2672.200273 2777.01236 2801.579922 1925.282768 1800.183498 0.907102739 1.211868713 1.181821032 1.261704899 1.264579519 1.484404382 1.542627384 1.556274639 1.069492511 1 10.81392826 -8.863856278 0.579362636 0.951646457 1.614214172 0.869760805 0.076848806 0.229986635 0.131170315 0.018061158 0.074209812 1.37E-09 8.863856278 0.662567715 LRLDTGS(ph)PEPETR ddPTM_HeLa_Romidepsin_16h_R1 1 LRLDTGSPEPETR 13 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 LRLDT(0.077)GS(0.91)PEPET(0.012)R 117.07 0.0020077 45935000 2872.8 2669.2 2540.1 2804.7 3042.2 3124.6 2728 3513.5 3302 2758.3 TRUE FALSE FALSE 2837.785209 2706.777068 2584.309375 3128.992611 2886.945182 2924.948144 2959.716252 3615.157579 3006.66085 2686.638968 1.056258486 1.007495648 0.961911669 1.164649455 1.074556431 1.0887016 1.101642717 1.345606024 1.119116072 1 11.39158675 -4 0.66949562 1.028516522 31.25938712 0.666020188 0.059089071 83.4314828 0.464517767 0.008776594 3760.780001 1.00E-04 4 30.2308706 LRLPLDK(ac)EPAR ddPTM_HeLa_Romidepsin_16h_R1 2 LRLPLDKEPAR 11 2 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 1 ; LRLPLDK(1)EPAR;LRLPLDK(1)EPAR 101.71 0.005772 649860 437 402.57 766.23 151.14 1015.78 1451.38 1033.01 729.27 871.89 396.54 FALSE TRUE FALSE 431.6736759 408.237391 779.5659117 168.6155179 963.9409562 1358.641502 1120.753844 750.3702769 793.9059747 386.2378336 1.117636954 1.056958577 2.018357198 0.436558781 2.495718628 3.517629253 2.901719474 1.942767413 2.055484744 1 8.593345679 -8.642966961 5.959189974 1.100681159 2.828683119 0.577632531 0.590965361 0.077896441 3.776256292 0.069185702 0.139477552 2.28E-09 8.642966961 1.72800196 LRLS(ph)PSPT(ph)SQR ddPTM_HeLa_Romidepsin_16h_R1 3 LRLSPSPTSQR 11 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 2 0 LRLS(0.936)PS(0.065)PT(0.934)S(0.066)QR;LRLS(0.944)PS(0.094)PT(0.737)S(0.224)QR;LRLS(0.954)PS(0.046)PT(0.987)S(0.012)QR ;; 161.87 0.0019286 455860000 42949.4 42915.8 39293.3 37169.8 38717 39433.9 33050.8 35031.7 45525.1 43675.2 TRUE FALSE FALSE 42425.91619 43519.96976 39977.1834 41467.54717 36741.12702 36914.20106 35858.13413 36045.28697 41453.22104 42540.51201 0.997306196 1.023024118 0.939743823 0.974777811 0.863673832 0.867742284 0.842917314 0.847316717 0.974441046 1 15.37654978 -8.836366704 1.227550191 0.999525 0.844026556 0.885066521 0.022680804 0.082347249 0.246245613 0.003059044 0.007897253 1.46E-09 8.836366704 -0.155498444 LRLSPS(ph)PTSQR ddPTM_HeLa_Romidepsin_16h_R1 1 LRLSPSPTSQR 11 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 LRLS(0.296)PS(0.63)PT(0.058)S(0.016)QR 79.639 0.02117 4375700 1380.6 1165.6 1125.4 1055.2 1116.7 1028 1257 938.16 1149.7 897.75 TRUE FALSE FALSE 1363.772716 1182.009347 1144.987115 1177.207189 1059.710632 962.3141177 1363.769549 965.3041794 1046.867953 874.4263256 1.55961992 1.351754073 1.309415192 1.346262292 1.211892416 1.100509088 1.559616298 1.103928543 1.197205438 1 9.772193025 -12.5927483 1.404262583 1.001148591 1.350348859 0.17271056 0.162586867 0.341470317 1.214284356 0.110878236 0.026092475 2.55E-13 12.5927483 0.349200268 LRLSPSPTSQR ddPTM_HeLa_Romidepsin_16h_R1 2 LRLSPSPTSQR 11 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 110.84 0.016151 19768700 2745 2654.8 2517.91 2394.9 2828.2 2870.9 2321.1 1926.82 2713.3 2324.5 FALSE FALSE TRUE 2711.542884 2692.174344 2561.733167 2671.809606 2683.866401 2687.458755 2518.254176 1982.569497 2470.615652 2264.109155 1.197620211 1.189065615 1.131453032 1.180071023 1.185396205 1.186982858 1.112249456 0.875651023 1.09120872 1 11.1447278 -4.059646082 21.30952519 1.111327963 0.005561964 0 0.099082318 0 0 0.014648765 0 8.72E-05 4.059646082 -1.105765999 LRQDLQDR ddPTM_HeLa_Romidepsin_16h_R1 1 LRQDLQDR 8 1 P12270 P12270 TPR Nucleoprotein TPR 0 0 109.48 0.026243 2901400 903.85 884.63 818.02 1228.4 1169.2 1007.8 1039 671.48 868.16 894.81 FALSE FALSE TRUE 892.8335285 897.0838444 832.257295 1370.433388 1109.531361 943.4048325 1127.252634 690.9082144 790.5095953 871.5627072 1.024405383 1.029282044 0.95490237 1.572386446 1.273036756 1.082429095 1.293369513 0.792723471 0.907002547 1 9.767460657 LRQERTHALK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 1 LRQERTHALKTK 12 3 D6REL6;I6L9I8;Q9H201-2;Q9H201 D6REL6 EPN3 Epsin-3 0 1 LRQERTHALK(1)TK 57.802 0.029772 0 1124.9 1187.7 1252.7 1420 1395.3 1527.4 1196.6 916.61 888.6 954.81 FALSE TRUE FALSE 1111.189286 1204.420472 1274.502718 1584.187081 1324.092634 1429.804069 1298.239174 943.1306642 809.1213905 930.0038986 1.194822181 1.295070347 1.370427285 1.703419828 1.423749553 1.537417286 1.395950249 1.014114743 0.870019353 1 9.861092954 -10.52992381 0.964917763 1.051364173 1.424367231 0.499451353 0.175094913 0.308406527 0.588074547 0.040434381 0.041691673 2.95E-11 10.52992381 0.373003058 LRS(ph)LEQLY(ph)LS(ph)YNK ddPTM_HeLa_Romidepsin_16h_R1 1 LRSLEQLYLSYNK 13 1 Q6NSJ5 Q6NSJ5 LRRC8E Volume-regulated anion channel subunit LRRC8E 3 0 LRS(1)LEQLY(0.771)LS(0.68)Y(0.548)NK 75.387 0.002668 0 338.86 557.5 707.66 366.23 599.28 693.74 337.13 587.68 448.22 431.54 TRUE FALSE FALSE 334.729844 565.3484996 719.9765255 408.5752358 568.6965054 649.4122529 365.7658138 604.6835936 408.1300806 420.3285286 0.796352903 1.34501577 1.712889981 0.972037842 1.352980982 1.545011125 0.870190313 1.438597555 0.970978777 1 8.715373568 -10.25477697 24.58080415 0.903833314 1.313972359 0.366697067 0.238684169 307.8537052 1135819.93 0.038664321 0.046760183 5.56E-11 10.25477697 0.410139044 LRSS(ph)SEGT(ph)AGS(ph)SRMILK ddPTM_HeLa_Romidepsin_16h_R1 1 LRSSSEGTAGSSRMILK 17 2 H0YA74;E7EUW0;Q9C0I3-2;Q9C0I3 H0YA74 CCSER1 Serine-rich coiled-coil domain-containing protein 1 3 0 LRS(0.132)S(0.483)S(0.483)EGT(0.781)AGS(0.821)S(0.299)RMILK 55.04 0.0041739 0 982.37 1136.4 754.38 757.64 840.04 1154.9 895.9 1552 1306.2 1092.8 TRUE FALSE FALSE 970.3964966 1152.398269 767.5096675 845.2419016 797.1696242 1081.105617 971.9977236 1596.904671 1189.370201 1064.408898 0.911676422 1.082665008 0.721066564 0.79409511 0.748931755 1.015686377 0.913180757 1.500273695 1.117399716 1 10.05583676 -7.260610557 24.62763867 0.926658279 1.500273918 0.644008096 0.128786325 25.15747413 747366.1478 0.016377547 0.132170063 5.49E-08 7.260610557 0.573615639 LRSY(ph)AS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 LRSYASR 7 1 P07101-6;P07101-5;P07101-3;P07101-4;P07101-2;P07101 P07101-6 TH Tyrosine 3-monooxygenase 2 0 LRS(0.267)Y(0.743)AS(0.99)R 56.122 0.0043352 0 0 0 0 0 0 120.47 0 58.446 186.78 116.6 TRUE FALSE FALSE 0 0 0 0 0 112.7723558 0 60.1370428 170.073929 113.5707152 0 0 0 0 0 0.992970376 0 0.529511879 1.497515699 1 6.827447066 -12.30776564 1.011852166 1.004116264 0.176251888 0.558369167 0.3574337 0.365736325 0.665504243 0.218145639 0.057038112 4.92E-13 12.30776564 -0.827864376 LRVQS(ph)PEPPAPER ddPTM_HeLa_Romidepsin_16h_R1 2 LRVQSPEPPAPER 13 1 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 LRVQS(1)PEPPAPER;LRVQS(1)PEPPAPER ; 107.73 0.0030358 44355000 2728.31 2968.29 2694.28 2736.7 2795.6 3229.8 2954.56 2291.3 3045.76 3298.36 TRUE FALSE FALSE 2695.056308 3010.077665 2741.172813 3053.130131 2652.9301 3023.426204 3205.520253 2357.59515 2773.339597 3212.668132 0.838884129 0.93694012 0.85323871 0.950340964 0.825771599 0.94109509 0.997775096 0.733843352 0.863251193 1 11.64955624 -12.48120759 1.185449849 1.000862044 0.885816645 0 0.083448576 0.509268564 1.265012856 0.048419051 0.011489341 3.30E-13 12.48120759 -0.1150454 LRYTEMT(ph)MDEKY(ph)VNS(ph)IWDLLK ddPTM_HeLa_Romidepsin_16h_R1 1 LRYTEMTMDEKYVNSIWDLLK 21 2 H7C1L6 H7C1L6 CUL3 3 0 LRY(0.322)T(0.427)EMT(0.404)MDEKY(0.924)VNS(0.923)IWDLLK 43.116 0.020887 10087000 1523.7 1364 1601.5 1052.8 1356.6 1536 1167 1495.5 1686.4 1782.8 TRUE FALSE FALSE 1505.128558 1383.202428 1629.373436 1174.52969 1287.36764 1437.854557 1266.124951 1538.769933 1535.56416 1736.482599 0.866768581 0.796554154 0.93831832 0.67638437 0.741365125 0.828027046 0.729131954 0.886141867 0.884295737 1 10.76195224 -11.17387138 0.460666574 1.007355149 0.778001934 0.319536866 0.078523869 0.528423377 0.260399939 0.051225242 0.025685102 6.70E-12 11.17387138 -0.229353215 LS(ph)ASPAQEK ddPTM_HeLa_Romidepsin_16h_R1 1 LSASPAQEK 9 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 LS(0.829)AS(0.171)PAQEK 154.15 0.0047647 40392000 6511.9 5854.6 5394.1 4670.8 6976.7 6971.5 6410.3 6518.8 6236 5581.1 TRUE FALSE FALSE 6432.530458 5937.021212 5487.982048 5210.859873 6620.652965 6526.043649 6954.790722 6707.411193 5678.236542 5436.102217 1.18329829 1.092146721 1.009543572 0.958565469 1.217904429 1.20050054 1.279370851 1.233864067 1.044541901 1 12.40835687 -8.628651065 8.467116353 1.074703489 1.236560231 0.664008841 0.06284001 0.173289864 12.6131735 0.012156214 0.02435052 2.35E-09 8.628651065 0.161856741 LS(ph)ASSSISSADLFEEPR ddPTM_HeLa_Romidepsin_16h_R1 1 LSASSSISSADLFEEPR 17 0 Q9NP61;Q9NP61-2;H0Y6A0 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 0 LS(0.418)AS(0.418)S(0.11)S(0.029)IS(0.02)S(0.005)ADLFEEPR 187.75 6.86E-12 0 607.25 549.74 556.63 412.64 531.4 666.93 501.89 635.76 521.63 486.61 TRUE FALSE FALSE 599.8486034 557.4792541 566.3179117 460.3513783 504.2806751 624.3153254 544.5205241 654.1547125 474.9741064 473.9678021 1.265589352 1.176196467 1.19484469 0.971271416 1.063955553 1.317210415 1.148855517 1.380166985 1.002123149 1 8.888645246 -12.47143747 1.186267667 0.999077833 1.189491479 0.313872357 0.111338508 0.515830885 1.288632977 0.080787451 0.019478416 3.38E-13 12.47143747 0.190413646 LS(ph)DGEINAQESTYK ddPTM_HeLa_Romidepsin_16h_R1 1 LSDGEINAQESTYK 14 0 A0A3B3IRW6;Q2KHR3-2;Q2KHR3 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 1 0 LS(1)DGEINAQESTYK 93.181 0.016279 3178000 1420.8 1029.3 1021.7 386.37 1369 1006.2 1402.7 1133.1 1940.9 1447.1 TRUE FALSE FALSE 1403.482743 1043.790512 1039.48226 431.0439173 1299.134822 941.9070674 1521.845303 1165.884461 1767.301043 1409.504133 0.995728008 0.74053739 0.737480817 0.305812454 0.921696355 0.668254207 1.079702618 0.827159306 1.253845946 1 10.46097199 -10.2636784 21.83012669 0.997982701 0.752110587 0.33156553 0.203407283 33.30100664 324681.205 0.031347637 0.036811321 5.45E-11 10.2636784 -0.245872115 LS(ph)DLEMNS(ph)PTKR ddPTM_HeLa_Romidepsin_16h_R1 1 LSDLEMNSPTKR 12 1 H0Y7F9;A0A0J9YXZ3;X6RFI8;A0A0J9YWV4;O75154-3 H0Y7F9 RAB11FIP3 2 0 LS(1)DLEMNS(0.633)PT(0.367)KR 73.877 0.0023225 0 612.83 584.38 619.85 315.82 498.24 623.49 431.69 454.12 726.18 485.26 TRUE FALSE FALSE 605.3605922 592.606917 630.6382292 352.3365944 472.8129536 583.6510012 468.3577378 467.2592457 661.228642 472.6528752 1.280772051 1.253788876 1.334252392 0.745444729 1.000338681 1.234840687 0.990912702 0.988588603 1.398973066 1 8.884637221 -9.283515584 24.98986272 1.160722933 1.005914842 0.33098259 0.160183851 1088.346786 1231985.389 0.025720049 0.039307303 5.21E-10 9.283515584 -0.154808092 LS(ph)GDQPAAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSGDQPAAR 9 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 LS(1)GDQPAAR 107.06 0.0014841 0 1245 1338 1190.3 2909.2 1253.7 1589.1 1442.3 923.99 1298.8 1698 TRUE FALSE FALSE 1229.825461 1356.836399 1211.016672 3245.575392 1189.719011 1487.561639 1564.808926 950.7241928 1182.632075 1653.885715 0.743597608 0.820393082 0.732225124 1.962393993 0.719347776 0.899434359 0.946140904 0.574842738 0.715062754 1 10.69164383 -7.259592935 22.33189741 0.929305959 0.574842226 0.089288581 0.353357797 74.32392234 898541.4479 0.04619606 0.394241242 5.50E-08 7.259592935 -0.354463734 LS(ph)GFSFK ddPTM_HeLa_Romidepsin_16h_R1 1 LSGFSFK 7 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 LS(1)GFSFK 111.06 0.028953 45255000 4148.3 4272.6 4869.6 2001 6515.5 7183.5 5134.3 5206.1 4121.5 4705.4 TRUE FALSE FALSE 4097.738924 4332.749775 4954.353345 2232.365035 6182.989722 6724.497534 5570.407314 5356.73029 3752.862718 4583.15303 0.894087301 0.945364413 1.080992346 0.487080623 1.34906901 1.467220817 1.215409409 1.168787133 0.818838623 1 12.16212474 LS(ph)KSQGGEEEGPLSDK ddPTM_HeLa_Romidepsin_16h_R1 2 LSKSQGGEEEGPLSDK 16 1 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 0 LS(0.978)KS(0.022)QGGEEEGPLSDK;LS(0.597)KS(0.403)QGGEEEGPLSDK ; 209.25 1.71E-21 43105000 6626.7 5602.7 4808.6 7231.2 5541.5 4523.1 5106.8 4640.6 6950.8 5934.5 TRUE FALSE FALSE 6545.931232 5681.574958 4892.291666 8067.305368 5258.696577 4234.088508 5540.571465 4774.868439 6329.103039 5780.320834 1.132451194 0.982916887 0.846370263 1.395650103 0.909758598 0.732500605 0.958523173 0.826055954 1.094939748 1 12.49693386 -8.538211423 24.99913332 1.063872582 0.8460017 0.370671732 0.141289321 190.839213 311152.5666 0.019602249 0.039214729 2.90E-09 8.538211423 -0.217870882 LS(ph)LDLSHR ddPTM_HeLa_Romidepsin_16h_R1 1 LSLDLSHR 8 0 Q8TDM6-4;Q8TDM6;A0A0J9YYG8;A0A0A0MSL1;Q8TDM6-2 Q8TDM6-4 DLG5 Disks large homolog 5 1 0 LS(0.706)LDLS(0.294)HR 94.409 0.0037574 0 2377.6 2082.6 2625.7 1877.2 2187.1 2756 2044.4 2024.7 3020.9 2247 TRUE FALSE FALSE 2348.620897 2111.918897 2671.399207 2094.250696 2075.484126 2579.900495 2218.051285 2083.2815 2750.703138 2188.622616 1.073104554 0.964953429 1.220584667 0.95688068 0.948306076 1.178778139 1.013446205 0.951868762 1.256819297 1 11.0958075 LS(ph)LGLSR ddPTM_HeLa_Romidepsin_16h_R1 1 LSLGLSR 7 0 Q9NR12-2;Q9NR12;D6RAN1;H0Y8W6;D6RF83;H7BYK4;D6RH06;Q9NR12-3;Q9NR12-5;Q9NR12-6;Q9NR12-4 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 1 0 LS(1)LGLSR 155.58 0.010481 3156300 3180 2986.1 3095.3 1575.7 2647.2 2951.4 2455.2 2660.7 2728.5 3311.6 TRUE FALSE FALSE 3141.240937 3028.138394 3149.172398 1757.889848 2512.103506 2762.815065 2663.744627 2737.683157 2484.456126 3225.564155 0.973857839 0.938793417 0.976316777 0.544986788 0.778810585 0.856537006 0.825822864 0.84874553 0.770239253 1 11.6553358 -9.4623182 24.99933093 0.982403384 0.777358954 0.310289856 0.107243183 127.0931424 52463.88458 0.012748148 0.019473099 3.45E-10 9.4623182 -0.205044429 LS(ph)LQGHPTDLQTSNVK ddPTM_HeLa_Romidepsin_16h_R1 1 LSLQGHPTDLQTSNVK 16 0 Q9P270;D6RIF6 Q9P270 SLAIN2 SLAIN motif-containing protein 2 1 0 LS(0.952)LQGHPT(0.048)DLQTSNVK 82.859 0.0018663 0 1677.5 1542.7 1400.7 1526.6 1768.7 2255.6 1739.1 2052.9 2042 1925.9 TRUE FALSE FALSE 1657.053985 1564.418171 1425.078596 1703.112675 1678.436639 2111.47444 1886.819111 2112.297423 1859.358406 1875.86484 0.883354679 0.83397169 0.759691511 0.907907989 0.894753504 1.12560052 1.005839584 1.126039242 0.991200627 1 10.87334017 -8.267360127 24.87807092 0.915210181 1.077827764 0.570136415 0.074178884 314.5478706 1321683.602 0.012273196 0.028124851 5.40E-09 8.267360127 0.162617584 LS(ph)NGSFSAPSLTNSR ddPTM_HeLa_Romidepsin_16h_R1 3 LSNGSFSAPSLTNSR 15 0 O94806;O94806-2 O94806 PRKD3 Serine/threonine-protein kinase D3 1 0 LS(0.85)NGS(0.145)FS(0.004)APSLT(0.001)NSR;LS(0.995)NGS(0.003)FS(0.002)APSLTNSR;LS(1)NGSFSAPSLTNSR ;; 181.51 3.43E-08 41404300 2976.1 3323.28 3165.06 2901.84 2972.36 2758.19 2236.64 2688.37 3425.3 2738.81 TRUE FALSE FALSE 2939.826148 3370.065223 3220.146542 3237.364394 2820.669378 2581.950561 2426.620146 2766.153744 3118.932589 2667.655321 1.102026234 1.263306094 1.207107423 1.213561725 1.057359006 0.967872626 0.909645308 1.03692322 1.169166258 1 11.38135656 -8.335005729 4.290710435 1.092110873 0.964875858 0.355654258 0.089667344 0.262632899 9.230301582 0.015492297 0.036482726 4.62E-09 8.335005729 -0.127235016 LS(ph)PDFAEELR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPDFAEELR 10 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 LS(1)PDFAEELR 137.4 0.0053772 3064800 345.88 431.57 645.36 175.96 554.2 559.35 443.27 430.38 533.46 463.68 TRUE FALSE FALSE 341.6642815 437.6456538 656.5922201 196.3053231 525.917106 523.6093402 480.9213427 442.8323663 485.7460015 451.6335268 0.756507791 0.969028267 1.453816382 0.434656223 1.164477557 1.159367738 1.064848631 0.980512606 1.075531316 1 8.819008778 -9.020746992 0.708664484 0.898787604 1.072942785 0 0.258111139 1.804568406 1.696354351 0.050664785 0.157942155 9.53E-10 9.020746992 0.174155182 LS(ph)PENNQVLTK ddPTM_HeLa_Romidepsin_16h_R1 2 LSPENNQVLTK 11 0 Q16514-2;Q16514 Q16514-2 TAF12 Transcription initiation factor TFIID subunit 12 1 0 LS(0.624)PENNQVLT(0.376)K;LS(0.999)PENNQVLT(0.001)K ; 120.9 0.0096293 74295000 9728.2 9972.2 10168.8 4467.8 9614.9 9522.4 8589.7 9461.4 10846.6 10048.8 TRUE FALSE FALSE 9609.628957 10112.58889 10345.7837 4984.388058 9124.215775 8913.949372 9319.308904 9735.150681 9876.45293 9787.730727 0.981803569 1.033190346 1.057015562 0.509248589 0.932209521 0.91072687 0.952141938 0.994627964 1.009064635 1 13.2567587 LS(ph)PEVAPPAHR ddPTM_HeLa_Romidepsin_16h_R1 2 LSPEVAPPAHR 11 0 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 0 LS(1)PEVAPPAHR;LS(1)PEVAPPAHR ; 100.19 0.0080003 125569000 18610.8 17850.1 17720.6 11536.6 21309.2 27375 26192 29167 18522.2 17546.5 TRUE FALSE FALSE 18383.96441 18101.39418 18029.01961 12870.51597 20221.71201 25625.82585 28416.74783 30010.90113 16865.52804 17090.6394 1.075674466 1.05914084 1.054906091 0.753073988 1.183203948 1.499407088 1.662708291 1.75598469 0.986828383 1 14.06091875 -8.189404875 2.237615668 1.021237829 1.703807949 0.904010482 0.09572361 0.067580902 0.650795655 0.014040683 0.044472518 6.47E-09 8.189404875 0.68257012 LS(ph)PGESAYQK ddPTM_HeLa_Romidepsin_16h_R1 4 LSPGESAYQK 10 0 A0A0G2JHC2;Q6NYC8-2;Q6NYC8 A0A0G2JHC2 PPP1R18 Phostensin 1 0 LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK;LS(1)PGESAYQK ;;; 147.62 0.0039068 204128000 18472.6 17197.7 17381.8 12598.4 18698.4 18212.5 16327.8 16395.9 19777.5 17765.8 TRUE FALSE FALSE 18247.44885 17439.80967 17684.32294 14055.08629 17744.15087 17048.78003 17714.68292 16870.2895 18008.55087 17304.24195 1.054507264 1.007834363 1.021964613 0.812233574 1.025422028 0.985237035 1.023719096 0.974922192 1.040701518 1 14.07883812 -9.47024243 24.99982307 1.02462965 0.966658932 0.217746384 0.057453686 425.5609055 202121.9551 0.008804812 0.013449523 3.39E-10 9.47024243 -0.057970717 LS(ph)PGSYPTVIQQQNATSQR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPGSYPTVIQQQNATSQR 19 0 Q13469-5;Q13469-3;Q13469-4;Q13469-2;Q13469 Q13469-5 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 0 LS(0.993)PGS(0.007)YPTVIQQQNATSQR 171.25 1.18E-07 6365900 718.53 1200.7 639.22 808.04 997.59 1212.3 785.56 881.33 971.2 875.18 TRUE FALSE FALSE 709.77228 1217.603486 650.345356 901.4693867 946.6792598 1134.837943 852.2854468 906.829893 884.3334396 852.4426974 0.832633422 1.428369895 0.762919734 1.057513179 1.110548853 1.331277687 0.999815529 1.063801585 1.03741101 1 9.735459047 LS(ph)PGTDSSSNLGGVK ddPTM_HeLa_Romidepsin_16h_R1 1 LSPGTDSSSNLGGVK 15 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JQF5;A0A3B3IT55;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3;A0A1W2PRR3;A0A1W2PPV8;A0A0G2JQF4;I3L233 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 0 LS(1)PGTDSSSNLGGVK 209.56 8.23E-21 0 3068.2 3041.4 2738.1 1678.6 1632.6 1335 1072.1 1375.7 3185.3 2700.5 TRUE FALSE FALSE 3030.803598 3084.216909 2785.755482 1872.68763 1549.28233 1249.697809 1163.164147 1415.503709 2900.39879 2630.340621 1.152247574 1.172554187 1.059085451 0.711956321 0.58900445 0.475108736 0.442210464 0.538144641 1.102670417 1 11.36103392 -9.056435171 2.008027827 1.084565671 0.49406432 0.960914441 0.056270501 0.058111581 0.463480424 0.011825762 0.022593666 8.78E-10 9.056435171 -0.590501351 LS(ph)PPVASGGIPHQS(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 1 LSPPVASGGIPHQSPPTK 18 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 2 0 LS(0.959)PPVAS(0.042)GGIPHQS(0.96)PPT(0.039)K 65.207 0.0036283 0 2733.6 2065.8 2317.1 1556.3 2019.3 2033.9 1938.7 1954.1 2478.4 2575.3 TRUE FALSE FALSE 2700.281832 2094.882387 2357.428154 1736.246729 1916.247586 1903.940354 2103.37313 2010.6388 2256.725697 2508.393335 1.076498568 0.83514908 0.939815985 0.692174829 0.763934252 0.759027832 0.838534013 0.801564401 0.899669787 1 11.29254788 -9.913167937 1.591716428 1.035616794 0.780964781 0.534900226 0.076702306 0.127484152 0.645350888 0.011522045 0.015760776 1.22E-10 9.913167937 -0.254652013 LS(ph)PQQAFPR ddPTM_HeLa_Romidepsin_16h_R1 2 LSPQQAFPR 9 0 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 LS(1)PQQAFPR;LS(1)PQQAFPR ; 129 0.0087862 16322700 3210.3 3445.4 3033.9 2614 2028.03 1802.59 1594.27 1745.59 3776.9 3091.8 TRUE FALSE FALSE 3171.171629 3493.904432 3086.703757 2916.242979 1924.532061 1687.410317 1729.687254 1796.095893 3439.084605 3011.47459 1.053029516 1.160197215 1.024980841 0.968377083 0.639066346 0.560326932 0.574365548 0.596417416 1.141993565 1 11.55625437 -8.76882153 3.076257744 1.037145027 0.577384329 0.948164621 0.053575075 0.036479426 0.712295376 0.007236363 0.014655594 1.70E-09 8.76882153 -0.459760699 LS(ph)PSPTSQR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPSPTSQR 9 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 LS(0.992)PS(0.008)PTSQR 139.15 0.0065083 2281600000 2057.5 1829 1990.2 1727.2 1893.4 1736.4 1617.5 1839.3 2127 1846.1 TRUE FALSE FALSE 2032.422399 1854.74871 2024.838596 1926.906991 1796.772733 1625.449644 1754.89041 1892.517244 1936.755793 1798.138056 1.130292745 1.03148293 1.126075158 1.071612374 0.999240702 0.903962651 0.975948651 1.052487175 1.077089596 1 10.81228808 -8.666603723 4.555009579 1.066440173 0.973819937 0.439925296 0.049604785 0.191961626 6.995891934 0.008914748 0.018150717 2.15E-09 8.666603723 -0.092620236 LS(ph)PTFPESIEHPLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPTFPESIEHPLAR 15 0 Q5U5Q3;M9T4I7 Q5U5Q3 MEX3C RNA-binding E3 ubiquitin-protein ligase MEX3C 1 0 LS(0.926)PT(0.074)FPESIEHPLAR 78.225 0.014516 4795100 3256.2 2938.4 3244.2 2576.8 2876 2809.2 2250.6 2490 3908.5 4227.4 TRUE FALSE FALSE 3216.512182 2979.766872 3300.66394 2874.74174 2729.226988 2629.701186 2441.765908 2562.044221 3558.913971 4117.571539 0.781167286 0.723670942 0.801604516 0.69816437 0.662824425 0.63865343 0.593011168 0.622222151 0.864323531 1 12.007578 -16.52287874 0.068644677 2.230802438 0.232434204 0.815303355 0.051256746 30.16331549 0.161087277 5.919416367 0.883850756 3.00E-17 16.52287874 -1.998368234 LS(ph)PTPSMQDGLDLPSETDLR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58-6;Q9UK58;Q9UK58-5;Q9UK58-4 Q9UK58-6 CCNL1 Cyclin-L1 1 0 LS(0.956)PT(0.034)PS(0.01)MQDGLDLPSETDLR 167.35 5.49E-10 6434200 1092.8 1067 1219.7 801.79 1128.2 766.94 1038.1 838.98 1291.5 1271.4 TRUE FALSE FALSE 1079.480533 1082.021254 1240.928367 894.4967323 1070.623744 717.9350092 1126.276188 863.2545626 1175.985005 1238.368845 0.871695487 0.873747154 1.00206685 0.722318505 0.864543507 0.579742467 0.909483627 0.69709002 0.949624185 1 10.27422537 -9.255757358 24.96778769 0.936175181 0.759627994 0.492527622 0.093689311 314.7637096 1383125.45 0.013936831 0.022701167 5.55E-10 9.255757358 -0.176547186 LS(ph)SDSFAR ddPTM_HeLa_Romidepsin_16h_R1 3 LSSDSFAR 8 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 0 LS(0.498)S(0.498)DS(0.005)FAR;LS(0.958)S(0.04)DS(0.002)FAR;LS(0.959)S(0.039)DS(0.002)FAR ;; 148.69 0.0073264 26550700 5326.2 6939.1 6722.1 5028.9 7696.1 9982.8 7206.8 9660.7 6595.8 6853.6 TRUE FALSE FALSE 5261.282226 7036.788832 6839.095331 5610.36508 7303.339299 9344.931298 7818.945412 9940.217112 6005.855129 6675.542484 0.788143022 1.054114905 1.024500308 0.840435829 1.094044314 1.399875938 1.171282399 1.489050086 0.899680459 1 12.70466937 -8.476276305 3.559456039 0.917504869 1.333200411 0.747633568 0.108125292 0.095786549 2.456464325 0.017256716 0.039576976 3.34E-09 8.476276305 0.415695541 LS(ph)SPVLHR ddPTM_HeLa_Romidepsin_16h_R1 7 LSSPVLHR 8 0 Q16643-3;Q16643;Q16643-2;D6RCR4;D6R9W4 Q16643-3 DBN1 Drebrin 1 0 LS(0.643)S(0.357)PVLHR;LS(0.5)S(0.5)PVLHR;LS(0.5)S(0.5)PVLHR;LS(0.5)S(0.5)PVLHR;LS(0.5)S(0.5)PVLHR;LS(0.5)S(0.5)PVLHR;LS(0.643)S(0.357)PVLHR ;;;;;; 113.66 0.0032269 2209906600 34284.39 40496.9 30717.59 32012.3 37346.1 36337.04 29934.47 32754.1 38685 34351 TRUE FALSE FALSE 33866.51867 41067.01642 31252.21677 35713.71275 35440.18916 34015.22042 32477.10313 33701.78821 35224.91671 33458.55607 1.012193072 1.227399543 0.934057546 1.067401494 1.059226498 1.016637429 0.970666608 1.007269654 1.052792495 1 15.03008757 -7.925936608 7.118015611 1.025697116 0.989500716 0.034814183 0.073617285 0.64504505 51.40830533 0.00991713 0.030122017 1.19E-08 7.925936608 -0.0361964 LS(ph)THHLRDFMDPT(ph)MDNT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LSTHHLRDFMDPTMDNTK 18 1 Q96BZ9;Q96BZ9-3 Q96BZ9 TBC1D20 TBC1 domain family member 20 3 0 LS(0.5)T(0.5)HHLRDFMDPT(1)MDNT(1)K 41.386 0.025418 10708000 1630.8 1454.6 1566.6 1183.2 1511.8 1258.1 1272 1238.3 1835 2036.3 TRUE FALSE FALSE 1610.923182 1475.077897 1593.866016 1320.007151 1434.647205 1177.71147 1380.043648 1274.128257 1670.873004 1983.396632 0.812204254 0.743713019 0.803604277 0.665528583 0.723328446 0.593785152 0.69579812 0.642397106 0.84243009 1 10.9537575 -11.08058864 0.245296661 1.0957679 0.593520125 0.689386641 0.062196242 0.4779932 0.086018122 0.091419712 0.050661958 8.31E-12 11.08058864 -0.502247775 LSAFPEPPEDGTLLS(ph)EAK ddPTM_HeLa_Romidepsin_16h_R1 2 LSAFPEPPEDGTLLSEAK 18 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 LSAFPEPPEDGT(0.003)LLS(0.997)EAK;LSAFPEPPEDGTLLS(1)EAK ; 229.93 6.06E-39 13386100 5632.1 5363.7 5780.4 4753.4 9614.5 11399.9 7511.8 9639.2 5057.4 4875.6 TRUE FALSE FALSE 5563.453799 5439.210309 5881.005437 5303.010473 9123.836188 10671.48318 8149.852105 9918.095044 4605.053478 4748.931209 1.171517033 1.145354622 1.238385055 1.116674519 1.921239914 2.247133663 1.716144485 2.088489937 0.969703134 1 12.21338714 -8.746507383 5.247745419 1.102015529 2.000592459 0.90265877 0.1427737 0.036999969 2.869913883 0.020235482 0.039704505 1.79E-09 8.746507383 0.89857693 LSAK(ac)PPAK ddPTM_HeLa_Romidepsin_16h_R1 2 LSAKPPAK 8 1 A6NEL0;P05114;F2Z2W6;F2Z2Y5;H7BXJ5;A0A494C035 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 0 1 ; LSAK(1)PPAK;LSAK(1)PPAK 118.33 0.0078598 26590000 14087.8 13766.8 13488.2 10606.5 15254.4 16846.8 15937.3 15353 15300.3 13346.7 FALSE TRUE FALSE 13916.09247 13960.60937 13722.95646 11832.87344 14475.91105 15770.34385 17291.01386 15797.21483 13931.80285 12999.95081 1.070472702 1.073897092 1.05561603 0.910224478 1.113535832 1.213107963 1.330083022 1.21517497 1.071681197 1 13.66621854 -8.300962198 2.795459778 1.031366479 1.269421752 0.762772417 0.055368819 0.09098137 1.401643711 0.007902925 0.021040255 5.00E-09 8.300962198 0.238055273 LSAMLVPVT(ph)PEVKPK ddPTM_HeLa_Romidepsin_16h_R1 2 LSAMLVPVTPEVKPK 15 1 Q5JSK7;Q5JSK8;Q5JSL0;Q5JSK6;P82970 Q5JSK7 HMGN5 High mobility group nucleosome-binding domain-containing protein 5 1 0 LS(0.003)AMLVPVT(0.997)PEVKPK;LS(0.001)AMLVPVT(0.999)PEVKPK ; 71.592 0.025548 548540000 14727.1 14041.2 14302.9 13901.2 17377 18009.8 13552 15040.6 14094.5 12879.5 TRUE FALSE FALSE 14547.60044 14238.87238 14551.83597 15508.52215 16490.18685 16859.0319 14703.10654 15475.77603 12833.85262 12544.88873 1.159643641 1.135033772 1.159981271 1.236242304 1.314494468 1.343896487 1.172039613 1.233631988 1.023034392 1 13.61481205 -11.14207125 0.318836237 0.962855031 1.279467085 0.749990926 0.052650899 0.672956153 0.17593597 0.084748216 0.042244487 7.21E-12 11.14207125 0.316612055 LSAS(ph)PAQEK ddPTM_HeLa_Romidepsin_16h_R1 2 LSASPAQEK 9 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 LS(0.001)AS(0.999)PAQEK;LS(0.091)AS(0.909)PAQEK ; 129 0.0087862 55249000 10233 9466.6 9980.5 8258.5 10312.4 10869 9200.9 9165.7 10010 9796.3 TRUE FALSE FALSE 10108.27626 9599.871043 10154.20642 9213.386627 9786.119747 10174.50598 9982.424216 9430.895068 9114.680529 9541.790714 1.059368892 1.006086942 1.064182471 0.965582552 1.025606203 1.066309908 1.04617933 0.9883779 0.955237943 1 13.22004433 -12.69492334 1.584876517 1.000045814 1.033145837 0.174609322 0.03525569 0.662626197 3.007357913 0.022605114 0.005033186 2.02E-13 12.69492334 0.033100023 LSAS(ph)SEDISER ddPTM_HeLa_Romidepsin_16h_R1 2 LSASSEDISER 11 0 Q13233 Q13233 MAP3K1 Mitogen-activated protein kinase kinase kinase 1 1 0 LS(0.007)AS(0.912)S(0.081)EDISER;LS(0.073)AS(0.464)S(0.464)EDISER ; 176.87 1.44E-05 14700300 2918.6 3054 2321.71 2571.2 3487.5 3382.9 2574 3036.7 2845.4 2916.2 TRUE FALSE FALSE 2883.026981 3096.994292 2362.118389 2868.494242 3309.519861 3166.743608 2792.635496 3124.562123 2590.900298 2840.436704 1.014994271 1.09032329 0.831603952 1.009877896 1.165144732 1.114879132 0.983171177 1.100028781 0.912148577 1 11.47189704 -8.965517424 24.71006719 0.999293119 1.085171617 0.312333715 0.078835529 177.4535395 127161.6211 0.010611566 0.01923504 1.08E-09 8.965517424 0.085878497 LSASTASELS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 LSASTASELSPK 12 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;H0YF21 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 LSAS(0.001)T(0.002)AS(0.12)ELS(0.878)PK;LS(0.065)AS(0.408)T(0.012)AS(0.001)ELS(0.514)PK;LSASTAS(0.004)ELS(0.996)PK ;; 179.93 1.40E-06 691843000 8580.1 7463.1 8238.2 6832.9 7962 6665.2 7139.4 6719.8 8176.8 8272.7 TRUE FALSE FALSE 8475.522441 7568.165718 8381.582415 7622.952048 7555.66943 6239.315231 7745.820458 6914.226811 7445.446529 8057.774061 1.051844142 0.939237767 1.040185832 0.946036956 0.937686931 0.774322435 0.961285387 0.858081495 0.924007855 1 12.97616564 -8.87505644 1.802338236 1.018799101 0.874237578 0.382239899 0.06136179 0.173683471 1.141423869 0.007957067 0.0170725 1.33E-09 8.87505644 -0.144561523 LSDLDS(ph)ETR ddPTM_HeLa_Romidepsin_16h_R1 2 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 1 0 LSDLDS(0.972)ET(0.028)R;LSDLDS(0.939)ET(0.061)R ; 129.88 0.0083368 13164800 5178.5 5473.3 5382.6 4439.1 5127.8 5766 4310.9 4873.8 5472.7 4662.6 TRUE FALSE FALSE 5115.38245 5550.353261 5476.281895 4952.369629 4866.109232 5397.571209 4677.067738 5014.815713 4983.208005 4541.46498 1.126372761 1.222150404 1.205840388 1.090478436 1.071484478 1.188508825 1.029858814 1.104228643 1.097268839 1 12.14894204 -11.96086338 0.940169268 1.005222841 1.128995842 0.144979984 0.064493103 0.423397958 0.718036607 0.031903859 0.011828567 1.09E-12 11.96086338 0.123773 LSDLDSETR ddPTM_HeLa_Romidepsin_16h_R1 2 LSDLDSETR 9 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 0 ; ; 195.05 9.80E-07 49500000 10672.1 9276 9035.1 6497.1 9707.4 9267.5 8393.1 9059.1 10114.1 9835.8 FALSE FALSE TRUE 10542.02434 9406.587771 9192.352125 7248.325272 9211.995155 8675.336659 9106.009705 9321.210766 9209.469565 9580.264498 1.100389696 0.981871406 0.959509221 0.756589265 0.961559585 0.9055425 0.950496691 0.972959647 0.961295961 1 13.22584977 -9.860772879 2.801383734 1.046984781 0.911820231 0.297938823 0.068144759 0.176837659 2.820779404 0.011157038 0.015166589 1.38E-10 9.860772879 -0.13516455 LSDQFHDILIR ddPTM_HeLa_Romidepsin_16h_R1 2 LSDQFHDILIR 11 0 A0A024QZ42;O75340-2;O75340;H0Y9X3;A0A087WZ38 A0A024QZ42 PDCD6 Programmed cell death protein 6 0 0 ; ; 132.03 0.0022004 36495000 10073.5 9387.9 8920.7 6949 14197.3 13631.3 13539.6 14079 12962.2 10647.4 FALSE FALSE TRUE 9950.720307 9520.063103 9075.961041 7752.476076 13472.7588 12760.30392 14689.65329 14486.35365 11802.82837 10370.77901 0.959495935 0.917969912 0.875147473 0.747530737 1.299107694 1.230409394 1.416446466 1.396843345 1.138085032 1 13.34023665 -8.662841782 7.336286953 0.952078957 1.338976327 0.777715611 0.103722312 0.073483102 4.795362105 0.013498066 0.027070331 2.17E-09 8.662841782 0.386897371 LSDVDANTAIKHEEQS(ph)NEDIPIAEQSSK ddPTM_HeLa_Romidepsin_16h_R1 2 LSDVDANTAIKHEEQSNEDIPIAEQSSK 28 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 LS(0.002)DVDANT(0.016)AIKHEEQS(0.978)NEDIPIAEQS(0.003)S(0.002)K;LSDVDANT(0.001)AIKHEEQS(0.999)NEDIPIAEQSSK ; 85.849 4.14E-08 14328000 2669.99 2454.43 2373.78 2498.3 2500.08 2318.21 2171.82 2319.03 3130.31 2745.25 TRUE FALSE FALSE 2637.447135 2488.98353 2415.094645 2787.165201 2372.491589 2170.083863 2356.294337 2386.127474 2850.327234 2673.928009 0.986356823 0.930834159 0.903201072 1.042348631 0.887268311 0.811571536 0.881210836 0.892367882 1.065970072 1 11.38474491 -8.905846618 0.543082795 0.996313578 0.847831476 0.513093497 0.053384201 0.688550477 0.344470518 0.011864934 0.048057144 1.24E-09 8.905846618 -0.148482101 LSEAVWQPEEHYSS(ph)SPEK ddPTM_HeLa_Romidepsin_16h_R1 1 LSEAVWQPEEHYSSSPEK 18 0 F5H269;Q9Y485 F5H269 DMXL1 DmX-like protein 1 1 0 LSEAVWQPEEHYS(0.01)S(0.495)S(0.495)PEK 98.562 0.0010349 3443500 1612.5 1719.7 1877.9 1579.4 2770.6 2998.2 2201.3 2317.8 2472.6 2243 TRUE FALSE FALSE 1592.84623 1743.909982 1910.584062 1762.017659 2629.205943 2806.624696 2388.278367 2384.861886 2251.444463 2184.726537 0.729082658 0.79822804 0.874518632 0.806516344 1.203448532 1.28465721 1.093170393 1.091606591 1.030538342 1 11.09323699 -8.759181662 24.99940412 0.85904215 1.171176886 0.676800006 0.099600256 29.48228246 326445.746 0.017057238 0.032842669 1.74E-09 8.759181662 0.312134736 LSEGPAAMAGPGS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 LSEGPAAMAGPGSPPR 16 0 Q8N2Y8 Q8N2Y8 RUSC2 Iporin 1 0 LSEGPAAMAGPGS(1)PPR 90.853 0.016443 11124000 2609.1 2537.8 2476 2195.8 1695.8 1421.4 1375.4 1449.6 2631 2641.1 TRUE FALSE FALSE 2577.299286 2573.527215 2519.093741 2449.688728 1609.256998 1330.577127 1492.226442 1491.541889 2395.676771 2572.483841 1.001871905 1.00040559 0.979245701 0.952265934 0.625565445 0.517234397 0.580072231 0.579806125 0.9312699 1 11.3289463 -8.749334328 3.403590951 0.998592224 0.5611748 0.980686665 0.027720877 0.013281188 0.322351128 0.002653616 0.005357015 1.78E-09 8.749334328 -0.437417424 LSEGS(ph)QPAEEEEDQETPSR ddPTM_HeLa_Romidepsin_16h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 LSEGS(1)QPAEEEEDQETPSR;LS(0.008)EGS(0.992)QPAEEEEDQETPSR ; 246.9 3.45E-62 21662500 3192.4 3191.6 2831.3 3381.9 2479.8 2492.4 2242.86 2283.7 3546.9 3144.5 TRUE FALSE FALSE 3153.489801 3236.531429 2880.577589 3772.93119 2353.246553 2333.143684 2433.368472 2349.775256 3229.656381 3062.805437 1.029608268 1.056721197 0.940502963 1.231854673 0.768330409 0.761766861 0.794490059 0.767197037 1.054476508 1 11.58063801 -8.723348155 24.99985624 1.025362707 0.773686095 0.775332736 0.072786037 56.733049 37234.53989 0.009471286 0.018942278 1.89E-09 8.723348155 -0.251676612 LSEGSQPAEEEEDQET(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 LSEGSQPAEEEEDQETPSR 19 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 LSEGSQPAEEEEDQET(0.993)PS(0.007)R;LSEGSQPAEEEEDQET(1)PSR ; 249.5 4.18E-62 21942000 2399.1 2229.24 1915.02 2262.57 2662 2977.4 2463.9 2347.8 1986.37 2273.6 TRUE FALSE FALSE 2369.858846 2260.623299 1948.35012 2524.178989 2526.148207 2787.153749 2673.183605 2415.729889 1808.704092 2214.531544 1.070140027 1.020813321 0.879802378 1.139825258 1.140714484 1.258574869 1.207110195 1.090853682 0.816743431 1 11.11278583 -9.022606108 21.99324598 1.021843635 1.177374142 0.526246941 0.090199818 88.95755829 86546.25757 0.009800173 0.016362928 9.49E-10 9.022606108 0.155530507 LSEK(ac)ITPLK ddPTM_HeLa_Romidepsin_16h_R1 1 LSEKITPLK 9 1 C9JXM5;G5E9W1;Q7Z3E1 C9JXM5 TIPARP TCDD-inducible poly [ADP-ribose] polymerase 0 1 LSEK(1)ITPLK 145.46 0.019369 540110 233.54 481.59 385.67 391.82 496.37 589.13 588.54 470.28 467.63 328.19 FALSE TRUE FALSE 230.6935247 488.3698367 392.3824246 437.124072 471.0383867 551.4864943 638.5305729 483.8868098 425.8040016 319.6635765 0.721675979 1.527761912 1.227485561 1.367450358 1.47354413 1.725209048 1.997508067 1.513737709 1.332037908 1 8.320410558 -9.36482881 0.749782473 0.873748641 1.76491024 0.452561558 0.251096505 0.256185977 0.285061065 0.046553469 0.104276344 4.32E-10 9.36482881 0.891161599 LSEK(ac)SVEER ddPTM_HeLa_Romidepsin_16h_R1 2 LSEKSVEER 9 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 1 ; LSEK(1)SVEER;LSEK(1)SVEER 142.83 0.015741 8897200 3579.2 3310.6 2550.3 2376.23 2389.82 1688.37 2274.71 1798.77 4928.7 3243.3 FALSE TRUE FALSE 3535.575334 3357.206714 2594.686902 2650.980893 2267.858568 1580.488606 2467.923811 1850.814572 4487.864728 3159.038598 1.119193458 1.062730514 0.821353339 0.839173315 0.717895175 0.500306836 0.781226229 0.585879062 1.420642575 1 11.62526985 -9.265590649 1.217470764 1.059014806 0.640204251 0.697510247 0.142242371 0.134150337 0.392151596 0.01496429 0.029424421 5.43E-10 9.265590649 -0.418810555 LSESQLS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 LSESQLSFR 9 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 0 LS(0.003)ES(0.183)QLS(0.814)FR 110.54 0.018821 2801000 1702.9 1530.1 1484.2 1237.3 1235.7 1461.6 1456.5 1751.3 1620.6 1659.3 TRUE FALSE FALSE 1682.1444 1551.640788 1510.031878 1380.362448 1172.637618 1368.208477 1580.215074 1801.971102 1475.649477 1616.191147 1.04080783 0.960060195 0.934315153 0.854083659 0.725556269 0.846563527 0.977740211 1.114949247 0.913041431 1 10.65838212 -9.874990097 2.330156802 1.018918495 0.896146633 0.072987971 0.100495553 0.325072454 3.598390064 0.016992089 0.023167072 1.33E-10 9.874990097 -0.122771861 LSESSAS(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 4 LSESSASPQPK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2;A0A3B3IU80;A0A3B3IUB0;A0A3B3IS72;A0A3B3ISB4;A0A3B3IRI6;A0A3B3ITV8;A0A3B3IRT2;A0A3B3ITF8;A0A3B3IT49;Q8N5Y2-5;A0A3B3ITX5 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 0 LSES(0.002)S(0.016)AS(0.982)PQPK;LS(0.014)ES(0.083)S(0.091)AS(0.812)PQPK;LSES(0.002)S(0.002)AS(0.997)PQPK;LSES(0.007)S(0.007)AS(0.985)PQPK ;;; 180.24 9.75E-06 67938000 21004.3 20528.2 19561.5 14875.8 11413 9647.6 8799.2 10014.7 21256.1 20078.1 TRUE FALSE FALSE 20748.29151 20817.19654 19901.9597 16595.80999 10830.55202 9031.149496 9546.603828 10304.45954 19354.90118 19556.46807 1.060942673 1.064466061 1.017666361 0.848609776 0.553809204 0.461798596 0.488155826 0.526908003 0.989693083 1 14.25535822 -8.875950425 2.184332826 1.032396749 0.488765281 0.987423804 0.027710146 0.02515833 0.243775356 0.004878558 0.009974928 1.33E-09 8.875950425 -0.543631468 LSFASETPLEKEPHS(ph)PADQPEQQAESTLTSAETR ddPTM_HeLa_Romidepsin_16h_R1 1 LSFASETPLEKEPHSPADQPEQQAESTLTSAETR 34 1 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 LSFAS(0.001)ET(0.024)PLEKEPHS(0.975)PADQPEQQAESTLTSAETR 87.498 1.54E-09 9676100 1319.1 1205.2 1285.6 1419.7 1012.4 1114.1 1107.2 1258.5 1521.2 1527.6 TRUE FALSE FALSE 1303.022302 1222.166837 1307.975329 1583.852394 960.7334502 1042.912606 1201.24554 1294.912712 1385.140062 1487.912732 0.875738391 0.821396854 0.879067233 1.064479361 0.645692069 0.700923235 0.807336018 0.870288078 0.930928295 1 10.5390742 -11.76385699 0.175221865 1.124351323 0.736176605 0.232823918 0.104614299 7.358044697 0.517941352 0.80329591 0.305993461 1.72E-12 11.76385699 -0.388174719 LSFS(ph)PENILIQNQDIVR ddPTM_HeLa_Romidepsin_16h_R1 2 LSFSPENILIQNQDIVR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 LS(0.203)FS(0.797)PENILIQNQDIVR;LS(0.032)FS(0.968)PENILIQNQDIVR ; 182.09 4.27E-09 132406000 2746.6 3289.5 2645.9 2495.42 3052.2 4127.4 3503.4 3597.1 3329.5 2853.3 TRUE FALSE FALSE 2713.123383 3335.809667 2691.95078 2783.952202 2896.434845 3863.672461 3800.978709 3701.176413 3031.701181 2779.170855 0.976234829 1.200289526 0.968616512 1.001720422 1.042193876 1.390224877 1.36766644 1.331755623 1.090865348 1 11.44043881 -8.296560045 5.327799752 1.006365265 1.364715 0.810200441 0.070470567 0.048400364 3.792244368 0.009442493 0.022083781 5.05E-09 8.296560045 0.358349735 LSFSDS(ph)ESDNSADSSLPSR ddPTM_HeLa_Romidepsin_16h_R1 2 LSFSDSESDNSADSSLPSR 19 0 Q03111 Q03111 MLLT1 Protein ENL 1 0 LSFS(0.089)DS(0.91)ESDNS(0.001)ADSSLPSR;LS(0.156)FS(0.156)DS(0.57)ES(0.109)DNS(0.009)ADSSLPSR ; 263.19 9.92E-77 14895500 2427.6 2221.62 2207 1375.91 1553.14 1663.99 1357.36 1632.73 2810.9 2710.6 TRUE FALSE FALSE 2398.011477 2252.896025 2245.411909 1534.999188 1473.87747 1557.666409 1472.654125 1679.970467 2559.486064 2640.178221 0.908276365 0.853312101 0.8504774 0.581399837 0.558249234 0.589985326 0.557785877 0.636309493 0.969436852 1 11.3664196 -9.494379996 1.322409972 0.957262723 0.57239347 0.933967776 0.044295476 0.076001748 0.265017895 0.00862163 0.014690993 3.20E-10 9.494379996 -0.384869253 LSGEHS(ph)ESSTPRPR ddPTM_HeLa_Romidepsin_16h_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 0 LSGEHS(0.918)ES(0.061)S(0.004)T(0.018)PRPR 78.244 0.01446 4492600 844.69 669.22 641.3 561.21 1067.1 1319.2 1111.9 894.37 1228.5 928.34 TRUE FALSE FALSE 834.3945934 678.6412967 652.4615575 626.0997408 1012.641905 1234.907378 1206.344758 920.2471849 1118.619883 904.221593 0.922776673 0.750525427 0.721572635 0.69241848 1.119904582 1.365713214 1.334125139 1.01772308 1.237108129 1 9.82053256 -8.53332387 21.07101398 0.90775881 1.247702388 0.463453856 0.172409386 18.91479933 38156.78174 0.022401462 0.044882034 2.93E-09 8.53332387 0.339943578 LSGEMPPAS(ph)PSFPR ddPTM_HeLa_Romidepsin_16h_R1 3 LSGEMPPASPSFPR 14 0 Q96JM7-2;Q96JM7 Q96JM7-2 L3MBTL3 Lethal(3)malignant brain tumor-like protein 3 1 0 LSGEMPPAS(0.965)PS(0.035)FPR;LSGEMPPAS(0.95)PS(0.05)FPR;LSGEMPPAS(0.924)PS(0.076)FPR ;; 108.97 0.008327 48285000 8043.5 7754.4 7777.6 9845.3 9443.1 8113.9 6162.8 7257.8 8134.4 6906.8 TRUE FALSE FALSE 7945.462728 7863.566647 7912.965865 10983.65991 8961.18337 7595.447976 6686.268078 7467.792992 7406.838891 6727.36034 1.181066916 1.168893332 1.176236364 1.632684939 1.33205045 1.129038373 0.99389177 1.11006288 1.101002253 1 12.71582482 -11.6117164 0.723025498 1.00775202 1.224433862 0.135733506 0.163388714 0.858261754 0.903891406 0.094440602 0.039906309 2.45E-12 11.6117164 0.216681842 LSGFSFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LSGFSFKK 8 1 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 0 1 LSGFSFK(1)K 92.062 0.015154 440180 293.46 121.17 314.68 177.36 450.19 299.49 287.42 157.07 0 162.13 FALSE TRUE FALSE 289.8831966 122.8758344 320.1568734 197.8671977 427.2151244 280.3535556 311.8334476 161.6145726 0 157.9178392 1.835658328 0.77809977 2.027363564 1.25297559 2.705299962 1.775312763 1.974656246 1.02340922 0 1 7.303030345 -9.722208608 24.99996108 1.35940272 1.817513497 0.196639273 0.659534829 231.5180528 147535.3898 0.082265888 0.116340471 1.90E-10 9.722208608 0.458110777 LSGINEIPRPFS(ph)PPVTSNT(ph)SPPPAAPLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9-3;Q0JRZ9 Q0JRZ9-3 FCHO2 F-BAR domain only protein 2 2 0 LSGINEIPRPFS(0.909)PPVT(0.121)S(0.076)NT(0.447)S(0.447)PPPAAPLAR 74.627 3.92E-05 26356000 1438.8 1271.3 1261.8 1327.7 1409.9 1415.9 870.39 1143.7 1375.7 1539.9 TRUE FALSE FALSE 1421.263352 1289.197395 1283.7611 1481.214921 1337.947542 1325.42856 944.3209049 1176.791155 1252.653946 1499.893176 0.947576384 0.859526142 0.855901687 0.987546943 0.892028555 0.883681972 0.629592107 0.784583312 0.835162108 1 10.55064404 -5.395970792 0.254245622 0.994935333 2.64E-16 0.302186311 0.085174167 11.71530654 0.273084351 0.03896353 4.374477835 4.02E-06 5.395970792 -0.994935333 LSGINEIPRPFS(ph)PPVTSNTSPPPAAPLAR ddPTM_HeLa_Romidepsin_16h_R1 2 LSGINEIPRPFSPPVTSNTSPPPAAPLAR 29 1 Q0JRZ9-3;Q0JRZ9 Q0JRZ9-3 FCHO2 F-BAR domain only protein 2 1 0 LSGINEIPRPFS(0.993)PPVT(0.002)S(0.003)NT(0.001)SPPPAAPLAR;LS(0.003)GINEIPRPFS(0.873)PPVT(0.074)S(0.034)NT(0.012)S(0.004)PPPAAPLAR ; 87.958 1.34E-07 115479000 2190.58 2224.55 1511.01 2128.02 1538.23 1421.32 1371.75 1555.54 2085.63 2173.09 TRUE FALSE FALSE 2163.880368 2255.867273 1537.308495 2374.071685 1459.728383 1330.502239 1488.266411 1600.547096 1899.086029 2116.632809 1.022322039 1.065781114 0.726299096 1.121626612 0.689646488 0.62859379 0.703129237 0.756176078 0.89722035 1 11.0475553 -8.74685386 24.99539874 0.998645774 0.690311301 0.615696925 0.106285308 97.47993628 167051.7618 0.013750873 0.02740618 1.79E-09 8.74685386 -0.308334474 LSGLAAPDYTRLS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 LSGLAAPDYTRLSPAK 16 1 Q8TEK3-1;Q8TEK3 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 LS(0.215)GLAAPDYT(0.159)RLS(0.626)PAK 106.36 0.026366 12989000 2428.3 2123.4 2138.6 1666.1 1262.8 1248.7 860.14 903.09 2037.7 1920.6 TRUE FALSE FALSE 2398.702946 2153.293281 2175.821436 1858.742321 1198.354604 1168.9121 933.2002701 929.2194843 1855.443008 1870.702535 1.282247124 1.151061294 1.163103912 0.993606566 0.640590677 0.624851936 0.498850166 0.496722203 0.99184289 1 10.86936446 -8.776335221 2.010336978 1.141364007 0.533688226 0.904089943 0.085916959 0.083147969 0.684443491 0.01687359 0.037042783 1.67E-09 8.776335221 -0.607675781 LSGSSES(ph)PSGPK ddPTM_HeLa_Romidepsin_16h_R1 2 LSGSSESPSGPK 12 0 A0A2R8YFS6;E5RIQ7;A0A2R8YGM9;A6NCB9;A0A2R8YET7;F8WB53;A0A2R8Y6K4;Q99502-3;Q99502 A0A2R8YFS6 EYA1 Eyes absent homolog;Eyes absent homolog 1 1 0 LSGS(0.003)S(0.019)ES(0.662)PS(0.316)GPK;LSGS(0.001)S(0.006)ES(0.958)PS(0.035)GPK ; 146.16 0.0015011 13666200 3497.3 3962 3355.6 2761.1 2663.97 2622.3 2120.96 2473.8 3787.7 3833.3 TRUE FALSE FALSE 3454.673562 4017.77714 3414.00281 3080.351373 2528.01767 2454.743493 2301.114289 2545.3755 3448.918626 3733.710313 0.92526556 1.076081646 0.914372708 0.825010811 0.677079221 0.657454191 0.616307666 0.68172817 0.923724214 1 11.86639428 -8.985701303 1.81604767 0.972276628 0.647300841 0.914127784 0.044947392 0.06874647 0.45292333 0.00721788 0.014584951 1.03E-09 8.985701303 -0.324975787 LSHPT(ph)T(ph)S(ph)RPK ddPTM_HeLa_Romidepsin_16h_R1 1 LSHPTTSRPK 10 1 Q5JPT2;Q96B97-2;Q96B97;Q96B97-3 Q5JPT2 SH3KBP1 SH3 domain-containing kinase-binding protein 1 3 0 LS(0.001)HPT(1)T(1)S(1)RPK 87.298 0.0030211 0 2760.7 2901.2 1769.3 1752.3 2208.3 2588.5 2168.6 3662 3185.9 3305.2 TRUE FALSE FALSE 2727.051527 2942.04317 1800.093924 1954.909171 2095.602211 2423.103204 2352.80083 3767.954192 2900.945125 3219.330428 0.847086557 0.913868034 0.559151651 0.60724092 0.650943498 0.752673035 0.730835459 1.170415488 0.901102012 1 11.65254495 -10.90654761 0.864739919 0.969571452 0.748399934 0.154813246 0.165797731 0.550189938 0.886367125 0.048904704 0.039423011 1.24E-11 10.90654761 -0.221171518 LSKSDEQLS(ph)SLDR ddPTM_HeLa_Romidepsin_16h_R1 1 LSKSDEQLSSLDR 13 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 0 LS(0.001)KS(0.011)DEQLS(0.985)S(0.002)LDR 148.18 0.0050764 14293000 1331.8 1255.2 1254.6 983.93 1093 1102.1 904.01 982.96 1463 1292.8 TRUE FALSE FALSE 1315.567509 1272.870739 1276.435787 1097.696616 1037.220131 1031.679367 980.7965868 1011.400397 1332.145616 1259.21287 1.044753863 1.010846354 1.013677526 0.871732368 0.823705155 0.819304974 0.778896571 0.803200492 1.057919314 1 10.29830648 -9.11235642 2.044410248 1.021748347 0.80263129 0.966513258 0.019474041 0.041841369 0.343271301 0.003204364 0.005951538 7.72E-10 9.11235642 -0.219117057 LSLDSQEGDS(ph)GLDSGTER ddPTM_HeLa_Romidepsin_16h_R1 1 LSLDSQEGDSGLDSGTER 18 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 LSLDS(0.025)QEGDS(0.974)GLDS(0.001)GTER 129.05 7.67E-09 0 503.74 528.61 483.4 387.19 567.04 519.2 444.82 524.2 439.88 516.26 TRUE FALSE FALSE 497.6002231 536.0517855 491.8133742 431.9587296 538.1018329 486.0247956 482.6029997 539.3668999 400.5360311 502.8474908 0.989564892 1.066032535 0.978056733 0.859025326 1.070109412 0.966545135 0.959740296 1.072625219 0.796535805 1 8.973977099 LSLEGDHS(ph)TPPSAYGSVK ddPTM_HeLa_Romidepsin_16h_R1 4 LSLEGDHSTPPSAYGSVK 18 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YNB8;H0YMW4;H0YKN4 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 0 LSLEGDHS(0.904)T(0.095)PPS(0.001)AYGSVK;LSLEGDHS(0.916)T(0.083)PPSAYGSVK;LSLEGDHS(0.842)T(0.158)PPSAYGSVK;LSLEGDHS(0.93)T(0.07)PPSAYGSVK ;;; 243.99 1.05E-61 262374000 13889.8 14102.7 13189.1 12428.9 27546.8 32187.5 25983.2 27589.3 19073.4 17485.8 TRUE FALSE FALSE 13720.50578 14301.23818 13418.65075 13865.9879 26140.984 30130.82263 28190.21236 28387.55287 17367.42733 17031.5164 0.805595078 0.839692594 0.787871757 0.814137014 1.534859457 1.769121547 1.65517924 1.666766024 1.019722903 1 14.05591927 -8.688382331 4.532537091 0.884099267 1.684821294 0.955442635 0.082743597 0.034512922 1.343203376 0.014033931 0.028448315 2.05E-09 8.688382331 0.800722027 LSLEGDHSTPPSAY(ph)GSVK ddPTM_HeLa_Romidepsin_16h_R1 2 LSLEGDHSTPPSAYGSVK 18 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YNB8;H0YMW4;H0YKN4 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 0 LSLEGDHST(0.001)PPS(0.055)AY(0.889)GS(0.055)VK;LSLEGDHSTPPS(0.365)AY(0.459)GS(0.175)VK ; 78.078 0.013302 33474000 15262 16320.2 13904.8 8725.5 20236 16469.8 12350.4 12600.5 20043.1 18078.3 TRUE FALSE FALSE 15075.98087 16549.9562 14146.80721 9734.383365 19203.28141 15417.43293 13399.44267 12965.07559 18250.39494 17608.62316 0.85617034 0.939877925 0.803402236 0.552819109 1.090561212 0.875561524 0.760959136 0.736291274 1.036446449 1 14.10399449 -16.52287875 0.144184029 1.654434184 0.76188096 0.271641887 0.130253399 81.9486399 0.815147114 15.09115296 0.345244698 3.00E-17 16.52287875 -0.892553224 LSLEGDHSTPPSAYGS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 LSLEGDHSTPPSAYGSVK 18 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YKS4;H0YMM1;H0YKX9;H0YMT9;H0YLV6;H0YKZ7;H0YKL9;H0YKV8;H0YMD9;H0YNB8;H0YMW4;H0YKN4 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 1 0 LSLEGDHSTPPS(0.009)AYGS(0.991)VK 100.47 0.00084431 5283300 1547.4 2566.9 959.25 1158.1 2833.3 2888.2 2469.6 2733.5 4143.7 3950 TRUE FALSE FALSE 1528.539694 2603.036886 975.9453439 1292.004971 2688.706129 2703.653341 2679.367762 2812.58951 3773.077094 3847.378431 0.397293825 0.676574174 0.253665025 0.335814372 0.698841088 0.702726126 0.696413886 0.731040515 0.980687801 1 11.90966003 -12.41786168 1.112441354 1.003265618 0.547307707 0.514532682 0.165767593 0.358538612 0.784470924 0.128051549 0.031399237 3.82E-13 12.41786168 -0.455957911 LSLFPAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LSLFPASPR 9 0 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 0 LSLFPAS(1)PR;LSLFPAS(1)PR ; 106.62 0.022319 36738000 4047.2 3397.2 5257.9 4126 6324.4 6753.8 5501.5 4669.4 4247.6 2756.8 TRUE FALSE FALSE 3997.87117 3445.025871 5349.411544 4603.067533 6001.642268 6322.253977 5968.797273 4804.501722 3867.684018 2685.177939 1.488866385 1.282978614 1.99220002 1.714250466 2.235100394 2.354500939 2.222868432 1.789267539 1.440382763 1 11.39080198 -9.95393993 0.48078743 1.074528172 2.228978625 0.669114935 0.246103348 0.302979589 0.161692443 0.084263472 0.130282576 1.11E-10 9.95393993 1.154450453 LSLFSDGDSS(ph)ESEDTLSSSER ddPTM_HeLa_Romidepsin_16h_R1 1 LSLFSDGDSSESEDTLSSSER 21 0 M0QZ79;M0QXD7;M0R025;M0QYG0;M0QYA8;Q8IV63-2;Q8IV63 M0QZ79 VRK3 Inactive serine/threonine-protein kinase VRK3 1 0 LSLFSDGDS(0.3)S(0.674)ES(0.027)EDTLSSSER 289.68 4.71E-129 5386300 1130.3 1220.8 1178.4 1089.2 2153.8 2495.2 2187.7 2278.8 1225.3 1144 TRUE FALSE FALSE 1116.523469 1237.986454 1198.909558 1215.138429 2043.883549 2335.764773 2373.523183 2344.733483 1115.706099 1114.278715 1.002014535 1.111020463 1.075951233 1.090515696 1.834265989 2.096212322 2.130098288 2.104261215 1.001280994 1 10.12189442 -8.685468623 2.616586387 1.01527169 2.108590727 0.992519761 0.042758287 0.017740949 0.2464221 0.007482259 0.016179694 2.06E-09 8.685468623 1.093319037 up LSLSPALQDALHTFPQLQVEQS(ph)GEGSPEEGAVR ddPTM_HeLa_Romidepsin_16h_R1 1 LSLSPALQDALHTFPQLQVEQSGEGSPEEGAVR 33 0 Q9ULL5;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 0 LSLSPALQDALHT(0.001)FPQLQVEQS(0.947)GEGS(0.052)PEEGAVR 61.751 0.00036388 6708300 742.38 769.95 609.79 792.81 610.87 664.6 623.57 489.47 930.51 807.49 TRUE FALSE FALSE 733.331587 780.7893763 620.4031392 884.4784225 579.6950244 622.1342049 676.5360202 503.6320422 847.2828551 786.5112934 0.932385324 0.99272494 0.788803854 1.124559088 0.737046028 0.791004796 0.860173307 0.640336695 1.077267246 1 9.619323671 -5.792001691 0.320148751 0.982533183 8.47E-17 0.493087684 0.105842307 10.51878956 0.370675636 0.032914446 4.883632965 1.61E-06 5.792001691 -0.982533183 LSLVIRS(ph)PSLLQSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 LSLVIRSPSLLQSGAK 16 1 I3L1L3;Q9BQG0;Q9BQG0-2;I3L2H8 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 LS(0.305)LVIRS(0.687)PS(0.008)LLQSGAK 80.102 0.0091847 19617000 1880.8 1808.7 1819.2 1974 2574 3103.7 2806.9 3247.2 1944.5 1826.4 TRUE FALSE FALSE 1857.876086 1834.162926 1850.862413 2202.243168 2442.639175 2905.383587 3045.318016 3341.152609 1770.57905 1778.949865 1.044366749 1.031036884 1.040424157 1.237945606 1.373079266 1.6332015 1.711862755 1.878160074 0.995294519 1 10.79681014 -8.362185315 0.867886365 1.015515916 1.892849805 0.990823607 0.03046972 0.04758303 0.058387905 0.005103274 0.027710459 4.34E-09 8.362185315 0.877333889 LSLVIRSPS(ph)LLQSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 LSLVIRSPSLLQSGAK 16 1 I3L1L3;Q9BQG0;Q9BQG0-2;I3L2H8 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 LSLVIRS(0.368)PS(0.63)LLQS(0.001)GAK 83.065 0.0077152 14421000 1848.2 1702.1 1593.9 1983 2803 3346.4 2942.8 3064.1 2019.1 1569.1 TRUE FALSE FALSE 1825.673428 1726.062208 1621.641161 2212.28379 2659.952451 3132.57584 3192.761359 3152.754899 1838.506639 1528.334556 1.194550905 1.129374587 1.061051165 1.447512773 1.740425511 2.049666304 2.08904611 2.062869604 1.202947766 1 10.57774467 -8.752239007 1.436979066 1.091271365 2.090220107 0.973382627 0.068987193 0.048759411 0.201883246 0.01280952 0.032398173 1.77E-09 8.752239007 0.998948742 LSMEDS(ph)KSPPPKATEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LSMEDSKSPPPKATEEK 17 2 Q9NQG5 Q9NQG5 RPRD1B Regulation of nuclear pre-mRNA domain-containing protein 1B 1 0 LS(0.029)MEDS(0.485)KS(0.485)PPPKATEEK 48.216 0.028835 45152000 6933.1 5971.2 5539.4 7161.1 5985.4 5706.8 4418.2 4986.8 7040.8 6229.1 TRUE FALSE FALSE 6848.59671 6055.26271 5635.810933 7989.100076 5679.942703 5342.153898 4793.481798 5131.08519 6411.053214 6067.267084 1.128777853 0.998021453 0.928887892 1.316754309 0.93616164 0.880487677 0.79005617 0.845699574 1.056662436 1 12.56683111 -8.529077636 24.99967992 1.064576355 0.846286275 0.528057785 0.099559584 96.55164127 389385.3437 0.014612656 0.029287279 2.96E-09 8.529077636 -0.21829008 LSMPQSAAVSTT(ph)PPHNR ddPTM_HeLa_Romidepsin_16h_R1 2 LSMPQSAAVSTTPPHNR 17 0 A2A2F0;Q86X10-4;Q86X10-2;Q86X10-3;Q86X10 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 0 LSMPQSAAVS(0.001)T(0.016)T(0.983)PPHNR;LSMPQSAAVS(0.224)T(0.224)T(0.553)PPHNR ; 132.67 0.00081676 18331300 3516.2 3631.8 3754.2 3179.4 4499 4556.9 3385.9 3960.5 4348.3 4086.6 TRUE FALSE FALSE 3473.343202 3682.928576 3819.540276 3547.017188 4269.399242 4265.728797 3673.498261 4075.090819 3959.377157 3980.429543 0.872605121 0.92525908 0.959579923 0.891114175 1.072597617 1.071675494 0.92288991 1.023781674 0.994711027 1 11.95870841 -8.765119195 24.99927208 0.935824807 1.019099962 0.354655402 0.054002081 91.26209817 620006.2573 0.009142957 0.017051573 1.72E-09 8.765119195 0.083275155 LSNGNSRGS(ph)VSKS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 LSNGNSRGSVSKSSR 15 2 Q5T5P2;Q5T5P2-2;Q5T5P2-7;Q5T5P2-10;Q5T5P1;A0A1B0GU17;A0A0U1RQK8 Q5T5P2 KIAA1217 Sickle tail protein homolog 2 0 LSNGNS(0.001)RGS(0.947)VS(0.176)KS(0.868)S(0.009)R 116.87 0.0067222 66808000 3448.5 3543.2 3354.5 3514.5 3511.6 4096.7 3057.9 3582.7 3592.2 3314.6 TRUE FALSE FALSE 3406.468356 3593.081263 3412.883665 3920.863026 3332.389948 3834.934091 3317.63795 3686.359772 3270.904635 3228.486214 1.055128667 1.112930651 1.057115762 1.214458655 1.032183422 1.187842796 1.027614098 1.141822987 1.013138796 1 11.65664215 -10.74891306 0.740163424 1.008881258 1.113681988 0.336921196 0.058425829 0.425563434 0.510805228 0.016403128 0.014063527 1.78E-11 10.74891306 0.10480073 LSNGS(ph)FSAPSLTNSR ddPTM_HeLa_Romidepsin_16h_R1 1 LSNGSFSAPSLTNSR 15 0 O94806;O94806-2 O94806 PRKD3 Serine/threonine-protein kinase D3 1 0 LS(0.136)NGS(0.799)FS(0.062)APS(0.002)LT(0.001)NSR 146.67 0.0004796 17169000 635.58 711.97 495.12 530.39 558.3 547.6 295.73 383.1 723.74 548.68 TRUE FALSE FALSE 627.8333065 721.9931323 503.7373559 591.7161874 529.8078677 512.6101273 320.8492988 394.1843941 659.0068818 534.4252145 1.174782345 1.35097131 0.942577824 1.107201104 0.991360163 0.959180281 0.600363325 0.737585697 1.233113378 1 9.061844266 -7.987579984 1.867920725 1.094146456 0.657169446 0.665627401 0.122968698 0.168644134 1.109729252 0.017774023 0.077759381 1.03E-08 7.987579984 -0.43697701 LSNIFVIGK ddPTM_HeLa_Romidepsin_16h_R1 1 LSNIFVIGK 9 0 P62701 P62701 RPS4X "40S ribosomal protein S4, X isoform" 0 0 107.15 0.029865 723320 162.03 292.75 300.34 172.66 251.98 344.93 220.76 304.49 222.38 250.57 FALSE FALSE TRUE 160.055116 296.8713422 305.5672917 192.6237616 239.1205203 322.8900862 239.5113489 313.2999377 202.4897758 244.0601553 0.65580191 1.216385943 1.252016296 0.789247066 0.979760584 1.322993857 0.981361946 1.283699658 0.829671585 1 7.931092973 -10.25181142 24.99676749 0.837462012 1.107760609 0.365910974 0.174120734 640.8765394 1663888.404 0.032779395 0.039876672 5.60E-11 10.25181142 0.270298597 LSPLPPGSPGS(ph)AAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPLPPGSPGSAAR 14 0 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 0 LSPLPPGS(0.431)PGS(0.569)AAR 152.11 0.00061547 28695000 3482.1 2781.9 2857.7 2605.2 3225.2 3841.2 3396.3 3894 3245.8 3392.6 TRUE FALSE FALSE 3439.658826 2821.063661 2907.43707 2906.425482 3060.606009 3595.759717 3684.781637 4006.666746 2955.487519 3304.459763 1.04091412 0.85371403 0.879852466 0.879546337 0.926204653 1.088153579 1.11509351 1.212502809 0.894393556 1 11.69019871 -7.846468887 2.096025093 0.980743359 1.185451699 0.581706921 0.074752715 0.240649027 2.012649869 0.012277323 0.059709158 1.42E-08 7.846468887 0.20470834 LSPPVASGGIPHQS(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 1 LSPPVASGGIPHQSPPTK 18 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 LSPPVASGGIPHQS(0.999)PPT(0.001)K 118.46 0.00063793 19217000 6123.4 6696.1 6126 5490.6 6457.6 5364 4793.1 4296.5 8218.8 7524.2 TRUE FALSE FALSE 6048.765646 6790.367872 6232.62046 6125.449006 6128.044575 5021.257712 5200.225794 4420.812449 7483.689944 7328.720199 0.825350877 0.926542109 0.85043777 0.835814281 0.836168445 0.685147962 0.709568063 0.603217523 1.02114554 1 12.83934557 -5.494220724 0.174995401 0.998314326 6.96E-19 0.858183101 0.047958183 11.39287006 0.194082031 0.084295253 2.732236129 3.20E-06 5.494220724 -0.998314326 LSPPYS(ph)SPQEFAQDVGR ddPTM_HeLa_Romidepsin_16h_R1 2 LSPPYSSPQEFAQDVGR 17 0 Q13263-2;Q13263;M0R0K9 Q13263-2 TRIM28 Transcription intermediary factor 1-beta 1 0 LSPPY(0.014)S(0.901)S(0.086)PQEFAQDVGR;LSPPYS(0.937)S(0.063)PQEFAQDVGR ; 178.22 7.45E-09 23823000 1676.61 1804.34 1650.75 1976.17 2355.67 2322.5 1809.56 2316 2239.64 1865.67 TRUE FALSE FALSE 1656.174832 1829.741546 1679.480611 2204.664074 2235.45137 2174.099746 1963.263981 2383.009806 2039.320989 1817.199624 0.911388496 1.006901785 0.924213602 1.21322063 1.230162795 1.196401164 1.080378817 1.311363801 1.122232782 1 10.8275012 -9.258276142 24.98893318 0.959210018 1.200084698 0.63575871 0.078631897 90.87731222 717911.4835 0.009100424 0.014681646 5.52E-10 9.258276142 0.240874679 LSPQT(ph)GT(ph)PRTTAVSSNRNPEDDGCLLK ddPTM_HeLa_Romidepsin_16h_R1 1 LSPQTGTPRTTAVSSNRNPEDDGCLLK 27 2 Q8N7P7 Q8N7P7 Uncharacterized protein FLJ40521 2 0 LS(0.192)PQT(0.571)GT(0.571)PRT(0.252)T(0.252)AVS(0.081)S(0.081)NRNPEDDGCLLK 49.577 0.0038116 0 370.26 406.97 250.87 2510.8 467.65 435.28 342.45 459.81 498.28 277.58 TRUE FALSE FALSE 365.7471287 412.6993343 255.2362871 2801.11051 443.7840755 407.4670128 371.5376945 473.1138769 453.7125888 270.3684316 1.352773053 1.526433141 0.944031393 10.36034604 1.641404926 1.50708058 1.374190368 1.749885791 1.678127088 1 8.078782901 LSPS(ph)PSSR ddPTM_HeLa_Romidepsin_16h_R1 4 LSPSPSSR 8 0 P20700;Q03252 P20700;Q03252 LMNB1;LMNB2 Lamin-B1;Lamin-B2 1 0 LS(0.002)PS(0.915)PS(0.083)S(0.001)R;LS(0.006)PS(0.991)PS(0.003)SR;LS(0.001)PS(0.923)PS(0.076)S(0.001)R;LS(0.002)PS(0.929)PS(0.069)S(0.001)R ;;; 145.46 0.0081773 1930920000 19886.4 19065.2 18163.4 14139.4 14799.4 14725.2 11465.2 10097.2 20258.9 18682.4 TRUE FALSE FALSE 19644.01691 19333.60039 18479.52636 15774.26396 14044.13139 13784.30724 12439.0538 10389.34655 18446.89324 18197.02855 1.079517837 1.062459199 1.015524392 0.866859329 0.771781577 0.757503194 0.683576099 0.570936432 1.013731071 1 14.15141527 -8.679177051 0.954284852 1.043314487 0.627725 0.938820625 0.041734137 0.11329168 0.192673942 0.008245965 0.02894951 2.09E-09 8.679177051 -0.415589487 LSPS(ph)PTSQR ddPTM_HeLa_Romidepsin_16h_R1 5 LSPSPTSQR 9 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 LS(0.001)PS(0.922)PT(0.076)S(0.001)QR;LS(0.007)PS(0.985)PT(0.008)SQR;LS(0.005)PS(0.931)PT(0.034)S(0.029)QR;LS(0.007)PS(0.993)PT(0.001)SQR;LS(0.008)PS(0.983)PT(0.009)SQR ;;;; 160.91 0.0034441 5386544300 13158.8 14663 12935.3 11370.2 13254.5 13325.3 11386.3 10850.7 14075.7 12991.5 TRUE FALSE FALSE 12998.41548 14869.4261 13160.43347 12684.87602 12578.07341 12473.85634 12353.45204 11164.64788 12816.73414 12653.97896 1.027219622 1.175079092 1.040023341 1.002441688 0.994001448 0.985765535 0.976250402 0.882303339 1.012861977 1 13.62730348 -6.472205907 0.762669641 1.026901614 0.530398065 0.476596405 0.049546321 5.760679023 1.009941889 0.008673238 3.249180276 3.37E-07 6.472205907 -0.496503549 LSPS(ph)PTTEDPR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPSPTTEDPR 11 0 E7EQY4;F6RRE2;E7EV10;Q9BTC8-2;Q9BTC8 E7EQY4 MTA3 Metastasis-associated protein MTA3 1 0 LS(0.001)PS(0.888)PT(0.023)T(0.088)EDPR 155.26 0.0020875 12946000 2843.6 3120.8 2800.3 1650.7 2499.1 2658.9 2027 2252.7 3406.9 3014.2 TRUE FALSE FALSE 2808.941109 3164.734704 2849.038047 1841.561701 2371.561602 2489.004871 2199.173329 2317.87832 3102.178331 2935.890649 0.956759445 1.077947063 0.970416949 0.627258274 0.807782675 0.847785278 0.749065136 0.789497497 1.056639603 1 11.51958252 -9.374935613 7.885107125 0.98803877 0.770800921 0.779393252 0.065356962 0.102722433 6.486770356 0.009292332 0.014207485 4.22E-10 9.374935613 -0.217237849 LSPTPS(ph)MQDGLDLPSETDLR ddPTM_HeLa_Romidepsin_16h_R1 1 LSPTPSMQDGLDLPSETDLR 20 0 Q9UK58-6;Q9UK58;Q9UK58-5;Q9UK58-4 Q9UK58-6 CCNL1 Cyclin-L1 1 0 LS(0.155)PT(0.155)PS(0.69)MQDGLDLPSETDLR 83.243 0.0048855 5076000 1257.9 1350.9 1505.3 981.71 1526.4 1322.9 1096.5 1340.4 1558.3 1439.4 TRUE FALSE FALSE 1242.568231 1369.918006 1531.499115 1095.219929 1448.502112 1238.370959 1189.636683 1379.182359 1418.921745 1402.00418 0.886279976 0.977114066 1.092364157 0.781181643 1.03316533 0.88328621 0.848525774 0.983722002 1.012066701 1 10.45327494 LSQSSQDSS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 4 LSQSSQDSSPVR 12 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 0 LSQSSQDS(0.004)S(0.996)PVR;LSQSSQDS(0.004)S(0.995)PVR;LSQSSQDS(0.004)S(0.996)PVR;LSQSSQDS(0.004)S(0.996)PVR ;;; 168 0.00020896 473068000 23274.1 21509.5 20644.5 15022.3 14754.3 13476.6 14285.6 12498.8 22975.1 21715.2 TRUE FALSE FALSE 22990.42632 21812.31131 21003.80886 16759.24901 14001.33302 12615.48875 15499.01851 12860.43306 20920.14951 21151.03597 1.086964551 1.031264442 0.993039248 0.792360669 0.661969136 0.596447794 0.732778221 0.608028518 0.989083917 1 14.36844071 -9.129971193 1.998898582 1.041634816 0.649378205 0.943533535 0.042941775 0.052482411 0.410953305 0.007118082 0.013172633 7.41E-10 9.129971193 -0.39225661 LSRLMSGSS(ph)RSLER ddPTM_HeLa_Romidepsin_16h_R1 2 LSRLMSGSSRSLER 14 2 B5MC67;Q7Z6J6-2;Q7Z6J6;F8WEJ8;F8WCI0 B5MC67 FRMD5 FERM domain-containing protein 5 1 0 LSRLMS(0.009)GS(0.226)S(0.756)RS(0.009)LER;LS(0.001)RLMS(0.172)GS(0.172)S(0.654)RS(0.001)LER ; 105.13 0.0072504 25473000 1995.3 2180.58 1766.14 1687.25 2108.31 2022.99 1708.26 2265.3 2194 2037.06 TRUE FALSE FALSE 1970.980516 2211.278262 1796.878926 1882.337784 2000.715074 1893.727468 1853.359562 2330.842881 1997.763145 1984.136888 0.993369222 1.114478682 0.905622458 0.948693508 1.008355364 0.95443388 0.934088557 1.174738949 1.006867599 1 10.95429585 -7.250289503 24.43246501 0.990154121 1.174739097 0.521739689 0.054275567 720.1075971 1577914.811 0.007080891 0.139986077 5.62E-08 7.250289503 0.184584976 LSS(ph)DSFAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSDSFAR 8 0 A0A087WSV0;Q9HB09-3;Q9HB09 A0A087WSV0 BCL2L12 Bcl-2-like protein 12 1 0 LS(0.16)S(0.84)DSFAR 177.7 0.00016451 13593000 2327.3 3006.1 2461.6 2162.9 4409.2 5165 3756 5062.7 3165.3 2660.7 TRUE FALSE FALSE 2298.933972 3048.419955 2504.443115 2412.984675 4184.182071 4834.973169 4075.034546 5209.181237 2882.18764 2591.57463 0.88707998 1.176280983 0.966378929 0.931088245 1.614532733 1.865650756 1.572416437 2.010044849 1.11213762 1 11.33961322 -8.687109117 4.007848539 0.964176239 1.784256343 0.882145277 0.135328377 0.044795412 1.398697992 0.017775538 0.036318106 2.06E-09 8.687109117 0.820080104 LSS(ph)EDEEEDEAEDDQSEASGKK ddPTM_HeLa_Romidepsin_16h_R1 2 LSSEDEEEDEAEDDQSEASGKK 22 1 Q8NEJ9-2;Q8NEJ9;G3V4G1 Q8NEJ9-2 NGDN Neuroguidin 1 0 LS(0.182)S(0.818)EDEEEDEAEDDQSEASGKK;LS(0.21)S(0.79)EDEEEDEAEDDQSEASGKK ; 130.16 2.06E-05 32670000 4787.4 4359.9 4029.8 4112.5 4685.8 4610.3 4152.8 4658 5130.2 4842 TRUE FALSE FALSE 4729.049327 4421.278787 4099.936979 4588.0066 4446.666141 4315.716709 4505.538728 4792.771881 4671.342063 4716.204142 1.002723628 0.937465524 0.869329837 0.972817644 0.94284853 0.915082676 0.955331574 1.016235035 0.990487672 1 12.20341045 -10.26308553 24.26362244 1.001286159 0.941643949 0.31724857 0.035772966 74.01801691 1090993.308 0.005906595 0.006946015 5.46E-11 10.26308553 -0.05964221 LSS(ph)GFDDIDLPSAVK ddPTM_HeLa_Romidepsin_16h_R1 2 LSSGFDDIDLPSAVK 15 0 E9PKC4;Q9Y446;Q9Y446-2 E9PKC4 PKP3 Plakophilin-3 1 0 LS(0.024)S(0.976)GFDDIDLPSAVK;LS(0.042)S(0.958)GFDDIDLPSAVK ; 178.22 5.39E-08 33955000 5348.6 8150.6 4122.2 4022.9 6273.4 4509.1 2520 3230.2 4897.9 4873.1 TRUE FALSE FALSE 5283.409206 8265.344361 4193.945162 4488.046626 5953.244989 4220.983062 2734.048737 3323.660741 4459.819557 4746.496159 1.113117767 1.74135701 0.883587602 0.945549406 1.254239925 0.889283994 0.576014105 0.700234579 0.939602479 1 12.2126472 -7.970566915 4.18597122 1.097590129 0.644760566 0.405594672 0.234977883 0.156779601 6.250015653 0.032326084 0.100939758 1.07E-08 7.970566915 -0.452829563 LSS(ph)MAMISGLS(ph)GRK ddPTM_HeLa_Romidepsin_16h_R1 1 LSSMAMISGLSGRK 14 1 Q15746-9;Q15746-11;Q15746-7;Q15746-4;Q15746-5;Q15746-2;Q15746-3;Q15746-6;Q15746 Q15746-9 MYLK "Myosin light chain kinase, smooth muscle;Myosin light chain kinase, smooth muscle, deglutamylated form" 2 0 LS(0.216)S(0.783)MAMIS(0.003)GLS(0.998)GRK 53.448 0.0042629 0 1099.5 1213.4 1044.9 712.67 1133.8 1157.4 1141.5 1070.3 1272.9 1247.4 TRUE FALSE FALSE 1086.098871 1230.482277 1063.086046 795.0722586 1075.937955 1083.445875 1238.458982 1101.267442 1159.048636 1214.992368 0.893914151 1.012748976 0.874973435 0.65438457 0.885551205 0.891730602 1.019314206 0.90639865 0.953955487 1 10.24673154 -12.03861982 0.561133853 1.011705489 0.886784254 0.113298929 0.094307564 1.770961141 0.892614044 0.113542544 0.024823255 9.15E-13 12.03861982 -0.124921235 LSS(ph)PVLHR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSPVLHR 8 0 Q16643-3;Q16643;Q16643-2;D6RCR4;D6R9W4 Q16643-3 DBN1 Drebrin 1 0 LS(0.075)S(0.925)PVLHR;LS(0.215)S(0.785)PVLHR ; 109.48 0.023053 1348210000 6734.6 7073.3 6782.7 5602.3 7827.9 7629.9 6016.2 6991.3 7891 7345.5 TRUE FALSE FALSE 6652.516105 7172.878103 6900.750048 6250.064286 7428.413053 7142.374014 6527.215878 7193.582235 7185.209197 7154.662851 0.929815456 1.002545927 0.964510864 0.873565172 1.038261789 0.998282402 0.91230237 1.005439723 1.004269432 1 12.80466807 LSS(ph)SPGLFGAFSVR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSSPGLFGAFSVR 14 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 LS(0.004)S(0.498)S(0.498)PGLFGAFSVR;LSS(0.661)S(0.339)PGLFGAFSVR ; 231.07 2.05E-34 47887000 6253.2 5566.8 7635.6 5828.9 6495.6 5352.8 4912 3644.5 5006.2 4329.6 TRUE FALSE FALSE 6176.983593 5645.169557 7768.494415 6502.864844 6164.105294 5010.773355 5329.225157 3749.947857 4558.432934 4217.116368 1.464741082 1.338632626 1.84213423 1.542016932 1.461687266 1.188198977 1.26371309 0.889220863 1.080936008 1 12.04204112 -5.692853266 17.31759068 1.290276681 1.248831416 0 0.270209723 0 0 0.039765438 0 2.03E-06 5.692853266 -0.041445265 LSS(ph)SSATLLNS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSSATLLNSPDR 14 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 2 0 LS(0.233)S(0.617)S(0.14)S(0.006)AT(0.003)LLNS(1)PDR 213.83 5.46E-23 10910000 4202.1 3649 3679.5 2885.1 4174.3 3578.8 2555.7 3515.3 3739.5 4020.5 TRUE FALSE FALSE 4150.883189 3700.370718 3743.540154 3218.688837 3961.269895 3350.12623 2772.781094 3617.009659 3405.029754 3916.04683 1.059967709 0.944925043 0.955948771 0.821922969 1.011548142 0.855486764 0.708056163 0.923637999 0.869506904 1 11.9351823 -9.220207733 0.73269401 1.028590813 0.828331213 0.156051893 0.090622403 0.410669236 0.428961647 0.01533721 0.039171658 6.02E-10 9.220207733 -0.2002596 LSS(ph)SSATLLNSPDR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSSATLLNSPDR 14 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 1 0 LSS(0.462)S(0.462)S(0.075)ATLLNSPDR 209.22 6.44E-19 27515000 2524.6 1739.9 1996.8 2057.1 2263.3 1869.4 1812.4 1928.4 1793.4 1362.3 TRUE FALSE FALSE 2493.829204 1764.394358 2031.553466 2294.951581 2147.795355 1749.951373 1966.345211 1984.195211 1632.993812 1326.90725 1.879429934 1.329704362 1.531044063 1.729549357 1.618647691 1.318819664 1.481901023 1.495353358 1.230676683 1 10.37385181 -12.54548486 1.306801453 0.999530427 1.58093968 0.473312266 0.175020352 0.255357395 0.780143607 0.131249771 0.031035645 2.85E-13 12.54548486 0.581409253 LSS(ph)TPPLSALGR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSTPPLSALGR 12 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 0 LS(0.1)S(0.774)T(0.1)PPLS(0.025)ALGR 92.112 0.025608 24353000 3407.7 3265.5 3392.1 3377.2 3473 3391.1 2264.3 3099.3 3263.9 2872 TRUE FALSE FALSE 3366.165642 3311.471795 3451.138078 3767.687754 3295.75985 3174.419654 2456.629585 3188.973356 2971.968609 2797.385026 1.203325824 1.183774048 1.233701491 1.346860628 1.178157393 1.134781099 0.878187866 1.139983708 1.062409565 1 11.44986312 -6.86748718 19.7861625 1.122930647 8.282420482 0 0.12427563 9579.14579 1445605.502 0.019066888 33321.53769 1.36E-07 6.86748718 7.159489835 TKPPRPDS(ph)PATTPNISVK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPPRPDSPATTPNISVK 18 2 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 0 T(0.1)KPPRPDS(0.702)PAT(0.188)T(0.01)PNISVK 75.239 0.016252 48608000 2561 3238.5 2756.7 2459.5 1385.7 1142.7 833.12 1320.4 3345.8 3546.1 TRUE FALSE FALSE 2529.785547 3284.091688 2804.679207 2743.878962 1314.982558 1069.685158 903.885192 1358.603691 3046.543268 3453.971811 0.732427966 0.950816008 0.812015662 0.794412668 0.380716066 0.30969713 0.261694432 0.393345333 0.882040571 1 11.75404059 -8.773157992 3.02641227 0.871867528 0.315537214 0.924074364 0.07422757 0.06622266 1.248962914 0.015751186 0.031907941 1.69E-09 8.773157992 -0.556330315 down LSSLGTGSS(ph)SGNGK ddPTM_HeLa_Romidepsin_16h_R1 1 LSSLGTGSSSGNGK 14 0 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 1 0 LSSLGTGS(0.008)S(0.883)S(0.109)GNGK 141.59 0.00080634 5526000 1581.6 1794.2 1820.5 1437.4 2043.5 2231.9 2148.5 2504.2 1616.6 1867 TRUE FALSE FALSE 1562.322851 1819.458795 1852.185039 1603.598951 1939.21257 2089.288793 2330.993536 2576.655076 1472.007247 1818.495071 0.859129549 1.000529957 1.018526291 0.881827494 1.066383187 1.148910892 1.281825601 1.416916173 0.809464524 1 10.8285293 -7.772865336 0.937333043 0.93867695 1.495353676 0.862162696 0.067126412 0.276424428 0.294572204 0.01039883 0.12987366 1.69E-08 7.772865336 0.556676726 LSSLGTGSSS(ph)GNGK ddPTM_HeLa_Romidepsin_16h_R1 1 LSSLGTGSSSGNGK 14 0 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 1 0 LSSLGTGS(0.007)S(0.187)S(0.806)GNGK 162.94 0.00021162 10601000 1066.5 1329.2 1303.4 1096.3 1433.2 1778.5 1530.4 1674.3 1337.4 1333.3 TRUE FALSE FALSE 1053.501088 1347.912512 1326.08513 1223.059364 1360.058456 1664.85959 1660.392138 1722.743229 1217.779594 1298.660674 0.811221214 1.037925102 1.021117492 0.941785171 1.047277771 1.281981986 1.27854194 1.326553782 0.937719621 1 10.3428088 -8.379997898 1.684390158 0.927723152 1.316138012 0.841613211 0.064658804 0.129312042 0.70269554 0.013040498 0.040582978 4.17E-09 8.379997898 0.38841486 LSSPAAFLPACNS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5;H0YFE9 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 LS(0.001)SPAAFLPACNS(0.978)PS(0.02)K 82.121 0.022152 15787000 2660 2916.8 2932.3 333.62 2914.1 2410.2 2413.8 2468.6 3405.9 2901 TRUE FALSE FALSE 2627.578897 2957.862787 2983.335451 372.1947141 2765.382603 2256.195999 2618.828112 2540.025046 3101.267774 2825.631602 0.929908519 1.046797036 1.055811893 0.131720892 0.978677688 0.798474931 0.926811588 0.898922933 1.097548517 1 11.46435767 LSSPAAFLPACNSPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LSSPAAFLPACNSPSK 16 0 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5;H0YFE9 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 LSS(0.001)PAAFLPACNS(0.14)PS(0.859)K 195.45 4.30E-13 15650000 2801.3 2608.5 3031 454.29 2946.9 2899 2501.7 3002.3 2762.4 2747.1 TRUE FALSE FALSE 2767.156678 2645.222531 3083.753284 506.8171473 2796.508697 2713.763256 2714.194336 3089.166814 2515.324025 2675.729946 1.034168894 0.98859847 1.152490478 0.189412668 1.045138618 1.014214181 1.014375288 1.154513675 0.940051528 1 11.3857168 LSSPVLHR ddPTM_HeLa_Romidepsin_16h_R1 3 LSSPVLHR 8 0 Q16643-3;Q16643;Q16643-2;D6RCR4;D6R9W4 Q16643-3 DBN1 Drebrin 0 0 ;; ;; 118.74 0.00098531 8510100 8144.5 7716.1 7701.1 7841.5 9504.1 8738.9 7596.7 8496.2 9943.8 8963.2 FALSE FALSE TRUE 8045.231701 7824.727458 7835.134415 8748.171125 9019.070312 8180.512494 8241.963508 8742.024142 9054.401623 8730.334772 0.92152614 0.89626889 0.897460936 1.002043032 1.033072677 0.937021627 0.94406042 1.001338937 1.037119636 1 13.09182126 LSSS(ph)KENLDASK ddPTM_HeLa_Romidepsin_16h_R1 2 LSSSKENLDASK 12 1 K7EN13;K7EQL6;Q8NFA0 K7EN13 USP32 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 32 1 0 LS(0.001)S(0.23)S(0.767)KENLDAS(0.002)K;LS(0.001)S(0.229)S(0.771)KENLDASK ; 148.85 0.0034062 17180000 4198.4 3933.5 4181 2968.14 3633.1 4064.9 3006.3 3976.1 3947.7 4376 TRUE FALSE FALSE 4147.228286 3988.875916 4253.768551 3311.330312 3447.68935 3805.166009 3261.655047 4091.14218 3594.607825 4262.310889 0.972999951 0.935848187 0.997995844 0.776886154 0.808877963 0.892747176 0.765231615 0.959841336 0.84334717 1 12.05742011 -9.272843431 24.81683644 0.982985899 0.837644971 0.327690946 0.070757696 297.6264979 647676.5027 0.007789618 0.011965114 5.34E-10 9.272843431 -0.145340927 LSSS(ph)SATLLNS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSSATLLNSPDR 14 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 2 0 LS(0.002)S(0.155)S(0.694)S(0.1)AT(0.049)LLNS(1)PDR 187.08 9.01E-08 11351000 3281.7 2748.9 3554.2 2309.6 2940.5 2922.9 2069.4 2524.3 3010.6 2873.1 TRUE FALSE FALSE 3241.701378 2787.599086 3616.05936 2576.646819 2790.435312 2736.136123 2245.174784 2597.336638 2741.324396 2798.456448 1.158389076 0.996120232 1.2921621 0.920738581 0.997133729 0.977730465 0.802290415 0.928131878 0.979584441 1 11.45041558 -8.473105726 1.244601383 1.081317912 0.875064619 0.33648969 0.103563064 0.376429359 1.10021683 0.015935826 0.055817128 3.36E-09 8.473105726 -0.206253293 LSSS(ph)TVAISYSPDR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSSTVAISYSPDR 14 0 Q96T17-2;Q96T17;Q96T17-5 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 LS(0.003)S(0.002)S(0.916)T(0.079)VAISYSPDR;LSS(0.012)S(0.976)T(0.012)VAISYSPDR ; 222.74 1.05E-32 15499400 5090.8 4684.8 5789.7 5311.7 5864.2 5597.6 4952.9 5100.3 5370.8 4758.8 TRUE FALSE FALSE 5028.751371 4750.752737 5890.4673 5925.863746 5564.927992 5239.931425 5373.599202 5247.869134 4890.422197 4635.16569 1.084912969 1.024936983 1.270821303 1.278457803 1.200588795 1.13047338 1.159311136 1.132185877 1.055069554 1 12.1784052 -9.775911651 24.9976011 1.040081094 1.194743 0.684973621 0.051185991 115.7011875 199847.2344 0.009677099 0.012749132 1.68E-10 9.775911651 0.154661906 LSSSDRY(ph)SDASDDS(ph)FSEPR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 0 LS(0.003)S(0.01)S(0.038)DRY(0.939)S(0.011)DAS(0.287)DDS(0.533)FS(0.179)EPR 81.226 0.0034178 10369000 2313.7 2341.4 2714.5 2309.8 2524.8 2798.2 1793.8 2316.2 2832.9 2697 TRUE FALSE FALSE 2285.499734 2374.362291 2761.744734 2576.869944 2395.950035 2619.404051 1946.165327 2383.215593 2579.518329 2626.931551 0.870026375 0.903853886 1.05131964 0.980942934 0.912071741 0.997134489 0.740851175 0.907224093 0.981951101 1 11.35916289 -7.771063596 24.99999954 0.947225555 0.824037618 0.409926972 0.064320264 150.8511007 391856.7714 0.009815714 0.03000006 1.69E-08 7.771063596 -0.123187936 LSSSDRYS(ph)DASDDS(ph)FSEPR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSDRYSDASDDSFSEPR 19 1 Q9NRF8 Q9NRF8 CTPS2 CTP synthase 2 2 0 LSSS(0.001)DRYS(0.995)DAS(0.004)DDS(0.89)FS(0.11)EPR 208.4 7.26E-21 8591700 1433.3 1220.7 1082.5 1332.5 1303.8 1463.2 1023.4 1479.9 1629.5 1201.2 TRUE FALSE FALSE 1415.830388 1237.885047 1101.340458 1486.56992 1237.262221 1369.706242 1110.32757 1522.718572 1483.753439 1169.992651 1.210119044 1.058028053 0.941322544 1.270580562 1.05749572 1.170696449 0.949003884 1.30147704 1.268173298 1 10.19228375 -9.253966888 24.97331865 1.087232332 1.134719819 0.034335389 0.128688469 1966.795721 6573088.27 0.01854566 0.030390875 5.57E-10 9.253966888 0.047487487 LSSSGAPPADFPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSSGAPPADFPSPR 15 0 Q8NG08 Q8NG08 HELB DNA helicase B 1 0 LSSSGAPPADFPS(1)PR;LSSSGAPPADFPS(1)PR ; 175.27 3.68E-06 17646100 4664.9 4636.6 3912.6 3901.9 3429.4 3335.6 2654.5 3067.3 4857.1 4754.2 TRUE FALSE FALSE 4608.042404 4701.874177 3980.697162 4353.056037 3254.384921 3122.465925 2879.973164 3156.047486 4422.668811 4630.685199 0.995110271 1.015373314 0.859634588 0.940045771 0.702786906 0.674298898 0.621932401 0.681550861 0.955078702 1 12.17700997 -8.834181029 1.147268656 0.997186954 0.637992465 0.901264139 0.046901009 0.081936147 0.212545265 0.006643426 0.017864637 1.46E-09 8.834181029 -0.359194489 LSSSSATLLNS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 3 LSSSSATLLNSPDR 14 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 1 0 LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR;LSSSSATLLNS(1)PDR ;; 238.67 2.73E-43 553840000 8318.7 8948.9 8759.2 5173.9 6325.1 5315.2 4628.6 3931.99 8683.5 8359.7 TRUE FALSE FALSE 8217.308485 9074.882849 8911.650202 5772.130662 6002.306545 4975.575874 5021.753168 4045.755927 7906.826012 8142.513789 1.009185701 1.114506292 1.094459332 0.708888043 0.737156448 0.6110614 0.616732535 0.49686817 0.971054667 1 12.99125854 -9.095749575 2.913597365 1.020565103 0.617773008 0.890231415 0.070990001 0.066049178 1.087119186 0.011179581 0.019870445 8.02E-10 9.095749575 -0.402792095 LSSSSATLLNS(ph)PDRAR ddPTM_HeLa_Romidepsin_16h_R1 3 LSSSSATLLNSPDRAR 16 1 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 1 0 LSSSSATLLNS(1)PDRAR;LSSSSATLLNS(1)PDRAR;LSSSSATLLNS(1)PDRAR ;; 213.71 4.00E-25 175895000 9382.8 7855.9 7059.8 11602.3 6480.5 4870.8 4657.9 4605.3 10175.3 8424.2 TRUE FALSE FALSE 9268.438825 7966.495566 7182.672858 12943.81252 6149.775903 4559.5716 5053.54191 4738.54709 9265.195683 8205.33807 1.129562091 0.970891814 0.875365865 1.577486803 0.749484768 0.555683576 0.615884668 0.577495656 1.129166843 1 13.00234706 -8.536131713 24.97985549 1.075531631 0.597353634 0.64880861 0.178030898 104.144644 196296.5442 0.024317254 0.048655064 2.91E-09 8.536131713 -0.478177996 LSSSSPGATVS(ph)PSSS(ph)DAEYDKLPDADLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSSPGATVSPSSSDAEYDKLPDADLAR 29 1 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 2 0 LSS(0.001)S(0.005)S(0.026)PGAT(0.058)VS(0.448)PS(0.413)S(0.412)S(0.637)DAEYDKLPDADLAR 112.42 3.38E-09 6281100 812.71 629.97 771.12 526.92 753.34 670.59 629.56 488.22 814.58 475.99 TRUE FALSE FALSE 802.8043779 638.8387342 784.5410201 587.8449696 714.8942487 627.7414632 683.0348107 502.3458754 741.7219246 463.6237112 1.731586109 1.377925069 1.692193478 1.267935516 1.541970851 1.353989125 1.473252541 1.083520673 1.599836045 1 8.856810542 -12.55161247 1.331363468 1.000956636 1.478867272 0 0.259318254 0.306692626 0.977044609 0.130809886 0.031211516 2.81E-13 12.55161247 0.477910636 LSSSSPGATVS(ph)PSSSDAEYDKLPDADLAR ddPTM_HeLa_Romidepsin_16h_R1 1 LSSSSPGATVSPSSSDAEYDKLPDADLAR 29 1 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 0 LSSSSPGAT(0.02)VS(0.62)PS(0.142)S(0.142)S(0.062)DAEY(0.013)DKLPDADLAR 75.868 9.34E-06 36218000 1252.6 1223.6 1310.4 1246.1 1340.6 1351.9 1123.5 1071.1 1447.5 1478 TRUE FALSE FALSE 1237.332829 1240.825873 1333.206962 1390.179945 1272.18418 1265.517953 1218.930062 1102.090589 1318.031975 1439.601347 0.859496854 0.861923251 0.926094551 0.965670078 0.883705883 0.879075277 0.846713616 0.765552624 0.915553446 1 10.49145364 -16.52287875 0.216602434 1.647853403 0.854169507 0.246270654 0.054230698 33.14811768 0.417230686 9.12250438 0.043733848 3.00E-17 16.52287875 -0.793683896 LSSSTVAISYS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 4 LSSSTVAISYSPDR 14 0 Q96T17-2;Q96T17;Q96T17-5 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 LSSSTVAISYS(1)PDR;LSSSTVAISYS(1)PDR;LSSSTVAIS(0.002)YS(0.998)PDR;LSSSTVAISYS(1)PDR ;;; 255.39 1.24E-67 229167000 6652.4 6713.6 7548.9 4200.06 7280.6 6745.4 5566.19 6143.4 6996.4 6606.7 TRUE FALSE FALSE 6571.31799 6808.114237 7680.285438 4685.690699 6909.043814 6314.39071 6038.98204 6321.149586 6370.624461 6435.056982 1.021174794 1.057972642 1.193506982 0.728150615 1.073656975 0.981248609 0.938450437 0.98229893 0.989987265 1 12.65173721 -9.293342682 24.9991178 1.02712629 0.950264946 0.220374619 0.09872728 1014.451805 794911.719 0.014278904 0.021812487 5.09E-10 9.293342682 -0.076861345 LSSWDQAET(ph)PGHTPSLR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 LSSWDQAET(1)PGHTPSLR;LSSWDQAET(1)PGHTPSLR ; 109.12 0.0015788 19853400 3358.7 3602.5 3814.1 2611.6 4215.8 4652 3076.9 3572.7 4197.5 3865 TRUE FALSE FALSE 3317.762873 3653.21609 3880.482811 2913.56548 4000.651995 4354.752214 3338.251809 3676.070438 3822.065087 3764.586743 0.881308653 0.970416234 1.030785867 0.773940323 1.062706817 1.156767664 0.886751199 0.976487112 1.015268168 1 11.87827579 LSSWDQAETPGHT(ph)PSLR ddPTM_HeLa_Romidepsin_16h_R1 2 LSSWDQAETPGHTPSLR 17 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 LSSWDQAET(0.03)PGHT(0.901)PS(0.069)LR;LSSWDQAET(0.027)PGHT(0.756)PS(0.217)LR ; 84.948 0.00098757 2752200 2333.3 2437.8 2459.2 2096.25 2687.2 2567.3 2162.76 2428.9 2949.9 2885.2 TRUE FALSE FALSE 2304.860842 2472.119412 2502.001344 2338.628288 2550.062157 2403.257816 2346.46478 2499.176389 2686.053556 2810.242088 0.820164516 0.879682011 0.890315235 0.832180366 0.907417253 0.855178216 0.834968913 0.889309999 0.9558086 1 11.4564787 -12.39805245 1.038825646 1.002773892 0.86071917 0.692544367 0.029952517 0.198478257 0.371051573 0.021338793 0.00503072 4.00E-13 12.39805245 -0.142054722 LST(ph)SSETVSSTAASK ddPTM_HeLa_Romidepsin_16h_R1 1 LSTSSETVSSTAASK 15 0 Q9P242 Q9P242 NYAP2 Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 2 1 0 LST(0.96)S(0.04)SETVSSTAASK 252.46 5.09E-58 6354600 2179.9 2149.5 2328.7 2461.1 2299.6 1665.9 1467.3 1454.4 2373.8 2010.5 TRUE FALSE FALSE 2153.33054 2179.760717 2369.230047 2745.663962 2182.242831 1559.454366 1591.932425 1496.480769 2161.481383 1958.26692 1.099610333 1.113107051 1.209860628 1.402088721 1.114374557 0.79634413 0.812929233 0.764186309 1.103772607 1 10.93536171 -8.258928811 23.42768301 1.096852606 0.793330772 0.680711315 0.108254159 54.74212819 510820.3077 0.018486566 0.044785043 5.51E-09 8.258928811 -0.303521834 ISFPGSSES(ph)PLSSK ddPTM_HeLa_Romidepsin_16h_R1 2 ISFPGSSESPLSSK 14 0 Q15911;Q15911-2 Q15911 ZFHX3 Zinc finger homeobox protein 3 1 0 ISFPGS(0.003)S(0.009)ES(0.988)PLSSK;ISFPGS(0.016)S(0.053)ES(0.925)PLS(0.005)S(0.001)K ; 150.12 0.00061627 50880000 6837.8 7386.5 7286.4 5885.1 3664.3 3203.4 2604 2851.1 7925.8 7848.1 TRUE FALSE FALSE 6754.458264 7490.487341 7413.216736 6565.562952 3477.297098 2998.713078 2825.183695 2933.59208 7216.896597 7644.205231 0.883605039 0.979890926 0.969782536 0.858894124 0.454893216 0.392285789 0.369585014 0.383766787 0.944100319 1 12.9001508 -8.772020796 3.081948494 0.948062451 0.383430244 0.987664695 0.029760289 0.027861985 0.546005986 0.006798065 0.013743646 1.69E-09 8.772020796 -0.564632207 down LSTGS(ph)FPEDLLESDSSR ddPTM_HeLa_Romidepsin_16h_R1 1 LSTGSFPEDLLESDSSR 17 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 LS(0.001)T(0.044)GS(0.955)FPEDLLESDSSR 174.35 9.85E-07 3322700 472.88 382.12 447.13 373.6 445.57 304.55 313.13 287.16 395.29 294.45 TRUE FALSE FALSE 467.1163567 387.4994954 454.9121101 416.7973898 422.8309002 285.0902379 339.7272544 295.4685215 359.9342724 286.8001466 1.628717287 1.35111331 1.586164148 1.453267702 1.474305036 0.994037978 1.184543517 1.030224444 1.255000308 1 8.163901951 -8.256873987 24.92377335 1.351961672 1.081096129 0.399950858 0.176301722 489.0027486 2669591.335 0.036397722 0.089400548 5.54E-09 8.256873987 -0.270865542 LSTS(ph)SETVSSTAASK ddPTM_HeLa_Romidepsin_16h_R1 1 LSTSSETVSSTAASK 15 0 Q9P242 Q9P242 NYAP2 Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 2 1 0 LST(0.019)S(0.979)S(0.001)ETVSSTAASK 203.11 3.02E-18 5187300 1932 1549.4 1723.2 2013.3 1816.6 1313.4 1317.5 1073.8 1798.5 1732.9 TRUE FALSE FALSE 1908.452041 1571.212494 1753.191573 2246.087219 1723.892123 1229.477979 1429.408417 1104.868709 1637.637656 1687.879008 1.130680595 0.930879812 1.038695051 1.330715773 1.021336313 0.728415943 0.846866636 0.654589993 0.970234032 1 10.72099578 -8.310524888 5.184379618 1.070661221 0.752970731 0.624477201 0.11274517 0.097365936 6.110354512 0.015904541 0.036935076 4.89E-09 8.310524888 -0.317690489 LSTTPSPTS(ph)S(ph)LHEDGVEDFRR ddPTM_HeLa_Romidepsin_16h_R1 1 LSTTPSPTSSLHEDGVEDFRR 21 1 O94842-3;O94842-2;O94842;C9J919;C9JNL1 O94842-3 TOX4 TOX high mobility group box family member 4 2 0 LS(0.021)T(0.037)T(0.056)PS(0.071)PT(0.134)S(0.837)S(0.844)LHEDGVEDFRR 59.547 0.0071931 10681000 1179.4 1334.7 1210.9 1066.3 1364.7 1532.1 1272.3 1636.5 1591.3 1236.2 TRUE FALSE FALSE 1165.025019 1353.489942 1231.975207 1189.590623 1295.054267 1434.203755 1380.36913 1683.849546 1448.970143 1204.083346 0.967561775 1.124083267 1.023164394 0.987963688 1.075552013 1.191116678 1.14640663 1.398449328 1.203380271 1 10.23371954 -4 0.435486296 0.989242283 9.067114977 0.535092344 0.085163033 19.31489275 0.214593267 0.011427463 138.6850316 1.00E-04 4 8.077872694 LSVAS(ph)TPISQR ddPTM_HeLa_Romidepsin_16h_R1 1 LSVASTPISQR 11 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6;Q9BXS6-7;H0YMD2 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 LS(0.004)VAS(0.493)T(0.493)PIS(0.01)QR 114.76 0.012408 12142000 2483.7 2397.2 2729.3 1853.3 4229.6 4510.1 3315.5 3475.3 2721.7 2336.7 TRUE FALSE FALSE 2453.427709 2430.947845 2776.802322 2067.587266 4013.747729 4221.919166 3597.118487 3575.852322 2478.264335 2275.992197 1.077959631 1.06808268 1.220040352 0.908433372 1.763515593 1.854979631 1.580461696 1.571118006 1.08887207 1 11.1522799 -8.757583242 24.99999986 1.047522188 1.696119111 0.89425984 0.106398637 21.53393528 139606.174 0.015510726 0.030111369 1.75E-09 8.757583242 0.648596922 LSVAST(ph)PISQR ddPTM_HeLa_Romidepsin_16h_R1 1 LSVASTPISQR 11 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6;Q9BXS6-7;H0YMD2 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 LS(0.001)VAS(0.081)T(0.459)PIS(0.459)QR 110.98 0.029141 10271000 3002.1 2915.1 3106.7 2734.2 5159.9 5296.5 3682.5 3959.5 3652.1 3071.8 TRUE FALSE FALSE 2965.50925 2956.138854 3160.77081 3050.341069 4896.571049 4958.070744 3995.291458 4074.061885 3325.447029 2991.994193 0.991148063 0.98801624 1.056409407 1.019500999 1.636557671 1.657112422 1.335327277 1.361654342 1.111448357 1 11.54689166 -8.772846051 24.96832173 1.001601424 1.497456759 0.833222215 0.102593545 55.19983367 120828.2075 0.014736971 0.026882263 1.69E-09 8.772846051 0.495855335 LSVDYGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LSVDYGKK 8 1 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VQQ4;C9JEV8;C9JQ00;C9JDS9;C9JJQ8;Q71U36-2;Q71U36;P68363;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1A;TUBA4A;TUBA1B Tubulin alpha-1C chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 1 ; LSVDYGK(1)K;LSVDYGK(1)K 135.83 0.0027627 10676000 5119 3712.6 8189.3 5243.2 18651.8 13319 11266.6 7153.4 9854.9 5605.4 FALSE TRUE FALSE 5056.607659 3764.86608 8331.831331 5849.443454 17699.92905 12467.95889 12223.58472 7360.372343 8973.453062 5459.7709 0.92615748 0.689564846 1.526040467 1.071371594 3.241881275 2.283604773 2.238845722 1.348110109 1.643558535 1 12.4146247 -8.871661133 9.485691135 0.99163339 2.274252383 0.532227116 0.51018099 0.130968264 10.52970443 0.06604835 0.119889802 1.34E-09 8.871661133 1.282618993 LSVEEFFMDLHNFR ddPTM_HeLa_Romidepsin_16h_R1 1 LSVEEFFMDLHNFR 14 0 A0A2R8Y5N1;A0A140T8Z0;A0A0G2JH68;O60610-2;O60610-3;O60610;H9KV28 A0A2R8Y5N1 DIAPH1 Protein diaphanous homolog 1 0 0 142.39 0.0029513 1677800 933.04 1015.4 1287.1 1001 1289.7 1591 1087.3 946.19 1175.8 779.35 FALSE FALSE TRUE 921.6677496 1029.694828 1309.501436 1116.74033 1223.881796 1489.340235 1179.655235 973.5665148 1070.633503 759.1023746 1.214154744 1.356463716 1.725065656 1.471132705 1.61227502 1.961975465 1.554013364 1.282523342 1.41039409 1 9.568150654 -10.2785838 1.041562576 1.063679688 1.620024997 0.377712922 0.204355735 0.209872536 0.447327626 0.03814053 0.044959171 5.27E-11 10.2785838 0.556345308 LSVGEQPDVTHDPYEFLQS(ph)PEPAASAK ddPTM_HeLa_Romidepsin_16h_R1 4 LSVGEQPDVTHDPYEFLQSPEPAASAK 27 0 Q9H8M2-2;Q9H8M2-3;Q9H8M2-1;Q9H8M2-6;Q9H8M2 Q9H8M2-2 BRD9 Bromodomain-containing protein 9 1 0 LSVGEQPDVTHDPY(0.385)EFLQS(0.614)PEPAAS(0.001)AK;LSVGEQPDVTHDPY(0.249)EFLQS(0.75)PEPAAS(0.001)AK;LSVGEQPDVTHDPY(0.009)EFLQS(0.989)PEPAAS(0.002)AK;LSVGEQPDVTHDPY(0.389)EFLQS(0.61)PEPAAS(0.001)AK ;;; 114.51 1.30E-09 93006800 8906.7 8009.9 7517.9 5771.32 7247.4 7532.3 6623.4 7706.6 8980.8 9308.3 TRUE FALSE FALSE 8798.141715 8122.663582 7648.745896 6438.627173 6877.538134 7051.010339 7185.991431 7929.578312 8177.534755 9066.469024 0.970404431 0.895901542 0.84363007 0.710158184 0.758568536 0.777701917 0.792589862 0.874604909 0.901953642 1 13.14632508 -9.922572599 1.702688936 0.987716855 0.781997413 0.702271049 0.048443553 0.096571304 0.560344672 0.0072906 0.009897271 1.20E-10 9.922572599 -0.205719442 LSVPT(ph)S(ph)DEEDEVPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 2 LSVPTSDEEDEVPAPKPR 18 1 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 2 0 LS(0.014)VPT(0.993)S(0.993)DEEDEVPAPKPR;LS(0.284)VPT(0.858)S(0.858)DEEDEVPAPKPR ; 84.41 0.0094325 16950100 14112.4 14624.4 13677 12528.9 12932.3 13125.9 12120.4 13908 15331.9 15148.2 TRUE FALSE FALSE 13940.39264 14830.28269 13915.04245 13977.55037 12272.31647 12287.19735 13149.90647 14310.40604 13960.57646 14754.64758 0.944813664 1.005126189 0.943095548 0.947332038 0.831759377 0.832767932 0.891238263 0.969891416 0.946181628 1 13.84888184 -8.933718123 5.414119332 0.972932025 0.878786049 0.495012191 0.041241552 0.12482789 7.003320902 0.006414484 0.01173652 1.16E-09 8.933718123 -0.094145976 LSVPTS(ph)DEEDEVPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 LSVPTSDEEDEVPAPK 16 0 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 LSVPT(0.27)S(0.73)DEEDEVPAPK;LSVPT(0.287)S(0.713)DEEDEVPAPK ; 150.9 0.00028232 18547300 17532.2 16597.9 18823.5 9562.1 14353.1 15511.3 15721 15858.7 20403.2 21202.3 TRUE FALSE FALSE 17318.5108 16831.56567 19151.11512 10667.71499 13620.60775 14520.17799 17056.34135 16317.54646 18578.28669 20651.46119 0.838609464 0.815030255 0.927349157 0.516559816 0.659546926 0.703106567 0.825914505 0.790140045 0.899611244 1 14.33395624 -10.88442114 0.51418437 0.991257941 0.719635855 0.39403934 0.103862303 0.521274878 0.332438406 0.055226915 0.037805061 1.30E-11 10.88442114 -0.271622085 LSVPTS(ph)DEEDEVPAPKPR ddPTM_HeLa_Romidepsin_16h_R1 6 LSVPTSDEEDEVPAPKPR 18 1 Q8NE71;Q5STZ8;Q8NE71-2;F5GYK6 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 LSVPT(0.053)S(0.947)DEEDEVPAPKPR;LSVPT(0.024)S(0.976)DEEDEVPAPKPR;LSVPT(0.065)S(0.935)DEEDEVPAPKPR;LSVPT(0.206)S(0.794)DEEDEVPAPKPR;LSVPT(0.029)S(0.971)DEEDEVPAPKPR;LSVPT(0.027)S(0.973)DEEDEVPAPKPR ;;;;; 221.78 2.90E-37 239509400 25760 23644.2 21833.9 18667.7 18978.3 20789.2 20043.1 22204.9 28401.6 26083.3 TRUE FALSE FALSE 25446.02721 23977.06367 22213.90987 20826.14731 18009.76653 19460.83721 21745.56041 22847.36375 25861.28976 25405.65211 1.001589217 0.943768873 0.874368813 0.819744647 0.708888182 0.766004239 0.85593396 0.899302394 1.0179345 1 14.63286187 -9.723785599 1.764769128 1.000866854 0.804807027 0.765254392 0.048061034 0.12222921 0.776976801 0.008658573 0.012732701 1.89E-10 9.723785599 -0.196059827 LSVQSNPS(ph)PQLR ddPTM_HeLa_Romidepsin_16h_R1 2 LSVQSNPSPQLR 12 0 E9PBY7;E9PQ61;O75152;A0A1W2PPR9 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 LSVQSNPS(1)PQLR;LSVQSNPS(0.999)PQLR ; 180.61 1.27E-06 40911000 4459.4 3536 3855.8 3371.1 4518 4357.3 4457.7 3545.4 4536.9 4081.8 TRUE FALSE FALSE 4405.047118 3585.779901 3922.908582 3760.882444 4287.429601 4078.882593 4836.336927 3647.980555 4131.108301 3975.754248 1.107977718 0.901911858 0.986708015 0.945954455 1.078394019 1.025939316 1.216457715 0.917556853 1.039075366 1 11.95701287 -6.954340292 19.15333579 1.040042247 3.07E-05 0.144067057 0.083539673 217.3935476 74551.56011 0.011501969 15988.39113 1.11E-07 6.954340292 -1.040011511 LSYLSAPGSEYSMY(ph)STDSR ddPTM_HeLa_Romidepsin_16h_R1 1 LSYLSAPGSEYSMYSTDSR 19 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 LSYLSAPGS(0.004)EY(0.016)S(0.023)MY(0.72)S(0.034)T(0.072)DS(0.132)R 107.09 0.012093 14284000 2728.2 2787.6 2782.2 1494.6 3072.6 2221.6 1632.3 2215.6 3120.7 2977 TRUE FALSE FALSE 2694.947649 2826.843906 2830.623024 1667.412684 2915.793757 2079.64693 1770.947521 2279.70489 2841.576776 2899.657111 0.929402183 0.974889029 0.976192327 0.575037882 1.005565019 0.717204432 0.610743772 0.786198093 0.97996993 1 11.50166659 -9.006678727 0.588282299 0.979901659 0.683505011 0.42679567 0.121057711 0.65293656 0.404685714 0.026192209 0.091990824 9.85E-10 9.006678727 -0.296396648 LSYLSAPGSEYSMYST(ph)DSR ddPTM_HeLa_Romidepsin_16h_R1 1 LSYLSAPGSEYSMYSTDSR 19 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 LSYLSAPGSEYS(0.004)MYS(0.042)T(0.904)DS(0.05)R 138.98 0.0010385 12085000 2619.9 2760.9 2613.1 1285.6 2477.3 2373.9 1888.1 1729.8 2578.3 2603.3 TRUE FALSE FALSE 2587.967651 2799.768023 2658.579909 1434.247121 2350.874137 2222.215451 2048.475167 1779.849034 2347.690391 2535.665891 1.02062644 1.104154941 1.048474059 0.565629378 0.927122988 0.876383383 0.80786478 0.701925692 0.925867402 1 11.30814895 -9.307069008 24.99890564 1.021211801 0.791563715 0.591208214 0.101035342 218.3041665 119600.8019 0.014196403 0.021685407 4.93E-10 9.307069008 -0.229648086 LSYS(ph)DSDLKR ddPTM_HeLa_Romidepsin_16h_R1 1 LSYSDSDLKR 10 1 A0A087WTF0;A2A3K4;A2A3K4-2 A0A087WTF0 PTPDC1 Protein tyrosine phosphatase domain-containing protein 1 1 0 LS(0.003)YS(0.916)DS(0.081)DLKR 100.09 0.0021344 0 2399 2451.7 2307.7 1968.2 2147.5 1896.7 1635.1 2150.5 1867.4 1810 TRUE FALSE FALSE 2369.760065 2486.215097 2347.86455 2195.772545 2037.905062 1775.506991 1773.985353 2212.721325 1700.375067 1762.975939 1.34418174 1.410237679 1.331762107 1.245492066 1.155946044 1.007107897 1.00624479 1.255105799 0.964491363 1 10.78379707 -8.501536939 8.055214068 1.20606944 1.080991976 0.12509761 0.148425519 0.416201309 129.6832245 0.024767251 0.053695465 3.15E-09 8.501536939 -0.125077465 LT(ph)GLGQSNAALR ddPTM_HeLa_Romidepsin_16h_R1 2 LTGLGQSNAALR 12 0 Q08378-2;Q08378 Q08378-2 GOLGA3 Golgin subfamily A member 3 1 0 LT(1)GLGQSNAALR;LT(1)GLGQSNAALR ; 104.24 0.010151 67629000 5179 3545.8 13652.8 7400.2 12083 12639.9 12538.8 5917.8 4444.2 2455.1 TRUE FALSE FALSE 5115.876356 3595.717865 13890.42126 8255.845943 11466.35942 11832.25118 13603.84536 6089.022206 4046.699621 2391.316148 2.139355919 1.503656415 5.808692953 3.452427631 4.794999369 4.948007896 5.688852714 2.546305812 1.692247855 1 11.22358916 -9.775942971 24.90363497 1.550483998 4.57282477 0.699675617 0.948534573 87.42843567 150120.0453 0.149036241 0.196360425 1.68E-10 9.775942971 3.022340772 LT(ph)LNSPIFDKPLSR ddPTM_HeLa_Romidepsin_16h_R1 1 LTLNSPIFDKPLSR 14 1 H0YBX5;E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4 H0YBX5 CDK16 Cyclin-dependent kinase 16 1 0 LT(0.5)LNS(0.5)PIFDKPLSR 139.21 0.0044989 35385000 3234 2728.2 2893.7 2919.2 4074.7 4213.6 4078.4 3861.6 2980.2 2612.9 TRUE FALSE FALSE 3194.582764 2766.607671 2944.063635 3256.731639 3866.752854 3944.364559 4424.819194 3973.329303 2713.643448 2545.016481 1.255230678 1.087068666 1.156795508 1.27965051 1.519342952 1.549838513 1.738621037 1.561219478 1.066257711 1 11.31345928 -8.787142834 1.379722802 1.119015033 1.643905325 0.898954388 0.076520204 0.120718485 0.459975947 0.016331345 0.041102369 1.63E-09 8.787142834 0.524890292 LT(ph)LS(ph)QIY(ph)EWMVKSVPY(ph)FKDK ddPTM_HeLa_Romidepsin_16h_R1 1 LTLSQIYEWMVKSVPYFKDK 20 2 Q12778 Q12778 FOXO1 Forkhead box protein O1 4 0 LT(0.998)LS(0.998)QIY(0.985)EWMVKS(0.021)VPY(0.998)FKDK 49.606 0.0036717 0 304.87 414.53 396.68 481.07 351.28 301.53 381.84 342.09 369.55 327.47 TRUE FALSE FALSE 301.1541272 420.3657642 403.584049 536.6935769 333.3528708 282.2632061 414.2734801 351.9878344 336.4965224 318.9622822 0.944168461 1.317916844 1.265303365 1.682623955 1.045116898 0.88494227 1.298816516 1.103540619 1.05497277 1 8.317242023 -10.26974958 24.4273004 0.9736351 1.229676324 0.213817598 0.198995174 458.5241599 1347798.435 0.034323638 0.039607012 5.37E-11 10.26974958 0.256041225 LT(ph)LSEGHPETPVDGDLGK ddPTM_HeLa_Romidepsin_16h_R1 1 LTLSEGHPETPVDGDLGK 18 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 LT(0.585)LS(0.415)EGHPETPVDGDLGK 78.708 0.010922 3363100 2087.2 1904.2 2112.3 2065.3 3076.5 3499.7 2399.4 2971.6 2209.7 2368.3 TRUE FALSE FALSE 2061.760404 1931.007378 2149.063695 2304.099704 2919.494725 3276.080465 2603.204976 3057.578558 2012.058898 2306.771225 0.89378625 0.837103982 0.931632783 0.998841879 1.265619535 1.420201722 1.128505917 1.325479755 0.872240332 1 11.17165922 -8.800886725 3.839639933 0.938213747 1.287044659 0.830394507 0.080601306 0.070778606 2.193517732 0.012177841 0.023620698 1.58E-09 8.800886725 0.348830913 LT(ph)PEEEEILNK ddPTM_HeLa_Romidepsin_16h_R1 1 LTPEEEEILNK 11 0 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 1 0 LT(1)PEEEEILNK 196.7 5.86E-09 3172300 1213.4 1368 1197.2 810.24 1475.1 1607.1 1312.9 1360.4 1395.5 1431 TRUE FALSE FALSE 1198.610614 1387.25874 1218.036764 903.9237611 1399.820143 1504.411497 1424.417693 1399.761028 1270.682985 1393.822414 0.859944999 0.995290882 0.873882319 0.64852147 1.00430308 1.079342305 1.02195063 1.004260668 0.91165343 1 10.44483104 -8.542068295 24.99993973 0.911081845 1.03518821 0.338532766 0.095402301 262.1830396 341568.1998 0.015282711 0.030568741 2.87E-09 8.542068295 0.124106365 LT(ph)QT(ph)VAHLK ddPTM_HeLa_Romidepsin_16h_R1 1 LTQTVAHLK 9 0 A0A096LNZ9;A0A096LPJ4;P05161 A0A096LNZ9 ISG15 Ubiquitin-like protein ISG15 2 0 LT(1)QT(1)VAHLK 79.148 0.0025694 0 2207 2423.4 2824.8 2567.1 2592.6 2513.5 3706 826.41 3072.5 2963.1 TRUE FALSE FALSE 2180.100235 2457.516689 2873.964459 2863.920181 2460.289948 2352.895462 4020.787547 850.3208695 2797.687905 2886.118235 0.75537454 0.8514955 0.995788885 0.992308682 0.852456396 0.815245694 1.393147203 0.294624406 0.969360115 1 11.49491469 -7.224548171 24.33008236 0.913422725 0.294622275 0.561087253 0.172028264 9557.899719 6303363.786 0.023447347 8.081544202 5.96E-08 7.224548171 -0.61880045 LT(ph)SDEEGEPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 LTSDEEGEPSGK 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 LT(0.926)S(0.074)DEEGEPSGK 194.06 5.59E-10 66102000 7987.9 7520.4 7515.9 5775.4 7767.1 7893.6 6960.2 8072.9 7785.9 8077.1 TRUE FALSE FALSE 7890.540402 7626.272389 7646.711087 6443.178922 7370.715904 7389.224435 7551.399214 8306.476625 7089.509604 7867.255778 1.002959688 0.969368812 0.971966757 0.818986837 0.936885251 0.939237854 0.959851749 1.055828978 0.901141364 1 12.94164477 -9.912138513 2.3974974 1.001133128 0.940614385 0 0.062662364 0.350025662 4.087265517 0.009176013 0.01233642 1.22E-10 9.912138513 -0.060518743 LT(ph)T(ph)IPNGAFVY(ph)LS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LTTIPNGAFVYLSK 14 0 Q9HCJ2 Q9HCJ2 LRRC4C Leucine-rich repeat-containing protein 4C 4 0 LT(1)T(1)IPNGAFVY(1)LS(1)K 58.592 0.02485 5195500 293.84 152.63 296.14 266.14 193.41 273.29 158.18 293 290.18 249.41 TRUE FALSE FALSE 290.2585651 154.7787291 301.2941925 296.912359 183.539566 255.827651 171.6158053 301.4774927 264.225574 242.9302922 1.194822442 0.637132272 1.240249578 1.222212167 0.755523588 1.05309078 0.706440533 1.241004117 1.087660051 1 7.924398588 -8.768560482 24.99455646 1.076728483 0.930550595 0.073547946 0.212922471 293.1448731 1028920.654 0.029943246 0.055104049 1.70E-09 8.768560482 -0.146177888 LTAGVPDT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 LTAGVPDTPTR 11 0 P16144-4;P16144-2;P16144-3;P16144 P16144-4 ITGB4 Integrin beta-4 1 0 LT(0.001)AGVPDT(0.698)PT(0.301)R 115.37 0.025031 11971000 2508.8 2969.2 2656.6 1632.2 2987.8 3322.1 2132.1 3484.6 2592.1 2971.7 TRUE FALSE FALSE 2478.221781 3011.000476 2702.837009 1820.922644 2835.321417 3109.828532 2313.200521 3585.421403 2360.256084 2894.494806 0.856184567 1.040250779 0.933785406 0.629098605 0.979556575 1.074394235 0.799172455 1.238703692 0.815429373 1 11.49909585 -7.246509873 24.40169002 0.923953034 1.238704005 0.372726159 0.128065836 1658.164108 2710143.759 0.016861398 0.50327458 5.67E-08 7.246509873 0.314750971 LTAIIEEAEEAPGARPQLQDAWR ddPTM_HeLa_Romidepsin_16h_R1 1 LTAIIEEAEEAPGARPQLQDAWR 23 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 0 0 96.561 7.54E-05 20713000 950.01 1174.1 1100.3 867.13 1532.6 1617.9 1426 1438.5 849.79 986.83 FALSE FALSE TRUE 938.4309127 1190.629011 1119.45026 967.3916506 1454.385703 1514.521412 1547.124404 1480.120728 773.7826541 961.1920143 0.976319922 1.238700481 1.164647899 1.006449946 1.513106311 1.57566999 1.609589324 1.539880384 0.805024014 1 9.908680852 -8.730621866 5.098011685 1.024436939 1.571486981 0.847007461 0.10995603 0.046170313 2.981675537 0.014454629 0.028709389 1.86E-09 8.730621866 0.547050043 LTALNDSSLDLSMDSDNSMS(ph)VPSPTSATK ddPTM_HeLa_Romidepsin_16h_R1 3 LTALNDSSLDLSMDSDNSMSVPSPTSATK 29 0 H0YJL4;G3XAH6;P51003 H0YJL4 PAPOLA Poly(A) polymerase alpha 1 0 LTALNDSSLDLS(0.003)MDS(0.2)DNS(0.142)MS(0.599)VPS(0.052)PT(0.003)S(0.001)ATK;LTALNDSSLDLS(0.004)MDS(0.042)DNS(0.117)MS(0.501)VPS(0.332)PT(0.003)SATK;LTALNDSSLDLS(0.011)MDS(0.16)DNS(0.107)MS(0.405)VPS(0.281)PT(0.033)S(0.003)ATK ;; 96.181 4.52E-10 0 3746.5 3580.18 3658.67 3460.96 4680.9 5475.1 4759.88 5648.1 4348.47 4236.6 TRUE FALSE FALSE 3700.836217 3630.581868 3722.347617 3861.13248 4442.016206 5125.25878 5164.184088 5811.518862 3959.531952 4126.532521 0.896839222 0.87981419 0.90205217 0.93568449 1.07645249 1.242025539 1.251458473 1.408329834 0.959530049 1 12.01071429 -8.246951174 1.415044553 0.937833061 1.349877867 0.929250732 0.046403154 0.101847444 0.373868385 0.008686817 0.034764345 5.66E-09 8.246951174 0.412044806 LTALNDSSLDLSMDSDNSMSVPS(ph)PTSATK ddPTM_HeLa_Romidepsin_16h_R1 1 LTALNDSSLDLSMDSDNSMSVPSPTSATK 29 0 H0YJL4;G3XAH6;P51003 H0YJL4 PAPOLA Poly(A) polymerase alpha 1 0 LTALNDS(0.001)S(0.001)LDLS(0.028)MDS(0.224)DNS(0.175)MS(0.185)VPS(0.357)PT(0.02)S(0.008)AT(0.001)K 57.184 0.0010015 0 551.13 544.69 565.07 531.1 657.46 749.31 598.99 920.75 589.2 692.43 TRUE FALSE FALSE 544.4126156 552.3581601 574.9048063 592.5082809 623.9073629 701.4315093 649.8681956 947.3904485 536.5004763 674.4405688 0.80720621 0.818987151 0.852417297 0.87851815 0.925073893 1.040019746 0.963566288 1.404705607 0.7954748 1 9.397547509 -4.291946944 0.959890173 0.895975101 199.9864143 0.817324414 0.073311085 252.5500738 0.753845747 0.013223197 109968.7911 5.11E-05 4.291946944 199.0904392 LTASPS(ph)DPK ddPTM_HeLa_Romidepsin_16h_R1 1 LTASPSDPK 9 0 E7EWD6;Q76L83-2;Q76L83;A0A5F9ZHN2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 0 LTAS(0.273)PS(0.726)DPK 107.55 0.021469 20741000 8240.8 7614.2 8134.7 6653.4 6890.3 6876.7 5781.1 5714.3 7848.1 7621.3 TRUE FALSE FALSE 8140.35796 7721.392907 8276.281041 7422.697413 6538.66228 6437.301064 6272.14649 5879.634255 7146.14628 7423.297527 1.096595944 1.040156733 1.114906281 0.999919158 0.880829881 0.867175408 0.844927267 0.792051542 0.962664672 1 12.85784448 -8.75390664 2.439194339 1.051467748 0.838105403 0.815744628 0.044735328 0.084060846 1.020915545 0.006724173 0.014259484 1.76E-09 8.75390664 -0.213362345 LTDS(ph)PGLFSAQDTSLNR ddPTM_HeLa_Romidepsin_16h_R1 1 LTDSPGLFSAQDTSLNR 17 0 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 0 LT(0.08)DS(0.828)PGLFS(0.089)AQDT(0.001)S(0.002)LNR 85.576 0.0030529 0 898.4 883.06 694.83 949.02 969.36 723.65 706.55 863.4 892.37 938.85 TRUE FALSE FALSE 887.4499552 895.4917419 706.9232247 1058.750158 919.889942 677.4111005 766.5643394 888.3811168 812.5541922 914.4585417 0.970464942 0.979258983 0.773051147 1.157789128 1.005939471 0.740778362 0.838271288 0.971483207 0.888563183 1 9.836773954 -8.288010449 24.60880107 0.983203551 0.848986961 0.197602661 0.105549562 563.0570253 521474.1284 0.013730919 0.030712164 5.15E-09 8.288010449 -0.134216591 LTDSS(ph)PSSTSTSNSQR ddPTM_HeLa_Romidepsin_16h_R1 2 LTDSSPSSTSTSNSQR 16 0 Q5VT06 Q5VT06 CEP350 Centrosome-associated protein 350 1 0 LTDS(0.041)S(0.679)PS(0.101)S(0.101)T(0.03)S(0.012)T(0.012)S(0.022)NS(0.002)QR;LT(0.007)DS(0.033)S(0.93)PS(0.008)S(0.016)T(0.005)S(0.001)TSNSQR ; 136.57 0.00025929 4873000 1393.84 985.63 1247.91 1110.13 1552.48 1781.8 1816.72 1374.48 1398.58 1336.17 TRUE FALSE FALSE 1376.851342 999.505725 1269.62935 1238.488454 1473.251152 1667.94873 1971.032151 1414.24841 1273.487502 1301.456111 1.057931444 0.767990343 0.975545268 0.951617533 1.132002178 1.281601982 1.514482229 1.086666234 0.978509756 1 10.34591094 -8.424505395 2.796066545 0.997758847 1.318476621 0.589236775 0.123914101 0.147461459 2.223872919 0.017605976 0.04332739 3.76E-09 8.424505395 0.320717774 LTEDLEYHELLDR ddPTM_HeLa_Romidepsin_16h_R1 3 LTEDLEYHELLDR 13 0 P22059;H0YCV6 P22059 OSBP Oxysterol-binding protein 1 0 0 ;; ;; 174.46 1.35E-05 15268100 8273.3 8029.3 8299 8284.8 8739.7 8740.3 7816.1 9322.5 8976.6 7755.8 FALSE FALSE TRUE 8172.461837 8142.336696 8443.440614 9242.727557 8293.680497 8181.823038 8479.999339 9592.231829 8173.710414 7554.303198 1.081828677 1.077840865 1.117699461 1.223504977 1.097874983 1.083067865 1.122538918 1.269770564 1.081993958 1 12.88308297 -4 0.019335035 4.07E-05 2.529160658 0.385428221 0.057552603 1524.88013 2.296149464 112.9226077 198.9151054 1.00E-04 4 2.529119919 LTEMQVESSYYS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 LTEMQVESSYYSPQK 15 0 Q7Z7G8-4;Q7Z7G8-3;Q7Z7G8-2;Q7Z7G8-6;Q7Z7G8 Q7Z7G8-4 VPS13B Vacuolar protein sorting-associated protein 13B 1 0 LTEMQVES(0.002)S(0.007)YYS(0.991)PQK 102.29 0.0024216 0 1533.7 1049.9 1423.4 1010.5 1110.1 1432.2 1113.5 1146.3 1563.6 1445.5 TRUE FALSE FALSE 1515.006674 1064.68052 1448.17368 1127.338765 1053.447455 1340.687042 1208.080662 1179.466382 1423.7477 1407.945702 1.076040555 0.756194304 1.028572109 0.800697614 0.748215967 0.952229224 0.858044924 0.837721498 1.011223443 1 10.45937598 -10.27432247 24.9395777 1.035908043 0.858953335 0.485030071 0.082248281 433.1976005 838598.7445 0.013609936 0.015616148 5.32E-11 10.27432247 -0.176954708 LTETKDGS(ph)GLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTETKDGSGLEEK 13 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 LT(0.006)ET(0.115)KDGS(0.879)GLEEK 99.927 0.0034856 0 956.36 1040.4 779.11 695.42 642.25 876.89 814.64 668.23 1119.3 1079.4 TRUE FALSE FALSE 944.7035165 1055.046779 792.6700827 775.8277324 609.4735859 820.859559 883.8355013 687.5641808 1019.187005 1051.357032 0.89855633 1.003509508 0.753949475 0.737929845 0.579701821 0.780761943 0.840661615 0.653977821 0.969401424 1 10.03803696 -9.695866502 5.803164455 0.954527948 0.724195984 0.735316861 0.071455347 0.087406608 5.530744292 0.011985447 0.016930703 2.01E-10 9.695866502 -0.230331964 LTEVPVEPVLTVHPES(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 LTEVPVEPVLTVHPESK 17 0 Q9H307 Q9H307 PNN Pinin 1 0 LTEVPVEPVLT(0.001)VHPES(0.999)K 133.74 0.00071246 3654300 2235.2 2074.6 2345.6 2042.1 2216.3 2371.9 2301.7 2066.7 2418.2 2078.8 TRUE FALSE FALSE 2207.956523 2103.806273 2386.424184 2278.21721 2103.193941 2220.343245 2497.206341 2126.496704 2201.910136 2024.792476 1.090460651 1.039023158 1.178601863 1.125160843 1.038720741 1.096578178 1.233314707 1.050229457 1.087474475 1 10.98355834 -12.58250038 0.25627575 0.924376305 1.132324319 0.077940284 0.064004771 5.139129912 0.403354273 0.336274502 0.046768625 2.62E-13 12.58250038 0.207948014 LTEVQDDKEEEEEENPLLVPLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTEVQDDKEEEEEENPLLVPLEEK 24 1 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 0 0 114.75 4.13E-06 3214000 924.86 913.03 833.63 962.93 939.83 1231.4 1031.9 1553.7 1026 874.86 FALSE FALSE TRUE 913.5874506 925.8836603 848.1389805 1074.268497 891.8669681 1152.717514 1119.54956 1598.653858 934.2319903 852.1310111 1.072120881 1.086550833 0.995315238 1.260684664 1.046631277 1.352746818 1.31382328 1.876065813 1.096347836 1 9.734931445 -4 0.561196306 1.037824102 40.0130943 0.879746067 0.087825181 25.04818433 0.202245204 0.013980536 1186.569035 1.00E-04 4 38.97527019 LTFDSS(ph)FSPNTGKK ddPTM_HeLa_Romidepsin_16h_R1 1 LTFDSSFSPNTGKK 14 1 C9JI87;P21796 C9JI87 VDAC1 Voltage-dependent anion-selective channel protein 1 1 0 LT(0.001)FDS(0.052)S(0.935)FS(0.013)PNTGKK 119.34 0.006598 63291000 3861.9 4463.1 4364.6 3211.3 4193.5 4793.3 3045.1 4414.4 3269.4 3927.1 TRUE FALSE FALSE 3814.829677 4525.931639 4440.564032 3582.605616 3979.490047 4487.0236 3303.750718 4542.123699 2976.976676 3825.073376 0.99732196 1.183227404 1.160909503 0.936610952 1.040369597 1.173055562 0.863709109 1.187460541 0.778279626 1 11.90127171 LTFDSSFS(ph)PNTGKK ddPTM_HeLa_Romidepsin_16h_R1 1 LTFDSSFSPNTGKK 14 1 C9JI87;P21796 C9JI87 VDAC1 Voltage-dependent anion-selective channel protein 1 1 0 LTFDS(0.183)S(0.183)FS(0.624)PNT(0.01)GKK 192.4 5.52E-11 61305000 4620.9 5336.9 5576.1 3423.1 4479.6 5694.2 3555.5 4893.9 4432.9 4253.5 TRUE FALSE FALSE 4564.578693 5412.033018 5673.149681 3818.894928 4250.989296 5330.358997 3857.504081 5035.497275 4036.410322 4142.993457 1.101758605 1.306309816 1.369335902 0.921771895 1.026067104 1.286596045 0.931091039 1.215424868 0.974273883 1 12.01645783 -11.33614886 1.263990953 1.019405903 1.141245428 0.14717929 0.146906141 0.655627975 2.127938586 0.040698113 0.028771891 4.61E-12 11.33614886 0.121839525 LTFDTT(ph)FSPNTGKK ddPTM_HeLa_Romidepsin_16h_R1 1 LTFDTTFSPNTGKK 14 1 Q5JSD2;Q5JSD1;A0A0A0MR02;P45880-2;P45880;P45880-1 Q5JSD2 VDAC2 Voltage-dependent anion-selective channel protein 2 1 0 LTFDT(0.062)T(0.65)FS(0.288)PNTGKK 169.4 0.0001578 15643000 1288 1231.9 1579.4 1009.4 1366.9 1730.5 893.58 1562.2 1369.9 1194.9 TRUE FALSE FALSE 1272.301361 1249.242721 1606.888794 1126.111577 1297.141992 1619.926635 969.4806629 1607.399792 1247.372713 1163.856326 1.093177339 1.073365065 1.380659072 0.967569237 1.114520722 1.391861348 0.832989985 1.381098128 1.071758331 1 10.18469726 -11.03745784 0.650072352 1.008345683 1.160197976 0.075184183 0.175789206 1.06192634 1.009661187 0.066567646 0.043641255 9.17E-12 11.03745784 0.151852293 LTGQQVAIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LTGQQVAIKK 10 1 S4R3I1;J3KT61;C9JUK9;Q13164-3;Q13164 S4R3I1 MAPK7 Mitogen-activated protein kinase 7 0 1 LTGQQVAIK(1)K 130.94 0.0020241 778780 708.7 676.41 629.26 638.97 556.19 647.51 715.49 384.79 679.85 589.44 FALSE TRUE FALSE 700.0620918 685.9325177 640.2120063 712.8507178 527.8055489 606.1362007 776.2637027 395.9232916 619.0425133 574.1262638 1.219352146 1.194741577 1.115106635 1.241627082 0.919319638 1.055754176 1.35207837 0.689610137 1.078234096 1 9.165224244 -8.759499866 24.99944716 1.123179427 1.03272285 0.12543966 0.16696217 125.8277954 1621828.932 0.024302555 0.046721849 1.74E-09 8.759499866 -0.090456577 LTGS(ph)QLSITQVASIK ddPTM_HeLa_Romidepsin_16h_R1 1 LTGSQLSITQVASIK 15 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 LT(0.061)GS(0.937)QLS(0.002)ITQVASIK 88.951 0.01697 17748000 1760.7 1801.8 1887.5 2231.9 1747.3 2148.4 1995.4 1833.7 2021.3 1767.4 TRUE FALSE FALSE 1739.239911 1827.165788 1920.351146 2489.962779 1658.128761 2011.124174 2164.889226 1886.755216 1840.509866 1721.482693 1.010315072 1.061390739 1.11552161 1.446405932 0.963198043 1.168251172 1.25757246 1.096005916 1.069142242 1 10.74943596 -9.781718313 2.90963663 1.006516193 1.183744733 0.257534676 0.11733048 0.211287195 3.687116505 0.017748549 0.024696008 1.65E-10 9.781718313 0.177228541 LTGS(ph)TSSLNK ddPTM_HeLa_Romidepsin_16h_R1 1 LTGSTSSLNK 10 0 Q9NV70-2;Q9NV70 Q9NV70-2 EXOC1 Exocyst complex component 1 1 0 LTGS(0.757)T(0.218)S(0.02)S(0.005)LNK 163.46 0.0018948 42660000 2500.4 2245.8 2664 2365.9 2216.1 2838.2 2224.2 2649.2 2733.2 2503 TRUE FALSE FALSE 2469.924163 2277.416431 2710.365803 2639.45649 2103.004148 2656.84818 2413.123492 2725.850422 2488.735747 2437.971699 1.013106167 0.934143916 1.111729805 1.082644434 0.862604003 1.089778106 0.989807836 1.118081241 1.020822246 1 11.25146566 -9.770682091 24.97466584 1.000958581 1.035853217 0.091601369 0.073999151 491.9301907 1329239.495 0.011231104 0.014867889 1.70E-10 9.770682091 0.034894636 LTGSTSS(ph)LNK ddPTM_HeLa_Romidepsin_16h_R1 4 LTGSTSSLNK 10 0 Q9NV70-2;Q9NV70 Q9NV70-2 EXOC1 Exocyst complex component 1 1 0 LTGST(0.007)S(0.043)S(0.95)LNK;LTGS(0.008)T(0.051)S(0.332)S(0.609)LNK;LTGS(0.004)T(0.035)S(0.262)S(0.699)LNK;LTGS(0.186)T(0.066)S(0.186)S(0.562)LNK ;;; 160.72 0.0023638 123649000 17374.1 16235.3 17117.9 15300.4 18209.3 18527.9 15521.1 17650.6 17045.5 15597.8 TRUE FALSE FALSE 17162.33779 16463.86098 17415.82987 17069.50424 17280.01147 17344.02699 16839.46185 18161.29226 15520.90779 15192.56691 1.129653593 1.083678688 1.146338863 1.123543134 1.13739907 1.141612678 1.108401362 1.195406436 1.021611942 1 13.89107803 -15.83641744 0.21078414 0.507506336 1.155850617 0.79594493 0.025363871 10.26542923 0.165052343 2.093670057 0.021237513 1.46E-16 15.83641744 0.648344281 LTHDVELNLDYER ddPTM_HeLa_Romidepsin_16h_R1 1 LTHDVELNLDYER 13 0 H7C3V5;G3V0E5;P02786 H7C3V5 TFRC "Transferrin receptor protein 1;Transferrin receptor protein 1, serum form" 0 0 107.99 0.0012247 0 1866.7 1933.6 1592.1 1991.6 1882 1966.1 1536.5 2267.2 2090 2232.3 FALSE FALSE TRUE 1843.947942 1960.821272 1619.809833 2221.878163 1785.954517 1840.472555 1667.010272 2332.797855 1903.065165 2174.304524 0.848063333 0.901815385 0.744978366 1.021879934 0.821391161 0.846464943 0.766686659 1.072893805 0.87525236 1 11.0863383 -12.29932098 0.918715474 1.0036336 0.871137478 0 0.104490717 0.752069004 1.088068527 0.068977935 0.016591569 5.02E-13 12.29932098 -0.132496122 LTK(ac)LTEK ddPTM_HeLa_Romidepsin_16h_R1 2 LTKLTEK 7 1 P23526-2;P23526 P23526-2 AHCY Adenosylhomocysteinase 0 1 ; LTK(1)LTEK;LTK(1)LTEK 131.22 0.017161 6779100 5784.7 5397.4 6438.6 5497.3 7004.3 6955.8 5288.6 5560.9 5446.4 4108.6 FALSE TRUE FALSE 5714.193851 5473.384739 6550.661132 6132.923692 6646.844434 6511.346829 5737.813552 5721.795868 4959.260343 4001.85798 1.427885217 1.36771089 1.636904949 1.532519076 1.660939611 1.627080936 1.433787401 1.429784839 1.239239465 1 11.96645425 -11.7516686 0.487934724 0.945588427 1.555480052 0.65499995 0.113038822 0.357243501 0.153326535 0.1009784 0.028378988 1.77E-12 11.7516686 0.609891624 LTLDK(ac)LDVK ddPTM_HeLa_Romidepsin_16h_R1 2 LTLDKLDVK 9 1 P00558 P00558 PGK1 Phosphoglycerate kinase 1 0 1 ; LTLDK(1)LDVK;LTLDK(1)LDVK 134.59 0.0072959 2019660 381.25 341.154 570.79 421.927 1299.32 1400.28 1118.32 934.61 855.34 581.84 FALSE TRUE FALSE 376.6031784 345.956775 580.7243605 470.712185 1233.010852 1310.806627 1213.310073 961.6514658 778.8362482 566.7237129 0.664526946 0.610450502 1.024704538 0.830584947 2.175682478 2.312955321 2.140919897 1.696861176 1.37427856 1 9.146501759 -8.763376735 24.99945048 0.833205351 2.102366704 0.831329561 0.255142244 11.14616793 143831.9538 0.030938832 0.05820156 1.72E-09 8.763376735 1.269161353 LTLEDLEDSWDR ddPTM_HeLa_Romidepsin_16h_R1 1 LTLEDLEDSWDR 12 0 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 160.77 0.0075658 9522900 1082.2 1114 1162.8 947.26 854.18 1025.3 989.83 1327.7 1334.4 1076.4 FALSE FALSE TRUE 1069.00973 1129.682921 1183.038046 1056.786658 810.5880072 959.786639 1073.906135 1366.114905 1215.047922 1048.434973 1.019624257 1.077494504 1.128384761 1.007965859 0.773140946 0.915446989 1.024294461 1.303003944 1.158915864 1 10.03402167 -7.267318443 4.801212222 0.999935782 1.318565108 0.414508003 0.103380184 0.115249844 7.568331138 0.013123347 0.121384697 5.40E-08 7.267318443 0.318629327 LTLNS(ph)PIFDKPLSR ddPTM_HeLa_Romidepsin_16h_R1 2 LTLNSPIFDKPLSR 14 1 H0YBX5;E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2;E5RIY8;E5RIU4 H0YBX5 CDK16 Cyclin-dependent kinase 16 1 0 LT(0.002)LNS(0.995)PIFDKPLS(0.003)R;LT(0.028)LNS(0.671)PIFDKPLS(0.301)R ; 174.59 0.00010668 170420000 5093.3 5327.5 4834.4 5427.3 7256.7 7392.1 6520.1 8199.2 5495.1 5450.4 TRUE FALSE FALSE 5031.220901 5402.500685 4918.540704 6054.829962 6886.363521 6919.768667 7073.917131 8436.430916 5003.604493 5308.797822 0.947713789 1.017650486 0.926488608 1.14052751 1.297160629 1.303453041 1.332489458 1.589141496 0.942511782 1 12.37416948 -8.33639372 0.744599825 0.969230592 1.541223624 0.901546964 0.066218993 0.213719463 0.177843859 0.011802423 0.07582906 4.61E-09 8.33639372 0.571993032 LTLT(ph)SDESTLIEDGGAR ddPTM_HeLa_Romidepsin_16h_R1 1 LTLTSDESTLIEDGGAR 17 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 1 0 LTLT(0.852)S(0.102)DES(0.044)T(0.002)LIEDGGAR 220.72 4.16E-35 7000900 962.32 924.39 1127 684.52 830.69 1147.2 709.5 1118.2 952.28 868.34 TRUE FALSE FALSE 950.5908737 937.4035867 1146.614962 763.6674232 788.2967896 1073.897622 769.7649123 1150.553353 867.1056918 845.7804016 1.123921614 1.108329757 1.355688734 0.902914541 0.932034826 1.269712115 0.910123846 1.360345251 1.025213744 1 9.72413932 -12.1781459 0.934733269 1.00030194 1.112100269 0.06314116 0.16233502 1.341488715 2.118467018 0.099613229 0.028623061 6.64E-13 12.1781459 0.111798329 LTNSMMMHGR ddPTM_HeLa_Romidepsin_16h_R1 1 LTNSMMMHGR 10 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 0 64.654 0.0030544 0 121.07 0 118.49 153.14 0 108.22 205.76 0 62.404 63.051 FALSE FALSE TRUE 119.5943523 0 120.5522687 170.8467673 0 101.3050913 223.2372493 0 56.82242995 61.41292593 1.947380791 0 1.962978753 2.781934988 0 1.649572785 3.635020574 0 0.925251958 1 5.940470435 -12.60812258 1.3625554 0.99506528 1.590364448 0.027374768 1.160571041 1.457165954 4.789125748 0.806140526 0.179050299 2.47E-13 12.60812258 0.595299169 LTPEEEEILNK ddPTM_HeLa_Romidepsin_16h_R1 2 LTPEEEEILNK 11 0 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 0 0 ; ; 221.68 4.24E-26 16585600 4565.1 4436.5 4446.6 3894 4296.9 4803.7 3595.4 4218.5 4494.7 4339.6 FALSE FALSE TRUE 4509.458805 4498.957163 4523.991208 4344.242602 4077.613159 4496.759073 3900.793186 4340.555642 4092.682775 4226.856566 1.066858725 1.064374221 1.070296836 1.027771474 0.964691632 1.063854191 0.922859133 1.026899204 0.968256838 1 12.04536944 -8.948578609 9.700842244 1.0384741 0.994543188 0.142715243 0.045585934 0.494256176 89.10284542 0.006241141 0.011320439 1.13E-09 8.948578609 -0.043930912 LTPEELER ddPTM_HeLa_Romidepsin_16h_R1 2 LTPEELER 8 0 Q5H8X8;O95399;O95399-2 Q5H8X8 UTS2 Urotensin-2 0 0 ; ; 195.81 8.25E-07 26455000 3734.58 3873.9 3611.1 3199.5 4231.4 4256.1 4145.4 4342.8 4103.6 3589.3 FALSE FALSE TRUE 3689.061502 3928.436866 3673.949681 3569.441244 4015.455868 3984.148946 4497.510173 4468.452066 3736.563738 3496.049469 1.055208611 1.123678856 1.050886068 1.020992774 1.148569522 1.13961458 1.286454958 1.27814326 1.068796014 1 11.77150988 -4.000000004 0.293219084 1.013134238 3.550398808 0.78010459 0.044400889 13.20084159 0.168800004 0.016304004 17.67281127 1.00E-04 4.000000004 2.537264569 LTPIHDR ddPTM_HeLa_Romidepsin_16h_R1 1 LTPIHDR 7 0 I3L3X7;A0A087X2I4;P28072 I3L3X7 PSMB6 Proteasome subunit beta type;Proteasome subunit beta type-6 0 0 82.241 0.003428 0 3396.9 3419.6 4713.5 3042.2 4690.7 4955.7 6075.8 1547.6 6007 4582.6 FALSE FALSE TRUE 3355.497276 3467.741219 4795.53649 3393.953478 4451.316076 4639.046764 6591.8783 1592.377364 5469.718875 4463.543391 0.751756392 0.776903217 1.074378822 0.760372014 0.997260626 1.039319293 1.476826306 0.35675185 1.225420791 1 12.12397374 -8.568180534 20.58038178 0.879509308 1.011008349 0 0.293091939 53.18137947 24159.20603 0.036764514 0.073529186 2.70E-09 8.568180534 0.131499041 LTPS(ph)PDIIVLSDNEAS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 0 LT(0.004)PS(0.993)PDIIVLS(0.053)DNEAS(0.642)S(0.307)PR 112.53 0.0082642 2871500 449.59 580.44 572.38 461.16 527.69 516.65 597.27 799.02 532.17 631.88 TRUE FALSE FALSE 444.1102242 588.6114496 582.3420338 514.481489 500.7600102 483.6377324 648.0020989 822.1383831 484.5713824 615.4636665 0.721586421 0.956370752 0.94618426 0.835925038 0.813630499 0.785810371 1.052868161 1.335803278 0.787327358 1 9.26552988 -7.410295399 2.838535976 0.867358798 1.354427983 0.751443587 0.085220508 0.156267317 2.011208374 0.015525975 0.145923005 3.89E-08 7.410295399 0.487069185 LTPS(ph)PDIIVLSDNEASS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 0 LT(0.247)PS(0.753)PDIIVLS(0.001)DNEAS(0.125)S(0.874)PR;LT(0.02)PS(0.656)PDIIVLS(0.323)DNEAS(0.135)S(0.865)PR ; 176.44 1.76E-12 22628000 3226.98 3299.56 2993.87 2921.69 4119.44 4046.33 3557.18 4144.5 3681.74 3250.28 TRUE FALSE FALSE 3187.648327 3346.011292 3045.977051 3259.509545 3909.209605 3787.782572 3859.32678 4264.414569 3352.435953 3165.837257 1.006889511 1.05691197 0.962139492 1.029588472 1.234810664 1.196455239 1.219054066 1.347010039 1.058941342 1 11.62837138 -8.774704477 4.446621107 1.005014255 1.245891265 0.858383975 0.045717835 0.045027177 2.12180415 0.00594233 0.011523587 1.68E-09 8.774704477 0.24087701 LTPS(ph)PDIIVLSDNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 0 LTPS(1)PDIIVLSDNEASSPR;LT(0.011)PS(0.988)PDIIVLS(0.001)DNEASSPR;LTPS(1)PDIIVLSDNEASSPR;LT(0.006)PS(0.994)PDIIVLSDNEASSPR ;;; 185.71 5.36E-11 38156900 6203.27 6264.03 6094.58 7632.5 8349.63 8329.6 7381.74 8395.9 6785.2 6463 TRUE FALSE FALSE 6127.662159 6352.215179 6200.653608 8515.005562 7923.517224 7797.365443 8008.744811 8638.82212 6178.314718 6295.090328 0.973403373 1.009074508 0.984998353 1.352642316 1.258682054 1.238642344 1.272220793 1.372311066 0.981449732 1 12.62001136 -9.268042262 24.99953434 0.988921671 1.291835609 0.939642325 0.039151107 86.21529816 326424.1632 0.005899332 0.009139735 5.39E-10 9.268042262 0.302913937 LTPSPDIIVLS(ph)DNEASSPR ddPTM_HeLa_Romidepsin_16h_R1 4 LTPSPDIIVLSDNEASSPR 19 0 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 1 0 LTPSPDIIVLS(1)DNEASSPR;LTPS(0.002)PDIIVLS(0.998)DNEASSPR;LTPSPDIIVLS(1)DNEASSPR;LTPSPDIIVLS(0.996)DNEAS(0.001)S(0.003)PR ;;; 245.74 4.08E-62 50981700 5839.48 5993.7 5569.88 5762.73 9695.6 9993.4 8627.1 9785.6 5918.53 5639.57 TRUE FALSE FALSE 5768.306172 6078.079466 5666.821425 6429.043957 9200.797353 9354.853992 9359.885659 10068.7309 5389.161854 5493.053158 1.050109294 1.106502939 1.031634186 1.170395365 1.67498786 1.703033581 1.703949587 1.83299353 0.981086783 1 12.42339254 -8.799921659 2.843465268 1.033009366 1.741517033 0.980681617 0.046602947 0.02438536 0.402938167 0.00713986 0.014418882 1.59E-09 8.799921659 0.708507667 LTPT(ph)S(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 LTPTSPR 7 0 Q9BSW2-2 Q9BSW2-2 2 0 LT(0.008)PT(0.996)S(0.996)PR 46.663 0.026429 1304700 641.72 739.98 493.66 595.9 887.18 757.32 956.91 993.15 557.43 500.62 TRUE FALSE FALSE 633.8984698 750.3974579 502.2519452 664.8007618 841.9038941 708.9296961 1038.189912 1021.885228 507.5720647 487.6138202 1.300001033 1.538917534 1.030019914 1.363375553 1.72657923 1.453875314 2.129123229 2.095685532 1.040930432 1 8.929595206 -4 0.245424949 1.051148079 8.200421262 0.776326865 0.185328518 15.41063084 0.191339298 0.104571654 45.73147583 1.00E-04 4 7.149273183 LTPVRPAAAS(ph)PIVSGAR ddPTM_HeLa_Romidepsin_16h_R1 2 LTPVRPAAASPIVSGAR 17 1 I3VM54;Q9Y2K7-3;Q9Y2K7;Q9Y2K7-4;Q9Y2K7-5;Q9Y2K7-2 I3VM54 KDM2A Lysine-specific demethylase 2A 1 0 LTPVRPAAAS(0.998)PIVS(0.002)GAR;LTPVRPAAAS(1)PIVSGAR ; 164.82 5.46E-05 35945000 2266.64 2448.7 1954.24 2062.1 2101.56 1770.16 1576.31 1663.91 2320.12 1853.99 TRUE FALSE FALSE 2239.01332 2483.172863 1988.252727 2300.529704 1994.309551 1657.052489 1710.201732 1712.052611 2112.602656 1805.823073 1.23988521 1.375092001 1.101022995 1.273950776 1.104377046 0.917616191 0.947048334 0.948073284 1.169883522 1 10.81844083 -8.340447459 4.635174874 1.148003314 0.938497917 0.536920252 0.10083203 0.186650323 7.319667225 0.018453039 0.042871049 4.57E-09 8.340447459 -0.209505396 TEQELPRPQSPS(ph)DLDSLDGR ddPTM_HeLa_Romidepsin_16h_R1 1 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 1 0 T(0.002)EQELPRPQS(0.126)PS(0.849)DLDS(0.023)LDGR 72.793 0.0028889 14515000 2354.2 1844.1 2246.2 1628.9 1329.5 1062.8 817.46 906.31 2875 2209.4 TRUE FALSE FALSE 2325.506105 1870.061288 2285.294169 1817.241082 1261.650654 994.89051 886.895032 932.5326499 2617.852799 2151.999469 1.08062578 0.868987802 1.061939931 0.84444309 0.586269036 0.462309831 0.412126046 0.433333123 1.216474649 1 11.07146201 -8.767323685 1.568978161 1.02841367 0.422270887 0.916472239 0.082357848 0.053773425 0.267117318 0.009190182 0.022099784 1.71E-09 8.767323685 -0.606142782 down AADKS(ph)PESQNLIDGTK ddPTM_HeLa_Romidepsin_16h_R1 2 AADKSPESQNLIDGTK 16 1 Q9HCE3 Q9HCE3 ZNF532 Zinc finger protein 532 1 0 AADKS(0.956)PES(0.01)QNLIDGT(0.034)K;AADKS(0.997)PES(0.003)QNLIDGTK ; 68.481 0.016138 81570000 13465.6 12949.8 13122.6 10409.6 5820.7 4955.9 3900.6 3685.7 12557.8 13096.3 TRUE FALSE FALSE 13301.47609 13132.10762 13350.99335 11613.20693 5523.647959 4639.233984 4231.916867 3792.339914 11434.59892 12756.05624 1.042757718 1.029480223 1.04663958 0.910407317 0.433021606 0.363688737 0.331757464 0.297297209 0.896405496 1 13.63889474 -8.767217509 2.838563589 1.023136586 0.334688373 0.9795103 0.045012445 0.013908729 0.229769702 0.003938073 0.008076255 1.71E-09 8.767217509 -0.688448213 down SPLVTGS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SPLVTGSPK 9 0 Q10571 Q10571 MN1 Probable tumor suppressor protein MN1 1 0 SPLVT(0.005)GS(0.995)PK 102.4 0.026153 11452000 6373.2 6403.6 6622 5055.5 3247.5 2450.4 2074.2 2376.8 6947.3 6745.9 TRUE FALSE FALSE 6295.520987 6493.750049 6737.253132 5640.040697 3081.767957 2293.827348 2250.382496 2445.568958 6325.916088 6570.640546 0.958128959 0.988297869 1.02535713 0.858369996 0.469020933 0.349102547 0.342490581 0.372196431 0.962754855 1 12.6818183 -8.766719425 2.592089766 0.983444544 0.355446079 0.994777873 0.020954946 0.01472646 0.202221772 0.00360366 0.007506235 1.71E-09 8.766719425 -0.627998465 down LTPVSLSNS(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 2 LTPVSLSNSPIK 12 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 LTPVSLS(0.012)NS(0.988)PIK;LTPVSLS(0.011)NS(0.989)PIK ; 213.99 3.88E-21 135110000 9623.1 9741.4 10856.6 4763 5471.4 5268.1 4124 4721.8 8511.4 9093.8 TRUE FALSE FALSE 9505.809956 9878.539685 11045.55457 5313.720471 5192.174041 4931.485412 4474.292457 4858.417833 7750.119067 8857.541765 1.073188274 1.115268767 1.247022578 0.599909163 0.586186798 0.556755536 0.505139301 0.548506342 0.874974036 1 13.11269065 -9.188973307 6.79260101 1.057004439 0.554505936 0.88634995 0.090046124 0.051944478 4.126864233 0.011655968 0.019390906 6.47E-10 9.188973307 -0.502498503 LTPVSLSNS(ph)PIKGADCQEVPQDKDGYK ddPTM_HeLa_Romidepsin_16h_R1 1 LTPVSLSNSPIKGADCQEVPQDKDGYK 27 2 P46100-4;P46100;P46100-2;P46100-5;P46100-3 P46100-4 ATRX Transcriptional regulator ATRX 1 0 LT(0.004)PVS(0.011)LS(0.086)NS(0.852)PIKGADCQEVPQDKDGY(0.047)K 47.806 0.0148 52013000 2041.2 2543.2 2407 843.69 1678.8 1723.1 1491.1 1442.1 2663.8 2196.1 TRUE FALSE FALSE 2016.321069 2579.003236 2448.892825 941.2414075 1593.124572 1612.999471 1617.753997 1483.824888 2425.543056 2139.045005 0.942626763 1.205679745 1.144853343 0.4400288 0.744783101 0.754074583 0.756297316 0.69368568 1.133937365 1 11.06275112 -9.274144746 24.99973804 1.005103653 0.69009796 0.712513337 0.124218211 384.1794786 755930.1199 0.018909303 0.029000492 5.32E-10 9.274144746 -0.315005693 LTPVSPESS(ph)STEEK ddPTM_HeLa_Romidepsin_16h_R1 2 LTPVSPESSSTEEK 14 0 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 LTPVSPES(0.091)S(0.892)S(0.016)T(0.002)EEK;LTPVSPES(0.204)S(0.787)S(0.007)T(0.001)EEK ; 188.92 5.71E-11 1275224200 8325.8 7478 6444.1 5497.2 5436.8 5104.8 4732.5 5138.3 8710.9 7714.9 TRUE FALSE FALSE 8224.321947 7583.27548 6556.256857 6132.812129 5159.339809 4778.619755 5134.478432 5286.968604 7931.775287 7514.465786 1.094465286 1.009156964 0.872484757 0.816134148 0.686587704 0.635922751 0.683279235 0.703572117 1.055534154 1 12.87545483 -9.323960436 1.325077727 1.045419332 0.672403128 0.955081801 0.035013865 0.072734911 0.251612857 0.007691544 0.014282328 4.74E-10 9.323960436 -0.373016204 LTPVSPESSS(ph)TEEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTPVSPESSSTEEK 14 0 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 LTPVSPES(0.006)S(0.036)S(0.784)T(0.173)EEK 153.14 0.00061505 6560300 2051 1640.6 1497.9 1055.7 989.17 1235.7 1497.1 1406.5 1943.3 2026.7 TRUE FALSE FALSE 2026.001623 1663.69641 1523.970321 1177.765001 938.6889638 1156.742758 1624.263637 1447.194858 1769.486381 1974.046042 1.026319336 0.842785008 0.772003433 0.596624889 0.475515233 0.585975572 0.822809399 0.733110995 0.896375436 1 10.94693992 -9.853298554 1.791935531 1.012909875 0.643977914 0.677550405 0.097431833 0.123785201 0.806158114 0.017005244 0.023684663 1.40E-10 9.853298554 -0.368931962 LTQAEISEQPTMAT(ph)VVPQVPTSPK ddPTM_HeLa_Romidepsin_16h_R1 1 LTQAEISEQPTMATVVPQVPTSPK 24 0 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 0 LTQAEIS(0.006)EQPT(0.126)MAT(0.667)VVPQVPT(0.057)S(0.143)PK 58.457 0.003639 5072800 1426.9 1107.3 1129.3 1564.4 1310.7 1470.9 1285.6 1396.5 1387.4 1267.5 TRUE FALSE FALSE 1409.508394 1122.888598 1148.954993 1745.283289 1243.810088 1376.914237 1394.798832 1436.905524 1263.307469 1234.570167 1.141699704 0.909538095 0.930651836 1.413676869 1.007484322 1.115298485 1.12978498 1.163891338 1.023277172 1 10.26979312 LTQAEISEQPTMATVVPQVPTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LTQAEISEQPTMATVVPQVPTSPK 24 0 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 1 0 LTQAEISEQPT(0.001)MAT(0.009)VVPQVPT(0.257)S(0.732)PK 59.567 0.0022534 3990600 1390.3 1373.6 1602 1174.4 1528.2 1625.6 1031.4 1478.5 1562.3 1665.5 TRUE FALSE FALSE 1373.354489 1392.937577 1629.882138 1310.189654 1450.210251 1521.729406 1119.00709 1521.278065 1422.563975 1622.23007 0.846584288 0.858655996 1.004717005 0.807647249 0.893960899 0.938047836 0.689795554 0.937769613 0.876918756 1 10.66376273 -12.39859589 0.756956432 1.015210147 0.868160834 0 0.089216932 0.920260272 0.78189879 0.088070276 0.015189943 3.99E-13 12.39859589 -0.147049313 LTQTS(ph)STEQLNVLETETEVLNK ddPTM_HeLa_Romidepsin_16h_R1 1 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 LT(0.002)QT(0.14)S(0.457)S(0.3)T(0.101)EQLNVLETETEVLNK 162.87 3.91E-09 69815000 5520.1 5471.8 5207.8 4176.1 5782.6 5539.5 5875.7 6163.1 5629.2 5488.7 TRUE FALSE FALSE 5452.818898 5548.832144 5298.439574 4658.960331 5487.492344 5185.543828 6374.781811 6341.419575 5125.710253 5346.102783 1.019961478 1.037920962 0.991084495 0.87146853 1.026447221 0.969967103 1.19241662 1.186176142 0.958775104 1 12.38427186 -7.756554126 24.99994741 0.999587368 1.189296474 0.750973483 0.046535374 43.43257214 222254.9634 0.006259791 0.022010201 1.75E-08 7.756554126 0.189709107 LTQTSS(ph)TEQLNVLETETEVLNK ddPTM_HeLa_Romidepsin_16h_R1 3 LTQTSSTEQLNVLETETEVLNK 22 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 LT(0.001)QT(0.063)S(0.188)S(0.56)T(0.188)EQLNVLETETEVLNK;LT(0.001)QT(0.061)S(0.185)S(0.568)T(0.185)EQLNVLETETEVLNK;LT(0.005)QT(0.069)S(0.216)S(0.676)T(0.034)EQLNVLETETEVLNK ;; 209.29 1.02E-32 105702800 10782.4 9698.5 11568.4 8318.8 11817 11923.1 11589.8 11281.3 11131.7 11092.6 TRUE FALSE FALSE 10650.97996 9835.035738 11769.74315 9280.658797 11213.93439 11161.25239 12574.23732 11607.70662 10136.05287 10804.41265 0.985799072 0.910279536 1.089345948 0.858969302 1.037903193 1.033027222 1.163805727 1.074348693 0.93814011 1 13.39933303 -8.056704686 2.437234977 0.986008688 1.117766667 0.425797308 0.06518447 0.195088208 2.2516264 0.008083988 0.027731264 8.78E-09 8.056704686 0.131757979 AQAVSEEEEEEEGKSSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 AQAVSEEEEEEEGKSSSPK 19 1 G3V529;Q9GZR7-2;Q9GZR7 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 0 AQAVSEEEEEEEGKS(0.003)S(0.245)S(0.752)PK;AQAVS(0.001)EEEEEEEGKS(0.318)S(0.318)S(0.363)PK ; 80.835 0.0031306 224720000 7051.1 6815.9 6844.2 5471.1 3526.7 2989 2782.2 2474.61 8206.5 6494.3 TRUE FALSE FALSE 6965.158481 6911.854419 6963.32043 6103.694324 3346.719339 2798.012547 3018.519999 2546.208936 7472.490086 6325.57715 1.101110352 1.092683601 1.100819777 0.964922912 0.529077309 0.442333163 0.47719282 0.402525948 1.181313564 1 12.6269814 -8.766012065 3.192169309 1.056453848 0.44748787 0.970829528 0.052208489 0.02601146 0.54961964 0.006984333 0.014094413 1.71E-09 8.766012065 -0.608965978 down LTRPAAS(ph)PAVGEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTRPAASPAVGEK 13 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 0 LT(0.004)RPAAS(0.996)PAVGEK 63.894 0.03043 127630000 7472.2 7211.8 6644.3 6570.6 6645.1 7254.2 6092.1 6413.5 6856.7 6522.7 TRUE FALSE FALSE 7381.125952 7313.32791 6759.941254 7330.323688 6305.975751 6790.680032 6609.562822 6599.064504 6243.419579 6353.239314 1.161789378 1.151117965 1.064014894 1.153793101 0.992560714 1.068853178 1.040345326 1.03869289 0.982714371 1 12.63327665 -8.746621617 24.9996142 1.088210831 1.037896795 0.142985797 0.060156914 439.3278528 741203.4423 0.010072137 0.020076469 1.79E-09 8.746621617 -0.050314036 LTS(ph)DEEGEPSGKR ddPTM_HeLa_Romidepsin_16h_R1 3 LTSDEEGEPSGKR 13 1 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 LT(0.051)S(0.949)DEEGEPSGKR;LT(0.001)S(0.999)DEEGEPSGKR;LT(0.004)S(0.996)DEEGEPSGKR ;; 157.56 0.00091129 43769300 6226.6 6097.3 5213.2 6962.1 6110.3 6689.9 5941.4 6924 6756.4 6069.2 TRUE FALSE FALSE 6150.707804 6183.137949 5303.933559 7767.09076 5798.46859 6262.436981 6446.062368 7124.335016 6152.090662 5911.521309 1.040461073 1.045946995 0.897219731 1.313890343 0.980875867 1.059361314 1.090423603 1.205161014 1.040694999 1 12.52931374 -9.299970915 24.99999051 1.013721529 1.1155446 0.305814261 0.092486483 584.3166903 379114.1996 0.013227519 0.020205634 5.01E-10 9.299970915 0.101823072 LTS(ph)PGALLFQ ddPTM_HeLa_Romidepsin_16h_R1 2 LTSPGALLFQ 10 0 O60566-2;O60566;O60566-3 O60566-2 BUB1B Mitotic checkpoint serine/threonine-protein kinase BUB1 beta 1 0 LT(0.042)S(0.958)PGALLFQ;LT(0.07)S(0.93)PGALLFQ ; 179.8 4.28E-05 29930000 4469.2 4039.6 4803.9 4205.7 8799.2 10689.9 8036.6 8889.3 4895.4 4502 TRUE FALSE FALSE 4414.727671 4096.469595 4887.509864 4691.982822 8350.14399 10006.84989 8719.228603 9146.497871 4457.543163 4385.037391 1.006770816 0.934192626 1.114587956 1.069998361 1.904235528 2.28204437 1.988404619 2.085842618 1.016534813 1 12.09837343 -8.722149878 3.563723134 1.006550417 2.105925546 0.975951652 0.080604234 0.021623203 0.569201602 0.011047472 0.022484888 1.90E-09 8.722149878 1.099375129 up LTSPVTSIS(ph)PIQASEK ddPTM_HeLa_Romidepsin_16h_R1 1 LTSPVTSISPIQASEK 16 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 LTSPVT(0.001)S(0.024)IS(0.975)PIQASEK 221.78 7.96E-35 11732000 2070.9 2509.1 1748.3 1754.8 1983.2 1782.6 1366 1425 2263.9 2324.9 TRUE FALSE FALSE 2045.659074 2544.423176 1778.728428 1957.698233 1881.989904 1668.697613 1482.028006 1466.230127 2061.411114 2264.498763 0.90336065 1.123614293 0.785484389 0.864517245 0.831084536 0.73689491 0.654461831 0.647485506 0.910316732 1 11.14497604 -8.217256446 0.561692404 0.968374661 0.560957424 0.704708413 0.076933533 0.647011542 0.25323286 0.01566294 0.141585048 6.06E-09 8.217256446 -0.407417237 LTTEATQT(ph)PVSNK ddPTM_HeLa_Romidepsin_16h_R1 1 LTTEATQTPVSNK 13 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 LTTEAT(0.017)QT(0.983)PVSNK 133.04 0.003926 9485400 1912.9 2073.3 2656.3 1407.1 3061.7 4841.7 4055.5 3913.5 2241.3 2197.5 TRUE FALSE FALSE 1889.584839 2102.487972 2702.531787 1569.795523 2905.450024 4532.330996 4399.974069 4026.730948 2040.832515 2140.408633 0.882814996 0.982283448 1.262624223 0.733409265 1.357427726 2.117507342 2.055670119 1.881290743 0.953477987 1 11.06367054 -8.437589196 3.494829121 0.960574561 2.018715267 0.918197362 0.139616694 0.044263811 1.02140657 0.019633455 0.045983478 3.65E-09 8.437589196 1.058140706 ETDSPST(ph)PGKDQR ddPTM_HeLa_Romidepsin_16h_R1 1 ETDSPSTPGKDQR 13 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 1 0 ETDS(0.017)PS(0.226)T(0.757)PGKDQR 127.78 0.013039 2089100 1962.4 1630.3 1610.5 1438.6 680.72 622.93 561.7 384.89 2142.7 1583.2 TRUE FALSE FALSE 1938.481514 1653.251406 1638.530077 1604.937701 645.9803183 583.1267834 609.410784 396.0261849 1951.051546 1542.068236 1.257065977 1.072100033 1.062553549 1.040769574 0.418905145 0.378145902 0.395190543 0.256814955 1.265217388 1 10.59065089 -8.764932808 3.824676618 1.114131207 0.353194074 0.94979607 0.085209708 0.040707206 1.300514434 0.015284336 0.030238861 1.72E-09 8.764932808 -0.760937133 down LTTTGQVT(ph)SPVKGASFVTSTNPR ddPTM_HeLa_Romidepsin_16h_R1 2 LTTTGQVTSPVKGASFVTSTNPR 23 1 K7ENR9;K7ERZ5;P49916-4;P49916-3;P49916-2;P49916 K7ENR9 LIG3 DNA ligase 3 1 0 LTT(0.001)T(0.006)GQVT(0.496)S(0.496)PVKGAS(0.001)FVTSTNPR;LTTT(0.002)GQVT(0.582)S(0.416)PVKGASFVTSTNPR ; 85.062 0.00015093 190679000 4340.6 3184.5 3365.3 3473.9 2440.24 1800.74 1953.31 1803.6 3836.1 3418.1 TRUE FALSE FALSE 4287.695098 3229.331475 3423.871635 3875.568663 2315.705447 1685.678526 2119.224103 1855.78432 3492.989608 3329.297269 1.287867905 0.969973905 1.028406705 1.16408009 0.695553824 0.506316616 0.636537963 0.557410219 1.049167234 1 11.70100198 -8.674714329 4.162297798 1.118412389 0.577728637 0.860314754 0.095746136 0.069066708 2.236291719 0.018232698 0.037279005 2.11E-09 8.674714329 -0.540683752 GSPSS(ph)PAGSTPAIPK ddPTM_HeLa_Romidepsin_16h_R1 2 GSPSSPAGSTPAIPK 15 0 Q9HCE3 Q9HCE3 ZNF532 Zinc finger protein 532 1 0 GS(0.003)PS(0.287)S(0.709)PAGS(0.001)TPAIPK;GS(0.033)PS(0.213)S(0.713)PAGS(0.024)T(0.017)PAIPK ; 123.1 0.0031869 27489000 17434.7 18236.6 16915.4 13999.4 5653.2 4348.7 3368.4 3602.5 18290.1 17443.7 TRUE FALSE FALSE 17222.19917 18493.33533 17209.80544 15618.0765 5364.696109 4070.832105 3654.511812 3706.732654 16654.18765 16990.51016 1.013636378 1.088450856 1.012906927 0.919223517 0.315746617 0.23959446 0.215091353 0.218164883 0.980205273 1 14.05244155 -8.764042863 3.456338779 1.013504514 0.227943303 0.994581995 0.027449339 0.012354662 0.311037309 0.004489924 0.008982458 1.72E-09 8.764042863 -0.785561211 down LTVENS(ph)PKQEAGISEGQGTAGEEEEK ddPTM_HeLa_Romidepsin_16h_R1 3 LTVENSPKQEAGISEGQGTAGEEEEK 26 1 F8VVL1;O43583 F8VVL1 DENR Density-regulated protein 1 0 LT(0.002)VENS(0.954)PKQEAGIS(0.035)EGQGT(0.009)AGEEEEK;LT(0.009)VENS(0.829)PKQEAGIS(0.155)EGQGT(0.007)AGEEEEK;LT(0.019)VENS(0.978)PKQEAGIS(0.002)EGQGTAGEEEEK ;; 80.904 2.47E-05 234521300 6020 5288.5 6098.5 4103.4 5836 6075.7 5609.5 6181.9 6143.2 6372 TRUE FALSE FALSE 5946.625924 5362.951642 6204.641834 4577.854415 5538.167143 5687.482378 6085.97079 6360.763523 5593.736806 6206.454521 0.958135745 0.864092635 0.999707935 0.73759574 0.89232381 0.916381866 0.98058735 1.024862665 0.901277337 1 12.59955364 -10.74795283 1.4822823 0.987705358 0.914260717 0 0.081628138 0.508832602 2.326227306 0.016738193 0.01615858 1.79E-11 10.74795283 -0.073444641 LTVENS(ph)PKQEAGISEGQGTAGEEEEKKK ddPTM_HeLa_Romidepsin_16h_R1 2 LTVENSPKQEAGISEGQGTAGEEEEKKK 28 3 F8VVL1;O43583 F8VVL1 DENR Density-regulated protein 1 0 LT(0.016)VENS(0.847)PKQEAGIS(0.135)EGQGT(0.003)AGEEEEKKK;LT(0.004)VENS(0.996)PKQEAGISEGQGTAGEEEEKKK ; 79.877 3.95E-06 114423000 5634.6 4985.4 4966.5 6839.6 5468.2 6281.1 5299 5467.8 5997.6 4877.2 TRUE FALSE FALSE 5565.923328 5055.584592 5052.939849 7630.426733 5189.137349 5879.757981 5749.096928 5626.002166 5461.159635 4750.489641 1.171652556 1.064223896 1.063667165 1.606240053 1.092337368 1.237716199 1.210211444 1.184299428 1.149599315 1 12.21386051 -11.61069579 0.366024706 0.963212705 1.240167045 0.105171227 0.150736144 1.965096814 0.505196444 0.22122404 0.068263083 2.45E-12 11.61069579 0.276954339 LTVPT(ph)GLS(ph)VT(ph)S(ph)PDK ddPTM_HeLa_Romidepsin_16h_R1 1 LTVPTGLSVTSPDK 14 0 P48751-2;P48751;P48751-3 P48751-2 SLC4A3 Anion exchange protein 3 4 0 LTVPT(1)GLS(1)VT(1)S(1)PDK 75.669 0.0025635 0 376.35 261.24 401.56 338.56 353.27 240.79 249.61 221.86 420.78 350.75 TRUE FALSE FALSE 371.7629014 264.9177436 408.5489834 377.7059002 335.2413137 225.4042961 270.8118672 228.2791691 383.1443829 341.6374644 1.088179547 0.775435282 1.195855332 1.105575177 0.981277959 0.659776282 0.79268785 0.668191264 1.121494048 1 8.416322381 -8.346928686 4.750437681 1.037239451 0.715878842 0.655980067 0.110394738 0.098351737 3.86857701 0.014864813 0.034357676 4.50E-09 8.346928686 -0.321360609 LVAIVDPHIK ddPTM_HeLa_Romidepsin_16h_R1 1 LVAIVDPHIK 10 0 F5H6X6;Q14697;Q14697-2;E9PKU7 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 76.465 0.015314 760790 664.87 713.46 903.58 701.69 721.29 651.34 541.05 913.09 773.57 682.67 FALSE FALSE TRUE 656.7663087 723.5041086 919.3064309 782.8226994 684.4798798 609.7214761 587.0067735 939.5088185 704.3799618 664.934135 0.987716338 1.088083873 1.382552621 1.177293597 1.029395009 0.916965221 0.88280439 1.41293516 1.059322908 1 9.377067631 -10.19592802 5.257744514 0.994195746 1.118710238 0.084158469 0.163925257 0.378190571 20.82716253 0.027529766 0.033683056 6.37E-11 10.19592802 0.124514492 LVARPEPATGYTLEFR ddPTM_HeLa_Romidepsin_16h_R1 3 LVARPEPATGYTLEFR 16 1 Q16658 Q16658 FSCN1 Fascin 0 0 ;; ;; 139.77 0.0009074 88961130 2720.68 2234.95 2753.51 2570.25 2599.96 2907.32 2562.68 2887.53 2841.89 2368.14 FALSE FALSE TRUE 2687.519306 2266.413685 2801.433687 2867.434398 2467.274339 2721.551635 2780.353975 2971.076125 2587.704241 2306.615381 1.165135431 0.982571131 1.214521376 1.243135037 1.069651386 1.179889659 1.205382569 1.288067421 1.121862042 1 11.17156175 -16.52287874 0.071389962 0.398196271 1.392889056 0.311927684 0.080329313 145.7975056 0.807263661 14.69470447 2.040118943 3.00E-17 16.52287874 0.994692786 LVDVS(ph)PDRGSPPSR ddPTM_HeLa_Romidepsin_16h_R1 1 LVDVSPDRGSPPSR 14 1 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 0 LVDVS(0.97)PDRGS(0.03)PPSR 141.65 3.31E-05 0 1843.5 1794.2 1941 1765.1 1521.8 1343.5 1294.7 1364.9 2094 2039.3 TRUE FALSE FALSE 1821.030713 1819.458795 1974.782291 1969.189167 1444.136867 1257.654686 1404.671786 1404.391228 1906.707395 1986.318692 0.916786778 0.915995405 0.994192069 0.991376245 0.727041876 0.633158562 0.707173422 0.707032177 0.95992018 1 10.9558814 -8.703329316 5.21192298 0.960831756 0.685491943 0.936274401 0.034509252 0.04159496 2.290531218 0.006155278 0.012365357 1.98E-09 8.703329316 -0.275339813 LVEDEERR ddPTM_HeLa_Romidepsin_16h_R1 1 LVEDEERR 8 1 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 112.41 0.013921 5020500 1814.1 1746.6 2710.8 2533.9 1950.9 2355 2922.1 909.52 2704.5 2042.8 FALSE FALSE TRUE 1791.989051 1771.188681 2757.980337 2826.88144 1851.338293 2204.5231 3170.303101 935.8355262 2462.602746 1989.727762 0.900620219 0.890166341 1.386109392 1.420737799 0.930448039 1.107952124 1.59333511 0.470333452 1.237658133 1 10.95835534 -9.791611955 24.99929401 0.947041543 1.171782923 0.034295292 0.305388502 305.8372522 253398.1709 0.043205267 0.05678684 1.62E-10 9.791611955 0.22474138 LVEPGS(ph)PAEK ddPTM_HeLa_Romidepsin_16h_R1 1 LVEPGSPAEK 10 0 O14745;J3QRP6 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 0 LVEPGS(1)PAEK 106.79 0.020144 8652600 2408.9 2424.3 2672.9 1527.2 3091.1 4657 4107.1 4840.5 3315.4 2951.2 TRUE FALSE FALSE 2379.5394 2458.429359 2719.420703 1703.78205 2933.349633 4359.43273 4455.956971 4980.55223 3018.86232 2874.527399 0.827801955 0.855246452 0.946040975 0.592717276 1.020463271 1.516573727 1.550152896 1.732650812 1.050211705 1 11.48910907 -8.262282649 3.171372658 0.890541613 1.619965995 0.871923128 0.124458047 0.061805078 1.278362927 0.017737548 0.047043785 5.47E-09 8.262282649 0.729424382 LVEPHS(ph)PSPSSK ddPTM_HeLa_Romidepsin_16h_R1 3 LVEPHSPSPSSK 12 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 LVEPHS(0.999)PS(0.001)PSSK;LVEPHS(0.997)PS(0.003)PSSK;LVEPHS(0.942)PS(0.039)PS(0.014)S(0.004)K ;; 148.96 0.00147 49886900 19985 19579.3 18236.5 18451.1 20266.5 18838.3 17121.8 17467.4 24338.2 22272.6 TRUE FALSE FALSE 19741.41513 19854.9379 18553.89863 20584.503 19232.22488 17634.59343 18576.12526 17972.79166 22161.33044 21693.95464 0.909996147 0.915229069 0.855256634 0.948858949 0.886524619 0.812880534 0.856281189 0.828470049 1.021544057 1 14.40500545 -16.5228787 0.032757034 1.775434252 0.374099847 0.789408128 0.030499074 321.7541697 0.845098256 28.5134116 11.32913438 3.00E-17 16.5228787 -1.401334405 LVEQANS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 LVEQANSPK 9 0 O95391 O95391 SLU7 Pre-mRNA-splicing factor SLU7 1 0 LVEQANS(1)PK;LVEQANS(1)PK ; 155.33 0.0045422 586180000 14605.2 14854.2 15117.3 11355.2 18679.4 21236 21552 16109.9 16354.6 15125 TRUE FALSE FALSE 14427.1862 15063.31782 15380.41027 12668.14165 17726.12052 19879.08814 23382.62634 16576.01454 14891.80362 14732.05032 0.979306063 1.022486177 1.044010164 0.859903501 1.203235132 1.349376883 1.587194303 1.125166842 1.010843928 1 13.84667061 -8.510789966 3.525171458 0.989179327 1.372085312 0.675602944 0.114882724 0.08826709 2.320493187 0.014950425 0.033615499 3.08E-09 8.510789966 0.382905985 LVESANEK(ac)AER ddPTM_HeLa_Romidepsin_16h_R1 2 LVESANEKAER 11 1 O14686-3;O14686 O14686-3 KMT2D Histone-lysine N-methyltransferase 2D 0 1 ; LVESANEK(1)AER;LVESANEK(1)AER 135.8 1.59E-09 13953000 2395.21 2327.67 2072.17 2078.05 4486.6 4636 4595.7 4056.9 2379 2194.22 FALSE TRUE FALSE 2366.016259 2360.438999 2108.23525 2318.323919 4257.63206 4339.774562 4986.058643 4174.280001 2166.216282 2137.213848 1.107056396 1.104446802 0.986440946 1.084741202 1.99214134 2.030575726 2.332971335 1.953141004 1.013570207 1 11.06151555 -8.73957556 4.388331498 1.050228921 2.109636517 0.963596891 0.09805057 0.024934628 1.111087697 0.014075203 0.027969967 1.82E-09 8.73957556 1.059407596 LVEVDSGR ddPTM_HeLa_Romidepsin_16h_R1 1 LVEVDSGR 8 0 P20700;E9PBF6;A0A0D9SFE5 P20700 LMNB1 Lamin-B1 0 0 113.41 0.0012443 0 2953.4 2774.7 2518.9 2374.2 2451.9 2362 2238.6 2438.1 2687.3 3032.6 FALSE FALSE TRUE 2917.402825 2813.762299 2562.740398 2648.716175 2326.770394 2211.075823 2428.746628 2508.642577 2446.941158 2953.812615 0.987673629 0.952586594 0.867604257 0.89671097 0.787717671 0.748549794 0.822241267 0.849289682 0.828400944 1 11.52836259 -9.544287764 1.035886366 0.996668262 0.80197246 0.392912451 0.062372293 0.119238887 0.255587872 0.006095234 0.01071244 2.86E-10 9.544287764 -0.194695802 LVFLGLDNAGK ddPTM_HeLa_Romidepsin_16h_R1 1 LVFLGLDNAGK 11 0 D6RD69;Q9Y6B6;X1WI22;D6RAA2;Q5SQT8;D6RDB2;Q9NR31 D6RD69 SAR1B;SAR1A GTP-binding protein SAR1b;GTP-binding protein SAR1a 0 0 135.43 0.0095166 324480 202.18 141.53 166.35 56.03 140.86 245.12 132.7 174.22 170.84 148.59 FALSE FALSE TRUE 199.7157524 143.5224631 169.245252 62.50845223 133.6713886 229.4576231 143.9715347 179.2607808 155.5596425 144.7296104 1.379923237 0.991659293 1.16938926 0.431898159 0.923593923 1.585422793 0.994762124 1.238590917 1.074829415 1 7.177216304 LVGATATSS(ph)PPPK ddPTM_HeLa_Romidepsin_16h_R1 3 LVGATATSSPPPK 13 0 H9KVD1;Q96QD9-4;Q96QD9 H9KVD1 FYTTD1 UAP56-interacting factor 1 0 LVGAT(0.001)AT(0.011)S(0.054)S(0.935)PPPK;LVGATAT(0.007)S(0.111)S(0.882)PPPK;LVGATAT(0.004)S(0.023)S(0.973)PPPK ;; 156.69 0.0006391 83913400 10790.8 12923.7 10705.6 11146.7 13592.4 12551.6 10446.7 11657.4 13113.2 12018.1 TRUE FALSE FALSE 10659.27758 13105.64019 10891.92648 12435.5339 12898.72911 11749.59327 11334.04244 11994.68848 11940.32255 11705.86803 0.910592666 1.119578672 0.930467219 1.062333342 1.10190283 1.003735326 0.968235966 1.024673134 1.020028803 1 13.5149443 -10.28887684 24.99110758 0.957779873 1.026902105 0.115621924 0.060528183 813.8813784 741312.4626 0.010313325 0.011795436 5.14E-11 10.28887684 0.069122232 LVHDS(ph)LEDLQMTR ddPTM_HeLa_Romidepsin_16h_R1 2 LVHDSLEDLQMTR 13 0 A0A087WYY3;A0A2R8Y635;A0A2R8YDN7;Q9H7F0-2;Q9H7F0 A0A087WYY3 ATP13A3 Probable cation-transporting ATPase 13A3 1 0 LVHDS(1)LEDLQMTR;LVHDS(0.997)LEDLQMT(0.003)R ; 123.95 0.005522 10055300 2953.81 3837.9 3562.7 2431.15 2835.17 4002.9 2486.98 3702.9 3510.6 3760.1 TRUE FALSE FALSE 2917.807828 3891.930057 3624.707299 2712.251002 2690.480695 3747.127609 2698.224019 3810.037569 3196.603144 3662.41206 0.796690208 1.062668535 0.989704938 0.74056413 0.734619877 1.023131081 0.736734145 1.040308274 0.872813624 1 11.8385784 -9.285863958 24.87405571 0.92182301 0.851142052 0.101753329 0.123642776 1703.407579 1734749.49 0.02007083 0.030667624 5.18E-10 9.285863958 -0.070680958 LVIFDT(ph)MLEIK ddPTM_HeLa_Romidepsin_16h_R1 1 LVIFDTMLEIK 11 0 B4DUK8;Q9UGI9-2;Q9UGI9 B4DUK8 PRKAG3 5-AMP-activated protein kinase subunit gamma-3 1 0 LVIFDT(1)MLEIK 112.17 0.028024 28704000 1592.6 1525.5 1749.7 1656.7 1444.6 1989.9 1689.9 1662.1 1976.2 1571.7 TRUE FALSE FALSE 1573.188779 1546.976029 1780.152795 1848.255449 1370.876671 1862.751812 1833.440064 1710.190241 1799.443723 1530.867007 1.027645622 1.010522809 1.16283961 1.20732594 0.895490376 1.216795321 1.197648166 1.117138349 1.175440919 1 10.58013324 -9.416458827 0.412878923 0.997067663 1.172826318 0 0.105923252 1.284841361 0.445377373 0.035019922 0.090388293 3.83E-10 9.416458827 0.175758654 LVIGDHK ddPTM_HeLa_Romidepsin_16h_R1 1 LVIGDHK 7 0 E9PM92;O00193;E9PRZ9 E9PM92 C11orf58;SMAP Small acidic protein 0 0 100.45 0.01634 3853600 2617.1 3133.3 3397.9 3021.1 2577.2 3208.3 3807.6 1212.5 4031.5 3375.7 FALSE FALSE TRUE 2585.201779 3177.41068 3457.039024 3370.413797 2445.675867 3003.299984 4131.017449 1247.581774 3670.912543 3287.998827 0.786253863 0.966366123 1.05141127 1.025065389 0.74381896 0.91341273 1.256392616 0.379434982 1.116457984 1 11.68299407 -7.237364758 24.81707494 0.928700751 0.379434268 0.56917028 0.151058651 3902.0819 4022359.767 0.019991354 1.713873 5.79E-08 7.237364758 -0.549266482 LVIIEGDLERTEER ddPTM_HeLa_Romidepsin_16h_R1 2 LVIIEGDLERTEER 14 1 J3KN67;A0A2R2Y2Q3;P06753;A0A494C0P6;P06753-7;P06753-4;P06753-3;P06753-6;P06753-5;P06753-2;A0A087WWU8 J3KN67;P06753-4 TPM3 Tropomyosin alpha-3 chain 0 0 ; ; 115.92 0.0053583 6153400 5883.5 6230.4 6150.7 6561.8 6413.6 6763.2 5645.6 6380.3 6403.1 6429.6 FALSE FALSE TRUE 5811.789639 6318.111735 6257.750353 7320.50619 6086.29006 6331.053347 6125.137123 6564.903914 5830.390699 6262.558065 0.928021677 1.008870763 0.999232309 1.168932266 0.971853673 1.010937269 0.97805674 1.048278331 0.930991879 1 12.61253636 -9.949380425 3.057339175 0.966121691 1.030063913 0.261916973 0.055730486 0.30276807 5.799700053 0.009505284 0.012537998 1.12E-10 9.949380425 0.063942222 LVIITAGAR ddPTM_HeLa_Romidepsin_16h_R1 2 LVIITAGAR 9 0 P00338;P00338-3;P00338-5;P00338-2;F5GYU2;F5GXY2;F5GXH2 P00338 LDHA L-lactate dehydrogenase A chain 0 0 ; ; 131.03 0.014276 3315500 465.39 432.07 2611.1 549.48 900.33 1601.57 998.6 452.19 493.088 427.69 FALSE FALSE TRUE 459.7176477 438.1526928 2656.5451 613.013463 854.3828005 1499.234846 1083.421059 465.2734042 448.9849743 416.5785521 1.103555729 1.05178889 6.377056828 1.471543506 2.050952446 3.598924712 2.600760537 1.116892365 1.077791864 1 8.702444753 LVINGNPITIFQER ddPTM_HeLa_Romidepsin_16h_R1 4 LVINGNPITIFQER 14 0 P04406;P04406-2 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ;;; ;;; 238.01 3.30E-42 47097300 3987.14 4168.97 4118.73 3138.71 4644.09 4063.16 3625.3 4239.84 3947.59 4123.03 FALSE FALSE TRUE 3938.543204 4227.660869 4190.414768 3501.622418 4407.084758 3803.537189 3933.232892 4362.513081 3594.507663 4015.913086 0.980734174 1.052727183 1.043452554 0.871936803 1.097405413 0.947116411 0.979411857 1.086306647 0.8950661 1 11.97151233 -7.255564074 23.62394969 0.994033402 1.086306737 0.162129761 0.066259004 362.2348994 1456408.195 0.007135234 0.083595675 5.55E-08 7.255564074 0.092273335 LVINGNPITIFQERDPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 LVINGNPIT(0.015)IFQERDPS(0.985)K;LVINGNPITIFQERDPS(1)K ; 115.39 0.00052801 59505000 6191.7 6453.5 6168.9 5233.9 6048 6609.5 5525.5 6894.8 6605.7 6379.1 TRUE FALSE FALSE 6116.233179 6544.352542 6276.267117 5839.068144 5739.347992 6187.174281 5994.835832 7094.29016 6014.869648 6213.370062 0.984366474 1.053269398 1.010122857 0.939758631 0.923709345 0.995783966 0.96482839 1.141778148 0.968052697 1 12.60116027 -7.256024789 24.84323538 0.988394307 1.141778219 0.64533122 0.035220929 274.1171886 1257662.524 0.00492391 0.056667822 5.55E-08 7.256024789 0.153383911 LVINGNPITIFQERDPS(ph)KIK ddPTM_HeLa_Romidepsin_16h_R1 1 LVINGNPITIFQERDPSKIK 20 2 P04406;P04406-2 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 LVINGNPITIFQERDPS(1)KIK 98.002 0.00077619 148010000 1912.6 1909.9 1890 2041.3 2048.4 2061.7 1670.2 2100.9 1960.9 1754 TRUE FALSE FALSE 1889.288496 1936.787622 1922.894657 2277.324711 1943.862504 1929.964024 1812.066746 2161.686227 1785.512193 1708.430827 1.105861862 1.133664642 1.125532639 1.33299205 1.1378058 1.129670569 1.060661466 1.265305093 1.045118225 1 10.73845612 -11.11140637 0.611407705 1.007040065 1.172517697 0.387020588 0.073848613 0.490615608 0.413611026 0.034374644 0.020561379 7.74E-12 11.11140637 0.165477632 LVINGNPITIFQERDPSK ddPTM_HeLa_Romidepsin_16h_R1 2 LVINGNPITIFQERDPSK 18 1 P04406;P04406-2 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ; ; 112.57 0.0015302 56256000 4061.4 3685.7 3201.8 4292.7 4273.2 3876.1 3386.6 3493.4 4292.8 3800 FALSE FALSE TRUE 4011.898095 3737.587381 3257.525986 4789.042172 4055.122658 3628.42972 3674.257719 3594.476017 3908.841216 3701.275452 1.083923136 1.009810653 0.88010904 1.293889697 1.095601425 0.980318749 0.992700426 0.971145235 1.056079524 1 11.85380679 -8.228970491 21.94502394 1.048704967 0.982519252 0.111494508 0.098059641 310.9637961 210170.6145 0.013889642 0.035404163 5.90E-09 8.228970491 -0.066185715 LVLAES(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 1 LVLAESPQPK 10 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 0 LVLAES(1)PQPK 160.18 0.0024561 29149000 5769.4 5395.5 5606 4505.9 3657.5 3128.2 3151.8 3168 5650.1 4939.3 TRUE FALSE FALSE 5699.080334 5471.457991 5703.570078 5026.893359 3470.844127 2928.318116 3419.513813 3259.661082 5144.740905 4810.976274 1.184599551 1.137286422 1.18553278 1.044880098 0.721442786 0.608674404 0.710773369 0.677546697 1.069375655 1 12.23211397 -8.763912072 3.81348724 1.101241236 0.669188696 0.93105268 0.056864218 0.055358591 1.756202117 0.011776766 0.023319401 1.72E-09 8.763912072 -0.43205254 LVLLTA ddPTM_HeLa_Romidepsin_16h_R1 2 LVLLTA 6 0 I3L0R3 I3L0R3 FLYWCH1 0 0 ; ; 57.986 0.022077 4272600 1485.5 1457.36 1385.02 1097.64 1423.29 1495.4 1221.05 1042.82 1596.12 1277.01 FALSE FALSE TRUE 1467.394155 1477.876752 1409.125692 1224.554301 1350.6542 1399.848766 1324.765957 1072.992351 1453.35903 1243.833096 1.179735576 1.188163233 1.132889691 0.984500497 1.085880577 1.125431355 1.065067299 0.862649784 1.168451808 1 10.28057719 -9.271977185 24.2684956 1.099694599 1.035942652 0.239523068 0.086039948 964.0970266 2220306.75 0.01542476 0.023718013 5.35E-10 9.271977185 -0.063751947 LVLPSNT(ph)PNVR ddPTM_HeLa_Romidepsin_16h_R1 1 LVLPSNTPNVR 11 0 H0Y8J2;Q03188;H0Y9W1 H0Y8J2 CENPC Centromere protein C 1 0 LVLPS(0.208)NT(0.792)PNVR 116.74 0.023755 4646100 2594.4 2088.6 2166.4 1643.8 1979.2 1804.1 1976.6 1739.9 2844.1 2637.8 TRUE FALSE FALSE 2562.778455 2118.003366 2204.105283 1833.86389 1878.194039 1688.823832 2144.492355 1790.241261 2589.716573 2569.269576 0.997473554 0.824360116 0.857872332 0.713768578 0.731022566 0.657316713 0.834670046 0.696789966 1.007958292 1 11.32714255 -9.912421638 1.237470603 1.002463328 0.729850615 0.830888292 0.052061485 0.106230729 0.32174929 0.009147596 0.012756417 1.22E-10 9.912421638 -0.272612713 LVNHFVEEFK ddPTM_HeLa_Romidepsin_16h_R1 2 LVNHFVEEFK 10 0 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 0 ; ; 123.62 0.0046955 82522000 12119.6 11213 11075.3 9969.2 14872.7 17012.1 14690.1 15323.3 11403.4 10035.2 FALSE FALSE TRUE 11971.88165 11370.85691 11268.06095 11121.88581 14113.69062 15925.08171 15937.87673 15766.65551 10383.45134 9774.484057 1.224809574 1.163320421 1.152803655 1.137848887 1.443932031 1.629250365 1.630559386 1.613042225 1.062301732 1 13.25480484 -8.618038236 2.350342527 1.116578898 1.626397908 0.939737393 0.057824348 0.07266414 0.809837394 0.013168923 0.030245524 2.41E-09 8.618038236 0.50981901 LVNHFVEEFKR ddPTM_HeLa_Romidepsin_16h_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 0 ; ; 77.533 0.013102 22782000 13101.3 12112 13901.6 13026.9 18806.3 20972 18191.5 18200.8 12963.4 9693.5 FALSE FALSE TRUE 12941.61632 12282.51305 14143.55152 14533.13147 17846.54434 19631.95688 19736.68556 18727.41143 11803.92104 9441.661473 1.370692685 1.300884711 1.497993924 1.539255725 1.890191084 2.079290487 2.090382674 1.983486856 1.250195325 1 13.20482504 -8.828081627 0.327849197 1.029308944 2.416951485 0.899841098 0.115849319 0.5236182 0.08811418 0.059723649 0.267590145 1.49E-09 8.828081627 1.387642542 LVNTTIT(ph)PEPEPKPQPNSR ddPTM_HeLa_Romidepsin_16h_R1 2 LVNTTITPEPEPKPQPNSR 19 1 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 LVNT(0.034)T(0.195)IT(0.771)PEPEPKPQPNSR;LVNT(0.002)T(0.029)IT(0.969)PEPEPKPQPNSR ; 152.32 8.98E-06 80675000 5189.3 4798.9 4173.5 4558.7 5137.3 4737 4401.9 4694.3 5285.2 4851.2 TRUE FALSE FALSE 5126.050816 4866.45904 4246.138017 5085.798343 4875.124411 4434.320988 4775.797276 4830.122164 4812.478475 4725.165125 1.084840568 1.029902429 0.898622144 1.076321824 1.031736306 0.938447836 1.010715425 1.022212354 1.01847837 1 12.20614903 -9.980904232 24.99990015 1.04097456 0.996663076 0.110295635 0.050533296 381.2847684 499171.522 0.008705973 0.011441262 1.04E-10 9.980904232 -0.044311483 LVPGGGATEIELAK ddPTM_HeLa_Romidepsin_16h_R1 1 LVPGGGATEIELAK 14 0 P50990-2;P50990;P50990-3 P50990-2 CCT8 T-complex protein 1 subunit theta 0 0 148.28 8.98E-06 431120 154.76 0 53.514 0 172.4 171.1 141.28 254.19 136.54 52.237 FALSE FALSE TRUE 152.8737256 0 54.44538872 0 163.6017847 160.1672622 153.2803197 261.5445866 124.3275204 50.87987521 3.004601033 0 1.070077088 0 3.215451768 3.147949195 3.012592288 5.140432942 2.443550027 1 5.669023227 -12.57136804 1.26375592 0.978475471 2.310429151 0 1.569877048 1.02651261 2.859656838 1.212106107 0.26506811 2.68E-13 12.57136804 1.33195368 LVPS(ph)QEETK ddPTM_HeLa_Romidepsin_16h_R1 2 LVPSQEETK 9 0 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 LVPS(0.994)QEET(0.006)K;LVPS(0.996)QEET(0.004)K ; 126.03 0.010313 187546000 13087.9 13421.2 14025.7 8442.4 9902.3 9966 8293.9 8633.6 13488.1 13461.8 TRUE FALSE FALSE 12928.37964 13610.14401 14269.81142 9418.550011 9396.94868 9329.204764 8998.383659 8883.399594 12281.69055 13112.0605 0.985991458 1.03798667 1.088296643 0.71831197 0.716664531 0.711497996 0.686267705 0.677498369 0.936671285 1 13.6786068 -9.249134682 24.45034193 1.00374279 0.702508409 0.941986573 0.038170576 85.10241603 169104.718 0.005171492 0.008533395 5.63E-10 9.249134682 -0.301234381 LVPS(ph)QEETKLSVEESEAAGDGVDTK ddPTM_HeLa_Romidepsin_16h_R1 2 LVPSQEETKLSVEESEAAGDGVDTK 25 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 LVPS(0.45)QEET(0.45)KLS(0.084)VEES(0.015)EAAGDGVDTK;LVPS(0.546)QEET(0.437)KLS(0.017)VEES(0.001)EAAGDGVDTK ; 61.109 0.001748 113968000 8998.2 8056 7888.7 9401.1 5978 5819.5 5147.2 5432.7 8622.1 9047.9 TRUE FALSE FALSE 8888.526477 8169.412579 8025.999514 10488.09942 5672.920353 5447.652732 5584.40304 5589.886603 7850.917782 8812.834254 1.008588863 0.926990381 0.910717175 1.190093801 0.643711227 0.618149913 0.63366709 0.634289315 0.890850498 1 13.10539036 -8.739997317 24.609449 1.001577296 0.631518999 0.829670503 0.078745795 47.16192032 54128.25998 0.009478347 0.018941556 1.82E-09 8.739997317 -0.370058298 LVPSQEETKLS(ph)VEESEAAGDGVDTK ddPTM_HeLa_Romidepsin_16h_R1 1 LVPSQEETKLSVEESEAAGDGVDTK 25 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 LVPS(0.086)QEET(0.052)KLS(0.779)VEES(0.061)EAAGDGVDT(0.023)K 48.337 0.017417 18109000 2304.4 2838.2 2011.6 1862.2 2720 1968 1396.7 1700.3 2206.3 2346.4 TRUE FALSE FALSE 2276.313086 2878.156254 2046.611054 2077.516326 2581.18825 1842.251151 1515.335663 1749.495498 2008.963002 2285.44019 0.996006413 1.259344378 0.895499722 0.9090224 1.129405294 0.806081542 0.663038862 0.765496076 0.879026724 1 11.15825635 -8.074426452 5.07759536 1.010605189 0.717522679 0.55380117 0.110852749 0.101022169 4.742366833 0.013837292 0.037114948 8.43E-09 8.074426452 -0.29308251 LVPVGYGIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LVPVGYGIKK 10 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 1 LVPVGYGIK(1)K 159.04 0.0036283 1825100 806.34 572.39 1949.2 1415.5 1826.6 1621.2 1131.8 560.56 647.6 222.27 FALSE TRUE FALSE 796.5120179 580.4481214 1983.125008 1579.16677 1733.381786 1517.610552 1227.935064 576.7789192 589.6770341 216.4953934 3.679117627 2.681110727 9.160125662 7.294228046 8.006552745 7.009897664 5.671876176 2.66416255 2.723739406 1 7.758192517 -10.36964419 1.073395423 1.851059267 6.573374401 0.472741437 1.919210554 0.271475422 0.618154915 0.436805575 0.492603691 4.27E-11 10.36964419 4.722315134 LVPVS(ph)PLPPK ddPTM_HeLa_Romidepsin_16h_R1 1 LVPVSPLPPK 10 0 O95396 O95396 MOCS3 Adenylyltransferase and sulfurtransferase MOCS3;Molybdopterin-synthase adenylyltransferase;Molybdopterin-synthase sulfurtransferase 1 0 LVPVS(1)PLPPK 103.91 0.021984 31251000 5368.8 5510.5 5032.8 4941.8 5654.7 6529.5 5052.2 6191.3 5354.8 5504.4 TRUE FALSE FALSE 5303.363001 5588.076964 5120.393773 5513.194168 5366.119558 6112.286023 5481.333742 6370.435497 4875.853277 5361.394894 0.989175971 1.042280428 0.955048802 1.028313392 1.000881238 1.14005518 1.022370829 1.188204865 0.909437445 1 12.38839269 -4 0.456970937 0.994312077 5.153993995 0.580153245 0.050549516 34.89311234 0.371015351 0.008038727 137.1353951 1.00E-04 4 4.159681919 LVQAEYWHDPIKEDVYR ddPTM_HeLa_Romidepsin_16h_R1 1 LVQAEYWHDPIKEDVYR 17 1 Q5T0S4;A0A286YFE3;A0A2C9F2P4;A0A286YFL8;A0A286YFF7;P50897-2;P50897 Q5T0S4 PPT1 Palmitoyl-protein thioesterase 1 0 0 99.069 0.0013976 16935000 1821.2 1557.9 1572.8 1800.7 1728 1695.3 1430.7 1925.3 1781.6 1549.1 FALSE FALSE TRUE 1799.002514 1579.832157 1600.173924 2008.905407 1639.813712 1586.975801 1552.223622 1981.005518 1622.249234 1508.854159 1.19229715 1.047040993 1.060522593 1.331411253 1.086794043 1.051775476 1.028743311 1.312920474 1.075153105 1 10.55923765 -12.47988821 1.143093988 0.997741214 1.137683365 0.113914776 0.105863645 0.666394006 1.516656778 0.076015344 0.017414767 3.31E-13 12.47988821 0.139942151 LVQAFQFTDK ddPTM_HeLa_Romidepsin_16h_R1 1 LVQAFQFTDK 10 0 Q06830;A0A0A0MSI0;A0A0A0MRQ5 Q06830 PRDX1 Peroxiredoxin-1 0 0 142.83 0.018461 665370 454.44 399.97 369.93 278.11 376.08 503.98 355.87 351.08 325.81 344.54 FALSE FALSE TRUE 448.9011105 405.6007882 376.3684765 310.2663867 356.8872343 471.7773045 386.0975889 361.2379459 296.6687376 335.5888011 1.337652237 1.208624325 1.121516794 0.924543327 1.063465864 1.405819571 1.150507966 1.076430276 0.884024546 1 8.390550762 -12.69749031 1.595187321 1.000396504 1.187772002 0.247155007 0.137507915 0.537173155 2.473010424 0.104123482 0.023231196 2.01E-13 12.69749031 0.187375499 LVQGSILKK ddPTM_HeLa_Romidepsin_16h_R1 1 LVQGSILKK 9 1 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 0 79.148 0.022044 0 188.35 193.2 154.55 282.22 200.74 245.66 0 128.37 263.42 139.13 FALSE FALSE TRUE 186.0543178 195.9198747 157.2398779 314.8516043 190.4954887 229.9631188 0 132.0841834 239.8590555 135.5153825 1.372938734 1.445739008 1.16031018 2.323364318 1.405711183 1.696952143 0 0.974680372 1.769976596 1 7.082312813 -7.766219561 24.99999487 1.324004508 0.487340166 0.415615446 0.443550237 84.90944454 444081.3616 0.06103786 0.192112334 1.71E-08 7.766219561 -0.836664342 LVS(ph)PEQPPK ddPTM_HeLa_Romidepsin_16h_R1 1 LVSPEQPPK 9 0 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3 O43491 EPB41L2 Band 4.1-like protein 2 1 0 LVS(1)PEQPPK 99.343 0.028937 15848000 5754.1 5349 4754.8 5714.2 7357.4 7567.6 6227.7 6405 5817.3 5999.8 TRUE FALSE FALSE 5683.966816 5424.303362 4837.555299 6374.90269 6981.924424 7084.054783 6756.680683 6590.31857 5296.986118 5843.924331 0.972628408 0.928195345 0.827792255 1.090859896 1.194732175 1.212208506 1.156188941 1.127721407 0.906409087 1 12.51272178 -9.021189456 7.654661821 0.969952399 1.170817293 0.803166538 0.055920299 0.072138315 20.39194563 0.008481395 0.014496218 9.52E-10 9.021189456 0.200864894 LVS(ph)PETEASEESLQFNLEKPATGER ddPTM_HeLa_Romidepsin_16h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 LVS(0.833)PET(0.126)EAS(0.033)EES(0.008)LQFNLEKPATGER 76 0.00012958 11662000 896.43 943.06 921 722.25 743.59 888.12 731.67 915.32 1280.5 1107.8 TRUE FALSE FALSE 885.5039664 956.3364234 937.0296187 805.7599433 705.6418276 831.3719983 793.8180315 941.8033401 1165.968873 1079.019196 0.82065636 0.886301585 0.868408664 0.746752186 0.653965963 0.770488608 0.735684809 0.872832794 1.080582141 1 10.07550482 -12.10688578 0.293293101 1.089952039 0.748559828 0.675285035 0.069035751 1.878810001 0.23902135 0.225358729 0.044691174 7.82E-13 12.10688578 -0.341392211 LVS(ph)PGSANETSSILVESVTR ddPTM_HeLa_Romidepsin_16h_R1 4 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 0 LVS(0.991)PGS(0.009)ANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR;LVS(0.998)PGS(0.002)ANETSSILVESVTR;LVS(1)PGSANETSSILVESVTR ;;; 239.13 2.77E-57 116128000 7146.9 5815.83 6084.9 8616.37 6858.2 7008.7 6317.38 6728.4 6963.02 6518.5 TRUE FALSE FALSE 7059.790834 5897.705407 6190.805132 9612.635241 6508.200463 6560.86669 6853.9781 6923.075638 6340.230052 6349.14843 1.1119272 0.928897075 0.975060703 1.514003861 1.025050924 1.03334593 1.079511398 1.09039436 0.998595343 1 12.63234739 -13.29659608 0.34087211 0.911418464 1.106708064 0.065992325 0.150146236 16.03662449 1.393691237 1.285145831 0.060264911 5.05E-14 13.29659608 0.1952896 LVSEK(ac)LASYQAAR ddPTM_HeLa_Romidepsin_16h_R1 2 LVSEKLASYQAAR 13 1 H0YBG3;A0A0B4J1R1;H0YBT0;A0A087WUS5;P01106;P01106-2;A0A494C1T8 H0YBG3 MYC Myc proto-oncogene protein 0 1 ; LVSEK(1)LASYQAAR;LVSEK(1)LASYQAAR 250.51 4.99E-53 30506000 1537.75 1065.81 1346.07 1492.78 653.58 425.56 260.768 408.89 1095.59 918.86 FALSE TRUE FALSE 1519.007312 1080.814501 1369.497784 1665.382247 620.2253738 398.3680894 282.9176274 420.720587 997.5976864 894.9878847 1.697237848 1.207630315 1.530185835 1.860787476 0.692998625 0.445110036 0.31611336 0.470085232 1.114649375 1 9.805724343 -8.58782951 6.071540165 1.375950225 0.426323883 0.771674672 0.24846917 0.087852103 6.070748623 0.04516869 0.091421677 2.58E-09 8.58782951 -0.949626342 LVSFHDDS(ph)DEDLLHI ddPTM_HeLa_Romidepsin_16h_R1 5 LVSFHDDSDEDLLHI 15 0 P11717 P11717 IGF2R Cation-independent mannose-6-phosphate receptor 1 0 LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI;LVSFHDDS(1)DEDLLHI ;;;; 138.01 0.00043824 28085500 4721.23 4865.43 4211.95 3981.38 8116.89 10055.24 5790.6 8764.68 6742.19 5413.26 TRUE FALSE FALSE 4663.685833 4933.925651 4285.257223 4441.725889 7702.654815 9412.742616 6282.453419 9018.272187 6139.15164 5272.622725 0.884509679 0.935763074 0.812737312 0.842412993 1.460877293 1.785210721 1.191523412 1.71039588 1.16434495 1 12.36430506 -8.714382497 6.041658558 0.925847931 1.536781639 0.741716985 0.172723597 0.06212584 5.24719318 0.021117723 0.04217887 1.93E-09 8.714382497 0.610933708 LVSPET(ph)EASEESLQFNLEKPATGER ddPTM_HeLa_Romidepsin_16h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 LVS(0.27)PET(0.442)EAS(0.275)EES(0.012)LQFNLEKPATGER 119.29 6.19E-07 18559000 1802.5 1778.3 1965.9 1504.4 1460.9 1256.3 1124.7 1390.8 1799.3 1783.2 TRUE FALSE FALSE 1780.530437 1803.334954 2000.115665 1678.345806 1386.344822 1176.026485 1220.23199 1431.040604 1638.366102 1736.872207 1.025136121 1.038265767 1.151561788 0.966303566 0.7981847 0.677094423 0.702545636 0.823918189 0.943285347 1 10.76227589 -8.746290964 3.162287431 1.025178927 0.732658709 0.830488595 0.060728622 0.064829252 1.340023956 0.008283609 0.016894488 1.79E-09 8.746290964 -0.292520218 LVSPETEAS(ph)EESLQFNLEKPATGER ddPTM_HeLa_Romidepsin_16h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 LVSPET(0.006)EAS(0.955)EES(0.039)LQFNLEKPATGER 128.75 5.77E-07 34903000 1566 1321.1 1533.9 1730.1 1495.6 1309.2 1544.3 1713.7 1806.2 1646.1 TRUE FALSE FALSE 1546.91299 1339.69848 1560.596886 1930.142302 1419.273951 1225.546345 1675.472803 1763.283206 1644.648948 1603.334085 0.964810144 0.835570386 0.973344795 1.203830394 0.885201634 0.764373662 1.044992943 1.09976032 1.025768094 1 10.64685935 -7.534115461 24.99550613 0.966566538 1.086068614 0.148614015 0.112167486 269.3302912 599113.0053 0.015230884 0.057084659 2.92E-08 7.534115461 0.119502077 LVSPETEASEES(ph)LQFNLEKPATGER ddPTM_HeLa_Romidepsin_16h_R1 1 LVSPETEASEESLQFNLEKPATGER 25 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 LVSPET(0.001)EAS(0.087)EES(0.912)LQFNLEKPATGER 77.1 9.37E-05 4555400 791.56 832.44 957.51 866.09 687.77 862.96 706.93 922.65 691.26 616.31 TRUE FALSE FALSE 781.9121623 844.1591122 974.1750599 966.2314009 652.6705305 807.8196411 766.9766166 949.345422 629.4319743 600.2981774 1.302539624 1.406233009 1.62281862 1.609585765 1.087243898 1.345697308 1.277659412 1.581456446 1.04853221 1 9.229535477 -11.48040068 0.754460003 1.020811848 1.407986203 0.482112243 0.158274965 0.402369933 0.475895242 0.076280511 0.037456267 3.31E-12 11.48040068 0.387174355 LVSPGS(ph)ANETSSILVESVTR ddPTM_HeLa_Romidepsin_16h_R1 2 LVSPGSANETSSILVESVTR 20 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 0 LVSPGS(1)ANETSSILVESVTR;LVSPGS(1)ANETSSILVESVTR ; 191.61 1.16E-17 27140000 3401.7 3306.4 3259.9 3410.1 4071.6 5239.9 4066.6 4776.9 3805.6 3416.7 TRUE FALSE FALSE 3360.238772 3352.947586 3316.637192 3804.391807 3863.811059 4905.087301 4412.016902 4915.112065 3465.217605 3327.933641 1.009707264 1.007516359 0.996605567 1.143169371 1.161024069 1.473913794 1.325752668 1.476926103 1.041252013 1 11.70041095 -8.570878484 1.368215087 1.004396108 1.431171184 0.907604052 0.055954015 0.073690545 0.269276693 0.007410247 0.02221591 2.69E-09 8.570878484 0.426775077 LVSS(ph)DPEINTK ddPTM_HeLa_Romidepsin_16h_R1 1 LVSSDPEINTK 11 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 1 0 LVS(0.07)S(0.93)DPEINTK 180.24 9.75E-06 4348000 3556 3254.8 3122 2594.5 3151.4 2773.7 2490.2 2616.8 3167.9 3754 TRUE FALSE FALSE 3512.658104 3300.62116 3176.3371 2894.488297 2990.572299 2596.469522 2701.717526 2692.512979 2884.55509 3656.470539 0.960669057 0.902679544 0.868689373 0.791607171 0.81788497 0.710102678 0.738886721 0.73636939 0.78889056 1 11.83623602 -9.436635609 0.634273037 0.992629353 0.718788832 0.480863891 0.067391141 0.087980331 0.070450648 0.00461034 0.01045042 3.66E-10 9.436635609 -0.273840521 LVSVQEDAGKS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 LVSVQEDAGKSPAR 14 1 E9PDH4;Q9Y2I7-2;Q9Y2I7-3;Q9Y2I7-4;Q9Y2I7 E9PDH4 PIKFYVE 1-phosphatidylinositol 3-phosphate 5-kinase 1 0 LVSVQEDAGKS(1)PAR 65.298 0.025763 13326000 2919.7 3345.7 3047.9 3299.8 3885.1 4335.4 3479.7 4196.2 3240.7 2687.4 TRUE FALSE FALSE 2884.113573 3392.800852 3100.947421 3681.338402 3686.82885 4058.381932 3775.265631 4317.610426 2950.843676 2617.580961 1.101824019 1.296158898 1.184661513 1.406389509 1.408487036 1.550432248 1.442272727 1.649465859 1.127317061 1 11.35401844 -9.18061145 0.412372978 0.999529801 1.654529173 0.86785069 0.072503936 0.256229297 0.080024759 0.020967384 0.068294926 6.60E-10 9.18061145 0.654999373 LVTSGAESGNLNT(ph)SPSSNQTR ddPTM_HeLa_Romidepsin_16h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 0 LVTSGAESGNLNT(0.497)S(0.497)PS(0.005)S(0.001)NQTR 185.66 1.43E-13 13050000 1525.2 1528 1485 1726.8 1820.6 1431.2 1012.1 1256.7 1868.7 1617.7 TRUE FALSE FALSE 1506.610276 1549.511224 1510.845802 1926.460741 1727.687988 1339.750939 1098.067749 1293.060632 1701.558792 1575.671921 0.956170035 0.983397117 0.958858111 1.222628084 1.09647698 0.850272777 0.696888568 0.820640779 1.079894088 1 10.62175146 -8.046898419 5.199462483 1.002691958 0.760568487 0.63076697 0.086874328 0.103442021 6.55305183 0.012613282 0.034346505 8.98E-09 8.046898419 -0.242123472 LVTSGAESGNLNTS(ph)PSSNQTR ddPTM_HeLa_Romidepsin_16h_R1 2 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 0 LVTSGAESGNLNT(0.211)S(0.782)PS(0.007)S(0.001)NQTR;LVTSGAESGNLNT(0.21)S(0.699)PS(0.088)S(0.004)NQTR ; 200.94 4.62E-24 102089000 5824.2 5140.7 5338.8 4950.2 5934.2 4765.3 4212.3 4774.3 6161.1 5070.6 TRUE FALSE FALSE 5753.21241 5213.07091 5431.719574 5522.565415 5631.35563 4460.812709 4570.092657 4912.436838 5610.035785 4938.865081 1.164885518 1.055520008 1.099791042 1.118185114 1.140212486 0.903206027 0.925332558 0.994648924 1.135895736 1 12.26996384 -8.257220078 24.99415361 1.086203105 0.939489503 0.671922968 0.050711617 226.9855686 1344601.526 0.00948691 0.023259501 5.53E-09 8.257220078 -0.146713602 LVTSGAESGNLNTSPS(ph)SNQTR ddPTM_HeLa_Romidepsin_16h_R1 1 LVTSGAESGNLNTSPSSNQTR 21 0 Q8NHV4-2;Q8NHV4;Q8NHV4-3 Q8NHV4-2 NEDD1 Protein NEDD1 1 0 LVTSGAESGNLNT(0.006)S(0.006)PS(0.765)S(0.223)NQTR 329.64 6.33E-194 14035000 2169.2 2160.8 2311.1 2202.3 2041.5 2069.1 2126.4 1894.6 2369.3 2199.6 TRUE FALSE FALSE 2142.760956 2191.219799 2351.323726 2456.940288 1937.314637 1936.891188 2307.016363 1949.417262 2157.383874 2142.454075 1.000143238 1.022761619 1.097490842 1.146787843 0.904250252 0.904052605 1.076810182 0.909899206 1.00696855 1 11.06504856 -7.229342015 22.73014035 1.008906354 0.909898606 0.153669341 0.073327005 6042.479325 4278812.691 0.01005266 1.562957962 5.90E-08 7.229342015 -0.099007749 LVVLGIRPIR ddPTM_HeLa_Romidepsin_16h_R1 1 LVVLGIRPIR 10 1 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 0 0 97.431 0.0030656 0 159.82 231.56 446.67 282.37 294.22 456.49 254.79 294.4 242.29 231.7 FALSE FALSE TRUE 157.8720524 234.8199078 454.444104 315.018948 279.2048555 427.3217623 276.4318562 302.9179995 220.6189756 225.6804006 0.699538161 1.040497567 2.013662253 1.39586312 1.237169266 1.893481938 1.224881981 1.342243273 0.977572598 1 7.818137322 -9.983368835 24.51948573 0.85874168 1.505311079 0.5618407 0.256442678 98.46898795 145173.2226 0.041021279 0.053904343 1.04E-10 9.983368835 0.646569399 LVVSSPT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 LVVSSPTSPK 10 0 Q9Y4G2 Q9Y4G2 PLEKHM1 Pleckstrin homology domain-containing family M member 1 1 0 LVVS(0.011)S(0.268)PT(0.453)S(0.268)PK 121.5 0.022533 11284000 4359.6 4518.9 3768 3792.6 5153.4 4954.2 4275.8 5125.2 4059 4162.3 TRUE FALSE FALSE 4306.463518 4582.517193 3833.580459 4231.118257 4890.402768 4637.642609 4638.986345 5273.489576 3695.952874 4054.162846 1.062232496 1.130323908 0.945591138 1.04364783 1.206266979 1.143921146 1.144252592 1.300759189 0.911643911 1 11.98518832 -4 0.298560785 1.01735553 3.228871145 0.628303691 0.069268103 23.08882001 0.295364512 0.023096497 27.60485093 1.00E-04 4 2.211515615 LVVVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 LVVVKK 6 1 Q9BW85 Q9BW85 CCDC94 Coiled-coil domain-containing protein 94 0 1 ; LVVVK(1)K;LVVVK(1)K 106.84 0.011406 8938600 12326.4 12413.4 11244.7 12164.2 11795.4 11139.8 10923.7 10855.2 14399.6 10683.3 FALSE TRUE FALSE 12176.1611 12588.15617 11440.40929 13570.68204 11193.43672 10428.00273 11851.55881 11169.27809 13111.66371 10405.74633 1.170138183 1.209731217 1.099431884 1.304152688 1.075697636 1.002138857 1.13894366 1.073375973 1.260040683 1 13.34509282 -6.073847821 16.22517294 1.103171859 1.116765614 0 0.102288242 0 0 0.013357505 0 8.44E-07 6.073847821 0.013593755 LWAPDS(ph)PNR ddPTM_HeLa_Romidepsin_16h_R1 2 LWAPDSPNR 9 0 E5RIM3;Q9Y263 E5RIM3 PLAA Phospholipase A-2-activating protein 1 0 LWAPDS(1)PNR;LWAPDS(1)PNR ; 119.34 0.01385 10650000 3969.4 3171.6 4285.1 2472.39 3978.1 4248.7 3222 3858.1 4226 3637.9 TRUE FALSE FALSE 3921.019426 3216.249868 4359.680368 2758.259365 3775.082713 3977.221782 3495.6766 3969.728036 3848.015976 3543.386834 1.106573911 0.907676756 1.23037099 0.778424568 1.065388254 1.122435108 0.986535415 1.120320254 1.085971179 1 11.79091326 LWHLDPDTEYEIR ddPTM_HeLa_Romidepsin_16h_R1 1 LWHLDPDTEYEIR 13 0 H0YDP9;Q5TG12;E9PGC5;Q15262;Q15262-2;Q15262-3;Q15262-4 H0YDP9 PTPRK Protein-tyrosine-phosphatase;Receptor-type tyrosine-protein phosphatase kappa 0 0 89.44 0.0025249 0 1095.3 750.68 885.51 1036 946.18 1024.8 803.86 937.2 1071.5 1003.5 FALSE FALSE TRUE 1081.950062 761.2480927 900.9219301 1155.787195 897.8929039 959.3185874 872.1398483 964.3164033 975.6623564 977.4289253 1.10693477 0.778827056 0.921726283 1.182476971 0.91862731 0.981471453 0.892279557 0.98658468 0.998192637 1 9.932847989 LWSVHGQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 4 LWSVHGQKR 9 1 A0A5F9ZI22;A0A5F9ZH29;A0A5K1VW85;O75419-2;O75419;O75419-3 A0A5F9ZI22 CDC45 Cell division control protein 45 homolog 0 1 ;;; LWSVHGQK(1)R;LWSVHGQK(1)R;LWSVHGQK(1)R;LWSVHGQK(1)R 113.41 0.0015901 197781100 69.537 0 0 0 0 64.34 92.878 114.36 0 62.83 FALSE TRUE FALSE 68.6894563 0 0 0 0 60.22888165 100.767055 117.6688262 0 61.19766754 1.122419515 0 0 0 0 0.984169562 1.646583261 1.922766519 0 1 5.935404763 LY(ph)DLTTLCEET(ph)EDK ddPTM_HeLa_Romidepsin_16h_R1 1 LYDLTTLCEETEDK 14 0 Q3B7T1-4;Q3B7T1-3;Q3B7T1-5;Q3B7T1 Q3B7T1-4 EDRF1 Erythroid differentiation-related factor 1 2 0 LY(0.99)DLT(0.01)T(0.184)LCEET(0.817)EDK 84.169 0.0018315 0 380.47 407.33 468.65 394.94 1251.7 3127.1 2634.3 3058.8 2902 3145.5 TRUE FALSE FALSE 375.8326853 413.0644024 476.8066567 440.604821 1187.821078 2927.288402 2858.057376 3147.301552 2642.437852 3063.779457 0.122669628 0.134821846 0.155626951 0.14381088 0.387697971 0.955450105 0.932853496 1.027261132 0.862476523 1 11.58109673 -6.223699861 19.69863533 0.548920026 0.708398241 0 0.392584356 0 0 0.061842554 0 5.97E-07 6.223699861 0.159478215 LY(ph)SS(ph)GSS(ph)T(ph)PTGLAGGSR ddPTM_HeLa_Romidepsin_16h_R1 1 LYSSGSSTPTGLAGGSR 17 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 4 0 LY(0.948)S(0.087)S(0.547)GS(0.547)S(0.807)T(0.717)PT(0.269)GLAGGS(0.079)R 46.796 0.0043219 0 526.45 358.98 389.54 435.13 631.78 634.16 476 435.66 622.78 512.72 TRUE FALSE FALSE 520.0334249 364.0337299 396.3197803 485.4417779 599.5379091 593.6392227 516.4314281 448.2651347 567.076997 499.3994605 1.041317554 0.728942978 0.793592728 0.972051066 1.200517735 1.188706175 1.034104898 0.897608368 1.135517841 1 8.964050452 -8.877766836 24.66985276 0.973954299 1.08490513 0.172480067 0.136266475 10.5009751 2186.07652 0.020969922 0.038011214 1.33E-09 8.877766836 0.11095083 LY(ph)VEPY(ph)AAAVVAQDEKPWASLSPPSGGR ddPTM_HeLa_Romidepsin_16h_R1 1 LYVEPYAAAVVAQDEKPWASLSPPSGGR 28 1 H3BM45;A0A590UK59 H3BM45 ANKFN1 2 0 LY(0.999)VEPY(0.998)AAAVVAQDEKPWAS(0.001)LS(0.001)PPS(0.001)GGR 41.423 0.0040976 0 0 0 0 248.07 117.1 185.03 140.54 0 178.49 182.82 TRUE FALSE FALSE 0 0 0 276.7530206 111.12395 173.2071802 152.4774641 0 162.5254074 178.07031 0 0 0 1.55417835 0.624045356 0.972689833 0.856276737 0 0.912703568 1 7.476303183 -7.242197816 24.99996772 0.569541403 8.65E-05 0.113532325 0.499340921 9783.656625 12711426.45 0.077367148 3.862284821 5.73E-08 7.242197816 -0.569454915 LYATMEK(ac)HK ddPTM_HeLa_Romidepsin_16h_R1 1 LYATMEKHK 9 1 A0A669KB12;Q09472;Q92793-2;Q92793 A0A669KB12;Q92793-2 EP300;CREBBP Histone acetyltransferase p300;CREB-binding protein 0 1 LYATMEK(1)HK 63.184 0.022495 711400 0 0 223.02 0 0 72.6 67.261 0 0 0 FALSE TRUE FALSE 0 0 226.9015695 0 0 67.96109431 72.97414766 0 0 0 0 LYAVFTDYEHDK ddPTM_HeLa_Romidepsin_16h_R1 1 LYAVFTDYEHDK 12 0 Q8TCS8 Q8TCS8 PNPT1 "Polyribonucleotide nucleotidyltransferase 1, mitochondrial" 0 0 90.731 0.012847 6424400 3107.8 2300 2738.7 1706.7 3085.2 2968.8 2611.5 2839.7 3256.5 3025 FALSE FALSE TRUE 3069.920938 2332.37946 2786.365925 1904.036684 2927.750732 2779.103261 2833.320745 2921.862239 2965.230484 2946.410064 1.041919105 0.791600426 0.945681648 0.64622257 0.993667096 0.943216729 0.961617929 0.991668565 1.006387577 1 11.52474251 -10.29002917 24.77576397 1.01979514 0.896593482 0.227951613 0.101016998 654.0779128 566818.1338 0.016881894 0.019307143 5.13E-11 10.29002917 -0.123201658 LYDDIDFDIEEFAK ddPTM_HeLa_Romidepsin_16h_R1 1 LYDDIDFDIEEFAK 14 0 Q96KP4-2;Q96KP4 Q96KP4-2 CNDP2 Cytosolic non-specific dipeptidase 0 0 125.97 0.00027483 0 454.41 477.95 409.16 301.95 549.78 367.2 437.36 195.33 531.35 594.95 FALSE FALSE TRUE 448.8714761 484.6785926 416.2812582 336.8628797 521.7226751 343.7371051 474.5093475 200.9815654 483.8247252 579.4931132 0.774593288 0.836383697 0.718354108 0.581306097 0.900308672 0.593168577 0.81883518 0.346823044 0.834910224 1 9.178647706 -12.03250873 0.059397669 1.791051302 1.30E-11 0.388000347 0.140118938 47.07588784 0.814051479 15.05652307 9.637659538 9.28E-13 12.03250873 -1.791051302 LYDLNHNEIGELIR ddPTM_HeLa_Romidepsin_16h_R1 1 LYDLNHNEIGELIR 14 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 0 158.31 0.00020021 9205000 3151.7 2994.3 2735.6 2440.8 2699.9 2801.4 2436 2632.3 3195.7 3376.4 FALSE FALSE TRUE 3113.285868 3036.453834 2783.21197 2723.01678 2562.114028 2622.399581 2642.913779 2708.461447 2909.868588 3288.680641 0.946667131 0.92330456 0.846300469 0.827996719 0.779070487 0.797401714 0.803639534 0.823570831 0.884813366 1 11.6832932 -9.873539642 0.914936305 0.982875061 0.797411138 0.749111444 0.034633995 0.076894365 0.128137029 0.003908339 0.005790797 1.34E-10 9.873539642 -0.185463924 ISDYFEYQGGNGSS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 2 ISDYFEYQGGNGSSPVR 17 0 C9JWT6;B3KRP1;Q9UKI8-4;Q9UKI8-5;Q9UKI8;Q9UKI8-2 C9JWT6 TLK1 Serine/threonine-protein kinase tousled-like 1 1 0 ISDYFEYQGGNGS(0.002)S(0.998)PVR;ISDYFEYQGGNGS(0.105)S(0.895)PVR ; 314.11 1.70E-158 110651000 8903 8857.7 8408.7 6733.2 4896.6 3724.7 3117.8 3659 9417.8 8559.7 TRUE FALSE FALSE 8794.486812 8982.398933 8555.049896 7511.724265 4646.70823 3486.703691 3382.625854 3764.867392 8575.448381 8337.31776 1.054834068 1.077372746 1.02611537 0.900976127 0.557338507 0.418204486 0.405721115 0.451568178 1.028562018 1 13.02536761 -8.758537158 2.191721418 1.031344512 0.422303807 0.993031725 0.023258646 0.021586047 0.211442913 0.004620013 0.010011488 1.74E-09 8.758537158 -0.609040704 down LYEALT(ph)PVH ddPTM_HeLa_Romidepsin_16h_R1 2 LYEALTPVH 9 0 G5E9W3;Q9UKF6 G5E9W3 CPSF3 Cleavage and polyadenylation specificity factor subunit 3 1 0 LYEALT(1)PVH;LYEALT(1)PVH ; 134.26 0.014272 37744000 11619.1 10537.2 10469.8 8064 11887.8 12971 10660.2 11736.4 11684.8 10627.7 TRUE FALSE FALSE 11477.48194 10685.54298 10652.02248 8996.397622 11281.12121 12142.19496 11565.67712 12075.97422 10639.68222 10351.59082 1.108765033 1.03226095 1.029022752 0.869083581 1.089795897 1.172978644 1.117284997 1.166581487 1.02783064 1 13.33756488 -8.522352889 24.99991892 1.035380715 1.145882928 0.504810864 0.060315338 15.83570239 752848.1255 0.01004369 0.020269244 3.00E-09 8.522352889 0.110502212 LYEEK(ac)TGNAWHSK ddPTM_HeLa_Romidepsin_16h_R1 1 LYEEKTGNAWHSK 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 1 LYEEK(1)TGNAWHSK 101.2 0.010839 684750 700.85 546.75 685.04 462.96 770.14 604.93 565.32 562.72 623.19 557.44 FALSE TRUE FALSE 692.3077706 554.4471609 696.9628338 516.4896135 730.836882 566.2769253 613.3382667 579.0014154 567.4503256 542.9576284 1.275067767 1.021161011 1.283641296 0.951252154 1.34602931 1.04294865 1.12962455 1.066384162 1.045109776 1 9.084695807 LYENFISEFEHR ddPTM_HeLa_Romidepsin_16h_R1 2 LYENFISEFEHR 12 0 J3KNQ3;A0A087WUL9;Q9UNM6;E9PPD2;E9PQG3 J3KNQ3 PSMD13 26S proteasome non-ATPase regulatory subunit 13 0 0 ; ; 136.01 0.0012271 10723800 6712.6 5532.5 7390.7 6502.9 8372.6 9462.6 7320.7 7821.9 7549.3 6939.5 FALSE FALSE TRUE 6630.784249 5610.38668 7519.332033 7254.795895 7945.31498 8857.970399 7942.520075 8048.214336 6874.0717 6759.21079 0.980999773 0.830035762 1.1124571 1.073319966 1.175479686 1.310503648 1.175066191 1.190703262 1.016993243 1 12.72263909 -9.036657795 1.559582389 0.981332705 1.221443231 0.704398768 0.070231569 0.152008076 0.732926228 0.010819825 0.022218671 9.19E-10 9.036657795 0.240110526 LYEVAIDGKEEDLGS(ph)PTGELTSK ddPTM_HeLa_Romidepsin_16h_R1 2 LYEVAIDGKEEDLGSPTGELTSK 23 1 Q8ND04;Q8ND04-2;Q8ND04-3 Q8ND04 SMG8 Protein SMG8 1 0 LYEVAIDGKEEDLGS(0.561)PT(0.43)GELT(0.007)S(0.002)K;LY(0.001)EVAIDGKEEDLGS(0.769)PT(0.228)GELT(0.002)S(0.001)K ; 66.925 0.00086545 12128600 2252.96 2038.04 2209.76 1661.46 1872.98 2028.96 2626.5 2434.3 2322.99 2216.23 TRUE FALSE FALSE 2225.500057 2066.731581 2248.219946 1853.565823 1777.394842 1899.316004 2849.594844 2504.73263 2115.215956 2158.652025 1.030967489 0.957417665 1.041492524 0.858668188 0.823381824 0.879862054 1.320080685 1.160322553 0.979878152 1 11.07591498 -7.758622885 24.9999725 0.980729315 1.240201659 0.648539119 0.083501105 38.52858532 341970.2348 0.012824227 0.044069142 1.74E-08 7.758622885 0.259472344 LYGDADYLEER ddPTM_HeLa_Romidepsin_16h_R1 2 LYGDADYLEER 11 0 B4E1E0;P17812-2;P17812;A0A3B3IRI2 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 0 0 ; ; 176.6 0.00015044 20989700 6534.5 6200.9 6603.7 4096.5 5762.8 5959.2 4683.3 4580.5 6025.1 6878.4 FALSE FALSE TRUE 6454.855001 6288.196433 6718.634628 4570.156605 5468.702812 5578.426352 5081.099385 4713.029541 5486.199966 6699.698176 0.963454596 0.938579062 1.002826463 0.682143655 0.816261071 0.832638457 0.758407208 0.703468935 0.818872705 1 12.70988039 -9.271562722 25 0.979658603 0.765892484 0.632169134 0.068345703 192.3292388 474964.0069 0.007070329 0.010876974 5.35E-10 9.271562722 -0.21376612 LYGGVCYAGIDTDPELKY(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 LYGGVCYAGIDTDPELKYPK 20 1 Q17RY0-2;B7ZLQ8;E5RJM0;Q17RY0;A0A5K1VW93;E5RFP2;A0A5K1VW71;A0A5K1VW79;A0A5K1VW61;A0A590UJI5;Q7Z5Q1-8;Q8NE35-2;Q8NE35;Q7Z5Q1;Q7Z5Q1-3;Q7Z5Q1-6;Q7Z5Q1-4;Q7Z5Q1-5;Q7Z5Q1-7;Q17RY0-3;Q7Z5Q1-9;H0Y9D9 Q17RY0-2;H0Y9D9 CPEB4;CPEB2;CPEB3 Cytoplasmic polyadenylation element-binding protein 4;Cytoplasmic polyadenylation element-binding protein 2;Cytoplasmic polyadenylation element-binding protein 3 1 0 LYGGVCYAGIDTDPELKY(1)PK 57.525 0.011339 2614500 1257.5 1246.8 1200.7 1052.4 1164.4 818.99 982.42 1112.2 1550.1 1297.1 TRUE FALSE FALSE 1242.173106 1264.352483 1221.59768 1174.08344 1104.976323 766.6591822 1065.86673 1144.379752 1411.455174 1263.401155 0.983197697 1.00075299 0.966911954 0.929303757 0.87460449 0.606821657 0.843648691 0.905792865 1.117186863 1 10.30309708 -8.758257824 2.463352505 0.989553106 0.787319466 0.57283107 0.08374472 0.140352442 1.738928183 0.010712943 0.022624537 1.74E-09 8.758257824 -0.202233641 LYGPS(ph)SVSFADDFVR ddPTM_HeLa_Romidepsin_16h_R1 1 LYGPSSVSFADDFVR 15 0 P50454;E9PPV6;E9PR70;E9PK86;E9PMI5;E9PQ34;E9PJH8;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 1 0 LYGPS(0.833)S(0.158)VS(0.009)FADDFVR 138.31 0.0010144 3570700 823.75 782.5 948.86 707.09 659.56 784.94 905.88 648.4 1055.9 830.55 TRUE FALSE FALSE 813.7098182 793.5160555 965.3745103 788.8470728 625.900192 734.7848673 982.8254246 667.160431 961.4576594 808.9721913 1.005856353 0.980894107 1.193334605 0.975122608 0.773698032 0.908294346 1.214906316 0.824701316 1.188492843 1 9.6599463 -9.002917022 24.99807844 1.016901127 0.939801345 0.144003982 0.13408594 247.8022993 2123635.557 0.01763777 0.031533154 9.93E-10 9.002917022 -0.077099781 LYGPSS(ph)VSFADDFVR ddPTM_HeLa_Romidepsin_16h_R1 1 LYGPSSVSFADDFVR 15 0 P50454;E9PPV6;E9PR70;E9PK86;E9PMI5;E9PQ34;E9PJH8;E9PIG2;E9PRS3;E9PNX1 P50454 SERPINH1 Serpin H1 1 0 LYGPS(0.039)S(0.907)VS(0.054)FADDFVR 100.11 0.0078769 3366500 1021 1059.1 1270.1 841.38 831.2 1001.2 1176.1 933.45 1331 1141.7 TRUE FALSE FALSE 1008.555659 1074.010038 1292.205558 938.6643144 788.7807624 937.2265512 1275.997905 960.457903 1211.952026 1112.038469 0.906943138 0.965802953 1.162015158 0.844093384 0.709310679 0.842800476 1.147440435 0.863691257 1.089847213 1 10.11899098 LYGS(ph)PTQIGPSYR ddPTM_HeLa_Romidepsin_16h_R1 1 LYGSPTQIGPSYR 13 0 E7EWD6;Q76L83-2;Q76L83 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 0 LYGS(0.947)PT(0.033)QIGPS(0.02)YR 128.73 0.0028514 8903200 1701.8 1540.2 1599.6 1486.1 1418.8 1551.1 1185.2 1249.1 1552.7 1270.6 TRUE FALSE FALSE 1681.057807 1561.882976 1627.440367 1657.929874 1346.393342 1451.989716 1285.870858 1285.240738 1413.822623 1237.589629 1.358332171 1.262036251 1.315008084 1.339644286 1.087915825 1.173240048 1.039012309 1.038503158 1.142400187 1 10.2733173 -8.613292972 24.9243554 1.204093772 1.087641648 0.297649547 0.107419614 31.54883499 8685.753865 0.022534269 0.045068538 2.44E-09 8.613292972 -0.116452123 LYGSAGPPPTGEEDTAEKDEL ddPTM_HeLa_Romidepsin_16h_R1 1 LYGSAGPPPTGEEDTAEKDEL 21 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 180.31 3.38E-13 4994700 3704.3 3640.3 3782.8 4005.9 4358.6 4618 3815.8 4753.3 3862.3 3906.5 FALSE FALSE TRUE 3659.150567 3691.548239 3848.638047 4469.081006 4136.164378 4322.924704 4139.913957 4890.829236 3516.846215 3805.008567 0.961666841 0.970181321 1.011466329 1.174525872 1.087031555 1.136114316 1.088016987 1.285366156 0.924267621 1 11.89368399 -9.357585923 4.380496822 0.980971258 1.145725415 0.72121889 0.056171923 0.092628122 3.083788224 0.007776907 0.012074342 4.39E-10 9.357585923 0.164754157 LYINHT(ph)PPPLSK ddPTM_HeLa_Romidepsin_16h_R1 1 LYINHTPPPLSK 12 0 H0Y7U4;A0A0C4DG98;Q8NI27-2;Q8NI27;B7ZBA0;H0Y594 H0Y7U4 THOC2 THO complex subunit 2 1 0 LYINHT(0.999)PPPLS(0.001)K 131.08 0.0074643 17996000 5231.3 5848.5 5892.6 4621.5 6482.3 7366.1 5378.9 6887.7 5847.1 5369.9 TRUE FALSE FALSE 5167.538903 5930.835337 5995.158231 5155.859575 6151.484042 6895.429983 5835.783632 7086.984733 5324.120732 5230.389224 0.987983625 1.133918545 1.146216462 0.98575065 1.17610445 1.318339743 1.115745575 1.354963164 1.017920561 1 12.35270259 -8.172872093 0.386586161 0.984758307 1.393571636 0.582942795 0.081362589 1.463194863 0.242713688 0.025929758 0.249616155 6.72E-09 8.172872093 0.40881333 LYKDDQLLDDGK ddPTM_HeLa_Romidepsin_16h_R1 1 LYKDDQLLDDGK 12 1 B8ZZU8;Q15370;Q15370-2 B8ZZU8 TCEB2 Transcription elongation factor B polypeptide 2 0 0 98.407 0.019551 9854600 2386 2084.3 2132.9 1818.7 2315.7 2291.2 1951.5 2387 2280.4 2366 FALSE FALSE TRUE 2356.918514 2113.64283 2170.02223 2028.986651 2197.521188 2144.799715 2117.260361 2456.064079 2076.435313 2304.530979 1.022732407 0.91716833 0.941632918 0.880433663 0.953565479 0.930688168 0.918738078 1.065754421 0.901022955 1 11.17025745 -10.26700863 24.98378812 1.010734749 0.94034621 0 0.057346664 353.0299841 1583698.234 0.007348803 0.008523417 5.41E-11 10.26700863 -0.070388538 LYKSEPELT(ph)TVAEVDESNGEEK ddPTM_HeLa_Romidepsin_16h_R1 2 LYKSEPELTTVAEVDESNGEEK 22 1 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 LY(0.001)KS(0.003)EPELT(0.498)T(0.498)VAEVDESNGEEK;LYKS(0.015)EPELT(0.762)T(0.222)VAEVDESNGEEK ; 100.59 0.00012987 58932000 5573.5 6148 6386.6 4209.3 7424.3 6617.2 4908.4 5669 6131.1 6551.6 TRUE FALSE FALSE 5505.568038 6234.551705 6497.756094 4695.999071 7045.410267 6194.382276 5325.319373 5833.023571 5582.71906 6381.388488 0.862753937 0.976989838 1.018235468 0.735889859 1.104056003 0.970695059 0.834507942 0.914068088 0.874843942 1 12.63965465 -12.65245592 1.498720638 0.99989343 0.919436157 0 0.104235445 0.835233918 3.381208465 0.066189486 0.015019316 2.23E-13 12.65245592 -0.080457272 LYNNHEIR ddPTM_HeLa_Romidepsin_16h_R1 1 LYNNHEIR 8 0 O60506-2;O60506;O60506-4;O60506-3;B7Z645;O60506-5 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 98.582 0.015145 6027800 2827.5 2798.3 4103.1 2190.8 3439.7 3583.1 2767.9 2424.7 2937.5 2268.4 FALSE FALSE TRUE 2793.037342 2837.694541 4174.512734 2444.110604 3264.159274 3354.151474 3003.005357 2494.854869 2674.762643 2209.466641 1.264122884 1.284334639 1.889375769 1.106199369 1.477351689 1.518081971 1.35915397 1.129166118 1.210592001 1 11.10948243 -11.19759289 0.803578944 1.034144641 1.403452517 0.197399663 0.217693812 0.447791659 0.622534554 0.073715312 0.047165866 6.34E-12 11.19759289 0.369307876 LYPPGDEEEAELADSSGLYHEGSPSPGS(ph)PWK ddPTM_HeLa_Romidepsin_16h_R1 1 LYPPGDEEEAELADSSGLYHEGSPSPGSPWK 31 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 0 LYPPGDEEEAELADS(0.006)S(0.006)GLY(0.016)HEGS(0.096)PS(0.267)PGS(0.609)PWK 67.917 1.41E-05 5443900 1749.8 1713.3 1463.8 1674.9 1746.8 1739.6 1257.3 995.48 2830.5 2502.2 TRUE FALSE FALSE 1728.472765 1737.419882 1489.276825 1868.559819 1657.654278 1628.445174 1364.095031 1024.282643 2577.332991 2437.192483 0.709206506 0.712877581 0.611062456 0.766685369 0.680149102 0.668164368 0.559699343 0.420271542 1.057500796 1 11.25100448 -16.52287875 0.084547194 2.251783267 0.280123035 0.846364109 0.070804471 48.15319987 0.310647616 11.12482992 1.094831086 3.00E-17 16.52287875 -1.971660232 LYS(ph)EVAEER ddPTM_HeLa_Romidepsin_16h_R1 1 LYSEVAEER 9 0 Q9UPN4-2;Q9UPN4;I3L2X7 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 LYS(1)EVAEER 108.9 0.020243 835710 366.92 373.95 556.59 410.76 487.54 586.53 498.37 739.25 511.22 484 TRUE FALSE FALSE 362.4478379 379.2144779 566.2772155 458.2540039 462.6590145 549.0526259 540.7015354 760.6390324 465.4952028 471.4256102 0.768833576 0.8043994 1.201201639 0.972060053 0.981404074 1.164664401 1.146949855 1.61348687 0.987420269 1 8.880886325 -4 0.519650703 0.899480314 25.79319908 0.7253605 0.119219496 41.65190421 0.379576841 0.02546674 1148.804781 1.00E-04 4 24.89371876 LYS(ph)VSYLLK ddPTM_HeLa_Romidepsin_16h_R1 1 LYSVSYLLK 9 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 LYS(0.982)VS(0.018)YLLK 119.34 0.01385 9057100 2088.2 1775.7 2543.8 2339.2 3002.4 2645.7 1863.3 2281.8 1866.9 1880.6 TRUE FALSE FALSE 2062.748215 1800.698351 2588.073772 2609.66931 2849.176325 2476.648309 2021.568655 2347.820283 1699.919788 1831.741741 1.126113015 0.983052529 1.412903203 1.424692822 1.555446524 1.352072868 1.103631921 1.281741978 0.928034641 1 10.8390004 -9.759666429 24.99965918 1.055479789 1.355786933 0.655218809 0.121040472 25.87732217 364882.0947 0.02031316 0.027884295 1.74E-10 9.759666429 0.300307144 LYSGS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 LYSGSPTR 8 0 H3BMH3;Q6PJI9-3;Q6PJI9;Q6PJI9-4 H3BMH3 WDR59 WD repeat-containing protein 59 1 0 LYS(0.026)GS(0.931)PT(0.044)R 106.88 0.025227 42295000 5131.9 5311 5451.1 3275.1 5635.2 5595.1 4957.8 4136.9 5770 5019.4 TRUE FALSE FALSE 5069.350429 5385.768397 5545.974109 3653.782472 5347.614716 5237.591167 5378.915408 4256.594675 5253.916749 4888.995264 1.036890026 1.101610475 1.134379112 0.747348335 1.093806483 1.071302156 1.100208758 0.870648148 1.074641407 1 12.25532229 LYSILQGDS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 LYSILQGDSPTK 12 0 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 0 LYSILQGDS(0.5)PT(0.5)K;LYSILQGDS(0.914)PT(0.086)K ; 148.48 0.0014754 34615000 4435.8 4346.3 4546.9 2494.2 4170.6 3731.6 3438.5 3741.6 4757.2 4896.9 TRUE FALSE FALSE 4381.734763 4407.487325 4626.036887 2782.59114 3957.758719 3493.162803 3730.566104 3849.857293 4331.704117 4769.677832 0.918664723 0.924063947 0.96988456 0.583391843 0.829774852 0.73236871 0.782142156 0.80715248 0.908175409 1 12.21967611 -9.296606012 24.99743746 0.957769893 0.752709753 0.676774197 0.067754482 241.9041141 171951.6246 0.009987692 0.015256817 5.05E-10 9.296606012 -0.20506014 LYSILQGDSPT(ph)KWR ddPTM_HeLa_Romidepsin_16h_R1 1 LYSILQGDSPTKWR 14 1 O15042-2;O15042;O15042-3 O15042-2 U2SURP U2 snRNP-associated SURP motif-containing protein 1 0 LYS(0.001)ILQGDS(0.007)PT(0.991)KWR 120.59 0.002252 14225000 1605 1592.7 1238.9 1760.4 1463.4 1483.7 1160.1 1164.5 1923.2 1316.5 TRUE FALSE FALSE 1585.437643 1615.122072 1260.462535 1963.945731 1388.717237 1388.896358 1258.638865 1198.19297 1751.184175 1282.29714 1.236404257 1.259553673 0.982972273 1.531583959 1.08299176 1.083131448 0.981550083 0.934411325 1.365661765 1 10.32451489 -7.833381965 2.11747235 1.145310525 0.940713964 0.217977776 0.164403526 0.448479543 3.826327576 0.022900252 0.112654116 1.47E-08 7.833381965 -0.204596561 LYSVS(ph)YLLK ddPTM_HeLa_Romidepsin_16h_R1 1 LYSVSYLLK 9 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 LY(0.003)S(0.496)VS(0.5)YLLK 108.47 0.020637 21475000 1054.6 820.07 1104.6 852.06 973.04 1243.1 1100.7 931.1 1301.4 988.67 TRUE FALSE FALSE 1041.74613 831.614967 1123.8251 950.5791863 923.3821379 1163.669922 1194.193431 958.0399095 1184.999525 962.9842109 1.081789419 0.863581103 1.167023391 0.987118143 0.958875678 1.208399794 1.240096584 0.994865646 1.230549277 1 9.911368334 -8.256846583 24.9955322 1.027302444 1.157018267 0.142602564 0.115534713 375.8234408 2045348.737 0.012787074 0.031436325 5.54E-09 8.256846583 0.129715822 LYTSAPNT(ph)SQGK ddPTM_HeLa_Romidepsin_16h_R1 1 LYTSAPNTSQGK 12 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 LYTS(0.001)APNT(0.727)S(0.272)QGK 144.28 0.0011943 0 1625.4 1821.5 1718.3 1324.5 1864.2 1639.1 1703.4 1577.4 1651.6 1796.1 TRUE FALSE FALSE 1605.589 1847.143125 1748.206291 1477.644922 1769.062918 1534.3668 1848.086753 1623.03958 1503.876759 1749.437063 0.917774656 1.055850001 0.999296475 0.844640229 1.011218383 0.877063161 1.056389391 0.927749626 0.859634674 1 10.77267505 LYVELHR ddPTM_HeLa_Romidepsin_16h_R1 3 LYVELHR 7 0 A0A087WTZ5;E9PJ81;E9PRQ7;Q04323;Q04323-2 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 0 0 ;; ;; 104.45 0.0048362 8151600 7636.2 6314.6 9198.8 6072.7 9932.1 10176.2 8993.7 7381.8 6869.4 5363 FALSE FALSE TRUE 7543.127057 6403.497105 9358.901255 6774.854147 9425.227875 9525.973662 9757.624654 7595.380736 6254.983659 5223.668487 1.44402867 1.225862078 1.791633845 1.296953312 1.80433117 1.823617576 1.867963995 1.454031923 1.197431207 1 12.35084763 -11.37523495 0.227081617 0.748196346 1.84746442 0.537921959 0.201659587 1.691359512 0.222452575 0.644559264 0.285583139 4.21E-12 11.37523495 1.099268074 MAASIVRRGMLLAR ddPTM_HeLa_Romidepsin_16h_R1 1 MAASIVRRGMLLAR 14 2 E5RJ73;Q92552;Q92552-2 E5RJ73 MRPS27 "28S ribosomal protein S27, mitochondrial" 0 0 48.277 0.028584 11409000 14050 3292.4 2669.5 24224 5979.1 2069.8 7043.1 5769.7 14039 15448 FALSE FALSE TRUE 13878.7532 3338.750494 2715.961528 27024.89286 5673.964216 1937.54646 7641.340738 5936.637166 12783.31668 15046.65873 0.922381071 0.221893149 0.180502634 1.796072692 0.377091308 0.128769217 0.507843028 0.394548535 0.849578428 1 13.87715554 -8.519372105 0.205648578 1.116380029 3.54E-16 0.107879762 0.461160635 10.02690102 0.66810369 0.725660141 3.088841604 3.02E-09 8.519372105 -1.116380029 MADK(ac)DGDLIATK ddPTM_HeLa_Romidepsin_16h_R1 1 MADKDGDLIATK 12 1 O43852;O43852-3;O43852-15;O43852-2;O43852-4;O43852-10;O43852-6;O43852-8 O43852 CALU Calumenin 0 1 MADK(1)DGDLIATK 132.86 0.00081092 1959200 532.94 591.03 483.72 203.6 1477.7 1263.5 1150.6 1117 1326.5 1266 FALSE TRUE FALSE 526.4443223 599.3505359 492.1389437 227.14119 1402.287455 1182.766428 1248.331935 1149.318633 1207.854518 1233.109137 0.426924354 0.486048248 0.399104125 0.184202017 1.137196548 0.959174165 1.012345053 0.932049401 0.979519558 1 10.26808478 -8.711520019 24.99993874 0.641203455 1.006701316 0.411010782 0.246076872 118.3364949 59263.0388 0.043240219 0.086480338 1.94E-09 8.711520019 0.365497861 MAEESSSSSSSS(ph)SPTAATSQQQQLK ddPTM_HeLa_Romidepsin_16h_R1 2 MAEESSSSSSSSSPTAATSQQQQLK 25 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 MAEES(0.001)S(0.001)S(0.001)S(0.006)S(0.03)S(0.025)S(0.025)S(0.445)S(0.445)PT(0.019)AATSQQQQLK;MAEESSSSSSS(0.003)S(0.555)S(0.439)PT(0.003)AATSQQQQLK ; 138.66 3.05E-07 38108000 4193.8 3568.6 3527.6 3742.6 3456.1 3368.5 3106 3657.3 3906.6 3335.5 TRUE FALSE FALSE 4142.684353 3618.838844 3588.996398 4175.337021 3279.722321 3153.263721 3369.823562 3763.118205 3557.183912 3248.843229 1.275125963 1.11388534 1.104699779 1.285176516 1.009504642 0.970580449 1.037237972 1.158294796 1.094907837 1 11.66571041 MAFYS(ph)YNSVLAIAR ddPTM_HeLa_Romidepsin_16h_R1 1 MAFYSYNSVLAIAR 14 0 E9PIC7;E9PN52;E5RK40;A8K1M9;E9PMA4;Q2VYF4 E9PIC7 LETM2 "LETM1 domain-containing protein LETM2, mitochondrial" 1 0 MAFY(0.293)S(0.413)Y(0.293)NSVLAIAR 98.943 0.01506 5849900 168.6 183.23 104.87 212.21 151.96 181.43 0 201.16 214.92 197.31 TRUE FALSE FALSE 166.5450383 185.8095167 106.6952184 236.7467187 144.2049142 169.8372085 0 206.9802472 195.6970169 192.1838578 0.866592233 0.966832069 0.555172633 1.231876191 0.750348733 0.883722548 0 1.076990803 1.018280199 1 7.586343354 -7.958011968 24.99996176 0.916654096 0.514336107 0.202919963 0.29344704 131.1271219 78072.72303 0.035024905 0.105074602 1.10E-08 7.958011968 -0.402317989 MALIGLGVSHPVLK ddPTM_HeLa_Romidepsin_16h_R1 2 MALIGLGVSHPVLK 14 0 H3BSJ9;H3BRG4;P22695 H3BSJ9 UQCRC2 "Cytochrome b-c1 complex subunit 2, mitochondrial" 0 0 ; ; 86.114 0.0073518 1655140 965.6 1009.46 1125.89 1253.68 1269.84 1573.09 1042.45 886.56 974.79 750.26 FALSE FALSE TRUE 953.8308958 1023.671204 1145.485643 1398.63638 1205.035326 1472.574626 1130.995677 912.2112148 887.602341 730.768137 1.305244232 1.400815324 1.567509016 1.913926332 1.648998178 2.015105136 1.547680611 1.248290899 1.214615548 1 9.513269921 -10.43701902 0.799656057 1.072296425 1.687328815 0.523422748 0.207835298 0.27632347 0.368367915 0.054993502 0.058765352 3.66E-11 10.43701902 0.61503239 MALIQMGSVEEAVQALIDLHNHDLGENHHLR ddPTM_HeLa_Romidepsin_16h_R1 4 MALIQMGSVEEAVQALIDLHNHDLGENHHLR 31 0 A0A0U1RRM4;A0A0D9SF20;A6NLN1;P26599;P26599-2;P26599-3 A0A0U1RRM4;A6NLN1 PTBP1 Polypyrimidine tract-binding protein 1 0 0 ;;; ;;; 102.65 5.04E-12 36064900 10427.32 10688.21 9418.78 10454.83 11397.13 10821.81 9397.34 9169.63 10942.09 7284.98 FALSE FALSE TRUE 10300.22781 10838.6789 9582.709915 11663.66664 10815.49193 10130.33127 10195.54983 9434.938777 9963.402065 7095.715169 1.451612356 1.527496333 1.350492471 1.643761955 1.52422859 1.427668815 1.436860074 1.329667067 1.404143462 1 12.79273238 -12.06161356 0.680943925 0.97189544 1.47117681 0.14115954 0.150117181 0.274893041 0.215283813 0.077627956 0.01919165 8.68E-13 12.06161356 0.499281369 MALPPQEDAT(ph)ASPPR ddPTM_HeLa_Romidepsin_16h_R1 6 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 MALPPQEDAT(0.572)AS(0.428)PPR;MALPPQEDAT(0.633)AS(0.367)PPR;MALPPQEDAT(0.834)AS(0.166)PPR;MALPPQEDAT(0.671)AS(0.329)PPR;MALPPQEDAT(0.5)AS(0.5)PPR;MALPPQEDAT(0.656)AS(0.344)PPR ;;;;; 174.24 1.83E-05 491770000 34525.3 35221.5 33145.3 22476.4 28028.1 29822.6 24647.3 26926.4 35472.7 35436.2 TRUE FALSE FALSE 34104.49236 35717.3492 33722.18004 25075.22712 26597.72147 27917.03211 26740.84105 27705.4729 32299.93287 34515.56242 0.988090298 1.034818693 0.977013778 0.726490469 0.770600842 0.808824488 0.774747365 0.802695102 0.93580781 1 15.07495937 -9.30871742 6.928230002 0.997102964 0.778103158 0.917739762 0.031444101 0.034317895 4.205136664 0.003702943 0.005696491 4.91E-10 9.30871742 -0.218999806 MALPPQEDATAS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 MALPPQEDATASPPR 15 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 MALPPQEDAT(0.309)AS(0.691)PPR;MALPPQEDAT(0.176)AS(0.824)PPR ; 174.24 1.02E-05 287764000 16439.1 17695.1 16116.8 11272.2 13855.8 14511.8 12313.9 13622.7 18243.7 17870.1 TRUE FALSE FALSE 16238.73393 17944.21208 16397.30614 12575.5448 13148.68682 13584.54281 13359.84236 14016.85133 16611.93778 17405.83223 0.93294786 1.030931003 0.942058152 0.722490292 0.755418451 0.780459253 0.767549761 0.805296245 0.95438917 1 14.08728317 -9.337869407 5.360556116 0.972458404 0.766743842 0.912135399 0.032015542 0.05066055 2.60992304 0.005521184 0.00851767 4.59E-10 9.337869407 -0.205714562 MALPPQEDATAS(ph)PPRQK ddPTM_HeLa_Romidepsin_16h_R1 1 MALPPQEDATASPPRQK 17 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 MALPPQEDAT(0.142)AS(0.858)PPRQK 109.1 0.0077224 6478100 2859 2956.7 2291.6 3995.6 2307 2218.7 1970.9 2422.5 3557.6 3018.4 TRUE FALSE FALSE 2824.153408 2998.3245 2331.484337 4457.590072 2189.265181 2076.932231 2138.308197 2492.591215 3239.399346 2939.981533 0.960602431 1.019844671 0.793026865 1.516196623 0.744652698 0.706443972 0.727320282 0.847825467 1.101843433 1 11.52159138 MAPALSGANLTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MAPALSGANLTSPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 MAPALS(0.017)GANLT(0.235)S(0.748)PR 94.781 0.020385 119960000 3918.9 4095.4 3498.2 2733.2 3716.1 3858 3344.1 3597.6 3585.8 4076 TRUE FALSE FALSE 3871.134939 4153.055149 3559.084704 3049.225444 3526.45355 3611.486251 3628.147771 3701.69088 3265.077067 3970.104932 0.97507119 1.04608196 0.896471193 0.768046562 0.888251976 0.909670226 0.913866971 0.932391194 0.822415811 1 11.95496142 -9.656160488 7.062456711 0.992103459 0.880967758 0.169482646 0.07033981 0.122130636 7.362281268 0.007377247 0.0104414 2.21E-10 9.656160488 -0.111135701 MAPPVDDLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 MAPPVDDLSPK 11 0 E7EVH3;Q92576-2;Q92576;E7ER40 E7EVH3 PHF3 PHD finger protein 3 1 0 MAPPVDDLS(1)PK;MAPPVDDLS(1)PK;MAPPVDDLS(1)PK;MAPPVDDLS(1)PK ;;; 122.34 0.01238 214277000 15878.5 15568.9 14596.7 13316.6 11852.4 10321.5 9386.1 10566.5 15367.4 15115.6 TRUE FALSE FALSE 15684.96673 15788.07938 14850.74944 14856.32795 11247.5278 9661.989461 10183.3551 10872.22501 13992.90126 14722.89453 1.065345316 1.072348875 1.008684088 1.009062988 0.763948134 0.656256108 0.691668006 0.738457032 0.950417815 1 13.84577371 -8.717763623 3.271750607 1.033450925 0.695946118 0.938462546 0.038472031 0.033908049 0.743203758 0.005059149 0.010410661 1.92E-09 8.717763623 -0.337504808 MAPT(ph)PIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_HeLa_Romidepsin_16h_R1 1 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643-3;Q16643;Q16643-2;D6R9Q9 Q16643-3 DBN1 Drebrin 2 0 MAPT(0.987)PIPT(0.603)RS(0.183)PS(0.065)DS(0.111)S(0.036)T(0.012)AS(0.002)T(0.002)PVAEQIER 70.704 6.28E-05 11494000 1398.5 1737.8 1538.8 1564.8 1082.9 1148.6 1016.2 1062.2 1173.5 1383.6 TRUE FALSE FALSE 1381.454544 1762.264794 1565.582169 1745.729539 1027.635572 1075.208167 1102.516003 1092.933081 1068.539221 1347.653873 1.025081122 1.307653864 1.161709398 1.295384204 0.762536726 0.797837033 0.818100274 0.810989456 0.792888473 1 10.39623429 -8.730165568 24.99995944 1.066980587 0.798880377 0.509593658 0.142222351 129.6044691 103603.9318 0.018959813 0.0379167 1.86E-09 8.730165568 -0.268100211 MAPTPIPT(ph)RSPSDSSTASTPVAEQIER ddPTM_HeLa_Romidepsin_16h_R1 4 MAPTPIPTRSPSDSSTASTPVAEQIER 27 1 Q16643-3;Q16643;Q16643-2;D6R9Q9 Q16643-3 DBN1 Drebrin 1 0 MAPT(0.011)PIPT(0.471)RS(0.471)PS(0.046)DS(0.001)S(0.001)TASTPVAEQIER;MAPT(0.023)PIPT(0.478)RS(0.478)PS(0.02)DSSTASTPVAEQIER;MAPT(0.043)PIPT(0.938)RS(0.014)PS(0.004)DSSTASTPVAEQIER;MAPT(0.024)PIPT(0.424)RS(0.424)PS(0.068)DS(0.006)S(0.003)T(0.004)AS(0.022)T(0.025)PVAEQIER ;;; 81.553 3.32E-06 749580600 3169.36 2879.91 2674.51 2931.4 3374.65 2741.08 2575.25 2970.11 3224.57 3005.14 TRUE FALSE FALSE 3130.730621 2920.453449 2721.058725 3270.342261 3202.429018 2565.933834 2793.991671 3056.045447 2936.156383 2927.06603 1.069579774 0.997740884 0.929619864 1.117276559 1.094074744 0.876623147 0.954536605 1.044064403 1.00310562 1 11.51523958 -8.271082384 24.98912636 1.032946333 0.958020904 0.211622645 0.063342889 757.9192196 1964090.997 0.009193332 0.020797301 5.36E-09 8.271082384 -0.074925429 MAS(ph)EELY(ph)EVER ddPTM_HeLa_Romidepsin_16h_R1 1 MASEELYEVER 11 0 Q9Y232-2 Q9Y232-2 CDYL Chromodomain Y-like protein 2 0 MAS(1)EELY(1)EVER 67.519 0.0028091 0 0 0 0 0 69.091 0 0 66.958 0 0 TRUE FALSE FALSE 0 0 0 0 65.56502846 0 0 68.89532409 0 0 0 MAS(ph)PPAPSPAPPAISPIIK ddPTM_HeLa_Romidepsin_16h_R1 1 MASPPAPSPAPPAISPIIK 19 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 MAS(1)PPAPSPAPPAISPIIK 106.44 0.0013818 10127000 2670.9 2929.7 2566.3 2041 2211.1 2042.7 1721.8 2315.2 2713.9 2476.1 TRUE FALSE FALSE 2638.346043 2970.944393 2610.965375 2276.990023 2098.259316 1912.178063 1868.049649 2382.186659 2471.161987 2411.770565 1.093945702 1.231852 1.082592769 0.944115521 0.870007847 0.792852392 0.77455529 0.987733532 1.024625652 1 11.23587695 -8.994369471 2.724086742 1.064755997 0.845298158 0.645504936 0.079882112 0.148860501 2.234683102 0.013318994 0.024905525 1.01E-09 8.994369471 -0.21945784 MAS(ph)S(ph)AKSAEMPT(ph)IS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MASSAKSAEMPTISK 15 1 D6RFL8;Q9BXG8 D6RFL8 SPZ1 Spermatogenic leucine zipper protein 1 4 0 MAS(0.978)S(0.98)AKS(0.08)AEMPT(0.984)IS(0.979)K 56.817 0.0043125 0 1440.9 1838.1 1773.8 1487.7 1629.4 1290.3 781.23 1026.5 1386.3 1303.8 TRUE FALSE FALSE 1423.337757 1863.97682 1804.672245 1659.714874 1546.245638 1207.853994 847.5876567 1056.200158 1262.305856 1269.927088 1.120802737 1.46778255 1.421083353 1.306937138 1.217586153 0.951120742 0.667430173 0.831701416 0.993998685 1 10.31052995 -8.002554065 3.995651628 1.145574855 0.753517599 0.547445589 0.164493358 0.158475028 5.817333149 0.027985415 0.085002891 9.94E-09 8.002554065 -0.392057256 MAS(ph)VNMDPALMFR ddPTM_HeLa_Romidepsin_16h_R1 1 MASVNMDPALMFR 13 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8;H0Y8T6 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 0 MAS(1)VNMDPALMFR 61.419 0.027602 8422800 2777.1 2359.1 2396.4 1924.8 2659.6 2169.3 2362.1 2174.3 2903.8 2746 TRUE FALSE FALSE 2743.251637 2392.311472 2438.108337 2147.354432 2523.870688 2030.688731 2562.736715 2237.20994 2644.076855 2674.658524 1.025645559 0.894436224 0.911558733 0.802851808 0.943623519 0.759232894 0.95815473 0.836446941 0.988566141 1 11.385139 -10.16106609 3.335820719 1.012355735 0.86976681 0.52092289 0.058289075 0.121566995 2.558781819 0.008793714 0.010816692 6.90E-11 10.16106609 -0.142588926 MAS(ph)VVEY(ph)KGLR ddPTM_HeLa_Romidepsin_16h_R1 1 MASVVEYKGLR 11 1 Q5SQQ1;F5GXE4 Q5SQQ1 ATE1 Arginyl-tRNA--protein transferase 1 2 0 MAS(1)VVEY(1)KGLR 82.426 0.0043171 0 1116.7 765.39 809.81 733.06 764.02 796.69 637.5 641.16 800.07 699.59 TRUE FALSE FALSE 1103.089231 776.1651805 823.9044034 817.8198464 725.0292084 745.7840802 691.6492341 659.710953 728.5097354 681.4145509 1.618822535 1.139049906 1.209108908 1.200179605 1.064006055 1.094464565 1.01501976 0.968149201 1.069113852 1 9.412388945 -8.842259064 1.125439034 1.284894491 1.010451065 0.15253875 0.163450163 0.632895355 1.577191258 0.038695221 0.104596091 1.44E-09 8.842259064 -0.274443426 MASNIFGT(ph)PEENQASWAK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 MASNIFGT(1)PEENQASWAK 168.68 9.26E-07 141550000 2151.7 2298.3 2453.6 2677.6 4601.1 6170.4 5393.6 5252.8 2298.3 2487.1 TRUE FALSE FALSE 2125.474253 2330.655528 2496.303879 2987.19671 4366.288698 5776.131354 5851.732249 5404.78148 2092.734292 2422.484783 0.877394264 0.962092948 1.03047247 1.233112683 1.802400877 2.384382925 2.415590921 2.231089961 0.863879231 1 11.24227189 -8.658515958 1.700803919 0.946617521 2.372691646 0.986153018 0.073163135 0.028273676 0.164446571 0.011669751 0.029177611 2.20E-09 8.658515958 1.426074125 up MASNLECQMSS(ph)KLLVKTVLFLT(ph)QR ddPTM_HeLa_Romidepsin_16h_R1 1 MASNLECQMSSKLLVKTVLFLTQR 24 2 H0YDE5;A0A5F9UK30;A0A590UJI0;Q6ZVL6-2;Q6ZVL6 H0YDE5 KIAA1549L UPF0606 protein KIAA1549L 2 0 MAS(0.069)NLECQMS(0.019)S(0.911)KLLVKT(0.026)VLFLT(0.974)QR 45.885 0.012473 21575000 1695.9 1361.1 1643 1109.4 1560.4 1254.9 1286.9 1552.8 1647.7 1627 TRUE FALSE FALSE 1675.229718 1380.261602 1671.595726 1237.674048 1480.766965 1174.71594 1396.209254 1597.727818 1500.325585 1584.730305 1.057107138 0.870975709 1.054814008 0.780999798 0.934396825 0.741271834 0.881039032 1.008201719 0.946738748 1 10.63002162 -9.671963571 1.284560902 1.024191402 0.870172244 0.180094386 0.093528639 0.327537694 1.08730707 0.015317215 0.023986111 2.13E-10 9.671963571 -0.154019158 MATFPGPGS(ph)SPAR ddPTM_HeLa_Romidepsin_16h_R1 1 MATFPGPGSSPAR 13 0 O43187 O43187 IRAK2 Interleukin-1 receptor-associated kinase-like 2 1 0 MAT(0.004)FPGPGS(0.904)S(0.092)PAR 99.669 0.017822 12316000 2562 2284.1 2336.8 2553.2 4338.6 4418.7 3735.1 3896.9 2212 2175.3 TRUE FALSE FALSE 2530.773359 2316.25562 2377.471024 2848.412997 4117.185052 4136.359331 4052.359301 4009.650653 2014.15318 2118.785392 1.19444535 1.09319973 1.122091474 1.344361259 1.943181724 1.95223138 1.91258601 1.892428873 0.95061689 1 11.04902175 -8.88534996 2.884079336 1.09788897 1.933756406 0.970074629 0.070639808 0.034598462 0.580741486 0.012099668 0.023518776 1.30E-09 8.88534996 0.835867436 MAY(ph)SQGGGKK ddPTM_HeLa_Romidepsin_16h_R1 1 MAYSQGGGKK 10 1 Q92769;E5RFP9 Q92769 HDAC2 Histone deacetylase 2 1 0 MAY(0.906)S(0.094)QGGGKK 75.109 0.021766 22798000 2550 2275 2220.4 1648 2203.2 2092.2 2076.8 1939.3 2291.2 1991.6 TRUE FALSE FALSE 2518.919619 2307.02751 2259.045131 1838.549514 2090.762483 1958.515172 2253.20334 1995.410586 2086.269334 1939.857945 1.298507257 1.189276522 1.164541526 0.947775335 1.07779154 1.009617832 1.161530073 1.028637479 1.075475315 1 10.92173529 -9.313331533 24.97856457 1.15054232 1.051388493 0.242816331 0.088155756 524.9049114 252664.5438 0.018729371 0.028609608 4.86E-10 9.313331533 -0.099153827 MCGVGEQMRKK ddPTM_HeLa_Romidepsin_16h_R1 1 MCGVGEQMRKK 11 2 Q14573 Q14573 ITPR3 "Inositol 1,4,5-trisphosphate receptor type 3" 0 0 64.82 0.029542 6471400 5800.6 1466 3226.4 636.91 3516.8 2574.2 5026.7 3132.6 6809 4110 FALSE FALSE TRUE 5729.900056 1486.638386 3282.554139 710.552531 3337.324573 2409.716928 5453.667773 3223.236839 6199.985987 4003.221608 1.431322224 0.371360502 0.819978123 0.177495178 0.833659712 0.601944425 1.362319728 0.805160732 1.548749131 1 11.96694577 -10.27028878 24.99383838 1.203679938 0.719659703 0.409366827 0.329374127 566.1260799 1598937.599 0.056410648 0.0650209 5.37E-11 10.27028878 -0.484020235 MCKDY(ph)VY(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 1 MCKDYVYDK 9 1 A6NNY8 A6NNY8 USP27X Ubiquitin carboxyl-terminal hydrolase 27 2 0 MCKDY(1)VY(1)DK 49.418 0.0040165 0 555.67 676.16 541.17 661 680.08 670.94 560.67 614.38 627.1 823.24 TRUE FALSE FALSE 548.8972803 685.6789982 550.5888368 737.4279301 645.3729799 628.0690994 608.2932958 632.156116 571.0106054 801.8521061 0.684536807 0.855119034 0.686646369 0.919655787 0.804852884 0.783272993 0.758610336 0.788369964 0.712114617 1 9.64719236 -12.48322749 1.200325616 1.001106025 0.777446827 0 0.110186662 0.26069962 0.666717608 0.048445254 0.011605472 3.29E-13 12.48322749 -0.223659198 MDAEAEDK(ac)TLRTRSK ddPTM_HeLa_Romidepsin_16h_R1 1 MDAEAEDKTLRTRSK 15 3 E5RFE8;E5RHY1;E5RID0;E5RHS3;O60284 E5RFE8 ST18 Suppression of tumorigenicity 18 protein 0 1 MDAEAEDK(1)TLRTRSK 47.037 0.030257 2147700 184.34 139.12 391.94 0 258.73 377.83 358 147.35 177.66 65.288 FALSE TRUE FALSE 182.0931932 141.078535 398.7615513 0 245.5260426 353.6878824 388.4085111 151.6133398 161.7696446 63.59180835 2.863469335 2.218501701 6.270643368 0 3.86096966 5.56184659 6.107838748 2.384164623 2.543875522 1 5.99076903 -10.77360412 0.208219482 5.90E-16 5.267343942 0.163739918 1.853616574 2.670481699 0.465206049 5.61788514 4.151942661 1.68E-11 10.77360412 5.267343942 MDKEETKDWILPSDYDHAEAEAR ddPTM_HeLa_Romidepsin_16h_R1 1 MDKEETKDWILPSDYDHAEAEAR 23 2 O43852;O43852-3;O43852-15;O43852-2;O43852-4;H0Y875 O43852 CALU Calumenin 0 0 42.209 0.021461 21768000 1321.6 1141.2 1157.6 1573.5 1589.6 1791.6 1434.4 1825 1578.4 1478.5 FALSE FALSE TRUE 1305.491831 1157.265844 1177.747542 1755.435474 1508.47678 1677.122542 1556.2379 1877.803496 1437.223951 1440.088357 0.906535925 0.803607527 0.817830057 1.218977617 1.047489047 1.164596974 1.080654456 1.303950196 0.998010951 1 10.49194162 -9.253939968 24.98588601 0.931490157 1.152208078 0.662313652 0.090960024 324.3602535 1080674.699 0.014303013 0.023420521 5.57E-10 9.253939968 0.220717921 MDRT(ph)PPPPT(ph)LSPAAITVGR ddPTM_HeLa_Romidepsin_16h_R1 5 MDRTPPPPTLSPAAITVGR 19 1 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7;H7C4H9 E7EX82 PHC3 Polyhomeotic-like protein 3 2 0 MDRT(1)PPPPT(0.604)LS(0.396)PAAITVGR;MDRT(1)PPPPT(0.736)LS(0.264)PAAITVGR;MDRT(1)PPPPT(0.882)LS(0.118)PAAITVGR;MDRT(1)PPPPT(0.998)LS(0.002)PAAITVGR;MDRT(1)PPPPT(0.819)LS(0.17)PAAIT(0.011)VGR ;;;; 102.78 0.00038958 46235400 8859.7 8698.4 8208.4 8863.1 9807.8 9762.6 8104.3 9269.2 8939.1 8830.4 TRUE FALSE FALSE 8751.714569 8820.856304 8351.263759 9887.893324 9307.271368 9138.801367 8792.67904 9537.389678 8139.564508 8600.984935 1.017524695 1.02556351 0.970965979 1.149623374 1.082116925 1.062529633 1.02228746 1.108871804 0.946352606 1 13.07028616 -9.278409694 24.98266918 1.007513557 1.080178983 0.577335612 0.038563396 459.8028265 676892.4792 0.00501544 0.007674054 5.27E-10 9.278409694 0.072665427 MDRT(ph)PPPPTLS(ph)PAAITVGR ddPTM_HeLa_Romidepsin_16h_R1 1 MDRTPPPPTLSPAAITVGR 19 1 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7;H7C4H9 E7EX82 PHC3 Polyhomeotic-like protein 3 2 0 MDRT(1)PPPPT(0.098)LS(0.898)PAAIT(0.004)VGR 70.027 0.026848 8949800 3797.7 4072.8 2062.5 963.07 2517.6 2376 2584.1 3857 4400.2 5543.2 TRUE FALSE FALSE 3751.412172 4130.136985 2098.396947 1074.424685 2389.117478 2224.181268 2803.59339 3968.59621 4006.635091 5399.186865 0.694810583 0.76495537 0.388650551 0.198997499 0.442495794 0.411947451 0.519262152 0.735035906 0.742081204 1 12.39852643 -10.77084743 0.680041548 0.951724334 0.450680018 0.472209681 0.163379432 0.301308351 0.311488513 0.055757771 0.045925396 1.69E-11 10.77084743 -0.501044316 MDRT(ph)PPPPTLSPAAITVGR ddPTM_HeLa_Romidepsin_16h_R1 1 MDRTPPPPTLSPAAITVGR 19 1 E7EX82;Q8NDX5-2;Q8NDX5;Q8NDX5-7;H7C4H9 E7EX82 PHC3 Polyhomeotic-like protein 3 1 0 MDRT(1)PPPPTLSPAAITVGR 105.02 0.00057707 54546000 1225.4 1406.3 1329.4 1575.8 1114.9 1043.2 1105.6 1133.3 1593.6 1446.6 TRUE FALSE FALSE 1210.464353 1426.097928 1352.537649 1758.00141 1058.002493 976.5428868 1199.509636 1166.090247 1451.064425 1409.017123 0.859084204 1.012122496 0.959915694 1.247679238 0.750879798 0.693066728 0.851309481 0.827591254 1.029841583 1 10.46047343 MDS(ph)DEDEKEGEEEK ddPTM_HeLa_Romidepsin_16h_R1 1 MDSDEDEKEGEEEK 14 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 MDS(1)DEDEKEGEEEK 146.84 7.34E-05 0 1877.2 1648 1611.3 1181.4 1652.5 1887.4 1330.9 1562.6 1732.9 1842.8 TRUE FALSE FALSE 1854.319964 1671.200587 1639.344001 1317.999027 1568.166759 1766.801231 1443.946613 1607.811366 1577.905084 1794.92379 1.033091195 0.931070498 0.913322342 0.734292472 0.873667599 0.984332171 0.804461237 0.895754669 0.87909308 1 10.80970688 -9.942929348 2.30344673 1.01541788 0.862701522 0.221047211 0.075646305 0.161162424 1.72774679 0.010475496 0.01394845 1.14E-10 9.942929348 -0.152716358 MDS(ph)DEDEKEGEEEKVAK ddPTM_HeLa_Romidepsin_16h_R1 1 MDSDEDEKEGEEEKVAK 17 2 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 MDS(1)DEDEKEGEEEKVAK 55.975 0.0042526 0 1315.8 1373.1 1096 1430.7 1129.1 1033.9 1066 1094.9 1146.4 1065.6 TRUE FALSE FALSE 1299.762523 1392.430538 1115.07542 1596.124266 1071.477814 967.8371268 1156.546013 1126.579204 1043.863113 1037.915558 1.252281569 1.341564375 1.074341175 1.537817073 1.03233621 0.932481567 1.114296827 1.08542472 1.005730287 1 10.01947336 YADSPGAS(ph)SPEQPK ddPTM_HeLa_Romidepsin_16h_R1 2 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 0 YADSPGAS(0.632)S(0.367)PEQPK;YADSPGAS(0.612)S(0.388)PEQPK ; 189.99 5.06E-11 17839900 10554.6 8761.9 9498.7 8531.9 4620 4537.6 3475.5 3964.8 10564.5 9603 TRUE FALSE FALSE 10425.95648 8885.250258 9664.020889 9518.398422 4384.22416 4247.662004 3770.708883 4079.515233 9619.584661 9353.512676 1.114656797 0.949937266 1.033196963 1.017628216 0.468724886 0.454124793 0.403132921 0.436147934 1.02844621 1 13.19129255 -8.758302409 5.197834009 1.044057458 0.433600952 0.978976417 0.041868242 0.020917027 1.626756498 0.007884484 0.01531863 1.74E-09 8.758302409 -0.610456506 down MDY(ph)LTT(ph)FT(ph)EKS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 MDYLTTFTEKSGR 13 1 E5RFD1;C9JY63;Q8N573-2 E5RFD1 OXR1 4 0 MDY(0.997)LT(0.014)T(0.995)FT(0.995)EKS(0.999)GR 60.918 0.016483 35684000 5778 5627.8 5497.1 5439.3 4993.9 4588.9 4047.7 4142.3 6345.6 5370.4 TRUE FALSE FALSE 5707.575514 5707.028316 5592.77472 6068.217459 4739.042648 4295.6841 4391.511537 4262.150915 5778.033643 5230.876234 1.091131822 1.091027212 1.06918506 1.160076665 0.905974914 0.821216926 0.839536502 0.814806301 1.104601483 1 12.35283692 -8.574943573 5.548734998 1.057340013 0.831745456 0.878513389 0.04377638 0.058864085 3.952019188 0.007462558 0.015239438 2.66E-09 8.574943573 -0.225594556 MEEEQHHWDDR ddPTM_HeLa_Romidepsin_16h_R1 1 MEEEQHHWDDR 11 0 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 0 68.515 0.024952 1886900 251.51 271.08 284.54 235.73 248.13 280.17 317.3 289.45 236.18 303.96 FALSE FALSE TRUE 248.4444994 274.8962714 289.4922993 262.9862117 235.4670002 262.2680412 344.2514541 297.8247791 215.0554693 296.0630754 0.839160706 0.928505762 0.977806162 0.888277646 0.795327144 0.885851911 1.162763893 1.005950434 0.726383961 1 8.20976076 -7.772177361 24.99795017 0.912894908 1.084357171 0.42173017 0.089287351 130.048176 302753.8826 0.011177664 0.034027585 1.69E-08 7.772177361 0.171462264 MEELHNQEVQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 MEELHNQEVQKR 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; MEELHNQEVQK(1)R;MEELHNQEVQK(1)R 77.597 0.012918 1174450 208.8 0 0 0 391.21 145.58 127.13 217.74 133.18 324.56 FALSE TRUE FALSE 206.2550653 0 0 0 371.2450939 136.2779078 137.928419 224.0399634 121.2680472 316.1278844 0.652441861 0 0 0 1.17435099 0.431084743 0.436305767 0.708700417 0.383604399 1 8.304364485 -10.92547642 1.556634127 0.902944819 0.402308064 0.027035809 0.387004113 0.339736516 1.703420129 0.08252515 0.074114599 1.19E-11 10.92547642 -0.500636755 MEIDESNAGSS(ph)KEEAGETSPADESGAPK ddPTM_HeLa_Romidepsin_16h_R1 1 MEIDESNAGSSKEEAGETSPADESGAPK 28 1 Q9UKY1 Q9UKY1 ZHX1 Zinc fingers and homeoboxes protein 1 1 0 MEIDES(0.005)NAGS(0.136)S(0.5)KEEAGET(0.077)S(0.282)PADES(0.001)GAPK 51.811 0.020438 8677900 1850.2 1615.6 1921.2 1323.2 1406.5 1442.2 1086.8 1092.8 2047.7 1785.1 TRUE FALSE FALSE 1827.649051 1638.344459 1954.63768 1476.19461 1334.721057 1350.048074 1179.112765 1124.418444 1864.548583 1738.722845 1.051144555 0.942268898 1.124180134 0.849010879 0.767644516 0.776459617 0.678148774 0.646692167 1.07236676 1 10.76381227 -8.909992892 2.031834398 1.024393507 0.706473225 0.866164026 0.059273712 0.07845222 0.654838282 0.008550797 0.01746802 1.23E-09 8.909992892 -0.317920282 MEIGDTLSTAEES(ph)SPPK ddPTM_HeLa_Romidepsin_16h_R1 2 MEIGDTLSTAEESSPPK 17 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 MEIGDTLSTAEES(0.869)S(0.131)PPK;MEIGDTLSTAEES(0.895)S(0.105)PPK ; 149.35 0.00015948 47041000 11861.2 11811.4 12030.2 6611.3 8187.7 7196.1 6724.2 6768 11907.7 11773 TRUE FALSE FALSE 11716.63113 11977.6812 12239.58058 7375.729613 7769.851116 6736.292434 7295.35338 6963.821402 10842.64549 11467.13576 1.021757427 1.04452249 1.067361618 0.64320592 0.677575576 0.587443331 0.636196652 0.607285162 0.945540867 1 13.48521746 -9.255804722 24.98342267 1.017541104 0.630907507 0.964875257 0.036774814 47.6720643 211372.3041 0.004595544 0.007482844 5.55E-10 9.255804722 -0.386633597 MEIGDTLSTAEESS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 MEIGDTLSTAEESSPPK 17 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 MEIGDTLSTAEES(0.227)S(0.773)PPK 176.43 1.23E-08 26892000 4123 3757.9 4268.7 2349.5 3216 2571.1 2584.3 2612.8 4270.3 4329.4 TRUE FALSE FALSE 4072.74729 3810.803815 4342.994933 2621.160245 3051.875519 2406.815008 2803.810377 2688.397246 3888.353673 4216.921564 0.965810539 0.903693312 1.029897015 0.621581456 0.723721196 0.570751666 0.664895075 0.637526026 0.922083471 1 12.04197447 -9.258631303 24.97845 0.979296684 0.645266333 0.911386258 0.049873748 42.6584663 379455.8728 0.006700031 0.010793699 5.51E-10 9.258631303 -0.334030352 MEIQVPPS(ph)PTDVAK ddPTM_HeLa_Romidepsin_16h_R1 1 MEIQVPPSPTDVAK 14 0 Q5T5U3;A0A087WW76;A0A452Q6Z5;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 MEIQVPPS(0.856)PT(0.144)DVAK 93.716 0.021747 5663900 2290.6 2619.3 2033.7 2173.8 2036.5 2043.7 1547.7 1912.4 2717.1 2455.2 TRUE FALSE FALSE 2262.681286 2656.174574 2069.095695 2425.144984 1932.569806 1913.114166 1679.161599 1967.732277 2474.075771 2391.41355 0.946168966 1.110713191 0.865218688 1.014105228 0.808128651 0.799993027 0.702162785 0.822832285 1.034566259 1 11.22364792 -8.677767529 4.706919108 0.978686427 0.773441536 0.703423145 0.066992448 0.084583347 3.353826594 0.008835616 0.017919679 2.10E-09 8.677767529 -0.205244892 MEIQVPPSPT(ph)DVAK ddPTM_HeLa_Romidepsin_16h_R1 1 MEIQVPPSPTDVAK 14 0 Q5T5U3;A0A087WW76;A0A452Q6Z5;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 MEIQVPPS(0.263)PT(0.737)DVAK 75.764 0.0041591 0 1354.2 1675.8 1196.5 1293.5 1216.6 1132.5 1045.5 1420.1 1361 1486.6 TRUE FALSE FALSE 1337.69449 1699.391956 1217.324581 1443.060556 1154.512362 1060.136905 1134.304744 1461.188353 1239.268751 1447.977918 0.92383625 1.173631128 0.840706592 0.99660398 0.797327327 0.732149912 0.783371576 1.009123368 0.855861637 1 10.49982389 -8.761118326 24.99999848 0.972421157 0.8201027 0.261876238 0.109753638 7.364819981 573400.8164 0.0145038 0.027630251 1.73E-09 8.761118326 -0.152318457 MEISAELPQT(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 1 MEISAELPQTPQR 13 0 H3BS20;H3BNQ6;A0A087WTJ9;Q8IWV7-2;Q8IWV7 H3BS20 UBR1 E3 ubiquitin-protein ligase UBR1 1 0 MEIS(0.001)AELPQT(0.999)PQR 120.6 0.011847 18703000 4152.4 4538 4285.9 3982 3659.3 4483.7 3249.7 4534.6 4327.9 4386.1 TRUE FALSE FALSE 4101.788952 4601.886083 4360.494292 4442.417576 3472.552266 4197.20604 3525.729437 4665.801497 3940.801785 4272.14849 0.960123217 1.077183083 1.020679478 1.03985561 0.812835105 0.982457902 0.825282512 1.092144037 0.922440265 1 12.06074608 -8.825537093 25 0.995692362 0.924696083 0.159033146 0.083448505 80.75423234 31495.82454 0.010904217 0.019765578 1.49E-09 8.825537093 -0.070996279 MEIVELEDHPFFVGVQYHPEFLSR ddPTM_HeLa_Romidepsin_16h_R1 2 MEIVELEDHPFFVGVQYHPEFLSR 24 0 B4E1E0;P17812-2;P17812;A0A3B3IRI2 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 0 0 ; ; 87.793 3.35E-05 16323200 2286.7 1293.72 1992.2 1551.38 2133.7 1975.29 1784.06 1458.29 1487.52 939.47 FALSE FALSE TRUE 2258.828821 1311.933024 2026.873405 1730.757855 2024.809327 1849.075344 1935.598012 1500.48332 1354.472486 915.062434 2.468496943 1.433708756 2.215011053 1.891409581 2.212755384 2.02070949 2.115263331 1.639760594 1.480196799 1 9.83772637 -12.48033664 1.167976136 0.988480215 2.045215166 0.454812675 0.315455675 0.241499692 0.578983724 0.209706077 0.049079901 3.31E-13 12.48033664 1.056734951 MELAGSNTTAS(ph)SPAR ddPTM_HeLa_Romidepsin_16h_R1 1 MELAGSNTTASSPAR 15 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 MELAGSNTT(0.002)AS(0.677)S(0.321)PAR 125.36 0.0038727 31104000 2956.4 2789.8 2644.6 2954.2 2747.4 2960.3 2793.2 2319.4 3132.2 3018.2 TRUE FALSE FALSE 2920.36626 2829.074878 2690.628154 3295.778504 2607.189926 2771.146384 3030.454338 2386.50818 2852.048187 2939.786729 0.993393919 0.962340176 0.915246037 1.121094422 0.886863629 0.942635177 1.03084156 0.811796365 0.970154794 1 11.52149578 -7.25255273 24.17248335 0.98810555 0.811796218 0.39497644 0.06188209 501.1900088 1363234.68 0.007715978 0.120896709 5.59E-08 7.25255273 -0.176309331 MEPITK(ac)ISHIPASR ddPTM_HeLa_Romidepsin_16h_R1 1 MEPITKISHIPASR 14 1 B5MBX1;A0A0C4DFT8;G3XAA4;Q9NQC1-3;Q9NQC1-2;Q9NQC1 B5MBX1 JADE2 Protein Jade-2 0 1 MEPITK(1)ISHIPASR 67.326 0.011617 894510 219.48 170.61 382.59 193.01 239.7 231.96 197.66 222.23 294.94 197.54 FALSE TRUE FALSE 216.8048933 173.0118521 389.2488185 215.3267243 227.4672146 217.1385046 214.4492355 228.6598744 268.5598277 192.4078823 1.126798397 0.899193162 2.023039876 1.119115921 1.182213597 1.128532272 1.114555354 1.188412198 1.395783917 1 7.588024093 MEREDS(ph)S(ph)EEEEEEIDDEEIER ddPTM_HeLa_Romidepsin_16h_R1 3 MEREDSSEEEEEEIDDEEIER 21 1 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 2 0 MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER;MEREDS(1)S(1)EEEEEEIDDEEIER ;; 96.79 0.0011697 29829000 1474.22 1483.21 1465.02 1438.71 1578.66 1350.14 1831.21 1761.7 2012.12 1958.11 TRUE FALSE FALSE 1456.25164 1504.090669 1490.518059 1605.06042 1498.095089 1263.870411 1986.752932 1812.67201 1832.150948 1907.23802 0.76353954 0.788622423 0.781506054 0.841562722 0.785478831 0.66267052 1.041691132 0.9504173 0.960630466 1 10.89726919 -12.39763903 1.11510678 1.000313874 0.820097018 0.270435632 0.09970089 0.507732081 1.126166909 0.071040436 0.017991651 4.00E-13 12.39763903 -0.180216856 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIK ddPTM_HeLa_Romidepsin_16h_R1 2 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIK 34 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7 P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 MES(0.092)EGGADDS(0.908)AEEGDLLDDDDNEDRGDDQLELIK;MES(0.022)EGGADDS(0.978)AEEGDLLDDDDNEDRGDDQLELIK ; 65.33 8.34E-05 7677700 1919.8 1641.07 2004.68 1190.52 1818.55 2284.84 1980.69 2057.89 2080.04 1849.16 TRUE FALSE FALSE 1896.400739 1664.173027 2039.570614 1328.173524 1725.742608 2138.846098 2148.929759 2117.4318 1893.996013 1801.118557 1.052901672 0.923966399 1.132391095 0.737415935 0.958150479 1.187509889 1.193108444 1.175620446 1.051566542 1 10.81467743 -8.253362585 23.8102906 1.000034139 1.186182514 0.463541456 0.09981938 233.8734271 689450.8014 0.013859222 0.034605519 5.58E-09 8.253362585 0.186148375 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQLELIKDDEK ddPTM_HeLa_Romidepsin_16h_R1 2 MESEGGADDSAEEGDLLDDDDNEDRGDDQLELIKDDEK 38 2 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7 P07910-2 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 MES(0.027)EGGADDS(0.973)AEEGDLLDDDDNEDRGDDQLELIKDDEK;MES(0.336)EGGADDS(0.664)AEEGDLLDDDDNEDRGDDQLELIKDDEK ; 57.67 0.00033855 146446000 5621.48 4862.44 5663.22 3263.23 5753.99 5577.94 5084.1 5835.67 5417.34 6064.23 TRUE FALSE FALSE 5552.96324 4930.893558 5761.785968 3640.540007 5460.342419 5221.527636 5515.943327 6004.515904 4932.799542 5906.68043 0.940115739 0.834799447 0.975469392 0.616342809 0.92443505 0.884003748 0.933848274 1.016563529 0.83512213 1 12.52813184 -10.766687 1.283431435 0.98367168 0.880238807 0 0.113129017 0.520214879 1.785802991 0.022906851 0.021610244 1.71E-11 10.766687 -0.103432873 MESEGGADDS(ph)AEEGDLLDDDDNEDRGDDQVK ddPTM_HeLa_Romidepsin_16h_R1 1 MESEGGADDSAEEGDLLDDDDNEDRGDDQVK 31 1 B4DY08 B4DY08 HNRNPC 1 0 MES(0.006)EGGADDS(0.994)AEEGDLLDDDDNEDRGDDQVK 81.566 1.87E-08 16144000 1352.5 1146.2 1137.3 1487.1 1449 1775.9 1410.9 1608.1 1279.2 1443.4 TRUE FALSE FALSE 1336.01521 1162.336234 1157.094229 1659.045499 1375.052123 1662.425721 1530.741811 1654.627836 1164.785148 1405.90026 0.950291602 0.826755828 0.823027253 1.180059174 0.97805809 1.182463485 1.088798298 1.176916943 0.828497712 1 10.45727853 -9.247084952 24.94983108 0.95184895 1.114900437 0.587639994 0.090467364 542.4422038 942834.159 0.012952115 0.021415059 5.66E-10 9.247084952 0.163051487 MET(ph)EADAPSPAPSLGER ddPTM_HeLa_Romidepsin_16h_R1 1 METEADAPSPAPSLGER 17 0 Q12873-2;Q12873;Q12873-3 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 MET(0.945)EADAPS(0.055)PAPSLGER 206.67 3.87E-19 141780000 4704.9 4634.6 4350.9 3536.3 3735.9 3845.7 3751.5 3560.3 4813.5 4718.6 TRUE FALSE FALSE 4647.554869 4699.84602 4426.625589 3945.183645 3545.243082 3599.972181 4070.152316 3663.311663 4382.968504 4596.010092 1.011215114 1.022592624 0.963145315 0.858393164 0.771374086 0.783282045 0.885583851 0.797063451 0.953646406 1 12.16616625 -9.264279789 2.570155961 1.006438349 0.812904459 0.864382244 0.034300166 0.059496353 0.776452933 0.004621621 0.007800078 5.44E-10 9.264279789 -0.193533891 METEADAPS(ph)PAPS(ph)LGER ddPTM_HeLa_Romidepsin_16h_R1 1 METEADAPSPAPSLGER 17 0 Q12873-2;Q12873;Q12873-3 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 2 0 MET(0.325)EADAPS(0.766)PAPS(0.908)LGER 89.502 0.021469 11989000 2443.4 1990.9 2588.6 1940.1 2392.2 2115.4 1744.8 2167.3 2569.5 2642.7 TRUE FALSE FALSE 2413.618901 2018.927942 2633.653497 2164.42349 2270.117107 1980.232767 1893.003268 2230.007406 2339.677485 2574.042273 0.937676481 0.784341409 1.023158603 0.840865557 0.881926894 0.769308565 0.735420427 0.866344516 0.908950684 1 11.32982003 -9.166482842 0.270345778 1.012760915 0.725885203 0.312263781 0.075469244 1.801833027 0.261834882 0.05967178 0.178237453 6.82E-10 9.166482842 -0.286875712 METEADAPS(ph)PAPSLGER ddPTM_HeLa_Romidepsin_16h_R1 2 METEADAPSPAPSLGER 17 0 Q12873-2;Q12873;Q12873-3 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 MET(0.004)EADAPS(0.762)PAPS(0.234)LGER;METEADAPS(1)PAPSLGER ; 161.26 3.93E-05 21749900 5756 5804.6 5320 4995.3 4854.8 5298.3 3863.4 5047.1 6585 5777.9 TRUE FALSE FALSE 5685.843658 5886.317311 5412.592368 5572.88009 4607.04144 4959.755729 4191.5571 5193.129875 5996.021108 5627.789325 1.010315655 1.045937751 0.961761725 0.990243196 0.81862365 0.881297334 0.744796377 0.922765508 1.065430982 1 12.45835261 -8.791823334 6.688449769 1.004217407 0.837610732 0.729827471 0.050637516 0.058058803 8.231429036 0.006123784 0.011357204 1.62E-09 8.791823334 -0.166606675 METEADAPSPAPS(ph)LGER ddPTM_HeLa_Romidepsin_16h_R1 1 METEADAPSPAPSLGER 17 0 Q12873-2;Q12873;Q12873-3 Q12873-2 CHD3 Chromodomain-helicase-DNA-binding protein 3 1 0 METEADAPS(0.347)PAPS(0.653)LGER 88.319 0.014253 150470000 2989.5 2858.6 2588.5 2577.4 2802.5 2939.4 2149.9 2743.3 3510.3 3155.4 TRUE FALSE FALSE 2953.062824 2898.843446 2633.551757 2875.411115 2659.477967 2751.581826 2332.512452 2822.673057 3196.329976 3073.422253 0.960838629 0.943197259 0.85687925 0.935573077 0.865314867 0.895282717 0.758930033 0.918413685 1.03999051 1 11.58563028 -9.697809723 0.456374514 0.997708979 0.837507058 0.603356489 0.04742848 0.474484798 0.217523816 0.015216342 0.029809397 2.01E-10 9.697809723 -0.160201921 METVSNASSS(ph)SNPSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 METVS(0.007)NAS(0.05)S(0.184)S(0.695)S(0.064)NPS(0.086)S(0.914)PGR 83.964 0.023691 12870000 5023.8 4988.2 4810.8 4362.9 5051 4789.6 4876.2 5959.3 5640.7 4782.5 TRUE FALSE FALSE 4962.567993 5058.424011 4894.529956 4867.359026 4793.228622 4483.560018 5290.384306 6131.722943 5136.181665 4658.249961 1.065328833 1.085906521 1.05072291 1.044890048 1.02897626 0.962498804 1.135702109 1.316314709 1.102598982 1 12.18557234 -7.384661639 3.038002035 1.034127732 1.328311136 0.809697973 0.040124966 0.084044415 1.230005246 0.005342111 0.049976597 4.12E-08 7.384661639 0.294183403 METVSNASSSS(ph)NPSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 2 0 METVS(0.01)NAS(0.074)S(0.095)S(0.355)S(0.465)NPS(0.086)S(0.914)PGR 80.508 0.029551 3934600 908.85 1007.9 964.69 1222 875.01 1000.1 824.83 1002.2 1007.7 742.65 TRUE FALSE FALSE 897.7725866 1022.089243 981.4800248 1363.29339 830.3549746 936.1968377 894.8910396 1031.197076 917.5687882 723.3558459 1.24112163 1.412982626 1.356842597 1.884678747 1.147920459 1.294241061 1.237138048 1.425573708 1.268488799 1 9.498561728 -11.09592676 0.857502741 1.037900511 1.390879972 0.174930634 0.200647371 0.400829896 0.633933002 0.061184516 0.043354955 8.02E-12 11.09592676 0.35297946 METVSNASSSSNPS(ph)SPGR ddPTM_HeLa_Romidepsin_16h_R1 2 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 METVSNASSSSNPS(0.5)S(0.5)PGR;METVS(0.003)NAS(0.01)S(0.01)S(0.003)S(0.001)NPS(0.486)S(0.486)PGR ; 147.53 9.43E-05 30399570 8275.26 8871.24 7457.78 6736.44 5642.5 5618.1 6128.25 6514.83 9394.22 8218.22 TRUE FALSE FALSE 8174.397948 8996.12955 7587.579533 7515.338889 5354.54217 5259.121542 6648.783402 6703.326327 8553.977435 8004.70946 1.021198582 1.1238546 0.947889436 0.938864668 0.668923987 0.657003426 0.83060896 0.837422815 1.068618103 1 12.96663332 -8.931512018 3.93436465 1.014411519 0.748558296 0.779333029 0.070825076 0.080848656 2.511963502 0.010610005 0.019692619 1.17E-09 8.931512018 -0.265853224 METVSNASSSSNPSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 6 METVSNASSSSNPSSPGR 18 0 Q9NTI5-2;Q9NTI5;A9IYQ1 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 METVSNASSS(0.001)S(0.009)NPS(0.043)S(0.947)PGR;METVSNASSSS(0.001)NPS(0.047)S(0.952)PGR;METVSNASSSSNPS(0.056)S(0.944)PGR;METVSNASSSSNPS(0.473)S(0.527)PGR;METVSNASSSSNPS(0.106)S(0.894)PGR;METVSNASSSSNPS(0.013)S(0.987)PGR ;;;;; 176.17 9.04E-09 486940000 20993.69 19837.85 19553.46 16231.49 15559.6 15889.66 14778.05 16458.32 23915.19 20449.89 TRUE FALSE FALSE 20737.81083 20117.12777 19893.77977 18108.25125 14765.53555 14874.36201 16033.2972 16934.51552 21776.15551 19918.59891 1.041127989 1.009967009 0.998753972 0.909112701 0.741293884 0.746757444 0.804941014 0.85018608 1.093257393 1 14.28182855 -9.035133123 2.733750308 1.017933698 0.784780426 0.890126597 0.039992041 0.056234816 0.839537436 0.005351251 0.009825108 9.22E-10 9.035133123 -0.233153272 MEVGPFS(ph)TGQESPTAENAR ddPTM_HeLa_Romidepsin_16h_R1 1 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 0 MEVGPFS(0.677)T(0.318)GQES(0.004)PTAENAR 142.4 5.79E-11 0 1001.5 971.84 1137.9 415.18 617.14 1080.4 810.16 891.97 961.58 940.42 TRUE FALSE FALSE 989.2933328 985.521589 1157.704672 463.1850651 585.6450429 1011.365927 878.9749702 917.7777447 875.5738765 915.9877528 1.080028996 1.075911316 1.263886628 0.505667312 0.639359032 1.104126036 0.959592492 1.001954166 0.955879458 1 9.839184499 -9.290299185 24.9990788 1.057632416 0.851953975 0.294807308 0.178840639 799.8350491 692834.6843 0.028118386 0.042956147 5.13E-10 9.290299185 -0.205678441 MEVGPFST(ph)GQESPTAENAR ddPTM_HeLa_Romidepsin_16h_R1 2 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 0 MEVGPFS(0.229)T(0.701)GQES(0.067)PT(0.003)AENAR;MEVGPFS(0.005)T(0.578)GQES(0.365)PT(0.051)AENAR ; 164.82 1.01E-06 11162500 1714.03 1737.71 1711.62 1023.53 1677.28 2011.33 1682.69 1959.77 1810.31 1798.05 TRUE FALSE FALSE 1693.138743 1762.173527 1741.410028 1141.875354 1591.682143 1882.812504 1825.617647 2016.472853 1648.39134 1751.336402 0.966769572 1.006187918 0.994332115 0.652002296 0.908838611 1.075071872 1.042414036 1.151390933 0.941219139 1 10.77424051 -8.193668826 6.97261011 0.956561693 1.086175575 0.318212525 0.103639559 0.314019653 27.60914195 0.015470518 0.039748266 6.40E-09 8.193668826 0.129613882 MEVGPFSTGQES(ph)PTAENAR ddPTM_HeLa_Romidepsin_16h_R1 1 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 0 MEVGPFS(0.123)T(0.088)GQES(0.394)PT(0.394)AENAR 131.48 4.28E-09 0 682.4 656.3 691.61 499.3 696.72 538.3 449.01 838.02 749.8 770.31 TRUE FALSE FALSE 674.0826463 665.5394086 703.6471819 557.0314153 661.1637786 503.9043673 487.1488982 862.2667865 682.7360101 750.2972352 0.898420805 0.887034334 0.93782457 0.742414325 0.881202472 0.671606323 0.649274548 1.149233592 0.909954053 1 9.551318432 -10.5919969 0.496645143 0.990467119 0.807895489 0.090084028 0.137101142 0.958801999 0.584824038 0.060498094 0.053431433 2.56E-11 10.5919969 -0.18257163 MEVGPFSTGQESPT(ph)AENAR ddPTM_HeLa_Romidepsin_16h_R1 1 MEVGPFSTGQESPTAENAR 19 0 Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2 Q9Y4W2-3 LAS1L Ribosomal biogenesis protein LAS1L 1 0 MEVGPFST(0.001)GQES(0.026)PT(0.973)AENAR 126.14 0.0022368 10529000 1095.8 1261.2 1249.6 467.98 1078 1181.1 1124.2 1060.7 1221.2 1099.3 TRUE FALSE FALSE 1082.443968 1278.955207 1271.348764 522.0900495 1022.985637 1105.631522 1219.68952 1091.389681 1111.972813 1070.740028 1.010930702 1.194459135 1.187355223 0.487597396 0.955400574 1.032586336 1.139108923 1.019285403 1.038508681 1 10.06439253 MFGS(ph)MFLQAVFSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 MFGSMFLQAVFSSPK 15 0 Q8NHY0-3 Q8NHY0-3 2 0 MFGS(1)MFLQAVFS(0.457)S(0.543)PK 48.14 0.0042495 0 633.65 635.74 574.42 405.48 558.3 567.57 408.58 709.26 741.87 582.74 TRUE FALSE FALSE 625.9268301 644.6899644 584.4175391 452.3635054 529.8078677 531.3041087 443.284775 729.7813191 675.5152892 567.6003308 1.102759805 1.135816752 1.029628609 0.796975408 0.933417123 0.936053205 0.780980473 1.285730962 1.190124904 1 9.14873162 -9.501114964 24.50556108 1.057680293 0.933826307 0.193529458 0.139620231 794.1460471 894192.5383 0.019292863 0.029295881 3.15E-10 9.501114964 -0.123853985 MFIFSEEKR ddPTM_HeLa_Romidepsin_16h_R1 1 MFIFSEEKR 9 1 E9PLT2 E9PLT2 UBTF 0 0 95.815 0.021605 12439000 1344.2 1254.8 1397.3 1385.3 1169.2 1197.8 1514 1443.4 1434.7 1100.4 FALSE FALSE TRUE 1327.816373 1272.465107 1421.61942 1545.474904 1109.531361 1121.264446 1642.599122 1485.162502 1306.376839 1071.811449 1.238852574 1.187209847 1.32637081 1.441927967 1.035192675 1.046139642 1.532544855 1.3856565 1.21884949 1 10.06583542 -16.44384478 0.146015696 1.63E-13 1.37568535 0.100539526 0.162997803 60.03752089 0.61555102 17.23011493 0.39760015 3.60E-17 16.44384478 1.37568535 MFLVIGTHVMEGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 MFLVIGTHVMEGSGR 15 0 E7ERY9 E7ERY9 ATP2B1 Calcium-transporting ATPase 0 0 70.622 0.023252 15953000 2608.1 2650.3 2465.9 2291.5 2964.7 2891.5 2493.6 2650.8 2647.9 2854.9 FALSE FALSE TRUE 2576.311474 2687.610993 2508.817955 2556.454012 2813.400296 2706.742482 2705.406322 2727.496716 2411.065192 2780.729286 0.926487698 0.966512996 0.902215821 0.919346599 1.01174908 0.973393021 0.972912514 0.980856615 0.867062178 1 11.44124758 -8.750044243 24.99963662 0.956452782 0.983074218 0.155727873 0.040285018 408.9048187 897084.4359 0.005414465 0.010753417 1.78E-09 8.750044243 0.026621437 MFVS(ph)SSGLPPSPVPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 2 0 MFVS(0.95)S(0.049)SGLPPS(0.001)PVPS(1)PR 93.342 0.015995 15018000 2797.9 2687.4 2883.4 3321 5434.4 6233.5 5583.3 4941.2 3097.2 2860 TRUE FALSE FALSE 2763.798119 2725.233288 2933.584367 3704.989646 5157.062289 5835.199468 6057.545363 5084.165826 2820.178675 2785.696788 0.99213889 0.978295018 1.053088183 1.330004637 1.851264758 2.094700146 2.174517122 1.825096632 1.012378191 1 11.44382252 -8.842031797 1.927678943 0.996283771 2.050543348 0.967468625 0.085303353 0.035321258 0.266614228 0.012249732 0.026254066 1.44E-09 8.842031797 1.054259577 MFVSSSGLPPS(ph)PVPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 2 0 MFVS(0.005)S(0.008)S(0.001)GLPPS(0.988)PVPS(0.998)PR 103.39 0.0063004 17438000 2215.9 2163.4 2270.8 1861.2 4601.1 4333.5 3560.4 4083.5 2163.1 1923.4 TRUE FALSE FALSE 2188.891758 2193.856402 2310.322321 2076.400701 4366.288698 4056.603336 3862.820287 4201.64963 1969.626918 1873.429791 1.168387398 1.171037427 1.233204646 1.108341883 2.330639087 2.165335128 2.061897545 2.242757989 1.051348136 1 10.8714662 -8.76619873 24.99792158 1.103603412 2.187794494 0.972499583 0.088773754 14.78798129 77672.6036 0.015311715 0.028418295 1.71E-09 8.76619873 1.084191082 MFVSSSGLPPS(ph)PVPSPR ddPTM_HeLa_Romidepsin_16h_R1 1 MFVSSSGLPPSPVPSPR 17 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 MFVS(0.049)S(0.008)SGLPPS(0.941)PVPS(0.001)PR 90.259 0.012528 33097000 690.04 682.02 686.83 680.73 1704.8 2245.5 1946.4 2555.9 715.65 668.96 TRUE FALSE FALSE 681.6295271 691.6214955 698.783988 759.4392055 1617.797695 2102.019797 2111.727167 2629.850934 651.6404716 651.5803228 1.046117421 1.061452397 1.072444891 1.165534285 2.482882982 3.226033266 3.240931461 4.036111654 1.000092312 1 9.347799226 -8.500727678 1.478167245 1.01491701 3.644765622 0.970690576 0.193119236 0.042205726 0.178953966 0.027126959 0.082303578 3.16E-09 8.500727678 2.629848611 up MGAGLGHGMDR ddPTM_HeLa_Romidepsin_16h_R1 1 MGAGLGHGMDR 11 0 A0A087X0X3;P52272-2;P52272;M0R2T0;M0QZM1 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 0 0 62.166 0.029155 2680200 2827.3 3044.8 3092.5 1758.9 3315.2 3226.1 3152.8 2935.3 2970.9 2721.3 FALSE FALSE TRUE 2792.83978 3087.664774 3146.323665 1962.272294 3146.012973 3019.962622 3420.598753 3020.228274 2705.175263 2650.600234 1.053663146 1.164892667 1.187023085 0.740312428 1.186905869 1.13935047 1.29049968 1.139450693 1.020589687 1 11.37210338 -8.577190754 24.99999928 1.030435078 1.193727834 0.302783339 0.119833328 81.3498301 37445.21653 0.016633677 0.033267359 2.65E-09 8.577190754 0.163292757 MGEIEGTYRVLQT(ph)AGMR ddPTM_HeLa_Romidepsin_16h_R1 2 MGEIEGTYRVLQTAGMR 17 1 O94887-3;O94887-2;O94887;C9JWM9;C9JVQ5 O94887-3 FARP2 "FERM, RhoGEF and pleckstrin domain-containing protein 2" 1 0 MGEIEGTYRVLQT(1)AGMR;MGEIEGTYRVLQT(1)AGMR ; 71.316 0.0037995 5434400 1977.21 1667.16 1811.61 1332.95 1534.8 1574.6 1745.59 1815.11 1621.87 1919.8 TRUE FALSE FALSE 1953.111004 1690.630322 1843.140312 1487.071951 1456.473429 1473.988142 1893.860371 1867.627344 1476.805885 1869.923319 1.044487217 0.90411746 0.985676949 0.795258252 0.778894735 0.788261276 1.012801087 0.998772155 0.789768152 1 10.86876339 -9.916663563 1.701902937 1.020393371 0.878487741 0 0.110981469 0.303006638 1.758387819 0.015762133 0.021450637 1.21E-10 9.916663563 -0.14190563 MGESDDSILR ddPTM_HeLa_Romidepsin_16h_R1 3 MGESDDSILR 10 0 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 0 ;; ;; 128.38 0.019881 22855600 7840.7 6673.9 7006.6 5588.4 6839.5 6941.1 6672.8 6453.4 8132.9 7917 FALSE FALSE TRUE 7745.134533 6767.855339 7128.546934 6234.557102 6490.454793 6497.586111 7239.587465 6640.118947 7405.473055 7711.315199 1.004385677 0.877652536 0.924426865 0.808494653 0.841679354 0.84260414 0.938826553 0.861087736 0.960338524 1 12.91276122 -10.24549258 5.198115225 1.002306768 0.870193688 0.655861177 0.038633137 0.066621713 5.675361467 0.006148113 0.007362914 5.68E-11 10.24549258 -0.13211308 MGGCAGS(ph)RRRFS(ph)DSEGR ddPTM_HeLa_Romidepsin_16h_R1 1 MGGCAGSRRRFSDSEGR 17 3 A0A1B0GTS8 A0A1B0GTS8 2 0 MGGCAGS(1)RRRFS(0.998)DS(0.002)EGR 80.719 0.0054409 10784000 2126 2585 2167.8 10.937 1081.2 1072 1769.7 1415.1 2646.7 2381.1 TRUE FALSE FALSE 2100.087494 2621.391698 2205.52965 12.2015874 1026.022329 1003.50266 1920.018274 1456.043686 2409.972523 2319.238679 0.905507274 1.130281123 0.950971398 0.005261031 0.442396179 0.432686238 0.827865752 0.627811057 1.039122254 1 11.17943558 -9.467445662 24.78265732 0.970743542 0.483361696 0.637452768 0.201894696 146.9578523 65700.94219 0.031308231 0.047823962 3.41E-10 9.467445662 -0.487381846 MGGEEK(ac)PIGAGEEK ddPTM_HeLa_Romidepsin_16h_R1 1 MGGEEKPIGAGEEK 14 1 P26639;P26639-2;D6RCA5;D6R9F8;D6RDJ6;D6RJ97;D6RHV7;D6RCS6 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 1 MGGEEK(1)PIGAGEEK 87.863 0.023182 3345700 564.4 698.36 924.87 795.27 1483.5 1310.1 1263.1 1397.6 1844.2 1779.1 FALSE TRUE FALSE 557.5208757 708.1915304 940.9669744 887.2228593 1407.791459 1226.388838 1370.387682 1438.037351 1679.250133 1732.878726 0.321731041 0.408679223 0.543007979 0.511993624 0.812400452 0.707717638 0.790815689 0.829854582 0.969052311 1 10.75895498 -8.739968053 24.90406593 0.62778933 0.780064215 0.125019994 0.206434742 553.1539528 641586.3874 0.039950859 0.079841586 1.82E-09 8.739968053 0.152274885 MGMGNNYSGGYGT(ph)PDGLGGYGR ddPTM_HeLa_Romidepsin_16h_R1 1 MGMGNNYSGGYGTPDGLGGYGR 22 0 P31942-4;P31942-3;P31942;P31942-2 P31942-4 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 1 0 MGMGNNY(0.027)S(0.034)GGY(0.127)GT(0.812)PDGLGGYGR 59.154 0.014163 4562000 1204.1 1075.5 1348.4 1168.1 1018.1 1008.2 921.14 706.38 1327.1 1648.7 TRUE FALSE FALSE 1189.423966 1090.640917 1371.868336 1303.161218 966.1425579 943.7792738 999.3816086 726.8179908 1208.400852 1605.866536 0.740674234 0.679160374 0.8542854 0.811500326 0.601633159 0.587707168 0.622331673 0.452601741 0.752491459 1 10.64913628 -10.05219622 0.078287523 1.501770137 1.00E-16 0.506356233 0.104106904 6.322589804 0.384899445 3.380267683 3.78104087 8.87E-11 10.05219622 -1.501770137 MGPSCPVFLSFT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MGPSCPVFLSFTK 13 0 E5RGT4;E5RGP6;E5RHQ4;E5RK67;A0A1B0GVX5;E5RJ54;Q15822-2;Q15822 E5RGT4 CHRNA2 Neuronal acetylcholine receptor subunit alpha-2 1 0 MGPSCPVFLS(0.256)FT(0.744)K 126.31 0.0085229 3797000 969.17 933.24 1012.2 885.11 1099.1 1431.5 1172 1390.5 1184.3 864.99 TRUE FALSE FALSE 957.3573833 946.3781772 1029.816916 987.4505828 1043.008826 1340.03177 1271.549651 1430.731924 1078.373242 842.5174351 1.136305723 1.123274294 1.222309324 1.172023915 1.237967052 1.590509245 1.509226513 1.698162986 1.279941752 1 9.718562732 -5.178648024 0.27108059 1.014664795 3.87163436 0.767400991 0.103585313 4.940793899 0.110432989 0.032808486 5.881760703 6.63E-06 5.178648024 2.856969565 MGS(ph)GVER ddPTM_HeLa_Romidepsin_16h_R1 1 MGSGVER 7 0 A0A087X0X3;P52272-2;P52272;M0QZM1;M0R2I7 A0A087X0X3 HNRNPM Heterogeneous nuclear ribonucleoprotein M 1 0 MGS(1)GVER 49.06 0.025355 745650 2365.5 2887.4 1866.6 1954.2 2542.2 2341 1726.3 1822.9 2562 2102.7 TRUE FALSE FALSE 2336.668376 2928.048893 1899.08739 2180.153799 2412.462048 2191.417655 1872.931879 1875.642735 2332.848303 2048.071551 1.140911496 1.429661426 0.927256369 1.064491032 1.177918831 1.06999077 0.91448557 0.915809184 1.139046291 1 11.0000504 -7.787303609 5.015244967 1.092438906 0.912794501 0.273675704 0.127390525 0.195652703 12.4601367 0.01834138 0.062140316 1.63E-08 7.787303609 -0.179644404 MGSKSPGNT(ph)SQPPAFFSK ddPTM_HeLa_Romidepsin_16h_R1 1 MGSKSPGNTSQPPAFFSK 18 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2;H7C184 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 MGS(0.26)KS(0.26)PGNT(0.374)S(0.105)QPPAFFSK 59.502 0.027413 56437000 3284.5 2643.3 2384.6 5348 2664.1 1823.5 1541.2 1934.7 3063.9 3224.7 TRUE FALSE FALSE 3244.467251 2680.512447 2426.102963 5966.360923 2528.141036 1706.984235 1672.10949 1990.677492 2789.85711 3140.921829 1.032966571 0.853415842 0.772417492 1.899557279 0.804904157 0.543466004 0.532362657 0.633787659 0.888228763 1 11.61697232 -8.524693963 24.99999007 1.049997277 0.584131714 0.370624527 0.295500468 46.84288586 645141.5681 0.040760568 0.081978298 2.99E-09 8.524693963 -0.465865563 MHY(ph)PGAFTYSPTPVTS(ph)GIGIGMSAMGSAT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 MHYPGAFTYSPTPVTSGIGIGMSAMGSATR 30 0 H9KVB1;Q01196-11;Q01196;Q01196-9;Q01196-10;Q01196-2;Q01196-8 H9KVB1 RUNX1 Runt-related transcription factor 1 3 0 MHY(0.804)PGAFT(0.067)Y(0.115)S(0.023)PT(0.025)PVT(0.462)S(0.503)GIGIGMS(0.055)AMGS(0.164)AT(0.782)R 45.803 0.0034189 0 253.68 323.08 276.05 235.11 226.31 258.03 194.41 185.67 339.44 341.58 TRUE FALSE FALSE 250.5880506 327.6283287 280.8545345 262.2945244 214.7605562 241.5427158 210.9231805 191.0420685 309.0796363 332.7057024 0.753182313 0.984739145 0.844153053 0.788367986 0.645497071 0.725995118 0.633963227 0.574207377 0.928988094 1 8.378102783 -6.06502031 0.111834035 1.098795577 1.86E-16 0.722338988 0.074795097 29.36774161 0.378389448 0.612715623 4.96637223 8.61E-07 6.06502031 -1.098795577 MIAILTENYGGK ddPTM_HeLa_Romidepsin_16h_R1 1 MIAILTENYGGK 12 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 0 0 99.283 0.027491 269630 167.36 73.633 142.52 0 168.37 302.25 130 182.02 172.84 252.25 FALSE FALSE TRUE 165.3201519 74.66960731 145.0005008 0 159.7774506 282.9372005 141.0421968 187.2864615 157.3807575 245.6965086 0.672863253 0.303909924 0.590161015 0 0.650304115 1.151571921 0.574050472 0.762267492 0.640549426 1 7.940733547 -11.54413347 0.961392934 0.96291611 0.584161609 0.047940878 0.298603077 0.558326247 1.053060099 0.109563197 0.059850503 2.86E-12 11.54413347 -0.378754501 MIDQVFGVLES(ph)PELSR ddPTM_HeLa_Romidepsin_16h_R1 1 MIDQVFGVLESPELSR 16 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 MIDQVFGVLES(0.941)PELS(0.059)R 100.69 0.007354 5087500 1773.1 1585.1 1428.8 1641.1 2199.8 2359.3 1892.6 2335.7 1947.6 1784.5 TRUE FALSE FALSE 1751.488775 1607.415079 1453.667665 1830.851704 2087.535997 2208.548344 2053.357397 2403.279794 1773.401778 1738.138433 1.007680828 0.924791173 0.836335954 1.053340556 1.201018261 1.270640073 1.181354349 1.382674561 1.020287996 1 10.76332727 -8.751653667 2.878256865 0.983929636 1.264405653 0.802819144 0.070439286 0.091332765 1.551785889 0.010595354 0.0218413 1.77E-09 8.751653667 0.280476017 MIFPWRT(ph)MWLSVT(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 MIFPWRTMWLSVTLK 15 1 A0A087WXF5 A0A087WXF5 TTLL9 2 0 MIFPWRT(0.939)MWLS(0.068)VT(0.993)LK 61.102 0.0038294 0 2494.6 2208.2 2267.4 2327.4 2400.4 2527 2559.2 2621.1 2712.6 2744 TRUE FALSE FALSE 2464.194856 2239.287098 2306.863146 2596.504939 2277.898631 2365.532856 2776.578384 2696.937393 2469.978262 2672.710484 0.921983458 0.837833769 0.863117483 0.971487542 0.852280351 0.885068873 1.038862383 1.009064547 0.924147332 1 11.38408785 -5.946688252 24.25599921 0.944023398 0.931398981 0 0.069070752 0 0 0.009933972 0 1.13E-06 5.946688252 -0.012624417 MIGGLFIYNHK ddPTM_HeLa_Romidepsin_16h_R1 2 MIGGLFIYNHK 11 0 C9JJD3;C9JPV8;C9JTK4;C9JGT8;C9JJ47;A0A087WY71;E9PFW3;Q96CW1-2;Q96CW1 C9JJD3 AP2M1 AP-2 complex subunit mu 0 0 ; ; 63.283 0.024398 728310 0 0 62.991 181.76 48.47 238.91 59.581 0 0 0 FALSE FALSE TRUE 0 0 64.08733193 202.7759464 45.99639503 223.644422 64.64180865 0 0 0 0 MK(ac)IELDQVK ddPTM_HeLa_Romidepsin_16h_R1 1 MKIELDQVK 9 1 H0YF06;J3KN19;E9PKQ5;Q9GZT6-3;Q9GZT6-2;Q9GZT6 H0YF06 CCDC90B "Coiled-coil domain-containing protein 90B, mitochondrial" 0 1 MK(1)IELDQVK 95.502 0.012535 59921000 2714.9 2041.5 2346.7 1785.4 2671.9 2580.2 2140.9 2389.3 2434.2 2626.2 FALSE TRUE FALSE 2681.809755 2070.240291 2387.543329 1991.836349 2535.542973 2415.333547 2322.747993 2458.430626 2216.479055 2557.970945 1.048412907 0.809329087 0.933373905 0.778678254 0.991232124 0.944238069 0.908043149 0.96108622 0.866498918 1 11.32078416 -10.28535694 24.98854718 1.022861654 0.905134913 0.027539711 0.079795434 513.8232785 536829.542 0.010402848 0.011899323 5.18E-11 10.28535694 -0.117726741 MK(ac)LLPSVVLK ddPTM_HeLa_Romidepsin_16h_R1 1 MKLLPSVVLK 10 1 Q99075 Q99075 HBEGF Proheparin-binding EGF-like growth factor;Heparin-binding EGF-like growth factor 0 1 MK(1)LLPSVVLK 72.928 0.015971 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 MKDTDSEEEIREAFR ddPTM_HeLa_Romidepsin_16h_R1 2 MKDTDSEEEIREAFR 15 2 P0DP25;P0DP24;P0DP23;E7EMB3;G3V361;A0A590UJI2;Q96HY3;A0A590UJC0;G3V226 P0DP25 CALM2;CALM1 0 0 ; ; 71.933 0.010231 66330000 5597.1 5211.7 5087.8 5964.7 6498.9 6877.3 5593.1 6096.4 6316.4 5611.2 FALSE FALSE TRUE 5528.880392 5285.070449 5176.351025 6654.366679 6167.236882 6437.862725 6068.177774 6272.789715 5751.445364 5465.420215 1.011611216 0.967001665 0.94710943 1.217539808 1.128410376 1.177926394 1.110285675 1.147723225 1.052333606 1 12.41611671 -9.264364439 24.99999788 0.998144018 1.153459939 0.82253185 0.037316152 70.46538465 602255.893 0.004989078 0.007829798 5.44E-10 9.264364439 0.15531592 MKEIAEAYLGYPVTNAVITVPAYFNDSQR ddPTM_HeLa_Romidepsin_16h_R1 1 MKEIAEAYLGYPVTNAVITVPAYFNDSQR 29 1 A0A0G2JIW1;P0DMV9;P0DMV8 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 0 58.712 0.003972 0 1038.5 679.99 790.95 1122.3 1077.2 1243.2 1101.4 1288.4 683.97 529.71 FALSE FALSE TRUE 1025.842363 689.5629171 804.716153 1252.065607 1022.226464 1163.763532 1194.952889 1325.677821 622.7940102 515.9480578 1.988266739 1.336496778 1.559684431 2.426728016 1.981258479 2.255582737 2.316033311 2.569401708 1.207086645 1 9.011082022 -10.96599226 0.11224002 4.96E-13 3.291031095 0.750103631 0.262148627 4.510964198 0.32773134 5.199568324 3.903587894 1.08E-11 10.96599226 3.291031095 up MKETAEAYLGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 MKETAEAYLGKK 12 2 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 1 MKETAEAYLGK(1)K 79.633 0.01035 592430 0 0 127.65 234.97 648.67 683.14 550.94 667.07 551.22 300.65 FALSE TRUE FALSE 0 0 129.8716947 262.138337 615.5659494 639.4895587 597.7368298 686.370618 501.9175026 292.8390697 0 0 0.443491693 0.89516176 2.102062235 2.183757651 2.041178558 2.343849196 1.713970418 1 8.193964236 -8.840450965 2.985738062 0.465589553 2.184610653 0.69269198 0.483100191 0.086455059 1.558247665 0.06327524 0.124640052 1.44E-09 8.840450965 1.7190211 MKETIQGT(ph)GSWGPEPPGPGIPPAYSSPR ddPTM_HeLa_Romidepsin_16h_R1 1 MKETIQGTGSWGPEPPGPGIPPAYSSPR 28 1 Q9H4L4 Q9H4L4 SENP3 Sentrin-specific protease 3 1 0 MKET(0.029)IQGT(0.42)GS(0.029)WGPEPPGPGIPPAYS(0.261)S(0.261)PR 73.11 5.07E-05 22909000 411.59 407.1 294.04 320.9 180.95 244.86 261.02 315.15 445.41 363.84 TRUE FALSE FALSE 406.5733828 412.8311645 299.1576429 358.0039679 171.7154463 229.2142362 283.1910323 324.268368 405.5714141 354.3873843 1.14725693 1.164914957 0.844154324 1.01020517 0.484541645 0.646790056 0.799100207 0.915011037 1.144429604 1 8.469183437 -9.229448216 1.804125949 1.074135306 0.724757622 0.567233739 0.141247318 0.198034083 1.257532482 0.022886025 0.041328917 5.90E-10 9.229448216 -0.349377684 MKETIQGTGSWGPEPPGPGIPPAYSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 MKETIQGTGSWGPEPPGPGIPPAYSSPR 28 1 Q9H4L4 Q9H4L4 SENP3 Sentrin-specific protease 3 1 0 MKETIQGTGSWGPEPPGPGIPPAY(0.001)S(0.044)S(0.955)PR 71.676 0.00013561 29578000 369.25 516.25 395.37 476.81 456.93 349.34 347.84 368.43 388.4 514.31 TRUE FALSE FALSE 364.749439 523.5177811 402.251249 531.9410157 433.6111571 327.0183014 377.3855209 379.0899408 353.6605312 500.9481521 0.728118145 1.045053822 0.802979804 1.061868406 0.865580909 0.652798698 0.753342475 0.756744863 0.705982305 1 8.968517483 -8.372953471 6.320413489 0.891931108 0.725081097 0.292929025 0.11855603 0.240558823 11.90142302 0.017757569 0.040052097 4.24E-09 8.372953471 -0.166850011 MKPLVVFVLGGPGAGK ddPTM_HeLa_Romidepsin_16h_R1 1 MKPLVVFVLGGPGAGK 16 1 P30085-2;P30085 P30085-2 CMPK1 UMP-CMP kinase 0 0 150.26 2.92E-10 565340 1448.3 987.67 1055 1102.7 1264.4 1098.9 1148.7 977.31 1148.6 1156.9 FALSE FALSE TRUE 1430.647563 1001.574444 1073.361832 1230.199362 1199.87295 1028.683837 1246.270549 1005.586923 1045.866339 1126.843571 1.269606181 0.888831839 0.952538453 1.091721508 1.064808799 0.912889653 1.105983635 0.892392652 0.928138001 1 10.13807154 -10.25158743 24.98800793 1.127314031 0.994440069 0.010237899 0.115307165 807.1522782 2047224.573 0.020142775 0.024510785 5.60E-11 10.25158743 -0.132873962 MKT(ph)FS(ph)S(ph)FLQIGR ddPTM_HeLa_Romidepsin_16h_R1 1 MKTFSSFLQIGR 12 1 Q8NH92 Q8NH92 OR1S1 Olfactory receptor 1S1 3 0 MKT(1)FS(1)S(1)FLQIGR 59.067 0.0042282 0 481.99 536.85 640.11 527.31 606.38 620 707.83 715.79 690.13 795.9 TRUE FALSE FALSE 476.1153205 544.4077884 651.250846 588.2800633 575.4341659 580.384001 767.9530625 736.5002543 628.4030443 775.2224033 0.614166101 0.702260133 0.840082592 0.75885328 0.742282684 0.748667735 0.990622896 0.950050271 0.810610016 1 9.598466454 -7.756410343 24.91963127 0.79419478 0.970336651 0.383099281 0.09614205 150.1306658 743892.6203 0.020419927 0.071893336 1.75E-08 7.756410343 0.176141871 MKTPVQY(ph)S(ph)QQQNSPQKHK ddPTM_HeLa_Romidepsin_16h_R1 1 MKTPVQYSQQQNSPQKHK 18 2 P46013 P46013 MKI67 Antigen KI-67 2 0 MKT(0.005)PVQY(0.986)S(0.922)QQQNS(0.087)PQKHK 43.408 0.026955 7248000 2353.1 2261.4 2016.3 2302 2243.8 1940.6 1955.8 2017.7 2143.1 2330.8 TRUE FALSE FALSE 2324.419512 2293.236049 2051.392856 2568.168071 2129.290513 1816.601923 2121.925603 2076.078966 1951.415769 2270.24548 1.023862632 1.010126909 0.903599577 1.131229241 0.937912015 0.800178632 0.934667912 0.91447334 0.85956157 1 11.14863259 -8.528497497 24.99767043 1.01094525 0.88505984 0.242168149 0.077282994 85.51064485 380433.8662 0.008019887 0.016078465 2.96E-09 8.528497497 -0.125885409 MKYDEITAT(ph)Y(ph)LLLGRK ddPTM_HeLa_Romidepsin_16h_R1 1 MKYDEITATYLLLGRK 16 2 H0YIY6;J3KNR0;P27448-8;P27448-6;P27448-3;P27448-4;P27448-2;P27448;P27448-7 H0YIY6 MARK3 MAP/microtubule affinity-regulating kinase 3 2 0 MKY(0.13)DEIT(0.184)AT(0.744)Y(0.942)LLLGRK 42.568 0.0043312 0 837.22 1070.5 1072.9 584.31 640.95 1036.2 716.67 921.08 758.67 642.36 TRUE FALSE FALSE 827.0156406 1085.570527 1091.573374 651.8706715 608.2399298 969.9901642 777.5439319 947.7299966 690.8126551 625.6713946 1.3218051 1.735048999 1.744643249 1.041873861 0.972139585 1.550318862 1.242735306 1.514740812 1.104114174 1 9.289261336 -11.67872015 0.99233446 1.031393566 1.381126741 0.223144646 0.248800511 0.539325571 1.067856086 0.103449232 0.051853241 2.10E-12 11.67872015 0.349733176 MLAESDES(ph)GDEESVSQTDKTELQNTLR ddPTM_HeLa_Romidepsin_16h_R1 1 MLAESDESGDEESVSQTDKTELQNTLR 27 1 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 MLAES(0.09)DES(0.873)GDEES(0.036)VS(0.001)QTDKTELQNTLR 102.27 3.80E-08 20085000 3598.9 2854.6 3486.4 3793.2 4338 4812.8 4039.8 4563.5 3764.2 2953 TRUE FALSE FALSE 3555.035223 2894.787134 3547.07933 4231.787632 4116.615673 4505.277613 4382.940511 4695.537672 3427.520524 2876.280634 1.235983436 1.006434177 1.233217401 1.471270773 1.431228797 1.566355368 1.523822279 1.632503316 1.191650246 1 11.48998873 -9.237590199 1.499713099 1.103639959 1.552224852 0.851800353 0.083110076 0.124511583 0.548395425 0.016696493 0.031314468 5.79E-10 9.237590199 0.448584893 MLDGLDPHPMLPNY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MLDGLDPHPMLPNYK 15 0 Q02880;Q02880-2;E9PCY5 Q02880 TOP2B DNA topoisomerase 2-beta;DNA topoisomerase 2 1 0 MLDGLDPHPMLPNY(1)K 59.248 0.0038771 0 625.71 568.85 467.25 658.37 670.45 609.68 477.96 731.43 699.17 516.6 TRUE FALSE FALSE 618.0836058 576.8582852 475.3822902 734.4938371 636.2344347 570.7234157 518.5579105 752.592773 636.6344841 503.1786575 1.228358152 1.146428364 0.944758453 1.459707852 1.264430486 1.134236135 1.0305642 1.495677056 1.265225531 1 8.974926921 -9.272553879 24.97831606 1.10296445 1.254615452 0.19836197 0.156375276 951.7823762 2138996.211 0.024096623 0.037021858 5.34E-10 9.272553879 0.151651002 MLDLLEDFLEHEGYKYER ddPTM_HeLa_Romidepsin_16h_R1 1 MLDLLEDFLEHEGYKYER 18 1 Q14839-2;A0A2R8Y8C1;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2R8YFD8;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8Y445;A0A2R8YER1;A0A2R8YDJ9;A0A2R8YD40;A0A2R8Y5Z7;Q14839;A0A2R8Y685;A0A2R8Y4X2;A0A2R8YDW2;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 0 0 108.34 0.00038262 4516100 1224.4 876.78 822.33 1211.1 942.87 1038.8 751.32 849.15 1412.6 1275.6 FALSE FALSE TRUE 1209.476542 889.1233319 836.6423087 1351.13308 894.7518256 972.4240326 815.137102 873.7188155 1286.253518 1242.459728 0.973453316 0.715615413 0.673375796 1.087466298 0.720145535 0.782660404 0.656067222 0.70321701 1.035247653 1 10.27898338 -8.847768882 0.251287676 1.043812307 0.562107857 0.427516513 0.121041697 2.964279028 0.318961872 0.120143103 0.457416563 1.42E-09 8.847768882 -0.48170445 MLGEDS(ph)DEEEEMDTSER ddPTM_HeLa_Romidepsin_16h_R1 1 MLGEDSDEEEEMDTSER 17 0 A0A087WWF4;A0A087X0M4;Q9BWU0;H7C256 A0A087WWF4 SLC4A1AP Kanadaptin 1 0 MLGEDS(1)DEEEEMDTSER 101.3 0.0023225 42495000 2755.1 2708 2703 2500.3 2534.6 2481.6 2470.6 2394.3 3036 2422.9 TRUE FALSE FALSE 2721.519781 2746.123295 2750.044581 2789.39645 2405.249904 2323.033769 2680.452702 2463.575293 2764.452556 2359.952709 1.153209457 1.163634883 1.165296479 1.181971334 1.019194111 0.984356068 1.135807803 1.043908755 1.171401675 1 11.20454223 -6.987901894 14.04953181 1.087141124 0.979981333 0 0.075868817 1458218.968 31021695.57 0.011751861 2960712.429 1.03E-07 6.987901894 -0.107159792 MLIS(ph)AVSPEIR ddPTM_HeLa_Romidepsin_16h_R1 1 MLISAVSPEIR 11 0 E9PMT9;A0AVK6 E9PMT9 E2F8 Transcription factor E2F8 1 0 MLIS(0.997)AVS(0.003)PEIR 65.234 0.027187 10854000 1203.2 1550.2 742.57 2367.2 1088.8 650.38 765.49 820.63 1390.6 1623 TRUE FALSE FALSE 1188.534936 1572.023756 755.4941194 2640.906802 1033.234473 608.822817 830.5107015 844.3736343 1266.221253 1580.834226 0.751840336 0.994426696 0.477908504 1.670577951 0.653600774 0.385127553 0.525362298 0.534131676 0.800982945 1 10.62647037 -8.531189941 24.99990304 0.915167573 0.491496134 0.350674382 0.287977739 159.2469145 479010.534 0.039285191 0.078673639 2.94E-09 8.531189941 -0.423671438 MLLADQGQSWKEEVVTVETWQEGSLK ddPTM_HeLa_Romidepsin_16h_R1 1 MLLADQGQSWKEEVVTVETWQEGSLK 26 1 P09211;A8MX94;A0A087X2E9 P09211 GSTP1 Glutathione S-transferase P 0 0 147.41 8.65E-08 17676000 3408 3167.6 3444.4 4979.2 4204.4 3498.2 2967.6 3576.2 3992.3 3760.1 FALSE FALSE TRUE 3366.461985 3212.193556 3504.348337 5554.918532 3989.833779 3274.67631 3219.66787 3679.671705 3635.218689 3662.41206 0.919192579 0.877070494 0.956841633 1.516737724 1.089400568 0.894131042 0.879111312 1.004712644 0.992575011 1 11.8385784 -5.894853428 13.37574843 0.990824616 1.148085311 0 0.181007582 0 0 0.02443067 0 1.27E-06 5.894853428 0.157260694 MLMS(ph)SVK ddPTM_HeLa_Romidepsin_16h_R1 1 MLMSSVK 7 0 A6QRH7;Q5HY75;D3DWX8;P98173-3;P98173-2;P98173 A6QRH7 FAM3A Protein FAM3A 1 0 MLMS(0.999)S(0.001)VK 74.335 0.0026284 0 1800.1 1648.3 1609.2 1597 2060.1 2191.8 2125.3 2125.5 1722.9 1728.3 TRUE FALSE FALSE 1778.159689 1671.504811 1637.207451 1781.652654 1954.96541 2051.751054 2305.822929 2186.997989 1568.799509 1683.398517 1.056291586 0.992934706 0.972560825 1.058366534 1.16132062 1.218814816 1.369742759 1.299156419 0.931924018 1 10.71716104 -8.35241615 1.385159661 1.020162923 1.336351294 0.901731549 0.044279825 0.084356343 0.302141239 0.00571836 0.020822261 4.44E-09 8.35241615 0.316188371 MLNS(ph)SFEDDPFFSESILAHR ddPTM_HeLa_Romidepsin_16h_R1 1 MLNSSFEDDPFFSESILAHR 20 0 A0A494C175;A0A0S2Z4A4;P58340 A0A494C175 MLF1 Myeloid leukemia factor 1 1 0 MLNS(0.733)S(0.267)FEDDPFFSESILAHR 79.021 0.0015031 5352200 868.03 776.06 936.67 876.96 3196.7 3622.6 2875.6 3139.2 1023.3 1002.3 TRUE FALSE FALSE 857.4501165 786.9853931 952.9723484 978.3582414 3033.56047 3391.127551 3119.853392 3230.027799 931.7734851 976.2601015 0.87830089 0.806122663 0.976145954 1.002149161 3.107328125 3.473590231 3.195719448 3.308572986 0.954431594 1 9.931121761 -8.749280589 5.023239982 0.931352215 3.305940108 0.994669251 0.083859312 0.009150584 0.622865331 0.012886949 0.025271447 1.78E-09 8.749280589 2.374587893 up MLNSS(ph)FEDDPFFSESILAHR ddPTM_HeLa_Romidepsin_16h_R1 1 MLNSSFEDDPFFSESILAHR 20 0 A0A494C175;A0A0S2Z4A4;P58340 A0A494C175 MLF1 Myeloid leukemia factor 1 1 0 MLNS(0.386)S(0.614)FEDDPFFSESILAHR 103.94 0.00017078 5186500 357.39 298.52 366.18 359.08 1313.2 1595.6 1325.9 1277.7 342.35 339.88 TRUE FALSE FALSE 353.0339932 302.7225724 372.5532093 400.5985191 1246.182504 1493.64631 1438.521913 1314.668234 311.7293586 331.0498686 1.06640729 0.914431936 1.125368848 1.210085117 3.764334688 4.511846858 4.345332983 3.971209048 0.941638672 1 8.370904747 -8.730686597 3.75925598 1.029226523 4.265785695 0.991458553 0.141842818 0.012893168 0.386015678 0.020083955 0.040523925 1.86E-09 8.730686597 3.236559172 up MLPHAPGVQMQAIPEDAIPEES(ph)GDEDEDDPDKR ddPTM_HeLa_Romidepsin_16h_R1 5 MLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKR 33 1 Q13547 Q13547 HDAC1 Histone deacetylase 1 1 0 MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR;MLPHAPGVQMQAIPEDAIPEES(1)GDEDEDDPDKR ;;;; 98.667 7.08E-13 189355000 11305.3 11154.5 11074 11334.6 15212.2 14998 13256.5 12197.9 12047.1 11263.4 TRUE FALSE FALSE 11167.50666 11311.53334 11266.73832 12645.15978 14435.86467 14039.6762 14382.50678 12550.82699 10969.5772 10970.77524 1.017932316 1.031060531 1.026977408 1.152622262 1.315847271 1.279734193 1.310983632 1.14402371 0.999890797 1 13.42137786 -9.085645181 2.676672356 1.011242128 1.266948698 0.863428002 0.046330283 0.064710695 0.908064327 0.006664349 0.012016836 8.21E-10 9.085645181 0.25570657 MLQGELGGIMGQEPENK(ac)GDHSKVR ddPTM_HeLa_Romidepsin_16h_R1 1 MLQGELGGIMGQEPENKGDHSKVR 24 2 H0YFP6;Q8TBY8-3;Q8TBY8-4;Q8TBY8;Q8TBY8-1 H0YFP6 PMFBP1 Polyamine-modulated factor 1-binding protein 1 0 1 MLQGELGGIMGQEPENK(0.886)GDHSK(0.114)VR 42.904 0.010818 0 0 0 122.17 356.27 483.97 344.75 342.89 349.67 0 0 FALSE TRUE FALSE 0 0 124.2963176 397.4636137 459.271205 322.7215876 372.015068 359.7871498 0 0 0 MLS(ph)EDLPS(ph)LELYVNKMKDK ddPTM_HeLa_Romidepsin_16h_R1 1 MLSEDLPSLELYVNKMKDK 19 2 Q96RY7-2;Q96RY7 Q96RY7-2 IFT140 Intraflagellar transport protein 140 homolog 2 0 MLS(0.929)EDLPS(0.924)LELY(0.148)VNKMKDK 42.277 0.0041885 0 396.97 405.91 364.02 356.33 425.94 398.36 357.65 567.77 370.66 407.08 TRUE FALSE FALSE 392.1315769 411.6244116 370.3556154 397.5305512 404.2026924 372.9060816 388.0287821 584.1975292 337.5072413 396.5040029 0.988972555 1.038134315 0.934052652 1.002588998 1.019416423 0.940485036 0.978625132 1.473371075 0.851207652 1 8.631191621 -7.260526881 24.9690981 0.991268181 1.473371229 0.885322163 0.053691508 9.504416764 260031.4168 0.003867999 0.031413906 5.49E-08 7.260526881 0.482103049 MLTTVGPASS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 MLTTVGPASSSPK 13 0 A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-4;Q8IVL1-8;Q8IVL1-9;Q8IVL1-10;Q8IVL1-13;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1 A0A0A0MTL4 NAV2 Neuron navigator 2 1 0 MLTTVGPAS(0.001)S(0.651)S(0.348)PK 96.059 0.022693 33036000 4722.8 4656.8 4403.1 3843.9 3731.6 3857.9 3605.1 4287.1 4413.8 4293.2 TRUE FALSE FALSE 4665.236697 4722.358553 4479.734108 4288.349804 3541.162527 3611.392641 3911.317104 4411.140475 4019.018673 4181.662045 1.115641734 1.129301819 1.071280764 1.025513243 0.846831353 0.863626138 0.935349883 1.054877326 0.961105568 1 12.02986076 -8.932169995 6.417818012 1.063309232 0.921961553 0.439222885 0.069681336 0.142671158 10.51280964 0.01064796 0.019408823 1.17E-09 8.932169995 -0.141347678 MLTTVGPASSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 MLTTVGPASSSPK 13 0 A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-4;Q8IVL1-8;Q8IVL1-9;Q8IVL1-10;Q8IVL1-13;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1 A0A0A0MTL4 NAV2 Neuron navigator 2 1 0 MLTTVGPASS(0.228)S(0.772)PK 126.5 0.0046717 28701000 3406.3 3128 3807.2 3474.4 2844.9 2924.4 2368.9 2883 3595.7 3513.1 TRUE FALSE FALSE 3364.782705 3172.036066 3873.462719 3876.126476 2699.714137 2737.540278 2570.114307 2966.415056 3274.091586 3421.829156 0.983328668 0.927000128 1.131986006 1.132764466 0.788968126 0.800022489 0.751093696 0.866909165 0.956824972 1 11.74055202 -8.739512435 24.99922727 1.00696154 0.798006796 0.705492953 0.069286462 106.2462071 121132.2875 0.010128118 0.020242646 1.82E-09 8.739512435 -0.208954743 MLVLVLGDLHIPHR ddPTM_HeLa_Romidepsin_16h_R1 1 MLVLVLGDLHIPHR 14 0 Q9UBQ0 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 0 56.936 0.020396 225800 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 MLY(ph)AAT(ph)RAT(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 MLYAATRATVK 11 1 D6RG15;Q6IBS0 D6RG15 TWF2 Twinfilin-2 3 0 MLY(1)AAT(1)RAT(1)VK 53.775 0.0040314 0 264.4 360.94 306.82 332.47 338.14 259.3 220.6 353.91 386.49 368.88 TRUE FALSE FALSE 261.1773911 366.0213228 312.1600734 370.9117457 320.883454 242.7315669 239.3377585 364.1498275 351.9213664 359.2964444 0.726913375 1.018716796 0.868809247 1.032327905 0.893088309 0.675574642 0.666128937 1.013508019 0.979473557 1 8.489030848 -8.307572671 21.43369028 0.893137059 0.773176446 0.175589225 0.126879766 126.4912679 58767.91929 0.020204565 0.045179442 4.93E-09 8.307572671 -0.119960614 MLY(ph)QT(ph)INS(ph)LKTK ddPTM_HeLa_Romidepsin_16h_R1 1 MLYQTINSLKTK 12 1 E9PRL9;E9PII8;E9PPX4;Q15782-5 E9PRL9 CHI3L2 3 0 MLY(0.999)QT(0.999)INS(0.999)LKT(0.002)K 62.408 0.029861 43365000 7409.2 2988.9 4432.1 697.55 4994.6 3288.5 7450.2 4273.9 7885.2 6036.8 TRUE FALSE FALSE 7318.893821 3030.977813 4509.238841 778.2040131 4739.706925 3078.375463 8083.019802 4397.558553 7179.927963 5879.963066 1.244717652 0.515475655 0.766882171 0.132348453 0.806077669 0.523536531 1.374671866 0.747888805 1.221083854 1 12.52159138 -10.26612834 24.90843897 1.115561116 0.700160005 0.327647061 0.300299803 357.2098485 1897545.777 0.051563271 0.059995835 5.42E-11 10.26612834 -0.415401111 MMAECLEK ddPTM_HeLa_Romidepsin_16h_R1 1 MMAECLEK 8 0 I3L268;I3L0K9 I3L268 ACAP1 0 0 49.358 0.029112 0 159.95 0 350.03 516.89 8047.9 12010 6394.4 7352.1 692.46 283.34 FALSE FALSE TRUE 158.0004679 0 356.1221253 576.6552538 7637.185632 11242.59976 6937.540176 7564.821414 630.5246433 275.978786 0.572509468 0 1.290396739 2.089491233 27.67308946 40.73718826 25.1379473 27.41088011 2.284685184 1 8.108413563 -8.745595873 4.716585489 0.774153628 31.02427463 0.932747395 3.826995239 0.03113908 1.727438602 0.530757733 1.046706944 1.80E-09 8.745595873 30.250121 MMEIMTR ddPTM_HeLa_Romidepsin_16h_R1 2 MMEIMTR 7 0 D6RAT0;P61247;D6R9B6;H0Y9Y4;D6RG13;H0Y8L7;D6RB09;E9PFI5 D6RAT0 RPS3A 40S ribosomal protein S3a 0 0 ; ; 60.788 0.017219 1248650 1326.11 1104.33 1032.51 909.94 1055.12 1378.24 985.79 1274.97 1253.59 1194.28 FALSE FALSE TRUE 1309.946861 1119.876787 1050.480403 1015.151544 1001.273289 1290.174912 1069.522978 1311.859245 1141.465771 1163.252433 1.126107132 0.962711751 0.903054551 0.872683792 0.86075323 1.109110005 0.919424664 1.127751129 0.981270907 1 10.18394849 -10.18198156 9.718987373 1.059527133 0.958766764 0.089438249 0.093241313 0.593126009 69.78565363 0.015696621 0.019230964 6.58E-11 10.18198156 -0.100760369 MMST(ph)GS(ph)KK ddPTM_HeLa_Romidepsin_16h_R1 1 MMSTGSKK 8 1 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 2 0 MMS(0.182)T(0.819)GS(0.999)KK 69.198 0.0028751 0 1488.1 1531.5 1125.3 10019 1574.3 1841.6 1192.5 1458.9 1841.4 1694 TRUE FALSE FALSE 1469.962465 1553.060497 1144.885374 11177.44392 1493.957596 1723.927703 1293.79092 1501.11097 1676.700572 1649.989636 0.890891938 0.941254699 0.693874282 6.774250988 0.905434534 1.044811232 0.784120635 0.909769939 1.016188548 1 10.68824125 MMT(ph)DT(ph)QDGPS(ph)ESSQIMR ddPTM_HeLa_Romidepsin_16h_R1 1 MMTDTQDGPSESSQIMR 17 0 Q9HC10-3 Q9HC10-3 OTOF Otoferlin 3 0 MMT(1)DT(1)QDGPS(0.489)ES(0.489)S(0.022)QIMR 49.934 0.0042662 0 705.44 728.9 595.47 500.6 589.3 736.82 645.66 749.27 693.72 717.7 TRUE FALSE FALSE 696.8418259 739.1614733 605.8339056 558.4817274 559.225822 689.73958 700.5023443 770.9489453 631.6719457 699.0540505 0.996835403 1.057373851 0.866648158 0.798910652 0.799975083 0.986675607 1.002071791 1.102845974 0.903609593 1 9.449260198 -9.761321299 24.99999998 1.002878969 0.920864318 0.088885384 0.094518957 4.763193408 1008284.932 0.015217717 0.020757547 1.73E-10 9.761321299 -0.082014651 MNEVS(ph)VIK ddPTM_HeLa_Romidepsin_16h_R1 1 MNEVSVIK 8 0 P31751;P31751-2;A0A1B0GXA2;C9JHS6;J3QLS6;M0QZK3;E7EVP8;A8MX96;C9JIF6;C9J258;A0A5F9ZHJ8;A0A0A0MRF1;C9JIJ1;C9JC83;J3KSY8;J3KRI8 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 0 MNEVS(1)VIK 114.97 0.028437 63773000 3972.9 3440.5 3587.9 3292.7 3523 4488 3915.9 4238.2 3764.3 3453.2 TRUE FALSE FALSE 3924.476767 3488.935449 3650.345894 3673.417467 3343.208164 4201.231284 4248.516448 4360.82563 3427.61158 3363.485366 1.166788715 1.037297645 1.085286688 1.092146112 0.993971372 1.249070778 1.263129161 1.296519876 1.019065406 1 11.71574127 -8.16355733 6.008267917 1.074052499 1.273109499 0.781096245 0.051206638 0.110065825 5.600308986 0.009321648 0.024181621 6.86E-09 8.16355733 0.199057 MNFADEFAKLQDY(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 MNFADEFAKLQDYR 14 1 E5RFS7;E5RGE3;E5RID3 E5RFS7 FAM92A1 1 0 MNFADEFAKLQDY(1)R;MNFADEFAKLQDY(1)R ; 97.472 0.0092256 34468000 7320.8 7420 7448.9 8387.8 8271.6 8007.9 7438.3 7240.8 7284.8 7107.2 TRUE FALSE FALSE 7231.571274 7524.458955 7578.54498 9357.636902 7849.469386 7496.221034 8070.109016 7450.301124 6633.229243 6922.553919 1.044639212 1.086948407 1.094761423 1.351760782 1.133897905 1.082869288 1.165770482 1.076235911 0.9582055 1 12.75708867 -10.00651649 1.757047984 1.01926659 1.157613522 0.440128509 0.075968998 0.253786908 1.543153589 0.013231844 0.017336679 9.85E-11 10.00651649 0.138346932 MNGVMFPGNS(ph)PSYTER ddPTM_HeLa_Romidepsin_16h_R1 2 MNGVMFPGNSPSYTER 16 0 Q9NY27-2;Q9NY27;Q9NY27-3 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 0 MNGVMFPGNS(0.961)PS(0.037)YT(0.003)ER;MNGVMFPGNS(0.974)PS(0.025)YT(0.001)ER ; 118.71 0.0022094 111768000 6520.3 6342.1 5648.5 5876.5 6455.8 5430.6 5100.2 4977.4 6379.3 6355 TRUE FALSE FALSE 6440.828076 6431.38425 5746.809773 6555.96858 6126.336436 5083.602186 5533.410861 5121.413216 5808.719431 6189.896184 1.04053895 1.039013266 0.928417796 1.059140313 0.989731694 0.821274224 0.893942434 0.827382732 0.938419524 1 12.5956995 -8.342321624 4.994211378 1.01632058 0.852428156 0.693992481 0.045386075 0.067410304 2.961423261 0.005263357 0.012112968 4.55E-09 8.342321624 -0.163892424 MNIAS(ph)PGTVHK ddPTM_HeLa_Romidepsin_16h_R1 1 MNIASPGTVHK 11 0 E7EUC4;Q9NRH2 E7EUC4 SNRK SNF-related serine/threonine-protein kinase 1 0 MNIAS(0.999)PGT(0.001)VHK 86.498 0.012494 8204400 2604.6 2283.5 2910.2 2022.2 3173.5 3146.9 2621.1 2785 2629.3 2703.5 TRUE FALSE FALSE 2572.854133 2315.647173 2960.85081 2256.016279 3011.544453 2945.823246 2843.736169 2865.579581 2394.128823 2633.26268 0.97705943 0.87938328 1.124403893 0.856738029 1.14365516 1.11869707 1.079928786 1.088223975 0.909187238 1 11.36263573 -8.730049159 24.99999699 0.982758955 1.106438672 0.47711183 0.074123936 134.2125652 106889.8735 0.009085362 0.018169349 1.86E-09 8.730049159 0.123679717 MNLIIICMAR ddPTM_HeLa_Romidepsin_16h_R1 2 MNLIIICMAR 10 0 Q13472-3 Q13472-3 0 0 ; ; 157.34 0.0072736 22386900 3116.5 2121.19 3947.7 3506.5 4555 4143 3794.8 3279.9 3245.6 2528.9 FALSE FALSE TRUE 3078.514899 2151.052168 4016.408063 3911.938029 4322.541353 3878.275671 4117.130217 3374.798732 2955.305407 2463.198813 1.249803663 0.873275903 1.630565929 1.588153586 1.754848748 1.574487471 1.671456723 1.370087836 1.199783546 1 11.26631736 -9.746347022 24.99998701 1.102907345 1.607170446 0.782113742 0.133570637 85.64717702 141871.4086 0.022057054 0.031123319 1.79E-10 9.746347022 0.504263101 MNTY(ph)MNS(ph)T(ph)T(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MNTYMNSTTSK 11 0 A2RUB6;A2RUB6-3;C9JYB8 A2RUB6 CCDC66 Coiled-coil domain-containing protein 66 5 0 MNT(0.04)Y(0.977)MNS(0.985)T(0.999)T(0.999)S(1)K 54.416 0.0040403 0 343.1 321.77 243.78 243.59 178.39 226.77 258.29 288.7 230.52 344.26 TRUE FALSE FALSE 338.9181652 326.2998865 248.0228886 271.7550219 169.2860926 212.2801289 280.2291462 297.053079 209.9017139 335.3160756 1.010742371 0.973111372 0.739668947 0.810444359 0.504855284 0.633074715 0.835716408 0.885889764 0.625981661 1 8.38937784 -9.777464257 3.778223707 1.004786472 0.725195043 0.095486401 0.156852816 0.111124486 3.433922134 0.017066724 0.023493724 1.67E-10 9.777464257 -0.27959143 MNYMQNHQAGAPAPS(ph)LSR ddPTM_HeLa_Romidepsin_16h_R1 1 MNYMQNHQAGAPAPSLSR 18 0 Q9HCK8-2;Q9HCK8;A0A2R8Y840;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 0 MNYMQNHQAGAPAPS(0.523)LS(0.477)R 64.749 0.0091062 10387000 546.55 685.74 554.08 900.47 678.93 700.78 593.86 635.37 641.61 646.14 TRUE FALSE FALSE 539.8884384 695.3938657 563.72353 1004.586578 644.2816687 656.0024197 644.3024536 653.7534285 584.2227947 629.3531897 0.857846512 1.104934204 0.895718873 1.596220683 1.023720352 1.042343839 1.023753378 1.038770343 0.92829083 1 9.297726067 MNYMQNHQAGAPAPSLS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 MNYMQNHQAGAPAPSLSR 18 0 Q9HCK8-2;Q9HCK8;A0A2R8Y840;H0YJG4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 0 MNYMQNHQAGAPAPS(0.333)LS(0.667)R;MNYMQNHQAGAPAPS(0.278)LS(0.722)R ; 76.693 0.0044625 14625400 2686.3 1662.79 2678.7 1962.48 1646.06 1627 2470.31 1449.18 2608.7 2348.6 TRUE FALSE FALSE 2653.558342 1686.198801 2725.32165 2189.391171 1562.055416 1523.039951 2680.13807 1491.109737 2375.371338 2287.583033 1.159983399 0.737109332 1.191354198 0.957076154 0.682840969 0.665785647 1.17160253 0.651827591 1.038376008 1 11.1596084 -8.983333525 10.24544071 1.055457357 0.811917163 0.260296353 0.180866022 0.307207346 178.9687183 0.025819434 0.046497648 1.04E-09 8.983333525 -0.243540193 MNYNSQSRK ddPTM_HeLa_Romidepsin_16h_R1 1 MNYNSQSRK 9 1 Q9UKZ4;Q9UKZ4-2 Q9UKZ4 TENM1 Teneurin-1;Ten-1 intracellular domain;Teneurin C-terminal-associated peptide 0 0 63.426 0.027711 9862100 9132 8664.2 10139 9617 10376 12099 13457 3967.8 12660 11367 FALSE FALSE TRUE 9020.695671 8786.174835 10315.46504 10728.96279 9846.474002 11325.91295 14600.03724 4082.602033 11527.65789 11071.6837 0.814753737 0.793571698 0.931697953 0.969045276 0.889338448 1.022962112 1.318682654 0.368742654 1.041183817 1 13.43458701 -9.543080358 24.81720374 0.899322677 0.941902044 0 0.230030741 1402.533012 1722971.925 0.033554716 0.04745704 2.86E-10 9.543080358 0.042579367 MPDEPEEPVVAVS(ph)SPAVPPPTK ddPTM_HeLa_Romidepsin_16h_R1 3 MPDEPEEPVVAVSSPAVPPPTK 22 0 O60885;O60885-2;O60885-3;M0QZD9 O60885 BRD4 Bromodomain-containing protein 4 1 0 MPDEPEEPVVAVS(0.5)S(0.5)PAVPPPTK;MPDEPEEPVVAVS(0.5)S(0.5)PAVPPPTK;MPDEPEEPVVAVS(0.499)S(0.499)PAVPPPT(0.002)K ;; 90.718 0.00018094 33689800 15072.6 14897.8 13779.3 13834 14624.8 14573.5 13144.1 14261.2 15719.5 14916 TRUE FALSE FALSE 14888.88935 15107.53162 14019.12294 15433.55217 13878.44188 13642.30038 14260.55953 14673.82532 14313.50855 14528.48017 1.024807081 1.039856299 0.964940777 1.062296399 0.955257654 0.939003958 0.981558935 1.010004154 0.985203434 1 13.82659617 -8.725156494 24.99976611 1.013595977 0.96985977 0.30232189 0.030755645 149.4657929 102984.9159 0.004098679 0.008197174 1.88E-09 8.725156494 -0.043736208 MPDEPEEPVVAVSS(ph)PAVPPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 MPDEPEEPVVAVSSPAVPPPTK 22 0 O60885;O60885-2;O60885-3;M0QZD9 O60885 BRD4 Bromodomain-containing protein 4 1 0 MPDEPEEPVVAVS(0.212)S(0.769)PAVPPPT(0.019)K 85.054 0.00034182 5692800 2730.4 2308.9 2424.3 2138.2 2723.3 2666.1 2465.7 2400.3 2538.5 2843 TRUE FALSE FALSE 2697.120835 2341.404755 2466.493925 2385.428745 2584.319839 2495.744814 2675.136496 2469.748893 2311.450202 2769.13845 0.973992772 0.845535461 0.890708056 0.861433542 0.933257721 0.901271229 0.966053718 0.8918835 0.834718178 1 11.43522147 -10.4210321 6.415316151 0.988672247 0.900974436 0 0.058269829 0.118720881 6.349562019 0.005657786 0.006432438 3.79E-11 10.4210321 -0.087697812 MPDPAK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 1 MPDPAKSAPAPK 12 1 P23527;Q5QNW6;Q5QNW6-2;Q93079 P23527;Q5QNW6;Q93079 HIST1H2BO;HIST2H2BF;HIST1H2BH Histone H2B type 1-O;Histone H2B type 2-F;Histone H2B type 1-H 0 1 MPDPAK(1)SAPAPK 66.663 0.026027 0 239.81 0 135.83 0 74.257 221.98 184.1 171.96 136.82 178.06 FALSE TRUE FALSE 236.8871035 0 138.1940642 0 70.4673882 207.7961944 199.7374494 176.9353913 124.5824765 173.4339755 1.365863308 0 0.796810796 0 0.406306711 1.198128531 1.151662751 1.020188753 0.718327976 1 7.438242738 -5.387010244 7.017245782 0.950901636 0.8624958 0 0.496354377 0 0 0.072410059 0 4.10E-06 5.387010244 -0.088405836 MPEMTENETPTKK ddPTM_HeLa_Romidepsin_16h_R1 1 MPEMTENETPTKK 13 1 C9JBW0;Q68DE3 C9JBW0 KIAA2018 Basic helix-loop-helix domain-containing protein KIAA2018 0 0 85.355 0.026239 24313000 3267 3419.7 3520.2 2900.1 3852.4 3497.4 3069 3423.4 4360.9 3877.4 FALSE FALSE TRUE 3227.180547 3467.842626 3581.467604 3235.423207 3655.797653 3273.927427 3329.680783 3522.450678 3970.850182 3776.664589 0.854505469 0.918228915 0.94831498 0.856687993 0.967996381 0.866883291 0.881645882 0.932688248 1.05141722 1 11.88289695 -12.49549288 1.219665777 1.00043146 0.898628837 0.561659836 0.041301983 0.307174998 0.812171728 0.026291397 0.006279115 3.20E-13 12.49549288 -0.101802623 MPETVPQEEMPGPPLNSES(ph)GEEAPTGR ddPTM_HeLa_Romidepsin_16h_R1 1 MPETVPQEEMPGPPLNSESGEEAPTGR 27 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 MPETVPQEEMPGPPLNS(0.285)ES(0.714)GEEAPT(0.002)GR 95.543 5.37E-08 6360700 1905 1773.8 1567 1792.9 2079.9 1885.8 2015.7 1987 2045.1 2000.4 TRUE FALSE FALSE 1881.781127 1798.771603 1594.272978 2000.203534 1973.754942 1765.303466 2186.913508 2044.49071 1862.181134 1948.42932 0.965793888 0.923190585 0.818234956 1.026572282 1.012997968 0.906013602 1.122398173 1.049301963 0.955734506 1 10.92809588 -7.753696228 24.99853447 0.968327034 1.085850089 0.414599016 0.061380465 141.0670029 455419.3845 0.008626034 0.031090193 1.76E-08 7.753696228 0.117523055 MPFLSISS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 MPFLSISSPK 10 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 MPFLS(0.008)IS(0.05)S(0.942)PK 107.11 0.027468 159300000 8452.3 9672.9 8038.4 7806.4 10025 9381 7488 7215 7338.6 7068.7 TRUE FALSE FALSE 8349.280117 9809.07534 8178.30498 8709.012698 9513.386842 8781.584376 8124.030533 7423.754642 6682.217236 6885.054155 1.212667312 1.424691095 1.187834517 1.264915642 1.381744664 1.275456108 1.179951581 1.078242012 0.970539532 1 12.74925229 -11.69591522 0.82382908 1.011614325 1.256392433 0.539751551 0.096314782 0.364741694 0.493326345 0.047771852 0.020631046 2.01E-12 11.69591522 0.244778108 MPFWGHS(ph)PES(ph)DMGSRVGY(ph)PAQVYK ddPTM_HeLa_Romidepsin_16h_R1 1 MPFWGHSPESDMGSRVGYPAQVYK 24 1 M0R2Q7 M0R2Q7 SIPA1L3 3 0 MPFWGHS(0.932)PES(0.934)DMGS(0.202)RVGY(0.69)PAQVY(0.242)K 41.615 0.023054 3218800 1326 882.05 1030.2 1475.7 1114.8 1071.5 767.4 1080.9 1087.2 1069 TRUE FALSE FALSE 1309.838202 894.4675231 1048.130199 1646.327377 1057.907596 1003.034608 832.5829368 1112.174136 989.9581091 1041.227226 1.257975367 0.859051224 1.006629651 1.581141308 1.016019914 0.963319613 0.799616948 1.068137779 0.950760876 1 10.02406923 -8.529603354 24.99988476 1.128937288 0.939348212 0.120043976 0.198493025 230.3115302 856221.2319 0.028780616 0.057667344 2.95E-09 8.529603354 -0.189589076 MPPCS(ph)GGDGS(ph)TPPGPS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 MPPCSGGDGSTPPGPSLR 18 0 P07900-2;G3V592;A0A0U1RR69 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 3 0 MPPCS(1)GGDGS(0.646)T(0.646)PPGPS(0.709)LR 48.568 0.022132 1882700 112.17 58.095 230.6 227.53 135.69 0 45.354 0 224.39 234.76 TRUE FALSE FALSE 110.8028289 58.91286293 234.6134963 253.8380892 128.765233 0 49.20636763 0 204.3199964 228.6609014 0.484572694 0.257642923 1.026032413 1.110107096 0.563127462 0 0.215193622 0 0.89355021 1 7.837065891 -8.388508133 4.302782392 0.75641055 0.088836296 0.618022985 0.252387281 0.142552799 4.317235496 0.042556817 0.098529936 4.09E-09 8.388508133 -0.667574255 MPPS(ph)RRDRS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MPPSRRDRSK 10 3 Q13129 Q13129 RLF Zinc finger protein Rlf 2 0 MPPS(1)RRDRS(1)K 53.968 0.0042675 0 3114.9 3008.4 2919.5 3210.3 2397.3 2666.1 2574.6 2847.1 3879.6 3416.2 TRUE FALSE FALSE 3076.934401 3050.752334 2970.312673 3581.489991 2274.956835 2495.744814 2793.28646 2929.476347 3532.598859 3327.446632 0.924713374 0.916844858 0.892670267 1.076347839 0.683694462 0.750048037 0.839468448 0.880397696 1.061654551 1 11.70019981 -8.759395969 25 0.960665514 0.789310182 0.600707534 0.075148928 29.33781476 358922.8896 0.01026865 0.019748975 1.74E-09 8.759395969 -0.171355332 MPQDGS(ph)DDEDEEWPTLEK ddPTM_HeLa_Romidepsin_16h_R1 3 MPQDGSDDEDEEWPTLEK 18 0 F8WBL2;Q13895 F8WBL2 BYSL Bystin 1 0 MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK;MPQDGS(1)DDEDEEWPTLEK ;; 94.019 0.0013951 70535700 15253 14678.1 15063.8 13721.9 13019.6 14085.1 12950 14786.9 16322.1 14948.4 TRUE FALSE FALSE 15067.09057 14884.73868 15325.97912 15308.49064 12355.16123 13185.10757 14049.97268 15214.73562 14862.2105 14560.03841 1.034824919 1.022300783 1.052605679 1.05140455 0.848566527 0.905568186 0.964968105 1.044965349 1.020753522 1 13.82972654 -8.796224312 24.99996605 1.022514341 0.94019554 0.443137547 0.04856654 138.4684973 99516.96843 0.007386995 0.013390466 1.60E-09 8.796224312 -0.082318801 MPSRT(ph)ARY(ph)ARYSPR ddPTM_HeLa_Romidepsin_16h_R1 1 MPSRTARYARYSPR 14 3 I3L267;Q86WC6 I3L267 PPP1R27 Protein phosphatase 1 regulatory subunit 27 2 0 MPS(0.003)RT(0.656)ARY(0.743)ARY(0.055)S(0.542)PR 64.313 0.015046 30073000 2601.5 2557.7 2483 2651.3 2091.1 2095.6 2194.3 2437.2 3099.7 2699.6 TRUE FALSE FALSE 2569.791917 2593.707368 2526.215573 2957.855781 1984.383364 1961.697923 2380.683787 2507.716537 2822.455069 2629.464003 0.977306369 0.98640155 0.96073404 1.124889246 0.754672192 0.746044791 0.90538748 0.953698752 1.073395592 1 11.36055303 -8.750767798 24.9998626 0.994890103 0.83791729 0.561612323 0.076134639 129.0667589 302357.3032 0.010378364 0.02058702 1.78E-09 8.750767798 -0.156972814 MQASIEK(ac)GGSLPK ddPTM_HeLa_Romidepsin_16h_R1 2 MQASIEKGGSLPK 13 1 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 1 ; MQASIEK(1)GGSLPK;MQASIEK(1)GGSLPK 183.06 3.70E-07 2072700 843.4 735.53 860.04 366.79 802.47 800.16 461.65 515.29 843.15 655.46 FALSE TRUE FALSE 833.1203164 745.8848106 875.0086354 409.1999856 761.5169615 749.0323584 500.8625395 530.1991032 767.7365523 638.4310547 1.304949548 1.1683091 1.370560891 0.640946242 1.19279436 1.173239229 0.784520953 0.830471982 1.202536353 1 9.318387019 -9.278320812 24.99404873 1.165318421 0.94535957 0.362992074 0.183094105 948.5385423 1404369.21 0.03081218 0.047141057 5.27E-10 9.278320812 -0.219958851 MQEAMTQEVSDVFS(ph)DTTTPIK ddPTM_HeLa_Romidepsin_16h_R1 2 MQEAMTQEVSDVFSDTTTPIK 21 0 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 MQEAMTQEVS(0.004)DVFS(0.728)DT(0.063)T(0.161)T(0.043)PIK;MQEAMTQEVS(0.123)DVFS(0.317)DT(0.317)T(0.121)T(0.121)PIK ; 82.034 0.00074099 21163500 3562.3 3552.5 4007.4 2256.85 3782.7 4476.7 3350.7 4141.1 3739.2 4040 TRUE FALSE FALSE 3518.881317 3602.512188 4077.147116 2517.797616 3589.654704 4190.653318 3635.308374 4260.916195 3404.756587 3935.040218 0.894242784 0.915495647 1.036113201 0.639840377 0.912228212 1.064958193 0.923830043 1.082813887 0.865240607 1 11.94216267 -4.770885576 1.048697754 0.932501438 32.87781792 0.153147712 0.111890007 580.278506 3.745218817 0.016660192 43977.83249 1.69E-05 4.770885576 31.94531648 MQEAMTQEVSDVFSDTTT(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 1 MQEAMTQEVSDVFSDTTTPIK 21 0 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 MQEAMTQEVS(0.041)DVFS(0.046)DT(0.046)T(0.201)T(0.667)PIK 78.645 0.0013694 15068000 1773.5 1958.3 1815 1112 1956.2 2373.6 1431.4 2062.4 1733.4 2392.8 TRUE FALSE FALSE 1751.8839 1985.868999 1846.589314 1240.574672 1856.367814 2221.93462 1552.98308 2122.07229 1578.360363 2330.634711 0.751676739 0.85207218 0.79231177 0.532290481 0.796507409 0.953360306 0.666334828 0.910512608 0.6772234 1 11.18650719 -12.27988935 0.762049395 1.017303544 0.775547162 0 0.150974722 0.708266177 0.653608468 0.108191378 0.022299291 5.25E-13 12.27988935 -0.241756382 MQEFRS(ph)SDGRPDS(ph)GGT(ph)LRIYADSLK ddPTM_HeLa_Romidepsin_16h_R1 1 MQEFRSSDGRPDSGGTLRIYADSLK 25 3 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 3 0 MQEFRS(0.541)S(0.541)DGRPDS(0.901)GGT(0.908)LRIY(0.049)ADS(0.06)LK 43.198 0.0041956 0 275.43 139.06 0 172.15 0 129.83 295.47 0 210.99 0 TRUE FALSE FALSE 272.0729532 141.0176903 0 192.054793 0 121.534282 320.5672144 0 192.118526 0 0 MQK(ac)GIDYVKNK ddPTM_HeLa_Romidepsin_16h_R1 1 MQKGIDYVKNK 11 2 A0A590UJW3;A0A590UJH3;A0A1W2PSB2;E7EUE6;A0A1W2PRD1;Q9NY46-4;Q9NY46-2;Q9NY46-3;Q9NY46 A0A590UJW3 SCN3A Sodium channel protein type 3 subunit alpha 0 1 MQK(0.967)GIDYVK(0.033)NK 56.359 0.02606 0 0 0 0 0 123.53 130.41 0 124.13 0 0 FALSE TRUE FALSE 0 0 0 0 117.2258031 122.0772219 0 127.7215057 0 0 0 PDPAK(ac)SAPAPK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PDPAKSAPAPKK 12 2 P23527;Q5QNW6;Q5QNW6-2;Q93079 P23527;Q5QNW6;Q93079 HIST1H2BO;HIST2H2BF;HIST1H2BH Histone H2B type 1-O;Histone H2B type 2-F;Histone H2B type 1-H 0 2 ; PDPAK(1)SAPAPK(1)K;PDPAK(1)SAPAPK(1)K 122.34 0.0042648 12938600 1399.04 1125.38 1741.34 7167.8 21744.7 24673.1 22520.2 23018.1 955.34 1598.39 FALSE TRUE FALSE 1381.987962 1141.223129 1771.647292 7996.574762 20634.98682 23096.56854 24433.06523 23684.09241 869.8919977 1556.863597 0.887674402 0.733027049 1.137959225 5.136336141 13.25420342 14.83531928 15.69377386 15.21269586 0.558746443 1 10.60442683 -8.833714547 2.084425962 0.920415245 15.35019644 0.997981159 0.29643191 0.009709374 0.085860163 0.048324077 0.101962322 1.47E-09 8.833714547 14.42978119 up MQNDTAENETTEKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 MQNDTAENETTEKEEK 16 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 0 0 90.853 0.016733 2859300 1507.2 1279.3 1078.7 923.22 1150.6 1461.1 1149.1 1337.5 1360.3 1279.3 FALSE FALSE TRUE 1488.829667 1297.310019 1097.474321 1029.96704 1091.880589 1367.740425 1246.704525 1376.198452 1238.631361 1246.063602 1.194826383 1.041126647 0.880753053 0.82657662 0.87626393 1.097648967 1.000514359 1.104436764 0.994035424 1 10.28316199 -9.992200632 23.29627619 1.093368462 0.96172765 0.153347794 0.100672772 91.88101901 274439.4848 0.018552903 0.024349309 1.02E-10 9.992200632 -0.131640812 MQQNIQELEEQLEEEESAR ddPTM_HeLa_Romidepsin_16h_R1 3 MQQNIQELEEQLEEEESAR 19 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ;; ;; 193.98 1.09E-14 9191600 2686.38 2743.04 2761.17 2995.69 3098.84 2766.11 2895.95 3124.87 3256.74 2712.94 FALSE FALSE TRUE 2653.637367 2781.656589 2809.227006 3342.065773 2940.694631 2589.364498 3141.931921 3215.283183 2965.449018 2642.457428 1.004230887 1.05267792 1.063111548 1.264756714 1.112863579 0.979907745 1.189018937 1.216777667 1.122231521 1 11.36766451 -9.70352611 2.382232975 1.003582409 1.143215485 0.224451514 0.081932278 0.204827764 2.381497566 0.012048049 0.017413534 1.98E-10 9.70352611 0.139633077 MQRRGALFGMPGGS(ph)GGRK ddPTM_HeLa_Romidepsin_16h_R1 2 MQRRGALFGMPGGSGGRK 18 3 Q92995 Q92995 USP13 Ubiquitin carboxyl-terminal hydrolase 13 1 0 MQRRGALFGMPGGS(1)GGRK;MQRRGALFGMPGGS(1)GGRK ; 59.345 0.013711 58803000 7986.4 7220.5 8407.2 3732.77 9986.1 10875.8 9659.5 10378 8477.8 7465.1 TRUE FALSE FALSE 7889.058685 7322.150389 8553.523789 4164.370431 9476.472054 10180.87148 10479.97769 10678.27106 7719.524335 7271.155626 1.084980035 1.007013295 1.176363735 0.572724701 1.303296552 1.400172408 1.441308401 1.468579632 1.061664023 1 12.82796896 -8.538032011 24.99761939 1.01714686 1.422913322 0.648010401 0.152571895 108.0252214 178203.5987 0.020690624 0.041392663 2.90E-09 8.538032011 0.405766461 MQYAPNTQVEILPQGHES(ph)PIFK ddPTM_HeLa_Romidepsin_16h_R1 1 MQYAPNTQVEILPQGHESPIFK 22 0 P40121-2;P40121;H7C0X8 P40121-2 CAPG Macrophage-capping protein 1 0 MQYAPNTQVEILPQGHES(1)PIFK 86.701 0.00027595 25421000 1970.1 1545.4 1569.9 1632.9 1555.9 1884.2 1540.7 1558.2 1563.7 1232.3 TRUE FALSE FALSE 1946.087663 1567.156182 1597.223451 1821.703581 1476.496617 1763.805701 1671.56702 1603.284059 1423.838756 1200.284668 1.621355096 1.305653753 1.330703868 1.517726277 1.230122034 1.469489487 1.392642149 1.335753177 1.18625089 1 10.22916089 -12.52002877 1.265435724 0.999266228 1.421527031 0.483110696 0.120918672 0.231071538 0.660601305 0.084153093 0.020066768 3.02E-13 12.52002877 0.422260803 MREDY(ph)DSVEQDGDEPGPQR ddPTM_HeLa_Romidepsin_16h_R1 1 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 0 MREDY(0.967)DS(0.033)VEQDGDEPGPQR 61.52 0.01085 29185000 1128.3 1045.8 1061.2 1078.7 1069.5 1369.1 1343.2 1166.6 1256.6 1194.7 TRUE FALSE FALSE 1114.547846 1060.5228 1079.669741 1203.424369 1014.919424 1281.618929 1457.291374 1200.35373 1144.206549 1163.661522 0.957793847 0.911367077 0.927821124 1.034170458 0.872177523 1.101367455 1.252332699 1.031531685 0.983281244 1 10.18445576 -8.070273219 6.70318621 0.968584355 1.15049026 0.585046432 0.066651382 0.110599647 8.816423326 0.008592378 0.022331607 8.51E-09 8.070273219 0.181905905 MREDYDS(ph)VEQDGDEPGPQR ddPTM_HeLa_Romidepsin_16h_R1 1 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 1 0 MREDYDS(1)VEQDGDEPGPQR 87.729 0.0052129 42312000 1799.6 1507.4 1301.4 1547.4 1488.5 1538.8 1382.2 1514.9 1993.3 1573 TRUE FALSE FALSE 1777.665783 1528.621217 1324.050321 1726.317669 1412.536291 1440.475646 1499.604033 1558.731241 1815.014256 1532.133233 1.160255351 0.99770776 0.864187456 1.12674122 0.921940899 0.940176491 0.978768687 1.017360114 1.18463213 1 10.58132604 -10.02122048 24.44667113 1.075850114 0.974043634 0.348158352 0.081151873 607.27263 699596.2692 0.01374531 0.016933094 9.52E-11 10.02122048 -0.10180648 MREDYDSVEQDGDEPGPQR ddPTM_HeLa_Romidepsin_16h_R1 2 MREDYDSVEQDGDEPGPQR 19 1 Q9Y5S9;Q9Y5S9-2 Q9Y5S9 RBM8A RNA-binding protein 8A 0 0 ; ; 94.61 0.0037843 29662000 1961.62 2030.44 1741.99 1976.53 2114.35 2277.1 1940.69 2093.9 2471.8 1850.63 FALSE FALSE TRUE 1937.711021 2059.024588 1772.308605 2205.065698 2006.44683 2131.600659 2105.53216 2154.483693 2250.716017 1802.550366 1.074983012 1.142284081 0.983222793 1.223303238 1.113115543 1.182547073 1.168085064 1.195241883 1.248628643 1 10.81582386 -8.129307488 0.136035119 0.932895636 1.381868018 0 0.09455305 9.753674199 0.315429426 0.249552421 0.903110042 7.42E-09 8.129307488 0.448972382 MRKQT(ph)CQEIDEELK ddPTM_HeLa_Romidepsin_16h_R1 1 MRKQTCQEIDEELK 14 2 A0A087X1X6;P32314-2;P32314 A0A087X1X6 FOXN2 Forkhead box protein N2 1 0 MRKQT(1)CQEIDEELK 134.23 2.37E-05 0 807.8 893.33 1032.8 616.48 771.39 815.24 685.2 848.21 855.46 849.72 TRUE FALSE FALSE 797.9542229 905.9063232 1050.775451 687.7603182 732.0230898 763.1487951 743.4008709 872.7516181 778.9455151 827.6441519 0.964127181 1.094560169 1.26959811 0.830985535 0.884465973 0.922073567 0.898213162 1.054501039 0.941159934 1 9.6928668 MRPNS(ph)NTPVNETATASDSK ddPTM_HeLa_Romidepsin_16h_R1 1 MRPNSNTPVNETATASDSK 19 1 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 MRPNS(0.5)NT(0.5)PVNETATASDSK 71.592 0.016291 3496900 2172.1 2125.3 2007.8 1780.2 1282.1 1217.6 1191.1 1003.9 2307.9 2294.6 TRUE FALSE FALSE 2145.62561 2155.220029 2042.744917 1986.0351 1216.669653 1139.79929 1292.272004 1032.946263 2101.475644 2234.985961 0.960017489 0.964310321 0.91398557 0.88861189 0.544374629 0.509980514 0.578201397 0.462171253 0.940263465 1 11.12605005 -8.816725064 2.891583005 0.973361936 0.518370223 0.96994003 0.036377696 0.029751454 0.50668723 0.005655356 0.011306353 1.53E-09 8.816725064 -0.454991714 MRPNSNTPVNETAT(ph)ASDS(ph)KGT(ph)S(ph)NSSK ddPTM_HeLa_Romidepsin_16h_R1 1 MRPNSNTPVNETATASDSKGTSNSSK 26 2 O15014 O15014 ZNF609 Zinc finger protein 609 4 0 MRPNS(0.034)NT(0.109)PVNET(0.109)AT(0.67)AS(0.204)DS(0.799)KGT(0.519)S(0.519)NS(0.519)S(0.518)K 42.325 0.0042659 0 684.33 533.88 559.53 557.8 398.05 618.07 273.4 705.24 573.04 662.09 TRUE FALSE FALSE 675.9891227 541.3959767 569.2683849 622.2954605 377.7360232 578.5773217 296.6225892 725.6450067 521.7858672 644.8888064 1.048225859 0.839518335 0.882738822 0.964965517 0.585738223 0.89717377 0.459959277 1.125224999 0.809109822 1 9.332906618 -9.672700577 0.988336586 1.022942007 0.768752291 0.040911134 0.19003444 0.454758671 0.887674911 0.030818136 0.050722817 2.12E-10 9.672700577 -0.254189716 MRSLSSTSSGSK(ac)DK ddPTM_HeLa_Romidepsin_16h_R1 1 MRSLSSTSSGSKDK 14 2 D6REY2;P23508;P23508-2;A0A096LNU0;A0A096LPB3 D6REY2 MCC Colorectal mutant cancer protein 0 1 MRSLSSTSSGSK(1)DK 64.224 0.017601 0 310.92 484.51 423.6 1203.7 392.96 406.16 238.44 335.95 490.44 311.26 FALSE TRUE FALSE 307.1303874 491.3309445 430.9725803 1342.877458 372.9057849 380.2076868 258.6930876 345.6701832 446.5738181 303.1734203 1.013051827 1.620626716 1.421538141 4.42940366 1.230008173 1.254093075 0.853284194 1.140173116 1.472997922 1 8.243999466 -10.1819171 2.813036339 1.001717196 1.750766353 0.056303856 0.95932393 0.473281995 7.237302282 0.168345684 0.20557241 6.58E-11 10.1819171 0.749049157 MRSNYETLVS(ph)LDDGLPK ddPTM_HeLa_Romidepsin_16h_R1 1 MRSNYETLVSLDDGLPK 17 1 Q8N393-2 Q8N393-2 1 0 MRSNYETLVS(1)LDDGLPK 69.148 0.0034968 0 784.9 728.97 755.18 697.11 892.76 953 651.27 830.04 898.51 741.74 TRUE FALSE FALSE 775.3333369 739.2324588 768.3235911 777.7131382 847.1991259 892.1063757 706.5888575 854.0558978 818.1450152 722.4694879 1.073171047 1.023202324 1.063468567 1.076465029 1.172643468 1.234801456 0.978018961 1.182134211 1.132428468 1 9.496792849 -9.082900288 2.594500309 1.035908533 1.135940451 0.19739985 0.071796956 0.25282394 3.340387084 0.010022795 0.018167042 8.26E-10 9.082900288 0.100031918 MS(ph)DVS(ph)TS(ph)VQS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 MSDVSTSVQSK 11 0 Q5T7N2 Q5T7N2 L1TD1 LINE-1 type transposase domain-containing protein 1 4 0 MS(0.994)DVS(0.559)T(0.559)S(0.913)VQS(0.975)K;MS(1)DVS(0.611)T(0.611)S(0.936)VQS(0.841)K ; 63.091 0.01685 27604200 8193.4 7264.8 6590.2 6935.9 6920.7 6707.2 4884.9 7833.5 8053.5 8573.4 TRUE FALSE FALSE 8093.535689 7367.074045 6704.899667 7737.861392 6567.510854 6278.631566 5299.823284 8060.149963 7333.17479 8350.661832 0.969208891 0.882214391 0.802918356 0.926616542 0.78646591 0.75187233 0.634659071 0.965210917 0.878154922 1 13.02767483 -9.808820996 0.708713902 0.995905908 0.775286745 0.269185682 0.093252814 0.357989877 0.366980525 0.01911374 0.031149194 1.55E-10 9.808820996 -0.220619162 MS(ph)DYSPNSTGSVQNTSR ddPTM_HeLa_Romidepsin_16h_R1 1 MSDYSPNSTGSVQNTSR 17 0 H7C1W4;Q93075 H7C1W4 TATDN2 Putative deoxyribonuclease TATDN2 1 0 MS(0.949)DYS(0.051)PNSTGSVQNTSR 198.52 8.92E-19 5345800 1940.4 2022.6 1666.7 1603.2 1384.3 1452.9 1132.2 1339.1 2350.5 1838.6 TRUE FALSE FALSE 1916.749658 2051.074216 1695.708214 1788.569527 1313.654005 1360.064379 1228.36904 1377.844746 2140.265393 1790.832907 1.070311837 1.145318588 0.94688243 0.99873613 0.733543593 0.759459117 0.685920521 0.769387663 1.195122887 1 10.80641502 -8.80077135 3.681069604 1.036268644 0.731675386 0.82477521 0.072418472 0.056167773 1.587306705 0.008228542 0.016041562 1.58E-09 8.80077135 -0.304593258 MS(ph)GGSTMSSGGGNTNNSNSK ddPTM_HeLa_Romidepsin_16h_R1 1 MSGGSTMSSGGGNTNNSNSK 20 0 A0A6E1WJ75;Q86U70-3;Q86U70-2;Q86U70 A0A6E1WJ75 LDB1 LIM domain-binding protein 1 1 0 MS(0.489)GGS(0.093)T(0.377)MS(0.038)S(0.003)GGGNTNNSNSK 96.562 0.0002745 6781200 687.6 588.27 465.75 534.77 453.21 459.12 473.47 472.6 616.7 657.31 TRUE FALSE FALSE 679.2192667 596.5516805 473.8561834 596.6026236 430.0810025 429.7837137 513.68653 486.2739354 561.5408074 640.2329914 1.060893887 0.93177279 0.740130843 0.931852359 0.671757014 0.671292669 0.802343111 0.759526519 0.877088208 1 9.322453211 -9.919887874 3.113581893 1.028430967 0.763048167 0.562429699 0.085495447 0.091230943 1.792517543 0.011957129 0.015912733 1.20E-10 9.919887874 -0.2653828 MS(ph)PMGTASGSNSPTSDSASVQR ddPTM_HeLa_Romidepsin_16h_R1 4 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 0 MS(0.998)PMGT(0.002)ASGSNSPTSDSASVQR;MS(1)PMGTASGSNSPTSDSASVQR;MS(0.905)PMGT(0.095)ASGSNSPTSDSASVQR;MS(0.999)PMGT(0.001)ASGSNSPTSDSASVQR ;;; 188.63 4.12E-18 36032600 4527.51 4592.37 3938.48 4196.48 5305.89 4742.75 4382.51 4299.46 5447.61 4943.96 TRUE FALSE FALSE 4472.326967 4657.021505 4007.027592 4681.696763 5035.110634 4439.703582 4754.76029 4423.858092 4960.362118 4815.515206 0.928732809 0.967086865 0.832107764 0.972210981 1.045601648 0.921958169 0.987383506 0.918667661 1.030079214 1 12.23347444 -12.41310319 1.137542986 1.000024937 0.946608305 0.193350903 0.053343609 0.847305487 1.959212927 0.035643707 0.009000599 3.86E-13 12.41310319 -0.053416632 MS(ph)PPS(ph)AS(ph)PPSSSGGR ddPTM_HeLa_Romidepsin_16h_R1 1 MSPPSASPPSSSGGR 15 0 P43681-2 P43681-2 3 0 MS(0.91)PPS(0.836)AS(0.907)PPS(0.159)S(0.153)S(0.035)GGR 50.158 0.026842 6034700 4060.4 2319.5 3168 607.29 2379.3 2103.3 3996.6 3168.7 4936.7 4091.9 TRUE FALSE FALSE 4010.910283 2352.153982 3223.137711 677.5077272 2257.875443 1968.905918 4336.071104 3260.381335 4495.149188 3985.591848 1.006352491 0.59016429 0.808697386 0.169989239 0.566509449 0.494005908 1.087936565 0.818041952 1.127849855 1 11.96057826 -10.26642612 24.42196381 1.002999799 0.643583569 0.382050925 0.229393718 252.4325732 1236256.571 0.039261567 0.045652517 5.41E-11 10.26642612 -0.359416229 MS(ph)S(ph)LSQS(ph)MRK ddPTM_HeLa_Romidepsin_16h_R1 1 MSSLSQSMRK 10 1 F5H2B9;H0YNH8;Q9BZF9-2;Q9BZF9 F5H2B9 UACA Uveal autoantigen with coiled-coil domains and ankyrin repeats 3 0 MS(0.668)S(0.668)LS(0.668)QS(0.996)MRK 43.246 0.0041799 0 1810.8 2222.9 1951.2 1700.2 2207.6 2719.9 2390.8 2375.1 1777.2 2439.6 TRUE FALSE FALSE 1788.729273 2254.194045 1985.159818 1896.785124 2094.937934 2546.107168 2593.874492 2443.819771 1618.242781 2376.21884 0.752762853 0.948647493 0.835428027 0.798236716 0.881626683 1.071495236 1.091597478 1.02844895 0.681015887 1 11.21445199 -8.267308663 8.782413604 0.875413099 1.066773438 0.533167222 0.091332343 0.091962379 88.26753542 0.013746861 0.03234205 5.40E-09 8.267308663 0.191360338 MS(ph)SPEDDSDTKR ddPTM_HeLa_Romidepsin_16h_R1 2 MSSPEDDSDTKR 12 1 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 MS(0.99)S(0.008)PEDDS(0.002)DTKR;MS(0.643)S(0.32)PEDDS(0.036)DT(0.001)KR ; 158.06 0.00075339 13370400 4198.4 3586 3728.1 3573.2 3866.2 4085.7 4167.4 3320.4 3903.4 4495.9 TRUE FALSE FALSE 4147.228286 3636.483802 3792.986017 3986.350196 3668.893387 3824.636956 4521.378852 3416.470535 3554.270128 4379.09587 0.947051266 0.83041886 0.866157337 0.910313525 0.837819837 0.873385071 1.032491406 0.78017715 0.81164474 1 12.09641732 -10.56349643 2.623724851 0.979953191 0.881392167 0 0.082628379 0.213890989 3.034498434 0.0113193 0.01205901 2.73E-11 10.56349643 -0.098561024 MS(ph)TIGS(ph)FEGFQAVS(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 MSTIGSFEGFQAVSLK 16 0 C9JDW1;C9IYC1;Q6ZUI0 C9JDW1 TPRG1 Tumor protein p63-regulated gene 1 protein 3 0 MS(0.997)T(0.022)IGS(0.981)FEGFQAVS(0.999)LK 56.359 0.0040951 0 854.91 979.12 973.52 189.93 1269.5 1336.2 1204.6 1451.3 906.87 1011.7 TRUE FALSE FALSE 844.4900281 992.9040771 990.4637072 211.8906002 1204.712678 1250.821132 1306.918694 1493.291076 825.7572759 985.4158882 0.856988443 1.007599014 1.005122527 0.215026572 1.222542373 1.26933323 1.326261033 1.515391718 0.837978447 1 9.944588923 -8.540039906 24.9999872 0.891186531 1.34592479 0.535404024 0.231200891 154.974346 225762.4397 0.032922604 0.065856552 2.88E-09 8.540039906 0.454738259 MSAQEST(ph)PIMNGVTGPDGEDYSPWADRK ddPTM_HeLa_Romidepsin_16h_R1 1 MSAQESTPIMNGVTGPDGEDYSPWADRK 28 1 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;I3L0Y9;Q9UQB8-6 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 MS(0.013)AQES(0.12)T(0.31)PIMNGVT(0.256)GPDGEDY(0.026)S(0.274)PWADRK 41.047 0.013632 10165000 695.3 667.47 693.26 708.51 1439.4 2536.7 2255.5 2437.9 747.53 757.85 TRUE FALSE FALSE 686.8254162 676.8666602 705.3258995 790.4312598 1365.942047 2374.613057 2447.082114 2508.43679 680.6690446 738.1609477 0.930454826 0.916963519 0.955517766 1.070811538 1.850466421 3.216931299 3.315106443 3.398224734 0.922114678 1 9.527791604 -8.418553171 2.037958457 0.960959202 3.38936839 0.99758817 0.051586002 0.011919417 0.096109881 0.00880472 0.024146304 3.81E-09 8.418553171 2.428409188 up MSDYS(ph)PNSTGSVQNTSR ddPTM_HeLa_Romidepsin_16h_R1 2 MSDYSPNSTGSVQNTSR 17 0 H7C1W4;Q93075 H7C1W4 TATDN2 Putative deoxyribonuclease TATDN2 1 0 MS(0.115)DY(0.006)S(0.872)PNS(0.003)T(0.003)GS(0.001)VQNTSR;MS(0.005)DYS(0.995)PNSTGSVQNTSR ; 137.91 0.0014275 6859000 2789.81 2924.27 2552.51 2803.6 2266.81 1994.44 2045.76 2215.74 3373.29 2794.86 TRUE FALSE FALSE 2755.806723 2965.43795 2596.935366 3127.765423 2151.126227 1867.001721 2219.526803 2279.848941 3071.574494 2722.249134 1.012327155 1.089333784 0.953966826 1.148963695 0.790201822 0.685830587 0.815328316 0.83748725 1.128322333 1 11.41058339 -8.694928632 9.477011647 1.017479366 0.776842473 0.763909302 0.072586752 0.115305194 15.43129793 0.00860889 0.017223143 2.02E-09 8.694928632 -0.240636894 MSFLT(ph)NDAS(ph)SES(ph)IAS(ph)FSK ddPTM_HeLa_Romidepsin_16h_R1 1 MSFLTNDASSESIASFSK 18 0 A0A1W2PR44;A0A1W2PQ00;A0A1W2PR00;Q7RTN6-2;Q7RTN6-3 A0A1W2PR44 4 0 MS(0.397)FLT(0.626)NDAS(0.916)S(0.067)ES(0.884)IAS(0.598)FS(0.512)K 47.281 0.020117 1508900 1012.5 937.34 979.03 1277.1 1106.8 1229.1 1119.8 1390.3 1329.8 907.81 TRUE FALSE FALSE 1000.159261 950.5358971 996.0696065 1424.764311 1050.315866 1150.564477 1214.915784 1430.526137 1210.859357 884.2249653 1.131114026 1.074993282 1.126488898 1.611314277 1.187837832 1.301212386 1.373989462 1.617830522 1.369401911 1 9.788269658 -4 0.159660169 0.941061693 3.267252353 0.267930148 0.174474595 30.41982205 0.307356473 0.235447014 16.7119504 1.00E-04 4 2.32619066 MSGGSTMS(ph)SGGGNTNNSNSK ddPTM_HeLa_Romidepsin_16h_R1 6 MSGGSTMSSGGGNTNNSNSK 20 0 A0A6E1WJ75;Q86U70-3;Q86U70-2;Q86U70 A0A6E1WJ75 LDB1 LIM domain-binding protein 1 1 0 MS(0.092)GGS(0.092)T(0.229)MS(0.567)S(0.019)GGGNTNNSNSK;MS(0.006)GGS(0.063)T(0.223)MS(0.344)S(0.344)GGGNT(0.019)NNS(0.001)NSK;MS(0.02)GGS(0.216)T(0.216)MS(0.243)S(0.243)GGGNT(0.062)NNSNSK;MS(0.001)GGS(0.033)T(0.276)MS(0.601)S(0.089)GGGNTNNSNSK;MS(0.053)GGS(0.262)T(0.198)MS(0.468)S(0.019)GGGNTNNSNSK;MS(0.173)GGS(0.173)T(0.173)MS(0.309)S(0.171)GGGNT(0.001)NNSNSK ;;;;; 105 0.00039875 23247470 2280.15 1972.54 1934.96 2039.93 2038.93 1936.17 1771.5 1837.09 2503.17 2533.97 TRUE FALSE FALSE 2252.358655 2000.30947 1968.637167 2275.796305 1934.875794 1812.454986 1921.971166 1890.243301 2279.280206 2468.137094 0.91257437 0.810453145 0.797620672 0.92207046 0.783941783 0.734341293 0.778713294 0.765858309 0.923482011 1 11.26920682 -10.24399125 0.302270365 1.024779526 0.729480909 0.656272359 0.049302099 0.482877063 0.1438091 0.045829582 0.053009612 5.70E-11 10.24399125 -0.295298617 MSHSS(ph)S(ph)GSAS(ph)LS(ph)QVSPGK ddPTM_HeLa_Romidepsin_16h_R1 1 MSHSSSGSASLSQVSPGK 18 0 H7C5F9;B4E2D5;R4GND2;F6S7C4;Q8NEM7-2;Q8NEM7;Q8NEM7-3 H7C5F9 SUPT20H Transcription factor SPT20 homolog 4 0 MS(0.246)HS(0.301)S(0.455)S(0.477)GS(0.6)AS(0.813)LS(0.799)QVS(0.309)PGK 44.998 0.0043329 0 441.25 434.66 387.03 656.7 431.38 483.43 479.47 569.58 604.44 533.25 TRUE FALSE FALSE 435.8718753 440.7791549 393.7660948 732.6307439 409.3650689 452.5403832 520.1961698 586.0598987 550.3773726 519.3960881 0.839189754 0.848637803 0.75812295 1.410543438 0.788155857 0.871281847 1.001540408 1.128348696 1.059648667 1 9.020691338 MSLVPAT(ph)NYIY(ph)T(ph)PLNQLK ddPTM_HeLa_Romidepsin_16h_R1 1 MSLVPATNYIYTPLNQLK 18 0 A0A590UJM4;Q5MJ33;A0A590UJR1;V9GZ00;Q5MJ35;A0A590UJP0;Q5MJ34;A0A590UJF7;A0A590UJF2;B7Z7M5;Q9NUX5-2;Q9NUX5 A0A590UJM4 POT1 Protection of telomeres protein 1 3 0 MS(0.129)LVPAT(0.87)NY(0.275)IY(0.758)T(0.967)PLNQLK 47.75 0.0041575 0 1012.2 858.03 852.07 810.64 755.54 763.05 687.23 909.24 830.94 1007.5 TRUE FALSE FALSE 999.8629171 870.1093689 866.8999209 904.370011 716.9819745 714.2935676 745.603299 935.5474249 756.6186453 981.3250048 1.018890696 0.886667887 0.883397362 0.921580523 0.730626419 0.727886851 0.759792419 0.953351255 0.771017391 1 9.938587211 -9.679256106 1.015644882 1.010332565 0.795883325 0.031193919 0.103456724 0.232348688 0.478982914 0.013488978 0.021980463 2.09E-10 9.679256106 -0.214449241 MSPAS(ph)PIDDIER ddPTM_HeLa_Romidepsin_16h_R1 2 MSPASPIDDIER 12 0 B4DWJ3;Q96CJ1-2;Q96CJ1 B4DWJ3 EAF2 ELL-associated factor 2 1 0 MSPAS(1)PIDDIER;MSPAS(1)PIDDIER ; 139.19 0.0029605 14583400 3125 2843.2 3543.9 2972.5 6487.9 6883.2 6643.2 7813.8 3266.5 3067.6 TRUE FALSE FALSE 3086.911298 2883.226644 3605.580093 3316.194436 6156.798253 6443.385735 7207.473242 8039.879975 2974.336059 2987.90331 1.033136276 0.964966515 1.206725827 1.10987341 2.060574796 2.156490712 2.412217697 2.690809956 0.995459274 1 11.54491775 -8.55592282 1.232356744 1.009987052 2.554820976 0.957401215 0.133801487 0.058029162 0.169128753 0.019040454 0.062068997 2.78E-09 8.55592282 1.544833924 up MSPMGT(ph)ASGSNSPTSDSASVQR ddPTM_HeLa_Romidepsin_16h_R1 2 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 0 MS(0.015)PMGT(0.464)AS(0.464)GS(0.003)NS(0.048)PT(0.005)SDSASVQR;MS(0.001)PMGT(0.974)AS(0.017)GS(0.008)NS(0.001)PTSDSASVQR ; 137.81 3.16E-16 31672000 248.432 144.51 458.05 483.21 391 509.71 337.48 389.42 380.22 356.6 TRUE FALSE FALSE 245.4040152 146.5444156 466.0221681 539.0810138 371.045811 477.141176 366.1455428 400.6872533 346.2121709 347.3354806 0.706533104 0.421910296 1.341706201 1.552047067 1.068263485 1.373718502 1.054155314 1.153603003 0.996765923 1 8.44018598 -9.72872222 24.99974756 0.824582996 1.258121305 0.553900599 0.207801211 125.01013 95522.22967 0.034660115 0.049014838 1.87E-10 9.72872222 0.433538309 MSPMGTASGS(ph)NSPTSDSASVQR ddPTM_HeLa_Romidepsin_16h_R1 1 MSPMGTASGSNSPTSDSASVQR 22 0 Q5QPB1;O76080 Q5QPB1 ZFAND5 AN1-type zinc finger protein 5 1 0 MS(0.021)PMGT(0.104)AS(0.329)GS(0.528)NS(0.017)PTSDSASVQR 132.52 1.39E-12 0 113.06 214.26 149.43 53.999 224.57 256.57 135.63 188.68 166.02 60.933 TRUE FALSE FALSE 111.6819812 217.2763579 152.0307665 60.24261845 213.1093549 240.176005 147.1504088 194.1391581 151.1707554 59.34995188 1.881753526 3.660935705 2.561598816 1.01504073 3.590724983 4.046776745 2.479368629 3.27109209 2.547108306 1 5.891174955 -10.71152848 0.338334448 0.75516649 3.329701634 0.118354753 0.950955713 0.857228661 0.293467493 0.852039055 0.640777611 1.94E-11 10.71152848 2.574535145 MSPNETLFLES(ph)TNK ddPTM_HeLa_Romidepsin_16h_R1 2 MSPNETLFLESTNK 14 0 Q9HB90;Q9NQL2 Q9HB90 RRAGC;RRAGD Ras-related GTP-binding protein C;Ras-related GTP-binding protein D 1 0 MSPNETLFLES(0.918)T(0.082)NK;MSPNETLFLES(0.894)T(0.106)NK ; 163.9 0.00023023 117375000 10379.4 8499.5 8996 8582.5 14998.6 13141.8 12158.9 13038 9187.2 8352.4 TRUE FALSE FALSE 10252.89188 8619.156184 9152.571606 9574.849032 14233.16547 12302.08139 13191.67666 13415.23396 8365.473822 8135.403444 1.260280692 1.059462661 1.125029836 1.176935981 1.749534067 1.512166112 1.621514748 1.648994306 1.028280144 1 12.98999818 -8.819932208 6.5791745 1.122564442 1.623014325 0.894551208 0.088214614 0.058519447 5.04854303 0.016055302 0.029462638 1.51E-09 8.819932208 0.500449883 MSS(ph)PEDDSDTKR ddPTM_HeLa_Romidepsin_16h_R1 2 MSSPEDDSDTKR 12 1 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 MS(0.325)S(0.674)PEDDSDTKR;MS(0.026)S(0.968)PEDDS(0.005)DT(0.001)KR ; 130.69 0.0027682 12283500 5851 5712.9 4968.9 4633.2 5773 5866.2 5710.1 4307.2 5989.1 6194.4 TRUE FALSE FALSE 5779.685761 5793.326356 5055.38162 5168.912384 5478.382268 5491.368752 6195.115751 4431.822036 5453.419896 6033.468595 0.95793749 0.960198311 0.837889771 0.856706603 0.907998804 0.910151212 1.026791746 0.734539671 0.903861487 1 12.55877192 -9.910629212 6.41009183 0.979082208 0.887623674 0.178801795 0.073298492 0.19976505 11.89528566 0.010610999 0.013985567 1.23E-10 9.910629212 -0.091458533 MSYEGPTAEVVEVSAGGDLSQAAS(ph)PTGASR ddPTM_HeLa_Romidepsin_16h_R1 1 MSYEGPTAEVVEVSAGGDLSQAASPTGASR 30 0 O15061 O15061 SYNM Synemin 1 0 MSYEGPTAEVVEVSAGGDLSQAAS(0.476)PT(0.476)GAS(0.048)R 141.61 1.41E-11 6474600 1614.8 1461.3 1503 1659.3 1955.8 1788.9 1461.1 1983.8 2003.7 1581.9 TRUE FALSE FALSE 1595.118196 1481.87222 1529.159085 1851.156073 1855.988228 1674.595063 1585.205798 2041.198123 1824.484054 1540.80201 1.035251892 0.961753821 0.992443594 1.201423714 1.204559843 1.086833385 1.02881862 1.324763409 1.184113236 1 10.58946577 -9.267250766 24.98392161 1.010429092 1.158856043 0.324155715 0.093331119 298.1731307 1281885.443 0.011099492 0.017236716 5.40E-10 9.267250766 0.148426952 MT(ph)DS(ph)KYFT(ph)T(ph)NK ddPTM_HeLa_Romidepsin_16h_R1 1 MTDSKYFTTNK 11 1 A0A087WXS3;K7EKZ5;K7EJX1;K7EN71;K7ERB2;A0A087WYD1;A0A087WU93;A0A087WZQ6;A0A087X253;P63010;P63010-2 A0A087WXS3 AP2B1 AP-2 complex subunit beta 4 0 MT(1)DS(0.979)KY(0.048)FT(0.973)T(1)NK 75.739 0.013977 25545000 2281.5 1046.9 1094.5 1303.1 11367 7527.6 3224.6 1830.9 5860.2 1710.5 TRUE FALSE FALSE 2253.6922 1061.638286 1113.549313 1453.770553 10786.89957 7046.610654 3498.497444 1883.874203 5336.049035 1666.060963 1.352706924 0.637214549 0.668372489 0.872579446 6.474492717 4.229503487 2.099861602 1.130735456 3.202793386 1 10.70222548 MT(ph)GASGPSVGVT(ph)GT(ph)TGPASK ddPTM_HeLa_Romidepsin_16h_R1 1 MTGASGPSVGVTGTTGPASK 20 0 Q7Z5P9-2;Q7Z5P9 Q7Z5P9-2 MUC19 Mucin-19 3 0 MT(0.717)GAS(0.1)GPS(0.193)VGVT(0.955)GT(0.549)T(0.473)GPAS(0.014)K 57.41 0.003225 0 1120.7 1207.8 1134.9 1099.2 1062 1175.9 946.44 1067.3 1316.7 1209.2 TRUE FALSE FALSE 1107.040477 1224.80344 1154.652458 1226.294676 1007.802177 1100.763785 1026.83059 1098.180642 1198.931054 1177.78481 0.939934416 1.03992124 0.980359442 1.041187376 0.855675985 0.934605181 0.871832088 0.932411959 1.017954251 1 10.20186026 -8.754682208 24.99995952 0.981739674 0.89928664 0.605293574 0.039133094 101.9150827 377058.6722 0.005760917 0.011316036 1.76E-09 8.754682208 -0.082453034 MT(ph)GSAPPPSPTPNK ddPTM_HeLa_Romidepsin_16h_R1 1 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 0 MT(0.994)GS(0.006)APPPSPTPNK 104.94 0.019678 3279100 2022.8 1560.1 2192.6 1581.3 1917.2 2293.7 1554.1 1794.8 2256 2078.6 TRUE FALSE FALSE 1998.145336 1582.063129 2230.761283 1764.137346 1819.35813 2147.139973 1686.105215 1846.729706 2054.21771 2024.597672 0.986934522 0.781420996 1.101829422 0.871352057 0.898626999 1.060526742 0.832810014 0.912146513 1.014630086 1 10.98341953 -4 0.071369767 1.09102955 0.597823807 0.09764783 0.092860274 355.947926 1.891215617 2.289532688 17.6802189 1.00E-04 4 -0.493205743 MT(ph)KLDS(ph)S(ph)DIY(ph)NELK ddPTM_HeLa_Romidepsin_16h_R1 1 MTKLDSSDIYNELK 14 1 A0A494C1S6;A0A494C0A3 A0A494C1S6 4 0 MT(1)KLDS(1)S(1)DIY(1)NELK 52.576 0.02711 1447200 276.43 294.65 244.56 260.39 124.6 291.72 429.06 309.26 165.36 367.46 TRUE FALSE FALSE 273.0607648 298.7980904 248.8164642 290.497517 118.2411971 273.0800335 465.5043457 318.2079502 150.5697874 357.9133362 0.762924253 0.834833632 0.695186345 0.811642058 0.330362647 0.76297809 1.300606316 0.889064245 0.420687838 1 8.483466491 -7.782797475 24.99739695 0.816244078 1.094835421 0.211576888 0.230585629 236.5276859 276831.0414 0.029855035 0.08968587 1.65E-08 7.782797475 0.278591342 MT(ph)NSPVLPVGSTTNGSR ddPTM_HeLa_Romidepsin_16h_R1 1 MTNSPVLPVGSTTNGSR 17 0 P37275-3;P37275-4;P37275-5;P37275;P37275-2 P37275-3 ZEB1 Zinc finger E-box-binding homeobox 1 1 0 MT(0.942)NS(0.057)PVLPVGSTTNGSR 88.224 0.0259 7752400 2320.4 2090.3 2156.3 1473.5 1681.1 1550.6 1257.5 1693.2 2223.3 2308.4 TRUE FALSE FALSE 2292.118072 2119.727298 2193.829497 1643.873003 1595.307194 1451.521664 1364.312019 1742.190071 2024.44248 2248.427435 1.019431642 0.942759933 0.975717278 0.731121217 0.709521317 0.645571941 0.60678499 0.774848253 0.900381506 1 11.13470061 -9.227421157 2.034697938 1.005446765 0.672936307 0.848782739 0.056999805 0.058747262 0.474556765 0.006891661 0.012192395 5.92E-10 9.227421157 -0.332510458 MT(ph)NTGLPGPATPAYSYAK ddPTM_HeLa_Romidepsin_16h_R1 1 MTNTGLPGPATPAYSYAK 18 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 MT(0.84)NT(0.156)GLPGPAT(0.003)PAYSYAK 92.856 0.00076725 0 1045.3 812.65 1091.6 1048.6 1282.2 1217 781.56 1298.5 797.7 885.22 TRUE FALSE FALSE 1032.559482 824.090508 1110.59884 1169.844066 1216.764549 1139.237628 847.9456869 1336.070049 726.3517141 862.2218568 1.197556607 0.955775479 1.288066211 1.356778486 1.411196596 1.321281314 0.983442579 1.549566435 0.842418582 1 9.751915324 -9.658014893 7.707594175 1.085777471 1.311050914 0.440736857 0.165097396 0.200502397 13.44453733 0.023251148 0.032897653 2.20E-10 9.658014893 0.225273443 MT(ph)SAQCPALACVMS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 1 MTSAQCPALACVMSPLR 17 0 A0A0J9YWT4;A0A0G2JS48;A0A0G2JRT3;A0A0G2JRB3;A0A0J9YVP4;A0A0G2JP19;A0A0G2JNP1;A0A0G2JNC9;A0A0G2JMZ2;O60309 A0A0J9YWT4 LRRC37A3 Leucine-rich repeat-containing protein 37A3 2 0 MT(0.751)S(0.249)AQCPALACVMS(1)PLR 48.555 0.0042381 0 519.95 554.71 476.73 624.21 485.03 365.74 347.2 493.6 398.86 676.32 TRUE FALSE FALSE 513.6126494 562.5192219 485.0272857 696.3840972 460.2771092 342.3703944 376.6911593 507.8815372 363.1849626 658.7491089 0.779678701 0.853920278 0.736285301 1.057130989 0.698713824 0.519728057 0.57182796 0.770978709 0.551325167 1 9.363585295 -8.83972659 0.06234945 1.478144024 1.66E-14 0 0.185149868 50.2876938 0.981343927 9.185370974 14.13865057 1.45E-09 8.83972659 -1.478144024 MT(ph)T(ph)DINALK ddPTM_HeLa_Romidepsin_16h_R1 2 MTTDINALK 9 0 F8VZ81;Q9Y2I9-3;Q9Y2I9-2;Q9Y2I9 F8VZ81 TBC1D30 TBC1 domain family member 30 2 0 MT(1)T(1)DINALK;MT(1)T(1)DINALK ; 98.458 0.016733 13203300 3006.6 2847.1 2884.2 2876.6 2536 2030.57 2034.58 1869.78 2901.5 3217.1 TRUE FALSE FALSE 2969.954403 2887.181549 2934.398291 3209.206027 2406.578457 1900.82313 2207.397174 1923.879134 2641.982573 3133.519278 0.947801542 0.921386241 0.93645452 1.024153912 0.768011377 0.606609681 0.704446655 0.613967544 0.843135892 1 11.61356815 -8.586608765 3.84163891 0.969835587 0.651097291 0.855818116 0.055815707 0.039189344 1.169032191 0.005926821 0.012557195 2.59E-09 8.586608765 -0.318738296 MT(ph)T(ph)LLSAMS(ph)EEQLARYEVCRQSAFPK ddPTM_HeLa_Romidepsin_16h_R1 1 MTTLLSAMSEEQLARYEVCRQSAFPK 26 2 A0A1W2PRN6 A0A1W2PRN6 3 0 MT(0.837)T(0.837)LLS(0.326)AMS(0.513)EEQLARY(0.484)EVCRQS(0.003)AFPK 42.041 0.0040694 0 649.02 366.76 391.72 399.32 297.5 354.17 269.65 430.34 494.36 427.49 TRUE FALSE FALSE 641.1094946 371.9232569 398.5377223 445.4912573 282.3174649 331.53968 292.5540643 442.7912089 450.1432035 416.3837482 1.539708256 0.893222318 0.957140436 1.069905488 0.678022296 0.79623588 0.702606827 1.063420969 1.081077745 1 8.70176995 -10.14546113 8.65137871 1.25469198 0.870941265 0.395893205 0.182090148 0.248404041 17.14449673 0.038458971 0.047139024 7.15E-11 10.14546113 -0.383750715 MTDQEAIQDLWQWR ddPTM_HeLa_Romidepsin_16h_R1 4 MTDQEAIQDLWQWR 14 0 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 0 ;;; ;;; 190.66 1.15E-10 395764000 4335.8 4760.61 4478.11 4059.22 4580.7 4304.41 3969.52 4156.16 4834.2 4055.36 FALSE FALSE TRUE 4282.953602 4827.629993 4556.049626 4528.566116 4346.929786 4029.372093 4306.69093 4276.411932 4401.817045 3950.001163 1.084291732 1.222184449 1.153429946 1.146472097 1.10048823 1.0200939 1.09030118 1.082635614 1.114383734 1 11.94763736 -11.43628061 1.079893989 1.012684684 1.112700813 0.021142116 0.060309141 0.357278964 0.851622744 0.018153857 0.011379269 3.66E-12 11.43628061 0.100016129 MTDRFS(ph)SLQHT(ph)TLKPPDVT(ph)CIS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MTDRFSSLQHTTLKPPDVTCISK 23 2 Q8N6P7 Q8N6P7 IL22RA1 Interleukin-22 receptor subunit alpha-1 4 0 MT(0.284)DRFS(0.36)S(0.36)LQHT(0.498)T(0.498)LKPPDVT(1)CIS(1)K 49.34 0.0038705 0 536.27 366.87 520.37 384.21 499.17 483.43 311.16 438.94 497.08 417.43 TRUE FALSE FALSE 529.733735 372.0348055 529.4268216 428.634168 473.6954922 452.5403832 337.5899226 451.6400364 452.6199198 406.5851084 1.302885236 0.915023196 1.30213038 1.054229875 1.165058637 1.113027442 0.830305674 1.11081303 1.113223063 1 8.667413566 -7.93875052 13.1301576 1.135384017 0.970643135 0.170044442 0.130402753 1.3258132 281.4951151 0.019788621 0.05939125 1.15E-08 7.93875052 -0.164740883 MTERGSVAR ddPTM_HeLa_Romidepsin_16h_R1 1 MTERGSVAR 9 1 A0A1B0GTU4;A0A1B0GU60 A0A1B0GTU4 0 0 69.628 0.0041239 0 3635.6 3041 3761.4 1210.4 4121.9 4011.9 3643.2 3215.2 4204.6 3324.2 FALSE FALSE TRUE 3591.287909 3083.811278 3826.865589 1350.352143 3911.544062 3755.552538 3952.653317 3308.226739 3828.530045 3237.836805 1.10916273 0.952429497 1.181920467 0.4170538 1.208073259 1.159895561 1.220769778 1.021739803 1.182434532 1 11.66081456 MTGSAPPPS(ph)PTPNK ddPTM_HeLa_Romidepsin_16h_R1 2 MTGSAPPPSPTPNK 14 0 Q9UBW7 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 0 MT(0.412)GS(0.012)APPPS(0.568)PT(0.008)PNK;MT(0.14)GS(0.011)APPPS(0.641)PT(0.207)PNK ; 92.269 0.023599 11944600 9074.3 8778.3 8960.4 7276.6 8598 8978.5 6929.5 8109.9 9430.9 9426.4 TRUE FALSE FALSE 8963.698941 8901.881138 9116.352003 8117.954729 8159.211976 8404.802827 7518.091557 8344.547161 8587.376684 9181.500769 0.976278189 0.969545324 0.992904345 0.884164249 0.888657768 0.915406211 0.818830357 0.908843486 0.935291179 1 13.16451427 -9.258571224 23.98252841 0.987043223 0.881700022 0.687771996 0.030302672 44.33192299 370686.915 0.003747807 0.00603784 5.51E-10 9.258571224 -0.105343201 MTMTT(ph)MPESLNS(ph)PVSGK ddPTM_HeLa_Romidepsin_16h_R1 1 MTMTTMPESLNSPVSGK 17 0 J3KP55;F8VXJ2;P56177-2;P56177 J3KP55 DLX1 Homeobox protein DLX-1 2 0 MT(0.242)MT(0.123)T(0.57)MPES(0.068)LNS(0.537)PVS(0.461)GK 53.565 0.0039892 0 658.01 578.9 623.5 612.81 898.22 780.46 523.04 759.62 646.26 623.91 TRUE FALSE FALSE 649.989921 587.0497694 634.351756 683.6659756 852.3804817 730.5911248 567.4670045 781.5984062 588.456887 607.7007283 1.069588847 0.96601788 1.043855514 1.125004371 1.40263199 1.202221901 0.933793524 1.286156771 0.968333358 1 9.247217211 -9.143497485 4.054382949 1.028427814 1.19351991 0.387048018 0.114611377 0.216005148 6.123778107 0.017093049 0.029059116 7.19E-10 9.143497485 0.165092097 MTNNEDS(ph)LSPTSSTLSNLELDAAEKDR ddPTM_HeLa_Romidepsin_16h_R1 1 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 0 MT(0.012)NNEDS(0.536)LS(0.024)PT(0.333)S(0.07)S(0.024)TLSNLELDAAEKDR 111.56 4.69E-09 64973000 3884.1 3952.7 3710.1 3672.9 4043.6 3997.8 3173.6 4177.1 4603.7 4168.1 TRUE FALSE FALSE 3836.759095 4008.346214 3774.672734 4097.57798 3837.240003 3742.353482 3443.165505 4297.957798 4191.933542 4059.812161 0.945058279 0.987323072 0.929765365 1.009302356 0.945176735 0.921804589 0.84810956 1.058659275 1.032543718 1 11.98719726 -16.52287875 0.232217429 1.281130322 0.944524087 0.150799913 0.054130681 78.86309774 1.019284107 10.10501139 0.035521185 3.00E-17 16.52287875 -0.336606235 MTNNEDSLS(ph)PTSSTLSNLELDAAEKDR ddPTM_HeLa_Romidepsin_16h_R1 2 MTNNEDSLSPTSSTLSNLELDAAEKDR 27 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 0 MT(0.003)NNEDS(0.08)LS(0.569)PT(0.071)S(0.246)S(0.03)T(0.001)LSNLELDAAEKDR;MT(0.01)NNEDS(0.359)LS(0.548)PT(0.077)S(0.007)STLSNLELDAAEKDR ; 112.25 4.38E-09 74129000 4190.6 3687.7 3321.8 4325.6 3728.6 4142.3 3030.1 3556.6 4210.8 3899.9 TRUE FALSE FALSE 4139.523355 3739.615537 3379.614536 4825.746225 3538.315629 3877.620399 3287.476618 3659.50461 3834.175502 3798.580036 1.089755466 0.984477226 0.889704706 1.270407936 0.931483764 1.020807871 0.865448822 0.963387522 1.00937073 1 11.8912445 -8.083992162 2.046745498 1.039190842 0.919030059 0.137750619 0.100946068 0.420333585 3.366019011 0.01388181 0.05098721 8.24E-09 8.083992162 -0.120160783 MTQKTPFECS(ph)QSEVMFLS(ph)LDKK ddPTM_HeLa_Romidepsin_16h_R1 1 MTQKTPFECSQSEVMFLSLDKK 22 2 Q9Y616-2;Q9Y616 Q9Y616-2 IRAK3 Interleukin-1 receptor-associated kinase 3 2 0 MT(0.02)QKT(0.153)PFECS(0.751)QS(0.171)EVMFLS(0.905)LDKK 48.112 0.0042561 0 678.58 859 916.77 536.58 1046.8 904.47 848.27 866.59 743.16 833.58 TRUE FALSE FALSE 670.309206 871.0930245 932.7259973 598.6219043 993.3778899 846.677286 920.3220326 891.6634144 676.6899083 811.9234714 0.825581757 1.072875776 1.148785606 0.737288581 1.223487096 1.042804298 1.133508348 1.098211156 0.833440505 1 9.665199941 -8.849830951 0.748676417 0.928309671 1.127715585 0.225234566 0.134223004 0.846650619 0.864931765 0.025568182 0.090850589 1.41E-09 8.849830951 0.199405914 MTT(ph)LLS(ph)AMSEEQLARYEVCRQS(ph)AFPK ddPTM_HeLa_Romidepsin_16h_R1 1 MTTLLSAMSEEQLARYEVCRQSAFPK 26 2 A0A1W2PRN6 A0A1W2PRN6 3 0 MT(0.488)T(0.576)LLS(0.934)AMS(0.002)EEQLARY(0.048)EVCRQS(0.952)AFPK 60.675 0.00073459 0 1419.1 1407.2 1163.6 1102.9 1171.3 1346.5 1154.8 1559.5 1287.3 1289.5 TRUE FALSE FALSE 1401.803463 1427.010599 1183.85197 1230.422487 1111.52419 1260.462996 1252.888683 1604.621672 1172.160664 1255.998604 1.1160868 1.136156198 0.942558348 0.979636827 0.884972473 1.003554456 0.997523946 1.277566445 0.933249973 1 10.29461915 -7.256585515 24.57801943 1.03116079 1.277566574 0.491835573 0.079097202 300.3285198 1520676.83 0.011733007 0.128402909 5.54E-08 7.256585515 0.246405784 MTTTTTFKGVDPNSR ddPTM_HeLa_Romidepsin_16h_R1 1 MTTTTTFKGVDPNSR 15 1 Q9UK76;J3KT51;Q9UK76-2;F2Z3M5 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 0 68.786 0.0041194 0 853.76 1030.8 840.36 692.85 989.28 1184.6 1110.2 842.19 1267.2 1247.8 FALSE FALSE TRUE 843.3540447 1045.311629 854.9861133 772.960577 938.7933501 1108.907883 1204.50036 866.5574389 1153.858458 1215.381976 0.693900404 0.860068398 0.703471115 0.635981603 0.772426586 0.912394543 0.991046752 0.712991846 0.949379274 1 10.24719409 -12.4681155 1.181724687 1.001070676 0.780971581 0.342355734 0.104324836 0.43838565 1.086596708 0.079123442 0.019101394 3.40E-13 12.4681155 -0.220099096 MTVQAT(ph)PSSTTEET(ph)ATQK ddPTM_HeLa_Romidepsin_16h_R1 1 MTVQATPSSTTEETATQK 18 0 H0YDV8 H0YDV8 CD44 2 0 MT(0.071)VQAT(0.916)PS(0.006)S(0.007)TTEET(0.5)AT(0.5)QK 72.167 0.0058387 24846000 902.3 420.44 1606.3 843.33 6117.7 3984.6 4371.3 3736.9 8167.3 2648.3 TRUE FALSE FALSE 891.3024205 426.3589654 1634.256978 940.8397826 5805.490941 3729.99692 4742.598113 3845.021306 7436.796233 2579.496784 0.345533449 0.165287651 0.633556509 0.364737723 2.250629261 1.446017278 1.838574927 1.490609071 2.883041482 1 11.33287393 -8.769628335 24.99999783 0.614774788 1.740148874 0.174751474 0.777810794 73.75218755 225157.945 0.05256121 0.096459148 1.70E-09 8.769628335 1.125374086 MVEPENAVTITPLRPEDDY(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 MVEPENAVTITPLRPEDDYSPR 22 1 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;A0A0G2JPP5;Q14160-3;A0A669KAX5;H0YDF9 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 MVEPENAVT(0.002)IT(0.002)PLRPEDDY(0.965)S(0.032)PR;MVEPENAVT(0.01)IT(0.015)PLRPEDDY(0.793)S(0.182)PR ; 67.214 0.001637 97080000 3905.4 4713.1 4626.6 2772.87 5006.9 6231.2 5019 6217.4 4797.7 4440.1 TRUE FALSE FALSE 3857.799483 4779.451146 4707.124032 3093.482276 4751.37921 5833.04643 5445.313735 6397.29066 4368.581696 4324.745562 0.892029237 1.105140424 1.088416409 0.715298098 1.098649421 1.348760603 1.25910615 1.479229372 1.010136119 1 12.07839954 -8.383279598 3.62542172 0.956428057 1.35351589 0.694027118 0.116094691 0.097266823 2.303583448 0.016294066 0.038734818 4.14E-09 8.383279598 0.397087834 MVFETGQFDDAED ddPTM_HeLa_Romidepsin_16h_R1 2 MVFETGQFDDAED 13 0 Q9NQ92;H9KV77 Q9NQ92 COPRS Coordinator of PRMT5 and differentiation stimulator 0 0 ; ; 106.88 0.021551 25916000 8375.7 8263.4 6699.1 6785.1 8299.3 8479.6 7379 6883.6 9016.6 8071.3 FALSE FALSE TRUE 8273.613747 8379.732362 6815.695025 7569.625187 7875.755752 7937.780927 8005.772076 7082.766105 8210.132714 7861.606462 1.052407518 1.065905856 0.866959579 0.962859846 1.001799796 1.009689427 1.018337933 0.900931144 1.044332701 1 12.94060843 MVIQGPS(ph)SPQGEAMVTDVLEDQK ddPTM_HeLa_Romidepsin_16h_R1 2 MVIQGPSSPQGEAMVTDVLEDQK 23 0 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 MVIQGPS(0.48)S(0.48)PQGEAMVT(0.04)DVLEDQK;MVIQGPS(0.5)S(0.5)PQGEAMVTDVLEDQK ; 84.324 8.35E-05 26816000 11222.1 11162.9 12176.9 7851.6 11734.9 12143.3 10615.8 13037.4 12775.2 13169.5 TRUE FALSE FALSE 11085.32073 11320.0516 12388.83384 8759.438935 11136.02426 11367.38232 11517.50579 13414.6166 11632.55412 12827.35449 0.86419384 0.882493082 0.965813632 0.682871822 0.868146606 0.886182909 0.897886294 1.045782013 0.906855277 1 13.64693604 -12.27209938 0.860223384 1.004717201 0.881011276 0.038229863 0.090720765 0.844956512 1.054020653 0.0696977 0.016319788 5.34E-13 12.27209938 -0.123705924 MVIQGPS(ph)SPQGEAMVTDVLEDQKEGR ddPTM_HeLa_Romidepsin_16h_R1 2 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 MVIQGPS(0.418)S(0.418)PQGEAMVT(0.163)DVLEDQKEGR;MVIQGPS(0.498)S(0.498)PQGEAMVT(0.005)DVLEDQKEGR ; 71.634 0.00017225 952680000 4256.4 4265.7 3819.6 4861.2 4500.5 4554.3 4211.8 4183.6 4651.7 4197 TRUE FALSE FALSE 4204.52136 4325.752637 3886.078536 5423.274817 4270.822691 4263.294928 4569.550187 4304.645865 4235.640302 4087.961335 1.028512996 1.058168677 0.950615287 1.326645331 1.044731675 1.042890228 1.117806606 1.053005523 1.036125334 1 11.99716584 MVIQGPSS(ph)PQGEAMVTDVLEDQKEGR ddPTM_HeLa_Romidepsin_16h_R1 1 MVIQGPSSPQGEAMVTDVLEDQKEGR 26 1 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 MVIQGPS(0.221)S(0.738)PQGEAMVT(0.041)DVLEDQKEGR 56.461 0.0026043 113230000 1175.6 1004.6 971.2 1165.4 1027.3 1159.5 1134.7 1165.9 1298.8 1174.7 TRUE FALSE FALSE 1161.271335 1018.742785 988.1033286 1300.149031 974.8730476 1085.411692 1231.08139 1199.633477 1182.632075 1144.181125 1.01493663 0.890368459 0.863589957 1.136314001 0.852026857 0.948636251 1.075949745 1.048464663 1.03360565 1 10.16009973 -5.696348739 20.94717103 0.991903038 0.986961527 0 0.090367962 0 0 0.011201787 0 2.01E-06 5.696348739 -0.00494151 MVNHFIAEFK ddPTM_HeLa_Romidepsin_16h_R1 2 MVNHFIAEFK 10 0 P11142;E9PKE3;P11142-2;E9PN89;A8K7Q2 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 ; ; 75.509 0.014353 2403700 3600.7 3031.7 4422.4 3230.4 4138.1 4207.8 3764.5 3072 3549.1 2654.1 FALSE FALSE TRUE 3556.813283 3074.380352 4499.370017 3603.914047 3926.917316 3938.93516 4084.256536 3160.883473 3231.659607 2585.146099 1.375865482 1.189248203 1.740470304 1.39408525 1.519031097 1.523679904 1.579893893 1.222709801 1.250087803 1 11.3360301 -11.75975821 0.456013795 0.941558916 1.490954916 0.346513756 0.168114272 0.695692868 0.257247331 0.172020471 0.046664897 1.74E-12 11.75975821 0.549395999 MVNVEDVAECPHFS(ph)S(ph)FADELT(ph)DY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MVNVEDVAECPHFSSFADELTDYK 24 0 P35913-2;P35913 P35913-2 PDE6B "Rod cGMP-specific 3,5-cyclic phosphodiesterase subunit beta" 4 0 MVNVEDVAECPHFS(1)S(1)FADELT(1)DY(1)K 43.198 0.0041134 0 614.26 515.44 534.78 600.11 490.54 611.09 633.38 534.25 594.34 521.88 TRUE FALSE FALSE 606.7731629 522.6963778 544.0876216 669.4975418 465.5059133 572.0433212 687.1792814 549.7076808 541.1807418 508.3214824 1.193679952 1.028279142 1.070361258 1.31707505 0.915770687 1.12535736 1.351859611 1.081417371 1.064642673 1 8.989597392 -12.47389033 1.083727842 0.995930149 1.1412671 0.090415163 0.124104232 0.819678206 1.64178417 0.09485377 0.020766451 3.36E-13 12.47389033 0.145336951 MVQQLQEDVDMEDAP ddPTM_HeLa_Romidepsin_16h_R1 1 MVQQLQEDVDMEDAP 15 0 Q9UHA3 Q9UHA3 RSL24D1 Probable ribosome biogenesis protein RLP24 0 0 63.408 0.0038986 0 667.74 643.52 707.14 593.36 514.45 648.04 630.28 606.11 726.43 490.97 FALSE FALSE TRUE 659.601328 652.5794915 719.4474751 661.967075 488.1956968 606.6323355 683.8159675 623.6468366 661.4562814 478.2145286 1.37930006 1.364616615 1.504445039 1.384247101 1.020871738 1.268535979 1.429935576 1.304115202 1.383178975 1 8.901514151 -12.23769733 0.92428559 0.995827077 1.332715171 0 0.168276639 0.405470469 0.610372634 0.09253952 0.024355213 5.78E-13 12.23769733 0.336888093 MVSGMVKHIT(ph)GSY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 MVSGMVKHITGSYK 14 1 Q15046;Q15046-2 Q15046 KARS Lysine--tRNA ligase 2 0 MVS(0.001)GMVKHIT(0.766)GS(0.274)Y(0.959)K 78.287 0.002965 0 1206.7 1381.4 1424.2 1097.8 1345.4 1254.3 1251.1 1783.2 1663.1 1101.3 TRUE FALSE FALSE 1191.992276 1400.847385 1448.987604 1224.732801 1276.739218 1174.154278 1357.368403 1834.794079 1514.348171 1072.688067 1.111219853 1.30592241 1.350800524 1.141741797 1.190224126 1.094590603 1.265389673 1.710463773 1.411732093 1 10.06701489 -4.40521019 0.967929352 1.104924461 199.9642738 0.418467745 0.147129101 262.007062 0.971614297 0.020576157 114677.6838 3.93E-05 4.40521019 198.8593493 MVSNPCMTS(ph)ATIDVTTVER ddPTM_HeLa_Romidepsin_16h_R1 1 MVSNPCMTSATIDVTTVER 19 0 Q9H158-2;Q9H158 Q9H158-2 PCDHAC1 Protocadherin alpha-C1 1 0 MVS(0.001)NPCMT(0.255)S(0.703)AT(0.04)IDVTTVER 69.289 0.016747 8981600 64.539 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 63.75237384 0 0 0 0 0 0 0 0 0 0 MVT(ph)GDNINT(ph)ARAIATK ddPTM_HeLa_Romidepsin_16h_R1 1 MVTGDNINTARAIATK 16 1 E7ERY9;P20020-1;P20020-4;P20020-6;P20020;P23634-7;P23634;P23634-8;P20020-2;P20020-5;P23634-2;P23634-3;P23634-4;P23634-5;P23634-6 E7ERY9 ATP2B1;ATP2B4 Calcium-transporting ATPase;Plasma membrane calcium-transporting ATPase 1;Plasma membrane calcium-transporting ATPase 4 2 0 MVT(1)GDNINT(0.597)ARAIAT(0.403)K 64.5 0.01774 765210 379.24 418.32 358.54 338.41 366.65 543.48 475.6 416.34 478.57 278.87 TRUE FALSE FALSE 374.617677 424.2091199 364.7802383 377.5385565 347.9384823 508.753382 515.9974521 428.386141 435.7655006 271.6249172 1.379172724 1.561745971 1.342955728 1.38992608 1.280952005 1.872999676 1.899669064 1.577123872 1.604291333 1 8.085472019 -5.997783047 0.056545733 7.17E-12 3.761810318 0.091037276 0.246417349 100.5684428 0.643632756 12.01906654 36.86629416 1.01E-06 5.997783047 3.761810318 MY(ph)YS(ph)SPPT(ph)CESPSSDK ddPTM_HeLa_Romidepsin_16h_R1 1 MYYSSPPTCESPSSDK 16 0 Q5VVY4 Q5VVY4 ZFAND4 3 0 MY(0.643)Y(0.643)S(0.695)S(0.24)PPT(0.769)CES(0.005)PS(0.002)S(0.003)DK 42.958 0.0043467 0 250.94 192.64 301.16 409.49 213.68 224.84 229.87 208.07 402.64 407.1 TRUE FALSE FALSE 247.8814468 195.351991 306.4015635 456.8371605 202.7751123 210.4734496 249.3951521 214.0901772 366.62687 396.5234833 0.625136864 0.492661845 0.772719842 1.152106192 0.511382354 0.530796935 0.628954306 0.539918028 0.924603171 1 8.631262499 -12.24750738 0.814018392 1.017351765 0.659660901 0.298399626 0.185495524 0.712337204 0.785402791 0.16447171 0.037750239 5.66E-13 12.24750738 -0.357690864 MYASVLLIT(ph)AMSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 MYASVLLITAMSLDR 15 0 G3V4Q5 G3V4Q5 LTB4R 1 0 MYASVLLIT(0.616)AMS(0.384)LDR 114.4 0.0097672 161870000 2268.2 2072.9 2093.1 1897.4 2349 2166 1925.7 2050.7 2174.8 1879.3 TRUE FALSE FALSE 2240.554306 2102.082341 2129.529527 2116.786316 2229.121765 2027.59959 2089.26891 2110.033769 1980.280441 1830.475515 1.224028558 1.148380475 1.163375041 1.156413346 1.217782891 1.107690091 1.141380419 1.152724389 1.08183935 1 10.83800276 -12.42465024 1.10812872 0.998329531 1.167742504 0.571280815 0.040459765 0.196804991 0.425417617 0.026164438 0.006325851 3.76E-13 12.42465024 0.169412973 MYEEHLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 MYEEHLKR 8 1 G3V279;P84090 G3V279 ERH Enhancer of rudimentary homolog 0 1 MYEEHLK(1)R 78.264 0.012558 1207000 311.4 354.81 337.33 199.87 744.99 595.44 517.89 635.59 657.81 540.96 FALSE TRUE FALSE 307.604537 359.8050245 343.2010871 222.9799098 706.9703804 557.3933057 561.8795637 653.9797939 598.9738261 526.9057812 0.583794196 0.682864067 0.65135191 0.423187442 1.341739654 1.057861435 1.06637578 1.241170276 1.136775962 1 9.041401199 -8.748248987 24.99999946 0.75239002 1.160405616 0.513755521 0.204857771 159.365895 302047.4376 0.030532772 0.060775407 1.79E-09 8.748248987 0.408015597 MYPESTTGS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 MYPESTTGSPAR 12 0 A0A590UJ15;A0A590UJK5;A0A5F9UN28;A0A590UJJ4;K7EKU4;K7EIR5;A0A590UJU4;Q5TG84;A0A590UJU1;A0A590UJY1;A0A590UK89;Q5TG78;A0A590UJX9;A0A590UJV4;A0A590UJ72;A0A590UJI8;Q13303-2;Q13303;Q13303-5 A0A590UJ15 KCNAB2 Voltage-gated potassium channel subunit beta-2 1 0 MYPES(0.002)T(0.011)T(0.297)GS(0.69)PAR 99.732 0.021658 17078000 2287.6 1612.1 2079.5 1601 2370 3146 2819.5 2996.8 1718 2038 TRUE FALSE FALSE 2259.717851 1634.795186 2115.692825 1786.115153 2249.050056 2944.980753 3058.98826 3083.50768 1564.337777 1985.052466 1.138366814 0.823552633 1.065812043 0.89978234 1.132992752 1.483578295 1.541011289 1.553363315 0.788058655 1 10.95496142 -8.285331664 3.219957928 1.035698186 1.541030466 0.816373269 0.117862932 0.068974354 1.466312827 0.013932522 0.036110356 5.18E-09 8.285331664 0.50533228 MYRQQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 MYRQQKR 7 2 M0QZW0;A0A0B4J2A7;P43119 M0QZW0 PTGIR Prostacyclin receptor 0 1 ; MYRQQK(1)R;MYRQQK(1)R 72.234 0.020276 12801700 0 0 0 60.211 60.557 184.79 68.459 0 0 0 FALSE TRUE FALSE 0 0 0 67.17287912 57.46655032 172.9825154 74.27390575 0 0 0 0 NAAALT(ph)TLLDLGASPDYK ddPTM_HeLa_Romidepsin_16h_R1 1 NAAALTTLLDLGASPDYK 18 0 A0A669KBA8;A0A0U1RQS4;A0A0U1RR93;Q9BYB0-3;Q9BYB0 A0A669KBA8 SHANK3 SH3 and multiple ankyrin repeat domains protein 3 1 0 NAAALT(0.5)T(0.5)LLDLGASPDYK 80.98 0.0011358 0 886.68 850.98 1081.4 975.72 1011 1021.4 1014.5 1113.9 1078.5 1032.7 TRUE FALSE FALSE 875.8728031 862.9601188 1100.221313 1088.537337 959.4048974 956.1358364 1100.671605 1146.128939 982.0362588 1005.870305 0.870761169 0.857923844 1.093800371 1.082184584 0.953805767 0.950555784 1.094248035 1.139440078 0.97630505 1 9.974228584 -9.753481623 24.99948151 0.931186813 1.046495366 0.440837892 0.06929354 161.7897098 508264.525 0.012773467 0.017875956 1.76E-10 9.753481623 0.115308553 NAASFPLRS(ph)PQPVCSPAGSEGTPK ddPTM_HeLa_Romidepsin_16h_R1 1 NAASFPLRSPQPVCSPAGSEGTPK 24 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 1 0 NAAS(0.002)FPLRS(0.996)PQPVCS(0.002)PAGSEGTPK 71.634 0.00021422 0 1486.7 1736.9 1191.9 1076.9 1332.3 1392 880.61 1128.6 1701.3 1641.5 TRUE FALSE FALSE 1468.579529 1761.352124 1212.64452 1201.416245 1264.30776 1303.055692 955.4089914 1161.25426 1549.131467 1598.853593 0.918520329 1.101634403 0.758446255 0.751423551 0.790758932 0.814993754 0.597558773 0.726304313 0.968901389 1 10.64282212 -9.668028396 7.890614937 0.970785344 0.738197783 0.759059711 0.070451763 0.098969457 7.370403236 0.011488964 0.016252685 2.15E-10 9.668028396 -0.232587562 NAEAVLQS(ph)PGLSGK ddPTM_HeLa_Romidepsin_16h_R1 2 NAEAVLQSPGLSGK 14 0 Q13045-2;Q13045-3;Q13045 Q13045-2 FLII Protein flightless-1 homolog 1 0 NAEAVLQS(1)PGLSGK;NAEAVLQS(0.99)PGLS(0.01)GK ; 199.61 1.63E-16 206306000 14597.2 13203.5 12984 12982.3 12312.4 9994 9236.8 10394.9 14183.9 13090.7 TRUE FALSE FALSE 14419.28371 13389.37922 13209.98107 14483.37461 11684.05228 9355.415654 10021.37356 10695.66003 12915.25646 12750.60173 1.130870842 1.050097831 1.036028052 1.135897342 0.916353011 0.733723463 0.785952991 0.838835708 1.012913487 1 13.63827771 -8.534981465 4.276507541 1.064400605 0.789066812 0.866981612 0.048433011 0.059459961 2.598023711 0.00841923 0.018138163 2.92E-09 8.534981465 -0.275333793 NAEEES(ph)ESEAEEGD ddPTM_HeLa_Romidepsin_16h_R1 1 NAEEESESEAEEGD 14 0 H0Y503;Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3 H0Y503 BZW1 Basic leucine zipper and W2 domain-containing protein 1 1 0 NAEEES(0.999)ES(0.001)EAEEGD 111.31 0.0052783 71847000 5171.6 5684 5507.5 5212.3 5397.6 6474.7 6315.4 5405.8 7054.1 5408.8 TRUE FALSE FALSE 5108.56655 5764.019501 5603.355727 5814.970651 5122.140331 6060.987566 6851.829918 5562.208294 6423.163629 5268.278596 0.969684206 1.09409922 1.063602774 1.103770529 0.972260718 1.150468309 1.300582305 1.05579236 1.219214875 1 12.36311592 -8.675098542 0.521237802 0.985790447 1.20027668 0 0.106957729 0.952598092 0.39377014 0.018402433 0.09772395 2.11E-09 8.675098542 0.214486233 NAEEESES(ph)EAEEGD ddPTM_HeLa_Romidepsin_16h_R1 3 NAEEESESEAEEGD 14 0 H0Y503;Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3 H0Y503 BZW1 Basic leucine zipper and W2 domain-containing protein 1 1 0 NAEEES(0.246)ES(0.754)EAEEGD;NAEEES(0.107)ES(0.893)EAEEGD;NAEEES(0.091)ES(0.909)EAEEGD ;; 194.86 2.08E-11 88884200 13197.3 13075.9 13001.4 12378.6 13362.9 14037.8 13478.5 13754.6 15885.7 13204.6 TRUE FALSE FALSE 13036.44623 13259.98286 13227.68391 13809.87198 12680.94135 13140.82988 14623.36345 14152.56765 14464.84321 12861.54259 1.013598963 1.030979198 1.028467917 1.073733721 0.985958042 1.021714914 1.136983636 1.100378711 1.124658501 1 13.65077607 -4 0.356699824 1.005486247 2.489567969 0.066213061 0.049051029 28.52502892 0.355197261 0.008734203 29.0270378 1.00E-04 4 1.484081722 NAEEESESEAEEGD ddPTM_HeLa_Romidepsin_16h_R1 2 NAEEESESEAEEGD 14 0 H0Y503;Q7L1Q6-2;Q7L1Q6;Q7L1Q6-4;Q7L1Q6-3 H0Y503 BZW1 Basic leucine zipper and W2 domain-containing protein 1 0 0 ; ; 178.46 3.96E-06 17992000 13036.8 11956.5 13215.6 12834.2 13990.1 15708.9 16757.1 15141.7 16645.5 13872.2 FALSE FALSE TRUE 12877.90247 12124.82392 13445.61197 14318.15059 13276.13299 14705.15199 18180.44766 15579.8012 15156.68479 13511.79824 0.953085758 0.897350871 0.995101594 1.059677649 0.982558558 1.088319387 1.345523914 1.153051646 1.121737057 1 13.72193207 -7.98287432 3.981457507 0.980007811 1.24859562 0.630390807 0.073582428 0.066833798 2.402347089 0.007983961 0.02483781 1.04E-08 7.98287432 0.268587808 NAEK(ac)ELTDR ddPTM_HeLa_Romidepsin_16h_R1 1 NAEKELTDR 9 1 Q9UKX7;F2Z3L9;X6RKQ2;B1AHA5;B0QY21 Q9UKX7 NUP50 Nuclear pore complex protein Nup50 0 1 NAEK(1)ELTDR 101.97 0.025264 1718800 1017.6 973.64 830 424.3 728.01 653.67 554.09 532.47 1085.1 1094.1 FALSE TRUE FALSE 1005.1971 987.3469295 844.4458018 473.3595624 690.8569331 611.9025966 601.1543908 547.8761794 988.0459383 1065.675124 0.943249098 0.926498993 0.792404535 0.444187494 0.648280998 0.574192437 0.564106618 0.514111822 0.927154923 1 10.05755198 -9.538902702 2.748063865 0.969922183 0.556834751 0.917919112 0.056317421 0.047649533 0.730214122 0.008640012 0.013077768 2.89E-10 9.538902702 -0.413087432 NAEK(ac)YAEEDR ddPTM_HeLa_Romidepsin_16h_R1 2 NAEKYAEEDR 10 1 P38646;H0Y8S0 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 1 ; NAEK(1)YAEEDR;NAEK(1)YAEEDR 160.91 2.44E-12 1293800 692.18 824.11 761.51 511.09 892.01 1130.95 1188.49 988.48 759.55 797.18 FALSE TRUE FALSE 683.7434439 835.7118422 774.7637621 570.1846306 846.4874012 1058.685945 1289.440311 1017.080109 691.6139457 776.4691487 0.88058031 1.07629755 0.997803665 0.734330052 1.090175189 1.363461699 1.660645903 1.309878327 0.890716581 1 9.600784793 -8.277225428 2.921239008 0.944360854 1.486611954 0.785308364 0.120340817 0.080743315 1.379633185 0.016369385 0.04382588 5.28E-09 8.277225428 0.542251099 NAEQYK(ac)DQADK ddPTM_HeLa_Romidepsin_16h_R1 1 NAEQYKDQADK 11 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 1 NAEQYK(1)DQADK 178.53 9.82E-05 2399100 399.61 456.43 464.81 409.65 860.69 1021.4 1181.8 403.85 1166.7 1055.9 FALSE TRUE FALSE 394.7393996 462.8556335 472.8998231 457.0156605 816.7657776 956.1358364 1282.182063 415.5347626 1062.34743 1028.467566 0.383813173 0.450043977 0.459810147 0.444365652 0.794158032 0.929670384 1.246691782 0.404032929 1.032942083 1 10.00628058 -8.530890441 23.43812137 0.642393457 0.89264218 0.1180102 0.286755234 143.4366155 419621.3712 0.045891503 0.091953768 2.95E-09 8.530890441 0.250248723 NAEQYKDQADK ddPTM_HeLa_Romidepsin_16h_R1 1 NAEQYKDQADK 11 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 106.16 0.0186 8908900 1493.7 1535 1770.2 2024.6 1609.4 1781.9 2517.2 741.21 2479.2 1833.8 FALSE FALSE TRUE 1475.49421 1556.60977 1801.009588 2258.693778 1527.266313 1668.042341 2731.010905 762.6557419 2257.454143 1786.157612 0.826071675 0.871485114 1.008315043 1.264554574 0.855056856 0.933871865 1.528986517 0.426981212 1.263860551 1 10.80264368 -9.662420631 6.493341298 0.912268304 1.030246647 0 0.291221838 0.587510983 33.25736884 0.038945386 0.055134738 2.18E-10 9.662420631 0.117978342 NAETPEATTQQETDT(ph)DLPEAPPPPLEPAVIAR ddPTM_HeLa_Romidepsin_16h_R1 1 NAETPEATTQQETDTDLPEAPPPPLEPAVIAR 32 0 G3V119;H0YB24;Q8N163-2;Q8N163 G3V119 CCAR2 Cell cycle and apoptosis regulator protein 2 1 0 NAET(0.116)PEAT(0.051)T(0.06)QQET(0.018)DT(0.754)DLPEAPPPPLEPAVIAR 73.548 1.18E-05 15031000 1683.9 1719.1 1560.6 1383.5 1396.3 1570.2 1158.5 1306.6 1933.3 2022.5 TRUE FALSE FALSE 1663.375979 1743.301535 1587.761588 1543.46678 1325.041601 1469.869288 1256.902961 1344.40441 1760.380806 1969.955158 0.844372509 0.88494478 0.805988696 0.783503509 0.67262526 0.746143526 0.638036331 0.682454321 0.893614658 1 10.94394708 -6.948034963 0.093387101 1.217474018 0.069685169 0.805929713 0.047691117 12.55120409 0.172886467 0.501509195 2.056533314 1.13E-07 6.948034963 -1.147788849 NAGVEGS(ph)LIVEK ddPTM_HeLa_Romidepsin_16h_R1 1 NAGVEGSLIVEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 1 0 NAGVEGS(1)LIVEK 101.62 0.014792 4167900 1048.2 1055.6 1050.3 1023.7 1042.2 1292.1 1061.4 1132.3 1304.6 1047.6 TRUE FALSE FALSE 1035.424135 1070.460765 1068.580031 1142.065011 989.012645 1209.53898 1151.55529 1165.061314 1187.913309 1020.383201 1.014740476 1.049077213 1.047234049 1.119251091 0.969256103 1.185377198 1.128551792 1.141788019 1.164183522 1 9.994895337 -7.940728456 0.354216402 0.998651787 1.2267402 0.031273634 0.07016587 2.136274563 0.26421638 0.016149824 0.194042478 1.15E-08 7.940728456 0.228088414 NAGVEGSLIVEK ddPTM_HeLa_Romidepsin_16h_R1 2 NAGVEGSLIVEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 159.99 0.0031763 2555520 1219.61 1005.99 1059.97 1013.84 1141.99 1292.09 1041.55 1111.95 1333.15 1233.43 FALSE FALSE TRUE 1204.744924 1020.152354 1078.418333 1131.064951 1083.709989 1209.529619 1130.019231 1144.122519 1213.909725 1201.385311 1.00279645 0.849146685 0.897645679 0.941467272 0.902050307 1.006779098 0.940596843 0.952336031 1.010424977 1 10.23048321 -10.39856745 19.69274137 1.001334149 0.928938737 0.453304278 0.038801836 2.442869127 377.322763 0.00667011 0.007627414 3.99E-11 10.39856745 -0.072395412 NAIS(ph)LPVIGGPQALTLPTAQAPPKPPR ddPTM_HeLa_Romidepsin_16h_R1 2 NAISLPVIGGPQALTLPTAQAPPKPPR 27 1 O14613 O14613 CDC42EP2 Cdc42 effector protein 2 1 0 NAIS(1)LPVIGGPQALTLPTAQAPPKPPR;NAIS(0.994)LPVIGGPQALT(0.006)LPTAQAPPKPPR ; 68.938 8.93E-05 24876000 3146.8 2788.2 3104.9 4245.1 3923.2 4112.6 3500.9 3918.8 3748.5 2956 TRUE FALSE FALSE 3108.445591 2827.452353 3158.939482 4735.938436 3722.984465 3849.818133 3798.266359 4032.184295 3413.224772 2879.202694 1.079620271 0.982026156 1.097157727 1.64487844 1.293060913 1.337112577 1.319207698 1.400451696 1.18547568 1 11.49145364 -9.443091067 8.341062019 1.034694884 1.384832642 0.707028556 0.105660831 0.115668691 11.17715239 0.013896674 0.021227872 3.61E-10 9.443091067 0.350137758 NALFPEVFS(ph)PTPDENSDQNSR ddPTM_HeLa_Romidepsin_16h_R1 2 NALFPEVFSPTPDENSDQNSR 21 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 NALFPEVFS(1)PTPDENSDQNSR;NALFPEVFS(0.995)PT(0.005)PDENSDQNSR ; 182.72 8.15E-14 17178900 4191.9 4890.8 5149.7 3553.6 3294.6 3113.4 2524.2 2819.7 3841.6 4379.1 TRUE FALSE FALSE 4140.80751 4959.652811 5239.328368 3964.483952 3126.464268 2914.463788 2738.605485 2901.283571 3497.997675 4265.330351 0.970805816 1.16278281 1.228352305 0.929467034 0.732994636 0.683291457 0.642061754 0.680201375 0.82010006 1 12.05844177 -8.781201032 3.186545087 1.020305279 0.672823097 0.716630104 0.104664419 0.093102601 1.95485375 0.014275615 0.028606759 1.66E-09 8.781201032 -0.347482182 NALLQLTDS(ph)QIADVAR ddPTM_HeLa_Romidepsin_16h_R1 2 NALLQLTDSQIADVAR 16 0 O75643 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 1 0 NALLQLT(0.214)DS(0.786)QIADVAR;NALLQLT(0.375)DS(0.625)QIADVAR ; 136.2 7.46E-08 3677400 3133 2941.9 3177.8 2742.7 3230.2 3386.1 2831 3197.2 3667.2 3386 TRUE FALSE FALSE 3094.813791 2983.316145 3233.108276 3059.823879 3065.35084 3169.739138 3071.465069 3289.705938 3339.196447 3298.031232 0.938382196 0.904574862 0.980314633 0.927772863 0.9294487 0.961100401 0.931302602 0.997475678 1.012481754 1 11.68738935 -12.19707982 0.946637252 0.999909886 0.944911636 0.442055921 0.026385697 0.434297582 0.702004428 0.016054294 0.004558256 6.35E-13 12.19707982 -0.05499825 NALPPVLTTVNGQS(ph)PPEHSAPAK ddPTM_HeLa_Romidepsin_16h_R1 2 NALPPVLTTVNGQSPPEHSAPAK 23 0 Q6PKG0;A0A0B4J210;H0YBM7 Q6PKG0 LARP1 La-related protein 1 1 0 NALPPVLTTVNGQS(1)PPEHSAPAK;NALPPVLT(0.07)T(0.07)VNGQS(0.861)PPEHSAPAK ; 110.78 4.37E-06 1144480000 12491.6 12566.9 12436.7 10447.2 10767.1 10248.5 9278.1 9550.2 14030.4 13274.3 TRUE FALSE FALSE 12339.34757 12743.81715 12653.15555 11655.15442 10217.61471 9593.653926 10066.18158 9826.519969 12775.48588 12929.43177 0.954361165 0.985644023 0.97863199 0.901443669 0.790260151 0.742001203 0.778547871 0.760011742 0.988093376 1 13.65837125 -8.87822337 2.171831743 0.978736965 0.760814692 0.980499581 0.014249503 0.03784945 0.362471604 0.002932827 0.005997234 1.32E-09 8.87822337 -0.217922272 NAMS(ph)LPQLNEK ddPTM_HeLa_Romidepsin_16h_R1 1 NAMSLPQLNEK 11 0 Q9H3Q1;J3KRZ9 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 1 0 NAMS(1)LPQLNEK 104.81 0.023373 34098000 4000.2 4146.9 3553.7 2828.9 3365.8 2995 2533.3 2827.2 4292.7 3758.8 TRUE FALSE FALSE 3951.444024 4205.280167 3615.550658 3155.990728 3194.030666 2803.629166 2748.478439 2909.000571 3908.750161 3661.145834 1.079291621 1.148624053 0.9875462 0.862022676 0.872412849 0.765779156 0.750715367 0.794560147 1.067630282 1 11.83807953 -9.070254562 1.582529208 1.047284213 0.78027863 0.876722558 0.04743857 0.110057907 0.544434663 0.00883258 0.017744178 8.51E-10 9.070254562 -0.267005582 NAPAAVDEGSIS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 NAPAAVDEGSISPR 14 0 A0A494C0S2;A0A090HNM7;A0A1W2PS85;R4GMW8;P28715 A0A494C0S2 ERCC5-201;BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 1 0 NAPAAVDEGSIS(1)PR;NAPAAVDEGSIS(1)PR;NAPAAVDEGS(0.006)IS(0.994)PR ;; 224.06 8.90E-33 489130600 4855.56 3897.59 4359.49 4698.97 4095.66 3848.46 4142.87 4177.27 4671.76 4489.05 TRUE FALSE FALSE 4796.378567 3952.460374 4435.365095 5242.287021 3886.643187 3602.555826 4494.765274 4298.132717 4253.906085 4372.423834 1.096961033 0.903951795 1.01439505 1.198943016 0.888899003 0.823926491 1.027980234 0.983009168 0.972894268 1 12.09421754 NAPT(ph)PPKR ddPTM_HeLa_Romidepsin_16h_R1 1 NAPTPPKR 8 1 P42684-2;P42684-3;P42684-4;P42684-10;P42684-6;P42684;P42684-7;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 NAPT(1)PPKR 80.916 0.0019289 0 2314.6 2550.6 1692.1 1831 2340 2474.5 2654.9 1919.7 2385.4 2721.4 TRUE FALSE FALSE 2286.388765 2586.507414 1721.550291 2042.708835 2220.581068 2316.387436 2880.40714 1975.243491 2172.04385 2650.697636 0.862561136 0.97578365 0.64947064 0.770630647 0.837734579 0.87387841 1.086660018 0.745178727 0.819423468 1 11.3721564 -11.91899688 0.69432691 1.003092455 0.850999761 0 0.126436253 1.018335306 0.887732944 0.085116432 0.025307656 1.21E-12 11.91899688 -0.152092694 NAPWTLTPEFLAEHR ddPTM_HeLa_Romidepsin_16h_R1 1 NAPWTLTPEFLAEHR 15 0 H7BZN1;H7C1T3;C9J2E1;C9J050;C9JEJ2;P49585 H7BZN1 PCYT1A Choline-phosphate cytidylyltransferase A 0 0 95.57 0.0016186 0 2151 1629 2025.8 2190.3 2013.5 1910.1 1877.4 2661.4 1910.2 1891.6 FALSE FALSE TRUE 2124.782785 1651.933105 2061.058199 2443.552792 1910.743582 1788.050775 2036.866309 2738.40341 1739.346928 1842.455959 1.153233961 0.896592994 1.1186472 1.326247599 1.037063367 0.970471378 1.105516959 1.486278896 0.94403718 1 10.84741442 -7.266526224 4.793607258 1.073619364 1.507802098 0.540522228 0.117387871 0.10242225 6.689088447 0.015745893 0.14699873 5.41E-08 7.266526224 0.434182734 NARCTSISWELR ddPTM_HeLa_Romidepsin_16h_R1 2 NARCTSISWELR 12 1 H7C2Y2;A0A1W2PPQ7;A0A1W2PPR6;A0A1W2PPS0;A0A1W2PPC3;A0A1W2PP57;A0A1W2PP53;A0A1W2PQ29;A0A1W2PRZ8;A0A1W2PR92;A0A1W2PP13;A0A1W2PRV7;A0A1W2PQN1;A0A1W2PQ52;A0A1W2PRH2;A0A1W2PPI8;A0A1W2PNP0;Q969N2-3;Q969N2-4;Q969N2-6;Q969N2-5;Q969N2 H7C2Y2 PIGT GPI transamidase component PIG-T 0 0 ; ; 60.434 0.021561 2261300 848.09 560.05 1183.49 31.506 456.14 1269.1 991.69 444.91 964.14 445.27 FALSE FALSE TRUE 837.7531529 567.9343986 1204.088147 35.14887196 432.8614737 1188.008606 1075.924124 457.7827689 877.9049037 433.7018212 1.931633929 1.309504297 2.776304106 0.081043865 0.998062384 2.739229 2.480792266 1.055524202 2.02421309 1 8.760559691 -12.42185586 1.07081379 0.987287237 1.704978336 0 0.870275037 1.092595668 2.176352204 0.606831259 0.142321582 3.79E-13 12.42185586 0.717691099 NAS(ph)ASFQELEDK ddPTM_HeLa_Romidepsin_16h_R1 1 NASASFQELEDK 12 0 F2Z3H0;F2Z3N9;H7C3L7;Q99543-2;Q99543 F2Z3H0 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 0 NAS(1)ASFQELEDK 98.654 0.016845 26447000 1911.7 1614.8 2009.6 1126.7 1413.8 1423.8 1577 1508.6 1899.4 1906.5 TRUE FALSE FALSE 1888.399465 1637.533197 2044.576245 1256.974355 1341.64851 1332.823775 1710.950341 1552.248961 1729.512907 1856.968855 1.01692576 0.881831266 1.101028829 0.676895766 0.722493814 0.717741588 0.921367279 0.835904682 0.931363443 1 10.8587339 -9.261758848 24.99972748 1.003069892 0.776934003 0.610083331 0.083935478 13.53847246 1059451.061 0.012268959 0.019492634 5.47E-10 9.261758848 -0.226135889 NAS(ph)ASFQELEDKK ddPTM_HeLa_Romidepsin_16h_R1 1 NASASFQELEDKK 13 1 F2Z3H0;F2Z3N9;H7C3L7;Q99543-2;Q99543 F2Z3H0 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 0 NAS(0.999)AS(0.001)FQELEDKK 94.387 0.0053928 22894000 4630.1 5220.2 4587 2360 4372.3 5077.6 4037 4104.5 5462.3 5373 TRUE FALSE FALSE 4573.66656 5293.690113 4666.834811 2632.874304 4149.165216 4753.157747 4379.902679 4223.257232 4973.738207 5233.408685 0.873936441 1.011518578 0.891739035 0.503089757 0.792822702 0.908233626 0.836912029 0.806980208 0.950382152 1 12.35353521 -9.508894339 24.97328781 0.944492135 0.773845607 0.422549045 0.104590029 554.4871687 990201.4994 0.017159993 0.025570323 3.10E-10 9.508894339 -0.170646527 NASAS(ph)FQELEDK ddPTM_HeLa_Romidepsin_16h_R1 1 NASASFQELEDK 12 0 F2Z3H0;F2Z3N9;H7C3L7;Q99543-2;Q99543 F2Z3H0 DNAJC2 "DnaJ homolog subfamily C member 2;DnaJ homolog subfamily C member 2, N-terminally processed" 1 0 NAS(0.133)AS(0.867)FQELEDK 153 0.0014252 3828700 1340.7 1270.9 1303.4 734.55 1139.4 1114.9 1186.1 1093.7 1381.9 1283.7 TRUE FALSE FALSE 1324.359033 1288.791764 1326.08513 819.4821272 1081.252166 1043.661488 1286.847304 1125.344484 1258.299403 1250.349289 1.059191255 1.030745388 1.060571747 0.655402562 0.864760092 0.83469595 1.029190256 0.900024092 1.006358315 1 10.28811546 NASCYFDIEWR ddPTM_HeLa_Romidepsin_16h_R1 1 NASCYFDIEWR 11 0 Q16658;C9JPH9;C9JFC0;A0A0A0MSB2 Q16658 FSCN1 Fascin 0 0 144.7 0.025546 8594300 1215.8 1122.1 1193.4 525.29 1126.5 1356.6 929.13 1053.2 1179.8 1154.9 FALSE FALSE TRUE 1200.981362 1137.896953 1214.170626 586.0265014 1069.010501 1269.917638 1008.050279 1083.67268 1074.275733 1124.895532 1.06763813 1.011557893 1.07936301 0.520960823 0.950319804 1.128920511 0.896127908 0.963354063 0.955000445 1 10.13557531 NASGVVNS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 NASGVVNSSPR 11 0 A0A3B3ITD2;Q8N5G2 A0A3B3ITD2 TMEM57 Macoilin 1 0 NASGVVNS(0.5)S(0.5)PR 117.2 0.001394 0 4207.8 5157.6 4134 2346.8 4255 5714.1 3652.2 6014.6 5055.8 5044.9 TRUE FALSE FALSE 4156.513715 5230.208828 4205.950536 2618.148058 4037.851472 5348.987451 3962.417777 6188.622962 4603.596586 4913.832771 0.845880173 1.064384783 0.855940919 0.532811795 0.821731561 1.08855708 0.806380266 1.259428892 0.936864725 1 12.26263304 -12.51656721 1.192906755 1.001637254 0.893653572 0.006076314 0.187369255 1.518959607 3.772027681 0.138331429 0.0312175 3.04E-13 12.51656721 -0.107983682 NASLSQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 NASLSQSPR 9 0 C9J1X0;A4D1P6-3;A4D1P6-2;A4D1P6 C9J1X0 WDR91 WD repeat-containing protein 91 1 0 NASLS(0.001)QS(0.999)PR;NASLSQS(1)PR ; 130.1 0.0082236 82592000 6805.6 6801 7091.5 5918.7 6514.1 7758.6 7360.8 3894.5 7310.3 7226.5 TRUE FALSE FALSE 6722.65073 6896.744657 7214.924583 6603.047942 6181.66117 7262.8505 7986.026168 4007.181213 6656.448459 7038.754488 0.955090953 0.979824579 1.025028589 0.938098914 0.878232247 1.031837452 1.134579446 0.569302597 0.945685557 1 12.78110445 -7.248091486 24.8916216 0.983457709 0.569302311 0.787092751 0.065233894 704.7807233 1314277.266 0.008680006 0.223817189 5.65E-08 7.248091486 -0.414155398 NASVYS(ph)PSGPVNR ddPTM_HeLa_Romidepsin_16h_R1 2 NASVYSPSGPVNR 13 0 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 0 NAS(0.241)VYS(0.379)PS(0.379)GPVNR;NAS(0.228)VYS(0.594)PS(0.177)GPVNR ; 155.37 0.00071084 34232000 3589.2 3293.4 3460.3 2674.4 3625.4 3524.4 3391.3 3564.8 3297.2 3540.7 TRUE FALSE FALSE 3545.45345 3339.764572 3520.52507 2983.626711 3440.38231 3299.202214 3679.356937 3667.941864 3002.290174 3448.712104 1.028051442 0.968409212 1.020823126 0.865142297 0.997584665 0.956647617 1.066878541 1.063568588 0.870554017 1 11.75184198 -7.7399804 24.86922797 0.996119751 1.065223652 0.17862068 0.060745653 242.6437613 281199.836 0.006606334 0.024670954 1.82E-08 7.7399804 0.069103901 NATDLQNSS(ph)MSEEELTK ddPTM_HeLa_Romidepsin_16h_R1 3 NATDLQNSSMSEEELTK 17 0 Q5QNY5;H0YJ60;P40855-5;P40855 Q5QNY5 PEX19 Peroxisomal biogenesis factor 19 1 0 NATDLQNS(0.159)S(0.49)MS(0.351)EEELTK;NATDLQNS(0.215)S(0.721)MS(0.064)EEELTK;NATDLQNS(0.223)S(0.749)MS(0.028)EEELTK ;; 119.21 0.0028513 163917000 13044.6 12548.2 13584.7 12738.7 12375.6 11723.4 9847.6 11350.9 13906.3 12538.3 TRUE FALSE FALSE 12885.6074 12724.85389 13821.136 14211.60843 11744.02695 10974.31258 10684.0549 11679.32038 12662.4857 12212.55316 1.055111673 1.0419487 1.131715525 1.163688563 0.961635687 0.898609196 0.874842038 0.956337322 1.036841808 1 13.57607722 -8.53158899 24.87332574 1.046061146 0.910371034 0.654669714 0.051953711 105.838193 302235.2415 0.008687503 0.017396472 2.94E-09 8.53158899 -0.135690112 NAVALSAS(ph)PQLK ddPTM_HeLa_Romidepsin_16h_R1 2 NAVALSASPQLK 12 0 A0A2R8YD63;Q92547 A0A2R8YD63 TOPBP1 DNA topoisomerase 2-binding protein 1 1 0 NAVALS(0.031)AS(0.969)PQLK;NAVALS(0.033)AS(0.967)PQLK ; 152 0.0014362 106629000 10524.2 9725.2 9562.8 8767.4 9136.7 8549.5 7732 8763.4 10514.6 9806.9 TRUE FALSE FALSE 10395.927 9862.111621 9729.236523 9781.12804 8670.420105 8003.214542 8388.755887 9016.955153 9574.147842 9552.115324 1.088337677 1.032453157 1.018542615 1.023975079 0.907696339 0.837847353 0.878209235 0.943974695 1.002306559 1 13.22160454 -8.749312527 3.594991379 1.039717329 0.883674059 0.790105874 0.034117086 0.081787676 2.247059091 0.006027697 0.01209876 1.78E-09 8.749312527 -0.15604327 NAVEEYVYEFR ddPTM_HeLa_Romidepsin_16h_R1 1 NAVEEYVYEFR 11 0 A0A0A0MSM0;Q92598-2;Q92598-3;Q92598;Q92598-4 A0A0A0MSM0 HSPH1 Heat shock protein 105 kDa 0 0 185.99 1.83E-05 17412000 2737.5 2534.9 2325 2193 3229.5 2725.4 2238.9 2833.6 3030.1 2358.6 FALSE FALSE TRUE 2704.134297 2570.586389 2365.46565 2446.564978 3064.686564 2551.255736 2429.07211 2915.585745 2759.080267 2297.323232 1.177080465 1.118948502 1.029661659 1.064963321 1.334024974 1.110534077 1.057348864 1.269122997 1.200997852 1 11.16573814 -12.41909867 0.862273987 0.988596925 1.143470383 0 0.109672841 0.818821563 0.953831805 0.089026415 0.016848255 3.81E-13 12.41909867 0.154873457 NAVIVALSSK ddPTM_HeLa_Romidepsin_16h_R1 1 NAVIVALSSK 10 0 P61086-2;P61086 P61086-2 UBE2K Ubiquitin-conjugating enzyme E2 K 0 0 121.83 0.028097 476490 745.51 667.29 1092.5 887.96 1097.9 1129.7 1009.6 620.59 744.31 298.09 FALSE FALSE TRUE 736.4234374 676.6841261 1111.514504 990.6301132 1041.870066 1057.515816 1095.355399 638.5457925 677.7370494 290.3455788 2.536368697 2.330616257 3.828246701 3.411900113 3.588379304 3.642265952 3.772591969 2.199261291 2.334242705 1 8.181627256 -11.16970321 0.497914498 0.979236854 3.471483949 0.468124804 0.643056364 0.318630158 0.181524332 0.338046318 0.174861557 6.77E-12 11.16970321 2.492247095 NDAPTPGTSTT(ph)PGLR ddPTM_HeLa_Romidepsin_16h_R1 2 NDAPTPGTSTTPGLR 15 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 NDAPTPGT(0.001)S(0.004)T(0.033)T(0.962)PGLR;NDAPTPGTST(0.041)T(0.959)PGLR ; 147.83 0.00098717 123313000 11233.7 11052.7 9942.7 11774.5 8039.4 7138.5 5206.9 5840.9 10662.3 9761.6 TRUE FALSE FALSE 11096.77934 11208.3002 10115.74852 13135.92309 7629.119419 6682.372888 5649.173956 6009.897226 9708.637184 9507.992225 1.16710017 1.17882934 1.063920572 1.381566453 0.802390162 0.702816402 0.59415004 0.632088993 1.021102769 1 13.21492501 -8.565916949 6.760952136 1.106917586 0.655832018 0.818761142 0.105718776 0.065271165 7.640861262 0.016530698 0.033444216 2.72E-09 8.565916949 -0.451085568 NDDDEEEAARER ddPTM_HeLa_Romidepsin_16h_R1 2 NDDDEEEAARER 12 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;C9JEK3;C9JE79;F8WE61;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 0 0 ; ; 145.81 0.0017133 17599000 6500.6 6071.7 5300 12375.4 7066.3 6883.2 6237 6397.8 7396.3 6317.3 FALSE FALSE TRUE 6421.368187 6157.177552 5392.244277 13806.30198 6705.680343 6443.385735 6766.770624 6582.910249 6734.756404 6153.175635 1.043586039 1.000650382 0.87633518 2.24376855 1.089791799 1.04716428 1.099720051 1.069839484 1.094517173 1 12.58711546 NDDIS(ph)ELEDLSELEDLKDAK ddPTM_HeLa_Romidepsin_16h_R1 2 NDDISELEDLSELEDLKDAK 20 1 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 0 NDDIS(0.981)ELEDLS(0.019)ELEDLKDAK;NDDIS(0.866)ELEDLS(0.134)ELEDLKDAK ; 110.03 0.00013241 9276400 3512.7 2922.5 3233.7 3347.3 2534.3 1740.62 1522.31 2072.8 2944.7 2897.7 TRUE FALSE FALSE 3469.885861 2963.643032 3289.981192 3734.330576 2404.965214 1629.4 1651.614973 2132.773198 2681.318657 2822.417336 1.229402122 1.050037141 1.165660779 1.323096527 0.852094119 0.577306545 0.585177448 0.755654796 0.950007861 1 11.46271561 -8.537627985 4.997695974 1.124033813 0.642854029 0.78989571 0.111867189 0.060404674 4.203064216 0.016910685 0.035708514 2.90E-09 8.537627985 -0.481179784 NDDISELEDLS(ph)ELEDLKDAK ddPTM_HeLa_Romidepsin_16h_R1 2 NDDISELEDLSELEDLKDAK 20 1 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 0 NDDIS(0.003)ELEDLS(0.997)ELEDLKDAK;NDDIS(0.446)ELEDLS(0.554)ELEDLKDAK ; 56.688 0.012211 8279800 1823.56 1750.73 1840.97 1659.49 1406.86 1466.41 1191.12 1334.99 2086.5 1602.94 TRUE FALSE FALSE 1801.333749 1775.376823 1873.011311 1851.368042 1335.062684 1372.711134 1292.293703 1373.615829 1899.878214 1561.295388 1.15374308 1.13711783 1.199652113 1.185789734 0.855099359 0.879212956 0.827706092 0.879792408 1.216860198 1 10.6085278 -8.748591645 24.98188634 1.097329673 0.8594536 0.790603828 0.069751154 103.4574182 201167.4514 0.011750125 0.023379747 1.78E-09 8.748591645 -0.237876073 NDEELNK(ac)LLGK ddPTM_HeLa_Romidepsin_16h_R1 1 NDEELNKLLGK 11 1 A0A0U1RR32;A0A0U1RRH7;Q99878;Q96KK5;Q16777;Q6FI13;P20671;P0C0S8;Q9BTM1;Q9BTM1-2;H0YFX9 A0A0U1RR32 HIST1H2AJ;HIST1H2AH;HIST2H2AC;HIST2H2AA3;HIST1H2AD;HIST1H2AG;H2AFJ Histone H2A type 1-J;Histone H2A type 1-H;Histone H2A type 2-C;Histone H2A type 2-A;Histone H2A type 1-D;Histone H2A type 1;Histone H2A.J;Histone H2A 0 1 NDEELNK(1)LLGK 144.7 0.0035393 452660 0 75.214 0 0 327.31 194.74 128.74 137.73 322.08 307.91 FALSE TRUE FALSE 0 76.27286467 0 0 310.6061493 182.2967425 139.6751724 141.7150002 293.2723581 299.9104538 0 0.254318793 0 0 1.035662963 0.60783724 0.46572292 0.472524377 0.977866408 1 8.228388 -12.51332673 1.284657811 0.997534291 0.320784624 0.398817983 0.30875922 0.400260486 1.189290175 0.233905013 0.057243558 3.07E-13 12.51332673 -0.676749667 NDEELNK(ac)LLGR ddPTM_HeLa_Romidepsin_16h_R1 1 NDEELNKLLGR 11 1 Q93077;Q7L7L0;P04908 Q93077 HIST1H2AC;HIST3H2A;HIST1H2AB Histone H2A type 1-C;Histone H2A type 3;Histone H2A type 1-B/E 0 1 NDEELNK(1)LLGR 107.11 0.00092372 0 0 58.542 157.03 0 118.24 0 0 0 131.87 145.81 FALSE TRUE FALSE 0 59.36615581 159.7630413 0 112.2057716 0 0 0 120.0752169 142.0218352 0 0.418007243 1.124918862 0 0.790060003 0 0 0 0.845470112 1 7.149968944 -12.47170129 1.141848577 1.010487876 0.279595454 0.310122896 0.374524221 0.475426364 1.083087105 0.281997368 0.065372429 3.38E-13 12.47170129 -0.730892422 NDELLSDLT(ph)RTPPPPSSTFPK ddPTM_HeLa_Romidepsin_16h_R1 1 NDELLSDLTRTPPPPSSTFPK 21 1 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;G5E9V3;A0A1W2PQ63;E9PGF6 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 NDELLS(0.028)DLT(0.731)RT(0.24)PPPPSST(0.001)FPK 64.377 0.0063965 12219000 850.39 929.37 842.66 1361.2 739.58 794.47 786.5 662.52 1144.6 841.73 TRUE FALSE FALSE 840.0251196 942.4536953 857.3261438 1518.588349 701.8364728 743.705931 853.3052904 681.6889709 1042.224109 819.8617333 1.024593642 1.149527606 1.045696011 1.852249333 0.856042482 0.907111408 1.040791704 0.831468214 1.271219362 1 9.679236815 NDELLSDLTRT(ph)PPPPSSTFPK ddPTM_HeLa_Romidepsin_16h_R1 1 NDELLSDLTRTPPPPSSTFPK 21 1 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;G5E9V3;A0A1W2PQ63;E9PGF6 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 NDELLS(0.003)DLT(0.037)RT(0.959)PPPPSSTFPK 83.934 0.0012383 12790000 1504.8 1440.6 1374.4 2249.3 1623.4 1283.8 1020.7 981.08 1464.1 1344.7 TRUE FALSE FALSE 1486.458919 1460.880805 1398.320855 2509.374649 1540.55184 1201.769323 1107.398233 1009.466002 1333.147229 1309.7645 1.134905488 1.115376699 1.067612426 1.91589759 1.176205219 0.917546111 0.845494157 0.770723288 1.017852621 1 10.35509172 -8.094748721 3.723643722 1.140739804 0.819798538 0.278935128 0.254333952 0.289861436 7.349060937 0.038335461 0.108866253 8.04E-09 8.094748721 -0.320941265 NDEPPRMT(ph)LQPLR ddPTM_HeLa_Romidepsin_16h_R1 1 NDEPPRMTLQPLR 13 1 Q86XX4;Q86XX4-2 Q86XX4 FRAS1 Extracellular matrix protein FRAS1 1 0 NDEPPRMT(1)LQPLR 112.71 0.0086914 25725000 391.31 292.9 441.79 477.52 482.08 556.98 426.43 519.1 416.31 408.59 TRUE FALSE FALSE 386.5405632 297.0234539 449.4791696 532.7331092 457.4776587 521.3907756 462.6509536 534.1193395 379.0741909 397.9747729 0.971269009 0.746337392 1.129416235 1.338610247 1.149514215 1.310110115 1.162513267 1.342093459 0.95250809 1 8.636533173 -9.528103655 24.99909418 0.966609699 1.249934413 0.741916919 0.093573419 57.61184552 275648.4921 0.013888344 0.019678507 2.96E-10 9.528103655 0.283324713 NDFTEEEEAQVR ddPTM_HeLa_Romidepsin_16h_R1 1 NDFTEEEEAQVR 12 0 E5RJR5;P63208 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 0 153.38 0.014455 7551600 816.01 964.92 655.18 855.4 1134.7 1066.8 840.24 1258.5 1711.1 1137.9 FALSE FALSE TRUE 806.0641563 978.5041691 666.5831331 954.3053728 1076.792025 998.6349229 911.6099646 1294.912712 1558.05493 1108.337194 0.727273397 0.882857829 0.601426296 0.861024405 0.971538292 0.901020852 0.822502366 1.168338227 1.40575895 1 10.11418115 -7.257422941 24.19000555 0.85716498 1.168338422 0.081925214 0.20506399 230.8210389 1390086.323 0.018014788 0.182681046 5.53E-08 7.257422941 0.311173442 NDGQASSS(ph)PPSESMGQAK ddPTM_HeLa_Romidepsin_16h_R1 1 NDGQASSSPPSESMGQAK 18 0 Q5VYV7 Q5VYV7 SLX4IP Protein SLX4IP 1 0 NDGQAS(0.013)S(0.11)S(0.84)PPS(0.025)ES(0.012)MGQAK 145.46 0.00011993 1908800 604.51 691.79 831.32 785.96 731.84 843.04 777.19 617.49 888.81 621.29 TRUE FALSE FALSE 597.1419996 701.5290378 845.7887759 876.8363933 694.4914739 789.1724648 843.2044992 635.3560989 809.3126075 605.1487962 0.98676888 1.159267014 1.397654232 1.448959989 1.147637537 1.304096562 1.39338375 1.049917149 1.337377869 1 9.241146111 -10.06223454 3.5585802 0.994271871 1.296122682 0.11018402 0.156565835 0.113804926 2.851968422 0.018023383 0.022728797 8.66E-11 10.06223454 0.301850812 NDHQEDFWK ddPTM_HeLa_Romidepsin_16h_R1 1 NDHQEDFWK 9 0 A6NKB8;Q9H4A4 A6NKB8 RNPEP Aminopeptidase B 0 0 96.015 0.015543 5668700 4598.6 4255.2 4400.6 4542.4 4953 4576 3729.6 3985.5 4757.2 3975 FALSE FALSE TRUE 4542.550494 4315.104817 4477.190597 5067.613661 4700.229928 4283.608368 4046.392131 4100.814154 4331.704117 3871.728927 1.173261502 1.114516253 1.156380181 1.308876152 1.213987347 1.10638127 1.045112457 1.059168716 1.118803563 1 11.91876223 -12.27484227 0.875350722 0.994687386 1.15072053 0.089628248 0.080771099 0.612202425 0.795860565 0.064230893 0.015241183 5.31E-13 12.27484227 0.156033144 NDK(ac)SEEEQSSSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 NDKSEEEQSSSSVK 14 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 1 NDK(1)SEEEQSSSSVK 259.1 1.03E-68 569920 174.13 152.61 180.25 0 178.21 66.707 330.8 135.56 156.31 179.57 FALSE TRUE FALSE 172.0076366 154.7584476 183.3871756 0 169.1152787 62.44463799 358.8981437 139.4822147 142.3292421 174.9047455 0.983436076 0.884815601 1.048497427 0 0.966899315 0.357020833 2.051963443 0.797475302 0.81375289 1 7.450425623 -10.13376292 2.168050216 0.993156199 0.86911278 0 0.49953238 1.644859371 14.89144783 0.085857616 0.106732665 7.35E-11 10.13376292 -0.124043419 NDKS(ph)EEEQSSSSVK ddPTM_HeLa_Romidepsin_16h_R1 4 NDKSEEEQSSSSVK 14 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 NDKS(1)EEEQSSSSVK;NDKS(0.926)EEEQS(0.071)S(0.003)S(0.001)SVK;NDKS(0.998)EEEQS(0.001)SSSVK;NDKS(0.987)EEEQS(0.008)S(0.001)S(0.001)S(0.002)VK ;;; 212.32 4.36E-23 789627000 8996.4 8479.8 12865.7 9220.2 10530.3 12063.1 18302.8 3901.99 13746.8 11238.6 TRUE FALSE FALSE 8886.748416 8599.178847 13089.62211 10286.28291 9992.899497 11292.30684 19857.43938 4014.887924 12517.25178 10946.61955 0.811825822 0.785555651 1.195768433 0.939676661 0.912875381 1.031579365 1.814024803 0.366769659 1.143481028 1 13.4181978 -7.994934867 24.99864668 0.925554583 1.173498278 0 0.349289135 253.6262803 1251720.828 0.042039925 0.125501338 1.01E-08 7.994934867 0.247943695 NDKS(ph)EEEQSSSSVKK ddPTM_HeLa_Romidepsin_16h_R1 1 NDKSEEEQSSSSVKK 15 2 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 NDKS(1)EEEQSSSSVKK 82.859 0.024326 9601500 1336.9 1640.8 2052.8 1305.5 1523.7 1983.4 3258.5 451.87 2058.4 1359.1 TRUE FALSE FALSE 1320.605349 1663.899225 2088.528123 1456.448053 1445.939903 1856.667141 3535.276909 464.9441455 1874.291549 1323.790386 0.997594002 1.256920463 1.577687937 1.100210477 1.092272552 1.40253862 2.670571524 0.351221878 1.415852214 1 10.37045898 -9.73325965 0.644297547 0.979430584 1.482792422 0 0.564302376 1.126921845 0.963060307 0.127997824 0.226227539 1.85E-10 9.73325965 0.503361838 NDKSEEEQS(ph)SSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 NDKSEEEQSSSSVK 14 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 1 0 NDKS(0.003)EEEQS(0.562)S(0.151)S(0.224)S(0.06)VK 74.793 0.017217 2218000 965.59 1366.8 1947.4 1122.9 1055.6 1375.8 1948.7 808.06 1798.2 1660.8 TRUE FALSE FALSE 953.8210177 1386.041846 1981.29368 1252.734981 1001.728793 1287.89082 2114.222529 831.4399412 1637.364488 1617.652177 0.589632946 0.856823158 1.224795855 0.774415538 0.619248567 0.79614817 1.306969792 0.513979428 1.012185754 1 10.65968572 -10.0106745 24.56735497 0.801847796 0.88687802 0 0.255101089 1678.80575 3863776.714 0.043285797 0.054885434 9.76E-11 10.0106745 0.085030224 NDKSEEEQSSSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 NDKSEEEQSSSSVK 14 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 0 117.08 0.0051944 2990700 964.26 864.65 996.29 797.12 913.39 1211.8 1483.7 850.07 1386.3 1213.1 FALSE FALSE TRUE 952.5072282 876.8225654 1013.63001 889.286765 866.7763 1134.369891 1609.725441 874.6654343 1262.305856 1181.583487 0.806127742 0.742074153 0.857857291 0.752622878 0.733571778 0.960042099 1.362345918 0.740248526 1.06831711 1 10.20650585 -7.995773498 24.98524837 0.866941583 1.078771409 0.171026924 0.174211907 137.2967934 811611.4559 0.022482341 0.067056532 1.01E-08 7.995773498 0.211829826 NDLQDTEIS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 NDLQDTEISPR 11 0 Q9NS91 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 0 NDLQDTEIS(1)PR;NDLQDTEIS(1)PR ; 173.06 0.00018973 66258000 7290.3 5914 7204.5 5205.4 6596.8 5236.6 4874.4 4780.3 7048 7226.4 TRUE FALSE FALSE 7201.443019 5997.257447 7329.8913 5807.27284 6260.14068 4901.99816 5288.431414 4918.610438 6417.609228 7038.657086 1.023127414 0.852045692 1.041376389 0.825054093 0.889394185 0.696439406 0.751340966 0.698799555 0.911766144 1 12.78108449 -8.685431678 0.690401682 1.009413984 0.679485867 0.672217995 0.069575592 0.272716341 0.219362545 0.010976259 0.049189884 2.06E-09 8.685431678 -0.329928118 NDQEPPPEALDFS(ph)DDEKEK ddPTM_HeLa_Romidepsin_16h_R1 2 NDQEPPPEALDFSDDEKEK 19 1 Q96HR8-2;Q96HR8 Q96HR8-2 NAF1 H/ACA ribonucleoprotein complex non-core subunit NAF1 1 0 NDQEPPPEALDFS(1)DDEKEK;NDQEPPPEALDFS(1)DDEKEK ; 84.127 0.0024778 256410000 9274.9 8594.3 8916.7 5998.6 7636.2 7915.4 6620.6 7221.7 9638 10134.5 TRUE FALSE FALSE 9161.853951 8715.290781 9071.891423 6692.186356 7246.496219 7409.631486 7182.953599 7430.648496 8775.953141 9871.204229 0.928139439 0.882900463 0.919025806 0.677950349 0.734104578 0.750630958 0.727667408 0.752760081 0.889045849 1 13.26901038 -9.599018377 1.193431712 0.968363986 0.727573332 0.773924154 0.049332967 0.117103847 0.334243435 0.008092385 0.013339316 2.52E-10 9.599018377 -0.240790654 NDQEPPPEALDFS(ph)DDEKEKEAK ddPTM_HeLa_Romidepsin_16h_R1 1 NDQEPPPEALDFSDDEKEKEAK 22 2 Q96HR8-2;Q96HR8 Q96HR8-2 NAF1 H/ACA ribonucleoprotein complex non-core subunit NAF1 1 0 NDQEPPPEALDFS(1)DDEKEKEAK 76.78 0.00084788 13030000 7279.4 6554.2 5764.9 8661.2 6321 5093.8 4318.2 5505.4 7853.3 6555.4 TRUE FALSE FALSE 7190.675873 6646.4702 5865.235666 9662.648696 5998.415783 4768.322619 4684.9878 5664.690063 7150.881179 6385.089763 1.126166763 1.040936063 0.918583118 1.513314465 0.939441105 0.746790225 0.733738753 0.887174695 1.119934323 1 12.64049119 -8.522486302 24.99998976 1.082035542 0.793590045 0.472801685 0.154612927 9.809331491 624876.0887 0.021855267 0.044105718 3.00E-09 8.522486302 -0.288445496 NDREYDS(ph)GDTDEIIAMK ddPTM_HeLa_Romidepsin_16h_R1 1 NDREYDSGDTDEIIAMK 17 1 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 NDREYDS(0.938)GDT(0.062)DEIIAMK 102.9 0.0031338 6121600 3183.5 2939.3 3237.3 1651.3 2864.9 3001.8 2820.3 3343.1 3413.3 3433.8 TRUE FALSE FALSE 3144.698278 2980.679543 3293.643849 1842.231076 2718.693463 2809.994668 3059.856212 3439.827324 3108.005899 3344.589381 0.940234486 0.891194465 0.984767777 0.550809342 0.812863151 0.840161332 0.914867526 1.028475227 0.929263818 1 11.70761339 -10.06323199 1.408855404 0.975620393 0.840610601 0.13063526 0.121003532 0.494179871 1.901907862 0.023045077 0.029726225 8.65E-11 10.06323199 -0.135009791 NDREYDSGDT(ph)DEIIAMK ddPTM_HeLa_Romidepsin_16h_R1 1 NDREYDSGDTDEIIAMK 17 1 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 NDREYDS(0.325)GDT(0.675)DEIIAMK 123.76 5.68E-06 0 912.09 929.06 906.84 586.86 1112 1030.9 950.9 1156.7 1212.2 1169.7 TRUE FALSE FALSE 900.9730963 942.1393311 922.6231698 654.7155145 1055.250491 965.0288171 1031.669422 1190.16729 1103.777796 1139.311025 0.790805211 0.826937781 0.809807989 0.574659158 0.926218098 0.847028419 0.905520441 1.044637735 0.968811651 1 10.15394593 -7.277329757 2.587661608 0.862945303 1.079081645 0.212999476 0.112593709 0.701812692 6.134604825 0.017866202 0.323472261 5.28E-08 7.277329757 0.216136342 NDS(ph)GEENVPLDLTR ddPTM_HeLa_Romidepsin_16h_R1 2 NDSGEENVPLDLTR 14 0 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 NDS(0.998)GEENVPLDLT(0.002)R;NDS(0.993)GEENVPLDLT(0.007)R ; 197.94 1.96E-12 106955000 5190.6 5296.2 5333.7 3188.05 6794.7 6898.7 5740 6711.1 5212.1 5384.2 TRUE FALSE FALSE 5127.334971 5370.760043 5426.530811 3556.667341 6447.941104 6457.895335 6227.555457 6905.27509 4745.916722 5244.317708 0.977693431 1.02411035 1.034744864 0.678194484 1.229510008 1.231408106 1.187486305 1.316715629 0.904963617 1 12.35653937 -8.581990299 24.99999822 0.975523526 1.237939757 0.662957273 0.104234718 34.50677685 14593.72308 0.0137331 0.027466203 2.62E-09 8.581990299 0.262416231 NDS(ph)GEENVPLDLTREPSDNLR ddPTM_HeLa_Romidepsin_16h_R1 1 NDSGEENVPLDLTREPSDNLR 21 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 NDS(0.672)GEENVPLDLT(0.207)REPS(0.121)DNLR 49.141 0.024423 11965000 1088.4 1171.6 785.11 1183.9 1290.1 1186.2 1169.5 1237.5 1105 1398.1 TRUE FALSE FALSE 1075.134162 1188.093816 798.7745102 1320.788088 1224.261383 1110.405648 1268.837301 1273.30511 1006.166032 1361.77716 0.789508147 0.872458321 0.58656771 0.969900309 0.899017415 0.815409217 0.931751051 0.935031918 0.738862467 1 10.41127493 -12.42338755 1.155306209 0.999878332 0.843927987 0 0.130374694 0.56227167 1.343753966 0.06976873 0.017620832 3.77E-13 12.42338755 -0.155950344 NDS(ph)LSSLDFDDDDVDLSR ddPTM_HeLa_Romidepsin_16h_R1 1 NDSLSSLDFDDDDVDLSR 18 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 NDS(0.972)LS(0.027)SLDFDDDDVDLSR 195.55 5.86E-15 2496600 339.02 257.51 258.63 477.06 307.98 461.45 347.13 495.14 484.57 386.58 TRUE FALSE FALSE 334.8878938 261.1352325 263.1313467 532.2199218 292.2626314 431.9648343 376.6152135 509.4660947 441.2288456 376.5365959 0.889390029 0.693518865 0.698820113 1.413461341 0.776186524 1.147205448 1.000208792 1.353032083 1.171808665 1 8.556646278 -9.278966492 24.99157404 0.906353563 1.110771333 0.250088864 0.210642512 966.8407661 1378596.99 0.0292378 0.044720432 5.26E-10 9.278966492 0.20441777 NDS(ph)WGSFDLR ddPTM_HeLa_Romidepsin_16h_R1 2 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 NDS(0.683)WGS(0.317)FDLR;NDS(0.992)WGS(0.008)FDLR ; 143.58 0.0041766 163449000 8517.7 7716 7964.2 7503.9 6651 7587.8 7100.6 7114.2 8415.7 7655.2 TRUE FALSE FALSE 8413.882996 7824.626051 8102.81356 8371.536225 6311.574652 7102.964069 7703.724787 7320.038153 7662.978714 7456.3168 1.128423486 1.049395601 1.086704572 1.122744171 0.84647351 0.952610284 1.033180992 0.981723061 1.027716354 1 12.86424744 -8.781859983 24.99956394 1.067171996 0.959125276 0.497080047 0.056863154 187.4602308 229494.3398 0.009839403 0.017850578 1.65E-09 8.781859983 -0.10804672 NDSGEENVPLDLT(ph)REPSDNLR ddPTM_HeLa_Romidepsin_16h_R1 1 NDSGEENVPLDLTREPSDNLR 21 1 Q6R327-3;Q6R327;Q6R327-4 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 NDS(0.003)GEENVPLDLT(0.742)REPS(0.255)DNLR 70.907 0.0034342 28535000 895.5 824.66 777.5 1150.5 1146.9 1034.2 1071 1058.1 1083.4 858.93 TRUE FALSE FALSE 884.5853016 836.2695851 791.0320614 1283.526223 1088.369413 968.1179577 1161.970713 1088.714454 986.4979906 836.6148748 1.057338721 0.999587278 0.945515177 1.534190058 1.300920467 1.15718473 1.388895594 1.301332892 1.179154256 1 9.708419839 -9.277443179 24.99987059 1.01970435 1.32747623 0.670098504 0.104894462 304.4736592 475623.6773 0.013866066 0.021221653 5.28E-10 9.277443179 0.30777188 NDSLS(ph)SLDFDDDDVDLSR ddPTM_HeLa_Romidepsin_16h_R1 1 NDSLSSLDFDDDDVDLSR 18 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 NDS(0.029)LS(0.709)S(0.261)LDFDDDDVDLSR 235.72 3.17E-49 2238600 409.41 511.25 388.16 458.98 439.93 631.11 475.75 531.11 432.01 476.22 TRUE FALSE FALSE 404.4199534 518.4473909 394.915762 512.0494272 417.4787305 590.7841078 516.1601931 546.4768299 393.3699436 463.8477357 0.87188084 1.117710298 0.851390945 1.103917057 0.900033995 1.27365957 1.112779374 1.178138401 0.848058346 1 8.857507489 -8.267291414 24.98142822 0.955500581 1.180651143 0.540374636 0.09799723 250.1810574 1067985.941 0.01286164 0.029498115 5.40E-09 8.267291414 0.225150562 NDSLVTPS(ph)PQQAR ddPTM_HeLa_Romidepsin_16h_R1 1 NDSLVTPSPQQAR 13 0 A0A0A0MS29;Q9GZY8-2;E9PQX8;H7C433 A0A0A0MS29 MFF Mitochondrial fission factor 1 0 NDSLVT(0.005)PS(0.995)PQQAR 111.81 0.0064168 6417600 1985.9 2317.6 2243.4 1683.6 2250.9 2665.5 1402.1 2234.9 2380.6 1898.3 TRUE FALSE FALSE 1961.695087 2350.227234 2282.445436 1878.265754 2136.028174 2495.183153 1521.194339 2299.563305 2167.673174 1848.981892 1.060959599 1.271092618 1.234433634 1.01583783 1.155245588 1.349490313 0.822719976 1.243691631 1.172360412 1 10.85251538 -10.48195274 9.33065447 1.026760161 1.149589628 0.026583644 0.14746596 0.593382979 130.1558375 0.022937642 0.025713653 3.30E-11 10.48195274 0.122829467 NDSVIVADQTPT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 4 NDSVIVADQTPTPTR 15 0 E9PEK8;H7C2N6;B8ZZU6;E9PBF9;P15336-3;P15336-7;P15336-5;P15336 E9PEK8 ATF2 Cyclic AMP-dependent transcription factor ATF-2 1 0 NDSVIVADQT(0.001)PT(0.975)PT(0.023)R;NDSVIVADQTPT(0.998)PT(0.002)R;NDSVIVADQT(0.001)PT(0.993)PT(0.006)R;NDS(0.002)VIVADQT(0.288)PT(0.698)PT(0.012)R ;;; 186.96 3.89E-09 19459100 7179.6 8946 6639.7 8038.2 7753.8 8399.1 5368.3 6853.3 6962 6798 TRUE FALSE FALSE 7092.092274 9071.942023 6755.261193 8967.614505 7358.094653 7862.424617 5824.283268 7051.589423 6339.301283 6621.38698 1.071088625 1.370096937 1.020218455 1.354340795 1.111261836 1.187428652 0.879616806 1.064971651 0.957397793 1 12.69291773 -10.5048046 13.20111998 1.031330047 1.141344982 0.157014379 0.140063325 1.357875785 989.1384716 0.023865713 0.025787775 3.13E-11 10.5048046 0.110014935 NDSWGS(ph)FDLR ddPTM_HeLa_Romidepsin_16h_R1 2 NDSWGSFDLR 10 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 NDS(0.342)WGS(0.658)FDLR;NDS(0.136)WGS(0.864)FDLR ; 125.36 0.0093074 13785600 4821.2 4537.7 4423.9 4246.7 4271.3 4327.7 4303 4038.6 4785.6 4910.3 TRUE FALSE FALSE 4762.43736 4601.58186 4500.896124 4737.723435 4053.319623 4051.173937 4668.496713 4155.450519 4357.56395 4782.729698 0.995757164 0.962124592 0.941072653 0.990589838 0.847490843 0.847042211 0.976115525 0.868844945 0.911103956 1 12.22361854 -9.336906243 0.992182127 0.997835415 0.892498126 0.243404921 0.050571156 0.296562119 0.57932704 0.007503654 0.015223139 4.60E-10 9.336906243 -0.105337289 NDTT(ph)S(ph)ARELS(ph)PS(ph)S(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 NDTTSARELSPSSLK 15 1 O15021;H7C1I9;O15021-2;O15021-3;O15021-6 O15021 MAST4 Microtubule-associated serine/threonine-protein kinase 4 5 0 NDT(0.047)T(0.962)S(0.993)ARELS(0.999)PS(1)S(0.999)LK 46.706 0.0043347 0 421.8 388.24 364.8 339.02 617.73 348.84 350.78 331.4 430.78 551.08 TRUE FALSE FALSE 416.6589394 393.7056529 371.149191 378.2190875 586.204933 326.5502498 380.5752444 340.9885361 392.2499579 536.7628622 0.776243978 0.733481544 0.691458402 0.704629761 1.092111572 0.608369678 0.709019329 0.635268496 0.730769555 1 9.068141047 -16.52287875 0.180480165 2.117031794 0.688154427 0 0.152359247 42.91402249 0.493280928 16.73357645 0.170302578 3.00E-17 16.52287875 -1.428877366 NDVLPLSNS(ph)VPEDVGK ddPTM_HeLa_Romidepsin_16h_R1 2 NDVLPLSNSVPEDVGK 16 0 Q96EQ0;D6RFW1 Q96EQ0 SGTB Small glutamine-rich tetratricopeptide repeat-containing protein beta 1 0 NDVLPLS(0.119)NS(0.881)VPEDVGK;NDVLPLS(0.013)NS(0.987)VPEDVGK ; 141.18 1.29E-07 2569700 3248 2901.4 3267.7 3285.3 4401.5 6115.5 5011.1 6822.2 3090 3149 TRUE FALSE FALSE 3208.412127 2942.245985 3324.572948 3665.161844 4176.875031 5724.739287 5436.742709 7019.589593 2813.622661 3067.188526 1.046043339 0.959264799 1.083915423 1.194958123 1.361792728 1.866445195 1.772549246 2.288607151 0.917329547 1 11.58270113 -8.060742086 0.79963342 1.010164084 2.325935121 0.949562952 0.099831259 0.141914396 0.121613859 0.014651028 0.130059716 8.69E-09 8.060742086 1.315771037 up NDVVEALTGS(ph)AASR ddPTM_HeLa_Romidepsin_16h_R1 1 NDVVEALTGSAASR 14 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 0 NDVVEALTGS(1)AASR 129.42 0.0001005 0 1689.5 1958.2 1638 1156.8 1657.3 1240.9 1123.1 1350 1823.1 1657 TRUE FALSE FALSE 1668.907724 1985.767591 1666.508703 1290.554659 1572.721797 1161.610495 1218.496086 1389.06012 1660.03737 1613.950901 1.034051112 1.230376705 1.032564684 0.799624485 0.974454549 0.719730999 0.754977171 0.860658226 1.028555062 1 10.65638097 -9.265852221 23.6764548 1.037093666 0.820972161 0.645593456 0.088898602 99.47143989 533700.2931 0.014070334 0.021972096 5.42E-10 9.265852221 -0.216121505 NEDEEEEEEEKDEAEDLLGR ddPTM_HeLa_Romidepsin_16h_R1 3 NEDEEEEEEEKDEAEDLLGR 20 1 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 0 ;; ;; 189.56 1.73E-17 67538500 2495.01 2177.57 2540 1987.13 2376.64 2706.25 1995.19 2108.86 2691.65 2706.43 FALSE FALSE TRUE 2464.599858 2208.225888 2584.207635 2216.89132 2255.351192 2533.329359 2164.661389 2169.876537 2450.902083 2636.116558 0.934935844 0.83768143 0.980308563 0.840968626 0.855558221 0.961008098 0.821155416 0.823133761 0.929739649 1 11.36419845 -10.75382898 0.022931026 1.867046484 7.39E-07 0.300277526 0.055310308 119.5014659 1.998737822 82.79270857 79.51985235 1.76E-11 10.75382898 -1.867045745 NEDS(ph)GSETAYLENR ddPTM_HeLa_Romidepsin_16h_R1 1 NEDSGSETAYLENR 14 0 J3QT39;Q49A88-5;Q49A88 J3QT39 CCDC14 Coiled-coil domain-containing protein 14 1 0 NEDS(0.812)GS(0.167)ET(0.021)AYLENR 134.08 0.0016179 8950100 1147.8 1163.4 1152 1170.3 1005.1 889.77 570.91 561.7 1212.6 1141.2 TRUE FALSE FALSE 1133.810172 1179.778376 1172.050077 1305.615592 953.8059965 832.9165686 619.4030811 577.9519033 1104.142019 1111.551459 1.020024905 1.061379899 1.054427185 1.174588528 0.858085326 0.749327943 0.557241931 0.519950649 0.993334145 1 10.11835902 -8.126880115 1.676259597 1.027067601 0.52509891 0.912997652 0.062206367 0.08019948 0.419336818 0.009338578 0.037460343 7.47E-09 8.126880115 -0.50196869 NEDY(ph)PRTCRMWNS(ph)T(ph)FQTYKK ddPTM_HeLa_Romidepsin_16h_R1 1 NEDYPRTCRMWNSTFQTYKK 20 3 H3BMH7 H3BMH7 3 0 NEDY(0.828)PRT(0.173)CRMWNS(0.508)T(0.508)FQT(0.508)Y(0.475)KK 45.257 0.0040104 0 791.29 1017.2 587.61 450.05 704.18 671.83 639.32 795.94 1144.1 881.7 TRUE FALSE FALSE 781.6454531 1031.520168 597.8371056 502.0868985 668.2430669 628.9022312 693.6238248 818.9692681 1041.768831 858.7933069 0.910167146 1.201127396 0.696136196 0.584642305 0.778118625 0.73230919 0.807672602 0.953627912 1.21306119 1 9.746167137 -9.726379496 24.99998702 0.974659931 0.752739161 0.519123612 0.137411882 120.9812243 86267.34333 0.018329525 0.02592125 1.88E-10 9.726379496 -0.221920769 NEEDAAELVALAQAVNAR ddPTM_HeLa_Romidepsin_16h_R1 1 NEEDAAELVALAQAVNAR 18 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 199.84 1.13E-19 3498000 964.36 1004.8 815.2 783.24 1154 1177.8 856.09 897.61 946.15 864.52 FALSE FALSE TRUE 952.6060094 1018.945601 829.388214 873.8018941 1095.107074 1102.542381 928.8062632 923.5809292 861.5239743 842.0596458 1.131280918 1.210063451 0.98495186 1.037695962 1.3005101 1.309340005 1.103017189 1.096811768 1.023115142 1 9.717778617 -8.780486952 24.9821143 1.067837609 1.202956765 0.360845473 0.089845764 223.0571607 292553.2102 0.014631039 0.026551133 1.66E-09 8.780486952 0.135119157 NEEDEGHSNS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 NEEDEGHSNSSPR 13 0 Q14103-3;D6RAF8;Q14103;D6RD83 Q14103-3 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 1 0 NEEDEGHSNS(0.681)S(0.319)PR;NEEDEGHS(0.001)NS(0.499)S(0.499)PR ; 139.21 0.00051188 8812100 5798.4 7270.3 10463.6 4262.5 7208.3 7348.1 9253.3 3516.5 6989.8 6740.6 TRUE FALSE FALSE 5727.726871 7372.651474 10645.71457 4755.350306 6840.433553 6878.580125 10039.27507 3618.244379 6364.614782 6565.47824 0.872400556 1.122942032 1.621468259 0.724296103 1.041878947 1.047689121 1.529100349 0.55110142 0.969406119 1 12.68068439 -10.24893109 23.21031944 0.93974471 1.110763918 0.04249219 0.302708012 625.6565237 1160964.642 0.046850537 0.057124957 5.64E-11 10.24893109 0.171019208 NEEPS(ph)EEEIDAPKPK ddPTM_HeLa_Romidepsin_16h_R1 4 NEEPSEEEIDAPKPK 15 1 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK;NEEPS(1)EEEIDAPKPK ;;; 170.79 0.00013006 1662302000 39566.7 36697.8 37253.2 29137.5 28445.6 26160.3 26649.5 27777 40997.4 39532.3 TRUE FALSE FALSE 39084.44584 37214.43259 37901.57632 32506.51485 26993.91489 24488.74126 28913.10786 28580.68367 37330.48986 38505.24515 1.015042125 0.966476968 0.984322426 0.844210048 0.701045138 0.635984557 0.750887516 0.742254297 0.969491032 1 15.23276736 -9.056083068 2.191644728 1.003620785 0.704130432 0.936683985 0.034121067 0.047981675 0.455957259 0.005199003 0.009776593 8.79E-10 9.056083068 -0.299490354 NEFWFS(ph)DGSLSDK ddPTM_HeLa_Romidepsin_16h_R1 1 NEFWFSDGSLSDK 13 0 Q9P2F8;Q9P2F8-2 Q9P2F8 SIPA1L2 Signal-induced proliferation-associated 1-like protein 2 1 0 NEFWFS(0.942)DGS(0.056)LS(0.002)DK 151.9 0.00076874 2634500 924.48 771.34 874.46 1161.6 1813.4 1737.6 1303.1 1444.5 945.57 920.55 TRUE FALSE FALSE 913.2120822 782.1989448 889.6796095 1295.909657 1720.855431 1626.572968 1413.785281 1486.294328 860.995851 896.6339783 1.018489266 0.872372633 0.992243916 1.445305095 1.919239593 1.814088031 1.576769692 1.657637748 0.960253428 1 9.808375362 -9.098572458 3.268914485 0.995292764 1.733552814 0.933083237 0.097789089 0.04704867 0.955821662 0.015414326 0.027016305 7.97E-10 9.098572458 0.73826005 NEGNLENEGKPEDEVEPDDEGKS(ph)DEEEKPDVEGK ddPTM_HeLa_Romidepsin_16h_R1 1 NEGNLENEGKPEDEVEPDDEGKSDEEEKPDVEGK 34 3 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 0 NEGNLENEGKPEDEVEPDDEGKS(1)DEEEKPDVEGK 51.07 0.0078214 3604500 639.45 588.96 810.56 721.66 899.39 933.65 797.4 719.29 838.49 906.58 TRUE FALSE FALSE 631.6561374 597.2513943 824.6674568 805.1017247 853.4907722 873.9927782 865.1311361 740.1015213 763.4933544 883.0269209 0.715330555 0.676368274 0.933909757 0.911752185 0.966551248 0.98976912 0.979733591 0.838141515 0.864632025 1 9.786313612 -9.564431862 24.9997563 0.845603157 0.941978474 0.271416645 0.092639537 244.7565063 147252.6884 0.020212352 0.028584598 2.73E-10 9.564431862 0.096375317 NEGS(ph)ESAPEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 NEGSESAPEGQAQQR 15 0 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NEGS(0.715)ES(0.285)APEGQAQQR 198.67 5.21E-18 28666000 3025 2878.5 3251.1 1450 2269.2 2581.4 1656.4 1949.2 2958.3 3018.8 TRUE FALSE FALSE 2988.130136 2919.023599 3307.684032 1617.655822 2153.394256 2416.456871 1797.094575 2005.597027 2693.702239 2940.371141 1.016242506 0.992739848 1.124920588 0.550153618 0.732354575 0.821820361 0.611179504 0.682089754 0.916109603 1 11.52178255 -9.264198841 24.99999984 1.014501962 0.686563769 0.802147401 0.082013401 70.27499626 636673.1281 0.011095957 0.017425122 5.44E-10 9.264198841 -0.327938193 NEGSES(ph)APEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 NEGSESAPEGQAQQR 15 0 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NEGS(0.042)ES(0.958)APEGQAQQR 210.2 1.80E-25 26927000 6219.6 6771.3 5930.6 3201.9 5548 4980.9 3674.7 4552.7 6676.2 6609.3 TRUE FALSE FALSE 6143.793123 6866.626539 6033.819605 3572.118743 5264.864858 4662.636565 3986.828926 4684.425192 6079.063951 6437.589433 0.954362372 1.066645615 0.937279345 0.554884523 0.817831723 0.724282997 0.619304628 0.727667591 0.944307495 1 12.65230485 -9.392926315 6.046588353 0.985130298 0.694960501 0.804007358 0.072285634 0.071497051 3.240141779 0.010310715 0.015797967 4.05E-10 9.392926315 -0.290169797 NEIIQS(ph)PISQVPSVEK ddPTM_HeLa_Romidepsin_16h_R1 2 NEIIQSPISQVPSVEK 16 0 Q7Z3T8 Q7Z3T8 ZFYVE16 Zinc finger FYVE domain-containing protein 16 1 0 NEIIQS(1)PISQVPSVEK;NEIIQS(0.865)PIS(0.135)QVPSVEK ; 199.61 2.50E-18 22846000 4505.3 4400.4 4180.1 4128.7 7123.3 8176.6 6912.7 8500.7 5158.7 4552.2 TRUE FALSE FALSE 4450.387671 4462.348947 4252.852887 4606.07972 6759.77142 7654.141649 7499.864565 8746.654343 4697.292952 4433.933188 1.003711035 1.006408703 0.959160345 1.038824792 1.52455419 1.726264543 1.691469909 1.972662639 1.059396421 1 12.11437132 -8.604214068 2.059240939 0.996104959 1.798621418 0.959229479 0.074026136 0.038481856 0.327829343 0.010037296 0.024182127 2.49E-09 8.604214068 0.802516459 PEPAK(ac)SAPAPK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PEPAKSAPAPKK 12 2 P06899;Q16778 P06899;Q16778 HIST1H2BJ;HIST2H2BE Histone H2B type 1-J;Histone H2B type 2-E 0 2 ; PEPAK(1)SAPAPK(1)K;PEPAK(1)SAPAPK(1)K 168.85 0.0001119 136428000 2268.53 2237.03 2879.4 12726.9 40739 43359 43053 43958 0 2269.9 FALSE TRUE FALSE 2240.880284 2268.522967 2929.514749 14198.44406 38659.93681 40588.49983 46709.92075 45229.85538 0 2210.927671 1.013547532 1.026050285 1.325016095 6.421939644 17.48584421 18.35813101 21.12684253 20.45741069 0 1 11.11043611 -8.826350095 1.991815109 0.989826861 20.20159956 0.992635697 0.755721054 0.016265939 0.131282888 0.104671048 0.224245576 1.49E-09 8.826350095 19.2117727 up NEIVTET(ph)SPFAPAFLQPDDKK ddPTM_HeLa_Romidepsin_16h_R1 1 NEIVTETSPFAPAFLQPDDKK 21 1 A0A669KB77;P11137-3;P11137;E7EV03 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 NEIVT(0.123)ET(0.542)S(0.335)PFAPAFLQPDDKK 103.51 0.00015922 17930000 1932.3 1748.8 1835.3 2040.5 3574.6 3901.8 3688.6 3957.1 1943.1 1944.7 TRUE FALSE FALSE 1908.748384 1773.419652 1867.242627 2276.432211 3392.174823 3652.487572 4001.909592 4071.592445 1769.304269 1894.176414 1.007693038 0.936248408 0.98578074 1.201805806 1.790844189 1.928272122 2.112743862 2.149531805 0.934075758 1 10.88735499 -8.688469433 1.698220172 0.993033676 2.092918223 0.987435396 0.055576874 0.025865006 0.150445316 0.008300454 0.02035155 2.05E-09 8.688469433 1.099884547 up NEKPTQSVS(ph)SPEATSGSTGSVEK ddPTM_HeLa_Romidepsin_16h_R1 1 NEKPTQSVSSPEATSGSTGSVEK 23 1 H0YE68;Q9BZ95-3;Q9BZ95-4;Q9BZ95-2;Q9BZ95-5;Q9BZ95 H0YE68 WHSC1L1 Histone-lysine N-methyltransferase NSD3 1 0 NEKPTQSVS(0.489)S(0.489)PEAT(0.019)S(0.002)GSTGSVEK 72.676 0.00050521 8255600 2615.6 2390.4 2894.4 2020.8 2570.1 2613.5 2175.9 2136.5 3290.5 2781.6 TRUE FALSE FALSE 2583.720061 2424.052114 2944.775818 2254.454404 2438.938207 2446.505785 2360.720892 2198.316257 2996.189439 2709.333631 0.953636729 0.894704176 1.086900404 0.832106603 0.90019855 0.902991701 0.871328974 0.811386324 1.105876886 1 11.40372234 -4 0.199386273 1.001910367 0.137731238 0.475939922 0.068912255 33.0546004 0.378618938 0.05266333 8.98482352 1.00E-04 4 -0.864179129 NELESYAYSLK ddPTM_HeLa_Romidepsin_16h_R1 2 NELESYAYSLK 11 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 ; ; 163.78 0.0084713 20769100 3767.7 2292.52 2655.56 2993 4060.3 4003.3 4291.2 3666.7 4158.5 3688.5 FALSE FALSE TRUE 3721.777823 2324.794157 2701.778908 3339.064742 3853.08774 3747.50205 4655.694421 3772.790179 3786.553345 3592.672238 1.035935809 0.647093306 0.75202488 0.929409788 1.072485182 1.043096003 1.295886213 1.05013481 1.05396571 1 11.81084161 -8.275162278 1.994532072 0.960829477 1.164591354 0.308145688 0.141879871 0.394701804 3.005998894 0.023030218 0.07154623 5.31E-09 8.275162278 0.203761877 NELMYQLEQDHDLQAILQER ddPTM_HeLa_Romidepsin_16h_R1 2 NELMYQLEQDHDLQAILQER 20 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 ; ; 125.23 1.68E-09 5427200 2737.9 2134.7 2823.5 1857.23 2587.6 2826.6 2005.14 2274 2505.7 2034.08 FALSE FALSE TRUE 2704.529422 2164.752363 2872.641833 2071.971671 2455.545116 2645.989382 2175.456542 2339.794602 2281.583916 1981.234308 1.36507298 1.092628143 1.449925342 1.045798401 1.239401673 1.335525723 1.098030926 1.180978238 1.151597217 1 10.95218379 -12.54786024 1.311808386 0.999873875 1.240499944 0.131814666 0.131068598 0.392686074 1.209514461 0.083749121 0.01980404 2.83E-13 12.54786024 0.240626069 NEMGIPQQTTS(ph)PENAGPQNTK ddPTM_HeLa_Romidepsin_16h_R1 4 NEMGIPQQTTSPENAGPQNTK 21 0 Q15398-1;Q15398-3;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 0 NEMGIPQQT(0.051)T(0.166)S(0.783)PENAGPQNTK;NEMGIPQQT(0.065)T(0.132)S(0.803)PENAGPQNTK;NEMGIPQQT(0.052)T(0.195)S(0.752)PENAGPQNT(0.001)K;NEMGIPQQTT(0.03)S(0.969)PENAGPQNTK ;;; 129.27 4.69E-12 24685800 16022.5 14271.4 14889.5 13107.8 15741.3 17540.4 16744.3 15177.8 18093 15446.1 TRUE FALSE FALSE 15827.21161 14472.31314 15148.6455 14623.38551 14937.96272 16419.62505 18166.56042 15616.9457 16474.71677 15044.8081 1.052004885 0.961947341 1.006901876 0.971988836 0.99289819 1.091381488 1.207496986 1.038028907 1.095043331 1 13.87697808 -8.10947893 4.647581804 1.013252916 1.128454068 0.438695806 0.052696985 0.126437751 4.323267584 0.006430189 0.017282019 7.77E-09 8.10947893 0.115201153 NENLAANFLLSQNFDDE ddPTM_HeLa_Romidepsin_16h_R1 2 NENLAANFLLSQNFDDE 17 0 P54725-2;P54725-3;P54725;K7EQ16 P54725-2 RAD23A UV excision repair protein RAD23 homolog A 0 0 ; ; 179.59 6.44E-08 33197000 12765.8 12127.4 12785.5 8489.4 12290.8 12498 9943.2 11163.3 13035.1 11008 FALSE FALSE TRUE 12610.20552 12298.12986 13008.02626 9470.984372 11663.55461 11699.41814 10787.77516 11486.29247 11869.20801 10722.01057 1.176104559 1.146998482 1.213207745 0.883321678 1.087814131 1.091158981 1.006133606 1.071281584 1.106994619 1 13.38828784 -9.283287667 24.9944188 1.099943155 1.033568664 0.254057077 0.078670403 1446.932405 1655284.964 0.014506771 0.022170787 5.21E-10 9.283287667 -0.066374491 NENTEGS(ph)PQEDGVELEGLK ddPTM_HeLa_Romidepsin_16h_R1 4 NENTEGSPQEDGVELEGLK 19 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 NENT(0.056)EGS(0.944)PQEDGVELEGLK;NENT(0.463)EGS(0.537)PQEDGVELEGLK;NENT(0.244)EGS(0.756)PQEDGVELEGLK;NENT(0.025)EGS(0.975)PQEDGVELEGLK ;;; 129.22 0.00038754 25260900 10527.6 8158.3 10972.9 6036.5 8963.4 9782.4 8188 9202.3 10884.5 10776.7 TRUE FALSE FALSE 10399.28556 8273.152762 11163.87872 6734.468533 8505.964251 9157.336211 8883.488516 9468.554032 9910.963059 10496.71978 0.990717651 0.788165535 1.063558803 0.641578386 0.810344987 0.872399798 0.846310914 0.902048852 0.944196212 1 13.35765094 -10.27914783 22.16501879 0.995616705 0.846439039 0.262409144 0.100130503 149.1336908 186664.4594 0.015836776 0.018142563 5.26E-11 10.27914783 -0.149177666 NENTEGS(ph)PQEDGVELEGLKQR ddPTM_HeLa_Romidepsin_16h_R1 2 NENTEGSPQEDGVELEGLKQR 21 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 NENT(0.076)EGS(0.924)PQEDGVELEGLKQR;NENT(0.264)EGS(0.736)PQEDGVELEGLKQR ; 76.909 0.001462 5808100 1146.83 778.75 839.91 1431.27 828.11 978.87 719.76 1224.46 1085.03 1066.31 TRUE FALSE FALSE 1132.851995 789.7132629 854.5282812 1596.760172 785.8484566 916.3233662 780.8963964 1259.887818 987.9821993 1038.607112 1.090741611 0.760358035 0.822763749 1.537405389 0.756636891 0.882261786 0.751868909 1.213055257 0.951256917 1 10.02043429 NESEDNKFS(ph)DDSDDDFVQPR ddPTM_HeLa_Romidepsin_16h_R1 1 NESEDNKFSDDSDDDFVQPR 20 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 0 NES(0.12)EDNKFS(0.803)DDS(0.077)DDDFVQPR 48.919 0.027644 2630500 971.45 740.71 576.27 620.04 824.57 704.96 719.94 721.32 1020 1048.4 TRUE FALSE FALSE 959.6095937 751.1377348 586.2997376 691.7319422 782.489116 659.9153312 781.0916856 742.1902561 928.7686454 1021.162417 0.939722788 0.735571269 0.57414935 0.677396593 0.766272929 0.646239345 0.764904459 0.726809217 0.909520983 1 9.995996631 -10.26379675 3.362234397 0.97420205 0.693406117 0.799177964 0.057798118 0.065934287 1.544024405 0.009838719 0.011636651 5.45E-11 10.26379675 -0.280795933 NESS(ph)PAPPDSDADKLK ddPTM_HeLa_Romidepsin_16h_R1 2 NESSPAPPDSDADKLK 16 1 Q8ND04;Q8ND04-2;J3KTD7 Q8ND04 SMG8 Protein SMG8 1 0 NES(0.162)S(0.838)PAPPDSDADKLK;NES(0.233)S(0.767)PAPPDSDADKLK ; 101.62 0.0018895 53171000 6771.4 6194.6 7530.7 4716 6558 7476.8 6563.5 6608.7 6478.3 7321 TRUE FALSE FALSE 6688.867572 6281.807741 7661.768675 5261.286109 6223.320789 6999.05661 7121.003526 6799.912308 5898.864623 7130.799365 0.93802493 0.880940189 1.074461401 0.737825571 0.87273817 0.981524827 0.998626264 0.95359748 0.827237498 1 12.7998481 -11.8021651 0.732167399 0.999498479 0.928250372 0 0.099979015 1.350340242 1.382078895 0.051979075 0.018361173 1.58E-12 11.8021651 -0.071248107 NESSDSALGDS(ph)ESEDTGHDMTR ddPTM_HeLa_Romidepsin_16h_R1 2 NESSDSALGDSESEDTGHDMTR 22 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 0 NES(0.003)S(0.007)DS(0.017)ALGDS(0.827)ES(0.137)EDT(0.005)GHDMT(0.003)R;NESSDSALGDS(0.967)ES(0.032)EDT(0.001)GHDMTR ; 73.299 0.00099223 15164500 3234.9 3260.1 3426.6 8688.2 4704.7 5711.6 4062.6 5077 4035.2 3999.5 TRUE FALSE FALSE 3195.471795 3305.995773 3486.238536 9692.770563 4464.601603 5346.647193 4407.677143 5223.894985 3674.281606 3895.592413 0.820278781 0.848650326 0.89491871 2.488137755 1.146064868 1.372486294 1.131452338 1.340975757 0.943189435 1 11.92762702 -9.419171166 22.6920468 0.905445401 1.473524013 0.403402941 0.36089823 13.11067955 2862.203059 0.053273194 0.081376123 3.81E-10 9.419171166 0.568078612 NETGLLSSIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 NETGLLSSIKK 11 1 Q05D32;H0YMH7;Q05D32-2;H0YNU2;H0YNW9 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 0 1 NETGLLSSIK(1)K 136.53 0.0010141 287980 0 0 65.096 0 133.7 0 0 0 172.23 0 FALSE TRUE FALSE 0 0 66.22896857 0 126.8767901 0 0 0 156.8253174 0 0 (ac)SETAPAAPAAAPPAEK(ac)APVK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAAPPAEKAPVK 20 1 P16403 P16403 HIST1H1C Histone H1.2 0 1 ; SETAPAAPAAAPPAEK(1)APVK;SETAPAAPAAAPPAEK(1)APVK 63.682 2.23E-19 3000300 827.06 1728.59 928.22 1397.17 2803.1 3353.7 1991.64 3610.6 1291.64 1134.76 FALSE TRUE FALSE 816.9794746 1752.925135 944.3752797 1558.717369 2660.047347 3139.409394 2160.809852 3715.067014 1176.112483 1105.278772 0.739161464 1.58595748 0.854422707 1.410248174 2.406675506 2.840377898 1.95499082 3.361203626 1.064086739 1 10.11019457 -8.826299876 2.311374347 0.935029391 2.658463142 0.789966294 0.390205129 0.08765722 0.954361558 0.055419584 0.114706969 1.49E-09 8.826299876 1.723433751 NEVNGTSEDIKSEGDTQS(ph)N ddPTM_HeLa_Romidepsin_16h_R1 1 NEVNGTSEDIKSEGDTQSN 19 1 O95232 O95232 LUC7L3 Luc7-like protein 3 1 0 NEVNGTSEDIKS(0.19)EGDT(0.004)QS(0.806)N 166.3 1.55E-06 10432000 4431.5 4533.4 4442.6 2335 4985.8 4506.3 3974.2 3956.1 4245.9 5075.7 TRUE FALSE FALSE 4377.487173 4597.221324 4519.921589 2604.983687 4731.356021 4218.361973 4311.768449 4070.563512 3866.13607 4943.832582 0.885444056 0.929890171 0.914254582 0.526915838 0.957021894 0.853257448 0.872150983 0.823361925 0.782011932 1 12.27141417 -11.19992512 0.512577618 0.999070436 0.827105233 0 0.129197448 0.958181473 0.571343129 0.070862837 0.036012824 6.31E-12 11.19992512 -0.171965203 NEVQGRDDALER ddPTM_HeLa_Romidepsin_16h_R1 1 NEVQGRDDALER 12 1 E7EPG1;Q13201 E7EPG1 MMRN1 Multimerin-1;Platelet glycoprotein Ia*;155 kDa platelet multimerin 0 0 100.93 0.0033569 0 1034 1149.8 1318.6 590.15 1011.9 1167.4 1879.5 925.56 1505.4 1008.1 FALSE FALSE TRUE 1021.39721 1165.986915 1341.54968 658.3859197 960.2589671 1092.806908 2039.144683 952.3396183 1370.753254 981.9094167 1.040215312 1.18746892 1.366266233 0.670515944 0.977950665 1.112940653 2.076713644 0.969885411 1.39600785 1 9.939446129 -7.971374139 24.99130446 1.030474445 1.541181988 0.209052536 0.318989724 157.3884974 137403.6412 0.036406153 0.109216093 1.07E-08 7.971374139 0.510707542 NEVQKSS(ph)SSEDGS(ph)MGS(ph)FS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 NEVQKSSSSEDGSMGSFSEK 20 1 Q8N766-4;Q8N766-3;Q8N766 Q8N766-4 EMC1 ER membrane protein complex subunit 1 4 0 NEVQKS(0.453)S(0.478)S(0.299)S(0.295)EDGS(0.731)MGS(0.86)FS(0.884)EK 40.104 0.027399 1831800 961.67 1435 712.82 1554.8 1060.6 1069.6 746.06 1261.9 1930.4 1112.7 TRUE FALSE FALSE 949.9487961 1455.201968 725.2263331 1734.573292 1006.473624 1001.256012 809.4303178 1298.411086 1757.740189 1083.791894 0.876504799 1.34269501 0.669156447 1.600467121 0.928659487 0.923845268 0.746850316 1.198026202 1.621842901 1 10.08187205 -6.021121789 20.35108417 0.987779056 1.025581666 0 0.335748985 0 0 0.032035038 0 9.53E-07 6.021121789 0.03780261 NFDFEGSLS(ph)PVIAPK ddPTM_HeLa_Romidepsin_16h_R1 2 NFDFEGSLSPVIAPK 15 0 Q9H1A4;H0Y564 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 0 NFDFEGS(0.024)LS(0.976)PVIAPK;NFDFEGS(0.02)LS(0.98)PVIAPK ; 144.15 0.00048202 291650000 11788.8 12613.7 12523.8 11758.9 11806.2 11868.7 9970.9 12546.2 13282.7 11739.4 TRUE FALSE FALSE 11645.11357 12791.276 12741.77149 13118.51935 11203.68556 11110.32837 10817.828 12909.2045 12094.66204 11434.4087 1.018427265 1.11866528 1.114335846 1.147284455 0.979822032 0.971657448 0.946076731 1.128978756 1.057742675 1 13.48109414 -7.223041542 22.43636545 1.024949691 1.128979779 0.107517767 0.066765422 7515.008923 4390793.976 0.009799498 2.721741944 5.98E-08 7.223041542 0.104030088 NFEDVAFDEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 NFEDVAFDEKK 11 1 P07237;H7BZ94;H0Y3Z3 P07237 P4HB Protein disulfide-isomerase 0 1 ; NFEDVAFDEK(1)K;NFEDVAFDEK(1)K 127.37 0.0027093 706930 158.72 377.19 467.26 204.43 914.2 1006.04 624.75 905.32 1085.87 634.33 FALSE TRUE FALSE 156.7854596 382.5000907 475.3924643 228.0671585 867.5449626 941.7572908 677.8162494 931.5140058 988.7470676 617.8500152 0.253759741 0.619082433 0.769430206 0.369130295 1.404135213 1.524249037 1.097056296 1.507670119 1.600302733 1 9.271112852 -8.750351854 24.99954812 0.629773268 1.372902873 0.35667268 0.37763336 117.6054911 265168.7526 0.04393752 0.087220104 1.78E-09 8.750351854 0.743129605 NFEHLIPDAPELIHDFLVNEK ddPTM_HeLa_Romidepsin_16h_R1 1 NFEHLIPDAPELIHDFLVNEK 21 0 E9PP73;P53618 E9PP73 COPB1 Coatomer subunit beta 0 0 95.206 0.00029353 1243500 1024.8 976.84 943.69 1153 831.74 1035.2 1124.9 1021.2 906.68 970.65 FALSE FALSE TRUE 1012.309343 990.5919792 960.1145286 1286.315285 789.2932042 969.054061 1220.448978 1050.746811 825.58427 945.4323731 1.070736916 1.047766088 1.015529567 1.360557689 0.834848929 1.024985064 1.290889769 1.111392883 0.87323461 1 9.884830455 -4 0.113221698 0.967916416 1.53566611 0.146998198 0.142734208 185.099824 1.459940548 0.711856097 16.53433704 1.00E-04 4 0.567749695 NFEHLNSDFDR ddPTM_HeLa_Romidepsin_16h_R1 2 NFEHLNSDFDR 11 0 P48163 P48163 ME1 NADP-dependent malic enzyme 0 0 ; ; 133.42 0.0020446 24426000 9525.2 8199 9933.2 8862.7 12660 12664.8 9359.6 9126.4 10859.1 8969.1 FALSE FALSE TRUE 9409.103199 8314.425737 10106.08318 9887.447074 12013.91296 11855.56015 10154.60419 9390.457985 9887.834899 8736.081489 1.077039312 0.951733995 1.156821075 1.131794282 1.375206146 1.35707985 1.162375168 1.074905036 1.131838675 1 13.0927706 -9.35575959 2.101051216 1.031920187 1.239958306 0.418939692 0.098381469 0.203383066 1.755780659 0.015478413 0.025833927 4.41E-10 9.35575959 0.208038119 NFERLRS(ph)S(ph)ASES(ph)RMS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 NFERLRSSASESRMSR 16 3 A0A1W2PR18;A0A1W2PR28;Q5JU85-3;Q5JU85 A0A1W2PR18 IQSEC2 IQ motif and SEC7 domain-containing protein 2 4 0 NFERLRS(0.958)S(0.525)AS(0.525)ES(0.995)RMS(0.997)R 67.299 0.002783 0 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 NFILDQTNVSAAAQR ddPTM_HeLa_Romidepsin_16h_R1 2 NFILDQTNVSAAAQR 15 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PQ74 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 231.69 4.67E-34 716540 454.7 339.29 732.49 233.07 785.08 907.82 586.59 500.76 589.57 424.24 FALSE FALSE TRUE 449.1579415 344.0665335 745.2386812 260.01865 745.0144381 849.8132319 636.41494 515.2487005 536.8373826 413.2181836 1.086975257 0.832650999 1.803499242 0.629252681 1.802956568 2.056572691 1.54014263 1.246916813 1.29916205 1 8.690759931 -8.742196439 24.9955571 1.062456507 1.681177407 0.372146891 0.348479197 166.8173994 216685.9121 0.046203771 0.09229403 1.81E-09 8.742196439 0.6187209 NFITAEELRR ddPTM_HeLa_Romidepsin_16h_R1 1 NFITAEELRR 10 1 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 111.86 0.01092 4875500 1851.9 1739 1171.2 3434 1849.7 1556.6 1354 1585.7 1760.7 1521.4 FALSE FALSE TRUE 1829.32833 1763.481688 1191.584245 3831.055237 1755.302907 1457.138284 1469.008726 1631.579728 1603.218582 1481.873809 1.23446971 1.190034993 0.804106421 2.58527765 1.184515778 0.983307941 0.991318368 1.101024742 1.081886037 1 10.53320688 -11.74354073 0.684839391 1.002197303 1.271913567 0.034407046 0.463937069 2.128391837 1.9205383 0.299473299 0.106397838 1.80E-12 11.74354073 0.269716264 NFLGEK(ac)YIR ddPTM_HeLa_Romidepsin_16h_R1 1 NFLGEKYIR 9 1 D6RAN4;A0A2R8Y5Y7;P32969;H0Y9V9;E7ESE0 D6RAN4 RPL9 60S ribosomal protein L9 0 1 NFLGEK(1)YIR 102.06 0.025103 411370 194.8 422.5 274.95 294.79 427.81 338.25 328.12 248 370.68 56.542 FALSE TRUE FALSE 192.4257027 428.4479661 279.7353894 328.8750068 405.9772593 316.6369167 355.9905046 255.1754887 337.5254524 55.07303069 3.494009686 7.779632984 5.079353468 5.971616283 7.371616456 5.749400618 6.463971569 4.633401967 6.128688547 1 5.783274098 -10.79079389 1.026443566 1.561023298 6.182374958 0.090622133 1.792546022 0.146340914 0.324710111 0.269707904 0.243005731 1.62E-11 10.79079389 4.621351659 NFPNAIEHTLQWAR ddPTM_HeLa_Romidepsin_16h_R1 1 NFPNAIEHTLQWAR 14 0 P22314;P22314-2 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 133.04 0.00080963 12649000 3198.8 2554 3410.8 2981.8 3477.8 3609.3 3242.5 3199.7 3205.1 2398.8 FALSE FALSE TRUE 3159.811795 2589.955279 3470.163543 3326.569746 3300.314889 3378.677378 3517.917869 3292.278271 2918.427829 2336.47883 1.352381949 1.108486516 1.485210779 1.423753429 1.412516495 1.446055207 1.505649366 1.409076868 1.249070949 1 11.19012025 -15.19160367 0.156622177 5.65E-11 1.54851886 0.455120549 0.117743336 14.06164715 0.218098586 4.637539208 0.198487992 6.43E-16 15.19160367 1.54851886 NFS(ph)DNQLQEGK ddPTM_HeLa_Romidepsin_16h_R1 2 NFSDNQLQEGK 11 0 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 1 0 NFS(1)DNQLQEGK;NFS(1)DNQLQEGK ; 155.09 0.0021127 33294000 6085.1 5372.4 5100.7 4587.4 6185 6570 6395.3 6185.4 5791 5593.5 TRUE FALSE FALSE 6010.932461 5448.032788 5189.475544 5117.816772 5869.356371 6150.198204 6938.516622 6364.36479 5273.038456 5448.180064 1.103291813 0.999972968 0.952515424 0.939362633 1.077305871 1.128853696 1.273547596 1.168163445 0.96785319 1 12.41155867 -8.119283425 2.52313091 1.031105779 1.219287662 0.681240647 0.058129292 0.15299015 1.875144511 0.009392688 0.029957429 7.60E-09 8.119283425 0.188181883 NFS(ph)PSTNSVK ddPTM_HeLa_Romidepsin_16h_R1 1 NFSPSTNSVK 10 0 D4PHA4;Q86WP2-4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 0 NFS(0.892)PS(0.084)T(0.015)NS(0.009)VK 111.79 0.01696 5803700 1407.3 1336.8 1360.6 1307.9 1396 1536.6 1380.8 1401.2 1252.7 1386.8 TRUE FALSE FALSE 1390.147286 1355.619505 1384.280672 1459.125552 1324.756911 1438.416219 1498.085118 1441.741511 1140.655375 1350.770736 1.029151172 1.003589632 1.024808012 1.080217029 0.980741495 1.064885536 1.1090595 1.06734731 0.844447799 1 10.39956711 -4 0.233962468 1.004442371 1.522345027 0.280043008 0.05936387 31.49424203 0.385324817 0.018228199 6.348569762 1.00E-04 4 0.517902656 NFTKPQDGDVIAPLIT(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 2 NFTKPQDGDVIAPLITPQK 19 1 Q9Y3Z3-3;Q9Y3Z3-4;Q9Y3Z3 Q9Y3Z3-3 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 0 NFTKPQDGDVIAPLIT(1)PQK;NFTKPQDGDVIAPLIT(1)PQK ; 88.504 0.0023965 27147000 4867 3740.9 4663.9 3446.1 4153.4 3084.9 3333.6 3288 5467.4 5370.5 TRUE FALSE FALSE 4807.679132 3793.564488 4745.073223 3844.554296 3941.4365 2887.784846 3616.755901 3383.133092 4978.382051 5230.973636 0.919079213 0.72521193 0.907110904 0.734959601 0.753480475 0.552054942 0.69141161 0.646750171 0.951712319 1 12.35286378 -9.499609811 0.418691984 0.999157747 0.59406653 0.758368284 0.068820699 0.375395283 0.13804717 0.025460624 0.060599714 3.17E-10 9.499609811 -0.405091217 NFTKPQDGDVIAPLIT(ph)PQKK ddPTM_HeLa_Romidepsin_16h_R1 3 NFTKPQDGDVIAPLITPQKK 20 2 Q9Y3Z3-3;Q9Y3Z3-4;Q9Y3Z3 Q9Y3Z3-3 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 0 NFTKPQDGDVIAPLIT(1)PQKK;NFTKPQDGDVIAPLIT(1)PQKK;NFTKPQDGDVIAPLIT(1)PQKK ;; 150.48 6.98E-05 368944000 18123.5 16392.3 17090.6 16994.8 13605.1 12673.5 9184.3 10405.7 16832 17405 TRUE FALSE FALSE 17902.60381 16623.07123 17388.05472 18959.81874 12910.78098 11863.70425 9964.414213 10706.77251 15326.50376 16952.81559 1.056025397 0.980549286 1.02567356 1.1183876 0.761571487 0.699807309 0.587773409 0.631563085 0.904068335 1 14.04923728 -8.587182074 3.524466956 1.028761102 0.64246147 0.888110062 0.060544992 0.040982407 1.030276528 0.007146646 0.015341201 2.59E-09 8.587182074 -0.386299632 KPS(ph)PEPEGEVGPPK ddPTM_HeLa_Romidepsin_16h_R1 4 KPSPEPEGEVGPPK 14 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 0 KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK;KPS(1)PEPEGEVGPPK ;;; 87.668 0.0065366 173130000 28687.2 26862.6 26199.2 23363.9 14766.2 12882.8 10885.3 11635.7 29563 28385.1 TRUE FALSE FALSE 28337.54937 27240.77239 26655.18609 26065.34405 14012.62571 12059.63066 11809.89711 11972.36062 26918.81124 27647.65101 1.024953236 0.985283429 0.964103101 0.942768846 0.506828797 0.436190064 0.427157342 0.433033556 0.973638275 1 14.75486929 -8.756451359 3.263215481 1.005361329 0.434096675 0.994412577 0.019563899 0.013397954 0.296844307 0.00341397 0.00690204 1.75E-09 8.756451359 -0.571264653 down NFVVVMVTK ddPTM_HeLa_Romidepsin_16h_R1 1 NFVVVMVTK 9 0 P54725-2;P54725-3;P54725;A0A494C0B4;Q5W0S4;K7ENJ0;K7ELW1;Q5W0S5;P54727 P54725-2;P54727 RAD23A;RAD23B UV excision repair protein RAD23 homolog A;UV excision repair protein RAD23 homolog B 0 0 101.65 0.015864 370810 276.12 224.14 172.45 297.77 187.72 249.47 317.61 172.86 261.58 155.44 FALSE FALSE TRUE 272.7545432 227.2954488 175.4514199 332.1995684 178.1399479 233.5296721 344.5877855 177.8614314 238.1836297 151.4016464 1.801529572 1.501274618 1.158847503 2.194160872 1.176605091 1.542451338 2.275984401 1.174765504 1.573190486 1 7.242237084 -12.40462775 0.989327646 0.978179292 1.626726755 0.010043108 0.415382858 0.592873855 0.980496207 0.286157127 0.063575921 3.94E-13 12.40462775 0.648547463 NFYES(ph)DDDQKEK ddPTM_HeLa_Romidepsin_16h_R1 2 NFYESDDDQKEK 12 1 O00203-3;O00203 O00203-3 AP3B1 AP-3 complex subunit beta-1 1 0 NFYES(1)DDDQKEK;NFYES(1)DDDQKEK ; 136.33 0.0035336 15569000 1814.77 1703.98 2009.94 1466.29 2101.72 2144.56 1715.05 2060.35 1829.52 1884.27 TRUE FALSE FALSE 1792.650885 1727.968675 2044.922163 1635.829349 1994.461386 2007.529537 1860.726304 2119.962977 1665.883149 1835.316394 0.97675305 0.941509966 1.114206885 0.891306455 1.086712565 1.093832946 1.013844975 1.155094012 0.907681724 1 10.84181308 -8.661268704 23.684218 0.989111599 1.082587241 0.403657314 0.066715315 6.630003421 1557.550762 0.007912458 0.015824914 2.18E-09 8.661268704 0.093475642 NFYQEHPDLAR ddPTM_HeLa_Romidepsin_16h_R1 4 NFYQEHPDLAR 11 0 P17844;J3KTA4;P17844-2;J3QRQ7;X6RLV5;J3QR02;J3KRX8;J3KTQ4 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 0 ;;; ;;; 179.94 4.76E-06 84528300 13924.7 13595.2 13214.2 11032.3 12055.4 12575.7 10066.8 10654 14288.4 13497.6 FALSE FALSE TRUE 13754.9804 13786.59358 13444.18761 12307.90643 11440.16795 11772.15336 10921.87374 10962.25668 13010.40972 13146.93041 1.046250339 1.048654945 1.022610388 0.936180998 0.870177874 0.895429807 0.830754663 0.833826326 0.989615775 1 13.68243837 -8.975901007 1.866153318 1.02550939 0.853108688 0.912886237 0.023891619 0.07189982 0.501095561 0.004066257 0.008201552 1.06E-09 8.975901007 -0.172400701 NFYVEHPEVAR ddPTM_HeLa_Romidepsin_16h_R1 1 NFYVEHPEVAR 11 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 0 82.774 0.023351 8276800 2724.8 2920.1 2202.3 2043.3 2381.9 1802.6 1906.9 2061.1 3191.5 2690.6 FALSE FALSE TRUE 2691.58909 2961.209244 2240.630108 2279.55596 2260.342755 1687.419678 2068.872038 2120.734677 2906.044247 2620.697824 1.02705053 1.129931584 0.854974613 0.869827852 0.862496521 0.643881817 0.789435554 0.809225183 1.108881848 1 11.3557353 -9.21395845 1.361992689 1.020204439 0.763891195 0.725644769 0.076288484 0.159444441 0.58106015 0.011504592 0.022437669 6.11E-10 9.21395845 -0.256313244 NGAGNGAK(ac)GK(ac)GK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 NGAGNGAKGKGKR 13 3 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 0 3 ; NGAGNGAK(1)GK(1)GK(1)R;NGAGNGAK(1)GK(1)GK(1)R 138.25 0.00024034 1693950 0 0 0 0 71.811 121.92 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 68.14621671 114.1297055 0 0 0 0 0 NGEFELMHVDEFIDELLHSER ddPTM_HeLa_Romidepsin_16h_R1 2 NGEFELMHVDEFIDELLHSER 21 0 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 0 0 ; ; 112.54 6.34E-05 6776700 746.96 579.96 802.81 691.93 939.83 682.92 704.84 823.1 574.19 565.62 FALSE FALSE TRUE 737.8557642 588.1246921 816.7825713 771.9342022 891.8669681 639.283616 764.709092 846.9150999 522.8330083 550.9251109 1.3393032 1.067522029 1.482565516 1.401159953 1.618853362 1.160382062 1.388045447 1.537259935 0.949009217 1 9.105712411 -15.18656778 0.173778629 0.043547126 1.487596768 0.569309951 0.146340987 21.72239308 0.371859868 7.478555726 0.241731226 6.51E-16 15.18656778 1.444049641 NGGHFVISIK ddPTM_HeLa_Romidepsin_16h_R1 2 NGGHFVISIK 10 0 M0R0P1;M0R299;M0QXL5;M0R2Q4;P22087 M0R0P1 FBL rRNA 2-O-methyltransferase fibrillarin 0 0 ; ; 72.2 0.019347 3791900 8295.5 6452.7 7366.3 6561.8 7304 7432.6 6635.9 7335.1 8490.6 7988.4 FALSE FALSE TRUE 8194.391255 6543.54128 7494.507361 7320.50619 6931.249625 6957.680848 7199.55318 7547.329546 7731.179471 7780.860216 1.053147213 0.840979159 0.96319779 0.940835073 0.890807627 0.894204581 0.925290132 0.969986523 0.993615006 1 12.92571395 -10.2791225 24.99062523 1.025097297 0.918855299 0.568954673 0.038693685 379.0766645 535727.7111 0.006595836 0.007551803 5.26E-11 10.2791225 -0.106241998 NGHVGISFVPK ddPTM_HeLa_Romidepsin_16h_R1 2 NGHVGISFVPK 11 0 Q60FE5;P21333-2;P21333 Q60FE5 FLNA Filamin-A 0 0 ; ; 128.88 0.00083738 12105500 13382.4 12696.1 11434.5 9538.6 22650 21563 18304.8 18100.1 18618.4 15693.6 FALSE FALSE TRUE 13219.29016 12874.83603 11633.51268 10641.49781 21494.08598 20185.19389 19859.60926 18623.79784 16953.12367 15285.87801 0.864804112 0.842269971 0.761062771 0.696165298 1.406140097 1.320512559 1.299212858 1.218366248 1.109070978 1 13.8999118 -8.752347359 24.99999558 0.897256265 1.310887248 0.76595128 0.116767743 71.98880157 197943.5181 0.016658682 0.032941598 1.77E-09 8.752347359 0.413630983 NGIDILVGTPGR ddPTM_HeLa_Romidepsin_16h_R1 1 NGIDILVGTPGR 12 0 Q9NR30;Q9NR30-2;A0A087WVC1;Q9BQ39 Q9NR30;A0A087WVC1 DDX21;DDX50 Nucleolar RNA helicase 2;ATP-dependent RNA helicase DDX50 0 0 99.539 0.0062967 0 285.97 215.31 341.38 162.77 145.98 169.42 282.18 189.5 240 273.61 FALSE FALSE TRUE 282.4844876 218.3411398 347.3215757 181.5902333 138.5300959 158.5946088 306.1483622 194.9828835 218.5337989 266.5015728 1.05997306 0.819286496 1.303262762 0.681385222 0.519809675 0.59509821 1.148767563 0.731638772 0.820009416 1 8.058000237 -9.227728382 24.99604987 1.028782973 0.738542949 0.297958207 0.201155469 530.4823226 393342.8745 0.02806329 0.046535975 5.92E-10 9.227728382 -0.290240023 NGIGPGSHSEFAAS(ph)IGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 NGIGPGSHSEFAASIGSPK 19 0 Q9H694;Q9H694-2;A6NGY7 Q9H694 BICC1 Protein bicaudal C homolog 1 1 0 NGIGPGSHS(0.003)EFAAS(0.56)IGS(0.437)PK 56.131 0.020144 12097000 2988.7 3062.3 3029.1 3184.3 3718.8 3004 2570.1 2625.3 3742.1 3288.7 TRUE FALSE FALSE 2952.272575 3105.41114 3081.820215 3552.483749 3529.015759 2812.054095 2788.40423 2701.258913 3407.397204 3203.2591 0.921646511 0.969453623 0.96208896 1.109021668 1.101695382 0.877872819 0.870489755 0.843284552 1.063728252 1 11.64532478 -8.032552153 24.46796354 0.982158316 0.861210643 0.495121393 0.064798699 367.1079775 275938.197 0.009740096 0.024858232 9.28E-09 8.032552153 -0.120947673 NGPSSS(ph)PFSSPASSR ddPTM_HeLa_Romidepsin_16h_R1 2 NGPSSSPFSSPASSR 15 0 A8CG34-2;A8CG34;C9JFL1;A6NF01;Q96HA1-2;Q96HA1-3;Q96HA1 A8CG34-2;Q96HA1 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 0 NGPS(0.001)S(0.092)S(0.907)PFSSPASSR;NGPSS(0.086)S(0.914)PFSSPASSR ; 217.79 4.39E-26 16579600 4545.2 4490.3 3788.2 2616.1 3257 3844.8 3317.3 3762.5 4234.6 4080.4 TRUE FALSE FALSE 4489.801354 4553.514561 3854.132032 2918.585791 3090.783136 3599.129689 3599.071379 3871.362001 3855.84677 3974.39062 1.129682959 1.145713896 0.969741629 0.734347997 0.777674726 0.905580259 0.905565588 0.974076877 0.970173075 1 11.95651796 -9.517841168 8.701895915 1.068823966 0.859130483 0.587187678 0.079887867 0.067441103 55.33860257 0.013377521 0.019545319 3.04E-10 9.517841168 -0.209693483 NGQAEAEEATEQTHIS(ph)PNAIFK ddPTM_HeLa_Romidepsin_16h_R1 1 NGQAEAEEATEQTHISPNAIFK 22 0 P48436 P48436 SOX9 Transcription factor SOX-9 1 0 NGQAEAEEATEQT(0.291)HIS(0.708)PNAIFK 94.08 0.0001938 2309000 760.86 711.98 717.12 913.36 1516.7 937.46 964.37 1091.4 733.05 744.66 TRUE FALSE FALSE 751.5863457 722.0032731 729.6011728 1018.966981 1439.297139 877.5593315 1046.283564 1122.977937 667.484172 725.3136259 1.036222565 0.995435971 1.005911301 1.404863971 1.984379016 1.209903275 1.442525725 1.548265326 0.920269726 1 9.502461142 -9.189146659 4.369824571 1.014432644 1.532154977 0.67885889 0.182049516 0.099344 3.65975318 0.02586449 0.04341156 6.47E-10 9.189146659 0.517722334 NGS(ph)EADIDEGLYSR ddPTM_HeLa_Romidepsin_16h_R1 3 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS1;Q5JRS3;Q5JRS2;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 1 0 NGS(0.978)EADIDEGLY(0.005)S(0.016)R;NGS(0.997)EADIDEGLY(0.002)SR;NGS(0.707)EADIDEGLY(0.241)S(0.052)R ;; 171.52 4.45E-05 70897500 4425.1 4430.3 4272.9 3882.8 4265.7 4312.2 3442.7 4513.7 4362.1 4342.3 TRUE FALSE FALSE 4371.165179 4492.66988 4347.268032 4331.747605 4048.005411 4036.664337 3735.122852 4644.296788 3971.942851 4229.48642 1.033497864 1.062225867 1.027847734 1.024178157 0.957091479 0.954410048 0.883114989 1.098075825 0.939107602 1 12.04626677 -8.765016809 24.75555222 1.02157897 0.965400143 0.095373997 0.058026686 91.15617492 630801.106 0.00712389 0.013295831 1.72E-09 8.765016809 -0.056178827 NGS(ph)PPPGAPSSR ddPTM_HeLa_Romidepsin_16h_R1 2 NGSPPPGAPSSR 12 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 0 NGS(1)PPPGAPSSR;NGS(1)PPPGAPSSR ; 123.95 0.0061693 38073000 6218.6 6216.2 5446.3 5759.5 5659.7 6335.7 5107.3 5698.1 6565 6867.3 TRUE FALSE FALSE 6142.805311 6303.711827 5541.090567 6425.440489 5370.86439 5930.869218 5541.113935 5862.965533 5977.809958 6688.886556 0.918359918 0.942415718 0.828402533 0.960614362 0.802953428 0.886675109 0.828406027 0.876523392 0.89369283 1 12.70755036 -11.08781987 0.237822856 1.041525528 0.828489705 0.181624442 0.054176474 1.306223438 0.223586683 0.105146465 0.05838848 8.17E-12 11.08781987 -0.213035823 NGSEADIDEGLYSR ddPTM_HeLa_Romidepsin_16h_R1 1 NGSEADIDEGLYSR 14 0 P22314;P22314-2;Q5JRR9;Q5JRS1;Q5JRS3;Q5JRS2;Q5JRS0 P22314 UBA1 Ubiquitin-like modifier-activating enzyme 1 0 0 190.34 4.93E-10 4611900 1334.1 1382.4 1476.7 949.14 1691.4 1328.1 1079.2 1696.5 1444.8 1328.2 FALSE FALSE TRUE 1317.839476 1401.861463 1502.401344 1058.884033 1605.081547 1243.238696 1170.867221 1745.585551 1315.573469 1293.693173 1.018664629 1.083612013 1.161327412 0.81849704 1.240697238 0.960999658 0.905057896 1.349304138 1.01691305 1 10.33727978 -7.248672332 24.32421261 1.018527842 1.349304445 0.423117922 0.114249758 944.6999488 1799829.312 0.014011591 0.328734002 5.64E-08 7.248672332 0.330776603 NGSGTLTGSHDYPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 NGSGTLTGSHDYPAKK 16 1 Q7Z7F0 Q7Z7F0 KIAA0907 UPF0469 protein KIAA0907 0 1 ; NGSGTLTGSHDYPAK(1)K;NGSGTLTGSHDYPAK(1)K 117.53 0.00056003 5412600 2780.9 2464.3 2008.6 3004 4300.3 3422.1 3332 2999.3 4429.2 3226.4 FALSE TRUE FALSE 2747.005321 2498.99248 2043.55884 3351.336614 4080.839644 3203.438854 3615.019997 3086.080013 4033.041259 3142.577663 0.87412488 0.795204685 0.650281094 1.06642921 1.298564453 1.019366647 1.150335929 0.982021876 1.283354523 1 11.61773268 -9.020092835 24.8653166 0.903969999 1.117847698 0.222738254 0.170907655 567.7981748 702662.196 0.019717668 0.032990328 9.55E-10 9.020092835 0.213877699 NGSLDSPGKQDT(ph)EEDEEEDEKDKGK ddPTM_HeLa_Romidepsin_16h_R1 1 NGSLDSPGKQDTEEDEEEDEKDKGK 25 3 Q9Y266;A0A0A0MSS4;A0A0A0MSU9 Q9Y266 NUDC Nuclear migration protein nudC 1 0 NGS(0.006)LDS(0.489)PGKQDT(0.505)EEDEEEDEKDKGK 51.777 0.010057 127020000 1334.8 1549.4 1358.4 1196.5 1050.2 1586.1 993.08 1120.2 1372.8 1169.1 TRUE FALSE FALSE 1318.530944 1571.212494 1382.042382 1334.84496 996.6043752 1484.753329 1077.43219 1152.61122 1250.01333 1138.726613 1.157899472 1.379797816 1.213673559 1.172226014 0.875191959 1.303871633 0.946172837 1.012193099 1.097729091 1 10.15320571 NGSMGS(ph)PVNQQPK ddPTM_HeLa_Romidepsin_16h_R1 1 NGSMGSPVNQQPK 13 0 A0A0A0MRW1;A0A0A0MRV9;Q5T586;A0A0A0MRW2;Q5T593;A0A0A0MRW0;A0A0A0MRW3;Q8IW50-3;Q8IW50-7;Q8IW50-2;Q8IW50-5;Q8IW50-6;Q8IW50-4;Q8IW50 A0A0A0MRW1 FAM219A Protein FAM219A 1 0 NGS(0.009)MGS(0.991)PVNQQPK 103.14 0.015028 3073900 634.24 988.76 843.35 663.76 1318.1 1483.3 1212.3 1329 827.78 692.41 TRUE FALSE FALSE 626.5096389 1002.679789 858.028153 740.5070543 1250.832438 1388.521917 1315.272732 1367.452518 753.7412836 674.4210884 0.928959147 1.486726626 1.272243955 1.097989175 1.854675751 2.05883526 1.950224799 2.027594543 1.11761227 1 9.397505838 -8.819761146 0.732498042 0.976128651 2.134477646 0.802958513 0.190972874 0.216836125 0.209068993 0.036390416 0.135387482 1.51E-09 8.819761146 1.158348996 up NGSPSLGRDSPDT(ph)MLASPQEEGEGPSSTTESSER ddPTM_HeLa_Romidepsin_16h_R1 2 NGSPSLGRDSPDTMLASPQEEGEGPSSTTESSER 34 1 Q5VVD7;Q8IWE5 Q5VVD7 PLEKHM2 Pleckstrin homology domain-containing family M member 2 1 0 NGS(0.026)PS(0.249)LGRDS(0.249)PDT(0.341)MLAS(0.134)PQEEGEGPSSTTESSER;NGS(0.002)PS(0.004)LGRDS(0.205)PDT(0.668)MLAS(0.121)PQEEGEGPSSTTESSER ; 76.109 3.49E-06 13862300 5846.12 5718.55 4741.17 1813.13 5548.37 5292.54 4360.63 5002.52 5474.72 5511.59 TRUE FALSE FALSE 5774.865241 5799.055897 4823.688075 2022.772622 5265.215975 4954.363775 4731.021803 5147.260024 4985.047332 5368.398097 1.075714792 1.080220914 0.898533974 0.37679259 0.980779719 0.92287563 0.881272536 0.958807438 0.928591219 1 12.39027594 -9.604526982 5.917924583 1.039111596 0.822496017 0.236164718 0.165296121 0.201058346 11.40289536 0.025435587 0.036129755 2.49E-10 9.604526982 -0.216615579 NGSTAVAESVAS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 3 NGSTAVAESVASPQK 15 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 NGSTAVAESVAS(1)PQK;NGST(0.001)AVAESVAS(0.999)PQK;NGSTAVAESVAS(1)PQK ;; 166.67 3.44E-05 66071000 19224 18304.5 18702.9 15859.1 14281.9 13429.2 10956.7 11706.3 20151.6 18893 TRUE FALSE FALSE 18989.69049 18562.19123 19028.41613 17692.80376 13553.04135 12571.11746 11887.36182 12045.00332 18349.19043 18402.15714 1.031927418 1.008696486 1.034031825 0.961452705 0.736491991 0.683132818 0.645976542 0.65454301 0.997121712 1 14.16758727 -8.728029415 2.407805457 1.016544061 0.660688378 0.991811282 0.014671194 0.019266587 0.22768532 0.002538041 0.005466986 1.87E-09 8.728029415 -0.355855683 NGT(ph)KSPEAATPVGK ddPTM_HeLa_Romidepsin_16h_R1 1 NGTKSPEAATPVGK 14 1 Q5VWN6;A0A2R8YH03 Q5VWN6 FAM208B Protein FAM208B 1 0 NGT(0.58)KS(0.114)PEAAT(0.306)PVGK 81.01 0.018611 8771200 5415.9 5872.6 5445.4 5215.8 4634.2 5149.2 4339.9 4776.4 6100.7 6515 TRUE FALSE FALSE 5349.888928 5955.274617 5540.174903 5818.875337 4397.699481 4820.182738 4708.530998 4914.597598 5555.038113 6345.739361 0.843067864 0.938468203 0.873054279 0.91697358 0.69301609 0.759593558 0.741998801 0.774472023 0.875396514 1 12.63157255 -6.490308682 0.048114658 1.438486104 2.35E-10 0.480797997 0.066634052 127.8357607 0.786179077 7.589623504 17.75527735 3.23E-07 6.490308682 -1.438486104 NGTSGSDS(ph)PGQAVEAEEIVK ddPTM_HeLa_Romidepsin_16h_R1 3 NGTSGSDSPGQAVEAEEIVK 20 0 Q05D32 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 NGT(0.001)S(0.001)GS(0.067)DS(0.931)PGQAVEAEEIVK;NGT(0.02)S(0.02)GS(0.22)DS(0.74)PGQAVEAEEIVK;NGTSGS(0.017)DS(0.983)PGQAVEAEEIVK ;; 184.95 1.52E-13 52379900 5924.55 5496.08 5201.99 4909.82 7781.6 8127 6421.06 7429.7 6385.33 5839.1 TRUE FALSE FALSE 5852.339306 5573.453959 5292.528454 5477.51649 7384.475915 7607.710929 6966.464676 7644.666647 5814.210092 5687.39934 1.029000947 0.979965293 0.930570923 0.963096868 1.298392371 1.337643178 1.224894589 1.344141002 1.022296791 1 12.47355339 -8.756969872 24.9999792 1.001113588 1.298410862 0.932093919 0.041390269 21.74520458 121629.2365 0.006285513 0.012235454 1.75E-09 8.756969872 0.297297274 NGVAAEVS(ph)PAKEENPR ddPTM_HeLa_Romidepsin_16h_R1 4 NGVAAEVSPAKEENPR 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR;NGVAAEVS(1)PAKEENPR ;;; 184.22 6.63E-08 96253000 16063.3 17487.6 16725.4 12741.2 14171.2 12877.8 10054.1 11086 18502.4 17883.9 TRUE FALSE FALSE 15867.51432 17733.79089 17016.49857 14214.39749 13447.99078 12054.95014 10908.095 11406.75592 16847.499 17419.2737 0.910917102 1.018055701 0.976877616 0.816015509 0.772017882 0.692046658 0.626208371 0.654835334 0.967175744 1 14.08839685 -8.741782788 1.256662654 0.964534883 0.643919191 0.936643136 0.035969175 0.094613961 0.295664442 0.007135444 0.019559204 1.81E-09 8.741782788 -0.320615691 NGVCY(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 NGVCYPR 7 0 E5RIW8;Q9Y561-2;Q9Y561 E5RIW8 LRP12 Low-density lipoprotein receptor-related protein 12 1 0 NGVCY(1)PR 62.842 0.018748 3406900 255.22 165.74 147.12 168.03 194.47 127.06 139.63 0 134.65 136.07 TRUE FALSE FALSE 252.1092805 168.0732921 149.6805619 187.4584192 184.5454702 118.9412761 151.4901687 0 122.6065668 132.5348818 1.902210777 1.268143826 1.129367302 1.414408167 1.392429433 0.897433751 1.143021118 0 0.925089042 1 7.050228302 -7.427117521 1.312717046 1.392339177 4.79E-27 0.529759824 0.317965003 0.680041836 1.24568053 0.054786974 1.159184582 3.74E-08 7.427117521 -1.392339177 NGYGFVEFDDLRDADDAVYELNGK ddPTM_HeLa_Romidepsin_16h_R1 1 NGYGFVEFDDLRDADDAVYELNGK 24 1 Q08170;A0A0D9SEM4 Q08170 SRSF4 Serine/arginine-rich splicing factor 4 0 0 104.52 2.12E-08 0 456.53 628.01 569.99 494.12 705.74 657.12 253.2 708.61 531.99 518.02 FALSE FALSE TRUE 450.9656368 636.8511413 579.9104369 551.2524793 669.7234543 615.1321528 274.7068017 729.1125123 484.407482 504.5617657 0.893776872 1.262186683 1.149334881 1.092537161 1.327336909 1.21914143 0.54444633 1.445041146 0.960055864 1 8.978887077 -10.27636405 24.70648922 0.949839076 1.132802709 0.134823562 0.2265728 1036.941701 1716562.791 0.036675892 0.042035341 5.29E-11 10.27636405 0.182963633 NGYGFVEFEDS(ph)RDADDAVYELNGK ddPTM_HeLa_Romidepsin_16h_R1 2 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJK4;A0A590UK01;A0A590UJP7;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 0 NGY(0.005)GFVEFEDS(0.993)RDADDAVY(0.001)ELNGK;NGYGFVEFEDS(0.987)RDADDAVY(0.013)ELNGK ; 69.525 0.00050737 4158800 1557.16 1412.39 1134.69 1323.13 1599.88 1526.79 1179.59 1133.99 1473.95 1317.44 TRUE FALSE FALSE 1538.180735 1432.273663 1154.438803 1476.116516 1518.232154 1429.233046 1279.784345 1166.800212 1342.11622 1283.212719 1.198695051 1.116162303 0.899647258 1.150328776 1.18314924 1.113792768 0.997328289 0.909280429 1.045903147 1 10.32554463 -7.534853276 3.166288034 1.094780062 0.916591263 0.309017672 0.085074498 0.264955466 5.104757123 0.013907435 0.084086398 2.92E-08 7.534853276 -0.178188799 NGYGFVEFEDSRDADDAVYELNGK ddPTM_HeLa_Romidepsin_16h_R1 1 NGYGFVEFEDSRDADDAVYELNGK 24 1 Q13247;Q13247-3;A0A590UJK4;A0A590UK01;A0A590UJP7;A0A590UK80;Q13247-2 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 0 0 66.467 0.002006 9512700 889.96 920.8 804.58 807.5 775.86 579.96 686.44 672.16 927.87 873.49 FALSE FALSE TRUE 879.1128252 933.7630466 818.5833774 900.8669494 736.2649691 542.9024277 744.7461965 691.6078891 844.8789833 850.7966039 1.03328201 1.097516189 0.96213757 1.058851135 0.865383061 0.638110713 0.875351633 0.812894511 0.993044612 1 9.732670464 -8.60688143 4.600271088 1.020726357 0.780292251 0.748328573 0.065636207 0.072792033 2.798536575 0.008918281 0.018347767 2.47E-09 8.60688143 -0.240434106 NHLLQFALES(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 NHLLQFALESPAK 13 0 Q9NS91;F8WE49 Q9NS91 RAD18 E3 ubiquitin-protein ligase RAD18 1 0 NHLLQFALES(1)PAK 198.14 1.62E-12 7178300 1975.6 1951.7 1720.7 1006.5 1158.1 1102 835.81 928.06 1981.5 1499.5 TRUE FALSE FALSE 1951.520627 1979.176084 1750.648062 1122.876266 1098.997836 1031.585757 906.8036805 954.9119519 1804.269677 1460.542774 1.336161229 1.355096283 1.198628409 0.768807519 0.752458507 0.706303009 0.620867596 0.653806221 1.235341895 1 10.51228889 -9.197053195 3.858506684 1.184037509 0.689014596 0.87155954 0.100388696 0.094277128 2.806866864 0.022632715 0.038079837 6.35E-10 9.197053195 -0.495022913 NHSDSSTSESEVS(ph)SVSPLK ddPTM_HeLa_Romidepsin_16h_R1 1 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;C9IZ04;Q9NY27-3;H7C559 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 0 NHSDSST(0.001)S(0.121)ESEVS(0.379)S(0.379)VS(0.121)PLK 122.5 0.00036647 12458000 2365.4 1871.8 1735.6 1090.1 2850.9 2243 2172.2 1779.4 4298.3 3704.4 TRUE FALSE FALSE 2336.569595 1898.15125 1765.80739 1216.142491 2705.407935 2099.679539 2356.706614 1830.884132 3913.849283 3608.159154 0.647579415 0.52607193 0.489392877 0.33705345 0.749802827 0.581925422 0.653160383 0.507428873 1.084721908 1 11.81704726 -11.64200204 0.682049624 0.99511359 0.552453594 0.745441722 0.111103003 0.289679827 0.267812831 0.064940939 0.025486976 2.28E-12 11.64200204 -0.442659996 NHSDSSTSESEVSSVS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 1 NHSDSSTSESEVSSVSPLK 19 0 Q9NY27-2;Q9NY27;C9IZ04;Q9NY27-3;H7C559 Q9NY27-2 PPP4R2 Serine/threonine-protein phosphatase 4 regulatory subunit 2 1 0 NHSDSSTS(0.009)ESEVS(0.241)S(0.241)VS(0.509)PLK 123.64 0.00037005 11937000 2509.3 2366.7 2260.6 1260.3 3148.9 2805 1868.5 1628.6 5309.1 3997.3 TRUE FALSE FALSE 2478.715686 2400.018465 2299.944795 1406.021816 2988.199883 2625.769553 2027.210343 1675.720971 4834.240799 3893.44957 0.636637419 0.616424695 0.590721609 0.361124959 0.767494179 0.674406977 0.520672043 0.430394934 1.241634369 1 11.92683322 -12.03608488 0.448730195 1.08794543 0.550485596 0.716950728 0.133391172 0.718906731 0.219927131 0.175511037 0.034650992 9.20E-13 12.03608488 -0.537459834 NHSVNEEEQEEQGEGS(ph)EDEWEQVGPR ddPTM_HeLa_Romidepsin_16h_R1 2 NHSVNEEEQEEQGEGSEDEWEQVGPR 26 0 Q14694;Q14694-3;Q14694-2;H3BNA1 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 0 NHSVNEEEQEEQGEGS(1)EDEWEQVGPR;NHSVNEEEQEEQGEGS(1)EDEWEQVGPR ; 156.9 8.93E-11 67006000 2582 2615 1938.83 2906.9 2430.9 2865.6 2460.9 2523.9 2977.3 2434.7 TRUE FALSE FALSE 2550.529591 2651.814039 1972.574523 3243.009455 2306.842102 2682.497408 2669.928785 2596.925064 2711.002831 2371.446143 1.075516557 1.11822655 0.83180237 1.367523975 0.972757534 1.131165224 1.125865242 1.095080768 1.143185494 1 11.21155139 -9.276930631 24.98433985 1.030172997 1.128164817 0.155766426 0.120580145 1115.612531 1799259.447 0.016278354 0.024924445 5.29E-10 9.276930631 0.09799182 LEEPPELNRQS(ph)PNPR ddPTM_HeLa_Romidepsin_16h_R1 3 LEEPPELNRQSPNPR 15 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 0 LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR;LEEPPELNRQS(1)PNPR ;; 91.14 0.0055835 943387000 17415.1 18326.7 15448.9 14281.5 7807.2 5918.1 5463 5453.65 19317.4 17949.1 TRUE FALSE FALSE 17202.83806 18584.70376 15717.78162 15932.79423 7408.769451 5539.95251 5927.027084 5611.442758 17589.60336 17482.77979 0.983987573 1.063029105 0.899043619 0.911342156 0.423775254 0.316880529 0.339020862 0.32096971 1.006110216 1 14.09364697 -8.756117078 2.87618172 0.990875815 0.327017057 0.984531927 0.038744998 0.020956309 0.355635108 0.005756195 0.011842342 1.75E-09 8.756117078 -0.663858758 down NIDDASQMDLFHRDS(ph)DDDQTEEQLDESEAR ddPTM_HeLa_Romidepsin_16h_R1 1 NIDDASQMDLFHRDSDDDQTEEQLDESEAR 30 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 0 NIDDAS(0.03)QMDLFHRDS(0.854)DDDQT(0.117)EEQLDESEAR 55.406 0.00073361 4207400 905.88 993.78 1024.9 626.7 612.53 766.13 487.43 526.45 1138.9 954.08 TRUE FALSE FALSE 894.8387861 1007.770461 1042.737955 699.1620027 581.2703084 717.1767656 528.832292 541.6820001 1037.033932 929.2928641 0.962924414 1.084448724 1.122076791 0.752359164 0.625497441 0.771744617 0.569069572 0.582896976 1.115938766 1 9.859989519 -9.078812913 4.491478968 1.000314306 0.64571956 0.858573301 0.079823456 0.063102561 2.333500866 0.011318396 0.019350125 8.34E-10 9.078812913 -0.354594746 NIDDGTSDRPYSHALVAGIDR ddPTM_HeLa_Romidepsin_16h_R1 3 NIDDGTSDRPYSHALVAGIDR 21 1 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 0 ;; ;; 79.467 0.001319 22552100 7351.1 6945 7196.8 6236 8790.9 8501.2 7305.5 8333.9 8536.1 9188.7 FALSE FALSE TRUE 7261.501966 7042.771892 7322.057285 6957.035661 8342.26757 7958.000756 7926.028988 8575.028248 7772.609837 8949.976249 0.811343155 0.786903976 0.81810913 0.777324483 0.932099409 0.889164455 0.885592181 0.958106257 0.868450331 1 13.12766814 -12.35949348 1.105981377 0.999238439 0.852617932 0.047910818 0.069467292 0.36765968 0.810965493 0.040981581 0.010875014 4.37E-13 12.35949348 -0.146620507 NIDDGTSDRPYSHALVAGIDRYPR ddPTM_HeLa_Romidepsin_16h_R1 1 NIDDGTSDRPYSHALVAGIDRYPR 24 2 P61353;K7ELC7 P61353 RPL27 60S ribosomal protein L27 0 0 74.324 0.00016891 21681000 1414.8 1788 1223.1 1924.9 1851.8 2068.2 1514.4 1784.6 1647.7 1666.2 FALSE FALSE TRUE 1397.555873 1813.171511 1244.387542 2147.465995 1757.295736 1936.048695 1643.033098 1836.234585 1500.325585 1622.911884 0.861140945 1.117233492 0.766762235 1.323217863 1.082804158 1.192947513 1.012398217 1.131444414 0.924465216 1 10.66436896 -9.263545597 24.99663106 0.937949041 1.139810351 0.473811201 0.112869357 132.3327442 1570530.547 0.016642317 0.026211558 5.45E-10 9.263545597 0.20186131 NIEDVIAQGIGK ddPTM_HeLa_Romidepsin_16h_R1 1 NIEDVIAQGIGK 12 0 P05387;H0YDD8 P05387 RPLP2 60S acidic ribosomal protein P2 0 0 136.96 2.58E-13 0 182.63 114.66 181 53.101 49.178 173.01 60.115 97.178 155.63 117.33 FALSE FALSE TRUE 180.4040353 116.2741865 184.1502291 59.24078747 46.66826315 161.9552194 65.2211666 99.98969211 141.710063 114.2817497 1.578590071 1.017434427 1.611370403 0.518374873 0.408361469 1.417157331 0.570705006 0.874940158 1.240006068 1 6.836451219 -9.255642727 24.96658736 1.279965232 0.764713355 0.411081245 0.317969762 408.273131 1758460.207 0.051608004 0.084106812 5.55E-10 9.255642727 -0.515251877 NIEDYIHR ddPTM_HeLa_Romidepsin_16h_R1 2 NIEDYIHR 8 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 0 ; ; 140.35 0.0041911 12568100 9491.9 9189 10099 8935.2 9381.2 10067.9 8900.3 9012.7 10242.4 9895.2 FALSE FALSE TRUE 9376.209072 9318.362983 10274.76886 9968.329865 8902.442358 9424.593683 9656.29126 9273.468255 9326.294091 9638.121278 0.972825388 0.966823587 1.066055154 1.03426068 0.923669884 0.977845517 1.00188522 0.962165549 0.967646476 1 13.23453624 -7.243200878 22.17092795 0.989852198 0.962165435 0.048213862 0.037234873 2204.734309 2679889.48 0.00506741 0.183091128 5.71E-08 7.243200878 -0.027686763 NIGLGFK(ac)TPK ddPTM_HeLa_Romidepsin_16h_R1 1 NIGLGFKTPK 10 1 M0QZC5;P62280 M0QZC5 RPS11 40S ribosomal protein S11 0 1 NIGLGFK(1)TPK 134.57 0.0083758 11644000 4937.4 4960.6 5106.4 3784.9 4787.7 5047.6 4524 4618.6 4805.1 4712.2 FALSE TRUE FALSE 4877.22107 5030.435457 5195.27475 4222.527946 4543.365804 4725.07465 4908.268447 4752.231904 4375.319821 4589.776365 1.06262717 1.096008837 1.131923287 0.919985553 0.989888274 1.029478187 1.069391634 1.035395088 0.953275165 1 12.16420815 -9.265623046 24.99961946 1.043343049 1.012287464 0.099824325 0.058390585 847.239439 5062731.26 0.00888314 0.013834434 5.42E-10 9.265623046 -0.031055585 NIGNGIIS(ph)SPLTGK ddPTM_HeLa_Romidepsin_16h_R1 1 NIGNGIISSPLTGK 14 0 Q9P275;A0A075B784;K7EMM6;E9PEW0 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36;Ubiquitin carboxyl-terminal hydrolase 1 0 NIGNGIIS(0.536)S(0.454)PLT(0.01)GK 102.33 0.0024001 0 2591.4 2442 2635.8 2014.6 2256.3 2895.1 2570.5 2283.1 2629.7 2770.5 TRUE FALSE FALSE 2559.81502 2476.37854 2681.674993 2247.537531 2141.152592 2710.112454 2788.838206 2349.157896 2394.493046 2698.522011 0.948598903 0.917679578 0.993756947 0.832877228 0.793453818 1.004295108 1.033468764 0.870535014 0.887335006 1 11.39795374 -11.19701809 0.689794303 0.99519739 0.921348573 0 0.079290417 0.984349579 1.027189797 0.031963628 0.018894171 6.35E-12 11.19701809 -0.073848817 NIGRDT(ph)PTSAGPNSFNK ddPTM_HeLa_Romidepsin_16h_R1 2 NIGRDTPTSAGPNSFNK 17 1 Q8WW12;Q8WW12-3 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 0 NIGRDT(0.982)PT(0.017)S(0.001)AGPNSFNK;NIGRDT(0.997)PT(0.002)S(0.001)AGPNSFNK ; 159.44 0.00016441 52725000 7138.5 6410.8 5754.4 8488.1 6568.2 5951.9 5554.5 5554.2 6802.6 6434 TRUE FALSE FALSE 7051.493216 6501.051411 5854.552918 9469.53406 6233.000245 5571.592799 6026.299091 5714.902014 6194.158419 6266.843752 1.125206483 1.037372506 0.934210769 1.511053161 0.994599593 0.889058834 0.961616298 0.911926679 0.988401604 1 12.61352331 -8.527847289 24.99998557 1.083577222 0.927756619 0.219113556 0.15094768 169.9624993 855191.2663 0.021376433 0.042872193 2.97E-09 8.527847289 -0.155820604 NIIFFVRPR ddPTM_HeLa_Romidepsin_16h_R1 1 NIIFFVRPR 9 1 F5H6Y0;H3BMM5;A0A2R8YF87;Q96AX1 F5H6Y0 VPS33A Vacuolar protein sorting-associated protein 33A 0 0 124.08 0.0009989 273420 0 0 0 0 0 48.727 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 45.61350196 0 0 0 0 0 NIIGSS(ph)PVADFSAIK ddPTM_HeLa_Romidepsin_16h_R1 2 NIIGSSPVADFSAIK 15 0 P42566;B1AUU8 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 0 NIIGS(0.132)S(0.867)PVADFS(0.001)AIK;NIIGS(0.027)S(0.973)PVADFSAIK ; 244 3.01E-57 51056000 8053.7 7866.6 8551 6130.6 8544.3 8920.8 7847.8 8000.8 7988.7 7953.8 TRUE FALSE FALSE 7955.538407 7977.346201 8699.826568 6839.448817 8108.252488 8350.789671 8514.391936 8232.290525 7274.170664 7747.159129 1.026897508 1.029712449 1.122969907 0.88283314 1.046609777 1.077916373 1.099034084 1.062620554 0.93894685 1 12.91945166 -8.523540825 24.99920155 1.013456542 1.078522787 0.250181968 0.0599227 23.90647053 902660.0054 0.007546593 0.015195876 3.00E-09 8.523540825 0.065066245 NIIHGS(ph)DSVESAEK ddPTM_HeLa_Romidepsin_16h_R1 3 NIIHGSDSVESAEK 14 0 P15531;P15531-2 P15531 NME1 Nucleoside diphosphate kinase A 1 0 NIIHGS(0.975)DS(0.024)VES(0.001)AEK;NIIHGS(0.997)DS(0.003)VESAEK;NIIHGS(0.988)DS(0.012)VESAEK ;; 106.76 0.0070792 29550300 9913.4 8318.7 10276.4 6064.5 10025.5 9209 7178.3 6542.4 12214.1 9315.4 TRUE FALSE FALSE 9792.571668 8435.810877 10455.25643 6765.706024 9513.861325 8620.574621 7788.024623 6731.694022 11121.64031 9073.384565 1.079263377 0.929731438 1.152299493 0.74566508 1.048546026 0.950094704 0.858337324 0.741916533 1.225743296 1 13.14742509 -6.032393542 0.454499533 1.033104011 2.80E-20 0.410477662 0.117546796 8.306493822 0.501565437 0.020533765 5.936054062 9.28E-07 6.032393542 -1.033104011 NIIHGS(ph)DSVK ddPTM_HeLa_Romidepsin_16h_R1 2 NIIHGSDSVK 10 0 Q32Q12;P22392-2;P22392;O60361 Q32Q12 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 1 0 NIIHGS(0.913)DS(0.087)VK;NIIHGS(0.889)DS(0.111)VK ; 103.11 0.0094291 32547900 10809.9 9039.2 8960.4 8364.1 13252.8 10597.2 9330.2 8782.6 14885.3 11340.2 TRUE FALSE FALSE 10678.14478 9166.454095 9116.352003 9331.196596 12576.46016 9920.073121 10122.70696 9036.710674 13553.92149 11045.57997 0.966734641 0.829875309 0.825339369 0.844790099 1.138596633 0.898103418 0.916448659 0.818129125 1.227090069 1 13.43118155 -10.46385139 8.706903902 0.985411144 0.901117536 0.231939343 0.116679864 0.532192928 74.27991981 0.015437886 0.017515152 3.44E-11 10.46385139 -0.084293608 NIIHGSDS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 NIIHGSDSVK 10 0 Q32Q12;P22392-2;P22392;O60361 Q32Q12 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 1 0 NIIHGS(0.002)DS(0.998)VK 150.51 0.0037143 27813000 5616.4 5070.2 4952.1 4454.1 4941.8 4404.4 3736 4097.5 6562.7 5158.8 TRUE FALSE FALSE 5547.945157 5141.578409 5038.289223 4969.103999 4689.601506 4122.973055 4053.335747 4216.054698 5975.715675 5024.773632 1.104118427 1.023245779 1.002689791 0.988920967 0.933296074 0.820529114 0.806670319 0.839053658 1.189250723 1 12.29484289 -8.620248431 1.197623602 1.046750551 0.809356153 0.791375509 0.053797548 0.133994758 0.371758328 0.006790162 0.02129146 2.40E-09 8.620248431 -0.237394398 NILDSKPTANK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 NILDSKPTANKK 12 2 H0YHL7;B4E3S0;Q9ULV4;Q9ULV4-2;Q9ULV4-3 H0YHL7 CORO1C Coronin;Coronin-1C 0 1 NILDSKPTANK(1)K 92.151 0.029659 1342200 588.86 672.05 704.26 636.82 1098.2 1134.4 1145 1139.2 996.35 881.24 FALSE TRUE FALSE 581.6827478 681.5111375 716.5173499 710.4521247 1042.154756 1061.915501 1242.256271 1172.160955 907.2339606 858.3452578 0.677679224 0.793982528 0.834765898 0.827699714 1.214144013 1.237165921 1.447268754 1.365605441 1.056956921 1 9.745414259 -8.579132243 1.94478919 0.834845573 1.373140242 0.789171443 0.1144833 0.11801271 0.891659292 0.019709115 0.049250104 2.64E-09 8.579132243 0.53829467 NILFVITKPDVYK ddPTM_HeLa_Romidepsin_16h_R1 1 NILFVITKPDVYK 13 1 F8VZJ2;F8W0W4;H0YHX9;Q13765;E9PAV3-2;E9PAV3;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 0 112.08 0.0018608 363990 436.35 494.1 537.05 327.36 460.86 364.36 324.36 419.75 477.88 264.82 FALSE FALSE TRUE 431.0315984 501.0559528 546.39713 365.2109035 437.3405945 341.0785719 351.9111303 431.894804 435.1372159 257.9399382 1.671054127 1.942529552 2.118311471 1.41587575 1.695513295 1.322317801 1.364314238 1.674400665 1.686971079 1 8.01089136 -12.07550153 0.931048328 1.013247699 1.643586953 0 0.31306392 0.378032851 0.61025005 0.151643352 0.049136725 8.40E-13 12.07550153 0.630339254 NILIDFTK ddPTM_HeLa_Romidepsin_16h_R1 1 NILIDFTK 8 0 P19367-4;P19367-2;P19367;P19367-3;E9PB90;P52789 P19367-4 HK1;HK2 Hexokinase-1;Hexokinase;Hexokinase-2 0 0 110.87 0.020223 180490 243.65 150.64 197.98 143.48 0 169.85 173.18 258.1 176.8 241.55 FALSE FALSE TRUE 240.6803001 152.7607139 201.4257589 160.0698327 0 158.9971332 187.8899049 265.5677163 160.9865652 235.2744962 1.022976583 0.649287179 0.856130869 0.680353524 0 0.675794171 0.798598692 1.128756923 0.684249963 1 7.87820113 -10.26215247 24.72335417 1.010850058 0.668370815 0.071517601 0.286074 57.19557352 1983003.397 0.0461112 0.054414765 5.47E-11 10.26215247 -0.342479243 NIMSK(ac)VHGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NIMSKVHGKR 10 2 Q99581 Q99581 FEV Protein FEV 0 2 NIMSK(1)VHGK(1)R 74.376 0.02247 29279000 0 0 0 0 154.11 98.342 0 136.4 0 0 FALSE TRUE FALSE 0 0 0 0 146.2451916 92.05826358 0 140.3465188 0 0 0 NINMDNDLEVLTS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 0 NINMDNDLEVLT(0.045)S(0.565)S(0.343)PT(0.046)R 94.845 0.0085116 8135600 2347.1 2160.7 2008.8 1822.5 1946.6 2181.9 1307.9 1783.2 2097.5 2407.7 TRUE FALSE FALSE 2318.492642 2191.118391 2043.762321 2033.226025 1847.257738 2042.483632 1418.992993 1834.794079 1909.894347 2345.147607 0.988633993 0.934320034 0.87148558 0.866992772 0.78769359 0.87094033 0.605076196 0.782378931 0.814402616 1 11.19546302 -8.860614758 0.525170319 1.003582601 0.682209766 0.411600363 0.083916291 0.382861487 0.174448897 0.013321267 0.057421201 1.38E-09 8.860614758 -0.321372834 NINMDNDLEVLTSS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 NINMDNDLEVLTSSPTR 17 0 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 0 NINMDNDLEVLT(0.003)S(0.047)S(0.925)PT(0.025)R;NINMDNDLEVLT(0.003)S(0.045)S(0.881)PT(0.072)R;NINMDNDLEVLT(0.006)S(0.22)S(0.647)PT(0.128)R ;; 130.95 0.0027209 158669000 11661.3 11751.3 10513.6 9643.5 9885.4 9738.4 8649.6 9938.4 11744.8 10713.5 TRUE FALSE FALSE 11519.16759 11916.73511 10696.5848 10758.52684 9380.91115 9116.147669 9384.296808 10225.95192 10694.31567 10435.16173 1.103880121 1.141978958 1.025052134 1.030988031 0.898971324 0.873599079 0.899295771 0.979951456 1.024834684 1 13.34916534 -8.831198373 4.169214701 1.056004812 0.908696012 0.693159518 0.04629061 0.110911929 3.769461558 0.008294045 0.015729092 1.48E-09 8.831198373 -0.1473088 NINPST(ph)ANSPK ddPTM_HeLa_Romidepsin_16h_R1 1 NINPSTANSPK 11 0 P46937-6;P46937-7;P46937;P46937-9;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 NINPS(0.007)T(0.649)ANS(0.344)PK 142.39 0.0056152 7362400 3421.4 3205.4 3181.4 3247.6 3707.2 3608.4 3024.3 2758.9 3300.6 3226.5 TRUE FALSE FALSE 3379.698661 3250.525705 3236.770932 3623.102792 3518.007751 3377.834886 3281.183967 2838.724419 3005.386069 3142.675065 1.075420968 1.034318101 1.029941329 1.152872224 1.119430955 1.074827914 1.044073568 0.903282828 0.956314607 1 11.6177774 -7.263495825 5.079592073 1.052514257 0.896470615 0.419281478 0.053317763 0.123004536 10.1814803 0.007261134 0.066962125 5.45E-08 7.263495825 -0.156043642 NINPSTANS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 NINPSTANSPK 11 0 P46937-6;P46937-7;P46937;P46937-9;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 NINPS(0.029)T(0.412)ANS(0.558)PK;NINPST(0.003)ANS(0.997)PK ; 144.88 0.0025059 42219400 9814.5 9569.1 9533.1 9578.4 10941.3 10280.3 9158.4 9368 11047.7 9905 TRUE FALSE FALSE 9694.877099 9703.814041 9699.019607 10685.89968 10382.92463 9623.422008 9936.314267 9639.0483 10059.56604 9647.666672 1.004893455 1.005819787 1.005322835 1.107614933 1.076210962 0.997486992 1.029918902 0.999106688 1.042694196 1 13.23596435 -9.476356714 24.99969418 1.002778153 1.042378507 0.146783183 0.033253723 431.7964978 232036.6134 0.004843914 0.007399076 3.34E-10 9.476356714 0.039600355 NINTFVET(ph)PVQK ddPTM_HeLa_Romidepsin_16h_R1 3 NINTFVETPVQK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 NINT(0.001)FVET(0.999)PVQK;NINT(0.002)FVET(0.998)PVQK;NINTFVET(1)PVQK ;; 135.94 0.0054344 55371000 11061.8 9883.1 10777.9 7582.2 7712.2 9107.4 7798 8150.8 12349.4 10995.3 TRUE FALSE FALSE 10926.97453 10022.23454 10965.48483 8458.889639 7318.617656 8525.466533 8460.361925 8386.630538 11244.83873 10709.64052 1.020293305 0.935814281 1.023889159 0.789838802 0.683367256 0.796055341 0.789976275 0.783091694 1.049973499 1 13.38662244 -9.226429926 5.616980662 1.004220572 0.764853207 0.895906905 0.040503879 0.040653099 3.685335402 0.005651794 0.009324552 5.94E-10 9.226429926 -0.239367366 SSQPS(ph)PTAVPASDS(ph)PPTKQEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSQPSPTAVPASDSPPTKQEVK 22 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 2 0 S(0.003)S(0.003)QPS(0.645)PT(0.346)AVPAS(0.02)DS(0.981)PPT(0.002)KQEVK 116.65 0.00016679 22599000 6387.2 5267.7 5957.1 5108.3 3642.4 3152.6 2805.4 2608.9 6586.6 6439.3 TRUE FALSE FALSE 6309.35035 5341.858819 6060.780827 5698.945681 3456.514736 2951.159035 3043.690606 2684.384405 5997.478 6272.006058 1.005954122 0.851698606 0.96632254 0.908632044 0.551101945 0.470528728 0.485281835 0.427994549 0.956229625 1 12.61471124 -8.755436766 2.549223558 0.986708035 0.463412835 0.958724277 0.04733082 0.037934291 0.503552948 0.007644414 0.016058902 1.76E-09 8.755436766 -0.5232952 down NIPSPGQLDPDT(ph)RIPVINLEDGTR ddPTM_HeLa_Romidepsin_16h_R1 2 NIPSPGQLDPDTRIPVINLEDGTR 24 1 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 0 NIPS(0.061)PGQLDPDT(0.932)RIPVINLEDGT(0.007)R;NIPS(0.001)PGQLDPDT(0.997)RIPVINLEDGT(0.002)R ; 83.727 0.00011646 18935700 1627.3 1585.45 1638.06 2093.59 1244.86 794.63 897.32 1030.26 1742.27 1436.77 TRUE FALSE FALSE 1607.465842 1607.770007 1666.569747 2335.660726 1181.330149 743.8557076 973.5383384 1060.068948 1586.437008 1399.442508 1.148647288 1.148864635 1.190881181 1.668993698 0.844143394 0.531537168 0.695661546 0.757493746 1.133620708 1 10.4506365 -8.531434173 24.99907317 1.131095062 0.66878488 0.640201609 0.183889643 106.92667 312440.5789 0.028379835 0.056829426 2.94E-09 8.531434173 -0.462310182 NISFNDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 NISFNDKK 8 1 E7EQR4;P15311;P26038;A0A2R8Y7M3;A0A2R8Y5S7;P35241-4;P35241;P35241-5 E7EQR4;P26038;A0A2R8Y7M3 EZR;MSN;RDX Ezrin;Moesin;Radixin 0 1 ; NISFNDK(1)K;NISFNDK(1)K 128.6 0.0021539 20895100 4084.4 3946.3 4201.2 4014.3 8924 8152.7 8712.7 4193.7 7618.3 5065.8 FALSE TRUE FALSE 4034.617762 4001.856115 4274.320124 4478.452254 8468.57498 7631.768782 9452.756521 4315.038093 6936.900168 4934.189786 0.81768597 0.811046248 0.866265853 0.907636805 1.716305077 1.546711641 1.915766708 0.874518063 1.405884344 1 12.26859749 -8.771429818 24.97976415 0.898968824 1.544455911 0.431025986 0.299812993 93.51393959 233819.4309 0.03442091 0.062928383 1.69E-09 8.771429818 0.645487086 NISSS(ph)PSVESLPGGR ddPTM_HeLa_Romidepsin_16h_R1 1 NISSSPSVESLPGGR 15 0 Q92609;Q92609-2;C9J3F6 Q92609 TBC1D5 TBC1 domain family member 5 1 0 NIS(0.004)S(0.035)S(0.603)PS(0.315)VES(0.043)LPGGR 118.55 0.0036637 4092600 799.15 934.64 661.24 789.59 985.58 1138.1 945.04 1066.9 1081 808.18 TRUE FALSE FALSE 789.4096524 947.7978865 672.7486048 880.8861109 935.2821749 1065.379083 1025.311674 1097.769068 984.3126526 787.1833671 1.002828166 1.204036983 0.854627566 1.119035472 1.188137623 1.353406497 1.302506782 1.39455318 1.250423591 1 9.620555927 -8.612517429 1.730312942 1.009354273 1.35145041 0.515285051 0.11405741 0.120905917 0.723889678 0.011942231 0.030594939 2.44E-09 8.612517429 0.342096137 NITLNFGPQHPAAHGVLR ddPTM_HeLa_Romidepsin_16h_R1 1 NITLNFGPQHPAAHGVLR 18 0 O75306-2;O75306 O75306-2 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" 0 0 58.246 0.019964 515320 134.3 126.59 196.5 212.11 149.17 137.53 139.95 208.55 166.33 115.08 FALSE FALSE TRUE 132.6630999 128.3721373 199.9200001 236.6351562 141.5572983 128.7422769 151.8373495 214.5840652 151.4530282 112.090205 1.183538739 1.145257405 1.783563515 2.1111136 1.262887317 1.148559563 1.354599624 1.914387303 1.351170945 1 6.808516404 -9.85138876 6.892905003 1.09123293 1.572011252 0.322029807 0.293328753 0.177291923 11.49751102 0.048336087 0.063753663 1.41E-10 9.85138876 0.480778322 NITSFCPDT(ph)PSEKTAK ddPTM_HeLa_Romidepsin_16h_R1 1 NITSFCPDTPSEKTAK 16 1 A9QM74 A9QM74 KPNA7 Importin subunit alpha-8 1 0 NIT(0.001)S(0.001)FCPDT(0.71)PS(0.288)EKTAK 72.321 0.020259 28906000 3586.5 2905.6 3226.9 3931.3 3385.7 3657 3281.1 3192.4 3282.7 3182.1 TRUE FALSE FALSE 3542.786358 2946.505113 3283.062841 4385.855403 3212.915095 3423.329502 3559.796552 3284.767057 2989.08709 3099.428583 1.143045004 0.950660754 1.059247778 1.415052899 1.036615301 1.10450343 1.148533175 1.059797627 0.964399408 1 11.59778655 -13.40436864 0.392163179 0.883485715 1.12633671 0.176301172 0.114827684 8.961780586 0.931022687 1.03128405 0.035863015 3.94E-14 13.40436864 0.242850995 NITSFCPDTPS(ph)EKTAK ddPTM_HeLa_Romidepsin_16h_R1 1 NITSFCPDTPSEKTAK 16 1 A9QM74 A9QM74 KPNA7 Importin subunit alpha-8 1 0 NIT(0.043)S(0.043)FCPDT(0.387)PS(0.527)EKTAK 63.374 0.021761 28225000 2545.4 2520 2249.1 3471.7 2827.6 2755.6 2698.9 2881.3 3100 2619.4 TRUE FALSE FALSE 2514.375686 2555.476626 2288.244642 3873.114289 2683.297021 2579.526053 2928.144499 2964.66587 2822.728236 2551.34761 0.985508864 1.001618367 0.896876863 1.518066089 1.051717535 1.011044533 1.147685438 1.161999979 1.106367562 1 11.31704376 NITSSS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 NITSSSPER 9 0 A6NF31;O75665-3;O75665 A6NF31 OFD1 Oral-facial-digital syndrome 1 protein 1 0 NITS(0.001)S(0.003)S(0.996)PER;NITS(0.001)SS(0.998)PER ; 126.03 0.010313 133960000 12561.2 11115.7 12200.1 8888.2 8605.3 7181 6861.9 5335.5 12461.1 12162.6 TRUE FALSE FALSE 12408.09926 11272.18712 12412.43762 9915.895504 8166.13943 6722.157276 7444.749615 5489.874274 11346.54801 11846.6139 1.047396274 0.951511311 1.047762485 0.837023608 0.689322662 0.567432798 0.628428484 0.463412948 0.957788285 1 13.53218713 -8.793487274 1.404423334 1.021035563 0.548244872 0.935533198 0.051865042 0.057387754 0.226906228 0.007102499 0.017640121 1.61E-09 8.793487274 -0.472790692 NKDQGTYEDYVEGLR ddPTM_HeLa_Romidepsin_16h_R1 2 NKDQGTYEDYVEGLR 15 1 F8VZU9;G3V1Y7;F8VPF3;F8W1R7;J3KND3;G8JLA2;G3V1V0;F8W180;B7Z6Z4;P60660-2;P60660 F8VZU9 MYL6 Myosin light polypeptide 6 0 0 ; ; 132.23 0.0018957 202750000 9911.4 8914.6 9232.3 9797.3 10610.1 10393.9 9979.9 10742.2 10771.3 9813.3 FALSE FALSE TRUE 9790.596044 9040.099973 9392.984309 10930.10992 10068.62701 9729.763335 10827.59246 11053.00861 9807.887951 9558.349051 1.024297815 0.945780482 0.982699445 1.143514415 1.053385574 1.017933461 1.132788978 1.156372146 1.026106904 1 13.22254574 -9.272033592 24.97535796 1.003831384 1.095338431 0.576032615 0.044661368 454.6019059 1071700.164 0.007067239 0.010861281 5.35E-10 9.272033592 0.091507047 NKDSGSDTASAIIPSTTPS(ph)VDSDDESVVK ddPTM_HeLa_Romidepsin_16h_R1 2 NKDSGSDTASAIIPSTTPSVDSDDESVVK 29 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 NKDSGSDTASAIIPS(0.274)T(0.167)T(0.042)PS(0.487)VDS(0.03)DDESVVK;NKDSGSDTASAIIPS(0.006)T(0.03)T(0.006)PS(0.662)VDS(0.289)DDES(0.006)VVK ; 148.84 1.17E-11 170615000 12211 12723 11498.4 12123.4 24658 31127 27597 31288 12279.6 10913.5 TRUE FALSE FALSE 12062.16764 12902.11473 11698.52483 13525.16455 23399.61025 29138.08516 29941.08849 32193.26892 11181.28182 10629.9657 1.134732508 1.213749423 1.100523291 1.272362013 2.201287466 2.741126923 2.816668402 3.028539304 1.051864337 1 13.37584932 -8.593716618 1.706662028 1.07507749 2.912317499 0.989636312 0.080956995 0.026407416 0.153261051 0.013779509 0.035995678 2.55E-09 8.593716618 1.837240009 up NKELYEINPPEISEEIIGS(ph)PIPEPR ddPTM_HeLa_Romidepsin_16h_R1 2 NKELYEINPPEISEEIIGSPIPEPR 25 1 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 NKELYEINPPEIS(0.389)EEIIGS(0.611)PIPEPR;NKELY(0.001)EINPPEIS(0.217)EEIIGS(0.782)PIPEPR ; 93.295 1.39E-05 28249000 2312.44 2505.6 2030.7 2465.9 2617.2 2469.7 2255.83 2594.2 2733.5 2375.8 TRUE FALSE FALSE 2284.255092 2540.873903 2066.043482 2751.01896 2483.634518 2311.894141 2447.440144 2669.259084 2489.008914 2314.076374 0.987113095 1.098007798 0.892815598 1.188819432 1.073272493 0.999056975 1.057631534 1.153487895 1.075594973 1 11.17622076 -9.261196531 24.99979525 0.996329858 1.085931439 0.240031957 0.071479447 20.54945386 2115422.678 0.009605673 0.015278163 5.48E-10 9.261196531 0.089601581 ASAGTPSLSAGVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ASAGTPSLSAGVSPK 15 0 Q8TEK3-1;Q8TEK3 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 ASAGTPSLSAGVS(1)PK;ASAGTPSLSAGVS(1)PK ; 190.82 2.10E-12 36054000 11030.7 9377.3 9208.9 8516.6 5917.3 4633.5 4032 4797.1 10367.1 10375.3 TRUE FALSE FALSE 10896.25359 9509.313876 9369.177042 9501.329364 5615.318101 4337.434304 4374.477979 4935.89652 9439.840611 10105.74821 1.07822334 0.940980685 0.927113643 0.940190589 0.555655849 0.429204668 0.432870272 0.488424649 0.934106057 1 13.30288852 -8.753396928 2.186121773 1.022158894 0.443602386 0.950088427 0.055298606 0.042306512 0.412227653 0.008579495 0.018653529 1.76E-09 8.753396928 -0.578556508 down NKGTSDSSSGNVS(ph)EGESPPDSQEDSFQGR ddPTM_HeLa_Romidepsin_16h_R1 1 NKGTSDSSSGNVSEGESPPDSQEDSFQGR 29 1 S5FZ81;Q8WUB8-3;Q8WUB8-2;Q8WUB8 S5FZ81 PHF10 PHD finger protein 10 1 0 NKGTSDSSS(0.002)GNVS(0.996)EGES(0.002)PPDSQEDSFQGR 110.7 7.49E-10 10467000 1672.3 1537.9 1235.8 1611.2 1074.2 900.41 878.38 726.51 1812.6 1232.6 TRUE FALSE FALSE 1651.917364 1559.550597 1257.308581 1797.494525 1019.379566 842.8767069 952.9895753 747.5304206 1650.476516 1200.576874 1.375936352 1.29900103 1.047253706 1.497192361 0.849074797 0.702059756 0.793776388 0.622642695 1.374736222 1 10.22951207 -8.582981536 7.429415539 1.200668364 0.724552182 0.730859112 0.154378935 0.11007796 11.47713831 0.02542217 0.051100443 2.61E-09 8.582981536 -0.476116182 NKPGPNIES(ph)GNEDDDASFK ddPTM_HeLa_Romidepsin_16h_R1 8 NKPGPNIESGNEDDDASFK 19 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(0.999)GNEDDDAS(0.001)FK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(1)GNEDDDASFK;NKPGPNIES(0.999)GNEDDDAS(0.001)FK ;;;;;;; 138.82 0.00015933 4824018000 41320.3 49013.5 37706.9 40987.9 38896.3 42154.4 38514.7 44129.1 42231.5 42196.8 TRUE FALSE FALSE 40816.67229 49703.51334 38363.17278 45727.11385 36911.27667 39460.86989 41786.13766 45405.90588 38454.20887 41100.52105 0.993093792 1.209315893 0.933398697 1.112567741 0.898073205 0.960106317 1.016681458 1.104752561 0.935613659 1 15.32686906 NKPLEQS(ph)VEDLSK ddPTM_HeLa_Romidepsin_16h_R1 1 NKPLEQSVEDLSK 13 1 O95466;O95466-2;O95466-3 O95466 FMNL1 Formin-like protein 1 1 0 NKPLEQS(0.771)VEDLS(0.229)K 107.62 0.0030598 41142000 4318.3 4186.4 4960.4 2737.5 3537.9 3902 3411.1 3523.6 5070.3 4458.3 TRUE FALSE FALSE 4265.666899 4245.336249 5046.733681 3054.02263 3357.347761 3652.674793 3700.838749 3625.549807 4616.799669 4342.472723 0.982312883 0.977631069 1.162179708 0.703291149 0.773141934 0.841150889 0.852242256 0.834904451 1.063172981 1 12.08430107 -9.250684346 24.999928 1.001788531 0.804484842 0.742183303 0.067994528 307.8376079 715564.3219 0.009665517 0.015926736 5.61E-10 9.250684346 -0.197303689 NKPLSPIKLTPTSVLDYFGTGSVQR ddPTM_HeLa_Romidepsin_16h_R1 1 NKPLSPIKLTPTSVLDYFGTGSVQR 25 2 P35251-2;P35251;A0A1W2PP02 P35251-2 RFC1 Replication factor C subunit 1 0 0 44.933 0.021446 10116000 1233.6 1041.7 1193.2 1554.7 1084.6 779.89 774.15 987.4 1416.9 1323.7 FALSE FALSE TRUE 1218.564409 1056.36508 1213.967145 1734.461729 1029.248815 730.057546 839.9062817 1015.968861 1290.168915 1289.310083 0.945129046 0.81932585 0.941563369 1.345263449 0.798294241 0.566238918 0.651438543 0.787994195 1.000666118 1 10.33238356 -8.529290652 24.99802063 0.984704559 0.66941551 0.55922204 0.136491179 90.38708454 352390.4427 0.019369432 0.038817588 2.96E-09 8.529290652 -0.31528905 NKPPPPPPASASPSAVPNGPQS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 NKPPPPPPASASPSAVPNGPQSPK 24 1 H0Y7W6 H0Y7W6 FNBP1 1 0 NKPPPPPPASAS(0.001)PS(0.002)AVPNGPQS(0.996)PK;NKPPPPPPASASPSAVPNGPQS(1)PK ; 129.8 1.04E-06 32798000 7316.3 7473 6547.2 7191.6 9797 10527.1 9744.3 11520.5 7941.1 7743.1 TRUE FALSE FALSE 7227.126121 7578.20509 6661.15127 8023.126629 9297.022532 9854.452285 10571.9806 11853.82749 7230.828127 7541.933146 0.958259107 1.00480937 0.883215369 1.063802406 1.232710812 1.306621538 1.401760052 1.571722695 0.958749963 1 12.88071865 -8.195441682 0.938844009 0.973041416 1.558703268 0.943747273 0.051239441 0.125206585 0.172780158 0.008533827 0.05345375 6.38E-09 8.195441682 0.585661852 NKS(ph)PAAVTEPETNK ddPTM_HeLa_Romidepsin_16h_R1 1 NKSPAAVTEPETNK 14 1 B7ZBC9;B7ZBC8;O75449 B7ZBC9 KATNA1 Katanin p60 ATPase-containing subunit A1 1 0 NKS(0.99)PAAVT(0.009)EPETNK 63.443 0.028271 5093800 1828 1459.6 1252.5 1272.8 1779.2 2093.3 1911.5 1840.8 1798.2 1703.5 TRUE FALSE FALSE 1805.719633 1480.148287 1274.299237 1419.967125 1688.400785 1959.544886 2073.862762 1894.060644 1637.364488 1659.242824 1.088279308 0.892062491 0.768000451 0.855792235 1.017573052 1.18098741 1.249885027 1.14152107 0.986814265 1 10.69630932 -8.266499438 4.580916038 0.993764906 1.199369315 0.537699872 0.097706236 0.160509579 9.235881388 0.01714869 0.042337292 5.41E-09 8.266499438 0.205604409 NKT(ph)Y(ph)Y(ph)KFEK ddPTM_HeLa_Romidepsin_16h_R1 1 NKTYYKFEK 9 2 Q8IZT8 Q8IZT8 HS3ST5 Heparan sulfate glucosamine 3-O-sulfotransferase 5 3 0 NKT(1)Y(1)Y(1)KFEK 55.806 0.0042023 0 618.71 736 849.86 618.87 614.23 512.01 859.28 656 715.36 827.63 TRUE FALSE FALSE 611.1689245 746.3614273 864.6514568 690.4266613 582.8835511 479.2942134 932.2672218 674.980325 651.3764099 806.1280533 0.758153648 0.925859638 1.072598148 0.856472689 0.723065707 0.594563372 1.156475349 0.837311544 0.808030942 1 9.654865219 -9.008946974 24.71451694 0.902110204 0.829051566 0.061242101 0.155653224 1129.09164 3118941.533 0.02493184 0.04356071 9.80E-10 9.008946974 -0.073058637 NKTIT(ph)AYHES(ph)GHAIIAY(ph)YT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 NKTITAYHESGHAIIAYYTK 20 1 Q96I63;Q96TA2-3;Q96TA2-2;Q96TA2 Q96I63 YME1L1 ATP-dependent zinc metalloprotease YME1L1 4 0 NKT(0.17)IT(0.788)AY(0.065)HES(0.959)GHAIIAY(0.659)Y(0.659)T(0.701)K 47.68 0.0040667 0 0 0 61.49 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 62.56020766 0 0 0 0 0 0 0 0 NLAANDLSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 NLAANDLSPSR 11 0 Q96CB9-4;Q96CB9 Q96CB9-4 NSUN4 5-methylcytosine rRNA methyltransferase NSUN4 1 0 NLAANDLS(0.407)PS(0.593)R 109.95 0.014591 5802900 2512.5 2085.1 2363.6 2198.5 1909.7 2298 1840.4 1790.7 2116.9 2095.7 TRUE FALSE FALSE 2481.876684 2114.454093 2404.737467 2452.700914 1812.240883 2151.165216 1996.72353 1842.511079 1927.559162 2041.253412 1.215859172 1.035860653 1.178069049 1.201566106 0.887807889 1.053845252 0.97818503 0.902637109 0.944301747 1 10.99523958 -8.758181768 24.99999987 1.111372546 0.964246869 0.342570432 0.093477364 73.89567992 567089.6387 0.014156953 0.027400553 1.75E-09 8.758181768 -0.147125677 NLAMGVNLTSMSK ddPTM_HeLa_Romidepsin_16h_R1 2 NLAMGVNLTSMSK 13 0 P12004 P12004 PCNA Proliferating cell nuclear antigen 0 0 ; ; 104.17 0.0019379 2341600 1505.65 869.51 1638.54 1080.94 1676.73 1580.83 1387.73 996.66 1360.8 892.72 FALSE FALSE TRUE 1487.298559 881.7509846 1667.058101 1205.923369 1591.160211 1479.820065 1505.603752 1025.496785 1239.08664 869.5270057 1.710468506 1.014058193 1.917201065 1.386872818 1.829914656 1.701867861 1.731520403 1.179373128 1.425012256 1 9.764087025 -12.48545538 0.746999191 0.913545381 1.584621978 0.103658793 0.303527896 0.768229836 0.598528702 0.340798277 0.050797949 3.27E-13 12.48545538 0.671076596 NLATSADT(ph)PPSTVPGTGK ddPTM_HeLa_Romidepsin_16h_R1 1 NLATSADTPPSTVPGTGK 18 0 Q96Q15;J3KRA9;Q96Q15-4;Q96Q15-3;Q96Q15-2 Q96Q15 SMG1 Serine/threonine-protein kinase SMG1 1 0 NLAT(0.013)S(0.479)ADT(0.507)PPS(0.002)TVPGTGK 279.12 8.69E-106 18158000 7394.2 7378 7481.4 6733.3 7309.4 7719.9 6101.4 7643.3 7413.2 6639.1 TRUE FALSE FALSE 7304.076646 7481.867678 7611.610629 7511.835827 6936.374043 7226.623305 6619.652764 7864.446826 6750.144825 6466.615225 1.129505374 1.156999051 1.177062553 1.161633338 1.072643694 1.117527958 1.023665787 1.216161246 1.043845132 1 12.65879505 -12.05214764 0.833948723 0.99976822 1.128715414 0.3992429 0.052799806 0.427406316 0.540037155 0.033610932 0.010114484 8.87E-13 12.05214764 0.128947194 NLATTVTEEILEK ddPTM_HeLa_Romidepsin_16h_R1 1 NLATTVTEEILEK 13 0 B4DT28;O43390-3;O43390;O43390-4;O43390-2 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 0 216.84 1.34E-22 1703100 840.77 928.44 750.08 735.45 862.12 726.22 720.18 782.75 1153.9 932 FALSE FALSE TRUE 830.5223718 941.5106027 763.1348278 820.4861894 818.1227994 679.8168858 781.3520712 805.3976363 1050.692294 907.7865056 0.914887329 1.037149811 0.840654518 0.903831666 0.901228201 0.74887309 0.86072228 0.887210408 1.157422244 1 9.826209232 -9.62026258 0.322395771 0.994199278 0.814080849 0.452129632 0.080074039 1.224399095 0.306065616 0.040319712 0.083871413 2.40E-10 9.62026258 -0.180118428 NLDDGIDDER ddPTM_HeLa_Romidepsin_16h_R1 2 NLDDGIDDER 10 0 A0A087WTT1;E7EQV3;P11940-2;P11940;H0YAR2;E7ERJ7;H0YAP2;Q9H361 A0A087WTT1 PABPC1;PABPC3 Polyadenylate-binding protein;Polyadenylate-binding protein 1;Polyadenylate-binding protein 3 0 0 ; ; 250.76 1.02E-46 119688000 10323.6 10355.5 9923.4 7527.1 10151.9 10195 8579.5 9283 10961.2 10604.4 FALSE FALSE TRUE 10197.77199 10501.285 10096.11261 8397.418718 9633.810661 9543.572403 9308.242516 9551.588959 9980.802819 10328.89616 0.987305113 1.016689958 0.977462883 0.813002531 0.932704765 0.923968278 0.901184635 0.924744407 0.966299076 1 13.33439846 -9.497847014 24.77921192 0.995612259 0.901756836 0.646304286 0.033539526 282.3705699 279522.3929 0.004617535 0.007032931 3.18E-10 9.497847014 -0.093855423 NLDDGIDDERLR ddPTM_HeLa_Romidepsin_16h_R1 3 NLDDGIDDERLR 12 1 A0A087WTT1;E7EQV3;P11940-2;P11940;H0YAR2;E7ERJ7;H0YAP2;Q9H361 A0A087WTT1 PABPC1;PABPC3 Polyadenylate-binding protein;Polyadenylate-binding protein 1;Polyadenylate-binding protein 3 0 0 ;; ;; 176.99 2.23E-06 124325000 17957.2 19002.8 15703 18567.2 19711.7 22038.5 18621.3 19218 22344 20725 FALSE FALSE TRUE 17738.33074 19270.32192 15976.30413 20714.02703 18705.73839 20630.31098 20202.99276 19774.04251 20345.49668 20186.56151 0.878719772 0.954611408 0.791432663 1.026129537 0.926643123 1.02198242 1.000813969 0.979564672 1.007873315 1 14.30110757 NLDDTIDDEKLR ddPTM_HeLa_Romidepsin_16h_R1 1 NLDDTIDDEKLR 12 1 H0Y5F5;B1ANR0;Q13310-2;Q13310;Q13310-3;H0YEU6;P0CB38 H0Y5F5 PABPC4;PABPC4L Polyadenylate-binding protein;Polyadenylate-binding protein 4;Polyadenylate-binding protein 4-like 0 0 146.67 0.0017023 8872200 3444.9 3538.8 3666.7 2649.8 3358.6 3324.7 2933.1 3129.5 3520.9 3820 FALSE FALSE TRUE 3402.912234 3588.619319 3730.517375 2956.182344 3187.198109 3112.2624 3182.237441 3220.047145 3205.981886 3720.755849 0.914575525 0.964486643 1.002623533 0.79451124 0.856599637 0.836459721 0.855266395 0.865428229 0.861648013 1 11.86138001 -9.263725308 24.9956968 0.962004015 0.842951189 0.597874203 0.043188341 84.34466321 922274.7478 0.005775393 0.009090374 5.45E-10 9.263725308 -0.119052825 NLDIERPTYTNLNR ddPTM_HeLa_Romidepsin_16h_R1 1 NLDIERPTYTNLNR 14 1 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;F8VQQ4;Q9NY65;C9J2C0;Q9NY65-2;Q6PEY2;C9JDS9;Q71U36-2;Q71U36;P68363;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA1A;TUBA8;TUBA3E;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 69.352 0.029782 2533800 1644.5 1464.8 1694.7 1570 1681.3 1961.5 1738.8 1578.8 1595 1372.8 FALSE FALSE TRUE 1624.456201 1485.421493 1724.195543 1751.530787 1595.496987 1836.16648 1886.493629 1624.480087 1452.339205 1337.134458 1.214878722 1.11089912 1.289470578 1.309913731 1.193221054 1.373210053 1.410848114 1.214896585 1.086157938 1 10.38492883 -13.25478155 0.153779875 0.633119942 1.408887785 0.609369751 0.077002908 8.535504823 0.247077953 1.388192104 0.222417084 5.56E-14 13.25478155 0.775767843 NLDK(ac)SIDNK ddPTM_HeLa_Romidepsin_16h_R1 2 NLDKSIDNK 9 1 A0A087WTT1;E7EQV3;P11940-2;P11940;E5RGH3;H0YEQ8;E5RH24;E5RJB9;B1ANR1;H0Y5F5;B1ANR0;Q13310-2;Q13310;Q13310-3;P0CB38 A0A087WTT1;H0Y5F5 PABPC1;PABPC4;PABPC4L Polyadenylate-binding protein;Polyadenylate-binding protein 1;Polyadenylate-binding protein 4;Polyadenylate-binding protein 4-like 0 1 ; NLDK(1)SIDNK;NLDK(1)SIDNK 189.18 4.89E-08 4790400 4000.5 3764.3 4022.5 3660.7 4350.9 4058.5 3552.4 3956.5 4068.3 3927.7 FALSE TRUE FALSE 3951.740367 3817.293914 4092.509925 4083.967358 4128.857338 3799.174948 3854.140767 4070.975085 3704.421059 3825.657788 1.032957098 0.997813742 1.069753269 1.067520302 1.079254227 0.993077572 1.00744525 1.064124214 0.968309573 1 11.90149211 -11.6564015 0.55161561 0.998670207 1.040797146 0.30470772 0.031379434 1.246925528 0.72950819 0.025181256 0.008382893 2.21E-12 11.6564015 0.042126939 NLDPDPEPPS(ph)PDS(ph)PTETFAAPAEVR ddPTM_HeLa_Romidepsin_16h_R1 2 NLDPDPEPPSPDSPTETFAAPAEVR 25 0 Q9BUA3;H0YGY5 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 2 0 NLDPDPEPPS(1)PDS(0.988)PT(0.011)ET(0.001)FAAPAEVR;NLDPDPEPPS(1)PDS(0.985)PT(0.015)ETFAAPAEVR ; 104.24 4.98E-09 2628200 1649.26 1370.48 1590.37 1536.91 1685.51 1756.41 1347.38 1716.36 1536.87 1532.43 TRUE FALSE FALSE 1629.158185 1389.773653 1618.049723 1714.614766 1599.492135 1644.18107 1461.826424 1766.020169 1399.408498 1492.617248 1.091477529 0.931098482 1.084035258 1.148730372 1.07160234 1.101542322 0.979371253 1.183170147 0.937553482 1 10.54362855 -9.554735783 24.99919962 1.034643446 1.091926658 0.271424019 0.070217232 275.5514512 216232.6739 0.010095809 0.01427769 2.79E-10 9.554735783 0.057283212 NLEEEENLGKGEYQESLRS(ph)LEEEGQELPQSADVQR ddPTM_HeLa_Romidepsin_16h_R1 2 NLEEEENLGKGEYQESLRSLEEEGQELPQSADVQR 35 2 P48681 P48681 NES Nestin 1 0 NLEEEENLGKGEY(0.057)QES(0.21)LRS(0.732)LEEEGQELPQSADVQR;NLEEEENLGKGEY(0.012)QES(0.054)LRS(0.927)LEEEGQELPQS(0.007)ADVQR ; 57.484 0.00066171 16857200 1941.07 1649.98 1598.17 2340.18 2073.46 2113.71 2035.81 1863.47 2125.59 1868 TRUE FALSE FALSE 1917.411492 1673.208462 1625.985478 2610.762622 1967.643599 1978.650753 2208.731651 1917.386564 1935.471907 1819.469091 1.053830209 0.919613568 0.893659302 1.434903531 1.081438321 1.087487973 1.213942936 1.053816508 1.063756409 1 10.82930183 NLEELEEKS(ph)TTPPPAEPVSLPQEPPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 NLEELEEKS(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR 58.877 0.00099802 25081000 3227.8 2712.9 2788.2 6615.5 3152.6 2939.5 2708.1 3026.2 3600.2 3212.6 TRUE FALSE FALSE 3188.458332 2751.092277 2836.727451 7380.415237 2991.711058 2751.675437 2938.125946 3113.758322 3278.189095 3129.136189 1.018957993 0.879185856 0.906552889 2.358611064 0.956082087 0.87937222 0.938957517 0.995085587 1.047633883 1 11.61154873 -6.038269979 19.58393756 1.062524175 1.136601611 0 0.425264794 0 0 0.054166047 0 9.16E-07 6.038269979 0.074077436 NLEELEEKST(ph)TPPPAEPVSLPQEPPK ddPTM_HeLa_Romidepsin_16h_R1 1 NLEELEEKSTTPPPAEPVSLPQEPPK 26 1 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 NLEELEEKS(0.003)T(0.499)T(0.499)PPPAEPVSLPQEPPK 105.71 1.45E-06 22434000 3912.3 3458.7 2925.4 9295.7 4727.4 4392.8 4422.3 4601.5 4890.2 3842 TRUE FALSE FALSE 3864.615383 3507.391669 2976.31536 10370.51257 4486.143138 4112.114257 4797.930052 4734.637143 4452.808264 3742.184286 1.03271648 0.937257869 0.79534174 2.771245823 1.198803371 1.098854023 1.282120196 1.265206837 1.189895506 1 11.86966489 NLEELEEKST(ph)TPPPAEPVSLPQEPPKPR ddPTM_HeLa_Romidepsin_16h_R1 2 NLEELEEKSTTPPPAEPVSLPQEPPKPR 28 2 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 NLEELEEKS(0.257)T(0.371)T(0.371)PPPAEPVSLPQEPPKPR;NLEELEEKS(0.049)T(0.476)T(0.476)PPPAEPVSLPQEPPKPR ; 78.254 1.92E-06 268910000 16032.6 14907.7 12216 32007 15623.8 14050.1 12830.3 14353.1 16945.7 13583.1 TRUE FALSE FALSE 15837.1885 15117.57099 12428.61436 35707.79994 14826.45919 13152.34395 13920.10536 14768.3843 15430.03415 13230.2091 1.197047483 1.142655484 0.939411785 2.698959605 1.120651916 0.994114594 1.052145529 1.11626235 1.166272886 1 13.69154824 -10.82784359 0.875231816 1.044051832 1.31407246 0.031284855 0.484028787 1.314354378 2.158595743 0.138359972 0.117691341 1.49E-11 10.82784359 0.270020629 NLEQILNGGES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 NLEQILNGGESPK 13 0 G3V340;Q13033-2;Q13033;G3V3G7 G3V340 STRN3 Striatin-3 1 0 NLEQILNGGES(1)PK;NLEQILNGGES(1)PK ; 211.49 3.38E-23 109164000 11438.7 13058.5 12580.8 6463.8 10361.4 10305.7 9396.3 9820.2 11930.7 12200.6 TRUE FALSE FALSE 11299.28072 13242.33791 12799.76355 7211.174969 9832.619094 9647.19903 10194.42149 10104.33199 10863.58831 11883.62665 0.950827643 1.114334731 1.077092366 0.606816015 0.827408954 0.811805967 0.857854406 0.85027343 0.91416439 1 13.53668757 -9.283075776 24.99912973 0.995534401 0.797752512 0.620801872 0.085620913 434.2066842 501689.7711 0.012931795 0.019764161 5.21E-10 9.283075776 -0.197781889 NLEQILNGGES(ph)PKQK ddPTM_HeLa_Romidepsin_16h_R1 1 NLEQILNGGESPKQK 15 1 G3V340;Q13033-2;Q13033 G3V340 STRN3 Striatin-3 1 0 NLEQILNGGES(1)PKQK 89.353 0.0061431 56184000 2256.5 2227.5 2146.2 2534.7 2369.6 2279.3 2085.8 1883 2371.6 2345.2 TRUE FALSE FALSE 2228.99691 2258.858803 2183.553711 2827.77394 2248.67047 2133.660086 2262.9678 1937.481634 2159.478156 2284.271366 0.97580215 0.988874981 0.955908192 1.237932578 0.984414769 0.934065942 0.990673802 0.848183654 0.945368483 1 11.15751833 -6.377627989 1.197855935 1.001749839 2.89E-10 0.244624932 0.08155387 11.82179606 2.844143765 0.011590093 24.47902182 4.19E-07 6.377627989 -1.001749839 NLFASFPTEESSINY(ph)TFKTPEK ddPTM_HeLa_Romidepsin_16h_R1 1 NLFASFPTEESSINYTFKTPEK 22 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 NLFASFPT(0.001)EES(0.019)S(0.027)INY(0.886)T(0.047)FKT(0.02)PEK 100.39 0.00044979 163160000 1781.1 1404.8 1844.3 1560.6 1597.9 1272.4 1221.4 1099.5 1774.6 1624.9 TRUE FALSE FALSE 1759.391268 1424.576811 1876.399268 1741.043915 1516.3532 1191.097746 1325.145686 1131.312298 1615.875331 1582.684864 1.111649772 0.900101368 1.18557984 1.100057222 0.958089153 0.752580488 0.837277032 0.714805786 1.02097099 1 10.62815831 -8.419092332 3.34273138 1.05493586 0.774743223 0.730603247 0.077086175 0.099014166 2.068226255 0.011321297 0.026913278 3.81E-09 8.419092332 -0.280192636 NLFASFPTEESSINYTFKT(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 1 NLFASFPTEESSINYTFKTPEK 22 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 NLFASFPT(0.033)EES(0.273)S(0.117)INY(0.102)T(0.117)FKT(0.357)PEK 53.481 0.017671 151460000 906.98 1172.3 1184.6 906.64 1100.6 1017.5 737.71 696.45 1047.4 1228.8 TRUE FALSE FALSE 895.9253789 1188.80367 1205.217466 1011.469983 1044.432275 952.4850338 800.371069 716.6006819 953.7179207 1196.875599 0.748553467 0.993255833 1.006969703 0.845091991 0.872632274 0.795809552 0.668717008 0.598726119 0.79683964 1 10.22505749 -7.779734754 1.369019031 0.895828921 0.575883572 0.624464527 0.08158592 0.381119867 1.103280861 0.015582581 0.129412873 1.66E-08 7.779734754 -0.319945349 NLFNQELLSPS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 1 NLFNQELLSPSKR 13 1 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 NLFNQELLS(0.041)PS(0.959)KR 98.508 0.0041496 15876000 1515.6 1768.5 1998.2 1538 2003.6 1818.2 1338.5 1413.2 2162.2 1780.6 TRUE FALSE FALSE 1497.127284 1793.396989 2032.977833 1715.830797 1901.348816 1702.022888 1452.192157 1454.088712 1968.807417 1734.339755 0.863226066 1.03405171 1.172191219 0.989327951 1.096295469 0.981366473 0.837316998 0.838410529 1.135191309 1 10.76017083 -7.760194672 24.95387922 0.975886326 0.837863707 0.266097715 0.097611667 34.87624856 699108.2966 0.014274338 0.048081885 1.74E-08 7.760194672 -0.138022619 NLGES(ph)PTGSAESAGIALR ddPTM_HeLa_Romidepsin_16h_R1 1 NLGESPTGSAESAGIALR 18 0 P51788-4;P51788-5;P51788-3;P51788 P51788-4 CLCN2 Chloride channel protein 2 1 0 NLGES(0.859)PT(0.123)GS(0.018)AESAGIALR 148.19 6.25E-05 3609300 607.68 769.04 709.69 615.51 831.24 1034.5 806.3 1118.8 904.95 763.83 TRUE FALSE FALSE 600.2733624 779.8665653 722.0418567 686.6781623 788.818721 968.3987887 874.7871019 1151.170713 824.0090055 743.9855865 0.806834666 1.048228056 0.970505168 0.9229724 1.060260757 1.301636492 1.175811894 1.547302439 1.107560443 1 9.539130862 -7.248442526 0.593172834 0.914087814 1.892830746 0.705793021 0.107734359 1.181717092 0.277661842 0.018791244 0.792283035 5.64E-08 7.248442526 0.978742932 NLGIGK(ac)VSSFEEK ddPTM_HeLa_Romidepsin_16h_R1 1 NLGIGKVSSFEEK 13 1 G3XAL0;P40926-2;P40926 G3XAL0 MDH2 "Malate dehydrogenase;Malate dehydrogenase, mitochondrial" 0 1 NLGIGK(1)VSSFEEK 121.04 0.0075039 231730 127.05 0 0 0 146.71 112.88 0 64.447 0 0 FALSE TRUE FALSE 125.5014657 0 0 0 139.2228412 105.6673323 0 66.31167226 0 0 0 NLGS(ph)INTELQDVQR ddPTM_HeLa_Romidepsin_16h_R1 1 NLGSINTELQDVQR 14 0 A0A087X1A9;O75396 A0A087X1A9 SEC22B Vesicle-trafficking protein SEC22b 1 0 NLGS(0.976)INT(0.024)ELQDVQR 99.747 0.010361 6719600 976.42 1188.8 956.12 349.51 924.01 1791.6 1292.9 1970 1038.5 744.07 TRUE FALSE FALSE 964.5190175 1205.535958 972.7608675 389.9219907 876.8543217 1677.122542 1402.718894 2026.998842 945.613959 724.7389541 1.330850249 1.663407149 1.342222413 0.538017156 1.209889874 2.314105696 1.935481577 2.796867521 1.304764914 1 9.50131763 -8.266885844 6.91487618 1.167665263 2.310589637 0.711208743 0.335309184 0.05613157 17.4005663 0.048302041 0.11487672 5.41E-09 8.266885844 1.142924374 NLHVVFTMNPSSEGLKDR ddPTM_HeLa_Romidepsin_16h_R1 1 NLHVVFTMNPSSEGLKDR 18 1 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 41.359 0.026225 602460 388.97 297.42 382.27 254.37 282.54 366.51 376.41 268.96 281.59 407.06 FALSE FALSE TRUE 384.229084 301.6070866 388.923249 283.7814562 268.1209295 343.0911939 408.382256 276.7419333 256.4038851 396.4845225 0.969089743 0.760703305 0.980929209 0.715744096 0.67624564 0.865333132 1.030008065 0.697989247 0.646693302 1 8.631120739 -10.35375041 6.047072328 0.986300268 0.825169398 0 0.154271727 0.205848891 11.06913839 0.018654016 0.021263568 4.43E-11 10.35375041 -0.161130869 NLHYFNSDSFASHPNYPYSDEY ddPTM_HeLa_Romidepsin_16h_R1 2 NLHYFNSDSFASHPNYPYSDEY 22 0 S4R3Z2;A0A0A0MSS8;P42330;P42330-2 S4R3Z2 AKR1C3 Aldo-keto reductase family 1 member C3 0 0 ; ; 106.31 7.84E-05 36494000 1885.89 1471.93 1464.49 1520.12 3106.2 3225.5 2537.3 2037.18 3588.8 2184.9 FALSE FALSE TRUE 1862.904047 1492.651869 1489.978834 1695.883427 2947.679023 3019.40096 2752.818199 2096.122589 3267.80874 2128.135983 0.875368897 0.701389329 0.700133284 0.796886778 1.385099001 1.418800765 1.293534915 0.984957073 1.535526285 1 11.05537462 -8.762189771 24.99997011 0.890695635 1.282822238 0.291755118 0.250345599 11.04571224 368018.9191 0.024070549 0.045575033 1.73E-09 8.762189771 0.392126603 NLLDEELQR ddPTM_HeLa_Romidepsin_16h_R1 1 NLLDEELQR 9 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 169.65 3.35E-06 0 4270.4 3733.3 3587.4 3414 4040.4 3867.8 3847.9 4153.3 3852.1 3440 FALSE FALSE TRUE 4218.350722 3785.857495 3649.837192 3808.742743 3834.203311 3620.660063 4174.74053 4273.469183 3507.558528 3350.628304 1.258973046 1.129894799 1.089299338 1.136724936 1.14432368 1.08059138 1.245957519 1.275423233 1.046836059 1 11.71021594 -12.52525521 1.269298377 0.999579112 1.174899646 0.431541212 0.06668435 0.339199536 0.974722288 0.051488548 0.012212798 2.98E-13 12.52525521 0.175320534 NLLEDDS(ph)DEEEDFFLR ddPTM_HeLa_Romidepsin_16h_R1 5 NLLEDDSDEEEDFFLR 16 0 O75379 O75379 VAMP4 Vesicle-associated membrane protein 4 1 0 NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR;NLLEDDS(1)DEEEDFFLR ;;;; 210.57 8.96E-26 12709100 3382.57 4463.05 3743.45 4163.48 4653.14 5243.49 3252.5 5289.3 4503.91 4060.14 TRUE FALSE FALSE 3341.341936 4525.880935 3808.603177 4644.881147 4415.672903 4908.447912 3528.767269 5442.33755 4101.069009 3954.656977 0.844913214 1.144443364 0.963067897 1.174534523 1.116575452 1.24118171 0.892306789 1.376184479 1.037022688 1 11.94933685 -9.73253187 1.326527656 0.930814416 1.14510531 0.209914522 0.137856859 0.344347412 1.220166365 0.023107759 0.03494036 1.85E-10 9.73253187 0.214290894 NLLEENFEEHSMS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 NLLEENFEEHSMSPER 16 0 P38398-8;P38398-4;P38398;P38398-7;Q5YLB2 P38398-8 BRCA1 Breast cancer type 1 susceptibility protein 1 0 NLLEENFEEHS(0.103)MS(0.897)PER;NLLEENFEEHS(0.003)MS(0.997)PER ; 139.02 0.0002728 15251100 7404.3 7383.4 7586.7 4536.6 6457 6899.4 6212.4 6127.8 7345.9 7918.5 TRUE FALSE FALSE 7314.053544 7487.343699 7718.743331 5061.143037 6127.475196 6458.550607 6740.081101 6305.098225 6688.864306 7712.776228 0.94830361 0.970771545 1.000773665 0.656202499 0.794457795 0.837383377 0.873885213 0.817487509 0.8672447 1 12.91303454 -9.291674277 24.93221019 0.976247104 0.802443066 0.601741233 0.064698781 275.3415828 227050.5503 0.008721538 0.013323402 5.11E-10 9.291674277 -0.173804038 NLLPAYRPNLS(ph)PPAEAGLALPPTGYR ddPTM_HeLa_Romidepsin_16h_R1 1 NLLPAYRPNLSPPAEAGLALPPTGYR 26 1 F8WCX2;Q8N1G0-2;Q8N1G0;H0Y5I5 F8WCX2 ZNF687 Zinc finger protein 687 1 0 NLLPAY(0.172)RPNLS(0.828)PPAEAGLALPPTGYR 77.894 3.15E-05 13290000 598.75 713.35 654.09 735.65 589.59 759.42 431.15 811.77 543.05 702.73 TRUE FALSE FALSE 591.4522047 723.39256 665.4741621 820.7093143 559.5010222 710.8955129 467.7718702 835.2572842 494.4782479 684.4729733 0.864098697 1.056860663 0.972243154 1.199038306 0.817418721 1.038602751 0.683404442 1.220292571 0.722421874 1 9.418849767 -6.894677624 9.469660628 0.949069866 3.915926257 0.239189245 0.15223384 14630.17231 46569.41636 0.017269401 829487.5646 1.27E-07 6.894677624 2.966856391 NLLSVAYK ddPTM_HeLa_Romidepsin_16h_R1 1 NLLSVAYK 8 0 P62258;P62258-2;B4DJF2;I3L3T1;K7EIT4;P63104;E7EX29;E7ESK7;E5RGE1;E5RIR4;E9PD24;E7EVZ2;P31946-2;P31946;Q4VY20;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2;E9PG15;P27348;P61981;Q04917;A2IDB2;P31947-2;P31947 P62258;P63104;P31946-2;E9PG15;P61981;Q04917;P31947-2 YWHAE;YWHAZ;YWHAB;YWHAQ;YWHAG;YWHAH;SFN "14-3-3 protein epsilon;14-3-3 protein zeta/delta;14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed;14-3-3 protein theta;14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed;14-3-3 protein eta;14-3-3 protein sigma" 0 0 110.87 0.020223 11198000 1118.2 986.85 2517.6 2350.1 2731.9 2501.5 1686.1 802.27 1063.8 513.05 FALSE FALSE TRUE 1104.570948 1000.7429 2561.417772 2621.82962 2592.480949 2341.662223 1829.317292 825.4824167 968.6510637 499.720887 2.210375786 2.002603706 5.125696841 5.246588021 5.187857895 4.68594026 3.660678069 1.651886959 1.938384184 1 8.96497871 -9.849748897 5.678475093 1.601099564 4.334392669 0.573012928 1.042638751 0.112178954 5.717884396 0.183084165 0.242468615 1.41E-10 9.849748897 2.733293105 NLLVY(ph)S(ph)Y(ph)FEKS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 NLLVYSYFEKSR 12 1 M0R1H8 M0R1H8 ZNF431 4 0 NLLVY(1)S(1)Y(1)FEKS(1)R 49.216 0.0043435 0 207.67 526.11 305.16 316.38 367.83 385.78 462.96 431.09 472.19 393.2 TRUE FALSE FALSE 205.1388382 533.5165904 310.4711818 352.9613442 349.0582625 361.129903 502.2838108 443.562909 429.9561438 382.9846073 0.53563207 1.393049695 0.810662298 0.921607129 0.911415905 0.942935816 1.31149869 1.158174247 1.122646016 1 8.581142599 -7.724036937 0.603764328 0.820121701 1.397809457 0 0.237725313 2.401990715 0.825832911 0.047490577 0.862233027 1.89E-08 7.724036937 0.577687756 NLNK(ac)QLEK(ac)K(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NLNKQLEKKR 10 3 F8VWZ8;Q52LW3;Q52LW3-2 F8VWZ8 ARHGAP29 Rho GTPase-activating protein 29 0 3 NLNK(1)QLEK(1)K(1)R 77.288 0.0069308 0 0 61.213 79.818 720.49 2751.4 2804 2799.9 2306.1 70.483 119.33 FALSE TRUE FALSE 0 62.07475822 81.20719881 803.7964438 2610.985791 2624.833449 3037.723436 2372.823365 64.17882395 116.2297894 0 0.534069265 0.698678017 6.915580317 22.4639983 22.58313865 26.13549807 20.41493302 0.552171903 1 6.860836065 -8.859116794 2.685719817 0.552211075 23.48477253 0.982291562 1.419732222 0.022145723 0.324066068 0.203938414 0.404874329 1.38E-09 8.859116794 22.93256145 NLNNSNLFS(ph)PVNR ddPTM_HeLa_Romidepsin_16h_R1 3 NLNNSNLFSPVNR 13 0 P52948-6;P52948-2;P52948-5;P52948;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 0 NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR;NLNNSNLFS(1)PVNR ;; 174.47 2.87E-05 111308000 3682.6 3237.18 3054.41 2743.52 5815.2 7792.4 6627 7394.3 3708.2 3506.04 TRUE FALSE FALSE 3637.715055 3282.753105 3107.570725 3060.738691 5518.428644 7294.490789 7189.897215 7608.242404 3376.529305 3414.952575 1.0652315 0.961288051 0.909989423 0.896275607 1.615960551 2.136044536 2.105416417 2.22792037 0.98874852 1 11.73764983 -8.514761265 2.717214077 1.007010304 2.153706683 0.981642387 0.072939992 0.028087041 0.415097023 0.012154538 0.02858525 3.06E-09 8.514761265 1.14669638 up NLNVILAK ddPTM_HeLa_Romidepsin_16h_R1 2 NLNVILAK 8 0 A0A3B3IRQ7;P30533 A0A3B3IRQ7 LRPAP1 Alpha-2-macroglobulin receptor-associated protein 0 0 ; ; 131.04 0.013729 2036570 1920.6 1604.53 2058.38 2198.26 2275.3 2350 2083 2247.26 1803.12 1480.18 FALSE FALSE TRUE 1897.190988 1627.118615 2094.20524 2452.433164 2159.182951 2199.842584 2259.929968 2312.280923 1641.844431 1441.72471 1.315917647 1.128591751 1.45256943 1.701041223 1.497638859 1.525840938 1.56751837 1.603829709 1.138805779 1 10.49358 -10.53201254 0.287085523 0.934053812 1.677156187 0.749731696 0.111511186 0.530051676 0.150663468 0.149062841 0.132139559 2.94E-11 10.53201254 0.743102375 NLQAHYEDFLQDSR ddPTM_HeLa_Romidepsin_16h_R1 1 NLQAHYEDFLQDSR 14 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;E9PNZ4;E9PLY5;A0A5F9ZGX0;A0A669KBB0 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 0 0 70.438 0.026446 5097600 1487.6 1424.9 1359 1501.7 1574.8 1571.2 1533.8 1517.3 1436.6 1523.9 FALSE FALSE TRUE 1469.468559 1444.95978 1382.652825 1675.33362 1494.43208 1470.805391 1664.080934 1561.200682 1308.106898 1484.308858 0.990001879 0.973489966 0.931512884 1.1286961 1.006820158 0.990902522 1.121115005 1.051803116 0.881290232 1 10.53557561 -9.269211889 24.9965124 0.988830282 1.056491578 0.408332586 0.056028965 492.7244074 1584609.084 0.006673696 0.010310937 5.38E-10 9.269211889 0.067661296 PEPAK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 5 PEPAKSAPAPK 11 1 P06899;Q16778 P06899;Q16778 HIST1H2BJ;HIST2H2BE Histone H2B type 1-J;Histone H2B type 2-E 0 1 ;;;; PEPAK(1)SAPAPK;PEPAK(1)SAPAPK;PEPAK(1)SAPAPK;PEPAK(1)SAPAPK;PEPAK(1)SAPAPK 163.84 0.00052188 9091230200 11720.31 13305.15 14017.89 46328 103717.1 126722.7 119981.2 128658 3386.3 7830.15 FALSE TRUE FALSE 11577.45835 13492.46025 14261.8655 51684.66134 98424.02937 118625.5284 130172.4001 132380.5162 3083.420847 7626.721574 1.518012457 1.769103555 1.869986384 6.776786177 12.9051557 15.55393458 17.06793658 17.35746021 0.404291781 1 12.89684732 -8.800813451 1.383357089 1.227002479 17.12612677 0.9959035 0.441623974 0.014919038 0.057176479 0.061519732 0.153127808 1.58E-09 8.800813451 15.89912429 up NLQDGQIS(ph)DTGDLGEDIASN ddPTM_HeLa_Romidepsin_16h_R1 1 NLQDGQISDTGDLGEDIASN 20 0 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 NLQDGQIS(0.975)DT(0.025)GDLGEDIASN 126.14 0.00027932 14598000 6287.3 5656.8 6378.3 4594.3 4313.2 4212.2 3502.7 3620.6 6697 6283.9 TRUE FALSE FALSE 6210.667969 5736.436579 6489.311636 5125.514583 4093.081309 3943.054014 3800.219251 3725.356349 6098.003547 6120.643372 1.014708355 0.937227711 1.06023358 0.837414349 0.668733834 0.644222147 0.620885587 0.608654372 0.996301071 1 12.57946759 -8.915773141 2.295908524 1.004722001 0.627043783 0.965921902 0.032381583 0.032661076 0.34863144 0.004547206 0.009036631 1.21E-09 8.915773141 -0.377678218 NLQDGQISDT(ph)GDLGEDIASN ddPTM_HeLa_Romidepsin_16h_R1 1 NLQDGQISDTGDLGEDIASN 20 0 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 NLQDGQIS(0.291)DT(0.703)GDLGEDIAS(0.006)N 84.208 0.0066535 16366000 2266.8 2193.3 2151.5 1904.5 1733 1583.4 1116.5 1435.5 2416 1984.4 TRUE FALSE FALSE 2239.17137 2224.177335 2188.945955 2124.707251 1644.558543 1482.22585 1211.335482 1477.033928 2199.906909 1932.845002 1.158484704 1.150727209 1.132499478 1.099264167 0.850848641 0.766862241 0.626711134 0.764176086 1.138170369 1 10.91651023 -8.556431227 2.296064257 1.090105525 0.70688574 0.901199307 0.059318786 0.085665353 0.903074855 0.011294983 0.027078412 2.78E-09 8.556431227 -0.383219785 NLQDGQISDTGDLGEDIAS(ph)N ddPTM_HeLa_Romidepsin_16h_R1 2 NLQDGQISDTGDLGEDIASN 20 0 H0YHT2;A0A1B0GV47;Q7Z4S6-6;Q7Z4S6-3;Q7Z4S6-5;Q7Z4S6-2;Q7Z4S6;Q7Z4S6-4;H0YI78 H0YHT2 KIF21A Kinesin-like protein KIF21A 1 0 NLQDGQISDTGDLGEDIAS(1)N;NLQDGQISDTGDLGEDIAS(1)N ; 217.67 1.24E-35 8160900 10464.9 10788.6 10606.1 8073.2 7148.6 6371.9 5298.6 5579.3 11630.4 10735.8 TRUE FALSE FALSE 10337.34977 10940.48219 10790.69472 9006.66137 6783.780267 5964.756154 5748.662952 5740.728243 10590.1479 10456.88237 0.988569003 1.046247037 1.031922742 0.861314209 0.648738317 0.570414388 0.549749222 0.54899042 1.012744289 1 13.35216517 -8.806556224 2.045234424 1.001910216 0.556240797 0.989146575 0.021691731 0.024627653 0.209823962 0.003725651 0.008010369 1.56E-09 8.806556224 -0.44566942 NLQEAEEWYK ddPTM_HeLa_Romidepsin_16h_R1 3 NLQEAEEWYK 10 0 P08670;B0YJC4;B0YJC5;H7C5W5;P41219;P41219-2;F8W835 P08670 VIM;PRPH Vimentin;Peripherin 0 0 ;; ;; 179.42 9.04E-05 187355000 7625.5 7228.5 6754 5272.6 7383.2 6981.272 6416.82 7095.6 7603.6 6881.3 FALSE FALSE TRUE 7532.557473 7330.263013 6871.550537 5882.24282 7006.407753 6535.19125 6961.864531 7300.899991 6923.514972 6702.522834 1.123839136 1.093657298 1.02521852 0.87761623 1.045338886 0.975034537 1.038693146 1.089276407 1.032971486 1 12.71048851 -9.531651967 23.53730261 1.062594113 1.001988957 0.166544777 0.060458272 142.8788792 383321.2766 0.010905587 0.015440082 2.94E-10 9.531651967 -0.060605156 NLQLDYVDLYLIHFPVSVKPGEEVIPK ddPTM_HeLa_Romidepsin_16h_R1 1 NLQLDYVDLYLIHFPVSVKPGEEVIPK 27 1 P52895;S4R3P0;H0Y804 P52895 AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C2 0 0 120.42 1.89E-10 854180 178.3 167.62 277.57 50.105 102.86 1683.8 689.39 796.25 403.14 151 FALSE FALSE TRUE 176.126811 169.9797588 282.4009894 55.89837585 97.61067038 1576.210614 747.9467694 819.2882375 367.0821487 147.0769982 1.197514317 1.155719527 1.920089428 0.380061985 0.663670537 10.7169077 5.085409536 5.570471572 2.495850154 1 7.200427827 -8.284412129 24.96048346 1.084033496 6.920377687 0.757709351 1.516330401 226.0546719 245613.7 0.189288328 0.423517025 5.20E-09 8.284412129 5.836344191 NLQLLTQASSEGS(ph)P ddPTM_HeLa_Romidepsin_16h_R1 2 NLQLLTQASSEGSP 14 0 B8ZZB7;H0YEJ0 B8ZZB7 SAMD12 1 0 NLQLLTQAS(0.001)S(0.029)EGS(0.969)P;NLQLLTQASS(0.001)EGS(0.999)P ; 123.28 0.0036424 7305000 3614.8 3374.5 3687.6 3259.6 3465.7 3452.3 2866 3317.8 3998.8 3661.7 TRUE FALSE FALSE 3570.741427 3422.0063 3751.781131 3636.490289 3288.832397 3231.709172 3109.437968 3413.795308 3641.137313 3566.568506 1.00117001 0.959467425 1.051930203 1.019604778 0.92212792 0.906111621 0.871829032 0.957165214 1.020907717 1 11.80032097 -8.697752635 5.699171747 1.002588566 0.90926654 0.708661492 0.029520552 0.079985963 4.975321078 0.003983861 0.007998987 2.01E-09 8.697752635 -0.093322026 NLQYYDISAK ddPTM_HeLa_Romidepsin_16h_R1 1 NLQYYDISAK 10 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 0 169.37 0.016126 567510 646.58 390.65 548.11 477.16 523.93 491.84 574.33 404.5 545.97 485.79 FALSE FALSE TRUE 638.6992343 396.149581 557.6496246 532.3314843 497.191897 460.4130113 623.1135759 416.2035693 497.1370758 473.1691058 1.349832917 0.837226218 1.178541916 1.125034322 1.050769991 0.973041151 1.316894041 0.879608504 1.050654131 1 8.88621207 -10.27835272 24.98822573 1.165198863 1.066447281 0.036762257 0.158001159 1842.522031 2722184.579 0.029704823 0.034009213 5.27E-11 10.27835272 -0.098751582 NLRGY(ph)Y(ph)NQSEAVDVWLR ddPTM_HeLa_Romidepsin_16h_R1 1 NLRGYYNQSEAVDVWLR 17 1 A0A140T9Z4 A0A140T9Z4 2 0 NLRGY(0.969)Y(0.988)NQS(0.044)EAVDVWLR 61.03 0.019847 42673000 2852.8 786.34 1347.7 973.3 3128.8 2242.1 3365.4 2234.1 4062.7 2631.8 TRUE FALSE FALSE 2818.028976 797.4101152 1371.156153 1085.837526 2969.125661 2098.837046 3651.256992 2298.740159 3699.321937 2563.425457 1.099321601 0.31107209 0.53489215 0.423588493 1.158264873 0.81876266 1.424366362 0.896745467 1.443116642 1 11.32385723 NLS(ph)FNELYPSGTLK ddPTM_HeLa_Romidepsin_16h_R1 1 NLSFNELYPSGTLK 14 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 NLS(1)FNELYPSGTLK 169.02 6.75E-05 35267000 3854.4 3292.1 3812.2 2950.1 2519.1 2601.2 2787.6 2694.5 3681.8 3183.7 TRUE FALSE FALSE 3807.42109 3338.44627 3878.549742 3291.204443 2390.540927 2434.991715 3024.378674 2772.461106 3352.490587 3100.987015 1.227809427 1.076575379 1.25074685 1.06134093 0.770896787 0.785231187 0.975295498 0.894057632 1.081104361 1 11.59851177 -8.887942919 5.737988302 1.118732082 0.861092205 0.686886144 0.086671162 0.11716239 5.501274824 0.015942252 0.029232047 1.29E-09 8.887942919 -0.257639877 NLS(ph)PGAVESDVR ddPTM_HeLa_Romidepsin_16h_R1 2 NLSPGAVESDVR 12 0 A0A3B3IU78;A0A3B3ISK1;A0A3B3ITV3;A0A3B3ISC6;A0A3B3IT15;A0A3B3IS84;P53621;P53621-2 A0A3B3IU78 COPA Coatomer subunit alpha;Xenin;Proxenin 1 0 NLS(0.942)PGAVES(0.058)DVR;NLS(0.993)PGAVES(0.007)DVR ; 143.64 0.0015291 106580000 5068.2 5120.7 4514 4765.7 4888.1 5344 4083.3 4872.7 5580.2 5066.9 TRUE FALSE FALSE 5006.426829 5192.789349 4592.564276 5316.732657 4638.642017 5002.535647 4430.1354 5013.683887 5081.092936 4935.261208 1.014419829 1.052181259 0.930561541 1.077295088 0.939897975 1.013631384 0.897649631 1.015890279 1.029548938 1 12.26891073 -8.682564084 25 1.008810345 0.965177878 0.195938813 0.048324012 41.31302248 13092.15154 0.006036739 0.012073478 2.08E-09 8.682564084 -0.043632467 NLS(ph)SDEATNPISR ddPTM_HeLa_Romidepsin_16h_R1 2 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 NLS(0.5)S(0.5)DEATNPISR;NLS(0.405)S(0.405)DEAT(0.19)NPISR ; 187.08 1.71E-08 94792000 6596.9 6438.5 4981.4 5468.5 5323.9 4640.3 3986.4 4655.5 6857.1 6824.7 TRUE FALSE FALSE 6516.494445 6529.141372 5068.099177 6100.7937 5052.201517 4343.799806 4325.004716 4790.199547 6243.783802 6647.39331 0.980308241 0.982210781 0.762419033 0.917772338 0.76002747 0.653459123 0.650631686 0.720613227 0.939283041 1 12.698573 -9.056131035 0.698220276 0.996998819 0.651605353 0.787232312 0.061649691 0.202923707 0.186020507 0.011411398 0.034710397 8.79E-10 9.056131035 -0.345393466 NLSELQDT(ph)SLQQLVSQR ddPTM_HeLa_Romidepsin_16h_R1 1 NLSELQDTSLQQLVSQR 17 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 NLSELQDT(0.5)S(0.5)LQQLVSQR 88.283 0.021415 4359000 2065.4 1836.9 1945.1 1799.3 1452.2 1578.4 1044 1465.6 1718.6 1726.4 TRUE FALSE FALSE 2040.22611 1862.759926 1978.95365 2007.343532 1378.088815 1477.545334 1132.677334 1508.004824 1564.884112 1681.547879 1.21330242 1.107765024 1.176864289 1.193747473 0.819535877 0.878681691 0.67359208 0.89679565 0.930621204 1 10.71557414 -8.751308142 24.94178038 1.115816733 0.811292022 0.666836927 0.098975091 87.43542182 215253.0478 0.014411702 0.028559073 1.77E-09 8.751308142 -0.304524711 YSSSGTPSSAS(ph)PALSR ddPTM_HeLa_Romidepsin_16h_R1 2 YSSSGTPSSASPALSR 16 0 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 YSSSGTPSSAS(1)PALSR;YSSSGT(0.001)PS(0.03)S(0.091)AS(0.878)PALSR ; 233.47 1.17E-45 17811900 2782.9 3502.9 2276.93 2047.02 1915.18 1135.5 1033.94 1209.72 3390.8 2877.4 TRUE FALSE FALSE 2748.980944 3552.213918 2316.559012 2283.706084 1817.441218 1062.945215 1121.762838 1244.72134 3087.518356 2802.644733 0.980852447 1.26745066 0.826561777 0.814839661 0.648473635 0.379265057 0.400251528 0.444123839 1.101644571 1 11.45257316 -8.752169837 1.331388237 1.007584515 0.395009841 0.872877455 0.105025428 0.103530466 0.365603457 0.015707614 0.041330589 1.77E-09 8.752169837 -0.612574674 down NLSLSSSTPPLPS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 2 NLSLSSSTPPLPSPGR 16 0 E9PB87;O43516-2;O43516;O43516-3 E9PB87 WIPF1 WAS/WASL-interacting protein family member 1 1 0 NLSLSSSTPPLPS(1)PGR;NLSLSSSTPPLPS(1)PGR ; 111.63 0.0030225 20127700 2180.3 2106.3 1712.75 1981.52 2395.7 2043.49 1831.91 1906.44 1760.05 1879.84 TRUE FALSE FALSE 2153.725665 2135.952547 1742.559695 2210.632666 2273.438489 1912.917584 1987.51239 1961.599834 1602.62672 1831.001486 1.176255553 1.166548778 0.951697587 1.207335266 1.241636616 1.044738412 1.085478305 1.071326183 0.875273304 1 10.83841725 -12.48272175 1.22054433 0.999901823 1.123903329 0.338659017 0.090986623 0.550620185 1.465897916 0.057034334 0.013907145 3.29E-13 12.48272175 0.124001507 NLSLTDFVGDES(ph)PSPER ddPTM_HeLa_Romidepsin_16h_R1 1 NLSLTDFVGDESPSPER 17 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 NLSLTDFVGDES(0.5)PS(0.5)PER 156.13 5.77E-05 40803000 995.76 973.39 726.91 877.54 1329.3 1519.4 1066.3 1245.2 758.32 840.72 TRUE FALSE FALSE 983.6232941 987.09341 739.5615636 979.0053037 1261.460861 1422.315244 1156.871495 1281.227897 690.49396 818.8779732 1.201184213 1.20542186 0.903140135 1.195544801 1.540474774 1.736907439 1.412752001 1.564613947 0.843219604 1 9.677504671 -8.810064987 3.98688286 1.093044919 1.569370866 0.768632268 0.13617477 0.075202199 2.480100061 0.017993818 0.034596156 1.55E-09 8.810064987 0.476325947 NLSLTDFVGDESPS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 NLSLTDFVGDESPSPER 17 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 NLSLTDFVGDES(0.015)PS(0.985)PER;NLSLTDFVGDESPS(1)PER ; 190.37 2.92E-13 38965000 3311.78 2964.61 3830.85 2794.49 4175.23 4189.03 3308.15 4285.1 3429.13 3348.38 TRUE FALSE FALSE 3271.414752 3006.345857 3897.524337 3117.602082 3962.152433 3921.364502 3589.144178 4409.082608 3122.420024 3261.388605 1.003074196 0.921799338 1.195050578 0.955912484 1.214866707 1.202360398 1.100495713 1.351903481 0.957389751 1 11.67127064 -6.838506349 0.366356052 0.990002499 1.624560157 0.575521696 0.089205307 4.099529529 0.302676577 0.024455071 1.219027013 1.45E-07 6.838506349 0.634557658 NLSLTDFVGDESPS(ph)PERLK ddPTM_HeLa_Romidepsin_16h_R1 1 NLSLTDFVGDESPSPERLK 19 1 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 NLSLTDFVGDES(0.037)PS(0.962)PERLK 64.152 0.0093744 14066000 896.25 937.7 642.52 1298.5 1093.1 984.07 845.05 867.28 932.89 748.09 TRUE FALSE FALSE 885.3261603 950.9009652 653.7027911 1448.63868 1037.315028 921.1911029 916.8285259 892.3733785 849.4499819 728.654514 1.215014995 1.305009366 0.897136817 1.988100879 1.423603379 1.264235773 1.258248605 1.224686544 1.165778796 1 9.509091123 -10.88642045 0.596052314 1.022836531 1.367619532 0.140084579 0.25704408 0.80460932 0.661128001 0.107669635 0.077363743 1.30E-11 10.88642045 0.344783 NLSSDEAT(ph)NPISR ddPTM_HeLa_Romidepsin_16h_R1 2 NLSSDEATNPISR 13 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 NLS(0.033)S(0.294)DEAT(0.673)NPISR;NLS(0.201)S(0.201)DEAT(0.598)NPISR ; 211.82 6.71E-23 103635000 3596.9 3816.1 3498.8 3056.2 3043.9 2709 2066.32 2477.22 3662.1 3626.7 TRUE FALSE FALSE 3553.059599 3869.823156 3559.695146 3409.572224 2888.558425 2535.903643 2241.833169 2548.894452 3334.552604 3532.477811 1.005826445 1.09549822 1.007704885 0.965206975 0.817714528 0.717882398 0.634634749 0.721559933 0.943969865 1 11.78646478 -8.584013977 1.771347308 1.01173985 0.67827613 0.925458902 0.040365907 0.054936471 0.343481132 0.00532903 0.013786427 2.61E-09 8.584013977 -0.33346372 NLT(ph)EDNSQNQDLIAK ddPTM_HeLa_Romidepsin_16h_R1 1 NLTEDNSQNQDLIAK 15 0 B1AHE3;Q9UBB4-2;Q9UBB4 B1AHE3 ATXN10 Ataxin-10 1 0 NLT(0.869)EDNS(0.131)QNQDLIAK 96.229 0.022283 5957700 2012.3 2006.6 1766 2137.9 1717.2 1689.2 1292.2 1667 2251.6 2089.8 TRUE FALSE FALSE 1987.773314 2034.848967 1796.736489 2385.094057 1629.564876 1581.265572 1401.959436 1715.232015 2050.211257 2035.506695 0.976549632 0.999676873 0.882697411 1.171744639 0.800569647 0.776841253 0.688752063 0.842656042 1.00722403 1 10.99117225 -8.596790418 10.03357395 0.992097243 0.765885542 0.688330978 0.07536749 0.144040358 18.4897532 0.009678839 0.019370926 2.53E-09 8.596790418 -0.226211701 NLTANDPSQEYVAS(ph)EGEEDPEVEFLK ddPTM_HeLa_Romidepsin_16h_R1 1 NLTANDPSQEYVASEGEEDPEVEFLK 26 0 Q86X95 Q86X95 CIR1 Corepressor interacting with RBPJ 1 1 0 NLTANDPSQEY(0.147)VAS(0.853)EGEEDPEVEFLK 101.71 1.66E-06 40398000 4198.6 4132.2 3630.6 3352.2 4881 5244.7 4903.2 5717.4 4826.9 4485.3 TRUE FALSE FALSE 4147.425848 4190.37322 3693.78907 3739.797137 4631.904356 4909.580596 5319.677686 5882.823948 4395.169975 4368.771259 0.94933463 0.959165168 0.845498391 0.856029514 1.060230459 1.123789804 1.217659925 1.346562591 1.006042595 1 12.09301186 -7.886275843 1.340277644 0.957210132 1.341192676 0.842498593 0.059135459 0.17777302 0.517777458 0.009746611 0.067799878 1.30E-08 7.886275843 0.383982544 NLTDTDLIK ddPTM_HeLa_Romidepsin_16h_R1 1 NLTDTDLIK 9 0 H3BNK2;O43325 H3BNK2 LYRM1 LYR motif-containing protein 1 0 0 89.029 0.0031582 0 945.64 899.99 609.12 910.96 914.37 1080.7 821.38 900.91 781.04 914.33 FALSE FALSE TRUE 934.114176 912.6600828 619.7214781 1016.289481 867.7062869 1011.646758 891.1479967 926.9764094 711.1818262 890.5755748 1.04888816 1.024798017 0.695866242 1.14116029 0.974320778 1.135947118 1.000642755 1.040873381 0.798564262 1 9.798594234 NLVPGESVYGEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NLVPGESVYGEKR 13 1 M0R0P1;M0R299;M0QXL5;M0R2Q4;P22087;M0R2U2;M0R1H0;M0R2B0 M0R0P1 FBL rRNA 2-O-methyltransferase fibrillarin 0 1 NLVPGESVYGEK(1)R 160.22 6.43E-05 870480 533.86 363.95 586.46 259.14 971.11 727.07 956.16 632 1170.6 897.01 FALSE TRUE FALSE 527.353109 369.0736977 596.6670903 289.1029861 921.550633 680.6125735 1037.376207 650.2859229 1065.898604 873.7055509 0.603582189 0.422423432 0.682915531 0.330892926 1.054761106 0.778995364 1.187329307 0.744284985 1.219974628 1 9.771003346 NLVYDQS(ph)PNR ddPTM_HeLa_Romidepsin_16h_R1 2 NLVYDQSPNR 10 0 I3L533;I3L2R9;Q9NXR1;Q9NXR1-1;I3L2T8 I3L533 NDE1 Nuclear distribution protein nudE homolog 1 1 0 NLVYDQS(1)PNR;NLVYDQS(1)PNR ; 118.87 0.012537 61222000 5368.7 5014.9 5817.9 5875.3 5945.2 5658.9 4854.5 4619.1 5117.3 4833.7 TRUE FALSE FALSE 5303.264219 5085.499894 5919.158109 6554.62983 5641.794259 5297.314553 5266.841109 4752.746371 4659.595871 4708.119777 1.126408093 1.080155165 1.257223348 1.392196915 1.19831154 1.12514439 1.11867186 1.009478644 0.98969357 1 12.20093531 -11.31873951 0.740435214 1.012527214 1.176306346 0.318827744 0.09881923 0.598652428 0.702341919 0.045301946 0.025201163 4.80E-12 11.31873951 0.163779133 NLWEQICKEY(ph)EAEQPPFPEGY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 NLWEQICKEYEAEQPPFPEGYK 22 1 H3BV97;H3BU74;I3L193;Q8N0W5-2;Q8N0W5-3;Q8N0W5 H3BV97 IQCK IQ domain-containing protein K 2 0 NLWEQICKEY(1)EAEQPPFPEGY(1)K 43.116 0.022653 7255100 689.18 710.92 652.78 484.12 748.29 988.37 468.3 766.62 1144 1423.1 TRUE FALSE FALSE 680.7800091 720.9283504 664.1413621 540.0962323 710.101969 925.2163468 508.0773903 788.8009402 1041.677775 1386.127657 0.491138032 0.520102421 0.479134341 0.389643933 0.512291899 0.667482784 0.366544443 0.569068034 0.751502049 1 10.43684441 -12.15799285 0.672819452 1.043532187 0.490599407 0.625065366 0.109764911 0.250011915 0.181465594 0.079556073 0.017247403 6.95E-13 12.15799285 -0.55293278 NLYIISVK ddPTM_HeLa_Romidepsin_16h_R1 1 NLYIISVK 8 0 C9JD32;J3KT29;P62829;B9ZVP7 C9JD32 RPL23 60S ribosomal protein L23 0 0 158.07 0.0060467 4536500 1691.1 1459.9 1659.6 1458.8 1349.4 1306.5 1447.5 1436.4 1572 1185.5 FALSE FALSE TRUE 1670.488223 1480.452511 1688.484642 1627.47332 1280.535083 1223.018867 1570.450614 1477.959968 1431.396383 1154.700539 1.446685237 1.282109482 1.462270593 1.409433238 1.108975911 1.059165407 1.360050126 1.279950877 1.23962563 1 10.17330304 -12.48510241 1.229800179 1.000149446 1.312832031 0.12308495 0.145047149 0.368486408 0.997904326 0.096608044 0.023649172 3.27E-13 12.48510241 0.312682585 NLYPSS(ph)SPYTR ddPTM_HeLa_Romidepsin_16h_R1 2 NLYPSSSPYTR 11 0 Q9Y2Z0-2;Q9Y2Z0 Q9Y2Z0-2 SUGT1 Suppressor of G2 allele of SKP1 homolog 1 0 NLYPS(0.208)S(0.713)S(0.079)PYTR;NLYPS(0.116)S(0.426)S(0.426)PYT(0.032)R ; 127.52 0.006696 92165000 6250.1 5558.2 5951 5247.4 6866.7 7247 6610.5 7067.2 5907.5 5920.6 TRUE FALSE FALSE 6173.921377 5636.448485 6054.574659 5854.129078 6516.266676 6783.940089 7171.995705 7271.678282 5379.118404 5766.781958 1.0706008 0.977399272 1.049905251 1.015146596 1.12996585 1.176382277 1.243673813 1.260959463 0.93277645 1 12.49355076 -8.278919176 1.342187856 1.028792608 1.259751312 0.850909854 0.041371037 0.11027062 0.362785682 0.005068889 0.020449834 5.26E-09 8.278919176 0.230958704 NLYPSSS(ph)PYTR ddPTM_HeLa_Romidepsin_16h_R1 2 NLYPSSSPYTR 11 0 Q9Y2Z0-2;Q9Y2Z0 Q9Y2Z0-2 SUGT1 Suppressor of G2 allele of SKP1 homolog 1 0 NLYPS(0.061)S(0.211)S(0.728)PYTR;NLYPS(0.054)S(0.2)S(0.744)PYT(0.001)R ; 171.49 0.00027455 85219000 5651.1 4755.8 5601.8 4759.9 6735 7215.5 6026.7 6256 5414.7 5454.7 TRUE FALSE FALSE 5582.22222 4822.752277 5699.296979 5310.262034 6391.287818 6754.452837 6538.607748 6437.00749 4930.395671 5312.986108 1.050675102 0.907729134 1.072710687 0.99948728 1.202955869 1.271310088 1.230684142 1.211561137 0.927989566 1 12.37530723 -8.706125138 4.868381242 1.017191567 1.236413348 0.828618655 0.051995171 0.054194645 2.649192085 0.006314185 0.012697722 1.97E-09 8.706125138 0.219221782 NLYSDDIPHALR ddPTM_HeLa_Romidepsin_16h_R1 2 NLYSDDIPHALR 12 0 P60228;E5RIT4;H0YBR5 P60228 EIF3E Eukaryotic translation initiation factor 3 subunit E 0 0 ; ; 132.86 0.0014472 13913100 9142.4 8782.5 8209.5 8495.6 9055.9 9194.5 7261.7 8519.1 9908.1 9301 FALSE FALSE TRUE 9030.968912 8906.140266 8352.382904 9477.901245 8593.743631 8607.001124 7878.508617 8765.586718 9021.894721 9059.358679 0.99686625 0.983087278 0.92196183 1.046200022 0.948603972 0.950067375 0.869654122 0.967572543 0.995864613 1 13.14519321 -8.396964448 2.585244576 0.993777993 0.921090877 0.342798165 0.037559908 0.195979638 2.529152866 0.005031979 0.012857725 4.01E-09 8.396964448 -0.072687116 NMGGPYGGGNYGPGGS(ph)GGSGGYGGR ddPTM_HeLa_Romidepsin_16h_R1 5 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 0 NMGGPYGGGNYGPGGS(0.5)GGS(0.5)GGYGGR;NMGGPY(0.001)GGGNY(0.002)GPGGS(0.948)GGS(0.05)GGYGGR;NMGGPYGGGNYGPGGS(0.985)GGS(0.015)GGYGGR;NMGGPY(0.001)GGGNYGPGGS(0.978)GGS(0.021)GGYGGR;NMGGPYGGGNYGPGGS(0.681)GGS(0.319)GGYGGR ;;;; 203.59 5.12E-29 174007100 17934.6 17986 17407.9 18826 18017.2 18921 18261.1 14493.2 20517.6 20174.2 TRUE FALSE FALSE 17716.0062 18239.20738 17710.8772 21002.7507 17097.71505 17712.00916 19812.19738 14912.53788 18682.45447 19650.07138 0.901574649 0.928200566 0.901313632 1.068838392 0.870109565 0.901371238 1.008250657 0.758905023 0.950757588 1 14.26224693 NMGGPYGGGNYGPGGSGGS(ph)GGYGGR ddPTM_HeLa_Romidepsin_16h_R1 1 NMGGPYGGGNYGPGGSGGSGGYGGR 25 0 P22626;P22626-2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 1 0 NMGGPYGGGNYGPGGS(0.262)GGS(0.738)GGYGGR 118.08 1.95E-06 18283000 1337.6 1637.8 1522.9 1294.6 1617 1533.3 1378.6 1237.2 1717.9 1491 TRUE FALSE FALSE 1321.296817 1660.856991 1549.405436 1444.287743 1534.478456 1435.327078 1495.69825 1272.99643 1564.246721 1452.263605 0.909818859 1.143633281 1.066889944 0.994507979 1.056611521 0.988337843 1.029908237 0.876560168 1.077109359 1 10.50408763 KTVTPAK(ac)AVTTPGK ddPTM_HeLa_Romidepsin_16h_R1 1 KTVTPAKAVTTPGK 14 2 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 K(0.158)TVTPAK(0.842)AVTTPGK 93.106 0.026321 2537400 1779.2 1605.3 1951.7 3731.7 9899.1 11609 9222.2 11859 2270.4 2250.2 FALSE TRUE FALSE 1757.514426 1627.899456 1985.66852 4163.176712 9393.911988 10867.22237 10005.53344 12202.12145 2067.329738 2191.73948 0.801881082 0.742743137 0.905978351 1.899485204 4.28605319 4.95826373 4.56511074 5.567322927 0.943236985 1 11.09786061 -8.795699573 2.178655788 0.886599974 4.998849609 0.98403331 0.241104441 0.024372686 0.235897916 0.035318524 0.075187018 1.60E-09 8.795699573 4.112249635 up NMQIT(ph)INRDS(ph)GEDVS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 NMQITINRDSGEDVSSPK 18 1 A3KMH1-3;A3KMH1 A3KMH1-3 VWA8 von Willebrand factor A domain-containing protein 8 3 0 NMQIT(1)INRDS(0.985)GEDVS(0.872)S(0.143)PK 59.513 0.023737 3079300 1484.1 1392.8 1089.7 946.08 1239.5 1209.7 1191 1146.9 1368.4 1372.6 TRUE FALSE FALSE 1466.011218 1412.407875 1108.665771 1055.470221 1176.24369 1132.404074 1292.16351 1180.083742 1246.006877 1336.939654 1.096542551 1.056448487 0.829256405 0.789467361 0.879803128 0.847012108 0.966508478 0.882675399 0.931984382 1 10.38471863 -9.766986156 24.99988832 1.047677797 0.866679981 0.60350647 0.060221076 54.77774062 246888.8258 0.009196171 0.012276506 1.71E-10 9.766986156 -0.180997816 NMSDEEK(ac)QK ddPTM_HeLa_Romidepsin_16h_R1 2 NMSDEEKQK 9 1 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 0 1 ; NMSDEEK(1)QK;NMSDEEK(1)QK 154.85 0.0026726 1365660 261.545 475.1 349.33 311.67 585.69 502.77 485.03 309.37 588.66 187.618 FALSE TRUE FALSE 258.3571889 481.7884703 355.4099421 347.7067519 555.8000538 470.6446196 526.2284361 318.3211328 536.0087753 182.7436573 1.413768296 2.636416921 1.944855145 1.902702162 3.041419122 2.575436141 2.879598908 1.74189976 2.933118354 1 7.513677524 -10.3708913 0.833397466 1.076827376 2.498855103 0 0.728033993 0.231289803 0.329564496 0.104407465 0.116482064 4.26E-11 10.3708913 1.422027727 NMSEREVSTAPAGT(ph)DMPAAK ddPTM_HeLa_Romidepsin_16h_R1 1 NMSEREVSTAPAGTDMPAAK 20 1 A0A5F9ZI63 A0A5F9ZI63 1 0 NMS(0.006)EREVS(0.04)T(0.04)APAGT(0.914)DMPAAK 45.395 0.021383 7557900 1280.7 1268.9 1173.7 2357.3 1288.7 1411.2 924.32 1343.9 1392.5 966.13 TRUE FALSE FALSE 1265.090336 1286.763608 1194.127756 2629.862117 1222.93283 1321.028874 1002.831718 1382.783626 1267.951312 941.0298033 1.34436798 1.36739942 1.268958488 2.794664003 1.299568649 1.403811941 1.065674768 1.469436591 1.347408241 1 9.878096605 -11.07563093 0.769210419 1.050073146 1.536581733 0.077584221 0.454842611 0.777011102 1.004484163 0.160126575 0.109881253 8.40E-12 11.07563093 0.486508587 NMSVIAHVDHGK ddPTM_HeLa_Romidepsin_16h_R1 3 NMSVIAHVDHGK 12 0 P13639 P13639 EEF2 Elongation factor 2 0 0 ;; ;; 77.674 0.010967 13870600 12960.1 11097 10913.9 10896.3 19236.8 18695.8 15433.3 15051.6 18335.9 14621.7 FALSE FALSE TRUE 12802.13732 11253.22386 11103.85185 12156.18147 18255.07431 17501.19872 16744.20412 15487.0943 16695.89118 14241.82613 0.898911221 0.790153156 0.779664894 0.85355497 1.28179309 1.228859176 1.175706259 1.087437395 1.172313932 1 13.79784652 -8.764393284 24.99998977 0.91709039 1.194710956 0.583655301 0.114890123 36.21425139 306498.5423 0.014709611 0.027524474 1.72E-09 8.764393284 0.277620567 NMTVEQLLT(ph)GSPTSPTVEPEKPTR ddPTM_HeLa_Romidepsin_16h_R1 1 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 0 NMT(0.002)VEQLLT(0.578)GS(0.42)PTSPTVEPEKPTR 79.304 5.29E-05 0 1779.4 1499.8 1766.7 1608.6 1491.1 1574.9 1301.8 1223.7 2077.5 1714.3 TRUE FALSE FALSE 1757.711988 1520.914224 1797.448672 1794.593901 1415.003603 1474.268973 1412.37486 1259.105829 1891.683197 1669.762239 1.05267202 0.910856761 1.076469829 1.074760142 0.847428197 0.882921495 0.845853875 0.754062944 1.132905723 1 10.70542697 -8.749182429 24.39786261 1.023368395 0.837112398 0.715848994 0.063797704 64.88829989 129161.1452 0.007790661 0.015485981 1.78E-09 8.749182429 -0.186255997 NMTVEQLLTGS(ph)PTSPTVEPEKPTR ddPTM_HeLa_Romidepsin_16h_R1 4 NMTVEQLLTGSPTSPTVEPEKPTR 24 1 Q9C0C9;K7ES11 Q9C0C9 UBE2O E2/E3 hybrid ubiquitin-protein ligase UBE2O 1 0 NMT(0.001)VEQLLT(0.164)GS(0.748)PT(0.079)S(0.007)PT(0.001)VEPEKPTR;NMT(0.003)VEQLLT(0.172)GS(0.777)PT(0.031)S(0.007)PT(0.009)VEPEKPTR;NMTVEQLLT(0.114)GS(0.882)PT(0.004)SPTVEPEKPTR;NMTVEQLLT(0.08)GS(0.291)PT(0.291)S(0.291)PT(0.047)VEPEKPTR ;;; 129.42 3.00E-06 153208000 6328.43 6321.4 6808.2 5817.69 6090.4 5628.6 4756.22 5615 6965.5 6492.9 TRUE FALSE FALSE 6251.296661 6410.392835 6926.693865 6490.358691 5779.584162 5268.950625 5160.213208 5777.461166 6342.488235 6324.213522 0.988470209 1.013626882 1.095265655 1.026271278 0.913881883 0.833139268 0.815945444 0.91354619 1.002889642 1 12.62667036 -8.572410996 3.705807447 1.0062121 0.85214965 0.7967188 0.037975723 0.083030794 2.366886513 0.005958189 0.012784134 2.68E-09 8.572410996 -0.15406245 NNASTDYDLSDK ddPTM_HeLa_Romidepsin_16h_R1 2 NNASTDYDLSDK 12 0 B5MCW2;G5E9G0;P39023 B5MCW2 RPL3 60S ribosomal protein L3 0 0 ; ; 140.45 0.01994 25675000 3897.6 3494.5 3602.1 3349.8 3588.2 3807.5 2847.5 3899.1 3989 3531.5 FALSE FALSE TRUE 3850.094552 3543.695663 3664.793039 3737.119637 3405.080765 3564.213038 3089.366579 4011.914307 3632.213849 3439.751121 1.119294512 1.030218623 1.065423896 1.086450591 0.989920679 1.036183408 0.898136659 1.166338542 1.055952516 1 11.74808847 -8.758594629 24.99335933 1.058108813 1.014718426 0.060825411 0.068128738 156.798926 1377577.798 0.010189472 0.019671815 1.74E-09 8.758594629 -0.043390387 NNGAGYFLEHLAFK ddPTM_HeLa_Romidepsin_16h_R1 1 NNGAGYFLEHLAFK 14 0 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 0 97.69 0.0056577 3643000 2022.7 1894.5 2536.7 2483.3 2256.3 2700.8 2288.3 2570.1 2219.7 1325.9 FALSE FALSE TRUE 1998.046554 1921.170821 2580.850199 2770.43083 2141.152592 2528.227596 2482.668145 2644.461789 2021.164473 1291.452927 1.547130765 1.487604218 1.998408262 2.145204655 1.657940872 1.95766144 1.922383769 2.047664095 1.56503147 1 10.33477934 -10.99117568 0.39128182 0.936594685 2.018739211 0.521821146 0.228469804 0.329070177 0.129608504 0.143969183 0.083496719 1.02E-11 10.99117568 1.082144526 NNK(ac)K(ac)TNK(ac)NK ddPTM_HeLa_Romidepsin_16h_R1 2 NNKKTNKNK 9 3 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 0 3 ; NNK(1)K(1)TNK(1)NK;NNK(1)K(1)TNK(1)NK 169.76 0.00013624 7000200 2817.8 2754.7 3046.3 2509.5 930.88 959.29 788.08 703.51 3234.3 2395.2 FALSE TRUE FALSE 2783.45557 2793.480739 3099.319574 2799.660198 883.37372 897.994465 855.0194955 723.8649519 2945.016108 2332.972359 1.193094106 1.197391271 1.328485338 1.200040021 0.378647315 0.384914318 0.366493624 0.310275837 1.262345049 1 11.1879535 -8.757448967 24.99915792 1.12873586 0.362314208 0.947395644 0.095795135 20.42831577 127977.6267 0.016871545 0.032768477 1.75E-09 8.757448967 -0.766421652 NNK(ac)K(ac)TSK(ac)NK ddPTM_HeLa_Romidepsin_16h_R1 2 NNKKTSKNK 9 3 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 0 3 ; NNK(1)K(1)TSK(1)NK;NNK(1)K(1)TSK(1)NK 174.98 4.14E-05 21178000 3407 3313 4521.6 3150.9 1009.29 862.17 811.74 591.19 3850.4 2764.4 FALSE TRUE FALSE 3365.474174 3359.640501 4600.296551 3515.221883 957.7821651 807.0801195 880.6891753 608.2951499 3506.01058 2692.580489 1.249906618 1.247740045 1.708508462 1.305521561 0.355711619 0.299742245 0.327079981 0.225915308 1.302100566 1 11.39477376 -8.753812189 21.3919484 1.19249752 0.30372464 0.871356535 0.185411889 9.659018763 27088.74447 0.032197156 0.063197765 1.76E-09 8.753812189 -0.88877288 NNPS(ph)PPPDSDLER ddPTM_HeLa_Romidepsin_16h_R1 2 NNPSPPPDSDLER 13 0 E7ESD5;E9PLN6;F2Z2Y1;O95677-3;O95677-5;O95677-2;O95677-4;O95677 E7ESD5 EYA4 Eyes absent homolog;Eyes absent homolog 4 1 0 NNPS(1)PPPDSDLER;NNPS(0.998)PPPDS(0.002)DLER ; 149.32 0.0007677 110101000 4233 4622.4 4314.1 4296.4 3333.7 3030.3 2871.4 2725.9 4911.6 4471.6 TRUE FALSE FALSE 4181.406568 4687.474269 4389.185101 4793.169983 3163.568849 2836.67361 3115.296644 2804.769616 4472.294195 4355.427187 0.960045109 1.076237546 1.00775077 1.100505135 0.72635099 0.651296299 0.715267759 0.643971187 1.026832502 1 12.08859851 -8.670274982 5.944362043 0.998023083 0.678109995 0.923879914 0.048057615 0.043841662 2.32359494 0.007214578 0.014522161 2.14E-09 8.670274982 -0.319913088 NNS(ph)PPTVGAFGHTR ddPTM_HeLa_Romidepsin_16h_R1 1 NNSPPTVGAFGHTR 14 0 F5H1D4;Q86XL3-3;Q86XL3 F5H1D4 ANKLE2 Ankyrin repeat and LEM domain-containing protein 2 1 0 NNS(0.999)PPT(0.001)VGAFGHTR 79.332 0.0032472 0 2229.6 2233.4 2130.8 2528.5 2661.6 2075.9 2329.5 2144.7 2624.1 2357.8 TRUE FALSE FALSE 2202.424778 2264.841864 2167.88568 2820.857067 2525.76862 1943.25669 2527.367672 2206.753511 2389.393924 2296.544016 0.959017011 0.986195713 0.943977413 1.228305248 1.09981285 0.846165663 1.100509136 0.960901901 1.040430276 1 11.16524872 NNS(ph)RVSPVPLSGAAAGTEQK ddPTM_HeLa_Romidepsin_16h_R1 1 NNSRVSPVPLSGAAAGTEQK 20 1 Q96JM2;Q96JM2-3;H3BLX4;Q96JM2-2;H0Y6H9 Q96JM2 ZNF462 Zinc finger protein 462 1 0 NNS(0.512)RVS(0.487)PVPLS(0.001)GAAAGTEQK 54.225 0.015892 7378000 3389.5 3120.5 2972.3 3200.3 2136.9 1707.2 1468.3 1579.7 3559.6 3634.2 TRUE FALSE FALSE 3348.18747 3164.430481 3024.031635 3570.333744 2027.846019 1598.11543 1593.017365 1625.406127 3241.220461 3539.78296 0.945873662 0.893961725 0.854298602 1.008630694 0.572872982 0.451472717 0.450032497 0.459182426 0.91565514 1 11.78944519 -8.664885867 3.953260524 0.959596647 0.460635415 0.953078646 0.049470379 0.033660625 0.987331926 0.008005329 0.016478525 2.16E-09 8.664885867 -0.498961232 NNSFT(ph)APSTVGK ddPTM_HeLa_Romidepsin_16h_R1 1 NNSFTAPSTVGK 12 0 O95453;O95453-3;O95453-2;A0A494C0W0;A0A494C0K5;A0A494C0Q6;O95453-4 O95453 PARN Poly(A)-specific ribonuclease PARN 1 0 NNS(0.022)FT(0.977)APSTVGK 138.31 0.004705 15700000 2815.2 2865.3 1854 1902.2 2243.8 1750.6 1444.3 1885.1 2251.5 2602.6 TRUE FALSE FALSE 2780.88726 2905.637769 1886.268092 2122.141314 2129.290513 1638.74231 1566.978806 1939.642394 2050.120201 2534.984077 1.097003837 1.146215393 0.744094651 0.837141871 0.839962086 0.646450731 0.618141479 0.765149735 0.808730997 1 11.30776097 -9.750579245 24.99208972 1.054617879 0.740659839 0.591054117 0.108303994 74.86296324 172279.3917 0.013483453 0.018961305 1.78E-10 9.750579245 -0.31395804 NNSRVS(ph)PVPLSGAAAGTEQK ddPTM_HeLa_Romidepsin_16h_R1 1 NNSRVSPVPLSGAAAGTEQK 20 1 Q96JM2;Q96JM2-3;H3BLX4;Q96JM2-2;H0Y6H9 Q96JM2 ZNF462 Zinc finger protein 462 1 0 NNS(0.088)RVS(0.909)PVPLS(0.002)GAAAGTEQK 58.479 0.010711 5866200 1168.3 1145.7 1178.6 1248 854.73 874.13 486.87 794.74 1439.1 1155 TRUE FALSE FALSE 1154.06031 1161.829195 1199.113039 1392.299632 811.1099387 818.2759141 528.2247256 817.734548 1310.383292 1124.992933 1.025837831 1.032743549 1.065884952 1.237607447 0.720991141 0.727360937 0.469536039 0.72687972 1.164792465 1 10.13570022 -8.614583979 6.261482563 1.03239007 0.640002552 0.798368965 0.103301128 0.066408194 3.741537259 0.013485765 0.027183654 2.43E-09 8.614583979 -0.392387518 NNTAAET(ph)EDDES(ph)DGEDRGGGTSGSLR ddPTM_HeLa_Romidepsin_16h_R1 1 NNTAAETEDDESDGEDRGGGTSGSLR 26 1 Q6KC79 Q6KC79 NIPBL Nipped-B-like protein 2 0 NNT(0.308)AAET(0.692)EDDES(0.997)DGEDRGGGT(0.002)S(0.001)GSLR 63.09 0.0021711 5608700 853.96 841.21 981.12 575.93 757.16 754.07 659.41 787.44 716.31 726.33 TRUE FALSE FALSE 843.5516071 853.0525765 998.195982 642.5217364 718.5192998 705.8873606 715.4202689 810.223334 652.2414396 707.4598419 1.192366771 1.205796465 1.4109578 0.908209482 1.01563263 0.997777286 1.011252126 1.145256997 0.921948358 1 9.466504447 NNTAAETEDDES(ph)DGEDRGGGT(ph)SGVR ddPTM_HeLa_Romidepsin_16h_R1 1 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 2 0 NNTAAET(0.025)EDDES(0.99)DGEDRGGGT(0.727)S(0.259)GVR 75.73 0.00034545 11674000 1901.6 1701.3 1571 1613.3 1248 1380.4 1090.4 1282.4 1809.6 1549.3 TRUE FALSE FALSE 1878.422568 1725.250946 1598.342596 1799.837337 1184.309903 1292.196895 1183.018549 1319.504221 1647.744844 1509.048963 1.244772446 1.143270357 1.059172125 1.192696447 0.784805485 0.856298852 0.783949745 0.874394571 1.091909464 1 10.5594239 -8.757602486 24.99997429 1.120703407 0.824185282 0.818449136 0.068550626 42.74931645 278536.8233 0.014118487 0.027407723 1.75E-09 8.757602486 -0.296518124 NNTAAETEDDES(ph)DGEDRGGGTSGSLR ddPTM_HeLa_Romidepsin_16h_R1 1 NNTAAETEDDESDGEDRGGGTSGSLR 26 1 Q6KC79 Q6KC79 NIPBL Nipped-B-like protein 1 0 NNTAAETEDDES(1)DGEDRGGGTSGSLR 80.245 2.62E-05 9795100 444.17 384.25 483.16 413.85 305.66 434.38 377.14 143.97 420.42 553 TRUE FALSE FALSE 438.7562852 389.6594816 491.5691971 461.7012842 290.0610296 406.6245199 409.1742622 148.1355448 382.8165822 538.6329803 0.814573747 0.723422991 0.912623651 0.857172325 0.538513311 0.754919462 0.759653191 0.275021304 0.710718794 1 9.073158758 -6.744426888 0.221442271 0.984101552 8.44E-24 0.385181505 0.151830418 8.698246492 0.29824432 0.117382833 2.445726416 1.80E-07 6.744426888 -0.984101552 NNTAAETEDDES(ph)DGEDRGGGTSGVR ddPTM_HeLa_Romidepsin_16h_R1 2 NNTAAETEDDESDGEDRGGGTSGVR 25 1 A0A590UJS4;Q6KC79-2 A0A590UJS4 NIPBL Nipped-B-like protein 1 0 NNTAAETEDDES(1)DGEDRGGGTSGVR;NNTAAETEDDES(0.975)DGEDRGGGT(0.023)S(0.002)GVR ; 125.79 4.45E-07 40896000 2399.69 2156.57 1842.32 1725.11 1697.3 1590.9 1820.52 1918.29 2431.1 2486.64 TRUE FALSE FALSE 2370.441655 2186.930249 1874.384807 1924.575335 1610.680448 1489.246624 1975.154923 1973.792695 2213.656327 2422.036734 0.978697648 0.902930256 0.773887852 0.7946103 0.665010743 0.614873674 0.81549338 0.814930949 0.913964803 1 11.24200503 -9.847723568 1.530108614 0.99248767 0.731832914 0.705242475 0.064616938 0.123256172 0.580897921 0.011060552 0.015610321 1.42E-10 9.847723568 -0.260654755 NNTAASPMSTAT(ph)SSSGRSTGK ddPTM_HeLa_Romidepsin_16h_R1 1 NNTAASPMSTATSSSGRSTGK 21 1 O75486 O75486 SUPT3H Transcription initiation protein SPT3 homolog 1 0 NNT(0.021)AAS(0.021)PMS(0.031)T(0.038)AT(0.635)S(0.189)S(0.058)S(0.005)GRS(0.001)TGK 51.827 0.027168 6215100 3668.9 2721.6 3212.7 403.99 3606.1 3858.8 2954.9 3848.2 3516.7 3156.9 TRUE FALSE FALSE 3624.182036 2759.914756 3268.615696 450.7012246 3422.067261 3612.235134 3205.889132 3959.541596 3202.157544 3074.883283 1.178640521 0.897567323 1.063004802 0.146575067 1.112909644 1.174755203 1.042605145 1.287704681 1.041391575 1 11.58631593 -10.24967181 23.53071654 1.084358026 0.950585212 0.028259592 0.296386841 986.3194374 1972267.602 0.049922575 0.060842322 5.63E-11 10.24967181 -0.133772815 NNVGERDDDVPADMVAEES(ph)GPGAQNSPYQLR ddPTM_HeLa_Romidepsin_16h_R1 1 NNVGERDDDVPADMVAEESGPGAQNSPYQLR 31 1 Q86XK2-4;Q86XK2;Q86XK2-5 Q86XK2-4 FBXO11 F-box only protein 11 1 0 NNVGERDDDVPADMVAEES(0.845)GPGAQNS(0.147)PY(0.008)QLR 59.011 0.001304 4688300 433.87 344.27 262.51 500.19 300.81 382.42 151.07 205.04 291.76 389 TRUE FALSE FALSE 428.5818256 349.1166421 267.0788764 558.0243213 285.4585432 357.9845962 163.901882 210.9725089 265.6642549 378.8937239 1.131139944 0.921410464 0.704891265 1.47277267 0.753400031 0.944815323 0.432580092 0.556811833 0.701157708 1 8.565649433 -7.920486117 1.788267547 1.042211595 0.470127702 0.327912496 0.234012167 0.223397281 1.322473496 0.028072993 0.139555241 1.20E-08 7.920486117 -0.572083893 NNVS(ph)SVS(ph)TTGT(ph)AT(ph)DLESS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 NNVSSVSTTGTATDLESSAK 20 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 5 0 NNVS(0.474)S(0.474)VS(0.443)T(0.443)T(0.443)GT(0.799)AT(0.91)DLES(0.204)S(0.811)AK 42.068 0.026623 10509000 598.31 870.82 757.63 751.55 647.46 840.97 474.16 792.63 1064.2 837.29 TRUE FALSE FALSE 591.0175676 883.0794268 770.8162323 838.4477471 614.4177002 787.2347311 514.4351386 815.5634985 969.0152867 815.5370851 0.724697354 1.082819461 0.945163925 1.028092729 0.753390264 0.965296055 0.630793066 1.000032388 1.188192793 1 9.671606672 -8.73080402 24.99956762 0.900849367 0.831758981 0.023302571 0.163514987 589.5084773 481057.9646 0.021893748 0.043783483 1.86E-09 8.73080402 -0.069090385 NPDDITNEEYGEFYK ddPTM_HeLa_Romidepsin_16h_R1 4 NPDDITNEEYGEFYK 15 0 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ;;; ;;; 242.07 5.23E-46 125137000 10929.2 10580.5 9508.6 10854.2 12350.2 13228.2 12471 14102.8 11493.8 10701.7 FALSE FALSE TRUE 10795.99071 10729.45256 9674.093194 12109.21367 11719.92321 12382.96071 13530.28643 14510.84227 10465.76574 10423.66829 1.035718943 1.029335571 0.928089126 1.161703667 1.124356885 1.18796573 1.298035015 1.392105146 1.004038641 1 13.34757546 -7.624281219 0.623053247 1.011043019 1.542261296 0.88761903 0.046447089 0.510260832 0.176298798 0.008292641 0.176530576 2.38E-08 7.624281219 0.531218276 NPDDITQEEYGEFYK ddPTM_HeLa_Romidepsin_16h_R1 3 NPDDITQEEYGEFYK 15 0 P08238 P08238 HSP90AB1 Heat shock protein HSP 90-beta 0 0 ;; ;; 174.94 4.96E-05 139593000 12028.9 12421.7 12537.2 11892.3 12669.9 12294.9 11162.8 12765.8 12882 12096.5 FALSE FALSE TRUE 11882.28714 12596.57302 12755.40471 13267.34368 12023.30773 11509.29557 12110.96795 13135.15828 11729.80166 11782.23119 1.008492106 1.069116097 1.082596709 1.126046796 1.020461026 0.97683498 1.027901062 1.11482775 0.995550119 1 13.52432515 -10.30662905 6.877579718 1.003895451 1.057186508 0.286832569 0.041974199 0.254466317 31.90616057 0.007577651 0.008682982 4.94E-11 10.30662905 0.053291057 NPDELAEALDER ddPTM_HeLa_Romidepsin_16h_R1 1 NPDELAEALDER 12 0 K7EM11;O14908-2;O14908 K7EM11 GIPC1 PDZ domain-containing protein GIPC1 0 0 152.96 0.014503 5118500 900.06 689.01 534.81 729.2 840.91 1048.3 1110.5 1127.7 785.15 512.67 FALSE FALSE TRUE 889.0897225 698.7099009 544.1181437 813.513535 797.9952248 981.3170132 1204.825842 1160.32822 714.9242176 499.3507595 1.780491379 1.399236684 1.089651179 1.629142481 1.598065507 1.965185783 2.41278464 2.323673687 1.43170748 1 8.963909755 -4 0.237669435 1.212396429 8.692666491 0.715864501 0.238415055 23.99166584 0.295037884 0.190213665 71.34227346 1.00E-04 4 7.480270062 up NPDVDTSFLPDRDREEEENR ddPTM_HeLa_Romidepsin_16h_R1 2 NPDVDTSFLPDRDREEEENR 20 2 B0S8I6;Q14320;Q9Y247 B0S8I6 FAM50A;FAM50B Protein FAM50A;Protein FAM50B 0 0 ; ; 63.998 0.0053787 20432800 3959.4 4244.6 4240.4 3531.6 4623.4 4686.1 4381.5 4737.9 5359.3 4840.4 FALSE FALSE TRUE 3911.14131 4304.35559 4314.202383 3939.940209 4387.450646 4386.673334 4753.664501 4874.983661 4879.950785 4714.64571 0.829572687 0.912975408 0.915063962 0.835681078 0.930600286 0.930435414 1.008276081 1.034008484 1.035062035 1 12.20293365 -7.7419053 2.28339523 0.911277136 1.034457425 0.289564826 0.059982893 0.305731122 3.00779478 0.009473909 0.050684886 1.81E-08 7.7419053 0.123180289 NPEAALS(ph)PTFR ddPTM_HeLa_Romidepsin_16h_R1 1 NPEAALSPTFR 11 0 B4E349;F5H6D8;B4DTN4;Q86U44 B4E349 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 0 NPEAALS(0.997)PT(0.003)FR 171.99 0.00024739 37597000 1740.7 1973.6 1743 1801 1882.9 2199.8 2367 1927 2062.1 1802.3 TRUE FALSE FALSE 1719.483679 2001.384393 1773.336184 2009.240094 1786.808587 2059.23988 2568.052921 1982.754705 1877.660611 1755.475986 0.979497124 1.140080758 1.010173991 1.144555727 1.017848493 1.173037909 1.462881259 1.129468429 1.069601992 1 10.77764655 -8.339806233 0.77166633 0.999500934 1.320450847 0.392812884 0.10457944 0.513131598 0.467164721 0.016756668 0.103988622 4.57E-09 8.339806233 0.320949914 NPEFFEHR ddPTM_HeLa_Romidepsin_16h_R1 2 NPEFFEHR 8 0 O43252 O43252 PAPSS1 Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1;Sulfate adenylyltransferase;Adenylyl-sulfate kinase 0 0 ; ; 114.5 0.009736 12894900 4769.1 3996.5 4819.4 5675.5 5619.7 5626.8 4549 4992.7 5473.1 4493.5 FALSE FALSE TRUE 4710.972375 4052.762832 4903.279635 6331.728014 5332.905739 5267.26564 4935.391946 5137.155897 4983.572228 4376.758222 1.076361118 0.92597366 1.120299406 1.44667073 1.218460209 1.203462785 1.127636414 1.173735362 1.138644626 1 12.09564697 -9.519567031 24.98911233 1.028540329 1.231321304 0.502896212 0.093342291 77.51761147 584923.9276 0.013874907 0.019856164 3.02E-10 9.519567031 0.202780976 NPGFEIIHGLLDR ddPTM_HeLa_Romidepsin_16h_R1 1 NPGFEIIHGLLDR 13 0 Q9NSD9-2;Q9NSD9 Q9NSD9-2 FARSB Phenylalanine--tRNA ligase beta subunit 0 0 124.81 0.0017771 3719100 2770.8 2645.9 3259.1 3358.7 3358.9 3402.8 2747.4 2757.2 2800.7 2420.3 FALSE FALSE TRUE 2737.028424 2683.14905 3315.823268 3747.048697 3187.482799 3185.372062 2980.764087 2836.975232 2550.198378 2357.420257 1.161026938 1.138171712 1.406547372 1.589469967 1.352106308 1.351210949 1.26441778 1.203423625 1.081775033 1 11.20299326 -9.866712098 4.111146916 1.079152291 1.366127755 0.625020605 0.101322761 0.120475853 3.745869856 0.019207793 0.02566312 1.36E-10 9.866712098 0.286975464 NPLPPILGS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 NPLPPILGSPTK 12 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 0 NPLPPILGS(0.982)PT(0.018)K 94.532 0.022366 35673000 1375.6 847.34 933.47 1073.6 1308.5 1573.6 1352.9 1653 1725.5 1216.6 TRUE FALSE FALSE 1358.833658 859.2688748 949.7166538 1197.734683 1241.722362 1473.052039 1467.815292 1700.826947 1571.166958 1184.992557 1.146702273 0.725125968 0.801453687 1.010752917 1.047873554 1.243089697 1.238670474 1.435306017 1.325887618 1 10.21066228 -7.93163293 1.425341779 1.016232549 1.39246926 0.432545102 0.160792984 0.361704387 1.252325634 0.022412253 0.135529934 1.17E-08 7.93163293 0.37623671 NPLPPSVGVVDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 NPLPPSVGVVDKK 13 1 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 NPLPPSVGVVDK(1)K 86.772 0.021755 355770 0 146.37 0 0 189.95 131.44 75.663 155.07 0 214.31 FALSE TRUE FALSE 0 148.4306007 0 0 180.2561427 123.0414082 82.08981333 159.5567058 0 208.7421953 0 0.711071379 0 0 0.863534766 0.589441957 0.393259318 0.764372079 0 1 7.705578447 -12.5767503 1.366487687 0.999167001 0.361918713 0 0.438221651 0.395517968 1.326893163 0.230154082 0.054101155 2.65E-13 12.5767503 -0.637248288 NPNNEFWEANRDIYLS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 NPNNEFWEANRDIYLSPDR 19 1 Q15696 Q15696 ZRSR2 U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 2 1 0 NPNNEFWEANRDIY(0.025)LS(0.975)PDR 60.352 0.013344 3277500 697.1 1010.7 1128.9 652.97 766.66 864.11 834.86 861.28 1052.6 1206.6 TRUE FALSE FALSE 688.6034771 1024.928661 1148.548031 728.4694637 727.5344794 808.8961598 905.7729876 886.1997779 958.4528197 1175.252358 0.585919673 0.87209241 0.977277793 0.619840887 0.619045326 0.688274441 0.770705101 0.754050627 0.815529374 1 10.19875486 -9.231122408 24.96391176 0.81742633 0.690765231 0.300570548 0.116639879 1184.432825 975299.0407 0.025429148 0.042165492 5.87E-10 9.231122408 -0.126661099 NPPGFAFVEFEDPRDAEDAVR ddPTM_HeLa_Romidepsin_16h_R1 1 NPPGFAFVEFEDPRDAEDAVR 21 1 Q16629-4;Q16629;A0A0B4J1Z1;C9JAB2;Q16629-3;Q16629-2 Q16629-4 SRSF7 Serine/arginine-rich splicing factor 7 0 0 93.5 0.0010144 22894000 295.47 355.12 426.15 430.53 330.39 446.82 355.48 223.55 424.1 479.66 FALSE FALSE TRUE 291.868698 360.1193887 433.566962 480.3099043 313.5289654 418.269644 385.6744623 230.0180665 386.1674338 467.1983641 0.624721147 0.770806185 0.928014726 1.028064183 0.671083183 0.895272065 0.825504736 0.492334914 0.826559902 1 8.867891412 -12.6126132 1.43496114 0.999366646 0.769954198 0.063229325 0.156453029 0.495515533 1.839799326 0.107719417 0.025056483 2.44E-13 12.6126132 -0.229412448 NPPPQDYES(ph)DDDSYEVLDLTEYAR ddPTM_HeLa_Romidepsin_16h_R1 1 NPPPQDYESDDDSYEVLDLTEYAR 24 0 Q8IVP5 Q8IVP5 FUNDC1 FUN14 domain-containing protein 1 1 0 NPPPQDY(0.079)ES(0.888)DDDS(0.008)Y(0.025)EVLDLTEYAR 100.14 8.75E-06 1635300 383.08 462.03 459.94 677.7 418.13 499.63 195.32 433.47 534.14 525.96 TRUE FALSE FALSE 378.4108736 468.5344705 467.9450628 756.0588627 396.7912658 467.7052555 211.9104759 446.0117705 486.3651806 512.2954834 0.738657447 0.91457857 0.913428047 1.475825744 0.774535944 0.912959943 0.413648925 0.870614294 0.949384089 1 9.000832362 -7.845065303 13.03927767 0.917025824 0.642253613 0.235514581 0.218345017 0.772296305 117.1658198 0.030976143 0.092978334 1.43E-08 7.845065303 -0.274772211 NPQMPQYSSPQPGSALS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 NPQMPQYSSPQPGSALSPR 19 0 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3;A0A087WUV6 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 NPQMPQY(0.003)S(0.001)SPQPGS(0.022)ALS(0.974)PR;NPQMPQY(0.014)S(0.009)S(0.126)PQPGS(0.034)ALS(0.816)PR;NPQMPQYSSPQPGS(0.053)ALS(0.947)PR;NPQMPQY(0.002)S(0.001)S(0.002)PQPGS(0.022)ALS(0.973)PR ;;; 120.15 0.0011822 38380800 5880.2 5868.3 5510.5 5681.51 4136.2 4459.8 4083.66 4190.96 5891.82 5362.9 TRUE FALSE FALSE 5808.529861 5950.914081 5606.407941 6338.432919 3925.11428 4174.833173 4430.525978 4312.218815 5364.840863 5223.571085 1.111984458 1.139242481 1.073290255 1.213429054 0.751423541 0.799229704 0.848179513 0.8255308 1.027044674 1 12.35082072 -8.750124118 24.99994155 1.073044552 0.808607093 0.836972336 0.061861324 77.91225025 172138.2677 0.010260447 0.020374028 1.78E-09 8.750124118 -0.264437458 NPSDSAVHS(ph)PFTK ddPTM_HeLa_Romidepsin_16h_R1 1 NPSDSAVHSPFTK 13 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 NPSDSAVHS(0.999)PFT(0.001)K 107.63 0.0034704 24457000 6934.5 6112.3 6728.8 5337 9975.6 11098 8786.9 7930.4 9308.7 8258.8 TRUE FALSE FALSE 6849.979647 6198.34912 6845.911941 5954.089051 9466.507908 10388.87362 9533.259067 8159.853612 8476.106558 8044.235185 0.851538958 0.770533056 0.851033291 0.740168445 1.176806457 1.29146816 1.185104469 1.01437283 1.053687064 1 12.97373955 -8.739429536 24.88869618 0.896551507 1.177130764 0.623812743 0.109295207 121.4876773 137377.373 0.016378683 0.032735811 1.82E-09 8.739429536 0.280579257 NPSS(ph)SVPPPSAGSVK ddPTM_HeLa_Romidepsin_16h_R1 1 NPSSSVPPPSAGSVK 15 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 NPS(0.216)S(0.391)S(0.391)VPPPS(0.001)AGSVK 99.069 0.0083937 3855400 1164.9 2071.8 946.91 1195.6 1470.3 802.05 639.72 929.85 1024.8 1016.2 TRUE FALSE FALSE 1150.701751 2100.966855 963.3905713 1333.840897 1395.265105 750.8015935 694.0578008 956.7537427 933.1393213 989.7989775 1.162561062 2.122619747 0.973319425 1.34758767 1.409644924 0.758539472 0.701210869 0.966614196 0.942756401 1 9.950991742 -8.243722325 24.13523721 1.190945025 0.798030373 0.26705963 0.335553665 641.9841793 874546.8909 0.048112188 0.122333293 5.71E-09 8.243722325 -0.392914652 NPVSLPSLPNPTKPNNVPSVPS(ph)PSIQR ddPTM_HeLa_Romidepsin_16h_R1 1 NPVSLPSLPNPTKPNNVPSVPSPSIQR 27 1 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 0 NPVS(0.004)LPS(0.085)LPNPT(0.056)KPNNVPS(0.148)VPS(0.515)PS(0.19)IQR 43.438 0.02359 11333000 659.33 770.8 585.8 689.79 718.16 622.04 415.01 440.81 666.58 855.75 TRUE FALSE FALSE 651.2938324 781.6513426 595.9956033 769.5467654 681.5096154 582.2936515 450.260939 453.5641419 606.9594153 833.5174916 0.781379922 0.937774372 0.715036708 0.923252089 0.81763085 0.698597999 0.540193749 0.544156717 0.728190376 1 9.703068665 -6.489451916 0.28256633 0.936939178 1.00E-41 0.524681255 0.102398186 5.939100836 0.251992184 0.045686375 2.084019951 3.24E-07 6.489451916 -0.936939178 NPVWYQALTHGLNEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 NPVWYQALTHGLNEEQR 17 0 O95373 O95373 IPO7 Importin-7 0 0 116.29 1.47E-05 0 933.41 976.89 782.33 867.75 910.53 836.65 732.06 765.96 1028.4 844.15 FALSE FALSE TRUE 922.0332399 990.6426831 795.9461255 968.0833379 864.0622564 783.1907652 794.2411581 788.1218441 936.4173283 822.2188613 1.121396362 1.204840621 0.968046542 1.177403467 1.050890824 0.952533203 0.965972925 0.958530485 1.138890595 1 9.683378657 -8.319877034 4.913754354 1.072397465 0.959487907 0.406012598 0.071970112 0.193090836 9.825852739 0.010814649 0.025152563 4.79E-09 8.319877034 -0.112909558 NPYLLS(ph)EEEDDDVDGDVNVEK ddPTM_HeLa_Romidepsin_16h_R1 2 NPYLLSEEEDDDVDGDVNVEK 21 0 G3V5V3;O60524-4;O60524-5;O60524-3;O60524 G3V5V3 NEMF Nuclear export mediator factor NEMF 1 0 NPYLLS(1)EEEDDDVDGDVNVEK;NPY(0.002)LLS(0.998)EEEDDDVDGDVNVEK ; 165.01 1.04E-09 13606200 10485.2 9630.2 9712 6733.8 10109.9 10428.6 8950.3 9651.5 11234.3 12024.1 TRUE FALSE FALSE 10357.40235 9765.774208 9881.033286 7512.393639 9593.954078 9762.246117 9710.538259 9930.750925 10229.47607 11711.71215 0.884362783 0.833846844 0.843688195 0.641442818 0.819176048 0.833545599 0.829130543 0.847933317 0.873439847 1 13.51566438 -10.96871579 0.701602289 0.985256977 0.799388348 0.340604804 0.067361804 0.296595823 0.325083507 0.02221055 0.015896434 1.07E-11 10.96871579 -0.18586863 NQAAIQGRPPYAAS(ph)AEEVAK ddPTM_HeLa_Romidepsin_16h_R1 1 NQAAIQGRPPYAASAEEVAK 20 1 A0A494C0Y9;A0A0C4DG79;Q9NZB2-4;Q9NZB2;Q9NZB2-6 A0A494C0Y9 FAM120A Constitutive coactivator of PPAR-gamma-like protein 1 1 0 NQAAIQGRPPY(0.146)AAS(0.854)AEEVAK 60.472 0.0090433 7813200 2112.3 2112.4 1993.1 1966.1 1784.5 1546 1273.9 1521.2 2446.9 2101.1 TRUE FALSE FALSE 2086.554475 2142.138423 2027.789069 2193.429733 1693.430306 1447.215589 1382.105034 1565.213522 2228.043136 2046.513119 1.019565648 1.046725967 0.990850755 1.071788748 0.827471024 0.707161648 0.675346286 0.764819686 1.088702103 1 10.9989522 -8.572520545 3.589851029 1.014776904 0.715792835 0.930251923 0.039762873 0.033565219 0.893934729 0.004583054 0.009883094 2.68E-09 8.572520545 -0.298984068 NQAIYAAVDDDDDDAA ddPTM_HeLa_Romidepsin_16h_R1 2 NQAIYAAVDDDDDDAA 16 0 Q9UK59-2;Q9UK59 Q9UK59-2 DBR1 Lariat debranching enzyme 0 0 ; ; 166.86 0.00019082 76061000 20426.2 19534.5 18866.9 18691.3 19734.2 18867.5 16368.1 17770.6 20424.2 19492 FALSE FALSE TRUE 20177.23762 19809.5072 19195.27048 20852.47605 18727.09014 17661.92764 17758.40601 18284.76427 18597.4084 18985.59503 1.062765617 1.0433967 1.011043923 1.098331446 0.986384156 0.930280437 0.935362098 0.963086184 0.979553623 1 14.21261759 -8.525452319 24.98388613 1.034545074 0.944851063 0.611098374 0.032168371 36.99321077 359124.1238 0.004590942 0.009224976 2.98E-09 8.525452319 -0.089694011 NQATSATSEKDNDDDQS(ph)DKGTYTIELENPNSEEVEAR ddPTM_HeLa_Romidepsin_16h_R1 1 NQATSATSEKDNDDDQSDKGTYTIELENPNSEEVEAR 37 2 H0Y2V6;Q5SW79;H0YB66 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 NQATSATSEKDNDDDQS(0.272)DKGT(0.272)Y(0.111)T(0.272)IELENPNS(0.071)EEVEAR 48.687 0.004501 25069000 637.25 489.09 369.09 582.26 490.59 370.04 423.19 422.23 555.5 630.71 TRUE FALSE FALSE 629.4829519 495.9754219 375.5138566 649.5836408 465.5533617 346.3956382 459.135748 434.4465589 505.8146887 614.3240633 1.02467572 0.807351448 0.611263467 1.057395729 0.757830255 0.563864675 0.747383629 0.707194435 0.823367859 1 9.262856085 -10.18046617 4.214819463 1.011871025 0.745965778 0.28427973 0.136640879 0.138586706 4.597092056 0.020472046 0.025084722 6.60E-11 10.18046617 -0.265905247 NQCCPICNMTFSSPVVAQS(ph)HY(ph)LGK ddPTM_HeLa_Romidepsin_16h_R1 1 NQCCPICNMTFSSPVVAQSHYLGK 24 0 D6RJ07;Q9UL40-3;Q9UL40;Q9UL40-2 D6RJ07 ZNF346 Zinc finger protein 346 2 0 NQCCPICNMT(0.003)FS(0.146)S(0.146)PVVAQS(0.728)HY(0.977)LGK 40.104 0.028986 30800000 3412.3 3586.4 3277 3033 3394.7 2938.1 2677 2939.2 4017.3 4059.2 TRUE FALSE FALSE 3370.709575 3636.889433 3334.03481 3383.689731 3221.455792 2750.364892 2904.384313 3024.241115 3657.982626 3953.741399 0.852536682 0.91986022 0.843260718 0.855819688 0.814786671 0.69563601 0.734591371 0.764906151 0.925195216 1 11.9490028 -5.69434553 0.057312462 1.34075307 2.42E-12 0.762884522 0.042971717 70.96621591 0.429260284 2.688701694 9.055937061 2.02E-06 5.69434553 -1.34075307 NQGGGLSS(ph)SGAGEGQGPK ddPTM_HeLa_Romidepsin_16h_R1 1 NQGGGLSSSGAGEGQGPK 18 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 NQGGGLS(0.06)S(0.47)S(0.47)GAGEGQGPK 185.59 1.80E-15 0 1677.2 1800.6 1666.2 1338.2 1758.8 1827.4 1420.1 2024.1 1682.6 1790.7 TRUE FALSE FALSE 1656.757641 1825.948894 1695.199512 1492.92898 1669.041873 1710.635038 1540.723259 2082.66414 1532.104042 1744.177356 0.949879114 1.046882582 0.97191923 0.855950214 0.956922109 0.980768975 0.883352403 1.194066723 0.878410694 1 10.76833103 -7.247966534 24.7538813 0.966627562 1.194066895 0.594335446 0.059265272 992.7305001 1823925.857 0.007249625 0.18588669 5.65E-08 7.247966534 0.227439332 NQGGGLSSS(ph)GAGEGQGPK ddPTM_HeLa_Romidepsin_16h_R1 1 NQGGGLSSSGAGEGQGPK 18 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 NQGGGLS(0.002)S(0.122)S(0.876)GAGEGQGPK 219.72 7.13E-30 2920600 1336.2 1156.7 1104.1 685.44 1249.5 1247.5 1062.6 1293.8 1255.9 1384.8 TRUE FALSE FALSE 1319.91388 1172.984053 1123.316397 764.6937979 1185.733352 1167.788776 1152.857217 1331.234062 1143.569159 1348.822696 0.978567371 0.869635465 0.832812497 0.56693426 0.879087634 0.865783753 0.854713685 0.98696001 0.847827636 1 10.397485 -10.17803265 2.648851567 0.991285292 0.824841494 0.126848736 0.109129073 0.227897025 3.082018869 0.017532612 0.021435678 6.64E-11 10.17803265 -0.166443798 NQGGYDRYS(ph)GGNYR ddPTM_HeLa_Romidepsin_16h_R1 1 NQGGYDRYSGGNYR 14 1 P98179 P98179 RBM3 RNA-binding protein 3 1 0 NQGGYDRYS(1)GGNYR 156.6 0.0033544 8347000 3465.6 2754.7 3066.4 1685.2 3119.9 2971.2 2560.3 2258.5 3449.5 3642.5 TRUE FALSE FALSE 3423.359934 2793.480739 3119.769406 1880.050753 2960.679861 2781.349909 2777.771818 2323.846134 3140.968081 3547.867325 0.964906413 0.787368998 0.879336548 0.529910107 0.834495653 0.783949808 0.782941289 0.654998037 0.885311595 1 11.79273634 -10.11643396 1.445618066 0.988948937 0.736400033 0.473743876 0.09612311 0.17960736 0.722206158 0.016018023 0.020181122 7.65E-11 10.11643396 -0.252548904 NQGGYGGS(ph)SSSSSYGSGR ddPTM_HeLa_Romidepsin_16h_R1 2 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-3;P09651-2;P09651;H0YH80;A0A2R8Y4L2 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 NQGGYGGS(0.358)S(0.358)S(0.124)S(0.036)S(0.124)SYGSGR;NQGGYGGS(0.244)S(0.244)S(0.022)S(0.244)S(0.244)SYGSGR ; 278.88 4.35E-106 168014000 3032.1 3404.1 3062.3 2816 3369.7 3350.9 2790.81 2931.23 3663.7 3587 TRUE FALSE FALSE 2995.143599 3452.023009 3115.598047 3141.59917 3197.731635 3136.788305 3027.861332 3016.040515 3336.009496 3493.809223 0.85727165 0.988039927 0.891748189 0.899190245 0.91525651 0.897813276 0.866636138 0.863252777 0.954834475 1 11.77058512 -12.47156495 1.077476615 1.003103634 0.895572456 0.404307398 0.037459968 0.340838647 0.673781719 0.029083394 0.006352929 3.38E-13 12.47156495 -0.107531178 NQGGYGGSSSSS(ph)SYGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-3;P09651-2;P09651;H0YH80;A0A2R8Y4L2 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 NQGGYGGS(0.022)S(0.022)S(0.113)S(0.113)S(0.609)S(0.113)Y(0.004)GS(0.003)GR 72.797 0.020586 6239900 622.54 775.33 732.19 722.77 627.72 608.19 527.53 582.85 835.27 832.81 TRUE FALSE FALSE 614.952243 786.2451161 744.9334598 806.3400681 595.6851061 569.3286218 572.338385 599.7138452 760.5613592 811.1734761 0.75810201 0.969268768 0.918340505 0.994041462 0.734349832 0.701858035 0.705568416 0.739316389 0.937606297 1 9.663866669 -8.66767745 7.448691569 0.899417913 0.715748783 0.681112993 0.068355215 0.163605787 11.29503237 0.014055245 0.028179417 2.15E-09 8.66767745 -0.18366913 NQGGYGGSSSSSSY(ph)GSGR ddPTM_HeLa_Romidepsin_16h_R1 1 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-3;P09651-2;P09651;H0YH80;A0A2R8Y4L2 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 NQGGYGGSSSSSS(0.008)Y(0.698)GS(0.294)GR 172.43 9.42E-06 1207400 247.05 299.87 225.41 306.34 286.99 190.79 226.15 174.43 256.14 387.97 TRUE FALSE FALSE 244.0388596 304.0915777 229.3331665 341.7604722 272.3438294 178.5991347 245.3591754 179.4768568 233.2301969 377.8904835 0.645792552 0.804708218 0.606877327 0.904390259 0.720695125 0.472621414 0.649286463 0.474944103 0.617189919 1 8.561824377 -16.52287875 0.156752755 2.292205743 0.545148407 0 0.163938789 35.71825651 0.376267067 14.25389667 0.24476745 3.00E-17 16.52287875 -1.747057336 NQGGYGGSSSSSSYGS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 4 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-3;P09651-2;P09651;H0YH80;A0A2R8Y4L2 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 NQGGYGGSSSSSSYGS(1)GR;NQGGYGGSSSSSSYGS(1)GR;NQGGYGGSSSSSS(0.001)YGS(0.999)GR;NQGGYGGSSSSSSYGS(1)GR ;;; 284.23 1.17E-106 45534600 7859.65 8199.7 6559.55 6512.83 7872.92 8791.17 9400.1 8723.6 9485.8 7526.4 TRUE FALSE FALSE 7763.853563 8315.135592 6673.716216 7265.874048 7471.135514 8229.442609 10198.54426 8976.003602 8637.36629 7330.863043 1.059064058 1.134264212 0.910358873 0.991134878 1.01913451 1.122574868 1.39117921 1.224412944 1.178219568 1 12.83976734 -7.94584051 4.307679785 1.025354227 1.305678499 0.619938439 0.081321763 0.071557219 2.772164302 0.009002274 0.028562595 1.13E-08 7.94584051 0.280324273 NQGGYGGSSSSSSYGSGR ddPTM_HeLa_Romidepsin_16h_R1 5 NQGGYGGSSSSSSYGSGR 18 0 F8W6I7;P09651-3;P09651-2;P09651;H0YH80;A0A2R8Y4L2 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 0 ;;;; ;;;; 288.06 2.98E-125 12804950 1545.66 1292.78 1434.96 1447.47 1057.8 1330 1162.09 1400.18 1531.08 1544.19 FALSE FALSE TRUE 1526.820901 1310.979791 1459.934877 1614.833292 1003.816519 1245.017292 1260.797896 1440.691999 1394.13637 1504.071721 1.015125063 0.87162053 0.970655093 1.07364115 0.66739937 0.827764577 0.838256499 0.957861237 0.926908172 1 10.55465765 -8.778935704 24.99964034 0.997130773 0.824276095 0.434422384 0.083805656 140.5892549 200880.7925 0.011678248 0.021202742 1.66E-09 8.778935704 -0.172854677 NQKPSQVNGAPGS(ph)PTEPAGQK ddPTM_HeLa_Romidepsin_16h_R1 4 NQKPSQVNGAPGSPTEPAGQK 21 1 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 NQKPSQVNGAPGS(0.999)PT(0.001)EPAGQK;NQKPSQVNGAPGS(0.878)PT(0.122)EPAGQK;NQKPSQVNGAPGS(0.944)PT(0.056)EPAGQK;NQKPSQVNGAPGS(0.996)PT(0.004)EPAGQK ;;; 138.59 4.84E-05 398268000 27385.2 26649.5 25817 24157.9 22857.9 23127.9 19057.4 23522.1 26015.2 26510.4 TRUE FALSE FALSE 27051.41865 27024.67236 26266.33406 26951.15006 21691.37607 21650.10183 20676.13508 24202.67485 23688.33536 25821.65599 1.047625244 1.046589435 1.017221129 1.043742124 0.840045893 0.838447458 0.80072847 0.937301421 0.917382501 1 14.65629391 -8.759731226 24.99997107 1.025910902 0.84919609 0.709134425 0.04904416 11.9360363 174686.8279 0.005130852 0.009851795 1.74E-09 8.759731226 -0.176714811 NQLVT(ph)PEPTSR ddPTM_HeLa_Romidepsin_16h_R1 1 NQLVTPEPTSR 11 0 Q14676-3;Q14676;Q14676-2 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 NQLVT(0.959)PEPT(0.041)SR 139.74 0.0066188 20402000 3583.4 3038.5 2795.3 2519.4 3219.9 3777.1 3056 3255.8 3001.6 2675.4 TRUE FALSE FALSE 3539.724142 3081.276083 2843.951024 2810.704882 3055.576488 3535.7555 3315.576564 3350.001436 2733.129378 2605.892722 1.358353747 1.182426297 1.091353838 1.078595776 1.17256419 1.356830797 1.272338088 1.285548483 1.048826513 1 11.34756198 -12.54934148 1.313475914 0.999848465 1.235764231 0.417829073 0.093552555 0.362700177 1.119863519 0.075934785 0.017935947 2.82E-13 12.54934148 0.235915766 NQLVTPEPT(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 3 NQLVTPEPTSR 11 0 Q14676-3;Q14676;Q14676-2 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 NQLVT(0.007)PEPT(0.989)S(0.004)R;NQLVT(0.293)PEPT(0.686)S(0.021)R;NQLVT(0.162)PEPT(0.676)S(0.162)R ;; 140.33 0.0063983 51767000 8920.8 8568.3 8048 7731.2 9427.8 10576.4 8668.8 9556.5 8932.6 7925.7 TRUE FALSE FALSE 8812.069858 8688.924752 8188.072064 8625.11772 8946.664186 9900.602174 9405.127656 9833.00225 8133.645884 7719.789171 1.141491 1.125539125 1.060660062 1.11727374 1.158925974 1.282496446 1.218314056 1.27373974 1.053609846 1 12.91434573 -4 0.099661519 0.918497518 1.939981031 0.768756679 0.0426509 47.22236819 0.335786879 0.403601588 6.626631783 1.00E-04 4 1.021483513 NQNYLVPS(ph)PVLR ddPTM_HeLa_Romidepsin_16h_R1 2 NQNYLVPSPVLR 12 0 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 0 NQNYLVPS(1)PVLR;NQNYLVPS(1)PVLR ; 117.48 0.0083039 23279000 5390 4890.2 4406.3 4043.8 3623.2 3058.5 2572.9 3262.1 5239.9 5287.5 TRUE FALSE FALSE 5324.304607 4959.044364 4482.989803 4511.363183 3438.294584 2863.071721 2791.442062 3356.483717 4771.23022 5150.129988 1.033819461 0.962896932 0.870461486 0.875970741 0.667613166 0.555922225 0.542013904 0.651727961 0.926429087 1 12.33039313 -8.940149389 1.075535075 1.013493045 0.564155532 0.910276313 0.05297821 0.076648289 0.174417923 0.007669753 0.019730685 1.15E-09 8.940149389 -0.449337514 NQPTVYIAAS(ph)PPNTDELMSR ddPTM_HeLa_Romidepsin_16h_R1 1 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8-2;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 0 NQPTVY(0.005)IAAS(0.899)PPNT(0.087)DELMS(0.009)R 67.168 0.014709 13437000 1532.2 1645.7 1715 1511 1060.5 1064.6 1012.8 712.89 1586.9 1544.9 TRUE FALSE FALSE 1513.524957 1668.868208 1744.848856 1685.708929 1006.378728 996.5754958 1098.827207 733.5163474 1444.96369 1504.763275 1.005822631 1.109056976 1.159550399 1.120248585 0.668795381 0.662280581 0.730232605 0.487462951 0.960259805 1 10.55532083 -8.750806723 24.21949572 1.032082967 0.645630353 0.858237516 0.083553536 43.23565166 98482.8403 0.012556182 0.024891633 1.77E-09 8.750806723 -0.386452614 NQPTVYIAASPPNT(ph)DELMSR ddPTM_HeLa_Romidepsin_16h_R1 2 NQPTVYIAASPPNTDELMSR 20 0 A0A1B0GV57;Q9NYJ8-2;Q9NYJ8 A0A1B0GV57 TAB2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 1 0 NQPTVYIAAS(0.065)PPNT(0.914)DELMS(0.02)R;NQPTVYIAAS(0.062)PPNT(0.748)DELMS(0.19)R ; 104.7 4.34E-05 15448000 3275.1 2710.6 2318.5 2773.6 2171.6 2087.56 1219.8 1629.71 2898.9 2609 TRUE FALSE FALSE 3235.181821 2748.759898 2358.85252 3094.296682 2060.775149 1954.171653 1323.409782 1676.863088 2639.615124 2541.217804 1.27308325 1.081670329 0.928237051 1.217643241 0.810939993 0.768990226 0.520777786 0.659865945 1.038720538 1 11.31130432 -8.4214944 1.54620883 1.119270345 0.596334083 0.748720125 0.11438666 0.155729278 0.713887268 0.019998642 0.063212681 3.79E-09 8.4214944 -0.522936263 NQQGFS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 NQQGFSPK 8 0 D6RCT7;C9JKA9;Q9NS87-4;Q9NS87-2;Q9NS87 D6RCT7 KIF15 Kinesin-like protein;Kinesin-like protein KIF15 1 0 NQQGFS(1)PK 107.55 0.024663 5180600 4427.5 4016 4732.4 3021.1 4473.4 4466.8 3721.2 2765.8 5096.2 4896.3 TRUE FALSE FALSE 4373.535927 4072.537353 4814.765437 3370.413797 4245.105705 4181.385896 4037.278635 2845.824059 4640.383108 4769.09342 0.917058137 0.853943715 1.009576666 0.70672002 0.890128444 0.876767454 0.846550545 0.59672223 0.973011577 1 12.21949933 -4.894650851 0.197256297 1.000808015 3.33E-19 0.517906001 0.085523878 22.23426036 0.34549832 0.084589677 6.411908674 1.27E-05 4.894650851 -1.000808015 NQS(ph)LVEENEK ddPTM_HeLa_Romidepsin_16h_R1 3 NQSLVEENEK 10 0 O95239;O95239-2;Q2VIQ3 O95239 KIF4A;KIF4B Chromosome-associated kinesin KIF4A;Chromosome-associated kinesin KIF4B 1 0 NQS(1)LVEENEK;NQS(1)LVEENEK;NQS(1)LVEENEK ;; 141.73 0.0045117 60832000 15599.9 14816.6 14196 9629.3 9255.1 8395.7 7372.5 7937.4 14909 13393.9 TRUE FALSE FALSE 15409.76242 15025.18848 14443.07543 10742.68497 8782.777711 7859.241866 7998.719966 8167.056146 13575.5017 13045.92455 1.181193588 1.151715115 1.107094815 0.823451411 0.67322003 0.602428892 0.613120208 0.626023561 1.040593302 1 13.67131157 -9.017590271 2.228364475 1.096110144 0.619834919 0.948781667 0.051359159 0.066812067 0.661310549 0.0115998 0.022124516 9.60E-10 9.017590271 -0.476275225 NQS(ph)SEDILR ddPTM_HeLa_Romidepsin_16h_R1 1 NQSSEDILR 9 0 Q13625-2;Q13625;Q13625-3;H0Y847 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 NQS(0.956)S(0.044)EDILR 101.72 0.026772 12005000 2703.5 1845.2 2497.4 2432.6 1923.6 2350.2 2441.2 2100.7 2309.8 2579.9 TRUE FALSE FALSE 2670.548702 1871.176774 2540.866199 2713.868658 1825.431514 2200.029805 2648.555467 2161.48044 2103.205703 2512.873826 1.062746834 0.744636183 1.011139586 1.079986042 0.726431823 0.87550349 1.05399461 0.860162742 0.836972267 1 11.29512252 NQSLGQS(ph)APSLTAGLK ddPTM_HeLa_Romidepsin_16h_R1 1 NQSLGQSAPSLTAGLK 16 0 Q6P0Q8;Q6P0Q8-2 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 NQSLGQS(0.453)APS(0.453)LT(0.094)AGLK 96.64 0.0076594 33007000 3135.3 2673.8 2913.8 3092.7 3067.3 2657 2246.4 2338.5 3895.7 3311.9 TRUE FALSE FALSE 3097.085758 2711.441827 2964.513467 3450.292526 2910.764235 2487.226275 2437.20916 2406.160808 3547.258835 3225.856361 0.960081731 0.840533962 0.918984956 1.069574135 0.902322952 0.771028216 0.75552315 0.74589831 1.099633226 1 11.65546648 -8.345456475 3.272514016 0.969765233 0.75408134 0.67337614 0.069285094 0.098590833 2.028545272 0.00857264 0.021200926 4.51E-09 8.345456475 -0.215683893 NQSPT(ph)EAEKPASSSLPSSPPPQLLTR ddPTM_HeLa_Romidepsin_16h_R1 3 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 NQS(0.249)PT(0.751)EAEKPASSSLPSSPPPQLLTR;NQS(0.032)PT(0.692)EAEKPAS(0.161)S(0.071)S(0.032)LPS(0.005)S(0.005)PPPQLLTR;NQS(0.067)PT(0.81)EAEKPAS(0.084)S(0.028)S(0.01)LPSSPPPQLLTR ;; 102.92 1.95E-06 60291000 3389.49 3374.59 2966.42 2851.65 3641.2 3136.43 3148.62 3742.82 3844.9 3029.96 TRUE FALSE FALSE 3348.177592 3422.097567 3018.049296 3181.37119 3455.375977 2936.022245 3416.063704 3851.112592 3501.002514 2951.241202 1.134498119 1.159545199 1.022637287 1.077977357 1.170821271 0.994843201 1.157500682 1.304912858 1.186281389 1 11.52710612 -16.52287584 0.020347282 1.13E-06 1.913402375 0.002403481 0.092436325 2574.374989 4.223806851 264.1941786 148.6266126 3.00E-17 16.52287584 1.91340125 NQSPTEAEKPAS(ph)SSLPSSPPPQLLTR ddPTM_HeLa_Romidepsin_16h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 NQSPTEAEKPAS(0.328)S(0.263)S(0.263)LPS(0.069)S(0.069)PPPQLLT(0.008)R 48.773 0.01483 41477000 1278.6 1366.7 1533.1 1109.6 1513.6 1443.8 1281.6 1368.9 1657.1 1610.6 TRUE FALSE FALSE 1263.015931 1385.940438 1559.782962 1237.897173 1436.355344 1351.54584 1390.459072 1408.506962 1508.884826 1568.75638 0.805106483 0.883464416 0.994279917 0.78909459 0.915601277 0.861539661 0.886344808 0.897849392 0.961835021 1 10.61540561 -12.54684203 1.31481176 0.999963212 0.871573638 0.340936587 0.055181436 0.339819516 1.052844131 0.038676012 0.009182385 2.84E-13 12.54684203 -0.128389574 NQSPTEAEKPASSSLPS(ph)SPPPQLLTR ddPTM_HeLa_Romidepsin_16h_R1 1 NQSPTEAEKPASSSLPSSPPPQLLTR 26 1 Q99567;I3L2W3 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 NQSPTEAEKPAS(0.002)S(0.072)S(0.072)LPS(0.427)S(0.427)PPPQLLT(0.001)R 86.492 1.19E-05 55308000 2146.3 2293.6 2386.4 2043 2608.1 2249.4 2297.8 2222.6 2731.4 2466.7 TRUE FALSE FALSE 2120.14007 2325.889361 2427.934291 2279.221273 2474.998925 2105.6706 2492.975075 2286.907424 2487.096743 2402.614778 0.882430296 0.968065868 1.010538315 0.948641993 1.030127238 0.876407911 1.037609149 0.951841071 1.035162509 1 11.23038964 -10.01887931 24.51495007 0.943468717 0.976536984 0 0.058737459 1332.697436 1730516.976 0.0095638 0.011819305 9.57E-11 10.01887931 0.033068267 NQSS(ph)EDILR ddPTM_HeLa_Romidepsin_16h_R1 1 NQSSEDILR 9 0 Q13625-2;Q13625;Q13625-3;H0Y847 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 NQS(0.037)S(0.963)EDILR 128.88 0.0088483 13224000 2966.7 2421.4 2807.9 2753.1 2131.9 2961.1 2925.2 2486.1 2780.1 2849.8 TRUE FALSE FALSE 2930.540719 2455.488533 2856.770322 3071.426376 2023.101188 2771.895267 3173.666415 2558.031381 2531.440893 2775.761785 1.055760885 0.88461789 1.029184254 1.106516558 0.728845392 0.998607042 1.143349704 0.921560126 0.911980598 1 11.43866805 NQT(ph)PAPSAAQTSAPSK ddPTM_HeLa_Romidepsin_16h_R1 1 NQTPAPSAAQTSAPSK 16 0 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 0 NQT(0.979)PAPS(0.01)AAQT(0.006)S(0.006)APSK 137.44 0.0022872 1906300 923.39 711.63 887.81 908 913.04 1078.4 838.89 836.59 1085.1 961.4 TRUE FALSE FALSE 912.1353675 721.6483458 903.2619606 1012.987232 866.4441618 1009.49372 910.1452957 860.7954117 988.0459383 936.4226894 0.974063719 0.770643806 0.964587863 1.081762802 0.925270363 1.078032102 0.971938534 0.919238098 1.055128148 1 9.871016081 NQTAEK(ac)EEFEHQQK ddPTM_HeLa_Romidepsin_16h_R1 2 NQTAEKEEFEHQQK 14 1 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PM13;E9PS65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 1 ; NQTAEK(1)EEFEHQQK;NQTAEK(1)EEFEHQQK 219.41 8.29E-25 13678900 2453.7 2741 2598.7 1167.09 6579.3 5772.6 4545.8 5577.1 6568.8 5868.4 FALSE TRUE FALSE 2423.793361 2779.58787 2643.929283 1302.034437 6243.53377 5403.74949 4931.920139 5738.464589 5981.270076 5715.938122 0.424041218 0.486287257 0.462553867 0.227790156 1.092302547 0.945382783 0.862836517 1.003940992 1.046419669 1 12.48077458 -8.705181784 24.99994178 0.648152055 0.965829363 0.34506806 0.24463576 102.1286699 45383.55492 0.041449889 0.082899751 1.97E-09 8.705181784 0.317677308 NQTYSFS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 NQTYSFSPSK 10 0 Q86YS7;Q86YS7-3;H0YFE9 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 NQT(0.128)YS(0.128)FS(0.429)PS(0.314)K;NQT(0.012)YS(0.22)FS(0.749)PS(0.02)K ; 130.69 0.0070776 74581000 7053.7 6553.1 8512.4 7677 8078.9 8705.7 6333.4 6561.8 7598.7 7074.2 TRUE FALSE FALSE 6967.726791 6645.354714 8660.554751 8564.650861 7666.603586 8149.433866 6871.358838 6751.65533 6919.053241 6890.411264 1.011220742 0.964435134 1.25689954 1.242981084 1.112648185 1.182720966 0.997234936 0.97986246 1.004156788 1 12.75037438 -9.791672467 24.99992521 1.002381955 1.129664957 0.367146417 0.085813267 181.8503296 150372.3633 0.014557421 0.019133483 1.62E-10 9.791672467 0.127283002 NQVALNPQNTVFDAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NQVALNPQNTVFDAKR 16 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2 A0A0G2JIW1 HSPA1B;HSPA1A Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A 0 1 NQVALNPQNTVFDAK(1)R 177.36 4.11E-55 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 NQVAMNPTNTVFDAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 NQVAMNPTNTVFDAKR 16 1 P11142;E9PKE3;P11142-2;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 1 ; NQVAMNPTNTVFDAK(1)R;NQVAMNPTNTVFDAK(1)R 176.4 3.53E-12 1286820 544.97 323.28 584.92 94.882 677.72 577.52 717.72 446.57 551.8 520.61 FALSE TRUE FALSE 538.327696 327.8311443 595.1002872 105.8527033 643.1334195 540.6183359 778.6831189 459.4907984 502.445626 507.0844771 1.06161344 0.646502031 1.173572282 0.20874767 1.268296405 1.066130714 1.535608274 0.906142505 0.990851916 1 8.986082301 NQVEEDAEDS(ph)GEADDEEKPEIHKPGQNSFSK ddPTM_HeLa_Romidepsin_16h_R1 2 NQVEEDAEDSGEADDEEKPEIHKPGQNSFSK 31 2 O75717-2;O75717 O75717-2 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 0 NQVEEDAEDS(0.998)GEADDEEKPEIHKPGQNS(0.001)FS(0.001)K;NQVEEDAEDS(0.98)GEADDEEKPEIHKPGQNS(0.016)FS(0.004)K ; 61.186 0.00026056 23707000 3794.89 3466.5 3522.9 3536.1 4537.7 4829.4 4388.8 4129.05 5454.7 4874.7 TRUE FALSE FALSE 3748.636421 3515.301478 3584.214597 3944.96052 4306.124237 4520.816926 4761.584562 4248.517547 4966.81797 4748.054591 0.789509966 0.740366693 0.754880663 0.83085829 0.90692391 0.95214089 1.002849582 0.894791217 1.046074318 1 12.21312081 -8.444357829 3.676703044 0.868404755 0.954504786 0.146149538 0.095839772 0.42664808 10.93718201 0.01580336 0.036660158 3.59E-09 8.444357829 0.086100032 NQVERS(ph)QMT(ph)FGRLQGIFPKIMPK ddPTM_HeLa_Romidepsin_16h_R1 1 NQVERSQMTFGRLQGIFPKIMPK 23 3 Q7RTT3 Q7RTT3 SSX9 Protein SSX9 2 0 NQVERS(1)QMT(1)FGRLQGIFPKIMPK 42.64 0.026144 20337000 1032.9 1090 973.98 808.94 917.58 953.5 895.07 835.97 999.12 1027.9 TRUE FALSE FALSE 1020.310618 1105.345049 990.9317133 902.473449 870.7524686 892.5744273 971.0972235 860.157473 909.7562049 1001.19501 1.019092792 1.104025727 0.989748954 0.901396272 0.869713153 0.891509065 0.969938138 0.859130803 0.908670335 1 9.96750729 -9.325589538 4.25969813 1.017437758 0.900019833 0.503336741 0.052337624 0.100777085 3.674101549 0.006159492 0.009657112 4.73E-10 9.325589538 -0.117417925 NQVLVFVHSR ddPTM_HeLa_Romidepsin_16h_R1 2 NQVLVFVHSR 10 0 O75643;A0A494C1A5 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 0 ; ; 90.05 0.0072205 1653430 1028.34 1113.36 1598.34 1600.69 1466.47 1540.74 1358.68 1336.28 1173.86 1017.51 FALSE FALSE TRUE 1015.806197 1129.033911 1626.158437 1785.769309 1391.630564 1442.291687 1474.086245 1374.943153 1068.867022 991.0749435 1.024953969 1.139201348 1.640802694 1.801850931 1.404162796 1.455280144 1.487361026 1.387325108 1.078492629 1 9.952850346 -9.885244279 4.560782414 1.014923605 1.5297913 0.795425005 0.116958811 0.066735642 2.385398686 0.019693485 0.026151472 1.30E-10 9.885244279 0.514867695 NQYDNDVTVWS(ph)PQGR ddPTM_HeLa_Romidepsin_16h_R1 1 NQYDNDVTVWSPQGR 15 0 P25786;P25786-2;B4DEV8 P25786 PSMA1 Proteasome subunit alpha type-1;Proteasome subunit alpha type 1 0 NQYDNDVTVWS(1)PQGR 163.34 0.00011624 4735000 1665.4 1538.5 1451.1 1178 1085.1 922 1127 967.14 1595.2 1566.7 TRUE FALSE FALSE 1645.101464 1560.159043 1476.355787 1314.205903 1029.723298 863.0871756 1222.727352 995.12267 1452.521317 1525.996908 1.078050326 1.022386766 0.96746971 0.86121138 0.674787277 0.565589072 0.801264633 0.652113163 0.95185076 1 10.57553632 -9.065156427 1.871051696 1.035350151 0.672350389 0.851496398 0.064608453 0.079985774 0.553172967 0.009620786 0.018576713 8.61E-10 9.065156427 -0.362999762 NREEEWDPEYT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 NREEEWDPEY(0.022)T(0.978)PK;NREEEWDPEY(0.016)T(0.984)PK;NREEEWDPEY(0.003)T(0.997)PK ;; 85.469 0.016333 202199300 12971.8 12410.9 12623.6 15360.7 13587.2 15386.2 13614 11485.1 14177.4 13074.8 TRUE FALSE FALSE 12813.69471 12585.62098 12843.30846 17136.77641 12893.79448 14403.07148 14770.37282 11817.40325 12909.33784 12735.11481 1.006170333 0.988261289 1.008495695 1.345631874 1.012460011 1.130973037 1.159814657 0.927938493 1.013680523 1 13.63652435 -9.474312226 24.99999393 1.00172852 1.119391474 0.2360956 0.100691807 391.9961071 201783.2935 0.014099173 0.021536612 3.35E-10 9.474312226 0.117662954 NREEEWDPEYTPK ddPTM_HeLa_Romidepsin_16h_R1 1 NREEEWDPEYTPK 13 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 0 119.88 0.0055892 7979700 4965.4 4902.5 4440.7 3585.2 5083.2 5452.4 4307.8 5490.2 5315.4 4994.1 FALSE FALSE TRUE 4904.879795 4971.517524 4517.988521 3999.737693 4823.785336 5104.009237 4673.704424 5649.050275 4839.977311 4864.352562 1.008331475 1.022030673 0.928795449 0.822254892 0.991660303 1.049267949 0.960807089 1.161315962 0.994989004 1 12.24803208 -7.255793691 24.48751887 0.988140414 1.161316062 0.443025518 0.061057097 365.4881308 1585197.853 0.008794163 0.101456258 5.55E-08 7.255793691 0.173175648 NREILDESLR ddPTM_HeLa_Romidepsin_16h_R1 2 NREILDESLR 10 1 Q8WUM4;Q8WUM4-2 Q8WUM4 PDCD6IP Programmed cell death 6-interacting protein 0 0 ; ; 144.77 0.0046641 7351900 2545.1 2591.14 2379.58 2894.36 2505.16 2379.39 2022.28 2353.54 2675.2 2223.72 FALSE FALSE TRUE 2514.079342 2627.618137 2420.995592 3229.019522 2377.312337 2227.354658 2194.052413 2421.635967 2435.923412 2165.947434 1.16072962 1.213149542 1.117753623 1.490811583 1.097585426 1.028351207 1.012975836 1.118049279 1.124645674 1 11.08078251 -6.159118429 16.16024896 1.110777718 1.136979808 0 0.136564951 0 0 0.019279482 0 6.93E-07 6.159118429 0.02620209 NRENS(ph)PSSQSAGLSSINK ddPTM_HeLa_Romidepsin_16h_R1 1 NRENSPSSQSAGLSSINK 18 1 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 NRENS(0.898)PS(0.092)S(0.007)QS(0.003)AGLSSINK 62.781 0.014776 11090000 2597.2 2346.2 2624.1 1689.5 2735.6 2632.3 2034.6 2818.7 2687.2 2505.1 TRUE FALSE FALSE 2565.544327 2379.229865 2669.77136 1884.847939 2595.992124 2464.104525 2207.418873 2900.254637 2446.850102 2440.017141 1.051445207 0.975087357 1.094160904 0.772473237 1.063923724 1.00987181 0.904673511 1.1886206 1.002800374 1 11.25267557 -14.77111364 16.58731522 0.39315234 1.012072464 0 0.106157102 0 0 0 0.012445513 1.69E-15 14.77111364 0.618920124 NRPDYVS(ph)EEEEDDEDFETAVK ddPTM_HeLa_Romidepsin_16h_R1 2 NRPDYVSEEEEDDEDFETAVK 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 NRPDYVS(1)EEEEDDEDFETAVK;NRPDY(0.027)VS(0.973)EEEEDDEDFETAVK ; 103.74 0.00014028 59206000 12984.8 12948.9 12860.4 12415.6 12610.5 12919.8 10789.9 12155.9 14603.8 14486.5 TRUE FALSE FALSE 12826.53626 13131.19495 13084.22987 13851.15009 11966.93913 12094.26648 11706.39384 12507.61179 13297.59955 14110.13864 0.909029783 0.930621257 0.927292793 0.981645216 0.848109252 0.857133072 0.82964414 0.886427278 0.942414521 1 13.78444454 -13.14899602 0.018671816 1.968026412 2.41E-08 0.482271422 0.038501367 675.4083975 2.226750238 131.9639003 103.966405 7.10E-14 13.14899602 -1.968026387 NRPT(ph)SISWDGLDSGK ddPTM_HeLa_Romidepsin_16h_R1 1 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 0 NRPT(0.841)S(0.158)IS(0.001)WDGLDSGK 111.93 0.0022365 41380000 6452.2 5103.7 5610.6 3354.3 7139.1 7024.5 5822.4 6583.6 5819 5329.4 TRUE FALSE FALSE 6373.558105 5175.550023 5708.250139 3742.139948 6774.765087 6575.657121 6316.954511 6774.086079 5298.534066 5190.94142 1.227823161 0.997034951 1.09965605 0.720898127 1.305112992 1.266756179 1.216918859 1.304982186 1.020727001 1 12.34178049 NRPTS(ph)ISWDGLDSGK ddPTM_HeLa_Romidepsin_16h_R1 1 NRPTSISWDGLDSGK 15 1 P30086 P30086 PEBP1 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide 1 0 NRPT(0.028)S(0.928)IS(0.044)WDGLDSGK 90.882 0.0056643 38613000 4813.2 4104.2 4789 2593 5598.7 5606.4 5088.5 4891.7 4851.4 4302.4 TRUE FALSE FALSE 4754.534867 4161.979035 4872.350536 2892.81486 5312.977447 5248.169134 5520.717063 5033.233622 4417.478633 4190.623028 1.134565155 0.993164741 1.162679273 0.69030663 1.267825193 1.252360114 1.317397682 1.201070482 1.0541341 1 12.03294903 NRS(ph)AEEGELAESK ddPTM_HeLa_Romidepsin_16h_R1 2 NRSAEEGELAESK 13 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 NRS(1)AEEGELAESK;NRS(1)AEEGELAESK ; 145.33 0.00028363 179307000 14944.3 14459.7 13013.1 14841.4 17297 16984.4 15232.5 16706.8 14220.5 12753.6 TRUE FALSE FALSE 14762.15312 14663.26404 13239.58755 16557.4325 16414.26955 15899.15165 16526.34817 17190.1849 12948.58286 12422.25963 1.188362952 1.180402316 1.06579543 1.332884112 1.321359401 1.279892075 1.330381803 1.383821093 1.042369363 1 13.60064001 -4.000000185 0.045462545 0.379958505 2.719885741 0.791971118 0.059707057 165.2924858 0.575565951 7.57103561 28.34783256 1.00E-04 4.000000185 2.339927236 NRS(ph)PSDS(ph)DMEDYS(ph)PPPSLSEVAR ddPTM_HeLa_Romidepsin_16h_R1 1 NRSPSDSDMEDYSPPPSLSEVAR 23 1 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 3 0 NRS(0.631)PS(0.515)DS(0.815)DMEDY(0.217)S(0.809)PPPS(0.006)LS(0.007)EVAR 49.707 0.0037688 0 255.2 227.8 272.58 206.86 315.14 248.1 245.77 103.14 456.01 364.56 TRUE FALSE FALSE 252.0895242 231.0069744 277.3241406 230.7781265 299.0572299 232.2472107 266.6456977 106.1241932 415.2233235 355.0886786 0.709933995 0.650561362 0.780999669 0.649916881 0.84220435 0.654054113 0.75092706 0.298866733 1.169351062 1 8.472035553 -16.52287875 0.115705431 2.101152209 0.485135284 0.598587199 0.139104788 56.07207149 0.472070829 14.53033522 0.653636173 3.00E-17 16.52287875 -1.616016924 NRSPS(ph)DS(ph)DMEDY(ph)SPPPSLSEVAR ddPTM_HeLa_Romidepsin_16h_R1 1 NRSPSDSDMEDYSPPPSLSEVAR 23 1 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 3 0 NRS(0.272)PS(0.773)DS(0.926)DMEDY(0.959)S(0.069)PPPS(0.001)LS(0.001)EVAR 54.457 0.0045931 3123700 407.27 321.4 253.17 219.14 396.55 220.16 294.34 321.91 358.3 245.54 TRUE FALSE FALSE 402.3060366 325.9246776 257.5763177 244.4779979 376.3125738 206.0924865 319.3412323 331.223958 326.2527506 239.1608354 1.682156846 1.362784492 1.077000409 1.02223258 1.573470728 0.861731755 1.33525722 1.384942302 1.364156259 1 7.901837345 -9.799640206 24.90601629 1.334179447 1.207117804 0.07536972 0.242310017 477.0636319 311031.8399 0.049648967 0.065252344 1.59E-10 9.799640206 -0.127061643 NRSVSGKRICS(ph)Y(ph)CNNILGK ddPTM_HeLa_Romidepsin_16h_R1 1 NRSVSGKRICSYCNNILGK 19 3 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;E9PMT2 E9PMS6 LMO7 LIM domain only protein 7 2 0 NRS(0.001)VS(0.001)GKRICS(0.999)Y(0.999)CNNILGK 41.348 0.029543 14853000 3133.8 2615 2788.6 2145.4 2381.9 2319 2246.3 1961.3 3279.7 3374.4 TRUE FALSE FALSE 3095.60404 2651.814039 2837.134413 2393.461242 2260.342755 2170.823384 2437.100666 2018.047121 2986.355418 3286.732602 0.94184846 0.806823785 0.863208164 0.728219035 0.687717265 0.66048068 0.741496483 0.613997963 0.908609181 1 11.68243837 -9.681766226 0.638503662 0.989961341 0.657265846 0.850734602 0.04747175 0.129316389 0.108115403 0.009427154 0.017399586 2.08E-10 9.681766226 -0.332695495 NS(ph)DADFQNNEK ddPTM_HeLa_Romidepsin_16h_R1 1 NSDADFQNNEK 11 0 E5RIM1;A0A087WTZ8;E5RFJ1;E5RHW9;Q96MF7 E5RIM1 NSMCE2 E3 SUMO-protein ligase NSE2 1 0 NS(1)DADFQNNEK 92.939 0.029542 4930100 832.29 1375.4 1419 898.9 1080.5 1593.2 1560.7 1572.1 1679.1 1431.9 TRUE FALSE FALSE 822.1457293 1394.762917 1443.6971 1002.835047 1025.358053 1491.399662 1693.265819 1617.586233 1528.917091 1394.699032 0.589478956 1.000045806 1.035131643 0.7190333 0.735182308 1.069334407 1.214072557 1.15981025 1.096234425 1 10.44573811 -8.086373384 4.124771619 0.82416978 1.180264865 0.340164395 0.160355102 0.164488132 5.056004992 0.025421599 0.070670082 8.20E-09 8.086373384 0.356095085 NS(ph)FTPLSSSNTIR ddPTM_HeLa_Romidepsin_16h_R1 1 NSFTPLSSSNTIR 13 0 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 0 NS(0.773)FT(0.226)PLS(0.001)SSNTIR 186.29 8.44E-08 14657000 1699.6 1185.3 1259.5 956.09 1649.9 1835.7 1267.4 1800.9 1530.9 1564.8 TRUE FALSE FALSE 1678.884621 1201.986685 1281.421069 1066.637624 1565.699446 1718.404694 1375.052924 1853.0062 1393.97247 1524.14627 1.101524607 0.788629483 0.84074678 0.699826286 1.027263247 1.127453925 0.902179109 1.215766647 0.914592318 1 10.57378565 -7.245594306 22.97262866 0.991160989 1.215767174 0.177031214 0.139440776 1383.160058 2005240.206 0.021042369 0.627899107 5.68E-08 7.245594306 0.224606186 NS(ph)GIWESPELDR ddPTM_HeLa_Romidepsin_16h_R1 2 NSGIWESPELDR 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 NS(0.956)GIWES(0.044)PELDR;NS(0.582)GIWES(0.418)PELDR ; 144.4 0.0015206 6371800 5068.2 6110 2912.3 1192.64 2693.2 3675.2 3153 5027.8 6305.7 6698.2 TRUE FALSE FALSE 5006.426829 6196.01674 2962.98736 1330.538648 2555.755954 3440.366581 3420.815741 5173.27146 5741.702399 6524.179798 0.767364938 0.949700488 0.454154768 0.203939605 0.391735978 0.527325532 0.524328858 0.792938211 0.880065016 1 12.67158083 -9.757908038 24.99954877 0.89154177 0.469572624 0.655608394 0.147801687 46.20302804 327084.7651 0.026249948 0.036283112 1.75E-10 9.757908038 -0.421969146 NS(ph)LTGEEGQLAR ddPTM_HeLa_Romidepsin_16h_R1 2 NSLTGEEGQLAR 12 0 Q9BX95 Q9BX95 SGPP1 Sphingosine-1-phosphate phosphatase 1 1 0 NS(0.976)LT(0.024)GEEGQLAR;NS(0.863)LT(0.137)GEEGQLAR ; 110.57 0.010455 9070100 1403.06 1910.29 1139.51 1133.1 1354.74 1547.93 1203.55 1942.91 1577.42 1577.54 TRUE FALSE FALSE 1385.958965 1937.183113 1159.342694 1264.114353 1285.602563 1449.022269 1305.779507 1999.125035 1436.331604 1536.555283 0.901990953 1.260731152 0.754507635 0.822693701 0.836678365 0.943032955 0.84980965 1.301043351 0.934773789 1 10.58548396 -12.65622416 1.437145866 1.000569884 0.942046043 0 0.174642758 2.173512156 7.943284484 0.123908587 0.026714553 2.21E-13 12.65622416 -0.058523841 NS(ph)MRADS(ph)VS(ph)S(ph)SNIKNR ddPTM_HeLa_Romidepsin_16h_R1 1 NSMRADSVSSSNIKNR 16 2 Q53F19;Q53F19-2 Q53F19 C17orf85 Uncharacterized protein C17orf85 4 0 NS(1)MRADS(0.999)VS(0.807)S(0.807)S(0.387)NIKNR 41.689 0.029746 4050300 1224.6 1487.2 1304.7 1340.7 914.26 601.16 509.2 701.16 1300.1 1364.6 TRUE FALSE FALSE 1209.674104 1508.136841 1327.407756 1495.718042 867.6019006 562.7478162 552.4514353 721.4469584 1183.8158 1329.147495 0.910112767 1.134664773 0.998691087 1.125321341 0.652750657 0.423390044 0.415643439 0.54278924 0.890657962 1 10.37628549 -8.575298451 4.263212017 0.984640413 0.464474118 0.899430381 0.083554249 0.047397499 1.808521077 0.01247292 0.026184058 2.66E-09 8.575298451 -0.520166295 NS(ph)NPVIAELSQAINS(ph)GTLLSKPSPPLPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 0 NS(0.993)NPVIAELS(0.15)QAINS(0.301)GT(0.23)LLS(0.232)KPS(0.094)PPLPPKR 60.218 0.00043363 4360500 903.87 708.74 871.82 568.66 814.53 1113.1 1082.2 954.01 734.83 709.3 TRUE FALSE FALSE 892.8532848 718.7176603 886.9936614 634.4111448 772.9614947 1041.976502 1174.122041 981.6127742 669.1049644 690.8722837 1.292356497 1.040304666 1.283875012 0.918275577 1.118819662 1.508204232 1.699477702 1.420831024 0.968492991 1 9.432275225 -8.226531287 4.946042606 1.126320168 1.566135325 0.696973399 0.135687538 0.092263284 5.837016899 0.020240318 0.051936444 5.94E-09 8.226531287 0.439815157 NS(ph)NPVIAELSQAINSGTLLSKPS(ph)PPLPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 0 NS(1)NPVIAELSQAINS(0.029)GT(0.205)LLS(0.196)KPS(0.57)PPLPPKR 93.764 1.52E-08 6072500 748.02 719.28 661.08 490.03 587.71 1041.7 1063.3 998.22 915 711.71 TRUE FALSE FALSE 738.9028445 729.4060427 672.5858201 546.6895743 557.7169657 975.1387319 1153.616675 1027.101921 833.1601083 693.2196716 1.065899995 1.052200439 0.970234758 0.788623861 0.804531361 1.406680699 1.664143017 1.481639894 1.201870262 1 9.437168784 -8.091877849 4.795555384 0.997839764 1.566516663 0.803583917 0.122490619 0.063494535 2.425689052 0.016305506 0.043838753 8.09E-09 8.091877849 0.568676899 NS(ph)PGLLVSPGNLNK ddPTM_HeLa_Romidepsin_16h_R1 2 NSPGLLVSPGNLNK 14 0 A0A0D9SGF3;D8L7E9;A0A0D9SFD0;A0A0R4J2G5;A0A1B0GV32;A0A0D9SGI5;Q06413-4;Q06413-3;Q06413-6;Q06413-2;Q06413;Q06413-5;A0A0D9SFV9;D6RC63;D6RJG6 A0A0D9SGF3 MEF2C Myocyte-specific enhancer factor 2C 1 0 NS(0.993)PGLLVS(0.007)PGNLNK;NS(0.999)PGLLVS(0.001)PGNLNK ; 140.49 0.00092528 86008000 3563.3 3852.4 3488.3 3955.5 4289.1 4087.9 3474.5 3455.1 3544.2 2767.6 TRUE FALSE FALSE 3519.869129 3906.634188 3549.012398 4412.853521 4070.211222 3826.696383 3769.623943 3555.067867 3227.197875 2695.697353 1.305736019 1.449210975 1.31654705 1.63699887 1.509891761 1.419557125 1.398385445 1.318793396 1.197166244 1 11.39644282 -11.37476536 0.589004136 1.002965041 1.450751776 0.594665774 0.105499717 0.271991677 0.201864392 0.055770931 0.02567999 4.22E-12 11.37476536 0.447786735 NS(ph)PGSQVASNPR ddPTM_HeLa_Romidepsin_16h_R1 4 NSPGSQVASNPR 12 0 Q9H0D6-2;Q9H0D6 Q9H0D6-2 XRN2 5-3 exoribonuclease 2 1 0 NS(0.999)PGS(0.001)QVASNPR;NS(0.966)PGS(0.034)QVASNPR;NS(0.759)PGS(0.231)QVAS(0.01)NPR;NS(0.789)PGS(0.208)QVAS(0.003)NPR ;;; 181.75 1.05E-06 424137000 12305.9 11868.8 12306.5 9558.2 12617.7 14251.1 11510.6 11660.9 12691.5 12184 TRUE FALSE FALSE 12155.91096 12035.88928 12520.68947 10663.36406 11973.77169 13340.5007 12488.31008 11998.28974 11556.34045 11867.45792 1.024306219 1.014192707 1.055043932 0.898538181 1.008958428 1.124124542 1.052315513 1.011024418 0.973783984 1 13.53472331 -8.470426064 24.99291967 1.006351374 1.062316039 0.27805644 0.046936787 362.4097511 172682.6258 0.006369109 0.014241586 3.39E-09 8.470426064 0.055964665 NS(ph)PGVPTGAK ddPTM_HeLa_Romidepsin_16h_R1 2 NSPGVPTGAK 10 0 R4GND7;B7ZC06;Q08379 R4GND7 GOLGA2 Golgin subfamily A member 2 1 0 NS(0.998)PGVPT(0.002)GAK;NS(0.999)PGVPT(0.001)GAK ; 133.88 0.0060805 184973000 24903.9 23172.4 22697.1 24153.5 24622.1 25616.5 22715.5 22680 24210.2 23374 TRUE FALSE FALSE 24600.36169 23498.62166 23092.1335 26946.24132 23365.54236 23979.68832 24644.954 23336.21002 22044.77908 22766.74011 1.080539487 1.032146963 1.01429249 1.183579256 1.026301624 1.053277202 1.082498148 1.025013239 0.968288783 1 14.47464011 -12.41238316 0.900207773 0.995881158 1.064444751 0.285740635 0.047571137 0.840988659 1.095503109 0.041252181 0.00823325 3.87E-13 12.41238316 0.068563593 NS(ph)PNNISGISNPPGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 NSPNNISGISNPPGTPR 17 0 Q9NW25;Q9BWW4-2;Q9BWW4-3;Q9BWW4;A0A087WVT6 Q9NW25 SSBP3 Single-stranded DNA-binding protein 3 2 0 NS(0.998)PNNIS(0.001)GIS(0.001)NPPGT(1)PR 193.51 7.32E-13 7000600 1339.5 1236.9 1373.7 1200.7 1483.4 1793.7 1339.9 1607 1666 1239.3 TRUE FALSE FALSE 1323.173659 1254.313111 1397.608672 1339.530583 1407.696563 1679.088359 1453.711073 1653.49601 1516.988787 1207.102807 1.096156558 1.039110425 1.157820745 1.109707123 1.166177855 1.391006921 1.204297649 1.369805454 1.256718797 1 10.23733284 -6.858009763 0.253770501 1.003443959 1.724120387 0.3695026 0.097870338 4.115153147 0.17704675 0.038952206 0.960690769 1.39E-07 6.858009763 0.720676427 NS(ph)PNNISGISNPPGTPR ddPTM_HeLa_Romidepsin_16h_R1 4 NSPNNISGISNPPGTPR 17 0 Q9NW25;Q9BWW4-2;Q9BWW4-3;Q9BWW4;A0A087WVT6 Q9NW25 SSBP3 Single-stranded DNA-binding protein 3 1 0 NS(1)PNNISGISNPPGTPR;NS(0.493)PNNIS(0.204)GIS(0.093)NPPGT(0.209)PR;NS(0.619)PNNIS(0.011)GIS(0.017)NPPGT(0.353)PR;NS(0.95)PNNIS(0.019)GIS(0.006)NPPGT(0.025)PR ;;; 291.75 9.97E-120 45274000 3809.6 3082.2 3247.92 2230.09 3687.07 3212.21 2956.72 3788.28 3363.78 3423.61 TRUE FALSE FALSE 3763.16713 3125.591293 3304.448685 2487.943499 3498.90506 3006.960148 3207.863723 3897.887905 3062.915092 3334.664119 1.128499602 0.937303183 0.990938987 0.746085186 1.049252619 0.901728042 0.961975062 1.168899705 0.918507827 1 11.70332574 -10.24393488 24.47025919 1.060680369 0.958404929 0 0.114395972 833.2566467 1164845.36 0.017650475 0.021589377 5.70E-11 10.24393488 -0.10227544 NS(ph)PQPLRR ddPTM_HeLa_Romidepsin_16h_R1 1 NSPQPLRR 8 1 Q9UL54-2 Q9UL54-2 1 0 NS(1)PQPLRR 70.808 0.024264 1618000 308.63 474.13 601.46 417.76 530.43 460.72 480.5 193.81 594.98 403.07 TRUE FALSE FALSE 304.8682988 480.8048146 611.928159 466.0633768 503.3601778 431.2814789 521.313658 199.4175866 541.7634986 392.5981833 0.776540269 1.224674069 1.558662737 1.187125658 1.282125591 1.09853152 1.327855503 0.507943223 1.379943978 1 8.616909687 -10.25087058 24.42035648 0.894477349 1.192886779 0 0.299964739 568.5863164 1313781.202 0.041896075 0.051008165 5.61E-11 10.25087058 0.29840943 NS(ph)PSNLSSSSDTGSVGGTYR ddPTM_HeLa_Romidepsin_16h_R1 1 NSPSNLSSSSDTGSVGGTYR 20 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 NS(0.496)PS(0.496)NLS(0.008)S(0.001)SSDTGSVGGTYR 260.98 2.03E-80 11569000 1372.7 1309.7 1404.6 2023.2 570.01 569.16 544.11 424.79 1377.7 1409.8 TRUE FALSE FALSE 1355.969004 1328.137991 1429.046474 2257.131903 540.9202627 532.7925129 590.3266898 437.0806284 1254.475061 1373.173193 0.987471217 0.967203553 1.040689173 1.643734319 0.393919912 0.388000957 0.429899661 0.31829971 0.913559242 1 10.42329788 -8.652877261 14.5007214 1.036175039 0.385106248 0.748797743 0.199776503 0.27689658 35.46675007 0.027588665 0.055178846 2.22E-09 8.652877261 -0.651068791 NS(ph)S(ph)TPSTANGNDS(ph)KK ddPTM_HeLa_Romidepsin_16h_R1 1 NSSTPSTANGNDSKK 15 1 O95758-1 O95758-1 3 0 NS(0.976)S(0.278)T(0.28)PS(0.281)T(0.185)ANGNDS(1)KK 71.354 0.0030189 0 1353.9 1337.3 1583.3 1123.3 1517.2 1581.8 1209 1604.9 1892.6 1337.1 TRUE FALSE FALSE 1337.398146 1356.126545 1610.856672 1253.181231 1439.771623 1480.728085 1311.69243 1651.335249 1723.321116 1302.361949 1.026902043 1.041282376 1.236873262 0.962237289 1.105508053 1.136955887 1.007164276 1.267954158 1.323227477 1 10.34691474 -4 0.147953168 0.974223116 1.657141604 0 0.133201729 66.94220759 0.64333381 0.181595267 9.823305861 1.00E-04 4 0.682918488 NS(ph)SEASSGDFLDLK ddPTM_HeLa_Romidepsin_16h_R1 2 NSSEASSGDFLDLK 14 0 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 NS(0.472)S(0.472)EAS(0.055)S(0.001)GDFLDLK;NS(0.91)S(0.09)EAS(0.001)SGDFLDLK ; 148.36 0.00013285 61919000 2960.92 3052.4 3084.18 1972.57 3387 4313.9 3487.8 3757 3173.3 3080 TRUE FALSE FALSE 2924.831168 3095.371767 3137.858859 2200.647825 3214.148751 4038.255712 3784.053645 3865.702867 2889.4721 2999.981156 0.974949847 1.03179707 1.045959523 0.733553883 1.071389647 1.346093693 1.261359138 1.288575716 0.963163417 1 11.55073772 -8.395729973 4.675599474 0.977926035 1.292674385 0.756266601 0.085677815 0.082463479 2.775992073 0.011779011 0.02700608 4.02E-09 8.395729973 0.31474835 NS(ph)SPGEASLLEK ddPTM_HeLa_Romidepsin_16h_R1 1 NSSPGEASLLEK 12 0 Q76FK4-2;Q76FK4-4;Q76FK4 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 NS(0.5)S(0.5)PGEASLLEK 176.43 2.07E-06 20710000 4349.3 3840.9 4828.7 2720.3 4198.3 4210.7 3302.9 3937.8 4433.7 3917.9 TRUE FALSE FALSE 4296.289059 3894.972291 4912.741498 3034.833885 3984.045085 3941.649859 3583.448244 4051.73403 4037.138768 3816.112393 1.125828753 1.020664983 1.287368136 0.795268476 1.044006223 1.03289669 0.939031107 1.061743893 1.057919252 1 11.89788795 -9.249857115 24.99936632 1.07294732 0.979709643 0.247152963 0.103159669 1068.696218 2306692.598 0.015339096 0.025291137 5.63E-10 9.249857115 -0.093237677 NS(ph)TELAPPLPVR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTELAPPLPVR 12 0 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 0 NS(0.774)T(0.226)ELAPPLPVR 175.6 1.91E-05 5049300 1052.7 1260 1498.9 717.65 1398.3 1737.3 1415.5 1503.3 1263.8 1248.2 TRUE FALSE FALSE 1039.869287 1277.738313 1524.987726 800.6280696 1326.939533 1626.292137 1535.732535 1546.795614 1150.762563 1215.771584 0.855316328 1.050969055 1.254337365 0.658534942 1.091438187 1.337662566 1.263175217 1.272274853 0.94652859 1 10.24765649 -8.518624024 24.89823556 0.946849949 1.275967865 0.515138163 0.142724141 98.90783049 578797.7646 0.020597852 0.042022151 3.03E-09 8.518624024 0.329117916 NS(ph)TKEPR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTKEPR 7 1 Q13873 Q13873 BMPR2 Bone morphogenetic protein receptor type-2 1 0 NS(0.5)T(0.5)KEPR 76.17 0.025727 21503000 7378.7 6744.5 7310.5 5395.6 6915.9 7548.9 6416 7380.5 7302.1 6688.3 TRUE FALSE FALSE 7288.765566 6839.449248 7437.736186 6019.464659 6562.955816 7066.549653 6960.97488 7594.043123 6648.981888 6514.537002 1.118846292 1.049874956 1.141713706 0.924004984 1.007432426 1.084735516 1.068529487 1.165707267 1.020637673 1 12.66944693 -12.61155642 1.43317423 1.000200074 1.0729401 0.114676657 0.065509837 0.675035319 2.500029032 0.046480187 0.010817452 2.45E-13 12.61155642 0.072740026 NS(ph)TPPSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTPPSLAR 9 0 H0YAP0;Q96GY0 H0YAP0 ZC2HC1A Zinc finger C2HC domain-containing protein 1A 1 0 NS(0.421)T(0.421)PPS(0.157)LAR 123.62 0.011548 8377700 4852.4 4676.3 5062.4 4689.2 7071.4 8024.8 7543.7 7817.8 5717.5 5268.8 TRUE FALSE FALSE 4793.257082 4742.133074 5150.508948 5231.387367 6710.520071 7512.041179 8184.46169 8043.995709 5206.11248 5131.915816 0.934009297 0.924047323 1.003623039 1.019382927 1.307605251 1.463788855 1.594816046 1.567444985 1.014457888 1 12.32528179 -8.519453155 1.500469575 0.964172337 1.58092342 0.981267303 0.035205917 0.036005589 0.158092057 0.005540735 0.016398023 3.02E-09 8.519453155 0.616751082 NS(ph)TPSEPGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTPSEPGSGR 11 0 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 NS(0.408)T(0.408)PS(0.172)EPGS(0.012)GR 128.21 0.0063893 189130000 8175.5 7218.8 8857.2 6967 7975 10882 11582 4813 9312.2 9315.1 TRUE FALSE FALSE 8075.853861 7320.426456 9011.355851 7772.557321 7568.005991 10186.67532 12565.77479 4952.256561 8479.293509 9073.092359 0.890088356 0.806828165 0.993195649 0.856660223 0.834115392 1.122734666 1.384949507 0.545817938 0.934553863 1 13.14737863 -8.254957662 24.95499745 0.925974475 1.054545581 0.046532994 0.202834567 1017.928322 3919070.886 0.026222516 0.065130412 5.56E-09 8.254957662 0.128571106 NS(ph)WDSPAFSNDVIR ddPTM_HeLa_Romidepsin_16h_R1 1 NSWDSPAFSNDVIR 14 0 A0A2R8Y7T6;A0A3B3IRZ4;Q6DN90-2;Q6DN90;Q6DN90-3;A0A2R8Y695;A0A3B3IU98;A0A0C4DGT3 A0A2R8Y7T6 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 0 NS(0.76)WDS(0.224)PAFS(0.016)NDVIR 203.92 9.01E-17 18302000 3151.2 3227.4 2862.6 2686.5 3164.1 3489.9 2682.9 2736 3555 2960.3 TRUE FALSE FALSE 3112.791962 3272.835422 2912.422352 2997.12577 3002.62417 3266.906653 2910.785459 2815.161843 3237.031896 2883.390979 1.079559444 1.135064736 1.010068483 1.039444804 1.041351725 1.133008557 1.009500786 0.976337189 1.122647577 1 11.49355076 NSADDEELT(ph)NDS(ph)LTLSQSK ddPTM_HeLa_Romidepsin_16h_R1 2 NSADDEELTNDSLTLSQSK 19 0 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 2 0 NSADDEELT(0.991)NDS(0.778)LT(0.194)LS(0.036)QS(0.001)K;NSADDEELT(1)NDS(0.999)LT(0.001)LSQSK ; 119.2 0.00092278 16547000 8294.4 7660 7768.5 7968.4 5329.9 4093 4002.5 3506.7 8177.1 8121.4 TRUE FALSE FALSE 8193.304662 7767.837681 7903.707484 8889.7439 5057.895314 3831.47051 4342.47225 3608.160832 7445.719696 7910.404857 1.035763 0.981977259 0.999153346 1.123803909 0.639397781 0.484358333 0.548957017 0.456128466 0.941256463 1 12.94953582 -8.634685801 4.427853211 1.019184196 0.509861535 0.95424683 0.052193935 0.025936286 0.885988303 0.006554585 0.01345103 2.32E-09 8.634685801 -0.50932266 NSADDEELTNDS(ph)LTLSQSK ddPTM_HeLa_Romidepsin_16h_R1 1 NSADDEELTNDSLTLSQSK 19 0 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 0 NSADDEELTNDS(0.845)LT(0.153)LS(0.002)QSK 103.99 0.00011026 0 2878.9 2713.1 2616.2 2385 2053.6 1620.9 1290.5 1649.8 2702.5 2931.5 TRUE FALSE FALSE 2843.810859 2751.295093 2661.733864 2660.764922 1948.797129 1517.329721 1400.115038 1697.53436 2460.781631 2855.339207 0.995962529 0.963561557 0.932195326 0.931855982 0.682509848 0.531400864 0.49034981 0.594512328 0.861817617 1 11.47944643 -8.669492593 1.896056025 0.991135576 0.528713467 0.926210657 0.052100718 0.034050599 0.247468795 0.004933184 0.011740414 2.14E-09 8.669492593 -0.462422108 NSADYSSESK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 NSADYSSESKK 11 1 Q04727-4;Q04727;Q04727-3;H7C4W5;H7C4P7;Q5JSY7;H7C4E4;Q04727-2 Q04727-4 TLE4 Transducin-like enhancer protein 4 0 1 NSADYSSESK(1)K 184.55 7.90E-06 805840 228.56 187.27 227.56 282.38 1007.7 1112.3 870.48 577.43 176.78 166.67 FALSE TRUE FALSE 225.7742228 189.906392 231.5205863 315.0301042 956.2733088 1041.22762 944.4185495 594.137026 160.968354 162.3398894 1.390750133 1.169807327 1.426147247 1.94055882 5.890562772 6.413874149 5.817538457 3.659833873 0.991551458 1 7.342873725 -8.825701669 4.574135349 1.225811096 5.550384244 0.894587444 0.695947874 0.044299962 1.824214211 0.101740592 0.191454739 1.49E-09 8.825701669 4.324573149 NSAPASVSPDGT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 NSAPASVSPDGTR 13 0 A0A590UJM5;C9J637;A0A590UJ51;H0Y7H7;H0Y599;Q8N1I0-2;Q8N1I0;Q8N1I0-3 A0A590UJM5 DOCK4 Dedicator of cytokinesis protein 4 1 0 NSAPASVS(0.012)PDGT(0.988)R;NSAPAS(0.002)VS(0.426)PDGT(0.572)R ; 190.18 2.09E-10 22066000 4382.6 4455.7 4458.7 4202.2 4930.6 5971.1 4373.2 5709.2 4516.5 4583.5 TRUE FALSE FALSE 4329.183185 4518.427462 4536.301803 4688.078136 4678.973083 5589.565981 4744.659499 5874.386694 4112.532928 4464.420009 0.969707863 1.012097305 1.016101037 1.050097913 1.048058443 1.252025116 1.062771757 1.315823037 0.921179665 1 12.12425705 -7.539228229 0.508329827 0.98307175 1.394854135 0.707051294 0.063486232 1.230751614 0.254578863 0.011651157 0.284812362 2.89E-08 7.539228229 0.411782385 NSASAT(ph)TPLSGNSSR ddPTM_HeLa_Romidepsin_16h_R1 1 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 NS(0.027)AS(0.091)AT(0.872)T(0.01)PLSGNSSR 194.67 2.10E-12 16117000 3527.9 3041.8 3187.7 2894.2 2361.6 2466.9 2288.1 2071.2 3367.9 3171.2 TRUE FALSE FALSE 3484.900598 3084.62254 3243.180581 3228.841022 2241.07874 2309.273052 2482.451157 2131.126904 3066.666589 3088.811767 1.128233399 0.998643742 1.049976763 1.045334344 0.725547204 0.74762505 0.803691304 0.689950397 0.992830519 1 11.59283624 -8.764966825 24.54777124 1.054972654 0.746554123 0.901435009 0.047384236 16.84929462 117257.1057 0.008109425 0.015138411 1.72E-09 8.764966825 -0.308418532 NSASATT(ph)PLSGNSSR ddPTM_HeLa_Romidepsin_16h_R1 1 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 NSAS(0.002)AT(0.051)T(0.947)PLS(0.001)GNSSR 102.15 0.014741 15164000 3924.2 3756.5 3648.6 3085.6 3021 2679.2 2095.7 2196.7 4211.4 3966.9 TRUE FALSE FALSE 3876.370341 3809.384106 3712.102352 3442.37159 2866.827097 2508.007767 2273.708706 2260.258049 3834.721836 3863.839366 1.003243141 0.985906438 0.960728954 0.890919954 0.741963323 0.649097317 0.588458393 0.58497723 0.992464094 1 11.9158194 -8.650655732 1.116714368 1.001698469 0.575864314 0.99805159 0.007495036 0.01232304 0.029529948 0.001063179 0.003407136 2.24E-09 8.650655732 -0.425834155 NSASATTPLS(ph)GNSSR ddPTM_HeLa_Romidepsin_16h_R1 2 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 NS(0.001)ASAT(0.001)T(0.087)PLS(0.9)GNS(0.007)S(0.004)R;NSASATTPLS(0.999)GNSSR ; 231.41 3.65E-45 155177000 4138.5 3780.6 3668.6 4292.9 7854.9 8790.9 8335.2 8631.4 4673.3 4341.7 TRUE FALSE FALSE 4088.05837 3833.823386 3732.450444 4789.265297 7454.035142 8229.189861 9043.19168 8881.135941 4255.308344 4228.902008 0.966694987 0.906576548 0.882605092 1.132507986 1.762640782 1.945940068 2.13842545 2.100104454 1.006244253 1 12.04606742 -8.672164259 2.023921993 0.967464561 2.07793644 0.986705215 0.058202165 0.026616916 0.220842207 0.009680256 0.022504308 2.13E-09 8.672164259 1.110471879 up NSASATTPLSGNS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 2 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 NSASATT(0.002)PLS(0.118)GNS(0.578)S(0.302)R;NSASAT(0.001)T(0.003)PLS(0.059)GNS(0.585)S(0.352)R ; 127.2 0.0025033 22042000 3286.2 3086.2 2877.4 3693.7 5086.3 5536.4 3958.8 5044.2 3071.03 3080.4 TRUE FALSE FALSE 3246.14653 3129.647605 2927.47994 4120.782973 4826.727131 5182.641908 4295.060373 5190.145969 2796.349385 3000.370764 1.081915132 1.043086955 0.975706061 1.373424586 1.608710227 1.727333825 1.431509874 1.729834869 0.932001278 1 11.55092507 -9.035324124 2.817098857 1.035700961 1.617560794 0.912856368 0.089955665 0.050907077 0.808465167 0.012289656 0.02247588 9.22E-10 9.035324124 0.581859833 NSASATTPLSGNSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 NSASATTPLSGNSSR 15 0 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 NSASATTPLS(0.047)GNS(0.223)S(0.73)R;NSASATT(0.002)PLS(0.015)GNS(0.232)S(0.751)R ; 161.2 0.00020056 177402000 11517.9 11097.3 9834.8 11550 20079 18942.4 15470.9 19255 10792 10273.8 TRUE FALSE FALSE 11377.5154 11253.52808 10005.97057 12885.46534 19054.2937 17732.04177 16784.99786 19812.11305 9826.736491 10006.88519 1.136968715 1.124578514 0.9999086 1.287659955 1.904118348 1.771984132 1.677344901 1.979848141 0.981997525 1 13.28870536 -8.891938729 3.791028899 1.069253938 1.817919586 0.940512195 0.093075562 0.038769068 1.060689676 0.013923893 0.026201842 1.28E-09 8.891938729 0.748665648 NSATFK(ac)SFEDR ddPTM_HeLa_Romidepsin_16h_R1 2 NSATFKSFEDR 11 1 O43399;O43399-5;O43399-7;O43399-2;O43399-4;O43399-3;O43399-6 O43399 TPD52L2 Tumor protein D54 0 1 ; NSATFK(1)SFEDR;NSATFK(1)SFEDR 173.04 0.0018838 2619300 988.66 1031.67 984.14 598.67 1366.28 940.6 1042.9 982.85 1381.58 959.66 FALSE TRUE FALSE 976.6098316 1046.193877 1001.268544 667.8910422 1296.553633 880.4986956 1131.4839 1011.287214 1258.008025 934.7278949 1.044806555 1.119249659 1.071187187 0.714529914 1.387092052 0.941983973 1.210495489 1.081905461 1.345854801 1 9.868402638 -8.744897351 24.99999665 1.014830263 1.144064853 0.056603337 0.179758589 332.3761668 502318.1367 0.01920929 0.038333272 1.80E-09 8.744897351 0.12923459 NSDDAPWS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 NSDDAPWSPK 10 0 H0Y589;H0Y3N9;Q9UPP1-5;Q9UPP1-4;Q9UPP1-3;Q9UPP1-2;Q9UPP1 H0Y589 PHF8 Histone lysine demethylase PHF8 1 0 NS(0.002)DDAPWS(0.998)PK;NSDDAPWS(1)PK ; 122.66 0.010436 41012000 15128.5 15671.6 14462.4 10766 10260.4 8668.6 7016.7 7949.1 16875.1 15203.5 TRUE FALSE FALSE 14944.10802 15892.2252 14714.11201 12010.81558 9736.773501 8114.704437 7612.698323 8179.094667 15365.74879 14808.51088 1.009156704 1.073181856 0.993625364 0.811075177 0.657511993 0.547975722 0.514075884 0.552323913 1.037629571 1 13.85413895 -8.856524124 1.594474012 1.011636949 0.533828784 0.984041536 0.027547004 0.032447512 0.166390894 0.00451774 0.010200951 1.39E-09 8.856524124 -0.477808165 NSDLLT(ph)SPDVGLLK ddPTM_HeLa_Romidepsin_16h_R1 2 NSDLLTSPDVGLLK 14 0 P05412 P05412 JUN Transcription factor AP-1 1 0 NS(0.027)DLLT(0.852)S(0.121)PDVGLLK;NS(0.004)DLLT(0.884)S(0.112)PDVGLLK ; 131.72 0.00033389 3405500 4330.3 4257.5 4257.5 5521.2 4270.2 3659.7 3323 3277.1 4917.4 4548.7 TRUE FALSE FALSE 4277.520638 4317.437197 4331.600002 6159.587122 4052.27576 3425.856981 3605.255537 3371.917718 4477.575428 4430.524118 0.965466054 0.974475498 0.977672141 1.390261504 0.914626724 0.773239664 0.813731162 0.761065199 1.010619807 1 12.11326166 -8.519594234 24.99931043 1.013253036 0.79547543 0.480788542 0.122222346 102.3429981 778958.8351 0.018003429 0.036600882 3.02E-09 8.519594234 -0.217777606 NSEPAGLET(ph)PEAK ddPTM_HeLa_Romidepsin_16h_R1 1 NSEPAGLETPEAK 13 0 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 NSEPAGLET(1)PEAK 121.95 0.0092605 5991900 873.52 970.98 942.63 546.56 994.9 1333.1 818.98 871.84 956.58 719.33 TRUE FALSE FALSE 862.8732023 984.6494819 959.0360797 609.7558388 944.1265405 1247.919212 888.5441408 897.0653149 871.021089 700.6417029 1.231547021 1.405353803 1.368796741 0.870281966 1.347516907 1.781108957 1.268186203 1.28034816 1.243176199 1 9.452533051 -12.81192313 0.183445457 0.664729133 1.447487087 0.078883838 0.220820893 13.13233015 0.570103086 2.517929793 0.429557957 1.54E-13 12.81192313 0.782757954 NSESESNKVAAET(ph)QSPSLFGSTK ddPTM_HeLa_Romidepsin_16h_R1 1 NSESESNKVAAETQSPSLFGSTK 23 1 Q9UKX7;Q9UKX7-2 Q9UKX7 NUP50 Nuclear pore complex protein Nup50 1 0 NSESESNKVAAET(0.994)QS(0.004)PS(0.001)LFGSTK 111.95 5.26E-06 23958000 4107.7 3837 3190.7 4671.8 5148.8 5419.5 4399.4 5192.2 3700.5 3631.8 TRUE FALSE FALSE 4057.633772 3891.017387 3246.232795 5211.975497 4886.037523 5073.211441 4773.084926 5342.428115 3369.518012 3537.445312 1.147052015 1.099951248 0.917677168 1.473372741 1.381233374 1.434145546 1.349302817 1.510250377 0.952528651 1 11.78849213 -9.251989619 24.99982455 1.063631198 1.422755364 0.864345911 0.079649284 196.332023 519406.4143 0.011990622 0.019714821 5.60E-10 9.251989619 0.359124166 NSESESNKVAAETQS(ph)PSLFGSTK ddPTM_HeLa_Romidepsin_16h_R1 1 NSESESNKVAAETQSPSLFGSTK 23 1 Q9UKX7;Q9UKX7-2 Q9UKX7 NUP50 Nuclear pore complex protein Nup50 1 0 NSESESNKVAAET(0.014)QS(0.638)PS(0.34)LFGS(0.006)T(0.002)K 76.762 0.0002493 23287000 2803.2 2609.4 2090.7 3084.6 3112.1 3430.8 3937.1 3515 2569.9 2216.7 TRUE FALSE FALSE 2769.03352 2646.135202 2127.087756 3441.255965 2953.277924 3211.582952 4271.517176 3616.700979 2340.041708 2159.109814 1.282488506 1.225567678 0.985168861 1.593830912 1.367822009 1.487456975 1.97836958 1.675088944 1.083799301 1 11.07622091 -4 0.202207497 1.010137572 5.252841791 0.687214265 0.169863971 20.55460654 0.237025948 0.154272014 27.94347484 1.00E-04 4 4.242704218 NSFNNPAYYVLEGVPHQLLPPEPPS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 NSFNNPAYYVLEGVPHQLLPPEPPSPAR 28 0 O15357;A0A0A0MTP6;O15357-2 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 1 0 NSFNNPAYYVLEGVPHQLLPPEPPS(1)PAR 105.38 6.96E-09 16382000 1106.4 1301.2 1200.4 12435 0 1437.7 1043.6 982.04 1155.2 1232 TRUE FALSE FALSE 1092.914771 1319.518328 1221.292458 13872.79321 0 1345.83561 1132.243358 1010.453778 1051.876019 1199.992462 0.91076803 1.099605513 1.017750108 11.56073362 0 1.12153672 0.943542058 0.842050104 0.876568855 1 10.22880963 -9.459049806 24.99987876 0.971593628 2.902351837 0.088100978 3.076917757 430.5454526 168631.4292 0.465582612 0.71118886 3.47E-10 9.459049806 1.930758208 NSGEPLPPKPGPGSPS(ph)HPGALDLDGVSR ddPTM_HeLa_Romidepsin_16h_R1 1 NSGEPLPPKPGPGSPSHPGALDLDGVSR 28 1 A1X283;G3V144;A0A1B0GUF2 A1X283 SH3PXD2B SH3 and PX domain-containing protein 2B 1 0 NSGEPLPPKPGPGS(0.386)PS(0.614)HPGALDLDGVSR 70.465 4.71E-05 42210000 2349.5 1950.1 2157.3 2102.5 2205.2 2807.9 2509.1 2467.4 2336.4 2150.4 TRUE FALSE FALSE 2320.86339 1977.553559 2194.846902 2345.600943 2092.660415 2628.484252 2722.222891 2538.790326 2127.426532 2094.532298 1.108058058 0.944150425 1.047893558 1.119868595 0.9991063 1.254926579 1.299680551 1.212103689 1.015704811 1 11.03241242 -8.252521032 24.10230167 1.045961813 1.25998134 0.780436269 0.053670021 150.9740792 408013.2371 0.008191918 0.020524133 5.59E-09 8.252521032 0.214019528 NSGLSK(ac)EQK ddPTM_HeLa_Romidepsin_16h_R1 2 NSGLSKEQK 9 1 O95251-4;O95251;O95251-2;E7EUP3;O95251-3;O95251-5 O95251-4 KAT7 Histone acetyltransferase KAT7;Histone acetyltransferase 0 1 ; NSGLSK(1)EQK;NSGLSK(1)EQK 164.66 0.0063751 26678000 7115 6591.6 8409.7 7228.9 7572 7334.5 8145.9 3423.2 8503.6 7503 FALSE TRUE FALSE 7028.279643 6684.396718 8556.067301 8064.739431 7185.572585 6865.849121 8837.812543 3522.244891 7743.016718 7308.070978 0.961714749 0.914659523 1.170769595 1.103538739 0.983237931 0.939488566 1.209322209 0.481966432 1.059515807 1 12.83527493 -7.247210296 24.91229895 1.006426824 0.481966055 0.737392349 0.097930814 950.648958 1664370.109 0.012923538 0.371383538 5.66E-08 7.247210296 -0.524460769 NSGSDGS(ph)PS(ph)PLLAR ddPTM_HeLa_Romidepsin_16h_R1 2 NSGSDGSPSPLLAR 14 0 Q9HCH0;Q9HCH0-2;H7C1V4 Q9HCH0 NCKAP5L Nck-associated protein 5-like 2 0 NS(0.045)GS(0.107)DGS(0.847)PS(1)PLLAR;NS(0.001)GS(0.002)DGS(0.996)PS(1)PLLAR ; 160.46 0.0033465 17062700 6334.7 6736.1 5375.8 5402.8 5886 5188.8 4372.2 5379.5 6701.7 6019.9 TRUE FALSE FALSE 6257.49024 6830.930993 5469.363544 6027.497157 5585.615456 4857.252426 4743.574559 5535.147345 6102.283167 5863.50213 1.067193309 1.164991645 0.932781028 1.027968784 0.952607389 0.828387595 0.809000228 0.944000228 1.04072328 1 12.51754689 -8.543593371 2.472638543 1.035840259 0.855346696 0.609027912 0.063953242 0.147889004 1.809526932 0.009589896 0.022692467 2.86E-09 8.543593371 -0.180493563 NSGSDGSPS(ph)PLLAR ddPTM_HeLa_Romidepsin_16h_R1 2 NSGSDGSPSPLLAR 14 0 Q9HCH0;Q9HCH0-2;H7C1V4 Q9HCH0 NCKAP5L Nck-associated protein 5-like 1 0 NSGSDGS(0.001)PS(0.999)PLLAR;NSGSDGS(0.005)PS(0.995)PLLAR ; 167.18 8.45E-05 54708000 2587.66 3336.2 2581.7 2625.16 3442.5 3565.1 3203.2 3783.8 3370.9 2903.8 TRUE FALSE FALSE 2556.120605 3383.167111 2626.633406 2928.693351 3266.816379 3337.301616 3475.279728 3893.278283 3069.398261 2828.358857 0.903746919 1.196159074 0.928677561 1.035474457 1.155021885 1.179942781 1.228726588 1.376514961 1.085222356 1 11.46574946 -7.431869242 0.475442665 0.959654159 1.598188996 0.608569009 0.086949651 1.469347609 0.246922792 0.018085688 0.508198958 3.70E-08 7.431869242 0.638534837 NSITEIS(ph)DNEDDLLEYHR ddPTM_HeLa_Romidepsin_16h_R1 2 NSITEISDNEDDLLEYHR 18 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 NSITEIS(1)DNEDDLLEYHR;NSIT(0.001)EIS(0.999)DNEDDLLEYHR ; 207.13 1.05E-21 7257900 4546.1 3968.6 4839.5 3573 3982.1 3946.5 2945.9 2868.58 5142.3 5279.5 TRUE FALSE FALSE 4490.690385 4024.470055 4923.729467 3986.127071 3778.878578 3694.331387 3196.124672 2951.577836 4682.359809 5142.337829 0.873277979 0.782614871 0.957488526 0.775158538 0.73485615 0.718414758 0.621531447 0.573975871 0.910550797 1 12.32820868 -6.339597449 0.20301057 1.012580983 2.64E-17 0.832904605 0.054365147 4.971096529 0.131771734 0.055358921 1.349703061 4.58E-07 6.339597449 -1.012580983 NSK(ac)LLSTSAK ddPTM_HeLa_Romidepsin_16h_R1 2 NSKLLSTSAK 10 1 C9J2P0;P51965-3;P51965 C9J2P0 UBE2E1 Ubiquitin-conjugating enzyme E2 E1 0 1 ; NSK(1)LLSTSAK;NSK(1)LLSTSAK 150.09 0.014777 3139400 2719.5 2204.09 3126.3 4314.3 5040.1 4541.8 4209.6 3449.6 2590 1933.8 FALSE TRUE FALSE 2686.353688 2235.119237 3180.71194 4813.139665 4782.88489 4251.593638 4567.163319 3549.408733 2358.343913 1883.559597 1.426211144 1.186646411 1.688670719 2.555342381 2.539279828 2.257212166 2.42475116 1.884415411 1.252067583 1 10.87924597 -9.499542602 3.197330155 1.206927215 2.341971848 0.869087877 0.204274892 0.069817229 1.461315642 0.037269941 0.056646511 3.17E-10 9.499542602 1.135044633 NSKYEYDPDIS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 NSKYEYDPDISPPR 14 1 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 0 NSKYEYDPDIS(1)PPR 164.66 9.31E-05 0 624 761.31 468.41 1166.1 630.77 641.35 700.42 569.12 714.56 597.5 TRUE FALSE FALSE 616.394448 772.0277422 476.5624796 1300.929969 598.5794532 600.3698049 759.9136573 585.5865893 650.647964 581.9768639 1.059139093 1.326560883 0.818868428 2.235363722 1.02852792 1.031604248 1.305745476 1.006202524 1.117996272 1 9.184817991 -10.30262757 1.508925655 1.019360107 1.26696072 0.047898238 0.365854609 0.723439184 3.144772835 0.067537989 0.07883483 4.98E-11 10.30262757 0.247600613 NSLEDNSWVFPS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 NSLEDNSWVFPSPPK 15 0 Q9H6S1 Q9H6S1 AZI2 5-azacytidine-induced protein 2 1 0 NSLEDNSWVFPS(1)PPK 118.52 0.00020625 0 614.63 639.48 793.93 538.13 685.23 593.15 287.93 491.91 594.94 759.35 TRUE FALSE FALSE 607.1386531 648.4826162 807.7480186 600.3511226 650.2601562 555.2496293 312.386767 506.1426397 541.7270763 739.6219775 0.820876977 0.876775753 1.092109271 0.811699951 0.879179062 0.750720836 0.422360039 0.684326122 0.732437776 1 9.530644284 -8.051475768 2.861003119 0.914658813 0.553277324 0.559319965 0.115085938 0.117383125 1.886903517 0.014996572 0.048133806 8.88E-09 8.051475768 -0.361381489 NSLESISS(ph)IDR ddPTM_HeLa_Romidepsin_16h_R1 1 NSLESISSIDR 11 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 NS(0.178)LES(0.252)IS(0.172)S(0.398)IDR 106.79 0.01605 14939000 2050.3 1858.4 2121 1147.6 2082.9 2730.4 1847.7 2017.2 1991.7 1934.9 TRUE FALSE FALSE 2025.310155 1884.562604 2157.915115 1280.290912 1976.601841 2555.936252 2004.643592 2075.564499 1813.557364 1884.631019 1.074645453 0.999963698 1.145006685 0.679332399 1.048800439 1.356199822 1.063679612 1.101310802 0.962287761 1 10.88006638 -8.501375053 24.97298044 1.013792598 1.169354231 0.27090273 0.136574654 883.4710347 1026005.291 0.018760882 0.04157299 3.15E-09 8.501375053 0.155561632 NSLESISSIDRELS(ph)PEGPGKEK ddPTM_HeLa_Romidepsin_16h_R1 1 NSLESISSIDRELSPEGPGKEK 22 2 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 NSLES(0.002)IS(0.009)S(0.009)IDRELS(0.98)PEGPGKEK 53.454 0.011991 6160300 2898.4 2760.5 2379.6 2244.2 3197.9 3494.3 2550.6 2933.5 3020.3 2607.6 TRUE FALSE FALSE 2863.073186 2799.362391 2421.01594 2503.684963 3034.69923 3271.025507 2767.2479 3018.376194 2750.156804 2539.854176 1.127258885 1.102174455 0.953210607 0.985759335 1.194832073 1.287879256 1.089530228 1.188405312 1.082801064 1 11.31052995 -4 0.113223636 0.977145396 1.622368011 0.234219602 0.086560589 116.7405459 0.920781324 0.51020765 11.85122806 1.00E-04 4 0.645222615 NSLESYAFNMK ddPTM_HeLa_Romidepsin_16h_R1 1 NSLESYAFNMK 11 0 P11142;E9PKE3;E9PNE6;A8K7Q2;E9PM13;E9PS65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 117.01 0.028156 10558000 1856.8 1750.8 1653.2 1681.5 2017.6 2426.1 2132.9 2104.1 1946.2 1417.3 FALSE FALSE TRUE 1834.168607 1775.447808 1681.973253 1875.922942 1914.634343 2271.08004 2314.068473 2164.978814 1772.126998 1380.478342 1.328647145 1.286110586 1.218398871 1.358893425 1.386935445 1.645139928 1.676280173 1.568281623 1.283705035 1 10.43095254 -4.000000001 0.083433945 0.655179745 3.409365141 0.670261013 0.112677435 48.03900282 0.29341643 1.427539779 15.28179964 1.00E-04 4.000000001 2.754185396 NSLLAGGDDDTMSVIS(ph)GISSR ddPTM_HeLa_Romidepsin_16h_R1 3 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 0 NSLLAGGDDDT(0.187)MS(0.12)VIS(0.635)GIS(0.056)S(0.002)R;NSLLAGGDDDTMS(0.025)VIS(0.974)GIS(0.001)SR;NSLLAGGDDDTMS(0.017)VIS(0.977)GIS(0.005)SR ;; 161.59 3.85E-08 47893200 12240.5 11641.9 12141.6 11459.2 6827.7 6384.5 6432.41 6963.6 13225.8 11230.1 TRUE FALSE FALSE 12091.30808 11805.79497 12352.91945 12784.16662 6479.256991 5976.551055 6978.778745 7165.080779 12042.85132 10938.34038 1.10540609 1.079304041 1.129323007 1.16874829 0.592343698 0.546385543 0.638010749 0.65504277 1.100976099 1 13.41710624 -8.75474038 24.99714484 1.067459644 0.605695936 0.952302842 0.053400651 29.455049 109909.735 0.009422175 0.018506762 1.76E-09 8.75474038 -0.461763708 NSLLAGGDDDTMSVISGIS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 2 NSLLAGGDDDTMSVISGISSR 21 0 Q8N3U4;Q8N3U4-2 Q8N3U4 STAG2 Cohesin subunit SA-2 1 0 NSLLAGGDDDT(0.001)MS(0.001)VIS(0.036)GIS(0.793)S(0.169)R;NSLLAGGDDDT(0.255)MS(0.255)VIS(0.021)GIS(0.374)S(0.096)R ; 97.589 0.00083154 34632000 6066.1 5482.1 5710.4 5440.2 3382.3 3832.7 2867.4 3407.7 7003.2 5639.8 TRUE FALSE FALSE 5992.16404 5559.277148 5809.787117 6069.221521 3209.68861 3587.802839 3110.956884 3506.296423 6376.816252 5493.277183 1.090817711 1.012014679 1.057617689 1.104845308 0.584293947 0.653126125 0.566320755 0.63828864 1.160840067 1 12.42345137 -8.758858296 24.99999402 1.046412182 0.610395306 0.948976539 0.052125568 8.97688749 86947.06315 0.00636436 0.012274514 1.74E-09 8.758858296 -0.436016876 NSLSDS(ph)PLVAGPEAAR ddPTM_HeLa_Romidepsin_16h_R1 1 NSLSDSPLVAGPEAAR 16 0 H0YBQ5;E5RFK5 H0YBQ5 CCNC 1 0 NS(0.133)LS(0.133)DS(0.735)PLVAGPEAAR 136.85 0.0011874 2404000 981.29 1075.9 939.63 1153 1404.8 1242.6 955.96 1001.6 1148.3 1030.6 TRUE FALSE FALSE 969.32966 1091.046548 955.983866 1286.315285 1333.107814 1163.20187 1037.159219 1030.579716 1045.593172 1003.824863 0.965636233 1.086889345 0.952341291 1.281414051 1.328028287 1.158769734 1.033207342 1.026652909 1.041609159 1 9.97129187 -9.277534911 24.9870247 0.990591666 1.166901244 0.395368739 0.095255083 589.6803644 915429.492 0.015486714 0.023701862 5.28E-10 9.277534911 0.176309578 NSNLVGAAHEELQQSR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNLVGAAHEELQQSR 16 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 154.47 4.46E-07 0 1820.3 1469.3 1429.7 1568 2019.8 2349.4 1940.9 2037.1 1646.3 1737.2 FALSE FALSE TRUE 1798.113483 1489.984844 1454.583329 1749.299538 1916.722069 2199.280922 2105.759998 2096.040274 1499.050805 1692.067294 1.062672561 0.880570678 0.859648629 1.033823858 1.13276941 1.299759726 1.24448951 1.238745222 0.885928598 1 10.72457123 -8.566612185 2.76905302 1.003643074 1.258200251 0.758993879 0.075344811 0.114593898 1.775026211 0.011327011 0.025732084 2.71E-09 8.566612185 0.254557177 NSNPVIAELSQAINSGT(ph)LLSKPSPPLPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 NS(0.001)NPVIAELS(0.067)QAINS(0.179)GT(0.753)LLSKPSPPLPPKR 104.03 1.43E-09 43728000 4324.2 4325.2 4036.1 4278.8 4563.3 5176.6 4036 4889.9 4991 4421.8 TRUE FALSE FALSE 4271.494987 4386.090279 4106.346627 4773.534988 4330.417773 4845.831967 4378.817739 5031.381542 4544.59246 4306.920999 0.991774632 1.018381874 0.953429754 1.108340504 1.005455585 1.125126736 1.016693304 1.168208459 1.055183613 1 12.07244115 -4 0.322211451 0.992099146 2.450565815 0.369730143 0.051467119 29.25571006 0.372665744 0.013984268 25.55301477 1.00E-04 4 1.45846667 NSNPVIAELSQAINSGTLLSKPS(ph)PPLPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 NSNPVIAELS(0.004)QAINS(0.086)GT(0.072)LLS(0.072)KPS(0.765)PPLPPKR 47.286 0.0102 3182700 311.61 240.67 322.81 468.84 385.04 410.63 459.09 400.63 473.78 476.57 TRUE FALSE FALSE 307.8119775 244.0581586 328.4283726 523.0494868 365.389972 384.3920682 498.0850931 412.221597 431.4039302 464.1886427 0.663118287 0.525773653 0.707532116 1.126803714 0.787158363 0.828094514 1.073023007 0.888047572 0.929372006 1 8.858567414 -9.296271175 24.88711721 0.799132283 0.93320336 0.220744841 0.158231574 1041.875484 744411.1132 0.02938495 0.044887483 5.06E-10 9.296271175 0.134071077 NSNPVIAELSQAINSGTLLSKPSPPLPPKR ddPTM_HeLa_Romidepsin_16h_R1 2 NSNPVIAELSQAINSGTLLSKPSPPLPPKR 30 2 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 0 0 ; ; 189.18 4.98E-30 8536100 2204.99 2152.26 2305.3 2231.6 2546.58 2336.12 2486.74 2631.09 2749.2 2171.31 FALSE FALSE TRUE 2178.114734 2182.559573 2345.422779 2489.628092 2416.61852 2186.849471 2697.963634 2707.216438 2503.304667 2114.899053 1.029890637 1.031992316 1.108999872 1.177185307 1.142663768 1.034020734 1.275693811 1.280068868 1.183652082 1 11.04637309 -4.000000002 0.229403452 0.990330068 2.669146045 0.333539206 0.079597061 18.43446827 0.224018811 0.036920299 11.73173756 1.00E-04 4.000000002 1.678815976 YISENES(ph)PRPSQK ddPTM_HeLa_Romidepsin_16h_R1 1 YISENESPRPSQK 13 1 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 YISENES(0.824)PRPS(0.176)QK 127.3 0.021127 4172600 2239.2 2111.8 2448.2 1870.8 1333.9 1085.1 832.41 943.14 2240.5 2629.8 TRUE FALSE FALSE 2211.907769 2141.529976 2490.809894 2087.110698 1265.826106 1015.765612 903.1148846 970.4282679 2040.104069 2561.477417 0.863528116 0.836052647 0.972411421 0.814807378 0.494178124 0.396554584 0.352575775 0.378854899 0.796456004 1 11.32276046 -8.747242129 2.245052671 0.928063784 0.37384234 0.934303793 0.062222741 0.048115959 0.49450999 0.009491758 0.020570091 1.79E-09 8.747242129 -0.554221443 down NSNSPPSPS(ph)SMNQR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 0 NSNS(0.005)PPS(0.013)PS(0.491)S(0.491)MNQR 95.775 0.019113 28445000 3675.1 3495.9 2910.1 3121.1 1966.6 1723.3 1189.3 1303.3 3393.8 2876.6 TRUE FALSE FALSE 3630.306468 3545.115372 2960.74907 3481.976267 1866.237064 1613.186692 1290.319112 1341.008929 3090.250028 2801.865517 1.295674773 1.265269639 1.056706345 1.242734973 0.666069464 0.575754504 0.460521429 0.478612882 1.102925893 1 11.452172 -8.646203282 3.851546981 1.15303237 0.514699598 0.911618669 0.094558276 0.062994944 1.752089272 0.018901507 0.039208486 2.26E-09 8.646203282 -0.638332772 NSPCLVY(ph)VT(ph)FNQK ddPTM_HeLa_Romidepsin_16h_R1 1 NSPCLVYVTFNQK 13 0 Q969R8;H0YFM4 Q969R8 ITFG2 Integrin-alpha FG-GAP repeat-containing protein 2 2 0 NSPCLVY(1)VT(1)FNQK 76.311 0.0031508 0 534.62 565.03 701.91 488.15 672.8 723.09 497.46 584.78 626.3 806.46 TRUE FALSE FALSE 528.1038458 572.9845072 714.1264491 544.5921998 638.4645054 676.8868827 539.71424 601.6996867 570.2821594 785.5080529 0.672308634 0.729444472 0.909126834 0.693299321 0.812804532 0.861718578 0.687089379 0.76600066 0.726004218 1 9.617482256 -12.44605553 1.154160164 1.001245838 0.760497111 0 0.110859844 0.277502529 0.655795163 0.053741576 0.013104991 3.58E-13 12.44605553 -0.240748727 NSPFQIPPPS(ph)PDSK ddPTM_HeLa_Romidepsin_16h_R1 3 NSPFQIPPPSPDSK 14 0 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 NSPFQIPPPS(0.915)PDS(0.085)K;NSPFQIPPPS(0.924)PDS(0.076)K;NSPFQIPPPS(0.753)PDS(0.247)K ;; 104.2 0.0082784 91186000 12247 13687.9 11242.9 11250.7 13015.4 12546.9 10021.5 12642.3 13538.5 12047.1 TRUE FALSE FALSE 12097.72885 13880.59862 11438.57796 12551.55887 12351.17557 11745.19358 10872.72596 13008.085 12327.58265 11734.11461 1.030987787 1.182926798 0.974813895 1.069663907 1.052586922 1.000944168 0.926591083 1.108569793 1.050576295 1 13.51842137 -6.922836511 19.48075933 1.024136383 3.798546103 0.10056731 0.064738576 5417429.139 15536370.44 5.068761776 646251837.5 1.19E-07 6.922836511 2.774409719 NSPNNISGISNPPGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 NSPNNISGISNPPGTPR 17 0 Q9NW25;Q9BWW4-2;Q9BWW4-3;Q9BWW4;A0A087WVT6 Q9NW25 SSBP3 Single-stranded DNA-binding protein 3 1 0 NSPNNISGISNPPGT(1)PR;NSPNNISGISNPPGT(1)PR;NSPNNISGISNPPGT(1)PR;NSPNNISGISNPPGT(1)PR ;;; 237.66 2.87E-46 104794000 4751.5 5121.94 4454.59 3401.68 4619.07 4412.33 3843.87 3788.49 5757 4755.82 TRUE FALSE FALSE 4693.58689 5194.046806 4532.12027 3794.998247 4383.341622 4130.396353 4170.368222 3898.103981 5242.079501 4632.263111 1.013238406 1.121276292 0.978381444 0.819253604 0.946263525 0.891658409 0.900287424 0.841511781 1.131645456 1 12.17750148 -9.468436653 7.628895543 1.016674466 0.886240788 0.660130492 0.058973277 0.134065755 16.86169356 0.00701424 0.010685259 3.40E-10 9.468436653 -0.130433678 PSSTTPTPLVS(ph)ETGGNSPSDKVDNELK ddPTM_HeLa_Romidepsin_16h_R1 1 PSSTTPTPLVSETGGNSPSDKVDNELK 27 1 A0A3B3IRW6;Q2KHR3-2;Q2KHR3;H0YCQ7 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 1 0 PSSTTPT(0.002)PLVS(0.418)ET(0.418)GGNS(0.158)PS(0.004)DKVDNELK 77.693 3.49E-06 20842000 3153.1 3078.7 3533.8 3006 1642 1334.2 1424.5 1159.3 2872.4 3719.3 TRUE FALSE FALSE 3114.668804 3122.042019 3595.304307 3353.567864 1558.202613 1248.948926 1545.496994 1192.842516 2615.48535 3622.67205 0.85977112 0.861806417 0.992445426 0.925716658 0.43012522 0.344759037 0.42661797 0.32927146 0.721976849 1 11.82283849 -8.742193296 5.126254874 0.931557424 0.376803561 0.900244557 0.082887227 0.028459281 2.004892688 0.009352939 0.018428446 1.81E-09 8.742193296 -0.554753863 down ATSDTLES(ph)PPKIIPK ddPTM_HeLa_Romidepsin_16h_R1 1 ATSDTLESPPKIIPK 15 1 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 AT(0.004)S(0.018)DT(0.01)LES(0.968)PPKIIPK 60.542 0.029874 32069000 6885.9 6455.7 5502.9 5541.2 2467.1 2038 1802.5 1743.7 6366.9 5844.7 TRUE FALSE FALSE 6801.972002 6546.583514 5598.675666 6181.899616 2341.194681 1907.778377 1955.604305 1794.151208 5797.428518 5692.853851 1.194826388 1.149965147 0.983456771 1.085905203 0.411251499 0.335118102 0.343519148 0.315158487 1.018369463 1 12.47493635 -8.741238401 4.937820026 1.090959489 0.340226343 0.968012008 0.064224887 0.028275738 1.768923771 0.012244164 0.024173471 1.81E-09 8.741238401 -0.750733146 down NSPS(ph)NLSSSSDTGSVGGTYR ddPTM_HeLa_Romidepsin_16h_R1 1 NSPSNLSSSSDTGSVGGTYR 20 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 NS(0.237)PS(0.6)NLS(0.123)S(0.026)S(0.007)S(0.007)DTGSVGGTYR 82.651 0.003742 9756600 299.03 349.21 420.69 597.65 210.88 155.1 279.67 138.48 357.88 415.9 TRUE FALSE FALSE 295.3853073 354.1261875 428.011933 666.753105 200.1180067 145.1896106 303.4251628 142.4867003 325.8703165 405.094858 0.729175652 0.8741809 1.05657212 1.64591846 0.494002831 0.35840892 0.749022499 0.35173663 0.804429654 1 8.662115962 NSPT(ph)FKS(ph)FEERVETTVTSLKVQMK ddPTM_HeLa_Romidepsin_16h_R1 1 NSPTFKSFEERVETTVTSLKVQMK 24 3 E9PNK6 E9PNK6 TPD52L1 2 0 NS(0.17)PT(0.829)FKS(0.813)FEERVET(0.167)T(0.008)VT(0.007)S(0.007)LKVQMK 47.808 0.012846 23577000 485.56 421.33 403.55 344.89 444.02 441.82 471.93 497.79 461.29 466.52 TRUE FALSE FALSE 479.641808 427.2614948 410.5736185 384.7678046 421.3600025 413.5891279 512.0157224 512.1927683 420.0310671 454.3997431 1.05555035 0.940276708 0.903551608 0.846760612 0.927289262 0.910187856 1.126795801 1.127185426 0.924364667 1 8.827818209 -7.740092439 24.37375798 0.985749695 1.126990856 0.458121271 0.067906485 164.174651 187449.1873 0.011470426 0.042824004 1.82E-08 7.740092439 0.141241162 NSQDDYDEER ddPTM_HeLa_Romidepsin_16h_R1 1 NSQDDYDEER 10 0 O76094-2;O76094;R4GNC1;D6RDY6 O76094-2 SRP72 Signal recognition particle subunit SRP72 0 0 187.42 9.34E-07 4598900 3163.8 2428.1 3228.3 2496.3 3151.9 2698.8 3025.8 2830.8 3697.6 3642.5 FALSE FALSE TRUE 3125.238389 2462.282856 3284.487207 2784.933951 2991.046782 2526.35539 3282.811376 2912.704732 3366.877395 3547.867325 0.880878032 0.694017738 0.92576382 0.784960005 0.843054857 0.712077189 0.925291471 0.820973409 0.948986275 1 11.79273634 -11.30485308 0.800400802 0.987753107 0.81875825 0.392827756 0.07514665 0.345742028 0.471546989 0.027078815 0.015938541 4.96E-12 11.30485308 -0.168994857 NSQEDS(ph)EDS(ph)EDKDVK ddPTM_HeLa_Romidepsin_16h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 2 0 NS(0.445)QEDS(0.555)EDS(1)EDKDVK 148.33 0.0072266 24004000 11178 10690 10369 9498.7 10130 10949 9856.4 10341 11195 10387 TRUE FALSE FALSE 11041.75824 10840.4941 10549.4681 10596.98439 9613.0283 10249.39424 10693.60237 10640.20052 10193.69116 10117.14424 1.091390809 1.071497435 1.042731807 1.047428418 0.950172111 1.01307187 1.056978344 1.051699992 1.00756606 1 13.3045145 -8.910715424 21.58042368 1.046768132 1.017714309 0.098441697 0.036911064 14.67235805 3537.870077 0.006598716 0.01196119 1.23E-09 8.910715424 -0.029053823 NSQEDS(ph)EDSEDKDVK ddPTM_HeLa_Romidepsin_16h_R1 3 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 NS(0.001)QEDS(0.995)EDS(0.004)EDKDVK;NSQEDS(0.986)EDS(0.013)EDKDVK;NS(0.011)QEDS(0.975)EDS(0.013)EDKDVK ;; 142.4 0.003835 1147981000 17831.9 19044.6 16697.7 16909 16452.3 16614.3 16670.2 11606.1 18723.7 17402.2 TRUE FALSE FALSE 17614.55794 19312.71038 16988.31646 18864.09814 15612.67774 15552.69985 18086.16637 11941.90419 17049.00538 16950.08834 1.039201543 1.139387005 1.002255335 1.112920344 0.921097131 0.917558631 1.067024904 0.704533449 1.005835783 1 14.04900517 -7.256333838 24.71395754 1.021326272 0.704533293 0.661667597 0.068269889 208.7200211 1010293.972 0.009164462 0.101901488 5.54E-08 7.256333838 -0.316792979 NSQEDSEDSEDKDVK ddPTM_HeLa_Romidepsin_16h_R1 1 NSQEDSEDSEDKDVK 15 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 0 113.4 0.004557 4428500 1130.2 1176 1233.6 1205.3 1033.5 1105.7 1122 603.91 1684.6 1672 FALSE FALSE TRUE 1116.424688 1192.555759 1255.070291 1344.662457 980.7566385 1035.049338 1217.302652 621.383183 1533.925157 1628.561199 0.685528237 0.73227568 0.770662037 0.825675116 0.602222771 0.635560604 0.747471236 0.381553474 0.941889785 1 10.66938222 -16.52287875 0.126088915 2.109034545 0.512616885 0.624461102 0.102084523 41.73033887 0.375878822 11.75351249 0.41143116 3.00E-17 16.52287875 -1.59641766 NSRPEANEALER ddPTM_HeLa_Romidepsin_16h_R1 1 NSRPEANEALER 12 1 Q9Y696 Q9Y696 CLIC4 Chloride intracellular channel protein 4 0 0 155.88 0.0014206 7264500 1577.2 1761 1645.3 1401.6 2180.6 2465.4 2107.5 2175.6 2127.1 2013.4 FALSE FALSE TRUE 1557.97648 1785.791404 1673.935756 1563.659587 2069.315845 2307.868897 2286.510997 2238.547553 1936.846849 1961.091578 0.794443512 0.910610919 0.853573477 0.797341442 1.055185728 1.176828723 1.165937901 1.141480377 0.987637125 1 10.93744119 -8.560009239 4.628960577 0.890854461 1.156819713 0.781110971 0.065064913 0.085113987 4.221235193 0.012189324 0.025533794 2.75E-09 8.560009239 0.265965252 NSS(ph)EASSGDFLDLK ddPTM_HeLa_Romidepsin_16h_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 0 NS(0.034)S(0.881)EAS(0.076)S(0.008)GDFLDLK;NS(0.255)S(0.738)EAS(0.006)S(0.001)GDFLDLK;NS(0.033)S(0.966)EAS(0.001)SGDFLDLK ;; 242.67 2.23E-54 201324000 8768.3 9060.7 9505.3 6937.6 14193.3 18566.5 18029.6 18783.1 9242.5 8875.5 TRUE FALSE FALSE 8661.428587 9188.256772 9670.735759 7739.757954 13468.96294 17380.16057 19561.03377 19326.55936 8415.827652 8644.913231 1.001910413 1.062851243 1.118661981 0.895296199 1.558021761 2.010449395 2.262721817 2.235598999 0.973500535 1 13.07763577 -8.40136375 1.912139992 1.006893143 2.239464855 0.976165053 0.081498122 0.030820115 0.217865263 0.010975671 0.031381825 3.97E-09 8.40136375 1.232571711 up NSS(ph)LLSFDNEDENE ddPTM_HeLa_Romidepsin_16h_R1 1 NSSLLSFDNEDENE 14 0 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 0 NS(0.189)S(0.811)LLSFDNEDENE 139.48 0.0010344 4901800 1903.4 1839.9 2065.6 1504.5 1493.4 1835.3 1611.8 1635.8 1941.5 1941.4 TRUE FALSE FALSE 1880.200629 1865.80216 2101.550902 1678.457369 1417.186225 1718.030253 1748.706252 1683.129292 1767.847377 1890.962148 0.994308972 0.986694611 1.111365927 0.887620818 0.749452456 0.908548199 0.924770627 0.890091477 0.934893054 1 10.88490477 -9.077673913 10.15598748 1.00393969 0.868106162 0.553324103 0.060102575 0.290113848 36.8402868 0.008279896 0.013744497 8.36E-10 9.077673913 -0.135833529 NSS(ph)MDEEIENPYWSVR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSMDEEIENPYWSVR 16 0 Q155Q3;Q155Q3-5;Q155Q3-4 Q155Q3 DIXDC1 Dixin 1 0 NS(0.034)S(0.966)MDEEIENPYWSVR 101.72 0.0070162 3738600 1065.1 969.42 1114.1 1077.3 1535.4 1537.7 1605.3 1885.4 1233.9 1043.4 TRUE FALSE FALSE 1052.118152 983.0675202 1133.490443 1201.862495 1457.042809 1439.445933 1741.654142 1939.951074 1123.536894 1016.292318 1.035251505 0.967307834 1.115319307 1.182595277 1.433684761 1.416369983 1.713733452 1.90885146 1.105525324 1 9.989099711 -7.678808985 0.559174511 1.002352142 2.271162483 0.955876131 0.06400026 0.281143232 0.078565715 0.010647548 0.21076414 2.10E-08 7.678808985 1.268810341 NSS(ph)PAPPQPAPGK ddPTM_HeLa_Romidepsin_16h_R1 3 NSSPAPPQPAPGK 13 0 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 NS(0.057)S(0.943)PAPPQPAPGK;NS(0.124)S(0.876)PAPPQPAPGK;NS(0.046)S(0.954)PAPPQPAPGK ;; 118.73 0.0051245 153598000 11035.8 9595.4 10215.1 6259.9 9319.1 9823.5 8408.8 9386.6 11155.1 11711.1 TRUE FALSE FALSE 10901.29142 9730.484293 10392.88953 6983.699092 8843.511553 9195.810054 9123.043262 9658.186461 10157.35992 11406.84393 0.955679896 0.853039136 0.911109996 0.61223763 0.775281191 0.806166027 0.799786805 0.846701026 0.8904619 1 13.47761206 -9.999201932 1.3528749 0.983248115 0.777373802 0.476139285 0.074296589 0.183701905 0.658234373 0.012666988 0.016842335 1.00E-10 9.999201932 -0.205874312 NSS(ph)PGEASLLEK ddPTM_HeLa_Romidepsin_16h_R1 1 NSSPGEASLLEK 12 0 Q76FK4-2;Q76FK4-4;Q76FK4 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 NS(0.003)S(0.997)PGEASLLEK 175.6 1.91E-05 19478000 5766.5 5827.2 6127.5 3736.7 5027 5498.8 4473.2 4748.9 5403.8 5445.5 TRUE FALSE FALSE 5696.21568 5909.235475 6234.146567 4168.754836 4770.453432 5147.444427 4853.153496 4886.301929 4920.470594 5304.025125 1.073942062 1.114103975 1.175361432 0.785960612 0.899402495 0.970478892 0.91499444 0.921244114 0.92768614 1 12.37287189 -9.260193326 24.99996306 1.052578574 0.903395419 0.529662268 0.075126716 69.90769937 1402575.564 0.010764411 0.017222349 5.49E-10 9.260193326 -0.149183155 NSS(ph)QDDLFPTSDTPR ddPTM_HeLa_Romidepsin_16h_R1 2 NSSQDDLFPTSDTPR 15 0 Q9H6T3-3;Q9H6T3;Q9H6T3-2 Q9H6T3-3 RPAP3 RNA polymerase II-associated protein 3 1 0 NS(0.001)S(0.998)QDDLFPTSDTPR;NS(0.084)S(0.916)QDDLFPTSDTPR ; 260.25 7.44E-71 9206500 1703.81 1805.15 1418.28 1637.68 2208.62 2577.5 2181.1 2616.8 1589.32 1901.15 TRUE FALSE FALSE 1683.043308 1830.562949 1442.964568 1827.036267 2095.90588 2412.806069 2366.36258 2692.512979 1447.167239 1851.757849 0.908889523 0.988554173 0.779240422 0.986649668 1.131846629 1.302981418 1.277900661 1.454030818 0.78150998 1 10.85467974 -8.427655684 1.723462946 0.944387481 1.362110244 0.834363578 0.087310395 0.098656833 0.566590312 0.011100236 0.032763258 3.74E-09 8.427655684 0.417722764 NSS(ph)SPVSPASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 NS(0.018)S(0.491)S(0.491)PVSPASVPGQR 165.89 3.72E-05 99819000 2960.9 2612.1 2494.8 2014.9 1738.5 1485.2 1292.6 1557.5 2627.5 2678.8 TRUE FALSE FALSE 2924.811412 2648.873212 2538.220947 2247.872218 1649.777858 1390.300513 1402.393412 1602.563805 2392.489819 2609.20439 1.120959103 1.015203417 0.972794986 0.861516341 0.632291538 0.532844617 0.537479324 0.614196347 0.916942279 1 11.34939425 -8.937021205 1.50307216 1.054441775 0.551412675 0.920429299 0.058860915 0.05907774 0.267092973 0.008458515 0.018599474 1.16E-09 8.937021205 -0.5030291 NSS(ph)YFVEWIPNNVK ddPTM_HeLa_Romidepsin_16h_R1 2 NSSYFVEWIPNNVK 14 0 Q5JP53;P07437;Q5ST81;P04350;P68371;A0A0B4J269;Q13509;Q13509-2;Q9BVA1;Q13885 Q5JP53;P04350;P68371;A0A0B4J269;Q9BVA1 TUBB;TUBB4A;TUBB4B;TUBB3;TUBB2B;TUBB2A Tubulin beta chain;Tubulin beta-4A chain;Tubulin beta-4B chain;Tubulin beta-3 chain;Tubulin beta-2B chain;Tubulin beta-2A chain 1 0 NS(0.097)S(0.903)YFVEWIPNNVK;NS(0.032)S(0.968)YFVEWIPNNVK ; 162.67 0.00022453 25815000 6296.3 5783.5 6510.8 4883.4 6248.5 6190.6 5670.4 6235 7029.7 5976.8 TRUE FALSE FALSE 6219.558274 5864.920265 6624.117743 5448.041685 5929.615729 5795.040639 6152.043634 6415.399888 6400.946026 5821.521874 1.068373255 1.007454819 1.137867019 0.935844922 1.018567972 0.995451149 1.056775834 1.10201422 1.099531388 1 12.50718064 -12.61621779 1.437341505 1.000087792 1.041774698 0 0.061955298 0.918963471 3.420341533 0.036400904 0.008429105 2.42E-13 12.61621779 0.041686906 NSSLLS(ph)FDNEDENE ddPTM_HeLa_Romidepsin_16h_R1 3 NSSLLSFDNEDENE 14 0 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 1 0 NS(0.001)S(0.004)LLS(0.995)FDNEDENE;NS(0.004)S(0.022)LLS(0.974)FDNEDENE;NSSLLS(1)FDNEDENE ;; 239.61 2.00E-43 23414600 9733.5 8976.2 8519.5 8180.8 10218.9 14078.8 12741.5 13909 11724 9907 TRUE FALSE FALSE 9614.864358 9102.567179 8667.778324 9126.702588 9697.391401 13179.21012 13823.76269 14311.43497 10675.37608 9649.614712 0.996398783 0.943308873 0.898251234 0.945810052 1.00495115 1.365775786 1.432571466 1.483109471 1.106300759 1 13.23625562 -8.210015949 3.176579688 0.980987271 1.449357627 0.937769342 0.052548973 0.033696285 0.67859426 0.006078161 0.016804069 6.17E-09 8.210015949 0.468370356 NSSLLSFDNEDENE ddPTM_HeLa_Romidepsin_16h_R1 3 NSSLLSFDNEDENE 14 0 Q96AT1 Q96AT1 KIAA1143 Uncharacterized protein KIAA1143 0 0 ;; ;; 199.68 1.65E-15 46541300 23024.4 20984.2 21539.4 19279.9 21494.1 21388 18107.8 21135.9 25150 23335.2 FALSE FALSE TRUE 22743.76976 21279.61612 21914.28422 21509.13275 20397.17587 20021.37583 19645.87608 21747.43392 22900.52101 22728.94814 1.000652103 0.936234092 0.96415743 0.946332079 0.897409583 0.8808756 0.864354829 0.956816558 1.00754865 1 14.4722433 -9.494253916 0.80808564 1.001465047 0.89452308 0.681026659 0.027377576 0.222799984 0.290532644 0.005376894 0.010578525 3.20E-10 9.494253916 -0.106941966 NSSNKPAVTTK(ac)SPAVKPAAAPK ddPTM_HeLa_Romidepsin_16h_R1 2 NSSNKPAVTTKSPAVKPAAAPK 22 3 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ; NSSNKPAVTTK(1)SPAVKPAAAPK;NSSNKPAVTTK(1)SPAVKPAAAPK 161.14 3.09E-24 17698500 4230.5 3885.4 4181.4 5741.3 6403.5 6008.6 6084 6261.7 4419.7 4059.3 FALSE TRUE FALSE 4178.937039 3940.098763 4254.175513 6405.13612 6076.7055 5624.669852 6600.774808 6442.87241 4024.390963 3953.838801 1.056931567 0.996524887 1.075960788 1.619979074 1.53691281 1.422584515 1.669459768 1.62952329 1.017843965 1 11.94903834 -9.293489448 5.882772661 1.026887923 1.570796722 0.945413257 0.065649643 0.030882114 3.343228979 0.010329485 0.016094247 5.09E-10 9.293489448 0.543908799 NSSNTSVGS(ph)PSNTIGR ddPTM_HeLa_Romidepsin_16h_R1 4 NSSNTSVGSPSNTIGR 16 0 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 NSSNTSVGS(0.92)PS(0.08)NTIGR;NSSNT(0.07)S(0.022)VGS(0.884)PS(0.025)NTIGR;NSSNTSVGS(0.998)PS(0.002)NTIGR;NSS(0.005)NT(0.008)S(0.004)VGS(0.89)PS(0.092)NT(0.001)IGR ;;; 265.93 2.68E-86 344243000 12867.8 13248.7 12236.7 13081.4 11992.2 11508.6 9412.1 10376.3 13397.1 12169.4 TRUE FALSE FALSE 12710.9623 13435.21555 12449.67463 14593.93302 11380.19328 10773.2376 10211.56354 10676.52187 12198.82982 11853.23723 1.072362094 1.133463819 1.050318524 1.231219179 0.960091582 0.908885682 0.861499972 0.900726245 1.029155967 1 13.53299351 -8.530139395 24.98649928 1.058452311 0.895317718 0.645356519 0.06431694 99.04292273 340841.6268 0.010216865 0.020468464 2.95E-09 8.530139395 -0.163134593 NSSQDDLFPTSDT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSQDDLFPTSDTPR 15 0 Q9H6T3-3;Q9H6T3;Q9H6T3-2 Q9H6T3-3 RPAP3 RNA polymerase II-associated protein 3 1 0 NSSQDDLFPTS(0.002)DT(0.998)PR 214.28 2.20E-25 1831100 571.99 590.22 584.15 556.21 865.63 967.73 710.46 1059.5 801.96 573.99 TRUE FALSE FALSE 565.0183659 598.5291327 594.3168857 620.5216172 821.453671 905.8951762 770.8064547 1090.154961 730.2306891 559.0776571 1.01062591 1.070565287 1.063031009 1.109902371 1.469301555 1.620338722 1.378710891 1.94991688 1.306134631 1 9.12690488 -8.212872298 0.637880625 0.995417078 1.889307619 0.718977596 0.157126067 0.355297578 0.188888722 0.02178759 0.185271589 6.13E-09 8.212872298 0.89389054 NSSQSGGKPGS(ph)SPITK ddPTM_HeLa_Romidepsin_16h_R1 1 NSSQSGGKPGSSPITK 16 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 NSSQSGGKPGS(0.907)S(0.047)PIT(0.047)K 187.56 1.08E-11 20833000 3635.2 3493.6 3240.4 2931.8 3198 3047 2127 2115.8 3664 4105.4 TRUE FALSE FALSE 3590.892784 3542.782993 3296.797803 3270.788511 3034.794127 2852.306534 2307.667327 2177.017335 3336.282663 3998.741116 0.898005817 0.885974583 0.824458925 0.817954555 0.758937385 0.713301124 0.577098457 0.544425676 0.834333248 1 11.96533017 -6.722649707 0.262600032 0.996694934 5.88E-16 0.859366609 0.050478371 1.198497449 0.051023953 0.013364458 0.404937815 1.89E-07 6.722649707 -0.996694934 NSSQSLMVPQS(ph)GSPEPESIR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSQSLMVPQSGSPEPESIR 20 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970;A0A075B6R8;B7ZB24;H0YGQ3 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 NSSQS(0.006)LMVPQS(0.975)GS(0.019)PEPESIR 119.37 1.14E-06 0 1169.9 1196.8 784.78 909.56 1222.7 1159.5 766.99 896.26 1141.7 1085.5 TRUE FALSE FALSE 1155.640809 1213.648582 798.4387667 1014.727607 1160.301056 1085.411692 832.1381115 922.191869 1039.583493 1057.298554 1.093012759 1.147876896 0.755168693 0.959736116 1.097420452 1.026589593 0.787041757 0.8722152 0.983244978 1 10.0461671 -9.785211524 24.98774887 1.05294649 0.925695482 0.295526574 0.105010032 250.1624687 262953.5967 0.017676645 0.023238702 1.64E-10 9.785211524 -0.127251008 NSSQSLMVPQSGS(ph)PEPESIR ddPTM_HeLa_Romidepsin_16h_R1 3 NSSQSLMVPQSGSPEPESIR 20 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970;A0A075B6R8;B7ZB24;H0YGQ3 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 NSSQSLMVPQS(0.388)GS(0.612)PEPESIR;NSSQSLMVPQS(0.009)GS(0.991)PEPESIR;NSSQSLMVPQS(0.056)GS(0.944)PEPESIR ;; 205.55 4.34E-24 28084000 6806 6439.2 6153.55 6362.99 7222.9 6363.9 5849.22 5960.2 6972.03 6435.3 TRUE FALSE FALSE 6723.045854 6529.851227 6260.649956 7098.708843 6854.288461 5957.267329 6346.052601 6132.648983 6348.434175 6268.109978 1.072579434 1.041757603 0.998809845 1.132511852 1.093517581 0.950408871 1.012434789 0.978388861 1.01281474 1 12.61381478 -8.251670231 24.96901923 1.043832688 0.983613237 0.355113023 0.042466748 739.2253538 1889385.507 0.006616883 0.016667606 5.60E-09 8.251670231 -0.060219451 NSSS(ph)PVSLDAALPESSNVYR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSSPVSLDAALPESSNVYR 20 0 H7C296;R4GN32;H7C1E9;Q70EL1-6;Q70EL1-7;Q70EL1 H7C296 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 0 NS(0.005)S(0.142)S(0.845)PVS(0.008)LDAALPESSNVYR 120.79 6.26E-07 0 641.26 697.66 521.56 586.29 482.61 712.38 782.41 642.85 647.3 577.66 TRUE FALSE FALSE 633.4440765 707.4816758 530.637533 654.0796084 457.9806108 666.8612171 848.8678859 661.4498505 589.4038668 562.6523099 1.125817961 1.25740473 0.943100248 1.162493421 0.813967352 1.185210129 1.508689951 1.175592526 1.047545449 1 9.136099876 -7.996129132 24.83569293 1.058477711 1.343343544 0.422178221 0.136763374 69.48391649 445794.9419 0.017678622 0.052693612 1.01E-08 7.996129132 0.284865833 NSSS(ph)PVSLDAALPESSNVYRDPSAK ddPTM_HeLa_Romidepsin_16h_R1 2 NSSSPVSLDAALPESSNVYRDPSAK 25 1 H7C296;R4GN32;H7C1E9;Q70EL1-6;Q70EL1-7;Q70EL1 H7C296 USP54 Inactive ubiquitin carboxyl-terminal hydrolase 54 1 0 NS(0.03)S(0.241)S(0.664)PVS(0.064)LDAALPESSNVYRDPSAK;NS(0.016)S(0.22)S(0.692)PVS(0.073)LDAALPESSNVYRDPSAK ; 108.02 1.96E-06 21123600 2536 2505.1 2292.72 2337.5 3307.4 2689.6 2978.7 3033.4 3075.6 2647.3 TRUE FALSE FALSE 2505.090257 2540.366864 2332.62383 2607.772748 3138.611036 2517.74324 3231.710704 3121.166643 2800.510633 2578.522764 0.971521482 0.985202418 0.904635733 1.011343698 1.217212848 0.976428549 1.253318663 1.210447581 1.086091103 1 11.33232907 -8.021468094 0.773709674 0.980516253 1.266277252 0.470513827 0.084824377 0.615948413 0.474106901 0.012513071 0.121416641 9.52E-09 8.021468094 0.285761 NSSS(ph)PVSPASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 2 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 NSS(0.009)S(0.988)PVS(0.001)PAS(0.001)VPGQR;NS(0.001)S(0.107)S(0.888)PVS(0.004)PASVPGQR ; 157.37 0.00035147 113438800 6434.4 6131.4 5624.5 5110.6 4411.2 3797.4 3729 3627.4 6530.9 5913.3 TRUE FALSE FALSE 6355.975058 6217.71801 5722.392063 5701.511618 4186.080004 3554.758396 4045.741167 3732.353096 5946.759947 5759.671614 1.103530806 1.079526478 0.993527487 0.989902203 0.726791436 0.617180741 0.702425666 0.648014912 1.032482465 1 12.49177084 -8.761626337 2.624343327 1.048356361 0.65841041 0.958782739 0.036848011 0.046596535 0.656025581 0.007126826 0.01484775 1.73E-09 8.761626337 -0.389945952 NSSSPVS(ph)PASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 2 NSSSPVSPASVPGQR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 NS(0.003)S(0.001)S(0.016)PVS(0.98)PASVPGQR;NSS(0.001)S(0.019)PVS(0.979)PAS(0.001)VPGQR ; 181.81 3.25E-08 23939000 2984.6 2766 2663.3 2311.9 2380.75 2207.31 1824.87 1817.83 3174.3 2847.5 TRUE FALSE FALSE 2948.222547 2804.939821 2709.653619 2579.212756 2259.251444 2066.270015 1979.874412 1870.426043 2890.382658 2773.52154 1.062988877 1.011327938 0.976972265 0.929941491 0.814578654 0.744998726 0.71384858 0.674386702 1.042134563 1 11.43750321 -8.679110917 1.017010494 1.030003156 0.683148603 0.98364877 0.017754205 0.066008771 0.129423617 0.004287518 0.014334891 2.09E-09 8.679110917 -0.346854553 NSSSSGTSLLT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 NSSSSGTSLLTPK 13 0 Q9NXV6 Q9NXV6 CDKN2AIP CDKN2A-interacting protein 1 0 NSSSSGTS(0.001)LLT(0.999)PK 113.65 0.012528 14510000 2611.6 2184.7 2251.4 2319.3 2902 3531.9 2598 2673.3 2196 2545.4 TRUE FALSE FALSE 2579.768815 2215.456264 2290.584673 2587.468379 2753.900111 3306.222989 2818.674055 2750.647718 1999.58426 2479.270141 1.040535588 0.893592121 0.923894752 1.043641165 1.110770491 1.333546891 1.136896705 1.109458656 0.806521333 1 11.27569976 -8.677701255 3.167644043 1.001840191 1.191146801 0.543930168 0.094650524 0.134982094 2.711223063 0.010972526 0.023057279 2.10E-09 8.677701255 0.18930661 NSSSSTIGS(ph)PSSR ddPTM_HeLa_Romidepsin_16h_R1 1 NSSSSTIGSPSSR 13 0 H3BLS7;Q5THJ4-2;Q5THJ4;A0A2R8YD87 H3BLS7 VPS13D Vacuolar protein sorting-associated protein 13D 1 0 NSSSSTIGS(0.864)PS(0.129)S(0.006)R 112.03 0.006375 1066900 683.24 764.35 820.08 569.66 1025.4 939.55 842.81 1003.8 944.41 981.2 TRUE FALSE FALSE 674.9124081 775.1105394 834.3531484 635.5267695 973.0700117 879.5157873 914.3982604 1032.843369 859.9396043 955.7082826 0.706190812 0.811032565 0.873020736 0.66497987 1.018166348 0.92027641 0.95677549 1.080709865 0.899792981 1 9.900426511 -7.669209331 0.995360586 0.847175335 1.098952095 0.335368533 0.103513123 1.295985654 1.48670392 0.020389559 0.29752958 2.14E-08 7.669209331 0.251776759 NSSTDQGS(ph)DEEGSLQK ddPTM_HeLa_Romidepsin_16h_R1 2 NSSTDQGSDEEGSLQK 16 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 NSSTDQGS(1)DEEGSLQK;NSSTDQGS(0.937)DEEGS(0.063)LQK ; 260.58 2.95E-72 40337000 6994.3 6619 7438.2 4255.6 6485.2 7403.5 5726.7 7348.9 7610.1 6654.9 TRUE FALSE FALSE 6909.050781 6712.182456 7567.658751 4747.652495 6154.236044 6930.440244 6213.125755 7561.528827 6929.433596 6482.004739 1.065881785 1.035510267 1.167487383 0.732435826 0.949434055 1.069181607 0.958519163 1.1665417 1.069026308 1 12.66222436 NST(ph)PSEPGSGR ddPTM_HeLa_Romidepsin_16h_R1 3 NSTPSEPGSGR 11 0 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 NS(0.023)T(0.67)PS(0.305)EPGS(0.001)GR;NS(0.012)T(0.452)PS(0.202)EPGS(0.334)GR;NS(0.002)T(0.715)PS(0.282)EPGS(0.001)GR ;; 124.6 0.016478 282673500 16090.5 14320 15832.9 11700 16537.1 18094.2 20116 9320.02 16651.9 16232.7 TRUE FALSE FALSE 15894.3828 14521.59734 16108.46498 13052.80905 15693.15008 16938.03902 21824.65254 9589.680074 15162.51236 15810.97211 1.005275494 0.918450632 1.018815596 0.825553859 0.992548084 1.071283846 1.380348557 0.606520586 0.958986724 1 13.94863845 -7.200794869 22.98999645 1.00904353 0.60651088 0.449331636 0.136596517 25278.85647 9582061.649 0.017676752 56.17931338 6.30E-08 7.200794869 -0.40253265 NSTDLDSAPEDPT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 3 NSTDLDSAPEDPTSPK 16 0 I3L2J0;A0A0A0MQR4;Q96RK0;I3L373;I3L135;I3L1Q4 I3L2J0 CIC Protein capicua homolog 1 0 NSTDLDSAPEDPT(0.962)S(0.038)PK;NSTDLDSAPEDPT(0.958)S(0.042)PK;NSTDLDSAPEDPT(0.973)S(0.027)PK ;; 241.66 1.54E-46 25149800 16883.1 16395 15434 10869.5 11841 11068.8 9084.9 9595.9 16997.8 17410.4 TRUE FALSE FALSE 16677.32228 16625.80924 15702.6223 12126.28273 11236.70959 10361.5394 9856.571179 9873.542227 15477.4742 16958.0753 0.983444288 0.980406617 0.925967247 0.715074236 0.662617036 0.611009164 0.581231714 0.582232479 0.912690498 1 14.04968482 -9.146324833 1.415707518 0.993799879 0.593072535 0.968472367 0.030323109 0.023971852 0.094484795 0.002732584 0.005456675 7.14E-10 9.146324833 -0.400727344 NSTDLDSAPEDPTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 NSTDLDSAPEDPTSPK 16 0 I3L2J0;A0A0A0MQR4;Q96RK0;I3L373;I3L135;I3L1Q4 I3L2J0 CIC Protein capicua homolog 1 0 NSTDLDSAPEDPT(0.177)S(0.823)PK 169.37 1.38E-05 17237000 3927.8 3029.2 2655.2 2610.9 2440.7 1972.2 1726.1 1947.6 3304 3224.2 TRUE FALSE FALSE 3879.926463 3071.845157 2701.412642 2912.784543 2316.141971 1846.182785 1872.714891 2003.950733 3008.481965 3140.434819 1.235474285 0.978159183 0.860203379 0.92750995 0.737522701 0.587874894 0.596323439 0.638112506 0.957982616 1 11.61674861 -9.037171978 0.922418398 1.10624743 0.591773267 0.783081228 0.092665714 0.18453888 0.306382417 0.019393024 0.050626108 9.18E-10 9.037171978 -0.514474163 NSTFSEIFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 NSTFSEIFKK 10 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 1 ; NSTFSEIFK(1)K;NSTFSEIFK(1)K 199.33 2.90E-13 8581700 1679.54 1450.86 1696.02 1164.75 4437.8 3647.09 3358.46 3132.46 3506.45 2877.14 FALSE TRUE FALSE 1659.06912 1471.285245 1725.538517 1299.423875 4211.322506 3414.052719 3643.727509 3223.092788 3192.82433 2802.391488 0.592019041 0.525010603 0.615737852 0.463683922 1.50276024 1.21826402 1.300220731 1.150122244 1.139321306 1 11.4524428 -8.757382773 24.99999991 0.741883087 1.288041906 0.629699349 0.213898443 56.36362325 347352.1888 0.032630192 0.063404504 1.75E-09 8.757382773 0.546158819 NSTGGTSVGWDS(ph)PPASPLQR ddPTM_HeLa_Romidepsin_16h_R1 3 NSTGGTSVGWDSPPASPLQR 20 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 0 NSTGGT(0.009)S(0.136)VGWDS(0.854)PPASPLQR;NSTGGTSVGWDS(0.998)PPAS(0.002)PLQR;NSTGGTSVGWDS(1)PPASPLQR ;; 292.29 4.69E-129 49278000 2528.1 2603.31 2108.06 2220.77 2397.97 2802.75 2365.88 2223.86 2494.9 2589.34 TRUE FALSE FALSE 2497.286545 2639.959467 2144.7499 2477.545876 2275.592643 2623.66332 2566.837788 2288.20388 2271.749895 2522.068574 0.990173927 1.04674373 0.850393174 0.982346754 0.902272312 1.04028231 1.01775099 0.907272667 0.900748663 1 11.30039179 NSTPS(ph)EPGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTPSEPGSGR 11 0 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 NST(0.154)PS(0.769)EPGS(0.078)GR 153.49 0.0022523 95571000 10040 10083 9980.9 6599.7 9792.2 10352 9818.8 7241.4 10013 9527.3 TRUE FALSE FALSE 9917.628618 10224.94874 10154.61338 7362.788367 9292.467494 9690.54061 10652.80863 7450.918484 9117.412202 9279.779373 1.068735389 1.101852569 1.094273147 0.793422782 1.001367287 1.044264117 1.147959256 0.802919788 0.982503122 1 13.17987479 NSTPS(ph)SSSSLQK ddPTM_HeLa_Romidepsin_16h_R1 1 NSTPSSSSSLQK 12 0 F8VRZ8;Q9P0U3-2;Q9P0U3 F8VRZ8 SENP1 Sentrin-specific protease 1 1 0 NST(0.041)PS(0.615)S(0.152)S(0.152)S(0.038)S(0.002)LQK 95.273 0.0036428 0 1515.9 1638.6 1487 1389.5 1319.3 1246.9 1226.8 934.29 1539.2 1502.2 TRUE FALSE FALSE 1497.423628 1661.668254 1512.880611 1550.160528 1251.971198 1167.227114 1331.004361 961.3222071 1401.530097 1463.172627 1.023408721 1.135661112 1.03397274 1.059451563 0.855655153 0.797737117 0.90967008 0.657012159 0.957870637 1 10.51488428 -8.65356829 4.270173642 1.0265799 0.803964829 0.712963025 0.07198354 0.088948698 2.894754678 0.009697566 0.0198853 2.22E-09 8.65356829 -0.222615072 NSTPSEPGS(ph)GRGPPQEEEEEEDEEEEATKEDAEAPGIR ddPTM_HeLa_Romidepsin_16h_R1 1 NSTPSEPGSGRGPPQEEEEEEDEEEEATKEDAEAPGIR 38 2 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 NS(0.001)T(0.007)PS(0.078)EPGS(0.913)GRGPPQEEEEEEDEEEEAT(0.001)KEDAEAPGIR 62.958 0.00020069 17474000 659.18 525.53 507.37 956.7 655.78 646.68 401.2 595.88 757.81 659.55 TRUE FALSE FALSE 651.1456606 532.9284251 516.200562 1067.318155 622.3130995 605.3592351 435.277918 613.1208477 690.0295756 642.4147959 1.013590697 0.829570596 0.803531558 1.661415899 0.968709163 0.942318326 0.677565213 0.954400259 1.074118436 1 9.327361311 -8.005830374 4.20554516 1.024153371 0.812583285 0.132490834 0.232026711 0.318451572 13.4892573 0.031622313 0.094607727 9.87E-09 8.005830374 -0.211570086 NSVEVALNK ddPTM_HeLa_Romidepsin_16h_R1 2 NSVEVALNK 9 0 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 0 ; ; 129.85 0.013896 2884300 2974.3 3059.9 3185.5 2553 3757 3366.6 2870.2 2915.7 3458.2 3062.2 FALSE FALSE TRUE 2938.048088 3102.977353 3240.942291 2848.189872 3565.266271 3151.485125 3113.994716 3000.061179 3148.889931 2982.643603 0.985048326 1.040344663 1.086600588 0.954921289 1.195337675 1.056608011 1.044038488 1.005839644 1.055737913 1 11.54237588 -10.13858505 4.202287114 0.992997043 1.058555571 0.062066256 0.061103029 0.257923377 7.666181874 0.009178828 0.01132805 7.27E-11 10.13858505 0.065558527 NSVLSDPGLDS(ph)PRT(ph)SPVIMAR ddPTM_HeLa_Romidepsin_16h_R1 1 NSVLSDPGLDSPRTSPVIMAR 21 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 2 0 NSVLS(0.001)DPGLDS(0.997)PRT(0.501)S(0.501)PVIMAR 77.037 0.0064918 12976000 810.24 758.01 748.2 713.22 925.24 807.65 513.17 601.74 979.02 708.31 TRUE FALSE FALSE 800.3644832 768.6812847 761.2221071 795.6858522 878.0215503 756.0437716 556.758647 619.1503975 891.4539992 689.9080041 1.1601032 1.114179398 1.103367554 1.153321671 1.272664681 1.095861719 0.807004186 0.89743907 1.292134595 1 9.430260188 -7.76889119 24.52961012 1.102563878 0.852221611 0.591095127 0.092491918 63.86916384 210246.2716 0.012390331 0.038294753 1.70E-08 7.76889119 -0.250342267 NSYATTENKT(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 1 NSYATTENKTLPR 13 1 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;I3L0Y9 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 NSYATT(0.001)ENKT(0.999)LPR 79.326 0.022868 19741000 1250.3 1263.1 1046.1 1325.7 3418.7 4191.2 3977.8 5536.7 1011.6 1237.7 TRUE FALSE FALSE 1235.060863 1280.881955 1064.306932 1478.983672 3244.230982 3923.395846 4315.674233 5696.895679 921.1199624 1205.544376 1.024483949 1.062492581 0.88284343 1.226818109 2.69109213 3.254459915 3.579855143 4.72557941 0.764069727 1 10.23546904 -8.285669512 1.005221873 0.980328468 4.480883279 0.959339401 0.271850058 0.083980716 0.142335693 0.041032848 0.213552136 5.18E-09 8.285669512 3.500554811 up NSYNNSQAPS(ph)PGLGSK ddPTM_HeLa_Romidepsin_16h_R1 4 NSYNNSQAPSPGLGSK 16 0 Q9UHB7 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 NSY(0.002)NNS(0.009)QAPS(0.989)PGLGSK;NSYNNS(0.119)QAPS(0.881)PGLGSK;NSYNNS(0.002)QAPS(0.995)PGLGS(0.003)K;NSYNNSQAPS(0.999)PGLGS(0.001)K ;;; 214.34 5.47E-26 67988000 20108.9 18395.2 18491.4 20304.6 28331.3 30516.8 28179.5 32043.9 20289.8 20878.7 TRUE FALSE FALSE 19863.80499 18654.16811 18813.23506 22652.31339 26885.44804 28566.87497 30573.06603 32971.03969 18475.02947 20336.26836 0.97676745 0.917285697 0.925107533 1.113887414 1.322044318 1.404725511 1.503376405 1.621292515 0.908476872 1 14.31176735 -8.530453778 1.228703379 0.976311611 1.561077461 0.958118407 0.052361274 0.067180153 0.193486037 0.008210032 0.027470462 2.95E-09 8.530453778 0.58476585 NT(ph)DT(ph)SVVVS(ph)WEES(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 NTDTSVVVSWEESK 14 0 A8MX12;P52179-2;P52179 A8MX12 MYOM1 Myomesin-1 4 0 NT(0.999)DT(0.501)S(0.501)VVVS(0.999)WEES(1)K 72.315 0.017636 6625800 1717.8 2234.3 1961.1 1800.4 2168.3 2476.8 1581.6 2077.1 2181.1 1977.1 TRUE FALSE FALSE 1696.862793 2265.754534 1995.232123 2008.570719 2057.64356 2318.540474 1715.941065 2137.197611 1986.016953 1925.734657 0.881150883 1.176566318 1.036088807 1.043015304 1.068497964 1.203977124 0.891057892 1.109808978 1.031303532 1 10.91119322 -10.2738899 24.98971473 0.943876806 1.070372089 0.206428108 0.08915796 662.1144773 1328942.231 0.014681307 0.016843126 5.32E-11 10.2738899 0.126495283 NT(ph)EDIT(ph)FPS(ph)VY(ph)VGLK ddPTM_HeLa_Romidepsin_16h_R1 1 NTEDITFPSVYVGLK 15 0 H0Y626;O95361;J3QKY5;K7EL43;K7ENN8;B3KP96;O95361-2 H0Y626 TRIM16 Tripartite motif-containing protein 16 4 0 NT(1)EDIT(1)FPS(1)VY(1)VGLK 57.532 0.024386 2721400 526.76 417.66 399.87 482.83 468.24 447.16 404.59 366.35 543.78 499.74 TRUE FALSE FALSE 520.3396465 423.5398284 406.8295696 538.6570764 444.3439656 418.5879191 438.9558645 376.9497592 495.1429549 486.7566828 1.068993329 0.870126376 0.835796578 1.106624923 0.912866698 0.859953102 0.901797305 0.774411061 1.017228879 1 8.927056976 -5.053534232 0.275956884 1.032941927 7.17E-09 0.36610277 0.081761751 19.74888496 0.421982614 0.039764511 8.824752292 8.84E-06 5.053534232 -1.03294192 NT(ph)ISNNS(ph)DMAEVKS(ph)MFREVLPK ddPTM_HeLa_Romidepsin_16h_R1 1 NTISNNSDMAEVKSMFREVLPK 22 2 E9PIK7;A0A494C180;A8MTZ0 E9PIK7 BBIP1 BBSome-interacting protein 1 3 0 NT(0.835)IS(0.176)NNS(0.991)DMAEVKS(0.999)MFREVLPK 44.089 0.026101 5269900 481.49 445.09 361.44 519.75 515.23 518.98 397.19 540.25 394.01 512.76 TRUE FALSE FALSE 475.6214147 451.3559887 367.7307116 579.8459405 488.9358905 485.8188529 430.9273087 555.8812814 358.7687588 499.4384213 0.952312426 0.903727005 0.736288391 1.160995862 0.97897132 0.972730235 0.862823704 1.113012651 0.718344331 1 8.964163 -6.129291443 17.09509463 0.967856388 0.968840343 0 0.138137528 0 0 0.013787975 0 7.43E-07 6.129291443 0.000983955 NT(ph)LQLHR ddPTM_HeLa_Romidepsin_16h_R1 1 NTLQLHR 7 0 P61313;E7ERA2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 1 0 NT(1)LQLHR 68.626 0.0038132 0 1039.6 1068.5 791.61 782.41 1257.3 1692.7 2277.2 1733.3 1101.8 682.23 TRUE FALSE FALSE 1026.928955 1083.542371 805.38764 872.8759255 1193.135289 1584.541933 2470.625311 1783.450301 1003.252248 664.5055663 1.54540309 1.63059939 1.212010374 1.31357203 1.795523394 2.384542754 3.717990393 2.683875638 1.509772528 1 9.376137474 -8.198919207 1.920575941 1.297408231 3.205518424 0.83260554 0.320562045 0.093718163 0.657180698 0.048441195 0.16468777 6.33E-09 8.198919207 1.908110193 up NTAELQPESGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 NTAELQPESGKR 12 1 O15355 O15355 PPM1G Protein phosphatase 1G 0 1 ; NTAELQPESGK(1)R;NTAELQPESGK(1)R 276.17 1.29E-95 5047300 1960.86 1831.99 1463.89 1322.31 1340.98 1363.63 1382.73 1381.71 2281.7 2008.49 FALSE TRUE FALSE 1936.960284 1857.780803 1489.368391 1475.201704 1272.544787 1276.498444 1500.179052 1421.687599 2077.619037 1956.30914 0.99010951 0.9496356 0.761315459 0.754073921 0.650482462 0.65250344 0.766841508 0.726719295 1.062009574 1 10.93391865 -9.73499839 2.077259056 0.996164373 0.706080474 0.920187926 0.041088232 0.053230949 0.470875025 0.006085996 0.008786776 1.84E-10 9.73499839 -0.290083899 NTASQNS(ph)ILEEGETK ddPTM_HeLa_Romidepsin_16h_R1 1 NTASQNSILEEGETK 15 0 Q15398-1;Q15398-3;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 0 NTAS(0.001)QNS(0.994)ILEEGET(0.005)K 141.22 0.00070534 8824600 1477.6 1583 1477.9 497.05 1912.1 1568 1674.6 1614.1 1573.5 1507.3 TRUE FALSE FALSE 1459.590443 1605.285516 1503.62223 554.5212597 1814.518402 1467.80986 1816.840482 1660.801437 1432.762219 1468.140129 0.994176519 1.093414371 1.024168061 0.377703224 1.235929981 0.999775043 1.237511629 1.131228147 0.975902907 1 10.51977396 NTDVAQS(ph)PEAPK ddPTM_HeLa_Romidepsin_16h_R1 1 NTDVAQSPEAPK 12 0 V9GY78;A0A087WVV2;Q9P2E9-3;Q9P2E9 V9GY78;A0A087WVV2 RRBP1 Ribosome-binding protein 1 1 0 NTDVAQS(1)PEAPK 143.97 0.0015254 21971000 5505.6 5267.8 5592.3 3096.3 5988.8 7758.5 6213.9 7064.5 5505.1 5878.3 TRUE FALSE FALSE 5438.49563 5341.960227 5689.631636 3454.308775 5683.169189 7262.756889 6741.708511 7268.900162 5012.710068 5725.580919 0.949859186 0.932998818 0.993721286 0.603311493 0.992592589 1.268475111 1.177471528 1.269548062 0.875493708 1 12.48320636 -8.318461835 5.567677341 0.945144067 1.232381371 0.623042275 0.115809147 0.115511075 7.79006049 0.016631587 0.038166256 4.80E-09 8.318461835 0.287237304 NTDVAQS(ph)PEAPKQEAPAK ddPTM_HeLa_Romidepsin_16h_R1 3 NTDVAQSPEAPKQEAPAK 18 1 V9GY78;A0A087WVV2;Q9P2E9-3;Q9P2E9 V9GY78;A0A087WVV2 RRBP1 Ribosome-binding protein 1 1 0 NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK;NTDVAQS(1)PEAPKQEAPAK ;; 98.684 0.0008912 182102000 14502.5 13752.5 13703.9 13283.5 16044.5 18432.4 16031.8 18519.3 15540.4 14626.1 TRUE FALSE FALSE 14325.73795 13946.10806 13942.41063 14819.40077 15225.68929 17254.62913 17393.54069 19055.12673 14150.4277 14246.11181 1.005589324 0.978941359 0.97868182 1.040241784 1.068761041 1.211181644 1.220932485 1.337566838 0.993283493 1 13.7982806 -8.071694814 1.03851238 0.998174824 1.33152719 0.963789655 0.022908395 0.086287813 0.144265099 0.003423582 0.023101499 8.48E-09 8.071694814 0.333352365 NTEDLTEEWLR ddPTM_HeLa_Romidepsin_16h_R1 1 NTEDLTEEWLR 11 0 G3V4P8;P60983 G3V4P8 GMFB Glia maturation factor beta 0 0 164.48 0.0074163 5855800 1226.7 1345.5 1379.4 1165 1625.5 1364.2 970.17 1299.1 1486.9 1391.7 FALSE FALSE TRUE 1211.748509 1364.441984 1403.407878 1299.702781 1542.544669 1277.032023 1052.576216 1336.687409 1353.90794 1355.543433 0.893920828 1.006564563 1.035310152 0.958805708 1.137952965 0.942081228 0.776497595 0.986089694 0.998793478 1 10.40465562 -7.987185371 24.94102662 0.973836848 0.875792553 0.226500556 0.078567784 278.5634484 542158.2819 0.011414952 0.034217831 1.03E-08 7.987185371 -0.098044295 NTEESSS(ph)PVRK ddPTM_HeLa_Romidepsin_16h_R1 1 NTEESSSPVRK 11 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 NT(0.005)EES(0.156)S(0.156)S(0.682)PVRK 100.02 0.029519 6335300 4401 4161.9 5818.6 5249.7 4602.2 4275.3 7410.2 3112.2 5899 4584.5 TRUE FALSE FALSE 4347.358919 4220.491337 5919.870292 5856.695015 4367.332561 4002.122128 8039.622203 3202.246597 5371.378666 4465.394029 0.973566698 0.945155413 1.325721818 1.311574069 0.978039683 0.896252851 1.800428395 0.717125202 1.202890189 1 12.12457177 -9.780932599 24.81021378 0.983991649 1.18516916 0.044908019 0.28451844 349.4525437 444768.0494 0.040575151 0.053370449 1.66E-10 9.780932599 0.201177511 NTFTAWS(ph)DEES(ph)DYEIDDRDVNK ddPTM_HeLa_Romidepsin_16h_R1 2 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 0 NT(0.02)FT(0.246)AWS(0.759)DEES(0.844)DY(0.131)EIDDRDVNK;NT(0.006)FT(0.334)AWS(0.823)DEES(0.823)DY(0.014)EIDDRDVNK ; 67.928 0.0028082 6269300 4133.3 3820.2 4472.9 3432.8 3031.1 3362.6 2862.9 2843.2 4347.3 3948.4 TRUE FALSE FALSE 4082.92175 3873.980876 4550.748948 3829.716488 2876.411656 3147.740712 3106.074655 2925.463506 3958.4666 3845.819999 1.061651807 1.007322464 1.183297437 0.995812724 0.747931951 0.81848363 0.807649514 0.760686539 1.029290659 1 11.90907552 -8.834175638 5.362681855 1.040151104 0.788119478 0.855340611 0.053046973 0.0583617 3.025187686 0.008059652 0.014924181 1.46E-09 8.834175638 -0.252031626 NTFTAWS(ph)DEESDY(ph)EIDDRDVNK ddPTM_HeLa_Romidepsin_16h_R1 1 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 2 0 NT(0.001)FT(0.041)AWS(0.698)DEES(0.28)DY(0.981)EIDDRDVNK 80.944 0.00068917 24117000 2781.4 2338.7 2139.5 2218 2188.7 1913.5 1700.7 1893.9 2274 2378.3 TRUE FALSE FALSE 2747.499227 2371.62428 2176.7371 2474.455596 2077.002472 1791.233526 1845.157416 1948.697008 2070.607745 2316.511423 1.186050368 1.023791317 0.939661716 1.06818191 0.896607913 0.773246144 0.796524203 0.841220548 0.893847414 1 11.17773808 -8.729625888 1.14074601 1.080356389 0.790842992 0.471380799 0.088962911 0.226375792 0.574876951 0.014084138 0.041443159 1.86E-09 8.729625888 -0.289513397 NTFTAWS(ph)DEESDYEIDDRDVNK ddPTM_HeLa_Romidepsin_16h_R1 4 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 0 NT(0.002)FT(0.061)AWS(0.863)DEES(0.063)DY(0.01)EIDDRDVNK;NT(0.002)FT(0.079)AWS(0.915)DEES(0.003)DY(0.001)EIDDRDVNK;NT(0.001)FT(0.013)AWS(0.986)DEESDYEIDDRDVNK;NT(0.007)FT(0.128)AWS(0.651)DEES(0.016)DY(0.197)EIDDRDVNK ;;; 106.06 8.70E-06 170150100 5724.72 4994.13 4285.23 4411.82 4232.99 4049.08 3806.6 4159.37 5442.11 5472.82 TRUE FALSE FALSE 5654.944911 5064.437493 4359.812631 4921.935387 4016.964725 3790.356856 4129.932509 4279.714809 4955.354052 5330.635347 1.06083882 0.95006264 0.81787861 0.923329972 0.753562092 0.711051612 0.774754272 0.802852668 0.929599143 1 12.38009178 -9.571021128 1.088503506 1.029921843 0.766119816 0.699949224 0.060301344 0.140694562 0.333313179 0.010079299 0.017220727 2.69E-10 9.571021128 -0.263802027 NTFTAWSDEES(ph)DYEIDDRDVNK ddPTM_HeLa_Romidepsin_16h_R1 1 NTFTAWSDEESDYEIDDRDVNK 22 1 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 1 0 NT(0.002)FT(0.017)AWS(0.263)DEES(0.565)DY(0.152)EIDDRDVNK 83.167 0.0005075 10151000 1104.2 1342.4 899.18 1013.2 897.62 892.91 904.08 682.97 1340.3 1216.5 TRUE FALSE FALSE 1090.741586 1361.298342 914.8298507 1130.350951 851.8111019 835.8559327 980.8725326 702.7306594 1220.420211 1184.895155 0.920538481 1.148876622 0.772076624 0.953967064 0.71889154 0.70542607 0.827813776 0.593074127 1.029981603 1 10.21054369 -8.900284829 1.165456875 0.971479427 0.703905739 0.599484017 0.103557727 0.250089676 0.671994487 0.015674018 0.039701477 1.26E-09 8.900284829 -0.267573688 NTGIICTIGPASR ddPTM_HeLa_Romidepsin_16h_R1 1 NTGIICTIGPASR 13 0 P14618;B4DNK4;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2;H3BU13 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 143.55 0.00022253 1332500 411.42 502.56 350.73 267.27 473.59 471.22 285.17 326.95 564.75 543.55 FALSE FALSE TRUE 406.4054548 509.6350529 356.8343085 298.1730149 449.4209351 441.1105628 309.3923327 336.4097824 514.2373456 529.4284926 0.767630493 0.962613573 0.673999064 0.563197899 0.848879389 0.833182515 0.584389274 0.635420623 0.971306518 1 9.048292029 -16.52287875 0.105806102 1.928392861 0.542623505 0.512391354 0.108922636 69.53703736 0.544186909 14.04948089 0.806491249 3.00E-17 16.52287875 -1.385769356 NTGNGTQSS(ph)MGSPLTRPTPR ddPTM_HeLa_Romidepsin_16h_R1 1 NTGNGTQSSMGSPLTRPTPR 20 1 E3W994;J3KR49;O75122;A0A0U1RQI6;H7C4I5;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 0 NTGNGT(0.001)QS(0.084)S(0.883)MGS(0.009)PLT(0.017)RPT(0.006)PR 67.655 0.011386 9727700 1481.1 1579.2 1231.5 1382.2 2018.6 2057.8 1809.9 1973.9 1450.1 1206.7 TRUE FALSE FALSE 1463.047784 1601.432019 1252.933741 1542.016467 1915.58331 1926.313221 1963.632861 2031.011682 1320.399424 1175.34976 1.24477652 1.36251529 1.066009271 1.311963911 1.629798529 1.638927651 1.670679595 1.728006208 1.123409787 1 10.19887442 -5.253023658 0.172821448 0.942142079 3.462409978 0.810681025 0.11237563 11.28149426 0.176114393 0.182601745 6.830125999 5.58E-06 5.253023658 2.520267899 NTGVSPASRPSPGTPT(ph)SPSNLTSGLK ddPTM_HeLa_Romidepsin_16h_R1 1 NTGVSPASRPSPGTPTSPSNLTSGLK 26 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 NTGVSPASRPS(0.001)PGT(0.024)PT(0.879)S(0.091)PS(0.004)NLT(0.001)SGLK 95.223 5.87E-06 86416000 2226.7 2123.7 2124.3 1998.7 1598.1 1304.7 1286.3 1336.9 2580 2268.7 TRUE FALSE FALSE 2199.560124 2153.597504 2161.27255 2229.799098 1516.542994 1221.333881 1395.55829 1375.581092 2349.238338 2209.758847 0.99538469 0.974584855 0.978058105 1.009068977 0.686293437 0.552700075 0.631543253 0.62250281 1.06311978 1 11.10967322 -8.691215541 4.067597801 0.995416999 0.607453657 0.970861877 0.032429552 0.017816672 0.577144242 0.003374701 0.006878949 2.04E-09 8.691215541 -0.387963342 NTKGS(ph)FLCS(ph)CPRGY(ph)LLEEDGRT(ph)CK ddPTM_HeLa_Romidepsin_16h_R1 1 NTKGSFLCSCPRGYLLEEDGRTCK 24 3 A0A494C0D8;Q75N90 A0A494C0D8 FBN3 Fibrillin-3 4 0 NT(0.05)KGS(0.96)FLCS(0.991)CPRGY(1)LLEEDGRT(1)CK 40.756 0.0042256 0 635.63 556.63 651.05 734.74 692.55 759.87 710.42 668.29 992.95 924.93 TRUE FALSE FALSE 627.8826971 564.4662518 662.3812521 819.6940959 657.2065892 711.3167594 770.7630571 687.6259168 904.1380651 900.9001853 0.696950347 0.626558037 0.735243774 0.909861169 0.729499894 0.78956223 0.855547673 0.763265374 1.003594049 1 9.815223462 -12.3515952 1.092176757 0.999087103 0.761265096 0.613855928 0.07526881 0.301913269 0.648267531 0.054158689 0.014355376 4.45E-13 12.3515952 -0.237822007 NTLDSEVPAAYQT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 NTLDSEVPAAYQTPK 15 0 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 NTLDSEVPAAYQT(1)PK;NTLDSEVPAAYQT(1)PK ; 178.22 1.11E-07 9503700 6657.7 6517.8 6889.1 5545.5 6269.7 5831.8 4863.2 4429.1 6069.5 6675.9 TRUE FALSE FALSE 6576.553392 6609.557759 7009.001896 6186.696802 5949.733814 5459.166801 5276.280087 4557.249021 5526.628719 6502.459156 1.011394802 1.016470477 1.07790018 0.951439548 0.914997491 0.839554186 0.811428409 0.70085008 0.849929017 1 12.66676972 -8.03408167 0.914964918 1.01153297 0.697819023 0.706999843 0.059575316 0.172385024 0.204952918 0.005058487 0.04114586 9.25E-09 8.03408167 -0.313713948 NTLETSSLNFKVT(ph)PDIEESLLEPENEK ddPTM_HeLa_Romidepsin_16h_R1 1 NTLETSSLNFKVTPDIEESLLEPENEK 27 1 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 1 0 NT(0.001)LET(0.045)S(0.045)S(0.045)LNFKVT(0.744)PDIEES(0.121)LLEPENEK 58.08 0.0016161 0 546.62 646.46 571.27 435.26 696.01 369.52 489.88 594.92 627.72 755.66 TRUE FALSE FALSE 539.9575852 655.5608808 581.2127147 485.5868092 660.4900125 345.9088646 531.490395 612.1330716 571.575151 736.0278443 0.733610269 0.890674023 0.789661314 0.659739727 0.897370959 0.469967091 0.72210637 0.831671079 0.776567294 1 9.523616535 -16.52287875 0.203500708 2.267399498 0.694635902 0.047765552 0.135637691 35.00785369 0.428551579 17.57321866 0.11005326 3.00E-17 16.52287875 -1.572763596 NTLQPEEALSTSDPRVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 NTLQPEEALSTSDPRVSPR 19 1 Q9BXL7 Q9BXL7 CARD11 Caspase recruitment domain-containing protein 11 1 0 NTLQPEEALSTSDPRVS(1)PR 110.06 0.00029904 7307400 1524.8 1260.6 1233 1833.3 1032.8 1163.9 987.38 1295.6 1377.3 1357.1 TRUE FALSE FALSE 1506.215151 1278.34676 1254.459848 2045.274772 980.0923621 1089.530546 1071.248033 1333.086142 1254.110838 1321.842346 1.13948169 0.967094725 0.949023801 1.547291005 0.741459346 0.824251507 0.810420422 1.008506155 0.948759768 1 10.3683344 NTNAAEES(ph)LPEIQK ddPTM_HeLa_Romidepsin_16h_R1 1 NTNAAEESLPEIQK 14 0 Q9NTJ3;E9PD53 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 0 NTNAAEES(1)LPEIQK 152.94 0.00061513 3654700 1622.4 1407.9 1581.9 1179 1642.7 1966.3 1714.4 2195.1 1433.9 1266.5 TRUE FALSE FALSE 1602.625565 1427.720453 1609.432306 1315.321527 1558.866889 1840.659776 1860.021093 2258.611755 1305.648393 1233.596147 1.299149295 1.157364553 1.304667098 1.066249704 1.263676846 1.492108888 1.507803909 1.830916674 1.058408293 1 10.26865445 -4 0.366498756 1.120166392 10.26527682 0.83502081 0.098376427 20.11512635 0.248051932 0.033320342 130.7280945 1.00E-04 4 9.145110432 NTPS(ph)PDVTLGTNPGTEDIQFPIQK ddPTM_HeLa_Romidepsin_16h_R1 1 NTPSPDVTLGTNPGTEDIQFPIQK 24 0 M0R3F6;M0R2Z9;Q8IX01-4;Q8IX01-3;Q8IX01 M0R3F6 SUGP2 SURP and G-patch domain-containing protein 2 1 0 NT(0.072)PS(0.815)PDVT(0.103)LGT(0.01)NPGTEDIQFPIQK 115.34 1.43E-06 4070200 2942.5 3085.4 2916 2746.2 3129.7 3089.4 3025.8 2977.3 3258.4 2962.3 TRUE FALSE FALSE 2906.635678 3128.836342 2966.751757 3063.728565 2969.97973 2891.997311 3282.811376 3063.443478 2966.960543 2885.339019 1.00738099 1.084391235 1.028216004 1.0618262 1.029334754 1.002307629 1.13775586 1.061727394 1.028288365 1 11.49452513 -4 0.138187261 0.979496452 1.356129393 0.188164652 0.03690854 56.52122803 0.518011269 0.098134989 4.211035426 1.00E-04 4 0.37663294 NTPSQHSHSIQHS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 NTPSQHSHSIQHSPER 16 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 NTPSQHSHS(0.003)IQHS(0.997)PER;NTPSQHS(0.009)HS(0.368)IQHS(0.622)PER ; 81.016 0.0077268 2340870 980.38 689.04 998.79 529.552 1292.2 1088.61 1293.27 855.04 1209.49 1052.4 TRUE FALSE FALSE 968.4307515 698.7403232 1016.173521 590.7812939 1226.254212 1019.051334 1403.120322 879.7792334 1101.310185 1025.058496 0.944756572 0.681658974 0.991332226 0.576339103 1.196277302 0.994139689 1.368819757 0.858272222 1.074387646 1 10.00149053 NTSGLPAEPESVS(ph)SPPTLHMK ddPTM_HeLa_Romidepsin_16h_R1 1 NTSGLPAEPESVSSPPTLHMK 21 0 Q8IWI9-3;Q8IWI9 Q8IWI9-3 MGA MAX gene-associated protein 1 0 NTSGLPAEPES(0.008)VS(0.462)S(0.462)PPT(0.068)LHMK 59.975 0.0060013 9976800 1986.2 1997.9 1856.9 1424.1 2303.8 2649.3 2253.3 2184 2156 2213.4 TRUE FALSE FALSE 1961.99143 2026.026489 1889.218566 1588.761143 2186.228489 2480.01828 2444.695246 2247.190594 1963.16196 2155.895549 0.910058667 0.939760968 0.876303384 0.736937902 1.014069763 1.150342502 1.133958112 1.042346692 0.910601611 1 11.07407157 -8.520778283 24.99998423 0.932142696 1.106526046 0.613050976 0.073231622 51.54969859 613549.7519 0.011943408 0.024193002 3.01E-09 8.520778283 0.17438335 NTSKFDGT(ph)RLY(ph)ES(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 NTSKFDGTRLYESTK 15 2 M0QYP4;M0R2M0;M0R2R8;M0QY05;M0QZR7;M0R0R6;M0QY14;M0QZ01;M0R1M2;P20273-2;P20273-4;P20273-3;P20273 M0QYP4 CD22 B-cell receptor CD22 4 0 NT(0.006)S(0.006)KFDGT(0.994)RLY(0.998)ES(0.998)T(0.998)K 44.925 0.03 14495000 935.7 906.67 1029.2 326.92 759.86 769.32 993.5 834.79 1092.1 1148.1 TRUE FALSE FALSE 924.2953285 919.4341241 1047.112794 364.7200286 721.0815088 720.1629349 1077.887865 858.9433316 994.4198408 1118.272196 0.826538772 0.822191705 0.936366653 0.326146022 0.644817524 0.643996101 0.96388685 0.768098621 0.889246682 1 10.12705568 -10.86043345 0.628106993 0.977429798 0.707556565 0.218732435 0.168959377 0.659191936 0.593894245 0.06825561 0.05105911 1.38E-11 10.86043345 -0.269873233 NTSLPPLWS(ph)PEAER ddPTM_HeLa_Romidepsin_16h_R1 5 NTSLPPLWSPEAER 14 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 NT(0.016)S(0.14)LPPLWS(0.844)PEAER;NT(0.001)S(0.003)LPPLWS(0.997)PEAER;NTSLPPLWS(1)PEAER;NT(0.001)S(0.047)LPPLWS(0.953)PEAER;NTSLPPLWS(1)PEAER ;;;; 203.92 9.01E-17 211685800 15020.75 14696.4 14657.86 13570.23 17302.36 17874.81 15810.91 17173.35 16667.62 14440 TRUE FALSE FALSE 14837.67132 14903.2963 14912.9739 15139.28384 16419.35601 16732.66733 17153.8883 17670.23379 15176.82632 14064.84672 1.054947247 1.059613134 1.060301204 1.07639167 1.167403836 1.189680035 1.219628528 1.256340303 1.079060912 1 13.77980621 -7.539422811 0.34665279 1.009907004 1.427609301 0.893271157 0.026319202 0.766106815 0.07420061 0.006879088 0.12990481 2.89E-08 7.539422811 0.417702297 NTSPS(ph)LGESR ddPTM_HeLa_Romidepsin_16h_R1 1 NTSPSLGESR 10 0 C9J052;Q9NSU2-2;Q9NSU2;Q9NSU2-1 C9J052 TREX1 Three-prime repair exonuclease 1 1 0 NT(0.025)S(0.206)PS(0.768)LGES(0.001)R 105.25 0.0023038 0 2060 1643 2008.3 1629.2 2127.2 2450.9 1831.9 1889.1 1912.4 1707.6 TRUE FALSE FALSE 2034.891928 1666.130197 2043.253619 1817.57577 2018.641046 2294.2954 1987.50154 1943.758128 1741.350154 1663.236306 1.223453288 1.001739916 1.228480651 1.09279467 1.213682649 1.379416377 1.194960411 1.168660233 1.046964973 1 10.69977744 -16.52287875 0.209210374 0.034637768 1.229789786 0.368866362 0.090136394 38.04699494 0.471747665 15.05494294 0.083852038 3.00E-17 16.52287875 1.195152018 NTTADK(ac)LAIK ddPTM_HeLa_Romidepsin_16h_R1 1 NTTADKLAIK 10 1 P38432 P38432 COIL Coilin 0 1 NTTADK(1)LAIK 118.23 0.015355 828310 600.32 403.17 914.1 228.42 708.76 718.47 711.6 729.24 1004.4 834.26 FALSE TRUE FALSE 593.0030689 408.8458378 930.0095271 254.8309951 672.5893325 672.5620858 772.0432862 750.3394088 914.5639484 812.5858049 0.729772863 0.503141743 1.144506243 0.313605029 0.827714844 0.827681313 0.950106784 0.923397141 1.125498308 1 9.666376352 -6.499438683 24.79945012 0.830830106 0.793130412 0 0.24935311 0 0 0.029870945 0 3.17E-07 6.499438683 -0.037699694 NVAEALGHS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 NVAEALGHSPK 11 0 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 NVAEALGHS(1)PK 126.56 0.0071187 5243900 1312.2 1188.4 1331.7 559.36 1492.6 1446.4 1272.1 1400.5 1341.2 1287.8 TRUE FALSE FALSE 1296.206402 1205.130326 1354.87768 624.0358351 1416.427052 1353.979708 1380.152142 1441.021258 1221.239713 1254.34277 1.033374953 0.960766351 1.080149471 0.497500245 1.129218493 1.079433581 1.100299037 1.148825737 0.973609241 1 10.29271593 NVAEALGHS(ph)PKDPGGGGGPVR ddPTM_HeLa_Romidepsin_16h_R1 1 NVAEALGHSPKDPGGGGGPVR 21 1 Q8IU81 Q8IU81 IRF2BP1 Interferon regulatory factor 2-binding protein 1 1 0 NVAEALGHS(1)PKDPGGGGGPVR 45.237 0.028379 39858000 2470.8 2313.8 2068 2630.7 2652 2485 2227.6 2542.2 2245.5 2198.8 TRUE FALSE FALSE 2440.684939 2346.373737 2103.992673 2934.873912 2516.658544 2326.21652 2416.812288 2615.754546 2044.656856 2141.674859 1.139615068 1.095578877 0.982405272 1.3703639 1.175088989 1.086166983 1.128468347 1.221359318 0.954699938 1 11.06452376 -15.04458883 0.18732827 0.632911135 1.188761206 0.367742058 0.093621738 30.60900434 0.589341364 4.372966533 0.127675257 9.02E-16 15.04458883 0.555850071 NVALLSQLY(ph)HSPARR ddPTM_HeLa_Romidepsin_16h_R1 1 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 0 NVALLS(0.001)QLY(0.951)HS(0.048)PARR 61.423 0.015567 7147500 2078.6 1643 1760.1 1818.9 2889.4 3223.4 2593.8 2591.1 2342.4 1890.9 TRUE FALSE FALSE 2053.265224 1666.130197 1790.733802 2029.209776 2741.943136 3017.435143 2814.117307 2666.06939 2132.889877 1841.774145 1.114830083 0.904633286 0.972287404 1.101769064 1.488751019 1.63833071 1.527938327 1.447555009 1.158062666 1 10.84688044 -8.769734928 3.932914587 1.03646815 1.541512932 0.900863432 0.079001011 0.045625473 1.559638249 0.011590583 0.02280603 1.70E-09 8.769734928 0.505044781 NVALLSQLYHS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 NVALLSQLYHSPAR 14 0 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 0 NVALLS(0.001)QLYHS(0.999)PAR 104.78 0.0080046 61432000 1438.4 1298.9 1422.7 1522 2202.3 2574.9 2150.2 2484.2 1957.6 2009.1 TRUE FALSE FALSE 1420.868228 1317.185948 1447.461497 1697.980801 2089.908413 2410.3722 2332.837934 2556.076408 1782.507353 1956.903292 0.726079941 0.673097109 0.739669406 0.867687641 1.06796714 1.231727807 1.192106909 1.306184326 0.910881677 1 10.93435675 -8.565416835 2.305985745 0.838798948 1.240835711 0.806074561 0.094036192 0.140751492 1.499095786 0.019577012 0.046618383 2.72E-09 8.565416835 0.402036763 NVALLSQLYHS(ph)PARR ddPTM_HeLa_Romidepsin_16h_R1 1 NVALLSQLYHSPARR 15 1 Q15717;Q15717-2 Q15717 ELAVL1 ELAV-like protein 1 1 0 NVALLSQLY(0.001)HS(0.999)PARR 105.02 0.0018154 41357000 1326.8 1079.5 1322.8 1434 2046.4 2209 1930.8 2412.2 1940.3 1516.3 TRUE FALSE FALSE 1310.628451 1094.697229 1345.822779 1599.805827 1941.964572 2067.852029 2094.802104 2481.993201 1766.754708 1476.906307 0.887414757 0.741209665 0.91124452 1.083214161 1.314886775 1.400124042 1.418371696 1.680535311 1.19625375 1 10.52836259 -8.600371144 1.300948262 0.923528788 1.534357564 0.794063711 0.125402967 0.115237103 0.380433036 0.016069445 0.048506162 2.51E-09 8.600371144 0.610828776 NVDAAVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 NVDAAVSPR 9 0 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 NVDAAVS(1)PR;NVDAAVS(1)PR ; 129 0.0087862 146186000 10714.1 10171.8 9800 9996.9 9320.6 9283.9 8293.6 8808.7 11631.9 10131.4 TRUE FALSE FALSE 10583.51243 10314.99887 9970.564889 11152.78861 8844.935002 8690.688752 8998.058177 9063.565837 10591.51373 9868.184767 1.072488272 1.045278246 1.010374767 1.130176307 0.896308208 0.880677547 0.911825061 0.918463329 1.07329909 1 13.26856901 -8.73650418 24.99752859 1.039956872 0.901023133 0.801272889 0.036968283 86.24549849 86460.6908 0.00571034 0.011416786 1.83E-09 8.73650418 -0.138933739 NVDNAEGS(ph)DTDY ddPTM_HeLa_Romidepsin_16h_R1 1 NVDNAEGSDTDY 12 0 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 NVDNAEGS(0.812)DT(0.188)DY 130.56 0.0038031 8127600 4448.8 4407.5 4319.6 3940.5 5076.7 5762.8 4893.6 5984.2 4300.1 3973.3 TRUE FALSE FALSE 4394.576314 4469.548901 4394.780826 4396.119151 4817.617055 5394.575679 5309.262262 6157.343385 3915.488286 3870.073093 1.135527988 1.154900384 1.135580833 1.135926647 1.244838777 1.393920877 1.371876482 1.591014753 1.01173497 1 11.9181451 -4 0.257197949 1.025108018 4.68170117 0.943510247 0.041770499 8.266034576 0.103852756 0.024289813 13.3639082 1.00E-04 4 3.656593152 NVFEVGPGDS(ph)PTFPR ddPTM_HeLa_Romidepsin_16h_R1 1 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 0 NVFEVGPGDS(0.71)PT(0.29)FPR 177.66 5.72E-08 7710500 4375.9 4144.5 3475.5 3462.4 3173.4 2986.6 2073.4 2746.8 4494.2 4394.4 TRUE FALSE FALSE 4322.564848 4202.84638 3535.98962 3862.738979 3011.449556 2795.765899 2249.514544 2826.274324 4092.227496 4280.232855 1.009890115 0.981920032 0.826120854 0.902460009 0.703571431 0.653180795 0.525558917 0.660308544 0.956075904 1 12.06347357 -8.834840687 0.832340434 1.006033973 0.570309917 0.890529158 0.054725196 0.119293817 0.154225718 0.008687686 0.029040988 1.46E-09 8.834840687 -0.435724055 NVFEVGPGDSPT(ph)FPR ddPTM_HeLa_Romidepsin_16h_R1 1 NVFEVGPGDSPTFPR 15 0 Q16584;Q16584-2 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 0 NVFEVGPGDS(0.244)PT(0.756)FPR 111.11 0.0085697 6328700 1822.7 2327.8 2166.1 1843.7 1519.9 1380.9 1241.1 1466.5 2248 1797.4 TRUE FALSE FALSE 1800.484231 2360.57083 2203.800062 2056.877269 1442.333831 1292.664947 1346.519003 1508.930864 2046.93325 1750.703289 1.028434825 1.348355741 1.258808432 1.174886277 0.823859669 0.738368949 0.769130333 0.861899828 1.169206263 1 10.77371888 -8.678123954 6.559783568 1.071971048 0.787997497 0.647005015 0.121356909 0.144786169 9.308457981 0.020630389 0.0414195 2.10E-09 8.678123954 -0.283973551 NVFHIASQK(ac)NFK ddPTM_HeLa_Romidepsin_16h_R1 2 NVFHIASQKNFK 12 1 E5RGR5;A0A087WWE7;Q8N0T1-2;Q8N0T1 E5RGR5 C8orf59 Uncharacterized protein C8orf59 0 1 ; NVFHIASQK(1)NFK;NVFHIASQK(1)NFK 115.92 0.0056611 2798500 1421.53 1423.71 1302.12 909.14 1935.48 1942.78 2253.77 1351.2 2655.5 1277.11 FALSE TRUE FALSE 1404.203846 1443.753027 1324.782852 1014.259044 1836.705233 1818.642628 2445.205168 1390.29484 2417.985429 1243.930498 1.128844295 1.160638017 1.064997485 0.81536633 1.476533646 1.462013055 1.965708833 1.117662797 1.943826792 1 10.28069016 -8.649221369 6.658861222 1.056046079 1.544549746 0.103415607 0.3511531 0.114662156 6.307084996 0.028056234 0.056378298 2.24E-09 8.649221369 0.488503667 NVFSSSGTSFS(ph)GRK ddPTM_HeLa_Romidepsin_16h_R1 2 NVFSSSGTSFSGRK 14 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 NVFS(0.017)S(0.054)S(0.054)GT(0.272)S(0.179)FS(0.423)GRK;NVFSSSGT(0.11)S(0.379)FS(0.511)GRK ; 192.32 1.00E-13 0 4837 4158 4739.7 4555.9 5555.2 6444 5317.7 5604.9 5727.8 4700.5 TRUE FALSE FALSE 4778.044784 4216.536433 4822.19249 5082.674594 5271.697415 6032.249197 5769.385305 5767.068938 5215.491222 4578.380332 1.043610281 0.920966833 1.053252928 1.11014687 1.151432828 1.317550915 1.260136748 1.259630813 1.139156392 1 12.1606216 -8.731580026 1.471331936 1.014118683 1.279192535 0.773260985 0.057062312 0.092731061 0.402751858 0.006538614 0.016592236 1.86E-09 8.731580026 0.265073853 NVGMPVAHMES(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 NVGMPVAHMESPER 14 0 Q9UPS8 Q9UPS8 ANKRD26 Ankyrin repeat domain-containing protein 26 1 0 NVGMPVAHMES(1)PER 71.929 0.014547 5709100 3049.1 2920.8 2716.9 2548.7 2528.8 2516.5 2322.8 2406.6 3225.2 2883.1 TRUE FALSE FALSE 3011.936396 2961.919099 2764.186505 2843.392686 2399.7459 2355.703772 2520.098574 2476.231174 2936.730034 2808.196646 1.07255181 1.05474063 0.98432797 1.012533324 0.854550518 0.838867098 0.897408156 0.881786956 1.045770793 1 11.45542825 -8.806839908 5.10195501 1.03199346 0.867778379 0.886093416 0.028156276 0.056498884 3.287658029 0.00530071 0.009947407 1.56E-09 8.806839908 -0.164215082 NVHS(ph)EDFENR ddPTM_HeLa_Romidepsin_16h_R1 2 NVHSEDFENR 10 0 Q9H2P0;A0A669KBJ7 Q9H2P0 ADNP Activity-dependent neuroprotector homeobox protein 1 0 NVHS(1)EDFENR;NVHS(1)EDFENR ; 115.34 0.0061783 39627000 5838.5 5572.7 5087.8 4503 5465 4798.1 3853.2 4284.5 5768.7 4994.3 TRUE FALSE FALSE 5767.338116 5651.152617 5176.351025 5023.658047 5186.100657 4491.516895 4180.490712 4408.465248 5252.733024 4864.547366 1.185585766 1.161701633 1.064097158 1.032708219 1.066101379 0.92331651 0.859379177 0.906243668 1.079798927 1 12.24808986 -8.258946263 1.733306639 1.091645941 0.875339129 0.72947456 0.052829897 0.208652211 1.184740428 0.011451395 0.039107208 5.51E-09 8.258946263 -0.216306812 NVIPDT(ph)PPSTPLVPSR ddPTM_HeLa_Romidepsin_16h_R1 2 NVIPDTPPSTPLVPSR 16 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 0 NVIPDT(0.961)PPS(0.034)T(0.005)PLVPSR;NVIPDT(0.444)PPS(0.444)T(0.067)PLVPS(0.044)R ; 146.86 0.0006277 28677000 6373.8 6021.5 5525.1 6803.3 11340 11705.9 9862.3 10836.9 5854.9 5990.3 TRUE FALSE FALSE 6296.113674 6106.270835 5621.262048 7589.929556 10761.27748 10957.93077 10700.00352 11150.4486 5331.22308 5834.671142 1.079086296 1.046549272 0.963423972 1.30083245 1.844367441 1.878071703 1.833865741 1.911067193 0.913714407 1 12.51043563 -8.874277587 2.871344969 1.035086481 1.875477286 0.982318838 0.05474477 0.019373867 0.322436058 0.006791722 0.013268116 1.34E-09 8.874277587 0.840390805 NVMILTNPVAAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 NVMILTNPVAAKK 13 1 F8W7T0;Q9UGI8-2;Q9UGI8 F8W7T0 TES Testin 0 1 NVMILTNPVAAK(1)K 189.33 3.98E-54 0 289.54 250.26 299.53 358.7 530.64 589.41 560.18 354.6 393.16 310.3 FALSE TRUE FALSE 286.0109751 253.7831668 304.743194 400.1745817 503.5594607 551.7486032 607.7616752 364.8597915 357.9947849 302.2383613 0.94630931 0.839678874 1.008287607 1.324036367 1.66610042 1.825541275 2.010868748 1.207192198 1.184478315 1 8.239542974 -8.988599191 2.216547451 0.96251476 1.720127697 0.705366228 0.20670466 0.101503611 0.999252374 0.027910141 0.053984535 1.03E-09 8.988599191 0.757612937 NVNIFK ddPTM_HeLa_Romidepsin_16h_R1 1 NVNIFK 6 0 P00338;P00338-3;P00338-5;P00338-2;F5GYU2;F5GXY2 P00338 LDHA L-lactate dehydrogenase A chain 0 0 121.87 0.024563 2884800 2593.6 1699 2029.3 1818.7 1966.9 2101.9 1927.7 1982.1 2459.1 2269.2 FALSE FALSE TRUE 2561.988206 1722.918567 2064.619115 2028.986651 1866.521753 1967.595374 2091.43879 2039.448936 2239.151937 2210.245857 1.15914173 0.779514442 0.934112877 0.917991383 0.844486032 0.890215614 0.946247126 0.922724922 1.013078219 1 11.10999114 -10.26729933 24.99959606 1.075150261 0.893805008 0.602202839 0.061529593 247.2598311 1054852.78 0.012327686 0.014297055 5.40E-11 10.26729933 -0.181345253 NVPNWHR ddPTM_HeLa_Romidepsin_16h_R1 2 NVPNWHR 7 0 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 0 ; ; 134.44 0.0064504 35213000 9833.1 8660.9 9059.8 9319.2 9247.2 9069.5 7608.1 6662.9 9666 8313.8 FALSE FALSE TRUE 9713.250395 8782.828378 9217.482019 10396.72975 8775.280878 8489.98822 8254.331824 6855.680499 8801.448751 8097.806277 1.199491574 1.08459354 1.13826902 1.2838946 1.083661498 1.04843064 1.019329377 0.846609596 1.086892974 1 12.98331541 -7.189936859 1.291767536 1.111370215 0.702532717 0.565423309 0.073665 1.203842969 1.514252884 0.013837315 0.675915405 6.46E-08 7.189936859 -0.408837499 NVPQEESLEDS(ph)DVDADFK ddPTM_HeLa_Romidepsin_16h_R1 5 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 1 0 NVPQEES(0.003)LEDS(0.997)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEESLEDS(1)DVDADFK;NVPQEES(0.039)LEDS(0.961)DVDADFK ;;;; 248.23 5.70E-62 278437000 46248.1 45422.2 46116.7 40094.6 43412 41723.6 34373.8 38389.3 48717.5 44683 TRUE FALSE FALSE 45684.41037 46061.65492 46919.34182 44730.5263 41196.52365 39057.59662 37293.50971 39500.03383 44360.08478 43522.12922 1.049682338 1.058350217 1.078057132 1.027765119 0.946564986 0.897419251 0.856886149 0.90758505 1.019253552 1 15.40946152 -8.549302955 2.38631287 1.031998336 0.883663894 0.889931782 0.024152333 0.086385976 0.983864606 0.004509107 0.010736913 2.82E-09 8.549302955 -0.148334441 NVPQEESLEDSDVDADFK ddPTM_HeLa_Romidepsin_16h_R1 1 NVPQEESLEDSDVDADFK 18 0 O00505 O00505 KPNA3 Importin subunit alpha-4 0 0 182.1 5.35E-15 0 1420 1634.4 1205.1 1047.7 1231.9 1319.2 1061.9 1246.8 1572.1 1658.2 FALSE FALSE TRUE 1402.692494 1657.409126 1226.07426 1168.840004 1169.031546 1234.907378 1152.097759 1282.874191 1431.487439 1615.119725 0.868475861 1.026183447 0.759122832 0.723686291 0.723804885 0.764591849 0.713320345 0.794290461 0.886304227 1 10.6574254 -9.696691108 7.997875442 0.94268115 0.742928341 0.798915319 0.048844925 0.093962053 10.22679209 0.008930627 0.012623544 2.01E-10 9.696691108 -0.19975281 NVPVGFGESWKKHLS(ph)GEFGK ddPTM_HeLa_Romidepsin_16h_R1 1 NVPVGFGESWKKHLSGEFGK 20 2 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 1 0 NVPVGFGES(0.002)WKKHLS(0.998)GEFGK 40.014 0.027516 1458200 2219.2 668.08 1226.7 1004.8 1414.5 914.81 2202.1 1074.8 2015.2 1418.4 TRUE FALSE FALSE 2192.151537 677.4852478 1248.050199 1120.979704 1342.312787 856.3565934 2389.146319 1105.897642 1834.955465 1381.549764 1.586733677 0.490380633 0.903369703 0.811392925 0.971599303 0.619852152 1.729323389 0.800476155 1.328186297 1 10.43207181 -10.27412645 24.99651892 1.277068669 0.923643072 0.226817278 0.336879754 1011.922423 1993720.23 0.062124597 0.071287513 5.32E-11 10.27412645 -0.353425597 NVQQTVSAK(ac)GPPEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NVQQTVSAKGPPEKR 15 2 G3V4A5;A0A087WYL7;O75586;O75586-2 G3V4A5 MED6 Mediator of RNA polymerase II transcription subunit 6 0 2 NVQQTVSAK(1)GPPEK(1)R 250.05 1.13E-69 27877000 731.23 812.79 461.35 661.95 961.17 1382.8 1163.6 1100.7 697.9 661.06 FALSE TRUE FALSE 722.3174875 824.232479 469.3796032 738.4877736 912.1179083 1294.443543 1262.436155 1132.547018 635.4780761 643.8855659 1.121810343 1.280091561 0.72897985 1.146923945 1.416583872 2.010362728 1.960652982 1.75892593 0.986942571 1 9.330660499 -8.50592954 2.622321909 1.054930929 1.915369028 0.872222232 0.148163547 0.067095583 0.918535446 0.021250305 0.050667168 3.12E-09 8.50592954 0.860438099 NVS(ph)QESLETK ddPTM_HeLa_Romidepsin_16h_R1 1 NVSQESLETK 10 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 NVS(0.999)QES(0.001)LETK 105.95 0.020678 3964600 1227.9 1557.1 1096.4 798.39 1044.9 1151.7 905.82 656.93 1280.8 1138.1 TRUE FALSE FALSE 1212.933883 1579.020895 1115.482382 890.7036083 991.5748539 1078.110087 982.7603282 675.9372331 1166.24204 1108.531998 1.094180308 1.424425184 1.006269899 0.803498329 0.894493669 0.972556578 0.886542139 0.609758883 1.05205988 1 10.1144347 -9.406883186 5.288402748 1.080034241 0.849023421 0.488267369 0.143222919 0.196988132 7.866005858 0.023205542 0.035607396 3.92E-10 9.406883186 -0.23101082 NVS(ph)SFPDDATSPLQENR ddPTM_HeLa_Romidepsin_16h_R1 1 NVSSFPDDATSPLQENR 17 0 J3QLL0;J3KS65;P52292 J3QLL0 KPNA2 Importin subunit alpha-1 1 0 NVS(0.768)S(0.106)FPDDAT(0.125)SPLQENR 147.37 0.00013472 6803000 920.04 1066 983.5 1002.9 1227.5 1273.7 983.07 1096.6 1276.9 1086.4 TRUE FALSE FALSE 908.8261986 1081.007176 1000.617405 1118.860017 1164.856095 1192.314681 1066.571941 1128.328391 1162.690866 1058.175171 0.858861768 1.021576772 0.94560658 1.057348582 1.100815939 1.126764937 1.007935142 1.066296414 1.098769748 1 10.04736276 -9.289590141 2.181629341 0.938220786 1.076200144 0.135035666 0.071446803 0.200264687 1.862638999 0.010203296 0.017401665 5.13E-10 9.289590141 0.137979358 NVS(ph)TGSAENEEK ddPTM_HeLa_Romidepsin_16h_R1 1 NVSTGSAENEEK 12 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 NVS(0.83)T(0.17)GSAENEEK 145.1 0.0015129 3857600 1200.4 1011 1355.7 569.95 907.8 1223.1 1019 935.85 1137.4 1209.8 TRUE FALSE FALSE 1185.769063 1025.232885 1379.29539 635.8503007 861.4715785 1144.947857 1105.553835 962.9273432 1035.668095 1178.369222 1.006279731 0.870043842 1.170512064 0.539601925 0.731071011 0.971637613 0.938206646 0.817169462 0.878899479 1 10.20257594 -9.283236437 24.97609171 1.002380598 0.812998568 0.313496214 0.135413586 684.9867957 784887.8737 0.019774231 0.030221587 5.21E-10 9.283236437 -0.18938203 NVSEELDR ddPTM_HeLa_Romidepsin_16h_R1 1 NVSEELDR 8 0 Q15393-3;Q15393 Q15393-3 SF3B3 Splicing factor 3B subunit 3 0 0 116.25 0.016089 3690300 633.86 650.95 730.38 645.38 789.3 1064.4 605.61 681.87 797.21 727.97 FALSE FALSE TRUE 626.1342705 660.1140912 743.0919575 720.0018722 749.0190757 996.3882752 657.0504983 701.5988326 725.905541 709.0572345 0.883051805 0.93097434 1.047999966 1.015435479 1.056359119 1.405229686 0.926653684 0.989481241 1.023761561 1 9.469758275 -9.352848437 1.595068809 0.943116651 1.096861069 0.161464792 0.125103293 0.426550138 2.129933149 0.020713829 0.036290323 4.44E-10 9.352848437 0.153744418 IDAGTMAEPSAS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 3 IDAGTMAEPSASPSK 15 0 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 0 IDAGTMAEPS(0.043)AS(0.953)PS(0.005)K;IDAGTMAEPS(0.081)AS(0.916)PS(0.003)K;IDAGTMAEPS(0.017)AS(0.882)PS(0.101)K ;; 157.37 0.00048431 54451000 18837.4 19996.8 19918.8 15148.3 8613.2 6230.2 5149.8 5771.4 20106.9 18499.4 TRUE FALSE FALSE 18607.80252 20278.31548 20265.47836 16899.81772 8173.636264 5832.110327 5587.223883 5938.386353 18308.48851 18018.78292 1.0326892 1.125398733 1.124686304 0.937900068 0.453617556 0.323668383 0.310077762 0.329566452 1.016077977 1 14.13721395 -8.740540421 3.049206943 1.03399949 0.326084678 0.983783534 0.043509261 0.025712416 0.491576128 0.007772082 0.015970677 1.82E-09 8.740540421 -0.707914812 down NVSHNPLLLLT(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 2 NVSHNPLLLLTPQK 14 0 P47712 P47712 PLA2G4A Cytosolic phospholipase A2;Phospholipase A2;Lysophospholipase 1 0 NVSHNPLLLLT(1)PQK;NVSHNPLLLLT(1)PQK ; 128.74 0.0019039 43862000 7695.2 8009.6 7537 6785.8 6970.1 7142.6 5996.5 6505.7 8254 7466.1 TRUE FALSE FALSE 7601.407943 8122.359359 7668.178323 7570.406124 6614.389788 6686.210912 6505.84256 6693.932165 7515.741567 7272.129646 1.045279487 1.116916193 1.054461168 1.041016386 0.909553337 0.919429553 0.894626867 0.920491313 1.033499392 1 12.8281622 -8.759666213 24.9996776 1.033824783 0.910454238 0.829037873 0.030149316 18.75992488 264487.2476 0.005438002 0.010439381 1.74E-09 8.759666213 -0.123370545 NVSIGIVGK ddPTM_HeLa_Romidepsin_16h_R1 1 NVSIGIVGK 9 0 P25786;P25786-2;F5GX11 P25786 PSMA1 Proteasome subunit alpha type-1 0 0 130.66 0.021241 5891900 2988.4 2246.1 2261.8 2244.9 2422.5 2104.1 2414.7 1946.3 2699.2 2304.1 FALSE FALSE TRUE 2951.976231 2277.720655 2301.16568 2504.465901 2298.870785 1969.654801 2619.804558 2002.61312 2457.776792 2244.23915 1.315357248 1.014918867 1.025365626 1.115953218 1.024343054 0.877649247 1.167346429 0.89233499 1.095149237 1 11.1320107 -10.12188814 18.28507459 1.1497866 1.021656279 0.196996286 0.109768636 3.503020882 510.423471 0.022700322 0.027802252 7.55E-11 10.12188814 -0.12813032 NVSS(ph)FPDDATSPLQENR ddPTM_HeLa_Romidepsin_16h_R1 2 NVSSFPDDATSPLQENR 17 0 J3QLL0;J3KS65;P52292 J3QLL0 KPNA2 Importin subunit alpha-1 1 0 NVS(0.216)S(0.784)FPDDATSPLQENR;NVS(0.048)S(0.952)FPDDAT(0.001)SPLQENR ; 172.95 1.69E-06 11511300 3405.4 3051.2 3256.4 3275.2 3988.8 3253.1 3037.7 3461.2 3637.9 2788.7 TRUE FALSE FALSE 3363.893675 3094.154874 3313.076276 3653.894034 3785.236652 3045.237409 3295.722162 3561.344361 3312.517113 2716.249172 1.238433392 1.139127774 1.219724726 1.345198398 1.393552805 1.121118578 1.213335726 1.311125797 1.219518867 1 11.40740011 -12.43863746 0.410579913 0.907581605 1.264620193 0.088364988 0.104244008 1.427683924 0.285492247 0.224542743 0.027173249 3.64E-13 12.43863746 0.357038588 NVSSFPDDAT(ph)SPLQENR ddPTM_HeLa_Romidepsin_16h_R1 3 NVSSFPDDATSPLQENR 17 0 J3QLL0;J3KS65;P52292 J3QLL0 KPNA2 Importin subunit alpha-1 1 0 NVSSFPDDAT(0.887)S(0.113)PLQENR;NVSSFPDDAT(0.5)S(0.5)PLQENR;NVSSFPDDAT(0.531)S(0.469)PLQENR ;; 199.05 1.27E-18 485755300 9968.9 9769.8 9774.8 9204.3 10980.9 12398 10584.4 11002.3 11674.9 10425.8 TRUE FALSE FALSE 9847.395212 9907.339501 9944.926294 10268.54447 10420.5037 11605.80781 11483.43867 11320.63419 10630.6677 10154.93621 0.969715122 0.975618093 0.979319425 1.011187491 1.026151566 1.142873532 1.130823319 1.114791265 1.046847315 1 13.30989356 -8.430800281 2.419039522 0.985370634 1.131204864 0.854529836 0.024080196 0.049204744 0.56018521 0.002454188 0.006265752 3.71E-09 8.430800281 0.14583423 NVSSFPDDATS(ph)PLQENR ddPTM_HeLa_Romidepsin_16h_R1 3 NVSSFPDDATSPLQENR 17 0 J3QLL0;J3KS65;P52292 J3QLL0 KPNA2 Importin subunit alpha-1 1 0 NVSSFPDDAT(0.013)S(0.987)PLQENR;NVSSFPDDAT(0.02)S(0.98)PLQENR;NVSSFPDDAT(0.006)S(0.994)PLQENR ;; 166.36 5.01E-06 489494700 10567.3 11012.8 10432.3 9637.16 11773.7 12856.3 10751.65 12330.5 12057.9 11625.4 TRUE FALSE FALSE 10438.50168 11167.83849 10613.86981 10751.45378 11172.84416 12034.82392 11664.89488 12687.26356 10979.41122 11323.37043 0.92185465 0.986264519 0.937341922 0.949492366 0.986706584 1.062830541 1.030161024 1.120449396 0.969623955 1 13.46701582 -8.140514719 1.417533703 0.960776932 1.087452945 0.745582568 0.029024953 0.215630205 0.77830474 0.005308867 0.024019657 7.24E-09 8.140514719 0.126676013 NVST(ph)GSAENEEK ddPTM_HeLa_Romidepsin_16h_R1 1 NVSTGSAENEEK 12 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 NVS(0.11)T(0.859)GS(0.031)AENEEK 132.65 0.0064476 3738100 1130.5 923.09 1181 614.16 1200.2 1115.6 1288.5 853.22 1166.6 1068.8 TRUE FALSE FALSE 1116.721031 936.0852852 1201.55481 685.1720689 1138.949315 1044.31676 1397.945158 877.9065745 1062.256374 1041.032422 1.072705333 0.899189368 1.154195378 0.658165927 1.094057487 1.003154886 1.342844976 0.843303778 1.020387408 1 10.02379929 NVSTGS(ph)AENEEK ddPTM_HeLa_Romidepsin_16h_R1 4 NVSTGSAENEEK 12 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 NVS(0.001)T(0.038)GS(0.961)AENEEK;NVS(0.026)T(0.144)GS(0.83)AENEEK;NVS(0.017)T(0.064)GS(0.919)AENEEK;NVS(0.001)T(0.006)GS(0.993)AENEEK ;;; 180.85 1.23E-06 69029000 11613.9 11621.8 12383.9 7331.2 10631.6 11798.9 10473.7 10036.9 11686.5 11753.4 TRUE FALSE FALSE 11472.34532 11785.41201 12599.43658 8178.867838 10089.02978 11044.98837 11363.33582 10327.30187 10641.23017 11448.04497 1.002122663 1.029469401 1.100575392 0.714433587 0.881288447 0.964792538 0.992600557 0.90210179 0.929523792 1 13.48281362 -9.307472822 24.99999538 1.010404798 0.900240106 0.366559739 0.079244578 369.4122228 200620.679 0.011669067 0.017824825 4.93E-10 9.307472822 -0.110164692 SRLT(ph)PVSPESSSTEEK ddPTM_HeLa_Romidepsin_16h_R1 5 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 SRLT(0.999)PVS(0.001)PESSSTEEK;S(0.019)RLT(0.981)PVSPESSSTEEK;S(0.034)RLT(0.966)PVSPESSSTEEK;S(0.14)RLT(0.854)PVS(0.005)PESSSTEEK;S(0.013)RLT(0.856)PVS(0.127)PES(0.003)S(0.001)STEEK ;;;; 147.64 0.00016366 1160558000 31970.4 31831.8 28105.7 26558.8 9795.1 7045.8 5285.03 5356.36 32611.7 31259.8 TRUE FALSE FALSE 31580.73247 32279.92892 28594.86792 29629.65342 9295.219496 6595.596119 5733.940316 5511.337826 29694.82787 30447.66589 1.037213578 1.060177454 0.939148111 0.97313382 0.305285125 0.216620747 0.188321178 0.181010191 0.97527436 1 14.89404402 -8.739137877 3.855682396 1.01532269 0.202831971 0.991909418 0.034370114 0.013539086 0.434901362 0.00540119 0.010829891 1.82E-09 8.739137877 -0.812490719 down NVTELNEPLSNEER ddPTM_HeLa_Romidepsin_16h_R1 2 NVTELNEPLSNEER 14 0 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 0 ; ; 298.91 1.58E-130 28365000 3998.8 4048.8 3659.7 4061.4 4870.4 4560.9 4053.4 4590.3 4228.6 3796.7 FALSE FALSE TRUE 3950.061088 4105.799113 3723.395543 4530.998177 4621.845314 4269.47321 4397.695695 4723.113088 3850.383425 3698.061187 1.068143789 1.110257215 1.006850713 1.22523613 1.249802283 1.154516649 1.189189544 1.277186301 1.041189756 1 11.85255338 -9.257119703 24.97980772 1.038367481 1.215627851 0.806972722 0.042439744 126.5574325 731854.9078 0.007107933 0.011522768 5.53E-10 9.257119703 0.17726037 NVTMET(ph)E ddPTM_HeLa_Romidepsin_16h_R1 1 NVTMETE 7 0 P49458 P49458 SRP9 Signal recognition particle 9 kDa protein 1 0 NVT(0.291)MET(0.709)E 72.23 0.014631 2765800 3141.3 2969.9 3408.9 3103.1 2984.7 2800.4 2264.2 2709.5 3069 3466.6 TRUE FALSE FALSE 3103.012627 3011.71033 3468.230475 3461.895023 2832.379622 2621.463478 2456.521091 2787.895108 2794.500954 3376.537232 0.91899257 0.891952353 1.027155999 1.025279683 0.838841519 0.776376298 0.72752673 0.825666923 0.82762332 1 11.72132875 -8.580751125 4.523257409 0.964249496 0.775891573 0.599111438 0.063267219 0.07822759 3.292704776 0.007650378 0.015902016 2.63E-09 8.580751125 -0.188357923 NVYATTVGT(ph)PYK ddPTM_HeLa_Romidepsin_16h_R1 2 NVYATTVGTPYK 12 0 Q13439-3;Q13439-4;Q13439;Q13439-5;H0Y6I0 Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 NVYAT(0.004)T(0.001)VGT(0.994)PYK;NVYAT(0.101)T(0.101)VGT(0.782)PY(0.015)K ; 131.53 0.0071314 17141000 3820 3781.1 4728.9 2928.8 4067.6 4897.9 3258.3 3614.1 3656.4 3429.4 TRUE FALSE FALSE 3773.440371 3834.330425 4811.204521 3267.441636 3860.015194 4584.939997 3535.059921 3718.668281 3329.362426 3340.303694 1.129669849 1.147898747 1.44034943 0.978186996 1.155588098 1.37261172 1.058304946 1.113272511 0.996724469 1 11.70576356 -11.3929499 0.789484396 1.012235019 1.181101062 0.226391869 0.129990338 0.647886636 0.850217549 0.052251728 0.02844779 4.05E-12 11.3929499 0.168866043 NWDEWVPESR ddPTM_HeLa_Romidepsin_16h_R1 1 NWDEWVPESR 10 0 H0YMJ0;B3KTM8;Q9UBU8-2;H0YLJ3 H0YMJ0 MORF4L1 Mortality factor 4-like protein 1 0 0 141.91 4.19E-05 0 1754.5 1695.1 1601.2 1096.9 1471.3 1331.6 1150.4 1523.9 2024.4 1866.9 FALSE FALSE TRUE 1733.115479 1718.963662 1629.068214 1223.728739 1396.214071 1246.515058 1248.114947 1567.991642 1843.332594 1818.397669 0.953100363 0.945317788 0.895881161 0.672970913 0.767826584 0.6855019 0.686381735 0.862293034 1.013712581 1 10.82845202 -9.4668161 3.063993968 0.974476702 0.731506634 0.812193674 0.055356762 0.075255478 1.40110176 0.0082915 0.012785097 3.41E-10 9.4668161 -0.242970068 NWEDEDFYDS(ph)DDDTFLDR ddPTM_HeLa_Romidepsin_16h_R1 1 NWEDEDFYDSDDDTFLDR 18 0 A0A087WWF4;A0A087X0M4;Q9BWU0 A0A087WWF4 SLC4A1AP Kanadaptin 1 0 NWEDEDFY(0.001)DS(0.985)DDDT(0.014)FLDR 80.683 0.0054674 2347900 929.05 795.28 861.31 913.47 938.37 869.44 601.26 604.56 944.3 973.68 TRUE FALSE FALSE 917.7263813 806.4759727 876.3007392 1019.089699 890.4814774 813.88559 652.3310094 622.0519898 859.839443 948.3836532 0.967674188 0.850368909 0.92399393 1.074554265 0.938946464 0.858181799 0.687834514 0.655907541 0.906636718 1 9.889326986 -7.896444558 1.97293619 0.974185464 0.650122433 0.778535951 0.058427554 0.106162239 0.782394021 0.008312399 0.039442971 1.27E-08 7.896444558 -0.324063031 NWRVRELT(ph)GFNR ddPTM_HeLa_Romidepsin_16h_R1 1 NWRVRELTGFNR 12 2 H7C411 H7C411 CCNT2 1 0 NWRVRELT(1)GFNR 68.676 0.0037881 0 433.46 518.63 492.21 385.82 434.47 559.77 368.23 555.15 353 392.55 TRUE FALSE FALSE 428.1768228 525.9312868 500.7767086 430.4303237 412.2973747 524.0025036 399.507447 571.2123894 321.4267959 382.3514944 1.119851312 1.375517801 1.309728655 1.125745106 1.078320291 1.370473272 1.044869584 1.493945748 0.840657878 1 8.578755703 -10.67931021 2.089116588 1.041251445 1.242516879 0.385438146 0.151291284 0.251443913 2.291774305 0.025806789 0.026146122 2.09E-11 10.67931021 0.201265435 NWTEDMEGGIS(ph)SPVK ddPTM_HeLa_Romidepsin_16h_R1 2 NWTEDMEGGISSPVK 15 0 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 NWTEDMEGGIS(0.865)S(0.134)PVK;NWTEDMEGGIS(0.648)S(0.352)PVK ; 104.94 0.0084682 58708700 9867.8 9871.4 9187.1 7666.8 6894.6 5577 4965.4 5152.4 10996.2 9484.6 TRUE FALSE FALSE 9747.527458 10010.36983 9346.997622 8553.271489 6542.742835 5220.647699 5387.160952 5301.476565 10012.67233 9238.188725 1.055134047 1.083585768 1.011778163 0.925860225 0.708227882 0.565115939 0.583140387 0.573865367 1.083835006 1 13.1733943 -8.728744564 1.858077564 1.031364966 0.571148114 0.982272994 0.028358195 0.031640711 0.221747221 0.004570992 0.010564259 1.87E-09 8.728744564 -0.460216852 NWTEDMEGGIS(ph)SPVKK ddPTM_HeLa_Romidepsin_16h_R1 1 NWTEDMEGGISSPVKK 16 1 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 NWTEDMEGGIS(0.877)S(0.123)PVKK 116.58 0.0021714 31948000 17142 16325 15429 14498 10658 8982.5 7686.7 7993.7 17220 15633 TRUE FALSE FALSE 16933.06671 16554.82378 15697.53527 16174.32698 10114.08249 8408.54724 8339.608106 8224.985098 15679.80007 15226.85241 1.112052988 1.087212468 1.03091137 1.062223928 0.664226737 0.552218345 0.547690874 0.540163185 1.029746638 1 13.89433013 -8.682572684 3.461197888 1.056969963 0.553112617 0.981302528 0.032545382 0.030385528 0.722239914 0.006896487 0.014304421 2.08E-09 8.682572684 -0.503857346 NYACYMS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 NYACYMSPTK 10 0 A0A2R8Y872;Q587J7-2;Q587J7 A0A2R8Y872 TDRD12 Putative ATP-dependent RNA helicase TDRD12 1 0 NYACYMS(0.999)PTK 97.597 0.0033455 0 3095.4 2255.7 3056.6 1816.6 2317.2 2778.8 2027.9 1946.8 3131 2697.8 TRUE FALSE FALSE 3057.672074 2287.455804 3109.798841 2026.643839 2198.944637 2601.243648 2200.149775 2003.127586 2850.955518 2627.710767 1.163625812 0.87051278 1.183463142 0.771258338 0.836829024 0.989927689 0.837287651 0.762309007 1.084957886 1 11.35959077 -9.255143477 24.99584833 1.067675118 0.847604414 0.548678641 0.099973756 318.4892912 1264458.127 0.015865256 0.025893712 5.56E-10 9.255143477 -0.220070704 NYDPKVT(ph)PDPER ddPTM_HeLa_Romidepsin_16h_R1 1 NYDPKVTPDPER 12 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 0 NYDPKVT(1)PDPER 128.35 0.019436 9600300 2882.4 2468.7 2322.3 2730.3 2544.5 2499.3 2175.9 2350.5 2375.3 2260.8 TRUE FALSE FALSE 2847.2682 2503.454423 2362.718657 3045.990132 2414.64467 2339.602796 2360.720892 2418.508009 2162.847219 2202.06409 1.292999696 1.136867194 1.072956354 1.383243179 1.096536963 1.062458993 1.07204913 1.09829138 0.982190858 1 11.10464074 -8.54228405 24.99853311 1.154855952 1.077453485 0.063415179 0.115220406 521.3726094 671646.3596 0.018926855 0.037857629 2.87E-09 8.54228405 -0.077402467 NYDPYKPLDIT(ph)PPPDQK ddPTM_HeLa_Romidepsin_16h_R1 1 NYDPYKPLDITPPPDQK 17 1 Q9UKK3 Q9UKK3 PARP4 Poly [ADP-ribose] polymerase 4 1 0 NY(0.005)DPY(0.019)KPLDIT(0.976)PPPDQK 73.405 0.014744 6628300 3082.8 3089.1 3407.3 3185.1 2758.3 2417.1 2134.1 2697.5 3276.2 3120.6 TRUE FALSE FALSE 3045.225648 3132.588431 3466.602627 3553.376248 2617.533658 2262.655111 2315.370401 2775.547907 2983.168467 3039.526362 1.001875057 1.030617293 1.140507505 1.169055907 0.86116498 0.744410425 0.761753683 0.913151451 0.98145833 1 11.56963082 -8.577421152 8.184409206 1.025391224 0.802034022 0.702678176 0.07372882 0.118143833 15.83652877 0.0113323 0.022742034 2.65E-09 8.577421152 -0.223357201 NYDYYASR ddPTM_HeLa_Romidepsin_16h_R1 1 NYDYYASR 8 0 O95861-3;O95861-4;O95861 O95861-3 BPNT1 "3(2),5-bisphosphate nucleotidase 1" 0 0 106.42 0.0030221 0 1622.8 1465 1624.4 1672.3 1817.6 1746.8 1520.7 1315.5 1767.9 1223.1 FALSE FALSE TRUE 1603.020689 1485.624308 1652.672001 1865.659194 1724.84109 1635.185118 1649.86822 1353.561917 1609.774596 1191.323686 1.345579467 1.247036659 1.387256898 1.566038867 1.447835807 1.372578366 1.384903398 1.136183166 1.351248712 1 10.21834974 -12.03827091 0.562322967 0.957489056 1.381868622 0.007719826 0.151520625 0.574337053 0.290952424 0.125222369 0.027426787 9.16E-13 12.03827091 0.424379565 NYGS(ph)PLISGSTPK ddPTM_HeLa_Romidepsin_16h_R1 2 NYGSPLISGSTPK 13 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 NYGS(0.998)PLIS(0.002)GSTPK;NYGS(0.971)PLIS(0.028)GS(0.001)TPK ; 182.7 3.92E-07 59187000 4518.3 4640.7 4001.9 3296.4 4501.5 4986 4172.8 4436.3 4848.8 4294.5 TRUE FALSE FALSE 4463.229222 4706.031896 4071.551391 3677.545278 4271.771658 4667.410692 4527.237528 4564.657341 4415.111184 4182.928271 1.0670107 1.1250568 0.973373466 0.879179618 1.02123952 1.115823746 1.082312972 1.091258813 1.055507266 1 12.03029754 -8.271742582 23.06240221 1.022699047 1.095049956 0.255679552 0.061378648 298.6587155 668511.7518 0.009582572 0.021694247 5.35E-09 8.271742582 0.072350908 NYGSPLIS(ph)GSTPK ddPTM_HeLa_Romidepsin_16h_R1 1 NYGSPLISGSTPK 13 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 NYGS(0.001)PLIS(0.984)GS(0.012)T(0.004)PK 137.73 0.0013852 3914000 1705.2 1916.3 1998.9 1648.3 1934.4 1778.5 1720.3 2010.4 2080.8 1936.1 TRUE FALSE FALSE 1684.416367 1943.277722 2033.690016 1838.884201 1835.68035 1664.85959 1866.422239 2068.567752 1894.688037 1885.799843 0.893210577 1.03047931 1.078423049 0.975121622 0.973422687 0.88284003 0.989724464 1.096917979 1.004713222 1 10.88096084 -10.24171683 24.53417101 0.949571657 0.999243047 0.048398925 0.063588171 1165.188716 1449456.217 0.011614394 0.014212253 5.73E-11 10.24171683 0.04967139 SVS(ph)ENSLVAMDFSGQTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSENSLVAMDFSGQTGR 18 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 0 S(0.012)VS(0.558)ENS(0.431)LVAMDFSGQTGR 146.81 0.00010327 27398000 3785.8 2893.5 2539.6 2587.1 2115.8 1654.4 1091 1278.6 2948.5 3295.8 TRUE FALSE FALSE 3739.657213 2934.234769 2583.800673 2886.232675 2007.822831 1548.689179 1183.669513 1315.594274 2684.778775 3210.174641 1.164938868 0.9140421 0.804878538 0.89908899 0.62545595 0.482431441 0.368724336 0.409820156 0.83633418 1 11.64843607 -8.737146502 0.762106027 1.073364945 0.334027152 0.821524721 0.10708185 0.164867804 0.17009711 0.0173345 0.06829151 1.83E-09 8.737146502 -0.739337794 down NYILDQTNVYGS(ph)AQR ddPTM_HeLa_Romidepsin_16h_R1 2 NYILDQTNVYGSAQR 15 0 M0R3F1;A0A0A0MRA5;B7Z4B8;Q9BUJ2-3;Q9BUJ2-4;Q9BUJ2-2;Q9BUJ2 M0R3F1 HNRNPUL1 Heterogeneous nuclear ribonucleoprotein U-like protein 1 1 0 NYILDQTNVYGS(1)AQR;NYILDQTNVYGS(1)AQR ; 241.68 2.26E-50 9954400 4079.9 4103.6 3951.6 3260.4 3523.5 3217.5 3077.5 2945.3 4081.7 3557.3 TRUE FALSE FALSE 4030.17261 4161.370589 4020.37594 3637.382789 3343.682647 3011.912134 3338.902773 3030.517609 3716.622529 3464.880833 1.163148981 1.201014058 1.160321562 1.049785826 0.965020966 0.869268607 0.963641445 0.874638337 1.072655225 1 11.75859002 -8.730892939 2.702656074 1.096058307 0.909567285 0.713058403 0.060040063 0.164178249 2.448011608 0.012154059 0.025561492 1.86E-09 8.730892939 -0.186491021 KLANDFPLDLS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 KLANDFPLDLSPVK 14 1 Q96JM2;Q96JM2-3 Q96JM2 ZNF462 Zinc finger protein 462 1 0 KLANDFPLDLS(1)PVK;KLANDFPLDLS(1)PVK ; 120.87 0.0012149 18703900 8469.7 8291 9424.9 7513.9 3336.9 2800.8 2038.05 2012.55 9479.4 8849.1 TRUE FALSE FALSE 8366.468039 8407.720916 9588.936431 8382.692472 3166.605541 2621.837919 2211.161916 2070.779959 8631.538722 8619.199106 0.970678126 0.975464288 1.112508983 0.972560486 0.367389766 0.304185793 0.256539139 0.240252016 1.001431643 1 13.07333811 -8.734966436 4.323960737 0.996452131 0.277479244 0.985616149 0.042330376 0.017950578 0.759917005 0.006778107 0.013516271 1.84E-09 8.734966436 -0.718972887 down NYQQNYQNS(ph)ESGEK ddPTM_HeLa_Romidepsin_16h_R1 4 NYQQNYQNSESGEK 14 0 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NYQQNYQNS(0.962)ES(0.038)GEK;NYQQNY(0.025)QNS(0.975)ESGEK;NYQQNYQNS(0.979)ES(0.021)GEK;NYQQNYQNS(0.999)ES(0.001)GEK ;;; 251.68 3.25E-55 64454000 13497.3 14379.7 15299.4 7379.7 10519.6 9991.5 8667.5 8332.5 14490.6 14265.1 TRUE FALSE FALSE 13332.78972 14582.13779 15565.67964 8232.975637 9982.745558 9353.075396 9403.717234 8573.587741 13194.52444 13894.49065 0.959573838 1.049490634 1.120277097 0.592535261 0.718467903 0.673149929 0.676794672 0.617049445 0.949622752 1 13.76222533 -9.255638389 24.99999999 0.996161885 0.661244665 0.909414355 0.056656969 106.6829454 459761.4932 0.008622271 0.014049502 5.55E-10 9.255638389 -0.33491722 NYQQNYQNS(ph)ESGEKNEGSESAPEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 3 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NYQQNY(0.015)QNS(0.806)ES(0.178)GEKNEGSESAPEGQAQQR;NYQQNY(0.092)QNS(0.749)ES(0.145)GEKNEGS(0.007)ES(0.007)APEGQAQQR;NYQQNY(0.326)QNS(0.382)ES(0.279)GEKNEGS(0.007)ES(0.007)APEGQAQQR ;; 111.33 7.08E-10 84030700 2188.62 1868.08 1765.93 2003.8 1515.59 1197.3 1469.64 1080.48 2000.03 1744.14 TRUE FALSE FALSE 2161.944258 1894.378879 1796.665271 2235.488784 1438.243787 1120.796394 1594.471185 1111.741984 1821.142308 1698.826991 1.272610024 1.115109949 1.057591668 1.315901381 0.846609922 0.659747225 0.938571846 0.654417424 1.071999866 1 10.73032322 -8.617134041 6.371114437 1.135877548 0.767177929 0.706574775 0.115914439 0.100107912 5.664674337 0.018983647 0.038237931 2.41E-09 8.617134041 -0.368699619 NYQQNYQNSES(ph)GEKNEGSESAPEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 2 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NYQQNY(0.001)QNS(0.091)ES(0.836)GEKNEGS(0.063)ES(0.009)APEGQAQQR;NYQQNY(0.144)QNS(0.144)ES(0.668)GEKNEGS(0.035)ES(0.009)APEGQAQQR ; 79.332 1.13E-06 261779100 1611.81 1905.01 1527.5 1391.66 1599.56 1325.61 1292.6 1232.08 1977.9 1684.82 TRUE FALSE FALSE 1592.16464 1931.828781 1554.085497 1552.570277 1517.928484 1240.907799 1402.393412 1267.728291 1800.99167 1641.048134 0.970212029 1.177192028 0.94700787 0.946084545 0.924974992 0.756167826 0.854571772 0.772511339 1.097464257 1 10.68040184 -8.576385715 1.675685906 0.998855293 0.797534649 0.65215783 0.073382438 0.178291263 0.993732569 0.009995043 0.026667902 2.65E-09 8.576385715 -0.201320644 NYQQNYQNSESGEKNEGS(ph)ESAPEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NYQQNY(0.001)QNS(0.102)ES(0.102)GEKNEGS(0.397)ES(0.397)APEGQAQQR 47.806 0.0096698 9795800 898.18 866.5 1001.9 726.15 787.38 669.56 596.96 710.05 807.52 821.5 TRUE FALSE FALSE 887.2326367 878.6986097 1019.337649 810.1108796 747.1970605 626.7772769 647.6657675 730.5941765 735.2933887 800.1573116 1.108822758 1.098157321 1.273921558 1.012439514 0.933812701 0.783317565 0.809423045 0.913063176 0.918936037 1 9.644139853 -8.6581225 2.738532282 1.073742363 0.835208821 0.573918106 0.091443763 0.137495676 2.081355709 0.012919343 0.028056236 2.20E-09 8.6581225 -0.238533543 NYQQNYQNSESGEKNEGSES(ph)APEGQAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 NYQQNYQNSESGEKNEGSESAPEGQAQQR 29 1 H0Y449;P67809;C9J5V9 H0Y449 YBX1 Nuclease-sensitive element-binding protein 1 1 0 NY(0.001)QQNY(0.069)QNS(0.139)ES(0.116)GEKNEGS(0.31)ES(0.365)APEGQAQQR 50.88 0.0071813 3098800 219.52 128.96 152.85 262.32 190.41 318.03 130.16 121.2 293.25 222.21 TRUE FALSE FALSE 216.8444058 130.7755023 155.5102901 292.6506727 180.6926672 297.7089094 141.2157872 124.7067308 267.0209855 216.4369522 1.001882551 0.604219848 0.718501571 1.352128967 0.834851283 1.375499453 0.65245692 0.576180405 1.233712556 1 7.757803021 -7.553552346 24.99091079 0.986675027 0.595249009 0.300979342 0.24244183 143.8393347 117190.8606 0.029847835 0.111682601 2.80E-08 7.553552346 -0.391426018 NYSEVIEVDES(ph)DVEEDIFPTTSK ddPTM_HeLa_Romidepsin_16h_R1 1 NYSEVIEVDESDVEEDIFPTTSK 23 0 F8W7U8;P49959-2;P49959;P49959-3 F8W7U8 MRE11A Double-strand break repair protein MRE11A 1 0 NYSEVIEVDES(0.964)DVEEDIFPT(0.011)T(0.013)S(0.011)K 59.228 0.0040217 2829400 4534.9 4693.8 4591 4748.2 5117.4 4925.7 4266.5 5360.9 5046.3 4296.6 TRUE FALSE FALSE 4479.626895 4759.87944 4670.904429 5297.209225 4856.239982 4610.963667 4628.896404 5516.009183 4594.946289 4184.973713 1.070407415 1.137373796 1.116113206 1.265768817 1.16039916 1.101790354 1.106075383 1.318051095 1.097962999 1 12.03100285 -10.43284013 0.705710162 1.012621636 1.181816047 0.363647207 0.070120562 0.343479125 0.367285747 0.018422898 0.019505151 3.69E-11 10.43284013 0.16919441 NYTDEAIETDDLTIK ddPTM_HeLa_Romidepsin_16h_R1 1 NYTDEAIETDDLTIK 15 0 O14818;O14818-2;H0Y586 O14818 PSMA7 Proteasome subunit alpha type-7 0 0 186.56 4.31E-08 8437500 1612.2 1362.7 1350 1367.4 1682.9 1692.8 1462.8 1784 1639.2 1474.3 FALSE FALSE TRUE 1592.549886 1381.884126 1373.496184 1525.505222 1597.015333 1584.635543 1587.050195 1835.617225 1492.585847 1435.997473 1.109019978 0.962316544 0.956475348 1.062331411 1.112129626 1.103508587 1.105190103 1.278287225 1.039407014 1 10.4878375 -4 0.664436849 1.040340836 23.72572768 0.686996383 0.049832908 120.6551074 0.684715793 0.010176294 4046.393452 1.00E-04 4 22.68538684 NYTEDIFPVT(ph)PPELEETIRDEK ddPTM_HeLa_Romidepsin_16h_R1 1 NYTEDIFPVTPPELEETIRDEK 22 1 Q5T3J3-2;Q5T3J3 Q5T3J3-2 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1 1 0 NYTEDIFPVT(1)PPELEETIRDEK 105.46 9.72E-05 4420000 2460.5 2190.8 2214.5 2483 2431 2741.4 2367.2 2392.8 2601 2909 TRUE FALSE FALSE 2430.51048 2221.64214 2253.042444 2770.096143 2306.936999 2566.233387 2568.269909 2462.031893 2368.360046 2833.423761 0.857799851 0.784083966 0.795166073 0.977649789 0.814187073 0.905700525 0.906419274 0.868924701 0.835865104 1 11.46833067 -12.09393218 0.930404665 0.997706728 0.864829797 0 0.074072293 0.394366471 0.632353738 0.033591476 0.010646659 8.06E-13 12.09393218 -0.132876931 NYTNSPEES(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 2 NYTNSPEESSK 11 0 J3QQU0;A0A3B3ITH3;Q9P2X3-2;Q9P2X3 J3QQU0 IMPACT Protein IMPACT 1 0 NYTNS(0.132)PEES(0.667)S(0.201)K;NYT(0.001)NS(0.25)PEES(0.676)S(0.073)K ; 138.2 0.003491 29535000 8676.2 8779.6 8963.8 7553.3 8578.1 9502.5 8585.4 6743.9 9721.5 9309.2 TRUE FALSE FALSE 8570.451137 8903.199439 9119.811179 8426.648085 8140.327548 8895.320918 9314.643662 6939.024106 8851.984692 9067.345642 0.945199563 0.981896995 1.005786207 0.92934012 0.897763013 0.981028106 1.027273474 0.765276232 0.976248733 1 13.14646457 -7.251694514 24.8331789 0.971311172 0.76527611 0.74338688 0.036368854 504.4306304 1285430.012 0.005362507 0.094260003 5.60E-08 7.251694514 -0.206035062 NYVPSYDPSS(ph)PQTSQSWYLG ddPTM_HeLa_Romidepsin_16h_R1 1 NYVPSYDPSSPQTSQSWYLG 20 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 NYVPSYDPS(0.075)S(0.925)PQTSQSWYLG 168.32 2.72E-12 0 6224.6 6714 5827.5 5941.2 4481.1 4550.4 3611.5 4191.3 6876.5 6206 TRUE FALSE FALSE 6148.732181 6808.519868 5928.925193 6628.149498 4252.412746 4259.644126 3918.26072 4312.568653 6261.448617 6044.767225 1.017199166 1.126349389 0.980835981 1.096510296 0.7034866 0.704682905 0.648207048 0.713438333 1.03584611 1 12.56147107 -8.751933295 24.99451727 1.021413694 0.690166656 0.930863806 0.046553722 36.39501614 95693.38451 0.006590561 0.013044489 1.77E-09 8.751933295 -0.331247039 NYYEQWGK ddPTM_HeLa_Romidepsin_16h_R1 1 NYYEQWGK 8 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 111.95 0.023545 0 1076.5 398.82 768.22 0 797.38 702.93 1016.7 718.46 1129.7 904.9 FALSE FALSE TRUE 1063.379204 404.4345984 781.5905468 0 756.6867232 658.0150416 1103.058473 739.2475066 1028.656803 881.3905676 1.206478992 0.458859685 0.886769811 0 0.85851466 0.746564651 1.251497932 0.838728634 1.16708397 1 9.783637647 -10.27722995 24.91292353 1.097503973 0.725621268 0.262653169 0.309405831 838.5291147 1322951.074 0.053456441 0.061237463 5.28E-11 10.27722995 -0.371882706 PAAAAAAGSAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 PAAAAAAGSASPR 13 0 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 0 PAAAAAAGS(0.001)AS(0.999)PR;PAAAAAAGS(0.003)AS(0.997)PR ; 148.78 0.00076828 7626200 2985.7 2877.1 2691.3 2401.9 2555.3 2765.6 2692.2 2258.8 2869.9 2774.1 TRUE FALSE FALSE 2949.30914 2917.603889 2738.140948 2679.618979 2424.893506 2588.887086 2920.875401 2324.154814 2613.208956 2702.028482 1.091516673 1.079782803 1.013364946 0.991706415 0.897434473 0.958127238 1.080993565 0.860151856 0.967128575 1 11.39982717 -9.283801032 2.671884778 1.046850906 0.958976532 0.243538709 0.063973181 0.268598129 3.800307572 0.009699222 0.01616513 5.20E-10 9.283801032 -0.087874374 PAAGTAAASANGAAIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PAAGTAAASANGAAIKK 17 1 A0A0G2JH30;A0A0G2JPX0;P49918-2;P49918 A0A0G2JH30 CDKN1C Cyclin-dependent kinase inhibitor 1C 0 1 ; PAAGTAAASANGAAIK(1)K;PAAGTAAASANGAAIK(1)K 228.93 3.83E-38 1457630 333.66 228.393 165.36 177.334 496.85 487.25 638.5 514.57 254.32 297.84 FALSE TRUE FALSE 329.5932236 231.6083226 168.2380214 197.8381915 471.4938905 456.1162975 692.7341741 529.4582711 231.5729822 290.1020739 1.136128464 0.79836838 0.579926986 0.681960625 1.625268941 1.572261416 2.387898042 1.825075788 0.798246559 1 8.180416799 -8.355407226 1.943233176 0.984025511 2.050577847 0.760546913 0.273526696 0.133614555 0.970396588 0.041047594 0.120777071 4.41E-09 8.355407226 1.066552336 PAAMISQPPT(ph)PPTGQPVREDAK ddPTM_HeLa_Romidepsin_16h_R1 1 PAAMISQPPTPPTGQPVREDAK 22 1 Q6PKG0;Q6PKG0-3 Q6PKG0 LARP1 La-related protein 1 1 0 PAAMIS(0.153)QPPT(0.834)PPT(0.013)GQPVREDAK 58.332 0.0088203 10476000 2710.2 2300.1 2665.5 2503.6 1421.8 1892.3 1662 1607.1 2035.5 2981.3 TRUE FALSE FALSE 2677.16704 2332.480868 2711.891909 2793.078012 1349.240241 1771.388137 1803.170239 1653.598903 1853.439782 2903.845396 0.921938559 0.803238654 0.933896795 0.961854931 0.464639144 0.610014617 0.620959449 0.569451426 0.63827082 1 11.50374893 -8.770309964 24.99731405 0.94643754 0.573297709 0.599230546 0.11609396 45.88062803 129291.8491 0.010340813 0.018946328 1.70E-09 8.770309964 -0.373139832 PAAS(ph)SPETPSAGQQEAK ddPTM_HeLa_Romidepsin_16h_R1 1 PAASSPETPSAGQQEAK 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 PAAS(0.936)S(0.064)PETPSAGQQEAK 257.04 1.33E-72 4041500 1822 1731.2 1901.6 1158.7 1402.9 1569.4 1266.3 1371.5 1485 1982.7 TRUE FALSE FALSE 1799.792763 1755.571879 1934.69655 1292.674346 1331.304778 1469.120405 1373.85949 1411.182189 1352.177881 1931.189168 0.931960883 0.909062617 1.001816177 0.669367024 0.689370467 0.760733557 0.711405963 0.730732241 0.700178886 1 10.91527377 -9.262345141 24.99999948 0.964022614 0.713685425 0.498464847 0.090249355 16.98587205 468829.9138 0.006067999 0.009607914 5.47E-10 9.262345141 -0.250337189 PAASS(ph)PETPSAGQQEAK ddPTM_HeLa_Romidepsin_16h_R1 1 PAASSPETPSAGQQEAK 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 PAAS(0.05)S(0.95)PETPSAGQQEAK 238.07 1.26E-46 4030600 2250.7 1853.3 1846.8 1286.9 1452.5 1789.6 1612.8 1802.7 2140.9 2247.4 TRUE FALSE FALSE 2223.267603 1879.390806 1878.942779 1435.697433 1378.373505 1675.250336 1749.791192 1854.85828 1949.412542 2189.012224 1.015648784 0.858556561 0.85835189 0.655865425 0.629678304 0.765299671 0.799351951 0.847349439 0.890544384 1 11.0960643 -9.902492369 1.720321841 1.008062079 0.742397191 0.601646561 0.075865956 0.125511174 0.746451427 0.01226038 0.016773879 1.25E-10 9.902492369 -0.265664888 PAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_HeLa_Romidepsin_16h_R1 3 PAEKPAETPVATSPTATDSTSGDSSR 26 1 P54727;H0Y579;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 0 PAEKPAETPVAT(0.489)S(0.489)PT(0.02)AT(0.001)DSTSGDSSR;PAEKPAETPVAT(0.452)S(0.452)PT(0.055)AT(0.018)DS(0.006)T(0.006)S(0.006)GDS(0.002)S(0.002)R;PAEKPAETPVAT(0.558)S(0.39)PT(0.047)AT(0.003)DSTSGDSSR ;; 131.81 3.76E-07 18291900 3504.95 3626.07 3814.89 2782.67 3813.23 3567.9 3723.48 4025.35 3418.24 3628.55 TRUE FALSE FALSE 3462.230321 3677.117909 3881.28656 3104.415398 3618.626644 3339.922705 4039.752298 4141.817151 3112.504053 3534.279748 0.979614113 1.040415069 1.098183176 0.878372857 1.023865371 0.945008019 1.143019961 1.171898505 0.880661486 1 11.78720052 -7.697370353 6.663172598 0.993482828 1.161574837 0.531483854 0.065556077 0.10021861 8.092549038 0.007067163 0.026794364 2.01E-08 7.697370353 0.168092009 PAETPVAT(ph)SPTATDSTSGDSSR ddPTM_HeLa_Romidepsin_16h_R1 1 PAETPVATSPTATDSTSGDSSR 22 0 P54727;H0Y579;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 0 PAETPVAT(0.489)S(0.489)PT(0.01)AT(0.01)DS(0.001)T(0.001)S(0.001)GDSSR 100.73 0.00048763 13670000 2308 1910.4 1819.8 1455 1988.8 2100.5 1664.7 1713.2 1874.5 2323.5 TRUE FALSE FALSE 2279.869208 1937.294661 1851.472856 1623.233946 1887.304115 1966.284829 1806.099576 1762.768739 1706.840025 2263.135135 1.0073942 0.856022529 0.818100884 0.717250119 0.833933461 0.868832267 0.798052025 0.778905648 0.754192712 1 11.14410702 -10.14395112 2.88170687 1.004260417 0.803734707 0.081021009 0.087357257 0.06863877 1.092921838 0.006557035 0.008109421 7.18E-11 10.14395112 -0.20052571 ANK(ac)K(ac)KPSMPNVSNDLSQK ddPTM_HeLa_Romidepsin_16h_R1 2 ANKKKPSMPNVSNDLSQK 18 3 Q92793-2;Q92793 Q92793-2 CREBBP CREB-binding protein 0 2 ; ANK(0.963)K(0.831)K(0.206)PSMPNVSNDLSQK;ANK(0.975)K(0.858)K(0.167)PSMPNVSNDLSQK 123.58 4.68E-06 3186400 69.277 299.39 337.95 438.03 1746.15 1913.13 1853.95 1636.19 421.01 257.689 FALSE TRUE FALSE 68.43262528 303.6048203 343.831878 488.6770896 1657.03745 1790.887167 2011.424467 1683.530576 383.3538112 250.9942026 0.272646239 1.209608896 1.36987976 1.946965645 6.601895312 7.135173437 8.01382839 6.707448055 1.527341298 1 7.971510232 -8.792643455 2.504076088 0.750040425 7.380367786 0.970709631 0.502446054 0.029208897 0.37392454 0.074200859 0.15363894 1.61E-09 8.792643455 6.630327361 up PAMPQDSVPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 PAMPQDSVPSPR 12 0 P53396 P53396 ACLY ATP-citrate synthase 1 0 PAMPQDSVPS(1)PR 101.61 0.020394 6728000 2708.3 2210.4 2221.3 1786.6 1995.2 2679.6 2215.7 2736.4 2144.4 2138.6 TRUE FALSE FALSE 2675.290198 2241.518069 2259.960795 1993.175098 1893.377499 2508.382208 2403.901503 2815.573417 1952.599493 2083.038864 1.284320828 1.076080772 1.084934532 0.956859295 0.908949675 1.204193667 1.154035839 1.351666292 0.937380251 1 11.02447404 -7.166019422 1.682150362 1.103980065 1.477633436 0.313714681 0.118654748 1.499934232 3.377620869 0.019725109 0.969716005 6.82E-08 7.166019422 0.373653371 PAPAVGEAEDKENQQATSGPNQPS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 3 PAPAVGEAEDKENQQATSGPNQPSVR 26 1 P16989-2;P16989;P16989-3 P16989-2 YBX3 Y-box-binding protein 3 1 0 PAPAVGEAEDKENQQAT(0.038)S(0.076)GPNQPS(0.886)VR;PAPAVGEAEDKENQQATS(0.001)GPNQPS(0.999)VR;PAPAVGEAEDKENQQAT(0.001)S(0.009)GPNQPS(0.991)VR ;; 118.67 7.45E-10 15704200 2836.79 3362.68 2640.69 3004.13 2445.77 2791.13 2329.9 2547.97 3380.97 2879.32 TRUE FALSE FALSE 2802.214112 3410.019897 2686.650102 3351.481645 2320.95323 2612.785801 2527.801648 2621.691492 3078.567575 2804.514851 0.99917963 1.215903669 0.957973213 1.195030807 0.827577443 0.931635573 0.901332951 0.934811057 1.097718407 1 11.45353551 -8.726921084 24.99994608 1.026371696 0.901360008 0.423178331 0.091132567 166.2998595 120442.3574 0.012390556 0.02478016 1.88E-09 8.726921084 -0.125011688 PAPEASSLEEPHS(ph)PETGEK ddPTM_HeLa_Romidepsin_16h_R1 1 PAPEASSLEEPHSPETGEK 19 0 Q5JTC6;Q5JTC6-2 Q5JTC6 AMER1 APC membrane recruitment protein 1 1 0 PAPEAS(0.007)S(0.082)LEEPHS(0.894)PET(0.017)GEK 72.207 0.0060491 4874900 1440.5 1394.9 1159.9 1150.9 1342.9 1126.9 1192.6 1348.8 1248.1 1637 TRUE FALSE FALSE 1422.942632 1414.537439 1180.087573 1283.972473 1274.366802 1054.894727 1293.899414 1387.8254 1136.46681 1594.470504 0.892423302 0.887151838 0.740112514 0.805265742 0.799241377 0.661595636 0.811491596 0.870398917 0.712754991 1 10.63886169 -10.58118547 0.631179483 0.983919183 0.773790748 0 0.102291113 0.280154931 0.251474097 0.019884213 0.018578508 2.62E-11 10.58118547 -0.210128435 PAPEPEAEGSAVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 PAPEPEAEGSAVKR 14 1 Q14814-6;Q14814-3;Q14814-5;Q14814-4;Q14814-2;Q14814 Q14814-6 MEF2D Myocyte-specific enhancer factor 2D 0 1 PAPEPEAEGSAVK(1)R 118.23 0.0012265 2710800 254.61 203.16 212.09 153.28 50.636 236.1 229.13 137.47 284.31 228.49 FALSE TRUE FALSE 251.5067154 206.0200918 215.7813375 171.0029548 48.05185597 221.013972 248.5922965 141.4474776 258.8806015 222.5537969 1.130094022 0.925709176 0.969569338 0.768366827 0.215911194 0.993081112 1.116998676 0.635565331 1.163227072 1 7.798010304 -9.497199917 2.33305344 1.054247429 0.754069911 0.291483641 0.230218788 0.315548948 3.425720332 0.037691122 0.058814208 3.18E-10 9.497199917 -0.300177518 PAPPPQSQS(ph)PEVEQLGR ddPTM_HeLa_Romidepsin_16h_R1 1 PAPPPQSQSPEVEQLGR 17 0 P52948-6;P52948-2;P52948-5;P52948;A0A3B3ITD8 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 0 PAPPPQS(0.071)QS(0.929)PEVEQLGR 153.92 7.17E-05 17328000 307.23 268.53 208.74 260.28 244.97 143.54 180.23 334.17 277.24 338.66 TRUE FALSE FALSE 303.4853626 272.3103724 212.3730321 290.3747983 232.4682668 134.3682573 195.5387317 343.8386817 252.44296 329.8615644 0.920038572 0.825529258 0.643824729 0.880292916 0.704744935 0.40734742 0.592790288 1.042372676 0.765299711 1 8.365716874 -10.11840189 0.900074293 0.979474714 0.683522224 0.12791542 0.174030734 0.405533584 0.653218699 0.035403515 0.045628316 7.61E-11 10.11840189 -0.295952489 PAPPQEES(ph)PSSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 PAPPQEESPSSEAK 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 PAPPQEES(0.333)PS(0.333)S(0.333)EAK 119.77 0.0042291 37202000 2882.5 2412.3 3033.3 1957.3 2199.8 1932.2 2216.1 2283.5 2956.8 3469 TRUE FALSE FALSE 2847.366981 2446.260423 3086.093314 2183.612235 2087.535997 1808.738656 2404.335479 2349.56947 2692.336403 3378.87488 0.84269678 0.723986685 0.913349391 0.646254245 0.617819858 0.535307971 0.711578725 0.695370368 0.796814472 1 11.72232721 -10.26966428 0.415217823 0.996261639 0.614718241 0.458814623 0.098534603 0.385600026 0.176021825 0.044183217 0.051221051 5.37E-11 10.26966428 -0.381543398 PAPPQEESPS(ph)SEAK ddPTM_HeLa_Romidepsin_16h_R1 3 PAPPQEESPSSEAK 14 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 PAPPQEES(0.003)PS(0.498)S(0.498)EAK;PAPPQEES(0.096)PS(0.807)S(0.096)EAK;PAPPQEES(0.273)PS(0.663)S(0.064)EAK ;; 186.42 3.80E-08 53764000 7735.7 6580.3 6510.9 4456.1 5081.6 6082.5 5702.3 5240.3 6229.1 7659.4 TRUE FALSE FALSE 7641.414313 6672.937636 6624.219483 4971.335249 4822.26699 5693.84788 6186.65322 5391.919813 5671.953695 7460.407684 1.024262297 0.894446781 0.887916554 0.666362411 0.646381162 0.763208677 0.829264764 0.722737958 0.76027396 1 12.86503876 -9.706431517 1.742985551 1.010151019 0.731371932 0.385934721 0.097359188 0.10098317 0.625637178 0.010071304 0.014935575 1.97E-10 9.706431517 -0.278779087 PARPPS(ph)PTEQEGAVPR ddPTM_HeLa_Romidepsin_16h_R1 1 PARPPSPTEQEGAVPR 16 1 Q8N8E2-2;Q8N8E2 Q8N8E2-2 ZNF513 Zinc finger protein 513 1 0 PARPPS(0.986)PT(0.014)EQEGAVPR 65.265 0.01906 4496800 1784.3 1568 1877.5 1172.1 1373.6 1917.8 1539.4 1830.7 1516.1 1870.8 TRUE FALSE FALSE 1762.552265 1590.074345 1910.1771 1307.623717 1303.500066 1795.258769 1670.156598 1883.668416 1380.496219 1822.196346 0.967268027 0.872614166 1.048282807 0.717608571 0.71534556 0.985216973 0.916562368 1.033735152 0.757600146 1 10.83146271 -10.26999237 1.167825263 0.989618319 0.887537526 0 0.13044851 0.656470398 1.737037529 0.022710373 0.026873964 5.37E-11 10.26999237 -0.102080793 PAS(ph)PDRFAVSAEAENK ddPTM_HeLa_Romidepsin_16h_R1 2 PASPDRFAVSAEAENK 16 1 G3V331;O15037 G3V331 KHNYN Protein KHNYN 1 0 PAS(1)PDRFAVSAEAENK;PAS(1)PDRFAVSAEAENK ; 93.115 0.0037911 17582300 7443.2 7715.1 7759 6358 6289.7 6513.9 5968.3 5470.2 7722.4 7822.6 TRUE FALSE FALSE 7352.479415 7823.71338 7894.04214 7093.141875 5968.713139 6097.682813 6475.247253 5628.471606 7031.689203 7619.367724 0.964972381 1.026819241 1.036049503 0.930935759 0.783360688 0.800287246 0.849840497 0.738705862 0.922870435 1 12.89545557 -8.88641074 3.820748692 0.99042989 0.797502623 0.848086604 0.039379974 0.05442141 1.503047107 0.005051966 0.009513956 1.30E-09 8.88641074 -0.192927268 PAS(ph)PVAGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 PASPVAGSPK 10 0 K7EN91;Q13057;Q13057-2 K7EN91 COASY Bifunctional coenzyme A synthase;Phosphopantetheine adenylyltransferase;Dephospho-CoA kinase 1 0 PAS(1)PVAGSPK 118.9 0.012512 13104000 3091.6 3019.7 2658.5 2695.7 2274.9 2506.5 2411.9 2146.5 2817.1 3172.4 TRUE FALSE FALSE 3053.91839 3062.211416 2704.770077 3007.389518 2158.803364 2346.342739 2616.766726 2208.605591 2565.13152 3089.980591 0.988329312 0.991013156 0.87533562 0.97327133 0.698646254 0.75933899 0.846855392 0.714763581 0.830144865 1 11.59338206 -9.047142604 1.375191453 0.992235197 0.761506187 0.49747863 0.078944768 0.142894547 0.535024642 0.009040772 0.019263678 8.97E-10 9.047142604 -0.23072901 PAS(ph)PVPGSER ddPTM_HeLa_Romidepsin_16h_R1 1 PASPVPGSER 10 0 A0A5E8;Q99501;Q99501-2;Q99501-4 A0A5E8 GAS2L1 GAS2-like protein 1 1 0 PAS(0.997)PVPGS(0.003)ER 102.05 0.023176 11778000 1600 1358.1 1413.4 1033.8 1308.5 1701.1 1399 1275.7 1381.5 1610.1 TRUE FALSE FALSE 1580.498585 1377.219367 1437.999634 1153.33282 1241.722362 1592.4052 1517.831025 1312.610367 1257.93518 1568.26937 1.007797904 0.878177814 0.916934081 0.735417552 0.791778751 1.015390105 0.967838213 0.836980172 0.802116782 1 10.61495767 -10.26049774 24.09840507 1.003682346 0.879034948 0 0.099289077 42.7153624 1093163.936 0.013414564 0.015925505 5.49E-11 10.26049774 -0.124647398 PASPAS(ph)NVVVLPSGSTVYVK ddPTM_HeLa_Romidepsin_16h_R1 1 PASPASNVVVLPSGSTVYVK 20 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 PAS(0.164)PAS(0.836)NVVVLPSGSTVYVK 127.97 2.12E-09 0 865.56 974.52 798.74 762.95 1051.2 814.17 659.32 814.45 971.4 1157.9 TRUE FALSE FALSE 855.0102218 988.2393181 812.6417346 851.1658688 997.5533414 762.1471646 715.3226243 838.0148258 884.5155511 1127.817591 0.758110379 0.876240383 0.720543589 0.754701714 0.884498831 0.675771659 0.634253828 0.743041102 0.784271817 1 10.13931804 -16.52287875 0.166847397 2.004773789 0.680770616 0.144675329 0.095499211 26.36906733 0.289179344 8.62054563 0.118152358 3.00E-17 16.52287875 -1.324003173 PASPDRFAVS(ph)AEAENK ddPTM_HeLa_Romidepsin_16h_R1 1 PASPDRFAVSAEAENK 16 1 G3V331;O15037 G3V331 KHNYN Protein KHNYN 1 0 PAS(0.438)PDRFAVS(0.562)AEAENK 106.6 0.025979 9099300 2523.1 2183.1 1910.3 1512.4 1230.7 1884.3 1566.6 1466.5 2061.7 2105.6 TRUE FALSE FALSE 2492.347487 2213.833739 1943.54797 1687.270804 1167.892787 1763.899311 1699.666965 1508.930864 1877.296388 2050.896208 1.215247986 1.07944699 0.947657888 0.822699265 0.569454847 0.860062691 0.828743531 0.735742188 0.915354166 1 11.00203877 -9.456807899 2.237794613 1.102958558 0.758662716 0.615621877 0.106108066 0.130813088 1.295197545 0.01736807 0.027643027 3.49E-10 9.456807899 -0.344295842 PASVDGSPVS(ph)PSTNR ddPTM_HeLa_Romidepsin_16h_R1 2 PASVDGSPVSPSTNR 15 0 P35568 P35568 IRS1 Insulin receptor substrate 1 1 0 PASVDGS(0.032)PVS(0.544)PS(0.354)T(0.07)NR;PASVDGS(0.002)PVS(0.333)PS(0.333)T(0.333)NR ; 137.73 0.001076 7969500 2440.5 2601.4 2530.9 1913.88 1562.83 1990.37 1529.74 1629.5 2585.7 2927.9 TRUE FALSE FALSE 2410.754247 2638.022577 2574.949253 2135.171811 1483.072953 1863.191781 1659.676077 1676.647012 2354.428516 2851.832736 0.845335078 0.925027104 0.902910336 0.748701627 0.520042054 0.653331367 0.58196824 0.587919127 0.825584364 1 11.47767365 -9.06887656 2.697838101 0.92405476 0.59047111 0.866700388 0.05740645 0.073764797 1.057452594 0.009956565 0.018055767 8.53E-10 9.06887656 -0.33358365 PAT(ph)PGASSVEQLRK ddPTM_HeLa_Romidepsin_16h_R1 1 PATPGASSVEQLRK 14 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 0 PAT(0.877)PGAS(0.097)S(0.026)VEQLRK 73.252 0.020727 61008000 4367.1 3963.4 3768.9 3363 3650 4396.3 3667 4524.9 3826.5 4040.2 TRUE FALSE FALSE 4313.872105 4019.196849 3834.496124 3751.845883 3463.72688 4115.390618 3978.474888 4655.820842 3484.248256 3935.235022 1.096217146 1.021335912 0.974400792 0.953398174 0.880182978 1.045780137 1.010987874 1.183111254 0.885397756 1 11.94223408 -7.259199774 24.19826259 1.021087736 1.183111341 0.313694201 0.071991926 118.6846483 1282208.159 0.009577039 0.08446948 5.51E-08 7.259199774 0.162023606 PATPAEDDEDDDIDLFGS(ph)DNEEEDKEAAQLREER ddPTM_HeLa_Romidepsin_16h_R1 1 PATPAEDDEDDDIDLFGSDNEEEDKEAAQLREER 34 2 P29692-2;E9PI39;P29692;P29692-3;E9PRY8;A0A087X1X7;E9PK01;E9PQ49;E9PL71;P29692-4;E9PQZ1;H0YE72 P29692-2 EEF1D Elongation factor 1-delta 1 0 PATPAEDDEDDDIDLFGS(1)DNEEEDKEAAQLREER 55.413 0.00077142 3034900 504.19 562.74 460.72 500.55 339.08 383.24 392.36 576.76 388.14 317.66 TRUE FALSE FALSE 498.0447383 570.6622685 468.7386383 558.4259462 321.7754823 358.7522009 425.6870486 593.4476406 353.4237863 309.4071474 1.609674316 1.844373258 1.51495737 1.804825618 1.039974303 1.159482591 1.375815175 1.918015293 1.142261222 1 8.273362714 -12.25054767 1.013663766 1.003962829 1.51980474 0.30740126 0.274077908 0.503563408 0.938758377 0.182637134 0.051657722 5.62E-13 12.25054767 0.515841911 PCSEETPAIS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 1 PCSEETPAISPSKR 14 1 P33316-2;H0YNJ9 P33316-2 DUT "Deoxyuridine 5-triphosphate nucleotidohydrolase, mitochondrial" 1 0 PCSEET(0.001)PAIS(0.548)PS(0.451)KR 59.003 0.027539 11965000 2130.6 2476.6 2330.8 918.46 1861.2 1766.4 1447.3 1953.8 2382.9 2368.1 TRUE FALSE FALSE 2104.631428 2511.46564 2371.366596 1024.656667 1766.216019 1653.532741 1570.233626 2010.33012 2169.767456 2306.576421 0.912448167 1.088828281 1.028089325 0.444232698 0.765730545 0.716877501 0.680763755 0.871564498 0.940687435 1 11.17153738 -9.294201959 24.99602703 0.974173835 0.700048755 0.644481115 0.110217827 318.1444078 242725.6346 0.016422252 0.025086413 5.08E-10 9.294201959 -0.274125079 YLTNQK(ac)NSNSK(ac)NDR ddPTM_HeLa_Romidepsin_16h_R1 2 YLTNQKNSNSKNDR 14 2 B1AK63;Q9HAF1-2;Q9HAF1;Q9HAF1-4;Q9HAF1-3 B1AK63 MEAF6 Chromatin modification-related protein MEAF6 0 2 ; YLTNQK(1)NSNSK(1)NDR;YLTNQK(1)NSNSK(1)NDR 360.11 1.23E-286 9398200 68.713 190.44 294.71 291.399 765.17 1003.56 830.04 884.44 162.88 194.159 FALSE TRUE FALSE 67.87549953 193.1210193 299.8393039 325.0919235 726.1205197 939.4357548 900.5435769 910.029876 148.3116049 189.1147212 0.358911771 1.021184486 1.585488967 1.719019659 3.839576925 4.967544298 4.761890408 4.812052019 0.784241459 1 7.563117861 -8.789920138 1.370491407 0.735059672 4.963555362 0.973041778 0.292579971 0.050974195 0.1915519 0.055315726 0.139408059 1.62E-09 8.789920138 4.22849569 up TLVLSDK(ac)HSPQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 TLVLSDKHSPQKK 13 2 Q8NEZ4;Q8NEZ4-3;H7BY37;Q8NEZ4-2 Q8NEZ4 KMT2C Histone-lysine N-methyltransferase 2C 0 2 TLVLSDK(1)HSPQK(1)K 86.738 0.0092459 3088400 1583.6 1279.9 1590.5 2081.2 4704.3 5322.4 4524.4 4787 1983.1 1921.9 FALSE TRUE FALSE 1564.298474 1297.918466 1618.181985 2321.838136 4464.222017 4982.315817 4908.702423 4925.504292 1805.726569 1871.968761 0.835643472 0.693344084 0.864427879 1.240318848 2.384773779 2.661537907 2.622213856 2.631189363 0.964613623 1 10.87034064 -8.78377024 2.731449914 0.897322591 2.634425017 0.990111195 0.08133874 0.022167074 0.338284911 0.015515006 0.031769334 1.65E-09 8.78377024 1.737102425 up PDPAK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 PDPAKSAPAPKKGSK 15 3 P23527;Q5QNW6;Q5QNW6-2;Q93079 P23527;Q5QNW6;Q93079 HIST1H2BO;HIST2H2BF;HIST1H2BH Histone H2B type 1-O;Histone H2B type 2-F;Histone H2B type 1-H 0 3 ; PDPAK(1)SAPAPK(1)K(1)GSK;PDPAK(1)SAPAPK(1)K(1)GSK 206.67 2.41E-24 49345000 259.043 158.81 338.72 1794.8 9069.8 12762.5 14421.1 15285.9 256.026 78.272 FALSE TRUE FALSE 255.8856843 161.0457313 344.6152795 2002.323221 8606.934262 11947.01744 15646.02787 15728.1734 233.1263933 76.23848216 3.356384821 2.11239425 4.520227446 26.26394393 112.8948796 156.7058669 205.2248081 206.3022893 3.057857223 1 6.252447492 -8.52233923 1.418416496 1.532760114 200 0.990833068 8.048700572 0.025276218 0.098720969 1.194036224 3.648610054 3.00E-09 8.52233923 198.4672399 EGRPPEPTPAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 EGRPPEPTPAKR 12 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 1 ; EGRPPEPTPAK(1)R;EGRPPEPTPAK(1)R 101.72 0.012768 44907000 3514.7 3426.1 3489.5 5359.8 8502.4 9744.7 9027 10204.7 3489.7 3532.2 FALSE TRUE FALSE 3471.861485 3474.332726 3550.233284 5979.525295 8068.490801 9122.04512 9793.753155 10499.95689 3177.572492 3440.432935 1.009135057 1.00985335 1.03191469 1.738015363 2.345196362 2.651423612 2.846663004 3.051928956 0.923596696 1 11.74837441 -8.780331555 1.259121182 0.992159406 2.924840262 0.990153901 0.082551576 0.02803417 0.088208237 0.012953431 0.034407918 1.66E-09 8.780331555 1.932680856 up PDPSK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PDPSKSAPAPKKGSK 15 3 Q8N257 Q8N257 HIST3H2BB Histone H2B type 3-B 0 3 PDPSK(1)SAPAPK(1)K(1)GSK 132.08 1.28E-15 0 0 0 0 128.99 396.16 599.2 531 621.05 0 0 FALSE TRUE FALSE 0 0 0 143.9044307 375.9424769 560.9130538 576.1031267 639.0191019 0 0 0 TVGK(ac)K(ac)QPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVGKKQPK 8 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 0 2 TVGK(1)K(1)QPK 82.75 0.023751 0 3740 3320.5 5152.3 8719.4 26486 28376 28267 27296 8475.7 7364.1 FALSE TRUE FALSE 3694.415441 3367.246086 5241.97362 9727.578054 25134.32059 26562.86518 30667.99827 28085.76669 7717.612164 7172.77962 0.515060498 0.469447866 0.730814816 1.356179692 3.504125586 3.70328751 4.275608606 3.915604296 1.075958355 1 12.80831659 -8.775507307 2.469387769 0.734832771 3.986477612 0.978253547 0.22075004 0.030418935 0.378798164 0.037490976 0.078477148 1.68E-09 8.775507307 3.25164484 up PALK(ac)IPQTK ddPTM_HeLa_Romidepsin_16h_R1 2 PALKIPQTK 9 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 0 1 ; PALK(1)IPQTK;PALK(1)IPQTK 129.38 0.0068747 1185890 938.92 758.27 899.43 1223.49 2289.8 2469.1 2392.5 2659.5 586.57 678.93 FALSE TRUE FALSE 927.4760819 768.944945 915.0842019 1364.95567 2172.942962 2311.332479 2595.71889 2736.448437 534.1057101 661.2913007 1.402522732 1.162793075 1.383783819 2.064076254 3.285908886 3.49518053 3.925227638 4.138037856 0.807670855 1 9.369142113 -8.770743421 1.233129885 1.177789283 3.996829622 0.976665332 0.189072529 0.04518595 0.13598134 0.029822078 0.080781043 1.70E-09 8.770743421 2.819040339 up PELAK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PELAKSAPAPKKGSK 15 3 Q99880 Q99880 HIST1H2BL Histone H2B type 1-L 0 3 PELAK(1)SAPAPK(1)K(1)GSK 116.58 0.0013556 1713700 0 91.911 0 508.54 2481.9 3842.5 3863.9 4119.6 276.02 131.68 FALSE TRUE FALSE 0 93.20492547 0 567.3397876 2355.239382 3596.976651 4192.09957 4238.794126 251.3320799 128.2589346 0 0.726693433 0 4.423393889 18.36316034 28.04464782 32.68465922 33.04872397 1.959567812 1 7.002915518 -8.539348148 1.560573602 0.402530717 32.86685681 0.995303435 0.935428646 0.01581475 0.075622449 0.133387649 0.379792463 2.89E-09 8.539348148 32.46432609 PEMT(ph)PVS(ph)LRS(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 PEMTPVSLRSTK 12 1 A0A5E8;Q99501;Q99501-2;Q99501-4 A0A5E8 GAS2L1 GAS2-like protein 1 4 0 PEMT(1)PVS(1)LRS(1)T(1)K 61.212 0.0039152 0 1062.4 1055.8 818.08 1092.2 1079.5 1065.8 1042.6 1124.6 1185.1 1301.8 TRUE FALSE FALSE 1049.45106 1070.66358 832.3183392 1218.485303 1024.409087 997.6988197 1131.158418 1157.138527 1079.101688 1267.979048 0.827656468 0.844385861 0.656413322 0.960966433 0.807906951 0.786841723 0.892095512 0.912584895 0.85104063 1 10.30831519 -12.10806682 0.834775385 1.001956579 0.833953384 0.042946154 0.089721496 0.506514854 0.628883596 0.052945562 0.014911133 7.80E-13 12.10806682 -0.168003195 TVANLLSGK(ac)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 TVANLLSGKSPR 12 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 0 1 ; TVANLLSGK(1)SPR;TVANLLSGK(1)SPR 171.26 0.00064588 11219600 977.02 934.36 1269.15 1559.71 3147 3838.8 3738.6 3489.8 1198.47 824.92 FALSE TRUE FALSE 965.1117044 947.5139446 1291.239023 1740.051009 2986.396847 3593.513069 4056.156591 3590.771857 1091.275842 803.4884595 1.201151918 1.179250222 1.607041157 2.165620412 3.716788725 4.472389151 5.048182762 4.468977513 1.35817239 1 9.650133492 -8.768532345 1.276721382 1.102456485 4.833056155 0.984593334 0.190225609 0.029772417 0.096383529 0.026743169 0.071126722 1.70E-09 8.768532345 3.73059967 up PDPAK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 PDPAKSAPAPK 11 1 P23527;Q5QNW6;Q5QNW6-2;Q93079 P23527;Q5QNW6;Q93079 HIST1H2BO;HIST2H2BF;HIST1H2BH Histone H2B type 1-O;Histone H2B type 2-F;Histone H2B type 1-H 0 1 ; PDPAK(1)SAPAPK;PDPAK(1)SAPAPK 150.09 0.0059039 770750000 2605.71 2205.66 2867.59 10737.3 22702.9 27635.4 27340.6 29660.2 704.89 2008.93 FALSE TRUE FALSE 2573.950604 2236.711339 2917.499201 11978.79715 21544.2863 25869.58713 29662.90988 30518.37109 641.842873 1956.737709 1.31542955 1.143081839 1.491001675 6.121820565 11.01030874 13.22077405 15.15936947 15.59655694 0.328016816 1 10.93423467 -8.768126466 1.291601047 1.073877723 15.23167614 0.993125782 0.505827406 0.021880636 0.072578134 0.075289055 0.199004546 1.71E-09 8.768126466 14.15779842 up VINDK(ac)HDDVMAK ddPTM_HeLa_Romidepsin_16h_R1 1 VINDKHDDVMAK 12 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 1 VINDK(1)HDDVMAK 70.54 0.013901 1258500 662.4 482.08 406.04 752.22 2940.6 3423.6 2738 2824.7 659.22 527.9 FALSE TRUE FALSE 654.326414 488.8667349 413.1069559 839.1952157 2790.530209 3204.843009 2970.565652 2906.428238 600.2577122 514.1850819 1.272550366 0.950760246 0.803420734 1.632087832 5.427092904 6.232858793 5.777230332 5.652494287 1.167396203 1 9.006143944 -8.766882666 3.949148045 1.097050618 5.879024072 0.993376867 0.186165743 0.012196937 0.421841478 0.029407629 0.057936809 1.71E-09 8.766882666 4.781973454 up PELAK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 PELAKSAPAPK 11 1 Q99880 Q99880 HIST1H2BL Histone H2B type 1-L 0 1 ; PELAK(1)SAPAPK;PELAK(1)SAPAPK 166.69 0.0045495 161989000 1192.41 1339.47 1550.87 5112.6 11309.8 12853.6 12996.3 14749.7 0 1141.39 FALSE TRUE FALSE 1177.876448 1358.327094 1577.862242 5703.742868 10732.6187 12032.29644 14100.2054 15176.4593 0 1111.736523 1.059492446 1.221806665 1.419277148 5.130480782 9.65392292 10.82297486 12.68304594 13.65112954 0 1 10.1185992 -8.765712115 1.237540843 0.970140212 12.97198712 0.986952651 0.592062895 0.028860473 0.087477837 0.081180073 0.22031246 1.72E-09 8.765712115 12.00184691 up ATVTPSPVK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 2 ATVTPSPVKGK 11 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 1 ; ATVTPSPVK(1)GK;ATVTPSPVK(1)GK 155.06 0.0080794 4596600 697.85 840.02 1343.09 2399 8118.5 11471.7 9872.2 8145 455.55 411.86 FALSE TRUE FALSE 689.3443358 851.8458236 1366.465918 2676.383668 7704.182651 10738.69539 10710.74442 8380.662724 414.8044671 401.1598178 1.718378325 2.123457499 3.406288111 6.671614525 19.20477154 26.76912023 26.69944482 20.89108219 1.034013001 1 8.648033295 -8.761392119 2.027851645 1.542836737 25.10025407 0.97398253 1.692435023 0.032051995 0.268457416 0.252806309 0.558207299 1.73E-09 8.761392119 23.55741733 up NEIVANVGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 NEIVANVGKR 10 1 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 0 1 NEIVANVGK(1)R 87.298 0.017525 0 718.05 684.56 902.58 1592.8 6252.1 7927.8 6758.5 6442.1 981.28 606.89 FALSE TRUE FALSE 709.2981304 694.1972536 918.2890263 1776.96703 5933.032007 7421.239166 7332.566821 6628.492 893.5118591 591.1229103 1.199916495 1.174370408 1.553465464 3.006087227 10.03688388 12.55447731 12.4044707 11.21339045 1.511550041 1 9.207314326 -8.757743239 2.540664721 1.143499161 12.09700973 0.993638343 0.395415705 0.014246336 0.187844969 0.059995095 0.125973851 1.75E-09 8.757743239 10.95351057 up SATDGNTSTTPPTSAK(ac)KR ddPTM_HeLa_Romidepsin_16h_R1 2 SATDGNTSTTPPTSAKKR 18 2 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 0 1 ; SATDGNTSTTPPTSAK(0.81)K(0.19)R;SATDGNTSTTPPTSAK(0.785)K(0.215)R 155.63 7.25E-16 2498700 368.92 465.46 341.58 987.14 1380.81 1689.54 1726.72 1810.82 360.18 500.93 FALSE TRUE FALSE 364.4234611 472.0127581 347.5250566 1101.277771 1310.342113 1581.583847 1873.387554 1863.21322 327.9645987 487.9157664 0.74689831 0.967406242 0.712264453 2.257106344 2.685590841 3.241510022 3.839571669 3.818719025 0.672174628 1 8.930488293 -8.756505165 1.15995956 0.855513611 3.788529542 0.966267057 0.231059415 0.057814599 0.152618051 0.037437301 0.106511907 1.75E-09 8.756505165 2.933015931 up LKATVTPSPVK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 2 LKATVTPSPVKGK 13 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 1 ; LKATVTPSPVK(1)GK;LKATVTPSPVK(1)GK 116.19 0.0035759 3108600 583.57 550.64 999.22 2385.76 5478.9 7698 7641.8 6437.2 465.78 398.63 FALSE TRUE FALSE 576.4572244 558.3919244 1016.611005 2661.612797 5199.291288 7206.122644 8290.894301 6623.450226 424.1194702 388.2735351 1.484667824 1.438140573 2.618285598 6.85499411 13.39079494 18.5593969 21.35323052 17.05872182 1.092321345 1 8.600929566 -8.748766839 1.405786243 1.241858672 19.64186183 0.982100454 1.04584762 0.032226741 0.127457978 0.153150237 0.392604081 1.78E-09 8.748766839 18.40000315 up ISLSAPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 ISLSAPAKK 9 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 0 1 ; ISLSAPAK(1)K;ISLSAPAK(1)K 129.42 0.0021843 8552300 4228 3437.5 3190.2 4739.2 11030.6 13264.2 12095.1 10731.1 4365.5 3617.5 FALSE TRUE FALSE 4176.46751 3485.893215 3245.724093 5287.168603 10467.66732 12416.66043 13122.45749 11041.58745 3975.038746 3523.516829 1.185312207 0.989322142 0.921160378 1.500537349 2.970801001 3.523939584 3.724249984 3.133683755 1.128145242 1 11.78280039 -8.745487877 2.570469803 1.069614975 3.477200142 0.98032217 0.156088182 0.025325631 0.341706092 0.023556601 0.04964677 1.80E-09 8.745487877 2.407585167 up K(ac)SAPSTGGVK(ac)KPHR ddPTM_HeLa_Romidepsin_16h_R1 2 KSAPSTGGVKKPHR 14 3 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243 K7EMV3 H3F3B;H3F3A Histone H3;Histone H3.3 0 2 ; K(1)SAPSTGGVK(0.5)K(0.5)PHR;K(1)SAPSTGGVK(0.5)K(0.5)PHR 70.68 0.0096582 13898400 1244.89 1172.31 1577.72 1633.75 6694.6 8250 6805.7 6680.2 1642.92 1234.95 FALSE TRUE FALSE 1229.716802 1188.813811 1605.179555 1822.651862 6352.949581 7722.851626 7383.775988 6873.481047 1495.97312 1202.865821 1.022322507 0.988317891 1.334462686 1.515257837 5.281511429 6.420376646 6.13848682 5.714254182 1.243674144 1 10.23226 -8.740804457 3.321822889 1.038775688 6.080960618 0.992430866 0.202357489 0.013119647 0.300885543 0.029709969 0.060389512 1.82E-09 8.740804457 5.042184929 up PEPVK(ac)SAPVPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PEPVKSAPVPKKGSK 15 3 Q99879 Q99879 HIST1H2BM Histone H2B type 1-M 0 3 PEPVK(1)SAPVPK(1)K(1)GSK 137.21 8.23E-06 1069900 0 0 0 0 783.23 1642.1 1305.8 1399.8 85.224 84.217 FALSE TRUE FALSE 0 0 0 0 743.2588505 1537.17511 1416.714619 1440.301004 77.60135199 82.0290302 0 0 0 0 9.060924512 18.73940367 17.27089319 17.55843024 0.946023034 1 6.358062667 -8.520653169 2.654743448 0.378736223 17.82825592 0.990898934 0.754043044 0.01884706 0.265781211 0.122596394 0.288881777 3.02E-09 8.520653169 17.44951969 PERWKK(ac)ANLEK ddPTM_HeLa_Romidepsin_16h_R1 2 PERWKKANLEK 11 3 A0A087WTD2;Q9NYL5 A0A087WTD2 CYP39A1 24-hydroxycholesterol 7-alpha-hydroxylase 0 1 ; PERWK(0.004)K(0.996)ANLEK;PERWK(0.001)K(0.999)ANLEK 101.66 0.0054072 3026400 0 0 65.153 0 2148.79 3307.1 1722.03 2622 97.848 0 FALSE TRUE FALSE 0 0 66.28696063 0 2039.129228 3095.786983 1868.299185 2697.863433 89.09622982 0 0 PETVDRRRS(ph)AET(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 PETVDRRRSAETTK 14 3 Q9Y6Q3;Q9Y6Q3-3;Q9Y6Q3-2 Q9Y6Q3 ZFP37 Zinc finger protein 37 homolog 3 0 PET(0.334)VDRRRS(0.72)AET(0.973)T(0.973)K 56.648 0.0043423 0 404.07 326.77 464.25 320.79 610.34 547.6 344.43 398.71 397.96 519 TRUE FALSE FALSE 399.1450394 331.3702766 472.3300765 357.8812492 579.1920723 512.6101273 373.6858756 410.2460448 362.3654609 505.5163052 0.789578962 0.655508582 0.934351814 0.70795194 1.145743602 1.014032826 0.739216266 0.811538699 0.716822498 1 8.981613816 -12.43457926 1.229007414 0.998068224 0.84727972 0 0.165094288 0.751639357 2.070310978 0.092500079 0.024422772 3.68E-13 12.43457926 -0.150788504 PFGIS(ph)ALIVGFDDDGISR ddPTM_HeLa_Romidepsin_16h_R1 1 PFGISALIVGFDDDGISR 18 0 Q8TAA3-5;Q8TAA3;A0A087WYS6;Q8TAA3-2 Q8TAA3-5 PSMA8 Proteasome subunit alpha type-7-like 1 0 PFGIS(0.999)ALIVGFDDDGIS(0.001)R 76.85 0.016125 9637100 1381.8 1383.4 1534.3 1539.3 1390.8 2023.8 1502.9 1610.4 1673.8 1361.6 TRUE FALSE FALSE 1364.95809 1402.875542 1561.003848 1717.281109 1319.822286 1894.485712 1630.556288 1656.994383 1524.091136 1326.225436 1.029205181 1.057795684 1.177027529 1.29486365 0.9951719 1.428479398 1.229471434 1.249406276 1.14919462 1 10.37311031 -9.590311909 0.767744319 1.004644873 1.265108732 0.340807713 0.110074258 0.335429504 0.396864644 0.019963692 0.037278659 2.57E-10 9.590311909 0.260463859 PFHS(ph)DLMNGT(ph)RPGMASTK ddPTM_HeLa_Romidepsin_16h_R1 1 PFHSDLMNGTRPGMASTK 18 1 H0Y2U9;Q6QNK2-3;Q6QNK2-2;Q6QNK2;Q6QNK2-4 H0Y2U9 ADGRD1;GPR133 Probable G-protein coupled receptor 133 2 0 PFHS(0.993)DLMNGT(0.96)RPGMAS(0.025)T(0.022)K 40.137 0.028942 6838200 129.27 220.61 290.85 24999 0 284.94 201.42 195.98 201.37 137.09 TRUE FALSE FALSE 127.6944075 223.7157534 295.9121222 27889.502 0 266.7332536 218.5286098 201.6503721 183.3589629 133.528382 0.956309105 1.675417241 2.216099062 208.8657226 0 1.997577216 1.636570491 1.510168617 1.373183439 1 7.061002615 -9.461206859 24.99999459 1.073501919 42.83721765 0.110365605 58.7147835 419.6300363 170105.7104 8.972443502 13.70562589 3.46E-10 9.461206859 41.76371573 PFISVTVQSS(ph)T(ph)ESAQDT(ph)Y(ph)LDSQDHK ddPTM_HeLa_Romidepsin_16h_R1 1 PFISVTVQSSTESAQDTYLDSQDHK 25 0 Q9Y2H0-3;Q9Y2H0-1;Q9Y2H0 Q9Y2H0-3 DLGAP4 Disks large-associated protein 4 4 0 PFIS(0.23)VT(0.23)VQS(0.23)S(0.516)T(0.516)ES(0.516)AQDT(0.828)Y(0.929)LDS(0.004)QDHK 45.395 0.0039089 0 1359.7 1203.6 1256.2 1239.9 1088.8 1302.5 1167.1 1206.7 1408.8 1255.9 TRUE FALSE FALSE 1343.127453 1220.544312 1278.063634 1383.263072 1033.234473 1219.274454 1266.233445 1241.613961 1282.7934 1223.271537 1.097979813 0.997770549 1.044791443 1.130789878 0.844648504 0.996732464 1.0351205 1.014994564 1.048657931 1 10.25652897 -8.795195416 24.99999322 1.048463596 0.979023764 0.291919499 0.060805132 218.6687501 161947.1188 0.009571099 0.017349726 1.60E-09 8.795195416 -0.069439832 PFSAPKPQTS(ph)PSPK ddPTM_HeLa_Romidepsin_16h_R1 2 PFSAPKPQTSPSPK 14 1 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 0 PFS(0.084)APKPQT(0.125)S(0.46)PS(0.332)PK;PFSAPKPQT(0.169)S(0.569)PS(0.262)PK ; 72.681 0.018994 125918000 7557 6828.3 7334.2 3865.4 6590.8 6149.1 6155.4 6492.8 6865.8 7724.9 TRUE FALSE FALSE 7464.892377 6924.428987 7461.848674 4312.335735 6254.446882 5756.192355 6678.239522 6680.658924 6251.705652 7524.205984 0.992116961 0.920287005 0.99171244 0.573128347 0.831243442 0.765023229 0.887567344 0.887888893 0.830879121 1 12.87732363 -9.405173058 21.94407344 0.988985739 0.794149449 0.35201559 0.09922067 4.208339273 772.3871416 0.012707902 0.019411642 3.93E-10 9.405173058 -0.19483629 PGEAAVASS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 PGEAAVASSPSK 12 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 PGEAAVAS(0.014)S(0.984)PS(0.002)K 91.093 0.026973 3418500 3335.4 3003 3306.7 1627.6 2459.5 2889.4 2666.5 2375.9 3575.4 3378.5 TRUE FALSE FALSE 3294.746862 3045.276313 3364.251726 1815.79077 2333.982537 2704.776665 2892.992443 2444.642918 3255.607269 3290.726083 1.001221852 0.925411668 1.022343289 0.551790311 0.709260655 0.82193917 0.87913499 0.742888608 0.989327944 1 11.68419023 -9.292246924 24.87307863 0.995242512 0.751409754 0.687720228 0.082879074 279.2254162 225437.346 0.012960973 0.019799515 5.10E-10 9.292246924 -0.243832758 PGELLFRS(ph)DPLAY(ph)TVCK ddPTM_HeLa_Romidepsin_16h_R1 1 PGELLFRSDPLAYTVCK 17 1 B0QZ88;Q9H7B4 B0QZ88 SMYD3 Histone-lysine N-methyltransferase SMYD3 2 0 PGELLFRS(0.999)DPLAY(0.685)T(0.316)VCK 58.49 0.02788 32651000 1211.6 1244.7 1205.4 1088.9 480.49 854.87 709.98 1098.1 1024.3 1320.4 TRUE FALSE FALSE 1196.832553 1262.222919 1226.379481 1214.803741 455.9688023 800.246566 770.2856835 1129.871791 932.6840426 1286.095818 0.930593613 0.981437698 0.953567739 0.944567057 0.354537194 0.622229351 0.598933355 0.87852847 0.725205719 1 10.32878242 -8.866709374 9.434607958 0.965877096 0.613557148 0.523781429 0.140864507 0.12049283 9.921845091 0.016662479 0.030247364 1.36E-09 8.866709374 -0.352319948 PGFSIADK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PGFSIADKK 9 1 P62913;Q5VVC8;P62913-2 P62913 RPL11 60S ribosomal protein L11 0 1 ; PGFSIADK(1)K;PGFSIADK(1)K 116.52 0.0014445 2540000 1958.82 1583.81 2081.85 1068.46 3578.9 3641.6 3117.3 2616.4 3386.5 2014.32 FALSE TRUE FALSE 1934.945148 1606.106919 2118.083726 1192.000372 3396.255378 3408.913513 3382.083384 2692.101406 3083.602958 1961.987676 0.98621677 0.818612134 1.079560158 0.607547329 1.731027886 1.737479575 1.723804602 1.372129621 1.57167295 1 10.93810026 -8.746701651 24.99972429 0.961817352 1.653900852 0.598104214 0.251211363 68.8987953 116872.9442 0.021727598 0.043308681 1.79E-09 8.746701651 0.6920835 PGPTPSGTNVGSS(ph)GRSPSK ddPTM_HeLa_Romidepsin_16h_R1 1 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 0 PGPTPSGTNVGS(0.047)S(0.473)GRS(0.473)PS(0.006)K 117.6 0.00031079 273000000 5745.3 7611.9 4900.2 4294.7 4231.1 5853.6 3815.6 6868.8 5634.7 6653.6 TRUE FALSE FALSE 5675.274074 7719.060528 4985.485925 4791.273421 4015.171179 5479.573852 4139.696969 7067.537891 5130.71832 6480.738513 0.875714097 1.1910773 0.769277439 0.739309789 0.619554572 0.845516887 0.638769326 1.09054514 0.791687291 1 12.66194251 -9.620841976 22.77840184 0.959443443 0.770450777 0.243805535 0.154800433 6.644449923 1535.048321 0.021654028 0.030623417 2.39E-10 9.620841976 -0.188992666 PGPTPSGTNVGSSGRS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 4 PGPTPSGTNVGSSGRSPSK 19 1 P60468 P60468 SEC61B Protein transport protein Sec61 subunit beta 1 0 PGPTPSGTNVGSS(0.003)GRS(0.996)PS(0.001)K;PGPTPS(0.001)GT(0.001)NVGS(0.022)S(0.049)GRS(0.685)PS(0.243)K;PGPTPSGT(0.001)NVGS(0.014)S(0.279)GRS(0.697)PS(0.009)K;PGPTPSGTNVGS(0.012)S(0.103)GRS(0.88)PS(0.004)K ;;; 165.88 9.01E-08 384782100 12547.8 16485.9 11769.5 8959.8 8342.3 11052.1 7720.6 12324.4 10690 12393.2 TRUE FALSE FALSE 12394.86259 16717.98893 11974.34321 9995.774233 7916.561302 10345.90648 8376.387571 12680.98707 9733.859626 12071.22288 1.026810847 1.384945759 0.991974329 0.828066413 0.655820987 0.857071946 0.693913753 1.050513871 0.806368976 1 13.55928422 -9.290546162 4.52082425 1.046579292 0.802162812 0.317290357 0.165565099 0.163184881 8.286162127 0.022439292 0.035582239 5.12E-10 9.290546162 -0.24441648 PGPTQTLS(ph)PNGENNNDIIQDNNGTIIPFRK ddPTM_HeLa_Romidepsin_16h_R1 1 PGPTQTLSPNGENNNDIIQDNNGTIIPFRK 30 1 Q15555-2;Q15555 Q15555-2 MAPRE2 Microtubule-associated protein RP/EB family member 2 1 0 PGPT(0.002)QT(0.027)LS(0.971)PNGENNNDIIQDNNGTIIPFRK 134.17 4.17E-11 7743800 929.28 854.43 645.87 335.26 1091.2 1396.5 1292.7 1209.3 969.86 778.36 TRUE FALSE FALSE 917.9535779 866.458688 657.1110964 374.0243386 1035.511992 1307.268157 1402.501906 1244.289188 883.1132925 758.138095 1.210799964 1.142877127 0.866743276 0.493345924 1.36586197 1.724314034 1.84992934 1.641243457 1.164844899 1 9.566316849 -8.444957515 4.135317237 1.044459282 1.74044614 0.726857084 0.205985392 0.102499429 3.26537075 0.032109347 0.073566062 3.59E-09 8.444957515 0.695986858 PGQATSHIFYEPDAYDDLDQEDPDDDLDI ddPTM_HeLa_Romidepsin_16h_R1 1 PGQATSHIFYEPDAYDDLDQEDPDDDLDI 29 0 Q8TE02;Q8TE02-4 Q8TE02 ELP5 Elongator complex protein 5 0 0 86.039 5.03E-07 3041700 1092.9 1039 1030.5 770.27 882.86 787.82 671.31 774.26 1064.2 1164.6 FALSE FALSE TRUE 1079.579314 1053.627069 1048.43542 859.3322416 837.8043598 737.4808446 728.3310546 796.6619915 969.0152867 1134.343524 0.951721671 0.928843024 0.924266237 0.757559084 0.738580811 0.650138894 0.64207274 0.70231105 0.854252055 1 10.1476419 -9.15511356 1.067546871 0.978578503 0.658425833 0.859102176 0.047224118 0.062878138 0.141444499 0.004788093 0.010611577 7.00E-10 9.15511356 -0.32015267 PGWLSS(ph)PTLGR ddPTM_HeLa_Romidepsin_16h_R1 2 PGWLSSPTLGR 11 0 C9J266;Q5XPI4;Q5XPI4-2;C9JS59 C9J266 RNF123 E3 ubiquitin-protein ligase RNF123 1 0 PGWLS(0.022)S(0.955)PT(0.023)LGR;PGWLS(0.002)S(0.921)PT(0.077)LGR ; 155.53 0.0020477 142392000 8792 8994.9 8325.1 7168.2 8053.5 8710.1 8665.1 9296.5 7754.8 7639.2 TRUE FALSE FALSE 8684.839722 9121.530438 8469.994873 7997.021011 7642.499843 8153.552721 9401.113378 9565.47956 7061.191266 7440.732483 1.167202254 1.225891464 1.1383281 1.074762603 1.027116599 1.09579974 1.263466117 1.285556171 0.948991417 1 12.86122894 -16.52287875 0.24496958 0.020739096 1.174031375 0.464958267 0.078984102 41.96292724 0.551515942 19.80089565 0.054363439 3.00E-17 16.52287875 1.153292278 PHS(ph)T(ph)SPLPDDS(ph)LFVAS(ph)LSSPR ddPTM_HeLa_Romidepsin_16h_R1 1 PHSTSPLPDDSLFVASLSSPR 21 0 Q96EN9-2 Q96EN9-2 4 0 PHS(0.84)T(0.84)S(0.321)PLPDDS(0.984)LFVAS(0.522)LS(0.368)S(0.125)PR 57.616 0.0066907 10861000 1249.1 1241.8 1272 966.91 1346.1 1289.9 1340.3 1496.7 1543.4 1667.3 TRUE FALSE FALSE 1233.875489 1259.282093 1294.138626 1078.708684 1277.403494 1207.479553 1454.145049 1540.004653 1405.354438 1623.983306 0.759783358 0.775427979 0.796891583 0.664236313 0.786586592 0.743529536 0.895418717 0.948288475 0.865374929 1 10.66532109 -12.25725549 0.914055131 1.004122298 0.791086798 0.239290762 0.084494898 0.401864527 0.584496772 0.058196111 0.014758942 5.53E-13 12.25725549 -0.2130355 PIPQT(ph)PESAGNK ddPTM_HeLa_Romidepsin_16h_R1 2 PIPQTPESAGNK 12 0 P52948-6;P52948-2;P52948-5;P52948;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 0 PIPQT(0.982)PES(0.018)AGNK;PIPQT(0.5)PES(0.5)AGNK ; 130.44 0.0079417 22336500 7356.7 6798.6 7278.3 4921.3 5681.5 5683.8 5043.6 5467.9 6273 6588.5 TRUE FALSE FALSE 7267.033711 6894.310869 7404.975758 5490.323861 5391.551854 5320.623524 5472.003258 5626.10506 5711.927169 6417.32982 1.132407701 1.074327027 1.153902942 0.855546468 0.840155019 0.829102395 0.852691604 0.876704987 0.89007848 1 12.64775742 -9.246120334 24.01472903 1.071417169 0.849141657 0.660771162 0.070577649 161.9366432 253857.9102 0.008552198 0.014142141 5.67E-10 9.246120334 -0.222275512 PIPQTPES(ph)AGNK ddPTM_HeLa_Romidepsin_16h_R1 1 PIPQTPESAGNK 12 0 P52948-6;P52948-2;P52948-5;P52948;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 0 PIPQT(0.225)PES(0.775)AGNK 169.09 0.00018175 18040000 4484.8 4315.6 4569.2 2757.7 3851.7 3180.6 3269.8 3503.1 3677.8 4325.6 TRUE FALSE FALSE 4430.137533 4376.35513 4648.725009 3076.558249 3655.133376 2977.369925 3547.53673 3604.456672 3348.848357 4213.220288 1.051484904 1.038719751 1.103366236 0.730215379 0.867539109 0.706673215 0.842001245 0.855511088 0.79484293 1 12.04070763 -9.261329619 24.9999719 1.031629683 0.80122409 0.516645035 0.092546581 2.964162462 675119.9068 0.008045566 0.012800055 5.48E-10 9.261329619 -0.230405593 PIS(ph)PSPSAILER ddPTM_HeLa_Romidepsin_16h_R1 2 PISPSPSAILER 12 0 Q5T5P2;Q5T5P2-2;Q5T5P2-7;Q5T5P2-10;Q5T5P2-3;Q5T5P2-9;Q5T5P1;Q5T5P2-4;Q5T5P2-8;Q5T5P2-6;Q5T5P0 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 PIS(0.999)PS(0.001)PSAILER;PIS(0.896)PS(0.103)PS(0.001)AILER ; 140.45 0.0019601 10788500 3202.2 3391.6 3115.2 2137.1 2509.6 2040.52 2059.15 1923.86 2758 3650.6 TRUE FALSE FALSE 3163.170355 3439.347034 3169.418749 2384.201557 2381.525747 1910.137357 2234.05415 1979.523854 2511.317572 3555.756886 0.88959129 0.967261583 0.891348551 0.67051872 0.669766192 0.537195714 0.628292153 0.556709561 0.706268075 1 11.79594097 -9.184222571 1.630739282 0.950060522 0.587691784 0.706133668 0.087622625 0.072133664 0.375356313 0.008123981 0.015308388 6.54E-10 9.184222571 -0.362368738 PK(ac)RLDSADAKVYSGYYHLDQK ddPTM_HeLa_Romidepsin_16h_R1 1 PKRLDSADAKVYSGYYHLDQK 21 3 Q2VWP7 Q2VWP7 PRTG Protogenin 0 1 PK(0.902)RLDSADAK(0.098)VYSGYYHLDQK 55.33 0.010736 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 PKPSS(ph)SPVIFAGGQDR ddPTM_HeLa_Romidepsin_16h_R1 1 PKPSSSPVIFAGGQDR 16 1 Q15366;Q15366-2;H3BSS4;Q15366-6;Q15366-3 Q15366 PCBP2 Poly(rC)-binding protein 2 1 0 PKPS(0.056)S(0.472)S(0.472)PVIFAGGQDR 149.97 0.0018993 14718000 1941.6 1739.7 1800.6 1366.7 1178.4 1038.6 1313.2 1091.9 1396.8 1695.1 TRUE FALSE FALSE 1917.935032 1764.191542 1831.938688 1524.724285 1118.261851 972.2368119 1424.743175 1123.492404 1271.86671 1651.061058 1.161637859 1.068519867 1.109552357 0.923481465 0.677298908 0.588855759 0.862925795 0.680466903 0.770332935 1 10.68917776 -8.956877407 3.21828263 1.079116715 0.706127594 0.583135535 0.122782881 0.078054265 1.667022405 0.013023016 0.024305883 1.10E-09 8.956877407 -0.372989121 PLEGSSSEDSPPEGQAPPS(ph)HSPR ddPTM_HeLa_Romidepsin_16h_R1 1 PLEGSSSEDSPPEGQAPPSHSPR 23 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 PLEGSSSEDSPPEGQAPPS(0.5)HS(0.5)PR 156.8 9.79E-10 8372500 1196.1 1004.1 1407.4 1349.7 989.96 1073.5 963.3 918.79 1421.6 1347.3 TRUE FALSE FALSE 1181.521473 1018.235746 1431.895207 1505.758665 939.4386472 1004.906815 1045.122678 945.373739 1294.448536 1312.296952 0.900346123 0.775918701 1.091136579 1.147422207 0.715873527 0.765761753 0.796407152 0.720396201 0.986399103 1 10.3578785 -8.730032988 24.99875198 0.960765012 0.75410594 0.57073941 0.09817137 132.6764427 105606.7926 0.015021756 0.030041235 1.86E-09 8.730032988 -0.206659073 PLEGSSSEDSPPEGQAPPSHS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 PLEGSSSEDSPPEGQAPPSHSPR 23 0 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 PLEGSSSEDSPPEGQAPPS(0.027)HS(0.973)PR 136.16 2.48E-06 9560000 2234.5 2408.8 2769.7 3283.9 2056.2 2233.3 2000.9 2147.4 2458.5 2958.9 TRUE FALSE FALSE 2207.265055 2442.71115 2817.905467 3663.599969 1951.264441 2090.599338 2170.856396 2209.531631 2238.605603 2882.027351 0.765872348 0.847566956 0.977751119 1.27118848 0.677045775 0.725391914 0.753239346 0.7666588 0.776746828 1 11.49286831 PLISVYSEK ddPTM_HeLa_Romidepsin_16h_R1 2 PLISVYSEK 9 0 P36578;H3BTP7;H3BU31 P36578 RPL4 60S ribosomal protein L4 0 0 ; ; 157.91 0.018621 1343380 1640.01 1320.51 1619.49 1042.26 1477.73 1384.26 1201.88 1326.54 1347.69 1487.2 FALSE FALSE TRUE 1620.020927 1339.100174 1647.676544 1162.771005 1402.315924 1295.810253 1303.967657 1364.921342 1227.149231 1448.56233 1.118364667 0.924433935 1.137456436 0.802706919 0.968074273 0.894549186 0.900180566 0.942259311 0.847149761 1 10.50040605 -9.265149637 24.99627114 1.050924296 0.904784156 0.15873026 0.093866354 201.6090306 1358254.027 0.010699789 0.016741415 5.43E-10 9.265149637 -0.14614014 PLLSQEDS(ph)EEEENELEAINR ddPTM_HeLa_Romidepsin_16h_R1 1 PLLSQEDSEEEENELEAINR 20 0 Q9H1H9-3;Q9H1H9-4;Q9H1H9-2 Q9H1H9-3 KIF13A Kinesin-like protein KIF13A 1 0 PLLSQEDS(1)EEEENELEAINR 114.64 7.86E-07 0 948.69 900.07 796.11 619.98 689.03 855.87 644.09 898.52 818.03 972.39 TRUE FALSE FALSE 937.1270014 912.7412091 809.9659606 691.6650047 653.866228 801.1826692 698.7989885 924.5172586 744.863348 947.1271676 0.98944158 0.963694465 0.855181847 0.730276808 0.690367936 0.845908233 0.737809042 0.976127906 0.786444918 1 9.887414334 -9.699240038 2.79457044 0.99424179 0.78973386 0.228147919 0.098889907 0.12114809 1.93312804 0.011341395 0.016246675 2.00E-10 9.699240038 -0.20450793 PLLSQEDS(ph)EEEENELEAINRK ddPTM_HeLa_Romidepsin_16h_R1 2 PLLSQEDSEEEENELEAINRK 21 1 Q9H1H9-3;Q9H1H9-4;Q9H1H9-2 Q9H1H9-3 KIF13A Kinesin-like protein KIF13A 1 0 PLLS(0.003)QEDS(0.997)EEEENELEAINRK;PLLS(0.018)QEDS(0.982)EEEENELEAINRK ; 149.12 4.09E-06 29360000 3313 3596.1 3242.7 3225.1 2489.8 2711.7 2504.16 2526.4 3582.2 3539.2 TRUE FALSE FALSE 3272.619882 3646.72599 3299.137833 3598.001237 2362.736215 2538.431122 2716.863288 2599.497398 3261.79906 3447.251074 0.949341899 1.057864923 0.957034391 1.043730543 0.685397195 0.736363864 0.788124575 0.754078349 0.946202928 1 11.75123066 -8.761421694 25 0.984977986 0.744027151 0.893216445 0.042527848 0.108544298 152561.814 0.00610202 0.011603749 1.73E-09 8.761421694 -0.240950835 PLPVES(ph)PDTQR ddPTM_HeLa_Romidepsin_16h_R1 1 PLPVESPDTQR 11 0 P57682 P57682 KLF3 Krueppel-like factor 3 1 0 PLPVES(0.969)PDT(0.031)QR 110.98 0.0020857 0 1611.4 1415.1 1565.2 1126 1003.4 963.9 955.78 949.37 1802 1561.8 TRUE FALSE FALSE 1591.759637 1435.021815 1592.441649 1256.193418 952.1927538 902.3099008 1036.963929 976.8385231 1640.824607 1521.224211 1.046367541 0.943333537 1.046815872 0.825777955 0.625938469 0.593147213 0.681664098 0.642139743 1.078621149 1 10.57101709 -8.999507898 2.722493356 1.017130921 0.635035992 0.951423828 0.041177411 0.036886833 0.552439227 0.005744381 0.01071804 1.00E-09 8.999507898 -0.382094929 PLTS(ph)PESLSR ddPTM_HeLa_Romidepsin_16h_R1 1 PLTSPESLSR 10 0 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 PLT(0.022)S(0.975)PES(0.003)LSR 158.47 0.002749 14347000 3078.4 3244.1 3070.1 2142.7 3269.3 3644.9 3538.9 3276.4 3027.6 3400.3 TRUE FALSE FALSE 3040.879277 3289.770525 3123.533803 2390.449056 3102.455422 3412.002653 3839.494078 3371.197465 2756.803873 3311.959716 0.918151046 0.993300284 0.943107426 0.721762721 0.936743103 1.030206568 1.159281636 1.017886011 0.832378444 1 11.69346941 -8.084448271 3.985750892 0.942049984 1.090251734 0.385534332 0.088025432 0.192355704 5.608778961 0.012207635 0.034261737 8.23E-09 8.084448271 0.14820175 PMFIVNTNVPR ddPTM_HeLa_Romidepsin_16h_R1 1 PMFIVNTNVPR 11 0 P14174 P14174 MIF Macrophage migration inhibitory factor 0 0 104.05 0.021303 2411000 419.35 249.28 346.75 241.93 435.13 347.71 160.69 143.93 236.9 237.44 FALSE FALSE TRUE 414.2388009 252.7893704 352.7850383 269.9030849 412.9236924 325.4924532 174.3390046 148.0943875 215.7110707 231.2712746 1.791138141 1.093042665 1.525416587 1.16704111 1.785451709 1.407405454 0.753829047 0.640349251 0.932718822 1 7.853442275 -7.735093117 5.597775961 1.388896137 0.680169795 0.432407072 0.289483715 0.122673567 10.75455869 0.044613777 0.164905005 1.84E-08 7.735093117 -0.708726343 PMGAQTDERLAQY(ph)KKR ddPTM_HeLa_Romidepsin_16h_R1 1 PMGAQTDERLAQYKKR 16 3 H0Y9T6;Q8IZQ1-2;Q8IZQ1 H0Y9T6 WDFY3 WD repeat and FYVE domain-containing protein 3 1 0 PMGAQTDERLAQY(1)KKR 62.081 0.013149 23058000 5434.1 4993.4 4224 3694.2 4537.6 4890.9 4259.7 5461.2 4631 4680.5 TRUE FALSE FALSE 5367.867099 5063.697216 4297.516948 4121.340786 4306.02934 4578.387275 4621.518812 5619.211206 4216.791761 4558.899935 1.177447888 1.11072787 0.942665338 0.904020892 0.944532541 1.004274571 1.013735523 1.23258051 0.924958174 1 12.15447003 -9.775696731 24.98675309 1.088156144 0.999635979 0 0.106205156 357.7249086 626929.9378 0.017272052 0.022759863 1.68E-10 9.775696731 -0.088520165 PMSPGDCPPETT(ph)ET(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 PMSPGDCPPETTETPK 16 0 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 2 0 PMSPGDCPPET(0.638)T(0.681)ET(0.681)PK 46.408 0.00426 0 876.81 883.18 973.79 7544.5 954.94 950.24 846.56 991.3 1058 1324.9 TRUE FALSE FALSE 866.1231025 895.6134312 990.7384065 8416.830588 906.2058484 889.5227308 918.4667853 1019.981701 963.3698302 1290.478907 0.671164091 0.694016327 0.767729252 6.522253516 0.702224456 0.689296606 0.711725531 0.790390061 0.746521175 1 10.33369085 PNNSGEAPS(ph)SPTPK ddPTM_HeLa_Romidepsin_16h_R1 2 PNNSGEAPSSPTPK 14 0 K7ENR9;K7ERZ5;P49916-4;P49916-3;P49916-2;P49916 K7ENR9 LIG3 DNA ligase 3 1 0 PNNSGEAPS(0.789)S(0.205)PT(0.005)PK;PNNS(0.005)GEAPS(0.618)S(0.375)PT(0.002)PK ; 198.38 1.84E-16 21065000 8047.3 7002 7586.2 4579.2 4570.1 4173.9 3484.6 4159.5 6549.7 7599.6 TRUE FALSE FALSE 7949.216412 7100.57434 7718.234629 5108.66865 4336.870744 3907.201261 3780.581837 4279.84857 5963.878428 7402.161296 1.073904782 0.959256906 1.042700141 0.690159056 0.585892494 0.527846004 0.510740267 0.578189045 0.805694201 1 12.85373086 -9.113194946 2.312517801 1.031806721 0.543551945 0.856268277 0.081230599 0.035946725 0.37666255 0.006553856 0.011925895 7.71E-10 9.113194946 -0.488254776 PNS(ph)SAS(ph)KFSPMSYPQMKPK ddPTM_HeLa_Romidepsin_16h_R1 1 PNSSASKFSPMSYPQMKPK 19 2 Q96JM2;Q96JM2-3 Q96JM2 ZNF462 Zinc finger protein 462 2 0 PNS(0.516)S(0.516)AS(0.828)KFS(0.107)PMS(0.017)Y(0.016)PQMKPK 41.554 0.027286 29840000 1662.5 1202.4 2415.7 1243.7 2030.8 1966.2 1602.1 1589 1789 1974 TRUE FALSE FALSE 1642.236811 1219.327419 2457.744245 1387.502446 1927.160698 1840.566166 1738.182334 1634.975208 1628.987359 1922.715195 0.854123801 0.634169544 1.278267448 0.721637011 1.002312096 0.957274468 0.904024859 0.850347057 0.84723279 1 10.90892936 -9.07056528 0.009457003 1.811166805 5.62E-05 0 0.167610517 11916.67025 39.7157019 3695.1014 3910.246602 8.50E-10 9.07056528 -1.811110624 PPAPPS(ph)PVQSQS(ph)PS(ph)T(ph)NWSPAVPVK ddPTM_HeLa_Romidepsin_16h_R1 1 PPAPPSPVQSQSPSTNWSPAVPVK 24 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 4 0 PPAPPS(0.88)PVQS(0.27)QS(0.973)PS(0.872)T(0.464)NWS(0.54)PAVPVK 48.229 0.0042277 0 304.64 260.81 260.15 191.23 184.07 263.46 260.42 221.39 394.05 389.44 TRUE FALSE FALSE 300.9269305 264.48169 264.6778016 213.3409124 174.676221 246.6257563 282.5400683 227.7955704 358.8051811 379.3222927 0.793327828 0.697247948 0.697764953 0.562426508 0.460495532 0.650174696 0.7448549 0.600533042 0.945911137 1 8.567280351 -10.82096934 0.596460008 0.980270604 0.605642229 0.778004287 0.074130041 0.236851378 0.195150739 0.03349326 0.025434997 1.51E-11 10.82096934 -0.374628375 PPGATSRPTT(ph)APPRTTTRR ddPTM_HeLa_Romidepsin_16h_R1 1 PPGATSRPTTAPPRTTTRR 19 3 D6RIE1;E9PB58;Q6UXF1-2;Q6UXF1 D6RIE1 TMEM108 Transmembrane protein 108 1 0 PPGAT(0.001)S(0.003)RPT(0.011)T(0.907)APPRT(0.052)T(0.013)T(0.013)RR 61.524 0.012253 124940000 10092 10304 9815.8 8865.4 5216 4527 4536.1 4391.6 8915.8 8795.9 TRUE FALSE FALSE 9968.994822 10449.05998 9986.639881 9890.459261 4949.808056 4237.73931 4921.396221 4518.664017 8118.348518 8567.38125 1.163598833 1.219632893 1.165658395 1.154432022 0.577750413 0.494636481 0.574434133 0.527426513 0.9475881 1 13.06463857 -8.743768258 8.352155429 1.10319889 0.540936496 0.923644017 0.079567251 0.03744164 13.53426587 0.012584293 0.024685807 1.80E-09 8.743768258 -0.562262394 PPPPMRS(ph)LS(ph)RLFSNK ddPTM_HeLa_Romidepsin_16h_R1 1 PPPPMRSLSRLFSNK 15 2 A0A0C4DGX6;Q86TI4;Q86TI4-1 A0A0C4DGX6 WDR86 WD repeat-containing protein 86 2 0 PPPPMRS(1)LS(0.997)RLFS(0.003)NK 66.989 0.017422 2496300 1395.2 1730.1 1408.1 1389 1476.4 1649.1 1077.6 1750.4 1698.7 1620.7 TRUE FALSE FALSE 1378.194766 1754.456393 1432.60739 1549.602715 1401.053799 1543.727832 1169.131317 1801.045062 1546.764018 1578.59398 0.873052085 1.111404462 0.907521128 0.981634755 0.887532713 0.977913163 0.740615593 1.140917224 0.979836511 1 10.62442444 -8.773992025 24.79428039 0.952823832 0.925676049 0.000188032 0.11050285 1010.524747 1996010.532 0.015484924 0.028210244 1.68E-09 8.773992025 -0.027147783 PQLELAES(ph)SPAASFLSSR ddPTM_HeLa_Romidepsin_16h_R1 2 PQLELAESSPAASFLSSR 18 0 H0YCR5;Q9BQC3-2;Q9BQC3-3;Q9BQC3 H0YCR5 DPH2 Diphthamide biosynthesis protein 2 1 0 PQLELAES(0.489)S(0.489)PAAS(0.01)FLS(0.003)S(0.01)R;PQLELAES(0.436)S(0.436)PAAS(0.088)FLS(0.01)S(0.03)R ; 106.87 0.0015369 8151600 2135.7 2166.18 2013.95 1476.02 2033.91 2446.02 1888.07 2086.1 2187.37 2162 TRUE FALSE FALSE 2109.669267 2196.675539 2049.001955 1646.684377 1930.111983 2289.727216 2048.442619 2146.458012 1991.726149 2105.830928 1.001822719 1.043139556 0.973013516 0.781964191 0.916556005 1.087327185 0.972747903 1.019292662 0.945814843 1 11.0401739 -9.530889853 24.84536098 1.004247163 0.953263636 0.060302982 0.076390003 340.9965805 1057550.353 0.012106383 0.017138408 2.95E-10 9.530889853 -0.050983527 PQSASTAHSTPSVPSPVSKSTLQGSVTPK ddPTM_HeLa_Romidepsin_16h_R1 1 PQSASTAHSTPSVPSPVSKSTLQGSVTPK 29 1 A0A096LNH2 A0A096LNH2 EFCAB8 0 0 30.337 0.02796 5659200 1163.9 1003.6 987.47 982.54 982.29 1973.7 1364.4 1128.9 1093 1103.4 FALSE FALSE TRUE 1149.713939 1017.728707 1004.656501 1096.145898 932.1600759 1847.58694 1480.292102 1161.56294 995.2393425 1074.733509 1.069766532 0.946959129 0.934795922 1.01992344 0.867340665 1.719111691 1.377357354 1.080791592 0.926033602 1 10.06976326 -8.279996989 24.99905612 1.008933335 1.390913972 0.601379318 0.156279495 408.3990939 550155.7797 0.021164558 0.047406151 5.25E-09 8.279996989 0.381980637 PQSPVIQAAAVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 PQSPVIQAAAVSPK 14 0 Q9Y6D5 Q9Y6D5 ARFGEF2 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 1 0 PQSPVIQAAAVS(1)PK 87.157 0.022949 8934800 2408.2 2902 2685.3 1502.4 2503.9 2368.9 1859.6 2534.5 2632 3035.7 TRUE FALSE FALSE 2378.847932 2942.854432 2732.03652 1676.114557 2376.11664 2217.534935 2017.554378 2607.831759 2396.587328 2956.832076 0.804525881 0.995272764 0.923974189 0.566861598 0.803602159 0.749969859 0.682336475 0.881968164 0.810525341 1 11.5298366 -9.316584685 24.98635213 0.914420038 0.738340008 0.432313236 0.097153447 218.0762558 98809.87374 0.01564332 0.023895576 4.82E-10 9.316584685 -0.17608003 PRDGTVS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 PRDGTVSK 8 1 Q6NSI8-2 Q6NSI8-2 1 0 PRDGTVS(1)K 72.848 0.028295 8442900 6667.4 6122.7 6364 5612.6 8041.9 8936.9 7146.2 7492.9 6707.5 5773 TRUE FALSE FALSE 6586.135164 6208.895531 6474.76275 6261.55522 7631.491835 8365.860933 7753.19805 7709.69524 6107.564401 5623.016628 1.171281467 1.104192988 1.151474943 1.113558012 1.357188203 1.487788759 1.378832496 1.371095935 1.086172211 1 12.4571286 -8.733296979 3.591867397 1.091172517 1.411704262 0.884777999 0.052219499 0.072102789 1.954065897 0.010842703 0.021938408 1.85E-09 8.733296979 0.320531745 PRPVS(ph)PSSLLDTAISEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 PRPVSPSSLLDTAISEEAR 19 1 A0A0B4J2F2;P57059 A0A0B4J2F2 LOC102724428;SIK1 Serine/threonine-protein kinase SIK1 1 0 PRPVS(0.849)PS(0.14)S(0.01)LLDTAISEEAR 79.455 0.0034043 3404000 514.72 388.85 395.58 502.76 318.21 225.44 199.39 317.6 360.2 468.36 TRUE FALSE FALSE 508.4463947 394.3242405 402.464904 560.8914768 301.9705563 211.0351116 216.3261816 326.7892549 327.9828099 456.1919397 1.114544889 0.864382305 0.882227126 1.229507644 0.661937509 0.462601579 0.474199921 0.71634158 0.718957924 1 8.833497146 -8.619567824 5.648079484 1.03551441 0.546359812 0.588854207 0.155137243 0.068094514 3.281019175 0.017378607 0.035166804 2.40E-09 8.619567824 -0.489154598 PS(ph)VLS(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 PSVLSSK 7 0 H3BS19;Q96JG9 H3BS19 ZNF469 Zinc finger protein 469 3 0 PS(1)VLS(1)S(1)K 74.743 0.0042565 0 1171.3 1140.9 1367.8 960.63 1132.2 1337.4 898.54 1463.2 1101.6 1512.4 TRUE FALSE FALSE 1157.023745 1156.96162 1391.605985 1071.702561 1074.419609 1251.944456 974.8619652 1505.535383 1003.070137 1473.10763 0.785430556 0.785388383 0.944673666 0.727511377 0.72935581 0.849866249 0.661772396 1.02201316 0.680921147 1 10.52464713 -12.28823096 0.746659095 1.01694561 0.804692328 0 0.141482884 0.706391271 0.617181377 0.093984161 0.018785893 5.15E-13 12.28823096 -0.212253282 PSADLTNSSAPSPS(ph)HK ddPTM_HeLa_Romidepsin_16h_R1 2 PSADLTNSSAPSPSHK 16 0 E7ETY4;E9PC69;Q7KZI7-10;Q7KZI7-12;Q7KZI7-8;Q7KZI7-11;Q7KZI7-6;Q7KZI7-3;Q7KZI7-14;Q7KZI7-9;Q7KZI7-13;Q7KZI7-4;Q7KZI7-16;Q7KZI7-5;Q7KZI7-15;Q7KZI7-2;Q7KZI7-7;Q7KZI7 E7ETY4 MARK2 Serine/threonine-protein kinase MARK2 1 0 PSADLTNSSAPS(0.005)PS(0.995)HK;PSADLTNSSAPS(0.358)PS(0.641)HK ; 93.237 0.0042634 17541100 3752 3866 3626.1 3629.7 3674.6 4464 3887.2 3682.2 3787.5 4087.2 TRUE FALSE FALSE 3706.269181 3920.425649 3689.210749 4049.382992 3487.07145 4178.764807 4217.378671 3788.738647 3448.736514 3981.013955 0.930986232 0.984780685 0.926701285 1.017173775 0.875925453 1.049673489 1.059372994 0.951701926 0.866296012 1 11.95892021 -8.161330219 23.90628476 0.963431027 1.024162095 0.233844615 0.055961685 30.29582763 7228.481861 0.006441739 0.016423275 6.90E-09 8.161330219 0.060731068 PSDVGNLDDFAES(ph)DEDEAHGPGAPEAR ddPTM_HeLa_Romidepsin_16h_R1 2 PSDVGNLDDFAESDEDEAHGPGAPEAR 27 0 Q8N3D4;E9PIH6;A0A0U1RQH4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 PSDVGNLDDFAES(1)DEDEAHGPGAPEAR;PSDVGNLDDFAES(1)DEDEAHGPGAPEAR ; 126.68 2.70E-10 20210000 4243.5 3925.9 4231.2 3412.1 4010.5 4717 3973.5 4788.3 3788.1 5100.7 TRUE FALSE FALSE 4191.77859 3981.168923 4304.842261 3806.623056 3805.82922 4415.598923 4311.008991 4926.841906 3449.282849 4968.183079 0.843724662 0.801332974 0.866482211 0.766200238 0.766040454 0.888775404 0.867723456 0.991678815 0.694274505 1 12.27850262 -12.05843803 0.821621409 1.001022145 0.844756624 0 0.11303851 0.459276642 0.55943594 0.043647327 0.012858325 8.74E-13 12.05843803 -0.156265521 PSGEAFVELES(ph)EDEVK ddPTM_HeLa_Romidepsin_16h_R1 2 PSGEAFVELESEDEVK 16 0 P31943;E9PCY7;G8JLB6;D6RDU3;D6RBM0;D6RIH9;D6RJ04;D6RIU0;D6RIT2;D6RFM3;D6R9T0;D6RAM1;E7EN40;D6RDL0;E7EQJ0 P31943;E7EQJ0 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 1 0 PS(0.008)GEAFVELES(0.992)EDEVK;PSGEAFVELES(1)EDEVK ; 156.13 0.00022374 4764600 3546.2 3107.8 3394.4 1560.13 2723.4 3264.1 2575.5 2982.6 3021.1 3616.6 TRUE FALSE FALSE 3502.97755 3151.55169 3453.478108 1740.519571 2584.414736 3055.534544 2794.262906 3068.896825 2750.88525 3522.640211 0.994418204 0.894656139 0.980366402 0.494095186 0.733658444 0.867398985 0.793229719 0.871192243 0.780915758 1 11.78244142 -9.462115464 24.99995712 0.987107895 0.757373442 0.299211759 0.121452058 138.4945702 56981.05891 0.015691234 0.023968737 3.45E-10 9.462115464 -0.229734453 TSVSQNVIPS(ph)SAQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSVSQNVIPSSAQK 14 0 H0Y8J2;Q03188;Q03188-2 H0Y8J2 CENPC Centromere protein C 1 0 TSVSQNVIPS(0.5)S(0.5)AQK 89.266 0.019914 12652000 3485.5 3246.4 3657 3076.9 1880.1 1548.8 1155.9 1681.3 4185.5 3815.5 TRUE FALSE FALSE 3443.017385 3292.102904 3720.648551 3432.665655 1784.151481 1449.836679 1254.082117 1729.945763 3811.138397 3716.37276 0.926445652 0.885837648 1.001150528 0.923660213 0.480078721 0.390121436 0.337447882 0.465493069 1.025499497 1 11.8596795 -8.734602128 3.765112481 0.960398421 0.397400381 0.968996609 0.047714155 0.025782124 0.778706506 0.007007458 0.014110325 1.84E-09 8.734602128 -0.56299804 down PSPGTPT(ph)SPSNLTSGLK ddPTM_HeLa_Romidepsin_16h_R1 1 PSPGTPTSPSNLTSGLK 17 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 PSPGT(0.002)PT(0.658)S(0.329)PS(0.011)NLTSGLK 166.64 5.82E-07 0 973.98 826.7 916.8 587.92 527.69 457.16 546.91 610.19 1081.9 976.28 TRUE FALSE FALSE 962.1087571 838.3383043 932.7565194 655.8980766 500.7600102 427.9489514 593.3645217 627.8448849 985.1321543 950.9161049 1.011770389 0.881611217 0.980903062 0.689753884 0.526607981 0.450038599 0.623992504 0.660252657 1.035982196 1 9.893174254 -9.160504446 2.548275458 0.99544274 0.561273722 0.900770195 0.065916007 0.060695548 0.76896744 0.010380643 0.018294464 6.91E-10 9.160504446 -0.434169018 PSQLSTPAAS(ph)PSASEPR ddPTM_HeLa_Romidepsin_16h_R1 1 PSQLSTPAASPSASEPR 17 0 K7EL01;Q5XUX1;Q5XUX1-2 K7EL01 FBXW9 F-box/WD repeat-containing protein 9 1 0 PSQLS(0.002)T(0.053)PAAS(0.847)PS(0.093)AS(0.005)EPR 155.49 6.13E-05 5603100 870.73 1072.5 806.82 581.5 674.55 919.27 817.83 794.4 999.62 935.2 TRUE FALSE FALSE 860.1172078 1087.598683 820.8623637 648.735766 640.1251964 860.5316138 887.2964598 817.3847106 910.2114836 910.9033692 0.944246379 1.19397811 0.901151968 0.712189446 0.702736666 0.944701318 0.974084068 0.897334161 0.99924044 1 9.831154207 -9.531729857 24.96743995 0.992226172 0.846400005 0.395922303 0.105037052 191.738005 540857.6511 0.017465579 0.024721391 2.94E-10 9.531729857 -0.145826167 PSQLSTPAASPS(ph)ASEPR ddPTM_HeLa_Romidepsin_16h_R1 1 PSQLSTPAASPSASEPR 17 0 K7EL01;Q5XUX1;Q5XUX1-2 K7EL01 FBXW9 F-box/WD repeat-containing protein 9 1 0 PSQLSTPAAS(0.009)PS(0.633)AS(0.358)EPR 135.79 0.0013738 6186600 1819.8 1421.1 1481.3 998.59 1501 1328.5 1830.4 1305.6 1701.6 1788.9 TRUE FALSE FALSE 1797.619578 1441.106283 1507.081405 1114.051674 1424.398369 1243.613138 1985.87413 1343.375476 1549.404634 1742.42412 1.031677395 0.827069751 0.864933737 0.639368832 0.81748086 0.713725851 1.139719146 0.770980762 0.889223592 1 10.76688011 -10.25816726 24.11871031 1.014958773 0.826733269 0.198829839 0.129151934 144.8875138 1067963.816 0.020020616 0.023979938 5.52E-11 10.25816726 -0.188225503 PSS(ph)PGGLPEEDSVLFNK ddPTM_HeLa_Romidepsin_16h_R1 2 PSSPGGLPEEDSVLFNK 17 0 A0A0U1RQY6;A0A0C4DG54;Q5R372-2;Q5R372-4;Q5R372;Q5R372-3 A0A0U1RQY6 RABGAP1L Rab GTPase-activating protein 1-like 1 0 PS(0.023)S(0.977)PGGLPEEDSVLFNK;PS(0.018)S(0.981)PGGLPEEDS(0.002)VLFNK ; 173.71 1.30E-06 7886700 3759.6 3579.6 4017.5 2867.2 3745.9 3606.8 3206.8 3674.5 3101.9 3747.5 TRUE FALSE FALSE 3713.776549 3629.993703 4087.422902 3198.719155 3554.732745 3376.33712 3479.185512 3780.81586 2824.458295 3650.13941 1.017434167 0.994480839 1.119799121 0.876327941 0.973862186 0.924988539 0.953165105 1.0358004 0.773794636 1 11.83373585 -9.244024655 24.99458018 1.014798545 0.952469363 0 0.091488621 821.5448824 1179128.175 0.007132208 0.011804844 5.70E-10 9.244024655 -0.062329182 PSSS(ph)Y(ph)AS(ph)DHDIIVS(ph)IFYTIVIPK ddPTM_HeLa_Romidepsin_16h_R1 1 PSSSYASDHDIIVSIFYTIVIPK 23 0 A0A2C9F2M2;Q8NGG3 A0A2C9F2M2 OR5T3 Olfactory receptor 5T3 4 0 PS(0.335)S(0.335)S(0.716)Y(0.702)AS(0.896)DHDIIVS(0.891)IFY(0.059)T(0.067)IVIPK 41.912 0.025274 10080000 2899 2909.1 2633.3 315.54 2599.9 2207 1932.3 2297.8 3078 3041 TRUE FALSE FALSE 2863.665873 2950.054386 2679.131482 352.0242195 2467.217401 2065.979823 2096.429514 2364.283218 2802.695971 2961.994382 0.966803276 0.995968934 0.904502554 0.118847025 0.832958164 0.697496199 0.70777633 0.798206517 0.946219206 1 11.53235319 -9.501537653 24.96820854 0.983115202 0.636371643 0.448063948 0.185359398 500.8166023 585935.876 0.02680327 0.040689205 3.15E-10 9.501537653 -0.346743559 IDAGTMAEPSAS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 2 IDAGTMAEPSASPSKR 16 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 0 IDAGTMAEPS(0.057)AS(0.939)PS(0.004)KR;IDAGTMAEPS(0.197)AS(0.755)PS(0.049)KR ; 102.63 0.0035892 8469800 4301.8 5018.4 4562.7 4231 2543.4 2115.46 2177.8 1998.77 5091.5 4937.6 TRUE FALSE FALSE 4249.368007 5089.049167 4642.11188 4720.208127 2413.600807 1980.288933 2362.782278 2056.601256 4636.103488 4809.32044 0.883569323 1.058163878 0.965232393 0.981470914 0.501859013 0.411760655 0.491292337 0.427628244 0.963983071 1 12.23161734 -8.7336406 5.734742465 0.957535425 0.452301512 0.965136105 0.04812892 0.02749377 2.561138532 0.008449724 0.016714008 1.85E-09 8.7336406 -0.505233912 down PSSTTPTPLVSETGGNS(ph)PSDKVDNELK ddPTM_HeLa_Romidepsin_16h_R1 1 PSSTTPTPLVSETGGNSPSDKVDNELK 27 1 A0A3B3IRW6;Q2KHR3-2;Q2KHR3;H0YCQ7 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 1 0 PSSTT(0.001)PT(0.003)PLVS(0.085)ET(0.093)GGNS(0.753)PS(0.064)DKVDNELK 58.938 0.0012183 24318000 1288.2 1310.3 1511.9 1117.2 762.11 864.54 843.48 569.57 1206.5 1525.2 TRUE FALSE FALSE 1272.498923 1328.746438 1538.213985 1246.375921 723.2166829 809.2986842 915.1251701 586.0496093 1098.587618 1485.575084 0.856569915 0.894432366 1.035433349 0.838985477 0.486826072 0.54477131 0.61600735 0.394493429 0.73950326 1 10.53680581 -8.849842983 4.250818877 0.934155905 0.51987739 0.798409183 0.094081334 0.055842188 1.866897214 0.011711425 0.022037355 1.41E-09 8.849842983 -0.414278515 PST(ph)T(ph)HTFRQSDT(ph)PRK ddPTM_HeLa_Romidepsin_16h_R1 1 PSTTHTFRQSDTPRK 15 2 H0Y965;A5PLN7-2;A5PLN7-4;A5PLN7 H0Y965 FAM149A Protein FAM149A 3 0 PS(0.128)T(0.744)T(0.797)HT(0.332)FRQS(0.234)DT(0.766)PRK 57.267 0.025222 22023000 2354.6 795.71 1107.9 1082.7 4422.8 2498 3426.5 1866.9 4841.3 2551.9 TRUE FALSE FALSE 2325.90123 806.9120263 1127.182535 1207.886868 4197.088012 2338.385862 3717.546824 1920.915806 4408.282003 2485.60127 0.935749936 0.324634541 0.453484856 0.485953593 1.688560455 0.940772718 1.495632815 0.772817358 1.773527418 1 11.27937917 -8.77164762 24.99996849 0.841954979 1.223554029 0.156377505 0.449472668 249.3133303 610568.5205 0.053141082 0.097110819 1.69E-09 8.77164762 0.38159905 PST(ph)VNELES(ph)GQIS(ph)YDEVGERIK ddPTM_HeLa_Romidepsin_16h_R1 1 PSTVNELESGQISYDEVGERIK 22 1 P15924-2;P15924-3;P15924 P15924-2 DSP Desmoplakin 3 0 PS(0.17)T(0.831)VNELES(0.958)GQIS(0.964)Y(0.078)DEVGERIK 56.327 0.0089476 50818000 1405.9 1488.8 1086.8 1148.1 1002.3 1141.2 1078.2 1004.7 1358.1 1278.2 TRUE FALSE FALSE 1388.76435 1509.759365 1105.715298 1280.848724 951.1488909 1068.281003 1169.782281 1033.769409 1236.628135 1244.99218 1.11548038 1.212665742 0.888130316 1.028800618 0.763979812 0.85806242 0.939590063 0.830342091 0.993281849 1 10.28192096 -9.235232718 1.752372149 1.064595964 0.862434645 0.495474945 0.091673057 0.22334621 1.338395664 0.014712259 0.026653953 5.82E-10 9.235232718 -0.202161319 PSTQPRPDS(ph)WGEDNWEGLETDSR ddPTM_HeLa_Romidepsin_16h_R1 2 PSTQPRPDSWGEDNWEGLETDSR 23 1 E9PPN3;E9PS17;Q96KG9-3;Q96KG9-2;Q96KG9;H0YDH0 E9PPN3 SCYL1 N-terminal kinase-like protein 1 0 PSTQPRPDS(1)WGEDNWEGLETDSR;PS(0.004)T(0.004)QPRPDS(0.991)WGEDNWEGLETDSR ; 170.32 9.64E-13 80076000 2577.8 2527 2311.4 2773.6 2647.1 2711.8 2854.4 2534.2 2293.5 2944.4 TRUE FALSE FALSE 2546.380782 2562.575172 2351.628947 3094.296682 2512.008609 2538.524732 3096.852665 2607.523079 2088.363616 2867.904064 0.887889108 0.893535877 0.819981734 1.078940095 0.875903989 0.885149808 1.079831332 0.909208614 0.728184615 1 11.48578105 -7.785609535 24.9996133 0.934123225 0.994520221 0.036392432 0.102410718 394.0968258 407621.3512 0.011200799 0.033625875 1.64E-08 7.785609535 0.060396996 PSVMTPT(ph)EGLDT(ph)GEMSNST(ph)SSLK ddPTM_HeLa_Romidepsin_16h_R1 1 PSVMTPTEGLDTGEMSNSTSSLK 23 0 Q9C000-7;Q9C000-6;Q9C000-5;Q9C000-3;Q9C000-2;Q9C000-4;Q9C000 Q9C000-7 NLRP1 "NACHT, LRR and PYD domains-containing protein 1" 3 0 PS(0.044)VMT(0.272)PT(0.702)EGLDT(0.752)GEMS(0.136)NS(0.186)T(0.373)S(0.373)S(0.163)LK 40.384 0.0041325 0 371.25 467.63 412.66 281.03 251.76 459.05 352.89 240.83 518.46 522.81 TRUE FALSE FALSE 366.7250622 474.2133074 419.8421742 313.5240109 238.9117478 429.7181865 382.8644678 247.7980361 472.0876391 509.2273208 0.720159833 0.931240898 0.824469067 0.615685762 0.46916522 0.84386318 0.751853744 0.486615753 0.927066596 1 8.992166014 -9.346501123 4.613400373 0.868993849 0.642785295 0.497183245 0.124393 0.191210045 7.241122686 0.022494701 0.034896863 4.50E-10 9.346501123 -0.226208553 PT(ph)PT(ph)FHS(ph)S(ph)RTSLAGDTSNSS(ph)SPASTGAK ddPTM_HeLa_Romidepsin_16h_R1 1 PTPTFHSSRTSLAGDTSNSSSPASTGAK 28 1 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5;H0Y4F5;H0Y6T5;H0Y314 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 5 0 PT(0.878)PT(0.684)FHS(0.61)S(0.61)RT(0.5)S(0.5)LAGDT(0.186)S(0.03)NS(0.075)S(0.417)S(0.221)PAS(0.136)T(0.153)GAK 44.183 0.028698 37687000 4958.3 1710.7 2735 105.27 3221.4 1991.6 4201.8 2848.2 5018.1 3775.2 TRUE FALSE FALSE 4897.866332 1734.78328 2782.601528 117.4418127 3056.999937 1864.343188 4558.700787 2930.608173 4569.268568 3677.11976 1.331984448 0.471777748 0.756733995 0.031938534 0.831357186 0.507011822 1.239747706 0.796984696 1.242621635 1 11.84436045 -10.2626656 24.99977981 1.156770436 0.66436324 0.391306793 0.301584511 90.45589805 1844183.355 0.052568064 0.061903431 5.46E-11 10.2626656 -0.492407196 PTEATVSLS(ph)SLVDYPHQAR ddPTM_HeLa_Romidepsin_16h_R1 2 PTEATVSLSSLVDYPHQAR 19 0 Q92619;K7ES92;F5H1R4;K7ES98;K7EM85;Q92619-2 Q92619 HMHA1 Minor histocompatibility protein HA-1;Minor histocompatibility antigen HA-1 1 0 PTEATVSLS(0.973)S(0.027)LVDYPHQAR;PTEATVS(0.001)LS(0.959)S(0.04)LVDYPHQAR ; 151.2 9.88E-06 5430600 7357.8 6897.5 7103.1 2549.6 7171.8 7657.2 6020.7 7158.7 6989.7 6985.2 TRUE FALSE FALSE 7268.120304 6994.603186 7226.726476 2844.396748 6805.796284 7167.929632 6532.098108 7365.82569 6364.523726 6803.723497 1.068256273 1.02805518 1.062172277 0.418064718 1.000304655 1.053530414 0.960076951 1.082616848 0.935447146 1 12.7321088 PTGGGS(ph)SPPEIR ddPTM_HeLa_Romidepsin_16h_R1 1 PTGGGSSPPEIR 12 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 0 PTGGGS(0.698)S(0.301)PPEIR 98.337 0.017268 3239600 2610.6 2206.4 2296.6 1837.6 2179.5 2317.2 1837.7 1989.9 1999.1 2122.3 TRUE FALSE FALSE 2578.781003 2237.461757 2336.57136 2050.071958 2068.271982 2169.138398 1993.794192 2047.474617 1820.295489 2067.16234 1.247498057 1.082383185 1.130327945 0.991732443 1.000536795 1.049331422 0.964507796 0.990475967 0.880576941 1 11.01343598 -9.260173175 24.58069814 1.117624583 1.0002294 0 0.095995856 93.43276896 1813779.473 0.014157798 0.022651649 5.49E-10 9.260173175 -0.117395183 PTHS(ph)GGGGGGGGGGGGGGGGR ddPTM_HeLa_Romidepsin_16h_R1 1 PTHSGGGGGGGGGGGGGGGGR 21 0 Q13595;Q13595-4;Q13595-3 Q13595 TRA2A Transformer-2 protein homolog alpha 1 0 PT(0.071)HS(0.929)GGGGGGGGGGGGGGGGR 53.865 0.015685 206540 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 PTLLANGGHGVEGS(ph)DTTGSPTEFLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 PTLLANGGHGVEGSDTTGSPTEFLEEK 27 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;H7C456;A0A0J9YW37 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 PTLLANGGHGVEGS(0.314)DT(0.244)T(0.244)GS(0.099)PT(0.099)EFLEEK 56.783 0.001744 12102000 1526.4 1708.5 1560 1299.5 2042.3 1781.8 1415.4 2027.7 1949.3 1736.1 TRUE FALSE FALSE 1507.79565 1732.552308 1587.151146 1449.754304 1938.07381 1667.94873 1535.624041 2086.3683 1774.949726 1690.995872 0.891661343 1.024575126 0.938589604 0.857337578 1.146113863 0.98637067 0.908118149 1.233810404 1.049647581 1 10.72365742 -7.254768456 24.83833538 0.959770099 1.233810541 0.452578853 0.082204291 440.9709351 1641852.423 0.01078337 0.139074668 5.56E-08 7.254768456 0.274040442 PTLLANGGHGVEGSDTTGS(ph)PTEFLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 PTLLANGGHGVEGSDTTGSPTEFLEEK 27 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;H7C456;A0A0J9YW37 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 PTLLANGGHGVEGS(0.133)DT(0.216)T(0.036)GS(0.451)PT(0.164)EFLEEK 91.151 1.55E-07 11561000 1639 1368.6 1631.3 1334.1 1629.6 1539.4 1544.2 1796.2 1708.6 1908 TRUE FALSE FALSE 1619.023238 1387.867187 1659.692092 1488.354919 1546.435431 1441.037308 1675.364309 1848.170213 1555.778537 1858.429885 0.871178004 0.74679556 0.893061452 0.800866867 0.83211933 0.775405798 0.901494494 0.994479387 0.837146749 1 10.85986854 -11.72503848 0.834544453 0.993134321 0.847545571 0 0.082765008 0.42311329 0.584295694 0.033388795 0.014175711 1.88E-12 11.72503848 -0.145588751 PTS(ph)PVST(ph)DSNMSAAVMQK ddPTM_HeLa_Romidepsin_16h_R1 1 PTSPVSTDSNMSAAVMQK 18 0 A0A0A0MSX4;Q9Y6N7-4;Q9Y6N7-3;Q9Y6N7;Q9Y6N7-2;A0A087WZ85;A0A087WTM1;Q9Y6N7-6;Q9Y6N7-5 A0A0A0MSX4 ROBO1 Roundabout homolog 1 2 0 PT(0.458)S(0.541)PVS(0.003)T(0.502)DS(0.263)NMS(0.233)AAVMQK 72.315 0.0017266 0 702.69 553.94 568.93 412.16 787.61 728.25 716.1 575.06 704.83 599.86 TRUE FALSE FALSE 694.125344 561.7383819 578.831988 459.8158785 747.4153227 681.7171753 776.9255161 591.6984538 641.7882395 584.2755507 1.188010252 0.961427157 0.990683227 0.786984631 1.279217181 1.166773408 1.329724503 1.012704456 1.098434187 1 9.19050511 NSNS(ph)PPS(ph)PSSMNQR ddPTM_HeLa_Romidepsin_16h_R1 1 NSNSPPSPSSMNQR 14 0 Q7Z5L9;Q7Z5L9-2;Q7Z5L9-3 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 2 0 NS(0.005)NS(0.977)PPS(0.962)PS(0.03)S(0.025)MNQR 123.72 0.0079667 42839000 9356.3 9966.3 8166.1 7817.8 3768.1 2679.6 2257.1 2554.4 10246 9303.5 TRUE FALSE FALSE 9242.261817 10106.60583 8308.227545 8721.73082 3575.799796 2508.382208 2448.818018 2628.307534 9329.572098 9061.793729 1.019915272 1.115298597 0.916841389 0.962472892 0.394601765 0.276808575 0.270235462 0.290042746 1.029550261 1 13.14558094 -8.733581396 3.36670966 1.011493424 0.28288897 0.982270382 0.046256901 0.020800268 0.489232979 0.006845534 0.01394075 1.85E-09 8.733581396 -0.728604454 down PTTQQS(ph)PQDEQEK ddPTM_HeLa_Romidepsin_16h_R1 1 PTTQQSPQDEQEK 13 0 Q96QK1;I3L4S0;A0A1W2PP10;A0A3B3ITD4 Q96QK1 VPS35 Vacuolar protein sorting-associated protein 35 1 0 PT(0.001)T(0.016)QQS(0.984)PQDEQEK 89.507 0.023127 3357900 1551.4 1796.2 1656.7 1226 1326.3 2225.3 1790.1 1915.4 1785.1 2109.8 TRUE FALSE FALSE 1532.49094 1821.486951 1685.534169 1367.755889 1258.613962 2083.110512 1942.151049 1970.819077 1625.436185 2054.987092 0.745742368 0.886373913 0.820216426 0.665578822 0.612468062 1.013685448 0.945091605 0.959042071 0.790971482 1 11.00491362 PTYPELMQHPFFTLHESK ddPTM_HeLa_Romidepsin_16h_R1 1 PTYPELMQHPFFTLHESK 18 0 P52564;P52564-2 P52564 MAP2K6 Dual specificity mitogen-activated protein kinase kinase 6 0 0 58.814 0.016968 1042100 233.21 214.24 164.4 288.91 302.79 379.46 368.21 248.56 248.55 229.58 FALSE FALSE TRUE 230.3675468 217.2560763 167.261313 322.3151336 287.3374964 355.2137307 399.4857482 255.7516914 226.3190655 223.6154785 1.030194995 0.971560993 0.747986294 1.441381141 1.284962465 1.588502428 1.786485224 1.143711934 1.012090339 1 7.804876244 -9.191376805 8.417755001 0.99272263 1.467775131 0.656600177 0.17814795 0.170482001 19.14244271 0.025614874 0.042533796 6.44E-10 9.191376805 0.475052501 PVATASLSSPS(ph)AVHMDAVEPTTPAS(ph)QAPK ddPTM_HeLa_Romidepsin_16h_R1 1 PVATASLSSPSAVHMDAVEPTTPASQAPK 29 0 Q9NWQ4-4;Q9NWQ4 Q9NWQ4-4 GPATCH2L G patch domain-containing protein 2-like 2 0 PVAT(0.008)AS(0.032)LS(0.137)S(0.137)PS(0.661)AVHMDAVEPT(0.325)T(0.325)PAS(0.375)QAPK 41.763 0.0041378 0 331.83 409.34 347.38 238.12 271.29 278.89 252.89 334.84 348.43 334.36 TRUE FALSE FALSE 327.7855283 415.1026993 353.4260032 265.6525548 257.445059 261.0698291 274.3704703 344.5280671 317.2655481 325.673279 1.006485793 1.274598581 1.085216461 0.815702644 0.790501019 0.801631101 0.842471544 1.057894796 0.974183541 1 8.347281543 -9.258692267 24.98041094 1.033427 0.853289273 0.463030398 0.107797495 198.0073852 1800544.458 0.017077586 0.027509102 5.51E-10 9.258692267 -0.180137727 PVDMS(ph)KY(ph)LYADS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 PVDMSKYLYADSSK 14 1 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 3 0 PVDMS(0.94)KY(0.93)LY(0.179)ADS(0.565)S(0.386)K 52.79 0.026109 2995700 939.26 1009 1117.7 172.13 1158.5 1139.9 897.74 1121.8 1093.8 1095.2 TRUE FALSE FALSE 927.8119378 1023.204728 1137.1531 192.0324805 1099.377422 1067.064069 973.9940132 1154.257513 995.9677885 1066.746546 0.869758558 0.959182603 1.066001201 0.18001697 1.030589155 1.000297655 0.913051012 1.082035388 0.933649884 1 10.05900172 -12.23038342 0.739621097 1.008457233 0.879712288 0.012840254 0.247749536 2.937763816 2.584462413 0.23225149 0.049823587 5.88E-13 12.23038342 -0.128744945 PVIPVLSS(ph)T(ph)ILPST(ph)Y(ph)QIR ddPTM_HeLa_Romidepsin_16h_R1 1 PVIPVLSSTILPSTYQIR 18 0 Q99570 Q99570 PIK3R4 Phosphoinositide 3-kinase regulatory subunit 4 4 0 PVIPVLS(0.623)S(0.689)T(0.689)ILPS(0.033)T(0.971)Y(0.997)QIR 50.376 0.0040456 0 1049.8 1114.2 1178.9 674.93 1053.1 1008 1097 1183.7 1075.8 1266.3 TRUE FALSE FALSE 1037.004634 1129.885737 1199.41826 752.9685822 999.3563773 943.5920532 1190.179153 1217.948492 979.5777536 1233.401343 0.840768205 0.916073055 0.972447668 0.610481403 0.810244275 0.765032451 0.964956913 0.987471352 0.794208437 1 10.26842661 -12.34710909 0.619802578 1.024507754 0.85049518 0 0.125900019 1.587647404 0.84967953 0.158066537 0.024879934 4.50E-13 12.34710909 -0.174012574 PVIVEPLEQLDDEDGLPEK ddPTM_HeLa_Romidepsin_16h_R1 2 PVIVEPLEQLDDEDGLPEK 19 0 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 0 ; ; 178.99 1.33E-10 6389700 9194.1 8594.2 9350.3 6206 7815.2 7396.2 7991.9 6872.9 8964.3 10346.9 FALSE FALSE TRUE 9082.038773 8715.189373 9513.038049 6923.56692 7416.361181 6923.60669 8670.731787 7071.756518 8162.510556 10078.08605 0.90116702 0.864766319 0.943933005 0.686992241 0.735889845 0.686996187 0.860355007 0.701696382 0.809926659 1 13.29893406 -9.89308629 0.578445969 0.977820492 0.730394287 0.363879704 0.085353562 0.334254419 0.239990409 0.019646833 0.031297988 1.28E-10 9.89308629 -0.247426204 PVS(ph)SAASVYAGAGGSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 PVS(0.499)S(0.499)AAS(0.003)VYAGAGGSGSR 165.16 6.27E-07 13518000 603.11 595.66 724.47 446.51 766.11 702.65 475.68 562.72 587.75 686.74 TRUE FALSE FALSE 595.7590633 604.0457171 737.0790964 498.1375871 727.0125479 657.7529327 516.0842473 579.0014154 535.180168 668.8983958 0.890657037 0.903045546 1.101929831 0.744713383 1.086880388 0.983337584 0.771543557 0.865604431 0.800091869 1 9.385643275 -11.92562949 0.012627479 1.911970715 3.19E-07 0 0.1226319 3755.261958 14.33092008 1134.10942 1036.141584 1.19E-12 11.92562949 -1.911970396 PVS(ph)VAGSPLSPGPVR ddPTM_HeLa_Romidepsin_16h_R1 1 PVSVAGSPLSPGPVR 15 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 PVS(0.964)VAGS(0.033)PLS(0.003)PGPVR 111.88 0.004103 19183000 3447.5 2796.5 2867.9 3001.8 2225.1 2054.3 2241.6 2202.9 3482.5 3439.8 TRUE FALSE FALSE 3405.480544 2835.8692 2917.814596 3348.88224 2111.544844 1923.03686 2432.001448 2266.637436 3171.016478 3350.4335 1.016429827 0.84641859 0.870876738 0.999536997 0.63023034 0.573966581 0.725876651 0.676520646 0.94644961 1 11.71013206 -8.761880866 24.99998343 0.982573539 0.651401806 0.811580868 0.068321961 3.562921497 201776.2638 0.011107687 0.021068151 1.73E-09 8.761880866 -0.331171733 PVSS(ph)AASVYAGAGGSGSR ddPTM_HeLa_Romidepsin_16h_R1 2 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 PVS(0.052)S(0.832)AAS(0.116)VYAGAGGSGSR;PVS(0.308)S(0.692)AASVYAGAGGSGSR ; 149.31 5.25E-05 55164000 2153.38 2203.68 1853.9 1836.39 2290.99 1908.25 1738.96 1763.98 1933.17 2073.74 TRUE FALSE FALSE 2127.133776 2234.703465 1886.166352 2048.722052 2174.072231 1786.318984 1886.667219 1815.017978 1760.262433 2019.863936 1.053107459 1.106363367 0.933808619 1.014287159 1.076345883 0.884375899 0.934056589 0.898584279 0.871475748 1 10.9800424 -8.253922747 24.99673434 1.026977086 0.908510683 0.303388398 0.066712594 314.3848231 1045490.941 0.006459882 0.016126145 5.57E-09 8.253922747 -0.118466403 PVSSAAS(ph)VYAGAGGSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 PVS(0.015)S(0.231)AAS(0.753)VYAGAGGS(0.002)GSR 139 0.00066761 35630000 1279.5 1370.1 1271.1 1258.4 1598.7 920.09 992.74 1213.1 1241.5 1073.3 TRUE FALSE FALSE 1263.904962 1389.388304 1293.222962 1403.902129 1517.112373 861.2992185 1077.063311 1248.199135 1130.457131 1045.415511 1.208997713 1.329029739 1.237042064 1.342913046 1.45120515 0.823882188 1.030272939 1.193974186 1.081347195 1 10.02986076 -6.101548992 15.2164874 1.143770752 1.159632107 0 0.179929461 0 0 0.025443323 0 7.92E-07 6.101548992 0.015861356 PVSSAASVYAGAGGS(ph)GSR ddPTM_HeLa_Romidepsin_16h_R1 2 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 PVSSAASVYAGAGGS(0.99)GS(0.01)R;PVSSAASVYAGAGGS(0.727)GS(0.273)R ; 220.78 4.85E-38 433000000 4399.2 3962.1 4203.2 4137.1 4616.1 3710.4 3063 3126.7 3935 4656 TRUE FALSE FALSE 4345.580858 4017.878548 4276.354933 4615.450968 4380.523192 3473.317415 3323.171144 3217.166131 3583.043745 4535.036449 0.95822402 0.885963893 0.94295933 1.017731835 0.965928993 0.765885226 0.732777163 0.709402486 0.790080473 1 12.14689843 -8.214586927 3.666005054 0.972358057 0.726974723 0.63256535 0.067134307 0.054452899 1.518002565 0.00560965 0.015022542 6.10E-09 8.214586927 -0.245383335 PVSSAASVYAGAGGSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 PVSSAASVYAGAGGSGSR 18 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 0 203.85 3.51E-26 2087200 333.01 136.64 140.61 214.04 428.13 426 356.16 475.47 265.68 214.07 FALSE FALSE TRUE 328.951146 138.5636215 143.0572581 238.7883119 406.2809285 398.7799749 386.4122215 489.2269743 241.9169154 208.5084305 1.577639548 0.664546854 0.686098196 1.145221377 1.948510799 1.912536456 1.853221093 2.346317475 1.160226063 1 7.703961907 -8.747979688 6.990861309 1.171121174 1.999774136 0.722484165 0.28951492 0.086679431 19.35296965 0.052000196 0.101371308 1.79E-09 8.747979688 0.828652962 PVSVAGS(ph)PLSPGPVR ddPTM_HeLa_Romidepsin_16h_R1 1 PVSVAGSPLSPGPVR 15 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 PVS(0.281)VAGS(0.513)PLS(0.205)PGPVR 90.476 0.015677 17781000 1918.8 1739.6 1605.4 1480.2 1209.3 832.84 877.5 852.41 1552 1713.7 TRUE FALSE FALSE 1895.412928 1764.090134 1633.341314 1651.347689 1147.584908 779.6242119 952.0348281 877.0731385 1413.185233 1669.177827 1.135536848 1.056861711 0.97853044 0.989318011 0.687515069 0.467070793 0.570361535 0.525452186 0.846635517 1 10.70492195 -8.694656236 2.171327498 1.058855907 0.52275738 0.873341737 0.082197513 0.0504113 0.482935004 0.009314687 0.020940439 2.02E-09 8.694656236 -0.536098527 PVSVAGSPLS(ph)PGPVR ddPTM_HeLa_Romidepsin_16h_R1 3 PVSVAGSPLSPGPVR 15 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 PVSVAGS(0.03)PLS(0.97)PGPVR;PVSVAGS(0.009)PLS(0.991)PGPVR;PVSVAGS(0.002)PLS(0.998)PGPVR ;; 132.23 0.0016652 154047000 4672.6 4959.62 5002.9 3917.8 4747.52 4899.25 4184.55 4751.2 4979.1 4621.48 TRUE FALSE FALSE 4615.648554 5029.441661 5089.973376 4370.79447 4505.236339 4586.203737 4539.985573 4888.668476 4533.756826 4501.413283 1.025377646 1.117302799 1.130750068 0.97098271 1.000849301 1.018836407 1.008568929 1.086029691 1.007185197 1 12.13616231 -10.78674883 2.661284653 1.008880974 1.044489787 0.104762974 0.049015085 0.480452887 7.017782815 0.010183409 0.010021919 1.63E-11 10.78674883 0.035608813 PWSS(ph)T(ph)DSDGS(ph)VRS(ph)MR ddPTM_HeLa_Romidepsin_16h_R1 2 PWSSTDSDGSVRSMR 15 1 H7C0E9;A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5-2;Q9Y2K5;H0YIX9 H7C0E9 R3HDM2 R3H domain-containing protein 2 4 0 PWS(0.445)S(0.559)T(0.81)DS(0.198)DGS(0.992)VRS(0.996)MR;PWS(0.171)S(0.83)T(0.99)DS(0.012)DGS(0.998)VRS(0.999)MR ; 86.214 0.008078 51178000 3340.95 3260.39 3714.7 1501.61 3523.5 3068.24 3027.55 3152.83 3582.02 3191.5 TRUE FALSE FALSE 3300.229216 3306.289856 3779.352795 1675.233213 3343.682647 2872.189366 3284.710021 3244.052162 3261.63516 3108.58437 1.061650199 1.063599846 1.215779386 0.5389055 1.075628726 0.92395413 1.056657832 1.043578612 1.049234884 1 11.60204202 PY(ph)KCNDCGKT(ph)FSQT(ph)SS(ph)LVYHR ddPTM_HeLa_Romidepsin_16h_R1 1 PYKCNDCGKTFSQTSSLVYHR 21 2 Q96IR2 Q96IR2 ZNF845 Zinc finger protein 845 4 0 PY(0.992)KCNDCGKT(0.87)FS(0.221)QT(0.727)S(0.269)S(0.715)LVY(0.206)HR 40.669 0.0043429 0 203.33 69.612 0 55.813 0 0 0 0 178.29 61.959 TRUE FALSE FALSE 200.8517358 70.59199956 0 62.26636167 0 0 0 0 162.3432959 60.34929625 3.328153736 1.169723658 0 1.03176616 0 0 0 0 2.690061127 1 5.915265042 -9.977607639 4.944550834 2.108483258 0.202862506 0.700082471 0.630283135 0.117841503 7.649840585 0.147835122 0.192300513 1.05E-10 9.977607639 -1.905620752 PY(ph)PLITPCY(ph)IK ddPTM_HeLa_Romidepsin_16h_R1 1 PYPLITPCYIK 11 0 Q9NZ56 Q9NZ56 FMN2 Formin-2 2 0 PY(1)PLIT(0.158)PCY(0.842)IK 69.721 0.0031294 0 1082.1 939.04 832.02 1627.7 1633.4 1386.7 1044 1124.1 1665.7 1036 TRUE FALSE FALSE 1068.910949 952.2598298 846.5009591 1815.902333 1550.041503 1298.094345 1132.677334 1156.62406 1516.71562 1009.084571 1.059287774 0.94368684 0.838880094 1.799554156 1.536086814 1.286407882 1.122480084 1.146211223 1.503060957 1 9.978831375 -9.293758573 24.99867 1.008149264 1.367622171 0.264624921 0.247201462 463.0924962 358197.5118 0.030963653 0.0473001 5.08E-10 9.293758573 0.359472907 PY(ph)T(ph)SLVPPLS(ph)PQPK ddPTM_HeLa_Romidepsin_16h_R1 1 PYTSLVPPLSPQPK 14 0 C9K0J5;Q70E73 C9K0J5 RAPH1 Ras-associated and pleckstrin homology domains-containing protein 1 3 0 PY(0.84)T(0.866)S(0.294)LVPPLS(1)PQPK 51.726 0.028341 3221700 925.3 1119.8 927.17 1093.9 805.16 762.9 780.8 716.32 1325.6 1114.2 TRUE FALSE FALSE 914.0220877 1135.564574 943.3070049 1220.381865 764.0696807 714.1531521 847.1211325 737.045589 1207.035016 1085.252923 0.842220341 1.046359378 0.869204758 1.124513778 0.704047567 0.658052272 0.780574845 0.679146375 1.112215402 1 10.08381559 -8.726249058 24.99322899 0.941578417 0.707434753 0.65009955 0.100341549 90.96180281 64603.4453 0.012976663 0.02595251 1.88E-09 8.726249058 -0.234143664 PYLQDYFTNANRELK ddPTM_HeLa_Romidepsin_16h_R1 1 PYLQDYFTNANRELK 15 1 Q6UVY6 Q6UVY6 MOXD1 DBH-like monooxygenase protein 1 0 0 79.089 0.013277 20654000 1719.5 1686.1 1532.2 1892 2828.6 2482.9 2408.3 2320.4 1849.3 1737.3 FALSE FALSE TRUE 1698.542073 1709.83696 1558.867298 2110.761942 2684.245987 2324.250703 2612.860942 2387.537113 1683.893976 1692.164696 1.003768769 1.010443584 0.9212267 1.247373821 1.586279394 1.373536931 1.544093757 1.410936606 0.995112344 1 10.72465428 -9.020603489 3.860349948 0.998137688 1.474294906 0.93085697 0.063203236 0.035363229 1.160553673 0.008414001 0.014982411 9.54E-10 9.020603489 0.476157219 PYQYPALT(ph)PEQK ddPTM_HeLa_Romidepsin_16h_R1 1 PYQYPALTPEQK 12 0 H3BQN4;J3KPS3;P04075;H3BUH7;H3BR04;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 1 0 PYQYPALT(1)PEQK 137.93 0.0048194 19075000 6158.2 5252.5 4943.1 4623 4556.4 4804.6 4858.7 4600.2 5361.7 5800.5 TRUE FALSE FALSE 6083.14149 5326.444833 5029.132582 5157.533012 4323.869906 4497.601566 5271.397857 4733.299529 4882.136123 5649.802174 1.07669991 0.942766608 0.890143128 0.912869664 0.765313505 0.796063548 0.93302344 0.837781463 0.864125145 1 12.46398464 -9.846635551 1.849839779 1.036066691 0.848264284 0.300904388 0.074066809 0.134481072 0.935376849 0.009544915 0.013304297 1.42E-10 9.846635551 -0.187802407 PYQYPALTPEQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PYQYPALTPEQKK 13 1 H3BQN4;J3KPS3;P04075;H3BUH7;H3BR04;H3BMQ8 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 1 ; PYQYPALTPEQK(1)K;PYQYPALTPEQK(1)K 196.27 5.89E-11 1387240 723.5 683.49 743.94 1231.88 1124.61 1076.41 977.19 771.55 795.11 593.34 FALSE TRUE FALSE 714.6817037 693.1121902 756.8879636 1374.315762 1067.216955 1007.630875 1060.192494 793.8735819 723.9933702 577.9249413 1.236634124 1.19931178 1.309664819 2.378017738 1.846635919 1.743532426 1.834481294 1.373662089 1.252746366 1 9.174738323 -9.473440918 9.08954743 1.12758704 1.832825253 0.642764035 0.237751105 0.199343679 35.34475759 0.036635467 0.055818529 3.36E-10 9.473440918 0.705238212 QAAPPIELDAVWEDIRER ddPTM_HeLa_Romidepsin_16h_R1 1 QAAPPIELDAVWEDIRER 18 1 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 0 108.96 0.0015712 2182500 857.69 822.08 645.21 677.25 791.5 729.58 706.09 817.05 872.97 791.7 FALSE FALSE TRUE 847.2361444 833.6532638 656.4396094 755.5568316 751.1068015 682.9621926 766.065267 840.6900527 794.8893768 771.1315199 1.098692146 1.081077926 0.851268029 0.979802812 0.974032032 0.8856624 0.993430105 1.090203203 1.030809086 1 9.590833129 -9.812173979 24.99999723 1.050492336 0.961640931 0.316449458 0.064940615 103.4455889 50973.38981 0.011209378 0.014732019 1.54E-10 9.812173979 -0.088851406 QAAS(ph)PLEPK ddPTM_HeLa_Romidepsin_16h_R1 2 QAASPLEPK 9 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;Q14980-4;Q14980-3;F5H6Y5;F5H4J1 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 QAAS(1)PLEPK;QAAS(1)PLEPK ; 107.97 0.021094 78498000 17217.4 16923.9 15470.1 12863.6 15359.1 15501.9 14266.8 14802.6 16998.9 15223.1 TRUE FALSE FALSE 17007.54771 17162.15511 15739.3506 14350.94996 14575.26781 14511.37862 15478.62164 15230.88988 15478.47581 14827.60167 1.147019463 1.157446463 1.06148998 0.967853755 0.982982153 0.978673352 1.043905952 1.027198479 1.043896117 1 13.85599764 -9.408847111 6.009603818 1.079331271 1.000811681 0.427805192 0.047666903 0.261281842 12.17011938 0.010192429 0.015609334 3.90E-10 9.408847111 -0.07851959 QADFEAHNILR ddPTM_HeLa_Romidepsin_16h_R1 1 QADFEAHNILR 11 0 P49915-2;P49915 P49915-2 GMPS GMP synthase [glutamine-hydrolyzing] 0 0 124.12 0.0038352 3802600 2776 2003.7 2933.8 2594.9 2818.1 2874.2 2142.6 2154.1 2800.4 2497.9 FALSE FALSE TRUE 2742.165044 2031.908141 2984.861558 2894.934547 2674.281841 2690.547896 2324.592391 2216.425485 2549.92521 2433.004198 1.12706959 0.835143705 1.226821376 1.189860071 1.09916861 1.105854194 0.955441175 0.910983009 1.048056231 1 11.24852309 -7.646309414 4.821434582 1.071467307 0.921769525 0.245636966 0.102486869 0.228430286 8.4072806 0.014530961 0.058516887 2.26E-08 7.646309414 -0.149697782 QADLYISEGLHPR ddPTM_HeLa_Romidepsin_16h_R1 3 QADLYISEGLHPR 13 0 P40227;Q92526-3;Q92526 P40227 CCT6A;CCT6B T-complex protein 1 subunit zeta;T-complex protein 1 subunit zeta-2 0 0 ;; ;; 164.92 8.88E-05 16515020 6395.28 5376.91 5075.22 5320.88 8002.64 7766.63 6391.3 6061.98 7654.05 7125 FALSE FALSE TRUE 6317.331867 5452.60628 5163.552075 5936.105181 7594.235419 7270.367409 6934.176862 6237.373827 6969.452598 6939.891473 0.910292602 0.785690425 0.744039312 0.855359944 1.094287346 1.047619756 0.999176556 0.898771091 1.004259595 1 12.76069739 -6.930554638 11.57468356 0.941754949 0.625240912 0.010476117 0.108153427 773077.6322 4480599.097 0.016174859 5439983.479 1.17E-07 6.930554638 -0.316514037 QADPQPQAWPPPDS(ph)PVRVDTVR ddPTM_HeLa_Romidepsin_16h_R1 2 QADPQPQAWPPPDSPVRVDTVR 22 1 K7ERU2;Q63ZY3-3;Q63ZY3;Q63ZY3-2 K7ERU2 KANK2 KN motif and ankyrin repeat domain-containing protein 2 1 0 QADPQPQAWPPPDS(1)PVRVDTVR;QADPQPQAWPPPDS(0.998)PVRVDT(0.002)VR ; 149.44 2.42E-06 80183000 5954.9 5706.8 5642.1 6134.2 6807.7 6277.2 6146.4 7093.3 6190.9 6121.1 TRUE FALSE FALSE 5882.319388 5787.14048 5740.298384 6843.465066 6460.277666 5876.107179 6668.475063 7298.533444 5637.170399 5962.07294 0.986623184 0.970659121 0.962802442 1.147833167 1.083562333 0.98558123 1.118482637 1.224160375 0.945505105 1 12.54159831 -9.266842168 24.96369469 0.989324115 1.103693635 0.576804395 0.058419362 282.3250464 1304486.861 0.008757887 0.013623326 5.41E-10 9.266842168 0.11436952 QAGAPGGSSGSGGS(ph)PELSALR ddPTM_HeLa_Romidepsin_16h_R1 2 QAGAPGGSSGSGGSPELSALR 21 0 Q9Y2J4;Q9Y2J4-2;Q9Y2J4-4 Q9Y2J4 AMOTL2 Angiomotin-like protein 2 1 0 QAGAPGGSS(0.001)GS(0.126)GGS(0.662)PELS(0.211)ALR;QAGAPGGS(0.001)S(0.001)GS(0.002)GGS(0.585)PELS(0.411)ALR ; 224.08 6.74E-42 28379000 6619.5 5923.4 5648.8 5389.2 4876 3713.8 3521.3 3775.1 6314.6 6836.2 TRUE FALSE FALSE 6538.818988 6006.789781 5747.114994 6012.324661 4627.159525 3476.500166 3820.399134 3884.326562 5749.806361 6658.594539 0.982011887 0.90211076 0.863112322 0.902941999 0.694915346 0.522107202 0.573754583 0.583355322 0.863516517 1 12.70100198 -8.776697643 0.972737525 0.986502797 0.534095851 0.870978996 0.060883309 0.095848187 0.173271375 0.008195149 0.025835168 1.67E-09 8.776697643 -0.452406946 QAGEVTYADAHK ddPTM_HeLa_Romidepsin_16h_R1 1 QAGEVTYADAHK 12 0 Q08170;A0A0D9SEM4;Q13247;Q13247-3;A0A590UJK4;A0A590UK01;A0A590UJP7;A0A590UK80 Q08170;Q13247 SRSF4;SRSF6 Serine/arginine-rich splicing factor 4;Serine/arginine-rich splicing factor 6 0 0 131.08 0.0016927 4188600 4686.4 4158.3 4192.1 2839 4149.6 3991.8 3823.3 3871.8 4991.3 4531.5 FALSE FALSE TRUE 4629.280354 4216.840657 4265.061742 3167.258538 3937.830428 3736.736863 4148.051007 3983.824424 4544.865627 4413.770977 1.048826588 0.955382751 0.966307895 0.71758561 0.892169179 0.84660869 0.939797517 0.902589746 1.029701281 1 12.10779606 -9.677057226 2.492072912 1.020817452 0.865143028 0.564020362 0.060973903 0.147486088 1.871421953 0.009855693 0.014328 2.10E-10 9.677057226 -0.155674424 QAGPAPAAATAASK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QAGPAPAAATAASKK 15 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 1 ; QAGPAPAAATAASK(1)K;QAGPAPAAATAASK(1)K 216.88 2.67E-25 12093700 3488.1 3673.5 2826.3 2677.83 2432.91 2633.27 2710.3 2322.69 4510.2 3201.3 FALSE TRUE FALSE 3445.585696 3725.215629 2875.490566 2987.453304 2308.749524 2465.012545 2940.512814 2389.893371 4106.796416 3118.129765 1.105016775 1.19469551 0.922184381 0.958091398 0.74042766 0.790542002 0.943037345 0.766450902 1.3170704 1 11.60646525 -9.234539694 2.000020597 1.059966521 0.822989994 0.586098866 0.114983797 0.162286056 1.266332075 0.013456599 0.023801619 5.83E-10 9.234539694 -0.236976527 QAGPASVPLRTEEEFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 QAGPASVPLRTEEEFKK 17 2 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 1 QAGPASVPLRTEEEFK(1)K 107.5 0.00017595 0 301.32 200.78 189.88 144.62 376.89 454.73 301.47 240.56 369.2 239.18 FALSE TRUE FALSE 297.6473959 203.6065861 193.1847817 161.3416449 357.6558969 425.6742206 327.0768543 247.5202241 336.1778273 232.9660691 1.277642693 0.873975283 0.829239994 0.692554265 1.535227419 1.827194072 1.403967777 1.062473282 1.443033437 1 7.863976035 -8.728109923 24.99999529 1.060168494 1.479839569 0.38215397 0.269130349 160.4137226 120323.6348 0.038798508 0.077593291 1.87E-09 8.728109923 0.419671076 QAHDLS(ph)PAAESSSTFSFSGR ddPTM_HeLa_Romidepsin_16h_R1 4 QAHDLSPAAESSSTFSFSGR 20 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 QAHDLS(0.996)PAAES(0.003)S(0.001)STFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR;QAHDLS(1)PAAESSSTFSFSGR ;;; 114.34 0.00012065 91591700 7377.3 6636 5997.6 6307.27 8437.4 7882.3 7560.2 7564.1 8526 7487 TRUE FALSE FALSE 7287.38263 6729.421782 6101.985712 7036.546234 8006.807994 7378.646469 8202.363199 7782.955299 7763.413206 7292.486661 0.999300097 0.922788357 0.836749657 0.964903545 1.097953053 1.011814874 1.124769037 1.067256707 1.06457695 1 12.83219513 -8.76537331 24.99433449 0.977505505 1.074426071 0.424315337 0.062118379 84.54472455 537161.2458 0.009229027 0.017183133 1.72E-09 8.76537331 0.096920566 QALDS(ph)EEEEEDVAAK ddPTM_HeLa_Romidepsin_16h_R1 2 QALDSEEEEEDVAAK 15 0 Q8NC44;H7C3D5 Q8NC44 FAM134A Protein FAM134A 1 0 QALDS(1)EEEEEDVAAK;QALDS(1)EEEEEDVAAK ; 186.17 6.59E-09 56387000 7440.5 7103.5 7376.5 4863.3 6637.5 8960.9 5937.4 8686.2 8052.1 7241.1 TRUE FALSE FALSE 7349.812324 7203.503259 7504.884888 5425.617629 6298.763607 8388.32741 6441.722608 8937.521492 7331.900009 7052.975178 1.042086799 1.021342494 1.064073628 0.769266514 0.893064763 1.189331764 0.913334082 1.267198773 1.039547116 1 12.78401625 -7.248666178 24.46145203 1.004098022 1.267198999 0.36387475 0.107997633 1299.533893 2488628.672 0.014257045 0.334120782 5.64E-08 7.248666178 0.263100977 QALDYVELSPLTQAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 QALDYVELSPLTQASPQR 18 0 F6WYE2;F6TR96;H0Y5J9;Q9H2D6-6;Q9H2D6-5;Q9H2D6-7;Q9H2D6-3;Q9H2D6-2;Q9H2D6 F6WYE2 TRIOBP TRIO and F-actin-binding protein 1 0 QALDYVELSPLTQAS(1)PQR;QALDYVELSPLTQAS(1)PQR ; 221.81 4.38E-38 91092000 8268.8 8080.5 7352.9 8805.5 7388.8 5486.5 4522 4476.2 8809.1 7773.1 TRUE FALSE FALSE 8168.016685 8194.257491 7480.87414 9823.633341 7011.721965 5135.930357 4906.098567 4605.711785 8021.192033 7571.153741 1.078833816 1.082299709 0.988075846 1.297508105 0.926110102 0.678355048 0.647998804 0.608323638 1.059441177 1 12.88629745 -8.33435274 3.353547938 1.055461829 0.638454128 0.83978939 0.085033952 0.071285232 1.56073013 0.012172883 0.030129268 4.63E-09 8.33435274 -0.417007701 QAPAPTVIRDPPSITPAVKS(ph)PLPGPSEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QAPAPTVIRDPPSITPAVKSPLPGPSEEK 29 2 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 QAPAPT(0.001)VIRDPPS(0.144)IT(0.144)PAVKS(0.71)PLPGPSEEK 72.935 2.43E-05 19868000 2417.6 2089.9 2466.6 2382.8 2503.1 2352.3 2142.7 2182.1 2566.2 2409.2 TRUE FALSE FALSE 2388.133361 2119.321667 2509.530138 2658.310547 2375.357467 2201.995622 2324.700885 2245.235621 2336.672645 2346.608637 1.017695633 0.903142362 1.069428493 1.132830804 1.012251225 0.938373612 0.990664079 0.956800203 0.995765808 1 11.19636154 -8.320321826 10.01078932 1.014959756 0.964844546 0.174703579 0.056037482 0.898653897 150.019266 0.008176665 0.018310061 4.78E-09 8.320321826 -0.05011521 QAPFRS(ph)PTAPSVFSPTGNR ddPTM_HeLa_Romidepsin_16h_R1 1 QAPFRSPTAPSVFSPTGNR 19 1 H0Y3X6;A0A0C4DFX9;Q9H3P2;C9JEM7;H7C2C7;C9JHL4 H0Y3X6 NELFA Negative elongation factor A 1 0 QAPFRS(0.918)PT(0.077)APS(0.004)VFS(0.002)PTGNR 56.039 0.01785 15962000 981.87 769.25 893.55 906.24 760.58 761.67 629.05 631.45 862.69 817.94 TRUE FALSE FALSE 969.9025908 780.0795217 909.1018629 1011.023733 721.7647645 713.0017452 682.4814913 649.7200095 785.5288458 796.6898009 1.217415599 0.979150883 1.141098909 1.269030596 0.905954568 0.894955282 0.856646452 0.815524447 0.98599084 1 9.637874296 -8.611458574 7.622420171 1.108207683 0.863135057 0.600490192 0.092509935 0.129370698 9.605202579 0.014866246 0.029824622 2.45E-09 8.611458574 -0.245072626 QAPGVGAVGGGS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 QAPGVGAVGGGSPER 15 0 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 0 QAPGVGAVGGGS(1)PER 112.01 0.0040942 8039400 1529 1485.9 1223.6 840.42 1274.8 1662.9 1038.9 1213.1 1461.9 1438.6 TRUE FALSE FALSE 1510.36396 1506.818539 1244.896245 937.5933147 1209.742199 1556.646057 1127.14414 1248.199135 1331.144003 1401.224965 1.077888275 1.075358045 0.888434246 0.669124044 0.863346165 1.110918015 0.804399128 0.89079139 0.949985931 1 10.45247288 -9.714442165 6.97608298 1.040666186 0.868673393 0.328095436 0.107651888 0.168432801 19.43724911 0.016890838 0.023806711 1.93E-10 9.714442165 -0.171992793 QAPGVGAVGGGS(ph)PEREEVGAGYNS(ph)EDEYEAAAAR ddPTM_HeLa_Romidepsin_16h_R1 1 QAPGVGAVGGGSPEREEVGAGYNSEDEYEAAAAR 34 1 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3 A0A087WXV6 OTUD5 OTU domain-containing protein 5 2 0 QAPGVGAVGGGS(0.97)PEREEVGAGY(0.28)NS(0.745)EDEY(0.006)EAAAAR 57.563 0.003329 85408000 830.1 1016.3 841.7 879.34 944.82 1196.9 786.9 842.71 977.99 1106.9 TRUE FALSE FALSE 819.9824219 1030.607498 856.3494354 981.0134282 896.6023098 1120.421953 853.7392664 867.0924843 890.516125 1078.142578 0.760551005 0.95591021 0.794282178 0.909910663 0.831617569 1.039215012 0.791861191 0.804246583 0.825972504 1 10.07433226 -12.60274952 1.407896682 0.999838005 0.851377609 0 0.097555402 0.417575386 1.48790348 0.058043458 0.013464492 2.50E-13 12.60274952 -0.148460396 QAPGVGAVGGGSPEREEVGAGYNS(ph)EDEYEAAAAR ddPTM_HeLa_Romidepsin_16h_R1 1 QAPGVGAVGGGSPEREEVGAGYNSEDEYEAAAAR 34 1 A0A087WXV6;Q96G74-2;Q96G74-3;Q96G74-5;Q96G74;H7BZQ3 A0A087WXV6 OTUD5 OTU domain-containing protein 5 1 0 QAPGVGAVGGGSPEREEVGAGY(0.458)NS(0.528)EDEY(0.013)EAAAAR 54.086 0.0017491 7706900 716.02 560.61 619.59 671.95 740.27 783.29 786.89 809.54 854.32 680.56 TRUE FALSE FALSE 707.2928728 568.5022823 630.373704 749.6440206 702.4912596 733.240297 853.728417 832.9627627 777.9074795 662.8789531 1.067001554 0.857626086 0.950963522 1.130891269 1.059757979 1.106145087 1.287909977 1.256583512 1.173528705 1 9.372601637 -7.945375142 1.165494713 1.016357862 1.30593869 0.538980001 0.085533543 0.317124502 0.666671786 0.011326965 0.082603843 1.13E-08 7.945375142 0.289580828 QAPLPS(ph)PESLDLGR ddPTM_HeLa_Romidepsin_16h_R1 2 QAPLPSPESLDLGR 14 0 H3BRS1;Q12968 H3BRS1 NFATC3 "Nuclear factor of activated T-cells, cytoplasmic 3" 1 0 QAPLPS(0.613)PES(0.387)LDLGR;QAPLPS(0.949)PES(0.051)LDLGR ; 109.1 0.0059814 6124400 3722.32 2825.07 2884.6 3072.38 3430.24 3946.48 3020.4 4056.9 3724.78 3452.04 TRUE FALSE FALSE 3676.950932 2864.84141 2934.805253 3427.623032 3255.182053 3694.312665 3276.952701 4174.280001 3391.626348 3362.355503 1.093564 0.85203406 0.872842045 1.019411252 0.968125485 1.098727562 0.974600306 1.241474912 1.008705458 1 11.71525655 -7.255187289 24.46207611 1.014208575 1.24147505 0.44777884 0.079798195 440.1354545 1722017.754 0.012157375 0.150393243 5.56E-08 7.255187289 0.227266475 QAPLPSPES(ph)LDLGR ddPTM_HeLa_Romidepsin_16h_R1 1 QAPLPSPESLDLGR 14 0 H3BRS1;Q12968 H3BRS1 NFATC3 "Nuclear factor of activated T-cells, cytoplasmic 3" 1 0 QAPLPS(0.321)PES(0.679)LDLGR 106.55 0.0071762 3676400 1145.9 1110.1 1141 1127.4 1206.4 1112.7 1110.4 1153.3 1494.2 1177.3 TRUE FALSE FALSE 1131.93333 1125.728017 1160.858626 1257.755293 1144.832906 1041.602061 1204.717348 1186.668916 1360.55501 1146.713576 0.987110778 0.981699389 1.012335295 1.096834745 0.998359948 0.908336731 1.050582616 1.034843347 1.186481993 1 10.16328937 -9.647015616 7.305298663 0.992869366 1.016533825 0 0.075946241 0.568415266 34.46864356 0.007208089 0.010201916 2.25E-10 9.647015616 0.023664459 QAQAQES(ph)EEEEESR ddPTM_HeLa_Romidepsin_16h_R1 3 QAQAQESEEEEESR 14 0 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 0 QAQAQES(0.826)EEEEES(0.174)R;QAQAQES(0.901)EEEEES(0.099)R;QAQAQES(1)EEEEESR ;; 239.51 2.09E-43 95351000 9759.3 9511.7 8973.5 8327.3 8543.6 8131 7350.1 8045.3 10498.9 9660.5 TRUE FALSE FALSE 9640.349898 9645.605962 9129.680003 9290.141607 8107.588211 7611.455342 7974.417311 8278.078062 9559.852089 9409.518817 1.024531656 1.025090246 0.970260029 0.987313144 0.861636856 0.808910157 0.847484071 0.879755726 1.015976723 1 13.19990523 -8.779099774 3.187912909 1.00943091 0.843042315 0.924732098 0.021668887 0.046638232 0.980683531 0.003424471 0.006868717 1.66E-09 8.779099774 -0.166388595 QAQAQESEEEEES(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 QAQAQESEEEEESR 14 0 H0YLQ7;Q9NVM6 H0YLQ7 DNAJC17 DnaJ homolog subfamily C member 17 1 0 QAQAQES(0.154)EEEEES(0.846)R 176.43 4.79E-07 23882000 2952.2 2376.4 2329 2538.8 2186.9 2163 1898.8 2072 3091.9 2392.3 TRUE FALSE FALSE 2916.217451 2409.855022 2369.535268 2832.348001 2075.294333 2024.791281 2060.084025 2131.950051 2815.35272 2330.147701 1.251516138 1.034206982 1.016903464 1.215522947 0.890627805 0.868954049 0.88410019 0.914942023 1.208229298 1 11.18620569 -8.743455937 24.89026178 1.112047934 0.887780351 0.652459333 0.082576988 143.1279586 198097.359 0.015059291 0.030068783 1.81E-09 8.743455937 -0.224267583 QAQIEVVPSAS(ph)ALIIK ddPTM_HeLa_Romidepsin_16h_R1 1 QAQIEVVPSASALIIK 16 0 P30050 P30050 RPL12 60S ribosomal protein L12 1 0 QAQIEVVPS(0.251)AS(0.749)ALIIK 122.01 0.002813 7201500 2788.3 2746.3 2593.5 2022.4 2080.4 2313.8 2188.4 2689.6 3348.1 2997.1 TRUE FALSE FALSE 2754.315127 2784.962483 2638.63878 2256.239404 1974.229425 2165.955647 2374.282641 2767.419333 3048.637551 2919.23491 0.94350582 0.954004241 0.90388025 0.772887237 0.676283165 0.741960039 0.813323598 0.947994738 1.044327587 1 11.51137459 -9.461536067 2.727560083 0.97110796 0.782821414 0.63131904 0.069914259 0.138864605 2.040928586 0.011168644 0.017399187 3.46E-10 9.461536067 -0.188286546 QAQQERDELADEIANS(ph)SGK ddPTM_HeLa_Romidepsin_16h_R1 1 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 QAQQERDELADEIANS(0.5)S(0.5)GK 108.37 0.00033228 8329400 2941.3 2763.4 2747.3 1992.4 2611.5 3042.1 2376 2653.4 3501.1 3195.6 TRUE FALSE FALSE 2905.450304 2802.303218 2795.115604 2222.770663 2478.22541 2847.719628 2577.817381 2730.171943 3187.952847 3112.577851 0.933454661 0.900315864 0.898006648 0.714125323 0.796197084 0.914907117 0.828193704 0.877141737 1.02421626 1 11.60389421 -10.25569488 1.000643785 0.979285668 0.832165749 0.599539917 0.05534595 0.261465333 0.516069499 0.012304313 0.014674611 5.55E-11 10.25569488 -0.147119919 QAQQERDELADEIANSS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 1 0 QAQQERDELADEIANS(0.265)S(0.735)GK 93.196 0.0011419 8583900 1538.9 1606 1805 1511.8 1844 1373.6 1252.9 1688.2 1861.5 1689.7 TRUE FALSE FALSE 1520.143295 1628.60931 1836.415268 1686.601429 1749.893799 1285.831393 1359.321295 1737.045403 1695.002778 1645.80135 0.923649318 0.989554 1.115818302 1.024790403 1.063247274 0.781279826 0.825932786 1.055440502 1.029895119 1 10.6845745 -8.269489892 24.99871225 0.987232314 0.881389211 0.286017855 0.085525274 663.9642035 2061764.167 0.012647569 0.028740784 5.38E-09 8.269489892 -0.105843102 QAQQERDELADEIANSSGK ddPTM_HeLa_Romidepsin_16h_R1 1 QAQQERDELADEIANSSGK 19 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 115.2 0.00093992 10255000 1508.1 1505.2 1297.4 1667.2 1572.4 1547.8 1180.1 1675.5 1856.9 1633.2 FALSE FALSE TRUE 1489.718697 1526.390245 1319.980703 1859.969508 1492.154561 1448.900575 1280.337665 1723.977949 1690.814213 1590.769229 0.936476939 0.959529653 0.829775104 1.169226482 0.938008187 0.910817578 0.804854432 1.083738557 1.062890948 1 10.63550885 -9.258765264 0.006474862 1.904778003 9.60E-08 0.026282011 0.105750292 19410.20475 50.279574 7272.39478 7517.579787 5.51E-10 9.258765264 -1.904777907 QAREES(ph)EESEAEPVQR ddPTM_HeLa_Romidepsin_16h_R1 1 QAREESEESEAEPVQR 16 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 QAREES(0.997)EES(0.003)EAEPVQR 81.016 0.0087314 3651800 793.14 576.74 511.86 816.93 780.22 533.5 771.84 632.66 939.02 819.17 TRUE FALSE FALSE 783.4729046 584.8593609 520.7687086 911.3872904 740.402462 499.4110718 837.4000703 650.9650189 855.0316994 797.8878453 0.981933625 0.733009488 0.652684098 1.142249873 0.927953053 0.62591638 1.049521026 0.815860303 1.071618905 1 9.640042159 -10.42463455 11.11856904 0.992041382 0.855383135 0.191541272 0.155539148 0.835211128 90.88955471 0.025501162 0.029138572 3.76E-11 10.42463455 -0.136658247 QAS(ph)LDGLQQLR ddPTM_HeLa_Romidepsin_16h_R1 3 QASLDGLQQLR 11 0 Q3MII6 Q3MII6 TBC1D25 TBC1 domain family member 25 1 0 QAS(1)LDGLQQLR;QAS(1)LDGLQQLR;QAS(1)LDGLQQLR ;; 132.51 0.0045374 35796200 2261.97 1905.16 2000.35 1979.45 2029.94 1794.47 1535.81 1988.6 2461.44 2152 TRUE FALSE FALSE 2234.40024 1931.980892 2035.165253 2208.323323 1926.344587 1679.809158 1666.261663 2046.137004 2241.282642 2096.09073 1.065984505 0.921706711 0.97093376 1.053543767 0.91901775 0.801400977 0.794937757 0.976168147 1.069267952 1 11.03348545 -8.57147873 4.384389398 1.018871969 0.851730754 0.557792921 0.062866941 0.105947279 4.365896292 0.009129031 0.019130952 2.68E-09 8.57147873 -0.167141214 QAS(ph)PTEVVER ddPTM_HeLa_Romidepsin_16h_R1 1 QASPTEVVER 10 0 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;A0A0A0MR59;Q8TB72-4;A0A0C4DG68 C9JW01 PUM2 Pumilio homolog 2 1 0 QAS(0.901)PT(0.099)EVVER 105.95 0.020678 25598000 2047.2 1981.9 1878.8 1852.6 1882 1755.1 1635 1732.3 2352.6 2020.3 TRUE FALSE FALSE 2022.247939 2009.80124 1911.499726 2066.806329 1785.954517 1642.954774 1773.876859 1782.421367 2142.177564 1967.812315 1.027663016 1.021337871 0.97138315 1.050306634 0.907583769 0.834914368 0.901446162 0.905788298 1.088608679 1 10.94237691 -8.654265745 5.45855732 1.012772494 0.881290016 0.783212584 0.035562608 0.054843326 2.447354662 0.003712568 0.007502926 2.22E-09 8.654265745 -0.131482479 QAS(ph)TDAGTAGALT(ph)PQHVR ddPTM_HeLa_Romidepsin_16h_R1 1 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 2 0 QAS(0.973)T(0.026)DAGT(0.104)AGALT(0.897)PQHVR 98.188 0.0012273 0 718.48 834.65 781.71 773.18 726.99 667.89 706.23 567.62 809.19 799.29 TRUE FALSE FALSE 709.7228894 846.4002246 795.3153346 862.5787095 689.8889875 625.2139845 766.2171586 584.0431891 736.8140197 778.5243306 0.91162583 1.087185321 1.021567732 1.107966284 0.886149553 0.803075716 0.984191667 0.750192597 0.946423883 1 9.604598317 -8.543928117 24.93192017 0.983245851 0.857149709 0.455877084 0.080682484 194.4498676 230315.2521 0.012051236 0.024104228 2.86E-09 8.543928117 -0.126096142 QAS(ph)TDAGTAGALTPQHVR ddPTM_HeLa_Romidepsin_16h_R1 3 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 QAS(0.382)T(0.382)DAGT(0.211)AGALT(0.024)PQHVR;QAS(0.606)T(0.074)DAGT(0.137)AGALT(0.184)PQHVR;QAS(0.896)T(0.095)DAGTAGALT(0.009)PQHVR ;; 246.9 7.22E-62 120957000 6943.8 6480.7 5740.2 6061.8 4196.8 3927.02 3384.6 3968.96 7041.4 5928.2 TRUE FALSE FALSE 6859.166295 6571.935465 5840.105773 6762.693838 3982.621636 3676.096096 3672.08784 4083.795596 6411.599548 5774.184509 1.187902168 1.138158203 1.01141655 1.171194621 0.689728849 0.636643337 0.635949169 0.707250624 1.110390487 1 12.49540149 -8.752373887 23.68503182 1.093627541 0.66295033 0.925207617 0.060657917 25.12657189 65646.04425 0.011597344 0.022905447 1.77E-09 8.752373887 -0.43067721 QASASYDS(ph)EEEEEGLPMSYDEK ddPTM_HeLa_Romidepsin_16h_R1 2 QASASYDSEEEEEGLPMSYDEK 22 0 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 1 0 QAS(0.015)AS(0.025)YDS(0.958)EEEEEGLPMS(0.001)Y(0.001)DEK;QAS(0.007)AS(0.016)YDS(0.977)EEEEEGLPMSYDEK ; 94.957 0.0001299 21577000 7659.8 8090.7 8575.1 6676.9 8898.9 8850.9 7934.8 9629.7 8548.4 9060.5 TRUE FALSE FALSE 7566.439411 8204.601087 8724.346018 7448.914594 8444.755927 8285.356055 8608.781714 9908.320176 7783.809694 8825.106904 0.857376516 0.929688578 0.988582474 0.844059418 0.956901261 0.938839172 0.975487528 1.122742227 0.882007411 1 13.10739804 -7.131883647 1.736157053 0.930273655 1.237739303 0.595202522 0.049071357 0.882930129 1.996939367 0.008479738 0.495218665 7.38E-08 7.131883647 0.307465648 QASASYDS(ph)EEEEEGLPMSYDEKR ddPTM_HeLa_Romidepsin_16h_R1 2 QASASYDSEEEEEGLPMSYDEKR 23 1 Q15059 Q15059 BRD3 Bromodomain-containing protein 3 1 0 QAS(0.126)AS(0.072)Y(0.002)DS(0.783)EEEEEGLPMS(0.009)Y(0.008)DEKR;QAS(0.103)AS(0.052)YDS(0.845)EEEEEGLPMSYDEKR ; 91.809 0.00010167 153915000 6191.5 5650.5 4796.6 7079.2 5994.5 7612.9 5528.4 6392.7 6114.4 5516.7 TRUE FALSE FALSE 6116.035617 5730.047887 4880.082811 7897.730413 5688.578296 7126.46026 5997.982158 6577.662688 5567.51275 5373.375339 1.13821113 1.066377747 0.908196897 1.469789455 1.058660142 1.326253948 1.116241055 1.224121204 1.036129509 1 12.3916129 -9.283171297 24.97243542 1.056315963 1.227019635 0.426029876 0.119053015 672.3951027 772656.0539 0.017521753 0.026777627 5.21E-10 9.283171297 0.170703672 QASPT(ph)EVVER ddPTM_HeLa_Romidepsin_16h_R1 1 QASPTEVVER 10 0 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;A0A0A0MR59;Q8TB72-4;A0A0C4DG68 C9JW01 PUM2 Pumilio homolog 2 1 0 QAS(0.1)PT(0.9)EVVER 130.15 0.015061 43020000 1390.3 1415.8 1113.6 1401.6 1255.2 1416.5 931.09 1119.5 1692.7 1165 TRUE FALSE FALSE 1373.354489 1435.73167 1132.981741 1563.659587 1191.14246 1325.990222 1010.176761 1151.890966 1541.300673 1134.733132 1.210288525 1.265259319 0.998456561 1.377997648 1.049711537 1.168548079 0.890232895 1.01512059 1.358293531 1 10.14813733 -7.765447102 24.99906249 1.12600961 0.952676727 0.237161134 0.138392498 101.0848341 630559.052 0.017478056 0.055411892 1.72E-08 7.765447102 -0.173332883 QASS(ph)DSDSILSLK ddPTM_HeLa_Romidepsin_16h_R1 2 QASSDSDSILSLK 13 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 QAS(0.072)S(0.684)DS(0.221)DS(0.024)ILSLK;QAS(0.223)S(0.75)DS(0.027)DSILSLK ; 154.13 0.00034192 10015000 3853.3 3781.4 3521.2 3643.6 3879.4 3805.1 2771 3621.2 3932.3 3895.4 TRUE FALSE FALSE 3806.334497 3834.634648 3582.485009 4064.890176 3681.419742 3561.96639 3006.368671 3725.973709 3580.585239 3794.196946 1.003198978 1.010657776 0.944201121 1.071344011 0.970276397 0.938793226 0.792359678 0.982019057 0.943700417 1 11.88957885 -8.17285786 3.017702585 1.001903017 0.884736259 0.348606453 0.055781965 0.151115816 2.651607219 0.006529852 0.018771585 6.72E-09 8.17285786 -0.117166758 QAST(ph)DAGTAGALTPQHVR ddPTM_HeLa_Romidepsin_16h_R1 1 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 QAS(0.105)T(0.894)DAGTAGALTPQHVR 222.93 7.96E-38 12154000 1017.8 1073.7 844.47 1053.7 866.95 787.81 613.08 962.36 1254.9 1047.6 TRUE FALSE FALSE 1005.394662 1088.815577 859.1676461 1175.533752 822.7063065 737.4714835 665.1549999 990.2043682 1142.658601 1020.383201 0.985310873 1.067065369 0.842004891 1.152051259 0.806271904 0.722739734 0.651867847 0.97042402 1.119832824 1 9.994895337 -8.610363416 8.101276197 0.996258716 0.768045439 0.513570044 0.111821778 0.133098044 10.81033332 0.013446964 0.026954373 2.45E-09 8.610363416 -0.228213276 QASTDAGTAGALT(ph)PQHVR ddPTM_HeLa_Romidepsin_16h_R1 2 QASTDAGTAGALTPQHVR 18 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 QASTDAGTAGALT(1)PQHVR;QASTDAGTAGALT(1)PQHVR ; 135.68 0.0008268 35292000 6340.6 7375.8 7003 7973.1 8481 9468.6 7175.7 8452.3 7195.3 7868.3 TRUE FALSE FALSE 6263.318328 7479.636706 7124.884277 8894.987337 8048.182923 8863.587019 7785.203779 8696.853965 6551.734347 7663.880432 0.817251572 0.975959473 0.929670595 1.160637541 1.050144636 1.156540358 1.015830538 1.134784662 0.854884729 1 12.90385934 -9.298305361 10.33389944 0.918212788 1.098662233 0.677149855 0.064860604 0.390003616 108.2463113 0.012025717 0.018418406 5.03E-10 9.298305361 0.180449445 QATDNSEIS(ph)SATK ddPTM_HeLa_Romidepsin_16h_R1 1 QATDNSEISSATK 13 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3 P46100-4;A0A096LNN3 ATRX Transcriptional regulator ATRX 1 0 QATDNSEIS(0.499)S(0.499)AT(0.001)K 222.88 2.06E-31 4320200 1857.7 1760.5 1559.5 1549.9 2249.5 2767 2388.5 2591 1855.4 1778.7 TRUE FALSE FALSE 1835.057638 1785.284365 1586.642443 1729.10673 2134.699621 2590.19763 2591.37913 2665.966497 1689.448377 1732.489118 1.059202981 1.030473639 0.915816687 0.998047672 1.232157593 1.495072958 1.495754925 1.538807067 0.975156704 1 10.75863057 -8.45085808 2.437652838 1.017501524 1.516089678 0.967651046 0.041960996 0.039865052 0.462922499 0.006870403 0.0172794 3.54E-09 8.45085808 0.498588154 QATDNSEISS(ph)ATK ddPTM_HeLa_Romidepsin_16h_R1 1 QATDNSEISSATK 13 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1;A0A096LNN3 P46100-4;A0A096LNN3 ATRX Transcriptional regulator ATRX 1 0 QATDNSEIS(0.101)S(0.893)AT(0.006)K 141.34 0.00098579 4334400 1052.5 1306 1146.1 1103.1 1746.7 1978.5 1425.4 1520.1 1469.6 1284.2 TRUE FALSE FALSE 1039.671725 1324.385902 1166.04739 1230.645612 1657.559381 1852.080235 1546.47344 1564.081695 1338.155295 1250.836299 0.831181287 1.058800343 0.932214224 0.98385825 1.32516092 1.48067356 1.236351585 1.25042877 1.069808493 1 10.28867728 -8.791703867 4.662020614 0.933048274 1.330669849 0.756919901 0.093611788 0.063495351 3.230546377 0.014120666 0.026956668 1.62E-09 8.791703867 0.397621575 QATINIGTIGHVAHGK ddPTM_HeLa_Romidepsin_16h_R1 2 QATINIGTIGHVAHGK 16 0 H7BZU1;Q2VIR3-2;Q2VIR3;P41091 H7BZU1 EIF2S3;EIF2S3L Putative eukaryotic translation initiation factor 2 subunit 3-like protein;Eukaryotic translation initiation factor 2 subunit 3 0 0 ; ; 80.387 0.010454 3921900 4324.2 4003.3 3694.6 4297.3 4421.4 4182.4 3630.9 4264.8 4855.2 4431.6 FALSE FALSE TRUE 4271.494987 4059.658562 3758.902963 4794.174045 4195.759459 3915.158138 3939.308555 4388.195259 4420.938752 4316.466393 0.98958143 0.940505078 0.870828734 1.110671 0.972035706 0.907028523 0.912623474 1.016617497 1.024203214 1 12.07563504 -10.4125898 6.003689144 0.995466252 0.9602187 0.083579994 0.063467516 0.540532696 25.33644295 0.010674336 0.01213044 3.87E-11 10.4125898 -0.035247552 QDDGSSSAS(ph)PSVQGAPR ddPTM_HeLa_Romidepsin_16h_R1 2 QDDGSSSASPSVQGAPR 17 0 Q9NQA3 Q9NQA3 WASH6P WAS protein family homolog 6 1 0 QDDGSSS(0.001)AS(0.792)PS(0.207)VQGAPR;QDDGSSS(0.011)AS(0.922)PS(0.067)VQGAPR ; 267.6 5.00E-87 27611000 4101.9 4086.9 3215.5 3710 3914.4 4248.9 3585.5 3796.4 4471.7 4221.2 TRUE FALSE FALSE 4051.904465 4144.435485 3271.464429 4138.967656 3714.633561 3977.409003 3890.052281 3906.242844 4071.739952 4111.532615 0.985497342 1.00800258 0.795680038 1.006672704 0.903466884 0.967378682 0.946131928 0.950069769 0.990321696 1 12.00546056 QDDS(ph)PPRPIIGPALPPGFIK ddPTM_HeLa_Romidepsin_16h_R1 2 QDDSPPRPIIGPALPPGFIK 20 1 A0A0A0MRI1;Q8IXQ4-4;Q8IXQ4 A0A0A0MRI1 GPALPP1 GPALPP motifs-containing protein 1 1 0 QDDS(1)PPRPIIGPALPPGFIK;QDDS(1)PPRPIIGPALPPGFIK ; 75.225 0.002433 141904000 2671.8 2915 3281.4 3277.6 3291.5 3754.2 3172.7 3771.9 3558.4 3095.5 TRUE FALSE FALSE 2639.235074 2956.037447 3338.511391 3656.571534 3123.522473 3514.318736 3442.189059 3881.033975 3240.127792 3015.078464 0.875345403 0.980418083 1.107271811 1.21276165 1.035967226 1.165581187 1.141658202 1.287208284 1.074641284 1 11.55797983 -9.735685513 3.082216242 0.940645271 1.159654171 0.53775508 0.078096525 0.110692175 2.172493631 0.011774884 0.016590321 1.84E-10 9.735685513 0.219008899 QDDSPSGASYGQDYDLS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 QDDSPSGASYGQDYDLSPSR 20 0 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 QDDSPSGASYGQDYDLS(1)PSR;QDDSPSGASYGQDYDLS(0.999)PS(0.001)R ; 354.05 1.52E-271 18652200 4569.3 5061.7 5365.3 3432.3 4004.5 4356 3781.4 4284.2 6186.9 5729.5 TRUE FALSE FALSE 4513.607614 5132.958745 5458.680796 3829.158675 3800.135422 4077.665658 4102.592022 4408.156568 5633.528169 5580.646764 0.808796508 0.919778471 0.978144833 0.686149623 0.680948926 0.730679764 0.735146336 0.789900661 1.009475856 1 12.44621662 -9.256236444 24.99647635 0.912997399 0.723069493 0.742672617 0.063113345 236.472638 1136085.313 0.011910292 0.019365275 5.54E-10 9.256236444 -0.189927906 QDEDYDEQVEESLQDEDDNDVYILTK ddPTM_HeLa_Romidepsin_16h_R1 1 QDEDYDEQVEESLQDEDDNDVYILTK 26 0 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 0 104.26 4.94E-09 0 463.08 457.41 458.53 292.73 490.1 425.86 235.53 296.94 278.82 316 FALSE FALSE TRUE 457.4358028 463.84943 466.5105223 326.5768199 465.0883682 398.6489204 255.5359123 305.5314904 253.8816409 307.7902744 1.486193167 1.507030821 1.515676618 1.061036839 1.511056089 1.295196611 0.830227377 0.992661288 0.824852706 1 8.265803836 -7.768221064 24.93799977 1.286004813 0.911444309 0.276719882 0.234664149 129.5126026 476259.2348 0.032755402 0.101579051 1.71E-08 7.768221064 -0.374560505 QDEHGFISR ddPTM_HeLa_Romidepsin_16h_R1 1 QDEHGFISR 9 0 E9PNH7;A0A024R3B9;E9PJL7;P02511 E9PNH7 CRYAB Alpha-crystallin B chain 0 0 103.26 0.0010993 0 5160.3 4828.2 4832.5 3607.4 4931.2 5251.5 4216.9 4973.4 4866 4348.7 FALSE FALSE TRUE 5097.404279 4896.171526 4916.607635 4024.504561 4679.542463 4915.946098 4575.083381 5117.297482 4430.772773 4235.720147 1.203432734 1.155924225 1.160748932 0.950134669 1.10478084 1.160592751 1.080119371 1.208129268 1.04604946 1 12.04839156 -12.55156654 1.340324068 1.000477284 1.132955098 0.247321918 0.071635932 0.431884673 1.39799751 0.051169642 0.012293836 2.81E-13 12.55156654 0.132477813 QDEHGYISR ddPTM_HeLa_Romidepsin_16h_R1 3 QDEHGYISR 9 0 P04792 P04792 HSPB1 Heat shock protein beta-1 0 0 ;; ;; 133.91 0.0032503 163429000 23898.8 22890.7 23993.1 19928.1 25017 23525.8 21086.6 15715 27341 23825.7 FALSE FALSE TRUE 23607.51223 23212.95588 24410.68984 22232.28069 23740.28914 22022.57731 22877.69528 16169.68873 24895.55248 23206.70488 1.017271188 1.000269362 1.05188091 0.958011092 1.022992677 0.948974765 0.985822649 0.696767974 1.072774123 1 14.50225407 -6.775538815 1.558100247 1.006586863 2.94E-13 0.866439146 0.036421143 0.815303512 0.646892499 0.003823537 1.827621999 1.68E-07 6.775538815 -1.006586863 QDGESK(ac)TIMLK ddPTM_HeLa_Romidepsin_16h_R1 1 QDGESKTIMLK 11 1 E9PGM9;P78332-2;P78332;C9JSL1;F8WF63;F8WCA5 E9PGM9 RBM6 RNA-binding protein 6 0 1 QDGESK(1)TIMLK 47.288 0.029347 3788000 0 0 0 0 264.35 249.14 252.67 364.93 0 0 FALSE TRUE FALSE 0 0 0 0 250.8592331 233.2207581 274.1317835 375.4886738 0 0 0 QDGGTAPVAS(ph)ASPK ddPTM_HeLa_Romidepsin_16h_R1 1 QDGGTAPVASASPK 14 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 QDGGT(0.001)APVAS(0.942)AS(0.056)PK 151.73 0.00061562 5141400 3067.2 3121.8 2623.4 2304.1 2267.4 2345.5 2039.3 2407.2 3238.9 2955.9 TRUE FALSE FALSE 3029.815787 3165.748782 2669.059177 2570.510883 2151.686117 2195.63012 2212.518091 2476.848534 2949.204672 2879.105292 1.052346295 1.099559919 0.927044657 0.892815866 0.747345407 0.762608483 0.768474184 0.86028411 1.024347626 1 11.49140484 -9.226875371 1.901992519 1.03003723 0.783983486 0.86118469 0.045405374 0.088591979 0.625115857 0.007416961 0.013276949 5.93E-10 9.226875371 -0.246053744 QDGGTAPVASAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QDGGTAPVASASPK 14 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 QDGGT(0.002)APVAS(0.128)AS(0.869)PK 119.08 0.0043156 5935400 2636.1 2745.6 2786.9 2416.1 2356.2 2038.6 1765.3 2228.1 2852.2 2783.2 TRUE FALSE FALSE 2603.970199 2784.252629 2835.404825 2695.46085 2235.954322 1908.340039 1915.244538 2292.566558 2597.092089 2710.892063 0.960558421 1.027061412 1.04593055 0.994307699 0.824803891 0.703952793 0.70649974 0.845687141 0.958021208 1 11.40455196 -8.643609658 3.520773312 0.991174184 0.749008704 0.863820996 0.044803076 0.060695606 1.458072339 0.006624646 0.013901892 2.27E-09 8.643609658 -0.24216548 QDKPLS(ph)PAGSSQEAADTPDTR ddPTM_HeLa_Romidepsin_16h_R1 1 QDKPLSPAGSSQEAADTPDTR 21 1 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 0 QDKPLS(0.651)PAGS(0.249)S(0.097)QEAADT(0.003)PDTR 69.581 0.0025164 13511000 1759 1509.1 1677 1539.4 2894.2 3113.1 2711.5 3243.6 1891.4 1861.8 TRUE FALSE FALSE 1737.560631 1530.345149 1706.187482 1717.392671 2746.498174 2914.182957 2941.814742 3337.448448 1722.228447 1813.430168 0.958162416 0.843895275 0.940861971 0.947040973 1.514532086 1.607000374 1.622237677 1.840406379 0.949707619 1 10.82450548 -8.674112425 3.316495971 0.961408773 1.671381069 0.956247271 0.074456166 0.037233926 0.813220045 0.011621834 0.02430672 2.12E-09 8.674112425 0.709972296 QDLPALEEK(ac)PR ddPTM_HeLa_Romidepsin_16h_R1 2 QDLPALEEKPR 11 1 A0A087WYC1;P34932;A0A087WTS8 A0A087WYC1 HSPA4 Heat shock 70 kDa protein 4 0 1 ; QDLPALEEK(1)PR;QDLPALEEK(1)PR 128.01 0.012001 1735820 954.08 593.24 576.93 282.08 1155.74 1204.32 894.27 1031.54 1083.83 830.96 FALSE TRUE FALSE 942.451306 601.5916483 586.9712246 314.6954168 1096.758275 1127.367839 970.2292715 1061.385982 986.8895303 809.3715394 1.164423581 0.743282435 0.725218513 0.388814533 1.355073933 1.392892861 1.198743994 1.311370527 1.219328185 1 9.660658309 QDMLTLQMIRIMS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 QDMLTLQMIRIMSK 14 1 F5GWN5;O00750 F5GWN5 PIK3C2B Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta 1 0 QDMLT(0.016)LQMIRIMS(0.984)K 69.979 0.02619 4104300 1690.5 1772 1758.9 1263.5 2258 2163.8 1528.1 1866.6 2025.2 1496.8 TRUE FALSE FALSE 1669.895536 1796.946263 1789.512917 1409.591815 2142.765834 2025.540163 1657.896776 1920.607126 1844.06104 1457.91292 1.145401425 1.232547046 1.227448424 0.966855973 1.469748847 1.38934235 1.137171331 1.317367519 1.264863638 1 10.50968884 -10.82233185 0.26688573 0.94473597 1.327643041 0.014610027 0.149699567 1.489662938 0.351270845 0.226873709 0.155338803 1.51E-11 10.82233185 0.382907071 QDPFQESGLHLS(ph)PTAAEAK ddPTM_HeLa_Romidepsin_16h_R1 2 QDPFQESGLHLSPTAAEAK 19 0 H3BN50;Q15599-3;H3BQS0;Q15599 H3BN50 SLC9A3R2 Na(+)/H(+) exchange regulatory cofactor NHE-RF2 1 0 QDPFQESGLHLS(0.5)PT(0.5)AAEAK;QDPFQESGLHLS(0.958)PT(0.042)AAEAK ; 116.04 0.00083117 21735000 5359.9 4939.1 5271.4 3485.7 7801.2 7659.2 5957.9 6724.4 7419.3 6635.2 TRUE FALSE FALSE 5294.571477 5008.632779 5363.146506 3888.733035 7403.075654 7169.801839 6463.963877 6918.959905 6755.699226 6462.816547 0.819235923 0.774992256 0.829846626 0.601708714 1.145487513 1.109392753 1.000177528 1.070579654 1.045318117 1 12.65794732 QDS(ph)DSDVVDIEEAEHDFMGEAHPVVFSR ddPTM_HeLa_Romidepsin_16h_R1 1 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 QDS(0.843)DS(0.157)DVVDIEEAEHDFMGEAHPVVFSR 64.502 0.00025982 1995400 456.13 563.97 473.6 48.918 354.75 404.5 474.38 679.55 498.67 671.08 TRUE FALSE FALSE 450.5705121 571.9095845 481.8428093 54.57412933 336.6457837 378.6537555 514.6738254 699.2117071 454.0677063 653.6452449 0.689319651 0.874954096 0.737162571 0.08349197 0.515028276 0.57929551 0.787390147 1.069711304 0.694669945 1 9.352364039 -11.80169662 0.574427338 1.017409507 0.636429132 0.025730966 0.260257015 1.186816294 0.710536971 0.225609424 0.065889245 1.58E-12 11.80169662 -0.380980376 QDS(ph)LDIYNER ddPTM_HeLa_Romidepsin_16h_R1 2 QDSLDIYNER 10 0 Q9ULQ0-2;Q9ULQ0 Q9ULQ0-2 STRIP2 Striatin-interacting protein 2 1 0 QDS(0.996)LDIY(0.004)NER;QDS(0.946)LDIY(0.054)NER ; 128.95 0.0078038 15885000 2453.2 2752.5 1926.71 3418.5 3777.6 4475.8 5403.2 4326 3873 2873 TRUE FALSE FALSE 2423.299455 2791.249767 1960.243579 3813.763055 3584.814976 4189.810825 5862.147673 4451.165985 3526.58918 2798.359046 0.865971598 0.997459483 0.700497523 1.362856943 1.281041824 1.497238473 2.094851868 1.590634337 1.260234703 1 11.45036537 -8.466787908 1.127948283 0.928250297 1.848762186 0.696048703 0.211965173 0.161400993 0.379114498 0.027359256 0.104262548 3.41E-09 8.466787908 0.920511889 QDS(ph)LEPVLR ddPTM_HeLa_Romidepsin_16h_R1 1 QDSLEPVLR 9 0 D6RDZ7;D6RD37;D6RAX8;D6RBL1;D6RDZ9;D6RCK9;Q99576-3;E7EWD5 D6RDZ7 TSC22D3 1 0 QDS(1)LEPVLR 109.72 0.0195 1874600 1480.7 1991.5 954.54 1274.4 1227.1 928.96 859.02 829.45 1615.4 1821.2 TRUE FALSE FALSE 1462.652659 2019.536389 971.1533683 1421.752124 1164.476508 869.6024541 931.9851374 853.4488271 1470.914578 1773.884961 0.82454764 1.138482164 0.547472575 0.801490601 0.656455482 0.49022483 0.525392096 0.481118475 0.829205168 1 10.79269674 -8.700854163 0.445472199 0.956324284 0.37435144 0.607022157 0.134985932 0.777765234 0.228510295 0.036980201 0.198162024 1.99E-09 8.700854163 -0.581972844 QDS(ph)WEVVEGLR ddPTM_HeLa_Romidepsin_16h_R1 1 QDSWEVVEGLR 11 0 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5;Q9H4L5-8;Q9H4L5-6;Q9H4L5-4;Q9H4L5-2;C9J8P4;C9JEF2;C9JZ19 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 QDS(1)WEVVEGLR 108.66 0.0022852 0 648.05 515.84 600.76 633.77 951.91 851.29 651.63 992.01 858.69 678.09 TRUE FALSE FALSE 640.1513173 523.1020091 611.2159758 707.0494694 903.3304806 796.8953164 706.9794359 1020.712244 781.8866158 660.473124 0.96923144 0.792011045 0.925421419 1.070519668 1.367702103 1.206552224 1.070413633 1.545425858 1.183828058 1 9.367356046 -8.940033282 4.655335845 0.96440629 1.273430452 0.523825074 0.144896614 0.110325071 4.890202233 0.018198505 0.033416414 1.15E-09 8.940033282 0.309024162 QDSDS(ph)DVVDIEEAEHDFMGEAHPVVFSR ddPTM_HeLa_Romidepsin_16h_R1 1 QDSDSDVVDIEEAEHDFMGEAHPVVFSR 28 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 QDS(0.25)DS(0.75)DVVDIEEAEHDFMGEAHPVVFSR 54.273 0.0016566 1263800 260.17 151.96 115.55 192.41 238.99 160.74 147.96 241.26 127.33 185.59 TRUE FALSE FALSE 256.998948 154.0992969 117.5610993 214.6573495 226.7934485 150.4692328 160.5277187 248.2404775 115.9412859 180.768345 1.421703274 0.852468372 0.650341183 1.187472007 1.254608203 0.832387068 0.888030029 1.373251923 0.641380469 1 7.497998254 -10.24729606 24.94711665 1.199137664 0.99725058 0 0.287140327 1266.383437 2233749.814 0.042423916 0.051819544 5.66E-11 10.24729606 -0.201887084 QDVDNAS(ph)LAR ddPTM_HeLa_Romidepsin_16h_R1 2 QDVDNASLAR 10 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 1 0 QDVDNAS(1)LAR;QDVDNAS(1)LAR ; 128.21 0.0081123 42594000 5532 4882.8 4943.3 4328.2 5197.1 4573.7 4327 5448.4 6237.1 5214 TRUE FALSE FALSE 5464.573856 4951.540187 5029.336063 4828.646849 4931.872594 4281.455331 4694.535272 5606.040858 5679.238155 5078.539528 1.076012863 0.97499294 0.990311493 0.950794381 0.971120253 0.843048539 0.924386873 1.103868706 1.118281766 1 12.31019796 -9.909599146 2.184181047 1.035420198 0.954132816 0.264933025 0.068941689 0.335400747 3.243881525 0.011273308 0.015220026 1.23E-10 9.909599146 -0.081287383 QDVDNASLAR ddPTM_HeLa_Romidepsin_16h_R1 2 QDVDNASLAR 10 0 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 0 ; ; 166.86 0.013885 42244400 4109.4 3564.77 3748.52 3604.28 4087.93 4400.4 3553.37 3747.74 4007.93 3544.68 FALSE FALSE TRUE 4059.313052 3614.954926 3813.761418 4021.023812 3879.307678 4119.228642 3855.193159 3856.174944 3649.450703 3452.588703 1.175730271 1.047027386 1.10460925 1.164640262 1.123593921 1.193084087 1.116609446 1.116893808 1.057018665 1 11.75346276 -12.44196514 1.007628262 0.994676002 1.133551257 0.459529177 0.042478777 0.320982637 0.545482703 0.033956776 0.007255838 3.61E-13 12.44196514 0.138875255 QEAGDS(ph)PPPAPGTPK ddPTM_HeLa_Romidepsin_16h_R1 5 QEAGDSPPPAPGTPK 15 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 0 QEAGDS(0.977)PPPAPGT(0.023)PK;QEAGDS(0.999)PPPAPGT(0.001)PK;QEAGDS(1)PPPAPGTPK;QEAGDS(0.996)PPPAPGT(0.004)PK;QEAGDS(0.634)PPPAPGT(0.366)PK ;;;; 171.33 1.17E-05 33723700 20919.4 19848.9 19012.4 16798.1 19184.7 21262.6 19278.2 19167.2 22214.9 21557.1 TRUE FALSE FALSE 20664.42631 20128.33334 19343.30285 18740.37536 18205.63317 19903.98848 20915.68983 19721.77269 20227.94371 20997.04343 0.984158859 0.958627028 0.92123936 0.892524484 0.867056985 0.947942435 0.996125473 0.939264271 0.963371046 1 14.35789858 -10.09673597 2.253526766 0.993178948 0.92725721 0.342764486 0.033513515 0.222663162 2.197221281 0.006253309 0.007876823 8.00E-11 10.09673597 -0.065921738 QEAGDSPPPAPGT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QEAGDSPPPAPGTPK 15 0 J3KR72;P49848-4;P49848-2;P49848;P49848-3 J3KR72 TAF6 Transcription initiation factor TFIID subunit 6 1 0 QEAGDS(0.004)PPPAPGT(0.996)PK 173.49 2.07E-05 5278600 5956.6 5645.6 5488 4719.1 4290.9 3623.6 2710.5 3112 5899.9 5978.2 TRUE FALSE FALSE 5883.998668 5725.078905 5583.516338 5264.744546 4071.919361 3392.063655 2940.729802 3202.04081 5372.198167 5822.885502 1.01049534 0.983203071 0.958891659 0.904147015 0.699295798 0.582539989 0.505029646 0.549906195 0.922600687 1 12.50751854 -8.65313166 1.341642089 1.003100396 0.520446996 0.975128412 0.030524905 0.02174897 0.077274454 0.002518951 0.007134855 2.22E-09 8.65313166 -0.4826534 QEAGKEGTAPS(ph)ENGETK ddPTM_HeLa_Romidepsin_16h_R1 1 QEAGKEGTAPSENGETK 17 1 Q15651;A0A087WZE9 Q15651 HMGN3 High mobility group nucleosome-binding domain-containing protein 3 1 0 QEAGKEGTAPS(0.991)ENGET(0.009)K 71.428 0.011015 4945900 1731.4 1930 1518.7 1333.8 1633.4 1444 1541.4 1482.6 2072.8 1678.7 TRUE FALSE FALSE 1710.297031 1957.170591 1545.132336 1488.020232 1550.041503 1351.73306 1672.326478 1525.496692 1887.403577 1635.087132 1.045997487 1.196982444 0.944984708 0.910055619 0.947987097 0.826703993 1.022775144 0.93297578 1.154313761 1 10.6751518 -9.552993438 24.99762028 1.037163564 0.928699854 0.465359891 0.077920868 163.4180518 135649.4203 0.010864218 0.015364412 2.80E-10 9.552993438 -0.10846371 QEAIPDLEDS(ph)PPVS(ph)DSEEQQESAR ddPTM_HeLa_Romidepsin_16h_R1 2 QEAIPDLEDSPPVSDSEEQQESAR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 2 0 QEAIPDLEDS(1)PPVS(0.995)DS(0.005)EEQQESAR;QEAIPDLEDS(1)PPVS(0.815)DS(0.183)EEQQES(0.003)AR ; 111.98 2.03E-05 7818100 3336.6 3098.3 2815.8 2966.4 3207.9 3465.3 2538.5 3154.1 3438.6 3087.4 TRUE FALSE FALSE 3295.932236 3141.917949 2864.807818 3309.389125 3044.188893 3243.878514 2754.120127 3245.358907 3131.043004 3007.188903 1.09601769 1.044802322 0.952653096 1.100492597 1.012303846 1.078707929 0.915845401 1.079200214 1.041186006 1 11.55419978 QEAIPDLEDS(ph)PPVSDSEEQQESAR ddPTM_HeLa_Romidepsin_16h_R1 1 QEAIPDLEDSPPVSDSEEQQESAR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 QEAIPDLEDS(0.76)PPVS(0.231)DS(0.01)EEQQESAR 101.2 8.07E-06 1925900 1334.6 1570.5 1247.8 1203.3 1359.1 1281 1048.9 1337.8 1686.9 1701.5 TRUE FALSE FALSE 1318.333382 1592.60954 1269.517436 1342.431208 1289.740055 1199.148234 1137.99354 1376.507132 1536.019439 1657.294785 0.795473077 0.960969379 0.766017879 0.810013535 0.778220065 0.723557598 0.686657287 0.830574708 0.926823311 1 10.69461452 -16.52287875 0.143427454 1.784002371 0.703332344 0.555745455 0.065177946 32.170586 0.318809662 7.12790199 0.16594415 3.00E-17 16.52287875 -1.080670026 QEAIPDLEDSPPVS(ph)DSEEQQESAR ddPTM_HeLa_Romidepsin_16h_R1 1 QEAIPDLEDSPPVSDSEEQQESAR 24 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 QEAIPDLEDS(0.059)PPVS(0.896)DS(0.046)EEQQESAR 93.494 2.57E-05 2533200 1056.6 1511.5 1182.4 1252 888.47 1104.4 1010.6 777.27 1590.2 1353.9 TRUE FALSE FALSE 1043.721753 1532.778937 1202.979176 1396.762131 843.1280606 1033.832404 1096.440339 799.7590811 1447.968529 1318.725483 0.791462489 1.162318433 0.912228657 1.05917581 0.6393507 0.783963317 0.831439411 0.606463659 1.098006028 1 10.36492856 -8.754809358 24.99992315 0.93170918 0.728503856 0.514709478 0.125820882 129.7189994 489128.7227 0.018377919 0.036083473 1.76E-09 8.754809358 -0.203205324 QEAKPQQAAGMLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QEAKPQQAAGMLSPK 15 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 QEAKPQQAAGMLS(1)PK 103.61 0.0021258 0 1733.5 1634.6 1483.8 1062.2 1538.6 1519.2 1367.6 1298.9 1457.7 1830.4 TRUE FALSE FALSE 1712.371435 1657.611942 1509.624917 1185.016562 1460.079501 1422.128023 1483.76391 1336.481622 1327.319661 1782.845944 0.96047078 0.929756128 0.846750064 0.664676926 0.818959992 0.797672972 0.8322446 0.749633824 0.744494871 1 10.79996633 -9.763357293 2.40077048 0.980412972 0.778476786 0.222203904 0.087408112 0.087653039 1.037555144 0.007559891 0.010696904 1.72E-10 9.763357293 -0.201936186 QEDAPVVY(ph)LGSFR ddPTM_HeLa_Romidepsin_16h_R1 1 QEDAPVVYLGSFR 13 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 QEDAPVVY(0.574)LGS(0.426)FR 87.216 0.0038747 0 511.69 639.32 463.89 580.34 707.53 794.12 477.03 492.07 842.57 548.01 TRUE FALSE FALSE 505.4533255 648.3203637 471.9638109 647.4416414 671.4221039 743.3782949 517.5489163 506.3072691 767.2084289 533.7726212 0.94694502 1.214600259 0.884203858 1.21295401 1.257880373 1.392687196 0.969605588 0.948544847 1.437331925 1 9.060081497 -9.249447646 24.73353424 0.989909612 1.164732737 0 0.202872109 725.9523466 1497312.129 0.02224019 0.036691172 5.63E-10 9.249447646 0.174823125 QEEAEEQGAGS(ph)PGQPAHLAR ddPTM_HeLa_Romidepsin_16h_R1 2 QEEAEEQGAGSPGQPAHLAR 20 0 Q96S99 Q96S99 PLEKHF1 Pleckstrin homology domain-containing family F member 1 1 0 QEEAEEQGAGS(1)PGQPAHLAR;QEEAEEQGAGS(1)PGQPAHLAR ; 174.76 2.87E-11 15025000 5375.8 4738.6 5085.8 5700.7 6638.6 7018.9 6894.7 6946.7 5114.4 4971.4 TRUE FALSE FALSE 5310.277682 4805.310135 5174.316216 6359.841757 6299.80747 6570.414942 7480.335646 7147.691804 4656.955255 4842.242311 1.096656743 0.992372919 1.068578539 1.313408406 1.301010372 1.356895116 1.544808204 1.476111963 0.961735278 1 12.24145956 -8.709561842 0.799294215 1.035233117 1.523836441 0.905906036 0.0620659 0.15689692 0.179332709 0.011265692 0.044060542 1.95E-09 8.709561842 0.488603324 QEEEAAQQGPVVVS(ph)PASDYKDK ddPTM_HeLa_Romidepsin_16h_R1 3 QEEEAAQQGPVVVSPASDYKDK 22 1 I3L0X5;I3L4C3;O75391 I3L0X5 SPAG7 Sperm-associated antigen 7 1 0 QEEEAAQQGPVVVS(0.999)PAS(0.001)DYKDK;QEEEAAQQGPVVVS(1)PASDYKDK;QEEEAAQQGPVVVS(0.981)PAS(0.015)DY(0.005)KDK ;; 123.88 2.86E-05 82387000 8653 8195.2 8013.9 6075.6 7769.8 8210.9 6924.8 7527.9 8881.7 7986.8 TRUE FALSE FALSE 8547.533908 8310.572241 8153.378568 6778.089459 7373.278113 7686.249989 7512.992339 7745.707909 8087.298507 7779.301785 1.098753351 1.06829282 1.048086164 0.871297919 0.947807183 0.988038542 0.965766922 0.995681634 1.039591821 1 12.92542496 -9.378540079 11.98481236 1.049964619 0.955980727 0.607384101 0.03906204 0.397505192 38.5887309 0.007476662 0.011421266 4.18E-10 9.378540079 -0.093983892 QEEEDRDS(ph)PGPQVPDPK ddPTM_HeLa_Romidepsin_16h_R1 1 QEEEDRDSPGPQVPDPK 17 1 M0R353;Q6NSJ2-2;Q6NSJ2 M0R353 PHLDB3 Pleckstrin homology-like domain family B member 3 1 0 QEEEDRDS(1)PGPQVPDPK 70.784 0.003904 0 1959.3 2264.9 2047.7 2231.8 2654.1 3165.6 2751.9 3062.8 2011.3 1778.6 TRUE FALSE FALSE 1935.419298 2296.785322 2083.33936 2489.851217 2518.651373 2963.328377 2985.646317 3151.417286 1831.404291 1732.391716 1.117194963 1.325788678 1.202579844 1.437233389 1.453857895 1.710541761 1.723424495 1.819113574 1.057153688 1 10.75854946 -8.411070499 0.376518732 1.002796926 2.07700805 0.955657509 0.058835062 0.321281341 0.057111364 0.019122181 0.139185296 3.88E-09 8.411070499 1.074211124 QEEEQDLDGEKGPS(ph)SEGPEEEDGEGFSFKYSPGK ddPTM_HeLa_Romidepsin_16h_R1 1 QEEEQDLDGEKGPSSEGPEEEDGEGFSFKYSPGK 34 2 P84157-2;P84157-3;P84157 P84157-2 MXRA7 Matrix-remodeling-associated protein 7 1 0 QEEEQDLDGEKGPS(0.398)S(0.398)EGPEEEDGEGFS(0.115)FKY(0.07)S(0.02)PGK 45.325 0.0082232 7660000 1374.4 1257.3 914.06 1007.3 1371.6 1170.9 953.4 1420.9 1676.9 1191.8 TRUE FALSE FALSE 1357.648284 1275.000302 929.9688309 1123.768765 1301.602134 1096.083269 1034.381772 1462.0115 1526.913864 1160.836864 1.169542703 1.098345807 0.801119313 0.96806778 1.121261888 0.944218178 0.891065579 1.259446133 1.315356112 1 10.18094952 QEEGADAS(ph)EEDPTPAGEEDVKDAR ddPTM_HeLa_Romidepsin_16h_R1 2 QEEGADASEEDPTPAGEEDVKDAR 24 1 Q86X53;E5RHA3;H0YB25 Q86X53 ERICH1 Glutamate-rich protein 1 1 0 QEEGADAS(0.903)EEDPT(0.097)PAGEEDVKDAR;QEEGADAS(0.972)EEDPT(0.028)PAGEEDVKDAR ; 82.413 9.12E-05 16760900 4043.3 3871.8 3514.3 1814.62 3371.8 3930.5 2865.4 3482.5 4528.2 3846.1 TRUE FALSE FALSE 3994.018704 3926.307302 3575.464917 2024.434902 3199.724464 3679.353735 3108.787004 3583.260643 4123.186451 3746.177768 1.066158349 1.048083552 0.954430126 0.540400117 0.85413044 0.982162076 0.829855708 0.956511107 1.100638226 1 11.87120365 -9.514822008 24.48031715 1.031847985 0.832507845 0.450555258 0.114351161 214.3342201 651252.9666 0.017550299 0.025503678 3.06E-10 9.514822008 -0.19934014 QEES(ph)ESPVERPLKENPPNK ddPTM_HeLa_Romidepsin_16h_R1 1 QEESESPVERPLKENPPNK 19 2 D6RBF8;H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 D6RBF8 SRPK1 SRSF protein kinase 1 1 0 QEES(0.577)ES(0.423)PVERPLKENPPNK 55.302 0.018665 5646300 1731.2 1674.7 1606.2 1278.1 2042.3 2024.9 1558.4 1963.8 2165.5 1998.2 TRUE FALSE FALSE 1710.099469 1698.276471 1634.155237 1425.879936 1938.07381 1895.515425 1690.770457 2020.619455 1971.812256 1946.286476 0.878647357 0.872572713 0.839627289 0.732615652 0.995780341 0.973913886 0.868716131 1.038192208 1.01311512 1 10.92650836 -7.245029478 23.05778288 0.917997341 1.038192486 0.167026406 0.084556123 1693.710692 2379741.377 0.01228245 0.392765321 5.69E-08 7.245029478 0.120195145 QEESES(ph)PVERPLK ddPTM_HeLa_Romidepsin_16h_R1 1 QEESESPVERPLK 13 1 D6RBF8;H3BLV9;Q96SB4-4;Q96SB4;Q96SB4-3 D6RBF8 SRPK1 SRSF protein kinase 1 1 0 QEES(0.097)ES(0.903)PVERPLK 68.329 0.025435 7670100 3504.3 3143.4 3496.5 1946.2 3371.2 3090.9 2793.9 3152.6 3820.7 3193.9 TRUE FALSE FALSE 3461.588244 3187.652868 3557.355116 2171.228801 3199.155084 2893.401465 3031.213796 3243.815507 3478.967023 3110.922018 1.112720995 1.024664987 1.143505075 0.697937392 1.028362352 0.93007843 0.974377943 1.042718361 1.118307371 1 11.60312652 QEETAVLEEDS(ph)ADWEK ddPTM_HeLa_Romidepsin_16h_R1 1 QEETAVLEEDSADWEK 16 0 Q96A49 Q96A49 SYAP1 Synapse-associated protein 1 1 0 QEETAVLEEDS(1)ADWEK 106.87 0.0038688 3610700 655.33 588.21 609.85 272.14 786.48 821.28 529.09 743.15 785.49 549.44 TRUE FALSE FALSE 647.3425859 596.4908358 620.4641834 303.6061073 746.3429908 768.8028586 574.0308914 764.6518728 715.2338071 535.1654696 1.209612022 1.114591411 1.159387551 0.567312587 1.394602293 1.436570374 1.072623187 1.428813921 1.336472265 1 9.063841222 QEK(ac)PAEKPAETPVATSPTATDSTSGDSSR ddPTM_HeLa_Romidepsin_16h_R1 1 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;H0Y579;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 0 1 QEK(0.977)PAEK(0.023)PAETPVATSPTATDSTSGDSSR 220.62 3.56E-62 2175900 264.31 353.52 359.24 143.98 464.98 404.97 432.38 382.13 612.84 374.23 FALSE TRUE FALSE 261.0884881 358.4968638 365.4924215 160.627645 441.2503355 379.093724 469.1063464 393.1863286 558.0260555 364.5074507 0.716277507 0.983510387 1.002702197 0.440670403 1.21053859 1.040016393 1.286959555 1.078678441 1.530904388 1 8.509804494 QEKPAEKPAETPVAT(ph)SPTATDSTSGDSSR ddPTM_HeLa_Romidepsin_16h_R1 2 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;H0Y579;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 0 QEKPAEKPAET(0.019)PVAT(0.679)S(0.205)PT(0.047)AT(0.028)DS(0.012)T(0.006)S(0.001)GDS(0.001)S(0.001)R;QEKPAEKPAET(0.123)PVAT(0.407)S(0.407)PT(0.051)AT(0.009)DS(0.001)T(0.001)SGDSSR ; 81.455 1.26E-05 396913000 3294 3004 2880.6 3298.9 4061.7 3729.7 3516.6 4247.8 2990.8 3853.3 TRUE FALSE FALSE 3253.851461 3046.290391 2930.735635 3680.33434 3854.416293 3491.384207 3815.299916 4370.703391 2723.295357 3753.190711 0.866956068 0.811653504 0.780865099 0.980588151 1.026970541 0.930244284 1.016548375 1.164530057 0.725594719 1 11.87390188 -6.000736948 0.772163655 0.919595832 2.613851144 0.435640361 0.095427749 10.9952575 1.05286748 0.014150844 25.17311489 9.98E-07 6.000736948 1.694255312 QEKPAEKPAETPVATS(ph)PTATDSTSGDSSR ddPTM_HeLa_Romidepsin_16h_R1 4 QEKPAEKPAETPVATSPTATDSTSGDSSR 29 2 P54727;H0Y579;P54727-2 P54727 RAD23B UV excision repair protein RAD23 homolog B 1 0 QEKPAEKPAET(0.005)PVAT(0.199)S(0.727)PT(0.057)AT(0.009)DS(0.001)T(0.001)S(0.001)GDSSR;QEKPAEKPAET(0.044)PVAT(0.209)S(0.736)PT(0.01)AT(0.001)DSTSGDSSR;QEKPAEKPAETPVAT(0.201)S(0.759)PT(0.031)AT(0.007)DS(0.001)T(0.001)S(0.001)GDSSR;QEKPAEKPAETPVAT(0.178)S(0.582)PT(0.143)AT(0.059)DS(0.018)T(0.014)S(0.006)GDSSR ;;; 108.24 2.03E-09 460575800 8196.76 8545.1 7835.33 8805.77 10050.3 10421.8 9678.75 10398.55 8395.35 7457.52 TRUE FALSE FALSE 8096.854736 8665.398142 7971.700632 9823.93456 9537.395688 9755.880615 10500.86278 10699.41564 7644.448869 7263.772555 1.114690015 1.192961106 1.097460111 1.352456246 1.31300858 1.343087293 1.445648622 1.472983296 1.052407521 1 12.82650331 -8.123970944 0.266431443 0.985532873 1.731378392 0.904055293 0.049577002 1.044881829 0.085188442 0.032166773 0.248940103 7.52E-09 8.123970944 0.745845519 QELGS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 2 QELGSPEER 9 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 QELGS(1)PEER;QELGS(1)PEER ; 110.93 0.0186 90128000 6361.9 5900.5 6343.4 6217.5 6804.8 6351.7 4839.7 5727.7 6738.9 6072 TRUE FALSE FALSE 6284.358716 5983.567394 6453.804216 6936.396604 6457.525664 5945.846869 5250.783997 5893.421963 6136.155906 5914.248565 1.062579404 1.011720649 1.091229789 1.172828049 1.091859024 1.005342742 0.887819296 0.996478572 1.037520801 1 12.52997916 -7.979309361 8.035635009 1.048210253 0.942775479 0.438466927 0.05400838 0.159923569 47.66242526 0.008496454 0.025212232 1.05E-08 7.979309361 -0.105434774 QEMEK(ac)MTKK ddPTM_HeLa_Romidepsin_16h_R1 1 QEMEKMTKK 9 2 P40222;Q9NUQ3;Q9NUQ3-2 P40222;Q9NUQ3 TXLNA;TXLNG Alpha-taxilin;Gamma-taxilin 0 1 QEMEK(1)MTKK 140.45 0.0013595 1316600 428.07 355.52 337.65 188.43 449.41 295.14 214.96 292.26 300.96 254.03 FALSE TRUE FALSE 422.8525182 360.5250199 343.5266566 210.2171632 426.4749307 276.2815065 233.218697 300.716082 274.0413838 247.430264 1.708976547 1.457077296 1.388377683 0.849601661 1.723616682 1.116603531 0.942563344 1.215356914 1.10754998 1 7.950878161 QEMLQTEGSQCAKTFINLMT(ph)HICK ddPTM_HeLa_Romidepsin_16h_R1 1 QEMLQTEGSQCAKTFINLMTHICK 24 1 E5RG49;E5RHH0;G3V126;Q9UI12-2;Q9UI12 E5RG49 ATP6V1H V-type proton ATPase subunit H 1 0 QEMLQTEGSQCAKT(0.001)FINLMT(0.998)HICK 53.475 0.0039977 0 204.94 228.65 336.03 192.47 248.01 448.84 353.6 210.55 165.01 193.04 TRUE FALSE FALSE 202.4421125 231.8689407 341.8784612 214.724287 235.3531242 420.1605726 383.6347752 216.6419321 150.2510923 188.024793 1.076677758 1.2331828 1.818262665 1.141999859 1.251713248 2.234601969 2.040341431 1.152198753 0.799102554 1 7.554779098 -9.541302399 0.609209939 1.002970542 1.762334601 0.391916799 0.35552209 0.576244544 0.432988019 0.087058878 0.183149107 2.88E-10 9.541302399 0.759364059 QENEDSSDAT(ph)TPVPR ddPTM_HeLa_Romidepsin_16h_R1 1 QENEDSSDATTPVPR 15 0 Q6P4R8-3;Q6P4R8;Q6P4R8-2 Q6P4R8-3 NFRKB Nuclear factor related to kappa-B-binding protein 1 0 QENEDS(0.227)S(0.127)DAT(0.52)T(0.127)PVPR 128.59 0.0046867 3248200 599.03 397.73 485.57 551.35 570.66 346.62 377.74 516.18 646.59 613.87 TRUE FALSE FALSE 591.7287919 403.3292534 494.0211422 615.0996812 541.5370908 324.4721007 409.8252262 531.1148539 588.757371 597.9215689 0.989642827 0.674552106 0.826230676 1.028729708 0.905699207 0.54266666 0.685416361 0.888268431 0.984673244 1 9.223812444 -9.602876257 0.423498466 1.016161198 0.71636789 0.252544333 0.136553122 1.049071727 0.409402389 0.057613239 0.124176894 2.50E-10 9.602876257 -0.299793308 QENGDLS(ph)PFSGTSLR ddPTM_HeLa_Romidepsin_16h_R1 1 QENGDLSPFSGTSLR 15 0 P19174-2 P19174-2 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 1 0 QENGDLS(0.997)PFS(0.003)GTSLR 194.05 3.83E-14 0 1912 2079.5 2072.4 1156.6 2167 1864.4 1759.9 2053.7 1986.9 1782.8 TRUE FALSE FALSE 1888.695809 2108.775256 2108.469253 1290.331534 2056.409904 1745.270857 1909.385862 2113.120569 1809.186688 1736.482599 1.087656052 1.214394695 1.214218475 0.743071963 1.184238705 1.005060954 1.099570974 1.21689706 1.041868596 1 10.76195224 -11.93298629 1.024830316 1.005474343 1.089941293 0.041806279 0.136028293 1.176831945 2.414514867 0.060936349 0.024918903 1.17E-12 11.93298629 0.08446695 QEPES(ph)EEEEEEKQEKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QEPESEEEEEEKQEKEEK 18 2 P49756 P49756 RBM25 RNA-binding protein 25 1 0 QEPES(1)EEEEEEKQEKEEK 80.738 0.011807 33597000 4310.4 3867.4 4069.5 3760.5 3529 3806.9 2986.9 3509.3 4481 3937.6 TRUE FALSE FALSE 4257.863187 3921.845359 4140.32794 4195.306704 3348.901961 3563.651376 3240.607211 3610.836059 4080.208137 3835.300584 1.11017718 1.022565317 1.079531538 1.093866468 0.873178487 0.929171338 0.844942173 0.941474072 1.063856156 1 11.90512394 -8.758037732 24.99999971 1.055691171 0.895743672 0.806148651 0.039444411 35.36035229 259872.6129 0.007068234 0.013688488 1.75E-09 8.758037732 -0.159947499 QEPGGSHGS(ph)ETEDTGR ddPTM_HeLa_Romidepsin_16h_R1 2 QEPGGSHGSETEDTGR 16 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 QEPGGS(0.001)HGS(0.959)ET(0.035)EDT(0.006)GR;QEPGGS(0.085)HGS(0.913)ET(0.002)EDTGR ; 175.16 2.27E-06 11218800 2027.59 1993.16 2301.71 1819.42 1766.23 2101.1 2083.25 2104.48 2208.2 2193.3 TRUE FALSE FALSE 2002.876953 2021.219759 2341.770297 2029.789901 1676.092692 1966.846491 2260.201203 2165.369808 2010.693061 2136.31775 0.937537009 0.946123187 1.096171343 0.95013483 0.784570878 0.920671324 1.057989245 1.013599128 0.941195691 1 11.06091053 -9.018230634 24.7941539 0.978151717 0.940241127 0.053873077 0.078936258 1924.134704 2616873.751 0.012493515 0.020985149 9.59E-10 9.018230634 -0.037910589 QEPIES(ph)DEEEAEPPREVEPGQR ddPTM_HeLa_Romidepsin_16h_R1 2 QEPIESDEEEAEPPREVEPGQR 22 1 P56524-2;P56524 P56524-2 HDAC4 Histone deacetylase 4 1 0 QEPIES(1)DEEEAEPPREVEPGQR;QEPIES(1)DEEEAEPPREVEPGQR ; 77.401 0.00078799 59007000 3140.9 3130.2 2718.68 2904.8 2768.9 2599.22 2436.7 2643.82 3091 3370.4 TRUE FALSE FALSE 3102.617503 3174.267038 2765.997485 3240.666643 2627.592701 2433.138231 2643.673237 2720.31476 2814.533218 3282.836522 0.945102652 0.966928148 0.842563273 0.987154438 0.800403152 0.741169478 0.805301519 0.828647647 0.857347967 1 11.68072719 -9.091280893 0.643217959 0.980638838 0.776007009 0.419178059 0.065272811 0.35414133 0.27352289 0.011266519 0.034721079 8.10E-10 9.091280893 -0.204631829 QEPLEEDS(ph)PSSSSAGLDK ddPTM_HeLa_Romidepsin_16h_R1 3 QEPLEEDSPSSSSAGLDK 18 0 P15408;P15408-3;P15408-2;C9JCN8 P15408 FOSL2 Fos-related antigen 2 1 0 QEPLEEDS(0.816)PS(0.176)S(0.007)S(0.001)SAGLDK;QEPLEEDS(0.917)PS(0.081)S(0.002)SSAGLDK;QEPLEEDS(0.857)PS(0.085)S(0.055)S(0.003)SAGLDK ;; 351.02 4.22E-237 99597000 13130.6 12171.2 11866.3 11131.4 9152.8 8290.5 7184.8 7944.3 12742.2 12586.4 TRUE FALSE FALSE 12970.5592 12342.54647 12072.82797 12418.46484 8685.698462 7760.763806 7795.076733 8174.155786 11602.50572 12259.40351 1.058008995 1.006781974 0.984781026 1.012974639 0.708492746 0.633045792 0.635844699 0.666766191 0.946416822 1 13.58160117 -8.719803518 3.779265237 1.023047527 0.647556204 0.96367289 0.032376621 0.023101225 0.688048794 0.00416111 0.00843474 1.91E-09 8.719803518 -0.375491323 PEPTK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPTKSAPAPK 11 1 P58876 P58876 HIST1H2BD Histone H2B type 1-D 0 1 ; PEPTK(1)SAPAPK;PEPTK(1)SAPAPK 158.08 0.0047139 1305450000 3852.3 3916.2 4508.1 15358.1 33876 39191 41346 44044 1038.4 2993.2 FALSE TRUE FALSE 3805.346686 3971.332366 4586.561589 17133.87578 32147.18131 36686.82158 44857.92821 45318.34365 945.5229033 2915.436233 1.305240925 1.36217432 1.573199077 5.876950966 11.02654243 12.58364741 15.38635203 15.54427538 0.324316098 1 11.50949605 -8.740067401 1.208506564 1.075950824 15.31743852 0.989736037 0.611741381 0.028000707 0.080534169 0.090642428 0.254767838 1.82E-09 8.740067401 14.24148769 up QEPQT(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 QEPQTSR 7 0 A0A3B3ISW0;A0A3B3IRF8 A0A3B3ISW0 1 0 QEPQT(0.5)S(0.5)R 78.939 0.0022275 0 840.56 1125.1 1145.4 758.2 949.17 1237.4 620.09 553.67 1058 926.65 TRUE FALSE FALSE 830.3149314 1140.939187 1165.335207 845.8666514 900.7303131 1158.334134 672.7604291 569.6895679 963.3698302 902.5754994 0.919939586 1.264092797 1.291122136 0.937169967 0.997955643 1.283365363 0.745378563 0.631182176 1.067356505 1 9.817903807 -7.579394361 9.020054818 1.024404905 0.659383059 0.51379935 0.147694844 0.184771137 27.36613675 0.022039962 0.083022857 2.63E-08 7.579394361 -0.365021846 QEQALLEEIER ddPTM_HeLa_Romidepsin_16h_R1 2 QEQALLEEIER 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 181.66 7.92E-05 6611300 2432.2 2873.9 2504.8 1724.56 2522 3100.9 2202.41 2731.1 2725.3 2412.9 FALSE FALSE TRUE 2402.555411 2914.35884 2548.394993 1923.961741 2393.292929 2902.762498 2389.48265 2810.12007 2481.542342 2350.21251 1.022271561 1.240040561 1.084325346 0.818633095 1.018330436 1.235106394 1.016709187 1.195687648 1.055879982 1 11.1985755 -4 0.41162261 1.019013459 3.682644179 0.089319547 0.116186023 103.1727083 1.196321258 0.027482727 227.239662 1.00E-04 4 2.66363072 QEQINTEPLEDTVLS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 QEQINTEPLEDTVLSPTK 18 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 QEQINTEPLEDT(0.178)VLS(0.821)PT(0.001)K;QEQINTEPLEDTVLS(0.792)PT(0.208)K ; 200.73 1.01E-20 103841000 35332.7 35391.4 32790.1 26121.5 26406.1 23968.2 20220.3 20120 36740.5 34773.2 TRUE FALSE FALSE 34902.05146 35889.64106 33360.79794 29141.79074 25058.49818 22436.70937 21937.81178 20702.14046 33454.33766 33869.78725 1.030477434 1.059635858 0.984972173 0.860406666 0.739848113 0.662440222 0.647710351 0.611227354 0.987733918 1 15.0477113 -8.843392578 1.385343498 1.019370525 0.633964227 0.982623693 0.022090954 0.036977977 0.142154811 0.003746629 0.009047054 1.43E-09 8.843392578 -0.385406298 QEQINTEPLEDTVLS(ph)PTKK ddPTM_HeLa_Romidepsin_16h_R1 1 QEQINTEPLEDTVLSPTKK 19 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 QEQINTEPLEDT(0.019)VLS(0.843)PT(0.138)KK 90.712 0.0011222 39205000 3076.4 3516.9 3356.1 2556.7 2803.9 2230.7 1820 2208.4 3838.6 3869.5 TRUE FALSE FALSE 3038.903653 3566.411011 3414.511513 2852.317684 2660.80652 2088.165469 1974.590755 2272.29657 3495.266002 3768.969832 0.806295563 0.946256184 0.905953527 0.756789736 0.705977134 0.554041439 0.523907286 0.602895929 0.927379671 1 11.87995453 -8.760508496 1.280408724 0.911431591 0.549087196 0.892327762 0.05370242 0.141182739 0.459599336 0.012310387 0.032891412 1.74E-09 8.760508496 -0.362344395 QERLS(ph)PEVAPPAHR ddPTM_HeLa_Romidepsin_16h_R1 2 QERLSPEVAPPAHR 14 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 0 QERLS(1)PEVAPPAHR;QERLS(1)PEVAPPAHR ; 119.04 0.0015957 253630000 5802.1 5986 5332.9 5579.5 7200.3 9225.1 8289.6 9521.1 6437 5900.4 TRUE FALSE FALSE 5731.381773 6070.271065 5425.716887 6224.628042 6832.841823 8635.645883 8993.718417 9796.578007 5861.258598 5747.106757 0.997263843 1.056230782 0.944077971 1.083088988 1.188918548 1.502607529 1.564912363 1.70461041 1.019862488 1 12.48862013 -8.261039027 1.294588947 0.998871708 1.677791208 0.97923682 0.037918804 0.040102983 0.121235587 0.00514447 0.021833237 5.48E-09 8.261039027 0.6789195 QES(ph)DEESRPQNANYPR ddPTM_HeLa_Romidepsin_16h_R1 1 QESDEESRPQNANYPR 16 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 0 QES(0.991)DEES(0.009)RPQNANYPR 63.16 0.022066 4413500 691.78 442.11 566.52 2396.8 1346.2 1226.9 1042.1 1158.6 556.11 690.78 TRUE FALSE FALSE 683.3483193 448.3340362 576.380043 2673.929293 1277.498391 1148.50505 1130.615948 1192.122263 506.3701288 672.833436 1.015627766 0.666337331 0.856645957 3.974132601 1.898684462 1.706967859 1.680380147 1.771794027 0.752593587 1 9.394105591 QES(ph)DPEDDDVK ddPTM_HeLa_Romidepsin_16h_R1 1 QESDPEDDDVK 11 0 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 1 0 QES(1)DPEDDDVK 98.676 0.02054 5539300 4141.1 3911.4 4448.9 1999.9 4234.1 3494.2 3280.9 3031.7 4290.7 4750.8 TRUE FALSE FALSE 4090.62668 3966.464792 4526.331238 2231.137848 4018.018077 3270.931897 3559.579564 3119.417456 3906.929046 4627.373531 0.884006154 0.857174111 0.978164224 0.48216074 0.86831505 0.706865758 0.769244052 0.674122682 0.84430812 1 12.17597785 -10.00810747 0.453069317 0.987833979 0.69647134 0.293295299 0.123198933 0.623423754 0.306789848 0.045386858 0.067019283 9.82E-11 10.00810747 -0.291362639 QES(ph)DPEDDDVKKPALQSSVVATSK ddPTM_HeLa_Romidepsin_16h_R1 1 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 0 QES(0.985)DPEDDDVKKPALQS(0.012)S(0.003)VVATSK 73.919 0.00073993 234010000 3266.4 2993.4 3071.2 2282.5 3271 2978.9 2621 3302.7 3393.1 3768.9 TRUE FALSE FALSE 3226.58786 3035.541164 3124.652948 2546.413389 3104.068664 2788.557904 2843.627675 3398.258414 3089.612638 3670.983435 0.878943727 0.826901352 0.851175987 0.693659733 0.845568693 0.759621489 0.774622857 0.925707913 0.841630776 1 11.84195089 -11.09546456 0.599402992 0.992772554 0.79860204 0.164363521 0.07479277 0.332586316 0.270948719 0.027167555 0.016326907 8.03E-12 11.09546456 -0.194170513 QESDPEDDDVKKPALQS(ph)SVVATSK ddPTM_HeLa_Romidepsin_16h_R1 1 QESDPEDDDVKKPALQSSVVATSK 24 2 Q9H307 Q9H307 PNN Pinin 1 0 QES(0.003)DPEDDDVKKPALQS(0.49)S(0.49)VVAT(0.012)S(0.005)K 70.15 0.00047662 250030000 3679.2 3440.2 3240.1 2469.2 3308.2 2952.3 2507.7 3349.3 3557.2 3273.9 TRUE FALSE FALSE 3634.356495 3488.631226 3296.492581 2754.700522 3139.370209 2763.657558 2720.703975 3446.206711 3239.035123 3188.843606 1.139709859 1.09401139 1.033757998 0.863855636 0.984485474 0.866664503 0.853194547 1.080707346 1.015739724 1 11.63881763 -9.427566704 5.297509479 1.069716551 0.92558996 0.431082116 0.073091302 0.16356888 7.15892528 0.012115591 0.018560054 3.74E-10 9.427566704 -0.14412659 QESSSSVNT(ph)SNKMNFK ddPTM_HeLa_Romidepsin_16h_R1 1 QESSSSVNTSNKMNFK 16 1 Q12923-2;Q12923-3;Q12923;Q12923-4 Q12923-2 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 0 QES(0.206)S(0.206)S(0.206)S(0.042)VNT(0.338)S(0.001)NKMNFK 80.96 0.012935 5645200 761.37 672.44 692.76 653.04 757.34 1065.4 1369.3 1356.5 836.23 517.37 TRUE FALSE FALSE 752.0901296 681.906628 704.8171972 728.5475574 718.6901138 997.3243784 1485.608308 1395.748187 761.4354944 503.9286528 1.492453595 1.3531809 1.398644815 1.445735529 1.42617434 1.979098376 2.948052863 2.76973373 1.510998611 1 8.977075678 -7.993974127 1.916950488 1.277798331 2.92120569 0.920666216 0.171071125 0.076543817 0.533426703 0.031276719 0.133116832 1.01E-08 7.993974127 1.64340736 up QETKLKLMAR ddPTM_HeLa_Romidepsin_16h_R1 1 QETKLKLMAR 10 2 D6RJ07;Q9UL40-3;Q9UL40;Q9UL40-2;B7Z4J8 D6RJ07 ZNF346 Zinc finger protein 346 0 0 83.998 0.017696 0 3858.6 3590.2 3793.1 3840.2 3368.5 3094.5 3630.9 3008.1 4931.2 3404 FALSE FALSE TRUE 3811.569899 3640.74293 3859.117314 4284.221993 3196.592875 2896.771437 3939.308555 3095.134628 4490.141122 3315.563589 1.149599396 1.098076641 1.163940069 1.292154977 0.964117499 0.873689 1.188126377 0.933516895 1.354261802 1 11.69503841 -7.225380164 22.53556107 1.080418011 0.933515676 0.076280139 0.143606281 8274.133679 5170654.376 0.016449293 3.812432165 5.95E-08 7.225380164 -0.146902334 QEVPSWLENMAYEHHYK ddPTM_HeLa_Romidepsin_16h_R1 1 QEVPSWLENMAYEHHYK 17 0 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1;O15523-2;O15523 A0A2R8Y4A4 DDX3X;DDX3Y ATP-dependent RNA helicase DDX3X;ATP-dependent RNA helicase DDX3Y 0 0 62.469 0.015864 15564000 2479 1975 2429.2 2466.8 2159.7 2283.7 1832.1 2237.4 2335.4 2313.9 FALSE FALSE TRUE 2448.784994 2002.804102 2471.479207 2752.023023 2049.48245 2137.77894 1987.718528 2302.135639 2126.515975 2253.784544 1.086521336 0.888640446 1.096590716 1.221067484 0.909351542 0.94852853 0.881947005 1.02145329 0.943531173 1 11.13813389 QEYDESGPS(ph)IVHR ddPTM_HeLa_Romidepsin_16h_R1 2 QEYDESGPSIVHR 13 0 P0CG38;P0CG39;P60709;Q6S8J3;A5A3E0;A0A2R8YFE2;Q9BYX7;P63261 P0CG38;P60709;P63261 POTEI;POTEJ;ACTB;POTEE;POTEF;POTEKP;ACTG1 "POTE ankyrin domain family member I;POTE ankyrin domain family member J;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 1 0 QEYDESGPS(1)IVHR;QEYDESGPS(1)IVHR ; 235.02 1.23E-41 34828000 10974.9 12441.4 11303 9352.2 16901.7 15235.4 13821.3 14435.9 13041.8 13301.6 TRUE FALSE FALSE 10841.1337 12616.55036 11499.72397 10433.54537 16039.14318 14261.90711 14995.28088 14853.57999 11875.30874 12956.02251 0.836764037 0.973798119 0.887596788 0.805304665 1.237968147 1.100793634 1.157398489 1.146461422 0.916585992 1 13.66133526 -8.757394338 24.99999166 0.915067629 1.156146956 0.8001879 0.062811834 43.39288177 268181.6464 0.011116434 0.021594849 1.75E-09 8.757394338 0.241079327 QEYDESGPSIVHR ddPTM_HeLa_Romidepsin_16h_R1 6 QEYDESGPSIVHR 13 0 P0CG38;P0CG39;P60709;Q6S8J3;A5A3E0;A0A2R8YFE2;Q9BYX7;P63261 P0CG38;P60709;P63261 POTEI;POTEJ;ACTB;POTEE;POTEF;POTEKP;ACTG1 "POTE ankyrin domain family member I;POTE ankyrin domain family member J;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 0 ;;;;; ;;;;; 278.35 1.99E-93 222746200 17032.7 18304.8 16658.5 16091.6 23430.2 26129.4 19832 22154.1 21983.8 22455.4 FALSE FALSE TRUE 16825.0989 18562.49545 16948.4342 17952.18651 22234.46946 24459.81567 21516.52958 22795.09393 20017.51387 21872.00547 0.769252683 0.8486874 0.774891641 0.820783742 1.016572051 1.118316091 0.983747449 1.042204107 0.915211634 1 14.41679789 -8.672236951 5.90796156 0.871054356 1.045020813 0.616422685 0.071151586 0.162150176 8.632730271 0.014536282 0.029260208 2.13E-09 8.672236951 0.173966456 QEYDESGPSIVHRK ddPTM_HeLa_Romidepsin_16h_R1 1 QEYDESGPSIVHRK 14 1 P0CG38;P0CG39;P60709;Q6S8J3;A5A3E0;A0A2R8YFE2;Q9BYX7;P63261 P0CG38;P60709;P63261 POTEI;POTEJ;ACTB;POTEE;POTEF;POTEKP;ACTG1 "POTE ankyrin domain family member I;POTE ankyrin domain family member J;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Putative beta-actin-like protein 3;Putative beta-actin-like protein 3, N-terminally processed;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed" 0 0 44.968 0.030147 7752300 2364.3 2199.7 1619.1 2955 2907.5 2849.4 1940.7 2301.7 2827.5 2978.1 FALSE FALSE TRUE 2335.483002 2230.667434 1647.279756 3296.671004 2759.119426 2667.332536 2105.54301 2368.296058 2574.601318 2900.728533 0.805136701 0.76900248 0.567884839 1.136497596 0.951181538 0.919538835 0.725866963 0.816448706 0.887570584 1 11.50219957 -12.27088579 1.050376386 0.998048388 0.837225058 0.060968849 0.145399554 0.794438205 1.598952334 0.091678245 0.026117191 5.36E-13 12.27088579 -0.16082333 QFDIQLLTHNDPK ddPTM_HeLa_Romidepsin_16h_R1 1 QFDIQLLTHNDPK 13 0 P48507-2;P48507 P48507-2 GCLM Glutamate--cysteine ligase regulatory subunit 0 0 59.227 0.028746 344840 406.63 195.1 242.12 252.77 189.27 149.53 140.23 141.15 179.21 145.3 FALSE FALSE TRUE 401.6738372 197.8466229 246.333997 281.9964567 179.6108456 139.9755156 152.1411327 145.2339526 163.1810088 141.5250851 2.83818121 1.397961519 1.740567737 1.992554582 1.269109611 0.98905092 1.075011774 1.026206432 1.15301827 1 7.14491398 -8.62613674 4.166843487 1.845743311 1.045812902 0.233813567 0.492411865 0.257422418 8.144495334 0.100194056 0.207206408 2.37E-09 8.62613674 -0.799930409 QFEDELHPDLK ddPTM_HeLa_Romidepsin_16h_R1 1 QFEDELHPDLK 11 0 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 0 0 81.494 0.024764 5231600 6983.4 7210.9 6248.4 6469.5 6518.3 6248.3 5934.7 5892.1 7683.8 7073.3 FALSE FALSE TRUE 6898.283635 7312.415239 6357.150781 7217.53403 6185.646828 5849.053795 6438.79327 6062.578617 6996.541684 6889.534646 1.001269895 1.061380139 0.922725715 1.047608351 0.897832313 0.848976614 0.934575933 0.879969247 1.015531824 1 12.75019082 -8.710443388 9.207922162 1.002104915 0.890210402 0.675322099 0.039870928 0.142594885 24.17120395 0.005119266 0.01023164 1.95E-09 8.710443388 -0.111894513 QFHLTDDDLLR ddPTM_HeLa_Romidepsin_16h_R1 1 QFHLTDDDLLR 11 0 E9PGM4;Q04446 E9PGM4 GBE1 "1,4-alpha-glucan-branching enzyme" 0 0 107.03 0.0074574 2807100 1527.9 1356 1203.9 734.75 1287.3 1361.2 1273.4 1496.3 1527.3 1377.9 FALSE FALSE TRUE 1509.277367 1375.089804 1224.853374 819.7052521 1221.604277 1274.223713 1381.562564 1539.59308 1390.694463 1342.101959 1.124562375 1.024579239 0.912638094 0.61076228 0.910217192 0.949423927 1.029402092 1.147150609 1.036206268 1 10.39027856 -9.843946361 4.636070467 1.059307054 0.917302904 0.168261193 0.130003633 0.275481847 10.77415989 0.022831547 0.030474748 1.43E-10 9.843946361 -0.14200415 QFKIFS(ph)DFR ddPTM_HeLa_Romidepsin_16h_R1 2 QFKIFSDFR 9 1 Q0VDD8-4;M9MMK7;Q0VDD8-2 Q0VDD8-4 DNAH14 "Dynein heavy chain 14, axonemal" 1 0 QFKIFS(1)DFR;QFKIFS(1)DFR ; 111.95 0.0066592 152216000 6151.5 4753.6 7730.9 7689 9088.4 8330.7 6133.6 4914.5 4839.5 3929.9 TRUE FALSE FALSE 6076.523152 4820.521306 7865.453072 8578.038358 8624.585035 7798.395156 6654.587831 5056.693304 4406.642999 3827.800631 1.587471171 1.259344927 2.054823077 2.240983579 2.253143741 2.037304423 1.738488618 1.321044064 1.151220616 1 11.90229997 -11.00206622 0.570678121 1.047323017 1.932488075 0.501663786 0.313221584 0.453571923 0.342181794 0.163145865 0.104263613 9.95E-12 11.00206622 0.885165059 QFLIS(ph)PPASPPVGWK ddPTM_HeLa_Romidepsin_16h_R1 1 QFLISPPASPPVGWK 15 0 H0YF64;V9GYW9;E9PD55;E9PDJ2;Q9UKA8-6;P53805-4;P53805-3;Q9UKA8-5;P53805-2;Q9UKA8-2;Q9UKA8;P53805 H0YF64 RCAN3;RCAN1 Calcipressin-3;Calcipressin-1 1 0 QFLIS(0.831)PPAS(0.169)PPVGWK 126.71 0.0025855 16912000 4619.8 4527.1 5306.1 5334.4 5856.4 6084 5130.4 5521.3 4859.1 4567.9 TRUE FALSE FALSE 4563.492101 4590.832633 5398.450445 5951.188427 5557.526055 5695.252035 5566.176048 5681.050104 4424.489926 4449.225299 1.025682404 1.031827413 1.213346163 1.337578573 1.249099715 1.280054763 1.251043872 1.276862762 0.994440521 1 12.11933844 -9.705578238 3.291464531 1.012560804 1.276111717 0.963272514 0.024676588 0.028884817 0.63872944 0.003798555 0.005388854 1.97E-10 9.705578238 0.263550912 QFLISPPAS(ph)PPVGWK ddPTM_HeLa_Romidepsin_16h_R1 2 QFLISPPASPPVGWK 15 0 H0YF64;V9GYW9;E9PD55;E9PDJ2;Q9UKA8-6;P53805-4;P53805-3;Q9UKA8-5;P53805-2;Q9UKA8-2;Q9UKA8;P53805 H0YF64 RCAN3;RCAN1 Calcipressin-3;Calcipressin-1 1 0 QFLIS(0.007)PPAS(0.993)PPVGWK;QFLIS(0.231)PPAS(0.769)PPVGWK ; 117.13 0.0014311 19632000 5681 5329.3 6234.7 6803 7133.7 6333.9 5652.3 6955.2 5766.6 5671.9 TRUE FALSE FALSE 5611.757787 5404.326025 6343.212338 7589.594869 6769.640669 5929.184232 6132.406221 7156.437739 5250.820853 5524.54322 1.015786747 0.978239433 1.148187657 1.373795908 1.225375637 1.073244248 1.110029549 1.295389945 0.950453394 1 12.43163947 -9.643084467 4.786918749 1.005737983 1.207342121 0.630539462 0.082309963 0.114795267 4.351666427 0.013073843 0.018600326 2.27E-10 9.643084467 0.201604138 QFS(ph)ALVPAFDPRPGR ddPTM_HeLa_Romidepsin_16h_R1 1 QFSALVPAFDPRPGR 15 1 H0YJD4;H0YJP0;A0A087X2H1;Q9ULT8 H0YJD4 HECTD1 E3 ubiquitin-protein ligase HECTD1 1 0 QFS(1)ALVPAFDPRPGR 86.179 0.0078206 4608600 1297.3 1423.5 897.95 1331.8 1239.6 846.07 787.36 927.72 1134.7 1008.9 TRUE FALSE FALSE 1281.488009 1443.54007 913.5784431 1485.788982 1176.338586 792.0088576 854.2383387 954.5621145 1033.20959 982.6886326 1.304063125 1.468969949 0.929672343 1.511963132 1.197061355 0.805961147 0.869286883 0.971377996 1.051410951 1 9.940590557 -8.269129844 24.2102408 1.186668123 0.880916494 0.399031734 0.182352391 318.1815611 1001664.753 0.027731528 0.063178115 5.38E-09 8.269129844 -0.305751629 QFS(ph)QYIK ddPTM_HeLa_Romidepsin_16h_R1 1 QFSQYIK 7 0 A0A2R8Y6J3;P46777 A0A2R8Y6J3 RPL5 60S ribosomal protein L5 1 0 QFS(1)QYIK 98.418 0.0042067 0 4645 2118.2 4008.8 868.11 2696.5 2216.2 5772.9 1271.6 4789.9 3596.6 TRUE FALSE FALSE 4588.384953 2148.020075 4078.571482 968.4849628 2558.887543 2074.591972 6263.249982 1308.39174 4361.479347 3503.159814 1.309784651 0.613166452 1.164255044 0.2764604 0.730451272 0.592205918 1.787885885 0.373489024 1.245012954 1 11.77444109 -10.26537132 24.95458619 1.146287195 0.814038482 0.156716385 0.413343527 509.1196577 3231188.683 0.067032458 0.078164576 5.43E-11 10.26537132 -0.332248714 QFSIQAEDERES(ph)TDDESNPLGR ddPTM_HeLa_Romidepsin_16h_R1 2 QFSIQAEDERESTDDESNPLGR 22 1 Q14669;Q14669-2;Q14669-3;Q14669-4 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 QFSIQAEDERES(0.679)T(0.317)DDES(0.004)NPLGR;QFS(0.001)IQAEDERES(0.713)T(0.284)DDES(0.003)NPLGR ; 59.792 0.0053324 14398800 1969.86 2209.57 2188.29 1865.35 1730.31 1947.29 1677.1 1700.97 2215.8 2375.4 TRUE FALSE FALSE 1945.850589 2240.676384 2226.37627 2081.030544 1642.005824 1822.864454 1819.552832 1750.184883 2017.613298 2313.686766 0.841017297 0.968444138 0.962263476 0.899443509 0.709692361 0.787861382 0.786430064 0.7564485 0.872033902 1 11.17597785 -8.869034602 5.706168348 0.929474695 0.764582778 0.737883481 0.047968342 0.107196034 5.037427401 0.009383623 0.017232416 1.35E-09 8.869034602 -0.164891918 QFTELLS(ph)DIGFAREGLR ddPTM_HeLa_Romidepsin_16h_R1 1 QFTELLSDIGFAREGLR 17 1 Q6P158;H7C109 Q6P158 DHX57 Putative ATP-dependent RNA helicase DHX57 1 0 QFT(0.019)ELLS(0.981)DIGFAREGLR 55.815 0.028718 241950000 2535.4 2413.8 2373 2545.4 2860.6 2930.2 2688 2549.8 3167.4 2554.2 TRUE FALSE FALSE 2504.49757 2447.78154 2414.30107 2839.711124 2714.612908 2742.969677 2916.318653 2623.57444 2884.099811 2487.841516 1.006694982 0.983897698 0.97044006 1.141435701 1.091151864 1.102550005 1.17222847 1.054558509 1.159277949 1 11.28067887 -9.261025257 24.99999994 0.999259559 1.113983557 0.318889092 0.059209553 12.17239625 734815.8606 0.004295847 0.006841442 5.48E-10 9.261025257 0.114723998 QFTQS(ph)PETEASADSFPDTK ddPTM_HeLa_Romidepsin_16h_R1 2 QFTQSPETEASADSFPDTK 19 0 O15061;H0YL34;A0A075B7B1;O15061-2 O15061 SYNM Synemin 1 0 QFT(0.292)QS(0.605)PET(0.102)EAS(0.001)ADSFPDTK;QFT(0.111)QS(0.58)PET(0.306)EAS(0.003)ADSFPDTK ; 82.627 0.0031489 15054300 7653.7 6188.3 6262.3 7516 7817.8 8376 6490.8 7241.2 7417.5 7408.1 TRUE FALSE FALSE 7560.41376 6275.41905 6371.292705 8385.035284 7418.828494 7840.800632 7042.12839 7450.712697 6754.060223 7215.636494 1.047781962 0.869697227 0.882984157 1.162064537 1.028159955 1.086640193 0.975953874 1.03257872 0.936031108 1 12.81691095 -9.256623844 24.99637273 0.999723107 1.052608095 0.22250487 0.075441881 797.9514047 4141988.352 0.011864865 0.019263976 5.54E-10 9.256623844 0.052884987 QGAIYHGLATLLNQPS(ph)PMMQR ddPTM_HeLa_Romidepsin_16h_R1 1 QGAIYHGLATLLNQPSPMMQR 21 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 QGAIYHGLATLLNQPS(1)PMMQR 76.959 0.0010784 22349000 1588.1 1697.2 1281.6 1978.3 2502.7 2198.1 2163.7 2109.9 1354.4 1338.1 TRUE FALSE FALSE 1568.743626 1721.093226 1303.90571 2207.040354 2374.97788 2057.648504 2347.484624 2170.946628 1233.259072 1303.335969 1.203637177 1.320529217 1.000437141 1.693377921 1.822229982 1.57875525 1.801135455 1.665684581 0.946232668 1 10.34799331 -9.253375089 24.42432986 1.112474941 1.71587062 0.868098739 0.120351285 117.5084466 355897.6014 0.018288967 0.029967521 5.58E-10 9.253375089 0.603395679 QGALIAS(ph)ALIMIQQT(ph)EIT(ph)CPK ddPTM_HeLa_Romidepsin_16h_R1 1 QGALIASALIMIQQTEITCPK 21 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 3 0 QGALIAS(1)ALIMIQQT(1)EIT(1)CPK 68.088 0.0021938 3967100 2847.4 2481.2 2627.9 1716.6 3115.7 2810.7 2511.5 2652.4 2596.1 2203.8 TRUE FALSE FALSE 2812.694794 2516.130399 2673.637497 1915.081369 2956.694203 2631.105341 2724.826747 2729.143009 2363.898314 2146.544958 1.310335841 1.172176892 1.245553925 0.892169233 1.377420115 1.225739685 1.269401201 1.271411996 1.101257304 1 11.06780067 -12.45957933 1.14735555 0.997721572 1.225085255 0.213402726 0.12535801 0.473839418 1.097824402 0.08706306 0.020669776 3.47E-13 12.45957933 0.227363684 QGDETPSTNNGS(ph)DDEKTGLK ddPTM_HeLa_Romidepsin_16h_R1 2 QGDETPSTNNGSDDEKTGLK 20 1 Q9Y3P9;C9JGR5;B5MCD9;Q9Y3P9-4;Q9Y3P9-3 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 0 QGDET(0.003)PS(0.079)T(0.079)NNGS(0.837)DDEKT(0.001)GLK;QGDET(0.002)PS(0.028)T(0.028)NNGS(0.941)DDEKT(0.001)GLK ; 79.236 0.0018014 27413000 2923.5 2901.9 2413.2 2875.2 3477.2 3189.4 2820.6 2857.1 3135.2 2915.5 TRUE FALSE FALSE 2887.867258 2942.753024 2455.200734 3207.644152 3299.745509 2985.607633 3060.181694 2939.765681 2854.77986 2839.75489 1.016942437 1.036270079 0.86458192 1.129549654 1.161982508 1.051361033 1.077621771 1.035218107 1.005290939 1 11.4715507 QGDGK(ac)WHLVYR ddPTM_HeLa_Romidepsin_16h_R1 1 QGDGKWHLVYR 11 1 Q5JX58;Q5JX59;Q5JX61;Q5JX60;Q5JX44;Q5JX52;Q5JX45;E7ENH5;A6PVH9;F2Z2V0;B0QZ18;Q99829 Q5JX58 CPNE1 Copine-1 0 1 QGDGK(1)WHLVYR 87.667 0.0055231 0 559.46 587.28 559.55 451.44 476.07 598.18 566.37 433.7 776.51 521.17 FALSE TRUE FALSE 552.6410863 595.5477433 569.288733 503.6376169 451.7743714 559.9582285 614.4774537 446.2484252 707.0570008 507.6299283 1.088669236 1.173192734 1.121464085 0.99213539 0.889967959 1.10308356 1.210483109 0.879082182 1.39285917 1 8.987633318 -7.209960368 22.88186023 1.055781169 0.879079427 0.104643879 0.13915081 22616.39383 10051917.18 0.012874395 16.77964032 6.17E-08 7.209960368 -0.176701742 QGDTGDWIGTFLGHK ddPTM_HeLa_Romidepsin_16h_R1 2 QGDTGDWIGTFLGHK 15 0 Q9Y3F4;Q9Y3F4-2 Q9Y3F4 STRAP Serine-threonine kinase receptor-associated protein 0 0 ; ; 117.53 0.0017455 12503400 11657.5 10821.4 11209.6 10483.5 12953.5 13373.1 11023 11901.4 13354.6 11416.2 FALSE FALSE TRUE 11515.41391 10973.74395 11404.69839 11695.6516 12292.43456 12518.60207 11959.29334 12245.74823 12160.13113 11119.60548 1.035595546 0.986882491 1.025638761 1.051804546 1.105473983 1.12581351 1.075514178 1.101275423 1.093575771 1 13.44081798 -8.989002365 2.490312049 1.015063187 1.102056071 0.552855241 0.030098682 0.088509199 1.104491575 0.002984566 0.005663621 1.03E-09 8.989002365 0.086992883 QGEVPES(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 1 QGEVPESPEAR 11 0 H7BYP4;U5Y3L1;Q9H930-3;Q9H930-1;Q9H930-2;Q9H930 H7BYP4 SP140L Nuclear body protein SP140-like protein 1 0 QGEVPES(1)PEAR 108.97 0.015044 13481000 3411.2 3433.7 3207.6 3363.5 3254 2863.6 2569.1 3102.2 3840.5 3450 TRUE FALSE FALSE 3369.622982 3482.039719 3263.426932 3752.403696 3087.936238 2680.625202 2787.31929 3191.957263 3496.996061 3360.368503 1.002754007 1.0362077 0.971151506 1.116664346 0.91892786 0.797717631 0.829468342 0.949883104 1.040658505 1 11.71440373 -8.529289011 24.99475134 1.009291892 0.856443413 0.67443736 0.052657657 66.43654453 259047.4362 0.006912184 0.013852396 2.96E-09 8.529289011 -0.152848479 QGGSQPSSFS(ph)PGQSQVTPQDQEK ddPTM_HeLa_Romidepsin_16h_R1 1 QGGSQPSSFSPGQSQVTPQDQEK 23 0 Q9H0L4 Q9H0L4 CSTF2T Cleavage stimulation factor subunit 2 tau variant 1 0 QGGS(0.001)QPS(0.013)S(0.013)FS(0.947)PGQS(0.027)QVTPQDQEK 100.17 1.01E-05 0 865.8 977.5 1083.7 1212 1113.1 1106 813.93 726.6 1054.7 947.73 TRUE FALSE FALSE 855.2472966 991.2612707 1102.561344 1352.137143 1056.294353 1035.330169 883.0651939 747.6230246 960.3649905 923.107838 0.926486876 1.073830413 1.194401454 1.464766181 1.14428056 1.121570121 0.956621922 0.809897819 1.040360563 1 9.850355384 -10.08867822 4.713700563 0.965751557 1.126238738 0.102493154 0.160294693 0.313888769 12.00108595 0.028359017 0.035146006 8.15E-11 10.08867822 0.160487181 QGLAETAS(ph)PVAVSLR ddPTM_HeLa_Romidepsin_16h_R1 1 QGLAETASPVAVSLR 15 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;Q15154-4;Q15154-2;Q15154 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 QGLAET(0.001)AS(0.85)PVAVS(0.149)LR 193.41 1.37E-12 46618000 2219.7 2096.2 2081.5 1814.4 2754.3 2558.7 2713.5 2451.3 2388.4 2542.8 TRUE FALSE FALSE 2192.645443 2125.710359 2117.727634 2024.189465 2613.737793 2395.207328 2943.984622 2522.224498 2174.775522 2476.737689 0.885295787 0.858270283 0.855047203 0.817280519 1.055314741 0.967081552 1.188654186 1.018365614 0.878080683 1 11.27422537 -8.260203068 1.851157916 0.923572772 1.091675857 0.479664916 0.078973602 0.278808552 1.816772877 0.012582784 0.041250773 5.49E-09 8.260203068 0.168103086 QGLAETASPVAVS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 QGLAETASPVAVSLR 15 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;Q15154-4;Q15154-2;Q15154 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 QGLAET(0.054)AS(0.294)PVAVS(0.652)LR 97.2 0.0099776 46158000 2240.7 1642 1572.4 1422.1 2548.3 2093.3 2286.9 2158.7 1978.3 2275.7 TRUE FALSE FALSE 2213.389487 1665.116119 1599.766962 1586.529893 2418.250742 1959.544886 2481.149229 2221.158579 1801.355893 2216.576986 0.998561972 0.751210596 0.721728581 0.715756729 1.090984323 0.884040978 1.119360728 1.002066968 0.812674635 1 11.11411776 -7.761677231 24.99999995 0.941874274 1.060713848 0.085205928 0.138451432 11.30973243 1189463.635 0.020675889 0.0684031 1.73E-08 7.761677231 0.118839574 QGPGPGGPK(ac)GGK ddPTM_HeLa_Romidepsin_16h_R1 1 QGPGPGGPKGGK 12 1 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 1 QGPGPGGPK(1)GGK 125.97 0.011583 338760 146.53 51.919 0 163.3 192.39 219.01 93.433 0 176.26 131.8 FALSE TRUE FALSE 144.744036 52.64991704 0 182.1815143 182.5716204 205.0159678 101.3691967 0 160.4948641 128.375817 1.127502355 0.410123326 0 1.419126426 1.422165207 1.596998349 0.789628444 0 1.250195464 1 7.004229648 QGPSPVS(ph)PNALDR ddPTM_HeLa_Romidepsin_16h_R1 2 QGPSPVSPNALDR 13 0 H0Y3A3;A0A3B3ITG3;Q5VWQ8-3;Q5VWQ8-4;Q5VWQ8-2;Q5VWQ8-5;Q5VWQ8 H0Y3A3 DAB2IP Disabled homolog 2-interacting protein 1 0 QGPS(0.002)PVS(0.998)PNALDR;QGPS(0.029)PVS(0.971)PNALDR ; 144.15 0.00076759 14728000 2386 2271.1 2184.21 2225 2593.7 2215.8 1746.48 1989.62 2692 2206.57 TRUE FALSE FALSE 2356.918514 2303.072605 2222.225259 2482.264969 2461.333811 2074.217531 1894.825968 2047.186516 2451.220778 2149.242993 1.096627288 1.071573858 1.033957196 1.154948499 1.145209647 0.965092145 0.88162482 0.952515152 1.140504254 1 11.06961289 -8.04533123 6.933007244 1.061781759 0.918233651 0.613893827 0.055016747 0.128010915 16.28431037 0.008311121 0.021810609 9.01E-09 8.04533123 -0.143548108 QGPVSQSATQQPVT(ph)ADKQQGHEPVSPR ddPTM_HeLa_Romidepsin_16h_R1 1 QGPVSQSATQQPVTADKQQGHEPVSPR 27 1 A0A0A0MRT2;Q9BTA9-5;Q9BTA9-2;Q9BTA9 A0A0A0MRT2 WAC WW domain-containing adapter protein with coiled-coil 1 0 QGPVS(0.001)QS(0.006)AT(0.094)QQPVT(0.755)ADKQQGHEPVS(0.144)PR 52.926 0.0042205 7153000 1934.3 1727.3 1520.3 1790.2 1672.5 1651.7 1427 1513.4 1711.8 1633.1 TRUE FALSE FALSE 1910.724008 1751.616975 1546.760184 1997.191347 1587.146084 1546.161701 1548.209344 1557.187841 1558.692321 1590.671827 1.201205664 1.101180612 0.972394279 1.25556467 0.997783488 0.972018033 0.973305316 0.978949784 0.979895598 1 10.63542051 -8.549778004 24.99958372 1.098720886 0.976327072 0.253731272 0.086583719 211.2828426 196360.8665 0.013507907 0.027016321 2.82E-09 8.549778004 -0.122393814 QGQDVAPPPNPVPQRT(ph)SPTGPK ddPTM_HeLa_Romidepsin_16h_R1 1 QGQDVAPPPNPVPQRTSPTGPK 22 1 Q9UPY8-2 Q9UPY8-2 MAPRE3 Microtubule-associated protein RP/EB family member 3 1 0 QGQDVAPPPNPVPQRT(0.462)S(0.462)PT(0.076)GPK 73.654 0.0017281 17253000 3279.8 2653.1 2446 4655.5 4995.9 4481.3 4021.8 5394.8 2791.7 2741 TRUE FALSE FALSE 3239.824536 2690.450411 2488.571604 5193.790815 4740.940581 4194.959393 4363.411592 5550.890026 2542.00336 2669.788425 1.21351359 1.007739185 0.932123153 1.945394162 1.775773892 1.57127035 1.634366061 2.079149784 0.952136632 1 11.3825097 -9.262258108 24.99888097 1.083422059 1.777737403 0.856153201 0.158708648 22.60953453 690355.668 0.024763645 0.039225136 5.47E-10 9.262258108 0.694315344 QGQSQAASSSSVT(ph)SPIK ddPTM_HeLa_Romidepsin_16h_R1 2 QGQSQAASSSSVTSPIK 17 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 0 QGQSQAASSSSVT(0.907)S(0.092)PIK;QGQSQAASSSSVT(0.5)S(0.5)PIK ; 216 1.86E-26 47092000 8597.9 7451.3 7764.3 6965.5 5918.2 5151.1 4193.2 4788.5 8631.6 7569.2 TRUE FALSE FALSE 8493.105488 7556.199597 7899.434385 7770.883884 5616.17217 4821.961334 4549.370303 4927.047692 7859.568078 7372.551093 1.151990048 1.024909764 1.071465533 1.054029167 0.76176782 0.654042444 0.617068671 0.668296175 1.066058136 1 12.8479482 -8.663875015 2.767357948 1.07023175 0.646358984 0.958435688 0.039880937 0.052222068 0.807309138 0.008783776 0.018985157 2.17E-09 8.663875015 -0.423872766 QGS(ph)FSEDVISHK ddPTM_HeLa_Romidepsin_16h_R1 4 QGSFSEDVISHK 12 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5;E9PNZ4 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 QGS(0.95)FS(0.048)EDVIS(0.002)HK;QGS(0.859)FS(0.14)EDVIS(0.001)HK;QGS(0.95)FS(0.05)EDVISHK;QGS(0.949)FS(0.051)EDVISHK ;;; 117.53 0.0034739 79285000 16036.7 15050.3 13782.3 14425.6 16657.6 17215.3 15010.9 16823.5 18171.4 16566.1 TRUE FALSE FALSE 15841.23853 15262.17852 14022.17515 16093.55575 15807.50051 16115.29789 16285.92547 17310.26143 16546.10447 16135.71033 0.981750304 0.945863442 0.869015052 0.997387497 0.979659413 0.998734952 1.009309484 1.072792029 1.025433906 1 13.97796947 -7.035091734 1.176589378 0.978234174 1.157342519 0.363413293 0.040237955 2.218745067 1.781350634 0.006092318 0.550439886 9.22E-08 7.035091734 0.179108345 QGS(ph)FTIEKPSPNIPIELIPHINK ddPTM_HeLa_Romidepsin_16h_R1 2 QGSFTIEKPSPNIPIELIPHINK 23 1 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 QGS(0.49)FT(0.49)IEKPS(0.021)PNIPIELIPHINK;QGS(0.499)FT(0.499)IEKPS(0.003)PNIPIELIPHINK ; 68.168 0.0006736 106513000 12387.5 12606.6 11801.1 12699.9 13034.8 11947.2 11651 12938.1 13476.9 12484.4 TRUE FALSE FALSE 12236.51639 12784.07605 12006.4932 14168.32219 12369.58552 11183.81248 12640.63565 13312.44351 12271.49231 12160.05349 1.00628804 1.051317419 0.987371742 1.16515295 1.017231177 0.919717375 1.039521385 1.094768499 1.009164337 1 13.56986195 -10.35685705 6.199101023 1.00278562 1.036658574 0.06119593 0.060537092 0.551575519 29.89823456 0.010369116 0.011818861 4.40E-11 10.35685705 0.033872954 QGS(ph)PDQVS(ph)PVSEMTSTSLYQDK ddPTM_HeLa_Romidepsin_16h_R1 2 QGSPDQVSPVSEMTSTSLYQDK 22 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 QGS(0.983)PDQVS(0.988)PVS(0.008)EMT(0.008)S(0.004)T(0.004)S(0.004)LYQDK;QGS(0.786)PDQVS(0.811)PVS(0.177)EMT(0.068)S(0.053)T(0.043)S(0.052)LY(0.009)QDK ; 72.103 0.0047701 9429600 4268.1 4155.8 4263.5 2807.4 4368.7 4803.7 3996.1 4364.1 4551.4 4468.5 TRUE FALSE FALSE 4216.078756 4214.305461 4337.704429 3132.004797 4145.748937 4496.759073 4335.528634 4490.368348 4144.311385 4352.407726 0.968677344 0.968269916 0.996621802 0.719602803 0.952518513 1.03316586 0.996121896 1.031697541 0.952188225 1 12.087598 -8.178945373 0.004226332 1.921077152 4.99E-05 0 0.086599765 114494.8229 106.8762982 23774.98836 24810.70566 6.62E-09 8.178945373 -1.921027262 QGS(ph)PDQVSPVSEMTSTSLYQDK ddPTM_HeLa_Romidepsin_16h_R1 2 QGSPDQVSPVSEMTSTSLYQDK 22 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGS(0.945)PDQVS(0.055)PVSEMTSTSLYQDK;QGS(0.829)PDQVS(0.171)PVSEMTSTSLYQDK ; 147.85 2.64E-06 36903000 7912.8 7893.8 8065.9 6061.6 7988.4 7625.9 6726.9 7216.4 8805.9 8400.5 TRUE FALSE FALSE 7816.35575 8004.929124 8206.283606 6762.470713 7580.722139 7138.629601 7298.282718 7425.195148 8018.278249 8182.253799 0.955281508 0.978328138 1.00293682 0.826480195 0.926483378 0.872452722 0.891964842 0.907475536 0.979959611 1 12.99828257 -9.276293672 24.99997795 0.979936141 0.886970607 0.764594172 0.027237004 308.279282 518837.2346 0.004288037 0.006565872 5.29E-10 9.276293672 -0.092965534 QGS(ph)PVAAGAPAK ddPTM_HeLa_Romidepsin_16h_R1 4 QGSPVAAGAPAK 12 0 Q9NZI8 Q9NZI8 IGF2BP1 Insulin-like growth factor 2 mRNA-binding protein 1 1 0 QGS(1)PVAAGAPAK;QGS(1)PVAAGAPAK;QGS(1)PVAAGAPAK;QGS(1)PVAAGAPAK ;;; 127.03 0.0050686 1722700000 54287.6 51303.2 51949.3 54395.2 53585.9 49246 45370.9 43976.6 50675.6 46068.6 TRUE FALSE FALSE 53625.92185 52025.4478 52853.45577 60684.62896 50851.21157 46099.33953 49224.70311 45248.99354 46143.04742 44871.73113 1.19509367 1.159425912 1.177878688 1.352402224 1.133257182 1.027358169 1.097009228 1.008407574 1.028332232 1 15.45351922 -8.269701863 23.29885239 1.128274712 1.049533418 0.183578286 0.094357631 465.0498884 1311370.576 0.016319839 0.037155282 5.37E-09 8.269701863 -0.078741295 QGS(ph)SLNLFEDVQITEPEAEPESK ddPTM_HeLa_Romidepsin_16h_R1 2 QGSSLNLFEDVQITEPEAEPESK 23 0 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 QGS(0.715)S(0.285)LNLFEDVQITEPEAEPESK;QGS(0.797)S(0.203)LNLFEDVQITEPEAEPESK ; 110.47 4.46E-06 4907900 3329.3 2738.6 3511.4 3689.4 5143.3 7291.6 6473.1 7260.3 3048 3451.1 TRUE FALSE FALSE 3288.721211 2777.154083 3572.514444 4115.985787 4880.818209 6825.690293 7022.924952 7470.365326 2775.379246 3361.439924 0.978366797 0.826179895 1.062792888 1.224471024 1.452002213 2.030585239 2.089260885 2.222370619 0.825651896 1 11.71486365 -8.443830996 1.265942894 0.978088369 2.212928247 0.974335671 0.083008837 0.041491917 0.124955674 0.010529439 0.037473036 3.60E-09 8.443830996 1.234839879 up QGSAQSQQQIRGEIDS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSAQSQQQIRGEIDSLR 18 1 Q2M1P5 Q2M1P5 KIF7 Kinesin-like protein KIF7 1 0 QGSAQS(0.003)QQQIRGEIDS(0.997)LR 58.755 0.019868 14819000 944.29 1112.1 774.76 1274.9 1191.9 1133.2 939.02 997.74 1218.6 971.99 TRUE FALSE FALSE 932.7806303 1127.756173 788.2443728 1422.309937 1131.072895 1060.792177 1018.780335 1026.608033 1109.605364 946.7375597 0.985257869 1.191202526 0.832590156 1.502327569 1.194705844 1.120471208 1.076095825 1.0843639 1.172030572 1 9.886820749 -9.300901403 24.99999928 0.99993689 1.184731937 0.202833492 0.148792076 483.2251019 306131.7095 0.020483398 0.031289249 5.00E-10 9.300901403 0.184795047 QGSFTIEKPS(ph)PNIPIELIPHINK ddPTM_HeLa_Romidepsin_16h_R1 1 QGSFTIEKPSPNIPIELIPHINK 23 1 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 QGS(0.291)FT(0.116)IEKPS(0.593)PNIPIELIPHINK 80.733 0.00013968 130260000 9450.6 8489.8 9087.6 9905.2 8842.7 8955 7322.1 8374.1 9254.4 8391.9 TRUE FALSE FALSE 9335.412452 8609.319627 9245.765866 11050.48583 8391.424022 8382.804401 7944.038991 8616.391371 8426.663286 8173.877228 1.142103336 1.053272442 1.131135887 1.351927062 1.026614884 1.025560351 0.971881369 1.054137606 1.030926089 1 12.99680486 -8.553415035 24.99999266 1.094596298 1.01489897 0.185671914 0.093821665 335.8654027 274970.9149 0.015152014 0.030304215 2.80E-09 8.553415035 -0.079697328 QGSGRES(ph)PSLASR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSGRESPSLASR 13 1 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 QGS(0.002)GRES(0.986)PS(0.012)LASR 76.341 0.01787 279800000 3177.6 2946.5 2663.8 2974.7 2607.6 2634.7 2211.4 2124.1 3266 2863.8 TRUE FALSE FALSE 3138.870189 2987.980904 2710.162322 3318.64881 2474.524442 2466.351173 2399.236261 2185.557482 2973.88078 2789.398063 1.125285857 1.071192005 0.971593964 1.189736544 0.887117717 0.884187598 0.860126883 0.78352298 1.066137107 1 11.44573811 -8.620133114 7.12299086 1.062234757 0.851149906 0.748127652 0.061860754 0.09506314 6.022865202 0.00985882 0.019798737 2.40E-09 8.620133114 -0.211084852 QGSIT(ph)SPQANEQSVTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QGS(0.005)IT(0.536)S(0.459)PQANEQSVTPQR 219.68 1.60E-29 6677900 1008.9 1053 1079.1 536.77 1005.4 995.03 1023.9 831.2 1241.2 1254.1 TRUE FALSE FALSE 996.6031387 1067.824162 1097.881283 598.833873 954.0906863 931.4507943 1110.87004 855.2494606 1130.183963 1221.518301 0.815872458 0.874177784 0.898784146 0.490237332 0.781069498 0.762535275 0.909417435 0.700152801 0.925228842 1 10.25445976 -11.77497286 0.411426698 1.037476882 0.755874399 0.31213034 0.113831036 1.354147753 0.400351859 0.16357653 0.042598148 1.68E-12 11.77497286 -0.281602483 QGSITS(ph)PQANEQSVT(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 QGS(0.042)IT(0.118)S(0.841)PQANEQS(0.129)VT(0.871)PQR 106.31 0.0065708 6920200 2607.1 2703.8 2803.7 1196.8 2641.3 2662.3 2629 2410.8 2937.4 3521.1 TRUE FALSE FALSE 2575.323662 2741.864167 2852.497222 1335.179647 2506.504605 2492.187622 2852.307194 2480.552694 2674.671587 3429.621314 0.750906128 0.799465572 0.831723669 0.389308184 0.730840048 0.726665539 0.831668261 0.723273058 0.779873736 1 11.74383357 -11.95297608 0.513662923 1.035240453 0.707736061 0.129368324 0.135378753 0.904056137 0.390436421 0.143623974 0.032963453 1.11E-12 11.95297608 -0.327504392 QGSITS(ph)PQANEQSVT(ph)PQRR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 QGS(0.044)IT(0.438)S(0.518)PQANEQS(0.152)VT(0.848)PQRR 58.054 0.023003 59475000 3062.3 2944.8 2564.3 2034.2 2561.1 2978.5 2634.3 2462.7 3361.8 3255.8 TRUE FALSE FALSE 3024.97551 2986.256972 2608.930566 2269.403775 2430.39751 2788.183463 2858.057376 2533.954339 3061.112188 3171.213847 0.95388569 0.941676316 0.822691465 0.715626219 0.766393447 0.879216476 0.901250283 0.799048712 0.96528091 1 11.63081945 -9.833042487 3.325532083 0.9771608 0.813370556 0.687473588 0.050266711 0.110467168 2.466318903 0.009203982 0.012516781 1.47E-10 9.833042487 -0.163790244 QGSITS(ph)PQANEQSVTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QGS(0.007)IT(0.126)S(0.867)PQANEQSVTPQR 180.93 4.54E-10 7505200 1022.6 846.29 1192.2 406.45 1018.1 1199.7 805.58 952.37 1221.5 1111.2 TRUE FALSE FALSE 1010.136158 858.2040928 1212.949741 453.4456614 966.1425579 1123.043042 874.0059451 979.9253234 1112.245981 1082.330864 0.933297009 0.792922129 1.120682946 0.418952907 0.892649919 1.03761528 0.807521964 0.905384256 1.02763953 1 10.07992588 -10.63368124 0.963921018 0.98413987 0.848635163 0.110455679 0.175474154 0.836681493 1.616845475 0.041619466 0.040513492 2.32E-11 10.63368124 -0.135504707 QGSITSPQANEQS(ph)VTPQRR ddPTM_HeLa_Romidepsin_16h_R1 1 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QGSITSPQANEQS(0.532)VT(0.468)PQRR 94.838 0.00078222 23119000 2132.5 1807 2011.4 1296.9 1308.4 1482.9 1116 1448.1 2242 2325.2 TRUE FALSE FALSE 2106.50827 1832.438993 2046.407573 1446.85368 1241.627466 1388.147476 1210.793012 1489.998489 2041.469905 2264.790969 0.930111564 0.809098508 0.903574591 0.638846454 0.548230491 0.612925208 0.53461579 0.657896693 0.901394404 1 11.14516219 -9.446162238 0.984133623 0.970638533 0.571374003 0.852513847 0.063282924 0.110079209 0.21239679 0.010884634 0.020640073 3.58E-10 9.446162238 -0.39926453 QGSITSPQANEQSVT(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 QGSITSPQANEQSVTPQR 18 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QGSITSPQANEQSVT(1)PQR;QGSITSPQANEQS(0.001)VT(0.999)PQR ; 244.18 2.13E-61 14623100 4299.3 3733.8 3947.2 3104.8 2741.5 2799.5 2498.1 2933.7 4330.3 4765.9 TRUE FALSE FALSE 4246.898478 3786.364534 4015.89936 3463.791585 2601.591025 2620.620985 2710.288552 3018.581981 3942.987123 4642.081231 0.914869488 0.815660982 0.865107515 0.746172118 0.560436342 0.564535788 0.58385203 0.650264791 0.849400716 1 12.18055605 -9.388708686 0.742910182 0.970583516 0.568334859 0.826790254 0.062395632 0.134878038 0.147612749 0.011125946 0.024549277 4.09E-10 9.388708686 -0.402248657 QGSITSPQANEQSVT(ph)PQRR ddPTM_HeLa_Romidepsin_16h_R1 2 QGSITSPQANEQSVTPQRR 19 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QGSITSPQANEQS(0.144)VT(0.856)PQRR;QGSITSPQANEQS(0.076)VT(0.924)PQRR ; 84.025 0.0027967 124056000 3795.2 3537 3806.1 2901.26 3375.4 3852.2 3020.9 2962.9 4105.3 3880.5 TRUE FALSE FALSE 3748.942643 3586.793979 3872.343574 3236.717332 3203.140743 3606.056852 3277.495171 3048.626837 3738.111686 3779.684051 0.991866673 0.948966615 1.02451515 0.856346004 0.847462566 0.954063039 0.867134693 0.806582454 0.989001101 1 11.88404993 -9.256620168 24.91456792 0.993704819 0.87019036 0.723008317 0.038489047 155.7212723 805053.6553 0.005673726 0.009210933 5.54E-10 9.256620168 -0.123514459 QGSPDQVS(ph)PVS(ph)EMTSTSLYQDKQEGK ddPTM_HeLa_Romidepsin_16h_R1 1 QGSPDQVSPVSEMTSTSLYQDKQEGK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 QGS(0.026)PDQVS(0.808)PVS(0.526)EMT(0.553)S(0.076)T(0.009)S(0.001)LYQDKQEGK 76.237 0.00026041 8466400 791.75 686.48 442.78 832.09 685.16 777.3 599.42 484.35 664.72 574.75 TRUE FALSE FALSE 782.0998465 696.1442835 450.4864002 928.3001609 650.1937285 727.6330386 650.3347198 498.3639031 605.2657784 559.8179121 1.397061133 1.243519131 0.804701655 1.65821804 1.161437879 1.29976734 1.161689731 0.890225004 1.081183301 1 9.128813838 -7.278007072 3.977151411 1.206345095 0.866232425 0.157499035 0.217365853 0.332877659 10.78406595 0.030941141 0.31668386 5.27E-08 7.278007072 -0.34011267 QGSPDQVS(ph)PVSEMT(ph)STSLYQDKQEGK ddPTM_HeLa_Romidepsin_16h_R1 1 QGSPDQVSPVSEMTSTSLYQDKQEGK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 QGS(0.191)PDQVS(0.5)PVS(0.413)EMT(0.776)S(0.1)T(0.017)S(0.003)LY(0.001)QDKQEGK 73.574 0.00046996 9988600 862.98 799 762.97 917.69 845.12 899.2 677.95 836.12 1090.4 901.35 TRUE FALSE FALSE 852.4616678 810.248343 776.2491728 1023.797636 801.9903728 841.744022 735.5350561 860.311813 992.871893 877.9327971 0.970987382 0.922904744 0.884178351 1.166145791 0.913498591 0.958779561 0.83780337 0.979929006 1.130920153 1 9.7779667 -4.000000002 0.203314547 0.99528999 0.604830995 0.09847547 0.092700804 105.0259262 1.214221014 0.071380431 13.23533501 1.00E-04 4.000000002 -0.390458995 QGSPDQVS(ph)PVSEMTSTSLYQDK ddPTM_HeLa_Romidepsin_16h_R1 1 QGSPDQVSPVSEMTSTSLYQDK 22 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGS(0.069)PDQVS(0.73)PVS(0.012)EMT(0.039)S(0.05)T(0.026)S(0.037)LY(0.037)QDK 53.088 0.010573 12130000 3141.8 3076.6 3005.9 2674.6 3897.9 3836.4 3159.7 3502.8 3351.9 3134 TRUE FALSE FALSE 3103.506533 3119.912456 3058.216429 2983.849836 3698.975618 3591.266421 3428.084839 3604.147991 3052.097669 3052.578228 1.016683702 1.02205815 1.001847029 0.977485133 1.21175457 1.176469906 1.123012936 1.180689805 0.999842573 1 11.57581255 -8.764162757 24.99999971 1.006841302 1.16966176 0.927302809 0.023295599 13.25014476 121634.9516 0.003401382 0.006373363 1.72E-09 8.764162757 0.162820458 QGSPDQVS(ph)PVSEMTSTSLYQDKQEGK ddPTM_HeLa_Romidepsin_16h_R1 1 QGSPDQVSPVSEMTSTSLYQDKQEGK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGS(0.001)PDQVS(0.566)PVS(0.067)EMT(0.34)S(0.023)T(0.002)SLYQDKQEGK 125.08 4.36E-07 39769000 3321 2493.7 2842.6 4197 3075.5 2576.1 2279.8 2502.1 2696.6 2867 TRUE FALSE FALSE 3280.522375 2528.806374 2892.074261 4682.276887 2918.545759 2411.495524 2473.446155 2574.494316 2455.409342 2792.514927 1.174755538 0.905565929 1.035652212 1.676724032 1.045131659 0.863556897 0.885741427 0.921926788 0.879282441 1 11.44734928 -8.365354578 5.423725049 1.111962178 0.891399326 0.179263397 0.210128502 0.285778953 12.23912998 0.029183441 0.066395863 4.31E-09 8.365354578 -0.220562852 QGSPDQVSPVS(ph)EMTSTSLYQDKQEGK ddPTM_HeLa_Romidepsin_16h_R1 2 QGSPDQVSPVSEMTSTSLYQDKQEGK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGS(0.001)PDQVS(0.157)PVS(0.761)EMT(0.073)S(0.005)T(0.001)SLYQDKQEGK;QGSPDQVS(0.14)PVS(0.655)EMT(0.14)S(0.031)T(0.031)S(0.003)LYQDKQEGK ; 100.94 2.59E-07 20028000 4455.1 4461.9 3531 4877.9 4616.4 3995.67 3663.76 4272.4 4704.5 4251.6 TRUE FALSE FALSE 4400.799528 4524.714745 3592.455574 5441.905749 4380.807882 3740.359582 3974.959683 4396.015153 4283.717737 4141.142819 1.062701703 1.092624655 0.867503424 1.314107237 1.057874136 0.903219171 0.959870223 1.061546376 1.034428882 1 12.01581324 -8.300644715 24.51578626 1.046138358 0.973377666 0.103842401 0.110197578 790.2616346 494162.9305 0.015168724 0.033918871 5.00E-09 8.300644715 -0.072760692 QGSPDQVSPVSEMT(ph)STSLYQDKQEGK ddPTM_HeLa_Romidepsin_16h_R1 4 QGSPDQVSPVSEMTSTSLYQDKQEGK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGS(0.007)PDQVS(0.189)PVS(0.144)EMT(0.591)S(0.048)T(0.016)S(0.005)LYQDKQEGK;QGS(0.001)PDQVS(0.032)PVS(0.387)EMT(0.567)S(0.009)T(0.003)S(0.001)LYQDKQEGK;QGS(0.001)PDQVS(0.267)PVS(0.267)EMT(0.435)S(0.023)T(0.007)SLYQDKQEGK;QGSPDQVS(0.006)PVS(0.032)EMT(0.667)S(0.142)T(0.142)S(0.01)LY(0.001)QDKQEGK ;;; 118.08 2.70E-07 70030200 8069.9 6836.56 6511.8 9623.2 7600.29 7412.47 6913.7 7411.4 7685.31 6818.67 TRUE FALSE FALSE 7971.540955 6932.805271 6625.135147 10735.87966 7212.418841 6938.83709 7500.949505 7625.837166 6997.916625 6641.51997 1.200258524 1.043858229 0.997532971 1.616479317 1.085959069 1.044766427 1.129402537 1.148206615 1.053661911 1 12.69729774 -12.44548549 0.825242983 0.983693823 1.161838339 0.088928762 0.164990462 1.45027925 1.489471879 0.178762349 0.031106811 3.59E-13 12.44548549 0.178144515 QGTAVEVEAES(ph)LDPTVKPVDVGGDEPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QGTAVEVEAESLDPTVKPVDVGGDEPEEK 29 1 P49321-4;P49321;P49321-3;E9PPR5 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 QGT(0.001)AVEVEAES(0.499)LDPT(0.499)VKPVDVGGDEPEEK 91.615 5.66E-08 4689100 1680.2 1703.5 1523.6 1742.2 1758.1 2109.8 1709.2 2082.8 1290.3 1523.2 TRUE FALSE FALSE 1659.721076 1727.481918 1550.117619 1943.641361 1668.377597 1974.990589 1854.379405 2143.062532 1174.892336 1483.627044 1.118691576 1.164363998 1.044816232 1.310060617 1.124526277 1.331190744 1.249895931 1.444475241 0.791905446 1 10.53491276 -4 0.165989784 0.976263552 2.65319989 0.675056806 0.101674103 20.44902987 0.211696443 0.103738633 8.505939836 1.00E-04 4 1.676936338 QGVDDIEKFEDEGAGFEES(ph)SETGDYEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QGVDDIEKFEDEGAGFEESSETGDYEEK 28 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 QGVDDIEKFEDEGAGFEES(0.431)S(0.431)ET(0.124)GDY(0.014)EEK 41.908 0.022109 4462900 1641.2 1724.7 1621.6 1110.5 1766 2076.5 1547.8 1548.7 1845.3 1934.1 TRUE FALSE FALSE 1621.196423 1748.980372 1649.823268 1238.901235 1675.87443 1943.818352 1679.270093 1593.509191 1680.251746 1883.851803 0.860575349 0.92840656 0.87577126 0.65764262 0.889599929 1.031831882 0.89140244 0.84587821 0.891923528 1 10.87946976 -12.25046864 0.760688091 1.008861339 0.87231512 0.039884844 0.093281647 1.008197242 0.940408343 0.086180463 0.018467766 5.62E-13 12.25046864 -0.136546219 QGVGK(ac)YINPAATK ddPTM_HeLa_Romidepsin_16h_R1 2 QGVGKYINPAATK 13 1 Q13356 Q13356 PPIL2 Peptidyl-prolyl cis-trans isomerase-like 2 0 1 ; QGVGK(1)YINPAATK;QGVGK(1)YINPAATK 222.2 4.59E-30 11143000 3197.25 3034.53 2856.63 2477.86 2431.33 2296.09 2155.36 1726.69 4530.6 2954.42 FALSE TRUE FALSE 3158.280687 3077.250193 2906.348447 2764.361832 2307.250158 2149.377259 2338.436225 1776.649051 4125.371789 2877.663742 1.097515544 1.069357113 1.009968053 0.96062712 0.80177893 0.746917448 0.812616217 0.617392861 1.433583684 1 11.49068231 -8.765818877 1.378386589 1.049223391 0.721005624 0.631703484 0.13136209 0.103477116 0.393167904 0.008687043 0.022215133 1.71E-09 8.765818877 -0.328217767 QGVGK(ac)YINPAATK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 QGVGKYINPAATKR 14 2 Q13356 Q13356 PPIL2 Peptidyl-prolyl cis-trans isomerase-like 2 0 2 QGVGK(1)YINPAATK(1)R 138.02 2.18E-05 924530 366.62 327.28 330.48 0 194.01 196.78 357.45 235.66 353.8 316.39 FALSE TRUE FALSE 362.1514944 331.8874564 336.2318658 0 184.1089457 184.2063931 387.8117941 242.4784503 322.1552419 308.1701422 1.175167366 1.076961753 1.09105919 0 0.597426293 0.597742506 1.25843403 0.786833042 1.045381099 1 8.267583279 QGVGK(ac)YINPAATKR ddPTM_HeLa_Romidepsin_16h_R1 2 QGVGKYINPAATKR 14 2 Q13356 Q13356 PPIL2 Peptidyl-prolyl cis-trans isomerase-like 2 0 1 ; QGVGK(1)YINPAATKR;QGVGK(1)YINPAATKR 163.33 1.91E-06 6126900 3661.3 3538.1 2385.31 3973 2375.89 1662.16 1857.2 1578.79 3748.3 2509.87 FALSE TRUE FALSE 3616.674667 3587.909465 2426.82532 4432.376954 2254.639468 1555.95334 2014.950522 1624.469798 3413.04266 2444.663216 1.479416324 1.467649794 0.992703332 1.813082851 0.922269969 0.636469404 0.824224175 0.664496356 1.396119776 1 11.25542001 -8.533306934 24.99666569 1.272910177 0.729877701 0.599725183 0.237156564 132.8401583 318421.0126 0.037796622 0.075654053 2.93E-09 8.533306934 -0.543032476 QGVTEAAEK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 1 QGVTEAAEKTK 11 1 F8W754;O76070;G4Y816;Q16143 F8W754;G4Y816 SNCG;SNCB Gamma-synuclein;Beta-synuclein 0 1 QGVTEAAEK(1)TK 137.01 0.0047048 1143800 650.7 606.03 616.47 534.81 821.32 633.19 669.6 672.39 819.22 787.3 FALSE TRUE FALSE 642.7690181 614.5617062 627.1994018 596.6472486 779.4049756 592.7312025 726.4758073 691.8445438 745.9469114 766.8458325 0.838198489 0.801414939 0.817895039 0.778053715 1.016377664 0.772947022 0.947355748 0.902195089 0.972746907 1 9.582792756 -12.21993034 0.97606355 0.999311498 0.858433189 0.318416139 0.073861134 0.480801095 0.828659101 0.046427613 0.013180521 6.03E-13 12.21993034 -0.140878309 QHFISFDTDR ddPTM_HeLa_Romidepsin_16h_R1 2 QHFISFDTDR 10 0 C9J0K6;P30626-3;P30626-2;P30626 C9J0K6 SRI Sorcin 0 0 ; ; 123.51 0.004716 26577000 1757.88 1356.36 1946.95 1799.89 2132.2 1851.73 1632.43 1208.81 1935.73 1311.69 FALSE FALSE TRUE 1736.454282 1375.454872 1980.835848 2008.001751 2023.385878 1733.410429 1771.088563 1243.78501 1762.593461 1277.612105 1.359140443 1.07658253 1.550420382 1.571683411 1.583724724 1.356757988 1.386249048 0.973523189 1.379599844 1 10.31923417 -12.08081957 0.556390901 0.953317709 1.385262894 0 0.222716182 1.05447499 0.509322981 0.234206921 0.048377229 8.30E-13 12.08081957 0.431945185 QHYIDLK ddPTM_HeLa_Romidepsin_16h_R1 2 QHYIDLK 7 0 Q32Q12;P22392-2;P22392;J3KPD9;F6XY72;O60361 Q32Q12 NME1-NME2;NME2;NME2P1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Putative nucleoside diphosphate kinase 0 0 ; ; 85.161 0.024542 59419000 20844.5 18595.7 20100.5 14893.1 18890.5 20716.6 17378.6 17372.4 20990.7 17556.4 FALSE FALSE TRUE 20590.43922 18857.49075 20450.34077 16615.1103 17926.44729 19392.87612 18854.73785 17875.04298 19113.23922 17100.2822 1.204099381 1.102759038 1.195906625 0.971627842 1.048312951 1.134067608 1.102598053 1.045306901 1.117714842 1 14.06173251 -9.265638378 24.96833439 1.106194199 1.06615104 0.157918553 0.06684597 1016.799901 6046149.17 0.013732021 0.021476825 5.42E-10 9.265638378 -0.040043158 QIANSQDGYVWQVT(ph)DMNR ddPTM_HeLa_Romidepsin_16h_R1 2 QIANSQDGYVWQVTDMNR 18 0 P10155-3;P10155-5;P10155-4;P10155;D6RDN1;D6RE09;P10155-2 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 1 0 QIANSQDGY(0.374)VWQVT(0.626)DMNR;QIANSQDGY(0.005)VWQVT(0.995)DMNR ; 130.44 0.0034208 22796000 4329 4576.2 4065.8 5288.7 4243.4 3859.6 2839.73 3642.6 4592 4308 TRUE FALSE FALSE 4276.236483 4640.623864 4136.563543 5900.204378 4026.843464 3612.984016 3080.936595 3747.992884 4181.280019 4196.077539 1.019103304 1.105943306 0.985816755 1.406123772 0.959668506 0.86103843 0.734242055 0.893213447 0.996473488 1 12.03482562 -8.31297874 3.834546628 1.044244999 0.816476368 0.427795486 0.126477321 0.176976335 5.384717309 0.018002649 0.043861187 4.86E-09 8.31297874 -0.227768631 KAPSK(ac)RPPISDSEELSAK ddPTM_HeLa_Romidepsin_16h_R1 1 KAPSKRPPISDSEELSAK 18 3 P42568-2;P42568 P42568-2 MLLT3 Protein AF-9 0 1 K(0.33)APSK(0.67)RPPISDSEELSAK 53.255 0.016362 5379300 1607.7 1919 1603 2173.7 4859.8 5207.6 5015.1 5614.1 1852.1 1710.9 FALSE TRUE FALSE 1588.104734 1946.015732 1630.899543 2425.033422 4611.786272 4874.851167 5441.082469 5776.535126 1686.443537 1666.450571 0.952986402 1.167760848 0.978666617 1.455208731 2.76743058 2.925289985 3.265072821 3.466370515 1.011997335 1 10.70256281 -8.731938811 1.715295001 0.985185907 3.270280422 0.982139694 0.134964584 0.029586471 0.176207599 0.020110951 0.047741949 1.85E-09 8.731938811 2.285094514 up QIASNS(ph)PGSSPK ddPTM_HeLa_Romidepsin_16h_R1 4 QIASNSPGSSPK 12 0 Q9C0D5-2;Q9C0D5 Q9C0D5-2 TANC1 Protein TANC1 1 0 QIAS(0.415)NS(0.585)PGSSPK;QIAS(0.026)NS(0.971)PGS(0.003)SPK;QIAS(0.355)NS(0.642)PGS(0.003)SPK;QIAS(0.03)NS(0.97)PGSSPK ;;; 184 6.26E-07 23145500 11234 10274.9 10331.9 10115.2 11323.4 13000.9 9611.6 9786 11230.8 10722.8 TRUE FALSE FALSE 11097.07569 10419.55031 10511.72239 11284.76702 10745.52464 12170.18445 10428.00906 10069.14247 10226.28912 10444.22011 1.062508791 0.997637947 1.006463123 1.080479624 1.028848926 1.165255454 0.998447845 0.96408754 0.979133819 1 13.35041715 -12.53279875 1.228452804 0.999467593 1.042336212 0.101777041 0.05386306 1.06986101 2.832213928 0.0394236 0.008930631 2.93E-13 12.53279875 0.042868619 QIATLHAQVADMK ddPTM_HeLa_Romidepsin_16h_R1 1 QIATLHAQVADMK 13 0 P35579 P35579 MYH9 Myosin-9 0 0 89.231 0.013411 0 2180.3 1705.8 2158.3 2060.7 2923.5 2890.9 2315.5 2113.7 2142.8 1891.2 FALSE FALSE TRUE 2153.725665 1729.814297 2195.864306 2298.96783 2774.302886 2706.18082 2512.178512 2174.856575 1951.142601 1842.066351 1.169190058 0.939061883 1.192065804 1.248037471 1.506081952 1.469100621 1.363782857 1.180661366 1.059214072 1 10.84710931 -9.236380737 2.336352815 1.072462933 1.382117477 0.665296586 0.103961315 0.14989802 1.603270045 0.017640723 0.030472783 5.80E-10 9.236380737 0.309654544 QIATLHAQVADMKK ddPTM_HeLa_Romidepsin_16h_R1 1 QIATLHAQVADMKK 14 1 P35579 P35579 MYH9 Myosin-9 0 0 40.475 0.028492 1670900 761.64 783.97 699.26 663.84 921.56 894.8 823.8 750.11 806.82 747.27 FALSE FALSE TRUE 752.3568387 795.0067502 711.430327 740.5963043 874.5293544 837.6251678 893.7735514 771.8132494 734.6559985 727.8558177 1.033661916 1.092258564 0.977433043 1.017504135 1.201514549 1.150811943 1.227954122 1.060393049 1.009342758 1 9.507508882 -8.770045244 24.99803183 1.01952485 1.164341934 0.655172588 0.049160453 76.08426008 221007.461 0.006760979 0.012396969 1.70E-09 8.770045244 0.144817084 QICLVMLETLSQS(ph)PQGR ddPTM_HeLa_Romidepsin_16h_R1 2 QICLVMLETLSQSPQGR 17 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 0 QICLVMLET(0.023)LS(0.116)QS(0.862)PQGR;QICLVMLET(0.011)LS(0.052)QS(0.937)PQGR ; 107.63 0.0031485 211090000 13223.3 10886.8 11103.7 1119.33 10837.9 11952.2 10323.4 10451.6 12791.1 11133.8 TRUE FALSE FALSE 13062.12933 11040.06466 11296.95524 1248.752201 10284.80152 11188.49299 11200.26934 10754.00056 11647.03198 10844.54227 1.204488766 1.018029566 1.041718033 0.115150291 0.948385028 1.031716481 1.032802405 0.991650942 1.073999408 1 13.40468154 -9.49702273 24.98651736 1.090348509 0.826444425 0.183520529 0.256809356 968.9309243 936348.7979 0.040674917 0.061990855 3.18E-10 9.49702273 -0.263904084 QICVVMLETLS(ph)QSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 QICVVMLETLSQSPPK 16 0 Q15366;Q15366-2;H3BRU6;F8VZX2;Q15366-8;Q15366-5 Q15366;Q15366-8 PCBP2 Poly(rC)-binding protein 2 1 0 QICVVMLET(0.004)LS(0.55)QS(0.446)PPK 156.11 1.15E-06 0 5435.5 4638.5 5507.1 414.9 4071.2 4360 3172.8 3559.8 4615.6 4315.8 TRUE FALSE FALSE 5369.250035 4703.800925 5602.948765 462.8726902 3863.431472 4081.410071 3442.297553 3662.797197 4202.769176 4203.674894 1.277275282 1.118973528 1.332869193 0.110111439 0.919060482 0.970914777 0.818878158 0.871332177 0.999784541 1 12.03743538 -9.378229753 23.93332435 1.146942408 0.761087419 0.406075796 0.245739931 11.05750057 2237.870705 0.03732014 0.05700746 4.19E-10 9.378229753 -0.385854989 QICVVMLETLSQS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 2 QICVVMLETLSQSPPK 16 0 Q15366;Q15366-2;H3BRU6;F8VZX2;Q15366-8;Q15366-5 Q15366;Q15366-8 PCBP2 Poly(rC)-binding protein 2 1 0 QICVVMLET(0.001)LS(0.004)QS(0.994)PPK;QICVVMLET(0.007)LS(0.494)QS(0.499)PPK ; 99.796 0.0022314 70394000 4326 4374.5 4751.5 1245.66 4253.6 4288.4 3049.4 3360.4 4137.3 3816 TRUE FALSE FALSE 4273.273048 4436.084326 4834.197864 1389.68907 4036.52292 4014.38508 3308.41596 3457.627872 3767.249526 3716.85977 1.149699831 1.19350328 1.300613465 0.373887947 1.086003554 1.080047494 0.890110514 0.930255131 1.013557078 1 11.85986854 QIDNPDYK ddPTM_HeLa_Romidepsin_16h_R1 1 QIDNPDYK 8 0 P27797;K7EJB9;K7EL50 P27797 CALR Calreticulin 0 0 122.33 0.00034467 0 4412.9 4177 4112.1 3630.9 5196.4 5504.4 4965.8 4715.7 4309.8 4686.2 FALSE FALSE TRUE 4359.113877 4235.803916 4183.669376 4050.721742 4931.208318 5152.686605 5387.594928 4852.141339 3924.320694 4564.451848 0.955013663 0.927998379 0.916576517 0.88744977 1.080350605 1.128873034 1.180337773 1.063028267 0.859757277 1 12.1562259 -8.592140482 5.781296025 0.963318384 1.126001269 0.732578474 0.053257113 0.078076024 4.743655025 0.006858448 0.013908411 2.56E-09 8.592140482 0.162682885 QIDS(ph)S(ph)EEDDDEEDYDNDKR ddPTM_HeLa_Romidepsin_16h_R1 1 QIDSSEEDDDEEDYDNDKR 19 1 O14646-2;O14646 O14646-2 CHD1 Chromodomain-helicase-DNA-binding protein 1 2 0 QIDS(0.999)S(0.999)EEDDDEEDY(0.002)DNDKR 63.894 0.0091439 8528300 913.41 1256.4 1114.6 1139.8 1219 1061.5 953.69 1179.2 1514.5 919.16 TRUE FALSE FALSE 902.2770076 1274.087632 1133.999145 1271.589039 1156.789881 993.6735758 1034.696405 1213.318292 1379.039327 895.2800907 1.007815338 1.423116235 1.266641755 1.420325384 1.292098298 1.109902461 1.155723684 1.355238773 1.540344012 1 9.806195294 -10.28278701 23.76914064 1.003690545 1.281301197 0 0.194528224 193.2237476 215140.7744 0.016722712 0.019135283 5.21E-11 10.28278701 0.277610652 QIDSS(ph)PVGGETDETTVSQNYR ddPTM_HeLa_Romidepsin_16h_R1 2 QIDSSPVGGETDETTVSQNYR 21 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 QIDS(0.153)S(0.847)PVGGETDETTVSQNYR;QIDS(0.238)S(0.762)PVGGETDETTVSQNYR ; 161.63 1.16E-08 49000000 8151.7 7433.4 6809.5 7631.9 7731.9 8316.4 7559.7 7979.4 8563 7956.4 TRUE FALSE FALSE 8052.343945 7538.0476 6928.016491 8514.336187 7337.312291 7785.00888 8201.820729 8210.27135 7797.103834 7749.691581 1.039053472 0.972690012 0.893973188 1.098667747 0.946787651 1.004557252 1.058341567 1.059432013 1.006117953 1 12.91992318 -7.759677479 23.6124186 1.006519794 1.058886835 0.16842936 0.05193835 32.38977576 433990.741 0.007016272 0.023769884 1.74E-08 7.759677479 0.05236704 QIESSDYDSSSSK(ac)GK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QIESSDYDSSSSKGKK 16 2 Q9UNL4-2;Q9UNL4-6;Q9UNL4-8;Q9UNL4-3;Q9UNL4 Q9UNL4-2;Q9UNL4-8 ING4 Inhibitor of growth protein 4 0 2 ; QIESSDYDSSSSK(1)GK(1)K;QIESSDYDSSSSK(1)GK(1)K 416.46 0 57091000 6311.3 6059.2 6631.1 7577.4 8051.1 8200.6 6514.3 7823.1 6264 5128.3 FALSE TRUE FALSE 6234.375448 6144.501577 6746.511514 8453.534641 7640.222324 7676.608126 7067.624479 8049.449056 5703.732152 4995.066027 1.248106715 1.230114185 1.350635102 1.692376957 1.52955382 1.536838169 1.414921132 1.611480011 1.141873225 1 12.28628803 -10.29391 0.507888378 1.029655442 1.570748044 0.775273226 0.099549008 0.251550128 0.154936156 0.04015848 0.046145645 5.08E-11 10.29391 0.541092602 QIESSDYDSSSSK(ac)GK(ac)K(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QIESSDYDSSSSKGKKK 17 3 Q9UNL4-8;Q9UNL4-3;Q9UNL4 Q9UNL4-8 ING4 Inhibitor of growth protein 4 0 3 ; QIESSDYDSSSSK(1)GK(1)K(1)K;QIESSDYDSSSSK(1)GK(1)K(1)K 297.28 5.07E-139 1802050 506.84 265.915 424.92 567.47 739.72 787.69 695.18 633.96 465.6 328.86 FALSE TRUE FALSE 500.6624391 269.6585583 432.3155544 633.0835514 701.9693281 737.3591512 754.2285718 652.3026324 423.9555699 320.3161698 1.563025805 0.84185122 1.349652609 1.976433322 2.191488892 2.301972928 2.354637833 2.036433667 1.323553445 1 8.323352818 -9.181747704 2.753494373 1.235056439 2.229066332 0.857716684 0.19713593 0.095036463 1.409503188 0.038795869 0.067233703 6.58E-10 9.181747704 0.994009893 QIESSDYDSSSSK(ac)GK(ac)K(ac)SR ddPTM_HeLa_Romidepsin_16h_R1 2 QIESSDYDSSSSKGKKSR 18 3 Q9UNL4-2 Q9UNL4-2 ING4 Inhibitor of growth protein 4 0 3 ; QIESSDYDSSSSK(1)GK(1)K(1)SR;QIESSDYDSSSSK(1)GK(1)K(1)SR 352.72 4.95E-296 2491700 124.58 384.99 299.33 443.56 607.04 591.73 550.46 517 194.38 345.94 FALSE TRUE FALSE 123.061571 390.4098993 304.5397131 494.8464942 576.0604836 553.9203627 597.2160587 531.9585793 176.994166 336.9524289 0.365219421 1.158649904 0.903806256 1.468594531 1.70961962 1.643912657 1.77240467 1.57873496 0.525279389 1 8.396401115 -9.323048439 1.438877952 0.716037892 1.695844723 0.814062387 0.205895448 0.152165025 0.618979386 0.044251101 0.080459007 4.75E-10 9.323048439 0.97980683 QIESSDYDSSSSK(ac)GKK ddPTM_HeLa_Romidepsin_16h_R1 2 QIESSDYDSSSSKGKK 16 2 Q9UNL4-2;Q9UNL4-6;Q9UNL4-8;Q9UNL4-3;Q9UNL4 Q9UNL4-2;Q9UNL4-8 ING4 Inhibitor of growth protein 4 0 1 ; QIESSDYDSSSSK(0.965)GK(0.035)K;QIESSDYDSSSSK(1)GKK 219.53 4.66E-29 9252000 4620.9 4080.5 3654.5 3750.8 1967.62 2051.77 1665.35 1776.61 4983.6 4409.3 FALSE TRUE FALSE 4564.578693 4137.945386 3718.10504 4184.485144 1867.205009 1920.668519 1806.804787 1828.013407 4537.854334 4294.74575 1.062828619 0.963490187 0.865733446 0.974326628 0.43476497 0.447213556 0.420701222 0.425639494 1.056606048 1 12.06835701 -8.771670379 5.565189692 1.009075628 0.429305936 0.962684921 0.053466003 0.024334234 2.363396093 0.009225901 0.017629128 1.69E-09 8.771670379 -0.579769692 down QILFFK(ac)MR ddPTM_HeLa_Romidepsin_16h_R1 1 QILFFKMR 8 1 Q9H788;H0YAT1 Q9H788 SH2D4A SH2 domain-containing protein 4A 0 1 QILFFK(1)MR 58.917 0.028764 0 209.95 124.47 203.1 149.39 324.45 262.91 499.2 222.24 514.87 271.99 FALSE TRUE FALSE 207.3910486 126.2222919 206.6348703 166.6631747 307.8921058 246.1108995 541.6020355 228.6701638 468.8187377 264.9236606 0.782833244 0.476447787 0.779978919 0.629098867 1.162191799 0.928987992 2.044370195 0.86315493 1.769637097 1 8.049432888 -7.965487804 24.97723886 0.855756533 1.461992801 0.165369253 0.430577001 127.6492925 92381.40345 0.041056318 0.123168282 1.08E-08 7.965487804 0.606236268 QILGVIDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 QILGVIDKK 9 1 E9PLA9;Q14444-2;Q14444 E9PLA9 CAPRIN1 Caprin-1 0 1 QILGVIDK(1)K 137.95 0.0034014 780830 847.53 740.32 732.16 655.49 1637.6 1312.6 1103.5 1221.9 1965.5 1337.6 FALSE TRUE FALSE 837.1999784 750.7422444 744.9029377 731.280838 1554.027161 1228.729096 1197.231262 1257.253749 1789.700757 1302.848959 0.642591739 0.576231219 0.571749267 0.561293643 1.192791498 0.943109397 0.918933276 0.965003456 1.373682455 1 10.34745412 -8.76023464 24.99965567 0.767551136 0.994396793 0.154902526 0.245576079 38.21736876 793019.6596 0.02986894 0.05718348 1.74E-09 8.76023464 0.226845657 QILIACS(ph)PVSSVR ddPTM_HeLa_Romidepsin_16h_R1 1 QILIACSPVSSVR 13 0 Q5QJE6;J3KP30;E9PRB3 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 QILIACS(0.965)PVS(0.031)S(0.004)VR 134.06 0.0017904 24669000 3120.8 2684.7 3079.1 182.36 2431.1 2425.9 1703.4 1831.6 2649.7 3056.1 TRUE FALSE FALSE 3082.762489 2722.495277 3132.690444 203.4453212 2307.031895 2270.892819 1848.086753 1884.594456 2412.704196 2976.702081 1.035630172 0.914601194 1.052403082 0.068345879 0.77502949 0.762888847 0.620850425 0.633114905 0.81052928 1 11.53949912 QIMQGAHSDFIVRLYR ddPTM_HeLa_Romidepsin_16h_R1 1 QIMQGAHSDFIVRLYR 16 1 A0A5F9ZGW0;Q13976-3;Q13976;Q13976-2 A0A5F9ZGW0 PRKG1 cGMP-dependent protein kinase 1 0 0 62.287 0.025257 15980000 2952 2326.7 2553.7 2043.7 2438 2485.8 2343.9 2378.7 3327.7 2945.3 FALSE FALSE TRUE 2916.019889 2359.455344 2598.146077 2280.00221 2313.579763 2326.965403 2542.990807 2447.523932 3030.062178 2868.780681 1.01646665 0.822459297 0.905662149 0.794763512 0.80646798 0.811133949 0.886436117 0.853158259 1.056219528 1 11.48622196 -10.26331345 24.99909908 1.007775921 0.840181055 0.839840245 0.036654619 43.33104549 578010.7956 0.00566732 0.006654802 5.45E-11 10.26331345 -0.167594866 QIPS(ph)AEDLETDGGGPGQVVDDGLEHR ddPTM_HeLa_Romidepsin_16h_R1 4 QIPSAEDLETDGGGPGQVVDDGLEHR 26 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;Q8WUI4-10 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 0 QIPS(1)AEDLETDGGGPGQVVDDGLEHR;QIPS(1)AEDLETDGGGPGQVVDDGLEHR;QIPS(1)AEDLETDGGGPGQVVDDGLEHR;QIPS(1)AEDLETDGGGPGQVVDDGLEHR ;;; 148.56 2.16E-08 13402300 3772.77 3679.36 3071.53 3087.59 2599.47 2521.02 2690.92 3101.53 4583.84 4612.13 TRUE FALSE FALSE 3726.786028 3731.158127 3124.988691 3444.591683 2466.809346 2359.934958 2919.486678 3191.267877 4173.84987 4492.306198 0.829593056 0.830566298 0.695631276 0.766775801 0.549118701 0.525328162 0.649885949 0.710385209 0.929110725 1 12.13324055 -10.21764241 0.445783499 0.987163177 0.593211851 0.774437047 0.069322309 0.296822981 0.14875908 0.033547188 0.040967274 6.06E-11 10.21764241 -0.393951326 QIQTS(ph)PVPVRK ddPTM_HeLa_Romidepsin_16h_R1 1 QIQTSPVPVRK 11 1 Q9NRM7 Q9NRM7 LATS2 Serine/threonine-protein kinase LATS2 1 0 QIQT(0.168)S(0.832)PVPVRK 113.61 0.0013558 0 1905.4 2512.6 1663.1 1852.5 1768.7 1760.1 1406.7 1508.5 2257.8 1899.2 TRUE FALSE FALSE 1882.176252 2547.972449 1692.045558 2066.694766 1678.436639 1647.63529 1526.185063 1552.146067 2055.856713 1849.85851 1.017470386 1.377387749 0.914689177 1.117217752 0.907332442 0.890681791 0.825027998 0.839062047 1.111358897 1 10.85319921 -8.590977643 5.012539243 1.038096547 0.855842519 0.421126017 0.121066332 0.176834646 8.499823381 0.017158693 0.035166173 2.56E-09 8.590977643 -0.182254028 QIS(ph)QDVKLEPDILLR ddPTM_HeLa_Romidepsin_16h_R1 1 QISQDVKLEPDILLR 15 1 E9PIJ1;E9PJF6;A0A590UK85;A0A590UJY6;A0A5F9UK94;H0Y360;Q01433-3;Q01433-5;Q01433-2;Q01433-4;Q01433 E9PIJ1 AMPD2 AMP deaminase 2 1 0 QIS(1)QDVKLEPDILLR 112.3 0.02693 13104000 779.79 1216.9 635.51 1112.2 1086.5 684.68 794 1048.9 1053.3 1071.3 TRUE FALSE FALSE 770.2856195 1234.03155 646.570785 1240.797797 1031.051851 640.9311577 861.4423402 1079.248267 959.09021 1043.467472 0.738198018 1.182625797 0.619636742 1.189110184 0.988101574 0.614232044 0.825557445 1.034290283 0.919137622 1 10.02716991 -9.478292638 0.008119638 1.765057547 7.30E-07 0 0.198365379 18549.33669 71.13428639 7601.04897 7858.889616 3.32E-10 9.478292638 -1.765056817 QISDGEREELNLTANR ddPTM_HeLa_Romidepsin_16h_R1 1 QISDGEREELNLTANR 16 1 O95816-2;O95816 O95816-2 BAG2 BAG family molecular chaperone regulator 2 0 0 118.08 0.0033325 3453200 899.68 868.12 917.85 850.8 930.74 939.96 869.92 836.83 1036.7 1007.9 FALSE FALSE TRUE 888.7143541 880.3414161 933.8247942 949.1734991 883.2408647 879.8995896 943.8109831 861.0423558 943.9749555 981.7146127 0.905267521 0.896738629 0.951218187 0.966852777 0.899692083 0.896288573 0.961390379 0.877080105 0.961557405 1 9.93915988 -12.30926806 0.934687924 1.002100322 0.920325497 0.359461939 0.031241059 0.388235301 0.58321941 0.022215333 0.005360098 4.91E-13 12.30926806 -0.081774825 QISGQYSGS(ph)PQLLK ddPTM_HeLa_Romidepsin_16h_R1 1 QISGQYSGSPQLLK 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GUE9;Q96N67-7 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 0 QISGQYS(0.051)GS(0.949)PQLLK 203.53 9.67E-17 17047000 859.99 947.31 845.16 963.98 910.63 792.56 547.03 908.21 995.83 1090 TRUE FALSE FALSE 849.5081111 960.646255 859.8696553 1075.439903 864.1571531 741.9179739 593.4947145 934.4876234 906.7604707 1061.681643 0.800153339 0.904834572 0.809912897 1.012958932 0.8139513 0.69881398 0.559013824 0.880195706 0.854079447 1 10.05213551 -16.52286232 0.031269406 2.183582168 1.92E-05 0.196927782 0.114465823 906.5226882 2.27473146 122.7693574 50.84638605 3.00E-17 16.52286232 -2.183562971 QISLAPETLDSS(ph)GDVSPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 QISLAPETLDSSGDVSPGPR 20 0 Q8TER5;Q8TER5-2 Q8TER5 ARHGEF40 Rho guanine nucleotide exchange factor 40 1 0 QISLAPET(0.031)LDS(0.276)S(0.48)GDVS(0.213)PGPR 171.83 1.99E-10 3362900 2961.3 3033.1 3225.3 3443.8 3868.7 3306.8 2494.1 2968.5 3519.8 3212.4 TRUE FALSE FALSE 2925.206537 3075.800061 3281.434994 3841.98836 3671.265803 3095.506152 2705.948792 3054.388864 3204.980272 3128.941385 0.934886972 0.983016197 1.048736486 1.22788761 1.173325209 0.989314203 0.864812874 0.976173245 1.024301794 1 11.61145892 -7.952392916 10.90790779 1.010160705 0.921932659 0.145444953 0.094035623 1.049350815 234.5526522 0.015467008 0.046445251 1.12E-08 7.952392916 -0.088228046 QITQEEDDS(ph)DEEVAPENFFSLPEK ddPTM_HeLa_Romidepsin_16h_R1 5 QITQEEDDSDEEVAPENFFSLPEK 24 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 0 QIT(0.001)QEEDDS(0.999)DEEVAPENFFSLPEK;QIT(0.006)QEEDDS(0.992)DEEVAPENFFS(0.001)LPEK;QITQEEDDS(1)DEEVAPENFFSLPEK;QIT(0.002)QEEDDS(0.998)DEEVAPENFFSLPEK;QIT(0.001)QEEDDS(0.978)DEEVAPENFFS(0.022)LPEK ;;;; 125.61 8.29E-07 36525500 13720.5 13686.9 14271.2 11133.4 14539.7 14387.5 12129.1 13274.1 14959.9 14856.1 TRUE FALSE FALSE 13553.26927 13879.58454 14519.58425 12420.69609 13797.68485 13468.18518 13159.34545 13658.16514 13621.84908 14470.13638 0.936637286 0.959188232 1.003417236 0.85836759 0.953528321 0.930757308 0.909414058 0.943886414 0.941376689 1 13.8207909 -16.52287875 0.169302119 1.266221574 0.91729525 0.047286632 0.038739389 47.27561778 0.523171869 4.148859565 0.053865513 3.00E-17 16.52287875 -0.348926324 QITT(ph)SPITVR ddPTM_HeLa_Romidepsin_16h_R1 1 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 QIT(0.139)T(0.684)S(0.176)PIT(0.001)VR 157.03 0.0061812 25739000 3800 3558.5 3520.6 2818.4 3134.6 2777.5 2203.6 2927.1 3908.6 3972.9 TRUE FALSE FALSE 3753.684138 3608.596656 3581.874566 3144.276669 2974.629665 2600.026714 2390.773729 3011.79102 3559.005027 3869.683485 0.970023557 0.932530185 0.925624687 0.812541047 0.768701026 0.67189648 0.617821519 0.778304229 0.919714762 1 11.91799985 -9.066954249 1.002995926 0.986266353 0.677208623 0.860156947 0.046107292 0.09933508 0.196505575 0.006779045 0.016489766 8.57E-10 9.066954249 -0.30905773 QITTS(ph)PITVR ddPTM_HeLa_Romidepsin_16h_R1 1 QITTSPITVR 10 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 QIT(0.003)T(0.099)S(0.897)PIT(0.001)VR 127.52 0.0084027 25541000 3978.6 4280.2 4943.8 3485.3 3603.4 3436.1 2837.9 3163.1 4245.1 4471 TRUE FALSE FALSE 3930.107293 4340.456768 5029.844765 3888.286785 3419.505052 3216.5443 3078.951155 3254.619308 3865.407624 4354.842775 0.90246824 0.99669655 1.155000312 0.892865021 0.785218945 0.738613187 0.707017753 0.747356329 0.887611292 1 12.08840492 -8.788900924 3.020930362 0.9718468 0.734733 0.724288818 0.070612488 0.108897039 2.04065655 0.011046 0.022218579 1.63E-09 8.788900924 -0.2371138 QITVNDLPVGR ddPTM_HeLa_Romidepsin_16h_R1 2 QITVNDLPVGR 11 0 P32119;Q06830;A0A0A0MSI0;A0A0A0MRQ5 P32119;Q06830 PRDX2;PRDX1 Peroxiredoxin-2;Peroxiredoxin-1 0 0 ; ; 169.58 0.0063559 12618000 5724.9 5671.4 4894.9 4761.9 5422 5933.8 5035.5 5754.9 5657.9 4629.9 FALSE FALSE TRUE 5655.122717 5751.242118 4980.093681 5312.493283 5145.295108 5554.64933 5463.215244 5921.408952 5151.843254 4509.614531 1.254014657 1.275328984 1.104328019 1.178037113 1.140961178 1.23173484 1.211459473 1.313063215 1.142413219 1 12.13878841 -12.31932731 0.94919405 0.994792263 1.211509242 0.317079006 0.072393448 0.304774553 0.473258704 0.046687648 0.011276779 4.79E-13 12.31932731 0.21671698 QIVGTPVNS(ph)EDSDTR ddPTM_HeLa_Romidepsin_16h_R1 1 QIVGTPVNSEDSDTR 15 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 QIVGT(0.117)PVNS(0.877)EDS(0.006)DTR 125.33 0.0028145 36992000 2858.1 2448.4 2851.4 2764.7 3377 3972 3241.5 3744.2 2575.8 2717 TRUE FALSE FALSE 2823.264378 2482.868639 2901.027421 3084.367622 3204.659089 3718.202019 3516.832929 3852.53252 2345.413997 2646.411948 1.066827249 0.93820187 1.096211579 1.165490363 1.210944914 1.404997442 1.32890608 1.455756925 0.886261868 1 11.36982194 -8.645883608 1.02232076 1.024680393 1.4185512 0.871947595 0.066071676 0.11299343 0.222615404 0.008219646 0.028267488 2.26E-09 8.645883608 0.393870808 QIVS(ph)ALDFCHS(ph)YS(ph)ICHR ddPTM_HeLa_Romidepsin_16h_R1 1 QIVSALDFCHSYSICHR 17 0 Q8TDC3-3;Q8TDC3;Q8TDC3-2 Q8TDC3-3 BRSK1 Serine/threonine-protein kinase BRSK1 3 0 QIVS(1)ALDFCHS(0.626)Y(0.378)S(0.996)ICHR 70.335 0.0039086 0 1735.8 1543.5 1361.6 1165.2 1222.3 1188.7 1202.9 1275.3 1322.2 1568.7 TRUE FALSE FALSE 1714.643402 1565.229434 1385.298077 1299.925906 1159.92147 1112.745906 1305.074296 1312.198793 1203.93912 1527.944948 1.122189254 1.024401721 0.906641354 0.850767502 0.759138261 0.728263088 0.854136988 0.858799785 0.787946661 1 10.57737685 -9.561311275 1.950482848 1.058437326 0.802745262 0.326175644 0.097763958 0.106998133 0.819928596 0.010058236 0.015625854 2.75E-10 9.561311275 -0.255692064 QIYYSDKYDDEEFEYR ddPTM_HeLa_Romidepsin_16h_R1 2 QIYYSDKYDDEEFEYR 16 1 Q5T179;P61024 Q5T179 CKS1B Cyclin-dependent kinases regulatory subunit;Cyclin-dependent kinases regulatory subunit 1 0 0 ; ; 119.77 0.0033041 41628000 3383.5 3188.5 3183.2 2498.4 2721.6 2760.2 2544.1 2697.3 3435 3036.3 FALSE FALSE TRUE 3342.260601 3233.387787 3238.602261 2787.276763 2582.706596 2583.832128 2760.19579 2775.34212 3127.764997 2957.416488 1.13012848 1.093314993 1.095078178 0.942470151 0.873298234 0.873678813 0.933313181 0.938434654 1.057600446 1 11.53012171 -9.147773313 4.316236877 1.06808652 0.904986558 0.825562283 0.037627051 0.104961842 3.267857298 0.008342549 0.01411946 7.12E-10 9.147773313 -0.163099962 QIYYSDKYFDEHYEYR ddPTM_HeLa_Romidepsin_16h_R1 1 QIYYSDKYFDEHYEYR 16 1 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 0 108.36 0.0014067 14571000 1813.7 1753.9 1479.7 1832.2 2072.6 2243.2 1818.4 1973.9 1825.7 1880.9 FALSE FALSE TRUE 1791.593927 1778.59145 1505.453558 2044.047585 1966.827488 2099.86676 1972.854851 2031.011682 1662.404819 1832.033947 0.977926162 0.970828872 0.821738899 1.115725824 1.073575897 1.146194241 1.076865881 1.108610288 0.907409397 1 10.83923052 QKDFLDGVYAFEYYPS(ph)TPGR ddPTM_HeLa_Romidepsin_16h_R1 1 QKDFLDGVYAFEYYPSTPGR 20 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 QKDFLDGVYAFEYYPS(0.5)T(0.5)PGR 121.65 6.98E-05 42650000 5276.2 5399.5 4791.4 4586.4 5741.8 5915.3 4616 4877.3 4944.7 5193.3 TRUE FALSE FALSE 5211.891645 5475.514303 4874.792307 5116.701148 5448.77452 5537.331421 5008.082925 5018.41698 4502.433648 5058.377317 1.030348532 1.082464585 0.963706739 1.011530146 1.077178348 1.094685326 0.990057208 0.992100167 0.890094464 1 12.30445894 QKDFLDGVYAFEYYPST(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 QKDFLDGVYAFEYYPSTPGR 20 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 1 0 QKDFLDGVYAFEYYPS(0.069)T(0.931)PGR 98.135 0.00045886 45726000 6147.8 5908.1 5381.2 5347 7336.7 6384.6 5742.3 6536.3 5320.8 5453.5 TRUE FALSE FALSE 6072.868249 5991.274387 5474.857529 5965.245298 6962.280822 5976.644665 6230.050819 6725.417528 4844.894322 5311.817284 1.143275065 1.127914246 1.030693873 1.123014023 1.31071542 1.125160062 1.172866175 1.266123658 0.912097322 1 12.37498981 -16.52287868 0.053232021 0.310751236 1.497769119 0.593931537 0.07174045 226.8330941 0.953968868 22.03972795 4.980898091 3.00E-17 16.52287868 1.187017883 QKEDVEVVGGS(ph)DGEGAIGLSSDPK ddPTM_HeLa_Romidepsin_16h_R1 2 QKEDVEVVGGSDGEGAIGLSSDPK 24 1 Q8NHZ8 Q8NHZ8 CDC26 Anaphase-promoting complex subunit CDC26 1 0 QKEDVEVVGGS(1)DGEGAIGLSSDPK;QKEDVEVVGGS(0.574)DGEGAIGLS(0.19)S(0.235)DPK ; 83.601 8.00E-05 148599000 17302.9 15902.1 16067.7 17454.2 16260.8 15604.8 13335.7 14974.3 17879.1 17091.1 TRUE FALSE FALSE 17092.0056 16125.97018 16347.35158 19472.33673 15430.9507 14607.70364 14468.43403 15407.55774 16279.94852 16647.07076 1.026727515 0.968697161 0.981995681 1.169715502 0.926946904 0.877493936 0.869127923 0.925541674 0.977946736 1 14.02298072 -8.538906735 24.99938776 1.017793517 0.890838241 0.541195218 0.055326445 125.4627797 195687.8804 0.007460165 0.014923792 2.89E-09 8.538906735 -0.126955276 QKEENNTDLPYLEESTLTTAALS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 QKEENNTDLPYLEESTLTTAALSPSK 26 1 A0A087WU78;A0A087WWC4;Q6T4R5-4;Q6T4R5-3;Q6T4R5-2;Q6T4R5 A0A087WU78 NHS Nance-Horan syndrome protein 1 0 QKEENNTDLPYLEEST(0.001)LT(0.001)T(0.003)AALS(0.849)PS(0.146)K;QKEENNTDLPYLEES(0.098)T(0.098)LT(0.03)T(0.088)AALS(0.57)PS(0.115)K ; 129.48 2.17E-07 16447900 5555.4 5829.2 5808.8 5288.3 4602.3 4901.8 3613 4083.9 6546.5 6484.5 TRUE FALSE FALSE 5487.688648 5911.263631 5909.899727 5899.758128 4367.427457 4588.5908 3919.88813 4202.061203 5960.964644 6316.031755 0.868850706 0.935914172 0.935698229 0.934092537 0.691482821 0.726499007 0.620625146 0.665300835 0.943783197 1 12.62480271 -8.748566008 5.371436497 0.93642858 0.673216621 0.918732417 0.037968995 0.04815237 4.075969008 0.007887819 0.015437703 1.78E-09 8.748566008 -0.263211959 QKFNDS(ph)EGDDTEETEDYR ddPTM_HeLa_Romidepsin_16h_R1 3 QKFNDSEGDDTEETEDYR 18 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 QKFNDS(0.965)EGDDT(0.023)EET(0.012)EDYR;QKFNDS(0.632)EGDDT(0.367)EET(0.001)EDYR;QKFNDS(0.983)EGDDT(0.011)EET(0.006)EDYR ;; 74.742 0.006814 174963500 6124.8 6028.6 5880.2 5164 5948.6 5764 4873.2 5348.9 5892.6 5619.7 TRUE FALSE FALSE 6050.148582 6113.470789 5982.542414 5761.085977 5645.020745 5395.699002 5287.129486 5503.661982 5365.551098 5473.699384 1.105312542 1.11688099 1.09296145 1.052503174 1.031299008 0.98574997 0.965915209 1.005473921 0.980242195 1 12.41830049 -8.44348725 2.435435335 1.060247833 0.982865951 0.377022165 0.041467945 0.265180013 3.068237129 0.007073485 0.017877452 3.60E-09 8.44348725 -0.077381882 QKKKY(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QKKKYPK 7 3 Q52LR7 Q52LR7 EPC2 Enhancer of polycomb homolog 2 1 0 QKKKY(1)PK 52.683 0.0043371 0 641.57 557.32 470.77 430.65 443.16 390.93 649.37 459.58 762.4 599.25 TRUE FALSE FALSE 633.7502981 565.1659656 478.9635544 480.4437793 420.5438915 365.9508347 704.5274716 472.8772222 694.2090345 583.6813986 1.085781215 0.968278186 0.820590746 0.823126761 0.720502474 0.626970185 1.207041159 0.810163256 1.189362958 1 9.189037281 -9.910624919 3.721506458 1.040213002 0.836606569 0.361416131 0.149049557 0.213284058 5.784436232 0.023289394 0.030945296 1.23E-10 9.910624919 -0.203606433 QKNS(ph)PLLSVSSQTITK ddPTM_HeLa_Romidepsin_16h_R1 1 QKNSPLLSVSSQTITK 16 1 Q8ND24;E9PRE9 Q8ND24 RNF214 RING finger protein 214 1 0 QKNS(0.991)PLLS(0.008)VSSQTITK 76.391 0.011157 10787000 2152.5 2515.5 2117.7 5080.1 2881.6 2616.5 2258.2 2260.2 2814.5 2818.3 TRUE FALSE FALSE 2126.264502 2550.913275 2154.55768 5667.485065 2734.541199 2449.314094 2450.011452 2325.595321 2562.764071 2745.08016 0.774572828 0.929267317 0.784879696 2.064597292 0.996160782 0.892255946 0.892509985 0.847186671 0.933584421 1 11.42263256 QKS(ph)DAEEDGGTVSQEEEDR ddPTM_HeLa_Romidepsin_16h_R1 2 QKSDAEEDGGTVSQEEEDR 19 1 P27824-3;P27824;P27824-2 P27824-3 CANX Calnexin 1 0 QKS(1)DAEEDGGTVSQEEEDR;QKS(0.999)DAEEDGGT(0.001)VSQEEEDR ; 91.547 0.0013109 26770400 2550.7 3165.5 3192.9 2177.23 2202.76 3438.1 1850.97 3326.55 2893.6 3786.5 TRUE FALSE FALSE 2519.611087 3210.063992 3248.471085 2428.971577 2090.344938 3218.416506 2008.191346 3422.798476 2634.789169 3688.126184 0.683168352 0.870378027 0.880791742 0.658592319 0.566776958 0.872642731 0.5445018 0.92805894 0.714397783 1 11.8486723 -12.45995862 0.778638321 1.032614197 0.739692704 0 0.156978167 0.759782698 0.667836491 0.149710421 0.024111394 3.47E-13 12.45995862 -0.292921493 QKSEEELK ddPTM_HeLa_Romidepsin_16h_R1 1 QKSEEELK 8 1 H0YM11;V9GY01;Q9Y448-3;Q9Y448-2;Q9Y448 H0YM11 KNSTRN Small kinetochore-associated protein 0 0 114.89 0.001309 1450100 834.36 967.23 871.12 920.52 1024.4 877.6 1013.4 1025 847.51 823.46 FALSE FALSE TRUE 824.1904994 980.8466893 886.2814782 1026.954854 972.1210454 821.5241923 1099.478171 1054.656758 771.706583 802.0663905 1.027583887 1.222899626 1.104997652 1.280386344 1.212020672 1.02425959 1.370806935 1.314924513 0.962148012 1 9.647577849 -8.620359917 0.249985466 0.961320079 1.432240802 0.552434912 0.092865515 2.746166957 0.25904769 0.087126893 0.404098237 2.40E-09 8.620359917 0.470920723 QKVDSLLENLEK ddPTM_HeLa_Romidepsin_16h_R1 1 QKVDSLLENLEK 12 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;P07910-4;G3V5V7;G3V4W0;G3V576;P0DMR1;B7ZW38;A0A0G2JPF8;A0A0G2JNQ3;B2RXH8;O60812;B4DY08 P07910-2;B4DY08 HNRNPC;HNRNPCL4;HNRNPCL3;HNRNPCL2;HNRNPCL1 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 1 0 0 160.48 0.00088066 10476000 8349.2 8441 7922.6 7786.2 9223.3 8756 8281.3 8442.7 8581.9 8483.2 FALSE FALSE TRUE 8247.436739 8559.83262 8060.48953 8686.477079 8752.600584 8196.519859 8984.713415 8686.976204 7814.31337 8262.805241 0.998140038 1.035947523 0.975514888 1.051274576 1.059277125 0.99197786 1.087368412 1.051334983 0.945721597 1 13.01241595 -8.515244615 0.477831285 0.997666236 1.072524039 0.400686592 0.032342213 1.259357603 0.394971951 0.006689505 0.04382159 3.05E-09 8.515244615 0.074857803 QLAELETEDGMQES(ph)P ddPTM_HeLa_Romidepsin_16h_R1 2 QLAELETEDGMQESP 15 0 Q96QG7-2;Q96QG7 Q96QG7-2 MTMR9 Myotubularin-related protein 9 1 0 QLAELETEDGMQES(1)P;QLAELETEDGMQES(1)P ; 141.46 0.00093619 11162600 5084.9 5109.3 4497.4 4329.7 4977.8 4994.4 4607.5 5010.2 5454.9 4655.2 TRUE FALSE FALSE 5022.923283 5181.22886 4575.67536 4830.320286 4723.764291 4675.273959 4998.860935 5155.162232 4967.000082 4534.257233 1.107772018 1.14268525 1.00913449 1.065294719 1.04179451 1.031100292 1.102465228 1.13693643 1.095438531 1 12.14665052 -12.42616734 1.174399153 1.000310718 1.079508866 0 0.050906228 0.465993658 1.156665741 0.029564559 0.007558059 3.75E-13 12.42616734 0.079198148 QLATK(ac)AAR ddPTM_HeLa_Romidepsin_16h_R1 2 QLATKAAR 8 1 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1 0 1 ; QLATK(1)AAR;QLATK(1)AAR 138.4 0.008658 31385000 396.64 598.64 17941.4 3120.4 10001.7 17293.3 11579.6 1753.22 541.71 261.912 FALSE TRUE FALSE 391.8055991 607.0676696 18253.66254 3481.19533 9491.275928 16188.31394 12563.17093 1803.946655 493.2581009 255.1074885 1.535845151 2.379654448 71.55282916 13.64599429 37.20500713 63.45683554 49.24657841 7.071319879 1.933530465 1 7.994961439 -9.85205008 11.37402269 1.304139579 40.4473069 0.511922729 18.48853136 0.252391008 30.05479435 2.793533982 3.672418274 1.41E-10 9.85205008 39.14316732 QLEAIDQLHLEYAK ddPTM_HeLa_Romidepsin_16h_R1 2 QLEAIDQLHLEYAK 14 0 O43707;O43707-2;O43707-3;F5GXS2 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 116.58 0.0021642 20170400 7954.6 6860.8 6800.5 5347.5 8428.2 8477 5937 7338.4 7047.1 7345.9 FALSE FALSE TRUE 7857.646276 6957.386522 6918.85985 5965.803111 7998.077504 7935.347058 6441.288632 7550.725026 6416.789726 7155.052459 1.098195481 0.972373936 0.966989395 0.833788871 1.117822343 1.109055049 0.900243383 1.055299744 0.896819382 1 12.80474663 -10.23710941 24.27220762 1.046370095 0.992100661 0 0.097570473 1133.559241 1130870.542 0.014769291 0.018082731 5.79E-11 10.23710941 -0.054269434 QLEEPGAGTPS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 2 QLEEPGAGTPSPVR 14 0 Q96P11-5;Q96P11;Q96P11-2;Q96P11-4;Q63ZY6-4;Q63ZY6-5;Q63ZY6 Q96P11-5 NSUN5;NSUN5P2 Probable 28S rRNA (cytosine-C(5))-methyltransferase;Putative methyltransferase NSUN5C 1 0 QLEEPGAGT(0.007)PS(0.993)PVR;QLEEPGAGTPS(1)PVR ; 169.06 6.72E-05 49074000 4632 4438.1 4304.9 3608.6 3986.1 3821.4 3466.8 3447.5 5041.5 4551.8 TRUE FALSE FALSE 4575.543402 4500.579688 4379.824979 4025.843311 3782.674443 3577.224873 3761.269905 3547.247973 4590.575613 4433.54358 1.032028516 1.01512021 0.987883597 0.908041894 0.853194375 0.806854564 0.848366513 0.800093178 1.03541908 1 12.11424454 -9.040202181 1.538652224 1.015932542 0.820725718 0.96958873 0.015799995 0.046223999 0.216844878 0.00265403 0.00546264 9.12E-10 9.040202181 -0.195206824 QLENTISEMS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QLENTISEMSPK 12 0 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 QLENTISEMS(1)PK 133.15 0.0042033 5812600 1963.6 2047.2 1675.4 2005.3 1810.6 1801.8 1572.5 1534 1943.2 1879.9 TRUE FALSE FALSE 1939.666888 2076.020535 1704.559634 2237.162221 1718.198326 1686.670795 1706.068111 1578.38387 1769.395325 1831.059927 1.059313712 1.133780771 0.930914171 1.221785365 0.938362694 0.921144508 0.931737998 0.862005577 0.966323002 1 10.83846329 -8.546393504 24.99998783 1.043038623 0.911325684 0.421450873 0.079815074 160.5029693 170639.9525 0.010382583 0.020766016 2.84E-09 8.546393504 -0.131712939 QLES(ph)GGFEAR ddPTM_HeLa_Romidepsin_16h_R1 1 QLESGGFEAR 10 0 Q8IYI6 Q8IYI6 EXOC8 Exocyst complex component 8 1 0 QLES(1)GGFEAR 97.273 0.02798 3943000 1220.5 1084.1 1270.4 1245.5 1604.4 1445.9 1077.9 1408.8 1219.6 1295.8 TRUE FALSE FALSE 1205.624077 1099.361988 1292.510779 1389.51057 1522.521481 1353.511656 1169.456799 1449.561405 1110.515921 1262.134929 0.955225982 0.871033645 1.024067038 1.10092078 1.20630643 1.072398541 0.926570347 1.148499556 0.879870999 1 10.30165044 -9.52115074 24.73716907 0.969101648 1.084717514 0.455277088 0.079374761 50.26918238 719628.9138 0.011964726 0.017068672 3.01E-10 9.52115074 0.115615866 QLFEELRR ddPTM_HeLa_Romidepsin_16h_R1 2 QLFEELRR 8 1 P30613-2;P30613 P30613-2 PKLR Pyruvate kinase PKLR 0 0 ; ; 131.5 0.0065825 10325700 4195.3 4312 4050.7 3132.8 4845.5 4226.5 3868.3 3179.3 4855.6 5875.6 FALSE FALSE TRUE 4144.16607 4372.704449 4121.200734 3495.029076 4598.216054 3956.44029 4196.873305 3271.288029 4421.302975 5722.951065 0.724130964 0.764064623 0.720118115 0.610703995 0.803469399 0.691328695 0.733340764 0.571608597 0.772556488 1 12.48254356 -12.84813456 0.332496768 1.197150565 0.675852032 0.261935733 0.09465521 1.548781791 0.163889625 0.311763973 0.025588388 1.42E-13 12.84813456 -0.521298534 QLFHPEQLITGK ddPTM_HeLa_Romidepsin_16h_R1 2 QLFHPEQLITGK 12 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q9NY65;C9J2C0;Q9NY65-2;Q6PEY2;F8VX09;F8VWV9;F8VRZ4;F8VS66;C9JEV8;C9JQ00;C9JJQ8;C9K0S6;C9JDL2;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA1A;TUBA8;TUBA3E;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 ; ; 96.604 0.0045931 872560 790.72 506.71 858.58 680.93 569.23 602.62 632.84 712.04 610.938 817.15 FALSE FALSE TRUE 781.0824005 513.8434767 873.5232247 759.6623305 540.180069 564.1145269 686.5934138 732.641754 556.2941752 795.9203252 0.981357525 0.645596626 1.097500839 0.954445196 0.67868611 0.708757534 0.862640885 0.92049635 0.698931988 1 9.636480208 -10.10503925 0.593391306 1.004082799 0.814516527 0 0.164790902 0.815070482 0.627656022 0.041185873 0.055263037 7.85E-11 10.10503925 -0.189566272 QLFHPEQLITGKEDAANNYAR ddPTM_HeLa_Romidepsin_16h_R1 1 QLFHPEQLITGKEDAANNYAR 21 1 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q9NY65;C9J2C0;Q9NY65-2;F8VX09;F8VWV9;F8VRZ4;F8VS66;C9JEV8;C9JQ00;C9JJQ8;C9K0S6;C9JDL2;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA1A;TUBA8;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 99.021 0.00020118 22783000 2452.9 2444.9 1773.9 3290.5 2620.2 2008.7 2066 2515.2 2289 2235.3 FALSE FALSE TRUE 2423.003111 2479.319366 1804.773985 3670.963092 2486.481417 1880.350553 2241.485988 2587.973344 2084.266107 2177.226584 1.11288514 1.138751191 0.828932551 1.686073062 1.142040721 0.863644862 1.02951434 1.188655955 0.95730326 1 11.08827584 -11.92402858 0.644933726 0.994666833 1.124748273 0.062688402 0.220596856 2.608159231 1.917245574 0.181582812 0.050445613 1.19E-12 11.92402858 0.13008144 QLHDDYFYHDEL ddPTM_HeLa_Romidepsin_16h_R1 3 QLHDDYFYHDEL 12 0 Q14257;Q14257-2;A8MXP8 Q14257 RCN2 Reticulocalbin-2 0 0 ;; ;; 144.7 0.00070991 43948400 7847.8 8385.37 8168 7806.5 8767.7 8616.7 7803.6 8581.7 9138.4 7255.1 FALSE FALSE TRUE 7752.147995 8503.419459 8310.160614 8709.124261 8320.251552 8066.120679 8466.437589 8829.99795 8321.038616 7066.611456 1.097010646 1.203323476 1.175975312 1.232432873 1.177403286 1.141441089 1.198090151 1.249537774 1.177514664 1 12.78680287 -10.79511554 0.725173973 1.013808622 1.201195437 0.216827519 0.060728712 0.162019641 0.187998127 0.011378094 0.009383242 1.60E-11 10.79511554 0.187386814 QLHLEGASLELS(ph)DDDTESK ddPTM_HeLa_Romidepsin_16h_R1 4 QLHLEGASLELSDDDTESK 19 0 P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35580 MYH10 Myosin-10 1 0 QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(1)DDDTESK;QLHLEGASLELS(0.999)DDDT(0.001)ESK;QLHLEGASLELS(0.985)DDDT(0.012)ES(0.002)K ;;; 181.65 8.07E-11 90698000 17032.3 16542.1 17304.3 12240.3 23844.9 26604.3 20224.3 22766 21936.7 20482.7 TRUE FALSE FALSE 16824.70378 16774.98012 17605.47408 13655.58108 22628.00578 24904.37109 21942.15154 23424.69829 19974.62661 19950.5565 0.843320023 0.840827679 0.882455288 0.684471186 1.13420424 1.248304582 1.09982654 1.174137588 1.001206488 1 14.28414137 -8.60673602 9.729653003 0.898564365 1.17072297 0.701186869 0.091858561 0.157125877 16.85836637 0.014355339 0.028732622 2.47E-09 8.60673602 0.272158606 QLHVLVPQS(ph)PPTDLPGLTR ddPTM_HeLa_Romidepsin_16h_R1 2 QLHVLVPQSPPTDLPGLTR 19 0 O95402 O95402 MED26 Mediator of RNA polymerase II transcription subunit 26 1 0 QLHVLVPQS(0.985)PPT(0.011)DLPGLT(0.004)R;QLHVLVPQS(0.995)PPT(0.004)DLPGLT(0.001)R ; 79.762 0.0037933 35946000 3419.6 3247 3256.1 3232.7 4189.7 5927.5 4936.9 5951.6 3450.5 3902.6 TRUE FALSE FALSE 3377.9206 3292.711351 3312.771055 3606.479984 3975.883975 5548.75188 5356.240163 6123.800156 3141.878638 3801.209889 0.888643537 0.866227187 0.871504377 0.948771599 1.045952234 1.459733096 1.409088243 1.611013423 0.826547002 1 11.89224297 -8.302224462 2.369429976 0.932796176 1.509948034 0.936860797 0.068706711 0.053228001 0.57937015 0.010041111 0.028262536 4.99E-09 8.302224462 0.577151858 QLIVGVNK ddPTM_HeLa_Romidepsin_16h_R1 2 QLIVGVNK 8 0 Q5VTE0;P68104;A0A087WV01;A0A2R8Y488;A0A2U3TZH3;Q05639 Q5VTE0;A0A2R8Y488 EEF1A1P5;EEF1A1;EEF1A2 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha;Elongation factor 1-alpha 2 0 0 ; ; 155.51 0.0013302 96130000 11460.7 10722.5 11171.53 11320.66 9518.24 8771.45 8826.44 8922.6 9977.04 9407.91 FALSE FALSE TRUE 11321.01258 10873.45164 11365.96579 12629.60797 9032.488695 8210.982654 9576.157593 9180.761353 9084.668554 9163.491142 1.235447539 1.186605789 1.240353225 1.378252871 0.985703872 0.896053974 1.045033759 1.001884676 0.991398192 1 13.16168163 -8.579988976 24.99974078 1.14889226 0.979638093 0.3930772 0.113409268 79.72387929 34898.36049 0.018880498 0.037761001 2.63E-09 8.579988976 -0.169254167 QLLDS(ph)DEEQEEDEGR ddPTM_HeLa_Romidepsin_16h_R1 2 QLLDSDEEQEEDEGR 15 0 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 0 QLLDS(1)DEEQEEDEGR;QLLDS(1)DEEQEEDEGR ; 244.18 2.95E-57 49606000 7029.7 5767.6 6941.7 3818.7 5034.5 4920 4676.9 5216.3 6195.1 6539.2 TRUE FALSE FALSE 6944.019313 5848.796424 7062.517377 4260.236062 4777.570679 4605.627879 5074.155769 5367.225411 5640.99474 6369.310641 1.090230906 0.918277778 1.108835441 0.668869255 0.75009227 0.723096758 0.796656978 0.842669751 0.885652319 1 12.63692152 -9.26336479 24.99979205 1.036903951 0.756333388 0.689611342 0.080126534 52.8282643 685929.5488 0.010084888 0.015890124 5.45E-10 9.26336479 -0.280570562 QLLDS(ph)DEEQEEDEGRNR ddPTM_HeLa_Romidepsin_16h_R1 1 QLLDSDEEQEEDEGRNR 17 1 Q9UNS1-2;Q9UNS1 Q9UNS1-2 TIMELESS Protein timeless homolog 1 0 QLLDS(1)DEEQEEDEGRNR 71.434 0.011012 10513000 1200.6 1043.1 1186.2 816.2 739.56 1011.5 945.84 818.64 1315.9 1204.6 TRUE FALSE FALSE 1185.966625 1057.784789 1206.845313 910.5728843 701.8174935 946.8684145 1026.179626 842.3260568 1198.202608 1173.304318 1.010792006 0.901543421 1.028586782 0.776075627 0.598154701 0.807010082 0.874606536 0.717909279 1.021220658 1 10.19636154 -9.231490157 7.009721519 0.997443699 0.754858729 0.722273973 0.073675666 0.084542043 15.23298656 0.011020858 0.018136495 5.87E-10 9.231490157 -0.24258497 QPGQVIGATTPST(ph)GSPTNK ddPTM_HeLa_Romidepsin_16h_R1 1 QPGQVIGATTPSTGSPTNK 19 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 QPGQVIGATT(0.088)PS(0.341)T(0.398)GS(0.173)PT(0.001)NK 254.02 2.05E-75 14635000 5125.2 5492.3 4816.1 4419.8 2547.9 2036 1842.3 1542.3 5442.2 5449.4 TRUE FALSE FALSE 5062.732091 5569.620744 4899.9222 4930.838072 2417.871155 1905.906171 1998.784916 1586.924017 4955.436002 5307.823802 0.953824445 1.049322839 0.923150877 0.928975463 0.455529657 0.359074875 0.376573336 0.298978277 0.93360974 1 12.37390476 -8.731851542 3.132161388 0.979621617 0.352166118 0.982252681 0.039223582 0.020690929 0.417277433 0.005619616 0.011552754 1.85E-09 8.731851542 -0.627455499 down QLLLTADDR ddPTM_HeLa_Romidepsin_16h_R1 2 QLLLTADDR 9 0 H3BQN4;J3KPS3;P04075;H3BUH7;P04075-2;H3BR04;H3BPS8;H3BMQ8;H3BU78 H3BQN4 ALDOA Fructose-bisphosphate aldolase;Fructose-bisphosphate aldolase A 0 0 ; ; 118.71 0.012079 2958500 2498.4 2117.89 3376.9 2265.3 3520.7 3465.8 2933.5 2217.18 2302.34 1663.68 FALSE FALSE TRUE 2467.94854 2147.705711 3435.673528 2527.224645 3341.025541 3244.346565 3182.671417 2281.330605 2096.412944 1620.457354 1.522995057 1.325370091 2.120187563 1.559574918 2.06177937 2.002117833 1.964057499 1.407831314 1.293716826 1 10.66218534 -11.03124679 0.452019244 0.985773747 1.885525286 0.492165931 0.261365109 0.459728791 0.228717594 0.169315227 0.097117409 9.31E-12 11.03124679 0.899751539 QLLTLS(ph)SELSQAR ddPTM_HeLa_Romidepsin_16h_R1 1 QLLTLSSELSQAR 13 0 E7EQR4;P15311 E7EQR4 EZR Ezrin 1 0 QLLT(0.024)LS(0.74)S(0.185)ELS(0.051)QAR 116.58 0.0055268 3879800 837.28 768.27 745.2 739.6 996.13 1019 887.79 660.8 917.06 633.85 TRUE FALSE FALSE 827.0749093 779.0857252 758.1698934 825.1160319 945.293769 953.8891887 963.1988604 679.9192054 835.0358568 617.3824856 1.33964751 1.261917439 1.228039199 1.336474635 1.531131496 1.545053854 1.560133115 1.101293317 1.352542186 1 9.270020746 -12.98194051 0.255477957 0.677555683 1.447645639 0.016918359 0.176352117 4.702091252 0.301820203 1.13547031 0.108075785 1.04E-13 12.98194051 0.770089956 QLLTLSSELSQAR ddPTM_HeLa_Romidepsin_16h_R1 1 QLLTLSSELSQAR 13 0 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 142.76 0.00032738 560230 0 0 0 0 0 52.474 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 49.12108075 0 0 0 0 0 QLMEQDASS(ph)SPSAQVIGLK ddPTM_HeLa_Romidepsin_16h_R1 2 QLMEQDASSSPSAQVIGLK 19 0 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5;Q9H4L5-8;Q9H4L5-6;Q9H4L5-4;Q9H4L5-2 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 QLMEQDAS(0.048)S(0.475)S(0.475)PS(0.001)AQVIGLK;QLMEQDAS(0.101)S(0.447)S(0.447)PS(0.005)AQVIGLK ; 135.95 6.88E-09 6391300 4883.6 4788.6 5071.1 4270.6 4943.1 4397.3 3570.1 4205.2 4963.1 4612.7 TRUE FALSE FALSE 4824.076805 4856.014036 5159.360368 4764.386866 4690.835162 4116.326722 3873.344205 4326.870827 4519.187906 4492.861389 1.073720373 1.080828812 1.148346214 1.060434866 1.044064073 0.916192681 0.862110773 0.9630546 1.005859633 1 12.13341884 -8.258223386 5.154133282 1.050581876 0.90722759 0.677696651 0.045634939 0.089807848 7.862573708 0.007364556 0.018142912 5.52E-09 8.258223386 -0.143354286 QLMEQDASSSPS(ph)AQVIGLK ddPTM_HeLa_Romidepsin_16h_R1 1 QLMEQDASSSPSAQVIGLK 19 0 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5;Q9H4L5-8;Q9H4L5-6;Q9H4L5-4;Q9H4L5-2 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 QLMEQDAS(0.028)S(0.282)S(0.282)PS(0.409)AQVIGLK 145.79 8.03E-05 8981700 2378.7 2294.4 2493 2247.9 2361.5 2403.6 1542.1 2703 2560.7 2159.7 TRUE FALSE FALSE 2349.707489 2326.700623 2536.389619 2507.812775 2240.983843 2250.017717 1673.085936 2781.20704 2331.664579 2103.590683 1.11699843 1.10606148 1.205742942 1.192158149 1.065313638 1.06960814 0.795347664 1.322123673 1.108421233 1 11.0386383 -6.949179293 19.68622449 1.067177736 3.874358552 0.317740655 0.109054716 143.9532053 68865.04871 0.014922454 3913.113265 1.12E-07 6.949179293 2.807180816 QLNK(ac)YDPFSR ddPTM_HeLa_Romidepsin_16h_R1 1 QLNKYDPFSR 10 1 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 0 1 QLNK(1)YDPFSR 186.78 4.05E-05 933210 682.3 678.79 862.66 810.81 893.38 1103.9 816.87 1271.2 832.54 852.99 FALSE TRUE FALSE 673.9838652 688.3460234 877.6742354 904.5596672 847.7874849 1033.364353 886.2549174 1307.980166 758.0755373 830.8291968 0.81121832 0.828504855 1.056383477 1.088743235 1.020411281 1.243774721 1.06671133 1.574306935 0.912432471 1 9.698408106 -4 0.447636209 0.911532352 14.30582457 0.749308131 0.105216006 30.14196121 0.326867065 0.025244082 371.6353739 1.00E-04 4 13.39429222 QLPALDGSLMGPES(ph)PPAQEEEAPVSPHK ddPTM_HeLa_Romidepsin_16h_R1 1 QLPALDGSLMGPESPPAQEEEAPVSPHK 28 0 A0A494C108;Q8N9T8 A0A494C108 KRI1 Protein KRI1 homolog 1 0 QLPALDGS(0.021)LMGPES(0.979)PPAQEEEAPVSPHK 67.848 6.16E-05 18798000 1768.8 1549.9 1463.5 1418.9 4100.5 3942.7 3398.4 4135.8 3145.4 2673.4 TRUE FALSE FALSE 1747.241185 1571.719533 1488.971604 1582.959894 3891.236184 3690.774194 3687.060011 4255.462848 2864.067546 2603.944683 0.670997812 0.603591752 0.571813838 0.607908419 1.494362077 1.417378111 1.415951743 1.634237039 1.099895695 1 11.34648309 -8.753257141 24.99999999 0.783402251 1.479937086 0.81031403 0.173101562 66.23429606 202370.6106 0.027614351 0.054479872 1.76E-09 8.753257141 0.696534834 QLPFRGDDGIFDDNFIEER ddPTM_HeLa_Romidepsin_16h_R1 1 QLPFRGDDGIFDDNFIEER 19 1 O60493-4;O60493;O60493-2 O60493-4 SNX3 Sorting nexin-3 0 0 96.447 0.0024915 4756100 1029.7 832.17 686.26 1725.5 1001.4 903.51 843.06 1049.4 999.59 863 FALSE FALSE TRUE 1017.14962 843.8853111 698.2040674 1925.010429 950.2948213 845.7786269 914.6694954 1079.762733 910.1841669 840.5791356 1.210058134 1.003933211 0.830622648 2.290100179 1.130523922 1.006185606 1.08814204 1.284546199 1.082806042 1 9.715239837 -11.66162448 0.471455114 0.983265644 1.254370924 0.044810075 0.375805647 3.244216555 1.355170715 0.398437292 0.121762734 2.18E-12 11.66162448 0.27110528 QLPLEPES(ph)PSGQVGPR ddPTM_HeLa_Romidepsin_16h_R1 1 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 QLPLEPES(0.912)PS(0.088)GQVGPR 239.19 4.06E-46 32971000 3153.9 2924.7 3042.9 2142.8 3292.3 2942.3 2709.3 3047.5 3205.2 3121 TRUE FALSE FALSE 3115.459054 2965.874003 3095.860398 2390.560618 3124.281646 2754.296526 2939.427874 3135.674604 2918.518884 3039.91597 1.024850385 0.975643417 1.018403281 0.786390361 1.027752634 0.906043638 0.966943792 1.031500421 0.960065644 1 11.56981573 QLPLEPES(ph)PSGQVGPRPAPPQEESPSSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 QLPLEPESPSGQVGPRPAPPQEESPSSEAK 30 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 QLPLEPES(0.669)PS(0.331)GQVGPRPAPPQEESPSSEAK 88.001 5.03E-08 46227000 2532.8 2685.8 2220.9 2424.8 2264.7 2499.6 2129.1 2349.2 2684.7 3078.1 TRUE FALSE FALSE 2501.929259 2723.610763 2259.553833 2705.166785 2149.123908 2339.883627 2309.945701 2417.170396 2444.573708 2998.130518 0.834496445 0.908436356 0.753654259 0.90228453 0.716821331 0.780447553 0.770462022 0.806225873 0.815366007 1 11.54984747 -14.40697843 0.17171413 1.369288519 0.740777182 0.067472782 0.078274013 10.76585429 0.234951485 1.540114705 0.091191143 3.92E-15 14.40697843 -0.628511337 QLPLEPESPS(ph)GQVGPR ddPTM_HeLa_Romidepsin_16h_R1 1 QLPLEPESPSGQVGPR 16 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 QLPLEPES(0.207)PS(0.793)GQVGPR 238.45 5.05E-46 36302000 2459.7 2257.8 2223.1 1759.3 2430.9 2790.3 2085.4 2595.5 2200.3 2667.9 TRUE FALSE FALSE 2429.72023 2289.585368 2261.792123 1962.718544 2306.842102 2612.008835 2262.533824 2670.596697 2003.499657 2598.587573 0.93501572 0.8810884 0.87039288 0.755302059 0.887729213 1.00516483 0.870678305 1.027710871 0.770995628 1 11.34351196 -11.10120088 1.043907566 0.987209479 0.897253461 0 0.099138293 0.510165757 1.168805316 0.020632638 0.015658247 7.92E-12 11.10120088 -0.089956018 QLPLEPESPS(ph)GQVGPRPAPPQEESPSSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 QLPLEPESPSGQVGPRPAPPQEESPSSEAK 30 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 QLPLEPES(0.134)PS(0.551)GQVGPRPAPPQEES(0.209)PS(0.08)S(0.025)EAK 58.858 0.00057315 45909000 1598.7 1320 1377.3 1276.4 1614 1367.5 1274.5 1288.3 1808.6 1467.9 TRUE FALSE FALSE 1579.214429 1338.582995 1401.271329 1423.983374 1531.631557 1280.121163 1382.755998 1325.574928 1646.834286 1429.763746 1.104528237 0.9362267 0.98007194 0.995957113 1.071248002 0.895337546 0.967122017 0.927128647 1.151822663 1 10.48156106 -8.364055651 0.564608125 1.042157751 0.912828398 0.320471052 0.064272688 1.461705986 0.626814131 0.01332925 0.099386323 4.32E-09 8.364055651 -0.129329353 QLPSQK(ac)TVVVEAGKK ddPTM_HeLa_Romidepsin_16h_R1 1 QLPSQKTVVVEAGKK 15 2 O94842-3;O94842-2;O94842 O94842-3 TOX4 TOX high mobility group box family member 4 0 1 QLPSQK(1)TVVVEAGKK 155.26 6.06E-07 1074100 570.07 602 495.43 441.85 309.87 604.38 565.34 642.22 818.25 741.5 FALSE TRUE FALSE 563.1217676 610.4749718 504.0527513 492.938776 294.0561776 565.7620685 613.3599655 660.8016224 745.0636707 722.2357231 0.779692488 0.845257237 0.697906148 0.682517854 0.407147096 0.783348221 0.849251769 0.914938989 1.031607337 1 9.49632597 -11.69150788 0.57965568 1.008432543 0.726135589 0.404427119 0.131550203 0.786722004 0.504469883 0.108908441 0.036065261 2.03E-12 11.69150788 -0.282296955 QLQPASELWSS(ph)DGAAGLVGSLQEVTIHEK ddPTM_HeLa_Romidepsin_16h_R1 1 QLQPASELWSSDGAAGLVGSLQEVTIHEK 29 0 Q9H1A4;F8WAS1 Q9H1A4 ANAPC1 Anaphase-promoting complex subunit 1 1 0 QLQPAS(0.017)ELWS(0.259)S(0.723)DGAAGLVGS(0.001)LQEVTIHEK 73.389 2.50E-05 13208000 1219.4 1005.3 1316.2 1116.2 943.13 1018.2 684.22 832.99 1407.4 1138.9 TRUE FALSE FALSE 1204.537484 1019.45264 1339.107909 1245.260296 894.9985568 953.1403061 742.3376297 857.0912514 1281.518619 1109.311214 1.0858427 0.918996064 1.207152594 1.122552698 0.806805652 0.859218129 0.669187889 0.772633721 1.155238136 1 10.11544845 -8.686735041 5.854384469 1.050204387 0.770659305 0.729178722 0.089842775 0.085251465 5.010539561 0.01245111 0.025031708 2.06E-09 8.686735041 -0.279545082 QLRTFVLPVT(ph)PPRLVAPR ddPTM_HeLa_Romidepsin_16h_R1 1 QLRTFVLPVTPPRLVAPR 18 2 K7EP52;K7ERN2;P32942 K7EP52 ICAM3 Intercellular adhesion molecule 3 1 0 QLRTFVLPVT(1)PPRLVAPR 48.883 0.026226 15399000 5487.3 5199.1 5553.9 3712.7 5357.7 5614.2 5288.1 5447.6 5721.5 5943.8 TRUE FALSE FALSE 5420.418677 5272.293066 5650.5633 4141.979843 5084.276577 5255.470739 5737.271082 5605.217711 5209.75471 5789.379219 0.936269412 0.910683662 0.976022314 0.715444556 0.878207556 0.90777794 0.990999357 0.968189766 0.899881406 1 12.49919294 -11.17804483 0.756682171 0.992173358 0.903521151 0 0.078536453 0.742692493 0.924027963 0.028962713 0.018246706 6.64E-12 11.17804483 -0.088652208 QLS(ph)ALHR ddPTM_HeLa_Romidepsin_16h_R1 1 QLSALHR 7 0 P61313;E7EX53;A0A2R8Y738;A0A2R8YEM3;E7EQV9;E7ENU7;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 1 0 QLS(1)ALHR 81.972 0.024438 2856600 1432 1729 1589.2 1847 1724.2 1700 1536.5 1703.1 1556.7 1827.6 TRUE FALSE FALSE 1414.546233 1753.340907 1616.859359 2060.55883 1636.20764 1591.375486 1667.010272 1752.376511 1417.464853 1780.118689 0.79463591 0.984957306 0.908287391 1.157540137 0.919156487 0.893971563 0.936460182 0.984415546 0.796275474 1 10.79775772 -9.434300075 24.96778517 0.908348668 0.974502129 0.158261688 0.09184593 140.2685366 39533.86602 0.015745407 0.024051503 3.68E-10 9.434300075 0.06615346 QLS(ph)LEGSGLGVEDLKDNTPSGK ddPTM_HeLa_Romidepsin_16h_R1 2 QLSLEGSGLGVEDLKDNTPSGK 22 1 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 QLS(0.995)LEGS(0.005)GLGVEDLKDNTPSGK;QLS(0.983)LEGS(0.017)GLGVEDLKDNTPSGK ; 121.48 2.27E-05 87143000 3677.5 3801.2 3291.8 3397.2 4574.9 4273 3249 3518.7 3895.6 3774.3 TRUE FALSE FALSE 3632.677215 3854.713393 3349.092398 3790.000248 4341.425782 3999.96909 3524.969979 3620.508033 3547.167779 3676.243142 0.988149335 1.048546912 0.911009492 1.030943847 1.180940872 1.088058906 0.958851154 0.984839112 0.964889329 1 11.84401647 -9.007404389 24.95306574 0.99251864 1.056054047 0.205784339 0.064623795 465.3024391 1568094.565 0.009672689 0.017024788 9.83E-10 9.007404389 0.063535407 QLS(ph)PEDSSSPVK ddPTM_HeLa_Romidepsin_16h_R1 1 QLSPEDSSSPVK 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 0 QLS(0.767)PEDS(0.141)S(0.091)S(0.001)PVK 155.09 0.0013296 13027000 2738.9 2832.3 2177.3 2616.7 2965.2 3318.1 2678.7 3590.9 2910.2 2738.2 TRUE FALSE FALSE 2705.517233 2872.173194 2215.194993 2919.255166 2813.874779 3106.084119 2906.228711 3694.797026 2649.904423 2667.061169 1.014418891 1.076905632 0.830575248 1.09455876 1.05504696 1.164609254 1.089674562 1.385343939 0.993567172 1 11.3810352 -4 0.600763972 1.00383758 23.84810261 0.686008187 0.075347236 62.02335937 0.440973824 0.012119031 1865.974173 1.00E-04 4 22.84426503 QLS(ph)SGVSEIR ddPTM_HeLa_Romidepsin_16h_R1 1 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 0 QLS(0.498)S(0.498)GVS(0.004)EIR 143.55 0.0041786 331810000 3377.1 4012.9 2207.5 2676.1 3902.6 2482.4 1841.4 2645.7 2996 3357.6 TRUE FALSE FALSE 3335.938606 4069.393712 2245.920611 2985.523273 3703.435759 2323.782652 1997.80847 2722.249155 2728.030256 3270.369068 1.020049584 1.244322468 0.686748365 0.912901025 1.132421351 0.7105567 0.610881655 0.832398148 0.834165869 1 11.67523774 -8.243837881 23.97267396 1.002577766 0.707239028 0.361910586 0.153858711 314.5428364 428395.7332 0.019328036 0.049132002 5.70E-09 8.243837881 -0.295338738 QLSEVFET(ph)EDSK ddPTM_HeLa_Romidepsin_16h_R1 1 QLSEVFETEDSK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 QLS(0.008)EVFET(0.93)EDS(0.062)K 127.79 0.0098909 3070900 1518.3 1269.2 1599.6 1073.4 1229.7 1266 1237.5 1439.5 1559 1641.4 TRUE FALSE FALSE 1499.794376 1287.067831 1627.440367 1197.511558 1166.94382 1185.106686 1342.613219 1481.149661 1419.559135 1598.756191 0.938100746 0.805043219 1.017941557 0.749027003 0.729907303 0.741267926 0.839786095 0.926438734 0.887914707 1 10.64273423 -10.1381937 0.73346638 0.985275048 0.802893571 0.241773442 0.088148632 0.412261138 0.458133749 0.021091591 0.027241708 7.27E-11 10.1381937 -0.182381477 QLSGQS(ph)TSSDTTYK ddPTM_HeLa_Romidepsin_16h_R1 1 QLSGQSTSSDTTYK 14 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 QLS(0.072)GQS(0.849)T(0.072)S(0.006)S(0.001)DTTYK 254.72 1.34E-67 7148200 3603.8 3389.1 3684.5 3224.7 4381 5241.8 4723.5 4915.1 4159 3716.5 TRUE FALSE FALSE 3559.875499 3436.811839 3748.627177 3597.554987 4157.421222 4906.865897 5124.713972 5057.310664 3787.008624 3619.944794 0.983406019 0.949410014 1.035548162 0.993814876 1.148476416 1.355508489 1.415688433 1.39706845 1.046150933 1 11.82175198 -8.398577609 1.908830667 0.990775924 1.410594898 0.975044593 0.027794989 0.025651033 0.180614442 0.003104494 0.008903122 3.99E-09 8.398577609 0.419818974 QLSLAAT(ph)AS(ph)PPQAPSPNR ddPTM_HeLa_Romidepsin_16h_R1 4 QLSLAATASPPQAPSPNR 18 0 Q8NEQ6 Q8NEQ6 C1orf64 Uncharacterized protein C1orf64 2 0 QLS(0.029)LAAT(0.989)AS(0.982)PPQAPSPNR;QLS(0.494)LAAT(0.825)AS(0.681)PPQAPSPNR;QLS(0.344)LAAT(0.872)AS(0.784)PPQAPSPNR;QLS(0.45)LAAT(0.841)AS(0.708)PPQAPSPNR ;;; 100.68 0.0083175 362108000 4908.53 5817.77 5193.52 5325.52 5408.51 5607.46 4728.15 5673.8 6128.62 5616.78 TRUE FALSE FALSE 4848.702948 5899.672719 5283.911037 5941.28168 5132.493553 5249.161403 5129.758943 5837.962451 5580.460878 5470.855246 0.886278786 1.078382164 0.965829071 1.085987732 0.938151957 0.959477297 0.937652106 1.067102343 1.02003446 1 12.41755067 -10.27440423 24.99277008 0.946298319 0.999417163 0.024008959 0.063660158 1210.895142 2334275.367 0.011100966 0.012732649 5.32E-11 10.27440423 0.053118845 QLSLPLT(ph)QSK ddPTM_HeLa_Romidepsin_16h_R1 1 QLSLPLTQSK 10 0 Q9C0I1-3;Q9C0I1-2;Q9C0I1 Q9C0I1-3 MTMR12 Myotubularin-related protein 12 1 0 QLS(0.005)LPLT(0.995)QSK 182.23 5.96E-05 78731000 3810.2 3585.5 3757.6 4516.3 4306.4 4024.3 3762 4057.6 3442.8 3225 TRUE FALSE FALSE 3763.759817 3635.976763 3822.999452 5038.495856 4086.628339 3767.160218 4081.544186 4175.000254 3134.867345 3141.214035 1.198186362 1.15750685 1.217045196 1.603996353 1.300970992 1.199268874 1.299352461 1.329104037 0.997979542 1 11.61710653 -11.01570777 0.492102226 1.002766761 1.330621064 0.555803153 0.110252438 0.525368052 0.30435994 0.070305677 0.041986347 9.64E-12 11.01570777 0.327854303 QLSPEDSS(ph)SPVK ddPTM_HeLa_Romidepsin_16h_R1 1 QLSPEDSSSPVK 12 0 Q96AY2;Q96AY2-2 Q96AY2 EME1 Crossover junction endonuclease EME1 1 0 QLS(0.057)PEDS(0.081)S(0.78)S(0.081)PVK 98.156 0.017511 10767000 1474.5 1480.9 1653.5 1777.7 1523.8 1644.6 1802.7 1860.7 1748.7 1692.3 TRUE FALSE FALSE 1456.528227 1501.748149 1682.278474 1983.246038 1446.0348 1539.515368 1955.821293 1914.536419 1592.291892 1648.333802 0.883636691 0.911070408 1.020593324 1.20318229 0.87727061 0.933982768 1.186544431 1.161498003 0.966000873 1 10.68679272 -9.587912867 5.75580195 0.941460642 1.065105715 0.270533532 0.101971793 0.231203804 14.60878335 0.017188448 0.024471991 2.58E-10 9.587912867 0.123645072 VAPVINNGS(ph)PTILGK ddPTM_HeLa_Romidepsin_16h_R1 2 VAPVINNGSPTILGK 15 0 H0Y4T7;E7ESY4;Q13330-3;Q13330;F8W9Y9 H0Y4T7 MTA1 Metastasis-associated protein MTA1 1 0 VAPVINNGS(0.998)PT(0.002)ILGK;VAPVINNGS(0.962)PT(0.038)ILGK ; 141.06 0.00072217 248580000 8715.4 8832.6 9045.2 6905.6 5386.8 3832.7 3853.3 3384.8 9287 8988 TRUE FALSE FALSE 8609.173353 8956.945575 9202.627912 7704.057964 5111.891495 3587.802839 4180.599206 3482.733848 8456.34746 8754.490464 0.983400849 1.023125859 1.051189438 0.880012149 0.583916507 0.40982429 0.477537696 0.397822565 0.965943991 1 13.0958075 -8.730054698 2.280325935 0.998895936 0.433841524 0.984973619 0.031964362 0.022227105 0.235527881 0.0044985 0.009800017 1.86E-09 8.730054698 -0.565054412 down QLSS(ph)GVSEIR ddPTM_HeLa_Romidepsin_16h_R1 3 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 1 0 QLS(0.035)S(0.944)GVS(0.02)EIR;QLS(0.092)S(0.849)GVS(0.06)EIR;QLS(0.16)S(0.42)GVS(0.42)EIR ;; 148.13 0.0038731 5046430000 11331.3 15267.3 7646.6 9508.7 12092.1 8774.2 7084.9 9428.5 11464.6 10061.8 TRUE FALSE FALSE 11193.18976 15482.23345 7779.685865 10608.14063 11474.99502 8213.556937 7686.691229 9701.298772 10439.17746 9800.392986 1.142116421 1.579756391 0.793813664 1.082419924 1.170870906 0.838084447 0.784324796 0.989888751 1.065179476 1 13.25862389 -8.253254115 24.53055387 1.094128235 0.862121857 0.254005188 0.191573919 540.6953641 1620412.27 0.026643474 0.066613246 5.58E-09 8.253254115 -0.232006378 QLSSGVSEIR ddPTM_HeLa_Romidepsin_16h_R1 1 QLSSGVSEIR 10 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 0 161.51 0.022673 5037400 1730.5 2599.7 1469 1664.3 1960.7 1327.9 1314.3 1974.8 1965.5 1746.8 FALSE FALSE TRUE 1709.408 2636.298645 1494.567329 1856.734197 1860.638163 1243.051476 1425.936609 2031.937722 1789.700757 1701.417884 1.004696152 1.549471573 0.878424603 1.091286399 1.093580936 0.730597396 0.838087234 1.194261411 1.051887825 1 10.73252181 S(ph)RLT(ph)PVSPESSSTEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 S(0.998)RLT(0.994)PVS(0.009)PESSSTEEK 91.969 0.010246 42874000 4877.7 4302.4 4143.1 3531 2041.2 1435.9 1040.8 1068.1 4441 4389.4 TRUE FALSE FALSE 4818.248716 4362.9693 4215.208918 3939.270834 1937.029947 1344.150624 1129.205526 1099.003788 4043.785837 4275.362755 1.126980093 1.02049102 0.985930121 0.921388677 0.453067975 0.314394521 0.264119232 0.257055097 0.945834557 1 12.06183112 -8.730048501 1.859399374 1.055110242 0.266354213 0.97542536 0.053246883 0.033966642 0.238408342 0.008416725 0.01943243 1.86E-09 8.730048501 -0.788756029 down QLVHELDEAEYR ddPTM_HeLa_Romidepsin_16h_R1 4 QLVHELDEAEYR 12 0 H0YKK6;Q06323-3;Q06323;Q06323-2 H0YKK6 PSME1 Proteasome activator complex subunit 1 0 0 ;;; ;;; 209.67 3.07E-21 14276000 5575.26 5395 5456.3 5749.99 6645.09 6796.8 5801.22 5927.37 5961.13 6102.91 FALSE FALSE TRUE 5507.306587 5470.950952 5551.264613 6414.830898 6305.966261 6362.506416 6293.975482 6098.869099 5427.951603 5944.355518 0.92647665 0.920360657 0.933871569 1.079146575 1.060832624 1.070344194 1.058815453 1.025993328 0.913127014 1 12.53730469 -9.259761958 24.9960994 0.958173568 1.059743824 0.802506668 0.02904087 68.10249338 1014825.309 0.005318138 0.008531643 5.50E-10 9.259761958 0.101570256 QLVNNKDTT(ph)SFEDISPQGVSDDSSTGSR ddPTM_HeLa_Romidepsin_16h_R1 1 QLVNNKDTTSFEDISPQGVSDDSSTGSR 28 1 Q3V6T2;A0A2R8Y7D4;A0A2U3TZV9;A0A2R8Y7B1;H7C2C6;A0A2R8Y820;A0A2R8YCU9;A0A2R8Y885;A0A2R8YDS8;H0Y470;H0Y7U8;A0A2R8Y5D7;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;A0A2R8Y802 Q3V6T2 CCDC88A Girdin 1 0 QLVNNKDT(0.088)T(0.456)S(0.456)FEDISPQGVSDDSSTGSR 70.465 8.13E-05 8512000 664.55 841.04 540.41 725.41 705.45 710.83 685.55 728.63 847.81 813.14 TRUE FALSE FALSE 656.450209 852.8801832 549.8156094 809.2853174 669.4482541 665.4102571 743.7805999 749.7117595 771.9797502 792.0145056 0.828836094 1.076849196 0.694198914 1.021806181 0.845247466 0.840149079 0.939099719 0.94658842 0.974704055 1 9.629383043 -12.5788551 1.338538224 1.000462401 0.890412918 0.100666575 0.102396041 0.671154716 2.141213726 0.067077675 0.015380027 2.64E-13 12.5788551 -0.110049483 QLVTS(ph)PSPMSSSDGK ddPTM_HeLa_Romidepsin_16h_R1 1 QLVTSPSPMSSSDGK 15 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 0 QLVT(0.038)S(0.589)PS(0.279)PMS(0.068)S(0.02)S(0.006)DGK 93.237 0.018378 5855100 4479.8 4459.4 3993.6 4604 1724.7 1379.7 1278.8 1183.4 4618.7 4830.5 TRUE FALSE FALSE 4425.198474 4522.17955 4063.106933 5136.336142 1636.682123 1291.541623 1387.42124 1217.639812 4205.591904 4705.002914 0.940530443 0.961142774 0.863571608 1.091675444 0.34785996 0.274503894 0.294882121 0.258796824 0.893855324 1 12.1999799 -8.726471782 7.549486704 0.968809401 0.289428542 0.965534915 0.061490905 0.022412601 3.855842697 0.00787982 0.015660613 1.88E-09 8.726471782 -0.679380859 QLVYVEQAGS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 QLVYVEQAGSSPK 13 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 QLVYVEQAGS(0.929)S(0.071)PK 260.73 3.55E-66 32673000 3207.8 3084.1 2528.5 3299.8 3547.6 4258.7 4374.6 4252.8 2997.8 2860.7 TRUE FALSE FALSE 3168.7021 3127.518041 2572.507482 3681.338402 3366.552734 3986.582814 4746.178415 4375.848058 2729.66926 2786.378602 1.137211611 1.122431115 0.923244056 1.321191025 1.208217983 1.430739818 1.703350152 1.570442744 0.979647654 1 11.44417558 -8.265381758 1.002444791 1.063790032 1.684289614 0.836670203 0.100465688 0.184853844 0.308710062 0.015667722 0.083889607 5.43E-09 8.265381758 0.620499582 QLVYVEQAGSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QLVYVEQAGSSPK 13 0 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 QLVYVEQAGS(0.227)S(0.773)PK 149.82 0.00076843 26515000 4576.4 4727.2 4298.4 4672.7 5814.3 6919.4 6262.4 6568 5149.3 4508.9 TRUE FALSE FALSE 4520.621077 4793.749646 4373.211849 5212.97956 5517.574575 6477.272671 6794.3281 6758.034717 4688.733711 4391.758128 1.029341996 1.091533164 0.995777026 1.186991498 1.256347552 1.474870082 1.547063363 1.538799387 1.067621115 1 12.10058289 -8.517231883 1.066947101 1.016381663 1.573654899 0.966504061 0.03885475 0.054307887 0.1141453 0.00540889 0.020471017 3.04E-09 8.517231883 0.557273237 QLWDS(ph)PETAPAAR ddPTM_HeLa_Romidepsin_16h_R1 2 QLWDSPETAPAAR 13 0 Q9Y613 Q9Y613 FHOD1 FH1/FH2 domain-containing protein 1 1 0 QLWDS(0.8)PET(0.2)APAAR;QLWDS(0.569)PET(0.431)APAAR ; 153.41 0.00076877 22567000 3204.3 3128.1 2921.1 4697.7 3290 3403.1 2769.6 3249 3303.2 2909.4 TRUE FALSE FALSE 3165.244759 3172.137474 2971.94052 5240.870177 3122.099023 3185.652893 3004.849755 3343.004689 3007.753519 2833.813369 1.11695597 1.11938828 1.048742501 1.849405552 1.101730643 1.12415762 1.060355558 1.179684141 1.061380242 1 11.46852903 -10.32611 1.155051962 1.040433582 1.229082071 0.113122683 0.219063913 0.716621109 1.865758466 0.046495212 0.053615527 4.72E-11 10.32611 0.188648488 QMADTGK(ac)LNTLLQR ddPTM_HeLa_Romidepsin_16h_R1 1 QMADTGKLNTLLQR 14 1 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;Q5RI18;A0A1W2PQL0;A0A1W2PP34;A0A1W2PPL4;A0A1W2PPH7;A0A1W2PRZ7;A0A1W2PQD4;A0A1W2PQ74;A0A1W2PPE9 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 1 QMADTGK(1)LNTLLQR 92.151 0.01855 823660 149.97 151.27 175.31 0 188.33 188.35 278.8 126.16 256.39 125.69 FALSE TRUE FALSE 148.142108 153.399583 178.361197 0 178.7188173 176.3150429 302.481265 129.8102406 233.4578363 122.4245557 1.210068578 1.25301319 1.45690704 0 1.459828188 1.440193447 2.470756486 1.06032846 1.906952694 1 6.93574915 -8.288598713 3.045888434 1.069654614 1.767729341 0.123326894 0.565669701 0.246067562 4.597944199 0.066186604 0.173578652 5.15E-09 8.288598713 0.698074727 QMDIIVS(ph)EVS(ph)MIR ddPTM_HeLa_Romidepsin_16h_R1 1 QMDIIVSEVSMIR 13 0 C9J4M6;C9J2Y9;P30876 C9J4M6 POLR2B DNA-directed RNA polymerase;DNA-directed RNA polymerase II subunit RPB2 2 0 QMDIIVS(1)EVS(1)MIR 46.41 0.029488 2270500 202.79 176.62 260.4 180.23 178.06 262.16 133.72 81.266 136.58 172.87 TRUE FALSE FALSE 200.3183175 179.106461 264.9321528 201.0690406 168.9729338 245.4088221 145.0781735 83.61730349 124.3639427 168.3788125 1.189688385 1.063711392 1.573429275 1.194146922 1.00352848 1.457480419 0.861617749 0.496602288 0.738596151 1 7.395566802 -7.482013805 4.32716507 1.146098715 0.545367185 0.452703587 0.224786341 0.123482129 4.940204792 0.026291511 0.151623172 3.30E-08 7.482013805 -0.600731531 QMGPVT(ph)PT(ph)S(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 QMGPVTPTSRR 11 1 M0R2L7 M0R2L7 ITPKC 3 0 QMGPVT(1)PT(1)S(1)RR 52.821 0.028109 1963600 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 QMGVTEWS(ph)VNGSPIDTLR ddPTM_HeLa_Romidepsin_16h_R1 1 QMGVTEWSVNGSPIDTLR 18 0 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785;O95785-2 B9EGQ5 WIZ Protein Wiz 1 0 QMGVT(0.003)EWS(0.586)VNGS(0.412)PIDTLR 144.08 8.63E-11 0 958.64 872.97 981.46 895.62 1102.6 1336.9 1006 1336.7 918.2 1056 TRUE FALSE FALSE 946.9557269 885.2596946 998.5418996 999.1757984 1046.330208 1251.476405 1091.449615 1375.375306 836.0738923 1028.564968 0.920657184 0.860674554 0.970810723 0.971427017 1.017271869 1.216720814 1.061138235 1.337178835 0.812854723 1 10.00641721 -7.799885856 0.808903368 0.951672444 1.333667791 0.701776158 0.0817773 0.539443784 0.401093222 0.011529353 0.155832959 1.59E-08 7.799885856 0.381995347 QMNLGFGDES(ph)PEPEASGR ddPTM_HeLa_Romidepsin_16h_R1 1 QMNLGFGDESPEPEASGR 18 0 Q9P227-2;Q9P227 Q9P227-2 ARHGAP23 Rho GTPase-activating protein 23 1 0 QMNLGFGDES(0.981)PEPEAS(0.019)GR 80.541 0.018123 3237700 900.2 905.5 844.94 785.49 804.99 696.75 786.44 555.67 927.82 900.57 TRUE FALSE FALSE 889.2280161 918.2476528 859.6458263 876.3120496 763.9083565 652.2299237 853.240194 571.7474347 844.8334554 877.1730616 1.01374296 1.046826097 0.980018498 0.999018424 0.870875304 0.743558999 0.972715911 0.651806878 0.963132012 1 9.776717697 -8.663436014 3.147444925 1.008010456 0.806712368 0.60094217 0.077640359 0.114761873 2.266385693 0.009854787 0.020848723 2.17E-09 8.663436014 -0.201298087 QMNMS(ph)PPPGNAGPVIMSIEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QMNMSPPPGNAGPVIMSIEEK 21 0 Q86U42-2;Q86U42;B4DEH8;G3V4T2;Q92843-2 Q86U42-2 PABPN1 Polyadenylate-binding protein 2 1 0 QMNMS(1)PPPGNAGPVIMSIEEK 60.382 0.0043119 10625000 2367.2 2049 1771.9 1828.4 2024.9 2344.8 2202.6 2001.1 2099.1 2363.3 TRUE FALSE FALSE 2338.347656 2077.845876 1802.739176 2039.808211 1921.561797 2194.974847 2389.688789 2058.998671 1911.351239 2301.901125 1.01583323 0.902665129 0.783152307 0.886140672 0.834771648 0.95354871 1.038137026 0.89447746 0.830335942 1 11.16861015 -10.25706836 22.03648307 1.007476804 0.899016491 0 0.084607633 58.15386722 293181.1942 0.011299879 0.013561172 5.53E-11 10.25706836 -0.108460313 QMNT(ph)SLCERIRKVY(ph)GDLECEYCGK ddPTM_HeLa_Romidepsin_16h_R1 1 QMNTSLCERIRKVYGDLECEYCGK 24 3 E5RH37;E9PBN4;F8W7M8;Q9P243-3;Q9P243-4;Q9P243-2;Q9P243 E5RH37 ZFAT Zinc finger protein ZFAT 2 0 QMNT(0.501)S(0.501)LCERIRKVY(0.989)GDLECEY(0.01)CGK 40.756 0.020028 3260400 1209.8 1228.3 1337.4 1476.3 1205.7 1391.4 1271.5 1158.5 1126.4 1128.4 TRUE FALSE FALSE 1195.054492 1245.59204 1360.676886 1646.996752 1144.16863 1302.494031 1379.501178 1192.01937 1025.651963 1099.084005 1.087318609 1.133300124 1.238009906 1.498517624 1.041020181 1.185072319 1.255137161 1.084557107 0.933187962 1 10.10208594 -10.30432792 1.555660105 1.032508588 1.219146406 0.374830377 0.120218303 0.313097237 1.444564493 0.022309402 0.02602608 4.96E-11 10.30432792 0.186637818 QMPSESLDPAFS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 QMPSESLDPAFSPR 14 0 Q15018 Q15018 FAM175B BRISC complex subunit Abro1 1 0 QMPSES(0.004)LDPAFS(0.996)PR;QMPSES(0.002)LDPAFS(0.998)PR ; 116.58 0.0063726 8251100 2904 2887 2893.9 2667.1 3378.3 4474.3 3600.3 4075 2905.5 3223.5 TRUE FALSE FALSE 2868.604931 2927.643262 2944.267116 2975.482651 3205.892745 4188.40667 3906.109392 4192.903696 2645.624803 3139.753005 0.913640317 0.932443812 0.93773845 0.947680485 1.021065268 1.333992407 1.244081743 1.335424694 0.842621951 1 11.61643536 -8.350580121 3.891204728 0.954442391 1.299571641 0.921028686 0.048804025 0.039043692 1.089617725 0.005923738 0.014086963 4.46E-09 8.350580121 0.34512925 QMVIDVLHPGK ddPTM_HeLa_Romidepsin_16h_R1 1 QMVIDVLHPGK 11 0 E7ETK0;A0A2R8Y849;A0A2R8YD14;P62847-2;P62847-3;P62847;P62847-4 E7ETK0 RPS24 40S ribosomal protein S24 0 0 69.672 0.019131 980780 525.55 477.67 665.48 462.87 677.6 685.49 646.15 536.53 683.29 632.88 FALSE FALSE TRUE 519.1443945 484.3946508 677.0624002 516.3892073 643.0195435 641.6894013 701.0339649 552.053649 622.1748311 616.4376864 0.842168488 0.785796621 1.098346865 0.837698958 1.043121726 1.040963938 1.137234112 0.89555467 1.009306934 1 9.267811255 -8.733023783 24.65799256 0.921014656 1.037773055 0.17993596 0.103479678 215.7300183 187201.2766 0.014940358 0.029875823 1.85E-09 8.733023783 0.116758399 QNAPPKGTDTQTPAVLS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 QNAPPKGTDTQTPAVLSPSK 20 1 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 QNAPPKGTDTQT(0.001)PAVLS(0.912)PS(0.087)K 97.059 0.0001631 0 2880.6 2914.4 1916.7 3610.1 1686.9 1577.7 1332.3 1128.8 2635.4 2319.5 TRUE FALSE FALSE 2845.490139 2955.429 1950.059359 4027.516748 1600.811198 1476.890062 1445.465529 1161.460047 2399.683224 2259.239056 1.259490505 1.308152403 0.863148747 1.782687289 0.708562113 0.653711283 0.639801939 0.514093471 1.062164368 1 11.14162122 -8.551076655 24.9998062 1.16390698 0.618740893 0.594440844 0.235185496 111.8943567 99203.29175 0.032725348 0.065451593 2.81E-09 8.551076655 -0.545166087 QNDTPKGPQPPTVS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 2 QNDTPKGPQPPTVSPIR 17 1 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 QNDTPKGPQPPT(0.11)VS(0.89)PIR;QNDTPKGPQPPT(0.056)VS(0.944)PIR ; 101.05 0.0011446 56958000 6699.2 7504.1 4554.6 10154.4 5493.7 4405.3 4357 4275 7625.4 6539.2 TRUE FALSE FALSE 6617.547574 7609.742917 4633.870902 11328.49951 5213.335989 4123.815547 4727.083471 4398.69038 6943.365126 6369.310641 1.038973909 1.194751417 0.727530994 1.778606845 0.818508671 0.647450844 0.742165634 0.690606979 1.090128197 1 12.63692152 -8.536310363 24.99960679 1.066471901 0.704066083 0.375985239 0.254763623 196.3361352 365429.8387 0.034307842 0.068643328 2.91E-09 8.536310363 -0.362405818 QNEVANVQPSSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 QNEVANVQPSSKR 13 1 Q6ZW49-2;Q6ZW49-1;Q6ZW49 Q6ZW49-2 PAXIP1 PAX-interacting protein 1 0 1 ; QNEVANVQPSSK(1)R;QNEVANVQPSSK(1)R 124.48 0.0011871 2414400 869.99 971.37 757.71 1265.03 1333.69 1292.35 1137.01 1250.66 950.45 781.11 FALSE TRUE FALSE 859.3862272 985.0449724 770.8976247 1411.298721 1265.626823 1209.773006 1233.587601 1286.845874 865.4393716 760.8166496 1.129557598 1.294720578 1.013250203 1.854978754 1.663510944 1.590097964 1.621399324 1.691400779 1.137513712 1 9.571405008 -9.26814192 24.99994574 1.080697029 1.674398422 0.884058479 0.102671845 126.8706641 473217.0097 0.016839275 0.026088234 5.39E-10 9.26814192 0.593701393 QNGSNDSDRYS(ph)DNEEDSKIELK ddPTM_HeLa_Romidepsin_16h_R1 1 QNGSNDSDRYSDNEEDSKIELK 22 2 G5E972;P42167;H0YJH7;P42167-3;P42167-2 G5E972 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin" 1 0 QNGS(0.008)NDS(0.036)DRY(0.336)S(0.6)DNEEDS(0.02)KIELK 66.448 0.0046891 7585700 1015.6 1168.7 1034.4 699.79 638.65 914.71 691.86 830.28 1265.1 1166.2 TRUE FALSE FALSE 1003.221477 1185.152989 1052.403298 780.7030124 606.0573074 856.2629831 750.6265711 854.3028418 1151.946287 1135.901956 0.883193722 1.043358525 0.926491316 0.687297885 0.533547199 0.753817685 0.66081986 0.75209206 1.01412475 1 10.1496226 -9.269581502 5.000172085 0.951903311 0.671455035 0.807255452 0.072006097 0.064683975 4.98694559 0.011293675 0.018064615 5.38E-10 9.269581502 -0.280448275 QNGSNDSDRYS(ph)DNEEGK ddPTM_HeLa_Romidepsin_16h_R1 3 QNGSNDSDRYSDNEEGK 17 1 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 QNGSNDS(0.001)DRY(0.013)S(0.986)DNEEGK;QNGSNDS(0.001)DRY(0.106)S(0.894)DNEEGK;QNGS(0.001)NDS(0.006)DRY(0.215)S(0.778)DNEEGK ;; 89.816 0.0034626 45462800 7332.4 8017.3 7812.3 5103.2 6650.5 6869.9 5313.63 5081.9 7970.9 8068.4 TRUE FALSE FALSE 7243.029888 8130.16776 7948.269804 5693.255995 6311.100169 6430.935562 5764.9696 5228.936759 7257.962741 7858.781805 0.921647918 1.034532827 1.011387007 0.724445103 0.803063417 0.818312013 0.733570386 0.665362252 0.923548066 1 12.94008998 -9.259994753 24.99994308 0.971862612 0.754955846 0.829774209 0.051846758 43.9764043 761031.4379 0.008464489 0.013550424 5.50E-10 9.259994753 -0.216906766 QNLAMT(ph)GEVS(ph)LT(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 QNLAMTGEVSLTGK 14 0 K7ERR6;K7EJE8;K7EKE6;P36776-3;P36776-2;P36776 K7ERR6 LONP1 "Lon protease homolog, mitochondrial" 3 0 QNLAMT(1)GEVS(1)LT(1)GK 68.283 0.018993 5122100 5289.2 4269.2 4300.2 3214.4 5282.1 6063.6 4150.5 4118.8 4119.4 4339.8 TRUE FALSE FALSE 5224.733196 4329.30191 4375.043177 3586.064052 5012.534727 5676.155529 4503.043366 4237.97098 3750.950547 4227.05137 1.236023114 1.024189566 1.035010648 0.848360651 1.185822998 1.342816785 1.065291848 1.002583269 0.887368101 1 12.04543593 -12.78407994 1.775622562 0.999809892 1.117905092 0.107949402 0.136917645 0.777383483 4.436644342 0.104435194 0.02204253 1.64E-13 12.78407994 0.118095201 QNLWFANPGGSNS(ph)MPSQSR ddPTM_HeLa_Romidepsin_16h_R1 2 QNLWFANPGGSNSMPSQSR 19 0 M0QZ22;Q5PRF9;M0QX45 M0QZ22 SAMD4B Protein Smaug homolog 2 1 0 QNLWFANPGGS(0.45)NS(0.46)MPS(0.079)QS(0.012)R;QNLWFANPGGS(0.156)NS(0.831)MPS(0.01)QS(0.002)R ; 100.69 0.00056697 9557200 2757.3 2272.36 2143.4 2589.8 3661.7 3652.4 2308.3 3028.4 2596.1 2166.3 TRUE FALSE FALSE 2723.692967 2304.350344 2180.704978 2889.244861 3474.829785 3419.023428 2504.366944 3116.021976 2363.898314 2110.019214 1.290837993 1.092099223 1.033500057 1.369297892 1.646823765 1.620375495 1.186892957 1.476774219 1.120320753 1 11.04304042 -9.093487081 4.922828026 1.130430252 1.475602534 0.627568954 0.137239932 0.139885891 5.560965042 0.024394644 0.041283874 8.06E-10 9.093487081 0.345172282 QNPEQS(ph)ADEDAEK ddPTM_HeLa_Romidepsin_16h_R1 2 QNPEQSADEDAEK 13 0 Q99613-2;Q99613;B5ME19;H3BPE3 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 0 QNPEQS(1)ADEDAEK;QNPEQS(1)ADEDAEK ; 143.94 0.00076756 7839200 3343.3 2588.24 2933.41 1470.54 2531.4 2693.77 2229.69 2394.67 2912.97 2969.1 TRUE FALSE FALSE 3302.550574 2624.677311 2984.464771 1640.570754 2402.213212 2521.646791 2419.079813 2463.955998 2652.426668 2891.962354 1.141975645 0.907576583 1.031986038 0.567286345 0.830651619 0.871950075 0.836483853 0.852001408 0.917171921 1 11.49783306 -9.453752197 15.11218363 1.052808385 0.80064301 0.451117817 0.107047592 1.888563831 412.3322371 0.016043745 0.024506707 3.52E-10 9.453752197 -0.252165374 QNPLPSSFPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 QNPLPSSFPGKK 12 1 Q8IUR6-2;Q8IUR6;Q8IUR6-3 Q8IUR6-2 CREBRF CREB3 regulatory factor 0 1 QNPLPSSFPGK(1)K 107.85 0.00099551 0 94.092 202.1 60.183 153.69 327.84 437.84 286.88 582.85 177.69 110.52 FALSE TRUE FALSE 92.94517051 204.9451691 61.23045987 171.4603609 311.1091015 409.8634371 311.24758 599.7138452 161.7969614 107.6486745 0.863412123 1.903833653 0.568799014 1.592777262 2.890041173 3.807417408 2.891327567 5.571028609 1.503009323 1 6.750186745 -7.566017715 0.519104429 0.896239999 6.999140596 0.81332043 0.636415105 0.820198348 0.180580589 0.120898002 2.847771582 2.72E-08 7.566017715 6.102900597 QNPQS(ph)PPQDSSVTSK ddPTM_HeLa_Romidepsin_16h_R1 2 QNPQSPPQDSSVTSK 15 0 C9JEF4;C9J172;Q9BRX7;A0A2R8YCS4;E7EP63;E7ER52;A6NDI8;Q9UBN7 C9JEF4 HDAC6 Histone deacetylase 6 1 0 QNPQS(0.583)PPQDS(0.404)S(0.013)VT(0.001)SK;QNPQS(0.98)PPQDS(0.015)S(0.005)VT(0.001)S(0.001)K ; 124.6 0.0029365 12515600 3728.9 3304.6 3642 2684.66 4027.5 4288.8 3551.2 4196.5 3796.1 3344.2 TRUE FALSE FALSE 3683.450733 3351.122246 3705.387482 2995.073021 3821.961646 4014.759521 3852.838839 4317.919107 3456.567308 3257.317202 1.130823467 1.028798253 1.137558074 0.919490745 1.173346472 1.232535634 1.182825804 1.325605963 1.061170004 1 11.6694685 -4.000000006 0.367341859 1.04885317 4.687119881 0.586294168 0.072921082 32.28874946 0.397813252 0.021041828 83.73703322 1.00E-04 4.000000006 3.638266712 QNSPVT(ph)QDGIQESPWQDR ddPTM_HeLa_Romidepsin_16h_R1 2 QNSPVTQDGIQESPWQDR 18 0 O75815 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 0 QNS(0.011)PVT(0.989)QDGIQESPWQDR;QNS(0.195)PVT(0.805)QDGIQESPWQDR ; 178.02 1.37E-09 11715600 3310.7 3323.7 2767.4 3143 2560.8 2359.8 1841.48 2197.36 3636.2 3435.3 TRUE FALSE FALSE 3270.347915 3370.491136 2815.565436 3506.408448 2430.11282 2209.016396 1997.895265 2260.937145 3310.969165 3346.050411 0.977375566 1.007304351 0.84145936 1.047924573 0.726263063 0.660186227 0.597090605 0.675703252 0.989515625 1 11.70824347 -8.641177241 4.259638456 0.981787026 0.64663354 0.888177892 0.054724068 0.046632675 1.505600827 0.007646192 0.015723507 2.28E-09 8.641177241 -0.335153487 QNSSS(ph)SDSGGSIVR ddPTM_HeLa_Romidepsin_16h_R1 1 QNSSSSDSGGSIVR 14 0 A0A2R8Y4W2;A0A2R8YE63;Q12929-2;Q12929 A0A2R8Y4W2 EPS8 Epidermal growth factor receptor kinase substrate 8 1 0 QNS(0.009)S(0.077)S(0.687)S(0.023)DS(0.203)GGS(0.001)IVR 201.75 1.27E-16 31322000 1276.3 1637.1 1284.8 1690.9 2330.7 2191.7 1960.9 2062.8 1538.6 1549.8 TRUE FALSE FALSE 1260.743965 1660.147137 1307.161405 1886.409814 2211.755682 2051.657443 2127.458797 2122.483863 1400.983763 1509.535973 0.835186433 1.099773153 0.865935909 1.249662047 1.465189119 1.359131204 1.409346207 1.406050536 0.928089021 1 10.55988942 -9.098482552 3.486523742 0.932563155 1.404297886 0.89788728 0.074153768 0.05933287 1.350101245 0.01278087 0.022249913 7.97E-10 9.098482552 0.471734731 QNTVSK(ac)GPFSK ddPTM_HeLa_Romidepsin_16h_R1 1 QNTVSKGPFSK 11 1 A0A3B3IS53;A0A3F2YNX6;Q92794;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 0 1 QNTVSK(1)GPFSK 140.24 0.0041058 1156400 196.25 187.97 360.39 603.16 1122 1284.5 1148.3 921.26 245.61 0 FALSE TRUE FALSE 193.8580295 190.6162466 366.6624368 672.9001972 1064.740153 1202.424596 1245.836573 947.9152046 223.6420265 0 0 QNTVSK(ac)GPFSK(ac)VR ddPTM_HeLa_Romidepsin_16h_R1 1 QNTVSKGPFSKVR 13 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A5PLL3 A0A3B3IS53 KAT6A;MYST3 Histone acetyltransferase KAT6A;Histone acetyltransferase 0 2 QNTVSK(1)GPFSK(1)VR 132.06 0.00024341 1171300 0 0 0 0 181.46 292.61 167.27 125.57 0 0 FALSE TRUE FALSE 0 0 0 0 172.1994191 273.9131654 181.4779096 129.2031698 0 0 0 QNVGTLESFS(ph)PGDFR ddPTM_HeLa_Romidepsin_16h_R1 2 QNVGTLESFSPGDFR 15 0 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9 Q6ULP2-7 AFTPH Aftiphilin 1 0 QNVGTLESFS(1)PGDFR;QNVGT(0.003)LES(0.014)FS(0.983)PGDFR ; 200 4.55E-18 5808200 1603.05 1664.41 1445.56 1595.26 3116.2 3561.2 3021.9 3022.7 1403.04 1546.34 TRUE FALSE FALSE 1583.51141 1687.841608 1470.719365 1779.711467 2957.168686 3333.650813 3278.580111 3110.157055 1277.548588 1506.165864 1.051352609 1.120621339 0.97646574 1.181617184 1.963375188 2.213335791 2.176772286 2.064949904 0.848212417 1 10.55666494 -8.749440229 3.102878409 1.030773753 2.150013052 0.979531326 0.07677855 0.015934821 0.316582531 0.007708613 0.015737339 1.78E-09 8.749440229 1.119239299 up QNVPSGGPVPS(ph)PQTYR ddPTM_HeLa_Romidepsin_16h_R1 1 QNVPSGGPVPSPQTYR 16 0 Q5JSZ5;Q5JSZ5-5;A0A494C0D3;A0A494C065;H3BLU0;Q5JSZ5-4;Q5JSZ5-2;Q5JSZ5-3 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 QNVPSGGPVPS(0.999)PQT(0.001)YR 123.76 1.41E-05 0 1019.4 1178.2 1011 1161.9 1035.4 1333 958.69 1036.4 1280.8 954.32 TRUE FALSE FALSE 1006.975161 1194.786731 1028.596031 1296.244345 982.5596744 1247.825602 1040.121105 1066.386599 1166.24204 929.5266288 1.083320401 1.28537117 1.106580488 1.394520936 1.057053821 1.342431258 1.118979352 1.147236201 1.254662324 1 9.860352385 -10.50757735 2.818612385 1.03245873 1.206813889 0.001084663 0.124880655 0.185734834 2.94801926 0.017305413 0.018845075 3.11E-11 10.50757735 0.17435516 QPAQELS(ph)PTPGGTAHQALK ddPTM_HeLa_Romidepsin_16h_R1 2 QPAQELSPTPGGTAHQALK 19 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 QPAQELS(0.966)PT(0.034)PGGTAHQALK;QPAQELS(0.407)PT(0.407)PGGT(0.186)AHQALK ; 111.53 0.00033607 44143000 7400.2 7208.6 7185.5 5291 6950.5 8430.4 6617 7758.3 7837.1 7389 TRUE FALSE FALSE 7310.003516 7310.08286 7310.560613 5902.770315 6595.790049 7891.724648 7179.047815 7982.77417 7136.130148 7197.032715 1.015696858 1.015707883 1.015774265 0.82016722 0.916459645 1.096524771 0.997501067 1.109175751 0.991537823 1 12.8131865 -6.898086301 1.236259914 0.992806194 1.253631874 0.223731134 0.068998387 4.307571291 3.02940357 0.010525824 1.7766554 1.26E-07 6.898086301 0.26082568 QPAQELSPT(ph)PGGTAHQALK ddPTM_HeLa_Romidepsin_16h_R1 1 QPAQELSPTPGGTAHQALK 19 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 QPAQELS(0.075)PT(0.802)PGGT(0.123)AHQALK 74.537 0.025962 7639400 2358.2 2229.7 2769.9 1699.9 2892.9 2357 1925.2 1909.7 2731 2914.1 TRUE FALSE FALSE 2329.457351 2261.089775 2818.108948 1896.450436 2745.264518 2206.395307 2088.72644 1964.954156 2486.73252 2838.391262 0.820696351 0.796609617 0.992854292 0.668142712 0.967190308 0.777340086 0.735883903 0.692277412 0.876106319 1 11.47085776 -16.52287875 0.085973738 1.649992406 0.617825758 0.268463068 0.099116137 110.7282017 0.725001262 13.59828182 1.289856102 3.00E-17 16.52287875 -1.032166648 QPASAQSTPSTTPHSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 QPASAQSTPSTTPHSSPK 18 0 A0A087WT18;Q96A73-2;Q96A73 A0A087WT18 KIAA1191 Putative monooxygenase p33MONOX 1 0 QPASAQSTPST(0.001)T(0.005)PHS(0.32)S(0.674)PK;QPASAQSTPSTTPHS(0.245)S(0.755)PK ; 147.41 2.91E-05 4585600 1650.35 1509.49 1957.15 1952.5 3073.7 3731.9 3351.1 3009.4 2211.54 2247.3 TRUE FALSE FALSE 1630.234899 1530.74064 1991.213375 2178.257237 2916.837619 3493.443634 3635.74235 3096.472241 2013.734323 2188.914822 0.744768541 0.69931485 0.909680612 0.99513111 1.332549622 1.595970569 1.660979365 1.414615228 0.919969248 1 11.0960001 -8.692845196 2.032378996 0.862760743 1.569312284 0.907365376 0.100145932 0.081875088 0.686385517 0.019098727 0.043807517 2.03E-09 8.692845196 0.706551541 QPEYSPES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 QPEYSPESPR 10 0 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 QPEYS(0.05)PES(0.95)PR;QPEYS(0.017)PES(0.983)PR;QPEYS(0.003)PES(0.997)PR;QPEYS(0.044)PES(0.956)PR ;;; 153.49 0.0035155 526851000 9873.4 8701.9 8831.2 7341.7 7375.6 7717.8 6929.6 7400.7 9101.7 9257.9 TRUE FALSE FALSE 9753.059203 8824.405577 8984.903331 8190.581898 6999.19561 7224.657488 7518.200051 7614.827578 8287.621156 9017.378423 1.081584774 0.978599895 0.996398611 0.908310765 0.776189629 0.801192669 0.833745652 0.844461352 0.919072126 1 13.13849235 -9.17406254 1.843816119 1.034754813 0.813820566 0.732255485 0.048950782 0.087317706 0.58018832 0.006411578 0.011816261 6.70E-10 9.17406254 -0.220934247 FIQELSGSS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 1 FIQELSGSSPKR 12 1 I3L254;Q01664 I3L254 TFAP4 Transcription factor AP-4 1 0 FIQELSGS(0.056)S(0.944)PKR 74.966 0.017825 20541000 2922.4 2404.9 2210.7 2161.3 1097.2 676.61 855.66 724.02 2674.6 2165.2 TRUE FALSE FALSE 2886.780665 2438.756245 2249.176306 2411.199675 1041.20579 633.3768047 928.339739 744.9683764 2435.377077 2108.947792 1.368825097 1.15638531 1.06649217 1.143318808 0.493708661 0.300328347 0.440190953 0.353241735 1.154783009 1 11.04230767 -8.72743349 3.961604747 1.168287642 0.375344351 0.937444825 0.095406253 0.053836081 1.808054656 0.021138732 0.042548481 1.87E-09 8.72743349 -0.792943291 down LLDLPAAAS(ph)SEDIER ddPTM_HeLa_Romidepsin_16h_R1 2 LLDLPAAASSEDIER 15 0 P22466 P22466 GAL Galanin peptides;Galanin;Galanin message-associated peptide 1 0 LLDLPAAAS(0.81)S(0.19)EDIER;LLDLPAAAS(0.986)S(0.014)EDIER ; 238.12 1.38E-45 23876000 7929.3 7522 8556.8 6039.8 4120.9 3099 2375.6 2930.6 7291.2 7206.8 TRUE FALSE FALSE 7832.654642 7627.894913 8705.727515 6738.150094 3910.595096 2900.983902 2577.383405 3015.392287 6639.056811 7019.566297 1.115831707 1.086661852 1.240208746 0.959909745 0.557099247 0.413271102 0.367171317 0.4295696 0.945793021 1 12.77716618 -8.72692898 2.759262882 1.073176853 0.406505607 0.944434058 0.074330569 0.041422024 0.643677756 0.011088212 0.023280729 1.88E-09 8.72692898 -0.666671246 down QPGVDSLS(ph)PVASLPK ddPTM_HeLa_Romidepsin_16h_R1 2 QPGVDSLSPVASLPK 15 0 Q9UBW7;A0A087X151;Q9UBW7-2 Q9UBW7 ZMYM2 Zinc finger MYM-type protein 2 1 0 QPGVDS(0.002)LS(0.973)PVAS(0.025)LPK;QPGVDS(0.036)LS(0.964)PVASLPK ; 211.29 1.60E-25 19939500 4441.9 3960.9 4044.3 3551.6 4949.3 5548.1 4241.6 4495.6 4767.2 4176.7 TRUE FALSE FALSE 4387.760414 4016.661654 4114.689345 3962.252703 4696.718753 5193.594316 4601.881398 4625.673093 4340.809692 4068.188732 1.0785538 0.987334148 1.011430299 0.973959903 1.154498737 1.276635539 1.131186801 1.137035029 1.06701286 1 11.9901709 -8.655996783 6.030721906 1.027906845 1.182327916 0.711039987 0.048427725 0.094789898 4.768010082 0.007496111 0.015096213 2.21E-09 8.655996783 0.154421071 QPGYQPPNPHPGPSS(ph)PPAAPASK ddPTM_HeLa_Romidepsin_16h_R1 2 QPGYQPPNPHPGPSSPPAAPASK 23 0 Q9BUL9 Q9BUL9 RPP25 Ribonuclease P protein subunit p25 1 0 QPGYQPPNPHPGPS(0.24)S(0.76)PPAAPASK;QPGYQPPNPHPGPS(0.06)S(0.94)PPAAPASK ; 74.665 0.0004319 60496000 4501.2 4379.1 4687.1 4110.5 4795.9 5052.7 4092.7 4813 5611.2 5169.1 TRUE FALSE FALSE 4446.337643 4440.749085 4768.677009 4585.77535 4551.147327 4729.848777 4440.333836 4952.256561 5109.320218 5034.806037 0.883119948 0.882009963 0.947142149 0.9108147 0.903936973 0.939430187 0.881927487 0.983604239 1.014799812 1 12.29772048 -12.41723595 1.138876013 1.000116557 0.912637743 0.555889182 0.031951468 0.301902737 0.698933762 0.020849161 0.005238744 3.83E-13 12.41723595 -0.087478813 QPLLLS(ph)EDEEDTK ddPTM_HeLa_Romidepsin_16h_R1 4 QPLLLSEDEEDTK 13 0 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 0 QPLLLS(0.836)EDEEDT(0.164)K;QPLLLS(0.999)EDEEDT(0.001)K;QPLLLS(1)EDEEDTK;QPLLLS(1)EDEEDTK ;;; 214.89 2.07E-23 85688200 17313 11591.9 14818.3 9570.9 13302 11481.2 13622.5 12417.2 17310.5 15501.2 TRUE FALSE FALSE 17101.9825 11755.09107 15076.2063 10677.53249 12623.1493 10747.58837 14779.59481 12776.47209 15762.20553 15098.47659 1.132695898 0.7785614 0.998524997 0.707192704 0.836054501 0.711832635 0.978879871 0.846209352 1.043959994 1 13.88211537 -10.25989215 24.99990329 1.062661953 0.838625039 0.531055414 0.095625839 78.8501118 1274053.791 0.016339068 0.019455857 5.50E-11 10.25989215 -0.224036914 QPLLLS(ph)EDEEDTKR ddPTM_HeLa_Romidepsin_16h_R1 11 QPLLLSEDEEDTKR 14 1 Q99613-2;Q99613;B5ME19;H3BPE4 Q99613-2 EIF3C;EIF3CL Eukaryotic translation initiation factor 3 subunit C;Eukaryotic translation initiation factor 3 subunit C-like protein 1 0 QPLLLS(0.998)EDEEDT(0.002)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(0.994)EDEEDT(0.006)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR;QPLLLS(0.999)EDEEDT(0.001)KR;QPLLLS(1)EDEEDTKR;QPLLLS(1)EDEEDTKR ;;;;;;;;;; 238.07 4.92E-43 5584190100 39711.9 42090.5 39810.7 41635.6 38763.1 38839.6 33012.69 39223 44375 42945.7 TRUE FALSE FALSE 39227.87609 42683.05116 40503.58853 46449.70397 36784.87436 36357.87491 35816.78706 40357.85562 40405.98886 41829.96452 0.937793673 1.020394152 0.968291248 1.110440912 0.879390523 0.869182542 0.85624713 0.964807312 0.965958 1 15.35224915 QPLLLSEDEEDT(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 2 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 0 QPLLLS(0.264)EDEEDT(0.736)KR;QPLLLS(0.346)EDEEDT(0.654)KR ; 141.65 0.0019706 38287900 3943.9 3726.6 3553.8 3721.7 3257.22 2620.45 2400.3 3747.1 3602.8 3981.1 TRUE FALSE FALSE 3895.83023 3779.063173 3615.652398 4152.020465 3090.991909 2453.011702 2604.181422 3855.516427 3280.556545 3877.670448 1.004683168 0.974570486 0.932429005 1.070751246 0.797125994 0.632599323 0.671583998 0.99428677 0.84601221 1 11.92097448 -8.660512622 5.677878302 0.998175529 0.750853952 0.439031283 0.1065064 0.10123478 4.824510432 0.012898342 0.026016638 2.19E-09 8.660512622 -0.247321577 QPLLLSEDEEDTKR ddPTM_HeLa_Romidepsin_16h_R1 2 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 0 0 ; ; 178.68 2.45E-07 18614300 7127.9 6954.5 7229.8 6719.8 6758.7 7078.5 5603.9 7055.2 7659.6 7421.9 FALSE FALSE TRUE 7041.022413 7052.405634 7355.631636 7496.774894 6413.778319 6626.206695 6079.895126 7259.331081 6974.506192 7229.077968 0.973986232 0.975560876 1.017506198 1.037030577 0.887219414 0.91660468 0.841033276 1.00418492 0.964785028 1 12.81959594 -8.750930433 24.97725651 0.991981505 0.90748319 0.469278078 0.042824046 128.4039706 305183.6056 0.005657083 0.011217689 1.77E-09 8.750930433 -0.084498315 QPLSEASNQQPLS(ph)GGEEK ddPTM_HeLa_Romidepsin_16h_R1 2 QPLSEASNQQPLSGGEEK 18 0 Q9NQW6;Q9NQW6-2;C9JJT6 Q9NQW6 ANLN Actin-binding protein anillin 1 0 QPLSEASNQQPLS(1)GGEEK;QPLSEASNQQPLS(1)GGEEK ; 275.68 6.26E-106 29908000 6024.6 5796.8 5915.1 5716.7 7603.5 6641.2 5434.3 6066 5994.5 6523.8 TRUE FALSE FALSE 5951.169858 5878.407503 6018.049834 6377.691752 7215.465022 6216.848753 5895.889306 6241.510139 5458.336906 6354.310736 0.936556317 0.925105452 0.947081451 1.003679552 1.135522848 0.978367129 0.927856624 0.982248178 0.85899748 1 12.63351993 -9.215090487 9.515254519 0.963633958 1.006981606 0.177604377 0.062439775 0.943900401 188.8345267 0.008829157 0.014633291 6.09E-10 9.215090487 0.043347648 QPPGTQQSHS(ph)SPGEITSSPQGLDNPALLR ddPTM_HeLa_Romidepsin_16h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0-2;Q5TDH0;Q5TDH0-3 Q5TDH0-2 DDI2 Protein DDI1 homolog 2 1 0 QPPGTQQS(0.001)HS(0.499)S(0.499)PGEITSSPQGLDNPALLR 130.51 1.58E-10 22166000 507.16 593.26 467.26 531.19 497.39 359.52 529.5 604.41 570.98 543.89 TRUE FALSE FALSE 500.9785388 601.6119299 475.3924643 592.6086871 472.0063323 336.5478323 574.4757168 621.8976497 519.9101188 529.7596594 0.945671362 1.135631827 0.897373848 1.11863687 0.890982022 0.635283994 1.084408196 1.173924135 0.98140753 1 9.049194178 QPPGTQQSHSS(ph)PGEITSSPQGLDNPALLR ddPTM_HeLa_Romidepsin_16h_R1 1 QPPGTQQSHSSPGEITSSPQGLDNPALLR 29 0 Q5TDH0-2;Q5TDH0;Q5TDH0-3 Q5TDH0-2 DDI2 Protein DDI1 homolog 2 1 0 QPPGTQQSHS(0.152)S(0.848)PGEITSSPQGLDNPALLR 137.94 1.00E-10 23296000 408.63 267.86 262.7 292.64 346.99 360.69 336.4 404.49 491.66 459.33 TRUE FALSE FALSE 403.6494604 271.6309401 267.2721833 326.4764137 329.2818055 337.6430731 364.9738076 416.19328 447.6846982 447.3965404 0.902218555 0.607136881 0.59739439 0.72972494 0.735995422 0.754684139 0.81577253 0.930255919 1.000644077 1 8.80541029 -10.45672049 4.965025265 0.958303922 0.736329776 0.571173844 0.091844864 0.129344386 5.921295646 0.017502232 0.019641013 3.49E-11 10.45672049 -0.221974146 QPPLPTS(ph)SPGVSSGDSVAR ddPTM_HeLa_Romidepsin_16h_R1 1 QPPLPTSSPGVSSGDSVAR 19 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 QPPLPT(0.013)S(0.636)S(0.343)PGVS(0.004)S(0.002)GDS(0.002)VAR 119.37 0.00085283 3534700 621.98 719.7 575.56 654.61 701.74 887.62 677.71 930.41 634.01 699.65 TRUE FALSE FALSE 614.3990685 729.8319555 585.5773804 730.2990882 665.9275892 830.9039467 735.2746705 957.3299454 577.3025577 681.4729921 0.901575082 1.070962406 0.85928186 1.071647881 0.977188527 1.219276415 1.078949098 1.404795137 0.847139306 1 9.412512672 -4 0.489977622 0.95527186 13.64847984 0.696896314 0.089310934 33.81364695 0.333008167 0.015488888 442.426881 1.00E-04 4 12.69320798 QPPVSPLTLS(ph)PGPEAHQGFSR ddPTM_HeLa_Romidepsin_16h_R1 1 QPPVSPLTLSPGPEAHQGFSR 21 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 0 QPPVSPLT(0.003)LS(0.996)PGPEAHQGFSR 113.13 8.47E-05 5997400 922.89 719.26 827.13 794.25 469.59 747.1 572.82 519.63 914.31 1315.7 TRUE FALSE FALSE 911.6414617 729.3857612 841.5258507 886.0849221 445.62507 699.3627212 621.4753165 534.6646742 832.5318237 1281.517924 0.711376286 0.569157674 0.656663348 0.691433889 0.347732218 0.545729957 0.484952496 0.417212014 0.649645087 1 10.32363794 -11.44350471 0.179173333 1.295759937 0.296818717 0.389887904 0.135307268 1.529964194 0.136958147 0.477578205 0.225179009 3.60E-12 11.44350471 -0.99894122 QPS(ph)DASETTGLVQR ddPTM_HeLa_Romidepsin_16h_R1 1 QPSDASETTGLVQR 14 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 QPS(1)DASETTGLVQR 115.26 0.004789 6492600 751.87 744.9 637 560.69 535.66 384.95 506.81 749.08 976.7 718.9 TRUE FALSE FALSE 742.7059192 755.3867218 648.0867178 625.5196159 508.3232714 360.3529374 549.8584287 770.7534479 889.3415058 700.2228744 1.060670747 1.078780413 0.925543483 0.893315027 0.725944967 0.514626058 0.78526202 1.100725892 1.270083481 1 9.451670381 -9.225030442 1.992808859 1.031692171 0.767687605 0.421243352 0.156853497 0.239450169 1.855119741 0.022049506 0.039182853 5.96E-10 9.225030442 -0.264004566 QPS(ph)EEEIIK ddPTM_HeLa_Romidepsin_16h_R1 3 QPSEEEIIK 9 0 Q15121-2;Q15121;B1AKZ5 Q15121-2 PEA15 Astrocytic phosphoprotein PEA-15 1 0 QPS(1)EEEIIK;QPS(1)EEEIIK;QPS(1)EEEIIK ;; 125.82 0.010419 209819000 10653.3 9140.9 8723.9 8298.8 9524.9 11528 12393.3 11561.7 11490 9463.4 TRUE FALSE FALSE 10523.45348 9269.58583 8875.73582 9258.346303 9038.808811 10791.398 13445.98659 11896.21955 10462.30562 9217.539504 1.141677069 1.005646445 0.962918121 1.004427082 0.980609718 1.170746054 1.458739242 1.290606842 1.13504321 1 13.17016598 -7.952258678 4.510936675 1.046429364 1.371015926 0.789684721 0.069824181 0.071736683 3.169415221 0.010785445 0.033819854 1.12E-08 7.952258678 0.324586562 QPS(ph)SPSHNTNLR ddPTM_HeLa_Romidepsin_16h_R1 1 QPSSPSHNTNLR 12 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 QPS(0.871)S(0.129)PSHNTNLR 106.55 0.0051901 1557600 272.53 301.86 324.42 201.23 513.18 506.54 301.8 290.68 574.51 396.56 TRUE FALSE FALSE 269.2082995 306.109593 330.066394 224.4971594 486.9905097 474.1737288 327.4348845 299.0903672 523.1243867 386.257314 0.696966219 0.792501739 0.854524645 0.581211413 1.260792979 1.227611003 0.847711804 0.77432933 1.354341698 1 8.593418441 -8.758309103 24.99999991 0.830773585 1.029046953 0.061663988 0.239973603 107.6204926 859497.7821 0.028816019 0.055749063 1.74E-09 8.758309103 0.198273368 QPS(ph)SPYEDK ddPTM_HeLa_Romidepsin_16h_R1 1 QPSSPYEDK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QPS(0.749)S(0.251)PYEDK 131.42 0.0075465 5045100 3369.6 3472.8 3751.9 1572.7 2767.2 3453.4 3235.7 1844.7 4034.2 4475 TRUE FALSE FALSE 3328.530019 3521.69017 3817.200246 1754.542974 2625.979458 3232.738885 3510.540277 1898.073484 3673.371048 4358.738855 0.763645203 0.807960809 0.87575796 0.402534548 0.602463131 0.741668403 0.805402754 0.435463915 0.842760067 1 12.08969505 -11.95973603 0.20257315 1.209579001 0.552868772 0.360273735 0.145316538 4.484564217 0.343986299 0.850616786 0.251481207 1.10E-12 11.95973603 -0.656710229 QPSPS(ph)PSPTER ddPTM_HeLa_Romidepsin_16h_R1 2 QPSPSPSPTER 11 0 P29590-12;P29590-11;H3BT57;P29590-13;P29590-14;P29590-10;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 QPS(0.016)PS(0.774)PS(0.21)PTER;QPS(0.042)PS(0.821)PS(0.132)PT(0.005)ER ; 120.9 0.0096293 53795000 1412.8 1219.1 1240.97 1067.76 1711.14 1711.86 1251.31 1393.17 1689.82 1390.29 TRUE FALSE FALSE 1395.58025 1236.262522 1262.568562 1191.219435 1623.814141 1602.477671 1357.59624 1433.479176 1538.678267 1354.170065 1.030579752 0.912930033 0.932355983 0.879667529 1.199121279 1.183365156 1.002530092 1.058566581 1.136251868 1 10.40319322 -8.755273818 24.99999347 0.991053796 1.108331735 0.35282029 0.08498461 131.6826925 533939.1371 0.011398012 0.022342906 1.76E-09 8.755273818 0.11727794 QPSS(ph)PGPTPR ddPTM_HeLa_Romidepsin_16h_R1 3 QPSSPGPTPR 10 0 Q13424-2;Q13424 Q13424-2 SNTA1 Alpha-1-syntrophin 1 0 QPS(0.229)S(0.771)PGPTPR;QPS(0.386)S(0.611)PGPT(0.003)PR;QPS(0.052)S(0.946)PGPT(0.001)PR ;; 124.48 0.0096731 121051000 10221.9 10276.6 9531.5 11885.7 10805 10913.1 10328.4 9635 10761.4 9400.7 TRUE FALSE FALSE 10097.31155 10421.27424 9697.391759 13259.98056 10253.58053 10215.78813 11205.69404 9913.773523 9798.873432 9156.468459 1.102751743 1.13813249 1.059075538 1.448154451 1.119818255 1.115690856 1.223800867 1.082707112 1.070158596 1 13.16057556 -10.86609086 0.661554075 1.013562601 1.182436027 0.211964667 0.104479881 0.573013285 0.565674927 0.037241399 0.0282444 1.36E-11 10.86609086 0.168873425 QPSS(ph)PYEDK ddPTM_HeLa_Romidepsin_16h_R1 1 QPSSPYEDK 9 0 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QPS(0.183)S(0.817)PYEDK 143 0.0061867 4552100 3286.1 3850.8 3853.4 1448.3 2305.3 3013.6 3362 2095.6 3961.6 5010 TRUE FALSE FALSE 3246.047749 3905.011663 3920.466811 1615.75926 2187.651939 2821.040686 3647.568196 2156.23288 3607.264574 4879.839478 0.6651956 0.800233631 0.803400773 0.331109101 0.448304078 0.578101124 0.747477087 0.441865535 0.739217876 1 12.25261798 -12.32057628 0.252618594 1.235951204 0.505166109 0.322491653 0.159788125 3.206083224 0.281940666 0.738505924 0.133114312 4.78E-13 12.32057628 -0.730785095 QPSS(ph)PYEDKDK ddPTM_HeLa_Romidepsin_16h_R1 1 QPSSPYEDKDK 11 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QPS(0.17)S(0.825)PY(0.005)EDKDK 69.314 0.029607 42687000 5688.3 6239.3 7918.5 3515.3 5666.9 6589 6473.4 3012.9 7581.9 8011.6 TRUE FALSE FALSE 5618.968812 6327.137029 8056.318171 3921.755526 5377.696947 6167.984165 7023.250434 3100.073508 6903.755875 7803.457477 0.720061438 0.810812008 1.032403674 0.502566399 0.689142853 0.790416836 0.900017775 0.397269225 0.884704747 1 12.92989777 -16.52287875 0.169932365 2.06897832 0.660156942 0.230322745 0.169506588 57.74149718 0.640451968 20.55626448 0.263210865 3.00E-17 16.52287875 -1.408821379 QPTVGGTSST(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 QPTVGGTSSTPR 12 0 F8W108;F8WCU9;Q68CP9-3;Q68CP9;A0A087WY37;F8VWP4 F8W108 ARID2 AT-rich interactive domain-containing protein 2 1 0 QPTVGGTSS(0.065)T(0.935)PR;QPTVGGTS(0.009)S(0.345)T(0.647)PR ; 157.09 0.0023184 12572600 3870.9 3671.1 3613.3 2987.5 1904.91 1856.75 1748.89 1877.55 3413.1 3270.8 TRUE FALSE FALSE 3823.719982 3722.781842 3676.187971 3332.928807 1807.695335 1738.109667 1897.440673 1931.873947 3107.823788 3185.824144 1.200229457 1.168545931 1.153920557 1.046174759 0.56741843 0.545576149 0.595588641 0.606396919 0.975516427 1 11.63745092 -8.790783239 5.048604077 1.106921951 0.575058211 0.930670324 0.06850585 0.03905346 2.482455794 0.012218862 0.023164914 1.62E-09 8.790783239 -0.531863741 QPVGGGQK(ac)LLTR ddPTM_HeLa_Romidepsin_16h_R1 1 QPVGGGQKLLTR 12 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 QPVGGGQK(1)LLTR 128.88 0.0081598 14940000 654.9 677.06 820.36 786.91 1007.2 953.32 1321.6 1211.3 726.28 666.05 FALSE TRUE FALSE 646.9178269 686.5916685 834.6380217 877.8962367 955.7988256 892.4059287 1433.856671 1246.347054 661.3196978 648.745925 0.997182105 1.058336773 1.286540677 1.353220426 1.473302242 1.37558618 2.210197576 1.921163596 1.01938166 1 9.341509761 -7.832766409 0.49641165 0.984015572 2.505641532 0.839064456 0.156590139 0.638472476 0.150181807 0.032320053 0.508698537 1.47E-08 7.832766409 1.52162596 QPVS(ph)PEPGPDADEDGPVLM ddPTM_HeLa_Romidepsin_16h_R1 1 QPVSPEPGPDADEDGPVLM 19 0 Q5T7W7 Q5T7W7 TSTD2 Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 2 1 0 QPVS(1)PEPGPDADEDGPVLM 78.225 0.013608 2136000 765.75 527.99 408.2 589.48 547.37 455.86 270.03 363.63 685.3 577.22 TRUE FALSE FALSE 756.4167445 535.4230571 415.3045498 657.6384512 519.4356664 426.7320172 292.9663415 374.1510603 624.0050516 562.2237412 1.345401642 0.952330928 0.738681986 1.1697095 0.923894934 0.759007466 0.52108497 0.665484278 1.109887409 1 9.135000566 -8.275849579 0.664125952 1.143026504 0.489574443 0.54751925 0.160529988 0.7152698 0.43470282 0.036271614 0.275756439 5.30E-09 8.275849579 -0.653452061 QPVSEPPADQVASDMPHS(ph)PTLR ddPTM_HeLa_Romidepsin_16h_R1 1 QPVSEPPADQVASDMPHSPTLR 22 0 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;H7C231;H7C2V9 H7BYY2 BCOR BCL-6 corepressor 1 0 QPVSEPPADQVASDMPHS(0.791)PT(0.209)LR 90.454 0.00018412 10511000 1891.1 1510.7 1893.2 1627.1 1494.7 1088.2 646.8 1226.4 2563.1 2084.7 TRUE FALSE FALSE 1868.050546 1531.967674 1926.150352 1815.232958 1418.419882 1018.667532 701.7391759 1261.883949 2333.849917 2030.539193 0.919977586 0.754463484 0.94859058 0.893965979 0.698543464 0.501673415 0.345592529 0.621452643 1.149374474 1 10.98764716 -8.544671395 1.934335592 0.941837693 0.467969135 0.776511128 0.110295749 0.095257639 0.70750924 0.013797303 0.0353602 2.85E-09 8.544671395 -0.473868557 QQAAYYAQT(ph)SPQGMPQHPPAPQGQ ddPTM_HeLa_Romidepsin_16h_R1 4 QQAAYYAQTSPQGMPQHPPAPQGQ 24 0 Q96AE4 Q96AE4 FUBP1 Far upstream element-binding protein 1 1 0 QQAAY(0.001)Y(0.008)AQT(0.495)S(0.495)PQGMPQHPPAPQGQ;QQAAY(0.003)Y(0.003)AQT(0.556)S(0.438)PQGMPQHPPAPQGQ;QQAAY(0.001)Y(0.003)AQT(0.569)S(0.427)PQGMPQHPPAPQGQ;QQAAY(0.001)Y(0.011)AQT(0.583)S(0.404)PQGMPQHPPAPQGQ ;;; 71.506 0.00048958 141854000 7826.4 7498.11 7106.59 7063.41 8473.75 8540.1 7350.17 8300.6 8371.22 7778.15 TRUE FALSE FALSE 7731.008826 7603.668589 7230.277218 7880.114699 8041.302918 7994.415172 7974.493256 8540.764765 7622.477117 7576.072542 1.020450739 1.003642527 0.954356915 1.040131896 1.061407857 1.055218931 1.052589348 1.127334079 1.006125149 1 12.88723443 -4.000000837 0.4194253 1.005291931 3.173167541 0.707210739 0.023981116 29.50274811 0.337594408 0.00577603 54.18082484 1.00E-04 4.000000837 2.16787561 QQASKS(ph)PYNGVR ddPTM_HeLa_Romidepsin_16h_R1 1 QQASKSPYNGVR 12 1 Q9UK58-6;Q9UK58 Q9UK58-6 CCNL1 Cyclin-L1 1 0 QQAS(0.002)KS(0.998)PYNGVR 145.29 0.0099833 9881100 2557.5 2190.6 2017.3 2108.3 2404.5 1999.8 1526 1760.7 2294.1 2173.5 TRUE FALSE FALSE 2526.328206 2221.439324 2052.41026 2352.071566 2281.789393 1872.019234 1655.618402 1811.643077 2088.90995 2117.032157 1.193334829 1.049317705 0.969475241 1.11102307 1.077824626 0.884265847 0.782046884 0.855746603 0.986716212 1 11.04782747 -8.177836198 3.360961341 1.081931725 0.820962646 0.672594447 0.067749784 0.114942663 2.491845365 0.011754063 0.032772392 6.64E-09 8.177836198 -0.260969079 QQDLHLES(ph)PQRQPEY(ph)S(ph)PESPR ddPTM_HeLa_Romidepsin_16h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 3 0 QQDLHLES(0.809)PQRQPEY(0.909)S(0.79)PES(0.492)PR 42.353 0.029551 10983000 1870.9 1610.5 1524.5 1595.9 1387.9 1358.9 951.42 1310.4 2049.6 2034.1 TRUE FALSE FALSE 1848.096751 1633.172661 1551.033283 1780.425467 1317.070284 1272.070676 1032.233591 1348.314357 1866.278643 1981.253789 0.932791529 0.824312701 0.782854419 0.898635741 0.664766065 0.642053372 0.521000185 0.680535913 0.941968491 1 10.95219798 -8.974869354 0.446664162 0.992393705 0.527645511 0.797166489 0.067181732 0.393061039 0.131892643 0.01957198 0.078074388 1.06E-09 8.974869354 -0.464748194 QQDLHLES(ph)PQRQPEYS(ph)PESPR ddPTM_HeLa_Romidepsin_16h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 2 0 QQDLHLES(0.986)PQRQPEY(0.408)S(0.486)PES(0.121)PR 51.942 0.014713 25990000 2078.2 2632.1 2405.9 2301.6 2372.2 2031.6 1928.8 2257.3 2679 2910.5 TRUE FALSE FALSE 2052.870099 2669.154773 2447.77368 2567.721821 2251.137782 1901.787317 2092.632224 2322.611414 2439.38353 2834.88479 0.724145865 0.941539064 0.863447322 0.905758791 0.794084398 0.670851713 0.738171876 0.81929658 0.860487713 1 11.46907439 -12.4788274 1.109990172 1.004751997 0.800733109 0.170818556 0.088971666 0.411757001 0.872656873 0.0676795 0.015068416 3.32E-13 12.4788274 -0.204018888 QQDLHLESPQRQPEY(ph)S(ph)PES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 QQDLHLESPQRQPEYSPESPR 21 1 Q9H6F5 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 3 0 QQDLHLES(0.364)PQRQPEY(0.91)S(0.793)PES(0.933)PR 44.054 0.026475 2389100 508.38 673.74 854.71 651.32 815.84 741.93 769.77 697.13 624.37 685.78 TRUE FALSE FALSE 502.183669 683.2249294 869.585869 726.628683 774.2046405 694.5230675 835.1542446 717.3003567 568.5247834 667.9633367 0.751813223 1.02284795 1.301846705 1.087827195 1.159052597 1.039762258 1.250299528 1.073861868 0.85113172 1 9.383625108 -10.00165696 24.90438569 0.883039099 1.149982798 0.651009116 0.093237761 33.65723962 505885.0437 0.018109188 0.02360838 9.96E-11 10.00165696 0.266943699 QQDPS(ph)PGSNLGGGDDLK ddPTM_HeLa_Romidepsin_16h_R1 1 QQDPSPGSNLGGGDDLK 17 0 J3KTD8;Q13951-2 J3KTD8 CBFB Core-binding factor subunit beta 1 0 QQDPS(0.889)PGS(0.111)NLGGGDDLK 127.78 0.002087 9306600 4106.6 3635.1 4017.6 3054.2 3360.9 3318.1 2879.3 3198.4 4692.7 4363.7 TRUE FALSE FALSE 4056.54718 3686.275033 4087.524643 3407.340974 3189.380732 3106.084119 3123.86767 3290.940658 4272.973159 4250.330445 0.954407482 0.867291398 0.961695731 0.801664957 0.750384181 0.730786502 0.734970542 0.774278777 1.005327283 1 12.05335929 -9.335721966 0.791303271 0.982805937 0.729654608 0.876359981 0.037721719 0.140614911 0.174161137 0.007412822 0.016580714 4.62E-10 9.335721966 -0.253151329 QQDS(ph)QPEEVMDVLEMVENVK ddPTM_HeLa_Romidepsin_16h_R1 3 QQDSQPEEVMDVLEMVENVK 20 0 Q9H307 Q9H307 PNN Pinin 1 0 QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK;QQDS(1)QPEEVMDVLEMVENVK ;; 69.845 0.0015168 6949800 3525.72 2700.59 3611.38 2403.16 3596.3 3240.8 2517.26 2752.49 3529.11 3394.61 TRUE FALSE FALSE 3482.747169 2738.608977 3674.234554 2681.024666 3412.767391 3033.723339 2731.076002 2832.128955 3213.457563 3306.417543 1.053329509 0.828270762 1.111243364 0.81085484 1.032164676 0.917525781 0.825992473 0.856555144 0.971884985 1 11.69105321 -7.60333179 0.386832964 1.023438055 0.728035896 0.199348882 0.09164534 3.734017987 0.459015232 0.025274303 0.487996544 2.49E-08 7.60333179 -0.295402159 QQEGFK(ac)GTFPDAR ddPTM_HeLa_Romidepsin_16h_R1 2 QQEGFKGTFPDAR 13 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; QQEGFK(1)GTFPDAR;QQEGFK(1)GTFPDAR 152.38 0.00029649 1684990 1065.15 593.99 872.23 731.46 964.86 523.99 861.18 724.68 1308.21 1156.38 FALSE TRUE FALSE 1052.167542 602.3522068 887.4107973 816.0348468 915.6195938 490.5087301 934.3286077 745.6474724 1191.200421 1126.337081 0.934149785 0.534788579 0.787873197 0.724503224 0.812917917 0.435490173 0.82952841 0.662010942 1.057587858 1 10.13742293 -10.39327569 6.278221795 0.971184783 0.690880802 0.58785285 0.119862243 0.121233248 5.698812866 0.018722375 0.021311418 4.04E-11 10.39327569 -0.280303981 QQFILT(ph)SPDGAGTGK ddPTM_HeLa_Romidepsin_16h_R1 1 QQFILTSPDGAGTGK 15 0 C9JKS0;P49116;P49116-2;C9JMI6 C9JKS0 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 0 QQFILT(0.486)S(0.486)PDGAGT(0.028)GK 96.707 0.021448 4220400 2207 2026.2 2114.4 1762.1 2072.7 1965.1 1527.2 1883.4 2358.6 2274.9 TRUE FALSE FALSE 2180.100235 2054.724897 2151.200245 1965.842293 1966.922385 1839.536452 1656.92033 1937.893207 2147.640909 2215.79777 0.983889534 0.927307051 0.970846832 0.887193913 0.887681363 0.83019149 0.747775971 0.874580358 0.969240487 1 11.1136105 -8.937249796 0.70148949 0.99413137 0.797280208 0.765398596 0.036240904 0.217852169 0.196389167 0.00647212 0.022019622 1.16E-09 8.937249796 -0.196851162 QQIGSSAMPYK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 QQIGSSAMPYKR 12 1 A0A1B0GTG9;A0A1B0GWF8;A0A1B0GWJ0;A0A1B0GTJ7;A0A0A6YY92;P30566-2;P30566;A0A096LPA2;A0A096LNY6 A0A1B0GTG9 ADSL Adenylosuccinate lyase 0 1 QQIGSSAMPYK(1)R 73.951 0.021414 1336800 266.06 203.41 288.54 81.425 315.86 222.46 408.94 226.35 449.5 265.47 FALSE TRUE FALSE 262.8171584 206.2736113 293.5619177 90.83974162 299.7404856 208.245524 443.6753534 232.8990801 409.2955942 258.5730511 1.016413571 0.797738242 1.135315209 0.351311713 1.159210073 0.805364376 1.715860765 0.900709023 1.582901205 1 8.014428113 -7.793705715 24.99971377 0.955104249 1.30828696 0.119922455 0.349002456 179.7836855 139294.8185 0.035569102 0.106718832 1.61E-08 7.793705715 0.353182711 QQLEEEEENFSRPQIDENPLDDNS(ph)EEEMEDAPK ddPTM_HeLa_Romidepsin_16h_R1 4 QQLEEEEENFSRPQIDENPLDDNSEEEMEDAPK 33 1 Q5F1R6;Q5F1R6-3;Q5F1R6-2;A0A2R8Y534;A0A2R8Y4Q0;A0A2R8Y4N5 Q5F1R6 DNAJC21 DnaJ homolog subfamily C member 21 1 0 QQLEEEEENFSRPQIDENPLDDNS(1)EEEMEDAPK;QQLEEEEENFSRPQIDENPLDDNS(1)EEEMEDAPK;QQLEEEEENFSRPQIDENPLDDNS(1)EEEMEDAPK;QQLEEEEENFSRPQIDENPLDDNS(1)EEEMEDAPK ;;; 89.381 1.17E-11 82220100 8716.33 8673.05 7552.54 8613.98 9517.47 9671.97 7978.95 8946.45 10084.34 8610.02 TRUE FALSE FALSE 8610.092017 8795.149426 7683.988791 9609.968898 9031.757991 9053.962332 8656.681814 9205.301416 9182.371374 8386.330439 1.026681703 1.048748256 0.916251613 1.145908686 1.076961856 1.079609538 1.032237148 1.097655462 1.094921246 1 13.03382396 -9.246228543 24.99977657 1.009636781 1.082551473 0.319065114 0.049720257 585.446993 962212.3842 0.005969524 0.009876682 5.67E-10 9.246228543 0.072914691 QQLLIGAYAK ddPTM_HeLa_Romidepsin_16h_R1 2 QQLLIGAYAK 10 0 Q99832-2;Q99832-4;Q99832-3;Q99832 Q99832-2 CCT7 T-complex protein 1 subunit eta 0 0 ; ; 164.57 0.01771 1905460 2148.57 1426.33 3604.7 2967.2 3879.6 3413.5 2370.5 1843.17 2008.29 1300.21 FALSE FALSE TRUE 2122.382402 1446.409911 3667.438291 3310.281625 3681.609535 3195.388367 2571.850211 1896.499216 1828.663513 1266.430357 1.675877707 1.142115635 2.895886277 2.613867875 2.907076189 2.523145745 2.030786926 1.4975156 1.443951105 1 10.30655203 -9.770755712 24.9999054 1.314803571 2.430896041 0.616415652 0.423345711 106.8366283 286690.2101 0.076799982 0.101700162 1.70E-10 9.770755712 1.11609247 QQLS(ph)PSPGQEAGILPETEK ddPTM_HeLa_Romidepsin_16h_R1 2 QQLSPSPGQEAGILPETEK 19 0 Q17RY0-2;B7ZLQ8;E5RJM0;Q17RY0 Q17RY0-2 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 0 QQLS(0.759)PS(0.241)PGQEAGILPETEK;QQLS(0.92)PS(0.08)PGQEAGILPETEK ; 265.42 2.75E-90 13815600 6239.7 5786.8 5817.9 5901.6 10726.5 13283.6 12133.7 13938.4 6360.1 6212.1 TRUE FALSE FALSE 6163.648136 5868.266722 5919.158109 6583.97076 10179.08668 12434.82083 13164.33618 14341.68561 5791.236727 6050.708746 1.018665481 0.969847826 0.97825864 1.088132157 1.682296588 2.055101535 2.175668459 2.370248877 0.957117087 1 12.56288843 -8.495439845 1.567526339 0.998334578 2.268306906 0.988180675 0.059595119 0.026905923 0.128754356 0.008754573 0.025766493 3.20E-09 8.495439845 1.269972327 up QQLSAEELDAQLDAYNAR ddPTM_HeLa_Romidepsin_16h_R1 1 QQLSAEELDAQLDAYNAR 18 0 Q86V81;E9PB61 Q86V81 ALYREF THO complex subunit 4 0 0 153.2 0.00017824 3754500 2227.9 2093.6 2490.1 1978 2312.4 2563.1 1781.9 2313.2 2555.8 2313.6 FALSE FALSE TRUE 2200.745498 2123.073756 2533.439146 2206.705667 2194.389599 2399.326182 1933.254542 2380.128792 2327.202847 2253.492338 0.97659329 0.942126015 1.124227983 0.979238149 0.973772824 1.064714595 0.857892662 1.056195644 1.032709456 1 11.13794683 -4.017097155 20.69875276 0.992424298 0.988537084 0 0.070531 0 0 0.008080237 0 9.61E-05 4.017097155 -0.003887214 QQLSPDRQPQS(ph)SGPDR ddPTM_HeLa_Romidepsin_16h_R1 1 QQLSPDRQPQSSGPDR 16 1 Q9H1H9-3;Q9H1H9-4;Q9H1H9-2;A0A1B0GUA8;Q9H1H9;H0Y307 Q9H1H9-3 KIF13A Kinesin-like protein KIF13A 1 0 QQLS(0.003)PDRQPQS(0.499)S(0.499)GPDR 128.82 0.014132 2399200 1152.8 701.58 880.31 848.8 778.53 806.81 670.86 562.51 1147.7 863.95 TRUE FALSE FALSE 1138.74923 711.4568617 895.6314263 946.9422497 738.798709 755.2574449 727.8428317 578.7853394 1045.046838 841.5044545 1.353230187 0.845458224 1.06432167 1.125296776 0.877949849 0.897508553 0.864930456 0.687798307 1.241879151 1 9.716827098 -8.291829492 0.653154018 1.14871433 0.695559077 0.51881689 0.133058455 0.896328068 0.527289395 0.031404909 0.236452043 5.11E-09 8.291829492 -0.453155253 QQLSPS(ph)PGQEAGILPETEK ddPTM_HeLa_Romidepsin_16h_R1 2 QQLSPSPGQEAGILPETEK 19 0 Q17RY0-2;B7ZLQ8;E5RJM0;Q17RY0 Q17RY0-2 CPEB4 Cytoplasmic polyadenylation element-binding protein 4 1 0 QQLS(0.164)PS(0.836)PGQEAGILPETEK;QQLS(0.041)PS(0.959)PGQEAGILPETEK ; 190.1 8.41E-15 12849600 5944.7 6346.9 6335.4 6118.1 8790.3 10078.1 9335.2 10235 7218.2 6743.6 TRUE FALSE FALSE 5872.24371 6436.251825 6445.664979 6825.503509 8341.69819 9434.141936 10128.13165 10531.13358 6572.586114 6568.4003 0.894014287 0.979881178 0.981314275 1.039142439 1.269974089 1.436292172 1.541947992 1.603302645 1.000637265 1 12.68132634 -8.448147598 1.165927396 0.949664968 1.596998752 0.982174516 0.033495567 0.054758293 0.137781349 0.006692543 0.0253089 3.56E-09 8.448147598 0.647333784 QQPPEPEWIGDGES(ph)TSPSDKVVK ddPTM_HeLa_Romidepsin_16h_R1 1 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q8NE71;Q5STZ8;Q8NE71-2;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 QQPPEPEWIGDGES(0.377)T(0.377)S(0.245)PS(0.001)DKVVK 119.48 1.69E-06 91972000 4616.1 4696.6 3598 4182.9 3607.1 3061.5 3596.5 3477.5 5071 3886.8 TRUE FALSE FALSE 4559.837198 4762.718858 3660.621681 4666.546579 3423.016227 2865.880031 3901.98662 3578.115976 4617.437059 3785.820376 1.204451544 1.258041424 0.966929573 1.232638138 0.904167627 0.7570037 1.030684563 0.945136224 1.219666176 1 11.88639025 -8.737735876 24.85556341 1.109956791 0.907047343 0.495386155 0.113908206 172.2611578 180632.5669 0.017416685 0.034817423 1.83E-09 8.737735876 -0.202909448 QQPPEPEWIGDGEST(ph)SPSDK ddPTM_HeLa_Romidepsin_16h_R1 1 QQPPEPEWIGDGESTSPSDK 20 0 Q8NE71;Q5STZ8;Q8NE71-2;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 QQPPEPEWIGDGES(0.088)T(0.443)S(0.443)PS(0.026)DK 89.297 0.0013132 6083000 1535.6 1539.3 1587.7 1033.8 1516.5 1405.7 985.76 1570.3 1689.1 1690.2 TRUE FALSE FALSE 1516.883517 1560.970306 1615.333252 1153.33282 1439.107346 1315.880307 1069.49043 1615.734153 1538.022666 1646.28836 0.921396004 0.94817551 0.981197032 0.700565495 0.874152658 0.799301227 0.649637363 0.981440549 0.934236494 1 10.68500134 -9.279016522 24.81778212 0.961850487 0.796576839 0.445543723 0.08684768 464.4646862 655792.488 0.012428332 0.019011185 5.26E-10 9.279016522 -0.165273648 QQPPEPEWIGDGEST(ph)SPSDKVVK ddPTM_HeLa_Romidepsin_16h_R1 2 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q8NE71;Q5STZ8;Q8NE71-2;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 QQPPEPEWIGDGES(0.028)T(0.568)S(0.377)PS(0.028)DKVVK;QQPPEPEWIGDGES(0.28)T(0.552)S(0.136)PS(0.032)DKVVK ; 115.79 3.85E-06 116743000 9186 7782 7499.7 8668.5 7238.8 7395.8 6393.8 6940.2 9611.1 8470.2 TRUE FALSE FALSE 9074.037499 7891.5552 7630.229133 9670.792757 6869.377024 6923.232249 6936.889212 7141.003737 8751.459145 8250.142983 1.099864271 0.956535568 0.924860229 1.172196988 0.83263733 0.839165123 0.840820484 0.865561209 1.060764542 1 13.01020341 -8.735644528 24.99973575 1.038327733 0.843895457 0.666438267 0.066236694 106.7965003 103504.037 0.010035564 0.020065603 1.84E-09 8.735644528 -0.194432276 QQPPEPEWIGDGESTS(ph)PSDK ddPTM_HeLa_Romidepsin_16h_R1 2 QQPPEPEWIGDGESTSPSDK 20 0 Q8NE71;Q5STZ8;Q8NE71-2;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 QQPPEPEWIGDGES(0.004)T(0.213)S(0.622)PS(0.161)DK;QQPPEPEWIGDGEST(0.188)S(0.755)PS(0.056)DK ; 116.92 0.00010441 75400000 9703.4 9162.7 10417.6 6416.1 8607.4 9684 8411.7 9066.3 10846.3 11531.1 TRUE FALSE FALSE 9585.131228 9291.692731 10598.91396 7157.959671 8168.132259 9065.223654 9126.189588 9328.619086 9876.179763 11231.52036 0.853413511 0.827287173 0.9436758 0.637309949 0.727250808 0.807123467 0.812551578 0.830574917 0.879327059 1 13.45526561 -11.37780127 0.430201047 1.016260936 0.776923261 0.312901471 0.080062795 0.703716728 0.280440278 0.072216018 0.028906227 4.19E-12 11.37780127 -0.239337675 QQPPEPEWIGDGESTS(ph)PSDKVVK ddPTM_HeLa_Romidepsin_16h_R1 1 QQPPEPEWIGDGESTSPSDKVVK 23 1 Q8NE71;Q5STZ8;Q8NE71-2;A0A0G2JIC2 Q8NE71 ABCF1 ATP-binding cassette sub-family F member 1 1 0 QQPPEPEWIGDGES(0.267)T(0.267)S(0.424)PS(0.042)DKVVK 96.234 2.57E-05 89229000 5709.1 4589.6 4353.1 5537.5 4365.6 4269.2 4266 4577 5660.3 5462 TRUE FALSE FALSE 5639.515293 4654.212509 4428.863879 6177.771805 4142.807142 3996.411898 4628.353934 4709.428274 5154.028592 5320.096453 1.060040047 0.874836114 0.832478117 1.161214249 0.778709029 0.751191625 0.869975568 0.885214829 0.968784803 1 12.37723669 -9.263905144 0.678905492 1.02569076 0.827516749 0.1995561 0.108994948 0.656723765 0.588642276 0.023540236 0.06016567 5.45E-10 9.263905144 -0.198174011 QQPPLGPSSS(ph)LLSLPGLK ddPTM_HeLa_Romidepsin_16h_R1 2 QQPPLGPSSSLLSLPGLK 18 0 Q4KMP7;Q4KMP7-2 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 QQPPLGPS(0.001)S(0.071)S(0.927)LLS(0.001)LPGLK;QQPPLGPS(0.054)S(0.188)S(0.708)LLS(0.05)LPGLK ; 157.84 5.35E-06 60753000 10307.1 9609.7 9396.9 9474.5 11655.8 12979.4 11242.9 13475.3 9655.5 9154 TRUE FALSE FALSE 10181.4731 9744.985609 9560.449103 10569.98627 11060.96103 12150.05823 12197.87165 13865.18654 8791.887897 8916.17776 1.141910062 1.09295551 1.072258692 1.185484022 1.240549631 1.36269807 1.368060617 1.555059457 0.986060186 1 13.12220966 -4 0.268932441 1.029598496 4.773909602 0.942682759 0.041436348 8.775517835 0.111216275 0.022398128 15.42930031 1.00E-04 4 3.744311106 QQQEK(ac)EMK ddPTM_HeLa_Romidepsin_16h_R1 2 QQQEKEMK 8 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 0 1 ; QQQEK(1)EMK;QQQEK(1)EMK 99.815 0.0073972 1657380 0 132.4 0 51.917 74.755 238.91 126.395 0 188.976 308.18 FALSE TRUE FALSE 0 134.2639307 0 57.91988782 70.9399734 223.644422 137.1309881 0 172.0735133 300.1734392 0 0.447287845 0 0.19295474 0.236329948 0.74505067 0.456839181 0 0.573246966 1 8.229652516 -12.4265968 1.110119946 1.007438049 0.252664854 0.359240178 0.259638559 0.293909217 0.637563803 0.174357495 0.042107342 3.74E-13 12.4265968 -0.754773195 QQSHFAMMHGGTGFAGIDS(ph)SSPEVK ddPTM_HeLa_Romidepsin_16h_R1 2 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 0 QQSHFAMMHGGT(0.007)GFAGIDS(0.492)S(0.125)S(0.375)PEVK;QQS(0.001)HFAMMHGGT(0.004)GFAGIDS(0.67)S(0.115)S(0.211)PEVK ; 70.701 9.94E-05 72887000 3933.94 3295.35 3223.77 3149.98 3853.3 3630.04 2805.28 2925.23 4012.63 3501.92 TRUE FALSE FALSE 3885.991626 3341.742024 3279.878365 3514.195509 3656.651722 3398.092159 3043.560413 3009.866915 3653.730323 3410.939614 1.139273064 0.979713042 0.961576204 1.03027198 1.072036487 0.996233456 0.892293842 0.882415773 1.071180008 1 11.7359535 -7.865051309 2.803580629 1.050086687 0.881500463 0.572485779 0.049724768 0.167267065 2.590977038 0.009355585 0.036648511 1.36E-08 7.865051309 -0.168586224 QQSHFAMMHGGTGFAGIDSSS(ph)PEVK ddPTM_HeLa_Romidepsin_16h_R1 2 QQSHFAMMHGGTGFAGIDSSSPEVK 25 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 0 QQSHFAMMHGGTGFAGIDS(0.151)S(0.107)S(0.742)PEVK;QQSHFAMMHGGTGFAGIDS(0.127)S(0.089)S(0.784)PEVK ; 97.813 5.32E-06 75873000 5172.8 4405.7 4370.4 3876.7 3984.9 4311.5 3696.2 3271.2 5294.2 4442.1 TRUE FALSE FALSE 5109.751924 4467.72356 4446.464979 4324.942294 3781.535683 4036.009065 4010.155136 3365.847011 4820.673492 4326.693602 1.180983077 1.032595319 1.027681964 0.999595232 0.874001266 0.932816011 0.926840563 0.777925899 1.114170296 1 12.07904924 -9.020115144 1.178832106 1.083831424 0.873252588 0.701999356 0.060023044 0.253634367 0.697174133 0.013094969 0.030301214 9.55E-10 9.020115144 -0.210578836 QQSLFS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 QQSLFSSPR 9 0 Q5T7B8-4;Q5T7B8-2;Q5T7B8 Q5T7B8-4 KIF24 Kinesin-like protein KIF24 1 0 QQS(0.003)LFS(0.907)S(0.09)PR 109.39 0.0012533 0 3362.9 3040 3258 2229.5 3130.4 3006.8 2183.1 2442.6 3722.6 3319.1 TRUE FALSE FALSE 3321.911681 3082.7972 3314.704123 2487.28528 2970.644007 2814.675184 2368.53246 2513.272777 3389.641333 3232.869304 1.027542833 0.953579285 1.025313371 0.769373905 0.918887752 0.870643048 0.732640957 0.777412429 1.048493154 1 11.65859947 -8.778806038 0.643358863 1.016186964 0.75127636 0.710313307 0.060577345 0.363430556 0.256101111 0.011771755 0.049923155 1.66E-09 8.778806038 -0.264910604 QQSTSSDRVS(ph)QTPESLDFLK ddPTM_HeLa_Romidepsin_16h_R1 1 QQSTSSDRVSQTPESLDFLK 20 1 Q12965 Q12965 MYO1E Unconventional myosin-Ie 1 0 QQS(0.017)T(0.017)S(0.017)S(0.017)DRVS(0.916)QT(0.017)PES(0.002)LDFLK 62.658 0.0072131 4704900 542.33 529.4 689.2 724.73 826.37 704.75 929.47 825.15 609.28 943.14 TRUE FALSE FALSE 535.7198734 536.8529071 701.1952369 808.5266926 784.1972553 659.7187495 1008.419159 849.0244134 554.7844708 918.6370868 0.583168131 0.584401517 0.763299509 0.880137221 0.853652946 0.718149484 1.097733994 0.924221791 0.603921264 1 9.843351218 -7.764463763 24.99934384 0.785311417 1.01097791 0.338934424 0.139259232 84.87109189 701568.6505 0.024521229 0.078485319 1.72E-08 7.764463763 0.225666493 QQT(ph)EKPESEDEWER ddPTM_HeLa_Romidepsin_16h_R1 1 QQTEKPESEDEWER 14 1 A2AB15;A0A140T947;O60231 A2AB15 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 0 QQT(0.665)EKPES(0.335)EDEWER 198.48 7.70E-16 6487700 2680.2 3084.7 2736.3 2000.9 2932 3359.6 2566.8 2781.7 3390.6 2854.7 TRUE FALSE FALSE 2647.532691 3128.126488 2783.924154 2232.253473 2782.369099 3144.932403 2784.823928 2862.184101 3087.336244 2780.534482 0.952166826 1.125009061 1.001219072 0.802814526 1.000659807 1.131053192 1.001542669 1.029364721 1.110339132 1 11.44114651 -8.509413167 24.88835938 0.977116671 1.051594792 0.042476963 0.090023173 884.8014162 1635372.915 0.011460787 0.024641705 3.09E-09 8.509413167 0.074478121 QQTEKPES(ph)EDEWER ddPTM_HeLa_Romidepsin_16h_R1 2 QQTEKPESEDEWER 14 1 A2AB15;A0A140T947;O60231 A2AB15 DHX16 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 1 0 QQTEKPES(1)EDEWER;QQTEKPES(1)EDEWER ; 86.222 0.0091056 355620000 6819.7 7318 6943.7 5404.9 8034.7 9004.2 7671.6 8830.7 7711.9 7935.7 TRUE FALSE FALSE 6736.578873 7421.022996 7064.552186 6029.839969 7624.659277 8428.86068 8323.225513 9086.202372 7022.128349 7729.52937 0.871538039 0.960087302 0.913969253 0.780104413 0.986432538 1.090475277 1.076808835 1.17551819 0.908480712 1 12.91616486 -8.315189754 3.279848637 0.926458844 1.114943281 0.690374641 0.061386558 0.134966512 2.899916489 0.010302905 0.025971448 4.84E-09 8.315189754 0.188484437 QQTST(ph)PVLTQPGR ddPTM_HeLa_Romidepsin_16h_R1 1 QQTSTPVLTQPGR 13 0 Q5T5U3;A0A087WW76;A0A452Q6Z5;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 QQT(0.001)S(0.003)T(0.969)PVLT(0.026)QPGR 139.64 0.0024227 28352000 3029.3 2700.6 2698.3 2441.8 2383.9 2170.1 1674.4 2798.4 3204.7 2896.1 TRUE FALSE FALSE 2992.377726 2738.619118 2745.26278 2724.132405 2262.240687 2031.437614 1816.623494 2879.367289 2918.063606 2820.858905 1.060803758 0.970845835 0.973201026 0.965710267 0.801968749 0.720148608 0.643996582 1.020741337 1.034459257 1 11.46191879 -8.838800921 2.432849284 1.020149723 0.775112582 0.531744446 0.093581468 0.144983367 1.747359361 0.013453053 0.027406952 1.45E-09 8.838800921 -0.245037142 QQVAFYGQTLGQAQAHS(ph)QEQ ddPTM_HeLa_Romidepsin_16h_R1 2 QQVAFYGQTLGQAQAHSQEQ 20 0 Q96I24;Q96I24-2 Q96I24 FUBP3 Far upstream element-binding protein 3 1 0 QQVAFYGQTLGQAQAHS(1)QEQ;QQVAFY(0.002)GQT(0.341)LGQAQAHS(0.657)QEQ ; 141.22 0.00011274 20357000 9420.1 8822.5 8249.1 6683.1 10221.2 12066 10760.5 13188.5 9722.9 9398.5 TRUE FALSE FALSE 9305.284198 8946.703387 8392.672125 7455.831467 9699.574023 11295.02154 11674.4966 13570.08844 8853.259473 9154.325615 1.01649041 0.977319768 0.916798514 0.814459937 1.059561832 1.23384529 1.275298377 1.482368993 0.967112144 1 13.16023789 -7.919141838 1.486198519 0.985292053 1.440781118 0.854222952 0.071904923 0.146404082 0.559031952 0.011505159 0.0680835 1.20E-08 7.919141838 0.455489065 QQVEQSSAS(ph)QTGIK ddPTM_HeLa_Romidepsin_16h_R1 1 QQVEQSSASQTGIK 14 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 QQVEQS(0.191)S(0.287)AS(0.522)QTGIK 178.85 3.72E-07 3020200 1393.9 1344.9 1062.1 1277.4 1323.8 1165.9 904.22 1167.3 1369.6 1358.1 TRUE FALSE FALSE 1376.910611 1363.833538 1080.585405 1425.098998 1256.241546 1091.402753 981.0244242 1201.073984 1247.099546 1322.816366 1.040893238 1.031007457 0.816882398 1.077321868 0.949671911 0.825059911 0.741617997 0.907967284 0.942760898 1 10.36939708 -8.357712497 3.425686465 1.007649962 0.815026676 0.435836683 0.078534623 0.132262842 2.917553003 0.010508418 0.025546071 4.39E-09 8.357712497 -0.192623286 QQVSWEQEFLVGS(ph)SPGGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 QQVSWEQEFLVGSSPGGSGR 20 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 0 QQVSWEQEFLVGS(0.5)S(0.5)PGGS(0.001)GR 108.23 0.00041849 8359800 1899.6 2103.9 2592.8 1963.3 2284.5 2139.7 2261.5 2412.9 2497.1 2322.4 TRUE FALSE FALSE 1876.446945 2133.518759 2637.926596 2190.305984 2167.91344 2002.980076 2453.591754 2482.713455 2273.753122 2262.063713 0.829528777 0.943173593 1.166159282 0.968277759 0.958378594 0.885465809 1.084669605 1.097543557 1.005167586 1 11.14342385 -9.980667175 24.93860674 0.917755023 1.020317025 0.149776432 0.088483628 289.7138572 373718.9748 0.015804987 0.020770317 1.05E-10 9.980667175 0.102562003 QQVSWEQEFLVGSS(ph)PGGSGR ddPTM_HeLa_Romidepsin_16h_R1 1 QQVSWEQEFLVGSSPGGSGR 20 0 Q9BUA3 Q9BUA3 C11orf84 Uncharacterized protein C11orf84 1 0 QQVSWEQEFLVGS(0.065)S(0.934)PGGS(0.001)GR 174.72 7.06E-11 8408300 1186.7 1258.4 1148.7 1044.4 1149.1 1449.7 872.08 1412.1 1221.5 1181.1 TRUE FALSE FALSE 1172.236044 1276.115788 1168.692642 1165.158442 1090.457139 1357.068849 946.1544534 1452.956886 1112.245981 1150.414852 1.018968107 1.109265746 1.015887999 1.01281589 0.94788166 1.179634326 0.822446313 1.26298516 0.966821646 1 10.16793849 -7.223089989 23.27608811 1.014511795 1.262986754 0.420327091 0.089488584 5756.910654 3493982.296 0.010370936 3.353336133 5.98E-08 7.223089989 0.248474958 QREEEIEAQEK ddPTM_HeLa_Romidepsin_16h_R1 1 QREEEIEAQEK 11 1 S4R3J5;O75937 S4R3J5 DNAJC8 DnaJ homolog subfamily C member 8 0 0 187.58 2.20E-08 3405100 1848.8 1798.4 1567.7 2381.6 1671.9 2028 1465.1 1813 1796.3 1911.4 FALSE FALSE TRUE 1826.266114 1823.717922 1594.985161 2656.971798 1586.576704 1898.417345 1589.545557 1865.456295 1635.634429 1861.741552 0.980945025 0.979576311 0.856716744 1.427143201 0.852200297 1.019699723 0.853794962 1.001995305 0.878550746 1 10.8624371 QRELEIEER ddPTM_HeLa_Romidepsin_16h_R1 1 QRELEIEER 9 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 0 125.74 0.011909 4527400 1226.7 1067.4 1194.7 1369.4 1312.8 1344.5 868.51 1174 1482.2 1408.3 FALSE FALSE TRUE 1211.748509 1082.426885 1215.493252 1527.736471 1245.802917 1258.590789 942.2812177 1207.967838 1349.62832 1371.712163 0.88338395 0.789106428 0.886113928 1.113744204 0.908210156 0.917532718 0.686938006 0.880627781 0.983900527 1 10.42176207 -16.11728135 0.017897959 2.070405761 1.62E-06 0.168165874 0.10048785 4288.187209 6.631311997 485.017139 302.268645 7.63E-17 16.11728135 -2.070404142 QRNK(ac)QVAMGRK ddPTM_HeLa_Romidepsin_16h_R1 2 QRNKQVAMGRK 11 3 K7ENH6;K7EKA2;Q15438-3 K7ENH6 CYTH1 0 1 ; QRNK(1)QVAMGRK;QRNK(1)QVAMGRK 97.431 0.0080968 3802300 1465.42 1455.78 1626.61 2504.83 1325.55 1298.66 764.98 933.96 1538.95 1121.04 FALSE TRUE FALSE 1447.558897 1476.274509 1654.920465 2794.45023 1257.902237 1215.679817 829.9573821 960.9826591 1401.302458 1091.915219 1.325706311 1.352004701 1.5156126 2.55921905 1.152014566 1.113346344 0.760093245 0.880089078 1.283343645 1 10.09264513 -7.993603478 2.826434419 1.306450751 0.822406073 0.225118735 0.417548933 0.395507726 6.335501669 0.066532722 0.227196272 1.01E-08 7.993603478 -0.484044678 QRPDLGS(ph)AQK ddPTM_HeLa_Romidepsin_16h_R1 1 QRPDLGSAQK 10 1 A0A3B3ITP6;A0A3B3IS57;A0A3B3IT92;P33991;E5RFR3;A0A3B3IU45 A0A3B3ITP6 MCM4 DNA replication licensing factor MCM4 1 0 QRPDLGS(1)AQK 93.649 0.012315 5642100 2978.8 2607.3 2692.4 2980.2 3101.1 2915.9 2365.6 2353.6 3261.9 2883.7 TRUE FALSE FALSE 2942.49324 2644.005638 2739.260093 3324.784746 2942.839295 2729.583401 2566.534005 2421.697703 2970.147494 2808.781058 1.047605057 0.941335612 0.975248706 1.183710897 1.047728262 0.971803549 0.913753672 0.862188135 1.057450699 1 11.45572846 -7.793705587 2.27136904 1.026554957 0.872339169 0.479771356 0.061572089 0.221861753 2.190831692 0.008946951 0.04421778 1.61E-08 7.793705587 -0.154215788 QRS(ph)DDESPSTSSGSSDADQR ddPTM_HeLa_Romidepsin_16h_R1 1 QRSDDESPSTSSGSSDADQR 20 1 R4GMM6;R4GN77;R4GNG6;R4GND1;A0A1B0GX65;Q969T4 R4GMM6 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 0 QRS(0.927)DDES(0.07)PS(0.002)T(0.001)SSGSSDADQR 70.767 0.0016323 0 223.23 199.24 119.72 135.87 107.36 124.36 161.25 186.09 288.51 202.15 TRUE FALSE FALSE 220.5091869 202.0449059 121.8036764 151.5799287 101.8810186 116.4137974 174.946571 191.4742205 262.704943 196.8981139 1.119915181 1.026139367 0.618612713 0.769839414 0.51743014 0.591238763 0.888513189 0.9724533 1.334217672 1 7.621305481 -9.813912393 7.605092238 1.056641117 0.720269267 0.589836358 0.157319185 0.123383355 15.22583426 0.022480058 0.029681957 1.53E-10 9.813912393 -0.33637185 QRS(ph)DDESPSTSSGSSDADQRDPAAPEPEEQEER ddPTM_HeLa_Romidepsin_16h_R1 1 QRSDDESPSTSSGSSDADQRDPAAPEPEEQEER 33 2 R4GMM6;R4GN77;R4GNG6;R4GND1;A0A1B0GX65;Q969T4 R4GMM6 UBE2E3 Ubiquitin-conjugating enzyme E2 E3 1 0 QRS(0.563)DDES(0.055)PS(0.2)T(0.073)S(0.073)S(0.027)GS(0.004)S(0.004)DADQRDPAAPEPEEQEER 51.729 0.0037661 9808300 430.24 276.43 403.45 431.9 293.59 331.88 312.97 350.99 446.34 549.55 TRUE FALSE FALSE 424.9960694 280.3215888 410.471878 481.8383102 278.6070068 310.6739391 339.553664 361.1453419 406.4182325 535.2726118 0.7939806 0.523698733 0.766846405 0.900173668 0.520495539 0.580403204 0.634356506 0.674694229 0.759273356 1 9.064130026 -11.35138062 0.357557257 1.059404308 0.616090189 0.212133169 0.133754217 0.854970434 0.243460921 0.153885024 0.061969003 4.45E-12 11.35138062 -0.443314118 QRS(ph)PAPGSPDEEGGAEAPAAGIR ddPTM_HeLa_Romidepsin_16h_R1 2 QRSPAPGSPDEEGGAEAPAAGIR 23 1 O15061;H0YL34;A0A075B7B1;O15061-2 O15061 SYNM Synemin 1 0 QRS(0.953)PAPGS(0.047)PDEEGGAEAPAAGIR;QRS(1)PAPGSPDEEGGAEAPAAGIR ; 92.147 4.12E-05 14968500 1331.39 1369.66 1041.31 1537.58 1365.21 776.65 1057.86 1065.45 1347.5 1315.55 TRUE FALSE FALSE 1315.162507 1388.942109 1059.433564 1715.362234 1295.538239 727.0245715 1147.714602 1096.277115 1226.976225 1281.371821 1.02637071 1.083949316 0.826796365 1.338692022 1.011055665 0.567379865 0.895692088 0.855549573 0.957548937 1 10.32347345 -8.434567826 12.37930235 1.029656557 0.785537378 0.406191734 0.145024745 0.724899708 99.97512394 0.018973526 0.04243144 3.68E-09 8.434567826 -0.244119179 QRS(ph)PIALPVK ddPTM_HeLa_Romidepsin_16h_R1 1 QRSPIALPVK 10 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 0 QRS(1)PIALPVK 82.515 0.020412 67561000 7254.6 6489.1 9264.3 7143.2 8234.5 8336.7 6594.9 5978.6 7067.5 6789 TRUE FALSE FALSE 7166.178145 6580.45372 9425.541255 7969.130394 7814.262738 7804.011775 7155.070641 6151.581358 6435.365099 6612.620801 1.083712247 0.995135502 1.425386626 1.20513948 1.181719468 1.180169257 1.082032504 0.930278863 0.973194334 1 12.69100646 QRS(ph)PIALPVKQEPPQIDAVK ddPTM_HeLa_Romidepsin_16h_R1 1 QRSPIALPVKQEPPQIDAVK 20 2 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 0 QRS(1)PIALPVKQEPPQIDAVK 55.437 0.013219 29766000 2355.1 1768 2151.1 3075 2229 1701.7 1702.3 1608.8 2082.4 2111.1 TRUE FALSE FALSE 2326.395135 1792.88995 2188.538993 3430.545968 2115.245812 1592.966862 1846.89332 1655.34809 1896.144929 2056.253318 1.131375748 0.871920758 1.064333355 1.668347931 1.028689313 0.774693881 0.898183752 0.805031207 0.922135863 1 11.00580229 -8.370230654 5.705158873 1.095090186 0.835003984 0.268879439 0.207305957 0.247878762 11.02893701 0.029508569 0.066889853 4.26E-09 8.370230654 -0.260086202 QRYDENEDLS(ph)DVEEIVSVR ddPTM_HeLa_Romidepsin_16h_R1 1 QRYDENEDLSDVEEIVSVR 19 1 Q8NHM5-2;Q8NHM5-3;Q8NHM5;Q8NHM5-4;S4R3G4;F8WBN2;F6SRV7;F5H0A1 Q8NHM5-2 KDM2B Lysine-specific demethylase 2B 1 0 QRY(0.021)DENEDLS(0.978)DVEEIVS(0.001)VR 71.905 0.0054202 1453300 368.55 335.76 197.98 452.74 325.31 300.84 160.38 351.47 364.97 303.43 TRUE FALSE FALSE 364.0579708 340.4868381 201.4257589 505.087929 308.7082168 281.6172949 174.0026732 361.6392299 332.3261691 295.5468449 1.231811394 1.15205709 0.681535812 1.708994489 1.04453227 0.952868555 0.588748201 1.223627443 1.12444499 1 8.207243009 -8.267694821 4.16383549 1.125525918 0.883399602 0.108990635 0.278350529 0.322820357 13.71711762 0.037558191 0.093895797 5.40E-09 8.267694821 -0.242126316 QS(ph)AGPNSPTGGGGGGGSGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 QSAGPNSPTGGGGGGGSGGTR 21 0 H7BZ52;S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2 H7BZ52 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 0 QS(0.727)AGPNS(0.189)PT(0.084)GGGGGGGSGGTR 224.8 6.06E-42 6605100 783.69 593.36 677.93 716.06 703.76 816.84 698 700.48 733.59 585.58 TRUE FALSE FALSE 774.1380848 601.7133377 689.7290873 798.8542264 667.8445011 764.6465602 757.2881026 720.7472836 667.9758731 570.3665472 1.357264182 1.054959027 1.209273389 1.400597967 1.170904052 1.340623085 1.327721807 1.263656305 1.171134381 1 9.155745558 -12.45419079 0.978988534 0.985990192 1.27182034 0.250663159 0.10920296 0.399614297 0.628112334 0.086341305 0.017569832 3.51E-13 12.45419079 0.285830147 QS(ph)GDGQESTEPVENK ddPTM_HeLa_Romidepsin_16h_R1 2 QSGDGQESTEPVENK 15 0 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 0 QS(0.999)GDGQES(0.001)TEPVENK;QS(0.834)GDGQES(0.127)T(0.038)EPVENK ; 245.67 2.46E-57 16253800 4557.2 4090 4051.1 2022.6 4500.1 4627.7 4210.3 4300 4042.4 4567 TRUE FALSE FALSE 4501.655094 4147.579127 4121.607696 2256.462529 4270.443105 4332.004905 4567.922777 4424.413716 3680.83762 4448.348682 1.011983416 0.932386246 0.926547803 0.507258466 0.960006378 0.973845626 1.026880558 0.994619359 0.827461578 1 12.11905416 -10.07083388 2.887854252 1.005681806 0.893735834 0 0.148658681 0.455207485 7.445640491 0.024251295 0.030695958 8.50E-11 10.07083388 -0.111945972 QS(ph)HRRLS(ph)S(ph)T(ph)LPDRR ddPTM_HeLa_Romidepsin_16h_R1 1 QSHRRLSSTLPDRR 14 3 H7C3G8 H7C3G8 IRAK1 4 0 QS(1)HRRLS(1)S(1)T(1)LPDRR 49.5 0.0043266 0 96.366 130.72 58.415 0 0 0 146.61 170.44 127.51 135.52 TRUE FALSE FALSE 95.19145413 132.5602796 59.43168857 0 0 0 159.0630497 175.3714125 116.1051862 131.9991709 0.72115191 1.00425085 0.450242893 0 0 0 1.205030673 1.328579652 0.879590269 1 7.044385057 -9.75103888 24.53099084 0.874837171 0.461663104 0.16010127 0.447182739 251.818036 593944.7711 0.076408022 0.107358158 1.77E-10 9.75103888 -0.413174067 QS(ph)PASPPPLGGGAPVR ddPTM_HeLa_Romidepsin_16h_R1 3 QSPASPPPLGGGAPVR 16 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 QS(0.585)PAS(0.415)PPPLGGGAPVR;QS(0.996)PAS(0.004)PPPLGGGAPVR;QS(0.995)PAS(0.005)PPPLGGGAPVR ;; 160.93 0.00011795 40268000 3389.05 3953.11 3379.56 3256.24 4380.2 4967.5 3809.43 5035.1 4012.1 3425.94 TRUE FALSE FALSE 3347.742955 4008.761986 3438.379824 3632.74179 4156.662049 4650.092782 4133.002889 5180.782674 3653.247728 3336.933585 1.003239312 1.201331068 1.030401036 1.088646716 1.245653215 1.393522725 1.238563125 1.552557923 1.09479186 1 11.70430726 -6.595857445 0.330353015 0.984953857 2.170705715 0.745854945 0.086436885 2.969595885 0.164769276 0.02718417 1.536138387 2.54E-07 6.595857445 1.185751858 QS(ph)PLTYEDHGAPFAGHLPR ddPTM_HeLa_Romidepsin_16h_R1 1 QSPLTYEDHGAPFAGHLPR 19 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 QS(0.996)PLT(0.004)YEDHGAPFAGHLPR 125.37 0.00029286 4295100 1554.8 1844.1 1575.9 1117.6 1596.5 1424 1189.7 1008.9 1746.7 1576 TRUE FALSE FALSE 1535.8495 1870.061288 1603.327878 1246.82217 1515.024648 1333.010996 1290.753088 1038.09093 1590.470777 1535.055293 1.00051738 1.218237087 1.044475652 0.812232743 0.98695119 0.868379792 0.840851202 0.676256376 1.036099992 1 10.58407491 -7.01920045 0.602146457 1.015971762 0.380827641 0.618163048 0.088941619 2.359252353 0.477091019 0.016478847 1.106521494 9.57E-08 7.01920045 -0.635144121 QS(ph)PNSSSAAASVASR ddPTM_HeLa_Romidepsin_16h_R1 1 QSPNSSSAAASVASR 15 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 QS(0.987)PNS(0.004)S(0.003)S(0.004)AAAS(0.002)VASR 150.92 0.00047551 8167900 1241.5 1245.8 1226 755.42 784.2 706.38 614.85 421.72 1146.5 1150.6 TRUE FALSE FALSE 1226.36812 1263.338405 1247.338016 842.7652148 744.1793477 661.2445977 667.0753437 433.9218028 1043.954169 1120.707246 1.094280531 1.127268883 1.112991836 0.75199408 0.664026534 0.59002438 0.595227117 0.387185685 0.931513713 1 10.13019375 -8.949224502 1.826419117 1.058468478 0.542602348 0.883456642 0.084984764 0.075267381 0.504098568 0.012535341 0.025765238 1.12E-09 8.949224502 -0.515866131 QS(ph)PPISTSK ddPTM_HeLa_Romidepsin_16h_R1 1 QSPPISTSK 9 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 0 QS(0.997)PPIS(0.003)TSK 119.03 0.014023 11458000 3885.3 3834.2 4082.1 2143 2570.8 3013.4 2598.4 2474 3880 3970.9 TRUE FALSE FALSE 3837.944469 3888.177968 4153.147238 2390.783743 2439.602483 2820.853465 2819.108031 2545.581287 3532.963082 3867.735446 0.992297566 1.005285398 1.073792998 0.618135283 0.63075733 0.729329476 0.728878195 0.658158068 0.913444865 1 11.9172734 -9.260089497 24.9999922 1.002360838 0.676929996 0.914478065 0.049507034 20.50691239 379789.6027 0.006360455 0.010180542 5.49E-10 9.260089497 -0.325430842 QS(ph)PS(ph)FKLSLSSGT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 QSPSFKLSLSSGTK 14 1 Q6IN85-4;Q6IN85-2;Q6IN85 Q6IN85-4 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 3 0 QS(0.999)PS(0.999)FKLS(0.002)LS(0.185)S(0.144)GT(0.671)K 82.663 0.0025199 0 1579 1485.8 1518.1 1383.3 1347.5 1725 1480.8 1498.1 1999.6 1671.1 TRUE FALSE FALSE 1559.754541 1506.717131 1544.521894 1543.243655 1278.732047 1614.778067 1606.579115 1541.44516 1820.750768 1627.684581 0.958265845 0.925681271 0.948907369 0.948122058 0.785614155 0.99207063 0.987033442 0.947017117 1.118614005 1 10.66860544 -11.12226732 0.764547838 0.994726377 0.932671688 0.261044313 0.066879071 0.745931313 0.950655629 0.019953997 0.013185915 7.55E-12 11.12226732 -0.062054689 QSACNLEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QSACNLEKK 9 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 1 ; QSACNLEK(1)K;QSACNLEK(1)K 135.55 3.85E-07 853830 874.04 482.32 914.03 44.919 815.09 1003.56 1168.98 495.74 1210.56 894.75 FALSE TRUE FALSE 863.3868643 489.1101136 929.9383087 50.11274613 773.4929158 939.4357548 1268.273132 510.0834548 1102.284482 871.504266 0.990685758 0.561225151 1.067049635 0.057501435 0.887537728 1.077947397 1.455268989 0.585290829 1.264806754 1 9.767363916 -10.46308564 24.99242336 0.99589174 0.827595666 0.090158387 0.362301424 659.527668 275671.816 0.059655354 0.068205964 3.44E-11 10.46308564 -0.168296075 QSAGPNS(ph)PTGGGGGGGSGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 QSAGPNSPTGGGGGGGSGGTR 21 0 H7BZ52;S4R3H3;S4R393;S4R410;A7E2V4-5;A7E2V4;A7E2V4-3;A7E2V4-4;A7E2V4-2 H7BZ52 ZSWIM8 Zinc finger SWIM domain-containing protein 8 1 0 QSAGPNS(0.959)PT(0.04)GGGGGGGSGGTR 109.12 0.00025787 6600900 790.25 764.02 647.57 891.73 726.53 1028.1 753.34 1207.8 724.33 782.42 TRUE FALSE FALSE 780.618129 774.7758936 658.8406842 994.8360183 689.452463 962.407728 817.3286808 1242.745787 659.5441107 762.0926156 1.024308743 1.016642699 0.864515245 1.305400417 0.904683301 1.262848778 1.072479465 1.630701783 0.865438265 1 9.573822526 -4.046284812 0.857737613 1.017162197 200 0.624771666 0.139970515 261.6226379 0.725698258 0.017807509 101592.4956 8.99E-05 4.046284812 198.9828378 QSELS(ph)AEESPEK ddPTM_HeLa_Romidepsin_16h_R1 1 QSELSAEESPEK 12 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 1 0 QS(0.181)ELS(0.724)AEES(0.095)PEK 175.6 1.91E-05 19293000 6505.1 6167.1 6253.9 3885.8 5230.4 6095.6 5690.6 7255.6 7176.8 7511.4 TRUE FALSE FALSE 6425.813339 6253.920596 6362.746506 4335.094479 4963.473171 5706.110833 6173.959422 7465.529339 6534.889033 7316.252745 0.878292968 0.854798326 0.869672868 0.592529349 0.678417401 0.779922596 0.843869073 1.020403422 0.893201651 1 12.8368892 -10.86475962 0.746697259 0.979473139 0.789290682 0.197237705 0.111368829 0.510629262 0.626496088 0.037612394 0.029768861 1.37E-11 10.86475962 -0.190182457 QSELSAEES(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 1 QSELSAEESPEK 12 0 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 1 0 QSELS(0.001)AEES(0.999)PEK 120.21 0.0074547 18282000 2839 2818.4 2893.8 1954.6 2500.4 3150.1 2583.1 4514.7 3407.7 3162.7 TRUE FALSE FALSE 2804.397176 2858.077509 2944.165375 2180.600049 2372.795258 2948.818776 2802.50845 4645.325721 3102.906777 3080.532598 0.910361143 0.927786809 0.955732582 0.707864624 0.770254877 0.957243166 0.909748026 1.507961878 1.007263088 1 11.58896409 -7.260623116 24.45986002 0.923187874 1.507962128 0.791645669 0.092361561 18.62358907 557930.798 0.013795466 0.111282836 5.49E-08 7.260623116 0.584774253 QSELSAEES(ph)PEKLGTSQLHR ddPTM_HeLa_Romidepsin_16h_R1 1 QSELSAEESPEKLGTSQLHR 20 1 F8W9X7;Q567U6 F8W9X7 CCDC93 Coiled-coil domain-containing protein 93 1 0 QS(0.001)ELS(0.014)AEES(0.984)PEKLGTS(0.001)QLHR 48.771 0.027971 5636500 1304.4 1158 943.53 887.89 1195.7 1192.7 984.62 1264.4 1133 1340.4 TRUE FALSE FALSE 1288.501471 1174.302354 959.9517439 990.5520194 1134.678967 1116.490319 1068.253598 1300.983419 1031.661642 1305.576215 0.98692168 0.8994514 0.735270552 0.75870869 0.869102052 0.855170542 0.818223851 0.99648217 0.790196413 1 10.35047096 -10.12294377 3.602805631 0.993908706 0.835312472 0.014987528 0.092696913 0.135209866 3.19336634 0.011125699 0.013804865 7.53E-11 10.12294377 -0.158596234 QSESSFISGDINS(ph)T(ph)STLNQGLT(ph)SHGLR ddPTM_HeLa_Romidepsin_16h_R1 1 QSESSFISGDINSTSTLNQGLTSHGLR 27 0 O95490-4;A0A6I8PLG0 O95490-4 3 0 QS(0.092)ES(0.092)S(0.094)FIS(0.096)GDINS(0.8)T(0.8)S(0.015)T(0.015)LNQGLT(0.827)S(0.169)HGLR 57.147 0.001385 0 647.26 663.87 541.72 456 380.88 518.5 508.6 425.89 567.46 554.49 TRUE FALSE FALSE 639.3709462 673.2159793 551.1484094 508.7248655 361.4422723 485.3695234 551.8004713 438.2124552 516.7049564 540.0842699 1.183835527 1.246501735 1.02048595 0.94193609 0.669233104 0.898692205 1.021693284 0.811377927 0.95671173 1 9.07704072 -9.271622143 3.067119006 1.101431757 0.862732912 0.475026074 0.114496417 0.175505215 3.368628286 0.018554343 0.030656281 5.35E-10 9.271622143 -0.238698845 QSETVDQNSDS(ph)DEMLAILK ddPTM_HeLa_Romidepsin_16h_R1 1 QSETVDQNSDSDEMLAILK 19 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1 P46100-4 ATRX Transcriptional regulator ATRX 1 0 QSETVDQNS(0.129)DS(0.871)DEMLAILK 78.021 0.0030333 5630300 3271.9 3023.8 2893.7 2746.1 2743.7 2512.5 2415 2594.8 3331.1 3179.3 TRUE FALSE FALSE 3232.020824 3066.369136 2944.063635 3063.617003 2603.678751 2351.959359 2620.13004 2669.876444 3033.158073 3096.701328 1.043697949 0.990204999 0.950709585 0.989316269 0.840791047 0.759504747 0.846103567 0.862167888 0.979480341 1 11.59651653 -8.777325495 3.355001835 1.01228482 0.820183882 0.834501669 0.035551423 0.065099826 1.529428625 0.005690488 0.011349253 1.67E-09 8.777325495 -0.192100939 QSFDDNDS(ph)EELEDKDSK ddPTM_HeLa_Romidepsin_16h_R1 3 QSFDDNDSEELEDKDSK 17 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 QSFDDNDS(0.971)EELEDKDS(0.028)K;QSFDDNDS(0.988)EELEDKDS(0.012)K;QS(0.004)FDDNDS(0.976)EELEDKDS(0.021)K ;; 74.703 0.0093079 1322767000 5673.1 4863.12 5204.52 5176.44 5388.56 5951.13 5328.19 5664.8 5956.8 6352.05 TRUE FALSE FALSE 5603.954075 4931.583131 5295.102487 5774.964349 5113.561676 5570.871999 5780.766326 5828.70205 5424.008889 6187.022825 0.905759399 0.797085007 0.855840141 0.933399554 0.826497949 0.900412388 0.93433732 0.942085105 0.876675106 1 12.59502964 -11.65574847 0.922789462 0.991825791 0.88597388 0 0.058245284 0.354585489 0.608504913 0.020161931 0.009808992 2.21E-12 11.65574847 -0.105851911 QSFTMVADT(ph)PENLR ddPTM_HeLa_Romidepsin_16h_R1 1 QSFTMVADTPENLR 14 0 C9J9W2;Q14847;Q14847-2;F6S2S5 C9J9W2 LASP1 LIM and SH3 domain protein 1 1 0 QSFTMVADT(1)PENLR 115.09 0.011933 50341000 3287.4 2824.3 2816.3 2176.1 3306.7 4088 2921.2 3442.7 3000.1 2908.1 TRUE FALSE FALSE 3247.331904 2864.06057 2865.31652 2427.710921 3137.94676 3826.789993 3169.326655 3542.309093 2731.763542 2832.547143 1.146435254 1.011125473 1.011568873 0.857076969 1.107818017 1.351006638 1.118896349 1.250573747 0.964419445 1 11.46788425 -8.51140528 24.7933762 1.045254759 1.228262623 0.553099564 0.091681581 359.1370582 776069.9184 0.014038196 0.029794846 3.08E-09 8.51140528 0.183007864 QSGLSSLVNGKS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 1 QSGLSSLVNGKSPIR 15 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 1 0 QS(0.045)GLS(0.047)S(0.044)LVNGKS(0.864)PIR 76.573 0.013924 56936000 3406.3 3460.4 3387.8 2961.6 2741.8 2325.7 1751.7 2035 3471.3 2945 TRUE FALSE FALSE 3364.782705 3509.115602 3446.763238 3304.034127 2601.875715 2177.095276 1900.489354 2093.879514 3160.818234 2868.488475 1.17301594 1.223332648 1.201595637 1.151838034 0.907054617 0.758969504 0.662540349 0.729959187 1.101910731 1 11.48607501 -8.460307592 2.3932698 1.109648023 0.704682896 0.886987573 0.067788965 0.09979792 1.119733255 0.013849762 0.0348207 3.46E-09 8.460307592 -0.404965126 QSHAASAAPQAS(ph)SPPDYTMAWAEYYR ddPTM_HeLa_Romidepsin_16h_R1 1 QSHAASAAPQASSPPDYTMAWAEYYR 26 0 Q96I24 Q96I24 FUBP3 Far upstream element-binding protein 3 1 0 QSHAASAAPQAS(0.585)S(0.409)PPDY(0.003)T(0.002)MAWAEYYR 73.839 8.18E-05 15929000 1166.1 1315.9 1095.4 1317.1 1543.8 1333.4 1070.8 1210.1 1416.9 1199 TRUE FALSE FALSE 1151.887125 1334.425275 1114.464978 1469.389299 1465.014125 1248.200043 1161.753725 1245.112334 1290.168915 1167.849807 0.986331562 1.142634324 0.954287932 1.258200575 1.254454225 1.068801858 0.994780081 1.066157931 1.104738732 1 10.18963903 -10.27127108 23.97112587 0.993545455 1.105710594 0.074430079 0.098671143 426.7890658 1040572.356 0.016187942 0.018645453 5.35E-11 10.27127108 0.112165139 QSHS(ph)ESPSLQSK ddPTM_HeLa_Romidepsin_16h_R1 1 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QS(0.325)HS(0.494)ES(0.144)PS(0.038)LQSK 196.37 1.22E-10 12773000 2635.7 2418.6 3135 1810.3 2791.3 2441.9 2515.6 1798.4 3217.9 2951.9 TRUE FALSE FALSE 2603.575075 2452.649114 3189.56336 2019.615404 2648.849545 2285.870471 2729.275001 1850.433867 2930.082965 2875.209212 0.905525436 0.853033269 1.109332617 0.702423808 0.921271932 0.795027527 0.949243968 0.643582338 1.019085134 1 11.48945122 -4 0.168557455 1.002040768 0.029343563 0.338117376 0.111517668 55.00834429 0.574814783 0.155754341 13.53360953 1.00E-04 4 -0.972697205 QSHSES(ph)PSLQSK ddPTM_HeLa_Romidepsin_16h_R1 4 QSHSESPSLQSK 12 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QSHS(0.017)ES(0.551)PS(0.432)LQSK;QSHSES(0.596)PS(0.404)LQSK;QSHS(0.001)ES(0.762)PS(0.237)LQSK;QSHS(0.011)ES(0.964)PS(0.024)LQSK ;;; 191.63 4.27E-10 563700000 33301.4 29391.7 29244.4 24838.9 31948.2 31793.3 30438.9 20658.8 36738.2 33147.3 TRUE FALSE FALSE 32895.50973 29805.47712 29753.38651 27710.89049 30317.76414 29761.81074 33024.37941 21256.52978 33452.24338 32286.12837 1.018874402 0.923166655 0.92155325 0.85829091 0.939033748 0.921814174 1.022865889 0.658379647 1.036118143 1 14.97862683 -10.11895099 2.80756315 1.009160459 0.896256668 0.300390584 0.088467784 0.260386951 3.952058656 0.013817924 0.017229678 7.60E-11 10.11895099 -0.112903791 QSHSGSIS(ph)PYPK ddPTM_HeLa_Romidepsin_16h_R1 5 QSHSGSISPYPK 12 0 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 QSHS(0.001)GS(0.059)IS(0.939)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK;QSHSGSIS(1)PYPK ;;;; 214.48 3.57E-21 387184000 36069.8 33562.9 31617.1 19295.3 34666.4 33881.2 28101.6 27221.9 44500.7 40359.4 TRUE FALSE FALSE 35630.1674 34035.39939 32167.38236 21526.31337 32897.24425 31716.30067 30488.5492 28009.52273 40520.44594 39310.85697 0.906369643 0.865801512 0.818282399 0.547592066 0.83684882 0.806807664 0.775575796 0.712513664 1.030769845 1 15.26264019 -10.1723314 1.115643803 0.968098361 0.746295154 0.629532169 0.080187191 0.228472574 0.55253414 0.016393716 0.020319831 6.72E-11 10.1723314 -0.221803208 QSNAS(ph)SDVEVEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QSNAS(0.5)S(0.5)DVEVEEK 291.13 1.83E-111 415360000 11977 12245 12917 6802.9 11331 11308 9934.8 10395 12074 11936 TRUE FALSE FALSE 11831.01972 12417.38543 13141.81497 7589.483307 10752.73679 10585.45529 10778.66166 10695.76292 10994.0712 11625.901 1.017643253 1.068079406 1.130391095 0.652808183 0.924894921 0.91050623 0.927124845 0.919994323 0.945653262 1 13.50505491 -9.298394155 24.99953557 1.022297024 0.876028177 0.463135602 0.088386236 410.758938 277873.1588 0.012749312 0.019475168 5.03E-10 9.298394155 -0.146268847 QSNAS(ph)SDVEVEEKETSVSK ddPTM_HeLa_Romidepsin_16h_R1 1 QSNASSDVEVEEKETSVSK 19 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QS(0.193)NAS(0.402)S(0.402)DVEVEEKET(0.001)S(0.001)VSK 53.96 0.021484 5974400 819.01 877 883.78 707.21 944.63 1174.7 849.8 1101.9 1130 1079 TRUE FALSE FALSE 809.0275911 889.346429 899.1618202 788.9809477 896.4220062 1099.640461 921.9819908 1133.781738 1028.92997 1050.967424 0.769793214 0.846216931 0.855556318 0.750718747 0.852949373 1.046312603 0.877269808 1.078798174 0.979031268 1 10.03750224 -6.112312778 0.848709398 0.874546915 2.150856246 0.295295161 0.090467207 15.62535177 1.866824285 0.016830768 29.38847954 7.72E-07 6.112312778 1.276309331 QSNASS(ph)DVEVEEK ddPTM_HeLa_Romidepsin_16h_R1 1 QSNASSDVEVEEK 13 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QSNAS(0.07)S(0.93)DVEVEEK 276.1 2.52E-94 237250000 41390 41008 40949 24596 36361 38348 32671 35308 39597 38251 TRUE FALSE FALSE 40885.52276 41585.3117 41661.70017 27439.90525 34505.36249 35897.68656 35446.07392 36329.58127 36055.34515 37257.23351 1.097384827 1.11616746 1.118217759 0.736498732 0.926138611 0.963509182 0.951387706 0.975101419 0.967740805 1 15.18523293 -9.304881346 24.99991845 1.05846023 0.916607632 0.483315037 0.07708753 321.6351915 185093.3047 0.011960367 0.018269829 4.96E-10 9.304881346 -0.141852598 QSNVAAPGDAT(ph)PPAEKK ddPTM_HeLa_Romidepsin_16h_R1 2 QSNVAAPGDATPPAEKK 17 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 0 QSNVAAPGDAT(1)PPAEKK;QS(0.003)NVAAPGDAT(0.997)PPAEKK ; 70.767 0.012717 24774000 5758.5 5548.3 5661 7076.2 6819.6 7010.6 6527.2 6784.9 6509.1 5557.8 TRUE FALSE FALSE 5688.313187 5626.409113 5759.52733 7894.383539 6471.570365 6562.645286 7081.620205 6981.210377 5926.909794 5413.407555 1.050782364 1.039347039 1.063937506 1.458302088 1.195470745 1.2122947 1.308163136 1.289614777 1.094857487 1 12.40232129 -9.415793249 7.253566021 1.026994585 1.283342193 0.744028778 0.070833717 0.088458415 5.324861598 0.01004262 0.015354988 3.84E-10 9.415793249 0.256347608 QSNVAAPGDATPPAEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QSNVAAPGDATPPAEKK 17 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 1 ; QSNVAAPGDATPPAEK(1)K;QSNVAAPGDATPPAEK(1)K 165.24 3.42E-11 1936440 1899.68 2030.2 1256.52 1736.68 1810.85 1431.77 2124.52 1513.9 2539.79 2225.37 FALSE TRUE FALSE 1876.525969 2058.781209 1278.389204 1937.483113 1718.435567 1340.284518 2304.976676 1557.702308 2312.624821 2167.554567 0.865734131 0.949817477 0.589784093 0.893856673 0.792799219 0.618339459 1.063399608 0.718645026 1.066928075 1 11.0818526 -11.22619183 0.585830251 0.994212831 0.797861477 0.295010018 0.137655625 0.793651291 0.605180931 0.068353581 0.036088503 5.94E-12 11.22619183 -0.196351354 NLQAPSK(ac)LTNSSSTGTVGK ddPTM_HeLa_Romidepsin_16h_R1 2 NLQAPSKLTNSSSTGTVGK 19 1 Q6ZU65 Q6ZU65 UBN2 Ubinuclein-2 0 1 ; NLQAPSK(1)LTNSSSTGTVGK;NLQAPSK(1)LTNSSSTGTVGK 252.1 2.06E-65 5274900 693.72 648.4 725.87 999.34 2327.33 2330.73 2375.69 2747.3 757.71 761.78 FALSE TRUE FALSE 685.2646738 657.5281922 738.5034629 1114.888393 2208.557666 2181.803875 2577.481049 2826.788791 689.9385199 741.9888458 0.92355118 0.886169915 0.995302648 1.502567591 2.976537556 2.940480693 3.473746356 3.809745668 0.929850258 1 9.535253689 -8.730919905 1.551754429 0.945088435 3.49718373 0.970888436 0.19494971 0.041863243 0.20296191 0.029570996 0.073231812 1.86E-09 8.730919905 2.552095294 up QSPSPSEVSQS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 2 QSPSPSEVSQSPGR 14 0 A0A5F9ZH11;P55201-3;P55201;P55201-2;C9JHC0;A0A5F9ZHX4;A0A5F9ZHW9;P55201-4 A0A5F9ZH11 BRPF1 Peregrin 1 0 QSPSPS(0.002)EVS(0.006)QS(0.992)PGR;QSPSPSEVS(0.005)QS(0.995)PGR ; 138.81 0.0011064 8099900 1551.2 1149.01 1280.39 849.55 1269.01 930.95 878.34 1044 1330.17 1589.11 TRUE FALSE FALSE 1532.293378 1165.185793 1302.674651 947.7789683 1204.247684 871.4652995 952.9461777 1074.206493 1211.196264 1547.824693 0.989965714 0.752789252 0.841616403 0.61232966 0.77802589 0.563025841 0.615668029 0.694010438 0.782515145 1 10.59602637 -9.860795763 0.962952021 1.003264002 0.643129266 0.516125419 0.09928767 0.131489605 0.242267118 0.013208515 0.019549868 1.38E-10 9.860795763 -0.360134736 QSQESLPGAVS(ph)PLSGR ddPTM_HeLa_Romidepsin_16h_R1 2 QSQESLPGAVSPLSGR 16 0 Q69YU3 Q69YU3 ANKRD34A Ankyrin repeat domain-containing protein 34A 1 0 QSQESLPGAVS(0.988)PLS(0.012)GR;QSQESLPGAVS(0.994)PLS(0.006)GR ; 208.07 3.07E-19 16447700 4486 4321.2 4221 5692.6 4321.6 3327.8 2647.3 2941.2 4506.2 4475.2 TRUE FALSE FALSE 4431.322907 4382.033967 4294.464734 6350.805196 4101.052626 3115.16432 2872.161596 3026.298982 4103.154186 4358.933659 1.0166071 1.005299532 0.985209932 1.456963031 0.940838505 0.714662017 0.658913813 0.694275072 0.941320632 1 12.08975953 -8.312459205 4.072227656 1.038950195 0.682424212 0.588612991 0.139520259 0.118729459 4.150343618 0.019596144 0.047194291 4.87E-09 8.312459205 -0.356525983 QSS(ph)FEIPDDVPLPAGWEMAK ddPTM_HeLa_Romidepsin_16h_R1 2 QSSFEIPDDVPLPAGWEMAK 20 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 QS(0.239)S(0.761)FEIPDDVPLPAGWEMAK;QS(0.206)S(0.794)FEIPDDVPLPAGWEMAK ; 82.831 0.0011187 13994100 6169.7 5239.7 5319.7 5568.2 3559.6 3334.78 2694.13 2819.8 6226.9 5803.8 TRUE FALSE FALSE 6094.501323 5313.464634 5412.287147 6212.021483 3377.940329 3121.698321 2922.969335 2901.386464 5669.950468 5653.016439 1.078097223 0.939934403 0.957415781 1.098886152 0.597546525 0.552218157 0.517063654 0.513245715 1.002995574 1 12.46480518 -8.708127109 5.650514133 1.026947242 0.536820865 0.955016587 0.049752779 0.029765351 2.02128038 0.007990251 0.016003762 1.96E-09 8.708127109 -0.490126377 QSS(ph)GASSSSFSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 QSSGASSSSFSSSR 14 0 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1 A0A2R8Y4A4 DDX3X ATP-dependent RNA helicase DDX3X 1 0 QS(0.226)S(0.761)GAS(0.002)S(0.006)S(0.005)S(0.001)FSSSR;QS(0.235)S(0.763)GASS(0.001)SSFSSSR ; 183.75 1.56E-07 8459900 1629.7 2062.3 1793.4 17738.6 1533.62 1033.65 1292.83 1279.04 1904.95 1801.47 TRUE FALSE FALSE 1609.83659 2091.333114 1824.613375 19789.62039 1455.353649 967.603101 1402.642948 1316.047004 1734.566501 1754.66755 0.917459601 1.191868576 1.039862722 11.27827342 0.829418455 0.551445259 0.799378177 0.750026411 0.988544241 1 10.776982 -8.558903019 24.99946247 1.807671426 0.706850213 0.045994244 3.046496374 632.5954921 438994.7138 0.459079772 0.918161727 2.76E-09 8.558903019 -1.100821213 QSS(ph)LTFQSSDPEQMR ddPTM_HeLa_Romidepsin_16h_R1 2 QSSLTFQSSDPEQMR 15 0 A0A0X1KG75;A0A590PXD8;A0A0D9SG04;Q53SF7;Q53SF7-3;Q53SF7-2 A0A0X1KG75 COBLL1 Cordon-bleu protein-like 1 1 0 QS(0.223)S(0.776)LT(0.001)FQSSDPEQMR;QS(0.032)S(0.795)LT(0.171)FQS(0.001)S(0.001)DPEQMR ; 152.94 0.00065258 13437000 3378.4 5117.6 2477.1 3481.9 3893.3 3209.2 2044.2 3022 3491 3788.8 TRUE FALSE FALSE 3337.222761 5189.645707 2520.212886 3884.493661 3694.610373 3004.142477 2217.834297 3109.436802 3178.756217 3690.36643 0.904306612 1.406268403 0.682916706 1.052603782 1.001150006 0.814049915 0.600979426 0.842582129 0.861366013 1 11.84954836 -8.097226775 3.98864492 0.977491285 0.718182344 0.267846857 0.180663284 0.210739787 5.950658882 0.02320333 0.064653105 7.99E-09 8.097226775 -0.25930894 QSS(ph)PAMPHK ddPTM_HeLa_Romidepsin_16h_R1 3 QSSPAMPHK 9 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 0 QS(0.098)S(0.902)PAMPHK;QS(0.093)S(0.907)PAMPHK;QS(0.025)S(0.975)PAMPHK ;; 81.92 0.017351 7712800 3151.95 2845.16 3063.03 3807.1 3055.04 3296.39 3326.3 2132.74 3555.4 3383.95 TRUE FALSE FALSE 3113.532821 2885.214237 3116.340752 4247.294815 2899.129909 3085.761318 3608.835839 2194.447467 3237.396119 3296.034491 0.944629927 0.875359237 0.945481839 1.288607515 0.879581181 0.936204195 1.094902328 0.665784133 0.982209418 1 11.68651562 -7.248420189 24.54280315 0.983149691 0.665783869 0.418085006 0.115555052 1240.768873 2338953.618 0.0150696 0.36630723 5.64E-08 7.248420189 -0.317365822 QSS(ph)PSTNAALPGPPAQLMDSSAVPGTALGTEPR ddPTM_HeLa_Romidepsin_16h_R1 1 QSSPSTNAALPGPPAQLMDSSAVPGTALGTEPR 33 0 H0Y760;Q9Y4B4 H0Y760 RAD54L2 Helicase ARIP4 1 0 QS(0.198)S(0.452)PS(0.173)T(0.173)NAALPGPPAQLMDS(0.004)S(0.001)AVPGTALGTEPR 53.395 0.0019701 5083100 470.48 325.18 523.16 483.81 467.09 404.77 307 530.34 559.88 584.71 TRUE FALSE FALSE 464.7456088 329.7578926 532.2653803 539.7503886 443.2526543 378.9065033 333.0765723 545.6845512 509.8029306 569.5191499 0.816031575 0.57901107 0.934587328 0.947730008 0.778292801 0.665309504 0.584838231 0.95814961 0.895146249 1 9.153600543 -11.99325008 0.493455809 1.037242519 0.767942996 0.159057662 0.137698347 1.406258444 0.543064429 0.180686976 0.038792004 1.02E-12 11.99325008 -0.269299523 QSS(ph)SSDTDLSLTPK ddPTM_HeLa_Romidepsin_16h_R1 1 QSSSSDTDLSLTPK 14 0 Q86YS7;Q86YS7-3;H0YFE9 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 QS(0.079)S(0.877)S(0.033)S(0.01)DT(0.001)DLSLTPK 172.42 3.62E-05 5003000 2206.9 2600.1 1616 1657.2 2266.4 1880.8 1375.7 2340.5 2404.8 2021.4 TRUE FALSE FALSE 2180.001454 2636.704276 1644.125802 1848.813261 2150.737151 1760.62295 1492.551924 2408.218675 2189.708665 1968.883737 1.107227112 1.339187392 0.835054794 0.939015965 1.092363714 0.894223929 0.758070117 1.223139097 1.112157424 1 10.94316221 QSS(ph)TPSAPELGQQPDVNISEWK ddPTM_HeLa_Romidepsin_16h_R1 1 QSSTPSAPELGQQPDVNISEWK 22 0 I3L213;Q93100-4;Q93100-2;Q93100-3;Q93100 I3L213 PHKB Phosphorylase b kinase regulatory subunit beta 1 0 QS(0.324)S(0.447)T(0.155)PS(0.074)APELGQQPDVNISEWK 75.005 0.0011709 5955300 2149.6 2073.7 1721.9 1754.2 2039.7 2174.3 1673.5 2045.1 2162.5 2110 TRUE FALSE FALSE 2123.399848 2102.893603 1751.868947 1957.028858 1935.606498 2035.369247 1815.647048 2104.271742 1969.080584 2055.181896 1.033193146 1.023215321 0.852415521 0.952241192 0.941817608 0.990359662 0.883448347 1.023885889 0.95810526 1 11.00505037 QSSGASSSS(ph)FSSSR ddPTM_HeLa_Romidepsin_16h_R1 3 QSSGASSSSFSSSR 14 0 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A0J9YVQ7;A0A2R8YDT5;A0A2R8Y7T2;A0A087WVZ1 A0A2R8Y4A4 DDX3X ATP-dependent RNA helicase DDX3X 1 0 QSSGAS(0.002)S(0.003)S(0.026)S(0.969)FSSSR;QSSGAS(0.051)S(0.249)S(0.118)S(0.571)FS(0.011)SSR;QSSGAS(0.013)S(0.02)S(0.174)S(0.681)FS(0.111)S(0.001)SR ;; 178.47 3.89E-07 24274800 7256.9 8374 7734 15315.2 5380.2 5333 4610.2 4942.7 8694.7 7711.1 TRUE FALSE FALSE 7168.450112 8491.889392 7868.607026 17086.01548 5105.628318 4992.238511 5001.790273 5085.709226 7917.024256 7510.76451 0.954423495 1.130629163 1.047643954 2.274870349 0.679774783 0.664677811 0.665949554 0.677122711 1.054090332 1 12.87474405 -8.585832147 25 1.093438854 0.669373303 0.31241537 0.378015776 74.44435085 29562.70333 0.056080862 0.112161734 2.60E-09 8.585832147 -0.424065551 QSSGPSSS(ph)PAAAAAPEKPGPK ddPTM_HeLa_Romidepsin_16h_R1 2 QSSGPSSSPAAAAAPEKPGPK 21 1 Q9UDT6-2;Q9UDT6 Q9UDT6-2 CLIP2 CAP-Gly domain-containing linker protein 2 1 0 QS(0.073)S(0.217)GPS(0.051)S(0.135)S(0.524)PAAAAAPEKPGPK;QS(0.002)S(0.002)GPS(0.016)S(0.183)S(0.796)PAAAAAPEKPGPK ; 86.32 0.00063634 7067000 3856.1 3737.6 3359.3 4016.1 6079.6 8904.5 6951.1 7578.4 3377 3690.2 TRUE FALSE FALSE 3809.10037 3790.218031 3417.767207 4480.460378 5769.335326 8335.531188 7541.52626 7797.669047 3074.952662 3594.328072 1.059753115 1.054499744 0.950877922 1.24653629 1.605122073 2.319079122 2.098174154 2.169437205 0.85550139 1 11.81150638 -8.58847972 2.013896206 1.028365932 2.194335914 0.964782597 0.100539994 0.031619751 0.256851584 0.011748677 0.02880878 2.58E-09 8.58847972 1.165969982 up QSSGS(ph)ATNVASTPDNR ddPTM_HeLa_Romidepsin_16h_R1 2 QSSGSATNVASTPDNR 16 0 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 QS(0.003)S(0.01)GS(0.962)AT(0.024)NVAS(0.002)TPDNR;QS(0.01)S(0.136)GS(0.569)AT(0.01)NVAS(0.229)T(0.047)PDNR ; 174.65 3.28E-06 7851700 1346.96 1415.32 1066.65 1450.42 1362.06 1264.53 881.97 1099.48 1297.65 1208.74 TRUE FALSE FALSE 1330.542733 1435.244912 1085.214596 1618.124385 1292.548996 1183.730614 956.8845098 1131.291719 1181.584934 1177.336761 1.13012927 1.219060646 0.921753768 1.374393835 1.097858352 1.005430777 0.812753446 0.960890509 1.003608291 1 10.20131133 -7.981475318 4.418352683 1.089512713 0.887643566 0.32747958 0.12430786 0.177301568 8.459820602 0.017163346 0.052498233 1.04E-08 7.981475318 -0.201869147 QSSLAEPVS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 QSSLAEPVSPSK 12 0 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 0 QSSLAEPVS(0.5)PS(0.5)K 131.24 0.0035626 12410000 4618.2 4696.9 4433.9 3480.7 4182.4 4097.9 3677.6 4092.1 4575.8 4717.3 TRUE FALSE FALSE 4561.911602 4763.023081 4511.07017 3883.154911 3968.956521 3836.057415 3989.975252 4210.498457 4166.528988 4594.743866 0.992854386 1.036624286 0.981789258 0.845129788 0.86380365 0.83487949 0.868378166 0.916372834 0.906803319 1 12.16576873 -9.317509273 5.345064366 0.99971511 0.864021608 0.703154175 0.037657015 0.047234682 2.956291599 0.003557272 0.005512967 4.81E-10 9.317509273 -0.135693502 QSSLAEPVS(ph)PSKK ddPTM_HeLa_Romidepsin_16h_R1 1 QSSLAEPVSPSKK 13 1 E7EMD6;O43572 E7EMD6 AKAP10 "A-kinase anchor protein 10, mitochondrial" 1 0 QS(0.001)S(0.004)LAEPVS(0.624)PS(0.371)KK 78.848 0.01272 17293000 3694.2 3253.5 3449.7 3077.4 3218.1 3538.3 3252.7 3260.5 3720.1 3826.7 TRUE FALSE FALSE 3649.173669 3299.302858 3509.740581 3433.223468 3053.868349 3312.214049 3528.984257 3354.837423 3387.364939 3727.281782 0.979044216 0.885176665 0.941635429 0.921106497 0.819328542 0.888640635 0.946798354 0.900076146 0.90880302 1 11.86390818 -10.33831497 4.549665227 0.990897187 0.900975058 0.241814691 0.042584375 0.114471097 4.369502146 0.00608168 0.006952492 4.59E-11 10.33831497 -0.089922129 QSSSSTTSQGGVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 QSSSSTTSQGGVKR 14 1 A0A0A0MSN9;P18615-4;P18615;P18615-3;A2ABK4;A0A0G2JI50;E9PD43;A0A0A0MT02 A0A0A0MSN9 NELFE Negative elongation factor E 0 1 QSSSSTTSQGGVK(1)R 106.79 0.0051236 341140 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 QSSTPGSLFLS(ph)PPAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 QSSTPGSLFLSPPAPAPK 18 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 QSSTPGS(0.01)LFLS(0.99)PPAPAPK;QSSTPGS(0.003)LFLS(0.997)PPAPAPK ; 171.25 2.47E-07 31828000 10269.7 8779.5 9611.8 9707.7 12523.4 13644.1 11457.5 12165 10609.2 10103.1 TRUE FALSE FALSE 10144.52895 8903.098031 9779.089347 10830.14995 11884.28417 12772.28604 12430.69976 12516.97508 9660.286581 9840.620006 1.030883109 0.904729379 0.993747278 1.10055565 1.207676362 1.297914769 1.263202904 1.271970168 0.981674587 1 13.2645335 -8.819789449 2.052889371 1.003837604 1.275146093 0.929604561 0.03607765 0.063775401 0.547235863 0.005899656 0.012584914 1.51E-09 8.819789449 0.271308488 QSSVTQVTEQS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 QSSVTQVTEQSPK 13 0 Q14966-3;Q14966;C9JWN0;Q14966-2;Q14966-6;Q14966-4 Q14966-3 ZNF638 Zinc finger protein 638 1 0 QSSVTQVT(0.001)EQS(0.999)PK;QSSVTQVT(0.003)EQS(0.997)PK;QSSVTQVTEQS(1)PK ;; 228.11 7.69E-32 25735800 7877.3 7959 7421.1 7469.5 7421.5 8458.4 8048.1 7861.7 8387.2 8371.6 TRUE FALSE FALSE 7781.288438 8071.047011 7550.261132 8333.158735 7042.753162 7917.935538 8731.705413 8089.165886 7637.027826 8154.104625 0.954278709 0.989814012 0.92594607 1.02195877 0.863706499 0.971036785 1.070835587 0.992036067 0.936586931 1 12.99331075 -7.795807144 20.06442395 0.96956818 1.031435347 0.259145682 0.046495934 20.35904943 11886.07809 0.006107864 0.018329754 1.60E-08 7.795807144 0.061867167 QSTLYSFFPKSPALS(ph)DANK ddPTM_HeLa_Romidepsin_16h_R1 1 QSTLYSFFPKSPALSDANK 19 1 A0A087WWJ1;P52701-2;P52701;F8WAX8;P52701-3;F8W7G9 A0A087WWJ1 MSH6 DNA mismatch repair protein Msh6 1 0 QSTLYSFFPKS(0.176)PALS(0.824)DANK 99.392 0.0005093 21683000 1811.5 1541.7 1766.6 3399.8 1936.1 1805.1 1244.3 1493 1744.7 1581 TRUE FALSE FALSE 1789.420741 1563.404093 1797.346932 3792.900873 1837.293592 1689.759936 1349.990811 1536.197599 1588.649662 1539.925392 1.162017816 1.015246648 1.167164943 2.463041971 1.193105589 1.097299872 0.876659881 0.997579238 1.031640669 1 10.58864474 -9.512573357 24.95078772 1.074868353 1.334016536 0.088781385 0.411287971 1055.891835 2556464.451 0.066253386 0.097193283 3.07E-10 9.512573357 0.259148184 QSVQPSK(ac)FNSYGR ddPTM_HeLa_Romidepsin_16h_R1 1 QSVQPSKFNSYGR 13 1 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 0 1 QSVQPSK(1)FNSYGR 161.87 0.00027889 1184700 0 119.22 67.183 53.534 264.57 534.15 350.11 492.04 219.2 246.58 FALSE TRUE FALSE 0 120.8983823 68.35229193 59.72385297 251.0680057 500.0195389 379.8483347 506.2764011 199.594203 240.1738161 0 0.503378696 0.284595103 0.248669293 1.045359606 2.081906958 1.581555979 2.10795835 0.831040645 1 7.907935066 -8.463565788 3.520740731 0.478726872 1.883280923 0.818868451 0.303336023 0.097549948 2.387178958 0.058496969 0.135245693 3.44E-09 8.463565788 1.404554051 QSWRRASMKET(ph)NR ddPTM_HeLa_Romidepsin_16h_R1 1 QSWRRASMKETNR 13 3 Q5JW53;Q9H410-4;Q9H410;Q5JW54;Q9H410-2 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 0 QSWRRAS(0.001)MKET(0.999)NR 44.829 0.028694 51672000 4046.9 3566.9 4016.6 2864.6 3520.9 3424.2 2844.8 3364.7 4072 4186 TRUE FALSE FALSE 3997.574826 3617.114912 4086.507238 3195.81853 3341.215335 3205.404671 3086.437241 3462.052286 3707.790121 4077.247117 0.980459293 0.887146354 1.00227117 0.783817718 0.819478251 0.786168849 0.756990477 0.849115147 0.909385675 1 11.99337968 -9.260121695 24.99704682 0.981901506 0.797186044 0.74274297 0.04482298 32.7498875 621276.6133 0.005907474 0.009455778 5.49E-10 9.260121695 -0.184715462 QT(ph)DQFSFS(ph)INES(ph)TEKDMNS(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 QTDQFSFSINESTEKDMNSEK 21 1 O95405-3;O95405-2;O95405 O95405-3 ZFYVE9 Zinc finger FYVE domain-containing protein 9 4 0 QT(0.926)DQFS(0.091)FS(0.956)INES(0.879)T(0.294)EKDMNS(0.856)EK 44.089 0.0040797 0 1298.4 1390.3 1476.1 388.46 1400.1 1502.9 1462.9 1509.7 1810.7 1459.3 TRUE FALSE FALSE 1282.574601 1409.87268 1501.790901 433.375573 1328.647673 1406.86954 1587.158689 1553.380788 1648.746457 1421.387176 0.902340068 0.991899114 1.056567083 0.304896217 0.934754228 0.989786291 1.116626572 1.092862532 1.159955912 1 10.47308387 -12.32104355 0.861298035 1.004119694 0.917341021 0.047186394 0.224267344 3.308658308 4.045696503 0.194844635 0.042635199 4.77E-13 12.32104355 -0.086778673 QT(ph)IETEETSPS(ph)T(ph)ES(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 QTIETEETSPSTESLK 16 0 H7C120 H7C120 ARHGAP4 4 0 QT(0.628)IET(0.372)EET(0.057)S(0.31)PS(0.772)T(0.96)ES(0.901)LK 69.935 0.013909 6764100 1634.5 2824.9 1816 2213.2 1628.4 784.34 812.7 1504.7 3161.4 5531.5 TRUE FALSE FALSE 1614.578085 2864.669016 1847.606718 2469.100597 1545.296672 734.2232053 881.7307177 1548.23612 2878.636466 5387.790833 0.299673491 0.531696405 0.34292473 0.458276996 0.286814526 0.136275373 0.16365348 0.287360101 0.534288831 1 12.39547813 -16.52287875 0.202334139 4.398137428 0.177059096 0.432413517 0.17873421 12.21350637 0.149103216 16.33013564 0.104763699 3.00E-17 16.52287875 -4.221078332 QTAEETGLT(ph)PLETSR ddPTM_HeLa_Romidepsin_16h_R1 2 QTAEETGLTPLETSR 15 0 Q5T8C6;Q13042-4;Q13042-3;Q13042-2;Q13042 Q5T8C6 CDC16 Cell division cycle protein 16 homolog 1 0 QTAEET(0.026)GLT(0.974)PLETSR;QT(0.038)AEET(0.167)GLT(0.744)PLET(0.05)S(0.001)R ; 182.91 5.36E-08 20311000 2986.9 3263.9 3567.4 2546 4051.7 4758 3088.2 3924.7 3272.3 3273.7 TRUE FALSE FALSE 2950.494514 3309.84927 3629.489101 2840.380499 3844.92663 4453.979156 3350.511631 4038.255002 2979.617292 3188.648802 0.925311847 1.038009977 1.138253011 0.89077872 1.205816905 1.396823367 1.0507622 1.266447092 0.934445114 1 11.63872949 -8.696549323 7.379174393 0.979969653 1.231100981 0.575974925 0.101733549 0.121553484 11.62559459 0.014238275 0.028509502 2.01E-09 8.696549323 0.251131329 QTAEETGLTPLETS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 QTAEETGLTPLETSR 15 0 Q5T8C6;Q13042-4;Q13042-3;Q13042-2;Q13042 Q5T8C6 CDC16 Cell division cycle protein 16 homolog 1 0 QTAEETGLT(0.002)PLET(0.245)S(0.754)R 113.14 0.0040198 2518700 1844.6 1775.6 1833.6 1479.3 1370 1364.4 883.33 991.34 1832.1 1571.5 TRUE FALSE FALSE 1822.117306 1800.596943 1865.513039 1650.343626 1300.083788 1277.219243 958.3600282 1020.022859 1668.232387 1530.672203 1.190403341 1.176343922 1.21875411 1.078182267 0.849354803 0.834417219 0.626104025 0.66638883 1.089869133 1 10.57994964 -8.408948128 1.453926056 1.11058372 0.657987065 0.871366301 0.073790619 0.141339708 0.568049217 0.01478178 0.049203452 3.90E-09 8.408948128 -0.452596656 QTDPSTPQQES(ph)SKPLGGIQPSSQTIQPK ddPTM_HeLa_Romidepsin_16h_R1 2 QTDPSTPQQESSKPLGGIQPSSQTIQPK 28 1 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YF61 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 QTDPST(0.001)PQQES(0.499)S(0.499)KPLGGIQPSSQTIQPK;QT(0.008)DPS(0.07)T(0.161)PQQES(0.38)S(0.38)KPLGGIQPS(0.001)S(0.001)QTIQPK ; 120.27 2.03E-10 41119000 8238.5 7949.1 7924.7 8650.1 6635.1 7066.8 6052.5 6581.5 9011.8 8429.5 TRUE FALSE FALSE 8138.085993 8061.007638 8062.626079 9650.265262 6296.486088 6615.254287 6566.599199 6771.925319 8205.762038 8210.500375 0.991180272 0.981792494 0.981989612 1.175356534 0.766882139 0.805706593 0.799780634 0.824788382 0.999422893 1 13.00325443 -8.733095431 24.99988272 1.004634257 0.799782785 0.784291206 0.056703774 74.12083003 65375.62329 0.00772844 0.015454511 1.85E-09 8.733095431 -0.204851473 QTESTSFLEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 QTESTSFLEKK 11 1 P60900-3;G3V5Z7;P60900-2;P60900;G3V295 P60900-3 PSMA6 Proteasome subunit alpha type-6;Proteasome subunit alpha type 0 1 ; QTESTSFLEK(1)K;QTESTSFLEK(1)K 167.84 0.0008602 2573900 822.8 839.29 860.52 993.06 1231.38 1026.6 1146.85 1151.49 1188.33 981.48 FALSE TRUE FALSE 812.7713971 851.1055467 875.4969896 1107.88227 1168.538084 961.0035732 1244.26341 1184.806546 1082.042789 955.9810081 0.850196176 0.890295455 0.915810024 1.15889569 1.222344454 1.005253834 1.301556621 1.239362013 1.131866407 1 9.900838147 -9.233027634 5.090598741 0.922708705 1.186107457 0.53798125 0.1032392 0.087753528 6.374113235 0.013544135 0.022278004 5.85E-10 9.233027634 0.263398752 QTGGEEGDGASGY(ph)DAY(ph)WKNLSSDK ddPTM_HeLa_Romidepsin_16h_R1 1 QTGGEEGDGASGYDAYWKNLSSDK 24 1 Q9Y3S2 Q9Y3S2 ZNF330 Zinc finger protein 330 2 0 QTGGEEGDGAS(0.08)GY(0.627)DAY(0.656)WKNLS(0.318)S(0.318)DK 44.963 0.016332 6113200 1468 1529.4 1488.9 1297.7 1759.4 1520.9 1040.5 1414.6 2070.2 1876.3 TRUE FALSE FALSE 1450.107451 1550.930933 1514.81368 1447.74618 1669.611253 1423.719398 1128.880044 1455.529219 1885.036127 1827.553456 0.79346924 0.848637794 0.828875169 0.7921772 0.913577246 0.779030235 0.61770015 0.796435921 1.031453346 1 10.83569789 -16.52287875 0.16212233 1.814287115 0.728945879 0.643631828 0.067367447 33.15307344 0.357013363 8.570246062 0.13046567 3.00E-17 16.52287875 -1.085341236 QTGIET(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 1 QTGIETPNK 9 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 QT(0.465)GIET(0.535)PNK 139.76 0.013323 29808000 7317.2 6328.5 6576 4239.2 4128.1 4361.1 3272.1 2864.6 8159.9 6841.5 TRUE FALSE FALSE 7228.015152 6417.592789 6690.452521 4729.35625 3917.427653 4082.439785 3550.032092 2947.482681 7430.058107 6663.756844 1.084675705 0.963059268 1.0040061 0.709713208 0.587870738 0.612633366 0.53273734 0.442315461 1.114995382 1 12.70212004 -9.085732299 1.466954029 1.038814856 0.527961134 0.947425346 0.055021539 0.059258369 0.251657631 0.008708654 0.017758826 8.21E-10 9.085732299 -0.510853723 QTIET(ph)EETSPS(ph)T(ph)ES(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 QTIETEETSPSTESLK 16 0 H7C120 H7C120 ARHGAP4 4 0 QT(0.044)IET(0.953)EET(0.003)S(0.003)PS(0.998)T(1)ES(1)LK 74.519 0.011271 6435600 4118.9 6432.6 3960.6 3997 4020.4 1902.4 2519.9 3733 6865.4 12998 TRUE FALSE FALSE 4068.697263 6523.158312 4029.532582 4459.151946 3815.223986 1780.84278 2733.940243 3841.008465 6251.341429 12660.31009 0.321374219 0.515244751 0.318280718 0.352215066 0.301353123 0.140663441 0.215945757 0.303389762 0.493774749 1 13.62802512 -13.79509822 0.268749742 1.958922862 0.210355137 0.376152842 0.179638172 2.077258436 0.098629179 1.247415544 0.048065507 1.60E-14 13.79509822 -1.748567725 QTPS(ph)PDVVLR ddPTM_HeLa_Romidepsin_16h_R1 4 QTPSPDVVLR 10 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 QT(0.045)PS(0.955)PDVVLR;QT(0.173)PS(0.827)PDVVLR;QT(0.3)PS(0.7)PDVVLR;QT(0.078)PS(0.922)PDVVLR ;;; 140.45 0.0047662 349648000 11864.9 11481.3 10642.1 9535.7 10308 9020.5 8228.6 9120.6 12525.7 11888.2 TRUE FALSE FALSE 11720.28604 11642.93404 10827.32129 10638.2625 9781.944296 8444.119162 8927.537079 9384.490171 11405.37002 11579.34285 1.01217195 1.005491779 0.935054901 0.918727655 0.844775427 0.729239929 0.770988233 0.810451015 0.984975587 1 13.49926576 -8.916360703 1.20080859 1.005400997 0.76690523 0.9269745 0.026937863 0.074378033 0.212648098 0.004275972 0.010533338 1.21E-09 8.916360703 -0.238495767 QTQS(ph)ASSTLQK ddPTM_HeLa_Romidepsin_16h_R1 1 QTQSASSTLQK 11 0 C9J840;E7EX83;A0A0D9SG62;H7C0P6;E7ENQ1;G3XAA2;H7C360;G5E948;A0A0D9SEY1;O95819-4;O95819-2;O95819;O95819-5;O95819-3 C9J840 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 0 QT(0.027)QS(0.958)AS(0.007)S(0.007)TLQK 121.45 0.0093797 6834900 2265 2818.4 3048.7 2100.4 2443.5 2546.2 2868 1374 2672.3 2748.8 TRUE FALSE FALSE 2237.393309 2858.077509 3101.761345 2343.258131 2318.799077 2383.506037 3111.607848 1413.754522 2433.282795 2677.38578 0.835663402 1.067488119 1.158503705 0.875203771 0.866068347 0.89023631 1.162181361 0.528035419 0.908827862 1 11.38660931 -7.241790574 24.59661238 0.949308103 0.528034934 0.560349731 0.116652297 2375.472267 2973591.661 0.016827722 0.856049271 5.73E-08 7.241790574 -0.421273169 QTQSESSNYDS(ph)ELEK ddPTM_HeLa_Romidepsin_16h_R1 4 QTQSESSNYDSELEK 15 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1 P46100-4 ATRX Transcriptional regulator ATRX 1 0 QTQSESSNYDS(1)ELEK;QTQSES(0.02)S(0.308)NYDS(0.672)ELEK;QTQSES(0.001)S(0.002)NYDS(0.997)ELEK;QTQSES(0.024)S(0.039)NYDS(0.937)ELEK ;;; 268.08 1.75E-84 28812500 8345.7 8205.9 9179.1 5437.5 6874.56 6573.01 5740.28 6992.9 8714 8739.9 TRUE FALSE FALSE 8243.979398 8321.422876 9338.858385 6066.209334 6523.725551 6153.015874 6227.85924 7195.228529 7934.598015 8512.836138 0.968417489 0.977514748 1.097032556 0.712595572 0.766339848 0.722792707 0.731584532 0.845221077 0.932074562 1 13.05542415 -9.25174814 24.99532207 0.991651625 0.753128785 0.840518877 0.052102642 175.0993786 451610.4041 0.007018564 0.011544188 5.60E-10 9.25174814 -0.238522839 QTQSESSNYDS(ph)ELEKEIK ddPTM_HeLa_Romidepsin_16h_R1 2 QTQSESSNYDSELEKEIK 18 1 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1 P46100-4 ATRX Transcriptional regulator ATRX 1 0 QT(0.001)QS(0.027)ES(0.091)S(0.217)NY(0.029)DS(0.636)ELEKEIK;QTQS(0.001)ES(0.018)S(0.013)NY(0.01)DS(0.958)ELEKEIK ; 69.619 0.0088972 29863000 2802.6 2535.9 2345 3115.9 2648.5 1994.98 1908.38 1877.65 2881.3 2316.7 TRUE FALSE FALSE 2768.440833 2571.600467 2385.813741 3476.175019 2513.337162 1867.507217 2070.47775 1931.97684 2623.589312 2256.5118 1.22686743 1.139635284 1.057301691 1.540508239 1.113815209 0.827607999 0.917556801 0.856178479 1.162674758 1 11.13987861 -8.298119823 7.178669749 1.142123804 0.872167652 0.493304175 0.140951555 0.177925069 29.25708698 0.022359227 0.050873615 5.03E-09 8.298119823 -0.269956152 QTS(ph)IETDR ddPTM_HeLa_Romidepsin_16h_R1 1 QTSIETDR 8 0 E9PFK9;Q9UJ41;Q9UJ41-4;Q9UJ41-3 E9PFK9 RABGEF1 Rab5 GDP/GTP exchange factor 1 0 QT(0.004)S(0.982)IET(0.014)DR 103.21 0.028296 17904000 2739.9 2451.3 2189.1 2558.8 2559.2 2471.4 2216.7 1621.6 2900.5 3046.2 TRUE FALSE FALSE 2706.505045 2485.809466 2227.200367 2854.660496 2428.594474 2313.485516 2404.986443 1668.518438 2641.072016 2967.059285 0.91218435 0.837802426 0.750642354 0.962117781 0.818519025 0.779723387 0.810562315 0.562347522 0.890131191 1 11.53481804 -5.227736132 0.172004865 1.02282269 2.92E-14 0.543425985 0.079291082 17.4331345 0.268868184 0.113538255 4.266781203 5.92E-06 5.227736132 -1.02282269 QTSGGPVDAS(ph)SEYQQELER ddPTM_HeLa_Romidepsin_16h_R1 2 QTSGGPVDASSEYQQELER 19 0 A8MUH2;P18859;P18859-2 A8MUH2 ATP5J "ATP synthase-coupling factor 6, mitochondrial" 1 0 QTSGGPVDAS(0.5)S(0.5)EYQQELER;QTSGGPVDAS(0.5)S(0.5)EYQQELER ; 184.97 5.18E-11 2529700 1438.74 1311.22 1291.84 1335.06 1537.38 1878.39 1285.2 1135.33 1127.32 1399.54 TRUE FALSE FALSE 1421.204083 1329.67939 1314.323933 1489.425919 1458.921762 1758.366941 1394.364856 1168.178982 1026.489676 1363.179749 1.042565432 0.975424841 0.964160401 1.092611536 1.070234327 1.289901014 1.022876739 0.856951538 0.753011242 1 10.41276009 -9.241265735 24.26962308 1.012735415 1.076707645 0.074330406 0.130075764 1160.844385 1396537.661 0.015219501 0.025214864 5.74E-10 9.241265735 0.063972231 QTVAVGVIK(ac)AVDKK ddPTM_HeLa_Romidepsin_16h_R1 1 QTVAVGVIKAVDKK 14 2 Q5VTE0;P68104;A0A087WVQ9 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1 0 1 QTVAVGVIK(0.999)AVDK(0.001)K 106.19 0.0090779 681590 401.98 275.68 49.622 193.34 342.59 196.87 63.205 278.35 184.9 290.77 FALSE TRUE FALSE 397.0805131 279.5610303 50.48565009 215.6948805 325.1063539 184.2906424 68.57363112 286.4036181 168.3620809 283.2157535 1.402042465 0.987095622 0.178258623 0.7615921 1.147910559 0.650707597 0.242125059 1.011255958 0.594465805 1 8.145757705 -9.991943093 24.9989985 1.190101595 0.664301591 0.111678499 0.348455957 144.7288238 449062.7478 0.049586429 0.065107435 1.02E-10 9.991943093 -0.525800005 QTVDK(ac)VMGIPK ddPTM_HeLa_Romidepsin_16h_R1 2 QTVDKVMGIPK 11 1 Q14676-3;Q14676 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 0 1 ; QTVDK(1)VMGIPK;QTVDK(1)VMGIPK 126.66 0.0031943 2213100 762.14 682.36 1062.25 945.39 1619.89 1546.05 1481.02 1300.36 994.07 867.67 FALSE TRUE FALSE 752.8507445 691.966282 1080.738016 1054.70044 1537.220969 1447.262395 1606.817802 1337.983865 905.1578895 845.1278083 0.890812889 0.818771167 1.278786481 1.247977442 1.818921296 1.712477545 1.901271957 1.583173399 1.071030773 1 9.723025726 -9.082528315 1.48156857 0.941680304 1.773945042 0.866279987 0.137568789 0.082659499 0.358131844 0.019901248 0.040524257 8.27E-10 9.082528315 0.832264737 QVAEQGGDLS(ph)PAANR ddPTM_HeLa_Romidepsin_16h_R1 2 QVAEQGGDLSPAANR 15 0 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 0 QVAEQGGDLS(1)PAANR;QVAEQGGDLS(1)PAANR ; 203.53 2.81E-18 311270000 6505.3 6955.5 6288.5 6655.6 6532.2 6607.7 5797.1 6689.5 7234.2 6448.8 TRUE FALSE FALSE 6426.010901 7053.419712 6397.948705 7425.151788 6198.837459 6185.489295 6289.505529 6883.050128 6587.155034 6281.259246 1.023045006 1.122930838 1.018577399 1.182111977 0.986878143 0.984753065 1.001312839 1.095807363 1.048699755 1 12.6168381 -10.49844222 15.15481647 1.010162924 1.053454173 0.043475798 0.061521804 5.260405682 3263.247741 0.010400777 0.011307404 3.17E-11 10.49844222 0.04329125 QVAGDAPVEQATAET(ph)ASPVHR ddPTM_HeLa_Romidepsin_16h_R1 1 QVAGDAPVEQATAETASPVHR 21 0 A0A087X055;Q92766;Q92766-2;Q92766-4 A0A087X055 RREB1 Ras-responsive element-binding protein 1 1 0 QVAGDAPVEQAT(0.061)AET(0.571)AS(0.368)PVHR 104.55 0.00027146 7350300 3124.1 2801.5 2830.7 1564.7 1686.7 1815.3 1731.5 1921.6 3511.9 3077.4 TRUE FALSE FALSE 3086.022268 2840.939591 2879.967146 1745.617976 1600.621405 1699.308189 1878.573567 1977.198464 3197.786868 2997.448704 1.029549651 0.947785891 0.960806149 0.582367923 0.533994594 0.566918188 0.626724175 0.659627123 1.066836228 1 11.54951935 -9.296793629 4.364982743 1.006815902 0.589157313 0.957768632 0.042797303 0.028775863 1.285182337 0.00656431 0.010399343 5.05E-10 9.296793629 -0.417658589 QVAGDAPVEQATAETAS(ph)PVHR ddPTM_HeLa_Romidepsin_16h_R1 1 QVAGDAPVEQATAETASPVHR 21 0 A0A087X055;Q92766;Q92766-2;Q92766-4 A0A087X055 RREB1 Ras-responsive element-binding protein 1 1 0 QVAGDAPVEQATAET(0.387)AS(0.613)PVHR 183.65 6.49E-14 6297700 1563.9 1393.8 1539.4 738.12 463.08 839.43 520.2 764.6 1932.7 1446.6 TRUE FALSE FALSE 1544.838585 1413.421953 1566.192611 823.4649074 439.4472996 785.7931321 564.385775 786.7224947 1759.834471 1409.017123 1.096394472 1.003126172 1.111549736 0.584425053 0.311882157 0.557688845 0.400552815 0.558348427 1.248980188 1 10.46047343 -9.169787291 4.22887646 1.047395975 0.459789787 0.902738616 0.099970072 0.038710524 1.240458573 0.011140283 0.01880221 6.76E-10 9.169787291 -0.587606188 QVAPEK(ac)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 QVAPEKPVK 9 1 P53999;D6RC37;D6R970 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 0 1 ; QVAPEK(1)PVK;QVAPEK(1)PVK 133.99 0.0080058 25861000 13389.8 13076.3 16746.6 14009.8 22497 25823 20757 20737 15566.8 13800.7 FALSE TRUE FALSE 13226.59997 13260.38849 17038.06755 15629.67899 21348.89414 24172.99364 22520.09906 21336.99238 14174.46642 13442.15582 0.98396419 0.986477814 1.267510046 1.162736037 1.588204632 1.798297383 1.675333879 1.587319226 1.054478657 1 13.71447691 -8.932727993 1.278921154 0.996230937 1.705932008 0.902065694 0.095026704 0.081445395 0.26501188 0.014680311 0.034645284 1.17E-09 8.932727993 0.709701071 QVCPDLLRK ddPTM_HeLa_Romidepsin_16h_R1 1 QVCPDLLRK 9 1 Q8IYW2 Q8IYW2 CFAP46 Cilia- and flagella-associated protein 46 0 0 97.431 0.021806 5089300 2631.1 2332.3 1760 3004.9 3683.6 3876.2 2315.3 3103.8 3875.3 3162.1 FALSE FALSE TRUE 2599.031141 2365.134181 1790.632062 3352.340676 3495.612147 3628.52333 2511.961524 3193.603556 3528.683462 3079.948186 0.843855476 0.767913626 0.581383826 1.088440608 1.134958102 1.178111809 0.815585644 1.036901715 1.145695722 1 11.58869037 QVDLESNPQNRS(ph)PESRPSVVYPSTK ddPTM_HeLa_Romidepsin_16h_R1 1 QVDLESNPQNRSPESRPSVVYPSTK 25 2 J3QS41;P42694 J3QS41 HELZ Probable helicase with zinc finger domain 1 0 QVDLES(0.058)NPQNRS(0.909)PES(0.029)RPS(0.001)VVY(0.002)PSTK 74.733 0.00042008 7409800 905.3 475.6 738.86 716.74 698.99 538.92 834.68 563.54 967.55 670.91 TRUE FALSE FALSE 894.2658554 482.2955093 751.7195484 799.6128512 663.317932 504.4847513 905.5776984 579.8451408 881.0099047 653.4796615 1.36846777 0.738042112 1.150333503 1.223623164 1.015055205 0.771997632 1.385777939 0.887319338 1.348182593 1 9.351998525 QVETEEAGVVT(ph)TATASVNLKVSPK ddPTM_HeLa_Romidepsin_16h_R1 2 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QVETEEAGVVT(0.482)T(0.482)AT(0.009)AS(0.027)VNLKVSPK;QVETEEAGVVT(0.951)T(0.035)AT(0.012)ASVNLKVS(0.001)PK ; 127.9 1.33E-06 56872000 2891.3 3001.9 3075.1 3031.6 3021.6 2761.6 1971.42 2147.37 3255.2 3079.9 TRUE FALSE FALSE 2856.059723 3044.160827 3128.620826 3382.127856 2867.396477 2585.142673 2138.872366 2209.500763 2964.046759 2999.883754 0.952056799 1.014759596 1.04291402 1.127419638 0.955835863 0.861747616 0.712985082 0.736528794 0.988053872 1 11.55069088 -8.029508778 2.328768991 0.995570501 0.721986609 0.847572429 0.048867318 0.097985256 1.033629381 0.008076752 0.029160102 9.34E-09 8.029508778 -0.273583892 QVETEEAGVVTT(ph)ATASVNLKVSPK ddPTM_HeLa_Romidepsin_16h_R1 2 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QVETEEAGVVT(0.011)T(0.831)AT(0.049)AS(0.007)VNLKVS(0.103)PK;QVETEEAGVVT(0.168)T(0.802)AT(0.03)AS(0.001)VNLKVSPK ; 120.31 8.23E-07 196569000 7548.9 6741.8 7472.5 7225.7 6332.6 5751.2 3997.5 5088.6 6883.1 6992.8 TRUE FALSE FALSE 7456.891103 6836.711237 7602.555728 8061.169432 6009.423792 5383.716881 4337.04755 5235.830613 6267.458297 6811.126048 1.094810322 1.003756382 1.116196599 1.183529621 0.882295196 0.790429783 0.636759255 0.768717327 0.920179461 1 12.73367762 -8.411271612 2.620230513 1.056606267 0.715225821 0.76457377 0.079634432 0.084232269 1.11760006 0.010274077 0.025921489 3.88E-09 8.411271612 -0.341380445 QVETEEAGVVTTAT(ph)ASVNLKVSPK ddPTM_HeLa_Romidepsin_16h_R1 1 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QVET(0.002)EEAGVVT(0.253)T(0.058)AT(0.265)AS(0.265)VNLKVS(0.157)PK 51.089 0.019661 70968000 1512.7 1541.2 1299.2 1607.9 955.67 1299.1 899.33 1287.4 1365.5 1355.2 TRUE FALSE FALSE 1494.262631 1562.897054 1321.812031 1793.812963 906.8985938 1216.091703 975.7190678 1324.648888 1243.36626 1319.991709 1.132024255 1.184020357 1.001379041 1.358957751 0.687048705 0.92128738 0.739185755 1.003528188 0.941950053 1 10.36631315 -8.742983001 24.99997967 1.087393945 0.836687413 0.470863865 0.137170413 160.7272791 217711.136 0.017954733 0.035857466 1.81E-09 8.742983001 -0.250706532 QVETEEAGVVTTATAS(ph)VNLKVSPK ddPTM_HeLa_Romidepsin_16h_R1 5 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QVETEEAGVVT(0.173)T(0.173)AT(0.089)AS(0.514)VNLKVS(0.052)PK;QVETEEAGVVT(0.014)T(0.13)AT(0.053)AS(0.614)VNLKVS(0.189)PK;QVETEEAGVVT(0.032)T(0.032)AT(0.237)AS(0.659)VNLKVS(0.039)PK;QVETEEAGVVT(0.027)T(0.205)AT(0.205)AS(0.496)VNLKVS(0.067)PK;QVETEEAGVVT(0.025)T(0.239)AT(0.065)AS(0.484)VNLKVS(0.187)PK ;;;; 99.971 6.14E-07 152004000 11557.69 11930.54 10599.18 11449.28 10595.38 9793.53 7584.71 9254.6 11647.43 11787.32 TRUE FALSE FALSE 11416.82043 12098.49846 10783.65428 12773.09962 10054.65822 9167.75504 8228.955078 9522.36725 10605.65469 11481.08373 0.99440268 1.053776694 0.939254041 1.112534315 0.875758636 0.798509553 0.716740272 0.829396203 0.923750313 1 13.48697121 -8.510249814 3.888392983 1.004498959 0.779356075 0.753829821 0.057290872 0.063237692 2.125354849 0.006710027 0.014904775 3.09E-09 8.510249814 -0.225142884 QVETEEAGVVTTATASVNLKVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 QVETEEAGVVTTATASVNLKVSPK 24 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 QVETEEAGVVTT(0.006)AT(0.074)AS(0.334)VNLKVS(0.586)PK;QVETEEAGVVT(0.002)T(0.004)AT(0.032)AS(0.417)VNLKVS(0.545)PK;QVETEEAGVVTTAT(0.001)AS(0.01)VNLKVS(0.988)PK ;; 112.6 1.56E-09 29792000 5480.6 5597.9 5130.4 5401.1 4662.8 4911.4 3710.4 4201.5 5280.6 5136.3 TRUE FALSE FALSE 5413.800339 5676.707383 5219.69246 6025.600595 4424.839917 4597.577391 4025.561283 4323.063774 4808.28991 5002.858186 1.082141476 1.134692844 1.043342079 1.204431621 0.884462392 0.918990149 0.804652288 0.864118792 0.961108577 1 12.28853684 -8.628452881 8.93487243 1.058338116 0.864299617 0.674391776 0.068846092 0.122141166 9.43880722 0.009707579 0.019437429 2.35E-09 8.628452881 -0.194038499 QVHPDTGIS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 QVHPDTGISSK 11 0 P06899;P23527;Q96A08;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99879;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 1 0 QVHPDT(0.107)GIS(0.576)S(0.318)K 126.71 0.0070544 32851000 3418.2 3064.3 3188.6 2848.6 3099.4 3165.9 3528.8 3788.9 4362.8 3522.7 TRUE FALSE FALSE 3376.537664 3107.439296 3244.096245 3177.968535 2941.226053 2963.609207 3828.536184 3898.525844 3972.580241 3431.179746 0.984074841 0.905647482 0.945475459 0.926202872 0.857205472 0.863728929 1.115807526 1.136205659 1.157788439 1 11.74448899 -7.668067038 8.1060936 0.961559466 1.129692935 0.414544418 0.081059812 0.14330291 10.91469977 0.008775217 0.033076161 2.15E-08 7.668067038 0.168133469 QVHPDTGISS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 QVHPDTGISSK 11 0 P06899;P23527;Q96A08;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99879;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 1 0 QVHPDT(0.001)GIS(0.184)S(0.815)K 188.13 1.83E-08 33987000 5652.3 5877.1 5573.1 4683.8 5748.8 5932 6657.1 6061.2 7223.3 6296.3 TRUE FALSE FALSE 5583.407594 5959.837968 5670.097468 5225.362994 5455.417284 5552.964345 7222.553908 6236.571259 6577.229957 6132.721218 0.910429057 0.9718097 0.924564686 0.852046393 0.889558989 0.905464988 1.177707848 1.016933762 1.072481485 1 12.58231165 -7.771818801 24.99995239 0.94028637 1.097320817 0.451241427 0.069043389 106.9362359 257569.6441 0.00854368 0.026034945 1.69E-08 7.771818801 0.157034446 QVHPDTGISSK ddPTM_HeLa_Romidepsin_16h_R1 4 QVHPDTGISSK 11 0 P06899;P23527;Q96A08;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99879;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99879;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BA;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BM;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-A;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-M;Histone H2B type 1-L 0 0 ;;; ;;; 155.88 0.00093388 61256200 41562.3 33560.1 34207.1 36107.4 53280.8 54026.8 43983.2 38275.4 51873 44985.5 FALSE FALSE TRUE 41055.7227 34032.55997 34802.46023 40282.30748 50561.68196 50574.66184 47719.13191 39382.83831 47233.34896 43816.77022 0.936986512 0.776701701 0.794272605 0.919335389 1.15393448 1.154230711 1.089060916 0.898807423 1.077974226 1 15.41919553 -8.77582988 24.97163949 0.935576251 1.080813731 0.332166666 0.106692189 222.385759 385902.8331 0.016131773 0.029339226 1.68E-09 8.77582988 0.14523748 QVLQSTQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 QVLQSTQSPR 10 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 QVLQS(0.004)T(0.001)QS(0.995)PR;QVLQS(0.003)T(0.001)QS(0.996)PR;QVLQS(0.011)T(0.005)QS(0.984)PR ;; 151.55 0.0036453 268804000 9776.7 9067.1 10416.7 10826.7 11325.9 11098.4 8886.1 8764 9078.6 8571.3 TRUE FALSE FALSE 9657.53782 9194.746872 10597.99829 12078.534 10747.89706 10389.24806 9640.885112 9017.572513 8266.587278 8348.61639 1.156783037 1.101349786 1.2694317 1.44677075 1.287386623 1.244427528 1.15478837 1.080127783 0.990174526 1 13.02732141 -11.09238454 0.664569829 1.016934992 1.241408117 0.463797873 0.098281862 0.474178881 0.467188455 0.044920004 0.028424778 8.08E-12 11.09238454 0.224473125 QVQVALETAQR ddPTM_HeLa_Romidepsin_16h_R1 1 QVQVALETAQR 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 133.75 0.010107 1818000 770.72 674.24 841.97 677.78 712.64 865.71 812.39 626.93 662.75 620.14 FALSE FALSE TRUE 761.3261682 683.7319684 856.6241347 756.1481127 676.2713216 810.393925 881.3943863 645.0692304 603.4719801 604.0286734 1.260413953 1.131952834 1.418184554 1.251841421 1.119601356 1.341648105 1.459192957 1.067944717 0.999078366 1 9.238473226 -12.34540353 0.485055294 0.9297943 1.275196018 0.421679438 0.120203222 1.342671509 0.40620347 0.226979842 0.031411866 4.51E-13 12.34540353 0.345401718 QVS(ph)ASELHTSGILGPETLR ddPTM_HeLa_Romidepsin_16h_R1 5 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 QVS(0.845)AS(0.154)ELHT(0.001)SGILGPETLR;QVS(0.986)AS(0.014)ELHTSGILGPETLR;QVS(0.755)AS(0.242)ELHT(0.003)SGILGPETLR;QVS(0.601)AS(0.244)ELHT(0.141)S(0.014)GILGPET(0.001)LR;QVS(0.499)AS(0.499)ELHT(0.002)SGILGPETLR ;;;; 145.83 2.43E-05 449103000 6615.63 6734.08 6932.29 7688.62 11036.9 11713.7 11668.4 11646 8829.4 7934.97 TRUE FALSE FALSE 6534.996157 6828.882555 7052.943599 8577.61442 10473.64581 10965.23237 12659.5136 11982.95864 8039.67635 7728.818336 0.845536261 0.883561013 0.912551349 1.109822233 1.355141932 1.418746294 1.637962371 1.550425707 1.040220639 1 12.91603214 -8.666755399 1.327439429 0.917867551 1.57717204 0.938102023 0.068702087 0.073582002 0.256098041 0.011600975 0.032703024 2.15E-09 8.666755399 0.659304489 QVSAS(ph)ELHTSGILGPETLR ddPTM_HeLa_Romidepsin_16h_R1 1 QVSASELHTSGILGPETLR 19 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 QVS(0.285)AS(0.712)ELHT(0.003)SGILGPETLR 52.926 0.02679 22369000 845.65 818.36 687.94 823.46 1001.1 879.3 837.99 922.1 898.09 776.33 TRUE FALSE FALSE 835.3428925 829.8808936 699.9133071 918.6723197 950.0101314 823.1155678 909.1688497 948.7795087 817.7625811 756.1608347 1.104715894 1.097492564 0.925614334 1.214916559 1.256359875 1.088545624 1.202348506 1.254732413 1.08146646 1 9.562549317 -9.231740973 24.88680486 1.046629526 1.199886852 0.603038837 0.065436798 391.0018679 327653.8697 0.010373118 0.017200512 5.86E-10 9.231740973 0.153257326 QVSS(ph)PSFTNR ddPTM_HeLa_Romidepsin_16h_R1 1 QVSSPSFTNR 10 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 QVS(0.016)S(0.981)PS(0.003)FTNR 147.24 0.0039321 29132000 2067.4 1858 2305.2 1631 3147.9 4356 3282.6 3189.5 2037.4 1949.3 TRUE FALSE FALSE 2042.201734 1884.156973 2345.321039 1819.583894 2987.250917 4077.665658 3561.423962 3281.78315 1855.169841 1898.656905 1.075603353 0.992363058 1.235252685 0.958353186 1.573349513 2.147657983 1.875759624 1.728476136 0.977095881 1 10.89076351 -8.592695582 3.746860059 1.045192347 1.910894383 0.91193547 0.123669998 0.042124018 1.182779299 0.017036708 0.03613043 2.55E-09 8.592695582 0.865702036 QVSS(ph)PSFTNRR ddPTM_HeLa_Romidepsin_16h_R1 1 QVSSPSFTNRR 11 1 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 QVS(0.003)S(0.858)PS(0.043)FT(0.096)NRR 105.13 0.025894 4354400 3652.3 3420.5 2917 3401.5 3545 3910.4 3938.2 3566.1 3434.9 3159.6 TRUE FALSE FALSE 3607.784363 3468.653889 2967.769161 3794.797435 3364.085422 3660.53806 4272.71061 3669.279477 3127.673941 3077.513137 1.172305106 1.127096371 0.964340047 1.233072701 1.093118136 1.18944677 1.388364702 1.192287186 1.016299136 1 11.5875493 -4 0.095493321 0.924054249 1.906763645 0.440290737 0.089974755 102.3378705 0.702106831 0.898143032 13.22930401 1.00E-04 4 0.982709396 QVVES(ph)AYEVIK ddPTM_HeLa_Romidepsin_16h_R1 1 QVVESAYEVIK 11 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 1 0 QVVES(0.984)AY(0.016)EVIK 138.21 0.0034892 4769600 1722.9 1478 1699.1 1688.1 1820.6 1644.1 1493.9 1862.9 1832.8 1743.8 TRUE FALSE FALSE 1701.900632 1498.807323 1728.672123 1883.286065 1727.687988 1539.047316 1620.791829 1916.800072 1668.869778 1698.495825 1.002004602 0.88243215 1.017766484 1.108796405 1.017187068 0.906123697 0.954251288 1.128527986 0.98255748 1 10.73004196 -7.250451747 23.90870401 0.993800999 1.128528131 0.329080724 0.0601929 833.2274731 1813009.309 0.008318746 0.157494159 5.62E-08 7.250451747 0.134727132 QVVSVVQDEEVGLPFEASPES(ph)PPPASPDGVTEIR ddPTM_HeLa_Romidepsin_16h_R1 2 QVVSVVQDEEVGLPFEASPESPPPASPDGVTEIR 34 0 Q96TA1-2;Q96TA1 Q96TA1-2 FAM129B Niban-like protein 1 1 0 QVVSVVQDEEVGLPFEAS(0.003)PES(0.997)PPPASPDGVTEIR;QVVSVVQDEEVGLPFEAS(0.178)PES(0.822)PPPASPDGVTEIR ; 139.72 2.86E-16 5088000 3223.5 3015.9 2905.6 2953.9 3476.8 3623.4 3400.3 3915.9 3574 2864.4 TRUE FALSE FALSE 3184.210742 3058.357919 2956.170749 3295.443817 3299.365922 3391.876434 3689.121397 4029.200388 3254.332489 2789.982475 1.141301342 1.09619252 1.059566064 1.181170078 1.182575859 1.215733957 1.322274039 1.444166917 1.166434742 1 11.44604034 -4 0.281305378 1.041380571 4.07256943 0.820333703 0.051376151 11.70668732 0.149259299 0.02036251 17.7053549 1.00E-04 4 3.031188859 QWS(ph)S(ph)S(ph)APNLGKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 QWSSSAPNLGKSPK 14 1 Q02779 Q02779 MAP3K10 Mitogen-activated protein kinase kinase kinase 10 4 0 QWS(1)S(1)S(1)APNLGKS(1)PK 59.908 0.0041625 0 1141.3 511.08 809.39 620.85 600.55 585.04 922.09 749.34 1222.4 716.48 TRUE FALSE FALSE 1127.389397 518.2749977 823.4770934 692.6355982 569.9016925 547.6578321 1000.412302 771.0209706 1113.065482 697.8657463 1.615481778 0.742657166 1.17999357 0.99250551 0.816635142 0.784761016 1.433531173 1.104827074 1.594956463 1 9.446805711 -10.2546658 24.98926162 1.290644173 1.014313797 0.305413378 0.256910389 736.6260221 2717580.305 0.049257059 0.059605051 5.56E-11 10.2546658 -0.276330376 QWVT(ph)LVVDVNQCLEGK ddPTM_HeLa_Romidepsin_16h_R1 1 QWVTLVVDVNQCLEGK 16 0 Q13576;D6RDK8;E9PDT6;D6R939;E7EWC2;F5H7S7;Q13576-3;Q13576-2 Q13576 IQGAP2 Ras GTPase-activating-like protein IQGAP2 1 0 QWVT(1)LVVDVNQCLEGK 72.815 0.027269 8517000 1196.3 1102.1 881.75 1111.3 1550.2 1722 1251.3 1213.2 1303.7 1315.8 TRUE FALSE FALSE 1181.719035 1117.615393 897.0964889 1239.793735 1471.087509 1611.969758 1357.585391 1248.302028 1187.093807 1281.615326 0.922054388 0.872036538 0.699973284 0.967368062 1.147838575 1.257764108 1.059276807 0.974006788 0.926248136 1 10.32374759 -8.83610084 5.715168783 0.932114279 1.116335574 0.485651093 0.103545281 0.167427592 9.474253461 0.016892267 0.031137606 1.46E-09 8.83610084 0.184221295 QWYESHYALPLGR ddPTM_HeLa_Romidepsin_16h_R1 2 QWYESHYALPLGR 13 0 Q5JR95;P62241 Q5JR95 RPS8 40S ribosomal protein S8 0 0 ; ; 188.96 5.45E-11 81791000 14238.7 15184 13610.2 16229.7 15676.4 19467.8 10800 14886.9 12294.7 10950.2 FALSE FALSE TRUE 14065.15325 15397.76075 13847.07982 18106.25428 14876.37481 18223.87041 11717.35173 15317.62896 11195.03124 10665.71223 1.318726115 1.443669248 1.298279902 1.697613239 1.394784942 1.708640738 1.098600026 1.436156221 1.049628098 1 13.38069269 -11.46397106 0.584144433 0.998050458 1.449906521 0.484370046 0.167935393 0.489592743 0.347675316 0.103468011 0.043466638 3.44E-12 11.46397106 0.451856063 QYDPPAESQQSES(ph)PPRR ddPTM_HeLa_Romidepsin_16h_R1 1 QYDPPAESQQSESPPRR 17 1 Q6P597;Q6P597-3;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 0 QYDPPAES(0.027)QQS(0.25)ES(0.723)PPRR 72.801 0.008276 9801500 1705.6 1515.3 1539.3 1396.6 2907.4 4041.9 3537.4 4514.1 1872.6 1514 TRUE FALSE FALSE 1684.811491 1536.632433 1566.090871 1558.081463 2759.024529 3783.635635 3837.866668 4644.708361 1705.109966 1474.666062 1.14250374 1.042020613 1.061996957 1.056565621 1.870948685 2.565757586 2.602532714 3.149667902 1.156268534 1 10.52617258 -8.390125986 1.538437396 1.05609474 2.902232278 0.969249545 0.136204001 0.043972929 0.198274534 0.019579294 0.063860652 4.07E-09 8.390125986 1.846137538 up QYPK(ac)FNFVGK ddPTM_HeLa_Romidepsin_16h_R1 1 QYPKFNFVGK 10 1 Q07666-2;Q07666;Q5VWX1 Q07666-2 KHDRBS1;KHDRBS2 "KH domain-containing, RNA-binding, signal transduction-associated protein 1;KH domain-containing, RNA-binding, signal transduction-associated protein 2" 0 1 QYPK(1)FNFVGK 90.657 0.014505 0 0 0 0 124.66 0 0 0 65.864 0 0 FALSE TRUE FALSE 0 0 0 139.0737757 0 0 0 67.76967092 0 0 0 QYRRSQCSDGERSVLS(ph)EVNS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 QYRRSQCSDGERSVLSEVNSK 21 3 Q9HCS5 Q9HCS5 EPB41L4A Band 4.1-like protein 4A 2 0 QY(0.006)RRS(0.005)QCS(0.007)DGERS(0.06)VLS(0.935)EVNS(0.987)K 49.708 0.0043348 0 511.64 542.54 464.77 472.42 582.58 506.37 318.85 443.82 513.36 463.74 TRUE FALSE FALSE 505.4039349 550.1778924 472.8591269 527.0434232 552.8487687 474.0145912 345.933111 456.6612315 467.4437959 451.6919679 1.118912823 1.218037803 1.046861933 1.166820445 1.223950851 1.049420014 0.765860665 1.011001443 1.034872942 1 8.81919545 -7.91846854 7.769894467 1.089077752 0.890231596 0.471948408 0.091930174 0.173699853 14.31735094 0.013634942 0.04127 1.21E-08 7.91846854 -0.198846155 QYT(ph)SPEEIDAQLQAEK ddPTM_HeLa_Romidepsin_16h_R1 1 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 0 QYT(0.994)S(0.006)PEEIDAQLQAEK 327.7 6.67E-180 25425000 2946.3 2788.8 3047.9 2657 3712.9 3912.6 3810.2 4187.4 3252.2 2851.2 TRUE FALSE FALSE 2910.389362 2828.0608 3100.947421 2964.214842 3523.416858 3662.597487 4133.838293 4308.555812 2961.315087 2777.125413 1.047986291 1.018341047 1.116603307 1.067368016 1.268728031 1.318844828 1.488531369 1.551444451 1.066323859 1 11.43937661 -8.027214803 0.688278864 1.01888282 1.666387208 0.96279885 0.036789457 0.144442876 0.083143702 0.005663879 0.059692335 9.39E-09 8.027214803 0.647504388 QYTS(ph)PEEIDAQLQAEK ddPTM_HeLa_Romidepsin_16h_R1 1 QYTSPEEIDAQLQAEK 16 0 Q13442;F8WBW6 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 0 QYT(0.033)S(0.967)PEEIDAQLQAEK 157.37 0.00019645 24530000 3462.4 3231.4 3070.2 2858.2 4095 4594.3 3926.2 4537.2 3631.4 3357.8 TRUE FALSE FALSE 3420.198937 3276.891734 3123.635543 3188.678532 3886.016869 4300.739057 4259.69133 4668.476723 3306.598489 3270.563872 1.045752069 1.001934792 0.955075536 0.974962929 1.188179477 1.314983968 1.30243331 1.427422581 1.011017861 1 11.67532367 -8.471411243 2.302204766 1.011891567 1.351039355 0.935942586 0.041152411 0.057024443 0.593435238 0.006488412 0.016397324 3.38E-09 8.471411243 0.339147788 RAAEDDEDDDVDTK ddPTM_HeLa_Romidepsin_16h_R1 3 RAAEDDEDDDVDTK 14 1 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 0 ;; ;; 249.82 4.64E-55 43279200 17502.3 16159.1 16709.2 15776.1 17393.5 16086.7 15215.4 12166.3 18427.1 17041.4 FALSE FALSE TRUE 17288.97524 16386.58823 17000.01662 17600.20691 16505.84479 15058.81179 16507.7957 12518.3127 16778.93402 16598.66197 1.041588489 0.987223444 1.02417994 1.060338896 0.994408153 0.907230463 0.994525687 0.754176012 1.010860638 1 14.01877933 -6.454613038 0.923483064 1.018241525 1.21E-12 0.782169668 0.039118377 2.542729583 0.554343152 0.005845666 3.723933753 3.51E-07 6.454613038 -1.018241525 RAAEDDEDDDVDTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RAAEDDEDDDVDTKK 15 2 B8ZZQ6;P06454-2;P06454;B8ZZA1;B8ZZW7;H7C2N1 B8ZZQ6 PTMA "Prothymosin alpha;Prothymosin alpha, N-terminally processed;Thymosin alpha-1" 0 1 ; RAAEDDEDDDVDTK(1)K;RAAEDDEDDDVDTK(1)K 209.6 5.20E-19 3601100 2905.1 3203.4 2588.35 2008.39 3278.51 3011 3032.4 1991.89 4378.9 4166.4 FALSE TRUE FALSE 2869.691524 3248.497549 2633.399146 2240.609502 3111.195401 2818.606818 3289.97198 2049.522194 3987.240217 4058.156327 0.70714169 0.800486055 0.648915156 0.552124985 0.766652428 0.694553534 0.810706073 0.505037763 0.982525042 1 11.98660873 -12.3016172 0.446921811 1.089030056 0.672338054 0.646536209 0.091578206 0.962411917 0.249709621 0.185205424 0.026576698 4.99E-13 12.3016172 -0.416692003 RAAELS(ph)PEER ddPTM_HeLa_Romidepsin_16h_R1 1 RAAELSPEER 10 1 Q5U5Q3 Q5U5Q3 MEX3C RNA-binding E3 ubiquitin-protein ligase MEX3C 1 0 RAAELS(1)PEER 76.357 0.020812 2405000 770.68 960.73 857.4 998.05 705.8 789.98 652.67 600.02 1005 1019.9 TRUE FALSE FALSE 761.2866557 974.2551822 872.3226873 1113.449237 669.7803923 739.5028275 708.1077735 617.380632 915.1102829 993.402851 0.76634233 0.980725172 0.878115748 1.120843609 0.674228377 0.744413837 0.712810289 0.621480632 0.921187494 1 9.956235077 -8.710173214 24.99999767 0.90816816 0.694001165 0.627865629 0.09416011 72.28251792 35248.23017 0.016282239 0.03256445 1.95E-09 8.710173214 -0.214166995 RAAGDGGSGPPEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 RAAGDGGSGPPEKK 14 2 H3BP71;O75150-3;O75150-4;O75150;H3BQ99;H3BUL6;I3L332 H3BP71 RNF40 E3 ubiquitin-protein ligase BRE1B 0 1 RAAGDGGSGPPEK(1)K 95.822 0.022152 483680 205.19 221.2 222.89 549.24 377.46 308.83 308.64 331.74 434.53 307.86 FALSE TRUE FALSE 202.6890654 224.3140594 226.769307 612.7457131 358.1968077 289.0967597 334.8558739 341.3383735 395.6645485 299.8617528 0.675941708 0.748058255 0.756246186 2.04342737 1.194539832 0.964100146 1.116700849 1.138319143 1.319489881 1 8.228153709 RAAS(ph)AATAAPTATPAAQESGTIPK ddPTM_HeLa_Romidepsin_16h_R1 1 RAASAATAAPTATPAAQESGTIPK 24 1 B8ZZ81;O00116 B8ZZ81 AGPS "Alkyldihydroxyacetonephosphate synthase, peroxisomal" 1 0 RAAS(0.631)AAT(0.359)AAPT(0.009)AT(0.002)PAAQESGTIPK 55.022 0.0023957 0 1570.1 1386.5 1122.3 1123.2 1199.2 1539.3 838.09 993.95 1178.8 1040.4 TRUE FALSE FALSE 1550.963017 1406.019183 1141.833161 1253.069669 1138.000349 1440.943698 909.2773437 1022.708375 1073.365176 1013.370258 1.53049984 1.387468373 1.126767982 1.236536852 1.12298574 1.421932099 0.897280472 1.009214911 1.059203354 1 9.984945677 -7.748128186 24.99274045 1.255532667 0.953247552 0.319323833 0.162886326 247.5877644 464855.906 0.028920515 0.106922789 1.79E-08 7.748128186 -0.302285115 RADDDRFPR ddPTM_HeLa_Romidepsin_16h_R1 1 RADDDRFPR 9 2 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 0 0 112.41 0.019682 2149300 960.3 947.8 985.27 859.52 1039.8 1126.7 928.13 891.68 1212.6 930.57 FALSE FALSE TRUE 948.5954942 961.1431533 1002.418211 958.9017466 986.735126 1054.707506 1006.965339 917.479354 1104.142019 906.3936573 1.046560164 1.060403662 1.105941335 1.057930778 1.088638604 1.163630723 1.11095806 1.012230554 1.218170505 1 9.823993955 -10.64788468 0.568413636 1.004684287 1.097398783 0 0.076529749 0.460187642 0.34868634 0.014927681 0.0129234 2.25E-11 10.64788468 0.092714496 RADLEETDK ddPTM_HeLa_Romidepsin_16h_R1 4 RADLEETDK 9 1 Q7Z6E1;K7EPW3;P10072-2;P10072 Q7Z6E1 HKR1 Krueppel-related zinc finger protein 1 0 0 ;;; ;;; 187.34 1.14E-06 284319000 17051.8 16563.1 17260.2 15742.7 16517.8 17725.9 17186.6 13536.9 17704.9 16192.8 FALSE FALSE TRUE 16843.9661 16796.27576 17560.60654 17562.94505 15674.83503 16593.2722 18646.42938 13928.56884 16121.3294 15772.10872 1.067959041 1.064935327 1.11339624 1.113544508 0.99383255 1.052064279 1.182240733 0.883113925 1.022141661 1 13.94508794 -12.11627582 0.884649605 1.000101425 1.064264366 0.053850645 0.0755782 1.111327312 1.575586667 0.045394879 0.013368227 7.65E-13 12.11627582 0.064162941 RADLNQGIGEPQS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 RADLNQGIGEPQS(0.752)PS(0.248)R;RADLNQGIGEPQS(0.5)PS(0.5)R ; 194.67 8.43E-13 31350000 4225.8 4468.5 4807.2 4040.1 4890.9 4729.5 3790.3 4105.3 4556.6 4295.4 TRUE FALSE FALSE 4174.294324 4531.40766 4890.867299 4507.235371 4641.299123 4427.300214 4112.247987 4224.080378 4149.046284 4183.804889 0.997726815 1.083082931 1.168999853 1.077305346 1.109348845 1.058199493 0.982896693 1.009626522 0.991692107 1 12.03059986 -10.26657265 23.73661665 0.998926548 1.071735743 0.3289949 0.047982209 195.3699109 903405.9426 0.008814624 0.010253467 5.41E-11 10.26657265 0.072809195 RADLNQGIGEPQS(ph)PSRR ddPTM_HeLa_Romidepsin_16h_R1 1 RADLNQGIGEPQSPSRR 17 2 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 RADLNQGIGEPQS(0.688)PS(0.312)RR 71.08 0.02752 22935000 2367.7 2518.6 2541.6 1919.3 2359.8 2672.2 2347.1 1992.4 2453.4 1899.1 TRUE FALSE FALSE 2338.841562 2554.056917 2585.835482 2141.218497 2239.3706 2501.455044 2546.462615 2050.046951 2233.961759 1849.761108 1.264401955 1.380749604 1.397929425 1.157564881 1.210626924 1.352312487 1.376644046 1.108276599 1.207702848 1 10.85312325 -11.91776767 0.780168336 1.001070734 1.286668901 0.206089601 0.112695041 0.371970461 0.422183924 0.06061013 0.01999442 1.21E-12 11.91776767 0.285598167 RADLNQGIGEPQSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RADLNQGIGEPQSPSR 16 1 Q96C19 Q96C19 EFHD2 EF-hand domain-containing protein D2 1 0 RADLNQGIGEPQS(0.194)PS(0.806)R 222.96 1.07E-34 16494000 969.74 979.07 936.51 1018.9 940.42 1100.7 776.08 796.17 869.78 798.64 TRUE FALSE FALSE 957.9204359 992.8533732 952.8095637 1136.710012 892.4268582 1030.368822 842.0002158 819.2059228 791.9846984 777.8912177 1.231432383 1.27633961 1.22486222 1.461271173 1.147238634 1.324566725 1.082413835 1.05311116 1.018117547 1 9.603424609 -12.05005287 0.83070133 0.999545809 1.230053024 0.369647656 0.112061342 0.533578928 0.668621826 0.074856935 0.022500673 8.91E-13 12.05005287 0.230507215 (ac)PEPSK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPSKSAPAPK 11 1 P33778;U3KQK0;Q99877 P33778;U3KQK0 HIST1H2BB;HIST1H2BN Histone H2B type 1-B;Histone H2B;Histone H2B type 1-N 0 1 ; PEPSK(1)SAPAPK;PEPSK(1)SAPAPK 64.42 1.66E-07 8961100 1512.56 2064.13 1412.39 6684.8 18244.7 25944 22176.9 23956 0 1179.99 FALSE TRUE FALSE 1494.124337 2093.188876 1436.972055 7457.728029 17313.60488 24286.26213 24060.60533 24649.12906 0 1149.33369 1.299991769 1.821219455 1.250265322 6.488740473 15.0640367 21.13073196 20.9343949 21.44645135 0 1 10.16658201 -8.730310459 1.668869307 1.161162651 21.44170655 0.996071952 0.561779202 0.011011404 0.061994401 0.065133029 0.156457418 1.86E-09 8.730310459 20.28054389 up RAEDGS(ph)VIDYELIDQDAR ddPTM_HeLa_Romidepsin_16h_R1 2 RAEDGSVIDYELIDQDAR 18 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33;H0YNA0 P07355 ANXA2 Annexin A2;Annexin 1 0 RAEDGS(0.901)VIDY(0.099)ELIDQDAR;RAEDGS(1)VIDYELIDQDAR ; 143.47 3.11E-05 16223200 2586.39 3198.04 2924.1 2675.64 2655.02 2484.24 2093.66 1699.16 3065.64 2985.84 TRUE FALSE FALSE 2554.866084 3243.062091 2974.992734 2985.010086 2519.524422 2325.505082 2271.495428 1748.322514 2791.44148 2908.267446 0.878483885 1.115118245 1.022943312 1.026387752 0.866331749 0.799618716 0.781047641 0.601156031 0.959829703 1 11.50594423 -7.713960769 1.029678567 0.96599437 0.57493497 0.760565848 0.07019917 0.45789075 0.59590629 0.012793022 0.164391763 1.93E-08 7.713960769 -0.3910594 RAEDGSVIDYELIDQDAR ddPTM_HeLa_Romidepsin_16h_R1 8 RAEDGSVIDYELIDQDAR 18 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;H0YN28;H0YM50;H0YNP5;H0YL33;H0YNA0 P07355 ANXA2 Annexin A2;Annexin 0 0 ;;;;;;; ;;;;;;; 203.17 4.63E-21 618923600 18484.5 20989.5 18194.6 19431.5 20543.1 21707.2 18438.3 20338.2 20144.6 18813.9 FALSE FALSE TRUE 18259.2038 21284.99073 18511.26938 21678.26146 19494.70895 20320.17998 20004.44874 20926.65373 18342.81652 18325.11217 0.996403386 1.161520352 1.010158585 1.182981106 1.063824809 1.108870701 1.091641271 1.141965928 1.000966125 1 14.16153441 -10.28117861 24.54249993 0.998301592 1.105398642 0.538796006 0.046389453 312.5494953 388602.7274 0.006924036 0.00792379 5.23E-11 10.28117861 0.10709705 RAEFTVETR ddPTM_HeLa_Romidepsin_16h_R1 2 RAEFTVETR 9 1 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 ; ; 117.52 0.0096005 12903900 8219.3 7592.4 10599.1 3187 9652.1 10442.4 7932.9 8514.6 8682.8 7703.3 FALSE FALSE TRUE 8119.12001 7699.286006 10783.57289 3555.495935 9159.51732 9775.164341 8606.720328 8760.956517 7906.188622 7503.167156 1.082092381 1.026138142 1.437202806 0.473866017 1.220753467 1.302805087 1.147078314 1.167634458 1.053713513 1 12.87328398 RAELPGS(ph)SSPLLAQPR ddPTM_HeLa_Romidepsin_16h_R1 1 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 RAELPGS(0.391)S(0.391)S(0.218)PLLAQPR 132.84 0.0026544 8955700 1281.6 1835.1 1397.7 1662.6 1832 2028.4 1730.3 1648.8 1817.5 1953.7 TRUE FALSE FALSE 1265.979366 1860.934586 1422.026382 1854.837635 1738.506204 1898.791786 1877.271639 1696.505427 1654.938248 1902.942592 0.665274597 0.977924712 0.747277605 0.974720752 0.913588361 0.997818743 0.986509864 0.891516872 0.869673239 1 10.89401632 -9.231225576 24.44054528 0.843828955 0.955021169 0.211778062 0.096541983 817.7976362 661533.1146 0.019900857 0.032998807 5.87E-10 9.231225576 0.111192215 RAELPGSSS(ph)PLLAQPR ddPTM_HeLa_Romidepsin_16h_R1 1 RAELPGSSSPLLAQPR 16 1 Q9C0H5;Q9C0H5-2 Q9C0H5 ARHGAP39 Rho GTPase-activating protein 39 1 0 RAELPGS(0.188)S(0.188)S(0.625)PLLAQPR 170.47 1.79E-05 11995000 1331.8 1490.4 1305.4 1366.6 1388.8 1676.2 1810.1 1525.1 1621.2 1551.1 TRUE FALSE FALSE 1315.567509 1511.38189 1328.119939 1524.612722 1317.924354 1569.09623 1963.849849 1569.226362 1476.195812 1510.802198 0.870774156 1.000383698 0.87908261 1.009141186 0.872334151 1.03858482 1.299872247 1.038670955 0.977094032 1 10.56109907 -7.985282417 8.169506821 0.939871656 1.170056992 0.570437156 0.077857441 0.079113867 30.92839534 0.010439049 0.030722875 1.03E-08 7.985282417 0.230185336 RAET(ph)GVSLSRCST(ph)QK ddPTM_HeLa_Romidepsin_16h_R1 1 RAETGVSLSRCSTQK 15 2 A0A2R8Y4M0 A0A2R8Y4M0 2 0 RAET(1)GVS(0.023)LS(0.073)RCS(0.074)T(0.83)QK 75.743 0.0021687 0 3629.8 2760.3 2405.7 1100.9 2718.2 2255.9 2325.3 2090.1 3380 4206.5 TRUE FALSE FALSE 3585.558601 2799.159576 2447.570199 1228.191238 2579.480111 2111.755271 2522.810924 2150.573746 3077.684335 4097.214524 0.875121032 0.683185994 0.597374188 0.299762492 0.62956921 0.515412424 0.61573806 0.524886782 0.751165046 1 12.00042772 -10.17402629 1.476733754 0.954602333 0.524058604 0.658163964 0.108644887 0.109608026 0.456914626 0.017032656 0.020943482 6.70E-11 10.17402629 -0.430543729 RAGDLLEDS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 6 RAGDLLEDSPK 11 1 P51858-2;P51858;P51858-3 P51858-2 HDGF Hepatoma-derived growth factor 1 0 RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK;RAGDLLEDS(1)PK ;;;;; 137.93 0.001051 382902700 25116.8 27974.4 25008 14271.1 22076.1 23517.8 21102 23073.4 26021.3 28279.7 TRUE FALSE FALSE 24810.66678 28368.22434 25443.25375 15921.19173 20949.47424 22015.08848 22894.40335 23740.99243 23693.88976 27544.98932 0.900732489 1.029886925 0.92369808 0.578006822 0.760554814 0.799241133 0.831163995 0.86189877 0.860188744 1 14.74950228 -9.496885975 24.90341044 0.958486449 0.769263052 0.527886556 0.083537973 398.9659891 382245.8499 0.012553535 0.019132696 3.19E-10 9.496885975 -0.189223396 RAGELTEDEVER ddPTM_HeLa_Romidepsin_16h_R1 2 RAGELTEDEVER 12 1 P62269 P62269 RPS18 40S ribosomal protein S18 0 0 ; ; 205.31 3.09E-15 16223200 4299.2 4432.5 4241.8 4637.5 4125.1 4123.7 3724.6 3911.6 4388 4091.7 FALSE FALSE TRUE 4246.799697 4494.900851 4315.62675 5173.70957 3914.580754 3860.208879 4040.967431 4024.775975 3995.52629 3985.397044 1.065590116 1.127842672 1.082859926 1.29816666 0.982231058 0.968588283 1.013943501 1.009880805 1.00254159 1 11.96050774 RAGQT(ph)DGR ddPTM_HeLa_Romidepsin_16h_R1 1 RAGQTDGR 8 1 J3KRY1 J3KRY1 ARHGDIA 1 0 RAGQT(1)DGR 44.395 0.027349 474420 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 RAGT(ph)VAARGDPGGER ddPTM_HeLa_Romidepsin_16h_R1 1 RAGTVAARGDPGGER 15 2 H0Y4T2;H3BTQ3 H0Y4T2 SLC19A1 1 0 RAGT(1)VAARGDPGGER 104.24 0.0011697 0 349.01 277.48 346.21 208.31 260.97 284.22 356.05 297.96 233.31 0 TRUE FALSE FALSE 344.7561319 281.3863707 352.2356398 232.3957823 247.6517271 266.0592593 386.2928781 306.5810025 212.4421693 0 0 RALLETAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 RALLETASPR 10 1 Q96BT3;H3BMP6;H3BQS6;H3BN05;H3BTS2;H3BQJ0;I3L4F8;H3BUW2;H3BTR4;Q96BT3-3;Q96BT3-2 Q96BT3 CENPT Centromere protein T 1 0 RALLET(0.01)AS(0.99)PR;RALLET(0.005)AS(0.995)PR;RALLET(0.01)AS(0.99)PR ;; 74.698 0.0029682 8617600 8170 7388.5 7459.5 7134.8 7141.8 6513.2 5752.7 5112.9 8660.4 7767.5 TRUE FALSE FALSE 8070.420898 7492.515497 7589.329468 7959.759146 6777.327296 6097.02754 6241.334194 5260.833695 7885.792134 7565.69923 1.066711833 0.990326904 1.003123338 1.052085062 0.895796554 0.8058776 0.824951403 0.695353269 1.042308436 1 12.88525771 -8.357529503 1.338182328 1.029500902 0.748679018 0.895465887 0.038552015 0.107061476 0.356305734 0.006238775 0.023206679 4.39E-09 8.357529503 -0.280821884 TVTPAK(ac)AVTTPGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TVTPAKAVTTPGKK 14 2 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 2 ; TVTPAK(1)AVTTPGK(1)K;TVTPAK(1)AVTTPGK(1)K 201.48 1.78E-17 2965500 98.098 173.24 161.36 838.61 2675.4 3067.2 3072.6 3372.4 331.46 487.51 FALSE TRUE FALSE 96.90234384 175.6788773 164.1684031 935.574034 2538.864355 2871.215819 3333.586567 3469.975073 301.8133874 474.8444199 0.204071775 0.369971447 0.34573093 1.970274883 5.34672884 6.046645382 7.020376417 7.307604191 0.635604789 1 8.89131109 -8.725190733 1.797293401 0.557202621 6.902323004 0.985132861 0.349012244 0.034284296 0.224512986 0.066708296 0.156305355 1.88E-09 8.725190733 6.345120382 up RALS(ph)SDSILSPAPDAR ddPTM_HeLa_Romidepsin_16h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 RALS(0.846)S(0.004)DS(0.114)ILS(0.036)PAPDAR 130.64 0.0030166 76444000 2177 1548.2 1515.4 1458.2 1482.2 1204.2 1115.9 920.92 1786.6 1553.4 TRUE FALSE FALSE 2150.465887 1569.9956 1541.774901 1626.803945 1406.557803 1127.255506 1210.684518 947.5653672 1626.802021 1513.042444 1.421285897 1.03764148 1.018989855 1.07518725 0.929622172 0.7450257 0.800165602 0.626264895 1.075185979 1 10.56323674 -8.586276016 0.856918169 1.188152984 0.668439746 0.661648551 0.121014279 0.389665509 0.504608577 0.029419331 0.124223502 2.59E-09 8.586276016 -0.519713238 RALSS(ph)DSILS(ph)PAPDAR ddPTM_HeLa_Romidepsin_16h_R1 1 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 2 0 RALS(0.228)S(0.725)DS(0.047)ILS(1)PAPDAR 149.19 0.00027184 4840400 1694.3 1920.1 1460.2 1605.7 1919 2419.2 2137.7 2056.6 1677.1 1672.3 TRUE FALSE FALSE 1673.64922 1947.131218 1485.614168 1791.358589 1821.066269 2264.620928 2319.276185 2116.104476 1527.095976 1628.853405 1.02750144 1.195399913 0.912061309 1.099766611 1.118005011 1.390315986 1.423870422 1.299137461 0.937528185 1 10.66964105 -8.408285638 2.432624103 1.025376115 1.381137278 0.780897091 0.080931547 0.087641751 1.00512326 0.010636504 0.027501549 3.91E-09 8.408285638 0.355761163 RALSSDS(ph)ILSPAPDAR ddPTM_HeLa_Romidepsin_16h_R1 3 RALSSDSILSPAPDAR 16 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 RALS(0.056)S(0.002)DS(0.941)ILSPAPDAR;RALS(0.361)S(0.026)DS(0.613)ILSPAPDAR;RALS(0.371)S(0.102)DS(0.527)ILSPAPDAR ;; 195.6 6.25E-13 154217000 6125.7 5732.9 5236.2 6230.3 4144.16 4090.47 3709.8 3741.68 5619.3 5280.8 TRUE FALSE FALSE 6051.037612 5813.607917 5327.333865 6950.6766 3932.668051 3829.102168 4024.910319 3849.939607 5116.695734 5143.604055 1.176419792 1.130259611 1.035720053 1.351324193 0.764574413 0.744439527 0.782507805 0.748490663 0.994768586 1 12.32856388 -8.726643077 23.85291635 1.101946782 0.760498205 0.758773378 0.097829619 43.50827069 29824.62183 0.014584751 0.029168037 1.88E-09 8.726643077 -0.341448577 RALVEFESNPEET(ph)REPGSPPSVQR ddPTM_HeLa_Romidepsin_16h_R1 2 RALVEFESNPEETREPGSPPSVQR 24 2 Q9H6F5;H0YG79 Q9H6F5 CCDC86 Coiled-coil domain-containing protein 86 1 0 RALVEFESNPEET(0.923)REPGS(0.032)PPS(0.045)VQR;RALVEFES(0.002)NPEET(0.611)REPGS(0.364)PPS(0.023)VQR ; 52.095 0.0089923 32916000 3115.5 2790.6 2331.15 5575.7 2781.4 2857.2 2594 2869.9 3190.5 3005.9 TRUE FALSE FALSE 3077.527088 2829.88614 2371.722688 6220.388668 2639.454779 2674.634141 2814.334295 2952.936029 2905.133689 2927.806285 1.051137537 0.966555115 0.810068173 2.124590244 0.901512779 0.913528383 0.961243341 1.008583131 0.992256115 1 11.51560439 -5.538576079 11.42732156 1.057128425 0.957739498 0 0.356736988 0 0 0.044047015 0 2.89E-06 5.538576079 -0.099388928 RAMRAFRMLLY(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RAMRAFRMLLYSK 13 3 Q9H4L4;A0A087X0R7 Q9H4L4 SENP3;SENP3-EIF4A1 Sentrin-specific protease 3 2 0 RAMRAFRMLLY(1)S(1)K 50.806 0.029192 15555000 741.86 812.91 410.88 769.23 1017.7 938.02 1101.1 646.9 1111.1 901.2 TRUE FALSE FALSE 732.817925 824.3541683 418.031194 858.1719919 965.7629714 878.0835493 1194.627407 665.6170309 1011.720433 877.7866941 0.834847384 0.939128121 0.476233232 0.977654364 1.100225121 1.000338186 1.360954107 0.758290181 1.152581191 1 9.777726591 -9.00048846 24.99084919 0.884051152 1.068662205 0.131122051 0.210891488 24.7103542 1264393.564 0.027987511 0.050319283 9.99E-10 9.00048846 0.184611054 RAPAPPPPQPPPPS(ph)PLIPNR ddPTM_HeLa_Romidepsin_16h_R1 1 RAPAPPPPQPPPPSPLIPNR 20 1 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2 COBL Protein cordon-bleu 1 0 RAPAPPPPQPPPPS(1)PLIPNR 98.973 0.00022417 12090000 2526.8 2621.2 2867.2 1618.2 2492.9 2302.5 2118.6 2500.7 3160.1 3279.9 TRUE FALSE FALSE 2496.00239 2658.101322 2917.102413 1805.303898 2365.678011 2155.377681 2298.553831 2573.053809 2877.452741 3194.687725 0.781297768 0.832037918 0.913110346 0.565095575 0.740503678 0.674675545 0.719492492 0.805416376 0.90069922 1 11.6414592 -12.50819398 0.275583522 1.15190515 0.702455443 0.452510445 0.089034105 2.84536093 0.26108008 0.424627684 0.059147502 3.10E-13 12.50819398 -0.449449707 RAPFDLFENK ddPTM_HeLa_Romidepsin_16h_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 0 ; ; 152.67 0.0023042 28757000 6987.3 4843.8 12626.3 9941.9 12174.3 10815.2 10927.9 6230.1 6505.2 5201.4 FALSE FALSE TRUE 6902.1361 4911.991144 12846.05546 11091.42926 11553.00004 10124.14362 11856.11555 6410.358114 5923.358619 5066.266878 1.362371203 0.969548439 2.535605755 2.189270625 2.280377311 1.998343922 2.340207462 1.265302099 1.169176193 1 12.30670736 -9.769729173 24.9999453 1.160783125 2.119796417 0.674556049 0.33168266 78.54512232 236872.153 0.052066515 0.069069998 1.70E-10 9.769729173 0.959013292 RAPFDLFENK(ac)K ddPTM_HeLa_Romidepsin_16h_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 1 RAPFDLFENK(1)K 117.95 0.0070443 1101700 953.92 686.97 764.57 690.67 1366.4 873.13 1241 1156.7 1609.3 1210.1 FALSE TRUE FALSE 942.2932561 696.6411817 777.8770201 770.5285151 1296.667509 817.3398109 1346.410509 1190.16729 1465.360177 1178.661428 0.799460502 0.591044354 0.659966469 0.65373185 1.100118727 0.693447492 1.142321686 1.009761804 1.243240971 1 10.20293365 -7.747241178 24.99840465 0.848037085 1.076041807 0.172504387 0.204215116 288.0855665 507216.0539 0.024783866 0.09183957 1.79E-08 7.747241178 0.228004721 RAPFDLFENR ddPTM_HeLa_Romidepsin_16h_R1 2 RAPFDLFENR 10 1 P07900-2;P07900 P07900-2 HSP90AA1 Heat shock protein HSP 90-alpha 0 0 ; ; 145.55 0.0026104 58334000 3573.5 2508.33 9855.4 6039.7 9282.7 10560.6 9217.4 3597.6 3312.5 1774.41 FALSE FALSE TRUE 3529.944807 2543.642336 10026.9291 6738.038532 8808.96918 9885.811743 10000.32573 3701.69088 3016.221704 1728.310572 2.04242505 1.471750724 5.801578294 3.898627156 5.096867034 5.71992783 5.786185588 2.141797278 1.74518501 1 10.75514677 -9.771809854 24.98695551 1.504472241 4.81075258 0.679459836 1.067701486 82.58581512 198984.5552 0.167096896 0.22094443 1.69E-10 9.771809854 3.306280339 RAPSTSPS(ph)FEGTQETYTVAHEENVR ddPTM_HeLa_Romidepsin_16h_R1 1 RAPSTSPSFEGTQETYTVAHEENVR 25 1 Q9BUT9 Q9BUT9 FAM195A Protein FAM195A 1 0 RAPS(0.166)T(0.166)S(0.166)PS(0.482)FEGT(0.013)QET(0.006)Y(0.001)TVAHEENVR 61.903 0.001074 5763100 1079.9 995.81 964.85 879.09 844.45 686.94 630.14 736.05 1303.2 1122.7 TRUE FALSE FALSE 1066.737763 1009.829039 981.6428095 980.734522 801.3545654 643.046751 683.6640759 757.3464455 1186.638528 1093.532092 0.975497446 0.923456245 0.897680842 0.896850243 0.73281303 0.588045614 0.625188854 0.692569016 1.085142847 1 10.09477984 -8.830961474 1.20786337 0.982501059 0.623813974 0.898825285 0.051328114 0.080022704 0.23128674 0.006754687 0.017669376 1.48E-09 8.830961474 -0.358687085 RAQS(ph)TDSLGTSGSLQSK ddPTM_HeLa_Romidepsin_16h_R1 2 RAQSTDSLGTSGSLQSK 17 1 I3L456;Q15276-2;Q15276 I3L456 RABEP1 Rab GTPase-binding effector protein 1 1 0 RAQS(0.931)T(0.069)DSLGTSGSLQSK;RAQS(0.773)T(0.226)DSLGTSGSLQSK ; 253.34 3.10E-72 9428200 5152.8 4732.7 3578.2 5511.2 5248.2 4761.8 4581.4 4748.2 4621.4 4264.4 TRUE FALSE FALSE 5089.995692 4799.327075 3640.47707 6148.430875 4980.36477 4457.536348 4970.544002 4885.581676 4208.050409 4153.610273 1.225438921 1.155459169 0.876460917 1.480261861 1.199044793 1.073171543 1.1966804 1.176225345 1.013106703 1 12.02015014 -12.42015757 0.968741941 0.992088008 1.175758633 0.182851367 0.140317392 0.851460055 1.326662498 0.11606925 0.024648759 3.80E-13 12.42015757 0.183670625 RAQST(ph)DSLGTSGSLQSK ddPTM_HeLa_Romidepsin_16h_R1 1 RAQSTDSLGTSGSLQSK 17 1 I3L456;Q15276-2;Q15276 I3L456 RABEP1 Rab GTPase-binding effector protein 1 1 0 RAQS(0.069)T(0.922)DS(0.007)LGT(0.001)SGS(0.001)LQSK 132.25 0.0047512 8621200 3168.5 3188.9 2189.7 3756.1 3342.5 3487.2 3181 3204.3 2988.5 2993.2 TRUE FALSE FALSE 3129.881103 3233.793418 2227.81081 4190.397955 3171.919752 3264.379174 3451.194061 3297.011365 2721.201075 2915.436233 1.073554986 1.109197101 0.764143213 1.43731422 1.08797432 1.119688072 1.183765922 1.130880974 0.933376983 1 11.50949605 -9.260522411 24.99990718 1.023936545 1.181683256 0.385557513 0.129056241 81.06298025 2210066.726 0.017920899 0.028635718 5.49E-10 9.260522411 0.157746711 RAQSTDSLGT(ph)SGSLQSK ddPTM_HeLa_Romidepsin_16h_R1 1 RAQSTDSLGTSGSLQSK 17 1 I3L456;Q15276-2;Q15276 I3L456 RABEP1 Rab GTPase-binding effector protein 1 1 0 RAQS(0.052)T(0.004)DS(0.124)LGT(0.572)S(0.124)GS(0.124)LQSK 90.793 0.021566 6085600 1727.7 1950.3 1303.1 1872.2 1703.5 2069.3 1832.3 1981.1 2310.3 1919.1 TRUE FALSE FALSE 1706.642128 1977.756375 1325.779909 2088.672573 1616.564038 1937.078408 1987.935516 2038.420003 2103.660982 1869.241505 0.913013178 1.058052889 0.709260898 1.117390432 0.864823531 1.036291139 1.063498489 1.090506495 1.125408876 1 10.86823726 -8.044138709 8.47628437 0.953068004 1.070469415 0.111818967 0.117988714 0.374521877 68.57378084 0.013333643 0.034518939 9.03E-09 8.044138709 0.117401411 RAQT(ph)PPISSLPTSPSDEVGR ddPTM_HeLa_Romidepsin_16h_R1 1 RAQTPPISSLPTSPSDEVGR 20 1 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 RAQT(0.995)PPIS(0.002)S(0.002)LPTSPSDEVGR 65.278 0.0017562 0 1042.1 1274.8 962.84 1030.9 1187.2 1160.6 1149.3 1592.8 1063.8 1308.3 TRUE FALSE FALSE 1029.398484 1292.746668 979.5978263 1150.097509 1126.612754 1086.441406 1246.921513 1638.885155 968.6510637 1274.310177 0.807808415 1.01446782 0.768727931 0.902525562 0.884096175 0.85257218 0.978507066 1.286095947 0.760137587 1 10.31550077 -7.283971452 3.023119211 0.899713791 1.338292173 0.676020491 0.084355479 0.162527021 2.238115729 0.011749851 0.165972339 5.20E-08 7.283971452 0.438578382 RAS(ph)DSVFQPK ddPTM_HeLa_Romidepsin_16h_R1 2 RASDSVFQPK 10 1 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 RAS(0.954)DS(0.046)VFQPK;RAS(0.86)DS(0.14)VFQPK ; 64.104 0.029705 17179600 6119.6 5285.7 5788.2 6269.9 8865.1 9337.2 8313 10231.5 6051.2 6000.8 TRUE FALSE FALSE 6045.011961 5360.112223 5888.941193 6994.855339 8412.680867 8740.583054 9019.106013 10527.53231 5509.965516 5844.898351 1.034237312 0.917058245 1.007535262 1.196745421 1.439320303 1.495420883 1.543073202 1.801148913 0.942696551 1 12.51296222 -8.572814785 1.035965052 1.002580897 1.68485812 0.938090459 0.072975226 0.095677611 0.19092358 0.011697556 0.04282238 2.67E-09 8.572814785 0.682277223 RAS(ph)DTSLTQGLK ddPTM_HeLa_Romidepsin_16h_R1 1 RASDTSLTQGLK 12 1 A0A0B4J2F2;P57059 A0A0B4J2F2 LOC102724428;SIK1 Serine/threonine-protein kinase SIK1 1 0 RAS(0.888)DT(0.021)S(0.081)LT(0.01)QGLK 58.781 0.0042408 0 1811.9 1536.3 1510.3 1393.6 1412.5 1620.2 1443 1945.2 1927.8 1579.3 TRUE FALSE FALSE 1789.815866 1557.928072 1536.586138 1554.734589 1340.414854 1516.674449 1565.568384 2001.481293 1755.37274 1538.269558 1.163525506 1.012779628 0.99890564 1.010703606 0.871378392 0.985961427 1.017746451 1.301125204 1.14113468 1 10.58709262 RAS(ph)GQAFELILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 6 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 2 0 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 ;;;;; 129.75 0.00081581 181014900 22548.68 21588.61 21581.5 21374.49 25869.54 30225.45 25632.2 27842.97 25617.15 21680.57 TRUE FALSE FALSE 22273.84802 21892.53502 21957.11695 23845.9091 24549.32084 28294.14129 27809.39843 28648.56241 23325.88794 21117.30567 1.054767515 1.036710619 1.039768865 1.129211722 1.162521452 1.339855649 1.316900881 1.356639093 1.104586367 1 14.36613815 -8.557165795 1.095285697 1.02616226 1.36013277 0.927198579 0.034725712 0.070096357 0.157824269 0.004413006 0.015700757 2.77E-09 8.557165795 0.33397051 RAS(ph)GQAFELILSPR ddPTM_HeLa_Romidepsin_16h_R1 5 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(1)GQAFELILSPR;RAS(0.998)GQAFELILS(0.002)PR ;;;; 146.1 0.0009518 644770000 5909.54 4847.86 5316.25 6231.22 6668.7 5406.98 5044.95 5380.1 5765.2 4175.7 TRUE FALSE FALSE 5837.512253 4916.1083 5408.777101 6951.702975 6328.371355 5061.491428 5473.467927 5535.764705 5249.546073 4067.214712 1.43526041 1.208716197 1.329847939 1.709204816 1.555947203 1.24446133 1.345753375 1.361070191 1.290698044 1 11.98982544 -12.38894854 0.591367019 0.919396713 1.411457988 0.193582074 0.164690403 0.849997375 0.396092253 0.234202875 0.033664235 4.08E-13 12.38894854 0.492061275 RAS(ph)ISEPSDTDPEPR ddPTM_HeLa_Romidepsin_16h_R1 1 RASISEPSDTDPEPR 15 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 0 RAS(0.992)IS(0.008)EPSDTDPEPR 132.5 0.00048393 25787000 991.02 1078.4 1110.5 778.28 519.67 680.76 656.59 755.78 928.23 1060.9 TRUE FALSE FALSE 978.9410671 1093.581744 1129.827787 868.2683955 493.1493007 637.2616331 712.3607382 777.6473019 845.206784 1033.337665 0.947358352 1.058300477 1.093377146 0.840256215 0.477239258 0.616702221 0.68937847 0.75255875 0.81793862 1 10.01309605 -8.979326106 6.234284347 0.989419656 0.637551119 0.752641276 0.094380946 0.050687198 7.041242298 0.011906639 0.021409178 1.05E-09 8.979326106 -0.351868537 RAS(ph)LSDIGFGK ddPTM_HeLa_Romidepsin_16h_R1 1 RASLSDIGFGK 11 1 D6R9B0;A0A0A0MSJ6;Q07002;Q07002-3;D6RA44 D6R9B0 CDK18 Cyclin-dependent kinase 18 1 0 RAS(0.996)LS(0.004)DIGFGK 101.61 0.0054718 13759000 3196.8 2834.5 3359.1 3478.8 6005.7 6808.7 6138.7 6480 2745 2575.5 TRUE FALSE FALSE 3157.836172 2874.404165 3417.563726 3881.035224 5699.206719 6373.646044 6660.121025 6667.488576 2499.480325 2508.588139 1.258810134 1.145825463 1.362345486 1.547099408 2.271878205 2.54073036 2.654928054 2.657864985 0.996369347 1 11.29265991 -8.781804067 1.236144795 1.124829014 2.688206393 0.982860418 0.08751481 0.046015581 0.139293833 0.016947872 0.045444893 1.65E-09 8.781804067 1.563377379 up RAS(ph)LSDLTDLEDIEGLTVR ddPTM_HeLa_Romidepsin_16h_R1 1 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;Q8WZ73-2;Q8WZ73;J3KSU7;K7EN88;Q8WZ73-3 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 0 RAS(0.992)LS(0.008)DLT(0.001)DLEDIEGLTVR 81.643 0.0018249 0 466.77 422.68 474.56 539.13 480.59 640.5 477.46 370.98 680.43 575.91 TRUE FALSE FALSE 461.0808277 428.6305001 482.8195177 601.4667473 456.063699 599.5741171 518.0154405 381.713721 619.5706366 560.9477752 0.821967477 0.764118371 0.860720978 1.072233056 0.813023456 1.06885907 0.923464649 0.680479962 1.104506808 1 9.13172265 -12.49233903 1.282598026 0.998944712 0.877164524 0.22448701 0.121770976 0.74042043 2.209049862 0.076923716 0.01942138 3.22E-13 12.49233903 -0.121780188 RAS(ph)LSEIGFGK ddPTM_HeLa_Romidepsin_16h_R1 3 RASLSEIGFGK 11 1 Q00537-2;Q00537;F5H6Z0 Q00537-2 CDK17 Cyclin-dependent kinase 17 1 0 RAS(0.817)LS(0.183)EIGFGK;RAS(0.993)LS(0.007)EIGFGK;RAS(0.7)LS(0.3)EIGFGK ;; 104.41 0.026407 56501000 13297.8 11625.7 13449.1 14938 14981.6 16235.5 15071.5 15271.2 15437 13603.1 TRUE FALSE FALSE 13135.7213 11789.36691 13683.17594 16665.20185 14217.03305 15198.10395 16351.67283 15713.04808 14056.27606 13249.6895 0.991398425 0.889784391 1.032716725 1.257780557 1.073008771 1.147053593 1.234117436 1.185918212 1.060875884 1 13.69367093 -9.426100254 5.8186522 0.986691767 1.174001211 0.701131532 0.060785197 0.08978267 4.426040748 0.008460814 0.012950501 3.75E-10 9.426100254 0.187309444 RAS(ph)LTLEEK ddPTM_HeLa_Romidepsin_16h_R1 1 RASLTLEEK 9 1 A0A0U1RQQ9;Q6P3W7 A0A0U1RQQ9 SCYL2 SCY1-like protein 2 1 0 RAS(0.989)LT(0.011)LEEK 71.268 0.024448 7458200 2792.1 2545.4 2884.8 2713.7 4451.9 4511.1 4040.9 4511.4 3412.5 2980.7 TRUE FALSE FALSE 2758.068811 2581.234208 2935.008734 3027.470762 4224.702931 4222.855269 4384.133945 4641.930241 3107.277453 2903.260984 0.949989969 0.88908101 1.010935203 1.04278285 1.455157822 1.454521413 1.510072284 1.59886771 1.070271488 1 11.50345855 -8.767387986 2.877262873 0.970785234 1.516772795 0.95332655 0.055567387 0.032491808 0.551922963 0.007354844 0.015050699 1.71E-09 8.767387986 0.545987561 RAS(ph)PNSDDTVLSPQELQK ddPTM_HeLa_Romidepsin_16h_R1 1 RASPNSDDTVLSPQELQK 18 1 Q9UH62 Q9UH62 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 0 RAS(0.962)PNS(0.037)DDTVLSPQELQK 92.551 0.0015669 12968000 2844.6 2502.5 2636.3 2776 3162.1 2925.4 2799.7 3174.9 2788.6 2788 TRUE FALSE FALSE 2809.928921 2537.730261 2682.183696 3096.974181 3000.726238 2738.476381 3037.506448 3266.760722 2539.180632 2715.567358 1.034748379 0.934511992 0.987706561 1.140451984 1.105008951 1.008436183 1.118553159 1.202975398 0.935046087 1 11.40703793 -9.265559827 24.94785297 1.007423601 1.108793074 0.570837629 0.05639043 235.2048298 1424081.974 0.008169996 0.012772201 5.43E-10 9.265559827 0.101369474 RAS(ph)PPDPSPS(ph)PSAASASER ddPTM_HeLa_Romidepsin_16h_R1 1 RASPPDPSPSPSAASASER 19 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 2 0 RAS(1)PPDPS(0.239)PS(0.701)PS(0.044)AAS(0.01)AS(0.007)ER 97.784 0.00063664 5807400 2381.7 2580.2 2072.7 1931.7 2290.6 2580.3 2065.4 1970.2 2454.9 2378.9 TRUE FALSE FALSE 2352.670924 2616.524123 2108.774474 2155.052243 2173.702135 2415.427158 2240.835024 2027.204629 2235.327596 2317.095835 1.015353309 1.129225681 0.910093766 0.930066081 0.938114903 1.042437314 0.967087762 0.874890282 0.964710894 1 11.178102 RAS(ph)PPDPSPSPSAASASER ddPTM_HeLa_Romidepsin_16h_R1 2 RASPPDPSPSPSAASASER 19 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 RAS(1)PPDPSPSPSAASASER;RAS(0.999)PPDPS(0.001)PSPSAASASER ; 134.8 0.00022301 57483000 5403.3 5825.7 4811.6 4444.1 6912.2 7466.9 6808.6 7890.1 6209.4 6178.7 TRUE FALSE FALSE 5337.442501 5907.714358 4895.34388 4957.947752 6559.444641 6989.789188 7386.922314 8118.387595 5654.015712 6018.176483 0.886887002 0.98164525 0.813426441 0.823828907 1.089938897 1.161446363 1.227435309 1.348977987 0.939489848 1 12.5551107 -8.202280725 1.618777128 0.930707803 1.294561486 0.822672827 0.070821376 0.140944361 0.68818127 0.011915993 0.04513802 6.28E-09 8.202280725 0.363853683 RAS(ph)QEANLLTLAQK ddPTM_HeLa_Romidepsin_16h_R1 1 RASQEANLLTLAQK 14 1 A0A1C7CYX1;Q6PJG2;A0A0A0MSU2;H7C1L3 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 0 RAS(1)QEANLLTLAQK 142.91 0.0010215 34089000 2070.8 2004.3 2136.3 2004.6 2603.3 2776 2087.2 2058 2535.9 2411 TRUE FALSE FALSE 2045.560293 2032.516588 2173.481405 2236.381284 2470.443887 2598.622559 2264.486716 2117.544983 2309.082753 2348.361872 0.871058382 0.865503997 0.925530869 0.952315446 1.051986032 1.106568195 0.964283547 0.901711533 0.983273822 1 11.19743902 -8.934806857 6.370366409 0.930298935 1.010060843 0.246947824 0.063496239 0.25922652 19.47649163 0.011002269 0.020052692 1.16E-09 8.934806857 0.079761908 RAS(ph)WASENGETDAEGTQMTPAK ddPTM_HeLa_Romidepsin_16h_R1 2 RASWASENGETDAEGTQMTPAK 22 1 Q12789-3;Q12789 Q12789-3 GTF3C1 General transcription factor 3C polypeptide 1 1 0 RAS(0.72)WAS(0.27)ENGET(0.003)DAEGT(0.006)QMT(0.001)PAK;RAS(0.738)WAS(0.262)ENGETDAEGTQMTPAK ; 93.529 0.00042811 25191000 4317.3 3575.8 3480.9 3197.4 4482.9 5131.6 5124.1 6407.7 4347.2 3769.5 TRUE FALSE FALSE 4264.679087 3626.140206 3541.483604 3567.098432 4254.120885 4803.707321 5559.340926 6593.09669 3958.375544 3671.567847 1.161541681 0.987627182 0.964569838 0.971546375 1.158666015 1.30835314 1.514159933 1.79571697 1.078115865 1 11.84218054 -7.645489746 1.185103658 1.055237336 1.893603212 0.936899428 0.065298171 0.191756188 0.340922354 0.012806788 0.166453571 2.26E-08 7.645489746 0.838365876 RAS(ph)YDYNQDR ddPTM_HeLa_Romidepsin_16h_R1 1 RASYDYNQDR 10 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 1 0 RAS(1)YDYNQDR 92.295 0.010489 3800500 1423.2 1469.2 1155.6 1452.5 1714 1653.1 1664.6 1421.7 1614.5 1381.5 TRUE FALSE FALSE 1405.853491 1489.883436 1175.712733 1620.444884 1626.528184 1547.472245 1805.991082 1462.834646 1470.095076 1345.608431 1.044771613 1.10721916 0.873740612 1.204246976 1.208767831 1.150016758 1.342137163 1.087117629 1.092513277 1 10.39404293 -9.220679369 22.75269483 1.019454271 1.204321352 0.517481918 0.084256088 92.68870332 51739.64281 0.011024339 0.018281496 6.02E-10 9.220679369 0.184867081 RASGLS(ph)TEGATGPSADTSGSELDGR ddPTM_HeLa_Romidepsin_16h_R1 1 RASGLSTEGATGPSADTSGSELDGR 25 1 Q7Z628 Q7Z628 NET1 Neuroepithelial cell-transforming gene 1 protein 1 0 RAS(0.25)GLS(0.375)T(0.375)EGATGPSADTSGSELDGR 85.013 3.26E-05 10304000 254.63 187.3 266.25 201.43 207.98 0 155.41 157.09 244.13 283.27 TRUE FALSE FALSE 251.5264716 189.9368143 270.8839696 224.7202844 197.3660045 0 168.6105215 161.6351513 222.2944014 275.9106046 0.911623067 0.688399834 0.981781653 0.814467732 0.715325911 0 0.611105622 0.585824353 0.805675453 1 8.108057097 -8.577767639 3.440946154 0.927733391 0.411730537 0.540633513 0.185423009 0.11303043 2.736645675 0.025952611 0.056201638 2.64E-09 8.577767639 -0.516002853 RASGQAFELILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RASGQAFELILSPR 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 RASGQAFELILS(1)PR 93.427 0.0047644 40275000 1065.4 1276.6 1059.3 1325.2 1620.7 1673.6 1454.1 1635.7 1148.1 1055.8 TRUE FALSE FALSE 1052.414495 1294.572008 1077.736672 1478.425859 1537.989631 1566.662361 1577.611218 1683.026399 1045.411061 1028.370164 1.023381008 1.258858001 1.04800461 1.437639783 1.49556034 1.523442061 1.534088865 1.636595905 1.016570781 1 10.00614394 -9.210084506 0.809633739 1.006233819 1.599270592 0.895745041 0.078241392 0.118011321 0.151583516 0.013973558 0.034150864 6.16E-10 9.210084506 0.593036773 RASLS(ph)DLTDLEDIEGLTVR ddPTM_HeLa_Romidepsin_16h_R1 1 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;Q8WZ73-2;Q8WZ73;J3KSU7;K7EN88;Q8WZ73-3 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 0 RAS(0.346)LS(0.653)DLT(0.002)DLEDIEGLTVR 72.399 0.0042389 3465300 903.44 1061.9 1088 1150.6 837.43 976.55 807.8 1083.2 916.53 843.99 TRUE FALSE FALSE 892.4285258 1076.849456 1106.936184 1283.637786 794.6928222 914.1516067 876.4145118 1114.540683 834.5532613 822.0630181 1.085596245 1.309935409 1.346534462 1.561483435 0.966705477 1.112021325 1.06611597 1.355784968 1.015193778 1 9.683105183 -10.44124913 3.874318293 1.035741804 1.238400869 0.271101391 0.160307877 0.254423235 6.862377794 0.02947821 0.033011608 3.62E-11 10.44124913 0.202659065 RASLSDLT(ph)DLEDIEGLTVR ddPTM_HeLa_Romidepsin_16h_R1 1 RASLSDLTDLEDIEGLTVR 19 1 J3KSI3;Q8WZ73-2;Q8WZ73;J3KSU7;K7EN88;Q8WZ73-3 J3KSI3 RFFL;hCG_2039718 E3 ubiquitin-protein ligase rififylin 1 0 RAS(0.039)LS(0.039)DLT(0.461)DLEDIEGLT(0.461)VR 124.99 7.31E-08 0 404.89 284.85 344.3 260.61 350.59 393.16 171.6 317.11 402.96 398.23 TRUE FALSE FALSE 399.9550449 288.8601258 350.2923971 290.7429544 332.6980841 368.0383449 186.1756997 326.2850775 366.9182484 387.8839272 1.031120438 0.744707645 0.903085621 0.749561748 0.857725883 0.948836286 0.479977866 0.84119257 0.945948575 1 8.599481186 -10.26577591 24.87362143 1.014695767 0.789017316 0.361588281 0.12257006 227.8723555 1307034.63 0.019554657 0.022775392 5.42E-11 10.26577591 -0.225678451 RASPNSDDT(ph)VLSPQELQK ddPTM_HeLa_Romidepsin_16h_R1 1 RASPNSDDTVLSPQELQK 18 1 Q9UH62 Q9UH62 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 0 RASPNS(0.002)DDT(0.887)VLS(0.111)PQELQK 152.07 6.83E-05 4581400 1043.3 1148.4 814.8 1451.6 1066.2 1355.4 1234.7 1159.8 1306.1 1286.7 TRUE FALSE FALSE 1030.583858 1164.567205 828.9812522 1619.440822 1011.787835 1268.794314 1339.575387 1193.356983 1189.279145 1253.271349 0.822315023 0.929221917 0.661453925 1.292170944 0.807317455 1.012385958 1.068863011 0.952193621 0.948939865 1 10.29148309 -9.273638678 24.9988855 0.897793645 1.015964426 0.215742476 0.142233864 1142.470815 2341155.454 0.021456929 0.032923566 5.33E-10 9.273638678 0.118170781 RASS(ph)ASVPAVGASAEGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RASSASVPAVGASAEGTR 18 1 A0A2R8YFI4;V9GYZ0;Q9BZ23-3;Q9BZ23-4;Q9BZ23 A0A2R8YFI4 PANK2 "Pantothenate kinase 2, mitochondrial" 1 0 RAS(0.061)S(0.916)AS(0.021)VPAVGASAEGT(0.001)R 93.342 0.0075615 3701500 1187.7 1068.1 969.56 1082.7 1241.6 982.22 765.67 1022.8 1534 1226.2 TRUE FALSE FALSE 1173.223856 1083.13674 986.4347851 1207.886868 1178.236519 919.459312 830.7059907 1052.393104 1396.795198 1194.343147 0.982317233 0.906889065 0.825922422 1.011339891 0.986514237 0.769845177 0.695533769 0.881148024 1.169509116 1 10.22200168 -8.144719915 0.415608876 0.996792372 0.701328597 0.429751201 0.098077638 1.882867842 0.357899756 0.024065397 0.245113713 7.17E-09 8.144719915 -0.295463775 RASS(ph)LNFLNK ddPTM_HeLa_Romidepsin_16h_R1 1 RASSLNFLNK 10 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 0 RAS(0.004)S(0.996)LNFLNK 132.56 0.0097702 36388000 2661.2 2259.2 2754.4 2385.5 2784.2 2815.6 2294.5 2019.4 2777.2 2032.1 TRUE FALSE FALSE 2628.764271 2291.005077 2802.339177 2661.322734 2642.111885 2635.692247 2489.394773 2077.828153 2528.800276 1979.305749 1.328124405 1.15747912 1.415819248 1.344573841 1.334867989 1.33162461 1.257711081 1.049776243 1.277619831 1 10.95077877 -12.30206223 0.814295039 0.981919786 1.287268349 0 0.131150731 0.454843608 0.488770189 0.091244246 0.019419579 4.99E-13 12.30206223 0.305348563 RASS(ph)LNVLNVGGK ddPTM_HeLa_Romidepsin_16h_R1 1 RASSLNVLNVGGK 13 1 Q07866-6;H0YG16;G3V5R9;Q07866-7;Q07866-4;Q07866-9;H0YJK1 Q07866-6 KLC1 Kinesin light chain 1 1 0 RAS(0.002)S(0.998)LNVLNVGGK 162.48 0.00049725 46275000 4165.3 3344.9 3248.6 3515.8 3092.2 2573 2517.1 3489.6 3635.1 2906.3 TRUE FALSE FALSE 4114.531721 3391.98959 3305.14052 3922.313338 2934.393495 2408.593604 2730.902411 3590.56607 3309.967552 2830.793907 1.453490383 1.198246747 1.167566636 1.385587742 1.036597362 0.850854454 0.964712551 1.268395435 1.169271823 1 11.466991 -8.616863299 9.082546349 1.22451241 1.008824487 0.289495579 0.15168009 0.337175063 29.38253145 0.028448828 0.056960491 2.42E-09 8.616863299 -0.215687923 RASS(ph)LQTSPGS(ph)S(ph)SHLSPR ddPTM_HeLa_Romidepsin_16h_R1 1 RASSLQTSPGSSSHLSPR 18 1 Q8NHM5-2;Q8NHM5-3;Q8NHM5;A0A0C4DGG3 Q8NHM5-2 KDM2B Lysine-specific demethylase 2B 3 0 RAS(0.469)S(0.526)LQT(0.165)S(0.049)PGS(0.792)S(0.447)S(0.399)HLS(0.152)PR 56.766 0.015354 56388000 977.54 590.71 777.54 598.82 697.87 947.48 855.37 1010.1 864.97 700.5 TRUE FALSE FALSE 965.6253665 599.0260309 791.0727575 668.0583859 662.2550898 886.9390859 928.0251064 1039.32565 787.6049168 682.300909 1.415248542 0.877949924 1.159419176 0.979125745 0.970620266 1.299923647 1.36014051 1.523265814 1.154336608 1 9.414264328 -7.769208939 2.230574458 1.143921669 1.486078438 0.450438617 0.153465312 0.325843096 3.070037233 0.027989856 0.145933385 1.70E-08 7.769208939 0.342156769 RASVFVK ddPTM_HeLa_Romidepsin_16h_R1 1 RASVFVK 7 1 H7C3I1;F6VDH7;Q3KNR6;Q8IZP2;Q8NFI4;P50502 H7C3I1 ST13;ST13P4;ST13P5 Putative protein FAM10A4;Putative protein FAM10A5;Hsc70-interacting protein 0 0 75.738 0.022732 0 245.08 259.78 487.33 518.28 493.47 483.7 618.61 179.55 476.52 166.45 FALSE FALSE TRUE 242.0928707 263.4371897 495.8117742 578.2059722 468.2863845 452.7931311 671.154718 184.744996 433.8988577 162.125605 1.493242666 1.624895646 3.058195368 3.566407491 2.88841719 2.792853918 4.139720669 1.139517697 2.676312959 1 7.340968148 -9.849264657 3.496945965 1.244037247 3.012722438 0.282871158 0.857228979 0.119623859 2.895550836 0.110104621 0.148709421 1.41E-10 9.849264657 1.768685191 RAT(ph)ISSPLELEGTVSR ddPTM_HeLa_Romidepsin_16h_R1 1 RATISSPLELEGTVSR 16 1 Q96GS4 Q96GS4 C17orf59 Uncharacterized protein C17orf59 1 0 RAT(0.896)IS(0.075)S(0.028)PLELEGTVSR 78.401 0.011227 3341700 549.59 686.8 508.44 415.58 661.89 1015.6 815.61 943.22 816.93 655.9 TRUE FALSE FALSE 542.8913857 696.4687884 517.2891849 463.631315 628.1112834 950.7064377 884.887893 970.5105825 743.8617348 638.8596234 0.849781964 1.090174998 0.809707119 0.72571704 0.983175741 1.488130417 1.385105367 1.519129629 1.164358659 1 9.319355153 -8.299874167 5.088669755 0.91651781 1.458217548 0.774540013 0.127624064 0.05369959 3.573689415 0.015403225 0.036132676 5.01E-09 8.299874167 0.541699738 RAT(ph)PEPGDEGEPGR ddPTM_HeLa_Romidepsin_16h_R1 1 RATPEPGDEGEPGR 14 1 M0QZR4;M0QZH8;M0QYS3;M0QYC1 M0QZR4 ARHGEF1 1 0 RAT(1)PEPGDEGEPGR 160.64 0.00013207 6091600 1719.3 1598.5 2258.7 2202 1952.7 1405.9 1320 1450.7 2411.9 1892.4 TRUE FALSE FALSE 1698.34451 1621.003725 2298.011726 2456.605601 1853.046432 1316.067527 1432.120767 1492.673716 2196.173623 1843.235175 0.921393283 0.879434023 1.246727361 1.332768403 1.005322846 0.713998705 0.776960415 0.809811865 1.191477709 1 10.84802444 -8.270442967 23.31121465 1.008399375 0.767927337 0.431840609 0.149853104 220.628886 571232.9785 0.022402614 0.050867004 5.36E-09 8.270442967 -0.240472038 RATVLEDS(ph)Y(ph)RRIMGVK ddPTM_HeLa_Romidepsin_16h_R1 1 RATVLEDSYRRIMGVK 16 3 H0Y8X6;P46934-4;P46934-3;P46934-2;P46934 H0Y8X6 NEDD4 E3 ubiquitin-protein ligase NEDD4 2 0 RAT(0.005)VLEDS(0.997)Y(0.998)RRIMGVK 43.408 0.0042454 0 857.43 747.35 793.42 764.16 688.12 684.89 745.46 730.67 938.74 974.98 TRUE FALSE FALSE 846.9793134 757.8712129 807.2291423 852.5157747 653.0026687 641.1277394 808.7793538 751.8107836 854.7767433 949.649879 0.891885875 0.798053293 0.850028163 0.897715878 0.687624653 0.675120119 0.851660566 0.791671542 0.900096722 1 9.891251902 -10.62980168 0.421639491 1.004220085 0.758048421 0.460117517 0.069572381 0.468780018 0.223169734 0.041713079 0.034620954 2.35E-11 10.62980168 -0.246171665 RAVS(ph)PSNPK ddPTM_HeLa_Romidepsin_16h_R1 2 RAVSPSNPK 9 1 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7;Q14244-2;Q14244-4 A0A087WZ40 MAP7 Ensconsin 1 0 RAVS(0.999)PS(0.001)NPK;RAVS(0.988)PS(0.012)NPK ; 84.169 0.015499 12300200 3593.8 3723.04 5151 3947.5 3471.27 2904.36 5519.9 1190.03 6312.2 3841.01 TRUE FALSE FALSE 3549.997383 3775.453055 5240.650994 4403.928524 3294.118139 2718.780769 5988.760168 1224.46164 5747.621023 3741.220006 0.948887629 1.009150237 1.400786638 1.177137008 0.88049303 0.726709673 1.600750599 0.327289397 1.536295918 1 11.86929309 -7.219030146 23.58542262 1.027655576 0.327284617 0.355803976 0.29466275 11145.64028 6198253.986 0.031902816 17.83568035 6.04E-08 7.219030146 -0.700370959 RAVSEGCAS(ph)EDEVEGEA ddPTM_HeLa_Romidepsin_16h_R1 2 RAVSEGCASEDEVEGEA 17 1 Q9BYX2-6;Q9BYX2-5;Q9BYX2-4;Q9BYX2-2;Q9BYX2 Q9BYX2-6 TBC1D2 TBC1 domain family member 2A 1 0 RAVS(0.038)EGCAS(0.962)EDEVEGEA;RAVS(0.133)EGCAS(0.867)EDEVEGEA ; 79.471 0.029733 21200000 3996.5 3652.8 3523.6 588.04 3726.8 3774.7 3131.9 3879.5 3890 3496.4 TRUE FALSE FALSE 3947.789121 3704.224214 3584.92678 656.0319516 3536.607489 3533.508852 3397.923508 3991.747212 3542.068657 3405.563024 1.159217754 1.087698036 1.052667872 0.192635387 1.03847953 1.037569655 0.997756754 1.172125485 1.040083132 1 11.73367762 -9.489608315 24.99987237 1.07784254 0.881740553 0.113218618 0.252131554 1070.871187 804668.952 0.038963198 0.059493268 3.24E-10 9.489608315 -0.196101986 RDAFTDS(ph)AIS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 RDAFTDSAISAK 12 1 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4;F8W0B5;A0A5F9ZH85;F8WB06 Q99700;F8WB06 ATXN2 Ataxin-2 2 0 RDAFT(0.216)DS(0.787)AIS(0.997)AK 89.189 0.0021295 0 726.95 728.27 387.49 446.55 446.71 501.54 399.49 470.12 872.01 766.7 TRUE FALSE FALSE 718.0896538 738.5226042 394.2341009 498.1822121 423.9127218 469.4932126 433.4226706 483.7221805 794.0152416 746.7810235 0.961579943 0.988941311 0.527911246 0.667106148 0.567653313 0.628689265 0.580387901 0.647743 1.063250426 1 9.544541457 -9.767931513 24.99998725 0.981881603 0.604650411 0.946564263 0.046468399 18.39080595 70819.49654 0.005680591 0.007565048 1.71E-10 9.767931513 -0.377231192 RDASEETST(ph)SVMQK ddPTM_HeLa_Romidepsin_16h_R1 1 RDASEETSTSVMQK 14 1 Q9H0W8-2;Q9H0W8;M0QZH1;M0QX70;M0QYR7;M0R2N0;M0QZC7 Q9H0W8-2 SMG9 Protein SMG9 1 0 RDAS(0.012)EET(0.158)S(0.158)T(0.577)S(0.095)VMQK 76.01 0.0026609 0 250.45 251.11 219.86 242.82 220.98 194.29 198.75 244.01 450.75 204.32 TRUE FALSE FALSE 247.3974191 254.6451332 223.6865711 270.8959909 209.702566 181.875496 215.63182 251.0700444 410.4337911 199.0117369 1.243129792 1.279548317 1.123986829 1.361206103 1.053719591 0.913893315 1.08351308 1.261584107 2.062359725 1 7.636709708 -7.249166974 22.90346876 1.125938203 1.261584385 0 0.322088324 1344.400391 2508843.949 0.019915272 0.416520121 5.63E-08 7.249166974 0.135646183 RDDGSWEVIEGYR ddPTM_HeLa_Romidepsin_16h_R1 2 RDDGSWEVIEGYR 13 1 P49448;P00367 P49448 GLUD2;GLUD1 "Glutamate dehydrogenase 2, mitochondrial;Glutamate dehydrogenase 1, mitochondrial" 0 0 ; ; 212.83 1.85E-23 9197000 2686 2077.56 2223.4 2647.6 2412.3 2990 2191.04 2547.7 2574 2294.4 FALSE FALSE TRUE 2653.261999 2106.807944 2262.097344 2953.727969 2289.191329 2798.94865 2377.146883 2621.41368 2343.774993 2234.791157 1.187252773 0.942731466 1.012218675 1.321702012 1.024342396 1.252443049 1.063699789 1.173001634 1.0487669 1 11.1259243 RDEFEFLEK ddPTM_HeLa_Romidepsin_16h_R1 2 RDEFEFLEK 9 1 A0A3B3IUA7;Q14258 A0A3B3IUA7 TRIM25 E3 ubiquitin/ISG15 ligase TRIM25 0 0 ; ; 133.75 0.004492 10710000 9866.4 10135.7 9988.8 9850.3 11547.7 11276 11371.8 11716.8 11382 10064 FALSE FALSE TRUE 9746.144522 10278.39065 10162.65087 10989.23803 10958.37778 10555.49999 12337.72041 12055.80712 10363.96541 9802.535829 0.994247274 1.048544053 1.036736927 1.121060736 1.117912545 1.076813202 1.258625383 1.229866162 1.057273913 1 13.25893929 -7.410978774 0.387469819 0.990683263 1.430342508 0.763978031 0.041406426 1.265198852 0.14062422 0.010177507 0.252703194 3.88E-08 7.410978774 0.439659245 RDELLAQHAAGALGLPDLVAVLTR ddPTM_HeLa_Romidepsin_16h_R1 2 RDELLAQHAAGALGLPDLVAVLTR 24 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 0 0 ; ; 106.63 2.31E-06 3257600 904.89 736.96 1080.98 991.01 1304.24 1498.14 1224.56 1492.69 860.18 732.6 FALSE FALSE TRUE 893.8608526 747.3349422 1099.794003 1105.595239 1237.679766 1402.413689 1328.574096 1535.87863 783.2433464 713.5669464 1.25266572 1.047322814 1.541262539 1.54939245 1.734497054 1.965356854 1.861877295 2.152395984 1.097645218 1 9.478904979 -8.726365946 0.447191268 1.051634542 2.261387218 0.921077287 0.109027149 0.321949076 0.096567501 0.032736 0.170471445 1.88E-09 8.726365946 1.209752676 up RDET(ph)MQPAKPSFLEY(ph)FEQKEK ddPTM_HeLa_Romidepsin_16h_R1 1 RDETMQPAKPSFLEYFEQKEK 21 3 F5H5B4;Q13043-2;Q13043 F5H5B4 STK4 Serine/threonine-protein kinase 4;Serine/threonine-protein kinase 4 37kDa subunit;Serine/threonine-protein kinase 4 18kDa subunit 2 0 RDET(0.999)MQPAKPS(0.073)FLEY(0.928)FEQKEK 40.186 0.023788 6665300 3282.2 3550.7 2704.4 2751.9 3218.1 3036.4 2381.4 3035.8 3006.9 3084.1 TRUE FALSE FALSE 3242.195284 3600.686848 2751.468948 3070.087626 3053.868349 2842.38384 2583.676057 3123.636083 2737.955333 3003.974637 1.079301817 1.198640895 0.915942802 1.022008504 1.016609232 0.946207669 0.860085842 1.039834373 0.911444224 1 11.55265692 -8.695573002 1.186725919 1.045006256 0.941862948 0.087756973 0.088295886 0.560086567 1.541649428 0.01267255 0.037410165 2.02E-09 8.695573002 -0.103143307 RDFSAT(ph)S(ph)GLLQHQAS(ph)LSS(ph)MKPHK ddPTM_HeLa_Romidepsin_16h_R1 1 RDFSATSGLLQHQASLSSMKPHK 23 2 Q8TAW3 Q8TAW3 ZNF671 Zinc finger protein 671 4 0 RDFS(0.503)AT(0.563)S(0.934)GLLQHQAS(0.98)LS(0.041)S(0.978)MKPHK 52.685 0.0031076 0 255.06 445.89 369.76 270.11 311.89 332.06 309.72 401.23 531.98 428.79 TRUE FALSE FALSE 251.9512306 452.1672511 376.1955177 301.3413891 295.9730895 310.8424377 336.0276091 412.838957 484.3983764 417.649974 0.603259299 1.082646425 0.900743544 0.7215166 0.708663014 0.74426543 0.804567533 0.988480744 1.159819003 1 8.706150538 -9.263355134 24.9551079 0.83844281 0.786665333 0 0.173605264 776.32048 10112576.57 0.027762338 0.043783211 5.45E-10 9.263355134 -0.051777477 RDLEIER ddPTM_HeLa_Romidepsin_16h_R1 1 RDLEIER 7 1 Q92597-3;Q92597-2;Q92597;F8WBF9;Q5TH30;Q9UGV2-3;Q9UGV2-2;Q9UGV2 Q92597-3 NDRG1;NDRG3 Protein NDRG1;Protein NDRG3 0 0 90.601 0.028611 3662500 1469.4 1647.1 1613.3 1394.8 1866.8 1787.7 1614.7 1388.7 1516.1 1628.2 FALSE FALSE TRUE 1451.490388 1670.287917 1641.37881 1556.073339 1771.53023 1673.47174 1751.852578 1428.879843 1380.496219 1585.899129 0.91524761 1.053211952 1.034983108 0.981193135 1.117051014 1.055219534 1.10464313 0.90099037 0.870481731 1 10.6310853 -10.24668117 24.40302448 0.959978038 1.039806413 0.31679073 0.067028827 590.6224421 976607.7998 0.010236836 0.012504763 5.67E-11 10.24668117 0.079828376 RDLFAFQES(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 RDLFAFQESPPR 12 1 E7EX48;P51957-3;P51957-2;P51957 E7EX48 NEK4 Serine/threonine-protein kinase Nek4 1 0 RDLFAFQES(1)PPR;RDLFAFQES(1)PPR ; 77.324 0.016213 6510000 3537.8 3348.8 3336.3 3342.5 3233.8 3365.8 3539.1 3556.2 4032.7 3521.3 TRUE FALSE FALSE 3494.679933 3395.944494 3394.366902 3728.975577 3068.767119 3150.736243 3839.711066 3659.093036 3672.005212 3429.816118 1.018911747 0.990124362 0.989664397 1.087223177 0.894732258 0.918631243 1.119509307 1.066848166 1.070612851 1 11.74391552 -7.73875749 24.99895741 0.998987167 1.093178784 0.317497766 0.056738076 199.996577 220423.9405 0.007085826 0.026474697 1.82E-08 7.73875749 0.094191617 RDLNES(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 RDLNESPVK 9 1 Q96RL1-2;Q96RL1-3;Q96RL1;Q96RL1-4 Q96RL1-2 UIMC1 BRCA1-A complex subunit RAP80 1 0 RDLNES(1)PVK;RDLNES(1)PVK ; 82.505 0.016575 19966600 8554.2 7684.5 9267.2 7788.7 7382.5 7416.6 6632.2 4404.9 9224.3 8191.4 TRUE FALSE FALSE 8449.93812 7792.682593 9428.491729 8689.266141 7005.743477 6942.703196 7195.538902 4532.348832 8399.255505 7978.586247 1.059077117 0.976699675 1.181724611 1.089073411 0.878068277 0.870167092 0.901856379 0.568064152 1.052724787 1 12.96191742 -6.796411267 0.755276962 1.0360066 4.04E-15 0.767641773 0.077402522 1.767661306 0.443481088 0.012855162 1.82374793 1.60E-07 6.796411267 -1.0360066 RDLQELR ddPTM_HeLa_Romidepsin_16h_R1 1 RDLQELR 7 1 Q9P253 Q9P253 VPS18 Vacuolar protein sorting-associated protein 18 homolog 0 0 107.66 0.019791 2449900 1709.6 1458.2 1592.1 1598.8 2006.3 1683.3 1613.2 1567.7 1645.9 1592.5 FALSE FALSE TRUE 1688.762738 1478.728578 1619.809833 1783.660779 1903.911024 1575.742563 1750.225168 1613.058926 1498.686582 1551.12662 1.088732999 0.953325511 1.044279565 1.149913073 1.227437528 1.015869718 1.128357379 1.039927305 0.96619229 1 10.59910074 -9.354732551 6.874678126 1.034812087 1.114071429 0.338151779 0.06707402 0.278274844 17.64610243 0.010229544 0.015664277 4.42E-10 9.354732551 0.079259343 RDNYVPEVSALDQEIIEVDPDTK ddPTM_HeLa_Romidepsin_16h_R1 2 RDNYVPEVSALDQEIIEVDPDTK 23 1 H0YN88;A0A075B716;H3BNC9;P08708 H0YN88 RPS17 40S ribosomal protein S17 0 0 ; ; 137.43 3.27E-06 5254400 2511.3 2354.7 2523.2 1918.71 2716.8 2836.3 2269 2421.4 2946.1 3053.1 FALSE FALSE TRUE 2480.69131 2387.849528 2567.115238 2140.560278 2578.151558 2655.069584 2461.728803 2491.459389 2682.593437 2973.780022 0.834187899 0.802967775 0.863249877 0.719811238 0.866961086 0.892826492 0.827811333 0.837808907 0.902082003 1 11.53808222 -12.05200127 0.727443692 1.006552425 0.829438015 0.408198218 0.052926923 0.345292513 0.317287868 0.035477609 0.009412542 8.87E-13 12.05200127 -0.177114409 RDPSSNDINGGMEPT(ph)PSTVSTPSPSADLLGLR ddPTM_HeLa_Romidepsin_16h_R1 1 RDPSSNDINGGMEPTPSTVSTPSPSADLLGLR 32 1 O95782-2;O95782 O95782-2 AP2A1 AP-2 complex subunit alpha-1 1 0 RDPS(0.001)S(0.001)NDINGGMEPT(0.437)PS(0.095)T(0.095)VS(0.047)T(0.108)PS(0.15)PS(0.066)ADLLGLR 67.758 1.34E-05 39759000 582.55 452 602.15 522.09 558.21 883.46 711.71 773.25 522.64 642.96 TRUE FALSE FALSE 575.4496565 458.3632679 612.6301682 582.4565023 529.7224607 827.0097572 772.1626296 795.6227688 475.8937694 626.2558065 0.918873167 0.731910608 0.978242695 0.93006164 0.845856366 1.320562219 1.232982787 1.27044374 0.759903165 1 9.290608265 -8.257333206 24.99965059 0.935348958 1.27049492 0.771340998 0.095084317 122.4556406 745543.6657 0.011867101 0.02909402 5.53E-09 8.257333206 0.335145962 RDQALTEEHAR ddPTM_HeLa_Romidepsin_16h_R1 2 RDQALTEEHAR 11 1 P12814-2;P12814;P12814-3;P12814-4;H9KV75;H0YJ11 P12814-2 ACTN1 Alpha-actinin-1 0 0 ; ; 155.47 0.00043268 4271700 1104.15 818.22 1740.66 1278.95 1403.47 1650.26 1470.16 401.21 1553.53 1181.94 FALSE FALSE TRUE 1090.692195 829.7389226 1770.955457 1426.828217 1331.845689 1544.813712 1595.035354 412.8183783 1414.578386 1151.233028 0.947412182 0.720739331 1.538311891 1.239391315 1.156886274 1.341877512 1.385501731 0.358588025 1.228750697 1 10.16896417 -9.779741277 24.99996591 0.955390979 1.190242281 0.080380416 0.317693243 373.1833249 509757.9182 0.046146277 0.060711068 1.66E-10 9.779741277 0.234851302 RDS(ph)DGVDGFEAEGK ddPTM_HeLa_Romidepsin_16h_R1 4 RDSDGVDGFEAEGK 14 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 1 0 RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK;RDS(1)DGVDGFEAEGK ;;; 155.24 0.00016946 47908400 17191.8 14659.7 16875.5 13934.3 15906 16612.9 16731.7 16675.6 18946.1 17872.8 TRUE FALSE FALSE 16982.25973 14866.07964 17169.211 15545.44933 15094.25747 15551.38931 18152.89018 17158.08218 17251.51336 17408.46208 0.975517519 0.853957091 0.986256622 0.892982347 0.867064385 0.893323559 1.042762428 0.985617345 0.990984343 1 14.08750114 -10.49391687 17.54685067 0.989200295 0.931348327 0.182485818 0.056153919 14.08747276 8536.410403 0.010059185 0.011006897 3.21E-11 10.49391687 -0.057851968 RDS(ph)GVGSGLEAQESWER ddPTM_HeLa_Romidepsin_16h_R1 1 RDSGVGSGLEAQESWER 17 1 A0A0A0MTG6;Q12770-4;Q12770-2;Q12770 A0A0A0MTG6 SCAP Sterol regulatory element-binding protein cleavage-activating protein 1 0 RDS(0.998)GVGS(0.002)GLEAQESWER 76.051 0.0043289 0 386.07 343.87 142.78 216.89 133.94 525.49 169.11 494.37 317.17 294.14 TRUE FALSE FALSE 381.3644303 348.7110109 145.265026 241.9678423 127.104542 491.9128849 183.4741992 508.673816 288.8015208 286.4982004 1.331123301 1.217149045 0.507036434 0.8445702 0.443648658 1.716984205 0.640402624 1.77548695 1.008039563 1 8.162382267 RDS(ph)IVAELDR ddPTM_HeLa_Romidepsin_16h_R1 4 RDSIVAELDR 10 1 M0QXB4;O14579-3;O14579 M0QXB4 COPE Coatomer subunit epsilon 1 0 RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR;RDS(1)IVAELDR ;;; 122.1 0.0031682 13239400 2501.49 2220.94 2398.68 1984.06 3227.62 3450.99 3043.71 3727.95 2583.11 2294.53 TRUE FALSE FALSE 2471.000878 2252.206452 2440.428019 2213.466352 3062.902507 3230.482877 3302.242651 3835.812352 2352.070172 2234.91778 1.105633907 1.007735708 1.091954273 0.990401693 1.370476594 1.445459384 1.477567847 1.716310276 1.052419106 1 11.12600604 -8.31162684 1.131043613 1.043452082 1.63624492 0.902770366 0.07571012 0.121764023 0.274811051 0.012001435 0.054175935 4.88E-09 8.31162684 0.592792838 RDS(ph)LASLFPSEEEER ddPTM_HeLa_Romidepsin_16h_R1 2 RDSLASLFPSEEEER 15 1 Q6P597;Q6P597-3;Q6P597-2;K7ENJ3;K7EL76 Q6P597 KLC3 Kinesin light chain 3 1 0 RDS(0.999)LAS(0.001)LFPSEEEER;RDS(0.998)LAS(0.002)LFPSEEEER ; 124.77 0.00086311 5441900 275.13 151.03 204.788 245.404 778.73 1742.68 1609.26 1957.95 297.506 355.96 TRUE FALSE FALSE 271.7766097 153.1562043 208.3522492 273.7787651 738.9885023 1631.328372 1745.950504 2014.600194 270.8963182 346.7121079 0.78386824 0.44173884 0.600937332 0.789642931 2.131418215 4.705138168 5.035735599 5.81058506 0.78132927 1 8.437594409 -8.314808798 1.960285327 0.818470406 5.454915739 0.986830307 0.230814957 0.028696843 0.211409513 0.03807663 0.11535045 4.84E-09 8.314808798 4.636445333 up RDS(ph)LEEGELR ddPTM_HeLa_Romidepsin_16h_R1 2 RDSLEEGELR 10 1 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;E7ESP2;J3KS35;A0A087X1I0;A0A087WYI9;E9PFJ2 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 1 0 RDS(1)LEEGELR;RDS(1)LEEGELR ; 125.36 0.0074771 30689000 3556.6 3591.6 3905.5 1934.68 3251.5 3753 3226.1 2859.8 4363.5 3863.9 TRUE FALSE FALSE 3513.250791 3642.162639 3973.473589 2158.376805 3085.563822 3513.195412 3500.124853 2942.543801 3973.217631 3763.515321 0.933502455 0.967755497 1.055787807 0.573500204 0.819862166 0.93348774 0.930014775 0.781860455 1.055719797 1 11.87786513 RDS(ph)LGTYSSR ddPTM_HeLa_Romidepsin_16h_R1 2 RDSLGTYSSR 10 1 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 RDS(0.971)LGT(0.006)YS(0.002)S(0.021)R;RDS(0.999)LGTYSS(0.001)R ; 92.906 0.010221 35291000 1769.98 1614.61 1866.15 1388.69 1987.27 1929.65 1732.71 1762.07 1946.3 1903.42 TRUE FALSE FALSE 1748.406803 1637.340522 1898.629558 1549.256872 1885.852196 1806.351593 1879.886344 1813.052715 1772.218053 1853.968874 0.943061573 0.883154267 1.024089231 0.83564341 1.017197334 0.97431603 1.013979453 0.977930504 0.955904966 1 10.85640131 RDS(ph)LTGSSDLYK ddPTM_HeLa_Romidepsin_16h_R1 3 RDSLTGSSDLYK 12 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;E9PR38;Q14671-4;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 0 RDS(0.973)LT(0.026)GS(0.002)SDLYK;RDS(0.905)LT(0.09)GS(0.002)S(0.002)DLYK;RDS(0.994)LT(0.005)GSSDLYK ;; 154.81 0.00040327 100194200 7004.5 6374.1 7828.2 6118.3 10780.1 14096 12416 14403.5 7441.9 6219.4 TRUE FALSE FALSE 6919.12646 6463.834747 7964.446537 6825.726633 10229.95127 13195.31109 13470.61473 14820.24255 6776.277825 6057.819091 1.142181098 1.067023404 1.314738261 1.126763036 1.688718517 2.178227988 2.223673987 2.446465027 1.118600229 1 12.56458278 -8.445580848 1.31754414 1.077183753 2.386070352 0.967536574 0.095175233 0.053767766 0.176603796 0.015070213 0.051959735 3.58E-09 8.445580848 1.308886599 up RDS(ph)PLQGSGQQNSQAGQR ddPTM_HeLa_Romidepsin_16h_R1 3 RDSPLQGSGQQNSQAGQR 18 1 C9J840;E7EX83;A0A0D9SG62;H7C0P6;E7ENQ1;G3XAA2;H7C360;G5E948;A0A0D9SEY1;O95819-4;O95819-2;O95819;O95819-5;O95819-3;E7EN19;O95819-6 C9J840 MAP4K4 Mitogen-activated protein kinase kinase kinase kinase 4 1 0 RDS(1)PLQGSGQQNSQAGQR;RDS(0.999)PLQGS(0.001)GQQNSQAGQR;RDS(1)PLQGSGQQNSQAGQR ;; 128.72 5.85E-09 5481500 1829.66 1558.89 1673.4 1560.23 1595.71 1628.46 1650.04 1599.63 1882.47 1735.36 TRUE FALSE FALSE 1807.3594 1580.836094 1702.524825 1740.631134 1514.274964 1524.406662 1790.194356 1645.91277 1714.097168 1690.275097 1.069269377 0.935253733 1.00724718 1.029791622 0.895874859 0.90186897 1.0591142 0.973754375 1.014093606 1 10.72304235 -10.26223601 24.99989956 1.032710539 0.973177371 0.193705141 0.051964686 88.34649877 2772532.931 0.009346487 0.011023751 5.47E-11 10.26223601 -0.059533168 RDS(ph)PPPPAR ddPTM_HeLa_Romidepsin_16h_R1 1 RDSPPPPAR 9 1 O96013;O96013-2;O96013-4;M0R2X4 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 0 RDS(1)PPPPAR 75.788 0.021077 13515000 363.07 417.46 769.14 792.97 619.9 666.05 888.69 211.06 1000.8 582.81 TRUE FALSE FALSE 358.6447632 423.3370128 782.5265591 884.6569224 588.2641898 623.4915546 964.1753064 217.1666881 911.2859415 567.6685122 0.63178555 0.745746864 1.378492099 1.558404075 1.03628117 1.098337394 1.69848298 0.382558982 1.605313527 1 9.148904909 -9.769176592 24.94681569 0.81523449 1.220417084 0 0.42607875 178.6792909 576108.5078 0.05369417 0.071307452 1.70E-10 9.769176592 0.405182594 RDS(ph)PTYDPYK ddPTM_HeLa_Romidepsin_16h_R1 1 RDSPTYDPYK 10 1 F5H0Q6;A0A0A0MQS2;Q8N2M8-3;Q8N2M8;Q8N2M8-4 F5H0Q6 CLASRP CLK4-associating serine/arginine rich protein 1 0 RDS(0.994)PT(0.006)YDPYK 99.941 0.0072796 12055000 7086.7 6598.4 7392.1 5535.8 7027.1 7199.2 6129.7 6048.2 6705.9 7507.7 TRUE FALSE FALSE 7000.324575 6691.292448 7520.7564 6175.875243 6668.480865 6739.194354 6650.356565 6223.195125 6106.107509 7312.648872 0.957289855 0.915029911 1.02845857 0.844546942 0.911910442 0.921580466 0.909431956 0.851017905 0.83500625 1 12.83617838 -4.000000053 0.104610726 1.046352443 0.521114531 0 0.066306944 67.72023384 0.501184499 0.275484065 5.13932802 1.00E-04 4.000000053 -0.525237912 RDS(ph)SDDWEIPDGQITVGQR ddPTM_HeLa_Romidepsin_16h_R1 2 RDSSDDWEIPDGQITVGQR 19 1 H7C560;A0A2U3TZI2;A0A2R8Y8E0;P15056;A0A2R8Y679;A0A2R8Y492;A0A2R8YDP5 H7C560 BRAF Serine/threonine-protein kinase B-raf 1 0 RDS(0.5)S(0.5)DDWEIPDGQITVGQR;RDS(0.768)S(0.232)DDWEIPDGQITVGQR ; 194.1 6.61E-15 31973300 2605.7 2311.25 2508.7 2381.8 2278.9 2167.29 2148.4 2335.28 2595.2 2066.66 TRUE FALSE FALSE 2573.940726 2343.787838 2552.362871 2657.194923 2162.599229 2028.807164 2330.885042 2402.847642 2363.078812 2012.967875 1.278679485 1.164344383 1.267960062 1.320038415 1.074333702 1.007868624 1.157934546 1.193684048 1.173927732 1 10.97510843 -6.257747061 18.26989532 1.149490978 1.152949715 0 0.105217005 0 0 0.017314345 0 5.52E-07 6.257747061 0.003458737 RDS(ph)SESQLASTESDKPTTGR ddPTM_HeLa_Romidepsin_16h_R1 3 RDSSESQLASTESDKPTTGR 20 2 A0A087WVF1;Q96B23-2;Q96B23;K7EQH1 A0A087WVF1 C18orf25 Uncharacterized protein C18orf25 1 0 RDS(0.759)S(0.151)ES(0.09)QLASTESDKPTTGR;RDS(0.843)S(0.12)ES(0.037)QLASTESDKPTTGR;RDS(0.857)S(0.076)ES(0.067)QLASTESDKPTTGR ;; 113.67 0.00027038 69573000 2375.31 2581.12 2188.37 1762.5 2919.89 3523.31 3045.1 3514.74 2399.76 2553.5 TRUE FALSE FALSE 2346.358808 2617.457075 2226.457662 1966.288543 2770.877118 3298.181862 3303.750718 3616.433457 2185.119455 2487.159702 0.943388881 1.05238802 0.89518082 0.790575909 1.114072858 1.326083669 1.328322711 1.454041513 0.878560172 1 11.28028343 -8.356562207 2.873406667 0.961065981 1.374945428 0.858493876 0.079584071 0.071744317 1.141086056 0.011100369 0.028204297 4.40E-09 8.356562207 0.413879447 RDS(ph)VLAASR ddPTM_HeLa_Romidepsin_16h_R1 1 RDSVLAASR 9 1 A0A3B3ISR4;A0A3B3IRZ9;A0A3B3IS59;A0A3B3IRP0;A0A3B3IU13;A0A3B3IU05;A0A3B3ITQ1;A0A3F2YNW8;A0A3B3ISE3;A0A3B3IU04;A0A3B3ITU8;Q14643-6;Q14643-2;Q14643-3;Q14643-5;Q14643-7;Q14643-8;Q14643-4;Q14643 A0A3B3ISR4 ITPR1 "Inositol 1,4,5-trisphosphate receptor type 1" 1 0 RDS(1)VLAASR 81.709 0.01709 4216800 979.49 1170.9 1463.1 990.35 1865.3 2587.8 1603.3 2118.9 935.24 938.37 TRUE FALSE FALSE 967.5515991 1187.383961 1488.564642 1104.858927 1770.106781 2422.447932 1739.484262 2180.207028 851.589792 913.9910121 1.058600781 1.299119953 1.628642538 1.208829094 1.936678542 2.650406732 1.903174363 2.385370315 0.931726659 1 9.836036168 -8.913407733 0.756505931 1.023483079 2.375540143 0.795476898 0.258589823 0.219217134 0.232738163 0.047355715 0.156896045 1.22E-09 8.913407733 1.352057064 up RDSFIGT(ph)PYWMAPEVVMCETSK ddPTM_HeLa_Romidepsin_16h_R1 1 RDSFIGTPYWMAPEVVMCETSK 22 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 0 RDS(0.085)FIGT(0.469)PY(0.446)WMAPEVVMCETSK 67.785 0.000848 28490000 942.54 989.28 978.83 0 872.67 1095.3 774.02 884.95 884.16 935.22 TRUE FALSE FALSE 931.0519599 1003.20711 995.8661256 0 828.1343935 1025.313865 839.7652395 910.554632 805.0785152 910.9228496 1.022097492 1.101308536 1.093249693 0 0.909115842 1.125577062 0.921884043 0.999595775 0.88380538 1 9.83118506 RDSS(ph)DDWEIPDGQITVGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RDSSDDWEIPDGQITVGQR 19 1 H7C560;A0A2U3TZI2;A0A2R8Y8E0;P15056;A0A2R8Y679;A0A2R8Y492;A0A2R8YDP5 H7C560 BRAF Serine/threonine-protein kinase B-raf 1 0 RDS(0.241)S(0.759)DDWEIPDGQITVGQR 87.468 0.0014588 4063200 898.64 891.96 910.77 1057.8 863.39 1056 556.35 1036.3 1035.1 960.49 TRUE FALSE FALSE 887.68703 904.5170363 926.6215698 1180.107813 819.3279865 988.5250081 603.6063551 1066.283705 942.5180635 935.5363313 0.948853615 0.966843303 0.990470962 1.26142382 0.875784252 1.056639892 0.645198198 1.139756597 1.007462812 1 9.869649871 RDT(ph)GGNT(ph)YTAKALK ddPTM_HeLa_Romidepsin_16h_R1 1 RDTGGNTYTAKALK 14 2 E9PAL5;A8TX70-2;A8TX70 E9PAL5 COL6A5 Collagen alpha-5(VI) chain 2 0 RDT(1)GGNT(1)YTAKALK 94.673 0.012604 13561000 1111.4 2440.4 1926.5 1642.5 2214.8 3335.2 1460.2 2913.7 1697 1859.6 TRUE FALSE FALSE 1097.853829 2474.756015 1960.029924 1832.413578 2101.770491 3122.091484 1584.229352 2998.003312 1545.21607 1811.287324 0.606117988 1.366296767 1.082119826 1.011663668 1.160373875 1.723686487 0.874642764 1.655178211 0.853103784 1 10.8227997 -9.39870483 0.830868519 0.830662899 1.35293782 0.301873532 0.281423293 0.500057772 0.686284187 0.057607736 0.120249802 3.99E-10 9.39870483 0.522274921 RDTSGPTPGT(ph)PSPAMAR ddPTM_HeLa_Romidepsin_16h_R1 1 RDTSGPTPGTPSPAMAR 17 1 Q9H6K5-2;Q9H6K5 Q9H6K5-2 PRR36 Proline-rich protein 36 1 0 RDT(0.004)S(0.004)GPT(0.01)PGT(0.835)PS(0.147)PAMAR 62.799 0.026606 5527600 4752.1 3135.6 2512.4 1262.5 2395.5 2341.2 3186.2 3892.4 5039.2 4393.9 TRUE FALSE FALSE 4694.179577 3179.743059 2556.127268 1408.47619 2273.248696 2191.604876 3456.835748 4005.020453 4588.481331 4279.745845 1.096836062 0.742974741 0.597261464 0.329102765 0.531164415 0.512087623 0.807719868 0.935808012 1.072138743 1 12.06330941 -10.10458201 3.458518988 1.045590169 0.607892198 0.60550219 0.157384541 0.127775317 2.85243481 0.028636362 0.035719209 7.86E-11 10.10458201 -0.437697971 RDTVSLY(ph)QRT(ph)LEQR ddPTM_HeLa_Romidepsin_16h_R1 1 RDTVSLYQRTLEQR 14 2 Q96JK9 Q96JK9 MAML3 Mastermind-like protein 3 2 0 RDTVSLY(1)QRT(1)LEQR 115.57 0.0044064 211340000 3937.2 4497.6 4032.2 3821.9 4772 4330.2 3430.6 4032.8 4484.1 3552.4 TRUE FALSE FALSE 3889.211892 4560.917331 4102.37875 4263.806061 4528.467033 4053.514195 3721.995078 4149.482705 4083.030865 3460.108136 1.124014551 1.318143004 1.185621544 1.232275378 1.308764598 1.171499281 1.075687502 1.199234978 1.180029844 1 11.75660141 -11.06222246 1.049216953 1.024579844 1.207999183 0.156412051 0.08481994 0.250098189 0.579791308 0.020371777 0.015836153 8.67E-12 11.06222246 0.183419339 RDVLSLLNLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RDVLSLLNLSPR 12 1 Q96AY4;A0A087WW06 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 0 RDVLSLLNLS(1)PR 117.48 0.00032796 0 1105.8 1240.2 1345.2 1363.2 1119.6 1384.4 907.41 962.71 1440.3 1128.7 TRUE FALSE FALSE 1092.322084 1257.659568 1368.612642 1520.819598 1062.462634 1295.941308 984.4853828 990.5644949 1311.475961 1099.376211 0.993583519 1.143975607 1.244899269 1.383347741 0.966423162 1.178796935 0.895494529 0.901024131 1.192927359 1 10.10246945 -6.259240858 14.42145325 1.044359832 1.074135379 0 0.160786806 0 0 0.021326798 0 5.51E-07 6.259240858 0.029775546 RDVYLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 RDVYLSPR 8 1 P38159;P38159-2;H3BUY5;H0Y6E7;H3BT71;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 0 RDVYLS(1)PR;RDVYLS(1)PR ; 97.214 0.010052 49160000 4925.9 4028.3 7420.4 5437.7 7254.1 7128.3 6500.6 4633.2 4860.3 3649.7 TRUE FALSE FALSE 4865.861236 4085.010513 7549.548949 6066.432459 6883.896208 6672.824636 7052.760802 4767.254332 4425.582595 3554.880268 1.368783438 1.149127454 2.123713988 1.706508237 1.936463591 1.877088434 1.98396578 1.341044978 1.244931548 1 11.79558525 -9.775848717 24.9943518 1.17713703 1.836835493 0.683124719 0.21254949 100.4741133 174281.3403 0.035858663 0.047245597 1.68E-10 9.775848717 0.659698463 RDWYVY(ph)AFLS(ph)S(ph)LPWVGK ddPTM_HeLa_Romidepsin_16h_R1 1 RDWYVYAFLSSLPWVGK 17 1 Q09161 Q09161 NCBP1 Nuclear cap-binding protein subunit 1 3 0 RDWY(0.451)VY(0.562)AFLS(0.994)S(0.994)LPWVGK 43.791 0.0043168 0 538.56 575.28 625.26 610.69 476.21 592.36 643.79 396.89 751.48 533.23 TRUE FALSE FALSE 531.9958236 583.3788069 636.142388 681.3008512 451.9072267 554.5101078 698.4735065 408.373386 684.2657467 519.3766077 1.024296851 1.123228883 1.224819098 1.311766531 0.870095457 1.067645519 1.344830507 0.786276047 1.317475097 1 9.020637228 -10.31279215 4.839649003 1.010799226 1.115645454 0 0.191909941 0.411240877 21.30400009 0.026868804 0.030891519 4.87E-11 10.31279215 0.104846228 RDY(ph)LWT(ph)S(ph)AKNT(ph)LSTPLPK ddPTM_HeLa_Romidepsin_16h_R1 1 RDYLWTSAKNTLSTPLPK 18 2 A0A087WZC3;Q15431 A0A087WZC3 SYCP1 Synaptonemal complex protein 1 4 0 RDY(0.972)LWT(0.845)S(0.845)AKNT(0.791)LS(0.275)T(0.271)PLPK 44.415 0.0043438 0 667.61 731.86 1079.8 1003.4 2086 2152.6 1217.2 1733.7 2679.9 1715.7 TRUE FALSE FALSE 659.4729125 742.1631443 1098.593466 1119.417829 1979.543636 2015.055807 1320.588938 1783.861874 2440.203032 1671.125867 0.394627913 0.444109662 0.6573972 0.669858478 1.184556876 1.205807323 0.790239062 1.067461111 1.460214985 1 10.70660468 -8.773471897 24.78711012 0.677477156 1.052874241 0.135224375 0.31008769 180.2468661 371310.5756 0.038987732 0.071071941 1.68E-09 8.773471897 0.375397084 RDYDDMS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RDYDDMSPR 9 1 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 RDYDDMS(1)PR 111.5 0.013458 8086800 4638.3 4004.9 3867.9 3904.9 4486.6 4386.1 3699.6 3841.4 4914.4 3790.2 TRUE FALSE FALSE 4581.766616 4061.281087 3935.219177 4356.402911 4257.63206 4105.842365 4013.843932 3952.544848 4474.843756 3691.730058 1.241089284 1.100102398 1.065955288 1.180043731 1.153289107 1.112172965 1.087252824 1.070648392 1.212126479 1 11.85008135 -7.687645042 3.102824589 1.119320501 1.07404514 0.067726519 0.067655464 0.856775518 15.91586392 0.012753075 0.059538847 2.05E-08 7.687645042 -0.045275361 RDYDDMSPR ddPTM_HeLa_Romidepsin_16h_R1 2 RDYDDMSPR 9 1 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 ; ; 65.627 0.026121 13626600 1563.69 1523.18 1523.21 1464.19 1523.97 1435.13 1180.18 1258.35 1960.58 1423.17 FALSE FALSE TRUE 1544.631145 1544.623368 1549.720831 1633.486537 1446.196124 1343.429825 1280.42446 1294.758372 1785.220814 1386.195838 1.114295038 1.114289428 1.117966732 1.178395211 1.043284134 0.96914865 0.923696656 0.934037122 1.287856135 1 10.43691538 -8.220023781 2.975892323 1.074348655 0.932743994 0.44145734 0.082236974 0.17303726 3.04920333 0.009103981 0.025391665 6.03E-09 8.220023781 -0.141604661 RDYEVDGR ddPTM_HeLa_Romidepsin_16h_R1 1 RDYEVDGR 8 1 A0A590UJ18;A0A590UJ08;A0A590UJR4;A0A590UJ68;A0A590UJR5;A0A590UJS9;A0A590UJX2;C9JUA9;A0A590UJ81;A0A590UJC5;A0A590UKA8;Q12959-2;A0A0C4DFT3;Q12959-7;A0A590UJD9;Q12959;Q12959-4;Q12959-3;Q12959-6;Q12959-8;Q12959-5;Q12959-9;A0A590UK48;A0A590UJ29;A0A590UK81;A0A3B3ISW2;B7Z2T4;E9PIW2;B5MCC5;H7C325;E9PN83;F8W750;Q15700-2;Q15700-5;Q15700-4;Q15700-3;F8VYC1;A0A3B3ITF1;Q15700 A0A590UJ18 DLG1;DLG2 Disks large homolog 1;Disks large homolog 2 0 0 107.57 0.0010991 0 1136.3 820.92 1130 1111.4 1085.4 1338.1 1038.1 670.86 1081.5 762.16 FALSE FALSE TRUE 1122.450339 832.4769333 1149.667176 1239.905297 1030.007988 1252.599729 1126.276188 690.2702757 984.7679313 742.3589733 1.51200481 1.121394047 1.548667447 1.670223358 1.387479676 1.687323483 1.517158448 0.929833545 1.326538732 1 9.535973172 -12.41079726 0.70381912 0.936576598 1.446411863 0.083878427 0.24574845 0.885087085 0.622500063 0.282508676 0.044865502 3.88E-13 12.41079726 0.509835265 REDEGEPGDEGQLEDEGS(ph)QEK ddPTM_HeLa_Romidepsin_16h_R1 2 REDEGEPGDEGQLEDEGSQEK 21 1 Q969E4 Q969E4 TCEAL3 Transcription elongation factor A protein-like 3 1 0 REDEGEPGDEGQLEDEGS(1)QEK;REDEGEPGDEGQLEDEGS(1)QEK ; 115.83 3.66E-08 7078500 2543.9 2455.7 3143.6 2669.75 2764.9 2896.3 2407.4 2602.2 2954.3 2702.4 TRUE FALSE FALSE 2512.893968 2490.271409 3198.313039 2978.439057 2623.796836 2711.235777 2611.884496 2677.490551 2690.060009 2632.191258 0.954677575 0.946083003 1.215076233 1.131543556 0.996810861 1.03002993 0.992285225 1.017209727 1.02198501 1 11.36204861 NYPS(ph)QEELIK ddPTM_HeLa_Romidepsin_16h_R1 2 NYPSQEELIK 10 0 P38398-8;P38398-4;P38398;P38398-7;K7EPC7;H0Y8B8;B7ZA85;E7EUM2;A0A2R8Y7V5;P38398-6;P38398-5;P38398-3 P38398-8 BRCA1 Breast cancer type 1 susceptibility protein 1 0 NYPS(1)QEELIK;NY(0.002)PS(0.998)QEELIK ; 122.46 0.010521 45106000 10061.9 9800.9 9025.8 7815.8 5723.2 4301 3498.7 3461.4 10614.5 10425.3 TRUE FALSE FALSE 9939.261693 9938.877327 9182.890263 8719.49957 5431.123748 4026.179981 3795.879491 3561.550148 9665.112535 10154.4492 0.978808549 0.978770697 0.904321847 0.858687596 0.534851634 0.396494177 0.373814415 0.350737896 0.951810614 1 13.30982437 -8.726288543 1.477766339 0.986996045 0.354747246 0.990211454 0.026414124 0.021902008 0.095955919 0.003689508 0.009378149 1.88E-09 8.726288543 -0.632248798 down REDIFYTS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 REDIFYTSK 9 1 S4R3Z2;A0A0A0MSS8;P42330;S4R3D5;P17516;P52895-2;P52895;S4R3P0;H0Y804;B4DK69 S4R3Z2;P52895 AKR1C3;AKR1C4;AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C3;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C2 1 0 REDIFYT(0.057)S(0.942)K 68.463 0.026539 10837000 3512.9 3231.9 2614.2 1852 3090.2 2987.2 2607.9 3182.7 3639.4 2916.8 TRUE FALSE FALSE 3470.083424 3277.398773 2659.699054 2066.136954 2932.495563 2796.327561 2829.414961 3274.786403 3313.882949 2841.021116 1.221421201 1.153598879 0.936177151 0.72725153 1.032197736 0.984268489 0.995914795 1.152679361 1.166440802 1 11.47219384 -9.758144194 24.99536521 1.111159459 0.96477725 0.326299475 0.113053016 98.17260935 744675.9082 0.020705898 0.028599141 1.75E-10 9.758144194 -0.146382209 REDIFYTSK ddPTM_HeLa_Romidepsin_16h_R1 2 REDIFYTSK 9 1 S4R3Z2;A0A0A0MSS8;P42330;S4R3D5;P17516;P52895-2;P52895;S4R3P0;H0Y804;B4DK69 S4R3Z2;P52895 AKR1C3;AKR1C4;AKR1C2;AKR1C1 Aldo-keto reductase family 1 member C3;Aldo-keto reductase family 1 member C4;Aldo-keto reductase family 1 member C2 0 0 ; ; 136.02 0.0043694 189459000 13362.2 11186.8 15705.1 15366.4 15092.7 13836.5 11272 9894.2 11678.7 8983 FALSE FALSE TRUE 13199.33637 11344.28806 15978.44068 17143.13547 14322.4632 12952.39231 12229.4434 10180.47307 10634.12782 8749.620365 1.508561036 1.296546318 1.826186739 1.95930049 1.636923958 1.480337634 1.397711316 1.163533118 1.215381626 1 13.09500471 -11.93268583 0.667614065 0.980259007 1.556556665 0.342677974 0.23018288 0.608349865 0.482157385 0.190570001 0.053948442 1.17E-12 11.93268583 0.576297657 REDPSFER ddPTM_HeLa_Romidepsin_16h_R1 1 REDPSFER 8 1 Q9NWH9;H7C3F4;Q9NWH9-3;H0YMM0 Q9NWH9 SLTM SAFB-like transcription modulator 0 0 105.52 0.017015 1083700 223.25 282.07 195.15 315.53 195.92 189 181.45 203.42 351.2 291.12 FALSE FALSE TRUE 220.5289431 286.0409889 198.5465039 352.0130632 185.9214713 176.92351 196.8623585 209.3056368 319.7877924 283.5566604 0.777724434 1.008761312 0.700200459 1.241420542 0.655676615 0.623944116 0.694261098 0.738143962 1.12777387 1 8.147493234 REDS(ph)FESLDSLGSR ddPTM_HeLa_Romidepsin_16h_R1 4 REDSFESLDSLGSR 14 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMP7 E9PMS6 LMO7 LIM domain only protein 7 1 0 REDS(1)FESLDSLGSR;REDS(1)FESLDSLGSR;REDS(0.991)FES(0.009)LDSLGSR;REDS(0.999)FES(0.001)LDSLGSR ;;; 234.36 9.30E-43 63551000 6006.96 5722.21 5957.6 6053.2 7280.3 7093.9 6575.3 6779.3 6930.5 6145.1 TRUE FALSE FALSE 5933.744861 5802.767423 6061.289529 6753.099465 6908.759124 6640.622685 7133.805818 6975.44835 6310.618722 5985.449416 0.991361625 0.969478985 1.012670747 1.1282527 1.154259045 1.109460998 1.191858008 1.165400936 1.054326632 1 12.54724386 -9.241075327 3.078501865 0.993525401 1.153762824 0.86848097 0.02812104 0.0449044 0.86668789 0.003174352 0.005316381 5.74E-10 9.241075327 0.160237423 REDS(ph)PGPEVQPMDK ddPTM_HeLa_Romidepsin_16h_R1 2 REDSPGPEVQPMDK 14 1 O75382-3;O75382-2;O75382;E9PMW5;E9PMK8 O75382-3 TRIM3 Tripartite motif-containing protein 3 1 0 REDS(1)PGPEVQPMDK;REDS(1)PGPEVQPMDK ; 132.51 0.0013163 19288000 7954.7 7111.3 7487.3 7532.8 8230.2 9649.5 8433.9 8948.6 8186.5 7303.9 TRUE FALSE FALSE 7857.745057 7211.413068 7617.613316 8403.777779 7810.182183 9032.928092 9150.275255 9207.513622 7454.278937 7114.143625 1.104524377 1.013672685 1.070770245 1.181277498 1.097838699 1.269714047 1.286208957 1.294254672 1.047811139 1 12.79647439 -5.996131835 0.266386853 1.017594422 1.892940298 0.820450499 0.045533488 5.341936244 0.16927394 0.025604112 1.734540095 1.01E-06 5.996131835 0.875345877 REDTLDVEVS(ph)AS(ph)GY(ph)T(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 REDTLDVEVSASGYTK 16 1 Q9BVS4;Q9BVS4-2 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 4 0 REDT(0.001)LDVEVS(1)AS(1)GY(1)T(1)K 57.973 0.003828 0 156.97 322.09 362.26 243.3 158.57 144.93 168.58 231.29 336.97 221.4 TRUE FALSE FALSE 155.0567893 326.6243915 368.5649833 271.4314908 150.4775812 135.6694407 182.899181 237.9820112 306.8305592 215.6479961 0.719027267 1.514618255 1.709104606 1.258678475 0.697792625 0.629124514 0.848137633 1.103566996 1.422830561 1 7.7525345 -8.733740366 24.99771642 1.012779644 0.808080562 0.069555755 0.344220565 543.8803581 490837.0186 0.055919393 0.111819475 1.85E-09 8.733740366 -0.204699081 REEDEENDNDNES(ph)DHDEADS ddPTM_HeLa_Romidepsin_16h_R1 2 REEDEENDNDNESDHDEADS 20 1 H0YBP8;Q9NRG0 H0YBP8 CHRAC1 Chromatin accessibility complex protein 1 1 0 REEDEENDNDNES(0.85)DHDEADS(0.15);REEDEENDNDNES(0.906)DHDEADS(0.094) ; 55.437 0.010653 9543900 2043.87 2016.38 2234.69 1409.56 1618.64 1656.13 1655.84 1601.02 2180.24 2191.94 TRUE FALSE FALSE 2018.958526 2044.766651 2273.583842 1572.539959 1536.034761 1550.308638 1796.487008 1647.342988 1985.233874 2134.993083 0.945651085 0.957739239 1.064913915 0.736555061 0.719456551 0.72614223 0.841448632 0.771591721 0.929854944 1 11.06001568 -9.251047684 24.99222613 0.978350415 0.759590545 0.847357563 0.046811076 199.2479084 479195.013 0.0070696 0.011639796 5.61E-10 9.251047684 -0.21875987 REEDEPEERS(ph)GDETPGSEVPGDK ddPTM_HeLa_Romidepsin_16h_R1 1 REEDEPEERSGDETPGSEVPGDK 23 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 REEDEPEERS(0.988)GDET(0.005)PGS(0.007)EVPGDK 65.111 0.0033709 39969000 1972.7 1528.7 1779.3 1284.4 2255.4 2422.9 1978.2 1935.3 1771.5 2353 TRUE FALSE FALSE 1948.655974 1550.221079 1810.26797 1432.908371 2140.298522 2268.08451 2146.228259 1991.294852 1613.052603 2291.868721 0.850247641 0.676400469 0.789865473 0.625213983 0.933866108 0.98962235 0.936453401 0.868852057 0.703815445 1 11.16230869 -6.289837594 14.92492003 0.886198453 0.84691819 0 0.135908098 0 0 0.018460794 0 5.13E-07 6.289837594 -0.039280263 REEEEDFIR ddPTM_HeLa_Romidepsin_16h_R1 1 REEEEDFIR 9 1 Q96A65 Q96A65 EXOC4 Exocyst complex component 4 0 0 110.53 0.012149 3058800 1376.1 1478.1 1588.3 1456 1611.4 2035.4 1667.5 1425.1 1659.9 1494.9 FALSE FALSE TRUE 1359.327564 1498.908731 1615.943695 1624.349571 1529.164245 1905.344509 1809.137408 1466.33302 1511.434387 1456.062282 0.933564162 1.029426247 1.109803966 1.115576985 1.050205244 1.308559759 1.24248628 1.007053776 1.038028665 1 10.50785635 -9.589557078 1.206128568 0.968152764 1.165860197 0.384428822 0.085604684 0.263507402 0.768134896 0.014995188 0.024790278 2.57E-10 9.589557078 0.197707433 REEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_HeLa_Romidepsin_16h_R1 1 REEGPPPPSPDGASSDAEPEPPSGR 25 1 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;E9PD53;Q9NTJ3-2;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 0 REEGPPPPSPDGAS(0.499)S(0.499)DAEPEPPS(0.001)GR 157.73 1.60E-10 7342400 740.83 826.97 980.11 646.55 854.51 880.89 669.7 694.43 892.37 986.36 TRUE FALSE FALSE 731.800479 838.6121054 997.1684034 721.3071531 810.9011661 824.6039719 726.5843013 714.5222364 812.5541922 960.734225 0.761709597 0.872886677 1.037923265 0.750787402 0.844043175 0.858306023 0.756280231 0.743725182 0.845763762 1 9.907993573 -12.46466602 1.108823633 1.003529594 0.826165955 0.047399751 0.095676994 0.466810292 0.993253233 0.066232507 0.015064953 3.43E-13 12.46466602 -0.17736364 REEGPPPPSPDGASS(ph)DAEPEPPSGR ddPTM_HeLa_Romidepsin_16h_R1 1 REEGPPPPSPDGASSDAEPEPPSGR 25 1 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;E9PD53;Q9NTJ3-2;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 0 REEGPPPPSPDGAS(0.26)S(0.74)DAEPEPPS(0.001)GR 146.36 1.70E-21 0 1245.3 1232.5 1180.6 872.76 1491.3 1144.6 929.17 929.67 1757.1 1325 TRUE FALSE FALSE 1230.121805 1249.851167 1201.147848 973.6726177 1415.193396 1071.463754 1008.093677 956.5685347 1599.940575 1290.576309 0.95315697 0.96844422 0.930706568 0.754447924 1.096559255 0.830221155 0.781119001 0.741194866 1.23971017 1 10.33379973 -5.503484088 0.322782767 0.986344299 1.24E-14 0.406388201 0.116633398 12.56857751 0.382923645 0.027496877 6.166910834 3.14E-06 5.503484088 -0.986344299 REELFIVSK ddPTM_HeLa_Romidepsin_16h_R1 1 REELFIVSK 9 1 E9PEF9;E9PCX2;P15121 E9PEF9 AKR1B1 Aldose reductase 0 0 129.88 0.0053804 6587200 3969.8 2577.1 3741 2863.9 5202.8 4175.5 3117 4102.2 3407.5 3867 FALSE FALSE TRUE 3921.414551 2613.380481 3806.110536 3195.037593 4937.281702 3908.699026 3381.757902 4220.890685 3102.724666 3766.534783 1.041119962 0.693842121 1.010507205 0.84826977 1.310828649 1.037744041 0.897843269 1.120629684 0.823761055 1 11.87902214 REELITNWEQIR ddPTM_HeLa_Romidepsin_16h_R1 2 REELITNWEQIR 12 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 ; ; 154.1 0.00091188 8473400 2642.97 1956.67 2371.34 2003.63 3006.59 2651.66 2198.16 2372.32 2817 3149.9 FALSE FALSE TRUE 2610.756465 1984.216052 2412.612178 2235.299128 2853.152493 2482.227484 2384.871656 2440.959336 2565.040465 3068.065144 0.850945577 0.646732047 0.786362761 0.728569643 0.929951732 0.809053057 0.777321062 0.795602186 0.836044981 1 11.5831134 -11.37006242 0.93122013 0.980441693 0.78855692 0.209808107 0.083198295 0.271987707 0.491200697 0.025245736 0.015384949 4.27E-12 11.37006242 -0.191884773 REEPEALY(ph)AAVNK ddPTM_HeLa_Romidepsin_16h_R1 3 REEPEALYAAVNK 13 1 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 0 REEPEALY(1)AAVNK;REEPEALY(1)AAVNK;REEPEALY(1)AAVNK ;; 151.66 0.00019524 14998400 10652.6 9810.2 11250.5 10081.8 10498.6 7887.4 5542.6 6285.2 12247.6 11555.4 TRUE FALSE FALSE 10522.76201 9948.308253 11446.31023 11247.50515 9962.817266 7383.420595 6013.388306 6467.052346 11152.14398 11255.18904 0.934925391 0.883886376 1.016980718 0.999317302 0.885175471 0.656001473 0.534276971 0.574584072 0.990844662 1 13.45830267 -8.235852689 2.318575673 0.967262206 0.555203916 0.952199445 0.0388175 0.047774544 0.496800138 0.006226646 0.018659875 5.81E-09 8.235852689 -0.41205829 REESPMDVDQPS(ph)PSAQDTQSIASDGTPQGEK ddPTM_HeLa_Romidepsin_16h_R1 2 REESPMDVDQPSPSAQDTQSIASDGTPQGEK 31 1 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 REESPMDVDQPS(0.499)PS(0.499)AQDT(0.001)QSIASDGTPQGEK;REES(0.001)PMDVDQPS(0.495)PS(0.495)AQDT(0.008)QSIASDGTPQGEK ; 105.9 9.46E-13 39608000 6314.8 6724.9 6577.4 5226.2 6402.6 5778.6 5294 6226.1 7399.2 7206.6 TRUE FALSE FALSE 6237.832789 6819.573319 6691.876888 5830.477834 6075.851431 5409.36611 5743.672228 6406.24238 6737.39702 7019.371493 0.888659732 0.971536173 0.95334417 0.830626765 0.865583398 0.770633968 0.818260187 0.91265185 0.9598291 1 12.77712614 -9.261654555 24.99963837 0.94868301 0.835985889 0.642860942 0.042745682 11.89848713 1382424.367 0.007976295 0.012668988 5.47E-10 9.261654555 -0.112697121 REESPMDVDQPSPS(ph)AQDTQSIASDGTPQGEKEK ddPTM_HeLa_Romidepsin_16h_R1 1 REESPMDVDQPSPSAQDTQSIASDGTPQGEKEK 33 2 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7;H0Y659 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 REES(0.015)PMDVDQPS(0.127)PS(0.412)AQDT(0.412)QS(0.033)IASDGTPQGEKEK 63.203 0.00015623 9519400 1366 1707.6 1238.7 1062.2 1500 1455.3 1089.1 1687.4 1691.5 1396.2 TRUE FALSE FALSE 1349.350667 1731.639638 1260.259054 1185.016562 1423.449403 1362.311027 1181.608127 1736.222257 1540.208004 1359.926523 0.992223215 1.273333234 0.926711137 0.871382786 1.046710524 1.001753407 0.868876448 1.276702989 1.132567075 1 10.40931299 -7.243083528 24.08242747 0.999103528 1.276703386 0.313498489 0.115692866 1935.265258 2538957.011 0.014063845 0.597925926 5.71E-08 7.243083528 0.277599858 REFITGDVEPTDAESEWHS(ph)ENEEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 REFITGDVEPTDAESEWHSENEEEEK 26 1 E9PNJ7;C9J6D1;Q99733;Q99733-2;E9PS34;E9PKT8;C9JZI7;A8MXH2 E9PNJ7 NAP1L4 Nucleosome assembly protein 1-like 4 1 0 REFITGDVEPT(0.004)DAES(0.02)EWHS(0.976)ENEEEEK;REFITGDVEPT(0.003)DAES(0.419)EWHS(0.578)ENEEEEK ; 132.8 1.75E-07 13688600 2084.68 1978.46 1961.22 1423.62 2666.9 2895 2496.8 2593.5 3039.7 2512.5 TRUE FALSE FALSE 2059.271118 2006.312812 1995.354211 1588.225643 2530.798141 2710.018843 2708.87813 2668.538831 2767.821619 2447.224888 0.841471958 0.819831811 0.815353841 0.648990475 1.034150214 1.107384473 1.106918348 1.090434657 1.131004197 1 11.25693097 -8.537772183 24.9869724 0.886346989 1.096888842 0.432096112 0.118677184 160.5069766 269284.531 0.016068433 0.032146257 2.90E-09 8.537772183 0.210541853 REGPGS(ph)EPDSQVDGGLSGASLGEK ddPTM_HeLa_Romidepsin_16h_R1 2 REGPGSEPDSQVDGGLSGASLGEK 24 1 Q5JSZ5;A0A494C0D3;A0A494C065;H0Y412 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 REGPGS(0.522)EPDS(0.47)QVDGGLS(0.005)GAS(0.003)LGEK;REGPGS(0.999)EPDS(0.001)QVDGGLSGASLGEK ; 92.377 2.04E-05 50600000 11231.3 11840.2 9538.7 10843.9 8728.3 8535.9 7143 9598.1 13258.6 14635 TRUE FALSE FALSE 11094.4086 12006.88665 9704.717072 12097.72274 8282.862281 7990.483538 7749.726242 9875.80588 12072.71761 14254.78059 0.778293887 0.84230596 0.680804381 0.848678285 0.58105856 0.560547634 0.543658052 0.692806586 0.846924127 1 13.79915821 -10.72421273 0.129217097 1.269801232 0.349640356 0.593394624 0.091178496 2.366525977 0.242161494 0.871903614 0.720810033 1.89E-11 10.72421273 -0.920160876 REGPVGGES(ph)DSEEMFEK ddPTM_HeLa_Romidepsin_16h_R1 1 REGPVGGESDSEEMFEK 17 1 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;J3QL92 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 REGPVGGES(0.831)DS(0.169)EEMFEK 88.637 0.0074524 21092000 7583.9 8181.8 8232.9 8397.8 8166.8 8393.6 6169.8 6931.2 8759.6 8394.6 TRUE FALSE FALSE 7491.46451 8296.983595 8376.190171 9368.793149 7750.017721 7857.276049 6693.862658 7131.743336 7976.119437 8176.507082 0.916218189 1.014734472 1.024421564 1.145818508 0.947839664 0.96095753 0.818670196 0.872223709 0.975492268 1 12.99726896 -7.839851254 5.132061992 0.981183801 0.845763782 0.484904201 0.061184074 0.150183997 6.876874132 0.009726552 0.031094815 1.45E-08 7.839851254 -0.135420019 REGT(ph)PPPPPPSR ddPTM_HeLa_Romidepsin_16h_R1 2 REGTPPPPPPSR 12 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;C9JQE8 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 REGT(1)PPPPPPSR;REGT(1)PPPPPPSR ; 106.76 0.0050795 38542000 5963.1 5767.4 5357.2 6833.5 4752.2 3752.4 3603.8 3672.7 6708.8 5583.1 TRUE FALSE FALSE 5890.419444 5848.593609 5450.439819 7623.621423 4509.677501 3512.63375 3909.906682 3778.96378 6108.748126 5438.050257 1.083185915 1.075494586 1.00227831 1.401903451 0.829282057 0.645936243 0.718990538 0.694911522 1.123334253 1 12.40887377 -8.533015382 24.99694683 1.064906696 0.697810268 0.741482829 0.113450403 81.52209715 201033.1113 0.015875181 0.031778096 2.93E-09 8.533015382 -0.367096429 REHLT(ph)LT(ph)FHS(ph)PEVPK ddPTM_HeLa_Romidepsin_16h_R1 1 REHLTLTFHSPEVPK 15 1 H3BUG9;A6NGA9 H3BUG9 TMEM202 Transmembrane protein 202 3 0 REHLT(1)LT(1)FHS(1)PEVPK 71.692 0.0025333 0 1616.1 1582.7 1821.9 442.09 1446.7 1599.3 1164.5 1352.1 1775.3 1923.3 TRUE FALSE FALSE 1596.402352 1604.981292 1853.609405 493.2065259 1372.869501 1497.109892 1263.412601 1391.22088 1616.512722 1873.332389 0.852172503 0.856752011 0.989471712 0.263277638 0.732848857 0.799169384 0.674419878 0.742644972 0.862907582 1 10.87139119 REHY(ph)VAVQLLK ddPTM_HeLa_Romidepsin_16h_R1 1 REHYVAVQLLK 11 1 H7BYL6;A0A0A0MRE9;A0A0A0MRF6;Q99996-5;Q99996-3;Q99996;Q99996-1;Q99996-6 H7BYL6 AKAP9 A-kinase anchor protein 9 1 0 REHY(1)VAVQLLK 140.35 0.0035023 86710000 2377.1 2350.2 2464.5 2399.9 2543.9 2772.4 2101.5 2179.6 2321.5 2217.7 TRUE FALSE FALSE 2348.126991 2383.286177 2507.393589 2677.38773 2414.07529 2595.252588 2280.001358 2242.663287 2113.859226 2160.083834 1.087053638 1.103330408 1.160785313 1.239483249 1.117584073 1.201459196 1.055515217 1.038229744 0.978600549 1 11.07687159 -11.13772095 0.769112908 1.011362617 1.135547788 0.45843799 0.059071232 0.414687589 0.533778725 0.022343809 0.014635082 7.28E-12 11.13772095 0.124185171 RELLMKENVK ddPTM_HeLa_Romidepsin_16h_R1 1 RELLMKENVK 10 2 P0C7W6 P0C7W6 CCDC172 Coiled-coil domain-containing protein 172 0 0 83.862 0.017894 0 7014.1 7252.2 6974.7 8043.1 6600.7 5955.9 6027.6 5711.4 7543.9 6692.6 FALSE FALSE TRUE 6928.609451 7354.296662 7096.091728 8973.081066 6263.841648 5575.337212 6539.584194 5876.650348 6869.15469 6518.725287 1.062877962 1.128180179 1.088570451 1.376508546 0.960899773 0.855280284 1.003199844 0.901502992 1.053757351 1 12.67037416 -8.542050679 24.99966669 1.069314784 0.924943939 0.384367055 0.107153356 244.6925519 319071.2043 0.016592298 0.033188144 2.87E-09 8.542050679 -0.144370845 REPEDEGEDDD ddPTM_HeLa_Romidepsin_16h_R1 1 REPEDEGEDDD 11 1 P39687 P39687 ANP32A Acidic leucine-rich nuclear phosphoprotein 32 family member A 0 0 143.04 0.0090916 9570900 3097.8 3193.4 3583.6 3538.8 2982.1 3006.6 3607.6 1524.2 3649.2 3608.8 FALSE FALSE TRUE 3060.042822 3238.356769 3645.971055 3947.972707 2829.912309 2814.487963 3914.029454 1568.300322 3322.806412 3515.042856 0.870556334 0.921285146 1.037247967 1.123164885 0.805086147 0.800698051 1.113508317 0.446168194 0.945310356 1 11.77932656 -7.249152112 24.64066792 0.946007795 0.446167816 0.664920232 0.108609147 756.1241811 1516285.87 0.015032195 0.340971832 5.63E-08 7.249152112 -0.499839978 REPLPSR ddPTM_HeLa_Romidepsin_16h_R1 2 REPLPSR 7 1 P38159;P38159-2;H3BUY5;H0Y6E7;H3BT71;Q8IZ40;Q96E39 P38159;Q96E39 RBMX;RCOR2;RBMXL1 "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed;REST corepressor 2;RNA binding motif protein, X-linked-like-1" 0 0 ; ; 157.33 0.0068187 3222400 2266.8 2822.1 3629.2 2146.61 2902.4 3209.7 3175 832.88 2715.7 2270.5 FALSE FALSE TRUE 2239.17137 2861.829598 3692.364704 2394.811148 2754.279698 3004.610529 3444.684421 856.9780687 2472.80099 2211.512083 1.012506957 1.294060123 1.669610911 1.082884044 1.245428284 1.358622705 1.557615013 0.387507749 1.118149437 1 11.11081741 -10.26838383 21.52116947 1.00590601 1.257744142 0.05381135 0.327378723 124.5196846 385891.191 0.05108431 0.059220597 5.39E-11 10.26838383 0.251838132 REQGGSGLGSGSS(ph)GGGGSTSGLGSGYIGR ddPTM_HeLa_Romidepsin_16h_R1 3 REQGGSGLGSGSSGGGGSTSGLGSGYIGR 29 1 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 REQGGSGLGS(0.011)GS(0.348)S(0.595)GGGGS(0.029)T(0.01)S(0.004)GLGS(0.002)GYIGR;REQGGS(0.009)GLGS(0.079)GS(0.079)S(0.829)GGGGS(0.003)T(0.001)SGLGSGYIGR;REQGGSGLGS(0.05)GS(0.38)S(0.533)GGGGS(0.013)T(0.006)S(0.018)GLGSGYIGR ;; 68.234 3.90E-05 20024100 1513.72 1345.39 1271.1 1318.47 1356.55 1470.73 1218.15 1426.74 1476.33 1486.15 TRUE FALSE FALSE 1495.270198 1364.330436 1293.222962 1470.917705 1287.320192 1376.7551 1321.619631 1468.020471 1344.283347 1447.539609 1.032973598 0.942516825 0.893393835 1.016150229 0.889316039 0.951100123 0.913011031 1.01414874 0.928667747 1 10.49938711 -10.25304405 24.39936563 1.015570866 0.943149293 0.044996324 0.049812723 309.0063712 898065.6762 0.006422935 0.007796973 5.58E-11 10.25304405 -0.072421573 RES(ph)AASGLGGLLEEEGAGAGAAQEEVLEPGR ddPTM_HeLa_Romidepsin_16h_R1 1 RESAASGLGGLLEEEGAGAGAAQEEVLEPGR 31 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 RES(0.808)AAS(0.192)GLGGLLEEEGAGAGAAQEEVLEPGR 72.438 5.23E-06 11387000 924.3 705.34 1082.5 888.83 1124.1 1311.8 1039.9 1245.1 1224.6 1068.9 TRUE FALSE FALSE 913.0342761 715.269795 1101.340458 991.6007067 1066.732982 1227.980214 1128.22908 1281.125004 1115.068709 1041.129824 0.876964866 0.687013069 1.057832014 0.95242753 1.024591706 1.179468867 1.083658401 1.230514173 1.07101793 1 10.02393426 -8.50513792 1.373789373 0.925614637 1.170730818 0.462875255 0.107218821 0.283531038 1.031531806 0.015948602 0.050517863 3.13E-09 8.50513792 0.245116181 RES(ph)EDDPES(ph)EPDDHEK ddPTM_HeLa_Romidepsin_16h_R1 1 RESEDDPESEPDDHEK 16 1 P16383-3;P16383-4;P16383 P16383-3 GCFC2 GC-rich sequence DNA-binding factor 2 2 0 RES(1)EDDPES(1)EPDDHEK 72.167 0.0131 22196000 3365 3291.9 3441.5 2616.6 3342.3 3263.6 2773.2 2985.9 3072.5 3127.3 TRUE FALSE FALSE 3323.986086 3338.243455 3501.397864 2919.143603 3171.729959 3055.066493 3008.755539 3072.292306 2797.687905 3046.052295 1.091243933 1.095924538 1.149487115 0.958336667 1.041259194 1.002959305 0.987755707 1.008614432 0.918463517 1 11.572725 -9.207428507 24.99999724 1.056240065 1.001597254 0.14657548 0.06109642 396.0905266 183338.2924 0.007915163 0.013125805 6.20E-10 9.207428507 -0.054642812 RES(ph)ESESDET(ph)PPAAPQLIK ddPTM_HeLa_Romidepsin_16h_R1 1 RESESESDETPPAAPQLIK 19 1 O60832 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 2 0 RES(0.374)ES(0.266)ES(0.373)DET(0.987)PPAAPQLIK 57.936 0.0037835 0 889.41 748.25 690.61 862.08 859.16 776.3 647.4 807.3 965.63 607.92 TRUE FALSE FALSE 878.5695288 758.7838831 702.6297774 961.7577458 815.3138592 726.6969354 702.3901398 830.6579518 879.2616343 592.1261508 1.483753973 1.281456464 1.186621764 1.624244672 1.376925944 1.227267086 1.186217057 1.402839497 1.484922821 1 9.20976076 -12.4515524 1.137697512 0.996413617 1.353465158 0 0.197521024 0.346406162 0.78902899 0.099260296 0.023655724 3.54E-13 12.4515524 0.357051541 RESDES(ph)GESAPDEGGEGAR ddPTM_HeLa_Romidepsin_16h_R1 1 RESDESGESAPDEGGEGAR 19 1 Q7Z3C6;H7C152;Q7Z3C6-2 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 RES(0.074)DES(0.864)GES(0.061)APDEGGEGAR 130.02 2.96E-09 0 228.57 221.1 237.95 283.45 270.76 497.94 445.81 454.06 146.45 325.77 TRUE FALSE FALSE 225.7841009 224.2126516 242.0914199 316.2238227 256.9421069 466.123241 483.6770903 467.1975097 133.3511452 317.3064484 0.711564804 0.706612339 0.762957769 0.996588075 0.809760117 1.469000215 1.524321654 1.472385802 0.420259802 1 8.30973303 -8.257520131 21.22656456 0.848116874 1.492144971 0.788820413 0.166591905 11.69102124 63313.9711 0.01850152 0.045125363 5.53E-09 8.257520131 0.644028096 RESDGAPGDLTSLENER ddPTM_HeLa_Romidepsin_16h_R1 1 RESDGAPGDLTSLENER 17 1 Q9BX66-11;Q9BX66;Q9BX66-7;Q9BX66-3;Q9BX66-2;A0A0U1RQI5;Q9BX66-4;Q9BX66-9;Q9BX66-8;Q9BX66-10;Q9BX66-6;Q9BX66-5;Q9BX66-12 Q9BX66-11;A0A0U1RQI5 SORBS1 Sorbin and SH3 domain-containing protein 1 0 0 49.049 0.022952 2436600 480.83 573.75 643.23 800.73 532.17 657.56 620.96 766.84 507.01 693.55 FALSE FALSE TRUE 474.969459 581.8272676 654.4251483 893.3141701 505.0113791 615.5440382 673.7043269 789.0273055 461.6617558 675.531471 0.703104858 0.861288175 0.968755974 1.3223872 0.747576391 0.911199647 0.997295249 1.168009692 0.683405253 1 9.399879172 -9.688434654 4.81323918 0.855943873 1.017352514 0.260816874 0.165777972 0.299630557 12.9849874 0.028008735 0.039622191 2.05E-10 9.688434654 0.161408641 RESS(ph)LGPWGIT(ph)NGS(ph)ATAIK ddPTM_HeLa_Romidepsin_16h_R1 1 RESSLGPWGITNGSATAIK 19 1 X6RID7;A0A087WSW1;Q5T0N1-2;Q5T0N1 X6RID7 CFAP70 Cilia- and flagella-associated protein 70 3 0 RES(0.237)S(0.763)LGPWGIT(0.854)NGS(0.626)AT(0.519)AIK 41.275 0.027433 1958000 1279.5 1172 1026.7 1261 1420.8 1636.6 1272.4 1314.1 1448.6 1258.6 TRUE FALSE FALSE 1263.904962 1188.499447 1044.569283 1406.802753 1348.291274 1532.026542 1380.477624 1352.12141 1319.033588 1225.901391 1.031000512 0.969490251 0.852082631 1.147565998 1.099836646 1.249714336 1.126091898 1.102960989 1.075970382 1 10.25962722 -9.135564514 24.99999994 0.999818623 1.147459592 0.583533304 0.066841511 7.636155504 1488.931983 0.009498503 0.015751483 7.32E-10 9.135564514 0.147640969 RET(ph)VSIMLT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RETVSIMLTK 10 1 Q9C091-3;Q9C091 Q9C091-3 GREB1L GREB1-like protein 2 0 RET(0.963)VS(0.039)IMLT(0.998)K 54.066 0.0041993 0 1475.4 1446 1227.9 1109 1262.8 1266.8 1259.2 1319.4 1467.2 1335.8 TRUE FALSE FALSE 1457.417257 1466.356826 1249.271084 1237.227798 1198.354604 1185.855568 1366.156417 1357.574757 1335.969957 1301.095723 1.120146067 1.127016867 0.960168466 0.950912201 0.921034926 0.911428381 1.05000454 1.043408823 1.026803742 1 10.34551139 -9.738760607 24.89864602 1.063591999 0.970193248 0.415609458 0.055399345 209.309822 229797.3221 0.010626401 0.015021994 1.82E-10 9.738760607 -0.093398751 RETCEHSSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 RETCEHSSEAK 11 1 D6RAC5;A0A087X159;P81877-2;P81877-4;P81877-5;P81877-3;P81877 D6RAC5 SSBP2 Single-stranded DNA-binding protein 2 0 0 105.78 0.0022771 0 800.88 638.73 685.79 511.15 839.11 671.93 819.39 816.78 882.26 754.9 FALSE FALSE TRUE 791.1185665 647.7220577 697.7258873 570.251568 796.2870855 628.9958416 888.9889661 840.4122406 803.3484559 735.2875892 1.075930803 0.88090982 0.948915632 0.775549018 1.082960052 0.85544194 1.209035729 1.142970795 1.092563601 1 9.522164824 -4.254386491 12.27902064 1.012607485 1.179154301 0 0.131677088 0 0 0.016782053 0 5.57E-05 4.254386491 0.166546815 REVLYDS(ph)EGLS(ph)GEER ddPTM_HeLa_Romidepsin_16h_R1 1 REVLYDSEGLSGEER 15 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 0 REVLY(0.002)DS(0.998)EGLS(1)GEER 134.08 0.0013635 15771000 3906.8 4293.4 4218.2 2250.2 4118 4154.8 3725.5 3577.3 3828 3927.6 TRUE FALSE FALSE 3859.182419 4353.842598 4291.616002 2510.378712 3907.843094 3889.321689 4041.943877 3680.803531 3485.614093 3825.560386 1.008788786 1.138092765 1.121826757 0.656212021 1.021508668 1.01666718 1.056562561 0.962160614 0.911138171 1 11.90145538 REVLYDS(ph)EGLSGEER ddPTM_HeLa_Romidepsin_16h_R1 1 REVLYDSEGLSGEER 15 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 REVLYDS(0.956)EGLS(0.044)GEER 69.922 0.015171 4721000 1281.6 1019.4 1092.2 802.78 1115.6 831.2 869.87 1046.6 824.56 1012.4 TRUE FALSE FALSE 1265.979366 1033.75114 1111.209283 895.6012008 1058.666769 778.0890026 943.7567361 1076.88172 750.8092885 986.0977021 1.283827519 1.04832527 1.126875441 0.908227652 1.073592167 0.789058732 0.957062099 1.092063918 0.761394421 1 9.945586785 -9.273777965 23.28944503 1.129155075 0.959984824 0 0.156411556 297.5033209 561545.4313 0.019887971 0.030538768 5.32E-10 9.273777965 -0.169170252 REVLYDSEGLS(ph)GEER ddPTM_HeLa_Romidepsin_16h_R1 1 REVLYDSEGLSGEER 15 1 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 REVLYDS(0.074)EGLS(0.925)GEER 58.339 0.026535 3670100 788.7 753.72 706.71 659.17 740.55 578.5 804.06 823.22 778.26 691.61 TRUE FALSE FALSE 779.087021 764.3308899 719.0099911 735.3863369 702.7569701 541.535717 872.3568363 847.0385719 708.6504764 673.6418725 1.15652998 1.134624971 1.067347534 1.0916577 1.043220439 0.803892601 1.294986063 1.257401902 1.051969162 1 9.395838007 REVS(ph)PAPAVAGQSK ddPTM_HeLa_Romidepsin_16h_R1 2 REVSPAPAVAGQSK 14 1 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 0 REVS(1)PAPAVAGQSK;REVS(1)PAPAVAGQSK ; 160.04 0.00053453 9745200 4179.56 4801.9 4243.25 4189.1 5585.6 5877.6 5353.4 6215.3 5139.3 4512.7 TRUE FALSE FALSE 4128.617915 4869.501274 4317.101986 4673.463452 5300.545989 5502.040329 5808.117662 6395.129899 4679.628136 4395.459403 0.939291559 1.107848083 0.9821731 1.063248007 1.20591399 1.251755465 1.321390355 1.454940044 1.064650519 1 12.10179825 -8.022536969 0.611444278 0.972684546 1.537342458 0.882322709 0.053837945 0.31417858 0.134774542 0.009176247 0.1045815 9.49E-09 8.022536969 0.564657912 RFDAQTGADR ddPTM_HeLa_Romidepsin_16h_R1 2 RFDAQTGADR 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 0 ; ; 150.15 0.0024126 3319100 1411.98 1194.52 2150.21 1518.21 1958.52 2080.87 2049.36 1005.46 1666.08 1212.37 FALSE FALSE TRUE 1394.770245 1211.336484 2187.633503 1693.752584 1858.569416 1947.909123 2223.432587 1034.551399 1517.061632 1180.872453 1.18113539 1.025797902 1.852556979 1.434323055 1.573895142 1.64955082 1.882872771 0.876090721 1.28469559 1 10.20563743 -9.780013782 24.99887316 1.083445712 1.561295937 0.361125775 0.272424694 157.1612087 211519.0261 0.039563496 0.052047702 1.66E-10 9.780013782 0.477850225 RFDDAVVQSDMK ddPTM_HeLa_Romidepsin_16h_R1 3 RFDDAVVQSDMK 12 1 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 ;; ;; 142.12 0.00046263 111775000 14433.7 12980.9 14699.3 14338 15623 14505.8 13047.9 12422.3 13633.8 11799.4 FALSE FALSE TRUE 14257.77651 13163.64545 14955.13515 15995.82702 14825.70001 13578.9262 14156.1883 12781.71965 12414.35878 11492.84989 1.240577981 1.145376959 1.301255589 1.391806835 1.289993357 1.181510794 1.231738728 1.112145358 1.080181061 1 13.48844897 -12.12476568 0.643816593 0.978161185 1.245609881 0.48427589 0.079687985 0.551910283 0.366789404 0.082495838 0.017977098 7.50E-13 12.12476568 0.267448696 RFDEGK(ac)LK ddPTM_HeLa_Romidepsin_16h_R1 1 RFDEGKLK 8 2 Q15417-3;Q15417;E9PDU6;Q15417-2 Q15417-3 CNN3 Calponin-3;Calponin 0 1 RFDEGK(1)LK 114.89 0.0030838 504560 0 0 228.74 227.16 165.93 249.38 128.7 0 0 0 FALSE TRUE FALSE 0 0 232.7211237 253.425308 157.4619729 233.4454228 139.6317748 0 0 0 0 RFDEILEASDGIMVAR ddPTM_HeLa_Romidepsin_16h_R1 5 RFDEILEASDGIMVAR 16 1 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BR70 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ;;;; ;;;; 138.77 0.00025145 125915900 7234.05 6420.56 6593.037 7593.89 7126.657 7721.984 6148.55 7237.01 8056.82 6615.03 FALSE FALSE TRUE 7145.878616 6510.948812 6707.786043 8471.931292 6762.9571 7228.574144 6670.807684 7446.401466 7336.197841 6443.170567 1.109062463 1.010519393 1.04106914 1.314869939 1.049631859 1.121897064 1.035329985 1.155704538 1.138600595 1 12.65355507 -13.10871086 0.331428152 0.915864029 1.115066781 0 0.092620437 7.25073542 0.664049275 0.567453043 0.034460821 7.79E-14 13.10871086 0.199202752 RFDGK(ac)LQSESTNNGK ddPTM_HeLa_Romidepsin_16h_R1 1 RFDGKLQSESTNNGK 15 2 H0Y8U3;P42285 H0Y8U3 SKIV2L2 Superkiller viralicidic activity 2-like 2 0 1 RFDGK(1)LQSESTNNGK 115.38 0.0021841 1498900 466.61 347.39 298.6 457.73 930.84 821.8 791.03 718.72 506.2 152.49 FALSE TRUE FALSE 460.9227778 352.2805655 303.7970077 510.6548963 883.3357614 769.2896322 858.2200685 739.5150292 460.9242042 148.5282878 3.103265948 2.371807894 2.04538147 3.438098586 5.94725607 5.179414935 5.778159037 4.978950745 3.103275551 1 7.214593914 -8.255197636 0.210817085 0.740754427 8.633756804 0.622122306 0.986724406 3.092749908 0.187348582 1.238009605 6.669717946 5.56E-09 8.255197636 7.893002378 RFDSEK(ac)AGDR ddPTM_HeLa_Romidepsin_16h_R1 1 RFDSEKAGDR 10 2 E9PM69;P17980;E9PKD5;R4GNH3 E9PM69;R4GNH3 PSMC3 26S protease regulatory subunit 6A 0 1 RFDSEK(1)AGDR 84.198 0.017732 0 150.1 130.95 62.529 129.18 58.417 0 63.438 0 0 0 FALSE TRUE FALSE 148.2705235 132.7935175 63.61729102 144.1163994 55.43576251 0 68.82642214 0 0 0 0 RFEK(ac)PLEEK ddPTM_HeLa_Romidepsin_16h_R1 2 RFEKPLEEK 9 2 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 1 ; RFEK(1)PLEEK;RFEK(1)PLEEK 105.13 0.0067819 12621900 3215.9 3519.4 3831.1 2209.06 6595.7 6745.3 6097.4 5172.1 7834.6 5763.3 FALSE TRUE FALSE 3176.703374 3568.946206 3897.778688 2464.481911 6259.096817 6314.297099 6615.313004 5321.746553 7133.853754 5613.568635 0.565897307 0.635771367 0.69434952 0.439022317 1.114994262 1.124827629 1.178450543 0.948014872 1.270823289 1 12.45470249 -8.720492296 24.97114929 0.746327064 1.100153399 0.327261292 0.226156443 113.9354154 69481.80816 0.0296658 0.059331091 1.90E-09 8.720492296 0.353826335 RFELYFQGPSSNKPR ddPTM_HeLa_Romidepsin_16h_R1 2 RFELYFQGPSSNKPR 15 2 P33993-2;P33993;C9J8M6 P33993-2 MCM7 DNA replication licensing factor MCM7 0 0 ; ; 100.73 0.0028311 4884400 1964.87 1678.18 1729.82 1335.88 1443.75 1674.66 1178.05 1147.77 1831.62 1490.67 FALSE FALSE TRUE 1940.921409 1701.805462 1759.926791 1490.340731 1370.07005 1567.654631 1278.113538 1180.978914 1667.79532 1451.942179 1.336775966 1.172089004 1.212119062 1.026446337 0.943611991 1.079694945 0.880278538 0.81337875 1.148665108 1 10.50376829 -9.027173703 2.819465461 1.167851271 0.935616886 0.57383721 0.099419409 0.223218073 3.564366771 0.021528401 0.039507333 9.39E-10 9.027173703 -0.232234385 RFPEAEALS(ph)PEQAAHYLR ddPTM_HeLa_Romidepsin_16h_R1 1 RFPEAEALSPEQAAHYLR 18 1 Q2NKX8 Q2NKX8 ERCC6L DNA excision repair protein ERCC-6-like 1 0 RFPEAEALS(1)PEQAAHYLR 139.2 0.00019071 6087800 607.4 753.12 766.78 700.7 694.33 958.86 712.29 848.28 925.01 818.41 TRUE FALSE FALSE 599.9967752 763.7224431 780.1254843 781.7182309 658.8957492 897.5919406 772.7918948 872.8236434 842.2747889 797.1475902 0.752679657 0.958069061 0.97864623 0.980644288 0.826566821 1.126004709 0.969446442 1.094933553 1.056610845 1 9.638703051 -8.216124593 0.780860146 0.891690295 1.083810186 0.064178123 0.10431965 1.120292087 0.986763547 0.019537363 0.14153348 6.08E-09 8.216124593 0.192119891 RFPGYDSESK ddPTM_HeLa_Romidepsin_16h_R1 1 RFPGYDSESK 10 1 A0A2R8Y6J3;P46777 A0A2R8Y6J3 RPL5 60S ribosomal protein L5 0 0 106.67 0.013049 27610000 3626.9 3365.9 3179.5 2915.3 3271.9 3256.1 2946.5 2765.3 3835.8 3385.4 FALSE FALSE TRUE 3582.693948 3413.285229 3234.837864 3252.380703 3104.922734 3048.045719 3196.775636 2845.309593 3492.716441 3297.44682 1.086505452 1.035129728 0.981012899 0.986333027 0.941614195 0.924365391 0.96946996 0.862882633 1.059218429 1 11.68713368 -9.110557386 1.120011925 1.041058633 0.92156237 0.71821801 0.033268738 0.238982598 0.591755387 0.006928169 0.015467739 7.75E-10 9.110557386 -0.119496263 RFPTDYASTS(ph)EDEFGSNR ddPTM_HeLa_Romidepsin_16h_R1 2 RFPTDYASTSEDEFGSNR 18 1 H0Y2V6;Q5SW79;Q5SW79-3 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 RFPTDYAS(0.067)T(0.219)S(0.713)EDEFGSNR;RFPTDYAS(0.035)T(0.346)S(0.62)EDEFGSNR ; 142.4 5.02E-11 6899200 1948.77 2126.27 1522.52 2070.04 1956.96 2052.66 1589.23 2041.58 1884.85 2051.76 TRUE FALSE FALSE 1925.017642 2156.203685 1549.018822 2309.387765 1857.089029 1921.501651 1724.219157 2100.649896 1716.264295 1998.454979 0.963252944 1.078935331 0.77510819 1.155586585 0.929262379 0.961493589 0.862776082 1.051136962 0.858795576 1 10.96466936 -9.143365127 0.004974596 1.938450414 3.53E-05 0 0.110708702 42981.0003 78.99928383 15174.61642 15607.41641 7.19E-10 9.143365127 -1.938415087 RFPWT(ph)TENT(ph)GNVNQQCIRSLLCT(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 1 RFPWTTENTGNVNQQCIRSLLCTPIK 26 2 G5E9C5;O76074-2;O76074 G5E9C5 PDE5A "cGMP-specific 3,5-cyclic phosphodiesterase" 3 0 RFPWT(0.502)T(0.502)ENT(0.936)GNVNQQCIRS(0.148)LLCT(0.913)PIK 42.863 0.017413 2297500 562.93 303.69 754.3 365.73 540.14 422.9 311.81 401.68 361.13 472.59 TRUE FALSE FALSE 556.0687926 307.9653558 767.4282751 408.0174234 512.5746403 395.8780548 338.2951336 413.3019771 328.8296283 460.3120437 1.20802573 0.669036059 1.667191388 0.886393109 1.113537322 0.860021067 0.734925662 0.897873481 0.714362426 1 8.84646838 -8.200838288 4.032918809 1.096118053 0.812209849 0.081384994 0.270995495 0.258437371 8.52002437 0.031874633 0.084915258 6.30E-09 8.200838288 -0.283908204 RFS(ph)EGVLQSPSQDQEK ddPTM_HeLa_Romidepsin_16h_R1 2 RFSEGVLQSPSQDQEK 16 1 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 RFS(1)EGVLQSPSQDQEK;RFS(1)EGVLQSPSQDQEK ; 260.97 4.05E-72 30360300 4022.7 4557.3 3297.6 4612.8 7434.2 8680.3 8837.2 10932.9 3944.3 3905.4 TRUE FALSE FALSE 3973.669785 4621.457789 3354.993345 5146.15364 7054.805033 8125.656844 9587.831547 11249.22621 3591.511929 3803.937145 1.044620254 1.214914341 0.881979175 1.352849283 1.8546061 2.136117537 2.520502096 2.957258699 0.944156486 1 11.89327769 -8.142931958 0.806120169 1.01188276 3.090958855 0.970858251 0.119061341 0.106590192 0.09773833 0.01940921 0.151493122 7.20E-09 8.142931958 2.079076095 up RFS(ph)FSQR ddPTM_HeLa_Romidepsin_16h_R1 4 RFSFSQR 7 1 Q92614;A0A0D9SFK2;Q92614-3;Q92614-4 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 RFS(0.986)FS(0.014)QR;RFS(0.928)FS(0.072)QR;RFS(0.996)FS(0.004)QR;RFS(0.936)FS(0.064)QR ;;; 86.882 0.001506 55617000 6278.83 6526.48 6020.61 6460.53 5797.31 5433.3 4060.24 4876.14 6794.5 6256.7 TRUE FALSE FALSE 6202.301205 6618.359957 6125.396192 7207.526876 5501.451638 5086.129665 4405.116684 5017.223418 6186.782903 6094.150032 1.01774672 1.086018546 1.005127238 1.182696002 0.902743058 0.834592132 0.722843491 0.823285182 1.015200294 1 12.5732093 -8.402195023 3.033606547 1.025926595 0.783506474 0.764641235 0.063146719 0.094668947 1.652791081 0.00889109 0.021720554 3.96E-09 8.402195023 -0.24242012 RFS(ph)LSVPR ddPTM_HeLa_Romidepsin_16h_R1 1 RFSLSVPR 8 1 D6R9B0;A0A0A0MSJ6;Q07002;Q07002-3;D6R9X1 D6R9B0 CDK18 Cyclin-dependent kinase 18 1 0 RFS(0.863)LS(0.137)VPR 63.408 0.029931 8074200 1377.2 1457.5 1718 1961.3 3110.1 2977.8 2799.7 3318.6 1541.4 1370.8 TRUE FALSE FALSE 1360.414157 1478.018723 1747.901069 2188.074734 2951.379992 2787.52819 3037.506448 3414.618455 1403.533323 1335.186418 1.018894544 1.106975553 1.309106388 1.638778454 2.210462862 2.087744567 2.274968054 2.557409518 1.051189036 1 10.38282547 -8.997488981 1.002510985 1.000955864 2.385592231 0.968516037 0.101996581 0.055534576 0.10942209 0.016532398 0.042395904 1.01E-09 8.997488981 1.384636368 up RFS(ph)PSQVPIQTR ddPTM_HeLa_Romidepsin_16h_R1 1 RFSPSQVPIQTR 12 1 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 RFS(0.952)PS(0.048)QVPIQTR 73.498 0.01883 18824000 914.99 1202.5 852.93 2046 981.3 836.14 1028.7 962.25 1205.8 1068 TRUE FALSE FALSE 903.8377499 1219.428827 867.7748889 2282.568147 931.2205993 782.7133525 1116.077752 990.0911856 1097.950228 1040.253206 0.86886322 1.172242315 0.834195832 2.194242838 0.895186474 0.752425802 1.072890471 0.951779028 1.055464402 1 10.02271902 -10.25622992 23.20646211 0.938074299 1.129531915 0.028292138 0.384316733 412.0983122 1835763.278 0.063085112 0.075955395 5.54E-11 10.25622992 0.191457615 RFVEVGR ddPTM_HeLa_Romidepsin_16h_R1 1 RFVEVGR 7 1 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 0 101.33 0.022205 3218400 1387.9 2026.8 1873.9 1578.6 2119.5 2231.6 1974.2 2072.5 1896 1385.1 FALSE FALSE TRUE 1370.983741 2055.333344 1906.514443 1761.12516 2011.334006 2089.007962 2141.888499 2132.464518 1726.417011 1349.114902 1.016209767 1.523467972 1.413159428 1.305393007 1.490854487 1.548428498 1.587624964 1.580639658 1.279666401 1 10.39779751 -10.26464613 24.74686372 1.0076546 1.488237101 0.688251489 0.116823832 56.99937146 439869.0606 0.014685865 0.017172526 5.44E-11 10.26464613 0.480582501 PEPSK(ac)SAPAPK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 PEPSKSAPAPKK 12 2 P33778;U3KQK0;Q99877 P33778;U3KQK0 HIST1H2BB;HIST1H2BN Histone H2B type 1-B;Histone H2B;Histone H2B type 1-N 0 2 ; PEPSK(1)SAPAPK(1)K;PEPSK(1)SAPAPK(1)K 114.71 0.006397 8197100 566.21 426.35 720.87 2227.3 8687.4 9864.2 10191.2 10318.7 1211.51 1020.45 FALSE TRUE FALSE 559.3088147 432.3521665 733.41644 2484.830906 8244.049561 9233.909455 11056.84027 10617.2553 1103.149511 993.9385619 0.562719705 0.434988824 0.737889109 2.499984407 8.294325099 9.290221558 11.12426934 10.68200361 1.109876962 1 9.957012867 -8.72250011 1.942548347 0.730229503 10.53274953 0.9888199 0.464889785 0.022723528 0.174221356 0.07190994 0.164406835 1.89E-09 8.72250011 9.802520024 up RGAT(ph)PPAPPR ddPTM_HeLa_Romidepsin_16h_R1 1 RGATPPAPPR 10 1 Q6SPF0 Q6SPF0 SAMD1 Atherin 1 0 RGAT(1)PPAPPR 84.892 0.020482 22513000 1492.5 1701.3 1715.6 2013.7 1554.2 1239.8 1045.6 1008 1849.2 1422.6 TRUE FALSE FALSE 1474.308836 1725.250946 1745.459298 2246.533469 1474.883374 1160.580781 1134.413238 1037.16489 1683.802921 1385.640647 1.063990753 1.245092622 1.259676744 1.621295878 1.064405391 0.837577033 0.818692235 0.748509285 1.215180086 1 10.43633744 -8.261652796 4.49860464 1.113296259 0.798195267 0.467862951 0.180771552 0.184439578 10.02332288 0.029657906 0.07382948 5.47E-09 8.261652796 -0.315100991 RGAYGGGYGGYDDYGGYNDGYGFGSDR ddPTM_HeLa_Romidepsin_16h_R1 1 RGAYGGGYGGYDDYGGYNDGYGFGSDR 27 1 P55795 P55795 HNRNPH2 Heterogeneous nuclear ribonucleoprotein H2 0 0 52.059 0.013113 7185300 282.7 195.85 321.33 241.61 251.13 312.52 189.95 115.76 263.68 313.2 FALSE FALSE TRUE 279.2543437 198.6071814 326.9226139 269.546085 238.313899 292.5509806 206.0843483 119.109333 240.0958004 305.0630188 0.915398873 0.65103657 1.071655998 0.883575092 0.781195636 0.958985398 0.675546807 0.39044173 0.787036729 1 8.25296349 -7.129514868 1.193744568 0.93232254 1.69E-11 0.573539064 0.124590983 0.865235733 0.828858536 0.017154464 1.072460173 7.42E-08 7.129514868 -0.93232254 RGAYGGGYGGYDDYNGYNDGYGFGSDR ddPTM_HeLa_Romidepsin_16h_R1 3 RGAYGGGYGGYDDYNGYNDGYGFGSDR 27 1 P31943;E9PCY7;G8JLB6;H0YB39;H0YBD7 P31943 HNRNPH1 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed" 0 0 ;; ;; 139.04 3.00E-10 30232800 2183.17 2193.26 1753.74 1904.84 1839.67 2104.09 1720.5 1881.13 2432.29 2207.1 FALSE FALSE TRUE 2156.560684 2224.136772 1784.263109 2125.086563 1745.784775 1969.64544 1866.639227 1935.557529 2214.739891 2149.759224 1.003163824 1.034598083 0.829982767 0.988523059 0.812083863 0.916216764 0.868301532 0.900360146 1.030226951 1 11.06995937 -9.769735635 24.99810165 1.004018582 0.887796798 0.646135224 0.047122366 81.83993874 246598.1228 0.006563841 0.008706663 1.70E-10 9.769735635 -0.116221783 RGDEEEFFEIR ddPTM_HeLa_Romidepsin_16h_R1 1 RGDEEEFFEIR 11 1 Q5TGL8 Q5TGL8 PXDC1 PX domain-containing protein 1 0 0 158.25 0.00048905 0 431.05 411.59 339.25 291.65 378.64 272.34 189.5 251.64 649.48 410.53 FALSE FALSE TRUE 425.7961968 417.3843748 345.1545039 325.3719453 359.3165879 254.9383529 205.5961253 258.9208064 591.3888821 399.8643714 1.064851553 1.043814865 0.863178939 0.813705768 0.898596158 0.637562061 0.514164652 0.647521572 1.478973683 1 8.64336693 -8.579586925 0.747176032 1.032506634 0.534921236 0.63663603 0.15756191 0.217813307 0.203302659 0.013249508 0.063063863 2.63E-09 8.579586925 -0.497585398 RGDFIPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 RGDFIPGLR 9 1 P08559-3;P08559;P08559-2;P08559-4 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 0 120.99 0.0002994 0 2971.2 2627.9 3640.5 3330.2 3246.6 4336.9 2777 2860.1 2959.6 2361.1 FALSE FALSE TRUE 2934.985872 2664.895645 3703.861375 3715.253393 3080.913887 4059.786087 3012.878311 2942.852481 2694.885964 2299.758282 1.276214937 1.158772062 1.610543771 1.615497343 1.339668569 1.765309911 1.310084775 1.279635562 1.171812701 1 11.16726652 -10.8380511 0.60237504 1.031497385 1.4822965 0.417659246 0.172957832 0.404352383 0.33880839 0.069298429 0.052050494 1.45E-11 10.8380511 0.450799115 RGDLPFVVPR ddPTM_HeLa_Romidepsin_16h_R1 3 RGDLPFVVPR 10 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ;; ;; 164.65 0.0010917 65416730 8214.5 9494.8 7823.2 8192.4 9016.35 9909.1 8183.45 9217.18 9201.79 8727.96 FALSE FALSE TRUE 8114.378514 9628.468044 7959.359514 9139.643834 8556.212015 9275.94049 8878.552039 9483.864561 8378.758856 8501.206341 0.954497302 1.132600205 0.93626236 1.075099635 1.006470337 1.09113226 1.044387312 1.115590445 0.985596458 1 13.05345186 -8.36677876 0.435003233 0.980762568 1.119529139 0.257902114 0.055541894 1.931688179 0.455367266 0.015176681 0.119282059 4.30E-09 8.36677876 0.138766571 RGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_HeLa_Romidepsin_16h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 0 RGDS(0.997)ES(0.604)EEDEQDS(0.398)EEVR 98.898 0.0033564 8168500 1230.9 1073.1 1281.5 1216.1 1530 1632.1 1517.3 1678.6 1553.7 1308 TRUE FALSE FALSE 1215.897317 1088.20713 1303.80397 1356.711204 1451.918391 1527.814077 1646.179424 1727.167643 1414.733181 1274.017971 0.954380036 0.854153673 1.023379575 1.06490743 1.139637292 1.199209204 1.292116329 1.355685462 1.110449941 1 10.31516991 -8.304822475 0.894423058 0.96876369 1.361315982 0.813097283 0.06302879 0.171407351 0.220757433 0.008128182 0.046149564 4.96E-09 8.304822475 0.392552292 RGDS(ph)ESEEDEQDS(ph)EEVR ddPTM_HeLa_Romidepsin_16h_R1 1 RGDSESEEDEQDSEEVR 17 1 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 0 RGDS(0.989)ES(0.029)EEDEQDS(0.982)EEVR 127.01 0.0019711 4417900 723.72 522.33 844.63 728.69 674.81 1045.1 777.81 977.17 683.99 735.47 TRUE FALSE FALSE 714.8990223 529.6833755 859.3304308 812.9445664 640.3719276 978.3214829 843.877162 1005.442872 622.8122213 716.3623834 0.997957233 0.73940702 1.199575035 1.13482308 0.893921767 1.365679586 1.178003175 1.403539459 0.869409444 1 9.484545772 -7.878499671 0.75204791 0.988921907 1.43990405 0.49955959 0.145197601 0.881313982 0.575513963 0.022375682 0.279547465 1.32E-08 7.878499671 0.450982143 RGEAHLAVNDFELAR ddPTM_HeLa_Romidepsin_16h_R1 4 RGEAHLAVNDFELAR 15 1 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 0 0 ;;; ;;; 127.07 0.00041616 18974600 4082.64 3811.21 3595.72 3847.22 4001.58 4284.63 3522.26 3666.81 4297.57 4541.02 FALSE FALSE TRUE 4032.879213 3864.864314 3658.301998 4292.053678 3797.364441 4010.855971 3821.440676 3772.903362 3913.184576 4423.043646 0.911788247 0.873801984 0.827100588 0.970384654 0.858541028 0.906809042 0.863984392 0.853010656 0.884726647 1 12.11082376 -11.64093041 0.51936996 1.008507436 0.877110435 0.006478142 0.05116445 0.517930123 0.2682868 0.031886674 0.010423495 2.29E-12 11.64093041 -0.131397001 RGEDVETSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RGEDVETSKK 10 2 O60869-2;O60869-3;O60869 O60869-2 EDF1 Endothelial differentiation-related factor 1 0 1 ; RGEDVETSK(1)K;RGEDVETSK(1)K 144.7 0.0035987 3146600 1566.44 1785.32 1836.72 1521.29 2056.5 2218.33 3152 928.97 2120.12 1504.4 FALSE TRUE FALSE 1547.347627 1810.453782 1868.687341 1697.188708 1951.549131 2076.585872 3419.730801 955.8482813 1930.491157 1465.315471 1.05598259 1.23553857 1.275279882 1.158241171 1.331828654 1.41715959 2.333784682 0.652315696 1.317457705 1 10.51699558 -9.23362336 0.68832933 1.018821776 1.530554265 0.054749617 0.397634185 0.815096162 0.748404607 0.074864035 0.195178175 5.84E-10 9.23362336 0.511732489 RGEGDAPFSEPGTTSTQRPS(ph)SPETATK ddPTM_HeLa_Romidepsin_16h_R1 1 RGEGDAPFSEPGTTSTQRPSSPETATK 27 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182;A0A087X1W1;I3L1I8;Q9UQ35-3 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 RGEGDAPFSEPGT(0.017)T(0.059)S(0.058)T(0.058)QRPS(0.396)S(0.396)PET(0.01)AT(0.005)K 103.71 1.09E-08 110720000 5261.8 5161.9 4756.4 3518.7 3803 4102.8 4036.9 4500.4 5293.7 5033.2 TRUE FALSE FALSE 5197.667158 5234.569364 4839.183147 3925.54865 3608.918719 3840.644321 4379.794185 4630.611974 4820.218214 4902.436738 1.060221158 1.067748478 0.98709752 0.800734178 0.736147943 0.783415376 0.89339127 0.944553132 0.983229049 1 12.2592833 -9.363410864 4.294379481 1.031874709 0.827326209 0.718040213 0.059144806 0.094990833 3.014709746 0.009819535 0.015246684 4.33E-10 9.363410864 -0.2045485 RGEK(ac)GEVVETVEDVIVR ddPTM_HeLa_Romidepsin_16h_R1 1 RGEKGEVVETVEDVIVR 17 2 H7C128;H7C179;H7C127;Q9H0E9-4;Q9H0E9-2;B5MCW3;Q9H0E9 H7C128 BRD8 Bromodomain-containing protein 8 0 1 RGEK(1)GEVVETVEDVIVR 105.53 0.013962 244650 66.731 138.78 0 0 0 74.105 0 60.495 72.812 72.811 FALSE TRUE FALSE 65.9176569 140.7337485 0 0 0 69.36992966 0 62.24532738 66.29951236 70.91935972 0.929473379 1.984419332 0 0 0 0.978152227 0 0.877691615 0.93485774 1 6.148107606 -9.71571416 24.99999372 1.042097542 0.297530904 0.470832062 0.454737763 94.54708648 51692.85122 0.068084102 0.096285262 1.92E-10 9.71571416 -0.744566638 RGES(ph)LDNLDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RGESLDNLDSPR 12 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 2 0 RGES(1)LDNLDS(1)PR 96.435 0.018474 15246000 3195.9 3508.4 3089.4 3120.5 4013.5 4712.7 4698.9 4432.4 3564.6 3388.6 TRUE FALSE FALSE 3156.947142 3557.791347 3143.169711 3481.306892 3808.676119 4411.57368 5098.024449 4560.644501 3245.773248 3300.563684 0.956487268 1.077934465 0.952313002 1.054761315 1.153947169 1.336612198 1.544592057 1.381777459 0.983399673 1 11.68849672 -8.354878069 1.51195992 0.98643088 1.472100538 0.924243117 0.054003946 0.067466184 0.291383848 0.007656653 0.026108384 4.42E-09 8.354878069 0.485669658 RGES(ph)LDNLDSPR ddPTM_HeLa_Romidepsin_16h_R1 4 RGESLDNLDSPR 12 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 RGES(1)LDNLDSPR;RGES(1)LDNLDSPR;RGES(0.999)LDNLDS(0.001)PR;RGES(0.987)LDNLDS(0.013)PR ;;; 169.94 0.00024724 680773000 12772.9 13727.3 10471.73 10335.01 9866.41 10262.07 8026.98 10118.7 13529.4 12715 TRUE FALSE FALSE 12617.21898 13920.55329 10653.98607 11529.99248 9362.890281 9606.356846 8708.791481 10411.46862 12319.29658 12384.66247 1.018777784 1.124015558 0.860256474 0.930989643 0.7560069 0.775665616 0.70319167 0.840674394 0.994722029 1 13.59626693 -9.111990512 1.41787659 1.015281263 0.761708036 0.746510054 0.064525268 0.134838023 0.534139229 0.009675699 0.019669905 7.73E-10 9.111990512 -0.253573227 RGESLDNLDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RGESLDNLDSPR 12 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 RGESLDNLDS(1)PR 152.94 0.00042324 30767000 2631.6 2294.7 2548.8 2487.1 2828 2980.6 2425.4 2446 2580.1 2311.5 TRUE FALSE FALSE 2599.525047 2327.004847 2593.160795 2774.670204 2683.676607 2790.149279 2631.413415 2516.771151 2349.329394 2251.446897 1.154601981 1.03355973 1.151775242 1.232394248 1.191978639 1.239269415 1.168765481 1.117846108 1.043475375 1 11.13663673 -12.92924219 0.263590306 0.866408101 1.195629719 0.547258708 0.053223877 3.888002493 0.268547769 0.411233809 0.03960151 1.18E-13 12.92924219 0.329221618 RGFS(ph)DSGGGPPAK ddPTM_HeLa_Romidepsin_16h_R1 1 RGFSDSGGGPPAK 13 1 Q9H307;G3V5F0;G3V579 Q9H307 PNN Pinin 1 0 RGFS(0.929)DS(0.071)GGGPPAK 61.962 0.026418 14330000 1930.7 2259.1 1450.3 1804.2 1959.8 1624.6 1423.4 1409.4 2272.2 2317.6 TRUE FALSE FALSE 1907.167886 2290.903669 1475.541863 2012.810093 1859.784093 1520.793303 1544.30356 1450.178765 2068.968741 2257.388418 0.844855883 1.014846914 0.653649966 0.891654302 0.823865347 0.673695892 0.684110695 0.642414373 0.916532009 1 11.14043896 -5.508474877 0.139271215 1.052506955 2.05E-16 0.578489097 0.088123236 23.23253616 0.319516329 0.261571763 4.605144211 3.10E-06 5.508474877 -1.052506955 RGGADVNIR ddPTM_HeLa_Romidepsin_16h_R1 2 RGGADVNIR 9 1 P08621;P08621-2;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 0 0 ; ; 107.21 0.01406 1485140 1073.7 873.96 903.15 1010.32 952.85 1272.54 1119.39 472.73 1117.02 1035.73 FALSE FALSE TRUE 1060.613331 886.2636318 918.8689469 1127.137952 904.2225089 1191.228801 1214.470959 486.4076967 1017.110934 1008.821585 1.051338856 0.878513748 0.910833948 1.117281756 0.896315585 1.180812166 1.203851084 0.482154331 1.008216863 1 9.978455334 -7.249402479 24.79279195 1.024511357 0.48215396 0.694919581 0.108377628 704.4180638 1450884.317 0.014464479 0.320186999 5.63E-08 7.249402479 -0.542357397 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR ddPTM_HeLa_Romidepsin_16h_R1 2 RGGDGYDGGYGGFDDYGGYNNYGYGNDGFDDR 32 1 P31942-4;P31942-3;P31942;P31942-5 P31942-4 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 0 ; ; 136.48 1.77E-15 96186000 3135.4 2893 2899.8 2874.2 3051.2 3201.3 2807.1 2878.5 3390.8 3003 FALSE FALSE TRUE 3097.184539 2933.72773 2950.269803 3206.528528 2895.485878 2996.747262 3045.535004 2961.784856 3087.518356 2924.981627 1.05887316 1.002990139 1.008645584 1.096255955 0.98991592 1.024535414 1.041215089 1.01258238 1.055568461 1 11.51421185 -7.202101983 19.59502106 1.027878897 1.012580949 0.021964324 0.031304317 17058.54991 5630358.439 0.004357778 5.683815183 6.28E-08 7.202101983 -0.015297948 RGGGSGGGEES(ph)EGEEVDED ddPTM_HeLa_Romidepsin_16h_R1 4 RGGGSGGGEESEGEEVDED 19 1 Q96QR8 Q96QR8 PURB Transcriptional activator protein Pur-beta 1 0 RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGSGGGEES(1)EGEEVDED;RGGGS(0.001)GGGEES(0.999)EGEEVDED ;;; 106.19 0.0015646 154173000 9855.45 9047.63 8009.3 8444.61 10621.32 10033.64 8789.62 9825.07 10121.07 9465.16 TRUE FALSE FALSE 9735.327985 9175.002773 8148.698507 9421.015541 10079.27441 9392.522786 9536.210103 10109.3429 9215.816151 9219.253779 1.055977872 0.995200153 0.883878316 1.021884826 1.093285275 1.018794255 1.034379824 1.096546764 0.999627125 1 13.17043427 -4.000014608 0.744567262 1.01644157 14.22265766 0.210364453 0.050810963 520.1375944 2.155616157 0.00889042 11524.89598 1.00E-04 4.000014608 13.20621609 RGGIPAS(ph)PIDPFQSR ddPTM_HeLa_Romidepsin_16h_R1 2 RGGIPASPIDPFQSR 15 1 Q96LD4-2;Q96LD4 Q96LD4-2 TRIM47 Tripartite motif-containing protein 47 1 0 RGGIPAS(0.997)PIDPFQS(0.003)R;RGGIPAS(1)PIDPFQSR ; 76.329 0.011334 9978100 5227.1 5532.4 4972.6 6400.7 5192.8 5158.1 4137.5 4829.2 5733.3 5935.2 TRUE FALSE FALSE 5163.390095 5610.285272 5059.146017 7140.77905 4927.792039 4828.514057 4488.939147 4968.925283 5220.499289 5781.002648 0.893165149 0.970469244 0.87513297 1.23521463 0.85241131 0.835238167 0.776498372 0.859526554 0.903043919 1 12.49710402 -8.54630011 24.99999894 0.965053022 0.823161213 0.355312095 0.097458834 198.1253187 211478.5033 0.013797278 0.027595624 2.84E-09 8.54630011 -0.141891809 RGILTLK ddPTM_HeLa_Romidepsin_16h_R1 3 RGILTLK 7 1 P0CG38;P0CG39;P60709;A0A2R8Y793;G5E9R0;E7EVS6;A0A2R8YGF8;C9JTX5;C9JUM1;C9JZR7;Q6S8J3;A5A3E0;P63261;I3L3I0;I3L1U9;I3L4N8;K7EM38;I3L3R2;J3KT65;P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P0CG38;P60709;P63261;P63267 POTEI;POTEJ;ACTB;POTEE;POTEF;ACTG1;ACTG2;ACTA1;ACTC1;ACTA2 "POTE ankyrin domain family member I;POTE ankyrin domain family member J;Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;POTE ankyrin domain family member E;POTE ankyrin domain family member F;Actin, cytoplasmic 2;Actin, cytoplasmic 2, N-terminally processed;Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ;; ;; 106.36 0.0059927 13982100 5293.6 4636.5 13833.6 8783 13401.7 15421.8 11356.1 6332.3 5033.3 2197.94 FALSE FALSE TRUE 5229.079567 4701.772769 14074.36801 9798.531785 12717.76124 14436.39675 12320.68685 6515.51511 4583.109042 2140.837202 2.442539565 2.196230878 6.574235534 4.57696259 5.940555045 6.743341688 5.755078826 3.043442586 2.140802223 1 11.06395938 -9.837659492 6.039186772 1.718769053 5.491363024 0.72313073 1.05716268 0.078415682 4.785715914 0.1777497 0.235278207 1.45E-10 9.837659492 3.772593971 RGMFEPY(ph)LKSFYIRSTDPTQIK ddPTM_HeLa_Romidepsin_16h_R1 1 RGMFEPYLKSFYIRSTDPTQIK 22 3 A0A590UK30;A0A590UJW5;A0A590UKD3;A0A590UJU7;A0A590UJU0;A0A590UJE5;A0A590UJ60;A0A590UK04;A0A5F9UJV3;A0A2R8Y2A8;A0A590UKC4;Q13367-3;Q13367;Q13367-4 A0A590UK30 AP3B2 AP-3 complex subunit beta-2 1 0 RGMFEPY(0.946)LKS(0.039)FY(0.01)IRS(0.002)T(0.002)DPT(0.002)QIK 44.788 0.017661 7481700 1230.3 1317.4 1416.2 1033.8 1273.1 1371.8 788.67 1188.7 1508.4 1301.3 TRUE FALSE FALSE 1215.30463 1335.946392 1440.848367 1153.33282 1208.128956 1284.146407 855.6596101 1223.093159 1373.484926 1267.492038 0.958826244 1.054007719 1.136771138 0.90993299 0.953164927 1.013139624 0.675080856 0.964971078 1.083624105 1 10.30776097 -7.792889706 24.99720807 0.991317857 0.820025728 0.396301026 0.092364368 120.1985823 95535.54841 0.011302074 0.03391081 1.61E-08 7.792889706 -0.17129213 RGNDPLTSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 4 RGNDPLTSSPGR 12 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 0 RGNDPLT(0.012)S(0.377)S(0.611)PGR;RGNDPLT(0.001)S(0.091)S(0.908)PGR;RGNDPLTS(0.06)S(0.94)PGR;RGNDPLT(0.002)S(0.208)S(0.79)PGR ;;; 145.81 0.0023183 550324800 9778.6 8908.3 9228.7 8392 8523.9 7950.7 7023.9 7085.2 10240.1 9399.1 TRUE FALSE FALSE 9659.414662 9033.711281 9389.321652 9362.322526 8088.893576 7442.67593 7620.509891 7290.199083 9324.199809 9154.910027 1.055107547 0.986761339 1.025605017 1.022655875 0.883557954 0.812970953 0.832395935 0.796315754 1.018491693 1 13.16032999 -8.629717649 2.776112123 1.023740828 0.816754205 0.956563791 0.019858295 0.045114713 0.700278516 0.003685877 0.008093581 2.35E-09 8.629717649 -0.206986623 RGPGLTSS(ph)PPLLPPS(ph)LQVNFHS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RGPGLTSSPPLLPPSLQVNFHSPR 24 1 P42892-2 P42892-2 3 0 RGPGLT(0.034)S(0.148)S(0.822)PPLLPPS(0.998)LQVNFHS(0.998)PR 47.155 0.014956 14657000 1898.6 1644.2 1761 1813.9 2234.1 2086.7 1615.5 1745.1 1586.5 1556.7 TRUE FALSE FALSE 1875.459133 1667.347091 1791.649466 2023.631653 2120.08554 1953.366605 1752.72053 1795.591715 1444.599467 1516.25671 1.236900797 1.099646966 1.181626736 1.334623379 1.398236543 1.288282249 1.155952365 1.184226724 0.952740692 1 10.56629831 -12.55404661 0.391891372 0.895169152 1.257397324 0.613951756 0.08277817 1.909729212 0.324738835 0.297154943 0.031517902 2.79E-13 12.55404661 0.362228172 RGPGT(ph)PGPVAR ddPTM_HeLa_Romidepsin_16h_R1 1 RGPGTPGPVAR 11 1 Q8N6S5 Q8N6S5 ARL6IP6 ADP-ribosylation factor-like protein 6-interacting protein 6 1 0 RGPGT(1)PGPVAR 81.185 0.022192 2382200 346.54 444.74 349.44 211.45 331.68 707.08 462.86 673.91 426.51 350.28 TRUE FALSE FALSE 342.3162372 451.0010614 355.5218566 235.8988439 314.7531319 661.89987 502.1753168 693.4085226 388.3618774 341.1796751 1.003331271 1.321887247 1.042037034 0.691421152 0.922543618 1.940033121 1.471879345 2.032385201 1.138291363 1 8.414387894 -8.265069773 24.99942959 1.000941827 1.780477254 0.764638563 0.202401595 102.0191307 702521.2484 0.026898356 0.062440763 5.43E-09 8.265069773 0.779535427 RGPNYTSGYGTNSELS(ph)NPSETESER ddPTM_HeLa_Romidepsin_16h_R1 1 RGPNYTSGYGTNSELSNPSETESER 25 1 E7EU85;E9PFF5;B4DXZ6;P51114-3;P51114-2;P51114 E7EU85 FXR1 Fragile X mental retardation syndrome-related protein 1 1 0 RGPNYTSGYGT(0.001)NS(0.025)ELS(0.809)NPS(0.125)ET(0.025)ES(0.013)ER 45.542 0.018528 17043000 314.86 329.46 251.96 189.6 482.55 271.58 373.08 552.06 480.93 356.74 TRUE FALSE FALSE 311.0223652 334.0981465 256.3452581 211.5224441 457.9236729 254.2269145 404.7694059 568.0329851 437.9144163 347.4718434 0.895100916 0.961511423 0.737743973 0.608747005 1.317872747 0.731647526 1.164898433 1.634759754 1.260287487 1 8.440752267 -7.362804663 2.956524732 0.925046734 1.682016685 0.493790203 0.212909738 0.159267219 2.158855272 0.02403758 0.248414871 4.34E-08 7.362804663 0.75696995 RGPPS(ph)PSASSPS(ph)SAGWR ddPTM_HeLa_Romidepsin_16h_R1 1 RGPPSPSASSPSSAGWR 17 1 H3BQ28 H3BQ28 SYNGR3 2 0 RGPPS(1)PSAS(0.219)S(0.219)PS(0.344)S(0.219)AGWR 68.413 0.011934 1193100 290.17 202.76 267.33 298.64 286.4 180.02 165.37 230.12 206.54 258.82 TRUE FALSE FALSE 286.6332964 205.6144606 271.9827665 333.1701619 271.7839393 168.517303 179.4165237 236.7781591 188.0665451 252.0958191 1.137001389 0.815620272 1.078886463 1.321601299 1.078097766 0.668465283 0.711699719 0.939238739 0.746012154 1 7.977828382 -8.272133771 24.69931516 1.0685529 0.766991095 0.29760122 0.168539983 361.2845691 834407.6938 0.019700544 0.044483426 5.34E-09 8.272133771 -0.301561805 RGPSTPGGK(ac)LILPAPQIPPPNNAR ddPTM_HeLa_Romidepsin_16h_R1 1 RGPSTPGGKLILPAPQIPPPNNAR 24 2 F8W108;F8WCU9;Q68CP9-3;Q68CP9 F8W108 ARID2 AT-rich interactive domain-containing protein 2 0 1 RGPSTPGGK(1)LILPAPQIPPPNNAR 44.258 0.029297 0 0 0 0 0 0 0 0 0 0 71.086 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 69.23917547 0 0 0 0 0 0 0 0 0 1 6.11351664 -12.15782943 0.67715094 1.083625667 2.50E-23 0 0.307667284 0.06659167 0.049088893 0.041658112 0.0090835 6.95E-13 12.15782943 -1.083625667 RGQS(ph)PLPR ddPTM_HeLa_Romidepsin_16h_R1 3 RGQSPLPR 8 1 H3BTS1;H3BN52;Q9BQ65-3;Q9BQ65-2;Q9BQ65 H3BTS1 USB1 U6 snRNA phosphodiesterase 1 0 RGQS(1)PLPR;RGQS(1)PLPR;RGQS(1)PLPR ;; 118.4 0.0057533 17419800 2320.88 2519.02 2336.83 2512.96 3541.81 4524.7 4547.4 1525.9 2769.89 2492.89 TRUE FALSE FALSE 2292.592222 2554.48283 2377.501546 2803.520259 3361.058219 4235.586273 4933.656042 1570.049509 2522.144101 2428.124358 0.944182374 1.052039539 0.979151475 1.154603243 1.384219967 1.744386056 2.031879473 0.646610007 1.03872114 1 11.2456266 -8.815949457 2.375265222 0.981677477 1.531656457 0.285141013 0.331005976 0.223859992 2.575311643 0.045847581 0.09484534 1.53E-09 8.815949457 0.54997898 RGS(ph)ALGPDEAGGELER ddPTM_HeLa_Romidepsin_16h_R1 1 RGSALGPDEAGGELER 16 1 O75145-2;O75145;R4GNF1;R4GN36 O75145-2 PPFIA3 Liprin-alpha-3 1 0 RGS(1)ALGPDEAGGELER 76.341 0.00899 2773000 408.03 381.17 481.63 660.69 588.33 639.7 709.17 666.79 445.12 476.09 TRUE FALSE FALSE 403.0567734 386.5361213 490.0125681 737.0820864 558.3053247 598.8252345 769.4068821 686.0825166 405.3073524 463.7211132 0.869179259 0.833552992 1.056696696 1.589494344 1.203967878 1.29134779 1.659201749 1.479515375 0.874032562 1 8.857113604 -9.411700498 4.708036814 0.929152607 1.432970201 0.797967979 0.131624076 0.082265462 2.881128286 0.021130968 0.032489724 3.88E-10 9.411700498 0.503817594 RGS(ph)FSSENYWR ddPTM_HeLa_Romidepsin_16h_R1 3 RGSFSSENYWR 11 1 Q6P6C2-3;Q6P6C2;K7ER58;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 0 RGS(0.983)FS(0.008)S(0.008)ENYWR;RGS(1)FSSENYWR;RGS(0.988)FS(0.011)SENYWR ;; 127.78 0.0019539 32726300 1358.46 1221.01 1411.95 1419.81 1418.13 1799.53 1293.51 1481.02 1588.96 1458.63 TRUE FALSE FALSE 1341.902567 1238.199411 1436.524397 1583.975113 1345.757534 1684.545841 1403.380707 1523.870977 1446.839438 1420.734582 0.9445132 0.871520568 1.011113839 1.114898682 0.947226562 1.185686519 0.98778528 1.07259371 1.018374196 1 10.47242134 -9.52266321 24.99999999 0.96424842 1.058564162 0.318576431 0.070803898 7.022535358 814564.8895 0.010239341 0.014571643 3.00E-10 9.52266321 0.094315741 RGS(ph)GDTSISIDTEASIR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSGDTSISIDTEASIR 17 1 Q32MZ4-3;Q32MZ4-2;Q32MZ4;Q32MZ4-4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 RGS(0.946)GDT(0.04)S(0.007)IS(0.002)IDT(0.004)EAS(0.001)IR;RGS(0.997)GDT(0.002)S(0.001)ISIDTEASIR ; 109.77 0.0031129 11800000 1174.97 772.52 932.25 1155.03 2398.03 2740.7 2311 2726.3 1146.83 1006.29 TRUE FALSE FALSE 1160.649014 783.3955568 948.4754202 1288.580003 2275.649581 2565.578115 2507.296282 2805.181189 1044.254653 980.1464407 1.18415878 0.799263788 0.967687461 1.314681102 2.321744472 2.617545714 2.558083342 2.862002118 1.065406769 1 9.936853504 -8.734079304 2.502897517 1.054173662 2.661314176 0.97506348 0.12191372 0.033725389 0.4309638 0.020564769 0.04380893 1.84E-09 8.734079304 1.607140514 up RGS(ph)GDTSSLIDPDTSLSELR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 RGS(0.479)GDT(0.479)S(0.034)S(0.007)LIDPDTSLSELR;RGS(0.981)GDT(0.008)S(0.008)S(0.002)LIDPDTSLSELR ; 126.04 5.83E-05 262098000 1565.72 1612.67 1650.82 1602.63 2548.02 2943.58 2706.75 3369.07 1737.6 2054.4 TRUE FALSE FALSE 1546.636402 1635.373211 1679.55183 1787.933621 2417.985031 2755.494738 2936.661277 3466.548725 1582.184704 2001.026392 0.772921541 0.817267187 0.839345166 0.893508266 1.208372384 1.377040677 1.467577484 1.732385309 0.790686575 1 10.96652448 -8.21144206 1.128850645 0.875456716 1.669324532 0.930068267 0.08469194 0.13697672 0.297539927 0.0166811 0.085287923 6.15E-09 8.21144206 0.793867816 RGS(ph)IGENQGEEK ddPTM_HeLa_Romidepsin_16h_R1 4 RGSIGENQGEEK 12 1 E7EX44;Q05682-3;Q05682-6;Q05682-2 E7EX44 CALD1 Caldesmon 1 0 RGS(1)IGENQGEEK;RGS(1)IGENQGEEK;RGS(1)IGENQGEEK;RGS(1)IGENQGEEK ;;; 172.09 3.17E-05 157433000 19255.6 17883.7 19316.4 17516.9 19745.3 20899.2 23476 10600 23139.7 21248.5 TRUE FALSE FALSE 19020.90534 18135.4672 19652.59384 19542.2864 18737.62366 19563.80857 25470.05085 10906.69428 21070.02728 20696.46091 0.919041445 0.876259341 0.949563016 0.944233243 0.905354 0.945273139 1.230647644 0.526983542 1.018049771 1 14.33709647 -16.52287057 0.01079317 2.041744674 1.02E-07 0.06557288 0.158801132 28773.79136 25.10661071 2765.035857 2036.934874 3.00E-17 16.52287057 -2.041744572 RGS(ph)IGENQIK ddPTM_HeLa_Romidepsin_16h_R1 1 RGSIGENQIK 10 1 E9PGZ1;Q05682-5;Q05682-4;C9J813 E9PGZ1 CALD1 Caldesmon 1 0 RGS(1)IGENQIK 118.76 0.019415 28207000 2207.8 1920.7 1869 1262.4 2230.6 2300.7 1991.4 2453.3 2630.9 2203.5 TRUE FALSE FALSE 2180.890484 1947.739665 1901.529161 1408.364628 2116.764158 2153.692695 2160.549466 2524.282365 2395.585715 2146.252752 1.016138701 0.907507125 0.885976341 0.656197005 0.986260428 1.00346648 1.006661244 1.176134713 1.116171295 1 11.06760427 -7.086279338 1.637981495 0.964441491 1.328990222 0.255962428 0.115325907 1.933920064 3.472592525 0.01679397 1.271037873 8.20E-08 7.086279338 0.364548731 RGS(ph)LEMSSDGEPLSR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSLEMSSDGEPLSR 15 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 0 RGS(0.958)LEMS(0.021)S(0.021)DGEPLSR;RGS(0.961)LEMS(0.02)S(0.02)DGEPLSR ; 98.676 0.0064248 46295000 6796.6 5907 5394.7 5517.7 8077.2 9329.3 9605.1 10192.3 6760.3 5949.9 TRUE FALSE FALSE 6713.760425 5990.158901 5488.592491 6155.682436 7664.990344 8733.187839 10420.95695 10487.19812 6155.641837 5795.32074 1.158479526 1.03361991 0.947073119 1.062181493 1.322617106 1.506937792 1.798167422 1.809597534 1.062174487 1 12.50067279 -8.184028464 1.40371664 1.060776726 1.835745051 0.956975259 0.064298396 0.080126643 0.285371873 0.012270466 0.053118721 6.55E-09 8.184028464 0.774968325 RGS(ph)LGEEGSEPPPPPPLPLAR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSLGEEGSEPPPPPPLPLAR 21 1 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 RGS(1)LGEEGSEPPPPPPLPLAR;RGS(0.934)LGEEGS(0.066)EPPPPPPLPLAR ; 165 7.43E-10 17782700 1221.66 1088.5 1010.9 862.38 874.98 824.48 486.23 722.13 1117.69 1296.18 TRUE FALSE FALSE 1206.769938 1103.823932 1028.49429 962.0924332 830.3265056 771.7983889 527.5303641 743.0236922 1017.721007 1262.505057 0.955853548 0.874312483 0.81464568 0.76205036 0.657681727 0.611323008 0.417844159 0.58853126 0.80611242 1 10.30207345 -8.933356952 0.594870391 0.991527551 0.463048504 0.803649832 0.075711891 0.144483261 0.089664904 0.009835301 0.037038626 1.17E-09 8.933356952 -0.528479047 RGS(ph)LPDQK ddPTM_HeLa_Romidepsin_16h_R1 2 RGSLPDQK 8 1 X6RKU3;Q6P3S6 X6RKU3 FBXO42 F-box only protein 42 1 0 RGS(1)LPDQK;RGS(1)LPDQK ; 87.789 0.013255 6032600 2922.8 3017.7 3413.7 4075.3 8546 12043 21921 3578.1 3476.6 2887.7 TRUE FALSE FALSE 2887.175789 3060.18326 3473.114017 4546.505361 8109.86573 11273.49117 23782.96919 3681.626678 3165.644189 2812.677138 1.026486741 1.087996635 1.234807213 1.616433433 2.883326217 4.008099976 8.455634269 1.308940379 1.125491492 1 11.45772824 -8.491658346 1.868785027 1.051385254 5.045106972 0.470579538 1.624357707 0.184044227 1.261604856 0.215341481 0.581338207 3.22E-09 8.491658346 3.993721718 RGS(ph)LSNAGDPEIVK ddPTM_HeLa_Romidepsin_16h_R1 4 RGSLSNAGDPEIVK 14 1 F5H7V1;O43847;O43847-2 F5H7V1 NRD1 Nardilysin 1 0 RGS(0.997)LS(0.003)NAGDPEIVK;RGS(0.917)LS(0.083)NAGDPEIVK;RGS(0.662)LS(0.338)NAGDPEIVK;RGS(0.519)LS(0.481)NAGDPEIVK ;;; 118.15 0.0013151 125070000 11322 10670.8 12116.8 9007.3 17854.8 25769.6 22625.8 30022.3 12034.5 11123.5 TRUE FALSE FALSE 11184.00311 10821.0238 12327.68782 10048.76641 16943.60293 24123.00573 24547.63489 30890.94788 10958.10418 10834.50987 1.032257411 0.998755268 1.137816844 0.927477711 1.563855046 2.226497186 2.265689467 2.851162467 1.011407467 1 13.40334627 -8.230490833 1.301190528 1.009794875 2.675314103 0.958689225 0.134229764 0.060138564 0.182496851 0.018663282 0.081698912 5.88E-09 8.230490833 1.665519227 up RGS(ph)MEQAPAVALPPTHK ddPTM_HeLa_Romidepsin_16h_R1 1 RGSMEQAPAVALPPTHK 17 1 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 RGS(1)MEQAPAVALPPTHK 77.681 0.0019864 0 1625.9 1983.2 2243.3 1790.9 2353.5 2595 2910.8 3313.5 1772.8 2354.9 TRUE FALSE FALSE 1606.082905 2011.119542 2282.343695 1997.972284 2233.392113 2429.187875 3158.043279 3409.370895 1614.236328 2293.719359 0.700208986 0.876794074 0.995040517 0.871062223 0.973698942 1.059060633 1.376822002 1.486394088 0.703763659 1 11.16347317 -7.729881706 1.099763201 0.866236333 1.60359389 0.842506003 0.096561487 0.300908837 0.471860427 0.018170071 0.211431518 1.86E-08 7.729881706 0.737357557 RGS(ph)PAPANPGR ddPTM_HeLa_Romidepsin_16h_R1 1 RGSPAPANPGR 11 1 E9PJN1;O75676-2;O75676 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 0 RGS(1)PAPANPGR 63.212 0.028123 7635800 145.76 118.9 174.73 77.087 160.34 122.7 223.81 56.065 136.15 116.73 TRUE FALSE FALSE 143.9834211 120.5738773 177.7711024 86.00016165 152.1572515 114.859866 242.8204158 57.68715232 123.972403 113.6973378 1.266374604 1.060481096 1.563546745 0.756395561 1.338265737 1.010224762 2.135673716 0.507374697 1.090372083 1 6.829054664 -12.42720938 0.702516866 0.965393869 1.231663729 0.017505487 0.421447613 2.996906548 2.077043512 0.501009292 0.077512426 3.74E-13 12.42720938 0.26626986 RGS(ph)PSAAFTFPDTDDFGK ddPTM_HeLa_Romidepsin_16h_R1 2 RGSPSAAFTFPDTDDFGK 18 1 H7C055;Q9ULT0-3;Q9ULT0;Q9ULT0-4 H7C055 TTC7A Tetratricopeptide repeat protein 7A 1 0 RGS(0.764)PS(0.233)AAFT(0.002)FPDTDDFGK;RGS(0.728)PS(0.255)AAFT(0.017)FPDTDDFGK ; 96.128 0.0010706 53555000 5580.5 5449.1 5052.7 4921.7 5412.1 6501.3 4749.8 6257.7 5676.2 5124.4 TRUE FALSE FALSE 5512.48272 5525.812573 5140.640124 5490.770111 5135.900342 6085.887912 5153.247893 6438.756676 5168.506456 4991.267349 1.104425456 1.107096091 1.029926823 1.100075337 1.028977208 1.219307139 1.032452789 1.290004367 1.03550984 1 12.28519047 RGS(ph)PTTGFIEQK ddPTM_HeLa_Romidepsin_16h_R1 2 RGSPTTGFIEQK 12 1 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 RGS(0.856)PT(0.099)T(0.045)GFIEQK;RGS(0.999)PT(0.001)TGFIEQK ; 135.91 0.0040634 35881000 7238.5 6770.3 6964.9 6055 6382.8 5913.9 5052.4 6169.3 7447.5 7301.1 TRUE FALSE FALSE 7150.274378 6865.612461 7086.121163 6755.10759 6057.061898 5536.020876 5481.55073 6347.798962 6781.376947 7111.416369 1.005464173 0.965435309 0.996443014 0.949896229 0.851737767 0.778469518 0.770809983 0.892620912 0.953590199 1 12.79592121 -8.793612566 2.250942152 0.9987864 0.809086147 0.820209398 0.035780054 0.069169424 0.71490686 0.004715662 0.009974624 1.61E-09 8.793612566 -0.189700253 RGS(ph)PVPPVPER ddPTM_HeLa_Romidepsin_16h_R1 4 RGSPVPPVPER 11 1 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER;RGS(1)PVPPVPER ;;; 68.283 0.024454 59526000 6476.5 6768 6147.2 5817.2 4486.82 4338.22 3479.51 3766.06 6533.5 6332.9 TRUE FALSE FALSE 6397.561927 6863.280082 6254.189437 6489.812035 4257.840833 4061.021743 3775.059493 3875.025004 5949.127397 6168.370345 1.037155937 1.112656941 1.013912766 1.052111283 0.690269973 0.658362179 0.61200273 0.628208876 0.964456909 1 12.59067367 -8.71531972 4.890438498 1.028093945 0.638824963 0.958857678 0.038919197 0.026066496 1.365668171 0.005496714 0.011014228 1.93E-09 8.71531972 -0.389268982 RGS(ph)SDPTVQR ddPTM_HeLa_Romidepsin_16h_R1 1 RGSSDPTVQR 10 1 Q2KHT3;A0A2R8YDG4;H7BZJ9;H7BZI2;Q2KHT3-2;H7BXG1 Q2KHT3;H7BXG1 CLEC16A Protein CLEC16A 1 0 RGS(0.619)S(0.381)DPTVQR 69.345 0.025858 1016100 436.92 489.91 309.64 320.62 559.23 537.25 1103.8 491.42 604.32 542.23 TRUE FALSE FALSE 431.594651 496.8069658 315.0291543 357.691593 530.6904063 502.9214589 1197.556744 505.6384624 550.2681057 528.1427864 0.817193119 0.9406679 0.596484819 0.677263047 1.004823733 0.952245248 2.267486701 0.957389697 1.041892685 1 9.044784213 -7.932417663 14.24486594 0.880344084 1.612463581 0.453588088 0.323037793 0.767111314 160.5565297 0.039226527 0.117708315 1.17E-08 7.932417663 0.732119497 RGS(ph)SGSVDETLFALPAASEPVIR ddPTM_HeLa_Romidepsin_16h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 0 RGS(0.676)S(0.252)GS(0.072)VDETLFALPAASEPVIR 105.37 6.79E-06 14049000 1761.9 1704.3 2067.9 1472.6 1917.2 2469.3 1883.5 2631.3 1868 2338.4 TRUE FALSE FALSE 1740.425285 1728.29318 2103.890932 1642.868941 1819.35813 2311.519699 2043.484443 2707.432514 1700.921402 2277.648031 0.764132676 0.758806083 0.92371205 0.721300622 0.798788094 1.014871336 0.897190617 1.188696619 0.74678852 1 11.15332911 -5.80810589 1.0606285 0.865167338 7.093308841 0.507252004 0.101167308 25.51669283 1.763801248 0.017436406 341.199201 1.56E-06 5.80810589 6.228141504 RGS(ph)SPGSLEIPK ddPTM_HeLa_Romidepsin_16h_R1 2 RGSSPGSLEIPK 12 1 A0A1B0GUI1;Q6GYQ0-3;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-2 A0A1B0GUI1 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 0 RGS(0.535)S(0.464)PGS(0.001)LEIPK;RGS(0.732)S(0.245)PGS(0.023)LEIPK ; 123.76 0.0018513 50120000 17653.8 17122.9 18551.2 13971 24188.1 27721 23430.8 28998 18496.5 18121.1 TRUE FALSE FALSE 17438.6287 17363.95664 18874.07585 15586.39276 22953.691 25949.71757 25421.01157 29837.01138 16842.12671 17650.31121 0.988006868 0.983776231 1.069333885 0.883066172 1.300469478 1.470213032 1.440258546 1.690452425 0.954211318 1 14.107406 -8.488578746 2.395686709 0.992322786 1.534176506 0.906135819 0.080252913 0.056400782 0.638758943 0.010573387 0.02610781 3.25E-09 8.488578746 0.54185372 RGSFDATGS(ph)GFSMTFSSSSYSSSGYGR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSFDATGSGFSMTFSSSSYSSSGYGR 27 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 RGS(0.047)FDAT(0.195)GS(0.409)GFS(0.318)MT(0.03)FSSSSYSSSGYGR;RGS(0.019)FDAT(0.127)GS(0.405)GFS(0.405)MT(0.042)FS(0.001)SSSYSSSGYGR ; 66.474 0.00027346 191243000 538.43 663.96 710.47 760.21 1047.83 1109.54 979.68 1044.07 736.61 572.41 TRUE FALSE FALSE 531.8674081 673.3072463 722.8354323 848.1090571 994.3553251 1038.643975 1062.893995 1074.278518 670.7257567 557.5387057 0.953956026 1.207642159 1.296475787 1.521166241 1.783473174 1.862909183 1.906403957 1.926823209 1.203012006 1 9.122928154 -9.209972109 0.907697137 0.973485855 1.934439198 0.948025208 0.082567655 0.039715164 0.064508907 0.008269348 0.019062255 6.17E-10 9.209972109 0.960953342 RGSGDTSS(ph)LIDPDTSLSELR ddPTM_HeLa_Romidepsin_16h_R1 1 RGSGDTSSLIDPDTSLSELR 20 1 C9JSU1;Q9Y608-2;Q9Y608-4;Q9Y608-5;Q9Y608 C9JSU1 LRRFIP2 Leucine-rich repeat flightless-interacting protein 2 1 0 RGS(0.005)GDT(0.224)S(0.317)S(0.454)LIDPDTSLSELR 89.049 0.0027315 132350000 499.15 603.3 561.97 406.48 761.25 696.82 1010.2 895.34 655.72 556.06 TRUE FALSE FALSE 493.0661678 611.7932732 571.7508521 453.4791301 722.4005719 652.2954509 1096.006363 921.2452503 597.0707609 541.613481 0.91036539 1.129575416 1.055643687 0.837274451 1.333793558 1.20435601 2.023595057 1.700927474 1.102392724 1 9.081119839 -8.012825222 1.495546959 0.976472309 1.896013751 0.766087277 0.169556433 0.126027615 0.501415192 0.021940211 0.111976631 9.71E-09 8.012825222 0.919541442 RGSIGENQIK(ac)DEK ddPTM_HeLa_Romidepsin_16h_R1 1 RGSIGENQIKDEK 13 2 E9PGZ1;Q05682-5;Q05682-4;C9J813 E9PGZ1 CALD1 Caldesmon 0 1 RGSIGENQIK(1)DEK 105.03 0.0093106 1993000 782.75 1170.5 1066.8 786.7 2447 2261.1 2055.9 1938 2478.8 1735 FALSE TRUE FALSE 773.2095419 1186.97833 1085.367206 877.6619555 2322.120459 2116.623007 2230.528095 1994.072972 2257.08992 1689.92445 0.457540893 0.702385441 0.642257828 0.519349818 1.374097202 1.252495641 1.319898114 1.179977586 1.335615873 1 10.72274304 -8.755237053 24.99995155 0.711924132 1.282271471 0.495114582 0.244932209 74.97880252 302216.9571 0.03144058 0.061639566 1.76E-09 8.755237053 0.570347339 RGSLGEEGS(ph)EPPPPPPLPLAR ddPTM_HeLa_Romidepsin_16h_R1 2 RGSLGEEGSEPPPPPPLPLAR 21 1 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 RGS(0.331)LGEEGS(0.669)EPPPPPPLPLAR;RGS(0.052)LGEEGS(0.948)EPPPPPPLPLAR ; 91.475 0.00030682 38484000 1730.28 1519.07 1461.86 1613.55 1190.16 1137.53 1013.04 1094.17 1540.81 1308 TRUE FALSE FALSE 1709.190682 1540.455507 1487.30306 1800.116243 1129.421694 1064.845504 1099.087592 1125.828083 1402.996095 1274.017971 1.341575017 1.209131693 1.167411366 1.412944153 0.886503738 0.835816706 0.862693947 0.883683047 1.101237287 1 10.31516991 -8.651165866 8.838408007 1.18512543 0.861370154 0.694459959 0.109480514 0.157777918 11.79541012 0.02104819 0.042142906 2.23E-09 8.651165866 -0.323755276 RGSLKS(ph)S(ph)T(ph)S(ph)GS(ph)QK ddPTM_HeLa_Romidepsin_16h_R1 1 RGSLKSSTSGSQK 13 2 Q7Z4N2-5;A0A0G2JN34 Q7Z4N2-5 5 0 RGS(0.005)LKS(0.997)S(0.999)T(0.999)S(0.999)GS(1)QK 50.102 0.0043391 0 822.29 636.87 901.83 644.52 800.22 857.97 584.17 488.02 886.98 844.57 TRUE FALSE FALSE 812.2676132 645.8358726 917.5259729 719.042435 759.3817874 803.148486 633.7893852 502.1400887 807.6462873 822.6279496 0.987405805 0.785088657 1.11535959 0.874079753 0.92311693 0.976320445 0.77044475 0.610409711 0.981788046 1 9.68409628 -6.765612976 0.848025005 0.979946405 2.95E-13 0.615899355 0.085771967 2.022310519 0.59905237 0.012542208 2.258481456 1.72E-07 6.765612976 -0.979946405 RGSS(ph)GSVDETLFALPAASEPVIR ddPTM_HeLa_Romidepsin_16h_R1 1 RGSSGSVDETLFALPAASEPVIR 23 1 Q9NQC3-5;Q9NQC3 Q9NQC3-5 RTN4 Reticulon-4 1 0 RGS(0.328)S(0.518)GS(0.152)VDET(0.002)LFALPAASEPVIR 140.42 9.00E-07 14083000 1273.3 1474.4 1386.4 843.29 1447.7 1944 1281.2 1821.1 1537.5 1522.6 TRUE FALSE FALSE 1257.78053 1495.156642 1410.52971 940.7951576 1373.818467 1819.784674 1390.025096 1873.790655 1399.982149 1483.042633 0.848108141 1.008168349 0.951105302 0.634368249 0.926351298 1.227061606 0.937279257 1.263477269 0.943993192 1 10.53434436 -8.331110296 8.477646337 0.911707676 1.121798404 0.419345337 0.128849641 0.29113729 33.20807913 0.018476221 0.041434545 4.67E-09 8.331110296 0.210090728 RGSSAAASPGS(ph)PPPGR ddPTM_HeLa_Romidepsin_16h_R1 4 RGSSAAASPGSPPPGR 16 1 Q86UX6 Q86UX6 STK32C Serine/threonine-protein kinase 32C 1 0 RGSSAAAS(0.185)PGS(0.815)PPPGR;RGSSAAAS(0.009)PGS(0.991)PPPGR;RGSSAAAS(0.022)PGS(0.978)PPPGR;RGSSAAAS(0.027)PGS(0.973)PPPGR ;;; 94.958 0.0026423 22138700 3669.63 3769.64 3953.04 2886.51 3518.25 3951.38 3733.53 3637.59 3945.89 3893.23 TRUE FALSE FALSE 3624.903138 3822.709091 4021.841003 3220.261868 3338.700574 3698.89957 4050.655945 3742.837927 3592.959716 3792.083323 0.955913367 1.008076238 1.060588774 0.849206516 0.880439666 0.975426765 1.068187484 0.98701363 0.947489654 1 11.88877495 -12.5622655 1.267791376 1.000375628 0.971013965 0 0.067088673 1.982236005 5.588842098 0.051400522 0.011454332 2.74E-13 12.5622655 -0.029361663 RGST(ph)S(ph)S(ph)S(ph)RSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RGSTSSSRSPSR 12 2 Q2M3A8 Q2M3A8 MRGPRG-AS1 Putative uncharacterized protein MRGPRG-AS1 5 0 RGS(0.458)T(0.569)S(0.98)S(0.978)S(0.742)RS(0.273)PS(0.999)R 56.286 0.0039565 0 0 0 0 65.975 260.01 59.366 0 113.96 150.02 230.94 TRUE FALSE FALSE 0 0 0 73.60333992 246.7407195 55.57270419 0 117.2572528 136.6018355 224.9401455 0 0 0 0.327213 1.096917222 0.247055518 0 0.521282017 0.607280818 1 7.813397354 -12.41201972 1.151632468 0.998004394 0.252069064 0.250136715 0.342902575 0.398006735 0.948030607 0.234641818 0.060074276 3.87E-13 12.41201972 -0.74593533 RGT(ph)GNTDT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RGTGNTDTK 9 1 P29536-2;P29536 P29536-2 LMOD1 Leiomodin-1 2 0 RGT(0.998)GNT(0.061)DT(0.942)K 49.418 0.0043508 0 640.13 671.42 728.45 506.04 470.12 517.3 523.24 481.04 539.31 447.89 TRUE FALSE FALSE 632.3278493 680.8722684 741.1283667 564.5507258 446.1280221 484.2461995 567.6839925 494.9581334 491.0727629 436.2537532 1.449449649 1.560725297 1.69884697 1.294087951 1.022634233 1.110010392 1.301270163 1.134564757 1.12565854 1 8.769023733 -8.814026138 24.14085325 1.291888643 1.15119402 0.168606515 0.204101219 166.2241096 76307.14765 0.038986531 0.070669177 1.53E-09 8.814026138 -0.140694623 RGT(ph)GQS(ph)DDSDIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 1 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 0 RGT(0.711)GQS(0.806)DDS(0.399)DIWDDT(0.083)ALIK 64.275 0.013507 8885200 2210 2168.5 1931.8 1891.3 1979.1 1912.7 1909.1 1932 1879.2 1997.3 TRUE FALSE FALSE 2183.06367 2199.0282 1965.422169 2109.981005 1878.099142 1790.484643 2071.258906 1987.899372 1711.119645 1945.409858 1.122161307 1.130367563 1.010286938 1.084594589 0.965400239 0.920363714 1.064690249 1.021840906 0.879567685 1 10.92585842 -8.764343298 24.98773491 1.062818862 0.992995662 0.017130425 0.078009242 89.38611474 769162.3773 0.009341065 0.01748925 1.72E-09 8.764343298 -0.0698232 RGT(ph)GQSDDS(ph)DIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 2 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 2 0 RGT(0.676)GQS(0.313)DDS(0.926)DIWDDT(0.085)ALIK;RGT(0.567)GQS(0.435)DDS(0.985)DIWDDT(0.013)ALIK ; 64.707 0.0026713 3163700 2040.55 2409 2297.6 2351.8 2483 2291 1975.34 2063 2570 2708.7 TRUE FALSE FALSE 2015.678992 2442.913965 2337.588764 2623.726182 2356.283245 2144.612494 2143.12533 2122.68965 2340.132763 2638.327584 0.763998756 0.925932769 0.88601157 0.99446566 0.893097301 0.812868162 0.812304485 0.804558791 0.886975817 1 11.36540799 -12.59698525 1.397188039 0.999865739 0.852568561 0.089143407 0.07272564 0.379280496 1.330313909 0.051999566 0.012086108 2.53E-13 12.59698525 -0.147297178 RGTGQSDDS(ph)DIWDDTALIK ddPTM_HeLa_Romidepsin_16h_R1 2 RGTGQSDDSDIWDDTALIK 19 1 B4DP61;A0A1W2PRV5;E7EQZ4;Q16637-4;Q16637-2;Q16637-3;Q16637 B4DP61 SMN2;SMN1 Survival motor neuron protein 1 0 RGT(0.047)GQS(0.072)DDS(0.88)DIWDDTALIK;RGT(0.046)GQS(0.122)DDS(0.821)DIWDDT(0.01)ALIK ; 90.084 0.0011739 65074000 6506 6228 5363.1 6253.8 5486.7 5343.3 5654.8 5480.6 6263.4 6538.7 TRUE FALSE FALSE 6426.70237 6315.677947 5456.442506 6976.893781 5206.693225 5001.880375 6135.118571 5639.172514 5703.185817 6368.823631 1.009087822 0.991655337 0.856742598 1.095476054 0.817528248 0.785369585 0.963304831 0.885433926 0.895484967 1 12.63681121 -8.747081646 24.99998216 0.996741687 0.864541719 0.316743551 0.076458637 159.2989353 277373.0721 0.009658225 0.019245447 1.79E-09 8.747081646 -0.132199968 RGY(ph)QEY(ph)AIQQTPY(ph)EQPMKS(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RGYQEYAIQQTPYEQPMKSSR 21 2 E5RH37;E9PBN4;F8W7M8;Q9P243-3;Q9P243-4;Q9P243-2;Q9P243 E5RH37 ZFAT Zinc finger protein ZFAT 5 0 RGY(0.996)QEY(0.989)AIQQT(0.026)PY(0.989)EQPMKS(1)S(1)R 44.468 0.015336 5088700 1987.8 2004.1 1891.6 1828.3 1724.7 1761.5 1373.1 1630.8 2053.9 2128.9 TRUE FALSE FALSE 1963.571929 2032.313772 1924.522505 2039.696648 1636.682123 1648.945835 1489.73108 1677.984625 1870.19404 2073.590871 0.946942792 0.980093904 0.928111004 0.983654335 0.78929848 0.795212719 0.718430574 0.809216827 0.901910819 1 11.01791556 -8.738038627 6.289694942 0.971550919 0.773621163 0.849730858 0.036506701 0.03602504 4.723104436 0.004566309 0.00899555 1.83E-09 8.738038627 -0.197929756 RHDEFERHAEGT(ph)FT(ph)SDVSS(ph)Y(ph)LEGQAAK ddPTM_HeLa_Romidepsin_16h_R1 1 RHDEFERHAEGTFTSDVSSYLEGQAAK 27 2 P01275 P01275 GCG Glucagon;Glicentin;Glicentin-related polypeptide;Oxyntomodulin;Glucagon;Glucagon-like peptide 1;Glucagon-like peptide 1(7-37);Glucagon-like peptide 1(7-36);Glucagon-like peptide 2 4 0 RHDEFERHAEGT(0.943)FT(0.779)S(0.277)DVS(0.144)S(0.932)Y(0.925)LEGQAAK 51.301 0.005028 25885000 1867.6 2157.2 1965.3 1215.1 2248.4 2327.7 1939.6 1973.5 1999.2 1946.8 TRUE FALSE FALSE 1844.836973 2187.569118 1999.505222 1355.595579 2133.655758 2178.967482 2104.349576 2030.600109 1820.386545 1896.221855 0.97290144 1.15364619 1.054467976 0.71489292 1.1252142 1.149109993 1.109759161 1.070866314 0.960007153 1 10.88891205 RHGAPAAPS(ph)PPPR ddPTM_HeLa_Romidepsin_16h_R1 2 RHGAPAAPSPPPR 13 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 RHGAPAAPS(1)PPPR;RHGAPAAPS(1)PPPR ; 117.48 0.0015902 13334900 1900.65 2093.71 1603.59 1768.26 2014.5 2430.49 1693.33 2248.6 2158.7 1879.21 TRUE FALSE FALSE 1877.484147 2123.185304 1631.499811 1972.714541 1911.692548 2275.189533 1837.161408 2313.659693 1965.620465 1830.387853 1.025730226 1.159964704 0.891341039 1.077757666 1.044419381 1.243009523 1.003700612 1.264027014 1.073881944 1 10.83793367 -4.000000001 0.318016741 1.007540353 2.948207632 0.267424212 0.093318809 41.65053624 0.531328895 0.028040473 47.56483051 1.00E-04 4.000000001 1.940667279 DPRGTK(ac)RGAEK ddPTM_HeLa_Romidepsin_16h_R1 2 DPRGTKRGAEK 11 3 F8WC68;O77932 F8WC68 DXO Decapping and exoribonuclease protein 0 1 ; DPRGTK(1)RGAEK;DPRGTK(1)RGAEK 89.886 0.014239 16792300 381.4 383.51 507.74 1237.93 8782 12387.3 9038.9 10283.2 538.11 457.59 FALSE TRUE FALSE 376.7513501 388.9090638 516.5770017 1381.065291 8333.82177 11595.79151 9806.66394 10580.72817 489.9800939 445.7017458 0.845299247 0.872576936 1.159019471 3.098631101 18.69820311 26.01693087 22.00274967 23.73948109 1.099345243 1 8.799934802 -8.716091159 3.044569021 0.946729374 23.658317 0.991499046 0.974869084 0.01374871 0.25998428 0.132438576 0.2752636 1.92E-09 8.716091159 22.71158763 up RIDFIPVS(ph)PAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 2 0 RIDFIPVS(1)PAPS(0.831)PT(0.169)R;RIDFIPVS(0.999)PAPS(0.794)PT(0.207)R ; 97.689 0.0033498 20001000 5267.3 4811 4975.4 4408.1 4732.4 4617.7 4023.5 4814.5 5140.6 5401.4 TRUE FALSE FALSE 5203.100122 4878.729384 5061.99475 4917.785263 4490.887969 4322.643873 4365.25599 4953.799961 4680.811861 5261.070849 0.988981192 0.927326304 0.962160536 0.934749864 0.853607202 0.821628143 0.829727657 0.941595372 0.889707057 1 12.36114076 -9.287537341 0.94143427 0.994324175 0.854790442 0.327849308 0.049578844 0.210043972 0.368682345 0.006699207 0.014359153 5.16E-10 9.287537341 -0.139533733 RIDFIPVS(ph)PAPSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 0 RIDFIPVS(1)PAPSPTR 82.578 0.0029852 0 1351.9 1040.7 935.14 769.1 1005.7 1027.9 855.96 910.33 1262.6 1233.1 TRUE FALSE FALSE 1335.422523 1055.351002 951.4157194 858.0269607 954.3753762 962.2205074 928.665221 936.6689623 1149.669894 1201.063884 1.111866355 0.878680157 0.792144141 0.714389111 0.794608337 0.801140156 0.773202186 0.779866063 0.957209611 1 10.23009717 -10.04292892 3.30869259 1.052476478 0.776178125 0.847945995 0.046193968 0.057496778 1.274356512 0.008100708 0.010309606 9.06E-11 10.04292892 -0.276298353 RIDFIPVSPAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFIPVSPAPSPTR 15 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 0 RIDFIPVSPAPS(0.782)PT(0.218)R 177.41 1.74E-08 32047000 1604.1 1321 1373.7 1502.9 1074.4 1093 765.98 984.11 1623.7 1466.5 TRUE FALSE FALSE 1584.548612 1339.597073 1397.608672 1676.672369 1019.569359 1023.160827 831.0423221 1012.58367 1478.472205 1428.400119 1.109317054 0.937830413 0.978443403 1.173811418 0.713784146 0.716298476 0.581799393 0.708893578 1.035054664 1 10.48018444 -8.684711196 6.574052525 1.044639525 0.671013303 0.858079658 0.071538337 0.058153714 4.004186518 0.01092932 0.021931865 2.07E-09 8.684711196 -0.373626223 RIDFT(ph)PVSPAPSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 RIDFT(0.869)PVS(0.127)PAPS(0.004)PTR 188 7.14E-12 12775000 817.86 880.68 835.27 576.99 1923.9 2354.5 2131.7 2325 934.99 781.9 TRUE FALSE FALSE 807.8916077 893.0782362 849.807524 643.7042986 1825.716204 2204.055049 2312.766545 2392.270207 851.3621527 761.5861253 1.060801374 1.172655602 1.115839031 0.84521537 2.397255075 2.894032567 3.036776102 3.141168316 1.117880335 1 9.572863385 -8.612242826 3.129240317 1.035293188 3.002334659 0.980892342 0.125950263 0.023337026 0.457447162 0.019369073 0.041928552 2.44E-09 8.612242826 1.967041471 up RIDFTPVS(ph)PAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 2 0 RIDFTPVS(1)PAPS(0.923)PT(0.077)R;RIDFTPVS(0.999)PAPS(0.948)PT(0.053)R;RIDFT(0.014)PVS(0.985)PAPS(0.602)PT(0.399)R ;; 193.27 1.31E-12 27238100 4983.3 5406.6 4373.1 4662.9 8074.2 9593.8 8064.8 10188.2 5472.3 5095.6 TRUE FALSE FALSE 4922.561623 5482.714257 4449.211971 5202.046438 7662.143445 8980.787143 8749.823911 10482.97949 4982.843782 4963.215577 0.991808948 1.104669779 0.89643738 1.048120187 1.543786145 1.809469487 1.762934488 2.112134629 1.003954736 1 12.2770594 -8.552028232 1.835396748 0.994514657 1.910648048 0.946016676 0.096428729 0.05004123 0.334487158 0.013534915 0.035267324 2.81E-09 8.552028232 0.91613339 RIDFTPVS(ph)PAPSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 2 0 RIDFT(0.297)PVS(0.685)PAPS(0.184)PT(0.834)R;RIDFT(0.082)PVS(0.918)PAPS(0.283)PT(0.717)R ; 116.61 0.0030783 13050000 2162.41 2570.2 2267.1 1564.94 4083.7 4942.9 4121.7 4346.8 2217.3 2122.76 TRUE FALSE FALSE 2136.053715 2606.383343 2306.557924 1745.885726 3875.293551 4627.064642 4471.797095 4472.5678 2018.979135 2067.610389 1.033102622 1.2605776 1.115567003 0.84439783 1.874286167 2.237880341 2.162785174 2.163157925 0.976479488 1 11.01374864 -8.637827978 4.207699427 1.034559319 2.168934885 0.959953028 0.108315214 0.029332828 0.931704485 0.016212408 0.033401454 2.30E-09 8.637827978 1.134375565 up RIDFTPVS(ph)PAPSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 RIDFTPVS(0.475)PAPS(0.395)PT(0.13)R 80.362 0.0092069 30290000 1178.1 1064.6 1191.1 622.19 1600.2 2013.6 1850.9 2264.4 1025.1 973.41 TRUE FALSE FALSE 1163.740864 1079.587467 1211.830596 694.1305353 1518.535823 1884.937459 2008.1154 2329.916841 933.4124886 948.1206679 1.227418517 1.138660408 1.278139626 0.732112018 1.601627171 1.988077597 2.117995597 2.457405392 0.984487018 1 9.888926873 -8.31552364 1.967982206 1.103313798 2.264984565 0.885023471 0.182100272 0.078506908 0.583073403 0.026183376 0.079117336 4.84E-09 8.31552364 1.161670767 up RIDFTPVSPAPS(ph)PT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 2 0 RIDFT(0.039)PVS(0.051)PAPS(0.926)PT(0.985)R 100.68 0.0062304 13407000 1622.8 1711.2 1585.9 1441.5 3317.6 4145.6 3271.4 3580 1876.4 1930.5 TRUE FALSE FALSE 1603.020689 1735.290319 1613.501924 1608.173012 3148.290492 3880.709539 3549.272634 3683.581652 1708.570084 1880.345332 0.852513984 0.922857248 0.858088085 0.855254078 1.674315052 2.063828103 1.887564255 1.958992101 0.908646968 1 10.87678193 -8.653614377 3.717952695 0.916581318 1.95185961 0.981738686 0.067319979 0.024529719 0.646238566 0.011758921 0.024433535 2.22E-09 8.653614377 1.035278291 RIDFTPVSPAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDFTPVSPAPSPTR 15 1 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309;Q7Z309-5 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 RIDFTPVSPAPS(0.987)PT(0.013)R 112.03 0.0063045 23909000 932.44 902.56 1268.6 1044.2 1564.1 1384 1395.7 1206.6 1277.7 1023.7 TRUE FALSE FALSE 921.0750626 915.2662634 1290.679451 1164.935317 1484.278141 1295.566867 1514.250723 1241.511067 1163.419312 997.1041264 0.923750126 0.917924457 1.294427951 1.16831862 1.488588906 1.299329561 1.518648537 1.245116768 1.166798212 1 9.961600361 -9.524528671 1.658925692 0.958411112 1.373972808 0.614180929 0.124782303 0.117132074 0.645007281 0.016289908 0.026269835 2.99E-10 9.524528671 0.415561696 RIDIS(ph)PSTFR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 RIDIS(0.973)PS(0.014)T(0.014)FR 64.313 0.029547 412480000 1603.6 1612 1621.9 1195.5 1611.6 1543.5 1497.9 1397 1844.5 1634 TRUE FALSE FALSE 1584.054706 1634.693778 1650.128489 1333.729335 1529.354038 1444.875331 1625.131589 1437.419991 1679.5233 1591.548444 0.995291543 1.02710903 1.03680695 0.838007376 0.960922078 0.907842508 1.021100925 0.903158177 1.055276266 1 10.63621536 -9.306088469 24.99996678 1.003047835 0.932386411 0.473727421 0.048543321 339.132861 189886.7283 0.006548119 0.010002434 4.94E-10 9.306088469 -0.070661424 RIDISPSTFR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDISPSTFR 10 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 0 131.42 0.0001208 0 1815.8 2013.8 1678.3 1423.9 1984.9 1886.5 1413 1600.2 2090.5 2031 FALSE FALSE TRUE 1793.668331 2042.150329 1707.510107 1588.538018 1883.603146 1765.958738 1533.020185 1646.499262 1903.520444 1978.234327 0.906701651 1.032309621 0.863148558 0.803008014 0.952163816 0.892694416 0.774943678 0.832307497 0.962232036 1 10.94999761 -4.000000021 0.101656816 1.058520423 0.332041514 0.454055878 0.059637658 79.22907822 0.572715687 0.466816993 8.070790802 1.00E-04 4.000000021 -0.726478909 RIDISPSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 RIDISPSTLR 10 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;Q9NYF8-4 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 0 0 88.155 0.026884 4185800 2513.8 2497.1 2597 2464.8 2499.9 2731.8 2531.5 2483.5 2821.8 2993.2 FALSE FALSE TRUE 2483.160839 2532.254239 2642.199696 2749.791773 2372.320775 2557.246796 2746.525547 2555.356154 2569.411141 2915.436233 0.851728743 0.86856787 0.906279364 0.943183645 0.813710397 0.877140363 0.942063324 0.87649187 0.881312756 1 11.50949605 -12.37639184 1.045369846 1.001502058 0.88377423 0 0.051603524 0.314026713 0.601540808 0.027777737 0.006804587 4.20E-13 12.37639184 -0.117727828 RIDT(ph)PSLEEPSDLEELEQFAK ddPTM_HeLa_Romidepsin_16h_R1 1 RIDTPSLEEPSDLEELEQFAK 21 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 0 RIDT(0.482)PS(0.482)LEEPS(0.036)DLEELEQFAK 80.362 0.0012779 5164900 1680.1 1588.4 1811.7 1443.9 1614.1 1544.8 1222.9 1450.2 1649.7 1763.1 TRUE FALSE FALSE 1659.622295 1610.761537 1843.231879 1610.850512 1531.726454 1446.092266 1326.773095 1492.159249 1502.1467 1717.294408 0.966416875 0.937964702 1.073334817 0.938016513 0.891941677 0.842075918 0.772595013 0.868901245 0.874717051 1 10.74592168 -8.612304319 1.931090622 0.985850605 0.82146636 0.563355148 0.053620605 0.114978356 0.860914974 0.005896392 0.014455895 2.44E-09 8.612304319 -0.164384245 RIDTPS(ph)LEEPSDLEELEQFAK ddPTM_HeLa_Romidepsin_16h_R1 1 RIDTPSLEEPSDLEELEQFAK 21 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 0 RIDT(0.067)PS(0.921)LEEPS(0.012)DLEELEQFAK 132.74 7.63E-05 6911400 3276 3443 2768.4 3347.4 2870.1 2685.9 2401.9 2225.4 3367.3 2961.6 TRUE FALSE FALSE 3236.070852 3491.470644 2816.582841 3734.442138 2723.628087 2514.279658 2605.917326 2289.788438 3066.120254 2884.657205 1.121821631 1.210358943 0.976401229 1.294587839 0.944177382 0.871604312 0.903371576 0.793781817 1.062906278 1 11.49418417 -8.533273525 24.97538858 1.081247185 0.868785499 0.594826437 0.094122383 123.9446257 297799.2931 0.013977291 0.027977129 2.93E-09 8.533273525 -0.212461686 RIDTPSLEEPS(ph)DLEELEQFAK ddPTM_HeLa_Romidepsin_16h_R1 1 RIDTPSLEEPSDLEELEQFAK 21 1 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6 A0A0C4DG88 POU2F1 "POU domain protein;POU domain, class 2, transcription factor 1" 1 0 RIDT(0.188)PS(0.243)LEEPS(0.569)DLEELEQFAK 44.641 0.027738 7394300 1026.1 980.79 1059.5 857.99 751.41 678.64 905.25 945.42 922.33 989.47 TRUE FALSE FALSE 1013.593499 994.5975874 1077.940153 957.1948408 713.0627438 635.2770942 982.1419124 972.7742361 839.8344948 963.7634268 1.051703634 1.031993495 1.118469661 0.993184442 0.739873214 0.659162899 1.019069499 1.009349607 0.87141146 1 9.912535244 -8.931760233 8.100568347 1.033154079 0.85491467 0.288899519 0.117156191 0.212068601 22.29077083 0.016171506 0.029381337 1.17E-09 8.931760233 -0.178239409 RIEQHYFEDR ddPTM_HeLa_Romidepsin_16h_R1 1 RIEQHYFEDR 10 1 C9JNK6;O75431-2;O75431 C9JNK6 MTX2 Metaxin-2 0 0 104.43 0.0045547 4631300 1469.1 1336.5 1341.3 1409.3 1193.7 1684.8 1523.8 1482.5 1508.2 1175.3 FALSE FALSE TRUE 1451.194044 1355.315282 1364.644764 1572.249897 1132.781035 1577.146717 1653.231534 1525.393799 1373.302815 1144.765537 1.267677964 1.183923903 1.192073591 1.373425253 0.989531042 1.377702828 1.444166059 1.332494515 1.199636756 1 10.16083643 -16.52287875 0.126013745 0.063836576 1.412007923 0.228919936 0.128762379 56.57047935 0.509314978 13.44653986 0.471542357 3.00E-17 16.52287875 1.348171347 RILS(ph)DVTHSAVFGVPASK ddPTM_HeLa_Romidepsin_16h_R1 1 RILSDVTHSAVFGVPASK 18 1 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 RILS(0.507)DVT(0.493)HSAVFGVPASK 67.877 0.0077182 10889000 3724.2 4237.4 3032.5 5498.4 4731.2 3932.1 3554.2 4577 3662.4 3762.8 TRUE FALSE FALSE 3678.808018 4297.054228 3085.27939 6134.150879 4489.749209 3680.8515 3856.093659 4709.428274 3334.825771 3665.041914 1.003756056 1.172443407 0.841812853 1.673691877 1.225019881 1.004313617 1.05212812 1.284958913 0.909901128 1 11.83961398 RILVATNLFGR ddPTM_HeLa_Romidepsin_16h_R1 1 RILVATNLFGR 11 1 O00148;H0Y400;A0A140T9X3;A0A0G2JJZ9;Q5STU3;Q13838;Q13838-2 O00148;Q5STU3 DDX39A;DDX39B ATP-dependent RNA helicase DDX39A;Spliceosome RNA helicase DDX39B 0 0 172.61 0.00036021 1278500 144.39 155.37 266.76 322.51 304.34 215.84 163.72 0 0 0 FALSE FALSE TRUE 142.6301191 157.5573029 271.4028459 359.8001237 288.8083942 202.0485206 177.6263727 0 0 0 0 RINPPSSGGTSS(ph)SPIK ddPTM_HeLa_Romidepsin_16h_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 0 RINPPS(0.007)S(0.007)GGT(0.001)S(0.056)S(0.464)S(0.464)PIK 157.37 0.00030247 6329800 1515 1325 1367 1130.9 1404.2 1329.1 1030.6 1335.2 1339.6 1404.8 TRUE FALSE FALSE 1496.534597 1343.653385 1390.792062 1261.659979 1332.538434 1244.174799 1118.139138 1373.831905 1219.782821 1368.303093 1.093715716 0.981985198 1.016435663 0.922061775 0.973862034 0.909283042 0.817172119 1.004040634 0.891456598 1 10.41817212 -9.292507198 1.190492269 1.042579329 0.910698256 0.063108192 0.071377633 0.279515616 0.782309201 0.00975239 0.019029596 5.10E-10 9.292507198 -0.131881073 RINPPSSGGTSSS(ph)PIK ddPTM_HeLa_Romidepsin_16h_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 0 RINPPSSGGT(0.016)S(0.35)S(0.218)S(0.416)PIK 75.743 0.0092924 17634000 2243.6 2106.8 2140.9 2342.3 2038.4 1641.9 1420.8 1880.7 2588.6 2160.7 TRUE FALSE FALSE 2216.25414 2136.459586 2178.161466 2613.127747 1934.372842 1536.987889 1541.482717 1935.115087 2357.069133 2104.564703 1.05307009 1.015155097 1.034970065 1.241647617 0.919132037 0.73031154 0.732447292 0.91948472 1.119979409 1 11.03930615 -8.522402425 24.99998102 1.0408297 0.79405177 0.682460615 0.085260939 7.452438126 391140.3518 0.011650369 0.02351345 3.00E-09 8.522402425 -0.24677793 RIPLAEWESR ddPTM_HeLa_Romidepsin_16h_R1 2 RIPLAEWESR 10 1 P31930 P31930 UQCRC1 "Cytochrome b-c1 complex subunit 1, mitochondrial" 0 0 ; ; 112.13 0.010811 28800000 3693.05 3901.07 4630.54 3818.17 2675.45 3175.51 2703.03 2281.21 3781.53 2703.37 FALSE FALSE TRUE 3648.037686 3955.989366 4711.132606 4259.64478 2538.911803 2972.605159 2932.625301 2347.213212 3443.300486 2633.136058 1.385434556 1.502386994 1.789171734 1.617707816 0.964215957 1.128921975 1.113738613 0.89141357 1.307680428 1 11.36256635 -8.674382935 24.01036214 1.290862086 1.038391663 0.342510742 0.231235186 25.9870905 7161.298502 0.04319516 0.086390588 2.12E-09 8.674382935 -0.252470423 RIPSIVS(ph)SPLNSPLDR ddPTM_HeLa_Romidepsin_16h_R1 1 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 RIPSIVS(0.497)S(0.497)PLNS(0.005)PLDR 94.188 0.0028111 33666000 1296.4 1205 905.31 1163.9 1193.6 1186.3 1021 1019.7 1277 1134.4 TRUE FALSE FALSE 1280.598978 1221.964022 921.0665408 1298.475594 1132.686138 1110.499259 1107.723715 1049.203411 1162.781922 1104.928124 1.15898849 1.105921729 0.833598603 1.175167475 1.025122008 1.005042078 1.00253011 0.949567114 1.052359783 1 10.10973681 -7.312092074 0.613728662 1.068672716 0.882885411 0.09805371 0.09075212 5.211323652 1.382405179 0.017852593 0.672425908 4.87E-08 7.312092074 -0.185787305 RIPSIVSS(ph)PLNSPLDR ddPTM_HeLa_Romidepsin_16h_R1 1 RIPSIVSSPLNSPLDR 16 1 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 RIPS(0.034)IVS(0.321)S(0.644)PLNS(0.001)PLDR 71.969 0.011202 30023000 1402.4 1318.7 1246 1442.9 1640.5 1373.3 1212 1491.5 1660.1 1648.1 TRUE FALSE FALSE 1385.307009 1337.264693 1267.686107 1609.734887 1556.779163 1285.550562 1314.94725 1534.654199 1511.616498 1605.282124 0.862967941 0.833040294 0.789696769 1.002773819 0.969785398 0.800825314 0.819137789 0.956002796 0.941651611 1 10.64861115 -12.19841494 0.935126121 1.000190176 0.877305288 0.187518908 0.072470712 0.592368877 0.929950266 0.048751715 0.013658011 6.33E-13 12.19841494 -0.122884888 RIS(ph)FSASHR ddPTM_HeLa_Romidepsin_16h_R1 1 RISFSASHR 9 1 E9PKY8;E9PJM0;Q03393 E9PKY8 PTS 6-pyruvoyl tetrahydrobiopterin synthase 1 0 RIS(0.998)FS(0.002)AS(0.001)HR 84.605 0.015217 3940800 1394.4 1488.1 1520.2 1078.3 1515.8 1614.7 1256.5 839.66 1169.5 1171.1 TRUE FALSE FALSE 1377.404516 1509.049511 1546.658443 1202.97812 1438.44307 1511.525881 1363.227079 863.9542373 1064.896991 1140.674653 1.207534955 1.322944721 1.355915501 1.054619839 1.261045878 1.325115691 1.195105962 0.75740636 0.933567681 1 10.15567164 -12.08359879 0.971810304 1.005687273 1.196492805 0.198764098 0.168051124 0.748293981 1.327899677 0.092250841 0.030776768 8.25E-13 12.08359879 0.190805531 RIS(ph)GLIYEETR ddPTM_HeLa_Romidepsin_16h_R1 3 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 1 0 RIS(1)GLIYEETR;RIS(1)GLIYEETR;RIS(1)GLIYEETR ;; 158.86 0.0024 114476000 6406.5 6205.6 6268.5 5938.9 6746.3 8703.1 7835.5 7754.5 7183 6114.1 TRUE FALSE FALSE 6328.415114 6292.9626 6377.600613 6625.583561 6402.011137 8146.999998 8501.047174 7978.864223 6540.53449 5955.254801 1.06266068 1.056707531 1.070919856 1.112560887 1.075018845 1.368035503 1.427486725 1.339802324 1.098279538 1 12.53994752 -8.275680742 3.633570297 1.042676251 1.389984931 0.929079527 0.038967189 0.040384022 1.164112449 0.006089824 0.015484091 5.30E-09 8.275680742 0.34730868 RISGLIYEETR ddPTM_HeLa_Romidepsin_16h_R1 1 RISGLIYEETR 11 1 P62805 P62805 HIST1H4A Histone H4 0 0 122.34 0.005798 7680000 1140.7 1267.4 1910.9 2115.9 1973.6 1843.6 1858.4 1764.6 1453.8 860.83 FALSE FALSE TRUE 1126.79671 1285.24249 1944.158413 2360.550314 1872.879827 1725.79991 2016.25245 1815.655917 1323.768487 838.4655125 1.343879614 1.532850751 2.318710053 2.815321893 2.233699299 2.058283715 2.404693359 2.165450922 1.578798969 1 9.711607634 -9.925236597 2.346342587 1.159765918 2.347724726 0.787066576 0.244678254 0.07778148 0.868068597 0.039637063 0.053082006 1.19E-10 9.925236597 1.187958808 up RITITGMYAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 RITITGMYAAGK 12 1 Q86X29-6 Q86X29-6 0 0 ; ; 78.149 0.025044 3198500 113.01 0 105.78 0 1784.25 2680.7 2536 2684.9 79.853 112.82 FALSE FALSE TRUE 111.6325907 0 107.6210565 0 1693.193065 2509.411922 2751.407777 2762.583345 72.71074768 109.8889201 1.015867573 0 0.979362218 0 15.40822371 22.83589573 25.03808185 25.13978063 0.661674968 1 6.77990212 -8.567171027 2.406849879 0.79743535 24.5316124 0.990327152 1.065361431 0.019461079 0.226192288 0.1643133 0.386176536 2.71E-09 8.567171027 23.73417705 RKADTTTPTPTAILAPGS(ph)PAS(ph)PPGSLEPK ddPTM_HeLa_Romidepsin_16h_R1 1 RKADTTTPTPTAILAPGSPASPPGSLEPK 29 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;H0YDJ7;U3KPW0;E9PIQ3;U3KQA6;A0A0G2JHL0;A0A140T9F7;A0A140T9V2 H0Y6K2 BRD2 Bromodomain-containing protein 2 2 0 RKADT(0.053)T(0.071)T(0.078)PT(0.095)PT(0.328)AILAPGS(0.447)PAS(0.892)PPGS(0.036)LEPK 65.155 0.0003382 0 1290.6 795.9 811.2 1334.5 1281.9 1351.4 1308.3 1067.8 1129.2 1097.9 TRUE FALSE FALSE 1274.869671 807.1047011 825.3185957 1488.801169 1216.47986 1265.049901 1419.426969 1098.695108 1028.201524 1069.3764 1.192161779 0.754743326 0.771775584 1.39221435 1.13756004 1.182979072 1.327340841 1.027416641 0.961496368 1 10.06255403 -9.241239415 24.99851609 1.040754801 1.213911797 0.336619983 0.164694927 1105.995493 1368728.932 0.02682342 0.04444174 5.74E-10 9.241239415 0.173156997 RKADTTTPTPTAILAPGS(ph)PASPPGSLEPK ddPTM_HeLa_Romidepsin_16h_R1 1 RKADTTTPTPTAILAPGSPASPPGSLEPK 29 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;H0YDJ7;U3KPW0;E9PIQ3;U3KQA6;A0A0G2JHL0;A0A140T9F7;A0A140T9V2 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 0 RKADTTTPTPTAILAPGS(0.491)PAS(0.491)PPGS(0.019)LEPK 65.223 0.00016995 22080000 1707.1 1781.5 1706.5 1849.1 2112.2 2595.4 2328.2 2776.3 1818 1690.3 TRUE FALSE FALSE 1686.293209 1806.580004 1736.200917 2062.901642 2004.406552 2429.562316 2525.95725 2856.62786 1655.393527 1646.385762 1.024239426 1.097300551 1.054552922 1.252988024 1.217458629 1.47569444 1.534243862 1.735090236 1.005471236 1 10.6850867 -7.628818293 0.497164223 1.001450557 2.069892301 0.9712167 0.041620551 0.289220148 0.060324603 0.007910773 0.167711634 2.35E-08 7.628818293 1.068441744 RKADTTTPTPTAILAPGSPAS(ph)PPGSLEPK ddPTM_HeLa_Romidepsin_16h_R1 1 RKADTTTPTPTAILAPGSPASPPGSLEPK 29 2 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;H0YDJ7;U3KPW0;E9PIQ3;U3KQA6;A0A0G2JHL0;A0A140T9F7;A0A140T9V2 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 0 RKADTTTPTPTAILAPGS(0.162)PAS(0.808)PPGS(0.031)LEPK 80.664 1.13E-06 21669000 1765.6 1573.7 1448.4 2145.1 2505.9 2241.8 2074.3 2026.9 1823.9 1615.5 TRUE FALSE FALSE 1744.080188 1595.85459 1473.608794 2393.126555 2378.014572 2098.556215 2250.49099 2085.545154 1660.765816 1573.529077 1.108387645 1.014188179 0.936499246 1.520865798 1.511261919 1.333662177 1.430218877 1.325393464 1.055440182 1 10.61978812 -9.260682551 24.99989074 1.041300636 1.424408322 0.883189707 0.072831969 18.46484267 609934.9113 0.012020699 0.019178029 5.49E-10 9.260682551 0.383107686 RKAMYT(ph)KDY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RKAMYTKDYK 10 3 Q5JVZ8;H0YCM7;Q5JVZ5;Q96JJ3-3;Q96JJ3 Q5JVZ8 ELMO2 Engulfment and cell motility protein 2 2 0 RKAMY(0.074)T(0.955)KDY(0.971)K 52.693 0.0041987 0 1137.1 939.03 979.37 900.85 905.54 1335.7 1033.1 924.81 851.08 1000.2 TRUE FALSE FALSE 1123.240588 952.249689 996.415524 1005.010516 859.3269148 1250.353081 1120.851488 951.5679182 774.9572732 974.2146598 1.15297032 0.977453664 1.022788473 1.031610955 0.882071427 1.283447204 1.150517986 0.976753849 0.795468704 1 9.928095883 -12.78060682 1.76548965 0.99986751 1.076786911 0.097510024 0.126477082 0.924573165 5.214007184 0.080549834 0.017017711 1.66E-13 12.78060682 0.076919401 RKAS(ph)PEPPDSAEGALK ddPTM_HeLa_Romidepsin_16h_R1 1 RKASPEPPDSAEGALK 16 2 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 RKAS(1)PEPPDSAEGALK 85.177 0.01639 34314000 6331.2 6017.7 5088.8 5934.7 4113.2 3690.7 2935.8 3286.8 5854.9 5988.8 TRUE FALSE FALSE 6254.032899 6102.417339 5177.368429 6620.897938 3903.288056 3454.876181 3185.166779 3381.898372 5331.22308 5833.210113 1.072142573 1.046150785 0.887567622 1.135035051 0.66914923 0.592276999 0.546040125 0.579766253 0.913943262 1 12.51007433 -8.656419201 4.882585342 1.029662889 0.579679743 0.889414673 0.071421688 0.039110709 1.530157756 0.008945826 0.018170303 2.21E-09 8.656419201 -0.449983146 RKDPELWGSVLLESNPYR ddPTM_HeLa_Romidepsin_16h_R1 1 RKDPELWGSVLLESNPYR 18 2 A0A087WVQ6;Q00610-2;Q00610 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 64.454 0.011178 9192800 3965.1 3909.3 3961.2 5339 4484.9 3808.8 3347.8 3837 3757.8 3544.3 FALSE FALSE TRUE 3916.771836 3964.335228 4030.143024 5956.320301 4256.018818 3565.429972 3632.162048 3948.017541 3421.692956 3452.218575 1.134566584 1.148344215 1.16740668 1.725360133 1.232835849 1.032793809 1.052124009 1.14361749 0.991157681 1 11.7533081 -10.95709897 0.897356047 1.026472898 1.219946436 0.178917065 0.18300586 0.717286343 1.239667878 0.057295676 0.045228957 1.10E-11 10.95709897 0.193473538 RKELEEVS(ph)PETPVVPATTQR ddPTM_HeLa_Romidepsin_16h_R1 1 RKELEEVSPETPVVPATTQR 20 2 Q15149 Q15149 PLEC Plectin 1 0 RKELEEVS(0.89)PET(0.11)PVVPATTQR 61.276 0.0083456 12802000 2711.1 2406.1 2223.5 2887.2 2393.2 2683.6 2651.7 2561.3 2904.6 2561.5 TRUE FALSE FALSE 2678.05607 2439.973139 2262.199085 3221.031649 2271.066074 2512.126621 2876.935332 2635.407174 2644.805301 2494.951861 1.073389877 0.977964015 0.906710514 1.291019558 0.910264486 1.006883804 1.153102542 1.056295801 1.060062658 1 11.28479626 RKLEGDSTDLSDQIAELQAQIAELK ddPTM_HeLa_Romidepsin_16h_R1 1 RKLEGDSTDLSDQIAELQAQIAELK 25 2 P35579 P35579 MYH9 Myosin-9 0 0 57.152 0.0024066 4648500 908.69 977.23 1056.9 1245.9 1250.9 1436.7 742.83 1100.6 993.3 1179.5 FALSE FALSE TRUE 897.6145368 990.9874696 1075.294901 1389.95682 1187.061905 1344.899507 805.9259617 1132.444125 904.4567602 1148.85642 0.781311329 0.862586005 0.935969789 1.209861212 1.033255231 1.170641939 0.701502771 0.985714233 0.787267011 1 10.16598279 -9.511982962 24.40520062 0.891664697 1.01770785 0.215328284 0.140435596 603.8971842 1352655.812 0.023363024 0.034371861 3.08E-10 9.511982962 0.126043153 RKPVLPALTINPTIAEGPS(ph)PTSEGASEANLVDLQK ddPTM_HeLa_Romidepsin_16h_R1 2 RKPVLPALTINPTIAEGPSPTSEGASEANLVDLQK 35 2 P36507 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 1 0 RKPVLPALTINPT(0.006)IAEGPS(0.732)PT(0.197)S(0.055)EGAS(0.009)EANLVDLQK;RKPVLPALTINPT(0.016)IAEGPS(0.863)PT(0.095)S(0.025)EGASEANLVDLQK ; 91.115 1.74E-12 64500000 4380.8 4062.2 4636.9 4718.4 6063.9 5828.1 4732.8 5897.3 5298.8 4935.2 TRUE FALSE FALSE 4327.405125 4119.387758 4717.603299 5263.963609 5754.436555 5455.703219 5134.803914 6067.929071 4824.862057 4806.982793 0.900233122 0.856959123 0.981406321 1.09506604 1.19709947 1.134953765 1.068196858 1.262315538 1.003719436 1 12.23091592 -9.204538794 2.890112957 0.9436656 1.155545836 0.736728129 0.06185726 0.111872277 1.848390975 0.010018837 0.017130125 6.24E-10 9.204538794 0.211880237 RKS(ph)EPAVGPPR ddPTM_HeLa_Romidepsin_16h_R1 1 RKSEPAVGPPR 11 2 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 RKS(1)EPAVGPPR 93.228 0.026413 14562000 3741.2 4134.8 3294.1 4106.1 5006.7 4778.7 3830.7 4246.1 4508.8 4336.2 TRUE FALSE FALSE 3695.600815 4193.009823 3351.432429 4580.866602 4751.189416 4473.356493 4156.079562 4368.954204 4105.521636 4223.544899 0.87499977 0.992770273 0.793511732 1.084602321 1.124929302 1.059147375 0.984026372 1.034428261 0.972055876 1 12.04423867 -9.206274643 24.99999607 0.934127343 1.057194716 0.492838516 0.066106371 230.9270149 104653.3207 0.010855269 0.018001421 6.22E-10 9.206274643 0.123067373 RKS(ph)LRTT(ph)GFYSGFSEVAEK ddPTM_HeLa_Romidepsin_16h_R1 1 RKSLRTTGFYSGFSEVAEK 19 3 H7C5R6;Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 2 0 RKS(0.778)LRT(0.232)T(0.926)GFY(0.024)S(0.038)GFS(0.003)EVAEK 53.255 0.021552 2723400 228.49 449.53 445.61 7439.9 0 440.45 351.66 294.21 352.32 378.95 TRUE FALSE FALSE 225.705076 455.8584951 453.3656551 8300.136244 0 412.3066665 381.5299916 302.7225022 320.8076168 369.1048244 0.611493162 1.23503803 1.228284285 22.48720606 0 1.117044913 1.033662977 0.820153198 0.86915043 1 8.527886784 -9.481908009 24.99998591 0.861306476 5.11201698 0.099986544 6.158442665 942.2005247 574923.4142 0.937961875 1.432656789 3.30E-10 9.481908009 4.250710504 RKS(ph)S(ph)S(ph)QPS(ph)PSGPK ddPTM_HeLa_Romidepsin_16h_R1 1 RKSSSQPSPSGPK 13 2 O14598 O14598 VCY Testis-specific basic protein Y 1 4 0 RKS(1)S(1)S(0.885)QPS(0.885)PS(0.23)GPK 100.11 0.002588 4322500 2260.8 4378.3 2379 2543.4 4813.4 3501.7 2542.8 1781.2 3719.9 2115.1 TRUE FALSE FALSE 2233.2445 4439.937822 2420.405497 2837.479875 4567.754237 3277.952671 2758.785369 1832.736212 3387.182827 2060.149397 1.084020656 2.155153325 1.17486892 1.377317528 2.217195628 1.591123768 1.339119082 0.889613255 1.64414427 1 11.00853325 -10.48307739 24.84846433 1.037067662 1.541856268 0.028761255 0.428116323 411.8344236 257115.3961 0.064443945 0.072644098 3.29E-11 10.48307739 0.504788606 RKS(ph)VPGPGNRTCT(ph)GT(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 RKSVPGPGNRTCTGTSK 17 3 B1B0D4;Q86TH1 B1B0D4 ADAMTSL2 ADAMTS-like protein 2 3 0 RKS(1)VPGPGNRT(0.14)CT(0.663)GT(0.598)S(0.598)K 63.062 0.026001 5629000 1001.6 1046 1311.6 277.33 944.07 995.71 1236.1 1105.3 1275.6 1288.3 TRUE FALSE FALSE 989.3921139 1060.725615 1334.427848 309.3961995 895.8905851 932.0873445 1341.094303 1137.280112 1161.507141 1254.82978 0.788467193 0.845314346 1.063433359 0.246564279 0.713953876 0.742799828 1.068745996 0.90632222 0.925629244 1 10.29327596 -12.1714716 0.631796297 1.022197886 0.788509804 0.0815119 0.218288934 1.89091231 1.172013963 0.246960602 0.049932612 6.74E-13 12.1714716 -0.233688083 RKS(ph)VSTPVS(ph)AQMT(ph)S(ph)KS(ph)CK ddPTM_HeLa_Romidepsin_16h_R1 1 RKSVSTPVSAQMTSKSCK 18 3 P51587 P51587 BRCA2 Breast cancer type 2 susceptibility protein 5 0 RKS(0.334)VS(0.334)T(0.334)PVS(1)AQMT(1)S(1)KS(1)CK 46.319 0.0043392 0 0 63.945 0 0 199.74 179.68 202.21 0 144.19 0 TRUE FALSE FALSE 0 64.84521939 0 0 189.5465225 168.1990279 219.3857124 0 131.2932853 0 0 RKSMQWARR ddPTM_HeLa_Romidepsin_16h_R1 1 RKSMQWARR 9 3 Q6UVM3-4;Q6UVM3-3;Q6UVM3-2;Q6UVM3 Q6UVM3-4 KCNT2 Potassium channel subfamily T member 2 0 0 68.557 0.0043027 0 1299.6 1135.9 1159.6 995.32 1306.5 1547.8 1100.8 1153.9 1309.3 1192.7 FALSE FALSE TRUE 1283.759975 1151.89123 1179.782352 1110.403582 1239.82443 1448.900575 1194.301925 1187.286276 1192.192929 1161.713482 1.10505731 0.991545031 1.015553637 0.955832569 1.067237704 1.247209917 1.028052048 1.022012996 1.02623663 1 10.18203858 -12.65718804 1.499961733 1.000003664 1.061420733 0.034081954 0.076033438 0.929586641 3.762853399 0.056420867 0.012705285 2.20E-13 12.65718804 0.061417069 RKTS(ph)SDDES(ph)EEDEDDLLQR ddPTM_HeLa_Romidepsin_16h_R1 1 RKTSSDDESEEDEDDLLQR 19 2 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 0 RKT(0.374)S(0.451)S(0.175)DDES(0.999)EEDEDDLLQR 79.172 0.0092636 3679900 1499.3 1819.3 1475.2 1771 1358 1240.5 1253.9 1229.8 1741.9 1900.8 TRUE FALSE FALSE 1481.025955 1844.912153 1500.875237 1975.771353 1288.696193 1161.236054 1360.406235 1265.382323 1586.100101 1851.416942 0.799941883 0.996486589 0.810663013 1.067167156 0.696059414 0.627214771 0.734791934 0.683466967 0.856695251 1 10.85441411 -8.671640424 9.353658333 0.913025934 0.683428185 0.654559461 0.084024242 0.16554192 15.77051015 0.013561663 0.027142256 2.13E-09 8.671640424 -0.229597749 RLAAAEETAVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 RLAAAEETAVSPR 13 1 Q9BUH6 Q9BUH6 C9orf142 Protein PAXX 1 0 RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR;RLAAAEETAVS(1)PR ;; 165.86 0.00024714 96633100 4791.6 5101 5091.6 4199 4120.7 4031.6 3270.68 3653.44 5359.1 5532.3 TRUE FALSE FALSE 4733.198136 5172.812012 5180.217162 4684.508137 3910.405303 3773.993771 3548.491478 3759.146522 4879.768674 5388.570048 0.878377398 0.959960057 0.96133429 0.869341605 0.725685157 0.700370179 0.658521917 0.697614857 0.905577663 1 12.39568676 -8.812474151 2.224145839 0.944081907 0.683476314 0.926403463 0.032884174 0.076220755 0.768673799 0.007106696 0.014930974 1.54E-09 8.812474151 -0.260605593 RLAEDEAFQR ddPTM_HeLa_Romidepsin_16h_R1 2 RLAEDEAFQR 10 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 141.89 0.0022954 4213400 2756.7 2851.9 2762.5 2897.2 3394 3494.1 2716.4 3091.6 3551.2 2820.9 FALSE FALSE TRUE 2723.10028 2892.049123 2810.580154 3232.187896 3220.791515 3270.838287 2947.130948 3181.050568 3233.571778 2747.612611 0.99107868 1.052568004 1.022917183 1.176362302 1.172214563 1.190429201 1.072615163 1.157750752 1.176865969 1 11.4239629 -9.348350527 4.145769018 1.001393905 1.152440905 0.281414746 0.06525376 0.071602736 2.255571312 0.005462505 0.008526344 4.48E-10 9.348350527 0.151047001 RLAS(ph)TSDIEEK ddPTM_HeLa_Romidepsin_16h_R1 2 RLASTSDIEEK 11 1 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 RLAS(0.743)T(0.129)S(0.129)DIEEK;RLAS(0.971)T(0.024)S(0.006)DIEEK ; 143.94 0.0039025 17177700 4187.6 5390.8 4098 3892.9 6642 6480.2 5523.6 6749.2 4374 4037.4 TRUE FALSE FALSE 4136.55992 5466.691824 4169.323971 4343.015415 6303.033955 6066.136134 5992.774446 6944.477454 3982.778485 3932.507766 1.051888557 1.390128678 1.060220149 1.104388261 1.602802672 1.542561768 1.523906576 1.765915763 1.012783374 1 11.9412339 -8.232663117 0.424852591 1.00193868 1.930237639 0.766757631 0.132734732 0.842770535 0.17592165 0.037725592 0.347083817 5.85E-09 8.232663117 0.928298959 RLAST(ph)SDIEEK ddPTM_HeLa_Romidepsin_16h_R1 1 RLASTSDIEEK 11 1 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 RLAS(0.082)T(0.836)S(0.082)DIEEK 161.25 0.0029687 7648500 1417.7 1499.4 1018.7 1265.8 1527.8 1358.2 1549.9 1918.2 1112 1167.8 TRUE FALSE FALSE 1400.420527 1520.508593 1036.430046 1412.157752 1449.830665 1271.415403 1681.548467 1973.700091 1012.539935 1137.460388 1.2311818 1.336757402 0.911179024 1.241500598 1.274620796 1.117766752 1.478335849 1.735181385 0.890175997 1 10.15160059 -4 0.601603878 1.117069621 42.21099976 0.650857203 0.14621584 69.74165333 0.494528403 0.024251442 3780.486981 1.00E-04 4 41.09393014 RLAVPTEVSTEVPEMDT(ph)ST ddPTM_HeLa_Romidepsin_16h_R1 2 RLAVPTEVSTEVPEMDTST 19 1 O00488 O00488 ZNF593 Zinc finger protein 593 1 0 RLAVPTEVSTEVPEMDT(0.333)S(0.333)T(0.333);RLAVPTEVSTEVPEMDT(0.691)S(0.155)T(0.155) ; 123.76 0.00046301 22413600 2062.77 1809.01 1666.29 1338.84 1430.84 1677.71 1461.9 1305.61 1800.65 1975.65 TRUE FALSE FALSE 2037.628166 1834.47729 1695.291078 1493.64298 1357.818896 1570.509746 1586.07375 1343.385765 1639.595354 1924.322328 1.058880904 0.953310817 0.880980828 0.77619168 0.705608866 0.816136529 0.824224573 0.698108496 0.852037795 1 10.91013476 -9.646174161 1.786463461 1.027297777 0.766198891 0.62398972 0.069515572 0.080195915 0.520357958 0.007491661 0.011361868 2.26E-10 9.646174161 -0.261098886 RLDEEEEDNEGGEWER ddPTM_HeLa_Romidepsin_16h_R1 1 RLDEEEEDNEGGEWER 16 1 Q99613-2;Q99613 Q99613-2 EIF3C Eukaryotic translation initiation factor 3 subunit C 0 0 126.07 0.0015562 39005000 1242.1 1307.9 1162.4 1123.5 1227.3 1217.5 1137.1 1362.3 1536.8 1387.4 FALSE FALSE TRUE 1226.960807 1326.312651 1182.631084 1253.404356 1164.666301 1139.705679 1233.685246 1401.716001 1399.344759 1351.355148 0.907948447 0.981468604 0.875144544 0.927516618 0.861850642 0.843379833 0.912924517 1.037266927 1.035512212 1 10.40019116 -12.41850765 0.542272532 1.020950168 0.91125178 0.328297824 0.055246519 1.713847635 0.639232903 0.099991533 0.013132375 3.81E-13 12.41850765 -0.109698388 RLDEELEDAEK ddPTM_HeLa_Romidepsin_16h_R1 3 RLDEELEDAEK 11 1 C9J0E9;Q15008-3;Q15008-2;Q15008;Q15008-4;C9J7B7 C9J0E9 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 0 ;; ;; 207.47 6.54E-14 16497400 10182.7 9952.7 11030.8 7262 10869 11670 10960.1 11905.3 11087.7 12023.5 FALSE FALSE TRUE 10058.58934 10092.81437 11222.78645 8101.666609 10314.31437 10924.32466 11891.05062 12249.76107 10095.98834 11711.12774 0.858891608 0.861814045 0.958301088 0.691792182 0.880727681 0.932815772 1.015363412 1.045993294 0.862085067 1 13.51559239 -7.760516074 3.035305891 0.906724599 1.039812576 0.32820855 0.080409072 0.287517631 5.289805669 0.012987573 0.055483631 1.74E-08 7.760516074 0.133087977 RLDEYTQEEIDAFPR ddPTM_HeLa_Romidepsin_16h_R1 1 RLDEYTQEEIDAFPR 15 1 H0YAX3;E5RJI7;Q9BYD1 H0YAX3 MRPL13 "39S ribosomal protein L13, mitochondrial" 0 0 103.66 0.0042631 2539200 848.77 1102.2 857.87 969 1290.6 858.09 1147.3 1026.9 1164.2 1131.2 FALSE FALSE TRUE 838.4248648 1117.716801 872.8008675 1081.040339 1224.735866 803.2608184 1244.751633 1056.611731 1060.071036 1101.811261 0.760951439 1.014435811 0.792150978 0.981148385 1.111565937 0.729036675 1.129732176 0.958977067 0.96211672 1 10.1056614 -9.062653389 24.80131723 0.889230856 0.983713816 0.074696809 0.127388549 363.6238465 143939.4073 0.020051403 0.033251517 8.66E-10 9.062653389 0.09448296 RLDLPIER ddPTM_HeLa_Romidepsin_16h_R1 1 RLDLPIER 8 1 B4E1E0;P17812-2;P17812;A0A3B3IRI2;A0A3B3ISY3;A0A3B3ITB8;A0A3B3IRQ8;A0A3B3ITF6 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 0 0 95.775 0.022867 9586700 3285.5 2760.3 3252.6 2807.6 2728.6 2547.7 2525.4 2730.6 3111.7 2964.4 FALSE FALSE TRUE 3245.455062 2799.159576 3309.210139 3132.227922 2589.34936 2384.910192 2739.907413 2809.605603 2833.381759 2887.384461 1.124012097 0.969444705 1.146092661 1.084797665 0.896780251 0.825975974 0.948923654 0.973062521 0.981297017 1 11.4955475 -8.758640346 24.99998654 1.061432508 0.907794748 0.5174568 0.065615542 43.07197294 384696.6364 0.009972998 0.019256139 1.74E-09 8.758640346 -0.153637759 RLDQLER ddPTM_HeLa_Romidepsin_16h_R1 1 RLDQLER 7 1 Q96CT7;M0R2F5 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 0 95.815 0.0032479 0 1461.4 1133.9 1472.6 1039.7 1529.3 1685.8 1333.9 1471.6 1748.8 1342.6 FALSE FALSE TRUE 1443.587895 1149.863074 1498.229985 1159.915006 1451.254114 1578.082821 1447.201433 1514.178424 1592.382948 1307.719058 1.103897573 0.879289069 1.145681846 0.886975684 1.109759856 1.20674453 1.10666081 1.157877462 1.217679698 1 10.35283692 -8.532930312 24.96232477 1.032554049 1.15308449 0.216966961 0.101469115 178.5441669 443400.3877 0.011646835 0.023314159 2.93E-09 8.532930312 0.120530441 RLDQVEQELNELR ddPTM_HeLa_Romidepsin_16h_R1 1 RLDQVEQELNELR 13 1 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 0 89.26 0.0031637 0 424.51 400.44 460.62 438.6 690.05 516.1 463.44 511.47 734.15 509.12 FALSE FALSE TRUE 419.3359088 406.0774048 468.6368979 489.3129957 654.8341736 483.1228756 502.804582 526.2685775 668.4857853 495.892989 0.84561774 0.818881117 0.945036345 0.986731022 1.320515087 0.974248248 1.01393767 1.061254321 1.348044437 1 8.953885018 -8.993097181 24.98976348 0.918772168 1.087831122 0 0.167362393 145.9109631 528225.3023 0.015718822 0.028446931 1.02E-09 8.993097181 0.169058954 RLEEFEGER ddPTM_HeLa_Romidepsin_16h_R1 2 RLEEFEGER 9 1 Q08378-2;Q08378;Q08378-4 Q08378-2;Q08378-4 GOLGA3 Golgin subfamily A member 3 0 0 ; ; 144.77 4.98E-06 0 1269.45 1281.53 1352.56 1053.44 1344.79 1464.81 1355.6 1449.42 1370.1 1357.68 FALSE FALSE TRUE 1253.977455 1299.571413 1376.100739 1175.243689 1276.160348 1371.213368 1470.74463 1491.356681 1247.554825 1322.407278 0.948253595 0.982731595 1.040602818 0.888715382 0.965028225 1.036907004 1.112172214 1.127758979 0.943396823 1 10.36895085 -7.919325239 2.544507766 0.973489921 1.124761071 0.722873406 0.037776546 0.115276022 1.473610322 0.005449706 0.021173533 1.20E-08 7.919325239 0.15127115 RLEEPEEPK ddPTM_HeLa_Romidepsin_16h_R1 1 RLEEPEEPK 9 1 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 0 0 128.03 0.0059904 5041900 3431.6 3158.2 2843.7 2512.1 3014.4 2778.9 2684.1 3129.2 3466.4 3215.8 FALSE FALSE TRUE 3389.774339 3202.661222 2893.193406 2802.560822 2860.56392 2601.337258 2912.087387 3219.738465 3156.356502 3132.253052 1.08221599 1.022478442 0.923678054 0.894742786 0.913260797 0.830500351 0.929710128 1.027930506 1.007695243 1 11.61298506 -9.776762766 4.314192622 1.039394646 0.914003076 0.525573988 0.04999082 0.116703223 5.047735038 0.008749218 0.011980129 1.67E-10 9.776762766 -0.12539157 RLEEPEEPKVLT(ph)PEEQLADK ddPTM_HeLa_Romidepsin_16h_R1 2 RLEEPEEPKVLTPEEQLADK 20 2 O75822;O75822-2 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 RLEEPEEPKVLT(1)PEEQLADK;RLEEPEEPKVLT(1)PEEQLADK ; 74.618 0.0020549 9311700 7629.5 6651.7 7655.7 7722.6 7834.5 8674.7 7699.7 8154 7633.7 7764 TRUE FALSE FALSE 7536.508719 6745.342807 7788.944247 8615.523348 7434.67623 8120.414666 8353.712326 8389.923125 6950.922753 7562.290161 0.996590789 0.891970906 1.02997162 1.139274369 0.983124962 1.073803635 1.104653769 1.109442106 0.919155786 1 12.88460749 -9.520100163 24.98189899 0.988964035 1.078086249 0.525937138 0.053786443 78.28490574 703852.0018 0.007539896 0.010771092 3.02E-10 9.520100163 0.089122214 RLEEWLGR ddPTM_HeLa_Romidepsin_16h_R1 1 RLEEWLGR 8 1 P56192;P56192-2 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 0 0 95.502 0.023059 12410000 3502.1 3457.1 3627 3209.6 3368 3726.3 3267.9 3477.8 3367.5 3049.4 FALSE FALSE TRUE 3459.415058 3505.769145 3690.126414 3580.709054 3196.118392 3488.201456 3545.475344 3578.424656 3066.302366 2970.176148 1.164717136 1.180323647 1.242393121 1.205554443 1.076070318 1.174408951 1.193691945 1.204785332 1.03236381 1 11.53633278 -11.9550316 0.660552262 0.991409449 1.182288938 0.711198474 0.04162806 0.344974645 0.264231985 0.035837442 0.009799179 1.11E-12 11.9550316 0.190879489 RLET(ph)PEPGQQGLQAAAR ddPTM_HeLa_Romidepsin_16h_R1 2 RLETPEPGQQGLQAAAR 17 1 I3L419;I3L156;Q9BSJ6-2;Q9BSJ6 I3L419 FAM64A Protein FAM64A 1 0 RLET(1)PEPGQQGLQAAAR;RLET(1)PEPGQQGLQAAAR ; 117.29 0.00034831 7898000 3058.21 2988.4 3396.92 1928.59 3051.52 3805.07 2944.95 2640.98 3171.39 3021.03 TRUE FALSE FALSE 3020.93536 3030.470774 3456.041968 2151.58265 2895.789548 3561.938307 3195.093979 2717.39259 2887.732936 2942.543205 1.026640953 1.029881488 1.174508487 0.731198321 0.98411114 1.210496519 1.08582738 0.923484347 0.981373164 1 11.52284788 RLFDDEAS(ph)VDEPR ddPTM_HeLa_Romidepsin_16h_R1 3 RLFDDEASVDEPR 13 1 A0A2R8Y549;Q8NI35-4;Q8NI35-3;Q8NI35-2;Q8NI35;A0A0U1RR46;A0A0X1KG69;A0A087WUZ6;Q8NI35-5 A0A2R8Y549 INADL InaD-like protein 1 0 RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR;RLFDDEAS(1)VDEPR ;; 111.58 0.0019176 10514800 3853.6 4368.3 4112.3 4065.1 4153.2 3938.1 3135.15 3657 4271.1 4066.9 TRUE FALSE FALSE 3806.630841 4429.797042 4183.872856 4535.125989 3941.246706 3686.46812 3401.449563 3762.809525 3889.082119 3961.241352 0.960969177 1.118285065 1.056202459 1.144874949 0.994952429 0.930634564 0.858682736 0.949906656 0.981783682 1 11.95173689 -8.215563146 3.814413882 1.010994128 0.903697801 0.41433396 0.062786122 0.220810673 6.764932105 0.010179276 0.027070543 6.09E-09 8.215563146 -0.107296327 RLGDS(ph)SLSR ddPTM_HeLa_Romidepsin_16h_R1 1 RLGDSSLSR 9 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 0 RLGDS(0.333)S(0.333)LS(0.333)R 95.618 0.010013 25873000 2102.3 1634.5 2154.1 2549.9 2376.7 2057.5 1406.9 1922.8 1785.5 1694.9 TRUE FALSE FALSE 2076.676359 1657.510534 2191.591207 2844.731436 2255.40813 1926.03239 1526.402051 1978.433184 1625.800408 1650.866254 1.257931316 1.004024724 1.327540134 1.723174987 1.366196762 1.166679848 0.924606731 1.198421241 0.98481655 1 10.68900753 -12.17003775 0.649678245 0.976252837 1.253555816 0.197844443 0.204706759 1.516527455 1.005693127 0.23840914 0.049403679 6.76E-13 12.17003775 0.277302979 RLGDSS(ph)LSR ddPTM_HeLa_Romidepsin_16h_R1 1 RLGDSSLSR 9 1 Q14152;Q14152-2 Q14152 EIF3A Eukaryotic translation initiation factor 3 subunit A 1 0 RLGDS(0.043)S(0.899)LS(0.058)R 89.561 0.012327 25694000 2385.6 2019.7 2444.5 2740.8 2555.9 2244.5 1560.1 1879.5 1763.2 1746.3 TRUE FALSE FALSE 2356.52339 2048.13339 2487.045497 3057.704192 2425.462886 2101.083694 1692.614855 1933.880367 1605.494976 1700.930874 1.385431604 1.204125 1.462167296 1.797665172 1.425962055 1.235255192 0.995110901 1.136954121 0.94389196 1 10.7321088 -12.25818749 0.875986147 0.989605232 1.337845743 0.318313571 0.207198411 0.76839162 1.008014503 0.178903495 0.043464778 5.52E-13 12.25818749 0.348240511 RLIFSTITSK ddPTM_HeLa_Romidepsin_16h_R1 1 RLIFSTITSK 10 1 P43686;P43686-2 P43686 PSMC4 26S protease regulatory subunit 6B 0 0 95.094 0.003805 0 623.05 526.97 624.02 539.41 610.08 543.19 358.88 430.72 621.54 381.75 FALSE FALSE TRUE 615.456027 534.3886975 634.8808063 601.7791222 578.9453411 508.4819121 389.3632582 443.1822036 565.9479057 371.83208 1.655198839 1.437177496 1.707439569 1.618416362 1.55700751 1.367504149 1.047148106 1.191888026 1.522052389 1 8.538507435 -5.75028232 15.19517727 1.364188769 1.321176303 0 0.244420491 0 0 0.04097679 0 1.78E-06 5.75028232 -0.043012466 RLIS(ph)PYK ddPTM_HeLa_Romidepsin_16h_R1 1 RLISPYK 7 1 O14929-2;O14929 O14929-2 HAT1 Histone acetyltransferase type B catalytic subunit 1 0 RLIS(1)PYK 68.371 0.026234 52734000 3994.3 4128.8 3211.6 4001 4495.9 4726.7 4040.5 4611.6 4518.2 3995.3 TRUE FALSE FALSE 3945.615935 4186.925355 3267.496551 4463.614445 4266.457446 4424.679125 4383.699969 4745.02937 4114.080876 3891.50153 1.013905791 1.075915125 0.839649304 1.147015981 1.096352504 1.137010763 1.126480341 1.219331236 1.057196263 1 11.92611121 RLKEDILENEDEQNS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 RLKEDILENEDEQNSPPK 18 2 Q9NTI5-2;Q9NTI5;A9IYQ1;Q9NTI5-5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 RLKEDILENEDEQNS(1)PPK 57.595 0.021273 12273000 5183.6 4194 4775.9 4099.4 3737.6 3485.6 3183.8 3098.8 5026.3 4923.4 TRUE FALSE FALSE 5120.420289 4253.043242 4859.022536 4573.391916 3546.856325 3262.881409 3454.231893 3188.458889 4576.735139 4795.489358 1.067757617 0.886884096 1.013248529 0.953686178 0.739623438 0.68040635 0.72030853 0.664887074 0.954383338 1 12.22746233 -8.786269471 2.432487168 1.018486019 0.690089077 0.874780949 0.051074643 0.063397752 0.76581447 0.007832912 0.01635937 1.64E-09 8.786269471 -0.328396942 RLLEDGEDFNLGDALDS(ph)SNSMQTIQK ddPTM_HeLa_Romidepsin_16h_R1 1 RLLEDGEDFNLGDALDSSNSMQTIQK 26 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 RLLEDGEDFNLGDALDS(0.597)S(0.176)NS(0.176)MQT(0.051)IQK 59.561 0.0036923 10755000 957.2 982.6 876.59 1036.4 1076.2 920.22 1077.9 1166.6 1099.9 1143 TRUE FALSE FALSE 945.5332782 996.4330686 891.8466812 1156.233444 1021.277498 861.4209119 1169.456799 1200.35373 1001.522189 1113.304695 0.849303234 0.895022785 0.801080499 1.038559749 0.917338715 0.773751261 1.050437319 1.078189767 0.899593969 1 10.12063278 -7.556722545 24.079917 0.914498345 1.071251762 0.414747156 0.07764223 88.07224415 62663.30652 0.011781742 0.044083847 2.78E-08 7.556722545 0.156753417 RLPATLLNAFPTAPS(ph)PRPPR ddPTM_HeLa_Romidepsin_16h_R1 2 RLPATLLNAFPTAPSPRPPR 20 2 Q93015;Q93015-2 Q93015 NAT6 N-acetyltransferase 6 1 0 RLPATLLNAFPT(0.015)APS(0.985)PRPPR;RLPATLLNAFPT(0.037)APS(0.963)PRPPR ; 124.7 0.0002274 17392400 1739.82 1556.17 1526.96 1638.88 1640.31 1243.19 1325.19 1551.91 1457.16 1339.09 TRUE FALSE FALSE 1718.614405 1578.077802 1553.536098 1828.375017 1556.59886 1163.754171 1437.751606 1596.812067 1326.82796 1304.300249 1.31765244 1.209903781 1.191087788 1.401805312 1.193435991 0.892244077 1.102316439 1.224267241 1.017271875 1 10.3490603 -7.19607242 18.68386264 1.159643393 1.224279492 0.018613841 0.144502765 14136.69594 4036996.347 0.022598177 34.09812848 6.37E-08 7.19607242 0.064636099 RLPENLYNDR ddPTM_HeLa_Romidepsin_16h_R1 3 RLPENLYNDR 10 1 E5RHG9;B7Z2R2;P14927;P14927-2 E5RHG9 UQCRB Cytochrome b-c1 complex subunit 7 0 0 ;; ;; 113.67 0.0023132 12636300 4010.36 3784.47 4185.37 3349.09 4881.32 5484.3 3935.68 4289.04 4358.85 3654.38 FALSE FALSE TRUE 3961.48019 3837.747868 4258.214609 3736.327544 4632.208026 5133.87093 4269.976561 4413.136605 3968.983539 3559.438681 1.112950818 1.078189066 1.196316327 1.049695719 1.301387225 1.442325993 1.199620767 1.239840604 1.115058832 1 11.79743403 -9.431198864 0.456133736 1.02429936 1.316560743 0.473931087 0.090539001 0.641925406 0.269599589 0.03044544 0.076651958 3.71E-10 9.431198864 0.292261382 RLPNNHIGISFIPR ddPTM_HeLa_Romidepsin_16h_R1 2 RLPNNHIGISFIPR 14 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 ; ; 63.181 0.016685 2182300 530.55 182.08 336.015 174.59 650.35 891.34 725.24 615.81 529.25 447.42 FALSE FALSE TRUE 524.0834525 184.643327 341.8632001 194.7769173 617.1602127 834.3862507 786.8418675 633.6274908 481.9125545 435.7959639 1.202589046 0.423692146 0.784457013 0.446945207 1.416167803 1.914625925 1.80552812 1.453954472 1.105821518 1 8.767509025 -8.52938316 24.76081135 0.973662918 1.721554008 0.660078106 0.283231868 80.52796083 306551.0121 0.045590608 0.091368699 2.96E-09 8.52938316 0.74789109 RLPQFDDDADTGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 RLPQFDDDADTGKK 14 2 O43257 O43257 ZNHIT1 Zinc finger HIT domain-containing protein 1 0 1 RLPQFDDDADTGK(1)K 113.37 1.93E-05 0 552.36 428.89 718.32 554.59 1028.9 1014.1 1002.9 842.39 701.4 458.07 FALSE TRUE FALSE 545.6276239 434.9279247 730.8220583 618.7143052 976.3913936 949.3022829 1088.086301 866.7632256 638.6650273 446.1692754 1.222916176 0.97480474 1.637992795 1.386725486 2.188387788 2.127672915 2.438729785 1.942677978 1.431441075 1 8.801447358 -9.023613725 1.090529441 1.096688418 2.244645076 0.781330866 0.229162447 0.121481768 0.284944812 0.032319046 0.077580638 9.47E-10 9.023613725 1.147956658 RLPT(ph)PEQIFQNIK ddPTM_HeLa_Romidepsin_16h_R1 1 RLPTPEQIFQNIK 13 1 H0YEQ5;Q9H9L7-2;Q9H9L7 H0YEQ5 AKIRIN1 Akirin-1 1 0 RLPT(1)PEQIFQNIK 77.74 0.002126 0 1951.3 1738.2 1668.9 1800.1 2392 2448.3 1766.1 1947.1 1812.8 1561.2 TRUE FALSE FALSE 1927.516805 1762.670425 1697.946504 2008.236032 2269.927314 2291.861532 1916.11249 2003.436266 1650.658628 1520.639799 1.267569615 1.15916368 1.116600069 1.320652026 1.492744906 1.507169241 1.260069933 1.317495615 1.085502713 1 10.57046274 -9.151952206 3.846711426 1.131780021 1.394066076 0.65590945 0.092850723 0.151094114 4.004520348 0.018721613 0.031881604 7.05E-10 9.151952206 0.262286054 RLQLS(ph)PWESSVVNR ddPTM_HeLa_Romidepsin_16h_R1 1 RLQLSPWESSVVNR 14 1 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7;Q14244-2;Q14244-4 A0A087WZ40 MAP7 Ensconsin 1 0 RLQLS(1)PWESSVVNR 68.123 0.018344 13610000 1265.1 1337.9 1254.5 1497 1493.3 1478.9 1536.3 1509 1374.6 1217.9 TRUE FALSE FALSE 1249.680475 1356.734991 1276.334046 1670.090184 1417.091329 1384.403063 1666.793284 1552.660534 1251.652333 1186.258782 1.053463623 1.143709123 1.075932221 1.407863283 1.194588693 1.16703293 1.405084041 1.308871687 1.055125873 1 10.21220305 -9.625661284 0.668464303 1.010575758 1.314364238 0.615104418 0.086792076 0.297252382 0.269564608 0.019619702 0.037333836 2.37E-10 9.625661284 0.30378848 RLS(ph)ASSTGSTR ddPTM_HeLa_Romidepsin_16h_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 1 0 RLS(0.888)AS(0.05)S(0.05)T(0.012)GS(0.001)TR 114.24 0.01948 12966000 2376.8 2218.3 2773.1 2994.9 3282 3737.6 4033.5 1211.4 3168.3 2765.4 TRUE FALSE FALSE 2347.830647 2249.529286 2821.364642 3341.184429 3114.507293 3498.779423 4376.105389 1246.449948 2884.919313 2693.554509 0.87164772 0.835152687 1.047450361 1.240436909 1.156281517 1.298945097 1.624658188 0.462752821 1.071045454 1 11.39529555 -9.492036675 4.515909961 0.92984906 1.188634193 0.108460577 0.277600551 0.269328338 13.01332158 0.039425767 0.059374272 3.22E-10 9.492036675 0.258785133 RLS(ph)DEHEPEQR ddPTM_HeLa_Romidepsin_16h_R1 2 RLSDEHEPEQR 11 1 Q9UK59-2;Q9UK59 Q9UK59-2 DBR1 Lariat debranching enzyme 1 0 RLS(1)DEHEPEQR;RLS(1)DEHEPEQR ; 82.55 0.014972 9192600 1787.95 1896.38 1792.64 1639.64 1374.09 1559.46 1449.79 1684.05 2350.1 1935.1 TRUE FALSE FALSE 1766.157778 1923.077287 1823.840147 1829.222892 1303.96506 1459.815539 1572.935126 1732.77533 2139.90117 1884.825823 0.937040312 1.020294429 0.967643867 0.970499698 0.691822578 0.774509518 0.834525454 0.919329154 1.135330991 1 10.88021549 -8.792798452 23.44858194 0.973541308 0.804971158 0.60786935 0.076236406 44.16110271 33021.07334 0.008647079 0.015675834 1.61E-09 8.792798452 -0.16857015 RLS(ph)EDYGVLK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSEDYGVLK 10 1 P32119;A6NIW5 P32119 PRDX2 Peroxiredoxin-2 1 0 RLS(1)EDYGVLK 90.689 0.011194 5480900 2363.3 2180.5 2787.9 3481.2 3741.7 3636.4 6156.7 3949.3 3029.3 2665.2 TRUE FALSE FALSE 2334.495191 2211.197136 2836.42223 3883.712724 3550.747087 3404.045776 6679.649944 4063.566765 2758.351821 2595.95772 0.899280898 0.851784726 1.092630365 1.496061625 1.367798504 1.311287064 2.573096585 1.565343971 1.062556528 1 11.34205117 -8.416650024 0.793531575 0.943747306 2.081483838 0.588928069 0.306169107 0.37740089 0.381190801 0.048922011 0.268945345 3.83E-09 8.416650024 1.137736532 RLS(ph)ELGITQADDNLMSQEMFVGIVGNQFK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSELGITQADDNLMSQEMFVGIVGNQFK 29 1 Q8NEM2 Q8NEM2 SHCBP1 SHC SH2 domain-binding protein 1 1 0 RLS(0.926)ELGIT(0.025)QADDNLMS(0.05)QEMFVGIVGNQFK 67.015 0.00011109 0 936.47 1042.6 1270.3 832.45 833.95 1075.3 574.88 698.41 1022 1056.7 TRUE FALSE FALSE 925.0559434 1057.27775 1292.409039 928.7017858 791.3904196 1006.5918 623.7102929 718.6173914 930.5897604 1029.246782 0.898769819 1.027234449 1.255684314 0.902312062 0.768902496 0.977988776 0.60598712 0.698197366 0.904146388 1 10.00737322 -7.88863759 1.108452825 0.974896265 0.61511593 0.472059632 0.126479064 0.516794975 0.924740225 0.019666956 0.16686711 1.29E-08 7.88863759 -0.359780336 RLS(ph)ESSALK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSESSALK 9 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 0 RLS(0.999)ES(0.001)SALK 128.88 0.01363 53435000 2402.6 2826.3 3321.1 2927.9 3163.6 3668.9 2980.8 3307 2885.6 2816.8 TRUE FALSE FALSE 2373.316187 2866.088726 3378.902352 3266.437574 3002.149687 3434.469131 3233.989078 3402.682827 2627.504709 2743.61913 0.865031214 1.044637973 1.231549349 1.190557953 1.094229754 1.251802443 1.178731057 1.240216906 0.957678375 1 11.4218645 -9.953201205 4.050745147 0.936578762 1.193560821 0.832217493 0.052244003 0.071239049 2.497729034 0.010433436 0.013696916 1.11E-10 9.953201205 0.256982058 RLS(ph)GNEYVFTK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSGNEYVFTK 11 1 A0A2R8Y4E6;O95263-2;O95263-3;O95263-6;O95263-4;O95263 A0A2R8Y4E6 PDE8B "High affinity cAMP-specific and IBMX-insensitive 3,5-cyclic phosphodiesterase 8B" 1 0 RLS(1)GNEYVFTK 101.04 0.0055498 16059000 2875.9 3431.3 3340.6 3727.9 3414.7 3273.7 2975.6 3189.3 3580.1 3219.9 TRUE FALSE FALSE 2840.847425 3479.605931 3398.741742 4158.937338 3240.435117 3064.521135 3228.34739 3281.577364 3259.886889 3136.246534 0.90581126 1.109480997 1.083697249 1.326087504 1.033220789 0.977130178 1.029366587 1.046339096 1.039423035 1 11.61482326 -10.25392548 24.38859662 0.955521984 1.087133447 0.190484157 0.094396816 397.7773493 1291105.005 0.016291582 0.019742287 5.57E-11 10.25392548 0.131611463 RLS(ph)ITSLTGK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSITSLTGK 10 1 G3V1S3;Q6ZUT9;Q6ZUT9-2 G3V1S3 DENND5B DENN domain-containing protein 5B 1 0 RLS(0.96)IT(0.033)S(0.007)LTGK 75.483 0.021441 18000000 2781.3 2949.9 3404.9 3111.8 4058.7 4363.3 3420.4 4065.8 2718.4 2523.8 TRUE FALSE FALSE 2747.400446 2991.42877 3464.160856 3471.600957 3851.569394 4084.499212 3710.928691 4183.437508 2475.259496 2458.231312 1.117633004 1.216902882 1.409208661 1.412235269 1.566805115 1.66156016 1.509592963 1.701807917 1.006927006 1 11.26340496 -9.592719373 0.654029594 1.024842738 1.64652937 0.94987651 0.055364988 0.09678736 0.083910546 0.012730653 0.025050596 2.55E-10 9.592719373 0.621686631 RLS(ph)LESEGAGEGAAASPELSALEEAFRR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLESEGAGEGAAASPELSALEEAFRR 28 2 O94811 O94811 TPPP Tubulin polymerization-promoting protein 1 0 RLS(0.99)LES(0.01)EGAGEGAAASPELSALEEAFRR 83.022 1.31E-06 3162300 317.93 357.59 252.73 289.2 423.76 620.57 680.06 738.84 344.99 417.58 TRUE FALSE FALSE 314.0549469 362.6241614 257.1286596 322.6386647 402.1339459 580.9175798 737.8242794 760.2171697 314.1332304 406.7312114 0.772143711 0.891557253 0.632183251 0.793247864 0.988697043 1.428259164 1.814034081 1.869089827 0.772336181 1 8.667931893 -8.064633136 1.904858644 0.861596316 1.873397399 0.945903556 0.098749016 0.069275181 0.476445194 0.017912044 0.070382254 8.62E-09 8.064633136 1.011801083 RLS(ph)LGQGDSTEAATEER ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLGQGDSTEAATEER 17 1 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 RLS(1)LGQGDSTEAATEER 67.902 0.010327 2721400 1348.9 1158.9 933.31 1121.5 1193.1 1278.4 983.36 1467.4 1332.7 1186 TRUE FALSE FALSE 1332.459088 1175.215025 949.553869 1251.173107 1132.211655 1196.714366 1066.886574 1509.856904 1213.499974 1155.187549 1.153456934 1.017336991 0.821991087 1.083090887 0.980110681 1.035948117 0.923561351 1.30702318 1.050478751 1 10.17391138 -14.27749586 12.69148527 1.057681283 1.048928986 0 0.124186375 0 0 0 0.01610704 5.28E-15 14.27749586 -0.008752297 RLS(ph)LPGLLS(ph)QVSPR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLPGLLSQVSPR 14 1 Q96Q42-3;Q96Q42 Q96Q42-3 ALS2 Alsin 2 0 RLS(0.999)LPGLLS(0.996)QVS(0.005)PR 88.108 0.019784 10083000 1239 1353.8 1539.1 1778.2 2955 3762.9 3824.2 4224.5 1336 1339.4 TRUE FALSE FALSE 1223.898591 1372.858832 1565.88739 1983.803851 2804.195323 3522.462834 4149.027453 4346.729242 1216.504814 1304.602195 0.938139301 1.052319885 1.200279592 1.52061974 2.149463901 2.700028291 3.180300837 3.331842656 0.932471844 1 10.34939425 -8.442084432 0.906997371 0.965051912 3.450628226 0.998395523 0.036528059 0.019972034 0.028133711 0.006900216 0.032676557 3.61E-09 8.442084432 2.485576314 up RLS(ph)LPGLLSQVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLPGLLSQVSPR 14 1 Q96Q42-3;Q96Q42 Q96Q42-3 ALS2 Alsin 2 0 RLS(1)LPGLLS(0.348)QVS(0.652)PR 80.277 0.012417 5487600 1206.1 1387.3 1152.2 1603 2547.3 2940.5 2869.7 3564.3 1463.5 1312.5 TRUE FALSE FALSE 1191.399589 1406.830446 1172.253558 1788.346402 2417.301776 2752.61154 3113.452246 3667.427397 1332.600895 1278.401061 0.931945088 1.10046095 0.916968543 1.398893084 1.890879044 2.153167441 2.435426833 2.868761228 1.042396581 1 10.3201248 -8.344503675 0.840941123 0.956918578 2.863072916 0.973997448 0.108952848 0.081562777 0.091952283 0.017898732 0.102286757 4.52E-09 8.344503675 1.906154337 up RLS(ph)LPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLPSSK 8 1 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 1 0 RLS(0.987)LPS(0.012)S(0.001)K 65.842 0.028009 7700400 6016.1 6231.1 6204.5 5469.9 4304.1 4157 4061.1 4242.3 6396.2 5813.3 TRUE FALSE FALSE 5942.773459 6318.821589 6312.48672 6102.355575 4084.445716 3891.381116 4406.049733 4365.044257 5824.107852 5662.269628 1.049539116 1.115952084 1.114833297 1.077722535 0.721344264 0.687247583 0.778141986 0.770900106 1.028581865 1 12.46716473 -8.759386913 24.99997189 1.042666951 0.738449336 0.92811781 0.04406412 12.7248335 154990.4204 0.007861068 0.015118759 1.74E-09 8.759386913 -0.304217615 RLS(ph)LTLR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLTLR 7 1 Q00537-2;Q00537;F8VUX2;F8W1S5;F8VZY6;F8VQZ9 Q00537-2 CDK17 Cyclin-dependent kinase 17 1 0 RLS(0.92)LT(0.08)LR 74.165 0.022102 7820100 1472.4 1662.9 1494.8 1468.4 1548.1 1543.9 1638.7 1713 1714.6 1453.1 TRUE FALSE FALSE 1454.453822 1686.31035 1520.816367 1638.183317 1469.09468 1445.249773 1777.891137 1762.562952 1561.241882 1415.348253 1.027629645 1.191445531 1.07451743 1.157441862 1.037973995 1.021126617 1.25615101 1.245321036 1.103079669 1 10.46694136 -4 0.197150319 0.990152842 2.12943481 0.265391092 0.077524284 33.44357544 0.380970345 0.072586906 11.80771273 1.00E-04 4 1.139281968 RLS(ph)PISGSR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSPISGSR 9 1 E9PQ01 E9PQ01 PCF11 1 0 RLS(1)PISGSR 83.226 0.016109 15791000 1829.4 1876.5 2036.8 2251.2 2044.5 1945.4 1607.8 1621 2184.6 1939.7 TRUE FALSE FALSE 1807.102569 1902.917416 2072.24965 2511.494336 1940.161536 1821.095218 1744.366492 1667.901077 1989.203905 1889.306314 0.956489985 1.007204285 1.096830955 1.329320882 1.026917404 0.963896222 0.923284106 0.88281136 1.052875275 1 10.88364091 -7.887314356 2.607163807 1.019252662 0.897511487 0.215960057 0.104196352 0.437511101 5.861750031 0.016777594 0.066696294 1.30E-08 7.887314356 -0.121741175 RLS(ph)PPSSSAASSYSFSDLNSTR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSPPSSSAASSYSFSDLNSTR 22 1 P50402 P50402 EMD Emerin 1 0 RLS(0.431)PPS(0.253)S(0.098)S(0.208)AAS(0.006)S(0.004)Y(0.001)SFSDLNSTR 43.801 0.027465 22761000 865.5 1033.2 1028.6 445.11 1283.6 1638.6 1197.9 1903.6 1147.1 1150.1 TRUE FALSE FALSE 854.9509531 1047.745417 1046.502352 496.5757125 1218.093102 1533.898748 1299.649596 1958.677663 1044.500503 1120.220236 0.76319899 0.935303062 0.9341934 0.443284005 1.087369307 1.369283199 1.160173289 1.748475522 0.932406387 1 10.12956668 -8.39135462 3.550857304 0.862888964 1.402090769 0.626366475 0.202269569 0.127981204 2.925143652 0.028837041 0.068592713 4.06E-09 8.39135462 0.539201805 RLS(ph)PQPQIR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSPQPQIR 9 1 J3QT39;Q49A88-5;Q49A88;C9JU82;A0A0A0MR27;Q49A88-2;Q49A88-3;Q49A88-6 J3QT39 CCDC14 Coiled-coil domain-containing protein 14 1 0 RLS(1)PQPQIR 77.124 0.020081 6550600 906.91 609.4 725.38 946.48 939.99 748.97 522.27 662.22 710.03 825 TRUE FALSE FALSE 895.8562321 617.9791492 738.0049346 1055.916471 892.0188027 701.1132342 566.6316008 681.3802909 646.5231385 803.5663811 1.114850314 0.76904555 0.91841191 1.31403764 1.110074816 0.87250195 0.705145977 0.847945244 0.804567182 1 9.650273397 -8.071538836 4.437349715 1.045691664 0.777578046 0.232810443 0.156415585 0.164848596 6.147608108 0.020069064 0.055344429 8.48E-09 8.071538836 -0.268113618 RLS(ph)PSASPPR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSPSASPPR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 RLS(0.817)PS(0.031)AS(0.152)PPR 63.602 0.030082 2095000 731.19 607.36 792.59 646.07 576 626.13 606.03 765.45 662.05 663.9 TRUE FALSE FALSE 722.277975 615.91043 806.3846965 720.7716533 546.6045706 586.1223137 657.5061731 787.5970881 602.8345899 646.6517823 1.116950413 0.952460732 1.247015347 1.114620995 0.845284256 0.906395575 1.016785527 1.217961675 0.932239895 1 9.336845229 RLS(ph)QPESAEK ddPTM_HeLa_Romidepsin_16h_R1 2 RLSQPESAEK 10 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 RLS(1)QPESAEK;RLS(1)QPESAEK ; 103.13 0.006673 233830000 9679.9 9509.4 9266.3 9793.5 11724.9 13786.3 14059.1 14779.9 11598.4 11123.8 TRUE FALSE FALSE 9561.917656 9643.273583 9427.576064 10925.87055 11126.5346 12905.39992 15253.2796 15207.53309 10561.01006 10834.80207 0.882518905 0.890027664 0.870119823 1.008405181 1.026925506 1.1911062 1.407804176 1.403581993 0.974730317 1 13.40338518 -8.067863152 1.379028006 0.935196783 1.442073544 0.943279599 0.045623221 0.095238662 0.317330178 0.008599164 0.043854636 8.55E-09 8.067863152 0.506876762 RLS(ph)QSDEDVIR ddPTM_HeLa_Romidepsin_16h_R1 3 RLSQSDEDVIR 11 1 H0Y917;A0A499FIZ0;Q9H7D7-3;Q9H7D7-4;Q9H7D7-2;Q9H7D7 H0Y917 WDR26 WD repeat-containing protein 26 1 0 RLS(1)QSDEDVIR;RLS(0.984)QS(0.016)DEDVIR;RLS(0.999)QS(0.001)DEDVIR ;; 148.85 0.00070912 124447000 5548.5 5625.5 4833.5 5126.1 5982.4 6998.1 6569.3 7694.6 6729.5 7070.9 TRUE FALSE FALSE 5480.872748 5704.695937 4917.62504 5718.803801 5677.095805 6550.943995 7127.296178 7917.231111 6127.596666 6887.196999 0.795806008 0.828304452 0.714024158 0.830352871 0.824296997 0.951177089 1.034861669 1.149557812 0.889708348 1 12.74970123 -7.658221787 1.828221136 0.871267963 1.150794489 0.643310115 0.074192955 0.316743436 1.759245963 0.014797941 0.116202592 2.20E-08 7.658221787 0.279526525 RLS(ph)SLRAS(ph)TSK ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSLRASTSK 11 2 A2A3R5;P62753 A2A3R5 RPS6 40S ribosomal protein S6 2 0 RLS(0.995)S(0.006)LRAS(0.973)T(0.02)S(0.006)K 105.19 0.029896 30074000 4997.6 5252 4239.2 3787.2 5296.8 4820.5 3611.6 4136.1 4722.8 4267.9 TRUE FALSE FALSE 4936.687329 5325.937794 4312.981498 4225.093883 5026.484531 4512.485607 3918.369214 4255.771528 4300.38094 4157.019343 1.187554573 1.281191487 1.037517784 1.016375806 1.209155916 1.08550989 0.942591047 1.023755527 1.034486632 1 12.02133375 -7.852460852 6.351455338 1.104239755 0.984065141 0.23324663 0.089766855 0.252519114 14.3298411 0.014328267 0.044132031 1.40E-08 7.852460852 -0.120174614 RLS(ph)SSESPQR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSSESPQR 10 1 J3KS33;Q9H2G4 J3KS33 TSPYL2 Testis-specific Y-encoded-like protein 2 1 0 RLS(0.491)S(0.251)S(0.251)ES(0.007)PQR 121.68 0.016709 1333700 1082.1 884.55 1192.6 873.02 1330.1 1643.6 1823.1 1086.2 1151 974.06 TRUE FALSE FALSE 1068.910949 897.0027181 1213.356703 973.9626801 1262.220034 1538.579264 1977.954068 1117.627483 1048.051677 948.7537808 1.126647367 0.945453643 1.278895249 1.026570539 1.330397896 1.621684462 2.084791764 1.177995288 1.104661397 1 9.889889919 -8.454094622 2.58727478 1.067736314 1.677102464 0.5480345 0.221459477 0.134388521 1.758765509 0.029385277 0.072519078 3.51E-09 8.454094622 0.60936615 RLS(ph)SSTVAISYS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSSTVAISYSPDR 15 1 Q96T17-2;Q96T17;Q96T17-5 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 2 0 RLS(0.97)S(0.027)S(0.002)T(0.001)VAISYS(1)PDR 102.03 0.0067032 5174600 1912.1 1798.9 1756.8 1619 1737.4 2355.2 1996.6 2000.5 1984.2 1919.5 TRUE FALSE FALSE 1888.79459 1824.224961 1787.376367 1806.196398 1648.733995 2204.710321 2166.191154 2058.381311 1806.728182 1869.631113 1.01024987 0.975713845 0.956004826 0.966070999 0.881849892 1.179222096 1.158619547 1.10095585 0.966355432 1 10.86853793 -8.243465883 24.9404542 0.988869345 1.147501218 0.786649849 0.041964606 309.9449992 430086.6854 0.006161059 0.015671264 5.71E-09 8.243465883 0.158631873 RLS(ph)STSLASGHSVR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSTSLASGHSVR 14 1 Q9BZL6-2;Q9BZL6;Q9BZL6-3;M0QZ82 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 0 RLS(0.958)S(0.034)T(0.008)SLASGHSVR 78.95 0.011238 3405200 724.08 339.81 622.67 540.66 508.72 616.78 700.63 449.49 583.77 581.73 TRUE FALSE FALSE 715.2546345 344.5938541 633.5073102 603.1736531 482.7581201 577.3697486 760.1414947 462.495284 531.5561491 566.6165707 1.262325656 0.608160566 1.118052918 1.064518202 0.852001415 1.018977874 1.341544766 0.816240308 0.938123198 1 9.146228984 RLS(ph)VLEEEATEGGTSR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSVLEEEATEGGTSR 16 1 A0A1B0GVE3;O75808-2;O75808 A0A1B0GVE3 CAPN15 Calpain-15 1 0 RLS(1)VLEEEATEGGTSR 53.768 0.028735 1949700 587.92 585.54 527.69 492.33 482.6 613.7 598.75 477.41 760.02 635.43 TRUE FALSE FALSE 580.7542049 593.7832475 536.8742231 549.2555111 457.9711212 574.4865506 649.6078101 491.2231051 692.0419077 618.921437 0.938332671 0.959383877 0.867435172 0.887439792 0.739950329 0.928205934 1.049580401 0.793676024 1.118141765 1 9.273612482 -10.60758876 0.739211668 0.987164658 0.884277756 0.312206687 0.089294878 0.662422757 0.783208598 0.023513554 0.022234016 2.47E-11 10.60758876 -0.102886902 RLSELGIT(ph)QADDNLMSQEMFVGIVGNQFK ddPTM_HeLa_Romidepsin_16h_R1 2 RLSELGITQADDNLMSQEMFVGIVGNQFK 29 1 Q8NEM2 Q8NEM2 SHCBP1 SHC SH2 domain-binding protein 1 1 0 RLS(0.162)ELGIT(0.573)QADDNLMS(0.265)QEMFVGIVGNQFK;RLS(0.205)ELGIT(0.409)QADDNLMS(0.385)QEMFVGIVGNQFK ; 45.856 0.0066665 16301400 2937.7 2482.02 2621 2557.65 2603.2 2642.67 2168.79 2523.97 2967 2841.3 TRUE FALSE FALSE 2901.894182 2516.961943 2666.617406 2853.377527 2470.34899 2473.811916 2353.006968 2596.99709 2701.624089 2767.482616 1.04856817 0.909477056 0.963553444 1.0310372 0.892633968 0.893885259 0.850233694 0.938396893 0.976202731 1 11.43435854 -8.972575994 0.721945091 1.019143828 0.879129192 0.369459122 0.048834211 0.433166024 0.419841233 0.009635152 0.03109072 1.07E-09 8.972575994 -0.140014636 RLSLPGLLSQVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSLPGLLSQVSPR 14 1 Q96Q42-3;Q96Q42 Q96Q42-3 ALS2 Alsin 1 0 RLSLPGLLSQVS(1)PR 107.63 0.0019804 6480300 2806.5 2809.6 2833.4 3704.5 2989.1 2753.6 2521.3 2921.8 2904.5 2796.4 TRUE FALSE FALSE 2772.293299 2849.153623 2882.714138 4132.83172 2836.555073 2577.653847 2735.459159 3006.337673 2644.714246 2723.749125 1.017822557 1.046041134 1.058362575 1.517332005 1.04141569 0.946362432 1.004299234 1.103749845 0.970983055 1 11.41137811 -9.699643713 4.113708975 1.011004693 1.116980471 0.113988641 0.145761096 0.406606315 13.8310408 0.023884804 0.033752878 2.00E-10 9.699643713 0.105975778 RLSSSSATLLNS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 2 RLSSSSATLLNSPDR 15 1 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7 A0A087WZ40 MAP7 Ensconsin 1 0 RLSSSSATLLNS(1)PDR;RLSSSSATLLNS(1)PDR ; 110.34 0.001249 29823000 4065.5 3966.4 3634.4 5005.5 3291.4 2860.67 2500.9 2470.21 4379.2 4200.9 TRUE FALSE FALSE 4015.948122 4022.239083 3697.655207 5584.259462 3123.427576 2677.882419 2713.326384 2541.681629 3987.513384 4091.760012 0.981472058 0.983009529 0.903683304 1.364757328 0.76334574 0.654457351 0.66311963 0.621170748 0.97452279 1 11.99850582 -8.537602622 24.96595375 1.008712891 0.658097091 0.689677462 0.119100162 95.00237378 161086.5749 0.016025702 0.032061124 2.90E-09 8.537602622 -0.3506158 RLSSST(ph)VAISYSPDR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSSTVAISYSPDR 15 1 Q96T17-2;Q96T17;Q96T17-5 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 RLS(0.255)S(0.255)S(0.097)T(0.392)VAISYSPDR 64.331 0.0036694 0 385.31 359.41 417.62 451.19 526.84 582.16 674.38 652.4 431.49 264.77 TRUE FALSE FALSE 380.6136935 364.4697834 424.8885009 503.3587107 499.9533889 544.9618548 731.6618204 671.2761647 392.8964537 257.8912372 1.475869043 1.413269359 1.647549197 1.951825568 1.93862108 2.113146072 2.837094537 2.602942899 1.523496719 1 8.010618943 -4 0.176419631 0.888851546 9.25414087 0.846389576 0.208481985 9.035202449 0.096985565 0.195637748 20.26682583 1.00E-04 4 8.365289323 up RLSSSTVAISYS(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 RLSSSTVAISYSPDR 15 1 Q96T17-2;Q96T17;Q96T17-5 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 RLSSSTVAISYS(1)PDR 109.55 0.0069153 5520900 630.05 615.51 633.51 832.02 692.4 777.66 765.65 519.5 861.47 768.07 TRUE FALSE FALSE 622.3707083 624.1751659 644.5359758 928.2220672 657.0642443 727.9700358 830.6842919 534.5309129 784.4179656 748.1154307 0.831918021 0.834330025 0.861546159 1.240747122 0.878292597 0.973071809 1.110369146 0.714503258 1.048525312 1 9.547117078 RLT(ph)VNEAVK ddPTM_HeLa_Romidepsin_16h_R1 2 RLTVNEAVK 9 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 RLT(1)VNEAVK;RLT(1)VNEAVK ; 126.71 0.0041202 16141800 5813 5346.1 6657.2 6367.1 7909.3 8231.4 5758.4 6651.8 5958.6 4549.4 TRUE FALSE FALSE 5742.14892 5421.362536 6773.065773 7103.29406 7505.658907 7705.440106 6247.518352 6844.259338 5425.647892 4431.205932 1.295843391 1.223450821 1.528492667 1.603016012 1.693818573 1.738903636 1.409891223 1.544559076 1.224417907 1 12.11348366 -10.42705813 0.538997267 1.039256508 1.621526997 0.69929598 0.123335573 0.257094225 0.176186809 0.047170326 0.048659193 3.74E-11 10.42705813 0.582270489 RLTLEDLEDSWDR ddPTM_HeLa_Romidepsin_16h_R1 2 RLTLEDLEDSWDR 13 1 Q6P2Q9;I3L3Z8 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 ; ; 168 8.25E-05 23238000 3126.2 3121.7 2813.2 2905.64 2872.04 2955.1 2214.62 2891 3255.3 3003 FALSE FALSE TRUE 3088.096672 3165.647375 2862.162566 3241.603768 2725.469082 2766.278647 2402.729768 2974.646524 2964.137815 2924.981627 1.055766178 1.082279405 0.978523263 1.108247566 0.931790154 0.94574223 0.821451234 1.016979559 1.013386815 1 11.51421185 -8.644519149 8.278628643 1.032681556 0.921042307 0.468722855 0.057296382 0.157202521 10.76455723 0.007764397 0.015554368 2.27E-09 8.644519149 -0.111639249 RLTVSSLQESGLK ddPTM_HeLa_Romidepsin_16h_R1 2 RLTVSSLQESGLK 13 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 187.74 2.71E-08 3108200 2476 2395.31 2979.6 2105.56 3001.9 2711.7 2726.32 2596.8 2733.5 2394.4 FALSE FALSE TRUE 2445.82156 2429.031237 3031.458688 2349.014754 2848.701841 2538.431122 2957.893553 2671.934311 2489.008914 2332.193143 1.048721701 1.04152233 1.299831747 1.007212787 1.221469092 1.088430917 1.268288418 1.145674542 1.067239616 1 11.18747156 -9.965139683 24.695248 1.024171381 1.167478348 0.385111427 0.081268624 102.3944065 72536.58776 0.011687962 0.015360953 1.08E-10 9.965139683 0.143306967 RMCVNGLCRARK ddPTM_HeLa_Romidepsin_16h_R1 1 RMCVNGLCRARK 12 3 Q96JE7-3 Q96JE7-3 0 0 53.08 0.029994 21555000 3003.2 1312.7 2234.5 421.52 2452.3 1772 2898.2 2362.8 3631.4 2608.1 FALSE FALSE TRUE 2966.595843 1331.180225 2273.390535 470.2581257 2327.14998 1658.774919 3144.373036 2431.16389 3306.598489 2540.341186 1.167794255 0.524016314 0.894915434 0.185116129 0.916077727 0.652973281 1.237775876 0.957022586 1.301635586 1 11.31080656 -10.28076762 24.89857783 1.079236181 0.768867313 0.280818901 0.277591072 857.6751061 1104850.84 0.045852187 0.052475136 5.24E-11 10.28076762 -0.310368868 RMEDEGGFPVPQENGQPES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RMEDEGGFPVPQENGQPESPR 21 1 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 RMEDEGGFPVPQENGQPES(1)PR 75.044 0.0041413 4941700 667.77 575.53 663.68 563.41 559.85 608.54 535.41 667.81 707.31 635.63 TRUE FALSE FALSE 659.6309624 583.6323264 675.231072 628.5541151 531.2787654 569.656258 580.887712 687.1320287 644.0464221 619.116241 1.065439604 0.942686184 1.090636988 1.015244107 0.85812442 0.92011196 0.938253067 1.109859479 1.040267367 1 9.274066495 -8.972913865 24.98464509 1.028835877 0.95067374 0.190931616 0.069668456 250.5795638 231137.1454 0.010071402 0.018255721 1.06E-09 8.972913865 -0.078162137 RMEELHNQEVQK ddPTM_HeLa_Romidepsin_16h_R1 1 RMEELHNQEVQK 12 1 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 0 64.224 0.025715 2788700 3363 2837.4 3106.5 3005.2 3138.5 3081.2 2699.7 2816.8 3376.4 3196 FALSE FALSE TRUE 3322.010462 2877.344992 3160.567329 3352.675364 2978.330634 2884.321264 2929.012451 2898.299664 3074.406328 3112.967459 1.067152325 0.92430937 1.015290834 1.077003023 0.956749684 0.926550406 0.940906864 0.931040784 0.987612742 1 11.60407478 -8.594560013 6.928491514 1.024883094 0.934899019 0.420068634 0.041053461 0.138358343 10.92879131 0.006295596 0.01266636 2.54E-09 8.594560013 -0.089984075 RMEELHNQEVQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 RMEELHNQEVQKR 13 2 Q15233;Q15233-2;H7C367;C9JYS8 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; RMEELHNQEVQK(1)R;RMEELHNQEVQK(1)R 56.956 0.021676 1000650 64.487 0 0 67.808 127.23 0 0 135.36 199.93 0 FALSE TRUE FALSE 63.70100764 0 0 75.64828001 120.7369783 0 0 139.276428 182.0477601 0 0 RMGESDDSILR ddPTM_HeLa_Romidepsin_16h_R1 2 RMGESDDSILR 11 1 Q8WVC2;P63220 Q8WVC2 RPS21 40S ribosomal protein S21 0 0 ; ; 122.7 0.0023855 19545800 2913.3 2366.3 2947.7 3838.4 3256.8 3407.2 3141 2860.7 3426.4 2485.1 FALSE FALSE TRUE 2877.791579 2399.612834 2999.003482 4282.213868 3090.593343 3189.490916 3407.796462 2943.469841 3119.934202 2420.536744 1.188906381 0.991355673 1.238982837 1.769117482 1.276821495 1.317679198 1.407868098 1.21604014 1.288943128 1 11.24111128 -9.522147471 24.72297868 1.085826649 1.398652409 0.397286872 0.161322251 14.65715368 495534.2276 0.023591952 0.033604101 3.01E-10 9.522147471 0.31282576 RMS(ph)ADMSEIEAR ddPTM_HeLa_Romidepsin_16h_R1 2 RMSADMSEIEAR 12 1 Q9UG54;O43318-4;O43318-3;O43318-2;O43318 Q9UG54 DKFZp586F0420;MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 0 RMS(0.976)ADMS(0.024)EIEAR;RMS(0.908)ADMS(0.092)EIEAR ; 55.314 0.024487 43255000 6738.9 7074 6978.2 8225.8 8788.5 8465.2 6887.4 7931.7 7699.4 6973 TRUE FALSE FALSE 6656.763695 7173.587958 7099.652644 9176.9057 8339.990051 7924.30104 7472.415584 8161.191225 7010.74638 6791.840455 0.980111906 1.056206783 1.04532088 1.351166265 1.227942574 1.166738396 1.100204817 1.20161704 1.032230723 1 12.72958685 -9.455246295 7.144360739 0.997729837 1.20247633 0.685569298 0.062817497 0.111306868 10.20900121 0.009938939 0.015168151 3.51E-10 9.455246295 0.204746493 RMYS(ph)FDDVLEEGK ddPTM_HeLa_Romidepsin_16h_R1 2 RMYSFDDVLEEGK 13 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;E9PJ10 E9PMS6 LMO7 LIM domain only protein 7 1 0 RMY(0.003)S(0.997)FDDVLEEGK;RMY(0.002)S(0.998)FDDVLEEGK ; 85.619 0.0019266 7125700 4774.9 4807.9 4207.7 3672.1 5338.6 5434.9 5150.9 5729.3 4812.1 4652 TRUE FALSE FALSE 4716.701682 4875.585742 4280.933253 4096.68548 5066.151321 5087.62743 5588.417317 5895.068256 4381.693724 4531.140369 1.040952453 1.07601737 0.944780542 0.90411798 1.118074239 1.122813909 1.23333573 1.301012058 0.967017873 1 12.14565847 -7.910596725 1.367174296 1.012778567 1.304469606 0.787071418 0.055511478 0.188677113 0.584216983 0.00833427 0.054456314 1.23E-08 7.910596725 0.291691039 RNALFPEVFS(ph)PTPDENSDQNSR ddPTM_HeLa_Romidepsin_16h_R1 1 RNALFPEVFSPTPDENSDQNSR 22 1 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 RNALFPEVFS(0.908)PT(0.091)PDENSDQNSR 75.82 0.00076221 6002200 827.13 931.55 822.54 1037.2 765.85 857.53 574.95 816.03 979.23 750.45 TRUE FALSE FALSE 817.0486214 944.6643854 836.8559637 1157.125944 726.7658167 802.7366006 623.7862386 839.6405406 891.6452163 730.9532008 1.117785134 1.29237328 1.144883096 1.583036975 0.994271338 1.098205192 0.853387382 1.148692611 1.219838993 1 9.513635231 -6.920374307 21.0622871 1.098926686 3.517398843 0 0.192328126 5830.34017 1510784.791 0.025903615 13653.28651 1.20E-07 6.920374307 2.418472156 RNAQVNS(ph)MHR ddPTM_HeLa_Romidepsin_16h_R1 1 RNAQVNSMHR 10 1 K7EPH7 K7EPH7 ELAC1 1 0 RNAQVNS(1)MHR 75.739 0.021257 17301000 1252.5 1018.2 1303.4 815.05 848.55 939.14 839.2 853.95 1314 987.05 TRUE FALSE FALSE 1237.234048 1032.534246 1326.08513 909.2899159 805.2453271 879.1319849 910.4816271 878.6576959 1196.472549 961.4062987 1.286900294 1.073983234 1.379318122 0.945791511 0.837570264 0.914422951 0.947031061 0.913929623 1.244502507 1 9.909002445 -9.028943765 24.28902163 1.150504417 0.905229819 0.628247737 0.107138984 328.5211525 275687.874 0.019255404 0.03197622 9.36E-10 9.028943765 -0.245274599 RNDDIS(ph)ELEDLSELEDLKDAK ddPTM_HeLa_Romidepsin_16h_R1 1 RNDDISELEDLSELEDLKDAK 21 2 D6RAY8;Q9H4L7;Q9H4L7-2 D6RAY8 SMARCAD1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 1 0 RNDDIS(0.999)ELEDLS(0.001)ELEDLKDAK 87.457 0.0005999 0 762.11 727.71 647.75 782.62 646.98 377.69 439.26 367.11 633.33 821.63 TRUE FALSE FALSE 752.8211102 737.9547205 659.023817 873.1102067 613.9621964 353.5568279 476.5707334 377.7317486 576.6833786 800.2839342 0.940692519 0.922116125 0.823487501 1.091000543 0.76718046 0.441789236 0.595502063 0.471997166 0.72059847 1 9.644368137 -8.480023391 3.993532742 0.962052608 0.516505839 0.742161444 0.106506432 0.050224652 1.688112764 0.0103388 0.023372199 3.31E-09 8.480023391 -0.445546769 RNDGQASSS(ph)PPSESMGQAK ddPTM_HeLa_Romidepsin_16h_R1 1 RNDGQASSSPPSESMGQAK 19 1 Q5VYV7 Q5VYV7 SLX4IP Protein SLX4IP 1 0 RNDGQAS(0.013)S(0.177)S(0.807)PPS(0.002)ESMGQAK 69.98 0.014322 1327900 545.25 444.23 547.78 592.3 597.77 511.64 464.69 460.36 548.12 675.28 TRUE FALSE FALSE 538.6042833 450.4838816 557.3138811 660.7845129 567.2635663 478.9478552 504.160757 473.6797903 499.0947744 657.7361283 0.818875929 0.684900619 0.847321376 1.004634662 0.862448544 0.728176292 0.766509145 0.720166903 0.758806994 1 9.361365107 -16.52287875 0.191907525 1.894062301 0.767407577 0 0.115641233 40.72403692 0.484126922 13.55827934 0.108147704 3.00E-17 16.52287875 -1.126654725 RNEES(ph)DDDLDFDIDLEDTGGDHQMN ddPTM_HeLa_Romidepsin_16h_R1 2 RNEESDDDLDFDIDLEDTGGDHQMN 25 1 Q96MD7-1 Q96MD7-1 1 0 RNEES(1)DDDLDFDIDLEDTGGDHQMN;RNEES(1)DDDLDFDIDLEDTGGDHQMN ; 57.02 0.0066011 21104000 1177.13 1455.74 1145.56 1524.48 1603.85 1627.01 1671.52 1397.22 1342.54 1171.46 TRUE FALSE FALSE 1162.782687 1476.233946 1165.497991 1700.74755 1521.99955 1523.049312 1813.498867 1437.646356 1222.45986 1141.0253 1.019068277 1.293778451 1.021447983 1.490543242 1.333887644 1.334807661 1.589359032 1.259960104 1.071369635 1 10.15611507 -9.62692994 0.862247046 1.002272001 1.419402397 0.574953912 0.128504621 0.226558361 0.337122635 0.023206401 0.040734735 2.36E-10 9.62692994 0.417130396 RNEIDAEPPAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 RNEIDAEPPAKR 12 2 Q8TDN6 Q8TDN6 BRIX1 Ribosome biogenesis protein BRX1 homolog 0 1 ; RNEIDAEPPAK(1)R;RNEIDAEPPAK(1)R 174.9 9.24E-05 5604000 2012.76 2234.7 1970.99 1745.37 2193.6 2288.5 2168.3 1949.85 3469.8 3069.1 FALSE TRUE FALSE 1988.227707 2266.160165 2005.294254 1947.177892 2081.652407 2142.272236 2352.475348 2006.265833 3159.452398 2989.36434 0.665100497 0.758074262 0.670809586 0.651368542 0.69635286 0.716631361 0.786948354 0.671134598 1.056897734 1 11.54562303 -12.28121545 0.79512798 1.01945521 0.700867503 0.884465698 0.04667099 0.193797741 0.19844255 0.039844627 0.008534522 5.23E-13 12.28121545 -0.318587708 VAVATPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VAVATPAKK 9 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 1 ; VAVATPAK(1)K;VAVATPAK(1)K 141.52 0.0021843 446710000 3546.6 3969.3 4591.2 10868.2 29955 39149 38217 37056 1571.4 3121 FALSE TRUE FALSE 3503.372675 4025.17991 4671.10791 12124.83242 28426.28457 36647.50525 41463.15103 38128.1569 1430.850048 3039.91597 1.152457078 1.324108939 1.536591128 3.988541966 9.351009979 12.05543364 13.63957143 12.54250357 0.470687368 1 11.56981573 -8.711728911 1.541192508 1.079357005 13.12094734 0.99483219 0.375680026 0.014487467 0.06916416 0.047756711 0.120232783 1.94E-09 8.711728911 12.04159034 up RNEVLDR ddPTM_HeLa_Romidepsin_16h_R1 1 RNEVLDR 7 1 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 98.458 0.0030858 0 340.78 560 769.31 512.16 381.79 451.69 1168.9 139.04 850.8 525.22 FALSE FALSE TRUE 336.6264423 567.8836947 782.6995178 571.378349 362.3058316 422.8284668 1268.186337 143.062903 774.7023171 511.5747087 0.658020103 1.110069918 1.52998087 1.116901089 0.708216856 0.826523398 2.478985601 0.279652025 1.514348352 1 8.998801132 -10.09179871 6.715828703 0.839488299 1.190696834 0 0.590773907 0.480963148 30.01786926 0.086220567 0.105956029 8.09E-11 10.09179871 0.351208535 RNLDIERPTYTNLNR ddPTM_HeLa_Romidepsin_16h_R1 1 RNLDIERPTYTNLNR 15 2 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;F8VQQ4;Q9NY65;C9J2C0;Q9NY65-2;Q6PEY2;C9JDS9;Q71U36-2;Q71U36;P68363;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA1B;TUBA1A;TUBA8;TUBA3E;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 57.267 0.030512 23444000 721.86 743.21 801.74 1172.5 860.12 1001.7 790.14 798.65 628.08 632.84 FALSE FALSE TRUE 713.0616927 753.6729299 815.6939484 1308.069967 816.2248668 937.6946028 857.2544719 821.7576777 571.9029517 616.3987256 1.156818895 1.222703582 1.323321925 2.122116598 1.324183249 1.521246823 1.390746665 1.333159274 0.927813326 1 9.267720069 -9.786724644 2.511313105 1.078194234 1.527776713 0.481475344 0.225412637 0.184119797 2.384426855 0.036309968 0.050834239 1.63E-10 9.786724644 0.449582479 RNLEVLR ddPTM_HeLa_Romidepsin_16h_R1 2 RNLEVLR 7 1 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 0 0 ; ; 152.47 0.0070003 14440300 5854.6 5831.7 6919 8102.4 7575.7 7009.5 5528.8 5545 5593 4584.9 FALSE FALSE TRUE 5783.241883 5913.798826 7039.422293 9039.237611 7189.08376 6561.615572 5998.416134 5705.435826 5092.748072 4465.783637 1.295011661 1.324246606 1.57630169 2.024110066 1.609814614 1.469308884 1.343194526 1.27758895 1.140392927 1 12.12469764 -10.74075293 0.866825752 1.064435757 1.545703695 0.45078141 0.200428307 0.33764472 0.540927962 0.06093263 0.054612055 1.82E-11 10.74075293 0.481267938 RNPNPSSS(ph)SIFGR ddPTM_HeLa_Romidepsin_16h_R1 3 RNPNPSSSSIFGR 13 1 Q9ULJ8-3 Q9ULJ8-3 1 0 RNPNPS(0.265)S(0.265)S(0.456)S(0.015)IFGR;RNPNPS(0.344)S(0.071)S(0.582)S(0.004)IFGR;RNPNPS(0.033)S(0.033)S(0.93)S(0.005)IFGR ;; 77.24 0.013677 154756000 10105.6 9467 9024 9321.7 9608.2 8941.2 8081.5 8292.6 10548.2 9653.4 TRUE FALSE FALSE 9982.42906 9600.276674 9181.058935 10399.51881 9117.857701 8369.886176 8767.942408 8532.533297 9604.742574 9402.603276 1.061666516 1.021023263 0.976437978 1.106025481 0.969716304 0.890166896 0.93250158 0.907464991 1.021498227 1 13.19884453 -8.524600544 24.98156161 1.029873214 0.915232089 0.71697552 0.034195035 23.12909884 335579.6388 0.005204376 0.010469426 2.99E-09 8.524600544 -0.114641124 RNQEIQQGEDAFPPS(ph)SPLFAEPYK ddPTM_HeLa_Romidepsin_16h_R1 1 RNQEIQQGEDAFPPSSPLFAEPYK 24 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3;C9JCE0 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 RNQEIQQGEDAFPPS(0.5)S(0.5)PLFAEPYK 69.72 0.00040033 8539700 905.85 1212.9 1051 1368.6 1333.4 1310.6 1291.4 1240.6 951.88 1248.1 TRUE FALSE FALSE 894.8091518 1229.975238 1069.292214 1526.843971 1265.351622 1226.85689 1401.091484 1276.494804 866.7414688 1215.674182 0.736060011 1.011763889 0.879587829 1.255964792 1.040864107 1.00919877 1.152522201 1.050030364 0.712971849 1 10.2475409 -9.295308598 23.95370113 0.884884042 1.096018102 0.523971865 0.110702631 270.8396121 191548.1256 0.018376182 0.028071283 5.07E-10 9.295308598 0.21113406 RNQEIQQGEDAFPPSS(ph)PLFAEPYK ddPTM_HeLa_Romidepsin_16h_R1 1 RNQEIQQGEDAFPPSSPLFAEPYK 24 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3;C9JCE0 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 RNQEIQQGEDAFPPS(0.444)S(0.556)PLFAEPYK 77.03 0.00012448 6507500 773.91 829.67 869.11 1076.2 1061.4 1065.4 1059.3 1258 951.21 1028.1 TRUE FALSE FALSE 764.4772872 841.350116 884.236495 1200.635308 1007.232797 997.3243784 1149.276916 1294.398245 866.1313953 1001.389814 0.763416281 0.840182419 0.883009277 1.198968964 1.005834874 0.995940207 1.147681851 1.292601769 0.864929305 1 9.96778797 -9.275378299 24.01431437 0.880710227 1.115141102 0.632942956 0.097785356 308.9756798 532309.9801 0.018588455 0.02849217 5.30E-10 9.275378299 0.234430875 RNRHCS(ph)SHQS(ph)RS(ph)MK ddPTM_HeLa_Romidepsin_16h_R1 1 RNRHCSSHQSRSMK 14 3 E7ES88 E7ES88 CLK4 3 0 RNRHCS(0.967)S(0.036)HQS(0.997)RS(1)MK 52.93 0.025553 6938400 7464.4 7549.8 6719.6 5971.6 5281.8 4839.2 4436.2 5009.5 7600.2 7582.7 TRUE FALSE FALSE 7373.421022 7656.086283 6836.551819 6662.064489 5012.250037 4529.990738 4813.010717 5154.441979 6920.419077 7385.700361 0.998337417 1.036609381 0.925647059 0.902022038 0.678642484 0.613346131 0.651666123 0.697894814 0.937002415 1 12.85051902 -8.887401642 1.96430785 0.99883677 0.647296972 0.940500059 0.038010221 0.041406272 0.32355289 0.004876151 0.010155928 1.30E-09 8.887401642 -0.351539798 RNS(ph)FSENEK ddPTM_HeLa_Romidepsin_16h_R1 2 RNSFSENEK 9 1 Q9HCG8 Q9HCG8 CWC22 Pre-mRNA-splicing factor CWC22 homolog 1 0 RNS(0.999)FS(0.001)ENEK;RNS(0.983)FS(0.017)ENEK ; 133.42 0.010764 25481000 5219 5868.7 7801.5 5796 5246.8 5801.4 7763.8 2386.13 7640.7 6207.2 TRUE FALSE FALSE 5155.388821 5951.319713 7937.281835 6466.160791 4979.036217 5430.709263 8423.256978 2455.168907 6957.296656 6045.936049 0.852703168 0.984350424 1.312829274 1.069505324 0.823534384 0.898241268 1.393209738 0.406085821 1.150739373 1 12.56175 -6.121044142 11.45618626 0.960837439 0.668631714 0 0.265144275 0 0 0.030768995 0 7.57E-07 6.121044142 -0.292205726 RNS(ph)FTPLSSSNTIR ddPTM_HeLa_Romidepsin_16h_R1 4 RNSFTPLSSSNTIR 14 1 O60825 O60825 PFKFB2 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 0 RNS(0.985)FT(0.015)PLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(1)FTPLSSSNTIR;RNS(0.988)FT(0.012)PLSSSNTIR ;;; 177.39 6.73E-07 104705000 4481.45 4132.42 4577.61 5171.56 5788.74 6471.12 5603.73 5339.5 4542.31 4214.36 TRUE FALSE FALSE 4426.828364 4190.596317 4657.281382 5769.5201 5493.318997 6057.636317 6079.710686 5493.990008 4136.034417 4104.87032 1.078433183 1.020883972 1.134574547 1.405530419 1.338244224 1.475719291 1.481096895 1.338407691 1.007591981 1 12.00312093 -9.34945372 2.524104742 1.036618355 1.417838184 0.929605338 0.050049413 0.054061046 0.672931475 0.008283949 0.013535746 4.47E-10 9.34945372 0.381219829 RNS(ph)LEGYSR ddPTM_HeLa_Romidepsin_16h_R1 2 RNSLEGYSR 9 1 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 RNS(1)LEGYSR;RNS(1)LEGYSR ; 120.03 0.003994 25126200 4240 4433.5 3808.3 3451.9 3056.6 3336.1 3621.9 3375.6 4745.4 4720.1 TRUE FALSE FALSE 4188.321249 4495.914929 3874.581864 3851.02492 2900.610296 3122.933977 3929.544096 3473.26766 4320.959539 4597.471122 0.91100545 0.977910423 0.84276372 0.837639828 0.630914305 0.679272125 0.854718603 0.755473513 0.939855722 1 12.1666248 -9.393226283 1.726436923 0.958900537 0.738904856 0.701104631 0.063867183 0.154104989 0.903251386 0.011260886 0.019091372 4.04E-10 9.393226283 -0.219995681 RNS(ph)LTGEEGQLAR ddPTM_HeLa_Romidepsin_16h_R1 1 RNSLTGEEGQLAR 13 1 Q9BX95 Q9BX95 SGPP1 Sphingosine-1-phosphate phosphatase 1 1 0 RNS(0.998)LT(0.002)GEEGQLAR 110.6 0.0019719 8103700 248.78 374.85 292.04 206.91 300.98 257.82 199.43 380.12 192.03 394.23 TRUE FALSE FALSE 245.7477737 380.1271481 297.1228337 230.8339077 285.6198675 241.3461341 216.3695792 391.1181725 174.8543559 383.9878478 0.639988414 0.989945777 0.773781867 0.601148992 0.743825278 0.628525448 0.563480278 1.018569142 0.455364296 1 8.584916844 -9.520565025 24.96119643 0.839365629 0.698870456 0 0.193065448 145.2547931 1567062.11 0.027336429 0.039036911 3.02E-10 9.520565025 -0.140495173 RNS(ph)SEASSGDFLDLK ddPTM_HeLa_Romidepsin_16h_R1 6 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 0 RNS(0.864)S(0.136)EASSGDFLDLK;RNS(0.856)S(0.128)EAS(0.016)SGDFLDLK;RNS(0.87)S(0.127)EAS(0.001)S(0.002)GDFLDLK;RNS(0.978)S(0.022)EASSGDFLDLK;RNS(0.764)S(0.229)EAS(0.002)S(0.005)GDFLDLK;RNS(0.49)S(0.49)EAS(0.004)S(0.015)GDFLDLK ;;;;; 176.44 1.91E-08 1808370000 27759.8 28627.84 28810.14 19946.89 44884.27 57812.37 53077.94 62003.2 30383.2 30222.12 TRUE FALSE FALSE 27421.45288 29030.86348 29311.5684 22253.24327 42593.65822 54118.34614 57586.3789 63797.16477 27665.6505 29436.94497 0.931531887 0.98620504 0.995740843 0.75596307 1.446945607 1.838449819 1.95626207 2.167248158 0.939827503 1 14.84534033 -8.385359575 2.066426184 0.95724433 2.035652654 0.953396766 0.104356276 0.044456735 0.367015204 0.014576764 0.040729364 4.12E-09 8.385359575 1.078408323 up RNS(ph)SSPVS(ph)PASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 0 RNS(0.995)S(0.144)S(0.347)PVS(0.503)PAS(0.01)VPGQR 76.574 0.027863 4741400 1224.4 1324.3 1133.9 1250.4 902.04 909.49 951.32 965.55 1123.9 1462.1 TRUE FALSE FALSE 1209.476542 1342.94353 1153.635054 1394.977131 856.0055328 851.3765242 1032.125097 993.4866659 1023.375569 1424.114431 0.849283257 0.943002543 0.810071879 0.979540057 0.601079179 0.597828732 0.72474871 0.697617161 0.718604872 1 10.47584936 -8.76106993 25 0.92162535 0.656171317 0.586947528 0.090392608 3.73469404 252687.259 0.011118704 0.021185598 1.73E-09 8.76106993 -0.265454033 RNS(ph)TTFPSR ddPTM_HeLa_Romidepsin_16h_R1 4 RNSTTFPSR 9 1 Q96E09 Q96E09 FAM122A Protein FAM122A 1 0 RNS(0.848)T(0.116)T(0.036)FPSR;RNS(0.995)T(0.004)T(0.001)FPSR;RNS(1)TTFPSR;RNS(0.971)T(0.022)T(0.007)FPSR ;;; 110.93 0.0055212 21747100 1918.51 1617.26 1496.15 1340.87 2008.87 2798.34 2259.45 2391.52 1756.84 1742.98 TRUE FALSE FALSE 1895.126462 1640.027829 1522.189863 1495.907698 1906.349868 2619.535105 2451.367627 2460.714858 1599.70383 1697.697128 1.116292436 0.966030867 0.896620391 0.881139323 1.122903394 1.542993189 1.443936958 1.449442787 0.942278692 1 10.72936339 -8.363027742 4.450150546 1.024206267 1.474402254 0.886007319 0.0803558 0.06434836 2.135939741 0.013226838 0.030682002 4.33E-09 8.363027742 0.450195988 RNS(ph)VDTATSSSLSTPSEPLSPTSSLGEERN ddPTM_HeLa_Romidepsin_16h_R1 1 RNSVDTATSSSLSTPSEPLSPTSSLGEERN 30 2 P13807-2;P13807 P13807-2 GYS1 "Glycogen [starch] synthase, muscle" 1 0 RNS(0.749)VDT(0.032)AT(0.032)S(0.032)S(0.032)S(0.032)LS(0.039)T(0.039)PS(0.014)EPLS(0.001)PTSSLGEERN 49.972 0.01749 6241200 569.44 597.41 457.26 470.91 680.41 1116 847.02 919.28 783.52 633.16 TRUE FALSE FALSE 562.4994463 605.8203537 465.2184185 525.3588299 645.6861387 1044.691202 918.9658577 945.8779164 713.4400088 616.7104119 0.912096562 0.982341699 0.754354734 0.851872807 1.046984332 1.693973673 1.490109199 1.533747279 1.156847679 1 9.268449393 -8.356090728 4.788189667 0.936724203 1.562756159 0.866591422 0.11087782 0.045102952 1.710243124 0.013157872 0.03031328 4.40E-09 8.356090728 0.626031956 RNS(ph)VERPAEPVAGAATPSLVEQQK ddPTM_HeLa_Romidepsin_16h_R1 1 RNSVERPAEPVAGAATPSLVEQQK 24 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 RNS(0.999)VERPAEPVAGAAT(0.001)PSLVEQQK 57.768 0.0032806 12289000 1380.1 1301.7 1293.6 1299.1 1257.8 1667.9 1333.4 1404.3 1564.4 1263.8 TRUE FALSE FALSE 1363.27881 1320.025367 1316.114565 1449.308054 1193.609773 1561.326573 1446.658963 1444.931205 1424.476146 1230.966294 1.10748671 1.072348913 1.069171895 1.17737428 0.969652685 1.268374756 1.175222238 1.173818659 1.157201585 1 10.26557554 -4.000000009 0.057890734 0.807013459 1.741763913 0.079627426 0.082842135 237.7085202 1.041155715 3.581053922 19.04298344 1.00E-04 4.000000009 0.934750454 RNS(ph)VTPLASPEPTK ddPTM_HeLa_Romidepsin_16h_R1 1 RNSVTPLASPEPTK 14 1 Q9H178;Q5W015;Q5VX20;A0A1W2PR17;Q16875-3;Q16875-2;Q16875;Q16875-4 Q9H178 PFKFB3 "6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3;6-phosphofructo-2-kinase;Fructose-2,6-bisphosphatase" 1 0 RNS(0.938)VT(0.062)PLASPEPTK 78.401 0.0018949 0 2993.4 2653.2 2857.9 2420 3727.8 4488.5 4265.4 4515 3097.6 3043.4 TRUE FALSE FALSE 2956.915289 2690.551819 2907.640551 2699.811786 3537.556456 4201.699336 4627.70297 4645.634402 2820.542898 2964.332029 0.997498006 0.907641854 0.980875463 0.91076565 1.193373894 1.417418594 1.561128417 1.567177481 0.951493581 1 11.53349133 -8.307655721 1.916621972 0.984025357 1.56128727 0.968089363 0.045409161 0.041271391 0.290094092 0.006685051 0.020612458 4.92E-09 8.307655721 0.577261914 RNSS(ph)EASSGDFLDLK ddPTM_HeLa_Romidepsin_16h_R1 8 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 0 RNS(0.1)S(0.9)EASSGDFLDLK;RNS(0.257)S(0.738)EAS(0.002)S(0.002)GDFLDLK;RNS(0.328)S(0.631)EAS(0.007)S(0.034)GDFLDLK;RNS(0.459)S(0.5)EAS(0.014)S(0.027)GDFLDLK;RNS(0.126)S(0.873)EAS(0.001)SGDFLDLK;RNS(0.144)S(0.782)EAS(0.043)S(0.03)GDFLDLK;RNS(0.114)S(0.789)EAS(0.011)S(0.086)GDFLDLK;RNS(0.32)S(0.679)EAS(0.001)SGDFLDLK ;;;;;;; 167.69 9.13E-06 1297674900 21576.87 22483.19 20637.62 16590.2 30225.72 37667.8 35160.72 38795.6 23659.24 23436.13 TRUE FALSE FALSE 21313.88281 22799.70894 20996.80912 18508.43698 28683.18872 35260.94915 38147.27068 39918.08948 21543.09832 22827.25596 0.933703238 0.99879324 0.919813102 0.810804286 1.256532488 1.544686282 1.671128178 1.748702934 0.943744546 1 14.47846982 -8.34778611 2.117875893 0.956735508 1.695154518 0.956556573 0.06878606 0.045480614 0.393383057 0.010275956 0.029233232 4.49E-09 8.34778611 0.738419009 RNSS(ph)SPVSPAS(ph)VPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 2 0 RNS(0.243)S(0.741)S(0.016)PVS(0.124)PAS(0.876)VPGQR 133.9 0.0014745 4049700 1982.2 2043.8 1353.1 1403.2 1324.4 1062 968.1 1122.2 1994.4 1891.2 TRUE FALSE FALSE 1958.040184 2072.57267 1376.650138 1565.444586 1256.810926 994.1416274 1050.33039 1154.669086 1816.015869 1842.066351 1.062958553 1.125134645 0.747340147 0.849830727 0.682283201 0.539688284 0.570191399 0.626833602 0.985858011 1 10.84710931 -9.121922724 1.084600823 1.036101884 0.576467111 0.845616199 0.080087888 0.12283142 0.285141132 0.013439959 0.030229348 7.55E-10 9.121922724 -0.459634774 RNSS(ph)SPVSPASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 RNS(0.026)S(0.751)S(0.223)PVSPASVPGQR 173.19 9.52E-06 3574700 1322.6 1296.2 1205.3 1914.3 791.15 716.01 581.38 761.51 1401.4 1285.7 TRUE FALSE FALSE 1306.479642 1314.447938 1226.277741 2135.640373 750.7746633 670.2592718 630.7624027 783.5430904 1276.055274 1252.297329 1.043266333 1.049629275 0.979222516 1.705378047 0.599517899 0.53522375 0.50368422 0.62568455 1.018971489 1 10.29036142 -8.562815777 24.99999382 1.066304769 0.552682066 0.633494722 0.207720611 75.0782698 46997.62403 0.028706223 0.057412506 2.74E-09 8.562815777 -0.513622703 RNSSEASSGDFLDLK ddPTM_HeLa_Romidepsin_16h_R1 3 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" 0 0 ;; ;; 118.19 0.0023796 33556900 14406.2 11046.5 12302.9 9114.7 18645.8 21914.2 20447.9 23085.8 14141.4 14274.1 FALSE FALSE TRUE 14230.61169 11202.01292 12517.02681 10168.5845 17694.23525 20513.95334 22184.74412 23753.7512 12876.55777 13903.25682 1.023545193 0.805711429 0.900294584 0.731381476 1.272668374 1.475478271 1.595650889 1.708502655 0.926154061 1 13.76313525 -8.358085651 2.309475787 0.968259988 1.623240239 0.881257435 0.113027388 0.082774951 0.853550796 0.017658445 0.048125676 4.38E-09 8.358085651 0.654980251 RNSSS(ph)PVSPASVPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RNSSSPVSPASVPGQR 16 1 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 RNS(0.181)S(0.181)S(0.637)PVSPASVPGQR 109.55 0.0049761 1983300 1223.9 1093.4 733.29 1381.6 421.89 435.38 658.53 620.12 945.27 793.07 TRUE FALSE FALSE 1208.982636 1108.792914 746.0526048 1541.347093 400.359379 407.5606231 714.4655218 638.0621938 860.7226837 772.4659271 1.565095098 1.435393944 0.965806489 1.995359327 0.518287429 0.527609839 0.924915257 0.82600691 1.114253268 1 9.593327488 -8.719928032 24.99990159 1.307554954 0.703069874 0.515890587 0.305573983 105.1579527 63330.14302 0.047101124 0.094201524 1.91E-09 8.719928032 -0.604485079 RNT(ph)IDSTSSFSQFR ddPTM_HeLa_Romidepsin_16h_R1 1 RNTIDSTSSFSQFR 14 1 Q8TDN4-2;Q8TDN4;Q8TDN4-4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 0 RNT(0.999)IDSTSSFSQFR 115.83 0.00068087 0 1018.6 834.68 1083.8 1070.4 1292 883.41 869.88 897.03 1199.5 931.12 TRUE FALSE FALSE 1006.184911 846.4306469 1102.663084 1194.164684 1226.064419 826.9629521 943.7675855 922.9841478 1092.213716 906.9293682 1.109441316 0.933292797 1.215820243 1.316711892 1.351885232 0.911827294 1.040618618 1.017702348 1.204298542 1 9.824846388 -11.83193009 0.606127749 0.996325732 1.12097646 0 0.153134488 1.944116688 1.294004349 0.12413988 0.036440907 1.47E-12 11.83193009 0.124650728 RNTIDSTS(ph)SFSQFR ddPTM_HeLa_Romidepsin_16h_R1 1 RNTIDSTSSFSQFR 14 1 Q8TDN4-2;Q8TDN4;Q8TDN4-4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 0 RNT(0.002)IDS(0.001)T(0.006)S(0.702)S(0.22)FS(0.069)QFR 106.76 0.010905 6371400 1326.6 1210.8 1429.6 1418.7 1542.3 1243.4 921.5 1101.1 1158.7 1137.6 TRUE FALSE FALSE 1310.430889 1227.845674 1454.481588 1582.736769 1463.590676 1163.950753 999.772187 1132.958591 1055.06297 1108.044988 1.182651339 1.108118973 1.312655717 1.428404791 1.320876581 1.050454418 0.902284833 1.022484289 0.952184236 1 10.11380074 -5.824822458 9.272420082 1.122599777 0.790902232 0 0.167513117 0 0 0.023670103 0 1.50E-06 5.824822458 -0.331697544 RNVPQEESLEDS(ph)DVDADFK ddPTM_HeLa_Romidepsin_16h_R1 2 RNVPQEESLEDSDVDADFK 19 1 O00505 O00505 KPNA3 Importin subunit alpha-4 1 0 RNVPQEESLEDS(1)DVDADFK;RNVPQEES(0.001)LEDS(0.999)DVDADFK ; 162.44 3.43E-07 8569400 5717.5 5628.8 5259.7 4821.4 5126.5 5027.6 4837.6 5084.6 5750.9 5546.3 TRUE FALSE FALSE 5647.812911 5708.042394 5351.242872 5378.872953 4864.875575 4706.352586 5248.505623 5231.714879 5236.525101 5402.206326 1.045464125 1.056613178 0.990566178 0.99568077 0.900534945 0.871190825 0.971548531 0.968440404 0.969330822 1 12.39933303 -8.959529544 3.166921048 1.022696626 0.927346451 0.525471474 0.037282463 0.131059645 2.708086641 0.005541223 0.01034596 1.10E-09 8.959529544 -0.095350175 RNWNLY(ph)PACLREMS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RNWNLYPACLREMSR 15 2 H7C3J3;Q9BV44 H7C3J3 THUMPD3 THUMP domain-containing protein 3 2 0 RNWNLY(1)PACLREMS(1)R 60.55 0.0038139 0 1497.3 1688.3 1438.4 1362.4 1620.7 1430.2 1508.2 1395.8 1944.5 1814.8 TRUE FALSE FALSE 1479.050332 1712.067932 1463.434749 1519.927098 1537.989631 1338.814836 1636.30647 1436.185271 1770.57905 1767.651234 0.836731988 0.968555277 0.827897902 0.859856893 0.870075274 0.757397619 0.925695317 0.812482261 1.001656331 1 10.78761794 -14.6251277 0.296209896 1.344027779 0.843381183 0.539992792 0.054024203 9.41958153 0.342214559 1.974559976 0.023643736 2.37E-15 14.6251277 -0.500646596 RNY(ph)MPLAFS(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 1 RNYMPLAFSDK 11 1 E5RK21;H9KVE0;Q9UJW0-2;Q9UJW0 E5RK21 DCTN4 Dynactin subunit 4 2 0 RNY(1)MPLAFS(1)DK 62.408 0.0036711 0 486.65 359.75 315.01 410.42 449.63 478.16 311.65 474.82 518.72 366.39 TRUE FALSE FALSE 480.7185226 364.8145699 320.4926169 457.8746915 426.6837033 447.6071192 338.1215432 488.5581676 472.324384 356.871135 1.347036719 1.022258553 0.898062593 1.28302529 1.195624026 1.254254198 0.94746117 1.369004438 1.323515235 1 8.479259406 -7.204730939 21.21157554 1.14503241 1.369014316 0.161159122 0.155669241 13900.26648 5198199.212 0.023048135 31.8432633 6.24E-08 7.204730939 0.223981906 RPAAAAAAGSAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 6 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 1 0 RPAAAAAAGS(0.022)AS(0.978)PR;RPAAAAAAGSAS(1)PR;RPAAAAAAGS(0.001)AS(0.999)PR;RPAAAAAAGS(0.004)AS(0.996)PR;RPAAAAAAGS(0.005)AS(0.995)PR;RPAAAAAAGS(0.003)AS(0.997)PR ;;;;; 170.79 1.52E-05 227108600 4902.86 4966.75 5098.88 4683.3 5046.65 5956.51 4721.73 5101.4 5304.7 5561.23 TRUE FALSE FALSE 4843.102056 5036.672037 5187.623868 5224.805182 4789.100619 5575.908235 5122.793628 5249.00096 4830.234346 5416.748443 0.894097651 0.929833107 0.957700717 0.964564856 0.884128305 1.029382903 0.945732238 0.969031702 0.891722109 1 12.40321138 -8.250890626 24.99785185 0.945279564 0.977817267 0.187036111 0.040929506 1461.986003 3464528.845 0.006591964 0.016600179 5.61E-09 8.250890626 0.032537703 RPAAAAAAGSASPR ddPTM_HeLa_Romidepsin_16h_R1 1 RPAAAAAAGSASPR 14 1 Q96S55-2;Q96S55 Q96S55-2 WRNIP1 ATPase WRNIP1 0 0 139.77 0.00064701 1291400 450.86 287.15 834.12 414.9 278.12 370.29 187.11 308.6 379.79 475.18 FALSE FALSE TRUE 445.3647449 291.1925052 848.6375087 462.8726902 263.9264986 346.6296641 203.0031187 317.5288541 345.8206312 462.8347551 0.962254325 0.629150041 1.833564786 1.000081962 0.570239153 0.748927474 0.4386082 0.686052313 0.747179479 1 8.854353393 -8.77437097 10.44329143 1.024500176 0.608425128 0.306158235 0.308045144 0.24221919 185.4480897 0.042203635 0.078230284 1.68E-09 8.77437097 -0.416075048 RPAEATSSPT(ph)SPERPR ddPTM_HeLa_Romidepsin_16h_R1 1 RPAEATSSPTSPERPR 16 2 Q9BU76 Q9BU76 MMTAG2 Multiple myeloma tumor-associated protein 2 1 0 RPAEATS(0.001)S(0.002)PT(0.995)S(0.002)PERPR 107.91 0.016362 44140000 544.72 477.79 505.82 443.18 507.32 546.6 525.78 483.88 597.3 376.6 TRUE FALSE FALSE 538.0807431 484.5163402 514.6235849 494.4225568 481.4295673 511.6740241 570.4397401 497.8803044 543.875992 366.8158777 1.466895998 1.320870686 1.402947953 1.347876651 1.312455639 1.394906969 1.55511191 1.357303036 1.482694793 1 8.518912277 -12.33888161 0.829365491 0.972799943 1.399754116 0 0.163939734 0.237551046 0.262150439 0.068019656 0.0139774 4.58E-13 12.33888161 0.426954173 RPAEDMEEEQAFK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 RPAEDMEEEQAFKR 14 2 P61978-3;P61978;P61978-2;Q5T6W2;S4R457 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 1 ; RPAEDMEEEQAFK(1)R;RPAEDMEEEQAFK(1)R 136.33 9.67E-06 22582000 267.44 257.448 277.6 0 420.35 403.65 286.62 348.54 542.09 354.55 FALSE TRUE FALSE 264.1803384 261.0723597 282.4315116 0 398.897971 377.8580677 310.9654956 358.624455 493.6041127 345.3387399 0.764989003 0.755989206 0.817839063 0 1.15509187 1.094166463 0.900465137 1.038471546 1.429333161 1 8.431868374 -5.459876688 17.71612249 0.855928495 0.931113795 0 0.358250372 0 0 0.040126175 0 3.47E-06 5.459876688 0.0751853 RPAEGPPTNPPAPGGGS(ph)SSSK ddPTM_HeLa_Romidepsin_16h_R1 1 RPAEGPPTNPPAPGGGSSSSK 21 1 A0A087WZ13;E9PAU2 A0A087WZ13 RAVER1 1 0 RPAEGPPTNPPAPGGGS(0.25)S(0.25)S(0.25)S(0.25)K 77.053 0.0011582 2633400 939.95 888.68 823.45 957.11 889.53 798.24 681.91 1042.6 1044.6 872.56 TRUE FALSE FALSE 928.4935279 901.1908604 837.7818018 1067.775562 844.1339648 747.2350402 739.8314184 1072.765986 951.1683598 849.8907654 1.092485724 1.06036081 0.98575233 1.256368 0.993226423 0.879213036 0.870501773 1.262239843 1.119165425 1 9.731133617 -8.5524891 24.99960323 1.057357863 0.981566729 0.065586853 0.124368232 407.2338951 343820.2126 0.017084066 0.03416847 2.80E-09 8.5524891 -0.075791134 RPAEGPPTNPPAPGGGSSSS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RPAEGPPTNPPAPGGGSSSSK 21 1 A0A087WZ13;E9PAU2 A0A087WZ13 RAVER1 1 0 RPAEGPPTNPPAPGGGS(0.223)S(0.223)S(0.223)S(0.33)K 87.468 0.00014957 0 762.55 846.68 741.58 831.03 574.59 871.4 497.6 613.3 735.08 800.12 TRUE FALSE FALSE 753.2557473 858.5995833 754.4868888 927.1175987 545.2665282 815.7203523 539.8661316 631.0448679 669.3326038 779.3327671 0.9665393 1.10171113 0.968119038 1.189629947 0.699658158 1.046690691 0.692728645 0.809724542 0.858853409 1 9.606095666 -8.028751205 1.125049676 0.999285313 0.748269478 0.265358308 0.134696829 0.545336632 1.091820935 0.017580503 0.116469213 9.36E-09 8.028751205 -0.251015835 RPAGAAGGGVAAR ddPTM_HeLa_Romidepsin_16h_R1 1 RPAGAAGGGVAAR 13 1 B3EWF7 B3EWF7 EPM2A "Laforin, isoform 9" 0 0 79.82 0.026257 1042700 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 RPAS(ph)TAGLPTAGLPTATGLPSGAPPGVATIR ddPTM_HeLa_Romidepsin_16h_R1 1 RPASTAGLPTAGLPTATGLPSGAPPGVATIR 31 1 Q765P7;A0A087WXN9 Q765P7 MTSS1L MTSS1-like protein 1 0 RPAS(0.373)T(0.342)AGLPT(0.095)AGLPT(0.034)AT(0.156)GLPSGAPPGVATIR 53.866 0.0017686 9389100 449.7 438.89 418.62 594.39 275.11 252.27 303.03 330.49 366.81 488.55 TRUE FALSE FALSE 444.2188834 445.0687049 425.9059055 663.1161685 261.0701101 236.1507612 328.7693606 340.0522067 334.0015949 475.8574006 0.933512609 0.935298483 0.895028437 1.393518663 0.548630976 0.496263714 0.690898913 0.714609474 0.701894295 1 8.894385498 -8.705579297 24.99999971 0.985524424 0.609882735 0.518499499 0.171675834 42.73769287 19126.81512 0.020189173 0.040378331 1.97E-09 8.705579297 -0.375641689 RPAS(ph)VSSSAAVEHEQR ddPTM_HeLa_Romidepsin_16h_R1 2 RPASVSSSAAVEHEQR 16 1 Q7Z5L9;Q7Z5L9-2 Q7Z5L9 IRF2BP2 Interferon regulatory factor 2-binding protein 2 1 0 RPAS(0.968)VS(0.027)S(0.005)SAAVEHEQR;RPAS(0.825)VS(0.13)S(0.041)S(0.003)AAVEHEQR ; 112.14 0.00089494 51152000 5201 4148.4 4075.2 2423.31 2822.5 2083.8 2717.65 2487.4 5379.7 4699.4 TRUE FALSE FALSE 5137.608211 4206.801284 4146.127147 2703.504504 2678.457293 1950.651905 2948.487123 2559.368995 4898.526158 4577.308911 1.122408016 0.919055577 0.905800161 0.590631866 0.585159828 0.426156928 0.644152969 0.559142729 1.070176004 1 12.16028394 -9.415692498 1.611393273 1.054263237 0.544969546 0.916173783 0.067975272 0.074529447 0.38194169 0.012209403 0.020755046 3.84E-10 9.415692498 -0.509293691 K(ac)QLTYK(ac)NN ddPTM_HeLa_Romidepsin_16h_R1 1 KQLTYKNN 8 2 Q07326 Q07326 PIGF Phosphatidylinositol-glycan biosynthesis class F protein 0 2 K(1)QLTYK(1)NN 48.796 0.027886 0 723.72 525.23 733.01 2880 6116.6 8762.4 7765.6 8822.5 552.89 612.72 FALSE TRUE FALSE 714.8990223 532.6242017 745.7677316 3212.999151 5804.447078 8202.510919 8425.20987 9077.765118 503.4381337 596.8014461 1.197884199 0.892464663 1.249607782 5.383698669 9.725926631 13.74412038 14.11727456 15.21069558 0.843560512 1 9.221107221 -8.710707097 1.356876738 1.022678623 14.79891924 0.995931668 0.375798202 0.017358376 0.063576875 0.05924647 0.159262546 1.95E-09 8.710707097 13.77624062 up RPDDVPLSLS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 2 RPDDVPLSLSPSKR 14 2 F8WDB4;Q9UFC0 F8WDB4 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 1 0 RPDDVPLS(0.006)LS(0.497)PS(0.497)KR;RPDDVPLS(0.131)LS(0.737)PS(0.131)KR ; 106.87 0.0063819 277660000 6239.6 5865.4 5926.4 5483.1 5481.6 5183.9 4621.9 5244.9 6127.8 6136.3 TRUE FALSE FALSE 6163.549355 5947.973255 6029.546506 6117.081821 5201.853497 4852.66552 5014.484071 5396.652906 5579.714221 5976.878041 1.031232244 0.995163899 1.008812036 1.023457695 0.870329537 0.811906398 0.83898049 0.902921704 0.933549954 1 12.54517639 -8.721546475 5.304715021 1.013633746 0.84942855 0.799410653 0.034553901 0.037806591 2.527081323 0.003512186 0.007004537 1.90E-09 8.721546475 -0.164205197 (ac)TTTTTFK(ac)GVDPNSR ddPTM_HeLa_Romidepsin_16h_R1 1 TTTTTFKGVDPNSR 14 1 Q9UK76;J3KT51;Q9UK76-2;F2Z3M5 Q9UK76 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 1 TTTTTFK(1)GVDPNSR 71.085 6.07E-07 1059400 328.61 421.14 369.46 1439.5 2698.1 3174.5 3295.6 3776 292.38 381.73 FALSE TRUE FALSE 324.6047749 427.06882 375.8902963 1605.941763 2560.405889 2971.659695 3575.528182 3885.252602 266.2288005 371.8125996 0.873033284 1.148613093 1.010967075 4.319223622 6.886280594 7.992358781 9.616479339 10.44949151 0.716029529 1 8.538431849 -8.709492669 1.085002784 0.876541129 10.02766735 0.985444214 0.455480682 0.040450679 0.091918194 0.075158318 0.232983242 1.95E-09 8.709492669 9.151126216 up RPDHSGGS(ph)PSPPTSEPAR ddPTM_HeLa_Romidepsin_16h_R1 2 RPDHSGGSPSPPTSEPAR 18 1 Q8TAD8 Q8TAD8 SNIP1 Smad nuclear-interacting protein 1 1 0 RPDHS(0.063)GGS(0.902)PS(0.034)PPT(0.001)S(0.001)EPAR;RPDHS(0.025)GGS(0.972)PS(0.003)PPTSEPAR ; 119.43 0.00046046 16322000 1508.03 1074.96 1147.28 988.35 1948.2 2038.26 1754.28 2088.25 1542.55 1325.48 TRUE FALSE FALSE 1489.64955 1090.093315 1167.247927 1102.627677 1848.776084 1908.021764 1903.288499 2148.670219 1404.580465 1291.043839 1.153833438 0.844350349 0.904111768 0.854059052 1.432001013 1.477890763 1.474224533 1.664289124 1.087941728 1 10.33432227 -8.64959393 5.657009606 1.028140643 1.519280423 0.843951892 0.112362041 0.075145018 3.461624912 0.019007734 0.038374276 2.24E-09 8.64959393 0.49113978 RPDPDS(ph)DEDEDYER ddPTM_HeLa_Romidepsin_16h_R1 2 RPDPDSDEDEDYER 14 1 H0Y6J6;Q5W012;Q96I25;Q5W011;Q5W010 H0Y6J6 RBM17 Splicing factor 45 1 0 RPDPDS(1)DEDEDYER;RPDPDS(1)DEDEDYER ; 166.3 0.0001426 138583000 4641.1 4175.1 4537 3399.1 4226 3907.3 3782 4085.1 5182.4 4299.4 TRUE FALSE FALSE 4584.532488 4233.877167 4615.964582 3792.119935 4010.331451 3657.63614 4103.242986 4203.295923 4718.873164 4187.700968 1.094761188 1.011026623 1.102267 0.905537421 0.957645133 0.873423429 0.979831897 1.00372399 1.126841004 1 12.03194271 -9.255285908 24.99868092 1.046741111 0.942854781 0.571716413 0.051739469 321.3586466 1305528.762 0.007685826 0.01253588 5.56E-10 9.255285908 -0.10388633 RPDPDS(ph)DEDEDYERER ddPTM_HeLa_Romidepsin_16h_R1 2 RPDPDSDEDEDYERER 16 2 H0Y6J6;Q5W012;Q96I25;Q5W011;Q5W010 H0Y6J6 RBM17 Splicing factor 45 1 0 RPDPDS(1)DEDEDYERER;RPDPDS(1)DEDEDYERER ; 108.47 0.0031676 126069000 5344.3 4663.7 4334 6259.9 4813.4 4656.9 4413.5 4289.6 5147.2 4729.6 TRUE FALSE FALSE 5279.161616 4729.355691 4409.431452 6983.699092 4567.754237 4359.339119 4788.38258 4413.712808 4686.821541 4606.72431 1.145968645 1.026620082 0.957172853 1.515979386 0.991540611 0.946299111 1.039433284 0.958102224 1.017387025 1 12.16952555 -8.567971471 24.99999973 1.092361178 0.984059486 0.14028312 0.149746959 224.8314076 124648.6355 0.021602068 0.04320415 2.70E-09 8.567971471 -0.108301692 RPDQQLQGEGK ddPTM_HeLa_Romidepsin_16h_R1 2 RPDQQLQGEGK 11 1 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 0 ; ; 136.93 1.50E-05 4689300 7729.7 7563.3 7865 7295.1 7667.5 7412.1 7664.2 6029.1 7634.1 7719.8 FALSE FALSE TRUE 7635.487443 7669.776336 8001.887026 8138.593786 7276.198864 6938.490731 8315.196957 6203.542496 6951.286976 7519.238483 1.015460204 1.020020359 1.064188487 1.082369419 0.967677629 0.922765084 1.105856261 0.825022708 0.924466885 1 12.87637084 -7.242703942 24.74083874 1.013732272 0.825022519 0.476230463 0.058599651 2060.868083 2721407.916 0.006709094 0.308420401 5.72E-08 7.242703942 -0.188709753 RPEGPGAQAPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 0 RPEGPGAQAPS(0.5)S(0.5)PR 69.805 0.017207 532330000 1857.9 1869.2 1303 1607.6 1920.7 1956.2 1342.3 1631.9 2017.9 1785 TRUE FALSE FALSE 1835.2552 1895.514647 1325.678168 1793.478276 1822.679512 1831.205133 1456.314928 1679.116452 1837.41397 1738.625443 1.055578249 1.090237495 0.76248635 1.03154954 1.048345128 1.053248784 0.837624305 0.965772392 1.056819902 1 10.76373145 RPEGPGAQAPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 1 0 RPEGPGAQAPS(0.01)S(0.99)PR;RPEGPGAQAPS(0.039)S(0.961)PR;RPEGPGAQAPS(0.002)S(0.998)PR;RPEGPGAQAPS(0.079)S(0.921)PR ;;; 177.39 6.73E-07 663760400 6399.14 5668.77 6019.83 5845.31 6518.23 5901.13 5280.62 5938.24 6079.35 5858.1 TRUE FALSE FALSE 6321.14482 5748.575093 6124.602616 6521.172245 6185.5804 5524.066838 5729.155731 6110.053605 5535.59771 5705.905718 1.107824968 1.007478107 1.073379568 1.142881178 1.084066353 0.968131461 1.004074728 1.070829752 0.970152327 1 12.47824019 -8.278336735 24.59925821 1.05938469 1.013318246 0.101480314 0.054535565 1052.707747 1532536.173 0.008055684 0.018060794 5.27E-09 8.278336735 -0.046066443 RPEGPGAQAPSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPEGPGAQAPSSPR 14 1 P40222 P40222 TXLNA Alpha-taxilin 0 0 ; ; 157.37 0.00012947 1953400 1028.34 752.39 851.1 679.47 1222.19 931.01 729.2 840.13 787.53 973.04 FALSE FALSE TRUE 1015.806197 762.9821662 865.9130385 758.0335184 1159.817084 871.5214657 791.1382298 864.437836 717.0913444 947.7602805 1.071796548 0.805037077 0.913641409 0.799815664 1.223745189 0.919558968 0.834745079 0.912084895 0.756616793 1 9.88837839 -10.29002781 24.91730661 1.033903928 0.919899638 0 0.143791806 874.4889805 762190.5941 0.019436571 0.022228674 5.13E-11 10.29002781 -0.114004289 RPEPSTLENITDDKYATVSS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 RPEPSTLENITDDKYATVSSPSK 23 2 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 0 RPEPSTLENIT(0.014)DDKY(0.002)AT(0.035)VS(0.241)S(0.613)PS(0.096)K 75.483 0.00032843 48374000 3460 3356.9 3515.7 2385.9 2811.4 2838.6 2380.4 2286 3605.6 3730.4 TRUE FALSE FALSE 3417.828189 3404.158526 3576.889284 2661.768984 2667.923767 2657.222621 2582.591117 2352.141803 3283.106106 3633.48367 0.940647736 0.936885599 0.984424208 0.732566657 0.734260564 0.731315416 0.710775485 0.647351692 0.903569798 1 11.82713771 -9.235051477 5.605128051 0.969108913 0.71207375 0.919596928 0.03561426 0.032997791 3.310365309 0.005192262 0.008522086 5.82E-10 9.235051477 -0.257035162 RPES(ph)PSEIS(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 1 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 2 0 RPES(0.998)PS(0.002)EIS(1)PIK 89.866 0.010024 7483800 2679.1 2774.7 3165.4 2099.6 2317.2 1978.7 1684.3 2047.6 3423.7 3221.4 TRUE FALSE FALSE 2646.446099 2813.762299 3220.492459 2342.365631 2198.944637 1852.267456 1827.3644 2106.844075 3117.475697 3137.707564 0.843432998 0.896757344 1.026383879 0.746521332 0.700812486 0.590325076 0.582388372 0.671459667 0.993552023 1 11.61549518 -8.935301362 2.276682475 0.928179071 0.621293191 0.844973359 0.063516177 0.100358168 1.05109587 0.011314391 0.022317905 1.16E-09 8.935301362 -0.30688588 RPES(ph)PSEISPIK ddPTM_HeLa_Romidepsin_16h_R1 4 RPESPSEISPIK 12 1 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 0 RPES(0.856)PS(0.143)EIS(0.001)PIK;RPES(0.999)PSEISPIK;RPES(0.985)PS(0.01)EIS(0.005)PIK;RPES(0.873)PS(0.12)EIS(0.007)PIK ;;; 143.56 0.0023567 143246000 9190.9 9626.1 8841.5 8795 11642.3 13896.8 12362.8 14158.9 9621.8 9481.4 TRUE FALSE FALSE 9078.877776 9761.616488 8995.382599 9811.919282 11048.14999 13008.83933 13412.89592 14568.56543 8761.20211 9235.071861 0.983086858 1.057015759 0.974045761 1.062462689 1.196325286 1.408634337 1.452386741 1.577525941 0.948688028 1 13.17290747 -8.305171301 1.144162214 0.993716831 1.556948466 0.97690459 0.033255212 0.046605097 0.107790745 0.004406669 0.019834013 4.95E-09 8.305171301 0.563231635 RPFDPNDR ddPTM_HeLa_Romidepsin_16h_R1 2 RPFDPNDR 8 1 Q16629-4;Q16629;A0A0B4J1Z1;C9JAB2;Q16629-3;Q16629-2;F8WEA1 Q16629-4 SRSF7 Serine/arginine-rich splicing factor 7 0 0 ; ; 112.11 0.013993 8723600 1735.8 1541.18 1713.32 1215.35 1671.05 1643.93 1445.53 1389.72 2016.2 2078.62 FALSE FALSE TRUE 1714.643402 1562.876772 1743.139616 1355.874485 1585.770083 1538.888179 1568.313282 1429.929356 1835.866022 2024.617153 0.846897597 0.771936941 0.860972463 0.66969426 0.783244418 0.760088482 0.774622145 0.706271481 0.906771939 1 10.98343341 -11.29526496 0.362210852 1.035032524 0.730341418 0.681508374 0.052256284 0.424124073 0.127441116 0.052708431 0.022459161 5.07E-12 11.29526496 -0.304691107 RPGAPSLS(ph)PAPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPGAPSLSPAPR 12 1 Q5QP82;Q5QP82-2 Q5QP82 DCAF10 DDB1- and CUL4-associated factor 10 1 0 RPGAPS(0.001)LS(0.999)PAPR;RPGAPS(0.004)LS(0.996)PAPR ; 113.65 0.0028186 31966000 3032.2 3438.9 3632.2 3912.2 4259.2 4369.3 4038.8 4036.2 3159.3 3153.1 TRUE FALSE FALSE 2995.24238 3487.312924 3695.416917 4364.546971 4041.837131 4090.115831 4381.855571 4152.981079 2876.724295 3071.182007 0.975273485 1.135495362 1.20325559 1.421129377 1.316052621 1.33177253 1.426765187 1.352241928 0.936683104 1 11.5845783 -9.744618169 1.55534784 0.987560527 1.369410251 0.934321834 0.045655258 0.054655944 0.268369807 0.007098055 0.010474544 1.80E-10 9.744618169 0.381849724 RPGEK(ac)TYTQR ddPTM_HeLa_Romidepsin_16h_R1 2 RPGEKTYTQR 10 2 P23246;P23246-2 P23246 SFPQ "Splicing factor, proline- and glutamine-rich" 0 1 ; RPGEK(1)TYTQR;RPGEK(1)TYTQR 174.77 0.0010058 4127300 724.98 725.66 932.59 1178.68 761.48 539.59 757.17 506.9 704.03 539.55 FALSE TRUE FALSE 716.1436649 735.8758605 948.8213377 1314.964527 722.6188341 505.1119404 821.4840009 521.5663517 641.0597935 525.5324132 1.362701228 1.400248285 1.805447797 2.50215685 1.375022389 0.961143267 1.563146212 0.992453251 1.21982922 1 9.037635938 -11.23675838 0.908264105 1.055886001 1.526703874 0.121829004 0.414409655 0.664108642 1.158555979 0.143633202 0.094823144 5.80E-12 11.23675838 0.470817873 RPGFS(ph)PTSHR ddPTM_HeLa_Romidepsin_16h_R1 2 RPGFSPTSHR 10 1 Q8WUA4;H0Y4Q6 Q8WUA4 GTF3C2 General transcription factor 3C polypeptide 2 1 0 RPGFS(0.987)PT(0.012)S(0.001)HR;RPGFS(0.955)PT(0.02)S(0.026)HR ; 64.945 0.029072 4959400 1258.92 1063.72 1260.88 973.3 969.02 1236.05 1171.94 1075.95 1228.84 1124.17 TRUE FALSE FALSE 1243.575799 1078.695078 1282.825087 1085.837526 919.5672935 1157.070394 1271.484554 1107.080916 1118.929473 1094.963901 1.135723102 0.985142137 1.171568383 0.991665135 0.839815169 1.056720128 1.16121139 1.011066131 1.021887088 1 10.09666759 RPHT(ph)PTPGIYMGR ddPTM_HeLa_Romidepsin_16h_R1 1 RPHTPTPGIYMGR 13 1 P62995;H7C2L4;P62995-3;H7BXF3 P62995 TRA2B Transformer-2 protein homolog beta 1 0 RPHT(0.747)PT(0.253)PGIYMGR 55.011 0.020095 15279000 1185.3 1388.6 1444.5 995.04 1473 1339.6 1258.1 1198 1350 1655.8 TRUE FALSE FALSE 1170.853108 1408.148747 1469.640917 1110.091207 1397.827313 1254.003883 1364.962983 1232.66224 1229.252619 1612.782077 0.725983457 0.873117805 0.911245814 0.688308248 0.866718035 0.77754081 0.84634062 0.764307997 0.762193874 1 10.6553358 -12.46788663 1.145335725 1.002516716 0.802289923 0 0.098152509 0.300371471 0.690510588 0.048770937 0.011409436 3.40E-13 12.46788663 -0.200226792 RPILQLS(ph)PPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 RPILQLSPPGPR 12 1 Q8N3X1-2;Q8N3X1;F5GXL1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 0 RPILQLS(1)PPGPR 83.869 0.011991 167450000 1646.5 1538.2 1307.5 1812.9 1625.9 2046 1558.6 1626.5 1722.7 1407.3 TRUE FALSE FALSE 1626.431825 1559.85482 1330.256489 2022.516028 1542.924256 1915.267203 1690.987445 1673.560211 1568.617397 1370.738143 1.186537219 1.137967035 0.970467259 1.475494089 1.125615614 1.397252431 1.233632735 1.220918977 1.144359632 1 10.42073728 -9.275329206 24.99951889 1.086839544 1.284180139 0.464845212 0.108642513 570.2540618 1026366.133 0.017122762 0.026240624 5.30E-10 9.275329206 0.197340594 RPLEEDFRRS(ph)PTEDFR ddPTM_HeLa_Romidepsin_16h_R1 1 RPLEEDFRRSPTEDFR 16 3 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 0 RPLEEDFRRS(0.851)PT(0.149)EDFR 73.022 0.026051 6876700 1958.5 2278.8 1550.5 2530.3 1636.8 1862.2 1482.5 1790.6 2233.5 2359.7 TRUE FALSE FALSE 1934.629049 2310.881006 1577.485802 2822.865191 1553.267988 1743.21143 1608.423513 1842.408186 2033.730166 2298.394654 0.841730573 1.005432641 0.686342443 1.22818994 0.675805604 0.758447392 0.699803017 0.80160654 0.88484811 1 11.16641083 -4 0.120587729 1.032499288 0.0709886 0.150470551 0.154423641 109.0838971 0.903753736 0.633828218 17.70349641 1.00E-04 4 -0.961510688 AGDT(ph)SDQEGHSLEEK ddPTM_HeLa_Romidepsin_16h_R1 2 AGDTSDQEGHSLEEK 15 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 0 AGDT(0.784)S(0.216)DQEGHSLEEK;AGDT(0.557)S(0.443)DQEGHSLEEK ; 85.054 0.017336 37809000 13490.4 12137 11564.9 10658.5 7902.7 6069.9 5759.1 5674.9 13306.1 12714.1 TRUE FALSE FALSE 13325.97382 12307.865 11766.18223 11890.88592 7499.39573 5682.05298 6248.27781 5839.094278 12115.96909 12383.78585 1.076082385 0.993869335 0.950128045 0.960197961 0.605581833 0.458830042 0.504553122 0.471511245 0.978373596 1 13.59616481 -8.722658235 2.284626713 1.027191016 0.478125158 0.975009248 0.038177186 0.033051701 0.351405143 0.00649772 0.014203664 1.89E-09 8.722658235 -0.549065858 down RPLSAS(ph)LGQLNEVGLPSAAILPDEGAVDLPSR ddPTM_HeLa_Romidepsin_16h_R1 1 RPLSASLGQLNEVGLPSAAILPDEGAVDLPSR 32 1 Q5TC82-2;Q5TC82 Q5TC82-2 RC3H1 Roquin-1 1 0 RPLS(0.135)AS(0.86)LGQLNEVGLPS(0.005)AAILPDEGAVDLPSR 69.229 9.88E-06 7585400 657.37 647.6 662.64 768.24 657.12 728.18 683.57 750.33 684.46 477.89 TRUE FALSE FALSE 649.3577216 656.7169298 674.1729712 857.0675235 623.5847143 681.6516481 741.6324187 772.0396147 623.2401833 465.4743489 1.395045126 1.410855252 1.44835687 1.841277668 1.339675786 1.464423657 1.593283111 1.658608292 1.338935614 1 8.862557857 -11.79641877 0.339398216 0.854995496 1.598594106 0.393771479 0.164966623 0.90681239 0.180834292 0.262210551 0.06732252 1.60E-12 11.79641877 0.74359861 RPLSS(ph)SHEASEGQAK ddPTM_HeLa_Romidepsin_16h_R1 1 RPLSSSHEASEGQAK 15 1 A0A0J9YVR0;Q8IZ21-3;Q8IZ21;Q8IZ21-2 A0A0J9YVR0;Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 RPLS(0.152)S(0.418)S(0.418)HEAS(0.013)EGQAK 75.017 0.0021731 0 9586.5 2517.5 5207.2 444.73 4917.4 3138 8391.7 4760.3 7642.3 5453.8 TRUE FALSE FALSE 9469.656051 2552.941431 5297.829132 496.1517751 4666.446729 2937.491927 9104.490789 4898.03177 6958.753548 5312.10949 1.782654531 0.480589008 0.997311735 0.093400141 0.878454546 0.552980305 1.713912487 0.922050229 1.309979314 1 12.37506917 -10.25639022 24.95778635 1.369586861 0.813544414 0.259533863 0.432267663 466.3363686 2305084.653 0.080617339 0.097132176 5.54E-11 10.25639022 -0.556042447 RPMEEDGEEKS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 RPMEEDGEEKSPSK 14 2 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 RPMEEDGEEKS(0.949)PS(0.051)K;RPMEEDGEEKS(0.994)PS(0.006)K ; 101.75 0.0087141 14366400 16738.1 15204.1 15613.3 14232.7 11590 11168.5 9962.5 8560 17057.9 16847.8 TRUE FALSE FALSE 16534.0896 15418.14372 15885.04294 15878.35174 10998.51905 10454.86889 10808.7145 8807.670095 15532.1987 16410.09173 1.007556196 0.939552562 0.968004518 0.967596769 0.670228981 0.637099967 0.65866265 0.536722783 0.946502857 1 14.00229568 -8.740297535 3.433927644 0.99501658 0.619298266 0.949609712 0.03900894 0.031492328 0.776435595 0.005419122 0.010977382 1.82E-09 8.740297535 -0.375718313 RPNEDS(ph)DEDEEKGAVVPPVHDIYR ddPTM_HeLa_Romidepsin_16h_R1 3 RPNEDSDEDEEKGAVVPPVHDIYR 24 2 Q12996;H0YE74;E9PLP8 Q12996 CSTF3 Cleavage stimulation factor subunit 3 1 0 RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR;RPNEDS(1)DEDEEKGAVVPPVHDIYR ;; 57.951 0.0032249 18686500 3808.36 4241.6 3508.25 4561.8 3904.64 3592.2 3009.06 3469.98 4220.3 3895.78 TRUE FALSE FALSE 3761.942243 4301.313356 3569.30962 5089.25678 3705.371651 3362.670013 3264.649481 3570.378397 3842.825798 3794.567074 0.991402226 1.133545217 0.94063685 1.341195631 0.976493913 0.886180149 0.86034834 0.94091851 1.012717847 1 11.88971958 -8.410784203 5.321618204 1.028950889 0.894605751 0.293178114 0.110839878 0.25784564 10.4286346 0.01576532 0.035755678 3.88E-09 8.410784203 -0.134345138 RPPEDDFR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPEDDFR 8 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 0 0 110.87 0.014284 2867800 666.99 619.71 397.84 596.17 697.68 702.14 512.1 528.58 745.24 495.1 FALSE FALSE TRUE 658.8604693 628.4342936 404.7642383 665.1019805 662.0747862 657.2755201 555.5977612 543.8736283 678.5838679 482.2372306 1.36625799 1.303164197 0.839346721 1.379200813 1.372923416 1.362971331 1.152125398 1.127813437 1.407157774 1 8.913599227 RPPEEDFR ddPTM_HeLa_Romidepsin_16h_R1 2 RPPEEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 0 ; ; 96.668 0.0024472 3342600 1728.23 2264.3 1476.92 1916.59 1812.63 1533.28 1613.1 1755.9 2250.1 1827.13 FALSE FALSE TRUE 1707.165668 2296.176875 1502.625173 2138.195154 1720.124727 1435.308356 1750.116674 1806.704196 2048.845421 1779.660899 0.959264582 1.290232806 0.844332296 1.201462118 0.966546339 0.806506654 0.983398958 1.015195758 1.151256074 1 10.79738666 -8.526971096 24.96843233 1.011548347 0.930979652 0.088911125 0.137627158 233.9700527 1427508.238 0.017933109 0.035990362 2.97E-09 8.526971096 -0.080568694 RPPEEDWR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPEEDWR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 0 0 106.6 0.016433 2871200 970.47 882.76 819.25 927.8 1040.3 867.22 932.5 780.02 924.19 861.62 FALSE FALSE TRUE 958.6415384 895.1875185 833.5087026 1035.076601 987.2096091 811.8074408 1011.706527 802.588648 841.5281317 839.2349882 1.142280234 1.066670874 0.993176779 1.233357303 1.176320843 0.967318394 1.205510424 0.956333636 1.002732421 1 9.712931016 -12.48725124 1.182686287 0.999024122 1.100474213 0.127560283 0.093492069 0.759727769 1.871763156 0.063839622 0.014969093 3.26E-13 12.48725124 0.101450091 RPPES(ph)PPIVEEWNSR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPESPPIVEEWNSR 15 1 A0A3B3IU46;Q9BTL3 A0A3B3IU46 FAM103A1 RNMT-activating mini protein 1 0 RPPES(1)PPIVEEWNSR 62.468 0.021791 39520000 1040.1 667.61 831.81 825.37 933.94 958.66 939.56 875.38 1098.8 968.46 TRUE FALSE FALSE 1027.422861 677.0086311 846.2873041 920.8031629 886.2775568 897.4047199 1019.366203 900.7077392 1000.520576 943.2992696 1.089180172 0.71770291 0.897156747 0.976151676 0.939550772 0.951346777 1.080639237 0.954848337 1.060660819 1 9.88157174 RPPGPTT(ph)SPASTSLSSPGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPGPTTSPASTSLSSPGQR 20 1 Q01970-2;Q01970 Q01970-2 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 0 RPPGPT(0.317)T(0.519)S(0.139)PAS(0.017)T(0.004)S(0.002)LS(0.002)S(0.001)PGQR 52.366 0.022402 18277000 969.56 672.61 661.05 641.47 989.21 873.01 793.59 888.92 1041.2 830.23 TRUE FALSE FALSE 957.7426298 682.0790212 672.555298 715.6397796 938.7269224 817.2274785 860.9975148 914.6394977 948.0724643 808.6605049 1.184356877 0.843467706 0.831690547 0.884969373 1.160841808 1.01059403 1.064720621 1.131054988 1.172398625 1 9.659390342 -7.322246988 3.101121802 1.039788073 1.139331755 0.0448455 0.127069175 0.993238948 14.9565959 0.01962356 0.22074263 4.76E-08 7.322246988 0.099543682 RPPS(ph)PDVIVLS(ph)DNEQPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 0 RPPS(1)PDVIVLS(0.714)DNEQPS(0.673)S(0.613)PR;RPPS(1)PDVIVLS(0.998)DNEQPS(0.543)S(0.459)PR ; 67.47 0.0026661 185475000 7816.2 8038.8 6646.1 13790.8 7022.6 6822.6 5836.1 6157.3 8441.1 8226.2 TRUE FALSE FALSE 7720.933148 8151.970437 6761.772583 15385.35718 6664.210517 6386.657879 6331.818188 6335.451761 7686.106875 8012.482138 0.963613149 1.017408875 0.843904856 1.920173664 0.831728596 0.797088564 0.790244281 0.79069777 0.959266647 1 12.96803352 -8.554036926 24.99985131 1.046054175 0.796093937 0.202384418 0.286754894 283.530538 227490.4714 0.040801642 0.081603838 2.79E-09 8.554036926 -0.249960238 RPPS(ph)PDVIVLS(ph)DNEQPSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 0 RPPS(1)PDVIVLS(0.84)DNEQPS(0.091)S(0.069)PR;RPPS(1)PDVIVLS(1)DNEQPSSPR ; 149.44 6.87E-06 63295000 2881.8 3338 3370.5 3082.86 5061.8 4838.9 3542.7 4259.2 3683.1 3522.9 TRUE FALSE FALSE 2846.675513 3384.992452 3429.162139 3439.314778 4803.477458 4529.709907 3843.61685 4382.433232 3353.674312 3431.37455 0.829602094 0.986482939 0.99935524 1.002314008 1.399869757 1.320086117 1.120139114 1.277165511 0.977355944 1 11.7445709 -8.893880919 5.409580078 0.931892855 1.269551748 0.775174492 0.082140168 0.080239561 3.568126694 0.014309882 0.026292976 1.28E-09 8.893880919 0.337658893 RPPS(ph)PDVIVLSDNEQPS(ph)S(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 3 0 RPPS(0.998)PDVIVLS(0.399)DNEQPS(0.809)S(0.794)PR 42.659 0.02851 5022800 998.29 833.66 854.31 554.13 789.37 839.8 766.17 881.37 874.35 696.69 TRUE FALSE FALSE 986.1224575 845.3962874 869.1789072 618.2011179 749.0855034 786.1394903 831.2484607 906.8710504 796.1459462 678.5898934 1.453193552 1.24581326 1.280860378 0.911008437 1.10388544 1.15848983 1.224964399 1.336405183 1.173235785 1 9.406396133 -7.30448606 3.355801036 1.192820878 1.348939034 0.094608327 0.143016366 0.779776431 14.58826135 0.026681683 0.291450684 4.96E-08 7.30448606 0.156118156 RPPS(ph)PDVIVLSDNEQPS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 0 RPPS(1)PDVIVLS(0.03)DNEQPS(0.531)S(0.439)PR;RPPS(1)PDVIVLSDNEQPS(0.557)S(0.442)PR ; 145.19 1.28E-05 67905000 1874.94 1614.33 1661.47 1764.11 1982.43 2150.8 1684.93 2272 2170.12 1831.02 TRUE FALSE FALSE 1852.08751 1637.05658 1690.387188 1968.084699 1881.2592 2013.370821 1828.047912 2337.736735 1976.019032 1783.449836 1.038485901 0.917915686 0.947818746 1.103526804 1.054842789 1.128919233 1.025006633 1.31079478 1.107975673 1 10.80045492 -4 0.726677421 1.012435173 41.60427809 0.579138752 0.06798027 148.0282638 0.659511259 0.009837528 9816.024471 1.00E-04 4 40.59184292 RPPS(ph)PDVIVLSDNEQPSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 2 0 RPPS(1)PDVIVLSDNEQPS(0.02)S(0.98)PR 210.31 6.36E-32 5244600 2797.8 2284.4 2741.3 3026.1 2714.4 2807.4 2740.7 2976.8 2992.2 2577.5 TRUE FALSE FALSE 2763.699337 2316.559843 2789.011177 3375.99192 2575.874039 2628.0162 2973.49499 3062.929011 2724.570138 2510.536178 1.100840275 0.922735097 1.110922519 1.344729444 1.026025461 1.046794793 1.184406349 1.220029824 1.085254282 1 11.2937798 -9.530019048 24.99304294 1.038499706 1.158941812 0.313877426 0.094919414 180.5818295 632084.337 0.015115396 0.021402272 2.95E-10 9.530019048 0.120442106 RPPS(ph)PDVIVLSDNEQPSSPR ddPTM_HeLa_Romidepsin_16h_R1 2 RPPSPDVIVLSDNEQPSSPR 20 1 Q86YP4-2;Q86YP4;Q86YP4-3;C9JMI3;C9JGN4;C9JHD7;C9JJK9 Q86YP4-2 GATAD2A Transcriptional repressor p66-alpha 1 0 RPPS(1)PDVIVLSDNEQPSSPR;RPPS(1)PDVIVLSDNEQPSSPR ; 229.48 6.05E-46 31767000 2488.3 2292.2 2739 3124 3781.3 4147.7 3829.7 4389.1 2707.9 2037.7 TRUE FALSE FALSE 2457.971643 2324.469652 2786.671146 3485.211579 3588.326151 3882.675356 4154.994622 4516.091684 2465.698642 1984.76026 1.238422439 1.171158904 1.40403413 1.755986176 1.807939338 1.956244003 2.093449121 2.275383972 1.242315604 1 10.95474904 -8.677055835 0.455294038 1.045178559 2.445638657 0.951422959 0.091799386 0.203932896 0.062140897 0.023115997 0.126848344 2.10E-09 8.677055835 1.400460097 up RPPS(ph)PEPSTK ddPTM_HeLa_Romidepsin_16h_R1 4 RPPSPEPSTK 10 1 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 RPPS(1)PEPSTK;RPPS(1)PEPSTK;RPPS(1)PEPSTK;RPPS(1)PEPSTK ;;; 92.906 0.010221 4120650000 31702 47536.3 33885.4 38297.5 32840.7 36667.9 36797 16281.8 39743.6 39276.6 TRUE FALSE FALSE 31315.60383 48205.51728 34475.16117 42725.63715 31164.71653 34324.93953 39922.53626 16752.88819 36188.83288 38256.18827 0.818576164 1.260071101 0.901165608 1.116829435 0.814632036 0.89723888 1.043557606 0.437913157 0.945960236 1 15.22340551 -7.254752517 24.91360401 0.947079868 0.437912914 0.588342324 0.133242662 423.3475247 1577245.379 0.018474224 0.239252585 5.56E-08 7.254752517 -0.509166953 RPPS(ph)PPGPEER ddPTM_HeLa_Romidepsin_16h_R1 1 RPPSPPGPEER 11 1 F5H1N7;Q6ZU35 F5H1N7 KIAA1211 Uncharacterized protein KIAA1211 1 0 RPPS(1)PPGPEER 71.279 0.022523 11439000 1244.8 1337.3 1126.4 1595.9 1508.9 1176.4 1266.2 1188.3 1627.3 1490.8 TRUE FALSE FALSE 1229.627899 1356.126545 1146.004519 1780.425467 1431.895203 1101.231837 1373.750996 1222.681586 1481.750212 1452.068801 0.846811045 0.933927196 0.789221915 1.22613024 0.986106995 0.758388195 0.946064674 0.842027309 1.020440775 1 10.5038941 -9.131591663 0.008836551 1.826954559 5.72E-07 0.048185717 0.126408887 11558.89273 37.46356917 3774.830081 3969.96376 7.39E-10 9.131591663 -1.826953987 RPPTPAPWPSSGLGTPLT(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 RPPTPAPWPSSGLGTPLTPPK 21 1 M0R0S1;M0R2P6;Q8TBC3;M0R1G0;M0QZE8;M0R0K4;M0QYB1;M0R0E3;M0R0S2 M0R0S1 SHKBP1 SH3KBP1-binding protein 1 1 0 RPPTPAPWPSSGLGT(0.004)PLT(0.996)PPK 109.03 0.00010746 11621000 1141.3 1349.4 1329.1 1266.3 1241.8 952.07 1091.2 1215.2 1420.8 1277.8 TRUE FALSE FALSE 1127.389397 1368.396889 1352.232428 1412.715564 1178.426312 891.2357997 1183.886501 1250.359895 1293.72009 1244.602572 0.905822808 1.099464937 1.086477289 1.135073634 0.946829405 0.716080635 0.951216499 1.004625832 1.039464419 1 10.28146942 -8.517155454 24.99459217 0.990714067 0.885824618 0.24395845 0.099352518 356.0181233 1554789.594 0.015800759 0.032426321 3.04E-09 8.517155454 -0.104889449 RPPVLRAGVNT(ph)VT(ph)T(ph)LVENK ddPTM_HeLa_Romidepsin_16h_R1 1 RPPVLRAGVNTVTTLVENK 19 2 P62424;Q5T8U2;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 3 0 RPPVLRAGVNT(1)VT(1)T(1)LVENK 51.606 0.0039424 0 705.2 914.01 833.56 759.79 708.52 799.86 701.92 791 912.53 567.72 TRUE FALSE FALSE 696.6047512 926.8774568 848.0677621 847.6404947 672.3615805 748.7515274 761.5410673 813.886337 830.9110313 552.9705526 1.259750176 1.676178691 1.533658091 1.532885415 1.215908474 1.354053166 1.377181956 1.471843904 1.502631609 1 9.111058844 -11.0282821 1.180399584 1.058221665 1.437285211 0 0.189532939 0.208779937 0.607399376 0.035886193 0.029311144 9.37E-12 11.0282821 0.379063545 RPQS(ph)PGASPSQAER ddPTM_HeLa_Romidepsin_16h_R1 1 RPQSPGASPSQAER 14 1 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 1 0 RPQS(1)PGASPSQAER 77.505 0.012017 4692900 61.59 254.75 126.09 161.02 84.956 104.32 112.53 126.88 204.47 160.88 TRUE FALSE FALSE 60.83931739 258.3363772 128.2845436 179.63789 80.62037831 97.65428868 122.0882954 130.5510726 186.1816911 156.7003144 0.388252682 1.648601524 0.818661686 1.146378619 0.514487661 0.623191402 0.779119658 0.833125786 1.188138593 1 7.291864264 RPRPTPGDGEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 RPRPTPGDGEKR 12 3 I3L4Q4;Q9BUL5-4;Q9BUL5;I3L410;I3L1N0;Q9BUL5-3 I3L4Q4 PHF23 PHD finger protein 23 0 1 RPRPTPGDGEK(1)R 54.772 0.02485 216830 0 0 0 65.069 0 0 61.655 0 0 65.147 FALSE TRUE FALSE 0 0 0 72.59258394 0 0 66.89197416 0 0 63.45447155 0 0 0 1.144010535 0 0 1.05417274 0 0 1 5.987649927 -12.43373604 1.177463775 0.997976458 0.266665343 0 0.523991868 0.483323042 1.203735769 0.284480771 0.072099322 3.68E-13 12.43373604 -0.731311115 RPRSNSSRWPSCTASYSPPR ddPTM_HeLa_Romidepsin_16h_R1 1 RPRSNSSRWPSCTASYSPPR 20 3 V9GY78 V9GY78 RRBP1 0 0 54.004 0.018333 15902000 1145.6 998.38 1192.1 1161.6 1023.1 1044.1 880.3 714.93 1304.6 961.65 FALSE FALSE TRUE 1131.636987 1012.43522 1212.848 1295.909657 970.8873893 977.3853797 955.07266 735.6153716 1187.913309 936.6661944 1.208153976 1.080892239 1.294856169 1.38353414 1.036535102 1.043472462 1.019651041 0.785354885 1.268235488 1 9.871391187 -7.091023192 1.178777259 1.130130326 0.527091803 0.474508834 0.121289485 1.78181767 1.566125235 0.019924477 1.443694431 8.11E-08 7.091023192 -0.603038523 NFVFHTLS(ph)PVKAEAAK ddPTM_HeLa_Romidepsin_16h_R1 1 NFVFHTLSPVKAEAAK 16 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 0 NFVFHT(0.084)LS(0.916)PVKAEAAK 82.265 0.0081119 46243000 4092.9 3860.8 3299.3 3506.9 2079.6 1787.3 1489.1 1585.7 4333 3916.5 TRUE FALSE FALSE 4043.014161 3915.152444 3356.722933 3912.384278 1973.470252 1673.097298 1615.584117 1631.579728 3945.445628 3814.748765 1.059837596 1.026319867 0.879932897 1.025594218 0.517326402 0.438586497 0.423509965 0.427703062 1.034260936 1 11.89737233 -8.720213528 4.271201325 1.01742592 0.436770041 0.969067119 0.048453643 0.026335761 1.032611079 0.007842349 0.015766329 1.90E-09 8.720213528 -0.580655879 down RPS(ph)LGELLLR ddPTM_HeLa_Romidepsin_16h_R1 1 RPSLGELLLR 10 1 Q8N612;Q8N612-2 Q8N612 FAM160A2 FTS and Hook-interacting protein 1 0 RPS(1)LGELLLR 83.869 0.015433 3916900 570.79 499.52 393.49 523.42 876.03 1284 1044.8 1283.6 634.84 429.74 TRUE FALSE FALSE 563.8329919 506.5522557 400.3385284 583.9402832 831.3229202 1201.956544 1133.545286 1320.738941 578.0583204 418.5752928 1.347028842 1.21018193 0.95643134 1.395066295 1.986077378 2.871542025 2.708103668 3.155319875 1.381013954 1 8.709343346 -8.504191039 1.764524965 1.156093146 2.951752904 0.955540783 0.164527342 0.051654184 0.315772215 0.026164148 0.071863804 3.13E-09 8.504191039 1.795659758 up RPS(ph)PHDEEEFEVEEAAEAQAEPK ddPTM_HeLa_Romidepsin_16h_R1 2 RPSPHDEEEFEVEEAAEAQAEPK 23 1 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 RPS(1)PHDEEEFEVEEAAEAQAEPK;RPS(1)PHDEEEFEVEEAAEAQAEPK ; 83.834 9.61E-05 26057000 4857.1 4614.4 4511.2 4029.8 5489.8 5387.7 4978.5 5545.8 5209 5310.4 TRUE FALSE FALSE 4797.899797 4679.361644 4589.715544 4495.744437 5209.635021 5043.443358 5401.373666 5706.258973 4743.093994 5172.435042 0.92759015 0.904672868 0.88734136 0.869173687 1.007191966 0.97506171 1.044261285 1.103205536 0.916994405 1 12.33662791 -7.573852925 1.356379309 0.949036369 1.125392887 0.6237329 0.043816876 0.507253861 1.201033876 0.007736925 0.104344433 2.67E-08 7.573852925 0.176356518 RPS(ph)PQPSPR ddPTM_HeLa_Romidepsin_16h_R1 3 RPSPQPSPR 9 1 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 RPS(0.999)PQPS(0.001)PR;RPS(1)PQPSPR;RPS(1)PQPSPR ;; 117.95 0.0043439 26377600 1498.07 1454.94 1318.16 1560.06 1319.83 992.55 1153.9 694.46 1103.36 1709.83 TRUE FALSE FALSE 1479.810947 1475.422684 1341.102022 1740.441478 1252.47415 929.1292583 1251.912237 714.5531044 1004.672718 1665.40837 0.888557409 0.885922462 0.805269174 1.045053879 0.752052273 0.557898756 0.75171487 0.42905579 0.603259078 1 10.70166026 -6.901744676 0.389148855 0.962081239 1.26E-12 0.348710557 0.150320422 2.873836163 0.242628536 0.027103067 1.362946798 1.25E-07 6.901744676 -0.962081239 RPS(ph)QEQSASASSGQPQAPLNR ddPTM_HeLa_Romidepsin_16h_R1 5 RPSQEQSASASSGQPQAPLNR 21 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 RPS(1)QEQSASASSGQPQAPLNR;RPS(1)QEQSASASSGQPQAPLNR;RPS(0.822)QEQS(0.167)AS(0.005)AS(0.005)S(0.001)GQPQAPLNR;RPS(0.453)QEQS(0.333)AS(0.097)AS(0.097)S(0.02)GQPQAPLNR;RPS(0.416)QEQS(0.296)AS(0.124)AS(0.124)S(0.04)GQPQAPLNR ;;;; 240.82 8.81E-54 63599300 3177.43 3130.5 3230.86 3567.34 3915.43 4082.74 3938.11 3641.25 3820.43 3921.34 TRUE FALSE FALSE 3138.702261 3174.571261 3287.091763 3979.812636 3715.610997 3821.86609 4272.612965 3746.603824 3478.721172 3819.463022 0.821765322 0.831156433 0.860616203 1.04198224 0.972809784 1.000629164 1.118642317 0.98092423 0.910788022 1 11.89915411 -9.254403889 24.50771362 0.902232957 1.024280254 0.553900557 0.060988805 377.9521023 1316572.84 0.012475883 0.020393095 5.57E-10 9.254403889 0.122047296 RPS(ph)QNAISFFNVGHSK ddPTM_HeLa_Romidepsin_16h_R1 1 RPSQNAISFFNVGHSK 16 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 0 RPS(0.996)QNAIS(0.004)FFNVGHSK 76.678 0.0088196 28399000 842.31 763.59 973.7 1599.5 4041.5 4913.7 3800 5336.9 1376.7 1273.3 TRUE FALSE FALSE 832.0436017 774.3398401 990.6468401 1784.441716 3835.247174 4599.730428 4122.771905 5491.314781 1253.564504 1240.219482 0.670884157 0.624357101 0.798767359 1.438811227 3.09239391 3.708803557 3.324227658 4.427695951 1.01076021 1 10.27637974 -8.742768631 2.024302114 0.81385108 3.791818058 0.959892392 0.277176094 0.041573122 0.3467906 0.041244132 0.092059283 1.81E-09 8.742768631 2.977966978 up RPS(ph)SPVISK ddPTM_HeLa_Romidepsin_16h_R1 1 RPSSPVISK 9 1 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 RPS(0.516)S(0.484)PVISK 66.989 0.027639 302240000 8421.9 8962.4 8431.2 11039 8395 6584.5 6119.1 4505.5 8234.2 8013.1 TRUE FALSE FALSE 8319.250643 9088.572902 8577.941499 12315.38112 7966.571824 6163.771701 6638.856201 4635.859534 7497.712529 7804.918507 1.065898463 1.164467367 1.099043057 1.577900027 1.020711724 0.789729155 0.850599042 0.593966424 0.960639438 1 12.93016785 -8.273276548 4.100424465 1.090024401 0.748918893 0.496604696 0.174807953 0.159724104 6.441423709 0.025892623 0.064509221 5.33E-09 8.273276548 -0.341105508 RPS(ph)TSQTVSTPAPVPVIESTEAIEAK ddPTM_HeLa_Romidepsin_16h_R1 1 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 RPS(0.32)T(0.136)S(0.136)QT(0.133)VS(0.133)T(0.143)PAPVPVIESTEAIEAK 58.251 0.0014404 5925400 871.93 921.43 922.81 660.35 1034.8 1099.4 1281.2 1382.3 900.45 926.79 TRUE FALSE FALSE 861.3025818 934.4019157 938.8711209 736.702774 981.9902946 1029.151888 1390.025096 1422.29467 819.9114968 902.7118622 0.954127909 1.035105392 1.040056257 0.816099583 1.087822522 1.140066871 1.539832536 1.575579904 0.908275975 1 9.818121755 -7.849656608 1.985892258 0.979699464 1.60520591 0.909373059 0.072305704 0.063700871 0.472270059 0.009363202 0.047366345 1.41E-08 7.849656608 0.625506446 RPS(ph)VDAPVTDVGFLR ddPTM_HeLa_Romidepsin_16h_R1 2 RPSVDAPVTDVGFLR 15 1 A0A1B0GTT1;A0A1B0GVM0;Q9BUH8;G3V536;G3V3S3 A0A1B0GTT1 BEGAIN Brain-enriched guanylate kinase-associated protein 1 0 RPS(1)VDAPVTDVGFLR;RPS(1)VDAPVTDVGFLR ; 138.28 0.00030182 11141000 2571 2796.3 2472.96 2248.7 1958.46 1619.33 1367.7 1643.59 3094.2 2786.1 TRUE FALSE FALSE 2539.663663 2835.666385 2516.000831 2508.705274 1858.512478 1515.860039 1483.872404 1691.144683 2817.447002 2713.71672 0.935861744 1.044938244 0.927142031 0.924453631 0.68485869 0.558591849 0.546804459 0.623183942 1.038224433 1 11.40605441 -8.695031556 2.294593089 0.972620586 0.572578799 0.952115908 0.041846183 0.040867803 0.437411377 0.005834484 0.01292729 2.02E-09 8.695031556 -0.400041787 RPSADSES(ph)PGTPSPDGAAWEPPAR ddPTM_HeLa_Romidepsin_16h_R1 1 RPSADSESPGTPSPDGAAWEPPAR 24 1 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 0 RPS(0.085)ADS(0.306)ES(0.609)PGTPSPDGAAWEPPAR 83.747 6.32E-05 2271000 346.44 373.05 319.26 359.85 264.07 583.39 275.27 291.77 307.08 458.23 TRUE FALSE FALSE 342.217456 378.3018077 324.8165864 401.4575501 250.5935225 546.1132618 298.6514269 300.2119046 279.6139957 446.3251185 0.766744783 0.847592466 0.7277578 0.899473351 0.5614596 1.223577251 0.669134258 0.672630538 0.626480528 1 8.801951191 -12.31041652 0.84528274 1.010990999 0.798580202 0 0.20555712 0.975326498 1.14454237 0.138882771 0.030291643 4.89E-13 12.31041652 -0.212410796 RPSASS(ph)PNNNTAAK ddPTM_HeLa_Romidepsin_16h_R1 1 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 0 RPS(0.068)AS(0.068)S(0.865)PNNNTAAK 68.243 0.018263 2375900 611.82 687.63 648.22 619.69 502.8 637.98 659.35 317.21 676.03 670.25 TRUE FALSE FALSE 604.3629025 697.3104732 659.5019972 691.3414735 477.1402398 597.215137 715.3551725 326.3879709 615.5641837 652.8368084 0.925748816 1.068123709 1.010209579 1.058980536 0.730872147 0.914800038 1.095764153 0.499953383 0.942906674 1 9.350578592 -8.768955757 24.99914995 0.982369861 0.838195235 0.274173493 0.147379773 208.7990508 694458.6583 0.020175458 0.037090446 1.70E-09 8.768955757 -0.144174626 RPSTSQTVS(ph)TPAPVPVIESTEAIEAK ddPTM_HeLa_Romidepsin_16h_R1 2 RPSTSQTVSTPAPVPVIESTEAIEAK 26 1 P12270;P12270-2 P12270 TPR Nucleoprotein TPR 1 0 RPS(0.019)T(0.019)S(0.019)QT(0.016)VS(0.463)T(0.463)PAPVPVIESTEAIEAK;RPS(0.109)T(0.109)S(0.109)QT(0.085)VS(0.294)T(0.294)PAPVPVIESTEAIEAK ; 78.736 2.38E-05 66298000 3231.1 3867.9 3725 3672.7 5415 5084 3744.2 4510.3 3267.7 3190.7 TRUE FALSE FALSE 3191.71811 3922.352398 3789.832062 4097.354855 5138.652344 4759.148808 4062.232255 4640.798414 2975.428728 3107.805154 1.027000713 1.262097269 1.219456135 1.318407896 1.653466704 1.531353663 1.30710648 1.493271999 0.957405172 1 11.60168034 -9.698541751 1.002952552 1.006219067 1.480220879 0.801259086 0.099756521 0.151058482 0.303539928 0.019377654 0.031302594 2.00E-10 9.698541751 0.474001812 RPTPNDDTLDEGVGLVHSNIAT(ph)EHIPSPAK ddPTM_HeLa_Romidepsin_16h_R1 1 RPTPNDDTLDEGVGLVHSNIATEHIPSPAK 30 1 Q01581 Q01581 HMGCS1 "Hydroxymethylglutaryl-CoA synthase, cytoplasmic" 1 0 RPTPNDDTLDEGVGLVHS(0.003)NIAT(0.571)EHIPS(0.426)PAK 94.72 1.10E-07 10245000 6062 5343.4 5414.8 5406.7 8181.6 8521.8 6295.1 7186.5 6414.4 5926.8 TRUE FALSE FALSE 5988.114012 5418.624525 5509.042323 6031.848093 7764.062422 7977.284483 6829.805637 7394.430039 5840.679999 5772.820882 1.037294268 0.938644146 0.954306817 1.044870128 1.344933886 1.381869392 1.183096752 1.280904118 1.011754932 1 12.49506075 -8.819174101 5.861676199 1.006740298 1.295364674 0.871282051 0.056492566 0.05318648 3.715496567 0.008702457 0.016076729 1.52E-09 8.819174101 0.288624376 RPTSNGVVSS(ph)PNSTSRPTLPVK ddPTM_HeLa_Romidepsin_16h_R1 1 RPTSNGVVSSPNSTSRPTLPVK 22 2 Q7Z422-2;Q7Z422-4;Q7Z422-3;Q7Z422-5;Q7Z422 Q7Z422-2 SZRD1 SUZ domain-containing protein 1 1 0 RPT(0.064)S(0.064)NGVVS(0.404)S(0.465)PNS(0.001)T(0.001)SRPTLPVK 55.049 0.020658 19624000 959.27 1120.3 1081.5 1167.9 996.9 1265.3 842.84 1064.9 1393.6 1059.2 TRUE FALSE FALSE 947.5780483 1136.071613 1100.323054 1302.938093 946.0244731 1184.451414 914.4308086 1095.711201 1268.952926 1031.681831 0.918478953 1.101184084 1.066533325 1.262926276 0.916973086 1.148078194 0.886349629 1.062063097 1.229984756 1 10.0107824 -10.26009563 24.99876093 0.96150395 1.062045523 0 0.132904766 154.0392165 2865702.408 0.016617514 0.019770638 5.49E-11 10.26009563 0.100541573 RPYDLDR ddPTM_HeLa_Romidepsin_16h_R1 2 RPYDLDR 7 1 Q15424-2;Q15424;Q15424-4;Q15424-3;K7EII0;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 0 0 ; ; 113.41 0.01841 3524400 691.62 492.08 1095.08 660.94 703.73 931.27 714.33 333.02 628.48 534.5 FALSE FALSE TRUE 683.1902694 499.0075152 1114.139408 737.3609926 667.8160321 871.7648525 775.0051724 342.6554083 572.2671747 520.6136129 1.312278919 0.958498784 2.140050472 1.416330604 1.282747926 1.674494925 1.488637932 0.658176044 1.099216695 1 9.024069225 -11.44763271 0.689642109 1.01978533 1.407918138 0.102843439 0.373420904 0.98041718 0.977002086 0.182109616 0.086594777 3.57E-12 11.44763271 0.388132809 RPYTVILIER ddPTM_HeLa_Romidepsin_16h_R1 3 RPYTVILIER 10 1 A0A087X020;Q9Y3A5 A0A087X020 SBDS Ribosome maturation protein SBDS 0 0 ;; ;; 146.16 0.0017583 8087620 1954.64 1608.97 2291.92 2147.27 2120.78 2114.18 2122.57 1805.13 2085.59 1587.29 FALSE FALSE TRUE 1930.816096 1631.621122 2331.809906 2395.547461 2012.548683 1979.090721 2302.861043 1857.358589 1899.049607 1546.051977 1.248868812 1.055346875 1.508235131 1.549461141 1.301734167 1.280093264 1.489510752 1.201355851 1.228321968 1 10.59437311 -11.19292896 0.479902982 0.995873521 1.37990049 0.250289583 0.151800877 0.603009632 0.318547862 0.098721247 0.049241944 6.41E-12 11.19292896 0.384026969 RQDEDYDEQVEESLQDEDDNDVYILTK ddPTM_HeLa_Romidepsin_16h_R1 1 RQDEDYDEQVEESLQDEDDNDVYILTK 27 1 H0Y8C6;O00410-2;O00410;O00410-3 H0Y8C6 IPO5 Importin-5 0 0 74.471 5.78E-05 8599600 2808.7 2546.5 2942.4 2986.5 2232 2721.7 1677.4 2786.1 3315 2908.9 FALSE FALSE TRUE 2774.466484 2582.349694 2993.611238 3331.813182 2118.092711 2547.792154 1819.878314 2866.711408 3018.498097 2833.326359 0.979225875 0.911419783 1.056571273 1.175936959 0.747563974 0.899222974 0.642311574 1.011782988 1.065354892 1 11.46828107 -8.738616267 24.99999945 1.000538385 0.817441347 0.431637005 0.112477765 173.2728247 189798.8303 0.014619638 0.029223446 1.83E-09 8.738616267 -0.183097039 RQDPQVVS(ph)PFSR ddPTM_HeLa_Romidepsin_16h_R1 2 RQDPQVVSPFSR 12 1 Q12986-3;Q12986-2;Q12986 Q12986-3 NFX1 Transcriptional repressor NF-X1 1 0 RQDPQVVS(1)PFSR;RQDPQVVS(0.939)PFS(0.061)R ; 111.72 0.015556 14491500 3210.6 3805.2 2908.5 3188.7 3597.7 3899.5 3038 3469.2 3805.9 3220.4 TRUE FALSE FALSE 3171.467972 3858.769705 2959.121222 3557.392497 3414.095944 3650.334535 3296.047644 3569.575829 3465.490772 3136.733544 1.011073439 1.23018728 0.943376663 1.134107328 1.08842396 1.163737526 1.05078981 1.13799141 1.104808784 1 11.61504727 -10.47611677 24.9984506 1.004885255 1.102412087 0.094015163 0.077794059 334.8279781 178996.6837 0.01086949 0.012386584 3.34E-11 10.47611677 0.097526832 RQDS(ph)MEALQMDR ddPTM_HeLa_Romidepsin_16h_R1 2 RQDSMEALQMDR 12 1 Q8TDR0-2;Q8TDR0 Q8TDR0-2 TRAF3IP1 TRAF3-interacting protein 1 1 0 RQDS(1)MEALQMDR;RQDS(1)MEALQMDR ; 58.071 0.022704 13157200 4968.5 4140.9 4362.4 3992.1 5653.4 6974.3 5625.5 5884.2 5327.1 4617.9 TRUE FALSE FALSE 4907.942011 4199.195699 4438.325742 4453.685385 5364.885902 6528.664739 6103.32983 6054.450043 4850.630834 4497.926292 1.091156611 0.933584818 0.986749327 0.990164155 1.192746513 1.451483265 1.356920819 1.346053637 1.078414923 1 12.1350443 -8.512733629 3.573436665 1.027431524 1.37980126 0.909917786 0.05229318 0.054181094 1.474172737 0.008530118 0.019118841 3.07E-09 8.512733629 0.352369736 RQEQPSIEST(ph)SPISR ddPTM_HeLa_Romidepsin_16h_R1 1 RQEQPSIESTSPISR 15 1 Q5T5P2;Q5T5P2-3 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 RQEQPSIES(0.221)T(0.386)S(0.386)PIS(0.007)R 109.13 0.0019198 10672000 1949.3 1514.9 1506.7 1565.3 1381.4 1333.7 1262.7 1497.8 2019.6 1770 TRUE FALSE FALSE 1925.541182 1536.226802 1532.923481 1746.287351 1310.902003 1248.480874 1369.953706 1541.13648 1838.961918 1724.015145 1.116893426 0.891075004 0.889158942 1.0129188 0.760377313 0.72417048 0.79462974 0.89392282 1.066673877 1 10.75155673 -9.439089843 0.950916504 1.051603451 0.797025965 0.586249175 0.080616706 0.27100421 0.488149988 0.016718578 0.032223225 3.64E-10 9.439089843 -0.254577486 RQFS(ph)APNLK ddPTM_HeLa_Romidepsin_16h_R1 1 RQFSAPNLK 9 1 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 0 RQFS(1)APNLK 113.44 0.026463 40099000 2284 2687.5 2353.6 2032.1 2383.2 2354.3 1882.5 2430.7 2566.5 2385.4 TRUE FALSE FALSE 2256.161729 2725.334696 2394.563421 2267.060963 2261.576411 2203.867828 2042.399503 2501.028469 2336.945812 2323.426964 0.971049129 1.172980575 1.03061704 0.975740145 0.973379601 0.9485419 0.879046139 1.076439461 1.005818495 1 11.18203858 -9.050040918 4.968737822 1.005980042 0.962626451 0.107385059 0.070724225 0.463469659 25.48727781 0.010958659 0.01877603 8.91E-10 9.050040918 -0.04335359 RQLAELETEDGMQES(ph)P ddPTM_HeLa_Romidepsin_16h_R1 1 RQLAELETEDGMQESP 16 1 Q96QG7-2;Q96QG7 Q96QG7-2 MTMR9 Myotubularin-related protein 9 1 0 RQLAELETEDGMQES(1)P 168.89 1.09E-05 14026000 1679.9 1556.6 1520.5 1784.2 1339.1 1457.7 1573.3 1569.2 1705.5 1465.7 TRUE FALSE FALSE 1659.424733 1578.513856 1546.963665 1990.497599 1270.76073 1364.557675 1706.936063 1614.602326 1552.955808 1427.620903 1.162370717 1.105695393 1.083595555 1.394276026 0.890124772 0.955826349 1.195650792 1.130974142 1.087792849 1 10.47939721 -6.016626704 20.34201306 1.090879233 1.09766282 0 0.132976725 0 0 0.017532545 0 9.62E-07 6.016626704 0.006783588 RQLEEAEEEAQR ddPTM_HeLa_Romidepsin_16h_R1 3 RQLEEAEEEAQR 12 1 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 ;; ;; 150.49 0.00036571 8012100 4766.75 4470.7 4537.1 5077.14 4800.48 4904.3 4137.8 4568.42 5191.4 4894.5 FALSE FALSE TRUE 4708.651018 4533.638632 4616.066322 5664.182815 4555.493593 4590.931058 4489.264629 4700.600025 4727.068182 4767.340184 0.987689327 0.950978629 0.968268708 1.188122223 0.955562938 0.962996321 0.941670713 0.986000546 0.991552522 1 12.21896886 RQLEEAEEESQR ddPTM_HeLa_Romidepsin_16h_R1 1 RQLEEAEEESQR 12 1 P35749-4;P35749-3;P35749;P35749-2 P35749-4 MYH11 Myosin-11 0 0 107.03 0.0078412 15523000 861.43 857.25 781.68 1604.6 1038.2 975.63 748.38 946.57 851.93 1102.6 FALSE FALSE TRUE 850.9305598 869.318388 795.2848125 1790.131402 985.2167799 913.2903917 811.9473785 973.9575095 775.7312471 1073.954293 0.792334055 0.809455666 0.740520167 1.666859952 0.917373101 0.850399684 0.756035321 0.906889163 0.722313093 1 10.06871688 -4.672765962 16.88210082 0.921018247 0.820448299 0 0.263819324 0 0 0.033338102 0 2.12E-05 4.672765962 -0.100569949 RQLPQT(ph)PLT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 RQLPQTPLTPR 11 1 B1AQK6;B1AQK7;F6RH32;Q00975 B1AQK6 CACNA1B Voltage-dependent N-type calcium channel subunit alpha-1B 2 0 RQLPQT(1)PLT(1)PR 68.626 0.02317 2824200 776.62 695.66 664.66 767.44 879.56 709.26 441.53 655.41 861.12 872.79 TRUE FALSE FALSE 767.1542567 705.4535197 676.2281285 856.1750237 834.6727711 663.940575 479.0335472 674.3732543 784.0992705 850.11479 0.902412552 0.829833251 0.79545508 1.007128724 0.981835372 0.781001087 0.563492781 0.79327317 0.92234517 1 9.73151385 -5.407866103 0.237071795 0.982120041 3.67E-16 0.355265089 0.103268871 18.53586402 0.407373931 0.071300253 6.266932581 3.91E-06 5.407866103 -0.982120041 RQQDPS(ph)PGSNLGGGDDLK ddPTM_HeLa_Romidepsin_16h_R1 1 RQQDPSPGSNLGGGDDLK 18 1 J3KTD8;Q13951-2 J3KTD8 CBFB Core-binding factor subunit beta 1 0 RQQDPS(0.999)PGS(0.001)NLGGGDDLK 145.99 4.03E-11 0 1996.7 1889.4 1353.6 1810.2 1564.3 1566.6 1128.8 1331.9 1931.9 1965.3 TRUE FALSE FALSE 1972.363452 1915.999023 1377.15884 2019.503841 1484.467934 1466.499316 1224.680244 1370.436425 1759.106025 1914.241223 1.030363064 1.000918275 0.719428055 1.054989213 0.775486347 0.766099538 0.639773206 0.715916264 0.918957342 1 10.90255693 -8.554866006 0.577749659 1.016884383 0.622417646 0.545681825 0.098811811 0.545069325 0.27140525 0.019004962 0.110845243 2.79E-09 8.554866006 -0.394466737 RQS(ph)FAVLR ddPTM_HeLa_Romidepsin_16h_R1 2 RQSFAVLR 8 1 C9JUG3;Q8TE77-4;Q8TE77-2;Q8TE77;A0A087WWG1 C9JUG3 SSH3 Protein phosphatase Slingshot homolog 3 1 0 RQS(1)FAVLR;RQS(1)FAVLR ; 87.568 0.013384 27635000 2359.78 2783.9 2400.36 3234.3 2453.6 2710.3 2464.03 2476.3 2559.6 2510.65 TRUE FALSE FALSE 2331.018094 2823.091817 2442.137259 3608.264984 2328.383636 2537.120577 2673.324647 2547.947834 2330.662965 2445.422951 0.95321674 1.154439078 0.998656391 1.475517755 0.952139439 1.037497655 1.093195206 1.041925215 0.953071519 1 11.25586829 -10.26733284 24.39119852 0.977907903 1.108350718 0.178849993 0.135921794 438.2323746 1813705.787 0.02195545 0.025473468 5.40E-11 10.26733284 0.130442815 RQS(ph)LELQK ddPTM_HeLa_Romidepsin_16h_R1 2 RQSLELQK 8 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 RQS(1)LELQK;RQS(1)LELQK ; 103.08 0.0084317 17944600 9189.2 8626 8494.8 7756.8 7852 8558 8147.2 8436.4 10550.8 10605.5 TRUE FALSE FALSE 9077.198496 8747.437054 8642.648431 8653.677713 7451.28314 8011.17142 8839.222965 8680.493924 9607.110023 10329.96758 0.878724781 0.846801985 0.836657846 0.837725544 0.721326866 0.775527257 0.855687387 0.840321507 0.93002325 1 13.33454811 -11.18657003 0.471369893 1.00567957 0.800028225 0.665776919 0.041786843 0.336678667 0.172376142 0.029416671 0.014674111 6.51E-12 11.18657003 -0.205651344 RQS(ph)LTSPDSQSAR ddPTM_HeLa_Romidepsin_16h_R1 2 RQSLTSPDSQSAR 13 1 Q15751 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 RQS(0.995)LT(0.004)S(0.001)PDSQSAR;RQS(0.964)LT(0.03)S(0.006)PDSQSAR ; 73.593 0.0026671 0 880.7 759.4 878.76 999.87 986.01 1469.5 1532.64 1381.81 908.13 1050.95 TRUE FALSE FALSE 869.9656896 770.0908531 894.0544492 1115.479674 935.6902304 1375.603693 1662.822403 1421.790492 826.9045783 1023.646167 0.849869532 0.752301799 0.873401843 1.089712158 0.91407584 1.343827327 1.624411302 1.388947214 0.80780313 1 9.999501406 -8.160207591 3.126994052 0.919677026 1.507025602 0.851785789 0.106840336 0.070566327 1.313427827 0.015548986 0.044622575 6.92E-09 8.160207591 0.587348576 RQS(ph)MAFSILNTPK ddPTM_HeLa_Romidepsin_16h_R1 1 RQSMAFSILNTPK 13 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 RQS(0.5)MAFS(0.5)ILNTPK 70.488 0.018799 1424800 1073.7 1083.4 1269.8 1083.3 824.06 984.09 745.24 803.98 1096.3 1247.2 TRUE FALSE FALSE 1060.613331 1098.652134 1291.900336 1208.556243 782.0051432 921.209825 808.540667 827.2418928 998.2441823 1214.797564 0.87307825 0.904391123 1.063469647 0.994862254 0.643732887 0.758323734 0.665576464 0.680970984 0.821737063 1 10.24650021 -8.761641294 25 0.949404973 0.690693718 0.760711357 0.070208746 1.908158815 236303.499 0.01015827 0.019291565 1.73E-09 8.761641294 -0.258711255 RQS(ph)PEPSPVTLGR ddPTM_HeLa_Romidepsin_16h_R1 2 RQSPEPSPVTLGR 13 1 Q9NRL2;Q9NRL2-2 Q9NRL2 BAZ1A Bromodomain adjacent to zinc finger domain protein 1A 1 0 RQS(0.999)PEPS(0.001)PVTLGR;RQS(0.992)PEPS(0.008)PVTLGR ; 140.33 0.0016912 52155000 4545.4 4488.2 4571.5 3073.8 3652.4 3610.8 3127.5 3747.3 5421.4 5419.5 TRUE FALSE FALSE 4489.998916 4551.384997 4651.06504 3429.207219 3466.004399 3380.081533 3393.149772 3855.722213 4936.496406 5278.700609 0.85058791 0.862216923 0.881100366 0.649630936 0.656601815 0.640324539 0.642800193 0.730430176 0.935172644 1 12.36596713 -9.87044076 0.428797137 0.981657469 0.624510616 0.800844448 0.057708005 0.328965549 0.143262707 0.026638443 0.044676942 1.35E-10 9.87044076 -0.357146853 RQS(ph)PLPPQK ddPTM_HeLa_Romidepsin_16h_R1 6 RQSPLPPQK 9 1 Q01105;B2REB7 Q01105 SET Protein SET 1 0 RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK;RQS(1)PLPPQK ;;;;; 131.12 0.00339 396554000 41624.2 42022.1 42768 44243 33723.4 30726.1 28451.4 16916.1 48489.9 43314.7 TRUE FALSE FALSE 41116.86824 42613.68823 43512.3591 49358.58383 32002.36906 28762.80137 30868.06121 17405.54066 44152.8419 42189.37785 0.974578682 1.01005728 1.03135816 1.16992917 0.75854091 0.681754575 0.731654809 0.412557415 1.046539298 1 15.36459219 -8.566677489 4.764543702 1.004424388 0.633338961 0.802231903 0.096359519 0.066891462 3.420945015 0.013467842 0.028009499 2.71E-09 8.566677489 -0.371085427 RQS(ph)SGSATNVASTPDNR ddPTM_HeLa_Romidepsin_16h_R1 4 RQSSGSATNVASTPDNR 17 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 RQS(0.495)S(0.495)GS(0.011)ATNVASTPDNR;RQS(0.954)S(0.015)GS(0.015)AT(0.015)NVASTPDNR;RQS(0.913)S(0.087)GSATNVASTPDNR;RQS(0.853)S(0.123)GS(0.008)AT(0.008)NVAS(0.004)T(0.004)PDNR ;;; 246.48 8.60E-59 13925100 3583.48 3493.132 3493.72 3682.2 4376.64 4008.73 3449.599 4052.7 3417.556 3198.07 TRUE FALSE FALSE 3539.803167 3542.308404 3554.526731 4107.953289 4153.283729 3752.585091 3742.607853 4169.95848 3111.881232 3114.98368 1.136379362 1.137183616 1.141106052 1.31877201 1.333324394 1.204688523 1.201485541 1.338677473 0.999004024 1 11.60500889 -10.50083937 0.367164933 0.991168997 1.296481982 0.763484058 0.057422413 0.432920479 0.17020119 0.046526244 0.042970028 3.16E-11 10.50083937 0.305312986 RQS(ph)SSYDDPWK ddPTM_HeLa_Romidepsin_16h_R1 2 RQSSSYDDPWK 11 1 E9PMG1;H0YDT0;Q96D71-2;Q96D71-4;Q96D71-3;Q96D71;H0YCF0;H7C1V2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 1 0 RQS(0.545)S(0.169)S(0.169)Y(0.118)DDPWK;RQS(0.656)S(0.166)S(0.166)Y(0.012)DDPWK ; 99.991 0.0056928 8541900 8051.7 6922.1 8132.6 4319.2 10907 13227.9 8755 11405.8 7664.6 8371.3 TRUE FALSE FALSE 7953.562783 7019.549505 8274.144492 4818.606226 10350.37509 12382.67988 9498.649481 11735.80883 6979.05898 8153.812419 0.975440981 0.860891709 1.014757768 0.590963586 1.269390876 1.518636834 1.16493353 1.439303264 0.855925869 1 12.99325905 -8.544565096 24.95637214 0.953875561 1.360131901 0.687490715 0.150246044 100.0387688 115122.9143 0.019890273 0.039782987 2.85E-09 8.544565096 0.40625634 RQS(ph)STPSAPELGQQPDVNISEWK ddPTM_HeLa_Romidepsin_16h_R1 2 RQSSTPSAPELGQQPDVNISEWK 23 1 I3L213;Q93100-4;Q93100-2;Q93100-3;Q93100 I3L213 PHKB Phosphorylase b kinase regulatory subunit beta 1 0 RQS(0.435)S(0.374)T(0.089)PS(0.102)APELGQQPDVNISEWK;RQS(0.447)S(0.447)T(0.054)PS(0.052)APELGQQPDVNISEWK ; 60.541 0.0024584 14709900 3040.3 2604.4 2842 3354.5 3379.7 3436.3 2330.3 3092.2 3063.6 2459.4 TRUE FALSE FALSE 3003.243654 2641.064812 2891.463818 3742.363073 3207.221298 3216.73152 2528.235624 3181.667928 2789.583943 2395.504433 1.253699894 1.102508839 1.207037556 1.562244269 1.338850078 1.342820107 1.055408451 1.328182859 1.164507944 1 11.22611377 -12.10632592 0.434668663 0.937072664 1.295232745 0.216424987 0.139769287 1.531911591 0.42010846 0.2456545 0.044378397 7.83E-13 12.10632592 0.358160081 RQSNS(ph)MGT(ph)TVS(ph)QSFLSYGK ddPTM_HeLa_Romidepsin_16h_R1 1 RQSNSMGTTVSQSFLSYGK 19 1 Q68CL5-5 Q68CL5-5 3 0 RQS(0.287)NS(0.798)MGT(0.903)T(0.25)VS(0.695)QS(0.05)FLS(0.012)Y(0.005)GK 44.312 0.023998 3654900 770.95 748.18 646.51 543.02 642.62 628.87 494.49 625.92 799.16 832.09 TRUE FALSE FALSE 761.5533649 758.7128977 657.7622354 605.8065274 609.8247035 588.6872366 536.4919683 644.0300077 727.6811281 810.4721818 0.939641584 0.936136878 0.81157904 0.74747356 0.752431381 0.726350947 0.661949886 0.79463555 0.897848371 1 9.662618858 -9.663778338 1.128723904 0.976731386 0.722654021 0.838747477 0.042133288 0.088625409 0.226134099 0.006393773 0.010286083 2.17E-10 9.663778338 -0.254077365 RQSSGS(ph)ATNVASTPDNR ddPTM_HeLa_Romidepsin_16h_R1 1 RQSSGSATNVASTPDNR 17 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 RQS(0.072)S(0.221)GS(0.682)AT(0.024)NVASTPDNR 104.3 0.00080048 1015900 1071.2 994.07 989.19 624.62 1476.8 1743.1 1368.1 1157.6 1016.7 1008.2 TRUE FALSE FALSE 1058.143802 1008.064544 1006.406437 696.8415033 1401.433385 1631.721536 1484.30638 1191.09333 925.7638056 982.0068187 1.077532032 1.026535177 1.024846689 0.709609638 1.427111664 1.661619354 1.51150313 1.212917575 0.942726454 1 9.939589232 -8.640005519 8.11701207 1.015533558 1.479198217 0.728103356 0.144491876 0.0962632 6.451868756 0.020118887 0.040313151 2.29E-09 8.640005519 0.463664659 SAGAAQK(ac)KPAATTAK ddPTM_HeLa_Romidepsin_16h_R1 2 SAGAAQKKPAATTAK 15 2 Q6PL18;E5RHW7;E5RIP2 Q6PL18 ATAD2 ATPase family AAA domain-containing protein 2 0 1 ; SAGAAQK(0.991)K(0.009)PAATTAK;SAGAAQK(0.987)K(0.013)PAATTAK 116.78 0.0017936 27497000 5532.8 4773.3 5330.8 10658.4 19165.9 26791 26208 23185 5931.4 5175.3 FALSE TRUE FALSE 5465.364105 4840.498643 5423.580338 11890.77436 18187.79261 25079.14156 28434.10687 23855.8214 5400.880729 5040.84496 1.08421587 0.96025541 1.07592683 2.358885158 3.608084111 4.975186058 5.640742195 4.732504488 1.071423694 1 12.29944987 -8.704555431 1.432903859 1.022363149 5.266467526 0.981444934 0.246283724 0.032926748 0.135072906 0.036089002 0.094657521 1.97E-09 8.704555431 4.244104377 up RQVDQLTNDK ddPTM_HeLa_Romidepsin_16h_R1 2 RQVDQLTNDK 10 1 P08670;B0YJC4 P08670 VIM Vimentin 0 0 ; ; 173.04 0.00033046 11322300 6630.5 6288.3 6551.2 6341.9 7238.4 7620.9 6794.4 4623.8 7109.8 6495.6 FALSE FALSE TRUE 6549.684916 6376.826852 6665.220888 7075.180318 6868.997438 7133.949085 7371.516166 4757.582358 6473.881681 6326.843376 1.035221599 1.007900224 1.053482834 1.118279669 1.085691083 1.127568467 1.165117536 0.751967778 1.02324039 1 12.62727017 -9.667294269 5.325875654 1.016489218 1.0645214 0.013788151 0.107655338 0.573316552 26.05486314 0.015883596 0.022511361 2.15E-10 9.667294269 0.048032182 RQVS(ph)ASELHTSGILGPETLR ddPTM_HeLa_Romidepsin_16h_R1 1 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 RQVS(0.884)AS(0.099)ELHT(0.013)S(0.004)GILGPET(0.001)LR 49.176 0.021755 18414000 1237.3 1443.3 1383.5 1575.6 1772.8 1676.6 1501.3 1372.7 1766.6 1632.5 TRUE FALSE FALSE 1222.219312 1463.618815 1407.579237 1757.778285 1682.327401 1569.470671 1628.820385 1412.416909 1608.590871 1590.087415 0.768649132 0.920464373 0.885221293 1.105460158 1.058009381 0.987034207 1.024359019 0.888263686 1.011636754 1 10.63489036 -9.292097553 24.19508487 0.890300117 1.014376779 0.216031684 0.083332495 464.3352085 366446.8205 0.015215337 0.023243579 5.10E-10 9.292097553 0.124076661 RQVSAS(ph)ELHTSGILGPETLR ddPTM_HeLa_Romidepsin_16h_R1 1 RQVSASELHTSGILGPETLR 20 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 RQVS(0.121)AS(0.878)ELHTSGILGPETLR 94.019 0.00037503 29487000 1045.1 1157.9 833.66 1104.9 1179 1092.4 1107.3 1569.4 1235.6 905.28 TRUE FALSE FALSE 1032.361919 1174.200947 848.1695026 1232.653737 1118.831231 1022.599166 1201.354034 1614.808113 1125.084841 881.7606951 1.170796028 1.331654896 0.961904412 1.397945887 1.268860403 1.159724142 1.362449065 1.831345082 1.275952589 1 9.784243359 -4 0.511985116 1.099503926 24.12745579 0.598502326 0.14633081 43.38401476 0.403655433 0.027100168 1087.010895 1.00E-04 4 23.02795186 RRDEDMLYSPELAQR ddPTM_HeLa_Romidepsin_16h_R1 1 RRDEDMLYSPELAQR 15 2 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 0 0 59.709 0.018286 8753300 895.84 938.06 952.26 1057.8 997.75 799.72 676.14 926.76 1198.2 1232.4 FALSE FALSE TRUE 884.9211575 951.2660333 968.8336858 1180.107813 946.8310944 748.620473 733.5713147 953.5743384 1091.029991 1200.38207 0.73719958 0.792469379 0.807104429 0.983110163 0.788774772 0.623651828 0.611114855 0.794392354 0.908902272 1 10.22927796 -16.52287875 0.207461712 2.173660332 0.718443241 0.361136052 0.09988101 36.26473221 0.447942064 17.27876785 0.09974344 3.00E-17 16.52287875 -1.455217091 RRDELSEEINNLR ddPTM_HeLa_Romidepsin_16h_R1 1 RRDELSEEINNLR 13 2 A0A087WZG9;B4DSP0;Q86TG7-2;A0A087WXK2;A0A087WUL4;A0A087WX23;Q86TG7;A0A087WYS2 A0A087WZG9 PEG10 Retrotransposon-derived protein PEG10 0 0 75.088 0.016824 2154000 907.68 950.51 863.05 1022.9 1478.2 1465.3 1406.3 1702.9 1320 1268.9 FALSE FALSE TRUE 896.616847 963.8913047 878.0710232 1141.172511 1402.761938 1371.672059 1525.751087 1752.170725 1201.935894 1235.933795 0.725457019 0.779889108 0.710451504 0.923328188 1.134981456 1.109826485 1.23449257 1.417689792 0.972492134 1 10.27138575 -8.204879643 1.032630903 0.848448732 1.37047525 0.764438596 0.105669927 0.298618198 0.522605442 0.021015873 0.118267931 6.24E-09 8.204879643 0.522026518 RREEEGLQLR ddPTM_HeLa_Romidepsin_16h_R1 1 RREEEGLQLR 10 2 C9J352;C9JWD9;F2Z3G4;C9J4U1;C9JYI4;P52294 C9J352 KPNA1 "Importin subunit alpha-5;Importin subunit alpha-5, N-terminally processed" 0 0 87.806 0.013862 2581800 1474.1 1160.1 1258.2 1267.7 1149.1 1473.9 1281.5 1238.3 1432.2 1248.8 FALSE FALSE TRUE 1456.133102 1176.431918 1280.098443 1414.277439 1090.457139 1379.722547 1390.350578 1274.128257 1304.100445 1216.355996 1.197127409 0.967177308 1.052404434 1.162716707 0.896495058 1.134308172 1.143045772 1.047496178 1.072137145 1 10.24834981 -10.25039989 24.94389 1.093087946 1.061534665 0.025132265 0.088616132 3011.356318 6804217.911 0.016980841 0.020699774 5.62E-11 10.25039989 -0.031553281 RREEGPPPPSPDGAS(ph)SDAEPEPPSGR ddPTM_HeLa_Romidepsin_16h_R1 1 RREEGPPPPSPDGASSDAEPEPPSGR 26 2 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;E9PD53;Q9NTJ3-2;F8WCB7 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4;Structural maintenance of chromosomes protein 1 0 RREEGPPPPS(0.356)PDGAS(0.365)S(0.272)DAEPEPPS(0.007)GR 80.554 6.26E-05 41436000 1041.6 935.2 1051.8 911.44 953.82 761.48 705.85 856.76 1300.6 1058.1 TRUE FALSE FALSE 1028.904579 948.3657701 1070.106138 1016.824981 905.1430062 712.8238856 765.8048814 881.5489989 1184.271079 1030.610409 0.998344834 0.920198129 1.038322656 0.986624016 0.878259134 0.691652131 0.743059525 0.855365898 1.149096756 1 10.00928335 -8.561119249 3.264052464 0.995039614 0.762043085 0.733039202 0.067853154 0.065848569 1.444340605 0.006591388 0.014539574 2.75E-09 8.561119249 -0.232996529 RREPES(ph)PPASAPIPLFGADTIGQR ddPTM_HeLa_Romidepsin_16h_R1 1 RREPESPPASAPIPLFGADTIGQR 24 2 Q96AY4 Q96AY4 TTC28 Tetratricopeptide repeat protein 28 1 0 RREPES(0.999)PPAS(0.001)APIPLFGADTIGQR 62.765 0.0034076 0 526.72 577.79 671.46 386.74 521.42 620.17 500.69 605.38 625.28 770.97 TRUE FALSE FALSE 520.300134 585.9241428 683.1464796 431.4566985 494.8099917 580.5431385 543.2185961 622.8957152 569.3533908 750.9400883 0.69286504 0.78025418 0.909721681 0.574555421 0.658920731 0.773088489 0.723384734 0.829487898 0.758187503 1 9.552554001 -12.36313199 0.795318194 1.023110079 0.736807345 0.025222523 0.114661781 0.47899705 0.47000743 0.090737137 0.017280688 4.33E-13 12.36313199 -0.286302734 RRGDS(ph)ES(ph)EEDEQDSEEVR ddPTM_HeLa_Romidepsin_16h_R1 2 RRGDSESEEDEQDSEEVR 18 2 Q9NZ63 Q9NZ63 C9orf78 Uncharacterized protein C9orf78 2 0 RRGDS(1)ES(1)EEDEQDSEEVR;RRGDS(1)ES(0.999)EEDEQDS(0.001)EEVR ; 77.575 0.0023649 3713000 718.24 719.17 772.24 654.59 986.8 959.29 942.91 1070.53 702.15 816.49 TRUE FALSE FALSE 709.4858146 729.2944941 785.6805133 730.2767757 936.4399137 897.994465 1023.000752 1101.504097 639.3479454 795.2774721 0.892123617 0.917031501 0.987932565 0.918266644 1.177500868 1.129158685 1.286344437 1.38505633 0.803930663 1 9.635314494 -7.987685204 0.85653763 0.943845071 1.427123502 0.844090829 0.07035762 0.25877186 0.252773989 0.00994862 0.092862261 1.03E-08 7.987685204 0.483278431 RRS(ph)PPADAIPK ddPTM_HeLa_Romidepsin_16h_R1 1 RRSPPADAIPK 11 2 M0R1Q8;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;C9JW69;P18754;P18754-2 M0R1Q8 RCC1 Regulator of chromosome condensation 1 0 RRS(1)PPADAIPK 100.18 0.017334 211610000 7628.6 7851.5 6695.5 7666 7966.2 8097 6059 7215.5 8346.9 7416 TRUE FALSE FALSE 7535.619689 7962.033623 6812.032369 8552.37899 7559.655088 7579.627832 6573.651309 7424.269108 7600.332359 7223.331251 1.043233299 1.102266163 0.943059668 1.183993741 1.046560766 1.049325798 0.910058127 1.027817893 1.052192139 1 12.81844862 -7.790288408 24.98724209 1.036244617 0.968937903 0.171701595 0.066106092 253.2793446 219374.5885 0.008808377 0.026431121 1.62E-08 7.790288408 -0.067306715 RRS(ph)QS(ph)IEQESQEK ddPTM_HeLa_Romidepsin_16h_R1 1 RRSQSIEQESQEK 13 2 A0A0A0MRN0;Q5VTL8 A0A0A0MRN0 PRPF38B Pre-mRNA-splicing factor 38B 2 0 RRS(1)QS(1)IEQESQEK 101.01 0.012015 23063000 5487.4 5636.5 5282.4 5913.9 5265.9 5195.6 4549.5 5862.3 6245.1 5553.4 TRUE FALSE FALSE 5420.517458 5715.850795 5374.337956 6597.692944 4997.161473 4863.617928 4935.934416 6031.916401 5686.522615 5409.121867 1.002106736 1.056705864 0.993569398 1.219734572 0.923839691 0.899151109 0.912520468 1.115137826 1.051283878 1 12.40117869 -7.219079639 22.42196951 1.002458091 1.115139198 0.118858948 0.088069851 11718.20127 6202205.464 0.01162494 5.150459943 6.04E-08 7.219079639 0.112681106 RRS(ph)RSS(ph)AAAK ddPTM_HeLa_Romidepsin_16h_R1 1 RRSRSSAAAK 10 3 A0A0M3HER2;Q7Z7K6-3;Q7Z7K6 A0A0M3HER2 CENPV Centromere protein V 2 0 RRS(0.973)RS(0.041)S(0.986)AAAK 101.39 0.026481 10315000 883.16 852.74 961.24 566.51 987.92 1064.3 907 586.16 1144.1 918.55 TRUE FALSE FALSE 872.3957062 864.7448961 977.969979 632.0125517 937.502756 996.2946649 984.0405574 603.1196148 1041.768831 894.6859386 0.97508597 0.966534578 1.093087459 0.706407159 1.047856813 1.113569155 1.099872609 0.674113215 1.164396114 1 9.805237532 -7.248925866 24.30103825 0.992683098 0.674112919 0.399063108 0.123172413 962.8574542 1869805.2 0.014382089 0.328981713 5.64E-08 7.248925866 -0.318570179 RRSQRVCAS(ph)GPS(ph)MLNSAR ddPTM_HeLa_Romidepsin_16h_R1 1 RRSQRVCASGPSMLNSAR 18 3 Q9NV92 Q9NV92 NDFIP2 NEDD4 family-interacting protein 2 2 0 RRS(0.001)QRVCAS(0.999)GPS(0.988)MLNS(0.012)AR 68.123 0.0023532 0 1321.3 1380 1085.2 4298 1573.8 1616.5 1285.8 1776.4 1168.7 1268.6 TRUE FALSE FALSE 1305.195487 1399.427676 1104.087451 4794.954983 1493.483113 1513.210867 1395.01582 1827.797331 1064.168545 1235.641589 1.056289703 1.132551452 0.89353374 3.880538681 1.208670157 1.224635752 1.128980954 1.479229372 0.861227523 1 10.27104462 RRYEDDGIS(ph)DDEIEGK ddPTM_HeLa_Romidepsin_16h_R1 1 RRYEDDGISDDEIEGK 16 2 I3VM54;Q9Y2K7-3;Q9Y2K7 I3VM54 KDM2A Lysine-specific demethylase 2A 1 0 RRYEDDGIS(1)DDEIEGK 81.788 0.020521 8140000 2596.6 2625.5 2038.4 1790.7 2446.9 2088.5 1787.6 2197 2423.1 2642.2 TRUE FALSE FALSE 2564.95164 2662.461858 2073.877497 1997.749159 2322.025562 1955.05159 1939.438699 2260.566729 2206.371867 2573.555263 0.996656912 1.034546216 0.805841447 0.776260447 0.902263727 0.759669558 0.753602896 0.87838282 0.857324457 1 11.32954705 -9.756067922 24.99764625 1.00108658 0.809993579 0.579220662 0.064704219 38.72056962 180196.6867 0.006865512 0.009547241 1.75E-10 9.756067922 -0.191093001 RS(ph)DSLLSFR ddPTM_HeLa_Romidepsin_16h_R1 2 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 RS(1)DSLLSFR;RS(0.967)DS(0.033)LLSFR ; 105.2 0.007007 60925000 3933.2 3498.3 3688.5 2809.9 2546.41 2147.65 2187.97 2150.38 3395.9 3038.7 TRUE FALSE FALSE 3885.260646 3547.549159 3752.696795 3134.793859 2416.457196 2010.422096 2373.816117 2212.597853 3092.162199 2959.754136 1.312697091 1.198595896 1.267908287 1.059139954 0.816438489 0.679253074 0.802031523 0.747561369 1.04473617 1 11.53126162 -8.79575865 3.004372512 1.164321108 0.74865297 0.813808529 0.091887072 0.105873037 1.958344117 0.018775352 0.037676939 1.60E-09 8.79575865 -0.415668139 RS(ph)ESPPAELPSLR ddPTM_HeLa_Romidepsin_16h_R1 1 RSESPPAELPSLR 13 1 Q14669;Q14669-2;Q14669-3;G5E9G6;H7C1L9 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 RS(0.979)ES(0.021)PPAELPSLR 152.38 0.00022822 9147000 1454.7 1655.7 1415.8 766.36 1009.3 1281.8 878.24 941.73 1554.5 1407.1 TRUE FALSE FALSE 1436.969557 1679.008988 1440.441405 854.970149 957.7916548 1199.897117 952.8376837 968.9774717 1415.461627 1370.543339 1.048467068 1.225068146 1.051000259 0.623818397 0.698840837 0.875490094 0.695226234 0.70700243 1.032774073 1 10.42053223 -9.272182252 24.97276288 1.043765476 0.726149509 0.813546047 0.083560898 253.5791697 589466.3902 0.013624018 0.020940272 5.34E-10 9.272182252 -0.317615967 RS(ph)ETPPHWR ddPTM_HeLa_Romidepsin_16h_R1 1 RSETPPHWR 9 1 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 0 RS(0.976)ET(0.024)PPHWR 69.672 0.025638 7496300 1129.8 1185.9 1679.1 1071.2 1099.5 1246.8 1526.5 799.26 1943.2 1476.9 TRUE FALSE FALSE 1116.029563 1202.595131 1708.324031 1195.057184 1043.388412 1167.133504 1656.160872 822.3853271 1769.395325 1438.529925 0.775812546 0.835988957 1.187548484 0.830748922 0.72531575 0.81133766 1.151287049 0.571684546 1.230002445 1 10.49037952 RS(ph)HLVEAHVR ddPTM_HeLa_Romidepsin_16h_R1 1 RSHLVEAHVR 10 1 Q9UNX9 Q9UNX9 KCNJ14 ATP-sensitive inward rectifier potassium channel 14 1 0 RS(1)HLVEAHVR 71.268 0.024474 6772500 3871.1 3366.6 4103.9 2558.1 4765.6 4814.1 3428.9 4028.5 3383.6 3785.6 TRUE FALSE FALSE 3823.917544 3413.995083 4175.326658 2853.879558 4522.393649 4506.494547 3720.15068 4145.058292 3080.962342 3687.249566 1.03706502 0.925892056 1.132368879 0.773986004 1.226495134 1.22218322 1.008922942 1.124159951 0.835571959 1 11.84832935 RS(ph)PILLPK ddPTM_HeLa_Romidepsin_16h_R1 1 RSPILLPK 8 1 Q8TD16;Q8TD16-2 Q8TD16 BICD2 Protein bicaudal D homolog 2 1 0 RS(1)PILLPK 68.132 0.02627 7913700 1024.4 944.77 1088.5 1186.9 1300.3 1584 1204.3 1301 981.84 919.12 TRUE FALSE FALSE 1011.914219 958.0704969 1107.444886 1324.134963 1233.940839 1482.787512 1306.593212 1338.642382 894.0217713 895.2411299 1.130325881 1.070181502 1.237035307 1.479081912 1.378333499 1.656299585 1.45948747 1.495286954 0.998637955 1 9.806132509 -9.409605054 1.332012652 1.057137894 1.517144225 0.891025861 0.073386708 0.096286742 0.338292216 0.012840673 0.022796 3.89E-10 9.409605054 0.460006331 RS(ph)PPADAIPK ddPTM_HeLa_Romidepsin_16h_R1 2 RSPPADAIPK 10 1 M0R1Q8;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;C9JW69;P18754;P18754-2 M0R1Q8 RCC1 Regulator of chromosome condensation 1 0 RS(1)PPADAIPK;RS(1)PPADAIPK ; 69.229 0.025941 17215300 6148.6 6414.4 3480.8 10445.4 6234.9 5065.1 4152.9 7364.4 6708.3 9517.1 TRUE FALSE FALSE 6073.658498 6504.702092 3541.381864 11653.1463 5916.709787 4741.456457 4505.647222 7577.477295 6108.292847 9269.84437 0.655206091 0.701705642 0.382032505 1.25710269 0.638274986 0.511492563 0.486054247 0.817433065 0.65894233 1 13.1783294 -12.23238383 0.728628031 1.026083299 0.674216974 0 0.249157049 1.007379803 0.853540034 0.216181776 0.045618105 5.86E-13 12.23238383 -0.351866325 RS(ph)PT(ph)SSPTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 RSPTSSPTPQR 11 1 A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 A0A0D9SFE4 DNM1 Dynamin-1 2 0 RS(0.99)PT(0.463)S(0.312)S(0.213)PT(0.022)PQR 94.538 0.021949 6789700 1387.7 1194.9 1178.9 1445.1 1334.4 1464.8 1526.9 930.87 1577.7 1409 TRUE FALSE FALSE 1370.786179 1211.721834 1199.41826 1612.189261 1266.300589 1371.204007 1656.594848 957.8032548 1436.586561 1372.393977 0.998828472 0.882925642 0.873960597 1.17472773 0.922694656 0.999132924 1.207084027 0.697906921 1.046774166 1 10.42247898 -10.17117182 0.003390607 1.975152736 0.000220759 0.014476427 0.139898919 83163.58347 234.2536545 68112.52985 68325.26333 6.74E-11 10.17117182 -1.974931977 RS(ph)PTEDFR ddPTM_HeLa_Romidepsin_16h_R1 2 RSPTEDFR 8 1 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 0 RS(0.999)PT(0.001)EDFR;RS(0.998)PT(0.002)EDFR ; 91.636 0.011858 34163000 3015.6 3025.1 3224.3 2241.64 2327.1 2513.5 2111.01 2555.7 3128.6 3113.5 TRUE FALSE FALSE 2978.844707 3067.687437 3280.417589 2500.828964 2208.339403 2352.895462 2290.319137 2629.645147 2848.77018 3032.610821 0.982270685 1.011566475 1.081714002 0.824645532 0.728197429 0.775864626 0.755230154 0.867122523 0.939378756 1 11.56634465 -9.124645321 5.299901417 0.999045408 0.779110852 0.837971219 0.04699655 0.057704943 2.270993235 0.006295471 0.010573994 7.51E-10 9.124645321 -0.219934556 RS(ph)PTS(ph)SPTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 RSPTSSPTPQR 11 1 A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 A0A0D9SFE4 DNM1 Dynamin-1 2 0 RS(1)PT(0.025)S(0.674)S(0.279)PT(0.022)PQR 102.5 0.0063119 13515000 4173.9 4181.9 4339.9 4780.6 4688.8 4814.3 4404.7 3283.2 4762.7 4253.1 TRUE FALSE FALSE 4123.026901 4240.772898 4415.434139 5333.355465 4449.51304 4506.681767 4778.835108 3378.194212 4336.712184 4142.603849 0.995274241 1.023697426 1.065859614 1.287440378 1.074086058 1.08788625 1.153582453 0.815476047 1.046856601 1 12.01632215 -9.778137429 3.583414549 0.998656115 1.09449592 0.064608746 0.110408756 0.329465697 8.996670194 0.016805439 0.023182236 1.67E-10 9.778137429 0.095839805 RS(ph)PTSSPTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 RSPTSSPTPQR 11 1 A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 A0A0D9SFE4 DNM1 Dynamin-1 1 0 RS(0.998)PT(0.001)SSPTPQR 58.172 0.0042182 0 917.25 680.14 605.54 1661.6 1091.7 922.22 657.13 816.68 777.2 1011.9 TRUE FALSE FALSE 906.0702042 689.7150288 616.0791697 1853.72201 1035.986475 863.2931183 712.9466058 840.3093473 707.6852855 985.6106921 0.91929827 0.699784443 0.625073545 1.880785207 1.051111239 0.875896665 0.723355186 0.852577345 0.718017054 1 9.944874097 -8.027662793 5.145690895 0.990343516 0.788929467 0.054698065 0.331997857 0.419369512 30.71655932 0.045179179 0.126145689 9.38E-09 8.027662793 -0.201414049 RS(ph)PTVEPSTLPR ddPTM_HeLa_Romidepsin_16h_R1 2 RSPTVEPSTLPR 12 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 RS(1)PTVEPSTLPR;RS(0.995)PT(0.005)VEPSTLPR ; 129.29 0.0012639 44400000 3916.5 3366.4 3032.2 3507.6 3048.4 3044.6 2734.4 3075.6 4169.7 3804.4 TRUE FALSE FALSE 3868.764192 3413.792268 3084.974169 3913.165216 2892.828773 2850.059886 2966.659868 3164.587634 3796.751589 3705.56114 1.044042736 0.921261892 0.832525508 1.056025004 0.780672256 0.769130444 0.800596659 0.854010368 1.02460908 1 11.85547631 -9.260130581 0.737038892 1.020535079 0.795998349 0.539285768 0.073825686 0.353035265 0.37519763 0.015164635 0.037323727 5.49E-10 9.260130581 -0.224536729 RS(ph)PVPAQIAITVPK ddPTM_HeLa_Romidepsin_16h_R1 2 RSPVPAQIAITVPK 14 1 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 0 RS(1)PVPAQIAITVPK;RS(1)PVPAQIAITVPK ; 76.526 0.012662 342950000 13901.3 13571.2 12917 12737.1 13966.8 14089.9 11481.3 13775.4 15060.2 13800.6 TRUE FALSE FALSE 13731.86561 13762.25571 13141.81497 14209.82343 13254.02208 13189.60086 12456.52134 14173.96947 13713.17799 13442.05842 1.021559733 1.023820555 0.977663878 1.057116625 0.986011343 0.981218832 0.926682577 1.054449328 1.020169498 1 13.71446646 -8.554387093 24.99971836 1.012169818 0.981747015 0.136219005 0.034590291 256.615432 203605.8018 0.004531145 0.009062339 2.79E-09 8.554387093 -0.030422803 RS(ph)QINVHR ddPTM_HeLa_Romidepsin_16h_R1 1 RSQINVHR 8 1 Q96LA6-4;Q96LA6-3;Q96LA6-2;Q96LA6 Q96LA6-4 FCRL1 Fc receptor-like protein 1 1 0 RS(1)QINVHR 74.255 0.0026595 0 1309.1 1441.9 1101.9 1411.4 1311 1224.9 889.3 1065.5 1513.6 1667.1 TRUE FALSE FALSE 1293.144186 1462.199106 1121.078107 1574.592709 1244.094778 1146.632843 964.8371198 1096.328561 1378.219825 1623.788502 0.796374765 0.900486181 0.690408946 0.969703078 0.766167993 0.70614667 0.59418891 0.675167092 0.848768065 1 10.66514802 -6.615175673 0.073216578 1.279957108 3.44E-15 0.457176841 0.093460718 60.40200154 0.58721962 2.693469158 9.246168779 2.43E-07 6.615175673 -1.279957108 RS(ph)SAIGIENIQEVQEK ddPTM_HeLa_Romidepsin_16h_R1 2 RSSAIGIENIQEVQEK 16 1 F2Z357;J3KPC5;P47736;P47736-3;P47736-4;A0A0A0MQY8;X6R8W7;P47736-2 F2Z357 RAP1GAP Rap1 GTPase-activating protein 1 1 0 RS(0.616)S(0.384)AIGIENIQEVQEK;RS(0.637)S(0.363)AIGIENIQEVQEK ; 108.28 0.0010489 12862300 2327.4 2438.1 2595.7 2645 5163.4 7204.7 6283 7271.9 2628.2 2713.5 TRUE FALSE FALSE 2299.032754 2472.423636 2640.87707 2950.827345 4899.892431 6744.342922 6816.677863 7482.300953 2393.12721 2643.002879 0.869856318 0.935460062 0.999195684 1.1164677 1.853911121 2.551772825 2.579141293 2.830984791 0.905457663 1 11.36796228 -8.520963915 1.609722993 0.936333123 2.723387101 0.992609446 0.065716399 0.023135899 0.117536264 0.010932962 0.031059531 3.01E-09 8.520963915 1.787053977 up RS(ph)SDGS(ph)LSHEEDLAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSDGSLSHEEDLAK 15 1 A0A2R8Y7R9;Q13136-2;Q13136;E9PJZ7;H0YEF9 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 2 0 RS(0.952)S(0.048)DGS(0.994)LS(0.005)HEEDLAK 139.81 0.00029934 18715000 3327.7 3249.8 2987.2 3375.8 4349 4817.1 4358.8 4778.7 4232.6 3779.8 TRUE FALSE FALSE 3287.140712 3295.55077 3039.190963 3766.12588 4127.054302 4509.302856 4729.036363 4916.964145 3854.025655 3681.600251 0.892856499 0.895140848 0.825508137 1.022958937 1.120994682 1.224821422 1.284505661 1.335550796 1.046834363 1 11.84611727 -8.480919211 1.470767468 0.934880919 1.306352393 0.862213636 0.061244279 0.107717499 0.450152793 0.009653163 0.029886516 3.30E-09 8.480919211 0.371471474 RS(ph)SDPALIGLSTSVSDSNFSSEEPSR ddPTM_HeLa_Romidepsin_16h_R1 2 RSSDPALIGLSTSVSDSNFSSEEPSR 26 1 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 RS(0.5)S(0.5)DPALIGLS(0.001)TSVSDSNFSSEEPSR;RS(0.5)S(0.5)DPALIGLSTSVSDSNFSSEEPSR ; 127.3 1.47E-07 24127000 3160.9 3061.4 3279.4 2852.7 3212.2 3487.1 2770.6 3040.1 3248 3300.2 TRUE FALSE FALSE 3122.373735 3104.49847 3336.476581 3182.542596 3048.269448 3264.285564 3005.934695 3128.060497 2957.490745 3214.460328 0.971352394 0.965791502 1.03795855 0.990070578 0.948298979 1.015500342 0.935128883 0.973121513 0.92005825 1 11.65036083 -7.75181108 24.99989952 0.987487903 0.954125204 0.071014333 0.033212268 228.8348541 594157.861 0.003438279 0.012538997 1.77E-08 7.75181108 -0.033362699 RS(ph)SDSWEVWGSASTNR ddPTM_HeLa_Romidepsin_16h_R1 2 RSSDSWEVWGSASTNR 16 1 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;Q8N6T3-4;E5RHH7 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 RS(0.496)S(0.496)DS(0.009)WEVWGSASTNR;RS(0.498)S(0.498)DS(0.003)WEVWGSASTNR ; 89.028 0.0039419 20741000 2254.45 2131.27 2228.77 2259.98 2564.3 3007 2972.22 3847.1 2416.01 2466.31 TRUE FALSE FALSE 2226.971896 2161.274075 2267.560807 2521.289521 2433.434202 2814.862405 3224.680293 3958.409769 2199.916015 2402.234911 0.927041684 0.899693059 0.943937996 1.049559937 1.012987611 1.17176817 1.34236676 1.647802949 0.915778888 1 11.23016152 -7.167971375 0.824917264 0.958653144 2.141224883 0.972733061 0.037350581 0.327237221 0.145583749 0.006720959 0.364882662 6.79E-08 7.167971375 1.182571739 RS(ph)SIGLR ddPTM_HeLa_Romidepsin_16h_R1 2 RSSIGLR 7 1 Q96GN5-5;Q96GN5-2;Q96GN5;C9IZR6;Q96GN5-4;C9J8L0 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 1 0 RS(0.999)S(0.001)IGLR;RS(0.7)S(0.3)IGLR ; 104.01 0.0097426 9554300 1760.61 1726.16 1983.15 2067.5 2430.9 3621 3801.2 1743.92 1944.85 2062.53 TRUE FALSE FALSE 1739.151008 1750.460926 2017.665894 2306.554078 2306.842102 3389.629786 4124.073833 1794.377574 1770.897745 2008.945173 0.86570357 0.871333349 1.004340945 1.148141875 1.148285246 1.687268439 2.052855343 0.8931939 0.881506259 1 10.97222248 -8.556372319 2.038342128 0.941961006 1.588119254 0.457767976 0.279795954 0.188056299 1.556795261 0.038649079 0.096347655 2.78E-09 8.556372319 0.646158248 RS(ph)SLLNAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSLLNAK 8 1 E9PCH4;Q8TEU7;Q8TEU7-4;B7Z7Y1;A0A5F9ZHG7;Q8TEU7-2;Q8TEU7-5;Q8TEU7-3;D6RE77 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 0 RS(0.834)S(0.166)LLNAK 80.916 0.017272 39356000 4940.5 5079.2 5670.1 6207.1 6101.2 7138.2 6565.4 3595.6 6054 5039 TRUE FALSE FALSE 4880.283286 5150.705111 5768.785712 6924.794107 5789.832997 6682.092057 7123.064912 3699.633013 5512.515077 4908.086054 0.994335314 1.049432519 1.175363604 1.410895007 1.179651892 1.361445579 1.451291773 0.753783241 1.123149639 1 12.26094483 -9.738603331 2.992552802 0.998636126 1.251065728 0.172344569 0.186361995 0.225729316 4.170553224 0.027255391 0.038416727 1.83E-10 9.738603331 0.252429603 RS(ph)SPAAFINPPIGTVTPALK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPAAFINPPIGTVTPALK 20 1 Q6R954;F8WEE2;Q8WUT1;F8WCX5;F6VRR5;Q9BY77-2;Q9BY77 Q6R954 PDIP46;POLDIP3 Polymerase delta-interacting protein 3 1 0 RS(0.5)S(0.5)PAAFINPPIGTVTPALK 87.352 0.00064736 69189000 2777.1 2595.1 2569.7 2545.6 2012.9 2331 2439.7 2632.8 2857.6 2789.8 TRUE FALSE FALSE 2743.251637 2631.633886 2614.424551 2839.934249 1910.174202 2182.056623 2646.928057 2708.975914 2602.009099 2717.320594 1.009542872 0.968466471 0.962133271 1.045122999 0.702962398 0.803017733 0.974094872 0.996929078 0.957564266 1 11.40796907 -8.831670346 24.9999991 1.00061551 0.871986554 0.344769987 0.081112368 37.81519058 13460.38719 0.012017822 0.021784159 1.47E-09 8.831670346 -0.128628956 RS(ph)SPETGTTGDVAWQISPK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPETGTTGDVAWQISPK 19 1 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 RS(0.251)S(0.251)PET(0.251)GT(0.123)T(0.123)GDVAWQISPK 93.583 0.00026494 0 2610 3058.2 2564.8 3041.6 2738.1 2341.8 2643.1 2153.5 3140.1 2623.8 TRUE FALSE FALSE 2578.188316 3101.25342 2609.439268 3393.284103 2598.36454 2192.166538 2867.604848 2215.808125 2859.241591 2555.633298 1.008825608 1.213497031 1.02105387 1.327766431 1.016720412 0.857778203 1.12207211 0.867028977 1.118799631 1 11.31946513 -7.240899671 22.82748318 1.037872348 0.867028425 0.137464403 0.128048287 2242.107606 2491711.387 0.01706714 0.817184011 5.74E-08 7.240899671 -0.170843922 RS(ph)SPPPPPSGSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 0 RS(0.981)S(0.019)PPPPPSGSSSR 113.65 0.0014806 10739000 310.6 214.21 211.44 282.81 205.72 261.63 207.31 325.9 412.81 272.41 TRUE FALSE FALSE 306.8142877 217.225654 215.1200245 315.5098229 195.2213408 244.9126874 224.9189062 335.3294023 375.8872397 265.3327489 1.156337802 0.818691454 0.810755647 1.189109992 0.735760442 0.923039799 0.847686187 1.263807064 1.416663571 1 8.051658942 -10.26962809 24.92867374 1.073826182 0.933573223 0.190789962 0.194691758 843.7959582 2568740.452 0.026688214 0.030788679 5.37E-11 10.26962809 -0.140252959 RS(ph)SQPSPTAVPASDSPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 RS(0.491)S(0.491)QPS(0.014)PT(0.004)AVPASDSPPTK 113.23 0.00024129 25233000 1220.2 1104.2 1486.2 1229.7 4348.8 7100.2 6947.4 8132.6 1323.8 1225.2 TRUE FALSE FALSE 1205.327733 1119.744957 1512.066688 1371.8837 4126.864508 6646.520135 7537.511983 8367.90395 1205.396012 1193.369127 1.010020877 0.938305618 1.267056984 1.14958873 3.45816262 5.569542552 6.31616137 7.011999689 1.010078093 1 10.22082464 -8.386783458 1.489021318 0.993178126 6.773730968 0.992468825 0.205990601 0.021077241 0.088683289 0.028485889 0.09524195 4.10E-09 8.386783458 5.780552842 up RS(ph)STSSEPTPTVK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSTSSEPTPTVK 13 1 F8WAN1;Q69YQ0-2;Q69YQ0;A0A494C1J1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 RS(0.494)S(0.494)T(0.004)S(0.004)S(0.004)EPTPTVK 82.942 0.01035 7509100 2847.9 2762.2 2813.2 3499.5 5586.6 6872.3 6709.5 7556.4 3072.7 3321.9 TRUE FALSE FALSE 2813.188699 2801.086324 2862.162566 3904.128656 5301.494956 6433.182209 7279.404763 7775.032512 2797.870016 3235.596559 0.869449775 0.86570939 0.884585737 1.206617878 1.638490726 1.988252272 2.249787521 2.402967233 0.864715352 1 11.65981602 -8.453735296 1.175070227 0.921649068 2.368674758 0.987759421 0.064960519 0.045213572 0.11592472 0.012500733 0.046703798 3.52E-09 8.453735296 1.44702569 up RS(ph)STVAPAQPDGAESEWTDVETR ddPTM_HeLa_Romidepsin_16h_R1 3 RSSTVAPAQPDGAESEWTDVETR 23 1 Q02241;A0A2U3TZL8;H7BYN4;Q02241-3;Q02241-2 Q02241;Q02241-3 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 0 RS(0.943)S(0.045)T(0.013)VAPAQPDGAESEWTDVETR;RS(0.906)S(0.069)T(0.025)VAPAQPDGAESEWTDVETR;RS(0.748)S(0.126)T(0.126)VAPAQPDGAESEWTDVETR ;; 171.96 5.62E-13 26816200 1569.85 1600.19 1424.52 1615.03 1599.52 1897.24 1760.79 1926.37 1791.49 1667.99 TRUE FALSE FALSE 1550.716064 1622.717517 1449.313173 1801.767368 1517.890526 1776.012487 1910.351459 1982.106477 1631.254648 1624.655379 0.954489231 0.998807216 0.892074216 1.109015112 0.934284615 1.093162593 1.175850265 1.220016566 1.00406195 1 10.66591801 -7.918228847 1.97704185 0.979796103 1.214951254 0.710310432 0.0547237 0.124092989 0.921370804 0.007170678 0.032945628 1.21E-08 7.918228847 0.235155151 RS(ph)TSPIIGSPPVR ddPTM_HeLa_Romidepsin_16h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 1 0 RS(0.542)T(0.25)S(0.208)PIIGSPPVR 116.79 0.0084527 32141000 3553.4 3493.2 3075.2 3064.4 4586 4911 4320.2 4824.1 3953.7 3794 TRUE FALSE FALSE 3510.089794 3542.377361 3128.722566 3418.720346 4351.959307 4597.20295 4687.15768 4963.677722 3600.07117 3695.431333 0.949845763 0.958582921 0.846646111 0.925120788 1.177659362 1.244023372 1.268365519 1.343193061 0.97419512 1 11.85152705 -8.596581382 3.145290975 0.960252874 1.279028759 0.914165036 0.04793083 0.060532758 1.206307136 0.008150131 0.017759543 2.53E-09 8.596581382 0.318775885 RS(ph)TVLGLPQHVQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSTVLGLPQHVQK 13 1 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 RS(0.5)T(0.5)VLGLPQHVQK 61.962 0.026418 11001000 3341 1991.6 2462.9 2030.8 2564.5 2052.5 2182.1 1753.8 2763.1 2220.1 TRUE FALSE FALSE 3300.278607 2019.637797 2505.765741 2265.610651 2433.623996 1921.351874 2367.44752 1804.543436 2515.961416 2162.421482 1.526195811 0.933970465 1.158777677 1.047719268 1.125416121 0.888518677 1.094813171 0.834501253 1.163492611 1 11.07843203 -9.345880054 1.097563836 1.23458402 0.979045278 0.182545752 0.166757874 0.60145831 1.436327139 0.039315178 0.076442703 4.51E-10 9.345880054 -0.255538742 RS(ph)YDVPPPPMEPDHPFYSNISK ddPTM_HeLa_Romidepsin_16h_R1 1 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 0 RS(0.542)Y(0.458)DVPPPPMEPDHPFYSNISK 65.149 0.0016515 9424800 1011.6 813.42 700.5 877.77 974.15 1084.9 889.95 975.75 861.55 981.23 TRUE FALSE FALSE 999.2702301 824.8713481 712.6919087 979.2618974 924.4354904 1015.578391 965.5423308 1003.981787 784.4908102 955.7375031 1.045548832 0.863073119 0.745698381 1.024613865 0.967248316 1.062612263 1.010258913 1.050478592 0.820822462 1 9.900470621 -8.265607503 24.60515657 0.985676257 1.038030822 0.019208158 0.10342813 742.064823 4380559.306 0.01442793 0.033340261 5.42E-09 8.265607503 0.052354565 RSAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_HeLa_Romidepsin_16h_R1 1 RSASPDDDLGSSNWEAADLGNEER 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 0 RS(0.271)AS(0.725)PDDDLGS(0.002)S(0.002)NWEAADLGNEER 50.158 0.012313 237430000 1376.7 1212.6 1126.7 1232.4 1168.3 1228.9 909 1091.8 1541.8 1348.6 TRUE FALSE FALSE 1359.920251 1229.671015 1146.309741 1374.895887 1108.677291 1150.377256 986.2104373 1123.38951 1403.897546 1313.563178 1.035291088 0.936133896 0.872671951 1.046691861 0.844022815 0.875768502 0.750790258 0.855223053 1.068770479 1 10.35926988 -8.632564649 0.593348193 1.015383856 0.777273535 0.604440712 0.062957627 0.534841169 0.293868076 0.012506187 0.065627341 2.33E-09 8.632564649 -0.238110321 RSDS(ph)AISVR ddPTM_HeLa_Romidepsin_16h_R1 2 RSDSAISVR 9 1 H3BR17;Q6Q0C0;Q6Q0C0-2 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 0 RS(0.434)DS(0.565)AIS(0.002)VR;RSDS(1)AISVR ; 152.38 0.0052338 18701400 4497.8 4826.5 4201.5 3693.1 3781.6 4781.5 4376.3 4369.7 5001.2 4683.6 TRUE FALSE FALSE 4442.979084 4894.447594 4274.625345 4120.113599 3588.610841 4475.977582 4748.022813 4496.130375 4553.880146 4561.919397 0.973927572 1.072892168 0.937023427 0.903153528 0.786644947 0.98116104 1.040794981 0.985578653 0.998237748 1 12.15542524 -9.612114189 23.35016952 0.994269322 0.936995542 0.199457379 0.067438816 19.26609916 5033.483391 0.01124959 0.015909324 2.44E-10 9.612114189 -0.05727378 RSDS(ph)LLSFR ddPTM_HeLa_Romidepsin_16h_R1 1 RSDSLLSFR 9 1 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 RS(0.368)DS(0.632)LLSFR 92.781 0.011096 13989000 1119.4 1148 1250.6 1232.8 795.11 677.24 533.38 685.15 1086.8 1021.7 TRUE FALSE FALSE 1105.756322 1164.161574 1272.366168 1375.342136 754.5325697 633.9665497 578.6852839 704.9737343 989.5938861 995.1560867 1.111138581 1.16982812 1.278559399 1.382036602 0.75820525 0.637052376 0.581502029 0.708405188 0.994410725 1 9.958779015 -8.589843777 7.222662681 1.102629314 0.646006658 0.794136194 0.120110642 0.08779683 7.883879195 0.019766781 0.03973839 2.57E-09 8.589843777 -0.456622656 RSDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_HeLa_Romidepsin_16h_R1 1 RSDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 32 1 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 RS(0.3)DS(0.7)PEIPFQAAAGPSDGLDASSPGNSFVGLR 93.317 9.37E-12 196060000 2840.3 2858.9 2399.3 2968.6 2921.1 2953.7 2728.2 2873.1 3056 2621.8 TRUE FALSE FALSE 2805.681331 2899.147669 2441.05881 3311.8435 2772.025367 2764.968103 2959.93324 2956.228615 2782.663706 2553.685258 1.098679378 1.135279949 0.955896504 1.296887895 1.085500008 1.082736447 1.159083027 1.15763233 1.089665885 1 11.31836501 -16.52287867 0.125814772 0.559680671 1.183511256 0.105353663 0.083443672 77.93097924 0.700774697 8.556075464 0.30147577 3.00E-17 16.52287867 0.623830585 RSDS(ph)VSASER ddPTM_HeLa_Romidepsin_16h_R1 2 RSDSVSASER 10 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 RS(0.007)DS(0.983)VS(0.01)ASER;RS(0.106)DS(0.745)VS(0.15)ASER ; 94.781 0.0093988 16438700 1360.42 1215.08 1148.57 1577.09 1337.17 1280.45 1725.88 1450.04 1358.58 1050.74 TRUE FALSE FALSE 1343.838678 1232.185928 1168.560379 1759.440566 1268.929225 1198.633377 1872.476204 1491.99462 1237.065202 1023.441623 1.313058456 1.203963079 1.141794854 1.719141108 1.239864782 1.17117904 1.829587698 1.45782093 1.208730595 1 9.999213099 -4.000000002 0.041899352 5.77E-13 3.607658178 0.313288339 0.207316462 430.7710178 1.386604641 32.15655806 108.7645097 1.00E-04 4.000000002 3.607658178 RSDSAS(ph)SEPVGIYQGFEK ddPTM_HeLa_Romidepsin_16h_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 0 RS(0.007)DS(0.089)AS(0.452)S(0.452)EPVGIYQGFEK 60.943 0.01374 4370900 1237.9 1294.6 1129.2 1012.3 1711.6 2164.1 1759.4 1529.2 1422.4 1395 TRUE FALSE FALSE 1222.811999 1312.825413 1148.853252 1129.346889 1624.250665 2025.820994 1908.843392 1573.444989 1295.176982 1358.757699 0.899948534 0.966195381 0.845517382 0.831161354 1.1953939 1.490936166 1.404844582 1.15800263 0.953206729 1 10.40807249 -8.574606218 4.744562723 0.937021125 1.356096609 0.818116501 0.093265369 0.062337728 3.001576066 0.013979131 0.028975123 2.66E-09 8.574606218 0.419075484 RSEDES(ph)ETEDEEEKSQEDQEQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSEDESETEDEEEKSQEDQEQK 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 RS(0.085)EDES(0.872)ET(0.041)EDEEEKS(0.002)QEDQEQK 71.872 0.0013487 120560000 1099.1 894.4 1076.2 820.97 825.55 1063.2 933.46 739.76 1159 1068.9 TRUE FALSE FALSE 1085.703746 906.9913867 1094.93081 915.8944142 783.4191029 995.2649513 1012.748069 761.1637885 1055.336137 1041.129824 1.04281303 0.8711607 1.051675578 0.879712014 0.752470139 0.955947019 0.972739466 0.73109402 1.013645093 1 10.02393426 -9.197737228 6.574318684 1.009269001 0.863374309 0.389403965 0.085211614 0.182333935 15.48226008 0.012430171 0.020668325 6.34E-10 9.197737228 -0.145894692 RSEPQPEEGS(ph)PAGGQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSEPQPEEGSPAGGQK 16 1 F8WE91;Q9Y6K1-3;Q9Y6K1 F8WE91 DNMT3A DNA (cytosine-5)-methyltransferase 3A 1 0 RSEPQPEEGS(1)PAGGQK 71.842 0.011266 1547600 1809.3 1549.1 1411.8 741.73 1691.9 1729.6 1380.5 1415.8 1889.3 1765.7 TRUE FALSE FALSE 1787.247556 1570.90827 1436.371787 827.4923125 1605.55603 1619.084142 1497.759636 1456.763939 1720.316276 1719.826859 1.039202025 0.913410709 0.835183948 0.481148616 0.933556783 0.941422756 0.870878151 0.847041044 1.000284573 1 10.74804762 -9.994359944 3.054296469 1.018106533 0.816925346 0.342106755 0.121353368 0.210798443 4.045925246 0.020860999 0.027086814 1.01E-10 9.994359944 -0.201181187 RSES(ph)PPAELPSLR ddPTM_HeLa_Romidepsin_16h_R1 1 RSESPPAELPSLR 13 1 Q14669;Q14669-2;Q14669-3;G5E9G6;H7C1L9 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 RS(0.172)ES(0.828)PPAELPSLR 150.9 0.00022815 11126000 2054.6 1747.5 1484.3 1277.6 1231.1 1471.2 1317.8 1374.6 2071.2 1682.8 TRUE FALSE FALSE 2029.557745 1772.101351 1510.133619 1425.322123 1168.272373 1377.195068 1429.733899 1414.371882 1885.946685 1639.080613 1.238229364 1.081155702 0.921329681 0.869586347 0.712760778 0.840224121 0.872277963 0.862905626 1.150612526 1 10.6786711 -9.635050402 2.50917596 1.114636984 0.829303046 0.792884681 0.069323154 0.132061532 1.692637956 0.016099596 0.023730573 2.32E-10 9.635050402 -0.285333938 RSFLQIVLHS(ph)LGQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSFLQIVLHSLGQK 14 1 F2Z2N5 F2Z2N5 PRSS16 1 0 RSFLQIVLHS(1)LGQK 58.32 0.02828 24304000 2227.2 2058.2 2223.9 2149.2 2712.2 2793.9 2190.5 2385.8 2477.6 2067.9 TRUE FALSE FALSE 2200.05403 2087.175394 2262.606047 2397.700616 2573.786313 2615.378807 2376.561015 2454.829359 2255.997251 2014.17566 1.092285084 1.036242983 1.123340974 1.190412864 1.277836072 1.298485956 1.179917453 1.218776201 1.120059832 1 10.97597379 -9.374096561 1.781297851 1.043358909 1.242711917 0.764811364 0.044944223 0.114060811 0.710001951 0.007650572 0.013006049 4.23E-10 9.374096561 0.199353007 RSGEPMVS(ph)MQAAEEIR ddPTM_HeLa_Romidepsin_16h_R1 1 RSGEPMVSMQAAEEIR 16 1 A0A087WXN0;Q9H0B3-3;Q9H0B3-5;Q9H0B3;Q9H0B3-4 A0A087WXN0 KIAA1683 Uncharacterized protein KIAA1683 1 0 RSGEPMVS(1)MQAAEEIR 54.859 0.019999 5464000 2938.5 3056.8 3473.8 1205.2 3309 3943 2329.2 3466 3362.9 3134 TRUE FALSE FALSE 2902.684432 3099.833711 3534.260032 1344.550895 3140.129382 3691.055025 2527.04219 3566.283242 3062.113801 3052.578228 0.950896002 1.015480515 1.157795073 0.440464026 1.028681052 1.209159848 0.827838634 1.168285618 1.003123777 1 11.57581255 -8.540307955 24.99995268 0.951995399 1.05679461 0.086979709 0.200258389 563.2069832 807845.4789 0.027551436 0.055111749 2.88E-09 8.540307955 0.10479921 RSGPTDDGEEEMEEDTVTNGS ddPTM_HeLa_Romidepsin_16h_R1 1 RSGPTDDGEEEMEEDTVTNGS 21 1 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 0 72.815 0.0048299 9028000 2556.5 2548.3 2515.7 2772.4 2620.9 3063.9 2513.5 2450.3 3125.2 2736.3 FALSE FALSE TRUE 2525.340395 2584.175034 2559.484703 3092.957933 2487.145693 2868.126678 2726.996627 2521.195565 2845.674285 2665.210532 0.947520042 0.969595086 0.960331153 1.160492913 0.933189203 1.076135129 1.023182445 0.945964881 1.067710881 1 11.38003378 RSIPETQVQGMKY(ph)GELNKGTQFK ddPTM_HeLa_Romidepsin_16h_R1 1 RSIPETQVQGMKYGELNKGTQFK 23 3 C9JG08 C9JG08 1 0 RS(0.001)IPET(0.16)QVQGMKY(0.837)GELNKGT(0.002)QFK 41.521 0.0042033 0 444.06 394.33 449.96 289.74 106.68 359.76 248.09 290.04 444.57 393.08 TRUE FALSE FALSE 438.6476259 399.8813881 457.7913651 323.2411021 101.2357215 336.7724971 269.1627584 298.4318498 404.8065458 382.8677249 1.145689744 1.044437444 1.195690666 0.844263125 0.264414352 0.879605344 0.703017624 0.779464631 1.057301306 1 8.580702238 -9.003933668 24.99982149 1.074504164 0.66067539 0.627177813 0.157277225 82.74742676 525894.9587 0.022528267 0.040180754 9.91E-10 9.003933668 -0.413828774 RSIT(ph)S(ph)PPSTSTT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RSITSPPSTSTTK 13 1 C9JWJ8;K7EN08;Q14938-6;Q14938-5;Q14938-3;Q14938-2;Q14938-4;Q14938 C9JWJ8 NFIX Nuclear factor 1;Nuclear factor 1 X-type 3 0 RS(0.029)IT(0.794)S(0.869)PPS(0.153)T(0.153)S(0.003)T(0.091)T(0.909)K 82.578 0.014523 4053300 4774.2 4542.8 4680.9 3053.7 3060.5 3200.7 2379 2683.6 5259.6 4834.4 TRUE FALSE FALSE 4716.010214 4606.753658 4762.369101 3406.783162 2904.311265 2996.1856 2581.072201 2761.245732 4789.168203 4708.801591 1.001530883 0.978328258 1.011376039 0.723492612 0.616783529 0.636294722 0.548137812 0.586400951 1.017067318 1 12.20114422 -9.104718373 2.451710942 1.000869695 0.594886592 0.981599443 0.026375484 0.025605826 0.301386429 0.004001192 0.007244912 7.86E-10 9.104718373 -0.405983102 RSLDT(ph)PQS(ph)LAS(ph)LS(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 RSLDTPQSLASLSSR 15 1 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 5 0 RS(0.067)LDT(0.945)PQS(0.989)LAS(0.999)LS(1)S(1)R 52.247 0.018837 20167000 834.14 724.2 829.41 607.12 656.37 825.16 730.24 734.35 929.38 827.78 TRUE FALSE FALSE 823.9731808 734.3953066 843.8455331 677.318071 622.8729896 772.4349391 792.2665674 755.5972586 846.2539251 806.2741563 1.021951621 0.910850609 1.046598761 0.84005926 0.7725325 0.958030135 0.982626767 0.937146816 1.049585825 1 9.65512667 -9.266964906 24.96834125 1.004052907 0.899131991 0.395479038 0.066565288 375.7720471 1698009.461 0.010389251 0.016155837 5.41E-10 9.266964906 -0.104920916 RSLTVSDDAES(ph)SEPER ddPTM_HeLa_Romidepsin_16h_R1 1 RSLTVSDDAESSEPER 16 1 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 RSLTVSDDAES(0.5)S(0.5)EPER 153.36 7.98E-05 6396100 1956.1 1519.1 1824.2 1082.7 1976.1 1393.3 1184.4 1472.4 1891.5 1526 TRUE FALSE FALSE 1932.258301 1540.48593 1855.949436 1207.886868 1875.252243 1304.272627 1285.002906 1515.001571 1722.319503 1486.3543 1.29999846 1.036419062 1.24865884 0.812650704 1.26164552 0.877497799 0.86453338 1.019273514 1.158754345 1 10.53756233 -8.601460608 0.963466059 1.13847322 0.921385492 0.211196261 0.14916444 0.741626379 1.264918262 0.027108952 0.10219831 2.50E-09 8.601460608 -0.217087729 RSMMQSPR ddPTM_HeLa_Romidepsin_16h_R1 4 RSMMQSPR 8 1 Q9C0H6;Q9C0H6-2 Q9C0H6 KLHL4 Kelch-like protein 4 0 0 ;;; ;;; 71.296 0.015321 201827900 7882.7 8176.5 6260 57242.8 5703.7 6235.24 6034.81 8430.3 9289 10053.6 FALSE FALSE TRUE 7786.62262 8291.608982 6368.952674 63861.48187 5412.618906 5836.828287 6547.406611 8674.21743 8458.168575 9792.406023 0.795169502 0.846738683 0.65039712 6.521531248 0.552736365 0.596056605 0.668620827 0.885810638 0.86374774 1 13.25744766 RSNATNSSYS(ph)PTTGR ddPTM_HeLa_Romidepsin_16h_R1 1 RSNATNSSYSPTTGR 15 1 Q13009-2;Q13009 Q13009-2 TIAM1 T-lymphoma invasion and metastasis-inducing protein 1 1 0 RS(0.001)NAT(0.001)NS(0.002)S(0.009)YS(0.547)PT(0.316)T(0.125)GR 55.707 0.029559 661010 138.54 122.84 0 234.53 252.57 172.02 46.862 183.96 123.31 115.79 TRUE FALSE FALSE 136.8514212 124.5693447 0 261.6474621 239.6804104 161.0284772 50.84245711 189.2825924 112.2808448 112.7817591 1.213418041 1.104516774 0 2.319944858 2.125169995 1.427788309 0.450803902 1.678308566 0.995558552 1 6.81738994 -9.242257509 24.99267788 1.028627013 1.556100382 0.271173341 0.570987925 1191.57474 1552542.419 0.087931111 0.145671244 5.72E-10 9.242257509 0.527473369 RSNS(ph)TTQVSQPR ddPTM_HeLa_Romidepsin_16h_R1 2 RSNSTTQVSQPR 12 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 RS(0.067)NS(0.919)T(0.014)TQVSQPR;RS(0.245)NS(0.545)T(0.161)T(0.05)QVSQPR ; 147.51 0.00044116 5714780 394.04 385.1 353.09 161.99 514.78 504.59 390.8 573.67 563.19 394.62 TRUE FALSE FALSE 389.2372889 390.5214479 359.2353833 180.720046 488.5088557 472.3483275 423.9945422 590.2682363 512.8168759 384.3677155 1.012669049 1.016010014 0.934613832 0.470174884 1.270941434 1.228896987 1.103096137 1.535686304 1.334183011 1 8.586343354 -8.614446116 21.49565974 0.96364031 1.268148527 0.338361486 0.221024168 4.917551274 1149.9641 0.026533554 0.05306712 2.43E-09 8.614446116 0.304508217 RSNVSSPATPTASSSS(ph)STTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 RSNVSSPATPTASSSSSTTPTR 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 RSNVSSPATPT(0.008)AS(0.023)S(0.017)S(0.057)S(0.204)S(0.204)T(0.204)T(0.204)PT(0.079)R 66.556 0.001524 1493400 514.03 379.2 348.94 358.05 503.19 151.49 297.05 176.8 417.27 414.35 TRUE FALSE FALSE 507.7648046 384.5383876 355.0131543 399.4494257 477.5103366 141.8102779 322.2814196 181.9154291 379.9483261 403.5851273 1.258135571 0.952806141 0.879648754 0.989752592 1.183171292 0.351376372 0.798546323 0.450748595 0.941432923 1 8.6567292 -8.268932745 24.99881249 1.086245854 0.560056014 0.663149687 0.157962728 237.4658159 792216.3969 0.023636158 0.053828763 5.38E-09 8.268932745 -0.52618984 RSPQQTVPYVVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 RSPQQTVPYVVPLSPK 16 1 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 0 RSPQQTVPY(0.009)VVPLS(0.991)PK;RSPQQTVPY(0.016)VVPLS(0.984)PK ; 94.911 0.0026526 65933000 7645.3 7723.8 7398.6 8110.4 9678 9966.9 9168.5 9928.1 9222.6 8281.8 TRUE FALSE FALSE 7552.116143 7832.535859 7527.369529 9048.162609 9184.095546 9330.047257 9947.272161 10215.35391 8397.707558 8066.637642 0.936216114 0.970979013 0.933148341 1.121677087 1.138528338 1.15662159 1.233137349 1.266370744 1.041041873 1 12.97775174 -8.765706382 1.119364904 0.965693791 1.235332144 0.85294751 0.043934254 0.117311478 0.287215361 0.006791247 0.019619198 1.72E-09 8.765706382 0.269638354 RSPS(ph)PLGTSVR ddPTM_HeLa_Romidepsin_16h_R1 1 RSPSPLGTSVR 11 1 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;G5E9V3;E9PDY7 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 RS(0.412)PS(0.588)PLGTSVR 99.732 0.029725 7666700 2860.6 2689 2984.1 2425.1 2345.2 2195.2 1798.6 1941.6 2855.2 2677.6 TRUE FALSE FALSE 2825.733907 2726.855813 3036.037009 2705.501472 2225.515693 2054.933805 1951.373039 1997.777133 2599.823761 2608.035566 1.083472152 1.045559289 1.164108745 1.037371387 0.85333027 0.787923996 0.748215655 0.766008393 0.996851345 1 11.34874783 -8.643164392 2.823313542 1.051896044 0.768704603 0.895763069 0.045116 0.066875972 1.072779687 0.007570508 0.016461144 2.27E-09 8.643164392 -0.283191442 RSPSAPAATSSASSSTSSYK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 RSPSAPAATSSASSSTSSYKR 21 2 A0A087X0S7;A0A0C4DH00;A0A087WTU1;A0A0B4J2G4;Q15345-3;Q15345 A0A087X0S7 LRRC41 Leucine-rich repeat-containing protein 41 0 1 RSPSAPAATSSASSSTSSYK(1)R 154.07 1.73E-16 533250 0 0 0 0 0 0 0 0 0 170.07 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 165.6515569 0 0 0 0 0 0 0 0 0 1 7.372007952 -12.15782943 0.67715094 1.083625667 2.50E-23 0 0.307667284 0.06659167 0.049088893 0.041658112 0.0090835 6.95E-13 12.15782943 -1.083625667 RSPSS(ph)PSHPHMAS(ph)QS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 RSPSSPSHPHMASQSGK 17 1 A6NC05 A6NC05 C5orf63 Glutaredoxin-like protein C5orf63 3 0 RS(0.005)PS(0.023)S(0.946)PS(0.053)HPHMAS(0.977)QS(0.996)GK 51.147 0.0041277 0 698.99 951.21 839.28 948.99 683.14 849.93 631.49 829.08 858.19 1062 TRUE FALSE FALSE 690.470441 964.6011593 853.8873163 1058.716689 648.2768167 795.622216 685.1287448 853.0681217 781.431337 1034.409087 0.667502296 0.932514197 0.825483193 1.023499022 0.626712221 0.769156252 0.662338289 0.824691249 0.755437425 1 10.01459114 -12.54305406 1.282589784 1.001036511 0.778929986 0 0.13851592 0.440634542 1.288560192 0.085867385 0.019997752 2.86E-13 12.54305406 -0.222106525 RSPT(ph)DSDVSLDSEDSGAK ddPTM_HeLa_Romidepsin_16h_R1 2 RSPTDSDVSLDSEDSGAK 18 1 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 0 RS(0.064)PT(0.898)DS(0.038)DVSLDSEDSGAK;RS(0.245)PT(0.754)DSDVSLDSEDSGAK ; 156.08 2.68E-06 16622900 5539.8 5968.2 5737.9 6335.9 4913.1 5009.7 3695.7 3860.3 6693.1 5932.5 TRUE FALSE FALSE 5472.278787 6052.220476 5837.765743 7068.486569 4662.366174 4689.596338 4009.612666 3971.99169 6094.452373 5778.372795 0.947027646 1.047391834 1.01027849 1.22326593 0.806864898 0.811577325 0.693899963 0.68738931 1.054700448 1 12.49644757 -8.541515186 24.98291007 0.999542179 0.740911797 0.747622132 0.082659531 100.2593575 134401.3314 0.012240835 0.024484657 2.87E-09 8.541515186 -0.258630382 RSQS(ph)IEQESQEK ddPTM_HeLa_Romidepsin_16h_R1 2 RSQSIEQESQEK 12 1 A0A0A0MRN0;Q5VTL8 A0A0A0MRN0 PRPF38B Pre-mRNA-splicing factor 38B 1 0 RS(0.006)QS(0.994)IEQESQEK;RSQS(1)IEQESQEK ; 156.2 0.0018724 12497400 5946.5 5611.2 5049.6 4439.63 4753.2 4425.4 4567.3 3631.7 6360.8 6011.5 TRUE FALSE FALSE 5874.021771 5690.194621 5137.48617 4952.96091 4510.626467 4142.631222 4955.246348 3736.77751 5791.874117 5855.320363 1.003193917 0.971799025 0.877404796 0.845890678 0.770346657 0.707498645 0.846280996 0.63818498 0.989164342 1 12.51553239 -9.290901252 0.983501045 1.00409458 0.73419021 0.837791004 0.04936393 0.125600515 0.240681178 0.007977253 0.016743318 5.12E-10 9.290901252 -0.26990437 RSS(ph)DGS(ph)LSHEEDLAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSDGSLSHEEDLAK 15 1 A0A2R8Y7R9;Q13136-2;Q13136;E9PJZ7;H0YEF9 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 2 0 RS(0.177)S(0.824)DGS(0.85)LS(0.148)HEEDLAK 89.507 0.0015475 0 2259.5 2521 1943 2067.6 3137.1 3500.5 2575.2 3023.7 2813.3 2205.3 TRUE FALSE FALSE 2231.960345 2556.490704 1976.8171 2306.66564 2977.002081 3276.829347 2793.937424 3111.185989 2561.671402 2148.005988 1.039084787 1.190169263 0.920303347 1.073863692 1.385937515 1.525521514 1.300712121 1.448406572 1.192581127 1 11.0687823 -8.771088716 4.390474312 1.02679721 1.419330879 0.750512883 0.096335632 0.052909583 2.419016056 0.011280019 0.021953063 1.69E-09 8.771088716 0.392533669 RSS(ph)FSEGQTLTVTSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSFSEGQTLTVTSGAK 17 1 H7C3H3;E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622 H7C3H3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 0 RS(0.016)S(0.936)FS(0.047)EGQTLTVTSGAK 109.13 0.0032352 5585100 1148.3 1400.2 1305.4 1120.2 1726.6 1731.5 1381.2 1613.9 1536.3 1275.3 TRUE FALSE FALSE 1134.304078 1419.912052 1328.119939 1249.722795 1638.485159 1620.862738 1498.519094 1660.59565 1398.88948 1242.167522 0.913165139 1.143092238 1.069195512 1.00608233 1.319053292 1.304866461 1.206374395 1.336853219 1.126168134 1 10.27864404 -9.035908613 0.878589153 0.965061449 1.304753504 0.547598044 0.094294357 0.225167685 0.337414972 0.014999476 0.040363601 9.21E-10 9.035908613 0.339692055 RSS(ph)GFISELPSEEGK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSGFISELPSEEGK 15 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 RS(0.019)S(0.981)GFISELPSEEGK 135.36 0.00039393 39305000 5453.2 6448.4 6389.4 7441.3 8565 8102.8 6284.8 7221.7 6238.3 5540 TRUE FALSE FALSE 5386.734301 6539.180744 6500.604827 8301.698118 8127.89609 7585.057231 6818.630755 7430.648496 5680.330824 5396.070001 0.998269907 1.211841348 1.204692457 1.538471168 1.506262166 1.405663238 1.26362904 1.377048202 1.052679232 1 12.39769335 -9.849244671 1.592743983 0.997951352 1.408522745 0.79365234 0.085878652 0.106923618 0.547129249 0.015415853 0.021676742 1.41E-10 9.849244671 0.410571394 RSS(ph)ITEPEGPNGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSITEPEGPNGPNIQK 17 1 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 RS(0.231)S(0.735)IT(0.034)EPEGPNGPNIQK 82.56 0.0048013 40135000 3599.4 3787 3502.6 3539.6 4118.6 3807.1 3443.5 3921.8 3829.8 3039.3 TRUE FALSE FALSE 3555.529128 3840.313485 3563.561284 3948.865206 3908.412473 3563.838597 3735.990804 4035.271095 3487.253096 2960.338548 1.201054903 1.297254832 1.203768159 1.333923517 1.320258616 1.203861835 1.262014713 1.363111357 1.177991314 1 11.53154646 -11.58809623 0.4440818 0.967952638 1.297292821 0.466787826 0.072885292 0.369740354 0.141595478 0.053583038 0.017359895 2.58E-12 11.58809623 0.329340184 RSS(ph)LPNGEGLQLK ddPTM_HeLa_Romidepsin_16h_R1 2 RSSLPNGEGLQLK 13 1 Q9ULR3 Q9ULR3 PPM1H Protein phosphatase 1H 1 0 RS(0.156)S(0.844)LPNGEGLQLK;RS(0.009)S(0.991)LPNGEGLQLK ; 128.35 0.0045316 14126900 2607.75 2592.99 2680.44 6624.1 4710.8 4878.7 4363.7 4257.8 2907.09 2614.17 TRUE FALSE FALSE 2575.96574 2629.494181 2727.091934 7390.009609 4470.390298 4566.966815 4734.352569 4380.992725 2647.072589 2546.253487 1.011669008 1.032691441 1.071021384 2.902307115 1.755673707 1.793602577 1.859340633 1.720564252 1.039595077 1 11.31416034 -9.475388734 24.60964494 1.009805402 1.973821022 0.699305851 0.319516655 136.0394603 70496.61929 0.045995115 0.070257409 3.35E-10 9.475388734 0.96401562 RSS(ph)LYGIAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSLYGIAK 9 1 Q5VZ89-5;Q5VZ89-3;Q5VZ89;Q5VZ89-7;X6RAE7 Q5VZ89-5 DENND4C DENN domain-containing protein 4C 1 0 RS(0.319)S(0.681)LYGIAK 71.806 0.024047 7594900 3537.8 3510.8 4786 5890.3 5280.5 6413.1 5561.7 3960.4 3691.9 3036.8 TRUE FALSE FALSE 3494.679933 3560.225135 4869.298322 6571.364201 5011.016381 6003.323607 6034.110659 4074.987926 3361.687217 2957.903498 1.181471923 1.203631267 1.646199183 2.221629003 1.69411084 2.029587379 2.039995782 1.377660876 1.136510106 1 11.53035927 -9.713125905 2.867628123 1.089902765 1.885524015 0.719961367 0.218834675 0.091661811 1.544143668 0.033931498 0.048324006 1.94E-10 9.713125905 0.79562125 RSS(ph)PAAFINPPIGTVTPALK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPAAFINPPIGTVTPALK 20 1 Q6R954;F8WEE2;Q8WUT1;F8WCX5;F6VRR5;Q9BY77-2;Q9BY77 Q6R954 PDIP46;POLDIP3 Polymerase delta-interacting protein 3 1 0 RS(0.236)S(0.762)PAAFINPPIGT(0.001)VTPALK 71.872 0.0024601 72500000 1513.8 1709.1 1263.5 1383.5 1209.6 1295.4 1326.9 1388.5 1749.4 1514.9 TRUE FALSE FALSE 1495.349223 1733.160755 1285.490687 1543.46678 1147.869598 1212.628121 1439.606853 1428.674057 1592.929283 1475.54268 1.013423227 1.174592086 0.87119858 1.046033301 0.777930462 0.821818398 0.975645688 0.968236349 1.079554868 1 10.52702994 -8.786011771 24.99961581 1.011726689 0.8877397 0.367879676 0.090995709 200.3208342 203803.1041 0.012680182 0.022992108 1.64E-09 8.786011771 -0.123986989 RSS(ph)PPGHYYQK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPPGHYYQK 11 1 D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;D6RDK6;D6RBN5;Q9NX40-3;Q9NX40-2;Q9NX40-4;Q9NX40 D6RI08 OCIAD1 OCIA domain-containing protein 1 1 0 RS(0.066)S(0.934)PPGHYYQK 78.653 0.0021357 0 2686.5 2782.5 3114.1 2874.1 3334.2 3656.3 2658.4 2424 3653.6 2805.6 TRUE FALSE FALSE 2653.755905 2821.672108 3168.299604 3206.416965 3164.043332 3422.67423 2884.20443 2494.134616 3326.812865 2732.710108 0.971107728 1.032554496 1.159398355 1.173346912 1.157840828 1.252483467 1.055437392 0.912696377 1.217404238 1 11.41611671 -9.927721564 4.404476656 0.986886077 1.125629386 0 0.11159874 0.175768718 6.642482712 0.014119374 0.018646026 1.18E-10 9.927721564 0.138743309 RSS(ph)PPPPPSGSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPPPPPSGSSSR 14 1 Q5VUA4;Q5VUA4-2 Q5VUA4 ZNF318 Zinc finger protein 318 1 0 RS(0.008)S(0.992)PPPPPSGSSSR 118.71 0.0012946 9945200 323.61 193.99 250.91 160.31 232.92 329.13 230.15 365.95 298.67 244.44 TRUE FALSE FALSE 319.6657168 196.7209963 255.2769833 178.8457965 221.0332233 308.0996552 249.6989353 376.5381859 271.9562072 238.0894136 1.342628856 0.826248397 1.072189559 0.751170721 0.928362248 1.294050208 1.048761184 1.581499069 1.142244013 1 7.895359664 RSS(ph)PSARPPDVPGQQPQAAK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSPSARPPDVPGQQPQAAK 20 2 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 0 RS(0.087)S(0.908)PS(0.005)ARPPDVPGQQPQAAK 81.329 0.0037967 10605000 3276.2 2890.7 2699.6 3023.7 2947.1 3119.5 2883.7 3144.6 3602.6 2874.1 TRUE FALSE FALSE 3236.268414 2931.39535 2746.585406 3373.314421 2796.69849 2920.174018 3128.641406 3235.58404 3280.374433 2799.430468 1.156045293 1.047139904 0.981122924 1.205000253 0.999024095 1.04313147 1.117599255 1.155800823 1.171800647 1 11.45091763 -12.62755665 1.452260355 1.000117162 1.094235366 0 0.086659113 0.539938879 2.049763925 0.04878679 0.011195791 2.36E-13 12.62755665 0.094118203 RSS(ph)QPS(ph)PTAVPASDSPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 2 0 RS(0.248)S(0.815)QPS(0.903)PT(0.034)AVPASDSPPTK 71.678 0.0052022 7872400 1547.8 1593.4 1821.5 1242.3 2603.1 2961.2 2854.8 3539.8 1717.8 2070.4 TRUE FALSE FALSE 1528.934818 1615.831927 1853.202443 1385.940571 2470.254093 2771.988877 3097.286641 3642.218528 1564.155666 2016.61071 0.758170534 0.801261205 0.918968859 0.687262328 1.224953374 1.37457808 1.535887232 1.806108889 0.775635902 1 10.97771689 -8.127259377 1.264839321 0.866416952 1.745019276 0.89229203 0.11845074 0.137710697 0.380615628 0.020174136 0.103127596 7.46E-09 8.127259377 0.878602323 RSS(ph)QPSPTAVPASDSPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 RS(0.349)S(0.557)QPS(0.076)PT(0.018)AVPASDSPPTK 98.067 0.00051621 8935400 2768.8 3234.3 2505.3 2331.5 2308.3 1974.7 1930.1 1765 3546.5 3327.6 TRUE FALSE FALSE 2735.052801 3279.83256 2548.903696 2601.079 2190.498838 1848.523043 2094.042646 1816.06749 3229.292158 3241.148472 0.843852981 1.011935303 0.786419912 0.802517695 0.675840325 0.570329641 0.646080445 0.560316044 0.99634194 1 11.66228939 -8.724874763 0.468110824 0.9551933 0.498043698 0.852543081 0.063534844 0.486635676 0.161329818 0.019277786 0.099824513 1.88E-09 8.724874763 -0.457149603 RSS(ph)SSGDQSSDSLNS(ph)PTLLAL ddPTM_HeLa_Romidepsin_16h_R1 1 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 2 0 RS(0.025)S(0.519)S(0.193)S(0.072)GDQS(0.13)S(0.047)DS(0.014)LNS(0.962)PT(0.038)LLAL 96.591 0.00062802 3481800 729.73 758.47 727.47 691.74 621.87 323.34 417.12 782.97 774.92 681.34 TRUE FALSE FALSE 720.8357701 769.1477606 740.1313102 771.7222335 590.1336534 302.6796175 452.5501624 805.6240016 705.6092144 663.6386886 1.086187081 1.158985716 1.115262451 1.162865045 0.889239376 0.456090977 0.681922513 1.213949722 1.063243036 1 9.374254184 -8.538490342 8.786837409 1.063964845 0.757001558 0.373761759 0.181942235 0.143116491 67.08067704 0.025683237 0.052138636 2.89E-09 8.538490342 -0.306963287 RSS(ph)SSGDQSSDSLNSPTLLAL ddPTM_HeLa_Romidepsin_16h_R1 2 RSSSSGDQSSDSLNSPTLLAL 21 1 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 0 RS(0.102)S(0.361)S(0.136)S(0.052)GDQS(0.136)S(0.136)DS(0.077)LNS(0.001)PTLLAL;RS(0.011)S(0.62)S(0.177)S(0.177)GDQS(0.006)S(0.009)DSLNSPTLLAL ; 72.09 0.0089873 13650100 3471.4 3470.1 2966 3143.2 1870.24 1510.84 1380.57 1668.29 3594.6 3359.7 TRUE FALSE FALSE 3429.089242 3518.952159 3017.621986 3506.631573 1774.794674 1414.3022 1497.835581 1716.559339 3273.089973 3272.41451 1.04787741 1.075338148 0.922139288 1.071573165 0.542350203 0.432189197 0.457715725 0.524554372 1.000206411 1 11.67613979 -8.717620249 5.417732238 1.022503425 0.475491469 0.96598728 0.048799845 0.022165507 1.505718481 0.00681002 0.013601209 1.92E-09 8.717620249 -0.547011956 RSSAWAEGGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 RSSAWAEGGSPR 12 1 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 0 RSSAWAEGGS(1)PR;RSSAWAEGGS(1)PR ; 78.326 0.002095 2464300 2841.3 2502.9 2525.2 3472.4 2545.8 2846 2644.4 2548.8 3044 2324.34 TRUE FALSE FALSE 2806.669143 2538.135892 2569.150047 3873.895226 2415.878326 2664.149785 2869.01527 2622.545507 2771.737016 2263.953312 1.239720417 1.121107877 1.134806992 1.711119751 1.067106072 1.176768872 1.267259027 1.158392045 1.224290714 1 11.14462849 -12.23573886 0.552194087 0.958418533 1.245806917 0.005836862 0.183128456 1.603159274 0.696607473 0.241308573 0.040830386 5.81E-13 12.23573886 0.287388384 RSSQPS(ph)PTAVPASDSPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSQPSPTAVPASDSPPTK 19 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 RS(0.067)S(0.067)QPS(0.644)PT(0.222)AVPAS(0.001)DSPPTK 68.192 0.0052295 8072500 2580.9 2721.3 3188.1 1964.4 1921.6 2247 1519.5 1611.3 2990.1 2934.2 TRUE FALSE FALSE 2549.442998 2759.610533 3243.587543 2191.533171 1823.533582 2103.423952 1648.566292 1657.920423 2722.657967 2857.969061 0.892047095 0.965584467 1.134927452 0.766814869 0.638052247 0.735985557 0.576831399 0.580104399 0.952654808 1 11.48077458 -9.023281508 4.835624146 0.96218018 0.64107266 0.839463574 0.073340144 0.064882039 3.988161225 0.012025458 0.020994556 9.48E-10 9.023281508 -0.32110752 RSST(ph)SSEPTPTVK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSTSSEPTPTVK 13 1 F8WAN1;Q69YQ0-2;Q69YQ0;A0A494C1J1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 RS(0.008)S(0.14)T(0.287)S(0.287)S(0.277)EPTPTVK 66.826 0.030064 19366000 3947.2 4003.9 3295.9 4673.7 7871.5 9588.4 9532.9 10520 5326.8 5735.3 TRUE FALSE FALSE 3899.090008 4060.267009 3353.263757 5214.095184 7469.787982 8975.732185 10342.62429 10824.3796 4850.357667 5586.296079 0.697974105 0.726826318 0.600266028 0.933372508 1.337162921 1.606741221 1.851427877 1.937666649 0.868260042 1 12.44767632 -8.408049882 1.499478942 0.821426003 1.890873992 0.938539195 0.116020101 0.093232968 0.399773642 0.023689058 0.07729952 3.91E-09 8.408049882 1.069447989 RSSTSS(ph)EPTPTVK ddPTM_HeLa_Romidepsin_16h_R1 1 RSSTSSEPTPTVK 13 1 F8WAN1;Q69YQ0-2;Q69YQ0;A0A494C1J1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 RS(0.194)S(0.194)T(0.153)S(0.153)S(0.306)EPTPTVK 87.148 0.0079151 10901000 3539.5 3291.4 2883.5 4004.5 8600.2 10319 9864.3 11516 4037.6 3025.1 TRUE FALSE FALSE 3496.359213 3337.736416 2933.686108 4467.519132 8161.299702 9659.649203 10702.1734 11849.19729 3676.466944 2946.507466 1.186611354 1.132777179 0.995648625 1.516208319 2.769821491 3.278338614 3.632155533 4.021438068 1.247737189 1 11.52479021 -8.575059915 1.386191776 1.074804216 3.806837873 0.982148306 0.153147376 0.035905324 0.1349673 0.023421942 0.069401592 2.66E-09 8.575059915 2.732033657 up RST(ph)QGVTLTDLQEAEK ddPTM_HeLa_Romidepsin_16h_R1 2 RSTQGVTLTDLQEAEK 16 1 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 RS(0.058)T(0.942)QGVTLTDLQEAEK;RS(0.069)T(0.931)QGVTLTDLQEAEK ; 178.22 9.02E-09 3837400 4037.1 2559.8 3246.4 2471.8 4562.4 3775.1 1684.35 2850.2 2394.1 2670.3 TRUE FALSE FALSE 3987.894272 2595.836932 3302.90223 2757.601146 4329.563703 3533.883294 1827.418647 2932.66604 2179.9657 2600.925221 1.533259872 0.998043662 1.269895114 1.060238535 1.664624445 1.358702382 0.702603301 1.127547234 0.838150087 1 11.34480921 -7.773460241 24.99946434 1.261535579 0.915075219 0.154971891 0.263385558 218.5224974 454458.4501 0.036208232 0.109831964 1.68E-08 7.773460241 -0.346460361 RST(ph)RPT(ph)QQFYQPPRAR ddPTM_HeLa_Romidepsin_16h_R1 1 RSTRPTQQFYQPPRAR 16 3 Q9H7E2-3;Q9H7E2-2;Q9H7E2 Q9H7E2-3 TDRD3 Tudor domain-containing protein 3 2 0 RS(0.052)T(0.96)RPT(0.988)QQFY(0.001)QPPRAR 59.367 0.0042092 0 224.99 144.81 226.39 178.35 244.4 111.19 148.36 251.14 309.58 292.97 TRUE FALSE FALSE 222.2477353 146.848639 230.330223 198.9716662 231.927356 104.0853178 160.9616947 258.4063397 281.8903894 285.3585972 0.778836655 0.514610881 0.807160623 0.697268868 0.812757556 0.364752697 0.564068145 0.905549516 0.987846143 1 8.156632218 -11.37883217 0.522065432 1.012588814 0.647466884 0.401337298 0.153196722 0.657798549 0.383678987 0.107792322 0.046317866 4.18E-12 11.37883217 -0.36512193 RST(ph)SPIIGS(ph)PPVR ddPTM_HeLa_Romidepsin_16h_R1 1 RSTSPIIGSPPVR 13 1 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 2 0 RS(0.111)T(0.773)S(0.117)PIIGS(0.999)PPVR 85.473 0.024303 26653000 4026.7 3263.8 3493.7 2966.6 2663.5 2410.8 2108 2333.9 3780.9 3495.8 TRUE FALSE FALSE 3977.621032 3309.747862 3554.506383 3309.61225 2527.571656 2256.757661 2287.053467 2401.427714 3442.726835 3404.978612 1.168177978 0.972031909 1.043914452 0.971992082 0.742316456 0.662781743 0.671679246 0.705269544 1.011086185 1 11.73343002 -8.815769725 1.943138461 1.070513215 0.674685782 0.899776759 0.054491573 0.08308822 0.638147811 0.010826306 0.023482465 1.53E-09 8.815769725 -0.395827433 RSVSDNDIR ddPTM_HeLa_Romidepsin_16h_R1 4 RSVSDNDIR 9 1 P55072 P55072 VCP Transitional endoplasmic reticulum ATPase 0 0 ;;; ;;; 131.52 0.0048376 12649000 6908.4 6025.4 6933.3 5138.5 6795.7 8539.6 8443.2 3272.9 7953.3 6622.5 FALSE FALSE TRUE 6824.197764 6110.225739 7053.971178 5732.637547 6448.890071 7993.94712 9160.365197 3367.596198 7241.936929 6450.446495 1.057941922 0.947256247 1.093563241 0.888719494 0.999758711 1.239285858 1.420113352 0.522071798 1.122703201 1 12.65518331 RSVSGS(ph)PESDELQELR ddPTM_HeLa_Romidepsin_16h_R1 1 RSVSGSPESDELQELR 16 1 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 RS(0.012)VS(0.07)GS(0.915)PES(0.004)DELQELR 62.792 0.018152 1607200 588.97 438.78 454 741.18 538.99 508.39 650.26 421.76 383.73 592.52 TRUE FALSE FALSE 581.7914071 444.9571564 461.9016796 826.878719 511.4833291 475.9055198 705.4930682 433.9629602 349.4082277 577.126245 1.008083434 0.770987562 0.800347729 1.432751891 0.886259001 0.824612507 1.222424165 0.751937663 0.605427722 1 9.172743129 -7.930053949 0.004960528 1.943936736 2.41E-05 0 0.241440664 171780.8341 169.9564779 32381.02571 34237.94937 1.17E-08 7.930053949 -1.943912654 RSY(ph)DVPPPPMEPDHPFYSNISK ddPTM_HeLa_Romidepsin_16h_R1 1 RSYDVPPPPMEPDHPFYSNISK 22 1 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 0 RS(0.44)Y(0.56)DVPPPPMEPDHPFYSNISK 98.543 8.23E-05 12736000 2972.1 3059.3 2607 3021.3 3253.1 3379.2 3310.4 2906.6 3528.6 3198.9 TRUE FALSE FALSE 2935.874902 3102.368906 2652.373741 3370.636922 3087.082168 3163.280026 3591.585293 2990.697885 3212.993178 3115.792117 0.942256348 0.995691878 0.851267877 1.081791338 0.990785666 1.015241039 1.152703762 0.959851548 1.03119626 1 11.60538327 RSYS(ph)SPDITQAIQEEEK ddPTM_HeLa_Romidepsin_16h_R1 1 RSYSSPDITQAIQEEEK 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 RS(0.225)Y(0.085)S(0.464)S(0.225)PDIT(0.002)QAIQEEEK 77.51 0.0063193 3519700 1280.2 1292.1 1253.7 1227 1430.8 1338.8 1155.2 1607.1 1443.8 1276.1 TRUE FALSE FALSE 1264.59643 1310.290218 1275.520123 1368.871513 1357.780937 1253.255001 1253.322659 1653.598903 1314.662912 1242.946738 1.017418037 1.054180503 1.026206581 1.101311481 1.092388672 1.008293407 1.008347841 1.330385971 1.057698509 1 10.27954876 -7.259595746 24.84926536 1.024468177 1.330386084 0.842552907 0.03698388 42.81981231 577092.7949 0.005583926 0.048176813 5.50E-08 7.259595746 0.305917907 RT(ph)AAT(ph)LAT(ph)HELR ddPTM_HeLa_Romidepsin_16h_R1 1 RTAATLATHELR 12 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 3 0 RT(1)AAT(1)LAT(1)HELR 55.335 0.022642 3322700 642.12 801.88 645.57 661.53 642.86 734.96 604.6 560.95 937.55 565.2 TRUE FALSE FALSE 634.2935945 813.1688877 656.805875 738.0192112 610.0524554 687.998428 655.9547089 577.1802032 853.6931799 550.5160225 1.152180079 1.477103035 1.193073132 1.340595334 1.108146594 1.249733704 1.191527008 1.048434886 1.550714502 1 9.104640743 -11.23983512 1.194473142 1.029761989 1.22608538 0 0.200497554 0.327833472 0.960796661 0.031322948 0.022940922 5.76E-12 11.23983512 0.196323391 RT(ph)ASPPPPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 RTASPPPPPKR 11 2 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 RT(0.855)AS(0.145)PPPPPKR 64.65 0.027126 5950600 2071.5 1895.1 1818.6 1871.3 1781.8 2036.8 1763.1 1822.8 2228.3 2206.7 TRUE FALSE FALSE 2046.251761 1921.779268 1850.25197 2087.668511 1690.868097 1906.655053 1912.85767 1875.539842 2028.995267 2149.369616 0.952024141 0.894112978 0.86083471 0.971293395 0.786680934 0.887076396 0.88996218 0.872599961 0.94399551 1 11.06969788 -10.47599868 0.687674291 0.992674516 0.871135402 0.410710607 0.045291478 0.309270058 0.317802187 0.012125029 0.012418375 3.34E-11 10.47599868 -0.121539114 RT(ph)ESVPSDINNPVDR ddPTM_HeLa_Romidepsin_16h_R1 1 RTESVPSDINNPVDR 15 1 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 RT(0.84)ES(0.16)VPSDINNPVDR 96.562 0.0043504 48417000 1559.8 1523.5 1733 1626.3 1572.4 1618.5 840.96 1435 1751.1 1468.9 TRUE FALSE FALSE 1540.788558 1544.947873 1763.162138 1814.340458 1492.154561 1515.083073 912.3911214 1476.519461 1594.47723 1430.737766 1.076918911 1.079826024 1.232344724 1.268115304 1.04292666 1.058952318 0.637706743 1.031998662 1.114444078 1 10.48254356 -7.883588239 10.50546879 1.072879697 0.83525493 0.424333646 0.122186628 0.240318516 20.94831218 0.017171173 0.051619104 1.31E-08 7.883588239 -0.237624767 RT(ph)FSLTEVR ddPTM_HeLa_Romidepsin_16h_R1 2 RTFSLTEVR 9 1 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 RT(0.999)FS(0.001)LTEVR;RT(1)FSLTEVR ; 107.11 0.0090449 10918600 3165.7 3540.6 2907.8 2672.3 2402.9 2539.6 2034.26 2393.6 3549.6 3029.3 TRUE FALSE FALSE 3127.115231 3590.44466 2958.409039 2981.2839 2280.271047 2377.327756 2207.049994 2462.85504 3232.114886 2950.598349 1.059824097 1.21685307 1.002647155 1.010399772 0.772816486 0.805710393 0.748000823 0.834696813 1.095409982 1 11.52679183 -8.806314556 4.786701113 1.042681607 0.787454381 0.810329287 0.064513557 0.06944197 3.492430578 0.009855152 0.018611509 1.56E-09 8.806314556 -0.255227227 RT(ph)PRRIK ddPTM_HeLa_Romidepsin_16h_R1 1 RTPRRIK 7 3 Q8WYP5;Q8WYP5-3;Q8WYP5-2;P18089;P08913 Q8WYP5 AHCTF1;ADRA2B;ADRA2A Protein ELYS;Alpha-2B adrenergic receptor;Alpha-2A adrenergic receptor 1 0 RT(1)PRRIK 65.803 0.0036691 0 1613.5 1832.4 1478.6 1081.3 2328.3 2566.8 2315.8 2410.9 2667.3 2814.3 TRUE FALSE FALSE 1593.834041 1858.196575 1504.334413 1206.324994 2209.478163 2402.789764 2512.503994 2480.655588 2428.730008 2741.18408 0.581439989 0.677880989 0.54879 0.44007442 0.806030569 0.876551772 0.916576166 0.904957681 0.886014925 1 11.4205835 -8.337800596 4.066845092 0.740039875 0.902355919 0.228585059 0.157153331 0.411674224 12.94230099 0.030216389 0.071708784 4.59E-09 8.337800596 0.162316044 RT(ph)PSDDEEDNLFAPPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTPSDDEEDNLFAPPK 16 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 RT(0.593)PS(0.407)DDEEDNLFAPPK 88.176 0.0058007 57819000 4392.8 4652.7 4284.3 4659.9 4662.9 4430.3 3889.8 4246.7 4881.9 4606.1 TRUE FALSE FALSE 4339.258864 4718.200833 4358.866444 5198.699563 4424.934813 4147.218128 4220.199515 4369.571564 4445.250637 4486.432858 0.967195766 1.051659744 0.971566182 1.158760139 0.986292441 0.924390994 0.940658124 0.973952292 0.990820721 1 12.13135311 -8.507553705 24.87707184 1.002475204 0.947362137 0.235039074 0.055195755 925.1716309 1501825.962 0.00817232 0.017737342 3.11E-09 8.507553705 -0.055113067 RT(ph)PTMPQEEAAEK ddPTM_HeLa_Romidepsin_16h_R1 2 RTPTMPQEEAAEK 13 1 Q9NYV4-2 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 RT(0.844)PT(0.156)MPQEEAAEK;RT(0.824)PT(0.176)MPQEEAAEK ; 82.202 0.019025 23440000 7629.8 7556.9 7333.8 4790.5 6557.3 6408.7 6491.6 6122.7 8407.9 8274.9 TRUE FALSE FALSE 7536.805063 7663.286237 7461.441713 5344.40015 6222.656512 5999.204753 7042.996342 6299.850664 7655.876366 8059.916905 0.935097117 0.950789732 0.925746729 0.663083778 0.77204971 0.744325881 0.873829895 0.781627247 0.949870384 1 12.97654925 -9.42829099 5.988612983 0.965886662 0.772361061 0.769682955 0.050813239 0.086181795 4.489233739 0.008308808 0.012713148 3.73E-10 9.42829099 -0.193525601 RT(ph)SFLEGTLR ddPTM_HeLa_Romidepsin_16h_R1 1 RTSFLEGTLR 10 1 E9PEW5;A0A0A0MQX1;Q9HD67-3;Q9HD67 E9PEW5 MYO10 Unconventional myosin-X 1 0 RT(0.973)S(0.025)FLEGT(0.002)LR 80.24 0.0021178 0 619.59 587.63 727.77 947.72 1802.7 2460.3 1948 1778.1 802.55 853.43 TRUE FALSE FALSE 612.0381988 595.9026706 740.4365316 1057.299846 1710.701492 2303.09477 2113.463071 1829.546518 730.767918 831.2577656 0.736279677 0.716868696 0.890742393 1.271927781 2.057967532 2.770614442 2.542488214 2.200937656 0.879111087 1 9.699152103 -8.763562951 2.180669804 0.860633426 2.51057337 0.957120668 0.157140006 0.045614957 0.442333613 0.026390007 0.057107297 1.72E-09 8.763562951 1.649939943 up RT(ph)SFSFQK ddPTM_HeLa_Romidepsin_16h_R1 2 RTSFSFQK 8 1 H0Y7F8;Q9BPZ7-4;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7 H0Y7F8 MAPKAP1 Target of rapamycin complex 2 subunit MAPKAP1 1 0 RT(0.976)S(0.023)FS(0.001)FQK;RT(0.873)S(0.126)FS(0.001)FQK ; 103.88 0.011473 136499000 6195.3 6921.1 5919.5 6989.3 7246.4 7886.1 7584.3 6664.8 8109.1 6526.1 TRUE FALSE FALSE 6119.789301 7018.535427 6022.526414 7797.435752 6876.589168 7382.203661 8228.510253 6857.635473 7383.801786 6356.550981 0.962753122 1.104142081 0.947451917 1.226677136 1.081811377 1.161353647 1.294492922 1.078829619 1.16160506 1 12.63402847 -9.312766008 1.201414514 0.985241759 1.179357945 0.183562098 0.096602229 0.239444003 0.682760718 0.012425045 0.023898213 4.87E-10 9.312766008 0.194116186 RT(ph)SFYLPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTSFYLPK 8 1 Q9NS23-3;Q9NS23-4;Q9NS23-2;Q9NS23-5;Q9NS23 Q9NS23-3 RASSF1 Ras association domain-containing protein 1 1 0 RT(0.5)S(0.5)FYLPK 105.4 0.010947 18798000 1714.8 1423.9 1593.1 1829 1955.6 1867.5 1772.1 1788.5 2003.5 2076.6 TRUE FALSE FALSE 1693.899358 1443.945702 1620.827237 2040.477586 1855.798435 1748.172777 1922.62213 1840.247426 1824.301942 2022.649633 0.837465536 0.713888198 0.801338606 1.008814158 0.917508601 0.864298368 0.950546303 0.909820167 0.901936704 1 10.98203072 -12.34665066 1.164049188 0.99748765 0.873355629 0.074977292 0.082437708 0.541485516 1.351807221 0.051585392 0.014636207 4.50E-13 12.34665066 -0.124132022 RT(ph)SPQVLGSILK ddPTM_HeLa_Romidepsin_16h_R1 1 RTSPQVLGSILK 12 1 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 RT(0.5)S(0.5)PQVLGSILK 82.837 0.017635 103900000 5343.3 4558.6 6402.3 6528.6 6446.5 5526.1 4552.4 3118.9 4625.3 4348.9 TRUE FALSE FALSE 5278.173804 4622.77609 6513.729346 7283.46745 6117.51105 5173.000045 4939.080742 3209.140451 4211.601584 4235.914951 1.246052828 1.091328826 1.537738463 1.719455545 1.444200632 1.221223774 1.166000923 0.757602664 0.994260185 1 12.04845791 -11.63936587 0.752627579 1.012592803 1.29586955 0.161515317 0.248074198 0.939901261 1.067982903 0.137438138 0.058340468 2.29E-12 11.63936587 0.283276747 RT(ph)SSLDTITGPYLTGQWPR ddPTM_HeLa_Romidepsin_16h_R1 1 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C0Q2;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 RT(0.524)S(0.221)S(0.221)LDT(0.033)IT(0.001)GPYLTGQWPR 52.849 0.026613 27379000 1391.4 1336.9 1446.4 1501.7 1365.5 1349.9 1314.7 1175 1728.4 1584.8 TRUE FALSE FALSE 1374.441082 1355.720913 1471.573985 1675.33362 1295.81344 1263.645747 1426.370585 1208.996771 1573.807575 1543.626668 0.890397342 0.878269948 0.953322469 1.085323061 0.839460387 0.81862135 0.924038574 0.783218376 1.019551948 1 10.59210816 -4 0.021110104 1.601689517 3.53E-07 0.318346576 0.075151705 2783.406386 4.572756998 127.0626951 235.7109287 1.00E-04 4 -1.601689165 RT(ph)T(ph)MT(ph)PIIR ddPTM_HeLa_Romidepsin_16h_R1 1 RTTMTPIIR 9 1 J3QLE7 J3QLE7 LRRC37B 3 0 RT(1)T(1)MT(1)PIIR 64.207 0.020187 8885700 1988.3 2202.3 2150.2 1110.5 1735.1 1856.4 1688.5 1483.3 2017.2 2161.8 TRUE FALSE FALSE 1964.065835 2233.304037 2187.623329 1238.901235 1646.551372 1737.782031 1831.921148 1526.216945 1836.77658 2105.636124 0.932766024 1.060631517 1.038937024 0.588373851 0.781973368 0.825300255 0.870008415 0.72482464 0.872314337 1 11.04004043 -9.284548708 24.94675172 0.980661949 0.769373514 0.630561215 0.085063362 370.3993488 399848.664 0.012315948 0.018820296 5.19E-10 9.284548708 -0.211288434 RTADSSSS(ph)EDEEEYVVEK ddPTM_HeLa_Romidepsin_16h_R1 2 RTADSSSSEDEEEYVVEK 18 1 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 1 0 RT(0.002)ADS(0.014)S(0.044)S(0.226)S(0.713)EDEEEYVVEK;RT(0.213)ADS(0.004)S(0.004)S(0.135)S(0.644)EDEEEYVVEK ; 136.64 0.0002897 17348100 14301.6 13257 12847.3 15735.5 11828.3 11122.6 8567.5 9110.2 15419.6 13953.5 TRUE FALSE FALSE 14127.2866 13443.63239 13070.90187 17554.91255 11224.65771 10411.90176 9295.223236 9373.789263 14040.43236 13590.98606 1.039460017 0.989157986 0.961733152 1.291658491 0.82588987 0.766088767 0.683925596 0.689706341 1.03306944 1 13.73036251 -8.535060026 24.99897311 1.030127394 0.724588827 0.747935513 0.089638565 82.35150835 169005.1139 0.012468242 0.024949869 2.92E-09 8.535060026 -0.305538567 RTDALTS(ph)SPGR ddPTM_HeLa_Romidepsin_16h_R1 1 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 0 RTDALT(0.002)S(0.962)S(0.036)PGR 133.04 0.0013179 327310000 3223 3080.7 3080.5 1848.1 3159.7 2847.8 2847.6 2830.7 3032.5 3112.1 TRUE FALSE FALSE 3183.716836 3124.070175 3134.11481 2061.786018 2998.448719 2665.834771 3089.475073 2912.601838 2761.265605 3031.247193 1.05029931 1.030622043 1.03393574 0.68017746 0.989179875 0.87945146 1.019209215 0.960859228 0.910933827 1 11.56569579 RTDALTSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 2 RTDALTSSPGR 11 1 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 0 RT(0.003)DALT(0.158)S(0.215)S(0.623)PGR;RTDALTS(0.014)S(0.986)PGR ; 147.7 0.00071923 381895500 2594.37 2805.4 2690.95 1735.23 2499.55 2810.66 2077.41 2068.34 2718.04 2851.89 TRUE FALSE FALSE 2562.748821 2844.894495 2737.784856 1935.865457 2371.988636 2631.067897 2253.865154 2128.184155 2474.931695 2777.797487 0.922583029 1.024154752 0.985595555 0.69690662 0.85390985 0.947177722 0.811385698 0.76614086 0.890969089 1 11.43972571 -9.296711987 24.98615731 0.969543198 0.824390837 0.534038668 0.069504883 355.0747976 251524.3362 0.010463955 0.015984346 5.05E-10 9.296711987 -0.145152361 RTDAY(ph)S(ph)RS(ph)S(ph)SVS(ph)SQEEK ddPTM_HeLa_Romidepsin_16h_R1 1 RTDAYSRSSSVSSQEEK 17 2 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 5 0 RT(0.041)DAY(0.942)S(0.961)RS(0.879)S(0.824)S(0.358)VS(0.498)S(0.498)QEEK 42.095 0.0042964 0 790.18 1021.3 993.33 569.56 1137.9 873.02 815.74 842.81 1159.6 1202 TRUE FALSE FALSE 780.5489822 1035.677888 1010.618492 635.4152071 1079.828717 817.2368395 885.0289352 867.1953776 1055.882472 1170.771867 0.666696053 0.884611185 0.863207018 0.542731872 0.922322057 0.698032523 0.755936285 0.740703977 0.901868675 1 10.19324427 -12.45340603 1.085464708 1.005610984 0.753737215 0.314241963 0.109938193 0.396635 0.805269572 0.078848842 0.017860253 3.52E-13 12.45340603 -0.251873769 RTDIFGVEETAIGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 RTDIFGVEETAIGKK 15 2 Q15459;Q15459-2 Q15459 SF3A1 Splicing factor 3A subunit 1 0 1 RTDIFGVEETAIGK(1)K 182.02 2.49E-09 1717900 830.95 709.88 527.58 676.8 648.16 616.39 655.61 564.69 1111.8 950.85 FALSE TRUE FALSE 820.8220618 719.8737093 536.7623086 755.0548004 615.0819766 577.0046683 711.297497 581.0284142 1012.357823 926.1467799 0.88627643 0.777278208 0.579565054 0.815264726 0.664130125 0.623016438 0.768018107 0.627361048 1.093085724 1 9.855097046 -10.38459412 1.1676455 0.965730867 0.682448463 0.747265586 0.081146245 0.146844617 0.393225464 0.014662681 0.016460989 4.12E-11 10.38459412 -0.283282404 RTDYVS(ph)PTASALR ddPTM_HeLa_Romidepsin_16h_R1 1 RTDYVSPTASALR 13 1 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 RT(0.001)DYVS(0.994)PT(0.004)ASALR 123.63 0.0062919 4718700 1706.6 1774.7 1697.3 1571.1 2005.5 1875.6 1872.7 1664.8 1770.3 1769.2 TRUE FALSE FALSE 1685.799303 1799.684273 1726.840795 1752.757974 1903.151851 1755.755213 2031.767091 1712.968361 1611.959934 1723.235929 0.978275391 1.044363249 1.002091916 1.017131749 1.104405856 1.018871057 1.179041742 0.994041694 0.935426141 1 10.75090452 -9.072976778 1.087213059 0.992115732 1.081060025 0.332910434 0.053413246 0.367640696 0.857313987 0.00768124 0.017839807 8.45E-10 9.072976778 0.088944293 RTES(ph)VPSDINNPVDR ddPTM_HeLa_Romidepsin_16h_R1 3 RTESVPSDINNPVDR 15 1 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 RT(0.397)ES(0.603)VPSDINNPVDR;RT(0.015)ES(0.984)VPS(0.001)DINNPVDR;RT(0.249)ES(0.749)VPS(0.002)DINNPVDR ;; 121.48 0.0010258 63316500 3015.93 3154.06 3253.85 3088.78 3528.9 3241.29 2842.71 3071.71 3835.34 2905.65 TRUE FALSE FALSE 2979.170685 3198.462939 3310.481894 3445.919277 3348.807065 3034.18203 3084.169716 3160.585082 3492.297585 2830.160794 1.05265068 1.130134707 1.169715128 1.217570141 1.183256821 1.072088214 1.089750704 1.116751066 1.233957304 1 11.46666831 -10.42050367 1.883224626 1.019326654 1.142402716 0 0.079563011 0.172878026 1.183178448 0.0091421 0.010215486 3.80E-11 10.42050367 0.123076061 RTIPWLEDR ddPTM_HeLa_Romidepsin_16h_R1 1 RTIPWLEDR 9 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 0 102.95 0.016553 9522300 2547.2 2501.9 2378.2 2135.4 2731.4 3274.7 2319.1 2113.1 2406.8 2639.3 FALSE FALSE TRUE 2516.153747 2537.121814 2419.591573 2382.304995 2592.006466 3065.457239 2516.084296 2174.239215 2191.52978 2570.730606 0.978769903 0.986926366 0.941207752 0.926703479 1.008276192 1.192445926 0.978742888 0.84576704 0.852492974 1 11.32796272 -8.539003502 24.74576291 0.980909696 1.019194392 0.012817457 0.091181191 583.3357376 895210.5999 0.011807017 0.023620656 2.89E-09 8.539003502 0.038284695 RTIQEVLEEQS(ph)EDEDR ddPTM_HeLa_Romidepsin_16h_R1 1 RTIQEVLEEQSEDEDR 16 1 M0R0Q7;P18858-2;P18858-3;P18858 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 RTIQEVLEEQS(1)EDEDR 136.61 0.00036182 3123200 1126.3 1135.5 1028.4 598.29 864.04 1017.3 768.09 812.23 863.14 1122.5 TRUE FALSE FALSE 1112.572222 1151.485599 1046.298871 667.4671048 819.9448146 952.2978132 833.3315454 835.7305936 785.9385966 1093.337288 1.017592864 1.053184238 0.956977213 0.610485997 0.749946813 0.871000947 0.76219073 0.764384973 0.718843677 1 10.09452282 -9.435104749 6.488478097 1.011645024 0.759388623 0.397666847 0.110679283 0.076999439 4.766900015 0.009270648 0.014172743 3.67E-10 9.435104749 -0.252256402 RTLEGELHDLR ddPTM_HeLa_Romidepsin_16h_R1 2 RTLEGELHDLR 11 1 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 108.35 0.0032254 11575100 7818 7423.5 6897.3 9399.8 9366.2 8944.5 7721.8 8245.4 8522.3 7115 FALSE FALSE TRUE 7722.711209 7528.008228 7017.344613 10486.6491 8888.207864 8372.975317 8377.689499 8483.96764 7760.044144 6930.151274 1.114364016 1.086268962 1.012581737 1.513191948 1.282541681 1.208195173 1.208875415 1.224211031 1.119751047 1 12.75867113 -9.306515303 24.99939232 1.055485734 1.278370133 0.597829679 0.090171903 231.4538685 128365.1594 0.014328579 0.021887327 4.94E-10 9.306515303 0.222884399 RTNS(ph)SSSSPVVLK ddPTM_HeLa_Romidepsin_16h_R1 1 RTNSSSSSPVVLK 13 1 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 RT(0.043)NS(0.886)S(0.043)S(0.01)S(0.017)S(0.002)PVVLK 110.44 0.0012545 0 1662.4 1469.3 1397.3 1411 1413.4 1485.8 1234.1 1386.6 1622.4 1567.8 TRUE FALSE FALSE 1642.138029 1489.984844 1421.61942 1574.146459 1341.268924 1390.862175 1338.924423 1426.719083 1477.288481 1527.06833 1.07535334 0.975715896 0.93094683 1.030829091 0.878329344 0.910805462 0.876794048 0.934286342 0.967401688 1 10.5765489 -9.259413651 0.921643337 1.033440274 0.898917307 0.398160915 0.047636773 0.290189348 0.487398576 0.008710051 0.019226418 5.50E-10 9.259413651 -0.134522967 RTPAPPEPGS(ph)PAPGEGPSGR ddPTM_HeLa_Romidepsin_16h_R1 3 RTPAPPEPGSPAPGEGPSGR 20 1 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 0 RT(0.001)PAPPEPGS(0.998)PAPGEGPS(0.001)GR;RTPAPPEPGS(1)PAPGEGPSGR;RTPAPPEPGS(0.999)PAPGEGPS(0.001)GR ;; 115.06 8.22E-05 61085000 4814.15 4750.64 4608.23 4453.88 3937.71 4086.23 3244.26 4056.28 4884.53 5092.38 TRUE FALSE FALSE 4755.473288 4817.519635 4688.43431 4968.858562 3736.753965 3825.133091 3519.827363 4173.642062 4447.645403 4960.079233 0.95874946 0.971258605 0.945233753 1.001769998 0.753365781 0.771183868 0.709631278 0.841446651 0.896688378 1 12.27614745 -8.759377348 24.99996324 0.977682708 0.764835529 0.829198271 0.04263761 11.18889867 135650.3711 0.004813341 0.009257222 1.74E-09 8.759377348 -0.21284718 RTPLGHGS(ph)PDTSETPQNPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTPLGHGSPDTSETPQNPK 19 1 Q9NXE4-5 Q9NXE4-5 1 0 RT(0.419)PLGHGS(0.581)PDTSETPQNPK 75.045 0.018764 5612400 2005.5 2850.7 2256.2 1956.7 2756.6 2889.3 2657.5 2908.3 2395.9 2444.3 TRUE FALSE FALSE 1981.056195 2890.832229 2295.468215 2182.942861 2615.920416 2704.683055 2883.227984 2992.447072 2181.604703 2380.796734 0.832097998 1.214228913 0.964159679 0.916895941 1.098758402 1.136041148 1.211034921 1.256909937 0.916333878 1 11.21722874 -7.995003783 0.623024039 0.935728901 1.340564536 0.524974417 0.097034109 0.993826492 0.438764906 0.020555818 0.241637031 1.01E-08 7.995003783 0.404835635 RTPS(ph)DDEEDNLFAPPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTPSDDEEDNLFAPPK 16 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 RT(0.088)PS(0.912)DDEEDNLFAPPK 124.43 0.0039632 76067000 1460.4 1207.3 1307.7 1086.8 1350.4 1065.4 1080.1 966.25 1456.1 1133.1 TRUE FALSE FALSE 1442.600083 1224.296401 1330.45997 1212.46093 1281.484049 997.3243784 1171.843667 994.2069193 1325.862769 1103.661899 1.307103276 1.109303857 1.205495969 1.098580037 1.161120132 0.903650275 1.061777768 0.900825625 1.201330562 1 10.10808256 -8.271180773 24.53494646 1.147398827 0.966053877 0.524877728 0.086516251 449.8738913 1133065.3 0.01696105 0.038384614 5.36E-09 8.271180773 -0.18134495 RTQS(ph)LSALPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTQSLSALPK 10 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 0 RT(0.035)QS(0.964)LSALPK 100.02 0.0072643 18246000 3328.1 3647 3404.3 3266.5 3294.2 3864.5 3113.7 3208.6 3711.2 3314.3 TRUE FALSE FALSE 3287.535837 3698.342562 3463.550413 3644.188099 3126.084682 3617.570922 3378.1776 3301.435779 3379.260977 3228.194008 1.018382361 1.145638259 1.072906524 1.128862791 0.96836952 1.120617569 1.046460526 1.022688156 1.046796125 1 11.65651157 -10.49001 21.84672683 1.008109716 1.072066728 0.156613239 0.051386662 89.17701942 59274.53059 0.008142509 0.008977976 3.24E-11 10.49001 0.063957012 RTQS(ph)SLTVSEVLTR ddPTM_HeLa_Romidepsin_16h_R1 1 RTQSSLTVSEVLTR 14 1 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 RT(0.086)QS(0.75)S(0.145)LT(0.017)VS(0.001)EVLTR 96.805 0.0038334 15003000 1024.2 955.05 959.22 1087.4 1466.6 1259.1 1294.7 1033.9 1311.4 1060 TRUE FALSE FALSE 1011.716656 968.495219 975.9148217 1213.130304 1391.753929 1178.647574 1404.671786 1063.814265 1194.1051 1032.461047 0.979907822 0.938045287 0.945231614 1.174988933 1.34799655 1.141590355 1.360508263 1.030367459 1.156561889 1 10.01187164 -9.165835527 4.694442235 0.982559135 1.227894222 0.482549809 0.106405726 0.099840736 3.694125543 0.012203787 0.020520071 6.83E-10 9.165835527 0.245335087 RTS(ph)FYLPK ddPTM_HeLa_Romidepsin_16h_R1 1 RTSFYLPK 8 1 Q9NS23-3;Q9NS23-4;Q9NS23-2;Q9NS23-5;Q9NS23 Q9NS23-3 RASSF1 Ras association domain-containing protein 1 1 0 RT(0.479)S(0.521)FYLPK 97.813 0.0098575 19522000 2326.3 2627.7 2533.4 2491.8 2559.6 2024.1 2033.1 2263.9 2634 2491.5 TRUE FALSE FALSE 2297.946161 2664.69283 2577.492764 2779.91364 2428.974061 1894.766542 2205.791463 2329.402375 2398.408443 2426.770471 0.94691533 1.098040734 1.062108178 1.145519807 1.000908034 0.78077699 0.908941117 0.959877501 0.988312851 1 11.24482195 -8.389159212 10.98917291 1.005341943 0.885856406 0.446367164 0.072286104 0.421758585 35.27109315 0.011623879 0.026001374 4.08E-09 8.389159212 -0.119485537 RTS(ph)SEDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 2 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 0 RT(0.008)S(0.496)S(0.496)EDNLYLAVLR;RT(0.091)S(0.598)S(0.311)EDNLYLAVLR ; 122.46 0.0011301 179251000 3004.5 2791 2804.3 3766.5 2851.7 2431.4 2525.2 2679.8 3463.3 2689.2 TRUE FALSE FALSE 2967.879998 2830.291771 2853.107665 4202.000452 2706.167108 2276.041387 2739.690425 2757.335785 3153.533774 2619.334196 1.133066564 1.080538625 1.089249195 1.604224638 1.033150757 0.868938904 1.045949169 1.052685751 1.203944796 1 11.35498443 -8.532059483 24.99992711 1.110487944 0.98756325 0.14806857 0.169793146 377.9665068 1029233.413 0.025757644 0.051570259 2.94E-09 8.532059483 -0.122924694 RTS(ph)STLDSEGTFNSYR ddPTM_HeLa_Romidepsin_16h_R1 1 RTSSTLDSEGTFNSYR 16 1 Q92609;Q92609-2;C9JNM0;C9JED7;F2Z3C3;C9K0P2;C9J397;C9JWX0;C9JW04;C9JDR8 Q92609 TBC1D5 TBC1 domain family member 5 1 0 RTS(0.9)S(0.087)T(0.013)LDSEGTFNSYR 130.47 0.0030422 7311300 731.94 919.74 636.56 693.36 1197.7 1500.2 1602.2 1954.7 841.52 860.14 TRUE FALSE FALSE 723.0188337 932.6881239 647.6390598 773.5295456 1136.5769 1404.342062 1738.290828 2011.25616 766.2523436 837.7934388 0.863003695 1.113267401 0.77302952 0.923293869 1.356631417 1.676239031 2.074844165 2.400658763 0.914607716 1 9.710450776 -8.001257285 1.11023911 0.930017014 2.456607112 0.962939068 0.102586587 0.088821331 0.169751204 0.016547893 0.116023543 9.97E-09 8.001257285 1.526590098 up RTSS(ph)EDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 3 RTSSEDNLYLAVLR 14 1 Q15149-4 Q15149-4 PLEC Plectin 1 0 RTS(0.039)S(0.961)EDNLYLAVLR;RT(0.002)S(0.003)S(0.995)EDNLYLAVLR;RT(0.009)S(0.143)S(0.848)EDNLYLAVLR ;; 144.4 0.00033892 113052900 6541.84 6521.3 6100.14 7552.81 7596.72 6544.15 6241.66 6246.81 7744.8 6518.26 TRUE FALSE FALSE 6462.105538 6613.107033 6206.310378 8426.101429 7209.031031 6125.999935 6771.826445 6427.551592 7052.085691 6348.914666 1.017828381 1.041612209 0.977538793 1.327171946 1.135474551 0.964889317 1.066611665 1.012385885 1.110754525 1 12.63229427 RTSS(ph)LDTITGPYLTGQWPR ddPTM_HeLa_Romidepsin_16h_R1 1 RTSSLDTITGPYLTGQWPR 19 1 Q86VQ1;H7C0Q2;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 RTS(0.002)S(0.997)LDTITGPYLTGQWPR 139.11 0.00062975 24780000 2456.3 2079.5 2045.8 2451.4 1909.7 1635.9 1425.8 1761.4 2069.2 1959.4 TRUE FALSE FALSE 2426.361671 2108.775256 2081.406291 2734.842402 1812.240883 1531.37127 1546.907416 1812.36333 1884.12557 1908.494506 1.271348523 1.104941748 1.090601144 1.432984163 0.94956568 0.802397526 0.810538051 0.949629839 0.98723133 1 10.89821932 -8.535517003 24.99235454 1.146958963 0.854183081 0.5268609 0.127683749 137.7404598 272383.3188 0.019828291 0.039676118 2.91E-09 8.535517003 -0.292775881 RTSVPS(ph)PEQPQPYR ddPTM_HeLa_Romidepsin_16h_R1 1 RTSVPSPEQPQPYR 14 1 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 0 RT(0.03)S(0.03)VPS(0.94)PEQPQPYR 64.298 0.021788 5795200 1036.1 1065 980.55 857.51 1208.6 860.45 854.26 1242.6 1139.2 1124.6 TRUE FALSE FALSE 1023.471615 1079.993098 997.6160614 956.6593409 1146.920632 805.470022 926.8208231 1278.552671 1037.307099 1095.38273 0.934350695 0.985950452 0.910746568 0.873356239 1.047050132 0.735332044 0.846115972 1.167220037 0.946981425 1 10.09721932 -12.03432952 0.462201156 1.012714442 0.924608875 0.002035256 0.111537224 3.987656998 1.302223154 0.162276942 0.032375759 9.24E-13 12.03432952 -0.088105568 RTVLYNDDS(ph)DNDNFVST(ph)EDPLNLGTSRSGR ddPTM_HeLa_Romidepsin_16h_R1 1 RTVLYNDDSDNDNFVSTEDPLNLGTSRSGR 30 2 Q6RI45-3;Q6RI45-4;Q6RI45-2;Q6RI45 Q6RI45-3 BRWD3 Bromodomain and WD repeat-containing protein 3 2 0 RT(0.034)VLY(0.083)NDDS(0.883)DNDNFVS(0.19)T(0.69)EDPLNLGT(0.037)S(0.037)RS(0.045)GR 54.3 0.0019353 0 559.9 621.81 721.67 487.22 627.37 778.61 629.39 529.52 751.58 611.83 TRUE FALSE FALSE 553.0757234 630.5638575 734.2303636 543.5546688 595.3529679 728.8593338 682.8503709 544.8408258 684.3568024 595.9345684 0.928081291 1.058109214 1.232065402 0.912104613 0.999024053 1.223052618 1.145847895 0.914262831 1.148375742 1 9.219010126 -10.16635042 6.222187625 0.966179158 1.076430532 0 0.120730514 0.298633997 16.37088493 0.017538979 0.021523522 6.82E-11 10.16635042 0.110251375 RVAAPQDGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 RVAAPQDGSPR 11 1 Q9HD15 Q9HD15 SRA1 Steroid receptor RNA activator 1 1 0 RVAAPQDGS(1)PR;RVAAPQDGS(1)PR ; 97.2 0.0067845 4855000 2816.88 2923.9 2905.24 2976.63 3570.4 4743.5 3924.6 3362.3 3539.1 3313.9 TRUE FALSE FALSE 2782.546783 2965.062741 2955.804484 3320.801966 3388.189165 4440.405659 4257.955426 3459.582846 3222.554032 3227.8044 0.862055576 0.918600502 0.915732218 1.028811401 1.049688502 1.375673711 1.319149148 1.071806843 0.998373393 1 11.65633744 -8.56979726 2.375047259 0.934126897 1.259690863 0.68972991 0.088957889 0.118206772 1.337709444 0.013585538 0.031996302 2.69E-09 8.56979726 0.325563967 RVAIFIEK ddPTM_HeLa_Romidepsin_16h_R1 1 RVAIFIEK 8 1 Q9P258 Q9P258 RCC2 Protein RCC2 0 0 100.02 0.005361 1792900 1565.2 1485.9 1783 1400.5 1340.9 1403.2 1335.4 1070.4 1735.9 1216.5 FALSE FALSE TRUE 1546.12274 1506.818539 1814.032367 1562.4324 1272.468869 1313.540049 1448.828843 1101.370335 1580.636756 1184.895155 1.304860379 1.271689342 1.530964457 1.318625022 1.073908408 1.108570698 1.222748559 0.929508683 1.333988708 1 10.21054369 -7.256759117 23.85326416 1.189512739 0.929508476 0.215826997 0.152028391 376.8927874 1920723.152 0.024532496 0.261279117 5.54E-08 7.256759117 -0.260004262 RVDIIPGFEFDR ddPTM_HeLa_Romidepsin_16h_R1 2 RVDIIPGFEFDR 12 1 A6NKB8;Q9H4A4 A6NKB8 RNPEP Aminopeptidase B 0 0 ; ; 122.78 0.00425 14339200 4479 4127.8 4513.4 4403.2 4703.2 4844.1 3618.4 4106 4612 3960.8 FALSE FALSE TRUE 4424.408225 4185.911277 4591.953834 4912.318702 4463.178154 4534.577644 3925.746806 4224.800632 4199.491169 3857.897845 1.146844319 1.085023877 1.190273568 1.273314872 1.156893815 1.175401171 1.017587029 1.095104329 1.088543901 1 11.91359923 -12.12107154 0.709122696 0.991492207 1.145759184 0.202082474 0.069898495 0.688004576 0.576832757 0.062054356 0.01477171 7.57E-13 12.12107154 0.154266977 RVFGWEEDEDF ddPTM_HeLa_Romidepsin_16h_R1 1 RVFGWEEDEDF 11 1 Q9BWD3;Q17RB0;A6ZKI3 Q9BWD3 FAM127B;FAM127C;FAM127A Protein FAM127B;Protein FAM127C;Protein FAM127A 0 0 127.68 0.023139 10029000 3088 2937.2 3155.2 2723.2 2997.5 3714.8 2974.9 3279.3 3421.5 2701.8 FALSE FALSE TRUE 3050.362268 2978.549979 3210.114932 3038.069197 2844.52639 3477.436269 3227.587932 3374.181372 3115.472471 2631.606847 1.159125373 1.131836993 1.219830742 1.154454056 1.080908569 1.321411773 1.226470411 1.282175328 1.183866988 1 11.36172826 -16.52287875 0.067744672 0.248980233 1.484723346 0.224854923 0.078582793 99.02447253 0.522425668 11.89337192 1.818852733 3.00E-17 16.52287875 1.235743113 RVGDPPQPLPEEPMEVQGAERAS(ph)PEPQR ddPTM_HeLa_Romidepsin_16h_R1 1 RVGDPPQPLPEEPMEVQGAERASPEPQR 28 2 A0A024RCR6;A0A0G2JK23;P46379-2;P46379;P46379-3;H0Y710;A0A0G2JL47;P46379-5 A0A024RCR6 BAT3;BAG6 Large proline-rich protein BAG6 1 0 RVGDPPQPLPEEPMEVQGAERAS(1)PEPQR 45.579 0.011364 11849000 1175.8 1427.3 1577.9 1191.8 1553.3 1757.8 1197.9 1641.4 1812.2 1649.2 TRUE FALSE FALSE 1161.468897 1447.393567 1605.362688 1329.601524 1474.029305 1645.482253 1299.649596 1688.891319 1650.112293 1606.353546 0.723046866 0.901042968 0.999383163 0.827714127 0.91762446 1.024358714 0.809068215 1.051382072 1.027241044 1 10.64957374 -8.703497028 1.0143831 0.87412782 0.952321252 0 0.108632902 1.394790368 2.731644733 0.020651548 0.067593454 1.98E-09 8.703497028 0.078193433 RVIISAPSADAPMFVMGVNHEK ddPTM_HeLa_Romidepsin_16h_R1 1 RVIISAPSADAPMFVMGVNHEK 22 1 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 91.547 0.00079121 5783600 314.91 425.04 453.21 351.69 501.44 455.37 389.19 354.47 358.09 409.97 FALSE FALSE TRUE 311.0717558 431.0237243 461.0979299 392.3540526 475.8496457 426.2733266 422.2477889 364.7260302 326.0615335 399.3189203 0.779005802 1.079397199 1.15471095 0.982558132 1.191653141 1.06750095 1.05741994 0.91337027 0.816544163 1 8.64139762 -10.23621629 24.56647536 0.895641628 1.068987513 0.484220557 0.092237472 485.829276 473182.7759 0.017653242 0.021615829 5.80E-11 10.23621629 0.173345885 RVLESEEQVLVMYHRY(ph)WEEY(ph)S(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 RVLESEEQVLVMYHRYWEEYSK 22 2 Q5T2B5;A0A0A0MTN0;Q13617;Q13617-2 Q5T2B5 CUL2 Cullin-2 3 0 RVLES(0.008)EEQVLVMY(0.025)HRY(0.968)WEEY(0.999)S(0.999)K 43.156 0.0040093 0 0 0 75.677 73.984 0 0 180.32 145.25 0 70.894 TRUE FALSE FALSE 0 0 76.99412644 82.53837819 0 0 195.6363763 149.4525796 0 69.05216366 0 0 1.11501396 1.195304735 0 0 2.83316794 2.164343181 0 1 6.109614715 -7.758472555 24.99999995 0.504308447 2.49875614 0.726675793 0.509062776 31.79632787 267917.4606 0.077367542 0.266300767 1.74E-08 7.758472555 1.994447692 RVLT(ph)AY(ph)AY(ph)RNPK ddPTM_HeLa_Romidepsin_16h_R1 1 RVLTAYAYRNPK 12 2 J3KN75;Q0IIM8-2;Q0IIM8-3;Q0IIM8 J3KN75 TBC1D8B TBC1 domain family member 8B 3 0 RVLT(1)AY(1)AY(1)RNPK 59.57 0.0039501 0 174.47 147.82 167.13 246.59 154.02 309.4 62.185 178.96 252.65 283.33 TRUE FALSE FALSE 172.3434925 149.9010138 170.0388275 275.101896 146.1597847 289.6303385 67.46699235 184.1379252 230.0523512 275.9690458 0.624502984 0.543180535 0.616151812 0.996857801 0.529623836 1.04950299 0.244473043 0.667241229 0.833616504 1 8.108362645 -12.21279584 0.859409067 1.009209494 0.658873616 0.1611514 0.222836072 0.685245922 0.875064164 0.156699053 0.039715604 6.13E-13 12.21279584 -0.350335878 RVNDAEPGS(ph)PEAPQGK ddPTM_HeLa_Romidepsin_16h_R1 4 RVNDAEPGSPEAPQGK 16 1 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 0 RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK;RVNDAEPGS(1)PEAPQGK ;;; 145.02 9.33E-05 77244000 26643.5 25895 24121.6 24475.9 24021.2 23532.4 22004.8 22121 26611.6 25103.4 TRUE FALSE FALSE 26318.75877 26259.55049 24541.42633 27305.91872 22795.30853 22028.75559 23873.88716 22761.03623 24231.39185 24451.21005 1.076378581 1.073957094 1.003689645 1.116751223 0.932277318 0.900927011 0.976388781 0.930875658 0.991009925 1 14.57761824 -8.733588382 24.99452351 1.042409481 0.935622929 0.631079446 0.040638588 111.8188165 100349.9279 0.006028184 0.012054329 1.85E-09 8.733588382 -0.106786551 RVNS(ph)GDTEVGSSLLR ddPTM_HeLa_Romidepsin_16h_R1 3 RVNSGDTEVGSSLLR 15 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 RVNS(0.992)GDT(0.006)EVGS(0.002)SLLR;RVNS(0.998)GDT(0.002)EVGSSLLR;RVNS(0.935)GDT(0.065)EVGSSLLR ;; 104.94 0.0026623 25179700 2789.92 3015.92 2285.29 3401.7 3260.95 2877.01 3227.92 3449.94 2946.06 2252.87 TRUE FALSE FALSE 2755.915382 3058.378201 2325.064514 3795.020559 3094.531553 2693.178346 3502.099444 3549.758571 2682.557015 2194.340113 1.255919885 1.393757596 1.059573446 1.729458682 1.410233325 1.227329497 1.595969296 1.617688411 1.222489166 1 11.09957144 -7.908794615 0.051888438 8.66E-11 2.969041301 0.387451029 0.179956205 81.51937021 0.847701531 17.88576103 31.95889689 1.23E-08 7.908794615 2.969041301 RVPLS(ph)PLSLLAGPADAR ddPTM_HeLa_Romidepsin_16h_R1 1 RVPLSPLSLLAGPADAR 17 1 Q5T4K5;H0YDQ8;Q53ET0 Q5T4K5 CRTC2 CREB-regulated transcription coactivator 2 1 0 RVPLS(0.883)PLS(0.117)LLAGPADAR 53.304 0.026466 11364000 1578.1 1523 1498.8 1865.7 1988.8 2057 1756.5 2229.4 1807 1414.3 TRUE FALSE FALSE 1558.86551 1544.440834 1524.885985 2081.421012 1887.304115 1925.564339 1905.697066 2293.904172 1645.377394 1377.556282 1.131616567 1.12114536 1.106950043 1.510951704 1.370037754 1.397811736 1.383389623 1.665198149 1.194417546 1 10.42789555 -7.859089393 0.261959476 0.98252951 1.916877163 0.688895674 0.111085436 2.203443584 0.154250161 0.066579949 0.650796287 1.38E-08 7.859089393 0.934347653 RVPS(ph)PTPAPK ddPTM_HeLa_Romidepsin_16h_R1 4 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 RVPS(0.993)PT(0.007)PAPK;RVPS(0.987)PT(0.013)PAPK;RVPS(0.996)PT(0.004)PAPK;RVPS(0.996)PT(0.004)PAPK ;;; 112.08 0.0049805 3745090000 66354 66017 56508 56936 50997.8 49362.2 46183.6 50095.1 65506 63314 TRUE FALSE FALSE 65545.25193 66946.38906 57491.49804 63519.20821 48395.19197 46208.11473 50106.43383 51544.52268 59646.9793 61669.09315 1.062854156 1.085574404 0.93225788 1.030000685 0.784756018 0.749291296 0.812504794 0.835824236 0.967210255 1 15.91226001 -8.762283336 25 1.026931386 0.79349462 0.83500388 0.047092825 5.88976192 174477.3977 0.006811783 0.012889663 1.73E-09 8.762283336 -0.233436765 RVPSPTPAPK ddPTM_HeLa_Romidepsin_16h_R1 1 RVPSPTPAPK 10 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 0 89.827 0.025161 6226700 4467.4 4233.3 3853.1 4715.7 3141.1 3575.7 3450.8 3770.1 4806.5 4578.8 FALSE FALSE TRUE 4412.94961 4292.896509 3920.161589 5260.951422 2980.797946 3347.22431 3743.910866 3879.181895 4376.594602 4459.842116 0.989485613 0.962566924 0.878991114 1.179627279 0.668364007 0.750525293 0.839471615 0.869802516 0.981333977 1 12.12277692 -8.749406562 24.9999927 0.994080322 0.78389196 0.603784609 0.085915557 114.529056 237949.9759 0.011680604 0.023218992 1.78E-09 8.749406562 -0.210188362 RVQS(ph)SPNLLAAGR ddPTM_HeLa_Romidepsin_16h_R1 2 RVQSSPNLLAAGR 13 1 O94875-12;O94875-11;O94875-9;C9J4Z9;C9IZT7;C9JWC3;C9JN77;C9JI79;C9J372;C9JZ60;C9JDX2;C9JBB0;C9JEA9;C9JG84;C9J9D3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 RVQS(0.918)S(0.082)PNLLAAGR;RVQS(0.967)S(0.033)PNLLAAGR ; 96.435 0.004775 8282200 600.34 742.13 518.34 490.77 435.36 524.46 372.62 457.77 724.29 732.24 TRUE FALSE FALSE 593.0228252 752.5777256 527.3614903 547.5151365 413.1419546 490.9486986 404.2703335 471.0148527 659.5076884 713.2162992 0.831476827 1.055188624 0.739413122 0.767670533 0.579266003 0.688358776 0.56682711 0.660409546 0.9246952 1 9.478195863 -9.308811019 1.550739594 0.927992125 0.62588597 0.760093691 0.078663801 0.152142384 0.716748607 0.014177994 0.025500116 4.91E-10 9.308811019 -0.302106155 RVS(ph)EVEEEKEPVPQPLPSDDTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVSEVEEEKEPVPQPLPSDDTR 22 2 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 0 RVS(0.999)EVEEEKEPVPQPLPS(0.001)DDTR 72.122 0.003262 30453000 1965.3 2078.6 2060 1522.5 1741.9 2024.3 1752.8 2116.1 2334.8 1971 TRUE FALSE FALSE 1941.346168 2107.862585 2095.853436 1698.538614 1653.004343 1894.953763 1901.682788 2177.326015 2125.96964 1919.793136 1.011226747 1.097963393 1.091707954 0.884750852 0.861032531 0.987061433 0.990566511 1.134146161 1.107395167 1 10.90673515 -9.268554675 24.98499075 1.019751336 0.967296274 0.147196348 0.081434569 1069.714017 3756245.502 0.012278115 0.019012152 5.39E-10 9.268554675 -0.052455062 RVS(ph)GDAAQDLDR ddPTM_HeLa_Romidepsin_16h_R1 2 RVSGDAAQDLDR 12 1 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 RVS(1)GDAAQDLDR;RVS(1)GDAAQDLDR ; 84.046 0.011877 23866000 3677.8 3658.2 3256.4 3606.1 4515.5 4206.6 3558.6 3823.6 3843.7 3212.6 TRUE FALSE FALSE 3632.973559 3709.700236 3313.076276 4023.054249 4285.057185 3937.811836 3860.867395 3934.229833 3499.909845 3129.136189 1.161014842 1.185534925 1.058783024 1.285675665 1.369405781 1.258434149 1.233844474 1.257289423 1.118490738 1 11.61154873 -11.0707313 0.265908773 0.941375722 1.309960715 0.510314287 0.073952787 1.016390199 0.207628583 0.145100706 0.079585787 8.50E-12 11.0707313 0.368584993 RVS(ph)LSEIGFGK ddPTM_HeLa_Romidepsin_16h_R1 1 RVSLSEIGFGK 11 1 H0YBX5;E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2 H0YBX5 CDK16 Cyclin-dependent kinase 16 1 0 RVS(1)LSEIGFGK 139.19 0.0050982 74613000 4170.8 3802.1 3875.2 3472.7 3741.6 3424.9 3322.5 3541.8 4149.7 3622.9 TRUE FALSE FALSE 4119.964685 3855.626064 3942.64623 3874.229914 3550.65219 3206.059943 3604.713067 3644.276395 3778.540439 3528.776536 1.167533462 1.092624037 1.117284189 1.097896077 1.006199218 0.908547172 1.021519224 1.032730851 1.070779178 1 11.78495236 -8.688822716 5.167104712 1.086419813 0.986272448 0.483810328 0.049982463 0.194280293 9.472175272 0.010196109 0.020558258 2.05E-09 8.688822716 -0.100147365 RVS(ph)LVGADDLR ddPTM_HeLa_Romidepsin_16h_R1 2 RVSLVGADDLR 11 1 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 RVS(1)LVGADDLR;RVS(1)LVGADDLR ; 101.72 0.0054561 10975400 3228.5 3507.3 3478.6 2877.8 4488.6 5223.5 4221.6 4866.6 3753.8 3827.6 TRUE FALSE FALSE 3189.1498 3556.675861 3539.143574 3210.544776 4259.529993 4889.735208 4580.182599 5007.407393 3418.050726 3728.1584 0.855422291 0.954003419 0.949300752 0.861161043 1.142529242 1.311568523 1.228537553 1.34313161 0.916820145 1 11.86424744 -8.562738437 3.639001322 0.929311857 1.283761751 0.918315553 0.05011819 0.05656027 1.573353284 0.009233944 0.019978796 2.74E-09 8.562738437 0.354449894 RVS(ph)PLNLSSVT(ph)P ddPTM_HeLa_Romidepsin_16h_R1 2 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 2 0 RVS(0.905)PLNLS(0.092)S(0.003)VT(1)P;RVS(0.985)PLNLS(0.015)S(0.001)VT(0.999)P ; 130.47 0.003116 15739800 4453.5 3846.8 4439.8 3936.7 4193.5 3817.4 2818.1 3168.1 4055.3 4206.5 TRUE FALSE FALSE 4399.219029 3900.955351 4517.072857 4391.879777 3979.490047 3573.48046 3057.469344 3259.763975 3692.583811 4097.214524 1.073709713 0.952099366 1.102474091 1.071918434 0.971267192 0.872173141 0.746231208 0.795604906 0.901242488 1 12.00042772 -8.17591454 2.026441233 1.036317113 0.770369384 0.716154952 0.060780169 0.089458245 0.701136383 0.006683165 0.022531928 6.67E-09 8.17591454 -0.265947729 RVS(ph)PLNLSSVTP ddPTM_HeLa_Romidepsin_16h_R1 1 RVSPLNLSSVTP 12 1 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 0 RVS(0.534)PLNLS(0.465)S(0.001)VTP 117.86 0.012608 68796000 3282.6 2523.8 3640.8 3288.8 3243.6 3035.7 2553.3 2494.1 3057.9 2494.5 TRUE FALSE FALSE 3242.590409 2559.330123 3704.166597 3669.06653 3078.066988 2841.728567 2770.177238 2566.262848 2784.393765 2429.69253 1.334568209 1.053355555 1.524541295 1.510094995 1.26685453 1.169583613 1.140134895 1.056208889 1.145986058 1 11.24655804 -12.37574047 0.974536951 0.99175824 1.266759633 0.146614561 0.162549466 0.654878888 1.057777785 0.131623188 0.030077579 4.21E-13 12.37574047 0.275001393 RVS(ph)STWTTTTSATGLPTLEPAPVR ddPTM_HeLa_Romidepsin_16h_R1 1 RVSSTWTTTTSATGLPTLEPAPVR 24 1 Q14432 Q14432 PDE3A "cGMP-inhibited 3,5-cyclic phosphodiesterase A" 1 0 RVS(0.408)S(0.143)T(0.058)WT(0.266)T(0.087)T(0.029)T(0.007)S(0.001)ATGLPTLEPAPVR 76.106 0.00015935 17513000 293.66 271.32 384.32 302.56 116.86 311.53 182.32 138.09 264.54 344.63 TRUE FALSE FALSE 290.080759 275.1396501 391.0089284 337.5434108 110.8961981 291.6242384 197.8062562 142.0854163 240.8788798 335.6764629 0.864167706 0.819657261 1.164838681 1.005561748 0.330366321 0.868765823 0.589276515 0.423280843 0.717592404 1 8.390927571 -8.781188558 24.99887696 0.948118529 0.578079304 0.527129578 0.17308954 127.3253168 161170.4145 0.022755589 0.041288524 1.66E-09 8.781188558 -0.370039225 RVS(ph)VCAETYNPDEEEEDTDPR ddPTM_HeLa_Romidepsin_16h_R1 1 RVSVCAETYNPDEEEEDTDPR 21 1 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 0 RVS(0.995)VCAET(0.005)YNPDEEEEDTDPR 109.84 7.17E-05 62990000 1116.2 1394.1 1381.7 71.266 1603.3 1654.9 1173.2 1722.6 1450 1310.2 TRUE FALSE FALSE 1102.595325 1413.726176 1405.747909 79.50611024 1521.477618 1549.157231 1272.851579 1772.440713 1320.308368 1276.160815 0.86399403 1.107796259 1.101544486 0.062301012 1.192230321 1.213920074 0.997406881 1.388885078 1.034594036 1 10.31759443 RVSSTWT(ph)TTTSATGLPTLEPAPVR ddPTM_HeLa_Romidepsin_16h_R1 1 RVSSTWTTTTSATGLPTLEPAPVR 24 1 Q14432 Q14432 PDE3A "cGMP-inhibited 3,5-cyclic phosphodiesterase A" 1 0 RVS(0.105)S(0.105)T(0.105)WT(0.361)T(0.149)T(0.149)T(0.02)S(0.003)AT(0.002)GLPTLEPAPVR 57.216 0.0038726 15182000 501.05 515.61 473.67 267.68 545.46 439.91 437.21 471.61 646.59 493.24 TRUE FALSE FALSE 494.9430099 522.8687711 481.9140277 298.6304211 517.6231408 411.8011707 474.3466065 485.2552913 588.757371 480.4255537 1.03021791 1.088345046 1.003098241 0.621595622 1.077426329 0.857159174 0.987346745 1.010053041 1.225491372 1 8.908169079 -9.49472507 24.99827648 1.021438149 0.910368458 0.226735601 0.132907078 914.8179719 812288.7545 0.016687355 0.025453692 3.20E-10 9.49472507 -0.111069691 RVT(ph)FGEDLSPEVFDESLPANTPLR ddPTM_HeLa_Romidepsin_16h_R1 1 RVTFGEDLSPEVFDESLPANTPLR 24 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 RVT(0.581)FGEDLS(0.417)PEVFDES(0.002)LPANT(0.001)PLR 49.088 0.019741 1079200 286.16 118.87 206.61 226.97 179.81 366.42 319.68 266.13 267.42 203.73 TRUE FALSE FALSE 282.6721719 120.543455 210.2059604 253.2133393 170.6336247 343.0069446 346.8336112 273.8300517 243.5012854 198.4370652 1.424492806 0.607464411 1.059307948 1.276038521 0.859887867 1.72854272 1.747826752 1.379933992 1.22709578 1 7.632537716 -8.248406063 24.91725597 1.134457261 1.63167375 0.514345895 0.239964973 553.6202247 1058416.204 0.037091925 0.093923718 5.64E-09 8.248406063 0.49721649 RVTFGEDLS(ph)PEVFDESLPANTPLR ddPTM_HeLa_Romidepsin_16h_R1 1 RVTFGEDLSPEVFDESLPANTPLR 24 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 RVT(0.023)FGEDLS(0.977)PEVFDESLPANTPLR 63.202 0.00080947 0 659.62 303.57 457.31 359.07 726.6 465.49 552.57 759.44 590.71 386.27 TRUE FALSE FALSE 651.5802977 307.8436664 465.2692887 400.5873629 689.5188907 435.7466913 599.505282 781.4131982 537.8754181 376.2346497 1.731845534 0.818222529 1.236646569 1.06472746 1.832683117 1.158177992 1.593434529 2.076930444 1.429627544 1 8.555488911 -4.460552637 0.869013148 1.300728172 129.6992917 0.394570277 0.300304598 273.8001809 1.636994844 0.05415816 68761.33866 3.46E-05 4.460552637 128.3985635 RVTNDIS(ph)PESSPGVGR ddPTM_HeLa_Romidepsin_16h_R1 1 RVTNDISPESSPGVGR 16 1 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154;E9PGW9;E5RGQ4;Q15154-3 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 RVT(0.001)NDIS(0.962)PES(0.007)S(0.031)PGVGR 77.631 0.0083646 5027300 1363.8 1004.3 1104.2 1313.5 1155.4 1385.9 1116.3 1091.7 1394.5 1376.4 TRUE FALSE FALSE 1347.177481 1018.438562 1123.418138 1465.37305 1096.435627 1297.345463 1211.118494 1123.286617 1269.772427 1340.64093 1.004875691 0.759665425 0.837970938 1.093039171 0.817844363 0.967705397 0.903387676 0.837872836 0.947138342 1 10.38870717 RVVLGDGVQLPPGDY(ph)STTPGGTLFS(ph)TTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.398)S(0.28)T(0.311)T(0.104)PGGT(0.053)LFS(0.423)T(0.137)T(0.267)PGGT(0.028)R 66.014 3.59E-05 98063000 1660.6 1433 1186.9 1466 1379.3 1446.5 1324 1267.7 1746.9 1473 TRUE FALSE FALSE 1640.359968 1453.173812 1207.557497 1635.505818 1308.909174 1354.073318 1436.460527 1304.378899 1590.652889 1434.731248 1.143322118 1.012854368 0.841661112 1.139938801 0.912302688 0.943781855 1.001205298 0.909145111 1.108676549 1 10.4865648 -10.00159107 24.99965969 1.0682277 0.96232703 0.322445194 0.080760572 64.24994805 1009543.559 0.013644742 0.017790827 9.96E-11 10.00159107 -0.10590067 RVVLGDGVQLPPGDYS(ph)TTPGGT(ph)LFSTTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.109)S(0.425)T(0.321)T(0.321)PGGT(0.57)LFS(0.159)T(0.046)T(0.047)PGGT(0.001)R 82.538 2.32E-08 99103000 1190.5 989.54 1117.4 1419 899.85 832.54 934.34 965.29 1459 1194.3 TRUE FALSE FALSE 1175.989728 1003.47077 1136.847878 1583.071457 853.9272967 779.3433809 1013.702816 993.2191432 1328.503386 1163.271914 1.010932796 0.862627867 0.97728473 1.360878259 0.734073682 0.669958048 0.871423787 0.853815115 1.142040283 1 10.18397265 RVVLGDGVQLPPGDYS(ph)TTPGGTLFSTTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 0 RVVLGDGVQLPPGDY(0.067)S(0.3)T(0.3)T(0.3)PGGT(0.016)LFS(0.006)T(0.007)T(0.002)PGGT(0.001)R;RVVLGDGVQLPPGDY(0.195)S(0.222)T(0.222)T(0.222)PGGT(0.122)LFS(0.005)T(0.006)T(0.005)PGGT(0.002)R ; 63.427 0.00015983 15935000 873.8 626.89 522.15 746.05 984.87 1176.05 851.29 966.73 943.84 772.75 TRUE FALSE FALSE 863.1497895 635.7153739 531.2378017 832.3118113 934.6084088 1100.904201 923.5985514 994.7008073 859.4205865 752.6738436 1.146777979 0.844609361 0.705800801 1.105806743 1.241717667 1.46265771 1.227090006 1.32155623 1.141823373 1 9.555881027 -8.746753466 3.384259878 1.022240514 1.326965264 0.564585323 0.139590791 0.163225679 3.908513212 0.022625915 0.045762789 1.79E-09 8.746753466 0.30472475 RVVLGDGVQLPPGDYST(ph)T(ph)PGGTLFSTTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.276)S(0.166)T(0.697)T(0.812)PGGT(0.014)LFS(0.019)T(0.007)T(0.007)PGGT(0.003)R 75.156 2.59E-06 26775000 1008.2 709.61 678.36 773.49 736.01 818.82 707.4 603.51 1021.3 904.33 TRUE FALSE FALSE 995.9116706 719.5999082 690.1665712 862.9245532 698.4486633 766.5000446 767.4865383 620.9716097 929.9523701 880.8353762 1.130644497 0.816951643 0.78353639 0.979666095 0.792938933 0.870196708 0.87131666 0.704980325 1.055761832 1 9.782728602 -10.25371163 24.94833799 1.061693235 0.836785187 0.67460192 0.073377823 259.9111202 839099.7221 0.013105839 0.015890805 5.58E-11 10.25371163 -0.224908048 RVVLGDGVQLPPGDYST(ph)TPGGTLFS(ph)TTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.071)S(0.079)T(0.439)T(0.439)PGGT(0.089)LFS(0.367)T(0.367)T(0.127)PGGT(0.023)R;RVVLGDGVQLPPGDY(0.09)S(0.136)T(0.394)T(0.394)PGGT(0.106)LFS(0.282)T(0.282)T(0.282)PGGT(0.035)R ; 58.622 0.00072249 76366000 1831.95 1653.28 1334.73 1744.63 1889.51 1608.54 1374.64 1684.99 2318.86 2003.71 TRUE FALSE FALSE 1809.621489 1676.554919 1357.960416 1946.352329 1793.081254 1505.759485 1491.401887 1733.742527 2111.455354 1951.653325 0.927224864 0.859043406 0.695800016 0.997283843 0.918749878 0.771530203 0.764173569 0.88834554 1.081880335 1 10.93048109 -10.60257022 1.404699731 0.977498796 0.839824391 0.408513179 0.088086083 0.310184534 1.246128658 0.017610782 0.018072687 2.50E-11 10.60257022 -0.137674405 RVVLGDGVQLPPGDYST(ph)TPGGTLFSTTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 2 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 1 0 RVVLGDGVQLPPGDY(0.085)S(0.093)T(0.285)T(0.285)PGGT(0.19)LFS(0.019)T(0.019)T(0.019)PGGT(0.006)R;RVVLGDGVQLPPGDY(0.198)S(0.216)T(0.258)T(0.258)PGGT(0.063)LFS(0.002)T(0.002)T(0.002)PGGT(0.001)R ; 50.413 0.0029306 19096000 901.37 945.79 858.61 1096.28 1154.57 1226.96 1260.63 1606.18 1316.03 1110.81 TRUE FALSE FALSE 890.3837557 959.1048564 873.5537469 1223.037052 1095.647985 1148.561216 1367.707881 1652.652284 1198.320981 1081.950996 0.822942776 0.886458684 0.807387534 1.130399673 1.012659528 1.061564914 1.264112594 1.527474248 1.107555689 1 10.07941944 -6.615323589 0.641056745 0.910943706 2.616562538 0.755120325 0.101817034 1.960967944 0.310071505 0.016446452 2.970549209 2.42E-07 6.615323589 1.705618832 RVVLGDGVQLPPGDYSTT(ph)PGGT(ph)LFSTTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.18)S(0.145)T(0.35)T(0.353)PGGT(0.34)LFS(0.267)T(0.274)T(0.078)PGGT(0.013)R 43.865 0.01353 92249000 2739.7 2520.3 1962.7 2477.3 2384.8 2127.7 1957.2 2201.9 2492.7 2656.1 TRUE FALSE FALSE 2706.307483 2555.78085 1996.85997 2763.737082 2263.094757 1991.746837 2123.444519 2265.608502 2269.746669 2587.094139 1.046080018 0.987896347 0.771854391 1.068278514 0.874763204 0.76987799 0.82078363 0.875734852 0.877334394 1 11.33711684 -9.204667478 0.690513804 1.022571233 0.820224131 0.172417847 0.094493534 0.485451169 0.446629593 0.017374105 0.046401338 6.24E-10 9.204667478 -0.202347102 RVVLGDGVQLPPGDYSTT(ph)PGGTLFS(ph)TTPGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 RVVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 32 1 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 RVVLGDGVQLPPGDY(0.107)S(0.099)T(0.296)T(0.411)PGGT(0.252)LFS(0.471)T(0.144)T(0.194)PGGT(0.026)R 57.826 0.00079408 115620000 1756.9 1963.8 1589.2 1570.7 1748.9 1581.6 1459.3 1575.2 2263.3 1885.1 TRUE FALSE FALSE 1735.486227 1991.446428 1616.859359 1752.311724 1659.647107 1480.540864 1583.252906 1620.775927 2060.864779 1836.12483 0.945189673 1.084592069 0.880582482 0.954353264 0.903885771 0.806339983 0.862279557 0.882715543 1.122399058 1 10.84244843 -8.869687843 1.272300381 0.978997566 0.851416393 0.488315712 0.067805363 0.25400042 0.818662783 0.008050238 0.019897673 1.35E-09 8.869687843 -0.127581173 RWDDDVVFK ddPTM_HeLa_Romidepsin_16h_R1 1 RWDDDVVFK 9 1 Q9P013 Q9P013 CWC15 Spliceosome-associated protein CWC15 homolog 0 0 112.36 0.011484 10657000 3486.3 2957.1 2998.2 2527 3116.3 2998.9 2589 2997.2 3323.4 3688.8 FALSE FALSE TRUE 3443.807635 2998.730131 3050.382413 2819.18363 2957.263582 2807.279969 2808.909595 3083.919253 3026.14678 3592.964444 0.958486422 0.834611691 0.848987643 0.784640002 0.823070651 0.781326955 0.781780515 0.858321673 0.84224234 1 11.81095894 -10.2403291 1.418690203 0.986703216 0.805585414 0.430099339 0.052836376 0.076642577 0.294696027 0.005016617 0.00600619 5.75E-11 10.2403291 -0.181117803 RWDQTADQTPGAT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 RWDQTADQTPGATPK 15 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 RWDQTADQTPGAT(1)PK 112.67 0.0099818 14330000 4283.3 5147.4 3882.6 3447.2 3181.9 3707 3352 3549.1 4048.2 4169.6 TRUE FALSE FALSE 4231.093492 5219.865232 3950.175024 3845.781484 3019.51577 3470.134664 3636.718796 3651.787609 3686.118853 4061.273191 1.041814548 1.285278036 0.972644498 0.946939864 0.743489942 0.854445023 0.895462734 0.899173101 0.907626422 1 11.98771636 -9.157392187 2.91936194 1.041929576 0.852742962 0.448221984 0.100424452 0.182054866 3.000261809 0.01450778 0.025221993 6.96E-10 9.157392187 -0.189186614 RWS(ph)GNEPTDEFSDLPLR ddPTM_HeLa_Romidepsin_16h_R1 1 RWSGNEPTDEFSDLPLR 17 1 E9PD99;Q96II8-3;Q96II8-4;Q96II8;Q96II8-2 E9PD99 LRCH3 Leucine-rich repeat and calponin homology domain-containing protein 3 1 0 RWS(1)GNEPTDEFSDLPLR 122.08 0.00067947 1870500 631.34 431.37 432.11 456.91 502.45 534.17 448.56 418.5 505.61 501.66 TRUE FALSE FALSE 623.6449852 437.4428382 439.6306933 509.740084 476.8081016 500.038261 486.6606752 430.6086372 460.3869753 488.6268009 1.276321692 0.895249375 0.899726934 1.043209425 0.975812421 1.023354143 0.995976222 0.88126283 0.942205737 1 8.932589186 -10.24404253 24.87992281 1.130485249 0.964686661 0.144232682 0.100227353 676.4091363 967361.0255 0.018746547 0.022929347 5.70E-11 10.24404253 -0.165798588 RY(ph)NFPVEVEVPMER ddPTM_HeLa_Romidepsin_16h_R1 2 RYNFPVEVEVPMER 14 1 P78527-2;P78527 P78527-2 PRKDC DNA-dependent protein kinase catalytic subunit 1 0 RY(1)NFPVEVEVPMER;RY(1)NFPVEVEVPMER ; 45.28 0.028573 14436900 5628.8 6266.8 5657.1 5707.9 7615.1 7239.6 5942.9 7294.8 6767.4 6075.2 TRUE FALSE FALSE 5560.194021 6355.024175 5755.559452 6367.874254 7226.473031 6777.012925 6447.689778 7505.863529 6162.106795 5917.365428 0.93964013 1.073961757 0.972655741 1.076133345 1.221231495 1.145275378 1.0896217 1.268446848 1.041359853 1 12.53073928 -9.033853794 3.221601458 0.980258056 1.171842001 0.651228461 0.058731148 0.09847045 2.07902183 0.008432138 0.015188559 9.25E-10 9.033853794 0.191583945 RY(ph)NVPAT(ph)PDGVEY(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 RYNVPATPDGVEYLK 15 1 Q8TCU5 Q8TCU5 GRIN3A "Glutamate receptor ionotropic, NMDA 3A" 3 0 RY(1)NVPAT(1)PDGVEY(1)LK 57.804 0.0043154 0 463.6 532.57 362.06 425.14 276.76 398.37 319.53 446.11 516.47 352.56 TRUE FALSE FALSE 457.9494649 540.0675344 368.3615024 474.2966871 262.6359045 372.9154427 346.6708702 459.017489 470.2756297 343.4004404 1.333572736 1.572704839 1.072687915 1.3811767 0.764809457 1.085949227 1.009523662 1.336682878 1.369467171 1 8.423748079 RY(ph)SDFEWLR ddPTM_HeLa_Romidepsin_16h_R1 1 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 0 RY(0.672)S(0.328)DFEWLR 60.064 0.028326 8455200 4027.4 5087.6 4744.2 2395.7 5131.8 4685.3 5342.2 5059.2 5850.7 5190.7 TRUE FALSE FALSE 3978.3125 5159.223366 4826.770811 2672.702106 4869.905097 4385.924451 5795.966335 5205.57997 5327.398739 5055.844866 0.786873926 1.020447325 0.954691241 0.528636099 0.96322281 0.867495852 1.146389276 1.029616238 1.053710879 1 12.30373648 -7.768346319 24.98971161 0.886325135 1.088002771 0.211525129 0.146465161 152.0928411 550289.5769 0.019939304 0.061769319 1.70E-08 7.768346319 0.201677636 RY(ph)SPPIQR ddPTM_HeLa_Romidepsin_16h_R1 1 RYSPPIQR 8 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 RY(0.598)S(0.402)PPIQR 71.379 0.020395 979420000 1262.7 1385.3 1286.1 1147.6 1483.6 1283.5 1244.1 1225.2 1415.1 1452.7 TRUE FALSE FALSE 1247.309727 1404.80229 1308.484031 1280.290912 1407.886356 1201.488492 1349.773823 1260.649229 1288.529912 1414.958645 0.881516737 0.992822154 0.924750724 0.904825676 0.99500177 0.849133292 0.953931642 0.890944222 0.910648461 1 10.46654417 -10.55908375 0.00934786 1.875105176 1.01E-06 0.054947101 0.048698684 1605.719153 12.50150914 1258.350398 1248.194767 2.76E-11 10.55908375 -1.875104168 RY(ph)T(ph)YERIDGRVR ddPTM_HeLa_Romidepsin_16h_R1 1 RYTYERIDGRVR 12 3 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 2 0 RY(0.874)T(1)Y(0.126)ERIDGRVR 94.402 0.0046238 22881000 1054.6 1258.5 973.82 850.63 845.8 492.18 545.13 644.94 1194.1 917.85 TRUE FALSE FALSE 1041.74613 1276.217196 990.7689286 948.9838429 802.6356699 460.7312864 591.4333286 663.6003214 1087.296705 894.0041247 1.165258751 1.427529427 1.108237536 1.061498283 0.897798621 0.515357003 0.661555481 0.742278814 1.216209943 1 9.804137677 -8.553206968 2.826581387 1.111257529 0.643041824 0.771433385 0.125987516 0.111508858 1.802594277 0.020454059 0.0466161 2.80E-09 8.553206968 -0.468215705 RYEDDGIS(ph)DDEIEGK ddPTM_HeLa_Romidepsin_16h_R1 2 RYEDDGISDDEIEGK 15 1 I3VM54;Q9Y2K7-3;Q9Y2K7 I3VM54 KDM2A Lysine-specific demethylase 2A 1 0 RYEDDGIS(1)DDEIEGK;RYEDDGIS(1)DDEIEGK ; 117.13 0.0057871 29411000 8197.6 7478.2 8681.6 5989 7578 7080.6 6276.7 7382.7 8461.5 9303.2 TRUE FALSE FALSE 8097.684498 7583.478296 8832.699606 6681.476359 7191.266383 6628.172512 6809.842741 7596.306777 7704.682248 9061.501523 0.893636058 0.836889811 0.97475011 0.737347595 0.793606486 0.731465143 0.751513723 0.838305523 0.850265514 1 13.14553441 -10.18914774 0.349720179 1.00443565 0.743126968 0.330597554 0.072741634 0.533507651 0.189406075 0.041374157 0.051043134 6.47E-11 10.18914774 -0.261308681 RYEEIVK ddPTM_HeLa_Romidepsin_16h_R1 1 RYEEIVK 7 1 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 0 90.37 0.0036147 0 2108.9 1712.2 1542.1 1337.6 1734.2 1944.2 1802.5 1493.1 1985.7 1806.1 FALSE FALSE TRUE 2083.195916 1736.304397 1568.939604 1492.259606 1645.697303 1819.971895 1955.604305 1536.300493 1808.094019 1759.177262 1.184187609 0.986997976 0.89185987 0.848271313 0.935492596 1.03455856 1.111658471 0.873306247 1.027806611 1 10.78068515 -10.02210878 21.71563939 1.086904649 0.953928325 0.279393518 0.085874733 140.544998 138045.922 0.016809409 0.020716522 9.50E-11 10.02210878 -0.132976324 RYETLVGTIGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RYETLVGTIGKK 12 2 H3BSB3;H3BNT4;Q99547 H3BSB3 MPHOSPH6 M-phase phosphoprotein 6 0 1 ; RYETLVGTIGK(1)K;RYETLVGTIGK(1)K 147.96 0.00013458 3354000 1846.91 2088.55 1874.48 2325.76 2212.99 1804.95 2373.6 2453.84 2622.06 2006.42 FALSE TRUE FALSE 1824.399151 2117.952662 1907.104538 2594.675314 2100.052862 1689.61952 2575.213525 2524.837989 2387.536387 1954.292919 0.933534135 1.083743712 0.975853988 1.327679842 1.074584491 0.864568205 1.317721361 1.2919445 1.221688091 1 10.93243101 -9.315343263 24.19304747 0.978776089 1.160353906 0.085020838 0.154095563 208.2156598 93450.43227 0.020747586 0.031692479 4.84E-10 9.315343263 0.181577816 RYFGGTEDR ddPTM_HeLa_Romidepsin_16h_R1 1 RYFGGTEDR 9 1 Q16658 Q16658 FSCN1 Fascin 0 0 89.679 0.026702 7008600 1680.6 1361.9 1612.6 1157.8 1660.5 1671.2 1674.6 1388.8 1687.1 1159.5 FALSE FALSE TRUE 1660.116201 1381.072864 1640.666627 1291.670284 1575.758489 1564.415714 1816.840482 1428.982737 1536.201551 1129.376023 1.469941071 1.222863631 1.452719549 1.143702591 1.395246983 1.385203583 1.608711754 1.265285173 1.360221502 1 10.14131019 -12.39334539 0.931417463 0.981661891 1.376446284 0 0.167301255 0.373515771 0.534984984 0.106427078 0.022630128 4.04E-13 12.39334539 0.394784394 RYPS(ph)SISSS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 RYPSSISSSPQK 12 1 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 2 0 RY(0.008)PS(0.918)S(0.051)IS(0.026)S(0.453)S(0.544)PQK 97.631 0.016981 11758000 5202 5290.8 5560.4 3699.7 4137.9 3528.8 2653.7 2598.5 4848.4 5117.2 TRUE FALSE FALSE 5138.596023 5365.284021 5657.17643 4127.476722 3926.727522 3303.321069 2879.105212 2673.683498 4414.746961 4984.254406 1.030965838 1.076446663 1.135009566 0.828103139 0.787826464 0.662751296 0.5776401 0.536425969 0.885738688 1 12.28316199 -8.57857077 1.250150778 1.027745947 0.56033715 0.867689832 0.072831308 0.093641236 0.282767068 0.00953265 0.030130412 2.64E-09 8.57857077 -0.467408797 RYPSS(ph)ISSS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 RYPSSISSSPQK 12 1 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 2 0 RYPS(0.029)S(0.961)IS(0.012)S(0.323)S(0.675)PQK 133.88 0.0027423 13035000 4921.2 5360.1 5580.3 3006.9 3984.9 3328.1 2195.2 2933 4710.4 4484.3 TRUE FALSE FALSE 4861.218522 5435.559628 5677.422781 3354.571926 3781.535683 3115.445151 2381.660233 3017.861727 4289.090027 4367.79724 1.112967992 1.244462444 1.299836615 0.76802373 0.86577638 0.713276047 0.545277196 0.690934483 0.981980113 1 12.09269017 -8.771516966 1.607351283 1.085133219 0.647864218 0.710990891 0.12706368 0.164715508 0.859939256 0.02068435 0.049110423 1.69E-09 8.771516966 -0.437269001 RYPSSISS(ph)SPQK ddPTM_HeLa_Romidepsin_16h_R1 1 RYPSSISSSPQK 12 1 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 RYPS(0.002)S(0.002)ISS(0.498)S(0.498)PQK 166.24 0.00038961 26554000 5442 3920.2 9258.9 3883.6 5001.1 5883.2 4378.1 3637.4 5531.4 3927.4 TRUE FALSE FALSE 5375.670811 3975.388678 9420.047271 4332.640105 4745.875205 5507.282507 4749.975705 3742.64243 5036.65773 3825.365582 1.405269822 1.039217976 2.462522096 1.132608116 1.240633112 1.43967482 1.241705035 0.978375099 1.316647422 1 11.90138191 -12.13304577 0.864426663 0.997626219 1.379745801 0.017480518 0.405327194 1.086071062 1.450309388 0.263775116 0.074452313 7.36E-13 12.13304577 0.382119582 RYPSSISS(ph)SPQKDLTQAK ddPTM_HeLa_Romidepsin_16h_R1 1 RYPSSISSSPQKDLTQAK 18 2 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 RYPS(0.05)S(0.066)IS(0.066)S(0.409)S(0.409)PQKDLTQAK 69.122 0.022366 145670000 2084.2 1836.2 1723.3 2194 1447.2 1234.9 1420.4 1323 1799.8 1943.8 TRUE FALSE FALSE 2058.796969 1862.050072 1753.293314 2447.680603 1373.343984 1155.993875 1541.048741 1361.278918 1638.82138 1893.299796 1.087412027 0.983494572 0.926051604 1.292811951 0.725370587 0.610570961 0.813948612 0.71899808 0.865590005 1 10.88668716 -8.675849882 11.11217147 1.043493678 0.715574836 0.625543228 0.116528795 0.175657761 21.72977831 0.013994015 0.027994177 2.11E-09 8.675849882 -0.327918842 RYS(ph)DFEWLK ddPTM_HeLa_Romidepsin_16h_R1 1 RYSDFEWLK 9 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 1 0 RYS(1)DFEWLK 134.99 0.0020354 15837000 4813.1 4155.7 4185 3349.9 4395.6 4090 4264.3 4362.1 4838.2 4152.7 TRUE FALSE FALSE 4754.436086 4214.204054 4257.838169 3737.2312 4171.27613 3828.6622 4626.509536 4488.310481 4405.459275 4044.812255 1.175440487 1.041878779 1.052666453 0.923956655 1.031265697 0.946561165 1.143813172 1.109646183 1.089162858 1 11.98185702 -10.02565977 24.32850745 1.08420546 1.031827888 0.0971106 0.073059247 1151.275006 1091542.628 0.014827852 0.018199819 9.43E-11 10.02565977 -0.052377572 RYS(ph)DFEWLR ddPTM_HeLa_Romidepsin_16h_R1 2 RYSDFEWLR 9 1 O60493-4;O60493;O60493-3 O60493-4 SNX3 Sorting nexin-3 1 0 RY(0.018)S(0.982)DFEWLR;RY(0.012)S(0.988)DFEWLR ; 95.417 0.010089 21944300 7372.3 8346.5 7450.5 2831.5 8928.2 8698.2 7866.4 7759.2 8929.2 7327 TRUE FALSE FALSE 7282.443572 8464.002246 7580.172827 3158.891353 8472.560638 8142.413092 8534.57182 7983.70021 8130.549988 7136.643484 1.020429784 1.185992023 1.062148172 0.442629838 1.187191242 1.140930342 1.195880366 1.118691193 1.139268062 1 12.80102999 RYS(ph)GDSDSSASSAQSGPLGTR ddPTM_HeLa_Romidepsin_16h_R1 2 RYSGDSDSSASSAQSGPLGTR 21 1 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 0 RYS(0.928)GDS(0.07)DS(0.001)S(0.001)ASSAQSGPLGTR;RY(0.001)S(0.928)GDS(0.009)DS(0.009)S(0.018)AS(0.018)S(0.018)AQSGPLGTR ; 220.48 1.56E-41 13902800 2510.8 2318.04 2367.8 2291.23 3053.4 3482.2 2684.3 2931.3 2420.39 2578.4 TRUE FALSE FALSE 2480.197404 2350.673428 2409.010566 2556.152793 2897.573604 3259.698658 2912.304375 3016.112541 2203.904256 2511.412796 0.987570585 0.935996437 0.959225249 1.017814673 1.15376238 1.297954149 1.159627911 1.20096248 0.877555557 1 11.29428347 -8.714821577 3.174410462 0.986456988 1.215187519 0.84202617 0.050999555 0.055404775 1.139632762 0.005502512 0.011379637 1.93E-09 8.714821577 0.228730531 RYS(ph)PDELR ddPTM_HeLa_Romidepsin_16h_R1 4 RYSPDELR 8 1 S5FZ81;Q8WUB8-3;Q8WUB8-2;Q8WUB8 S5FZ81 PHF10 PHD finger protein 10 1 0 RY(0.38)S(0.62)PDELR;RY(0.023)S(0.977)PDELR;RY(0.022)S(0.978)PDELR;RY(0.43)S(0.57)PDELR ;;; 105.36 0.0078665 20977300 4339.4 4671.3 4615.9 4078.48 4672.6 4517.94 4234.41 4749.19 5204.61 4481.66 TRUE FALSE FALSE 4286.509724 4737.062684 4696.237803 4550.053047 4434.139786 4229.258215 4594.08068 4886.60032 4739.096646 4365.225827 0.981967461 1.085181585 1.07582929 1.042340815 1.015787032 0.968852101 1.052426807 1.119438149 1.085647532 1 12.09184058 -10.28100008 24.56949486 0.991484632 1.047492439 0 0.048651617 600.044541 753692.5243 0.006900577 0.007896598 5.24E-11 10.28100008 0.056007807 RYS(ph)SSGTPSSASPALSR ddPTM_HeLa_Romidepsin_16h_R1 1 RYSSSGTPSSASPALSR 17 1 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 RYS(0.998)S(0.002)SGTPSSASPALSR 170.47 4.53E-06 3064500 931.97 976.89 1203.9 774.24 723.04 896.49 585.92 670 1171.4 1035.4 TRUE FALSE FALSE 920.6107912 990.6426831 1224.853374 863.7612717 686.1405708 839.2071823 635.6880302 689.3853929 1066.62705 1008.500159 0.912851409 0.982293036 1.214529679 0.856481047 0.680357425 0.832133912 0.630330124 0.683574898 1.057636968 1 9.977995596 -8.969937887 5.539499957 0.979798783 0.714247611 0.713862768 0.094602707 0.087081011 7.438034865 0.014111364 0.025532252 1.07E-09 8.969937887 -0.265551171 RYT(ph)Y(ph)ERIDGRVR ddPTM_HeLa_Romidepsin_16h_R1 1 RYTYERIDGRVR 12 3 Q8TD26 Q8TD26 CHD6 Chromodomain-helicase-DNA-binding protein 6 2 0 RY(0.224)T(1)Y(0.776)ERIDGRVR 73.273 0.013119 20209000 2487.5 2213.7 2089.1 2123.9 1381.6 1235.8 892.14 1323.5 2086.8 2242.5 TRUE FALSE FALSE 2457.181393 2244.864527 2125.459909 2369.475311 1311.091797 1156.836368 967.9183493 1361.793384 1900.151382 2184.239527 1.124959677 1.027755656 0.973089207 1.084805619 0.600250925 0.529628896 0.443137457 0.623463392 0.869937275 1 11.09291536 -8.715932602 4.905819771 1.052722098 0.531356811 0.882851125 0.082235964 0.034476182 1.826782179 0.009761018 0.019552141 1.92E-09 8.715932602 -0.521365287 RYWEEETVPTTAGAS(ph)PGPPR ddPTM_HeLa_Romidepsin_16h_R1 3 RYWEEETVPTTAGASPGPPR 20 1 O15213 O15213 WDR46 WD repeat-containing protein 46 1 0 RYWEEETVPTTAGAS(1)PGPPR;RYWEEETVPTTAGAS(1)PGPPR;RYWEEETVPTTAGAS(1)PGPPR ;; 253.09 7.90E-68 5799500 1995.28 1731.41 1856.75 1895.41 1740.98 1917.02 1502.52 1328.66 1931.75 1794.35 TRUE FALSE FALSE 1970.96076 1755.784835 1889.065955 2114.566222 1652.131294 1794.528609 1630.144011 1367.102681 1758.969442 1747.732528 1.127724482 1.004607288 1.080866737 1.209891209 0.945299848 1.02677531 0.932719386 0.782215046 1.006429424 1 10.7712687 -7.126492489 1.014205523 1.064718853 0.57503001 0.596127472 0.069986308 1.243586224 0.828177861 0.011176928 0.702297328 7.47E-08 7.126492489 -0.489688843 S(ph)AAQAAAQTNSNAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 SAAQAAAQTNSNAAGK 16 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 S(0.99)AAQAAAQT(0.01)NSNAAGK;S(1)AAQAAAQTNSNAAGK ; 253.73 8.52E-72 5347200 1513.04 1670.29 1270.78 1050.09 1200.3 1181.31 1515.88 1353.18 1782.39 1570.99 TRUE FALSE FALSE 1494.598487 1693.804386 1292.897393 1171.506347 1139.044212 1105.828104 1644.638809 1392.332128 1622.968574 1530.175453 0.976749747 1.106934752 0.844934083 0.765602627 0.744387978 0.722680593 1.074804073 0.909916654 1.060642145 1 10.57948137 -9.691945524 11.64015223 0.997538024 0.840498642 0.441260439 0.102396386 0.518291872 84.91663195 0.016431632 0.02323678 2.03E-10 9.691945524 -0.157039383 S(ph)AAVETASLSPSLVPAR ddPTM_HeLa_Romidepsin_16h_R1 2 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 0 S(0.989)AAVET(0.005)ASLS(0.005)PSLVPAR;S(0.999)AAVETASLS(0.001)PSLVPAR ; 285.81 5.71E-104 51468000 3385.3 3916.2 3172 3593.7 6795.6 8925.9 8105 8392.1 3876.3 3586.8 TRUE FALSE FALSE 3344.038661 3971.332366 3227.207329 4009.220503 6448.795174 8355.563797 8793.438498 8634.912173 3529.59402 3493.614419 0.957185957 1.136740318 0.923744564 1.147585286 1.845880627 2.391667424 2.51700315 2.471627128 1.010298675 1 11.77050468 -8.571195297 1.863244557 0.986563671 2.497493384 0.991574243 0.059838187 0.019941478 0.137915944 0.009049301 0.023120967 2.68E-09 8.571195297 1.510929713 up S(ph)ADSENALSVQER ddPTM_HeLa_Romidepsin_16h_R1 2 SADSENALSVQER 13 0 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 1 0 S(0.698)ADS(0.262)ENALS(0.04)VQER;S(1)ADSENALSVQER ; 174.24 3.23E-05 13490500 1060.17 1040.76 837.21 941.49 1151.28 1481.87 1118.18 1006.97 1115.59 979.53 TRUE FALSE FALSE 1047.24824 1055.411847 851.7812889 1050.349504 1092.525886 1387.18329 1213.158181 1036.105088 1015.808836 954.0816694 1.09765052 1.106207027 0.892776076 1.100901042 1.145107301 1.453946066 1.271545424 1.085971067 1.064697991 1 9.897968956 -8.606492466 3.284386209 1.042540308 1.273762124 0.491060011 0.102487228 0.148997754 3.210562431 0.014935749 0.03214668 2.47E-09 8.606492466 0.231221816 S(ph)AEEGELAESK ddPTM_HeLa_Romidepsin_16h_R1 4 SAEEGELAESK 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK;S(1)AEEGELAESK ;;; 205.31 2.23E-13 77529000 6018.8 6095.3 5663.67 3764.7 7584.8 8140.3 6279.9 7365 5775 5925.5 TRUE FALSE FALSE 5945.440551 6181.109793 5762.243801 4199.992327 7197.719353 7620.161102 6813.314549 7578.094655 5258.469536 5771.554656 1.030128086 1.070960974 0.998386768 0.727705545 1.247102346 1.3202961 1.180499009 1.313007518 0.911101055 1 12.49474427 -8.56777365 24.99993061 0.999552282 1.265775835 0.685117113 0.100117599 57.11072803 31802.15261 0.013393588 0.026787185 2.71E-09 8.56777365 0.266223553 S(ph)AEEMY(ph)EEMMHK ddPTM_HeLa_Romidepsin_16h_R1 1 SAEEMYEEMMHK 12 0 Q9Y6V0-6;Q9Y6V0 Q9Y6V0-6 PCLO Protein piccolo 2 0 S(1)AEEMY(1)EEMMHK 49.536 0.024146 1329600 341.99 215.76 272.62 253.83 331.78 353.86 366.63 355.47 427.68 273.85 TRUE FALSE FALSE 337.8216943 218.7974749 277.3648367 283.1790189 314.8480286 331.249488 397.771543 365.7549636 389.4272297 266.7353375 1.266505209 0.820279296 1.03985036 1.06164793 1.180376142 1.24186578 1.491259264 1.371228001 1.459976144 1 8.059265158 -8.077970688 1.941420931 1.093734145 1.434370512 0.358826432 0.163480476 0.228043041 1.633297996 0.020319605 0.077666029 8.36E-09 8.077970688 0.340636367 S(ph)AEVDDGAAEKETLPEFGEGK ddPTM_HeLa_Romidepsin_16h_R1 2 SAEVDDGAAEKETLPEFGEGK 21 1 H7C5W6;F5H619;Q86XA9-2;Q86XA9 H7C5W6 HEATR5A HEAT repeat-containing protein 5A 1 0 S(0.995)AEVDDGAAEKET(0.005)LPEFGEGK;S(0.999)AEVDDGAAEKET(0.001)LPEFGEGK ; 78.758 0.0012774 12701100 3181.4 3288.4 3719.9 3028 4025.7 4577 3875 4715.3 3934.2 3893.9 TRUE FALSE FALSE 3142.623873 3334.694182 3784.643299 3378.111607 3820.253507 4284.544472 4204.142403 4851.729766 3582.315299 3792.735917 0.828590216 0.879231841 0.997866285 0.890679362 1.00725534 1.129671183 1.10847222 1.279216342 0.944520098 1 11.88902321 -7.900529411 0.89783926 0.915820217 1.288594409 0.795029287 0.058184359 0.42518998 0.44341709 0.012087073 0.124638371 1.26E-08 7.900529411 0.372774191 S(ph)AGEEEDGPVLTDEQK ddPTM_HeLa_Romidepsin_16h_R1 4 SAGEEEDGPVLTDEQK 16 0 F5GYV5;H7BZV4;A0A0C4DG62;F8WCT1;F5H7X4;Q66PJ3-7;Q66PJ3-4;Q66PJ3-3;Q66PJ3-2;Q66PJ3 F5GYV5 ARL6IP4 ADP-ribosylation factor-like protein 6-interacting protein 4 1 0 S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK;S(1)AGEEEDGPVLTDEQK ;;; 385.82 0 412317000 19439.9 18635.8 17161.2 17486.1 17524.8 14275.9 12755.9 13838.8 19730.9 18315.5 TRUE FALSE FALSE 19202.95902 18898.15528 17459.88349 19507.92516 16630.44406 13363.71606 13839.38583 14239.20384 17966.11889 17839.66067 1.076419523 1.059333786 0.978711636 1.093514362 0.932217511 0.749101472 0.775765082 0.798176832 1.0070886 1 14.12280055 -8.453682028 3.494618051 1.037470271 0.775612995 0.912936657 0.036030816 0.051599887 1.222111095 0.005711539 0.013281684 3.52E-09 8.453682028 -0.261857276 S(ph)APAMQSSGSFNYARPK ddPTM_HeLa_Romidepsin_16h_R1 1 SAPAMQSSGSFNYARPK 17 1 Q8WX93-3;Q8WX93;Q8WX93-4;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 S(0.999)APAMQS(0.001)SGSFNYARPK 89.859 0.010205 12426000 2397.4 2647.1 2117.8 1785.4 2434.8 2137.6 1685.3 1839.6 3069.1 2648.6 TRUE FALSE FALSE 2368.179567 2684.365943 2154.659421 1991.836349 2310.543071 2001.014259 1828.44934 1892.825924 2794.592009 2579.78899 0.917974135 1.040537018 0.835207619 0.772092739 0.895632581 0.77565036 0.708759262 0.733713467 1.083263794 1 11.33303735 -8.128589362 0.321898693 0.991638384 0.586557532 0.722582183 0.066268342 1.668179405 0.18943922 0.027190223 0.247639707 7.44E-09 8.128589362 -0.405080853 S(ph)APASPT(ph)HPGLMS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPASPTHPGLMSPR 15 0 P85037-2;P85037 P85037-2 FOXK1 Forkhead box protein K1 3 0 S(0.913)APAS(0.38)PT(0.709)HPGLMS(0.999)PR 64.843 0.020884 15778000 946.05 1030.4 1194.6 904.69 1036 657.47 858.6 943.58 980.91 1174.2 TRUE FALSE FALSE 934.5191787 1044.905998 1215.391512 1009.294514 983.1290542 615.4597889 931.5294626 970.8809986 893.1749529 1143.694115 0.817105874 0.913623656 1.062689312 0.882486411 0.859608388 0.538133213 0.814491786 0.848899182 0.78095615 1 10.15948553 -8.508422939 21.7949843 0.920054296 0.734733784 0.344610138 0.107787892 98.94211318 149173.0673 0.015634355 0.033702744 3.10E-09 8.508422939 -0.185320512 S(ph)APASQASLR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPASQASLR 10 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 S(1)APASQASLR 100.09 0.024431 16309000 321.91 118.8 176.4 263.21 393.72 549.34 413.28 310.04 384.13 166.77 TRUE FALSE FALSE 317.9864371 120.4724695 179.470168 293.6435786 373.6269992 514.2389469 448.3839929 319.0105182 349.7724507 162.4372914 1.957595048 0.741655247 1.104858167 1.807735011 2.300130691 3.165769034 2.760351328 1.963899518 2.153276799 1 7.343739065 -8.801890884 2.63337222 1.37832072 2.646330929 0.558561265 0.486715236 0.150307521 2.127662082 0.075314864 0.15387545 1.58E-09 8.801890884 1.26801021 S(ph)APGTPGTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPGTPGTPR 10 0 Q16584;Q16584-2;E9PID4 Q16584 MAP3K11 Mitogen-activated protein kinase kinase kinase 11 1 0 S(1)APGTPGTPR 121.61 0.010878 3295200 898.22 755.4 927.4 1068.9 878.85 1170.2 755.87 454.78 1056.6 901.03 TRUE FALSE FALSE 887.2721491 766.034541 943.541008 1192.491247 833.9990051 1095.427997 820.0735789 467.9383418 962.0950497 877.6211107 1.010996817 0.872853367 1.075112023 1.358776849 0.950295059 1.248178722 0.934427817 0.533189478 1.096253312 1 9.777454419 -7.299321559 3.765988556 1.036539344 0.49907675 0.569919396 0.138427474 0.128515333 3.368523903 0.01849791 0.177750042 5.02E-08 7.299321559 -0.537462594 S(ph)APPNLWAAQR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPPNLWAAQR 11 0 Q92934;F5H3B1;F5H1R6 Q92934 BAD Bcl2-associated agonist of cell death 1 0 S(1)APPNLWAAQR 101.56 0.018458 22424000 626.99 545.64 600.35 499.65 630.87 643.36 405.76 544.48 586.4 569.31 TRUE FALSE FALSE 619.3480047 553.3215342 610.7988399 557.4218839 598.6743498 602.2513723 440.2252443 560.2336698 533.9509153 554.5192441 1.116909848 0.997840093 1.101492593 1.005234516 1.079627725 1.086078398 0.793886324 1.010305189 0.962907818 1 9.115093719 -7.780893499 24.85735106 1.0553463 0.902095695 0.391211522 0.069497086 120.7266495 154257.9083 0.008823526 0.026526784 1.66E-08 7.780893499 -0.153250604 S(ph)APS(ph)SPAPR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPSSPAPR 9 0 E9PAK5;O75064 E9PAK5 DENND4B DENN domain-containing protein 4B 2 0 S(1)APS(0.62)S(0.38)PAPR 117.02 0.0012738 0 1964.6 2207.9 2426.2 1821.9 1861.7 2145.4 2142 1282 2389.3 2406.9 TRUE FALSE FALSE 1940.6547 2238.982874 2468.426993 2032.55665 1766.690502 2008.315864 2323.941427 1319.092647 2175.595024 2344.368391 0.827794261 0.955047373 1.052917708 0.866995417 0.753589115 0.856655409 0.991286794 0.562664406 0.928009025 1 11.19498358 -9.00189075 24.81200032 0.930416358 0.810069601 0.294138062 0.114193487 88.43090926 1160501.401 0.017392069 0.031179392 9.96E-10 9.00189075 -0.120346756 S(ph)APT(ph)SPTATNISSK ddPTM_HeLa_Romidepsin_16h_R1 1 SAPTSPTATNISSK 14 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 2 0 S(1)APT(0.989)S(0.011)PTATNISSK 158.65 0.0017139 6660700 1610.7 1781.3 1993.9 1297.3 2655.7 2676.5 2240.7 2359.6 1880.2 1669 TRUE FALSE FALSE 1591.068169 1806.377188 2028.602993 1447.29993 2520.169719 2505.480288 2431.025002 2427.871303 1712.030203 1625.639139 0.978733921 1.111179686 1.247880261 0.890295943 1.550263929 1.541227833 1.49542721 1.493487235 1.053142829 1 10.66679133 -8.754865668 24.99978263 1.015090374 1.519848223 0.862567803 0.092015798 38.78732699 147506.589 0.01375364 0.027000639 1.76E-09 8.754865668 0.50475785 S(ph)APTS(ph)PTATNISSK ddPTM_HeLa_Romidepsin_16h_R1 1 SAPTSPTATNISSK 14 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 2 0 S(1)APT(0.001)S(0.95)PT(0.048)ATNISSK 165.89 0.00098534 7522600 3235.1 3005.4 2605.1 2945.8 4423.7 4413.4 4128.8 4449.8 3021.7 2872.7 TRUE FALSE FALSE 3195.669357 3047.7101 2650.440673 3286.407256 4197.942082 4131.397984 4479.500169 4578.547942 2751.431584 2798.06684 1.142099006 1.089219906 0.947239943 1.174527788 1.500300858 1.47651869 1.600926792 1.636325436 0.983333044 1 11.45021471 -8.784218658 2.754962891 1.061838662 1.566519182 0.930865352 0.067270547 0.055264737 0.858148062 0.011295448 0.023091854 1.64E-09 8.784218658 0.50468052 S(ph)AQWLDQEEAPK ddPTM_HeLa_Romidepsin_16h_R1 2 SAQWLDQEEAPK 12 0 Q53H47-3;Q53H47 Q53H47-3 SETMAR Histone-lysine N-methyltransferase SETMAR;Histone-lysine N-methyltransferase;Transposon Hsmar1 transposase 1 0 S(1)AQWLDQEEAPK;S(1)AQWLDQEEAPK ; 127.57 0.0048737 13095400 4348.5 3758.6 4204.2 3496 3623.2 4340.8 2884.9 3511.7 4657.4 4323.7 TRUE FALSE FALSE 4295.498809 3811.513669 4277.372337 3900.223969 3438.294584 4063.436889 3129.943334 3613.305499 4240.830479 4211.369651 1.019976674 0.905053222 1.015672499 0.926117699 0.816431439 0.964873005 0.743212682 0.857988208 1.006995546 1 12.0400738 -8.80324226 0.649260699 1.009553935 0.806863978 0.547313343 0.060516278 0.444829047 0.322930362 0.011360619 0.046654106 1.57E-09 8.80324226 -0.202689957 S(ph)ASADNLTLPR ddPTM_HeLa_Romidepsin_16h_R1 2 SASADNLTLPR 11 0 Q8ND76-3;Q8ND76-2;Q8ND76 Q8ND76-3 CCNY Cyclin-Y 1 0 S(0.966)AS(0.034)ADNLTLPR;S(0.995)AS(0.005)ADNLTLPR ; 129.76 0.005705 34466000 4649.3 5346.7 4731.5 4928.3 4709.5 5659.8 3686.4 5614.9 5395.4 5125 TRUE FALSE FALSE 4592.632543 5421.970983 4813.849773 5498.133234 4469.156641 5298.157046 3999.522724 5777.358273 4912.821911 4991.851761 0.920025827 1.086164262 0.964341492 1.101421576 0.895290336 1.061361054 0.801210235 1.15735774 0.98416823 1 12.28535938 S(ph)ASAPTLAETEKETAEHLDLAGASSRPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASAPTLAETEKETAEHLDLAGASSRPK 28 2 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 S(0.328)AS(0.298)APT(0.298)LAET(0.07)EKET(0.006)AEHLDLAGASSRPK 47.919 0.012831 4733400 582 651.72 728.43 698.44 705.16 760.68 626.99 657.29 982.76 564.63 TRUE FALSE FALSE 574.9063601 660.8949313 741.1080186 779.1969191 669.1730539 712.075003 680.246515 676.3076491 894.8594842 549.9608312 1.045358737 1.201712729 1.347565093 1.416822571 1.216764933 1.294774032 1.236899932 1.229737848 1.627133122 1 9.103185062 -10.17171102 2.706924685 1.019152866 1.290254448 0 0.200553501 0.082626676 1.166878175 0.010438634 0.012791422 6.73E-11 10.17171102 0.271101582 S(ph)ASASHQADIK ddPTM_HeLa_Romidepsin_16h_R1 1 SASASHQADIK 11 0 C9JXK0;A0A494C1L1;Q14739 C9JXK0 LBR Lamin-B receptor 1 0 S(0.743)AS(0.255)AS(0.002)HQADIK 126.1 0.0073248 2696500 686 1187.6 998.96 527.29 669.78 1238.5 1370.3 335.03 1148.9 1010.1 TRUE FALSE FALSE 677.6387681 1204.319064 1016.34648 588.2577508 635.5986273 1159.363847 1486.693248 344.7235645 1046.139507 983.8574564 0.688757059 1.22407881 1.033022084 0.597909531 0.646027149 1.178385994 1.51108602 0.350379582 1.063303937 1 9.942305499 -8.242634569 24.80985262 0.860687494 1.063064061 0.013903982 0.329976862 1621.323384 2139066.956 0.044085222 0.112173848 5.72E-09 8.242634569 0.202376567 S(ph)ASDLSEDLFK ddPTM_HeLa_Romidepsin_16h_R1 1 SASDLSEDLFK 11 0 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 1 0 S(1)ASDLSEDLFK 137.84 0.0035587 4160800 1070.1 1435.3 1243.1 889.69 1504 1958 1884.9 1955.1 1411.3 1439.1 TRUE FALSE FALSE 1057.05721 1455.506191 1264.735634 992.5601439 1427.245268 1832.890119 2045.003359 2011.667734 1285.069793 1401.711975 0.754118698 1.038377511 0.902279254 0.708105632 1.018215792 1.307608234 1.458932645 1.435150566 0.916785914 1 10.45297422 -8.246567201 2.534481417 0.883994597 1.43878579 0.853690505 0.095963788 0.089562075 1.124209104 0.016760979 0.048109304 5.67E-09 8.246567201 0.554791193 S(ph)ASLSHPGGEGEPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SASLSHPGGEGEPAR 15 0 C9JXU1;A6NN40;Q2M3G4-2;Q2M3G4 C9JXU1 SHROOM1 Protein Shroom1 1 0 S(0.82)AS(0.172)LS(0.007)HPGGEGEPAR 132.24 2.22E-05 0 1216.1 1149.3 1316 962.07 858.74 1084.5 1216.5 789.43 1675.9 1265.5 TRUE FALSE FALSE 1201.277705 1165.479876 1338.904428 1073.30906 814.9152934 1015.20395 1319.82948 812.2709115 1526.003307 1232.622128 0.97457094 0.945528925 1.08622456 0.870752712 0.661123369 0.823613277 1.070749462 0.658978038 1.238013883 1 10.26751488 -9.014245516 24.2078594 0.990000957 0.816851962 0.391042775 0.136663985 349.6576027 594185.8487 0.015778363 0.026869171 9.68E-10 9.014245516 -0.173148995 S(ph)ASPDDDLGSSNWEAADLGNEERK ddPTM_HeLa_Romidepsin_16h_R1 1 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 0 S(0.5)AS(0.5)PDDDLGSSNWEAADLGNEERK 173.24 5.43E-15 442880000 17581 18731 14437 17930 15455 14405 13114 13848 18048 16162 TRUE FALSE FALSE 17366.71601 18994.69551 14688.26993 20003.15096 14666.27368 13484.56699 14227.90283 14248.67003 16433.74168 15742.10891 1.103201363 1.206616954 0.933056048 1.270677968 0.931658761 0.856592155 0.903811739 0.905130952 1.043935204 1 13.94234121 -8.543857822 24.99906213 1.068613759 0.890722197 0.504307639 0.092901942 155.2381255 184984.0304 0.01315655 0.026315011 2.86E-09 8.543857822 -0.177891561 S(ph)ASPDYNRTNSPSS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 SASPDYNRTNSPSSAK 16 1 Q14669;Q14669-2;Q14669-3;G5E9G6;F8W9P3;C9JLJ5;C9JSX9;C9JLD7 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 2 0 S(0.794)AS(0.205)PDYNRT(0.004)NS(0.069)PS(0.393)S(0.536)AK 96.805 0.0010446 0 1114.4 957.27 731.66 1692.5 570.66 666.11 537.33 404.93 1165.1 1041.9 TRUE FALSE FALSE 1100.817264 970.7464722 744.3942354 1888.194813 541.5370908 623.5477208 582.9707968 416.6460107 1060.890538 1014.831288 1.084729331 0.956559463 0.733515259 1.860599723 0.533622778 0.614434861 0.574450949 0.410556923 1.045386116 1 9.987024189 -8.618343625 21.77661654 1.065236936 0.541414981 0.503307201 0.279852818 3.750167978 850.2874536 0.03721558 0.074431179 2.41E-09 8.618343625 -0.523821955 S(ph)ASPY(ph)PSHSLS(ph)SPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SASPYPSHSLSSPQR 15 0 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 3 0 S(0.998)AS(0.428)PY(0.574)PS(0.386)HS(0.059)LS(0.476)S(0.079)PQR 103.04 0.010111 15810000 2260.7 2459.1 2236.8 1831 2282.1 2201.1 1876 2032 2644.7 2603.2 TRUE FALSE FALSE 2233.145719 2493.719274 2275.730566 2042.708835 2165.635921 2060.456814 2035.347393 2090.792714 2408.151408 2535.568489 0.880727824 0.983495135 0.897522814 0.805621636 0.854102711 0.812621242 0.802718366 0.824585383 0.949748121 1 11.30809353 -16.52287874 0.024326741 2.166777669 2.45E-12 0.679611879 0.040047115 674.75646 1.321588022 82.72304901 41.61147001 3.00E-17 16.52287874 -2.166777669 S(ph)ASWGSADQLK ddPTM_HeLa_Romidepsin_16h_R1 2 SASWGSADQLK 11 0 Q86VQ1;H7C0Q2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 S(0.493)AS(0.47)WGS(0.036)ADQLK;S(0.881)AS(0.084)WGS(0.035)ADQLK ; 163.71 0.00084251 182819000 11184.6 9977.1 11327.1 8088.2 10030.5 9213.6 7957.5 7817.8 10017.5 9863.6 TRUE FALSE FALSE 11048.27779 10117.55788 11524.24342 9023.39574 9518.606156 8624.880696 8633.409851 8043.995709 9121.509711 9607.34225 1.149982743 1.053106844 1.199524606 0.939218725 0.990763721 0.897738466 0.898626241 0.837275856 0.94943112 1 13.22992167 -8.628094464 1.344897021 1.078044934 0.872425755 0.517013911 0.07548181 0.239388374 0.851805838 0.011713139 0.033819137 2.35E-09 8.628094464 -0.205619178 S(ph)ATASPQQPQAQQR ddPTM_HeLa_Romidepsin_16h_R1 2 SATASPQQPQAQQR 14 0 A0A0U1RQI5;Q9BX66-4;Q9BX66-9;Q9BX66-8;Q9BX66-10;Q9BX66-6;Q9BX66-5;Q9BX66-12 A0A0U1RQI5 SORBS1 Sorbin and SH3 domain-containing protein 1 1 0 S(0.992)AT(0.008)ASPQQPQAQQR;S(0.662)AT(0.336)AS(0.002)PQQPQAQQR ; 147.52 1.97E-05 1325100 344.029 260.82 221.16 191.77 1057.86 1365.32 1299.29 1440.52 335.22 468.95 TRUE FALSE FALSE 339.8358422 264.4918308 225.009197 213.9433497 1003.873457 1278.080458 1409.65166 1482.199173 305.2370836 456.7666114 0.744003247 0.579052462 0.492613058 0.468386577 2.197782044 2.798103947 3.086153027 3.244981434 0.66825612 1 8.835313387 -8.550338445 2.815952921 0.793244471 3.039921215 0.958622336 0.224361686 0.044457447 0.712929701 0.039003949 0.089112799 2.82E-09 8.550338445 2.246676743 up S(ph)ATPEPVTDNR ddPTM_HeLa_Romidepsin_16h_R1 1 SATPEPVTDNR 11 0 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 S(0.687)AT(0.306)PEPVT(0.007)DNR 115 0.012299 7137700 6445.4 3413.1 5164 3517.2 2776.2 2520 4535.2 4019.6 6003.6 6814 TRUE FALSE FALSE 6366.840986 3461.149711 5253.877254 3923.875213 2634.520155 2358.980133 4920.419775 4135.900784 5466.62298 6636.971298 0.959299159 0.521495356 0.79160765 0.591214733 0.396946143 0.355430215 0.741365233 0.623160866 0.82366229 1 12.69630932 -10.26860053 22.53562845 0.980780209 0.574624013 0.577486458 0.136187552 60.38583103 190029.4702 0.022409933 0.025949628 5.39E-11 10.26860053 -0.406156196 S(ph)ATRAVST(ph)SLPRREQVT(ph)WCCCSGS(ph)WPR ddPTM_HeLa_Romidepsin_16h_R1 1 SATRAVSTSLPRREQVTWCCCSGSWPR 27 3 C9J1B9;Q5XG99-2 C9J1B9 LYSMD4 4 0 S(0.374)AT(0.374)RAVS(0.353)T(0.512)S(0.512)LPRREQVT(0.843)WCCCS(0.192)GS(0.841)WPR 43.162 0.015019 3957800 283.3 439.6 374.48 443.18 439.32 541.74 511.72 386.69 579.92 421.21 TRUE FALSE FALSE 279.8470306 445.7887003 380.9976673 494.4225568 416.8998611 507.1245624 555.185484 397.8782651 528.0505028 410.2669035 0.682109691 1.086582165 0.928658062 1.205124159 1.016167421 1.236084505 1.353230005 0.969803466 1.28709018 1 8.680418965 -9.548177027 1.406198123 0.85613666 1.170274912 0 0.196044281 0.288901932 1.144758265 0.027998336 0.045908575 2.83E-10 9.548177027 0.314138252 S(ph)AVLLVDETATTPIFANR ddPTM_HeLa_Romidepsin_16h_R1 3 SAVLLVDETATTPIFANR 18 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;A0A087WX73 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR;S(1)AVLLVDETATTPIFANR ;; 268.17 4.14E-90 112919300 4313 3398.93 4319.3 4211.9 6599.9 6603.7 5518.2 6465.3 4467.2 4599.7 TRUE FALSE FALSE 4260.431497 3446.780226 4394.475605 4698.899696 6263.082475 6181.744882 5986.91577 6652.363255 4067.642444 4480.199131 0.950946905 0.76933639 0.980866135 1.048814921 1.397947344 1.379792438 1.33630573 1.484836513 0.907915547 1 12.12934714 -8.831901605 3.444645143 0.95919669 1.397909108 0.904059857 0.073276603 0.055948138 1.331361241 0.01130602 0.021925013 1.47E-09 8.831901605 0.438712418 S(ph)AVLLVDETATTPIFANRR ddPTM_HeLa_Romidepsin_16h_R1 1 SAVLLVDETATTPIFANRR 19 1 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;A0A087WX73 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 S(0.995)AVLLVDET(0.003)AT(0.001)T(0.001)PIFANRR 49.425 0.024766 12767000 1375.9 806.77 1068.2 5277.2 1063.7 652.75 1302.2 1135.2 1211 1049.9 TRUE FALSE FALSE 1359.130002 818.1277292 1086.791573 5887.374694 1009.41542 611.0413817 1412.808835 1168.045221 1102.685127 1022.623447 1.329062037 0.800028331 1.062748538 5.757128602 0.987084174 0.597523344 1.381553337 1.142204616 1.07829048 1 9.998059294 S(ph)CASSAACLIASAGY(ph)QS(ph)FCS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 SCASSAACLIASAGYQSFCSPGK 23 0 Q8N2G4-4;Q8N2G4;Q8N2G4-3;Q8N2G4-2 Q8N2G4-4 LYPD1 Ly6/PLAUR domain-containing protein 1 4 0 S(0.809)CAS(0.111)S(0.111)AACLIAS(0.129)AGY(0.872)QS(0.975)FCS(0.993)PGK 46.027 0.017948 4443500 882.6 741.25 874.84 1118.2 1017.2 925.79 723.49 1066.4 924.21 916.14 TRUE FALSE FALSE 871.8425317 751.685337 890.0662232 1247.491545 965.2884883 866.6350069 784.9432225 1097.254601 841.5463429 892.3385507 0.977031118 0.842376849 0.997453514 1.398002523 1.081751413 0.9711953 0.879647329 1.229639357 0.943079667 1 9.801447358 -9.49634249 24.98801044 0.975083807 1.100437879 0.243360945 0.13794892 1056.810582 995152.8319 0.02134739 0.03254403 3.19E-10 9.49634249 0.125354072 S(ph)CFRAGVRY(ph)Y(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 SCFRAGVRYYVR 12 2 F8WDN7;E9PGZ4;A0A5F9ZHN7;Q9NTJ5-2;Q9NTJ5 F8WDN7 SACM1L Phosphatidylinositide phosphatase SAC1 3 0 S(1)CFRAGVRY(1)Y(1)VR 60.901 0.028133 3113600 123.75 61.705 50.491 62.708 0 115.97 112.92 60.28 121.85 109.1 TRUE FALSE FALSE 122.2416874 62.57368461 51.36977468 69.95859401 0 108.5598913 122.511422 62.02410669 110.9514308 106.2655663 1.150341467 0.588842527 0.48340941 0.658337376 0 1.021590484 1.152879774 0.583670787 1.044095794 1 6.731530379 -10.25957537 24.88655438 1.070994584 0.645477228 0.304232135 0.293441306 144.8128797 1933409.195 0.05080646 0.060541426 5.50E-11 10.25957537 -0.425517356 S(ph)DEEDEDSDFGEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 SDEEDEDSDFGEEQR 15 0 Q5VW52;Q9HCL2 Q5VW52 GPAM "Glycerol-3-phosphate acyltransferase 1, mitochondrial" 1 0 S(0.566)DEEDEDS(0.434)DFGEEQR 211.82 1.50E-25 7646500 1997.5 1942.6 1897.8 2158.8 1554.1 1639.6 1283.2 1758.2 1974.8 1580.2 TRUE FALSE FALSE 1973.153702 1969.947974 1930.830413 2408.410613 1474.788478 1534.834852 1392.194976 1809.070743 1798.168942 1539.146176 1.281979407 1.27989661 1.254481506 1.564770553 0.958186104 0.997198886 0.904524208 1.175372925 1.168289906 1 10.58791454 S(ph)DENIPGGVMR ddPTM_HeLa_Romidepsin_16h_R1 2 SDENIPGGVMR 11 0 O75976-2;O75976 O75976-2 CPD Carboxypeptidase D 1 0 S(1)DENIPGGVMR;S(1)DENIPGGVMR ; 107.03 0.0024254 5475400 645.22 587.85 502.07 599.97 524.76 562.75 530.78 491.33 600.22 715.3 TRUE FALSE FALSE 637.3558105 596.1257677 510.8083177 669.3413543 497.9795391 526.7920912 575.86444 505.5458584 546.5348199 696.7164029 0.914799491 0.855621836 0.733165339 0.960708477 0.714752139 0.756106917 0.826540666 0.725612109 0.784443739 1 9.444427719 -10.28894057 0.407265324 1.00518391 0.751659143 0.066957968 0.094076761 0.462338278 0.206012347 0.03577602 0.040681278 5.14E-11 10.28894057 -0.253524767 S(ph)DEPSPQWLK ddPTM_HeLa_Romidepsin_16h_R1 1 SDEPSPQWLK 10 0 Q9BY89;A0A1B0GVJ7;Q9BY89-2 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 S(0.982)DEPS(0.018)PQWLK 127.51 0.008405 3431200 1267.3 1509.4 1648.9 1288.9 2291 2476.7 1946.9 2319.6 1607.9 1806.1 TRUE FALSE FALSE 1251.85366 1530.649373 1677.598413 1437.928682 2174.081721 2318.446863 2112.269637 2386.713966 1464.085397 1759.177262 0.711613143 0.870093882 0.953626703 0.817387033 1.235851422 1.317915433 1.200714495 1.356721701 0.832255753 1 10.78068515 -8.722868817 6.13062833 0.865646329 1.279048367 0.858266529 0.082407566 0.07009993 6.870940602 0.016749455 0.033331454 1.89E-09 8.722868817 0.413402038 S(ph)DKSPDLAPTPAPQSTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-2;Q9BY44-4;Q9BY44-3;Q9BY44 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 0 S(0.874)DKS(0.126)PDLAPTPAPQSTPR 112.64 0.00049734 758670000 5946.5 5406.1 5365.8 5640.6 5712 5922.2 5308.8 5817.2 6320.9 5838.3 TRUE FALSE FALSE 5874.021771 5482.207218 5459.189498 6292.792712 5420.495326 5543.790533 5759.729339 5985.511504 5755.542873 5686.620124 1.032954838 0.964053708 0.96000601 1.106596286 0.953201587 0.974883219 1.012856356 1.052560462 1.012120161 1 12.47335572 S(ph)DLNGLPSPVEER ddPTM_HeLa_Romidepsin_16h_R1 1 SDLNGLPSPVEER 13 0 E7EWN3;Q9C0A6 E7EWN3 SETD5 SET domain-containing protein 5 1 0 S(0.97)DLNGLPS(0.03)PVEER 154.13 0.00076907 11691000 2231.2 1674.4 1800.7 1615.5 1452.3 1520.7 1335.2 1631.8 1792 2203.8 TRUE FALSE FALSE 2204.005276 1697.972247 1832.040428 1802.291711 1378.183712 1423.532178 1448.611855 1679.013558 1631.719032 2146.544958 1.026768747 0.791025709 0.853483372 0.839624488 0.642047448 0.663173707 0.674857449 0.782193521 0.76016066 1 11.06780067 -9.713183402 0.911444935 1.016301583 0.693868108 0.32683999 0.1028232 0.155914542 0.258861188 0.013059826 0.021363753 1.94E-10 9.713183402 -0.322433475 S(ph)DSAPPTPVNR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSAPPTPVNR 11 0 A2A2F0;Q86X10-4;Q86X10-2;Q86X10-3;Q86X10 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 0 S(0.61)DS(0.211)APPT(0.179)PVNR;S(0.539)DS(0.448)APPT(0.013)PVNR ; 143 0.0026109 18204600 5499.1 5471.3 5568.9 5097 5440.7 6940.4 6382.4 5922.5 5901.8 5795 TRUE FALSE FALSE 5432.074854 5548.325105 5665.824368 5686.339122 5163.040777 6496.930839 6924.520897 6093.858193 5373.928227 5644.445065 0.962375361 0.982970875 1.003787672 1.007422175 0.914711848 1.151030928 1.226785063 1.079620427 0.952073794 1 12.46261603 -8.244411428 23.14565246 0.981607983 1.159909522 0.783288732 0.042676923 94.34749228 128243.2231 0.005416546 0.013757998 5.70E-09 8.244411428 0.178301539 S(ph)DSDSSTLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSDSSTLPR 10 0 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 0 S(0.838)DS(0.162)DSSTLPR 138.25 0.0052072 40315000 1855 1804 1967.6 2221.4 2208.4 2574.5 2029.9 2285.5 2160.5 1940 TRUE FALSE FALSE 1832.390546 1829.396759 2001.845253 2478.24872 2095.697107 2409.997759 2202.319655 2351.627337 1967.259469 1889.59852 0.9697248 0.968140449 1.059402424 1.311521306 1.10907004 1.275402014 1.165496073 1.244511631 1.041099179 1 10.88386402 -9.462184686 4.825954263 0.984869564 1.214291972 0.785741912 0.056341206 0.059534054 2.819009344 0.00737745 0.011240107 3.45E-10 9.462184686 0.229422408 S(ph)DSDTEGLLFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSDTEGLLFSR 12 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 S(0.966)DS(0.026)DT(0.007)EGLLFSR;S(0.996)DS(0.002)DT(0.002)EGLLFSR ; 195.72 1.64E-10 12580800 2683.2 2663.4 2797.2 1666.98 2871.4 2661.2 2045.43 1850.03 2960.6 2806.7 TRUE FALSE FALSE 2650.496126 2700.895415 2845.884093 1859.724071 2724.861743 2491.157909 2219.168773 1903.557699 2695.796521 2733.781529 0.969534726 0.987970467 1.041006409 0.680275308 0.996737199 0.911249813 0.811757907 0.696309372 0.986105324 1 11.41668224 -5.715216819 0.34737396 0.993605522 1.35E-12 0.462142249 0.091675156 10.91807123 0.401424912 0.026795609 5.72650079 1.93E-06 5.715216819 -0.993605522 S(ph)DSDYDLSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SDSDYDLSPK 10 0 Q08499;Q08499-2;A0A1B0GW84;A0A087WSZ7;Q08499-10;Q08499-11;Q08499-6;Q08499-9;A0A1W2PQN6;Q08499-12;Q08499-7;Q07343;E9PMG3;Q07343-3 Q08499 PDE4D;PDE4B "cAMP-specific 3,5-cyclic phosphodiesterase 4D;cAMP-specific 3,5-cyclic phosphodiesterase 4B" 1 0 S(0.801)DS(0.199)DYDLSPK 185.99 7.42E-06 41905000 11960 11159 10714 10759 7248.5 6647.7 6560 6005.8 11512 11256 TRUE FALSE FALSE 11814.22692 11316.09669 10900.47268 12003.0062 6878.581997 6222.933424 7117.206236 6179.568347 10482.33789 10963.5675 1.077589655 1.032154606 0.994245046 1.094808438 0.627403626 0.567601141 0.649168826 0.563645761 0.956106476 1 13.4204297 -8.75467566 24.57451761 1.037221625 0.602873281 0.954934401 0.045068324 15.83422277 57529.54456 0.005843381 0.011474356 1.76E-09 8.75467566 -0.434348344 S(ph)DSEATISR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSEATISR 9 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2;H0Y4T4 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 S(0.993)DS(0.007)EATISR 152.64 0.0049593 106740000 1549.7 1534.5 1454.6 1132.4 1116 1311.3 1262.2 824.32 1511.6 1232 TRUE FALSE FALSE 1530.81166 1556.102731 1479.916703 1263.333416 1059.046356 1227.512162 1369.411236 848.1703986 1376.39871 1199.992462 1.275684397 1.296760421 1.233271666 1.05278446 0.882544173 1.022933227 1.141183199 0.706813105 1.14700613 1 10.22880963 -9.007258677 6.180458829 1.155359281 0.959264608 0.438390528 0.130983059 0.161113119 26.35799128 0.02294 0.040156398 9.83E-10 9.007258677 -0.196094673 S(ph)DSELEVKPAESLLR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSELEVKPAESLLR 15 1 Q92539 Q92539 LPIN2 Phosphatidate phosphatase LPIN2 1 0 S(1)DSELEVKPAESLLR;S(0.519)DS(0.481)ELEVKPAESLLR ; 142.91 0.0034767 13360200 2968.57 2981.99 2696.07 1781.21 2974.38 2531.29 1907.05 2766.06 2685.01 2629.16 TRUE FALSE FALSE 2932.387927 3023.970533 2742.993967 1987.161881 2822.58629 2369.548738 2069.034779 2846.091582 2444.855981 2560.854044 1.145082022 1.180844547 1.07112468 0.775976236 1.102205062 0.925296287 0.807947171 1.111383754 0.954703368 1 11.32240931 -9.478308945 24.91385503 1.081094789 0.942548709 0.222165362 0.116941254 447.5704257 250185.5177 0.017088013 0.026101403 3.32E-10 9.478308945 -0.13854608 S(ph)DSLLSFR ddPTM_HeLa_Romidepsin_16h_R1 6 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 S(0.582)DS(0.405)LLS(0.013)FR;S(0.999)DS(0.001)LLSFR;S(0.984)DS(0.016)LLSFR;S(0.695)DS(0.304)LLS(0.001)FR;S(0.679)DS(0.32)LLS(0.001)FR;S(0.985)DS(0.015)LLSFR ;;;;; 182.16 8.81E-05 137214900 13198.19 12456 13515.3 15269.89 10118.68 8770.82 7544.06 7543.82 13374.54 12753.34 TRUE FALSE FALSE 13037.32538 12631.35589 13750.52813 17035.46653 9602.286002 8210.392909 8184.852268 7762.08853 12178.28765 12422.00639 1.04953459 1.016853115 1.106949046 1.371394121 0.773006043 0.660955457 0.658899377 0.624865926 0.980380082 1 13.60061059 -8.538737074 24.98107404 1.052908314 0.660585228 0.778292726 0.107239662 84.64139421 133332.2803 0.015724489 0.03145628 2.89E-09 8.538737074 -0.392323085 S(ph)DSQASLTVPLSPQVVR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSQASLTVPLSPQVVR 17 0 Q8TEV9-2;Q8TEV9 Q8TEV9-2 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 0 S(0.628)DS(0.357)QAS(0.014)LT(0.002)VPLSPQVVR 115.2 0.0021108 3570100 797.98 678.74 577.57 570.21 793.36 840.06 600.99 838.74 816.36 631.75 TRUE FALSE FALSE 788.2539128 688.2953195 587.6223636 636.1403631 752.8718788 786.3828772 652.0380756 863.0076186 743.342717 615.3370439 1.281011635 1.118566363 0.954960163 1.033808007 1.223511385 1.277970967 1.059643787 1.402495798 1.2080253 1 9.265233037 -12.60147329 1.403888593 1.000130289 1.174739763 0 0.141653356 0.566049 2.004372755 0.092385215 0.021414493 2.50E-13 12.60147329 0.174609474 S(ph)DVDQLY(ph)LIRK ddPTM_HeLa_Romidepsin_16h_R1 1 SDVDQLYLIRK 11 1 H0YE65;A0A5H1ZRP5;Q00532-3;Q00532;Q00532-2 H0YE65 CDKL1 Cyclin-dependent kinase-like 1 2 0 S(1)DVDQLY(1)LIRK 66.27 0.0034112 0 848.26 949.6 722.92 1090.9 658.22 648.37 536.5 597.14 847.75 843.14 TRUE FALSE FALSE 837.9210808 962.9684937 735.5021193 1217.034991 624.6285772 606.9412495 582.0702966 614.4173038 771.9251168 821.2351013 1.020318152 1.172585648 0.895604825 1.481956859 0.760596541 0.739059069 0.708774254 0.748162497 0.939956312 1 9.681651482 -8.563509395 24.99999973 1.046538323 0.733033319 0.534053167 0.155988747 86.01402295 52924.03985 0.020531831 0.041063696 2.73E-09 8.563509395 -0.313505003 S(ph)EAASPALPVITK ddPTM_HeLa_Romidepsin_16h_R1 1 SEAASPALPVITK 13 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 1 0 S(1)EAASPALPVITK 182.72 3.89E-07 159490000 10209 9647.8 8653.1 8391.9 5800.8 4867.2 4554.3 4695.1 10030 8933 TRUE FALSE FALSE 10084.56878 9783.621982 8803.703576 9362.210963 5504.76353 4556.201628 4941.142128 4830.945311 9132.891679 8700.919372 1.159023357 1.124435426 1.011813028 1.076002496 0.632664583 0.523646 0.56788736 0.555222397 1.049646743 1 13.08695213 -8.720615098 4.197241111 1.076907653 0.555188295 0.96460306 0.047096817 0.036535929 1.377955454 0.009689548 0.019494949 1.90E-09 8.720615098 -0.521719358 S(ph)EAEDEDDEDYVPYVPLR ddPTM_HeLa_Romidepsin_16h_R1 2 SEAEDEDDEDYVPYVPLR 18 0 D6RD33;D6RGI7;A0A499FJW5;Q9UJV9 D6RD33 DDX41 Probable ATP-dependent RNA helicase DDX41 1 0 S(1)EAEDEDDEDYVPYVPLR;S(1)EAEDEDDEDYVPYVPLR ; 274.02 6.93E-91 58374000 2557.39 3182.16 2502.58 1454.78 2992.1 2636.28 2477.79 3059.2 2804.55 3490.08 TRUE FALSE FALSE 2526.219547 3226.958532 2546.136355 1622.988509 2839.401972 2467.830216 2688.253421 3147.713125 2553.704024 3399.407218 0.743135313 0.949270954 0.748994219 0.477432801 0.835263853 0.725958986 0.790800645 0.925959417 0.751220392 1 11.73106748 -12.39436463 0.618562665 1.042691462 0.763419427 0 0.144815879 1.154507941 0.597418542 0.185915778 0.02733861 4.03E-13 12.39436463 -0.279272035 S(ph)EDDSAVPLAK ddPTM_HeLa_Romidepsin_16h_R1 2 SEDDSAVPLAK 11 0 Q9Y2W2 Q9Y2W2 WBP11 WW domain-binding protein 11 1 0 S(0.789)EDDS(0.211)AVPLAK;S(0.998)EDDS(0.002)AVPLAK ; 131.17 0.0050813 6233100 4130.9 4395.2 4017.2 2417.4 4554 5270.9 4388.9 5441.9 4383 3830.7 TRUE FALSE FALSE 4080.551002 4457.075741 4087.117681 2696.911162 4321.592387 4934.106501 4761.693056 5599.352791 3990.973503 3731.177862 1.093636153 1.194549257 1.095396101 0.722804236 1.158238108 1.322399168 1.276190317 1.500693078 1.069628319 1 11.86541542 -8.336534618 3.447806072 1.039331396 1.362903329 0.576751095 0.128124817 0.136962096 3.155659781 0.018429733 0.045260766 4.61E-09 8.336534618 0.323571933 S(ph)EGEGEAASADDGSLNTSGAGPK ddPTM_HeLa_Romidepsin_16h_R1 1 SEGEGEAASADDGSLNTSGAGPK 23 0 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 S(0.981)EGEGEAAS(0.006)ADDGS(0.003)LNT(0.007)S(0.003)GAGPK 55.686 0.005506 4945000 2314.7 2346.3 1896 1362.2 2199.5 2147 1647.1 2242.2 2394.6 2200.7 TRUE FALSE FALSE 2286.487546 2379.331273 1928.999085 1519.703973 2087.251308 2009.813629 1787.004633 2307.074519 2180.420979 2143.525497 1.066694821 1.110008384 0.89991889 0.70897406 0.9737469 0.937620584 0.833675473 1.07629908 1.017212523 1 11.06576986 -9.740351394 24.13102126 1.038263289 0.897487286 0.358826135 0.093208313 133.371216 152616.2716 0.014288668 0.020193367 1.82E-10 9.740351394 -0.140776003 S(ph)EGSEYEEIPK ddPTM_HeLa_Romidepsin_16h_R1 2 SEGSEYEEIPK 11 0 P48634 P48634 PRRC2A Protein PRRC2A 1 0 S(1)EGSEYEEIPK;S(0.975)EGS(0.025)EYEEIPK ; 193.15 9.26E-09 19375500 6131.8 6691.9 5634.6 2151.13 4463.1 4741.6 4596.4 4210.2 6576.4 5735.8 TRUE FALSE FALSE 6057.063263 6786.108744 5732.667849 2399.853772 4235.331353 4438.627063 4986.818101 4332.015494 5988.190313 5586.783089 1.084177275 1.214671956 1.02611248 0.429559146 0.758098406 0.794487094 0.892609937 0.775404276 1.071849438 1 12.44780209 -9.484006732 24.71776063 1.057142667 0.742567093 0.663546182 0.123907199 247.2098931 157194.9181 0.019443783 0.029697118 3.28E-10 9.484006732 -0.314575574 S(ph)EGSEYEEIPKR ddPTM_HeLa_Romidepsin_16h_R1 1 SEGSEYEEIPKR 12 1 P48634 P48634 PRRC2A Protein PRRC2A 1 0 S(1)EGSEYEEIPKR 94.781 0.0065401 3694500 1547.1 2456.3 1618.6 891.29 1803.5 1748.8 1446.6 1564.8 1824.8 2173.3 TRUE FALSE FALSE 1528.24335 2490.879856 1646.771054 994.3451434 1711.460665 1637.057324 1569.474168 1610.075019 1661.585318 2116.837353 0.721946515 1.176698745 0.77793934 0.46973148 0.808498897 0.773350547 0.741424071 0.760604029 0.784937641 1 11.04769471 -9.532348712 24.9958891 0.892375511 0.711588545 0.314707525 0.144223905 228.8944814 604162.8009 0.024662291 0.034903076 2.94E-10 9.532348712 -0.180786966 S(ph)EGSPVLPHEPAK ddPTM_HeLa_Romidepsin_16h_R1 2 SEGSPVLPHEPAK 13 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 0 S(0.912)EGS(0.088)PVLPHEPAK;S(0.5)EGS(0.5)PVLPHEPAK ; 177.36 8.48E-07 24604000 6985.5 7130.6 6525.3 5780 7685.1 8196 7554 7419.5 7051 7527.9 TRUE FALSE FALSE 6900.358039 7230.984774 6638.870109 6448.310796 7292.90067 7672.302051 8195.636571 7634.171526 6420.3409 7332.324073 0.941087433 0.986179103 0.90542508 0.879436142 0.994623341 1.046367015 1.117740636 1.041166682 0.875621541 1 12.84005484 -8.254528128 3.043282637 0.96086587 1.078419349 0.584744051 0.048153268 0.14370133 2.699071709 0.006449146 0.017394638 5.57E-09 8.254528128 0.117553479 S(ph)EISPEGEK ddPTM_HeLa_Romidepsin_16h_R1 1 SEISPEGEK 9 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 0 S(0.826)EIS(0.174)PEGEK 118.03 0.014586 7950200 5200.2 4942.7 5422.3 4090.4 6639.6 7953.6 7211.2 7527.6 5278.9 5038.3 TRUE FALSE FALSE 5136.817962 5012.28346 5516.672857 4563.351294 6300.756436 7445.390629 7823.719148 7745.399229 4806.741963 4907.40424 1.046748487 1.021371629 1.12415293 0.929891053 1.283928555 1.517174919 1.594268327 1.578308786 0.979487674 1 12.2607444 -8.438600122 2.402245904 1.025074805 1.577830784 0.952875891 0.054416463 0.038352097 0.431334013 0.007234918 0.018420309 3.64E-09 8.438600122 0.552755979 S(ph)ELEFETLK ddPTM_HeLa_Romidepsin_16h_R1 2 SELEFETLK 9 0 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 S(1)ELEFETLK;S(1)ELEFETLK ; 164.65 0.0027081 9280500 3304.4 2826.4 3654.7 1752.64 3335.1 4012.1 3356.3 3168.5 3876.1 3294.5 TRUE FALSE FALSE 3264.124702 2866.190133 3718.30852 1955.288483 3164.897402 3755.739758 3641.384038 3260.175548 3529.411908 3208.908415 1.017207187 0.893197861 1.158745604 0.609331346 0.98628474 1.170410393 1.134773439 1.015976503 1.09987929 1 11.6478669 -8.305925358 11.32081652 0.979089425 1.109797256 0.163975176 0.143529133 1.393366875 353.1942517 0.019008492 0.042571952 4.94E-09 8.305925358 0.130707831 S(ph)ELVVEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SELVVEVK 8 0 P43121 P43121 MCAM Cell surface glycoprotein MUC18 1 0 S(1)ELVVEVK 131.82 0.0099482 3844200 1025.4 1547.2 1096.6 874.5 2125.7 3491.9 1634 3865 1165.4 1178.2 TRUE FALSE FALSE 1012.90203 1568.981522 1115.685863 975.6138046 2017.217597 3268.77886 1772.791919 3976.827677 1061.163705 1147.590194 0.882633919 1.367196696 0.972198846 0.850141287 1.757785669 2.848385143 1.544795283 3.465372654 0.924688718 1 10.16439183 -8.539048585 3.387535445 0.975977066 2.506856697 0.706508358 0.465788645 0.089811821 2.160712846 0.060123522 0.133544373 2.89E-09 8.539048585 1.530879631 S(ph)EPAVGPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SEPAVGPPR 9 0 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 S(1)EPAVGPPR 117.02 0.015157 8565700 655.34 652.29 603.18 629 591.5 806.83 629.14 947.55 745.52 731.37 TRUE FALSE FALSE 647.352464 661.4729557 613.6780949 701.7279395 561.3135478 755.2761669 682.5791359 974.9658643 678.838824 712.368902 0.908732066 0.928553947 0.861461096 0.985062567 0.787953469 1.060231805 0.958182108 1.368624966 0.952931581 1 9.476480728 -6.858329203 1.703406217 0.941520132 2.120144568 0.759051845 0.072433111 1.243129141 1.39393885 0.010158398 3.35993942 1.39E-07 6.858329203 1.178624436 S(ph)ESELIDELSEDFDR ddPTM_HeLa_Romidepsin_16h_R1 1 SESELIDELSEDFDR 15 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;A0A0A0MR45;H0YD33;E7EQA0;E7EQ12;D6RC54;P20810-3 P20810-6;P20810-3 CAST Calpastatin 1 0 S(0.608)ES(0.392)ELIDELSEDFDR 148.18 0.00047815 14445000 612.75 677.05 636.89 598.79 514.24 426.31 495.31 379.48 776.16 726.46 TRUE FALSE FALSE 605.2815673 686.5815277 647.9748033 668.0249172 487.9964139 399.0701669 537.381619 390.4596551 706.7383057 707.5864645 0.855417108 0.970314671 0.915753531 0.944089452 0.689663297 0.563987847 0.759457177 0.551819 0.998801335 1 9.466762641 -8.705033905 4.474202795 0.933142505 0.637502411 0.834041808 0.06702095 0.068071946 2.779960385 0.010356961 0.020903057 1.97E-09 8.705033905 -0.295640095 S(ph)ESFSSEDLIPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SESFSSEDLIPSR 13 0 Q9P219;A0A0A0MR69;Q9P219-3;Q9P219-2 Q9P219 CCDC88C Protein Daple 1 0 S(0.991)ES(0.009)FSSEDLIPSR 173.59 4.21E-05 3285200 721.58 726.24 637.95 584.15 618.15 565.84 504.99 450.44 603.49 583.67 TRUE FALSE FALSE 712.7851054 736.4640258 649.0532521 651.6921715 586.6034989 529.6846502 547.883838 463.4727707 549.5123429 568.5061693 1.253786052 1.295437175 1.141681986 1.146323834 1.031833128 0.931713109 0.963725405 0.815246686 0.966589938 1 9.151032195 -8.35667979 1.565099898 1.141495617 0.886711217 0.523189421 0.099003727 0.284064774 1.319741095 0.017468651 0.058101688 4.40E-09 8.35667979 -0.2547844 S(ph)ESPPAELPSLR ddPTM_HeLa_Romidepsin_16h_R1 2 SESPPAELPSLR 12 0 Q14669;Q14669-2;Q14669-3;G5E9G6;H7C1L9 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 S(0.614)ES(0.386)PPAELPSLR;S(0.949)ES(0.051)PPAELPSLR ; 128.36 0.0045904 108559000 3338.1 2842.6 3018.1 2317.2 2520 2469.6 2353.9 2648.9 3759.2 3442.6 TRUE FALSE FALSE 3297.413953 2882.618197 3070.628764 2585.125567 2391.394997 2311.80053 2553.840207 2725.541742 3422.967737 3353.160756 0.983374849 0.859671936 0.915741591 0.770951873 0.713176364 0.689439218 0.761621763 0.81282764 1.020818263 1 11.71130593 -9.636912897 1.04245313 0.994490037 0.73837446 0.852624517 0.044397353 0.119524507 0.259745221 0.008289743 0.013769257 2.31E-10 9.636912897 -0.256115576 S(ph)ESPPAELPSLRR ddPTM_HeLa_Romidepsin_16h_R1 2 SESPPAELPSLRR 13 1 Q14669;Q14669-2;Q14669-3;G5E9G6;H7C1L9 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 S(0.558)ES(0.437)PPAELPS(0.005)LRR;S(0.804)ES(0.194)PPAELPS(0.002)LRR ; 89.466 0.0068775 22763000 5375.6 4910.6 3694.7 5326.9 3327.4 3492.3 3030.6 3096.7 5216.3 4378.7 TRUE FALSE FALSE 5310.08012 4979.731556 3759.004704 5942.821242 3157.590362 3269.153301 3288.019088 3186.298129 4749.741064 4264.940743 1.245053669 1.167596892 0.881373255 1.393412383 0.740359726 0.766517872 0.77094133 0.747090832 1.113671057 1 12.05830998 -8.731030911 24.99229021 1.120564258 0.758013171 0.674169356 0.128305066 101.6085753 83510.23428 0.019740378 0.039477051 1.86E-09 8.731030911 -0.362551087 S(ph)ESPQAEALLLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SESPQAEALLLPR 13 0 A0A087WXB3;A0A087X223;A0A087WYW1;Q96NU1-4;Q96NU1-5 A0A087WXB3 SAMD11 Sterile alpha motif domain-containing protein 11 1 0 S(0.602)ES(0.398)PQAEALLLPR 134.02 0.0017942 2179700 660.82 782.02 705.19 697.41 548.31 315.1 290.5 497.41 1052.1 891.9 TRUE FALSE FALSE 652.7656717 793.0292981 717.4635361 778.0478256 520.3276947 294.9661269 315.1750627 511.8017736 957.997541 868.7283094 0.751403707 0.912862272 0.825877928 0.895616981 0.598953308 0.339537832 0.362800497 0.589139053 1.102758516 1 9.762761241 -8.604753361 3.288623752 0.878845001 0.426067102 0.792801382 0.112059708 0.082336793 1.780462373 0.016172184 0.034828035 2.48E-09 8.604753361 -0.452777899 S(ph)ESPVPQNEK ddPTM_HeLa_Romidepsin_16h_R1 1 SESPVPQNEK 10 0 Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8-3;Q9UIF8 Q9UIF8-4 BAZ2B Bromodomain adjacent to zinc finger domain protein 2B 1 0 S(0.5)ES(0.5)PVPQNEK 187.85 8.81E-08 6023100 4979.6 4539.7 4540.7 3877.6 2999.9 2841.7 2455.8 1747.9 4716.7 4766.3 TRUE FALSE FALSE 4918.90672 4603.610016 4619.728979 4325.946357 2846.803909 2660.124541 2664.395591 1798.472729 4294.826539 4642.470839 1.05954499 0.99162928 0.995101346 0.931819823 0.613208786 0.572997577 0.573917572 0.38739559 0.925116536 1 12.18067713 -8.724933003 1.572725418 1.02643965 0.500057064 0.928398549 0.06117685 0.05430719 0.270578629 0.007976303 0.019716223 1.88E-09 8.724933003 -0.526382586 S(ph)ESSPIVR ddPTM_HeLa_Romidepsin_16h_R1 1 SESSPIVR 8 0 H0Y8J2;Q03188;Q03188-2 H0Y8J2 CENPC Centromere protein C 1 0 S(0.86)ES(0.07)S(0.07)PIVR 114.89 0.020664 4767700 4781.1 3872.2 4203.5 4939 3571.9 3638.4 3001.6 2701.9 4554.8 4205.9 TRUE FALSE FALSE 4722.826114 3926.712933 4276.660154 5510.070419 3389.612614 3405.917982 3256.555829 2780.075214 4147.40728 4096.630112 1.152856369 0.958522695 1.043945887 1.345025123 0.827414856 0.831395047 0.794935286 0.678624903 1.012394863 1 12.00022192 -8.552590884 24.63750199 1.079376167 0.780717522 0.656518669 0.10761501 81.37621631 67477.38912 0.01584088 0.031682124 2.80E-09 8.552590884 -0.298658645 S(ph)ESVEGFLS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 2 0 S(0.91)ES(0.09)VEGFLS(0.958)PS(0.042)R 139.21 0.021937 4128500 2044.1 2101.6 1961.4 2013.9 1856.9 2478.6 2237.7 2041.4 2158.6 2282.3 TRUE FALSE FALSE 2019.185723 2131.18638 1995.537344 2246.756594 1762.135464 2320.225459 2427.770182 2100.464688 1965.52941 2223.005517 0.908313411 0.958695947 0.89767539 1.010684219 0.792681552 1.043733559 1.092111632 0.944876057 0.884176577 1 11.11829581 S(ph)ESVEGFLSPSR ddPTM_HeLa_Romidepsin_16h_R1 2 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 S(0.821)ES(0.176)VEGFLS(0.004)PSR;S(0.991)ES(0.009)VEGFLSPSR ; 156.52 0.0011826 10599200 2209.75 2270.37 2118.73 2076.49 2278.21 2125.94 1702.56 2293.74 2395.33 2470.2 TRUE FALSE FALSE 2182.816717 2302.332328 2155.605607 2316.583544 2161.944443 1990.099295 1847.175404 2360.105748 2181.085686 2406.023848 0.907229876 0.95690337 0.8959203 0.96282651 0.898554869 0.827131991 0.767729466 0.98091536 0.906510419 1 11.23243523 -16.52287874 0.083022595 1.374359553 0.781688966 0.081073088 0.064715016 133.7391586 0.84892953 9.13625416 0.935326379 3.00E-17 16.52287874 -0.592670587 S(ph)ETSWESPK ddPTM_HeLa_Romidepsin_16h_R1 1 SETSWESPK 9 0 E5RJU9;Q86UE4 E5RJU9 MTDH Protein LYRIC 1 0 S(0.563)ET(0.004)S(0.002)WES(0.431)PK 139.38 0.0064891 36562000 2986.8 4511.7 3001 1908.9 2504.6 3738.2 2347.5 3980.3 3579.7 4053.1 TRUE FALSE FALSE 2950.395733 4575.215831 3053.231146 2129.616 2376.780916 3499.341084 2546.896591 4095.463701 3259.522666 3947.799878 0.747351898 1.158928004 0.773400689 0.539443757 0.602052026 0.886402855 0.645143287 1.03740408 0.825655496 1 11.94683314 -9.541238133 24.99718304 0.901463024 0.728888975 0.21672648 0.16866458 310.8700613 423262.7334 0.027423834 0.038786654 2.88E-10 9.541238133 -0.172574049 S(ph)FAGNLNTYK ddPTM_HeLa_Romidepsin_16h_R1 1 SFAGNLNTYK 10 0 Q01813;Q01813-2;B1APP6 Q01813 PFKP "ATP-dependent 6-phosphofructokinase, platelet type" 1 0 S(1)FAGNLNTYK 148.13 0.0038731 25216000 1752 1361.9 2348.5 1798.2 2154.6 1789.6 1492.2 1432.4 1484.7 1087.6 TRUE FALSE FALSE 1730.64595 1381.072864 2389.374657 2006.116345 2044.642722 1675.250336 1618.947431 1473.844234 1351.904714 1059.343995 1.633695908 1.303705756 2.255522916 1.89373457 1.930102716 1.581403532 1.528254692 1.391280114 1.276171593 1 10.04895543 -11.87744321 0.627179111 0.969523735 1.720115049 0.384324918 0.274465576 0.574199856 0.404421269 0.225821251 0.064676632 1.33E-12 11.87744321 0.750591314 S(ph)FDASDTLALPR ddPTM_HeLa_Romidepsin_16h_R1 3 SFDASDTLALPR 12 0 Q5JXC2 Q5JXC2 MIIP Migration and invasion-inhibitory protein 1 0 S(1)FDASDTLALPR;S(1)FDASDTLALPR;S(0.995)FDAS(0.001)DT(0.004)LALPR ;; 190.35 5.09E-10 7305300 2260.68 2420.12 2828.16 2676.69 2561.17 3094.01 2351.18 2658.94 2906.09 2518.99 TRUE FALSE FALSE 2233.125963 2454.190513 2877.382938 2986.181492 2430.463938 2896.312746 2550.889171 2735.872234 2646.162032 2453.546277 0.910162561 1.000262573 1.172744515 1.217087903 0.990592255 1.1804598 1.039674366 1.115068527 1.078505043 1 11.26065277 -9.911427008 5.464576515 0.957452015 1.116461692 0.348698643 0.07614839 0.115695045 5.619258585 0.010947825 0.014453464 1.23E-10 9.911427008 0.159009677 S(ph)FDHLISDTK ddPTM_HeLa_Romidepsin_16h_R1 2 SFDHLISDTK 10 0 J3QSG6;H0Y465;P21359-2;P21359-6;P21359 J3QSG6 NF1 Neurofibromin;Neurofibromin truncated 1 0 S(1)FDHLISDTK;S(1)FDHLISDTK ; 155.33 0.0032855 20482100 5084.1 4178.2 5335.9 4570.7 5042.3 5151.6 3838.5 4386.7 4852.5 4288.1 TRUE FALSE FALSE 5022.133034 4237.020809 5428.769101 5099.18584 4784.972616 4822.429386 4164.542094 4513.622243 4418.480247 4176.694544 1.20241808 1.014443543 1.299776425 1.220866354 1.145636236 1.154604277 0.997090415 1.080668504 1.057889247 1 12.02814592 -5.267152011 13.1645109 1.112737499 1.132195611 0 0.098658813 0 0 0.014592644 0 5.41E-06 5.267152011 0.019458112 S(ph)FDYNYR ddPTM_HeLa_Romidepsin_16h_R1 4 SFDYNYR 7 0 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 0 S(1)FDYNYR;S(0.963)FDY(0.001)NY(0.036)R;S(0.998)FDY(0.001)NY(0.001)R;S(0.904)FDY(0.076)NY(0.02)R ;;; 125.57 0.022041 866844600 12599.2 11880.4 12099.4 7191.5 10554.7 10484.1 10241.4 11101.8 12008.7 11424.1 TRUE FALSE FALSE 12445.6361 12047.65258 12309.98498 8023.015067 10016.05427 9814.199846 11111.30426 11423.01307 10934.6118 11127.30024 1.118477604 1.082711199 1.106286765 0.721020813 0.900133371 0.881992904 0.998562457 1.026575434 0.982683271 1 13.44181598 -9.322407604 24.99999427 1.063234165 0.909195319 0.43951675 0.085888396 174.1084989 71392.68286 0.013736493 0.020982842 4.76E-10 9.322407604 -0.154038846 S(ph)FDYNYRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFDYNYRR 8 1 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 0 S(0.89)FDYNY(0.11)RR 71.03 0.024098 14509000 4201.2 3986.8 2825.2 4393.1 3171 3083.6 2667.7 3384.5 3542.6 2900.6 TRUE FALSE FALSE 4149.994158 4042.926275 2874.371421 4901.050892 3009.172037 2886.567912 2894.294371 3482.425168 3225.740983 2825.241994 1.468898653 1.431001763 1.017389458 1.734736671 1.065102403 1.02170643 1.024441226 1.232611286 1.141757411 1 11.46415873 S(ph)FEMTEFNQALEEIK ddPTM_HeLa_Romidepsin_16h_R1 1 SFEMTEFNQALEEIK 15 0 Q9BVS4;Q9BVS4-2;H0Y919 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 1 0 S(0.991)FEMT(0.009)EFNQALEEIK 96.103 0.015031 3312400 1136.8 1080.3 1160.6 504.22 1422.9 1167.1 1236.6 1325.8 975.43 1162.3 TRUE FALSE FALSE 1122.944244 1095.508492 1180.799756 562.5202888 1350.284103 1092.526077 1341.636773 1364.159931 888.1850978 1132.103278 0.991909719 0.967675399 1.043014165 0.496880717 1.192721662 0.965040997 1.185083374 1.204978342 0.784544233 1 10.14478986 -7.73361198 1.842309496 0.97074211 1.226182926 0.232030038 0.178377284 0.471876801 2.805938106 0.022752377 0.151159217 1.85E-08 7.73361198 0.255440817 S(ph)FEVEEVETPNST(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPR 16 0 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 S(0.805)FEVEEVET(0.071)PNS(0.378)T(0.746)PPR 146.67 0.0012707 6235300 1920.3 1919.3 2166.7 1753.1 1867.3 2358.5 1999.6 2138.1 2320.3 2155.2 TRUE FALSE FALSE 1896.894645 1946.319956 2204.410505 1955.801671 1772.004713 2207.799462 2169.445974 2199.96255 2112.766557 2099.207593 0.903624135 0.927168881 1.050115535 0.931685688 0.844130289 1.051729933 1.033459473 1.047996662 1.006459086 1 11.03562913 S(ph)FEVEEVETPNST(ph)PPRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 S(0.98)FEVEEVET(0.02)PNS(0.311)T(0.689)PPRR 127.9 0.0011239 8489200 1020.2 623.84 808.23 1458.7 725.75 1329.2 1165.4 1103 732.85 905.79 TRUE FALSE FALSE 1007.76541 632.6224359 822.2969041 1627.361757 688.7122694 1244.26841 1264.389047 1134.913565 667.3020605 882.2574452 1.142257756 0.717049699 0.932037365 1.844542958 0.780625058 1.410323502 1.433129359 1.286374596 0.756357528 1 9.785055889 S(ph)FEVEEVETPNSTPPR ddPTM_HeLa_Romidepsin_16h_R1 3 SFEVEEVETPNSTPPR 16 0 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 1 0 S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR;S(1)FEVEEVETPNSTPPR ;; 276.34 6.69E-102 69299900 2273.97 2547.21 1925.34 2100.19 2427.15 3318.6 2567.51 2542.06 2576.86 2251.27 TRUE FALSE FALSE 2246.253979 2583.069689 1958.849735 2343.023849 2303.283479 3106.55217 2785.594235 2615.610495 2346.379188 2192.781681 1.024385601 1.177987627 0.893317266 1.068516702 1.050393433 1.416717495 1.270347276 1.192827593 1.070046876 1 11.09854647 -8.3649577 6.331353427 1.021079327 1.289990335 0.645830643 0.08502206 0.094388953 4.908207727 0.011252736 0.025389449 4.32E-09 8.3649577 0.268911008 S(ph)FLNYYADLETSAR ddPTM_HeLa_Romidepsin_16h_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 0 S(0.991)FLNYYADLET(0.002)S(0.007)AR 164.82 0.0001242 4916800 773.14 1106.5 634.26 477.11 627.26 711.74 539.14 847.84 1164.6 1069.2 TRUE FALSE FALSE 763.7166723 1122.077336 645.2990292 532.2757031 595.2485816 666.262111 584.9345381 872.3709127 1060.435259 1041.42203 0.733340231 1.077447283 0.61963259 0.511104709 0.571572873 0.639761876 0.561669065 0.837672805 1.018256988 1 10.02433912 -9.70309808 13.76070741 0.885800849 0.613930933 0.611555952 0.125066667 0.859901771 201.9205563 0.021163567 0.029928202 1.98E-10 9.70309808 -0.271869916 S(ph)FNGTDNHIR ddPTM_HeLa_Romidepsin_16h_R1 2 SFNGTDNHIR 10 0 Q5T0W9 Q5T0W9 FAM83B Protein FAM83B 1 0 S(1)FNGTDNHIR;S(0.998)FNGT(0.002)DNHIR ; 105.95 0.0086668 7088300 396.2 469.13 719.29 585.04 637 342.53 442.36 336.75 726.24 617.24 TRUE FALSE FALSE 391.370962 475.7344245 731.8089407 652.6850775 604.491513 320.6434385 479.9340474 346.4933299 661.2832755 601.2040158 0.650978622 0.791302806 1.217238943 1.085629936 1.005468189 0.53333549 0.79828816 0.576332361 1.099931567 1 9.231710836 -8.261462527 25 0.886744356 0.652215619 0.363342595 0.180852334 2.526418171 2730262.856 0.029545245 0.070330944 5.48E-09 8.261462527 -0.234528737 S(ph)FQDYTGQK ddPTM_HeLa_Romidepsin_16h_R1 3 SFQDYTGQK 9 0 A0A087WXU5;A0A087WYV3;A0A0D9SEW3;A0A087WXF8;Q9NP64-2;Q9NP64-3;Q9NP64 A0A087WXU5 ZCCHC17 Nucleolar protein of 40 kDa 1 0 S(0.992)FQDYT(0.008)GQK;S(1)FQDYTGQK;S(0.996)FQDYT(0.003)GQK ;; 134.18 0.0069243 24762700 5495.5 4238.81 4694.9 4196.57 7332.7 9677.6 8997.1 9131.2 5225.7 4693.27 TRUE FALSE FALSE 5428.518732 4298.484078 4776.612765 4681.797169 6958.484957 9059.232593 9761.313449 9395.396865 4758.300304 4571.338169 1.187511956 0.940311987 1.044904706 1.024163384 1.522198687 1.98174632 2.135329544 2.055283709 1.040898776 1 12.15840083 -8.440112899 2.188117963 1.069386711 2.091755384 0.974656581 0.073571602 0.041279251 0.385389497 0.013565719 0.035622173 3.63E-09 8.440112899 1.022368673 up S(ph)FQY(ph)S(ph)VQIEK ddPTM_HeLa_Romidepsin_16h_R1 1 SFQYSVQIEK 10 0 Q9UPM8-2;Q9UPM8 Q9UPM8-2 AP4E1 AP-4 complex subunit epsilon-1 3 0 S(1)FQY(1)S(1)VQIEK 66.682 0.0032609 0 880.67 202.76 538.72 0 581.24 465.97 541.55 580.9 646.76 520.23 TRUE FALSE FALSE 869.9360553 205.6144606 548.0961956 0 551.5771539 436.1960208 587.5492435 597.707425 588.9121658 506.7143496 1.716817485 0.405779826 1.08166701 0 1.088536676 0.860832185 1.15952754 1.179574696 1.162217265 1 8.985028875 -10.26440713 24.99712349 1.338497139 0.827627589 0.229846153 0.389800059 281.0575824 2367323.617 0.071984697 0.084206759 5.44E-11 10.26440713 -0.51086955 S(ph)FS(ph)EDKSK ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEDKSK 8 1 F5GYN0;A6NE01 F5GYN0 FAM186A Protein FAM186A 2 0 S(0.999)FS(0.985)EDKS(0.016)K 77.533 0.0040727 0 1760.1 1442.5 1648.2 1632.3 1333.6 1001.4 1244 863.78 1921.3 1826.4 TRUE FALSE FALSE 1738.647224 1462.807553 1676.88623 1821.034206 1265.541416 937.4137719 1349.665329 888.7721115 1749.454116 1778.949865 0.977344701 0.822287115 0.942627031 1.023656845 0.711398022 0.526947831 0.758686546 0.499604924 0.983419573 1 10.79681014 -8.640498082 4.254671778 0.973229106 0.612252502 0.796873233 0.083622851 0.066340853 2.13867927 0.011711637 0.024089701 2.29E-09 8.640498082 -0.360976604 S(ph)FS(ph)NT(ph)QNS(ph)RK ddPTM_HeLa_Romidepsin_16h_R1 1 SFSNTQNSRK 10 1 F8VV00;A0A087X203;A0A087WY58;P51956-2;P51956 F8VV00 NEK3 Serine/threonine-protein kinase Nek3 4 0 S(1)FS(1)NT(1)QNS(1)RK 49.423 0.0043448 0 397.91 406.4 283.96 290.47 505.33 477.66 460.62 422.05 524.62 412.81 TRUE FALSE FALSE 393.0601199 412.1213099 288.9022047 324.0555081 479.5411245 447.1390676 499.7450513 434.2613509 477.6966733 402.0851367 0.977554463 1.024960319 0.718510033 0.805937545 1.19263579 1.112050725 1.242883672 1.080023386 1.188048574 1 8.651357197 -8.737815103 24.99964187 0.958076535 1.159836872 0.389726527 0.125164791 168.2830274 178079.3656 0.015825707 0.031637159 1.83E-09 8.737815103 0.201760337 S(ph)FSEDVISHK ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEDVISHK 10 0 F6QMI7;E9PHM6;F8W9J4;Q03001-14;Q03001;Q03001-8;H0YC82;Q03001-10;A0A494C1D7 F6QMI7;A0A494C1D7 DST Dystonin 1 0 S(0.576)FS(0.424)EDVISHK 113.77 0.0065911 11016000 7340 7631.7 7098.3 6249.8 7427 8403.6 6776.3 7981.7 8172.9 7721.3 TRUE FALSE FALSE 7250.537257 7739.139273 7221.842934 6972.431282 7047.972476 7866.637081 7351.878753 8212.637896 7441.895355 7520.699513 0.96407751 1.029045139 0.96026213 0.927098772 0.937143209 1.045998057 0.977552519 1.092004525 0.989521698 1 12.87665114 S(ph)FSGNPR ddPTM_HeLa_Romidepsin_16h_R1 2 SFSGNPR 7 0 Q9NQS3-3 Q9NQS3-3 1 0 S(0.993)FS(0.007)GNPR;S(0.993)FS(0.007)GNPR ; 109.48 0.029596 74922000 8151.3 6305.9 10986.6 5830.7 9885.6 13137.6 15801.6 3288.4 8060.3 7308.1 TRUE FALSE FALSE 8051.94882 6394.674626 11177.81716 6504.872968 9381.100944 12298.14976 17143.78751 3383.544666 7339.366581 7118.234508 1.131172176 0.898351216 1.570307518 0.91383235 1.317897146 1.727696628 2.408432525 0.475334813 1.031065578 1 12.79730375 -8.488372766 4.440780499 1.083064256 1.617372482 0.14489837 0.475004372 0.233339212 10.56803889 0.061675691 0.137546915 3.25E-09 8.488372766 0.534308226 S(ph)FSPLQPGQAPTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSPLQPGQAPTGR 14 0 Q7Z3C6;H7C152;Q7Z3C6-2;H7C1G6 Q7Z3C6 ATG9A Autophagy-related protein 9A 1 0 S(0.976)FS(0.023)PLQPGQAPT(0.001)GR 102.72 0.0089702 37364000 742.59 783.16 737.09 662.19 660.34 778.68 719.23 895.85 792.2 687.44 TRUE FALSE FALSE 733.5390275 794.185347 749.9187423 738.7555235 626.6403857 728.9248611 780.3213782 921.7700063 721.3436479 669.5802097 1.095520771 1.186094415 1.119983433 1.103311467 0.93587053 1.088629638 1.165388951 1.376638666 1.0773073 1 9.387113078 -7.317051724 2.001693147 1.059893681 1.446337721 0.657326911 0.065190075 0.317844395 1.481353528 0.010458514 0.214412143 4.82E-08 7.317051724 0.386444041 S(ph)FSSPENFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSSPENFQR 10 0 G3V1T9;I3L521;F5GXV8;F5GY08;J3KPD3;Q9Y580 G3V1T9 RBM7 RNA-binding protein 7 1 0 S(0.333)FS(0.333)S(0.333)PENFQR 192.44 4.93E-08 13196000 3022.7 2798.5 3080.4 2176.3 3545.9 3419.6 3002.6 3088.8 3016.3 3176.8 TRUE FALSE FALSE 2985.85817 2837.897356 3134.01307 2427.934046 3364.939491 3201.098596 3257.640769 3178.169555 2746.514574 3094.266278 0.964964842 0.917147104 1.012845304 0.784655821 1.087475734 1.034525897 1.052799105 1.027115726 0.887614163 1 11.59538164 S(ph)FTGGLGQLVVPSK ddPTM_HeLa_Romidepsin_16h_R1 1 SFTGGLGQLVVPSK 14 0 Q9Y3Q8 Q9Y3Q8 TSC22D4 TSC22 domain family protein 4 1 0 S(0.788)FT(0.212)GGLGQLVVPSK 94.007 0.015512 37687000 2758.5 3844.5 3252.6 3147.9 3419.2 2030.5 1336.9 1607.1 3098.5 3168.2 TRUE FALSE FALSE 2724.878341 3898.622972 3309.210139 3511.875009 3244.705465 1900.757603 1450.456253 1653.598903 2821.3624 3085.889707 0.883012226 1.263370808 1.072368248 1.138042945 1.051465144 0.615951244 0.470028546 0.53585807 0.914278431 1 11.59147078 -8.162991999 4.073502964 0.998902813 0.512076369 0.81100428 0.110810614 0.088428109 2.597869441 0.018216286 0.049281878 6.87E-09 8.162991999 -0.486826444 S(ph)FTLDDESLK ddPTM_HeLa_Romidepsin_16h_R1 2 SFTLDDESLK 10 0 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 0 S(0.983)FT(0.015)LDDES(0.002)LK;S(0.896)FT(0.083)LDDES(0.021)LK ; 151.1 0.0036753 17603800 3586.3 3568 3744.8 2911.9 3515.7 3620 2701.4 3269.6 3595.9 3393.1 TRUE FALSE FALSE 3542.588796 3618.230398 3809.976673 3248.587579 3336.28071 3388.693683 2930.856849 3364.200717 3274.273698 3304.946773 1.071904947 1.094792336 1.152810298 0.982947019 1.00948092 1.025339867 0.886809093 1.017928865 0.990719041 1 11.69041132 -7.926691165 8.524144448 1.042232618 0.952454356 0.277068176 0.057875397 0.265455656 27.69810679 0.008186267 0.024697286 1.18E-08 7.926691165 -0.089778262 S(ph)FTPDHVVYAR ddPTM_HeLa_Romidepsin_16h_R1 3 SFTPDHVVYAR 11 0 Q6NZI2-3;Q6NZI2-2;Q6NZI2 Q6NZI2-3 PTRF Polymerase I and transcript release factor 1 0 S(0.996)FT(0.004)PDHVVYAR;S(0.933)FT(0.067)PDHVVYAR;S(0.95)FT(0.05)PDHVVYAR ;; 178.53 1.21E-05 47706000 5189.9 4947.9 4881.4 4973.4 6230.1 7535 5655.17 7095.3 5684.2 5118.8 TRUE FALSE FALSE 5126.643503 5017.556666 4966.358719 5548.447909 5912.154749 7053.537818 6135.519999 7300.591311 5175.790916 4985.812838 1.02824628 1.006366831 0.996098105 1.11284721 1.185795565 1.414721741 1.230595732 1.464273038 1.038103732 1 12.28361301 -8.636345459 1.563811723 1.011747751 1.364230053 0.862466534 0.061175439 0.086334669 0.421312523 0.008212891 0.021680602 2.31E-09 8.636345459 0.352482302 S(ph)FVDAEVDVTR ddPTM_HeLa_Romidepsin_16h_R1 2 SFVDAEVDVTR 11 0 A0A2R8YHB3;A0A1B0GUB2;A0A3B3IRP5;Q6P1J9 A0A2R8YHB3 CDC73 Parafibromin 1 0 S(1)FVDAEVDVTR;S(1)FVDAEVDVTR ; 187.62 1.93E-08 15413100 2049.46 2204.78 1982.48 1593.17 1746.33 1811.26 1749.76 1731.7 1830.88 2443.27 TRUE FALSE FALSE 2024.480393 2235.818951 2016.984233 1777.379811 1657.208264 1695.526332 1898.384571 1781.804007 1667.121507 2379.793493 0.850695827 0.939501245 0.847545906 0.746863044 0.696366415 0.712467841 0.797709791 0.748722111 0.700532005 1 11.21662067 -10.5420883 0.278344515 1.029059538 0.699135825 0 0.103242425 0.635786069 0.173568842 0.080175383 0.070413544 2.87E-11 10.5420883 -0.329923712 S(ph)FVLNLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SFVLNLGK 8 0 P09382 P09382 LGALS1 Galectin-1 1 0 S(1)FVLNLGK 105.98 0.025985 6851800 2650.5 2003.6 2501.2 2090.9 2870.6 2206.3 2309.9 1728.8 2200.3 1990.9 TRUE FALSE FALSE 2618.194687 2031.806733 2544.732337 2332.659696 2724.10257 2065.324551 2506.102848 1778.8201 2003.499657 1939.176131 1.350158268 1.047768019 1.312274989 1.202912752 1.404773154 1.065052585 1.292354422 0.917307135 1.033170544 1 10.92122813 -4.006398305 4.935902797 1.177426793 0.00365301 0 0.16215924 0 0 0.022141732 0 9.85E-05 4.006398305 -1.173773783 S(ph)GAEVEAGDAAER ddPTM_HeLa_Romidepsin_16h_R1 1 SGAEVEAGDAAER 13 0 A0A087WZ13;E9PAU2;Q8IY67-2;Q8IY67;Q8IY67-3;K7EKR9 A0A087WZ13 RAVER1 Ribonucleoprotein PTB-binding 1 1 0 S(1)GAEVEAGDAAER 137.93 0.0013621 7164900 1210.4 1652.8 1510.9 1208.6 1747.9 1683.3 2003.6 2140.7 1947.4 1906.7 TRUE FALSE FALSE 1195.647179 1676.068162 1537.196581 1348.344019 1658.698141 1575.742563 2173.785734 2202.637777 1773.219667 1857.163659 0.643802808 0.902488132 0.827711965 0.726023262 0.893135149 0.848467261 1.1704869 1.186022441 0.954799895 1 10.85888524 -7.764422501 5.274438056 0.830188196 1.184279665 0.632003624 0.099582119 0.095374433 7.852668958 0.018570295 0.065024618 1.72E-08 7.764422501 0.354091468 S(ph)GAQASSTPLSPTR ddPTM_HeLa_Romidepsin_16h_R1 2 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 S(0.644)GAQAS(0.02)S(0.164)T(0.095)PLS(0.067)PT(0.009)R;S(0.594)GAQAS(0.035)S(0.255)T(0.114)PLS(0.002)PTR ; 159.41 0.00037638 102737000 8954.6 9451.5 7979.7 7907.7 8720.7 8128 6572.3 7245.3 9421.3 8241.9 TRUE FALSE FALSE 8845.457891 9584.558465 8118.583331 8822.025481 8275.650138 7608.647032 7130.550998 7454.931324 8578.635332 8027.77425 1.10185683 1.193924763 1.011311863 1.098937913 1.030877287 0.947790358 0.888235117 0.928642372 1.068619404 1 12.97078433 -8.232827101 2.632088367 1.061611588 0.909461619 0.633703098 0.052959368 0.170707553 2.318807689 0.008951488 0.025643765 5.85E-09 8.232827101 -0.152149969 S(ph)GASEANLIVAK ddPTM_HeLa_Romidepsin_16h_R1 1 SGASEANLIVAK 12 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 S(0.97)GAS(0.03)EANLIVAK 119.77 0.0075892 9431000 2430.8 1773.1 2016.8 1343.9 1458.2 1328.4 1578.8 1792.3 1909.1 2065.1 TRUE FALSE FALSE 2401.172475 1798.061748 2051.901558 1499.288041 1383.782613 1243.519527 1712.903233 1844.157373 1738.345315 2011.448404 1.193752954 0.89391393 1.020111455 0.74537733 0.687953322 0.618220942 0.851577017 0.916830563 0.864225655 1 10.97401902 -9.520860871 1.659533939 1.085154587 0.755823169 0.370265056 0.127613944 0.184044008 1.013703596 0.020271164 0.032740401 3.01E-10 9.520860871 -0.329331418 S(ph)GDETPGSEVPGDK ddPTM_HeLa_Romidepsin_16h_R1 2 SGDETPGSEVPGDK 14 0 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(1)GDETPGSEVPGDK;S(0.995)GDET(0.005)PGSEVPGDK ; 192.54 3.50E-11 481220000 13963.3 13924.4 15578.4 5258.5 13719.3 16449.1 13382.3 15751.8 12956.2 14793 TRUE FALSE FALSE 13793.10993 14120.42807 15849.53552 5866.512512 13019.15293 15398.0556 14518.99223 16207.55348 11797.36502 14408.67573 0.957278114 0.979994854 1.09999946 0.407151401 0.903563462 1.068665566 1.007656255 1.124846848 0.818768168 1 13.81465013 S(ph)GDGAT(ph)EQT(ph)GS(ph)GS(ph)VTQAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGDGATEQTGSGSVTQAR 18 0 E9PNK2 E9PNK2 CSTF3 5 0 S(1)GDGAT(1)EQT(1)GS(0.997)GS(0.812)VT(0.191)QAR 46.069 0.004324 0 577.97 1005 668.49 525.57 496.93 956.24 510.78 652.73 775.36 638.78 TRUE FALSE FALSE 570.9254793 1019.148416 680.124788 586.3388763 471.5698078 895.1393501 554.1656405 671.6157127 706.0098597 622.1844035 0.917614579 1.638016657 1.093124135 0.942387615 0.757926115 1.438704257 0.890677486 1.079448004 1.134727672 1 9.281198421 S(ph)GEQAEGSPGGPGDSQGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGEQAEGSPGGPGDSQGR 18 0 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 0 S(0.722)GEQAEGS(0.278)PGGPGDSQGR 216.88 4.60E-29 19457000 1404.3 1370.1 1421.6 2632.2 7455.7 7990.6 6787.3 7260.6 1028.1 1234.9 TRUE FALSE FALSE 1387.183851 1389.388304 1446.342352 2936.547349 7075.207808 7480.026448 7363.813093 7470.674006 936.1441611 1202.81712 1.153279105 1.155111846 1.202462392 2.44139138 5.88219746 6.218756222 6.122138578 6.210980773 0.778293014 1 10.23220159 -8.847377734 2.63558718 1.095703002 6.214060617 0.996100866 0.149798514 0.011177698 0.157781661 0.022710807 0.045453449 1.42E-09 8.847377734 5.118357614 up S(ph)GEQITSS(ph)PVSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGEQITSSPVSPK 13 0 A0A087WWN8;A0A087WZV0;O43314-2;O43314 A0A087WWN8 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 2 0 S(1)GEQIT(0.084)S(0.183)S(0.403)PVS(0.331)PK 138.91 0.01283 12096000 2564.9 2153.1 2352.3 1933 2017.8 2587.1 2057.8 2517.3 2642.2 2480.6 TRUE FALSE FALSE 2533.638012 2183.411398 2393.240795 2156.502555 1914.824137 2421.792659 2232.589481 2590.134104 2405.875014 2416.153654 1.048624539 0.903672411 0.990516804 0.892535353 0.792509257 1.002333877 0.924026283 1.072007196 0.995745867 1 11.23849649 -10.26408631 24.9980751 1.022961589 0.935950965 0.183387713 0.071740143 243.796648 2302454.858 0.011912311 0.013941875 5.44E-11 10.26408631 -0.087010623 S(ph)GEQITSSPVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SGEQITSSPVSPK 13 0 A0A087WWN8;A0A087WZV0;O43314-2;O43314 A0A087WWN8 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 2 0 S(1)GEQIT(0.017)S(0.033)S(0.056)PVS(0.895)PK 147.6 0.0078529 7255100 2745.9 2950.8 2852.7 2728.4 2763.2 3061.6 2446.3 3389.7 2818.3 3015.8 TRUE FALSE FALSE 2712.431915 2992.34144 2902.350047 3043.870446 2622.183593 2865.973641 2654.088661 3487.775621 2566.224189 2937.449081 0.923397084 1.018687084 0.988051185 1.036229178 0.892673718 0.975667513 0.903535206 1.187348453 0.873623378 1 11.52034813 -7.251161496 24.66499568 0.966283131 1.187348601 0.617511504 0.053961154 555.5104956 1333090.748 0.006437445 0.118368262 5.61E-08 7.251161496 0.22106547 S(ph)GEQITSSPVSPK ddPTM_HeLa_Romidepsin_16h_R1 4 SGEQITSSPVSPK 13 0 A0A087WWN8;A0A087WZV0;O43314-2;O43314 A0A087WWN8 PPIP5K2 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 1 0 S(0.999)GEQIT(0.001)SSPVSPK;S(0.994)GEQIT(0.004)S(0.001)SPVSPK;S(0.891)GEQIT(0.064)S(0.036)S(0.01)PVSPK;S(0.663)GEQIT(0.222)S(0.068)S(0.046)PVSPK ;;; 155.37 0.00071084 50013000 11556.8 10570.3 10752.5 9386.5 10633.7 12837.2 9906.3 13158.3 11573.6 11560 TRUE FALSE FALSE 11415.94128 10719.10896 10939.64275 10471.81129 10091.02261 12016.94435 10747.74087 13539.01465 10538.42823 11259.66953 1.013878892 0.951991435 0.971577604 0.930028298 0.896209483 1.06725551 0.954534309 1.20243446 0.935944718 1 13.45887687 -7.255597122 24.79857948 0.989694538 1.202434563 0.644893174 0.0498812 284.6147934 1208062.515 0.006610549 0.079669035 5.55E-08 7.255597122 0.212740025 S(ph)GGGAGSNGSVLDPAER ddPTM_HeLa_Romidepsin_16h_R1 2 SGGGAGSNGSVLDPAER 17 0 Q15149-3;Q15149-2;H0YDN1;E9PMV1 Q15149-3 PLEC Plectin 1 0 S(1)GGGAGSNGSVLDPAER;S(1)GGGAGSNGSVLDPAER ; 193.71 1.68E-13 55130000 1144.9 1203.24 1210.68 1437.16 1441.7 1957.03 1862.23 1721.24 1220.9 1196.6 TRUE FALSE FALSE 1130.945518 1220.179244 1231.751378 1603.331201 1368.124669 1831.982099 2020.40777 1771.041364 1111.699646 1165.512159 0.970342102 1.046903916 1.056832713 1.375645194 1.173839894 1.571825814 1.733493515 1.519539156 0.953829299 1 10.18674834 -8.630839379 0.803397867 0.983986535 1.681890934 0.859623293 0.101756075 0.173751497 0.196189173 0.016883818 0.071577547 2.34E-09 8.630839379 0.697904399 S(ph)GGGDLTLGLEPSEEEAPR ddPTM_HeLa_Romidepsin_16h_R1 2 SGGGDLTLGLEPSEEEAPR 19 0 B4DTR1;P04626-3;P04626-2;P04626-5;P04626-4;P04626 B4DTR1 ERBB2 Receptor protein-tyrosine kinase;Receptor tyrosine-protein kinase erbB-2 1 0 S(1)GGGDLTLGLEPSEEEAPR;S(1)GGGDLTLGLEPSEEEAPR ; 197.51 7.77E-16 25298000 2221.6 3452.2 2806 1908.97 1883.91 2860 1503.91 2517.6 2680.3 3344.4 TRUE FALSE FALSE 2194.522285 3500.800162 2854.837253 2129.694093 1787.767043 2677.25523 1631.652078 2590.442784 2440.567255 3257.512006 0.67368049 1.074685268 0.876385796 0.653779354 0.548813647 0.821871178 0.500889045 0.795221255 0.749212052 1 11.66955478 -9.260116932 24.9999999 0.864866986 0.657405399 0.361535774 0.139531558 118.2615296 2235646.273 0.023886251 0.038221052 5.49E-10 9.260116932 -0.207461587 S(ph)GGGSGGSGGQVSLK ddPTM_HeLa_Romidepsin_16h_R1 1 SGGGSGGSGGQVSLK 15 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 1 0 S(0.996)GGGS(0.004)GGSGGQVSLK 101.01 0.001942 0 1061.9 1196.7 1177.2 833.75 1181.7 1225.7 1086.3 1179.3 1099.5 1119.3 TRUE FALSE FALSE 1048.957154 1213.547174 1197.688672 930.1520979 1121.393439 1147.381726 1178.570295 1213.421185 1001.157966 1090.220425 0.962151443 1.113120931 1.098574788 0.853178015 1.028593314 1.052430958 1.081038539 1.113005368 0.918307843 1 10.09040414 -8.055476099 2.070013881 0.993369767 1.099007769 0.245802102 0.072774775 0.350259212 2.876603928 0.01016814 0.038236125 8.80E-09 8.055476099 0.105638002 S(ph)GGNEVSIEER ddPTM_HeLa_Romidepsin_16h_R1 1 SGGNEVSIEER 11 0 Q15061 Q15061 WDR43 WD repeat-containing protein 43 1 0 S(1)GGNEVSIEER 130.95 0.005178 22110000 1121.5 1241.9 944.85 1200.5 1279.2 1367.1 1121.2 1387.2 1101.4 1322.4 TRUE FALSE FALSE 1107.830727 1259.383501 961.2947179 1339.307459 1213.917651 1279.746722 1216.4347 1427.336443 1002.888025 1288.043857 0.860087737 0.977748928 0.746321418 1.039799577 0.942450557 0.993558344 0.944404721 1.108142735 0.778613259 1 10.330966 -4.000000552 0.814810257 0.929765139 47.4757836 0.274053304 0.091799913 543.1218543 1.66977526 0.012914603 46756.92184 1.00E-04 4.000000552 46.54601846 S(ph)GLNGSILAER ddPTM_HeLa_Romidepsin_16h_R1 1 SGLNGSILAER 11 0 Q96H22-5;Q96H22-4;Q96H22;Q96H22-3 Q96H22-5 CENPN Centromere protein N 1 0 S(0.984)GLNGS(0.016)ILAER 103.14 0.01773 9504100 1905.8 1881.1 1880.1 1314.4 1504.4 1469.3 1032.6 1176.4 1969.5 1621.1 TRUE FALSE FALSE 1882.571377 1907.582175 1912.822352 1466.377112 1427.624854 1375.416472 1120.309018 1210.437278 1793.342987 1578.983588 1.192267855 1.208107665 1.211426367 0.928684201 0.904141667 0.871077117 0.709512769 0.766592691 1.135757839 1 10.62478046 -8.670401396 1.392742152 1.110049028 0.763366264 0.799115358 0.079249346 0.185336055 0.713892666 0.016016748 0.043788992 2.14E-09 8.670401396 -0.346682764 S(ph)GMS(ph)KY(ph)FETS(ph)ALKEEATK ddPTM_HeLa_Romidepsin_16h_R1 1 SGMSKYFETSALKEEATK 18 2 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 4 0 S(0.993)GMS(0.993)KY(0.963)FET(0.203)S(0.846)ALKEEAT(0.002)K 48.899 0.024476 7628000 1835.4 1952 1797 1753.8 1829.3 1808.6 1432.7 1899.2 2074.7 2185.4 TRUE FALSE FALSE 1813.029439 1979.480307 1828.276031 1956.582608 1735.943995 1693.036297 1554.393502 1954.150356 1889.133636 2128.622993 0.851738164 0.929934664 0.858900819 0.919177616 0.815524403 0.795366912 0.730234291 0.918034975 0.887490947 1 11.05570474 -16.52287874 0.143587063 1.563712508 0.786161901 0.213291999 0.065207733 40.13800927 0.398081229 6.407258736 0.148617249 3.00E-17 16.52287874 -0.777550607 S(ph)GNSDSIER ddPTM_HeLa_Romidepsin_16h_R1 1 SGNSDSIER 9 0 A0A5F9ZI51;A0A5F9ZGW5;C9J8U3;A0A0A0MRW7;Q7Z2E3-13;Q7Z2E3-4;Q7Z2E3-5;Q7Z2E3-9;Q7Z2E3-10;Q7Z2E3-11;Q7Z2E3-8;Q7Z2E3-7;Q7Z2E3 A0A5F9ZI51 APTX Aprataxin 1 0 S(1)GNSDSIER 121.21 0.012791 15976000 2274 2157.6 3790.8 2222.5 1851.3 2679.7 4664.6 804.24 3109.6 2507.1 TRUE FALSE FALSE 2246.283613 2187.974749 3856.777284 2479.475907 1756.821253 2508.475818 5060.811008 827.5094155 2831.469588 2441.965181 0.919867176 0.895989331 1.579374397 1.015360877 0.71942928 1.027236522 2.07243373 0.338870276 1.159504489 1 11.25382691 S(ph)GPGPPELDSEQPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGPGPPELDSEQPSR 15 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 S(1)GPGPPELDSEQPSR 88.311 0.017561 3729400 713.58 648.61 565.25 569.56 533.4 521.08 481.39 541.64 529.54 574.4 TRUE FALSE FALSE 704.8826125 657.7411486 575.0879391 635.4152071 506.1786076 487.7846697 522.2792546 557.3114988 482.1766161 559.4770052 1.259895592 1.175635714 1.027902727 1.135730693 0.904735321 0.871858298 0.933513352 0.99612941 0.861834556 1 9.127935027 -8.762412669 24.97190093 1.122905561 0.923148605 0.252809697 0.110636337 17.85295962 458076.3179 0.015550508 0.029404133 1.73E-09 8.762412669 -0.199756956 S(ph)GPLEESER ddPTM_HeLa_Romidepsin_16h_R1 1 SGPLEESER 9 0 A0A2R8Y4Z8;Q9Y3X0 A0A2R8Y4Z8;Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 0 S(1)GPLEESER 99.343 0.028937 14596000 338.04 410.95 385.48 80.077 351.9 409.24 498.77 421.67 414.77 301.55 TRUE FALSE FALSE 333.9198385 416.7353649 392.1891177 89.33587951 333.9412299 383.0908848 541.1355114 433.8703562 377.6719324 293.7156875 1.136881184 1.418839315 1.335267861 0.304157671 1.136954014 1.304291534 1.842378648 1.477178015 1.285841882 1 8.198276513 -7.997717128 3.416746543 1.06164131 1.657258066 0.354731614 0.302547577 0.173116338 4.258644233 0.041233361 0.131123346 1.01E-08 7.997717128 0.595616757 S(ph)GPTDDGEEEMEEDTVTNGS ddPTM_HeLa_Romidepsin_16h_R1 1 SGPTDDGEEEMEEDTVTNGS 20 0 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 1 0 S(0.994)GPT(0.006)DDGEEEMEEDTVTNGS 80.508 0.0061372 5345700 571.04 615.05 720.66 708.23 923.62 885.42 805.43 859.82 821.81 949.48 TRUE FALSE FALSE 564.0799448 623.70869 733.202785 790.1188849 876.4842249 828.8445196 873.8432041 884.6975351 748.3052553 924.8123727 0.609939877 0.674416464 0.792812474 0.854355876 0.947742754 0.896229921 0.944887017 0.95662381 0.809142781 1 9.853016889 -8.95995866 3.141068136 0.797044385 0.934217357 0.3656408 0.096881587 0.385629086 7.831541416 0.023348453 0.043620083 1.10E-09 8.95995866 0.137172972 S(ph)GRSPTGNTPPVIDSVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGRSPTGNTPPVIDSVSEK 19 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 S(0.82)GRS(0.132)PT(0.041)GNT(0.006)PPVIDSVSEK 98.002 0.00064908 16756000 1765.4 1833.5 1620.3 2228.8 2487.2 2014.8 1913.1 2016 1963.7 1760.9 TRUE FALSE FALSE 1743.882626 1859.312061 1648.500642 2486.504343 2360.268903 1886.060782 2075.598666 2074.329779 1788.061754 1715.151564 1.016751325 1.084051171 0.961139923 1.449728639 1.376128473 1.099646715 1.210154665 1.209414854 1.042509473 1 10.74412035 -9.282726234 24.99835489 1.011844273 1.262286117 0.632787676 0.094312744 393.1572402 461705.5267 0.014741323 0.022530513 5.22E-10 9.282726234 0.250441843 S(ph)GS(ph)RLIFGTLYPAY(ph)Y(ph)SYK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSRLIFGTLYPAYYSYK 18 1 Q9H902-3 Q9H902-3 4 0 S(0.998)GS(0.998)RLIFGT(0.033)LY(0.448)PAY(0.565)Y(0.565)S(0.252)Y(0.14)K 44.998 0.0043168 0 425 457.63 389.52 390.49 626.4 540.57 356.08 512.55 548.9 448.79 TRUE FALSE FALSE 419.8199365 464.0725272 396.2994322 435.6402911 594.4324706 506.0293216 386.3254263 527.3798256 499.8050093 437.1303711 0.960399836 1.061634144 0.906593223 0.996591223 1.359851682 1.15761648 0.883776218 1.206458897 1.143377451 1 8.771919807 -8.960842975 24.99970833 0.981667172 1.138809185 0.208587448 0.125618955 147.8026194 94363.69141 0.01644541 0.029809808 1.09E-09 8.960842975 0.157142013 S(ph)GSCHRT(ph)SLTVS(ph)SAT(ph)RLCNSRLK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSCHRTSLTVSSATRLCNSRLK 23 3 B1AL88 B1AL88 FAM155A Transmembrane protein FAM155A 4 0 S(0.529)GS(0.529)CHRT(0.546)S(0.27)LT(0.256)VS(0.452)S(0.452)AT(0.96)RLCNS(0.006)RLK 47.75 0.0042399 0 441.47 512.65 263.87 541.76 330.6 341.52 347.07 315.05 528.31 525.87 TRUE FALSE FALSE 436.0891938 519.8671002 268.4625467 604.4008403 313.7282484 319.6979742 376.5501171 324.1654747 481.0566304 512.2078216 0.851391126 1.014953459 0.524128167 1.179991431 0.61250187 0.62415676 0.735151049 0.632878806 0.939182516 1 9.000585473 -5.716038026 0.141543867 1.058567595 5.80E-14 0.284951431 0.174453258 39.44196336 0.584171868 0.492826491 7.954914991 1.92E-06 5.716038026 -1.058567595 S(ph)GSESEEAELSLSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSESEEAELSLSLAR 16 0 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 0 S(0.993)GS(0.007)ESEEAELSLSLAR 174.47 3.64E-06 1404800 335.94 322.31 370.85 500.06 449.59 304.85 340.89 282.13 415.63 279.59 TRUE FALSE FALSE 331.8454341 326.8474886 377.3044887 557.8792901 426.6457446 285.3710689 369.8451881 290.2929864 378.4550118 272.3262115 1.218558552 1.200205764 1.385487231 2.048569937 1.566671612 1.047901586 1.358096182 1.065975195 1.389712029 1 8.089192039 -10.59624612 1.020197506 1.060657775 1.410635876 0.045563058 0.287697097 0.530652256 1.136405894 0.068185658 0.068250291 2.53E-11 10.59624612 0.349978101 S(ph)GSPISSEERR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPISSEERR 11 1 H8Y6P7;P0CAP2-3;P0CAP2;P0CAP1-11;P0CAP2-2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 0 S(0.496)GS(0.496)PIS(0.007)S(0.001)EERR 65.809 0.026122 3917400 1619 1653.1 1418.4 1572.4 1532.2 1654.6 1019.1 1257.4 1660.9 1480.7 TRUE FALSE FALSE 1599.267005 1676.372385 1443.086657 1754.208286 1454.006117 1548.8764 1105.662329 1293.780885 1512.344944 1442.231201 1.108883933 1.162346498 1.000593148 1.216315585 1.008164375 1.073944593 0.766633206 0.897068989 1.048614774 1 10.49408674 -7.77019032 24.99572667 1.066632568 0.831851092 0.636896313 0.073794209 79.94706142 228359.2139 0.010476696 0.032132774 1.70E-08 7.77019032 -0.234781476 S(ph)GSSS(ph)PDSEITELK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSSSPDSEITELK 14 0 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 2 0 S(0.872)GS(0.127)S(0.005)S(0.99)PDS(0.005)EITELK 177.93 4.23E-06 9213900 3172.1 3050.3 3611.6 1360.5 2350.1 2569.8 1871 2496.6 2956.7 3582.9 TRUE FALSE FALSE 3133.437225 3093.242203 3674.458383 1517.807411 2230.165628 2405.598074 2029.922693 2568.835182 2692.245347 3489.815741 0.89788042 0.886362614 1.052908994 0.434924799 0.639049678 0.689319509 0.58167045 0.736094789 0.771457735 1 11.76893515 -9.270352489 24.99050847 0.951500571 0.619623182 0.682371728 0.103210425 213.3935704 598310.4205 0.013166565 0.020293726 5.37E-10 9.270352489 -0.331877389 S(ph)GSSSSSSGTPASQLYPQSR ddPTM_HeLa_Romidepsin_16h_R1 2 SGSSSSSSGTPASQLYPQSR 20 0 O15066-2;O15066 O15066-2 KIF3B "Kinesin-like protein KIF3B;Kinesin-like protein KIF3B, N-terminally processed" 1 0 S(0.949)GS(0.051)S(0.001)SSSSGTPASQLYPQSR;S(0.964)GS(0.014)S(0.014)S(0.006)S(0.001)SSGTPASQLYPQSR ; 206.45 2.39E-24 12162900 3138.8 2924.3 3133.1 3260 3668.4 3924.3 3598.2 3561.8 3520 2621.1 TRUE FALSE FALSE 3100.543098 2965.468372 3187.630291 3636.936539 3481.187859 3673.549895 3903.831018 3664.855063 3205.162384 2553.003444 1.214468827 1.161560663 1.24858049 1.424571732 1.363565673 1.43891302 1.529113103 1.435507293 1.255447732 1 11.31797977 -9.294437821 0.199885406 0.916860373 1.712474831 0.636335178 0.091517312 1.009617963 0.101537499 0.111175216 0.254380591 5.08E-10 9.294437821 0.795614459 S(ph)GTNSPPPPFSDWGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTNSPPPPFSDWGR 15 0 D6RAU6;D6REP2;D6RAJ6;Q9UKT5-2;Q9UKT5 D6RAU6 FBXO4 F-box only protein 4 1 0 S(0.799)GT(0.045)NS(0.155)PPPPFSDWGR 217.79 4.39E-26 40535000 6405.8 6325.8 6294.8 5743.1 5727.1 5302.1 4533.3 4356.5 6607.9 6296.4 TRUE FALSE FALSE 6327.723646 6414.854778 6404.358353 6407.144244 5434.824716 4963.312922 4918.358389 4482.548454 6016.872874 6132.81862 1.03178066 1.045988016 1.044276498 1.044730758 0.886187095 0.80930372 0.801973561 0.73091163 0.981094216 1 12.58233457 -8.488849528 2.177933021 1.022517538 0.776810019 0.935236219 0.028957721 0.052822385 0.493401641 0.004222869 0.010749955 3.24E-09 8.488849528 -0.245707519 S(ph)GTPPRQGSITSPQANEQSVTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.452)GT(0.086)PPRQGS(0.452)IT(0.007)S(0.002)PQANEQSVTPQR 52.321 0.010658 9979200 643.35 548.85 612.61 787.62 460.47 474.19 583.34 510.26 851.98 788.24 TRUE FALSE FALSE 635.5086027 556.5767247 623.2722201 878.6883303 436.9704976 443.8907894 632.888885 525.023568 775.776775 767.7614112 0.827742308 0.724934487 0.811804567 1.144480977 0.569148815 0.578162412 0.824330158 0.68383688 1.010439915 1 9.58451424 -16.52287708 0.058434047 1.956319786 0.349161562 0.32868267 0.147259645 294.4206424 1.352712997 41.23622161 8.093874073 3.00E-17 16.52287708 -1.607158225 S(ph)GYLLPDTK ddPTM_HeLa_Romidepsin_16h_R1 1 SGYLLPDTK 9 0 P14625;H0YIV0 P14625 HSP90B1 Endoplasmin 1 0 S(1)GYLLPDTK 102.05 0.026474 3659200 2648.1 3018.2 3021 2178.3 2519.3 3058.6 2796.2 3433.8 3818.3 2852 TRUE FALSE FALSE 2615.823939 3060.690299 3073.579238 2430.165295 2390.73072 2863.165331 3033.709158 3533.151585 3476.781685 2777.904629 0.941653616 1.101798192 1.106437999 0.874819556 0.860623758 1.030692451 1.092085425 1.271876489 1.251584251 1 11.43978135 -7.382396217 1.866971774 0.978182482 1.321008921 0.247097579 0.11595026 0.363888008 1.564578935 0.011585808 0.198333091 4.15E-08 7.382396217 0.342826439 S(ph)HEAEVLK ddPTM_HeLa_Romidepsin_16h_R1 2 SHEAEVLK 8 0 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 S(1)HEAEVLK;S(1)HEAEVLK ; 123.51 0.0069469 25987000 19701.7 16509.7 16446.1 11845.9 21998 26910 26721 10846.9 20813 16428.1 TRUE FALSE FALSE 19461.5681 16742.12399 16732.33747 13215.57869 20875.35997 25190.53785 28990.68107 11160.73794 18951.43315 16001.29559 1.216249521 1.046298026 1.045686418 0.825906791 1.304604359 1.574281139 1.81177086 0.697489642 1.184368668 1 13.9659011 -8.536669043 23.66647144 1.077373156 1.411773473 0.199138861 0.282583506 126.5966517 217260.4309 0.038321918 0.076683598 2.91E-09 8.536669043 0.334400317 S(ph)HLDSPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 SHLDSPEAR 9 0 K7ER08;K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8 K7ER08 RBM42 RNA-binding protein 42 1 0 S(0.999)HLDS(0.001)PEAR 133.57 0.0029236 6815200 1493 1415.3 1470.7 1182.2 2023.6 2674.3 3521.9 1321.9 1945.2 1538.7 TRUE FALSE FALSE 1474.802742 1435.224631 1496.296917 1318.891526 1920.328141 2503.420861 3821.050098 1360.147091 1771.21644 1498.724352 0.984038686 0.95763082 0.998380332 0.880009406 1.281308426 1.670367775 2.549534938 0.907536525 1.181816014 1 10.54951935 -8.384275371 2.869032676 0.984561766 1.801379093 0.407537383 0.37759509 0.155572136 2.450093684 0.047614134 0.119056041 4.13E-09 8.384275371 0.816817326 S(ph)HSAPSEVGFSDAR ddPTM_HeLa_Romidepsin_16h_R1 1 SHSAPSEVGFSDAR 14 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 S(0.732)HS(0.261)APS(0.007)EVGFSDAR 152 0.00061551 5657800 2152.9 1826.9 2543 1932.3 2246.4 2667.4 3087.1 1583 2797.6 2342.3 TRUE FALSE FALSE 2126.659627 1852.619146 2587.259848 2155.721618 2131.757826 2496.961749 3349.318197 1628.801607 2547.375649 2281.446708 0.932153979 0.812037002 1.134043517 0.944892383 0.934388613 1.094464201 1.468067689 0.713933664 1.11656154 1 11.15573324 -8.173812474 5.57523397 0.964471752 1.133829388 0.049150114 0.191680891 0.313686192 15.57888062 0.023222852 0.060479404 6.70E-09 8.173812474 0.169357636 S(ph)HSPSIDGTPK ddPTM_HeLa_Romidepsin_16h_R1 2 SHSPSIDGTPK 11 0 A0A0C4DH56;Q9BWT3-2;Q9BWT3 A0A0C4DH56 PAPOLG Poly(A) polymerase gamma 1 0 S(0.592)HS(0.406)PS(0.001)IDGTPK;S(0.689)HS(0.31)PS(0.001)IDGTPK ; 94.547 0.011325 14149700 10230 9755.6 9170.8 8499.4 10327.9 11324.6 8509.4 9829.5 11543 10770.4 TRUE FALSE FALSE 10105.31283 9892.939593 9330.413927 9482.140619 9800.828724 10600.99461 9232.188224 10113.90107 10510.56517 10490.58346 0.963274623 0.943030446 0.889408484 0.903871616 0.934250108 1.010524787 0.880045258 0.964093286 1.001904729 1 13.3568073 -10.78714211 1.095854862 0.990821343 0.930818203 0.351835467 0.036195282 0.358239103 0.902265832 0.008729449 0.007972421 1.63E-11 10.78714211 -0.06000314 S(ph)HTSEGAHLDITPNSGAAGNSAGPK ddPTM_HeLa_Romidepsin_16h_R1 2 SHTSEGAHLDITPNSGAAGNSAGPK 25 0 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 1 0 S(0.331)HT(0.331)S(0.331)EGAHLDIT(0.005)PNSGAAGNSAGPK;S(0.561)HT(0.218)S(0.218)EGAHLDIT(0.002)PNSGAAGNSAGPK ; 53.525 0.0061445 15408000 4267.7 3911.4 3785.4 2702.4 5970.7 5706.9 4919.8 5210.1 5902.8 5223 TRUE FALSE FALSE 4215.683631 3966.464792 3851.283299 3014.864203 5665.992899 5342.247508 5337.687689 5360.846023 5374.838784 5087.305707 0.82866725 0.779678875 0.757037914 0.592624933 1.113751212 1.050113324 1.049217011 1.053769192 1.056519717 1 12.31268608 S(ph)HWDDSTSDS(ph)ELEK ddPTM_HeLa_Romidepsin_16h_R1 1 SHWDDSTSDSELEK 14 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 2 0 S(0.995)HWDDS(0.005)T(0.008)S(0.006)DS(0.986)ELEK 146.27 0.0063165 4910800 1347.6 1299.8 955.81 1214.4 1764.5 2142.2 2174.1 2180.5 1477.3 1228.3 TRUE FALSE FALSE 1331.174933 1318.098619 972.4454721 1354.814642 1674.450981 2005.320334 2358.768 2243.589327 1345.166588 1196.388589 1.112661008 1.101731186 0.812817408 1.132420231 1.39958789 1.676144651 1.971573468 1.87530151 1.124355916 1 10.22447034 -8.357112036 1.564231036 1.040380719 1.927627529 0.93498874 0.095054159 0.067870933 0.314979534 0.014529902 0.048325466 4.39E-09 8.357112036 0.88724681 S(ph)IDDEDVDENEDDVYGNSSGRK ddPTM_HeLa_Romidepsin_16h_R1 1 SIDDEDVDENEDDVYGNSSGRK 22 1 Q8IUI4;Q8TEQ0-2;Q8TEQ0 Q8IUI4 SNX29P2;SNX29 Putative protein SNX29P2;Sorting nexin-29 1 0 S(0.988)IDDEDVDENEDDVY(0.002)GNS(0.005)S(0.005)GRK 89.392 0.0001924 3230200 685.41 758.93 788.21 791.02 712 829.28 623.6 680.35 945.56 926.74 TRUE FALSE FALSE 677.0559593 769.6142365 801.9284644 882.4814543 675.6639832 776.2916844 676.5685684 700.0348538 860.9867454 902.6631612 0.750064906 0.852604016 0.888402783 0.97764204 0.748522829 0.860001513 0.749524958 0.775521683 0.953829493 1 9.81804392 -12.47345391 1.171145677 1.001531725 0.821351572 0.416413153 0.07115889 0.363839393 0.880585889 0.053735496 0.012748194 3.36E-13 12.47345391 -0.180180153 S(ph)IDDLEEK ddPTM_HeLa_Romidepsin_16h_R1 4 SIDDLEEK 8 0 Q6ZN40;P09493-3;P09493-7;P09493-8;P09493-9;P09493-2;H7BYY1 Q6ZN40 TPM1 Tropomyosin alpha-1 chain 1 0 S(1)IDDLEEK;S(1)IDDLEEK;S(1)IDDLEEK;S(1)IDDLEEK ;;; 132.32 0.0095492 126166000 21858 19386.7 21354.4 17354.8 13318.8 13759.1 13220 13196.2 22067.3 20166 TRUE FALSE FALSE 21591.58629 19659.62647 21726.06437 19361.44363 12639.09194 12879.93792 14342.90647 13578.01123 20093.54542 19642.08441 1.099251273 1.000893085 1.106097699 0.985712271 0.643469994 0.655731726 0.730213055 0.691271402 1.022984374 1 14.26166042 -8.827529065 4.883745783 1.047495176 0.681666161 0.947241288 0.041235041 0.035591401 1.639076836 0.007063103 0.013201034 1.49E-09 8.827529065 -0.365829015 S(ph)IDDSEMESPVDDVFYPGTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SIDDSEMESPVDDVFYPGTGR 21 0 C9JWJ8;K7EN08;Q14938-6;Q14938-5;Q14938-3;Q14938-2;Q14938-4;Q14938 C9JWJ8 NFIX Nuclear factor 1;Nuclear factor 1 X-type 1 0 S(0.959)IDDS(0.041)EMESPVDDVFYPGTGR 68.158 0.0022377 1066900 154.34 223.52 243.89 283.46 287.52 243.85 257.55 268.36 326.07 254.42 TRUE FALSE FALSE 152.4588447 226.6667204 248.1348031 316.2349789 272.8467815 228.268772 279.4262906 276.1245732 296.9054825 247.8101317 0.615224421 0.914678988 1.001310162 1.276118037 1.101031583 0.921143823 1.127582188 1.114258611 1.198116802 1 7.953091363 -9.755759511 3.024825463 0.817270826 1.099518791 0.06279964 0.170263495 0.19677493 3.726170559 0.026799587 0.037541479 1.75E-10 9.755759511 0.282247965 S(ph)IDST(ph)KSRS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SIDSTKSRSR 10 2 Q8N2Y8 Q8N2Y8 RUSC2 Iporin 3 0 S(0.866)IDS(0.504)T(0.627)KS(0.003)RS(1)R 101.35 0.018292 23339000 0 204.21 0 0 0 0 0 125.17 0 0 TRUE FALSE FALSE 0 207.0848737 0 0 0 0 0 128.7915965 0 0 0 S(ph)IEDLHR ddPTM_HeLa_Romidepsin_16h_R1 3 SIEDLHR 7 0 Q96PY5;Q96PY5-3 Q96PY5 FMNL2 Formin-like protein 2 1 0 S(1)IEDLHR;S(1)IEDLHR;S(1)IEDLHR ;; 166.3 0.0022418 66630000 9053.3 9967.2 8307.7 9009.4 10754.3 12283.4 9246.1 10952.9 9444.5 9093.9 TRUE FALSE FALSE 8942.954897 10107.5185 8452.292034 10051.10922 10205.46794 11498.53038 10031.4635 11269.80488 8599.760266 8857.639167 1.009631881 1.141107502 0.954237565 1.134739069 1.15216569 1.298148431 1.132521128 1.27232603 0.970886272 1 13.11270651 -8.915197893 1.778123143 1.012906536 1.223289093 0.674513879 0.065369425 0.138050953 0.879359282 0.009181404 0.019351518 1.22E-09 8.915197893 0.210382557 S(ph)IEDLQPPSALSAPFTNSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 SIEDLQPPSALSAPFTNSLAR 21 0 F8W1F5;Q8IVF7-3;Q8IVF7 F8W1F5 FMNL3 Formin-like protein 3 1 0 S(0.995)IEDLQPPS(0.005)ALSAPFTNSLAR 123.43 0.0001479 5851600 2453.6 2589.7 2538.8 2759.9 2748.7 2746.9 2181.8 2403.7 3108.7 2525 TRUE FALSE FALSE 2423.694579 2626.157865 2582.986749 3079.012624 2608.423582 2571.381955 2367.122038 2473.247267 2830.650086 2459.400136 0.985482006 1.067804228 1.050250714 1.251936429 1.060593412 1.045532168 0.962479429 1.005630288 1.150951423 1 11.26409076 -10.25872788 23.80899208 0.99314428 1.065518163 0 0.086386416 162.6781142 1428436.493 0.012424478 0.014846061 5.51E-11 10.25872788 0.072373883 S(ph)IELEHFEER ddPTM_HeLa_Romidepsin_16h_R1 2 SIELEHFEER 10 0 G5E9L9;Q8N568-2;Q8N568;A0A0U1RR70;Q8N568-3 G5E9L9 DCLK2 Serine/threonine-protein kinase DCLK2 1 0 S(1)IELEHFEER;S(1)IELEHFEER ; 134.68 0.0024809 4216000 2547.6 2340.1 2388.5 2217.7 2522.3 2082.63 1745.72 1572.86 2779.1 2680 TRUE FALSE FALSE 2516.548871 2373.043989 2430.070841 2474.120909 2393.577619 1949.556664 1894.001413 1618.368223 2530.530336 2610.373214 0.964057116 0.909082263 0.930928508 0.947803515 0.91694843 0.746849782 0.725567288 0.6199758 0.969413233 1 11.35004037 -6.952228915 0.46608903 0.985924082 0.223246975 0.933791237 0.031257902 0.956185618 0.113849226 0.007163149 0.42613849 1.12E-07 6.952228915 -0.762677107 S(ph)IEVENDFLPVEK ddPTM_HeLa_Romidepsin_16h_R1 4 SIEVENDFLPVEK 13 0 Q5JPT2;Q96B97-2;Q96B97;Q5VSN0;Q5JPT1 Q5JPT2 SH3KBP1 SH3 domain-containing kinase-binding protein 1 1 0 S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK;S(1)IEVENDFLPVEK ;;; 204.52 1.83E-16 131206300 23115.6 22625.1 22590.7 25103.9 30186 28098.4 26008.5 26941 25162.5 23456.9 TRUE FALSE FALSE 22833.85818 22943.61675 22983.88166 28006.53104 28645.49578 26303.00292 28217.66134 27720.49533 22911.90298 22847.48636 0.999403515 1.004207482 1.005969816 1.2258036 1.253770123 1.151242746 1.235044455 1.213284249 1.002819418 1 14.47974783 -9.264063669 24.39763239 1.00054551 1.215416276 0.948824142 0.024772107 23.45103258 218021.2153 0.003543129 0.005570176 5.44E-10 9.264063669 0.214870766 S(ph)IFASPESVTGK ddPTM_HeLa_Romidepsin_16h_R1 1 SIFASPESVTGK 12 0 O75940 O75940 SMNDC1 Survival of motor neuron-related-splicing factor 30 1 0 S(0.987)IFAS(0.008)PES(0.005)VTGK 143.42 0.0015315 53479000 3778.8 3242.2 3455.5 2655.6 4360.9 5046.1 4635.9 4348.4 3946 3470.2 TRUE FALSE FALSE 3732.742532 3287.843777 3515.641528 2962.652967 4138.347 4723.670496 5029.67323 4474.214093 3593.059877 3380.043704 1.104347417 0.972722268 1.040117181 0.876513213 1.224347187 1.39751758 1.488049762 1.323714865 1.063021722 1 11.72282619 -8.482924174 3.644942807 1.032386318 1.407390698 0.85784437 0.071704512 0.065805346 1.802143701 0.010893321 0.024817567 3.29E-09 8.482924174 0.37500438 S(ph)IGSAVDQGNESIVAK ddPTM_HeLa_Romidepsin_16h_R1 4 SIGSAVDQGNESIVAK 16 0 Q9H0H5;F8VRD2;F8W1E5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 0 S(0.999)IGS(0.001)AVDQGNESIVAK;S(0.704)IGS(0.283)AVDQGNES(0.013)IVAK;S(1)IGSAVDQGNESIVAK;S(0.95)IGS(0.05)AVDQGNESIVAK ;;; 270.78 1.28E-86 93230700 10182.5 9743.8 9659.3 8120 6633.7 6844.76 5697.8 6348.48 9738 9526.7 TRUE FALSE FALSE 10058.39177 9880.973472 9827.416065 9058.872606 6295.157535 6407.401926 6181.77099 6532.163253 8867.008891 9279.194961 1.083972458 1.064852448 1.059080675 0.976256307 0.678416346 0.690512696 0.666196908 0.703957971 0.955579544 1 13.17978393 -8.820708023 3.900197076 1.043337289 0.681266326 0.95335878 0.036767834 0.029248008 0.899346795 0.005229558 0.010033694 1.51E-09 8.820708023 -0.362070962 S(ph)IHEVDISNLEAALR ddPTM_HeLa_Romidepsin_16h_R1 4 SIHEVDISNLEAALR 15 0 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR;S(1)IHEVDISNLEAALR ;;; 204.23 2.47E-18 10801100 2549.34 2527.76 2332.48 2990.58 2527.44 2000.67 1957.16 2426.39 3039.13 3189.68 TRUE FALSE FALSE 2518.267664 2563.345872 2373.075836 3336.364931 2398.455306 1872.833644 2123.401122 2496.593766 2767.302601 3106.811654 0.810563351 0.825072826 0.763829965 1.073887091 0.771998941 0.602815314 0.683466318 0.8035871 0.89072107 1 11.60121907 -16.52287875 0.076469249 1.751780516 0.534010533 0.272185208 0.112355306 154.7740789 0.912431203 20.21866482 2.45557689 3.00E-17 16.52287875 -1.217769984 S(ph)IHVDSLEPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SIHVDSLEPQR 11 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 0 S(1)IHVDSLEPQR 126.1 0.0030701 1619900 883.58 957.98 545.03 597.93 784.55 1032.1 1009 978.37 866.73 761.42 TRUE FALSE FALSE 872.8105871 971.4664676 554.5160185 667.0654799 744.5114859 966.152141 1094.704435 1006.677592 789.207498 741.6381986 1.176868436 1.309892707 0.747690747 0.899448655 1.003874244 1.302727048 1.476062637 1.357370203 1.064140843 1 9.534571743 -8.105116585 3.936960129 1.05853479 1.41288876 0.546870435 0.146270749 0.15233417 4.150378693 0.022696097 0.063193451 7.85E-09 8.105116585 0.35435397 S(ph)IKYDSLLEQGLVEAALVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SIKYDSLLEQGLVEAALVSK 20 1 O96028;D6RIS1;D6R9V2;O96028-7;O96028-6;O96028-3;O96028-5 O96028;O96028-3;O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 S(0.52)IKY(0.386)DS(0.094)LLEQGLVEAALVSK 70.414 0.0016612 0 247.6 378.11 349.46 322.67 372.18 481.85 289.74 400.35 294.75 283.59 TRUE FALSE FALSE 244.582156 383.4330425 355.5422047 359.9786236 353.1862658 451.0613401 314.3505084 411.9334956 268.3868218 276.2222909 0.885454085 1.38813215 1.287159713 1.303220759 1.278630572 1.632965025 1.138034542 1.49131156 0.971633466 1 8.109685938 -10.25921241 24.99849449 0.94590887 1.353783608 0.67933478 0.128245629 76.44810049 858159.5115 0.020232753 0.024148829 5.51E-11 10.25921241 0.407874738 S(ph)ILPYPVSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 0 S(0.939)ILPYPVS(0.061)PK 127.46 0.008427 41034000 9746.4 9647.3 9329.1 6340.4 7489.5 8270.3 8243.1 8799.5 10658 9404.8 TRUE FALSE FALSE 9627.607128 9783.114943 9491.469072 7073.50688 7107.282868 7741.854521 8943.268708 9054.099649 9704.721787 9160.46194 1.050995811 1.067971791 1.036134328 0.772177967 0.775865116 0.845138004 0.976290144 0.988388982 1.059414018 1 13.16120464 -9.284836412 24.46462982 1.029504891 0.870604107 0.601081176 0.069357863 363.6659296 380258.7769 0.01163439 0.017778734 5.19E-10 9.284836412 -0.158900784 S(ph)IPQLDLGWPDTIAYR ddPTM_HeLa_Romidepsin_16h_R1 1 SIPQLDLGWPDTIAYR 16 0 A6ND36 A6ND36 FAM83G Protein FAM83G 1 0 S(1)IPQLDLGWPDTIAYR 126.14 0.0024038 40235000 506.95 654.29 495.4 232.51 525.2 509.26 282.72 542.69 547.03 492.58 TRUE FALSE FALSE 500.7710984 663.5011118 504.0222292 259.3939002 498.3970842 476.7199296 306.7342297 558.3918789 498.1022667 479.7827006 1.043745633 1.382920041 1.05052189 0.540648714 1.03879753 0.993616337 0.63931907 1.163843295 1.038183049 1 8.906237329 -9.463471844 24.99997441 1.056420557 0.869578887 0.228000618 0.200525528 338.6178724 142499.1455 0.029521899 0.045095387 3.44E-10 9.463471844 -0.18684167 S(ph)IQDLTVTGTEPGQVS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 SIQDLTVTGTEPGQVSSR 18 0 Q9UG54;O43318-4;O43318-3;O43318-2;O43318 Q9UG54 DKFZp586F0420;MAP3K7 Mitogen-activated protein kinase kinase kinase 7 2 0 S(1)IQDLTVTGTEPGQVS(0.733)S(0.267)R 160.47 3.73E-05 5732200 1332.9 1555.8 1567 1289.4 2425.6 3033.9 2296.7 2681.9 1547.3 1590.1 TRUE FALSE FALSE 1316.654102 1577.702593 1594.272978 1438.486495 2301.812581 2840.043581 2491.781641 2759.496545 1408.905613 1548.788973 0.850118464 1.018668535 1.029367464 0.928781467 1.486201556 1.833718881 1.608858072 1.781712418 0.909682105 1 10.59692487 -8.646268954 3.255806343 0.941768385 1.724123339 0.955173393 0.077830352 0.03713555 0.777928249 0.012582674 0.026669666 2.26E-09 8.646268954 0.782354954 S(ph)IQDLTVTGTEPGQVSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SIQDLTVTGTEPGQVSSR 18 0 Q9UG54;O43318-4;O43318-3;O43318-2;O43318 Q9UG54 DKFZp586F0420;MAP3K7 Mitogen-activated protein kinase kinase kinase 7 2 0 S(0.984)IQDLT(0.015)VTGTEPGQVS(0.311)S(0.689)R 136.11 0.010683 5421500 1759.6 1760 1700.2 1757.2 3125.2 3618.4 2745.2 3485.9 1761.8 1706.6 TRUE FALSE FALSE 1738.153318 1784.777326 1729.791268 1960.375732 2965.709382 3387.195918 2978.377219 3586.759017 1604.220195 1662.262286 1.045655269 1.073703796 1.040624745 1.179342002 1.78414045 2.037702441 1.791761291 2.157757561 0.965082472 1 10.69893233 -8.745840132 2.580895434 1.028601393 1.97619793 0.96097027 0.089238075 0.032153226 0.437393062 0.011800413 0.024846888 1.80E-09 8.745840132 0.947596537 S(ph)IQDLTVTGTEPGQVSSR ddPTM_HeLa_Romidepsin_16h_R1 4 SIQDLTVTGTEPGQVSSR 18 0 Q9UG54;O43318-4;O43318-3;O43318-2;O43318 Q9UG54 DKFZp586F0420;MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 0 S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(1)IQDLTVTGTEPGQVSSR;S(0.433)IQDLT(0.002)VT(0.058)GT(0.121)EPGQVS(0.089)S(0.297)R ;;; 268.49 3.95E-90 242411300 4812.99 5640.5 4774.7 4505.35 8308.7 9414.8 8451.48 10050.99 5160.26 5312.59 TRUE FALSE FALSE 4754.327427 5719.907107 4857.801651 5026.279765 7884.676035 8813.224665 9169.3485 10341.79954 4698.713421 5174.568146 0.918787287 1.105388304 0.938783975 0.971342849 1.523736052 1.703180713 1.772002656 1.998582151 0.908039722 1 12.33722275 -8.537546235 1.750788511 0.966285052 1.856061451 0.949686332 0.089334313 0.051403022 0.311223771 0.012980386 0.034907104 2.90E-09 8.537546235 0.889776399 S(ph)ISADDDLQESSR ddPTM_HeLa_Romidepsin_16h_R1 1 SISADDDLQESSR 13 0 A0A0A0MSN9;P18615-4;P18615;P18615-3;A2ABK4;A0A0G2JI50;E9PD43;A0A0A0MT02 A0A0A0MSN9 NELFE Negative elongation factor E 1 0 S(0.987)IS(0.013)ADDDLQESSR 222.56 2.14E-31 118460000 2445.6 3310.2 1946.7 1817.4 2644.5 2108 1562.6 2408.7 2122.9 2666.9 TRUE FALSE FALSE 2415.792087 3356.801082 1980.581497 2027.536339 2509.541297 1973.305603 1695.327205 2478.391934 1933.022507 2597.613554 0.93000442 1.292263462 0.762461951 0.780538097 0.966094935 0.759660959 0.652647967 0.954103404 0.744153227 1 11.3429711 S(ph)ISNPPGSNLR ddPTM_HeLa_Romidepsin_16h_R1 1 SISNPPGSNLR 11 0 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;Q9H4A3-4 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 S(0.997)IS(0.002)NPPGSNLR 96.334 0.024215 8872000 1545.2 1576.2 1441.2 1694.6 1902 1575.3 1299.8 1667.5 2087.2 1600.9 TRUE FALSE FALSE 1526.366508 1598.389785 1466.283481 1890.537625 1804.933843 1474.643414 1410.20498 1715.746482 1900.515605 1559.308387 0.978874045 1.02506329 0.940342201 1.21242061 1.157522051 0.945703509 0.9043785 1.100325308 1.218819587 1 10.60669057 S(ph)ISPEVSASR ddPTM_HeLa_Romidepsin_16h_R1 1 SISPEVSASR 10 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 S(0.989)IS(0.011)PEVSASR 172.21 0.00062543 12777000 3171.4 2568.4 2571.8 2690.7 2927 3059.2 2390.8 2926 2981.3 2811.7 TRUE FALSE FALSE 3132.745757 2604.558003 2616.5611 3001.811394 2777.624268 2863.726993 2593.874492 3010.659194 2714.645061 2738.651629 1.143900788 0.951036625 0.955419475 1.096090997 1.014230594 1.045670418 0.947135614 1.099321711 0.991234165 1 11.41925004 -10.25333296 24.97566014 1.06795315 1.014817827 0.005708793 0.0656864 1054.102514 3247662.399 0.011920232 0.014441328 5.58E-11 10.25333296 -0.053135324 S(ph)ISTSGPLDKEDTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SISTSGPLDKEDTGR 15 1 A0A0U1RR27;Q7Z401;Q7Z401-2 A0A0U1RR27 DENND4A C-myc promoter-binding protein 1 0 S(0.827)IS(0.064)T(0.092)S(0.017)GPLDKEDTGR 87.157 0.007209 24591000 1797 2002 2090.6 1955.2 2311.9 2082.3 1970.1 2420.5 2306.9 2540.3 TRUE FALSE FALSE 1775.097473 2030.184209 2126.986016 2181.269423 2193.915116 1949.24775 2137.440245 2490.533349 2100.565086 2474.30264 0.71741324 0.820507636 0.8596305 0.881569372 0.886680182 0.78779682 0.863855622 1.00655971 0.848952368 1 11.27280626 -5.936581735 20.02097904 0.864594379 0.871928037 0 0.083089363 0 0 0.014653457 0 1.16E-06 5.936581735 0.007333658 S(ph)ITSTPLSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 S(0.978)IT(0.02)S(0.002)TPLSGK 119.03 0.012435 37118000 2248 1965.7 2243.7 2167.2 2347.7 2136.8 2087.9 2666.3 2349.6 2170.6 TRUE FALSE FALSE 2220.600511 1993.373176 2282.750657 2417.781861 2227.888109 2000.265376 2265.246174 2743.445184 2139.445891 2114.207499 1.050322881 0.942846517 1.079719308 1.14358778 1.053769845 0.946106462 1.071439854 1.297623429 1.011937519 1 11.04590126 -7.282907059 3.83655198 1.02847545 1.318820977 0.664761283 0.056939377 0.104951984 2.999488227 0.007967683 0.082349548 5.21E-08 7.282907059 0.290345527 S(ph)IVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_HeLa_Romidepsin_16h_R1 1 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 1 0 S(0.829)IVDY(0.171)KPNLDLLEQQHQLIQEALIFDNK 86.946 3.79E-07 1797100 483.4 359.6 404.92 490.3 632.09 529.94 486.37 547.96 406.7 401.12 TRUE FALSE FALSE 477.5081349 364.6624582 411.9674627 546.9907929 599.8320886 496.0785443 527.6822557 563.8143581 370.3237334 390.6988446 1.22218978 0.933359449 1.054437372 1.400031765 1.535279914 1.269721043 1.350611252 1.443091951 0.947849574 1 8.609913179 -9.257815994 24.46450259 1.088549223 1.39732335 0.745148443 0.105044338 113.6753588 767514.8738 0.017305018 0.027957533 5.52E-10 9.257815994 0.308774127 S(ph)IVVIHPDTGR ddPTM_HeLa_Romidepsin_16h_R1 4 SIVVIHPDTGR 11 0 K7EQ71;K7EKI8;O60437 K7EQ71 PPL Periplakin 1 0 S(1)IVVIHPDTGR;S(1)IVVIHPDTGR;S(1)IVVIHPDTGR;S(1)IVVIHPDTGR ;;; 100.11 0.0080143 16682400 6751.9 7132.6 6949.9 8037.4 11453.4 11206.2 11025.3 11347 7639.1 7184.8 TRUE FALSE FALSE 6669.605246 7233.01293 7070.860094 8966.722005 10868.89026 10490.15999 11961.78871 11675.30754 6955.839764 6998.13786 0.953054281 1.03356251 1.010391655 1.281301138 1.553111767 1.498993046 1.709281661 1.668344891 0.993955807 1 12.77275537 -8.920769102 1.360347334 0.977367663 1.650050242 0.968416733 0.052032455 0.045951078 0.169733669 0.008183551 0.018924482 1.20E-09 8.920769102 0.672682579 S(ph)KFDSDEEEEDTENVEAASSGK ddPTM_HeLa_Romidepsin_16h_R1 2 SKFDSDEEEEDTENVEAASSGK 22 1 Q8TF01;Q8TF01-2 Q8TF01 PNISR Arginine/serine-rich protein PNISR 1 0 S(0.778)KFDS(0.214)DEEEEDT(0.008)ENVEAASSGK;S(0.774)KFDS(0.115)DEEEEDT(0.111)ENVEAASSGK ; 71.265 0.0014147 23206000 3541.7 3660.5 3337.5 2894.2 2337.3 2524.9 2065.59 2313.1 3875.9 3944.3 TRUE FALSE FALSE 3498.532398 3712.032615 3395.587787 3228.841022 2218.018859 2363.567039 2241.041163 2380.025899 3529.229797 3841.826517 0.910642993 0.966215574 0.883847246 0.840444254 0.577334466 0.615219617 0.583327007 0.619503741 0.918633306 1 11.90757666 -8.953208173 1.974314484 0.954568975 0.593310789 0.945051295 0.038169463 0.054573755 0.427514292 0.006673014 0.013432419 1.11E-09 8.953208173 -0.361258186 S(ph)KSATLLYDQPLQVFTGSSSSSDLISGTK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSATLLYDQPLQVFTGSSSSSDLISGTK 29 1 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8 Q96RT1-7 ERBB2IP Protein LAP2 1 0 S(0.374)KS(0.279)AT(0.334)LLY(0.014)DQPLQVFTGSSSSSDLISGTK 86.902 2.79E-07 6475300 1602.2 1987.9 2187.4 1648.5 1988.5 2391.6 1852.3 2017 2026.6 2443.5 TRUE FALSE FALSE 1582.67177 2015.885708 2225.470779 1839.107326 1887.019425 2238.784479 2009.634316 2075.358713 1845.33582 2380.017518 0.664983244 0.847004568 0.935064874 0.772728483 0.792859469 0.940658824 0.844377951 0.871993041 0.775345478 1 11.21675648 -12.68162335 1.561773154 0.999600841 0.810097863 0 0.104077622 0.34699198 1.529756692 0.066863304 0.015024871 2.08E-13 12.68162335 -0.189502977 S(ph)KSDATASISLSSNLK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 S(0.908)KS(0.091)DAT(0.001)ASISLSSNLK 234.36 6.94E-45 18602000 1925.8 2117.1 2136.8 1931.5 2850 2832.9 2189.5 2771.1 2568.5 2380.2 TRUE FALSE FALSE 1902.327609 2146.904589 2173.990108 2154.829118 2704.553865 2651.886833 2375.476075 2851.277406 2338.766927 2318.362061 0.820548111 0.926043704 0.937726744 0.929461862 1.166579591 1.143862245 1.024635503 1.229867178 1.008801415 1 11.17889018 -8.769584916 23.04663791 0.916944392 1.133095105 0.671225409 0.069039876 32.21481819 91148.1925 0.011611678 0.021348277 1.70E-09 8.769584916 0.216150713 S(ph)KSPASVNGTPSSQLSTPK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPASVNGTPSSQLSTPK 19 1 G5E9L9;Q8N568-2;Q8N568 G5E9L9 DCLK2 Serine/threonine-protein kinase DCLK2 1 0 S(0.447)KS(0.447)PAS(0.106)VNGTPSSQLSTPK 75.524 0.0043597 8664300 3564.2 4340 3300.8 4048.4 3110.8 3515.1 2494.4 2375.4 4001.1 4167.7 TRUE FALSE FALSE 3520.758159 4401.098634 3358.249039 4516.495056 2952.044268 3290.496454 2706.274274 2444.128451 3643.231595 4059.422553 0.867305168 1.084168641 0.827272597 1.112595449 0.727207929 0.810582395 0.666664837 0.602087715 0.89747533 1 11.98705881 -8.076920761 1.129356313 0.948352224 0.600261882 0.603324301 0.101586163 0.317595561 0.655732796 0.01501471 0.092196625 8.38E-09 8.076920761 -0.348090342 S(ph)KSPLPPEEEAK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPLPPEEEAK 12 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.807)KS(0.193)PLPPEEEAK 108.36 0.0026045 0 1063.1 1170.8 1093.1 775.97 1002.6 1186.7 1119.5 1068.4 1144.2 988.79 TRUE FALSE FALSE 1050.142528 1187.282553 1112.124947 865.6913024 951.4335808 1110.8737 1214.590302 1099.312468 1041.859886 963.1010933 1.090376219 1.232770434 1.154733345 0.898858187 0.987885475 1.153434159 1.261124414 1.141429987 1.081776247 1 9.91154343 -4.000006253 0.015622462 7.25E-08 2.437292625 0.074056115 0.103014979 6271.595005 7.640272373 473.441194 748.2919872 1.00E-04 4.000006253 2.437292553 S(ph)KSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.492)KS(0.429)PLPPEEEAKDEEEDQT(0.079)LVNLDTYTSDLHFQVSK 69.783 1.45E-05 99303000 6223.4 5459.6 4951.9 5039.2 7493.9 7583.5 5822.4 7102.3 7195.9 6392.8 TRUE FALSE FALSE 6147.546807 5536.460392 5038.085742 5621.856014 7111.458319 7098.938825 6316.954511 7307.793845 6552.280682 6226.714134 0.987285858 0.88914639 0.809108244 0.902860785 1.142088454 1.140077844 1.014492455 1.173619615 1.052285449 1 12.60425533 -8.754070996 24.9978672 0.964015548 1.111814691 0.554004326 0.076142191 123.844353 420149.1482 0.011790062 0.023204637 1.76E-09 8.754070996 0.147799144 S(ph)KSPPKVPIVIQDDSLPAGPPPQIR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPPKVPIVIQDDSLPAGPPPQIR 25 2 Q7Z422-2;Q7Z422-4;Q7Z422-3;Q7Z422-5;Q7Z422 Q7Z422-2 SZRD1 SUZ domain-containing protein 1 1 0 S(0.5)KS(0.5)PPKVPIVIQDDSLPAGPPPQIR 74.308 0.00018423 276920000 2776.2 2835.2 2919.3 2490.3 2300.9 2728.3 2017.9 2162.5 3045.5 3039.1 TRUE FALSE FALSE 2742.362607 2875.11402 2970.109192 2778.240203 2183.476487 2553.970435 2189.300376 2225.068526 2773.102852 2960.143744 0.926428864 0.971275137 1.003366542 0.938549085 0.737625155 0.862785951 0.739592589 0.751675837 0.936813578 1 11.53145152 -8.83535369 5.538744599 0.967449738 0.777205638 0.841846303 0.040369711 0.06055292 3.278994738 0.006316088 0.011666983 1.46E-09 8.83535369 -0.190244099 S(ph)KSPVGNPQLIQFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPVGNPQLIQFSR 15 1 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 0 S(1)KSPVGNPQLIQFSR 101.61 0.0027119 26878000 1075.6 991.74 1041.3 652.67 866.38 1058.8 1040 1282 1530.8 1286 TRUE FALSE FALSE 1062.490173 1005.701742 1059.42339 728.1347763 822.1653957 991.1460971 1128.337574 1319.092647 1393.881414 1252.589535 0.848234912 0.802898087 0.845786557 0.581303576 0.656372557 0.791277645 0.900803929 1.053092502 1.112799824 1 10.29069802 -11.45320569 0.740740919 0.988971633 0.795960194 0.345781852 0.127865821 0.644120535 0.738630937 0.060171428 0.029878462 3.52E-12 11.45320569 -0.19301144 S(ph)KSVPGLNVDMEEEEEEEDIDHLVK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSVPGLNVDMEEEEEEEDIDHLVK 25 1 Q96C24-2;Q96C24 Q96C24-2 SYTL4 Synaptotagmin-like protein 4 1 0 S(0.5)KS(0.5)VPGLNVDMEEEEEEEDIDHLVK 52.754 0.0075887 4238900 1753 1631.7 1673 2088.1 1649.7 1325.9 1458.2 1505.9 2045.2 1736.6 TRUE FALSE FALSE 1731.633762 1654.671115 1702.117863 2329.535947 1565.509653 1241.179269 1582.059472 1549.470841 1862.27219 1691.482882 1.023737089 0.978236986 1.006287372 1.377215207 0.925524976 0.73378175 0.935309183 0.916042874 1.100970166 1 10.72407286 -8.532628626 24.99830264 1.035995007 0.862501377 0.373777815 0.122903961 186.5109369 478205.6088 0.017422151 0.034876784 2.93E-09 8.532628626 -0.17349363 S(ph)KTPPPPPQTAQTK ddPTM_HeLa_Romidepsin_16h_R1 2 SKTPPPPPQTAQTK 14 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 S(0.5)KT(0.5)PPPPPQTAQTK;S(0.5)KT(0.5)PPPPPQTAQTK ; 128.35 0.00096523 92361000 9840.1 9712.5 9629.6 10369.1 10202.4 11497.6 10495 10804.1 11027.9 11264.1 TRUE FALSE FALSE 9720.165076 9849.23283 9797.199149 11568.02413 9681.733458 10762.94047 11386.44504 11116.69959 10041.537 10971.45706 0.885950246 0.897714203 0.892971562 1.054374462 0.882447373 0.980994631 1.037824327 1.013238217 0.915241882 1 13.42146751 -7.986271426 5.956071519 0.941428304 1.022761965 0.325657951 0.052937761 0.170327903 22.23656244 0.008338844 0.024616314 1.03E-08 7.986271426 0.081333661 S(ph)KTPVQAAAVSIVEKPVTR ddPTM_HeLa_Romidepsin_16h_R1 1 SKTPVQAAAVSIVEKPVTR 19 2 Q96T58 Q96T58 SPEN Msx2-interacting protein 1 0 S(0.5)KT(0.5)PVQAAAVSIVEKPVTR 57.708 0.016059 11055000 1735.8 1595.4 1696.3 1684.1 1892.8 1550.4 1133.8 1494.6 1523.8 1845.2 TRUE FALSE FALSE 1714.643402 1617.860083 1725.82339 1878.823566 1796.203353 1451.334444 1230.104944 1537.843893 1387.507512 1797.261438 0.954031153 0.900180713 0.960251722 1.045381338 0.999411279 0.807525501 0.684432948 0.855659539 0.772012064 1 10.81158457 -8.181711958 4.611109083 0.976793176 0.766119559 0.424513828 0.083409326 0.078707546 3.052598066 0.007340168 0.019407566 6.58E-09 8.181711958 -0.210673617 S(ph)LASIEAK ddPTM_HeLa_Romidepsin_16h_R1 3 SLASIEAK 8 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 S(0.999)LAS(0.001)IEAK;S(0.999)LAS(0.001)IEAK;S(0.984)LAS(0.016)IEAK ;; 140.11 0.0089753 46678000 13339.9 17305.9 11762 10095.5 13295 17473.1 14512.4 16708.7 15758.9 13875.4 TRUE FALSE FALSE 13177.30817 17549.53291 11966.71268 11262.78921 12616.50654 16356.6253 15745.08289 17192.13987 14349.38452 13514.91511 0.975019677 1.298530755 0.885444901 0.833359967 0.933524661 1.210264746 1.165015301 1.272086412 1.061744332 1 13.72226483 -8.251970469 23.5633864 0.988851359 1.210711522 0.404483987 0.120547528 229.4334751 570941.1311 0.016694114 0.04188245 5.60E-09 8.251970469 0.221860163 S(ph)LDGAAAVDSADR ddPTM_HeLa_Romidepsin_16h_R1 2 SLDGAAAVDSADR 13 0 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A3B3ITP0;A0A2R8Y7Y3;A0A2R8Y5G2;A0A2U3TZH6;A0A2R8Y420;A0A2R8YCW8;A0A2R8Y5Z6;P11171-5;P11171-7;P11171-6;A0A3B3IU06;A0A2R8Y570;A0A2R8Y6G5;A0A2R8YFR9;A0A2R8Y7N0;A0A3B3IUD6;A0A2R8Y4N6 P11171 EPB41 Protein 4.1 1 0 S(1)LDGAAAVDSADR;S(1)LDGAAAVDSADR ; 247.73 8.42E-53 24582000 2778.2 2721.9 2431.71 2302.51 2712.8 2491.7 2009.39 2712.6 2799.9 2493.9 TRUE FALSE FALSE 2744.33823 2760.21898 2474.032892 2568.73704 2574.355693 2332.488412 2180.067536 2791.084801 2549.469932 2429.108118 1.129771956 1.136309643 1.018494349 1.057481559 1.059794611 0.960224205 0.897476535 1.149016291 1.049549797 1 11.24621099 -8.324391069 8.066841404 1.06477778 0.991859578 0.133821899 0.071128814 0.450569583 53.46093999 0.010931047 0.02455083 4.74E-09 8.324391069 -0.072918202 S(ph)LDGAEFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLDGAEFSR 9 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;H7C2K6 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 S(1)LDGAEFSR 120.77 0.013039 4651700 1266.6 1419.5 1505.2 894.14 1128.1 1240.6 1254.1 1223.2 1316.8 1449.6 TRUE FALSE FALSE 1251.162192 1439.483758 1531.397375 997.5246739 1070.528847 1161.329664 1360.623223 1258.591362 1199.02211 1411.939183 0.886130371 1.01950833 1.084605763 0.706492663 0.758197563 0.82250686 0.963655686 0.891392049 0.849202377 1 10.46346223 -9.261866343 24.99999543 0.960959028 0.83172748 0.375160993 0.089705055 36.51362176 2137993.71 0.014218745 0.022561947 5.47E-10 9.261866343 -0.129231547 S(ph)LDNNYSTPNER ddPTM_HeLa_Romidepsin_16h_R1 2 SLDNNYSTPNER 12 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-9;A0A669KB05;O60716-13;O60716-21;O60716-18;O60716-17;O60716-19;O60716-25;O60716-27;O60716-29;O60716-26;H0YC95 O60716 CTNND1 Catenin delta-1 1 0 S(1)LDNNYSTPNER;S(1)LDNNYSTPNER ; 162.88 0.00052607 15374700 1025.79 1146.69 898.63 957.28 827.91 996.93 904.73 979.9 1211.88 934.33 TRUE FALSE FALSE 1013.287277 1162.833132 914.2702782 1067.965218 785.6586633 933.2293904 981.5777436 1008.25186 1103.486418 910.0559719 1.113434017 1.277760015 1.004630821 1.173515971 0.863308069 1.025463729 1.07859052 1.107900933 1.212547856 1 9.829811469 S(ph)LDTPQSLASLSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLDTPQSLASLSSR 14 0 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 1 0 S(0.999)LDT(0.001)PQSLASLSSR 103.13 0.0087748 3410000 794.63 806.89 717.59 662.19 1056.5 856.57 910.57 1338.1 905.06 789.2 TRUE FALSE FALSE 784.9447439 818.2494186 730.0793529 738.7555235 1002.582863 801.8379415 987.9137931 1376.815812 824.1091668 768.6964702 1.021137438 1.064463609 0.949762853 0.961049715 1.304263648 1.043113859 1.285180603 1.791104637 1.072086576 1 9.586270234 -4.000000002 0.754518098 1.013271815 143.6172141 0.855286959 0.092620235 84.79820669 0.337589357 0.01373739 20584.8071 1.00E-04 4.000000002 142.6039423 S(ph)LDYLNLDK ddPTM_HeLa_Romidepsin_16h_R1 2 SLDYLNLDK 9 0 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 0 S(0.999)LDY(0.001)LNLDK;S(1)LDYLNLDK ; 132.86 0.0070349 32430000 9147.4 8980.9 8492.4 7322.6 7387.3 6157.2 5859.8 6512 9116.8 8588.8 TRUE FALSE FALSE 9035.90797 9107.333346 8640.20666 8169.273466 7010.298515 5763.774791 6357.531266 6700.414446 8301.370575 8365.661738 1.080118735 1.088656658 1.032818076 0.976524479 0.837984936 0.68898014 0.759955574 0.80094255 0.992314874 1 13.03026395 -8.742595768 2.277704304 1.042496224 0.750519782 0.914856344 0.039276489 0.062514542 0.66129818 0.006549254 0.014178988 1.81E-09 8.742595768 -0.291976441 S(ph)LEAT(ph)VS(ph)GKMAS(ph)TMLRASLAPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SLEATVSGKMASTMLRASLAPVK 23 2 H7BZY2 H7BZY2 ARMC9 4 0 S(0.998)LEAT(0.998)VS(0.998)GKMAS(0.784)T(0.209)MLRAS(0.012)LAPVK 47.499 0.013705 14077000 1302.9 1604.8 1584.5 1342.6 874.45 924.25 838.27 671.79 1577.6 1757.6 TRUE FALSE FALSE 1287.019754 1627.392417 1612.077558 1497.837729 829.8235535 865.1934079 909.4726329 691.2271837 1436.495505 1711.937299 0.751791409 0.950614498 0.941668576 0.87493726 0.484727773 0.505388491 0.531253471 0.403768984 0.839105209 1 10.74141415 -8.76704658 7.15462632 0.890511856 0.48562593 0.891752221 0.070277985 0.043488944 12.14528945 0.014432161 0.027384217 1.71E-09 8.76704658 -0.404885925 S(ph)LEDVTAEYIHK ddPTM_HeLa_Romidepsin_16h_R1 2 SLEDVTAEYIHK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 S(1)LEDVTAEYIHK;S(1)LEDVTAEYIHK ; 180.95 5.06E-07 8428400 3281.6 3766.8 3740.7 3173.3 2816 2948.9 2288.98 2707 3254.3 3427.9 TRUE FALSE FALSE 3241.602597 3819.829109 3805.805314 3540.211877 2672.289012 2760.474807 2483.405904 2785.322774 2963.227257 3338.842664 0.970876116 1.144057835 1.139857639 1.060311082 0.800363863 0.826775948 0.743792432 0.834218037 0.887501316 1 11.7051324 -8.754082362 24.87802789 1.016507611 0.799001314 0.690008311 0.075803648 74.20934308 250939.3079 0.011046677 0.021742184 1.76E-09 8.754082362 -0.217506297 S(ph)LEEDLETLK ddPTM_HeLa_Romidepsin_16h_R1 4 SLEEDLETLK 10 0 P48681 P48681 NES Nestin 1 0 S(1)LEEDLETLK;S(1)LEEDLETLK;S(1)LEEDLETLK;S(1)LEEDLETLK ;;; 203.03 1.68E-12 27061300 8251.36 8736.91 8309.08 5181.43 7253.16 6341.21 5949.18 6563.25 7995.73 8447.2 TRUE FALSE FALSE 8150.789251 8859.908448 8453.696052 5780.531316 6883.00418 5936.027146 6454.503201 6753.147284 7280.571883 8227.740526 0.990647338 1.076833721 1.027462646 0.702566069 0.836560676 0.72146504 0.784480646 0.820777863 0.884881075 1 13.00628058 -9.269010002 24.99282927 1.005031252 0.774447623 0.782350043 0.058656922 139.5709772 460763.8934 0.006609347 0.010215539 5.38E-10 9.269010002 -0.230583628 S(ph)LEEEGQELPQSADVQR ddPTM_HeLa_Romidepsin_16h_R1 2 SLEEEGQELPQSADVQR 17 0 P48681 P48681 NES Nestin 1 0 S(1)LEEEGQELPQSADVQR;S(1)LEEEGQELPQSADVQR ; 266.39 5.79E-87 8076800 924.23 1031.45 1055.42 836.17 1042.79 1058.96 793.4 1154.68 1199.1 1167.53 TRUE FALSE FALSE 912.9651293 1045.97078 1073.789142 932.8519097 989.5725351 991.2958736 860.7913762 1188.088844 1091.849493 1137.197402 0.802820273 0.919779431 0.944241642 0.820307809 0.870185364 0.87170079 0.756941033 1.044751634 0.960123098 1 10.15126699 -12.5286678 1.269677003 1.000431067 0.867177299 0.199105754 0.077429735 0.445652653 1.279727562 0.051517309 0.012156062 2.96E-13 12.5286678 -0.133253768 S(ph)LELNGAVEPSEGAPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLELNGAVEPSEGAPR 16 0 M0R2A7;M0QYS2;M0R0P4;R4GN16;F5GYK2;Q9NRL3-2;Q9NRL3;Q9NRL3-3 M0R2A7 STRN4 Striatin-4 1 0 S(1)LELNGAVEPSEGAPR;S(1)LELNGAVEPSEGAPR ; 183.71 1.17E-08 15784600 1460.29 1137.55 1197.57 1400.66 1485.12 1720.11 1463.77 1439.34 1643.04 1641.62 TRUE FALSE FALSE 1442.491424 1153.564459 1218.413203 1562.6109 1409.328785 1610.200522 1588.102587 1480.985032 1496.082387 1598.970476 0.902137623 0.721442 0.761998562 0.977260633 0.881397628 1.007023298 0.993203196 0.926211618 0.935653541 1 10.64292759 -6.915160329 16.75060863 0.927967538 0.880152997 0 0.095507855 423341.3527 811864.0575 0.014346634 759506.1534 1.22E-07 6.915160329 -0.047814541 S(ph)LELSSLAGPGEDPLSADSLGKPTR ddPTM_HeLa_Romidepsin_16h_R1 3 SLELSSLAGPGEDPLSADSLGKPTR 25 1 G5E953;Q13615-3;Q13615-2;Q13615 G5E953 MTMR3 Myotubularin-related protein 3 1 0 S(0.999)LELSS(0.001)LAGPGEDPLSADSLGKPTR;S(0.989)LELS(0.009)S(0.003)LAGPGEDPLSADSLGKPTR;S(0.615)LELS(0.292)S(0.093)LAGPGEDPLSADSLGKPTR ;; 176.61 1.98E-18 67973700 2475.49 2748.13 2327.64 2309.23 3592.2 3405.3 3324.7 3474.5 2953.35 2571 TRUE FALSE FALSE 2445.317776 2786.818246 2368.151598 2576.234038 3408.87663 3187.71232 3607.099935 3575.029176 2689.194979 2504.205049 0.976484644 1.112855454 0.945670004 1.028763215 1.361260984 1.272943811 1.440417164 1.427610401 1.073871718 1 11.29013698 -8.771364069 4.656822869 0.996492513 1.37648371 0.880653752 0.063271225 0.039330188 2.131213863 0.00847974 0.016418793 1.69E-09 8.771364069 0.379991197 S(ph)LEQDALR ddPTM_HeLa_Romidepsin_16h_R1 1 SLEQDALR 8 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 S(1)LEQDALR 115 0.020624 2370600 841.4 1154.7 1113 698.15 1414.8 1443.2 901.63 1059.3 1080 815.27 TRUE FALSE FALSE 831.1446932 1170.955897 1132.371298 778.8733879 1342.597477 1350.984178 978.2144297 1089.949174 983.4020951 794.0891679 1.046664187 1.474589938 1.426000182 0.980838701 1.690738938 1.701300348 1.231869756 1.372577814 1.238402606 1 9.633157206 -10.27244242 18.42824781 1.022035224 1.410172826 0.309094724 0.208161668 13.97837778 23411.16062 0.033429685 0.038576524 5.34E-11 10.27244242 0.388137602 S(ph)LEQEEPFDLSQKR ddPTM_HeLa_Romidepsin_16h_R1 1 SLEQEEPFDLSQKR 14 1 Q8N895 Q8N895 ZNF366 Zinc finger protein 366 1 0 S(1)LEQEEPFDLSQKR 59.898 0.026566 9642100 1331.4 1054.5 947 2260.1 1451.2 1331.9 1249.5 1455.9 1351.6 1301.3 TRUE FALSE FALSE 1315.172385 1069.345279 963.4821378 2521.423396 1377.139849 1246.795889 1355.632499 1498.024169 1230.709511 1267.492038 1.037617866 0.843670214 0.760148473 1.989301171 1.086507692 0.983671574 1.069539262 1.181880536 0.970980072 1 10.30776097 S(ph)LESINSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLESINSR 8 0 E5RJH3;A0A0C4DH44;E5RI99;P62888 E5RJH3 RPL30 60S ribosomal protein L30 1 0 S(0.999)LES(0.001)INSR 121.36 0.018292 7340000 741.7 408.92 613.31 716.37 657.29 541.04 554.49 455.26 849.1 772.27 TRUE FALSE FALSE 732.6598751 414.6767865 623.9844033 799.20007 623.7460386 506.4692901 601.5883668 468.4322298 773.1543694 752.2063141 0.974014524 0.551280651 0.829538907 1.062474557 0.829222019 0.673311671 0.799765112 0.622744347 1.027848816 1 9.554984606 -5.293221238 0.134860809 1.091782457 2.19E-09 0.341292655 0.137839962 45.64087866 0.574170252 0.494361269 9.129108744 5.09E-06 5.293221238 -1.091782455 S(ph)LESVLSLGPR ddPTM_HeLa_Romidepsin_16h_R1 1 SLESVLSLGPR 11 0 Q13470-2;Q13470 Q13470-2 TNK1 Non-receptor tyrosine-protein kinase TNK1 1 0 S(0.999)LES(0.001)VLSLGPR 132.86 0.0044724 7513600 673.16 248.91 503.74 696.65 584.64 537.95 360.39 422.3 631.1 512.9 TRUE FALSE FALSE 664.955267 252.4141615 512.5073834 777.1999508 554.8036392 503.5767312 391.0015176 434.5185842 574.6528354 499.5747841 1.331042495 0.505258011 1.025887214 1.555722938 1.110551727 1.008010707 0.782668642 0.869776854 1.150283909 1 8.964556849 -7.963222812 3.254436065 1.126754806 0.827051552 0.142954838 0.253770569 0.333358965 7.25091487 0.038139382 0.12751407 1.09E-08 7.963222812 -0.299703254 S(ph)LGDEGLNR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGDEGLNR 9 0 Q01970-2;Q01970 Q01970-2 PLCB3 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3" 1 0 S(1)LGDEGLNR 115 0.016298 7104300 1075.2 827.93 825.21 696.72 1061.5 1092 872.18 1145.5 922.44 864.69 TRUE FALSE FALSE 1062.095049 839.5856203 839.5724339 777.2780446 1007.327694 1022.224724 946.2629474 1178.643235 839.9346561 842.2252291 1.261058221 0.996865911 0.996850254 0.922886204 1.19603125 1.213718954 1.123527193 1.399439478 0.997280332 1 9.718062282 -4.000001027 0.923817455 1.09856037 173.3499401 0.435646395 0.10895478 975.108744 1.821079118 0.02000614 354640.4208 1.00E-04 4.000001027 172.2513797 S(ph)LGEEIQESLK ddPTM_HeLa_Romidepsin_16h_R1 2 SLGEEIQESLK 11 0 P48681 P48681 NES Nestin 1 0 S(1)LGEEIQESLK;S(1)LGEEIQESLK ; 182.37 6.81E-06 7550100 4071.2 3305.9 3497.5 2051.15 3911.5 4420.3 3346.7 4144.9 3454.1 3617.1 TRUE FALSE FALSE 4021.578648 3352.440547 3558.37252 2288.313614 3711.881559 4137.857096 3630.968614 4264.826142 3145.156645 3523.127221 1.141479826 0.951552509 1.010003982 0.649512059 1.053575794 1.174484155 1.030609566 1.210522889 0.892717307 1 11.78264086 -8.509004743 24.67011876 1.020889754 1.125459971 0.175956056 0.138884751 1046.558865 1860941.572 0.021002535 0.045198639 3.10E-09 8.509004743 0.104570217 S(ph)LGGAVGSVASGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGGAVGSVASGAR 14 0 Q8NHG8 Q8NHG8 ZNRF2 E3 ubiquitin-protein ligase ZNRF2 1 0 S(1)LGGAVGSVASGAR 122.63 0.0037733 20829000 375.48 245.69 281.89 283.15 370.22 261.93 238 312.23 265.93 217.4 TRUE FALSE FALSE 370.9035053 249.1488303 286.7961772 315.8891353 351.3262919 245.1935183 258.2157141 321.2638824 242.1445548 211.7519167 1.75159456 1.176607202 1.354397078 1.491788789 1.659141024 1.157928212 1.219425629 1.517171072 1.143529459 1 7.726231218 -12.62877047 1.456727317 1.000742904 1.453053204 0.313233038 0.195051112 0.347510524 1.328238215 0.151159064 0.034725601 2.35E-13 12.62877047 0.4523103 S(ph)LGSAGPSGTLPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGSAGPSGTLPR 13 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 S(0.714)LGS(0.049)AGPS(0.096)GT(0.142)LPR;S(0.977)LGS(0.023)AGPSGTLPR ; 104.41 0.010161 27411000 1442.09 1514.22 1404.79 1285.24 1364.38 1506.24 1402.99 1449.92 1871.78 1787.24 TRUE FALSE FALSE 1424.513252 1535.537229 1429.239781 1433.845496 1294.750597 1409.996125 1522.159936 1491.871148 1704.363309 1740.807247 0.818306136 0.882083431 0.821021272 0.823667008 0.74376448 0.809966829 0.874398896 0.856999619 0.97906492 1 10.76554075 -12.32307266 0.594823692 1.030506859 0.823395832 0.749642625 0.037128964 0.49231283 0.24214478 0.056645096 0.008952728 4.75E-13 12.32307266 -0.207111028 S(ph)LGSVQAPSYGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 S(0.853)LGS(0.147)VQAPSYGAR;S(0.926)LGS(0.068)VQAPS(0.006)YGAR ; 186.29 8.44E-08 37308000 1780.56 1809.77 1810.38 1748.71 2705.46 2490.28 1418.53 1576.77 1570.41 1596.5 TRUE FALSE FALSE 1758.85785 1835.24799 1841.888904 1950.904078 2567.390281 2331.159145 1539.019903 1622.391352 1429.948596 1555.0227 1.131081784 1.180206559 1.184477181 1.254582379 1.651030741 1.49911583 0.989708962 1.04332326 0.919567667 1 10.60271993 -10.37203236 0.850257732 1.03537119 1.28931438 0.279753662 0.187192547 0.606517536 0.896261736 0.04914226 0.054843464 4.25E-11 10.37203236 0.25394319 S(ph)LIAQDHR ddPTM_HeLa_Romidepsin_16h_R1 2 SLIAQDHR 8 0 H0YAN8;O15013-7;O15013-4;O15013-5;O15013-6;O15013;E9PB39 H0YAN8 ARHGEF10 Rho guanine nucleotide exchange factor 10 1 0 S(1)LIAQDHR;S(1)LIAQDHR ; 98.353 0.013672 7464800 2763.8 3340.2 2461.5 1963.32 3480.2 2253.71 1518.39 1945.22 2459.72 2528.6 TRUE FALSE FALSE 2730.113743 3387.223423 2504.341375 2190.328296 3302.592408 2109.705205 1647.362009 2001.501872 2239.716483 2462.906607 1.108492597 1.375295114 1.016823524 0.889326574 1.340932863 0.856591638 0.668869052 0.812658452 0.90937938 1 11.26614621 -8.0135398 22.57149438 1.079610594 0.746255169 0.467049833 0.155697649 104.3352501 173935.9159 0.02019305 0.054260282 9.69E-09 8.0135398 -0.333355426 S(ph)LIYTDTLVR ddPTM_HeLa_Romidepsin_16h_R1 1 SLIYTDTLVR 10 0 Q5SYE7-2 Q5SYE7-2 NHSL1 NHS-like protein 1 1 0 S(0.999)LIYT(0.001)DTLVR 105.2 0.021156 3373000 759.54 717.65 765 512.5 569.21 800.08 578.86 728.17 669.73 680.81 TRUE FALSE FALSE 750.2824343 727.7530955 778.3145041 571.7576614 540.1610897 748.9574701 628.028354 749.2384501 609.8276714 663.1224581 1.131438734 1.097464106 1.173711574 0.862220325 0.814572155 1.129440665 0.947077491 1.129864388 0.919630551 1 9.373131506 -9.265993595 24.97706084 1.074474733 0.974478634 0.125873818 0.114116333 536.0922333 2940129.487 0.016598689 0.025894274 5.42E-10 9.265993595 -0.099996099 S(ph)LLDASEEAIKK ddPTM_HeLa_Romidepsin_16h_R1 3 SLLDASEEAIKK 12 1 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 S(1)LLDASEEAIKK;S(1)LLDASEEAIKK;S(0.995)LLDAS(0.005)EEAIKK ;; 164.68 0.00052335 99066000 7841.3 6715.4 7381.4 2816.2 8216.7 9156.3 5979.7 8437.9 7519.5 8100.5 TRUE FALSE FALSE 7745.72722 6809.939577 7509.870171 3141.822295 7797.371138 8571.241981 6487.615569 8682.037324 6846.937087 7890.047842 0.981708524 0.863104979 0.951815543 0.398200665 0.988253974 1.086335869 0.822253008 1.100378286 0.867794115 1 12.94581833 -10.30615482 5.663048226 0.991790362 0.879879878 0.007186358 0.1895545 0.435404061 35.47635677 0.031290821 0.035952566 4.94E-11 10.30615482 -0.111910484 S(ph)LLGIDTEDAIQGR ddPTM_HeLa_Romidepsin_16h_R1 4 SLLGIDTEDAIQGR 14 0 P49454 P49454 CENPF Centromere protein F 1 0 S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR;S(1)LLGIDTEDAIQGR ;;; 241.41 6.25E-44 44695800 3730.86 3800.56 3581.98 2880.12 2864.5 3510.78 2331.42 2771.15 3834.5 3585.17 TRUE FALSE FALSE 3685.386843 3854.064383 3644.322859 3213.133026 2718.313876 3286.452489 2529.450757 2851.328853 3491.532716 3492.026767 1.055371877 1.103675499 1.043612522 0.920134134 0.778434433 0.941130383 0.724350335 0.816525486 0.99985852 1 11.7698489 -9.036240111 3.147715539 1.034844941 0.81788737 0.768800078 0.058147038 0.091692889 1.83749738 0.008773363 0.015827433 9.20E-10 9.036240111 -0.216957571 S(ph)LLPPPLLS(ph)AGAS(ph)RES(ph)APRQPGPGER ddPTM_HeLa_Romidepsin_16h_R1 1 SLLPPPLLSAGASRESAPRQPGPGER 26 2 Q5SZB4 Q5SZB4 C9orf50 Uncharacterized protein C9orf50 4 0 S(1)LLPPPLLS(1)AGAS(1)RES(1)APRQPGPGER 44.632 0.018343 1166800 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 NVT(ph)PNSYAEPLAAPGGGER ddPTM_HeLa_Romidepsin_16h_R1 2 NVTPNSYAEPLAAPGGGER 19 0 Q9NYD6 Q9NYD6 HOXC10 Homeobox protein Hox-C10 1 0 NVT(0.968)PNS(0.032)YAEPLAAPGGGER;NVT(0.749)PNS(0.25)YAEPLAAPGGGER ; 205 4.95E-21 25208000 5246.7 4426.7 3681.8 3765.3 2411.5 1796.05 1576.58 1599.53 4071.5 3981.2 TRUE FALSE FALSE 5182.751202 4489.019199 3745.880185 4200.661702 2288.432156 1681.288201 1710.494666 1645.809877 3707.334843 3877.76785 1.33652952 1.157629691 0.965988767 1.083267969 0.590141609 0.433571133 0.441102906 0.424421972 0.956048682 1 11.92101072 -8.718624795 1.940997878 1.151471245 0.422970536 0.868251423 0.1159793 0.090310892 0.691135286 0.021208589 0.048611585 1.91E-09 8.718624795 -0.728500709 down S(ph)LNLEDYK ddPTM_HeLa_Romidepsin_16h_R1 2 SLNLEDYK 8 0 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 1 0 S(0.999)LNLEDY(0.001)K;S(0.639)LNLEDY(0.361)K ; 109.72 0.022849 29967000 4699.2 4261.2 5219.1 4378.3 8698.6 10937.2 10011.5 9898.6 5406.2 4462.6 TRUE FALSE FALSE 4641.924343 4321.189285 5309.936246 4884.539647 8254.677983 10238.34822 10861.87656 10185.00037 4922.655932 4346.661009 1.06792877 0.994139933 1.22161269 1.123745246 1.89908483 2.355451276 2.498901234 2.343177983 1.132514342 1 12.08569187 -8.600401096 1.954238011 1.040116073 2.430693737 0.981253408 0.082219242 0.025999256 0.199075512 0.011329721 0.027869117 2.51E-09 8.600401096 1.390577664 up S(ph)LPAGDALYLSFNPPQPSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLPAGDALYLSFNPPQPSR 19 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF0 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 S(1)LPAGDALYLSFNPPQPSR;S(1)LPAGDALYLSFNPPQPSR ; 271.73 9.76E-91 63718000 746.15 594.22 752.67 721.58 1125.89 990.72 1089.78 1003.61 857.45 852.14 TRUE FALSE FALSE 737.0556368 602.5854448 765.7699056 805.0124747 1068.431632 927.4161894 1182.345886 1032.647872 780.7575245 830.00128 0.88801747 0.72600544 0.922612921 0.969893052 1.287265041 1.11736718 1.424510919 1.244152144 0.940670266 1 9.696969751 -8.80485782 4.665634965 0.925033162 1.270310796 0.764600708 0.097887674 0.081609829 3.897437962 0.01550123 0.02937084 1.57E-09 8.80485782 0.345277634 S(ph)LPAPQDNDFLSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLPAPQDNDFLSR 13 0 O43353-2;O43353 O43353-2 RIPK2 Receptor-interacting serine/threonine-protein kinase 2 1 0 S(1)LPAPQDNDFLSR;S(1)LPAPQDNDFLSR ; 128.73 0.00014966 6457600 1052.62 1128.43 1176.21 1248.44 1067.21 1181.46 984.37 927.2 1195.74 1312.62 TRUE FALSE FALSE 1039.790263 1144.316067 1196.681442 1392.790507 1012.746291 1105.968519 1067.982363 954.0270691 1088.79002 1278.517943 0.813277802 0.895033248 0.93599112 1.089378928 0.792125208 0.865039497 0.835328412 0.746197638 0.851603238 1 10.32025669 -7.59496719 1.018923277 0.918012952 0.722463639 0.294513244 0.081713703 1.321564376 1.508093063 0.014585908 0.246135359 2.54E-08 7.59496719 -0.195549313 S(ph)LPEEDVAEIQHAEEFLIKPESK ddPTM_HeLa_Romidepsin_16h_R1 3 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;H7C2Q9;H7C0M1;C9IYT0;O60832-2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 1 0 S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK;S(1)LPEEDVAEIQHAEEFLIKPESK ;; 130.43 1.38E-06 110478000 11275.4 9830.4 10756.4 8910.17 11520.9 12926.39 11715.84 11704.5 12951.3 11311.6 TRUE FALSE FALSE 11137.97109 9968.792629 10943.61063 9940.405779 10932.94548 12100.4354 12710.98316 12043.15124 11792.90329 11017.723 1.01091406 0.904796084 0.99327335 0.902219613 0.99230535 1.098270069 1.153685127 1.093070795 1.070357577 1 13.42753848 -8.213733249 4.132217316 0.987776778 1.122904854 0.611317071 0.048670798 0.103485642 3.802829568 0.006250294 0.016465161 6.11E-09 8.213733249 0.135128077 S(ph)LPPDDIQDDFDWDSIV ddPTM_HeLa_Romidepsin_16h_R1 1 SLPPDDIQDDFDWDSIV 17 0 Q9UPW0-2;Q9UPW0;F6VXT0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 0 S(1)LPPDDIQDDFDWDSIV 88.73 0.0026247 0 0 0 0 0 0 0 0 62.499 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 64.30730996 0 0 0 S(ph)LPPGLLR ddPTM_HeLa_Romidepsin_16h_R1 2 SLPPGLLR 8 0 Q14432 Q14432 PDE3A "cGMP-inhibited 3,5-cyclic phosphodiesterase A" 1 0 S(1)LPPGLLR;S(1)LPPGLLR ; 106.6 0.025462 37775000 3088.6 3057.7 3203.7 2667 2635 3005 2472.8 2321.1 3442.7 2850.7 TRUE FALSE FALSE 3050.954955 3100.746381 3259.459055 2975.371089 2500.526117 2812.990198 2682.83957 2388.257366 3134.77629 2776.638403 1.098794482 1.11672675 1.173886759 1.071573124 0.900558789 1.013092016 0.966218564 0.860125454 1.128982545 1 11.43912359 -8.772093931 24.89396107 1.065739053 0.94280679 0.602635571 0.061524761 144.1368367 336770.663 0.010220341 0.018663904 1.69E-09 8.772093931 -0.122932264 S(ph)LPSTSSTSSTK ddPTM_HeLa_Romidepsin_16h_R1 1 SLPSTSSTSSTK 12 0 A0A590UJA3;S4R3W2;A0A590UJU2;A0A590UK38;A0A590UK73;B1AKN7;B1AKN5;A0A590UK09;B1AKN8;Q12857-2;Q12857-3;Q12857;Q12857-4 A0A590UJA3 NFIA Nuclear factor 1;Nuclear factor 1 A-type 1 0 S(0.994)LPS(0.002)T(0.003)S(0.001)STSSTK 122.46 0.006701 4167100 1267.3 854.55 1131.6 957.87 1111 1168.5 1036.5 874.83 958.02 1267.2 TRUE FALSE FALSE 1251.85366 866.5803773 1151.295023 1068.623436 1054.301524 1093.836621 1124.540284 900.1418258 872.3322918 1234.277961 1.01423966 0.702094994 0.932768031 0.865788315 0.854184841 0.886215792 0.911091601 0.729286153 0.706755139 1 10.26945161 -10.31137852 24.99719842 1.006724325 0.849782171 0 0.117755044 188.8392655 94523.59443 0.010868961 0.012429144 4.88E-11 10.31137852 -0.156942153 S(ph)LPTTVPES(ph)PNYR ddPTM_HeLa_Romidepsin_16h_R1 4 SLPTTVPESPNYR 13 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 2 0 S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR;S(1)LPTTVPES(1)PNYR ;;; 252.12 1.71E-52 1405435000 18024.2 16730.6 16477.9 15133.2 11756.6 9048.4 8235.6 8718.8 18642.5 16750 TRUE FALSE FALSE 17804.51412 16966.13383 16764.69094 16882.97179 11156.61683 8470.236442 8935.131658 8971.064722 16975.06811 16314.83259 1.091308417 1.039920804 1.027573581 1.034823477 0.68383275 0.519173972 0.547669221 0.5498717 1.040468422 1 13.99389656 -8.660133849 3.003759931 1.043675346 0.543372706 0.987817548 0.025581771 0.026615566 0.481267778 0.005532713 0.011807242 2.19E-09 8.660133849 -0.50030264 S(ph)LPTTVPESPNYR ddPTM_HeLa_Romidepsin_16h_R1 4 SLPTTVPESPNYR 13 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 0 S(1)LPTTVPESPNYR;S(0.999)LPTTVPESPNYR;S(1)LPTTVPESPNYR;S(0.995)LPT(0.004)TVPESPNYR ;;; 269.44 8.74E-80 909600000 7216.8 6847.5 5973.32 5747.46 4861.04 4374.83 4110.73 4111.26 7193.61 6605.95 TRUE FALSE FALSE 7128.838866 6943.899285 6077.283129 6412.008368 4612.96299 4095.292482 4459.895304 4230.212822 6550.195505 6434.326467 1.107938632 1.079195984 0.944509602 0.996531401 0.716930205 0.636475706 0.693140972 0.657444543 1.018007951 1 12.65157342 -8.775942891 2.354713212 1.047220133 0.660936319 0.933193113 0.045721751 0.05837259 0.660618881 0.008305643 0.017550751 1.68E-09 8.775942891 -0.386283814 S(ph)LPVSVPVWGFK ddPTM_HeLa_Romidepsin_16h_R1 2 SLPVSVPVWGFK 12 0 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 S(0.99)LPVS(0.01)VPVWGFK;S(0.999)LPVS(0.001)VPVWGFK ; 148.78 0.001472 18864300 5441 5057.9 5323.3 5294.5 4775.3 4252.8 3052.6 4154.4 5371.8 4613.8 TRUE FALSE FALSE 5374.682999 5129.105249 5415.949803 5906.675001 4531.598622 3981.059805 3311.887768 4274.601009 4891.332754 4493.932811 1.195986506 1.141339994 1.205169287 1.314366558 1.008381481 0.885874349 0.736968688 0.951193796 1.088430326 1 12.13376284 -8.367836939 3.334064471 1.122809749 0.843003899 0.649638798 0.096164112 0.145778561 3.034459095 0.016568836 0.040314564 4.29E-09 8.367836939 -0.27980585 S(ph)LQEEHVAVAQLR ddPTM_HeLa_Romidepsin_16h_R1 2 SLQEEHVAVAQLR 13 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 S(1)LQEEHVAVAQLR;S(1)LQEEHVAVAQLR ; 85.576 0.012461 18467200 4366.6 4834.1 3791.2 3886.7 3631 3917.6 3263.6 3741.1 4629.5 4066.8 TRUE FALSE FALSE 4313.3782 4902.154587 3857.184246 4336.098541 3445.696521 3667.278003 3540.810103 3849.342826 4215.425925 3961.14395 1.088922355 1.237560323 0.973755131 1.094658158 0.869874098 0.925812859 0.893885743 0.971775546 1.064194076 1 11.95170142 -8.763123439 24.99815487 1.056871643 0.914553088 0.540061023 0.071501324 30.98962416 460020.3509 0.011064812 0.02084423 1.73E-09 8.763123439 -0.142318554 S(ph)LQLPASPAPDPSPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLQLPASPAPDPSPR 15 0 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 S(1)LQLPASPAPDPSPR;S(1)LQLPASPAPDPSPR ; 144.08 0.00048208 21948000 4737.7 4615.5 5765.9 4339.2 4851.5 4360.6 3871.9 3969.3 6119.3 6179.1 TRUE FALSE FALSE 4679.95509 4680.47713 5866.253071 4840.918721 4603.909852 4081.971733 4200.779089 4084.145433 5571.974482 6018.566091 0.777586392 0.77767313 0.974692806 0.804330907 0.764951283 0.678229942 0.697970086 0.678591108 0.925797673 1 12.55520409 -16.52287875 0.064940962 1.857616177 0.414831047 0.639457462 0.067915243 126.9555341 0.644004443 17.23447655 2.840284794 3.00E-17 16.52287875 -1.44278513 S(ph)LQQLAEER ddPTM_HeLa_Romidepsin_16h_R1 1 SLQQLAEER 9 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 1 0 S(1)LQQLAEER 116.19 0.015629 4669800 654.83 610.95 598.65 789.84 712.34 837.75 737.1 664.71 746.88 645.13 TRUE FALSE FALSE 646.8486801 619.5509701 609.0692521 881.1650171 675.9866317 784.2204787 799.7092556 683.9423351 680.0771822 628.3694296 1.029408258 0.985966123 0.969285302 1.402304084 1.075778992 1.248024557 1.272673714 1.088439862 1.082288778 1 9.295469184 -9.293150217 24.99899997 1.00866065 1.214341203 0.556264782 0.091054924 322.5401452 254271.1583 0.012138473 0.01854283 5.09E-10 9.293150217 0.205680553 S(ph)LS(ph)SY(ph)RGKY(ph)SESWLR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSYRGKYSESWLR 15 2 Q86W71 Q86W71 GOLGA4 4 0 S(0.723)LS(0.723)S(0.723)Y(0.83)RGKY(0.455)S(0.38)ES(0.165)WLR 49.62 0.023638 7207000 1299.8 1212.3 1320.7 721.88 1226.2 1495.5 1280.4 1487.4 1616.7 1319.1 TRUE FALSE FALSE 1283.957538 1229.366791 1343.686229 805.3471621 1163.622438 1399.942377 1389.157144 1530.435572 1472.098303 1284.829592 0.999321269 0.956832563 1.045808906 0.626812433 0.905662857 1.089593815 1.081199525 1.191158409 1.145753734 1 10.32736131 -8.098598117 4.585825252 0.966027928 1.125998682 0.259219571 0.128918957 0.241395313 8.386446278 0.017155833 0.046379166 7.97E-09 8.098598117 0.159970755 S(ph)LSAPLHPEFEEVYR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSAPLHPEFEEVYR 15 0 Q53HC0-2;Q53HC0 Q53HC0-2 CCDC92 Coiled-coil domain-containing protein 92 1 0 S(0.62)LS(0.38)APLHPEFEEVYR 67.418 0.023539 1948200 1309.8 1176.6 1345 1186.7 2081.1 2091.5 1874.6 1893.4 1436 1289 TRUE FALSE FALSE 1293.835654 1193.164206 1368.409161 1323.911838 1974.893701 1957.8599 2033.828477 1948.182542 1307.560563 1255.511594 1.030524656 0.950341049 1.089921564 1.054479978 1.572979262 1.559412043 1.619920108 1.551704143 1.041456383 1 10.29405964 -8.77237465 5.396549664 1.016760846 1.581214376 0.980999869 0.037386184 0.014935117 1.297673061 0.005370858 0.01027693 1.69E-09 8.77237465 0.564453531 S(ph)LSASPALGSTK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSASPALGSTK 12 0 O95544;O95544-2 O95544 NADK NAD kinase 1 0 S(0.453)LS(0.268)AS(0.268)PALGS(0.011)TK;S(0.841)LS(0.108)AS(0.05)PALGSTK ; 156.52 0.0011826 146298000 5871.6 5273.2 6222.2 6314.9 6187 4993.4 4439.8 4248.3 5832.9 5073.9 TRUE FALSE FALSE 5800.034681 5347.436248 6330.494781 7045.05845 5871.254303 4674.337855 4816.916501 4371.217858 5311.190815 4942.079347 1.173602096 1.082021528 1.280937504 1.42552516 1.188012958 0.945824121 0.974674052 0.884489615 1.074687483 1 12.27090246 -8.248158781 22.30825299 1.131592561 0.938963614 0.433173395 0.118722429 196.985731 330884.596 0.020361042 0.051460932 5.65E-09 8.248158781 -0.192628946 S(ph)LSDSESDDSK ddPTM_HeLa_Romidepsin_16h_R1 5 SLSDSESDDSK 11 0 S4R2Y4;Q13185 S4R2Y4 CBX3 Chromobox protein homolog 3 1 0 S(0.995)LS(0.002)DS(0.002)ESDDSK;S(0.938)LS(0.013)DS(0.046)ES(0.003)DDSK;S(0.999)LS(0.001)DSESDDSK;S(0.465)LS(0.068)DS(0.465)ES(0.001)DDSK;S(0.625)LS(0.366)DS(0.009)ESDDSK ;;;; 171.26 0.00028711 784186800 15565.8 15363.6 18667.7 11693.1 10605.38 12611.4 14444.4 6226 19332.7 18655.1 TRUE FALSE FALSE 15376.07804 15579.88916 18992.60349 13045.11124 10064.14788 11805.57224 15671.30698 6406.139487 17603.53489 18170.43781 0.846213955 0.857430587 1.045247433 0.717930485 0.553874815 0.649713142 0.862461716 0.352558345 0.968800811 1 14.14930556 -9.075423708 5.139089492 0.926684063 0.626788074 0.602070633 0.130191987 0.123113531 5.892417642 0.019120072 0.03238489 8.41E-10 9.075423708 -0.299895989 TTT(ph)SPFFSEDTFR ddPTM_HeLa_Romidepsin_16h_R1 1 TTTSPFFSEDTFR 13 0 A0A5F9ZHK5;A0A5F9ZGT0;H0Y9K9;G5E9Z1;A0A590UJE4;A0A494C0H4;H0Y9M2;Q17R98-3;Q17R98-2;Q17R98 A0A5F9ZHK5 ZNF827 Zinc finger protein 827 1 0 T(0.054)T(0.004)T(0.471)S(0.471)PFFSEDTFR 217.91 1.86E-23 14516000 2478.1 2326 2393.6 2000.5 1169.2 1032 703.66 642.06 2241.6 2386.8 TRUE FALSE FALSE 2447.895964 2358.745489 2435.259604 2231.807223 1109.531361 966.0585306 763.4288628 660.6369931 2041.105682 2324.790592 1.052953317 1.014605572 1.047517833 0.960003551 0.477260776 0.415546473 0.328386077 0.284170538 0.877973994 1 11.18288505 -8.717068304 2.697327939 1.027251388 0.346495833 0.964158268 0.058478495 0.022078979 0.32728732 0.005942962 0.012585436 1.92E-09 8.717068304 -0.680755555 down S(ph)LSLESTDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSLESTDR 9 0 H0Y7V8;A0A0A0MRJ1;H0Y5V1;A0A0A0MRJ0;Q5VT25-3;Q5VT25-4;Q5VT25-5;Q5VT25;Q5VT25-2;Q5VT25-6 H0Y7V8 CDC42BPA Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase MRCK alpha 1 0 S(1)LSLESTDR 115.7 0.015905 5278200 2565.8 2464.8 3049.2 2643.6 2073.8 2571.7 2667.1 928.64 2970.2 2695.9 TRUE FALSE FALSE 2534.527043 2499.499519 3102.270047 2949.265471 1967.966248 2407.37667 2893.643407 955.5087332 2704.537873 2625.860129 0.96521784 0.951878393 1.181430044 1.123161679 0.749455855 0.916795469 1.101979262 0.363884094 1.029962656 1 11.35857436 -7.255084312 24.83959273 0.989512413 0.363883787 0.731587732 0.115763116 259.7257384 1015141.03 0.015521057 0.195129856 5.56E-08 7.255084312 -0.625628626 S(ph)LSPGGAALGYR ddPTM_HeLa_Romidepsin_16h_R1 4 SLSPGGAALGYR 12 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 S(0.992)LS(0.008)PGGAALGYR;S(0.999)LS(0.001)PGGAALGYR;S(0.999)LS(0.001)PGGAALGYR;S(0.999)LS(0.001)PGGAALGYR ;;; 208.33 1.12E-15 1364960000 18736.4 16138.5 18458.6 16271.7 19321 18909.9 16369.2 16688.7 17854.2 15637.4 TRUE FALSE FALSE 18508.03355 16365.69823 18779.86419 18153.11051 18334.97727 17701.61842 17759.59944 17171.5612 16257.27564 15231.13809 1.215144491 1.074489518 1.232991525 1.191842028 1.203782486 1.162199325 1.166006068 1.127398432 1.067371035 1 13.89473613 -12.38184562 0.89468156 0.990002939 1.1754337 0.559427149 0.047575417 0.292709316 0.381528081 0.038295976 0.007958019 4.15E-13 12.38184562 0.185430761 S(ph)LSPIIGK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSPIIGK 8 0 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;H7C2K6;X6RC15 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 S(0.796)LS(0.204)PIIGK;S(0.883)LS(0.117)PIIGK ; 126.31 0.014341 644550000 17912 18277.9 17843.1 14687.4 17871.1 17838.5 16127.8 17017.5 17765.8 15881 TRUE FALSE FALSE 17693.68165 18535.21676 18153.65167 16385.62629 16959.07108 16698.67742 17497.69493 17509.87451 16176.78235 15468.40933 1.143859157 1.198262624 1.173595247 1.05929614 1.096368134 1.079534234 1.131189029 1.131976413 1.04579482 1 13.91703723 -12.21588122 0.984638731 1.000959425 1.126022496 0.490924967 0.04139452 0.327335369 0.576588553 0.028091378 0.008083403 6.08E-13 12.21588122 0.125063071 S(ph)LSPILPGR ddPTM_HeLa_Romidepsin_16h_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 0 S(0.628)LS(0.372)PILPGR 102.06 0.026461 53874000 3649.4 3760.3 3526.2 3233.2 5357.4 5852.3 5223.8 5959 4231.4 3884.3 TRUE FALSE FALSE 3604.919709 3813.237602 3587.572032 3607.037797 5083.991887 5478.356917 5667.509442 6131.414263 3852.932986 3783.385326 0.95282912 1.007890361 0.948243893 0.953388959 1.343767935 1.448003956 1.49799953 1.62061586 1.018382389 1 11.885462 -8.583560661 2.307534439 0.97410151 1.524708315 0.959471667 0.050878389 0.038568829 0.412463504 0.007389813 0.017403329 2.61E-09 8.583560661 0.550606805 S(ph)LSPPQSQSK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPPQSQSK 10 0 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;I3L0Y9;Q9UQB8-6;I3L3C6 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 S(0.781)LS(0.151)PPQS(0.066)QS(0.002)K 100.09 0.0029272 0 1429.4 1304.7 1262.4 983.67 2925.6 5260.6 5305.2 5273.3 1388.9 1335.4 TRUE FALSE FALSE 1411.977923 1323.067601 1284.371542 1097.406554 2776.295715 4924.464638 5755.823556 5425.874616 1264.673305 1300.706115 1.085547232 1.017191805 0.987441765 0.843700618 2.134452727 3.785993299 4.42515299 4.171483897 0.972297501 1 10.34507932 -8.355280903 2.147219716 1.020767474 4.299011204 0.991751577 0.128463339 0.017885697 0.159158188 0.018154458 0.051047721 4.41E-09 8.355280903 3.27824373 up S(ph)LSPQEDALTGSR ddPTM_HeLa_Romidepsin_16h_R1 3 SLSPQEDALTGSR 13 0 Q96EN8 Q96EN8 MOCOS Molybdenum cofactor sulfurase 1 0 S(0.848)LS(0.152)PQEDALTGSR;S(0.998)LS(0.002)PQEDALTGSR;S(0.985)LS(0.015)PQEDALTGSR ;; 236.03 2.52E-41 97188000 6898.13 6262.23 5562.96 6397.34 6390.37 6418.44 4958.8 5613.22 6421.4 6822.5 TRUE FALSE FALSE 6814.052938 6350.389838 5659.780985 7137.030551 6064.245573 6008.322399 5380.000348 5775.629665 5847.053901 6645.250466 1.025401973 0.955628365 0.851703185 1.074004748 0.912568398 0.904152888 0.809600838 0.86913649 0.879884653 1 12.69810786 -7.961636068 0.466114028 1.011044863 0.768629126 0.159651993 0.072863808 1.587128347 0.349867064 0.014363016 0.188396621 1.09E-08 7.961636068 -0.242415737 S(ph)LSRTPETLLPFAEAEAFLKK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSRTPETLLPFAEAEAFLKK 21 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 S(0.427)LS(0.427)RT(0.139)PET(0.008)LLPFAEAEAFLKK 80.082 0.0011618 10360000 2090.9 1572.7 1823.8 2239.7 2132.4 2154.1 1999.5 1616.1 2106.6 1889.6 TRUE FALSE FALSE 2065.415307 1594.840512 1855.542474 2498.664652 2023.575671 2016.459962 2169.33748 1662.859304 1918.18042 1840.50792 1.122198543 0.86652195 1.008168699 1.357595165 1.099465886 1.09559972 1.178662399 0.903478483 1.042201666 1 10.84588824 S(ph)LSS(ph)SPVKK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSSPVKK 9 1 Q9H3Q1;Q9H3Q1-2 Q9H3Q1 CDC42EP4 Cdc42 effector protein 4 2 0 S(0.999)LS(0.008)S(0.945)S(0.049)PVKK 98.754 0.027683 19316000 5502.6 5373.3 5488 5275 5066.4 3926.5 3937.6 4234.9 6151.2 5620.9 TRUE FALSE FALSE 5435.532195 5448.945458 5583.516338 5884.92032 4807.842703 3675.609322 4272.059646 4357.43015 5601.021266 5474.868208 0.992815167 0.995265137 1.019844885 1.074897166 0.878165925 0.671360329 0.78030365 0.795896812 1.023042209 1 12.41860852 -8.523880862 4.995180784 1.002862448 0.753944533 0.902849835 0.039467211 0.037900476 2.733360523 0.005469058 0.011706079 2.99E-09 8.523880862 -0.248917915 AQSS(ph)PAAPASLSAPEPASQAR ddPTM_HeLa_Romidepsin_16h_R1 1 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;Q8WUI4-10;H0YI15 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 0 AQS(0.075)S(0.925)PAAPASLSAPEPASQAR 88.57 0.001238 8728200 1187.5 1273.4 1283.9 1081.7 675.34 754.81 467.36 389.67 1380.4 1175.9 TRUE FALSE FALSE 1173.026293 1291.326959 1306.245741 1206.771244 640.8748798 706.580077 507.0575467 400.9444867 1256.933567 1145.349948 1.024164095 1.127451885 1.140477408 1.053626662 0.559545037 0.616911956 0.442709713 0.350062867 1.097423166 1 10.16157275 -8.715744262 4.457593945 1.0355159 0.486511955 0.926084587 0.080219875 0.044504872 1.890852798 0.012730426 0.025591006 1.92E-09 8.715744262 -0.549003945 down S(ph)LSVPVDLSR ddPTM_HeLa_Romidepsin_16h_R1 3 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 0 S(0.945)LS(0.055)VPVDLSR;S(0.5)LS(0.5)VPVDLS(0.001)R;S(0.92)LS(0.079)VPVDLSR ;; 149.94 0.0037522 123430000 6180.8 6314 7078.4 7803.5 19484.2 21053.5 17885 18749.5 6566 5423.2 TRUE FALSE FALSE 6105.466032 6402.888658 7201.596583 8705.777387 18489.84857 19708.2493 19404.15145 19291.9872 5978.720515 5282.304482 1.155833794 1.212139262 1.363343709 1.648102152 3.500337519 3.730994562 3.6734254 3.652191438 1.131839434 1 12.36695175 -8.820026172 2.649823425 1.111363073 3.7053647 0.991766313 0.1072338 0.020100503 0.287582531 0.020716576 0.041932574 1.51E-09 8.820026172 2.594001627 up S(ph)LSYSPVER ddPTM_HeLa_Romidepsin_16h_R1 2 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.734)LS(0.134)YS(0.132)PVER;S(0.593)LS(0.152)YS(0.255)PVER ; 125.68 0.010489 94594500 7561.3 7190.3 6854.1 4913 5198 4845.6 3927.21 4595.8 7748.9 6847.9 TRUE FALSE FALSE 7469.139967 7291.525232 6973.392735 5481.064176 4932.726664 4535.981798 4260.787119 4728.772222 7055.818977 6669.990571 1.119812673 1.093183739 1.045487645 0.821749914 0.739540275 0.680058203 0.638799572 0.708962355 1.05784542 1 12.70346901 -9.05753925 1.935896919 1.062615231 0.680048474 0.959488828 0.036329297 0.063191624 0.468344452 0.008161763 0.015701055 8.76E-10 9.05753925 -0.382566757 S(ph)LTFTGGAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLTFTGGAK 9 0 F5H8C5;F5H0S5;F5H7J1;Q8NHQ8-2;Q8NHQ8 F5H8C5 RASSF8 Ras association domain-containing protein 8 1 0 S(0.997)LT(0.001)FT(0.002)GGAK 103.26 0.025376 16470000 1574.2 1409.2 1643.4 1332.2 2516.2 2416.7 1485.1 1889.7 1502.6 1486.4 TRUE FALSE FALSE 1555.013045 1429.038755 1672.002688 1486.235232 2387.788925 2262.28067 1611.244357 1944.375488 1368.203693 1447.783114 1.074064914 0.987053061 1.154870969 1.026559309 1.649272534 1.562582578 1.11290451 1.343001911 0.945033603 1 10.49962978 -8.787117837 24.98567109 1.041261235 1.40562655 0.638250261 0.142023543 109.2144822 106267.6165 0.020856214 0.037814666 1.63E-09 8.787117837 0.364365315 S(ph)LTNLSFLTDSEK ddPTM_HeLa_Romidepsin_16h_R1 2 SLTNLSFLTDSEK 13 0 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 S(0.874)LT(0.011)NLS(0.115)FLTDSEK;S(0.997)LT(0.003)NLSFLTDSEK ; 172.09 6.52E-05 45992000 6009.1 4775.9 6117.3 5830.7 4783.2 4531.3 3959.2 4056.3 6067.6 5412.5 TRUE FALSE FALSE 5935.858778 4843.135246 6223.76904 6504.872968 4539.095455 4241.764554 4295.494349 4173.662641 5524.898659 5271.88247 1.125946721 0.918672841 1.180559141 1.233880498 0.861000882 0.804601502 0.814793269 0.791683552 1.047993519 1 12.36410249 -8.605524514 7.398879532 1.069918317 0.809365059 0.707194316 0.084247675 0.105155177 8.003856432 0.01313404 0.026368071 2.48E-09 8.605524514 -0.260553258 S(ph)LTNLSFLTDSEKK ddPTM_HeLa_Romidepsin_16h_R1 2 SLTNLSFLTDSEKK 14 1 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 S(0.863)LT(0.133)NLS(0.004)FLTDSEKK;S(0.748)LT(0.192)NLS(0.06)FLTDSEKK ; 107.51 0.0019967 87673000 6945.2 5709 6829.1 7777.2 5628.3 4975.8 4517.9 4703.7 6947.1 6451.4 TRUE FALSE FALSE 6860.549231 5789.371452 6947.957621 8676.436457 5341.066849 4657.862439 4901.650313 4839.794138 6325.733977 6283.791698 1.091784954 0.921318167 1.105695089 1.380764493 0.849975159 0.741250293 0.780046594 0.770202828 1.006674677 1 12.61741964 -8.539983282 24.98769121 1.062664326 0.770480856 0.622189438 0.114836308 121.7500235 177861.7726 0.016716529 0.033438944 2.88E-09 8.539983282 -0.29218347 S(ph)LTNPTPIQQQLR ddPTM_HeLa_Romidepsin_16h_R1 1 SLTNPTPIQQQLR 13 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 S(0.939)LT(0.005)NPT(0.056)PIQQQLR 166.45 0.00015153 13049000 1427.9 1817.3 1767.4 2096.6 1902.5 1733.3 1220.1 1389.5 1408 1334.5 TRUE FALSE FALSE 1410.496206 1842.883997 1798.160856 2339.018757 1805.408326 1622.547724 1323.735264 1429.70299 1282.064954 1299.829498 1.085139403 1.417789026 1.383382097 1.79948121 1.388957805 1.248277352 1.018391463 1.099915791 0.986333174 1 10.34410668 -10.36541614 4.606294789 1.036861399 1.342195982 0.342277272 0.198989581 0.213997293 7.351508852 0.037863879 0.043088451 4.31E-11 10.36541614 0.305334583 S(ph)LTNSHLEK ddPTM_HeLa_Romidepsin_16h_R1 2 SLTNSHLEK 9 0 F8VX12;F8VX04;Q9H2H9 F8VX12 SLC38A1 Sodium-coupled neutral amino acid transporter 1 1 0 S(0.994)LT(0.002)NS(0.004)HLEK;S(0.804)LT(0.125)NS(0.071)HLEK ; 117.93 0.0061373 19469200 6363.4 12509.2 7610 5265.3 6439.7 8237.9 4230.9 7484.1 8832.1 8799.8 TRUE FALSE FALSE 6285.840433 12685.30485 7742.448858 5874.09876 6111.058079 7711.524777 4590.27254 7700.640626 8042.134856 8571.179927 0.733369324 1.479995164 0.903311904 0.685331402 0.712977458 0.89970399 0.535547332 0.898434135 0.938276284 1 13.06527811 -9.322930061 7.256473729 0.928315002 0.741519654 0.240873052 0.210731623 0.419350853 43.50517344 0.034361724 0.052675223 4.75E-10 9.322930061 -0.186795349 S(ph)LTPAVPVESKPDKPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PCH5;P20810-2;E9PSG1;H0Y944;E7EQK6;P20810-3 P20810-6;P20810-3 CAST Calpastatin 1 0 S(0.757)LT(0.241)PAVPVES(0.002)KPDKPSGK 65.416 0.028124 17672000 1742 1654.2 1650.4 1968.7 2121.5 2535.8 1771.6 2236.2 1922.7 2117.6 TRUE FALSE FALSE 1720.767834 1677.487871 1679.12452 2196.330357 2013.231939 2373.770564 1922.07966 2300.900919 1750.728897 2062.584447 0.834277519 0.813294153 0.814087647 1.064843847 0.976072491 1.15087194 0.931879256 1.11554265 0.8488035 1 11.01023747 -9.243336985 24.77538726 0.902555337 1.043136356 0.537666276 0.081876266 638.9597105 874496.7548 0.014095107 0.023342271 5.71E-10 9.243336985 0.140581019 S(ph)LTPPPSSTESK ddPTM_HeLa_Romidepsin_16h_R1 1 SLTPPPSSTESK 12 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 S(0.872)LT(0.11)PPPS(0.014)S(0.003)T(0.001)ESK 113.24 0.0096244 83116000 2778 2225.6 2146.1 2506.5 2311 1836.3 1860.4 2281 2433.8 2635.3 TRUE FALSE FALSE 2744.140667 2256.932055 2183.45197 2796.313323 2193.061046 1718.966356 2018.42233 2346.997136 2216.114832 2566.834526 1.069075797 0.879266674 0.850639941 1.089401477 0.854383492 0.669683355 0.786346883 0.91435467 0.863364899 1 11.32577458 -9.072209491 0.74064756 1.027472137 0.787384408 0.140023926 0.112382499 0.494830394 0.517211335 0.020552914 0.059463704 8.47E-10 9.072209491 -0.240087729 S(ph)LTSSLENIFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 S(0.568)LT(0.216)S(0.216)S(0.001)LENIFSR 166.86 0.00023731 8289300 807.49 854.33 1059.2 785.31 1330.5 873.88 483.51 665.75 978.33 1037.9 TRUE FALSE FALSE 797.6480013 866.3572802 1077.634932 876.1112372 1262.59962 818.0418883 524.5793273 685.0124259 890.8257145 1010.935208 0.789019904 0.85698596 1.065978238 0.866634409 1.248942177 0.809193192 0.518904993 0.677602699 0.881189721 1 9.981474821 -7.945766253 5.952194357 0.92878176 0.607039813 0.538957783 0.130560649 0.125339766 9.46433017 0.019393777 0.059315999 1.13E-08 7.945766253 -0.321741947 S(ph)LVPAAELLESR ddPTM_HeLa_Romidepsin_16h_R1 2 SLVPAAELLESR 12 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 S(1)LVPAAELLESR;S(1)LVPAAELLESR ; 130.15 0.0039499 3205400 1844.19 1832.97 1883.95 1238.19 2071.9 1925.16 1874.73 1952.26 2203.6 1850 TRUE FALSE FALSE 1821.712303 1858.7746 1916.739359 1381.355354 1966.163212 1802.148489 2033.969519 2008.745563 2006.504497 1801.936733 1.010974619 1.031542654 1.063710686 0.766594813 1.09113887 1.000117516 1.128768553 1.114770306 1.113526607 1 10.81533264 -7.76344823 24.69900357 1.000175776 1.121769463 0.193137672 0.089954407 39.8316215 489772.9143 0.01058958 0.034265165 1.72E-08 7.76344823 0.121593687 S(ph)LYASS(ph)PGGVYATR ddPTM_HeLa_Romidepsin_16h_R1 2 SLYASSPGGVYATR 14 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 2 0 S(1)LYAS(0.01)S(0.985)PGGVYAT(0.005)R;S(1)LYAS(0.009)S(0.991)PGGVYATR ; 176.43 4.90E-06 16562200 6572.1 5585.8 5777.4 5391.4 7004.1 7152.1 5775.7 6714.8 6505.8 5840.9 TRUE FALSE FALSE 6491.996717 5664.437039 5877.953223 6014.779035 6646.654641 6695.103892 6266.287814 6909.082144 5923.904954 5689.152576 1.141118406 0.995655673 1.033186076 1.057236373 1.168303109 1.176819184 1.101444851 1.214430805 1.041263154 1 12.47399806 -8.7631798 24.92242212 1.058900149 1.161518432 0.605442635 0.046789614 34.44038479 493189.0839 0.008895237 0.016749675 1.73E-09 8.7631798 0.102618283 S(ph)LYYYIQQDTK ddPTM_HeLa_Romidepsin_16h_R1 1 SLYYYIQQDTK 11 0 P07355;P07355-2;A6NMY6 P07355 ANXA2;ANXA2P2 Annexin A2;Putative annexin A2-like protein 1 0 S(0.943)LY(0.055)Y(0.002)YIQQDTK 119.21 0.0011162 0 1127.1 983.8 1176.6 943.96 1367.6 1366.6 932.74 814.2 1100.9 1170.7 TRUE FALSE FALSE 1113.362472 997.6499622 1197.078229 1053.105097 1297.806269 1279.27867 1011.966912 837.7575924 1002.432747 1140.285045 0.976389611 0.874912783 1.049806129 0.923545478 1.138141971 1.121893754 0.887468372 0.734691379 0.879107159 1 10.15517879 -7.460238041 4.040174393 0.998320944 0.749681459 0.46611271 0.086144 0.13371228 4.099894536 0.010608866 0.066546927 3.47E-08 7.460238041 -0.248639485 S(ph)MDEFTASTPADLGEAGR ddPTM_HeLa_Romidepsin_16h_R1 2 SMDEFTASTPADLGEAGR 18 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 0 S(0.999)MDEFTASTPADLGEAGR;S(0.994)MDEFT(0.005)AS(0.001)TPADLGEAGR ; 124.04 0.0021925 13482200 2748.5 2396.78 2606.04 2040.27 2400.1 2548.19 2081.68 2398.11 2820.32 2375.76 TRUE FALSE FALSE 2715.000225 2430.521932 2651.397033 2276.175617 2277.613941 2385.368883 2258.497847 2467.495529 2568.063516 2314.037413 1.173274127 1.050338218 1.145788317 0.983638209 0.984259774 1.030825548 0.975998847 1.066316178 1.109776143 1 11.17619647 -9.243305827 24.83954749 1.085401186 1.006344433 0.411909026 0.051580298 874.2052742 1197497.555 0.010492142 0.017374539 5.71E-10 9.243305827 -0.079056753 S(ph)MDELNHDFQALALEGR ddPTM_HeLa_Romidepsin_16h_R1 4 SMDELNHDFQALALEGR 17 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;E9PR38;Q14671-4 Q5T1Z4 PUM1 Pumilio homolog 1 1 0 S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR;S(1)MDELNHDFQALALEGR ;;; 83.894 0.0045034 12336100 4485.08 4271.4 3863.53 2594.31 4186.73 4587.3 3778.53 3927.74 4398.42 4459.91 TRUE FALSE FALSE 4430.41412 4331.532881 3930.773119 2894.276329 3973.065545 4294.186335 4099.478244 4041.38296 4005.014299 4344.040895 1.019883152 0.99712065 0.904865588 0.666263601 0.914601322 0.98852346 0.943701577 0.930328019 0.921955938 1 12.08482197 -9.756097624 5.039553544 1.00912215 0.888246667 0.205122554 0.085315804 0.167337931 11.69229723 0.013535105 0.018655988 1.75E-10 9.756097624 -0.120875482 S(ph)MDLGIADETK ddPTM_HeLa_Romidepsin_16h_R1 2 SMDLGIADETK 11 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 S(1)MDLGIADETK;S(1)MDLGIADETK ; 116.71 0.015881 45036000 11847.8 11890.5 12024.7 7907.5 10031 9034.7 8132.5 8611 11583.6 12708.7 TRUE FALSE FALSE 11703.39446 12057.89477 12233.98486 8821.802356 9519.080639 8457.411828 8823.274347 8860.145699 10547.5338 12378.52614 0.945459445 0.974097775 0.988323224 0.712669849 0.768999518 0.683232538 0.712788764 0.715767418 0.852083171 1 13.59555193 -9.260450257 24.99945544 0.974537066 0.719188607 0.866638737 0.045330125 12.77843138 322965.5032 0.004224163 0.006749691 5.49E-10 9.260450257 -0.255348459 S(ph)MDLGIADETKLNTVDDQK ddPTM_HeLa_Romidepsin_16h_R1 1 SMDLGIADETKLNTVDDQK 19 1 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 S(0.998)MDLGIADET(0.001)KLNT(0.001)VDDQK 90.706 0.0041296 17065000 2079.3 2214.4 1899 1643.5 1362.3 1417.5 1238.7 1218.2 2028.6 1804.5 TRUE FALSE FALSE 2053.956692 2245.574381 1932.051298 1833.529203 1292.776748 1326.926325 1343.915147 1253.446695 1847.156935 1757.61883 1.168601893 1.277623079 1.099243628 1.043189326 0.735527366 0.754956821 0.764622638 0.71315047 1.050942846 1 10.77940652 -8.811658616 4.222109843 1.09975292 0.742440894 0.862916411 0.071421457 0.073439294 2.724448252 0.013592964 0.025945887 1.54E-09 8.811658616 -0.357312026 S(ph)MDSSDLSDGAVTLQEYLELKK ddPTM_HeLa_Romidepsin_16h_R1 2 SMDSSDLSDGAVTLQEYLELKK 22 1 J3QRU8;A0A0C4DGN6;Q9Y2X7;Q9Y2X7-3;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 0 S(0.938)MDS(0.043)S(0.012)DLS(0.008)DGAVTLQEYLELKK;S(0.662)MDS(0.271)S(0.067)DLSDGAVTLQEYLELKK ; 129.66 0.0001028 94389000 2819.9 2386.85 2519.6 2221.26 3025.2 3270.4 2502.4 3182 2738.1 2926.8 TRUE FALSE FALSE 2785.529974 2420.452137 2563.452581 2478.092533 2870.812755 3061.431995 2714.953794 3274.06615 2493.197478 2850.761314 0.977117923 0.849054646 0.89921684 0.869273945 1.007033715 1.073899796 0.952360964 1.148488347 0.87457251 1 11.47713154 -4.000000033 0.987873474 0.966637989 157.7357223 0.382720318 0.071980894 1339.136853 1.880888275 0.010873206 475083.2073 1.00E-04 4.000000033 156.7690843 S(ph)MGETESGDAFLDLK ddPTM_HeLa_Romidepsin_16h_R1 1 SMGETESGDAFLDLK 15 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2;B1AKL5;B1AKL6 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 S(0.999)MGET(0.001)ESGDAFLDLK 99.069 0.011566 5290300 1704.2 1422.4 1278.3 1108 1470.9 1611.1 1263.1 1386.1 1298.4 1516 TRUE FALSE FALSE 1683.428555 1442.424585 1300.548275 1236.112173 1395.834484 1508.15591 1370.387682 1426.204617 1182.267852 1476.614101 1.14005992 0.976846004 0.880763819 0.837126079 0.945294023 1.021360901 0.928060812 0.965861436 0.800661358 1 10.52807713 -10.04020753 7.140226809 1.065931623 0.930109099 0 0.100568957 0.158925203 23.48681771 0.011648221 0.014425772 9.12E-11 10.04020753 -0.135822524 S(ph)MGGAAIAPPTSLVEK ddPTM_HeLa_Romidepsin_16h_R1 1 SMGGAAIAPPTSLVEK 16 0 H0Y6J6;Q5W012;Q96I25;Q5W011;Q5W010 H0Y6J6 RBM17 Splicing factor 45 1 0 S(1)MGGAAIAPPTSLVEK 91.14 0.01615 13080000 1232.1 1456 1489.1 984.4 1295.4 1856.1 1500.2 1586.6 1377.1 1272.9 TRUE FALSE FALSE 1217.082691 1476.497606 1515.017161 1098.22096 1229.290904 1737.5012 1627.626951 1632.505768 1253.928727 1239.829875 0.98165298 1.190887263 1.221955683 0.885783592 0.991499664 1.401402915 1.312782491 1.31671756 1.011371602 1 10.27592646 -8.265336979 24.98704205 1.016129973 1.340549147 0.660644306 0.098496078 143.7807985 921764.6896 0.014889367 0.034508596 5.43E-09 8.265336979 0.324419174 S(ph)MGYDDLDYGMMSDYGTAR ddPTM_HeLa_Romidepsin_16h_R1 2 SMGYDDLDYGMMSDYGTAR 19 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 S(0.901)MGY(0.026)DDLDY(0.05)GMMS(0.023)DYGTAR;S(0.89)MGY(0.068)DDLDY(0.026)GMMS(0.015)DY(0.001)GTAR ; 52.93 0.010961 115963000 4162.4 3644.4 3921 2223.7 3715.8 4388.6 3178.8 3181.3 3653.3 3530.9 TRUE FALSE FALSE 4111.667068 3695.705959 3989.24336 2480.814657 3526.16886 4108.182624 3448.807193 3273.345896 3326.539698 3439.166709 1.195541658 1.074593433 1.159944748 0.721341786 1.025297451 1.194528492 1.002803145 0.951784596 0.967251657 1 11.74784333 S(ph)MPTSGALDRVAS(ph)ATKIALY(ph)ETPTGWK ddPTM_HeLa_Romidepsin_16h_R1 1 SMPTSGALDRVASATKIALYETPTGWK 27 2 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 3 0 S(0.434)MPT(0.153)S(0.424)GALDRVAS(0.96)AT(0.082)KIALY(0.667)ET(0.122)PT(0.158)GWK 45.572 0.0038703 0 2235.4 2208.3 1920.6 2055.8 1546.2 1526.4 1558.6 1524.4 2036.2 2057.5 TRUE FALSE FALSE 2208.154085 2239.388505 1954.027237 2293.501269 1467.291644 1428.867966 1690.987445 1568.506109 1854.077172 2004.045853 1.101848085 1.117433766 0.975041182 1.144435525 0.732164707 0.712991653 0.843786804 0.782669771 0.925167041 1 10.9686998 -8.755006149 24.99995423 1.054926501 0.769401185 0.782536119 0.071158063 44.87004527 174366.2456 0.00914326 0.017939754 1.76E-09 8.755006149 -0.285525316 S(ph)NESVDIQDQEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNESVDIQDQEEK 13 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 S(0.584)NES(0.416)VDIQDQEEK 153.2 0.00076893 7460800 2230 2234.2 2319.8 1777.1 1900.5 2947.2 2159.1 2864.5 2237.6 2522.3 TRUE FALSE FALSE 2202.819902 2265.653126 2360.175146 1982.576664 1803.510393 2758.883432 2342.4939 2947.379788 2037.463452 2456.770282 0.896632428 0.922207966 0.960682064 0.806984958 0.734098099 1.122971672 0.953485117 1.199696939 0.829325992 1 11.26254725 -8.19638615 24.99991476 0.925021755 1.078194783 0.445593689 0.099784712 183.5473176 70536.59879 0.014041423 0.035798743 6.36E-09 8.19638615 0.153173029 S(ph)NFSNSADDIK ddPTM_HeLa_Romidepsin_16h_R1 2 SNFSNSADDIK 11 0 P45973 P45973 CBX5 Chromobox protein homolog 5 1 0 S(0.995)NFS(0.005)NSADDIK;S(1)NFSNSADDIK ; 158.31 0.001639 121037000 5169.3 4679.1 4660.4 3577.5 4928.4 5672.6 5137.8 4905.8 5060.2 4584.2 TRUE FALSE FALSE 5106.294583 4744.972493 4741.512307 3991.147383 4676.885358 5310.139167 5574.204604 5047.741583 4607.603038 4465.101823 1.143600927 1.062679572 1.061904632 0.89385361 1.047430841 1.189253768 1.248393614 1.130487452 1.031914438 1 12.12447736 -8.25310698 9.521890926 1.053851286 1.195405089 0.518344281 0.066541699 0.158037532 153.2114595 0.011196711 0.027338 5.58E-09 8.25310698 0.141553803 S(ph)NLNS(ph)T(ph)IS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 SNLNSTISK 9 0 P56715 P56715 RP1 Oxygen-regulated protein 1 4 0 S(1)NLNS(1)T(1)IS(1)K 56.81 0.0042173 0 793.25 621 836.02 1238.9 801.07 758.58 793.29 711.33 1153.7 758.24 TRUE FALSE FALSE 783.5815639 629.7424543 850.5705774 1382.147447 760.1884087 710.1091862 860.6720328 731.9112113 1050.510183 738.5408155 1.060986133 0.852684701 1.151690685 1.871457092 1.029311302 0.961502968 1.16536827 0.991023375 1.42241317 1 9.528533844 -9.537238096 24.70536807 1.015718545 1.211765959 0.016301421 0.278616308 333.9245372 574517.2945 0.039084487 0.055288109 2.90E-10 9.537238096 0.196047414 S(ph)NPSIQATLNK ddPTM_HeLa_Romidepsin_16h_R1 1 SNPSIQATLNK 11 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 0 S(1)NPSIQATLNK 150.9 0.0003892 0 1722.5 1568.2 1570.9 1451.7 1026.7 966.17 1024 770.37 1801.5 1374.9 TRUE FALSE FALSE 1701.505507 1590.277161 1598.240856 1619.552384 974.3036679 904.4348552 1110.978534 792.6594405 1640.369328 1339.1799 1.27055783 1.187500769 1.193447464 1.20936133 0.727537553 0.675364718 0.829596184 0.591899147 1.224905876 1 10.38713406 -8.755103925 24.898344 1.146289961 0.712725148 0.868536512 0.089887079 51.43791766 202149.0124 0.016954472 0.033254893 1.76E-09 8.755103925 -0.433564813 S(ph)NSDESNFSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSDESNFSEK 11 0 A0A087WWW9;O95999 A0A087WWW9 BCL10 B-cell lymphoma/leukemia 10 1 0 S(0.613)NS(0.384)DES(0.003)NFSEK 175.29 6.89E-05 20216000 2932.7 2906.8 2238.1 2438 3548.9 4355.1 3743.7 4470.2 3065.3 2952.6 TRUE FALSE FALSE 2896.955124 2947.722007 2277.053192 2719.893031 3367.78639 4076.823165 4061.689785 4599.538184 2791.131891 2875.891026 1.007324373 1.024976948 0.791773113 0.945756639 1.17104103 1.417586107 1.412323954 1.599343696 0.970527696 1 11.48979329 -8.344803806 2.046952997 0.984178961 1.498312407 0.898119388 0.078247727 0.077964123 0.629015248 0.0119579 0.034620533 4.52E-09 8.344803806 0.514133446 S(ph)NSFNNPLGNR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 S(0.991)NS(0.009)FNNPLGNR;S(0.845)NS(0.155)FNNPLGNR ; 176.99 1.42E-05 64629000 4311.3 4673.7 4540.2 3833.1 3575.9 3196.2 2243.81 2719.3 4712.2 3819.3 TRUE FALSE FALSE 4258.752217 4739.496471 4619.220276 4276.301057 3393.408479 2991.973135 2434.399165 2797.978655 4290.72903 3720.074035 1.144803081 1.274032835 1.241701168 1.149520417 0.912188426 0.804277847 0.654395354 0.752129831 1.153398827 1 11.86111562 -8.418091811 2.180689837 1.106160447 0.715139441 0.821506602 0.087253271 0.130390674 1.204656386 0.01624448 0.043364784 3.82E-09 8.418091811 -0.391021006 S(ph)NSLNNGQPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSLNNGQPK 10 0 O60333-3 O60333-3 KIF1B Kinesin-like protein KIF1B 1 0 S(0.626)NS(0.374)LNNGQPK 135.1 0.0058365 7689200 3506.5 4564.5 6430.9 4240.9 2617.9 3872.2 7360.8 1393.8 5393.9 6016.1 TRUE FALSE FALSE 3463.761429 4628.759151 6542.827117 4731.252812 2484.298794 3624.778917 7986.026168 1434.127404 4911.456075 5859.800855 0.591105656 0.789917484 1.116561344 0.807408465 0.423956181 0.618583977 1.362849415 0.244739956 0.83816092 1 12.51663592 -8.970642916 24.97713483 0.827678939 0.697699212 0.082784038 0.299906928 640.4131669 544863.9192 0.04518718 0.081907965 1.07E-09 8.970642916 -0.129979727 S(ph)NSLSTPRPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNSLSTPRPTR 11 1 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 S(0.644)NS(0.354)LS(0.002)TPRPTR 70.628 0.028553 13278000 787.64 624.63 575.26 496.77 813.17 600.75 731.73 570.41 739.37 680.99 TRUE FALSE FALSE 778.0399407 633.4235575 585.272159 554.2088848 771.6709005 562.3640138 793.8831279 586.9139134 673.2388954 663.2977816 1.172987401 0.954961067 0.882367129 0.835535562 1.163385318 0.847830385 1.196872883 0.884842268 1.014987407 1 9.373512891 -10.23183344 24.45682523 1.081688502 0.970129799 0.104303129 0.125098666 771.3335419 637182.9336 0.020734061 0.02539188 5.86E-11 10.23183344 -0.111558703 S(ph)NSPLPVPPSK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 0 S(0.903)NS(0.097)PLPVPPSK;S(0.5)NS(0.5)PLPVPPSK ; 140.31 0.0031046 1312180000 74906 78650 64763 54455 55502 51970 49495 51282 76948 73894 TRUE FALSE FALSE 73993.01686 79757.23676 65890.17285 60751.34332 52669.52583 48649.28473 53699.10406 52765.76376 70065.57816 71974.22323 1.028048842 1.108136124 0.915469037 0.844070844 0.731783178 0.675926499 0.746087997 0.733120295 0.973481547 1 16.13519269 -9.168275976 1.782992952 1.020061585 0.719210695 0.910624007 0.042550907 0.065898393 0.409727202 0.00646379 0.012025936 6.79E-10 9.168275976 -0.30085089 S(ph)NSRLEDQVIGVALQASK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSRLEDQVIGVALQASK 18 1 A0A3B3IRW6;Q2KHR3-2;Q2KHR3 A0A3B3IRW6 QSER1 Glutamine and serine-rich protein 1 1 0 S(0.5)NS(0.5)RLEDQVIGVALQASK 96.848 0.00049515 0 1969.7 2135.2 1559.4 1446.6 1467.7 789.16 638.71 1042.1 1951 1927 TRUE FALSE FALSE 1945.692539 2165.259402 1586.540703 1613.862698 1392.797792 738.7352229 692.9620115 1072.251519 1776.497674 1876.936262 1.036632185 1.153613708 0.845282141 0.85983884 0.742059185 0.393585674 0.369198478 0.571277534 0.946488013 1 10.87416394 -8.673335913 1.29907587 1.021356846 0.424616796 0.865723763 0.093702533 0.099119647 0.329866412 0.013922764 0.039547761 2.12E-09 8.673335913 -0.59674005 S(ph)NTPMGDKDDDDDDDADEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNTPMGDKDDDDDDDADEK 19 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6RE05;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 S(0.569)NT(0.431)PMGDKDDDDDDDADEK 70.942 0.016854 3118800 1092.3 984.27 954.31 729.73 1101.4 1487.5 997.44 1085 1366.5 1276.9 TRUE FALSE FALSE 1078.986627 998.1265789 970.9193652 814.1048161 1045.191448 1392.453551 1082.162529 1116.392763 1244.276818 1243.725954 0.867543709 0.802529348 0.780653778 0.654569291 0.84037118 1.119582289 0.870097247 0.897619576 1.000442914 1 10.28045292 S(ph)PAGGESATVAAK ddPTM_HeLa_Romidepsin_16h_R1 3 SPAGGESATVAAK 13 0 Q147X3 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 0 S(0.999)PAGGESATVAAK;S(1)PAGGESATVAAK;S(1)PAGGESATVAAK ;; 162.67 0.0003127 30924500 4271.5 4334.11 3782.5 2959.83 3829.5 4075.08 3569.72 4267.9 4763.3 4925.5 TRUE FALSE FALSE 4219.437315 4395.125714 3848.332826 3302.059471 3634.066325 3814.69554 3872.931928 4391.384953 4337.258518 4797.5348 0.879501138 0.916121695 0.802147975 0.688282547 0.757486183 0.795136606 0.807275421 0.91534197 0.904059835 1 12.22807756 -10.83955829 0.612759908 0.985264426 0.792426509 0.43247346 0.065955621 0.360930327 0.311504176 0.026469689 0.019971676 1.45E-11 10.83955829 -0.192837917 S(ph)PAGPAATPAQAQAASTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPAGPAATPAQAQAASTPR 19 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 S(1)PAGPAATPAQAQAASTPR 127.91 0.00091483 2790800 782.21 570.23 622.28 438.41 500.38 481.9 476.78 452.81 656.84 515.69 TRUE FALSE FALSE 772.6761237 578.2577129 633.1105224 489.101027 474.8437414 451.1081453 517.2776813 465.9113429 598.0905853 502.2922995 1.53829976 1.151237464 1.260442422 0.973737856 0.945353417 0.898098867 1.029833987 0.927570149 1.190722187 1 8.972383347 -9.243491755 5.529543354 1.252041427 0.953761056 0.520592137 0.130137415 0.160350238 16.81072032 0.030630208 0.04996309 5.71E-10 9.243491755 -0.298280371 S(ph)PALPPVWDVSASAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPALPPVWDVSASAK 15 0 G3V471;P56179;P56179-2;P56179-3 G3V471 DLX6 Homeobox protein DLX-6 1 0 S(1)PALPPVWDVSASAK 101.2 0.0074878 22960000 4056.2 2865.1 3626.7 2727.6 2035.4 1909.3 1849.6 2024.6 3961.8 3795.4 TRUE FALSE FALSE 4006.761474 2905.434953 3689.821192 3042.977946 1931.525943 1787.301892 2006.704978 2083.178607 3607.446685 3696.794961 1.083847364 0.785933487 0.998113564 0.823139497 0.522486631 0.483473363 0.542822904 0.563509372 0.975830882 1 11.85205931 -8.976174021 1.790237568 1.019520628 0.515781914 0.858789125 0.082830515 0.084589079 0.542169004 0.013633658 0.027783714 1.06E-09 8.976174021 -0.503738714 S(ph)PALSDANK ddPTM_HeLa_Romidepsin_16h_R1 2 SPALSDANK 9 0 A0A087WWJ1;P52701-2;P52701;F8WAX8;P52701-3;F8W7G9 A0A087WWJ1 MSH6 DNA mismatch repair protein Msh6 1 0 S(1)PALSDANK;S(1)PALSDANK ; 155.53 0.004503 144226000 6625.1 6915.5 7717.9 4956.4 7204.2 7656 6270.5 4221.2 6811.7 7136.8 TRUE FALSE FALSE 6544.350733 7012.856591 7852.226812 5529.482289 6836.542791 7166.806309 6803.116113 4343.333762 6202.444492 6951.384907 0.9414456 1.008843084 1.129591717 0.795450455 0.983479247 1.03098971 0.978670611 0.624815604 0.892260258 1 12.76308472 -7.261361855 23.69614151 0.977924165 0.624815398 0.611873608 0.083222222 1.361454875 414424.5735 0.010226733 0.078856302 5.48E-08 7.261361855 -0.353108766 S(ph)PAQILISLESEER ddPTM_HeLa_Romidepsin_16h_R1 1 SPAQILISLESEER 14 0 A0A075B6G3;H0Y304;A0A087WTU7;A0A5H1ZRP8;A0A5H1ZRP7;A0A087WV90;A0A5H1ZRQ1;A0A5H1ZRP9;A0A5H1ZRQ8;P11532;P11532-11;P11532-4;P11532-2;P11532-3;P11532-14;P11532-8;P11532-12;P11532-17;P11532-6;P11532-5;P11532-7;P11532-15 A0A075B6G3 DMD Dystrophin 1 0 S(1)PAQILISLESEER 127.66 0.00012607 0 396.4 216.49 403.32 325.48 406.56 233.61 403.35 185.43 269.29 401.82 TRUE FALSE FALSE 391.5685243 219.5377519 410.3396154 363.113529 385.8117261 218.6830749 437.6105389 190.7951245 245.204028 391.3806585 1.000480008 0.560931531 1.048441221 0.927775865 0.985771059 0.558747782 1.118119993 0.487492471 0.626510336 1 8.612428651 -5.251066543 0.22078277 1.017789378 3.45E-12 0 0.236530435 36.97128926 0.717210477 0.149198399 12.06481935 5.61E-06 5.251066543 -1.017789378 S(ph)PAQQEPPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPAQQEPPQR 10 0 A0A669KBI3;F5GXF9;P51825;P51825-3;P51825-2 A0A669KBI3 AFF1 AF4/FMR2 family member 1 1 0 S(1)PAQQEPPQR 101.89 0.023278 3124500 918 825.69 514.14 530.88 766.59 649.3 681.47 702.53 580.77 1004.1 TRUE FALSE FALSE 906.8110629 837.3140855 523.088391 592.2628435 727.4680518 607.8118255 739.3540448 722.8565971 528.8244766 978.0133373 0.927197031 0.856137696 0.534847912 0.605577471 0.74382222 0.621476009 0.755975421 0.739107096 0.54071295 1 9.933710329 -9.971128085 4.513219582 0.963108059 0.669491756 0.023112187 0.149815386 0.066042397 3.208913531 0.011941711 0.015574588 1.07E-10 9.971128085 -0.293616303 S(ph)PARTPPSEEDSAEAER ddPTM_HeLa_Romidepsin_16h_R1 1 SPARTPPSEEDSAEAER 17 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 0 S(0.985)PART(0.015)PPSEEDSAEAER 78.249 0.007588 11820000 574.35 599.91 482.72 708.8 574.06 578.21 444.7 587.12 704.66 761.22 TRUE FALSE FALSE 567.3496013 608.3555487 491.1215391 790.754791 544.7635761 541.2642471 482.4728069 604.1073909 641.6334447 741.4433947 0.76519611 0.820501677 0.66238575 1.066507297 0.734733872 0.730014255 0.650721027 0.814772099 0.865384262 1 9.534192744 -16.52287736 0.233438171 2.303696224 0.748814061 0.15835341 0.118312805 36.7267071 0.475531248 21.8920682 0.075138012 3.00E-17 16.52287736 -1.554882163 S(ph)PASAEAPGDSGER ddPTM_HeLa_Romidepsin_16h_R1 1 SPASAEAPGDSGER 14 0 H7BY64;Q8NB15;Q8NB15-1 H7BY64 PRAP1;ZNF511 Zinc finger protein 511 1 0 S(1)PASAEAPGDSGER 145.81 0.00061802 5008000 196.97 146.04 225.81 0 182.79 149.53 192.79 114.49 228.34 206.96 TRUE FALSE FALSE 194.5692539 148.095955 229.7401283 0 173.4615442 139.9755156 209.1655778 117.8025875 207.9166985 201.5831494 0.965205944 0.734664358 1.139679229 0 0.860496251 0.694381033 1.037614396 0.584387077 1.031419041 1 7.655231237 S(ph)PDEEDYDYESYEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPDEEDYDYESYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.725)PDEEDY(0.267)DY(0.009)ESYEK 142.97 0.00065679 15038000 2007.9 1678.6 1920.8 1000.4 1853.8 2206.5 1982.7 1930.1 2068.1 2307.6 TRUE FALSE FALSE 1983.426942 1702.231375 1954.230718 1116.070955 1759.193669 2065.511771 2151.110489 1985.944398 1883.123956 2247.648219 0.882445449 0.757338875 0.869455772 0.496550548 0.78268194 0.918965768 0.957049448 0.883565489 0.8378197 1 11.13420054 -11.08604774 1.000601837 0.977651896 0.810293945 0.061139188 0.129333338 0.501449609 1.061082907 0.037173306 0.028075172 8.20E-12 11.08604774 -0.167357951 S(ph)PDEVTLTSIVPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SPDEVTLTSIVPTR 14 0 A0A0C4DGG1;Q9UKS6;H0YDM6 A0A0C4DGG1 PACSIN3 Protein kinase C and casein kinase substrate in neurons protein 3 1 0 S(1)PDEVTLTSIVPTR 93.228 0.016235 11687000 571.81 348.27 303.13 370.91 451.03 491.45 702.04 522.43 653.45 589.09 TRUE FALSE FALSE 564.8405598 353.1729542 308.4058505 413.7963594 428.0122561 460.0479311 761.6712601 537.5456878 595.0037954 573.7853569 0.9844109 0.615514059 0.537493414 0.721169257 0.745944892 0.801777051 1.327449805 0.93684107 1.036979749 1 9.16436734 -10.47087835 24.82913519 0.993122597 0.81401165 0.161864704 0.202470408 490.8233468 234359.6906 0.037569217 0.042914598 3.38E-11 10.47087835 -0.179110947 S(ph)PDLSNQNSDQANEEWETASESSDFTSER ddPTM_HeLa_Romidepsin_16h_R1 1 SPDLSNQNSDQANEEWETASESSDFTSER 29 0 P48634;P48634-2;P48634-3 P48634 PRRC2A Protein PRRC2A 1 0 S(0.993)PDLS(0.006)NQNSDQANEEWETASESSDFTSER 114.06 6.00E-10 4361400 564.88 629.09 532.43 579.09 410.35 490.12 523.63 448.16 487.77 676.2 TRUE FALSE FALSE 557.9950253 637.9463455 541.6967208 646.0471105 389.4083083 458.8029138 568.1071191 461.1268025 444.1426296 658.6322265 0.847202737 0.968592668 0.822457054 0.980892043 0.59123786 0.696599552 0.862555909 0.700127907 0.674340871 1 9.363329294 -8.774826372 24.99933429 0.924094263 0.722194208 0.313182042 0.112951327 129.5785517 241979.404 0.01311802 0.023876317 1.68E-09 8.774826372 -0.201900055 S(ph)PDPGIVPQEAPVGNSLSELSEENFDGK ddPTM_HeLa_Romidepsin_16h_R1 1 SPDPGIVPQEAPVGNSLSELSEENFDGK 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;A0A0C4DH09;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 S(0.998)PDPGIVPQEAPVGNS(0.002)LSELSEENFDGK 77.308 3.53E-06 17403000 2712.3 3190 2471 1799.6 3992.5 4270.4 3886.5 4460.9 3074.3 2582.4 TRUE FALSE FALSE 2679.241444 3234.908904 2514.006718 2007.678219 3788.747827 3997.535222 4216.619213 4589.969103 2799.326908 2515.308876 1.065173932 1.286088136 0.999482307 0.798183571 1.506275378 1.58928204 1.676382274 1.824813305 1.112915768 1 11.29651986 -8.606056677 4.981638112 1.036312053 1.674039639 0.84799322 0.127162891 0.056336551 2.45130522 0.018737003 0.038286965 2.48E-09 8.606056677 0.637727586 S(ph)PDTLAPVASER ddPTM_HeLa_Romidepsin_16h_R1 1 SPDTLAPVASER 12 0 O43310;O43310-2 O43310 CTIF CBP80/20-dependent translation initiation factor 1 0 S(1)PDTLAPVASER 100.04 0.015568 2060400 351.61 353.9 254.8 270.07 260.63 342.29 383.95 258.35 356.31 343.28 TRUE FALSE FALSE 347.3244421 358.8822135 259.2346871 301.2967641 247.3290786 320.4187737 416.5627034 265.8249496 324.4407412 334.3615361 1.03876913 1.07333582 0.775312526 0.901110719 0.739705534 0.95830034 1.245845166 0.795022516 0.970329138 1 8.385265084 -9.799371196 24.99927448 1.022946296 0.913220172 0.152487126 0.134907174 252.1538171 166182.952 0.021600004 0.028388309 1.59E-10 9.799371196 -0.109726124 S(ph)PDVISSASTALSQDIPEIASEALSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPDVISSASTALSQDIPEIASEALSR 26 0 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 S(0.94)PDVIS(0.022)S(0.007)AS(0.007)T(0.02)ALS(0.003)QDIPEIASEALSR 54.521 0.0045303 5440000 432.08 499.5 499.54 491.69 471.23 432.38 407.69 436.25 529.34 438.63 TRUE FALSE FALSE 426.8136428 506.5319741 508.2342842 548.5415113 447.1813747 404.7523134 442.3191784 448.8722055 481.9945046 427.2343294 0.999015326 1.185606912 1.1895914 1.283935942 1.04668877 0.947377787 1.035308139 1.050646389 1.128173631 1 8.738883766 -10.30020187 22.617771 0.999534963 1.104629534 0.028367866 0.099136229 212.7828364 124157.1561 0.017024986 0.019469228 5.01E-11 10.30020187 0.105094571 S(ph)PEAVGPELEAEEK ddPTM_HeLa_Romidepsin_16h_R1 3 SPEAVGPELEAEEK 14 0 Q96N64-3;Q96N64-2;Q96N64 Q96N64-3 PWWP2A PWWP domain-containing protein 2A 1 0 S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK;S(1)PEAVGPELEAEEK ;; 212.03 6.83E-24 75085100 3231.07 3150.82 3404.33 3617.23 3450.98 3523.1 3260.05 3657.47 3783.46 3120.15 TRUE FALSE FALSE 3191.688476 3195.177327 3463.580936 4035.471152 3274.863613 3297.98528 3536.958566 3763.293124 3445.057862 3039.088053 1.05021257 1.051360563 1.139677717 1.327855949 1.077581023 1.085189117 1.163822339 1.238296837 1.133582773 1 11.56942276 -9.766161642 3.455412412 1.025094934 1.172432681 0.321170193 0.076506928 0.147999762 3.736690588 0.011352605 0.015753657 1.71E-10 9.766161642 0.147337747 S(ph)PEDQLGK ddPTM_HeLa_Romidepsin_16h_R1 2 SPEDQLGK 8 0 Q9UK61-3;Q9UK61;Q9UK61-2 Q9UK61-3 FAM208A Protein FAM208A 1 0 S(1)PEDQLGK;S(1)PEDQLGK ; 115.7 0.02037 58026000 8578.9 7991.6 8036.6 4709.1 7096.3 7709 6172.9 5965.5 8801.2 8567.6 TRUE FALSE FALSE 8474.337067 8104.105955 8176.473652 5253.588299 6734.149331 7216.41978 6697.225972 6138.10233 8013.998629 8345.012517 1.015497227 0.971131672 0.979803641 0.629548283 0.806966954 0.864758413 0.802542352 0.735541417 0.960333926 1 13.0266985 -9.391502004 7.282736148 1.003396713 0.777725322 0.764431008 0.059941613 0.08680838 4.774602497 0.008825736 0.013498404 4.06E-10 9.391502004 -0.225671391 S(ph)PEPDGPAPAFLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPEPDGPAPAFLR 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 S(1)PEPDGPAPAFLR 120.59 0.0047776 5763900 242.68 355.25 310.1 263.67 395.4 432.28 398.48 353.23 335.31 346.99 TRUE FALSE FALSE 239.7221228 360.2512188 315.4971604 294.156766 375.2212626 404.6587031 432.3268813 363.4501527 305.3190338 337.9751498 0.709289198 1.065910376 0.933492183 0.870350279 1.110203702 1.197303125 1.279167659 1.075375373 0.903377168 1 8.400773363 -8.658301189 3.314940421 0.882194036 1.190153246 0.591956497 0.101409171 0.142393777 3.086666455 0.01920935 0.040421211 2.20E-09 8.658301189 0.30795921 S(ph)PEPDPYLSYR ddPTM_HeLa_Romidepsin_16h_R1 2 SPEPDPYLSYR 11 0 H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BUL5;H3BVF8;H3BQG1;P49761-2;P49761-3;P49761-1;P49761 H3BRT8 CLK3 Dual specificity protein kinase CLK3 1 0 S(1)PEPDPYLSYR;S(1)PEPDPYLSYR ; 154.15 0.00051599 1773300 1834.42 1782.1 1976.67 3368.7 2086.33 2316.1 2035.12 2296.5 1938.77 2017.08 TRUE FALSE FALSE 1812.061383 1807.188451 2011.073112 3758.204944 1979.856795 2168.108685 2207.983042 2362.945604 1765.361555 1964.675971 0.922320734 0.919840461 1.023615671 1.912887927 1.007726884 1.103545173 1.123840814 1.202715175 0.898550999 1 10.94007568 -9.50008543 24.99620996 0.959636876 1.2611882 0.319085692 0.233329555 750.5892922 823132.4622 0.03472077 0.052795693 3.16E-10 9.50008543 0.301551324 S(ph)PEPEATLTFPFLDK ddPTM_HeLa_Romidepsin_16h_R1 2 SPEPEATLTFPFLDK 15 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 S(1)PEPEATLTFPFLDK;S(1)PEPEATLTFPFLDK ; 180.74 3.89E-08 11632100 1477.36 1416.93 1572.91 1201.62 1777.72 1652.55 1310.37 1418.8 1726.03 1702.63 TRUE FALSE FALSE 1459.353368 1436.877578 1600.285839 1340.556958 1686.996315 1546.957388 1421.672795 1459.85074 1571.649554 1658.395427 0.879979132 0.866426399 0.964960354 0.808345788 1.017246121 0.932803699 0.857258029 0.880279043 0.947692889 1 10.69557233 -12.31908688 0.985855707 1.001426293 0.90108653 0.182608883 0.057932272 0.542287858 0.923027574 0.039023547 0.009789771 4.80E-13 12.31908688 -0.100339763 S(ph)PEPEVLSTQEDLFDQSNK ddPTM_HeLa_Romidepsin_16h_R1 2 SPEPEVLSTQEDLFDQSNK 19 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 S(1)PEPEVLSTQEDLFDQSNK;S(0.999)PEPEVLSTQEDLFDQSNK ; 119.8 0.00034696 66385000 10706.9 11133.7 10536.1 6515.3 11212.7 9985.7 9237.6 10685.2 10850.4 10786.9 TRUE FALSE FALSE 10576.40018 11290.44052 10719.4764 7268.629641 10640.47408 9347.645997 10022.24151 10994.3594 9879.913049 10506.65478 1.006638212 1.074598981 1.020255888 0.691811979 1.012736622 0.889688125 0.953894624 1.046418639 0.940348118 1 13.35901578 S(ph)PEPGQTWTR ddPTM_HeLa_Romidepsin_16h_R1 4 SPEPGQTWTR 10 0 Q09666;E9PJZ0;E9PKR9;E9PJC6;E9PLK4;Q09666-2 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 S(0.996)PEPGQT(0.001)WT(0.003)R;S(1)PEPGQTWTR;S(1)PEPGQTWTR;S(1)PEPGQTWTR ;;; 120.57 0.011468 280186000 2495.17 3301.4 2479.93 1236.41 2792.13 2446.35 2118.08 2263.43 2758.17 2551.81 TRUE FALSE FALSE 2464.757908 3347.877196 2523.092141 1379.369542 2649.637187 2290.03613 2297.989662 2328.918776 2511.472367 2485.513608 0.991649332 1.346955891 1.015119021 0.554963585 1.066032058 0.921353286 0.924553241 0.936996993 1.010444022 1 11.27932829 -9.484963735 24.99846686 1.029824638 0.884685951 0.249055958 0.158293491 782.2985122 515792.9533 0.024108311 0.036821222 3.27E-10 9.484963735 -0.145138687 S(ph)PESQVIGENTK ddPTM_HeLa_Romidepsin_16h_R1 2 SPESQVIGENTK 12 0 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 S(0.972)PES(0.028)QVIGENTK;S(0.998)PES(0.002)QVIGENTK ; 168.45 0.00019759 9399100 2699.2 2513.72 2715.7 1408.69 2238.6 2265.12 2246.89 2318.66 2486.07 2783.31 TRUE FALSE FALSE 2666.301112 2549.108216 2762.965619 1571.569366 2124.355889 2120.386142 2437.740781 2385.746769 2263.709673 2710.999205 0.983512318 0.940283646 1.019168731 0.579701153 0.783606238 0.782141927 0.899203798 0.880024887 0.835009346 1 11.40460897 -9.315620689 24.9998312 0.989133279 0.791054284 0.422421099 0.09571285 163.1566378 75281.79676 0.01260437 0.019253501 4.83E-10 9.315620689 -0.198078996 S(ph)PFEGAVTESQSLFSDNFR ddPTM_HeLa_Romidepsin_16h_R1 2 SPFEGAVTESQSLFSDNFR 19 0 O95628-5;O95628-3;O95628-2;O95628;O95628-8;O95628-4;O95628-7;O95628-9;O95628-10;O95628-6 O95628-5 CNOT4 CCR4-NOT transcription complex subunit 4 1 0 S(1)PFEGAVTESQSLFSDNFR;S(0.782)PFEGAVT(0.197)ES(0.014)QS(0.006)LFSDNFR ; 214.46 3.79E-29 134382000 523.65 865.82 700.67 694.13 898.07 753.2 763.32 1035.64 976.06 614.85 TRUE FALSE FALSE 517.2675524 878.0090367 712.8648674 774.3885766 852.2381367 705.0729508 828.1563817 1065.604609 888.758749 598.8761084 0.863730486 1.466094614 1.190337797 1.293069745 1.423062508 1.177326898 1.382850927 1.779340659 1.484044424 1 9.226113768 -10.26343392 24.96180449 0.935650502 1.369342209 0.088700775 0.237761928 84.62231597 1059053.176 0.02739368 0.032162933 5.45E-11 10.26343392 0.433691707 S(ph)PGALETPSAAGSQGNTASQGK ddPTM_HeLa_Romidepsin_16h_R1 4 SPGALETPSAAGSQGNTASQGK 22 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 S(1)PGALETPSAAGSQGNTASQGK;S(1)PGALETPSAAGSQGNTASQGK;S(0.985)PGALET(0.015)PSAAGSQGNTASQGK;S(0.615)PGALET(0.357)PS(0.028)AAGSQGNTASQGK ;;; 285.96 5.11E-113 116422000 8446.8 8332.1 7771.7 5229.7 6672.8 6804.6 6207.7 6593.1 8072.5 7840.7 TRUE FALSE FALSE 8343.847153 8449.399523 7906.963178 5834.38252 6332.262116 6369.808021 6734.981883 6783.860946 7350.475382 7636.997484 1.092555965 1.106377152 1.035349716 0.763962871 0.829155978 0.834072295 0.881888713 0.888289012 0.962482363 1 12.89878983 -9.311157262 8.588072547 1.050109405 0.841043256 0.796360358 0.050391386 0.120925807 19.90208145 0.007933906 0.012149773 4.88E-10 9.311157262 -0.209066149 S(ph)PGAPGPLTLK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGAPGPLTLK 11 0 Q15942;Q15942-2;H0Y2Y8;C9JJK5 Q15942 ZYX Zyxin 1 0 S(1)PGAPGPLTLK 96.342 0.024203 725460000 12169 12092 11312 10464 12613 13817 12707 12105 12370 11897 TRUE FALSE FALSE 12020.67955 12262.23149 11508.88061 11673.89691 11969.31154 12934.13829 13786.33226 12455.23908 11263.59622 11587.91422 1.037346266 1.058191427 0.993179652 1.007420032 1.032913371 1.116174839 1.189716458 1.074847366 0.972012392 1 13.50033329 -8.248334385 3.644512815 1.01884693 1.136388336 0.690474269 0.034577484 0.086415573 2.514811107 0.004368191 0.011386689 5.65E-09 8.248334385 0.117541406 S(ph)PGASNFSTLPK ddPTM_HeLa_Romidepsin_16h_R1 4 SPGASNFSTLPK 12 0 Q9Y4E8 Q9Y4E8 USP15 Ubiquitin carboxyl-terminal hydrolase 15 1 0 S(1)PGASNFSTLPK;S(0.999)PGAS(0.001)NFSTLPK;S(1)PGASNFSTLPK;S(0.998)PGAS(0.002)NFSTLPK ;;; 158.31 0.00099775 177321000 14801.8 14021.2 12596.4 10544.4 15103.1 15537 14062.7 15354.3 14902.8 14800.5 TRUE FALSE FALSE 14621.38997 14218.59082 12815.63506 11763.59314 14332.33245 14544.23584 15257.18539 15798.55245 13569.85624 14415.98088 1.014248707 0.986307553 0.888988073 0.816010596 0.994197521 1.008896721 1.058352222 1.09590548 0.941306482 1 13.81538138 -7.728689864 2.126632787 0.98130409 1.092504062 0.334850454 0.062588383 0.400422938 3.334451875 0.010137946 0.05911048 1.87E-08 7.728689864 0.111199971 S(ph)PGDFTSAAQLASTPFHK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGDFTSAAQLASTPFHK 18 0 A0A590UJ99;O43683-2;O43683-3;O43683 A0A590UJ99 BUB1 Mitotic checkpoint serine/threonine-protein kinase BUB1 1 0 S(0.95)PGDFT(0.025)S(0.025)AAQLASTPFHK 78.234 0.0062434 17915000 1262.9 1145.9 1276.5 1027.6 2227.3 2179.6 1738.3 1927.1 1572.2 1529.4 TRUE FALSE FALSE 1247.507289 1162.03201 1298.716947 1146.415947 2113.63257 2040.330594 1885.951159 1982.857598 1431.578494 1489.665968 0.837440954 0.780062132 0.871817559 0.769579202 1.418863434 1.369656446 1.266022853 1.331075316 0.961006377 1 10.54077315 -8.757572615 24.99999896 0.895629025 1.342323875 0.89874731 0.078050331 28.02804213 181208.5742 0.01387749 0.026940517 1.75E-09 8.757572615 0.44669485 S(ph)PGEPGGAAPER ddPTM_HeLa_Romidepsin_16h_R1 1 SPGEPGGAAPER 12 0 Q96EB6;Q96EB6-2 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 S(1)PGEPGGAAPER 95.183 0.021493 96313000 325.44 504.41 345.69 362.55 357.67 415.32 440.46 402.2 496.67 379.3 TRUE FALSE FALSE 321.4734121 511.5110972 351.7065894 404.4697368 339.4167652 388.7823924 477.8726614 413.8370224 452.2465913 369.4457313 0.870150566 1.384536493 0.951984445 1.094801489 0.918718871 1.052339652 1.293485405 1.12015646 1.224121848 1 8.529218649 -6.795889681 0.296164393 0.947487941 1.472739242 0 0.172294696 12.3921093 0.646134696 0.069374587 2.473246593 1.60E-07 6.795889681 0.525251301 S(ph)PGEYINIDFGEPGAR ddPTM_HeLa_Romidepsin_16h_R1 3 SPGEYINIDFGEPGAR 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR;S(1)PGEYINIDFGEPGAR ;; 206.62 6.84E-19 57848000 1854.3 1942.69 1730.82 1638 2077.91 1781.3 1376.02 1649.31 1816.88 1780.05 TRUE FALSE FALSE 1831.699078 1970.039241 1760.944196 1827.393267 1971.866499 1667.480679 1492.899104 1697.030183 1654.373702 1733.804044 1.056462571 1.136252535 1.015653529 1.053979123 1.137306436 0.961746908 0.861054114 0.97879007 0.954187244 1 10.75972514 -8.011227228 24.01896444 1.043534072 0.917791669 0.454717596 0.05938145 194.2976543 415676.0299 0.00761734 0.020852699 9.74E-09 8.011227228 -0.125742403 S(ph)PGGGSEANGLALVSGFK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGGGSEANGLALVSGFK 18 0 O95049-5;O95049;O95049-4;O95049-3 O95049-5 TJP3 Tight junction protein ZO-3 1 0 S(0.995)PGGGS(0.005)EANGLALVSGFK;S(0.999)PGGGS(0.001)EANGLALVSGFK ; 120.71 0.0015899 20003900 591.38 459.73 548.37 1036.39 2999.3 3389.6 3724.1 4143.4 499.56 373.5 TRUE FALSE FALSE 584.1720331 466.202091 557.9141498 1156.222288 2846.234529 3173.015499 4040.424961 4263.282742 454.8781024 363.7964162 1.605766322 1.281491709 1.533588911 3.17821242 7.823701396 8.721953704 11.10628028 11.71886954 1.250364441 1 8.506987521 -8.579836726 1.169708792 1.231248399 11.4540143 0.98284802 0.547771379 0.04186343 0.109491307 0.087442232 0.289470585 2.63E-09 8.579836726 10.2227659 up S(ph)PGHMVILDQTK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGHMVILDQTK 12 0 Q9NWH9;H7C3F4;Q9NWH9-3 Q9NWH9 SLTM SAFB-like transcription modulator 1 0 S(1)PGHMVILDQTK;S(1)PGHMVILDQTK ; 121.42 0.0021488 135373000 22994.9 20342.9 25308.4 16414.5 19812.6 21991.2 18027.4 16591.7 23169.7 20493.8 TRUE FALSE FALSE 22714.62931 20629.28788 25748.88209 18312.42172 18801.48909 20586.03329 19558.64691 17071.75466 21097.344 19961.36812 1.137929483 1.03346062 1.289935736 0.917393117 0.941893811 1.031293705 0.979824969 0.855239709 1.056908719 1 14.28492298 S(ph)PGKAEAESDALPDDTVIESEALPSDIAAEAR ddPTM_HeLa_Romidepsin_16h_R1 4 SPGKAEAESDALPDDTVIESEALPSDIAAEAR 32 1 G3V529;Q9GZR7-2;Q9GZR7;A0A1W2PRR2;F5GYL3 G3V529 DDX24 ATP-dependent RNA helicase DDX24 1 0 S(0.987)PGKAEAES(0.009)DALPDDT(0.004)VIESEALPSDIAAEAR;S(0.962)PGKAEAES(0.038)DALPDDTVIESEALPSDIAAEAR;S(0.848)PGKAEAES(0.15)DALPDDT(0.002)VIESEALPSDIAAEAR;S(0.794)PGKAEAES(0.188)DALPDDT(0.017)VIESEALPSDIAAEAR ;;; 80.245 2.21E-08 180746500 8814.71 8638.62 9552.29 7259.91 8556.11 8839.14 8474.25 8466.03 10593.66 9857.22 TRUE FALSE FALSE 8707.272924 8760.234719 9718.5436 8099.334953 8119.459779 8274.347481 9194.052583 8710.981221 9646.136517 9601.128003 0.906901035 0.912417241 1.012229354 0.843581603 0.845677693 0.861809933 0.957601292 0.907287271 1.004687836 1 13.2289882 -9.252864017 24.78641648 0.954785811 0.884053462 0.440124066 0.046343162 550.2197389 1590366.126 0.007888482 0.012950688 5.59E-10 9.252864017 -0.070732348 S(ph)PGLVPPS(ph)PEFAPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGLVPPSPEFAPR 14 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 2 0 S(1)PGLVPPS(1)PEFAPR 128.82 0.025747 11768000 1909.5 1899.1 1969.1 1543.3 1708.5 2448.8 2076.3 2367.6 1790.9 2025.1 TRUE FALSE FALSE 1886.22628 1925.83558 2003.37136 1721.743607 1621.30887 2292.329583 2252.66087 2436.102771 1630.717419 1972.48761 0.956267745 0.976348632 1.015657259 0.872879302 0.821961497 1.162151575 1.142040568 1.235040848 0.826731387 1 10.94580052 -8.145754662 7.701697732 0.964299402 1.17910589 0.691463197 0.074997723 0.11502746 6.97448785 0.009044346 0.023215983 7.15E-09 8.145754662 0.214806488 S(ph)PGMLEPLGSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGMLEPLGSSR 12 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(1)PGMLEPLGSSR 96.23 0.027686 33702000 2933 2788.1 2812.3 1981.8 2311.2 2324.5 1929.1 2196.4 2856.7 2881.4 TRUE FALSE FALSE 2897.251468 2827.350945 2861.246902 2210.945041 2193.25084 2175.971952 2092.957706 2259.949369 2601.189597 2806.540813 1.03232116 1.007414869 1.019492355 0.787782964 0.781478334 0.775321685 0.745742836 0.805243722 0.926831203 1 11.45457732 -9.251451119 6.434184728 1.015394883 0.776479492 0.919043298 0.032140783 0.015013812 3.107216512 0.00265038 0.004285523 5.60E-10 9.251451119 -0.238915391 S(ph)PGNTSQPPAFFSK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGNTSQPPAFFSK 14 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2;H7C184 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 S(0.923)PGNT(0.075)S(0.002)QPPAFFSK;S(0.995)PGNT(0.005)SQPPAFFSK ; 139.6 0.0010205 304320000 4520.2 4663.8 4114.5 2893.8 3092.5 2768 2426.9 2592.1 4719.7 4014.6 TRUE FALSE FALSE 4465.106064 4729.457099 4186.111147 3228.394772 2934.678185 2591.133733 2633.040825 2667.098324 4297.558211 3910.300113 1.141883215 1.209486986 1.070534492 0.825613042 0.750499476 0.662643188 0.673360292 0.682069981 1.09903539 1 11.93306362 -9.06223286 2.209736918 1.082860117 0.684801618 0.924734523 0.055871096 0.080765581 0.779347191 0.011687397 0.02188842 8.66E-10 9.06223286 -0.398058498 S(ph)PGNVNNTIVVPLLEDGR ddPTM_HeLa_Romidepsin_16h_R1 2 SPGNVNNTIVVPLLEDGR 18 0 Q9Y4X4-2;Q9Y4X4-3;Q9Y4X4 Q9Y4X4-2 KLF12 Krueppel-like factor 12 1 0 S(1)PGNVNNTIVVPLLEDGR;S(1)PGNVNNTIVVPLLEDGR ; 203.23 7.11E-21 4269500 238.05 332.43 112.473 266.37 241.56 153.71 250.72 223.34 60.98 59.181 TRUE FALSE FALSE 235.148555 337.1099583 114.4305454 297.1689527 229.2322918 143.8884271 272.0161505 229.8019905 55.52579607 57.64346909 4.079361613 5.848189979 1.985143282 5.155292653 3.976726166 2.496179174 4.718941362 3.98660931 0.963262568 1 5.849085257 -12.0945512 0.812979295 0.947432161 4.024561146 0.553279725 1.087301792 0.39027952 0.457709665 0.736672997 0.205739243 8.04E-13 12.0945512 3.077128985 S(ph)PGPAADGPIDLSK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGPAADGPIDLSK 14 0 Q8IX07 Q8IX07 ZFPM1 Zinc finger protein ZFPM1 1 0 S(1)PGPAADGPIDLSK;S(1)PGPAADGPIDLSK ; 188.09 6.22E-11 15142800 2129.2 1898.38 1992.64 1505.36 2377 2571.2 2573.1 3050.3 2010.66 2275.1 TRUE FALSE FALSE 2103.248491 1925.105443 2027.321063 1679.416806 2255.69282 2406.908618 2791.65905 3138.555618 1830.821534 2215.992574 0.949122536 0.868732804 0.914859141 0.757862109 1.017915334 1.086153738 1.259778161 1.416320458 0.826185771 1 11.11373733 -7.721838578 1.540499309 0.947778967 1.433032819 0.820105343 0.080867587 0.170354369 0.642840351 0.011685459 0.096226042 1.90E-08 7.721838578 0.485253853 S(ph)PGPGPDLYSAPIFSSNYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGPGPDLYSAPIFSSNYSSR 21 0 Q8NEA6;Q8NEA6-2 Q8NEA6 GLIS3 Zinc finger protein GLIS3 1 0 S(1)PGPGPDLYSAPIFSSNYSSR 85.087 0.00068902 0 337.86 430.36 313.13 319.94 279.46 374.21 432.32 280.46 461.51 436.36 TRUE FALSE FALSE 333.7420324 436.4186194 318.5798963 356.9329682 265.1981134 350.2991887 469.04125 288.5746676 420.2313897 425.0233043 0.785232313 1.026811036 0.749558655 0.839796229 0.623961347 0.824188192 1.103565958 0.678961988 0.988725525 1 8.731398137 -12.47612966 0.834185192 1.018260162 0.829925643 0.189524438 0.136900692 1.135021686 1.175991443 0.150210772 0.025152454 3.34E-13 12.47612966 -0.188334519 S(ph)PGSPPGPELPIETALDDR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSPPGPELPIETALDDR 19 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;F5GZI3;B1AP52 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 S(0.814)PGS(0.186)PPGPELPIETALDDR 132.67 0.0003859 1468800 1545.6 1918.9 1729.9 1060.4 1485.9 1331.9 1399.3 1494.3 1967.3 1613.6 TRUE FALSE FALSE 1526.761633 1945.914325 1760.008184 1183.008437 1410.068978 1246.795889 1518.156507 1537.535213 1791.339761 1571.678439 0.971421122 1.238112247 1.119827148 0.752703866 0.897173966 0.793289427 0.965946003 0.978275947 1.139762254 1 10.61809036 -9.267590375 24.99338832 1.018125239 0.878809835 0.430078418 0.108204833 502.1380243 2040338.92 0.016700249 0.025912477 5.40E-10 9.267590375 -0.139315405 S(ph)PGSPPGPELPIETALDDRER ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSPPGPELPIETALDDRER 21 1 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;F5GZI3;B1AP52 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 S(0.499)PGS(0.499)PPGPELPIET(0.003)ALDDRER 48.224 0.02648 7377800 2905.4 2448.8 2765 2819.9 2241.4 2453.7 2281.5 2115 2975.6 2800.8 TRUE FALSE FALSE 2869.987867 2483.274271 2813.123665 3145.950106 2127.012994 2296.916489 2475.290553 2176.194188 2709.454883 2728.034812 1.052034913 0.910279539 1.03119053 1.153192801 0.779686896 0.841967441 0.907352993 0.797714963 0.993189263 1 11.41364634 -8.747535466 24.99999973 1.024210154 0.837820503 0.677771943 0.064674639 106.115438 190800.3106 0.009145491 0.018216379 1.79E-09 8.747535466 -0.186389651 S(ph)PGSPVGEGTGSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSPVGEGTGSPPK 15 0 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 S(0.861)PGS(0.054)PVGEGT(0.073)GS(0.012)PPK 112.42 0.0040671 6304200 1649.8 1861.6 1586.5 1571.4 1719.2 1607.8 1341.3 1667.1 1541.9 1494.6 TRUE FALSE FALSE 1629.691603 1887.807654 1614.112367 1753.092662 1631.462809 1505.066769 1455.229989 1715.334908 1403.988602 1455.770077 1.119470464 1.29677597 1.108768749 1.204237324 1.120687144 1.033862966 0.999629002 1.178300706 0.964430184 1 10.5075668 -11.84408863 1.00965958 1.008901454 1.128852253 0.341762107 0.080871954 0.517143288 1.040828644 0.036505639 0.016055701 1.43E-12 11.84408863 0.119950799 S(ph)PGSQAPDEGAGGALR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSQAPDEGAGGALR 16 0 P10075 P10075 GLI4 Zinc finger protein GLI4 1 0 S(0.998)PGS(0.002)QAPDEGAGGALR 94.82 0.0090037 11148000 322.76 145.98 242.55 213.22 309.77 317.95 306.96 302.37 223.46 239.44 TRUE FALSE FALSE 318.826077 148.0351103 246.771481 237.8734996 293.961281 297.6340211 333.0331747 311.1185989 203.4731779 233.2193143 1.367065494 0.634746358 1.05810911 1.01995626 1.260449984 1.276197994 1.427982823 1.334017295 0.872454233 1 7.865543461 -8.385449996 2.243714811 1.114102574 1.365849338 0.312773886 0.198014624 0.393837813 3.837373 0.031902007 0.086198063 4.12E-09 8.385449996 0.251746764 S(ph)PGSTPTTPT(ph)SSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 0 S(0.637)PGS(0.091)T(0.282)PT(0.218)T(0.102)PT(0.545)S(0.104)S(0.022)QAPQK 148.36 0.0005211 26271000 1916.6 1972.1 2172.8 1837.3 2023.9 1833.7 1736.4 2169.9 1902.4 1860.7 TRUE FALSE FALSE 1893.239742 1999.863276 2210.616673 2049.737271 1920.612831 1716.532488 1883.889773 2232.682633 1732.244579 1812.358746 1.044627476 1.103458838 1.219745637 1.13097767 1.059731047 0.94712622 1.03946847 1.231920909 0.955795636 1 10.82365284 -10.53174738 2.31022628 1.01676085 1.099216227 0.253273536 0.081106167 0.386004497 4.148473772 0.015777734 0.016969951 2.94E-11 10.53174738 0.082455377 S(ph)PGSTPTTPTSSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 S(0.929)PGS(0.071)TPTTPTSSQAPQK 245.96 6.01E-59 4687800 1655.9 1821.3 1735.4 1551.3 1592.1 1732.6 1399.7 1851.9 1978.2 1829.2 TRUE FALSE FALSE 1635.717254 1846.940309 1765.603909 1730.668605 1510.849196 1621.892452 1518.590483 1905.481805 1801.264838 1781.67712 0.918077263 1.0366302 0.990978606 0.971370506 0.847992702 0.910317831 0.852337646 1.069487722 1.010993977 1 10.7990202 -8.889785799 19.95738053 0.969803987 0.913885512 0.173738612 0.065235443 3.548042525 625.6523275 0.009446635 0.017123555 1.29E-09 8.889785799 -0.055918476 S(ph)PGVAAAVAEDGGLK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGVAAAVAEDGGLK 15 0 Q9BTE7;E9PLH8;E9PM78;H0YD80;E9PLS2;E9PQV9;E9PM04 Q9BTE7 DCUN1D5 DCN1-like protein 5;DCN1-like protein 1 0 S(1)PGVAAAVAEDGGLK 130.95 0.0018776 4295000 740.82 1000.9 922.65 712.44 812.75 717.6 571.17 734.79 1041.9 1112 TRUE FALSE FALSE 731.7906009 1014.990696 938.7083362 794.8156649 771.2723347 671.7476759 619.6851655 756.0499893 948.7098545 1083.11008 0.675638252 0.937107608 0.866678608 0.733827226 0.712090441 0.620202589 0.572134982 0.698036149 0.875912682 1 10.08096416 -16.52287875 0.146031796 1.994989916 0.607494747 0.497340401 0.095572887 42.47305188 0.426292503 12.34634478 0.270669081 3.00E-17 16.52287875 -1.38749517 S(ph)PGVAAAVAEDGGLKK ddPTM_HeLa_Romidepsin_16h_R1 5 SPGVAAAVAEDGGLKK 16 1 Q9BTE7;E9PLH8;E9PM78;H0YD80;E9PLS2;E9PQV9;E9PM04 Q9BTE7 DCUN1D5 DCN1-like protein 5;DCN1-like protein 1 0 S(1)PGVAAAVAEDGGLKK;S(1)PGVAAAVAEDGGLKK;S(1)PGVAAAVAEDGGLKK;S(1)PGVAAAVAEDGGLKK;S(1)PGVAAAVAEDGGLKK ;;;; 103.17 0.001409 61362600 13365.1 11340.65 10611.44 9485.06 10358.82 9642.92 8970.94 9776.05 12397.21 12224.45 TRUE FALSE FALSE 13202.20102 11500.30397 10796.12766 10581.76727 9830.170761 9026.768533 9732.93142 10058.90458 11288.37249 11906.85703 1.10878975 0.965855552 0.906715151 0.888712046 0.825589048 0.758115136 0.817422381 0.844799309 0.94805644 1 13.53950502 -9.564914022 1.33444126 1.050691617 0.813011802 0.733852527 0.05042492 0.124953699 0.446146602 0.008951568 0.01469767 2.72E-10 9.564914022 -0.237679815 S(ph)PGYESESSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGYESESSR 10 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 S(1)PGYESESSR 139.76 0.0049048 28694000 800.41 745.72 553.7 737.11 569.71 537.6 454.16 370.8 802.77 615.27 TRUE FALSE FALSE 790.6542951 756.2182657 563.3369162 822.3381264 540.6355728 503.249095 492.7363391 381.528513 730.9682406 599.2851967 1.319328926 1.261867087 0.940014736 1.372198297 0.902134035 0.839748917 0.822206759 0.636639308 1.219733517 1 9.227098927 -8.573356954 6.201558391 1.159841712 0.786773897 0.662921695 0.136159866 0.10921289 9.448520207 0.022913172 0.046467156 2.67E-09 8.573356954 -0.373067815 S(ph)PGYESESSRYESQNTELK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGYESESSRYESQNTELK 19 1 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 S(0.646)PGY(0.045)ES(0.046)ES(0.257)S(0.002)RY(0.001)ES(0.002)QNTELK 67.685 0.0066569 5112400 840.76 845.67 709.52 861.39 892.4 836.13 745.44 1100.8 866.6 826.58 TRUE FALSE FALSE 830.5124937 857.5753645 721.868898 960.9879648 846.857498 782.7039915 808.757655 1132.649911 789.0891256 805.1053324 1.031557562 1.065171636 0.89661423 1.193617687 1.051859259 0.972175888 1.004536453 1.406834442 0.980106694 1 9.653033734 -7.25989115 24.95133275 1.021656668 1.406834572 0.715591411 0.072833265 49.33495361 795004.7631 0.009133765 0.078092392 5.50E-08 7.25989115 0.385177904 S(ph)PHQLLSPSSFSPSATPSQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPHQLLSPSSFSPSATPSQK 20 0 E9PIQ6;A0A3B3ITS5;Q14181 E9PIQ6 POLA2 DNA polymerase alpha subunit B 1 0 S(0.997)PHQLLS(0.003)PSSFSPSATPSQK 86.997 0.00096355 20666000 1859.7 1682.9 1647.3 1337.7 2258.4 1878.4 1431.3 1474 2745.2 2242.1 TRUE FALSE FALSE 1837.033261 1706.59191 1675.970565 1492.371168 2143.145421 1758.376302 1552.874586 1516.647864 2499.662437 2183.849919 0.841190251 0.781460253 0.767438527 0.683367092 0.981361128 0.805172685 0.711072026 0.694483559 1.144612739 1 11.092658 -16.52287875 0.133499615 1.80045281 0.690336024 0.612828041 0.090298479 45.02381096 0.423470819 9.415978059 0.276417545 3.00E-17 16.52287875 -1.110116787 S(ph)PILEEKDIPPLEFPK ddPTM_HeLa_Romidepsin_16h_R1 2 SPILEEKDIPPLEFPK 16 1 E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-4;Q12830;A0A0A0MR81;F5GXF5;Q12830-2 E7ETD6 BPTF Nucleosome-remodeling factor subunit BPTF 1 0 S(1)PILEEKDIPPLEFPK;S(1)PILEEKDIPPLEFPK ; 75.017 0.012022 85072000 6544.5 6245 6482.8 7864 5043.7 4498 4239.9 4525.8 6915.6 6074.1 TRUE FALSE FALSE 6464.733117 6332.917274 6595.630415 8773.272681 4786.301168 4210.592317 4600.037 4656.746882 6297.051416 5916.294006 1.092699773 1.070419636 1.114824653 1.482900051 0.809003265 0.711694232 0.777520014 0.787105387 1.064357418 1 12.53047803 -8.552992067 24.99967608 1.083003576 0.760597665 0.640354102 0.131072494 108.5909357 90150.3432 0.019642339 0.03928502 2.80E-09 8.552992067 -0.322405911 S(ph)PISPELHSAPLTPVAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPISPELHSAPLTPVAR 17 0 A0A1W2PRB5;A0A0J9YVS1;A0A0G2JQF5;A0A3B3IT55;A0A0G2JNB1;A0A0G2JNT7;Q7Z3B3-4;Q7Z3B3;A0A0G2JQF4;Q7Z3B3-2 A0A1W2PRB5 KANSL1 KAT8 regulatory NSL complex subunit 1 1 0 S(0.862)PIS(0.138)PELHSAPLTPVAR 91.725 0.0034201 6438700 1157.2 1076.3 1024.2 804.35 833.43 662.83 606.87 754.56 1418 1337.6 TRUE FALSE FALSE 1143.095601 1091.45218 1042.025771 897.3527316 790.8969571 620.4773022 658.4175227 776.3920031 1291.170529 1302.848959 0.877381521 0.837742681 0.799805506 0.688761905 0.607051916 0.476246535 0.505367501 0.595918658 0.991036236 1 10.34745412 -9.322421359 0.583331696 0.966530043 0.486512675 0.943076273 0.043226968 0.145987867 0.096655882 0.011878925 0.030844723 4.76E-10 9.322421359 -0.480017368 S(ph)PISVPGGSALISNLGK ddPTM_HeLa_Romidepsin_16h_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 0 S(0.999)PIS(0.001)VPGGSALISNLGK;S(1)PISVPGGSALISNLGK ; 199.61 5.81E-19 63968000 5101.5 5357.9 4849.3 2389.89 4386.2 5112.7 4065.22 4937.9 4897.47 4797.5 TRUE FALSE FALSE 5039.320956 5433.328657 4933.700032 2666.220327 4162.355847 4786.01497 4410.519685 5080.770346 4459.428017 4672.860258 1.078423209 1.162741524 1.055820153 0.57057566 0.890751192 1.0242153 0.943858674 1.087293449 0.954325139 1 12.19009018 S(ph)PKPAAPAAPPFSSSSGVLGTGLCELDR ddPTM_HeLa_Romidepsin_16h_R1 2 SPKPAAPAAPPFSSSSGVLGTGLCELDR 28 1 H3BQC4;O43294-2;O43294;H3BS04;H3BN49;H3BSN4 H3BQC4 TGFB1I1 Transforming growth factor beta-1-induced transcript 1 protein 1 0 S(1)PKPAAPAAPPFSSSSGVLGTGLCELDR;S(1)PKPAAPAAPPFSSSSGVLGTGLCELDR ; 147.74 2.30E-11 109780000 3189.2 3236.3 3155.8 332.597 1976.03 2116.05 1950.59 1672.52 3167.2 2861.5 TRUE FALSE FALSE 3150.328804 3281.860716 3210.725375 371.0534301 1875.185816 1980.841234 2116.273066 1720.911727 2883.9177 2787.157817 1.130301551 1.17749368 1.151971142 0.133129681 0.67279499 0.710702933 0.759294308 0.617443231 1.034716327 1 11.44457898 -9.302438246 24.9999794 1.079802684 0.601271291 0.700659606 0.169464959 225.5080958 137508.0381 0.026049184 0.039791026 4.98E-10 9.302438246 -0.478531393 S(ph)PLELEPEAK ddPTM_HeLa_Romidepsin_16h_R1 4 SPLELEPEAK 10 0 A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5;Q92466-4;Q92466 A0A087WTQ7 DDB2 DNA damage-binding protein 2 1 0 S(1)PLELEPEAK;S(1)PLELEPEAK;S(1)PLELEPEAK;S(1)PLELEPEAK ;;; 179.94 4.20E-05 92159700 15513 14947.3 15721.1 9319.4 14064.1 15063.1 11565.8 13840.2 16221.8 15111.4 TRUE FALSE FALSE 15323.92159 15157.72848 15994.71915 10396.95288 13346.3565 14100.61652 12548.19876 14240.64435 14770.88158 14718.80365 1.041111897 1.029820687 1.086686088 0.706372143 0.906755523 0.958000179 0.852528443 0.967513712 1.00353819 1 13.84537279 -9.300370276 24.99990944 1.025439892 0.882821728 0.538156912 0.071128278 323.0165455 207427.8689 0.010404877 0.015893865 5.01E-10 9.300370276 -0.142618164 S(ph)PLGSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLGSVR 7 0 Q92620;J3KSA8;H3BMS7;Q92620-2 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 0 S(1)PLGSVR 114.89 0.028257 30624000 1233.5 831 774.99 1054.2 1115.7 1346.5 1296.7 1193.7 976.51 947.41 TRUE FALSE FALSE 1218.465628 842.6988398 788.4783759 1176.091564 1058.761666 1260.462996 1406.841666 1228.237826 889.1684999 922.7961516 1.320406057 0.913201511 0.854444803 1.274486854 1.14734079 1.365917048 1.52454219 1.330995826 0.96355896 1 9.849868177 -8.252337595 2.30788902 1.119013683 1.435887691 0.490621079 0.153254881 0.25310666 2.608681726 0.025400931 0.075224316 5.59E-09 8.252337595 0.316874009 S(ph)PLPGPSEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPLPGPSEEK 10 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 S(1)PLPGPSEEK 105.46 0.020992 2783800 2337.8 2397 2030.5 1166.4 2336.6 2407.9 2058.4 2279.3 2075.4 2137.8 TRUE FALSE FALSE 2309.305994 2430.745029 2065.840001 1301.264656 2217.354583 2254.042961 2233.240445 2345.247949 1889.771026 2082.259648 1.109038441 1.167359235 0.992114505 0.624929104 1.064879005 1.082498508 1.072508151 1.126299476 0.90755782 1 11.02393426 -9.570239344 24.99939579 1.062482016 0.987513162 0.023761146 0.146298639 291.2038198 153711.319 0.022926145 0.032422473 2.69E-10 9.570239344 -0.074968854 S(ph)PLPSRVRRS(ph)S(ph)GS(ph)CR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLPSRVRRSSGSCR 15 3 M0QYJ4 M0QYJ4 PLD3 4 0 S(0.973)PLPS(0.041)RVRRS(0.996)S(0.996)GS(0.995)CR 45.083 0.0043335 0 503.92 392.24 407.48 430.46 298.39 380.6 283.4 423.13 493.96 454.04 TRUE FALSE FALSE 497.7780292 397.761965 414.5720185 480.2318106 283.1620449 356.2808883 307.4719889 435.372599 449.7789805 442.2439753 1.125573342 0.899417487 0.937428301 1.085897915 0.640284686 0.805620671 0.695254217 0.984462476 1.017038118 1 8.788698679 -8.773835139 24.99997994 1.038862453 0.776981495 0.523538854 0.105207181 117.3135808 236600.019 0.015798734 0.028783151 1.68E-09 8.773835139 -0.261880959 S(ph)PLSALAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLSALAR 8 0 I3L1L3;Q9BQG0;Q9BQG0-2;I3L2H8 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 S(1)PLSALAR 114.86 0.020677 45874000 730.47 678.13 935.45 742.86 1302.9 1442.5 1014 942.55 826.11 510.98 TRUE FALSE FALSE 721.5667507 687.6767319 951.7311148 828.7529685 1236.408151 1350.328905 1100.129135 969.8211972 752.2206526 497.7046659 1.449789002 1.381696373 1.912240692 1.665150088 2.484220534 2.713112811 2.210405507 1.948587714 1.511379547 1 8.959146102 -9.643150631 0.649348068 1.131223661 2.37453893 0.680520541 0.284668383 0.250351379 0.215194643 0.067349857 0.12755716 2.27E-10 9.643150631 1.243315269 S(ph)PLSGIPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SPLSGIPVR 9 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 0 S(1)PLSGIPVR;S(0.999)PLS(0.001)GIPVR ; 107.55 0.021469 78875000 1500.62 1223.8 1648.27 1209.03 1826.67 2156.52 1821.96 1865.19 1453.69 1535.11 TRUE FALSE FALSE 1482.329866 1241.028689 1676.957448 1348.823737 1733.448214 2018.725332 1976.717237 1919.15633 1323.668326 1495.227621 0.991374053 0.829993154 1.121539908 0.902085889 1.159320621 1.350112387 1.322017604 1.283521186 0.885262088 1 10.54614941 -8.51974199 3.758709489 0.98683716 1.315351313 0.804497629 0.079968149 0.063940778 1.981866368 0.009751338 0.021603562 3.02E-09 8.51974199 0.328514153 S(ph)PLSPTETFSWPDVR ddPTM_HeLa_Romidepsin_16h_R1 3 SPLSPTETFSWPDVR 15 0 G3V311;A1L390-2;A1L390-3;A1L390 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 S(0.994)PLS(0.006)PTETFSWPDVR;S(0.998)PLS(0.002)PTETFSWPDVR;S(1)PLSPTETFSWPDVR ;; 216.27 7.10E-26 60292000 2879.98 3053.24 2746.13 2610.26 2519.62 2340.84 1669.8 1459.38 2756.85 2858.15 TRUE FALSE FALSE 2844.877696 3096.223593 2793.925241 2912.070543 2391.034389 2191.267879 1811.63277 1501.604858 2510.270431 2783.894851 1.021905585 1.112191285 1.003603006 1.046041858 0.858880999 0.787123076 0.65075474 0.539389933 0.901711654 1 11.44288901 -7.996434054 1.075970894 1.02193408 0.520101625 0.897394442 0.056209816 0.114679626 0.201920612 0.006649285 0.048555609 1.01E-08 7.996434054 -0.501832456 S(ph)PLTILQDDNS(ph)PGTLTLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLTILQDDNSPGTLTLR 18 0 Q99618;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 2 0 S(0.999)PLT(0.001)ILQDDNS(0.99)PGT(0.009)LT(0.001)LR 118.02 0.015425 2365200 465.37 338.68 505.65 477.02 276.43 516.28 504.08 366.1 457.89 462.41 TRUE FALSE FALSE 459.6978914 343.4479459 514.4506261 532.1752968 262.3227456 483.2913742 546.8965426 376.6925259 416.9351716 450.3965215 1.020651514 0.762545734 1.142217139 1.181570619 0.582426225 1.073035317 1.214255698 0.836357538 0.925706909 1 8.815051875 S(ph)PLTILQDDNSPGTLTLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLTILQDDNSPGTLTLR 18 0 Q99618;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 S(0.998)PLT(0.002)ILQDDNSPGTLTLR 90.872 0.0017908 0 176.92 249.51 267.88 989.58 286.44 219.43 158.13 221.94 323.79 208.15 TRUE FALSE FALSE 174.763631 253.0226083 272.542339 1103.999896 271.8218979 205.4091312 171.5615583 228.3614837 294.8294115 202.742233 0.861999143 1.248001487 1.34428005 5.445337557 1.340726567 1.013154132 0.84620533 1.126363661 1.454208169 1 7.663502836 -9.513884744 24.78995125 0.972672955 1.965253066 0.082567269 1.252365541 650.8583808 1793947.208 0.197876795 0.288611643 3.06E-10 9.513884744 0.992580111 S(ph)PMQEEEDLAAGVGR ddPTM_HeLa_Romidepsin_16h_R1 2 SPMQEEEDLAAGVGR 15 0 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 0 S(1)PMQEEEDLAAGVGR;S(1)PMQEEEDLAAGVGR ; 95.477 0.015762 3860600 619.52 719.53 779.26 589.59 656.71 682.47 667.38 655.53 874.87 687.05 TRUE FALSE FALSE 611.9690519 729.6595622 792.8226934 657.7611699 623.1956382 638.8623696 724.0672405 674.4967263 796.619436 669.200342 0.914478092 1.090345471 1.184731453 0.982906207 0.931254214 0.954665336 1.081988749 1.007914497 1.190405004 1 9.386294372 -10.26775627 24.93112694 0.959614656 1.032190913 0 0.102605861 697.9128424 2754478.884 0.013635619 0.015800857 5.40E-11 10.26775627 0.072576257 S(ph)PPADAIPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPADAIPK 9 0 M0R1Q8;C9JRH2;C9J3R0;C9JMJ4;C9JQZ4;C9JW69;P18754;P18754-2 M0R1Q8 RCC1 Regulator of chromosome condensation 1 0 S(1)PPADAIPK 99.568 0.028727 56710000 6021.4 5615.8 5850.6 3710 6014.2 6307.8 5026.4 6039.3 6182.5 5837.3 TRUE FALSE FALSE 5948.008861 5694.85938 5952.427239 4138.967656 5707.272932 5904.751937 5453.342291 6214.037617 5629.521716 5685.646105 1.046144757 1.001620445 1.046921868 0.727967865 1.003803759 1.038536664 0.959142055 1.092934295 0.990128758 1 12.47310859 -13.36531748 18.0686956 0.999994677 1.003717399 0 0.095375759 619.0390634 369401.2514 0.846310762 0.0130261 4.31E-14 13.36531748 0.003722721 S(ph)PPEGDTTLFLSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPPEGDTTLFLSR 13 0 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 S(1)PPEGDTTLFLSR;S(1)PPEGDTTLFLSR ; 133.04 0.0019029 80855000 522.73 514.21 434.42 455.27 474.19 513.74 369.58 506.52 673.29 456.83 TRUE FALSE FALSE 516.3587657 521.4490619 441.9808979 507.9104595 449.9903149 480.913672 400.972116 521.175357 613.0692561 444.9614907 1.1604572 1.171897058 0.993301459 1.141470599 1.011301706 1.080798411 0.901138917 1.171281938 1.377802953 1 8.797536673 -8.72855671 24.98940185 1.082779949 1.033964304 0.021201121 0.1259061 470.1216578 357270.4645 0.013126589 0.026251536 1.87E-09 8.72855671 -0.048815645 S(ph)PPGAEEPQAPPASR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPGAEEPQAPPASR 15 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 0 S(1)PPGAEEPQAPPASR 82.651 0.027141 3363700 103.72 0 125.57 123.04 216.9 102.82 0 0 152.45 173.55 TRUE FALSE FALSE 102.4558207 0 127.7554932 137.2664637 205.8307836 96.25013384 0 0 138.8144902 169.041146 0.606099894 0 0.75576566 0.812029893 1.217637176 0.569388792 0 0 0.821187584 1 7.401230643 -12.68746111 0.101416682 1.757539256 3.62E-22 0.207807205 0.370826722 48.24745845 1.084962608 14.9013701 5.334741274 2.05E-13 12.68746111 -1.757539256 S(ph)PPGSGASTPVGPWDQAVQR ddPTM_HeLa_Romidepsin_16h_R1 2 SPPGSGASTPVGPWDQAVQR 20 0 C9JUG3;Q8TE77-4;Q8TE77-2;Q8TE77 C9JUG3 SSH3 Protein phosphatase Slingshot homolog 3 1 0 S(1)PPGSGASTPVGPWDQAVQR;S(1)PPGSGASTPVGPWDQAVQR ; 220.78 1.51E-41 42198000 624.09 557.58 678.78 409.635 414.28 546.56 439.69 389.92 525.6 564.11 TRUE FALSE FALSE 616.483351 565.4296259 690.5938812 456.9989261 393.1377457 511.6365799 477.0372576 401.20172 478.5890196 549.4543409 1.121991957 1.029074818 1.256872191 0.831732306 0.71550576 0.93117215 0.868201818 0.730182092 0.871026005 1 9.101855789 -9.150482057 8.925365125 1.06997486 0.817930109 0.550266996 0.108342422 0.159654943 11.83573965 0.013645093 0.022659552 7.07E-10 9.150482057 -0.252044751 S(ph)PPKEYIDEEGVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPKEYIDEEGVR 13 1 H7BXF5;A0A2R8YDB8;Q9H0E3;Q9H0E3-3;Q9H0E3-2 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 0 S(0.999)PPKEY(0.001)IDEEGVR 67.749 0.025982 3773700 1382.2 1191.2 1209.6 780.16 1451 1629.6 1312.4 1246.3 1433.8 1240.3 TRUE FALSE FALSE 1365.353215 1207.969745 1230.652581 870.36577 1376.950056 1525.473819 1423.875223 1282.359724 1305.557337 1208.076827 1.130187405 0.999911361 1.018687349 0.720455645 1.139786829 1.262729145 1.178629696 1.061488554 1.080690654 1 10.23849649 -8.543251275 24.99988872 1.028787563 1.174140841 0.317793203 0.114178623 256.5864508 314865.8498 0.017652912 0.035308626 2.86E-09 8.543251275 0.145353279 S(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_HeLa_Romidepsin_16h_R1 2 SPPKVPIVIQDDSLPAGPPPQIR 23 1 Q7Z422-2;Q7Z422-4;Q7Z422-3;Q7Z422-5;Q7Z422 Q7Z422-2 SZRD1 SUZ domain-containing protein 1 1 0 S(1)PPKVPIVIQDDSLPAGPPPQIR;S(1)PPKVPIVIQDDSLPAGPPPQIR ; 118.9 1.83E-06 93853000 1970.42 1994.16 1823.15 1295.88 1699.3 1596.61 1558.22 1517.72 2057.7 2080.97 TRUE FALSE FALSE 1946.403763 2022.233837 1854.881161 1445.715743 1612.57838 1494.591774 1690.575168 1561.632834 1873.654158 2026.906099 0.960283145 0.99769488 0.915129301 0.713262318 0.79558613 0.737375932 0.834066841 0.770451495 0.924391198 1 10.98506354 -9.446222368 4.185892398 0.981326751 0.77398739 0.868594587 0.037141284 0.04753473 1.564159399 0.005031193 0.007710929 3.58E-10 9.446222368 -0.207339361 S(ph)PPLIGSESAYESFLSADDK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPLIGSESAYESFLSADDK 20 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.993)PPLIGS(0.003)ES(0.003)AYESFLSADDK 83.849 0.0014017 10827000 677.65 666.79 777.41 553.35 713.24 595.03 536.22 552.9 648.62 641.95 TRUE FALSE FALSE 669.3905411 676.1770871 790.9404949 617.3309306 676.8407013 557.0095034 581.7665134 568.8972892 590.6058027 625.2720465 1.070558879 1.081412628 1.26495419 0.987299743 1.082473949 0.890827451 0.930421433 0.909839633 0.944558142 1 9.288340211 -8.259954392 24.98964072 1.054848999 0.912368692 0.418116003 0.081480961 100.2374855 1686796.512 0.011122215 0.026763704 5.50E-09 8.259954392 -0.142480307 S(ph)PPLIGSESAYESFLSADDKASGR ddPTM_HeLa_Romidepsin_16h_R1 2 SPPLIGSESAYESFLSADDKASGR 24 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(1)PPLIGSESAYESFLSADDKASGR;S(0.998)PPLIGS(0.001)ESAYESFLSADDKASGR ; 177.38 3.06E-18 43396000 2602 3157.8 2261.09 2423.49 3001.8 2559.46 2464.34 3065.7 2705.22 2669.63 TRUE FALSE FALSE 2570.285823 3202.255591 2300.443323 2703.705317 2848.606945 2395.918766 2673.660978 3154.401193 2463.258348 2600.272628 0.988467823 1.231507634 0.884693127 1.039777632 1.095503185 0.921410602 1.028223329 1.213104026 0.947307725 1 11.34444718 -7.270691045 4.816543098 1.009014449 1.223004203 0.291859361 0.092428614 0.144712539 9.565933315 0.011412318 0.101903327 5.36E-08 7.270691045 0.213989754 S(ph)PPLPAVIR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPLPAVIR 9 0 Q9Y6X9-2;Q9Y6X9 Q9Y6X9-2 MORC2 MORC family CW-type zinc finger protein 2 1 0 S(1)PPLPAVIR 107.55 0.021469 193290000 606.73 508.52 739.67 622.28 729.14 772.36 647.63 646.01 612.81 574.64 TRUE FALSE FALSE 599.3349414 515.6789579 752.5436461 694.2309415 691.929265 723.0086887 702.639676 664.7012801 557.9987388 559.71077 1.070794013 0.921331133 1.344522361 1.240338723 1.236226462 1.291754112 1.255362079 1.187579936 0.996941222 1 9.128537698 -9.75862858 24.99999999 1.025957139 1.258683297 0.848462788 0.053705041 21.83517847 194206.661 0.008484057 0.011696979 1.74E-10 9.75862858 0.232726158 S(ph)PPPGPDGHAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPPGPDGHAK 11 0 P57081-3;P57081-2;P57081 P57081-3 WDR4 tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4 1 0 S(1)PPPGPDGHAK 88.224 0.015531 3786800 2533.4 2729.1 3211.2 1832.5 2606 3083.2 3113 1815.5 3412.1 3178 TRUE FALSE FALSE 2502.521946 2767.520341 3267.089589 2044.382272 2473.006096 2886.193471 3377.418142 1868.028628 3106.91323 3095.435102 0.808455634 0.894065051 1.055454074 0.660450698 0.79892035 0.93240316 1.091096415 0.603478531 1.003708082 1 11.5959265 -12.45951843 1.112477931 1.002524748 0.85994094 0.138874227 0.144989345 0.918412296 1.974449671 0.104630209 0.024072784 3.47E-13 12.45951843 -0.142583807 S(ph)PPREGSQGELTPANSQSR ddPTM_HeLa_Romidepsin_16h_R1 3 SPPREGSQGELTPANSQSR 19 1 J3QQX0;C9JFE4;A0A096LP07;A0A096LPJ3;A8K070;Q13098-5;Q13098;Q13098-7 J3QQX0 GPS1 COP9 signalosome complex subunit 1 1 0 S(0.676)PPREGS(0.317)QGELT(0.007)PANSQSR;S(0.728)PPREGS(0.271)QGELTPANSQSR;S(0.925)PPREGS(0.075)QGELTPANSQSR ;; 80.835 0.0012568 35515000 243.39 232.584 179.35 108.59 239.538 128.83 345.22 337.14 307.09 220.214 TRUE FALSE FALSE 240.4234691 235.8583237 182.4715115 121.1456867 227.313482 120.5981788 374.5429782 346.894614 279.6231013 214.4928085 1.120892913 1.099609471 0.850711559 0.564800692 1.059772044 0.562248122 1.746179654 1.61727853 1.303647909 1 7.744785468 -7.741682886 24.9997775 0.985042706 1.681729725 0.621609097 0.228168801 114.8954242 145385.9319 0.029315473 0.109381385 1.81E-08 7.741682886 0.696687019 S(ph)PPSSSEIFTPAHEENVR ddPTM_HeLa_Romidepsin_16h_R1 3 SPPSSSEIFTPAHEENVR 18 0 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 0 S(1)PPSSSEIFTPAHEENVR;S(0.996)PPS(0.004)SSEIFTPAHEENVR;S(0.968)PPS(0.029)S(0.003)SEIFTPAHEENVR ;; 196.76 1.36E-15 90158000 2336.2 2285.1 2681.43 2049.93 2261.12 2597.72 2140.06 2635.4 3649.69 2476.86 TRUE FALSE FALSE 2307.725496 2317.269698 2728.099164 2286.952552 2145.726609 2431.734076 2321.836643 2711.651141 3323.252586 2412.51082 0.956565863 0.960521992 1.130813235 0.947955355 0.889416367 1.007968153 0.962415017 1.123995432 1.377507847 1 11.2363197 -7.25682239 24.39021721 0.980868849 1.123995514 0 0.138455125 294.534445 1555860.483 0.007842939 0.083975053 5.54E-08 7.25682239 0.143126665 S(ph)PPSTGSTYGSSQK ddPTM_HeLa_Romidepsin_16h_R1 2 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.624)PPS(0.287)T(0.087)GS(0.002)TYGSSQK;S(0.995)PPS(0.001)T(0.004)GSTYGSSQK ; 128.85 0.002513 15595100 2676.64 2719.49 3175 1427.94 2086.05 3068.61 2279.46 2316.09 2952.89 2778.26 TRUE FALSE FALSE 2644.016082 2757.775052 3230.259543 1593.045141 1979.591084 2872.535724 2473.077276 2383.10241 2688.776123 2706.080405 0.977064864 1.019103145 1.193704199 0.588690986 0.731534466 1.061511594 0.91389645 0.880647303 0.993605407 1 11.40198899 -9.277756161 24.96447196 1.005561189 0.846432467 0.36332342 0.1296844 849.1182486 1299137.359 0.020318202 0.031094365 5.28E-10 9.277756161 -0.159128721 S(ph)PPSTGSTYGSSQKEESAASGGAAYTK ddPTM_HeLa_Romidepsin_16h_R1 3 SPPSTGSTYGSSQKEESAASGGAAYTK 27 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.985)PPS(0.011)T(0.003)GS(0.001)TYGSSQKEESAASGGAAYTK;S(0.967)PPS(0.027)T(0.005)GSTYGSSQKEESAASGGAAYTK;S(0.94)PPS(0.026)T(0.023)GS(0.004)T(0.004)Y(0.001)GS(0.001)S(0.001)QKEESAASGGAAYTK ;; 85.573 1.24E-06 94334000 2143.88 2056.39 2678.01 1290.47 2241.14 2263.18 2011.93 2044.52 2092.03 2491.37 TRUE FALSE FALSE 2117.749566 2085.339912 2724.619641 1439.680213 2126.766263 2118.570102 2182.823284 2103.67496 1904.913597 2426.643848 0.872707203 0.859351451 1.122793377 0.593280392 0.87642291 0.873045339 0.899523548 0.866907174 0.784999248 1 11.24474667 -9.282110071 24.9977215 0.943511705 0.832029386 0.15980375 0.117890377 991.7936235 1199404.365 0.016525546 0.025259258 5.22E-10 9.282110071 -0.111482319 S(ph)PPSYPGAPSSAPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPSYPGAPSSAPAR 15 0 H0Y8X4 H0Y8X4 DNPH1 1 0 S(1)PPSYPGAPSSAPAR 137.93 0.0010538 7279900 76.241 200.84 0 174.82 115.91 135.47 57.064 0 0 147.09 TRUE FALSE FALSE 75.31174537 203.6674308 0 195.033511 109.9946802 126.8139042 61.91101474 0 0 143.2685806 0.525668259 1.42157778 0 1.361313905 0.767751587 0.885148046 0.432132534 0 0 1 7.162578445 -7.479421047 2.694812981 0.809330025 2.95E-11 0.190884745 0.460619605 0.286299198 3.544027402 0.050174469 0.408526301 3.32E-08 7.479421047 -0.809330025 S(ph)PPSYSVLYPSSDPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPSYSVLYPSSDPK 15 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 0 S(0.674)PPS(0.326)YSVLYPSSDPK 172.09 1.50E-05 23863000 2466.9 2365.3 2208 2186 2100.6 2097 2035.3 2218.7 2128.3 2168.4 TRUE FALSE FALSE 2436.832474 2398.598755 2246.429314 2438.755605 1993.398544 1963.008468 2208.178331 2282.894584 1937.939518 2112.064655 1.153767934 1.135665402 1.063617682 1.15467848 0.943815114 0.929426314 1.045506976 1.080882907 0.917556909 1 11.04443828 -8.754704838 24.99731751 1.083937304 0.998130525 0.146381227 0.080287086 188.9011397 701157.9205 0.011169127 0.021938413 1.76E-09 8.754704838 -0.085806779 S(ph)PPTQVAISSDSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPTQVAISSDSAR 14 0 H0YM82;Q6ZUT6-3;Q6ZUT6-4;Q6ZUT6 H0YM82 C15orf52 Uncharacterized protein C15orf52 1 0 S(0.999)PPT(0.001)QVAISSDSAR 114.06 0.0049371 9890900 355.19 251.43 285.1 170.45 382.88 222.17 151.64 200.17 282.4 435.31 TRUE FALSE FALSE 350.8608077 254.9696381 290.0620459 190.158231 363.3402049 207.974054 164.5202978 205.9616031 257.1414367 424.0005834 0.827500766 0.601342659 0.684107657 0.448485777 0.856933266 0.490504169 0.388019036 0.48575783 0.606464818 1 8.72792244 -9.779340441 0.237109152 1.091177198 0.307905092 0.184149413 0.172015547 1.015951583 0.178597021 0.178926839 0.298283806 1.66E-10 9.779340441 -0.783272106 S(ph)PPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPVQPHTPVTISLGTAPSLQNNQPVEFNHAINYVNK 37 0 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 1 0 S(0.536)PPVQPHT(0.12)PVT(0.105)IS(0.105)LGT(0.105)APS(0.028)LQNNQPVEFNHAINYVNK 48.538 0.0040696 25756000 1882 1851.7 1536.7 2587.1 2096.1 1827 2126.7 2533.7 2196.9 2067.2 TRUE FALSE FALSE 1859.06146 1877.768281 1563.445619 2886.232675 1989.128195 1710.260596 2307.341845 2607.008612 2000.403762 2013.493846 0.923301287 0.932592014 0.776483932 1.433444994 0.98789882 0.849399465 1.145939358 1.294768602 0.993498821 1 10.97548535 -9.30521735 24.99877397 0.947255554 1.11764481 0.305411673 0.159864056 537.7504997 307073.2617 0.024324774 0.03715685 4.95E-10 9.30521735 0.170389256 S(ph)PPYTAFLGNLPYDVTEESIK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPYTAFLGNLPYDVTEESIK 21 0 E7EX17;P23588-2;P23588;F8VP89;F8VX11;F8W0K0;F8VSC7;F8VRU1;F8VYE9 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.506)PPY(0.418)T(0.076)AFLGNLPYDVTEESIK 101.49 0.00018046 4525800 111.84 113.11 0 0 98.415 0 0 124.96 0 0 TRUE FALSE FALSE 110.4768511 114.7023655 0 0 93.39251531 0 0 128.5755204 0 0 0 S(ph)PQESTGDPGNSSSVSEGK ddPTM_HeLa_Romidepsin_16h_R1 2 SPQESTGDPGNSSSVSEGK 19 0 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YAV4 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 0 S(0.766)PQES(0.105)T(0.105)GDPGNS(0.021)S(0.002)SVSEGK;S(0.505)PQES(0.438)T(0.057)GDPGNSSSVSEGK ; 179.69 2.60E-10 7123400 3261.7 3504.7 3599.8 1979.02 2734.9 2673.34 2242.06 2357.9 4155.7 3449.9 TRUE FALSE FALSE 3221.945146 3554.039259 3662.453009 2207.843604 2595.327848 2502.522202 2432.50052 2426.122116 3784.003784 3360.271101 0.958834882 1.057664442 1.089927836 0.657043297 0.772356685 0.744738185 0.723900081 0.722001899 1.126100743 1 11.71436192 -9.258225732 24.99999648 0.994533391 0.727839739 0.863277798 0.06247315 69.46633652 540400.2644 0.007563928 0.012205851 5.52E-10 9.258225732 -0.266693652 S(ph)PQQSAALPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPQQSAALPR 10 0 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 0 S(1)PQQSAALPR 111.31 0.01726 81765000 382.96 292.66 486.68 378.78 248.05 283.26 360.3 283.41 373.43 621.97 TRUE FALSE FALSE 378.2923362 296.7800752 495.1504612 422.5763258 235.3910829 265.1606002 390.903873 291.6100212 340.0294855 605.8111297 0.624439396 0.48988878 0.817334705 0.697538069 0.38855523 0.437695161 0.645257001 0.481354678 0.561279694 1 9.242724273 -14.73498537 0.197951923 1.935449384 0.473858122 0 0.183219384 11.62456206 0.263277401 4.549879215 0.147167945 1.84E-15 14.73498537 -1.461591263 S(ph)PQQTVPYVVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 2 0 S(0.989)PQQT(0.011)VPY(0.002)VVPLS(0.998)PK 136.92 0.011873 14567000 3855 3358.8 3417.8 2742.6 4117.3 4370.5 3676.9 4022.3 3422.3 3306.8 TRUE FALSE FALSE 3808.013777 3406.085275 3477.285375 3059.712316 3907.178817 4091.239155 3989.215794 4138.678904 3116.200917 3220.888859 1.182286612 1.057498543 1.079604273 0.949958986 1.213074709 1.27022053 1.238545001 1.284949306 0.967497189 1 11.65324316 -4 0.262674651 1.056186841 2.801481596 0.544925543 0.082147705 35.04968289 0.44231184 0.045516758 27.82640766 1.00E-04 4 1.745294755 S(ph)PQSDPADT(ph)PTNTK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQSDPADTPTNTK 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 2 0 S(0.995)PQS(0.005)DPADT(0.999)PT(0.001)NTK 193.19 1.29E-10 4687200 2925.4 2642.2 2771 2023.7 1533.1 1964.5 1750.7 1443.6 3034.3 2575 TRUE FALSE FALSE 2889.7441 2679.396961 2819.228093 2257.689716 1454.860186 1838.97479 1899.404414 1485.368288 2762.904608 2508.101129 1.152164108 1.06829702 1.124048811 0.900158965 0.580064404 0.733213972 0.757307747 0.592228228 1.101592187 1 11.2923798 -8.983366975 3.927461009 1.075825939 0.678412074 0.902873224 0.065223911 0.056851464 1.973322024 0.011460353 0.020815863 1.04E-09 8.983366975 -0.397413866 S(ph)PQSDPADTPTNTK ddPTM_HeLa_Romidepsin_16h_R1 2 SPQSDPADTPTNTK 14 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 S(0.997)PQS(0.003)DPADTPTNTK;S(0.906)PQS(0.094)DPADTPTNTK ; 163.9 0.00016707 8801200 2992.5 3141.8 3285.6 1664.29 1834.64 2156 2724.9 2066.33 4006.7 4298.4 TRUE FALSE FALSE 2956.026259 3186.030343 3342.78449 1856.723041 1741.011475 2018.238558 2956.352938 2126.115998 3648.330717 4186.726948 0.706047061 0.760983552 0.79842429 0.443478417 0.415840702 0.482056409 0.706125089 0.507822943 0.871404026 1 12.03160712 -11.21166744 0.301570125 1.082265655 0.489967081 0.630581592 0.114415589 0.881399909 0.20192471 0.203893982 0.095780345 6.14E-12 11.21166744 -0.592298574 S(ph)PQTLAPVGEDAMK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQTLAPVGEDAMK 14 0 Q92797 Q92797 SYMPK Symplekin 1 0 S(0.992)PQT(0.008)LAPVGEDAMK 99.796 0.014245 10284000 3541.1 3421.4 3602.3 1609.6 2505.7 3071.3 2919.3 3157.4 3493.5 3664.7 TRUE FALSE FALSE 3497.939711 3469.566559 3664.99652 1795.709525 2377.824779 2875.053842 3167.265269 3248.754387 3181.03261 3569.490566 0.979954883 0.972006087 1.026756186 0.503071655 0.66615242 0.805452148 0.88731577 0.910145111 0.891172718 1 11.80150247 -9.326988194 24.99999907 0.991079201 0.759738469 0.482660848 0.112891782 120.737019 46048.17171 0.017318879 0.026455027 4.71E-10 9.326988194 -0.231340732 S(ph)PRPASPASNVVVLPSGSTVYVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPRPASPASNVVVLPSGSTVYVK 23 1 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 S(0.609)PRPAS(0.373)PAS(0.018)NVVVLPSGSTVYVK 105.55 8.29E-06 14551000 2030.1 1839.1 1846.5 1958.9 2120.9 1594.3 1728 1953.4 2297.8 2024.7 TRUE FALSE FALSE 2005.35636 1864.990898 1878.637558 2185.397235 2012.662559 1492.429375 1874.776277 2009.918547 2092.279013 1972.098002 1.016864455 0.945688752 0.952608621 1.108158536 1.02056924 0.756772419 0.950650665 1.019177822 1.060940689 1 10.94551553 S(ph)PRPPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPRPPPR 7 1 Q9HB15 REV__H3BV60 KCNK12 Potassium channel subfamily K member 12 1 0 S(1)PRPPPR 93.143 0.015438 105570000 603.32 519.52 451.35 404.04 541.23 444.77 668.02 226.12 406.39 339.34 TRUE FALSE FALSE 595.9665038 526.8338162 459.2055574 450.7570059 513.6090135 416.3506324 724.7616021 232.6624254 370.0414606 330.5238979 1.803096562 1.593935626 1.38932634 1.363765249 1.553923988 1.259668772 2.192766111 0.703920131 1.11956038 1 8.368610777 -12.53466043 1.30771891 1.00120471 1.534735449 0.163715227 0.365396607 0.490462077 1.507513701 0.229974566 0.055384871 2.92E-13 12.53466043 0.533530739 S(ph)PRPTGSDLLPGAPILSLR ddPTM_HeLa_Romidepsin_16h_R1 2 SPRPTGSDLLPGAPILSLR 19 1 Q8N1F8 Q8N1F8 STK11IP Serine/threonine-protein kinase 11-interacting protein 1 0 S(0.997)PRPT(0.002)GS(0.002)DLLPGAPILSLR;S(0.981)PRPT(0.019)GS(0.001)DLLPGAPILSLR ; 126.32 0.00033356 42824000 2687.4 2545.49 2935.3 2315.9 2407.3 2574.18 2256.72 2319.76 3020.1 2855.52 TRUE FALSE FALSE 2654.644935 2581.325475 2986.387665 2583.675255 2284.446498 2409.698206 2448.40574 2386.878596 2749.974692 2781.333179 0.954450533 0.928089268 1.073725251 0.928934108 0.821349458 0.866382433 0.880299332 0.858177875 0.988725376 1 11.44156086 -8.978334866 7.045416938 0.980790832 0.860413049 0.726577272 0.038099505 0.07154051 14.45877875 0.005653653 0.010174404 1.05E-09 8.978334866 -0.120377783 S(ph)PS(ph)PAPAPAPAAAAGPPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPAPAPAPAAAAGPPTR 19 0 Q9H7N4 Q9H7N4 SCAF1 "Splicing factor, arginine/serine-rich 19" 2 0 S(1)PS(1)PAPAPAPAAAAGPPTR 147.37 0.00049226 7017600 1158.2 1240.5 966.14 927.83 1101.3 1068.6 982.74 1208.4 1428.8 1196.6 TRUE FALSE FALSE 1144.083413 1257.963792 982.9552614 1035.11007 1045.096551 1000.319909 1066.213911 1243.363147 1301.00455 1165.512159 0.981614309 1.079322752 0.843367659 0.888116063 0.896684383 0.858266386 0.914802906 1.066795518 1.116251374 1 10.18674834 -9.754560063 24.99998717 0.997675646 0.907362212 0.386232545 0.073112467 140.6857888 511261.8737 0.009661861 0.013491864 1.76E-10 9.754560063 -0.090313434 S(ph)PS(ph)PAPPPRR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPAPPPRR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 2 0 S(1)PS(1)PAPPPRR;S(1)PS(1)PAPPPRR ; 73.273 0.027176 37554000 5095.9 4710.7 4631.6 3719.1 5193.5 4388.7 4173.2 4677 5390.2 4963.1 TRUE FALSE FALSE 5033.789211 4777.017358 4712.211055 4149.119841 4928.456315 4108.276234 4527.671504 4812.321616 4908.087012 4834.157947 1.041295975 0.988179826 0.974773912 0.858292155 1.019506679 0.849843195 0.936599829 0.995482909 1.01529306 1 12.2390489 -9.718806692 2.572283695 1.018902403 0.931897309 0.34800005 0.050733653 0.20470542 2.777524796 0.007833713 0.011205659 1.91E-10 9.718806692 -0.087005094 S(ph)PS(ph)PEPIYNSEGK ddPTM_HeLa_Romidepsin_16h_R1 3 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-4;Q15637-3;Q15637-2;Q15637;Q15637-7;Q15637-5 Q15637-6 SF1 Splicing factor 1 2 0 S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK;S(1)PS(1)PEPIYNSEGK ;; 133.04 0.019455 11795200 4594.23 4734.21 5141.3 1927.96 3817.87 4406.92 3506.71 4194.98 4185.8 5025.38 TRUE FALSE FALSE 4538.233758 4800.858333 5230.78217 2150.879807 3623.029847 4125.332035 3804.56986 4316.355128 3811.411564 4894.819903 0.927150303 0.980803876 1.068636288 0.439419601 0.740176333 0.842795469 0.777264524 0.88182103 0.778662267 1 12.25704006 -9.316245731 24.9999828 0.973132506 0.744702043 0.394701822 0.131353388 193.431255 88233.41796 0.017655672 0.026969491 4.83E-10 9.316245731 -0.228430464 S(ph)PS(ph)QSSLPAVVVETFPATVNGTVEGGSGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSQSSLPAVVVETFPATVNGTVEGGSGAGR 31 0 O00499-9;O00499-10 O00499-9 BIN1 Myc box-dependent-interacting protein 1 2 0 S(0.755)PS(0.491)QS(0.427)S(0.327)LPAVVVETFPATVNGTVEGGSGAGR 82.55 8.67E-09 0 0 220.27 187.85 233.8 145.02 203.66 145.33 142.84 64.149 143.12 TRUE FALSE FALSE 0 223.3709668 191.1194505 260.8330561 137.6190883 190.6467833 157.6743266 146.97285 58.41135278 139.4017218 0 1.602354433 1.370997776 1.8710892 0.987212256 1.367607092 1.13107876 1.054311584 0.419014572 1 7.12310457 -10.24957869 24.95149094 0.527777772 1.341613023 0.584875689 0.334022452 506.2107536 1064923.631 0.072460051 0.088364709 5.63E-11 10.24957869 0.813835252 S(ph)PSAGILR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSAGILR 8 0 Q99618;F5GX58;F8WDL1;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 S(0.998)PS(0.002)AGILR;S(0.999)PS(0.001)AGILR ; 102.07 0.029255 24644000 2347.56 2419 2726.7 2269.7 2863.6 2218 2305.8 1879.24 2722.5 2186.7 TRUE FALSE FALSE 2318.947036 2453.054745 2774.15707 2532.133393 2717.459806 2076.276958 2501.654594 1933.612844 2478.992781 2129.889219 1.088764155 1.151728796 1.302488902 1.188856853 1.275869084 0.974828615 1.174546813 0.907846675 1.163906911 1 11.05656268 -11.01871536 1.178815806 1.020401918 1.144618574 0 0.123583755 0.517471455 1.502421607 0.029043758 0.023832895 9.58E-12 11.01871536 0.124216656 S(ph)PSAIPEQNHSLNDQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSAIPEQNHSLNDQAK 17 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 0 S(0.568)PS(0.432)AIPEQNHSLNDQAK 98.804 0.0015342 15844000 2595.2 3034.1 3206.9 2429.5 3208.8 3581.7 2755.3 3516.4 2881.9 2963 TRUE FALSE FALSE 2563.568704 3076.814139 3262.714749 2710.410221 3045.042962 3352.840929 2989.335113 3618.141486 2624.135646 2886.020833 0.888271032 1.06610947 1.13052363 0.939151301 1.055100825 1.161752158 1.035798176 1.253678229 0.909257347 1 11.494866 -6.578940731 0.355030358 0.951786183 1.544583032 0.501180667 0.077796536 6.298943902 0.38488995 0.02629789 1.763093186 2.64E-07 6.578940731 0.592796849 S(ph)PSAPAATSSASSSTSSYK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSAPAATSSASSSTSSYK 19 0 A0A087X0S7;A0A0C4DH00;A0A087WTU1;A0A0B4J2G4;Q15345-3;Q15345 A0A087X0S7 LRRC41 Leucine-rich repeat-containing protein 41 1 0 S(0.994)PS(0.002)APAATSS(0.003)AS(0.001)S(0.001)S(0.001)TSSYK;S(0.588)PS(0.412)APAATSSASSSTSSYK ; 209.19 3.62E-23 46913000 5561.8 4925.1 5850.6 4800.6 4199.9 4350.8 3467.7 4233.8 6173.6 5853.3 TRUE FALSE FALSE 5494.010642 4994.435687 5952.427239 5355.66796 3985.563431 4072.797922 3762.246351 4356.298323 5621.417754 5701.230422 0.963653499 0.876027685 1.044060106 0.93938809 0.699070751 0.714371744 0.659900771 0.764097923 0.986000799 1 12.4770576 -8.799811735 4.835513549 0.977215787 0.704936827 0.882039196 0.046434142 0.04303742 2.306292844 0.00661905 0.012530422 1.59E-09 8.799811735 -0.27227896 S(ph)PSAPAATSSASSSTSSYKR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSAPAATSSASSSTSSYKR 20 1 A0A087X0S7;A0A0C4DH00;A0A087WTU1;A0A0B4J2G4;Q15345-3;Q15345 A0A087X0S7 LRRC41 Leucine-rich repeat-containing protein 41 1 0 S(0.964)PS(0.036)APAATSSASSSTSSYKR;S(0.861)PS(0.139)APAATSSASSSTSSYKR;S(0.962)PS(0.038)APAATSSASSSTSSYKR ;; 186.17 2.15E-14 15899500 3816.7 3920.92 3484.05 2861.24 3475.89 3084.78 2872.38 2772.79 4160.66 3903.41 TRUE FALSE FALSE 3770.180592 3976.118815 3544.688429 3192.070031 3298.502363 2887.672514 3116.359886 2853.016304 3788.520149 3801.998845 0.991631178 1.045796955 0.932322332 0.839576802 0.867570585 0.759514306 0.819663554 0.750399045 0.996454839 1 11.89254238 -9.167263178 1.34489657 1.000372576 0.788693073 0.892001944 0.033396642 0.088858916 0.316185734 0.005207034 0.010454277 6.80E-10 9.167263178 -0.211679503 S(ph)PSDSSTASTPVAEQIER ddPTM_HeLa_Romidepsin_16h_R1 2 SPSDSSTASTPVAEQIER 18 0 Q16643-3;Q16643;Q16643-2;D6R9Q9 Q16643-3 DBN1 Drebrin 1 0 S(0.994)PS(0.006)DSSTASTPVAEQIER;S(0.984)PS(0.016)DSSTASTPVAEQIER ; 187.5 2.32E-14 274780000 1143.2 1264.63 1044.13 553.76 1240.9 1217.48 978.74 1271.14 1306.13 1307.55 TRUE FALSE FALSE 1129.266239 1282.433494 1062.302645 617.7883367 1177.572243 1139.686957 1061.874151 1307.91843 1189.306462 1273.579663 0.886686771 1.006951926 0.834107733 0.485080247 0.924616086 0.894868999 0.833771285 1.026962403 0.933829659 1 10.31467349 -11.22966287 0.639355276 0.989945537 0.843945556 0.088010451 0.140807583 1.059745743 0.953357816 0.068426652 0.037739511 5.89E-12 11.22966287 -0.145999981 S(ph)PSELFAQHIVTIVHHVK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.5)PS(0.5)ELFAQHIVTIVHHVK;S(0.663)PS(0.337)ELFAQHIVTIVHHVK ; 136.81 0.00031162 19641400 3550.83 3834.47 3535.91 2847.41 3480.1 3699.25 2997.99 3814.08 3693.17 3070.2 TRUE FALSE FALSE 3507.551118 3888.451769 3597.45103 3176.640942 3302.497511 3462.879864 3252.639196 3924.434387 3362.843625 2990.435761 1.172923078 1.300296037 1.202985557 1.062266905 1.10435327 1.157985036 1.087680678 1.312328604 1.124532976 1 11.54614001 -12.05316342 0.916597369 1.003394414 1.168917232 0.15789694 0.08661331 0.453595332 0.711068345 0.047143153 0.015452691 8.85E-13 12.05316342 0.165522818 S(ph)PSFASEWDEIEK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 0 S(0.87)PS(0.086)FAS(0.044)EWDEIEK;S(0.965)PS(0.035)FASEWDEIEK ; 195.71 3.20E-11 85221700 3354.59 3485.73 3142.27 3283.07 3034.43 3686.1 3667.35 3667.83 3314.44 3382.2 TRUE FALSE FALSE 3313.702967 3534.802198 3196.959891 3662.674001 2879.571714 3450.570106 3978.854617 3773.952874 3017.988185 3294.329956 1.005880713 1.072995797 0.970443135 1.111811521 0.874099362 1.047426989 1.207788737 1.145590431 0.91611594 1 11.68576935 -7.869969656 5.099819776 1.00526254 1.175274512 0.534433104 0.066800523 0.095302172 3.849423976 0.007483089 0.023695374 1.35E-08 7.869969656 0.170011973 S(ph)PSFGAGEGLLR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSFGAGEGLLR 12 0 Q96PE2 Q96PE2 ARHGEF17 Rho guanine nucleotide exchange factor 17 1 0 S(0.995)PS(0.005)FGAGEGLLR;S(0.998)PS(0.002)FGAGEGLLR ; 104.94 0.013172 10370000 988.67 877.21 1215.3 769.74 1072.91 1394.11 884.24 1121.4 1186.04 836.89 TRUE FALSE FALSE 976.6197098 889.5593854 1236.451787 858.7409605 1018.155399 1305.03087 959.3473235 1153.84594 1079.957612 815.1474772 1.198089594 1.091286436 1.516844278 1.053479259 1.249044409 1.600975169 1.176900316 1.415505748 1.324861626 1 9.670917286 -11.77445358 0.133158879 0.694018165 1.530299123 0.022682642 0.187604455 10.31056819 0.507398024 2.159860151 0.984227437 1.68E-12 11.77445358 0.836280958 S(ph)PSFGDPQLS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 2 0 S(1)PSFGDPQLS(1)PEAR 171.78 0.00042955 8500400 1480.1 1323.7 1485.5 519.89 1130.2 1056 948.28 860.75 1454.9 1636.9 TRUE FALSE FALSE 1462.059972 1342.335083 1511.354504 580.002128 1072.521677 988.5250081 1028.82688 885.6544432 1324.7701 1594.373102 0.917012442 0.841920302 0.947930257 0.363780678 0.672691778 0.620008583 0.645286149 0.555487572 0.830903443 1 10.63877356 -9.28644558 24.33697324 0.948129483 0.583875056 0.750498298 0.095338324 168.2127543 163710.4717 0.013513808 0.020648549 5.17E-10 9.28644558 -0.364254426 S(ph)PSFGEDYYGPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSFGEDYYGPSR 13 0 H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BUL5;H3BVF8;H3BQG1;P49761-2;P49761-3;P49761-1;P49761 H3BRT8 CLK3 Dual specificity protein kinase CLK3 1 0 S(0.998)PS(0.002)FGEDYYGPSR 113.52 0.0060967 3002800 721.61 522.7 732.04 902.56 958.94 974.05 1077.6 992.55 1615.1 1073.1 TRUE FALSE FALSE 712.8147398 530.0585843 744.7808491 1006.918234 910.0017135 911.8113486 1169.131317 1021.267868 1470.641411 1045.220707 0.681975333 0.507125988 0.712558452 0.963354655 0.870631157 0.872362499 1.118549708 0.977083463 1.407015189 1 10.0295919 -8.093054774 1.294724047 0.813429505 1.052537665 0.023732743 0.234278112 0.680435237 1.967135507 0.027213301 0.142424795 8.07E-09 8.093054774 0.23910816 S(ph)PSFGGASEASAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSFGGASEASAR 13 0 Q8WVT3;H7C2F7 Q8WVT3 TRAPPC12 Trafficking protein particle complex subunit 12 1 0 S(0.982)PS(0.018)FGGASEASAR 85.45 0.029977 6860800 819.07 1001.9 616.11 793.73 784.04 895.75 963.33 1021.3 828.06 731.2 TRUE FALSE FALSE 809.0868598 1016.004774 626.8331361 885.5047972 744.0275131 838.5144659 1045.155226 1050.849704 753.9962397 712.2033186 1.136033544 1.426565628 0.880132288 1.243331467 1.044684142 1.177352652 1.467495586 1.475491165 1.058681166 1 9.476145348 -4 0.401786666 1.068007081 8.744322325 0.435838717 0.148494892 40.12393373 0.472586914 0.035037107 246.8391965 1.00E-04 4 7.676315244 S(ph)PSGGAAGPLLTPSQSLDGSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSGGAAGPLLTPSQSLDGSR 21 0 Q96CX2 Q96CX2 KCTD12 BTB/POZ domain-containing protein KCTD12 1 0 S(0.774)PS(0.226)GGAAGPLLTPSQSLDGSR;S(0.971)PS(0.029)GGAAGPLLTPSQSLDGSR ; 137.86 0.00012567 113615000 777.88 508.74 733.53 853.03 649.84 671.63 589.82 650.1 628.31 561.65 TRUE FALSE FALSE 768.3988994 515.9020551 746.2967819 951.6613422 616.6762399 628.7150106 639.9192961 668.9096178 572.11238 547.058252 1.404601606 0.943047753 1.364199844 1.739597819 1.12725882 1.149265198 1.169746172 1.222739288 1.045797916 1 9.095550652 -12.51675628 1.209834877 0.996684763 1.278197405 0.185581176 0.201051457 0.637819566 1.638856368 0.152218323 0.034844957 3.04E-13 12.51675628 0.281512642 S(ph)PSGGAAGPLLTPSQSLDGSRR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSGGAAGPLLTPSQSLDGSRR 22 1 Q96CX2 Q96CX2 KCTD12 BTB/POZ domain-containing protein KCTD12 1 0 S(0.963)PS(0.037)GGAAGPLLTPSQSLDGSRR;S(0.96)PS(0.04)GGAAGPLLTPSQSLDGSRR;S(0.5)PS(0.5)GGAAGPLLTPSQSLDGSRR ;; 160.47 5.47E-09 103373900 2612.04 1797.56 2258.14 2021.16 1895.58 1429.38 1883 1921.63 2231.32 2384.35 TRUE FALSE FALSE 2580.203452 1822.866097 2297.441979 2254.856029 1798.841479 1338.047231 2042.941973 1977.229332 2031.745151 2322.404243 1.111005312 0.784904739 0.989251542 0.970914532 0.774560021 0.576147428 0.879666828 0.851371736 0.874845607 1 11.1814034 -9.334467967 0.908634 1.045045987 0.769467753 0.213726321 0.12580255 0.359642158 0.589064974 0.022529969 0.047448136 4.63E-10 9.334467967 -0.275578234 S(ph)PSGHPHVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSGHPHVR 9 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;Q8WX93-7 Q8WX93-3 PALLD Palladin 1 0 S(0.999)PS(0.001)GHPHVR 95.483 0.0018258 0 0 0 0 54.325 0 45.934 0 0 0 0 TRUE FALSE FALSE 0 0 0 60.60631211 0 42.99896565 0 0 0 0 0 S(ph)PSGLRPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSGLRPR 8 1 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4 P49815 TSC2 Tuberin 1 0 S(1)PSGLRPR 89.029 0.015808 5778700 520.92 574.2 598.67 563.7 728.14 786.65 850.89 585.38 586.79 596.65 TRUE FALSE FALSE 514.5708267 582.2836027 609.0896002 628.8776463 690.9802987 736.3856038 923.1645754 602.3170467 534.3060328 581.148947 0.88543708 1.001952435 1.0480783 1.08212817 1.188990021 1.267120258 1.588516301 1.036424569 0.919396027 1 9.18276416 -8.844485347 1.143716859 0.950023767 1.329354374 0.551608131 0.130496943 0.235671997 0.607683578 0.020207011 0.053997741 1.43E-09 8.844485347 0.379330606 S(ph)PSGSAFGS(ph)QENLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSGSAFGSQENLR 14 0 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 2 0 S(0.995)PS(0.005)GSAFGS(1)QENLR 130.47 0.00017374 0 1526.5 1142.1 1294.3 1361.9 1169.4 957.32 996.78 981.99 1414 1206.6 TRUE FALSE FALSE 1507.894431 1158.178514 1316.826749 1519.369286 1109.721154 896.1503416 1081.446468 1010.402331 1287.528299 1175.252358 1.283038847 0.985472189 1.120462971 1.292802584 0.944240738 0.762517374 0.920182343 0.859732231 1.095533474 1 10.19875486 -8.565543067 7.641785132 1.133037633 0.854343086 0.62014876 0.100948308 0.130266138 19.68372355 0.018117612 0.036482816 2.72E-09 8.565543067 -0.278694546 S(ph)PSKPLPEVTDEYK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSKPLPEVTDEYK 14 1 P05455;E9PGX9;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 1 0 S(0.623)PS(0.377)KPLPEVTDEYK;S(0.5)PS(0.5)KPLPEVTDEYK ; 67.685 0.023199 11678700 2827.5 2512.6 2552 1947.24 2509.7 2368.52 1963.82 2087.89 2956.6 2495.6 TRUE FALSE FALSE 2793.037342 2547.972449 2596.416489 2172.389051 2381.620644 2217.179216 2130.626822 2148.299803 2692.154291 2430.763952 1.149036845 1.04821879 1.068148344 0.893706297 0.979782772 0.912132671 0.876525596 0.883796142 1.107534234 1 11.24719409 -9.265922793 24.0761317 1.069999628 0.911459523 0.773374374 0.044724544 113.9525646 611930.557 0.009363539 0.014613307 5.42E-10 9.265922793 -0.158540105 S(ph)PSLGSDLTFATR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSLGSDLTFATR 13 0 Q13425 Q13425 SNTB2 Beta-2-syntrophin 1 0 S(0.855)PS(0.144)LGSDLTFATR 180.3 5.97E-07 46747000 134.54 142.86 202.31 220.96 203.52 85.988 215.41 134.74 123.7 63.194 TRUE FALSE FALSE 132.9001747 144.8711868 205.8311207 246.5084348 193.133615 80.49364431 233.70692 138.6384893 112.6359622 61.55221077 2.159145432 2.353630926 3.344008576 4.004867279 3.137720198 1.307729541 3.79688913 2.252372215 1.829925534 1 5.94373877 -10.9986916 0.723407294 1.154264419 2.958803458 0.354593835 0.778132953 0.370442667 0.42899145 0.273186189 0.193477141 1.00E-11 10.9986916 1.80453904 S(ph)PSPAHLPDDPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPAHLPDDPK 12 0 Q92615;A0A087X183;H0Y4V9;H0Y641 Q92615 LARP4B La-related protein 4B 1 0 S(0.5)PS(0.5)PAHLPDDPK 75.316 0.024831 99019000 13853 12769 12137 10027 15347 14441 12398 13365 14455 14188 TRUE FALSE FALSE 13684.15431 12948.76232 12348.23939 11186.36892 14563.78532 13518.26671 13451.08581 13751.69519 13162.1086 13819.39371 0.990213796 0.936999306 0.893544221 0.809468863 1.053865721 0.978209825 0.973348476 0.995101194 0.952437485 1 13.7544067 -10.32361963 5.752079414 0.995601255 0.947339354 0.037606853 0.06258506 0.373462281 25.27214453 0.010825529 0.012380515 4.75E-11 10.32361963 -0.048261902 S(ph)PSPEPIYNSEGK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPEPIYNSEGK 13 0 Q15637-6;Q15637-4;Q15637-3;Q15637-2;Q15637;Q15637-7;Q15637-5 Q15637-6 SF1 Splicing factor 1 1 0 S(0.779)PS(0.22)PEPIYNS(0.001)EGK;S(0.5)PS(0.5)PEPIYNSEGK ; 129.17 0.0027449 49558000 6846.7 6191.7 5776.8 3385.2 7603.9 9854.2 8703.1 9284.6 7243.2 6351.8 TRUE FALSE FALSE 6763.249787 6278.866915 5877.342781 3776.612752 7215.844609 9224.548423 9442.341097 9553.235252 6595.350051 6186.77932 1.093177797 1.014884577 0.949984229 0.610432756 1.166332955 1.491009772 1.526212688 1.544137064 1.066039325 1 12.59497286 -8.340788062 3.711055652 1.004485181 1.52594869 0.777565475 0.133018383 0.089959555 2.364633262 0.020266564 0.04886734 4.56E-09 8.340788062 0.521463508 S(ph)PSPISNQPSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPISNQPSPR 12 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 0 S(0.593)PS(0.406)PIS(0.001)NQPSPR 106.54 0.012386 4216300 651.7 498.2 565.92 664.1 667.53 673.25 745.65 770.71 626.13 609.68 TRUE FALSE FALSE 643.7568297 505.2136727 575.7696002 740.8863667 633.4634532 630.2314978 808.9854924 793.0092779 570.1273646 593.8404257 1.084056932 0.850756619 0.96956956 1.24761861 1.066723358 1.061280894 1.36229441 1.335391199 0.960068294 1 9.213931498 -7.577408893 0.850456166 1.027807909 1.487434048 0.591488933 0.102500638 0.856047499 0.606202003 0.016393458 0.330180688 2.65E-08 7.577408893 0.45962614 S(ph)PSPLSGHVAQAFPTK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPLSGHVAQAFPTK 16 0 Q6P0Q8;A0A669KBJ4 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 S(0.788)PS(0.16)PLS(0.052)GHVAQAFPTK 110.32 0.00042006 0 1363.7 1195.6 1012.9 1176.7 1280.6 1394.5 1403.1 1090.5 1762.3 1469 TRUE FALSE FALSE 1347.0787 1212.431688 1030.5291 1312.755591 1215.246203 1305.395951 1522.279279 1122.051897 1604.675474 1430.835168 0.941463231 0.847359441 0.720229082 0.917475066 0.849326485 0.912331469 1.063909605 0.784193681 1.12149569 1 10.48264177 -10.58457012 2.373681936 0.978343002 0.875700362 0.309454977 0.097151729 0.311533073 3.622786297 0.016558756 0.017465802 2.60E-11 10.58457012 -0.10264264 S(ph)PSPLVSLQAVK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPLVSLQAVK 12 0 Q9UPZ3-2;Q9UPZ3 Q9UPZ3-2 HPS5 Hermansky-Pudlak syndrome 5 protein 1 0 S(0.971)PS(0.029)PLVSLQAVK;S(0.966)PS(0.034)PLVSLQAVK ; 194.06 2.71E-10 46229000 3155 2936.8 3575.3 3710.7 3096 2668.3 1987.94 2334.1 2515.97 2240.08 TRUE FALSE FALSE 3116.545646 2978.144347 3637.526597 4139.748593 2937.999567 2497.804242 2156.795574 2401.633501 2290.935342 2181.882399 1.428374714 1.364942652 1.667150621 1.897328928 1.346543503 1.14479325 0.98850221 1.100716291 1.049981128 1 11.09135763 -6.194137272 14.53210531 1.275780348 1.23261321 0 0.288636375 0 0 0.04307568 0 6.40E-07 6.194137272 -0.043167139 S(ph)PSPPDGS(ph)PAATPEIR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPPDGSPAATPEIR 16 0 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 2 0 S(0.959)PS(0.041)PPDGS(0.985)PAAT(0.015)PEIR;S(0.999)PS(0.002)PPDGS(0.999)PAATPEIR ; 178.02 3.11E-07 95276900 2628.52 2536.66 2362.02 2066.05 2732.92 2523.34 1947.72 2224.06 2715.11 2599.11 TRUE FALSE FALSE 2596.482587 2572.371166 2403.129967 2304.936422 2593.448894 2362.106718 2113.159288 2288.409667 2472.263761 2531.584748 1.025635263 1.016111022 0.949259143 0.910471761 1.024436925 0.93305457 0.834717973 0.903943536 0.976567648 1 11.30582507 -8.008438653 0.533378396 1.012390284 0.827339481 0.497367017 0.042270584 1.086504392 0.333968421 0.008834275 0.107909814 9.81E-09 8.008438653 -0.185050803 S(ph)PSPPDGSPAATPEIR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPPDGSPAATPEIR 16 0 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 S(0.967)PS(0.033)PPDGSPAATPEIR;S(0.955)PS(0.045)PPDGSPAATPEIR ; 207.08 5.65E-19 502830000 2611.5 2516.64 2561.4 2353.6 2591.4 2903.4 2499.1 2118.2 2765.3 2711.7 TRUE FALSE FALSE 2579.670034 2552.069324 2605.980093 2625.734306 2459.151188 2717.88211 2711.373492 2179.486775 2517.964642 2641.249643 0.976685426 0.966235558 0.986646643 0.994125759 0.931055947 1.029013716 1.026549497 0.825172577 0.95332323 1 11.36700495 -7.253087576 24.98276481 0.988138278 0.825172495 0.731045003 0.028993754 369.882518 1106405.575 0.003619886 0.055349635 5.58E-08 7.253087576 -0.162965783 S(ph)PSPPLPTHIPPEPPRT(ph)PPFPAK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPPLPTHIPPEPPRTPPFPAK 23 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 0 S(0.47)PS(0.47)PPLPT(0.06)HIPPEPPRT(1)PPFPAK;S(0.499)PS(0.499)PPLPT(0.003)HIPPEPPRT(1)PPFPAK ; 123 2.13E-06 45002000 4822.4 4305.7 4427.8 4723.1 5303.4 5365.1 5098.3 5332.4 5825.4 5100.4 TRUE FALSE FALSE 4763.622734 4366.315758 4504.864002 5269.207045 5032.747708 5022.287425 5531.349475 5486.684581 5304.361634 4967.890873 0.958882322 0.878907341 0.906796087 1.060652736 1.013055205 1.010949627 1.113420084 1.104429369 1.067729097 1 12.27841777 -7.964289375 0.950959362 0.969675883 1.131497352 0.432887636 0.056378937 0.5594838 0.704828368 0.00825159 0.072180445 1.09E-08 7.964289375 0.161821469 S(ph)PSPVLR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSPVLR 7 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3;O43432-2 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 0 S(0.996)PS(0.004)PVLR;S(0.94)PS(0.06)PVLR;S(0.885)PS(0.115)PVLR ;; 110.12 0.0041212 188680000 3770.22 3256.36 3193.9 3175.56 3786.22 3473.73 3162.13 3488.58 4572.58 3991.63 TRUE FALSE FALSE 3724.267108 3302.203122 3249.48849 3542.733189 3592.995065 3251.769864 3430.721243 3589.516558 4163.596993 3887.926877 0.957905646 0.849348053 0.835789507 0.911213945 0.924141626 0.836376292 0.882403747 0.923246931 1.070904141 1 11.92478537 -10.43299865 3.695612599 0.982490218 0.880094392 0.649451644 0.042363423 0.10525808 2.573143243 0.006042542 0.006774763 3.69E-11 10.43299865 -0.102395826 S(ph)PSPYYSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPYYSR 8 0 P62995;H7C2L4;P62995-3;H7BXF3;Q13595;Q13595-4;Q13595-3 P62995;Q13595 TRA2B;TRA2A Transformer-2 protein homolog beta;Transformer-2 protein homolog alpha 1 0 S(1)PSPYYSR;S(1)PSPYYSR ; 139.98 0.008985 99158000 2406.29 1946.62 2500.45 2319.46 2715.3 2477.69 2334.41 2027.95 2280.11 2108.49 TRUE FALSE FALSE 2376.961212 1974.024567 2543.969283 2587.646879 2576.728109 2319.373605 2532.694727 2086.625534 2076.171251 2053.711126 1.15739803 0.96119875 1.238718168 1.259985811 1.254669207 1.129357277 1.233228323 1.016026795 1.01093636 1 11.00401755 -12.23814822 0.393074884 0.949761655 1.178701413 0.299835696 0.094696979 2.322327304 0.477670503 0.224885903 0.034720362 5.78E-13 12.23814822 0.228939758 S(ph)PSQESIGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSQESIGAR 10 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 0 S(0.995)PS(0.005)QESIGAR;S(0.989)PS(0.011)QESIGAR ; 107.39 0.019759 33641000 1006.97 931.48 873.84 573.25 898.44 816.72 887.96 698.73 1095.12 970.75 TRUE FALSE FALSE 994.6966623 944.5933999 889.0488186 639.5318622 852.5892543 764.5342278 963.3833002 718.9466501 997.1697244 945.5297751 1.051999301 0.999009682 0.94026528 0.676374112 0.901705347 0.808577633 1.018882034 0.76036384 1.054614832 1 9.88497908 -9.570900186 4.108782775 1.022712079 0.842735464 0.525584767 0.086014248 0.128139855 4.607337902 0.012781525 0.018574491 2.69E-10 9.570900186 -0.179976615 S(ph)PSSKPSLAVAVDSAPEVAVK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSSKPSLAVAVDSAPEVAVK 21 1 Q5SRN1;O60508 Q5SRN1 CDC40 Pre-mRNA-processing factor 17 1 0 S(0.641)PS(0.219)S(0.078)KPS(0.026)LAVAVDS(0.036)APEVAVK;S(0.817)PS(0.146)S(0.027)KPS(0.009)LAVAVDS(0.002)APEVAVK ; 105.2 0.00012803 64048000 8642.4 8395.9 10228.7 5756.8 7658.2 7738.6 6445.9 7419.9 9302.1 9524.8 TRUE FALSE FALSE 8537.063105 8514.097701 10406.72623 6422.428303 7267.373477 7244.128435 6993.414585 7634.5831 8470.096878 9277.344323 0.920205482 0.917730053 1.121735474 0.692270124 0.783346314 0.780840743 0.753816431 0.822927643 0.912987228 1 13.17949617 -9.247136972 24.99970747 0.968177851 0.767644845 0.720497661 0.064679505 327.5396563 572518.8492 0.009401617 0.015544451 5.66E-10 9.247136972 -0.200533005 S(ph)PSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSSKPSLAVAVDSAPEVAVKEDLETGVHLDPAVK 35 2 Q5SRN1;O60508 Q5SRN1 CDC40 Pre-mRNA-processing factor 17 1 0 S(0.299)PS(0.299)S(0.299)KPS(0.1)LAVAVDS(0.003)APEVAVKEDLETGVHLDPAVK 45.253 0.0074599 15814000 1342.2 1413 1566.4 1834.5 1339.1 1204.2 810.45 1394.3 1479.1 1539.6 TRUE FALSE FALSE 1325.84075 1432.892251 1593.662535 2046.613522 1270.76073 1127.255506 879.2896028 1434.641871 1346.805592 1499.60097 0.884129029 0.955515687 1.062724396 1.364772071 0.847399245 0.751703639 0.586349049 0.95668241 0.898109309 1 10.55036295 -8.530058735 24.99983876 0.985875402 0.755804707 0.362195221 0.154184556 157.9240556 549871.2737 0.022967081 0.046012231 2.95E-09 8.530058735 -0.230070695 S(ph)PSSVTGNALWK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSSVTGNALWK 12 0 Q9NYB0;A0A590UJT3 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 0 S(0.984)PS(0.012)S(0.003)VT(0.001)GNALWK 96.464 0.019778 36443000 1205.1 944.93 1033.3 681.61 1363 1315.1 1338.6 1498.6 1365.2 1224.8 TRUE FALSE FALSE 1190.411778 958.2327493 1051.284153 760.4209553 1293.441024 1231.069354 1452.300651 1541.959627 1243.093093 1192.979519 0.997847623 0.803226488 0.881225651 0.637413252 1.084210586 1.031928323 1.21737266 1.292528163 1.042007069 1 10.22035356 -7.788905109 1.722674396 0.951946888 1.300520688 0.528337327 0.124188009 0.297169527 1.54432999 0.019053751 0.121922321 1.63E-08 7.788905109 0.3485738 S(ph)PSTTYLHTPTPSEDAAIPSK ddPTM_HeLa_Romidepsin_16h_R1 4 SPSTTYLHTPTPSEDAAIPSK 21 0 Q13111 Q13111 CHAF1A Chromatin assembly factor 1 subunit A 1 0 S(0.382)PS(0.14)T(0.14)T(0.14)Y(0.063)LHT(0.071)PT(0.059)PS(0.006)EDAAIPSK;S(0.535)PS(0.118)T(0.118)T(0.138)YLHT(0.089)PT(0.001)PSEDAAIPSK;S(0.388)PS(0.128)T(0.128)T(0.128)Y(0.032)LHT(0.143)PT(0.037)PS(0.014)EDAAIPSK;S(0.498)PS(0.15)T(0.15)T(0.15)Y(0.038)LHT(0.013)PTPSEDAAIPSK ;;; 83.992 0.00094584 156160000 14197.4 14425 13547.9 11630.2 14965.8 13958.6 11919.8 12108.9 16721.7 16085.8 TRUE FALSE FALSE 14024.35663 14628.07553 13783.69552 12974.93845 14202.03938 13066.69051 12932.26751 12459.25192 15226.06927 15667.8886 0.895101886 0.933634129 0.879741736 0.82812297 0.906442453 0.833979028 0.825399506 0.795209376 0.971800966 1 13.93552316 -16.52283613 0.023122271 2.160255778 1.23E-05 0.833178385 0.02619394 494.2192052 0.920513223 59.44128923 30.92916787 3.00E-17 16.52283613 -2.160243453 S(ph)PSWQRPNQGVPSTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSWQRPNQGVPSTGR 16 1 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4;Q96HC4-6;A0A0A0MSP3 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 S(0.973)PS(0.019)WQRPNQGVPS(0.004)T(0.004)GR 59.733 0.026959 38333000 327.41 264.5 388.8 252.87 315.43 293.44 187.16 284.56 213.13 420.46 TRUE FALSE FALSE 323.419401 268.2236379 395.5669009 282.1080192 299.3324301 274.690131 203.0573657 292.7932946 194.067119 409.5363886 0.789720792 0.65494458 0.965889508 0.68884726 0.730905576 0.670734369 0.495822524 0.71493841 0.47387027 1 8.677847835 -16.52287875 0.048075971 2.376474254 1.67E-11 0 0.191002949 208.5883632 0.795722293 38.08757915 9.908568389 3.00E-17 16.52287875 -2.376474254 S(ph)PTDDEVTPSAVVR ddPTM_HeLa_Romidepsin_16h_R1 2 SPTDDEVTPSAVVR 14 0 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 S(0.998)PT(0.002)DDEVTPSAVVR;S(0.997)PT(0.003)DDEVTPSAVVR ; 141.59 0.00080634 8132100 3815.9 4978.6 3996.2 3634.8 3776.3 4068.1 2940.1 3737 3837.6 4218 TRUE FALSE FALSE 3769.390343 5048.688861 4065.752185 4055.072678 3583.58132 3808.161539 3189.832021 3845.124199 3494.355445 4108.415752 0.917480258 1.228865131 0.989615567 0.987016145 0.872253817 0.926917276 0.776414125 0.935914092 0.850535987 1 12.00436647 -8.761866791 23.67174993 0.986450339 0.874130643 0.249517964 0.0991686 6.382414102 353558.1707 0.013695617 0.025981656 1.73E-09 8.761866791 -0.112319695 S(ph)PTDSDVSLDSEDSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTDSDVSLDSEDSGAK 17 0 Q8N3V7-2 Q8N3V7-2 SYNPO Synaptopodin 1 0 S(1)PTDSDVSLDSEDSGAK 334.51 4.08E-204 34155000 5084.8 5117.3 5236.4 4462.1 3743 3239.8 3384 3180.9 5727.4 4670.9 TRUE FALSE FALSE 5022.824502 5189.341484 5327.537345 4978.028997 3551.980743 3032.787236 3671.436876 3272.934323 5215.126999 4549.549345 1.104026821 1.140627585 1.171003311 1.09418068 0.780732436 0.66661267 0.806989132 0.719397478 1.146295293 1 12.15150793 -8.720409881 5.460471699 1.071053011 0.738147636 0.891353153 0.061808843 0.054300037 3.862285016 0.010264819 0.020473002 1.90E-09 8.720409881 -0.332905375 S(ph)PTEDFR ddPTM_HeLa_Romidepsin_16h_R1 1 SPTEDFR 7 0 Q8IXT5 Q8IXT5 RBM12B RNA-binding protein 12B 1 0 S(0.997)PT(0.003)EDFR 126.24 0.021237 80475000 3753.9 3448.7 3544.1 1805.6 3239.2 2747.4 2611.6 2958.7 3691.8 3355.5 TRUE FALSE FALSE 3708.146023 3497.250889 3605.783574 2014.371968 3073.891537 2571.850007 2833.429239 3044.305316 3361.596162 3268.323626 1.13457125 1.070044246 1.103251693 0.616331856 0.940510148 0.78690188 0.866936559 0.931457733 1.028538341 1 11.67433513 -9.298104947 24.98892856 1.068459439 0.83448677 0.630658301 0.091333136 284.4082381 193833.8863 0.014048958 0.021460547 5.03E-10 9.298104947 -0.233972669 S(ph)PTGNTPPVIDSVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTGNTPPVIDSVSEK 16 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 S(0.786)PT(0.213)GNT(0.001)PPVIDSVSEK 78.166 0.02746 9846200 1081.9 1308 1078.3 827.32 1037.5 1036.3 975.83 928.58 1253.5 902 TRUE FALSE FALSE 1068.713387 1326.414058 1097.067359 922.9786311 984.5525036 970.0837745 1058.716976 955.4469972 1141.383821 878.56591 1.216429382 1.509749062 1.248702399 1.050551382 1.120635905 1.104167329 1.205051282 1.087507478 1.299144216 1 9.779006711 -12.14731859 1.089048549 1.008236501 1.193678161 0 0.151955278 0.548480952 1.237432737 0.069612651 0.023849291 7.12E-13 12.14731859 0.18544166 S(ph)PTGPSNSFLANMGGTVAHK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 0 S(0.819)PT(0.175)GPS(0.005)NSFLANMGGTVAHK 143.47 1.32E-05 206480000 3630.8 3744 3398.5 1801.8 4075.3 3782.3 4002.7 3742.7 4070.4 3947.9 TRUE FALSE FALSE 3586.546413 3796.70813 3457.649467 2010.132594 3867.322234 3540.623237 4342.689238 3850.989119 3706.333229 3845.332989 0.932701127 0.987354838 0.899180767 0.52274604 1.005718424 0.920758553 1.129340229 1.001470908 0.963852348 1 11.90889282 -11.65450312 0.833019599 0.994984691 0.92146817 0.022011016 0.14880515 1.851601699 2.583286549 0.071893161 0.032517597 2.22E-12 11.65450312 -0.073516522 S(ph)PTKAPHLQLIEGK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTKAPHLQLIEGK 14 1 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3;H0Y5B0 O43491 EPB41L2 Band 4.1-like protein 2 1 0 S(0.863)PT(0.137)KAPHLQLIEGK 67.234 0.023577 44208000 2596 2587.8 2715.9 2219.4 2888.6 3692.7 2995.6 2947.3 2983.9 2899.4 TRUE FALSE FALSE 2564.358953 2624.231116 2763.1691 2476.017471 2741.183963 3456.748388 3250.046189 3032.575475 2717.012511 2824.07317 0.908035592 0.929236234 0.978433962 0.876754008 0.970649058 1.224029329 1.150836396 1.073830348 0.962089984 1 11.46356175 -8.339470556 6.609842387 0.949384079 1.149154641 0.794007518 0.047442117 0.086090133 6.083437499 0.007522516 0.016976912 4.58E-09 8.339470556 0.199770562 S(ph)PTMEQAVQTASAHLPAPAAVGR ddPTM_HeLa_Romidepsin_16h_R1 2 SPTMEQAVQTASAHLPAPAAVGR 23 0 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.597)PT(0.403)MEQAVQTASAHLPAPAAVGR;S(0.545)PT(0.455)MEQAVQTASAHLPAPAAVGR ; 126.75 6.06E-07 24065000 497.8 647.86 445.03 386.02 760.39 585.39 520.31 509.13 775.88 947.6 TRUE FALSE FALSE 491.7326221 656.9805901 452.7755605 430.6534487 721.5844609 547.9854683 564.5051184 523.8608733 706.4833496 922.9812154 0.53276558 0.711802775 0.49055772 0.466589614 0.781797559 0.593712482 0.611610625 0.567574794 0.765436325 1 9.850157476 -12.30470765 0.823493592 1.024731765 0.592289947 0.457904276 0.114349638 0.28571639 0.315245334 0.081674735 0.017507435 4.96E-13 12.30470765 -0.432441818 S(ph)PTPESSTIASYVTLR ddPTM_HeLa_Romidepsin_16h_R1 4 SPTPESSTIASYVTLR 16 0 A0JP02;B4DJX4;Q9HAU0-8;Q9HAU0;Q9HAU0-2;Q9HAU0-4;Q9HAU0-6;H0YGJ6;Q9HAU0-5 A0JP02 PLEKHA5 Pleckstrin homology domain-containing family A member 5 1 0 S(0.989)PT(0.011)PESSTIASYVTLR;S(0.999)PT(0.001)PESSTIASYVTLR;S(0.981)PT(0.019)PESSTIASYVTLR;S(0.954)PT(0.006)PES(0.033)S(0.005)T(0.002)IASYVTLR ;;; 184.01 1.07E-08 69200500 1441.21 1517.92 1742.12 1289.16 1415.83 1593.16 1433.42 1530.14 1759.96 1834.88 TRUE FALSE FALSE 1423.643978 1539.289318 1772.440868 1438.218745 1343.574912 1491.362218 1555.174659 1574.412187 1602.54477 1787.209553 0.796573617 0.861280825 0.991736456 0.804728658 0.751772454 0.834464104 0.870169173 0.880933175 0.896674241 1 10.80349309 -12.42224122 1.044990556 1.003821674 0.845024275 0.20037093 0.06781087 0.409948096 0.769238404 0.049913259 0.011412894 3.78E-13 12.42224122 -0.158797399 S(ph)PTPPLFSLPEAR ddPTM_HeLa_Romidepsin_16h_R1 1 SPTPPLFSLPEAR 13 0 A0A087WWS1;Q96FV9;J3KRD7;J3QQZ3;J3KT14;Q96FV9-2 A0A087WWS1 THOC1 THO complex subunit 1 1 0 S(0.996)PT(0.004)PPLFSLPEAR 106.55 0.0089101 10033000 307.4 351.93 302.89 314.47 366.5 368.94 278.1 375.94 265.66 234.38 TRUE FALSE FALSE 303.6532906 356.8844798 308.1616734 350.830501 347.7961374 345.3659247 301.7218071 386.8172308 241.8987042 228.2907738 1.330116349 1.563289106 1.349864772 1.536770388 1.523478727 1.512833475 1.32165572 1.694405886 1.059607886 1 7.834728745 -11.41788223 0.470491138 0.965496373 1.519694999 0.761308174 0.103438714 0.341600019 0.159466549 0.083492365 0.03296435 3.82E-12 11.41788223 0.554198625 S(ph)PTPSAASSSASNSELEAGSEEDRK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTPSAASSSASNSELEAGSEEDRK 25 1 Q8WYL5;Q8WYL5-2;F8VS18 Q8WYL5 SSH1 Protein phosphatase Slingshot homolog 1 1 0 S(0.374)PT(0.32)PS(0.275)AAS(0.009)S(0.009)S(0.009)AS(0.004)NS(0.001)ELEAGSEEDRK 50.189 0.0036613 0 815.34 474.76 646.59 481.15 718.96 557.98 663.87 664.73 1077.5 739.4 TRUE FALSE FALSE 805.4023225 481.4436837 657.8436277 536.7828269 682.2687884 522.3268788 720.2591012 683.9629138 981.1257014 720.1902814 1.118318788 0.668495113 0.913430304 0.745334727 0.947345175 0.725262326 1.000095558 0.949697506 1.362314553 1 9.492234321 -10.28565555 24.99629032 1.055872765 0.853094221 0.450772464 0.143674313 507.6601783 524012.3987 0.017796697 0.020356361 5.18E-11 10.28565555 -0.202778544 S(ph)PTSSPTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPTSSPTPQR 10 0 A0A0D9SFE4;A0A0D9SFB1;A0A0U1RQP1;Q05193-5;Q05193-3;Q05193-2;Q05193 A0A0D9SFE4 DNM1 Dynamin-1 1 0 S(0.999)PT(0.001)SSPTPQR 108.9 0.018789 16289000 587.6 349.38 361.12 277.85 425.3 560.73 470.34 425.22 278.78 515.22 TRUE FALSE FALSE 580.4381052 354.2985808 367.4051421 309.9763243 403.595354 524.9011627 510.2906679 437.5230698 253.8452186 501.8345101 1.156632502 0.706006808 0.732124106 0.617686345 0.804239935 1.04596466 1.016850491 0.871847314 0.50583452 1 8.971067875 -10.26752521 24.98336567 1.07396535 0.830808634 0 0.2211575 389.0474067 1597103.351 0.025467715 0.029517516 5.40E-11 10.26752521 -0.243156715 S(ph)PTVPSQNPSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPTVPSQNPSR 11 0 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 0 S(0.978)PT(0.014)VPS(0.007)QNPSR;S(1)PTVPSQNPSR ; 94.538 0.027033 17196700 1886.52 1828.57 1518.11 1496.75 1420.45 1197.08 1332.77 1438.61 1373.93 1650.38 TRUE FALSE FALSE 1863.526369 1854.312656 1544.532068 1669.811277 1347.959136 1120.590451 1445.975451 1480.233911 1251.04226 1607.50289 1.159267819 1.153536126 0.960826931 1.03876098 0.838542279 0.697100116 0.899516548 0.920828149 0.778251951 1 10.65060562 -8.816880533 3.389905037 1.074097164 0.830846 0.265540745 0.12261747 0.124366945 2.908021244 0.013838487 0.027059699 1.52E-09 8.816880533 -0.243251164 S(ph)PVDSGTILR ddPTM_HeLa_Romidepsin_16h_R1 2 SPVDSGTILR 10 0 P49454 P49454 CENPF Centromere protein F 1 0 S(1)PVDSGTILR;S(1)PVDSGTILR ; 135.8 0.0056972 9795500 1382.17 1227.47 1195.57 743.26 1235.86 1356.41 1122.41 1241.1 1203.51 1237.13 TRUE FALSE FALSE 1365.32358 1244.750355 1216.378394 829.1992183 1172.789453 1269.739779 1217.747477 1277.00927 1095.865051 1204.989184 1.133058784 1.032997118 1.009451711 0.688138308 0.973277991 1.053735415 1.01058789 1.059768243 0.909439741 1 10.23480448 -9.521496164 23.30117786 1.060392853 0.954585778 0.016240847 0.113065863 30.09380506 507186.7624 0.017537853 0.025030331 3.01E-10 9.521496164 -0.105807075 S(ph)PVEGLGR ddPTM_HeLa_Romidepsin_16h_R1 1 SPVEGLGR 8 0 Q9Y5U2-2;Q9Y5U2;A6NCC9;E9PME3;C9JHT9;C9JJV1 Q9Y5U2-2 TSSC4 Protein TSSC4 1 0 S(1)PVEGLGR 114.97 0.020637 33179000 676.39 506.09 756.77 427.53 522.13 514.29 489.61 671.51 720.38 787.12 TRUE FALSE FALSE 668.1458985 513.2147483 769.9412644 476.9630302 495.4837578 481.4285288 531.1974612 690.9390824 655.9474086 766.6705089 0.871490283 0.669407186 1.004266181 0.622122574 0.646279923 0.627947108 0.692862781 0.901220373 0.855579289 1 9.582462875 -10.5733985 0.564524669 0.987528517 0.703791996 0.264688722 0.12496945 0.469278943 0.35022818 0.044978221 0.041367249 2.67E-11 10.5733985 -0.283736521 S(ph)PVGLSSDGISSSSSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPVGLSSDGISSSSSSSR 18 0 O60583-2;O60583 O60583-2 CCNT2 Cyclin-T2 1 0 S(1)PVGLSSDGISSSSSSSR;S(0.961)PVGLS(0.035)S(0.004)DGISSSSSSSR ; 188.71 2.06E-14 22423000 463.15 257.39 322.9 322.94 499.76 453.81 221.99 402.14 681.69 467.87 TRUE FALSE FALSE 457.5049497 261.0135432 328.519939 360.2798423 474.2553823 424.8130056 240.8458251 413.7752864 620.7179391 455.71467 1.00392851 0.572756508 0.720889541 0.790582059 1.040684915 0.932190762 0.528501365 0.907970082 1.362075834 1 8.831987003 -10.3729588 24.99992865 1.001857208 0.788198803 0.360258866 0.186276084 20.98507809 4681.311264 0.025191416 0.028807429 4.24E-11 10.3729588 -0.213658405 S(ph)PVISRPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPVISRPK 8 1 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2 A0A0U1RRM6 ENAH Protein enabled homolog 1 0 S(1)PVISRPK 93.162 0.014142 64660000 3852.5 4033.2 3572.2 2646 4853.7 4669.1 4056.6 3311.5 4231.4 4093.6 TRUE FALSE FALSE 3805.544248 4089.979495 3634.372643 2951.94297 4605.997577 4370.759579 4401.167503 3407.313028 3852.932986 3987.247682 0.954428857 1.025765095 0.911499092 0.740346024 1.155182207 1.096184618 1.103810913 0.854552639 0.966313932 1 11.96117751 S(ph)PVPAQIAITVPK ddPTM_HeLa_Romidepsin_16h_R1 2 SPVPAQIAITVPK 13 0 A0A0A0MSA7;A0A0U1RQK7;O43432;O43432-3 A0A0A0MSA7 EIF4G3 Eukaryotic translation initiation factor 4 gamma 3 1 0 S(1)PVPAQIAITVPK;S(1)PVPAQIAITVPK ; 181.51 4.93E-07 363480000 12865.5 11883.9 11608.1 10643.1 12304.9 10640.2 9466.7 11559.9 12244.6 11809 TRUE FALSE FALSE 12708.69034 12051.20186 11810.13411 11873.7053 11676.93504 9960.32556 10270.80126 11894.36747 11149.41231 11502.20048 1.104892091 1.047730117 1.026771715 1.032298587 1.015191403 0.86594957 0.892942292 1.034094953 0.969328637 1 13.48962227 -8.448565305 5.226525919 1.046822543 0.927519242 0.388820306 0.053478323 0.140834001 6.977021158 0.007860025 0.017737918 3.56E-09 8.448565305 -0.119303301 S(ph)PVPSAFSDQSR ddPTM_HeLa_Romidepsin_16h_R1 4 SPVPSAFSDQSR 12 0 Q9UQ35;Q9UQ35-2;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.995)PVPS(0.004)AFSDQSR;S(1)PVPSAFSDQSR;S(1)PVPSAFSDQSR;S(0.999)PVPS(0.001)AFSDQSR ;;; 159.58 0.00086681 380972000 3048.31 2927.41 2794.77 1501.14 2620.02 2435.58 2250.16 1948.83 2962.25 3299.38 TRUE FALSE FALSE 3011.156025 2968.622155 2843.411799 1674.70887 2486.310603 2279.954298 2441.288534 2005.216321 2697.298941 3213.661632 0.936986021 0.923750692 0.884788794 0.521121718 0.773669069 0.709456862 0.759659483 0.623966226 0.839322633 1 11.65000232 -9.463888529 5.700413908 0.963537777 0.688955196 0.681782396 0.080178775 0.072145409 4.923669008 0.010639992 0.016201086 3.44E-10 9.463888529 -0.274582581 S(ph)PVPTTLPGLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPVPTTLPGLR 11 0 Q63HR2-5;Q63HR2-6;Q63HR2;Q63HR2-4;F8VV64;Q63HR2-2 Q63HR2-5 TNS2 Tensin-2 1 0 S(1)PVPTTLPGLR 103.21 0.017694 7289300 610.51 672.19 732.75 554.09 377.29 379.47 327.13 432.82 679.35 885.08 TRUE FALSE FALSE 603.0688693 681.6531085 745.5032064 618.1564929 358.0354834 355.2230917 354.916414 445.3429638 618.5872345 862.085494 0.699546476 0.790702446 0.864767139 0.717047784 0.415313198 0.412050886 0.411695147 0.516587933 0.717547434 1 9.75168714 -8.896612028 3.173440817 0.847960131 0.433122074 0.804104459 0.086959061 0.097344874 1.960137342 0.017789697 0.034029162 1.27E-09 8.896612028 -0.414838057 S(ph)PVQLEEAPFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPVQLEEAPFSR 12 0 Q9BZL4-5;Q9BZL4-4;Q9BZL4;Q9BZL4-2 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 0 S(1)PVQLEEAPFSR;S(1)PVQLEEAPFSR ; 132.08 0.003261 11496400 532.98 649.03 529.65 288.56 477.51 377.81 423.45 610.42 720.74 586.05 TRUE FALSE FALSE 526.4838348 658.1670614 538.8683361 321.9246649 453.1408829 353.6691603 459.4178324 628.0815396 656.2752093 570.8243365 0.922321984 1.153011565 0.944017803 0.563964506 0.793835956 0.619576177 0.804832245 1.10030617 1.149697319 1 9.156903034 -9.494737941 24.46195176 0.979949045 0.768688557 0.389197685 0.154448525 479.7372438 417021.5642 0.021800845 0.033250841 3.20E-10 9.494737941 -0.211260488 S(ph)PVREPIDNLTPEER ddPTM_HeLa_Romidepsin_16h_R1 3 SPVREPIDNLTPEER 15 1 Q14498-2;Q14498;G3XAC6;Q5QP22;H0Y4X3;Q14498-3;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 0 S(1)PVREPIDNLTPEER;S(1)PVREPIDNLTPEER;S(1)PVREPIDNLTPEER ;; 69.081 0.019507 59234700 2893.28 2730.68 2467.43 2311.52 2745.68 2543.2 2332.35 2217.17 2737.69 2959.24 TRUE FALSE FALSE 2858.01559 2769.122585 2510.374584 2578.788818 2605.557704 2380.697728 2530.459751 2281.320316 2492.82415 2882.358518 0.991554511 0.96071414 0.870944599 0.894680104 0.90396725 0.825954756 0.877912909 0.791476946 0.864855685 1 11.49303408 -9.462419858 0.629300718 1.002584461 0.831395895 0.351085755 0.052148178 0.200916117 0.158990354 0.00665047 0.014790299 3.45E-10 9.462419858 -0.171188566 LAERLS(ph)PFLAESK ddPTM_HeLa_Romidepsin_16h_R1 1 LAERLSPFLAESK 13 1 H9KVB4;O15417-2;O15417 H9KVB4 TNRC18 Trinucleotide repeat-containing gene 18 protein 1 0 LAERLS(0.999)PFLAES(0.001)K 73.597 0.020461 13859000 4183.1 4405 3893.7 3681.3 1808.1 1266.7 1116.3 1224.6 4065.6 4176.4 TRUE FALSE FALSE 4132.114768 4467.013706 3961.468215 4106.949227 1715.82591 1185.761958 1211.118494 1260.031869 3701.962554 4067.896526 1.015786597 1.098113897 0.973837016 1.00960022 0.421796842 0.291492655 0.297725984 0.309750226 0.910043441 1 11.99006727 -8.715247313 3.983459058 1.014236473 0.307667206 0.980087934 0.047030113 0.014731591 0.487272418 0.005121628 0.010362236 1.93E-09 8.715247313 -0.706569267 down S(ph)PVSTRPLPSASQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPVSTRPLPSASQK 14 1 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.973)PVS(0.026)T(0.001)RPLPSASQK 132.23 0.012078 253140000 2001.3 1650.6 1873 1793.8 1947.5 1583.4 1498.2 1847.8 2356.2 1925.2 TRUE FALSE FALSE 1976.907386 1673.83719 1905.598779 2001.207596 1848.111808 1482.22585 1625.457071 1901.263178 2145.455571 1875.183026 1.054247696 0.892626035 1.016220152 1.067206543 0.985563426 0.790443295 0.866825823 1.013908056 1.144131288 1 10.8728157 -8.501126532 22.39891144 1.017324662 0.888030247 0.379192381 0.078486055 143.8834189 148160.0862 0.009530172 0.021082343 3.15E-09 8.501126532 -0.129294416 S(ph)PYQEFTDHLVK ddPTM_HeLa_Romidepsin_16h_R1 2 SPYQEFTDHLVK 12 0 E9PQD7;P15880;H0YEN5 E9PQD7 RPS2 40S ribosomal protein S2 1 0 S(0.995)PY(0.005)QEFTDHLVK;S(1)PYQEFTDHLVK ; 160.03 0.00034389 22939000 10577.8 10616.6 8788.3 2573.58 7532.3 9005.2 7501.5 9531.7 10540.9 10272.8 TRUE FALSE FALSE 10448.8737 10766.06077 8941.256675 2871.149429 7147.898624 8429.796783 8138.677223 9807.484701 9598.095504 10005.91118 1.044270084 1.075970053 0.893597446 0.286945324 0.714367587 0.842481673 0.813386915 0.980169075 0.959242525 1 13.28856493 -9.51814403 24.79348954 1.023674766 0.723141543 0.399889489 0.169311707 136.6983196 715826.3618 0.026581738 0.03818067 3.03E-10 9.51814403 -0.300533223 S(ph)QAELETLVLSR ddPTM_HeLa_Romidepsin_16h_R1 2 SQAELETLVLSR 12 0 Q00G26 Q00G26 PLIN5 Perilipin-5 1 0 S(1)QAELETLVLSR;S(1)QAELETLVLSR ; 152.94 0.0014258 6287100 0 174.38 120.8 267.53 346.78 874.3 834.5 1032.85 114.1 162.866 TRUE FALSE FALSE 0 176.8349262 122.9024733 298.4630774 329.0825226 818.4350517 905.3824092 1062.733885 103.8946102 158.6347178 0 1.114730298 0.774751423 1.88144866 2.074467223 5.159242963 5.707340874 6.699251587 0.654929839 1 7.309564735 -8.244768211 1.023234034 0.564318292 6.909030594 0.96751324 0.412414151 0.087591413 0.152411126 0.076685964 0.413294545 5.69E-09 8.244768211 6.344712302 S(ph)QAGVSSGAPPGR ddPTM_HeLa_Romidepsin_16h_R1 1 SQAGVSSGAPPGR 13 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 S(0.993)QAGVS(0.004)S(0.003)GAPPGR 123.63 0.0040847 4294800 668.9 565.89 678.41 313.65 734.14 686.3 489.04 712.01 748.97 497.92 TRUE FALSE FALSE 660.7471895 573.8566143 690.2174415 349.9156888 696.6740963 642.4476449 530.5790454 732.610886 681.9802474 484.9839666 1.362410378 1.18324863 1.423175793 0.721499499 1.436488924 1.324678111 1.09401358 1.510587847 1.406191327 1 8.921793243 -12.47746227 1.191799396 0.998644507 1.257186563 0 0.247777943 0.667797056 1.682845706 0.142674954 0.034239893 3.33E-13 12.47746227 0.258542056 S(ph)QDDAMVDYFFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SQDDAMVDYFFQR 13 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;E9PR38;Q14671-4;E9PM68;E9PL65;E9PMX1 Q5T1Z4 PUM1 Pumilio homolog 1 1 0 S(0.954)QDDAMVDY(0.046)FFQR 90.725 0.030162 5295000 1478.1 1191.6 1387 1160 1293.8 1239.8 930.04 1122.6 1459.7 1243.1 TRUE FALSE FALSE 1460.084349 1208.375376 1411.140153 1294.124658 1227.772558 1160.580781 1009.037574 1155.08066 1329.140776 1210.804083 1.205879935 0.997994137 1.165457049 1.06881425 1.01401422 0.958520704 0.833361556 0.953978167 1.097733973 1 10.24174973 -8.375901843 1.696602831 1.095627361 0.894271296 0.580486407 0.067032967 0.2455453 1.353487318 0.012893192 0.040097972 4.21E-09 8.375901843 -0.201356066 S(ph)QDSYPGSPSLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;R4GMX8;Q6VN20-3;Q6VN20;Q6VN20-2 A0A0D9SEU5 RANBP10 Ran-binding protein 10 2 0 S(0.965)QDS(0.005)YPGS(0.029)PSLS(1)PR 183.71 1.61E-06 18597000 4135.3 3836.7 3584.9 3213.5 5353.2 6030.7 5340.9 6425 3919.5 3841.2 TRUE FALSE FALSE 4084.897373 3890.713163 3647.293681 3585.05999 5080.006228 5645.357733 5794.555913 6610.897238 3568.930103 3741.40507 1.09180837 1.039906957 0.974845977 0.958212202 1.357780335 1.50888707 1.54876465 1.76695576 0.953901018 1 11.86936446 -8.41400305 1.784490532 1.03241305 1.640730107 0.923325098 0.078632192 0.069200041 0.425761468 0.011593196 0.033967365 3.85E-09 8.41400305 0.608317057 S(ph)QDVELWEGEVVK ddPTM_HeLa_Romidepsin_16h_R1 2 SQDVELWEGEVVK 13 0 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 S(1)QDVELWEGEVVK;S(1)QDVELWEGEVVK ; 125.86 0.0035448 6257000 3413.6 3794.2 3439.9 2597 4462.1 6058.3 5518.1 5781.3 3848.6 3466.3 TRUE FALSE FALSE 3371.99373 3847.614847 3499.770017 2897.277359 4234.382387 5671.194182 5986.807276 5948.572794 3504.371577 3376.245026 0.998740821 1.139613629 1.0365865 0.858135987 1.254169159 1.679734183 1.77321469 1.761890132 1.037949423 1 11.72120389 -8.355147131 2.651403299 1.005561042 1.761532415 0.955640419 0.069923566 0.036509506 0.496236728 0.009821871 0.025578801 4.41E-09 8.355147131 0.755971373 S(ph)QEADVQDWEFR ddPTM_HeLa_Romidepsin_16h_R1 2 SQEADVQDWEFR 12 0 Q9C0C2;Q9C0C2-2;A0A2R8Y5C4 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 S(1)QEADVQDWEFR;S(1)QEADVQDWEFR ; 183.76 6.71E-07 105559000 2715.8 2806.5 1874.32 2232.9 3122.7 3016.4 2412 3853.8 2462.4 2483.6 TRUE FALSE FALSE 2682.698785 2846.009981 1906.941753 2491.078404 2963.336967 2823.661775 2616.87522 3965.303623 2242.156777 2419.075714 1.108976776 1.176486525 0.788293538 1.029764546 1.224987275 1.167248201 1.081766563 1.639181279 0.926865068 1 11.24024021 -4.741127212 1.123602847 1.05283834 199.9941593 0.663917566 0.123949229 241.2248958 1.129132108 0.017620432 122692.7166 1.81E-05 4.741127212 198.941321 S(ph)QEDLNEPIKR ddPTM_HeLa_Romidepsin_16h_R1 2 SQEDLNEPIKR 11 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 S(1)QEDLNEPIKR;S(1)QEDLNEPIKR ; 81.526 0.015689 59296000 8818.4 9297.8 7726 5911.8 7950.8 8276.7 6501.9 7651.6 8527.2 9088.4 TRUE FALSE FALSE 8710.917949 9428.694672 7860.467789 6595.350132 7545.041007 7747.845582 7054.171224 7872.986974 7764.505875 8852.282058 0.984030772 1.065114578 0.887959482 0.745045186 0.852327226 0.875237089 0.796876012 0.889373714 0.877119123 1 13.1118337 -9.57551213 6.158043212 0.997294937 0.831684056 0.592246848 0.058022324 0.063573767 5.277576172 0.006473838 0.009216803 2.66E-10 9.57551213 -0.165610881 S(ph)QEEPKDTFEHDPSESIDEFNK ddPTM_HeLa_Romidepsin_16h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 S(0.496)QEEPKDT(0.496)FEHDPS(0.008)ES(0.001)IDEFNK 52.541 0.01206 11483000 4514.2 4453.7 4086.2 2715.2 4042.5 3688.8 2672.4 2869 4936.4 5503 TRUE FALSE FALSE 4459.179194 4516.399306 4157.318597 3029.144199 3836.19614 3453.097585 2899.393589 2952.009988 4494.876021 5360.031267 0.831931564 0.842606896 0.775614617 0.565135547 0.71570406 0.644230866 0.540928484 0.550744919 0.838591381 1 12.3880257 -8.939050197 0.202866046 1.068706882 0.320073837 0.759898173 0.071422971 1.335571704 0.109863679 0.096445477 0.292589164 1.15E-09 8.939050197 -0.748633045 S(ph)QEGLRPR ddPTM_HeLa_Romidepsin_16h_R1 2 SQEGLRPR 8 1 Q27J81-2 Q27J81-2 INF2 Inverted formin-2 1 0 S(1)QEGLRPR;S(1)QEGLRPR ; 75.652 0.025679 23269700 2778.5 2952.7 3793.7 2041.9 2535.8 3378.1 3544 1089.48 3902.4 3010 TRUE FALSE FALSE 2744.634573 2994.268188 3859.727757 2277.994085 2406.388664 3162.250312 3845.027272 1121.002385 3553.35957 2931.799766 0.936160308 1.021307193 1.316504559 0.776995111 0.820788886 1.078603781 1.311490408 0.382359804 1.212006226 1 11.51757086 S(ph)QEMVHLVNK ddPTM_HeLa_Romidepsin_16h_R1 2 SQEMVHLVNK 10 0 P16070;P16070-17;H0Y2P0;P16070-8;P16070-5;P16070-7;P16070-3;H0YD13;P16070-6;P16070-4;P16070-13;P16070-16;P16070-10;P16070-11;P16070-14;P16070-12;P16070-18;H0YE40 P16070 CD44 CD44 antigen 1 0 S(1)QEMVHLVNK;S(1)QEMVHLVNK ; 79.639 0.018892 65613000 11414.1 21350.4 16865.4 5908.4 14317 21308.8 9356.7 16173.3 13022.2 15408.6 TRUE FALSE FALSE 11274.98056 21650.97149 17158.93521 6591.557008 13586.35007 19947.23645 10151.45786 16641.24892 11857.46182 15008.28235 0.751250563 1.442601557 1.143297735 0.43919463 0.905256827 1.329081902 0.676390384 1.108804361 0.790061217 1 13.87347125 -6.912415947 18.68155776 0.925396818 9.046589023 0.026497892 0.288262705 669.857578 143224.9428 0.038008183 551.9118339 1.22E-07 6.912415947 8.121192205 S(ph)QEQEVLER ddPTM_HeLa_Romidepsin_16h_R1 2 SQEQEVLER 9 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 S(1)QEQEVLER;S(1)QEQEVLER ; 136.93 0.0066942 19700100 1497.15 1421.57 1142.25 1270.57 1455.46 1690.23 1013.75 1220 1577 1327.32 TRUE FALSE FALSE 1478.90216 1441.5829 1162.130382 1417.479282 1381.182445 1582.229758 1099.8579 1255.298775 1435.94917 1292.836035 1.143920899 1.115054702 0.898900054 1.096410715 1.068335356 1.223844103 0.850732707 0.970965181 1.11069705 1 10.3363236 -7.738484369 24.99993704 1.071016308 0.910848908 0.380786252 0.08644811 204.4204477 222627.7327 0.012349559 0.046145204 1.83E-08 7.738484369 -0.1601674 S(ph)QESGYYDR ddPTM_HeLa_Romidepsin_16h_R1 1 SQESGYYDR 9 0 D6REM6;A0A0R4J2E8;A8MXP9;P43243;D6R991 D6REM6 MATR3 Matrin-3 1 0 S(0.952)QES(0.048)GYYDR 107.39 0.021621 61982000 1303.8 858.1 1059.8 579.92 1054.6 825.27 852.36 895.53 1108.6 1271.7 TRUE FALSE FALSE 1287.908784 870.1803543 1078.245374 646.973079 1000.779827 772.5379104 924.7594371 921.4407476 1009.444039 1238.661051 1.039758846 0.702516927 0.870492677 0.522316479 0.807952931 0.623687901 0.746579895 0.743900639 0.814947753 1 10.27456574 -10.26061 24.99135284 1.018775014 0.716283541 0.454682388 0.11072009 26.26239985 791356.9187 0.01375677 0.016333906 5.49E-11 10.26061 -0.302491473 S(ph)QGGEEEGPLSDK ddPTM_HeLa_Romidepsin_16h_R1 2 SQGGEEEGPLSDK 13 0 E9PR76;E9PSH4;Q9H063 E9PR76 MAF1 Repressor of RNA polymerase III transcription MAF1 homolog 1 0 S(1)QGGEEEGPLSDK;S(1)QGGEEEGPLSDK ; 229.69 3.81E-32 98564000 2931.3 3334.2 2915.4 2398.7 2413.95 2676.9 2325.2 2447.6 3287.3 3191 TRUE FALSE FALSE 2895.572188 3381.138955 2966.141314 2676.04898 2290.757124 2505.854729 2522.70243 2518.417444 2993.275655 3108.09736 0.9316221 1.087848469 0.954327027 0.860992649 0.737028754 0.80623431 0.811654893 0.810276241 0.963057237 1 11.60181598 -9.14795466 3.11026006 0.97730936 0.794262843 0.812461661 0.044545224 0.092642373 1.711121681 0.007349863 0.012741802 7.11E-10 9.14795466 -0.183046518 S(ph)QNSSISSTTGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQNSSISSTTGK 12 0 A0A3B3IU55;Q8WXE9;Q8WXE9-3 A0A3B3IU55 STON2 Stonin-2 1 0 S(1)QNSSISSTTGK 103.76 0.0028398 0 834.57 881.11 1009.4 871.4 1100.1 1041.3 860.96 655.57 1205.6 814.71 TRUE FALSE FALSE 824.3979398 893.5142897 1026.968184 972.1553681 1043.957792 974.7642906 934.0899209 674.5378836 1097.768117 793.5437168 1.038881567 1.125979919 1.294154515 1.225081048 1.31556431 1.228368734 1.177112113 0.850032417 1.383374467 1 9.632165894 -10.17058768 3.056204018 1.017236155 1.192515633 0 0.167576959 0.240471889 4.319574176 0.020685451 0.025365282 6.75E-11 10.17058768 0.175279478 S(ph)QPAPVSPQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SQPAPVSPQQK 11 0 Q13118-2;Q13118 Q13118-2 KLF10 Krueppel-like factor 10 1 0 S(0.93)QPAPVS(0.07)PQQK 94.302 0.027403 2704400 1767.6 1738.5 1717.5 1561.2 1345.4 1256.7 1112.2 1395.7 1743 1782.7 TRUE FALSE FALSE 1746.055811 1762.974649 1747.392367 1741.71329 1276.739218 1176.400926 1206.67024 1436.082377 1587.101715 1736.385197 1.005569395 1.015313107 1.006339129 1.003068497 0.735285707 0.677499974 0.694932347 0.82705288 0.914026287 1 10.76187131 -8.757552344 7.243010866 1.004276331 0.726085983 0.878049708 0.046737148 0.022229307 6.64037008 0.005100767 0.009811706 1.75E-09 8.757552344 -0.278190348 S(ph)QRYSGAYGASVSDEELK ddPTM_HeLa_Romidepsin_16h_R1 1 SQRYSGAYGASVSDEELK 18 1 A0A286YEX5;C9JRZ6;F8WAR4;Q9NX63 A0A286YEX5 CHCHD3 MICOS complex subunit MIC19 1 0 S(0.771)QRY(0.083)S(0.146)GAYGASVSDEELK 94.45 0.0014992 0 937.58 858.73 743.57 990.53 966.89 993.71 750.28 952.57 847.85 665.51 TRUE FALSE FALSE 926.1524143 870.8192235 756.5115239 1105.059739 917.5459953 930.2151381 814.0087645 980.13111 772.0161725 648.2199543 1.42876258 1.343400828 1.167059914 1.704760447 1.415485576 1.435030088 1.255760115 1.512034771 1.190978722 1 9.340339622 -12.45048817 0.53186357 0.891339998 1.418881176 0.391804957 0.147927213 0.939627475 0.328488888 0.261458138 0.032569742 3.54E-13 12.45048817 0.527541178 S(ph)QSAAVTPSSTTSSTR ddPTM_HeLa_Romidepsin_16h_R1 3 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 0 S(0.904)QS(0.066)AAVT(0.025)PS(0.003)S(0.001)T(0.001)TSSTR;S(0.983)QS(0.017)AAVTPSSTTSSTR;S(0.989)QS(0.011)AAVTPSSTTSSTR ;; 185.71 5.15E-09 19903500 3455.52 3582.79 3570.89 2380.39 3763.25 4523.54 3014.79 3668.41 4069.68 3609.37 TRUE FALSE FALSE 3413.402793 3633.228612 3633.039843 2655.621892 3571.19731 4234.500393 3270.866187 3774.549656 3705.677628 3515.598047 0.970930905 1.033459617 1.033405922 0.755382685 1.015815023 1.204489346 0.930386848 1.073657911 1.054067495 1 11.77955442 -8.51947661 24.99916085 0.975631291 1.064691137 0.153358298 0.099810431 193.8823565 1424659.213 0.013392378 0.027223985 3.02E-09 8.51947661 0.089059846 S(ph)QSIEQES(ph)QEK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSIEQESQEK 11 0 A0A0A0MRN0;Q5VTL8 A0A0A0MRN0 PRPF38B Pre-mRNA-splicing factor 38B 2 0 S(1)QS(0.029)IEQES(0.971)QEK 130.61 0.00030599 0 2605.4 2451 2241.1 1699.2 2232.2 2774.2 2394 2837.8 2589.8 2412.2 TRUE FALSE FALSE 2573.644383 2485.505242 2280.105405 1895.669499 2118.282505 2596.937573 2597.3463 2919.907266 2358.161802 2349.530696 1.095386575 1.057873066 0.970451422 0.806828999 0.901576859 1.105300551 1.105474512 1.242761914 1.003673544 1 11.1981569 -7.490573763 1.772144061 1.016113626 1.257805248 0.450761713 0.085504521 0.523936442 2.275065147 0.014344752 0.181640845 3.23E-08 7.490573763 0.241691622 S(ph)QSIEQESQEK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSIEQESQEK 11 0 A0A0A0MRN0;Q5VTL8 A0A0A0MRN0 PRPF38B Pre-mRNA-splicing factor 38B 1 0 S(0.855)QS(0.013)IEQES(0.133)QEK;S(0.983)QS(0.017)IEQESQEK ; 190.34 1.43E-08 96765000 6504.4 7273.1 6272.3 5385.4 5439.8 6020.4 5041.8 5183.1 7158.6 6294.9 TRUE FALSE FALSE 6425.121871 7375.490893 6381.46675 6008.085287 5162.186707 5635.71587 5470.050366 5333.064821 6518.316887 6131.357591 1.047911784 1.202913186 1.040791808 0.979894778 0.841932089 0.91916281 0.892143426 0.869801629 1.06311152 1 12.58199083 -8.965637675 3.924294419 1.040171018 0.884762256 0.70015408 0.056800726 0.120209822 4.041656171 0.009396362 0.017218893 1.08E-09 8.965637675 -0.155408763 S(ph)QSLPTTLLSPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSLPTTLLSPVR 13 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 S(0.912)QS(0.071)LPT(0.005)T(0.012)LLSPVR;S(0.966)QS(0.012)LPT(0.001)T(0.001)LLS(0.02)PVR ; 196.67 1.99E-11 163690000 3999.6 3471.2 5356.3 4574.5 4699.2 4897.1 3802.1 3029.3 3589.5 2348.4 TRUE FALSE FALSE 3950.851337 3520.067645 5449.524155 5103.425214 4459.382289 4584.191115 4125.050279 3116.948016 3268.44613 2287.388229 1.72723252 1.538902579 2.38242205 2.231114573 1.949551996 2.004115898 1.803388785 1.362666807 1.428898727 1 11.15948553 -11.61274851 0.620465679 0.996755882 1.930748602 0.416019551 0.30556692 0.424385377 0.324516579 0.194797265 0.073402893 2.44E-12 11.61274851 0.933992721 S(ph)QSLQDQPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSLQDQPTR 10 0 Q8N4C8-2;Q8N4C8-3;Q8N4C8 Q8N4C8-2 MINK1 Misshapen-like kinase 1 1 0 S(0.499)QS(0.499)LQDQPT(0.002)R 129.76 0.00022074 0 2154.2 2229.8 1781.6 2086.1 2309.2 2684.7 2097.9 2379.5 2423.6 2102.9 TRUE FALSE FALSE 2127.943782 2261.191183 1812.608001 2327.304697 2191.352907 2513.156334 2276.095574 2448.347078 2206.827146 2048.266355 1.038899934 1.103953681 0.884947408 1.136231473 1.069857395 1.226967542 1.11123027 1.195326512 1.077412193 1 11.00018762 -8.783296805 1.850727113 1.018370532 1.166175481 0.435731738 0.069521144 0.199691991 1.390259551 0.009356506 0.020967381 1.65E-09 8.783296805 0.147804949 S(ph)QSSDTEQQSPTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.301)QS(0.301)S(0.301)DT(0.096)EQQSPTSGGGK 148.19 5.32E-05 36697000 6205.9 6025.9 5780.8 5601.7 5418.8 4518.6 4307.4 4067.7 7054.8 6631.3 TRUE FALSE FALSE 6130.260104 6110.732778 5881.412399 6249.394911 5142.258416 4229.876043 4673.270448 4185.392482 6423.801019 6459.01787 0.949100967 0.946077701 0.910573793 0.967545691 0.796136273 0.654879136 0.723526478 0.647992089 0.994547646 1 12.6570991 -8.592340593 2.535374385 0.968001087 0.679691366 0.941753247 0.032098838 0.048326584 0.625903157 0.005158118 0.011788714 2.56E-09 8.592340593 -0.28830972 S(ph)QVNGEAGSYEMTNQHVK ddPTM_HeLa_Romidepsin_16h_R1 1 SQVNGEAGSYEMTNQHVK 18 0 Q05D32;H0YMH7;Q05D32-2 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 S(0.857)QVNGEAGS(0.024)Y(0.07)EMT(0.048)NQHVK 61.111 0.013888 16141000 1663 1537.3 1695.8 1115.3 1923.1 1805.9 1346.9 1472.8 1621.9 1742.9 TRUE FALSE FALSE 1642.730716 1558.94215 1725.314688 1244.256234 1824.957031 1690.508818 1461.305652 1515.413144 1476.833202 1697.619207 0.967667372 0.918310858 1.016314307 0.732941892 1.075009651 0.995811553 0.860797078 0.892669651 0.86994374 1 10.72929717 -10.63154374 0.656017846 0.995927361 0.924031621 0 0.096790512 1.147130668 1.103972808 0.028541755 0.025873313 2.34E-11 10.63154374 -0.071895741 S(ph)QWESPSPTPSYR ddPTM_HeLa_Romidepsin_16h_R1 1 SQWESPSPTPSYR 13 0 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 0 S(0.983)QWES(0.015)PS(0.001)PTPSYR 111.31 0.0065092 4680300 2577.4 2909.2 2637 2177.1 2591.6 2830.7 2461.4 2830.3 2856.3 2875.7 TRUE FALSE FALSE 2545.985657 2950.155794 2682.895879 2428.826546 2459.340981 2649.827406 2670.471255 2912.190265 2600.825374 2800.988899 0.908959567 1.053255082 0.957838812 0.8671318 0.878025965 0.946032812 0.953403012 1.039700752 0.928538265 1 11.45172055 -12.60615322 1.37791436 1.000285418 0.943342982 0 0.061386909 0.814592936 2.752899723 0.043217703 0.009745956 2.48E-13 12.60615322 -0.056942436 S(ph)REDLSAQPVQTK ddPTM_HeLa_Romidepsin_16h_R1 2 SREDLSAQPVQTK 13 1 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 S(0.959)REDLS(0.041)AQPVQTK;S(0.745)REDLS(0.255)AQPVQTK ; 130.47 0.016066 220782000 8606.1 8784.9 7736.6 7718 7459.2 8046 7215.4 6637.9 9481.9 8558.5 TRUE FALSE FALSE 8501.205543 8908.574053 7871.252278 8610.391474 7078.52919 7531.886567 7828.275896 6829.957164 8633.815116 8336.148936 1.019800103 1.068667813 0.944231244 1.032897989 0.849136603 0.903521113 0.93907582 0.819318035 1.035707877 1 13.02516534 -8.764882791 24.99999761 1.010556089 0.883982253 0.719925993 0.042328923 35.28975074 256214.8178 0.005667805 0.010582314 1.72E-09 8.764882791 -0.126573835 S(ph)REDSPELNPPPGIEDNR ddPTM_HeLa_Romidepsin_16h_R1 1 SREDSPELNPPPGIEDNR 18 1 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 0 S(0.604)REDS(0.396)PELNPPPGIEDNR 112.58 0.00049666 4527900 1064.7 1081.9 624.16 559.74 770.52 721.03 714.39 612.12 971.69 995.47 TRUE FALSE FALSE 1051.723027 1097.131017 635.023243 624.4597725 731.1974892 674.95851 775.0702688 629.8307264 884.7796128 969.6075459 1.0846894 1.131520708 0.654928116 0.644033532 0.754116954 0.696115158 0.799364931 0.649572839 0.912513126 1 9.921257116 -9.757945594 24.99999996 1.04797429 0.704001113 0.841906318 0.070437283 20.6217134 147559.0652 0.009648906 0.013334976 1.75E-10 9.757945594 -0.343973177 S(ph)RESLNVDVVK ddPTM_HeLa_Romidepsin_16h_R1 4 SRESLNVDVVK 11 1 E7EVH7;H0YJU9;H0YJL0;H0YJT3;G5E9S8;G3V2E7;F8W6L3;Q07866-8;Q07866-2;Q07866-3;Q07866;Q07866-5;Q07866-10;H0YGB8;Q07866-6;H0YG16;G3V5R9;Q07866-7;Q07866-4;Q07866-9;G3V3H3 E7EVH7;Q07866-6 KLC1 Kinesin light chain 1 1 0 S(0.954)RES(0.046)LNVDVVK;S(0.782)RES(0.218)LNVDVVK;S(0.5)RES(0.5)LNVDVVK;S(0.5)RES(0.5)LNVDVVK ;;; 95.195 0.0017657 87555000 11214.8 11168.3 11271.9 9942.2 9546.5 9916.8 9616.6 7975.8 13162.4 11893.5 TRUE FALSE FALSE 11078.1097 11325.52762 11468.08269 11091.76394 9059.306482 9283.148485 10433.43376 8206.567189 11985.12198 11584.50516 0.956286829 0.977644489 0.989950156 0.957465493 0.782019289 0.801341823 0.900636982 0.708408955 1.034582126 1 13.4999088 -8.811708005 5.73159947 0.978899332 0.805592045 0.782281765 0.04846593 0.062653179 4.541119492 0.006294331 0.011674905 1.54E-09 8.811708005 -0.173307287 S(ph)RFIQVSPPFPIWGDAK ddPTM_HeLa_Romidepsin_16h_R1 1 SRFIQVSPPFPIWGDAK 17 1 H7C526 H7C526 CFB 1 0 S(0.715)RFIQVS(0.285)PPFPIWGDAK 84.169 0.0037163 0 349.96 434.05 383.22 511.49 542.41 417.07 346.72 377.52 470.64 521.58 TRUE FALSE FALSE 345.6945529 440.1605673 389.8897833 570.6308804 514.7287937 390.420573 376.1703881 388.4429456 428.5447797 508.0292764 0.680461873 0.866407878 0.767455345 1.123224402 1.013187266 0.768500146 0.740450217 0.764607403 0.843543472 1 8.988767828 -12.69100786 1.580328071 0.999651534 0.820865814 0 0.136883992 0.558488327 2.521820466 0.102545117 0.022929811 2.04E-13 12.69100786 -0.17878572 S(ph)RFSGGFGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SRFSGGFGAR 10 1 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;A0A0J9YVQ7;A0A2R8YDT5 A0A2R8Y4A4 1 0 S(0.941)RFS(0.059)GGFGAR;S(0.994)RFS(0.006)GGFGAR ; 71.888 0.029903 51649000 3545 2705.1 3388.5 4197.1 3244.5 3750.8 3427.5 3277.1 3055.3 3048.5 TRUE FALSE FALSE 3501.792176 2743.182469 3447.475421 4682.38845 3078.921058 3511.135985 3718.631764 3371.917718 2782.026316 2969.299531 1.179332748 0.923848349 1.161039964 1.576933685 1.036918312 1.182479554 1.252359934 1.135593659 0.936930171 1 11.53590692 -12.57893229 0.282190731 0.887769599 1.220402079 0.23606355 0.157693132 7.293247224 0.670773014 0.81881664 0.10397859 2.64E-13 12.57893229 0.332632481 S(ph)RFTPELQPK ddPTM_HeLa_Romidepsin_16h_R1 1 SRFTPELQPK 10 1 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 S(0.977)RFT(0.023)PELQPK 85.672 0.0176 31829000 5011.4 4543.2 5021.1 3934.1 4844.7 5451.8 4788.8 5046.9 4733.9 4908.5 TRUE FALSE FALSE 4950.319129 4607.159289 5108.490139 4388.979152 4597.456881 5103.447575 5195.560552 5192.924089 4310.488128 4780.976462 1.035420101 0.963644001 1.068503512 0.918008944 0.961614624 1.067448797 1.086715359 1.08616391 0.901591581 1 12.22308959 -8.090085124 6.189935235 1.006278678 1.084325145 0.376305504 0.052295261 0.169589869 9.510383351 0.005817499 0.015154237 8.13E-09 8.090085124 0.078046467 S(ph)RGQGYVGGQR ddPTM_HeLa_Romidepsin_16h_R1 1 SRGQGYVGGQR 11 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(1)RGQGYVGGQR 139.32 0.021712 1756200 637.98 656.26 606.76 587 527.69 667.98 437.16 420.38 699.62 501.45 TRUE FALSE FALSE 630.2040544 665.4988455 617.3204033 654.8717019 500.7600102 625.2982338 474.2923595 432.5430321 637.044235 488.4222567 1.290285293 1.362548157 1.263907193 1.34079005 1.025260424 1.280241073 0.971070325 0.885592387 1.304289938 1 8.931985133 -7.62069756 5.378183738 1.178917915 0.905755328 0.441050166 0.127310291 0.172371317 7.516271991 0.021040362 0.083235608 2.39E-08 7.62069756 -0.273162587 SESSTSAFST(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 SESSTSAFSTPTR 13 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 0 SESSTSAFS(0.001)T(0.998)PTR;SESSTSAFS(0.002)T(0.998)PTR;SESSTSAFS(0.002)T(0.998)PTR ;; 215.77 3.57E-23 42524000 15912.4 14815.3 15449.8 11619 9409.6 8366 5604.7 5948.6 16895.2 15480.9 TRUE FALSE FALSE 15718.45355 15023.87018 15718.69729 12962.44345 8929.393 7831.4396 6080.763078 6120.713356 15384.051 15078.70399 1.042427357 0.996363494 1.042443522 0.859652359 0.592185708 0.519370869 0.403268284 0.405917734 1.020250216 1 13.88022481 -8.714717964 1.494463167 1.022435069 0.420877209 0.986606463 0.030210263 0.030839694 0.138179135 0.00496672 0.0126609 1.93E-09 8.714717964 -0.60155786 down VLS(ph)PLIIK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPLIIK 8 0 Q8NCN4 Q8NCN4 RNF169 E3 ubiquitin-protein ligase RNF169 1 0 VLS(1)PLIIK 112.11 0.021682 91652000 13682 12098 12690 10796 6930.6 5148.4 4766.1 4656.2 12873 12192 TRUE FALSE FALSE 13515.23852 12268.31596 12910.86413 12044.28432 6576.90562 4819.433856 5170.932415 4790.919801 11721.60664 11875.25008 1.138101381 1.033099587 1.087207767 1.014234162 0.55383302 0.405838515 0.43543777 0.403437382 0.987061877 1 13.53567028 -8.713745322 3.104444822 1.066001101 0.421919817 0.978578791 0.0433634 0.028671989 0.56340883 0.007915318 0.016424915 1.93E-09 8.713745322 -0.644081284 down S(ph)RNRGPPPS(ph)WGRR ddPTM_HeLa_Romidepsin_16h_R1 1 SRNRGPPPSWGRR 13 3 P84103-2;P84103 P84103-2 SRSF3 Serine/arginine-rich splicing factor 3 2 0 S(1)RNRGPPPS(1)WGRR 87.083 0.03007 30367000 414.08 493.47 501.05 376.2 603.22 443.94 501.63 445.01 544.48 459.86 TRUE FALSE FALSE 409.0330337 500.4170836 509.7705651 419.6980141 572.4354325 415.5736668 544.2384397 457.8856622 495.7803451 447.9127709 0.913197971 1.11721995 1.138102323 0.937008367 1.2780065 0.927800442 1.215054526 1.022265253 1.106868072 1 8.807073991 -10.25589256 24.84608208 0.959010153 1.092397858 0.056416187 0.115757479 389.6459352 1745359.49 0.016031817 0.01933989 5.55E-11 10.25589256 0.133387705 S(ph)RNSPLLER ddPTM_HeLa_Romidepsin_16h_R1 1 SRNSPLLER 9 1 E7ETY4;E9PC69;Q7KZI7-10;Q7KZI7-12;Q7KZI7-8;Q7KZI7-11;Q7KZI7-6;Q7KZI7-3;Q7KZI7-14;Q7KZI7-9;Q7KZI7-13;Q7KZI7-4;Q7KZI7-16;Q7KZI7-5;Q7KZI7-15;Q7KZI7-2;Q7KZI7-7;Q7KZI7 E7ETY4 MARK2 Serine/threonine-protein kinase MARK2 1 0 S(0.998)RNS(0.002)PLLER 87.667 0.016472 155870000 941.88 1071 803.09 786.31 914.54 965.85 855.87 896.23 1120.8 760.04 TRUE FALSE FALSE 930.4000043 1086.077566 817.0674446 877.2268619 867.8676112 904.1353021 928.5675764 922.161001 1020.552841 740.2940512 1.256797894 1.467089414 1.103706619 1.184970838 1.172328225 1.221319151 1.254322623 1.245668528 1.37857766 1 9.531954625 -12.14908505 0.949401301 1.002682226 1.236078022 0 0.145946568 0.369084557 0.609959204 0.056823139 0.017176311 7.09E-13 12.14908505 0.233395796 S(ph)RQPSPLLLLPPPAGLTSDPGPSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 0 S(0.86)RQPS(0.14)PLLLLPPPAGLTSDPGPSVR 71.608 0.00027291 21816000 834.49 822.99 753.61 789.24 660.02 611.06 496.32 623.72 778.76 873.75 TRUE FALSE FALSE 824.3189149 834.5760748 766.7262659 880.4956423 626.3367165 572.0152381 538.4774084 641.7663541 709.1057552 851.049849 0.968590636 0.980642997 0.900918162 1.034599375 0.735957732 0.672128946 0.632721349 0.754087854 0.83321295 1 9.733099828 -8.679231653 5.040610475 0.980425089 0.685340404 0.791201719 0.06325325 0.038989173 1.727607243 0.005946651 0.012021055 2.09E-09 8.679231653 -0.295084685 S(ph)RS(ph)PESQVIGENTK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 0 S(0.971)RS(0.997)PES(0.031)QVIGENTK 114.31 0.00037725 0 3576.5 3701 3368.2 2257.6 3532.8 3114.7 3089.8 3288.4 3098.2 3894.8 TRUE FALSE FALSE 3532.908242 3753.102775 3426.822108 2518.634334 3352.508033 2915.680722 3352.247535 3383.544666 2821.089232 3793.612535 0.931278092 0.989321588 0.903313682 0.663914491 0.883724419 0.76857631 0.883655751 0.891905706 0.7436419 1 11.88935662 -9.517323952 21.70861246 0.967228771 0.818925744 0.116605223 0.096500807 25.14633619 98274.14673 0.010115902 0.014601072 3.04E-10 9.517323952 -0.148303027 S(ph)RS(ph)PESQVIGENTKQP ddPTM_HeLa_Romidepsin_16h_R1 2 SRSPESQVIGENTKQP 16 2 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 2 0 S(0.993)RS(0.983)PES(0.025)QVIGENTKQP;S(0.993)RS(0.735)PES(0.272)QVIGENT(0.001)KQP ; 123.4 0.0047659 36507000 10565.6 10459.4 9288 12351.3 10748.8 10026.4 8957.5 9784 11448.1 10484.3 TRUE FALSE FALSE 10436.8224 10606.64771 9449.653744 13779.41542 10200.24863 9385.745399 9718.349826 10067.0846 10424.15326 10211.91637 1.022023881 1.038653992 0.925355575 1.349346676 0.998857438 0.919097362 0.951667588 0.985817376 1.020783258 1 13.31796601 -8.517847285 24.99972286 1.032974232 0.95328076 0.143658208 0.107373706 389.8884246 1937226.076 0.015275251 0.031246227 3.03E-09 8.517847285 -0.079693473 S(ph)RSESDLSQPESDEEGYALSGR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSESDLSQPESDEEGYALSGR 22 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 S(0.333)RS(0.333)ES(0.333)DLS(0.001)QPESDEEGYALSGR 121.84 2.36E-05 8979900 421.21 476.09 498.72 324.31 577.16 722.21 430.03 622.44 473.46 376.24 TRUE FALSE FALSE 416.0761305 482.7924075 507.4000124 361.8082481 547.7053715 676.0631118 466.5567375 640.4493194 431.1125518 366.4652306 1.135376827 1.317430324 1.384578863 0.987292157 1.494562992 1.844821979 1.273126885 1.747640065 1.176407789 1 8.517532515 -8.246975508 0.272565132 0.977239356 1.948678461 0.467959876 0.201132259 2.8923757 0.260003562 0.129743989 0.912844726 5.66E-09 8.246975508 0.971439105 S(ph)RSFTLDDESLK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 0 S(0.93)RS(0.07)FTLDDESLK 101.72 0.0054474 22518000 5082 4837.3 4794.4 7083.6 6168.6 6212.3 5244.2 5383 5515.2 4850.4 TRUE FALSE FALSE 5020.058629 4905.399636 4877.844521 7902.639161 5853.793324 5815.354079 5689.642217 5538.748612 5021.906699 4724.385909 1.062584371 1.038314763 1.032482235 1.672733624 1.239059094 1.230922747 1.204313603 1.172374298 1.062975548 1 12.2059111 -9.434766184 24.99999999 1.031225581 1.296886797 0.497763614 0.132682396 45.45132171 12894.71259 0.019819366 0.030274579 3.67E-10 9.434766184 0.265661216 S(ph)RSLGPGAGPR ddPTM_HeLa_Romidepsin_16h_R1 2 SRSLGPGAGPR 11 1 P78549-3;P78549-2;P78549;H3BUV2 P78549-3 NTHL1 Endonuclease III-like protein 1 1 0 S(0.855)RS(0.145)LGPGAGPR;S(0.943)RS(0.057)LGPGAGPR ; 69.352 0.029576 21043000 2542.36 3147 2132.64 2961.98 2912.04 2611.95 2187.02 2382.9 2931.48 2539.21 TRUE FALSE FALSE 2511.372738 3191.303549 2169.757705 3304.458064 2763.427732 2445.054825 2372.785424 2451.845452 2669.281087 2473.240958 1.015417738 1.290332646 0.877293293 1.336084158 1.117330571 0.988603564 0.959383038 0.991349203 1.079264468 1 11.27218709 -5.80415991 8.262435144 1.03949428 0.702283166 0 0.140818983 0 0 0.017571925 0 1.57E-06 5.80415991 -0.337211114 S(ph)RSPFSTTR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPFSTTR 9 1 K7EPI8;Q8NG27-2;Q8NG27-3;Q8NG27 K7EPI8 PJA1 E3 ubiquitin-protein ligase Praja-1 1 0 S(1)RSPFSTTR 71.451 0.030256 3618900 460.35 432.67 312.3 579.11 385.34 392.73 322.99 315.57 308.67 419.62 TRUE FALSE FALSE 454.7390771 438.7611396 317.7354505 646.069423 365.6746619 367.6358205 350.4247625 324.7005201 281.0617821 408.7182119 1.112598029 1.073505234 0.777394893 1.580720908 0.894686489 0.899484803 0.857374965 0.794436144 0.687666402 1 8.674962719 -8.550714095 24.99999019 1.072958671 0.858785426 0.120719085 0.225016527 225.7628137 202765.3569 0.025725192 0.051451147 2.81E-09 8.550714095 -0.214173245 S(ph)RSPGSPVGEGTGSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPGSPVGEGTGSPPK 17 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 S(0.991)RS(0.009)PGSPVGEGTGSPPK 176.68 5.76E-08 6886500 1592.6 1879.8 1336.3 2109.4 1728.1 1660.5 1644.2 1697 1718.1 1472.9 TRUE FALSE FALSE 1573.188779 1906.263874 1359.557741 2353.298753 1639.908609 1554.399409 1783.858307 1746.100018 1564.428833 1434.633846 1.096578603 1.328745923 0.947668804 1.640347996 1.143085125 1.083481624 1.243424106 1.217104994 1.090472553 1 10.48646686 -10.65083885 1.083163013 1.024055673 1.230557588 0.151433174 0.172697287 0.481333436 1.166798534 0.03803184 0.037253767 2.23E-11 10.65083885 0.206501915 S(ph)RSPQAFR ddPTM_HeLa_Romidepsin_16h_R1 2 SRSPQAFR 8 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;H3BSK8 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 S(0.921)RS(0.079)PQAFR;S(0.921)RS(0.079)PQAFR ; 79.451 0.022561 27197000 2254.62 2223.97 2074.5 2174.81 2016.04 2323.53 2170.49 1306.81 2471.8 2404.5 TRUE FALSE FALSE 2227.139824 2255.279108 2110.605802 2426.271765 1913.153956 2175.063932 2354.851366 1344.620486 2250.716017 2342.030743 0.950943889 0.962958797 0.901186207 1.035969221 0.816878242 0.928708531 1.005474148 0.57412589 0.961010449 1 11.1935443 -7.257501571 24.86769754 0.961936943 0.574125728 0.785198714 0.058978494 117.9513748 744843.368 0.007987659 0.081014984 5.53E-08 7.257501571 -0.387811214 S(ph)RSPSSPELNNK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPSSPELNNK 12 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.524)RS(0.416)PS(0.049)S(0.011)PELNNK 75.788 0.021485 3390600 1234.1 1212.1 1262.8 878.48 988.55 1369.8 858.15 771.91 1273.4 1194.5 TRUE FALSE FALSE 1219.058315 1229.163976 1284.778504 980.053991 938.1006047 1282.274201 931.0412396 794.243998 1159.503915 1163.466718 1.047780994 1.056466813 1.104267518 0.842356705 0.806297757 1.102115068 0.80023023 0.682652959 0.99659397 1 10.18421423 -9.249036838 24.35079974 1.031789266 0.856088942 0.471616751 0.102354246 410.5152177 805993.458 0.015288998 0.025227619 5.64E-10 9.249036838 -0.175700323 S(ph)RSSDIVSSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSSDIVSSVR 11 1 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 S(0.817)RS(0.153)S(0.031)DIVSSVR 79.804 0.021026 56804000 1126.8 1143.3 1363.3 1196.5 1659 1356.8 1239.4 1341.3 984.29 965.04 TRUE FALSE FALSE 1113.066128 1159.395407 1387.027665 1334.84496 1574.335039 1270.104859 1344.674605 1380.108399 896.2526372 939.9681217 1.184153061 1.233441199 1.475611388 1.420095989 1.67488131 1.351221206 1.430553414 1.468250218 0.953492588 1 9.876468019 -10.25288484 0.824036544 1.047958382 1.483221976 0.808348851 0.093690749 0.16891504 0.2331219 0.02220416 0.02656947 5.59E-11 10.25288484 0.435263594 S(ph)RT(ph)GSESSQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 S(0.599)RT(0.734)GS(0.186)ES(0.462)S(0.019)QTGTSTTSSR 102.57 0.0017129 34916000 4143.4 4311.6 3901 5109.2 2997.9 2668.5 2291.1 2856 4941.2 4492 TRUE FALSE FALSE 4092.898647 4372.298818 3968.895269 5699.949744 2844.905976 2497.991462 2485.705977 2938.633854 4499.246697 4375.297192 0.935456146 0.999314704 0.907114441 1.30275716 0.650220054 0.570930694 0.568122774 0.671642114 1.028329391 1 12.0951653 -8.603465331 10.46847161 0.986840774 0.601782791 0.773144461 0.108550583 0.13467874 16.54413583 0.01460289 0.029219706 2.49E-09 8.603465331 -0.385057982 S(ph)RT(ph)PPSAPSQSR ddPTM_HeLa_Romidepsin_16h_R1 2 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 S(1)RT(1)PPSAPSQSR;S(0.999)RT(1)PPS(0.001)APSQSR ; 95.618 0.019287 91248000 2672.4 2491.7 2326.6 1886.2 2132.39 2211.7 2202.6 2726 2583.8 2879.9 TRUE FALSE FALSE 2639.827761 2526.778218 2367.093497 2104.291319 2023.566181 2070.379508 2389.688789 2804.872509 2352.698457 2805.079783 0.941088299 0.900786578 0.843859598 0.750171646 0.72139345 0.738082218 0.851914731 0.999926108 0.838727822 1 11.45382609 -10.04412376 1.434842137 0.976722025 0.805598966 0.19971136 0.086878693 0.250976217 1.004928298 0.014892305 0.019353933 9.03E-11 10.04412376 -0.17112306 S(ph)RTAS(ph)GSSVTSLDGTR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 2 0 S(0.914)RT(0.086)AS(0.793)GS(0.11)S(0.075)VT(0.017)S(0.004)LDGT(0.002)R 152.68 0.0041227 10495000 1916.1 1942 1933.3 1710.6 2201 2247 2232.1 2492.8 1902.6 1942.4 TRUE FALSE FALSE 1892.745836 1969.339527 1966.948276 1908.387621 2088.674757 2103.423952 2421.694518 2564.925235 1732.426691 1891.936168 1.000427957 1.040912247 1.039648329 1.008695564 1.103987963 1.111783784 1.280008575 1.355714468 0.915689821 1 10.8856477 -7.377754836 0.709060954 1.002882646 1.564617263 0.919611709 0.036447901 0.284337003 0.109648858 0.00371797 0.123281402 4.19E-08 7.377754836 0.561734617 S(ph)RTGSESSQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.497)RT(0.497)GS(0.006)ESSQTGTSTTSSR;S(0.879)RT(0.06)GS(0.06)ES(0.001)SQTGTSTTSSR ; 120.99 0.00059048 35572280 58.359 197.31 161.55 323.79 0 167.028 107.56 0 199.41 150.01 TRUE FALSE FALSE 57.64769806 200.0877354 164.36171 361.2281233 0 156.3554499 116.6961437 0 181.5742702 146.1127186 0.394542642 1.369406697 1.124896666 2.472256535 0 1.070101572 0.798672045 0 1.242699964 1 7.190937955 -7.281282227 5.056098848 0.87934521 2.13E-12 0.153605393 0.634912051 0.235063954 17.84447667 0.086670764 0.679466695 5.23E-08 7.281282227 -0.87934521 S(ph)RTLTAVHDAILEDLVFPSEIVGK ddPTM_HeLa_Romidepsin_16h_R1 2 SRTLTAVHDAILEDLVFPSEIVGK 24 1 A0A2R8Y623;P62081;B5MCP9 A0A2R8Y623 RPS7 40S ribosomal protein S7 1 0 S(0.333)RT(0.333)LT(0.333)AVHDAILEDLVFPSEIVGK;S(0.333)RT(0.333)LT(0.333)AVHDAILEDLVFPSEIVGK ; 72.231 0.0003803 5825300 1632.69 1795.93 1855.69 2004.18 1948.42 2023.64 2498.8 2152.73 2744.6 1950.15 TRUE FALSE FALSE 1612.790146 1821.21315 1887.987506 2235.912722 1848.984857 1894.335935 2711.04801 2215.015846 2499.116102 1899.484822 0.849067141 0.95879321 0.99394714 1.17711534 0.973413862 0.997289325 1.427254368 1.166114001 1.315681006 1 10.89139247 -7.98921058 0.649013969 0.933212493 1.358488611 0.060948343 0.165778299 0.957017674 0.465255214 0.021719644 0.251764363 1.03E-08 7.98921058 0.425276118 S(ph)RTPPSAPSQSR ddPTM_HeLa_Romidepsin_16h_R1 3 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.999)RT(0.001)PPSAPSQSR;S(0.994)RT(0.006)PPSAPSQSR;S(0.985)RT(0.015)PPSAPSQSR ;; 125.73 0.0020439 363250000 10561.1 11379.1 9986.1 9253.6 7607.4 7347.6 6647.1 6233.4 10152.7 10851.8 TRUE FALSE FALSE 10432.37725 11539.29527 10159.90388 10323.54477 7219.165991 6878.112073 7211.704508 6413.753594 9244.617084 10569.86867 0.986992135 1.091716049 0.961213824 0.976695652 0.682994862 0.650728243 0.682288942 0.606795959 0.874619862 1 13.36766983 -8.755450537 4.225682332 0.999377717 0.652127655 0.898783268 0.053574781 0.028439182 1.173766492 0.00519683 0.010250803 1.76E-09 8.755450537 -0.347250062 S(ph)RTSPITR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTSPITR 8 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.991)RT(0.009)SPITR 80.455 0.021831 21223000 825.67 846.15 1053.7 777.75 657.74 763.28 1340.9 340.33 1201.3 1015.6 TRUE FALSE FALSE 815.6064165 858.0621219 1072.039206 867.6771144 624.1730734 714.5088714 1454.796013 350.1769116 1093.852719 989.2145656 0.824498996 0.867417598 1.08372768 0.877137423 0.63097845 0.722299182 1.470657695 0.3539949 1.105779026 1 9.950139672 -8.999038935 24.99989737 0.924406535 0.82717898 0.06825712 0.276529435 115.4274785 3002390.32 0.037298578 0.067209034 1.00E-09 8.999038935 -0.097227555 S(ph)RTSVQTEDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 2 SRTSVQTEDDQLIAGQSAR 19 1 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 0 S(0.545)RT(0.227)S(0.227)VQTEDDQLIAGQSAR;S(0.353)RT(0.353)S(0.291)VQT(0.003)EDDQLIAGQSAR ; 229.48 2.57E-38 37849000 3182.8 3418.5 3002.1 3445.9 4245.2 4236.2 4329.5 3761.4 3748.9 3120.5 TRUE FALSE FALSE 3144.006809 3466.625733 3054.350291 3844.331171 4028.551603 3965.520492 4697.247622 3870.230174 3413.588995 3039.42896 1.034407071 1.140551656 1.004909255 1.264820209 1.32543042 1.304692606 1.545437542 1.273341218 1.123102082 1 11.56958458 -9.033452294 1.076435978 1.018467041 1.401877817 0.719189639 0.087154894 0.141416104 0.323032039 0.01248358 0.029960809 9.26E-10 9.033452294 0.383410776 S(ph)RVFDLQFSTDSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SRVFDLQFSTDSPR 14 1 Q15003;E9PHA2;C9JZP1;C9J470 Q15003 NCAPH Condensin complex subunit 2 1 0 S(1)RVFDLQFSTDSPR 83.891 0.01067 5241700 1071.4 1349.9 938.05 1044.7 890.3 1145 1142.4 960.44 1334.8 953.99 TRUE FALSE FALSE 1058.341365 1368.903928 954.3763668 1165.493129 844.8646688 1071.838195 1239.435427 988.2288161 1215.412145 929.2052023 1.138974859 1.473198734 1.027088919 1.254290362 0.909233684 1.153499994 1.333866216 1.063520537 1.308012635 1 9.859853421 -11.62031961 1.072031283 1.01664572 1.169504561 0 0.176702956 0.625375997 1.45082825 0.051928029 0.028539056 2.40E-12 11.62031961 0.152858841 S(ph)S(ph)LGLDNSLSTSS(ph)EVGAT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SSLGLDNSLSTSSEVGATR 19 0 A0A087WVY1 A0A087WVY1 MLLT6 4 0 S(0.973)S(0.986)LGLDNS(0.284)LS(0.032)T(0.02)S(0.168)S(0.553)EVGAT(0.984)R 56.424 0.013135 2536700 865.47 960.16 1074.4 664.26 696.84 673.56 558.98 809.01 903.28 1165.1 TRUE FALSE FALSE 854.9213187 973.6771577 1093.099481 741.0648666 661.2776545 630.5216898 606.4597472 832.4174279 822.4883745 1134.830534 0.753347124 0.857993443 0.963227062 0.653018089 0.582710488 0.555608675 0.53440556 0.733516946 0.724767575 1 10.14826116 -9.141014422 4.737222074 0.883378024 0.596288028 0.633857584 0.093781962 0.112915672 3.921632978 0.016017498 0.027002007 7.23E-10 9.141014422 -0.287089995 S(ph)S(ph)LSGDEEDELFK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 0 S(1)S(0.958)LS(0.042)GDEEDELFK 142.39 0.0088909 39422000 7571.1 7484.8 7703.2 6821 8836.2 9383.5 7814 9629 8380.6 7154.8 TRUE FALSE FALSE 7478.820521 7590.171211 7837.270965 7609.676114 8385.255742 8783.924634 8477.720965 9907.599923 7631.018146 6968.917265 1.073168218 1.089146409 1.124603818 1.091945251 1.203236518 1.260443237 1.216504751 1.421684251 1.095007712 1 12.76671881 -4 0.235923615 1.00275991 3.245567163 0.85635024 0.043518573 8.633562408 0.105920474 0.021041186 7.621633743 1.00E-04 4 2.242807253 S(ph)S(ph)S(ph)PREMQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPREMQK 9 1 A0A087X0J8;A0A087WUF5;A0A087WTH4;A0A087WVG8;A0A087WUW2;A0A087WW93;A0A075B764;A0A087WY24;Q86T75-2;Q86T75;Q3BBV2;Q5TAG4 A0A087X0J8 NBPF12;NBPF11;NBPF8 Neuroblastoma breakpoint family member 11;Putative neuroblastoma breakpoint family member 8;Neuroblastoma breakpoint family member 12 3 0 S(1)S(1)S(1)PREMQK 53.597 0.029264 1638200 491.13 689.2 563.78 579.43 742.9 680.44 420.11 707.17 609.14 657.66 TRUE FALSE FALSE 485.1439187 698.9025757 573.5923544 646.4264229 704.9870409 636.96208 455.7941329 727.6308482 554.6569928 640.5738984 0.757358237 1.091056906 0.895435103 1.009136377 1.100555365 0.99436159 0.711540283 1.135904616 0.865875107 1 9.323221203 -10.25458929 24.98316232 0.885419168 0.981730742 0.146395245 0.126929849 999.863407 3646635.337 0.02324585 0.028130863 5.56E-11 10.25458929 0.096311574 S(ph)SDEDAAGEPK ddPTM_HeLa_Romidepsin_16h_R1 2 SSDEDAAGEPK 11 0 E9PHH9;Q9BUI4 E9PHH9 POLR3C DNA-directed RNA polymerase III subunit RPC3 1 0 S(0.988)S(0.012)DEDAAGEPK;S(0.985)S(0.015)DEDAAGEPK ; 188.15 1.83E-08 28885000 6933.6 6376 8921.9 6506.4 6104.1 7362.2 9144.5 3028.6 8226.3 8128.3 TRUE FALSE FALSE 6849.090616 6465.761495 9077.181927 7258.700582 5792.584999 6891.77918 9921.233602 3116.227763 7490.519125 7917.125594 0.865098139 0.816680425 1.146524937 0.916835346 0.731652534 0.870490066 1.253135811 0.393605953 0.946115991 1 12.95076102 -7.238107669 24.65348392 0.937665115 0.393605211 0.563656756 0.146421339 3237.568387 3420923.258 0.019399017 1.514481748 5.78E-08 7.238107669 -0.544059904 S(ph)SDELDAWTDFR ddPTM_HeLa_Romidepsin_16h_R1 1 SSDELDAWTDFR 12 0 O43524;O43524-2 O43524 FOXO3 Forkhead box protein O3 1 0 S(0.844)S(0.156)DELDAWTDFR 97.779 0.018016 4641800 534.57 577.29 523.04 11208 584.28 2635.4 530.86 606.96 684.31 635.39 TRUE FALSE FALSE 528.0544552 585.4171038 532.1432918 12503.9217 554.4620114 2467.006445 575.9512351 624.52143 623.1035997 618.8824762 0.853238661 0.945926127 0.859845467 20.20403255 0.895908404 3.986227661 0.930631028 1.00911151 1.006820557 1 9.273521662 S(ph)SDGGSEEPPDRR ddPTM_HeLa_Romidepsin_16h_R1 2 SSDGGSEEPPDRR 13 1 Q9HCD6;Q9HCD6-2;Q9HCD6-3;Q9HCD6-4 Q9HCD6 TANC2 Protein TANC2 1 0 S(0.5)S(0.5)DGGSEEPPDRR;S(0.46)S(0.46)DGGS(0.079)EEPPDRR ; 155.39 0.00010689 2087900 782.66 1018.46 853.96 1102.31 1199.89 1350.3 1255.24 921.81 994.97 1148.04 TRUE FALSE FALSE 773.1206389 1032.797907 868.8228156 1229.764269 1138.655136 1264.020188 1361.860054 948.481118 905.9773913 1118.213755 0.691388954 0.923614024 0.776973822 1.099757773 1.018280387 1.130392272 1.217888841 0.84821092 0.810200543 1 10.12698028 -9.253791905 24.85895507 0.851599516 1.072786236 0.469299693 0.117755995 456.279356 1483185.506 0.021308984 0.034902074 5.57E-10 9.253791905 0.221186719 S(ph)SDGSLSHEEDLAK ddPTM_HeLa_Romidepsin_16h_R1 2 SSDGSLSHEEDLAK 14 0 A0A2R8Y7R9;Q13136-2;Q13136;E9PJZ7;H0YEF9 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 S(0.406)S(0.406)DGS(0.176)LS(0.012)HEEDLAK;S(0.5)S(0.5)DGSLSHEEDLAK ; 96.135 0.0077678 8277100 2379.33 2652.28 2318.7 2695.7 4347.5 5078.9 3893.5 4073.2 3930.8 3178.3 TRUE FALSE FALSE 2350.329811 2689.618867 2359.056001 3007.389518 4125.630852 4754.374681 4224.213793 4191.051616 3579.219403 3095.727308 0.759217327 0.868816469 0.762036112 0.971464609 1.332685486 1.535786007 1.364530326 1.353818085 1.156180454 1 11.59606268 -8.771911325 3.374806964 0.873104583 1.415979614 0.7919932 0.119874256 0.063485039 1.513323021 0.015729982 0.031433403 1.69E-09 8.771911325 0.542875031 S(ph)SDIISLLVSIYGSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSDIISLLVSIYGSK 15 0 Q9UJX6-2;Q9UJX6 Q9UJX6-2 ANAPC2 Anaphase-promoting complex subunit 2 1 0 S(0.5)S(0.5)DIISLLVSIYGSK 90.731 0.015461 5169200 1041.4 1092.1 941.75 631.54 970.81 1032.7 909.52 1239 1046.5 1243.7 TRUE FALSE FALSE 1028.707016 1107.474612 958.1407637 704.5616263 921.2659431 966.7138029 986.7746061 1274.84851 952.898419 1211.388495 0.849196621 0.914219193 0.790944249 0.581614923 0.760504122 0.798021285 0.814581458 1.05238618 0.786616699 1 10.2424459 -11.49318523 0.622768562 0.996335145 0.802040375 0 0.128307731 0.746594054 0.598459774 0.069204667 0.029435753 3.21E-12 11.49318523 -0.19429477 S(ph)SDIVSSVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSDIVSSVR 9 0 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 S(0.982)S(0.018)DIVSSVR;S(0.98)S(0.02)DIVSSVR ; 195.27 8.97E-08 91429000 3394.3 3810.6 3243 2875.7 4677.7 4546.1 3195 3930.6 3005.2 2767.3 TRUE FALSE FALSE 3352.928966 3864.245727 3299.443055 3208.201965 4438.979514 4255.618882 3466.38322 4044.32571 2736.407385 2695.405147 1.243942481 1.433641889 1.224099115 1.190248512 1.646869124 1.578842011 1.286034207 1.500451876 1.015211902 1 11.39628643 -10.99380228 0.273156235 0.903573073 1.523191165 0.612268147 0.131640165 1.048871663 0.233531941 0.255440208 0.149422083 1.01E-11 10.99380228 0.619618092 S(ph)SDSEEAFETPESTTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSDSEEAFETPESTTPVK 18 0 E9PGB3;E7EMZ9;E9PBC6;O95359-5;O95359-3;O95359 E9PGB3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 0 S(0.449)S(0.449)DS(0.102)EEAFETPESTTPVK 133.78 2.64E-09 0 804.43 1116.8 798.49 781.88 825.04 871.8 718.89 792.32 1024.8 1050.3 TRUE FALSE FALSE 794.6252977 1132.52234 812.3873835 872.2846445 782.9351302 816.0947936 779.9524987 815.2445291 933.1393213 1023.013055 0.77674991 1.107045834 0.794112431 0.852662281 0.765322717 0.797736441 0.762407181 0.796905304 0.912148009 1 9.99860884 -9.611515496 22.97990854 0.909614697 0.794706138 0.420265525 0.083719924 12.55222617 3249.124883 0.016029999 0.022669844 2.45E-10 9.611515496 -0.114908559 S(ph)SDSWEVWGSASTNR ddPTM_HeLa_Romidepsin_16h_R1 2 SSDSWEVWGSASTNR 15 0 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;Q8N6T3-4;E5RHH7 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 S(0.524)S(0.106)DS(0.37)WEVWGSASTNR;S(0.495)S(0.361)DS(0.145)WEVWGSASTNR ; 134.02 0.0014687 11509500 1686.72 1616.23 1283.56 1485.15 2142.84 2266.07 1955.25 2027.3 1888.1 2038.02 TRUE FALSE FALSE 1666.161608 1638.983328 1305.899823 1656.870031 2033.482879 2121.27544 2121.328886 2085.956727 1719.223607 1985.071947 0.839345703 0.82565437 0.657860198 0.834664977 1.024387495 1.068613883 1.068640807 1.050821725 0.86607622 1 10.95497558 -8.644563172 5.330639923 0.886600589 1.060393924 0.567490759 0.086444532 0.181928009 7.795212908 0.016266433 0.032935077 2.27E-09 8.644563172 0.173793335 S(ph)SEDLAGPLPSSVSSSSTTSSKPK ddPTM_HeLa_Romidepsin_16h_R1 3 SSEDLAGPLPSSVSSSSTTSSKPK 24 1 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 0 S(0.811)S(0.171)EDLAGPLPS(0.014)S(0.004)VSSSSTTSSKPK;S(0.826)S(0.174)EDLAGPLPSSVSSSSTTSSKPK;S(0.873)S(0.108)EDLAGPLPS(0.017)S(0.001)VSSSSTTSSKPK ;; 168.92 1.63E-14 141588000 13059.2 13518.6 13075.9 8382.9 12885.1 12752.2 11680.8 11949.3 15028.7 14012.9 TRUE FALSE FALSE 12900.02945 13708.91521 13303.48055 9352.170341 12227.52527 11937.37558 12672.96686 12295.03414 13684.49543 13648.84284 0.945137225 1.004401279 0.974696589 0.685198771 0.895865343 0.874607153 0.928501193 0.900811467 1.002612133 1 13.73649102 -9.44934205 24.99999942 0.976306113 0.860690934 0.495570017 0.06438209 99.3585055 33778.253 0.009763479 0.014913959 3.55E-10 9.44934205 -0.115615179 S(ph)SEGSLGGQNSGIGGR ddPTM_HeLa_Romidepsin_16h_R1 1 SSEGSLGGQNSGIGGR 16 0 C9JRJ5;Q9UGP4 C9JRJ5 LIMD1 LIM domain-containing protein 1 1 0 S(0.968)S(0.031)EGS(0.001)LGGQNSGIGGR 104.26 0.00098791 0 822.77 949.48 994.96 720 836.31 792.01 486.12 628.38 1009.4 921.56 TRUE FALSE FALSE 812.7417628 962.8468044 1012.276861 803.2497877 793.62998 741.4031171 527.4110207 646.5611839 919.1167359 897.6177383 0.905443072 1.072669092 1.12773714 0.894868443 0.8841514 0.825967542 0.587567511 0.72030794 1.023951173 1 9.809957376 -8.156519306 1.521207379 0.974174554 0.648683925 0.740955926 0.079266413 0.18119684 0.768169644 0.012546647 0.052461415 6.97E-09 8.156519306 -0.325490629 S(ph)SELLVR ddPTM_HeLa_Romidepsin_16h_R1 1 SSELLVR 7 0 Q9NSK0-5;Q9NSK0;Q9NSK0-3 Q9NSK0-5 KLC4 Kinesin light chain 4 1 0 S(0.991)S(0.009)ELLVR 128.12 0.018997 12163000 2092.3 1724.7 1562.1 1639.1 1528.4 1696.8 1561.7 1884.3 2327 1804.1 TRUE FALSE FALSE 2066.798243 1748.980372 1589.287695 1828.620454 1450.400045 1588.379956 1694.350759 1938.819248 2118.867292 1757.229222 1.176168833 0.995305763 0.904428219 1.04062716 0.825390351 0.903911645 0.964217268 1.103338838 1.205800169 1 10.77908668 -10.01398851 22.357198 1.08332488 0.95248418 0.389772601 0.090580747 152.2449235 243327.1199 0.015534834 0.019469413 9.68E-11 10.01398851 -0.1308407 S(ph)SETLTFK ddPTM_HeLa_Romidepsin_16h_R1 1 SSETLTFK 8 0 Q9NPF5;Q5TG37;Q5TG36;Q5TG38;Q5TG39;Q5TG40 Q9NPF5 DMAP1 DNA methyltransferase 1-associated protein 1 1 0 S(0.985)S(0.015)ETLTFK 105.2 0.026637 2333500 1221.3 1352.6 1294.1 836.88 1599.2 1710.5 1723.1 1945.2 1417 1565.6 TRUE FALSE FALSE 1206.414326 1371.641938 1316.623268 933.6440032 1517.586857 1601.20457 1869.460071 2001.481293 1290.259971 1524.925486 0.791130017 0.899481287 0.863401707 0.612255492 0.995187549 1.050021516 1.225935357 1.312510881 0.846113454 1 10.57452303 -7.925469286 1.717449359 0.878181034 1.304480703 0.724579008 0.102482764 0.195370047 1.054508297 0.017490062 0.089408157 1.19E-08 7.925469286 0.426299669 S(ph)SFSMEEGDVL ddPTM_HeLa_Romidepsin_16h_R1 1 SSFSMEEGDVL 11 0 B0QYS6;B0QYS7;P19484;B1AKB5;P19484-2 B0QYS6 TFEB Transcription factor EB 1 0 S(0.49)S(0.49)FS(0.021)MEEGDVL 153.1 0.0031195 1020300 964.25 776.22 782.26 876.34 663.7 611.26 765.62 838.06 737.43 685.03 TRUE FALSE FALSE 952.4973501 787.1476455 795.8749072 977.6665541 629.8289124 572.2024588 830.6517437 862.3079439 671.4724139 667.2328218 1.427533717 1.179719612 1.192799396 1.465255488 0.943941742 0.857575407 1.244920388 1.292364398 1.006353992 1 9.382046448 -8.725621016 24.99956391 1.220447233 1.079921727 0.101330997 0.184379272 352.5272212 246046.1917 0.030660675 0.061319594 1.88E-09 8.725621016 -0.140525506 S(ph)SFSSDPDEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSFSSDPDEK 10 0 P46013 P46013 MKI67 Antigen KI-67 1 0 S(0.916)S(0.083)FSSDPDEK 136.53 0.0055502 11874000 3526.6 3198.9 3734.2 2005.1 2738.5 2687.7 2708.8 2490.2 3401.2 3597.9 TRUE FALSE FALSE 3483.616443 3243.934198 3799.192185 2236.939096 2598.744126 2515.964644 2938.885404 2562.250008 3096.988154 3504.426039 0.99406191 0.925667759 1.084112531 0.63831825 0.741560557 0.717939148 0.838621038 0.731146835 0.883736201 1 11.77496246 -9.263201609 24.99999993 0.996548251 0.738937678 0.761486967 0.067827566 43.24621964 613515.8331 0.008266596 0.013039461 5.46E-10 9.263201609 -0.257610574 S(ph)SFSSDPDEKAQDSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSFSSDPDEKAQDSK 15 1 P46013 P46013 MKI67 Antigen KI-67 1 0 S(0.467)S(0.467)FS(0.011)S(0.056)DPDEKAQDSK 81.656 0.010649 5133200 2603.2 2657.2 2349.5 2349.3 1978.6 1834.7 1800.3 2087.7 3508.6 2602.7 TRUE FALSE FALSE 2571.471197 2694.608131 2390.392062 2620.93712 1877.624659 1717.468591 1953.217437 2148.104306 3194.782029 2535.081479 1.014354457 1.062927623 0.942925141 1.033867014 0.740656533 0.677480628 0.770475211 0.847351189 1.260228539 1 11.3078164 -8.759721676 24.99999981 1.007987348 0.753988997 0.691930154 0.093097174 11.08505756 161330.6448 0.006813947 0.013081208 1.74E-09 8.759721676 -0.253998351 S(ph)SGFISELPSEEGK ddPTM_HeLa_Romidepsin_16h_R1 3 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 S(0.909)S(0.091)GFISELPSEEGK;S(0.944)S(0.056)GFISELPSEEGK;S(0.991)S(0.009)GFISELPSEEGK ;; 286.74 3.51E-113 42372300 7749 8023.7 8156.9 7342.6 10921.8 9466.2 7759.9 9295.2 8462.7 8103.9 TRUE FALSE FALSE 7654.552207 8136.657859 8298.867423 8191.58596 10364.41979 8861.340371 8419.025712 9564.141947 7705.774917 7893.35951 0.969745797 1.030823168 1.051373298 1.037781942 1.313055585 1.122632304 1.066596004 1.21166937 0.976235139 1 12.94642374 -8.980161194 24.88890417 0.996130258 1.16762042 0.623129565 0.063783918 112.6992578 141386.9098 0.009351561 0.016949688 1.05E-09 8.980161194 0.171490162 S(ph)SGFLNLIK ddPTM_HeLa_Romidepsin_16h_R1 2 SSGFLNLIK 9 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 S(0.982)S(0.018)GFLNLIK;S(0.952)S(0.048)GFLNLIK ; 121.29 0.012746 9267100 3745.2 3540.9 4406.5 5363.5 5002.2 5097 4426.1 4761.5 3866.3 3291.4 TRUE FALSE FALSE 3699.552062 3590.748883 4483.193284 5983.653106 4746.919068 4771.31815 4802.052824 4899.26649 3520.488445 3205.888954 1.153986341 1.120047804 1.398424384 1.866456759 1.480687303 1.48829801 1.497884953 1.528208419 1.098131749 1 11.64650874 -9.677952985 3.392251723 1.076263848 1.56397706 0.800697807 0.112444123 0.078167026 1.794339942 0.019150755 0.027350278 2.10E-10 9.677952985 0.487713212 S(ph)SGGGYGGGPAGGHGGNR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-3;Q9H2U1-2;Q9H2U1 Q9H2U1-3 DHX36 ATP-dependent RNA helicase DHX36 1 0 S(0.5)S(0.5)GGGYGGGPAGGHGGNR 130.02 0.00065046 514960 354.67 266.83 314.95 301.27 387.49 299.8 201.9 261.34 363.73 430.8 TRUE FALSE FALSE 350.3471456 270.5864397 320.4315726 336.1042549 367.7149394 280.6437476 219.049381 268.9014606 331.1970778 419.6077539 0.834939637 0.644855671 0.763645499 0.800996292 0.876330182 0.668824027 0.522033682 0.640840066 0.789301615 1 8.712897527 -8.700190894 0.073752903 1.435650283 5.97E-15 0.328554993 0.107265614 23.53155717 0.507093145 3.638737873 6.322511729 1.99E-09 8.700190894 -1.435650283 S(ph)SGGREDLESSGLQR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGGREDLESSGLQR 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 S(0.956)S(0.044)GGREDLESSGLQR 92.236 0.0052406 76478000 679.49 520.57 662.86 695.08 1103.8 1514.2 1029.7 1459.6 772.85 753.21 TRUE FALSE FALSE 671.2081145 527.8985981 674.3968002 775.44842 1047.468967 1417.447507 1117.162692 1501.831223 703.7243604 733.6414956 0.914899332 0.719559351 0.919245714 1.056985496 1.427766795 1.932071066 1.522763774 2.047091436 0.959221043 1 9.518931432 -8.616331749 2.209730324 0.93528607 1.807786079 0.885195869 0.147455877 0.070116544 0.690027745 0.020897756 0.048881926 2.42E-09 8.616331749 0.872500009 S(ph)SGPYGGGGQYFAKPR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-3;P09651-2;P09651;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 S(0.498)S(0.498)GPY(0.005)GGGGQYFAKPR;S(0.607)S(0.392)GPYGGGGQYFAKPR ; 147.39 0.0019916 139767000 2962.1 3374.72 3182 2865.63 2437.8 2947 2301.54 2369.8 2692 2971.9 TRUE FALSE FALSE 2925.996786 3422.229397 3237.381375 3196.967624 2313.389969 2758.696211 2497.03275 2438.366424 2451.220778 2894.68961 1.010815383 1.182243991 1.11838636 1.104425018 0.79918412 0.953019696 0.862625389 0.842358509 0.846799177 1 11.49919294 -8.761973988 24.99999734 1.035634863 0.87051487 0.479363135 0.091306679 8.969012832 419451.1253 0.011526307 0.021849909 1.73E-09 8.761973988 -0.165119993 S(ph)SGREEDDEELLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGREEDDEELLR 13 1 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 S(0.849)S(0.151)GREEDDEELLR 171.11 0.00053004 39105000 2006.6 1508.5 1630.3 1508.7 2061.1 2021.4 1544.8 1415.1 1829.5 1651.9 TRUE FALSE FALSE 1982.142787 1529.736703 1658.674688 1683.142993 1955.914376 1892.239064 1676.015273 1456.043686 1665.864938 1608.9834 1.23192246 0.950747349 1.030883655 1.046090962 1.215621228 1.176046356 1.04166101 0.904946369 1.03535247 1 10.65193373 -7.351289838 3.418051157 1.101508761 0.896572646 0.249539055 0.090316514 0.295008547 5.561427485 0.014957926 0.133431226 4.45E-08 7.351289838 -0.204936115 S(ph)SGSETEQVVDFSDR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 0 S(0.618)S(0.051)GS(0.328)ET(0.002)EQVVDFSDR 278.89 1.58E-99 21333000 824.37 1061.6 660.31 653.37 571.28 612.57 511.88 557.72 1156 1081.9 TRUE FALSE FALSE 814.3222614 1076.545233 671.8024186 728.9157136 542.1254499 573.428754 555.3590744 573.8567483 1052.604465 1053.792082 0.772754204 1.021591689 0.637509458 0.691707336 0.514452005 0.544157395 0.527010104 0.544563542 0.998873006 1 10.04137453 -9.26994272 0.284953154 1.001088305 0.375815312 0.771186912 0.095481205 0.996524771 0.167589776 0.079869478 0.222121846 5.37E-10 9.26994272 -0.625272993 S(ph)SGSPYGGGYGSGGGSGGYGSR ddPTM_HeLa_Romidepsin_16h_R1 8 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 S(0.794)S(0.009)GS(0.197)PYGGGYGSGGGSGGYGSR;S(0.333)S(0.333)GS(0.333)PYGGGYGSGGGSGGYGSR;S(0.477)S(0.477)GS(0.046)PYGGGYGSGGGSGGYGSR;S(0.91)S(0.015)GS(0.075)PYGGGYGSGGGSGGYGSR;S(0.674)S(0.012)GS(0.314)PYGGGYGSGGGSGGYGSR;S(0.559)S(0.221)GS(0.221)PYGGGYGSGGGSGGYGSR;S(0.744)S(0.016)GS(0.239)PYGGGYGSGGGSGGY(0.001)GSR;S(0.981)S(0.015)GS(0.004)PYGGGYGSGGGSGGYGSR ;;;;;;; 292.29 1.52E-129 203589500 10931.12 10451.91 9692.92 8011.8 9195.7 9484.84 7607.03 8836.05 10745.5 10277.44 TRUE FALSE FALSE 10797.8873 10599.05226 9861.621207 8938.162013 8726.409115 8878.789335 8253.170938 9091.707166 9784.395567 10010.43063 1.078663617 1.058800831 0.985134564 0.892884866 0.871731641 0.886953785 0.824457133 0.908223383 0.977420046 1 13.28921642 -9.347051919 2.438987934 1.039684918 0.87098122 0.820857411 0.033786756 0.084222613 0.979279125 0.005609193 0.00921138 4.50E-10 9.347051919 -0.168703698 S(ph)SIDSQASLSGPLSGGAPGAGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SSIDSQASLSGPLSGGAPGAGAR 23 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 0 S(0.5)S(0.5)IDSQASLSGPLSGGAPGAGAR 218.88 9.04E-35 8474700 1512.4 1197 1288.2 1009 2130.1 2501.3 2074.2 2326.4 1387 1481.6 TRUE FALSE FALSE 1493.966287 1213.851397 1310.620581 1125.665327 2021.393049 2341.475003 2250.382496 2393.710714 1262.943246 1443.107818 1.035242321 0.841137011 0.908193112 0.78002857 1.400722124 1.622522567 1.559400114 1.658719247 0.875155155 1 10.49496338 -8.590549726 4.70519974 0.979337032 1.59609704 0.921466256 0.093417369 0.044616222 1.921688167 0.014364892 0.029622099 2.57E-09 8.590549726 0.616760009 S(ph)SITEPEGPGGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSITEPEGPGGPNIQK 16 0 H0YJL1;A0A3B3ISJ2;Q96KQ4 H0YJL1 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 0 S(0.898)S(0.089)IT(0.013)EPEGPGGPNIQK 167.37 1.93E-07 0 605.74 539.32 483.54 920.36 648.5 790.27 983.58 929.03 626.71 570.74 TRUE FALSE FALSE 598.3570079 546.9125611 491.9558109 1026.776354 615.4046251 739.7742975 1067.125261 955.9100173 570.655488 555.9120925 1.076351848 0.983811233 0.884952527 1.847012086 1.107017878 1.330739711 1.919593538 1.719534491 1.026521091 1 9.118712955 -7.795945895 0.482402455 1.011547387 2.165472726 0.550987255 0.249220157 1.518004898 0.32796506 0.054582046 0.902372384 1.60E-08 7.795945895 1.153925339 S(ph)SITEPEGPNGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 2 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 S(0.333)S(0.333)IT(0.333)EPEGPNGPNIQK;S(0.497)S(0.497)IT(0.007)EPEGPNGPNIQK ; 211.82 7.81E-26 20663400 3697.7 4427.3 4448.3 3555.6 5618.4 4890.5 3439.4 4135.3 4126.9 4308.3 TRUE FALSE FALSE 3652.63101 4489.627646 4525.720796 3966.715202 5331.672083 4578.012833 3731.54255 4254.948381 3757.779728 4196.369745 0.8704264 1.069883713 1.078484755 0.945273044 1.270543924 1.090946011 0.889231116 1.01395936 0.895483467 1 12.03492608 -10.24419274 24.13869289 0.938812465 1.051901723 0.255037304 0.099963934 634.1770882 887605.6659 0.017608444 0.021534157 5.70E-11 10.24419274 0.113089257 S(ph)SKAS(ph)LGSLEGEAEAEASSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 2 0 S(0.503)S(0.503)KAS(0.497)LGS(0.497)LEGEAEAEASSPK 66.045 0.017055 12550000 4006.9 4044.9 3294.5 3693.8 2663.7 3141.5 3181.3 3617.8 4090.7 3704.4 TRUE FALSE FALSE 3958.062362 4101.844208 3351.839391 4120.894536 2527.761449 2940.768289 3451.519543 3722.475335 3724.817547 3608.159154 1.096975547 1.136824634 0.928961071 1.142104425 0.700568168 0.815032864 0.956587389 1.031682688 1.032331831 1 11.81704726 -8.780191968 24.99987331 1.050729494 0.877373741 0.435347188 0.100435415 180.765263 240985.4101 0.015073633 0.027357212 1.66E-09 8.780191968 -0.173355753 S(ph)SLETLEDIEENAPLR ddPTM_HeLa_Romidepsin_16h_R1 2 SSLETLEDIEENAPLR 16 0 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 0 S(0.987)S(0.012)LET(0.001)LEDIEENAPLR;S(0.922)S(0.078)LETLEDIEENAPLR ; 273.84 3.91E-87 5611300 902.35 877.68 800.31 771.11 892.2 823.43 738.19 772.91 1019.03 678.21 TRUE FALSE FALSE 891.3518111 890.0360021 814.2390598 860.2693664 846.6677047 770.8154805 800.8918402 795.2729314 927.8854046 660.5900064 1.349326818 1.347334948 1.232593669 1.302274267 1.281684095 1.16685913 1.212388671 1.203882777 1.404631308 1 9.367611334 -12.38956522 1.105190037 0.999452675 1.267778863 0 0.136546559 0.221863425 0.483205215 0.045901156 0.011658869 4.08E-13 12.38956522 0.268326188 S(ph)SLETLEDIEENAPLRR ddPTM_HeLa_Romidepsin_16h_R1 3 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 0 S(0.5)S(0.5)LETLEDIEENAPLRR;S(0.458)S(0.458)LET(0.084)LEDIEENAPLRR;S(0.38)S(0.38)LET(0.24)LEDIEENAPLRR ;; 221.81 5.36E-36 8166000 1026.88 1051.5 882.04 744.44 709.68 783.39 767.2 799.68 893.74 895.32 TRUE FALSE FALSE 1014.363992 1066.303045 897.3915362 830.5156555 673.4623814 733.3339073 832.3659489 822.8174791 813.801656 872.0594573 1.163182147 1.22274122 1.029048568 0.952361274 0.772266588 0.840921913 0.954483025 0.943533692 0.93319515 1 9.768282692 -9.23368528 2.973467245 1.090639688 0.880566514 0.497654617 0.090406188 0.158778218 2.827461482 0.014409602 0.024281863 5.84E-10 9.23368528 -0.210073174 S(ph)SLGSHQLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 0 S(0.989)S(0.009)LGS(0.003)HQLPR 103.44 0.0093404 5701800 1232.7 1315.8 1122.6 930.57 1528.8 2020.2 1634.9 1466.3 1657.8 1615.1 TRUE FALSE FALSE 1217.675378 1334.323867 1142.138382 1038.166882 1450.779631 1891.11574 1773.768365 1508.725077 1509.522216 1573.139469 0.774041591 0.848191717 0.726024872 0.659933148 0.922219333 1.202128468 1.127534081 0.959053604 0.959560322 1 10.61943087 -8.44092392 6.209652945 0.856004296 1.096518646 0.526982927 0.111713861 0.180853162 11.0958107 0.01900107 0.042719495 3.62E-09 8.44092392 0.24051435 S(ph)SLGSLQT(ph)PEAVTTR ddPTM_HeLa_Romidepsin_16h_R1 2 SSLGSLQTPEAVTTR 15 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 2 0 S(0.843)S(0.047)LGS(0.111)LQT(0.993)PEAVT(0.003)T(0.003)R;S(0.988)S(0.012)LGS(0.061)LQT(0.939)PEAVTTR ; 158.14 0.0013371 24755000 6369.8 5139 5648.2 5016.1 4342.5 4037.7 2945.5 4067.3 5694.7 4907.5 TRUE FALSE FALSE 6292.162428 5211.346977 5746.504552 5596.085083 4120.886021 3779.704001 3195.690696 4184.980908 5185.351769 4780.002443 1.3163513 1.090239396 1.202196991 1.170728499 0.862109606 0.790732651 0.668554197 0.875518571 1.084801071 1 12.22279564 -8.668301606 3.617840226 1.154179738 0.774169701 0.773604263 0.091922368 0.106013581 2.693275122 0.018472086 0.03831891 2.15E-09 8.668301606 -0.380010037 S(ph)SLGSLQTPEAVTTR ddPTM_HeLa_Romidepsin_16h_R1 3 SSLGSLQTPEAVTTR 15 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 S(0.977)S(0.01)LGS(0.003)LQT(0.01)PEAVTTR;S(0.98)S(0.019)LGSLQTPEAVTTR;S(0.985)S(0.015)LGSLQTPEAVTTR ;; 244.18 2.95E-57 72696000 4465.41 4634 4658.6 4782.5 4269 4736.3 3796.05 3719.8 4674.8 4116.3 TRUE FALSE FALSE 4410.983865 4699.237574 4739.680979 5335.475152 4051.137 4433.665716 4118.486392 3827.426544 4256.67418 4009.357933 1.100172132 1.172067362 1.182154614 1.330755508 1.010420389 1.10582936 1.027218438 0.954623311 1.061684751 1 11.9691555 -5.734617308 10.76173848 1.077824234 0.725683542 0 0.106594712 0 0 0.015080698 0 1.84E-06 5.734617308 -0.352140692 S(ph)SLS(ph)GDEEDELFK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 2 0 S(0.952)S(0.048)LS(1)GDEEDELFK 161.87 0.0036416 22410000 3589 3698.9 3395.2 2772.1 3765.8 4054.7 4233.5 4536.7 3596.5 3156.3 TRUE FALSE FALSE 3545.255888 3750.973211 3454.292032 3092.623245 3573.617174 3795.617756 4593.093384 4667.962257 3274.820032 3074.298871 1.153191682 1.220106882 1.123603194 1.005960505 1.162416968 1.234628745 1.494029558 1.518382712 1.065225006 1 11.58604171 -7.894106003 1.760504956 1.087336178 1.542500725 0.854283549 0.065522799 0.124477371 0.706839511 0.01195174 0.06268007 1.28E-08 7.894106003 0.455164546 S(ph)SLSGDEEDELFK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 S(0.983)S(0.016)LS(0.001)GDEEDELFK 182.72 3.89E-07 134680000 8201 7282.7 7540.7 6687.4 6833.8 6519.5 5220.4 6189.3 8118 7260 TRUE FALSE FALSE 8101.043058 7385.226042 7671.94272 7460.628653 6485.045686 6102.924991 5663.820646 6368.37763 7391.905748 7071.384153 1.145609245 1.04438196 1.084928008 1.055045022 0.917082928 0.863045319 0.800949365 0.900584312 1.045326571 1 12.78777692 -8.648623782 2.477074721 1.069967979 0.850330003 0.840176299 0.041653738 0.10597956 1.315617131 0.008615334 0.019206099 2.25E-09 8.648623782 -0.219637976 S(ph)SLSGDEEDELFKGATLK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFKGATLK 18 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 S(0.494)S(0.096)LS(0.41)GDEEDELFKGATLK 74.505 0.0069104 5025000 1187.2 1479.7 715.98 2619.7 1323.1 906.59 911.69 979.17 1569.1 1149.5 TRUE FALSE FALSE 1172.72995 1500.531255 728.4413316 2922.60204 1255.57727 848.6618249 989.1289258 1007.500739 1428.755766 1119.635824 1.047420888 1.340195823 0.650605595 2.610314869 1.12141577 0.757980235 0.883438083 0.899846823 1.276089721 1 10.12881384 -5.726620153 11.50103974 1.093893619 1.044509998 0 0.528811362 0 0 0.065900521 0 1.88E-06 5.726620153 -0.04938362 S(ph)SPAAFINPPIGTVTPALK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPAAFINPPIGTVTPALK 19 0 Q6R954;F8WEE2;Q8WUT1;F8WCX5;F6VRR5;Q9BY77-2;Q9BY77 Q6R954 PDIP46;POLDIP3 Polymerase delta-interacting protein 3 1 0 S(0.5)S(0.5)PAAFINPPIGTVTPALK;S(0.5)S(0.5)PAAFINPPIGTVTPALK ; 145.79 5.82E-05 52320000 7373.8 6717.6 6636.4 5757.1 5426.7 6172.8 6084.3 6083.3 8570.8 7277.1 TRUE FALSE FALSE 7283.925289 6812.170549 6751.903758 6422.76299 5149.755249 5778.378002 6601.10029 6259.310688 7804.206182 7088.039893 1.027636046 0.961079601 0.952576997 0.90614092 0.726541516 0.815229328 0.931301233 0.883080623 1.101038693 1 12.79117101 -9.414535495 1.741513426 1.010651956 0.844353351 0.648187541 0.0600508 0.164000604 0.980295371 0.009140247 0.015332176 3.85E-10 9.414535495 -0.166298605 S(ph)SPAFGDRR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPAFGDRR 9 1 P13716;P13716-2 P13716 ALAD Delta-aminolevulinic acid dehydratase 1 0 S(0.5)S(0.5)PAFGDRR;S(0.5)S(0.5)PAFGDRR ; 103.31 0.0075174 11722700 1193.17 1062.17 742.75 761.68 1205.79 1421.39 1261.28 986.13 1135.19 1018.65 TRUE FALSE FALSE 1178.627185 1077.123257 755.6772522 849.7490254 1144.254037 1330.567766 1368.413092 1014.662116 1033.655763 992.1853262 1.187910317 1.085606921 0.761629135 0.856441839 1.153266438 1.341047616 1.37919102 1.022653822 1.041797068 1 9.954465811 -8.523044646 24.99981767 1.047007271 1.258515224 0.352303691 0.14776371 6.028168182 908407.6328 0.023985747 0.048360968 3.00E-09 8.523044646 0.211507953 S(ph)SPAGNSPAPL ddPTM_HeLa_Romidepsin_16h_R1 1 SSPAGNSPAPL 11 0 A0A087WZG9;B4DSP0;Q86TG7-2 A0A087WZG9 PEG10 Retrotransposon-derived protein PEG10 1 0 S(0.497)S(0.497)PAGNS(0.006)PAPL 98.182 0.021315 3411900 1504.8 1890.5 1808.9 1104.5 2227.5 2514 1928.8 2240.5 2027.9 2238 TRUE FALSE FALSE 1486.458919 1917.114509 1840.383146 1232.207487 2113.822363 2353.363514 2092.632224 2305.325333 1846.519545 2179.856437 0.681906796 0.879468242 0.844268051 0.565270018 0.969707145 1.079595644 0.959986258 1.05755833 0.847083098 1 11.09001741 -8.539210519 24.99692557 0.828001089 1.025059222 0.452430384 0.114672269 227.4312135 348098.4725 0.021002007 0.042012734 2.89E-09 8.539210519 0.197058133 S(ph)SPASSPELPWRPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPASSPELPWRPR 14 1 Q9NYF3 Q9NYF3 FAM53C Protein FAM53C 1 0 S(0.491)S(0.491)PAS(0.014)S(0.005)PELPWRPR 91.592 0.0065589 3676300 1354.4 1290 1337.6 1264.2 1661.5 1516.6 1309.4 1431 1797.7 1540.8 TRUE FALSE FALSE 1337.892052 1308.160654 1360.880367 1410.372752 1576.707455 1419.694155 1420.620403 1472.403727 1636.90921 1500.769794 0.891470536 0.87165977 0.906788218 0.939766217 1.05059914 0.945977298 0.94659448 0.981098989 1.090713057 1 10.55148698 -8.954453091 24.99962562 0.936956974 0.97848419 0.028957702 0.064914795 226.2739554 124195.5887 0.008262713 0.014977446 1.11E-09 8.954453091 0.041527216 S(ph)SPEIQEPIKPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPEIQEPIKPLEK 14 1 A0A075B785;A0A2R8Y566;Q9P260;Q9P260-2 A0A075B785 KIAA1468 LisH domain and HEAT repeat-containing protein KIAA1468 1 0 S(0.5)S(0.5)PEIQEPIKPLEK 78.529 0.014269 6366500 1843 1743.2 1753.7 1231.2 1682.2 1941 1535 1849.8 2059.3 1993.4 TRUE FALSE FALSE 1820.536807 1767.740815 1784.222413 1373.557137 1596.351057 1816.976364 1665.382862 1903.321044 1875.11105 1941.611181 0.937642318 0.910450472 0.918939091 0.707431617 0.822178546 0.935808561 0.857732423 0.980279195 0.965750027 1 10.92303861 -10.46498988 1.009717023 0.982081829 0.865195515 0.287465264 0.0699799 0.40739858 0.837833157 0.016512611 0.017694563 3.43E-11 10.46498988 -0.116886314 S(ph)SPELEDTATSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPELEDTATSSK 13 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 S(0.802)S(0.198)PELEDTATSSK 161.21 0.00039249 6078800 1751.4 1964.4 2224.4 951.69 1065.7 1496.8 2120.1 1451 2043.5 2438.9 TRUE FALSE FALSE 1730.053263 1992.054875 2263.114749 1061.728876 1011.313352 1401.159311 2300.181241 1492.982396 1860.724242 2375.537026 0.728278803 0.838570333 0.952675005 0.446942676 0.425719886 0.589828445 0.968278421 0.628482057 0.783285725 1 11.21403798 -9.27473308 24.95517157 0.870939202 0.620087839 0.388134023 0.155692408 694.0396133 1302860.981 0.027469246 0.042110207 5.31E-10 9.27473308 -0.250851362 S(ph)SPELLPSGVTDENEVTTAVTEK ddPTM_HeLa_Romidepsin_16h_R1 4 SSPELLPSGVTDENEVTTAVTEK 23 0 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 0 S(0.5)S(0.5)PELLPSGVTDENEVTTAVTEK;S(0.5)S(0.5)PELLPSGVTDENEVTTAVTEK;S(0.5)S(0.5)PELLPS(0.001)GVTDENEVTTAVTEK;S(0.5)S(0.5)PELLPSGVTDENEVTTAVTEK ;;; 190.92 5.17E-20 25062000 21221.6 20470.5 21473.2 14402.5 21700.1 22742.4 19321.3 20107.7 22474.1 21420 TRUE FALSE FALSE 20962.94298 20758.68424 21846.93204 16067.78482 20592.66292 21289.23404 20962.45074 20689.48457 20463.96021 20863.50531 1.004766105 0.994975865 1.047136218 0.770138315 0.987018366 1.020405427 1.004742512 0.991659084 0.98084957 1 14.34869395 S(ph)SPEQPIGQGR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPEQPIGQGR 11 0 Q8N201 Q8N201 INTS1 Integrator complex subunit 1 1 0 S(0.999)S(0.001)PEQPIGQGR;S(0.998)S(0.002)PEQPIGQGR ; 193.62 8.41E-09 97801000 6087 6239.5 6376.8 5539.7 5664.8 5660.2 4174 5699.6 6146.4 5631.9 TRUE FALSE FALSE 6012.809303 6327.339845 6487.785529 6180.226179 5375.704118 5298.531487 4528.539456 5864.508934 5596.65059 5485.582426 1.096111376 1.153449051 1.182697665 1.126630811 0.979969619 0.965901353 0.825534848 1.069076805 1.020247287 1 12.42142909 -8.595816398 5.302765199 1.071842939 0.945377794 0.405061225 0.077813198 0.184692078 9.434030949 0.012484647 0.025442524 2.54E-09 8.595816398 -0.126465145 S(ph)SPEQPRPSTSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPEQPRPSTSK 12 1 P29590-12;P29590-11;H3BT57;P29590-13;H3BUJ5;H3BRN3;P29590-5;P29590;P29590-4;P29590-9;P29590-3;P29590-8;H3BVD2;P29590-2 P29590-12;P29590-5;P29590-2 PML Protein PML 1 0 S(0.93)S(0.07)PEQPRPSTSK 75.02 0.022139 328100000 4716.8 4656.1 4965.4 5060.1 7180.8 8616.2 7790.4 5590.6 7242.5 6934.1 TRUE FALSE FALSE 4659.309827 4721.648698 5051.820704 5645.17257 6814.336981 8065.652628 8452.116382 5752.35519 6594.712661 6753.951082 0.689864314 0.699094299 0.747980055 0.835832611 1.008940826 1.194212473 1.251432869 0.851702229 0.976422923 1 12.72151601 -8.631564661 3.40188808 0.827052602 1.113495395 0.454055911 0.137306102 0.184026011 4.175120981 0.023326638 0.049404168 2.34E-09 8.631564661 0.286442793 S(ph)SPGAVAGLSNAPGTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;U3KPY3;Q9BWG4-2;Q9BWG4 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 0 S(0.998)S(0.002)PGAVAGLSNAPGTPR 191.36 2.55E-13 31898000 884.75 769.94 1007.4 823.81 796.82 909.07 664.66 835.83 824.88 941.81 TRUE FALSE FALSE 873.9663267 780.7792355 1024.933374 919.0627883 756.1553021 850.9833609 721.1162038 860.0134223 751.1006669 917.3416404 0.952716293 0.851132447 1.117286439 1.001876234 0.82428974 0.927662414 0.786093394 0.937506142 0.81877965 1 9.841315319 -8.767920393 24.99958273 0.979754119 0.867172202 0.162185157 0.089454124 123.415212 476058.6178 0.010374165 0.019133258 1.71E-09 8.767920393 -0.112581917 S(ph)SPGLYTSPGQDSLQPTAVSPPYGGDISPVSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGLYTSPGQDSLQPTAVSPPYGGDISPVSPSR 34 0 Q8N3V7-2;Q8N3V7-3;Q8N3V7 Q8N3V7-2 SYNPO Synaptopodin 1 0 S(0.295)S(0.295)PGLY(0.054)T(0.159)S(0.159)PGQDS(0.033)LQPT(0.006)AVSPPYGGDISPVSPSR 47.674 0.0073807 5583800 736.52 768.95 497.31 642.23 727.24 669.69 525.68 793.71 600.75 813.89 TRUE FALSE FALSE 727.5430109 779.7752983 505.9654719 716.4876544 690.1262291 626.8989703 570.3312461 816.6747466 547.0174154 792.7450205 0.9177516 0.983639478 0.638244907 0.903805935 0.870552588 0.790795217 0.719438447 1.030185905 0.690029456 1 9.6307131 S(ph)SPGPDTLVVLEFNPASK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGPDTLVVLEFNPASK 18 0 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 0 S(0.5)S(0.5)PGPDTLVVLEFNPASK 168.42 3.86E-07 12843000 1532.9 1370.7 1808.4 793.32 1831 2576.9 2316 2068.8 1520.8 1821.5 TRUE FALSE FALSE 1514.216425 1389.996751 1839.874443 885.0473911 1737.557238 2412.244407 2512.720982 2128.657464 1384.775839 1774.177167 0.85347532 0.783459948 1.037029716 0.498849499 0.979359485 1.359641219 1.416273994 1.19979983 0.780517225 1 10.79293437 -8.320469227 4.889436381 0.893753298 1.33513335 0.65867611 0.155802872 0.100159745 5.0178334 0.021874955 0.050894063 4.78E-09 8.320469227 0.441380053 S(ph)SPGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR 36 1 P40222 P40222 TXLNA Alpha-taxilin 1 0 S(0.459)S(0.459)PGQPEAGPEGAQERPS(0.08)QAAPAVEAEGPGS(0.001)S(0.001)QAPR 50.439 0.0037724 48748000 562.43 393.69 482.32 234.37 291.96 286.79 221.93 356.34 360.45 316.59 TRUE FALSE FALSE 555.5748868 399.2323782 490.7145773 261.4689621 277.0601917 268.4650446 240.7807287 366.6501357 328.2104492 308.3649462 1.801679775 1.294674972 1.59134358 0.847920509 0.898481475 0.87060818 0.780830414 1.189013668 1.064357195 1 8.268494964 -9.251154671 24.51314888 1.395067423 0.906137905 0.441423568 0.2407935 455.9500668 1086736.193 0.047265397 0.077787919 5.61E-10 9.251154671 -0.488929518 S(ph)SPGQTPEEGAQALAEFAALHGPALR ddPTM_HeLa_Romidepsin_16h_R1 5 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 1 0 S(0.44)S(0.44)PGQT(0.12)PEEGAQALAEFAALHGPALR;S(0.483)S(0.483)PGQT(0.035)PEEGAQALAEFAALHGPALR;S(0.5)S(0.5)PGQTPEEGAQALAEFAALHGPALR;S(0.476)S(0.476)PGQT(0.049)PEEGAQALAEFAALHGPALR;S(0.499)S(0.499)PGQT(0.001)PEEGAQALAEFAALHGPALR ;;;; 185.64 1.22E-19 1409189700 8256.03 7835.19 7310.55 7769.56 7979.75 7854.59 6090.46 7870.9 8455.16 7568.28 TRUE FALSE FALSE 8155.402331 7945.49401 7437.787056 8667.913084 7572.513581 7352.707049 6607.78352 8098.632073 7698.909313 7371.654995 1.106319047 1.077843987 1.008971128 1.175843564 1.027247421 0.997429621 0.896377208 1.098617892 1.044393602 1 12.84777284 -8.386389196 4.273575679 1.059383812 0.987843886 0.17714004 0.065911343 0.306799347 9.217890851 0.009803379 0.022726338 4.11E-09 8.386389196 -0.071539926 S(ph)SPGSVAASPSGGGGR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGSVAASPSGGGGR 16 0 Q9BXB5-2;Q9BXB5 Q9BXB5-2 OSBPL10 Oxysterol-binding protein-related protein 10 1 0 S(0.998)S(0.002)PGSVAASPSGGGGR 187.08 6.52E-10 25965000 1671.3 1608.6 1599.5 1245.6 1285.6 1350.7 1230.1 954.27 1447.4 1423.6 TRUE FALSE FALSE 1650.929553 1631.245913 1627.338627 1389.622133 1219.991035 1264.394629 1334.584663 981.8802969 1317.940919 1386.614667 1.190618845 1.17642338 1.17360552 1.002168927 0.879834221 0.911857244 0.962476956 0.708113307 0.950473805 1 10.43735121 -8.933604671 3.193097872 1.105721793 0.875013531 0.570380641 0.09468402 0.145108791 3.008456961 0.01485942 0.028017364 1.17E-09 8.933604671 -0.230708262 S(ph)SPKSEIEVISEPPEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPKSEIEVISEPPEEK 17 1 B7ZM87;O75044;A0A075B7E6;A0A075B7E9;Q5VZB4 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 0 S(0.497)S(0.497)PKS(0.005)EIEVISEPPEEK;S(0.495)S(0.495)PKS(0.009)EIEVISEPPEEK ; 87.208 0.0042366 27695000 6426.3 5763.4 6066.2 6945.6 7757 7710 7143 8595.5 7617.6 6256.8 TRUE FALSE FALSE 6347.973784 5844.537296 6171.779666 7748.682952 7361.131345 7217.355883 7749.726242 8844.197231 6936.262777 6094.247434 1.041633746 0.959025271 1.0127222 1.27147495 1.207881929 1.184289933 1.271646143 1.451236978 1.138165598 1 12.57323236 -5.723073518 0.315024203 0.996700856 2.478121077 0.704847371 0.079545219 5.678623596 0.189827084 0.025496154 3.936738691 1.89E-06 5.723073518 1.48142022 S(ph)SPLSWR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPLSWR 7 0 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 S(0.991)S(0.009)PLSWR 132.76 0.01394 19049000 3451.4 3141.9 2921.3 2845.1 3040.5 2846 2201.5 1992.3 3337.8 3170 TRUE FALSE FALSE 3409.333009 3186.131751 2972.144001 3174.063849 2885.331939 2664.149785 2388.495355 2049.944057 3039.258808 3087.642943 1.104186291 1.031897732 0.962593168 1.027989281 0.934477202 0.862842574 0.77356592 0.663918755 0.984329751 1 11.59229021 -7.650241966 0.6935086 1.047271817 0.537143671 0.905287203 0.038785753 0.430307136 0.195383253 0.007886691 0.154420015 2.24E-08 7.650241966 -0.510128146 S(ph)SPNPFITGLTR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPNPFITGLTR 12 0 A0A0D9SGJ6;J3KQV8;O43426 A0A0D9SGJ6 SYNJ1 Synaptojanin-1 1 0 S(0.896)S(0.104)PNPFITGLTR 128.57 0.004518 17523000 1875.6 1877.5 1641.9 730.86 1647.2 1816.7 1585.2 1357.2 1873.8 1928.9 TRUE FALSE FALSE 1852.739466 1903.931494 1670.476581 815.365472 1563.137237 1700.618733 1719.846848 1396.468441 1706.202635 1878.7869 0.986136036 1.01338342 0.889125095 0.433985074 0.831992834 0.905168507 0.915402832 0.743281977 0.908140585 1 10.87558572 -9.520817849 23.64330187 0.992693074 0.773258419 0.373963941 0.128348598 30.200421 346471.6313 0.019883996 0.028408673 3.01E-10 9.520817849 -0.219434655 S(ph)SPNPFVGS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPNPFVGSPPK 12 0 P98082-3;P98082 P98082-3 DAB2 Disabled homolog 2 2 0 S(0.769)S(0.231)PNPFVGS(1)PPK 153.41 0.014524 15003000 3581.6 3169 3195.6 2614.5 3476.5 3343 2896.9 2696 3873.4 3518.3 TRUE FALSE FALSE 3537.946082 3213.613265 3251.218078 2916.800792 3299.081232 3129.393089 3142.962614 2774.004506 3526.953403 3426.894059 1.032406027 0.937762653 0.948736092 0.851149975 0.962703012 0.913186412 0.917146127 0.809480672 1.02919826 1 11.74268588 -9.940938127 1.847186199 1.015277236 0.899158729 0.616475898 0.04239447 0.16090961 1.099245971 0.007145585 0.009593695 1.15E-10 9.940938127 -0.116118507 S(ph)SPNPFVGSPPK ddPTM_HeLa_Romidepsin_16h_R1 3 SSPNPFVGSPPK 12 0 P98082-3;P98082 P98082-3 DAB2 Disabled homolog 2 1 0 S(0.5)S(0.5)PNPFVGSPPK;S(0.907)S(0.093)PNPFVGSPPK;S(0.847)S(0.14)PNPFVGS(0.014)PPK ;; 172.58 9.47E-05 271953400 14170.4 13981 14357.5 10343.8 12192.5 11772.1 9851.7 10614.9 14618.4 14247 TRUE FALSE FALSE 13997.68571 14177.82488 14607.38626 11539.79883 11570.27123 11019.9008 10688.50315 10922.02538 13310.89369 13876.86089 1.008706928 1.02168819 1.052643417 0.831585682 0.833781597 0.794120579 0.770239267 0.787067441 0.959215042 1 13.76039363 -9.168403007 4.585832246 1.009028942 0.79872698 0.935706708 0.026948015 0.034972236 1.264129802 0.003659763 0.00615704 6.79E-10 9.168403007 -0.210301962 S(ph)SPNVANQPPS(ph)PGGK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPNVANQPPSPGGK 15 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 2 0 S(0.921)S(0.079)PNVANQPPS(1)PGGK;S(0.689)S(0.311)PNVANQPPS(1)PGGK ; 151.22 7.20E-05 0 2877.8 2845.2 2673.9 2959.1 3488 3921.5 2986.7 3356.2 2888.7 3151.7 TRUE FALSE FALSE 2842.724267 2885.2548 2720.438108 3301.245065 3309.994344 3670.928806 3240.390223 3453.306352 2630.327437 3069.81838 0.9260236 0.939878013 0.886188618 1.075387745 1.078237842 1.195813026 1.055564148 1.124922039 0.856834872 1 11.58393759 -9.091399561 4.843942249 0.956654182 1.111589331 0.728329418 0.054528864 0.093957613 3.685877711 0.007359973 0.012473582 8.10E-10 9.091399561 0.15493515 S(ph)SPNVANQPPSPGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPNVANQPPSPGGK 15 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 S(0.831)S(0.06)PNVANQPPS(0.109)PGGK 122.5 0.00011928 0 1796.7 1706.8 1666.6 2042 2719.8 2182.3 2410.7 2087.5 1663 1879.3 TRUE FALSE FALSE 1774.801129 1730.828375 1695.606474 2278.105648 2580.998457 2042.858073 2615.464798 2147.898519 1514.257115 1830.475515 0.969584742 0.945562156 0.926320216 1.244543087 1.410015286 1.116025894 1.428844459 1.173410134 0.827247949 1 10.83800276 -9.204407542 5.664118493 0.977622618 1.284530805 0.727808977 0.102505774 0.075530525 5.282152178 0.012147259 0.020203535 6.25E-10 9.204407542 0.306908187 S(ph)SPPGHYYQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPPGHYYQK 10 0 D6RI08;D6RDK1;D6RIV2;D6R9T5;D6RG39;D6RIT9;D6RDK6;D6RBN5;Q9NX40-3;Q9NX40-2;Q9NX40-4;Q9NX40 D6RI08 OCIAD1 OCIA domain-containing protein 1 1 0 S(0.988)S(0.012)PPGHYYQK 124.39 0.00025392 0 3352.6 2767.5 3080.2 5638.3 4593.7 4185.2 2841.6 3284.1 4822 4169.1 TRUE FALSE FALSE 3311.737222 2806.460938 3133.809589 6290.226775 4359.266348 3917.779227 3082.965433 3379.120252 4390.708243 4060.786181 0.815540901 0.691112709 0.771724846 1.549016987 1.073503049 0.964783432 0.759204079 0.832134494 1.081245859 1 11.98754335 S(ph)SPPLPPPAEER ddPTM_HeLa_Romidepsin_16h_R1 3 SSPPLPPPAEER 12 0 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 0 S(0.999)S(0.001)PPLPPPAEER;S(0.999)S(0.001)PPLPPPAEER;S(0.962)S(0.038)PPLPPPAEER ;; 180.24 1.34E-06 119146000 7449.7 7179.6 5762.2 6286.1 5772 5720.1 5810.9 6009.1 7973.9 7383.9 TRUE FALSE FALSE 7358.900191 7280.674597 5862.488674 7012.928459 5477.433302 5354.604071 6304.477701 6182.963828 7260.694413 7192.065214 1.023197089 1.012320437 0.815132858 0.975092446 0.761593943 0.744515506 0.87658795 0.859692403 1.009542349 1 12.81219039 -9.624380371 1.398633775 1.013279741 0.825854723 0.611472736 0.064637783 0.186375501 0.73466411 0.010947943 0.01731993 2.37E-10 9.624380371 -0.187425018 S(ph)SPPLRTPDVLESSGPAVR ddPTM_HeLa_Romidepsin_16h_R1 4 SSPPLRTPDVLESSGPAVR 19 1 E9PJN1;O75676-2;O75676;A0A0A6YYC0 E9PJN1 RPS6KA4 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-4 1 0 S(0.442)S(0.407)PPLRT(0.151)PDVLESSGPAVR;S(0.48)S(0.474)PPLRT(0.046)PDVLESSGPAVR;S(0.459)S(0.459)PPLRT(0.082)PDVLESSGPAVR;S(0.48)S(0.48)PPLRT(0.041)PDVLESSGPAVR ;;; 82.635 0.0027738 80730000 2385.97 1973.85 1661.59 1751.48 2693.25 2205.99 2066.57 2164.21 2584.76 2451.57 TRUE FALSE FALSE 2356.88888 2001.637912 1690.509277 1953.994359 2555.803403 2065.034359 2242.104404 2226.828002 2353.572592 2387.877858 0.987022377 0.838249706 0.707954668 0.818297449 1.070324177 0.864798989 0.938952718 0.932555237 0.985633576 1 11.22151333 -10.30291554 10.15670487 0.993914112 0.881310694 0.243195885 0.088304715 0.70221234 169.7598214 0.015796486 0.018074682 4.98E-11 10.30291554 -0.112603418 GGHMIAVS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 2 GGHMIAVSPQK 11 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 GGHMIAVS(1)PQK;GGHMIAVS(1)PQK ; 71.933 0.022619 13530200 10686.9 10285.9 11203.8 9372.1 5689.6 4791.6 4236.7 3577.6 10786.7 10257.2 TRUE FALSE FALSE 10556.64395 10430.70517 11398.79744 10455.7463 5399.238481 4485.432224 4596.565192 3681.112211 9821.910536 9990.716465 1.056645336 1.044039755 1.140938939 1.046546195 0.540425554 0.448960016 0.460083639 0.368453276 0.983103721 1 13.28637243 -8.708403024 4.133033155 1.040627488 0.439527578 0.97376522 0.047707745 0.024957459 0.876151602 0.007477491 0.015135454 1.96E-09 8.708403024 -0.60109991 down S(ph)SPQLDPLR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPQLDPLR 9 0 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.775)S(0.225)PQLDPLR;S(0.674)S(0.326)PQLDPLR ; 131.62 0.0074446 16449000 5662.6 4905.5 8201.4 4792.1 7154.8 7449.5 6806.9 5999.1 6292.1 5131.8 TRUE FALSE FALSE 5593.582053 4974.559758 8344.141927 5346.18515 6789.663858 6973.500992 7385.077916 6172.674493 5729.318817 4998.475096 1.119057702 0.995215473 1.669337501 1.069563226 1.358347041 1.395125685 1.477466182 1.234911523 1.146213336 1 12.28727232 -9.801697823 24.99999526 1.053217024 1.359762176 0.487208218 0.151633362 86.9924187 54020.85889 0.022433601 0.029483729 1.58E-10 9.801697823 0.306545152 S(ph)SPQLDPLRK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPQLDPLRK 10 1 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.828)S(0.172)PQLDPLRK;S(0.985)S(0.015)PQLDPLRK ; 109.11 0.022006 181035000 9207.6 8889.1 9858 5134.7 8765.7 8524.1 6383 6052.7 9185.9 8981.4 TRUE FALSE FALSE 9095.37423 9014.240983 10029.57435 5728.398173 8318.35362 7979.43752 6925.171861 6227.825325 8364.290097 8748.061933 1.039701628 1.030427202 1.146491009 0.654819115 0.950879599 0.912137749 0.791623552 0.711909149 0.956130645 1 13.09474772 -9.269023832 24.99367443 1.028995706 0.817708243 0.607045577 0.09226602 309.8453152 1021057.829 0.013376943 0.020680441 5.38E-10 9.269023832 -0.211287464 S(ph)SPSARPPDVPGQQPQAAK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSARPPDVPGQQPQAAK 19 1 A0A0A6YYC7;Q96JP5-2;Q96JP5 A0A0A6YYC7 ZFP91-CNTF;ZFP91 E3 ubiquitin-protein ligase ZFP91 1 0 S(0.358)S(0.358)PS(0.285)ARPPDVPGQQPQAAK 68.676 0.0063664 22208000 1499.1 1403.8 1641.2 1132.1 963.96 1085.3 948.62 1066 1582.3 1743.5 TRUE FALSE FALSE 1480.828393 1423.562733 1669.764398 1262.998729 914.7655242 1015.952833 1029.195759 1096.843028 1440.775125 1698.203619 0.87199696 0.838275645 0.98325335 0.74372632 0.538666573 0.598251483 0.60604968 0.645884284 0.848411291 1 10.72979374 -9.041093059 3.594568358 0.931347572 0.599153114 0.863105588 0.057973549 0.06233215 1.660773157 0.009820101 0.017422713 9.10E-10 9.041093059 -0.332194458 S(ph)SPSPALEQPFR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSPALEQPFR 12 0 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 S(0.813)S(0.084)PS(0.102)PALEQPFR 156.52 0.0011826 12930000 1651.6 1482.3 1600.6 1244.8 1570.7 1493.6 1078 1647.9 1656.2 1684.8 TRUE FALSE FALSE 1631.469664 1503.167858 1628.457772 1388.729633 1490.541318 1398.16378 1169.565293 1695.579387 1508.065324 1641.028653 0.994175002 0.915991232 0.992339633 0.846255567 0.908296948 0.85200449 0.712702542 1.033241792 0.91897562 1 10.68038471 -9.460228763 0.970223093 0.997633841 0.85543347 0.177791758 0.082648756 0.381086385 0.715019966 0.013374954 0.025254124 3.47E-10 9.460228763 -0.14220037 S(ph)SPSPEVVKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSPEVVKPK 11 1 A0A1W2PNZ9;Q15652-3;Q15652;Q15652-2 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 0 S(0.677)S(0.115)PS(0.208)PEVVKPK 69.229 0.029675 18369000 2666.5 2994.4 2902.2 3082.3 2375.8 1928 1883.1 2136.7 3103.6 3207.7 TRUE FALSE FALSE 2633.999672 3036.555242 2952.711574 3438.690029 2254.554061 1804.807022 2043.050467 2198.522043 2826.006243 3124.363492 0.84305161 0.971895636 0.945060196 1.100604983 0.721604278 0.577655906 0.653909339 0.703670379 0.90450623 1 11.60934659 -8.593183733 6.765505472 0.940182208 0.646428433 0.811979464 0.070203686 0.078521392 6.081928521 0.011855836 0.023873332 2.55E-09 8.593183733 -0.293753775 S(ph)SPVGGGPR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPVGGGPR 9 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 S(0.66)S(0.34)PVGGGPR;S(0.654)S(0.346)PVGGGPR ; 133.99 0.0069402 29908000 2747.7 3394.5 5987.5 3266.7 2444.3 2111.6 4082.3 638.9 5308.7 4312.3 TRUE FALSE FALSE 2714.209976 3442.28786 6091.709926 3644.411224 2319.55825 1976.675575 4429.05046 657.3855635 4833.876576 4200.265824 0.646199571 0.819540478 1.450315333 0.867662043 0.552240822 0.470607256 1.054469085 0.156510466 1.150850155 1 12.03626492 -8.768245263 21.57048179 0.881541844 0.587611339 0.295335978 0.298031971 37.44014862 118666.2888 0.043316438 0.080052765 1.71E-09 8.768245263 -0.293930505 S(ph)SPVTVNQTDKEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPVTVNQTDKEK 13 1 Q8IVL0-3;Q8IVL0-2;Q8IVL0;H0YHA8;A0A2R8YFX5 Q8IVL0-3 NAV3 Neuron navigator 3 1 0 S(0.5)S(0.5)PVT(0.001)VNQTDKEK 70.41 0.023469 5341600 2319.8 1768.8 2300.7 2097.9 2470.1 2145.2 1922.4 1677.9 2574.4 1937.6 TRUE FALSE FALSE 2291.525385 1793.701213 2340.742718 2340.469069 2344.04158 2008.128643 2085.688608 1726.447389 2344.139216 1887.260873 1.214207012 0.950425688 1.240285724 1.240140726 1.242033687 1.064044019 1.105140597 0.914790008 1.242085421 1 10.88207814 -7.098821363 2.107399036 1.12036395 0.786100542 0.271054322 0.106697498 1.567214312 5.13557569 0.016250211 1.155031772 7.96E-08 7.098821363 -0.334263408 S(ph)SPVVNDGVVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPVVNDGVVR 11 0 H0YAM1;H0Y8R1;F5H5I6;H0YAK1;Q12849-5;Q12849 H0YAM1 GRSF1 G-rich sequence factor 1 1 0 S(0.732)S(0.268)PVVNDGVVR;S(0.961)S(0.039)PVVNDGVVR ; 161.87 0.0011142 16716200 3982.9 3372.5 3527.7 3431.8 3689.4 3988.9 3392.2 3425.8 3910.7 3529.5 TRUE FALSE FALSE 3934.354883 3419.978144 3589.098139 3828.600863 3501.116151 3734.022164 3680.333383 3524.920118 3560.917197 3437.803081 1.144438698 0.994815021 1.044009227 1.113676605 1.018416724 1.086165227 1.07054805 1.025340904 1.035811858 1 11.74727119 -7.254793534 22.28032306 1.063997864 1.025340851 0.016135016 0.046504443 524.2470113 1757308.75 0.007952095 0.095743865 5.56E-08 7.254793534 -0.038657013 S(ph)SRGQEEISGALPVASPASSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSRGQEEISGALPVASPASSR 21 1 H0Y9D5;H0Y8S9;Q9UBK8;Q9UBK8-1 H0Y9D5 MTRR Methionine synthase reductase 1 0 S(0.5)S(0.5)RGQEEISGALPVASPASSR;S(0.499)S(0.499)RGQEEIS(0.002)GALPVASPASSR ; 113.33 0.0013233 75863000 4358.3 4026.1 3760.9 5200.2 5467.3 4947.7 4533 5188.4 4844.8 4451.8 TRUE FALSE FALSE 4305.179363 4082.779541 3826.356887 5801.471592 5188.28328 4631.557938 4918.032907 5338.518168 4411.468954 4336.141594 0.992859497 0.9415697 0.882433565 1.337934075 1.196520724 1.068128851 1.134195644 1.23116786 1.017371979 1 12.08219615 -9.270909857 24.99994343 0.983751147 1.183482596 0.694990564 0.074536388 325.065854 858099.9257 0.011565325 0.017807882 5.36E-10 9.270909857 0.199731449 S(ph)SRIKRSAPLS(ph)DY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 SSRIKRSAPLSDYK 14 3 A0A0A0MSD0;Q4LDE5-4;Q4LDE5 A0A0A0MSD0 SVEP1 "Sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1" 3 0 S(0.494)S(0.494)RIKRS(0.029)APLS(0.992)DY(0.991)K 46.481 0.025716 3087700 1411.1 1390.7 1345 927.09 1384.9 1620.9 1468.7 1353.6 1422.7 1434.8 TRUE FALSE FALSE 1393.90097 1410.278311 1368.409161 1034.284508 1314.223385 1517.329721 1593.451341 1392.76428 1295.450149 1397.523689 0.997407759 1.009126587 0.979167059 0.740083704 0.940394353 1.085727371 1.140196301 0.996594398 0.926961138 1 10.44865702 -8.250990983 23.69428118 0.974769849 1.080775074 0.288810033 0.084578655 408.8778399 927224.3358 0.012442654 0.031307227 5.61E-09 8.250990983 0.106005225 S(ph)SS(ph)PVTELASRS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 0 S(0.777)S(0.403)S(0.82)PVT(0.002)ELAS(0.367)RS(0.632)PIR 73.346 0.024054 7282400 2623.4 1783.4 2043.4 1797.8 1740.7 1709.5 1915.1 2054 2298.5 2223.7 TRUE FALSE FALSE 2591.424992 1808.506752 2078.96452 2005.670095 1651.865584 1600.268467 2077.768546 2113.429249 2092.916403 2165.927953 1.196450227 0.834980106 0.959849341 0.926009608 0.762659525 0.738837349 0.959297165 0.975761565 0.966290869 1 11.08076954 -10.25124279 24.8417209 1.092768163 0.87764757 0.3851966 0.097494871 416.1545857 1013868.629 0.017924731 0.021819441 5.61E-11 10.25124279 -0.215120593 S(ph)SS(ph)VGSSSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.92)S(0.057)S(0.986)VGS(0.013)S(0.019)S(0.004)S(0.001)YPISPAVSR 173.77 4.98E-12 0 1371.7 1365.9 1126.1 1016.4 1267 991.31 867.18 1013 1320.5 1366.7 TRUE FALSE FALSE 1354.981193 1385.129176 1145.699298 1133.92095 1202.340262 927.9684903 940.8382476 1042.309557 1202.391173 1331.192937 1.017869878 1.040517221 0.860656082 0.851808118 0.903205109 0.697095413 0.706763251 0.782989098 0.903243354 1 10.37850397 -8.9842129 0.834593193 1.012256008 0.724215924 0.70344282 0.063078399 0.18277861 0.24390321 0.009620715 0.027955494 1.04E-09 8.9842129 -0.288040084 S(ph)SSAASMAEEEASAVSTAAAQFTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSAASMAEEEASAVSTAAAQFTK 24 0 Q9HCK8-2;Q9HCK8;H0YJG4;H0YJA4 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 1 0 S(0.428)S(0.428)S(0.137)AAS(0.006)MAEEEASAVSTAAAQFTK 73.519 0.00026301 3183700 968.17 889.58 539.31 589.28 652.12 586.66 706.84 472.29 913.27 736.02 TRUE FALSE FALSE 956.3695716 902.1035306 548.6964643 657.4153262 618.839883 549.1743194 766.878972 485.954966 831.5848439 716.8980943 1.334038379 1.258342766 0.765375817 0.917027582 0.863218759 0.766042376 1.069718246 0.677857801 1.159976363 1 9.485624247 -9.761465233 24.99999855 1.169692985 0.854260382 0.637694619 0.126886269 0.441781113 426773.4558 0.024797678 0.03378935 1.73E-10 9.761465233 -0.315432603 S(ph)SSDPPAVHPPLPPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSDPPAVHPPLPPLR 16 0 O43150 O43150 ASAP2 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2" 1 0 S(0.465)S(0.071)S(0.465)DPPAVHPPLPPLR 118.5 0.0012244 6977200 3872.8 3735.6 3616.8 3991.1 4874.1 4836.8 3910.1 3918 4540.2 3894.3 TRUE FALSE FALSE 3825.596824 3788.189875 3679.748887 4452.569761 4625.356489 4527.74409 4242.223796 4031.361148 4134.113141 3793.125525 1.008560565 0.998698791 0.970109969 1.173852469 1.219405068 1.19367104 1.118397946 1.062807208 1.089896212 1 11.8891714 -9.25810603 24.98535121 1.0013458 1.15754863 0.66094431 0.049782831 103.9677709 779296.4306 0.006529721 0.0105444 5.52E-10 9.25810603 0.15620283 S(ph)SSERSTPPYLFPEYPEASK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSERSTPPYLFPEYPEASK 20 1 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 1 0 S(0.196)S(0.196)S(0.196)ERS(0.196)T(0.196)PPY(0.022)LFPEYPEASK 52.272 0.020216 7636700 2107 1912 2325.9 3268.9 1668.2 1445.9 1347.4 1302.9 2134.9 1877.6 TRUE FALSE FALSE 2081.319074 1938.917186 2366.381314 3646.865599 1583.065529 1353.511656 1461.848122 1340.597356 1943.949197 1828.819681 1.138066861 1.0602014 1.293939112 1.994108898 0.865621442 0.740101209 0.799339671 0.733039659 1.062952907 1 10.83669712 -8.54184397 24.99959076 1.154876418 0.768541541 0.385905624 0.277191253 236.5643073 311833.5004 0.042867698 0.085745225 2.87E-09 8.54184397 -0.386334877 S(ph)SSESLIFSGNQGR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSESLIFSGNQGR 14 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 0 S(0.893)S(0.092)S(0.015)ESLIFSGNQGR;S(0.455)S(0.455)S(0.09)ESLIFSGNQGR ; 170.74 5.16E-05 13580100 4093.9 4528.9 3625.6 3917.5 3398.7 2768.9 2374.1 2555.9 4946.8 4218.1 TRUE FALSE FALSE 4044.001972 4592.657973 3688.702047 4370.459782 3225.251657 2591.976226 2575.755995 2629.850934 4504.345819 4108.513154 0.984298168 1.117839423 0.897819213 1.063757038 0.785016753 0.630879379 0.626931422 0.640097971 1.096344505 1 12.00440067 -8.547898129 3.169408391 0.999381799 0.634815434 0.886423867 0.063518194 0.048720659 1.006951943 0.007463786 0.016680949 2.83E-09 8.547898129 -0.364566365 S(ph)SSESYTQSFQSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSESYTQSFQSR 13 0 Q9BTU6;E9PAM4 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 0 S(0.761)S(0.12)S(0.12)ESYTQSFQSR;S(0.785)S(0.107)S(0.107)ESYTQSFQSR ; 288.29 2.69E-111 56701000 3199.1 3128.6 3396.6 2707 3824.6 5642 3563.4 5041.8 3520.2 2922 TRUE FALSE FALSE 3160.108139 3172.644513 3455.716398 3019.996077 3629.41639 5281.494409 3866.075107 5187.676528 3205.344495 2846.086019 1.110334726 1.114739503 1.214199562 1.06110499 1.275230744 1.855704421 1.358383085 1.822740597 1.126228959 1 11.47476355 -8.473056607 4.163323093 1.074374429 1.644835974 0.771595287 0.138565813 0.070068388 2.530732962 0.018655937 0.042194882 3.36E-09 8.473056607 0.570461545 S(ph)SSKDSRPSQAAGDNQGDEAK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSKDSRPSQAAGDNQGDEAK 21 2 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.309)S(0.309)S(0.309)KDS(0.065)RPS(0.009)QAAGDNQGDEAK 49.176 0.024273 6018000 2298.6 2423.1 2315.5 1778.5 2500.8 2294.6 2188.7 2343.4 2586.5 2182.1 TRUE FALSE FALSE 2270.583779 2457.212465 2355.800306 1984.138538 2373.174844 2147.982465 2374.608123 2411.202582 2355.156962 2125.408727 1.068304534 1.156112908 1.108398717 0.933532695 1.116573398 1.010620893 1.117247752 1.134465362 1.108096025 1 11.05352459 -11.78361746 0.893141162 1.003954324 1.078095985 0 0.070287044 0.708058102 1.11380952 0.029460508 0.012486891 1.65E-12 11.78361746 0.074141662 S(ph)SSLGNLK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLGNLK 8 0 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YGH8 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 S(0.401)S(0.401)S(0.199)LGNLK 104.42 0.027283 46653000 6394.4 7204.3 7129.9 4612.9 7426.1 8514 8078.3 7351.8 8867.1 8429.2 TRUE FALSE FALSE 6316.462593 7305.722325 7253.992919 5146.265202 7047.118406 7969.982878 8764.4706 7564.512734 8074.004368 8210.208169 0.769342563 0.889833994 0.883533373 0.626812999 0.858336142 0.970740658 1.067508938 0.92135456 0.983410433 1 13.00320309 -8.189773627 4.78505609 0.865874382 0.998388727 0.235952952 0.104966322 0.285674188 12.45727551 0.017028164 0.044735831 6.46E-09 8.189773627 0.132514345 S(ph)SSPAPADIAQTVQEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 0 S(0.333)S(0.333)S(0.333)PAPADIAQTVQEDLR 73.707 0.019584 84782 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 S(ph)SSPVQVEEEPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPVQVEEEPVR 13 0 A0A0J9YVR0;Q8IZ21-3;Q8IZ21;Q8IZ21-2 A0A0J9YVR0;Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 S(0.479)S(0.041)S(0.479)PVQVEEEPVR;S(0.333)S(0.333)S(0.333)PVQVEEEPVR ; 235.93 2.56E-41 245314700 4348.9 4287 3408.2 3982 4990.1 5590 4722 5155.5 4567.2 3877.8 TRUE FALSE FALSE 4295.893934 4347.352499 3467.518291 4442.417576 4735.436576 5232.817041 5123.086562 5304.666258 4158.698193 3777.054197 1.137366241 1.150990235 0.918048328 1.176159341 1.253738053 1.38542281 1.356370943 1.404445365 1.101042764 1 11.88304577 -8.686751611 1.947717939 1.064228019 1.379413293 0.805937249 0.068010425 0.113976428 0.87624207 0.011513995 0.026865951 2.06E-09 8.686751611 0.315185274 S(ph)SSPVTELASR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.333)S(0.333)S(0.333)PVTELASR 184.44 3.94E-06 124010000 5337.3 5412.3 5593.2 2399.7 4110.9 3944.5 3352 3833.5 5422.2 5306.8 TRUE FALSE FALSE 5272.246935 5488.494501 5690.5473 2677.164605 3901.105433 3692.45918 3636.718796 3944.416274 4937.224852 5168.928571 1.019988352 1.061824404 1.100914285 0.517934146 0.754722256 0.714356782 0.703573042 0.763101331 0.955173743 1 12.33564955 -9.272293214 24.99718379 1.020677977 0.696317484 0.842586784 0.072745909 190.2795928 438227.3149 0.010242343 0.015742056 5.34E-10 9.272293214 -0.324360493 S(ph)SSSSQESLNRPFSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSQESLNRPFSSK 16 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 0 S(0.457)S(0.026)S(0.086)S(0.362)S(0.069)QESLNRPFSSK 73.984 0.012673 106420000 4865.6 5068.2 4361.6 5117.5 6055.8 5658.7 5310.7 5750.1 5617.9 5233.9 TRUE FALSE FALSE 4806.296196 5139.550253 4437.511818 5709.209429 5746.749929 5297.127333 5761.790725 5916.470071 5115.420954 5097.922523 0.942795065 1.008165626 0.870454935 1.119909022 1.127272904 1.039075684 1.130223282 1.160564925 1.003432463 1 12.31569373 -9.235351345 24.67895509 0.968507692 1.11265054 0.716530382 0.047269539 269.8205825 255247.087 0.006928517 0.011486895 5.82E-10 9.235351345 0.144142848 S(ph)SSTGNLLDKDDLAIPPPDYGAASR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;Q9UQB8-6;I3L3C6 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 S(0.304)S(0.304)S(0.304)T(0.087)GNLLDKDDLAIPPPDYGAASR 131.83 7.15E-07 261070000 3696.6 3404.3 3038.1 2750 7084.8 14512 15235 18202 3975.4 3888.2 TRUE FALSE FALSE 3651.544417 3452.225825 3090.976856 3067.967939 6723.236219 13584.73004 16529.06052 18728.64615 3619.830267 3787.184003 0.96418458 0.911554818 0.816167594 0.810092126 1.775259985 3.587026673 4.364472522 4.945269661 0.955810508 1 11.8869098 -8.182207131 1.684264512 0.944654695 4.777373672 0.992564561 0.13358014 0.02329338 0.123601101 0.021360275 0.080347662 6.57E-09 8.182207131 3.832718977 up S(ph)SSVGS(ph)SSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.986)S(0.01)S(0.011)VGS(0.569)S(0.382)S(0.038)S(0.004)YPISPAVSR;S(0.994)S(0.005)S(0.013)VGS(0.594)S(0.367)S(0.024)S(0.004)YPISPAVSR;S(0.94)S(0.059)S(0.422)VGS(0.577)S(0.001)SSYPISPAVSR ;; 207.21 2.47E-20 52775800 5919.2 6695.8 6137.9 5593.3 5224.1 5147.5 4260.5 5286.9 6918.6 6996.8 TRUE FALSE FALSE 5847.054514 6790.063648 6244.727575 6240.023663 4957.494683 4818.591363 4622.386764 5439.86811 6299.783088 6815.022127 0.857965595 0.996337726 0.916318019 0.915627792 0.72743633 0.707054397 0.678264381 0.798217234 0.924396571 1 12.73450263 -8.776717902 4.77173262 0.934980586 0.721052095 0.821894011 0.047334932 0.072277146 4.160341305 0.008915454 0.017158908 1.67E-09 8.776717902 -0.213928491 S(ph)SSVGSSSSYPIS(ph)PAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.884)S(0.078)S(0.038)VGSSS(0.005)S(0.016)YPIS(0.979)PAVSR 243.99 1.08E-60 116110000 5005.3 5122.7 4350.6 4517.4 4895.2 5320.8 4791.3 5609.8 5437.2 4746.7 TRUE FALSE FALSE 4944.293478 5194.817505 4426.320368 5039.723043 4645.379677 4980.818052 5198.272902 5772.110712 4950.883214 4623.38005 1.069410999 1.123597336 0.957377572 1.090051648 1.004758343 1.077310971 1.12434471 1.248461223 1.070836306 1 12.17473224 -7.242109949 1.311145978 1.0371769 1.348221256 0.634840222 0.04662544 0.644823876 0.910130154 0.006801648 0.270526653 5.73E-08 7.242109949 0.311044356 S(ph)SSVGSSSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 S(0.485)S(0.03)S(0.485)VGSSSSYPISPAVSR 364.82 4.21E-292 2749300000 2034 1973.9 1702.7 2064.9 1586.4 1903.6 1830.8 2187.7 2011.7 2059.2 TRUE FALSE FALSE 2009.208826 2001.688616 1732.334779 2303.653454 1505.440088 1781.966104 1986.308106 2250.997648 1831.768514 2005.701687 1.001748584 0.997999168 0.863705101 1.148552384 0.750580257 0.888450219 0.990330775 1.122299324 0.913280637 1 10.96989133 -9.952641493 24.99874437 1.000775958 0.955473846 0 0.11352405 354.4360204 187092.6193 0.016977763 0.022313149 1.12E-10 9.952641493 -0.045302112 S(ph)SSVLSLEGSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVLSLEGSEK 12 0 G3V311;A1L390-2;A1L390-3;A1L390;A0A0U1RR71 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 S(0.984)S(0.008)S(0.008)VLSLEGSEK 182.25 9.60E-07 42092000 4553.4 4602.1 4508.1 3586.1 3512.8 3493.7 2942.2 3166 4802.7 4578.9 TRUE FALSE FALSE 4497.901409 4666.888485 4586.561589 4000.741755 3333.528708 3270.463845 3192.110395 3257.603215 4373.134483 4459.939518 1.00851175 1.046401743 1.028390984 0.897039464 0.747438097 0.733297802 0.715729525 0.730414213 0.980536724 1 12.12280843 -8.908771707 2.447781827 1.009545484 0.725909014 0.981276142 0.018292324 0.025781238 0.313196907 0.002795436 0.005511635 1.23E-09 8.908771707 -0.28363647 S(ph)ST(ph)SSYRSRS(ph)YSRSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTSSYRSRSYSRSR 15 3 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 3 0 S(0.872)S(0.044)T(0.285)S(0.289)S(0.289)Y(0.216)RS(0.104)RS(0.641)Y(0.137)S(0.062)RS(0.061)R 66.663 0.0039607 0 170.97 126.15 109.99 155.65 162.5 143.9 140.07 146.3 168.79 222.26 TRUE FALSE FALSE 168.8861519 127.925943 111.9043298 173.6469854 154.2070186 134.7052544 151.9675423 150.5329597 153.6929997 216.4856532 0.780126301 0.590921113 0.516913376 0.802117752 0.712319807 0.622236404 0.70197512 0.695348433 0.709945428 1 7.758127608 -11.27483871 0.811698487 0.9748385 0.66724852 0.165164501 0.114431005 0.225226476 0.316587705 0.03180692 0.019306119 5.31E-12 11.27483871 -0.307589979 S(ph)STDSLPGPISR ddPTM_HeLa_Romidepsin_16h_R1 3 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 0 S(0.921)S(0.078)TDSLPGPISR;S(0.49)S(0.49)T(0.02)DSLPGPISR;S(0.461)S(0.461)T(0.079)DSLPGPISR ;; 176.87 1.99E-06 41913000 5803.3 6092.5 5803.9 5066.4 5559.6 6189.5 5681.4 6128.4 6692.7 5962 TRUE FALSE FALSE 5732.567147 6178.270375 5904.914445 5652.201006 5275.872866 5794.010926 6163.977974 6305.715585 6094.08815 5807.106381 0.987164135 1.06391548 1.016842823 0.97332486 0.908520099 0.997744926 1.061454289 1.085861903 1.049419065 1 12.50360375 -7.707061315 4.010180549 0.992945069 1.079261643 0.344729518 0.040578883 0.152141822 4.892498305 0.005284142 0.021537246 1.96E-08 7.707061315 0.086316574 S(ph)STPLPTISSSAENTR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPLPTISSSAENTR 16 0 G5E972;P42167;H0YJH7;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 S(0.972)S(0.014)T(0.014)PLPTISSSAENTR 202.92 1.64E-18 14085000 1242.8 1326.9 1148.9 795.62 1345.7 1381.4 1090.7 1195.1 1496.1 1581.7 TRUE FALSE FALSE 1227.652276 1345.580133 1168.896123 887.6133279 1277.023908 1293.132998 1183.344031 1229.678333 1362.285069 1540.607206 0.796862608 0.873408957 0.758724299 0.576145123 0.828909473 0.839365799 0.76810236 0.798177711 0.884252043 1 10.58928336 -12.01834206 0.524847691 1.029892618 0.768700003 0.360038214 0.082433142 0.744634555 0.325711751 0.096145764 0.020673943 9.59E-13 12.01834206 -0.261192615 S(ph)STPSHGQTTATEPTPAQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPSHGQTTATEPTPAQK 19 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 S(0.212)S(0.212)T(0.212)PS(0.178)HGQT(0.178)T(0.009)ATEPTPAQK 78.234 0.004137 3151800 1751 1508.4 1452.5 1472 2536.2 2132.2 1903.7 1809.9 2529.7 1807.9 TRUE FALSE FALSE 1729.658138 1529.635295 1477.780153 1642.199566 2406.76825 1995.959301 2065.40023 1862.266601 2303.437296 1760.930497 0.982241003 0.868651714 0.839204134 0.932574891 1.366759366 1.133468529 1.172902754 1.057546907 1.30807962 1 10.78212225 -8.793744478 24.999976 0.964780919 1.178457599 0.305929603 0.140562709 106.1642544 82157.09665 0.013738074 0.024903761 1.61E-09 8.793744478 0.21367668 S(ph)STVAPAQPDGAESEWTDVETR ddPTM_HeLa_Romidepsin_16h_R1 2 SSTVAPAQPDGAESEWTDVETR 22 0 Q02241;A0A2U3TZL8;H7BYN4;Q02241-3;Q02241-2 Q02241;Q02241-3 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 0 S(0.455)S(0.089)T(0.455)VAPAQPDGAESEWTDVETR;S(0.85)S(0.145)T(0.006)VAPAQPDGAESEWTDVETR ; 147.76 3.69E-06 11599300 3616.8 3315.8 2764.9 2316.2 2444 2404.4 1849.12 2105.89 3180.8 3778.7 TRUE FALSE FALSE 3572.71705 3362.479919 2813.021925 2584.009942 2319.27356 2250.7666 2006.184207 2166.820605 2896.301282 3680.528829 0.97070753 0.913586084 0.764298299 0.702075724 0.630146826 0.611533479 0.545080422 0.588725345 0.786925308 1 11.84569736 -9.452613018 0.908685917 0.993654475 0.57323672 0.80834332 0.068294504 0.038077709 0.062664625 0.003798178 0.007372277 3.53E-10 9.452613018 -0.420417755 S(ph)STVASLDTDSTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSTVASLDTDSTK 13 0 C9IZZ8;C9J6Y2;C9J0J6;C9JZ07;G3V1A3;C9J5T5;C9JBU8;A8MPU2;O14713-2;O14713 C9IZZ8 ITGB1BP1 Integrin beta-1-binding protein 1 1 0 S(0.873)S(0.059)T(0.059)VAS(0.008)LDTDSTK 257.2 7.17E-66 23764000 4611.1 4621.2 3979.5 3664.6 4947.9 5423.2 4708 4998.8 5427.9 4625 TRUE FALSE FALSE 4554.89814 4686.257375 4048.761528 4088.318294 4695.3902 5076.675023 5107.897402 5143.432391 4942.41503 4504.841833 1.011111668 1.040271234 0.898757754 0.907538699 1.04229857 1.126937462 1.133868311 1.141756488 1.097133976 1 12.13726074 -8.365348758 3.539419214 0.992859066 1.135207892 0.568519383 0.054927727 0.115673612 2.675672295 0.00689225 0.01658068 4.31E-09 8.365348758 0.142348826 S(ph)SVDLEESSTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSVDLEESSTK 11 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 S(0.992)S(0.008)VDLEESSTK 260.57 1.77E-61 48248000 5356.7 6106.1 5695.4 4452.1 7319.9 7275.2 6028.1 6420.4 6301.5 5898.6 TRUE FALSE FALSE 5291.41048 6192.061836 5794.526048 4966.87275 6946.338189 6810.3382 6540.126664 6606.164144 5737.878058 5745.353522 0.920989537 1.077751232 1.00855866 0.864502546 1.209035817 1.185364517 1.138333201 1.149827268 0.998698868 1 12.48817995 -8.749752583 24.99991902 0.969094975 1.169384329 0.735979025 0.05623442 86.49708126 185029.8243 0.008514778 0.016917549 1.78E-09 8.749752583 0.200289355 S(ph)T(ph)EMALRVASLDY(ph)LGTVAAR ddPTM_HeLa_Romidepsin_16h_R1 1 STEMALRVASLDYLGTVAAR 20 1 A0A590UJS4;Q6KC79-2;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 3 0 S(1)T(1)EMALRVAS(0.104)LDY(0.792)LGT(0.104)VAAR 47.397 0.004314 0 1115.1 460.47 621.67 303.93 816.91 487.09 823.57 608.12 1043.4 1112.5 TRUE FALSE FALSE 1101.508732 466.9525087 632.4899056 339.0718166 775.2200344 455.966521 893.5240152 625.7149927 950.0756908 1083.59709 1.0165298 0.430928168 0.583694725 0.312913185 0.715413544 0.420789725 0.824590638 0.577442482 0.876779478 1 10.08161271 -10.27070158 24.69169649 1.007805754 0.555950739 0.626702584 0.144602473 206.5235127 550560.855 0.022089521 0.025446813 5.36E-11 10.27070158 -0.451855015 S(ph)T(ph)NAT(ph)S(ph)AILT(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 STNATSAILTAK 12 0 Q86SJ6;Q86SJ6-2 Q86SJ6 DSG4 Desmoglein-4 5 0 S(1)T(1)NAT(1)S(1)AILT(1)AK 49.715 0.004339 0 290.65 222.95 311.6 258.82 355.49 281.61 403.51 405.37 345.36 231.71 TRUE FALSE FALSE 287.107446 226.088696 317.0232673 288.7459862 337.3480188 263.6160299 437.7841293 417.0987414 314.4701366 225.6901408 1.272131095 1.00176594 1.404683723 1.279391227 1.494739724 1.168044067 1.939757438 1.84810351 1.393371175 1 7.818199586 -4 0.28512892 1.075276088 7.865891385 0.570371072 0.196697928 18.7649783 0.239547412 0.069350732 64.74723008 1.00E-04 4 6.790615297 S(ph)T(ph)VKMVQTPY(ph)GIVPDVY(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 STVKMVQTPYGIVPDVYEK 19 1 O95147 O95147 DUSP14 Dual specificity protein phosphatase 14 4 0 S(0.998)T(0.998)VKMVQT(0.247)PY(0.76)GIVPDVY(0.999)EK 40.137 0.023655 45837000 336.71 311.08 260.06 211.34 240.85 325.18 278.23 280.93 380.07 178.99 TRUE FALSE FALSE 332.606049 315.4593924 264.5862352 235.7761252 228.5585258 304.4020475 301.8628493 289.0582663 346.0755873 174.339814 1.907803165 1.809451239 1.517646653 1.352394039 1.310994434 1.746027144 1.731462495 1.658016374 1.985063419 1 7.445758265 -12.46567777 1.203995857 1.000156373 1.64788679 0 0.351770384 0.276460886 0.717224339 0.147587752 0.036443314 3.42E-13 12.46567777 0.647730417 S(ph)TAALEEDAQILK ddPTM_HeLa_Romidepsin_16h_R1 2 STAALEEDAQILK 13 0 B1ALK7;A0A2R8YG42;Q14155-1;Q14155-5;E9PDQ5;Q14155-6;Q14155-2;Q14155-3;Q14155;Q15052-2;Q15052 B1ALK7 ARHGEF7;ARHGEF6 Rho guanine nucleotide exchange factor 7;Rho guanine nucleotide exchange factor 6 1 0 S(0.948)T(0.052)AALEEDAQILK;S(0.985)T(0.015)AALEEDAQILK ; 217.39 1.10E-23 50350000 5632.9 5377.6 6237.8 6583.4 7471.8 6693.4 5659 6426.5 6399.8 5791.2 TRUE FALSE FALSE 5564.244048 5453.305994 6346.366292 7344.603684 7090.486165 6265.713342 6139.675319 6612.440638 5827.385859 5640.743789 0.986438005 0.966770731 1.125093876 1.302062983 1.257012626 1.110795593 1.088451372 1.172263958 1.033088202 1 12.46166969 -9.636653309 4.582125028 0.9916432 1.183231059 0.684097072 0.060673411 0.094363848 3.390942959 0.010114191 0.01441632 2.31E-10 9.636653309 0.191587859 S(ph)TDSSSVSGSLQQETK ddPTM_HeLa_Romidepsin_16h_R1 4 STDSSSVSGSLQQETK 16 0 Q9H8G2;A0A3B3ISJ3 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 0 S(1)TDSSSVSGSLQQETK;S(0.964)T(0.036)DSSSVSGSLQQETK;S(0.634)T(0.137)DS(0.185)S(0.043)S(0.001)VSGSLQQETK;S(0.974)T(0.026)DSSSVSGSLQQETK ;;; 368.4 0 66187000 5762.3 5892.8 5385.1 5705 8287.3 9360.3 8722.7 9524.9 6037.9 5590.8 TRUE FALSE FALSE 5692.066871 5975.758993 5478.825407 6364.638943 7864.368157 8762.207039 9463.60592 9800.487954 5497.855102 5445.55021 1.045269376 1.097365512 1.00611053 1.168777937 1.444182471 1.609058167 1.737860373 1.799724101 1.00960507 1 12.41086211 -8.514167185 1.153731548 1.02243094 1.790303719 0.986924108 0.035076645 0.038946996 0.097375573 0.005807951 0.020708269 3.06E-09 8.514167185 0.767872778 S(ph)TELLLGVK ddPTM_HeLa_Romidepsin_16h_R1 1 STELLLGVK 9 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 S(0.974)T(0.026)ELLLGVK 164.33 0.0027704 2736500 1943.7 1771.5 1852.1 1370.3 1731.4 2030 2003.1 1851.8 2033.8 1967.1 TRUE FALSE FALSE 1920.009437 1796.439223 1884.335024 1528.740533 1643.040197 1900.289552 2173.243264 1905.378911 1851.891834 1915.994458 1.002095506 0.937601471 0.983476239 0.797883588 0.857539118 0.991803261 1.134263857 0.994459511 0.966543419 1 10.90387767 -7.975784189 20.81059583 0.969176384 1.064030486 0.252975068 0.074039925 44.32010976 38083.66523 0.011457372 0.034363895 1.06E-08 7.975784189 0.094854102 S(ph)TFSTNYR ddPTM_HeLa_Romidepsin_16h_R1 2 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 S(0.847)T(0.014)FS(0.036)T(0.102)NYR;S(0.886)T(0.013)FS(0.073)T(0.029)NYR ; 112.83 0.021417 162106000 1579.18 1126.83 1226.8 1481.42 2577.2 1693.52 895.8 1102.1 926.73 1343.56 TRUE FALSE FALSE 1559.932347 1142.693542 1248.151939 1652.708751 2445.675867 1585.309538 971.8892296 1133.987525 843.8409478 1308.654118 1.192012714 0.873182247 0.953767632 1.262907233 1.868848181 1.211404539 0.742663181 0.866529597 0.644815873 1 10.35386812 -14.30335892 17.85416596 1.095606817 1.104796815 0 0.33386782 0 0 0 0.040996814 4.97E-15 14.30335892 0.009189998 S(ph)TGDIAGTVVPETNKEPR ddPTM_HeLa_Romidepsin_16h_R1 1 STGDIAGTVVPETNKEPR 18 1 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IRI3;Q9UDY2-5;A0A3B3IRV6;A0A3B3ISF1;A0A3B3ISZ5;A0A3B3IS03;A0A3B3IT83 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 S(0.816)T(0.184)GDIAGTVVPETNKEPR 103.73 0.00065408 4772700 979.25 1144.3 970.88 1004.3 1003.6 980.08 964.53 1079.5 829.22 1320.4 TRUE FALSE FALSE 967.3145243 1160.409485 987.7777591 1120.421891 952.3825471 917.4560511 1046.457154 1110.733629 755.0524864 1286.095818 0.752132548 0.902272964 0.768043676 0.871180729 0.740522233 0.71336524 0.813669666 0.863647649 0.587088828 1 10.32878242 -12.39919391 0.87433602 1.013909291 0.798232259 0 0.141293539 0.368305987 0.449140126 0.055773521 0.011033704 3.99E-13 12.39919391 -0.215677031 S(ph)TLSPPEASPGPPAAPR ddPTM_HeLa_Romidepsin_16h_R1 1 STLSPPEASPGPPAAPR 17 0 Q6NUJ5-2;Q6NUJ5 Q6NUJ5-2 PWWP2B PWWP domain-containing protein 2B 1 0 S(0.623)T(0.139)LS(0.216)PPEAS(0.022)PGPPAAPR 82.85 0.015881 6571000 1229.1 1186.9 1237.7 1069.1 1356.4 1170.3 906.07 1328.4 1235.4 1340 TRUE FALSE FALSE 1214.119256 1203.609209 1259.241649 1192.714372 1287.177847 1095.521607 983.0315632 1366.835158 1124.90273 1305.186607 0.930226567 0.922174042 0.96479817 0.913826702 0.986202157 0.839360135 0.753173192 1.047233515 0.861871187 1 10.35004037 -14.02124876 0.122465452 1.163436413 0.85471589 0 0.086789054 54.92669417 0.942395978 2.87683173 0.421728874 9.52E-15 14.02124876 -0.308720523 S(ph)TPEHTWSSR ddPTM_HeLa_Romidepsin_16h_R1 1 STPEHTWSSR 10 0 O14646-2;O14646 O14646-2 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 0 S(0.84)T(0.16)PEHTWSSR 90.434 0.002484 0 1242 1162.7 1150.8 852.02 1782.9 1807.2 1633.3 1794.4 1701.5 1505.8 TRUE FALSE FALSE 1226.862026 1179.068521 1170.829191 950.5345613 1691.91196 1691.725752 1772.032461 1846.318133 1549.313579 1466.679099 0.836489746 0.803903541 0.798285864 0.648086253 1.153566558 1.1534396 1.20819371 1.258842602 1.056341213 1 10.51833754 -8.611355202 8.857119312 0.883658195 1.19809545 0.69061048 0.109801103 0.134889344 12.12907831 0.016896308 0.033837653 2.45E-09 8.611355202 0.314437254 S(ph)TPESGDS(ph)DKESVGSSSTSNEGGR ddPTM_HeLa_Romidepsin_16h_R1 1 STPESGDSDKESVGSSSTSNEGGR 24 1 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 2 0 S(0.408)T(0.408)PES(0.564)GDS(0.609)DKES(0.008)VGS(0.003)S(0.001)STSNEGGR 60.464 0.013111 10346000 2131.5 2139.6 2288.5 2304.5 2403.8 2135.7 2332.3 2662.2 2766.6 2350 TRUE FALSE FALSE 2105.520458 2169.721345 2328.330383 2570.957133 2281.125116 1999.235663 2530.405504 2739.226557 2519.148367 2288.946661 0.919864361 0.947912584 1.017206046 1.123205349 0.996582906 0.873430428 1.105489065 1.196719261 1.100571022 1 11.16046813 -9.606782543 4.808277151 0.960271037 1.049846831 0.059691046 0.093356966 0.267926795 11.09008197 0.013779121 0.019684278 2.47E-10 9.606782543 0.089575795 S(ph)TPKEDDSSASTSQSTR ddPTM_HeLa_Romidepsin_16h_R1 1 STPKEDDSSASTSQSTR 17 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.681)T(0.319)PKEDDSSASTSQSTR 138.98 0.0057122 8292600 1211.8 999.06 781.98 944.22 817.08 1030.7 808.01 651.25 1001.8 850.32 TRUE FALSE FALSE 1197.030115 1013.124793 795.5900339 1053.395159 775.3813587 964.8415964 876.6423492 670.0928912 912.1964989 828.2285638 1.445289583 1.223243 0.960592364 1.271865286 0.936192487 1.164946053 1.058454619 0.809067594 1.101382564 1 9.693885149 -6.319703506 0.578703026 1.198148192 6.63E-13 0.271832906 0.150418711 10.12294641 1.04381381 0.035021432 10.45189236 4.79E-07 6.319703506 -1.198148192 S(ph)TPLSQPSANGVQTEGLDYDR ddPTM_HeLa_Romidepsin_16h_R1 4 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6 ENAH Protein enabled homolog 1 0 S(0.818)T(0.161)PLS(0.021)QPSANGVQTEGLDYDR;S(0.841)T(0.159)PLSQPSANGVQTEGLDYDR;S(0.875)T(0.125)PLSQPSANGVQTEGLDYDR;S(0.775)T(0.205)PLS(0.02)QPSANGVQTEGLDYDR ;;; 231.93 4.19E-53 51177500 4068.18 3885.94 3963.56 3391.84 4999.46 4666.83 4092.8 3760.29 4373.8 4522.84 TRUE FALSE FALSE 4018.595457 3940.646365 4032.544099 3784.0205 4744.318901 4368.634625 4440.44233 3869.088058 3982.596374 4405.335965 0.912210894 0.894516649 0.9153772 0.858962978 1.07694826 0.99166889 1.007969055 0.878273096 0.904039194 1 12.10503633 -7.231301964 22.67563212 0.956559983 0.878272658 0.102023078 0.063286452 5712.815886 4298121.737 0.009013376 1.153527591 5.87E-08 7.231301964 -0.078287325 S(ph)TPPPNNLVNPVQELETER ddPTM_HeLa_Romidepsin_16h_R1 2 STPPPNNLVNPVQELETER 19 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 0 S(0.5)T(0.5)PPPNNLVNPVQELETER;S(0.726)T(0.274)PPPNNLVNPVQELETER ; 145.82 5.81E-05 10633200 4560.9 4096.6 4360.6 3896.9 3567.6 3811.6 2935 3163.3 4631.8 4472.3 TRUE FALSE FALSE 4505.309997 4154.272042 4436.494414 4347.477913 3385.532059 3568.051061 3184.298827 3254.825095 4217.520207 4356.109001 1.034250978 0.953665769 1.01845349 0.998018624 0.777191769 0.819091318 0.730996131 0.747186329 0.968185187 1 12.08882434 -8.764120537 5.23902456 1.010980481 0.767686772 0.922643723 0.032016681 0.029589436 2.366325135 0.004491918 0.008677409 1.72E-09 8.764120537 -0.24329371 S(ph)TPSSSTPSSR ddPTM_HeLa_Romidepsin_16h_R1 2 STPSSSTPSSR 11 0 H3BUV9;Q96S82 H3BUV9 UBL7 Ubiquitin-like protein 7 1 0 S(0.908)T(0.092)PSSSTPSSR;S(0.855)T(0.145)PSSSTPSSR ; 144.7 0.0025112 5124600 1657.72 2141 3740 2235.6 2041.06 2470.5 3996.2 834.88 3462.1 3358.7 TRUE FALSE FALSE 1637.515071 2171.141054 3805.093131 2494.090591 1936.897092 2312.643023 4335.637128 859.0359356 3152.441105 3271.44049 0.500548635 0.663665153 1.163124667 0.762382993 0.592062456 0.706918873 1.325299097 0.262586447 0.963624775 1 11.67571031 -7.039157947 18.67503922 0.792360694 0.16425062 0.303517456 0.253765621 6894326.187 475424388 0.037284414 33374761.99 9.14E-08 7.039157947 -0.628110073 S(ph)TQGVTLTDLQEAEK ddPTM_HeLa_Romidepsin_16h_R1 1 STQGVTLTDLQEAEK 15 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 S(0.883)T(0.11)QGVT(0.006)LTDLQEAEK 96.447 0.010616 4618700 1233 1339.7 985.79 1069.7 1065.6 1121.2 981.24 1031.1 1278.9 1324.2 TRUE FALSE FALSE 1217.971722 1358.560332 1002.947261 1193.383747 1011.218456 1049.558939 1064.586501 1060.933252 1164.511981 1289.797093 0.944312658 1.053313222 0.777600808 0.925249214 0.784013595 0.813739575 0.825390681 0.822558259 0.902864479 1 10.33292841 -9.755676608 24.99991839 0.978939189 0.827002242 0.666553627 0.052058324 54.02037122 234348.8529 0.007168365 0.009979414 1.76E-10 9.755676608 -0.151936947 S(ph)TSATDTHHVEMAR ddPTM_HeLa_Romidepsin_16h_R1 1 STSATDTHHVEMAR 14 0 H3BQP2;H3BNP3;H3BTL2;H3BS02;O14874-2;O14874-3;O14874 H3BQP2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 0 S(0.674)T(0.155)S(0.155)AT(0.016)DT(0.001)HHVEMAR 105.63 0.002311 34585000 1131.9 1035.2 1040.7 1278.2 1466 2045.3 1600.3 1700.4 1640.7 1271.8 TRUE FALSE FALSE 1118.103967 1049.773573 1058.812947 1425.991498 1391.18455 1914.611931 1736.229442 1749.598391 1493.951683 1238.758453 0.902600475 0.847440089 0.854737213 1.151145726 1.123047473 1.545589398 1.401588371 1.412380588 1.206007256 1 10.27467919 -8.612095252 1.677814278 0.939629135 1.449776694 0.739263524 0.12025347 0.093433669 0.525163753 0.013452202 0.034952429 2.44E-09 8.612095252 0.510147559 S(ph)TSPIIGS(ph)PPVR ddPTM_HeLa_Romidepsin_16h_R1 1 STSPIIGSPPVR 12 0 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 2 0 S(0.654)T(0.037)S(0.309)PIIGS(1)PPVR 138.31 0.023315 3867700 3117.5 3002.3 2810.2 3050.3 2464.9 2483 1840.3 2252.8 3416.3 3065.5 TRUE FALSE FALSE 3079.502711 3044.566458 2859.110352 3402.990038 2339.106955 2324.344314 1996.615036 2317.981214 3110.737572 2985.857868 1.031362793 1.019662219 0.95755072 1.139702621 0.783395278 0.778451091 0.668690582 0.776320011 1.041823727 1 11.54392978 -8.651531702 6.295684031 1.018315828 0.742026005 0.871079359 0.052739689 0.049974986 2.601903373 0.007019648 0.014123185 2.23E-09 8.651531702 -0.276289823 S(ph)TSPIIGSPPVR ddPTM_HeLa_Romidepsin_16h_R1 2 STSPIIGSPPVR 12 0 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 1 0 S(0.459)T(0.078)S(0.459)PIIGS(0.003)PPVR;S(0.459)T(0.081)S(0.459)PIIGS(0.001)PPVR ; 123.26 0.0064163 39173000 3941.8 3921.7 4304.7 4100.4 5191 6549.9 5612.1 6424 4897.2 4595 TRUE FALSE FALSE 3893.755825 3976.909796 4379.621498 4574.507541 4926.0839 6131.382529 6088.791634 6609.868305 4459.182167 4475.621238 0.869992258 0.888571571 0.978550522 1.022094431 1.100648075 1.369951165 1.360434968 1.476860519 0.996326975 1 12.12787223 -8.373471827 1.25014137 0.934677059 1.450156685 0.944193243 0.048499752 0.090124812 0.259452387 0.009047906 0.034952037 4.23E-09 8.373471827 0.515479627 S(ph)TSPPPSPEVWADSR ddPTM_HeLa_Romidepsin_16h_R1 1 STSPPPSPEVWADSR 15 0 E5RJ61;E5RGQ7;E5RJC0;E5RGQ0;E5RFK4;Q08495-3;Q08495-2;Q08495 E5RJ61 DMTN Dematin 1 0 S(0.362)T(0.362)S(0.273)PPPS(0.003)PEVWADSR 101.35 0.0018921 0 986.4 1339.8 1238.4 783.11 1387.9 1129.4 1083.4 1049.9 1438.1 1150.8 TRUE FALSE FALSE 974.3773774 1358.66174 1259.953833 873.6568628 1317.070284 1057.234985 1175.423969 1080.2772 1309.472734 1120.90205 0.869279682 1.2121146 1.124053464 0.779423022 1.175009256 0.943200153 1.048641109 0.963757003 1.168231189 1 10.1304445 S(ph)TSTPNVHMVSTTLPVDSR ddPTM_HeLa_Romidepsin_16h_R1 1 STSTPNVHMVSTTLPVDSR 19 0 H7C155;P04049;P04049-2 H7C155 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 0 S(0.336)T(0.336)S(0.282)T(0.045)PNVHMVSTTLPVDSR 92.492 0.0013982 0 797.48 591.15 436.42 561.27 679.69 579.48 322.5 537.78 871.57 719.36 TRUE FALSE FALSE 787.760007 599.4722252 444.015707 626.1666783 645.002883 542.4530982 349.893142 553.3398158 793.6145963 700.6709235 1.124293846 0.855568863 0.633700775 0.89366728 0.920550377 0.774190965 0.49936872 0.789728526 1.132649536 1 9.452593218 -10.08950364 4.503889589 1.057892042 0.754486824 0.60650453 0.119370214 0.123468536 4.378088945 0.020922904 0.025965778 8.14E-11 10.08950364 -0.303405218 S(ph)TTELDDYSTNK ddPTM_HeLa_Romidepsin_16h_R1 4 STTELDDYSTNK 12 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 S(0.87)T(0.126)T(0.004)ELDDYSTNK;S(0.998)T(0.001)T(0.001)ELDDYSTNK;S(0.969)T(0.031)T(0.001)ELDDYSTNK;S(0.841)T(0.136)T(0.023)ELDDYSTNK ;;; 217.46 1.73E-21 128128000 15475.5 15404.6 14468.1 9294.1 11541.6 11376.5 9779.5 11129.3 15298.5 15875.9 TRUE FALSE FALSE 15286.87865 15621.46636 14719.91121 10368.72757 10952.58908 10649.57837 10610.17049 11451.30874 13930.16384 15463.44183 0.988581897 1.010219234 0.951916874 0.670531676 0.708289216 0.68869392 0.686145465 0.740540745 0.900844973 1 13.91657385 -9.321286163 4.570502032 0.994730901 0.697656046 0.934530903 0.035740155 0.018072349 0.781853663 0.002881903 0.004502267 4.77E-10 9.321286163 -0.297074855 S(ph)TTPPPAEPVSLPQEPPK ddPTM_HeLa_Romidepsin_16h_R1 1 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPK 198.61 1.26E-20 71422000 17264 16233 16252 12121 17999 18525 16185 18746 17159 17280 TRUE FALSE FALSE 17053.57973 16461.5286 16534.85924 13522.48705 17080.44387 17341.31229 17559.7535 19288.38593 15624.25606 16831.06311 1.013220592 0.978044494 0.982401357 0.803424416 1.014816697 1.030315921 1.043294377 1.145999264 0.928298822 1 14.03883868 -7.271333881 1.390426783 0.988696939 1.206558324 0.41285482 0.06351877 1.051762486 1.790287304 0.009235751 0.318161828 5.35E-08 7.271333881 0.217861386 S(ph)TTPPPAEPVSLPQEPPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 S(0.333)T(0.333)T(0.333)PPPAEPVSLPQEPPKPR 177.29 2.41E-13 1860100000 12867 13020 11226 10303 11963 11284 10906 11845 13199 12857 TRUE FALSE FALSE 12710.17205 13203.2959 11421.38382 11494.28134 11352.48347 10562.98882 11832.35537 12187.71639 12018.44838 12522.97329 1.014948428 1.054325966 0.912034511 0.917855614 0.906532595 0.843488888 0.944851921 0.97322865 0.959712051 1 13.61228952 -9.745444166 24.95202131 1.010801239 0.913941138 0.582688558 0.037611471 108.5150343 169279.6576 0.005444195 0.007685233 1.80E-10 9.745444166 -0.096860101 S(ph)VASNQS(ph)EMEFSSLQDMPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVASNQSEMEFSSLQDMPK 19 0 G3V119;H0YB24;Q8N163-2;Q8N163;A0A087X2B6 G3V119 CCAR2 Cell cycle and apoptosis regulator protein 2 2 0 S(0.519)VAS(0.162)NQS(0.895)EMEFS(0.332)S(0.092)LQDMPK 47.796 0.0040262 0 1181.9 1364.3 1454.1 996.74 1412.5 1192.3 1297.6 1155 1567 1775.3 TRUE FALSE FALSE 1167.494548 1383.506651 1479.408001 1111.987769 1340.414854 1116.115878 1407.818112 1188.418103 1426.843595 1729.17745 0.67517336 0.800095242 0.855555918 0.643073253 0.775174841 0.645460579 0.814154795 0.687273653 0.825157415 1 10.75587021 -12.38362714 0.896940313 1.015097294 0.735269617 0.323387225 0.087654651 0.309520982 0.405611804 0.06122157 0.012719933 4.13E-13 12.38362714 -0.279827678 S(ph)VAVSDEEEVEEEAER ddPTM_HeLa_Romidepsin_16h_R1 2 SVAVSDEEEVEEEAER 16 0 Q9Y6X9-2;Q9Y6X9 Q9Y6X9-2 MORC2 MORC family CW-type zinc finger protein 2 1 0 S(1)VAVSDEEEVEEEAER;S(0.999)VAVS(0.001)DEEEVEEEAER ; 220.52 9.02E-35 61152000 11603.9 10397.1 10104.7 10459.3 10694.8 10618.3 8575.3 9862.3 11092.2 9803.2 TRUE FALSE FALSE 11462.4672 10543.47065 10280.56806 11668.65348 10149.00445 9939.824899 9303.685768 10147.65009 10100.08585 9548.511451 1.200445458 1.104200451 1.076667093 1.22203901 1.06288865 1.040981618 0.974359806 1.062746811 1.057765486 1 13.22106013 -8.365553132 3.600204905 1.105057566 1.020140553 0.247021176 0.064613775 0.340574219 8.104673126 0.01220244 0.029254292 4.31E-09 8.365553132 -0.084917013 S(ph)VDEVNYWDK ddPTM_HeLa_Romidepsin_16h_R1 3 SVDEVNYWDK 10 0 F5GXU9;F5H5P2;P12694;P12694-2 F5GXU9 BCKDHA "2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial" 1 0 S(1)VDEVNYWDK;S(1)VDEVNYWDK;S(1)VDEVNYWDK ;; 183.89 1.94E-05 25063500 4194.5 4858 4940.8 1818.38 4438.8 5638 4454.3 4552.9 4185.3 4652.3 TRUE FALSE FALSE 4143.375821 4926.391052 5026.792551 2028.629651 4212.271473 5277.749996 4832.648131 4684.630978 3810.956286 4531.432575 0.914363339 1.087159738 1.109316418 0.44767954 0.929567284 1.164697898 1.066472479 1.03380794 0.841004742 1 12.1457515 -8.280724055 22.97692353 0.938920463 1.08614074 0.165847995 0.177660588 441.7404653 526316.0141 0.025137262 0.056320712 5.24E-09 8.280724055 0.147220277 S(ph)VDFDSLTVR ddPTM_HeLa_Romidepsin_16h_R1 4 SVDFDSLTVR 10 0 Q9Y5K6 Q9Y5K6 CD2AP CD2-associated protein 1 0 S(0.998)VDFDS(0.002)LTVR;S(1)VDFDSLTVR;S(1)VDFDSLTVR;S(0.953)VDFDS(0.047)LTVR ;;; 185.3 1.14E-05 133480000 5752.4 4626.95 5211.33 5008.8 6572.8 7535.3 8018.1 7752.4 6022.22 5871.13 TRUE FALSE FALSE 5682.287536 4692.088324 5302.031013 5587.941023 6237.36549 7053.818649 8699.157214 7976.703463 5483.57756 5718.597196 0.9936506 0.820496384 0.927155879 0.977152408 1.090716005 1.233487586 1.521204749 1.394870663 0.958902572 1 12.48144557 -8.132390277 1.785643529 0.975990537 1.465549928 0.899356886 0.066989858 0.084683059 0.507707361 0.010259584 0.039088414 7.37E-09 8.132390277 0.489559392 S(ph)VEAAAELSAK ddPTM_HeLa_Romidepsin_16h_R1 2 SVEAAAELSAK 11 0 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 1 0 S(0.994)VEAAAELS(0.006)AK;S(0.999)VEAAAELS(0.001)AK ; 153.49 0.0022523 12704400 3203.1 3664.2 3149.6 1632.68 3258.3 3364.8 2458.8 2788.1 3176.7 3010.6 TRUE FALSE FALSE 3164.059385 3715.784704 3204.417467 1821.458144 3092.016793 3149.800139 2667.650411 2868.769275 2892.567996 2932.384178 1.079005749 1.267154806 1.092768639 0.62115263 1.054437824 1.074143069 0.90972064 0.978306081 0.986421908 1 11.51785841 S(ph)VEDLVR ddPTM_HeLa_Romidepsin_16h_R1 1 SVEDLVR 7 0 Q7L9B9 Q7L9B9 EEPD1 Endonuclease/exonuclease/phosphatase family domain-containing protein 1 1 0 S(1)VEDLVR 116.05 0.028048 1136400 472.65 613.74 611.24 404.27 1018.4 2258.8 767.15 1897.5 647.88 685.63 TRUE FALSE FALSE 466.88916 622.3802478 621.8783758 451.0135995 966.4272478 2114.46997 832.3117019 1952.401169 589.9319902 667.8172338 0.699127151 0.931961945 0.931210434 0.675354838 1.447143319 3.166240497 1.246316596 2.923556132 0.883373415 1 9.383309514 -8.497840923 5.77888186 0.861208184 2.331146717 0.68420995 0.481701811 0.072500149 7.730254763 0.061109346 0.133582408 3.18E-09 8.497840923 1.469938533 S(ph)VEEPTQPGGTGLSDSR ddPTM_HeLa_Romidepsin_16h_R1 2 SVEEPTQPGGTGLSDSR 17 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 0 S(0.997)VEEPT(0.003)QPGGTGLSDSR;S(1)VEEPTQPGGTGLSDSR ; 253.34 2.01E-72 27635000 3186.5 3455.7 3643.8 2023.51 3066.7 3068 2592 2667.4 3722.1 3545.1 TRUE FALSE FALSE 3147.661712 3504.349435 3707.21881 2257.477747 2910.194856 2871.964702 2812.164415 2744.577011 3389.186054 3452.997791 0.911573625 1.014871612 1.073623279 0.653773296 0.842802409 0.831730825 0.814412457 0.794838913 0.981519902 1 11.7536337 -9.268941851 24.98710751 0.970197306 0.794534409 0.719499088 0.064084462 283.7903455 945167.7188 0.010391341 0.016066963 5.38E-10 9.268941851 -0.175662897 S(ph)VELDLNQAHMEETPK ddPTM_HeLa_Romidepsin_16h_R1 3 SVELDLNQAHMEETPK 16 0 Q14680-3;Q14680-4;Q14680-5;Q14680-2;Q14680-8;Q14680-6;Q14680;Q14680-7 Q14680-3 MELK Maternal embryonic leucine zipper kinase 1 0 S(0.999)VELDLNQAHMEET(0.001)PK;S(0.994)VELDLNQAHMEET(0.006)PK;S(1)VELDLNQAHMEETPK ;; 117.53 0.0040452 44456100 7121.2 6608.7 6718.2 6423.7 4838.7 4204.7 3535.7 4086.2 7337.9 7465.7 TRUE FALSE FALSE 7034.404075 6701.737452 6835.127453 7166.438418 4591.763083 3936.03324 3836.02227 4204.42775 6681.579846 7271.740038 0.967361875 0.921614004 0.939957619 0.985519062 0.63145314 0.541278046 0.527524671 0.578187302 0.918841957 1 12.82808491 -8.69788648 3.902061054 0.976128797 0.552191332 0.970437704 0.033059483 0.023287342 0.708875565 0.004749381 0.009688276 2.00E-09 8.69788648 -0.423937465 S(ph)VEPQDAGPLER ddPTM_HeLa_Romidepsin_16h_R1 3 SVEPQDAGPLER 12 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 0 S(1)VEPQDAGPLER;S(1)VEPQDAGPLER;S(1)VEPQDAGPLER ;; 148.18 0.0014787 46324200 6519.2 6531.1 5890.3 5617.1 5824.1 5895.3 5463.4 5906.2 6261.2 6435.4 TRUE FALSE FALSE 6439.741483 6623.044997 5992.818201 6266.575531 5526.874444 5518.609356 5927.46106 6077.086579 5701.182591 6268.20738 1.027365735 1.056609106 0.95606572 0.999739663 0.881731268 0.880412696 0.945638952 0.969509496 0.909539561 1 12.6138372 -9.081582993 1.980635843 1.014681107 0.920340492 0.256644579 0.048999189 0.175864874 1.35967069 0.005684697 0.01076696 8.29E-10 9.081582993 -0.094340615 S(ph)VEYEGDLK ddPTM_HeLa_Romidepsin_16h_R1 1 SVEYEGDLK 9 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 S(1)VEYEGDLK 133.42 0.0069882 12535000 2205.7 1914.8 1627.1 1223.5 1986.4 1909.6 1795.6 1759.6 2032.5 2092.2 TRUE FALSE FALSE 2178.81608 1941.756605 1655.418993 1364.966827 1885.026596 1787.582723 1948.118219 1810.51125 1850.70811 2037.844342 1.069176892 0.952848343 0.812338292 0.66980917 0.925010098 0.877192966 0.95597008 0.888444329 0.908169516 1 10.99282814 -9.980863785 4.427047261 1.032128141 0.855849893 0.333433142 0.084143221 0.121894562 5.813345916 0.013197709 0.017139579 1.05E-10 9.980863785 -0.176278248 S(ph)VGGSGGGSFGDNLVTR ddPTM_HeLa_Romidepsin_16h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 S(0.988)VGGS(0.005)GGGS(0.007)FGDNLVTR 172.56 1.89E-06 87479000 857.64 862.07 1006.4 901.16 768.08 871.98 852.6 1058.4 730.92 904.8 TRUE FALSE FALSE 847.1867538 874.2062441 1023.91597 1005.356359 728.8820115 816.2632922 925.0198227 1089.023134 665.5446846 881.2931656 0.961299584 0.991958497 1.161833553 1.140774034 0.827059644 0.92621085 1.049616471 1.235710405 0.75519102 1 9.783478207 -7.310862471 3.37634139 0.992211182 1.255183812 0.301854349 0.118350467 0.219671267 4.162592606 0.013046211 0.137099558 4.89E-08 7.310862471 0.26297263 S(ph)VGSDERR ddPTM_HeLa_Romidepsin_16h_R1 2 SVGSDERR 8 1 C9IZQ1 C9IZQ1 SSR1 1 0 S(1)VGSDERR;S(1)VGSDERR ; 71.342 0.023864 6665100 2332.77 3570.09 2782.73 136.49 1395.79 2531.05 2175.21 2375.8 3133.71 2465.19 TRUE FALSE FALSE 2304.337302 3620.349821 2831.162248 152.271616 1324.557628 2369.324074 2359.972283 2444.540025 2853.423129 2401.144008 0.95968309 1.507760388 1.1790889 0.063416278 0.551636063 0.986748011 0.982853288 1.018073059 1.188359848 1 11.22950622 S(ph)VNFSLTPNEIK ddPTM_HeLa_Romidepsin_16h_R1 1 SVNFSLTPNEIK 12 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.592)VNFS(0.032)LT(0.376)PNEIK 187.62 6.85E-10 126700000 6484.1 6246.9 6195.1 4873.4 6900.9 7401.2 6651.9 6623.2 6435.5 6116.5 TRUE FALSE FALSE 6405.069295 6334.844022 6302.923117 5436.885438 6548.721322 6928.287206 7216.91222 6814.831842 5859.892762 5957.592448 1.075110349 1.063322823 1.057964802 0.912597746 1.099222778 1.162934065 1.211380651 1.143890238 0.983600811 1 12.54051372 -8.42384187 3.804255673 1.032066221 1.175695116 0.663071108 0.049350605 0.11687227 3.054287966 0.007247252 0.016869285 3.77E-09 8.42384187 0.143628896 S(ph)VPEDDGHALLAER ddPTM_HeLa_Romidepsin_16h_R1 2 SVPEDDGHALLAER 14 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 S(1)VPEDDGHALLAER;S(1)VPEDDGHALLAER ; 165.58 4.16E-05 7541400 1974.06 1822.17 1636.57 1792.47 1971.01 2091.23 1952.16 1787.23 2024.16 1814.14 TRUE FALSE FALSE 1949.999397 1847.822557 1665.053814 1999.723815 1870.422005 1957.607152 2117.976422 1838.94068 1843.11406 1767.008381 1.10355979 1.045735027 0.942301028 1.131700243 1.058524693 1.107865233 1.198622737 1.040708522 1.043070355 1 10.78709317 S(ph)VPNTPLRPNQQSVVNSSFSELFVK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 H0YJ97;Q15643-2;Q15643 H0YJ97 TRIP11 Thyroid receptor-interacting protein 11 1 0 S(0.988)VPNT(0.009)PLRPNQQS(0.001)VVNS(0.001)SFSELFVK 59.211 0.002217 32505000 1532.1 1734.9 1686.3 1644 1570.7 1517.3 1256.8 1387.5 1924.7 1706.6 TRUE FALSE FALSE 1513.426176 1759.323968 1715.649344 1834.087015 1490.541318 1420.349427 1363.552561 1427.645123 1752.550012 1662.262286 0.910461718 1.058391316 1.032117108 1.103368001 0.896694421 0.854467697 0.820299283 0.858856713 1.054316173 1 10.69893233 -8.532443768 24.75017764 0.981210228 0.847694353 0.623706517 0.059240869 117.0503426 302875.484 0.009595855 0.019212046 2.93E-09 8.532443768 -0.133515875 S(ph)VPSETVVEDSR ddPTM_HeLa_Romidepsin_16h_R1 3 SVPSETVVEDSR 12 0 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 S(0.927)VPS(0.028)ET(0.04)VVEDS(0.005)R;S(1)VPSETVVEDSR;S(1)VPSETVVEDSR ;; 172.33 0.00010077 43458500 1203.35 848.15 798.52 1340.14 1556.21 2460.61 1981.68 2471.03 958.47 867.1 TRUE FALSE FALSE 1188.683107 860.090278 812.4179056 1495.093292 1476.790797 2303.384962 2150.00385 2542.525354 872.7420427 844.572617 1.407437423 1.018373389 0.961927831 1.770236522 1.748565804 2.727278763 2.5456708 3.010428355 1.033353468 1 9.722077662 -8.469847982 1.196517399 1.167304977 2.878821438 0.91651141 0.214663474 0.107465316 0.28794134 0.036173712 0.131043449 3.39E-09 8.469847982 1.711516461 up S(ph)VQEGENPDDGVR ddPTM_HeLa_Romidepsin_16h_R1 1 SVQEGENPDDGVR 13 0 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 0 S(1)VQEGENPDDGVR 108.66 0.0076783 10923000 463.05 317.58 363.21 328.42 363.7 462.82 495.75 393.6 539.12 422.17 TRUE FALSE FALSE 457.4061685 322.0508996 369.5315177 366.3934657 345.1390318 433.2472957 537.8589926 404.988195 490.8997569 411.2019625 1.112363778 0.783193975 0.898661853 0.89103044 0.839341889 1.053611936 1.308016599 0.98488877 1.193816668 1 8.68370334 -7.990477895 24.94256308 0.994908748 1.155043125 0.197308077 0.139577117 257.5550324 674637.3911 0.019292779 0.057776559 1.02E-08 7.990477895 0.160134377 S(ph)VS(ph)PPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSPPPKR 8 1 Q13247 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 2 0 S(1)VS(1)PPPKR 74.533 0.0042847 0 7427.1 8129.6 8704.4 7004.5 6191 7922.3 8705.3 3639.3 9997.9 9320.5 TRUE FALSE FALSE 7336.575648 8244.048722 8855.896431 7814.393247 5875.050168 7416.090598 9444.727965 3744.597404 9103.662784 9078.352066 0.808139582 0.908099693 0.975496033 0.860772218 0.647149408 0.816898325 1.040357093 0.412475455 1.00278803 1 13.14821472 -4 0.130942581 1.007595126 2.48E-10 0.30617151 0.152836365 96.65636521 0.851996504 0.501703548 18.07481125 1.00E-04 4 -1.007595125 S(ph)VS(ph)PS(ph)KT(ph)LSVPDK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSPSKTLSVPDK 13 1 C9JWC4;Q8NCD3-3;Q8NCD3-2;Q8NCD3 C9JWC4 HJURP Holliday junction recognition protein 4 0 S(0.998)VS(0.999)PS(0.999)KT(0.578)LS(0.426)VPDK 63.709 0.004313 0 1467.1 1843 1418.6 1103.5 1192.6 582.36 714.67 291.7 651.28 505.17 TRUE FALSE FALSE 1449.218421 1868.945802 1443.290138 1231.091862 1131.737172 545.1490755 775.374052 300.1398793 593.0278856 492.0456106 2.945292854 3.798318209 2.933244616 2.501987287 2.300065578 1.107923867 1.575817435 0.609983857 1.205229501 1 8.942648243 -8.260307362 24.39822325 2.227878253 1.145699206 0.333423497 0.811527511 94.40946191 2034738.434 0.145297442 0.348772934 5.49E-09 8.260307362 -1.082179047 S(ph)VSEINS(ph)DDELSGK ddPTM_HeLa_Romidepsin_16h_R1 3 SVSEINSDDELSGK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 2 0 S(1)VSEINS(1)DDELSGK;S(0.985)VS(0.015)EINS(1)DDELSGK;S(0.987)VS(0.013)EINS(1)DDELSGK ;; 254.72 1.37E-66 20974900 7706.36 8935.3 8115.03 6393.22 9062.1 8009.3 6908.88 8119.02 7786.88 7916.3 TRUE FALSE FALSE 7612.43192 9061.091388 8256.268693 7132.434177 8599.627222 7497.531579 7495.720095 8353.931034 7090.40195 7710.633385 0.987264151 1.175142292 1.070764006 0.925012748 1.115294528 0.972362607 0.972127674 1.083429936 0.919561545 1 12.91263366 S(ph)VSEINSDDELSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSEINSDDELSGK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 S(0.999)VS(0.001)EINSDDELSGK 340.47 1.75E-198 165010000 7476.7 7389.8 7419.4 6863.1 9287.4 8430.7 8760.4 8232.1 7331.9 6904.1 TRUE FALSE FALSE 7385.571105 7493.833798 7548.531545 7656.643914 8813.429322 7892.005479 9504.508157 8470.282825 6676.116501 6724.730487 1.098270201 1.114369388 1.122503208 1.138580041 1.310599635 1.173579446 1.413366406 1.259572089 0.992770865 1 12.71526073 -8.238440789 0.267939577 0.995929782 1.493538369 0.756761036 0.062040646 1.744565281 0.151780038 0.039911798 0.27867601 5.78E-09 8.238440789 0.497608587 S(ph)VSGSPEPAAK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 S(0.819)VS(0.02)GS(0.162)PEPAAK;S(0.983)VS(0.005)GS(0.012)PEPAAK ; 171.49 0.00027455 106374300 17279.2 16316.1 16228.9 13984.1 13546.6 15009.3 17109.5 8017.7 19736.1 19190.1 TRUE FALSE FALSE 17068.59446 16545.79848 16511.3572 15601.00744 12855.26645 14050.25417 18562.7805 8249.6795 17970.85379 18691.53844 0.913172264 0.885202603 0.88335999 0.834656146 0.687758608 0.751690623 0.993111432 0.441359042 0.961443267 1 14.1900977 -5.437020049 0.176885712 1.026796101 1.62E-13 0.460260927 0.119087958 22.95469223 0.387937377 0.164848899 5.749401666 3.66E-06 5.437020049 -1.026796101 S(ph)VSPQNSDSSGFADVNGWHLR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSPQNSDSSGFADVNGWHLR 21 0 S4R3E2;Q9UKB3 S4R3E2 DNAJC12 DnaJ homolog subfamily C member 12 1 0 S(0.5)VS(0.5)PQNSDSSGFADVNGWHLR 195.94 1.11E-18 7730000 793.8 958.62 1069.2 1274.3 1498.9 1650 1506.3 1445.1 1112.1 1322.2 TRUE FALSE FALSE 784.1248603 972.1154775 1087.808977 1421.640562 1422.40554 1544.570325 1634.245084 1486.911689 1012.630991 1287.849053 0.608863949 0.754836504 0.844671178 1.10388757 1.104481566 1.199341119 1.26897254 1.15456985 0.786296335 1 10.33074779 -9.163604705 2.155838776 0.804280017 1.191322224 0.785443685 0.096890401 0.171786278 1.56047303 0.024016095 0.043252831 6.86E-10 9.163604705 0.387042207 S(ph)VSSFPVPQDNVDTHPGSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSFPVPQDNVDTHPGSGK 20 0 C9JAY7;E7EVC7;Q676U5-4;Q676U5-5;Q676U5-3;Q676U5-2;Q676U5 C9JAY7 ATG16L1 Autophagy-related protein 16-1 1 0 S(0.839)VS(0.08)S(0.08)FPVPQDNVDTHPGSGK 73.461 0.0031358 9904900 6503.7 5864.1 5594.3 1898.5 7125 7967.5 5864.6 6747.3 6427.5 5254.4 TRUE FALSE FALSE 6424.430403 5946.654954 5691.666445 2118.013503 6761.384663 7458.402464 6362.738978 6942.52248 5852.608302 5117.889931 1.255288896 1.161934906 1.112111929 0.413845067 1.321127409 1.457319826 1.243234822 1.356520475 1.143558846 1 12.3213334 -8.560564233 24.99999521 1.073357964 1.349411809 0.320974182 0.225982665 179.4180438 119022.6253 0.034324435 0.06864897 2.75E-09 8.560564233 0.276053845 S(ph)VSVVTGSEQK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSVVTGSEQK 11 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.999)VS(0.001)VVTGSEQK;S(0.978)VS(0.021)VVT(0.001)GSEQK ; 184.98 3.20E-06 64322000 8062.5 10646.2 4964.3 6105.9 13681.4 7885.6 4701 9413 5931.1 6312.6 TRUE FALSE FALSE 7964.231149 10796.07748 5050.701559 6811.892887 12983.18711 7381.73561 5100.302823 9685.350304 5400.607561 6148.597742 1.295292274 1.755860106 0.821439582 1.107877466 2.111568792 1.200555951 0.829506667 1.575212871 0.878347843 1 12.58604171 -11.87939027 0.811305735 1.005400674 1.327628806 0.139937345 0.381156794 1.182339571 1.480715411 0.216875576 0.077159244 1.32E-12 11.87939027 0.322228132 S(ph)VTLEEAIAEQNESER ddPTM_HeLa_Romidepsin_16h_R1 1 SVTLEEAIAEQNESER 16 0 H7BYY2;Q6W2J9-4;Q6W2J9-2;Q6W2J9;H7C231 H7BYY2 BCOR BCL-6 corepressor 1 0 S(0.999)VT(0.001)LEEAIAEQNESER 181.69 1.84E-08 2332700 215.72 139.05 215.68 242.92 245.38 150.27 0 163.59 236.45 240.38 TRUE FALSE FALSE 213.0907217 141.0075495 219.4338199 271.0075534 232.857343 140.668232 0 168.3232185 215.3013198 234.1348929 0.910119457 0.60224919 0.937211097 1.157484687 0.99454353 0.60079995 0 0.718915564 0.919561015 1 7.871196144 -8.067702096 4.264198803 0.943725378 0.344800942 0.554156038 0.208357131 0.103063469 3.626347647 0.027701655 0.077298448 8.56E-09 8.067702096 -0.598924436 S(ph)VTPASTLTK ddPTM_HeLa_Romidepsin_16h_R1 2 SVTPASTLTK 10 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 S(0.889)VT(0.004)PAS(0.006)T(0.099)LT(0.002)K;S(0.792)VT(0.199)PAS(0.001)T(0.008)LTK ; 107.34 0.0041275 9430000 9124.3 8934.2 8475.9 11727.5 12879.7 13470.5 11994.9 12132.1 9170.7 8334.2 TRUE FALSE FALSE 9013.089522 9059.975902 8623.419484 13083.48873 12222.40085 12609.77852 13013.74651 12483.12317 8350.449624 8117.676283 1.110304132 1.11607997 1.062301474 1.611728317 1.505652655 1.553372922 1.603136914 1.537770507 1.028674874 1 12.98685109 -9.265140519 24.99056373 1.059924961 1.560952588 0.97146073 0.04274963 44.02244508 297245.0884 0.008154735 0.012760105 5.43E-10 9.265140519 0.501027627 S(ph)VVGTPAYLAPEVLLNQGYNR ddPTM_HeLa_Romidepsin_16h_R1 2 SVVGTPAYLAPEVLLNQGYNR 21 0 Q9BZL6-2;Q9BZL6;Q9BZL6-3 Q9BZL6-2 PRKD2 Serine/threonine-protein kinase D2 1 0 S(0.985)VVGT(0.015)PAYLAPEVLLNQGYNR;S(0.992)VVGT(0.008)PAYLAPEVLLNQGYNR ; 265.93 1.62E-90 4449900 1443.15 1451.57 1395.77 1495.78 2498.7 2233.5 1107.43 1877.13 1248.18 1127.25 TRUE FALSE FALSE 1425.560333 1472.005241 1420.062791 1668.729121 2371.182015 2090.786558 1201.495077 1931.441795 1136.539655 1097.963882 1.298367237 1.34066818 1.293360204 1.519839722 2.1596175 1.904239831 1.094293807 1.759112322 1.035133917 1 10.10061488 -10.11009682 0.612124884 1.068118937 1.689426671 0.459759686 0.272056347 0.506046748 0.410675863 0.084319186 0.112472354 7.76E-11 10.11009682 0.621307734 S(ph)VVGTPAYLAPEVLR ddPTM_HeLa_Romidepsin_16h_R1 2 SVVGTPAYLAPEVLR 15 0 O94806;H0Y5M6;F8WBA3;Q15139 O94806 PRKD3;PRKD1 Serine/threonine-protein kinase D3;Serine/threonine-protein kinase;Serine/threonine-protein kinase D1 1 0 S(0.977)VVGT(0.008)PAY(0.014)LAPEVLR;S(0.97)VVGT(0.018)PAY(0.011)LAPEVLR ; 99.238 0.0082507 19954400 959.92 973.74 429.52 659.14 1126.72 889.34 555.94 811.1 972.65 767.73 TRUE FALSE FALSE 948.2201258 987.4483373 436.9956154 735.3528681 1069.219274 832.5140442 603.1615297 834.5678988 885.653748 747.7842639 1.268039689 1.320498953 0.584387285 0.983375692 1.429849925 1.113307787 0.806598318 1.116054374 1.184370668 1 9.546478302 S(ph)VVSDLEADDVK ddPTM_HeLa_Romidepsin_16h_R1 6 SVVSDLEADDVK 12 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 S(0.999)VVS(0.001)DLEADDVK;S(0.988)VVS(0.012)DLEADDVK;S(0.988)VVS(0.012)DLEADDVK;S(0.987)VVS(0.013)DLEADDVK;S(0.982)VVS(0.018)DLEADDVK;S(0.996)VVS(0.004)DLEADDVK ;;;;; 176.99 1.96E-06 189612800 25415.5 22639.9 26889.1 13761.48 20916.4 19860.8 16479.13 18387.4 27201.9 25655.5 TRUE FALSE FALSE 25105.72611 22958.62511 27357.09351 15352.64707 19848.95806 18591.75898 17878.86689 18919.41041 24768.89394 24988.96641 1.00467245 0.918750489 1.094766909 0.614377034 0.794308885 0.743998718 0.715470444 0.757110562 0.991193214 1 14.60900361 -9.264165347 24.99998594 1.000986519 0.729420831 0.848128634 0.058555453 60.30233154 553036.0448 0.007986973 0.012540075 5.44E-10 9.264165347 -0.271565688 S(ph)VVSFDK ddPTM_HeLa_Romidepsin_16h_R1 1 SVVSFDK 7 0 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 S(1)VVSFDK 141.52 0.013143 78453000 6949 6941.3 7089.1 3807.5 7586.2 7761.6 6136.3 7437.5 6906.7 7109.7 TRUE FALSE FALSE 6864.302915 7039.019804 7212.482812 4247.741065 7199.047906 7265.658809 6657.517169 7652.692328 6288.947454 6924.988969 0.991236657 1.016466573 1.041515422 0.613393189 1.039575361 1.049194279 0.961375852 1.105083685 0.908152703 1 12.75759606 -8.840311092 0.002251324 1.961224133 5.76E-06 0 0.131320504 751774.5442 517.9544679 223818.9156 227393.8908 1.44E-09 8.840311092 -1.961218373 S(ph)WASPVYTEADGTFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SWASPVYTEADGTFSR 16 0 E9PMS6;Q8WWI1-3;E9PMP7;E9PJ10;E9PK58;E9PLU6 E9PMS6 LMO7 LIM domain only protein 7 1 0 S(0.994)WAS(0.006)PVYTEADGTFSR;S(0.777)WAS(0.222)PVYTEADGTFSR ; 197.73 8.19E-14 117610000 2431.63 2288.34 2323.82 2646.7 3159.1 3336.16 2846.95 3013 2621.79 2876.57 TRUE FALSE FALSE 2401.992358 2320.555311 2364.265112 2952.723907 2997.879339 3122.990143 3088.769862 3100.176401 2387.290536 2801.836297 0.857292184 0.828226586 0.843826998 1.053853114 1.069969485 1.11462263 1.102409111 1.106480205 0.852044975 1 11.45215695 -9.098947408 4.73375138 0.915581935 1.096139442 0.788452775 0.053633869 0.118200762 4.333300712 0.010691229 0.018122996 7.96E-10 9.098947408 0.180557508 S(ph)WDSSSPVDRPEPEAASPTTR ddPTM_HeLa_Romidepsin_16h_R1 1 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 S(0.998)WDS(0.001)SSPVDRPEPEAASPTTR 94.359 0.00030686 4618900 183.74 220.25 164.97 170.01 257.12 218.05 149.19 317.22 191.62 212.97 TRUE FALSE FALSE 181.5005062 223.3506853 167.8412336 189.6673561 243.998207 204.1173087 161.8621949 326.3982602 174.4810273 207.4370087 0.874966851 1.076715706 0.809119041 0.914337115 1.176252051 0.983996588 0.780295647 1.573481329 0.841127764 1 7.696529497 -7.251816517 24.97889735 0.948866204 1.573481666 0.72318818 0.117518045 502.0023443 1303065.084 0.01519533 0.264742668 5.60E-08 7.251816517 0.624615462 S(ph)WGQQAQEYQEQK ddPTM_HeLa_Romidepsin_16h_R1 2 SWGQQAQEYQEQK 13 0 Q5VZK9;Q5VZK9-2 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 S(1)WGQQAQEYQEQK;S(1)WGQQAQEYQEQK ; 270.07 7.78E-80 6629500 1669.38 1807.35 1952.98 2061.1 2685.2 2179.2 1727.16 1771.57 1671.99 1904.05 TRUE FALSE FALSE 1649.032954 1832.793921 1986.970798 2299.41408 2548.164224 2039.956153 1873.864927 1822.827583 1522.443027 1854.582507 0.889166672 0.988251487 1.071384417 1.23985537 1.37398267 1.099954381 1.010397176 0.982877589 0.820908761 1 10.85687874 -9.69193607 3.046815323 0.947917541 1.145059498 0.438723222 0.114761081 0.206245141 3.891025878 0.019433339 0.027774403 2.03E-10 9.69193607 0.197141956 S(ph)WSPPPEVSR ddPTM_HeLa_Romidepsin_16h_R1 2 SWSPPPEVSR 10 0 F8WCJ4;C9JXD9;C9IYL0;B4DEH9;C9JY31;Q9NR19;Q9NR19-2 F8WCJ4 ACSS2 "Acetyl-coenzyme A synthetase, cytoplasmic" 1 0 S(0.753)WS(0.247)PPPEVSR;S(0.999)WS(0.001)PPPEVSR ; 144.17 0.0041369 188488000 6753.9 6859.4 7299.6 6707.4 9359.7 9846.9 8527.8 10297.2 7512.2 7194.6 TRUE FALSE FALSE 6671.580869 6955.966813 7426.646476 7482.941147 8882.039583 9217.714869 9252.151119 10595.13324 6840.290017 7007.683255 0.952038017 0.992620037 1.059786267 1.067819545 1.267471611 1.315372647 1.320286717 1.511930955 0.976112899 1 12.77472185 -8.43614115 0.76179162 0.974265896 1.478288608 0.944648526 0.042906235 0.139221373 0.128376536 0.007714409 0.042866902 3.66E-09 8.43614115 0.504022712 S(ph)YDVPPPPMEPDHPFYSNISK ddPTM_HeLa_Romidepsin_16h_R1 3 SYDVPPPPMEPDHPFYSNISK 21 0 P18669;Q8N0Y7 P18669 PGAM1;PGAM4 Phosphoglycerate mutase 1;Probable phosphoglycerate mutase 4 1 0 S(0.965)Y(0.035)DVPPPPMEPDHPFYSNISK;S(0.989)Y(0.011)DVPPPPMEPDHPFYSNISK;S(0.691)Y(0.309)DVPPPPMEPDHPFYSNISK ;; 106.72 9.48E-05 750893400 9945.5 9728.9 8826.4 8272.8 10962.3 11132.3 9559.1 10847.8 10916.7 10171.6 TRUE FALSE FALSE 9824.280421 9865.86371 8980.01979 9229.340061 10402.85293 10420.98196 10371.04972 11161.66398 9940.283011 9907.340366 0.991616323 0.995813543 0.906400654 0.931565861 1.05001469 1.051844549 1.046804625 1.126605483 1.003325075 1 13.2742821 -8.59681641 7.157917731 0.984471576 1.068826104 0.615456005 0.037139973 0.13833884 11.15419274 0.005754961 0.011566784 2.53E-09 8.59681641 0.084354529 S(ph)YEDLTESEDGAASGDSHK ddPTM_HeLa_Romidepsin_16h_R1 2 SYEDLTESEDGAASGDSHK 19 0 A0A0A0MSQ9;Q86VX9-5;Q86VX9 A0A0A0MSQ9 MON1A Vacuolar fusion protein MON1 homolog A 1 0 S(0.83)YEDLT(0.17)ESEDGAASGDSHK;S(0.999)YEDLT(0.001)ESEDGAASGDSHK ; 283.19 3.57E-107 32491000 10807.6 10946.6 9446 7093 9983.3 11850.6 10090.5 12059.6 13200.5 13153.8 TRUE FALSE FALSE 10675.87281 11100.70652 9610.403668 7913.126034 9473.814948 11093.38491 10947.58682 12408.5255 12019.81422 12812.06238 0.833267315 0.8664262 0.750105907 0.617630932 0.73944496 0.865854737 0.854474986 0.968503363 0.938163885 1 13.64521511 -11.7390317 0.689520388 0.998926712 0.802426574 0.32050526 0.090635815 0.599071644 0.549437477 0.061444544 0.022052862 1.82E-12 11.7390317 -0.196500138 S(ph)YELPDGQVITIGNER ddPTM_HeLa_Romidepsin_16h_R1 1 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;Q6S8J3;A5A3E0;Q562R1;A0A2R8YEA7;Q9BYX7;P63261;P63267;P68133;P68032;P62736 P60709;P63261;P63267 ACTB;ACTG2;POTEE;POTEF;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;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" 1 0 S(1)YELPDGQVITIGNER 99.813 0.0055444 8212100 1285 1410.5 1371.7 1259.1 1605.2 1443.7 1181.9 1388.6 1433.5 1460.2 TRUE FALSE FALSE 1269.337926 1430.357056 1395.573863 1404.683066 1523.280654 1351.452229 1282.290556 1428.77695 1305.28417 1422.263793 0.892477142 1.005690409 0.981234191 0.987638912 1.071025404 0.950212074 0.901584194 1.004579429 0.917751106 1 10.47397336 S(ph)YMERLS(ph)LRNKAT(ph)AEILK ddPTM_HeLa_Romidepsin_16h_R1 1 SYMERLSLRNKATAEILK 18 3 A0A0G2JQE0;A0A0G2JNC7;A0A0G2JS53;Q13075-2;Q13075;E7EQW0;B7ZLE8 A0A0G2JQE0 NAIP Baculoviral IAP repeat-containing protein 1 3 0 S(0.526)Y(0.482)MERLS(0.994)LRNKAT(0.999)AEILK 43.408 0.028872 2876900 1423.9 993.96 1105.8 186.94 1037.6 861.33 1161.8 808.69 1336.3 1168.1 TRUE FALSE FALSE 1406.544959 1007.952995 1125.045985 208.5548824 984.6474002 806.2937928 1260.483263 832.0881692 1216.777981 1137.752594 1.236248519 0.885915796 0.988831835 0.183304247 0.86543191 0.70867234 1.10787114 0.73134368 1.069457444 1 10.15197116 -9.829797492 2.372832847 1.108247146 0.746610786 0.295203219 0.234166122 0.255649457 2.946789125 0.03956033 0.054742539 1.48E-10 9.829797492 -0.36163636 S(ph)YPGHVQPATAR ddPTM_HeLa_Romidepsin_16h_R1 1 SYPGHVQPATAR 12 0 Q86VS8;H0YDK4 Q86VS8 HOOK3 Protein Hook homolog 3 1 0 S(0.994)Y(0.006)PGHVQPATAR 78.191 0.022101 3299900 1434.6 1362.5 1487 1621 2044.7 2368.2 1805.6 1841 1464.7 1423.5 TRUE FALSE FALSE 1417.114543 1381.681311 1512.880611 1808.427647 1940.351329 2216.879663 1958.967619 1894.26643 1333.693564 1386.517265 1.022067723 0.996512157 1.091137233 1.30429508 1.399442602 1.598883562 1.412869258 1.366204719 0.96190188 1 10.43724987 -9.153669311 1.791601124 1.009032346 1.457120451 0.923844876 0.059313172 0.062248491 0.391144056 0.009102386 0.017030733 7.02E-10 9.153669311 0.448088105 S(ph)YSLSELSVLQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 0 S(0.585)YS(0.026)LS(0.074)ELS(0.315)VLQAK 212.83 2.86E-23 149890000 3306.5 3600 3089.3 2727.8 2871.4 2318.3 2050 2405.3 3734.7 3241.8 TRUE FALSE FALSE 3266.199106 3650.680894 3143.067971 3043.201071 2724.861743 2170.168112 2224.126949 2474.893561 3400.659078 3157.577569 1.034400275 1.156165071 0.995404832 0.963777138 0.862959558 0.687288931 0.704377612 0.783795016 1.076983543 1 11.62460246 -8.637848407 1.941002039 1.026871253 0.722036394 0.875615594 0.053432844 0.083610798 0.63485326 0.008040271 0.019357275 2.30E-09 8.637848407 -0.304834859 S(ph)YSPDGK ddPTM_HeLa_Romidepsin_16h_R1 1 SYSPDGK 7 0 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2 D6REM6 MATR3 Matrin-3 1 0 S(0.991)YS(0.009)PDGK 115.7 0.028111 36722000 4807.8 6408.7 13236 4345.7 4229.1 3775.5 8703.8 2085.9 8148.4 6774.8 TRUE FALSE FALSE 4749.200684 6498.921847 13466.36703 4848.170281 4013.273246 3534.257735 9443.100555 2146.252225 7419.586696 6598.789719 0.719707838 0.984865729 2.040732862 0.734705982 0.60818323 0.535591811 1.431035229 0.325249374 1.124385988 1 12.68798573 S(ph)YTLVVAK ddPTM_HeLa_Romidepsin_16h_R1 1 SYTLVVAK 8 0 O43491;O43491-4;E9PHY5;E9PK52;O43491-3;O43491-2;E9PII3;A0A2R8Y5B3;E9PJP4;E9PQD2;E9PIG0;E9PRG1;E9PQN0 O43491 EPB41L2 Band 4.1-like protein 2 1 0 S(0.993)YT(0.007)LVVAK 167.12 0.0017976 44563000 2991.9 2269.3 3637.2 3101.5 3281.6 3337.8 3377.1 2427.5 2784.8 2604.2 TRUE FALSE FALSE 2955.433572 2301.247265 3700.50394 3460.110023 3114.127707 3124.525352 3663.95079 2497.735883 2535.720513 2536.542509 1.165142536 0.907237808 1.458877164 1.364104883 1.227705704 1.231804845 1.444466543 0.984700975 0.999675939 1 11.30864762 -10.50136663 0.648008577 1.034907757 1.275416226 0.26284751 0.16385558 0.650121524 0.605464099 0.050868833 0.050722121 3.15E-11 10.50136663 0.240508469 S(ph)YVTTSTR ddPTM_HeLa_Romidepsin_16h_R1 3 SYVTTSTR 8 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 S(0.967)YVT(0.024)T(0.007)S(0.002)TR;S(0.994)YVT(0.005)TSTR;S(1)YVTTSTR ;; 135.43 0.0093163 161611000 4426.72 3808.11 3705.74 2821.03 5157.1 4355.18 3820.83 3813.62 4334.94 3506.88 TRUE FALSE FALSE 4372.765434 3861.720673 3770.23685 3147.210762 4893.913943 4076.898054 4145.371205 3923.961078 3947.212109 3415.770752 1.28016947 1.130556162 1.103773386 0.921376459 1.432740748 1.193551426 1.213597605 1.148777644 1.155584609 1 11.73799544 -12.53146257 1.275661426 0.999461164 1.18813165 0.032254998 0.131799958 0.537056116 1.557850122 0.0881755 0.02081182 2.94E-13 12.53146257 0.188670486 SAAAGALGS(ph)PGLPLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SAAAGALGSPGLPLRK 16 1 O75145-2;O75145;A0A0C4DGR8;A0A0C4DGR7 O75145-2 PPFIA3 Liprin-alpha-3 1 0 SAAAGALGS(1)PGLPLRK 61.684 0.019424 23152000 1203.2 1160.3 936.74 1477.5 2131.2 1870.5 1740.4 1592.2 1177.1 1167.2 TRUE FALSE FALSE 1188.534936 1176.634734 953.0435668 1648.335502 2022.436911 1750.981087 1888.229533 1638.267795 1071.817228 1136.875976 1.045439398 1.03497194 0.838300384 1.44988155 1.77894243 1.540168958 1.660893161 1.441025961 0.942774103 1 10.15085916 -9.111369209 4.76499344 1.011722427 1.605886285 0.897732864 0.102049357 0.047102664 1.673034599 0.013920762 0.02354256 7.74E-10 9.111369209 0.594163858 SAADSIS(ph)ESVPVGPK ddPTM_HeLa_Romidepsin_16h_R1 2 SAADSISESVPVGPK 15 0 P45974-2;P45974 P45974-2 USP5 Ubiquitin carboxyl-terminal hydrolase 5 1 0 S(0.001)AADS(0.167)IS(0.679)ES(0.153)VPVGPK;SAADS(0.19)IS(0.783)ES(0.027)VPVGPK ; 188.25 2.83E-12 43384000 13867.7 13052.3 13303.9 11601.1 12032.2 11081 7524.5 9266 12704.2 12066.2 TRUE FALSE FALSE 13698.67514 13236.05062 13535.4488 12942.47377 11418.15194 10372.95986 8163.630842 9534.097091 11567.90453 11752.71838 1.165575035 1.126211842 1.151686644 1.101232357 0.971532846 0.882600903 0.694616392 0.81122484 0.9842748 1 13.52070687 -8.26098798 1.773103555 1.091252187 0.753665773 0.805072886 0.065352313 0.126638606 0.754248975 0.011071798 0.037209264 5.48E-09 8.26098798 -0.337586414 SAAEMYGSSFDLDYDFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SAAEMYGSSFDLDYDFQR 18 0 P07910-2;G3V4C1;G3V2D6;B2R5W2;P07910-4;G3V4W0;G3V251;G3V3K6;G3V5X6;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 0 83.243 0.027464 6593900 2102.6 1851.1 1724.2 1760.9 1988.5 2105.4 1859.1 1841.7 1990.8 1902.9 FALSE FALSE TRUE 2076.972702 1877.159834 1754.208978 1964.503543 1887.019425 1970.871735 2017.011908 1894.986684 1812.737862 1853.462384 1.120590696 1.012785504 0.946449733 1.059910123 1.018105057 1.063345958 1.088240002 1.022403638 0.978027867 1 10.85600712 -12.84132635 1.917259664 0.999740782 1.055738027 0.098095222 0.047172481 0.592150012 3.94310507 0.040393177 0.008200021 1.44E-13 12.84132635 0.055997246 SAAQAAAQT(ph)NSNAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 SAAQAAAQTNSNAAGK 16 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 SAAQAAAQT(0.992)NS(0.008)NAAGK;SAAQAAAQT(0.995)NS(0.005)NAAGK ; 227 3.87E-40 1074300 1050 1392.76 1104 1024.18 1267.5 1200.42 1183.1 607.09 1217.82 1277.97 TRUE FALSE FALSE 1037.202196 1412.367312 1123.214657 1142.600511 1202.814745 1123.717036 1283.592484 624.6551913 1108.895129 1244.768155 0.833249302 1.13464287 0.902348483 0.91792235 0.966296206 0.902752076 1.031190008 0.501824528 0.890844712 1 10.28166134 -7.254040543 24.86194739 0.939798424 0.501824303 0.728791285 0.082247087 359.2645313 1207187.477 0.012010628 0.166811836 5.57E-08 7.254040543 -0.437974121 SAAQAAAQTNS(ph)NAAGK ddPTM_HeLa_Romidepsin_16h_R1 2 SAAQAAAQTNSNAAGK 16 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 SAAQAAAQT(0.167)NS(0.833)NAAGK;SAAQAAAQT(0.003)NS(0.997)NAAGK ; 200.71 2.22E-18 9218500 5131 6833.3 4918.5 4879.2 5330.9 4937.8 4521.6 4958.7 6214 5967.3 TRUE FALSE FALSE 5068.461398 6929.499377 5004.104429 5443.356061 5058.844281 4622.290516 4905.664591 5102.172161 5658.204277 5812.268686 0.872028062 1.192219381 0.860955455 0.936528635 0.870373438 0.795264425 0.844018895 0.877827994 0.97349324 1 12.50488568 -8.81743466 1.892080341 0.955184979 0.838407909 0.323449921 0.088186009 0.375038112 2.729091278 0.014178113 0.030957889 1.52E-09 8.81743466 -0.116777071 SAAQPSTS(ph)PAEVQSLKK ddPTM_HeLa_Romidepsin_16h_R1 1 SAAQPSTSPAEVQSLKK 17 1 Q14789-4;Q14789-3;Q14789;Q14789-2 Q14789-4 GOLGB1 Golgin subfamily B member 1 1 0 SAAQPS(0.002)T(0.028)S(0.97)PAEVQSLKK 107.06 0.00069943 9534200 1840.5 2025.8 1592.8 1483.2 1767.5 2661.1 1634.9 3350.9 1783.7 1924.4 TRUE FALSE FALSE 1818.067278 2054.319266 1620.522016 1654.694563 1677.29788 2491.064298 1773.768365 3447.853005 1624.161405 1874.403811 0.969944293 1.09598543 0.864553308 0.882784464 0.8948434 1.328990202 0.946310691 1.839439818 0.866494933 1 10.87221608 -5.183613835 1.304596413 0.982559898 199.9999979 0.763547757 0.140877172 111.4442109 1.025826033 0.018105675 65530.03072 6.55E-06 5.183613835 199.017438 SAAS(ph)PVVSSMPER ddPTM_HeLa_Romidepsin_16h_R1 3 SAASPVVSSMPER 13 0 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 S(0.006)AAS(0.989)PVVS(0.004)S(0.001)MPER;S(0.015)AAS(0.981)PVVS(0.003)SMPER;S(0.004)AAS(0.985)PVVS(0.009)S(0.002)MPER ;; 103.11 0.01505 118306000 16190.8 14981.3 14690.3 12380.8 13488.6 12389.4 11531.6 12986.6 15964.6 15451.5 TRUE FALSE FALSE 15993.4603 15192.20713 14945.97851 13812.32635 12800.22641 11597.75732 12511.09382 13362.34678 14536.68619 15050.0678 1.062683605 1.009444431 0.993083799 0.917758413 0.850509551 0.770611633 0.83129817 0.887859574 0.965888419 1 13.87748237 -9.092077419 1.672274618 1.028712541 0.827333441 0.826187417 0.036693433 0.091267957 0.502811376 0.005724676 0.011206001 8.09E-10 9.092077419 -0.2013791 SAAS(ph)REDLVGPEVGASPQS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 SAASREDLVGPEVGASPQSGR 21 1 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 0 S(0.01)AAS(0.902)REDLVGPEVGAS(0.1)PQS(0.987)GR 91.643 0.015447 1870200 664.83 416.86 581.26 501.49 736.54 787.94 637.48 630.38 765.57 796.16 TRUE FALSE FALSE 656.7267962 422.728566 591.3765865 559.4746334 698.9516154 737.593177 691.6275353 648.6190507 697.0955018 775.4756484 0.846869657 0.545121651 0.762598526 0.721459964 0.901319876 0.951149373 0.891875247 0.836414466 0.89892636 1 9.598937668 -11.56257019 1.112415846 0.979169228 0.809333508 0.192146672 0.111805815 0.440389786 1.10264508 0.040020261 0.023374553 2.74E-12 11.56257019 -0.16983572 SAAS(ph)REDLVGPEVGASPQSGR ddPTM_HeLa_Romidepsin_16h_R1 1 SAASREDLVGPEVGASPQSGR 21 1 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 0 S(0.023)AAS(0.977)REDLVGPEVGASPQSGR 159.47 3.55E-16 0 689.73 474.26 743.81 612.19 738.02 967.42 886.81 797.06 841.56 837.92 TRUE FALSE FALSE 681.3233055 480.9366447 756.755701 682.9742882 700.3560855 905.6049842 962.1356193 820.1216735 766.2887659 816.1507176 0.834800841 0.589274302 0.927225431 0.836823731 0.858121019 1.109605082 1.178870028 1.004865469 0.938905951 1 9.672691787 -8.257721675 24.45508908 0.884885999 1.105889199 0.481306744 0.112440637 189.4321266 1246075.133 0.017952543 0.043874437 5.52E-09 8.257721675 0.2210032 SAATWDER ddPTM_HeLa_Romidepsin_16h_R1 1 SAATWDER 8 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 118.74 0.00065385 0 2348.4 2156.4 2534 1329.9 2738 2489.4 2557.3 2034.6 2446.3 2521.9 FALSE FALSE TRUE 2319.776798 2186.757856 2578.103207 1483.669295 2598.269643 2330.335374 2774.516998 2093.467941 2227.496801 2456.380674 0.944388149 0.890235735 1.049553611 0.604006256 1.057763428 0.948686577 1.129514259 0.852257129 0.906820683 1 11.26231844 -8.145881925 0.006450049 1.880743034 3.25E-07 0 0.139246513 48986.09022 68.81250527 9704.253791 10366.95991 7.15E-09 8.145881925 -1.880742709 SAAVETAS(ph)LSPSLVPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 0 SAAVET(0.037)AS(0.557)LS(0.381)PS(0.026)LVPAR 130.47 0.0019914 19635000 1035.7 864.21 1004.6 735.99 1913.8 2596.5 1836.4 2326.9 1249.9 917.18 TRUE FALSE FALSE 1023.07649 876.3763711 1022.084642 821.0886267 1816.131645 2430.59203 1992.38377 2394.22518 1138.105814 893.3515314 1.145211548 0.980998342 1.144101292 0.919110337 2.032941771 2.720756549 2.230234908 2.680048219 1.273973093 1 9.803084173 -8.619762398 3.66886685 1.059730336 2.501320219 0.943758309 0.163160011 0.030318542 0.789157604 0.020105054 0.042310025 2.40E-09 8.619762398 1.441589883 up SAAVETASLS(ph)PSLVPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SAAVETASLSPSLVPAR 17 0 Q2KHT3;Q2KHT3-3 Q2KHT3 CLEC16A Protein CLEC16A 1 0 S(0.196)AAVETAS(0.001)LS(0.784)PS(0.019)LVPAR 233.48 2.66E-46 35284000 1035.6 827.16 945.51 658.07 1907.8 2012.2 1793 2279.7 814.6 945.61 TRUE FALSE FALSE 1022.977709 838.8047802 961.9662049 734.1591497 1810.437847 1883.626914 1945.297375 2345.659523 741.7401358 921.0429159 1.110673228 0.910711939 1.044431468 0.797095485 1.965638968 2.045102222 2.112059429 2.546742917 0.805326357 1 9.84712457 -8.663029158 4.683693911 1.025602134 2.188802802 0.924790252 0.170680568 0.039123109 1.469707623 0.022957625 0.046694254 2.17E-09 8.663029158 1.163200668 up SADAGS(ph)FSPTPGQIGGAVK ddPTM_HeLa_Romidepsin_16h_R1 1 SADAGSFSPTPGQIGGAVK 19 0 O00443 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 0 SADAGS(0.914)FS(0.085)PT(0.001)PGQIGGAVK 254.59 9.36E-76 9279300 1723.4 1575.6 1457.2 1708.1 2145.5 2180.4 1771.2 2375.9 1683.7 1618 TRUE FALSE FALSE 1702.394538 1597.781338 1482.561955 1905.598559 2036.007129 2041.079477 1921.645684 2444.642918 1533.105655 1575.964127 1.080224168 1.013843723 0.940733313 1.209163665 1.291912103 1.295130671 1.219346082 1.551204673 0.972804919 1 10.62201898 -8.99654006 2.91839894 1.030218068 1.328524919 0.755976565 0.089875989 0.102387895 1.777879819 0.012947377 0.023985435 1.01E-09 8.99654006 0.298306851 SADAGSFS(ph)PTPGQIGGAVK ddPTM_HeLa_Romidepsin_16h_R1 1 SADAGSFSPTPGQIGGAVK 19 0 O00443 O00443 PIK3C2A Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha 1 0 S(0.008)ADAGS(0.051)FS(0.829)PT(0.112)PGQIGGAVK 224.86 1.41E-38 6093500 2361.8 2415.8 2070.5 2693.5 3344 2613.9 2626.1 2944.7 2697.6 2651.3 TRUE FALSE FALSE 2333.013473 2449.809696 2106.536184 3004.935143 3173.343202 2446.880226 2849.160868 3029.900249 2456.3199 2582.418844 0.903421797 0.948649249 0.815722124 1.163612615 1.228825916 0.947514859 1.103291542 1.173279949 0.95117022 1 11.3345073 -9.243713127 24.97461437 0.943258082 1.118289282 0.589643304 0.082370529 521.7960457 735161.8533 0.01289345 0.021349853 5.71E-10 9.243713127 0.1750312 SADEADELPPDLPKPPS(ph)PAPSSEDPGLAQPR ddPTM_HeLa_Romidepsin_16h_R1 1 SADEADELPPDLPKPPSPAPSSEDPGLAQPR 31 1 Q8TBE0-3;Q8TBE0-2;Q8TBE0 Q8TBE0-3 BAHD1 Bromo adjacent homology domain-containing 1 protein 1 0 SADEADELPPDLPKPPS(0.646)PAPS(0.245)S(0.109)EDPGLAQPR 70.572 8.95E-06 6842600 2769.2 2894.1 2668.5 3213.3 4082.4 4713.8 4057.8 4604.3 2848.7 3006.6 TRUE FALSE FALSE 2735.447925 2934.843216 2714.944123 3584.836865 3874.059894 4412.603393 4402.469431 4737.518156 2593.905137 2928.488099 0.934081968 1.002170102 0.92708047 1.224125468 1.322887362 1.506785496 1.50332502 1.617735158 0.885748909 1 11.51594032 -8.729761358 1.225950042 0.965232075 1.563684458 0.958503858 0.053850055 0.05608217 0.166119869 0.007691701 0.021610663 1.86E-09 8.729761358 0.598452383 SADGS(ph)APAGEGEGVTLQR ddPTM_HeLa_Romidepsin_16h_R1 2 SADGSAPAGEGEGVTLQR 18 0 Q01650 Q01650 SLC7A5 Large neutral amino acids transporter small subunit 1 1 0 S(0.078)ADGS(0.922)APAGEGEGVTLQR;S(0.013)ADGS(0.987)APAGEGEGVTLQR ; 286.85 1.14E-123 12424400 2699.74 5001.2 3668.3 2217.8 3458 4256.2 2007.37 4506.9 3960.1 3726.9 TRUE FALSE FALSE 2666.83453 5071.607025 3732.145223 2474.232471 3281.525356 3984.242556 2177.875958 4637.300041 3605.898738 3630.074601 0.734650062 1.397108209 1.028118051 0.681592734 0.903982898 1.097564925 0.599953499 1.277466871 0.99334012 1 11.82578348 SADVS(ph)PTTEGVK ddPTM_HeLa_Romidepsin_16h_R1 1 SADVSPTTEGVK 12 0 A0A0J9YX34;Q9C040;Q9C040-2 A0A0J9YX34 TRIM2 Tripartite motif-containing protein 2 1 0 SADVS(0.416)PT(0.416)T(0.167)EGVK 100.02 0.015576 13590000 2507.5 3057.4 2609.7 2398.8 3233.5 3363.3 2655.7 2966 3055.5 2730.5 TRUE FALSE FALSE 2476.937626 3100.442157 2655.120734 2676.160543 3068.482429 3148.395985 2881.275092 3051.81653 2782.208427 2659.561216 0.931333188 1.16577206 0.99833037 1.006241378 1.153755142 1.183802789 1.083364833 1.147488733 1.046115581 1 11.37697253 -9.318387736 0.743496322 0.971497932 1.143868772 0.292372497 0.069974889 0.419019597 0.45630822 0.014319242 0.033434285 4.80E-10 9.318387736 0.17237084 SADVS(ph)PTTEGVKR ddPTM_HeLa_Romidepsin_16h_R1 1 SADVSPTTEGVKR 13 1 A0A0J9YX34;Q9C040;Q9C040-2 A0A0J9YX34 TRIM2 Tripartite motif-containing protein 2 1 0 S(0.14)ADVS(0.647)PT(0.096)T(0.117)EGVKR 58.658 0.029782 7670700 2438.8 2469.6 2195.9 2796.1 3144.7 3286 2692.6 2809.4 2701.2 2822.3 TRUE FALSE FALSE 2409.074968 2504.367094 2234.118718 3119.398238 2984.214225 3076.035205 2921.309377 2890.685557 2459.597907 2748.976239 0.876353507 0.911018094 0.812709359 1.134749073 1.085572942 1.118974825 1.062689934 1.051549852 0.894732327 1 11.42467872 -9.24494737 24.99607948 0.928558261 1.090435982 0.759056604 0.052712268 423.5489538 641951.3513 0.009638034 0.015953673 5.69E-10 9.24494737 0.161877721 SADVSPT(ph)TEGVKR ddPTM_HeLa_Romidepsin_16h_R1 1 SADVSPTTEGVKR 13 1 A0A0J9YX34;Q9C040;Q9C040-2 A0A0J9YX34 TRIM2 Tripartite motif-containing protein 2 1 0 SADVS(0.308)PT(0.516)T(0.176)EGVKR 81.713 0.015412 8707400 2567.5 2515.5 2329.6 2851.3 3004.7 3425 2844.5 2903.4 2698.4 2941.6 TRUE FALSE FALSE 2536.206322 2550.913275 2370.145711 3180.980722 2851.358947 3206.153554 3086.111759 2987.405298 2457.048346 2865.176808 0.885183182 0.890316182 0.827224939 1.11022144 0.995177309 1.119007227 1.077110407 1.042660017 0.857555575 1 11.48440845 -9.244402574 24.85250556 0.931278107 1.067990234 0.666766307 0.059329701 473.8327336 691205.6991 0.009816498 0.016251834 5.70E-10 9.244402574 0.136712127 SADVSPTT(ph)EGVK ddPTM_HeLa_Romidepsin_16h_R1 1 SADVSPTTEGVK 12 0 A0A0J9YX34;Q9C040;Q9C040-2 A0A0J9YX34 TRIM2 Tripartite motif-containing protein 2 1 0 SADVS(0.315)PT(0.315)T(0.37)EGVK 158.25 0.00207 21406000 3153.4 3180.3 3272.4 2694.8 3182.1 3437.4 3161.5 3230.8 3507.6 2727 TRUE FALSE FALSE 3114.965148 3225.072347 3329.354749 3006.385455 3019.705563 3217.761234 3430.037731 3324.278101 3193.871471 2656.152147 1.172735964 1.214189613 1.253450317 1.131857397 1.136872211 1.211437092 1.291355894 1.251539037 1.202442968 1 11.37512207 -16.52287875 0.157470345 0.172026947 1.272672384 0 0.079706408 23.82351405 0.25172394 6.023395541 0.101774395 3.00E-17 16.52287875 1.100645438 SAEALGPGALVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SAEALGPGALVSPR 14 0 Q9P227-2;Q9P227 Q9P227-2 ARHGAP23 Rho GTPase-activating protein 23 1 0 SAEALGPGALVS(1)PR 172.09 3.92E-05 20566000 2857.7 3393.7 2539 2360.3 2759.4 2450.4 1912.2 2055.2 2993.5 3149.5 TRUE FALSE FALSE 2822.869253 3441.476598 2583.19023 2633.208992 2618.577521 2293.827348 2074.62222 2114.663969 2725.753863 3067.675536 0.920198117 1.121851564 0.842067618 0.858372719 0.853603157 0.747741188 0.676284762 0.68933756 0.88854047 1 11.58293018 -8.473479281 0.753307252 0.972461137 0.649403284 0.710480837 0.069834823 0.326222238 0.297499882 0.011827874 0.063383124 3.36E-09 8.473479281 -0.323057853 SAEKEISLWFKPEELVDYK ddPTM_HeLa_Romidepsin_16h_R1 1 SAEKEISLWFKPEELVDYK 19 2 Q32Q12;P22392-2;P22392 Q32Q12 NME1-NME2;NME2 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B 0 0 51.76 0.022971 1105900 551.41 417.41 667.34 735.7 629.93 478.17 428.36 560.11 639.78 391.33 FALSE FALSE TRUE 544.6892028 423.2863089 678.9547728 820.7650956 597.7823215 447.6164802 464.7448877 576.3158991 582.5564744 381.1631902 1.429018375 1.110512032 1.781270569 2.153316786 1.568310731 1.174343409 1.219280612 1.511992538 1.528364988 1 8.574264991 -11.72104001 0.618938097 0.99212768 1.51383733 0 0.330197852 0.880109503 0.642799205 0.231321123 0.077780728 1.90E-12 11.72104001 0.52170965 SAENPPSGS(ph)VRK ddPTM_HeLa_Romidepsin_16h_R1 1 SAENPPSGSVRK 12 1 Q5JXX1;Q5JXX2;Q15014 Q5JXX1 MORF4L2 Mortality factor 4-like protein 2 1 0 SAENPPS(0.06)GS(0.94)VRK 115.1 0.0026849 10893000 2222.9 2674.9 1923 2420.8 2590.6 3103.9 2446 2300.5 3545.8 3143.4 TRUE FALSE FALSE 2195.80644 2712.557312 1956.469008 2700.704286 2458.392015 2905.570807 2653.763179 2367.061338 3228.654767 3061.734015 0.7171774 0.885954593 0.63900685 0.882083249 0.80294108 0.948995175 0.866751705 0.773111357 1.054518372 1 11.58013324 -12.5148743 1.264655937 1.000097676 0.807404386 0.472335941 0.087927784 0.365834717 1.04652116 0.060615641 0.01456473 3.06E-13 12.5148743 -0.19269329 SAEPRPELGPGQETGTNS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SAEPRPELGPGQETGTNSR 19 1 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;Q9Y4B5-4 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 SAEPRPELGPGQET(0.001)GTNS(0.999)R;SAEPRPELGPGQET(0.001)GT(0.005)NS(0.995)R ; 138.04 0.00018235 18857500 2744.3 2753.9 2854.7 2104.6 2082.16 1919.23 1939.73 1682.27 2881.4 2827.7 TRUE FALSE FALSE 2710.851416 2792.669476 2904.384856 2347.943754 1975.899606 1796.597397 2104.490618 1730.943828 2623.680367 2754.235946 0.984248071 1.013954335 1.054515631 0.852484609 0.717403899 0.652303373 0.76409235 0.628466065 0.952598259 1 11.42743644 -8.941526204 2.701709926 0.998314388 0.690272768 0.922805988 0.042268324 0.045015126 0.666794503 0.005616491 0.010758909 1.14E-09 8.941526204 -0.308041621 SAEPSANTTLVS(ph)ETEEEGSVPAFGAAAK ddPTM_HeLa_Romidepsin_16h_R1 4 SAEPSANTTLVSETEEEGSVPAFGAAAK 28 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 SAEPSANT(0.003)T(0.006)LVS(0.586)ET(0.193)EEEGS(0.212)VPAFGAAAK;SAEPSANT(0.001)T(0.002)LVS(0.611)ET(0.229)EEEGS(0.157)VPAFGAAAK;SAEPSANT(0.001)T(0.002)LVS(0.465)ET(0.465)EEEGS(0.068)VPAFGAAAK;SAEPS(0.001)ANT(0.011)T(0.009)LVS(0.456)ET(0.456)EEEGS(0.067)VPAFGAAAK ;;; 73.968 3.23E-05 81213000 13919.4 12903.1 15401.1 8980.8 15440.6 16809 13866.1 15694.4 13970.4 17043.4 TRUE FALSE FALSE 13749.745 13084.75018 15669.14969 10019.20235 14652.60857 15734.95915 15043.88619 16148.4927 12720.85243 16600.61001 0.828267455 0.788208998 0.943889994 0.603544228 0.882654827 0.947854274 0.906224902 0.972765018 0.766288252 1 14.01894864 -8.26788436 22.17579697 0.882679834 0.938675744 0.054632839 0.110977124 308.8727681 1062780.763 0.017168339 0.039392982 5.40E-09 8.26788436 0.05599591 SAEPSPTVMS(ph)TSLGSNLSELDR ddPTM_HeLa_Romidepsin_16h_R1 1 SAEPSPTVMSTSLGSNLSELDR 22 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;F5H836 A0A1B0GTU4 PXN Paxillin 1 0 SAEPSPT(0.002)VMS(0.445)T(0.445)S(0.107)LGS(0.001)NLS(0.001)ELDR 76.909 0.00068844 3265900 1421 1386.6 1568.9 1199.9 1298.3 1158.1 791.13 1210.6 1808.4 1446.6 TRUE FALSE FALSE 1403.680305 1406.120591 1596.206046 1338.638084 1232.042906 1084.101148 858.3285625 1245.626801 1646.652175 1409.017123 0.996212382 0.997944289 1.132850708 0.950050969 0.874398817 0.769402394 0.609168298 0.884039505 1.168653061 1 10.46047343 -8.54106063 2.072597526 1.007548345 0.738081241 0.665810238 0.090605657 0.120649176 1.030176277 0.010406544 0.026047623 2.88E-09 8.54106063 -0.269467103 SAEPSPTVMSTS(ph)LGSNLSELDR ddPTM_HeLa_Romidepsin_16h_R1 2 SAEPSPTVMSTSLGSNLSELDR 22 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;F5H836 A0A1B0GTU4 PXN Paxillin 1 0 SAEPSPTVMS(0.132)T(0.117)S(0.722)LGS(0.028)NLSELDR;SAEPSPTVMS(0.003)T(0.051)S(0.921)LGS(0.024)NLS(0.001)ELDR ; 123.85 2.35E-05 28132000 6468.1 6563.4 5938.4 5093.3 4123.1 4051 3149.7 3515.7 6049.2 5608.4 TRUE FALSE FALSE 6389.264309 6655.799717 6041.755361 5682.211311 3912.682822 3792.154174 3417.235439 3617.421233 5508.144402 5462.692959 1.169618054 1.218409998 1.106003102 1.040185006 0.716255307 0.694191345 0.625558761 0.662204751 1.008320336 1 12.41539662 -8.760131345 3.184696243 1.096245422 0.661430472 0.913352075 0.063139351 0.062632445 1.316833115 0.011979495 0.024250172 1.74E-09 8.760131345 -0.43481495 SAEQEK(ac)DPISLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SAEQEKDPISLKR 13 2 Q9Y3Y4-2 Q9Y3Y4-2 0 2 SAEQEK(1)DPISLK(1)R 111.27 0.0039308 2282000 2275.7 2872 1689.4 2446.4 2042.5 1520.1 1240.6 1114.7 2672.6 2182.4 FALSE TRUE FALSE 2247.962893 2912.432091 1718.803298 2729.264279 1938.263603 1422.970516 1345.976533 1146.952086 2433.555962 2125.700933 1.057516068 1.370104348 0.808581899 1.283936153 0.911823283 0.669412378 0.633191862 0.539564182 1.144825184 1 11.05372292 -8.313700807 2.874116226 1.055311401 0.601506584 0.670759752 0.152716882 0.119728222 1.945715632 0.020226319 0.052898953 4.86E-09 8.313700807 -0.453804818 SAES(ph)PSWTPAEHVAK ddPTM_HeLa_Romidepsin_16h_R1 1 SAESPSWTPAEHVAK 15 0 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 1 0 SAES(0.92)PS(0.08)WTPAEHVAK 219.41 1.50E-26 7742900 1413.6 1300 1254.8 1129.8 1120 1051.1 1125.9 1092.2 1374.7 1350.5 TRUE FALSE FALSE 1396.370499 1318.301434 1276.639268 1260.432792 1062.842221 983.9381023 1221.533918 1123.801084 1251.743389 1315.413815 1.061544651 1.002195217 0.970522928 0.958202489 0.807990769 0.748006514 0.928630902 0.854332736 0.951596657 1 10.36130101 -9.071732092 1.900663944 1.025772877 0.83617122 0.648590077 0.054339444 0.129420335 0.922764755 0.008208584 0.01574839 8.48E-10 9.071732092 -0.189601656 SAES(ph)PTSPVTSETGSTFK ddPTM_HeLa_Romidepsin_16h_R1 4 SAESPTSPVTSETGSTFK 18 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 SAES(0.498)PT(0.498)S(0.004)PVTSETGSTFK;S(0.001)AES(0.991)PT(0.009)SPVTSETGSTFK;S(0.003)AES(0.803)PT(0.194)SPVTSETGSTFK;SAES(0.8)PT(0.199)S(0.001)PVTSETGSTFK ;;; 243.83 1.07E-61 52454000 8926.1 7918.1 9429.4 7372.4 10350.1 10558 8999.7 10014.8 8790.6 9391 TRUE FALSE FALSE 8817.30526 8029.57122 9593.514752 8224.831576 9821.895775 9883.377874 9764.134293 10304.56244 8004.34672 9147.020466 0.963953813 0.877834618 1.048813085 0.899181499 1.07378089 1.080502434 1.067466103 1.126548528 0.875076944 1 13.15908616 -8.635994357 7.988675585 0.974143417 1.087038079 0.569743713 0.057502239 0.128828323 8.548571334 0.006642627 0.013312907 2.31E-09 8.635994357 0.112894662 SAES(ph)PTSPVTSETGSTFKK ddPTM_HeLa_Romidepsin_16h_R1 2 SAESPTSPVTSETGSTFKK 19 1 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 S(0.002)AES(0.426)PT(0.324)S(0.247)PVTSETGSTFKK;S(0.008)AES(0.941)PT(0.049)S(0.001)PVTSETGSTFKK ; 155.08 1.51E-11 41532000 2970 2873.6 2480.4 3412.3 3919.2 3838.4 3489.3 3608.5 2982 3140.1 TRUE FALSE FALSE 2933.800498 2914.054616 2523.570322 3806.846181 3719.188599 3593.138628 3785.681055 3712.906254 2715.282451 3058.519749 0.959222349 0.952766323 0.825095317 1.244669478 1.216009346 1.174796608 1.237749423 1.213955298 0.887776661 1 11.57861788 -9.244351491 24.99521019 0.967098943 1.216116452 0.86934788 0.05549981 221.8136315 324456.9033 0.007734602 0.012805925 5.70E-10 9.244351491 0.249017509 SAESPT(ph)SPVTSETGSTFKK ddPTM_HeLa_Romidepsin_16h_R1 1 SAESPTSPVTSETGSTFKK 19 1 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 S(0.009)AES(0.059)PT(0.461)S(0.461)PVT(0.009)S(0.001)ETGSTFKK 78.661 0.00091501 0 842.57 447.22 670.1 811.27 985.71 1159.6 1034.4 923.95 831.09 796.68 TRUE FALSE FALSE 832.3004328 453.5159749 681.7628094 905.0728545 935.4055405 1085.505302 1122.26191 950.6830355 756.7552289 775.9821388 1.072576792 0.584441255 0.878580544 1.166357844 1.205447257 1.398879237 1.44624709 1.225135204 0.975222484 1 9.599879635 -8.778753016 2.085952302 0.985749273 1.356528481 0.615815559 0.149444189 0.194844606 1.727980483 0.024707305 0.053636456 1.66E-09 8.778753016 0.370779208 SAESPTS(ph)PVTSETGSTFK ddPTM_HeLa_Romidepsin_16h_R1 2 SAESPTSPVTSETGSTFK 18 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 SAESPT(0.064)S(0.781)PVT(0.001)S(0.154)ETGSTFK;SAESPT(0.173)S(0.819)PVTS(0.007)ETGSTFK ; 253.79 2.12E-75 51168000 4684.1 5142.6 4873.9 4070.2 7992.7 8077.6 6597.9 7032.3 4803.4 5043.3 TRUE FALSE FALSE 4627.008388 5214.997658 4958.728185 4540.815675 7584.802694 7561.467429 7158.325461 7235.768505 4373.771874 4912.274339 0.941927928 1.061625898 1.009456688 0.924381531 1.54405112 1.53930072 1.457232428 1.472997639 0.890376142 1 12.26217542 -8.760532759 25 0.97942035 1.50266285 0.962516953 0.051426316 2.843521637 78405.6612 0.00680172 0.012999648 1.74E-09 8.760532759 0.5232425 LNTITPVVGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 LNTITPVVGKK 11 1 Q9HCK8-2;Q9HCK8;A0A2R8Y840;A0A2R8YFT4;A0A2R8Y808;A0A2R8Y4P3 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 0 1 LNTITPVVGK(1)K 152.7 0.0014905 1244100 355.55 351.61 392.34 598.21 1286.2 1633.3 1401.8 1606.5 366.53 502.58 FALSE TRUE FALSE 351.2164198 356.5599748 399.1685131 667.3778549 1220.560415 1528.937401 1520.868857 1652.981543 333.7466388 489.5228991 0.717466783 0.728382626 0.815423576 1.363323056 2.493367351 3.123321511 3.106839046 3.376719548 0.681779421 1 8.935232538 -8.703223675 1.802022756 0.843408576 3.22346434 0.988985136 0.11381983 0.02879963 0.189327463 0.020935226 0.049683332 1.98E-09 8.703223675 2.380055764 up AAPGAEFAPNK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AAPGAEFAPNKR 12 1 Q15233;Q15233-2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; AAPGAEFAPNK(1)R;AAPGAEFAPNK(1)R 145.99 0.00013088 133848000 1368.73 1594.82 1332.64 1647.72 3402.6 3879.4 3343.8 4217 1739.21 1245.18 FALSE TRUE FALSE 1352.047392 1617.271918 1355.83404 1838.237139 3228.952625 3631.51886 3627.822289 4339.012242 1583.650702 1212.830044 1.114787186 1.333469537 1.117909345 1.515659303 2.662329022 2.994252062 2.991204173 3.577592972 1.305748245 1 10.24416168 -8.702093059 1.452704981 1.070493511 3.255231495 0.960375238 0.184665196 0.04506895 0.190197306 0.025681571 0.067008754 1.99E-09 8.702093059 2.184737984 up SAGEALGSSGT(ph)PPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SAGEALGSSGTPPVR 15 0 E7ER32;A0A087X287;A0A087WU73;A0A494BZX7;W0Z7M9;B0QY83;A0A499FIJ6;Q969V6 E7ER32 MKL1;mkl1 MKL/myocardin-like protein 1 1 0 SAGEALGS(0.003)S(0.018)GT(0.979)PPVR;SAGEALGS(0.002)S(0.016)GT(0.981)PPVR ; 102.5 0.014481 17785300 3167 2946.42 2679.73 2768.34 4284.4 5215.8 4923.1 4907 3145.77 2792.82 TRUE FALSE FALSE 3128.399386 2987.899778 2726.369577 3088.428496 4065.751081 4882.527213 5341.267991 5048.976303 2864.404452 2720.262134 1.150036001 1.098386711 1.002245167 1.135342237 1.494617386 1.794873793 1.963512238 1.856062414 1.052988393 1 11.40952997 -8.500232163 1.805546581 1.068420691 1.90884211 0.979290802 0.052523349 0.042626126 0.272879029 0.010265121 0.027972795 3.16E-09 8.500232163 0.840421419 SAGGRPGS(ph)GPQLGTGR ddPTM_HeLa_Romidepsin_16h_R1 2 SAGGRPGSGPQLGTGR 16 1 K7EM11;O14908-2;O14908;K7ESN1 K7EM11 GIPC1 PDZ domain-containing protein GIPC1 1 0 S(0.112)AGGRPGS(0.813)GPQLGT(0.075)GR;SAGGRPGS(0.999)GPQLGT(0.001)GR ; 120.9 0.019071 14520300 2324.57 2062.65 1722.76 2140.68 2790.67 3051.7 2326.57 3093.8 2170.66 1957.86 TRUE FALSE FALSE 2296.237247 2091.688041 1752.743915 2388.195494 2648.251696 2856.706219 2524.188798 3183.314222 1976.510733 1906.994515 1.204113189 1.096850581 0.919113244 1.252334747 1.388704412 1.498014911 1.323647644 1.669283365 1.036453287 1 10.89708498 -8.844146723 2.545807203 1.086677064 1.472658966 0.761533655 0.10961723 0.118025723 1.556153579 0.017722243 0.035726379 1.43E-09 8.844146723 0.385981901 SAGIARPEEGRPVVSGTGNDIT(ph)TPPNK ddPTM_HeLa_Romidepsin_16h_R1 1 SAGIARPEEGRPVVSGTGNDITTPPNK 27 2 E7EVA0;P27816-5;P27816-4;B5MEG9;H7C4C5 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 S(0.011)AGIARPEEGRPVVS(0.004)GT(0.032)GNDIT(0.477)T(0.477)PPNK 40.237 0.026701 9913200 2201.5 2021 1726.8 1561.1 1462.4 1742.9 1560 1748.6 2156.3 2274.8 TRUE FALSE FALSE 2174.667271 2049.451691 1756.85423 1741.601727 1387.768271 1631.534315 1692.506361 1799.192982 1963.435127 2215.700368 0.981480756 0.924967889 0.792911467 0.786027638 0.626333908 0.736351511 0.763869694 0.812019986 0.886146501 1 11.11354708 -9.779337333 1.704492141 0.992589532 0.737945441 0.738309611 0.056564185 0.08700486 0.514742548 0.007947004 0.011453524 1.66E-10 9.779337333 -0.254644091 SAGQGEVLVYVEDPAGHQEEAK ddPTM_HeLa_Romidepsin_16h_R1 2 SAGQGEVLVYVEDPAGHQEEAK 22 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 ; ; 198.61 1.37E-24 8720000 4458.3 5271.7 4997.2 4265.1 5502.6 5787.1 4075.6 5955.4 4900.6 5199.6 FALSE FALSE TRUE 4403.960525 5345.915131 5084.17417 4758.25093 5221.781789 5417.322987 4421.781362 6127.710103 4462.278062 5064.513642 0.86957225 1.055563379 1.003882017 0.939527715 1.031052961 1.069663026 0.873091016 1.209930614 0.881087184 1 12.30620801 -7.248371255 24.59941609 0.961172166 1.209930815 0.498110537 0.072059665 1151.113812 2166808.672 0.010499913 0.257759336 5.64E-08 7.248371255 0.248758649 SAHS(ph)IAQLQK ddPTM_HeLa_Romidepsin_16h_R1 1 SAHSIAQLQK 10 0 F8VQF2;G3V207;Q9ULS5 F8VQF2 TMCC3 Transmembrane and coiled-coil domains protein 3 1 0 S(0.107)AHS(0.893)IAQLQK 105.14 0.0212 7965700 1036.3 820.47 884.2 696.18 900.32 830.51 687.55 954.57 731.68 739.49 TRUE FALSE FALSE 1023.669177 832.0205982 899.5891301 776.6756072 854.3733108 777.4430913 745.9504798 982.1889769 666.2367083 720.2779432 1.421214111 1.155138244 1.248947213 1.078299863 1.186171698 1.079365401 1.035642542 1.363624954 0.924971693 1 9.492409916 -9.271324644 23.96430664 1.20339201 1.140582943 0 0.155306694 1379.630557 3344558.459 0.026591504 0.040950869 5.35E-10 9.271324644 -0.062809067 SAKDLMRMEKIVLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SAKDLMRMEKIVLEK 15 3 E7ERZ1 E7ERZ1 CCNG1 0 0 46.282 0.02806 1231600 72.549 0 0 0 556.74 765.51 557.63 1052.3 0 0 FALSE FALSE TRUE 71.66474488 0 0 0 528.3274803 716.5963816 604.9950783 1082.74664 0 0 0 SALAPNLLT(ph)SGK ddPTM_HeLa_Romidepsin_16h_R1 1 SALAPNLLTSGK 12 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 SALAPNLLT(0.926)S(0.074)GK 199.13 2.53E-14 38322000 5065.9 4364.5 4675.3 4274.4 6841.3 8982.5 7415.3 8807.3 4478.4 4205.6 TRUE FALSE FALSE 5004.154862 4425.943546 4756.671635 4768.62624 6492.162933 8408.54724 8045.155397 9062.12533 4077.840688 4096.337906 1.221616717 1.080463489 1.161200991 1.164119355 1.58486997 2.052698638 1.963987245 2.212250439 0.99548445 1 12.00011901 -8.502399065 1.820313951 1.107190738 2.09735156 0.963016001 0.085771617 0.051209571 0.333450713 0.014627957 0.039648262 3.14E-09 8.502399065 0.990160822 SALAPNLLT(ph)SGKK ddPTM_HeLa_Romidepsin_16h_R1 1 SALAPNLLTSGKK 13 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 SALAPNLLT(0.882)S(0.118)GKK 113.52 0.015022 13319000 1386.9 1321.1 1445.4 1465.1 2070.2 2721.8 2188.5 2335.9 1653.3 1316.3 TRUE FALSE FALSE 1369.995929 1339.69848 1470.556581 1634.501756 1964.549969 2547.885764 2374.391135 2403.485581 1505.424707 1282.102336 1.068554273 1.044923204 1.146988457 1.274860601 1.532287957 1.987271758 1.851951337 1.874644101 1.174184513 1 10.32429571 -8.700845695 1.405067058 1.037564863 1.919391929 0.958113683 0.074310487 0.043010493 0.169307392 0.009630739 0.025594295 1.99E-09 8.700845695 0.881827065 SALAPNLLTS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 SALAPNLLTSGK 12 0 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 SALAPNLLT(0.078)S(0.922)GK 171.99 0.00010929 30828000 6200.2 6081 6150.7 5070.7 8349.2 11780 9353.4 10248 6745.7 5638.2 TRUE FALSE FALSE 6124.629578 6166.608478 6257.750353 5656.998192 7923.109169 11027.29602 10147.87756 10544.50971 6142.347697 5491.718751 1.115248223 1.12289226 1.139488498 1.030096123 1.442737607 2.0079863 1.847850923 1.920074605 1.118474557 1 12.42304203 -8.493308176 2.894991757 1.067003329 1.917616801 0.971262703 0.064280254 0.031618868 0.529245802 0.010460996 0.024576134 3.21E-09 8.493308176 0.850613472 SALAPNLLTSGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SALAPNLLTSGKK 13 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 0 1 ; SALAPNLLTSGK(1)K;SALAPNLLTSGK(1)K 156.69 7.57E-05 1144460 946.83 867.52 960.2 1128.06 1342.97 952.56 1005.93 922.57 1207.5 1256.16 FALSE TRUE FALSE 935.2896718 879.7329693 976.9118782 1258.491605 1274.43323 891.6944902 1091.373669 949.2631074 1099.498176 1223.524782 0.764422336 0.719015244 0.798440614 1.028578761 1.041608023 0.728791524 0.89199147 0.775842975 0.898631717 1 10.25682761 -12.50354189 1.292130385 0.998792496 0.839057607 0.100316471 0.112386841 0.565077645 1.708539982 0.077661719 0.019413039 3.14E-13 12.50354189 -0.15973489 SALCLAIS(ph)NS(ph)SRGPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SALCLAISNSSRGPSR 16 1 F8VSD5;F8VU56;P23467-3 F8VSD5 PTPRB Protein-tyrosine-phosphatase 2 0 SALCLAIS(0.991)NS(0.493)S(0.494)RGPS(0.022)R 86.189 0.0016493 0 655.38 602.54 458.01 351.3 537.64 604.91 565.07 590.1 548.61 565 TRUE FALSE FALSE 647.3919765 611.0225739 465.9814719 391.9189589 510.2022246 566.2582033 613.0670317 607.1736125 499.5409476 550.3212186 1.17638927 1.110301681 0.846744513 0.712163998 0.927098951 1.028959423 1.114016707 1.103307654 0.907726126 1 9.104130145 -9.787113044 24.97655331 1.087647818 0.953596006 0.078648429 0.131407385 292.40639 284465.4807 0.022607445 0.029717844 1.63E-10 9.787113044 -0.134051812 SALLTQNGT(ph)GSLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SALLTQNGTGSLPR 14 0 Q86UU1-2;Q86UU1;Q86UU1-3;A0A087WZL0 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 S(0.003)ALLTQNGT(0.842)GS(0.155)LPR 122.93 0.0076586 16474000 1899.7 1703.5 1554.9 1682.6 1376.3 1484.8 1053.8 1185.1 1629.2 1599.9 TRUE FALSE FALSE 1876.545726 1727.481918 1581.962382 1877.150129 1306.062275 1389.926072 1143.309746 1219.388999 1483.480272 1558.334367 1.204199667 1.108543811 1.015162352 1.204587519 0.838114273 0.891930577 0.733674216 0.782495095 0.951965318 1 10.60578911 -8.689268056 6.891970296 1.099505823 0.808648321 0.69744733 0.086401759 0.093414684 7.278829075 0.013346813 0.02675715 2.05E-09 8.689268056 -0.290857502 SALLTQNGTGS(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 1 SALLTQNGTGSLPR 14 0 Q86UU1-2;Q86UU1;Q86UU1-3;A0A087WZL0 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 S(0.001)ALLT(0.096)QNGT(0.156)GS(0.747)LPR 137.27 0.0012729 18515000 1410.6 1442.6 1695.8 1821.8 1367.9 1133 955.08 853.74 1689.1 1405.7 TRUE FALSE FALSE 1393.407065 1462.908961 1725.314688 2032.445088 1298.090959 1060.604957 1036.204471 878.4416199 1538.022666 1369.179711 1.017694794 1.068456499 1.260108277 1.484425361 0.948079312 0.774628011 0.756806767 0.641582411 1.123316868 1 10.4190961 -8.315531484 3.605900161 1.068425307 0.721182066 0.584237437 0.153003182 0.16581185 4.371730795 0.024738863 0.060964402 4.84E-09 8.315531484 -0.347243241 SALNLNQPVSVSS(ph)VSPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SALNLNQPVSVSSVSPVK 18 0 Q86XJ1;G3V1N3;H0YIT6 Q86XJ1 GAS2L3 GAS2-like protein 3 1 0 SALNLNQPVS(0.005)VS(0.349)S(0.574)VS(0.071)PVK 108.47 0.0014174 22576000 1269.2 1566.6 1606.7 1176.8 2329.7 2295.5 2136.4 2111.5 1883.3 1974.9 TRUE FALSE FALSE 1253.730502 1588.654636 1634.66394 1312.867153 2210.806716 2148.824958 2317.865763 2172.592921 1714.852931 1923.591813 0.651765356 0.825879287 0.849797721 0.682508183 1.149311772 1.117089885 1.204967575 1.129445918 0.891484835 1 10.90958698 -8.745279871 24.90309546 0.82254186 1.15175035 0.746833169 0.095031302 127.4434236 196399.427 0.019717073 0.039335178 1.80E-09 8.745279871 0.32920849 SALNLNQPVSVSSVS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 SALNLNQPVSVSSVSPVK 18 0 Q86XJ1;G3V1N3;H0YIT6 Q86XJ1 GAS2L3 GAS2-like protein 3 1 0 SALNLNQPVSVS(0.16)S(0.337)VS(0.503)PVK 253.09 1.36E-63 14317000 1321 1532.2 1972.1 1200.2 2081.6 2037.3 1880.6 1781.7 1852.4 1846 TRUE FALSE FALSE 1304.899144 1553.770352 2006.423573 1338.972771 1975.368184 1907.123105 2040.338117 1833.250678 1686.716705 1798.040654 0.725733949 0.864146397 1.115894443 0.74468437 1.098622648 1.0606674 1.134756388 1.019582441 0.938085966 1 10.81220993 -8.738288188 24.97748874 0.879529736 1.081165127 0.381188284 0.111028227 201.4293766 217318.2427 0.019019318 0.038019263 1.83E-09 8.738288188 0.201635391 SALSSS(ph)LRDLSEAGK ddPTM_HeLa_Romidepsin_16h_R1 1 SALSSSLRDLSEAGK 15 1 A0A2R8Y7T6;A0A3B3IRZ4;Q6DN90-2;Q6DN90;Q6DN90-3 A0A2R8Y7T6 IQSEC1 IQ motif and SEC7 domain-containing protein 1 1 0 SALSS(0.004)S(0.996)LRDLSEAGK 188 1.91E-11 7667800 3764.8 3440.4 3490.1 3383.1 3482.6 3683.8 2875.4 3591 3885.3 3331.1 TRUE FALSE FALSE 3718.91317 3488.834042 3550.843726 3774.26994 3304.869927 3448.417069 3119.636404 3694.899919 3537.789037 3244.557542 1.146200405 1.075288078 1.094399985 1.163261829 1.018588786 1.062831226 0.961498252 1.138799319 1.09037642 1 11.66380604 -6.926769096 20.50339831 1.068933529 3.355765667 0.114217345 0.059061593 858.7494668 273481.6215 0.009319674 12353.34438 1.18E-07 6.926769096 2.286832138 SALVTSSS(ph)SLPSFPSTLSWSR ddPTM_HeLa_Romidepsin_16h_R1 1 SALVTSSSSLPSFPSTLSWSR 21 0 F8VXI9;Q14161-6;Q14161-4;Q14161-3;Q14161 F8VXI9 GIT2 ARF GTPase-activating protein GIT2 1 0 SALVTSS(0.009)S(0.495)S(0.495)LPSFPSTLSWSR 206.63 1.74E-32 0 627.5 718.97 628.14 905.26 967.02 867.39 532.5 864.4 850.61 716.19 TRUE FALSE FALSE 619.8517886 729.0916785 639.0725132 1009.930421 917.669361 811.9665784 577.7305367 889.4100502 774.5293112 697.5832806 0.888570305 1.045167937 0.91612361 1.447756058 1.315497929 1.163970813 0.828188623 1.274987625 1.11030372 1 9.446221652 -9.322290095 24.99972417 0.952802385 1.188826892 0.286618427 0.161934636 203.091136 83436.81298 0.02443374 0.037323161 4.76E-10 9.322290095 0.236024506 SALVTSSSS(ph)LPSFPSTLSWSR ddPTM_HeLa_Romidepsin_16h_R1 1 SALVTSSSSLPSFPSTLSWSR 21 0 F8VXI9;Q14161-6;Q14161-4;Q14161-3;Q14161 F8VXI9 GIT2 ARF GTPase-activating protein GIT2 1 0 SALVTSS(0.001)S(0.02)S(0.962)LPS(0.015)FPSTLSWSR 86.222 0.0017449 5858700 896.03 1168.2 897.12 1233.1 1338.8 1136.2 849.62 1014.5 1180.4 967.21 TRUE FALSE FALSE 885.1088417 1184.64595 912.7339973 1375.676824 1270.47604 1063.600487 921.7867016 1043.852957 1074.822068 942.0817448 0.939524459 1.257476813 0.968847982 1.460252076 1.348583652 1.128989594 0.978457238 1.108028006 1.140901067 1 9.879708438 -10.26955734 24.85043726 0.971442102 1.178347563 0.142275938 0.153782258 520.6195962 1593699.423 0.025295036 0.029182837 5.38E-11 10.26955734 0.206905461 SAMDSPVPASMFAPEPS(ph)SPGAAR ddPTM_HeLa_Romidepsin_16h_R1 1 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 0 SAMDSPVPASMFAPEPS(0.784)S(0.216)PGAAR 82.339 0.00010425 12550000 3378 3661.3 3604.7 2799 3389.4 3307.7 3012.4 3258.3 3624.7 3393.9 TRUE FALSE FALSE 3336.827637 3712.843878 3667.438291 3122.63355 3216.42627 3096.348645 3268.273181 3352.57377 3300.497754 3305.725989 1.009408417 1.123155364 1.109419929 0.944613546 0.972986352 0.936662221 0.988670323 1.014171707 0.998418431 1 11.69075143 SAMDSPVPASMFAPEPSS(ph)PGAAR ddPTM_HeLa_Romidepsin_16h_R1 1 SAMDSPVPASMFAPEPSSPGAAR 23 0 O00178;F8WAZ4 O00178 GTPBP1 GTP-binding protein 1 1 0 SAMDSPVPAS(0.003)MFAPEPS(0.146)S(0.852)PGAAR 88.108 4.39E-05 11786000 2083 1785.9 1757.2 1603.5 1810.8 2070.1 1568.1 1618.9 2258.9 2088 TRUE FALSE FALSE 2057.611595 1811.041947 1787.783329 1788.904215 1718.388119 1937.827291 1701.294375 1665.740317 2056.858326 2033.753459 1.011731086 0.890492375 0.879056073 0.879607214 0.844934331 0.952832942 0.836529309 0.819047319 1.011360702 1 10.98992908 -10.20795744 4.187906732 1.005788725 0.871594847 0.770264696 0.034114427 0.073345362 2.707783573 0.005638182 0.006854718 6.20E-11 10.20795744 -0.134193878 SAMPFTAS(ph)PASSTTAR ddPTM_HeLa_Romidepsin_16h_R1 3 SAMPFTASPASSTTAR 16 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 0 S(0.365)AMPFT(0.06)AS(0.389)PAS(0.016)S(0.126)T(0.041)T(0.002)AR;S(0.006)AMPFT(0.246)AS(0.73)PAS(0.001)S(0.013)T(0.004)TAR;S(0.032)AMPFT(0.077)AS(0.667)PAS(0.022)S(0.192)T(0.009)TAR ;; 154.81 0.00034831 283436000 8315.1 7654.8 7510.4 6873.7 11048.4 13305.2 10102.1 10896.2 8479.4 7291.4 TRUE FALSE FALSE 8213.752363 7762.564475 7641.115362 7668.469536 10484.55892 12455.04066 10960.17212 11211.46436 7720.981227 7101.968377 1.156545894 1.093015917 1.075915149 1.079766781 1.476289159 1.753744877 1.543258367 1.57864183 1.087160744 1 12.79400322 -8.676963752 3.648399872 1.076721947 1.617271891 0.939786796 0.063458823 0.044627774 1.160248041 0.011133371 0.023008718 2.10E-09 8.676963752 0.540549944 SANAFLTPSYTWT(ph)PLKTEVDESQATK ddPTM_HeLa_Romidepsin_16h_R1 2 SANAFLTPSYTWTPLKTEVDESQATK 26 1 Q15398-1;Q15398-3;Q15398 Q15398-1 DLGAP5 Disks large-associated protein 5 1 0 SANAFLT(0.005)PS(0.144)Y(0.11)T(0.12)WT(0.616)PLKT(0.004)EVDESQATK;SANAFLT(0.001)PS(0.015)Y(0.01)T(0.11)WT(0.845)PLKT(0.012)EVDES(0.006)QATK ; 66.545 0.00035028 41726000 4737.5 4924.3 5054 5266.9 6528.9 8292 6371.1 7456.7 4859.6 4649.2 TRUE FALSE FALSE 4679.757528 4993.624425 5141.96275 5875.88376 6195.70587 7762.167961 6912.261075 7672.44785 4424.945205 4528.413114 1.033421071 1.102731641 1.135488883 1.297559125 1.368184773 1.714103322 1.526420161 1.694290617 0.977151398 1 12.14478986 -8.826644369 0.85518084 1.013631328 1.677419909 0.942121784 0.064188719 0.089826683 0.1231676 0.010191703 0.033669724 1.49E-09 8.826644369 0.663788582 SANGGSES(ph)DGEENIGWSTVNLDEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SANGGSESDGEENIGWSTVNLDEEK 25 0 O43290 O43290 SART1 U4/U6.U5 tri-snRNP-associated protein 1 1 0 S(0.003)ANGGS(0.083)ES(0.914)DGEENIGWSTVNLDEEK 106.61 2.76E-06 6926600 2309.3 2287.7 2176.6 1298.4 2277.3 2110.6 1862.9 2213.5 2414.1 2682.7 TRUE FALSE FALSE 2281.153363 2319.906301 2214.48281 1448.527117 2161.080883 1975.739472 2021.13468 2277.54413 2198.17685 2613.003067 0.873000645 0.887831449 0.847485729 0.554353393 0.827048736 0.756118313 0.773491124 0.871619386 0.841245415 1 11.3514931 -10.69294028 0.622183346 0.981457984 0.76500421 0.236071691 0.095920422 0.409726428 0.361751014 0.031573572 0.026945402 2.03E-11 10.69294028 -0.216453774 SANPPHTIQASEEQSS(ph)TPAPVKK ddPTM_HeLa_Romidepsin_16h_R1 1 SANPPHTIQASEEQSSTPAPVKK 23 1 E9PS53;E9PHZ9;B7Z524;H0YDX7;J3QT46;Q9Y450-4;Q9Y450 E9PS53 HBS1L HBS1-like protein 1 0 SANPPHT(0.001)IQAS(0.065)EEQS(0.221)S(0.357)T(0.357)PAPVKK 60.454 0.0021397 7402000 1610.6 1568.3 1572.1 1775.8 2502.3 2712.3 2160.8 2089.6 1981.4 1470 TRUE FALSE FALSE 1590.969388 1590.378569 1599.461741 1981.126351 2374.598294 2538.992784 2344.338298 2150.059279 1804.178621 1431.809188 1.111160203 1.110747565 1.117091407 1.383652492 1.658460019 1.77327594 1.637325921 1.501638135 1.260069174 1 10.48362353 -9.075374056 2.054039318 1.059134621 1.655122922 0.86789258 0.094768286 0.05948911 0.49502459 0.012390249 0.023370484 8.41E-10 9.075374056 0.595988301 SNLPDNLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SNLPDNLKK 9 1 Q14204;A0A2R8YFZ7 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 1 SNLPDNLK(1)K 92.239 0.016832 0 292.93 187.2 292.04 315.36 1208.9 1388.9 1218.7 1521.7 392.5 336.02 FALSE TRUE FALSE 289.3596565 189.8354065 297.1228337 351.823407 1147.205322 1300.153772 1322.216348 1565.727989 357.393817 327.290152 0.884107434 0.580021749 0.907826991 1.074958733 3.505162973 3.972480579 4.039890414 4.783914149 1.091978524 1 8.354426383 -8.694848587 2.879623827 0.902154652 4.21215421 0.97571463 0.245727058 0.027081083 0.455142471 0.036641884 0.077534458 2.02E-09 8.694848587 3.309999559 up VLTANSNPSSPSAAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 VLTANSNPSSPSAAKR 16 1 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 0 1 ; VLTANSNPSSPSAAK(1)R;VLTANSNPSSPSAAK(1)R 338.47 6.54E-208 8385600 145.98 69.622 299.56 217.194 858.69 1088.6 914.34 991.81 299.77 257.46 FALSE TRUE FALSE 144.2007396 70.60214034 304.7737161 242.3069922 814.8678451 1019.041973 992.0040168 1020.506458 272.9578204 250.7711521 0.575029219 0.28154012 1.215345998 0.966247474 3.249448106 4.063633176 3.95581393 4.069473099 1.088473766 1 7.970227584 -8.693765681 2.762432618 0.777786511 4.010659884 0.969863916 0.259845092 0.031406512 0.486212765 0.040509661 0.086368076 2.02E-09 8.693765681 3.232873374 up K(ac)DILAELTK(ac)SQK ddPTM_HeLa_Romidepsin_16h_R1 11 KDILAELTKSQK 12 2 C9J266;Q5XPI4;Q5XPI4-2 C9J266 RNF123 E3 ubiquitin-protein ligase RNF123 0 2 ;;;;;;;;;; K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK;K(1)DILAELTK(1)SQK 133.23 1.01E-05 392761170 1638.802 2054.46 2729.62 7129.451 37174.29 50315.11 46050.27 44349.6 2915.56 1973.177 FALSE TRUE FALSE 1618.827651 2083.382742 2777.127891 7953.79167 35277.14726 47100.13686 49961.77878 45632.7857 2654.785011 1921.913577 0.842299919 1.08401479 1.44498063 4.138475197 18.35522038 24.50689636 25.9958509 23.7434119 1.381323824 1 10.90832775 -8.693665344 2.228043876 0.954095837 24.92565824 0.99646903 0.637388304 0.011837872 0.119425756 0.099391336 0.222033747 2.02E-09 8.693665344 23.97156241 up SAPGGGSKVPQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SAPGGGSKVPQKK 13 2 P06748;P06748-2;P06748-3;E5RI98 P06748;E5RI98 NPM1 Nucleophosmin 0 1 SAPGGGSKVPQK(1)K 94.688 0.0119 0 2953.4 3396.2 1655.8 14693 5260.8 5354.2 4911.2 6374 2926.8 2459.9 FALSE TRUE FALSE 2917.402825 3444.011793 1684.618504 16391.87379 4992.321745 5012.0839 5328.357205 6558.421633 2665.019678 2395.991443 1.217618215 1.437405715 0.703098715 6.841374095 2.083614179 2.091862187 2.223863203 2.737247519 1.112282636 1 11.22640704 SAPGST(ph)PVRR ddPTM_HeLa_Romidepsin_16h_R1 1 SAPGSTPVRR 10 1 A0A087WW42;A0A087WX51;F5H1D6;Q07864 A0A087WW42 POLE DNA polymerase;DNA polymerase epsilon catalytic subunit A 1 0 SAPGS(0.029)T(0.971)PVRR 89.266 0.016467 647110 257.8 127.23 222.36 236.21 158.6 231.74 252.61 58.834 180.02 172.78 TRUE FALSE FALSE 254.6578344 129.0211473 226.2300825 263.5217116 150.5060502 216.9325619 274.0666871 60.53626897 163.9185603 168.2911507 1.513198011 0.766654377 1.344277947 1.565867905 0.894319455 1.289031307 1.628527026 0.35971154 0.974017705 1 7.394815507 -7.244744701 24.37006449 1.242729149 0.359710559 0.44674385 0.286011889 1667.418041 2433961.844 0.03933043 1.420054466 5.69E-08 7.244744701 -0.88301859 SAPT(ph)SPTATNISSK ddPTM_HeLa_Romidepsin_16h_R1 1 SAPTSPTATNISSK 14 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 SAPT(0.94)S(0.059)PT(0.001)ATNISSK 178.68 7.84E-07 7949900 2061.2 2447.4 2271.3 2451.8 3524.1 4123.7 4113.9 4341.9 2210.3 2353.5 TRUE FALSE FALSE 2036.077302 2481.854561 2310.831024 2735.288652 3344.252027 3860.208879 4463.334563 4467.526026 2012.605232 2292.355731 0.888203028 1.082665543 1.008059523 1.193221722 1.458871318 1.68394845 1.947051456 1.948879908 0.877963749 1 11.16261523 -8.437130036 0.925146169 0.950734985 2.024747901 0.981379951 0.054465053 0.06249669 0.092107201 0.009531974 0.044602532 3.65E-09 8.437130036 1.074012916 SAPTAPT(ph)PPPPPPPATPR ddPTM_HeLa_Romidepsin_16h_R1 3 SAPTAPTPPPPPPPATPR 18 0 A6NHN7;A6NHB5;Q14202-2;Q14202 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 0 SAPT(0.021)APT(0.979)PPPPPPPATPR;SAPT(0.219)APT(0.781)PPPPPPPATPR;S(0.012)APT(0.002)APT(0.987)PPPPPPPATPR ;; 221.34 1.12E-34 9021900 5268.4 4800 4338.2 4656.6 3790.8 4247.4 3861.6 3931.2 5216.8 4898.4 TRUE FALSE FALSE 5204.186714 4867.574526 4413.704551 5195.018002 3597.341331 3976.004848 4189.604208 4044.94307 4750.196342 4771.138862 1.090764043 1.020212295 0.925084069 1.08884234 0.753979592 0.833345028 0.878114079 0.847794035 0.995610583 1 12.22011796 -8.765645751 24.99984857 1.035030531 0.832225515 0.74608978 0.054371578 39.87632962 236999.9645 0.008581866 0.015965222 1.72E-09 8.765645751 -0.202805016 SAPTS(ph)PTATNISSK ddPTM_HeLa_Romidepsin_16h_R1 3 SAPTSPTATNISSK 14 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 SAPT(0.067)S(0.932)PTATNISSK;SAPT(0.127)S(0.872)PTATNISSK;SAPT(0.015)S(0.972)PT(0.009)AT(0.004)NISSK ;; 247.73 1.16E-54 51678000 5811.8 6090.5 5970.1 6018 10229.2 11538.3 11071.9 10847.3 6429.2 5862.7 TRUE FALSE FALSE 5740.963546 6176.242219 6074.007086 6713.829476 9707.165754 10801.03987 12012.34691 11161.14951 5854.15625 5710.386209 1.005354688 1.081580473 1.063677108 1.175722487 1.699914051 1.891472743 2.103596232 1.954534965 1.025176938 1 12.47937261 -8.661783227 1.577631519 1.009417299 2.024680815 0.984917053 0.052896368 0.027226536 0.135740039 0.007576528 0.019549519 2.18E-09 8.661783227 1.015263516 SAQGSSS(ph)PVPSMVQK ddPTM_HeLa_Romidepsin_16h_R1 2 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SAQGS(0.036)S(0.167)S(0.784)PVPS(0.013)MVQK;SAQGS(0.002)S(0.012)S(0.738)PVPS(0.248)MVQK ; 116.58 0.0052267 125235000 9269.6 9397.4 9160.3 7983.7 9667 8957.3 7658.8 8677.2 10039.1 10010.9 TRUE FALSE FALSE 9156.61855 9529.696844 9319.731179 8906.812958 9173.656917 8384.957438 8309.338281 8928.261092 9141.177753 9750.815375 0.939061832 0.977323073 0.955789934 0.913442888 0.940809211 0.859923721 0.852168558 0.915642513 0.937478293 1 13.25130715 -4 0.106177795 1.038277747 0.52658081 0.461152793 0.032416286 48.83662425 0.365838618 0.188874081 3.668001784 1.00E-04 4 -0.511696937 SAQGSSSPVPS(ph)MVQK ddPTM_HeLa_Romidepsin_16h_R1 2 SAQGSSSPVPSMVQK 15 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SAQGSS(0.002)S(0.049)PVPS(0.949)MVQK;SAQGSS(0.005)S(0.277)PVPS(0.718)MVQK ; 138.25 0.0014065 40203000 10979.5 10646.4 10172.4 8768.2 10862.4 10841.3 9157.7 10294.3 11117.8 11331.5 TRUE FALSE FALSE 10845.67763 10796.2803 10349.44635 9782.02054 10308.05119 10148.57592 9935.554809 10592.14933 10123.39612 11037.106 0.982655928 0.978180358 0.937695657 0.886284914 0.933945112 0.9194961 0.90019565 0.959685386 0.917214723 1 13.43007432 -9.752678027 2.740693976 0.991450522 0.91893814 0.289290488 0.030034395 0.088950024 1.37488496 0.002950133 0.004157456 1.77E-10 9.752678027 -0.072512382 SAQGSSSPVPSMVQKS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SAQGSSSPVPSMVQKSPR 18 1 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;A0A494BZU9 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SAQGSSSPVPS(0.077)MVQKS(0.922)PR 92.136 0.0059753 24954000 3915.1 3865.3 3672.9 4102.5 3814.5 2709.8 2323.5 2755.3 4989.9 4340.3 TRUE FALSE FALSE 3867.381255 3919.715795 3736.825284 4576.850353 3619.831831 2536.652525 2520.858032 2835.020258 4543.590847 4227.53838 0.914806894 0.92718633 0.883924626 1.082627747 0.856250495 0.600030632 0.596294535 0.670607811 1.074760401 1 12.04560214 -8.382834122 3.803438782 0.957845702 0.619690203 0.850239784 0.066622681 0.057065893 1.455973947 0.008302834 0.019582524 4.14E-09 8.382834122 -0.3381555 SAQQEASADVAT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SAQQEASADVATPK 14 0 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 SAQQEASADVAT(1)PK;SAQQEAS(0.001)ADVAT(0.999)PK ; 188.9 1.18E-10 18167700 5068.2 4601.6 5071.6 4651.3 4619 6028.9 5055.3 5391.9 5124.1 4380.3 TRUE FALSE FALSE 5006.426829 4666.381446 5159.869071 5189.105191 4383.275194 5643.672747 5484.697056 5547.906119 4665.787662 4266.499175 1.173427352 1.093726087 1.209391789 1.216244274 1.027370454 1.322787727 1.285526337 1.300341543 1.093586913 1 12.05883705 -4 0.025990722 1.20E-13 2.816388176 0.515589036 0.075678527 800.4380098 1.615321014 59.63740574 127.5105544 1.00E-04 4 2.816388176 SAS(ph)EPSLHR ddPTM_HeLa_Romidepsin_16h_R1 2 SASEPSLHR 9 0 H7C155;P04049;P04049-2;Q96II5;P10398 H7C155;Q96II5 RAF1;ARAF RAF proto-oncogene serine/threonine-protein kinase;Serine/threonine-protein kinase A-Raf 1 0 S(0.004)AS(0.861)EPS(0.135)LHR;S(0.007)AS(0.993)EPSLHR ; 117.71 0.014771 27821000 2506.2 2066.79 2189.84 1932.29 3042.9 3230.2 2277.66 2348.62 3842 3022.8 TRUE FALSE FALSE 2475.65347 2095.886324 2227.953247 2155.710461 2887.609458 3023.800645 2471.124384 2416.573614 3498.361898 2944.26722 0.840838581 0.711853296 0.756708913 0.73217215 0.980756583 1.027012978 0.839300308 0.820772516 1.188194425 1 11.5236929 -11.99249273 0.981119342 0.992863386 0.841627658 0.38319349 0.114411175 0.573004972 1.05965945 0.053990151 0.020069918 1.02E-12 11.99249273 -0.151235729 SAS(ph)EPSLNR ddPTM_HeLa_Romidepsin_16h_R1 1 SASEPSLNR 9 0 H7C560;A0A2U3TZI2;A0A2R8Y8E0;P15056 H7C560 BRAF Serine/threonine-protein kinase B-raf 1 0 S(0.026)AS(0.967)EPS(0.008)LNR 105.4 0.02343 53656000 2059.2 1998.9 1882.3 2251.2 1874.2 1575.3 1486.4 1612.7 2219.7 1931.8 TRUE FALSE FALSE 2034.101678 2027.040567 1915.060642 2511.494336 1778.55258 1474.643414 1612.654779 1659.36093 2021.164473 1881.611558 1.081042296 1.077289602 1.017776828 1.334757074 0.945228346 0.783712987 0.857060413 0.881882833 1.074166697 1 10.87775311 -8.525804582 24.99999154 1.062465673 0.846164173 0.598522914 0.092756733 51.1670289 437199.9872 0.013640549 0.027399143 2.98E-09 8.525804582 -0.216301501 SAS(ph)LPAYR ddPTM_HeLa_Romidepsin_16h_R1 1 SASLPAYR 8 0 A0A0C4DGA7;O94929-2;O94929-3;O94929;A0A0A0MRD5;O94929-4 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 S(0.025)AS(0.975)LPAYR 104.01 0.027626 4245800 2247.2 2269 2196.1 2510 2544.9 2857.8 2110.8 2329.3 2625.7 2226.6 TRUE FALSE FALSE 2219.810262 2300.943042 2234.322199 2800.21801 2415.024257 2675.195803 2290.091299 2396.69462 2390.850816 2168.752611 1.023542404 1.060952287 1.03023378 1.291165251 1.113554513 1.233518194 1.055948607 1.105102817 1.102408271 1 11.08264978 -9.483481561 24.51414653 1.016614422 1.156114471 0.386228455 0.069517807 240.976945 149943.4383 0.009404721 0.014364324 3.28E-10 9.483481561 0.139500049 SAS(ph)PDDDLGSSNWEAADLGNEER ddPTM_HeLa_Romidepsin_16h_R1 4 SASPDDDLGSSNWEAADLGNEER 23 0 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 0 S(0.111)AS(0.889)PDDDLGSSNWEAADLGNEER;S(0.038)AS(0.962)PDDDLGSSNWEAADLGNEER;S(0.198)AS(0.802)PDDDLGSSNWEAADLGNEER;S(0.025)AS(0.975)PDDDLGSSNWEAADLGNEER ;;; 210.84 2.61E-34 474896400 7495.3 7515.9 6028.1 6578.8 6407.3 6429.7 4832 5941.6 7360.5 7452 TRUE FALSE FALSE 7403.944401 7621.709037 6133.016552 7339.47181 6080.311572 6018.862921 5242.429959 6113.510822 6702.158445 7258.395966 1.020052424 1.050054182 0.844954806 1.01116994 0.837693562 0.82922769 0.722257367 0.842267472 0.92336633 1 12.82543505 -8.742966151 0.886130073 1.010173366 0.770911896 0.581256312 0.066630685 0.239720371 0.349862809 0.00965792 0.033706349 1.81E-09 8.742966151 -0.23926147 SAS(ph)PDYNR ddPTM_HeLa_Romidepsin_16h_R1 1 SASPDYNR 8 0 Q14669;Q14669-2;Q14669-3;G5E9G6;F8W9P3;C9JLJ5;C9JSX9;C9JLD7 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 S(0.028)AS(0.972)PDYNR 107.45 0.024746 5517500 3124.7 4093.1 3202.9 1607 2167.7 2304.3 2267.3 1981.4 2793.8 3875.3 TRUE FALSE FALSE 3086.614955 4150.722769 3258.645131 1792.808901 2057.07418 2157.062667 2459.884405 2038.728683 2543.915531 3774.619147 0.817728845 1.099640151 0.86330435 0.474964183 0.544975294 0.571464983 0.651690756 0.540115069 0.673952903 1 11.88211537 -9.353834804 5.265923929 0.927409999 0.56282281 0.680538663 0.113655453 0.076584717 3.396622588 0.014517623 0.022365559 4.43E-10 9.353834804 -0.36458719 SAS(ph)PSVPGPTKPKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASPSVPGPTKPKPK 15 2 Q03164-2;Q03164;Q03164-3;A0A3B3ITZ6 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 0 S(0.03)AS(0.93)PS(0.04)VPGPTKPKPK 86.488 0.018748 31785000 3813.9 3611.5 3499.8 3507.5 2947.8 3317.7 2875.1 3044 3662.1 3606.4 TRUE FALSE FALSE 3767.41472 3662.342792 3560.712551 3913.053653 2797.362766 3105.709677 3119.310922 3132.073337 3334.552604 3512.705208 1.072510927 1.042598959 1.013666772 1.113971547 0.796355686 0.884136155 0.88800817 0.891641385 0.94928336 1 11.77836679 -8.760772115 24.9999766 1.039003631 0.868040604 0.74057953 0.048293239 5.850989381 219199.8858 0.0062019 0.01183638 1.73E-09 8.760772115 -0.170963027 SAS(ph)QSS(ph)LDKLDQELK ddPTM_HeLa_Romidepsin_16h_R1 1 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 0 S(0.011)AS(0.891)QS(0.101)S(0.997)LDKLDQELK 132.65 0.024412 6899100 2155.3 2139.9 2419.1 1727.3 3412 4234.6 3496.5 4074 2688.5 2111.2 TRUE FALSE FALSE 2129.030375 2170.025568 2461.203421 1927.018553 3237.872908 3964.022727 3793.492623 4191.874762 2448.033827 2056.35072 1.035343998 1.055279893 1.196879208 0.937105978 1.574572313 1.927697785 1.844769273 2.038501858 1.190474856 1 11.00587063 -8.56634847 2.831124454 1.02934252 1.925354729 0.940703974 0.098061555 0.033830352 0.54862991 0.011932367 0.02698143 2.71E-09 8.56634847 0.896012209 SAS(ph)SDTSEELNSQDSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASSDTSEELNSQDSPPK 18 0 O14745;J3QRP6;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 0 S(0.045)AS(0.767)S(0.172)DT(0.015)SEELNSQDSPPK 324.91 5.72E-187 90567000 1591.7 1582.1 1208.3 958.66 2892.3 3418.1 2597.2 3006.6 1548.3 1748.4 TRUE FALSE FALSE 1572.299748 1604.372845 1229.329955 1069.50478 2744.695138 3199.694441 2817.806103 3093.591227 1409.81617 1702.976316 0.923265775 0.942099329 0.721871434 0.628020936 1.611704821 1.8788837 1.654636108 1.816579126 0.827854244 1 10.73384266 -8.651449968 5.751131336 0.920928309 1.764639686 0.916876315 0.131951058 0.046745484 2.201195842 0.020296908 0.040947551 2.23E-09 8.651449968 0.843711377 SAS(ph)SGAEGDVSSEREP ddPTM_HeLa_Romidepsin_16h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 0 SAS(0.5)S(0.5)GAEGDVSSEREP;SAS(0.927)S(0.073)GAEGDVSSEREP ; 257.81 3.44E-71 109491000 6422.6 6599.3 5808.9 5836.3 6801 6107.7 5293.4 6143.5 6175.3 6113.7 TRUE FALSE FALSE 6344.318881 6692.205119 5910.001468 6511.120467 6453.919592 5717.437682 5743.021264 6321.25248 5622.965702 5954.865193 1.065400924 1.12382143 0.992466039 1.0934119 1.083806162 0.960128818 0.964425067 1.061527386 0.944264147 1 12.53985313 -8.255930828 24.97199287 1.043604473 0.992266891 0.130420926 0.056565743 622.097362 2820149.789 0.007130264 0.017650298 5.55E-09 8.255930828 -0.051337583 SAS(ph)SSWLEGTSTQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SASSSWLEGTSTQAK 15 0 Q9BZL4-5;Q9BZL4-4;Q9BZL4;K7EL81;Q9BZL4-2;Q9BZL4-3 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 0 S(0.047)AS(0.341)S(0.341)S(0.271)WLEGTSTQAK 267.07 2.00E-84 27503000 1926.5 1527.4 1736.7 1664.1 2121.9 2437.8 2327.3 2382.6 1722.6 1884.9 TRUE FALSE FALSE 1903.019077 1548.902777 1766.926535 1856.511072 2013.611525 2282.032448 2524.980804 2451.536772 1568.526342 1835.930026 1.03654227 0.843661117 0.962414967 1.011210147 1.096780104 1.242984436 1.375314292 1.335310571 0.854349741 1 10.84229536 -8.239863932 1.735522203 0.997952266 1.360064343 0.841573605 0.070383352 0.09681294 0.550210272 0.008837399 0.03071872 5.76E-09 8.239863932 0.362112077 SAS(ph)TDLGTADVVLGR ddPTM_HeLa_Romidepsin_16h_R1 1 SASTDLGTADVVLGR 15 0 H7C0E9;A0A0U1RRA6;B5MCU0;B5MCG9;Q9Y2K5-2;Q9Y2K5;Q9Y2K5-3 H7C0E9 R3HDM2 R3H domain-containing protein 2 1 0 S(0.003)AS(0.912)T(0.08)DLGT(0.005)ADVVLGR 207.64 7.94E-19 4085100 1518.9 1430.6 1024.8 1323.7 1876.3 1984.9 1343.4 1782.4 1314.3 1164.5 TRUE FALSE FALSE 1500.387063 1450.740024 1042.636214 1476.752422 1780.54541 1858.071296 1457.508362 1833.970932 1196.745716 1134.246122 1.322805547 1.279034591 0.919232778 1.301968235 1.569805155 1.6381553 1.285001848 1.616907385 1.055102321 1 10.14751801 -4.000000103 0.064440374 0.545218114 3.067329972 0.512357307 0.168712873 185.1159857 0.895792444 6.789393467 43.32382351 1.00E-04 4.000000103 2.522111858 SAS(ph)TLCLPSVGAARPQVK ddPTM_HeLa_Romidepsin_16h_R1 1 SASTLCLPSVGAARPQVK 18 1 Q8IUC4-2;A8MT19;Q8IUC4 Q8IUC4-2 RHPN2;RHPN2P1 Rhophilin-2;Putative rhophilin-2-like protein RHPN2P1 1 0 S(0.018)AS(0.803)T(0.179)LCLPSVGAARPQVK 78.418 0.0021388 0 993.54 1158.2 1225.6 715.19 1902.2 2274.1 1970.6 1976.4 1024.5 1091 TRUE FALSE FALSE 981.4303523 1174.50517 1246.931054 797.8836329 1805.123636 2128.792349 2137.982715 2033.584016 932.8661541 1062.655663 0.923563847 1.105254704 1.173410257 0.750839299 1.698691024 2.003275778 2.011924267 1.913681061 0.877863062 1 10.05345847 -8.623473059 4.431985018 0.979864617 1.963191108 0.94036339 0.116642635 0.033430154 1.160995933 0.016376364 0.03368192 2.38E-09 8.623473059 0.983326491 SASAPT(ph)LAETEKETAEHLDLAGASSRPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASAPTLAETEKETAEHLDLAGASSRPK 28 2 Q86W92-2 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 S(0.005)AS(0.036)APT(0.944)LAET(0.015)EKET(0.001)AEHLDLAGASSRPK 77.675 2.02E-06 19816000 1457.1 1247.4 1339.7 1492.8 1608.4 1701.6 1597.5 1567.9 2092.6 2108.6 TRUE FALSE FALSE 1439.340305 1264.96093 1363.016917 1665.40456 1526.317346 1592.873252 1733.19161 1613.264713 1905.432615 2053.818268 0.700811911 0.615906943 0.663650206 0.810882144 0.743160858 0.775566795 0.843887523 0.785495357 0.927751323 1 11.00409282 -12.23801652 0.990804202 0.998780536 0.741740052 0.623133938 0.068072227 0.27091823 0.480736596 0.048337142 0.013598016 5.78E-13 12.23801652 -0.257040484 SASNKS(ph)PLVLEANR ddPTM_HeLa_Romidepsin_16h_R1 1 SASNKSPLVLEANR 14 1 Q92560;F8W6N3 Q92560 BAP1 Ubiquitin carboxyl-terminal hydrolase BAP1;Ubiquitin carboxyl-terminal hydrolase 1 0 SASNKS(0.999)PLVLEANR 140.8 2.83E-05 0 691.79 797.51 576.52 606.59 929.69 769.74 724.7 626.28 856.42 782.1 TRUE FALSE FALSE 683.3581974 808.7373667 586.5540888 676.7267899 882.2444501 720.5560982 786.2559999 644.4004237 779.8196503 761.7809293 0.897053432 1.061640343 0.769977386 0.888348295 1.158134073 0.945883614 1.032128752 0.845913043 1.02367967 1 9.573232361 SASPDDDLGS(ph)SNWEAADLGNEERK ddPTM_HeLa_Romidepsin_16h_R1 3 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 0 S(0.006)AS(0.201)PDDDLGS(0.397)S(0.397)NWEAADLGNEERK;S(0.018)AS(0.304)PDDDLGS(0.534)S(0.144)NWEAADLGNEERK;SASPDDDLGS(0.752)S(0.247)NWEAADLGNEERK ;; 166.28 1.78E-14 491456000 6054.8 6141.7 4890.3 6851.3 5042.9 4760.7 4145.53 5195.3 5800.5 6312 TRUE FALSE FALSE 5981.001769 6228.163014 4975.41362 7643.479542 4785.541995 4456.506634 4497.651215 5345.617809 5281.688752 6148.01333 0.972834873 1.01303668 0.809271768 1.243243814 0.778388357 0.724869384 0.731561721 0.869487023 0.859088696 1 12.58590458 -8.574833692 24.99999073 0.991032661 0.767713068 0.442880611 0.113337058 53.0421614 25522.91951 0.01353801 0.027076025 2.66E-09 8.574833692 -0.223319592 SASPDDDLGSS(ph)NWEAADLGNEERK ddPTM_HeLa_Romidepsin_16h_R1 1 SASPDDDLGSSNWEAADLGNEERK 24 1 E9PM92;O00193;E9PQA1 E9PM92 C11orf58;SMAP Small acidic protein 1 0 S(0.032)AS(0.264)PDDDLGS(0.153)S(0.552)NWEAADLGNEERK 41.256 0.029562 16293000 644.91 713.35 578.92 825.85 746.4 508.05 481.29 459.76 775.21 736.87 TRUE FALSE FALSE 637.0495889 723.39256 588.9958598 921.3386627 708.3084228 475.5872447 522.1707606 473.0624302 705.8732761 717.7260112 0.887594401 1.007895142 0.820641652 1.283691337 0.986878575 0.662630638 0.727534954 0.659112841 0.983485711 1 9.487289396 -8.262308381 24.84200008 0.9689663 0.687537013 0.599553852 0.115633796 40.38277694 1154440.153 0.016597415 0.039266707 5.47E-09 8.262308381 -0.281429288 SASQES(ph)T(ph)LSDDS(ph)T(ph)PPSSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SASQESTLSDDSTPPSSSPK 20 0 J3KN99;Q8IZD0 J3KN99 SAMD14 Sterile alpha motif domain-containing protein 14 4 0 S(0.016)AS(0.157)QES(0.858)T(0.896)LS(0.076)DDS(0.554)T(0.551)PPS(0.325)S(0.296)S(0.271)PK 52.321 0.023339 20666000 1046 1120.3 1080.4 1174.5 1121.8 954.29 863.42 928.62 1237.3 1391.7 TRUE FALSE FALSE 1033.25095 1136.071613 1099.203909 1310.301216 1064.55036 893.3139488 936.7588732 955.4881546 1126.632789 1355.543433 0.762241124 0.838093111 0.810895381 0.966624295 0.785331059 0.659007987 0.691057808 0.704874614 0.831129982 1 10.40465562 -16.52287875 0.129882826 1.763061972 0.665940993 0.305529749 0.088388739 48.95103771 0.451007933 9.801288152 0.313435935 3.00E-17 16.52287875 -1.097120979 SASQS(ph)S(ph)LDKLDQELKEQQK ddPTM_HeLa_Romidepsin_16h_R1 2 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 2 0 S(0.002)AS(0.034)QS(0.973)S(0.991)LDKLDQELKEQQK;SAS(0.001)QS(1)S(1)LDKLDQELKEQQK ; 82.349 0.0075771 8191100 4033.3 4255.3 3294.54 4240.3 4990 5940.6 5915.3 6718.9 4723.1 4191.7 TRUE FALSE FALSE 3984.140588 4315.206225 3351.880087 4730.583437 4735.34168 5561.014832 6417.745434 6913.300771 4300.654107 4082.79903 0.975835587 1.056923496 0.820976017 1.15866184 1.159827277 1.362059409 1.571898442 1.693274815 1.053359246 1 11.99534284 -8.00530386 0.963720255 0.983900085 1.762554624 0.919853775 0.074090934 0.13666999 0.182517621 0.010433695 0.084251737 9.88E-09 8.00530386 0.778654539 SASQS(ph)SLDKLDQELK ddPTM_HeLa_Romidepsin_16h_R1 1 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 S(0.197)AS(0.197)QS(0.448)S(0.158)LDKLDQELK 62.556 0.026994 13981000 1414.3 1327.1 1465.8 1258.4 2127.6 2411.6 1815.2 2243.8 1560.5 1777.1 TRUE FALSE FALSE 1397.061968 1345.782949 1491.311634 1403.902129 2019.020633 2257.506543 1969.383043 2308.720813 1420.924972 1730.930686 0.807116067 0.777490953 0.861566351 0.811067792 1.166436443 1.30421545 1.137759622 1.333803157 0.820902295 1 10.75733224 -8.655045339 4.88047625 0.886066052 1.244273767 0.845055806 0.081077998 0.078936354 3.078864816 0.014368605 0.029190816 2.21E-09 8.655045339 0.358207716 SASQS(ph)SLDKLDQELKEQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 S(0.029)AS(0.082)QS(0.626)S(0.263)LDKLDQELKEQQK 54.171 0.020986 24925000 2641.7 2214.8 2497.6 2984.7 3166.8 3833.8 3719.1 4060.8 2824 2638.1 TRUE FALSE FALSE 2609.501944 2245.980013 2541.06968 3329.805057 3005.186379 3588.832553 4035.000261 4178.292841 2571.414367 2569.561782 1.01554357 0.874071224 0.988911689 1.295864953 1.169532642 1.396671051 1.57030677 1.626072146 1.000720973 1 11.32730662 -8.191809342 0.79234305 0.994259043 1.704707652 0.903851137 0.07792783 0.209915074 0.189307013 0.013459338 0.099552011 6.43E-09 8.191809342 0.710448609 SASQSS(ph)LDKLDQELK ddPTM_HeLa_Romidepsin_16h_R1 2 SASQSSLDKLDQELK 15 1 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 SAS(0.002)QS(0.138)S(0.86)LDKLDQELK;S(0.002)AS(0.006)QS(0.11)S(0.883)LDKLDQELK ; 162.41 0.0010112 160569000 3893.1 4225 4208.5 3238.4 5395.3 6546.4 6145.3 6563.4 4761.2 4451 TRUE FALSE FALSE 3845.6494 4284.479661 4281.747177 3612.839045 5119.957708 6128.106168 6667.281629 6753.301624 4335.346347 4335.362378 0.887042204 0.98826333 0.987633052 0.833341882 1.18097572 1.41351648 1.537883352 1.55772483 0.999996302 1 12.08193687 -8.342390323 2.066002177 0.945099461 1.539429714 0.944349586 0.060270641 0.051820132 0.425986892 0.009243032 0.026698583 4.55E-09 8.342390323 0.594330253 SASQSS(ph)LDKLDQELKEQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SASQSSLDKLDQELKEQQK 19 2 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 SAS(0.002)QS(0.162)S(0.836)LDKLDQELKEQQK 96.591 0.0019511 39325000 1683.2 1483.1 1358.9 1757.4 1738.9 1769.3 1925.7 2509.2 1852 1967.8 TRUE FALSE FALSE 1662.684511 1503.979121 1382.551084 1960.598857 1650.157444 1656.24744 2089.26891 2581.799743 1686.352482 1916.676272 0.867483223 0.784680826 0.721327386 1.022916016 0.860947395 0.864124769 1.090047881 1.347019202 0.879831668 1 10.90439097 -7.418103359 2.537577461 0.906651036 1.374129643 0.726629309 0.089242436 0.174548705 1.73422803 0.014230947 0.148500408 3.82E-08 7.418103359 0.467478608 SASS(ph)DTSEELNSQDSPPK ddPTM_HeLa_Romidepsin_16h_R1 2 SASSDTSEELNSQDSPPK 18 0 O14745;J3QRP6;O14745-2 O14745 SLC9A3R1 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 1 0 S(0.002)AS(0.089)S(0.767)DT(0.142)SEELNSQDSPPK;S(0.132)AS(0.132)S(0.723)DT(0.009)S(0.003)EELNSQDSPPK ; 197.51 1.62E-15 106778000 7169.7 7861.5 6978.5 5172.5 13008.1 15916.6 13510.2 15239.4 8294 8448.9 TRUE FALSE FALSE 7082.312939 7972.174403 7099.957865 5770.568787 12344.24812 14899.58063 14657.75605 15680.328 7552.163867 8229.39636 0.860611475 0.968743521 0.862755609 0.701214103 1.500018662 1.810531414 1.781145956 1.905404395 0.91770569 1 13.0065709 -8.57986792 3.901933431 0.915791203 1.811194395 0.958119106 0.0901258 0.034625244 1.082593041 0.014873336 0.03154107 2.63E-09 8.57986792 0.895403192 SASSASSLFS(ph)PSSTLFSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SASSASSLFSPSSTLFSSSR 20 0 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2;E9PR38;Q14671-4;H0YDK8 Q5T1Z4 PUM1 Pumilio homolog 1 1 0 SASSASS(0.034)LFS(0.939)PS(0.01)S(0.016)TLFSSSR;SASSASSLFS(0.951)PS(0.047)S(0.002)TLFSSSR ; 263.47 4.60E-81 103886000 2557.7 2329 2715 2398 3415.4 3056.9 3044.1 2799.5 2714.5 2498.3 TRUE FALSE FALSE 2526.525769 2361.787723 2762.253436 2675.268043 3241.099393 2861.573956 3302.665778 2880.499116 2471.708321 2433.393806 1.038272458 0.970573574 1.135144435 1.099397901 1.331925554 1.175960072 1.357226179 1.183737342 1.0157453 1 11.2487541 -9.157504279 1.457829516 1.01582598 1.263820488 0.725822605 0.066676143 0.132975966 0.555098508 0.009565594 0.018820381 6.96E-10 9.157504279 0.247994509 SASSESS(ph)S(ph)SS(ph)SKKK ddPTM_HeLa_Romidepsin_16h_R1 1 SASSESSSSSSKKK 14 2 E5RK24;E5RIW4;E5RH41;P29084 E5RK24 GTF2E2 Transcription initiation factor IIE subunit beta 3 0 S(0.168)AS(0.042)S(0.049)ES(0.356)S(0.423)S(0.96)S(0.038)S(0.526)S(0.439)KKK 63.682 0.0037371 0 2656.5 2806.4 2891.5 1979.3 2953 3175.5 2375.4 2742.5 2890 3479.2 TRUE FALSE FALSE 2624.121556 2845.908573 2941.825345 2208.155979 2802.297391 2972.595798 2577.166417 2821.849911 2631.511162 3388.809882 0.774349004 0.839795879 0.868099848 0.651602201 0.826926705 0.877179866 0.760493066 0.832696436 0.776529594 1 11.72656299 -12.32073969 0.776448435 1.016532207 0.800922711 0 0.092583681 0.438080249 0.414375034 0.06096037 0.012070572 4.78E-13 12.32073969 -0.215609496 SASSGAEGDVSS(ph)EREP ddPTM_HeLa_Romidepsin_16h_R1 2 SASSGAEGDVSSEREP 16 1 Q8TEA8 Q8TEA8 DTD1 D-tyrosyl-tRNA(Tyr) deacylase 1 1 0 SASSGAEGDVS(0.019)S(0.981)EREP;SASSGAEGDVS(0.033)S(0.967)EREP ; 218.21 1.25E-25 32202000 5700.9 5946.9 4744.3 5862.6 5829.6 5441.7 4833.8 4845.3 5532.2 5918.6 TRUE FALSE FALSE 5631.415238 6030.620614 4826.872551 6540.461396 5532.093759 5093.992932 5244.382851 4985.491111 5037.386176 5764.833919 0.976856457 1.046104831 0.83729603 1.134544635 0.959627604 0.883632209 0.909719677 0.864810883 0.873812888 1 12.49306333 -8.363179222 4.604951523 0.991838312 0.888684932 0.199097071 0.079230215 0.189872981 6.611214765 0.009008841 0.020811141 4.33E-09 8.363179222 -0.10315338 SASSSAAGS(ph)PGGLTSLQQQK ddPTM_HeLa_Romidepsin_16h_R1 2 SASSSAAGSPGGLTSLQQQK 20 0 E5RJ10;E5RHB8;E5RJX6;E5RG91;Q8NEZ2-3;Q8NEZ2-2;Q8NEZ2 E5RJ10 VPS37A Vacuolar protein sorting-associated protein 37A 1 0 SAS(0.003)S(0.12)S(0.12)AAGS(0.757)PGGLTSLQQQK;SASSS(0.001)AAGS(0.448)PGGLT(0.443)S(0.108)LQQQK ; 300.2 2.02E-148 24779000 3551 3212.7 3477.2 3760.8 5158.9 6500.9 5392.6 6612.8 3788.6 3251.5 TRUE FALSE FALSE 3507.719046 3257.928475 3537.719207 4195.641391 4895.622082 6085.513471 5850.647309 6804.130935 3449.738127 3167.025561 1.107575224 1.02870293 1.117047886 1.324789241 1.545810726 1.92152332 1.847363463 2.148429434 1.089267535 1 11.6289128 -8.536545206 0.975092557 1.044000202 2.074650885 0.971345988 0.068078671 0.065851255 0.113378842 0.011084298 0.044309087 2.91E-09 8.536545206 1.030650683 up SAST(ph)EKLEQGTSALIR ddPTM_HeLa_Romidepsin_16h_R1 1 SASTEKLEQGTSALIR 16 1 A0A0A0MRP0;Q8IWC1-2;Q8IWC1-4;Q8IWC1 A0A0A0MRP0 MAP7D3 MAP7 domain-containing protein 3 1 0 S(0.002)AS(0.4)T(0.598)EKLEQGTSALIR 100.77 0.022496 38715000 685.39 1026.4 748.38 1438.5 1011.7 723.2 770.12 810.51 1087.1 890.41 TRUE FALSE FALSE 677.0362031 1040.849686 761.40524 1604.826138 960.0691738 676.989854 835.5339736 833.9608281 989.8670533 867.2770198 0.780645846 1.200135207 0.877926225 1.850419303 1.10699252 0.780592404 0.963399184 0.961585294 1.141350492 1 9.760349073 -10.25756076 24.91710467 0.896416094 1.107787694 0.021316809 0.290907528 569.649266 3659552.061 0.048430924 0.058127054 5.53E-11 10.25756076 0.2113716 SASVVSSDSISTSADNFS(ph)PDLR ddPTM_HeLa_Romidepsin_16h_R1 2 SASVVSSDSISTSADNFSPDLR 22 0 Q13614 Q13614 MTMR2 Myotubularin-related protein 2 1 0 SASVVSSDSIS(0.001)T(0.001)S(0.047)ADNFS(0.951)PDLR;SASVVSSDSIS(0.01)T(0.01)S(0.303)ADNFS(0.676)PDLR ; 235.21 1.42E-53 150851000 15549.5 16346.6 15317 14913.9 13336.6 10697.1 10148.3 10694.8 17515.7 15672 TRUE FALSE FALSE 15359.97671 16576.72786 15583.58596 16638.31529 12655.98354 10013.58983 11010.29635 11004.23716 15949.05192 15264.83918 1.006232462 1.085941861 1.02088111 1.089976455 0.829093801 0.655990523 0.721284792 0.720887854 1.044822794 1 13.89792477 -8.564721802 4.172360782 1.016465543 0.705106048 0.939933459 0.038987651 0.037205534 1.407034767 0.005823634 0.01233082 2.72E-09 8.564721802 -0.311359495 SAT(ph)TTGSPGTEK ddPTM_HeLa_Romidepsin_16h_R1 1 SATTTGSPGTEK 12 0 A0A1B0GUI1;Q6GYQ0-3;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-2 A0A1B0GUI1 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 0 S(0.001)AT(0.616)T(0.364)T(0.018)GS(0.001)PGTEK 168.98 0.0003804 2540200 1500.3 1361 2405.4 1267.3 1263.4 1303.1 2096.1 780.01 2203.4 1763.2 TRUE FALSE FALSE 1482.013767 1380.160194 2447.264978 1413.831189 1198.923984 1219.836116 2274.142682 802.5783587 2006.322385 1717.39181 0.862944471 0.803637345 1.424989315 0.823243235 0.698107431 0.710284111 1.324183957 0.46732397 1.168238007 1 10.7460035 SATAS(ph)PQQPQAQQR ddPTM_HeLa_Romidepsin_16h_R1 1 SATASPQQPQAQQR 14 0 A0A0U1RQI5;Q9BX66-4;Q9BX66-9;Q9BX66-8;Q9BX66-10;Q9BX66-6;Q9BX66-5;Q9BX66-12 A0A0U1RQI5 SORBS1 Sorbin and SH3 domain-containing protein 1 1 0 S(0.073)AT(0.162)AS(0.766)PQQPQAQQR 111.66 0.0052351 420060 0 0 0 0 0 196.21 172.07 290.76 0 0 TRUE FALSE FALSE 0 0 0 0 0 183.6728142 186.6856215 299.1726819 0 0 0 SATDGNTST(ph)TPPTS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 2 0 SATDGNT(0.17)S(0.238)T(0.565)T(0.026)PPT(0.387)S(0.613)AK 128.74 0.0089352 9320900 2286.1 2152.9 2156.5 2030.9 2116.2 2136.3 1435.8 1756.5 2182.1 1820.8 TRUE FALSE FALSE 2258.236134 2183.208583 2194.032978 2265.722214 2008.202417 1999.797325 1557.756816 1807.321556 1986.927511 1773.495354 1.273325092 1.231020188 1.237123612 1.27754618 1.132341516 1.127602235 0.878354044 1.019073184 1.120345484 1 10.79237984 -7.857182789 5.910735543 1.158430646 0.950167204 0.5126859 0.087364876 0.171721001 8.643418879 0.016949387 0.052605103 1.39E-08 7.857182789 -0.208263442 SATDGNTST(ph)TPPTSAK ddPTM_HeLa_Romidepsin_16h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 SATDGNT(0.054)S(0.187)T(0.652)T(0.097)PPT(0.008)S(0.001)AK 112.03 0.0062235 8670500 3900.7 3312.3 3136.4 2891.2 1794.6 1667.7 1390.9 1875.5 3779.7 3378.4 TRUE FALSE FALSE 3853.156768 3358.930646 3190.987726 3225.494148 1703.014865 1561.139352 1509.043011 1929.764633 3441.634166 3290.628681 1.170948515 1.020756509 0.969719782 0.980206052 0.517534803 0.474419785 0.458588056 0.586442537 1.045889555 1 11.68414752 -8.803771522 3.42256273 1.067094639 0.495532849 0.944337948 0.062017884 0.046299088 1.116884312 0.012186935 0.023940374 1.57E-09 8.803771522 -0.57156179 SATDGNTSTT(ph)PPTS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 SATDGNTSTTPPTSAK 16 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 2 0 SAT(0.002)DGNT(0.089)S(0.338)T(0.397)T(0.376)PPT(0.219)S(0.579)AK 98.408 0.026448 15209000 1603.9 1312.6 1524.5 1266.4 1641 1393.5 1215.5 1256.6 1568.2 1149.2 TRUE FALSE FALSE 1584.35105 1331.078817 1551.033283 1412.827127 1557.253647 1304.459847 1318.74454 1292.957738 1427.936264 1119.343618 1.415428671 1.189160143 1.38566322 1.262192506 1.391220373 1.165379269 1.178140937 1.155103506 1.275690718 1 10.12843727 -12.51295094 1.258622082 0.999669263 1.283634082 0 0.126176588 0.293777552 0.831497137 0.07154467 0.017159934 3.07E-13 12.51295094 0.28396482 SATDGNTSTT(ph)PPTSAK ddPTM_HeLa_Romidepsin_16h_R1 3 SATDGNTSTTPPTSAK 16 0 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 SATDGNT(0.028)S(0.086)T(0.086)T(0.796)PPT(0.004)SAK;SATDGNTST(0.005)T(0.984)PPT(0.005)S(0.005)AK;SAT(0.001)DGNT(0.009)S(0.023)T(0.043)T(0.893)PPT(0.024)S(0.007)AK ;; 161.94 0.00019743 245810000 9778.8 9407.6 8877.4 7057.9 5632.5 4761.5 4291.64 4696.9 10091.5 9599.7 TRUE FALSE FALSE 9659.612224 9540.04044 9031.907423 7873.967606 5345.052507 4457.255517 4656.171794 4832.797391 9188.890965 9350.29841 1.033080636 1.020292618 0.965948575 0.842108697 0.571645125 0.476696606 0.497970395 0.51686023 0.982737723 1 13.19079669 -8.873936704 1.82595736 1.015126102 0.491840922 0.992167993 0.020426952 0.019407739 0.130968857 0.003244654 0.006939708 1.34E-09 8.873936704 -0.523285179 SATDGNTSTT(ph)PPTSAKK ddPTM_HeLa_Romidepsin_16h_R1 2 SATDGNTSTTPPTSAKK 17 1 A0A669KAU9;A0A669KAX4;Q13620-1;K4DI93;Q13620 A0A669KAU9 CUL4B Cullin-4B 1 0 SATDGNT(0.001)S(0.026)T(0.163)T(0.811)PPTSAKK;SATDGNT(0.001)S(0.044)T(0.182)T(0.739)PPT(0.026)S(0.009)AKK ; 81.665 0.0070645 15258200 8693.3 9268.8 7574.2 9633.5 4807 3680.5 3449.6 3654.6 8617.1 7894.7 TRUE FALSE FALSE 8587.342716 9399.28641 7706.025774 10747.3706 4561.680853 3445.327928 3742.608938 3760.340085 7846.364994 7689.594556 1.116748439 1.222338361 1.002136812 1.39765114 0.593227747 0.448050662 0.486710829 0.489016691 1.020387348 1 12.90869182 -8.627231726 6.542865195 1.086672739 0.483465152 0.870825119 0.117375577 0.05505679 3.041758335 0.016862496 0.03392329 2.36E-09 8.627231726 -0.603207587 NMK(ac)IK(ac)ADMEVPK ddPTM_HeLa_Romidepsin_16h_R1 1 NMKIKADMEVPK 12 2 A0A0A0MS79;O14513 A0A0A0MS79 NCKAP5 Nck-associated protein 5 0 2 NMK(1)IK(1)ADMEVPK 58.592 0.023483 0 144.58 489.1 290.37 673.02 3170.7 4313.5 3713.9 3953.3 176.02 366.39 FALSE TRUE FALSE 142.8178033 495.9855626 295.423768 750.8377391 3008.887347 4037.881271 4029.358573 4067.682498 160.2763303 356.871135 0.400194326 1.389816979 0.827816371 2.103946398 8.431299291 11.31467601 11.29079429 11.39818298 0.449115422 1 8.479259406 -8.6910191 2.292438959 0.769082213 11.34513793 0.995992128 0.302728834 0.014130999 0.15090847 0.053255303 0.118276382 2.04E-09 8.6910191 10.57605572 up RALPFSEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RALPFSEKK 9 2 A0A1C7CYX1;Q6PJG2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 0 1 ; RALPFSEK(1)K;RALPFSEK(1)K 110.54 0.0032878 1971370 574.55 578.68 757.64 874.65 2212.96 3333.2 2916.8 2280.4 717.95 558.75 FALSE TRUE FALSE 567.5471636 586.8266722 770.8264064 975.7811484 2100.024394 3120.219277 3164.552919 2346.379776 653.7347539 544.2335945 1.042837431 1.078262493 1.416352122 1.792945453 3.858682035 5.733235341 5.814696027 4.311346819 1.201202499 1 9.088082204 -8.688206247 2.061409382 1.055829666 5.35229247 0.95172282 0.415833904 0.041625692 0.358954615 0.059524006 0.136313902 2.05E-09 8.688206247 4.296462804 up SATPEPVTDNRDVEDMELS(ph)DVEDDGSK ddPTM_HeLa_Romidepsin_16h_R1 1 SATPEPVTDNRDVEDMELSDVEDDGSK 27 1 Q5VT52-2;Q5VT52-3;Q5VT52;Q5VT52-5 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 SATPEPVTDNRDVEDMELS(0.999)DVEDDGS(0.001)K 67.194 0.00031613 14613000 2497.2 2192.7 2411.5 2155.9 1277.9 1441.3 1392.2 1391.3 2543 2204.5 TRUE FALSE FALSE 2466.763166 2223.568888 2453.471146 2405.175302 1212.683994 1349.205582 1510.453433 1431.55507 2315.547711 2147.226772 1.148813529 1.035553821 1.142623209 1.120131014 0.564767546 0.628347969 0.703443834 0.666699526 1.078389922 1 11.06825885 -8.764463528 24.99999435 1.078161367 0.644397712 0.942081583 0.054236193 16.38661403 135466.2949 0.010172658 0.019030451 1.72E-09 8.764463528 -0.433763655 SATSTSAS(ph)PTLR ddPTM_HeLa_Romidepsin_16h_R1 2 SATSTSASPTLR 12 0 O75061-4;O75061;O75061-2 O75061-4 DNAJC6 Putative tyrosine-protein phosphatase auxilin 1 0 S(0.045)AT(0.001)S(0.001)T(0.002)S(0.01)AS(0.916)PT(0.026)LR;SATSTSAS(0.968)PT(0.031)LR ; 157.03 0.00113 50043000 3149.1 2467.8 3090.5 3275.5 6702.6 7969 7069.8 8165.2 3140.8 2639.9 TRUE FALSE FALSE 3110.717558 2502.541753 3144.288856 3654.228722 6360.541311 7459.806619 7670.308636 8401.447179 2859.878982 2571.315017 1.209776918 0.973253661 1.222833 1.421151705 2.473653079 2.901164022 2.983029533 3.267373746 1.112224275 1 11.32829065 -8.667522073 1.610535125 1.090948021 3.102092116 0.985974656 0.104652398 0.031580452 0.164396158 0.017713435 0.045083712 2.15E-09 8.667522073 2.011144095 up SATTTPSGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SATTTPSGSPR 11 0 Q2M2I8-2;Q2M2I8;A0A096LP60;A0A096LNZ0;A0A096LP25 Q2M2I8-2;A0A096LNZ0 AAK1 AP2-associated protein kinase 1 1 0 SATTTPS(0.006)GS(0.994)PR;SATTT(0.001)PS(0.024)GS(0.975)PR ; 98.182 0.021315 4813900 1868.34 1461.05 1755.43 1899.25 1740.1 2376.1 3170 1326.11 2434.2 1932.26 TRUE FALSE FALSE 1845.567953 1481.6187 1785.982523 2118.850221 1651.296204 2224.274879 3439.259721 1364.478901 2216.479055 1882.059607 0.980610788 0.787232612 0.948951094 1.12581462 0.877387835 1.181830198 1.827391496 0.724992394 1.177688022 1 10.8780966 -8.005194075 24.99124161 0.977599415 1.333296613 0.162316796 0.269031678 211.835328 1019263.889 0.03160331 0.09108388 9.88E-09 8.005194075 0.355697198 SAVEAQNEVT(ph)ENPK ddPTM_HeLa_Romidepsin_16h_R1 1 SAVEAQNEVTENPK 14 0 Q32MZ4-3;Q32MZ4-2;Q32MZ4 Q32MZ4-3 LRRFIP1 Leucine-rich repeat flightless-interacting protein 1 1 0 S(0.107)AVEAQNEVT(0.893)ENPK 167.03 0.00017716 2729600 1113.1 1091.8 853.21 1030.4 1188.8 1106 983.96 1266.8 1085.6 998.64 TRUE FALSE FALSE 1099.533109 1107.170389 868.0597621 1149.539696 1128.1311 1035.330169 1067.537538 1303.452859 988.5012171 972.6951888 1.130398425 1.138250093 0.892427322 1.181808761 1.159799198 1.064393225 1.097504696 1.340042466 1.016249724 1 9.925843972 SAVQKPPS(ph)TGSAPAIESVD ddPTM_HeLa_Romidepsin_16h_R1 1 SAVQKPPSTGSAPAIESVD 19 1 Q9NUQ3;Q9NUQ3-2 Q9NUQ3 TXLNG Gamma-taxilin 1 0 SAVQKPPS(0.646)T(0.141)GS(0.213)APAIESVD 94.281 0.018435 7173500 3201 3338.4 3318 3070.2 2499.7 2341.4 1881.4 2183 3341.8 3528.8 TRUE FALSE FALSE 3161.984981 3385.398083 3375.748398 3425.19097 2372.130981 2191.792097 2041.206069 2246.161661 3042.901038 3437.121267 0.919951534 0.984951597 0.982144107 0.996528986 0.690150506 0.637682504 0.593870833 0.653500847 0.885305115 1 11.74698504 -8.691246415 4.473893305 0.967219426 0.631354837 0.944286418 0.037927751 0.031530376 1.213430603 0.005368507 0.010881448 2.04E-09 8.691246415 -0.335864589 SAVS(ph)PDLHITPIYEGR ddPTM_HeLa_Romidepsin_16h_R1 2 SAVSPDLHITPIYEGR 16 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 S(0.004)AVS(0.995)PDLHITPIYEGR;S(0.01)AVS(0.959)PDLHIT(0.025)PIY(0.005)EGR ; 81.316 0.0097374 5543800 2343.59 2344.31 2105.78 2109.7 4698.5 4738 3960 3838.4 3299.3 3110.6 TRUE FALSE FALSE 2315.025424 2377.313258 2142.430218 2353.63344 4458.718012 4435.257091 4296.362301 3949.458048 3004.202345 3029.786164 0.764088717 0.784647209 0.707122583 0.776831536 1.471627954 1.463884529 1.418041429 1.303543496 0.9915559 1 11.56500026 -8.759903788 24.99973981 0.855232707 1.418087092 0.889482996 0.099498191 11.73070548 190972.1544 0.017872347 0.034277341 1.74E-09 8.759903788 0.562854385 SAVVAAAAPASVADDT(ph)PPPERR ddPTM_HeLa_Romidepsin_16h_R1 1 SAVVAAAAPASVADDTPPPERR 22 1 D6RCN9;D6R966;D6RHG9;D6RHC6;D6RIR8;D6R9V1;E7EV55;D6RDY2;D6RBE0;E7EVI8;Q7LFL8 D6RCN9 CXXC5 CXXC-type zinc finger protein 5 1 0 SAVVAAAAPAS(0.02)VADDT(0.98)PPPERR 52.192 0.0034134 0 2293.8 1386.1 1958.9 1197.2 1982.1 1305.8 2026 1252.2 2779.3 2213.2 TRUE FALSE FALSE 2265.842283 1405.613552 1992.993833 1335.625897 1880.946041 1222.363594 2198.088389 1288.430431 2530.712447 2155.700745 1.051093149 0.652044842 0.924522496 0.619578529 0.872545062 0.567037701 1.019663047 0.5976852 1.173962784 1 11.0739412 -10.27250225 24.91707525 1.024127327 0.760099133 0.485103841 0.150294807 418.3496641 942253.0521 0.021117738 0.024269623 5.34E-11 10.27250225 -0.264028194 SAYPPPAPAYALS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 SAYPPPAPAYALSSPR 16 0 O14497-2;O14497 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 SAYPPPAPAY(0.001)ALS(0.5)S(0.5)PR;SAYPPPAPAYALS(0.5)S(0.5)PR ; 165.89 2.07E-05 29719000 4478.6 4720.8 3636.1 3868.6 4129.8 3934.4 3099 3643.9 4770.7 4517.7 TRUE FALSE FALSE 4424.013101 4787.259546 3699.384795 4315.905734 3919.040896 3683.004538 3362.228983 3749.330497 4343.996644 4400.329503 1.005382233 1.087932061 0.840706314 0.980814217 0.890624416 0.836983807 0.764085731 0.85205676 0.987198036 1 12.10339584 -8.723771461 0.834175589 1.005893019 0.795938927 0.629912207 0.058623857 0.294695877 0.373140564 0.009634006 0.035915 1.89E-09 8.723771461 -0.209954093 SAYQEYDS(ph)DSDVPEELKR ddPTM_HeLa_Romidepsin_16h_R1 4 SAYQEYDSDSDVPEELKR 18 1 H0Y7Q2;Q96JG6-3;Q96JG6 H0Y7Q2 CCDC132 Coiled-coil domain-containing protein 132 1 0 SAYQEYDS(0.962)DS(0.038)DVPEELKR;SAYQEY(0.001)DS(0.923)DS(0.076)DVPEELKR;SAYQEYDS(0.962)DS(0.038)DVPEELKR;SAYQEY(0.003)DS(0.951)DS(0.045)DVPEELKR ;;; 132.24 0.00045634 127667000 11430.7 11681.5 12970.1 9150.9 11069.5 11827.3 9450.1 12660.2 12957.3 11418.7 TRUE FALSE FALSE 11291.37823 11845.95246 13195.83915 10208.97011 10504.58211 11071.5737 10252.79126 13026.50291 11798.36664 11122.04053 1.015225417 1.065088051 1.186458467 0.917904416 0.944483351 0.995462449 0.921844443 1.171233182 1.060809535 1 13.44113388 -7.240292591 24.08964975 1.007952964 1.171233451 0.282185527 0.075991062 3253.436894 3706106.542 0.010043678 0.596021925 5.75E-08 7.240292591 0.163280487 SDADSGFLGLRPT(ph)SVDPALRR ddPTM_HeLa_Romidepsin_16h_R1 1 SDADSGFLGLRPTSVDPALRR 21 2 Q9NZM5 Q9NZM5 GLTSCR2 Glioma tumor suppressor candidate region gene 2 protein 1 0 SDADS(0.003)GFLGLRPT(0.498)S(0.498)VDPALRR 51.786 0.014918 4720100 1269 1813.9 1462 1473.8 1360.6 1362.8 1251.4 1327.7 1572.5 1374.1 TRUE FALSE FALSE 1253.53294 1839.436132 1487.445497 1644.20769 1291.163505 1275.721478 1357.693885 1366.114905 1431.851662 1338.400684 0.936590182 1.374353849 1.111360383 1.228486888 0.96470625 0.953168579 1.014415116 1.020706969 1.069822871 1 10.38629437 SDAEEDGGTVS(ph)QEEEDRKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SDAEEDGGTVSQEEEDRKPK 20 2 P27824-3;P27824;P27824-2 P27824-3 CANX Calnexin 1 0 SDAEEDGGT(0.113)VS(0.887)QEEEDRKPK 71.634 0.0030971 33722000 2781.1 5084.3 3661.2 1874.5 2896.8 4711.8 1948.7 4952.3 3925.4 4485.9 TRUE FALSE FALSE 2747.202883 5155.876909 3724.92165 2091.23851 2748.965487 4410.731187 2114.222529 5095.586987 3574.302393 4369.355671 0.62874325 1.180008518 0.852510514 0.47861485 0.629146651 1.009469478 0.483875127 1.166210162 0.818038782 1 12.09320483 -12.62003949 1.414151265 1.000647435 0.772965763 0 0.249747365 0.779205584 2.785241144 0.168105684 0.038020091 2.40E-13 12.62003949 -0.227681672 SDAGLESDT(ph)AMK ddPTM_HeLa_Romidepsin_16h_R1 1 SDAGLESDTAMK 12 0 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 SDAGLES(0.162)DT(0.838)AMK 108.68 0.028131 42550000 8534.7 7497.1 8395.6 5786 5955.3 4698.3 4944.2 5818.1 8356.6 8053.5 TRUE FALSE FALSE 8430.675794 7602.644371 8541.721896 6455.004544 5651.378819 4398.093793 5364.160225 5986.437544 7609.164767 7844.268909 1.074756092 0.969197316 1.088912427 0.822894347 0.720446849 0.560676061 0.683831761 0.763160674 0.970028546 1 12.93742328 -9.004686972 2.500062428 1.034059774 0.670937232 0.867394092 0.062302883 0.065199623 0.817547627 0.009200199 0.01732835 9.89E-10 9.004686972 -0.363122542 SDAGLESDTAMK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SDAGLESDTAMKK 13 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 1 ; SDAGLESDTAMK(1)K;SDAGLESDTAMK(1)K 132.5 0.0001199 3097600 1401.82 1161.03 1234.43 853.58 1167.78 1178.15 1115.96 1052.68 1540.66 1535.27 FALSE TRUE FALSE 1384.734079 1177.375011 1255.914736 952.2749358 1108.183829 1102.870017 1210.749615 1083.137635 1402.859511 1495.383464 0.926006012 0.787339862 0.839861324 0.636809861 0.741070004 0.737516526 0.809658287 0.724320993 0.938126938 1 10.54629977 -10.24916103 1.099551089 0.97805405 0.738243861 0.769842254 0.051347425 0.132128985 0.311389027 0.010441033 0.012480993 5.63E-11 10.24916103 -0.239810189 SDATNYASHS(ph)PPVNR ddPTM_HeLa_Romidepsin_16h_R1 1 SDATNYASHSPPVNR 15 0 Q96FJ0;Q96FJ0-2 Q96FJ0 STAMBPL1 AMSH-like protease 1 0 SDAT(0.004)NY(0.001)AS(0.003)HS(0.993)PPVNR 68.625 0.022518 20366000 1494.4 1866.7 1710.3 1125.6 1751.6 1564.4 1339.6 1451.8 1982.6 1969.4 TRUE FALSE FALSE 1476.185678 1892.979452 1740.067054 1255.747168 1662.209316 1464.439889 1453.385591 1493.805542 1805.27129 1918.234704 0.769554255 0.986834118 0.907118952 0.654636873 0.866530729 0.763431026 0.757668281 0.778739713 0.941110744 1 10.90556354 -9.302292331 24.7842551 0.89819706 0.769480517 0.496290079 0.077175252 441.2764982 267708.0137 0.015089172 0.023049233 4.99E-10 9.302292331 -0.128716543 SDDY(ph)MPMSPASVSAPK ddPTM_HeLa_Romidepsin_16h_R1 3 SDDYMPMSPASVSAPK 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 S(0.027)DDY(0.97)MPMS(0.003)PASVSAPK;S(0.006)DDY(0.974)MPMS(0.018)PAS(0.001)VSAPK;S(0.001)DDY(0.997)MPMS(0.002)PASVSAPK ;; 100.19 0.00040726 10026300 5641.5 5851.2 5122.07 6574.6 8221.9 8162.7 6290.4 7044.2 6260.9 6019 TRUE FALSE FALSE 5572.739228 5933.573347 5211.21748 7334.786186 7802.305763 7641.129814 6824.706419 7248.012813 5700.909423 5862.625512 0.950553505 1.012101717 0.888888002 1.251109451 1.330855219 1.303363109 1.164104104 1.23630834 0.972415757 1 12.51733119 -9.249830861 24.99911682 0.973296227 1.258641303 0.889237506 0.051545494 182.4178079 392839.5693 0.007980106 0.013160456 5.63E-10 9.249830861 0.285345076 SDDYMPMS(ph)PASVSAPK ddPTM_HeLa_Romidepsin_16h_R1 3 SDDYMPMSPASVSAPK 16 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 SDDY(0.002)MPMS(0.996)PAS(0.001)VSAPK;SDDYMPMS(0.996)PAS(0.003)VSAPK;SDDY(0.001)MPMS(0.998)PAS(0.001)VSAPK ;; 110.35 0.0023029 43092400 13250.5 13155.4 11504.1 13679.3 12179.3 11471.7 9457.7 10191.1 12646.3 12534.8 TRUE FALSE FALSE 13088.99781 13340.60207 11704.32403 15260.96503 11557.74487 10738.69539 10261.0368 10485.9634 11515.18325 12209.14409 1.072065143 1.092672997 0.958652298 1.249961907 0.946646611 0.879561689 0.840438669 0.858861467 0.943160566 1 13.57567444 -8.52721883 24.99843662 1.048979362 0.866936009 0.536773447 0.080943412 64.58825962 372021.5009 0.010526691 0.021121317 2.97E-09 8.52721883 -0.182043353 SDEEDEDS(ph)DFGEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 SDEEDEDSDFGEEQR 15 0 Q5VW52;Q9HCL2 Q5VW52 GPAM "Glycerol-3-phosphate acyltransferase 1, mitochondrial" 1 0 SDEEDEDS(1)DFGEEQR 120.59 0.0035294 4623100 1305.1 1331.2 1308.9 1504.5 1147.4 1253.5 1039.8 1367.8 1281.8 1327.4 TRUE FALSE FALSE 1289.192939 1349.940669 1331.680855 1678.457369 1088.843896 1173.405395 1128.120586 1407.375135 1167.152598 1292.913957 0.997121991 1.044107121 1.029984129 1.29819727 0.842162691 0.907566501 0.872541116 1.088529618 0.902730295 1 10.33641055 SDEGQLS(ph)PATR ddPTM_HeLa_Romidepsin_16h_R1 2 SDEGQLSPATR 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;E9PMV1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 SDEGQLS(0.98)PAT(0.02)R;SDEGQLS(0.991)PAT(0.009)R ; 127.02 0.0069179 361300000 5894.2 5503.8 5772.3 4628.1 5850.6 6337.2 5146 5839.7 6207.4 5545.8 TRUE FALSE FALSE 5822.359223 5581.282641 5872.76446 5163.222698 5552.02205 5932.273372 5583.101112 6008.662506 5652.194597 5401.719317 1.077871485 1.033241884 1.087202817 0.955848017 1.02782498 1.098219479 1.03357853 1.112361112 1.046369548 1 12.39920296 -12.50745601 1.241430277 0.999835342 1.05356099 0.028711195 0.044860336 0.64742352 1.777133224 0.029606595 0.007063994 3.11E-13 12.50745601 0.053725648 SDES(ph)DQQESLHK ddPTM_HeLa_Romidepsin_16h_R1 1 SDESDQQESLHK 12 0 H0YJJ8;G3V5E5;P49770 H0YJJ8 EIF2B2 Translation initiation factor eIF-2B subunit beta 1 0 S(0.26)DES(0.74)DQQESLHK 121.13 0.0030044 5060200 2625.4 1861.8 2042.3 1571.2 4468.2 4119.8 2587.7 2759.5 3333.7 3138.6 TRUE FALSE FALSE 2593.400615 1888.010469 2077.845375 1752.869537 4240.171081 3856.558076 2807.499173 2839.341779 3035.525523 3057.05872 0.84833196 0.617590515 0.679687754 0.573384321 1.387010022 1.261525679 0.918366126 0.928782218 0.992956237 1 11.57792855 -8.759231557 24.99940453 0.857900871 1.119067367 0.392027982 0.194308956 64.22461092 727204.7024 0.03172317 0.061062939 1.74E-09 8.759231557 0.261166496 SDESPKPGK(ac)FQR ddPTM_HeLa_Romidepsin_16h_R1 1 SDESPKPGKFQR 12 2 Q9NQW6;Q9NQW6-2 Q9NQW6 ANLN Actin-binding protein anillin 0 1 SDESPK(0.001)PGK(0.999)FQR 89.266 0.020977 0 1336.4 820.11 962.52 1268 1735.4 1568 1429 1498.5 1567.5 1206.4 FALSE TRUE FALSE 1320.111443 831.6555301 979.2722568 1414.612126 1646.836062 1467.80986 1550.379224 1541.856733 1427.298874 1175.057554 1.123444071 0.707757273 0.833382376 1.203866246 1.401493958 1.249138696 1.319407053 1.312154224 1.214662949 1 10.19851571 -9.03095481 7.655680964 1.012614633 1.314141843 0.579456875 0.137927859 0.143464575 30.53210486 0.020943056 0.03542368 9.31E-10 9.03095481 0.301527211 SDGAPAEGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SDGAPAEGKR 10 1 F8WES8;C9JXU6;F5GZF3;C9JCL9;C9JXG5;F8WCP5;Q13769 F8WES8 THOC5 THO complex subunit 5 homolog 0 1 ; SDGAPAEGK(1)R;SDGAPAEGK(1)R 134.77 0.001779 7181800 5265.4 4831.85 5315.8 5763.8 6680 6512.2 6035.6 4279.21 5995 4589.04 FALSE TRUE FALSE 5201.22328 4899.872911 5408.319269 6430.237675 6339.094673 6096.091437 6548.263713 4403.02219 5458.792185 4469.816079 1.163632505 1.096213541 1.20996461 1.43859111 1.418200338 1.363834961 1.464996232 0.985056681 1.221256555 1 12.12599975 -9.566423565 3.101114001 1.080506618 1.347454739 0.327034328 0.139062834 0.167744521 3.311267018 0.021153816 0.031399925 2.71E-10 9.566423565 0.26694812 SDGAPASDS(ph)KPGSSEAAPSSK ddPTM_HeLa_Romidepsin_16h_R1 2 SDGAPASDSKPGSSEAAPSSK 21 1 P80723;P80723-2 P80723 BASP1 Brain acid soluble protein 1 1 0 S(0.001)DGAPAS(0.021)DS(0.519)KPGS(0.353)S(0.102)EAAPS(0.002)S(0.001)K;SDGAPAS(0.027)DS(0.877)KPGS(0.069)S(0.018)EAAPS(0.006)S(0.002)K ; 69.07 0.00259 35059000 4118.7 5140.2 4143.7 3835.5 4400.5 5714.3 3707.7 4898.4 4990.6 4271.1 TRUE FALSE FALSE 4068.4997 5212.563871 4215.81936 4278.978557 4175.926064 5349.174672 4022.631945 5040.127476 4544.228237 4160.136206 0.977972715 1.252979136 1.013384935 1.028566937 1.003795515 1.285817196 0.966947173 1.211529437 1.092326792 1 12.02241505 -9.698586172 0.414515166 0.981538305 1.133514991 0 0.115107854 1.523131371 0.593289392 0.045758849 0.090186811 2.00E-10 9.698586172 0.151976686 SDGEAKPEPSPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SDGEAKPEPSPSPR 14 1 P26358;K7ERQ1;K7ENQ6;K7EJL0 P26358 DNMT1 DNA (cytosine-5)-methyltransferase 1 1 0 SDGEAKPEPS(0.027)PS(0.973)PR 146.1 5.81E-05 0 959.76 794.1 761.2 730.69 799.07 672.64 554.26 559.03 1029.4 752.89 TRUE FALSE FALSE 948.062076 805.2793606 774.4483667 815.1758158 758.2904762 629.6604748 601.3388306 575.204651 937.3278858 733.3298093 1.292818134 1.098113496 1.05607103 1.111608727 1.034037437 0.858632046 0.820011437 0.784373748 1.278180532 1 9.518318375 -8.3017001 1.320311206 1.133308698 0.781640749 0.742306803 0.084524222 0.245060388 0.781662632 0.017073577 0.068103643 4.99E-09 8.3017001 -0.351667949 SDGS(ph)LEDGDDVHR ddPTM_HeLa_Romidepsin_16h_R1 2 SDGSLEDGDDVHR 13 0 Q9NRX5 Q9NRX5 SERINC1 Serine incorporator 1 1 0 S(0.141)DGS(0.859)LEDGDDVHR;S(0.231)DGS(0.769)LEDGDDVHR ; 165.86 6.72E-05 23574600 6472.7 6157.4 6482.6 5651.3 5604.3 6855.2 4449.4 6609.4 6650.5 6205.3 TRUE FALSE FALSE 6393.808243 6244.084039 6595.426934 6304.729896 5318.291658 6417.174844 4827.331925 6800.632561 6055.662624 6044.085411 1.057861994 1.033089974 1.091220008 1.043123892 0.879916695 1.061728021 0.798686914 1.125171486 1.001915461 1 12.56130833 SDGSDTTEQESTNLPS(ph)PNK ddPTM_HeLa_Romidepsin_16h_R1 2 SDGSDTTEQESTNLPSPNK 19 0 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 0 SDGSDTTEQESTNLPS(1)PNK;SDGSDTTEQESTNLPS(1)PNK ; 304.2 6.30E-144 5916100 9425 8836.8 8539.4 7858.3 7087.7 6651.6 5538.1 5802.9 10207.1 9379.6 TRUE FALSE FALSE 9310.124475 8961.204702 8688.024675 8766.91362 6725.988221 6226.584227 6008.506076 5970.797756 9294.151412 9135.91664 1.019068457 0.980876365 0.9509746 0.959609634 0.736213835 0.681550026 0.657679608 0.653552127 1.017320076 1 13.15733377 -8.72129952 1.806091758 1.004122659 0.657190037 0.979190045 0.022013214 0.032377068 0.214093141 0.003452528 0.008095026 1.90E-09 8.72129952 -0.346932621 SDGSGESAQPPEDS(ph)SPPASSESSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SDGSGESAQPPEDSSPPASSESSSTR 26 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 SDGSGESAQPPEDS(0.767)S(0.212)PPAS(0.002)S(0.002)ES(0.003)S(0.002)S(0.002)T(0.007)R 68.291 0.00023175 5284800 1449.8 1295.7 1192 1509.6 1562.9 1912.3 1242 1764 1503.9 1490.9 TRUE FALSE FALSE 1432.12928 1313.940899 1212.74626 1684.147055 1483.139381 1790.110202 1347.495449 1815.038557 1369.387417 1452.166203 0.986202046 0.904814405 0.835129104 1.159748141 1.021328948 1.232717163 0.927920954 1.249883486 0.942996342 1 10.50399087 -9.234009764 24.9752986 0.974460935 1.108709067 0.422776734 0.102116099 665.2083662 605688.3173 0.014130098 0.023428624 5.83E-10 9.234009764 0.134248132 KIDAGTMAEPSAS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 KIDAGTMAEPSASPSK 16 1 Q8IXQ3 Q8IXQ3 C9orf40 Uncharacterized protein C9orf40 1 0 KIDAGTMAEPS(0.232)AS(0.745)PS(0.023)K;KIDAGTMAEPS(0.065)AS(0.927)PS(0.008)K ; 109.42 0.0028837 26035400 9959.3 10131.9 8876 8533.8 4394.1 3554.7 2539.7 2902 10514.8 9166.8 TRUE FALSE FALSE 9837.912221 10274.53715 9030.483057 9520.518109 4169.85268 3327.566142 2755.422055 2985.964791 9574.329953 8928.645215 1.101837063 1.150738652 1.011405744 1.066289216 0.467019641 0.372684328 0.30860472 0.334425293 1.072316093 1 13.12422557 -8.706404702 3.926771253 1.05736858 0.347204993 0.981866141 0.046536789 0.024733584 0.777230282 0.008523536 0.017324267 1.97E-09 8.706404702 -0.710163586 down SDIDEIVLVGGS(ph)TR ddPTM_HeLa_Romidepsin_16h_R1 1 SDIDEIVLVGGSTR 14 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 1 0 SDIDEIVLVGGS(0.774)T(0.226)R 107.5 0.0017022 0 852.85 643.4 551.78 618.57 555.61 550.21 662.77 776.67 1043 837.88 TRUE FALSE FALSE 842.4551362 652.4578021 561.3834994 690.0919739 527.2551484 515.0533567 719.0656673 799.1417211 949.7114678 816.1117568 1.032279132 0.799471147 0.687875765 0.84558514 0.646057533 0.631106405 0.881087255 0.979206235 1.163702716 1 9.672622915 -10.22582056 5.522769461 1.015417861 0.771972221 0.561647541 0.112240297 0.11020401 9.459344308 0.017475207 0.021198378 5.95E-11 10.22582056 -0.24344564 SDISPLT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SDISPLTPR 9 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SDISPLT(1)PR 131.09 0.015919 158190000 5491.4 5870.1 5182.2 5162.2 5532.1 4571.6 4584.8 4925.7 6009.8 5262.2 TRUE FALSE FALSE 5424.468705 5952.739422 5272.394017 5759.077853 5249.776294 4279.489514 4974.232798 5068.217358 5472.268436 5125.487285 1.058332292 1.161399705 1.028662003 1.123615674 1.024249208 0.834942958 0.970489735 0.988826442 1.067658182 1 12.32347345 -8.497866459 24.17800832 1.0465788 0.934371576 0.497230398 0.060288892 386.2239104 373341.0972 0.009063304 0.02017132 3.18E-09 8.497866459 -0.112207224 SDK(ac)PDMAEIEK(ac)FDK ddPTM_HeLa_Romidepsin_16h_R1 2 SDKPDMAEIEKFDK 14 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 2 ; SDK(1)PDMAEIEK(1)FDK;SDK(1)PDMAEIEK(1)FDK 148.52 8.46E-07 3617140 1003.73 951.72 840.43 819.17 1978.81 1685.14 1943.19 1783.66 2177.42 1543.07 FALSE TRUE FALSE 991.4961527 965.1183391 855.0573316 913.8862897 1877.823942 1577.464993 2108.24451 1835.267388 1982.666102 1502.980819 0.659686498 0.642136165 0.568907681 0.608049203 1.249399805 1.049557634 1.402708859 1.221085036 1.319155958 1 10.55361088 -8.748904195 24.96385372 0.782139168 1.230037315 0.465893477 0.225624557 128.9964728 256895.2695 0.028068464 0.055827978 1.78E-09 8.748904195 0.447898146 SDKGS(ph)PGEDGFVPSALGTR ddPTM_HeLa_Romidepsin_16h_R1 1 SDKGSPGEDGFVPSALGTR 19 1 G3V238;A0A494BZY7;Q5JPI9 G3V238 METTL10 Protein-lysine N-methyltransferase METTL10 1 0 S(0.03)DKGS(0.97)PGEDGFVPSALGTR 96.723 0.0007802 23365000 3603.6 3406.4 3619.7 3868 3277.6 3136.7 2827.8 3380.7 3805.8 3566.7 TRUE FALSE FALSE 3559.677937 3454.355389 3682.69936 4315.236359 3110.331842 2936.274993 3067.993261 3478.515221 3465.399716 3474.03662 1.024651818 0.994334766 1.060063483 1.242138996 0.89530773 0.845205539 0.883120588 1.001289163 0.997513871 1 11.76239725 NYGYNPS(ph)PVKPEGLR ddPTM_HeLa_Romidepsin_16h_R1 3 NYGYNPSPVKPEGLR 15 1 E9PRF4;Q15047-3;Q15047 E9PRF4 SETDB1 Histone-lysine N-methyltransferase SETDB1 1 0 NYGY(0.003)NPS(0.996)PVKPEGLR;NYGYNPS(1)PVKPEGLR;NYGYNPS(1)PVKPEGLR ;; 190.18 1.51E-11 80059000 10853.3 9922.4 9931 9761 5634.7 4441.1 4137.4 4293.8 10937.8 10436 TRUE FALSE FALSE 10721.01581 10062.08781 10103.84489 10889.61275 5347.140233 4157.328043 4488.830653 4418.034329 9959.495774 10164.87122 1.054712409 0.989888371 0.99399635 1.071298644 0.526041119 0.408989741 0.441602314 0.434637511 0.979795569 1 13.31130432 -8.705352339 4.82758206 1.024015029 0.437477956 0.985112479 0.033932304 0.015870651 0.758761886 0.004927757 0.009914905 1.97E-09 8.705352339 -0.586537072 down SDKS(ph)PDLAPTPAPQSTPR ddPTM_HeLa_Romidepsin_16h_R1 5 SDKSPDLAPTPAPQSTPR 18 1 F8WAE5;Q9BY44-2;Q9BY44-4;Q9BY44-3;Q9BY44 F8WAE5 EIF2A "Eukaryotic translation initiation factor 2A;Eukaryotic translation initiation factor 2A, N-terminally processed" 1 0 S(0.069)DKS(0.931)PDLAPTPAPQSTPR;S(0.217)DKS(0.783)PDLAPTPAPQSTPR;S(0.042)DKS(0.958)PDLAPTPAPQSTPR;S(0.258)DKS(0.742)PDLAPTPAPQSTPR;S(0.203)DKS(0.797)PDLAPTPAPQSTPR ;;;; 121.14 0.00047691 838358100 16230.2 16710.7 14174.5 17052.1 17752.7 17514.4 15174.6 18181.6 17846 16160.8 TRUE FALSE FALSE 16032.38008 16945.95367 14421.20123 19023.74403 16846.71347 16395.28637 16463.53015 18707.65591 16249.80906 15740.94009 1.018514777 1.076552835 0.916158828 1.208551963 1.070248243 1.041569708 1.04590514 1.188471324 1.032327737 1 13.94223408 -9.267004012 24.99846828 1.008817134 1.101220123 0.387198942 0.063724646 387.4754253 1740689.704 0.00910712 0.014158905 5.41E-10 9.267004012 0.092402989 SDKTEEIAEEEETVFPK ddPTM_HeLa_Romidepsin_16h_R1 1 SDKTEEIAEEEETVFPK 17 1 Q9NR30 Q9NR30 DDX21 Nucleolar RNA helicase 2 0 0 119.04 1.96E-05 0 1562.2 1388.9 1484.7 1440 1291.9 1276.7 1176.5 1165.2 1665.5 1839.1 FALSE FALSE TRUE 1543.159306 1408.452971 1510.540581 1606.499575 1225.969522 1195.12299 1276.431881 1198.913224 1516.533509 1791.319917 0.86146494 0.786265456 0.843255616 0.896824493 0.684394513 0.667174511 0.712565002 0.6692904 0.846601154 1 10.8068073 -6.10218511 0.090757491 1.205326274 2.21E-09 0.583091076 0.068642689 25.98349358 0.273890936 0.739257519 4.108444104 7.90E-07 6.10218511 -1.205326272 AVVPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 AVVPSKR 7 1 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;G3V5V7;G3V4W0;G3V576;G3V555;G3V575;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 1 ; AVVPSK(1)R;AVVPSK(1)R 117.93 0.0037668 150482000 1908.79 1638.47 2033.82 3205.2 7067.8 10250.2 9759.9 8434.2 1633.58 1252.06 FALSE TRUE FALSE 1885.524933 1661.536424 2069.217784 3575.800305 6707.103792 9595.245301 10588.90566 8678.23027 1487.468513 1219.531301 1.546106223 1.362438523 1.696732001 2.932110314 5.499738948 7.867977883 8.682766614 7.116037337 1.219705072 1 10.25211107 -8.686463637 1.537766401 1.282290657 8.105684026 0.980031433 0.411711025 0.035126081 0.16655325 0.064968439 0.166706177 2.06E-09 8.686463637 6.823393369 up SDLNGLPS(ph)PVEER ddPTM_HeLa_Romidepsin_16h_R1 1 SDLNGLPSPVEER 13 0 E7EWN3;Q9C0A6 E7EWN3 SETD5 SET domain-containing protein 5 1 0 S(0.008)DLNGLPS(0.992)PVEER 124.46 0.00028266 0 1969.6 1569.3 1457 1376.3 1461.8 1292.2 1198.2 1363.2 2046.8 2058.1 TRUE FALSE FALSE 1945.593758 1591.392647 1482.358474 1535.434282 1387.198891 1209.63259 1299.975078 1402.642041 1863.729082 2004.630265 0.970549927 0.793858436 0.739467272 0.765943879 0.69199738 0.603419299 0.648486207 0.69970112 0.929712134 1 10.96912045 -9.929581959 0.940017173 0.996667773 0.661882762 0.886843454 0.044070415 0.089326163 0.15657941 0.008433473 0.012041349 1.18E-10 9.929581959 -0.334785011 SDNENDGYVPDVEMS(ph)DSESEASEKK ddPTM_HeLa_Romidepsin_16h_R1 1 SDNENDGYVPDVEMSDSESEASEKK 25 1 Q6IE81-2;Q6IE81 Q6IE81-2 JADE1 Protein Jade-1 1 0 SDNENDGY(0.007)VPDVEMS(0.975)DS(0.018)ESEASEKK 81.65 1.34E-05 0 821.72 773.64 812.92 621.52 355.64 460.19 318.32 334.35 924.28 581.58 TRUE FALSE FALSE 811.7045606 784.5313242 827.0685316 693.3830667 337.4903637 430.7853442 345.3580929 344.0238897 841.6100819 566.4704678 1.432915936 1.384946557 1.460038217 1.22404098 0.595777508 0.760472732 0.609666545 0.607311253 1.485708664 1 9.145856935 -8.76603689 24.23132011 1.246761497 0.649273034 0.822229749 0.153719025 32.97638956 173805.0487 0.028512226 0.052986635 1.71E-09 8.76603689 -0.597488462 SDS(ph)AISVR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSAISVR 8 0 H3BR17;Q6Q0C0;Q6Q0C0-2 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 0 S(0.001)DS(0.999)AISVR 99.013 0.0028934 0 1985.7 1527.5 1758.5 2275.3 1378.9 1567.1 1280.1 1426.1 1849.5 2079.7 TRUE FALSE FALSE 1961.497525 1549.004185 1789.105955 2538.380892 1308.529588 1466.967368 1388.831662 1467.361953 1684.076088 2025.669094 0.968320803 0.764687673 0.883217284 1.25310738 0.64597401 0.724189045 0.685616257 0.724383838 0.831367815 1 10.9841828 -8.721270844 24.99999067 0.974598478 0.696449355 0.49537822 0.124657617 83.33898219 51867.94436 0.016429957 0.032859574 1.90E-09 8.721270844 -0.278149123 SDS(ph)FENPVLQQHFR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSFENPVLQQHFR 14 0 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 1 0 S(0.288)DS(0.712)FENPVLQQHFR;S(0.088)DS(0.912)FENPVLQQHFR ; 101.3 0.0040373 58655000 5780.2 6605.8 5327.6 6700.3 5126.2 5633.4 8746 6312.5 8756.2 6283.9 TRUE FALSE FALSE 5709.748699 6698.796626 5420.324643 7475.020212 4864.590886 5273.443921 9488.885022 6495.142228 7973.023542 6120.643372 0.932867405 1.094459556 0.885580864 1.221280143 0.794784239 0.861583268 1.550308431 1.061186191 1.302644682 1 12.57946759 -7.776332635 24.99971944 0.970728247 1.305747418 0.257569106 0.189811494 128.8321414 216257.7412 0.019474485 0.058769211 1.67E-08 7.776332635 0.335019171 SDS(ph)LLSFR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSLLSFR 8 0 Q00587-2;Q00587 Q00587-2 CDC42EP1 Cdc42 effector protein 1 1 0 S(0.143)DS(0.856)LLSFR 139.38 0.0090285 7245200 3286 3212.5 3308.1 3904 2433.9 1918.6 1626.6 1903.7 3612.5 3554.7 TRUE FALSE FALSE 3245.948968 3257.725659 3365.676093 4355.398849 2309.689001 1796.007652 1764.763363 1958.780556 3289.388952 3462.348382 0.937499238 0.940900597 0.972078983 1.257932007 0.667087406 0.518725285 0.509701269 0.565737569 0.950045631 1 11.75753518 -8.576049655 7.313261705 0.9852725 0.539246864 0.854460912 0.090784612 0.057940453 6.604096648 0.01297514 0.026113698 2.65E-09 8.576049655 -0.446025637 SDS(ph)PEIPFQAAAGPSDGLDASS(ph)PGNSFVGLR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 S(0.482)DS(0.518)PEIPFQAAAGPS(0.006)DGLDAS(0.158)S(0.708)PGNS(0.129)FVGLR 67.184 0.00015697 2817600 1149.4 1214 1168 1257.5 1392.5 1085.1 1263.6 1213.7 1596.8 1202.2 TRUE FALSE FALSE 1135.390671 1231.090724 1188.32855 1402.898067 1321.435529 1015.765612 1370.930152 1248.816495 1453.978209 1170.966671 0.969618264 1.051345657 1.014826963 1.198068316 1.128499693 0.86745903 1.170767868 1.066483382 1.241690515 1 10.1934843 -9.912051142 2.037942203 0.986133509 1.079529059 0 0.118177596 0.386823959 3.247801154 0.014440581 0.019530334 1.22E-10 9.912051142 0.09339555 SDS(ph)PEIPFQAAAGPSDGLDASSPGNSFVGLR ddPTM_HeLa_Romidepsin_16h_R1 3 SDSPEIPFQAAAGPSDGLDASSPGNSFVGLR 31 0 A6NNK5;Q12888;Q12888-3;Q12888-2 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 S(0.198)DS(0.802)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.28)DS(0.72)PEIPFQAAAGPSDGLDASSPGNSFVGLR;S(0.263)DS(0.722)PEIPFQAAAGPS(0.015)DGLDASSPGNSFVGLR ;; 105.75 4.62E-13 207717900 6500.3 6480.8 6211.1 5435.2 6435.3 6854.5 5259.9 6727.4 6682.3 6548.1 TRUE FALSE FALSE 6421.071843 6572.036873 6319.20159 6063.643397 6106.882628 6416.519572 5706.675775 6922.046705 6084.618352 6377.979418 1.006756438 1.030426165 0.990784256 0.950715423 0.957494878 1.00604269 0.894746659 1.08530402 0.954004074 1 12.63888373 -9.520797771 24.71728782 1.005573925 0.974134745 0.018718867 0.048799686 117.4244498 1394740.444 0.006361939 0.00907891 3.01E-10 9.520797771 -0.03143918 SDS(ph)PSVGETER ddPTM_HeLa_Romidepsin_16h_R1 2 SDSPSVGETER 11 0 A0A0C4DH56;Q9BWT3-2;Q9BWT3 A0A0C4DH56 PAPOLG Poly(A) polymerase gamma 1 0 S(0.027)DS(0.972)PS(0.001)VGETER;SDS(0.999)PSVGETER ; 202 4.11E-13 16856100 5422.2 5774 5560.6 5114.4 5223.3 5545.6 4569.1 4883.2 5725 5621.7 TRUE FALSE FALSE 5356.112141 5855.286524 5657.37991 5705.750992 4956.73551 5191.254058 4957.19924 5024.487688 5212.941661 5475.647424 0.978169653 1.069332276 1.033189224 1.04202308 0.905232775 0.948062148 0.905317464 0.917606138 0.952022886 1 12.41881384 -8.751017909 24.99848252 1.002983521 0.920145356 0.643704229 0.033598065 114.2624309 274085.0844 0.004925971 0.009766219 1.77E-09 8.751017909 -0.082838165 SDS(ph)PVPTAPTSGGPK ddPTM_HeLa_Romidepsin_16h_R1 2 SDSPVPTAPTSGGPK 15 0 B4E349;F5H6D8;B4DTN4;Q86U44 B4E349 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 0 S(0.385)DS(0.615)PVPTAPTSGGPK;S(0.008)DS(0.991)PVPTAPTSGGPK ; 209.56 1.91E-25 23557000 10344.9 9613.9 10622.4 7592.8 6561.1 5956.7 5643.5 6340.8 10343.4 10589.6 TRUE FALSE FALSE 10218.81238 9749.244737 10807.27842 8470.715261 6226.262584 5576.086094 6122.858749 6524.261044 9418.260398 10314.48067 0.990724857 0.945199768 1.047777272 0.82124496 0.603642858 0.540607547 0.593617745 0.632534129 0.913110481 1 13.33238356 -8.930413554 2.741029499 0.994228333 0.585551576 0.949293873 0.041994411 0.029018184 0.442364925 0.004838982 0.009295773 1.17E-09 8.930413554 -0.408676757 SDS(ph)PVPTAPTSGGPKPSTASAVPELATDPELEKK ddPTM_HeLa_Romidepsin_16h_R1 1 SDSPVPTAPTSGGPKPSTASAVPELATDPELEKK 34 2 B4E349;F5H6D8;B4DTN4;Q86U44 B4E349 METTL3 N6-adenosine-methyltransferase 70 kDa subunit 1 0 S(0.043)DS(0.192)PVPT(0.135)APT(0.135)S(0.124)GGPKPS(0.124)T(0.124)AS(0.124)AVPELATDPELEKK 59.678 0.00047973 64652000 4362.2 4160.8 3843.4 3922.7 2796.3 2585.3 1948.4 2406.5 4234.2 4546.6 TRUE FALSE FALSE 4309.031829 4219.375852 3910.292765 4376.261031 2653.594377 2420.107674 2113.897047 2476.128281 3855.482547 4428.478677 0.973027566 0.952782244 0.882987827 0.988208672 0.59921128 0.546487372 0.477341589 0.559137451 0.870611067 1 12.11259546 -8.709774263 4.098709796 0.976332898 0.529853381 0.934850281 0.051368738 0.028052869 0.971760675 0.006225087 0.012600026 1.95E-09 8.709774263 -0.446479517 SDS(ph)QASLTVPLSPQVVR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSQASLTVPLSPQVVR 17 0 Q8TEV9-2;Q8TEV9 Q8TEV9-2 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 0 S(0.05)DS(0.936)QAS(0.014)LTVPLSPQVVR 148.2 2.07E-07 0 962.05 856.96 1085.9 995.64 1323.9 1249.9 889.23 1121.5 1271.6 920.92 TRUE FALSE FALSE 950.3241646 869.0243054 1104.799634 1110.760581 1256.336443 1170.035424 964.761174 1153.948833 1157.864911 896.9943656 1.059453884 0.96881802 1.231668421 1.238313889 1.400606839 1.304395511 1.075548756 1.286461629 1.290827407 1 9.808955113 -9.7028291 6.408119555 1.024504393 1.2575058 0.319832805 0.115447349 0.093418172 7.668622783 0.012825547 0.018104998 1.98E-10 9.7028291 0.233001407 SDS(ph)RAQAVSEDAGGNEGR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSRAQAVSEDAGGNEGR 18 1 P55884;P55884-2;C9JZG1 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 0 S(0.003)DS(0.997)RAQAVSEDAGGNEGR 178.1 4.34E-09 7162200 1491.9 1187.8 994.03 3901.2 1342 565.22 667.54 731.98 1484.2 1374.2 TRUE FALSE FALSE 1473.716149 1204.52188 1011.330675 4352.2751 1273.512732 529.1042662 724.2408309 753.1586864 1351.449435 1338.498086 1.101022231 0.899905567 0.755571252 3.251611 0.95144905 0.395296991 0.541084697 0.562689401 1.009676031 1 10.38639936 -8.512907347 24.94472961 1.187963927 0.532086851 0.216144433 0.679925371 658.6773836 1647764.226 0.098334076 0.206616214 3.07E-09 8.512907347 -0.655877076 SDS(ph)VSASER ddPTM_HeLa_Romidepsin_16h_R1 1 SDSVSASER 9 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 S(0.093)DS(0.774)VS(0.131)AS(0.001)ER 99.343 0.028937 21033000 1909.6 2200.7 1982.1 2166.5 1584.7 1525.4 2594.6 2082.1 2209.7 2182.9 TRUE FALSE FALSE 1886.325061 2231.681512 2016.597619 2417.000924 1503.826846 1427.931863 2814.985259 2142.342278 2012.058898 2126.187943 0.887186416 1.049616295 0.948456897 1.136776705 0.707287825 0.671592494 1.32395881 1.007597793 0.946322221 1 11.05405341 -7.744375183 24.99999393 0.934869325 1.165778175 0.292199224 0.152287672 242.6459324 355484.0453 0.020475154 0.076215698 1.80E-08 7.744375183 0.230908849 SDSAFFWEER ddPTM_HeLa_Romidepsin_16h_R1 1 SDSAFFWEER 10 0 Q13464;C9JFJ0;D6REE7;A0A0U1RQV4;O75116 Q13464;O75116 ROCK1;ROCK2 Rho-associated protein kinase 1;Rho-associated protein kinase 2 0 0 119.22 0.0021585 0 1193.4 1072 1261.1 934.4 1240.2 962.62 956.14 1064.2 1120.9 1126.8 FALSE FALSE TRUE 1178.854382 1087.091644 1283.048916 1042.439724 1176.907966 901.1116887 1037.354508 1094.990948 1020.643897 1097.525574 1.074101971 0.990493224 1.169037831 0.949809052 1.072328513 0.821039355 0.945175705 0.9976906 0.92994999 1 10.10003884 -8.285450597 24.98946134 1.03823426 0.923689244 0.273025743 0.077018783 574.1954738 597587.474 0.009407237 0.021045809 5.18E-09 8.285450597 -0.114545016 SDSAPPT(ph)PVNR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSAPPTPVNR 11 0 A2A2F0;Q86X10-4;Q86X10-2;Q86X10-3;Q86X10 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 0 S(0.002)DSAPPT(0.998)PVNR 128.57 0.012861 3453600 1664.2 1789.6 1903.3 1714.1 1873 2905.9 2067.4 2331.4 1993.1 1483.4 TRUE FALSE FALSE 1643.91609 1814.794036 1936.426138 1912.292307 1777.413821 2720.222368 2243.004904 2398.855381 1814.832144 1444.861054 1.137767597 1.256033603 1.340216163 1.323512944 1.230162455 1.882687862 1.552401802 1.660267175 1.256059978 1 10.49671505 -8.613074553 0.356132192 1.005506454 1.888995148 0.624864009 0.152434417 0.899613715 0.158646779 0.053393568 0.30699695 2.44E-09 8.613074553 0.883488694 SDSDS(ph)STLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSDSSTLPR 10 0 Q9ULE0 Q9ULE0 WWC3 Protein WWC3 1 0 S(0.073)DS(0.064)DS(0.431)S(0.431)TLPR 174.57 0.00029993 23200000 2988.7 3129.7 2849.1 2656.7 3599.3 3820.4 3077.4 3381.3 2867.4 2961.7 TRUE FALSE FALSE 2952.272575 3173.759999 2898.68739 2963.880154 3415.61429 3576.28877 3338.794279 3479.132581 2610.932562 2884.754607 1.023405099 1.100183701 1.004829798 1.027428866 1.184022475 1.239720273 1.157392823 1.206041087 0.905079606 1 11.49423289 -8.753804231 5.040833953 1.018828728 1.198856001 0.779576527 0.048564176 0.045794435 3.190812069 0.00493819 0.009646573 1.76E-09 8.753804231 0.180027274 SDSDYDLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 SDSDYDLSPK 10 0 Q08499;Q08499-2;A0A1B0GW84;A0A087WSZ7;Q08499-10;Q08499-11;Q08499-6;Q08499-9;A0A1W2PQN6;Q08499-12;Q08499-7;Q07343;E9PMG3;Q07343-3 Q08499 PDE4D;PDE4B "cAMP-specific 3,5-cyclic phosphodiesterase 4D;cAMP-specific 3,5-cyclic phosphodiesterase 4B" 1 0 SDS(0.001)DYDLS(0.999)PK;S(0.008)DS(0.007)DYDLS(0.985)PK;SDS(0.02)DYDLS(0.979)PK;S(0.002)DS(0.346)DYDLS(0.653)PK ;;; 126.34 0.0088949 770010000 26063.3 23660.4 23787.2 20307 21813.7 21498.2 18548.9 19391.9 23622.8 22872.1 TRUE FALSE FALSE 25745.63047 23993.49173 24201.20624 22654.99089 20700.46549 20124.5344 20124.4431 19952.97403 21509.9176 22277.87954 1.155658932 1.077009672 1.086333472 1.016927614 0.929193708 0.903341557 0.903337459 0.895640628 0.96552805 1 14.4433243 -8.847115009 2.15979237 1.076643223 0.901286621 0.661802043 0.049765736 0.143099979 1.358201901 0.008860622 0.018418449 1.42E-09 8.847115009 -0.175356602 SDSFENPVLQQHFR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSFENPVLQQHFR 14 0 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 0 ; ; 140.31 0.00044189 41100000 6506.9 5313.8 6410 6727.5 7136.1 7664.1 5509.5 6406.1 6573.8 5743.1 FALSE FALSE TRUE 6427.5914 5388.607816 6521.563361 7505.365204 6771.918189 7174.388745 5977.476792 6591.450396 5985.822864 5593.893434 1.149037156 0.963301836 1.165836182 1.341706862 1.210591204 1.282539403 1.068571803 1.178329633 1.0700638 1 12.44963705 -11.47372194 0.346235642 0.972344906 1.207272219 0.288453391 0.095780857 1.654653746 0.414412947 0.15532053 0.055359845 3.36E-12 11.47372194 0.234927313 SDSGGS(ph)SSEPFDR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSGGSSSEPFDR 13 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 S(0.001)DS(0.003)GGS(0.983)S(0.011)S(0.003)EPFDR 190.78 9.37E-11 32705000 2473.2 2186.9 1975.2 1683.6 1805.5 1336.8 1552 1686.7 2315.9 2144.2 TRUE FALSE FALSE 2443.055687 2217.687236 2009.577527 1878.265754 1713.358598 1251.382794 1683.826841 1735.502003 2108.760104 2088.493375 1.169769422 1.061859837 0.962213982 0.899340058 0.820380193 0.599179681 0.806239973 0.830982767 1.009703995 1 11.02824685 -9.164238683 1.42970047 1.080362682 0.751427804 0.750275506 0.076233313 0.153574355 0.616677087 0.014500988 0.02859852 6.85E-10 9.164238683 -0.328934878 SDSGGSS(ph)SEPFDR ddPTM_HeLa_Romidepsin_16h_R1 1 SDSGGSSSEPFDR 13 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 SDS(0.01)GGS(0.013)S(0.488)S(0.488)EPFDR 176.32 9.37E-07 24916000 3086.7 2774.1 2689.4 2726.8 2390.5 2185.4 2119.2 2080.9 3118.2 3304 TRUE FALSE FALSE 3049.078113 2813.153853 2736.207879 3042.085446 2268.503865 2045.759993 2299.204795 2141.107558 2839.300382 3218.161604 0.947459602 0.874149343 0.850239427 0.945286726 0.704906759 0.635692126 0.714446656 0.665320087 0.882274022 1 11.65202106 -8.902453644 0.554708924 0.985215973 0.622034268 0.741525371 0.063155047 0.304628784 0.159654286 0.013038568 0.052505983 1.25E-09 8.902453644 -0.363181705 SDSLS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSLSPPR 8 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46;Q6NVB9;D6RJ93;Q9UPQ0-7;D6R8Y0 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 S(0.001)DS(0.008)LS(0.991)PPR;SDS(0.002)LS(0.998)PPR ; 120.27 0.018699 172885000 4903 4788.4 4498 3733.4 4058.7 3960.7 2903.3 3487.2 4875.7 5163.2 TRUE FALSE FALSE 4843.24035 4855.811221 4576.285803 4165.073274 3851.569394 3707.624053 3149.90623 3588.09663 4439.605181 5029.05932 0.963050949 0.965550595 0.909968547 0.828201262 0.765862788 0.737240072 0.626341037 0.71347272 0.882790379 1 12.29607286 -8.918514592 0.8090094 0.98668192 0.66143754 0.877719718 0.04153467 0.081113476 0.100056674 0.004512291 0.014212166 1.21E-09 8.918514592 -0.32524438 SDSPES(ph)DAER ddPTM_HeLa_Romidepsin_16h_R1 2 SDSPESDAER 10 0 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 0 SDS(0.007)PES(0.993)DAER;SDS(0.001)PES(0.999)DAER ; 122.18 0.010639 6027500 2736.9 2753.6 3017.4 1086.5 2097.71 2070.4 1606.85 1610.36 2852 2894.8 TRUE FALSE FALSE 2703.54161 2792.365253 3069.916581 1212.126242 1990.656031 1938.108122 1743.335799 1656.953226 2596.909977 2819.592679 0.958841194 0.99034349 1.088780165 0.429894095 0.70600837 0.687371668 0.61829349 0.587656947 0.921023096 1 11.46127105 -9.269655043 24.99999648 0.988337638 0.6166304 0.85247284 0.080209417 156.8805929 477381.9152 0.011342452 0.017508735 5.37E-10 9.269655043 -0.371707238 SDSPES(ph)DAEREK ddPTM_HeLa_Romidepsin_16h_R1 1 SDSPESDAEREK 12 1 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 1 0 SDS(0.004)PES(0.996)DAEREK 175.6 0.00012626 34447000 2922.8 2722 2512.4 1900.8 1761.7 1922.1 1660.4 1787.5 2761.5 2268.7 TRUE FALSE FALSE 2887.175789 2760.320387 2556.127268 2120.57944 1671.793875 1799.284013 1801.434335 1839.218492 2514.504524 2209.758847 1.306556955 1.249150056 1.156744896 0.959642923 0.756550371 0.814244512 0.815217614 0.832316384 1.13790902 1 11.10967322 -9.065643147 2.978311046 1.15879818 0.807063518 0.830990554 0.077700893 0.124678618 2.177842976 0.018689526 0.033517832 8.60E-10 9.065643147 -0.351734662 SDSQASLTVPLS(ph)PQVVR ddPTM_HeLa_Romidepsin_16h_R1 2 SDSQASLTVPLSPQVVR 17 0 Q8TEV9-2;Q8TEV9 Q8TEV9-2 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 0 SDSQASLTVPLS(1)PQVVR;SDSQASLTVPLS(1)PQVVR ; 300.28 7.41E-132 71827000 5654.4 5989.9 4938.9 5875.6 5751.8 5357.9 4853.3 5259.2 5687.6 5409.4 TRUE FALSE FALSE 5585.481998 6074.225969 5024.859483 6554.964518 5458.264183 5015.547482 5265.539181 5411.366654 5178.886811 5268.863008 1.06009247 1.152853274 0.953689529 1.244094695 1.035947257 0.951922165 0.999369157 1.027046375 0.982923034 1 12.36327595 -8.504020714 24.79486365 1.050403227 0.993520961 0.120559793 0.082123379 1299.78799 1708982.414 0.011365634 0.024998224 3.13E-09 8.504020714 -0.056882266 SDTSISDFLS(ph)EEDDIVPSKK ddPTM_HeLa_Romidepsin_16h_R1 2 SDTSISDFLSEEDDIVPSKK 20 1 Q4AC94;Q4AC94-2;Q4AC94-4;Q4AC94-1;Q4AC94-3 Q4AC94 C2CD3 C2 domain-containing protein 3 1 0 S(0.001)DT(0.005)S(0.004)IS(0.016)DFLS(0.973)EEDDIVPSKK;S(0.04)DT(0.037)S(0.034)IS(0.029)DFLS(0.861)EEDDIVPSKK ; 83.059 0.0010706 20275100 5163.9 5123.4 5257.1 5779.3 7601.6 8747.2 8193.8 8636.2 6130.5 5463.9 TRUE FALSE FALSE 5100.960401 5195.52736 5348.59762 6447.529858 7213.661987 8188.28215 8889.781167 8886.074821 5582.172726 5321.94709 0.958476346 0.976245587 1.005007665 1.211498301 1.355455412 1.538587666 1.670400141 1.669703714 1.048896697 1 12.37773845 -8.59532691 1.05393287 0.975965744 1.691759392 0.985255413 0.033721669 0.03529248 0.073590082 0.004676062 0.016507394 2.54E-09 8.59532691 0.715793648 SDTSS(ph)PEVR ddPTM_HeLa_Romidepsin_16h_R1 1 SDTSSPEVR 9 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.018)DT(0.024)S(0.137)S(0.821)PEVR 109.83 0.019401 29087000 6607 7027.5 8431.4 4458.6 3753.9 4466 6566.3 1689.1 9478.8 8148.7 TRUE FALSE FALSE 6526.471343 7126.433329 8578.14498 4974.12431 3562.324475 4180.637013 7124.041358 1737.971444 8630.992388 7936.995599 0.822284863 0.897875429 1.080779858 0.626701155 0.448825306 0.526727899 0.897574059 0.218970947 1.087438223 1 12.95437729 -9.117296813 5.527007485 0.922956074 0.548767381 0.597576237 0.176173316 0.13197633 5.519500081 0.024448948 0.041015434 7.63E-10 9.117296813 -0.374188693 SDVEIPATVTAFSFEDDT(ph)VPLSPLK ddPTM_HeLa_Romidepsin_16h_R1 1 SDVEIPATVTAFSFEDDTVPLSPLK 25 0 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 0 SDVEIPAT(0.002)VT(0.097)AFS(0.345)FEDDT(0.414)VPLS(0.142)PLK 90.464 3.68E-05 3548300 569.39 316.63 522.66 383.32 427.33 479.94 514.46 467.17 507.09 274.89 TRUE FALSE FALSE 562.4500557 321.0875255 531.7566781 427.641262 405.5217555 449.2733829 558.1582196 480.6868269 461.7346004 267.7483182 2.100666998 1.199213977 1.986031814 1.597176277 1.514563222 1.67796902 2.08463763 1.795293543 1.724509807 1 8.064733703 -12.49649669 1.189456865 0.991717208 1.771127366 0.011577182 0.340933573 0.302374981 0.752311787 0.196525166 0.045674947 3.19E-13 12.49649669 0.779410158 SDVLELTDDNFESR ddPTM_HeLa_Romidepsin_16h_R1 4 SDVLELTDDNFESR 14 0 H7BZJ3 H7BZJ3 PDIA3 0 0 ;;; ;;; 369.42 1.87E-278 116851000 12271.28 11802.77 11308.49 10973.86 11682.78 12073.13 10154.42 11497 12869 11140.89 FALSE FALSE TRUE 12121.71292 11968.92971 11505.30952 12242.70933 11086.56414 11301.69596 11016.93618 11829.64756 11717.96441 10851.44807 1.117059478 1.102979955 1.060255686 1.128209733 1.021666792 1.041491963 1.015250325 1.090144604 1.0798526 1 13.40559996 -6.875696772 18.60722511 1.059300522 7.434047686 0.029916589 0.041959723 1018.39107 153306.5347 0.007071137 1563.229701 1.33E-07 6.875696772 6.374747163 SDVMMKYMGLKLGPALK ddPTM_HeLa_Romidepsin_16h_R1 1 SDVMMKYMGLKLGPALK 17 2 Q9UQR0;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 0 0 41.014 0.0043122 0 1358.3 1420.6 1265.8 1295.6 1380.2 1372 883.35 1265.2 1496.9 1330.1 FALSE FALSE TRUE 1341.744517 1440.599244 1287.830718 1445.403368 1309.763244 1284.333628 958.381727 1301.806566 1363.013515 1295.54381 1.035661246 1.111964901 0.994046444 1.115673092 1.010975649 0.991347122 0.739752465 1.004834075 1.052078289 1 10.33934209 -7.979041285 24.1663567 1.028960929 0.8706072 0.461809626 0.072463099 97.64832795 112590.8841 0.009005284 0.027011425 1.05E-08 7.979041285 -0.158353729 SDVYYFSPS(ph)GK ddPTM_HeLa_Romidepsin_16h_R1 1 SDVYYFSPSGK 11 0 Q9UBB5;X6RBL6;Q9UBB5-3 Q9UBB5 MBD2 Methyl-CpG-binding domain protein 2 1 0 S(0.282)DVYYFS(0.106)PS(0.613)GK 96.82 0.023453 12735000 2385.1 2333.1 2465.1 1623 2171 3461.5 2525 2591.6 2344.1 2445.3 TRUE FALSE FALSE 2356.029484 2365.945443 2508.004031 1810.658896 2060.205769 3240.321321 2739.473437 2666.583857 2134.437825 2381.770753 0.989192381 0.993355653 1.05299976 0.760215438 0.864989112 1.36046734 1.150183507 1.119580402 0.896155863 1 11.21781884 -8.268747172 24.99932882 0.973590646 1.204087727 0.582784077 0.102693 327.5412149 1120491.047 0.014479571 0.03298042 5.39E-09 8.268747172 0.230497081 SEAAAPHTDAGGGLS(ph)S(ph)DEEEGTSSQAEAAR ddPTM_HeLa_Romidepsin_16h_R1 1 SEAAAPHTDAGGGLSSDEEEGTSSQAEAAR 30 0 Q01831-2;Q01831 Q01831-2 XPC DNA repair protein complementing XP-C cells 2 0 SEAAAPHT(0.004)DAGGGLS(0.998)S(0.998)DEEEGTSSQAEAAR 110.01 4.43E-09 8700800 2704 1909.1 1962.8 1611.1 2116.6 2382.2 2153.3 2409.2 3209.4 3014 TRUE FALSE FALSE 2671.042608 1935.97636 1996.961711 1797.382962 2008.582004 2229.985108 2336.201248 2478.906401 2922.343226 2935.695846 0.909849912 0.65946081 0.680234539 0.612251084 0.684192815 0.759610404 0.795791312 0.844401645 0.995451634 1 11.51948679 -10.40564386 3.697635121 0.962273468 0.717202241 0.747009413 0.066784842 0.098945215 2.353807341 0.013413706 0.015137591 3.93E-11 10.40564386 -0.245071227 SEAAGSPDQGSTYS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 SEAAGSPDQGSTYSPAR 17 0 Q96S66-4;Q96S66-3;Q96S66-2;Q96S66 Q96S66-4 CLCC1 Chloride channel CLIC-like protein 1 1 0 SEAAGSPDQGSTYS(1)PAR;SEAAGSPDQGSTYS(1)PAR ; 248.01 8.12E-66 4340900 2291.5 4298.6 3322.1 1856.35 2324.01 3106.9 2013.77 2625.8 3856.3 4274.8 TRUE FALSE FALSE 2263.570317 4359.115804 3379.919757 2070.989921 2205.407098 2908.379117 2184.819574 2701.77338 3511.38287 4163.74008 0.543638717 1.046923132 0.8117509 0.497386936 0.529669733 0.698501602 0.524725255 0.648881373 0.843324224 1 12.0236643 -9.27440908 23.70094802 0.804737334 0.580577296 0.464441792 0.140604184 418.3697256 764531.4991 0.029144088 0.044714961 5.32E-10 9.27440908 -0.224160038 SEAEEGEVRT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 SEAEEGEVRTPTK 13 1 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0;Q9H4G0-4;H7C2K6 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 SEAEEGEVRT(1)PTK 143.25 0.0032795 33512000 1723.3 1953.7 1670.8 1727.5 1932.8 1700.2 1551.8 1750.7 1952.3 1895 TRUE FALSE FALSE 1702.295757 1981.20424 1699.879573 1927.241678 1834.162004 1591.562707 1683.609853 1801.353742 1777.681398 1845.767627 0.922269809 1.073376849 0.920960769 1.044141012 0.993712305 0.862276857 0.91214616 0.975937445 0.963112243 1 10.85000522 -8.286274866 24.61527724 0.97569054 0.916322737 0.258095849 0.052577058 742.2738966 735690.8922 0.007777336 0.017398606 5.17E-09 8.286274866 -0.059367803 SEANDAVNS(ph)STK ddPTM_HeLa_Romidepsin_16h_R1 2 SEANDAVNSSTK 12 0 O15234;J3KSY7;K7EQ38 O15234 CASC3 Protein CASC3 1 0 SEANDAVNS(0.919)S(0.08)T(0.001)K;SEANDAVNS(0.897)S(0.08)T(0.024)K ; 156.2 0.00079881 9608400 5142.9 5597.5 7005.8 2678.3 4837.5 5777 5603.8 3302.5 6158 6641.1 TRUE FALSE FALSE 5080.216357 5676.301752 7127.73301 2987.977648 4590.624324 5407.868344 6079.786632 3398.052627 5607.213057 6468.563265 0.785370128 0.877521255 1.101903579 0.461922923 0.709682218 0.836023105 0.93989753 0.525317986 0.866840568 1 12.65922959 -9.27294968 24.99284888 0.908010403 0.716896331 0.361900266 0.151462323 786.5444085 1707857.49 0.024449011 0.037538744 5.33E-10 9.27294968 -0.191114073 SEANDAVNS(ph)STKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SEANDAVNSSTKEEK 15 1 O15234;J3KSY7;K7EQ38 O15234 CASC3 Protein CASC3 1 0 SEANDAVNS(0.721)S(0.107)T(0.172)KEEK 68.82 0.019702 18091000 2901.7 2801.2 2635.2 1733.3 2233.2 2534.2 2331.9 2960.3 2928.9 2754.9 TRUE FALSE FALSE 2866.332964 2840.635367 2681.064551 1933.712301 2119.231471 2372.272799 2529.971528 3045.95161 2666.931848 2683.327301 1.068201022 1.058624256 0.999156737 0.720639745 0.789777479 0.884078807 0.942848652 1.135139798 0.99388988 1 11.38980732 -9.502608814 24.43060288 1.034792204 0.887697733 0.284878536 0.103124515 542.1357009 653416.8518 0.016348103 0.02476675 3.14E-10 9.502608814 -0.14709447 SEAPAEVTHFS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 SEAPAEVTHFSPK 13 0 Q6PID6 Q6PID6 TTC33 Tetratricopeptide repeat protein 33 1 0 SEAPAEVT(0.005)HFS(0.995)PK;SEAPAEVT(0.004)HFS(0.996)PK;SEAPAEVT(0.001)HFS(0.999)PK;SEAPAEVT(0.316)HFS(0.684)PK ;;; 139.88 0.00048064 311373000 38490.2 37492.2 36301.3 37790.9 40234.3 38571.3 33103.6 36771.8 40861.5 35245 TRUE FALSE FALSE 38021.06664 38020.01618 36933.1089 42160.46167 38180.99354 36106.71841 35915.41896 37835.73402 37206.7451 34329.32982 1.107538855 1.107508255 1.07584707 1.228117819 1.112197463 1.051774637 1.046202159 1.102140188 1.083817986 1 15.06715407 -12.12713277 0.780268874 0.996487795 1.104280311 0.101285443 0.053648916 0.595574271 0.625594678 0.039174097 0.010108916 7.46E-13 12.12713277 0.107792516 SEDDESGAGELTR ddPTM_HeLa_Romidepsin_16h_R1 1 SEDDESGAGELTR 13 0 P33993-2;P33993;P33993-3 P33993-2 MCM7 DNA replication licensing factor MCM7 0 0 155.26 0.00067958 0 722.59 744.64 720.28 579.14 644.31 650.61 568.5 707.44 749.87 920.69 FALSE FALSE TRUE 713.7827951 755.1230615 732.8161713 646.1028917 611.4284564 609.0381207 616.7883758 727.9086602 682.7997491 896.7703411 0.795948263 0.842047319 0.817172622 0.720477543 0.681811639 0.679146146 0.687788554 0.811700194 0.761398675 1 9.808594754 -12.16232624 0.259080383 1.131926181 0.68927517 0.104671935 0.088305304 1.531014465 0.152928883 0.219621999 0.044920629 6.88E-13 12.16232624 -0.442651011 SEDDSAKFDS(ph)NEEDSASVFSPSFGLK ddPTM_HeLa_Romidepsin_16h_R1 3 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 SEDDSAKFDS(0.996)NEEDS(0.002)AS(0.002)VFSPSFGLK;SEDDS(0.004)AKFDS(0.97)NEEDS(0.024)AS(0.001)VFSPSFGLK;S(0.001)EDDS(0.031)AKFDS(0.951)NEEDS(0.014)AS(0.002)VFSPSFGLK ;; 104.23 1.16E-06 59632000 10302.4 9329.8 10338.1 8058.2 9199 10382.3 8990.1 9882.6 12802.2 11123 TRUE FALSE FALSE 10176.83039 9461.145169 10518.03029 8989.926999 8729.540704 9718.904537 9753.71887 10168.53744 11657.13917 10834.02286 0.939339941 0.873280894 0.970833312 0.829786601 0.805752473 0.897072552 0.900285979 0.938574486 1.075975132 1 13.40328142 -10.79054312 0.667055292 0.992029137 0.880243169 0.521495641 0.05278288 0.396587121 0.39664601 0.016507961 0.013315732 1.62E-11 10.79054312 -0.111785968 SEDDSAKFDSNEEDS(ph)ASVFSPSFGLK ddPTM_HeLa_Romidepsin_16h_R1 1 SEDDSAKFDSNEEDSASVFSPSFGLK 26 1 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 SEDDSAKFDS(0.085)NEEDS(0.626)AS(0.255)VFS(0.03)PS(0.003)FGLK 83.826 1.80E-05 11690000 2520.4 2143.5 2458.8 2055.5 1898.1 2369.9 2296.8 2211.3 2703.1 2495.8 TRUE FALSE FALSE 2489.680395 2173.676249 2501.594383 2293.166581 1801.232874 2218.471039 2491.890135 2275.280477 2461.327966 2430.958756 1.024155753 0.894164183 1.029056695 0.943317765 0.740955752 0.912590982 1.025064752 0.935960131 1.012492688 1 11.2473097 -9.809170604 1.175644704 1.010346374 0.915086734 0.190184632 0.076473224 0.518904873 1.430496712 0.014874994 0.021983773 1.55E-10 9.809170604 -0.09525964 SEDES(ph)ET(ph)EDEEEKSQEDQEQK ddPTM_HeLa_Romidepsin_16h_R1 2 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 0 S(0.006)EDES(0.993)ET(0.97)EDEEEKS(0.031)QEDQEQK;S(0.025)EDES(0.964)ET(0.95)EDEEEKS(0.061)QEDQEQK ; 65.808 0.0084083 122073000 5923.1 5334.8 6239.4 4797.5 5028.9 4792.5 3769.7 4235.1 6017 5271.2 TRUE FALSE FALSE 5850.906979 5409.903454 6347.99414 5352.209523 4772.256468 4486.274717 4089.898224 4357.635937 5478.82445 5134.253464 1.139582808 1.053688427 1.236400615 1.042451363 0.929493743 0.873792996 0.796590634 0.848737984 1.067112188 1 12.3259388 -8.579224078 2.180205208 1.07997489 0.833849068 0.772526242 0.062130265 0.135910652 1.294700927 0.011205847 0.026914468 2.63E-09 8.579224078 -0.246125822 SEDES(ph)ETEDEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SEDESETEDEEEK 13 0 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 SEDES(1)ETEDEEEK;SEDES(0.993)ET(0.007)EDEEEK ; 273.72 2.24E-80 8893200 3512.9 2964.4 3517 1823.1 2542.89 3067.1 2440.2 2581.1 3457.9 3556.9 TRUE FALSE FALSE 3470.083424 3006.132901 3578.21191 2033.8954 2413.116834 2871.122209 2647.470527 2655.780056 3148.616764 3464.491225 1.001614147 0.867698229 1.032824642 0.587069 0.696528488 0.828728382 0.764172964 0.766571448 0.908825152 1 11.75842779 -9.276603539 24.99980736 0.990870948 0.734368924 0.695586572 0.076039517 287.9810661 474767.9609 0.011031806 0.016890191 5.29E-10 9.276603539 -0.256502024 SEDES(ph)ETEDEEEKSQEDQEQK ddPTM_HeLa_Romidepsin_16h_R1 3 SEDESETEDEEEKSQEDQEQK 21 1 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 S(0.001)EDES(0.96)ET(0.039)EDEEEKSQEDQEQK;S(0.016)EDES(0.775)ET(0.206)EDEEEKS(0.004)QEDQEQK;S(0.004)EDES(0.939)ET(0.057)EDEEEKSQEDQEQK ;; 119.16 5.24E-05 171496600 4558.53 4595.7 4788.48 3497.38 3377.51 3919.87 3756.97 3860.47 4882.37 4532.92 TRUE FALSE FALSE 4502.968883 4660.398385 4871.821486 3901.763531 3205.143061 3669.402958 4076.086938 3972.166609 4445.678599 4415.154085 1.019889407 1.055546034 1.103431815 0.883720807 0.725941383 0.831092842 0.923203779 0.899666587 1.006913578 1 12.10824807 -9.103149573 6.132584217 1.019902062 0.844384023 0.723036835 0.056933533 0.106359288 5.360504693 0.009041585 0.015124142 7.89E-10 9.103149573 -0.17551804 SEDESET(ph)EDEEEKS(ph)QEDQEQKR ddPTM_HeLa_Romidepsin_16h_R1 1 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 2 0 S(0.004)EDES(0.342)ET(0.675)EDEEEKS(0.979)QEDQEQKR 64.2 0.0013765 0 1328 1538.9 1152.9 1076.9 1065.5 1040.4 864.67 1040.3 1261.6 1287.7 TRUE FALSE FALSE 1311.813825 1560.564675 1172.965741 1201.416245 1011.123559 973.9217977 938.1150482 1070.399439 1148.759336 1254.245368 1.045898879 1.244225982 0.93519639 0.957879754 0.806160887 0.776500215 0.747951774 0.853421082 0.915896814 1 10.2926039 -8.938375405 1.865287367 1.037403485 0.78559304 0.62027929 0.086258949 0.148405997 1.038577666 0.012204835 0.0250894 1.15E-09 8.938375405 -0.251810444 SEDESET(ph)EDEEEKSQEDQEQKR ddPTM_HeLa_Romidepsin_16h_R1 1 SEDESETEDEEEKSQEDQEQKR 22 2 P25205;P25205-2;J3KQ69;A0A499FHX9;Q7Z6P5 P25205 MCM3 DNA replication licensing factor MCM3 1 0 S(0.008)EDES(0.238)ET(0.745)EDEEEKS(0.009)QEDQEQKR 43.696 0.027802 5509400 797.19 710.74 745.2 630.21 684.78 656.92 470.69 763.87 689.93 873.19 TRUE FALSE FALSE 787.4735416 720.7458164 758.1698934 703.0778454 649.8331213 614.9449321 510.6703969 785.9713733 628.2209328 850.5043979 0.925890029 0.84743338 0.891435594 0.826659859 0.764056156 0.72303557 0.6004324 0.92412382 0.738645131 1 9.732174886 -9.680513173 0.544436585 0.985305698 0.725242546 0.048545178 0.110158674 0.399105019 0.248807382 0.021453298 0.041370473 2.09E-10 9.680513173 -0.260063152 SEDFGVNEDLADSDAR ddPTM_HeLa_Romidepsin_16h_R1 2 SEDFGVNEDLADSDAR 16 0 P04083 P04083 ANXA1 Annexin A1 0 0 ; ; 318.07 1.64E-157 231930000 8037.7 7603.3 8578.5 6359 9929.1 10805.7 7962.1 9580.7 8826.5 8564.9 FALSE FALSE TRUE 7939.733421 7710.339457 8727.805194 7094.2575 9422.380976 10115.25064 8638.400575 9857.902439 8037.035734 8342.382663 0.951734503 0.924237088 1.046200534 0.850387448 1.129459215 1.212513385 1.035483617 1.181665099 0.963398115 1 13.02624377 -8.665592599 9.573816002 0.970141535 1.138547534 0.658236648 0.0644137 0.143665971 13.15329289 0.008567896 0.017146693 2.16E-09 8.665592599 0.168405998 SEDPPGQEAGS(ph)EEEGSSASGLAK ddPTM_HeLa_Romidepsin_16h_R1 2 SEDPPGQEAGSEEEGSSASGLAK 23 0 K7EIG1;I3L2B0;A0A494C0R8;O75153 K7EIG1 CLUH Clustered mitochondria protein homolog 1 0 SEDPPGQEAGS(1)EEEGSSASGLAK;SEDPPGQEAGS(0.956)EEEGS(0.037)S(0.007)ASGLAK ; 129.8 3.07E-06 13644400 8606.4 8225.5 8769.7 8285.2 7826.3 7989.7 6522.5 7587.1 8728.2 8372.8 TRUE FALSE FALSE 8501.501886 8341.298805 8922.33295 9243.173807 7426.894707 7479.183956 7076.520987 7806.620768 7947.527932 8155.273449 1.042454547 1.022810438 1.094056871 1.133398391 0.910686166 0.917097876 0.867723324 0.957248192 0.974526235 1 12.99351754 -8.721690585 24.4279296 1.033996787 0.910220315 0.644609297 0.047373225 62.5949945 38467.85255 0.006875874 0.013751555 1.90E-09 8.721690585 -0.123776472 SEDPPTT(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 1 SEDPPTTPIR 10 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C151 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SEDPPT(0.033)T(0.967)PIR 144.55 0.008483 225110000 8066.5 8118.9 7799.9 6750.9 7668.2 7426.5 6458.7 7426.5 8341.8 7803.2 TRUE FALSE FALSE 7968.182395 8233.198087 7935.653988 7531.470822 7276.86314 6951.970618 7007.301817 7641.37406 7595.688516 7600.471739 1.048379978 1.0832483 1.04410019 0.990921495 0.957422564 0.914676201 0.92195617 1.00538155 0.999370668 1 12.89187325 -8.918141523 2.725921811 1.030182603 0.944440336 0.602862412 0.032374774 0.153099685 2.306345647 0.005335591 0.010310402 1.21E-09 8.918141523 -0.085742266 SEDS(ph)TIYDLLKDPVSLR ddPTM_HeLa_Romidepsin_16h_R1 1 SEDSTIYDLLKDPVSLR 17 1 H0YAN8;O15013-7;O15013-4;O15013-5;O15013-6;O15013 H0YAN8 ARHGEF10 Rho guanine nucleotide exchange factor 10 1 0 S(0.007)EDS(0.932)T(0.031)IY(0.031)DLLKDPVSLR 110.57 0.00072291 4648900 1385.3 1716.5 1800.7 1867.6 817.58 688.32 603.46 501.76 1816.5 1587.2 TRUE FALSE FALSE 1368.415431 1740.664932 1832.040428 2083.540699 775.8558418 644.3385735 654.7178773 516.277634 1654.02769 1545.964315 0.88515331 1.12594121 1.185047035 1.347728844 0.50185883 0.416787482 0.423501287 0.333951844 1.069900304 1 10.5942913 -8.628492819 7.022051309 1.00401608 0.405591717 0.848621854 0.138156289 0.077695699 4.615199692 0.022975747 0.046143632 2.35E-09 8.628492819 -0.598424362 EVQQK(ac)IEK ddPTM_HeLa_Romidepsin_16h_R1 1 EVQQKIEK 8 1 P37802;P37802-2;X6RJP6 P37802 TAGLN2 Transgelin-2 0 1 EVQQK(1)IEK 125.57 0.0085225 3838600 2072.3 963.4 2209.4 1406.1 6098.5 7762.1 6566.5 6295.9 2060.8 1582.8 FALSE TRUE FALSE 2047.042011 976.9627705 2247.85368 1568.679898 5787.270788 7266.126861 7124.258346 6478.061933 1876.476887 1541.678628 1.327800732 0.633700664 1.45805594 1.017514201 3.753876251 4.713126802 4.621104696 4.201953518 1.217164753 1 10.59028634 -8.682257644 3.754238444 1.125964922 4.48823534 0.974000805 0.258946965 0.024138002 0.664739131 0.038038484 0.078258586 2.08E-09 8.682257644 3.362270418 up SEEDNEIES(ph)EEEVQPK ddPTM_HeLa_Romidepsin_16h_R1 2 SEEDNEIESEEEVQPK 16 0 A0A087WWJ1;P52701-2;P52701;P52701-3;C9J7Y7;A0A494C0M1 A0A087WWJ1 MSH6 DNA mismatch repair protein Msh6 1 0 SEEDNEIES(1)EEEVQPK;SEEDNEIES(1)EEEVQPK ; 185.14 7.01E-09 31508000 10423.2 9552.2 10032.8 5377.2 10055 10737.7 8652 10891.5 10658.7 10011.3 TRUE FALSE FALSE 10296.15803 9686.676122 10207.41668 5998.937164 9541.85583 10051.59562 9386.900664 11206.62837 9705.359177 9751.204983 1.055885713 0.993382473 1.046785161 0.615199575 0.978530945 1.030805489 0.962640072 1.149255747 0.995298447 1 13.25136479 SEEEFIHINNK ddPTM_HeLa_Romidepsin_16h_R1 2 SEEEFIHINNK 11 0 Q15046;Q15046-2;J3KRL2;H3BVA8 Q15046 KARS Lysine--tRNA ligase 0 0 ; ; 123.11 0.0040446 10257000 9680.5 8714.3 9146.7 7458.2 10217 10061.3 8230.5 8918.8 10121.6 10137.7 FALSE FALSE TRUE 9562.510343 8836.980144 9305.894477 8320.552176 9695.588365 9418.415401 8929.598465 9176.851406 9216.298746 9874.321093 0.968422057 0.894945593 0.942433853 0.842645494 0.981899239 0.953829161 0.904325308 0.929365302 0.933360244 1 13.26946584 -10.50601698 2.812909081 0.987683987 0.922088005 0.171732483 0.0397329 0.184629121 2.914641117 0.006458698 0.007037075 3.12E-11 10.50601698 -0.065595983 APS(ph)PASFQR ddPTM_HeLa_Romidepsin_16h_R1 2 APSPASFQR 9 0 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GV63;A0A1B0GWJ2;A0A1B0GTJ8;A0A1B0GVK1;H0Y7H8;Q8NFD5-4 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 0 APS(0.998)PAS(0.002)FQR;APS(0.996)PAS(0.004)FQR ; 110.54 0.018821 13467200 5013.5 4860.4 5047.8 4852.1 2163.9 1563.25 1511.06 1625.23 5542.6 4706.7 TRUE FALSE FALSE 4952.393534 4928.824839 5135.654842 5413.122632 2053.468108 1463.36337 1639.409399 1672.253466 5046.855974 4584.419255 1.08026628 1.075125237 1.120241094 1.180765181 0.44792328 0.319203652 0.357604597 0.364768878 1.100871385 1 12.16252327 -8.703210241 5.817602977 1.057572671 0.357979114 0.975576584 0.055745017 0.024418206 1.669601235 0.009214972 0.01847353 1.98E-09 8.703210241 -0.699593557 down SEEIS(ph)ESESEETNAPKK ddPTM_HeLa_Romidepsin_16h_R1 2 SEEISESESEETNAPKK 17 1 P54259 P54259 ATN1 Atrophin-1 1 0 S(0.039)EEIS(0.746)ES(0.171)ES(0.043)EETNAPKK;S(0.002)EEIS(0.973)ES(0.025)ESEETNAPKK ; 131.48 0.00058048 11136700 4825.3 4215 3955 3912.4 3237.4 3276 2876.6 3035.8 4961.8 4942.8 TRUE FALSE FALSE 4766.487388 4274.338881 4023.835116 4364.770096 3072.183398 3066.674173 3120.938332 3123.636083 4518.004181 4814.385343 0.990051076 0.887826498 0.835794152 0.906610042 0.638125779 0.636981453 0.648252707 0.648813059 0.938438421 1 12.2331359 -9.110439765 0.76070236 0.998286603 0.614415329 0.864495522 0.053672658 0.138007161 0.153690674 0.009579299 0.026363193 7.75E-10 9.110439765 -0.383871275 SEES(ph)PVYSNSSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SEESPVYSNSSVR 13 0 H0Y8J2;Q03188 H0Y8J2 CENPC Centromere protein C 1 0 S(0.003)EES(0.997)PVYSNSSVR 111.88 0.0064039 28399000 1666 1187.4 1199.9 886.17 1175.5 1109.3 899.51 1004.9 1720.5 1427.1 TRUE FALSE FALSE 1645.694151 1204.116248 1220.783756 988.633145 1115.509849 1038.41931 975.9143569 1033.975196 1566.614171 1390.023736 1.183932409 0.86625589 0.878246698 0.711234722 0.802511367 0.747051495 0.702084671 0.743854345 1.127041309 1 10.4408938 -9.90605863 2.012881477 1.085668261 0.750396781 0.838694988 0.066019197 0.106315577 0.871260971 0.014152235 0.019193565 1.24E-10 9.90605863 -0.33527148 SEEVPAFGVAS(ph)PPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK ddPTM_HeLa_Romidepsin_16h_R1 1 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 0 SEEVPAFGVAS(0.849)PPPLT(0.071)DT(0.025)PDT(0.025)T(0.025)ANAEGDLPT(0.003)T(0.003)MGGPLPPHLALK 58.089 7.88E-05 17781000 5026.2 4775.4 5248.7 4104.4 4994.9 6352.1 5044.6 5987.6 5865 4964 TRUE FALSE FALSE 4964.938741 4842.628207 5340.051422 4578.97004 4739.991614 5946.22131 5473.088198 6160.841759 5340.419711 4835.034564 1.02686727 1.001570546 1.104449482 0.947039774 0.98034286 1.229819814 1.131964648 1.274208421 1.104525653 1 12.23931049 -8.260337405 24.99876677 1.012247665 1.203994339 0.686591065 0.057921829 32.79256506 743899.1247 0.00655958 0.015750759 5.49E-09 8.260337405 0.191746674 SEEVPAFGVASPPPLTDTPDTTANAEGDLPT(ph)TMGGPLPPHLALK ddPTM_HeLa_Romidepsin_16h_R1 1 SEEVPAFGVASPPPLTDTPDTTANAEGDLPTTMGGPLPPHLALK 44 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 1 0 SEEVPAFGVAS(0.009)PPPLT(0.009)DT(0.009)PDT(0.009)T(0.009)ANAEGDLPT(0.478)T(0.478)MGGPLPPHLALK 66.878 1.24E-06 16255000 8203 9082.1 8214.3 6431.9 8623.4 9493.8 7232.4 8764 9247 8119.8 TRUE FALSE FALSE 8103.018681 9209.958042 8357.266446 7175.586541 8183.31572 8887.17682 7846.719875 9017.572513 8419.92516 7908.846425 1.024551274 1.164513451 1.056698537 0.907286114 1.034704087 1.12370077 0.992144676 1.140188092 1.064621148 1 12.94925156 -4.000000021 0.008284008 2.25E-08 2.199819145 0 0.074238107 30161.7457 19.52071471 2294.571091 2925.519294 1.00E-04 4.000000021 2.199819123 SEGDNYSATLLEPAASS(ph)LSPDHK ddPTM_HeLa_Romidepsin_16h_R1 4 SEGDNYSATLLEPAASSLSPDHK 23 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 SEGDNYSATLLEPAAS(0.008)S(0.642)LS(0.35)PDHK;SEGDNYSATLLEPAAS(0.234)S(0.692)LS(0.074)PDHK;SEGDNYSATLLEPAAS(0.04)S(0.615)LS(0.344)PDHK;SEGDNYSATLLEPAAS(0.058)S(0.846)LS(0.096)PDHK ;;; 167.11 1.68E-12 201472000 17306.5 15844.8 15843.8 12950.6 17876.8 17844.5 15216.5 16228.9 21742.8 18868.6 TRUE FALSE FALSE 17095.56172 16067.86351 16119.55469 14448.00931 16964.48019 16704.29404 16508.98913 16698.45762 19798.06951 18378.39105 0.93019904 0.874280206 0.877092812 0.786141141 0.923066668 0.90890949 0.898282613 0.90859192 1.077247157 1 14.16572285 -11.02622825 0.890771954 0.987838231 0.881968251 0.591571322 0.046870717 0.26607324 0.453157014 0.011931792 0.008987134 9.41E-12 11.02622825 -0.10586998 SEGEGEAASADDGSLNT(ph)SGAGPK ddPTM_HeLa_Romidepsin_16h_R1 2 SEGEGEAASADDGSLNTSGAGPK 23 0 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R2I2 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 SEGEGEAASADDGSLNT(0.5)S(0.5)GAGPK;SEGEGEAASADDGSLNT(0.843)S(0.157)GAGPK ; 164.02 2.66E-10 19572400 6203 6140.7 5421.2 6233.2 6273.3 5957.7 4794.1 4622 6719 5824.3 TRUE FALSE FALSE 6127.39545 6227.148936 5515.553712 6953.911912 5953.150092 5577.022198 5201.310734 4755.730278 6118.035812 5672.983846 1.080100987 1.09768494 0.972249148 1.225794414 1.049386047 0.983084449 0.916856257 0.838311972 1.078451125 1 12.46989204 -7.742840134 1.853461938 1.05274428 0.844135573 0.579184689 0.066089681 0.244455273 1.482348353 0.009824477 0.063715604 1.81E-08 7.742840134 -0.208608707 SEGETIMSSS(ph)MGK ddPTM_HeLa_Romidepsin_16h_R1 1 SEGETIMSSSMGK 13 0 B0YIW6;P48444-2;P48444 B0YIW6 ARCN1 Coatomer subunit delta 1 0 SEGETIMS(0.012)S(0.148)S(0.84)MGK 73.985 0.0025658 0 1435.9 1573.1 1960.1 1045.3 1471.9 1618.6 796.21 1381.7 1792.9 1688.8 TRUE FALSE FALSE 1418.398698 1595.246143 1994.214718 1166.162504 1396.783451 1515.176684 863.8400575 1421.67731 1632.538534 1644.924733 0.862287903 0.969798868 1.212344054 0.708945814 0.849147334 0.921122197 0.525154763 0.864281071 0.992470051 1 10.68380586 SEGGGTGESSQGGTSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SEGGGTGESSQGGTSKR 17 1 Q9H6E5;F5H0R1 Q9H6E5 TUT1 Speckle targeted PIP5K1A-regulated poly(A) polymerase 0 1 ; SEGGGTGESSQGGTSK(1)R;SEGGGTGESSQGGTSK(1)R 208.39 1.38E-22 683010 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 SEIDLFNIRK ddPTM_HeLa_Romidepsin_16h_R1 2 SEIDLFNIRK 10 1 P08758;D6RBE9;D6RBL5 P08758 ANXA5 Annexin A5;Annexin 0 0 ; ; 139.43 0.0032076 16761700 5977.6 6192.3 5834.5 8848.2 8360.6 6420.4 8247.1 6386.3 7045.7 5842.2 FALSE FALSE TRUE 5904.742712 6279.475362 5936.047025 9871.270516 7933.927384 6010.157161 8947.608468 6571.077515 6415.514946 5690.418802 1.037663996 1.10351726 1.043165228 1.734717753 1.394260714 1.056188898 1.572398936 1.154761669 1.127424038 1 12.47431912 -9.470220185 24.981773 1.027028165 1.376885969 0.427006105 0.183174823 205.9504971 97705.12956 0.025925747 0.039602026 3.39E-10 9.470220185 0.349857804 SEIDLLDIR ddPTM_HeLa_Romidepsin_16h_R1 1 SEIDLLDIR 9 0 P12429;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 0 172.25 0.010858 5717300 2885.6 2762.9 3239.4 3028.7 3058.5 3085.2 2786.6 2225.5 3102.8 2705.4 FALSE FALSE TRUE 2850.429197 2801.796179 3295.780398 3378.892544 2902.413332 2888.065677 3023.293734 2289.891331 2825.277797 2635.113318 1.081710292 1.063254532 1.250716763 1.282257018 1.101437768 1.095992972 1.147310711 0.868991597 1.072165579 1 11.36364929 -11.10601432 0.942485621 1.014982577 1.124263131 0.066453007 0.107541055 0.671852385 1.268357137 0.032364977 0.023642367 7.83E-12 11.10601432 0.109280554 SEIS(ph)PEGEK ddPTM_HeLa_Romidepsin_16h_R1 1 SEISPEGEK 9 0 Q96PY6-4;Q96PY6-2;Q96PY6-6;Q96PY6;Q96PY6-3 Q96PY6-4 NEK1 Serine/threonine-protein kinase Nek1 1 0 SEIS(1)PEGEK 108.7 0.020431 5548800 3767.9 3343.1 3402.8 2762.9 5184.4 5739.5 5227.8 5619.8 4027 3657.3 TRUE FALSE FALSE 3721.975386 3390.16425 3462.024307 3082.359498 4919.820722 5372.764473 5671.849202 5782.400046 3666.815034 3562.282819 1.044828717 0.95168307 0.971855544 0.865276469 1.381086503 1.50823636 1.592195087 1.623228795 1.029344165 1 11.79858634 -8.581348689 3.671715708 1.002376906 1.56486275 0.952249517 0.06101295 0.037799128 1.040635907 0.009837536 0.021040302 2.62E-09 8.581348689 0.562485844 SELELTLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SELELTLGK 9 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 164.96 0.011862 328380 338.76 430.39 480.86 422.75 460.15 369.41 338.13 322.8 499.69 389.57 FALSE FALSE TRUE 334.6310628 436.4490417 489.2291666 471.6303441 436.6668284 345.8058932 366.8507538 332.1397087 454.9964749 379.4489152 0.881886993 1.150218183 1.28931497 1.242935017 1.150792138 0.911337151 0.966798794 0.875321276 1.199098104 1 8.56776186 -5.885402763 16.17275378 1.005398667 1.035636309 0 0.160998551 0 0 0.022711463 0 1.30E-06 5.885402763 0.030237642 SELGNQS(ph)PSTSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SELGNQSPSTSSR 13 0 A0A0A0MSK5;J3KN66;Q5JTV8;Q5JTV8-3;H0YD16 A0A0A0MSK5 TOR1AIP1 Torsin-1A-interacting protein 1 1 0 SELGNQS(0.999)PS(0.001)TSSR;SELGNQS(1)PSTSSR ; 211.82 3.25E-23 58631000 4014.6 5375.4 4708.5 2738.5 4920.1 8382.3 5025.4 8649 5051.8 4286.2 TRUE FALSE FALSE 3965.668511 5451.075022 4790.449467 3055.138255 4669.008938 7846.698083 5452.257351 8899.245169 4599.954356 4174.843906 0.949896236 1.305695529 1.147455947 0.731797002 1.118367307 1.879518914 1.305978732 2.131635426 1.101826669 1 12.02750654 -6.675609364 0.540412937 0.98352415 3.564879844 0.619713363 0.250322553 2.944440034 0.37137108 0.045750352 5.514421323 2.11E-07 6.675609364 2.581355694 SELNEIKENQRS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 1 SELNEIKENQRSPVR 15 2 Q13427;E9PG73;C9JM79 Q13427 PPIG Peptidyl-prolyl cis-trans isomerase G 1 0 SELNEIKENQRS(1)PVR 87.363 0.017404 76527000 3303.3 3116.9 2532.7 2793.4 2845.9 3181.4 2488.2 2684.1 2934.5 2799.1 TRUE FALSE FALSE 3263.038109 3160.7798 2576.780581 3116.386051 2700.663103 2978.118807 2699.547646 2761.760199 2672.03097 2726.378978 1.19683952 1.159332516 0.945129273 1.143049472 0.990567755 1.092334863 0.99015862 1.012977367 0.980065864 1 11.4127704 -9.777967926 24.99915319 1.100527713 1.033580099 0.0855236 0.080479841 407.673123 616596.5045 0.014448964 0.019019917 1.67E-10 9.777967926 -0.066947614 SELSQDAEPAGS(ph)QETK ddPTM_HeLa_Romidepsin_16h_R1 2 SELSQDAEPAGSQETK 16 0 Q9BVJ6-3;Q9BVJ6;X6RJY0;Q9BVJ6-2 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 SELS(0.001)QDAEPAGS(0.745)QET(0.254)K;SELSQDAEPAGS(0.992)QET(0.008)K ; 140.96 0.00063816 54559000 10693.7 9743.9 9774.8 7725.2 8208.3 8142.6 6729.2 6842.4 11585.8 11230.9 TRUE FALSE FALSE 10563.36107 9881.07488 9944.926294 8618.423972 7789.399822 7622.314139 7300.77808 7040.374048 10549.53703 10939.1196 0.965650021 0.903278805 0.909115784 0.787853528 0.712068257 0.696794113 0.667400883 0.643596039 0.964386296 1 13.41720901 -9.129161437 0.747891448 0.989494024 0.642119047 0.980648725 0.018209667 0.052893323 0.056967011 0.003311261 0.009052073 7.43E-10 9.129161437 -0.347374976 SENPGEIS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 SENPGEISLR 10 0 Q96RF0-3;Q96RF0-2;Q96RF0 Q96RF0-3 SNX18 Sorting nexin-18 1 0 SENPGEIS(1)LR 113.95 0.015614 4376800 1481.9 1728.2 1656.1 1058.5 2139.3 2409.6 1760.9 2279.8 1896.8 1890.3 TRUE FALSE FALSE 1463.838033 1752.529645 1684.923726 1180.88875 2030.123538 2255.634337 1910.470802 2345.762416 1727.145457 1841.189733 0.795050073 0.951846305 0.9151277 0.641372656 1.102615065 1.225096086 1.037628424 1.274047087 0.938059466 1 10.84642259 -8.544373144 24.99269254 0.888938025 1.164637905 0.621411537 0.110114285 128.4096486 149308.2725 0.016998193 0.033998457 2.86E-09 8.544373144 0.275699879 SENSEDGAAWMQEPGRYS(ph)PPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SENSEDGAAWMQEPGRYSPPPR 22 1 P35548 P35548 MSX2 Homeobox protein MSX-2 1 0 SENS(0.001)EDGAAWMQEPGRY(0.454)S(0.545)PPPR 55.621 0.022148 6431700 827.41 769.5 806.57 1513.4 2741 2094.7 1866.8 1784.6 960.53 984.82 TRUE FALSE FALSE 817.3252087 780.3330412 820.6080125 1688.386429 2601.116542 1960.85543 2025.365945 1836.234585 874.6177911 959.2342344 0.852060091 0.813495821 0.855482408 1.760139878 2.711659414 2.044188333 2.111440431 1.914271321 0.911787507 1 9.905739338 -9.127488242 3.748686532 0.912953252 2.184524637 0.900570163 0.206287573 0.051963409 1.303285649 0.030876647 0.052971598 7.46E-10 9.127488242 1.271571385 SEPAVVS(ph)LEYGVAR ddPTM_HeLa_Romidepsin_16h_R1 2 SEPAVVSLEYGVAR 14 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 0 SEPAVVS(1)LEYGVAR;SEPAVVS(1)LEYGVAR ; 195.94 1.42E-11 7120900 1931.05 1296.11 1168.8 1339.4 1502.71 941.29 894.05 1112.04 1172.72 1429.71 TRUE FALSE FALSE 1907.51362 1314.356671 1189.142474 1494.26773 1426.021101 881.1446069 969.9905847 1144.215123 1067.828986 1392.565928 1.369783348 0.943838022 0.85392185 1.073031948 1.024024122 0.632748934 0.696549129 0.821659571 0.766806773 1 10.44352992 -8.810393921 0.777217173 1.158337959 0.702012019 0.099517651 0.192947437 0.498966755 0.54951328 0.034880316 0.1255583 1.55E-09 8.810393921 -0.45632594 SEPFS(ph)PSLRPEPPKHPESIK ddPTM_HeLa_Romidepsin_16h_R1 1 SEPFSPSLRPEPPKHPESIK 20 2 O60885 O60885 BRD4 Bromodomain-containing protein 4 1 0 S(0.025)EPFS(0.727)PS(0.248)LRPEPPKHPESIK 52.227 0.020257 19922000 2324.3 2072.6 2341.3 2313.6 3389.5 3135 2623.8 2599.9 2088.5 2432.3 TRUE FALSE FALSE 2295.970538 2101.778117 2382.049344 2581.109318 3216.521167 2934.683618 2846.665507 2675.124005 1901.699329 2369.108495 0.96912849 0.887159926 1.005462329 1.089485485 1.35769264 1.238729093 1.201576674 1.129169057 0.802706728 1 11.21012855 -9.027565449 3.74170948 0.978415605 1.23076482 0.729459643 0.083304498 0.077203282 2.316042897 0.009517365 0.016931776 9.39E-10 9.027565449 0.252349215 SEPHS(ph)PGIPEIFR ddPTM_HeLa_Romidepsin_16h_R1 2 SEPHSPGIPEIFR 13 0 Q9UJJ2;Q8ND82 Q9UJJ2 ZNF280C Zinc finger protein 280C 1 0 S(0.005)EPHS(0.995)PGIPEIFR;SEPHS(1)PGIPEIFR ; 107.82 0.0034221 14042600 3868.7 3772.1 3675.8 4034.7 7680.2 9594.5 7808.4 8817.1 4318.6 4085.2 TRUE FALSE FALSE 3821.546796 3825.203723 3739.775757 4501.210998 7288.250735 8981.442415 8471.645301 9072.208877 3932.3336 3979.065915 0.960413041 0.961332083 0.939862731 1.131223029 1.831648656 2.25717357 2.129053773 2.279984567 0.988255456 1 11.95821408 -8.674767641 2.338729209 0.975415097 2.213506227 0.993392186 0.046006594 0.015165439 0.168312712 0.006749045 0.015045012 2.11E-09 8.674767641 1.23809113 up SEPIS(ph)PPRDR ddPTM_HeLa_Romidepsin_16h_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 0 S(0.081)EPIS(0.919)PPRDR 86.699 0.016685 38788000 2021.7 1826.7 1944.3 1733.9 2147.2 2107.9 1743.3 1735.7 2165.8 1693.3 TRUE FALSE FALSE 1997.058743 1852.416331 1978.139726 1934.381676 2037.620372 1973.211993 1891.375858 1785.919741 1972.085424 1649.307822 1.210846584 1.123147727 1.199375702 1.172844542 1.235439707 1.196387943 1.146769471 1.08282985 1.195704888 1 10.68764497 -12.34467439 0.898863034 0.991986824 1.17538842 0 0.073458774 0.290293764 0.389921506 0.037140078 0.008192783 4.52E-13 12.34467439 0.183401596 SEPRPPIS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 SEPRPPISSPR 11 1 Q6WKZ4;E7EX40;Q6WKZ4-2;Q6WKZ4-3 Q6WKZ4 RAB11FIP1 Rab11 family-interacting protein 1 1 0 SEPRPPIS(0.5)S(0.5)PR;SEPRPPIS(0.79)S(0.21)PR ; 93.649 0.010502 72962000 4572.5 4741.5 3943.3 5214.6 9223.4 12141.9 9465.6 11474.4 4859.3 4597.4 TRUE FALSE FALSE 4516.768611 4808.250961 4011.931482 5817.536587 8752.695481 11366.07178 10269.60783 11806.39366 4424.672038 4477.958885 1.008666834 1.073759515 0.895928611 1.299149174 1.954617205 2.538226024 2.293368048 2.636556959 0.988100193 1 12.12862557 -8.67403274 1.961425208 1.002106322 2.481604878 0.978402118 0.098571785 0.027598765 0.214950307 0.0131043 0.030741027 2.12E-09 8.67403274 1.479498556 up SEPSLEPESFRS(ph)PTFGK ddPTM_HeLa_Romidepsin_16h_R1 1 SEPSLEPESFRSPTFGK 17 1 Q9C0B5;Q9C0B5-2;H0YEF4 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5;Palmitoyltransferase 1 0 SEPSLEPES(0.019)FRS(0.899)PT(0.082)FGK 86.539 0.0013789 0 663.31 1365.8 937.64 639.23 1091 1270 808.27 1144.7 869.71 788.68 TRUE FALSE FALSE 655.2253226 1385.027768 953.9592309 713.1407803 1035.322199 1188.851099 876.9244336 1177.820088 791.9209594 768.1899799 0.852946979 1.802975572 1.241827225 0.928339081 1.347742389 1.547600372 1.141546306 1.53324063 1.030892071 1 9.585319336 -10.32231763 24.99999494 0.93055816 1.339881532 0.38379005 0.231145974 166.5140962 68379.46929 0.038446051 0.043964411 4.76E-11 10.32231763 0.409323372 SEPTQALELTEDDIKEDGIVPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SEPTQALELTEDDIKEDGIVPLR 23 1 K7ER96;O43396 K7ER96 TXNL1 Thioredoxin-like protein 1 0 0 83.251 0.00028351 0 415.55 320.36 288.12 220.16 308.86 237.35 163.67 241.7 268.72 335.29 FALSE FALSE TRUE 410.4851168 324.8700365 293.1346077 245.6159351 293.0977217 222.184101 177.5721257 248.6932082 244.6850102 326.5791175 1.256923958 0.994766717 0.897591401 0.752087081 0.897478455 0.680337747 0.543733865 0.76150983 0.749236547 1 8.351288733 -9.470296709 1.270070714 1.120491548 0.698497637 0.339821392 0.154933669 0.183927657 0.59062095 0.022255376 0.038738511 3.39E-10 9.470296709 -0.421993911 SEPVKEES(ph)SELEQPFAQDTSSVGPDR ddPTM_HeLa_Romidepsin_16h_R1 4 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 SEPVKEES(0.5)S(0.5)ELEQPFAQDTSSVGPDR;SEPVKEES(0.499)S(0.499)ELEQPFAQDT(0.001)SSVGPDR;SEPVKEES(0.5)S(0.5)ELEQPFAQDTSSVGPDR;SEPVKEES(0.5)S(0.5)ELEQPFAQDTSSVGPDR ;;; 103.71 1.22E-06 151980000 10735.6 10697.6 10264.9 8785.19 8786.02 7771.9 6290.19 7199.14 11040.2 10540.6 TRUE FALSE FALSE 10604.75038 10848.20109 10443.55628 9800.975003 8337.636614 7275.300673 6824.478582 7407.435758 10052.73686 10266.75369 1.032921476 1.056634007 1.017220885 0.95463233 0.812100579 0.708627176 0.664716305 0.721497367 0.979154381 1 13.32569246 -8.656197292 1.762785691 1.02003884 0.690155751 0.973247091 0.023503581 0.035504595 0.222122443 0.003475246 0.008574623 2.21E-09 8.656197292 -0.329883089 SEPVKEESS(ph)ELEQPFAQDTSSVGPDR ddPTM_HeLa_Romidepsin_16h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 SEPVKEES(0.191)S(0.808)ELEQPFAQDTSSVGPDR 65.197 0.00046774 9097800 1249 834.25 953.08 1141.4 833.89 743.8 616.83 812.77 973.91 1038.4 TRUE FALSE FALSE 1233.776708 845.9945934 969.6679576 1273.374038 791.3334816 696.2735805 669.2235248 836.2862176 886.8010504 1011.422218 1.21984339 0.836440586 0.95871728 1.258993539 0.782396775 0.688410407 0.661665833 0.82684185 0.876786207 1 9.982169661 -8.636715495 6.532987299 1.08116341 0.722297832 0.483604537 0.137992381 0.108769361 5.837765339 0.019754103 0.039728556 2.31E-09 8.636715495 -0.358865578 SEPVKEESSELEQPFAQDT(ph)SSVGPDR ddPTM_HeLa_Romidepsin_16h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDR 26 1 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 SEPVKEESSELEQPFAQDT(0.594)S(0.203)S(0.203)VGPDR 84.665 2.38E-05 49951000 1907 2155.8 2348.5 1803.8 2097.4 2251.2 2015.4 2135.9 2418.7 2041.9 TRUE FALSE FALSE 1883.75675 2186.149409 2389.374657 2012.363843 1990.361852 2107.355585 2186.588026 2197.698897 2202.365414 1988.851144 0.947158241 1.099202128 1.20138436 1.011822252 1.000759588 1.05958437 1.099422666 1.105009243 1.107355581 1 10.95771959 -10.25827092 24.99831233 0.975046946 1.08094335 0.062391268 0.068065742 198.0862455 1562852.836 0.009707701 0.011629362 5.52E-11 10.25827092 0.105896404 SEPVKEESSELEQPFAQDT(ph)SSVGPDRK ddPTM_HeLa_Romidepsin_16h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 SEPVKEESSELEQPFAQDT(0.66)S(0.17)S(0.17)VGPDRK 114.39 1.42E-08 8376600 1546.5 1511.5 1798.6 2014.9 1800.2 1332.3 1279.5 1570.4 1744.7 1652.6 TRUE FALSE FALSE 1527.650663 1532.778937 1829.903879 2247.872218 1708.329077 1247.17033 1388.180698 1615.837046 1588.649662 1609.665214 0.94904869 0.952234616 1.136822653 1.396484312 1.061294648 0.77480107 0.862403366 1.003834234 0.986944148 1 10.65254495 -6.853842176 17.56627751 0.997143174 3.477168425 0 0.159728513 10136.47662 1229873.559 0.022848667 9651.207844 1.40E-07 6.853842176 2.480025251 SEPVKEESSELEQPFAQDTS(ph)SVGPDRK ddPTM_HeLa_Romidepsin_16h_R1 1 SEPVKEESSELEQPFAQDTSSVGPDRK 27 2 Q15424-2;Q15424;Q15424-4;Q15424-3;Q14151 Q15424-2;Q14151 SAFB;SAFB2 Scaffold attachment factor B1;Scaffold attachment factor B2 1 0 SEPVKEESSELEQPFAQDT(0.289)S(0.355)S(0.355)VGPDRK 43.241 0.024103 19501000 843.87 796.93 903.6 714.57 735.22 736.91 636.27 712.87 864.96 999.62 TRUE FALSE FALSE 833.5845879 808.1492015 919.326779 797.1919456 697.6989799 689.8238293 690.3147579 733.4957687 787.5958113 973.6497283 0.856144221 0.830020466 0.944206887 0.81876667 0.716581086 0.708492807 0.708997022 0.753346658 0.808910831 1 9.927259044 -6.067755739 0.066715472 1.308547931 1.54E-11 0.35329444 0.075846979 54.49956342 0.418396548 2.099302456 7.652451928 8.56E-07 6.067755739 -1.308547931 SEPVS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 SEPVSPSR 8 0 Q14814-6;Q14814-3;Q14814-5;Q14814-4;Q14814-2;Q14814 Q14814-6 MEF2D Myocyte-specific enhancer factor 2D 1 0 SEPVS(0.997)PS(0.003)R;SEPVS(1)PSR ; 159.34 0.0041405 86990000 9685.2 10971 10899.5 5106.2 8812.6 7625.8 6368.7 3851.6 11654.3 11183.7 TRUE FALSE FALSE 9567.153057 11125.45003 11089.20123 5696.602869 8362.860138 7138.535991 6909.657219 3963.039969 10611.91022 10893.14586 0.878272739 1.021325719 1.017998048 0.52295296 0.767717631 0.655323639 0.634312375 0.36381042 0.97418233 1 13.41113303 -9.263176263 24.99859673 0.953368329 0.60498359 0.770275104 0.105741434 63.0226216 907071.6433 0.016502815 0.026037038 5.46E-10 9.263176263 -0.348384738 SEPVSPS(ph)RER ddPTM_HeLa_Romidepsin_16h_R1 1 SEPVSPSRER 10 1 Q14814-6;Q14814-3;Q14814-5;Q14814-4;Q14814-2;Q14814 Q14814-6 MEF2D Myocyte-specific enhancer factor 2D 1 0 SEPVS(0.185)PS(0.815)RER 80.312 0.022374 31204000 1977.1 1968.7 1670.1 1705.2 1473.8 1271 1267.3 1195.6 1823.7 1958 TRUE FALSE FALSE 1953.002345 1996.41541 1699.16739 1902.363247 1398.586486 1189.787202 1374.94443 1230.1928 1660.583704 1907.130878 1.024052606 1.046816154 0.89095479 0.997500103 0.733345835 0.623862377 0.720949174 0.645048965 0.870723517 1 10.89718814 -8.710346861 3.442317962 1.004990681 0.669057133 0.836435104 0.062460239 0.043446737 1.050325759 0.006620561 0.013590565 1.95E-09 8.710346861 -0.335933549 SEQSSMSIEFGQES(ph)PEQSLAMDFSR ddPTM_HeLa_Romidepsin_16h_R1 3 SEQSSMSIEFGQESPEQSLAMDFSR 25 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SEQSSMSIEFGQES(0.907)PEQS(0.092)LAMDFSR;SEQSSMSIEFGQES(0.904)PEQS(0.094)LAMDFS(0.001)R;SEQSSMS(0.001)IEFGQES(0.797)PEQS(0.196)LAMDFS(0.006)R ;; 89.805 1.41E-05 49001600 4219.96 4119.63 4137.56 3148.32 4022.02 3679.82 3314.71 3425.4 4508.83 4193.64 TRUE FALSE FALSE 4168.525504 4177.626259 4209.572496 3512.343572 3816.761311 3444.691378 3596.261385 3524.508545 4105.548952 4084.688628 1.020524668 1.022752684 1.030573657 0.859880371 0.934406918 0.843317984 0.880424853 0.862858559 1.005106956 1 11.99601039 -9.261418354 24.99994677 1.01254945 0.877823097 0.895967883 0.023770662 0.421362688 500895.5274 0.003499275 0.005565327 5.48E-10 9.261418354 -0.134726352 SES(ph)APTLHPYSPLSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 S(0.17)ES(0.691)APT(0.139)LHPYSPLSPK 71.263 0.016322 15873000 2241.1 2223.6 1732.6 1747.7 2803.7 2209.8 2100 2176.2 2678.8 2222.5 TRUE FALSE FALSE 2213.784611 2254.903899 1762.755176 1949.777297 2660.616727 2068.600912 2278.373948 2239.164914 2439.201419 2164.75913 1.022647084 1.04164194 0.81429622 0.900690183 1.229059017 0.955580177 1.052483815 1.034371392 1.126777287 1 11.07999079 SES(ph)DQEDNDDINDNDWSYGSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SESDQEDNDDINDNDWSYGSEK 22 0 K7EKG9;Q14CW9;Q14CW9-2 K7EKG9 ATXN7L3 Ataxin-7-like protein 3 1 0 S(0.178)ES(0.822)DQEDNDDINDNDWSYGSEK 131.62 3.26E-12 0 1020.9 937.25 867.83 564.78 605.33 783.33 933.11 801.94 927.46 1070 TRUE FALSE FALSE 1008.456878 950.4446301 882.9342171 630.082521 574.4377513 733.2777411 1012.36834 825.1428686 844.5056547 1042.201246 0.967622023 0.911958831 0.847182078 0.604568958 0.551177379 0.703585554 0.971375101 0.791730841 0.810309581 1 10.02541817 -9.705217923 2.367923626 0.98260712 0.728263083 0.337131379 0.120557152 0.180715243 2.076271425 0.019306698 0.027900463 1.97E-10 9.705217923 -0.254344038 SES(ph)ELIDELSEDFDR ddPTM_HeLa_Romidepsin_16h_R1 1 SESELIDELSEDFDR 15 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;A0A0A0MR45;H0YD33;E7EQA0;E7EQ12;D6RC54;P20810-3 P20810-6;P20810-3 CAST Calpastatin 1 0 S(0.004)ES(0.994)ELIDELS(0.002)EDFDR 169.98 2.26E-05 34798000 4103.8 4346.2 4298 2888.6 3390.1 3314.8 2788.5 3169.1 4735.8 4005.4 TRUE FALSE FALSE 4053.781307 4407.385918 4372.804887 3222.593523 3217.090547 3102.994978 3025.35512 3260.792908 4312.218187 3901.339131 1.039074321 1.129711048 1.120847161 0.826022403 0.824611868 0.795366635 0.775465813 0.835813755 1.105317442 1 11.9297537 -9.201527877 7.573506679 1.035943962 0.808454749 0.873158823 0.049646419 0.089281505 10.13074377 0.007867653 0.013063692 6.29E-10 9.201527877 -0.227489213 SES(ph)ENWR ddPTM_HeLa_Romidepsin_16h_R1 2 SESENWR 7 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3;C9JH78;C9IYH5 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 0 S(0.071)ES(0.929)ENWR;S(0.018)ES(0.982)ENWR ; 119.75 0.027377 57263000 5805.5 8472.6 4017.5 5006.1 6842.4 4406.7 3161.9 5758.9 5661.6 6190.7 TRUE FALSE FALSE 5734.740333 8591.877485 4087.422902 5584.928836 6493.206795 4125.126092 3430.471707 5925.524685 5155.212316 6029.864722 0.951056217 1.424887271 0.677863118 0.926211299 1.076841205 0.68411586 0.568913544 0.982696123 0.854946596 1 12.55790992 -8.255570927 24.86820591 0.989718891 0.727608997 0.229509321 0.2025237 436.5208081 1849796.952 0.02603528 0.064448248 5.55E-09 8.255570927 -0.262109893 SES(ph)FSSEDLIPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SESFSSEDLIPSR 13 0 Q9P219;A0A0A0MR69;Q9P219-3;Q9P219-2 Q9P219 CCDC88C Protein Daple 1 0 S(0.001)ES(0.852)FS(0.085)S(0.063)EDLIPSR 163.33 0.00027638 3238600 829.8 790.51 725.12 556.09 424.92 462.62 490.65 618.32 816.02 909.36 TRUE FALSE FALSE 819.6860784 801.6388205 737.7404094 620.3877423 403.2347468 433.060075 532.3257988 636.2101137 743.0331274 885.7346961 0.925430698 0.905055232 0.832913527 0.700421633 0.455254546 0.488927528 0.600999149 0.718285189 0.838889038 1 9.790730823 -9.335570516 1.651195058 0.961646724 0.563710751 0.783135511 0.082346122 0.100074077 0.53442977 0.012773518 0.022395967 4.62E-10 9.335570516 -0.397935973 SES(ph)LDPDSSMDTTLILK ddPTM_HeLa_Romidepsin_16h_R1 1 SESLDPDSSMDTTLILK 17 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 S(0.032)ES(0.968)LDPDSSMDTTLILK 99.344 0.0045709 6329400 3012.5 3672.4 2824.7 2894.5 3652.2 3544 3301 3812.1 3914.2 3502.6 TRUE FALSE FALSE 2975.782491 3724.100144 2873.862719 3229.175709 3465.814606 3317.549838 3581.386858 3922.397099 3564.104149 3411.601947 0.872253721 1.091598669 0.842379259 0.94652769 1.015890675 0.972431687 1.049766917 1.149722963 1.044701054 1 11.73623361 -6.714886849 0.767688215 0.944645698 1.491204854 0.329331173 0.073383822 3.661027743 0.862621296 0.011423686 2.090806086 1.93E-07 6.714886849 0.546559155 SES(ph)LIDASEDSQLEAAIR ddPTM_HeLa_Romidepsin_16h_R1 2 SESLIDASEDSQLEAAIR 18 0 C9JAT7;O94888 C9JAT7 UBXN7 UBX domain-containing protein 7 1 0 S(0.01)ES(0.973)LIDASEDS(0.017)QLEAAIR;S(0.028)ES(0.972)LIDASEDSQLEAAIR ; 258.13 1.24E-75 16482900 1044.73 1419.34 834.29 1018.9 1366.42 1339.27 934.88 1401.41 1115.28 1019.67 TRUE FALSE FALSE 1031.996429 1439.321506 848.8104675 1136.710012 1296.686489 1253.694969 1014.288684 1441.957587 1015.526564 993.1788264 1.039084203 1.449206797 0.854640116 1.144516961 1.305592159 1.262305373 1.02125484 1.451860983 1.022501222 1 9.955909695 -4 0.121129725 0.909140962 2.158657532 0.214816948 0.170930554 93.95466813 0.781094361 0.703522753 19.91637456 1.00E-04 4 1.249516571 SES(ph)LSNCSIGKK ddPTM_HeLa_Romidepsin_16h_R1 1 SESLSNCSIGKK 12 1 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 0 S(0.019)ES(0.948)LS(0.033)NCSIGKK 162.31 0.00090124 9472700 1881.1 1675.4 1339.4 276.26 1594.1 1682.9 1491.8 1790.5 1627.3 1546.7 TRUE FALSE FALSE 1858.17243 1698.986325 1362.711695 308.202481 1512.747129 1575.368121 1618.513455 1842.305293 1481.750212 1506.516511 1.233423209 1.127758184 0.904544813 0.204579557 1.004135778 1.045702526 1.074341664 1.222890874 0.983560553 1 10.55700077 -9.754751167 13.34378356 1.114626717 0.895315828 0.092160475 0.263745691 0.885942675 1747.334407 0.04396202 0.060775645 1.76E-10 9.754751167 -0.219310889 SES(ph)LTAESR ddPTM_HeLa_Romidepsin_16h_R1 1 SESLTAESR 9 0 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 S(0.021)ES(0.903)LT(0.076)AESR 104.43 0.024305 6210000 1155 1299.9 757.23 930.17 985.35 1498.6 1006.2 1868.3 1066.7 1158.1 TRUE FALSE FALSE 1140.922416 1318.200026 770.4092705 1037.720632 935.0639127 1402.844297 1091.666603 1922.356313 971.2916804 1128.012395 1.011444928 1.168604203 0.682979437 0.91995499 0.82894826 1.243642625 0.967778907 1.704197863 0.861064723 1 10.13956721 -5.235775485 1.382739579 0.984186199 199.9519615 0.65896893 0.157265098 175.5816123 1.542470995 0.020817496 109636.5676 5.81E-06 5.235775485 198.9677753 SES(ph)PFRETEPLVSPHQDK ddPTM_HeLa_Romidepsin_16h_R1 1 SESPFRETEPLVSPHQDK 18 1 Q9BYW2;H7C3H4;C9JG86;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 S(0.145)ES(0.849)PFRET(0.005)EPLVSPHQDK 92.913 0.0018875 6031300 1643.8 1376.5 1417.2 1637.6 2116.9 1661.9 1705 1604.5 1959.4 2130.9 TRUE FALSE FALSE 1623.764733 1395.878403 1441.865772 1826.947017 2008.866694 1555.709954 1849.822657 1650.923676 1784.146357 2075.538911 0.782334036 0.672537815 0.694694647 0.880227785 0.967877154 0.749545068 0.891249327 0.795419285 0.859606316 1 11.01927026 -12.18051642 0.998797722 0.996531644 0.805980204 0.164367557 0.095042842 0.429025632 0.789600466 0.055493083 0.016917906 6.60E-13 12.18051642 -0.190551439 SES(ph)PIPVAEQGTLMR ddPTM_HeLa_Romidepsin_16h_R1 1 SESPIPVAEQGTLMR 15 0 P86452 P86452 ZBED6 Zinc finger BED domain-containing protein 6 1 0 SES(0.999)PIPVAEQGTLMR 101.2 0.010318 23366000 3393.6 3739.6 3533.4 3824.9 2719.5 2602.8 2062.3 2791.6 3482.3 3370.8 TRUE FALSE FALSE 3352.237498 3792.246187 3594.897345 4267.152935 2580.713767 2436.48948 2237.471711 2872.370542 3170.834366 3283.22613 1.021019377 1.155036551 1.094928343 1.299682923 0.786029857 0.742102244 0.681485716 0.874862232 0.965767888 1 11.6808984 -8.605086447 11.94846045 1.047414316 0.758749814 0.685359619 0.10335487 0.262478536 36.87007224 0.015241027 0.030487362 2.48E-09 8.605086447 -0.288664502 SES(ph)PKEPEQLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SESPKEPEQLRK 12 2 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 1 0 S(0.034)ES(0.966)PKEPEQLRK 73.877 0.023043 842720000 3468.8 3339.5 3277.3 3371.3 3723.3 3521.9 3549.2 3722.6 3726.1 3567.7 TRUE FALSE FALSE 3426.520931 3386.513569 3334.340032 3761.105568 3533.286107 3296.861956 3850.668959 3830.307558 3392.828284 3475.01064 0.98604617 0.974533295 0.959519373 1.082329224 1.016769867 0.948734349 1.108102783 1.102243404 0.976350474 1 11.76280168 -7.7469231 24.99915138 0.99513645 1.105173183 0.618409067 0.035203947 113.5246636 195502.7579 0.004679125 0.01734677 1.79E-08 7.7469231 0.110036733 SES(ph)PPAELPSLR ddPTM_HeLa_Romidepsin_16h_R1 1 SESPPAELPSLR 12 0 Q14669;Q14669-2;Q14669-3;G5E9G6;H7C1L9 Q14669 TRIP12 E3 ubiquitin-protein ligase TRIP12 1 0 S(0.09)ES(0.91)PPAELPSLR 138.42 0.0022632 44587000 2638 2165.8 2499.9 1524.9 1857.6 1547.7 1748.5 1804.1 2842.4 2640.5 TRUE FALSE FALSE 2605.847041 2196.290189 2543.409711 1701.216113 1762.79974 1448.806965 1897.017546 1856.298787 2588.168625 2571.899429 1.013199432 0.853956482 0.988922693 0.661462922 0.685407726 0.56332178 0.737593984 0.72176181 1.006325751 1 11.32861851 -9.262883589 24.34277753 0.99136782 0.671942664 0.851525827 0.062084138 23.398612 394395.5564 0.009699654 0.0153276 5.46E-10 9.262883589 -0.319425157 SES(ph)PPPLSDPK ddPTM_HeLa_Romidepsin_16h_R1 3 SESPPPLSDPK 11 0 Q15059;Q15059-2 Q15059 BRD3 Bromodomain-containing protein 3 1 0 S(0.042)ES(0.958)PPPLSDPK;SES(1)PPPLSDPK;SES(1)PPPLSDPK ;; 187.78 1.90E-08 700830000 21871.7 22983.9 21615.6 22718.1 23275.2 22152.7 22549.1 23996.5 23915.2 23817 TRUE FALSE FALSE 21605.11931 23307.46795 21991.81045 25344.87361 22087.37969 20737.21396 24464.41999 24690.80087 21776.16462 23198.23091 0.93132616 1.004708852 0.947995153 1.092534759 0.952114831 0.893913594 1.054581278 1.064339818 0.938699365 1 14.50172717 SES(ph)PSLTQER ddPTM_HeLa_Romidepsin_16h_R1 2 SESPSLTQER 10 0 Q9BXW9;Q9BXW9-1;H7BZJ7;Q9BXW9-3 Q9BXW9 FANCD2 Fanconi anemia group D2 protein 1 0 S(0.141)ES(0.843)PS(0.005)LT(0.011)QER;S(0.132)ES(0.825)PS(0.009)LT(0.034)QER ; 132.56 0.0063428 49652000 5580.7 4512.7 5178.7 3653.2 4791 4889 3629.3 4353 5344.1 5199.2 TRUE FALSE FALSE 5512.680282 4576.229909 5268.833101 4075.600173 4546.497392 4576.608679 3937.572651 4478.947187 4866.110311 5064.124034 1.088575289 0.903656758 1.040423391 0.804798647 0.897785552 0.903731553 0.777542695 0.884446581 0.960898722 1 12.30609703 -9.496584104 1.321915354 1.038372997 0.85206161 0.461457621 0.068238284 0.20183124 0.703385917 0.011087431 0.018873213 3.19E-10 9.496584104 -0.186311386 SES(ph)PVPQNEK ddPTM_HeLa_Romidepsin_16h_R1 2 SESPVPQNEK 10 0 Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8-3;Q9UIF8 Q9UIF8-4 BAZ2B Bromodomain adjacent to zinc finger domain protein 2B 1 0 S(0.307)ES(0.693)PVPQNEK;S(0.023)ES(0.977)PVPQNEK ; 144.1 0.0041415 8236200 7055.9 6461.8 6381.7 6146.4 4982.2 4652.6 4014.2 3184.9 6904 7137.8 TRUE FALSE FALSE 6969.899977 6552.76939 6492.770812 6857.075688 4727.939743 4355.313876 4355.166048 3277.050057 6286.488949 6952.358927 1.002523036 0.942524611 0.933894651 0.986294833 0.680048282 0.626451241 0.626429978 0.471358008 0.904223878 1 12.76328685 -8.608937395 1.503380806 0.995098959 0.556594241 0.898727782 0.059061658 0.066012497 0.295698801 0.007498413 0.020625501 2.46E-09 8.608937395 -0.438504718 SES(ph)TENQSYAK ddPTM_HeLa_Romidepsin_16h_R1 2 SESTENQSYAK 11 0 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8 Q96RT1-7 ERBB2IP Protein LAP2 1 0 SES(0.818)T(0.182)ENQSYAK;SES(0.996)T(0.004)ENQSYAK ; 215.72 2.00E-19 6361800 2380.4 3568.8 2009.27 2218.4 2441.1 2218.3 1778.71 1445.37 2280.1 2797.2 TRUE FALSE FALSE 2351.386769 3619.04166 2044.240502 2474.901846 2316.521558 2076.557789 1929.793583 1487.189501 2076.162145 2724.528341 0.863043608 1.328318596 0.750309869 0.908378088 0.85024682 0.762171477 0.708303729 0.545852094 0.762026261 1 11.41179078 -7.353526362 0.611678133 0.95766489 0.322901495 0.415036328 0.151582203 1.991721775 0.541350049 0.024902948 0.866241819 4.43E-08 7.353526362 -0.634763395 SES(ph)VEGFLSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 2 0 S(0.048)ES(0.952)VEGFLS(0.208)PS(0.792)R 143.64 0.015633 4181700 1368.7 1655.8 1572.2 1466.7 1383.2 1569.5 1434.9 1459.6 1714.4 1743.9 TRUE FALSE FALSE 1352.017758 1679.110396 1599.563481 1636.286755 1312.610143 1469.214015 1556.78037 1501.831223 1561.05977 1698.593227 0.795963234 0.98853002 0.941698964 0.96331878 0.772763085 0.864959304 0.916511585 0.884161787 0.919030964 1 10.73012469 -8.804347686 24.99999376 0.915379359 0.864045988 0.213840118 0.064239301 299.3394896 174405.4095 0.012886654 0.023359183 1.57E-09 8.804347686 -0.051333371 SESAEQQIS(ph)PPNTNAK ddPTM_HeLa_Romidepsin_16h_R1 2 SESAEQQISPPNTNAK 16 0 P31629 P31629 HIVEP2 Transcription factor HIVEP2 1 0 SESAEQQIS(0.998)PPNT(0.002)NAK;SESAEQQIS(0.926)PPNT(0.074)NAK ; 113.52 0.00011986 0 1211.11 1361.14 1313.03 1080.96 975.78 834.62 944.52 952.83 1354.68 1001.14 TRUE FALSE FALSE 1196.348525 1380.302165 1335.882736 1205.945681 925.9823055 781.2904756 1024.747505 980.3986327 1233.514028 975.1302385 1.226860247 1.415505448 1.369953144 1.236702169 0.949598596 0.80121654 1.050882708 1.00540276 1.26497362 1 9.929451108 -8.749076188 24.51835138 1.165321357 0.948099982 0.479416324 0.136394698 187.2854309 371416.4756 0.024654649 0.049016284 1.78E-09 8.749076188 -0.217221375 SESAPTLHPYS(ph)PLSPK ddPTM_HeLa_Romidepsin_16h_R1 2 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 SESAPTLHPY(0.022)S(0.923)PLS(0.055)PK;SESAPTLHPY(0.424)S(0.568)PLS(0.008)PK ; 98.175 0.0027354 20058800 8814.7 8691.3 8363.2 10968.6 5396.3 3903.4 3671.6 3412.5 10253.9 9571.4 TRUE FALSE FALSE 8707.263046 8813.65635 8508.757988 12236.84114 5120.906675 3653.985338 3983.465612 3511.235303 9336.765503 9322.733648 0.933981746 0.945393989 0.912689165 1.312580795 0.549292393 0.391943552 0.427285146 0.376631516 1.001505122 1 13.18653733 -8.595676311 6.867684746 0.982479625 0.412410974 0.871565747 0.109902289 0.052413504 4.028128793 0.015171938 0.030530354 2.54E-09 8.595676311 -0.570068651 SESAPTLHPYSPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SESAPTLHPYSPLSPK 16 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 SESAPTLHPYS(0.028)PLS(0.971)PK;SESAPTLHPYS(0.398)PLS(0.602)PK ; 190.19 1.23E-12 74037000 8282.9 7360.1 7443.4 8151.4 10676.4 8664 7430.6 7634.2 10034.7 8331.1 TRUE FALSE FALSE 8181.944829 7463.715681 7572.949255 9093.903221 10131.54347 8110.398362 8061.754979 7855.083532 9137.1713 8114.656821 1.008292157 0.919782049 0.933243318 1.120676256 1.248548607 0.999475214 0.993480705 0.968011797 1.126008345 1 12.98631437 -9.258687698 24.99876987 0.991548113 1.068449013 0.12267887 0.090890037 348.6476 3167416.742 0.012942575 0.02086897 5.51E-10 9.258687698 0.0769009 SESDLEDVGPTAEWNGDGS(ph)GSLRR ddPTM_HeLa_Romidepsin_16h_R1 1 SESDLEDVGPTAEWNGDGSGSLRR 24 1 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 0 SESDLEDVGPT(0.003)AEWNGDGS(0.498)GS(0.498)LRR 57.902 0.002611 4151500 1195.1 1197.9 1124 1287.9 1294.8 1408.3 1151.9 1155.5 1476.3 1140 TRUE FALSE FALSE 1180.533662 1214.764068 1143.562749 1436.813058 1228.721524 1318.314175 1249.742357 1188.932569 1344.256031 1110.382636 1.063177344 1.094004921 1.029881693 1.293980121 1.106574873 1.187261159 1.125506035 1.07074132 1.210624146 1 10.1168412 -10.26657338 0.782869238 1.016685307 1.147624725 0 0.089683083 0.40568207 0.511323932 0.015937141 0.018915065 5.41E-11 10.26657338 0.130939419 SESDLSQPES(ph)DEEGYALSGR ddPTM_HeLa_Romidepsin_16h_R1 2 SESDLSQPESDEEGYALSGR 20 0 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 SESDLSQPES(0.999)DEEGY(0.001)ALSGR;SESDLSQPES(1)DEEGYALSGR ; 182.47 3.14E-13 14204300 2973.2 2990.8 3555.2 2816.5 3717.2 4947.8 3619.2 4621.8 3626.5 3072.2 TRUE FALSE FALSE 2936.961495 3032.904561 3617.076765 3142.156982 3527.497413 4631.651548 3926.614758 4755.524491 3302.136757 2992.383801 0.981478878 1.013541298 1.208760976 1.050051461 1.178825193 1.547813334 1.312202919 1.589209409 1.103513779 1 11.54707951 -8.374476624 0.701147271 0.990878325 1.577588955 0.760654036 0.102605867 0.303396828 0.221749426 0.016493666 0.105890032 4.22E-09 8.374476624 0.58671063 SESELIDELSEDFDR ddPTM_HeLa_Romidepsin_16h_R1 4 SESELIDELSEDFDR 15 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;A0A0A0MR45;H0YD33;E7EQA0;E7EQ12;D6RC54;P20810-3 P20810-6;P20810-3 CAST Calpastatin 0 0 ;;; ;;; 414.59 0 62038000 6874.7 7163.1 7012.3 5323.01 8035.4 8711.4 7319.2 7255.2 7292.31 6793.6 FALSE FALSE TRUE 6790.908512 7263.94231 7134.34614 5938.481462 7625.323554 8154.769655 7940.892665 7465.117765 6640.06753 6617.101293 1.026266368 1.097752927 1.07816789 0.897444545 1.152366152 1.232377939 1.200056084 1.128155281 1.00347074 1 12.69198365 -8.586623112 8.915498182 1.018184504 1.188893253 0.671819888 0.055527499 0.124752884 16.1128842 0.007832441 0.015691625 2.59E-09 8.586623112 0.170708749 SESETSTMAAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SESETSTMAAKK 12 1 A0A087WVF1;Q96B23-2;Q96B23 A0A087WVF1 C18orf25 Uncharacterized protein C18orf25 0 1 ; SESETSTMAAK(1)K;SESETSTMAAK(1)K 163.9 0.00012924 2063300 210.548 200.26 161.01 284.63 581.3 662.84 674.5 533.54 343.87 296.21 FALSE TRUE FALSE 207.98176 203.0792655 163.8123115 317.5402598 551.6340919 620.4866632 731.7920132 548.9771381 313.113406 288.5144215 0.720871279 0.70387908 0.56777859 1.100604463 1.911980999 2.150626163 2.536413984 1.902771914 1.085260849 1 8.172499624 -8.738972721 2.566653362 0.827877116 2.217137209 0.907444725 0.20057537 0.055727826 0.749346921 0.029848658 0.063123979 1.82E-09 8.738972721 1.389260093 SESGGLGVSMVEYVLSSS(ph)PGDSCLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SESGGLGVSMVEYVLSSSPGDSCLRK 26 1 Q5T1Z4;Q5T1Z8;Q14671-2;Q14671;Q14671-3;H0YEH2 Q5T1Z4 PUM1 Pumilio homolog 1 1 0 SESGGLGVS(0.074)MVEY(0.053)VLS(0.098)S(0.098)S(0.591)PGDS(0.085)CLRK 58.622 0.0041206 13222000 980.71 1126.1 824.01 183.67 1204.6 985.64 776.72 944.15 1251 1376.4 TRUE FALSE FALSE 968.7567293 1141.953265 838.3515484 204.9067896 1143.124767 922.660785 842.6945774 971.4674906 1139.107427 1340.64093 0.722607156 0.85179651 0.625336382 0.152842409 0.852670347 0.688223643 0.628575899 0.724629145 0.849673765 1 10.38870717 -11.51724753 0.529250299 1.010726622 0.625393461 0.256805211 0.186724654 0.803493643 0.456917741 0.143071552 0.053791167 3.04E-12 11.51724753 -0.385333161 SESLDPDS(ph)SMDTTLILK ddPTM_HeLa_Romidepsin_16h_R1 2 SESLDPDSSMDTTLILK 17 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 S(0.001)ES(0.033)LDPDS(0.478)S(0.478)MDT(0.007)T(0.002)LILK;S(0.001)ES(0.023)LDPDS(0.485)S(0.485)MDT(0.005)T(0.002)LILK ; 104.07 0.0037556 29250300 5379.2 6501.7 4321.2 4523.3 5340.2 6085.6 4904.9 6301 5833.1 5784.5 TRUE FALSE FALSE 5313.636241 6593.231103 4396.408673 5046.305229 5067.669667 5696.7498 5321.522084 6483.309494 5311.372927 5634.217856 0.943100955 1.170212312 0.780305055 0.895653196 0.899445104 1.011098602 0.944500589 1.150702663 0.942699246 1 12.45999963 -7.257625056 23.77446992 0.963936266 1.150702807 0.273957688 0.094804887 196.7590282 1226280.803 0.012377721 0.123302396 5.53E-08 7.257625056 0.186766541 SESPKEPEQLR ddPTM_HeLa_Romidepsin_16h_R1 2 SESPKEPEQLR 11 1 F8W6I7;P09651-3;P09651-2;P09651;F8VTQ5;F8W646 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 0 ; ; 108.43 0.017408 13745100 5124.2 5308.7 4797.4 4242 5502.3 5459.6 4853.3 5272.2 5615 5023.7 FALSE FALSE TRUE 5061.744279 5383.436018 4880.896735 4732.479999 5221.497099 5110.74918 5265.539181 5424.742789 5112.780337 4893.18355 1.03444807 1.100190901 0.997488994 0.96715767 1.067096103 1.044463002 1.076096804 1.108632597 1.044878101 1 12.25655769 -4.000000008 0.447120945 1.01759342 3.14377713 0.316403058 0.036034265 58.78631279 0.638180079 0.007868152 114.886413 1.00E-04 4.000000008 2.126183711 SESQESLVT(ph)SPSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SESQESLVTSPSKPK 15 1 E7EWD6;Q76L83-2;Q76L83;A0A5F9ZHN2 E7EWD6 ASXL2 Putative Polycomb group protein ASXL2 1 0 SESQESLVT(0.519)S(0.373)PS(0.108)KPK 75.239 0.022029 24442000 4229.8 4332.2 3388.3 2695.6 2550.9 2699.7 2161.2 2124 4745.7 4214.2 TRUE FALSE FALSE 4178.245571 4393.188825 3447.27194 3007.277955 2420.718054 2527.197883 2344.772274 2185.454589 4321.232706 4104.714476 1.017913815 1.070278786 0.839832334 0.732639986 0.589740911 0.615681772 0.571238825 0.532425483 1.05274867 1 12.00306616 -9.241019209 1.506265471 1.013904548 0.573877256 0.96284791 0.040089993 0.046243194 0.205426958 0.006101394 0.011411448 5.74E-10 9.241019209 -0.440027292 SESS(ph)DFEVVPK ddPTM_HeLa_Romidepsin_16h_R1 1 SESSDFEVVPK 11 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-3;Q9Y520-2 E7EPN9 PRRC2C Protein PRRC2C 1 0 S(0.001)ES(0.104)S(0.895)DFEVVPK 169.89 0.00036098 16080000 5590.5 5414.6 5160.8 4071 5175.1 5107.3 3963.8 4824.7 5040.4 5324.6 TRUE FALSE FALSE 5522.360836 5490.826881 5250.621559 4541.708175 4910.995336 4780.960013 4300.485073 4964.295082 4589.574 5186.266124 1.064804756 1.058724475 1.012408818 0.875718304 0.946923127 0.921850113 0.829206402 0.957200221 0.884947646 1 12.34048052 -9.35187493 5.029707217 1.03352689 0.905224116 0.354714687 0.060285917 0.093564977 3.930059084 0.006262944 0.009667621 4.45E-10 9.35187493 -0.128302775 SESS(ph)PIVR ddPTM_HeLa_Romidepsin_16h_R1 1 SESSPIVR 8 0 H0Y8J2;Q03188;Q03188-2 H0Y8J2 CENPC Centromere protein C 1 0 S(0.042)ES(0.213)S(0.745)PIVR 109.44 0.023086 5394600 4370.3 3836.4 3987.7 4347.7 3339.4 3272 2903.8 2543.9 4752.2 3880.2 TRUE FALSE FALSE 4317.033103 3890.40894 4057.104246 4850.401531 3168.977957 3062.92976 3150.4487 2617.503733 4327.15133 3779.391845 1.142256024 1.029374328 1.073480711 1.283381488 0.838488859 0.810429266 0.833586151 0.692572731 1.144933235 1 11.88393839 -8.608237835 8.281818864 1.079483256 0.790960869 0.772048764 0.084027503 0.102718113 8.797987339 0.012764654 0.025580872 2.46E-09 8.608237835 -0.288522388 LGFSS(ph)SPTKK ddPTM_HeLa_Romidepsin_16h_R1 1 LGFSSSPTKK 10 1 Q8IVF2;Q8IVF2-3;Q8IVF2-2 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 LGFS(0.039)S(0.461)S(0.461)PT(0.039)KK 138.25 0.0080211 113680000 6207.3 5633 5709.8 3983.7 4179.7 3317.6 2612.6 2318.9 6342.1 5764.5 TRUE FALSE FALSE 6131.64304 5712.301522 5809.176674 4444.314138 3966.394312 3105.616067 2834.514179 2385.993713 5774.846692 5614.737459 1.092062289 1.017376425 1.034630153 0.791544426 0.706425606 0.553118661 0.504834678 0.424951964 1.028515889 1 12.45500285 -8.702527221 1.046122305 1.046929809 0.454436519 0.974173531 0.038537 0.066090407 0.138505239 0.007643783 0.024479347 1.98E-09 8.702527221 -0.59249329 down SESVEGFLS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 4 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 SESVEGFLS(0.954)PS(0.046)R;SESVEGFLS(0.995)PS(0.005)R;SESVEGFLS(0.99)PS(0.01)R;SESVEGFLS(0.714)PS(0.286)R ;;; 178.22 1.73E-06 184646000 7030.2 6439.5 6313.3 6187.9 6871 5938.4 5217.46 5700.8 7694.8 6822.2 TRUE FALSE FALSE 6944.513218 6530.15545 6423.180338 6903.374113 6520.347231 5558.955405 5660.630922 5865.743654 7006.557816 6644.958261 1.045080036 0.982723321 0.966624633 1.038889011 0.981247282 0.836567393 0.851868545 0.882735967 1.05441713 1 12.69804442 -8.360394103 4.171072001 1.014913301 0.8565909 0.861174217 0.028308484 0.058581027 1.780959545 0.004163295 0.009751235 4.36E-09 8.360394103 -0.158322401 SESVEGFLSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SESVEGFLSPSR 12 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 SESVEGFLS(0.016)PS(0.984)R 137.09 0.0024618 16731000 2275.6 2342.5 2220.3 2297.6 1861.3 1830.8 1089.6 1305.3 2157 2000.9 TRUE FALSE FALSE 2247.864112 2375.477776 2258.94339 2563.259323 1766.310916 1713.817789 1182.150597 1343.066796 1964.072518 1948.91633 1.153391799 1.218871093 1.15907664 1.315222867 0.906304128 0.879369608 0.606568162 0.689135175 1.007776726 1 10.92845644 -8.16057924 1.842806866 1.106685269 0.650315278 0.757044619 0.106916981 0.145086054 0.931234631 0.017065103 0.061804276 6.91E-09 8.16057924 -0.456369992 SESVVSGLDS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 4 SESVVSGLDSPAK 13 0 H7BYJ3;O14578;O14578-4;O14578-2 H7BYJ3 CIT Citron Rho-interacting kinase 1 0 SESVVSGLDS(1)PAK;SESVVSGLDS(1)PAK;S(0.29)ES(0.084)VVS(0.001)GLDS(0.624)PAK;SESVVSGLDS(1)PAK ;;; 198.48 4.15E-16 154993000 14688.2 13121.3 14055 11671.2 9926.7 9968.2 8851.8 8996.3 14893 13213.3 TRUE FALSE FALSE 14509.17457 13306.02201 14299.62138 13020.67906 9420.103457 9331.264191 9603.671671 9256.593747 13560.93278 12870.01656 1.127362541 1.033877613 1.111080263 1.011706473 0.731941829 0.72503902 0.746205075 0.719237128 1.053684175 1 13.65172629 -8.800742965 4.324694752 1.062552686 0.728943007 0.954622727 0.03491732 0.041566015 1.690542002 0.007343789 0.014055862 1.58E-09 8.800742965 -0.333609679 SESVVY(ph)ADIR ddPTM_HeLa_Romidepsin_16h_R1 1 SESVVYADIR 10 0 O95297-4;O95297-2;O95297;O95297-5 O95297-4 MPZL1 Myelin protein zero-like protein 1 1 0 SESVVY(1)ADIR 172.94 0.026093 7033500 1886.6 3113.7 2129 1540.5 2982.9 3210 1114.5 2638.6 2155.9 2201 TRUE FALSE FALSE 1863.605394 3157.53475 2166.054352 1718.619858 2830.671482 3004.89136 1209.165602 2714.943728 1963.070904 2143.817703 0.869292847 1.472855993 1.010372453 0.801663246 1.320388146 1.401654327 0.564024451 1.266406059 0.915689287 1 11.06596652 SET(ph)SPVAPR ddPTM_HeLa_Romidepsin_16h_R1 1 SETSPVAPR 9 0 A0A2R8Y661;A0A2R8YGD3;Q9Y4G8;H0Y8T6;H0Y8H7 A0A2R8Y661 RAPGEF2 Rap guanine nucleotide exchange factor 2 1 0 S(0.01)ET(0.925)S(0.065)PVAPR 140.11 0.013262 52989000 3814.9 4449.8 4126.2 3760.2 3902.1 3949.7 3766 3900 3935.4 3670.2 TRUE FALSE FALSE 3768.402531 4512.444401 4198.01478 4194.972016 3702.961276 3697.326917 4085.883946 4012.840347 3583.407968 3574.847675 1.054143526 1.262275994 1.174319904 1.173468745 1.035837499 1.034261388 1.1429533 1.122520653 1.002394589 1 11.80366605 -10.49089095 12.70049772 1.02385978 1.132651802 0.41876246 0.063637512 1.147444916 454.9877635 0.011949474 0.013223888 3.23E-11 10.49089095 0.108792021 SETAPAAPAAPAPAEKT(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAPAPAEKTPVK 20 1 P10412 P10412 HIST1H1E Histone H1.4 1 0 SETAPAAPAAPAPAEKT(1)PVK;S(0.004)ET(0.02)APAAPAAPAPAEKT(0.975)PVK ; 89.392 0.00094817 50458000 7990.3 14081.1 8479.4 7750.8 8057.2 8072.4 6018.7 6770 9840.4 10721.4 TRUE FALSE FALSE 7892.91115 14279.3341 8626.9804 8646.983965 7646.011018 7556.599692 6529.928228 6965.879269 8960.249978 10442.85648 0.755819173 1.36737818 0.826113086 0.828028613 0.732176204 0.723614243 0.625300964 0.667047305 0.858026728 1 13.35022877 -8.814500257 1.679876652 0.92041009 0.668281437 0.395027148 0.157996435 0.352247787 2.012650258 0.026570209 0.060387924 1.53E-09 8.814500257 -0.252128653 SETAPAAPAAPAPAEKT(ph)PVKK ddPTM_HeLa_Romidepsin_16h_R1 1 SETAPAAPAAPAPAEKTPVKK 21 2 P10412 P10412 HIST1H1E Histone H1.4 1 0 SETAPAAPAAPAPAEKT(1)PVKK 73.928 0.0015257 8201900 2438.6 4662.1 2484.3 2594.3 2881.6 2186.8 1744.6 2465.6 3370.2 3306.9 TRUE FALSE FALSE 2408.877405 4727.733166 2527.538199 2894.265173 2734.541199 2047.070538 1892.78628 2536.938246 3068.760871 3220.986261 0.747869506 1.467790541 0.784709401 0.898564892 0.848976362 0.63554153 0.587641836 0.787627776 0.95273951 1 11.65328679 -8.410546485 3.126058941 0.919627536 0.661657243 0.305837337 0.194685474 0.288400674 5.326241023 0.029321872 0.070875121 3.89E-09 8.410546485 -0.257970292 SETAPAETATPAPVEKS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAETATPAPVEKSPAK 20 1 P16401 P16401 HIST1H1B Histone H1.5 1 0 SETAPAET(0.001)AT(0.007)PAPVEKS(0.992)PAK;SETAPAETAT(0.123)PAPVEKS(0.877)PAK ; 165.88 1.71E-10 351580000 6806.5 12137.7 5868 6095.4 5206.3 4498.2 4048.3 3924.5 7260.6 8449 TRUE FALSE FALSE 6723.53976 12308.57486 5970.130078 6800.178828 4940.603084 4210.779537 4392.162501 4038.049216 6611.193751 8229.493762 0.817005268 1.495666102 0.725455326 0.826318 0.600353221 0.511669327 0.533709925 0.490680148 0.803353638 1 13.00658797 -8.867338047 1.649827666 0.952160474 0.511385861 0.52924891 0.196023171 0.229111847 1.258772531 0.030175984 0.06688023 1.36E-09 8.867338047 -0.440774612 SETDTS(ph)LIR ddPTM_HeLa_Romidepsin_16h_R1 1 SETDTSLIR 9 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 1 0 SET(0.006)DT(0.086)S(0.908)LIR 103.88 0.02481 5713000 3676.2 3809 3751.4 3183.4 4130.4 3847.5 3224.2 3497.8 4000.2 3554.4 TRUE FALSE FALSE 3631.39306 3862.623202 3816.691543 3551.479686 3919.610275 3601.657167 3498.063468 3599.003324 3642.412093 3462.056176 1.048912229 1.115702059 1.102434897 1.025829596 1.132162529 1.040323145 1.010400551 1.039556593 1.052095029 1 11.75741342 -11.45816493 1.020290542 1.006707711 1.064964295 0.085850194 0.040814848 0.452667493 0.965775518 0.013363087 0.008030057 3.48E-12 11.45816493 0.058256583 SETELK(ac)DTYAR ddPTM_HeLa_Romidepsin_16h_R1 2 SETELKDTYAR 11 1 Q13200;Q13200-2;Q13200-3;H7C1H2 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 0 1 ; SETELK(1)DTYAR;SETELK(1)DTYAR 144.55 0.0034743 1545200 705.55 584.27 610.93 383.93 1056.81 1096.4 1007.18 1098.33 1099.75 986.07 FALSE TRUE FALSE 696.9504852 592.4953684 621.5629804 428.321793 1002.877042 1026.343578 1092.729844 1130.108446 1001.385606 960.4517592 0.725648611 0.616892377 0.647156897 0.445958674 1.044172216 1.068605027 1.137724861 1.17664259 1.042619367 1 9.907569343 -8.544073164 24.98736114 0.798917552 1.116618417 0.50654397 0.170965249 184.8544469 217935.1625 0.02816553 0.056334915 2.86E-09 8.544073164 0.317700865 SETIQDTDTQSLVGS(ph)PSTR ddPTM_HeLa_Romidepsin_16h_R1 2 SETIQDTDTQSLVGSPSTR 19 0 E9PMR6;Q9NZN5-2;Q9NZN5 E9PMR6 ARHGEF12 Rho guanine nucleotide exchange factor 12 1 0 SETIQDTDTQSLVGS(0.999)PS(0.001)TR;SETIQDTDT(0.001)QS(0.039)LVGS(0.954)PS(0.006)TR ; 313.74 8.55E-165 13454300 3769.2 3575.3 3737.7 2459.4 4848.6 5714.1 4114.5 5103 3965.8 3859.7 TRUE FALSE FALSE 3723.259541 3625.633167 3802.753101 2743.7674 4601.157849 5348.987451 4463.985527 5250.647254 3611.088915 3759.424438 0.990380204 0.964411768 1.011525345 0.729837092 1.223899543 1.422820844 1.187411957 1.396662532 0.960543023 1 11.87629609 -8.541127895 22.10511989 0.977476616 1.321234902 0.767025955 0.098759052 21.19464707 25672.82779 0.013092111 0.026191937 2.88E-09 8.541127895 0.343758286 SETSWES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SETSWESPK 9 0 E5RJU9;Q86UE4 E5RJU9 MTDH Protein LYRIC 1 0 SETSWES(1)PK 154.84 0.0046388 36676000 4785.9 6866.6 4753 3075.8 4235 6112 3739.9 5660.6 5669.2 6656.5 TRUE FALSE FALSE 4727.56761 6963.268175 4835.723971 3431.438468 4018.872147 5721.462926 4057.567013 5824.38053 5162.132553 6483.56317 0.729161957 1.073987866 0.745843581 0.529251953 0.619855478 0.882456571 0.625823626 0.898330189 0.796187593 1 12.66257118 -9.543808019 24.68594165 0.884921698 0.703519199 0.291738069 0.139462923 218.5192981 257740.8904 0.023771261 0.033619588 2.86E-10 9.543808019 -0.181402499 SEVQQPVHPKPLS(ph)PDSR ddPTM_HeLa_Romidepsin_16h_R1 3 SEVQQPVHPKPLSPDSR 17 1 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3;F8VRN8 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 SEVQQPVHPKPLS(0.723)PDS(0.277)R;SEVQQPVHPKPLS(0.986)PDS(0.014)R;SEVQQPVHPKPLS(0.953)PDS(0.047)R ;; 114.87 0.00077575 214517000 8328.7 7967.6 7247.5 8587.3 9016.4 10460.9 8761.2 10118.8 9078.4 8196.5 TRUE FALSE FALSE 8227.186601 8079.768082 7373.639697 9580.20403 8556.259463 9792.482251 9505.376109 10411.57151 8266.405167 7983.553748 1.030516843 1.012051567 0.923603689 1.199992426 1.071735687 1.226581866 1.190619667 1.30412744 1.035429262 1 12.96281537 -8.366046221 0.781013465 1.00879868 1.288057724 0.717533804 0.061647785 0.333378176 0.316556923 0.00988669 0.058712149 4.30E-09 8.366046221 0.279259044 SEVSSDEDIQFR ddPTM_HeLa_Romidepsin_16h_R1 1 SEVSSDEDIQFR 12 0 H0YFD6;P40939;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 0 133.91 0.029872 2899200 1427.4 1394.6 1220.4 1184.1 1155 1453.3 1236.2 1431.6 1139.4 1294.5 FALSE FALSE TRUE 1410.0023 1414.233215 1241.64055 1321.011213 1096.05604 1360.43882 1341.202797 1473.021087 1037.48921 1260.868703 1.11827845 1.121634006 0.984750075 1.047699265 0.869286419 1.078969457 1.06371329 1.168258902 0.822836833 1 10.30020234 -16.52283316 0.00366624 3.91E-05 2.051643225 0.012409117 0.104599764 436078.5352 129.3656623 38122.62508 34361.96689 3.00E-17 16.52283316 2.051604133 SEWLDPS(ph)QKSPLHVGETR ddPTM_HeLa_Romidepsin_16h_R1 1 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 0 SEWLDPS(0.953)QKS(0.046)PLHVGET(0.001)R 65.652 0.011144 38470000 2305.4 2127.7 2091.2 1770.1 2357.4 2087 1877.5 1852.7 2196.6 2068 TRUE FALSE FALSE 2277.300898 2157.653816 2127.596459 1974.767291 2237.093081 1953.647435 2036.974803 1906.304951 2000.130595 2014.273062 1.130582015 1.071182382 1.056260196 0.980387083 1.110620563 0.969901982 1.011270439 0.946398474 0.992978873 1 10.97604356 -7.659856587 0.813380418 1.061581148 0.927191319 0.236087131 0.05140646 1.570698895 1.064782594 0.009530408 0.16701605 2.19E-08 7.659856587 -0.134389829 SEWLDPSQKS(ph)PLHVGETR ddPTM_HeLa_Romidepsin_16h_R1 1 SEWLDPSQKSPLHVGETR 18 1 O15164-2;O15164 O15164-2 TRIM24 Transcription intermediary factor 1-alpha 1 0 SEWLDPS(0.19)QKS(0.81)PLHVGETR 60.307 0.015314 57517000 2136 2420.2 2307.6 2360.7 2621.4 2446.8 1931.4 2172.5 2584.7 2565.8 TRUE FALSE FALSE 2109.96561 2454.271639 2347.76281 2633.655241 2487.620176 2290.457377 2095.453068 2235.35786 2353.517959 2499.140146 0.844276626 0.982046422 0.939428232 1.053824551 0.995390427 0.916498172 0.838469612 0.894450783 0.941731084 1 11.28721609 -7.956044284 6.401358523 0.944369958 0.867993783 0.29336834 0.055435959 0.273654859 27.81264054 0.010218441 0.03099127 1.11E-08 7.956044284 -0.076376175 SEYSELDEDESQAPYDPNGKPER ddPTM_HeLa_Romidepsin_16h_R1 1 SEYSELDEDESQAPYDPNGKPER 23 1 P19387 P19387 POLR2C DNA-directed RNA polymerase II subunit RPB3 0 0 71.651 0.0017548 3047500 656.77 682.32 637.68 557.94 832.91 753.42 577.15 728.02 743.52 681.93 FALSE FALSE TRUE 648.7650346 691.9257189 648.7785529 622.451648 790.4034947 705.2788936 626.1731066 749.0841101 677.017709 664.2133603 0.976741923 1.041722073 0.976762275 0.937126058 1.189984336 1.061825816 0.942728864 1.127776336 1.019277463 1 9.375502932 -8.805677144 24.99999979 0.988888978 1.069394198 0.309318571 0.063925127 126.2648563 71355.35153 0.00893143 0.016189664 1.56E-09 8.805677144 0.08050522 SFDY(ph)NYR ddPTM_HeLa_Romidepsin_16h_R1 1 SFDYNYR 7 0 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 0 S(0.064)FDY(0.935)NY(0.001)R 56.026 0.021636 16254000 5787.3 5326 6815.8 4347.3 6088.8 6001.4 5747.4 6043.7 6613.8 7078.9 TRUE FALSE FALSE 5716.762162 5400.979568 6934.42614 4849.955281 5778.065816 5617.929909 6235.584013 6218.564924 6022.245163 6894.989158 0.829118369 0.783319516 1.005719658 0.703402887 0.838009413 0.814784444 0.904364586 0.901896259 0.873423442 1 12.75133257 -12.23212653 0.840096949 1.005782868 0.845561453 0.075368139 0.085103798 0.559343638 0.670576866 0.058347488 0.014097965 5.86E-13 12.23212653 -0.160221416 SFDYNY(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 2 SFDYNYRR 8 1 Q5JRI1;O75494-5;O75494-4;O75494-6;O75494-3;O75494-2;O75494 Q5JRI1 SRSF10 Serine/arginine-rich splicing factor 10 1 0 S(0.09)FDYNY(0.91)RR;S(0.002)FDYNY(0.998)RR ; 66.073 0.023809 33313000 7123.4 7243.1 5416.5 8179 6201.2 5741.7 5267.1 4953.2 6374.4 4986.3 TRUE FALSE FALSE 7036.577261 7345.068552 5510.77191 9124.694463 5884.729624 5374.8239 5714.487343 5096.513027 5804.257699 4856.755207 1.448822714 1.512340696 1.134661245 1.878763511 1.211658684 1.106669715 1.176606005 1.049365844 1.195089613 1 12.24577706 -8.520527525 24.99640784 1.287870559 1.124404871 0.149510287 0.234322027 205.562826 2185382.931 0.03959461 0.080243052 3.02E-09 8.520527525 -0.163465688 SFELPPYTPPPILS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 1 SFELPPYTPPPILSPVR 17 0 A0A1C7CYX1;Q6PJG2;A0A0A0MSU2 A0A1C7CYX1 ELMSAN1 ELM2 and SANT domain-containing protein 1 1 0 SFELPPYTPPPILS(1)PVR 142.4 0.00031965 26341000 3656.2 3394.8 3777.7 2379.2 2675.3 4053.8 3839.2 3728.3 4428.7 4478.3 TRUE FALSE FALSE 3611.636828 3442.592084 3843.449284 2654.294298 2538.769458 3794.775263 4165.301552 3836.172478 4032.58598 4361.95312 0.827986163 0.789231793 0.881130351 0.608510506 0.582025847 0.869971583 0.954916625 0.879462106 0.924490903 1 12.09075855 -11.71483276 0.675969412 0.999523221 0.791487792 0.240696126 0.114371693 0.732586765 0.649013479 0.078605927 0.028468457 1.93E-12 11.71483276 -0.208035429 SFEVEEVET(ph)PNS(ph)TPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPR 16 0 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 SFEVEEVET(1)PNS(0.598)T(0.403)PPR 138.28 0.0041455 8969900 1616.3 1556.6 1433.4 1574.5 2301.5 2230.9 1993.3 1596.9 1634.6 1530.2 TRUE FALSE FALSE 1596.599914 1578.513856 1458.347726 1756.551098 2184.045867 2088.35269 2162.610852 1643.103782 1488.397282 1490.445183 1.071223505 1.059088837 0.978464516 1.178541229 1.465364772 1.401160347 1.450983153 1.102424833 0.99862598 1 10.5415276 -8.981369859 4.480147139 1.034036547 1.363892492 0.718991773 0.097929223 0.075934634 3.755634437 0.013872148 0.025061013 1.04E-09 8.981369859 0.329855945 SFEVEEVET(ph)PNS(ph)TPPRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 S(0.04)FEVEEVET(0.956)PNS(0.564)T(0.441)PPRR 90.442 0.004844 6322300 1579.8 1832.9 1690.3 1772.2 1890.3 1961.4 1616.9 1384.5 1897.2 1861.1 TRUE FALSE FALSE 1560.54479 1858.703614 1719.718962 1977.110102 1793.830937 1836.07287 1754.239446 1424.558323 1727.50968 1812.748354 0.86087227 1.025351153 0.948680471 1.09066992 0.989564235 1.012866936 0.967723646 0.785855533 0.952978209 1 10.82396295 -7.260050698 23.55993079 0.961123381 0.785855402 0.458467215 0.060183222 48.93373223 829980.6071 0.010296324 0.085572404 5.49E-08 7.260050698 -0.175267979 SFEVEEVET(ph)PNST(ph)PPRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 SFEVEEVET(0.997)PNS(0.258)T(0.746)PPRR 70.538 0.0088187 5893900 2416.1 1885.2 2146.9 2443.5 2311.1 2686.9 2255.7 2255.6 2546.5 2341.7 TRUE FALSE FALSE 2386.651644 1911.739895 2184.265894 2726.028967 2193.155943 2515.215762 2447.299102 2320.862227 2318.734662 2280.862296 1.046381295 0.838165416 0.957649174 1.195174725 0.961546844 1.102747748 1.072971001 1.017537197 1.016604407 1 11.15536363 SFEVEEVET(ph)PNSTPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPR 16 0 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 1 0 S(0.068)FEVEEVET(0.652)PNS(0.272)T(0.008)PPR 107.11 0.0078603 28815000 226.42 378.84 257.41 361.57 288.58 435 297.36 237.24 313.11 197.86 TRUE FALSE FALSE 223.660306 384.1733195 261.8901131 403.3764246 273.8526858 407.2049039 322.617751 244.1041651 285.1046574 192.7195687 1.160547979 1.993431814 1.358918115 2.093074551 1.420990549 2.112940096 1.674026946 1.266628847 1.479375755 1 7.59035926 -10.38388716 5.613908149 1.070058238 1.70735922 0.315813723 0.311268019 0.123189634 5.161666201 0.044812217 0.050971465 4.13E-11 10.38388716 0.637300982 SFEVEEVETPNS(ph)T(ph)PPRR ddPTM_HeLa_Romidepsin_16h_R1 2 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 2 0 SFEVEEVET(0.002)PNS(0.999)T(0.999)PPRR;S(0.005)FEVEEVET(0.007)PNS(0.998)T(0.991)PPRR ; 106.4 0.0019791 5440500 1392 1175.75 1356.39 1072.08 1162.2 1698.97 1011.85 1313.19 1580.93 1480.55 TRUE FALSE FALSE 1375.033769 1192.302239 1379.997399 1196.038934 1102.888597 1590.4113 1097.796514 1351.185081 1439.527661 1442.085098 0.953503903 0.826790486 0.956945884 0.829381661 0.764787459 1.102855374 0.761256403 0.93696626 0.99822657 1 10.49394059 -10.47796254 4.04358716 0.980682257 0.882663965 0.191805119 0.096172029 0.265260907 8.62338951 0.015735725 0.017430246 3.33E-11 10.47796254 -0.098018293 SFEVEEVETPNS(ph)TPPRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 1 0 SFEVEEVET(0.052)PNS(0.474)T(0.474)PPRR 76.176 0.0068625 84345000 1164.4 814.25 1123.6 882.37 1328.4 1040.9 1186.5 1358.1 1560.5 1308.3 TRUE FALSE FALSE 1150.207845 825.7130329 1143.155787 984.3937711 1260.606791 974.3898494 1287.28128 1397.394481 1420.924972 1274.310177 0.902612147 0.64796864 0.897078127 0.772491493 0.989246428 0.764641032 1.010178921 1.096588967 1.115054244 1 10.31550077 -7.531195182 24.83111325 0.905912069 1.074986513 0.21451145 0.128213325 166.5897188 497403.4844 0.01647977 0.061876279 2.94E-08 7.531195182 0.169074444 SFEVEEVETPNST(ph)PPRR ddPTM_HeLa_Romidepsin_16h_R1 1 SFEVEEVETPNSTPPRR 17 1 K7EJV0;K7EPY1;K7ENL0;Q9UHD8-7;Q9UHD8-2;Q9UHD8-5;Q9UHD8 K7EJV0 Sep-09 Septin-9 1 0 SFEVEEVET(0.01)PNS(0.133)T(0.857)PPRR 82.859 0.00096695 0 1521.7 1147.5 1169.2 1031.5 1794.6 1937 1765 1725.2 1635.1 1226.4 TRUE FALSE FALSE 1503.152935 1163.654535 1189.549436 1150.766883 1703.014865 1813.231951 1914.919056 1775.11594 1488.852561 1194.537951 1.25835511 0.974146141 0.995823895 0.963357323 1.425668279 1.517935826 1.603062552 1.486027245 1.246383641 1 10.22223697 -8.626812107 4.879037103 1.092602879 1.532101045 0.808417189 0.104350631 0.080461585 3.156241367 0.018067558 0.03684692 2.36E-09 8.626812107 0.439498166 SFGDKDLILPNGGT(ph)PAGTSSPASSSSLLNR ddPTM_HeLa_Romidepsin_16h_R1 1 SFGDKDLILPNGGTPAGTSSPASSSSLLNR 30 1 Q5VWJ9 Q5VWJ9 SNX30 Sorting nexin-30 1 0 SFGDKDLILPNGGT(0.912)PAGT(0.021)S(0.021)S(0.021)PAS(0.013)S(0.006)S(0.002)S(0.003)LLNR 66.633 4.45E-05 9794000 1278.9 1541.5 1225.5 1576.1 2290.2 2532.6 2488.7 2670.8 1704.1 1499.6 TRUE FALSE FALSE 1263.312275 1563.201277 1246.829313 1758.336098 2173.322548 2370.775034 2700.090116 2748.075384 1551.681028 1460.640176 0.86490314 1.070216542 0.853618389 1.20381195 1.487924668 1.623106822 1.848566239 1.881418456 1.062329418 1 10.5123851 -8.570401889 1.126870799 0.935475343 1.874497182 0.945808623 0.086311829 0.071235441 0.171330264 0.013091747 0.044972667 2.69E-09 8.570401889 0.939021839 SFGTRPLSSGFS(ph)PEEAQQQDEEFEK ddPTM_HeLa_Romidepsin_16h_R1 2 SFGTRPLSSGFSPEEAQQQDEEFEK 25 1 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 S(0.006)FGT(0.007)RPLS(0.282)S(0.282)GFS(0.422)PEEAQQQDEEFEK;S(0.015)FGT(0.033)RPLS(0.228)S(0.175)GFS(0.55)PEEAQQQDEEFEK ; 56.461 0.0028963 292820000 4511.7 4720.1 4864.6 4968.5 5197.4 6371 5027.4 5591.5 4609.3 4756.8 TRUE FALSE FALSE 4456.709665 4786.549692 4949.266322 5542.981347 4932.157284 5963.913661 5454.427231 5753.281231 4197.032664 4633.21765 0.9619038 1.033094073 1.068213647 1.19635678 1.064520956 1.287207749 1.177243903 1.241746377 0.905857005 1 12.17779874 -9.281000127 0.911749615 0.980308212 1.21942329 0.76993701 0.057455817 0.172202247 0.283292439 0.009196035 0.020086373 5.24E-10 9.281000127 0.239115078 SFIKDYPVVSIEDPFDQDDWGAWQK ddPTM_HeLa_Romidepsin_16h_R1 1 SFIKDYPVVSIEDPFDQDDWGAWQK 25 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 63.883 0.0023404 0 823.61 1013.1 786.3 931.52 1075.1 844.94 774.54 950.63 1358.1 854.12 FALSE FALSE TRUE 813.5715245 1027.362448 799.9852217 1039.226725 1020.233635 790.9510609 840.3294083 978.1349792 1236.628135 831.9298393 0.977932857 1.234914773 0.961601789 1.249175924 1.226345765 0.950742507 1.010096487 1.175742152 1.486457242 1 9.700318054 -10.33048418 24.99905598 0.989579323 1.108609228 0 0.18906364 184.2208561 66700.17674 0.017458769 0.019964861 4.67E-11 10.33048418 0.119029905 SFISPIPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SFISPIPSKR 10 1 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 0 1 ; SFISPIPSK(1)R;SFISPIPSK(1)R 123.86 0.0029096 10182400 446.69 415.17 1035.75 1246.8 3874.1 6550.1 4258.7 2026.28 722.32 254.78 FALSE TRUE FALSE 441.2455705 421.0147742 1053.776794 1390.960882 3676.390221 6131.569749 4620.433872 2084.907215 657.7138901 248.1607789 1.778063288 1.696540348 4.246347062 5.605079452 14.81454982 24.70805329 18.61871119 8.401437263 2.650353908 1 7.955131309 -8.825685085 2.465868088 1.641560014 17.74196019 0.762284112 3.817847527 0.092184664 1.142261567 0.565731084 1.156668449 1.49E-09 8.825685085 16.10040018 SFLEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 SFLEDIR 7 0 P52209-2;P52209;K7ELN9 P52209-2 PGD "6-phosphogluconate dehydrogenase, decarboxylating" 0 0 124.34 0.0010175 0 4954.4 4354 5854 3882.3 5288.8 6074.7 5230.7 4812.8 4812.8 4238.6 FALSE FALSE TRUE 4894.013867 4415.295726 5955.886414 4331.189793 5018.892801 5686.546275 5674.995527 4952.050775 4382.331114 4128.480561 1.185427373 1.06947233 1.442633997 1.049100203 1.215675532 1.377394465 1.374596645 1.199485065 1.061487646 1 12.0113952 -15.2225046 0.099803138 0.326953546 1.457393469 0.376414511 0.117184883 58.81361711 0.588874222 9.190808324 1.092356678 5.99E-16 15.2225046 1.130439923 SFLSEPSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 4 SFLSEPSSPGR 11 0 H0YC41;Q69YN4-3;Q69YN4 H0YC41 KIAA1429 Protein virilizer homolog 1 0 SFLSEPS(0.001)S(0.999)PGR;SFLSEPS(0.005)S(0.995)PGR;SFLSEPS(0.002)S(0.998)PGR;SFLSEPS(0.002)S(0.998)PGR ;;; 179.94 1.02E-05 486113000 31510.1 28997.1 27390.7 20695.1 27096.2 26309.3 24158.1 27325.6 30607.2 28546.1 TRUE FALSE FALSE 31126.04278 29405.32193 27867.42364 23087.96484 25713.3798 24628.22064 26210.08841 28116.22312 27869.61537 27804.46821 1.119461899 1.057575413 1.00226422 0.83036887 0.92479308 0.885764851 0.942657425 1.011212403 1.002343047 1 14.76302912 -9.501451369 5.440656287 1.057151847 0.91803691 0.554460974 0.053187119 0.10585837 9.573077333 0.009473637 0.014154133 3.15E-10 9.501451369 -0.139114937 SFLVASVLPGPDGNINS(ph)PTR ddPTM_HeLa_Romidepsin_16h_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 0 SFLVASVLPGPDGNINS(0.878)PT(0.122)R;S(0.001)FLVAS(0.218)VLPGPDGNINS(0.648)PT(0.134)R ; 106.75 0.00046819 25743000 5187.9 5663.1 5406.9 4787.5 4357.1 4667.1 4193 4342.6 5841.1 5111.1 TRUE FALSE FALSE 5124.667879 5742.82527 5501.004826 5341.053276 4134.740928 4368.887372 4549.153315 4468.24628 5318.657387 4978.312885 1.029398513 1.153568569 1.104993791 1.072864121 0.830550635 0.877583927 0.913794175 0.897542276 1.06836543 1 12.28144119 -8.76500214 24.99964932 1.037125318 0.882127932 0.758678512 0.050771653 46.00903798 322845.5549 0.008788122 0.01639462 1.72E-09 8.76500214 -0.154997386 SFNSDSPSIIGVPSETQT(ph)SPVER ddPTM_HeLa_Romidepsin_16h_R1 1 SFNSDSPSIIGVPSETQTSPVER 23 0 Q8N8K9;Q8N8K9-2;Q8N8K9-3 Q8N8K9 KIAA1958 Uncharacterized protein KIAA1958 1 0 SFNSDSPS(0.001)IIGVPS(0.028)ET(0.064)QT(0.453)S(0.453)PVER 55.413 0.010075 3278900 950 759.9 819.55 685.47 1061.1 1016.5 601.11 833.71 1034.5 860.95 TRUE FALSE FALSE 938.4210346 770.5978921 833.813924 764.7272666 1006.948107 951.5489306 652.1682684 857.8320835 941.971729 838.5823949 1.119056446 0.918929251 0.994313652 0.911928597 1.200774204 1.134711313 0.777703267 1.022955035 1.123290609 1 9.711808732 -10.27007196 24.86193727 1.056221096 0.99628373 0.09332202 0.115835284 1506.460668 4338610.214 0.02021178 0.023306904 5.37E-11 10.27007196 -0.059937366 SFPSS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 SFPSSPSK 8 0 A0A0G2JIS2;A2ABF8;A0A0G2JIR1;Q96KQ7-2;A2ABF9;A0A0G2JK64;Q96KQ7;Q96KQ7-3 A0A0G2JIS2 EHMT2 Histone-lysine N-methyltransferase EHMT2 1 0 SFPS(0.013)S(0.983)PS(0.004)K 133.23 0.0094767 12566000 8351.3 7687.4 8181.3 5703.6 6672.7 5846.3 5138.9 5200.2 8782.9 8398.2 TRUE FALSE FALSE 8249.511143 7795.623419 8323.692095 6363.077068 6332.16722 5472.740298 5575.398038 5350.659582 7997.335427 8180.013553 1.008496024 0.953008619 1.017564585 0.777880993 0.774102289 0.669038048 0.681587873 0.65411378 0.977667748 1 12.99788752 -9.003471732 1.365449026 1.003827462 0.671221282 0.940633062 0.035562826 0.055479724 0.205428563 0.004991407 0.010943635 9.92E-10 9.003471732 -0.332606179 SFQGDDS(ph)DLLLK ddPTM_HeLa_Romidepsin_16h_R1 1 SFQGDDSDLLLK 12 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 S(0.272)FQGDDS(0.728)DLLLK 146.84 0.0014935 13729000 1385.7 1520.4 1165.5 1311.8 1179.4 1092.1 1123 1254.4 1211.1 1027.2 TRUE FALSE FALSE 1368.810555 1541.804231 1185.785039 1463.476488 1119.210817 1022.318335 1218.387592 1290.694085 1102.776183 1000.513196 1.368108448 1.541013389 1.185176811 1.462725823 1.118636737 1.021793954 1.217762641 1.290032046 1.102210533 1 9.96652448 -12.38733751 1.163835097 1.00303727 1.279235537 0.257719956 0.149400851 0.464208889 1.143484798 0.100427214 0.026922081 4.10E-13 12.38733751 0.276198266 SFQQSS(ph)LSR ddPTM_HeLa_Romidepsin_16h_R1 1 SFQQSSLSR 9 0 D6REM6;A0A0R4J2E8;A8MXP9;P43243;Q68E03;D6R991;D6RB45;A0A1B0GX04;D6R9F3;D6RBS2;D6RCM3;D6REK4;D6R8Z5 D6REM6 MATR3;DKFZp686L22104 Matrin-3 1 0 SFQQS(0.205)S(0.794)LSR 128.88 0.0088483 8352600 2525.5 2245 2347.2 1716.9 2840.6 2967.6 2545.4 2338.4 2974.8 2495.3 TRUE FALSE FALSE 2494.718235 2276.605169 2388.052031 1915.416056 2695.633582 2777.979937 2761.606212 2406.057915 2708.726437 2430.471746 1.026433752 0.936692711 0.982546715 0.788084066 1.109098917 1.142979729 1.136242878 0.989955106 1.114485878 1 11.24702065 SFS(ph)ADNFIGIQR ddPTM_HeLa_Romidepsin_16h_R1 2 SFSADNFIGIQR 12 0 Q8N7R7-3;Q8N7R7-2;Q8N7R7 Q8N7R7-3 CCNYL1 Cyclin-Y-like protein 1 1 0 S(0.003)FS(0.997)ADNFIGIQR;S(0.39)FS(0.61)ADNFIGIQR ; 157.09 0.0011237 46976000 2131.41 2635.73 2415.5 1604.78 3508.7 5721.2 3524.1 6187.8 2385 2584.1 TRUE FALSE FALSE 2105.431555 2672.835876 2457.540764 1790.332214 3329.637946 5355.633784 3823.436966 6366.83423 2171.679627 2516.964709 0.836496256 1.061928229 0.976390632 0.711306046 1.32287828 2.127814412 1.519066577 2.529568335 0.862816876 1 11.29746927 -8.436080329 3.41637696 0.92455981 2.004466326 0.80722354 0.250277075 0.072692077 1.606063453 0.032542656 0.076525773 3.66E-09 8.436080329 1.079906515 up SFS(ph)ASQSTDREGASPVTEVR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSASQSTDREGASPVTEVR 20 1 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 S(0.029)FS(0.859)AS(0.021)QS(0.021)T(0.036)DREGAS(0.025)PVT(0.008)EVR 96.561 0.0066258 3702900 2307.7 2290.6 1798.5 3030.6 1609.3 1527 1622.4 1547.4 2638.2 2229 TRUE FALSE FALSE 2279.572865 2322.847127 1829.802138 3381.012231 1527.171416 1429.429628 1760.206616 1592.171578 2402.232785 2171.090259 1.04996688 1.069898922 0.842803348 1.557287735 0.703412219 0.658392539 0.810747784 0.733351168 1.106463803 1 11.08420399 SFS(ph)EDVISHK ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEDVISHK 10 0 F6QMI7;E9PHM6;F8W9J4;Q03001-14;Q03001;Q03001-8;H0YC82;Q03001-10;A0A494C1D7 F6QMI7;A0A494C1D7 DST Dystonin 1 0 S(0.074)FS(0.926)EDVISHK 105.17 0.0088762 10830000 5332 5103.2 4362.2 3926.2 4964.6 5554.9 4411.2 4567.9 5666.3 4724.1 TRUE FALSE FALSE 5267.011533 5175.042984 4438.122261 4380.165717 4711.237937 5199.959818 4785.887218 4700.06498 5159.491936 4601.367201 1.144662293 1.124675071 0.964522514 0.951927009 1.023877846 1.130090165 1.040101128 1.021449664 1.121295413 1 12.16784688 -9.768429204 24.98246706 1.074448656 1.024631869 0.245584683 0.059548684 308.0580212 1101036.288 0.012026719 0.01600068 1.70E-10 9.768429204 -0.049816787 SFS(ph)EGGER ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEGGER 8 0 G3V2D5;G3V515;G3V2P5;Q07352 G3V2D5 ZFP36L1 "Zinc finger protein 36, C3H1 type-like 1" 1 0 S(0.017)FS(0.983)EGGER 104.42 0.027283 10331000 3847.3 4721.5 3504 3998.3 1765.1 1748.4 1517.7 1871.2 3922.1 4098.1 TRUE FALSE FALSE 3800.407628 4787.969401 3564.98565 4460.602259 1675.020361 1636.682883 1646.6134 1925.34022 3571.297553 3991.630771 0.95209398 1.199502077 0.893115084 1.117488694 0.419633091 0.410028627 0.412516461 0.482344267 0.894696368 1 11.96276256 -8.754524666 24.99997522 0.997096388 0.42829361 0.906838818 0.090759581 30.3485611 109723.4736 0.011656163 0.022909573 1.76E-09 8.754524666 -0.568802778 SFS(ph)LEGLTGGAGVGNKPSSSLEVSSANAEELR ddPTM_HeLa_Romidepsin_16h_R1 2 SFSLEGLTGGAGVGNKPSSSLEVSSANAEELR 32 1 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;H0YMW2;H0YLH1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 S(0.049)FS(0.667)LEGLT(0.203)GGAGVGNKPS(0.039)S(0.005)S(0.037)LEVS(0.001)SANAEELR;S(0.152)FS(0.434)LEGLT(0.412)GGAGVGNKPS(0.001)S(0.001)SLEVSSANAEELR ; 106.03 2.92E-13 61459000 1874.98 2055.71 2208.34 1779.14 2926.5 3676.5 2768.09 2946.2 2109.97 2178.7 TRUE FALSE FALSE 1852.127023 2084.650339 2246.775231 1984.852538 2777.149785 3441.583515 3003.211496 3031.443649 1921.248999 2122.09706 0.872781485 0.982353908 1.058752342 0.935325992 1.308681793 1.621784215 1.4152093 1.428513194 0.90535397 1 11.05127493 -8.639481495 3.496207179 0.951019912 1.481027166 0.916394237 0.072994557 0.048813255 1.159108636 0.011616016 0.024434733 2.29E-09 8.639481495 0.530007254 SFS(ph)SPENFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSSPENFQR 10 0 G3V1T9;I3L521;F5GXV8;F5GY08;J3KPD3;Q9Y580 G3V1T9 RBM7 RNA-binding protein 7 1 0 S(0.001)FS(0.499)S(0.499)PENFQR 197.73 4.50E-09 14831000 2701.8 2014.1 2469.4 1901 2782.7 2420.4 2411.1 2438.4 2483.6 2445.1 TRUE FALSE FALSE 2668.869422 2042.454553 2512.378871 2120.802564 2640.688435 2265.744251 2615.898774 2508.951257 2261.460596 2381.57595 1.120631665 0.857606306 1.054922843 0.890503855 1.10879875 0.951363425 1.098389818 1.053483622 0.94956476 1 11.21770084 SFS(ph)SSAEEHS ddPTM_HeLa_Romidepsin_16h_R1 2 SFSSSAEEHS 10 0 Q96EQ0 Q96EQ0 SGTB Small glutamine-rich tetratricopeptide repeat-containing protein beta 1 0 S(0.002)FS(0.76)S(0.202)S(0.036)AEEHS;SFS(1)SSAEEHS ; 227.99 6.80E-27 50653000 7726.4 7248.6 8005.8 7794.8 15129.8 17237.9 14343.6 16394 9612.6 7974.7 TRUE FALSE FALSE 7632.227665 7350.645981 8145.137591 8696.071452 14357.66985 16136.45382 15561.94503 16868.33452 8752.824981 7767.516144 0.982582787 0.9463316 1.04861547 1.119543402 1.848424848 2.07742778 2.00346478 2.171651041 1.126849924 1 12.92323762 -8.724720693 2.594486018 0.99152929 2.074354112 0.983378355 0.063499213 0.016360711 0.22453975 0.006855563 0.014568704 1.88E-09 8.724720693 1.082824822 up SFSASQSTDREGAS(ph)PVTEVR ddPTM_HeLa_Romidepsin_16h_R1 2 SFSASQSTDREGASPVTEVR 20 1 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 SFS(0.001)AS(0.005)QS(0.054)T(0.172)DREGAS(0.718)PVT(0.05)EVR;S(0.002)FS(0.004)AS(0.032)QS(0.066)T(0.066)DREGAS(0.415)PVT(0.415)EVR ; 69.649 0.0034785 17022200 1920.43 1731.94 1842.36 1861.46 1923.65 1757.85 1544.8 1401.02 2061.75 1984.01 TRUE FALSE FALSE 1897.02306 1756.322297 1874.425503 2076.690764 1825.478962 1645.529058 1676.015273 1441.556303 1877.341916 1932.465134 0.981659657 0.908850704 0.969966014 1.074632979 0.944637463 0.85151811 0.867293926 0.745967561 0.971475181 1 10.91622667 -7.942639096 1.300663048 0.988154707 0.770113999 0.722242927 0.046065936 0.217403272 0.602440665 0.006904979 0.045054481 1.14E-08 7.942639096 -0.218040709 SFSEDAVTDSSGSGT(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEDAVTDSSGSGTLPR 18 0 Q27J81-2;A0A0A0MQU1;Q27J81 Q27J81-2 INF2 Inverted formin-2 1 0 SFSEDAVT(0.022)DS(0.017)S(0.01)GS(0.043)GT(0.908)LPR 108.96 0.0028486 1628600 809.13 859.39 888.09 694.83 1039.3 549.96 599.06 639.22 566.1 472.43 TRUE FALSE FALSE 799.2680123 871.488515 903.5468339 775.1695139 986.2606428 514.8193309 649.9441414 657.7148222 515.4665982 460.1562005 1.736949348 1.893897146 1.963565487 1.684579091 2.143317077 1.118792554 1.412442429 1.429329479 1.120199179 1 8.845979858 -12.15396794 0.92735782 1.003747379 1.676792811 0.422785646 0.284376533 0.434917448 0.679615832 0.192044253 0.056447959 7.02E-13 12.15396794 0.673045432 SFSEDT(ph)LMDGPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSEDTLMDGPAR 13 0 Q9BRG2;M0QZQ6 Q9BRG2 SH2D3A SH2 domain-containing protein 3A 1 0 SFS(0.003)EDT(0.997)LMDGPAR 141.73 0.00234 26160000 3778.8 3581.7 3802.2 4080.8 4788.8 5172.4 4945 5170.2 3985.2 3564.2 TRUE FALSE FALSE 3732.742532 3632.123267 3868.375696 4552.641297 4544.409667 4841.900333 5365.028177 5319.79158 3628.753731 3471.60157 1.075222043 1.046238514 1.114291378 1.311395102 1.309023969 1.394716598 1.545404352 1.532373883 1.045267914 1 11.76138567 -8.589700839 0.590728145 1.021415271 1.613295135 0.961810996 0.038518267 0.15376439 0.082026217 0.008530463 0.047176465 2.57E-09 8.589700839 0.591879864 SFSKEELMS(ph)SDLEETAGSTSIPK ddPTM_HeLa_Romidepsin_16h_R1 3 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 0 SFSKEELMS(0.285)S(0.233)DLEET(0.285)AGS(0.065)T(0.065)S(0.065)IPK;S(0.001)FSKEELMS(0.498)S(0.498)DLEET(0.002)AGS(0.001)T(0.001)SIPK;S(0.001)FS(0.005)KEELMS(0.497)S(0.497)DLEET(0.001)AGSTSIPK ;; 70.15 0.0019609 383797100 8505.1 7709.5 8349.7 9329.5 7687.8 7416.7 7377.2 7937 9554.8 9070.3 TRUE FALSE FALSE 8401.43657 7818.034543 8495.023026 10408.22069 7295.462879 6942.796806 8003.819184 8166.644572 8700.194758 8834.652298 0.950964032 0.88492838 0.961557143 1.178113222 0.825778155 0.785859655 0.905957463 0.924387774 0.984780664 1 13.10895764 SFSKEELMS(ph)SDLEETAGSTSIPKR ddPTM_HeLa_Romidepsin_16h_R1 1 SFSKEELMSSDLEETAGSTSIPKR 24 2 O00567 O00567 NOP56 Nucleolar protein 56 1 0 S(0.002)FS(0.004)KEELMS(0.495)S(0.495)DLEET(0.002)AGSTSIPKR 54.626 0.010984 9084400 835.99 826.11 896.63 1393.9 833.85 871.47 763.99 861.71 954.67 989.41 TRUE FALSE FALSE 825.8006323 837.7399983 912.235469 1555.069276 791.295523 815.7858795 828.8832915 886.6422193 869.2819242 963.7049856 0.856901899 0.869290925 0.946592041 1.613636227 0.82109726 0.846509971 0.860100657 0.920034899 0.902020781 1 9.912447758 SFSKEELMSS(ph)DLEETAGSTSIPK ddPTM_HeLa_Romidepsin_16h_R1 1 SFSKEELMSSDLEETAGSTSIPK 23 1 O00567 O00567 NOP56 Nucleolar protein 56 1 0 SFS(0.001)KEELMS(0.412)S(0.571)DLEET(0.012)AGS(0.002)T(0.001)SIPK 63.158 0.0061859 255870000 3996.3 3716.3 3686.1 4380.1 4163 3412.8 3409.6 4188.3 4674.2 4277.3 TRUE FALSE FALSE 3947.591558 3768.618169 3750.255024 4886.547771 3950.546576 3194.733094 3699.211339 4309.481852 4256.127845 4166.175129 0.947533754 0.904575072 0.900167398 1.172909832 0.948243041 0.766826404 0.887915468 1.034397671 1.021591199 1 12.02450777 -9.813481908 0.009615434 1.904939571 3.19E-05 0.050194351 0.100193105 3944.142103 23.7939602 2326.860083 2384.966409 1.54E-10 9.813481908 -1.904907639 SFSLASSSNS(ph)PISQR ddPTM_HeLa_Romidepsin_16h_R1 3 SFSLASSSNSPISQR 15 0 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 0 SFSLASS(0.004)S(0.001)NS(0.992)PIS(0.003)QR;SFSLASSSNS(0.923)PIS(0.077)QR;SFSLASSSNS(0.993)PIS(0.007)QR ;; 278.89 1.58E-99 470117000 9339.1 8143.24 9778.8 7543.94 9441 8582.41 7553.6 7850.24 8823.13 8371.7 TRUE FALSE FALSE 9225.271457 8257.880746 9948.995912 8416.205838 8959.190541 8034.021699 8195.202595 8077.374309 8033.967155 8154.202027 1.131351839 1.01271476 1.220106625 1.03213114 1.098720698 0.985261546 1.005028152 0.990578144 0.985254857 1 12.99332799 -8.253184301 24.66279722 1.071544333 0.994763161 0.210018129 0.066466682 635.1648173 1897603.571 0.009569031 0.023971491 5.58E-09 8.253184301 -0.076781171 SFT(ph)PDHVVYAR ddPTM_HeLa_Romidepsin_16h_R1 3 SFTPDHVVYAR 11 0 Q6NZI2-3;Q6NZI2-2;Q6NZI2 Q6NZI2-3 PTRF Polymerase I and transcript release factor 1 0 S(0.235)FT(0.765)PDHVVYAR;S(0.005)FT(0.995)PDHVVYAR;S(0.201)FT(0.799)PDHVVYAR ;; 110.92 0.01063 48938000 9963 10244.7 9819.8 10482.9 17468.3 21215.6 17336.7 17443.5 13060.2 11286.6 TRUE FALSE FALSE 9841.567124 10388.92516 9990.7095 11694.98222 16576.82747 19859.99163 18809.27887 17948.20015 11892.063 10993.3725 0.895227294 0.945017114 0.908793866 1.063821154 1.50789282 1.806542225 1.710965298 1.632638223 1.081748389 1 13.42434642 -8.713093366 2.612881041 0.946295581 1.71453138 0.963730687 0.065852216 0.028683567 0.398743459 0.008543176 0.018232936 1.94E-09 8.713093366 0.7682358 SFTPDHVVYAR ddPTM_HeLa_Romidepsin_16h_R1 1 SFTPDHVVYAR 11 0 Q6NZI2-3;Q6NZI2-2;Q6NZI2 Q6NZI2-3 PTRF Polymerase I and transcript release factor 0 0 106.62 0.0075452 7800900 2744.7 2614.9 2213.5 1978.7 3200.1 3006.8 2500.6 2353.7 2979.3 2541 FALSE FALSE TRUE 2711.246541 2651.712631 2252.025039 2207.486604 3036.786956 2814.675184 2713.000902 2421.800596 2712.823946 2474.984454 1.095460029 1.071405773 0.909914822 0.891919382 1.226992336 1.137249642 1.096168866 0.978511438 1.096097368 1 11.27320375 -8.753234193 24.99930522 1.027485853 1.110727477 0.222732334 0.08725119 268.5802823 818295.6946 0.013367014 0.026370548 1.77E-09 8.753234193 0.083241624 SFTSS(ph)SPSS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 SFTSSSPSSPSR 12 0 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 2 0 S(0.002)FT(0.019)S(0.314)S(0.529)S(0.136)PS(0.003)S(0.947)PS(0.051)R 148.78 0.015049 20479000 5858.5 5889.3 5708.4 4373.7 4904.8 3546.4 2940.3 2892.6 5665.1 5326.2 TRUE FALSE FALSE 5787.094349 5972.20972 5807.752307 4879.407773 4654.489754 3319.796485 3190.049009 2976.292817 5158.399267 5187.824556 1.115514661 1.151197319 1.119496669 0.940549882 0.897194904 0.639920732 0.614910735 0.5737073 0.99432801 1 12.34091398 -8.437299695 1.443136184 1.067507102 0.578966899 0.929459302 0.055294823 0.086144024 0.342832806 0.009786935 0.031896088 3.65E-09 8.437299695 -0.488540203 SFTSSSPS(ph)SPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SFTSSSPSSPSR 12 0 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 SFT(0.03)S(0.03)S(0.29)S(0.29)PS(0.352)S(0.007)PSR 132.86 0.0030931 175010000 3181.3 3453 3245.7 2621.7 2733.5 2589.3 2691.4 3003.1 3511.4 3437.3 TRUE FALSE FALSE 3142.525092 3501.611425 3302.190047 2924.833289 2593.999295 2423.852087 2920.007449 3089.98996 3197.33159 3347.99845 0.938628001 1.045882033 0.986317675 0.873606524 0.774791068 0.723970492 0.872165114 0.922936497 0.95499793 1 11.70908314 -9.115904074 3.700498844 0.978019567 0.820077449 0.64695908 0.056692879 0.125134289 3.090270959 0.009205733 0.015855678 7.66E-10 9.115904074 -0.157942118 SFTSSSPSS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 SFTSSSPSSPSR 12 0 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 SFT(0.002)S(0.013)S(0.164)S(0.164)PS(0.045)S(0.565)PS(0.047)R 171.67 0.00011744 190300000 2561.9 2418.3 2412.2 2410.4 2165.7 2068.2 2268.1 2079 2862.5 2754.6 TRUE FALSE FALSE 2530.674577 2452.344891 2454.183329 2689.101789 2055.176248 1936.048695 2460.752357 2139.152585 2606.470831 2683.035095 0.943213371 0.914018939 0.914704147 1.002261131 0.765989327 0.721589031 0.917152505 0.797288335 0.971463562 1 11.38965021 -8.761336616 25 0.964573263 0.803199924 0.667963529 0.054117417 1.276210568 310304.2125 0.008305136 0.015801803 1.73E-09 8.761336616 -0.161373338 SFVLNLGK ddPTM_HeLa_Romidepsin_16h_R1 2 SFVLNLGK 8 0 P09382 P09382 LGALS1 Galectin-1 0 0 ; ; 125.96 0.014465 13610300 2133.91 1488.22 7509 4091.4 6730.3 6426.4 3756.9 1450.13 1496.29 726.56 FALSE FALSE TRUE 2107.901084 1509.1712 7639.690995 4564.466919 6386.827677 6015.77378 4076.010992 1492.087224 1362.458075 707.6838665 2.978591408 2.132549959 10.7953443 6.449867144 9.024972844 8.500651301 5.75964945 2.108409269 1.925235461 1 9.466961219 -9.835889092 11.05650142 1.971237664 7.164411847 0.562646286 2.201319878 0.267396678 38.36829631 0.3614202 0.475177911 1.46E-10 9.835889092 5.193174182 SGADPVTSVGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SGADPVTSVGKR 12 1 Q92994-9;Q92994-3;Q92994-7;Q92994-8;Q92994-5;Q92994 Q92994-9 BRF1 Transcription factor IIIB 90 kDa subunit 0 1 ; SGADPVTSVGK(1)R;SGADPVTSVGK(1)R 187.42 2.98E-07 21627000 8133.1 7906.8 6231.8 5799 6685.8 5935.7 7861.8 6806.8 10253.8 7857.3 FALSE TRUE FALSE 8033.970649 8018.112138 6340.261865 6469.507665 6344.598678 5556.427927 8529.581096 7003.744019 9336.674447 7653.166213 1.049757764 1.047685613 0.828449519 0.845337405 0.829016188 0.726029956 1.11451664 0.915143331 1.219975391 1 12.90184102 -9.767736253 24.93433849 1.025967423 0.87683542 0.410299625 0.112104071 118.3876066 468790.3724 0.015313425 0.020404049 1.71E-10 9.767736253 -0.149132004 SGALLLALLLQASMEVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGALLLALLLQASMEVR 17 0 E9PHK5;P01189 E9PHK5 POMC Pro-opiomelanocortin;NPP;Melanotropin gamma;Potential peptide;Corticotropin;Melanotropin alpha;Corticotropin-like intermediary peptide;Lipotropin beta;Lipotropin gamma;Melanotropin beta;Beta-endorphin;Met-enkephalin 0 0 41.743 0.026705 879330 952.3 484.56 711.69 566 721.85 1059.7 703.1 797.79 508.04 750.87 FALSE FALSE TRUE 940.6930013 491.3816484 724.0766659 631.4435831 685.0113009 991.98859 762.8212965 820.8727949 462.59963 731.3622892 1.28622027 0.671871733 0.990038284 0.863380014 0.936623765 1.356357314 1.04301426 1.122388736 0.632517751 1 9.514442429 -8.292883741 24.99172274 1.058903786 1.160829777 0 0.223216259 1754.569251 1394513.984 0.029869765 0.066797821 5.09E-09 8.292883741 0.10192599 SGAMS(ph)PMSWNSDASTSEAS ddPTM_HeLa_Romidepsin_16h_R1 4 SGAMSPMSWNSDASTSEAS 19 0 Q13158 Q13158 FADD FAS-associated death domain protein 1 0 S(0.068)GAMS(0.931)PMSWNSDASTSEAS;S(0.068)GAMS(0.931)PMSWNSDASTSEAS;S(0.022)GAMS(0.96)PMS(0.018)WNSDASTSEAS;S(0.06)GAMS(0.939)PMS(0.001)WNSDASTSEAS ;;; 66.436 0.014393 36141500 8988.1 8412 7049.2 6717.6 6830.5 6408.7 5149.9 5478.6 8781.5 8086 TRUE FALSE FALSE 8878.54958 8530.424357 7171.888369 7494.320519 6481.914097 5999.204753 5587.332377 5637.114647 7996.060646 7875.924554 1.127302518 1.08310133 0.910609074 0.951548033 0.823003579 0.76171435 0.709419236 0.715740052 1.015253586 1 12.94323358 -8.829431562 0.971291379 1.06160718 0.706375634 0.889152188 0.047740989 0.148409307 0.269450417 0.01022715 0.030771506 1.48E-09 8.829431562 -0.355231546 SGAMVK(ac)MAAAGGGGGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 SGAMVKMAAAGGGGGGGR 18 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 0 1 ; SGAMVK(1)MAAAGGGGGGGR;SGAMVK(1)MAAAGGGGGGGR 97.273 0.0030354 1222280 572.31 424.74 218.91 187.585 412.4 523.57 392.24 298.35 786.98 555.63 FALSE TRUE FALSE 565.3344656 430.7195009 222.7200367 209.2744603 391.3536891 490.1155667 425.5568558 306.9822865 716.5905378 541.1946525 1.044604678 0.795867991 0.411534068 0.386689815 0.723129261 0.905617904 0.786328641 0.56723082 1.324090204 1 9.080003774 -10.08431677 4.150758948 1.019969213 0.640094452 0.587365071 0.177946155 0.131530233 4.156816424 0.027461024 0.034214681 8.24E-11 10.08431677 -0.37987476 SGAQASS(ph)TPLSPTR ddPTM_HeLa_Romidepsin_16h_R1 3 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 SGAQAS(0.178)S(0.356)T(0.356)PLS(0.104)PT(0.005)R;S(0.003)GAQAS(0.316)S(0.541)T(0.138)PLS(0.001)PTR;SGAQAS(0.385)S(0.557)T(0.052)PLS(0.003)PT(0.003)R ;; 159.4 0.00037718 44372400 7405.4 9525.9 6323.5 7368 7793.8 6944.5 6202.6 7416.1 8031.1 7440.2 TRUE FALSE FALSE 7315.140136 9660.00587 6433.557865 8219.922827 7396.053303 6500.768862 6729.448689 7630.673153 7312.778302 7246.902531 1.009416106 1.332984103 0.887766578 1.13426706 1.020581313 0.897041023 0.92859655 1.052956504 1.009090197 1 12.82314878 -8.486820733 20.49858127 1.032202802 0.956833105 0.102591234 0.117239446 141.4423446 80406.09768 0.016056924 0.035870254 3.26E-09 8.486820733 -0.075369696 SGAQASST(ph)PLS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 2 0 SGAQAS(0.071)S(0.375)T(0.554)PLS(0.685)PT(0.315)R 151.73 0.0025624 150870000 4103.4 3559.4 3550.2 3931.3 5801 7738.9 5156.4 6137.9 3642.1 3189.3 TRUE FALSE FALSE 4053.386182 3609.509327 3611.989742 4385.855403 5504.953323 7244.409266 5594.384487 6315.490452 3316.341454 3106.441526 1.304832603 1.161943431 1.162741906 1.411858349 1.772109108 2.332060399 1.80089805 2.033030527 1.067569251 1 11.60104718 -8.790180844 2.145061667 1.1514456 2.03507926 0.884793195 0.146057225 0.079936369 0.749926019 0.024630693 0.052779067 1.62E-09 8.790180844 0.883633661 SGAQASST(ph)PLSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 2 0 SGAQAS(0.01)S(0.4)T(0.589)PLS(0.141)PT(0.859)R 140.49 0.01837 34326000 4677.3 4047 4364.1 4833.5 6661.6 8483.2 7877.6 8233 5413.3 5143.5 TRUE FALSE FALSE 4620.291269 4103.973772 4440.05533 5392.372012 6321.633694 7941.150898 8546.723147 8471.208865 4929.12089 5009.871129 0.922237549 0.819177513 0.886261386 1.076349446 1.261835591 1.585100833 1.705976647 1.690903548 0.983881773 1 12.29055778 -8.445631004 1.537566703 0.9447226 1.709957707 0.972277928 0.054495583 0.052617705 0.239540141 0.0099422 0.030874919 3.58E-09 8.445631004 0.765235106 SGAQASST(ph)PLSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 S(0.195)GAQAS(0.034)S(0.3)T(0.47)PLS(0.001)PT(0.001)R 168.47 0.00014975 12090000 3446.3 3129.7 3296.1 3105.4 3358.9 2777.1 2842.3 3107 3456.4 3205.1 TRUE FALSE FALSE 3404.29517 3173.759999 3353.467238 3464.460959 3187.482799 2599.652273 3083.724891 3196.896143 3147.250927 3121.83104 1.090480275 1.016634135 1.074198826 1.109752871 1.021029889 0.832733175 0.987793654 1.024045216 1.008142621 1 11.60817674 -8.506186146 24.95310612 1.049040365 0.947939398 0.394104532 0.056406472 570.7130455 853135.7067 0.008412248 0.018380975 3.12E-09 8.506186146 -0.101100968 SGAQASSTPLS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 6 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 SGAQAS(0.001)S(0.003)T(0.003)PLS(0.551)PT(0.441)R;SGAQASSTPLS(0.968)PT(0.032)R;SGAQASS(0.001)T(0.002)PLS(0.98)PT(0.017)R;SGAQASS(0.001)TPLS(0.5)PT(0.5)R;SGAQASST(0.001)PLS(0.956)PT(0.043)R;SGAQASSTPLS(0.679)PT(0.321)R ;;;;; 142.19 0.00074081 4406105700 10844.83 10727 10807.65 9824.7 11952.16 12643.43 10759.36 10805.17 12391.63 10772.8 TRUE FALSE FALSE 10712.64904 10878.01499 10995.75261 10960.67804 11342.19668 11835.55563 11673.25977 11117.80055 11283.29158 10492.9211 1.020940588 1.036700351 1.047921023 1.044578334 1.080937955 1.12795622 1.112489044 1.059552477 1.075324161 1 13.35712874 -9.293267923 0.684281909 1.007035946 1.104475841 0.402998752 0.029007871 0.238386675 0.218158519 0.004296288 0.010661358 5.09E-10 9.293267923 0.097439895 SGAQASSTPLSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 S(0.007)GAQAS(0.004)S(0.03)T(0.042)PLS(0.1)PT(0.817)R;SGAQASSTPLS(0.23)PT(0.77)R ; 169.15 0.00013684 565280000 6934.9 7749.9 6897.9 7022.5 7869 7250.8 5796 6642.8 7355.6 7432.5 TRUE FALSE FALSE 6850.374771 7859.003296 7017.955056 7834.474492 7467.415567 6787.497281 6288.312095 6834.998937 6697.696714 7239.402579 0.946262443 1.085587272 0.969410801 1.082199036 1.031496106 0.93757699 0.86862307 0.944138534 0.925172573 1 12.82165493 -8.043746739 6.044762157 0.993600554 0.905289596 0.365413633 0.053070595 0.16427798 15.78164616 0.007388065 0.019716821 9.04E-09 8.043746739 -0.088310958 SGAQASSTPLSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SGAQASSTPLSPTR 14 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 157.5 0.00032412 0 1562.3 1616.6 1668 1628 1969.2 2006.1 1607.6 1481.5 1827.8 1741.7 FALSE FALSE TRUE 1543.258087 1639.358537 1697.03084 1816.23702 1868.704376 1877.916684 1744.149504 1524.364865 1664.31699 1696.450383 0.909698334 0.966346292 1.00034216 1.070610162 1.10153789 1.106968234 1.028117015 0.89856142 0.981058454 1 10.72830352 -9.559825065 3.132462428 0.956856327 1.047094631 0.269564489 0.058632228 0.24119416 4.873843426 0.01032657 0.015354 2.76E-10 9.559825065 0.090238305 SGCSEAQPPES(ph)PETR ddPTM_HeLa_Romidepsin_16h_R1 1 SGCSEAQPPESPETR 15 0 A0A494BZT8;Q9Y6A5;H0Y8F2;A0A494C117 A0A494BZT8 TACC3 Transforming acidic coiled-coil-containing protein 3 1 0 SGCSEAQPPES(0.951)PET(0.049)R 160.63 0.00022317 10499000 1082.3 1097.5 1127.4 137.73 2012.7 1662 1698.6 1758.2 1496.5 1332.1 TRUE FALSE FALSE 1069.108511 1112.950634 1147.021924 153.6549906 1909.984409 1555.803564 1842.879042 1809.070743 1362.649292 1297.49185 0.823980907 0.857770809 0.884030157 0.118424629 1.472058887 1.199085423 1.42033959 1.394282934 1.050217997 1 10.34150976 SGDAAIVDMVPGKPMCVESFSDYPPLGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGDAAIVDMVPGKPMCVESFSDYPPLGR 28 1 Q5VTE0;P68104;A0A087WVQ9 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1 0 0 51.22 0.0094513 13240000 1384.5 1124.7 1100.1 248.86 1306.2 1007.7 937.83 1184.6 1300 1500.6 FALSE FALSE TRUE 1367.625181 1140.533556 1119.246779 277.6343641 1239.53974 943.3112222 1017.489257 1218.874532 1183.724744 1461.614196 0.935695059 0.78032463 0.765760747 0.189950512 0.848062193 0.645390025 0.696140787 0.833923573 0.809874964 1 10.51334684 -10.07271242 1.907437534 0.973490657 0.650519243 0.271576907 0.180221514 0.23360248 1.653239403 0.029767301 0.037925188 8.46E-11 10.07271242 -0.322971414 SGDEGS(ph)EDEAPSGED ddPTM_HeLa_Romidepsin_16h_R1 2 SGDEGSEDEAPSGED 15 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 S(0.002)GDEGS(0.998)EDEAPSGED;S(0.003)GDEGS(0.996)EDEAPS(0.001)GED ; 170.95 1.91E-05 15816300 6961 7028.1 6645.4 5160.2 5322.3 6165 5392.7 4928.4 7350.4 6844.6 TRUE FALSE FALSE 6876.156655 7127.041776 6761.060399 5756.846603 5050.683171 5771.076397 5850.755803 5070.995478 6692.961815 6666.776305 1.031406536 1.069038685 1.014142382 0.863512789 0.757590016 0.865647223 0.877598938 0.760636812 1.003927762 1 12.7027736 -9.205416208 3.877891925 1.020507001 0.822536832 0.859241085 0.040487633 0.063121755 1.950608916 0.006118999 0.010262935 6.23E-10 9.205416208 -0.197970169 SGDET(ph)PGSEVPGDKAAEEQGDDQDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGDETPGSEVPGDKAAEEQGDDQDSEK 27 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.066)GDET(0.481)PGS(0.452)EVPGDKAAEEQGDDQDSEK 55.629 0.0025223 15818000 2997.3 2971.4 2744.5 2868 2661 2920.3 2385.8 2775.9 3398.2 2588.2 TRUE FALSE FALSE 2960.767755 3013.231447 2792.266871 3199.611654 2525.19924 2733.702255 2588.449792 2856.216287 3094.256481 2520.958191 1.174461269 1.195272281 1.107621253 1.269204569 1.001682316 1.08439016 1.026772202 1.13298836 1.227412851 1 11.29975648 -6.911235844 19.18362415 1.096984872 2.950847179 0 0.092749292 1386.054249 334701.7078 0.012844354 13058.90487 1.23E-07 6.911235844 1.853862307 SGDETPGS(ph)EVPGDKAAEEQGDDQDSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGDETPGSEVPGDKAAEEQGDDQDSEK 27 1 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.061)GDET(0.418)PGS(0.519)EVPGDKAAEEQGDDQDS(0.002)EK 48.489 0.013665 22213000 1518 1603.1 1487.4 1045.8 1606.8 1600.1 1023.7 1544.7 1545.1 1537 TRUE FALSE FALSE 1499.498032 1625.668484 1513.287573 1166.720317 1524.799 1497.858774 1110.653052 1589.393457 1406.902386 1497.068518 1.001622847 1.085901189 1.010833876 0.779336618 1.018523188 1.000527869 0.74188525 1.061670483 0.939771539 1 10.54792454 SGEDESQEDVLMDEAPS(ph)NLSQASTLQANR ddPTM_HeLa_Romidepsin_16h_R1 1 SGEDESQEDVLMDEAPSNLSQASTLQANR 29 0 Q7Z6Z7-2;Q7Z6Z7-3;Q7Z6Z7 Q7Z6Z7-2 HUWE1 E3 ubiquitin-protein ligase HUWE1 1 0 SGEDES(0.007)QEDVLMDEAPS(0.526)NLS(0.439)QAS(0.023)T(0.005)LQANR 62.683 0.00034171 2833400 750.46 876.72 815.83 649.83 720.26 679.48 436.31 641.79 727.07 847.32 TRUE FALSE FALSE 741.3131049 889.0624872 830.0291789 724.9664021 683.5024445 636.0634209 473.3701605 660.3591811 662.0390382 825.3065043 0.898227629 1.077251279 1.005722328 0.878420803 0.828180126 0.770699634 0.57356892 0.800138103 0.802173538 1 9.6887862 -8.537811553 1.495862627 0.964560189 0.690047274 0.582168466 0.088552579 0.167892797 0.735067898 0.011557877 0.033749972 2.90E-09 8.537811553 -0.274512916 SGEEDEEILFK ddPTM_HeLa_Romidepsin_16h_R1 1 SGEEDEEILFK 11 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 0 0 157.66 0.0011908 0 1010.7 892.33 993.1 1073.9 1122.1 1042.1 950.59 1085.7 1259.8 1129.8 FALSE FALSE TRUE 998.3811996 904.8922452 1010.384489 1198.069371 1064.83505 975.5131732 1031.333091 1117.113017 1147.120333 1100.447633 0.907250077 0.82229469 0.918157719 1.088710934 0.967638094 0.886469418 0.937194156 1.015144186 1.042412468 1 10.10387478 SGEHDFGAAFDGDGDR ddPTM_HeLa_Romidepsin_16h_R1 2 SGEHDFGAAFDGDGDR 16 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 0 ; ; 137.39 0.00052143 26892000 6236.6 5915.3 5771.1 4639.4 8493.4 8277.2 6485.8 7155.3 8723.6 7877.4 FALSE FALSE TRUE 6160.58592 5998.575749 5871.543575 5175.829257 8059.950105 7748.313633 7036.70369 7362.327316 7943.339367 7672.744012 0.802918214 0.78180319 0.765246901 0.674573431 1.050465139 1.0098491 0.91710393 0.959542936 1.03526709 1 12.90552691 SGEISLPIKEEPS(ph)PISK ddPTM_HeLa_Romidepsin_16h_R1 2 SGEISLPIKEEPSPISK 17 1 Q9ULH7-4;Q9ULH7;Q9ULH7-5;I3L2A0 Q9ULH7-4 MKL2 MKL/myocardin-like protein 2 1 0 SGEISLPIKEEPS(0.952)PIS(0.048)K;SGEISLPIKEEPS(0.969)PIS(0.03)K ; 84.403 0.005286 112109000 5693.7 5449.1 6097.7 6283.2 6227.5 6803.3 6082.1 6486.8 6464.3 5607.7 TRUE FALSE FALSE 5624.302994 5525.812573 6203.827911 7009.693147 5909.687437 6368.591087 6598.713422 6674.485324 5886.116818 5462.011146 1.029712837 1.011680941 1.13581385 1.283353871 1.081961805 1.165979145 1.208110574 1.221983102 1.077646431 1 12.41521654 -9.663531248 3.96319249 1.014064251 1.187487532 0.678168977 0.052213876 0.080304534 2.375252297 0.007456298 0.010628311 2.17E-10 9.663531248 0.173423281 SGEQAEGS(ph)PGGPGDSQGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGEQAEGSPGGPGDSQGR 18 0 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 0 SGEQAEGS(0.961)PGGPGDS(0.039)QGR 243.09 1.16E-61 16987000 730.93 805.51 899.67 1546.2 4889.7 4556.5 4015.2 4341 833.84 663.64 TRUE FALSE FALSE 722.021144 816.8499909 915.328379 1724.978919 4640.160363 4265.354355 4356.250988 4466.599986 759.259262 646.3985371 1.116990684 1.263694059 1.416043395 2.668599664 7.178482154 6.598644815 6.739264923 6.909978488 1.174599289 1 9.336280123 -8.88083802 3.155021498 1.116351391 6.864881594 0.990205728 0.26649493 0.018092038 0.359469162 0.045639203 0.08786193 1.32E-09 8.88083802 5.748530203 up SGEQAEGS(ph)PGGPGDSQGRK ddPTM_HeLa_Romidepsin_16h_R1 1 SGEQAEGSPGGPGDSQGRK 19 1 P38936 P38936 CDKN1A Cyclin-dependent kinase inhibitor 1 1 0 S(0.001)GEQAEGS(0.998)PGGPGDS(0.001)QGRK 72.158 0.0042956 2833800 711.53 558.49 453.38 674.32 1338.9 1364.2 1195.6 1365.2 573.15 467.42 TRUE FALSE FALSE 702.8575987 566.3524369 461.2708887 752.2880512 1270.570937 1277.032023 1297.154234 1404.699908 521.8860285 455.276361 1.543804289 1.243975056 1.013166789 1.6523767 2.790768521 2.80496009 2.849157886 3.085378527 1.146306009 1 8.830598743 -8.82567259 3.10807545 1.246530607 2.900746477 0.959845777 0.164020461 0.04681223 0.916896804 0.033716338 0.066450871 1.49E-09 8.82567259 1.654215871 up SGFEPASLKEEVGEEAIVELVENGKK ddPTM_HeLa_Romidepsin_16h_R1 1 SGFEPASLKEEVGEEAIVELVENGKK 26 2 P35579;B1AH99;Q5BKV1 P35579 MYH9 Myosin-9 0 0 121.35 7.79E-08 2958300 846.86 789.95 974.87 991.43 844.62 925.03 717.13 867.45 1026.4 998.07 FALSE FALSE TRUE 836.5381446 801.0709368 991.8372034 1106.063801 801.5158897 865.9235684 778.0430043 892.5482971 934.5962133 972.1399975 0.860512011 0.824028369 1.020261697 1.137761849 0.824486074 0.890739575 0.800340492 0.918127327 0.96138027 1 9.925020281 SGFGEISS(ph)PVIR ddPTM_HeLa_Romidepsin_16h_R1 4 SGFGEISSPVIR 12 0 G3V1T4;P57740 G3V1T4 NUP107 Nuclear pore complex protein Nup107 1 0 SGFGEIS(0.397)S(0.603)PVIR;SGFGEIS(0.208)S(0.792)PVIR;SGFGEIS(0.014)S(0.986)PVIR;SGFGEIS(0.017)S(0.983)PVIR ;;; 210.95 5.76E-21 289401900 17565.6 16285.7 17463.3 16165 22947.2 27217.7 23112.7 25448.8 19219.8 17611.4 TRUE FALSE FALSE 17351.50371 16514.97051 17767.24141 18034.07336 21776.11876 25478.57681 25075.89216 26185.12088 17500.73295 17153.85329 1.011522217 0.962755728 1.035758037 1.051313256 1.26945931 1.485297582 1.461822702 1.526486232 1.020221676 1 14.06624507 -8.557816447 1.818840984 1.003271309 1.500309216 0.98805615 0.02373085 0.022336479 0.146725862 0.003262843 0.008500265 2.77E-09 8.557816447 0.497037907 SGGDFKPTS(ph)PSLPASK ddPTM_HeLa_Romidepsin_16h_R1 1 SGGDFKPTSPSLPASK 16 1 Q5T5P2;Q5T5P2-2;Q5T5P2-7;Q5T5P2-10;Q5T5P2-9 Q5T5P2 KIAA1217 Sickle tail protein homolog 1 0 S(0.006)GGDFKPT(0.136)S(0.832)PS(0.023)LPAS(0.003)K 114.06 7.89E-05 0 2430.5 2330.3 2177.4 2177.7 2485.6 2121.5 1803.4 2051.3 2786.2 2199.2 TRUE FALSE FALSE 2400.876131 2363.106025 2215.296734 2429.49592 2358.750557 1985.942997 1956.580751 2110.651129 2536.995294 2142.064467 1.120823471 1.103190899 1.034187704 1.134184315 1.101157595 0.927116353 0.913408901 0.985335018 1.184369254 1 11.06478618 -8.255849422 24.97101007 1.06854898 0.939098963 0.58659767 0.056159895 272.8553604 1218871.943 0.007881182 0.019514621 5.55E-09 8.255849422 -0.129450017 SGGGGGGGGSS(ph)WGGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGGGGGGGGSSWGGR 15 0 Q13151 Q13151 HNRNPA0 Heterogeneous nuclear ribonucleoprotein A0 1 0 SGGGGGGGGS(0.044)S(0.956)WGGR 89.26 0.016708 2682600 1695 1567.2 1847.8 1091.9 1771.1 1715 1878.8 1223.1 1827.4 1932.9 TRUE FALSE FALSE 1674.340688 1589.263083 1879.960184 1218.150616 1680.714158 1605.417035 2038.385225 1258.488469 1663.952767 1882.682979 0.88933756 0.844148006 0.998553768 0.647029069 0.892722873 0.852728289 1.082702318 0.668454797 0.883819945 1 10.87857437 -11.74907455 0.529694109 1.010500577 0.858092426 0.036802551 0.128225043 1.484680234 0.762414324 0.108458522 0.03188663 1.78E-12 11.74907455 -0.152408151 SGGGPGPSGSET(ph)PPPPR ddPTM_HeLa_Romidepsin_16h_R1 2 SGGGPGPSGSETPPPPR 17 0 P27987-2;P27987 P27987-2 ITPKB Inositol-trisphosphate 3-kinase B 1 0 SGGGPGPS(0.004)GS(0.004)ET(0.992)PPPPR;SGGGPGPSGS(0.002)ET(0.998)PPPPR ; 142.19 0.00072869 7799600 1178.48 1174.08 943.24 853.76 673.46 688.6 618.18 671.87 1268.69 1068.41 TRUE FALSE FALSE 1164.116232 1190.608729 959.6566965 952.4757483 639.0908232 644.6006824 670.6881938 691.3094984 1155.215189 1040.652554 1.118640634 1.144098214 0.922168204 0.915267775 0.61412507 0.61941969 0.644488106 0.66430385 1.110087305 1 10.02327276 -9.005264721 1.760766047 1.06066555 0.629278207 0.913357694 0.061562011 0.077749348 0.480044632 0.010660403 0.021499385 9.88E-10 9.005264721 -0.431387343 SGGIVIS(ph)PFR ddPTM_HeLa_Romidepsin_16h_R1 2 SGGIVISPFR 10 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 SGGIVIS(1)PFR;SGGIVIS(1)PFR ; 126.66 0.0087633 36892000 5868.5 5667.1 6040.1 2776.5 5617.1 6608.8 5512.5 6757.3 6590.2 6552.1 TRUE FALSE FALSE 5796.972465 5746.881583 6145.225407 3097.531994 5330.438427 6186.519009 5980.731612 6952.811814 6000.756007 6381.875497 0.908349351 0.900500423 0.96291841 0.485363902 0.835246383 0.969388859 0.937143261 1.089462152 0.940280958 1 12.63976475 -11.36889994 0.801800006 0.989943907 0.875579808 0.045355237 0.149389645 1.134316627 1.53904798 0.0615352 0.0344806 4.28E-12 11.36889994 -0.114364099 SGGIVIS(ph)PFRLEELTNR ddPTM_HeLa_Romidepsin_16h_R1 1 SGGIVISPFRLEELTNR 17 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 SGGIVIS(0.998)PFRLEELT(0.001)NR 60.541 0.02198 90807000 3063.9 2895 2543.5 3497.7 3440.6 2710.8 2876.6 2954.2 3177.2 2939.1 TRUE FALSE FALSE 3026.556008 2935.755886 2587.768551 3902.120531 3265.013343 2537.588629 3120.938332 3039.675116 2893.023275 2862.741758 1.057222853 1.025504965 0.903947603 1.363071091 1.14051969 0.88641898 1.090192059 1.06180556 1.010577802 1 11.48318182 -11.36685944 0.491913988 0.999714815 1.074735265 0.04293377 0.123979412 2.944657481 1.533422433 0.097718779 0.041367266 4.30E-12 11.36685944 0.07502045 SGIETFS(ph)PPPPPPK ddPTM_HeLa_Romidepsin_16h_R1 2 SGIETFSPPPPPPK 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 S(0.011)GIET(0.023)FS(0.966)PPPPPPK;SGIET(0.006)FS(0.993)PPPPPPK ; 114.4 0.0048953 28678000 6557.6 6094.9 5789.8 7271.6 12291.3 13335.7 10847.8 11816.2 7103.7 6277.2 TRUE FALSE FALSE 6477.673449 6180.704162 5890.56904 8112.376606 11664.0291 12483.59181 11769.21186 12158.0831 6468.32728 6114.117439 1.059461732 1.010890652 0.96343734 1.326827083 1.907720814 2.041765133 1.924924076 1.988526263 1.057933111 1 12.57792855 -8.864336859 2.661406235 1.023743011 1.984668886 0.991374197 0.041783018 0.017373607 0.249651805 0.006671931 0.013234697 1.37E-09 8.864336859 0.960925875 SGK(ac)FMNPTDQAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGKFMNPTDQAR 12 1 F5H5G4;F5GXS9;Q9Y2W2 F5H5G4;Q9Y2W2 WBP11 WW domain-binding protein 11 0 1 SGK(1)FMNPTDQAR 110.64 0.0049328 47886000 761.3 589.28 1335.4 786.37 873.45 1022.9 1849.1 763.95 1403.2 717.92 FALSE TRUE FALSE 752.0209828 597.5758993 1358.642077 877.2937994 828.8745872 957.5399913 2006.162508 786.0536879 1277.694278 699.2683349 1.075439778 0.854573087 1.942948092 1.254588197 1.185345519 1.369345562 2.868945164 1.124108799 1.827187381 1 9.449702367 -8.608166011 0.509526066 1.009605653 2.022885406 0.035257142 0.565684864 1.374658324 0.522642229 0.114919961 0.664282901 2.47E-09 8.608166011 1.013279753 SGK(ac)LKGDDLQAIK ddPTM_HeLa_Romidepsin_16h_R1 1 SGKLKGDDLQAIK 13 2 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;G3V5V7;G3V4W0;G3V576;P0DMR1;B7ZW38;A0A0G2JPF8;A0A0G2JNQ3;B2RXH8;O60812;B4DY08 P07910-2;B4DY08 HNRNPC;HNRNPCL4;HNRNPCL3;HNRNPCL2;HNRNPCL1 Heterogeneous nuclear ribonucleoproteins C1/C2;Heterogeneous nuclear ribonucleoprotein C-like 4;Heterogeneous nuclear ribonucleoprotein C-like 3;Heterogeneous nuclear ribonucleoprotein C-like 2;Heterogeneous nuclear ribonucleoprotein C-like 1 0 1 SGK(0.733)LK(0.267)GDDLQAIK 90.229 0.028421 1172600 818.87 906.2 879.37 692.79 967.27 1063.9 695.02 789.85 1027.4 815.42 FALSE TRUE FALSE 808.8892975 918.9575074 894.675066 772.8936395 917.9066025 995.9202236 754.0549815 812.7030636 935.5067708 794.2352708 1.018450486 1.157034371 1.126461011 0.973129333 1.155711206 1.253936031 0.949410092 1.023252295 1.177871098 1 9.63342262 -10.4245059 8.432396595 1.008099104 1.091345397 0 0.101870168 0.437107386 34.15406042 0.014860388 0.016950717 3.76E-11 10.4245059 0.083246293 SGK(ac)LKGDDLQAIKK ddPTM_HeLa_Romidepsin_16h_R1 2 SGKLKGDDLQAIKK 14 3 P07910-2;G3V4C1;P07910;G3V2D6;G3V2Q1;B2R5W2;P07910-3;G3V5V7;G3V4W0;G3V576;B4DY08 P07910-2;B4DY08 HNRNPC Heterogeneous nuclear ribonucleoproteins C1/C2 0 1 ; SGK(0.605)LK(0.395)GDDLQAIKK;SGK(0.917)LK(0.083)GDDLQAIKK 79.886 0.00769 7068100 1421.06 1355.19 1286.86 2062.58 1737.31 1614.77 1399.65 1609.15 1579.57 1411.44 FALSE TRUE FALSE 1403.739574 1374.2684 1309.257258 2301.065204 1648.648588 1511.591408 1518.536236 1655.708216 1438.289303 1374.770585 1.021071871 0.999634714 0.952345993 1.673781232 1.199217241 1.099522658 1.104574285 1.204352373 1.04620314 1 10.42497517 SGK(ac)YDLDFK ddPTM_HeLa_Romidepsin_16h_R1 1 SGKYDLDFK 9 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 1 SGK(1)YDLDFK 116.77 0.0067726 13071000 1563.4 1412.6 1527.9 628.83 4549.2 3499.6 3618.3 3287.7 4367.8 3491.9 FALSE TRUE FALSE 1544.344679 1432.48662 1554.492459 701.5382833 4317.037349 3275.986854 3925.638312 3382.824412 3977.133029 3401.179935 0.454061446 0.42117343 0.457045052 0.206263208 1.269276378 0.96319128 1.154198951 0.99460319 1.169339201 1 11.73181962 -8.73685878 24.99919657 0.652182586 1.090085711 0.409145872 0.279178724 207.1318221 210658.2217 0.042943403 0.085855793 1.83E-09 8.73685878 0.437903125 SGKNSQEDS(ph)EDSEDKDVK ddPTM_HeLa_Romidepsin_16h_R1 1 SGKNSQEDSEDSEDKDVK 18 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 S(0.021)GKNS(0.3)QEDS(0.535)EDS(0.143)EDKDVK 89.831 0.0059475 14299000 1378.8 1420 1285.2 1698.1 1228.5 1442.6 1269.1 789.34 1329.4 1467.9 TRUE FALSE FALSE 1361.994655 1439.990797 1307.568367 1894.442312 1165.805061 1350.422516 1376.897322 812.1783075 1210.495134 1429.763746 0.952601196 1.007152966 0.914534566 1.32500374 0.815383006 0.944507454 0.963024364 0.568050707 0.846639969 1 10.48156106 -7.255116242 4.271906925 0.985463877 0.533818217 0.462333769 0.131146235 0.131603814 5.477167092 0.015596501 0.181375955 5.56E-08 7.255116242 -0.45164566 SGKRVGK(ac)PSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGKRVGKPSPK 11 3 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 0 1 SGK(0.469)RVGK(0.531)PSPK 67.207 0.021089 0 1389.1 1409.7 1217.1 1811.7 2818.9 2986.4 2944.7 2907.9 1882.2 1857.3 FALSE TRUE FALSE 1372.169115 1429.545794 1238.283115 2021.177278 2675.041014 2795.578678 3194.822744 2992.035499 1713.851318 1809.047078 0.758503818 0.790220338 0.684494688 1.117260741 1.478701713 1.545332187 1.766025209 1.653929041 0.947377953 1 10.82101424 -8.773949223 2.076989412 0.860269421 1.660579667 0.927556184 0.102700758 0.07074249 0.621945978 0.019292942 0.042037255 1.68E-09 8.773949223 0.800310246 SGLAESSSK(ac)FKPTQSSLTR ddPTM_HeLa_Romidepsin_16h_R1 1 SGLAESSSKFKPTQSSLTR 19 2 Q14966-3;Q14966;Q14966-5 Q14966-3 ZNF638 Zinc finger protein 638 0 1 SGLAESSSK(1)FKPTQSSLTR 66.779 0.028982 907700 105.06 0 0 0 60.147 0 163.21 60.447 0 0 FALSE TRUE FALSE 103.7794883 0 0 0 57.07747415 0 177.0730533 62.19593858 0 0 0 SGLEELVLSEMNS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 SGLEELVLSEMNSPSR 16 0 Q4V328-4;Q4V328;A0A087WXA6;A0A087WT45;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 0 SGLEELVLSEMNS(0.891)PS(0.109)R;SGLEELVLS(0.002)EMNS(0.908)PS(0.09)R ; 89.506 0.017813 10453700 4231.6 4193.6 3883.5 4027.9 5811 6963.6 5540.8 6613.6 4422.7 4413.1 TRUE FALSE FALSE 4180.023632 4252.637611 3951.090688 4493.62475 5514.442986 6518.648434 6011.435414 6804.954081 4027.122635 4298.447026 0.972449726 0.989342799 0.919190271 1.045406567 1.282891927 1.516512451 1.398513318 1.583119215 0.936878508 1 12.06959981 -8.609522061 2.181505948 0.981603992 1.492605612 0.955873332 0.05096925 0.038982485 0.373469246 0.006735264 0.015879185 2.46E-09 8.609522061 0.511001621 SGLEPAS(ph)SPSK ddPTM_HeLa_Romidepsin_16h_R1 1 SGLEPASSPSK 11 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 SGLEPAS(0.479)S(0.479)PS(0.043)K 151.13 0.0023219 83446000 12352 11505 12034 7646.6 7961.6 6666.5 5432 5524.4 13065 11803 TRUE FALSE FALSE 12201.44907 11666.96769 12243.44672 8530.73587 7555.289843 6240.532165 5893.393944 5684.239798 11896.43368 11496.35636 1.061331842 1.01484047 1.064984969 0.742038225 0.657189949 0.542826959 0.51263146 0.494438379 1.034800358 1 13.48888907 -8.928142285 1.562500929 1.033159536 0.519295963 0.969853336 0.04049945 0.044792121 0.21926043 0.006710733 0.014628145 1.18E-09 8.928142285 -0.513863572 SGLEPAS(ph)SPSKGSEPR ddPTM_HeLa_Romidepsin_16h_R1 1 SGLEPASSPSKGSEPR 16 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 SGLEPAS(0.56)S(0.438)PS(0.002)KGSEPR 118.72 0.001078 16773000 4337.3 4333.6 4011.3 3214.9 2958.1 2412.2 2198.2 2601.6 4301.8 4380.2 TRUE FALSE FALSE 4284.435319 4394.608535 4081.114994 3586.621865 2807.137119 2258.068205 2384.915053 2676.873191 3917.036234 4266.401773 1.004226875 1.030050326 0.956570715 0.840666692 0.657963612 0.529267595 0.558999171 0.627431108 0.918112368 1 12.05880412 -8.886368793 1.710054081 1.003550531 0.567773748 0.957967866 0.038604414 0.031884312 0.188161037 0.004265289 0.009240714 1.30E-09 8.886368793 -0.435776783 SGLEPASS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 SGLEPASSPSK 11 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 SGLEPAS(0.022)S(0.963)PS(0.015)K 115.29 0.012171 82834000 10632 10596 11426 6710.6 7129.9 6432.8 5325.5 5663.5 10804 10804 TRUE FALSE FALSE 10502.41309 10745.17077 11624.86474 7486.511146 6766.034598 6021.764841 5777.847837 5827.364437 9837.663181 10523.31052 0.998014177 1.021082742 1.104677536 0.71142167 0.642956851 0.572231032 0.549052299 0.55375772 0.934844901 1 13.36130101 -9.063622366 3.079373371 1.00806255 0.57907586 0.945856616 0.049158246 0.037135063 0.69423687 0.006909757 0.012352681 8.64E-10 9.063622366 -0.42898669 SGLEPASS(ph)PSKGSEPR ddPTM_HeLa_Romidepsin_16h_R1 3 SGLEPASSPSKGSEPR 16 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 SGLEPAS(0.149)S(0.851)PSKGSEPR;SGLEPAS(0.146)S(0.852)PS(0.002)KGSEPR;SGLEPAS(0.162)S(0.757)PS(0.079)KGS(0.003)EPR ;; 213 4.44E-25 24019000 12982.2 12738.2 12182.2 10304.3 9888.7 7978.5 6909.3 6783.6 14145.5 13313.4 TRUE FALSE FALSE 12823.96795 12917.52871 12394.22608 11495.73165 9384.042739 7468.699599 7496.17577 6979.872763 12880.29105 12967.51595 0.988930186 0.996145196 0.955790309 0.886502218 0.723657698 0.575954534 0.57807338 0.538258275 0.993273585 1 13.66261452 -8.667329111 1.329401633 0.994804974 0.546863335 0.996392312 0.011260411 0.015871581 0.055416662 0.001702652 0.004793303 2.15E-09 8.667329111 -0.44794164 SGLQLS(ph)LEQGTGENSFR ddPTM_HeLa_Romidepsin_16h_R1 2 SGLQLSLEQGTGENSFR 17 0 P23497;E9PHV6;P23497-7;P23497-5;P23497-2;P23497-3;P23497-4;P23497-6;C9JBL0 P23497 SP100 Nuclear autoantigen Sp-100 1 0 SGLQLS(0.984)LEQGT(0.015)GENS(0.001)FR;SGLQLS(0.994)LEQGT(0.006)GENSFR ; 192.72 2.04E-16 3446000 2282.2 1688.68 2330.5 1959.06 1784.51 1832.91 1940.11 1703.16 2203.6 2637.5 TRUE FALSE FALSE 2254.383669 1712.453281 2371.061375 2185.575735 1693.439796 1715.792966 2104.902895 1752.438247 2006.504497 2568.97737 0.877541272 0.666589477 0.92295923 0.850757099 0.659188289 0.667889483 0.819354394 0.682154023 0.781051838 1 11.32697847 -10.69668759 0.303541761 1.039231282 0.69051464 0.118000476 0.108260157 0.787244037 0.232601166 0.107225853 0.081683118 2.01E-11 10.69668759 -0.348716642 SGLS(ph)LEELR ddPTM_HeLa_Romidepsin_16h_R1 3 SGLSLEELR 9 0 A0A087WWA3;Q4R9M9;O60333-2;O60333;O60333-4 A0A087WWA3 KIF1B;KIF1Bbeta Kinesin-like protein;Kinesin-like protein KIF1B 1 0 S(0.276)GLS(0.724)LEELR;S(0.001)GLS(0.999)LEELR;S(0.001)GLS(0.999)LEELR ;; 129.88 0.0083368 73157300 8286.3 7454.3 7322.2 6836.5 9801.6 11592.4 10550 11630.8 8151.5 8062.6 TRUE FALSE FALSE 8185.303388 7559.241831 7449.639819 7626.968297 9301.387777 10851.68305 11446.11674 11967.31885 7422.409424 7853.13249 1.042297885 0.962576633 0.948620163 0.971200767 1.184417529 1.381828597 1.457522428 1.523891118 0.945152706 1 12.93905252 -8.322926191 1.847435106 1.006321441 1.489501172 0.963611443 0.041457516 0.047827499 0.312066002 0.00633226 0.01965133 4.75E-09 8.322926191 0.48317973 SGLTVPT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGLTVPTSPK 10 0 Q53EL6;Q53EL6-2;Q5VZS7 Q53EL6 PDCD4 Programmed cell death protein 4 1 0 SGLTVPT(0.928)S(0.072)PK 161.19 0.0047118 1433500000 23760 22010 22057 20004 16132 12525 11189 12067 23064 21126 TRUE FALSE FALSE 23470.40398 22319.85736 22440.89283 22316.9566 15308.72384 11724.69292 12139.39338 12416.13961 21001.09808 20577.14347 1.140605547 1.08469173 1.090573765 1.08455076 0.743967396 0.569792058 0.589945509 0.603394714 1.02060318 1 14.3287551 -8.631475146 3.109037742 1.073473721 0.592221104 0.968434376 0.039882219 0.040910294 0.788361504 0.008297833 0.017827378 2.34E-09 8.631475146 -0.481252618 SGNQVSEFISNTFLDKQHEVEIPS(ph)PTQK ddPTM_HeLa_Romidepsin_16h_R1 1 SGNQVSEFISNTFLDKQHEVEIPSPTQK 28 1 Q08499;Q08499-2;A0A1B0GW84;A0A087WSZ7;Q08499-10;Q08499-11;Q08499-6;Q08499-9;Q08499-3;D6RHE0;Q08499-4;Q08499-8;Q08499-5 Q08499 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 0 SGNQVSEFISNTFLDKQHEVEIPS(0.972)PT(0.027)QK 68.589 5.93E-05 46389000 2151.4 1613.8 1543 2134 1986.2 1667.2 1622.3 1459.8 1895.3 1817 TRUE FALSE FALSE 2125.177909 1636.519119 1569.855268 2380.743121 1884.836802 1560.671301 1760.098122 1502.03701 1725.779621 1769.794078 1.200805187 0.924694652 0.887027077 1.345209112 1.065003452 0.881837791 0.994521421 0.848707219 0.975130182 1 10.78936579 -8.31125949 6.741090447 1.08561389 0.917099601 0.185154651 0.133323141 0.252559389 28.07629828 0.019622184 0.044511536 4.88E-09 8.31125949 -0.168514289 SGPKPFSAPKPQT(ph)SPSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 0 SGPKPFSAPKPQT(0.822)S(0.172)PS(0.006)PK 91.774 0.025488 983170000 6086.5 4847.8 4908.9 800.22 5324 5409.4 5355.9 5342.2 5590.5 5173.6 TRUE FALSE FALSE 6012.315397 4916.047456 4994.337345 892.7452015 5052.296413 5063.756798 5810.830012 5496.768128 5090.471678 5039.189126 1.193111679 0.975563197 0.991099405 0.177160487 1.002601071 1.004875322 1.153127987 1.090804094 1.010176747 1 12.29897589 -9.904272046 3.150568514 1.090534821 0.89078993 0.069675458 0.260735037 0.453788025 9.067215429 0.044948016 0.060070752 1.25E-10 9.904272046 -0.199744891 SGPKPFSAPKPQTSPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SGPKPFSAPKPQTSPSPK 18 2 Q01518-2;Q01518 Q01518-2 CAP1 Adenylyl cyclase-associated protein 1 1 0 SGPKPFSAPKPQT(0.089)S(0.089)PS(0.821)PK 63.674 0.013605 14397000 3851.1 3712.7 3712.1 835.12 3518.5 3624.9 3305.9 3305.1 5146.5 4236 TRUE FALSE FALSE 3804.161312 3764.967488 3776.707543 931.6805038 3338.937816 3393.280589 3586.703063 3400.727854 4686.18415 4125.948109 0.922009005 0.912509656 0.915355076 0.225810039 0.809253468 0.822424446 0.869303968 0.824229429 1.135783589 1 12.01050996 -9.495239957 24.99624683 0.956227574 0.714760565 0.347912903 0.182400298 676.8930465 612176.3645 0.026650467 0.040646148 3.20E-10 9.495239957 -0.241467009 SGPLFNFDVHDDVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGPLFNFDVHDDVR 14 0 B0S8I6;Q14320 B0S8I6 FAM50A Protein FAM50A 0 0 125.22 0.00152 3382700 1249.5 1300.7 1271.4 978.03 1690.4 1693 1258.2 1425.4 1388.6 1027.2 FALSE FALSE TRUE 1234.270613 1319.011289 1293.528184 1091.11443 1604.13258 1584.822764 1365.071477 1466.6417 1264.400138 1000.513196 1.233637516 1.318334725 1.292864691 1.090554762 1.603309768 1.584009857 1.364371287 1.465889412 1.263751586 1 9.96652448 -10.34033109 0.185011144 0.844463831 1.651723262 0.365173877 0.146828097 1.490273294 0.254628885 0.465607811 0.480086461 4.57E-11 10.34033109 0.80725943 SGPPS(ph)PPSTATSFGGPRPR ddPTM_HeLa_Romidepsin_16h_R1 3 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 SGPPS(0.999)PPS(0.001)TATSFGGPRPR;SGPPS(0.935)PPS(0.065)TATSFGGPRPR;S(0.002)GPPS(0.994)PPS(0.003)T(0.001)ATSFGGPRPR ;; 172.55 3.24E-08 158023000 3539.43 3650.66 3294.68 3537.07 3616.29 3076.06 2927.29 2985.99 3710.59 3377.85 TRUE FALSE FALSE 3496.290066 3702.054087 3352.022523 3946.042676 3431.737227 2879.509694 3175.93394 3072.38491 3378.705537 3290.09297 1.062672118 1.125212607 1.018823041 1.199371176 1.043051749 0.875206178 0.965302187 0.933829207 1.02693315 1 11.68391264 -8.313054328 9.552181765 1.050645982 0.928899759 0.530271597 0.060208628 0.363372133 65.79715808 0.009211918 0.0206521 4.86E-09 8.313054328 -0.121746223 SGPPSPPS(ph)TATSFGGPRPR ddPTM_HeLa_Romidepsin_16h_R1 1 SGPPSPPSTATSFGGPRPR 19 1 A0A0A0MS59;A0A0C4DFX4;Q6ZRS2-3;Q6ZRS2-2;Q6ZRS2;A0A087X0E3 A0A0A0MS59 SRCAP Helicase SRCAP 1 0 SGPPS(0.204)PPS(0.649)T(0.13)AT(0.007)S(0.009)FGGPRPR 86.367 0.0021147 0 831.27 958.15 859.59 713.86 792.57 701.67 671.54 805.4 997.82 979.38 TRUE FALSE FALSE 821.1381615 971.6388608 874.5508034 796.399852 752.1221954 656.8355515 728.5805908 828.7029783 908.5724801 953.9355664 0.860789964 1.018558166 0.91678184 0.83485707 0.788441297 0.688553373 0.763762896 0.868720077 0.952446383 1 9.897748012 -9.095283278 2.308785356 0.93970169 0.770254827 0.6694028 0.057535795 0.170125555 1.781219886 0.010746009 0.019704996 8.03E-10 9.095283278 -0.169446864 SGPQILT(ph)PLGDR ddPTM_HeLa_Romidepsin_16h_R1 2 SGPQILTPLGDR 12 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 SGPQILT(1)PLGDR;S(0.002)GPQILT(0.998)PLGDR ; 115.09 0.018666 14321700 3717.3 3631.8 3953.4 3224.8 4558.2 5292.5 4542.4 4783.5 3938.3 3368 TRUE FALSE FALSE 3671.992118 3682.928576 4022.207269 3597.666549 4325.578045 4954.326331 4928.231343 4921.903025 3586.048584 3280.498874 1.119339545 1.122673324 1.22609622 1.096682757 1.318573245 1.510235644 1.502281065 1.500351993 1.093141233 1 11.67969951 -8.316364046 0.467106784 1.036495535 1.680598903 0.875788098 0.065291472 0.479802114 0.129029776 0.017375061 0.144908843 4.83E-09 8.316364046 0.644103368 SGPS(ph)PLSSPNGK ddPTM_HeLa_Romidepsin_16h_R1 4 SGPSPLSSPNGK 12 0 O75179-4;O75179-6;O75179-2;O75179;H0YM23;O75179-7 O75179-4 ANKRD17 Ankyrin repeat domain-containing protein 17 1 0 S(0.275)GPS(0.725)PLSSPNGK;S(0.002)GPS(0.998)PLSSPNGK;S(0.224)GPS(0.776)PLSSPNGK;S(0.073)GPS(0.927)PLSSPNGK ;;; 187.62 6.85E-10 74095200 16235.8 15204.9 15243.9 12637 11350.7 9988.2 8168.3 8953.2 16106.7 16039.3 TRUE FALSE FALSE 16037.91182 15418.95498 15509.21368 14098.1494 10771.43142 9349.986255 8862.115198 9212.246716 14666.07641 15622.59667 1.026584259 0.986964927 0.992742372 0.902420365 0.689477662 0.598491176 0.567262625 0.589674489 0.938773286 1 13.93134665 -8.756331543 1.680392047 1.010785543 0.576771377 0.980203047 0.025786014 0.017332496 0.099077363 0.002220034 0.005230139 1.75E-09 8.756331543 -0.434014166 SGPT(ph)DDGEEEMEEDTVTNGS ddPTM_HeLa_Romidepsin_16h_R1 1 SGPTDDGEEEMEEDTVTNGS 20 0 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 1 0 S(0.251)GPT(0.749)DDGEEEMEEDTVTNGS 95.197 0.0028346 6106200 955.38 898.52 957.18 785.55 979.88 1293.9 921.9 1207.1 1040 1170.6 TRUE FALSE FALSE 943.7354611 911.1693881 973.8393164 876.3789871 929.8730672 1211.223966 1000.206163 1242.025534 946.9797953 1140.187643 0.827701885 0.799139855 0.854104429 0.768626982 0.815543891 1.062302309 0.877229436 1.089316782 0.830547323 1 10.15505556 -4.180421022 1.009614498 0.891036669 134.6210992 0.329171206 0.08929171 1327.386556 2.482599557 0.015748605 410046.4273 6.60E-05 4.180421022 133.7300625 SGPTDDGEEEMEEDTVTNGS ddPTM_HeLa_Romidepsin_16h_R1 1 SGPTDDGEEEMEEDTVTNGS 20 0 P09661 P09661 SNRPA1 U2 small nuclear ribonucleoprotein A 0 0 138.45 0.0005028 9651000 5511.9 5540 4554.1 4271.3 5500.1 5542.8 4454.1 5200.7 6016.7 5479.5 FALSE FALSE TRUE 5444.718843 5617.992265 4633.3622 4765.167803 5219.409373 5188.632969 4832.431143 5351.174049 5478.551283 5337.1418 1.020156302 1.052621886 0.868135488 0.892831403 0.977940922 0.972174464 0.90543428 1.002629169 1.026495358 1 12.38185163 -9.775264168 24.99998013 1.013016976 0.936628092 0.518173655 0.041084698 157.3081146 284466.4791 0.006558319 0.008643894 1.68E-10 9.775264168 -0.076388883 SGQGFHGNSEVNAILS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SGQGFHGNSEVNAILSPR 18 0 C9JW01;Q8TB72-2;Q8TB72-3;Q8TB72;A0A0A0MR59;Q8TB72-4 C9JW01 PUM2 Pumilio homolog 2 1 0 SGQGFHGNSEVNAILS(1)PR;SGQGFHGNS(0.02)EVNAILS(0.98)PR ; 147.75 2.79E-05 14472600 4092.5 3990 3512.8 3249 5777.5 4891.6 4140.6 4192.1 6551.6 5470.1 TRUE FALSE FALSE 4042.619036 4046.171325 3573.93881 3624.664667 5482.652616 4579.042547 4492.302461 4313.391799 5965.608487 5327.986013 0.758751811 0.759418533 0.670786072 0.680306716 1.029029093 0.859432164 0.843152075 0.809572658 1.119674202 1 12.37937458 -12.29512915 1.028635473 0.999614424 0.800580476 0.467942568 0.10479338 0.480417848 0.913175357 0.068897982 0.018624865 5.07E-13 12.29512915 -0.199033948 SGQSALYDALFSS(ph)QSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGQSALYDALFSSQSPK 17 0 P49792;J3KNE0;A6NKT7;Q7Z3J3 P49792;Q7Z3J3 RANBP2;RGPD3;RGPD4 E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RanBP2-like and GRIP domain-containing protein 4 1 0 SGQS(0.001)ALY(0.001)DALFS(0.07)S(0.871)QS(0.057)PK 133.94 7.49E-07 0 1177.4 1320.3 1161.7 874.12 1149.3 1267.9 1193 1276.6 1405.4 1166.9 TRUE FALSE FALSE 1163.049396 1338.887218 1181.918901 975.1898673 1090.646932 1186.885282 1294.33339 1313.536407 1279.697504 1136.58377 1.02328524 1.177992554 1.039887189 0.858000873 0.959583412 1.044256757 1.138792779 1.155688161 1.125915694 1 10.1504883 -7.806624641 3.537445441 1.011310072 1.151872392 0.236874891 0.082658597 0.197133304 4.986830549 0.010904185 0.040680455 1.56E-08 7.806624641 0.140562321 SGRS(ph)PTGNTPPVIDSVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGRSPTGNTPPVIDSVSEK 19 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 S(0.142)GRS(0.854)PT(0.003)GNTPPVIDSVSEK 168.42 1.22E-06 5796300 1759 1633.6 1432.6 2207.9 2057.8 1415.3 1598.5 1748.5 1830.5 1888.2 TRUE FALSE FALSE 1737.560631 1656.597864 1457.533802 2463.187786 1952.782787 1324.866898 1734.27655 1799.090089 1666.775495 1839.144292 0.944765802 0.900743825 0.792506498 1.339311873 1.061788787 0.720371372 0.942980145 0.978221283 0.90627772 1 10.84481896 -8.315269157 24.99992701 0.986949979 0.886767719 0.1041237 0.149220901 590.8061931 274384.2756 0.020942405 0.046828667 4.84E-09 8.315269157 -0.10018226 SGRSPT(ph)GNTPPVIDSVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGRSPTGNTPPVIDSVSEK 19 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 S(0.274)GRS(0.274)PT(0.44)GNT(0.011)PPVIDSVSEK 64.249 0.013693 15698000 2893.6 3090.1 2736.6 3950.9 3485.8 3181 2850 3361.9 3025.3 3303.5 TRUE FALSE FALSE 2858.33169 3133.602509 2784.229375 4407.721648 3307.906619 2977.744366 3092.078929 3459.171272 2754.709591 3217.674594 0.888322174 0.973871788 0.865292401 1.369846925 1.02804262 0.925433657 0.960966946 1.07505317 0.856118141 1 11.65180272 SGS(ph)ESEEAELSLSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSESEEAELSLSLAR 16 0 Q8IV50 Q8IV50 LYSMD2 LysM and putative peptidoglycan-binding domain-containing protein 2 1 0 S(0.268)GS(0.731)ES(0.001)EEAELSLSLAR 211.9 7.73E-26 1993200 363.35 392.89 246.51 393.15 412.2 338.05 461.67 377.33 478.15 491.15 TRUE FALSE FALSE 358.9213504 398.4211157 250.8004031 438.6078528 391.1638959 316.449696 500.8842383 388.2474482 435.3830665 478.3898522 0.750269574 0.832837724 0.524259455 0.916841883 0.817667628 0.661489149 1.047021035 0.811571246 0.910100966 1 8.902042977 -12.30796086 0.998990236 1.001669528 0.793830545 0.174099074 0.13436824 0.604376987 1.066562164 0.0900982 0.023257831 4.92E-13 12.30796086 -0.207838983 SGS(ph)GGGSAKEPQEER ddPTM_HeLa_Romidepsin_16h_R1 1 SGSGGGSAKEPQEER 15 1 F5GWT4;Q9H4A3-2;Q9H4A3;Q9H4A3-5;Q9H4A3-6;Q9H4A3-7;F6UYG0 F5GWT4 WNK1 Serine/threonine-protein kinase WNK1 1 0 S(0.293)GS(0.707)GGGSAKEPQEER 141.1 0.0047444 15150000 1641.5 1727.1 1495.9 2024.4 1759.9 1689.7 1901.5 1190.5 1906.9 1635.5 TRUE FALSE FALSE 1621.492767 1751.414159 1521.935512 2258.470653 1670.085736 1581.733623 2063.013363 1224.945239 1736.342088 1593.009474 1.017880178 1.099437378 0.955383842 1.417738369 1.048384057 0.992921667 1.29504149 0.768950379 1.089975996 1 10.63753913 -10.13374292 1.550668814 1.006679255 1.099951476 0.001263192 0.170363223 0.850727764 3.923251326 0.028954756 0.036156922 7.35E-11 10.13374292 0.093272221 SGS(ph)LDDSFSDFQELPASSK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 S(0.116)GS(0.856)LDDS(0.011)FS(0.017)DFQELPASSK 224.86 3.88E-45 0 1889 1803.7 1739 1667.4 1656.2 1728.7 1809.3 2139.7 2103.6 2038.8 TRUE FALSE FALSE 1865.976141 1829.092536 1769.266566 1860.192633 1571.677934 1618.241649 1962.981897 2201.608844 1915.448747 1985.831682 0.939644663 0.921071283 0.890944878 0.936732277 0.791445694 0.814893661 0.988493594 1.108658334 0.964557452 1 10.95552763 -11.35633611 0.781126067 0.993920206 0.91534743 0.065465541 0.083890482 0.964915929 1.247377364 0.035698728 0.019889173 4.40E-12 11.35633611 -0.078572776 SGS(ph)LLQVEETEREEGLGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSLLQVEETEREEGLGAGR 20 1 Q8WYL5;Q8WYL5-2;Q8WYL5-4;Q8WYL5-5 Q8WYL5 SSH1 Protein phosphatase Slingshot homolog 1 1 0 S(0.262)GS(0.737)LLQVEETEREEGLGAGR 55.718 0.013023 4885700 974.72 1027.8 1038.6 931.97 797.61 1064.2 1012.7 938.5 1158.6 935.89 TRUE FALSE FALSE 962.8397377 1042.269395 1056.676397 1039.728756 756.9049854 996.2010545 1098.718713 965.6540168 1054.971914 911.5754429 1.056237029 1.143371515 1.159176024 1.140584429 0.830326213 1.092834457 1.205296524 1.059324299 1.157306203 1 9.83221825 -11.133445 1.22556142 1.012154661 1.087801381 0 0.106746754 0.721753825 2.239662848 0.025886366 0.020208364 7.35E-12 11.133445 0.07564672 SGS(ph)MDPSGAHPSVR ddPTM_HeLa_Romidepsin_16h_R1 3 SGSMDPSGAHPSVR 14 0 Q07666-2;Q07666;Q07666-3 Q07666-2 KHDRBS1 "KH domain-containing, RNA-binding, signal transduction-associated protein 1" 1 0 S(0.208)GS(0.79)MDPSGAHPS(0.002)VR;S(0.415)GS(0.585)MDPSGAHPSVR;S(0.382)GS(0.616)MDPS(0.001)GAHPS(0.001)VR ;; 88.224 0.0063826 19982500 5163.7 5517.7 4162.2 4609.5 9300.5 9035.9 7130.6 7493.7 6910 5803.5 TRUE FALSE FALSE 5100.762838 5595.378325 4234.641345 5142.472078 8825.86078 8458.535152 7736.272986 7710.518386 6291.952294 5652.724233 0.902354799 0.989855173 0.749132838 0.909733407 1.561346426 1.496364373 1.368591969 1.364035829 1.113083185 1 12.4647306 -8.767618782 24.99987718 0.935990358 1.445426601 0.854377326 0.101812202 34.48502329 139515.9315 0.013574107 0.025059754 1.71E-09 8.767618782 0.509436244 SGS(ph)NGSVVSLEQQQK ddPTM_HeLa_Romidepsin_16h_R1 2 SGSNGSVVSLEQQQK 15 0 Q2M1P5 Q2M1P5 KIF7 Kinesin-like protein KIF7 1 0 S(0.001)GS(0.999)NGSVVSLEQQQK;S(0.001)GS(0.999)NGSVVSLEQQQK ; 270.99 1.04E-84 29395000 6378.8 6789 6250.5 7597.8 6925 8082.7 5838.5 7399.7 7233.7 6902 TRUE FALSE FALSE 6301.052732 6884.57572 6359.287331 8476.293385 6571.591409 7566.241556 6334.422044 7613.798645 6586.699755 6722.685045 0.937282156 1.024081252 0.945944558 1.260849397 0.977524808 1.125479106 0.942245844 1.132553227 0.979772176 1 12.71482185 SGS(ph)PISSEER ddPTM_HeLa_Romidepsin_16h_R1 2 SGSPISSEER 10 0 H8Y6P7;P0CAP2-3;P0CAP2;P0CAP1-11;P0CAP2-2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 0 S(0.043)GS(0.953)PIS(0.004)SEER;S(0.043)GS(0.952)PIS(0.003)S(0.003)EER ; 155.33 0.0032855 93162000 6405.8 6504.2 6065 5547.4 5725.1 5348.3 4405.8 4884.2 6743.1 6711 TRUE FALSE FALSE 6327.723646 6595.766298 6170.558781 6188.816489 5432.926784 5006.560891 4780.028542 5025.516621 6139.980248 6536.647253 0.968038109 1.009044246 0.943994458 0.946787589 0.83114884 0.76592184 0.7312661 0.768821756 0.939316443 1 12.67433513 -8.659762375 1.498460453 0.985021249 0.74559823 0.945889869 0.023223335 0.046578496 0.20870707 0.002936046 0.00778204 2.19E-09 8.659762375 -0.239423019 SGS(ph)PISSEERR ddPTM_HeLa_Romidepsin_16h_R1 2 SGSPISSEERR 11 1 H8Y6P7;P0CAP2-3;P0CAP2;P0CAP1-11;P0CAP2-2 H8Y6P7 GCOM1;POLR2M DNA-directed RNA polymerase II subunit GRINL1A 1 0 S(0.17)GS(0.828)PIS(0.001)S(0.001)EERR;S(0.158)GS(0.842)PISSEERR ; 97.957 0.0064319 14405300 4490.3 4521.1 4136.1 4329.6 3960.9 3936.1 3227.5 3696 4879.1 4150.2 TRUE FALSE FALSE 4435.570496 4584.748164 4208.087085 4830.208723 3758.760493 3684.595913 3501.643769 3802.937929 4442.701076 4042.377206 1.097267838 1.134171289 1.040993176 1.194893123 0.929839127 0.911492354 0.8662338 0.940767706 1.099031795 1 11.98098823 -8.581790977 12.45989997 1.063254052 0.905248465 0.698404894 0.056669841 0.436672014 91.52183755 0.009066819 0.018136857 2.62E-09 8.581790977 -0.158005586 SGS(ph)PLEKDSDGLR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPLEKDSDGLR 13 1 B1AKL4;Q9NRA8;Q9NRA8-3;B1AKL5 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 S(0.215)GS(0.785)PLEKDSDGLR 132.65 0.012862 7226000 1178.8 1427 941.59 1592.3 907.03 777.7 1005.4 785.83 1060 1285.3 TRUE FALSE FALSE 1164.432332 1447.089343 957.977979 1776.409218 860.7408745 728.0074799 1090.798651 808.5667512 965.1909452 1251.907721 0.930126329 1.155907356 0.765214531 1.418961788 0.687543387 0.581518484 0.871309149 0.645867693 0.77097611 1 10.28991251 SGS(ph)PRPTEPTDFLMLFEGS(ph)PSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 2 0 S(0.162)GS(0.799)PRPT(0.037)EPT(0.002)DFLMLFEGS(0.943)PS(0.057)GK 95.867 0.0001301 11178000 3482.5 3040.2 3119 2737.5 3718 4307.4 3350 3957.2 3475.4 2979 TRUE FALSE FALSE 3440.05395 3083.000015 3173.284887 3054.02263 3528.256586 4032.171041 3634.548916 4071.695339 3164.55152 2901.605151 1.185569287 1.062515351 1.093630843 1.052528677 1.215967164 1.389634644 1.252599416 1.403256173 1.090621003 1 11.5026355 -4 0.229598674 1.041512177 3.081824114 0.699142814 0.073179016 23.75247359 0.288731089 0.05765282 18.39201898 1.00E-04 4 2.040311937 SGS(ph)PRPTEPTDFLMLFEGSPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.12)GS(0.488)PRPT(0.174)EPT(0.215)DFLMLFEGS(0.003)PSGK 55.587 0.014452 65532000 2375 2005 2251.6 2920.8 4429 5342.3 5154.5 6034.8 2226.6 2552.5 TRUE FALSE FALSE 2346.052586 2033.226443 2290.788153 3258.516639 4202.971603 5000.944271 5592.323101 6209.407417 2027.447319 2486.185682 0.943635306 0.81780957 0.921406703 1.310648944 1.690530049 2.011492668 2.249358582 2.497563823 0.815485076 1 11.27971833 -8.451202612 1.073705692 0.949828231 2.4347056 0.976231964 0.093315363 0.058651708 0.122734466 0.015008452 0.060610801 3.54E-09 8.451202612 1.484877369 up SGS(ph)SS(ph)PDSEITELK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSSSPDSEITELK 14 0 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 2 0 S(0.438)GS(0.56)S(0.047)S(0.869)PDS(0.072)EIT(0.014)ELK 159.58 0.0037697 7144300 2454.2 2650.8 2990.7 993.81 2338.8 2222.5 1839.5 1881.9 2406.1 2926.9 TRUE FALSE FALSE 2424.287266 2688.118032 3042.751879 1108.718988 2219.442309 2080.489423 1995.747084 1936.349807 2190.89239 2850.858716 0.850370891 0.942915205 1.067310653 0.388907027 0.778517117 0.729776404 0.700051207 0.679216335 0.768502619 1 11.47718083 -9.28339943 24.99958301 0.938187927 0.668763792 0.543617875 0.123368179 426.8862973 485971.0741 0.017374252 0.02655263 5.21E-10 9.28339943 -0.269424134 SGS(ph)YSYLEER ddPTM_HeLa_Romidepsin_16h_R1 2 SGSYSYLEER 10 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;A0A0U1RQZ1;H0YIM2;H0YIS3 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 S(0.006)GS(0.99)YS(0.004)YLEER;S(0.349)GS(0.531)YS(0.12)YLEER ; 145.23 0.0040667 17701800 3525.8 2969.8 2454.4 2527.3 3396.4 2979.3 2145.91 2870.1 3377.3 3170.6 TRUE FALSE FALSE 3482.826193 3011.608922 2497.117802 2819.518317 3223.069034 2788.932345 2328.183542 2953.141815 3075.225829 3088.227355 1.12777519 0.975190158 0.808592605 0.912989231 1.043663132 0.903085176 0.753889942 0.956257903 0.995789971 1 11.59256325 -10.00149434 23.89654972 1.059872206 0.897201827 0.387535284 0.081187628 22.72781855 363462.6904 0.014015382 0.018263675 9.97E-11 10.00149434 -0.162670379 SGSAS(ph)PAPGDTLPWNLPK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSASPAPGDTLPWNLPK 18 0 F6QMI7;Q5T0V7;E7ETB9;Q03001-11 F6QMI7 DST Dystonin 1 0 S(0.149)GS(0.012)AS(0.834)PAPGDT(0.006)LPWNLPK 111.7 0.0013178 18211000 3130.8 2619.6 3024.3 3082 3207.1 3060.7 2886.4 2987.8 3572.3 3142.1 TRUE FALSE FALSE 3092.640605 2656.478798 3076.936673 3438.355341 3043.42972 2865.131148 3131.570744 3074.247279 3252.784541 3060.467789 1.010512385 0.867997633 1.005381166 1.123473788 0.994432855 0.936174254 1.023232708 1.004502413 1.062839005 1 11.57953647 SGSDAGEARPPTPAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSDAGEARPPTPASPR 17 1 Q96FS4;F6RY50;E9PIB3 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 0 SGSDAGEARPPT(0.018)PAS(0.982)PR 166.67 3.21E-05 9336600 1645.5 1536.8 1632.2 1703.5 1760.9 2055.3 1990.4 1968 2139.2 1750.4 TRUE FALSE FALSE 1625.444013 1558.435111 1660.607756 1900.466685 1671.034702 1923.972963 2159.464526 2024.940975 1947.864594 1704.924356 0.953381895 0.914078742 0.974006706 1.114692672 0.980122488 1.128479957 1.266604304 1.187701359 1.142493265 1 10.73549202 -8.14424219 1.100515919 0.975474767 1.250755572 0.536551748 0.075542696 0.21978637 0.437922548 0.008444714 0.048401332 7.17E-09 8.14424219 0.275280805 SGSIGAADS(ph)PENWEK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSIGAADSPENWEK 15 0 D6RAI0;D6RGK7;D6RAZ3;D6R9T3;E7EMP6;Q96FZ2 D6RAI0 HMCES Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein 1 0 SGSIGAADS(1)PENWEK 120.92 0.00015382 0 963.1 805.7 704.88 914.52 771.3 644.36 698.77 817.91 976.54 969.94 TRUE FALSE FALSE 951.3613668 817.0426657 717.1481407 1020.261105 731.9376829 603.1874756 758.1235064 841.5749354 889.1958166 944.740819 1.007007793 0.864832607 0.759095115 1.079937571 0.774749718 0.638468735 0.802467186 0.890799803 0.941206095 1 9.883774783 -9.709161913 0.685513115 1.009797249 0.786080606 0.26725859 0.109779359 0.505248668 0.483784097 0.025832155 0.04572333 1.95E-10 9.709161913 -0.223716643 SGSLDDS(ph)FSDFQELPASSK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 S(0.073)GS(0.277)LDDS(0.647)FS(0.003)DFQELPASSK 96.805 0.0020893 4317900 1570.1 1345.9 1351.6 1141.1 1510.4 1441.9 1435.9 1398.1 1833.6 1261 TRUE FALSE FALSE 1550.963017 1364.847616 1375.124031 1273.039351 1433.318652 1349.767244 1557.86531 1438.551818 1669.598224 1228.239038 1.262753397 1.111223119 1.119589907 1.036475239 1.166970441 1.098945076 1.268373062 1.171231147 1.359343069 1 10.26237565 -12.58843752 1.385712933 1.000221863 1.16559297 0 0.130241129 0.347248505 1.198543828 0.053037346 0.012401522 2.58E-13 12.58843752 0.165371107 SGSLDDSFS(ph)DFQELPASSK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSLDDSFSDFQELPASSK 19 0 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 SGSLDDS(0.484)FS(0.516)DFQELPASSK 170 1.48E-07 7677600 5142.8 4321.1 4578.4 4237.5 5495.9 5179.6 3933.1 4243.1 5499.8 5391.9 TRUE FALSE FALSE 5080.117575 4381.932559 4658.085131 4727.459688 5215.423715 4848.640276 4267.177416 4365.867404 5007.884113 5251.817661 0.967306541 0.834364946 0.886947231 0.900156859 0.993070219 0.923230887 0.812514389 0.831305976 0.953552548 1 12.35860111 -4.000000016 0.093288774 1.081548221 0.398583345 0.32166288 0.053630474 92.23480407 0.620396233 0.582326477 8.0958748 1.00E-04 4.000000016 -0.682964876 SGSLDSELS(ph)VSPK ddPTM_HeLa_Romidepsin_16h_R1 3 SGSLDSELSVSPK 13 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 SGSLDSELS(0.737)VS(0.263)PK;SGSLDS(0.007)ELS(0.594)VS(0.398)PK;SGS(0.001)LDS(0.013)ELS(0.944)VS(0.042)PK ;; 182.72 3.89E-07 413526000 6998.9 6800.7 6980.3 5352.1 8599.5 10754.3 8992.5 10546 7065.1 7262.4 TRUE FALSE FALSE 6913.594715 6896.440433 7101.789193 5970.934984 8160.635426 10067.13494 9756.322726 10851.13187 6433.179761 7073.721801 0.977363107 0.974938035 1.003967839 0.844100906 1.153655127 1.423173715 1.379234723 1.534006026 0.909447663 1 12.78825377 -8.391889356 2.959854662 0.980012448 1.44497435 0.923046407 0.063340456 0.045208007 0.754077716 0.008023373 0.01982069 4.06E-09 8.391889356 0.464961902 SGSLDSELSVS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 3 SGSLDSELSVSPKR 14 1 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 SGSLDSELSVS(1)PKR;SGSLDSELS(0.001)VS(0.999)PKR;SGSLDSELS(0.058)VS(0.942)PKR ;; 176.43 7.38E-07 91220000 5995.6 5361.16 4493.89 7011.7 8653.4 9291.1 8039.4 8938.7 6872.6 6052.7 TRUE FALSE FALSE 5922.523321 5436.634551 4572.10427 7822.425745 8211.784708 8697.428696 8722.266435 9197.327182 6257.897443 5895.449981 1.004592243 0.922174655 0.775531009 1.326858131 1.392902108 1.475278176 1.479491211 1.560072125 1.061479185 1 12.52538622 -9.066860799 4.261800713 0.979863416 1.468053469 0.899291778 0.083455394 0.052041591 1.846037652 0.012817749 0.022102698 8.57E-10 9.066860799 0.488190052 SGSMEEDVDTS(ph)PGGDYYTSPSS(ph)PTSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSMEEDVDTSPGGDYYTSPSSPTSSSR 28 0 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 2 0 SGSMEEDVDT(0.188)S(0.812)PGGDYYTS(0.001)PS(0.268)S(0.678)PT(0.038)S(0.011)S(0.003)S(0.001)R 124.34 4.84E-10 14186000 2082.3 2478.6 2311.5 1643.1 1747 2019.3 1895.6 1853.1 2826.6 2227.6 TRUE FALSE FALSE 2056.920127 2513.493796 2351.730688 1833.082953 1657.844071 1890.273247 2056.612217 1906.716525 2573.781817 2169.726631 0.948008886 1.158438008 1.083883405 0.844845119 0.764079699 0.871203413 0.947866974 0.878781916 1.186224006 1 11.08329757 -9.242184411 24.68978011 0.998853687 0.861304513 0.491924852 0.093814415 545.2739449 699180.6125 0.012304668 0.020384307 5.73E-10 9.242184411 -0.137549174 SGSMEEDVDTSPGGDYYTSPSS(ph)PTSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SGSMEEDVDTSPGGDYYTSPSSPTSSSR 28 0 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 SGSMEEDVDTSPGGDY(0.001)Y(0.001)T(0.001)S(0.001)PS(0.071)S(0.561)PT(0.228)S(0.094)S(0.039)S(0.004)R;SGSMEEDVDTSPGGDYYTSPS(0.074)S(0.854)PT(0.047)S(0.018)S(0.007)SR ; 135.6 1.57E-10 35647000 6264.1 6296.6 6253.7 5252.4 4343.7 4153.5 3438.1 3830.5 7061.2 6564 TRUE FALSE FALSE 6187.75074 6385.2437 6362.543025 5859.707201 4122.02478 3888.104755 3730.132128 3941.329474 6429.628587 6393.466334 0.967824091 0.998713901 0.995163295 0.916514907 0.644724562 0.608137206 0.583428759 0.616462067 1.005656126 1 12.64238261 -8.787322968 2.989456098 0.98595446 0.601773898 0.994241596 0.013822385 0.014679842 0.26929546 0.002397435 0.00483315 1.63E-09 8.787322968 -0.384180562 SGSMSLDPAVADGS(ph)ES(ph)ETEDSVLETR ddPTM_HeLa_Romidepsin_16h_R1 2 SGSMSLDPAVADGSESETEDSVLETR 26 0 O60447-2;O60447 O60447-2 EVI5 Ecotropic viral integration site 5 protein homolog 2 0 SGSMSLDPAVADGS(0.999)ES(0.984)ET(0.017)EDSVLETR;SGSMSLDPAVADGS(0.992)ES(0.908)ET(0.096)EDS(0.004)VLETR ; 119.28 6.42E-12 0 1111.56 906.9 1055.28 1069.29 1532.71 1244.4 1054.01 1452.02 1302.78 988.59 TRUE FALSE FALSE 1098.011879 919.667362 1073.646706 1192.926341 1454.490089 1164.886856 1143.537583 1494.031908 1186.256094 962.9062893 1.140310216 0.955095394 1.115006432 1.238881036 1.510520915 1.209761395 1.187589692 1.55158599 1.231953833 1 9.911251591 -9.190423441 3.060518171 1.05969628 1.343095578 0.492862205 0.129679821 0.147340199 2.712419386 0.018106735 0.030976149 6.45E-10 9.190423441 0.283399298 SGSPMVPSYETS(ph)VSPQANR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPMVPSYETSVSPQANR 19 0 E9PDH4;Q9Y2I7-2;Q9Y2I7-3;Q9Y2I7-4;Q9Y2I7 E9PDH4 PIKFYVE 1-phosphatidylinositol 3-phosphate 5-kinase 1 0 SGSPMVPSYET(0.058)S(0.584)VS(0.358)PQANR 132.5 3.37E-09 0 1007.8 883.18 980.72 841.67 1296.4 1086.9 1020.7 1288 1091.5 808.76 TRUE FALSE FALSE 995.516546 895.6134312 997.7890202 938.9878456 1230.23987 1017.450598 1107.398233 1325.266248 993.8735063 787.7482986 1.263749535 1.136928423 1.266634307 1.191989684 1.56171695 1.29159352 1.405776737 1.682347331 1.261663793 1 9.621590923 -4 0.11760149 0.893966568 2.993203048 0.546564454 0.127357298 38.45548981 0.312482192 0.51091552 13.24688041 1.00E-04 4 2.09923648 SGSPMVPSYETSVS(ph)PQANR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPMVPSYETSVSPQANR 19 0 E9PDH4;Q9Y2I7-2;Q9Y2I7-3;Q9Y2I7-4;Q9Y2I7 E9PDH4 PIKFYVE 1-phosphatidylinositol 3-phosphate 5-kinase 1 0 SGSPMVPSYET(0.005)S(0.085)VS(0.91)PQANR 135.69 5.09E-10 0 779.35 913.6 968.19 866.33 1077.4 1186.2 869.55 1030.4 1016 851.85 TRUE FALSE FALSE 769.8509824 926.4616848 985.0409408 966.4991508 1022.416258 1110.405648 943.4095553 1060.212998 925.1264154 829.7188142 0.927845638 1.116597176 1.187198511 1.164851434 1.232244274 1.338291514 1.137023217 1.277797948 1.114987872 1 9.69647869 -9.975158071 2.222015065 0.965735048 1.22564094 0.597767337 0.073557271 0.091817617 0.908757558 0.01000391 0.013178557 1.06E-10 9.975158071 0.259905893 SGSPRPT(ph)EPTDFLMLFEGSPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.069)GS(0.329)PRPT(0.463)EPT(0.138)DFLMLFEGSPSGK 50.924 0.022078 216230000 1776.2 1386.7 1596 2003.7 3121.8 3815.9 3756.2 4270.5 2095.6 1755.5 TRUE FALSE FALSE 1754.550991 1406.221999 1623.777711 2235.377222 2962.482897 3572.076305 4075.251534 4394.06018 1908.164287 1709.891857 1.026118105 0.822404056 0.949637665 1.307320818 1.732555708 2.089065628 2.383338758 2.569788354 1.115956123 1 10.73968937 -8.427309088 1.129253273 0.986693277 2.534385116 0.977576538 0.091663148 0.052231422 0.121658279 0.014533192 0.057695597 3.74E-09 8.427309088 1.547691839 up SGSPRPTEPT(ph)DFLMLFEGSPSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.189)GS(0.189)PRPT(0.285)EPT(0.337)DFLMLFEGSPSGK 51.956 0.018644 3327700 495.95 582.27 375.1 617.56 671.83 765.99 828.15 842.63 637.38 571.45 TRUE FALSE FALSE 489.9051706 590.4672123 381.6284582 688.9651929 637.5440082 717.0457111 898.4930403 867.0101696 580.3711365 556.6036466 0.880168812 1.06083964 0.685637725 1.237802154 1.14541831 1.28825191 1.614242102 1.557679643 1.042700924 1 9.12050655 -8.187521937 0.967624421 0.93893525 1.651086462 0.768735207 0.130726523 0.225537882 0.334100725 0.019385621 0.119133822 6.49E-09 8.187521937 0.712151213 SGSPRPTEPTDFLMLFEGS(ph)PSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSPRPTEPTDFLMLFEGSPSGK 23 1 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 SGSPRPTEPTDFLMLFEGS(0.761)PS(0.239)GK 59.189 0.010519 4155700 1558 1635.9 1203.7 1313.2 1476 1804.8 1518.9 1415.2 1625.4 1441.9 TRUE FALSE FALSE 1539.010497 1658.930243 1224.649894 1465.038363 1400.674212 1689.479105 1647.915328 1456.146579 1480.020153 1404.43923 1.095818504 1.181204717 0.871984965 1.043148277 0.997319202 1.20295636 1.173361789 1.036817078 1.05381573 1 10.45577849 -14.94530074 0.011622432 1.10E-05 1.999713578 0.051174189 0.093775218 11556.16271 14.56486886 1415.014815 1107.897058 1.13E-15 14.94530074 1.99970256 SGSPSDNS(ph)GAEEMEVSLAKPK ddPTM_HeLa_Romidepsin_16h_R1 2 SGSPSDNSGAEEMEVSLAKPK 21 1 P31749-2;P31749 P31749-2 AKT1 RAC-alpha serine/threonine-protein kinase 1 0 S(0.008)GS(0.007)PS(0.026)DNS(0.958)GAEEMEVS(0.001)LAKPK;S(0.002)GS(0.019)PS(0.074)DNS(0.906)GAEEMEVSLAKPK ; 69.747 0.0073671 134531000 4849.3 4301.7 4812.5 4271.3 5878.7 5422.3 5246.7 5915.4 4574.8 4517.5 TRUE FALSE FALSE 4790.194866 4362.259446 4896.259544 4765.167803 5578.688003 5075.83253 5692.354567 6086.552766 4165.61843 4400.134699 1.088647324 0.991392251 1.112752195 1.082959529 1.267844824 1.153562988 1.293677343 1.3832651 0.94670248 1 12.10333197 -4 0.272591264 1.015274963 3.75674041 0.828539485 0.056225779 12.83615314 0.163021549 0.022793465 16.82823539 1.00E-04 4 2.741465447 SGSS(ph)PGLR ddPTM_HeLa_Romidepsin_16h_R1 2 SGSSPGLR 8 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SGS(0.338)S(0.662)PGLR;S(0.005)GS(0.41)S(0.585)PGLR ; 117.81 0.019598 10129100 3318.3 3804.9 6549.6 2787 2144.99 2923.2 5835.9 1447.14 5142.3 4335.6 TRUE FALSE FALSE 3277.855283 3858.465482 6663.593041 3109.246053 2035.523156 2736.416954 6331.6012 1489.010713 4682.359809 4222.960487 0.776198426 0.913687328 1.577943497 0.736271642 0.482013309 0.647985451 1.499327597 0.352598779 1.108786081 1 12.04403903 SGSS(ph)QELDVKPSAS(ph)PQER ddPTM_HeLa_Romidepsin_16h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 S(0.007)GS(0.093)S(0.9)QELDVKPS(0.348)AS(0.652)PQER 175.77 3.97E-07 6849400 3047.5 2837.3 2713.7 1913.7 2398.3 2336.9 2023.8 2382.2 2783.4 2769 TRUE FALSE FALSE 3010.355898 2877.243584 2760.93081 2134.970998 2275.905802 2187.579632 2195.701521 2451.125199 2534.445733 2697.060981 1.116161599 1.066807019 1.02368127 0.791591667 0.843846623 0.811097579 0.814108964 0.908813414 0.939706499 1 11.39717243 -9.337094974 4.957064291 1.056507987 0.832212012 0.758377027 0.054230049 0.066661207 3.020781285 0.007944856 0.012301347 4.60E-10 9.337094974 -0.224295975 VNNGNTAPEDSS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 VNNGNTAPEDSSPAK 15 0 E9PJ27;G3V167;Q9UGN5-2;Q9UGN5 E9PJ27 PARP2 Poly [ADP-ribose] polymerase 2 1 0 VNNGNTAPEDS(0.209)S(0.791)PAK 166.64 3.45E-05 3753000 2765.9 2883.6 2795 2227.1 1479.3 1304.9 877.73 906.76 2619.9 2595.9 TRUE FALSE FALSE 2732.188147 2924.195396 2843.645803 2484.607781 1403.805801 1221.521101 952.2843643 932.99567 2385.569582 2528.458144 1.080574798 1.15651327 1.124656071 0.982657272 0.55520231 0.483109085 0.376626509 0.36899787 0.943487868 1 11.30404218 -8.701950626 2.531872889 1.057150466 0.410626238 0.957198082 0.06309236 0.039685545 0.517390793 0.009739144 0.021029549 1.99E-09 8.701950626 -0.646524228 down SGSS(ph)SPDSEITELK ddPTM_HeLa_Romidepsin_16h_R1 1 SGSSSPDSEITELK 14 0 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 1 0 SGS(0.001)S(0.538)S(0.461)PDSEITELK 274.39 1.58E-82 116080000 9878.2 8915.3 10175 5572.7 8661.5 9224.6 7950.4 8374.1 10367 9946.7 TRUE FALSE FALSE 9757.800699 9040.809827 10352.09161 6217.041794 8219.471334 8635.177831 8625.706778 8616.391371 9439.749555 9688.2833 1.007175409 0.933169432 1.068516608 0.641707267 0.848392959 0.891301128 0.89032355 0.889362037 0.974346978 1 13.24202534 -9.300463753 24.99997638 1.001531478 0.839626394 0.541492625 0.075429823 302.4826302 193777.0598 0.011085846 0.01693406 5.01E-10 9.300463753 -0.161905084 SGSSQELDVKPSAS(ph)PQER ddPTM_HeLa_Romidepsin_16h_R1 1 SGSSQELDVKPSASPQER 18 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SGS(0.001)S(0.006)QELDVKPS(0.029)AS(0.963)PQER 98.408 0.016792 4741400 758.62 508.22 795.24 440.8 404.79 456.71 497.17 525.94 753.05 792.99 TRUE FALSE FALSE 749.3736476 515.3747345 809.0808186 491.76737 384.1320558 427.527705 539.3996074 541.1572441 685.695322 772.3880055 0.970203631 0.667248495 1.047505674 0.636684369 0.497330426 0.553514169 0.698353164 0.700628752 0.887760189 1 9.59318195 -9.567359267 0.943177278 0.987015713 0.607187548 0.510218787 0.129647535 0.250692343 0.44560559 0.023976696 0.042639678 2.71E-10 9.567359267 -0.379828165 SGSSS(ph)PDSEITELK ddPTM_HeLa_Romidepsin_16h_R1 2 SGSSSPDSEITELK 14 0 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 1 0 SGSS(0.497)S(0.503)PDSEITELK;SGS(0.003)S(0.027)S(0.968)PDS(0.002)EITELK ; 297.03 4.91E-115 238170000 13982.1 12870.2 14704.6 8295.4 12460 13043.3 11506 12382.3 14787.2 14581.6 TRUE FALSE FALSE 13811.68079 13051.38701 14960.52739 9254.553179 11824.11971 12209.87523 12483.31935 12740.56231 13464.5958 14202.76793 0.972464019 0.918932639 1.053352943 0.651602084 0.832522207 0.859682795 0.87893567 0.897047841 0.948026178 1 13.7938845 -9.291866247 24.99319569 0.985003222 0.829472847 0.541144606 0.070964343 379.5331345 311754.53 0.010476825 0.016004799 5.11E-10 9.291866247 -0.155530374 SGSSS(ph)PDSEITELKFPSINHD ddPTM_HeLa_Romidepsin_16h_R1 4 SGSSSPDSEITELKFPSINHD 21 1 B4E1E0;P17812-2;P17812 B4E1E0 CTPS1 CTP synthase;CTP synthase 1 1 0 S(0.015)GS(0.053)S(0.194)S(0.723)PDS(0.014)EITELKFPSINHD;S(0.038)GS(0.032)S(0.132)S(0.562)PDS(0.189)EIT(0.047)ELKFPSINHD;S(0.041)GS(0.048)S(0.179)S(0.684)PDS(0.048)EITELKFPSINHD;S(0.061)GS(0.061)S(0.187)S(0.617)PDS(0.074)EIT(0.001)ELKFPSINHD ;;; 125.08 5.62E-05 555039000 5769.79 4802.82 4635.24 5065.1 8371.23 8275.5 5812.74 6577.32 8645.1 6720.3 TRUE FALSE FALSE 5699.46558 4870.434226 4715.914408 5650.750694 7944.014896 7746.722258 6306.473991 6767.624377 7871.860604 6545.705637 0.870718284 0.744065575 0.720459286 0.863276017 1.213622386 1.183481612 0.963452123 1.033902951 1.202599237 1 12.67633301 -8.777192215 24.99996105 0.898351166 1.095022223 0.317176851 0.142576351 197.2607457 313055.1055 0.018787467 0.034138027 1.67E-09 8.777192215 0.196671057 SGST(ph)SPLGFAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSTSPLGFAR 11 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 0 S(0.037)GS(0.024)T(0.707)S(0.232)PLGFAR 121.68 0.019141 16255000 3666.1 3454.5 3445.9 2146 3266.1 3930.5 3630.3 4507.3 3766.3 4070.9 TRUE FALSE FALSE 3621.416163 3503.132542 3505.874444 2394.130617 3099.41873 3679.353735 3938.657591 4637.711614 3429.432695 3965.137431 0.91331416 0.883483259 0.884174762 0.603795117 0.781667416 0.927925904 0.993321836 1.16962191 0.8648963 1 11.95315516 -7.340189323 2.243955254 0.907955636 1.210487292 0.385594603 0.109683922 0.528646584 3.460518845 0.01818606 0.293992347 4.57E-08 7.340189323 0.302531656 SGSTS(ph)PLGFAR ddPTM_HeLa_Romidepsin_16h_R1 1 SGSTSPLGFAR 11 0 O75385 O75385 ULK1 Serine/threonine-protein kinase ULK1 1 0 S(0.001)GS(0.003)T(0.331)S(0.666)PLGFAR 126.66 0.0070768 17891000 3690.3 3582.6 3251.7 2078 3845.6 3795.1 3482.8 5029.8 4238.6 3918.8 TRUE FALSE FALSE 3645.321204 3633.035937 3308.294474 2318.268137 3649.344682 3552.605358 3778.628945 5175.329327 3859.489 3816.989011 0.955025334 0.951806758 0.866728844 0.607355203 0.956079431 0.930735024 0.989950176 1.355866971 1.011134428 1 11.89821932 -7.25558502 3.281263904 0.937929444 1.416707686 0.579183389 0.111566308 0.208559567 3.551849166 0.01651752 0.253927856 5.55E-08 7.25558502 0.478778242 SGSYS(ph)YLEER ddPTM_HeLa_Romidepsin_16h_R1 2 SGSYSYLEER 10 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;A0A0U1RQZ1;H0YIM2;H0YIS3 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 S(0.021)GS(0.231)YS(0.748)YLEER;S(0.108)GS(0.211)YS(0.68)YLEER ; 168.22 0.0011774 30885000 4070.4 4202.6 3632.7 3206.7 3853.8 4046.5 3487.1 3753.6 4056.5 4000 TRUE FALSE FALSE 4020.788399 4261.764313 3695.92562 3577.473742 3657.126205 3787.941709 3783.294187 3862.204494 3693.67648 3896.079423 1.032008838 1.093859711 0.948626868 0.918224028 0.938668289 0.972244479 0.971051607 0.99130538 0.948049585 1 11.92780737 -9.673045035 24.99999487 1.021453068 0.955478724 0.382427952 0.038376056 13.56789544 3834.274692 0.005214177 0.007373959 2.12E-10 9.673045035 -0.065974344 SGT(ph)FDLLEMDR ddPTM_HeLa_Romidepsin_16h_R1 2 SGTFDLLEMDR 11 0 H0YA31;H0YA26;E9PHT6;Q9NVE7 H0YA31 PANK4 Pantothenate kinase 4 1 0 SGT(1)FDLLEMDR;SGT(1)FDLLEMDR ; 144.1 0.0062737 12442800 9991.7 8287.5 10887.9 5574.4 7254.3 8605.4 7333.1 7242.1 10352.4 9199.2 TRUE FALSE FALSE 9869.917317 8404.171643 11077.39933 6218.938356 6884.086001 8055.542713 7955.973331 7451.638737 9426.455416 8960.203458 1.101528259 0.937944287 1.236288817 0.694062181 0.768295724 0.899035692 0.88792329 0.831637225 1.052035867 1 13.12931578 -9.252765046 24.99918413 1.052003462 0.822117617 0.653745814 0.090421285 328.5172109 946777.0955 0.013581138 0.022299526 5.59E-10 9.252765046 -0.229885845 SGT(ph)PPRQGS(ph)ITSPQANEQS(ph)VTPQRR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTPPRQGSITSPQANEQSVTPQRR 25 2 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 3 0 S(0.152)GT(0.587)PPRQGS(0.781)IT(0.397)S(0.086)PQANEQS(0.856)VT(0.142)PQRR 62.325 0.0013998 30956000 1865.6 1841.1 1452.8 1998.4 1509.1 1529.8 1150.3 1399.9 1950.7 1776 TRUE FALSE FALSE 1842.86135 1867.019054 1478.085375 2229.464411 1432.084996 1432.050717 1248.006453 1440.403898 1776.224506 1729.859264 1.065324439 1.079289566 0.85445412 1.288812597 0.827862142 0.827842326 0.721449704 0.832671147 1.026802899 1 10.75643895 -8.554369679 24.99941964 1.037878597 0.793586832 0.579484738 0.104183876 95.96173094 76179.9137 0.013612485 0.027225144 2.79E-09 8.554369679 -0.244291765 SGTAETEPVEQDSS(ph)QPS(ph)LPLVR ddPTM_HeLa_Romidepsin_16h_R1 2 SGTAETEPVEQDSSQPSLPLVR 22 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 SGTAETEPVEQDS(0.461)S(0.555)QPS(0.984)LPLVR;SGTAETEPVEQDS(0.526)S(0.593)QPS(0.881)LPLVR ; 86.248 0.00013946 0 1274.71 1481.96 1268.94 1207.18 1438.89 1556 1376.72 1490.66 1337.26 1361.79 TRUE FALSE FALSE 1259.173344 1502.823072 1291.025368 1346.759832 1365.458074 1456.576622 1493.658562 1533.789895 1217.652116 1326.410499 0.949308939 1.132999982 0.973322639 1.015341655 1.029438529 1.098134116 1.126090726 1.156346316 0.918005487 1 10.37331162 -7.412417013 0.46517701 0.980985054 1.278548388 0.581304774 0.05129795 2.030568725 0.322514842 0.011271365 0.322260356 3.87E-08 7.412417013 0.297563333 SGTAETEPVEQDSS(ph)QPSLPLVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTAETEPVEQDSSQPSLPLVR 22 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SGTAETEPVEQDS(0.214)S(0.785)QPSLPLVR 163.61 2.75E-09 13127000 2715.5 2835 2785.3 2340.1 2999.7 2766.1 2218.4 2276.1 2774.3 3075.5 TRUE FALSE FALSE 2682.402442 2874.911204 2833.776978 2610.673373 2846.614116 2589.355137 2406.830841 2341.955362 2526.15966 2995.598067 0.895448048 0.959711931 0.945980374 0.871503224 0.950265707 0.864386703 0.803455867 0.78179893 0.84329059 1 11.54862835 -4.258786518 0.230452274 0.974163237 1.65E-17 0.429447599 0.051290044 18.94149504 0.256459021 0.027476084 6.868129292 5.51E-05 4.258786518 -0.974163237 SGTAETEPVEQDSSQPS(ph)LPLVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTAETEPVEQDSSQPSLPLVR 22 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SGTAETEPVEQDS(0.102)S(0.323)QPS(0.575)LPLVR 151 1.87E-06 14262000 2981 2957.4 3315.6 2865.7 2973.5 2675.8 2183.3 3116.6 3192.8 2907.3 TRUE FALSE FALSE 2944.666425 2999.034355 3373.306627 3197.045718 2821.751199 2504.825016 2368.749448 3206.773904 2907.227971 2831.767927 1.039868556 1.059067845 1.191236964 1.128992841 0.99646273 0.884544596 0.836491375 1.132428217 1.02664768 1 11.46748732 -8.520022887 24.65079928 1.044625749 0.939824261 0.239918628 0.090547412 113.4030311 978854.0765 0.013494032 0.027403123 3.02E-09 8.520022887 -0.104801487 SGTGATATVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SGTGATATVSPK 12 0 C9K0W5;Q6NXR6;Q86TU7-3;Q86TU7-2;Q86TU7 C9K0W5 SETD3 Histone-lysine N-methyltransferase setd3 1 0 SGTGATATVS(1)PK;SGTGATAT(0.001)VS(0.999)PK ; 135.94 0.00074653 3242900 4126.8 3681.5 3814.1 2997.8 3353.7 4160.6 3305.5 3254.9 4211.2 4025.1 TRUE FALSE FALSE 4076.500974 3733.328254 3880.482811 3344.419741 3182.548175 3894.751088 3586.269087 3349.075396 3834.539725 3920.527322 1.039783845 0.952251559 0.989785937 0.853053548 0.811765335 0.993425315 0.914741511 0.854241055 0.978067339 1 11.936832 -9.575314963 1.979759392 1.016342615 0.890480836 0.474724312 0.052498148 0.182705934 1.445786464 0.008548873 0.013184315 2.66E-10 9.575314963 -0.125861779 SGTNS(ph)PPPPFSDWGR ddPTM_HeLa_Romidepsin_16h_R1 2 SGTNSPPPPFSDWGR 15 0 D6RAU6;D6REP2;D6RAJ6;Q9UKT5-2;Q9UKT5 D6RAU6 FBXO4 F-box only protein 4 1 0 S(0.182)GT(0.044)NS(0.774)PPPPFSDWGR;S(0.278)GT(0.163)NS(0.558)PPPPFSDWGR ; 200 4.55E-18 44328000 7571.1 7490.9 7124.6 7404.4 7237.5 6640.5 5312.8 6186.7 8289.3 8311.4 TRUE FALSE FALSE 7478.820521 7596.357087 7248.600674 8260.531567 6868.143368 6216.193481 5764.069099 6365.702404 7547.884247 8095.46863 0.923827991 0.9383468 0.895389879 1.020389547 0.84839355 0.767860857 0.712011789 0.78632908 0.93235915 1 12.98289888 -8.484344824 3.028724964 0.958797975 0.751344158 0.829406525 0.039813825 0.076894409 1.407623371 0.006346761 0.014856527 3.28E-09 8.484344824 -0.207453817 SGTPPRQGS(ph)ITSPQANEQSVTPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTPPRQGSITSPQANEQSVTPQR 24 1 Q9UQ35;Q9UQ35-2;I3L4D8;I3L182 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.08)GT(0.215)PPRQGS(0.597)IT(0.045)S(0.02)PQANEQS(0.041)VT(0.003)PQR 46.295 0.023659 15539000 450.57 408.61 177.69 467.67 369.65 423.45 316.93 450.24 544.07 445.27 TRUE FALSE FALSE 445.0782795 414.3624223 180.7826199 521.7442059 350.7853811 396.3929116 343.8500263 463.266984 495.4070166 433.7018212 1.02623106 0.955408537 0.416836202 1.20300211 0.808816943 0.913975668 0.792825876 1.068169331 1.14227562 1 8.760559691 -9.991170873 24.99994147 1.011251809 0.862572702 0.145946326 0.196152484 307.2196958 869897.9621 0.028375888 0.037263812 1.02E-10 9.991170873 -0.148679107 SGTSSPQS(ph)PVFR ddPTM_HeLa_Romidepsin_16h_R1 3 SGTSSPQSPVFR 12 0 Q8N556;Q8N556-2 Q8N556 AFAP1 Actin filament-associated protein 1 1 0 S(0.001)GTS(0.002)S(0.043)PQS(0.953)PVFR;SGTS(0.001)S(0.016)PQS(0.984)PVFR;S(0.011)GT(0.005)S(0.038)S(0.025)PQS(0.921)PVFR ;; 135.04 0.0027677 435999000 6584.2 6237.8 5569.51 4760.16 6903.5 6843.7 6202.4 6575.9 6687.8 6755.5 TRUE FALSE FALSE 6503.949238 6325.615912 5666.444985 5310.552096 6551.188634 6406.409657 6729.231701 6766.163291 6089.626418 6579.991136 0.988443465 0.961341099 0.861163012 0.807075874 0.995622714 0.9736198 1.022680967 1.028293679 0.925476386 1 12.68386993 -7.7696586 2.956413582 0.967639723 1.029017881 0.116934756 0.064199153 0.500111693 8.69667206 0.010234891 0.043808905 1.70E-08 7.7696586 0.061378159 SGTSTPTTPGS(ph)TAITPGTPPSYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTSTPTTPGSTAITPGTPPSYSSR 25 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 S(0.001)GT(0.001)S(0.001)T(0.003)PT(0.008)T(0.027)PGS(0.389)T(0.346)AIT(0.092)PGT(0.113)PPS(0.006)Y(0.001)S(0.006)S(0.005)R 48.077 0.020356 76578000 1073.3 1065.9 1047.1 971.57 1520.4 1529 1594.2 1659.8 1180.4 1188.5 TRUE FALSE FALSE 1060.218207 1080.905768 1065.324336 1083.907495 1442.808315 1431.301835 1729.611308 1707.823694 1074.822068 1157.622599 0.915858249 0.93372898 0.920269125 0.93632199 1.246354655 1.236414904 1.494106378 1.475285379 0.92847364 1 10.17694928 -8.282009788 1.227495984 0.950596677 1.498030464 0.926025804 0.06054292 0.097931431 0.264076608 0.009646711 0.041873634 5.22E-09 8.282009788 0.547433787 SGTSTPTTPGST(ph)AITPGT(ph)PPSYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTSTPTTPGSTAITPGTPPSYSSR 25 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 2 0 S(0.118)GT(0.14)S(0.152)T(0.181)PT(0.039)T(0.088)PGS(0.122)T(0.177)AIT(0.381)PGT(0.551)PPS(0.028)Y(0.001)S(0.012)S(0.01)R 41.174 0.025793 7924800 1669.8 1453.1 1502.6 1146.7 2263.4 2292 1710.2 1786.8 2001.2 1806.4 TRUE FALSE FALSE 1649.447835 1473.55678 1528.752123 1279.286849 2147.890252 2145.548597 1855.464345 1838.498239 1822.20766 1759.469468 0.93746886 0.837500626 0.868871072 0.7270867 1.220760173 1.219429286 1.05455899 1.04491625 1.035657449 1 10.78092476 -8.736733712 24.99998382 0.935024661 1.135213034 0.552821922 0.100274427 161.6764168 163601.7194 0.015345542 0.030680189 1.83E-09 8.736733712 0.200188373 SGTSTPTTPGSTAITPGT(ph)PPSYSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGTSTPTTPGSTAITPGTPPSYSSR 25 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 SGTSTPTTPGS(0.011)T(0.01)AIT(0.112)PGT(0.794)PPS(0.045)Y(0.001)S(0.014)S(0.012)R 73.227 0.00044759 89325000 1256.2 1382.6 1240.1 1220.3 2059.3 2081.4 1988.4 2046.3 1358.7 1385.1 TRUE FALSE FALSE 1240.888951 1402.064279 1261.68342 1361.396828 1954.206237 1948.405257 2157.294646 2105.506462 1237.174469 1349.114902 0.919780034 1.039247492 0.93519345 1.009103691 1.448509859 1.444210018 1.599044412 1.560657627 0.917026761 1 10.39779751 -8.732010707 3.22363474 0.965387109 1.531477316 0.965484348 0.050541745 0.031814754 0.681580048 0.007927791 0.01623793 1.85E-09 8.732010707 0.566090207 SGTTESFT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SGTTESFTR 9 0 Q7Z5P9-2;Q7Z5P9 Q7Z5P9-2 MUC19 Mucin-19 1 0 SGTTESFT(1)R;SGTTES(0.001)FT(0.999)R ; 128.61 0.018544 3907400 5756.1 5314.6 4891.6 4447.4 5668.6 4466.8 4508.5 5335.9 6063.7 5962.1 TRUE FALSE FALSE 5685.942439 5389.419078 4976.736246 4961.629314 5379.31019 4181.385896 4891.451877 5490.285848 5521.347485 5807.203783 0.979118807 0.928057509 0.85699356 0.854392148 0.926316759 0.720034297 0.842307599 0.945426758 0.95077557 1 12.50362795 -9.997439605 1.637984183 0.992163946 0.850976257 0.455284746 0.058126095 0.193610125 1.022406451 0.009965462 0.013137701 1.01E-10 9.997439605 -0.141187689 SGVAITFLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SGVAITFLTK 10 0 Q9BUQ8 Q9BUQ8 DDX23 Probable ATP-dependent RNA helicase DDX23 0 0 138.66 0.017196 137330 141.49 0 137.74 151.43 136.59 274.26 136.72 0 0 0 FALSE FALSE TRUE 139.7654655 0 140.1373069 168.9390491 129.6193026 256.7356711 148.3329934 0 0 0 0 SGVS(ph)ITIDDPVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGVSITIDDPVR 12 0 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 S(0.002)GVS(0.993)IT(0.005)IDDPVR 99.669 0.015748 3566400 1558.1 1877.6 1740.1 1673.2 1674 1881.5 1223.7 1645.7 1908.6 1823.1 TRUE FALSE FALSE 1539.109278 1904.032902 1770.385711 1866.663257 1588.569533 1761.278222 1327.641047 1693.315733 1737.890036 1775.735599 0.86674462 1.072250229 0.996987227 1.051205629 0.89459801 0.991858373 0.747656942 0.953585508 0.978687388 1 10.79420107 -7.787953723 24.99877403 0.957806125 0.850621005 0.275645982 0.077603336 219.7467077 207185.825 0.011547581 0.034657127 1.63E-08 7.787953723 -0.10718512 SGVSLAALK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SGVSLAALKK 10 1 P10412;P16402;P16403 P10412;P16402;P16403 HIST1H1E;HIST1H1D;HIST1H1C Histone H1.4;Histone H1.3;Histone H1.2 0 1 ; SGVSLAALK(1)K;SGVSLAALK(1)K 120.68 0.003162 2641800 1088.32 1350.06 1917.11 1144.26 5402.3 4254.5 3394.9 1790.17 1698.06 1157.89 FALSE TRUE FALSE 1075.055137 1369.06618 1950.476495 1276.564725 5126.600472 3982.651181 3683.262721 1841.965745 1546.181261 1127.807851 0.953225442 1.213917937 1.729440431 1.13189913 4.5456329 3.531320675 3.265860154 1.633226567 1.370961604 1 10.13930558 -8.78722777 23.92885995 1.069315637 3.266092282 0.658683593 0.703113388 54.43302501 50507.84557 0.100939173 0.183025641 1.63E-09 8.78722777 2.196776644 SGVSLAALKK ddPTM_HeLa_Romidepsin_16h_R1 1 SGVSLAALKK 10 1 P10412;P16402;P16403 P10412;P16402;P16403 HIST1H1E;HIST1H1D;HIST1H1C Histone H1.4;Histone H1.3;Histone H1.2 0 0 93.556 0.0049333 0 203.44 406.79 461.46 554.36 607.88 643.7 459.97 275.53 328.76 161.45 FALSE FALSE TRUE 200.960395 412.5168003 469.4915177 618.4577115 576.8576153 602.5696474 499.0398403 283.5020258 299.3548822 157.2555057 1.277922793 2.623226439 2.985533101 3.932820722 3.668282472 3.831787286 3.173433185 1.802811447 1.903620995 1 7.296966718 -10.12776198 1.926333669 1.100944854 3.322899 0.629553657 0.618822766 0.115919192 0.827066017 0.102897467 0.128347072 7.45E-11 10.12776198 2.221954146 SGVSSDNEDDDDEEDGNY(ph)LHPSLFASK ddPTM_HeLa_Romidepsin_16h_R1 1 SGVSSDNEDDDDEEDGNYLHPSLFASK 27 0 Q12872;Q12872-2 Q12872 SFSWAP "Splicing factor, suppressor of white-apricot homolog" 1 0 S(0.009)GVS(0.111)S(0.425)DNEDDDDEEDGNY(0.454)LHPSLFASK 79.36 6.81E-06 0 1308.7 1442.6 1226.1 987.22 1704.1 1931.2 1438.4 1754.1 1857.2 1857.3 TRUE FALSE FALSE 1292.749061 1462.908961 1247.439756 1101.367021 1617.133418 1807.802553 1560.57766 1804.852116 1691.087381 1809.047078 0.714602222 0.808662736 0.68955627 0.608810591 0.893914502 0.999312055 0.862651768 0.99768112 0.934794567 1 10.82101424 -8.528557161 24.97630451 0.823697463 0.944567794 0.26456875 0.115000603 235.3813314 1035314.827 0.021208891 0.042518508 2.96E-09 8.528557161 0.120870331 SGYIS(ph)ESENSEISQQVR ddPTM_HeLa_Romidepsin_16h_R1 2 SGYISESENSEISQQVR 17 0 A0A075B754;Q96QE3-2;Q96QE3 A0A075B754 ATAD5 ATPase family AAA domain-containing protein 5 1 0 SGYIS(0.876)ES(0.124)ENSEISQQVR;SGYIS(0.992)ES(0.008)ENSEISQQVR ; 194.67 1.33E-13 2933900 1783.68 1809.03 1843.46 1223.84 1840.73 2236.6 1428.69 2052.32 2563.1 2404.8 TRUE FALSE FALSE 1761.939822 1834.497572 1875.544648 1365.346139 1746.790679 2093.688478 1550.042893 2111.700641 2333.849917 2342.322949 0.752218998 0.783195832 0.800719921 0.582902601 0.745751426 0.893851328 0.66175456 0.901541199 0.996382637 1 11.19372429 -12.17548124 0.705667599 1.017951898 0.758324943 0.5118199 0.090571645 0.537660203 0.433843458 0.08257867 0.018252505 6.68E-13 12.17548124 -0.259626956 SGYISES(ph)ENSEISQQVR ddPTM_HeLa_Romidepsin_16h_R1 1 SGYISESENSEISQQVR 17 0 A0A075B754;Q96QE3-2;Q96QE3 A0A075B754 ATAD5 ATPase family AAA domain-containing protein 5 1 0 SGYIS(0.376)ES(0.624)ENSEISQQVR 177.07 8.39E-09 3185900 774.6 741.59 851.86 453.5 875.54 761.21 531.45 749.86 1099.2 623.99 TRUE FALSE FALSE 765.1588773 752.0301235 866.686266 505.9358038 830.8579267 712.5711377 576.5913497 771.556016 1000.884799 607.7786498 1.25894333 1.237342121 1.425989982 0.832434315 1.367040331 1.172418837 0.948686417 1.269468772 1.646791639 1 9.247402186 -12.42712795 1.17925038 1.000907858 1.190639103 0 0.26313491 0.706606483 1.77048636 0.107593109 0.027578915 3.74E-13 12.42712795 0.189731245 SGYS(ph)SPGSPGTPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGYSSPGSPGTPGSR 15 0 I3L170;A0A0G2JQJ7;A0A0G2JPD5;A0A0G2JS76;A0A0G2JMX7;P10636-3;P10636-2;P10636-4;P10636-6;P10636-5;P10636-7;P10636-8;P10636;P10636-9 I3L170 MAPT Microtubule-associated protein;Microtubule-associated protein tau 1 0 S(0.008)GYS(0.472)S(0.472)PGS(0.047)PGTPGSR 174.94 4.87E-06 16889000 1024.7 1085.3 977.78 1614.9 3963.4 5253.9 4554.1 5211.8 979.29 977.9 TRUE FALSE FALSE 1012.210562 1100.578882 994.7978507 1801.622336 3761.132909 4918.192746 4940.92514 5362.59521 891.6998497 952.494017 1.062694929 1.155470651 1.044413753 1.891478901 3.94872077 5.163489385 5.187355565 5.630056582 0.936173702 1 9.89556622 -8.676769568 1.699318968 1.031394308 5.400466823 0.996050259 0.120663396 0.013753897 0.08001457 0.017479545 0.043182705 2.10E-09 8.676769568 4.369072515 up SGYSS(ph)PGSPGTPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGYSSPGSPGTPGSR 15 0 I3L170;A0A0G2JQJ7;A0A0G2JPD5;A0A0G2JS76;A0A0G2JMX7;P10636-3;P10636-2;P10636-4;P10636-6;P10636-5;P10636-7;P10636-8;P10636;P10636-9 I3L170 MAPT Microtubule-associated protein;Microtubule-associated protein tau 1 0 S(0.001)GYS(0.308)S(0.628)PGS(0.062)PGTPGSR 180.3 4.15E-08 15701000 1445 1448.8 1179.5 2624.4 8032.2 9654.8 9097.4 9718.1 1616 1238.7 TRUE FALSE FALSE 1427.387784 1469.196244 1200.028703 2927.845476 7622.286862 9037.889439 9870.132929 9999.277891 1471.460913 1206.518395 1.183063424 1.217715577 0.994621141 2.426689462 6.317588601 7.490884079 8.180673387 8.287712752 1.219592605 1 10.2366342 -8.7202616 1.926300182 1.079816301 8.071704763 0.995578233 0.207157034 0.014864739 0.112030279 0.033349098 0.076550702 1.90E-09 8.7202616 6.991888462 up SGYSSPGS(ph)PGTPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SGYSSPGSPGTPGSR 15 0 I3L170;A0A0G2JQJ7;A0A0G2JPD5;A0A0G2JS76;A0A0G2JMX7;P10636-3;P10636-2;P10636-4;P10636-6;P10636-5;P10636-7;P10636-8;P10636;P10636-9 I3L170 MAPT Microtubule-associated protein;Microtubule-associated protein tau 1 0 SGYS(0.002)S(0.002)PGS(0.685)PGT(0.31)PGS(0.001)R 109.99 0.004332 4007200 720.51 602.05 549.51 696.78 838.99 1256.7 1202.2 1070.6 597.48 685.12 TRUE FALSE FALSE 711.728147 610.5256757 559.073991 777.344982 796.1732096 1176.400926 1304.314838 1101.576122 544.0398924 667.3204836 1.066546231 0.914891256 0.837789345 1.16487505 1.193089721 1.762872495 1.954555375 1.650745255 0.815260292 1 9.382235978 -8.347396559 2.379452881 1.014956299 1.828824539 0.896807899 0.124245612 0.057660955 0.631558215 0.015551358 0.042239654 4.49E-09 8.347396559 0.81386824 SHEGETAYIR ddPTM_HeLa_Romidepsin_16h_R1 2 SHEGETAYIR 10 0 J3KTL2;Q07955;J3KSR8 J3KTL2 SRSF1 Serine/arginine-rich splicing factor 1 0 0 ; ; 197.79 1.87E-09 21606000 1564.71 1285.03 1535.52 1016.68 1746.83 1504.88 1444.31 948.7 1368.37 1422.95 FALSE FALSE TRUE 1545.638713 1303.120686 1562.245081 1134.233325 1657.682747 1408.723025 1566.989655 976.1491377 1245.97956 1385.981554 1.115194288 0.940215028 1.127175955 0.818361054 1.196035216 1.016408206 1.130599214 0.704301681 0.898987116 1 10.43669234 -7.252661815 24.39456863 1.047634611 0.704301432 0.410197957 0.113684901 481.8183603 1339026.129 0.013005839 0.202498933 5.59E-08 7.252661815 -0.34333318 SHEVQAMS(ph)ELISSIADY(ph)YGIK ddPTM_HeLa_Romidepsin_16h_R1 1 SHEVQAMSELISSIADYYGIK 21 0 H0YIW7;F8VZA8;Q8N6Q8 H0YIW7 METTL25 Methyltransferase-like protein 25 2 0 S(0.003)HEVQAMS(0.515)ELIS(0.255)S(0.255)IADY(0.485)Y(0.485)GIK 42.529 0.0041421 0 361.28 245.98 372.56 380.86 423.01 369.75 495.86 436.33 493.06 564.17 TRUE FALSE FALSE 356.8765804 249.4429129 379.0442505 424.8968252 401.4222212 346.1241683 537.978336 448.9545201 448.9594787 549.5127821 0.649441818 0.453934687 0.689782409 0.773224644 0.730505703 0.629874645 0.979009686 0.81700469 0.817013714 1 9.102009229 -12.28846376 1.079374981 0.995775045 0.711915281 0.197547788 0.138923598 0.416040583 0.887306588 0.086151906 0.024607247 5.15E-13 12.28846376 -0.283859764 SHGLAT(ph)VRMLPT(ph)YVCGLPDGT(ph)EK ddPTM_HeLa_Romidepsin_16h_R1 1 SHGLATVRMLPTYVCGLPDGTEK 23 1 Q2TB90-3;Q2TB90-2;Q2TB90 Q2TB90-3 HKDC1 Putative hexokinase HKDC1 3 0 S(0.522)HGLAT(0.499)VRMLPT(0.972)Y(0.119)VCGLPDGT(0.888)EK 42.309 0.025487 4087700 408.32 475.39 665.56 448.15 974.23 951.3 776.29 846.82 1065.7 837.26 TRUE FALSE FALSE 403.3432388 482.0825529 677.1437926 499.9672116 924.5114077 890.5150002 842.2280532 871.3214006 970.3811229 815.5078645 0.494591476 0.591143965 0.83033386 0.613074666 1.133663387 1.091975981 1.03276509 1.068440218 1.189910196 1 9.67155498 -8.754170577 24.99901188 0.738078786 1.078948276 0.3373176 0.195748353 131.4955443 452238.1484 0.029223886 0.057506473 1.76E-09 8.754170577 0.340869489 SHGLEPAAPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SHGLEPAAPSPR 12 0 Q9ULL5;Q9ULL5-2;A0A3Q5ADB5 Q9ULL5 PRR12 Proline-rich protein 12 1 0 SHGLEPAAPS(1)PR 85.576 0.015377 13105000 2219.5 1853.6 1885.1 1583.3 1086 1189.6 1256.1 1423.6 2069.3 2262.4 TRUE FALSE FALSE 2192.44788 1879.695029 1917.909375 1766.368596 1030.577368 1113.588399 1362.793103 1464.78962 1884.216625 2203.622522 0.994928967 0.853002277 0.87034388 0.801574942 0.467674185 0.505344445 0.618433098 0.664718937 0.85505417 1 11.1056614 -9.260778321 1.258886842 0.992293658 0.564366287 0.765726763 0.087083873 0.112832387 0.352251984 0.013103555 0.025550524 5.49E-10 9.260778321 -0.427927371 GRLT(ph)PSPDIIVLSDNEAS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 GRLTPSPDIIVLSDNEASSPR 21 1 A0A0U1RRM1;Q8WXI9;A0A0U1RRK3;A0A0U1RR34 A0A0U1RRM1 GATAD2B Transcriptional repressor p66-beta 2 0 GRLT(0.983)PS(0.017)PDIIVLS(0.102)DNEAS(0.508)S(0.39)PR;GRLT(1)PSPDIIVLS(0.02)DNEAS(0.555)S(0.425)PR ; 158.33 4.82E-08 23537000 7627.3 6614.5 6947.4 6255.9 4344.2 3233.3 2933.6 2925.2 8267.5 7608.5 TRUE FALSE FALSE 7534.335534 6707.619105 7068.316583 6979.236593 4122.499264 3026.702565 3182.779911 3009.836047 7528.034094 7410.830073 1.016665537 0.905110364 0.953782034 0.94176179 0.556280366 0.408416134 0.429476844 0.406140205 1.015815235 1 12.85541943 -8.700876974 2.541830637 0.9951626 0.416661024 0.982274551 0.03471858 0.026571549 0.349098962 0.005847228 0.01262236 1.99E-09 8.700876974 -0.578501575 down SHISDQSPLS(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 SHISDQSPLSSK 12 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 SHISDQSPLS(0.922)S(0.078)K 169.58 0.00016951 5611100 2260.7 2690.8 1887.1 2260.3 2374 2115.6 1970.1 2007.7 2531.9 2347.3 TRUE FALSE FALSE 2233.145719 2728.681153 1919.944184 2521.646521 2252.845921 1980.419988 2137.440245 2065.789632 2305.440523 2286.316808 0.976743779 1.193483398 0.839754218 1.102929617 0.985360346 0.86620541 0.934883669 0.903544787 1.00836442 1 11.15880961 -8.375428239 6.129043634 1.002045852 0.905431967 0.254666571 0.087369796 0.262850775 12.41737812 0.011360896 0.025653067 4.21E-09 8.375428239 -0.096613885 SHLDS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 1 SHLDSPEAR 9 0 K7ER08;K7EP90;Q9BTD8-4;Q9BTD8-2;Q9BTD8-3;Q9BTD8 K7ER08 RBM42 RNA-binding protein 42 1 0 S(0.004)HLDS(0.996)PEAR 120.55 0.005517 3549800 1398.4 1508.1 1393 1325.2 1754.8 3133.4 3547 1070.7 1911.9 1579.7 TRUE FALSE FALSE 1381.355763 1529.331071 1417.244581 1478.425859 1665.246008 2933.185853 3848.282091 1101.679015 1740.894876 1538.659166 0.897765921 0.993937517 0.921090656 0.960853379 1.082270879 1.906325921 2.501062078 0.715999384 1.131436327 1 10.58745798 -8.333878957 4.895671231 0.955679545 1.78612741 0.376415708 0.41426178 0.131320427 5.928236593 0.052555703 0.1215494 4.64E-09 8.333878957 0.830447865 SHNVAAGSY(ph)EAPLPPGSFHGDFAYGTYR ddPTM_HeLa_Romidepsin_16h_R1 1 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 S(0.001)HNVAAGS(0.231)Y(0.555)EAPLPPGS(0.206)FHGDFAY(0.002)GT(0.003)Y(0.002)R 42.738 0.017197 8683900 633.41 482.56 580.03 691.86 592.24 707.92 563.43 474.42 455.35 655.69 TRUE FALSE FALSE 625.6897553 489.3534923 590.1251788 771.8561085 562.0157828 662.6861967 611.2877301 488.1465942 414.6223556 638.6550793 0.97969902 0.766225007 0.924012347 1.208564894 0.879998924 1.037627693 0.957148467 0.764335257 0.649211709 1 9.31889317 -7.27059737 4.313976948 0.980194391 0.749919962 0.029146396 0.149807587 0.201635528 8.771757689 0.014110003 0.139913627 5.36E-08 7.27059737 -0.230274428 SHNVAAGSYEAPLPPGS(ph)FHGDFAYGTYR ddPTM_HeLa_Romidepsin_16h_R1 1 SHNVAAGSYEAPLPPGSFHGDFAYGTYR 28 0 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;X6RGP5;O15027-4;A0A3F2YNZ0;A0A3F2YNX0 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 SHNVAAGSYEAPLPPGS(0.998)FHGDFAYGT(0.001)YR 99.311 1.11E-08 12836000 1973.5 1710.7 1620.1 2007.2 2312.5 1814.9 1685.6 2167.1 1861.8 1866.7 TRUE FALSE FALSE 1949.446223 1734.78328 1648.297161 2239.281908 2194.484496 1698.933747 1828.774822 2229.801619 1695.275945 1818.202865 1.072183011 0.954119759 0.906552945 1.231590793 1.206952501 0.934402745 1.005814509 1.226376694 0.932390977 1 10.82829746 -9.265370761 24.94633645 1.018987096 1.109032302 0.288781321 0.103472932 501.789238 3184072.679 0.015916432 0.024894048 5.43E-10 9.265370761 0.090045206 SHPAMS(ph)PGTPGPTMGR ddPTM_HeLa_Romidepsin_16h_R1 1 SHPAMSPGTPGPTMGR 16 0 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GUC6;A0A1B0GUG2;A0A1B0GU09;A0A6I8PTU7 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 1 0 S(0.006)HPAMS(0.981)PGT(0.012)PGPTMGR 56.347 0.023565 5325400 610.5 770.21 608.21 668.99 460.45 697.12 622.79 487.46 666 753.89 TRUE FALSE FALSE 603.0589912 781.0530366 618.7956399 746.3417715 436.9515183 652.5762819 675.6897671 501.563886 606.431292 734.3038291 0.821266303 1.063664665 0.842697008 1.016393681 0.595055481 0.888700639 0.920177371 0.683046807 0.825858817 1 9.520233313 -8.79759337 24.99987642 0.926196254 0.790700483 0.295510288 0.116946547 186.348458 128856.2006 0.017047598 0.030902105 1.59E-09 8.79759337 -0.135495771 SHPLDLS(ph)PNVQSR ddPTM_HeLa_Romidepsin_16h_R1 1 SHPLDLSPNVQSR 13 0 H0YBF7;A0A0A0MRE5;Q9ULH1;Q9ULH1-2;H0YBM4 H0YBF7 ASAP1 "Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1" 1 0 SHPLDLS(0.986)PNVQS(0.014)R 78.166 0.0038478 0 11981 11962 11395 7501.1 12369 12543 11039 12494 12631 13613 TRUE FALSE FALSE 11834.97096 12130.40135 11593.3252 8368.412476 11737.76377 11741.54278 11976.65238 12855.49418 11501.25173 13259.3323 0.892576692 0.914857632 0.874352112 0.631133777 0.885245464 0.885530471 0.903262104 0.969543103 0.867408062 1 13.69472051 -11.52733527 0.668727951 0.996085085 0.860766164 0.008123176 0.092604424 0.736740179 0.676171787 0.048649332 0.021029852 2.97E-12 11.52733527 -0.135318921 SHS(ph)APSEVGFSDAR ddPTM_HeLa_Romidepsin_16h_R1 1 SHSAPSEVGFSDAR 14 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 S(0.005)HS(0.992)APS(0.002)EVGFSDAR 111.88 0.0052084 4757900 1782.2 2031.1 2267.9 1734 2001.1 2711.5 2407.1 1769.5 2461.6 2615.7 TRUE FALSE FALSE 1760.477861 2059.693879 2307.371848 1934.493239 1898.9764 2538.243901 2611.559014 1820.697691 2241.428331 2547.743737 0.690994873 0.808438403 0.905653035 0.759296632 0.745356125 0.996271275 1.025047761 0.714631407 0.879769931 1 11.31500446 -6.982937447 15.52816796 0.856658475 0.453229799 0.139909546 0.110889689 2152241.941 43983737.36 0.019101749 19664213.48 1.04E-07 6.982937447 -0.403428676 SHS(ph)DTSIASR ddPTM_HeLa_Romidepsin_16h_R1 1 SHSDTSIASR 10 0 H7C3H3;E9PEM3;H7C357;H0Y6E6;Q92622-3;Q92622-2;Q92622 H7C3H3 KIAA0226 Run domain Beclin-1 interacting and cysteine-rich containing protein 1 0 S(0.29)HS(0.71)DTSIASR 101.35 0.023623 1850300 428.43 330.04 393.7 317.53 475.24 737.4 945.06 285.06 631.04 490.68 TRUE FALSE FALSE 423.2081304 334.6863118 400.5521834 354.2443126 450.9867294 690.2825198 1025.333373 293.3077613 574.5982019 477.9320629 0.885498512 0.700280098 0.838094396 0.741202234 0.943620997 1.444310967 2.145353812 0.613701788 1.202259163 1 8.900661746 -8.264969511 5.599335302 0.900807997 1.479271356 0.271300804 0.369364375 0.127165672 15.434437 0.045806527 0.110896532 5.43E-09 8.264969511 0.57846336 SHS(ph)PSASQSGSQLR ddPTM_HeLa_Romidepsin_16h_R1 3 SHSPSASQSGSQLR 14 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 S(0.035)HS(0.656)PS(0.042)AS(0.035)QS(0.209)GS(0.022)QLR;S(0.291)HS(0.699)PS(0.01)ASQSGSQLR;S(0.03)HS(0.965)PS(0.005)AS(0.001)QSGSQLR ;; 178.67 3.81E-07 12067900 1822.71 1193.79 1669.97 1439.77 2568.45 2414.34 1525.43 1696.98 2880.21 2076.26 TRUE FALSE FALSE 1800.494109 1210.596207 1699.035127 1606.242982 2437.372412 2260.071466 1654.999986 1746.079439 2622.596804 2022.318466 0.890311857 0.598617986 0.840142221 0.794258179 1.205236689 1.11756457 0.818367638 0.863404784 1.29682681 1 10.98179449 SHS(ph)SPSQIPK ddPTM_HeLa_Romidepsin_16h_R1 1 SHSSPSQIPK 10 0 Q9H792;H0YN99 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 SHS(0.582)S(0.378)PS(0.04)QIPK 103.26 0.022403 14670000 3634.3 3474.9 3763.3 3810.4 5214.7 5566.5 4724.4 3916 4315.7 3987.9 TRUE FALSE FALSE 3590.003754 3523.819733 3828.798658 4250.976376 4948.5744 5210.818615 5125.690418 4029.303282 3929.692983 3884.293783 0.924235898 0.907197017 0.985712943 1.094401354 1.273995912 1.341509913 1.319593909 1.037332269 1.01168789 1 11.92343661 -9.009511955 2.573221728 0.959350277 1.255676113 0.709508456 0.083256839 0.107127587 1.423662926 0.012536419 0.023465199 9.78E-10 9.009511955 0.296325836 SHS(ph)SSEAYEPR ddPTM_HeLa_Romidepsin_16h_R1 2 SHSSSEAYEPR 11 0 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 SHS(0.851)S(0.148)SEAYEPR;S(0.001)HS(0.642)S(0.299)S(0.058)EAYEPR ; 132.06 0.0019655 8420300 1825.55 1327.73 1562.96 1054.7 2707.2 2524.5 1943.82 1495.83 2651 1775.63 TRUE FALSE FALSE 1803.299494 1346.421818 1590.162663 1176.649377 2569.041482 2363.192597 2108.928022 1539.109481 2413.88792 1729.498877 1.042671677 0.778504014 0.919435499 0.68034122 1.485425355 1.366403083 1.219386755 0.889916439 1.395715229 1 10.75613836 -8.754722737 24.99999773 0.970851497 1.247798848 0.256363082 0.225826274 141.6454548 527213.1053 0.027096539 0.053224038 1.76E-09 8.754722737 0.276947351 SHS(ph)VPENMVEPPLSGR ddPTM_HeLa_Romidepsin_16h_R1 1 SHSVPENMVEPPLSGR 16 0 G3V311;A1L390-2;A1L390-3;A1L390 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 S(0.062)HS(0.938)VPENMVEPPLSGR 67.396 0.013832 11307000 2256.3 3196.8 1406 1628.8 1921.8 1456 1358.5 1517 2330.9 1985.3 TRUE FALSE FALSE 2228.799348 3241.804634 1430.47084 1817.12952 1823.723375 1362.966299 1473.890956 1560.892002 2122.418466 1933.72162 1.152595764 1.676458804 0.739750141 0.939705851 0.943115781 0.70484101 0.762204312 0.807195816 1.097582219 1 10.9171644 SHSS(ph)LPPNNSYADFER ddPTM_HeLa_Romidepsin_16h_R1 1 SHSSLPPNNSYADFER 16 0 O43293 O43293 DAPK3 Death-associated protein kinase 3 1 0 S(0.01)HS(0.386)S(0.604)LPPNNSYADFER 62.861 0.02552 8787300 2577.9 2353.1 1907.1 1693.2 2370.7 2516.2 2215.8 2446.6 2404.7 2759.9 TRUE FALSE FALSE 2546.479563 2386.227004 1940.292276 1888.975751 2249.714333 2355.422941 2404.009997 2517.388511 2189.617609 2688.1974 0.947281462 0.887668072 0.721781918 0.702692351 0.836885838 0.876209069 0.894283283 0.936459693 0.814530067 1 11.39242337 -10.21297235 2.72231071 0.977082649 0.827259887 0.095272114 0.08596815 0.189960599 2.730266471 0.013420651 0.016200617 6.12E-11 10.21297235 -0.149822762 SHSS(ph)PSQIPK ddPTM_HeLa_Romidepsin_16h_R1 1 SHSSPSQIPK 10 0 Q9H792;H0YN99 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 S(0.001)HS(0.082)S(0.835)PS(0.081)QIPK 131.42 0.0067711 15880000 4140.8 4160.5 4257.9 4553.2 5796.6 5804.2 5136.4 4737.2 5060.1 4574 TRUE FALSE FALSE 4090.330337 4219.071628 4332.006963 5079.662407 5500.777872 5433.330352 5572.685688 4874.263408 4607.511983 4455.166821 0.918109355 0.947006431 0.972355725 1.140173334 1.234696274 1.219557105 1.250836593 1.094069786 1.034195164 1 12.12126374 -9.179388428 3.025206792 0.958836479 1.204023497 0.822243969 0.049953405 0.069987926 1.248938124 0.00737987 0.012688468 6.62E-10 9.179388428 0.245187018 SHTPS(ph)PTSPK ddPTM_HeLa_Romidepsin_16h_R1 3 SHTPSPTSPK 10 0 B7Z385;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;P40123 B7Z385 CAP2 Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 2 1 0 SHT(0.024)PS(0.939)PT(0.03)S(0.007)PK;SHT(0.011)PS(0.932)PT(0.056)S(0.002)PK;SHT(0.011)PS(0.573)PT(0.208)S(0.208)PK ;; 138.63 0.0051314 5614400 5895 6656.8 6542.8 5241.8 6354.8 6288.8 6768.5 3345.1 7781.2 6710.4 TRUE FALSE FALSE 5823.149473 6750.514605 6656.674689 5847.881579 6030.490843 5886.965976 7343.416221 3441.885191 7085.229984 6536.062841 0.890926176 1.032810542 1.018453288 0.894710122 0.922648847 0.900689929 1.123522891 0.526599158 1.084021093 1 12.67420614 -7.24735581 24.92217453 0.958074845 0.526598853 0.730808684 0.082034319 877.318677 1552470.831 0.009968127 0.281335885 5.66E-08 7.24735581 -0.431475992 SHTPSPTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 SHTPSPTSPK 10 0 B7Z385;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;P40123 B7Z385 CAP2 Adenylyl cyclase-associated protein;Adenylyl cyclase-associated protein 2 1 0 SHTPS(0.005)PT(0.184)S(0.81)PK;SHTPSPT(0.131)S(0.869)PK;SHTPSPT(0.058)S(0.942)PK ;; 122.52 0.0043991 165864400 16781.7 16237.3 16918.7 14447.5 16361.3 18344.5 19513.2 7321.8 21459 18714.9 TRUE FALSE FALSE 16577.15819 16465.88914 17213.16288 16117.98793 15526.32181 17172.34565 21170.65072 7533.644731 19539.65329 18228.6842 0.909399604 0.90329554 0.944289927 0.884210168 0.851752197 0.942050752 1.161392149 0.413285164 1.071917922 1 14.15392281 -7.246890303 24.99288413 0.949262726 0.41328479 0.771374199 0.089518948 866.8056789 1489004.479 0.011133443 0.330048734 5.66E-08 7.246890303 -0.535977936 SHVEDGDIAGAPAS(ph)SPEAPPAEQDPVQLK ddPTM_HeLa_Romidepsin_16h_R1 3 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 A0A087WVV2;Q9P2E9-3;Q9P2E9;A0A087WU26;F8W7S5 A0A087WVV2 RRBP1 Ribosome-binding protein 1 1 0 SHVEDGDIAGAPAS(0.5)S(0.5)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.5)S(0.5)PEAPPAEQDPVQLK;SHVEDGDIAGAPAS(0.5)S(0.5)PEAPPAEQDPVQLK ;; 106.88 3.24E-09 93893000 6317 6916.3 6031.4 5944 7417.2 8041.7 7606.4 8776.8 7546.9 7517.5 TRUE FALSE FALSE 6240.005974 7013.667853 6136.373987 6631.273247 7038.672607 7527.861323 8252.487426 9030.742861 6871.886362 7322.194266 0.852204373 0.957864214 0.83805124 0.905640168 0.96127914 1.028088173 1.127051144 1.233338332 0.938500962 1 12.83806034 -7.704296316 1.268755424 0.921988921 1.261868466 0.844104516 0.045519895 0.273734704 0.613637601 0.00926463 0.098024419 1.98E-08 7.704296316 0.339879545 SHVEDGDIAGAPASS(ph)PEAPPAEQDPVQLK ddPTM_HeLa_Romidepsin_16h_R1 1 SHVEDGDIAGAPASSPEAPPAEQDPVQLK 29 0 A0A087WVV2;Q9P2E9-3;Q9P2E9;A0A087WU26;F8W7S5 A0A087WVV2 RRBP1 Ribosome-binding protein 1 1 0 SHVEDGDIAGAPAS(0.223)S(0.777)PEAPPAEQDPVQLK 131.26 1.66E-10 16224000 2611.1 2491.3 2445.7 2648.9 2447.6 3027.7 2674.2 2977 2720.7 2404.3 TRUE FALSE FALSE 2579.274909 2526.372587 2488.266383 2955.178281 2322.689839 2834.239741 2901.346481 3063.134798 2477.353778 2341.835939 1.101390095 1.078799989 1.062528054 1.261906623 0.99182432 1.210264004 1.238919615 1.308005717 1.057868203 1 11.19342429 -4 0.207790106 1.012425491 2.421665819 0.569214645 0.070862457 25.37412296 0.296295699 0.058307186 11.87858022 1.00E-04 4 1.409240328 SHVTEEEEEEEEEES(ph)DS ddPTM_HeLa_Romidepsin_16h_R1 2 SHVTEEEEEEEEEESDS 17 0 O75971;O75971-2 O75971 SNAPC5 snRNA-activating protein complex subunit 5 1 0 SHVTEEEEEEEEEES(0.5)DS(0.5);SHVTEEEEEEEEEES(0.5)DS(0.5) ; 164.65 9.21E-06 20032800 2153.5 2069.53 1777.04 1827.98 2637.6 2479.5 2349.4 2636.4 2793.9 1965.09 TRUE FALSE FALSE 2127.252314 2098.664898 1807.968636 2039.339649 2502.99343 2321.067952 2548.957977 2712.680074 2544.006587 1914.036679 1.111395794 1.096460126 0.944584112 1.065465292 1.307704005 1.212655942 1.33171846 1.417256056 1.329131576 1 10.90240276 -8.769621306 5.716501947 1.048742729 1.312266059 0.484201078 0.109278758 0.059385003 6.417315545 0.010497207 0.020066169 1.70E-09 8.769621306 0.263523329 SHWDDST(ph)SDSELEK ddPTM_HeLa_Romidepsin_16h_R1 2 SHWDDSTSDSELEK 14 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 SHWDDST(0.943)S(0.057)DSELEK;SHWDDS(0.01)T(0.495)S(0.495)DSELEK ; 256.13 2.35E-67 53062000 5130.7 5012.7 3979.5 6255.9 12811.8 15368.5 14370.5 16063.3 5247 4520.7 TRUE FALSE FALSE 5068.165055 5083.268922 4048.761528 6979.236593 12157.96604 14386.50245 15591.12991 16528.06624 4777.695179 4403.251562 1.151005111 1.154435274 0.919493577 1.585018819 2.761133646 3.267245181 3.540821979 3.75360481 1.08503798 1 12.10435355 -8.657955246 1.603108982 1.062210024 3.59590738 0.988992513 0.116085264 0.027252367 0.140366074 0.019130752 0.049127127 2.20E-09 8.657955246 2.533697356 up SIDAVIATASAPPSSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 SIDAVIATASAPPSSSPGR 19 0 Q9NR48-2;Q9NR48 Q9NR48-2 ASH1L Histone-lysine N-methyltransferase ASH1L 1 0 SIDAVIATASAPPS(0.011)S(0.41)S(0.579)PGR 259.22 4.85E-76 24673000 1503.8 1567 1349.9 1722.1 1330.7 1632.8 966.02 1099.1 1797.7 1627.1 TRUE FALSE FALSE 1485.471107 1589.060267 1373.394443 1921.217305 1262.789413 1528.46935 1048.073715 1130.900724 1636.90921 1584.827707 0.937307633 1.002670675 0.866589117 1.212256257 0.796799177 0.964438811 0.661317132 0.713579602 1.032862564 1 10.63011029 -7.765300942 24.7994684 0.969252065 0.687448307 0.552872271 0.103850161 39.82048928 255741.9344 0.012770245 0.040546697 1.72E-08 7.765300942 -0.281803758 SIDKDEEFAGSS(ph)PQSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SIDKDEEFAGSSPQSSK 17 1 A0A590UJ38;H3BQ24;A0A590UJL5;Q9Y2M0-2;Q9Y2M0 A0A590UJ38 FAN1 Fanconi-associated nuclease 1 1 0 SIDKDEEFAGS(0.192)S(0.788)PQS(0.008)S(0.011)K 69.255 0.012148 5759100 1551.2 1664.6 1486.2 1811.3 1538.8 1542 1202.1 1421.1 1845 2045.7 TRUE FALSE FALSE 1532.293378 1688.034282 1512.066688 2020.731028 1460.269294 1443.471177 1304.206344 1462.217286 1679.978579 1992.552419 0.769010322 0.847171832 0.758859176 1.014141966 0.732863678 0.724433226 0.654540544 0.733841314 0.843128925 1 10.96040196 -16.52287875 0.142259806 1.797189738 0.685679194 0.264006519 0.096961667 46.16094721 0.454794857 10.41732992 0.249173007 3.00E-17 16.52287875 -1.111510544 SIEAVHEDIR ddPTM_HeLa_Romidepsin_16h_R1 4 SIEAVHEDIR 10 0 H7C312;H7BZ20;P23919-2;P23919 H7C312 DTYMK Thymidylate kinase 0 0 ;;; ;;; 136.49 0.0026007 17527400 18078.1 16612 17402.2 15102.9 18125.1 17172 13513.8 16913.9 19795.9 18189.9 FALSE FALSE TRUE 17857.75716 16845.86417 17705.07799 16849.16836 17200.10851 16074.76462 14661.66183 17403.27701 18025.30512 17717.32378 1.007926332 0.950813136 0.999308824 0.95099963 0.970807371 0.907290786 0.827532534 0.982274594 1.017383063 1 14.11287308 -8.720202428 0.95942288 1.000766604 0.896881236 0.44522599 0.040672598 0.337166173 0.585341449 0.006323796 0.02124064 1.90E-09 8.720202428 -0.103885368 SIEEGDGAFGRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SIEEGDGAFGRSPR 14 1 O75420 O75420 GIGYF1 PERQ amino acid-rich with GYF domain-containing protein 1 1 0 SIEEGDGAFGRS(1)PR;SIEEGDGAFGRS(1)PR ; 78.763 0.014112 5994900 3713.2 3687.7 3699.3 3921.9 3777 4110.8 4009 3665.2 4190.5 3822.9 TRUE FALSE FALSE 3667.94209 3739.615537 3763.684765 4375.368531 3584.245596 3848.133147 4349.52436 3771.246779 3815.691185 3723.580507 0.985057818 1.004306347 1.010770348 1.175043355 0.962580395 1.033449697 1.168102677 1.012801193 1.024737125 1 11.86247483 -9.500367102 24.7419294 0.994262765 1.070293924 0.215069218 0.061604641 659.9223982 725303.3633 0.008723249 0.013258103 3.16E-10 9.500367102 0.076031158 SIGS(ph)AVDQGNESIVAK ddPTM_HeLa_Romidepsin_16h_R1 1 SIGSAVDQGNESIVAK 16 0 Q9H0H5;F8VRD2;F8W1E5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 0 S(0.213)IGS(0.787)AVDQGNESIVAK 176.17 2.70E-07 6684600 2589.8 1815 2033.5 1815.4 2050.8 2039.8 1598.2 1829.9 2021.5 2156.2 TRUE FALSE FALSE 2558.234521 1840.551618 2068.892214 2025.30509 1946.140023 1909.463363 1733.951068 1882.845269 1840.691977 2100.181613 1.218101571 0.87637736 0.985101575 0.964347596 0.926653205 0.909189639 0.825619583 0.896515453 0.876444192 1 11.03629837 -10.24629222 24.99307416 1.10299241 0.913935565 0.136792871 0.096169482 497.5834085 821022.3531 0.015072965 0.018421723 5.67E-11 10.24629222 -0.189056845 SIGS(ph)PESTPK ddPTM_HeLa_Romidepsin_16h_R1 1 SIGSPESTPK 10 0 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-6;Q8NEY1-5;H0Y6F6 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 S(0.033)IGS(0.928)PES(0.019)T(0.019)PK 111.63 0.0019922 0 6557.9 6554.1 5985.3 5815.6 6629.1 6091.6 4662.4 5760.3 6759 5761.8 TRUE FALSE FALSE 6477.969792 6646.368792 6089.471636 6488.027035 6290.79229 5702.36642 5058.42414 5926.965192 6154.458112 5612.107605 1.154284673 1.184291047 1.085059672 1.156076735 1.12093223 1.016082873 0.90134126 1.05610327 1.096639363 1 12.45432696 -8.077697871 4.93964787 1.092805079 0.974060671 0.436575405 0.061463785 0.19973108 8.717170152 0.010981411 0.029546674 8.36E-09 8.077697871 -0.118744407 SIGVSNFNHR ddPTM_HeLa_Romidepsin_16h_R1 1 SIGVSNFNHR 10 0 P52895;S4R3P0;B4DK69 P52895 AKR1C2 Aldo-keto reductase family 1 member C2 0 0 179.57 2.06E-05 7966300 2351 1781.1 3205.3 2264.7 5059 5169.4 3068.8 2391.2 2771.7 1942.7 FALSE FALSE TRUE 2322.345108 1806.174373 3261.086902 2526.55527 4800.820352 4839.092023 3329.463795 2460.385599 2523.79221 1892.228374 1.227306989 0.954522402 1.723410846 1.335227452 2.537125232 2.557350947 1.759546491 1.300258274 1.333767237 1 10.8858705 -9.344038419 1.575349872 1.100930728 2.016218491 0.446159861 0.405875334 0.23295686 1.134310257 0.066782085 0.117774822 4.53E-10 9.344038419 0.915287763 SIKYDS(ph)LLEQGLVEAALVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SIKYDSLLEQGLVEAALVSK 20 1 O96028;D6RIS1;D6R9V2;O96028-7;O96028-6;O96028-3;O96028-5 O96028;O96028-3;O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 S(0.422)IKY(0.004)DS(0.574)LLEQGLVEAALVSK 63.573 0.0064476 1329000 694.5 693.2 751.2 789.91 814.07 598.5 452.92 648.77 826.64 827.05 TRUE FALSE FALSE 686.0351669 702.9588878 764.2743209 881.2431108 772.5249702 560.2577816 491.3910135 667.5411364 752.703248 805.5631218 0.851621863 0.872630423 0.948745418 1.09394669 0.958987507 0.695485886 0.609996908 0.828663972 0.934381463 1 9.653853829 -8.259459765 24.80748988 0.939758583 0.701243703 0.649107694 0.080468478 83.68198409 1048647.371 0.012899581 0.031162787 5.50E-09 8.259459765 -0.238514879 SILAKPSS(ph)SPDPR ddPTM_HeLa_Romidepsin_16h_R1 1 SILAKPSSSPDPR 13 1 Q9BTC0;Q9BTC0-1 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 SILAKPS(0.016)S(0.492)S(0.492)PDPR 90.697 0.0080969 73671000 7381.2 6948.7 5758.2 7670.7 8435.3 8247.2 6957.5 7663.1 7300 6939.3 TRUE FALSE FALSE 7291.235095 7046.523981 5858.419056 8557.622426 8004.815165 7720.230537 7548.469876 7884.819708 6647.069717 6759.015986 1.0787421 1.04253696 0.866756207 1.266104777 1.184316649 1.142212203 1.116800122 1.166563258 0.98343749 1 12.72259751 -9.244560302 24.99947471 1.026994864 1.170628882 0.633150656 0.066517913 511.2422489 757197.5567 0.01020502 0.016894019 5.69E-10 9.244560302 0.143634019 SILLES(ph)DNEDEKLSR ddPTM_HeLa_Romidepsin_16h_R1 1 SILLESDNEDEKLSR 15 1 Q8IWY7;Q6IQ55-2;Q6IQ55 Q8IWY7 TTBK2 Tau-tubulin kinase 2 1 0 SILLES(1)DNEDEKLSR 107.63 0.0019137 7449700 1110.2 1313.3 889.71 1619.4 1699 1859.9 1599.1 1774.4 1355.4 1226.5 TRUE FALSE FALSE 1096.668455 1331.788672 905.1950293 1806.642648 1612.29369 1741.058393 1734.927514 1825.739464 1234.169629 1194.635353 0.917994309 1.114807684 0.757716593 1.512296319 1.349611566 1.457397345 1.452265337 1.528281797 1.033093174 1 10.22235461 -9.251008364 24.98796587 0.960369956 1.45326843 0.867694059 0.096668744 163.0233418 390529.739 0.013094345 0.021563348 5.61E-10 9.251008364 0.492898475 SILNNK(ac)LISK ddPTM_HeLa_Romidepsin_16h_R1 1 SILNNKLISK 10 1 Q9ULX6-2;Q9ULX6 Q9ULX6-2 AKAP8L A-kinase anchor protein 8-like 0 1 SILNNK(1)LISK 112.15 0.00095662 0 0 0 0 0 0 0 69.726 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 75.6485247 0 0 0 0 SILPYPVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SILPYPVSPK 10 0 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 0 SILPYPVS(1)PK 109.22 0.018585 38681000 6354.4 5627.7 5885.6 4064.9 4526.8 6001.1 5544.6 5012.3 6446 6261.9 TRUE FALSE FALSE 6276.950129 5706.926908 5988.036399 4534.902864 4295.780504 5617.649078 6015.558186 5157.322992 5869.453616 6099.214935 1.029140667 0.93568221 0.981771664 0.74352239 0.704316957 0.921044616 0.986284014 0.84557161 0.962329362 1 12.57440784 -9.414067989 6.475988454 1.006072564 0.845437323 0.428892997 0.079600573 0.168514704 8.778408237 0.013002174 0.01989487 3.85E-10 9.414067989 -0.16063524 SILVS(ph)PTGPSR ddPTM_HeLa_Romidepsin_16h_R1 4 SILVSPTGPSR 11 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 S(0.024)ILVS(0.902)PT(0.075)GPSR;S(0.003)ILVS(0.977)PT(0.02)GPSR;S(0.208)ILVS(0.624)PT(0.169)GPSR;S(0.263)ILVS(0.679)PT(0.058)GPSR ;;; 110.93 0.014145 179934000 6191.7 5839.3 6126.8 5281.8 8238.4 10713.7 9982.1 9598.8 6689.6 6115.9 TRUE FALSE FALSE 6116.233179 5921.505819 6233.434384 5892.506568 7817.963706 10029.12915 10829.97932 9876.526134 6091.265422 5957.008036 1.026729046 0.99404026 1.046403555 0.98917217 1.31239771 1.683584962 1.818023286 1.657967569 1.022537721 1 12.54037219 -8.432565036 2.266994467 1.01188538 1.7458705 0.980890408 0.044145298 0.024885421 0.249065165 0.005996304 0.015625768 3.69E-09 8.432565036 0.73398512 SINHQIES(ph)PSER ddPTM_HeLa_Romidepsin_16h_R1 3 SINHQIESPSER 12 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 SINHQIES(0.5)PS(0.5)ER;SINHQIES(0.664)PS(0.336)ER;S(0.003)INHQIES(0.91)PS(0.087)ER ;; 198.81 1.27E-14 22361000 3952.9 3368.66 3153.74 3112.97 4503.7 4464.59 2639.82 3286.45 5233.6 4314.4 TRUE FALSE FALSE 3904.720534 3416.084084 3208.629522 3472.906238 4273.859383 4179.317108 2864.046245 3381.538246 4765.493708 4202.311266 0.929184034 0.81290601 0.763539233 0.826427653 1.017025897 0.994528212 0.68154072 0.804685334 1.134017308 1 12.03696731 -10.60029247 2.007923369 0.975106759 0.846296443 0.343912197 0.107623873 0.3216829 2.66499548 0.019972988 0.02084618 2.51E-11 10.60029247 -0.128810315 SINKLDS(ph)PDPFK ddPTM_HeLa_Romidepsin_16h_R1 1 SINKLDSPDPFK 12 1 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 0 S(0.001)INKLDS(0.999)PDPFK 134.04 0.019275 20810000 1784.2 1860.3 1923.7 1451.9 2164.1 1826.1 1599.1 1874.1 1791.3 1829.2 TRUE FALSE FALSE 1762.453484 1886.489352 1957.181192 1619.775509 2053.657902 1709.418103 1734.927514 1928.324127 1631.081642 1781.67712 0.98921037 1.058827849 1.098504981 0.909129657 1.15265436 0.959443259 0.973760899 1.082308407 0.915475438 1 10.7990202 -10.28874329 23.4874441 0.994904893 1.03066852 0.114281956 0.072382729 770.9928191 663221.7596 0.01065188 0.012183841 5.14E-11 10.28874329 0.035763627 SINKLDS(ph)PDPFKLNDPFQPFPGNDSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SINKLDSPDPFKLNDPFQPFPGNDSPK 27 2 P42566;B1AUU8;P42566-2 P42566 EPS15 Epidermal growth factor receptor substrate 15 1 0 S(0.028)INKLDS(0.971)PDPFKLNDPFQPFPGNDSPK 46.399 0.01722 13317000 1743.7 1793.8 1453.3 1455.3 1638.9 1722.9 1381.5 1333.4 1827.4 1618.2 TRUE FALSE FALSE 1722.447114 1819.053163 1478.594077 1623.568633 1555.260817 1612.81225 1498.844576 1371.979825 1663.952767 1576.158931 1.092813091 1.154105165 0.938099609 1.030079265 0.986741113 1.023254837 0.950947615 0.870457794 1.055701132 1 10.6221973 -5.77801591 0.571925384 1.046004804 1.67E-14 0.505799742 0.054025947 11.15290868 0.67288665 0.010786889 11.36694471 1.67E-06 5.77801591 -1.046004804 SIPAGAEPGEKGS(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 1 SIPAGAEPGEKGSAR 15 1 A6NGP5;Q9H910;Q9H910-3;H3BU16;Q9H910-2 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 0 SIPAGAEPGEKGS(1)AR 114.06 0.026162 12794000 2151.1 2190.7 1985.8 1958.3 2057.3 2187.6 1193.2 2282.6 2649.5 2235.8 TRUE FALSE FALSE 2124.881566 2221.540732 2020.362016 2184.72786 1952.308304 2047.81942 1294.550378 2348.64343 2412.522084 2177.713594 0.97573968 1.0201253 0.927744595 1.003220932 0.896494521 0.940352958 0.594453918 1.078490503 1.107823403 1 11.08859851 -8.414935904 1.892717051 0.98675559 0.837527878 0.195580328 0.12099677 0.347976975 2.414323025 0.014958168 0.042526953 3.85E-09 8.414935904 -0.149227712 TVANLLSGKS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TVANLLSGKSPR 12 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 TVANLLS(0.005)GKS(0.995)PR;TVANLLS(0.005)GKS(0.995)PR ; 150.12 0.0050774 1006800000 11960.6 12134.7 10690.4 11030.5 6392.9 5460.2 4427.5 4532 13252 11889.2 TRUE FALSE FALSE 11814.81961 12305.53263 10876.46193 12305.89831 6066.646458 5111.310842 4803.571739 4663.12627 12066.70793 11580.31687 1.020250114 1.062624863 0.939219716 1.062656441 0.523875687 0.441379187 0.414804862 0.402676915 1.042001533 1 13.49938711 -8.697751884 4.58541161 1.012062864 0.429950395 0.980752546 0.039598933 0.018271548 0.757179165 0.005475884 0.011065776 2.01E-09 8.697751884 -0.582112469 down SIQEIQELDKDDESLR ddPTM_HeLa_Romidepsin_16h_R1 2 SIQEIQELDKDDESLR 16 1 J3KRY1;J3KTF8;J3QQX2;P52565-2;P52565;J3KS60;J3KRE2 J3KRY1 ARHGDIA Rho GDP-dissociation inhibitor 1 0 0 ; ; 169.98 1.43E-05 97009000 4375.2 4282.5 4350.2 4432.9 4683.3 4354 3949.6 4470.3 5177.7 5085.5 FALSE FALSE TRUE 4321.87338 4342.789147 4425.913406 4945.452755 4444.293725 4075.793452 4285.078925 4599.641078 4714.593544 4953.377977 0.872510315 0.876732841 0.893514169 0.998400037 0.897224832 0.8228311 0.865082161 0.928586734 0.951793618 1 12.274197 -12.31504264 0.920460914 1.003425608 0.892692814 0.31856815 0.045638023 0.471826658 0.681077999 0.036413209 0.00858272 4.84E-13 12.31504264 -0.110732794 SIQPQVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SIQPQVSPR 9 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 0 SIQPQVS(1)PR 134.38 0.0069077 72896000 3445.2 3305.3 2917.6 2593.8 2474.4 2036.3 1850.3 1963.7 3944.9 3718.6 TRUE FALSE FALSE 3403.208577 3351.8321 2968.379604 2893.70736 2348.122135 1906.187002 2007.464436 2020.516561 3592.058264 3621.990236 0.939596287 0.925411689 0.81954379 0.798927433 0.648296097 0.526281651 0.55424347 0.557847048 0.991736043 1 11.82256694 -8.993951722 0.782689789 0.977340531 0.515386722 0.973636744 0.029210895 0.074142846 0.086201148 0.005939763 0.017834015 1.01E-09 8.993951722 -0.461953809 SIS(ph)ADDDLQESSR ddPTM_HeLa_Romidepsin_16h_R1 1 SISADDDLQESSR 13 0 A0A0A0MSN9;P18615-4;P18615;P18615-3;A2ABK4;A0A0G2JI50;E9PD43;A0A0A0MT02 A0A0A0MSN9 NELFE Negative elongation factor E 1 0 S(0.001)IS(0.975)ADDDLQES(0.016)S(0.007)R 143.58 0.00076751 96545000 1481.1 1619.4 935.07 1158.7 1538.5 1307.9 1030.1 1437 1352.3 1353.5 TRUE FALSE FALSE 1463.047784 1642.197956 951.3445011 1292.674346 1459.984604 1224.329411 1117.596668 1478.577328 1231.346901 1318.335875 1.109768619 1.245659765 0.721625285 0.980534908 1.107445099 0.928693085 0.84773288 1.121548276 0.934016076 1 10.36450226 -9.779546184 24.99963448 1.067820315 0.95396101 0.1676252 0.13196274 337.4808002 465950.2088 0.02017341 0.026542548 1.66E-10 9.779546184 -0.113859305 SIS(ph)LGDSEGPIVATLAQPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SISLGDSEGPIVATLAQPLR 20 0 O43379;O43379-4 O43379 WDR62 WD repeat-containing protein 62 1 0 S(0.013)IS(0.969)LGDS(0.017)EGPIVATLAQPLR 94.639 0.0011998 97688000 302.14 197.84 175.54 147.26 270.41 146.73 0 140.04 133.38 241.95 TRUE FALSE FALSE 298.4574015 200.6251967 178.5952001 164.2868941 256.6099687 137.3544265 0 144.0918365 121.4501587 235.6641041 1.266452532 0.851318437 0.757837944 0.697123114 1.088880165 0.582839831 0 0.611428868 0.515352812 1 7.880588217 -8.342006473 0.587538806 1.111781435 0.183339633 0.190780543 0.301083566 0.762161071 0.355556418 0.050889225 0.382657556 4.55E-09 8.342006473 -0.928441801 SIS(ph)NEGLTLNNSHVSK ddPTM_HeLa_Romidepsin_16h_R1 2 SISNEGLTLNNSHVSK 16 0 Q08AD1-2;Q08AD1-3;Q08AD1 Q08AD1-2 CAMSAP2 Calmodulin-regulated spectrin-associated protein 2 1 0 S(0.002)IS(0.998)NEGLTLNNSHVSK;S(0.071)IS(0.929)NEGLTLNNSHVSK ; 202.96 1.63E-18 29112100 6087.7 6663.9 4804.9 4121 7119.3 6454.2 4574.1 5530.1 7332.8 6824.6 TRUE FALSE FALSE 6013.500771 6757.714559 4888.527269 4597.48941 6755.975555 6041.79745 4962.62394 5690.104718 6676.936003 6647.295908 0.90465369 1.016611063 0.735415925 0.69163303 1.016349452 0.908910561 0.746562814 0.856002922 1.00445897 1 12.69855186 -10.83637369 0.504727601 0.994730765 0.834518025 0.269380712 0.10210956 0.894489383 0.555625879 0.054952047 0.039088356 1.46E-11 10.83637369 -0.16021274 SIS(ph)PEVSASRR ddPTM_HeLa_Romidepsin_16h_R1 2 SISPEVSASRR 11 1 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 S(0.237)IS(0.763)PEVSASRR;S(0.065)IS(0.933)PEVS(0.002)ASRR ; 103.97 0.00090645 7518600 3473 3282.4 3266.2 4341.4 3553.5 3782.8 3304.6 3485.9 3500.3 2727.7 TRUE FALSE FALSE 3430.66974 3328.609713 3323.046841 4843.373095 3372.151635 3541.091288 3585.292642 3586.759017 3187.224401 2656.833961 1.291262379 1.252848226 1.250754428 1.822986745 1.269236875 1.332823707 1.349460559 1.350012485 1.199632513 1 11.37549235 -11.57830012 0.487954794 0.974195384 1.398133911 0.288322347 0.165284765 0.745783003 0.348760276 0.143800837 0.04873733 2.64E-12 11.57830012 0.423938526 SIS(ph)VGENLGLVAEPQAHAPIR ddPTM_HeLa_Romidepsin_16h_R1 2 SISVGENLGLVAEPQAHAPIR 21 0 O60336-4;O60336-3;O60336-6;O60336 O60336-4 MAPKBP1 Mitogen-activated protein kinase-binding protein 1 1 0 S(0.167)IS(0.833)VGENLGLVAEPQAHAPIR;S(0.051)IS(0.949)VGENLGLVAEPQAHAPIR ; 150.17 4.61E-06 28621000 1891.55 1831.77 1500.31 2350.21 3638.6 3600.9 2969.2 4112.9 2078.1 1694.45 TRUE FALSE FALSE 1868.495061 1857.557706 1526.422266 2621.952338 3452.908665 3370.814111 3221.403774 4231.900272 1892.229531 1650.427945 1.13212762 1.125500639 0.92486453 1.58864999 2.092129302 2.042387929 1.951859688 2.564123012 1.146508418 1 10.68862444 -8.958733771 2.452422782 1.05980162 2.153077943 0.90631339 0.165913558 0.05714892 0.694187525 0.023982595 0.046232193 1.10E-09 8.958733771 1.093276323 up SISASKAS(ph)PPGDLQNPK ddPTM_HeLa_Romidepsin_16h_R1 1 SISASKASPPGDLQNPK 17 1 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 0 SIS(0.001)AS(0.001)KAS(0.998)PPGDLQNPK 79.695 0.007047 264340000 2797.1 2326 2592.5 2876.8 2993.4 2925.3 2558.4 2547.3 3256.7 2621.5 TRUE FALSE FALSE 2763.007869 2358.745489 2637.621375 3209.429152 2840.635628 2738.382771 2775.710432 2621.002107 2965.412595 2553.393052 1.082092656 0.923769056 1.032986822 1.256927189 1.112494461 1.072448587 1.087067434 1.026478123 1.161361582 1 11.31819992 -9.472370409 24.99980444 1.028707723 1.111408601 0.160379303 0.079236137 400.5796938 198272.5236 0.010888067 0.016631687 3.37E-10 9.472370409 0.082700878 SISASKAS(ph)PPGDLQNPKR ddPTM_HeLa_Romidepsin_16h_R1 1 SISASKASPPGDLQNPKR 18 2 O00273 O00273 DFFA DNA fragmentation factor subunit alpha 1 0 SIS(0.006)AS(0.022)KAS(0.972)PPGDLQNPKR 117.84 0.0013649 12341000 820.47 876.15 713.09 1779.1 982.82 1001.2 938.86 773.05 1025.8 803.56 TRUE FALSE FALSE 810.4697961 888.4844627 725.5010323 1984.807913 932.663028 937.2265512 1018.606745 795.4169821 934.0498788 782.6833954 1.035501457 1.13517735 0.926940621 2.535901393 1.191622351 1.197452963 1.301428842 1.016269141 1.193394269 1 9.612285028 SISGPSVGVMEMRS(ph)PLLAGGS(ph)PPQPVVPAHK ddPTM_HeLa_Romidepsin_16h_R1 1 SISGPSVGVMEMRSPLLAGGSPPQPVVPAHK 31 1 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 0 S(0.002)IS(0.005)GPS(0.048)VGVMEMRS(0.947)PLLAGGS(0.999)PPQPVVPAHK 67.899 9.53E-05 11648000 957.23 1107.9 1079.7 1315 1500 1448 1219.1 1599.1 1164.9 1159.7 TRUE FALSE FALSE 945.5629126 1123.497045 1098.491726 1467.046487 1423.449403 1355.477473 1322.650324 1645.367436 1060.708426 1129.570827 0.837099268 0.99462293 0.972485921 1.298764497 1.260168348 1.199993344 1.170931731 1.456630604 0.939036669 1 10.14155902 -9.322419998 4.338148472 0.928794695 1.266790951 0.794042165 0.08344518 0.080507021 3.09787421 0.014318015 0.0224422 4.76E-10 9.322419998 0.337996256 SISGTSTS(ph)EKPNSMDTANTSPFK ddPTM_HeLa_Romidepsin_16h_R1 1 SISGTSTSEKPNSMDTANTSPFK 23 1 Q9UJF2-2;Q9UJF2 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 S(0.033)IS(0.037)GT(0.174)S(0.194)T(0.194)S(0.216)EKPNS(0.141)MDT(0.01)ANT(0.001)SPFK 59.661 0.010003 45562000 2734.3 2978 2850.1 3255.6 4840.9 5108.5 4092 4274.1 3145.2 2644.1 TRUE FALSE FALSE 2700.9733 3019.924362 2899.704795 3632.02779 4593.850809 4782.083337 4439.574378 4397.76434 2863.885435 2575.405901 1.048756353 1.172601321 1.125921469 1.410273926 1.783738559 1.856827048 1.723834824 1.707600475 1.11201323 1 11.33058411 -9.070501217 1.736708596 1.035131052 1.78137957 0.95589937 0.067994292 0.045987871 0.273867863 0.010899499 0.021357864 8.50E-10 9.070501217 0.746248518 SISGTSTSEKPNS(ph)MDTANTSPFK ddPTM_HeLa_Romidepsin_16h_R1 1 SISGTSTSEKPNSMDTANTSPFK 23 1 Q9UJF2-2;Q9UJF2 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 S(0.003)IS(0.012)GT(0.012)S(0.012)T(0.006)S(0.017)EKPNS(0.854)MDT(0.083)ANTSPFK 71.434 0.0017232 23942000 925.02 1195.1 1081.8 1084 1988.1 2198 1364.9 1962.5 1413.6 1288.7 TRUE FALSE FALSE 913.7455004 1211.924649 1100.628275 1209.33718 1886.639838 2057.554894 1480.834572 2019.281841 1287.164076 1255.219388 0.727956809 0.96550823 0.87684136 0.963446862 1.503035928 1.63919942 1.179741634 1.608708294 1.025449485 1 10.29372383 -8.808027135 4.854847495 0.879497126 1.47408025 0.784483867 0.14194018 0.065725534 3.379574867 0.021812927 0.041102666 1.56E-09 8.808027135 0.594583124 SISLYYTGEK ddPTM_HeLa_Romidepsin_16h_R1 1 SISLYYTGEK 10 0 P19338;H7BY16 P19338 NCL Nucleolin 0 0 192.26 1.37E-07 8233400 2885.1 2500.5 3258.3 2510.3 3027.1 2991.4 2858.1 2396.9 2557.4 2071.1 FALSE FALSE TRUE 2849.935291 2535.702105 3315.009345 2800.552697 2872.615791 2800.259194 3100.866943 2466.25052 2328.659739 2017.292523 1.412752617 1.25698285 1.643296302 1.388272977 1.423995657 1.388127484 1.537142931 1.222554732 1.154349065 1 10.97820459 -12.16220838 0.605491177 0.949189406 1.42529479 0.524143851 0.123114566 0.476100559 0.26803307 0.123620274 0.02447268 6.88E-13 12.16220838 0.476105385 SISSPSVSSET(ph)MDKPVDLSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SISSPSVSSETMDKPVDLSTR 21 1 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 SIS(0.002)S(0.007)PS(0.05)VS(0.165)S(0.165)ET(0.606)MDKPVDLS(0.002)T(0.002)R 59.996 0.010552 63209000 2570.4 2686 2706.2 2250.6 3126.7 4128.6 3627.2 3360 2617.5 2411.9 TRUE FALSE FALSE 2539.070976 2723.813579 2753.300276 2510.824961 2967.132832 3864.795784 3935.294277 3457.216299 2383.384244 2349.23849 1.080805966 1.159445322 1.17199692 1.068782489 1.263018993 1.645127049 1.675136132 1.47163275 1.014534818 1 11.19797747 -8.454614994 2.736711633 1.062165503 1.607193852 0.903586959 0.074753384 0.059777711 0.874857459 0.012087551 0.029398947 3.51E-09 8.454614994 0.545028349 SISSS(ph)NPDLAVAPGSVDDEVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SISSSNPDLAVAPGSVDDEVSR 22 0 K7ESB7;Q96HP0;K7EKT0;K7EP20 K7ESB7 DOCK6 Dedicator of cytokinesis protein 6 1 0 SISS(0.08)S(0.919)NPDLAVAPGSVDDEVSR 264.1 2.20E-82 20579000 1325.4 1123.8 1632.7 1624.2 1844.2 2115.4 1878.1 1852.4 1728.9 1264 TRUE FALSE FALSE 1309.245515 1139.620886 1661.116459 1811.997646 1750.083592 1980.232767 2037.625767 1905.996271 1574.262854 1231.161098 1.063423395 0.925647251 1.349227539 1.471779485 1.421490328 1.608427013 1.655043983 1.548129059 1.278681447 1 10.26580384 -9.487007833 2.013025788 1.021936585 1.556064295 0.793698285 0.111779269 0.06545687 0.527651605 0.012846056 0.020472433 3.26E-10 9.487007833 0.53412771 SIT(ph)SPPSTSTTK ddPTM_HeLa_Romidepsin_16h_R1 1 SITSPPSTSTTK 12 0 C9JWJ8;K7EN08;Q14938-6;Q14938-5;Q14938-3;Q14938-2;Q14938-4;Q14938 C9JWJ8 NFIX Nuclear factor 1;Nuclear factor 1 X-type 1 0 S(0.014)IT(0.919)S(0.067)PPSTSTTK 123.84 0.012809 10679000 2746.7 2776.5 2601.7 2832.5 2699.3 1746.8 1814.3 1706.7 2950.7 2483.7 TRUE FALSE FALSE 2713.222164 2815.58764 2646.981497 3160.006977 2561.544649 1635.185118 1968.406597 1756.080672 2686.782002 2419.173116 1.121549403 1.163863645 1.094167871 1.306234331 1.058851321 0.675927286 0.813669176 0.725901202 1.110619982 1 11.2402983 -8.299070327 7.515598908 1.089198686 0.746103168 0.80530069 0.085372461 0.095001213 16.70263881 0.013876399 0.031475295 5.02E-09 8.299070327 -0.343095518 SITS(ph)TPLSGK ddPTM_HeLa_Romidepsin_16h_R1 2 SITSTPLSGK 10 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 S(0.001)IT(0.023)S(0.908)T(0.068)PLSGK;S(0.001)IT(0.019)S(0.681)T(0.299)PLSGK ; 160.72 0.0023638 52000000 11637.5 11667.5 11412.5 12492.2 7677 7822.2 6531.6 8183.9 11955.6 10666.6 TRUE FALSE FALSE 11495.65767 11831.75537 11611.12978 13936.60694 7285.214043 7322.386665 7086.393941 8420.688234 10886.26119 10389.48019 1.106470917 1.138820725 1.117585246 1.341415228 0.701210639 0.704788548 0.682073964 0.810501399 1.04781577 1 13.34283585 -8.73376886 24.97791524 1.082632217 0.720184477 0.805890138 0.094954082 80.84164086 72974.63147 0.014845085 0.029684775 1.85E-09 8.73376886 -0.36244774 SIVDYKPNLDLLEQQHQLIQEALIFDNK ddPTM_HeLa_Romidepsin_16h_R1 1 SIVDYKPNLDLLEQQHQLIQEALIFDNK 28 1 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 87.881 2.54E-07 6533500 1992.9 2018.2 2411 1739.1 2049.9 2025.8 1571.5 1939.1 1882.7 1983.6 FALSE FALSE TRUE 1968.609768 2046.612273 2452.962444 1940.182925 1945.285954 1896.357918 1704.983171 1995.204799 1714.306597 1932.065786 1.018914461 1.059287053 1.269606067 1.004201274 1.006842504 0.981518296 0.882466417 1.032679536 0.887292042 1 10.9159285 -8.353554733 2.391433263 1.034096889 0.954965351 0.10664399 0.095697272 0.491133604 5.432942739 0.0129406 0.034929136 4.43E-09 8.353554733 -0.079131538 SIVEGIIEEEEEDEEGSESISKR ddPTM_HeLa_Romidepsin_16h_R1 2 SIVEGIIEEEEEDEEGSESISKR 23 1 Q9Y570-4;Q9Y570;Q9Y570-2 Q9Y570-4 PPME1 Protein phosphatase methylesterase 1 0 0 ; ; 289.81 4.39E-131 5515400 1217.4 911.91 761.2 1187.83 1224.95 1257.58 879.81 1184.37 991.03 1188.96 FALSE FALSE TRUE 1202.561861 924.7478929 774.4483667 1325.172494 1162.436231 1177.224697 954.5410394 1218.637877 902.3897947 1158.070648 1.038418393 0.798524593 0.668740174 1.144293309 1.003769703 1.01653962 0.824251129 1.052300116 0.77921826 1 10.17750755 SIVIRPLEPQPAPHLAR ddPTM_HeLa_Romidepsin_16h_R1 1 SIVIRPLEPQPAPHLAR 17 1 Q15029-3;Q15029;K7EP67;Q15029-2 Q15029-3 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component 0 0 44.807 0.024513 519700 398.4 400.61 543.94 421.1 389.87 309.78 475.87 455.61 473.12 424.48 FALSE FALSE TRUE 393.5441476 406.2497981 553.4070475 469.7895633 369.9734791 289.9860578 516.2903859 468.7923565 430.8029622 413.4519484 0.951849783 0.982580442 1.338503905 1.136261578 0.894840333 0.701377896 1.248731293 1.133849673 1.041966216 1 8.691575858 SIVPS(ph)SPQPQR ddPTM_HeLa_Romidepsin_16h_R1 1 SIVPSSPQPQR 11 0 H7C5K2;H7C5C6;H7C5A5;A0A1X7SBY3;H0Y860;Q9P246-3;Q9P246;Q9P246-2 H7C5K2 STIM2 Stromal interaction molecule 2 1 0 S(0.001)IVPS(0.499)S(0.499)PQPQR 114.76 0.012408 7361000 2716.3 3531.3 2522.2 1886.5 2931 3176.9 2062.9 3595.6 3119.9 3424.4 TRUE FALSE FALSE 2683.192691 3581.013734 2566.097833 2104.626006 2781.420133 2973.906343 2238.122675 3699.633013 2840.84833 3335.433594 0.80445094 1.073627651 0.769344603 0.630990229 0.833900617 0.891610119 0.671014011 1.109191027 0.85171785 1 11.7036586 -12.69653519 0.556806116 1.057858362 0.832328064 0 0.151815406 2.829010147 0.937595429 0.361650721 0.032085808 2.01E-13 12.69653519 -0.225530297 SIYDDIS(ph)SPGLGSTPLTSR ddPTM_HeLa_Romidepsin_16h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 SIYDDIS(0.924)S(0.075)PGLGSTPLTSR 175.7 1.42E-08 18642000 3164.7 2848 3289.5 2901.4 4423 5134.8 5264.1 5610.5 4066.2 3599.5 TRUE FALSE FALSE 3126.127419 2888.094219 3346.752368 3236.873519 4197.277806 4806.702852 5711.232523 5772.830966 3702.508888 3505.984471 0.891654668 0.823761269 0.95458277 0.923242401 1.197175241 1.37099947 1.628995385 1.646564899 1.05605399 1 11.77560389 -8.208661453 1.348115232 0.933832146 1.670075212 0.943913779 0.067865282 0.070929288 0.231920017 0.010001491 0.043548494 6.18E-09 8.208661453 0.736243066 SIYDDISS(ph)PGLGST(ph)PLTSR ddPTM_HeLa_Romidepsin_16h_R1 2 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 2 0 S(0.002)IYDDIS(0.393)S(0.606)PGLGS(0.309)T(0.663)PLT(0.025)S(0.003)R;S(0.014)IYDDIS(0.415)S(0.571)PGLGS(0.321)T(0.679)PLT(0.001)SR ; 177.07 1.45E-09 29060000 5144.7 4920.1 5322.9 4539.4 8546.3 9830.7 6733.1 8134.6 5592.9 4994.4 TRUE FALSE FALSE 5081.994418 4989.365297 5415.542842 5064.266787 8110.15042 9202.549997 7305.009346 8369.961817 5092.657016 4864.644768 1.044679449 1.025638158 1.113245283 1.041035271 1.667161901 1.891720863 1.501653192 1.720569993 1.046871305 1 12.24811874 -8.756415749 6.275644927 1.030108706 1.698843246 0.922587279 0.092223762 0.026410859 4.162129639 0.012779208 0.024694948 1.75E-09 8.756415749 0.66873454 SIYDDISS(ph)PGLGSTPLTSR ddPTM_HeLa_Romidepsin_16h_R1 2 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 SIYDDIS(0.09)S(0.91)PGLGSTPLTSR;SIYDDIS(0.452)S(0.548)PGLGSTPLTSR ; 255.72 8.26E-76 30418400 3467.3 3963.8 3601.9 3463.8 5256.1 5775 6125 5536.5 4146.6 3870.9 TRUE FALSE FALSE 3425.039214 4019.60248 3664.589559 3864.300854 4987.861604 5405.996138 6645.257347 5696.689892 3775.717711 3770.33346 0.908418115 1.066113256 0.971953701 1.024922834 1.322923199 1.433824407 1.762511836 1.510924684 1.001428057 1 11.88047641 -8.471376892 1.397943656 0.963624975 1.63654338 0.912501642 0.080895569 0.076192604 0.285575713 0.011766717 0.037979338 3.38E-09 8.471376892 0.672918405 SIYDDISSPGLGS(ph)TPLTSR ddPTM_HeLa_Romidepsin_16h_R1 1 SIYDDISSPGLGSTPLTSR 19 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 SIYDDISS(0.001)PGLGS(0.765)T(0.234)PLTSR 214.34 3.87E-29 19204000 2659.5 2391.6 2224.7 1954.9 1637 1266.1 954.1 1387.7 2337.7 2004.1 TRUE FALSE FALSE 2627.084991 2425.269008 2263.41997 2180.934736 1553.457782 1185.200296 1035.14123 1427.85091 2128.610257 1952.033193 1.345819836 1.242432258 1.159519202 1.117263141 0.795815249 0.607161958 0.530288744 0.731468561 1.090458023 1 10.93076187 -8.658435986 2.359773564 1.174421285 0.614334608 0.866522548 0.09666639 0.102814232 1.159827643 0.020733342 0.04652186 2.20E-09 8.658435986 -0.560086676 SIYFSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SIYFSSPK 8 0 A2IDA3;P29372-5;P29372-4;P29372-2;P29372 A2IDA3 MPG DNA-3-methyladenine glycosylase 1 0 SIYFS(0.497)S(0.503)PK 152.11 1.09E-07 0 3337 3581.4 3951.4 3179.7 6126.3 7858.1 6565.7 6635.5 3627.6 3714.4 TRUE FALSE FALSE 3296.32736 3631.819043 4020.172459 3547.351875 5813.652051 7355.992771 7123.390394 6827.487723 3303.138371 3617.899353 0.91111638 1.003847451 1.11118969 0.980500431 1.606913704 2.033222059 1.968929951 1.887141421 0.912998967 1 11.82093656 -8.618950835 2.699829989 0.971616498 1.961168642 0.976606588 0.068795709 0.028171338 0.414030941 0.010796544 0.023975418 2.40E-09 8.618950835 0.989552144 SIYGEKFEDENFILK ddPTM_HeLa_Romidepsin_16h_R1 2 SIYGEKFEDENFILK 15 1 F8WE65;C9J5S7;P62937;P62937-2 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 0 ; ; 153.32 0.00053869 257440000 6815.1 5947.9 5909.3 10514.9 6965.5 6495.8 6163.5 6360.9 7544.5 5572.3 FALSE FALSE TRUE 6732.03494 6031.634692 6012.148888 11730.68221 6610.024543 6080.739344 6687.027536 6544.942606 6869.701024 5427.530843 1.240349458 1.111303624 1.107713445 2.161329443 1.21786955 1.120350952 1.232057031 1.205878473 1.265713862 1 12.4060803 -11.35484064 0.591090377 1.009254725 1.327411017 0.033642068 0.303041297 1.200083586 0.901937877 0.173989826 0.081822013 4.42E-12 11.35484064 0.318156291 SK(ac)FADLSEAANR ddPTM_HeLa_Romidepsin_16h_R1 1 SKFADLSEAANR 12 1 P08670;B0YJC4;B0YJC5 P08670 VIM Vimentin 0 1 SK(1)FADLSEAANR 155.88 0.0020315 1580700 814.78 845.06 854.91 827.26 1093.1 1082.6 756.63 832.89 942.86 798.28 FALSE TRUE FALSE 804.849148 856.9567769 869.7893499 922.9116936 1037.315028 1013.425354 820.8981333 856.9883581 858.5282402 777.5405705 1.03512174 1.102137701 1.118641757 1.18696275 1.334097624 1.303372959 1.055762444 1.102178318 1.10415877 1 9.602774144 -9.868180371 1.337123514 1.01398644 1.19967649 0.359307701 0.083390686 0.258523002 0.921626947 0.015559868 0.022006059 1.35E-10 9.868180371 0.18569005 RPATADSPKPSAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 RPATADSPKPSAKK 14 3 Q03111 Q03111 MLLT1 Protein ENL 0 1 ; RPATADSPK(0.239)PSAK(0.761)K;RPATADSPK(0.019)PSAK(0.981)K 57.52 0.019431 7999600 2837 3014.2 2974.3 5392.4 9301 11974.6 11648.4 12101.3 3116.6 3167.5 FALSE TRUE FALSE 2802.421553 3056.633987 3026.066444 6015.89466 8826.335263 11209.46171 12637.81481 12451.43202 2837.84349 3085.207893 0.908341237 0.990738418 0.980830644 1.94991549 2.860855919 3.633292178 4.096260363 4.035848621 0.919822452 1 11.59115199 -8.677564868 1.24327643 0.942251806 4.092413516 0.995029292 0.092401538 0.021641196 0.065645326 0.015469865 0.04499948 2.10E-09 8.677564868 3.15016171 up SK(ac)IPNEHKK(ac)PAEVFR ddPTM_HeLa_Romidepsin_16h_R1 1 SKIPNEHKKPAEVFR 15 3 F2Z2B6;F2Z3N8;Q92613 F2Z2B6 JADE3 Protein Jade-3 0 2 SK(1)IPNEHK(0.225)K(0.775)PAEVFR 44.807 0.025798 3262500 494.08 619.49 599.3 723.19 1075.1 1138.9 944.11 1031.2 669 621.34 FALSE TRUE FALSE 488.0579629 628.2111965 609.7305651 806.8086305 1020.233635 1066.127966 1024.30268 1061.036145 609.1629645 605.1974972 0.80644412 1.038026759 1.007490229 1.333132794 1.685786276 1.761619918 1.692509775 1.753206432 1.006552352 1 9.241262211 -9.037749637 1.630930857 0.915190964 1.744402606 0.965079934 0.067264162 0.051682102 0.272510814 0.013059032 0.026449047 9.17E-10 9.037749637 0.829211642 SK(ac)LLFSNTAAQK ddPTM_HeLa_Romidepsin_16h_R1 1 SKLLFSNTAAQK 12 1 Q96ST3 Q96ST3 SIN3A Paired amphipathic helix protein Sin3a 0 1 SK(1)LLFSNTAAQK 120.87 0.016424 290680 234.1 96.247 121.78 0 258.47 127.89 136.76 168.33 208.07 260.71 FALSE TRUE FALSE 231.2466992 97.60196779 123.8995298 0 245.2793114 119.7182417 148.376391 173.200363 189.4596981 253.9367166 0.910646961 0.384355477 0.487914987 0 0.965907233 0.471449121 0.584304597 0.682061126 0.746090209 1 7.988325199 -10.33530002 5.736793145 0.960149988 0.509536171 0.328737052 0.238710365 0.143470641 8.477789097 0.037903765 0.043274079 4.62E-11 10.33530002 -0.450613817 SK(ac)LNTITPVVGK ddPTM_HeLa_Romidepsin_16h_R1 1 SKLNTITPVVGK 12 1 Q9HCK8-2;Q9HCK8;A0A2R8Y840;A0A2R8YFT4;A0A2R8Y808;A0A2R8Y4P3 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 0 1 SK(1)LNTITPVVGK 134.98 0.0025678 435040 203.38 251.83 171.25 265.5 327.98 301.59 323.46 302 167.51 279.72 FALSE TRUE FALSE 200.9011263 255.3752694 174.2305344 296.1983592 311.2419567 282.3193723 350.9346843 310.7378935 152.5274861 272.4528341 0.73737947 0.937319189 0.639488794 1.087154627 1.142370047 1.036213748 1.288056648 1.140519953 0.559830793 1 8.089862688 -9.059286428 9.432578007 0.862182187 1.148563161 0.581445079 0.146086709 0.287528812 44.49577942 0.019418724 0.032284831 8.72E-10 9.059286428 0.286380975 SK(ac)YQTDLYER ddPTM_HeLa_Romidepsin_16h_R1 1 SKYQTDLYER 10 1 Q8WUA2 Q8WUA2 PPIL4 Peptidyl-prolyl cis-trans isomerase-like 4 0 1 SK(1)YQTDLYER 90.685 0.014462 0 75.88 252.79 173.36 113.95 349.03 333.86 449.98 284.74 234.62 204.85 FALSE TRUE FALSE 74.95514537 256.3487843 176.3772581 127.1254352 331.2176967 312.5274235 488.20129 292.9785027 213.6349996 199.5279675 0.375662351 1.284776202 0.88397261 0.637130908 1.660006368 1.56633392 2.446781252 1.468358077 1.070702029 1 7.64044717 -8.678014897 4.007767465 0.756392409 1.851805521 0.611801576 0.347847969 0.101404827 3.105610652 0.053498907 0.109600719 2.10E-09 8.678014897 1.095413112 SKDDQVTVIGAGVTLHEALAAAELLK ddPTM_HeLa_Romidepsin_16h_R1 1 SKDDQVTVIGAGVTLHEALAAAELLK 26 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 74.873 8.67E-05 2048000 1278.1 1024.5 1913.1 1259.5 2144.2 1809.4 890.64 1209.8 1601.5 1320.7 FALSE FALSE TRUE 1262.522026 1038.922938 1946.396703 1405.129316 2034.773473 1693.78518 966.2909394 1244.803654 1458.257829 1286.388024 0.981447279 0.807627962 1.513071225 1.092305969 1.581772712 1.316698499 0.751165995 0.967673541 1.133606503 1 10.32911016 -9.787818482 24.99996489 0.97722341 1.200455174 0.171117348 0.240446249 300.4100084 284702.8057 0.038756553 0.050944374 1.63E-10 9.787818482 0.223231764 SKDDQVTVIGAGVTLHEALAAAELLKK ddPTM_HeLa_Romidepsin_16h_R1 1 SKDDQVTVIGAGVTLHEALAAAELLKK 27 2 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 53.96 0.011036 1547700 379.06 259.78 286.71 365.35 259.82 388.14 430.07 157.22 470 400.36 FALSE FALSE TRUE 374.4398709 263.4371897 291.7000673 407.593486 246.5604159 363.3391067 466.6001351 161.7689126 427.9620229 389.9585895 0.960204188 0.675551704 0.748028317 1.045222485 0.63227333 0.931737668 1.196537652 0.414836131 1.097455049 1 8.607177119 -10.47887705 17.74226664 0.982444963 0.825788566 0.166528326 0.2110248 24.63963194 9935.648143 0.032930354 0.037299239 3.32E-11 10.47887705 -0.156656397 SKDEEEDEES(ph)DDADDTPILKPVSLLR ddPTM_HeLa_Romidepsin_16h_R1 1 SKDEEEDEESDDADDTPILKPVSLLR 26 2 A0A3B3IS53;A0A3F2YNX6;Q92794;A0A3B3ITI3 A0A3B3IS53 KAT6A Histone acetyltransferase KAT6A 1 0 S(0.003)KDEEEDEES(0.979)DDADDT(0.017)PILKPVSLLR 55.247 0.0026169 17760000 556.65 727 625.59 674.5 759.4 837.29 668.89 998.59 701.57 713.66 TRUE FALSE FALSE 549.8653357 737.2347251 636.4781315 752.4888636 720.6449843 783.7898712 725.7054999 1027.482626 638.8198221 695.1190103 0.791037689 1.060587776 0.915639081 1.082532419 1.036721732 1.127562129 1.044001803 1.478139154 0.919007843 1 9.44111619 -4 0.469679187 0.915303416 13.89694828 0.709753896 0.09257554 36.48099111 0.377096923 0.022239268 463.1338173 1.00E-04 4 12.98164486 SKDHFGLEGDEESTMLEDSVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SKDHFGLEGDEESTMLEDSVSPK 23 1 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 SKDHFGLEGDEESTMLEDS(0.024)VS(0.976)PK 81.904 0.00013105 34785000 2911.6 2422.5 2150.4 2113.1 4445 4297 2753.9 2453.9 3769.5 3260.1 TRUE FALSE FALSE 2876.112299 2456.604019 2187.82681 2357.426564 4218.155063 4022.435568 2987.816197 2524.899725 3432.346479 3175.402132 0.905747423 0.773635564 0.688992045 0.742402526 1.328384528 1.266748399 0.940925298 0.795143298 1.080917105 1 11.63272359 -7.272286946 6.295125616 0.955605874 0.792203011 0.059664274 0.201419289 0.31362874 65.31773507 0.028755147 0.211639432 5.34E-08 7.272286946 -0.163402862 SKEFVS(ph)SDESSSGENK ddPTM_HeLa_Romidepsin_16h_R1 1 SKEFVSSDESSSGENK 16 1 Q08945 Q08945 SSRP1 FACT complex subunit SSRP1 1 0 S(0.043)KEFVS(0.862)S(0.078)DES(0.017)SSGENK 184.21 6.66E-08 10163000 3239.5 3078.8 2941.9 2886.5 2140.1 2035 1725.2 1795.1 3036 3106.8 TRUE FALSE FALSE 3200.015728 3122.143427 2993.102535 3220.250711 2030.882711 1904.970068 1871.738445 1847.038386 2764.452556 3026.084888 1.057477185 1.031743504 0.989100652 1.064164037 0.671125493 0.629516401 0.618534679 0.610372298 0.913540981 1 11.56323674 -8.721726559 5.644369021 1.027493051 0.62649478 0.94714278 0.043543229 0.018305216 1.434408785 0.004214085 0.008395973 1.90E-09 8.721726559 -0.400998271 SKEGDVEEPTDDS(ph)LPTTGDAGGREPMEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SKEGDVEEPTDDSLPTTGDAGGREPMEEK 29 2 Q9UKN8 Q9UKN8 GTF3C4 General transcription factor 3C polypeptide 4 1 0 SKEGDVEEPT(0.032)DDS(0.721)LPT(0.124)T(0.124)GDAGGREPMEEK 48.84 0.0068515 10096000 2470.9 2240.1 2273.4 2555.5 2362.8 2640.3 1866 2112.6 2673.4 2199.5 TRUE FALSE FALSE 2440.78372 2271.636187 2312.967573 2850.978934 2242.217499 2471.593351 2024.497993 2173.724748 2434.284408 2142.356673 1.139298489 1.060344533 1.07963702 1.33076764 1.046612605 1.153679675 0.944986434 1.014641855 1.136264768 1 11.06498297 -7.75210646 24.99381472 1.089961769 0.979814127 0.232675112 0.089446929 262.768694 703686.7018 0.013254183 0.048257536 1.77E-08 7.75210646 -0.110147643 SKENMAQESSIQEQGVTSNTS(ph)DSESSSK ddPTM_HeLa_Romidepsin_16h_R1 3 SKENMAQESSIQEQGVTSNTSDSESSSK 28 1 Q92796-3;Q92796-2 Q92796-3 1 0 SKENMAQESSIQEQGVTS(0.001)NT(0.251)S(0.427)DS(0.251)ES(0.045)S(0.019)S(0.006)K;SKENMAQESSIQEQGVT(0.001)S(0.01)NT(0.32)S(0.541)DS(0.103)ES(0.021)S(0.003)S(0.001)K;SKENMAQESSIQEQGVT(0.002)S(0.005)NT(0.251)S(0.598)DS(0.107)ES(0.02)S(0.009)S(0.009)K ;; 83.026 3.88E-06 24177900 5468 5658.4 6018.7 4862.4 5084.2 5971.8 4421.81 4514.29 5573.9 6215.7 TRUE FALSE FALSE 5401.353913 5738.059104 6123.452949 5424.613566 4824.734302 5590.221253 4797.398431 4644.903859 5075.356424 6054.215218 0.892164173 0.947779175 1.011436285 0.896006067 0.796921505 0.92336018 0.792406325 0.76721816 0.838317807 1 12.56372425 -4.337449964 0.221159269 0.977962247 5.55E-12 0.362276741 0.065441885 23.81290464 0.325909456 0.042025921 8.149821117 4.60E-05 4.337449964 -0.977962247 SKESVPEFPLS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 5 SKESVPEFPLSPPK 14 1 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK;SKESVPEFPLS(1)PPK ;;;; 110.84 0.0014091 4592442000 21649.02 26206.73 20954.91 18750.39 21714.84 20051.55 17218.26 18567.16 22578.5 21433.71 TRUE FALSE FALSE 21385.15342 26575.66903 21319.62142 20918.39832 20606.65069 18770.32067 18680.77857 19104.37148 20559.02241 20876.85912 1.024347259 1.272972571 1.021208281 1.001989724 0.987057036 0.899096965 0.894807905 0.915097974 0.984775645 1 14.34961706 -8.487546908 1.893741115 1.034714828 0.899602125 0.407070517 0.078683311 0.310598008 2.185541976 0.012395585 0.033367177 3.25E-09 8.487546908 -0.135112703 SKESVPEFPLS(ph)PPKKK ddPTM_HeLa_Romidepsin_16h_R1 2 SKESVPEFPLSPPKKK 16 3 P16949;P16949-2;A2A2D0 P16949 STMN1 Stathmin 1 0 SKESVPEFPLS(1)PPKKK;SKESVPEFPLS(1)PPKKK ; 72.793 0.025794 374960000 17128.7 15319.8 11472.7 24654.8 16241.3 14529.1 12299.8 12956.6 16564.4 14886.3 TRUE FALSE FALSE 16919.92882 15535.47255 11672.37753 27505.50398 15412.44586 13600.7374 13344.5447 13331.47878 15082.83858 14499.55178 1.166927714 1.07144502 0.805016438 1.896989948 1.062960158 0.938010885 0.920341877 0.919440751 1.040227919 1 13.82372068 -8.308196821 5.346174998 1.121578181 0.924738785 0.121233566 0.270130746 0.371141643 25.73542822 0.038019898 0.088101249 4.92E-09 8.308196821 -0.196839396 SKETSSPGTDDVFTPAPS(ph)DSPSSQR ddPTM_HeLa_Romidepsin_16h_R1 2 SKETSSPGTDDVFTPAPSDSPSSQR 25 1 P19634 P19634 SLC9A1 Sodium/hydrogen exchanger 1 1 0 SKETSSPGTDDVFT(0.047)PAPS(0.523)DS(0.348)PS(0.064)S(0.018)QR;SKETSSPGTDDVFTPAPS(0.709)DS(0.25)PS(0.033)S(0.008)QR ; 146.36 7.36E-08 13027000 2244.7 4416.8 3235.4 2408.5 4795 9575.6 4364.8 10640.6 3003.5 3453 TRUE FALSE FALSE 2217.340733 4478.979826 3291.71078 2686.982102 4550.293257 8963.750064 4735.546003 10948.46897 2734.859438 3363.290562 0.659277185 1.331725506 0.978717336 0.79891465 1.352928976 2.665172663 1.40800978 3.255284897 0.813149916 1 11.71565771 -6.637599432 0.485194674 0.837533542 6.05085229 0.698352477 0.447360267 2.876874502 0.295650039 0.089636951 9.785305024 2.30E-07 6.637599432 5.213318748 SKGEPVISVK(ac)TTSR ddPTM_HeLa_Romidepsin_16h_R1 2 SKGEPVISVKTTSR 14 2 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 0 1 ; SKGEPVISVK(1)TTSR;SKGEPVISVK(1)TTSR 134.37 7.24E-05 3304300 1706.07 1813.42 882.67 1142.16 1113.51 1118.26 1514.8 1141.65 1953.78 1451.72 FALSE TRUE FALSE 1685.275763 1838.949374 898.0325011 1274.221913 1056.68343 1046.806795 1643.467074 1174.681842 1779.029023 1414.004105 1.191846443 1.300526192 0.635098935 0.901144423 0.7472987 0.74031383 1.162278856 0.830748537 1.258149829 1 10.46557059 -9.763920797 24.99999757 1.108870354 0.845531175 0.523919554 0.156970325 50.47756907 508557.27 0.025364069 0.034216279 1.72E-10 9.763920797 -0.263339179 SKGHYEVT(ph)GSDDETGK ddPTM_HeLa_Romidepsin_16h_R1 1 SKGHYEVTGSDDETGK 16 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 S(0.001)KGHY(0.001)EVT(0.979)GS(0.014)DDET(0.006)GK 70.538 0.021917 7353700 2265.1 1606.8 1831.2 724.56 2161.6 1643 2258.6 1394.3 2763.5 2011.8 TRUE FALSE FALSE 2237.49209 1629.420573 1863.071268 808.3370364 2051.285486 1538.017603 2450.445428 1434.641871 2516.325639 1959.533146 1.141849575 0.831535091 0.950773031 0.412515113 1.046823571 0.784889812 1.250525123 0.732134526 1.284145483 1 10.93629426 -10.25392621 24.34324068 1.066984522 0.864350588 0.241617517 0.218214082 515.6827485 1670850.688 0.033197587 0.040219401 5.57E-11 10.25392621 -0.202633935 SKGHYEVTGSDDET(ph)GKLQGSGVSLASK ddPTM_HeLa_Romidepsin_16h_R1 1 SKGHYEVTGSDDETGKLQGSGVSLASK 27 2 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 SKGHYEVT(0.006)GS(0.142)DDET(0.85)GKLQGS(0.002)GVSLASK 68.158 7.84E-05 12088000 1723.7 1420 1426.6 1541 2529.1 2014.9 1650.5 1897.1 2444.6 1805.6 TRUE FALSE FALSE 1702.690881 1439.990797 1451.429375 1719.177671 2400.03059 1886.154393 1790.693429 1951.989595 2225.948853 1758.690252 0.96815848 0.81878591 0.825289941 0.97753295 1.364669297 1.072476743 1.018197165 1.109910966 1.265685558 1 10.7802857 -8.96555161 24.98343837 0.956101839 1.133040011 0.236543235 0.143152288 148.5690119 107748.0394 0.016245551 0.029450738 1.08E-09 8.96555161 0.176938172 SKGQESFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SKGQESFKK 9 2 P06748;P06748-3 P06748 NPM1 Nucleophosmin 0 1 SKGQESFK(1)K 108.31 0.0047275 5296500 2523.1 2475.2 4485.6 4177.2 3767.7 4559.1 9082.9 805.87 5086.6 3176.3 FALSE TRUE FALSE 2492.347487 2510.045931 4563.669986 4660.187518 3575.42021 4267.788224 9854.401299 829.186577 4631.641756 3093.779268 0.805599647 0.811320302 1.475111697 1.506308988 1.155680448 1.379474052 3.185230892 0.268017368 1.497082162 1 11.59515455 -9.709414475 5.558893409 0.898260299 1.557537599 0.08141354 0.699773653 0.241455977 16.08690243 0.09813264 0.138242683 1.95E-10 9.709414475 0.6592773 SKHEEEEWT(ph)DDDLVESL ddPTM_HeLa_Romidepsin_16h_R1 3 SKHEEEEWTDDDLVESL 17 1 D6RHI7;P51946 D6RHI7 CCNH Cyclin-H 1 0 SKHEEEEWT(0.998)DDDLVES(0.002)L;SKHEEEEWT(0.999)DDDLVES(0.001)L;SKHEEEEWT(1)DDDLVESL ;; 91.789 0.0044291 27584900 7919.8 7145.8 7406.2 7246.9 15991.8 17456.1 13033.6 13399.6 12838.9 10578.7 TRUE FALSE FALSE 7823.270431 7246.39876 7535.101804 8084.820676 15175.67877 16340.71155 14140.67366 13787.29628 11690.55663 10303.86385 0.759255998 0.703270042 0.731288953 0.784639704 1.472814373 1.585881936 1.372366121 1.338070503 1.134579882 1 13.33089782 -8.759158187 24.9998266 0.84914088 1.447546305 0.815493135 0.13749666 18.21664967 199633.7632 0.019971375 0.038461488 1.74E-09 8.759158187 0.598405425 SKHMPKSTIETALK ddPTM_HeLa_Romidepsin_16h_R1 1 SKHMPKSTIETALK 14 2 Q9BSH4 Q9BSH4 TACO1 Translational activator of cytochrome c oxidase 1 0 0 50.563 0.027113 603670 407.54 476.52 534.64 0 452.16 527.47 541.23 535.35 565.25 432.66 FALSE FALSE TRUE 402.5727457 483.2284611 543.9451849 0 429.084588 493.7663693 587.2020627 550.8395076 514.6926243 421.4194308 0.955278082 1.146668677 1.290745384 0 1.018188903 1.171674425 1.393391049 1.307105148 1.221331022 1 8.719113025 -8.089395351 3.114730818 0.942953865 1.341818209 0.189880226 0.338030398 0.305881012 5.670785866 0.045579368 0.137264174 8.14E-09 8.089395351 0.398864344 RQTEPVSPVLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 RQTEPVSPVLKR 12 2 Q8IYH5-2;Q8IYH5;Q8IYH5-4 Q8IYH5-2 ZZZ3 ZZ-type zinc finger-containing protein 3 0 1 ; RQTEPVSPVLK(1)R;RQTEPVSPVLK(1)R 140.33 6.23E-14 0 379.61 529.65 401.91 847.92 2151.99 2797.4 2588.7 2957.2 306.88 248.7 FALSE TRUE FALSE 374.9831673 537.1064266 408.905075 945.9605 2042.16592 2618.655168 2808.584113 3042.761916 279.4318842 242.2387381 1.547990095 2.217260669 1.68802512 3.905075246 8.430385395 10.81022461 11.59428147 12.56100465 1.153539216 1 7.920285785 -8.675025646 1.298664599 1.300789099 12.18345037 0.992844527 0.384297866 0.025301891 0.084165403 0.064841828 0.183963475 2.11E-09 8.675025646 10.88266127 up SKLT(ph)YMCRVDLR ddPTM_HeLa_Romidepsin_16h_R1 2 SKLTYMCRVDLR 12 2 Q96QB1-4;Q96QB1-1;Q96QB1-6;Q96QB1 Q96QB1-4 DLC1 Rho GTPase-activating protein 7 1 0 S(0.002)KLT(0.599)Y(0.399)MCRVDLR;S(0.001)KLT(0.624)Y(0.375)MCRVDLR ; 101.9 0.0026266 4752200 1996.69 2204.5 1869.97 1894.98 2247.2 2337.7 1793.79 1857.46 2189.18 2161.5 TRUE FALSE FALSE 1972.353574 2235.535009 1902.516043 2114.086504 2132.516999 2188.328515 1946.154478 1911.202675 1993.374258 2105.343918 0.93683201 1.061838396 0.903660455 1.004152569 1.012906718 1.039416171 0.924387916 0.907786447 0.946816451 1 11.03984021 -7.550569757 23.64127864 0.980607977 0.911936774 0.275113304 0.045854924 101.3414053 86520.31898 0.006267489 0.023452293 2.81E-08 7.550569757 -0.068671203 SKNFMLES(ph)S(ph)PAHCS(ph)T(ph)PGDAGK ddPTM_HeLa_Romidepsin_16h_R1 1 SKNFMLESSPAHCSTPGDAGK 21 1 H3BLU5;A0A669KAW8;A0A669KBC5;Q8N2C7-6;Q8N2C7-5;Q8N2C7-4;Q8N2C7-7;Q8N2C7 H3BLU5 UNC80 Protein unc-80 homolog 4 0 S(0.07)KNFMLES(0.965)S(0.965)PAHCS(1)T(1)PGDAGK 47.204 0.018314 46303000 4266 4403.8 5012.5 3964.7 4515.7 5657.3 5212.5 5484.4 4684.7 3942.8 TRUE FALSE FALSE 4214.004351 4465.796812 5099.74046 4423.117268 4285.246979 5295.816788 5655.24962 5643.082461 4265.688699 3840.365488 1.097292527 1.16285724 1.32793102 1.151743833 1.115843529 1.378987704 1.472581096 1.469412867 1.110750712 1 11.9070279 -4 0.189382665 0.973803899 3.429938598 0.727308261 0.083605926 16.97455707 0.189450976 0.089046025 12.25675451 1.00E-04 4 2.456134699 SKNFMLESSPAHCS(ph)T(ph)PGDAGK ddPTM_HeLa_Romidepsin_16h_R1 1 SKNFMLESSPAHCSTPGDAGK 21 1 H3BLU5;A0A669KAW8;A0A669KBC5;Q8N2C7-6;Q8N2C7-5;Q8N2C7-4;Q8N2C7-7;Q8N2C7 H3BLU5 UNC80 Protein unc-80 homolog 2 0 S(0.003)KNFMLES(0.018)S(0.035)PAHCS(0.972)T(0.971)PGDAGK 50.215 0.0042116 0 431.85 609.22 454.69 410.38 633.41 588.35 554.25 708.09 597.77 592 TRUE FALSE FALSE 426.5864461 617.7966152 462.6036887 457.8300665 601.0847241 550.7563338 601.3279812 728.577467 544.3039541 576.6197547 0.739805466 1.07141077 0.802268193 0.793989562 1.042428254 0.955146488 1.042850121 1.263531922 0.94395648 1 9.171476453 -6.312938028 0.722026569 0.882769893 2.440888346 0.51408871 0.103557316 5.992606547 0.809444997 0.019826114 10.50312713 4.86E-07 6.312938028 1.558118453 SKPIPIMPAS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 SKPIPIMPASPQK 13 1 O00429-7;O00429-4;O00429-5;O00429-3;O00429-9;O00429-2;O00429;O00429-8;O00429-6 O00429-7 DNM1L Dynamin-1-like protein 1 0 SKPIPIMPAS(1)PQK 110.34 0.0073107 327340000 12004 11154 12811 8847.3 9579 9835.1 8650.1 9063.5 11309 12297 TRUE FALSE FALSE 11857.69063 11311.0263 13033.97008 9870.266454 9090.147886 9206.668851 9384.839278 9325.738073 10297.49472 11977.52217 0.989995298 0.944354446 1.088202543 0.824065806 0.758933923 0.768662226 0.783537625 0.778603282 0.859734975 1 13.54804186 -9.108992621 5.202725122 0.996554957 0.774903723 0.75374668 0.055295812 0.042786861 1.709921686 0.004738881 0.007977489 7.78E-10 9.108992621 -0.221651233 SKPIPIMPAS(ph)PQKGHAVNLLDVPVPVAR ddPTM_HeLa_Romidepsin_16h_R1 2 SKPIPIMPASPQKGHAVNLLDVPVPVAR 28 2 O00429-7;O00429-4;O00429-5;O00429-3;O00429-9;O00429-2;O00429;O00429-8;O00429-6 O00429-7 DNM1L Dynamin-1-like protein 1 0 S(0.001)KPIPIMPAS(0.999)PQKGHAVNLLDVPVPVAR;S(0.002)KPIPIMPAS(0.998)PQKGHAVNLLDVPVPVAR ; 62.582 0.00030554 52180000 3960.2 3522.3 3394.6 4671.1 3001.2 3043.1 2542.7 2629.6 3776.1 3141.2 TRUE FALSE FALSE 3911.931559 3571.887032 3453.681589 5211.19456 2848.037565 2848.655731 2758.676875 2705.683327 3438.356159 3059.591171 1.27857983 1.167439319 1.128804927 1.703232317 0.930855597 0.931057639 0.901648854 0.884328388 1.123795947 1 11.57912317 -8.565498232 24.99999085 1.178863966 0.909552173 0.416165204 0.179924385 129.2738963 75829.7811 0.028349205 0.056698437 2.72E-09 8.565498232 -0.269311792 SKPPPTYES(ph)EEEDK ddPTM_HeLa_Romidepsin_16h_R1 1 SKPPPTYESEEEDK 14 1 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 1 0 SKPPPTYES(1)EEEDK 228.84 1.97E-32 8053200 1733.4 1514.2 1717.8 1742.5 1713.9 1613.8 1430.8 1496 1388.5 1509.7 TRUE FALSE FALSE 1712.272654 1535.516947 1747.697588 1943.976049 1626.433288 1510.683388 1552.332116 1539.2844 1264.309082 1470.477776 1.164432868 1.044229958 1.188523633 1.322003012 1.106057714 1.02734187 1.055665132 1.046792019 0.859794757 1 10.52206927 -5.938172469 9.56175044 1.094931589 0.74503453 0 0.118564225 0 0 0.01386704 0 1.15E-06 5.938172469 -0.349897059 SKPVLEPLT(ph)PPLGSPRPR ddPTM_HeLa_Romidepsin_16h_R1 1 SKPVLEPLTPPLGSPRPR 18 2 H7BXC7;Q9H7P9-3;Q9H7P9;E7ESZ3;Q9H7P9-2 H7BXC7 PLEKHG2 Pleckstrin homology domain-containing family G member 2 1 0 S(0.004)KPVLEPLT(0.996)PPLGSPRPR 72.797 0.0061359 17136000 4913.4 4073.6 4188.4 4833.4 3739.9 2936.4 3245.6 3345.9 4790.3 4057.9 TRUE FALSE FALSE 4853.513591 4130.948248 4261.297345 5392.26045 3549.038948 2748.773517 3521.281183 3442.708338 4361.84357 3952.475173 1.227968141 1.045154762 1.078133868 1.364274338 0.897928208 0.695456239 0.890905326 0.871025923 1.103572668 1 11.94854069 -8.541371906 24.90697742 1.119032168 0.821370997 0.648688653 0.108029683 120.6797016 162533.4523 0.017550487 0.035105645 2.87E-09 8.541371906 -0.297661171 SKS(ph)DATASISLSSNLK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSDATASISLSSNLK 16 1 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 S(0.007)KS(0.988)DAT(0.004)AS(0.001)ISLSSNLK 188.58 9.75E-12 15223000 706.24 822.32 752.8 675.12 974.25 920.92 699.36 977.17 749.16 820.2 TRUE FALSE FALSE 697.6320752 833.8966425 765.9021682 753.1805509 924.5303871 862.0761841 758.7636209 1005.442872 682.1532533 798.8910858 0.873250544 1.043817684 0.958706615 0.94278252 1.157267121 1.079091004 0.949771044 1.258548118 0.85387516 1 9.641855021 -8.774606714 24.97793628 0.949103206 1.097349562 0.454282502 0.088432684 166.4630522 315774.0378 0.01256202 0.022868122 1.68E-09 8.774606714 0.148246356 SKS(ph)DATASISLSSNLKR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSDATASISLSSNLKR 17 2 Q9UBF8-2;A0A0B4J1S8;Q9UBF8 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 S(0.198)KS(0.801)DATASISLSSNLKR 109.83 0.0018287 56004000 2976 2622.1 2412.2 2888.5 3031.6 2886.3 2615.2 3080.6 3042.1 2638.4 TRUE FALSE FALSE 2939.727367 2659.013993 2454.183329 3222.481961 2876.88614 2701.874745 2837.335023 3169.732301 2770.006957 2569.853988 1.14392778 1.03469458 0.954989404 1.253955274 1.119474551 1.051372863 1.104084137 1.233428948 1.077884958 1 11.32747068 -9.264640022 24.9844232 1.058964698 1.142326601 0.347186647 0.073124094 355.5787794 2775674.879 0.012748202 0.019976662 5.44E-10 9.264640022 0.083361904 SKS(ph)PASTSSVNGTPGSQLSTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPASTSSVNGTPGSQLSTPR 22 1 Q5VZY9;O15075-2;O15075 Q5VZY9 DCLK1 Serine/threonine-protein kinase DCLK1 1 0 S(0.154)KS(0.805)PAS(0.031)T(0.01)SSVNGTPGSQLSTPR 94.234 0.00016856 9337000 1067.8 950.89 719.86 1170.4 1464.6 1202.1 890.45 1269.8 1063.3 1257.3 TRUE FALSE FALSE 1054.785243 964.2766544 732.3888613 1305.727155 1389.855997 1125.28969 966.0848008 1306.53966 968.1957849 1224.635165 0.861305696 0.787399123 0.598046571 1.066217264 1.134914329 0.918877493 0.7888756 1.066880731 0.790599366 1 10.2581363 SKS(ph)PLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.289)KS(0.684)PLPPEEEAKDEEEDQT(0.027)LVNLDT(0.001)YTSDLHFQVSK 60.843 0.0002324 396110000 2635.5 2629.8 1999 2341.2 3512.3 3139.6 2423.4 2794.1 2986.3 2776.5 TRUE FALSE FALSE 2603.377512 2666.822393 2033.791756 2611.90056 3333.054225 2938.989693 2629.243536 2874.942875 2719.197849 2704.36613 0.962657195 0.986117362 0.752040093 0.965808783 1.232471516 1.086757322 0.972221737 1.063074575 1.005484361 1 11.40107477 -8.941180877 24.99996789 0.96187471 1.082552524 0.363926816 0.091115247 78.16702233 33222.86118 0.013785296 0.02498797 1.15E-09 8.941180877 0.120677814 SKS(ph)PPKVPIVIQDDSLPAGPPPQIR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPPKVPIVIQDDSLPAGPPPQIR 25 2 Q7Z422-2;Q7Z422-4;Q7Z422-3;Q7Z422-5;Q7Z422 Q7Z422-2 SZRD1 SUZ domain-containing protein 1 1 0 S(0.228)KS(0.769)PPKVPIVIQDDS(0.002)LPAGPPPQIR 57.216 0.0027019 113570000 1350.2 1608.6 1333.2 1222 1228.3 1175.6 1080.3 1377.5 1746.9 1587.5 TRUE FALSE FALSE 1333.743243 1631.245913 1356.403787 1363.29339 1165.615268 1100.482954 1172.060655 1417.355789 1590.652889 1546.256521 0.862562728 1.054964613 0.877217828 0.881673494 0.753830462 0.711707882 0.757998844 0.916636903 1.028712162 1 10.59456396 -9.053226996 2.224565332 0.941274085 0.77896313 0.535110236 0.077051058 0.208068944 2.038220945 0.012317558 0.023133269 8.85E-10 9.053226996 -0.162310955 SKSDPIMLLK(ac)DR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSDPIMLLKDR 12 2 P08559-3;P08559;P08559-2;P08559-4;Q5JPU3 P08559-3 PDHA1 "Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial" 0 1 SKSDPIMLLK(1)DR 59.975 0.022284 3979200 2209.4 2121.2 2448.4 2424.2 2700.1 2950.5 2382.4 2185.2 1776.9 1913.3 FALSE TRUE FALSE 2182.470983 2151.062309 2491.013375 2704.49741 2562.303822 2761.972572 2584.760997 2248.425314 1617.969614 1863.59219 1.171109749 1.154255915 1.336673006 1.451228131 1.374927323 1.482069192 1.3869778 1.206500717 0.868199396 1 10.86387047 -10.27914037 0.702949725 1.039577313 1.394167693 0.734169272 0.098005369 0.22450727 0.234538096 0.023536773 0.027682363 5.26E-11 10.27914037 0.354590381 SKSDSYT(ph)LDPDTLR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSDSYTLDPDTLR 14 1 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 SKS(0.006)DS(0.009)YT(0.829)LDPDT(0.156)LR 178.14 1.71E-06 14231000 1254.7 1230.4 1224.8 976.8 1063.3 1206.4 984.3 976.6 1150.5 1055.1 TRUE FALSE FALSE 1239.407234 1247.721603 1246.11713 1089.742212 1009.035833 1129.314933 1067.906417 1004.85638 1047.596399 1027.68835 1.206014677 1.214105038 1.212543793 1.060381985 0.981850026 1.098888524 1.039134498 0.977783177 1.019371679 1 10.00518711 -9.01172314 23.84956148 1.119026991 1.02957647 0.293891205 0.077010756 443.770032 902809.9123 0.014585465 0.02513385 9.73E-10 9.01172314 -0.089450522 SKSPAST(ph)SSVNGTPGSQLSTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPASTSSVNGTPGSQLSTPR 22 1 Q5VZY9;O15075-2;O15075 Q5VZY9 DCLK1 Serine/threonine-protein kinase DCLK1 1 0 S(0.073)KS(0.315)PAS(0.027)T(0.512)S(0.067)S(0.006)VNGTPGSQLSTPR 87.496 0.00043837 15577000 1538.2 1396.4 1469.9 1418.6 1698.5 1831.3 1748.5 1946.6 1687.6 1448.1 TRUE FALSE FALSE 1519.451827 1416.058556 1495.482993 1582.625207 1611.819207 1714.28584 1897.017546 2002.9218 1536.656829 1410.478153 1.077260093 1.003956391 1.060266683 1.12204872 1.142746666 1.215393401 1.344946423 1.42003036 1.089458086 1 10.4619686 -7.286438052 0.530954083 1.028700592 1.715671766 0.94597325 0.030907141 0.55331563 0.106102733 0.006216227 0.233674718 5.17E-08 7.286438052 0.686971174 SKSPLPPEEEAKDEEEDQT(ph)LVNLDTYTSDLHFQVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SKSPLPPEEEAKDEEEDQTLVNLDTYTSDLHFQVSK 36 2 Q1KMD3;H3BQZ7 Q1KMD3 HNRNPUL2;HNRNPUL2-BSCL2 Heterogeneous nuclear ribonucleoprotein U-like protein 2 1 0 S(0.007)KS(0.02)PLPPEEEAKDEEEDQT(0.931)LVNLDT(0.02)Y(0.014)T(0.006)S(0.002)DLHFQVSK 59.434 0.0004016 19702000 3124.7 3354.3 2560.7 2510.2 3954.8 3861.7 2748.9 3464.2 3673.3 3199.3 TRUE FALSE FALSE 3086.614955 3401.521923 2605.267909 2800.441135 3752.971799 3614.949833 2982.391497 3564.431161 3344.750848 3116.181725 0.990511859 1.091567252 0.836044923 0.898677093 1.204349467 1.160057452 0.957065974 1.143845731 1.073349099 1 11.60556365 -8.764493573 24.9996563 0.98407695 1.108077088 0.336760312 0.092238485 73.02531616 597745.8254 0.012859171 0.024058187 1.72E-09 8.764493573 0.124000137 SKT(ph)PTGPELDTSYK ddPTM_HeLa_Romidepsin_16h_R1 1 SKTPTGPELDTSYK 14 1 Q8NF91;A0A0C4DG40;Q8NF91-4;Q8NF91-2;E7ENN3;H0Y326;A0A5F9ZHE1;Q5JV20;F8WAI0;A0A5F9ZH87;H0Y325;Q8NF91-11;Q8NF91-8;Q8NF91-3;Q8NF91-9;A0A5F9ZH86 Q8NF91 SYNE1 Nesprin-1 1 0 S(0.332)KT(0.649)PT(0.019)GPELDTSYK 78.674 0.020927 13987000 1592.6 1902.8 1888.1 2062.9 1527.5 1891.3 1345 1827.2 1989.7 2214.4 TRUE FALSE FALSE 1573.188779 1929.587668 1920.961588 2301.422204 1449.545975 1770.452034 1459.244266 1880.067149 1811.736249 2156.869569 0.729385217 0.89462418 0.890624828 1.067019646 0.672060099 0.820843346 0.676556565 0.871664739 0.839984149 1 11.07472322 -8.727004454 24.99988893 0.884812466 0.758626793 0.312774713 0.101805136 238.7932799 173363.8757 0.017918536 0.035835713 1.87E-09 8.727004454 -0.126185674 SKTDNSSLS(ph)SPLNPK ddPTM_HeLa_Romidepsin_16h_R1 2 SKTDNSSLSSPLNPK 15 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 SKTDNSSLS(0.5)S(0.5)PLNPK;SKTDNSSLS(0.641)S(0.359)PLNPK ; 85.362 0.0083313 43358000 8587.5 6778.8 7400.2 8305.3 8453.7 9254.6 8242 9068.8 8692.3 7593.2 TRUE FALSE FALSE 8482.832247 6874.232124 7528.997377 9265.597864 8022.276144 8663.260928 8942.075274 9331.19142 7914.838918 7395.927569 1.146959887 0.929461796 1.017992308 1.252797269 1.084688306 1.171355567 1.209053927 1.261666144 1.070161767 1 12.85251538 -4 0.230403337 1.034828535 2.324630239 0.468856547 0.07765296 37.34552785 0.45452518 0.056645313 18.36636526 1.00E-04 4 1.289801705 SKTDNSSLSS(ph)PLNPK ddPTM_HeLa_Romidepsin_16h_R1 1 SKTDNSSLSSPLNPK 15 1 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 SKTDNSSLS(0.029)S(0.971)PLNPK 193.98 8.00E-12 9744600 1988.8 1509.2 1655.7 1548.9 2018.2 2084.5 2022.6 2320.6 2031.8 1677.6 TRUE FALSE FALSE 1964.559741 1530.446557 1684.516764 1727.991106 1915.203723 1951.307177 2194.399594 2387.7429 1850.070719 1634.01571 1.202289383 0.936616795 1.030906101 1.057511929 1.172084033 1.194178958 1.342948896 1.461272915 1.132223337 1 10.67420614 -7.664634031 1.092347779 1.077823817 1.526629845 0.777470879 0.071586376 0.431344653 0.629068972 0.013960833 0.188426837 2.16E-08 7.664634031 0.448806028 SKYDEIFYNLAPADGKLS(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 SKYDEIFYNLAPADGKLSGSK 21 2 Q9NZN4-2;Q9NZN4 Q9NZN4-2 EHD2 EH domain-containing protein 2 1 0 SKYDEIFYNLAPADGKLS(0.741)GS(0.259)K;SKYDEIFYNLAPADGKLS(0.633)GS(0.367)K ; 89.859 0.0004226 215895000 12013.8 11245.1 10265 11227.1 10365.9 9258.7 7445.5 8459.8 12183.1 11166.2 TRUE FALSE FALSE 11867.37118 11403.40881 10443.65802 12525.23013 9836.889442 8667.098951 8077.920584 8704.570966 11093.41302 10876.10051 1.091142103 1.048483213 0.960239197 1.151628758 0.904450031 0.796893973 0.742722134 0.800339327 1.019980737 1 13.40887377 -8.476922783 3.325279242 1.044412187 0.777772923 0.838840721 0.052130853 0.070717413 1.567008249 0.007879111 0.018233045 3.33E-09 8.476922783 -0.266639264 SLAALDALNT(ph)DDENDEEEYEAWK ddPTM_HeLa_Romidepsin_16h_R1 6 SLAALDALNTDDENDEEEYEAWK 23 0 P55081 P55081 MFAP1 Microfibrillar-associated protein 1 1 0 SLAALDALNT(0.999)DDENDEEEY(0.001)EAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(1)DDENDEEEYEAWK;SLAALDALNT(0.999)DDENDEEEY(0.001)EAWK ;;;;; 137.31 2.30E-13 69623800 31229.6 30529.3 29358.5 28648.5 37631.2 39223.5 35673.5 41782.4 34097.9 31787.7 TRUE FALSE FALSE 30848.96162 30959.09229 29869.47238 31960.97437 35710.73944 36717.24494 38703.6062 42991.30782 31048.09842 30961.85097 0.996353921 0.999910901 0.964718563 1.032269498 1.153378701 1.185886625 1.250041744 1.38852512 1.002785604 1 14.9182041 -7.841211465 0.745682666 0.993439482 1.449369341 0.957333408 0.027636956 0.201114725 0.12531152 0.004836304 0.064746702 1.44E-08 7.841211465 0.455929858 SLADELALVDVLEDK ddPTM_HeLa_Romidepsin_16h_R1 1 SLADELALVDVLEDK 15 0 A0A5F9ZHM4;P07195;F5H793;C9J7H8;A8MW50;A0A3B3IS95 A0A5F9ZHM4 LDHB L-lactate dehydrogenase B chain;L-lactate dehydrogenase 0 0 193 1.51E-11 4809400 2927.9 2575.1 2578.5 2102.7 2792.4 3062.5 2319.7 2781 2804.5 2833.1 FALSE FALSE TRUE 2892.213629 2611.352325 2623.377711 2345.824068 2649.893408 2866.816134 2516.73526 2861.463847 2553.658496 2759.495654 1.048095011 0.946315071 0.950672891 0.850091597 0.960281784 1.038891339 0.91202726 1.03695175 0.925407689 1 11.4301889 -10.25196743 24.42139269 1.022711533 0.953756149 0 0.061149638 490.092598 1263599.502 0.008850938 0.010761032 5.60E-11 10.25196743 -0.068955384 SLANGT(ph)PPMGAASK ddPTM_HeLa_Romidepsin_16h_R1 1 SLANGTPPMGAASK 14 0 A0A1B0GV68 A0A1B0GV68 1 0 SLANGT(0.999)PPMGAAS(0.001)K 101.2 0.024014 4597800 3348.8 4061.2 3870.2 3187.4 3905.1 3810.6 2781.7 3253.3 3369.4 2730.7 TRUE FALSE FALSE 3307.983538 4118.37368 3937.559208 3555.942185 3705.808175 3567.114958 3017.977529 3347.429103 3068.032425 2659.75602 1.243716909 1.548402804 1.480421203 1.336942997 1.393288763 1.341143673 1.134682093 1.25854743 1.15350145 1 11.3770782 -11.3340758 0.9924875 1.036681924 1.347486782 0.440159797 0.117948857 0.271264742 0.554881296 0.040674391 0.026217894 4.63E-12 11.3340758 0.310804859 SLAPDRS(ph)DDEHDPLDNTSRPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLAPDRSDDEHDPLDNTSRPR 21 2 Q92614;A0A0D9SFK2;Q92614-2;Q92614-3;Q92614-4;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 S(0.003)LAPDRS(0.997)DDEHDPLDNTSRPR;S(0.027)LAPDRS(0.973)DDEHDPLDNTSRPR ; 79.172 0.0012387 47119000 3483.5 3183.3 2826.4 3478.7 3454 3737 2870.9 3531.6 3564.8 3341.4 TRUE FALSE FALSE 3441.041762 3228.114581 2875.592306 3880.923662 3277.729491 3498.217761 3114.754174 3633.781274 3245.95536 3254.589946 1.057288881 0.991865222 0.883549803 1.192446276 1.007109819 1.074856685 0.957034289 1.116509709 0.997346951 1 11.66826007 -9.262265599 24.99999616 1.014757052 1.060159501 0.191505772 0.073762759 152.2616386 4607232.489 0.010898892 0.017276864 5.47E-10 9.262265599 0.045402448 SLASEAPSQPSLNGGS(ph)PEGVESQDGVDHFR ddPTM_HeLa_Romidepsin_16h_R1 1 SLASEAPSQPSLNGGSPEGVESQDGVDHFR 30 0 P38935 P38935 IGHMBP2 DNA-binding protein SMUBP-2 1 0 SLASEAPSQPS(0.001)LNGGS(0.998)PEGVES(0.001)QDGVDHFR 126.5 4.51E-11 4058500 1167.9 1067 1273.9 1302.2 1202.2 1421.7 907.22 1074.8 1370.8 1544.8 TRUE FALSE FALSE 1153.665186 1082.021254 1296.071695 1452.766491 1140.847248 1330.857958 984.2792442 1105.897642 1248.192215 1504.665873 0.766725162 0.71911065 0.861368439 0.965507703 0.758206369 0.884487368 0.654151371 0.734978883 0.829547767 1 10.55522744 -12.26961038 0.859572987 1.00827828 0.794405265 0.101722491 0.099870547 0.507807309 0.63299757 0.072331831 0.016982312 5.38E-13 12.26961038 -0.213873015 SLATMDS(ph)PPHQK ddPTM_HeLa_Romidepsin_16h_R1 1 SLATMDSPPHQK 12 0 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 S(0.001)LAT(0.065)MDS(0.933)PPHQK 61.649 0.028523 20264000 5768 5431.1 5145.1 4398.1 6448.3 6122.9 5589.5 6046.9 6094.6 6135.3 TRUE FALSE FALSE 5697.697397 5507.559168 5234.648307 4906.629016 6119.219189 5731.666451 6064.27199 6221.857511 5549.483712 5975.904022 0.953445266 0.921627782 0.875959234 0.821068912 1.023982174 0.959129603 1.014787381 1.041157537 0.92864338 1 12.54494126 -7.625621823 1.626490056 0.956164339 1.048465585 0.242724372 0.057581478 0.775928892 3.114270938 0.00936354 0.090490824 2.37E-08 7.625621823 0.092301246 SLDGAAAVDSADRS(ph)PRPTSAPAITQGQVAEGGVLDASAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLDGAAAVDSADRSPRPTSAPAITQGQVAEGGVLDASAK 39 2 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A3B3ITP0;A0A2R8Y7Y3;A0A2R8Y5G2;A0A2U3TZH6;A0A2R8Y420;A0A2R8YCW8;A0A2R8Y5Z6;P11171-5;P11171-7;P11171-6;A0A3B3IU06;A0A2R8Y570;A0A2R8Y6G5;A0A2R8YFR9;A0A2R8Y7N0;A0A3B3IUD6;A0A2R8Y4N6 P11171 EPB41 Protein 4.1 1 0 S(0.005)LDGAAAVDS(0.114)ADRS(0.293)PRPT(0.293)S(0.293)APAIT(0.003)QGQVAEGGVLDASAK 57.731 0.00042412 40547000 2547.1 2365.5 2403.4 1906.9 2395 2715.8 2729.9 2611.6 2954.6 2711.9 TRUE FALSE FALSE 2516.054965 2398.801571 2445.230169 2127.38475 2272.774213 2542.269145 2961.777638 2687.162526 2690.333176 2641.444447 0.952529957 0.90814008 0.925717053 0.805386898 0.860428549 0.96245414 1.121271977 1.017307984 1.018508331 1 11.36711135 -4.873908066 17.74849405 0.961422781 1.070441569 0 0.084948812 0 0 0.011831174 0 1.34E-05 4.873908066 0.109018788 SLDGAAAVDSADRSPRPTSAPAIT(ph)QGQVAEGGVLDASAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLDGAAAVDSADRSPRPTSAPAITQGQVAEGGVLDASAK 39 2 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A3B3ITP0;A0A2R8Y7Y3;A0A2R8Y5G2;A0A2U3TZH6;A0A2R8Y420;A0A2R8YCW8;A0A2R8Y5Z6;P11171-5;P11171-7;P11171-6;A0A3B3IU06;A0A2R8Y570;A0A2R8Y6G5;A0A2R8YFR9;A0A2R8Y7N0;A0A3B3IUD6;A0A2R8Y4N6 P11171 EPB41 Protein 4.1 1 0 S(0.04)LDGAAAVDS(0.031)ADRS(0.105)PRPT(0.114)S(0.114)APAIT(0.597)QGQVAEGGVLDASAK 42.461 0.011005 21550000 1051.3 1263.2 1297.8 1084.9 1406 1342.6 835.42 1119.5 1410.1 1255.5 TRUE FALSE FALSE 1038.486351 1280.983363 1320.387665 1210.341243 1334.246573 1256.812193 906.3805539 1151.890966 1283.977124 1222.881929 0.84921228 1.047511892 1.079734383 0.989744974 1.091067373 1.027746149 0.741184028 0.941947819 1.049960012 1 10.2560694 -7.772991023 24.99997798 0.967880249 0.841565892 0.272296847 0.089495002 233.229709 504757.7339 0.014306899 0.043453533 1.69E-08 7.772991023 -0.126314357 SLDLFNCEVTNLNDYR ddPTM_HeLa_Romidepsin_16h_R1 1 SLDLFNCEVTNLNDYR 16 0 P39687;H0YN26;Q92688-2;Q92688 P39687 ANP32A;ANP32B Acidic leucine-rich nuclear phosphoprotein 32 family member A;Acidic leucine-rich nuclear phosphoprotein 32 family member B 0 0 146.79 0.003099 6885600 2207.8 2363.1 2123.8 576.61 2544.8 2233.4 2155.1 2442.2 2899.4 2727.5 FALSE FALSE TRUE 2180.890484 2396.367784 2160.763848 643.2803612 2414.92936 2090.692948 2338.15414 2512.861204 2640.070402 2656.639157 0.820920854 0.902029836 0.813344877 0.242140661 0.9090167 0.786969108 0.880117322 0.945879758 0.993763265 1 11.37538657 -11.5503992 0.658248243 0.994381214 0.772698946 0.165989557 0.189566833 1.026146839 0.90576797 0.111417679 0.046583472 2.82E-12 11.5503992 -0.221682267 SLDNNYST(ph)PNER ddPTM_HeLa_Romidepsin_16h_R1 1 SLDNNYSTPNER 12 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-9;A0A669KB05;O60716-13;O60716-21;O60716-18;O60716-17;O60716-19;O60716-25;O60716-27;O60716-29;O60716-26;H0YC95 O60716 CTNND1 Catenin delta-1 1 0 SLDNNYS(0.003)T(0.997)PNER 174.46 9.82E-05 39902000 7208.5 7391.6 6198 6533.2 4186.1 5791.7 5019.4 6079.3 6674.7 6868.6 TRUE FALSE FALSE 7120.640029 7495.659139 6305.87359 7288.599324 3972.467697 5421.629062 5445.747711 6255.194954 6077.698115 6690.152782 1.0643464 1.120401788 0.942560476 1.08945185 0.593778323 0.810389424 0.813994521 0.934985367 0.908454308 1 12.70782344 -8.784964259 24.99998659 1.034967518 0.791701827 0.568881025 0.098715891 105.0408882 111627.0682 0.012845595 0.023294189 1.64E-09 8.784964259 -0.24326569 SLDS(ph)DESEDEEDDY(ph)QQK ddPTM_HeLa_Romidepsin_16h_R1 1 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 0 S(0.026)LDS(0.509)DES(0.511)EDEEDDY(0.954)QQK 95.554 0.0048551 44004000 6062.3 5810.1 6122.5 4977.7 6005 5924.3 5760.5 5458.2 6664.7 6042.9 TRUE FALSE FALSE 5988.410356 5891.89474 6229.059544 5553.245095 5698.542442 5545.75635 6249.796726 5616.124405 6068.59254 5885.904587 1.017415466 1.001017712 1.058301142 0.943482011 0.968167655 0.942209692 1.061824335 0.954165043 1.031038212 1 12.52304844 -9.246651755 24.99743712 1.011192107 0.976763775 0.281131778 0.036058561 1034.113241 1748098.758 0.005104608 0.00843752 5.67E-10 9.246651755 -0.034428332 SLDS(ph)DESEDEEDDY(ph)QQKR ddPTM_HeLa_Romidepsin_16h_R1 1 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 2 0 S(0.075)LDS(0.71)DES(0.261)EDEEDDY(0.954)QQKR 57.414 0.019532 57156000 3435.4 3492.5 2982.5 3189 3623.2 2824.9 3123 3508 3264.5 3597.9 TRUE FALSE FALSE 3393.528023 3541.667507 3034.409161 3557.727185 3438.294584 2644.398007 3388.267542 3609.498445 2972.514944 3504.426039 0.96835487 1.010626981 0.86587907 1.015209665 0.981129162 0.754588049 0.966853774 1.029982772 0.848217343 1 11.77496246 -10.12454787 0.656656909 0.992149351 0.932118902 0 0.08979709 1.2952041 1.185763578 0.021210914 0.027860347 7.51E-11 10.12454787 -0.06003045 SLDSDES(ph)EDEEDDYQQK ddPTM_HeLa_Romidepsin_16h_R1 2 SLDSDESEDEEDDYQQK 17 0 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 0 SLDS(0.001)DES(0.999)EDEEDDYQQK;SLDS(0.002)DES(0.997)EDEEDDYQQK ; 195.6 9.84E-14 23282000 12671.2 12209.3 11663.7 11505.1 12134 13762.2 12172.4 14108.4 13317.7 13531.9 TRUE FALSE FALSE 12516.75854 12381.18285 11866.70181 12835.3738 11514.7567 12882.83984 13206.32335 14516.60429 12126.53156 13180.33929 0.949653743 0.939367536 0.900333561 0.973827268 0.873631281 0.977428544 1.001971426 1.101383203 0.920046995 1 13.68609989 -7.299442473 2.105411343 0.960312332 1.132839189 0.585935282 0.039063275 0.394168668 2.038793383 0.005949729 0.124475941 5.02E-08 7.299442473 0.172526857 SLDSDES(ph)EDEEDDYQQKR ddPTM_HeLa_Romidepsin_16h_R1 2 SLDSDESEDEEDDYQQKR 18 1 Q13442 Q13442 PDAP1 28 kDa heat- and acid-stable phosphoprotein 1 0 SLDS(0.004)DES(0.996)EDEEDDYQQKR;SLDS(0.027)DES(0.972)EDEEDDYQQKR ; 173.21 4.49E-08 25977900 3090.2 3053.6 2788.4 3387.9 3165.7 3507.9 3270.7 3930 3415.1 3545.9 TRUE FALSE FALSE 3052.535454 3096.588661 2836.930932 3779.624939 3004.142516 3283.756511 3548.513176 4043.708349 3109.644903 3453.777007 0.883825287 0.896580368 0.821399565 1.094345388 0.869813688 0.95077259 1.02742973 1.170807595 0.900360648 1 11.75395922 -7.354012594 1.933533342 0.936917093 1.216118595 0.519705705 0.072494684 0.41887314 1.891118542 0.010592828 0.194035367 4.43E-08 7.354012594 0.279201502 SLDSEPSVPSAAKPPS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 2 SLDSEPSVPSAAKPPSPEK 19 1 Q7Z3K3-5;Q7Z3K3-7;Q7Z3K3-2;Q7Z3K3-3;Q7Z3K3-6;Q7Z3K3 Q7Z3K3-5 POGZ Pogo transposable element with ZNF domain 1 0 SLDSEPSVPS(0.011)AAKPPS(0.989)PEK;SLDSEPSVPS(0.023)AAKPPS(0.977)PEK ; 92.096 0.0012546 479240000 5837 5029.1 5411.2 3836.7 4215.4 4198.1 3757.2 4874.2 5978.7 5962.1 TRUE FALSE FALSE 5765.856399 5099.899802 5505.379666 4280.317306 4000.272408 3929.854959 4076.336474 5015.227287 5443.950098 5807.203783 0.992879984 0.878202314 0.948025913 0.737070278 0.68884657 0.676720691 0.701944796 0.863621714 0.937447746 1 12.50362795 -9.43893315 1.492119462 0.992904601 0.720802147 0.731910295 0.063678874 0.118392617 0.522217429 0.00999563 0.017064724 3.64E-10 9.43893315 -0.272102454 SLDSESIS(ph)PGDFHR ddPTM_HeLa_Romidepsin_16h_R1 2 SLDSESISPGDFHR 14 0 F8VWZ8;Q52LW3 F8VWZ8 ARHGAP29 Rho GTPase-activating protein 29 1 0 SLDSES(0.001)IS(0.999)PGDFHR;SLDSES(0.015)IS(0.985)PGDFHR ; 173.77 9.94E-06 11300100 4468 4847.9 4908.6 5101.1 7306.8 7706.5 5841.4 6470.9 5622.2 4599.2 TRUE FALSE FALSE 4413.542297 4916.148863 4994.032124 5690.913183 6933.906731 7214.079522 6337.56837 6658.125282 5119.336351 4479.712121 0.985229001 1.097425176 1.11481095 1.270374754 1.547846501 1.610389089 1.414726705 1.486284186 1.142782441 1 12.12919031 -9.160795831 1.52647981 0.999344351 1.518880253 0.881241 0.075873231 0.06546063 0.299240809 0.010141106 0.019659059 6.91E-10 9.160795831 0.519535902 SLENETLNKEEDCHS(ph)PTSKPPKPDQPLK ddPTM_HeLa_Romidepsin_16h_R1 1 SLENETLNKEEDCHSPTSKPPKPDQPLK 28 3 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.001)LENET(0.011)LNKEEDCHS(0.84)PT(0.074)S(0.074)KPPKPDQPLK 57.051 0.00070566 39560000 2211.4 1861.8 1978.4 403.08 2517.7 2239.2 2101.7 2271.1 2643.4 2319.5 TRUE FALSE FALSE 2184.446606 1888.010469 2012.833222 449.6860061 2389.212374 2096.122347 2280.218346 2336.810695 2406.967683 2259.239056 0.966894849 0.835684238 0.890934148 0.199043127 1.057529688 0.927800155 1.009285998 1.034335295 1.065388666 1 11.14162122 -10.32121154 3.699707302 0.98596861 0.843654266 0.087356526 0.232626387 0.511654372 13.79510835 0.040569353 0.04676714 4.77E-11 10.32121154 -0.142314344 SLENPTPPFT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SLENPTPPFTPK 12 0 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 SLENPT(0.143)PPFT(0.857)PK;SLENPT(0.023)PPFT(0.977)PK ; 138.73 0.0045757 28371000 9519.6 9520.8 8643.5 8426.1 7983.1 7501.3 5526.8 5731.6 9230 8458 TRUE FALSE FALSE 9403.571454 9654.834072 8793.936492 9400.365328 7575.692618 7021.991139 5996.246254 5897.434803 8404.445683 8238.259941 1.141451171 1.171950648 1.067450718 1.141061996 0.919574361 0.852363386 0.727853491 0.715859277 1.020172432 1 13.00812393 -8.274125654 1.58357129 1.081742602 0.720351055 0.864006396 0.058497445 0.124627832 0.585829383 0.010592679 0.037846855 5.32E-09 8.274125654 -0.361391547 SLEPEES(ph)PGKR ddPTM_HeLa_Romidepsin_16h_R1 1 SLEPEESPGKR 11 1 Q9BVI0;Q5JWZ0;Q5JXL1 Q9BVI0 PHF20 PHD finger protein 20 1 0 SLEPEES(1)PGKR 116.74 0.017736 5509100 2988.8 2303.5 3473.9 2580 1754.5 1730.8 1470.1 1552.5 2778.3 2995.3 TRUE FALSE FALSE 2952.371356 2335.928733 3534.361772 2878.311739 1664.961318 1620.207466 1594.970257 1597.419138 2529.80189 2917.481674 1.011958835 0.80066612 1.211442664 0.98657406 0.570684413 0.555344522 0.546694182 0.547533564 0.867118348 1 11.51050788 -8.761243373 6.028784429 1.005331962 0.552095237 0.805548697 0.101796498 0.039410704 5.332247005 0.0126042 0.024251286 1.73E-09 8.761243373 -0.453236725 SLES(ph)LDTSLFAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLESLDTSLFAK 12 0 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 1 0 SLES(0.999)LDT(0.001)SLFAK 103.14 0.014053 12456000 1377.8 1012 1142 1132.5 1291.1 1471.3 960.86 1417.6 1235.8 1274.6 TRUE FALSE FALSE 1361.006844 1026.246963 1161.876031 1263.444979 1225.210349 1377.288678 1042.475424 1458.616019 1125.266953 1241.485708 1.096272663 0.826628092 0.935875478 1.017687896 0.986890418 1.109387462 0.839699899 1.174895538 0.906387359 1 10.27785194 SLESLADGGS(ph)ASPIKDQPVMAVK ddPTM_HeLa_Romidepsin_16h_R1 1 SLESLADGGSASPIKDQPVMAVK 23 1 A0A3B3ITU7;Q9HB96 A0A3B3ITU7 FANCE Fanconi anemia group E protein 1 0 SLESLADGGS(0.539)AS(0.461)PIKDQPVMAVK 80.102 0.00050903 38196000 2267.8 2273.1 2323 2161.4 2181.1 2462.9 1928.8 2295.3 2618.7 2846.6 TRUE FALSE FALSE 2240.159181 2305.100761 2363.430841 2411.311238 2069.790328 2305.528639 2092.632224 2361.710884 2384.476913 2772.644922 0.807950259 0.831372508 0.85241021 0.869679063 0.746503929 0.831526829 0.754742235 0.85178988 0.860000823 1 11.43704715 -12.51934421 0.501374455 1.059088708 0.809946531 0.232239782 0.058355243 0.678509494 0.198666248 0.086425385 0.009589644 3.02E-13 12.51934421 -0.249142177 SLESLADGGSAS(ph)PIKDQPVMAVK ddPTM_HeLa_Romidepsin_16h_R1 1 SLESLADGGSASPIKDQPVMAVK 23 1 A0A3B3ITU7;Q9HB96 A0A3B3ITU7 FANCE Fanconi anemia group E protein 1 0 SLES(0.001)LADGGS(0.187)AS(0.813)PIKDQPVMAVK 77.445 0.0006199 44949000 2424.4 2283.8 2079.5 2456.7 1757.2 2002.9 1838.2 2539.8 2562.5 2376.6 TRUE FALSE FALSE 2394.85048 2315.951396 2115.692825 2740.755213 1667.523527 1874.921154 1994.336662 2613.285106 2333.303582 2314.855589 1.034557184 1.00047338 0.913963201 1.183985397 0.720357475 0.809951672 0.861538262 1.12891928 1.007969392 1 11.17670648 -8.758240769 24.99999992 1.017327742 0.87384218 0.269869542 0.115014399 83.51959468 652768.8147 0.01585526 0.03068107 1.74E-09 8.758240769 -0.143485562 SLETSSALS(ph)PSLK ddPTM_HeLa_Romidepsin_16h_R1 1 SLETSSALSPSLK 13 0 Q7Z333-3;Q7Z333;Q7Z333-4 Q7Z333-3 SETX Probable helicase senataxin 1 0 SLET(0.001)S(0.014)S(0.306)ALS(0.467)PS(0.211)LK 99.834 0.012836 18927000 1770.1 1615.1 1743.6 1733.9 2916.7 3977.8 3215.1 3796.2 1994.3 2058.8 TRUE FALSE FALSE 1748.52534 1637.83742 1773.946627 1934.381676 2767.849915 3723.631418 3488.190514 3906.037058 1815.924813 2005.312079 0.871946745 0.816749391 0.884623718 0.964628746 1.380258935 1.856883752 1.739475142 1.947844975 0.905557211 1 10.96961106 -8.520998649 2.20021537 0.92168067 1.849649536 0.97372821 0.069466808 0.039038255 0.374796489 0.01198874 0.029783045 3.01E-09 8.520998649 0.927968866 SLEVGT(ph)VMT(ph)LFY(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 SLEVGTVMTLFYSK 14 0 P19174-2;P19174 P19174-2;P19174 PLCG1 "1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1" 3 0 S(0.003)LEVGT(0.996)VMT(0.966)LFY(0.857)S(0.178)K 45.79 0.03051 14675000 904.51 1300.2 3270.8 1571.2 4596.1 4829.7 2769.1 2762.4 6180.1 2364.1 TRUE FALSE FALSE 893.4854842 1318.50425 3327.726902 1752.869537 4361.543867 4521.097757 3004.307285 2842.325686 5627.336378 2302.680341 0.388019765 0.572595434 1.445153651 0.761230078 1.894116082 1.96340659 1.304700106 1.234355301 2.443820046 1 11.16909843 -9.274127005 1.432546901 0.70381959 1.56225785 0 0.655980043 0.260633945 1.049262111 0.065607153 0.122318384 5.32E-10 9.274127005 0.85843826 SLFS(ph)PQNTLAAPTGHPPTSGVEK ddPTM_HeLa_Romidepsin_16h_R1 1 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 S(0.041)LFS(0.705)PQNT(0.192)LAAPT(0.063)GHPPTSGVEK 80.832 0.0001837 11873000 1990.8 1962.4 2080.7 1634.5 2362.2 2229.4 2152.9 2575.6 2289.5 2379.6 TRUE FALSE FALSE 1966.535364 1990.026719 2116.913711 1823.488581 2241.648119 2086.948535 2335.767272 2650.120922 2084.721386 2317.777649 0.848457299 0.858592592 0.913337702 0.786740083 0.967154084 0.900409293 1.007761583 1.143388764 0.899448395 1 11.17852646 -7.371468528 2.0046157 0.91159254 1.182827623 0.630957196 0.05831779 0.373289518 1.903031628 0.010335063 0.169520649 4.25E-08 7.371468528 0.271235083 SLFSPQNT(ph)LAAPTGHPPTSGVEK ddPTM_HeLa_Romidepsin_16h_R1 1 SLFSPQNTLAAPTGHPPTSGVEK 23 0 Q5VT52-2;Q5VT52-3;Q5VT52 Q5VT52-2 RPRD2 Regulation of nuclear pre-mRNA domain-containing protein 2 1 0 S(0.03)LFS(0.177)PQNT(0.786)LAAPT(0.008)GHPPTSGVEK 72.913 0.00099732 14825000 1533.1 1432.4 1340 1227.8 1972.7 1852.1 1486.4 1552.5 1894.2 1627.6 TRUE FALSE FALSE 1514.413988 1452.565365 1363.322138 1369.764013 1872.025758 1733.756787 1612.654779 1597.419138 1724.778008 1585.314717 0.955276559 0.916263092 0.859969395 0.864032862 1.180854336 1.093635711 1.017245826 1.007635342 1.08797199 1 10.63055356 -8.766486704 24.99973706 0.956083476 1.072071081 0.399089815 0.076208557 100.9925538 500225.091 0.010650917 0.019747602 1.71E-09 8.766486704 0.115987605 SLGAWNLENLRS(ph)PEEVDKESQR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGAWNLENLRSPEEVDKESQR 22 2 P48681 P48681 NES Nestin 1 0 S(0.001)LGAWNLENLRS(0.998)PEEVDKES(0.001)QR;S(0.001)LGAWNLENLRS(0.999)PEEVDKES(0.001)QR ; 59.561 0.0054358 49737000 2211.51 2109.28 2028.59 2376.1 3026.1 3456.1 2514.3 3020.8 2341.84 2075.13 TRUE FALSE FALSE 2184.555265 2138.974499 2063.896758 2650.835862 2871.666825 3235.266364 2727.864579 3108.202082 2132.379965 2021.217823 1.0808114 1.05826026 1.021115455 1.311504298 1.420760688 1.600652006 1.34961435 1.537786797 1.054997606 1 10.98100909 -9.04681609 2.226786801 1.03845827 1.480955727 0.906737693 0.065961861 0.061826658 0.607609169 0.009981136 0.018794776 8.98E-10 9.04681609 0.442497457 SLGDDISSETSGDFRK ddPTM_HeLa_Romidepsin_16h_R1 1 SLGDDISSETSGDFRK 16 1 P12429;D6RFG5;D6RA82 P12429 ANXA3 Annexin A3;Annexin 0 0 91.076 0.0075944 8185400 1236.8 966.48 1086.3 1435.3 1360.8 1206.3 1195 1086 1505.4 1366.1 FALSE FALSE TRUE 1221.725406 980.0861308 1105.206596 1601.256139 1291.353298 1129.221323 1296.50327 1117.421697 1370.753254 1330.608525 0.918170433 0.736569857 0.830602371 1.203401383 0.97049829 0.848650299 0.974368679 0.839782457 1.030170202 1 10.37787047 -10.47948066 0.009812894 1.882157577 1.98E-07 0.054034144 0.121170874 3356.617017 28.37311247 2726.326145 2712.969588 3.32E-11 10.47948066 -1.882157379 SLGGEAAVR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGGEAAVR 9 0 Q9UG01-2;Q9UG01 Q9UG01-2 IFT172 Intraflagellar transport protein 172 homolog 0 0 101.64 0.0039939 0 1436.8 1102.2 5014.5 2023.8 3702.5 4927.2 3430.6 1391.3 1045.3 835.38 FALSE FALSE TRUE 1419.287729 1117.716801 5101.775269 2257.801278 3513.547609 4612.367822 3721.995078 1431.55507 951.80575 813.6767072 1.74428949 1.373662034 6.270027425 2.774813705 4.31811256 5.668550889 4.574292278 1.759365922 1.169759121 1 9.668311882 -9.792588608 24.47317408 1.362953699 4.246874997 0.576207179 1.22048533 80.20708501 63016.34647 0.187434625 0.246353128 1.61E-10 9.792588608 2.883921297 SLGGIS(ph)PSEDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGGISPSEDR 11 0 H3BV44;H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BMM1 H3BV44 MYO9A Unconventional myosin-IXa 1 0 SLGGIS(0.918)PS(0.082)EDR 132.17 0.0046398 2087800 1490.4 1530.7 1820.4 1755.9 1622.4 1880 1598.4 1709.2 1450.2 1762.6 TRUE FALSE FALSE 1472.234432 1552.249235 1852.083298 1958.92542 1539.602874 1759.874067 1734.168056 1758.653005 1320.49048 1716.807398 0.857541989 0.904148734 1.078795036 1.141028063 0.896782525 1.025085324 1.010112176 1.024374084 0.7691547 1 10.74551248 -9.771159296 24.99887662 0.928705046 1.027342716 0.384179448 0.083147432 202.6123865 521102.6417 0.012591785 0.01666462 1.69E-10 9.771159296 0.09863767 SLGGIS(ph)PSEDRR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGGISPSEDRR 12 1 H3BV44;H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BMM1 H3BV44 MYO9A Unconventional myosin-IXa 1 0 SLGGIS(0.918)PS(0.082)EDRR;SLGGIS(0.826)PS(0.174)EDRR ; 87.863 0.0094162 8234200 3486.9 4044.2 3345.4 3115.4 3303 3754.5 3384.8 3952.7 4266.5 3605.8 TRUE FALSE FALSE 3444.400322 4101.134354 3403.625284 3475.617206 3134.435585 3514.599567 3672.304828 4067.065138 3884.893554 3512.120796 0.980718068 1.167708798 0.969108263 0.989606397 0.892462352 1.000705776 1.045608919 1.15800833 1.106138934 1 11.77812675 -7.329882681 2.38239935 0.995368852 1.182498176 0.232586329 0.073200705 0.38519408 2.910754882 0.008863879 0.138562059 4.68E-08 7.329882681 0.187129323 SLGNILQAKPTS(ph)SPAKGPPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SLGNILQAKPTSSPAKGPPQK 21 2 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 SLGNILQAKPT(0.173)S(0.414)S(0.414)PAKGPPQK 99.454 0.0004329 115620000 2708.9 2510.3 2428.1 2725.7 1968.3 1602.5 1164.2 1479 2996.8 2781 TRUE FALSE FALSE 2675.882885 2545.640069 2470.360062 3040.858259 1867.850306 1500.105422 1263.087119 1521.792532 2728.758702 2708.749219 0.987866601 0.93978433 0.911992902 1.122606049 0.689561918 0.553800039 0.466299025 0.561806357 1.007386983 1 11.40341112 -8.573268837 3.942099788 0.990425788 0.530743129 0.928420358 0.059196149 0.037599227 1.22137353 0.008360079 0.017761691 2.67E-09 8.573268837 -0.459682659 SLGNILQAKPTSS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLGNILQAKPTSSPAK 16 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 SLGNILQAKPTS(0.009)S(0.991)PAK 225.37 3.26E-34 40560000 4968.3 4622.3 6422.4 3198.3 3865.6 3295.1 3425.9 2611.5 5545.9 4458.9 TRUE FALSE FALSE 4907.744449 4687.372861 6534.179178 3568.102494 3668.324007 3084.553744 3716.89586 2687.059632 5049.860814 4343.057135 1.130020696 1.079279575 1.504511448 0.821564714 0.844640974 0.710226379 0.855824767 0.618702345 1.162743353 1 12.08449522 -9.029308633 24.87625958 1.097763086 0.770027418 0.635081002 0.148327438 377.8284419 320688.4265 0.022325527 0.037065582 9.35E-10 9.029308633 -0.327735668 SLGNILQAKPTSS(ph)PAKGPPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SLGNILQAKPTSSPAKGPPQK 21 2 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 SLGNILQAKPT(0.28)S(0.187)S(0.533)PAKGPPQK 87.808 0.00050861 191830000 8206.9 7722.3 6556.6 6837.6 4865.6 4148.7 4252.7 4348.4 7961.5 8042.7 TRUE FALSE FALSE 8106.871146 7831.014742 6670.714873 7628.195484 4617.290276 3883.611459 4613.924232 4474.214093 7249.4035 7833.749495 1.034864742 0.999650901 0.851535383 0.973760456 0.589409998 0.495753848 0.588980313 0.571145924 0.925406602 1 12.93548728 -8.757865621 4.239336108 1.000777406 0.552392198 0.918239459 0.058412706 0.036541931 1.523391612 0.008651949 0.017035594 1.75E-09 8.757865621 -0.448385208 SLGS(ph)PLLHER ddPTM_HeLa_Romidepsin_16h_R1 3 SLGSPLLHER 10 0 H7C3L4;E7EQA9;Q92844;E7EV32;E7EMT6;E7ENY2;E7EVA2;E7EW82 H7C3L4 TANK TRAF family member-associated NF-kappa-B activator 1 0 S(0.012)LGS(0.988)PLLHER;S(0.001)LGS(0.999)PLLHER;S(0.001)LGS(0.999)PLLHER ;; 99.844 0.010305 11930000 2912.28 2568.36 2900.73 3014.91 4301.9 5006 3570.37 3693.6 3683.3 2778.91 TRUE FALSE FALSE 2876.784011 2604.517439 2951.215989 3363.50808 4082.35799 4686.132756 3873.637139 3800.468488 3353.856423 2706.713518 1.062832839 0.962243482 1.090331862 1.242653889 1.508234235 1.731299868 1.431121954 1.40408967 1.239088068 1 11.40232648 -8.984773374 2.238653363 1.027207342 1.531051395 0.782953268 0.110044104 0.075019223 0.754020972 0.01379329 0.026678828 1.04E-09 8.984773374 0.503844053 SLGS(ph)VQAPSYGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 S(0.311)LGS(0.689)VQAPSYGAR 115.12 0.0057994 44968000 215.95 248.63 238.98 356.16 319.63 334 143.22 207.36 227.67 339.73 TRUE FALSE FALSE 213.3179183 252.1302197 243.1393467 397.340895 303.3180884 312.6584779 155.3851032 213.3596344 207.306625 330.9037656 0.644652435 0.761944244 0.734773586 1.200774776 0.916635348 0.944862254 0.469577924 0.644778502 0.626486147 1 8.370267899 -12.59458374 1.409036201 0.999211133 0.778034218 0 0.221375399 0.685710503 2.456292323 0.141332035 0.033271727 2.54E-13 12.59458374 -0.221176915 SLGSAGPSGT(ph)LPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGSAGPSGTLPR 13 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 SLGSAGPS(0.13)GT(0.87)LPR;SLGSAGPS(0.235)GT(0.765)LPR ; 105 0.02025 13073200 4059 3490.13 3845.3 2490.89 4929.7 3391.48 2888.75 3569.4 4428.76 3992.92 TRUE FALSE FALSE 4009.527347 3539.264142 3912.225833 2778.898422 4678.119014 3174.775374 3134.120353 3672.674957 4032.640614 3889.183363 1.030943253 0.910027585 1.005924758 0.714519775 1.202853807 0.816308998 0.805855641 0.944330625 1.036886214 1 11.92525154 -10.04734766 1.829072756 1.014642543 0.907192864 0.128583794 0.124994748 0.501516674 3.27857815 0.020796491 0.026781129 8.97E-11 10.04734766 -0.107449679 SLGSASPGPGQPPLS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGSASPGPGQPPLSSPTR 19 0 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 0 SLGSASPGPGQPPLS(0.915)S(0.067)PT(0.018)R 200.94 3.01E-21 0 548.87 1067.6 760.17 520.5 1111.8 1713.2 751.43 1146.5 948.08 882.13 TRUE FALSE FALSE 542.1801613 1082.629701 773.40044 580.682659 1055.060697 1603.732049 815.2564454 1179.672169 863.2813503 859.2121354 0.631020139 1.260026082 0.900127463 0.675831538 1.227939706 1.866514663 0.948841865 1.372969631 1.004735984 1 9.74687056 -8.605678642 5.884995427 0.855918392 1.382014204 0.396124916 0.267450632 0.141522708 7.843983961 0.039298806 0.079475386 2.48E-09 8.605678642 0.526095812 SLGSASPGPGQPPLSSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 SLGSASPGPGQPPLSSPTR 19 0 Q9C0B5;Q9C0B5-2 Q9C0B5 ZDHHC5 Palmitoyltransferase ZDHHC5 1 0 SLGSASPGPGQPPLS(0.04)S(0.317)PT(0.642)R;SLGS(0.001)AS(0.018)PGPGQPPLS(0.265)S(0.265)PT(0.452)R ; 175.56 5.33E-12 8841200 2447.66 2503 2490.24 2493.37 3271.4 3382.7 2118.67 3244.5 2614.91 2282.3 TRUE FALSE FALSE 2417.826978 2538.2373 2533.581583 2781.665171 3104.448251 3166.556387 2298.629777 3338.374489 2381.0259 2223.005517 1.087638767 1.141804319 1.139709984 1.251308263 1.396509467 1.424448281 1.034018926 1.501739183 1.071084117 1 11.11829581 -9.664628585 0.800108439 1.029299253 1.329661808 0.502686463 0.119314045 0.332319956 0.427182097 0.023974411 0.04191169 2.16E-10 9.664628585 0.300362555 SLGSVQAPS(ph)YGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGSVQAPSYGAR 13 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 S(0.183)LGS(0.258)VQAPS(0.559)YGAR 134.02 0.0017942 88367000 1896.3 1428.4 1825.8 1232.5 2426.3 1839.3 1765.2 2087.2 2128.6 2089.6 TRUE FALSE FALSE 1873.187166 1448.509053 1857.577283 1375.007449 2302.476857 1721.774666 1915.136044 2147.589839 1938.212685 2035.311891 0.920344039 0.711688985 0.91267451 0.675575795 1.131264878 0.845951264 0.940954579 1.055164984 0.952292714 1 10.99103417 -7.277849086 4.646022238 0.924600359 1.061538844 0.090716277 0.127637074 0.350633033 19.71583391 0.017326836 0.150337003 5.27E-08 7.277849086 0.136938485 SLGSVQAPSYGARPVS(ph)SAASVYAGAGGSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 SLGS(0.003)VQAPS(0.239)Y(0.216)GARPVS(0.353)S(0.133)AAS(0.049)VY(0.004)AGAGGS(0.002)GS(0.001)R 51.66 0.0044317 18011000 959.75 1146.4 943.8 918.63 741.5 767.91 871.84 801.05 1003.9 1015.3 TRUE FALSE FALSE 948.0521978 1162.539049 960.2264431 1024.846323 703.6584881 718.8430293 945.8940678 824.2271179 914.1086697 988.9223596 0.958672022 1.175561497 0.97098264 1.036326374 0.71154068 0.726895314 0.956489717 0.833459887 0.924348267 1 9.949713449 -8.773656632 24.9999689 0.998984428 0.812038695 0.554978098 0.08901063 134.0105195 274223.5552 0.012928644 0.023559936 1.68E-09 8.773656632 -0.186945733 SLGSVQAPSYGARPVSSAASVYAGAGGS(ph)GSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLGSVQAPSYGARPVSSAASVYAGAGGSGSR 31 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 SLGSVQAPSYGARPVSSAASVYAGAGGS(0.769)GS(0.23)R;SLGSVQAPS(0.001)Y(0.001)GARPVS(0.097)S(0.097)AAS(0.197)VY(0.171)AGAGGS(0.343)GS(0.094)R ; 76.678 9.51E-07 58867000 1756.33 2052.2 1154.4 2705.6 1510.24 1852.83 1312.52 1515.31 1502.58 1598.84 TRUE FALSE FALSE 1734.923174 2081.090925 1174.491848 3018.434202 1433.166817 1734.440143 1424.005416 1559.153104 1368.185482 1557.301906 1.114057054 1.336343914 0.754183786 1.938246007 0.92028836 1.113746882 0.914405492 1.001188721 0.878561489 1 10.60483294 -5.827694995 9.031714542 1.093210291 0.83170521 0 0.318449057 0 0 0.037165886 0 1.49E-06 5.827694995 -0.261505081 SLGTADVHFER ddPTM_HeLa_Romidepsin_16h_R1 3 SLGTADVHFER 11 0 Q86V81;E9PB61 Q86V81 ALYREF THO complex subunit 4 0 0 ;; ;; 127.17 0.0032044 17540500 12887.19 12308.65 11854.45 9291.06 13227.36 13326.1 12570.6 12489.37 15291.6 13918.18 FALSE FALSE TRUE 12730.11597 12481.9315 12060.77173 10365.33607 12552.31846 12474.60522 13638.34645 12850.73022 13923.881 13556.58368 0.939035695 0.920728393 0.889661586 0.764597949 0.92592048 0.92018797 1.006031223 0.947932792 1.027093649 1 13.72670604 -11.23171173 0.885461405 0.990947768 0.910422838 0.302160286 0.058788427 0.571339986 0.950493884 0.021018168 0.013758785 5.87E-12 11.23171173 -0.08052493 SLGVLPFTLNSGS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 2 SLGVLPFTLNSGSPEK 16 0 P42695 P42695 NCAPD3 Condensin-2 complex subunit D3 1 0 SLGVLPFT(0.001)LNS(0.072)GS(0.927)PEK;SLGVLPFTLNS(0.066)GS(0.934)PEK ; 195.28 4.55E-13 261260000 16588.6 16182.8 18696.2 5113.7 10126.6 9476.4 8000.5 10171.4 19159.4 16893.6 TRUE FALSE FALSE 16386.41176 16410.62188 19021.59952 5704.970055 9609.801814 8870.888624 8680.06227 10465.69341 17445.73528 16454.70184 0.995849814 0.997321133 1.155997824 0.346707592 0.584015554 0.539109655 0.527512583 0.636030571 1.060227979 1 14.00621226 -9.264103417 24.9999973 1.008694881 0.530598089 0.900641446 0.085200342 49.99448635 469160.9629 0.011887067 0.018679067 5.44E-10 9.264103417 -0.478096793 SLHPWYGITPTS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 SLHPWYGITPTSSPK 15 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 0 SLHPWYGIT(0.009)PT(0.094)S(0.588)S(0.309)PK 144.27 0.00048191 8099000 2458 1972.7 1984.9 1625.1 2582.6 2596.9 1960.3 2234.8 3219.9 2787.1 TRUE FALSE FALSE 2428.040951 2000.471722 2019.446352 1813.001708 2450.800285 2430.966471 2126.807833 2299.460412 2931.90408 2714.69074 0.894407939 0.736905937 0.743895547 0.667848341 0.902791706 0.895485602 0.783443875 0.84704323 1.080014027 1 11.40657214 -10.7984488 1.419770844 0.969957585 0.798850779 0.555439566 0.079908091 0.225292222 0.946912252 0.017282541 0.016244883 1.59E-11 10.7984488 -0.171106806 SLIEEGGDWDR ddPTM_HeLa_Romidepsin_16h_R1 2 SLIEEGGDWDR 11 0 C9J0E9;Q15008-3;Q15008-2;Q15008;Q15008-4;H7C531 C9J0E9 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 0 ; ; 169.93 8.13E-05 5284100 3791.4 3789.1 3606.7 3050.3 4205.1 3830.9 3717.3 4195.9 4109.8 3957.2 FALSE FALSE TRUE 3745.188958 3842.443049 3669.473101 3402.990038 3990.498056 3586.117854 4033.047369 4317.301746 3742.209195 3854.391374 0.971668052 0.996900075 0.952024002 0.882886481 1.035312107 0.930397956 1.046351286 1.120099473 0.970894969 1 11.91228735 -7.50312454 3.871402821 0.977683158 1.111444133 0.582868037 0.040574463 0.118057868 3.746146535 0.005448667 0.031194099 3.14E-08 7.50312454 0.133760975 SLIEEGGDWDRR ddPTM_HeLa_Romidepsin_16h_R1 4 SLIEEGGDWDRR 12 1 C9J0E9;Q15008-3;Q15008-2;Q15008;Q15008-4;H7C531 C9J0E9 PSMD6 26S proteasome non-ATPase regulatory subunit 6 0 0 ;;; ;;; 211.37 3.55E-21 81576000 10793.5 9793.2 9984.4 9572.7 11374.1 11443.9 10311.1 10297.9 11228 10889.8 FALSE FALSE TRUE 10661.94467 9931.068927 10158.17429 10679.54061 10793.63723 10712.67172 11186.92458 10595.85349 10223.73956 10606.88143 1.005191276 0.936285467 0.957696601 1.006850193 1.017607042 1.009973742 1.054685551 0.998960304 0.963877991 1 13.37271293 -8.878075942 3.72145223 0.99310124 1.022186435 0.294427448 0.027075661 0.301319431 7.966862735 0.00416852 0.007888037 1.32E-09 8.878075942 0.029085195 SLIPDIKPLAGQEAVVDLHADDS(ph)RISEDETER ddPTM_HeLa_Romidepsin_16h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 S(0.001)LIPDIKPLAGQEAVVDLHADDS(0.79)RIS(0.152)EDET(0.057)ER 40.453 0.024101 178960000 1764.2 1410.2 1671.4 1060.8 1560.6 1590.4 1212.8 1727.8 1797.3 1500.8 TRUE FALSE FALSE 1742.697252 1430.052833 1700.490016 1183.454687 1480.956759 1488.778573 1315.815202 1777.791167 1636.544987 1461.809 1.192151131 0.978276117 1.16327784 0.809582297 1.013098674 1.018449451 0.900127993 1.216158313 1.119534075 1 10.51353911 SLIPDIKPLAGQEAVVDLHADDSRISEDET(ph)ER ddPTM_HeLa_Romidepsin_16h_R1 1 SLIPDIKPLAGQEAVVDLHADDSRISEDETER 32 2 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2 S4R3H4 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 SLIPDIKPLAGQEAVVDLHADDS(0.298)RIS(0.298)EDET(0.404)ER 59.673 0.00030946 55907000 1466.4 1520.7 1775.7 948.7 1309 1805.7 1394 1471.3 1645.9 1821.4 TRUE FALSE FALSE 1448.526953 1542.108455 1806.605314 1058.393158 1242.196845 1690.321598 1512.406325 1513.869744 1498.686582 1774.079765 0.816494828 0.869244148 1.018333757 0.596587131 0.700192218 0.952787823 0.852501874 0.853326763 0.844768432 1 10.79285516 -12.47113695 0.547735457 1.044347189 0.825765607 0.011217263 0.121622284 1.892588718 0.699154397 0.223274796 0.027390663 3.38E-13 12.47113695 -0.218581583 PDPSK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 2 PDPSKSAPAPK 11 1 Q8N257 Q8N257 HIST3H2BB Histone H2B type 3-B 0 1 ; PDPSK(1)SAPAPK;PDPSK(1)SAPAPK 126.03 0.014492 15951800 887.33 886.43 1111.43 4761.4 10329 12348.8 13902.5 14517.4 655.87 772.11 FALSE TRUE FALSE 876.5148807 898.9091848 1130.773973 5311.935471 9801.872587 11559.75153 15083.378 14937.43806 597.2073445 752.0504709 1.165500076 1.195277737 1.50358788 7.063269922 13.03353028 15.37097839 20.05633742 19.86228138 0.794105406 1 9.554685676 -8.654476343 1.089587121 0.954861046 20.07740238 0.988557153 0.830422081 0.03520755 0.080001413 0.133388551 0.433644512 2.22E-09 8.654476343 19.12254134 up SLIVEGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SLIVEGKR 8 1 D6R9L5;H0Y8X0;A0A494C198;B4DFG0;H0Y993;P35659;A0A494C028 D6R9L5 DEK Protein DEK 0 1 SLIVEGK(1)R 89.355 0.018102 534330 197.21 0 299.98 63.551 142.9 345.64 203.5 131.78 145.55 0 FALSE TRUE FALSE 194.8063287 0 305.2010261 70.89906564 135.6072798 323.5547195 220.7852849 135.5928464 132.5316435 0 0 SLKESEQES(ph)EEEILAQK ddPTM_HeLa_Romidepsin_16h_R1 2 SLKESEQESEEEILAQK 17 1 Q9BW71 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 S(0.001)LKES(0.001)EQES(0.998)EEEILAQK;SLKESEQES(0.999)EEEILAQK ; 70.452 0.011524 60226000 5972.5 5989.8 5398.1 5844 5123.9 4703.4 4760.7 5472 6121 5828.6 TRUE FALSE FALSE 5899.704873 6074.124562 5492.051666 6519.710777 4862.408263 4402.86792 5165.073739 5630.323687 5573.52243 5677.172132 1.039197815 1.069920802 0.967392134 1.148408156 0.856484206 0.775538916 0.909796923 0.991747926 0.981742723 1 12.47095677 -8.733245335 24.99985476 1.02708412 0.877574186 0.530873458 0.069270299 125.9600614 111689.1152 0.009553174 0.019103341 1.85E-09 8.733245335 -0.149509934 SLLAFIAFLFFASIIS(ph)LSLIFY(ph)Y(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 SLLAFIAFLFFASIISLSLIFYYSK 25 0 Q9UEF7 Q9UEF7 KL Klotho;Klotho peptide 3 0 S(0.002)LLAFIAFLFFAS(0.004)IIS(0.497)LS(0.497)LIFY(0.924)Y(0.924)S(0.151)K 51.431 0.0027669 0 751.57 792.78 797.91 535 813.85 1012.9 828.65 942.64 995.98 870.65 TRUE FALSE FALSE 742.4095758 803.9407776 811.7972888 596.8592173 772.3161976 948.178959 899.0355103 969.9138012 906.8970543 848.0303875 0.875451619 0.948009399 0.95727382 0.703818196 0.910717598 1.118095499 1.060145395 1.14372529 1.069415752 1 9.727972152 -8.262312137 24.985147 0.921667067 1.102604403 0.459388789 0.091309935 51.65796273 1478885.667 0.0125023 0.029568628 5.47E-09 8.262312137 0.180937336 SLLDASEEAIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SLLDASEEAIKK 12 1 P18206-2;P18206 P18206-2 VCL Vinculin 0 1 SLLDASEEAIK(1)K 105.2 0.006462 243020 0 123.17 0 0 310.88 271.72 157.35 142.12 130.14 138.12 FALSE TRUE FALSE 0 124.9039905 0 0 295.0146335 254.3579689 170.7153051 146.232018 118.4999525 134.5316225 0 0.928435919 0 0 2.192901773 1.890692792 1.268960427 1.08697134 0.880833445 1 7.071801517 -8.764952387 24.99999976 0.473202987 1.605588029 0.594765923 0.461647494 55.08819885 392034.0382 0.077800581 0.145201693 1.72E-09 8.764952387 1.132385042 SLLFGAMSEMIS(ph)PSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SLLFGAMSEMISPSEK 16 0 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 SLLFGAMS(0.025)EMIS(0.812)PS(0.163)EK 96.773 0.005725 9333000 3492.8 3169.8 3568.5 3263.3 3499.8 2866.8 2215.8 2313.9 3622.9 3930.5 TRUE FALSE FALSE 3450.22841 3214.424528 3630.608246 3640.6181 3321.192146 2683.620732 2404.009997 2380.849046 3298.85875 3828.385043 0.901222936 0.839629371 0.948339366 0.950954008 0.867517794 0.700979839 0.627943629 0.621893832 0.86168416 1 11.90252022 -8.247853934 1.916056174 0.94268451 0.62123405 0.863610419 0.047560922 0.087602777 0.612826827 0.00774265 0.025177684 5.65E-09 8.247853934 -0.32145046 SLLGDSAPT(ph)LHLNKGT(ph)PSQSPVVGR ddPTM_HeLa_Romidepsin_16h_R1 1 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 C9J2I0;B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 C9J2I0 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 0 S(0.002)LLGDS(0.051)APT(0.44)LHLNKGT(0.779)PS(0.35)QS(0.378)PVVGR 55.02 0.0092385 97078000 2860.6 2675.2 2639.7 3337.6 3656.5 3570.5 3007.7 2979.2 3402.4 3246.3 TRUE FALSE FALSE 2825.733907 2712.861536 2685.642871 3723.509016 3469.895161 3342.356573 3263.173963 3065.398452 3098.080823 3161.960658 0.893665106 0.85796815 0.849359989 1.177594986 1.097387202 1.057051916 1.032009666 0.969461288 0.979797397 1 11.6266037 -9.268804368 24.99555557 0.933316467 1.065942443 0.551374254 0.067007184 424.349658 1440171.94 0.011763535 0.018188422 5.39E-10 9.268804368 0.132625976 SLLGDSAPTLHLNKGT(ph)PS(ph)QSPVVGR ddPTM_HeLa_Romidepsin_16h_R1 1 SLLGDSAPTLHLNKGTPSQSPVVGR 25 1 C9J2I0;B8ZZY2;P52594-2;P52594-3;P52594;P52594-4 C9J2I0 AGFG1 Arf-GAP domain and FG repeat-containing protein 1 2 0 SLLGDS(0.003)APT(0.011)LHLNKGT(0.938)PS(0.524)QS(0.524)PVVGR 51.577 0.0153 35000000 1737.4 1679.1 1929.7 1955.9 1871.1 1853 1781.2 1607.3 2140.6 1970.9 TRUE FALSE FALSE 1716.223901 1702.738414 1963.285619 2182.050361 1775.610785 1734.59928 1932.495084 1653.80469 1949.139375 1919.695734 0.89400829 0.886983486 1.022706664 1.136664692 0.924943861 0.903580317 1.006667385 0.861493132 1.01533766 1 10.90666195 -7.241794603 22.59879795 0.960194455 0.861492787 0.144824945 0.074848335 1960.809095 2255525.026 0.010859013 0.463631486 5.73E-08 7.241794603 -0.098701668 SLLLEPPRGT(ph)PDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLLLEPPRGTPDR 13 1 Q53GT1-3;Q53GT1 Q53GT1-3 KLHL22 Kelch-like protein 22 1 0 SLLLEPPRGT(1)PDR 81.709 0.020333 9841900 3377.2 2598 2702.8 2744.6 3574.9 3414.6 3273.2 3420.2 2999.1 3356.9 TRUE FALSE FALSE 3336.037387 2634.574712 2749.8411 3061.943566 3392.459513 3196.41808 3551.225526 3519.158091 2730.852985 3269.687254 1.020292501 0.805757404 0.841010435 0.936463743 1.037548625 0.977591382 1.086105566 1.076298073 0.835203117 1 11.67493693 -7.762929464 24.10960299 0.978234993 1.081201858 0.19409328 0.08751641 29.56871427 478496.5518 0.011964179 0.038982662 1.73E-08 7.762929464 0.102966865 SLLS(ph)AEEAAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLLSAEEAAK 10 0 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 0 S(0.003)LLS(0.997)AEEAAK 102.05 0.0025976 0 1885.5 1620.5 1981.7 1695.3 2432.6 2220.6 1898.2 2798.3 2114.3 2154.4 TRUE FALSE FALSE 1862.518801 1643.313442 2016.190657 1891.318563 2308.455345 2078.710827 2059.433061 2879.264396 1925.191713 2098.428377 0.887577971 0.783116288 0.960809851 0.901302414 1.100087746 0.990603658 0.981416894 1.372105156 0.917444566 1 11.03509351 -4.479518322 1.059682118 0.939647029 200 0.723929213 0.078913319 326.5442505 1.008473623 0.012714027 157163.4632 3.31E-05 4.479518322 199.060353 SLLSS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 SLLSSPTK 8 0 I3NI36;Q92667-2;Q92667 I3NI36 AKAP1 "A-kinase anchor protein 1, mitochondrial" 1 0 SLLS(0.107)S(0.893)PT(0.001)K;SLLS(0.038)S(0.962)PTK ; 138.08 0.0091233 70322000 25168.3 34681 32879 13863.8 18553.2 25265.8 15146.6 19824.9 30642.6 28952.8 TRUE FALSE FALSE 24861.53908 35169.24003 33451.2452 15466.79779 17606.36097 23651.39692 16433.15183 20398.5022 27901.84911 28200.60208 0.881596038 1.247109545 1.186189043 0.548456297 0.624325712 0.838684112 0.582723439 0.723335698 0.989406149 1 14.78343834 -9.252411218 24.99462246 0.986721228 0.666572721 0.677945006 0.132074128 388.9397906 1076786.541 0.021878568 0.035947925 5.59E-10 9.252411218 -0.320148507 SLMS(ph)S(ph)PEDLTKDFEELKAEEVDVTK ddPTM_HeLa_Romidepsin_16h_R1 3 SLMSSPEDLTKDFEELKAEEVDVTK 25 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 S(0.004)LMS(0.979)S(0.979)PEDLT(0.038)KDFEELKAEEVDVTK;S(0.024)LMS(0.672)S(0.672)PEDLT(0.632)KDFEELKAEEVDVTK;S(0.003)LMS(0.908)S(0.908)PEDLT(0.18)KDFEELKAEEVDVTK ;; 70.315 0.00037346 243410000 15647.4 15164.1 15524.5 17305 15442.9 14727.6 12738.3 14290.4 16705.2 16274.9 TRUE FALSE FALSE 15456.68347 15377.5806 15794.69741 19305.88552 14654.79119 13786.55389 13820.29088 14703.87018 15211.04507 15852.07575 0.975057381 0.970067317 0.996380389 1.217877445 0.924471433 0.869700228 0.871828466 0.927567494 0.95956172 1 13.95238415 -8.537176981 24.99998091 1.004256093 0.889440658 0.401737399 0.072032477 189.2534022 330902.3746 0.010336399 0.020679568 2.90E-09 8.537176981 -0.114815435 SLMS(ph)SPEDLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SLMSSPEDLTK 11 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SLMS(0.5)S(0.5)PEDLTK 119.03 0.014435 17118000 5931.6 6031.8 5841 2727.5 3578.2 2950.4 2701.9 3037.5 6349.6 6493.6 TRUE FALSE FALSE 5859.303378 6116.715839 5942.660155 3042.866383 3395.591102 2761.878962 2931.399319 3125.38527 5781.675873 6324.895336 0.926387405 0.967085701 0.93956656 0.481093555 0.536861232 0.436667931 0.463470012 0.494140235 0.914114079 1 12.62682589 -9.270246584 5.711794695 0.963619622 0.480448955 0.980268217 0.033106972 0.01636361 2.091535106 0.005496163 0.008735475 5.37E-10 9.270246584 -0.483170667 SLMS(ph)SPEDLTKDFEELKAEEVDVTK ddPTM_HeLa_Romidepsin_16h_R1 3 SLMSSPEDLTKDFEELKAEEVDVTK 25 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.017)LMS(0.473)S(0.473)PEDLT(0.037)KDFEELKAEEVDVT(0.001)K;S(0.002)LMS(0.498)S(0.498)PEDLT(0.002)KDFEELKAEEVDVTK;S(0.02)LMS(0.48)S(0.48)PEDLT(0.02)KDFEELKAEEVDVTK ;; 84.156 7.74E-06 72396000 8272.42 7422.2 7839.6 8329.65 6262.41 5965.81 6190.69 6498.73 9075.6 8383.61 TRUE FALSE FALSE 8171.592563 7526.689926 7976.044949 9292.763325 5942.815849 5584.613995 6716.527054 6686.760499 8263.855606 8165.802604 1.00070905 0.921733024 0.97676191 1.138009792 0.727768737 0.683902644 0.82251891 0.81887364 1.012007761 1 12.99537898 -8.745296854 24.99999972 1.000432753 0.76182946 0.782215036 0.063234235 83.75033435 129703.8407 0.008963468 0.017882464 1.80E-09 8.745296854 -0.238603293 SLMSS(ph)PEDLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SLMSSPEDLTK 11 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SLMS(0.08)S(0.92)PEDLTK 112.64 0.018422 12700000 6537.1 5965.7 6585.4 3586.1 3464.2 3468.8 3047.9 3413.2 6251.7 6838.5 TRUE FALSE FALSE 6457.423311 6049.685281 6700.016125 4000.741755 3287.408947 3247.154875 3306.78855 3511.955557 5692.532294 6660.834784 0.969461565 0.908247311 1.005882347 0.60063669 0.493543085 0.487499687 0.49645257 0.527254567 0.854627457 1 12.70148728 -9.175494872 3.51442957 0.98041385 0.50332564 0.947465494 0.05024591 0.022700802 0.536491395 0.004983533 0.008484102 6.68E-10 9.175494872 -0.47708821 SLMSSPEDLTKDFEELKAEEVDVTK ddPTM_HeLa_Romidepsin_16h_R1 1 SLMSSPEDLTKDFEELKAEEVDVTK 25 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 0 0 59.614 0.0012464 18931000 1279.6 1198.3 1190.7 1018.6 628.15 696.26 671.38 692.3 1302.4 1110.8 FALSE FALSE TRUE 1264.003743 1215.169699 1211.423634 1136.375325 596.0931615 651.7712331 728.4070004 712.3306082 1185.910082 1081.941256 1.168273912 1.123138333 1.119675978 1.050311483 0.550947806 0.602409077 0.673240804 0.658381963 1.096094705 1 10.07940645 -8.789435451 8.091368158 1.086929062 0.623552052 0.951377837 0.052231246 0.04269151 10.33667228 0.01075602 0.019792905 1.62E-09 8.789435451 -0.46337701 SLPAPVAQRPDS(ph)PGGGLQAPGQK ddPTM_HeLa_Romidepsin_16h_R1 2 SLPAPVAQRPDSPGGGLQAPGQK 23 1 Q5JVS0-2;Q5JVS0 Q5JVS0-2 HABP4 Intracellular hyaluronan-binding protein 4 1 0 SLPAPVAQRPDS(1)PGGGLQAPGQK;SLPAPVAQRPDS(1)PGGGLQAPGQK ; 93.229 3.71E-05 158770000 3657.1 3934.2 3892.5 3656.7 6026 7044.5 6755.8 7367 4097.7 4237.8 TRUE FALSE FALSE 3612.525859 3989.585771 3960.24733 4079.504859 5718.470734 6594.379185 7329.637483 7580.152522 3731.191449 4127.701345 0.875190707 0.966539349 0.959431654 0.98832365 1.385388684 1.597591161 1.775718946 1.83641012 0.903939296 1 12.01112287 -8.431374884 1.364549842 0.938593474 1.817943654 0.982589926 0.047773823 0.045618732 0.161009575 0.008824951 0.030068715 3.70E-09 8.431374884 0.87935018 SLPEEDVAEIQHAEEFLIKPESK ddPTM_HeLa_Romidepsin_16h_R1 1 SLPEEDVAEIQHAEEFLIKPESK 23 1 O60832;H7C2Q9;H7C0M1;C9IYT0;O60832-2 O60832 DKC1 H/ACA ribonucleoprotein complex subunit 4 0 0 109.5 5.12E-06 3214500 1128.1 1278.6 1358 1395.8 1367.9 1857.1 1547.2 1638 1557.9 1356 FALSE FALSE TRUE 1114.350283 1296.600164 1381.63542 1557.188963 1298.090959 1738.437304 1678.619129 1685.392946 1418.557522 1320.770925 0.843712004 0.981699506 1.046082553 1.179000033 0.982828237 1.316229235 1.270938887 1.276067571 1.074037515 1 10.36716455 -8.740320574 0.762959363 0.927984232 1.308483376 0.606000639 0.093127074 0.313171583 0.324249202 0.017007805 0.066724192 1.82E-09 8.740320574 0.380499144 SLPELDRDKS(ph)DSDTEGLLFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLPELDRDKSDSDTEGLLFSR 21 2 A0A0C4DH22;A0A1B0GTW6;Q9H4G0-3;Q9H4G0-2;Q9H4G0 A0A0C4DH22 EPB41L1 Band 4.1-like protein 1 1 0 S(0.016)LPELDRDKS(0.895)DS(0.085)DT(0.004)EGLLFSR;SLPELDRDKS(0.842)DS(0.116)DT(0.042)EGLLFSR ; 66.606 0.0029358 142793000 3407.6 4941.2 3804.9 3440.13 3276.7 3610.4 2999.5 4077 6202.8 7895.4 TRUE FALSE FALSE 3366.066861 5010.762343 3871.122688 3837.894017 3109.477772 3379.707092 3254.277455 4194.961563 5648.006033 7690.27637 0.437704277 0.651571166 0.503378878 0.499058009 0.404338885 0.439477976 0.423167816 0.545489051 0.734434728 1 12.90881973 -12.50397127 0.548085673 1.142990426 0.468975833 0.63303646 0.106971947 0.389630302 0.141184948 0.142529917 0.016697957 3.13E-13 12.50397127 -0.674014592 SLPSS(ph)SQLKGSPQAISR ddPTM_HeLa_Romidepsin_16h_R1 1 SLPSSSQLKGSPQAISR 17 1 Q8WYP5;Q8WYP5-3;Q8WYP5-2 Q8WYP5 AHCTF1 Protein ELYS 1 0 S(0.005)LPS(0.169)S(0.789)S(0.037)QLKGSPQAISR 99.796 0.001202 75853000 2384.7 2197.2 2243.4 1618.1 1447.5 1557 1465.3 1656.3 2386.5 2265.2 TRUE FALSE FALSE 2355.634359 2228.132239 2282.445436 1805.192335 1373.628674 1457.512725 1589.762545 1704.222427 2173.045463 2206.349777 1.06766134 1.009872624 1.03448939 0.818180487 0.622579741 0.660599122 0.720539672 0.772417159 0.984905243 1 11.10744581 -9.11051871 3.133896921 1.031335154 0.694318544 0.923915078 0.044081691 0.048224162 0.902517544 0.007064445 0.0123883 7.75E-10 9.11051871 -0.33701661 K(ac)FNILGTNTK ddPTM_HeLa_Romidepsin_16h_R1 1 KFNILGTNTK 10 1 G8JLH9;P40763-3;P40763-2;P40763 G8JLH9 STAT3 Signal transducer and activator of transcription;Signal transducer and activator of transcription 3 0 1 K(1)FNILGTNTK 157.38 0.0038939 666420 303.31 349.9 473.65 293.92 653.59 566.72 639.92 635.42 409.28 294.1 FALSE TRUE FALSE 299.6131411 354.8259014 481.8936796 327.9044133 620.2348634 530.508421 694.2747888 653.8048752 372.6729717 286.4592396 1.045918929 1.238661046 1.682241705 1.144680876 2.165176673 1.851950811 2.423642504 2.282366162 1.300963349 1 8.162186062 -8.642759246 0.552615734 0.994467905 2.546610039 0.77239531 0.244483932 0.318849178 0.148799279 0.045623242 0.245375464 2.28E-09 8.642759246 1.552142134 SLPTPAVLLS(ph)PTKEPPPLLAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLPTPAVLLSPTKEPPPLLAK 21 1 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 S(0.002)LPT(0.062)PAVLLS(0.885)PT(0.051)KEPPPLLAK 81.854 0.001015 45135000 1165.3 1200.2 1251 1015.2 1000.9 723.64 694.56 719.92 1412.4 1091.2 TRUE FALSE FALSE 1151.096875 1217.096447 1272.77313 1132.582201 949.8203381 677.4017394 753.5559091 740.7497494 1286.071407 1062.850467 1.083028057 1.145124818 1.197509123 1.065608226 0.893653781 0.63734435 0.708995228 0.696946346 1.210021021 1 10.05372292 -8.503415685 2.988010103 1.06352888 0.684815468 0.869530538 0.074169871 0.070232017 1.263922975 0.010587738 0.024572485 3.14E-09 8.503415685 -0.378713412 SLPTPAVLLS(ph)PTKEPPPLLAKPK ddPTM_HeLa_Romidepsin_16h_R1 2 SLPTPAVLLSPTKEPPPLLAKPK 23 2 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 1 0 SLPT(0.001)PAVLLS(0.812)PT(0.187)KEPPPLLAKPK;S(0.001)LPT(0.018)PAVLLS(0.491)PT(0.491)KEPPPLLAKPK ; 77.357 0.00021146 234153000 6934.7 6012.1 6038.5 6829.1 4659.3 3983.2 3589.9 3149.8 6852.8 6965.1 TRUE FALSE FALSE 6850.177209 6096.738502 6143.597559 7618.712674 4421.518535 3728.686375 3894.826016 3240.934493 6239.868405 6784.145698 1.009733209 0.898674464 0.905581606 1.123017254 0.651742862 0.549617674 0.574107071 0.477721829 0.919772169 1 12.72795144 -8.632378562 4.891774405 0.994553046 0.547131519 0.898523237 0.068464006 0.040647015 1.583791221 0.009273688 0.018894153 2.33E-09 8.632378562 -0.447421527 SLPTPAVLLSPTKEPPPLLAKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SLPTPAVLLSPTKEPPPLLAKPK 23 2 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;A0A3B3ISX8 Q8WX93-3 PALLD Palladin 0 0 118.46 1.71E-06 20617000 1640.6 1506.2 1723 1396 1187.8 1112.4 780.64 599.76 1734.6 1580 FALSE FALSE TRUE 1620.603736 1527.404323 1752.988092 1557.412088 1127.182134 1041.32123 846.9475421 617.1131093 1579.453032 1538.951372 1.053057144 0.992496807 1.139079586 1.011995646 0.732435185 0.676643362 0.550340678 0.400995847 1.026317699 1 10.58773193 -8.281990276 1.163475149 1.034235491 0.444953505 0.931371111 0.061966818 0.100254174 0.239224948 0.009956843 0.045358884 5.22E-09 8.281990276 -0.589281987 down SLPTTVPES(ph)PNYR ddPTM_HeLa_Romidepsin_16h_R1 6 SLPTTVPESPNYR 13 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50;H0YC33 Q6PKG0 LARP1 La-related protein 1 1 0 S(0.041)LPT(0.001)TVPES(0.958)PNYR;S(0.038)LPT(0.025)T(0.016)VPES(0.921)PNYR;SLPTTVPES(1)PNYR;S(0.02)LPT(0.015)T(0.015)VPES(0.951)PNYR;SLPTTVPES(1)PNYR;SLPTTVPES(1)PNYR ;;;;; 241.76 1.87E-42 1864423600 22087.3 20986.21 19339.27 18943.1 19794.22 19494.37 18115.53 18140 21925.7 21314.5 TRUE FALSE FALSE 21818.09149 21281.65442 19675.86188 21133.39035 18784.04709 18248.74267 19654.26267 18664.85228 19964.61048 20760.74622 1.050930023 1.025091015 0.947743481 1.017949458 0.904786702 0.879002252 0.946703093 0.899045347 0.961651873 1 14.34157068 -9.003685915 1.225051943 1.023202784 0.90608827 0.538029873 0.037848907 0.193997922 0.576791178 0.005700711 0.013095569 9.92E-10 9.003685915 -0.117114514 SLQS(ph)VAEER ddPTM_HeLa_Romidepsin_16h_R1 1 SLQSVAEER 9 0 P61313;E7EX53;A0A2R8Y738;A0A2R8YEM3;E7EQV9;P61313-2 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 1 0 SLQS(1)VAEER 92.295 0.0041459 0 1379.8 1321.9 1105 1239.3 1123.8 1442.7 965.15 1234.9 1458.7 1374.4 TRUE FALSE FALSE 1362.982467 1340.509743 1124.232061 1382.593697 1066.448293 1350.516126 1047.129817 1270.629883 1328.230219 1338.69289 1.018144249 1.001357184 0.839798336 1.032793785 0.796634016 1.008831926 0.782203166 0.949157116 0.992184413 1 10.38660931 -9.845966746 8.617841578 1.00851907 0.902316051 0.288544667 0.077799732 0.222937286 20.41189767 0.010923321 0.014375605 1.43E-10 9.845966746 -0.106203019 SLQTTS(ph)PPVVAPGNENGLAVPVPLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SLQTTSPPVVAPGNENGLAVPVPLRK 26 1 O94804 O94804 STK10 Serine/threonine-protein kinase 10 1 0 S(0.006)LQT(0.048)T(0.188)S(0.758)PPVVAPGNENGLAVPVPLRK 107.13 6.50E-07 10403000 1071.9 1162.8 928.52 1194.6 1870.9 2286.5 1819 2190.7 1369.8 1194.7 TRUE FALSE FALSE 1058.835271 1179.169929 944.6805011 1332.725273 1775.420992 2140.400029 1973.505815 2254.084448 1247.281657 1163.661522 0.909916888 1.013327249 0.811817254 1.14528602 1.525719428 1.839366508 1.695944893 1.937061943 1.0718595 1 10.18445576 -8.690207111 2.050397208 0.950859633 1.814645357 0.948407186 0.089220024 0.040648492 0.346819248 0.011651268 0.026694306 2.04E-09 8.690207111 0.863785724 SLRS(ph)LEEQDQETLR ddPTM_HeLa_Romidepsin_16h_R1 3 SLRSLEEQDQETLR 14 1 P48681 P48681 NES Nestin 1 0 S(0.017)LRS(0.983)LEEQDQETLR;S(0.079)LRS(0.921)LEEQDQETLR;S(0.036)LRS(0.964)LEEQDQETLR ;; 103.97 0.0030963 7468000 3932.49 3975.73 3929.25 4233.43 3499.68 3915.96 3632.77 3494.87 4165.71 3949.13 TRUE FALSE FALSE 3884.559299 4031.700431 3997.636948 4722.919095 3321.07827 3665.742794 3941.337393 3595.988549 3793.118464 3846.531033 1.00988638 1.048139323 1.039283685 1.227838552 0.863395678 0.952999667 1.024647236 0.934865342 0.986114094 1 11.90934223 SLS(ph)AIDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSAIDR 7 0 O95831-6;O95831-4;O95831-3;O95831 O95831-6 AIFM1 "Apoptosis-inducing factor 1, mitochondrial" 1 0 S(0.052)LS(0.948)AIDR 120.31 0.027275 23288000 5669.5 4719.7 4994.8 4888 5547.2 6252.8 4135.5 5284 5005.4 3968.5 TRUE FALSE FALSE 5600.397953 4786.14406 5081.732399 5453.173559 5264.105685 5853.26626 4486.769267 5436.884203 4557.704488 3865.397798 1.448854231 1.238202201 1.314672555 1.410766458 1.361853543 1.514272674 1.16075227 1.40655231 1.179103607 1 11.91640118 -12.38533052 0.941108421 0.984325821 1.360049746 0.457513799 0.110095901 0.294362927 0.434293235 0.079945859 0.017386503 4.12E-13 12.38533052 0.375723926 SLS(ph)ARQLARMSESSPESR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSARQLARMSESSPESR 18 2 K7ESJ9;Q8NCQ7-2;Q8NCQ7-3;Q8NCQ7 K7ESJ9 PROCA1 Protein PROCA1 1 0 S(0.004)LS(0.996)ARQLARMSESSPESR 100.04 0.0050286 29483000 1460.1 1297 1359.8 1292.3 1283.4 1570.6 1292.2 1449.8 1350.3 1327.4 TRUE FALSE FALSE 1442.30374 1315.2592 1383.466749 1441.721806 1217.903309 1470.243729 1401.959436 1491.747676 1229.525786 1292.913957 1.115545031 1.017282854 1.070037756 1.115094937 0.941983264 1.137155123 1.084340863 1.153787279 0.95097263 1 10.33641055 -12.5070568 1.200372122 0.99909354 1.080172509 0.29681469 0.060923397 0.609522458 1.543248357 0.041569174 0.009588477 3.11E-13 12.5070568 0.081078969 SLS(ph)DSESDDSK ddPTM_HeLa_Romidepsin_16h_R1 3 SLSDSESDDSK 11 0 S4R2Y4;Q13185 S4R2Y4 CBX3 Chromobox protein homolog 3 1 0 SLS(0.999)DS(0.001)ESDDSK;S(0.218)LS(0.737)DS(0.041)ES(0.004)DDS(0.001)K;S(0.334)LS(0.638)DS(0.028)ESDDSK ;; 187.78 1.90E-08 459632600 10655.1 11011.6 12810.2 9043.2 8605.8 9784.2 10379.1 4476.07 14041.6 14175 TRUE FALSE FALSE 10525.23154 11166.62159 13033.15616 10088.81733 8166.613913 9159.021197 11260.70049 4605.578023 12785.68413 13806.73146 0.762326085 0.808780965 0.943971149 0.730717286 0.591495093 0.663373603 0.815594953 0.333574825 0.926047136 1 13.7530842 -6.663183204 0.128088274 1.088335704 1.42E-16 0.571401976 0.121575819 23.36158573 0.412478978 0.585833012 4.448558041 2.17E-07 6.663183204 -1.088335704 SLS(ph)ELCLAVPAPGIR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSELCLAVPAPGIR 15 0 A0A5F9ZHW8;O94827-5;O94827-3;O94827;O94827-7;O94827-2;O94827-6 A0A5F9ZHW8 PLEKHG5 Pleckstrin homology domain-containing family G member 5 1 0 S(0.29)LS(0.71)ELCLAVPAPGIR 132.24 2.22E-05 0 616.84 546.16 500.17 449.45 663.12 662.37 580.15 675.3 461.61 514.97 TRUE FALSE FALSE 609.3217168 553.8488548 508.875249 501.4175237 629.278512 620.0466947 629.4279265 694.8387401 420.3224455 501.5910052 1.214777998 1.104184184 1.014522278 0.999654138 1.254564985 1.236159916 1.254862866 1.385269538 0.837978435 1 8.970367667 -4 0.375840606 1.083043788 5.367033207 0.514808932 0.109670561 38.36091854 0.468094843 0.026304026 120.7171263 1.00E-04 4 4.283989419 SLS(ph)EQPVMDTATATEQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSEQPVMDTATATEQAK 18 0 A0A0A0MSN9;P18615-4;P18615;P18615-3;A2ABK4;A0A0G2JI50;E9PD43;A0A0A0MT02 A0A0A0MSN9 NELFE Negative elongation factor E 1 0 S(0.097)LS(0.537)EQPVMDT(0.333)AT(0.03)AT(0.003)EQAK 105.5 0.0022581 4460300 1764.3 2170.2 1049.3 1235.2 1730.6 1451.5 1015.8 1608.4 1529.6 1509.2 TRUE FALSE FALSE 1742.796033 2200.752133 1067.562626 1378.019636 1642.281024 1358.753835 1102.082027 1654.936516 1392.788745 1469.990766 1.18558298 1.497119698 0.726237641 0.937434212 1.117204993 0.924328142 0.749720374 1.125814226 0.947481288 1 10.52159138 SLS(ph)ESSVIMDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSESSVIMDR 11 0 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BNX5 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 S(0.001)LS(0.849)ES(0.075)S(0.075)VIMDR 108.72 0.020891 36328000 5324.1 4643.9 4793.8 4276.2 5084.6 5058.9 4960.2 5285.5 5444.4 4840.6 TRUE FALSE FALSE 5259.207821 4709.276946 4877.234078 4770.634364 4825.113889 4735.652617 5381.519264 5438.427603 4957.439228 4714.840514 1.115458265 0.998819988 1.034443066 1.011833666 1.023388569 1.004414169 1.141400064 1.153470109 1.051454278 1 12.20299326 -7.743530883 21.52158578 1.042239891 1.147435816 0.635720052 0.034582745 34.02820906 40889.19695 0.006637607 0.024651888 1.80E-08 7.743530883 0.105195925 SLS(ph)IEIGHEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSIEIGHEVK 11 0 A0A3B3IU16;C9JTT8;Q68DU7;H7C1N3;O15155-2;O15155 A0A3B3IU16 BET1;DKFZp781C0425 BET1 homolog 1 0 S(0.179)LS(0.821)IEIGHEVK 86.498 0.017238 6368400 6219.4 7823.2 6116.3 5476.7 9521.5 9082.4 5770.7 10543 6298.8 6834.9 TRUE FALSE FALSE 6143.595561 7933.335215 6222.751636 6109.941823 9035.582325 8502.063952 6260.863114 10848.04507 5735.419552 6657.328313 0.922831994 1.191669517 0.93472206 0.917776852 1.357238505 1.277098492 0.940446801 1.629489273 0.861519709 1 12.7007276 -4 0.393211952 0.969828614 8.750129704 0.470054918 0.173866906 40.96158333 0.488600374 0.040573 248.3460101 1.00E-04 4 7.780301091 SLS(ph)LESTDR ddPTM_HeLa_Romidepsin_16h_R1 2 SLSLESTDR 9 0 H0Y7V8;A0A0A0MRJ1;H0Y5V1;A0A0A0MRJ0;Q5VT25-3;Q5VT25-4;Q5VT25-5;Q5VT25;Q5VT25-2;Q5VT25-6 H0Y7V8 CDC42BPA Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase MRCK alpha 1 0 S(0.04)LS(0.952)LES(0.002)T(0.005)DR;SLS(0.976)LES(0.023)T(0.001)DR ; 141.91 0.0062775 27659000 5075.6 5016.2 4800.1 4524.3 4615.5 5888.2 4840.7 5783.6 5009.6 4791.9 TRUE FALSE FALSE 5013.736635 5086.818195 4883.643727 5047.420853 4379.953812 5511.963023 5251.868937 5950.939341 4561.528829 4667.405747 1.07420201 1.089859865 1.046329373 1.081418914 0.938412911 1.180947902 1.12522228 1.27499936 0.977315682 1 12.18840517 -7.347467296 1.044569518 1.039662205 1.357254288 0.617143847 0.058210573 0.776348602 0.727181003 0.008362514 0.263808709 4.49E-08 7.347467296 0.317592083 SLS(ph)MDSQVPVYSPSIDLK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSMDSQVPVYSPSIDLK 18 0 Q9ULJ3-2;Q9ULJ3 Q9ULJ3-2 ZBTB21 Zinc finger and BTB domain-containing protein 21 1 0 S(0.036)LS(0.952)MDS(0.012)QVPVYSPSIDLK;S(0.033)LS(0.955)MDS(0.013)QVPVYSPSIDLK ; 129.42 0.0021439 33419000 7599.3 7152.4 7397.6 7177.5 5903.6 4845 4481 4981.7 8176.1 7767.5 TRUE FALSE FALSE 7506.676809 7253.091675 7526.352125 8007.396321 5602.317263 4535.420137 4861.616028 5125.83763 7444.809139 7565.69923 0.992198683 0.958680943 0.994799277 1.058381529 0.740489027 0.599471377 0.642586479 0.677510098 0.984021293 1 12.88525771 -8.631828387 4.288118709 0.996599727 0.643874127 0.965051222 0.031405762 0.025736173 0.843181512 0.004458378 0.009181297 2.33E-09 8.631828387 -0.352725601 SLS(ph)PDEER ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPDEER 8 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 S(0.097)LS(0.903)PDEER 112.3 0.021613 19507000 4652 5210.9 5847.7 3614.2 4025.1 4770.9 3981.1 4074.8 5034.8 4858.5 TRUE FALSE FALSE 4595.299635 5284.259187 5949.476766 4032.090809 3819.684127 4466.054887 4319.254535 4192.697909 4584.474878 4732.27547 0.971054974 1.116642347 1.257212688 0.852040596 0.807155913 0.943743642 0.91272255 0.885979258 0.968767543 1 12.20831834 SLS(ph)PEDAESLSVLSVPSPDTANQEPTPK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSPEDAESLSVLSVPSPDTANQEPTPK 28 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 S(0.185)LS(0.815)PEDAESLSVLSVPSPDTANQEPTPK;S(0.165)LS(0.835)PEDAESLSVLSVPSPDTANQEPTPK ; 169.36 4.36E-18 12323700 5075.2 4117.4 4293.1 4279.6 7482.1 8629 6705.4 8083.2 5026.5 4867.2 TRUE FALSE FALSE 5013.34151 4175.364865 4367.819605 4774.427488 7100.260517 8077.634749 7274.956509 8317.074639 4576.917251 4740.749442 1.057499784 0.88073941 0.921335257 1.00710395 1.497708454 1.703872952 1.534558322 1.754379711 0.965441711 1 12.21089943 -8.684758419 3.627734838 1.004185997 1.645331053 0.948083689 0.075000499 0.038425524 0.998029219 0.011369737 0.023447813 2.07E-09 8.684758419 0.641145057 SLS(ph)PGAASSSSGDGDGKEGLEEPK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSPGAASSSSGDGDGKEGLEEPK 24 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 0 S(0.04)LS(0.924)PGAAS(0.005)S(0.005)S(0.005)S(0.022)GDGDGKEGLEEPK;S(0.021)LS(0.458)PGAAS(0.138)S(0.138)S(0.038)S(0.206)GDGDGKEGLEEPK ; 92.412 2.53E-05 30985300 8066.6 7612.7 8585.1 5893.3 8102.2 7852.9 6868.4 7306.1 8856.6 8464.5 TRUE FALSE FALSE 7968.281176 7719.87179 8734.520064 6574.711075 7688.714501 7351.125034 7451.801725 7517.490476 8064.443514 8244.59107 0.966485919 0.936355936 1.059424293 0.797457511 0.932576817 0.891630036 0.903841277 0.911808774 0.978149607 1 13.00923222 -9.268520327 24.99853645 0.984555525 0.891110632 0.562130043 0.044289642 316.2375531 1116441.55 0.006337521 0.009811699 5.39E-10 9.268520327 -0.093444893 SLS(ph)PILPGR ddPTM_HeLa_Romidepsin_16h_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 0 S(0.004)LS(0.996)PILPGR 101.97 0.02654 50579000 2876.1 1641.8 2293.9 2023.1 2820 2560.2 2818.4 3107.4 2387.3 2205.7 TRUE FALSE FALSE 2841.044987 1664.913303 2333.824367 2257.020341 2676.084877 2396.611483 3057.794826 3197.307716 2173.773909 2148.395596 1.322403096 0.77495658 1.086310348 1.050560867 1.245620165 1.115535466 1.423292261 1.488230437 1.011812681 1 11.06904395 -7.719713076 4.195910019 1.120390447 1.473358254 0.508416744 0.144593522 0.154358507 5.710399925 0.022911061 0.090892833 1.91E-08 7.719713076 0.352967808 SLS(ph)PPQSQSK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPPQSQSK 10 0 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;I3L0Y9;Q9UQB8-6;I3L3C6 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 S(0.41)LS(0.586)PPQS(0.005)QSK 98.156 0.026674 50974000 851.74 770.34 696.17 1020.9 2048.9 3825.7 3615.8 3538 840.04 765.4 TRUE FALSE FALSE 841.3586653 781.1848667 708.2865468 1138.941261 1944.336988 3581.250117 3922.925962 3640.366448 764.9047185 745.5147977 1.128560651 1.047846225 0.9500637 1.527724554 2.608046136 4.803727744 5.262036346 4.88302373 1.026008767 1 9.542093179 -8.440014729 1.828540733 1.059283477 5.161494529 0.992961607 0.146103173 0.019042716 0.123690151 0.022121133 0.062717987 3.63E-09 8.440014729 4.102211052 up SLS(ph)PQEDALTGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPQEDALTGSR 13 0 Q96EN8 Q96EN8 MOCOS Molybdenum cofactor sulfurase 1 0 S(0.398)LS(0.602)PQEDALTGSR 134.02 0.0017942 14066000 1224.9 1364.5 1007.6 1143.8 1266.3 1295.8 989.9 1309.5 1146.3 1619.5 TRUE FALSE FALSE 1209.970448 1383.709467 1025.136855 1276.051538 1201.675986 1213.002562 1073.982081 1347.388316 1043.772057 1577.425157 0.767054109 0.877195004 0.64987987 0.808945852 0.76179588 0.768976301 0.680845032 0.854169411 0.661693553 1 10.62335584 -12.33526535 0.508327831 1.056490786 0.758553421 0 0.124366504 0.723332655 0.244698029 0.108630042 0.015489719 4.62E-13 12.33526535 -0.297937365 SLS(ph)PVAAPPLREPR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPVAAPPLREPR 14 1 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 S(0.274)LS(0.726)PVAAPPLREPR 61.821 0.030464 122270000 4272.1 4256.7 4042.8 4143.3 3537.6 3459.5 3411.3 3145.9 4699.3 3962.8 TRUE FALSE FALSE 4220.030002 4316.625934 4113.163238 4622.367841 3357.063071 3238.449115 3701.055737 3236.921653 4278.982838 3859.845885 1.093315673 1.118341525 1.065628878 1.197552436 0.869740184 0.839009953 0.958861013 0.838614222 1.108589039 1 11.91432753 -8.732440189 24.98147971 1.062671278 0.879753229 0.742737181 0.061633454 100.8633057 86888.72002 0.009607216 0.019211916 1.85E-09 8.732440189 -0.182918049 QPGQVIGATTPSTGSPT(ph)NK ddPTM_HeLa_Romidepsin_16h_R1 1 QPGQVIGATTPSTGSPTNK 19 0 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 QPGQVIGATT(0.001)PS(0.005)T(0.06)GS(0.24)PT(0.694)NK 291.28 6.40E-124 11334000 4635 4020.6 3892 3685.7 1927.5 1231.8 1176 1125.4 4736.9 3869.3 TRUE FALSE FALSE 4578.506837 4077.202112 3959.738627 4111.857976 1829.132483 1153.091955 1275.889411 1157.961673 4313.2198 3768.775028 1.214852785 1.081837489 1.050669939 1.091033013 0.485338729 0.305959349 0.338542206 0.307251472 1.144461998 1 11.87987996 -8.696504747 3.499540542 1.099551075 0.327427475 0.976565491 0.056382018 0.035097229 0.863833524 0.012335594 0.025421293 2.01E-09 8.696504747 -0.7721236 down SLS(ph)SPTDNLELSLR ddPTM_HeLa_Romidepsin_16h_R1 2 SLSSPTDNLELSLR 14 0 J3QRU8;A0A0C4DGN6;Q9Y2X7;Q9Y2X7-3 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 0 S(0.027)LS(0.479)S(0.479)PT(0.016)DNLELSLR;S(0.036)LS(0.895)S(0.069)PTDNLELSLR ; 260.73 4.90E-68 152745000 7756.3 7623.7 7518.7 6097 7901.7 8054.5 7226.8 7873.4 8489.9 7293.1 TRUE FALSE FALSE 7661.763232 7731.026649 7649.55982 6801.963827 7498.446764 7539.843445 7840.644212 8101.204407 7730.542081 7103.624211 1.078571023 1.088321457 1.076853109 0.957534299 1.055580439 1.061407983 1.103752673 1.140432569 1.088253242 1 12.79433955 -15.47236008 0.010392808 2.55E-05 1.984489228 0.051096123 0.048193272 8879.797297 8.985661116 968.6514835 758.9085637 3.37E-16 15.47236008 1.98446369 SLS(ph)SPTVTLSAPLEGAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-9;Q96PU5-4;A0A1B0GVY1;Q96PU5-2;Q96PU5-6;Q96PU5-5;Q96PU5-7;Q96PU5 Q96PU5-9 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 0 S(0.003)LS(0.7)S(0.085)PT(0.209)VTLS(0.003)APLEGAK 174.4 9.59E-07 313070000 4879.3 5169.1 5098 4808.3 7220.1 8066.5 7119.8 6934.5 5324.4 4980.7 TRUE FALSE FALSE 4819.829215 5241.870725 5186.728551 5364.25827 6851.631355 7551.076683 7724.555634 7135.138817 4848.172329 4851.300696 0.993512775 1.080508312 1.06914184 1.105736091 1.412328731 1.556505596 1.592264862 1.470768205 0.999355149 1 12.24415589 -8.740692036 1.871788057 1.007910789 1.550942017 0.968090489 0.042071734 0.03878446 0.276055737 0.006662971 0.0152523 1.82E-09 8.740692036 0.543031228 SLS(ph)TSGESLYHVLGLDK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 0 S(0.281)LS(0.553)T(0.108)S(0.041)GES(0.017)LYHVLGLDK;S(0.139)LS(0.843)T(0.018)S(0.001)GESLYHVLGLDK ; 161.08 1.24E-05 75649000 3121.4 3522.7 3215 2484.3 8048.4 10485.6 5173.4 7131.9 4428 4160.6 TRUE FALSE FALSE 3083.355176 3572.292663 3270.955726 2771.546455 7637.660115 9815.604001 5612.828467 7338.250274 4031.94859 4052.507012 0.760851287 0.881501908 0.807143755 0.683909108 1.884675361 2.422106605 1.38502622 1.810792739 0.994926987 1 11.98459897 -8.755360896 24.98283801 0.864617344 1.879638494 0.799799163 0.250199638 47.14772288 193777.2641 0.036046274 0.070638142 1.76E-09 8.755360896 1.01502115 SLS(ph)VEHLETK ddPTM_HeLa_Romidepsin_16h_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 0 S(0.128)LS(0.872)VEHLETK 79.886 0.025815 7535300 10379 10633 10023 10776 13695 12691 10118 11972 11650 10580 TRUE FALSE FALSE 10252.49676 10782.69165 10197.44611 12021.97182 12996.09305 11880.08606 10977.42267 12318.39093 10607.99482 10305.13007 0.994892513 1.04634212 0.989550451 1.166600687 1.261128482 1.152832227 1.065238632 1.195364915 1.029389706 1 13.33107509 -9.258819334 24.24481237 1.001411022 1.166816353 0.722466897 0.048176966 57.83996571 535225.9328 0.007252974 0.011669489 5.51E-10 9.258819334 0.165405331 SLS(ph)VPVDLSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSVPVDLSR 10 0 Q9NYF3;D6RHW3 Q9NYF3 FAM53C Protein FAM53C 1 0 S(0.02)LS(0.98)VPVDLSR 119.03 0.012435 92168000 2742.4 2432.9 2611.3 3296.5 7218.8 7692.4 7413.1 8597.6 2588 2383.8 TRUE FALSE FALSE 2708.974574 2467.15043 2656.748581 3677.65684 6850.397699 7200.880466 8042.768529 8846.357991 2356.522798 2321.868532 1.166721774 1.062571113 1.144228687 1.583921221 2.950381386 3.10132997 3.463920725 3.810016746 1.014925163 1 11.18107057 -8.710708347 1.506464813 1.070156607 3.547597239 0.979459415 0.156838437 0.036593796 0.16664662 0.024387501 0.062106716 1.95E-09 8.710708347 2.477440632 up SLS(ph)YEEPR ddPTM_HeLa_Romidepsin_16h_R1 2 SLSYEEPR 8 0 F5GZK9;Q8IZD4-2;Q8IZD4 F5GZK9 DCP1B mRNA-decapping enzyme 1B 1 0 SLS(1)YEEPR;S(0.046)LS(0.954)YEEPR ; 128.91 0.012272 120553000 8224.4 9908.4 6377.6 7579.2 9188.5 6858.9 6007.8 6647.8 7792.7 8050.4 TRUE FALSE FALSE 8124.157849 10047.89072 6488.599453 8455.542765 8719.576558 6420.638426 6518.102382 6840.143605 7095.701395 7841.249447 1.036079505 1.281414497 0.827495605 1.078341254 1.112013668 0.818828488 0.831258134 0.872328275 0.904919738 1 12.93686784 -8.250689622 24.81785447 1.033355337 0.839850265 0.374551148 0.114590015 478.3388738 1104333.266 0.014269029 0.035983345 5.61E-09 8.250689622 -0.193505072 SLSAIYLEK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSAIYLEK 9 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ; ; 123.86 0.01112 631540 443.19 285.483 338.23 312.29 332.742 497.11 356.94 175.9 406.28 277.33 FALSE FALSE TRUE 437.7882298 289.5020372 344.1167513 348.3984392 315.7609341 465.3462753 387.2584747 180.989389 369.9412993 270.1249266 1.62068801 1.071733885 1.273917056 1.289767825 1.168944081 1.722707642 1.43362732 0.670021057 1.369519296 1 8.077482965 SLSDNGQPGT(ph)PDPADSGGTSAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSDNGQPGTPDPADSGGTSAK 22 0 O75691 O75691 UTP20 Small subunit processome component 20 homolog 1 0 SLSDNGQPGT(1)PDPADSGGTSAK 151.19 3.16E-06 11096000 3941.9 3546.8 3920.7 3068.6 3005.2 3040.6 2318.1 3225.5 3737.6 3589.5 TRUE FALSE FALSE 3893.854607 3596.731943 3988.938139 3423.40597 2851.83343 2846.315473 2514.999356 3318.824754 3403.299695 3496.244273 1.113724987 1.028741605 1.140920893 0.979166701 0.815684834 0.814106582 0.719343147 0.949254255 0.97341588 1 11.77159027 -8.875625969 3.559235295 1.058907259 0.815276263 0.698330776 0.070111746 0.088797685 2.18177078 0.010081553 0.019179253 1.33E-09 8.875625969 -0.243630996 SLSDSES(ph)DDSK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSDSESDDSK 11 0 S4R2Y4;Q13185 S4R2Y4 CBX3 Chromobox protein homolog 3 1 0 SLSDS(0.004)ES(0.994)DDS(0.001)K 155.88 0.001996 7020200 1679 1995.5 2369.8 1101.9 1244.1 1324.5 2311.8 581.07 3034.6 2239.2 TRUE FALSE FALSE 1658.535702 2023.592701 2411.045375 1229.306863 1180.608935 1239.868725 2508.164234 597.8823437 2763.177776 2181.025261 0.760438557 0.927817177 1.105464213 0.56363715 0.541309152 0.568479763 1.149993207 0.274129032 1.266916906 1 11.09079076 -9.243264201 24.86862045 0.902626264 0.641801495 0.342765077 0.248839473 836.6805159 1144808.714 0.03250766 0.053838425 5.71E-10 9.243264201 -0.260824769 SLSEQPVMDT(ph)ATATEQAK ddPTM_HeLa_Romidepsin_16h_R1 3 SLSEQPVMDTATATEQAK 18 0 A0A0A0MSN9;P18615-4;P18615;P18615-3;A2ABK4;A0A0G2JI50;E9PD43;A0A0A0MT02 A0A0A0MSN9 NELFE Negative elongation factor E 1 0 SLS(0.003)EQPVMDT(0.994)AT(0.002)ATEQAK;SLS(0.001)EQPVMDT(0.958)AT(0.04)AT(0.002)EQAK;S(0.004)LS(0.021)EQPVMDT(0.95)AT(0.024)ATEQAK ;; 130.56 0.0038063 58930500 12149.9 14340.5 9038 8586.7 11631.7 9448.3 7292.82 10337.4 10425.9 10737 TRUE FALSE FALSE 12001.81235 14542.38594 9195.302599 9579.534656 11038.09095 8844.584123 7912.271949 10636.49636 9493.381392 10458.05119 1.14761461 1.390544535 0.879255841 0.915996153 1.055463465 0.845720102 0.75657231 1.017062946 0.907758168 1 13.35232642 SLSES(ph)SVIMDR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSESSVIMDR 11 0 A0A0C4DGM5;H3BSS6;Q9H2Y7-2;Q9H2Y7;H3BNX5 A0A0C4DGM5 ZNF106 Zinc finger protein 106 1 0 SLS(0.014)ES(0.493)S(0.493)VIMDR 118.9 0.014512 35501000 5705.8 5098.5 5180 4532.6 5382.7 5344.7 4741 5586.4 5756.6 5147.3 TRUE FALSE FALSE 5636.255515 5170.276817 5270.155727 5056.680539 5108.000733 5003.190919 5143.700422 5748.03367 5241.715278 5013.572404 1.124199485 1.031256039 1.051177744 1.008598287 1.01883454 0.997929324 1.025955149 1.146494596 1.045505052 1 12.29162324 SLSFPILNPALSQPSQPS(ph)SPLPGSHGR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSFPILNPALSQPSQPSSPLPGSHGR 27 0 Q8ND24;E9PN76;Q8ND24-2 Q8ND24 RNF214 RING finger protein 214 1 0 SLSFPILNPALSQPS(0.005)QPS(0.479)S(0.244)PLPGS(0.272)HGR 113.79 1.42E-09 15669000 791.57 992.98 922.21 687.57 864.69 1158.1 612.53 758.98 1072.5 837.63 TRUE FALSE FALSE 781.9220404 1006.959199 938.2606782 767.0700785 820.5616427 1084.101148 664.5582829 780.9398888 976.5729139 815.8682518 0.958392533 1.234217898 1.150014939 0.94018866 1.005752633 1.328769866 0.814541173 0.957188721 1.19697379 1 9.672192391 DTTKLEPAS(ph)PPEDTSAEVSR ddPTM_HeLa_Romidepsin_16h_R1 2 DTTKLEPASPPEDTSAEVSR 20 1 E9PFE2;Q9UHL9-2;Q9UHL9;Q9UHL9-3 E9PFE2 GTF2IRD1 General transcription factor II-I repeat domain-containing protein 1 1 0 DT(0.008)T(0.032)KLEPAS(0.959)PPEDT(0.001)SAEVSR;DTTKLEPAS(1)PPEDTSAEVSR ; 111.33 0.00012301 65451000 6552.7 6353.8 5140.7 6155.7 2251.56 1354.92 1436.79 1359.99 6568.8 5600.6 TRUE FALSE FALSE 6472.833172 6443.248963 5230.171727 6867.450997 2136.654491 1268.344985 1558.830907 1399.339165 5981.270076 5455.095605 1.186566403 1.181143179 0.958768114 1.258905709 0.391680485 0.232506463 0.285756845 0.256519641 1.096455591 1 12.41338877 -8.691755395 5.533725401 1.097558378 0.272851067 0.954088024 0.088467658 0.032969443 1.844590441 0.014372188 0.028908108 2.03E-09 8.691755395 -0.824707311 down SLSLASTSRDS(ph)PGAVAAPLISGVEIK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSLASTSRDSPGAVAAPLISGVEIK 26 1 H3BLS7;Q5THJ4-2;Q5THJ4;A0A2R8YD87 H3BLS7 VPS13D Vacuolar protein sorting-associated protein 13D 1 0 S(0.002)LS(0.005)LAS(0.228)T(0.228)S(0.228)RDS(0.309)PGAVAAPLISGVEIK 68.97 0.00019144 12130000 1713.2 1675.7 1624.4 1761.8 2022.9 1740.1 1661.2 1810 2088.8 1597.3 TRUE FALSE FALSE 1692.318859 1699.290549 1652.672001 1965.507606 1919.663865 1628.913226 1802.302287 1862.369494 1901.972497 1555.801916 1.087746996 1.092228086 1.062263765 1.263340523 1.233874213 1.046992686 1.158439431 1.19704795 1.222502992 1 10.60344267 -10.62895978 0.464062246 1.003768501 1.173401735 0 0.091703106 0.57822513 0.31784913 0.034848026 0.029398184 2.35E-11 10.62895978 0.169633235 SLSNS(ph)NPDISGTPTSPDDEVR ddPTM_HeLa_Romidepsin_16h_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 0 SLS(0.015)NS(0.981)NPDISGT(0.003)PTSPDDEVR;S(0.005)LS(0.018)NS(0.799)NPDIS(0.052)GT(0.014)PT(0.088)S(0.024)PDDEVR;SLS(0.002)NS(0.998)NPDISGTPTSPDDEVR ;; 378.15 0 47013700 3739.4 3736.97 3663.17 3459.7 3716.36 3320.24 3104.66 3546.39 3937.88 3371.25 TRUE FALSE FALSE 3693.822754 3789.579162 3726.925937 3859.726792 3526.700282 3108.08738 3368.369743 3648.999199 3585.66615 3283.664439 1.124908718 1.154070165 1.134989889 1.175432772 1.074013605 0.946530146 1.025795968 1.11125825 1.091970942 1 11.68109099 -6.929997801 16.55820897 1.071015187 1.691785781 0 0.069159982 14243960.48 59684631.18 0.011183743 309684673.9 1.17E-07 6.929997801 0.620770594 SLSNSNPDIS(ph)GTPTSPDDEVR ddPTM_HeLa_Romidepsin_16h_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 0 SLSNS(0.093)NPDIS(0.509)GT(0.387)PT(0.008)S(0.002)PDDEVR;SLSNS(0.318)NPDIS(0.623)GT(0.053)PT(0.004)S(0.001)PDDEVR;SLSNS(0.024)NPDIS(0.898)GT(0.078)PTSPDDEVR ;; 241.11 4.54E-54 269530000 11860.3 11962.7 12318.1 11771.9 9975.1 10341.4 9876.7 10031.8 12774.5 11738.9 TRUE FALSE FALSE 11715.7421 12131.1112 12532.49136 13133.02247 9466.033425 9680.617915 10715.62665 10322.05431 11631.91673 11433.92169 1.024647748 1.060975537 1.096079867 1.148601751 0.82789035 0.846657707 0.937178594 0.902757128 1.017316459 1 13.48103269 -8.74563542 24.99999064 1.031618473 0.880520533 0.725815815 0.052513189 125.3713542 198321.6064 0.008520931 0.016997932 1.80E-09 8.74563542 -0.15109794 SLSPGAAS(ph)SSSGDGDGKEGLEEPK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPGAASSSSGDGDGKEGLEEPK 24 1 Q6ZN18-2;Q6ZN18 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 0 S(0.039)LS(0.14)PGAAS(0.245)S(0.245)S(0.245)S(0.085)GDGDGKEGLEEPK 78.419 0.00012875 14897000 2111.9 1884.7 1889.8 1698.2 2023.8 2172.7 1794.3 1754 2686.5 2247.2 TRUE FALSE FALSE 2086.15935 1911.232856 1922.691176 1894.553874 1920.517934 2033.871482 1946.707797 1804.749223 2446.212712 2188.81742 0.953098843 0.873180576 0.878415513 0.865560488 0.877422629 0.929210204 0.889387931 0.824531643 1.117595597 1 11.0959359 -10.50264858 1.480028304 0.984879025 0.877694686 0.625724935 0.049462138 0.130741827 0.568955397 0.005652583 0.00607583 3.14E-11 10.50264858 -0.107184339 SLSPQEDALT(ph)GSR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSPQEDALTGSR 13 0 Q96EN8 Q96EN8 MOCOS Molybdenum cofactor sulfurase 1 0 S(0.22)LS(0.22)PQEDALT(0.487)GS(0.074)R 98.654 0.028535 1329000 1042.6 1025.8 734.55 909.85 1117.3 1304.5 740.96 947.3 1083.1 1237 TRUE FALSE FALSE 1029.89239 1040.241239 747.3345346 1015.051138 1060.280012 1221.14666 803.8971239 974.7086309 986.2248233 1204.862562 0.854779975 0.863369211 0.62026538 0.842462178 0.880000795 1.013515316 0.667210643 0.8089791 0.818537196 1 10.23465287 -11.61436906 0.685418812 0.996936607 0.814261239 0.006833612 0.116878305 0.659119908 0.620835447 0.060556209 0.024511323 2.43E-12 11.61436906 -0.182675367 SLSQS(ph)FENLLDEPAYGLIQK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSQSFENLLDEPAYGLIQK 20 0 Q8TC07-2;Q8TC07-3;C9JA93 Q8TC07-2 TBC1D15 TBC1 domain family member 15 1 0 S(0.074)LS(0.262)QS(0.664)FENLLDEPAYGLIQK 84.214 0.0013509 4909100 1784.1 1750.6 1571.5 1029.1 1536.9 1934.4 1628.5 1787.2 1897 1636.6 TRUE FALSE FALSE 1762.354703 1775.244993 1598.851298 1148.089384 1458.466258 1810.798083 1766.824749 1838.909812 1727.327569 1594.080896 1.105561648 1.113647994 1.002992572 0.720220277 0.914926126 1.135951185 1.108365801 1.153586256 1.083588401 1 10.63850913 SLSRTPETLLPFAEAEAFLKK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSRTPETLLPFAEAEAFLKK 21 2 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 0 0 111.09 7.26E-05 2749200 630.91 583.22 461.29 748.13 560.01 533.93 572.67 651.82 542.71 631.71 FALSE FALSE TRUE 623.2202262 591.4305865 469.3185589 834.6323107 531.4306 499.8135962 621.3125755 670.6793833 494.1686584 615.2980831 1.012875293 0.961209863 0.762749912 1.356468244 0.863696174 0.812311317 1.009774925 1.090007269 0.803137003 1 9.265141688 -10.27191234 22.18883276 1.006079998 0.975909759 0 0.168898905 989.8571609 2097183.219 0.025487263 0.029354754 5.35E-11 10.27191234 -0.030170239 SLSS(ph)PGGPSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSPGGPSKPK 12 1 J3KRY8;Q9BZE9-3;Q9BZE9;Q9BZE9-2;J3QL04;J3QR12;Q9BZE9-4 J3KRY8 ASPSCR1 Tether containing UBX domain for GLUT4 1 0 SLS(0.027)S(0.972)PGGPSKPK 152.96 0.009421 7532700 2777.4 2759.3 2641.2 1782.4 2599.8 2722.6 2775.4 2612.5 2818 2740.3 TRUE FALSE FALSE 2743.547981 2798.145498 2687.168978 1988.489474 2467.122505 2548.634647 3011.142407 2688.088566 2565.951022 2669.106611 1.027889995 1.048345348 1.006767196 0.745001892 0.924325201 0.954864312 1.128146172 1.007111726 0.961352016 1 11.38214122 -9.493209313 24.99513316 1.016718332 0.951872652 0.087805381 0.09064052 1303.925941 1098499.484 0.014410111 0.021987499 3.21E-10 9.493209313 -0.064845679 SRLT(ph)PVS(ph)PESSSTEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 S(0.221)RLT(0.78)PVS(0.801)PES(0.138)S(0.023)S(0.029)T(0.008)EEK;S(0.065)RLT(0.927)PVS(0.421)PES(0.301)S(0.218)S(0.028)T(0.038)EEK ; 111.11 0.0047191 95236000 13717.7 12868 12409.7 11251.7 6249.9 4050.62 3348.16 3100.91 14632.2 13558.2 TRUE FALSE FALSE 13550.5034 13049.15604 12625.68562 12552.67449 5930.944281 3791.798455 3632.552627 3190.629938 13323.45938 13205.95601 1.026090302 0.988126572 0.956059949 0.950531297 0.449111316 0.287127903 0.275069266 0.241605374 1.008897756 1 13.68890112 -8.691163848 2.540359223 1.00707891 0.270044084 0.994326388 0.025251511 0.015603362 0.204533526 0.004363936 0.009466949 2.04E-09 8.691163848 -0.737034826 down SLSS(ph)PTVTLSAPLEGAK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSPTVTLSAPLEGAK 17 0 Q96PU5-9;Q96PU5-4;A0A1B0GVY1;Q96PU5-2;Q96PU5-6;Q96PU5-5;Q96PU5-7;Q96PU5 Q96PU5-9 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 0 S(0.004)LS(0.24)S(0.756)PTVTLSAPLEGAK 238.83 1.03E-46 382600000 4179 4695 4424.4 4440.1 5972.5 6685.5 6137.7 6567.7 4798.4 4519.2 TRUE FALSE FALSE 4128.064741 4761.096333 4501.404826 4953.485253 5667.701039 6258.318126 6659.036085 6757.726037 4369.219086 4401.790533 0.937814898 1.081627192 1.022630403 1.12533416 1.287589902 1.421766456 1.512801674 1.535222085 0.99260041 1 12.10387478 -8.553356492 0.900021724 0.974061974 1.564324983 0.977804132 0.032270897 0.069282777 0.099585865 0.006146664 0.025822165 2.80E-09 8.553356492 0.590263009 SLSS(ph)S(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WXA6;A0A087WT45 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 2 0 S(0.082)LS(0.301)S(0.811)S(0.805)PQAQPPRPAELS(0.001)DEEVAELFQR 65.753 0.00055602 0 335.4 398.33 382 355.39 410.48 479.43 304.92 359.39 356.83 296.89 TRUE FALSE FALSE 331.3120158 403.9377002 388.6485498 396.481864 389.5316739 448.7959703 330.8198972 369.7883826 324.9142311 289.176755 1.145707634 1.396853977 1.343982679 1.371071005 1.347036604 1.551978029 1.144005842 1.278762474 1.123583502 1 8.175807778 -10.57312314 1.475211532 1.045812049 1.35023876 0.553697376 0.104132303 0.169590567 0.746536566 0.021443784 0.022356942 2.67E-11 10.57312314 0.304426711 SLSS(ph)SLDDTEVKK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSSSLDDTEVKK 13 1 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 0 S(0.016)LS(0.355)S(0.549)S(0.079)LDDTEVKK;S(0.002)LS(0.016)S(0.819)S(0.163)LDDT(0.001)EVKK ; 81.992 0.0109 30604000 6204.3 8774.6 6901.4 4572.5 5706.3 8254 5323.1 7939.4 7356.4 8210.9 TRUE FALSE FALSE 6128.679605 8898.129049 7021.515972 5101.193964 5415.086218 7726.596039 5775.243981 8169.114013 6698.42516 7997.579634 0.766316797 1.112602744 0.877955118 0.637842222 0.677090628 0.966116799 0.722123973 1.021448286 0.837556544 1 12.96534774 -9.505580344 24.93011243 0.907668294 0.797749721 0.13986073 0.141299673 1281.727081 1847201.836 0.023075062 0.034749895 3.12E-10 9.505580344 -0.109918573 SLSSS(ph)PQAQPPRPAELSDEEVAELFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WXA6;A0A087WT45 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 0 S(0.003)LS(0.02)S(0.059)S(0.557)PQAQPPRPAELS(0.361)DEEVAELFQR 56.416 0.0015916 88026000 413.62 458.5 300.72 447.49 452.04 678.93 487.43 537.56 450.53 375.79 TRUE FALSE FALSE 408.5786403 464.954775 305.9539055 499.2308993 428.970712 635.5485641 528.832292 553.1134505 410.2334684 366.0269216 1.116252975 1.270274801 0.835878148 1.363918526 1.17196492 1.736343768 1.444790699 1.511127783 1.120774031 1 8.515805954 -8.652988644 1.593166115 1.064132342 1.546261848 0.604850268 0.157806638 0.168275939 0.855164911 0.02233599 0.057730599 2.22E-09 8.652988644 0.482129506 SLSSSPQAQPPRPAELS(ph)DEEVAELFQR ddPTM_HeLa_Romidepsin_16h_R1 2 SLSSSPQAQPPRPAELSDEEVAELFQR 27 1 Q4V328-4;Q4V328;A0A087WXA6;A0A087WT45 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 0 S(0.002)LS(0.008)S(0.018)S(0.109)PQAQPPRPAELS(0.862)DEEVAELFQR;S(0.003)LS(0.027)S(0.097)S(0.361)PQAQPPRPAELS(0.512)DEEVAELFQR ; 76.744 1.00E-05 113972300 1675.71 1411.95 1488.21 1806.4 2161.79 2031.46 1937.45 2023.57 1811.58 1721.28 TRUE FALSE FALSE 1655.285802 1431.827469 1514.111671 2015.264467 2051.46579 1901.656262 2102.016955 2082.118805 1649.547748 1676.560897 0.987310276 0.85402652 0.903105681 1.202022826 1.223615434 1.134260178 1.253767136 1.241898704 0.983887761 1 10.71128917 -9.248644071 23.97799074 0.974932004 1.209907564 0.853251371 0.054367904 151.0056199 282979.2448 0.009061039 0.014954429 5.64E-10 9.248644071 0.234975561 SLST(ph)NGENMGLAVQYLDPR ddPTM_HeLa_Romidepsin_16h_R1 1 SLSTNGENMGLAVQYLDPR 19 0 J3KRN4;J3QRB6;Q99759;Q99759-2 J3KRN4 MAP3K3 Mitogen-activated protein kinase kinase kinase 3 1 0 SLS(0.371)T(0.629)NGENMGLAVQYLDPR 125.23 0.0022199 8925300 916.76 1029 1136.7 968 1350.8 1468.2 1361 1295.2 1411.4 905.68 TRUE FALSE FALSE 905.5861765 1043.486289 1156.483787 1079.924715 1281.863635 1374.386758 1476.603306 1332.674569 1285.160849 882.150303 1.026566758 1.182889453 1.310982701 1.224195821 1.453112504 1.55799613 1.673868162 1.510711456 1.456850204 1 9.784880677 -9.09248609 0.616411812 0.998546069 1.645811305 0.456069921 0.159439497 0.151824778 0.106898839 0.014763966 0.046480638 8.08E-10 9.09248609 0.647265237 SLSTS(ph)GESLYHVLGLDK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSTSGESLYHVLGLDK 17 0 Q9H3Z4-2;Q9H3Z4 Q9H3Z4-2 DNAJC5 DnaJ homolog subfamily C member 5 1 0 SLS(0.17)T(0.042)S(0.787)GES(0.001)LYHVLGLDK;S(0.001)LS(0.021)T(0.127)S(0.825)GES(0.026)LYHVLGLDK ; 167.29 4.54E-06 52011000 2676.1 3834.6 3642.1 2069.43 7932.5 11134.4 4873 8744.6 5080.8 4657.4 TRUE FALSE FALSE 2643.482664 3888.583599 3705.489223 2308.707234 7527.674925 10422.94777 5286.912498 8997.611204 4626.360523 4536.400077 0.582726968 0.857195912 0.81683475 0.50892937 1.659393968 2.297625341 1.165442291 1.983425415 1.019830801 1 12.14733217 -8.69563272 6.592515971 0.786150551 1.781118766 0.714795986 0.303278781 0.084105314 6.600796264 0.042580098 0.0853473 2.02E-09 8.69563272 0.994968215 SLSVS(ph)SDFLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSVSSDFLGK 11 0 Q3V6T2;A0A2R8Y7D4;A0A2U3TZV9;A0A2R8Y7B1;H7C2C6;A0A2R8Y820;A0A2R8YCU9;A0A2R8Y885;A0A2R8YDS8;H0Y470;H0Y7U8;A0A2R8Y5D7;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H0Y7K3;A0A2R8Y4Z5;A0A2R8Y4C6 Q3V6T2 CCDC88A Girdin 1 0 SLS(0.003)VS(0.855)S(0.142)DFLGK 115.14 0.012239 9918900 1090 1172.1 1012.9 952.71 917.03 1430.8 1073.2 1370.7 1256 856.51 TRUE FALSE FALSE 1076.714661 1188.600855 1030.5291 1062.866813 870.2305372 1339.376498 1164.357581 1410.359042 1143.660214 834.2577467 1.290625907 1.424740566 1.235264645 1.274026902 1.043119516 1.605470855 1.395680874 1.690555524 1.370871555 1 9.704349368 -4 0.039525054 4.73E-08 3.481712816 0.194450412 0.185162313 409.4759731 1.245715423 30.60859995 96.72505005 1.00E-04 4 3.481712768 SLSVSS(ph)DFLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSVSSDFLGK 11 0 Q3V6T2;A0A2R8Y7D4;A0A2U3TZV9;A0A2R8Y7B1;H7C2C6;A0A2R8Y820;A0A2R8YCU9;A0A2R8Y885;A0A2R8YDS8;H0Y470;H0Y7U8;A0A2R8Y5D7;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H0Y7K3;A0A2R8Y4Z5;A0A2R8Y4C6 Q3V6T2 CCDC88A Girdin 1 0 S(0.036)LS(0.036)VS(0.253)S(0.674)DFLGK 140.78 0.00010412 0 1207.5 1050.6 1197 1277.1 1386.1 1546.6 1129.6 1625.3 1314.9 1063.5 TRUE FALSE FALSE 1192.782526 1065.390374 1217.833283 1424.764311 1315.362145 1447.777251 1225.548196 1672.325491 1197.292051 1035.870117 1.151478845 1.02849803 1.175662145 1.375427564 1.269813776 1.397643612 1.183109905 1.614416194 1.155832214 1 10.01662741 -4 0.154257817 0.953845433 2.9317908 0.584253509 0.113281438 28.11340635 0.277803452 0.200746436 12.58010049 1.00E-04 4 1.977945368 SLSYS(ph)PVER ddPTM_HeLa_Romidepsin_16h_R1 1 SLSYSPVER 9 0 Q9UQ35;Q9UQ35-2;I3L4U6 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SLS(0.003)YS(0.997)PVER 136.49 0.0067313 87304000 4742.3 4949 4600.8 3006.5 3510 3188.7 2719.4 2693.8 5411.6 4473.7 TRUE FALSE FALSE 4684.499024 5018.672152 4680.874994 3354.125676 3330.871602 2984.952361 2950.385768 2771.740853 4927.572942 4357.472629 1.075049558 1.151739226 1.074217876 0.769741077 0.764404481 0.685019188 0.677086472 0.636089102 1.130832793 1 12.08927589 -9.146361593 3.158265313 1.049940109 0.693697476 0.921035637 0.055382566 0.058949377 1.11856135 0.009163681 0.015872005 7.14E-10 9.146361593 -0.356242633 SLT(ph)PPPSSTESK ddPTM_HeLa_Romidepsin_16h_R1 2 SLTPPPSSTESK 12 0 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 1 0 S(0.072)LT(0.927)PPPS(0.001)STESK;S(0.002)LT(0.99)PPPS(0.007)S(0.001)TESK ; 125.82 0.011348 116943000 5861.8 5836.8 5042.7 5226.2 5429 5211.5 4274.4 4949.1 6159.6 5419.3 TRUE FALSE FALSE 5790.354127 5918.970624 5130.466078 5830.477834 5151.937872 4878.501969 4637.467429 5092.2944 5608.669949 5278.505805 1.096968411 1.121334492 0.971954236 1.104569749 0.976022015 0.924220253 0.878556849 0.964722705 1.062548789 1 12.36591389 -8.523925027 3.996652944 1.050693294 0.920588532 0.624460822 0.047882226 0.122678918 4.474606939 0.007757601 0.017000289 2.99E-09 8.523925027 -0.130104762 SLTDPSQESHT(ph)EAISDAETSSSDISFSGIATR ddPTM_HeLa_Romidepsin_16h_R1 1 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 SLTDPSQES(0.001)HT(0.498)EAIS(0.498)DAET(0.001)SSSDISFS(0.001)GIATR 103.85 8.66E-13 19293000 4764.7 4149.1 3840.3 3963.1 4674.4 4994.9 4206.8 4779.5 4991.8 4242.9 TRUE FALSE FALSE 4706.626004 4207.511139 3907.138811 4421.332269 4435.847925 4675.74201 4564.125487 4917.787292 4545.320906 4132.668846 1.13888293 1.018109918 0.945427508 1.069849154 1.073361571 1.131409795 1.104401455 1.189978552 1.099851228 1 12.01285805 -7.753845789 1.04700246 1.05406611 1.187848662 0.404551193 0.053238299 0.977830025 1.372444122 0.010275835 0.119629638 1.76E-08 7.753845789 0.133782551 SLTDPSQESHTEAIS(ph)DAETSSSDISFSGIATR ddPTM_HeLa_Romidepsin_16h_R1 1 SLTDPSQESHTEAISDAETSSSDISFSGIATR 32 0 Q5QJE6;J3KP30 Q5QJE6 DNTTIP2 Deoxynucleotidyltransferase terminal-interacting protein 2 1 0 SLTDPSQESHT(0.014)EAIS(0.984)DAET(0.001)SSSDISFSGIATR 123.03 8.55E-16 17444000 3683.1 3745.8 3034.1 3355.4 4430.4 4955.1 4226.5 3869.3 4573.4 4564.2 TRUE FALSE FALSE 3638.208961 3798.533471 3086.907238 3743.367136 4204.300156 4638.485102 4585.498805 3981.252091 4164.34365 4445.621426 0.818380292 0.854443756 0.694370245 0.842034617 0.945717089 1.043382838 1.031464078 0.895544562 0.936729256 1 12.11816938 -8.540000124 6.358727261 0.884612001 0.99457034 0.307687308 0.085380137 0.204646101 32.17722645 0.01539922 0.031760209 2.88E-09 8.540000124 0.109958338 SLTEISTDFDRSS(ph)PPLQPPPVNSLTTENR ddPTM_HeLa_Romidepsin_16h_R1 1 SLTEISTDFDRSSPPLQPPPVNSLTTENR 29 1 J3KRR7;Q9NQC7-2;Q9NQC7 J3KRR7 CYLD Ubiquitin carboxyl-terminal hydrolase CYLD 1 0 SLT(0.002)EIS(0.018)T(0.044)DFDRS(0.245)S(0.687)PPLQPPPVNS(0.001)LT(0.001)T(0.001)ENR 49.835 0.0085837 60418000 1147 806.48 938.99 1100.5 1489.4 1263.2 1474.6 1733.9 1020.1 1182.2 TRUE FALSE FALSE 1133.019923 817.8336466 955.3327271 1227.744988 1413.39036 1182.485597 1599.852487 1784.067661 928.8597011 1151.486274 0.98396303 0.710241768 0.829651859 1.066226334 1.227448727 1.02692114 1.389380424 1.549360771 0.806661549 1 10.1692815 -7.340787433 0.805378889 0.96299408 1.875738338 0.724785656 0.131265483 0.928573938 0.464833511 0.020895036 0.736187709 4.56E-08 7.340787433 0.912744257 SLTLGPSLS(ph)LGSISGVSVK ddPTM_HeLa_Romidepsin_16h_R1 1 SLTLGPSLSLGSISGVSVK 19 0 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;A0A0J9YWK3;A0A3B3IU00;O75128-5;O75128-4 H7C1N2 COBL Protein cordon-bleu 1 0 SLT(0.001)LGPS(0.008)LS(0.974)LGS(0.016)ISGVSVK 140.28 0.00031584 5128000 2467 2546.8 2372.4 2273.4 2956.6 2491.8 1914.9 2285.3 2531.8 2264.6 TRUE FALSE FALSE 2436.931255 2582.653917 2413.690627 2536.261205 2805.713669 2332.582022 2077.551558 2351.42155 2305.349467 2205.765366 1.104800761 1.170865205 1.094264451 1.149832727 1.271990989 1.057493267 0.941873325 1.066034306 1.045147187 1 11.10706362 -6.001553268 20.29702857 1.07546557 1.100928728 0 0.089073483 0 0 0.012964689 0 9.96E-07 6.001553268 0.025463158 SLTLS(ph)FVSER ddPTM_HeLa_Romidepsin_16h_R1 1 SLTLSFVSER 10 0 Q86V48-2;Q86V48-3;Q86V48;E5RFK8 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 SLTLS(0.963)FVS(0.037)ER 101.97 0.023223 1131400 341.25 494.35 975.58 518.45 1976.2 2495.4 1336.7 1553.8 1453.7 682.87 TRUE FALSE FALSE 337.0907137 501.3094723 992.5595607 578.3956284 1875.34714 2335.951994 1450.239265 1598.756752 1323.677431 665.128939 0.506805063 0.753702693 1.492281425 0.869599253 2.8195242 3.512028806 2.180388162 2.403679434 1.99010651 1 9.377490232 -8.763581639 24.56123962 0.827400392 2.745663053 0.665609812 0.544334173 13.33706278 152914.5207 0.063462358 0.119282091 1.72E-09 8.763581639 1.91826266 SLTNDWEDHLAVK ddPTM_HeLa_Romidepsin_16h_R1 3 SLTNDWEDHLAVK 13 0 P08238;P07900-2;P07900 P08238;P07900-2 HSP90AB1;HSP90AA1 Heat shock protein HSP 90-beta;Heat shock protein HSP 90-alpha 0 0 ;; ;; 175.15 8.57E-06 155893900 12479.11 11867.31 11455.91 12083.94 13819.97 13005.84 14038.39 13357.52 14444.27 13503.94 FALSE FALSE TRUE 12327.00981 12034.3783 11655.29531 13481.142 13114.68536 12174.8088 15230.8105 13743.99877 13152.33831 13153.10569 0.937193853 0.914945761 0.886124964 1.024939837 0.997078992 0.925622365 1.157963059 1.044924225 0.999941658 1 13.68311587 -7.766232153 24.99853432 0.96319133 1.101443652 0.564433236 0.049406264 58.80710763 306738.276 0.006955453 0.021890418 1.71E-08 7.766232153 0.138252321 SLTNPT(ph)PIQQQLR ddPTM_HeLa_Romidepsin_16h_R1 3 SLTNPTPIQQQLR 13 0 Q9UJF2-2;Q9UJF2;H0Y638 Q9UJF2-2 RASAL2 Ras GTPase-activating protein nGAP 1 0 S(0.044)LT(0.001)NPT(0.955)PIQQQLR;S(0.002)LT(0.002)NPT(0.996)PIQQQLR;S(0.071)LT(0.001)NPT(0.928)PIQQQLR ;; 157.09 0.0012736 37615000 6134.2 5672.4 6194.9 7615 7598.1 6314.8 4944.3 5544.6 5531.6 5769.1 TRUE FALSE FALSE 6059.434011 5752.256196 6302.719636 8495.48213 7210.340605 5911.30466 5364.268719 5705.024253 5036.839842 5619.21795 1.078341161 1.02367558 1.121636443 1.511862007 1.283157313 1.051979957 0.954629054 1.01527015 0.89635958 1 12.45615364 -9.633423405 5.540106591 1.037432239 1.167268676 0.185885664 0.154084117 0.342403239 15.5329376 0.025571703 0.036303113 2.33E-10 9.633423405 0.129836437 SLTPAVPVESKPDK(ac)PSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLTPAVPVESKPDKPSGK 18 2 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PCH5;P20810-2;E9PSG1;H0Y944;E7EQK6;P20810-3 P20810-6;P20810-3 CAST Calpastatin 0 1 SLTPAVPVESKPDK(1)PSGK 181.81 4.88E-18 1529700 725.45 670.07 666.15 445.21 1609.1 1342.7 1050.4 1588.7 1428.1 1058.6 FALSE TRUE FALSE 716.6079364 679.503263 677.7440613 496.687275 1526.981623 1256.905803 1139.62095 1634.666528 1300.367159 1031.097419 0.694995374 0.65900976 0.657303615 0.481707417 1.480928566 1.218998108 1.105250511 1.585365744 1.26114869 1 10.00996493 -8.75088063 24.99585598 0.796256086 1.321134148 0.569421094 0.236086064 113.7790142 269348.6301 0.030806864 0.061099348 1.77E-09 8.75088063 0.524878062 SLTS(ph)SLENIFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 SLT(0.056)S(0.59)S(0.354)LENIFSR;S(0.001)LT(0.054)S(0.89)S(0.054)LENIFSR ; 286.53 9.04E-109 167084000 5969.3 5880.2 5832.6 5365.3 5405.1 5343.4 4612.6 4789.6 6384.6 5656.9 TRUE FALSE FALSE 5896.543876 5962.98161 5934.113956 5985.66123 5129.257578 5001.973985 5004.394129 4928.179519 5813.545385 5509.932923 1.070166181 1.082223993 1.076984791 1.086340127 0.930911075 0.907810323 0.908249556 0.894417335 1.055102751 1 12.42781904 -8.659545716 5.513934972 1.044842424 0.90672688 0.881320512 0.02688964 0.076524533 3.508301314 0.005446231 0.010997474 2.19E-09 8.659545716 -0.138115544 SLTSS(ph)LENIFSR ddPTM_HeLa_Romidepsin_16h_R1 2 SLTSSLENIFSR 12 0 O60343-2;O60343-3;O60343;A0A3B3IRT3;Q5JU47 O60343-2 TBC1D4 TBC1 domain family member 4 1 0 SLTS(0.025)S(0.975)LENIFSR;SLTS(0.02)S(0.98)LENIFSR ; 253.97 2.92E-63 186266000 5097.2 5031.3 5026.1 4608.1 4903 4479.3 4102.1 4417.6 5429.4 4999.2 TRUE FALSE FALSE 5035.073366 5102.130773 5113.577162 5140.910204 4652.781614 4193.087186 4450.532272 4545.416286 4943.780866 4869.320063 1.034040338 1.047811749 1.050162465 1.055775783 0.955530044 0.861123757 0.913994606 0.933480697 1.015291828 1 12.24950462 -8.554710396 4.90362849 1.024172181 0.904096417 0.855377447 0.024240016 0.059832472 3.562572151 0.004037769 0.008429719 2.79E-09 8.554710396 -0.120075764 SLTVSDDAESS(ph)EPER ddPTM_HeLa_Romidepsin_16h_R1 3 SLTVSDDAESSEPER 15 0 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 SLTVSDDAES(0.022)S(0.978)EPER;SLTVSDDAES(0.014)S(0.986)EPER;SLTVSDDAES(0.021)S(0.979)EPER ;; 274.45 1.84E-85 37922700 6270.8 7029.3 5946.9 5650.1 6289 7070 6292.7 6876 6626.2 6407.3 TRUE FALSE FALSE 6194.369078 7128.25867 6050.4033 6303.391147 5968.048863 6618.249817 6827.201781 7074.946211 6033.536076 6240.837422 0.992554149 1.142195861 0.969485806 1.01002329 0.956289751 1.06047464 1.093956038 1.133653344 0.966783088 1 12.60752391 -7.874699128 2.529498226 1.004302797 1.120567041 0.430800237 0.050089798 0.189231068 2.378966089 0.006715765 0.027576521 1.33E-08 7.874699128 0.116264244 SLVESVSS(ph)SPNK ddPTM_HeLa_Romidepsin_16h_R1 1 SLVESVSSSPNK 12 0 Q9H2U2-4;Q9H2U2-6;Q9H2U2-3;Q9H2U2;Q9H2U2-2 Q9H2U2-4 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 0 SLVESVS(0.02)S(0.911)S(0.069)PNK 193.62 2.99E-10 8580300 2942 2858.7 3142.3 1715.1 2630.3 2891 2776.3 2442.1 2719.6 3032.9 TRUE FALSE FALSE 2906.141772 2898.944854 3196.990413 1913.407932 2496.065976 2706.27443 3012.118853 2512.758311 2476.352165 2954.104821 0.983763931 0.981327688 1.082219693 0.64771159 0.844948344 0.916106433 1.019638447 0.8505989 0.838274982 1 11.5285053 SLVESVSS(ph)SPNKESNEEEQVWHFLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-4;Q9H2U2-6;Q9H2U2-3;Q9H2U2;Q9H2U2-2 Q9H2U2-4 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 0 SLVES(0.014)VS(0.075)S(0.478)S(0.426)PNKES(0.007)NEEEQVWHFLGK 72.532 0.00012419 38776000 2132.1 2294.5 2253.7 2570.7 2471.4 2394.4 2159.4 2097.9 2497.7 2267.2 TRUE FALSE FALSE 2106.113145 2326.802031 2292.924703 2867.93643 2345.275236 2241.405568 2342.819382 2158.599427 2274.299456 2208.297817 0.953726951 1.053663149 1.038322225 1.298709081 1.062028508 1.01499243 1.060916405 0.977494706 1.029888015 1 11.10871904 -10.05946941 3.01339708 0.978288889 1.080694443 0.147275696 0.083065078 0.283621594 5.0917168 0.01411149 0.017909262 8.72E-11 10.05946941 0.102405554 SLVESVSSSPNKES(ph)NEEEQVWHFLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SLVESVSSSPNKESNEEEQVWHFLGK 26 1 Q9H2U2-4;Q9H2U2-6;Q9H2U2-3;Q9H2U2;Q9H2U2-2 Q9H2U2-4 PPA2 "Inorganic pyrophosphatase 2, mitochondrial" 1 0 S(0.02)LVES(0.029)VS(0.131)S(0.121)S(0.111)PNKES(0.587)NEEEQVWHFLGK 50.029 0.010658 154620000 4138.5 4375.7 3973.7 3931.7 5158.9 4800.4 4491.3 4661.1 4696.9 4305.8 TRUE FALSE FALSE 4088.05837 4437.301219 4042.860582 4386.301653 4895.622082 4493.669933 4872.79091 4795.961575 4276.7975 4193.934695 0.974754894 1.05802821 0.963977953 1.045867895 1.167310041 1.071468742 1.161866186 1.143547032 1.019757772 1 12.03408868 -8.948285957 4.339445564 0.992749595 1.132673006 0.758864841 0.035037216 0.065759928 2.629079548 0.004818313 0.008849616 1.13E-09 8.948285957 0.139923411 SLVGT(ph)PYWMAPELISR ddPTM_HeLa_Romidepsin_16h_R1 1 SLVGTPYWMAPELISR 16 0 O96013;O96013-2;O96013-4;M0R1R1;O96013-3 O96013 PAK4 Serine/threonine-protein kinase PAK 4 1 0 S(0.027)LVGT(0.931)PY(0.041)WMAPELIS(0.001)R 108.36 0.0087196 180020000 1990.6 1764.3 1881.7 1667.8 2144.6 2064.5 1484.3 2052.1 1721.5 1646.1 TRUE FALSE FALSE 1966.337802 1789.137862 1914.450199 1860.638883 2035.153059 1932.585113 1610.376405 2111.474276 1567.524728 1603.334085 1.226405538 1.115885877 1.194043224 1.160481088 1.269325638 1.205353975 1.004392297 1.316927206 0.977665693 1 10.64685935 -12.37487842 0.908812376 0.990647814 1.184589462 0.484051715 0.081117204 0.479205225 0.651727345 0.06588049 0.014052332 4.22E-13 12.37487842 0.193941648 SLYAS(ph)SPGGVYATR ddPTM_HeLa_Romidepsin_16h_R1 2 SLYASSPGGVYATR 14 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 S(0.011)LYAS(0.495)S(0.495)PGGVYATR;SLYAS(0.89)S(0.11)PGGVYATR ; 223.58 9.50E-33 4774400000 4654.3 4381.6 4640.9 4037.4 5145.1 5109.2 4227 4796.8 4534.3 4903.3 TRUE FALSE FALSE 4597.571601 4443.28428 4721.672918 4504.223185 4882.526348 4782.738609 4586.041274 4935.58784 4128.740852 4775.911559 0.962658446 0.930353133 0.98864329 0.943112771 1.022323443 1.001429476 0.960244179 1.033433676 0.864492736 1 12.22156041 -8.744832138 24.99973682 0.975691163 1.00099756 0.132474589 0.044247521 362.9094438 546303.8424 0.004149462 0.008280565 1.80E-09 8.744832138 0.025306397 SLYASS(ph)PGGVYATR ddPTM_HeLa_Romidepsin_16h_R1 4 SLYASSPGGVYATR 14 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 SLYAS(0.48)S(0.52)PGGVYATR;SLYAS(0.063)S(0.937)PGGVYATR;SLYAS(0.022)S(0.978)PGGVYATR;SLYAS(0.015)S(0.985)PGGVYATR ;;; 258.02 8.72E-68 7345442000 51609.5 45141.7 49923.7 42133.2 56777.7 61993 51142 47369.8 46630.8 39579.9 TRUE FALSE FALSE 50980.46356 45777.20604 50792.60106 47004.83883 53880.1221 58031.84737 55486.0002 48740.37043 42460.02446 38551.60849 1.32239524 1.187426617 1.317522227 1.219270496 1.397610222 1.505302882 1.439265503 1.264288893 1.101381398 1 15.23450343 -15.60948393 0.172477423 5.86E-15 1.43851195 0.632778261 0.089013528 17.25696587 0.256666209 6.014943918 0.14491663 2.46E-16 15.60948393 1.43851195 SLYASSPGGVYATR ddPTM_HeLa_Romidepsin_16h_R1 3 SLYASSPGGVYATR 14 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 0 0 ;; ;; 203.03 1.67E-16 19015800 3147.92 2192.41 3248.54 2390.46 3038.35 3412.21 3234.32 2634.64 2883.99 2427.97 FALSE FALSE TRUE 3109.55194 2223.274806 3305.079476 2666.856233 2883.291662 3194.180793 3509.04306 2710.869152 2626.038711 2364.890989 1.314881724 0.940117247 1.397561025 1.127686749 1.219207006 1.350667243 1.483807531 1.146297721 1.11042696 1 11.20755797 -15.7220146 0.243317414 6.41E-15 1.295570163 0.213857174 0.148019098 29.01763598 0.538283529 14.04476596 0.093152058 1.90E-16 15.7220146 1.295570163 SLYGDVDS(ph)PLPTGEAGGPPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SLYGDVDSPLPTGEAGGPPSTR 22 0 Q9Y4B5;Q9Y4B5-2;Q9Y4B5-3;J3QL92 Q9Y4B5 MTCL1 Microtubule cross-linking factor 1 1 0 SLYGDVDS(0.999)PLPT(0.001)GEAGGPPSTR 122.1 6.55E-05 12019000 1107.6 939.34 1157.4 1277.5 1368.5 1396 1399.8 1749.2 1289.4 1099.6 TRUE FALSE FALSE 1094.100145 952.5640532 1177.544061 1425.210561 1298.660338 1306.800105 1518.698977 1799.810342 1174.072835 1071.032233 1.021538018 0.889388782 1.099447827 1.330688766 1.212531517 1.220131444 1.41797691 1.680444608 1.096206816 1 10.06478618 -4 0.339961439 0.989157702 8.578943425 0.823718509 0.092473333 14.03725249 0.177140841 0.027490835 68.53811327 1.00E-04 4 7.589785723 SMDAMS(ph)SPTKTETVK ddPTM_HeLa_Romidepsin_16h_R1 1 SMDAMSSPTKTETVK 15 1 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 S(0.029)MDAMS(0.483)S(0.483)PT(0.003)KT(0.001)ETVK 89.992 0.0073186 6665700 2982.4 2891.2 3137.1 3114.6 2831.5 2507.7 2159.9 2746.3 3291.7 3200.9 TRUE FALSE FALSE 2946.049362 2931.902389 3191.69991 3474.724707 2686.997989 2347.466063 2343.361852 2825.759858 2997.282108 3117.740157 0.944931012 0.94039344 1.023722231 1.114501059 0.861841544 0.752938329 0.751621923 0.906348738 0.961363666 1 11.60628498 -8.53507589 24.10916222 0.983701358 0.799927383 0.66971764 0.062225766 65.38952566 129250.144 0.009117092 0.018246201 2.92E-09 8.53507589 -0.183773975 SMEAEMIQLQEELAAAER ddPTM_HeLa_Romidepsin_16h_R1 1 SMEAEMIQLQEELAAAER 18 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 90.476 0.027866 10630000 863.4 974.09 659.05 759.03 976.79 1074.4 732.49 1016 771.57 802.71 FALSE FALSE TRUE 852.8765487 987.8032646 670.5204888 846.7926199 926.9407614 1005.749307 794.7076823 1045.396357 702.5588468 781.8554785 1.09083657 1.263409021 0.857601574 1.083055172 1.185565347 1.286362167 1.016438081 1.33707109 0.898578914 1 9.610758148 -4 0.16847552 0.998279051 1.960897097 0.304593548 0.129619512 65.57004022 0.684978655 0.183961104 15.95504197 1.00E-04 4 0.962618045 SMGSQEDDSGNKPSSYS(ph) ddPTM_HeLa_Romidepsin_16h_R1 1 SMGSQEDDSGNKPSSYS 17 1 H7C3P9;Q9UNS2-2;Q9UNS2 H7C3P9 COPS3 COP9 signalosome complex subunit 3 1 0 SMGSQEDDSGNKPS(0.058)S(0.206)YS(0.736) 95.954 0.020089 7417000 3226.9 3261.9 3624.3 3273.1 3319.8 3083.1 2344.2 2646.8 3746.2 2943.5 TRUE FALSE FALSE 3187.569302 3307.821114 3687.379421 3651.551222 3150.378218 2886.09986 2543.316289 2723.380982 3411.130489 2867.027446 1.111802856 1.153745884 1.286133283 1.273636647 1.098830855 1.006652331 0.887091714 0.949897074 1.189779503 1 11.48534 -8.032074225 3.286606502 1.098963481 0.919941967 0.450923059 0.094394885 0.233466616 5.12493883 0.016289027 0.050601446 9.29E-09 8.032074225 -0.179021514 SMGTGDTPGLEVPS(ph)SPLRK ddPTM_HeLa_Romidepsin_16h_R1 3 SMGTGDTPGLEVPSSPLRK 19 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 SMGTGDT(0.002)PGLEVPS(0.499)S(0.499)PLRK;S(0.001)MGT(0.004)GDT(0.408)PGLEVPS(0.426)S(0.161)PLRK;SMGTGDTPGLEVPS(0.523)S(0.477)PLRK ;; 129.43 0.00063825 366638000 11756.6 12264.2 11656.2 9741.6 9347.6 8895.1 7522.2 8670.9 13264.9 12496.8 TRUE FALSE FALSE 11613.30604 12436.85573 11859.07127 10867.96963 8870.557091 8326.731818 8161.13548 8921.778811 12078.45412 12172.13133 0.954089774 1.021748401 0.974280588 0.89285675 0.728759561 0.684081661 0.670477113 0.732967676 0.99230396 1 13.57129418 -8.852339504 2.270081352 0.981426695 0.692280629 0.971914645 0.022869371 0.037238545 0.390476751 0.003919664 0.008041678 1.40E-09 8.852339504 -0.289146066 SMGTGDTPGLEVPSS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 4 SMGTGDTPGLEVPSSPLR 18 0 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 SMGTGDTPGLEVPS(0.244)S(0.756)PLR;SMGTGDTPGLEVPS(0.239)S(0.761)PLR;SMGTGDTPGLEVPS(0.006)S(0.994)PLR;SMGTGDTPGLEVPS(0.047)S(0.953)PLR ;;; 200.33 1.45E-20 163915000 19008.6 18346.1 17580.7 15057.1 14048.7 12975.6 11522.5 11406.5 20513.3 19498.7 TRUE FALSE FALSE 18776.91587 18604.37688 17886.68471 16798.07275 13331.74242 12146.50104 12501.22086 11736.52908 18678.53907 18992.12096 0.988668717 0.97958395 0.941795008 0.884475872 0.701961747 0.639554743 0.658231952 0.61796832 0.983488843 1 14.21311341 -8.848005145 1.458601027 0.992891824 0.631566674 0.989745967 0.015742418 0.024173482 0.103325408 0.002387102 0.005615125 1.42E-09 8.848005145 -0.361325151 SMIGMSTKLWK ddPTM_HeLa_Romidepsin_16h_R1 1 SMIGMSTKLWK 11 1 G5E9Z2;Q96KA5-2 G5E9Z2 CLPTM1L 0 0 68.371 0.0040387 0 486.14 782.01 684.3 553.21 640.13 634.28 367.1 589.85 691.28 696.79 FALSE FALSE TRUE 480.2147387 793.0191573 696.2099544 617.1747431 607.4617774 593.751555 398.2814648 606.9163791 629.4501855 678.6872954 0.707564061 1.168460295 1.025818458 0.909365399 0.895053999 0.87485291 0.586840902 0.894250391 0.927452436 1 9.406603197 -7.970056893 24.49709887 0.900107394 0.73812068 0.219735912 0.135273455 232.9060997 190542.4307 0.021914152 0.065741204 1.07E-08 7.970056893 -0.161986714 SMMS(ph)PMADR ddPTM_HeLa_Romidepsin_16h_R1 4 SMMSPMADR 9 0 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 S(0.011)MMS(0.989)PMADR;S(0.043)MMS(0.957)PMADR;S(0.011)MMS(0.989)PMADR;S(0.154)MMS(0.846)PMADR ;;; 58.596 0.019805 63882000 15481.1 15505 13894.9 10205.6 17720.8 20553.1 17002.2 19108.4 15649 14681.8 TRUE FALSE FALSE 15292.4104 15723.2798 14136.73491 11385.61949 16816.44145 19239.82324 18446.36644 19661.27141 14249.31425 14300.36472 1.069372054 1.099502013 0.988557648 0.796176861 1.175944934 1.34540787 1.289922796 1.374879018 0.996430128 1 13.80376432 -8.524322664 24.99956902 1.019231751 1.32015875 0.784592301 0.080676863 17.51476327 303245.2479 0.012158228 0.02446493 2.99E-09 8.524322664 0.300926999 SMMS(ph)PMAER ddPTM_HeLa_Romidepsin_16h_R1 1 SMMSPMAER 9 0 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;H7C1M2 P18583-6 SON Protein SON 1 0 S(0.306)MMS(0.694)PMAER 48.188 0.02422 23113000 1012.7 936.63 843.7 577.03 911.19 1028.7 1032.4 965.21 874.56 784.93 TRUE FALSE FALSE 1000.356823 949.8159017 858.3842446 643.7489236 864.6885742 962.96939 1120.09203 993.1368285 796.3371632 764.5374054 1.308447194 1.242340656 1.122749833 0.842011024 1.130995773 1.259545162 1.465058508 1.299003582 1.041593462 1 9.578443278 -8.04081353 3.662191216 1.130874583 1.381364929 0.428796472 0.129330226 0.212336802 5.880355959 0.022309713 0.066412687 9.10E-09 8.04081353 0.250490347 SMPPSLET(ph)SPITDTDLAK ddPTM_HeLa_Romidepsin_16h_R1 2 SMPPSLETSPITDTDLAK 18 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 S(0.008)MPPS(0.219)LET(0.544)S(0.228)PITDTDLAK;S(0.001)MPPS(0.314)LET(0.342)S(0.333)PIT(0.009)DTDLAK ; 131.61 0.0038243 13368200 4034.1 3562.8 4339.1 2842.3 3154.9 3480.2 2864.4 3766.5 4067 4235.9 TRUE FALSE FALSE 3984.930838 3612.957192 4414.620215 3170.940099 2993.89368 3257.826452 3107.702065 3875.477735 3703.237334 4125.850707 0.965844651 0.875687815 1.069990295 0.768554251 0.725642757 0.789613266 0.753226979 0.939316037 0.897569398 1 12.0104759 -9.247874263 24.7614299 0.979498315 0.78875237 0.553047956 0.0738969 312.5026699 570434.818 0.009844897 0.016266463 5.65E-10 9.247874263 -0.190745946 SMS(ph)DVSAEDVQNLR ddPTM_HeLa_Romidepsin_16h_R1 6 SMSDVSAEDVQNLR 14 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;E9PJ10;E9PK58;E9PLU6 E9PMS6 LMO7 LIM domain only protein 7 1 0 SMS(1)DVSAEDVQNLR;S(0.009)MS(0.991)DVSAEDVQNLR;S(0.342)MS(0.658)DVSAEDVQNLR;S(0.072)MS(0.928)DVSAEDVQNLR;S(0.08)MS(0.92)DVSAEDVQNLR;S(0.216)MS(0.784)DVSAEDVQNLR ;;;;; 190.34 6.68E-11 115148000 12483.6 14194.3 12946 12748 13706 13222.3 10368.4 11120.9 13120.2 12732.8 TRUE FALSE FALSE 12331.44508 14394.12773 13171.3197 14221.98374 13006.53168 12377.4377 11249.09164 11442.6657 11946.69645 12402.00002 0.994311003 1.160629552 1.062031904 1.146749211 1.048744691 0.998019487 0.907038511 0.922646805 0.963287892 1 13.59828518 -7.867582872 3.841738049 1.02911318 0.914235504 0.400141603 0.062649313 0.206194886 5.646418327 0.009774383 0.033344572 1.36E-08 7.867582872 -0.114877677 SMSQVDVDS(ph)GIENMEVDENDRR ddPTM_HeLa_Romidepsin_16h_R1 1 SMSQVDVDSGIENMEVDENDRR 22 1 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 0 S(0.055)MS(0.062)QVDVDS(0.883)GIENMEVDENDRR 42.052 0.028833 11818000 1583.8 1918.9 1567.7 1476.1 1964.4 1710.6 1474.8 1889.9 1838.3 1802.8 TRUE FALSE FALSE 1564.496036 1945.914325 1594.985161 1646.773627 1864.149338 1601.298181 1600.069475 1944.581275 1673.877844 1755.962996 0.890961848 1.108175018 0.908325041 0.937817956 1.061610832 0.911920231 0.911220498 1.107415862 0.953253484 1 10.77804673 -7.249811874 24.22885997 0.958039518 1.107416001 0.276767985 0.068374075 1152.117229 2400660.504 0.009549425 0.198365101 5.63E-08 7.249811874 0.149376482 SMSSIPPYPASSLASSS(ph)PPGSGR ddPTM_HeLa_Romidepsin_16h_R1 3 SMSSIPPYPASSLASSSPPGSGR 23 0 A0A2R8Y7R9;Q13136-2;Q13136;H0YDW2 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 SMSSIPPYPAS(0.007)S(0.007)LAS(0.195)S(0.195)S(0.595)PPGSGR;SMSSIPPYPAS(0.021)S(0.021)LAS(0.189)S(0.189)S(0.578)PPGS(0.004)GR;SMSSIPPYPAS(0.221)S(0.221)LAS(0.108)S(0.108)S(0.341)PPGSGR ;; 149.72 9.11E-17 43199000 10729.8 10573.8 10324.6 8942.3 13451.4 16601.6 15075.2 16245.2 10886.6 11392.1 TRUE FALSE FALSE 10599.02107 10722.65823 10504.29533 9976.250801 12764.92486 15540.81134 16355.68711 16715.22923 9912.87523 11096.1316 0.955199655 0.966342021 0.946662829 0.899074665 1.150394149 1.400561196 1.473999021 1.506401495 0.893363164 1 13.43776918 -8.344886926 2.233069203 0.969645424 1.484496519 0.969142019 0.04118352 0.032859964 0.316484318 0.005367462 0.014967356 4.52E-09 8.344886926 0.514851095 SMTEAEQQQLIDDHFLFDKPVS(ph)PLLLASGMAR ddPTM_HeLa_Romidepsin_16h_R1 1 SMTEAEQQQLIDDHFLFDKPVSPLLLASGMAR 32 1 P12277;G3V4N7 P12277 CKB Creatine kinase B-type 1 0 SMTEAEQQQLIDDHFLFDKPVS(0.959)PLLLAS(0.041)GMAR 55.984 0.00034623 25901000 813.04 709.9 816.85 943.98 981.77 1171.9 1243.6 1087.8 1055.1 945.38 TRUE FALSE FALSE 803.1303558 719.8939908 831.0669316 1053.127409 931.6666134 1097.019372 1349.231353 1119.273777 960.7292135 920.8188913 0.872191441 0.781797591 0.90253028 1.143685712 1.011780516 1.19135194 1.465251599 1.215519998 1.043342206 1 9.846773622 -8.354821271 1.158757372 0.926572431 1.352647843 0.669741161 0.108470972 0.224503208 0.542658068 0.016885772 0.070989491 4.42E-09 8.354821271 0.426075412 SNEDS(ph)LILEK ddPTM_HeLa_Romidepsin_16h_R1 3 SNEDSLILEK 10 0 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 0 S(0.137)NEDS(0.863)LILEK;SNEDS(1)LILEK;S(0.013)NEDS(0.987)LILEK ;; 127.3 0.0084954 29697100 9236.5 8944.8 9434.1 6925 7506.7 7616.8 6329.6 6642.1 9872.3 8393.2 TRUE FALSE FALSE 9123.921985 9070.725129 9598.296553 7725.701083 7123.605088 7130.111062 6867.236066 6834.278684 8989.296762 8175.143454 1.116056499 1.109549353 1.174082951 0.945023305 0.871373711 0.872169535 0.840014136 0.835982723 1.099588871 1 12.99702833 -9.000271545 3.919232546 1.06943945 0.857241396 0.85357605 0.047214581 0.085108876 2.962908764 0.009167655 0.01649668 9.99E-10 9.000271545 -0.212198053 SNEDVNS(ph)SELDEEYLIELEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNEDVNSSELDEEYLIELEK 20 0 Q99614 Q99614 TTC1 Tetratricopeptide repeat protein 1 1 0 S(0.01)NEDVNS(0.495)S(0.495)ELDEEYLIELEK 72.946 0.0032452 1140600 256.96 506.94 357.02 349.92 353.72 429.6 491.34 519.29 406.25 348.59 TRUE FALSE FALSE 253.8280727 514.0767146 363.2337833 390.3793968 335.6683485 402.1499465 533.0744073 534.3148368 369.9139825 339.5335815 0.747578698 1.514067363 1.069802232 1.149751948 0.988616051 1.184418768 1.570019687 1.573673021 1.089476867 1 8.407410461 -4.145788068 0.305502644 0.895769703 7.115029002 0.379816114 0.207644843 26.15490822 0.363768521 0.080279379 89.33133888 7.15E-05 4.145788068 6.219259299 SNEEEET(ph)SDSSLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNEEEETSDSSLEK 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 SNEEEET(0.425)S(0.425)DS(0.118)S(0.033)LEK 138.81 7.47E-05 0 1143 1120.6 972 1098.5 1104.8 1051.2 928.05 1113.6 1274.6 1175.5 TRUE FALSE FALSE 1129.068676 1136.375836 988.9172523 1225.513739 1048.417933 984.0317126 1006.878544 1145.820259 1160.596584 1144.960341 0.986120337 0.992502357 0.863713106 1.07035475 0.915680567 0.859446112 0.879400367 1.000751047 1.013656581 1 10.16108191 -9.349988206 0.610126402 0.996598703 0.912119399 0.185628174 0.062434232 0.953818252 0.696097832 0.014301753 0.035548523 4.47E-10 9.349988206 -0.084479304 SNEEGSEEK(ac)GPEVR ddPTM_HeLa_Romidepsin_16h_R1 2 SNEEGSEEKGPEVR 14 1 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 1 ; SNEEGSEEK(1)GPEVR;SNEEGSEEK(1)GPEVR 252.08 1.78E-55 3307100 612.45 447.72 452.79 285.089 1030.95 931.36 940.04 815.21 1199.41 1158.55 FALSE TRUE FALSE 604.9852238 454.0230139 460.67062 318.0523316 978.3367745 871.8491018 1019.886974 838.7968152 1092.131766 1128.450704 0.536120206 0.402341912 0.408232826 0.281848671 0.866973427 0.772607167 0.903793999 0.743317198 0.967815219 1 10.14012768 SNGELSES(ph)PGAGK ddPTM_HeLa_Romidepsin_16h_R1 1 SNGELSESPGAGK 13 0 E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-4;Q12830;A0A0A0MR81;F5GXF5;Q12830-2;F5H176 E7ETD6 BPTF Nucleosome-remodeling factor subunit BPTF 1 0 SNGELS(0.005)ES(0.995)PGAGK 155.37 0.00071084 36238000 7563.8 6974.9 7564.7 4970.9 4637.9 4397.4 3869.7 4139.8 7207.6 6770.4 TRUE FALSE FALSE 7471.609496 7073.092825 7696.36043 5545.658847 4401.210657 4116.420332 4198.392221 4259.578581 6562.934204 6594.504032 1.133005524 1.072573887 1.167087076 0.84095162 0.667405863 0.624219852 0.636650186 0.645928573 0.995212706 1 12.68704844 -8.981407205 2.89606382 1.072109576 0.640386997 0.937484929 0.052286424 0.050718256 0.868207141 0.009240326 0.017249226 1.04E-09 8.981407205 -0.43172258 SNGVTPGTQSS(ph)PAPSTR ddPTM_HeLa_Romidepsin_16h_R1 2 SNGVTPGTQSSPAPSTR 17 0 Q8TDW5;Q8TDW5-2 Q8TDW5 SYTL5 Synaptotagmin-like protein 5 1 0 SNGVT(0.002)PGT(0.024)QS(0.222)S(0.752)PAPSTR;SNGVTPGTQS(0.068)S(0.905)PAPS(0.013)T(0.013)R ; 228.26 5.70E-36 8113200 4316.2 3798.2 4819.4 4456.26 4367.9 4220.9 3430.77 4125.5 4697 4712 TRUE FALSE FALSE 4263.592494 3851.671159 4903.279635 4971.513749 4144.989764 3951.198112 3722.179518 4244.864834 4276.888556 4589.581561 0.928971942 0.839220549 1.068350038 1.083217213 0.903130211 0.860905958 0.811006291 0.924891469 0.931868951 1 12.16414691 -8.532553021 24.97549596 0.971755531 0.863787784 0.334019296 0.070757828 180.2214476 465265.9676 0.010632569 0.021286517 2.93E-09 8.532553021 -0.107967747 SNILSDNPDFS(ph)DEADIIK ddPTM_HeLa_Romidepsin_16h_R1 1 SNILSDNPDFSDEADIIK 18 0 O75717-2;O75717 O75717-2 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 0 SNILSDNPDFS(1)DEADIIK 192.62 1.22E-14 1617500 869.43 947.33 603.34 901.26 888.93 643.77 582.62 637.67 935.14 806.53 TRUE FALSE FALSE 858.8330527 960.6665366 613.8408796 1005.467922 843.564585 602.6351747 632.1077283 656.1199754 851.4987363 785.5762343 1.093252335 1.222881364 0.78138932 1.279911329 1.073816325 0.767125008 0.804642122 0.835208534 1.08391611 1 9.617607475 -8.264202652 24.63761606 1.058398447 0.802556902 0.491821568 0.126766156 124.7895031 1112644.538 0.016948815 0.039589218 5.44E-09 8.264202652 -0.255841545 SNIS(ph)PNFNFMGQLLDFER ddPTM_HeLa_Romidepsin_16h_R1 2 SNISPNFNFMGQLLDFER 18 0 F8VW29;Q16828-2;Q16829-2;Q16828;Q99956;Q16829 F8VW29 DUSP6;DUSP7;DUSP9 Dual specificity protein phosphatase 6;Dual specificity protein phosphatase 7;Dual specificity protein phosphatase 9 1 0 S(0.002)NIS(0.998)PNFNFMGQLLDFER;S(0.03)NIS(0.97)PNFNFMGQLLDFER ; 99.011 0.0031137 16432500 1965.3 2093.99 2268.5 3888.4 5012.1 4394.3 3434.9 4196 2297.39 1930.25 TRUE FALSE FALSE 1941.346168 2123.469246 2307.982291 4337.995103 4756.313834 4113.518412 3726.66032 4317.40464 2091.905684 1880.101827 1.032575013 1.129443744 1.227583665 2.307319232 2.529817144 2.187923204 1.982158768 2.296367451 1.112655525 1 10.87659509 -9.324934659 3.930299099 1.030661227 2.260270237 0.94764687 0.136446011 0.036179816 1.120994829 0.022385974 0.035328627 4.73E-10 9.324934659 1.22960901 up SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 SAPAPKKGSK 10 2 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 2 ; SAPAPK(1)K(1)GSK;SAPAPK(1)K(1)GSK 118.9 0.0054002 231100000 949.22 675.92 1303.19 4571.4 20816.7 31855 33002 24201 428.19 727.4 FALSE TRUE FALSE 937.6505415 685.4356195 1325.871475 5099.966777 19754.34612 29819.56831 35805.18906 24901.21775 389.891614 708.5020431 1.323426729 0.967443392 1.871372832 7.198238631 27.88184778 42.08818958 50.5364655 35.14628926 0.550304149 1 9.468628203 -8.637187698 1.957378948 1.160398078 43.74500225 0.964792702 3.53829511 0.035987525 0.277923281 0.48611078 1.167363348 2.31E-09 8.637187698 42.58460418 up SNNWS(ph)LEDVTASDK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 SNNWS(0.959)LEDVT(0.041)ASDK 142.4 0.00071844 18368000 2623.2 2535.9 2933.1 1906.8 1816.8 1718 1505.7 1498.4 2692.4 2712.6 TRUE FALSE FALSE 2591.227429 2571.600467 2984.149375 2127.273188 1724.081917 1608.225345 1633.59412 1541.75384 2451.585001 2642.126261 0.980735655 0.973307182 1.129449951 0.80513684 0.652535778 0.60868603 0.618287682 0.583527692 0.927883363 1 11.3674837 -8.93938186 2.929810232 0.998411081 0.612693553 0.922253548 0.052759425 0.042191828 0.736873092 0.006895272 0.013089246 1.15E-09 8.93938186 -0.385717528 SNNWSLEDVT(ph)ASDK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 SNNWS(0.002)LEDVT(0.992)AS(0.006)DK 282.09 1.49E-96 20687000 4378.7 4863.9 5128.2 3031.9 2838.7 3162 2466.8 2583.8 4749.1 4741.7 TRUE FALSE FALSE 4325.33072 4932.374112 5217.45417 3382.462544 2693.830546 2959.958405 2676.32993 2658.558176 4324.328602 4618.50995 0.936520819 1.067957884 1.129683432 0.732370955 0.583268321 0.640890338 0.579479087 0.575631146 0.93630384 1 12.17321176 -9.058182082 4.410275974 0.988563365 0.601320715 0.916528574 0.059926273 0.049093613 1.950109498 0.009823086 0.016942523 8.75E-10 9.058182082 -0.38724265 SNPTPMEPT(ph)SPGEHQQNSK ddPTM_HeLa_Romidepsin_16h_R1 1 SNPTPMEPTSPGEHQQNSK 19 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 0 SNPT(0.008)PMEPT(0.496)S(0.496)PGEHQQNSK 86.8 0.0023017 6320900 2223.5 1773.4 1786.2 1685.5 1704.3 1793.1 1709.7 1574.3 2487.8 2362.2 TRUE FALSE FALSE 2196.399127 1798.365972 1817.288062 1880.385441 1617.323211 1678.526697 1854.921875 1619.849887 2265.284937 2300.829703 0.954611775 0.781616288 0.789840317 0.817264067 0.702930429 0.729531045 0.806196944 0.704028588 0.984551327 1 11.16793849 -10.26410349 1.937719727 0.983791689 0.75705431 0.87138589 0.038461865 0.075986463 0.539902203 0.007102389 0.008413725 5.44E-11 10.26410349 -0.22673738 SNPTPMEPTS(ph)PGEHQQNSK ddPTM_HeLa_Romidepsin_16h_R1 1 SNPTPMEPTSPGEHQQNSK 19 0 E7EUR8;A0A1B0GVL4;P78312-4;P78312-6;P78312-2;P78312-5;P78312 E7EUR8 FAM193A Protein FAM193A 1 0 SNPT(0.003)PMEPT(0.075)S(0.923)PGEHQQNSK 99.964 0.00040955 4428400 1407.6 1285.5 1188.7 1371.8 1081.6 1070.3 780.86 1011.4 1794.3 1525.2 TRUE FALSE FALSE 1390.44363 1303.597303 1209.388825 1530.413971 1026.401916 1001.911284 847.1862289 1040.663263 1633.813314 1485.575084 0.935963214 0.877503478 0.814087984 1.030182848 0.690912177 0.674426554 0.570274931 0.700512061 1.099785081 1 10.53680581 -8.683030903 5.717578932 0.952006407 0.648492895 0.76837461 0.08087577 0.065045445 3.573817551 0.010298542 0.020724981 2.07E-09 8.683030903 -0.303513512 SNQSLGWGDS(ph)SKPVSSPDWNK ddPTM_HeLa_Romidepsin_16h_R1 2 SNQSLGWGDSSKPVSSPDWNK 21 1 Q8NDV7-2;Q8NDV7-6;Q8NDV7-5;Q8NDV7 Q8NDV7-2 TNRC6A Trinucleotide repeat-containing gene 6A protein 1 0 S(0.001)NQS(0.007)LGWGDS(0.301)S(0.237)KPVS(0.207)S(0.246)PDWNK;SNQS(0.004)LGWGDS(0.483)S(0.483)KPVS(0.026)S(0.004)PDWNK ; 67.579 0.0028045 23820000 3394.6 2808.2 3426.5 2252.7 3075.7 3015.3 2879 2840.9 3020.7 2962.6 TRUE FALSE FALSE 3353.22531 2847.733913 3486.136795 2513.167773 2918.735552 2822.632061 3123.542188 2923.096959 2750.521027 2885.631225 1.162042218 0.98686689 1.20810198 0.870924792 1.011472127 0.978167978 1.082446766 1.012983549 0.953178287 1 11.49467122 -9.260147182 24.99995797 1.079284849 0.996670701 0.122458241 0.08841368 162.3884033 3141690.657 0.013156644 0.021076018 5.49E-10 9.260147182 -0.082614148 SNS(ph)APLIHGLSDT(ph)SPVFQAEAPSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 2 0 S(0.42)NS(0.579)APLIHGLS(0.027)DT(0.506)S(0.467)PVFQAEAPS(0.001)AR 61.583 0.0012214 0 553.24 470.9 466.22 595.66 693.87 644.09 630.81 835.98 566.87 491.13 TRUE FALSE FALSE 546.4968981 477.5293426 474.3343635 664.5330119 658.4592247 602.9347277 684.3909857 860.1677623 516.1677274 478.3703718 1.142413766 0.998241887 0.991563005 1.389160055 1.376463225 1.260393125 1.430671768 1.798120898 1.079012744 1 8.901984228 -4 0.326966938 1.036778078 8.259853795 0.805271367 0.108263448 16.61401807 0.211207395 0.036881742 73.28950561 1.00E-04 4 7.223075716 SNS(ph)APLIHGLSDTSPVFQAEAPSAR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSAPLIHGLSDTSPVFQAEAPSAR 25 0 Q96E09 Q96E09 FAM122A Protein FAM122A 1 0 S(0.269)NS(0.731)APLIHGLSDTSPVFQAEAPSAR;S(0.203)NS(0.788)APLIHGLS(0.009)DTSPVFQAEAPSAR ; 97.106 9.33E-06 194408000 5411.8 5349.2 4974.7 4568.2 7652.7 8235.1 7427.8 8340 7339.8 6377.9 TRUE FALSE FALSE 5345.8389 5424.506178 5061.282567 5096.396778 7262.154163 7708.903688 8058.717147 8581.304742 6683.309905 6212.201239 0.860538591 0.873201941 0.814732552 0.82038501 1.169014635 1.240929486 1.297240195 1.381362968 1.075836028 1 12.60088885 -8.565625114 3.298949916 0.910708849 1.29955192 0.825203314 0.083599792 0.073298609 1.640634104 0.012338023 0.027094381 2.72E-09 8.565625114 0.388843071 SNS(ph)DESNFSEK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSDESNFSEK 11 0 A0A087WWW9;O95999 A0A087WWW9 BCL10 B-cell lymphoma/leukemia 10 1 0 S(0.329)NS(0.544)DES(0.002)NFS(0.124)EK;SNS(0.717)DES(0.272)NFS(0.011)EK ; 158.31 0.001639 21443900 2825.2 3016.1 2442.14 2610.3 4419.2 5013.7 4533.2 5386.4 3547.5 2975.4 TRUE FALSE FALSE 2790.765376 3058.560735 2484.644422 2912.115168 4193.671734 4693.340751 4918.249895 5542.246986 3230.202715 2898.098679 0.962964234 1.055368044 0.857336032 1.004836443 1.447042423 1.619455122 1.69706088 1.912373456 1.114593764 1 11.500891 -8.492994595 1.637830835 0.974960374 1.783941354 0.932584181 0.090927707 0.05480402 0.286973292 0.01175818 0.033839115 3.21E-09 8.492994595 0.80898098 HAPS(ph)PEPAVQGTGVAGVPEESGDAAAIPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 HAPSPEPAVQGTGVAGVPEESGDAAAIPAKK 31 1 P13051 P13051 UNG Uracil-DNA glycosylase 1 0 HAPS(1)PEPAVQGTGVAGVPEESGDAAAIPAKK 85.002 7.17E-09 19356000 963.36 1143.4 946.53 768.29 623.13 738.21 381.31 456.29 1166 1185.8 TRUE FALSE FALSE 951.6181978 1159.496815 963.0039576 857.1233047 591.3293509 691.0407635 413.6984619 469.4920312 1061.71004 1154.992745 0.823917035 1.003899652 0.833774897 0.742102761 0.51197668 0.598307449 0.358182736 0.40648916 0.919235246 1 10.17366807 -8.690787128 0.79439649 0.929864636 0.365030463 0.896741017 0.072583499 0.186360724 0.208833898 0.015148019 0.060725729 2.04E-09 8.690787128 -0.564834173 down SNS(ph)FNNPLGNR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSFNNPLGNR 11 0 O95835;O95835-2 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 S(0.065)NS(0.935)FNNPLGNR;S(0.067)NS(0.933)FNNPLGNR ; 141.73 0.0028439 12084400 3666.1 2803.16 3333.7 2613.8 3122.7 1973.17 2662.49 2549.77 3754.1 2984 TRUE FALSE FALSE 3621.416163 2842.62296 3391.72165 2916.019854 2963.336967 1847.090805 2888.641834 2623.543572 3418.323894 2906.47525 1.24598211 0.978031022 1.166953564 1.00328391 1.019563806 0.635508871 0.993864247 0.902654709 1.176106314 1 11.50505491 -8.683745184 2.347378139 1.107822 0.85896698 0.461515491 0.118585663 0.215554271 2.412089111 0.019365836 0.042926374 2.07E-09 8.683745184 -0.24885502 SNS(ph)GLGGEVSGVMSKPNVDPQPWFQDGPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSGLGGEVSGVMSKPNVDPQPWFQDGPK 29 1 C9JRJ5;Q9UGP4 C9JRJ5 LIMD1 LIM domain-containing protein 1 1 0 S(0.031)NS(0.476)GLGGEVS(0.109)GVMS(0.384)KPNVDPQPWFQDGPK 57.985 0.0025676 13002000 2919.8 3738.5 1955.5 2252 2616.7 1956.5 1451.1 1808.8 2415.9 2910 TRUE FALSE FALSE 2884.212355 3791.130701 1989.534657 2512.386836 2483.160035 1831.485964 1574.356398 1861.134774 2199.815853 2834.39778 1.017575012 1.337543632 0.701924998 0.88639176 0.876080292 0.646164055 0.555446525 0.656624411 0.776114019 1 11.46882653 -8.602522918 0.89772834 1.023009268 0.577682767 0.455393413 0.162213842 0.339024249 0.491735632 0.023457213 0.09362202 2.50E-09 8.602522918 -0.445326501 SNS(ph)GRELTDEEILASVMIK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSGRELTDEEILASVMIK 19 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 S(0.015)NS(0.901)GRELT(0.084)DEEILASVMIK 84.156 0.0073066 48017000 2287.1 2578.7 1917.2 2581.2 2732.5 2671.8 2050.2 2314.6 2705.5 2774.9 TRUE FALSE FALSE 2259.223945 2615.003006 1950.568062 2879.650489 2593.050329 2501.080603 2224.343937 2381.569299 2463.513304 2702.807698 0.835880387 0.967513526 0.721682147 1.065429291 0.959391351 0.925363874 0.822975285 0.88114641 0.911464514 1 11.40024315 -12.5484819 1.315539664 1.000000093 0.892012949 0.024620208 0.092434765 0.630955598 1.956123858 0.060466731 0.014325521 2.83E-13 12.5484819 -0.107987144 SNS(ph)IDGSNVTVTPGPGEQTVDVEPR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSIDGSNVTVTPGPGEQTVDVEPR 25 0 Q05GC8;Q96PN7-2;Q96PN7-3;Q96PN7-4;Q96PN7-5;Q96PN7 Q05GC8 BCAR2;TRERF1 Transcriptional-regulating factor 1 1 0 S(0.162)NS(0.76)IDGS(0.078)NVTVTPGPGEQTVDVEPR;S(0.188)NS(0.784)IDGS(0.028)NVT(0.001)VTPGPGEQTVDVEPR ; 127.77 6.06E-07 12261700 2293.7 2309 2113.55 2008.95 2328.4 2097.5 1731.29 2040.5 2661.7 2490.7 TRUE FALSE FALSE 2265.743502 2341.506163 2150.335451 2241.234251 2209.57306 1963.476519 1878.345729 2099.538648 2423.630886 2425.991255 0.933945453 0.965175022 0.88637395 0.923842675 0.910791849 0.809350205 0.774259069 0.865435374 0.99902705 1 11.24435863 -7.995084844 0.252609441 1.000383796 0.697714745 0.747091922 0.035856002 2.517174416 0.177182338 0.028367599 0.233981809 1.01E-08 7.995084844 -0.302669052 SNS(ph)KDIQNLSVGLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SNSKDIQNLSVGLPR 15 1 A0A1B0GTX4;A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A1B0GTX4 CDKL5 Cyclin-dependent kinase-like 5 1 0 S(0.011)NS(0.989)KDIQNLSVGLPR 120.08 0.023545 6827400 685.19 593.89 828.94 701.19 1244.8 1476.8 1011.5 1356 797.11 657.1 TRUE FALSE FALSE 676.8386407 602.250799 843.367353 782.264887 1181.273211 1382.437246 1097.416785 1395.233721 725.8144852 640.0284473 1.057513371 0.940975048 1.317702919 1.222234559 1.845657355 2.159962189 1.714637512 2.179955792 1.134034727 1 9.32199222 -8.831424252 1.710187817 1.033576787 2.012164309 0.88105226 0.156070769 0.073173131 0.433384738 0.021759026 0.048653184 1.47E-09 8.831424252 0.978587522 SNS(ph)LPHPAGGGK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSLPHPAGGGK 12 0 G5E9A7;Q09019 G5E9A7 DMWD Dystrophia myotonica WD repeat-containing protein 1 0 S(0.001)NS(0.999)LPHPAGGGK;S(0.013)NS(0.987)LPHPAGGGK ; 92.039 0.0039645 9923500 6107.1 7138.1 5341.8 6387.7 8608.6 7802.2 6143 7150.5 7337.9 7003.4 TRUE FALSE FALSE 6032.664316 7238.590359 5434.771788 7126.275929 8169.271019 7303.6646 6664.786267 7357.388436 6681.579846 6821.450658 0.884366774 1.061151172 0.796717892 1.044686282 1.197585591 1.07069082 0.977033567 1.07856654 0.979495445 1 12.73586286 -9.019199058 24.59036041 0.943364441 1.078851618 0.387001286 0.082403906 489.7039997 627218.1486 0.012485158 0.020929768 9.57E-10 9.019199058 0.135487177 SNS(ph)LPHSAVSNAGSK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSLPHSAVSNAGSK 15 0 A0A088AWN2;Q8TBZ3-4;Q8TBZ3-5;Q8TBZ3-6;Q8TBZ3;Q8TBZ3-2;Q8TBZ3-7 A0A088AWN2 WDR20 WD repeat-containing protein 20 1 0 S(0.006)NS(0.994)LPHSAVSNAGSK;S(0.082)NS(0.91)LPHS(0.007)AVS(0.001)NAGSK ; 177.04 9.12E-07 4018300 1409.9 1589.46 1081.25 1060.3 2257.79 2398.24 1780.12 2094.57 2049.75 1825.08 TRUE FALSE FALSE 1392.715596 1611.83646 1100.068703 1182.896875 2142.566551 2245.000204 1931.323348 2155.173078 1866.415226 1777.664158 0.783452594 0.906715958 0.618828195 0.66542202 1.205270715 1.262893327 1.086438819 1.21236234 1.049925666 1 10.79576708 -8.740675065 24.95931566 0.858345614 1.189302138 0.629118299 0.132698538 135.9736183 163443.4859 0.020681973 0.041328236 1.82E-09 8.740675065 0.330956525 SNS(ph)PLPVPPSK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSPLPVPPSK 11 0 Q13247;Q13247-3 Q13247 SRSF6 Serine/arginine-rich splicing factor 6 1 0 S(0.001)NS(0.999)PLPVPPSK;S(0.074)NS(0.926)PLPVPPSK ; 147.52 0.0024281 78018000 14766.9 14081 13107.7 10686.8 11134.5 10827.3 9493.1 10619.1 14580.4 14341.1 TRUE FALSE FALSE 14586.91534 14279.23269 13335.83402 11922.4581 10566.26492 10135.47047 10299.44368 10926.3469 13276.29251 13968.51615 1.044270929 1.022244062 0.954706561 0.853523593 0.756434313 0.725593926 0.737332696 0.782212426 0.95044401 1 13.76989115 -9.161009579 1.648257607 1.021750501 0.744374994 0.93928907 0.029342553 0.042772102 0.227621354 0.003697636 0.007026621 6.90E-10 9.161009579 -0.277375508 SNS(ph)SEALLVDR ddPTM_HeLa_Romidepsin_16h_R1 1 SNSSEALLVDR 11 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 0 S(0.004)NS(0.498)S(0.498)EALLVDR 155.37 0.0020711 17411000 2602.8 2432 2488.7 2689.9 1950.3 2150.2 2071.3 1961.9 2969.5 2494.6 TRUE FALSE FALSE 2571.076072 2466.23776 2532.01478 3000.918894 1850.768913 2012.809159 2247.23617 2018.664481 2703.900483 2429.789932 1.058147471 1.015000403 1.042071475 1.235052814 0.761699145 0.828388139 0.9248685 0.830797944 1.112812448 1 11.24661588 -8.738981988 24.99999999 1.04125213 0.842179833 0.689864068 0.076805641 116.3510082 129523.5855 0.010623944 0.021235778 1.82E-09 8.738981988 -0.199072296 SNS(ph)TTQVSQPR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSTTQVSQPR 11 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 SNS(0.642)T(0.187)T(0.171)QVSQPR;S(0.003)NS(0.764)T(0.173)T(0.06)QVSQPR ; 181.67 7.77E-06 119878000 3247.7 4243.5 2847.3 3019.7 4663.3 4592.7 4327.8 4087.4 3795.9 3365.8 TRUE FALSE FALSE 3208.115783 4303.240104 2896.856062 3368.851922 4425.3144 4299.241292 4695.403224 4205.66247 3456.385197 3278.356031 0.978574552 1.312621346 0.883630708 1.027604046 1.349857782 1.311401584 1.432243228 1.282857149 1.054304403 1 11.67875682 -8.769848547 6.650298261 1.00960191 1.349042076 0.630992828 0.111176368 0.060512258 11.91917733 0.015617765 0.029611134 1.70E-09 8.769848547 0.339440166 SNS(ph)VGIQDAFNDGSDSTFQK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSVGIQDAFNDGSDSTFQK 20 0 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3;A0A087WUV6 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 S(0.249)NS(0.751)VGIQDAFNDGSDSTFQK 65.171 0.0057975 4456100 1953.6 1936.9 1888.7 1411.5 1607.7 1532.8 934.86 1492.7 2222 1772.7 TRUE FALSE FALSE 1929.788772 1964.167729 1921.572031 1574.704271 1525.65307 1434.859027 1014.266985 1535.888919 2023.258755 1726.644998 1.11765231 1.137563153 1.112893521 0.912002336 0.883593947 0.831009865 0.587420683 0.88952212 1.171786185 1 10.75375578 -8.713701618 1.445077515 1.067345115 0.748298016 0.716392975 0.091403954 0.166630315 0.696243514 0.013864367 0.035962159 1.93E-09 8.713701618 -0.319047099 SNS(ph)VGIQDAFNDGSDSTFQKR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSVGIQDAFNDGSDSTFQKR 21 1 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3;A0A087WUV6 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 S(0.187)NS(0.773)VGIQDAFNDGS(0.04)DSTFQKR;S(0.069)NS(0.782)VGIQDAFNDGS(0.148)DSTFQKR ; 76.267 0.001249 24382000 4652.6 4495.2 3266.3 5493.9 3081.96 2690.17 2195.12 2755.58 4547.8 3759.1 TRUE FALSE FALSE 4595.892322 4558.483544 3323.148581 6129.130568 2924.676081 2518.276819 2381.573438 2835.30836 4141.033378 3661.43804 1.255215102 1.244998138 0.907607488 1.673968124 0.79877798 0.687783541 0.65044756 0.77437016 1.130985512 1 11.83819467 -8.546243448 24.99985509 1.15397894 0.706234176 0.582385351 0.195436485 127.9929881 136949.9355 0.028093407 0.056189098 2.84E-09 8.546243448 -0.447744764 SNS(ph)WVNTGGPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSWVNTGGPK 11 0 Q96N67-2;Q96N67-6;Q96N67;A0A0U1RRC1;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 0 S(0.084)NS(0.63)WVNT(0.287)GGPK 161.76 0.0011308 42941000 4662.9 5590.1 4584.7 4512.1 4368.4 3912.4 3335.5 3616.2 4593.7 4588.2 TRUE FALSE FALSE 4606.066781 5668.797575 4664.49478 5033.810232 4145.464247 3662.410267 3618.817287 3720.829042 4182.827967 4468.997903 1.030671055 1.268471746 1.043745126 1.126384559 0.927604876 0.819514877 0.809760346 0.832586885 0.935965525 1 12.12573565 -8.503258254 3.770528867 1.045381616 0.822518692 0.628594296 0.084626309 0.120854835 3.719574981 0.01236025 0.027690028 3.14E-09 8.503258254 -0.222862924 SNSDES(ph)NFSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSDESNFSEK 11 0 A0A087WWW9;O95999 A0A087WWW9 BCL10 B-cell lymphoma/leukemia 10 1 0 S(0.006)NS(0.122)DES(0.597)NFS(0.274)EK 151.99 0.0022964 8951400 2079.5 1885.3 1494.2 1417.8 2610.3 2444.5 2415.8 2398.2 1648.3 1536.9 TRUE FALSE FALSE 2054.154254 1911.841303 1520.205924 1581.732707 2477.086651 2288.304339 2620.997992 2467.588133 1500.87192 1496.971116 1.372207006 1.27713974 1.015521213 1.056622061 1.654732428 1.528622907 1.750867444 1.648387271 1.002605797 1 10.54783067 -4 0.204727528 1.063732255 4.571404671 0.633825759 0.173036979 29.3841577 0.340809529 0.175742021 33.57183189 1.00E-04 4 3.507672416 SNSFS(ph)DER ddPTM_HeLa_Romidepsin_16h_R1 3 SNSFSDER 8 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 S(0.028)NS(0.053)FS(0.918)DER;SNSFS(1)DER;SNS(0.004)FS(0.996)DER ;; 180.66 0.0001138 1793424800 29167.1 29898.8 32340.7 15320.4 24724.3 25751.2 24378 14569.2 30170.5 31756.3 TRUE FALSE FALSE 28811.60017 30319.71609 32903.57632 17091.81673 23462.52671 24105.78143 26448.66671 14990.73682 27471.97492 30931.26675 0.931471718 0.980228723 1.063764268 0.552574095 0.758537531 0.779333793 0.855078679 0.484646715 0.888161973 1 14.9167783 -9.269676905 24.99990896 0.974515879 0.704636801 0.62817263 0.109815108 298.1290442 904784.855 0.015556654 0.024013723 5.37E-10 9.269676905 -0.269879079 SNSGLGGEVSGVMS(ph)KPNVDPQPWFQDGPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSGLGGEVSGVMSKPNVDPQPWFQDGPK 29 1 C9JRJ5;Q9UGP4 C9JRJ5 LIMD1 LIM domain-containing protein 1 1 0 S(0.056)NS(0.194)GLGGEVS(0.121)GVMS(0.629)KPNVDPQPWFQDGPK 64.502 0.00070948 19406000 2715.4 3626.5 1669.4 1788.3 2368.3 1576.5 981.45 1664.9 2381.3 2397.5 TRUE FALSE FALSE 2682.30366 3677.553962 1698.455207 1995.07166 2247.436814 1475.766738 1064.814339 1713.071255 2168.310564 2335.212604 1.1486336 1.574826187 0.727323587 0.854342622 0.962412077 0.631962475 0.455981754 0.733582566 0.928528118 1 11.18933819 -8.663343053 1.016580687 1.095765765 0.575803341 0.457127607 0.216132103 0.365937129 0.714566741 0.035293968 0.119847833 2.17E-09 8.663343053 -0.519962424 SNSLDDSTEEVQSMDVS(ph)PVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSLDDSTEEVQSMDVSPVSK 21 0 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 SNSLDDSTEEVQS(0.047)MDVS(0.869)PVS(0.083)K 62.303 0.0047115 3329300 1434.8 1822.6 1420 1219.6 1809.1 1948.2 1215.1 1602.7 1635.4 1692.2 TRUE FALSE FALSE 1417.312106 1848.258611 1444.714504 1360.61589 1716.774876 1823.716308 1318.310564 1649.071596 1489.125728 1648.2364 0.859896132 1.121355293 0.876521417 0.825498023 1.041582916 1.106465254 0.799830997 1.000506721 0.90346611 1 10.68670746 SNSLSEQLAINTS(ph)PDAVK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSLSEQLAINTSPDAVK 18 0 Q5T1M5;Q5T1M5-2;Q5T1M5-3 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 SNSLSEQLAINT(0.302)S(0.698)PDAVK;SNSLSEQLAINT(0.004)S(0.996)PDAVK ; 234.12 3.95E-49 68412000 7961.4 6814.6 7746.6 6550.2 8593.5 8435.7 7201.2 8006.8 7987.2 7689.4 TRUE FALSE FALSE 7864.363395 6910.536118 7881.426323 7307.564944 8154.941628 7896.685995 7812.869748 8238.464125 7272.804828 7489.62828 1.050033874 0.922680787 1.052312081 0.975691272 1.088831291 1.054349522 1.043158546 1.099983046 0.971050172 1 12.8706784 -8.748480255 24.99855564 1.015159478 1.068319665 0.402808816 0.041392726 226.2964618 436530.2492 0.005678057 0.011297687 1.78E-09 8.748480255 0.053160187 SNSQSDSHDEEVS(ph)PTPPNPVVK ddPTM_HeLa_Romidepsin_16h_R1 2 SNSQSDSHDEEVSPTPPNPVVK 22 0 C9J4C2;C9IZL8;C9JR00;C9JSK5;P31321 C9J4C2 PRKAR1B cAMP-dependent protein kinase type I-beta regulatory subunit 1 0 SNSQSDSHDEEVS(0.961)PT(0.039)PPNPVVK;SNSQSDSHDEEVS(0.989)PT(0.011)PPNPVVK ; 104.55 7.93E-05 17925600 3737.9 3117.5 2922.8 2867.5 5188.6 5019.6 3311.7 3316.7 5694.4 5396.6 TRUE FALSE FALSE 3692.341037 3161.388247 2973.670108 3199.053842 4923.806381 4698.86376 3592.995715 3412.663482 5185.078602 5256.395554 0.702447333 0.601436519 0.565724188 0.608602189 0.936726761 0.893932679 0.683547438 0.649240234 0.986432347 1 12.35985813 -12.05775862 0.891163533 0.996112762 0.70925315 0.492861754 0.115970009 0.439970633 0.646174932 0.078747508 0.025027714 8.75E-13 12.05775862 -0.286859612 SNSS(ph)EALLVDR ddPTM_HeLa_Romidepsin_16h_R1 1 SNSSEALLVDR 11 0 Q96HB5-2;Q96HB5;Q96HB5-5;Q96HB5-3;Q96HB5-4 Q96HB5-2 CCDC120 Coiled-coil domain-containing protein 120 1 0 S(0.11)NS(0.049)S(0.841)EALLVDR 141.06 0.0029663 17560000 1741.2 1972.8 2320.2 2210.4 1622.1 1638.3 1577.1 1336.6 2018.6 1880.1 TRUE FALSE FALSE 1719.977585 2000.57313 2360.582108 2465.976848 1539.318184 1533.617917 1711.058835 1375.272412 1838.05136 1831.254731 0.93923448 1.09246032 1.289051746 1.346605039 0.840581137 0.837468372 0.934364185 0.75100006 1.00371146 1 10.83861677 SNSS(ph)SEAVLGQEELSAQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSSSEAVLGQEELSAQAK 19 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 0 S(0.009)NS(0.049)S(0.858)S(0.009)EAVLGQEELS(0.075)AQAK 183.6 1.26E-10 53352000 4583.9 4195.1 4221.3 4836.8 5005.5 4755.5 3778.3 4369.2 5218.7 4116 TRUE FALSE FALSE 4528.029664 4254.158728 4294.769956 5396.053574 4750.050657 4451.638898 4099.228708 4495.615909 4751.926402 4009.065727 1.1294476 1.061134693 1.071264541 1.345962861 1.184827334 1.110393094 1.022489774 1.121362486 1.18529521 1 11.96905035 -12.14080747 0.552314923 0.980876034 1.13653278 0 0.101141927 1.440496402 0.661473896 0.115844481 0.022115861 7.23E-13 12.14080747 0.155656747 SNSSSEAVLGQEELS(ph)AQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSSSEAVLGQEELSAQAK 19 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 0 SNS(0.002)S(0.264)S(0.081)EAVLGQEELS(0.652)AQAK 190.66 7.84E-15 47144000 4856.6 4597.7 4265.2 5685.5 5734.2 5278.6 4274 5250.2 5382.8 4929.9 TRUE FALSE FALSE 4797.405891 4662.426541 4339.434017 6342.884261 5441.562377 4941.314496 4637.033453 5402.106254 4901.348887 4801.820487 0.999080641 0.970970605 0.903706007 1.320933233 1.133229031 1.029050234 0.965682383 1.125012122 1.020727222 1 12.22936576 SNST(ph)SSMSSGLPEQDR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSTSSMSSGLPEQDR 16 0 P42684-2;P42684-3;P42684-6;P42684 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 SNS(0.014)T(0.795)S(0.045)S(0.038)MS(0.083)S(0.025)GLPEQDR;SNS(0.063)T(0.846)S(0.053)S(0.031)MS(0.007)SGLPEQDR ; 126.91 0.0057738 21265200 6130.7 5678.9 7215.8 6665 5543.9 5677.5 6039 5522.8 7471.6 6327.7 TRUE FALSE FALSE 6055.97667 5758.847703 7341.387972 7435.63866 5260.974096 5314.726073 6551.952509 5682.593504 6803.321383 6163.305442 0.982585843 0.93437649 1.191144596 1.206436827 0.853596199 0.862317489 1.06305822 0.9220042 1.10384297 1 12.58948857 SNST(ph)TQVSQPR ddPTM_HeLa_Romidepsin_16h_R1 2 SNSTTQVSQPR 11 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.023)NS(0.24)T(0.679)T(0.058)QVS(0.001)QPR;SNS(0.259)T(0.74)TQVSQPR ; 167.22 0.0010424 130746000 3168.53 4231.94 2828.82 3229.87 5262.1 5151.8 4402.52 4969.68 3676.45 3808.73 TRUE FALSE FALSE 3129.910738 4291.517362 2878.054425 3603.322766 4993.555401 4822.616607 4776.469939 5113.46985 3347.619104 3709.778646 0.843692047 1.156812245 0.775802198 0.971303981 1.346052118 1.299974222 1.287535024 1.378376 0.902377048 1 11.85711739 -8.78832345 6.107071607 0.93305214 1.323916368 0.791423504 0.097170429 0.057458121 6.585386031 0.014567743 0.027247302 1.63E-09 8.78832345 0.390864227 SNSWVNT(ph)GGPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNSWVNTGGPK 11 0 Q96N67-2;Q96N67-6;Q96N67;A0A0U1RRC1;A0A1B0GWE0 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 1 0 S(0.008)NS(0.453)WVNT(0.539)GGPK 153.75 0.0046309 37722000 4159.9 3800.9 3777.7 3905.2 3644.3 3230.7 2460.4 3339.2 4557.2 3365.9 TRUE FALSE FALSE 4109.197539 3854.40917 3843.449284 4356.737599 3458.317772 3024.268697 2669.386315 3435.814484 4149.592618 3278.453433 1.253395122 1.175679097 1.172336092 1.328900254 1.054862557 0.922468096 0.814221208 1.047998562 1.265716504 1 11.67879969 -8.405825649 4.003287224 1.145924946 0.918164369 0.540000803 0.10554073 0.178958091 4.934025 0.017834246 0.041473802 3.93E-09 8.405825649 -0.227760576 SNT(ph)MPPNLGNAGLLGR ddPTM_HeLa_Romidepsin_16h_R1 1 SNTMPPNLGNAGLLGR 16 0 M0R0S1;M0R2P6;Q8TBC3;M0QXA4;Q8TBC3-2 M0R0S1 SHKBP1 SH3KBP1-binding protein 1 1 0 S(0.072)NT(0.928)MPPNLGNAGLLGR 82.663 0.0018508 0 1247 1268.9 1518.2 1253 1236.5 1101.1 966.81 1104.1 1274.4 1317.5 TRUE FALSE FALSE 1231.801084 1286.763608 1544.623634 1397.877756 1173.396791 1030.743264 1048.930817 1136.045392 1160.414472 1283.27116 0.959891504 1.002721519 1.203661145 1.089308167 0.91437946 0.803215482 0.817388289 0.885273064 0.904262878 1 10.32561033 -8.531871068 5.755514752 1.007785608 0.836648255 0.541036639 0.078763777 0.105395006 12.42998168 0.011880662 0.024904813 2.94E-09 8.531871068 -0.171137353 SNT(ph)PESIAETPPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SNTPESIAETPPAR 14 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 S(0.177)NT(0.771)PESIAET(0.052)PPAR 164.7 0.00026786 32993000 2514.6 2972.2 2257.7 3017.8 2901 2760.5 2254.9 2185 3176.7 3064.5 TRUE FALSE FALSE 2483.951088 3014.04271 2296.994321 3366.732235 2752.951145 2584.112959 2446.43115 2248.219528 2892.567996 2984.883848 0.8321768 1.009768843 0.76954228 1.127927386 0.922297578 0.865733171 0.819606817 0.75320168 0.969072213 1 11.54345908 -16.52283386 0.015646423 2.038670822 2.98E-06 0.17461473 0.103423817 7099.19255 8.969946032 728.2117981 467.7181769 3.00E-17 16.52283386 -2.038667841 SNT(ph)PMGDKDDDDDDDADEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNTPMGDKDDDDDDDADEK 19 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;X6RE05;A0A0A0MSW0 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 S(0.027)NT(0.973)PMGDKDDDDDDDADEK 81.723 0.0042801 22425000 2676.2 2569.3 3091.6 2161.1 2857.7 2719.4 2259.8 3465.3 2837.2 2984.3 TRUE FALSE FALSE 2643.581445 2605.470673 3145.408001 2410.97655 2711.860905 2545.639116 2451.747356 3565.562988 2583.433726 2906.767456 0.909457494 0.896346444 1.082098258 0.829435649 0.932947319 0.875762907 0.843461816 1.22664198 0.888765189 1 11.50519994 -12.50653091 1.26839713 0.999855729 0.937997809 0 0.119562348 1.371325648 3.963676749 0.072678701 0.017748935 3.12E-13 12.50653091 -0.061857919 SNTAGS(ph)QSQVETEA ddPTM_HeLa_Romidepsin_16h_R1 2 SNTAGSQSQVETEA 14 0 Q02790 Q02790 FKBP4 "Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed" 1 0 SNT(0.002)AGS(0.914)QS(0.084)QVETEA;S(0.002)NT(0.002)AGS(0.912)QS(0.084)QVETEA ; 130.66 0.0021459 25068000 5366.4 5471.7 4840 4903.2 5112.1 5166 4545.5 4970.2 4661.3 4817.8 TRUE FALSE FALSE 5300.992253 5548.730736 4924.23817 5470.131054 4851.210461 4835.909273 4931.594657 5114.004895 4244.381654 4692.632861 1.129641378 1.182434446 1.049355088 1.165684854 1.033792884 1.030532201 1.050922755 1.089794375 0.904477674 1 12.19618188 -6.934331015 14.09484811 1.072164852 1.238294535 0 0.078557545 1493030.575 8295323.759 0.009386496 7009605.401 1.16E-07 6.934331015 0.166129683 SNTEPQS(ph)PPIASPK ddPTM_HeLa_Romidepsin_16h_R1 1 SNTEPQSPPIASPK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 SNTEPQS(1)PPIASPK 212.35 6.57E-24 7072100 5541.2 5600.8 5032.6 4442.2 6958.2 6751.3 6802.6 7717.3 6108.3 5301.4 TRUE FALSE FALSE 5473.661723 5679.648209 5120.190292 4955.828065 6603.097089 6319.913719 7380.412674 7940.5879 5561.958349 5163.668864 1.060033451 1.099924949 0.991579907 0.959749394 1.278760754 1.223919249 1.429296275 1.537780231 1.077133042 1 12.33418077 -7.875152924 0.89544034 1.026921223 1.61160608 0.867199404 0.06794465 0.246124143 0.250596511 0.010542136 0.113903206 1.33E-08 7.875152924 0.584684857 SNTEPQSPPIAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 SNTEPQSPPIASPK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK;SNTEPQSPPIAS(1)PK ;; 131.18 0.0020393 29943800 10528.9 11206 9639.9 11905.7 12543.4 12508.1 10570.8 12637.3 11504.8 11707.2 TRUE FALSE FALSE 10400.56972 11363.75836 9807.678416 13282.29305 11903.26349 11708.87278 11468.68349 13002.94034 10475.78187 11403.04526 0.912087033 0.996554702 0.860092913 1.164802275 1.043867075 1.026819811 1.005756202 1.140304195 0.918682829 1 13.47713154 -9.262317969 24.9996638 0.954183277 1.067838429 0.559562322 0.060452068 55.49604309 1579096.099 0.009277483 0.014697089 5.47E-10 9.262317969 0.113655151 SNTPESIAET(ph)PPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SNTPESIAETPPAR 14 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 SNTPESIAET(1)PPAR 164.7 0.00026786 18410000 1763.8 1596.5 1392.2 1228.3 1370.8 1288.4 1470.9 1465.9 1946.5 1582.5 TRUE FALSE FALSE 1742.302127 1618.975569 1416.430657 1370.321825 1300.842961 1206.075398 1595.838209 1508.313504 1772.400165 1541.386422 1.130347395 1.050337246 0.918932876 0.889019006 0.843943441 0.782461413 1.0353265 0.978543396 1.149873996 1 10.59001287 -9.755025979 4.623864698 1.063001611 0.90305478 0.555512381 0.075829974 0.132057938 7.042234783 0.013235297 0.018283721 1.76E-10 9.755025979 -0.159946831 YADSPGASS(ph)PEQPK ddPTM_HeLa_Romidepsin_16h_R1 1 YADSPGASSPEQPK 14 0 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 0 YADSPGAS(0.134)S(0.866)PEQPK 206.46 4.72E-17 5841400 5603.2 5609.3 5137.8 5107.1 2990.6 2397.9 2078.1 2183.2 5906.2 5259.3 TRUE FALSE FALSE 5534.906043 5688.267873 5227.221254 5697.606932 2837.978523 2244.681929 2254.613762 2246.367447 5377.93468 5122.662628 1.080474442 1.110412355 1.020410992 1.112235442 0.554004573 0.438186563 0.440125366 0.438515594 1.049831908 1 12.32267817 -8.688804484 4.604707456 1.048311684 0.448945252 0.981740601 0.039837363 0.022688271 0.909115683 0.00694318 0.014062359 2.05E-09 8.688804484 -0.599366432 down SNVSS(ph)PATPTASSSSSTTPTR ddPTM_HeLa_Romidepsin_16h_R1 3 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVS(0.251)S(0.747)PATPT(0.002)ASSSSSTTPTR;SNVS(0.029)S(0.969)PAT(0.002)PTASSSSSTTPTR;SNVS(0.031)S(0.969)PATPTASSSSSTTPTR ;; 220.89 9.75E-42 21028900 7121 6885.5 6737.2 6056.4 5627.7 4895.1 4334 4381.03 7703.6 7159.1 TRUE FALSE FALSE 7034.206513 6982.43425 6854.45814 6756.669464 5340.497469 4582.318908 4702.129852 4507.788191 7014.570722 6973.10555 1.008762375 1.001337811 0.982984997 0.968961307 0.765870734 0.657141768 0.674323631 0.646453457 1.005946443 1 12.7675856 -8.663782433 2.226856719 1.002825681 0.65932223 0.994970601 0.010960139 0.014209768 0.142802759 0.001696793 0.003853991 2.17E-09 8.663782433 -0.34350345 SNVSS(ph)PATPTASSSSSTTPTRK ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 S(0.006)NVS(0.199)S(0.586)PAT(0.2)PT(0.009)ASSSSSTTPTRK 104.55 5.62E-05 12000000 2805.1 2676.8 2225.4 2738.7 2168.7 1769.1 1930.5 1872.7 2849.9 2648.8 TRUE FALSE FALSE 2770.910362 2714.484061 2264.132153 3055.36138 2058.023146 1656.06022 2094.476622 1926.88362 2594.997806 2579.983794 1.074003011 1.052132214 0.877576114 1.184256036 0.797688401 0.641887838 0.811817743 0.746858807 1.005819421 1 11.33314629 -8.619694462 6.588023005 1.033038052 0.738039097 0.746771954 0.081227706 0.073143387 4.238564554 0.010969212 0.022069997 2.40E-09 8.619694462 -0.294998955 TGQAGSLSGS(ph)PKPFSPQLSAPITTK ddPTM_HeLa_Romidepsin_16h_R1 2 TGQAGSLSGSPKPFSPQLSAPITTK 25 1 Q9ULU4-9;A0A087WV57;A0A087WYS3;Q9ULU4-11;Q9ULU4-23;Q9ULU4;Q9ULU4-21;H7C4X9;A0A087WVZ6;Q9ULU4-10;Q9ULU4-13;Q9ULU4-12;Q9ULU4-20;Q9ULU4-7;Q9ULU4-5;Q9ULU4-19;Q9ULU4-16;Q9ULU4-22;Q9ULU4-14;Q9ULU4-8;Q9ULU4-17;Q9ULU4-6;Q9ULU4-3;Q9ULU4-4 Q9ULU4-9 ZMYND8 Protein kinase C-binding protein 1 1 0 T(0.001)GQAGS(0.027)LS(0.204)GS(0.571)PKPFS(0.157)PQLS(0.037)APIT(0.002)T(0.001)K;TGQAGS(0.007)LS(0.095)GS(0.892)PKPFS(0.004)PQLS(0.001)APITTK ; 76.959 9.83E-05 157257000 5663.4 5109.6 4343.4 4633 3255.5 2356.2 2157.11 2214.9 5866.5 5384.2 TRUE FALSE FALSE 5594.372302 5181.533083 4418.995055 5168.689259 3089.359687 2205.646424 2340.33487 2278.984637 5341.785547 5244.317708 1.066749311 0.988028066 0.842625352 0.985578973 0.589087057 0.420578338 0.446261077 0.434562657 1.018585418 1 12.35653937 -8.681724658 1.986154313 1.016639961 0.426635616 0.943020912 0.06194065 0.052845785 0.422473085 0.010110562 0.023512206 2.08E-09 8.681724658 -0.590004345 down TVKEPEGPPPS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 TVKEPEGPPPSPGK 14 1 P58012 P58012 FOXL2 Forkhead box protein L2 1 0 TVKEPEGPPPS(1)PGK;TVKEPEGPPPS(1)PGK ; 93.115 0.0060364 26101000 23819.5 22576.7 22281.8 21937.5 14059.3 10943.8 9580.8 11139 24435.4 23699.6 TRUE FALSE FALSE 23529.17877 22894.53538 22669.60538 24474.01697 13341.80146 10244.5265 10394.59291 11461.28939 22249.83662 23083.88098 1.019290422 0.991797497 0.982053469 1.060221069 0.577970467 0.443795673 0.450296591 0.496506173 0.963868972 1 14.49459818 -8.678912866 4.294122944 1.009079665 0.469746627 0.9836309 0.032446438 0.015950402 0.548901397 0.004258424 0.00867922 2.09E-09 8.678912866 -0.539333038 down SNVSSPAT(ph)PTASSSSSTTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVS(0.005)S(0.041)PAT(0.47)PT(0.107)AS(0.217)S(0.068)S(0.022)S(0.022)S(0.022)T(0.022)T(0.004)PT(0.002)R 101.61 0.00088293 2430300 891.61 701.17 837.62 746.8 730.81 841.64 681.93 669.8 828.97 894.17 TRUE FALSE FALSE 880.7427144 711.0410897 852.1984247 833.1485298 693.5140387 787.8619203 739.8531172 689.1796062 754.824847 870.9393345 1.0112561 0.816407138 0.978481957 0.956609142 0.796282831 0.90461171 0.849488693 0.791306098 0.866679018 1 9.766428421 -9.054696899 0.419202976 1.013547691 0.796152468 0.131035535 0.075097638 0.85204756 0.259786996 0.020692102 0.076507243 8.82E-10 9.054696899 -0.217395223 SNVSSPAT(ph)PTASSSSSTTPTRK ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 S(0.005)NVS(0.089)S(0.089)PAT(0.8)PT(0.015)AS(0.002)SSSSTTPTRK 76.133 0.0010261 9716100 2471.3 2231.5 1818.4 2024.7 1881.4 1698.5 1282 1513.2 2560.8 2313.9 TRUE FALSE FALSE 2441.178845 2262.915116 1850.048489 2258.80534 1785.385138 1589.971332 1390.893048 1556.982055 2331.755634 2253.784544 1.083146502 1.004051217 0.820863065 1.002227718 0.792172057 0.705467315 0.617136652 0.690830034 1.034595627 1 11.13813389 -8.657350586 0.787817796 1.036751388 0.618607501 0.830322814 0.065933602 0.213612473 0.232337332 0.012408102 0.051905989 2.20E-09 8.657350586 -0.418143886 SPTTVLFTS(ph)SPIK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTTVLFTSSPIK 13 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 0 SPTTVLFT(0.093)S(0.585)S(0.322)PIK 168.83 0.00011508 12648000 2918.1 2969.4 3660.1 2746.8 1413.1 1131.2 1029.2 803.4 2477.5 2347.5 TRUE FALSE FALSE 2882.533075 3011.203291 3723.802505 3064.39794 1340.984234 1058.919971 1116.620222 826.6451114 2255.906195 2286.511612 1.260668461 1.316942051 1.628595493 1.340206594 0.586476022 0.463115938 0.488350996 0.361531123 0.986614799 1 11.15893253 -8.676428998 5.137513765 1.197408914 0.457988813 0.817751197 0.179905366 0.080920513 3.635977082 0.030938747 0.062523261 2.11E-09 8.676428998 -0.739420101 down NSPQS(ph)SPTSTPK ddPTM_HeLa_Romidepsin_16h_R1 1 NSPQSSPTSTPK 12 0 Q9Y6Y0 Q9Y6Y0 IVNS1ABP Influenza virus NS1A-binding protein 1 0 NSPQS(0.958)S(0.042)PTSTPK 134.18 0.002896 19774000 9269.1 8498.6 8067.8 7287.4 5539.2 4691.6 3771.9 3437.5 10180 8653.9 TRUE FALSE FALSE 9156.124644 8618.243514 8208.216675 8130.003476 5256.513954 4391.821901 4092.285092 3536.958639 9269.475304 8429.07043 1.086255563 1.022442935 0.973798563 0.964519581 0.623617278 0.521032768 0.485496607 0.419614318 1.09970315 1 13.04115782 -8.674689693 1.643076513 1.038276295 0.459884577 0.974287745 0.041418747 0.040457065 0.219618491 0.006638417 0.016661523 2.11E-09 8.674689693 -0.578391717 down SNVSSPATPTASSSSS(ph)TTPTRK ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSSPATPT(0.001)AS(0.053)S(0.015)S(0.015)S(0.037)S(0.391)T(0.391)T(0.097)PT(0.002)RK 94.49 0.00013244 36777000 3801.2 3665.3 3740 3398 2115.4 1615.7 1258.9 1313.5 3877.4 3900.8 TRUE FALSE FALSE 3754.869512 3716.90019 3805.093131 3790.892748 2007.443244 1512.461984 1365.830935 1351.50405 3530.595633 3799.456654 0.988264864 0.978271508 1.001483496 0.997746018 0.528350085 0.398073231 0.359480594 0.355709822 0.929236982 1 11.8915774 -8.668832172 3.172432664 0.995455452 0.377538309 0.989236793 0.029507326 0.014097705 0.282987738 0.003736182 0.00787778 2.14E-09 8.668832172 -0.617917143 down SNVSSPATPTASSS(ph)SSTTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSSPATPT(0.017)AS(0.017)S(0.055)S(0.579)S(0.082)S(0.082)T(0.082)T(0.082)PT(0.006)R 162.82 1.88E-08 14672000 6137.1 5937.8 5597 5213 3690 2458.6 2270.9 2399.9 7372.7 6315.6 TRUE FALSE FALSE 6062.298665 6021.392504 5694.413437 5815.751588 3501.685531 2301.503395 2463.790189 2469.33732 6713.267247 6151.519802 0.985496082 0.978846317 0.925692125 0.945417031 0.569239089 0.374135737 0.400517314 0.401419064 1.091318481 1 12.58672717 -8.665995082 2.447884025 0.987122864 0.392610097 0.978115029 0.041064268 0.018137143 0.220272777 0.003978253 0.008812796 2.16E-09 8.665995082 -0.594512767 down SRLT(ph)PVSPES(ph)SSTEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 S(0.003)RLT(0.997)PVS(0.012)PES(0.638)S(0.296)S(0.047)T(0.008)EEK 118.31 7.97E-05 0 2408.6 2403.2 2015.5 2193.9 1160.6 705.89 699.08 759.83 2781 2187.2 TRUE FALSE FALSE 2379.243057 2437.032313 2050.578932 2447.569041 1101.370251 660.7859072 758.4598378 781.8144822 2532.260395 2130.376229 1.116818252 1.143944567 0.962543097 1.148890514 0.516983919 0.310173339 0.356021546 0.366984231 1.188644691 1 11.05689252 -8.660427487 4.182966489 1.062082525 0.35491243 0.956723202 0.073881 0.029165168 0.928041861 0.01003897 0.020588599 2.19E-09 8.660427487 -0.707170095 down SNVSSPATPTASSSSSTT(ph)PTRK ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSSPATPT(0.002)AS(0.078)S(0.057)S(0.057)S(0.057)S(0.132)T(0.132)T(0.43)PT(0.057)RK 62.831 0.0042072 44569000 3976.6 3701 3496.2 3048.1 2268.9 2026.8 1504.8 1238.6 3978 3773 TRUE FALSE FALSE 3928.13167 3753.102775 3557.049894 3400.535664 2153.109567 1897.294021 1632.617674 1274.436937 3622.197717 3674.976916 1.06888608 1.021258871 0.967910813 0.925321639 0.585883834 0.516273725 0.444252498 0.346787739 0.985638223 1 11.84351947 -8.659570737 1.301298119 1.033112952 0.399636673 0.973130894 0.043245211 0.045723794 0.152440608 0.006788682 0.019483677 2.19E-09 8.659570737 -0.633476279 down SNY(ph)VPPPET(ph)Y(ph)TTEK ddPTM_HeLa_Romidepsin_16h_R1 1 SNYVPPPETYTTEK 14 0 Q8N6N3;Q8N6N3-2 Q8N6N3 C1orf52 UPF0690 protein C1orf52 3 0 S(0.143)NY(0.86)VPPPET(0.998)Y(0.999)TTEK 81.703 0.025863 2933700 889.67 1060.4 993.74 897.04 1098.7 1103.7 854.84 1033.4 1055.6 1003.9 TRUE FALSE FALSE 878.8263598 1075.328339 1011.035628 1000.759986 1042.629239 1033.177132 927.4500883 1063.299799 961.1844922 977.8185333 0.898762224 1.099721781 1.033970613 1.023461871 1.066280914 1.056614389 0.948488965 1.087420377 0.982988622 1 9.93342294 -10.26334172 24.99604565 0.952193273 1.041411287 0.406527118 0.046332931 127.9571256 1681305.481 0.008768242 0.010303563 5.45E-11 10.26334172 0.089218014 SNYNFEKPFLWLAR ddPTM_HeLa_Romidepsin_16h_R1 2 SNYNFEKPFLWLAR 14 1 F5H018;B5MDF5;J3KQE5;P62826;B4DV51 F5H018 RAN GTP-binding nuclear protein Ran 0 0 ; ; 132.24 0.0020769 16464500 3109.4 2306.4 4142.3 3657 4012.8 4619.7 3718.3 2481.41 2559.78 1179.58 FALSE FALSE TRUE 3071.501437 2338.86956 4214.394994 4079.839547 3808.011842 4324.516079 4034.132309 2553.205683 2330.826866 1148.934342 2.673348098 2.035686005 3.66809037 3.550977109 3.314385953 3.763936652 3.511194821 2.222238113 2.028685871 1 10.16608064 -11.54873827 0.424955613 0.755832403 3.388660459 0.526657303 0.606872339 0.531575867 0.18996764 0.604339714 0.201840506 2.83E-12 11.54873827 2.632828056 SLS(ph)SPPSSK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSSPPSSK 9 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 SLS(0.938)S(0.061)PPSSK;S(0.223)LS(0.375)S(0.375)PPS(0.025)S(0.001)K ; 142.83 0.0062008 83929000 14783.1 16117.1 12524.5 11035.5 10247.6 7693.3 5691.3 6085.3 15073 14986.6 TRUE FALSE FALSE 14602.91789 16343.99696 12742.48367 12311.47643 9724.626733 7201.722959 6174.71888 6261.368554 13724.83313 14597.24597 1.000388561 1.119663051 0.872937518 0.843410905 0.66619599 0.49336176 0.423005743 0.428941772 0.940234422 1 13.83340858 -8.657037519 1.105779015 1.007796143 0.407311273 0.952776651 0.053072487 0.063792086 0.149784168 0.007711846 0.024743727 2.20E-09 8.657037519 -0.60048487 down SPALK(ac)SPLQSVVVR ddPTM_HeLa_Romidepsin_16h_R1 2 SPALKSPLQSVVVR 14 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 1 ; SPALK(1)SPLQSVVVR;SPALK(1)SPLQSVVVR 179.59 5.03E-08 2198900 206.294 161.62 164.024 185.591 263.76 0 237.144 68.742 252.52 0 FALSE TRUE FALSE 203.7796094 163.8952906 166.8787689 207.0499047 250.299343 0 257.2870054 70.73094131 229.9339788 0 0 SPAPGAPTRS(ph)PSTPAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPAPGAPTRSPSTPAK 16 1 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 SPAPGAPT(0.072)RS(0.901)PS(0.014)T(0.014)PAK 64.331 0.020394 41069000 4261.7 4163.9 3850.5 3680.3 3589.7 2742.8 2542 2573.8 3771.1 4221.9 TRUE FALSE FALSE 4209.756761 4222.519493 3917.516337 4105.833602 3406.504214 2567.543932 2757.917417 2648.268842 3433.803371 4112.214429 1.023720147 1.026823763 0.952653711 0.998448323 0.828386815 0.624370148 0.670664788 0.644000669 0.835025369 1 12.00569978 -8.535250406 2.321746591 1.008409979 0.646038901 0.850065237 0.06019075 0.029766088 0.319717458 0.003713203 0.008989056 2.92E-09 8.535250406 -0.362371078 SPAPGS(ph)PDEEGGAEAPAAGIR ddPTM_HeLa_Romidepsin_16h_R1 1 SPAPGSPDEEGGAEAPAAGIR 21 0 O15061;H0YL34;A0A075B7B1;O15061-2 O15061 SYNM Synemin 1 0 S(0.007)PAPGS(0.993)PDEEGGAEAPAAGIR 140.33 9.35E-05 104220000 1074.8 826.74 839.77 909.07 973.94 1066.2 792.65 1023.6 849.18 1004.5 TRUE FALSE FALSE 1061.699924 838.3788674 854.3858446 1014.180951 924.2362075 998.073261 859.9776712 1053.216251 773.227214 978.4029452 1.085135658 0.856885061 0.873245373 1.036567761 0.944637597 1.020104514 0.878960632 1.076464719 0.790295264 1 9.934284936 -10.28622454 24.98992786 1.040202949 0.954388941 0 0.106742345 816.0450361 822784.2486 0.012276752 0.014041969 5.17E-11 10.28622454 -0.085814008 SPART(ph)PPSEEDSAEAER ddPTM_HeLa_Romidepsin_16h_R1 1 SPARTPPSEEDSAEAER 17 1 O43765;K7EMD6 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 0 S(0.063)PART(0.936)PPSEEDSAEAER 68.481 0.018534 7080600 1808.4 2086.8 1853.5 2000.1 1683.5 1580.6 1597.5 1626.5 1814.7 1702.8 TRUE FALSE FALSE 1786.358525 2116.178025 1885.75939 2231.360973 1597.584713 1479.604761 1733.19161 1673.560211 1652.388687 1658.561011 1.077053249 1.275912078 1.136985241 1.345359597 0.963235421 0.892101497 1.044997199 1.009043503 0.996278507 1 10.69571637 SPAS(ph)PLNNQGIPTPAQLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SPASPLNNQGIPTPAQLTK 19 0 J3QLL6;J3KSG1;J3QRK1;A0A2U3U043;Q719H9 J3QLL6 KCTD1 BTB/POZ domain-containing protein KCTD1 1 0 S(0.156)PAS(0.844)PLNNQGIPTPAQLTK 113.23 2.31E-05 0 2000.3 2075.2 2033.8 1402.6 1984.6 1330.8 1543 1390.9 2428.4 2025.4 TRUE FALSE FALSE 1975.919574 2104.41472 2069.197436 1564.775211 1883.318456 1245.766175 1674.062381 1431.143497 2211.197822 1972.779816 1.00159154 1.066725593 1.048873989 0.793182898 0.954652132 0.631477555 0.848580449 0.725445123 1.120853835 1 10.94601423 -8.868756636 1.387353833 1.00904097 0.75698315 0.653362353 0.090256995 0.179562579 0.6919957 0.011993635 0.02845024 1.35E-09 8.868756636 -0.252057821 SPAVATSTAAPPPPSS(ph)PLPSK ddPTM_HeLa_Romidepsin_16h_R1 3 SPAVATSTAAPPPPSSPLPSK 21 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 SPAVATSTAAPPPPS(0.232)S(0.767)PLPSK;SPAVATSTAAPPPPS(0.21)S(0.664)PLPS(0.126)K;SPAVATSTAAPPPPS(0.235)S(0.764)PLPS(0.001)K ;; 183.71 1.52E-13 432114000 20021.4 18631.8 17476 18859.8 15486.4 13725.1 11430 12486.4 20299.6 19568 TRUE FALSE FALSE 19777.37148 18894.09897 17780.16245 21040.45881 14696.07122 12848.11041 12400.86391 12847.67428 18483.95293 19059.62054 1.037658197 0.991315589 0.932870747 1.103928526 0.771057912 0.67410106 0.650635404 0.674078178 0.969796481 1 14.21823178 -8.607661449 4.348404705 1.013979147 0.671738627 0.925239884 0.044250757 0.035717141 1.254300268 0.006098002 0.012615501 2.47E-09 8.607661449 -0.34224052 SPDASSAFSPAS(ph)PATPNGTK ddPTM_HeLa_Romidepsin_16h_R1 1 SPDASSAFSPASPATPNGTK 20 0 Q53GS7-2;Q53GS7 Q53GS7-2 GLE1 Nucleoporin GLE1 1 0 SPDASSAFS(0.124)PAS(0.876)PATPNGTK 201.9 6.24E-24 4830400 2846.6 2923.6 2720.7 2952.7 2894 2703.7 2127.4 2461.8 2921.2 2592.5 TRUE FALSE FALSE 2811.904544 2964.758518 2768.052642 3294.105067 2746.308381 2530.942296 2308.101303 2533.028299 2659.920556 2525.146476 1.113560964 1.174093679 1.096194881 1.30452039 1.087583792 1.002295241 0.914046502 1.003121333 1.053372777 1 11.30215136 -8.127436795 3.822768093 1.088436831 0.958757644 0.365070255 0.082441463 0.256118658 6.552301917 0.013695267 0.038016405 7.46E-09 8.127436795 -0.129679187 SPDEEDY(ph)DYESYEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPDEEDYDYESYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.353)PDEEDY(0.644)DY(0.002)ESYEK 158.08 0.02178 15410000 2606 2744 3016 1493 2713.2 3137.8 2377.5 3035.7 3052.6 2900.3 TRUE FALSE FALSE 2574.23707 2782.630104 3068.492215 1665.627685 2574.73528 2937.304707 2579.444791 3123.53319 2779.567811 2824.949788 0.911250558 0.985019315 1.086211241 0.5896132 0.911426918 1.03977236 0.913094032 1.105695118 0.983935298 1 11.46400951 -8.708523326 0.004613481 1.881847731 2.45E-07 0 0.138096528 107392.2522 140.9459194 28239.60884 29254.88925 1.96E-09 8.708523326 -1.881847486 SPDEEDYDYES(ph)YEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPDEEDYDYESYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SPDEEDYDYES(1)YEK 150.34 9.33E-05 0 594.77 582.37 729.38 769.23 539.43 758.97 686.21 928.08 654.97 630.65 TRUE FALSE FALSE 587.5207145 590.5686201 742.0745529 858.1719919 511.9008742 710.4742665 744.4966603 954.9325305 596.3878428 614.2656221 0.956460354 0.961422223 1.208067856 1.397069869 0.833354262 1.156623846 1.21201095 1.554592177 0.970895686 1 9.262718834 -4 0.478714701 0.996201285 15.15479056 0.488364615 0.152347106 52.76064038 0.534010388 0.031198644 748.1194718 1.00E-04 4 14.15858927 SPDEEDYDYESYEK ddPTM_HeLa_Romidepsin_16h_R1 2 SPDEEDYDYESYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 0 0 ; ; 171.49 0.00045496 33090000 4886.4 4698.9 5109.9 4730.2 4939.3 4603.1 4348 4607 5816.3 5598.9 FALSE FALSE TRUE 4826.842677 4765.051238 5198.835666 5277.12798 4687.22909 4308.976766 4717.319011 4740.296276 5296.075561 5453.439771 0.885100575 0.873769848 0.953313117 0.967669618 0.859499561 0.790139242 0.865017165 0.869230518 0.971144045 1 12.41295079 -16.52287875 0.136458375 1.421829279 0.829574562 0.494277227 0.044496971 49.18235496 0.470149899 5.62978714 0.154162878 3.00E-17 16.52287875 -0.592254717 SPDKPGGS(ph)PSASR ddPTM_HeLa_Romidepsin_16h_R1 1 SPDKPGGSPSASR 13 1 Q9Y3T9 Q9Y3T9 NOC2L Nucleolar complex protein 2 homolog 1 0 SPDKPGGS(0.994)PS(0.005)ASR 129.29 0.017941 19365000 1025.6 1087.3 844.26 777.52 1020.3 934.87 864.09 587.93 1147 871.36 TRUE FALSE FALSE 1013.099593 1102.607038 858.9539911 867.4205207 968.2302837 875.1348242 937.485783 604.9408269 1044.409447 848.7219416 1.193676684 1.299138132 1.012055832 1.022031455 1.140809771 1.031120773 1.104585303 0.712766805 1.230567275 1 9.729148165 -7.260730905 24.15572613 1.097009339 0.71276663 0.596232551 0.098287903 21.11977645 719841.4004 0.01414944 0.113195894 5.49E-08 7.260730905 -0.384242709 RHQGTFTDEK(ac)SK ddPTM_HeLa_Romidepsin_16h_R1 1 RHQGTFTDEKSK 12 2 Q92922 Q92922 SMARCC1 SWI/SNF complex subunit SMARCC1 0 1 RHQGTFTDEK(1)SK 99.973 0.018206 3044900 1964.4 618.94 1552.1 291.19 4934.5 5977 5415.2 5832.6 1657 1404.5 FALSE TRUE FALSE 1940.457137 627.6534536 1579.113649 324.8587579 4682.674052 5595.08899 5875.166953 6001.357079 1508.79377 1368.010888 1.418451531 0.458807353 1.154313656 0.237467962 3.422980105 4.089944781 4.294678505 4.386922015 1.102910645 1 10.417864 -8.627508823 4.694627077 1.080231484 4.189706662 0.945883464 0.371117149 0.037144188 1.384381369 0.058445109 0.119521932 2.36E-09 8.627508823 3.109475178 up SPEKIEEVLSPEGS(ph)PSKSPSK ddPTM_HeLa_Romidepsin_16h_R1 2 SPEKIEEVLSPEGSPSKSPSK 21 2 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 0 SPEKIEEVLS(0.111)PEGS(0.643)PS(0.111)KS(0.111)PS(0.024)K;SPEKIEEVLS(0.014)PEGS(0.739)PS(0.111)KS(0.111)PS(0.024)K ; 72.421 0.0021016 131359000 5828.7 5458 6020.5 9218.4 7683.8 7438.5 7924.1 8869.7 6766.7 5572.9 TRUE FALSE FALSE 5757.657562 5534.837867 6125.284277 10284.27478 7291.667014 6963.203857 8597.172856 9126.330775 6161.469404 5428.115255 1.060710264 1.019661081 1.128436665 1.89463088 1.3433147 1.282803244 1.583822829 1.681307479 1.135102907 1 12.40623564 -9.445840947 7.926984266 1.030833377 1.531212155 0.690051742 0.163502269 0.128566032 12.03782161 0.024031398 0.03670559 3.58E-10 9.445840947 0.500378778 SPFEIIS(ph)PPAS(ph)PPEMVGQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPFEIISPPASPPEMVGQR 19 0 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 2 0 SPFEIIS(1)PPAS(1)PPEMVGQR 87.157 0.0024778 0 649.36 478.89 529.03 712.69 717.87 1280.6 1187.1 1095.1 644.31 794.22 TRUE FALSE FALSE 641.4453506 485.631826 538.2375452 795.0945711 681.2344152 1198.773793 1287.932244 1126.784991 586.6812999 773.5860499 0.829184227 0.627767042 0.695769456 1.027803657 0.880618795 1.549632123 1.664885561 1.456573565 0.758391778 1 9.595417969 -8.256758885 6.998771652 0.883744617 1.570127088 0.86061408 0.132642192 0.04027774 13.17981044 0.020538981 0.049841501 5.54E-09 8.256758885 0.68638247 SPFEVSVDK ddPTM_HeLa_Romidepsin_16h_R1 1 SPFEVSVDK 9 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 98.582 0.00629 0 213.96 161.08 347.2 130.86 222.08 304.36 199.72 205.65 238.16 178.09 FALSE FALSE TRUE 211.3521732 163.3476885 353.2428704 145.9906489 210.7464289 284.9123783 216.6842118 211.6001583 216.8583731 173.4631961 1.218426605 0.941684992 2.036413938 0.841623193 1.214934543 1.642494688 1.249165337 1.219856217 1.250169361 1 7.438485787 -11.25083238 0.526725731 1.000107749 1.330316955 0.032927851 0.325955714 1.339431314 0.828749886 0.193202558 0.094577315 5.61E-12 11.25083238 0.330209206 SPFEVYVDK ddPTM_HeLa_Romidepsin_16h_R1 1 SPFEVYVDK 9 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 111.06 0.016097 338740 306.66 282.21 367.07 179.54 327.38 323.34 163.71 189.58 340.33 361.31 FALSE FALSE TRUE 302.92231 286.1829598 373.4586994 200.2992596 310.672577 302.6796175 177.6155233 195.0651982 309.8900324 351.9231141 0.860762757 0.813197395 1.061194006 0.569156306 0.882785371 0.860073139 0.504699794 0.554283565 0.880561748 1 8.459116462 -6.566786661 0.297939139 0.963869716 8.22E-16 0.477205447 0.131325999 6.722937764 0.317673384 0.054142006 2.544072629 2.71E-07 6.566786661 -0.963869716 SPFNSPSPQDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 SPFNSPSPQDSPR 13 0 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 SPFNS(0.009)PS(0.059)PQDS(0.931)PR;SPFNSPSPQDS(1)PR;SPFNS(0.015)PS(0.331)PQDS(0.654)PR ;; 146.27 0.00076791 80947000 4382.54 4372.2 4195.69 3994.65 3510.9 3902.32 3202.22 3402.11 5022.16 4876.4 TRUE FALSE FALSE 4329.123917 4433.751946 4268.714224 4456.530228 3331.725672 3652.974346 3474.216487 3500.544685 4572.965431 4749.710425 0.911450074 0.93347837 0.898731468 0.93827409 0.701458694 0.769094117 0.731458589 0.737001706 0.962788259 1 12.21362384 -8.769180919 24.8468476 0.948953414 0.736970854 0.915184969 0.030664039 40.46887223 129887.2137 0.006084939 0.011180937 1.70E-09 8.769180919 -0.21198256 SPGAGSLGS(ph)PASQR ddPTM_HeLa_Romidepsin_16h_R1 2 SPGAGSLGSPASQR 14 0 E9PC47;P53667-4;P53667-2;P53667 E9PC47 LIMK1 LIM domain kinase 1 1 0 SPGAGSLGS(0.908)PAS(0.092)QR;SPGAGS(0.008)LGS(0.967)PAS(0.025)QR ; 103.66 0.0085305 60454000 2648.4 2513.7 2670 2313.94 2644.4 2795.2 2295.28 2170.1 2744.2 2670.5 TRUE FALSE FALSE 2616.120282 2549.087935 2716.47023 2581.48863 2509.4464 2616.595741 2490.241026 2232.88842 2498.751879 2601.120025 1.005766845 0.979996275 1.04434636 0.992452715 0.964756096 1.005949636 0.957372594 0.858433443 0.96064459 1 11.34491726 -6.413870225 1.044960839 1.002261288 0.258048361 0.743507778 0.02366733 2.382533654 0.552994097 0.002786727 3.026805496 3.86E-07 6.413870225 -0.744212927 SPGAPSAGEAEARPSPSTTPLPDS(ph)SPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGAPSAGEAEARPSPSTTPLPDSSPSR 28 1 Q5SYE7-2;Q5SYE7 Q5SYE7-2 NHSL1 NHS-like protein 1 1 0 SPGAPSAGEAEARPS(0.001)PS(0.001)T(0.002)T(0.002)PLPDS(0.45)S(0.45)PS(0.094)R 63.433 0.00044611 7924500 2120.1 910.32 1503.3 575.91 1299 1015.8 1423.2 1050.3 2073.3 1558.8 TRUE FALSE FALSE 2094.259406 923.1355089 1529.464306 642.4994239 1232.707183 950.8936583 1544.086572 1080.688773 1887.858855 1518.302151 1.379342975 0.608005138 1.007351735 0.423169672 0.811898463 0.6262875 1.016982404 0.711774512 1.243401291 1 10.56824321 -10.2567025 24.99847187 1.179134183 0.750080691 0.55420961 0.190104631 249.4892714 1316658.856 0.034461124 0.04147743 5.54E-11 10.2567025 -0.429053493 SPGGGGGGGSGNDNNQAATK(ac)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGGGGGGGSGNDNNQAATKSPR 23 1 Q9NS37;E9PIM0;J3KN20 Q9NS37 CREBZF CREB/ATF bZIP transcription factor 0 1 SPGGGGGGGSGNDNNQAATK(1)SPR 85.636 9.19E-06 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 SPGLVPPS(ph)PEFAPR ddPTM_HeLa_Romidepsin_16h_R1 2 SPGLVPPSPEFAPR 14 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 S(0.001)PGLVPPS(0.999)PEFAPR;S(0.051)PGLVPPS(0.949)PEFAPR ; 107.13 0.0069055 21241000 3835.9 4406.5 4788.6 2212.42 3416.23 4919.1 4526.5 5571.4 5035 3965.83 TRUE FALSE FALSE 3789.146575 4468.534823 4871.943574 2468.23041 3241.887035 4604.785386 4910.980797 5732.599669 4584.65699 3862.797165 0.980933353 1.156813219 1.261247579 0.638974894 0.839258935 1.192085732 1.271353526 1.484054022 1.186874898 1 11.91543021 -7.765826509 2.082335949 0.98997554 1.441821271 0.419361286 0.174895808 0.225466359 1.816197219 0.023491487 0.130717494 1.71E-08 7.765826509 0.451845731 SPGS(ph)PPGPELPIETALDDRER ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSPPGPELPIETALDDRER 21 1 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-8;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;Q5VWU8;Q8TEW0-9;Q8TEW0-10;F5GZI3;B1AP52 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 S(0.421)PGS(0.498)PPGPELPIET(0.081)ALDDRER 55.718 0.010167 6445000 2080.9 1895.2 1992.2 1621.1 1831.8 1657.5 1443.7 1838.2 2589.2 2211.6 TRUE FALSE FALSE 2055.53719 1921.880675 2026.873405 1808.53921 1738.316411 1551.591099 1566.327842 1891.385417 2357.615467 2154.142313 0.954225344 0.892179065 0.940918988 0.839563477 0.806964517 0.720282541 0.72712366 0.878022499 1.094456691 1 11.07289785 -9.360390367 0.79219795 0.982553319 0.764210331 0.720721254 0.059161503 0.20442043 0.254227948 0.009404739 0.020625903 4.36E-10 9.360390367 -0.218342988 SPGS(ph)PVGEGTGSPPK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGSPVGEGTGSPPK 15 0 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 S(0.001)PGS(0.987)PVGEGT(0.01)GS(0.001)PPK;S(0.169)PGS(0.83)PVGEGT(0.001)GSPPK ; 137.39 0.0011111 270428600 4183 4070.9 3819.8 3195.9 3864.2 4107.9 3545.5 3983.3 4382.3 3740.8 TRUE FALSE FALSE 4132.015987 4128.210237 3886.282017 3565.424995 3666.995455 3845.418448 3846.654682 4098.550501 3990.336112 3643.613477 1.134043447 1.132998948 1.066601066 0.978540951 1.00641725 1.055385944 1.055725232 1.12485875 1.095159006 1 11.83115421 -9.494826308 24.81292848 1.071699504 1.041272744 0.11358125 0.050872799 1850.540316 1636841.532 0.010149793 0.015478342 3.20E-10 9.494826308 -0.03042676 SPGS(ph)TPTT(ph)PTSSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 0 S(0.368)PGS(0.481)T(0.151)PT(0.046)T(0.905)PT(0.038)S(0.009)S(0.002)QAPQK 111.81 0.0083162 20519000 2385.6 2703.5 2597.4 1941 2732.8 2955.4 2368.2 2850 2918.6 2920.2 TRUE FALSE FALSE 2356.52339 2741.559944 2642.606657 2165.427553 2593.335019 2766.559478 2569.354849 2932.460253 2657.553106 2844.332783 0.828497778 0.963867505 0.929077875 0.76131301 0.911755134 0.972656749 0.903324275 1.03098353 0.934332692 1 11.47387455 -4.759199732 1.332038975 0.911583985 115.0050931 0.216173551 0.067119216 2117.926579 4.986907393 0.011673018 737574.0846 1.74E-05 4.759199732 114.0935091 SPGS(ph)TPTTPT(ph)SSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 3 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 2 0 S(0.008)PGS(0.977)T(0.015)PT(0.032)T(0.367)PT(0.476)S(0.102)S(0.022)QAPQK;S(0.083)PGS(0.825)T(0.11)PT(0.008)T(0.08)PT(0.398)S(0.397)S(0.098)QAPQK;S(0.086)PGS(0.786)T(0.141)PT(0.103)T(0.058)PT(0.632)S(0.158)S(0.036)QAPQK ;; 115.66 0.0022879 47534000 8687.03 8627.36 8145.96 7461.59 8904.4 8892.2 8447.34 9809.04 9738.79 9144.18 TRUE FALSE FALSE 8581.149137 8748.816201 8287.737017 8324.334144 8449.975241 8324.017118 9164.856849 10092.8491 8867.728231 8906.612885 0.963458191 0.982283199 0.930515014 0.934623998 0.948730494 0.934588404 1.028994632 1.133186008 0.995634182 1 13.12066118 -7.384386421 2.966453397 0.970286609 1.140968381 0.805335205 0.025751941 0.118158282 1.63873784 0.00420102 0.040454305 4.13E-08 7.384386421 0.170681772 SPGS(ph)TPTTPTSSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 S(0.001)PGS(0.921)T(0.061)PT(0.016)TPTSSQAPQK 138.98 0.0008644 56096000 5728.6 5562.8 5565 4831.2 5213.9 5312.5 5017.6 5646.2 5931.2 5121.6 TRUE FALSE FALSE 5658.77762 5641.113244 5661.856491 5389.806075 4947.815227 4973.048395 5443.794819 5809.563889 5400.698617 4988.540094 1.134355445 1.130814454 1.134972634 1.080437558 0.991836316 0.996894543 1.091260111 1.164581978 1.082621071 1 12.28440195 -12.50222929 1.281754172 1.000549042 1.09204216 0.032233784 0.059774424 0.524168201 1.555717284 0.041129169 0.010219325 3.15E-13 12.50222929 0.091493118 SPGSNSKVPEIEVT(ph)VEGPNNNNPQTSAVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPGSNSKVPEIEVTVEGPNNNNPQTSAVR 29 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347 A0A494C1K3 GTF2I General transcription factor II-I 1 0 S(0.004)PGS(0.03)NS(0.03)KVPEIEVT(0.936)VEGPNNNNPQTSAVR 63.563 0.00048825 19363000 954.59 1351 617.94 2385.3 724.8 859.9 477.32 622.77 1136.2 903.04 TRUE FALSE FALSE 942.9550899 1370.019413 628.6949865 2661.099609 687.8107514 804.9551652 517.8635489 640.7888674 1034.575426 879.5788906 1.072052888 1.557585599 0.714768161 3.025424595 0.781977329 0.915159713 0.588763048 0.728517788 1.176216753 1 9.780669171 -8.566923243 24.99999855 1.20540031 0.74858166 0.172988651 0.615772531 225.9265754 128236.8495 0.08824852 0.17649711 2.71E-09 8.566923243 -0.45681865 SPGSTPT(ph)TPTSSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SPGS(0.015)T(0.152)PT(0.621)T(0.162)PT(0.011)S(0.017)S(0.021)QAPQK;SPGS(0.178)T(0.178)PT(0.627)T(0.017)PTSSQAPQK ; 156.57 1.99E-06 6521000 2914.65 2896.81 2807.16 2362.03 2840.15 3657.6 3223.3 3093.25 3511.6 3365.8 TRUE FALSE FALSE 2879.125125 2937.591367 2856.017442 2635.139022 2695.206547 3423.891164 3497.087022 3182.748308 3197.513701 3278.356031 0.878222224 0.896056237 0.871173666 0.803798916 0.822121369 1.044392718 1.066719718 0.970836687 0.975340589 1 11.67875682 -8.232338533 24.74262988 0.914586139 1.031256739 0.462055393 0.063593454 587.6411042 499633.9478 0.010996042 0.02802905 5.86E-09 8.232338533 0.1166706 SPGSTPTT(ph)PTSSQAPQK ddPTM_HeLa_Romidepsin_16h_R1 2 SPGSTPTTPTSSQAPQK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SPGS(0.001)T(0.008)PT(0.101)T(0.822)PT(0.043)S(0.021)S(0.003)QAPQK;SPGST(0.004)PT(0.263)T(0.725)PT(0.005)S(0.002)SQAPQK ; 200 1.15E-18 21297300 9119.7 8327 8645.5 6745.1 8881.2 10265.9 10404.4 10203.3 9734.5 9114.9 TRUE FALSE FALSE 9008.545589 8444.227725 8795.971301 7525.000199 8427.959224 9609.942122 11288.14948 10498.51639 8863.821939 8878.093584 1.014693696 0.95113074 0.990750009 0.847591899 0.949298309 1.082433073 1.27146097 1.18251923 0.998392488 1 13.1160342 -7.955715262 3.962708268 0.986460629 1.224824383 0.79427295 0.052500909 0.077940931 2.605753319 0.008042383 0.025721894 1.11E-08 7.955715262 0.238363754 SPGT(ph)S(ph)GEGVSPVIT(ph)VRPVNVT(ph)AEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPGTSGEGVSPVITVRPVNVTAEK 24 1 A0A075B6G6;Q7Z7B0-3;Q7Z7B0-2;Q7Z7B0 A0A075B6G6 FILIP1 Filamin-A-interacting protein 1 4 0 S(0.076)PGT(0.946)S(0.947)GEGVS(0.094)PVIT(0.953)VRPVNVT(0.983)AEK 40.381 0.027874 29060000 2648.1 2726.4 2160.7 2565.6 2366.6 2246.4 2274 2384.5 2964.8 2552.4 TRUE FALSE FALSE 2615.823939 2764.782331 2198.306077 2862.246744 2245.823571 2102.86229 2467.153503 2453.491745 2699.620863 2486.08828 1.052184655 1.11210143 0.884242967 1.151305352 0.903356324 0.845851817 0.992383707 0.986888424 1.08589099 1 11.27966181 -8.689238012 25 1.028726182 0.93026216 0.323618666 0.079000513 42.68009072 14777.11683 0.010472821 0.020945641 2.05E-09 8.689238012 -0.098464022 SPITSS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPITSSPPK 9 0 G3V5T8;Q52LA3 G3V5T8 LIN52 Protein lin-52 homolog 1 0 SPIT(0.001)S(0.032)S(0.967)PPK 102.95 0.025649 51797000 6879.4 7007 6603.2 4682.4 4750.3 4957.9 4353.4 4541.8 7013.9 6422.2 TRUE FALSE FALSE 6795.551227 7105.64473 6718.125926 5223.801119 4507.874465 4641.106191 4723.177687 4673.209817 6386.559217 6255.350318 1.086358218 1.135930742 1.073980766 0.835093297 0.720643007 0.741941851 0.755062058 0.747074037 1.020975468 1 12.61087497 -9.124799305 3.42342425 1.052776573 0.744356841 0.944255074 0.037307686 0.053137786 1.153839762 0.00739768 0.012801335 7.50E-10 9.124799305 -0.308419731 SLSS(ph)PPSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SLSSPPSSK 9 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 S(0.005)LS(0.169)S(0.822)PPS(0.004)SK 115.57 0.015976 41678000 7458 9484.4 5351.1 5078.7 5280.8 3584.6 2910 2716.8 6930.6 6649.9 TRUE FALSE FALSE 7367.099027 9617.921632 5444.233651 5665.92319 5011.301071 3355.555629 3157.175327 2795.406322 6310.709778 6477.134639 1.13740094 1.484903768 0.840531185 0.874757668 0.773691045 0.518061738 0.487433951 0.431580703 0.974305789 1 12.66114002 -8.647292775 1.125566943 1.091287617 0.443016005 0.750187918 0.153796005 0.192660199 0.469419624 0.025456787 0.081370118 2.25E-09 8.647292775 -0.648271612 down SPLDPMTS(ph)PGSGLILQANFVHSQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLDPMTSPGSGLILQANFVHSQR 24 0 Q08499;Q08499-2;A0A1B0GW84;A0A087WSZ7;Q08499-10;Q08499-11;Q08499-6;Q08499-9;A0A1W2PQN6;Q08499-12;Q08499-7 Q08499 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 0 S(0.007)PLDPMT(0.33)S(0.643)PGS(0.02)GLILQANFVHSQR 81.329 8.34E-05 47658000 3343.8 3112.5 2954.8 3141.8 2588.7 2197.6 2065.9 2148.6 3243.9 3071.7 TRUE FALSE FALSE 3303.044479 3156.317857 3006.227055 3505.069699 2456.588979 2057.180452 2241.377494 2210.766351 2953.75746 2991.896791 1.103996799 1.05495546 1.004789692 1.171520926 0.821080789 0.68758403 0.749149336 0.738917986 0.987252457 1 11.54684469 -8.605212499 5.258303358 1.054247789 0.731317718 0.887288349 0.053904981 0.047085394 2.228698749 0.008014578 0.016314346 2.48E-09 8.605212499 -0.322930071 SPLELGEKLS(ph)PLPGGPGAGDPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLELGEKLSPLPGGPGAGDPR 22 1 Q15742;Q15742-3;Q15742-2 Q15742 NAB2 NGFI-A-binding protein 2 1 0 SPLELGEKLS(1)PLPGGPGAGDPR 71.418 0.0013991 32319000 2154.6 2239.3 1610.8 1673.5 1684.8 1297.4 1244 1429.4 1851.6 1810.6 TRUE FALSE FALSE 2128.338906 2270.824924 1638.835298 1866.997944 1598.818369 1214.500327 1349.665329 1470.757434 1685.988259 1763.560351 1.206842116 1.28763664 0.929276561 1.05865271 0.906585572 0.688663888 0.76530714 0.833970571 0.956013928 1 10.78427523 -8.697194346 1.675860003 1.106029296 0.759746938 0.612038091 0.109795112 0.17831056 1.010161441 0.01789198 0.043853425 2.01E-09 8.697194346 -0.346282358 SPLLAGGS(ph)PPQPVVPAHK ddPTM_HeLa_Romidepsin_16h_R1 2 SPLLAGGSPPQPVVPAHK 18 0 Q8NFH5-2;Q8NFH5;C9IYQ7;F8WCF5;F8WEL4;C9JIY9 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 S(0.001)PLLAGGS(0.999)PPQPVVPAHK;S(0.003)PLLAGGS(0.997)PPQPVVPAHK ; 110.34 0.00053562 283430000 13849.9 14306.1 13751 10205.6 10612.7 9848.8 8010.9 9267.4 14253.9 13543.6 TRUE FALSE FALSE 13681.09209 14507.50165 13990.33039 11385.61949 10071.09432 9219.493466 8691.345646 9535.537597 12978.99548 13191.73532 1.037095709 1.099741717 1.06053753 0.863087321 0.76343969 0.698884054 0.658847789 0.722841792 0.983873249 1 13.68734674 -8.914672243 2.051813309 1.02834722 0.695760708 0.942443556 0.037951998 0.053900509 0.458645343 0.006184957 0.012578346 1.22E-09 8.914672243 -0.332586512 SPLS(ph)PTETFSWPDVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLSPTETFSWPDVR 15 0 G3V311;A1L390-2;A1L390-3;A1L390 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 SPLS(0.988)PT(0.012)ETFSWPDVR 184 1.95E-08 13078000 1274.1 1267.5 1378.4 1539.8 1267.2 1351.3 1000.9 1175.2 1264 1379.4 TRUE FALSE FALSE 1258.570779 1285.343898 1402.390474 1717.838921 1202.530055 1264.956291 1085.916421 1209.202558 1150.944674 1343.562989 0.936741179 0.956668134 1.043784687 1.278569695 0.89503065 0.94149385 0.808236331 0.899996924 0.856636186 1 10.39184824 -8.223939882 2.585208554 0.994668143 0.863679198 0.204623788 0.110137314 0.342813319 4.475400069 0.015253886 0.044283563 5.97E-09 8.223939882 -0.130988945 SPLTILQDDNS(ph)PGTLTLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLTILQDDNSPGTLTLR 18 0 Q99618;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 SPLTILQDDNS(0.652)PGT(0.322)LT(0.026)LR 149.74 6.27E-11 0 787.48 649.78 526.33 621.6 738.28 760.45 771.91 684.06 727.84 566.59 TRUE FALSE FALSE 777.8818909 658.9276199 535.4905529 693.4723167 700.6028167 711.8596992 837.4760161 703.8521968 662.7401675 551.8699101 1.40953851 1.193990844 0.970320257 1.256586569 1.269507186 1.289904896 1.517524331 1.275395132 1.200899261 1 9.108184417 -12.50524296 1.210715316 0.997531635 1.283943691 0.127612836 0.146076853 0.439448161 1.13683263 0.106091364 0.024760178 3.12E-13 12.50524296 0.286412056 NIPSPGQLDPDT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 NIPSPGQLDPDTR 13 0 Q9P2D1 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 0 NIPS(0.391)PGQLDPDT(0.609)R 130.66 0.0049209 12114000 2872.5 2483.2 2919.8 2316.3 1895.1 1768.8 1311.5 1243.3 2887.9 3186.1 TRUE FALSE FALSE 2837.488865 2518.158555 2970.617894 2584.121505 1798.385975 1655.779389 1422.898777 1279.272924 2629.598991 3103.324663 0.914338387 0.811438966 0.957237227 0.832694541 0.579503008 0.533550166 0.458507869 0.412226584 0.847348981 1 11.59959892 -8.643123616 0.934949253 0.955646126 0.406422063 0.903543127 0.064040022 0.109549471 0.176363189 0.010069633 0.037259902 2.27E-09 8.643123616 -0.549224062 down SPLWRGGGVAHGPRGPTS(ph)Y(ph)YYMLPMK ddPTM_HeLa_Romidepsin_16h_R1 1 SPLWRGGGVAHGPRGPTSYYYMLPMK 26 2 K7EJ73;K7ELQ0;K7ES61;X6RAY8;Q9BYD3-2;Q9BYD3 K7EJ73 MRPL4 "39S ribosomal protein L4, mitochondrial" 2 0 S(0.001)PLWRGGGVAHGPRGPT(0.134)S(0.486)Y(0.46)Y(0.46)Y(0.46)MLPMK 43.162 0.0040401 0 287.6 218.54 168.14 315.77 309.94 192.94 160.76 167.5 221.29 245.72 TRUE FALSE FALSE 284.0946206 221.6166119 171.0664062 352.2808131 294.1226053 180.6117567 174.4149504 172.3463482 201.4972682 239.336159 1.187010863 0.925963769 0.714753704 1.471908025 1.228910026 0.754636313 0.728744671 0.720101588 0.841900651 1 7.902894566 -8.217098912 10.0053379 1.086579473 0.733376022 0.332860942 0.202701914 0.492133907 108.7293246 0.027229547 0.069375708 6.07E-09 8.217098912 -0.353203451 SPMFPALGEAS(ph)SDDDLFQSAKPK ddPTM_HeLa_Romidepsin_16h_R1 1 SPMFPALGEASSDDDLFQSAKPK 23 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;Q5SRD0;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21D;FAM21A WASH complex subunit FAM21C;Putative WASH complex subunit FAM21;WASH complex subunit FAM21A 1 0 SPMFPALGEAS(0.819)S(0.181)DDDLFQSAKPK 102.07 3.38E-05 25446000 2036.8 1944.5 2399.1 1488.7 2094.4 2466.8 1953.3 2060.1 2349.3 2271.7 TRUE FALSE FALSE 2011.974698 1971.874722 2440.855329 1660.830499 1987.514953 2309.179441 2119.213253 2119.705743 2139.172724 2212.680907 0.909292746 0.891169945 1.103121251 0.750596479 0.898238398 1.043611591 0.957758187 0.957980763 0.966778679 1 11.1115797 -12.47990688 1.227326204 0.999919874 0.936191247 0.032957899 0.089389307 1.111944227 3.002960555 0.059213838 0.014582994 3.31E-13 12.47990688 -0.063728627 SPMFPALGEAS(ph)SDDDLFQSAKPKPAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPMFPALGEASSDDDLFQSAKPKPAK 26 2 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;Q5SRD0;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21D;FAM21A WASH complex subunit FAM21C;Putative WASH complex subunit FAM21;WASH complex subunit FAM21A 1 0 S(0.001)PMFPALGEAS(0.496)S(0.496)DDDLFQS(0.007)AKPKPAK 42.289 0.020211 19063000 780.39 985.93 760.91 719.08 718.38 882.88 951.7 939.58 1056.6 776.63 TRUE FALSE FALSE 770.8783065 999.8099484 774.1533194 802.223413 681.718388 826.4668174 1032.537374 966.7652649 962.0950497 756.4530406 1.019069612 1.321707885 1.023399045 1.060506561 0.901203844 1.092555351 1.364972204 1.278024164 1.27185033 1 9.563106715 -7.851202493 4.914761765 1.031107618 1.320578359 0.287432689 0.128861363 0.108537074 4.405301699 0.014622537 0.046950967 1.41E-08 7.851202493 0.289470741 SPPAEEAAS(ph)PEKEAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPAEEAASPEKEAK 15 1 P12036-2;P12036 P12036-2 NEFH Neurofilament heavy polypeptide 1 0 SPPAEEAAS(1)PEKEAK 104.26 0.0017115 0 549.67 705.1 779.76 1049.7 628.96 597.64 535.54 405.57 812.14 593.67 TRUE FALSE FALSE 542.9704106 715.0264163 793.3313957 1171.071253 596.8618242 559.4527328 581.0287542 417.3045281 739.5001644 578.2463678 0.938994935 1.236542858 1.37196088 2.025211602 1.03219295 0.967498914 1.004811766 0.721672545 1.278866942 1 9.175540489 -6.030220112 16.3377466 1.072194469 1.082168602 0 0.350820032 0 0 0.048026609 0 9.33E-07 6.030220112 0.009974133 SPPAS(ph)PESWK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPASPESWK 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 S(0.437)PPAS(0.531)PES(0.032)WK 96.334 0.029367 12133000 2311.4 2582.8 2205.7 2478.1 1525.8 1032.6 1193.1 1308.3 2619.6 2236.4 TRUE FALSE FALSE 2283.227768 2619.160726 2244.089283 2764.629582 1447.932732 966.6201926 1294.441884 1346.153596 2385.296415 2178.298006 1.048170527 1.202388617 1.030203066 1.269169588 0.664708285 0.443750208 0.594244626 0.617984129 1.09502759 1 11.08898562 -8.622965806 5.986894172 1.053591259 0.556171867 0.876221529 0.096420669 0.054635951 2.779450031 0.014090421 0.028434027 2.38E-09 8.622965806 -0.497419393 SPPLIGSESAYESFLSADDKAS(ph)GR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPLIGSESAYESFLSADDKASGR 24 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SPPLIGSESAYES(0.001)FLS(0.392)ADDKAS(0.606)GR 57.156 0.0029602 0 839.51 921.73 1159.5 993.31 862.12 748.06 741.64 708.32 1221.2 1231.2 TRUE FALSE FALSE 829.2777292 934.7061391 1179.680611 1108.161176 818.1227994 700.2613803 804.6348831 728.8141217 1111.972813 1199.213247 0.691518153 0.779432801 0.983712125 0.924073495 0.68221628 0.583933994 0.670968975 0.607743555 0.927251943 1 10.22787251 -16.52287875 0.078477172 1.830925748 0.44828851 0.477124804 0.109538072 149.2958325 0.901011778 22.64102256 2.608978184 3.00E-17 16.52287875 -1.382637238 SPPLLES(ph)PDATR ddPTM_HeLa_Romidepsin_16h_R1 3 SPPLLESPDATR 12 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 0 SPPLLES(1)PDATR;S(0.163)PPLLES(0.837)PDATR;S(0.001)PPLLES(0.722)PDAT(0.276)R ;; 123.95 0.0026988 13400700 2668.39 2780.2 2573.93 2834.3 2625.51 2373.58 2114.48 1969.61 3002.39 3056.37 TRUE FALSE FALSE 2635.866636 2819.339729 2618.728172 3162.015102 2491.520428 2221.915898 2294.083878 2026.597558 2733.848719 2976.965067 0.885420748 0.947051667 0.879663722 1.062160634 0.836933041 0.74636949 0.770611622 0.680759603 0.918334162 1 11.53962658 -8.494192579 4.108951611 0.946852919 0.740192647 0.754757126 0.055239435 0.088589636 3.337138354 0.008764012 0.019582559 3.20E-09 8.494192579 -0.206660272 SPPLS(ph)PVGTTPVK ddPTM_HeLa_Romidepsin_16h_R1 2 SPPLSPVGTTPVK 13 0 C9J4K0;Q9BVC5-2;Q9BVC5 C9J4K0 C2orf49 Ashwin 1 0 S(0.038)PPLS(0.885)PVGT(0.033)T(0.044)PVK;SPPLS(0.975)PVGT(0.018)T(0.006)PVK ; 116.79 0.0054875 20502100 5065.8 4830.4 4687.3 4405.1 4637 4213.6 3858.7 4124.6 5218.8 5002.6 TRUE FALSE FALSE 5004.056081 4898.402498 4768.88049 4914.438389 4400.356587 3944.364559 4186.457882 4243.938793 4752.017457 4872.631731 1.026971944 1.005288881 0.97870735 1.008579893 0.903075962 0.809493673 0.859177979 0.870974666 0.975246585 1 12.25048547 -8.639888887 3.189962533 1.009691888 0.847987424 0.905897022 0.022210458 0.043949794 0.887261859 0.00304158 0.006483848 2.29E-09 8.639888887 -0.161704463 SPPPS(ph)PPTHR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPPSPPTHR 10 0 Q96HA1 Q96HA1 POM121 Nuclear envelope pore membrane protein POM 121 1 0 SPPPS(0.825)PPT(0.175)HR 81.278 0.024409 1942400 169.04 236.58 178.33 191.66 209.62 141.1 133.14 60.059 188.46 160.62 TRUE FALSE FALSE 166.9796755 239.9105794 181.4337588 213.820631 198.9223092 132.0841654 144.4489083 61.79671241 171.6036656 156.4470692 1.067323768 1.5334936 1.159713376 1.366728262 1.271499109 0.844273824 0.923308496 0.395000767 1.096880027 1 7.289530822 -7.16604213 1.321738177 1.114448058 6.28E-12 0.622539405 0.182778726 1.011012567 1.291377363 0.029971696 1.599831282 6.82E-08 7.16604213 -1.114448058 SPPREGS(ph)QGELTPANSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPREGSQGELTPANSQSR 19 1 J3QQX0;C9JFE4;A0A096LP07;A0A096LPJ3;A8K070;Q13098-5;Q13098;Q13098-7 J3QQX0 GPS1 COP9 signalosome complex subunit 1 1 0 S(0.301)PPREGS(0.693)QGELT(0.006)PANSQSR 60.334 0.013363 13220000 227.71 209.48 304.76 142.84 295.11 332.72 143.04 192.03 160.84 273.08 TRUE FALSE FALSE 224.9345829 212.4290649 310.06422 159.3558329 280.0494355 311.4602658 155.189814 197.5860851 146.4540676 265.9853422 0.845665333 0.798649516 1.165719198 0.599115092 1.052875445 1.17096778 0.583452504 0.742845765 0.550609542 1 8.055202934 -4.000004592 0.027130578 1.505944543 9.25E-09 0 0.235867248 3513.834764 7.397579016 137.5622964 304.0170377 1.00E-04 4.000004592 -1.505944534 SPPS(ph)PATDQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPSPATDQR 10 0 Q6F5E8;Q6F5E8-2 Q6F5E8 RLTPR Leucine-rich repeat-containing protein 16C 1 0 S(0.025)PPS(0.857)PAT(0.118)DQR 101.56 0.023491 12472000 1022.9 881.39 867.64 1442.5 1696.2 2207.6 2095.2 1929.3 1362.7 1078.5 TRUE FALSE FALSE 1010.432501 893.7982316 882.7409102 1609.288637 1609.636585 2066.541485 2273.166236 1985.121252 1240.816699 1050.480415 0.961876573 0.850847116 0.84032115 1.531954918 1.532286145 1.967234663 2.163930145 1.889727047 1.181189751 1 10.03683355 -8.758391009 1.361805785 0.960168806 2.033097416 0.894755709 0.151958605 0.077150095 0.285725288 0.020920061 0.054131036 1.74E-09 8.758391009 1.072928609 SPPS(ph)TGSTYGSSQK ddPTM_HeLa_Romidepsin_16h_R1 2 SPPSTGSTYGSSQK 14 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.117)PPS(0.648)T(0.117)GS(0.117)T(0.001)YGSSQK;S(0.036)PPS(0.654)T(0.273)GS(0.03)T(0.008)YGSSQK ; 168.93 6.84E-05 121213000 4506.8 4641.6 4508.9 1562.8 4221.5 4307.3 3605.8 3980.3 3942.8 4496.8 TRUE FALSE FALSE 4451.869388 4706.944567 4587.375513 1743.498289 4006.061102 4032.077431 3912.076562 4095.463701 3590.146093 4379.972488 1.016414921 1.074651628 1.047352586 0.39806147 0.914631568 0.920571406 0.893173775 0.935043248 0.819673206 1 12.09670609 SPPVLGSAAAS(ph)PVHLK ddPTM_HeLa_Romidepsin_16h_R1 1 SPPVLGSAAASPVHLK 16 0 O00512 O00512 BCL9 B-cell CLL/lymphoma 9 protein 1 0 SPPVLGS(0.002)AAAS(0.998)PVHLK 110.6 0.0012732 16077000 4072.4 4898.8 4054.2 4572.3 4773.3 4465 4048.3 3889.2 5358.8 4928.8 TRUE FALSE FALSE 4022.764022 4967.765435 4124.76165 5100.970839 4529.700689 4179.70091 4392.162501 4001.727866 4879.495507 4800.749065 0.837945072 1.034789648 0.859191262 1.062536444 0.943540399 0.870635156 0.914891081 0.833563223 1.016402949 1 12.22904381 -7.793371146 0.009107663 1.801179626 2.63E-05 0.125370342 0.076605547 13258.43259 22.87899366 2142.354476 2386.839817 1.61E-08 7.793371146 -1.80115337 SPPY(ph)TAFLGNLPYDVTEESIKEFFR ddPTM_HeLa_Romidepsin_16h_R1 1 SPPYTAFLGNLPYDVTEESIKEFFR 25 1 E7EX17;P23588-2;P23588;F8VP89;F8VX11;F8W0K0;F8VSC7;F8VRU1;F8VYE9 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.277)PPY(0.522)T(0.2)AFLGNLPYDVTEESIKEFFR 74.308 0.00093536 65687000 66.562 146.87 0 0 0 0 0 0 120.7 0 TRUE FALSE FALSE 65.75071674 148.9376397 0 0 0 0 0 0 109.9042897 0 0 SPQQEEET(ph)GMT(ph)NGFGK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQQEEETGMTNGFGK 16 0 H0Y7I6;E9PI60;Q9ULD4 H0Y7I6 BRPF3 Bromodomain and PHD finger-containing protein 3 2 0 SPQQEEET(1)GMT(1)NGFGK 75.739 0.0038657 0 200.6 276.72 231.28 261.26 324.58 172.08 270.32 227.93 289.35 167.87 TRUE FALSE FALSE 198.15501 280.6156714 235.3053314 291.4681105 308.0154714 161.0846434 293.2809741 234.5247949 263.4698113 163.5087132 1.211892664 1.716212341 1.439099647 1.782584578 1.883786285 0.985174675 1.793671837 1.434325978 1.611350283 1 7.353223707 -10.46215714 2.771388748 1.083308565 1.57668539 0.088392515 0.298374152 0.171372451 2.535493527 0.043507743 0.048121971 3.45E-11 10.46215714 0.493376825 SPQQTVPY(ph)VVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 2 0 S(0.04)PQQT(0.262)VPY(0.704)VVPLS(0.993)PK 141.06 0.0016697 19445000 4396.7 4364.4 3961.9 3261.3 4491.1 5085.5 4537.3 4908.5 4359.6 4425.3 TRUE FALSE FALSE 4343.111329 4425.842138 4030.855208 3638.386851 4261.902408 4760.552963 4922.698149 5050.519703 3969.666457 4310.330068 1.007605279 1.026798892 0.93516161 0.84410864 0.988764744 1.104452069 1.142069881 1.171724583 0.920965772 1 12.07358263 -8.127090058 3.13778131 0.987029864 1.152628258 0.679162603 0.054984591 0.131481452 2.434338049 0.008153574 0.023866913 7.46E-09 8.127090058 0.165598394 SPQQTVPYVVPLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SPQQTVPYVVPLSPK 15 0 Q9UQR0;H0Y6S1;B4DRC2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 0 SPQQTVPYVVPLS(1)PK 115.29 0.0038785 26449000 2187.1 1875.8 1991.9 2478.4 2500.2 2476.4 2372.2 2282.6 2380.9 1783.1 TRUE FALSE FALSE 2160.442784 1902.207562 2026.568184 2764.964269 2372.605464 2318.166032 2573.694609 2348.64343 2167.946341 1736.774805 1.243939501 1.095252854 1.166857199 1.592010813 1.366098505 1.334753375 1.48188159 1.352301647 1.248259898 1 10.76219499 -10.65757446 0.227221991 0.906353496 1.513535756 0.357568129 0.134292995 1.177482564 0.24195272 0.287222596 0.230405142 2.20E-11 10.65757446 0.60718226 SPRPAS(ph)PASNVVVLPSGSTVYVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPRPASPASNVVVLPSGSTVYVK 23 1 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 S(0.083)PRPAS(0.76)PAS(0.157)NVVVLPSGSTVYVK 129.22 2.60E-06 24727000 3154.8 3274.3 2994.9 3458.2 3464.3 3115.3 3027.5 3788 3500.6 3121 TRUE FALSE FALSE 3116.348084 3320.395681 3047.024978 3858.053355 3287.503844 2916.242384 3284.655774 3897.599804 3187.497569 3039.91597 1.025142838 1.092265613 1.002338554 1.269131579 1.081445631 0.959316775 1.08050874 1.282140639 1.04854792 1 11.56981573 -4 0.15931161 0.979002732 1.702020758 0.196451893 0.092989963 69.38596217 0.700087358 0.167800481 11.8155795 1.00E-04 4 0.723018026 SPRPT(ph)SAPAITQGQVAEGGVLDASAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPRPTSAPAITQGQVAEGGVLDASAK 26 1 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A3B3ITP0;A0A2R8Y7Y3;A0A2R8Y5G2;A0A2U3TZH6;A0A2R8Y420;A0A2R8YCW8;A0A2R8Y5Z6;P11171-5;P11171-7;P11171-6;A0A3B3IU06;A0A2R8Y570;A0A2R8Y6G5;A0A2R8YFR9;A0A2R8Y7N0;A0A3B3IUD6;A0A2R8Y4N6;A0A2R8Y5C8;A0A2R8Y6D0;A0A1B0GWG0 P11171 EPB41 Protein 4.1 1 0 S(0.01)PRPT(0.495)S(0.495)APAITQGQVAEGGVLDASAK 89.239 1.06E-05 13182000 2379.5 1895.4 2265 1513.2 2709.3 2806.1 2234 2584.9 2509.8 2570.2 TRUE FALSE FALSE 2350.497739 1922.083491 2304.421375 1688.163304 2571.034311 2626.799266 2423.755904 2659.690003 2285.317202 2503.425833 0.938912472 0.76778128 0.920507148 0.674341249 1.027006383 1.049281841 0.968175638 1.062420131 0.912875936 1 11.289688 SPS(ph)AIPEQNHSLNDQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSAIPEQNHSLNDQAK 17 0 Q13129 Q13129 RLF Zinc finger protein Rlf 1 0 S(0.268)PS(0.732)AIPEQNHSLNDQAK 101.62 0.0012691 15734000 3065.7 3067.2 2683.5 2649.6 3195.9 3138.7 2735.2 3195.2 3168.9 2796 TRUE FALSE FALSE 3028.334069 3110.380122 2730.205192 2955.959219 3032.801297 2938.1472 2967.52782 3287.648071 2885.465647 2723.359517 1.111984683 1.142111463 1.002513688 1.085409106 1.11362502 1.078868648 1.089657022 1.207203107 1.059524323 1 11.41117173 -16.52287874 0.23676921 0.397591551 1.11482686 0.216990725 0.051833828 36.13700821 0.470087188 10.12782671 0.032574947 3.00E-17 16.52287874 0.71723531 SPS(ph)ELFAQHIVTIVHHVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSELFAQHIVTIVHHVK 18 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.449)PS(0.551)ELFAQHIVTIVHHVK 109.85 0.0004297 11369000 4206.2 4025.2 4035 4049.7 3787.2 4148.9 3393.8 4224.9 4175.2 4033.3 TRUE FALSE FALSE 4154.933217 4081.866871 4105.227482 4517.945368 3593.925052 3883.79868 3682.069287 4347.140816 3801.759655 3928.514285 1.057634748 1.039035772 1.044982196 1.150039186 0.914830593 0.988617681 0.937267634 1.106561031 0.967734716 1 11.93976809 -8.723641193 24.99996041 1.037992213 0.983408419 0.15213327 0.064339329 239.0251329 158091.652 0.008571307 0.017142332 1.89E-09 8.723641193 -0.054583794 SPS(ph)FASEWDEIEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSFASEWDEIEK 13 0 Q92625;A0A3B3ISP1 Q92625 ANKS1A Ankyrin repeat and SAM domain-containing protein 1A 1 0 S(0.001)PS(0.9)FAS(0.099)EWDEIEK 153.32 0.00076895 80259000 2787.5 2292.8 2301.9 2613.1 3301 2986.6 2857.8 3438.2 2737.1 2314.6 TRUE FALSE FALSE 2753.524878 2325.078099 2341.963604 2915.238917 3132.537652 2795.765899 3100.541461 3537.678892 2492.286921 2254.466358 1.221364368 1.031320822 1.038810624 1.293094885 1.38948077 1.240100962 1.375288413 1.569186819 1.105488628 1 11.13857027 -4 0.222496578 1.041383567 3.663406408 0.728474021 0.091753178 22.08423141 0.26535185 0.076295453 21.07023601 1.00E-04 4 2.622022842 SPS(ph)KPLPEVTDEYKNDVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSKPLPEVTDEYKNDVK 18 2 P05455;E9PGX9;E7ERC4;E9PFL9 P05455 SSB Lupus La protein 1 0 S(0.344)PS(0.656)KPLPEVTDEYKNDVK 79.514 0.0051303 59366000 4338.6 3655.3 4456.9 3555.5 3498.6 3118 2812.3 2900.5 4851.3 3985.6 TRUE FALSE FALSE 4285.719474 3706.759409 4534.470475 3966.603639 3320.053387 2918.769863 3051.176692 2984.421391 4417.387578 3882.053537 1.103982579 0.954845 1.168059748 1.021779736 0.855231221 0.751862342 0.785969761 0.768773888 1.137899706 1 11.9226043 -8.674499338 2.96745586 1.051683947 0.773236143 0.834222155 0.0606648 0.074838067 1.32630073 0.008625463 0.01832861 2.12E-09 8.674499338 -0.278447804 SPS(ph)PISNQPSPR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSPISNQPSPR 12 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 0 S(0.002)PS(0.997)PIS(0.001)NQPSPR;S(0.026)PS(0.53)PIS(0.281)NQPS(0.164)PR;S(0.39)PS(0.595)PIS(0.003)NQPS(0.012)PR ;; 143.56 0.0015299 47026500 2160.03 1751.64 1931.26 2436.93 2338.36 2340.95 1878.73 2413.81 2308.56 1971.81 TRUE FALSE FALSE 2133.702724 1776.299634 1964.87277 2718.699313 2219.024764 2191.37085 2038.309279 2483.649784 2102.076612 1920.582092 1.110966687 0.924875662 1.02306107 1.415560066 1.155391781 1.140993066 1.06129766 1.29317554 1.094499746 1 10.90732792 SPS(ph)PLGTSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPLGTSVR 10 0 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;G5E9V3;E9PDY7 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 S(0.126)PS(0.866)PLGT(0.008)SVR 123.62 0.010036 11789000 1367.7 1148.3 1027.2 1610 1091.3 919.97 797.05 649.89 1038.7 958.9 TRUE FALSE FALSE 1351.029946 1164.465798 1045.077985 1796.155775 1035.606889 861.1868861 864.7514071 668.6935418 945.7960705 933.9876398 1.446518015 1.246767889 1.118941987 1.923104438 1.108801492 0.922053836 0.92587029 0.715955451 1.012643027 1 9.867259647 -8.32085677 3.803137453 1.263119043 0.855503662 0.359635941 0.256692852 0.218246195 6.365169571 0.039358442 0.095538142 4.78E-09 8.32085677 -0.407615381 SPS(ph)PSAPSCPGVGASSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPSAPSCPGVGASSPR 18 0 Q6ZRN7 Q6ZRN7 Putative uncharacterized protein FLJ46214 1 0 S(0.044)PS(0.468)PS(0.468)APS(0.02)CPGVGASSPR 81.327 0.012558 4898000 2071.9 1859.2 1738 1699.3 1239.8 1239.3 1048.8 1149.6 1686.5 1755 TRUE FALSE FALSE 2046.646886 1885.373866 1768.249161 1895.781061 1176.52838 1160.11273 1137.885046 1182.861862 1535.655216 1709.404847 1.197286231 1.102941687 1.03442386 1.109029885 0.688267839 0.678664701 0.66566153 0.691972919 0.898356652 1 10.7392784 -8.759269144 24.48241693 1.092243851 0.679858981 0.843992204 0.078291058 10.65704416 120218.0874 0.010992582 0.021152897 1.74E-09 8.759269144 -0.412384871 SPS(ph)PSPTPEAK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPSPTPEAK 11 0 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 0 S(0.015)PS(0.976)PS(0.009)PTPEAK;S(0.138)PS(0.834)PS(0.028)PTPEAK ; 125.36 0.0076513 19566900 8322.2 8668.5 8000.5 8186.2 8929 9525.7 7955 8119 8883.3 8329.9 TRUE FALSE FALSE 8220.765825 8790.535371 8139.745346 9132.726961 8473.319811 8917.038513 8630.697501 8353.910455 8088.755399 8113.487997 1.013222159 1.083447141 1.003236259 1.125622786 1.04434983 1.099038849 1.063746875 1.029632441 0.996951669 1 12.98610655 -10.32405347 1.271285075 1.003479846 1.067425894 0.390683769 0.033633771 0.27396353 0.856728811 0.006232115 0.007201486 4.74E-11 10.32405347 0.063946048 SPS(ph)SPVPVVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSSPVPVVK 10 0 A2RUB6;A2RUB6-3 A2RUB6 CCDC66 Coiled-coil domain-containing protein 66 1 0 S(0.076)PS(0.866)S(0.058)PVPVVK 103.08 0.022513 7815800 4690 4189.7 5127.7 5426 3507.6 2944.4 2536.9 3014.7 4812.3 4015.6 TRUE FALSE FALSE 4632.836476 4248.682707 5216.945468 6053.37965 3328.594083 2756.262343 2752.384223 3101.925588 4381.875835 3911.274133 1.184482682 1.086265642 1.333822506 1.547674605 0.851025515 0.704696794 0.703705271 0.793072918 1.120319284 1 11.93342294 -8.539339422 24.99796482 1.140855326 0.738654295 0.665288294 0.152715266 133.6869509 203022.7769 0.025186144 0.050382375 2.89E-09 8.539339422 -0.40220103 SPS(ph)WQRPNQGVPSTGR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSWQRPNQGVPSTGR 16 1 Q96HC4;H0Y8Y3;Q96HC4-7;Q96HC4-4;Q96HC4-6;A0A0A0MSP3 Q96HC4 PDLIM5 PDZ and LIM domain protein 5 1 0 S(0.17)PS(0.83)WQRPNQGVPSTGR 144.15 0.0021075 7286800 798.91 845.23 915.42 702.14 914.91 1169.1 707.74 1038.1 725.54 822.19 TRUE FALSE FALSE 789.1725776 857.1291701 931.3525011 783.3247305 868.2187287 1094.398283 767.8554179 1068.135786 660.6458853 800.8293853 0.985444081 1.070301847 1.162984923 0.978141843 1.084149439 1.366581076 0.958825228 1.333786953 0.824952103 1 9.645351103 -8.46278456 0.419673281 0.986497164 1.267950051 0.366105897 0.128097955 1.915990975 0.439039673 0.03314397 0.232487563 3.45E-09 8.46278456 0.281452887 SPSAPAATSSASSSTSSYK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SPSAPAATSSASSSTSSYKR 20 1 A0A087X0S7;A0A0C4DH00;A0A087WTU1;A0A0B4J2G4;Q15345-3;Q15345 A0A087X0S7 LRRC41 Leucine-rich repeat-containing protein 41 0 1 SPSAPAATSSASSSTSSYK(1)R 239.51 1.99E-54 1021600 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 SPSDSSTAS(ph)TPVAEQIER ddPTM_HeLa_Romidepsin_16h_R1 2 SPSDSSTASTPVAEQIER 18 0 Q16643-3;Q16643;Q16643-2;D6R9Q9 Q16643-3 DBN1 Drebrin 1 0 SPSDS(0.015)S(0.065)T(0.214)AS(0.491)T(0.214)PVAEQIER;SPSDSSTAS(0.688)T(0.312)PVAEQIER ; 169.02 3.57E-07 60822000 3372 3320.2 3371.8 3737.2 3776.4 3697.8 3426.9 3309 3683.2 3290.7 TRUE FALSE FALSE 3330.900767 3366.941863 3430.484765 4169.312648 3583.676216 3461.522514 3717.9808 3404.740694 3353.765367 3205.20714 1.039215446 1.050459991 1.070284888 1.300793511 1.118079444 1.079968427 1.159981442 1.062252936 1.046349026 1 11.64620188 -9.513419341 21.04306311 1.023285697 1.144616746 0.413904856 0.061936279 36.94146363 82178.41249 0.009515449 0.013924748 3.07E-10 9.513419341 0.121331049 SPSEGQTATTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSEGQTATTSPR 13 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 SPSEGQTATT(0.019)S(0.981)PR 115.83 0.0056667 7011000 2876.6 3377.1 3436.3 3538.8 4119.5 3813.6 3182 2825.5 3532.2 3315.3 TRUE FALSE FALSE 2841.538893 3424.642902 3496.10736 3947.972707 3909.266543 3569.923268 3452.279001 2907.251385 3216.271185 3229.168028 0.87996006 1.060534129 1.082665049 1.222597484 1.210611064 1.105524159 1.069092401 0.900309727 0.996006141 1 11.6569468 -10.07495607 4.37550895 0.943537656 1.106200061 0.32409656 0.088878977 0.17613873 6.341690202 0.016116306 0.020082757 8.41E-11 10.07495607 0.162662404 SPSFGDPQLS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSFGDPQLSPEAR 14 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 SPSFGDPQLS(1)PEAR;SPSFGDPQLS(1)PEAR ; 142.19 0.00074081 21444000 3276.1 3450.9 3353.1 1940.9 3458.9 3542.6 3386.8 3510.4 3680.8 3646.4 TRUE FALSE FALSE 3236.169633 3499.481861 3411.459299 2165.31599 3282.379426 3316.239293 3674.474707 3611.967886 3351.580029 3551.666002 0.911169471 0.985307137 0.96052368 0.609662054 0.924180208 0.933713725 1.034577774 1.016978478 0.943664192 1 11.7942802 -8.370954507 0.007841943 1.845693548 1.48E-06 0 0.115134753 23229.27739 43.81368759 4971.57983 5343.793811 4.26E-09 8.370954507 -1.845692069 SPSFGDPQLS(ph)PEARPR ddPTM_HeLa_Romidepsin_16h_R1 4 SPSFGDPQLSPEARPR 16 1 O95425-2;O95425-3 O95425-2 SVIL Supervillin 1 0 SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;SPSFGDPQLS(1)PEARPR;S(0.001)PS(0.063)FGDPQLS(0.936)PEARPR ;;; 139 0.00093064 118387000 8286.42 7877.65 7342.93 8960.59 8640.6 9317.49 8293.29 8933 8357.69 7584.7 TRUE FALSE FALSE 8185.421926 7988.551763 7470.730616 9996.655577 8199.637939 8722.13246 8997.721846 9191.462261 7610.157274 7387.648401 1.107987479 1.081338923 1.011246098 1.353158006 1.109911774 1.180637192 1.217941266 1.244166176 1.030119039 1 12.85089949 -4.000000006 0.072023839 0.813024927 1.939452593 0.480516496 0.078038716 130.0632355 0.696785209 1.891143576 14.86740421 1.00E-04 4.000000006 1.126427666 SPSGGAAGPLLTPS(ph)QSLDGSRR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSGGAAGPLLTPSQSLDGSRR 22 1 Q96CX2 Q96CX2 KCTD12 BTB/POZ domain-containing protein KCTD12 1 0 SPSGGAAGPLLT(0.199)PS(0.595)QS(0.199)LDGS(0.007)RR;S(0.004)PS(0.001)GGAAGPLLT(0.014)PS(0.489)QS(0.489)LDGS(0.004)RR ; 109.77 0.00019254 37916000 1757.12 1483.09 1676.29 1346.19 1345.35 1565.32 1523.48 1496.27 1877.55 1775.39 TRUE FALSE FALSE 1735.703546 1503.96898 1705.465124 1501.842822 1276.691769 1465.301104 1652.884353 1539.562212 1709.617226 1729.265112 1.00372322 0.869715678 0.986236935 0.868486163 0.738285738 0.847354806 0.95583051 0.890298544 0.988638014 1 10.75594335 -9.92180725 1.134520306 1.003233098 0.864006592 0.420018027 0.062749097 0.296837998 0.754104052 0.012588505 0.01762783 1.20E-10 9.92180725 -0.139226506 SPSGSAFGS(ph)QENLR ddPTM_HeLa_Romidepsin_16h_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 0 SPSGSAFGS(1)QENLR;SPSGSAFGS(1)QENLR;SPSGS(0.018)AFGS(0.982)QENLR;SPSGSAFGS(1)QENLR ;;; 172.43 3.61E-05 62195000 5622.22 6273.42 4950.94 3898.69 4667.11 4781.41 4451.75 4661.06 6256.34 5958.01 TRUE FALSE FALSE 5553.69422 6361.737371 5037.109034 4349.474882 4428.929961 4475.893332 4829.881534 4795.920417 5696.757281 5803.220041 0.957002178 1.096242659 0.867985187 0.749493359 0.763184909 0.771277549 0.832276133 0.826424017 0.981654537 1 12.50263792 -9.548475359 7.02176442 0.987877508 0.790351923 0.850054531 0.043294629 0.051064441 9.35845945 0.006983667 0.009980809 2.83E-10 9.548475359 -0.197525586 SPSLS(ph)PSPPSPLEK ddPTM_HeLa_Romidepsin_16h_R1 2 SPSLSPSPPSPLEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SPS(0.01)LS(0.81)PS(0.179)PPSPLEK;SPS(0.116)LS(0.825)PS(0.058)PPSPLEK ; 163.62 0.00018023 18739400 7991.7 8793.3 7447.9 7876.6 6696.8 6451 5797.4 5604.3 8858.2 8909 TRUE FALSE FALSE 7894.294086 8917.092308 7577.527575 8787.329553 6355.037307 6038.80192 6289.831011 5766.451578 8065.900406 8677.542896 0.909738411 1.027605673 0.87323424 1.012651814 0.732354468 0.695911503 0.724840094 0.664525851 0.929514323 1 13.08307088 -8.703584752 6.155609952 0.95861835 0.702224517 0.873927355 0.047383107 0.051607891 3.953422171 0.007061566 0.014145189 1.98E-09 8.703584752 -0.256393833 SPSLSPS(ph)PPSPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSLSPSPPSPLEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SPSLS(0.293)PS(0.498)PPS(0.209)PLEK 119.77 0.0042291 47115000 2587 2316.6 2428.5 2442 2859.2 3004.4 2787.3 3171.9 2622 2518.7 TRUE FALSE FALSE 2555.468649 2349.213156 2470.767024 2724.35553 2713.284355 2812.428536 3024.053192 3263.673922 2387.481753 2453.263811 1.041660761 0.957586846 1.007134664 1.110502473 1.105989638 1.146402814 1.232665309 1.330339569 0.973185901 1 11.26048667 -7.241851589 0.560151907 1.011963396 1.556532484 0.919326133 0.032440934 0.745210842 0.154626489 0.006339944 0.264471594 5.73E-08 7.241851589 0.544569087 SPSLSPSPPS(ph)PLEK ddPTM_HeLa_Romidepsin_16h_R1 3 SPSLSPSPPSPLEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 S(0.229)PS(0.267)LS(0.017)PS(0.186)PPS(0.301)PLEK;SPS(0.001)LS(0.054)PS(0.075)PPS(0.87)PLEK;S(0.002)PSLS(0.018)PS(0.008)PPS(0.972)PLEK ;; 170.78 5.13E-05 511055000 8701.6 8077.4 7965.1 8287.4 10100.6 9994.2 9233.9 10115 9131.7 8267 TRUE FALSE FALSE 8595.541552 8191.113849 8103.729224 9245.628181 9585.128691 9355.602875 10018.22724 10407.66157 8314.937881 8052.222148 1.067474468 1.017248866 1.006396629 1.148208285 1.190370623 1.161865967 1.244156837 1.292520422 1.032626488 1 12.97517126 -8.117940086 0.509738546 1.021373377 1.354252973 0.878978707 0.0349239 0.557375423 0.164242928 0.008926993 0.094785803 7.62E-09 8.117940086 0.332879595 SPSMAVPSPGWVAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSMAVPSPGWVASPK 16 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 S(0.001)PSMAVPS(0.026)PGWVAS(0.973)PK 101.08 0.0072268 13224000 2852.7 2597.6 2512.6 2554.4 2023.3 1592.6 1337.4 1503.1 2786.5 2801.6 TRUE FALSE FALSE 2817.930195 2634.169081 2556.330749 2849.751747 1920.043451 1490.838 1450.998723 1546.589827 2537.268461 2728.814028 1.032657472 0.965316454 0.936791853 1.044318784 0.703618287 0.546331844 0.53173236 0.566762634 0.929806295 1 11.41405836 -8.606027828 3.055229244 1.007438421 0.550402729 0.955404734 0.042764784 0.029315901 0.549913424 0.005570525 0.012147054 2.48E-09 8.606027828 -0.457035693 SPSPGGPQLS(ph)PQLPR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPGGPQLSPQLPR 15 0 Q9HCH0;Q9HCH0-2;H7C1V4 Q9HCH0 NCKAP5L Nck-associated protein 5-like 1 0 SPS(0.001)PGGPQLS(0.999)PQLPR;S(0.04)PS(0.04)PGGPQLS(0.92)PQLPR ; 130.64 0.0019298 54534000 1345.16 1387.94 1178.74 1297.18 1567.5 1729.01 1225.64 1206.41 1328.09 1429.61 TRUE FALSE FALSE 1328.764673 1407.479456 1199.255475 1447.166055 1487.504626 1618.531841 1329.745831 1241.31557 1209.302304 1392.468526 0.954251136 1.010780085 0.861244224 1.03928098 1.068250088 1.162347163 0.954955754 0.891449643 0.868459345 1 10.443429 SPSPPDGS(ph)PAATPEIR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSPPDGSPAATPEIR 16 0 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 S(0.002)PSPPDGS(0.985)PAAT(0.013)PEIR;SPSPPDGS(0.997)PAAT(0.003)PEIR;SPS(0.018)PPDGS(0.981)PAATPEIR ;; 146.67 0.00030528 298660700 2953.36 3359.08 2978 2605.08 2384.08 2924.53 2471.44 2572.91 3840.7 3288.21 TRUE FALSE FALSE 2917.363312 3406.369216 3029.830841 2906.291607 2262.411501 2737.661971 2681.364052 2647.353091 3497.178173 3202.78183 0.910884184 1.063565799 0.945999759 0.907427281 0.706389514 0.85477629 0.837198471 0.826579278 1.09191895 1 11.64510981 -8.972882174 7.786155916 0.964031765 0.810939647 0.637128402 0.066711921 0.099644816 22.73330411 0.008423397 0.015211134 1.06E-09 8.972882174 -0.153092118 SPSPPLPT(ph)HIPPEPPRT(ph)PPFPAK ddPTM_HeLa_Romidepsin_16h_R1 1 SPSPPLPTHIPPEPPRTPPFPAK 23 1 Q8IZ21-3;Q8IZ21;Q8IZ21-2 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 2 0 S(0.075)PS(0.101)PPLPT(0.842)HIPPEPPRT(0.982)PPFPAK 101.66 3.27E-06 0 837.93 664.48 789.94 865.29 1100.4 825.89 820.62 909.54 880.42 910.51 TRUE FALSE FALSE 827.7169869 673.8345669 803.6885743 965.3389011 1044.242482 773.1182944 890.3234423 935.8561049 801.6730301 886.8548189 0.933317347 0.759802566 0.906223383 1.088497103 1.177467224 0.871752939 1.003911151 1.055252883 0.903950695 1 9.79255414 -9.267029238 24.83006052 0.944490742 1.03576529 0.295623213 0.095696564 605.6563139 2690314.001 0.015709134 0.024416728 5.41E-10 9.267029238 0.091274547 SPSPPT(ph)QHTGQPPGQPSAPSQLSAPR ddPTM_HeLa_Romidepsin_16h_R1 3 SPSPPTQHTGQPPGQPSAPSQLSAPR 26 0 Q68EM7-7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7;I3L460;Q68EM7-2 Q68EM7-7 ARHGAP17 Rho GTPase-activating protein 17 1 0 S(0.029)PS(0.029)PPT(0.47)QHT(0.47)GQPPGQPSAPSQLSAPR;S(0.033)PS(0.033)PPT(0.581)QHT(0.351)GQPPGQPSAPSQLSAPR;S(0.028)PS(0.028)PPT(0.472)QHT(0.472)GQPPGQPSAPSQLSAPR ;; 80.082 1.35E-05 141470000 1618.23 1665.16 1799.66 1765.02 1995.49 1842.99 1664.13 1747.93 2310.61 1925.3 TRUE FALSE FALSE 1598.50639 1688.602166 1830.982327 1969.099917 1893.652699 1725.228887 1805.481161 1798.503597 2103.943255 1875.280428 0.852409254 0.900453149 0.976377879 1.050029578 1.009797079 0.919984478 0.962779291 0.95905848 1.12193527 1 10.87289064 -9.690815882 8.279530387 0.926147467 0.980973216 0 0.077478298 0.412787025 43.23897091 0.010289331 0.014548414 2.04E-10 9.690815882 0.054825749 SPSPPTQHT(ph)GQPPGQPSAPSQLSAPR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSPPTQHTGQPPGQPSAPSQLSAPR 26 0 Q68EM7-7;Q68EM7-3;Q68EM7-6;Q68EM7-5;Q68EM7;I3L460;Q68EM7-2 Q68EM7-7 ARHGAP17 Rho GTPase-activating protein 17 1 0 S(0.001)PS(0.001)PPT(0.028)QHT(0.97)GQPPGQPSAPSQLSAPR;S(0.012)PS(0.012)PPT(0.152)QHT(0.823)GQPPGQPSAPSQLSAPR ; 130.98 4.90E-07 135323000 1280.58 1538.19 1366.79 1375.26 1659.57 1872.36 1447.91 1782.87 1954.43 1795.11 TRUE FALSE FALSE 1264.971798 1559.844679 1390.578407 1534.274032 1574.87595 1752.722239 1570.895439 1834.454531 1779.620886 1748.472783 0.723472399 0.892118364 0.795310296 0.877493803 0.900715164 1.002430381 0.8984386 1.049175342 1.017814462 1 10.77187962 -8.472463517 2.897850821 0.862682982 0.975183845 0.171107178 0.089600509 0.363798847 6.029149521 0.015794706 0.037546256 3.37E-09 8.472463517 0.112500863 SPSQS(ph)SLPAVVVETFPATVNGTVEGGSGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 SPSQSSLPAVVVETFPATVNGTVEGGSGAGR 31 0 O00499-9;O00499-10 O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 S(0.23)PS(0.23)QS(0.27)S(0.27)LPAVVVETFPATVNGTVEGGSGAGR 108.58 2.03E-13 2971500 1902.9 1661.2 1791.8 1351.2 2254.2 1883.6 1628.2 1650.7 2092.4 1887.6 TRUE FALSE FALSE 1879.706723 1684.586417 1822.985527 1507.432102 2139.159762 1763.244039 1766.499267 1698.4604 1905.250503 1838.55988 1.022379931 0.916253224 0.991529048 0.81989829 1.163497467 0.959035416 0.960805947 0.923799338 1.036273294 1 10.84436045 -10.30246759 24.79673901 1.010568304 0.96535467 0.090789364 0.081371739 977.0829411 590528.9863 0.012993234 0.0148584 4.98E-11 10.30246759 -0.045213634 SPSS(ph)DLDTDAEGDDFELLDQSELSQLDPASSR ddPTM_HeLa_Romidepsin_16h_R1 2 SPSSDLDTDAEGDDFELLDQSELSQLDPASSR 32 0 K7EQI9;Q86VR2-2;Q86VR2 K7EQI9 FAM134C Protein FAM134C 1 0 S(0.07)PS(0.235)S(0.695)DLDTDAEGDDFELLDQSELSQLDPASSR;S(0.176)PS(0.176)S(0.647)DLDTDAEGDDFELLDQSELSQLDPASSR ; 174.55 6.99E-24 8204300 209.72 295.812 179.92 251.84 257.216 385.28 305.54 531.53 164.18 425.09 TRUE FALSE FALSE 207.163852 299.9764491 183.0514321 280.9589257 244.0893077 360.6618514 331.49256 546.9089819 149.4953296 414.0461005 0.500340063 0.724500119 0.442103988 0.678569187 0.589522054 0.871066896 0.800617515 1.320889102 0.361059625 1 8.693647598 -6.79639205 1.403336103 0.718014365 2.490847941 0.501289136 0.192245588 3.048595119 2.176146129 0.030956334 10.50669447 1.60E-07 6.79639205 1.772833577 SPSSSVGS(ph)PPVLYMQPSPL ddPTM_HeLa_Romidepsin_16h_R1 1 SPSSSVGSPPVLYMQPSPL 19 0 F5H148;Q9NYV6;Q9NYV6-3;Q9NYV6-4 F5H148;Q9NYV6-4 RRN3 RNA polymerase I-specific transcription initiation factor RRN3 1 0 S(0.001)PS(0.006)S(0.029)S(0.029)VGS(0.934)PPVLYMQPSPL 137.27 0.00076455 4747800 1815.1 1797.3 1404.9 1305.3 1571.8 1447.3 1585.5 1947 1798.9 1624.8 TRUE FALSE FALSE 1792.976863 1822.602437 1429.351695 1456.224928 1491.585181 1354.822201 1720.17233 2003.333373 1638.001879 1582.587462 1.132940142 1.151659849 0.903173903 0.92015447 0.942497787 0.856080459 1.08693666 1.2658595 1.035015074 1 10.62806952 -9.763139136 24.99999766 1.071197547 0.987717175 0.10769925 0.116171246 86.56115745 1273146.365 0.019955597 0.027000646 1.73E-10 9.763139136 -0.083480372 SPT(ph)FSEELPVLGDGQQLR ddPTM_HeLa_Romidepsin_16h_R1 1 SPTFSEELPVLGDGQQLR 18 0 Q8N0Z3 Q8N0Z3 SPICE1 Spindle and centriole-associated protein 1 1 0 S(0.275)PT(0.671)FS(0.054)EELPVLGDGQQLR 163.9 2.97E-06 6276500 141.87 67.27 171.65 132.94 188.23 202 149.52 221.61 190.1 142.72 TRUE FALSE FALSE 140.1408339 68.21702883 174.6374962 148.3111483 178.6239207 189.0928519 162.2202251 228.0219357 173.0969799 139.0121138 1.00811958 0.490727225 1.256275381 1.066893699 1.284952194 1.360261683 1.166950279 1.640302629 1.245193495 1 7.119066798 -8.791671359 1.237006399 0.971995229 1.38900193 0.393003597 0.221407055 0.318797456 0.967000949 0.031452257 0.083657551 1.62E-09 8.791671359 0.417006701 SPT(ph)GPSNSFLANMGGTVAHK ddPTM_HeLa_Romidepsin_16h_R1 1 SPTGPSNSFLANMGGTVAHK 20 0 H0Y6J6;Q5W012;Q96I25 H0Y6J6 RBM17 Splicing factor 45 1 0 S(0.325)PT(0.637)GPS(0.026)NS(0.012)FLANMGGTVAHK 79.88 0.0020352 218770000 2030.7 2361.7 2039.5 1413.7 2127.4 2513.9 1846.4 2351.1 2704.1 2740.8 TRUE FALSE FALSE 2005.949047 2394.948075 2074.996642 1577.158646 2018.83084 2353.269903 2003.23317 2419.125369 2462.238523 2669.593621 0.751406143 0.897120841 0.777270602 0.590786041 0.756231519 0.881508663 0.750388806 0.906177386 0.922327093 1 11.38240443 -12.34250425 0.761273982 1.020658717 0.782204562 0.351319434 0.091085834 0.618835362 0.550742492 0.09485233 0.017866968 4.54E-13 12.34250425 -0.238454155 SPTAPSVFS(ph)PTGNR ddPTM_HeLa_Romidepsin_16h_R1 2 SPTAPSVFSPTGNR 14 0 H0Y3X6;A0A0C4DFX9;Q9H3P2;C9JEM7;H7C2C7;C9JHL4 H0Y3X6 NELFA Negative elongation factor A 1 0 SPTAPS(0.076)VFS(0.867)PT(0.057)GNR;SPTAPSVFS(0.98)PT(0.02)GNR ; 165.78 9.73E-05 16956900 2366.88 2434.63 2016.4 1147.19 1715.85 1688.72 1780.61 1714.53 2544.9 3197 TRUE FALSE FALSE 2338.031556 2468.904785 2051.494596 1279.833505 1628.283772 1580.816242 1931.854969 1764.13722 2317.27777 3113.941479 0.75082707 0.792855229 0.658809618 0.411001142 0.522901211 0.507657659 0.620388977 0.566528701 0.744162273 1 11.60452612 -10.652401 0.461544664 0.990211924 0.515220036 0.583423625 0.104637587 0.272680133 0.14856819 0.046538795 0.038385009 2.23E-11 10.652401 -0.474991888 KFELLPTPPLS(ph)PSRR ddPTM_HeLa_Romidepsin_16h_R1 1 KFELLPTPPLSPSRR 15 2 H0YBG3;A0A0B4J1R1;H0YBT0;A0A087WUS5;P01106;P01106-2 H0YBG3 MYC Myc proto-oncogene protein 1 0 KFELLPTPPLS(0.736)PS(0.264)RR 82.859 0.024326 32092000 6486.5 6022.5 5221.1 6081 2807.9 1815.8 1672.1 1580.4 5479.5 5100 TRUE FALSE FALSE 6407.440043 6107.284913 5311.971055 6784.113832 2664.602385 1699.77624 1814.128132 1626.126381 4989.399796 4967.501265 1.289871849 1.229448084 1.069344681 1.365699467 0.536406987 0.342179327 0.36519933 0.327352988 1.00440836 1 12.27830462 -8.642545226 4.929375721 1.155678023 0.361274611 0.916980651 0.113882489 0.047648613 1.860718311 0.019276411 0.039201729 2.28E-09 8.642545226 -0.794403412 down SPVDES(ph)GDEVQYGDVPVENGMAPFFEMK ddPTM_HeLa_Romidepsin_16h_R1 3 SPVDESGDEVQYGDVPVENGMAPFFEMK 28 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;D6R9F5;F8WA26 Q8WX93-3 PALLD Palladin 1 0 S(0.022)PVDES(0.978)GDEVQYGDVPVENGMAPFFEMK;S(0.027)PVDES(0.973)GDEVQYGDVPVENGMAPFFEMK;S(0.041)PVDES(0.959)GDEVQYGDVPVENGMAPFFEMK ;; 77.119 3.37E-06 58481000 9366.6 8725.3 8292.6 8982.2 10720.9 9061.3 8678.1 8410.3 10573.2 8922.1 TRUE FALSE FALSE 9252.436276 8848.135002 8436.929224 10020.76423 10173.77247 8482.312174 9415.217597 8653.638761 9627.506511 8690.302556 1.064685173 1.018161905 0.97084413 1.153097279 1.170704058 0.976066382 1.083416548 0.995781068 1.107844802 1 13.08519069 -12.86872681 0.442575248 0.969144314 1.059736601 0 0.073283031 6.186850787 1.114945118 0.273217953 0.018626018 1.35E-13 12.86872681 0.090592287 SPVDIVTGGIS(ph)PVRDLDR ddPTM_HeLa_Romidepsin_16h_R1 1 SPVDIVTGGISPVRDLDR 18 1 E9PEM5;A0A494C1L5;P50851-2;P50851;H0YAC6;A0A494BZW2;A0A494C0R9;H0Y9N9 E9PEM5 LRBA Lipopolysaccharide-responsive and beige-like anchor protein 1 0 SPVDIVT(0.006)GGIS(0.994)PVRDLDR 78.413 0.0054529 3632300 893.27 1052 1052.7 1053.1 1161.8 900.06 722.11 1108.9 1190 723.26 TRUE FALSE FALSE 882.3824817 1066.810084 1071.021802 1174.864377 1102.509011 842.5490708 783.4460054 1140.984272 1083.56342 704.4696009 1.252548698 1.514345093 1.52032366 1.667728991 1.565019994 1.196004866 1.112107612 1.619635922 1.538126582 1 9.460393643 -10.94718906 1.040581032 1.05441476 1.444695493 0 0.23066974 0.299794919 0.686556284 0.049759968 0.041198544 1.13E-11 10.94718906 0.390280732 SPVGKS(ph)PPSTGSTYGSSQK ddPTM_HeLa_Romidepsin_16h_R1 2 SPVGKSPPSTGSTYGSSQK 19 1 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 S(0.151)PVGKS(0.573)PPS(0.142)T(0.053)GS(0.031)T(0.048)Y(0.001)GSSQK;S(0.045)PVGKS(0.926)PPS(0.016)T(0.004)GS(0.006)T(0.002)YGS(0.001)SQK ; 93.115 0.0011501 103993000 3791.1 3778.3 3820.4 2454.11 3743.4 4468 3920.3 4735.5 3366.1 3817.7 TRUE FALSE FALSE 3744.892615 3831.491007 3886.892459 2737.865745 3552.360329 4182.50922 4253.290184 4872.514221 3065.027585 3718.515604 1.007093425 1.030381855 1.045280664 0.736279214 0.955316774 1.124779258 1.143813994 1.310338517 0.824261053 1 11.86051111 -7.668163269 1.618726285 0.987207409 1.304856784 0.550492479 0.102748622 0.296410388 1.219167701 0.013190755 0.115843229 2.15E-08 7.668163269 0.317649374 S(ph)RLTPVSPES(ph)SSTEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 2 0 S(0.963)RLT(0.037)PVS(0.263)PES(0.585)S(0.132)S(0.016)T(0.004)EEK 132.9 1.17E-06 0 3886.7 3819.1 3934.2 3536.2 1850.6 1416.8 697.87 893.7 4082 3849.9 TRUE FALSE FALSE 3839.327405 3872.86539 4002.673101 3945.072082 1756.156976 1326.271053 757.1470604 919.5577995 3716.895696 3749.879043 1.023853666 1.032797417 1.067413923 1.052053156 0.468323633 0.353683689 0.201912395 0.245223323 0.991204157 1 11.87262835 -8.642393981 3.017138174 1.022091549 0.270387654 0.981454926 0.048316981 0.025269747 0.460061308 0.0078861 0.016948151 2.28E-09 8.642393981 -0.751703894 down SPVPSPGS(ph)SSPQLQVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 0 SPVPSPGS(0.443)S(0.278)S(0.278)PQLQVK 103.31 0.0047132 48740000 7127.7 7567.6 7659.9 6391.4 5824.3 5673.4 4341.3 5664 7479.3 7672.6 TRUE FALSE FALSE 7040.824851 7674.136871 7793.217346 7130.40374 5527.064238 5310.88805 4710.049914 5827.878904 6810.332676 7473.264746 0.942135076 1.026878765 1.042812962 0.954121657 0.739578273 0.710651667 0.63025332 0.779830382 0.911292843 1 12.86752292 -8.749096013 3.755443231 0.982524667 0.702853457 0.876256281 0.048898874 0.049884456 1.518589697 0.006770696 0.013535343 1.78E-09 8.749096013 -0.279671211 SPVPSPGSS(ph)SPQLQVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPVPSPGSSSPQLQVK 16 0 Q8N3F8 Q8N3F8 MICALL1 MICAL-like protein 1 1 0 SPVPSPGS(0.192)S(0.735)S(0.073)PQLQVK 178.68 2.82E-08 43020000 3323.2 2954.6 2961.9 2930.2 2428 2145.6 1897.1 1899 2884.1 2870 TRUE FALSE FALSE 3282.69556 2996.194936 3013.450627 3269.003511 2304.0901 2008.503085 2058.239627 1953.944569 2626.138873 2795.436986 1.174304975 1.071816303 1.077989109 1.169406975 0.82423253 0.718493421 0.736285467 0.698976431 0.939437693 1 11.44885811 -8.62303798 4.370656004 1.088115122 0.726373045 0.849622958 0.068231447 0.057422278 1.956754234 0.010300197 0.021214908 2.38E-09 8.62303798 -0.361742078 SPWASDFKDFQES(ph)SPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPWASDFKDFQESSPQK 17 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 SPWASDFKDFQES(0.5)S(0.5)PQK 55.536 0.029116 14588000 893.73 761.14 766.28 894.72 1149.9 1209.3 1399.5 1418.4 912.59 933.05 TRUE FALSE FALSE 882.836875 771.8553489 779.616782 998.1717362 1091.216312 1132.029633 1518.373495 1459.439166 830.9656648 908.8092265 0.971421558 0.849304041 0.857844264 1.098329228 1.200709984 1.245618552 1.670728521 1.605880666 0.914345542 1 9.827833671 -8.050228433 1.103187286 0.968247388 1.710059325 0.904797277 0.086080827 0.141279778 0.271984477 0.013367853 0.087490069 8.91E-09 8.050228433 0.741811937 SPWASDFKDFQESS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 SPWASDFKDFQESSPQK 17 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 SPWASDFKDFQES(0.09)S(0.91)PQK 57.537 0.026263 14567000 582.04 788.34 806.99 892.02 1140.1 1179.5 978.47 1111.5 789.09 875.1 TRUE FALSE FALSE 574.9458726 799.4382712 821.0353224 995.1595495 1081.916443 1104.133757 1061.581217 1143.659499 718.5118141 852.3647758 0.674530305 0.937906274 0.963244078 1.167527774 1.269311536 1.295377036 1.245454115 1.341748898 0.842962819 1 9.735327164 -9.265908405 1.606633684 0.847856556 1.290002845 0.857903826 0.079626736 0.146676205 0.740094172 0.020244425 0.036846888 5.42E-10 9.265908405 0.44214629 SPYQEFTDHLVK ddPTM_HeLa_Romidepsin_16h_R1 1 SPYQEFTDHLVK 12 0 E9PQD7;P15880;H0YEN5 E9PQD7 RPS2 40S ribosomal protein S2 0 0 104.81 0.0061928 9471200 3696.4 3219.4 3720.3 3474.7 3453.9 3561.9 2820.4 3554.4 3971 3533.8 FALSE FALSE TRUE 3651.346855 3264.722798 3785.050261 3876.461163 3277.634595 3334.306086 3059.964706 3657.240956 3615.823814 3441.991367 1.060823944 0.948498253 1.099668726 1.126226289 0.952249511 0.96871425 0.889009989 1.062536354 1.050503453 1 11.74902776 SQALGQS(ph)APSLTASLK ddPTM_HeLa_Romidepsin_16h_R1 1 SQALGQSAPSLTASLK 16 0 O15021;H7C0U3;H7C2V7;H7C3S4;E7EX28;O15021-4 O15021 MAST4 Microtubule-associated serine/threonine-protein kinase 4 1 0 SQALGQS(0.934)APS(0.06)LT(0.006)ASLK 115.34 0.0029678 13486000 1426.5 1263.9 932.8 1900.9 1398.1 1484.7 1099.6 1336.5 1311.1 1152.8 TRUE FALSE FALSE 1409.113269 1281.693217 949.0349927 2120.691002 1326.74974 1389.832462 1192.999997 1375.169519 1193.831932 1122.85009 1.254943364 1.141464234 0.845201867 1.888667972 1.18159116 1.237772054 1.062474864 1.224713371 1.063215778 1 10.13294961 -12.57089384 0.508968447 0.922901835 1.240427991 0.091061483 0.249631714 3.591426369 1.052974605 0.593471987 0.061565747 2.69E-13 12.57089384 0.317526156 SQANGAGALSYVS(ph)PNTSK ddPTM_HeLa_Romidepsin_16h_R1 1 SQANGAGALSYVSPNTSK 18 0 O95453;O95453-3;O95453-2;A0A494C0W0;A0A494C0K5;A0A494C0Q6;A0A494C002;A0A494C1N1;A0A494C0Q2;F5H1Z4;A0A494C1K5;A0A494C0P9;A0A494BZU6;A0A494C1G3;A0A494C156;A0A494BZW7 O95453 PARN Poly(A)-specific ribonuclease PARN 1 0 SQANGAGALSYVS(0.994)PNT(0.005)S(0.001)K 209.73 1.44E-28 26722000 2690.1 2299.8 2435.8 2375.1 2279.7 2068.2 1894.5 1697.3 2587.3 2913.8 TRUE FALSE FALSE 2657.312026 2332.176645 2478.194077 2649.720237 2163.358402 1936.048695 2055.418783 1746.408698 2355.885408 2838.099056 0.936299958 0.821738988 0.873188014 0.933625002 0.76225613 0.682163891 0.724223765 0.615344519 0.830092735 1 11.47070923 -6.09884777 0.224100042 1.016328017 8.45E-14 0.636579764 0.070074139 4.848499622 0.131633247 0.038832822 1.491853492 7.96E-07 6.09884777 -1.016328017 SQAPLES(ph)SLDSLGDVFLDSGRK ddPTM_HeLa_Romidepsin_16h_R1 1 SQAPLESSLDSLGDVFLDSGRK 22 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 S(0.001)QAPLES(0.498)S(0.498)LDS(0.003)LGDVFLDSGRK 110.38 3.49E-05 1951700 761.42 643.63 718.74 810.69 683.43 661.3 642.72 810.12 889.75 721.75 TRUE FALSE FALSE 752.1395202 652.69104 731.2493682 904.4257922 648.5520169 619.0450642 697.3126208 833.559544 810.1685316 702.998831 1.069901523 0.928438301 1.040185753 1.286525315 0.922550634 0.880577658 0.991911494 1.185719673 1.152446485 1 9.45737848 -7.253892152 23.54364642 1.024451209 1.185719853 0.14218969 0.113726619 568.1533834 1772256.453 0.014528326 0.197493476 5.57E-08 7.253892152 0.161268645 SQAPLESS(ph)LDSLGDVFLDSGRK ddPTM_HeLa_Romidepsin_16h_R1 1 SQAPLESSLDSLGDVFLDSGRK 22 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 S(0.009)QAPLES(0.425)S(0.557)LDS(0.009)LGDVFLDSGRK 72.474 0.0010374 2890800 1019.1 887.18 941.04 1033.4 979.27 844.6 1241.2 1176.7 1210.5 1007.7 TRUE FALSE FALSE 1006.678817 899.6697433 957.4184065 1152.88657 929.2941977 790.6327858 1346.627497 1210.745958 1102.229848 981.5198087 1.025632706 0.91660885 0.975444813 1.174593279 0.946791078 0.80551893 1.371981987 1.233542051 1.122982785 1 9.938873574 -7.74638512 24.99864721 0.998780307 1.302762148 0.591460052 0.101976222 109.6768253 182122.9932 0.012406039 0.046043778 1.79E-08 7.74638512 0.30398184 SQDADS(ph)PGSSGAPENLTFK ddPTM_HeLa_Romidepsin_16h_R1 2 SQDADSPGSSGAPENLTFK 19 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;H0Y948;H0Y8L4;H0Y8U8 A8MQ02 MLLT4 Afadin 1 0 S(0.467)QDADS(0.522)PGS(0.01)SGAPENLTFK;SQDADS(1)PGSSGAPENLTFK ; 204.51 2.68E-21 14017500 7724.5 8178 8038.6 8356.4 8364.1 9001.5 6474.2 7612.6 9200.8 8385.1 TRUE FALSE FALSE 7630.350823 8293.130099 8178.508461 9322.606286 7937.248766 8426.333201 7024.118386 7832.85857 8377.857404 8167.253893 0.934261494 1.015412305 1.001378011 1.14146155 0.971838132 1.031721716 0.860034288 0.959056578 1.025786331 1 12.99563536 -7.764759084 24.99927183 0.989861286 0.909545435 0.265292063 0.059357158 92.46893803 696371.1802 0.008746614 0.027918473 1.72E-08 7.764759084 -0.080315851 SQDADSPGSSGAPENLT(ph)FK ddPTM_HeLa_Romidepsin_16h_R1 1 SQDADSPGSSGAPENLTFK 19 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;H0Y948;H0Y8L4;H0Y8U8 A8MQ02 MLLT4 Afadin 1 0 S(0.001)QDADS(0.108)PGS(0.257)S(0.055)GAPENLT(0.579)FK 72.496 0.029303 5071400 1271.6 1353.1 1058.2 1147.7 1236.6 1377.1 1053.1 1462.3 1525.6 1320.3 TRUE FALSE FALSE 1256.10125 1372.148977 1076.617527 1280.402474 1173.491688 1289.107754 1142.550288 1504.609343 1389.146515 1285.998416 0.976751787 1.066991188 0.837184178 0.995648563 0.912514101 1.00241784 0.888453884 1.169993155 1.080208574 1 10.32867315 -7.244513673 24.52556738 0.975098623 1.169993356 0.401996813 0.071922409 1774.995645 2571941.134 0.008027744 0.307139227 5.69E-08 7.244513673 0.194894734 SQDAT(ph)FSPGSEQAEK ddPTM_HeLa_Romidepsin_16h_R1 1 SQDATFSPGSEQAEK 15 0 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 SQDAT(0.931)FS(0.066)PGS(0.004)EQAEK 329.21 1.97E-177 46608000 7182.4 7401.8 7122.1 5595 4360.9 3653.9 3214.8 3428.1 7367.4 6665.1 TRUE FALSE FALSE 7094.858146 7506.002735 7246.057163 6241.920225 4138.347 3420.427582 3487.865032 3527.286665 6708.441292 6491.939741 1.092871842 1.15620339 1.116162111 0.961487702 0.637459244 0.526872972 0.537260845 0.543333242 1.033349285 1 12.66443389 -8.757456328 2.730514725 1.060089209 0.538811826 0.970535013 0.043169055 0.040426491 0.616808456 0.008456942 0.017532974 1.75E-09 8.757456328 -0.521277383 SQDATFS(ph)PGSEQAEK ddPTM_HeLa_Romidepsin_16h_R1 1 SQDATFSPGSEQAEK 15 0 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 S(0.004)QDAT(0.237)FS(0.424)PGS(0.335)EQAEK 237.34 1.65E-45 42850000 5550.9 5384 5032.1 4011.3 3353.1 2500.7 2179.4 2792.6 5556.5 5205.2 TRUE FALSE FALSE 5483.243496 5459.796093 5119.68159 4475.10538 3181.978795 2340.913341 2364.518182 2873.399475 5059.512723 5069.968154 1.081514386 1.076889623 1.009805473 0.882669327 0.627613172 0.461721508 0.466377324 0.566749019 0.997937772 1 12.30776097 -8.799431083 1.874413506 1.04179559 0.492553614 0.973977897 0.039278347 0.038503955 0.275034656 0.006782001 0.014999731 1.59E-09 8.799431083 -0.549241976 SQDATFSPGSEQAEKS(ph)PGPIVSR ddPTM_HeLa_Romidepsin_16h_R1 2 SQDATFSPGSEQAEKSPGPIVSR 23 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 SQDATFSPGSEQAEKS(0.991)PGPIVS(0.009)R;SQDATFS(0.002)PGS(0.007)EQAEKS(0.988)PGPIVS(0.004)R ; 105.75 8.11E-06 192325000 4195.1 4192.5 4288.5 3881.2 3869.5 3856.3 3114.2 3379.7 4428.8 4632.7 TRUE FALSE FALSE 4143.968508 4251.522125 4363.139544 4329.962606 3672.024976 3609.894876 3378.72007 3477.486287 4032.677036 4512.341786 0.91836317 0.942198603 0.966934632 0.959582144 0.813773679 0.800004753 0.748773083 0.770661101 0.893699375 1 12.13966063 -8.676468188 3.040609046 0.959895001 0.773541267 0.868844236 0.031103157 0.06399357 1.188829557 0.005005877 0.010587667 2.11E-09 8.676468188 -0.186353734 SQDKS(ph)LLDGEGPQAVGGQDVAFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQDKSLLDGEGPQAVGGQDVAFSR 24 1 A1X283 A1X283 SH3PXD2B SH3 and PX domain-containing protein 2B 1 0 S(0.158)QDKS(0.842)LLDGEGPQAVGGQDVAFSR 51.871 0.011627 4637700 500.58 677.71 460.43 575.48 759.57 661 730.17 950.01 498.01 446.99 TRUE FALSE FALSE 494.4787384 687.2508192 468.443591 642.0197053 720.8063086 618.7642333 792.1906216 977.4970405 453.4667383 435.3771354 1.135748064 1.5785184 1.075948994 1.474628898 1.655590636 1.421214352 1.819550356 2.245173118 1.041549272 1 8.766121833 -4 0.24095524 0.989733572 8.030177144 0.802237994 0.168566825 13.4969051 0.166684395 0.096107981 38.47891062 1.00E-04 4 7.040443572 SQDQDS(ph)EVNELSR ddPTM_HeLa_Romidepsin_16h_R1 2 SQDQDSEVNELSR 13 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 S(0.001)QDQDS(0.999)EVNELSR;S(0.001)QDQDS(0.997)EVNELS(0.002)R ; 220.52 2.64E-31 19113500 1902.45 1884.42 1849.06 1434.37 2314.2 2345.9 1886.34 2387.9 1789.96 1648.44 TRUE FALSE FALSE 1879.262208 1910.948914 1881.242114 1600.218608 2196.097739 2196.004561 2046.565673 2456.990119 1629.861495 1605.613291 1.170432643 1.190167598 1.171665758 0.996640111 1.367762556 1.367704523 1.274631746 1.530250237 1.015102144 1 10.64890875 -4 0.188044183 1.008526217 3.06738608 0.699065805 0.093016785 23.88647802 0.265599959 0.107133757 14.32454468 1.00E-04 4 2.058859863 SQDSS(ph)PVLSELK ddPTM_HeLa_Romidepsin_16h_R1 1 SQDSSPVLSELK 12 0 F6U4U2;P51955-3;P51955-2;P51955-4;P51955 F6U4U2 NEK2 Serine/threonine-protein kinase Nek2 1 0 S(0.004)QDS(0.198)S(0.77)PVLS(0.029)ELK 97.203 0.018787 1841900 818.81 766.73 740.34 695.2 1346.8 1828 1284.7 1420.4 851.07 661.41 TRUE FALSE FALSE 808.8300288 777.5240451 753.2253071 775.582295 1278.06777 1711.1967 1393.822386 1461.497033 774.9481677 644.2264729 1.255505731 1.206911044 1.169193349 1.203896964 1.98387962 2.656203636 2.163559625 2.268607539 1.202912641 1 9.331424136 -8.673791575 3.197148123 1.135723971 2.343835807 0.940184734 0.137476781 0.042401211 0.86515865 0.022086318 0.046425155 2.12E-09 8.673791575 1.208111835 up SQDSYPGSPS(ph)LSPR ddPTM_HeLa_Romidepsin_16h_R1 2 SQDSYPGSPSLSPR 14 0 A0A0D9SEU5;R4GMX8;Q6VN20-3;Q6VN20;Q6VN20-2 A0A0D9SEU5 RANBP10 Ran-binding protein 10 1 0 SQDSYPGS(0.024)PS(0.747)LS(0.229)PR;SQDSYPGS(0.376)PS(0.623)LS(0.001)PR ; 184.01 1.45E-07 30294000 4380.3 4381.8 3885.9 3956.8 6916.1 8372.5 7691.5 8201.6 4455.4 4124.9 TRUE FALSE FALSE 4326.911219 4443.487095 3953.532459 4414.303833 6563.145609 7837.524271 8344.815818 8438.900356 4056.897865 4017.734503 1.076952998 1.105968324 0.984020337 1.098704713 1.63354388 1.950732251 2.076995334 2.100412645 1.009747623 1 11.97216652 -8.544569156 1.860455888 1.036252567 2.074544681 0.989293677 0.047116871 0.025620766 0.175806478 0.007910422 0.020601002 2.85E-09 8.544569156 1.038292115 up SQEDEIS(ph)SPVNK ddPTM_HeLa_Romidepsin_16h_R1 1 SQEDEISSPVNK 12 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 SQEDEIS(0.928)S(0.072)PVNK 220.37 6.88E-29 35302000 8826.8 8814.9 9265.7 7837.2 5690.1 5473.1 4195.5 5109.6 9883.1 8416.9 TRUE FALSE FALSE 8719.215566 8938.996394 9426.965622 8743.373939 5399.712964 5123.386574 4551.865665 5257.438214 8999.130783 8198.227725 1.063548838 1.090357172 1.149878478 1.066495617 0.658643934 0.624938309 0.55522557 0.641289604 1.097692219 1 13.00109635 -8.729027466 5.344621819 1.048415639 0.610376428 0.956624451 0.047568552 0.031493598 2.290922649 0.008022422 0.01593278 1.87E-09 8.729027466 -0.438039211 SQEDEISS(ph)PVNK ddPTM_HeLa_Romidepsin_16h_R1 2 SQEDEISSPVNK 12 0 Q5UIP0-2;Q5UIP0;H7C2B5 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 SQEDEIS(0.063)S(0.937)PVNK;SQEDEIS(0.068)S(0.932)PVNK ; 240.37 2.07E-39 55058000 13749 13748.4 13578.5 11065.1 8260.2 8221 6676.3 7685.2 15447.1 13291.9 TRUE FALSE FALSE 13581.4219 13941.95034 13814.8281 12344.49892 7838.651171 7695.704632 7243.384755 7907.559137 14065.47269 12946.57452 1.049035934 1.076883334 1.067064348 0.953495375 0.605461403 0.594420139 0.559482722 0.610783889 1.086424263 1 13.66028281 -8.80227136 3.68580302 1.030982825 0.584978654 0.980524011 0.030986514 0.021838349 0.617568055 0.004686777 0.009128891 1.58E-09 8.80227136 -0.446004171 SQEEPKDT(ph)FEHDPSESIDEFNK ddPTM_HeLa_Romidepsin_16h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 S(0.311)QEEPKDT(0.66)FEHDPS(0.028)ES(0.001)IDEFNK 59.574 0.0038241 7236700 2175 2575 2147.4 1520 2264.1 1884.9 1503.1 1691.6 2453.1 2566.7 TRUE FALSE FALSE 2148.490263 2611.250918 2184.774596 1695.749552 2148.554528 1764.460973 1630.773276 1740.543777 2233.688592 2500.016764 0.859390343 1.044493363 0.873903978 0.678295272 0.859416048 0.705779657 0.652304937 0.696212842 0.893469446 1 11.28772205 -7.177673353 0.22230161 0.999613758 0.331087281 0.597773677 0.082782929 5.978552346 0.244548935 0.078364549 1.122806241 6.64E-08 7.177673353 -0.668526477 SQEEPKDTFEHDPS(ph)ESIDEFNK ddPTM_HeLa_Romidepsin_16h_R1 1 SQEEPKDTFEHDPSESIDEFNK 22 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 SQEEPKDT(0.005)FEHDPS(0.497)ES(0.497)IDEFNK 73.21 0.0012157 6080000 1606.3 1602.5 1489.3 1523.4 1734.5 1632.4 1260 1444.9 1679.1 1546.2 TRUE FALSE FALSE 1586.721798 1625.060037 1515.220642 1699.542676 1645.981993 1528.094908 1367.024369 1486.705902 1528.917091 1506.029501 1.053579493 1.079035992 1.006102896 1.128492287 1.092928121 1.014651378 0.907700923 0.987169176 1.015197305 1 10.55653432 -7.929102781 6.300962641 1.040820688 0.948779059 0.469344036 0.043290214 0.15585052 10.68482333 0.006553855 0.020045306 1.18E-08 7.929102781 -0.092041629 SQETPATK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SQETPATKK 9 1 M0QXK2;M0R221;M0R2B8;M0QZG7;M0R268;P09012 M0QXK2 SNRPA U1 small nuclear ribonucleoprotein A 0 1 ; SQETPATK(1)K;SQETPATK(1)K 160.36 0.0018074 2393000 1768.61 2159.84 2401.3 2523 1978.6 1980.54 4590.3 623.34 3057.6 2260.7 FALSE TRUE FALSE 1747.053501 2190.246284 2443.093619 2814.721131 1877.624659 1853.989886 4980.199967 641.3753594 2784.120598 2201.966688 0.793405963 0.994677302 1.109505258 1.278275982 0.85270348 0.841969997 2.261705408 0.29127387 1.264379072 1 11.10457693 -9.863009787 3.273728858 0.902219797 1.144231902 0 0.482157559 0.578936061 12.37057574 0.070617103 0.095310732 1.37E-10 9.863009787 0.242012105 SQGS(ph)GNEAEPLGK ddPTM_HeLa_Romidepsin_16h_R1 3 SQGSGNEAEPLGK 13 0 B8ZZZ7;Q9NUQ6-2;Q9NUQ6;Q9NUQ6-4;Q9NUQ6-3 B8ZZZ7 SPATS2L SPATS2-like protein 1 0 S(0.084)QGS(0.916)GNEAEPLGK;SQGS(1)GNEAEPLGK;SQGS(1)GNEAEPLGK ;; 157.07 0.00061843 23007600 9082.7 8439.8 8316 7082.4 6632.2 6075.4 5108.1 5211.6 8695.7 9566.3 TRUE FALSE FALSE 8971.996559 8558.615726 8460.736492 7901.300412 6293.734086 5687.201547 5541.981887 5362.389423 7917.934813 9317.766147 0.962891364 0.918526564 0.908021983 0.847982262 0.675455253 0.610361052 0.594775808 0.57550161 0.849767497 1 13.18576841 -8.837904585 0.922727174 0.982414933 0.562373424 0.910089779 0.046520224 0.049826091 0.080980813 0.003882432 0.012017104 1.45E-09 8.837904585 -0.420041509 SQGSPEDS(ph)APQASPGPSK ddPTM_HeLa_Romidepsin_16h_R1 1 SQGSPEDSAPQASPGPSK 18 0 Q9P107-2;Q9P107 Q9P107-2 GMIP GEM-interacting protein 1 0 S(0.022)QGS(0.486)PEDS(0.491)APQASPGPSK 171.04 2.58E-07 5860600 4717.3 4178.6 4029.2 4101.1 4049.4 4185.6 3718.1 4148 4560.4 4045.4 TRUE FALSE FALSE 4659.803733 4237.42644 4099.326536 4575.288478 3842.744008 3918.153668 4033.915321 4268.015836 4152.506402 3940.299925 1.18260128 1.075407081 1.040359012 1.16115234 0.9752415 0.994379551 1.023758444 1.083170296 1.053855412 1 11.94408973 -8.74534756 24.99892411 1.088194683 1.017699109 0.245942867 0.056845712 346.9522443 538993.4913 0.0109653 0.021875169 1.80E-09 8.74534756 -0.070495575 SQGSPEDSAPQAS(ph)PGPSK ddPTM_HeLa_Romidepsin_16h_R1 2 SQGSPEDSAPQASPGPSK 18 0 Q9P107-2;Q9P107 Q9P107-2 GMIP GEM-interacting protein 1 0 SQGSPEDSAPQAS(0.999)PGPS(0.001)K;S(0.019)QGS(0.236)PEDS(0.276)APQAS(0.468)PGPSK ; 243.99 1.05E-61 10545200 4448.7 4068.8 4030.3 3755.8 4504 4322.9 3482.5 4204.5 4335.6 4349.3 TRUE FALSE FALSE 4394.477533 4126.080673 4100.445681 4190.063268 4274.144073 4046.680642 3778.303463 4326.150574 3947.813077 4236.304559 1.037337489 0.973981123 0.967929861 0.989084521 1.008932199 0.955238365 0.891886646 1.021208583 0.931900203 1 12.0485906 -9.360992817 0.755395641 1.016373465 0.958273446 0 0.04450968 0.635885002 0.71811375 0.007555386 0.016918711 4.36E-10 9.360992817 -0.058100019 SQIDVALS(ph)QDS(ph)TYQGER ddPTM_HeLa_Romidepsin_16h_R1 1 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 2 0 SQIDVALS(0.928)QDS(0.987)T(0.081)Y(0.004)QGER 105.66 0.025855 4448700 2351.7 2502.5 2778 2182 2716 2062.9 1511.9 2233.8 2063.1 2196.1 TRUE FALSE FALSE 2323.036576 2537.730261 2826.349925 2434.293107 2577.392385 1931.087348 1640.320748 2298.431479 1878.571169 2139.045005 1.086015755 1.186384697 1.321313912 1.138027999 1.204926675 0.902780139 0.766847235 1.074512912 0.878228912 1 11.06275112 -8.234120012 22.48403741 1.091268645 0.899926593 0.309802376 0.133796341 201.6500409 165957.759 0.018297659 0.046627294 5.83E-09 8.234120012 -0.191342052 SQIDVALS(ph)QDSTYQGER ddPTM_HeLa_Romidepsin_16h_R1 2 SQIDVALSQDSTYQGER 17 0 Q92900-2;Q92900 Q92900-2 UPF1 Regulator of nonsense transcripts 1 1 0 SQIDVALS(0.813)QDS(0.185)T(0.002)YQGER;SQIDVALS(0.955)QDS(0.045)TYQGER ; 223.86 1.41E-35 268470000 11058.1 9651.3 9475.7 8319.8 9891.4 10187.9 7746.4 9774.4 10527.6 9387.7 TRUE FALSE FALSE 10923.31962 9787.171255 9640.620584 9281.774422 9386.604948 9536.92607 8404.379023 10057.20684 9585.985089 9143.806201 1.194614079 1.070360749 1.054333433 1.015088708 1.026553357 1.042993023 0.919133547 1.099892826 1.048358296 1 13.15857911 -9.57303349 2.467852493 1.092986302 1.016876483 0.146730115 0.062102993 0.414426706 5.113126719 0.013178191 0.019884315 2.67E-10 9.57303349 -0.076109819 SQIHDIVLVGGSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQIHDIVLVGGSTR 14 0 P11142;E9PKE3;P11142-2;E9PN89;E9PNE6;A8K7Q2 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 69.878 0.027043 10105000 2912.8 2391.3 2562.2 2409.3 3634.3 3039.8 2983.9 3093.8 3963.6 3424.3 FALSE FALSE TRUE 2877.297673 2424.964784 2606.794016 2687.874602 3448.82811 2845.566591 3237.352392 3183.314222 3609.085689 3335.336192 0.862670959 0.72705258 0.781568593 0.805878163 1.03402713 0.853157351 0.970622511 0.954420795 1.082075533 1 11.70361647 SQLDDHPES(ph)DDEENFIDANDDEDMEK ddPTM_HeLa_Romidepsin_16h_R1 2 SQLDDHPESDDEENFIDANDDEDMEK 26 0 Q03701 Q03701 CEBPZ CCAAT/enhancer-binding protein zeta 1 0 S(0.005)QLDDHPES(0.995)DDEENFIDANDDEDMEK;S(0.006)QLDDHPES(0.994)DDEENFIDANDDEDMEK ; 49.745 0.010688 94126000 5094.7 4442.2 4939.2 3054.4 5011 5722 4681 5490.9 5628 6059.2 TRUE FALSE FALSE 5032.603837 4504.737408 5025.164704 3407.564099 4755.269971 5356.382667 5078.604023 5649.770528 5124.617584 5901.781111 0.852726277 0.763284392 0.851465788 0.577378936 0.805734724 0.907587484 0.860520566 0.957299233 0.868317121 1 12.5269347 -11.60755792 0.816202372 0.989829799 0.816163734 0.11906933 0.103361547 0.514230448 0.694487716 0.046225108 0.021473437 2.47E-12 11.60755792 -0.173666065 SQLPTLEQDGGTQNPVS(ph)SPGMSQELR ddPTM_HeLa_Romidepsin_16h_R1 1 SQLPTLEQDGGTQNPVSSPGMSQELR 26 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 SQLPTLEQDGGT(0.001)QNPVS(0.481)S(0.481)PGMS(0.037)QELR 72.035 0.00010984 19683000 1746.2 2000.6 2040.1 2004.5 2169.4 2098.8 1735.2 1812.1 1795.2 2157.1 TRUE FALSE FALSE 1724.916643 2028.764499 2075.607085 2236.269721 2058.687423 1964.693454 1882.587845 1864.530254 1634.632816 2101.058231 0.820975172 0.965591752 0.987886511 1.064353995 0.979833587 0.935097098 0.896018881 0.887424359 0.778004527 1 11.03690043 -7.747721305 4.660101228 0.938918864 0.890133815 0.05802754 0.080040508 0.51132509 27.44332962 0.011901017 0.044215435 1.79E-08 7.747721305 -0.048785049 SQNIVTDSSS(ph)LSAEAIR ddPTM_HeLa_Romidepsin_16h_R1 1 SQNIVTDSSSLSAEAIR 17 0 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 SQNIVTDS(0.034)S(0.449)S(0.514)LS(0.003)AEAIR 181.34 4.89E-09 3296300 1797.8 1725.3 1525 1521.1 1678.2 1691.6 1318.6 1346.4 1794.8 1666 TRUE FALSE FALSE 1775.887722 1749.588819 1551.541985 1696.976739 1592.555192 1583.512219 1430.601851 1385.35596 1634.268593 1622.71708 1.094391465 1.078184756 0.956138322 1.045762542 0.981412725 0.97583999 0.881608919 0.853726122 1.007118624 1 10.66419577 -7.672889756 0.761560631 1.044005642 0.787217635 0.714426188 0.039215 0.708994239 0.411884648 0.00765704 0.136654156 2.12E-08 7.672889756 -0.256788007 SQNSQESTADES(ph)EDDMSSQASK ddPTM_HeLa_Romidepsin_16h_R1 2 SQNSQESTADESEDDMSSQASK 22 0 Q9BXW9;Q9BXW9-1 Q9BXW9 FANCD2 Fanconi anemia group D2 protein 1 0 SQNSQESTADES(0.998)EDDMS(0.001)SQASK;SQNSQESTADES(0.944)EDDMS(0.045)S(0.011)QASK ; 142.65 6.67E-06 34693000 13356.2 13845.1 14059.6 11767.4 13372 14579.2 11913.1 14477 13946.5 13467.2 TRUE FALSE FALSE 13193.4095 14040.01168 14304.30144 13128.00216 12689.57694 13647.63617 12924.99842 14895.86915 12699.09011 13117.3202 1.005800674 1.070341462 1.090489614 1.00081434 0.967390957 1.040428682 0.985338333 1.135587828 0.968116194 1 13.67918539 SQPAPVS(ph)PQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SQPAPVSPQQK 11 0 Q13118-2;Q13118 Q13118-2 KLF10 Krueppel-like factor 10 1 0 S(0.007)QPAPVS(0.993)PQQK 99.834 0.01925 5163300 2832.8 3397.1 2884.5 3003.2 2484.4 2113.9 1915.2 1690.1 3133.1 2752 TRUE FALSE FALSE 2798.272744 3444.924463 2934.703513 3350.444114 2357.611797 1978.828612 2077.87704 1739.000377 2852.867689 2680.502643 1.043935827 1.285178536 1.094833284 1.249931285 0.879540934 0.738230428 0.775181866 0.648759061 1.064303255 1 11.38828784 -8.525815998 5.041958325 1.064334427 0.735795516 0.7599661 0.099319068 0.083672236 6.218210052 0.016097539 0.034357303 2.98E-09 8.525815998 -0.328538911 SQPDPVDT(ph)PTSSKPQSK ddPTM_HeLa_Romidepsin_16h_R1 4 SQPDPVDTPTSSKPQSK 17 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 SQPDPVDT(0.778)PT(0.174)S(0.04)S(0.007)KPQSK;S(0.002)QPDPVDT(0.58)PT(0.388)S(0.023)S(0.008)KPQSK;S(0.002)QPDPVDT(0.966)PT(0.026)S(0.006)S(0.001)KPQSK;SQPDPVDT(0.901)PT(0.026)S(0.036)S(0.036)KPQSK ;;; 103.04 0.0015561 30252000 12024.4 11455 11679.2 9136.8 8995.9 9636 9283.3 8876.3 12318.8 11060.2 TRUE FALSE FALSE 11877.84199 11616.26379 11882.47158 10193.23981 8536.805655 9020.290699 10071.82327 9133.121736 11216.97567 10772.85441 1.102571476 1.078290242 1.103001222 0.946196748 0.792436742 0.837316681 0.934926147 0.847790325 1.04122596 1 13.39511294 -9.029382956 4.616488245 1.055566606 0.858051968 0.837880877 0.043886598 0.07409749 3.850374597 0.00811332 0.014153992 9.35E-10 9.029382956 -0.197514638 SQPERDWVLNEFR ddPTM_HeLa_Romidepsin_16h_R1 1 SQPERDWVLNEFR 13 1 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2;A0A0U1RQJ0 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 0 143.76 0.00087375 5171600 1861 1475.9 1449.8 2731.2 1904.2 1674.2 1201.4 1753.6 1976.3 1334 FALSE FALSE TRUE 1838.317416 1496.677759 1475.033161 3046.994195 1807.021568 1567.224023 1303.446886 1804.337649 1799.534778 1299.342488 1.414805899 1.151873177 1.135215061 2.345027753 1.390719988 1.206166995 1.003158827 1.38865439 1.384958004 1 10.34356604 -12.29659298 0.662766335 0.951717732 1.387099124 0 0.368307328 1.696943186 1.101163002 0.435152775 0.077413803 5.05E-13 12.29659298 0.435381392 SQPSK(ac)TLFVK ddPTM_HeLa_Romidepsin_16h_R1 2 SQPSKTLFVK 10 1 P19338;H7BY16 P19338 NCL Nucleolin 0 1 ; SQPSK(1)TLFVK;SQPSK(1)TLFVK 150.1 0.015255 1116790 1114.32 889.61 1705.47 254.37 1871.95 1625.88 1431.61 852.73 1118.16 813.63 FALSE TRUE FALSE 1100.738239 902.1339529 1735.15299 283.7814562 1776.417406 1521.991515 1553.210918 877.4023972 1018.148969 792.4917753 1.388958565 1.138351187 2.189490218 0.358087573 2.241559423 1.920513957 1.959907934 1.107143852 1.284743894 1 9.630252152 -10.74687287 0.28973888 0.914988772 1.766782524 0.092690621 0.546729229 2.189797336 0.597184071 0.737358159 0.537031988 1.79E-11 10.74687287 0.851793751 SQQENPESQPQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SQQENPESQPQKR 13 1 J3KSV9;J3KS37;O94762-4;O94762 J3KSV9 RECQL5 ATP-dependent DNA helicase Q5 0 1 SQQENPESQPQK(1)R 93.011 0.020003 0 0 0 0 0 0 57.604 128.49 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 53.92329031 139.4039374 0 0 0 0 SQQENPESQPQK(ac)RPR ddPTM_HeLa_Romidepsin_16h_R1 1 SQQENPESQPQKRPR 15 2 J3KSV9;J3KS37;O94762-4;O94762 J3KSV9 RECQL5 ATP-dependent DNA helicase Q5 0 1 SQQENPESQPQK(1)RPR 110.25 0.0047718 446850 0 58.774 103.1 0 160.6 281.45 169.64 285.6 0 55.598 FALSE TRUE FALSE 0 59.60142191 104.8944123 0 152.4039827 263.4662533 184.0492174 293.8633854 0 54.15355595 0 1.100600337 1.936981061 0 2.814293172 4.865169955 3.398654329 5.42648364 0 1 5.758984169 -8.553813644 3.497239469 0.650731428 4.416967951 0.843632831 0.753948477 0.064757426 1.663227752 0.109355657 0.239412975 2.79E-09 8.553813644 3.766236523 (ac)MNY(ph)EGSPIKVTLATLK ddPTM_HeLa_Romidepsin_16h_R1 1 MNYEGSPIKVTLATLK 16 1 E5RI98 E5RI98 NPM1 1 0 MNY(0.897)EGS(0.102)PIKVTLATLK 71.085 0.0026566 0 2549.2 1875.4 1937.7 2416.4 1239.6 933.36 801.51 891.7 2461.5 2086.8 TRUE FALSE FALSE 2518.12937 1901.80193 1971.424856 2695.795538 1176.338586 873.7213083 869.5902394 917.4999326 2241.337275 2032.584635 1.238880451 0.935656945 0.969910341 1.32628944 0.578740273 0.429857283 0.427824861 0.451395684 1.102703049 1 10.98909971 -8.640910056 5.459444212 1.101350673 0.446913183 0.880216404 0.11338188 0.055673115 2.450212092 0.018786584 0.038007856 2.29E-09 8.640910056 -0.65443749 down SQRYS(ph)GAYGASVSDEELK ddPTM_HeLa_Romidepsin_16h_R1 1 SQRYSGAYGASVSDEELK 18 1 A0A286YEX5;C9JRZ6;F8WAR4;Q9NX63 A0A286YEX5 CHCHD3 MICOS complex subunit MIC19 1 0 S(0.015)QRYS(0.985)GAYGASVSDEELK 135.26 0.0076358 13605000 1298.2 1467.8 1385.4 1565.3 1158.4 1508.7 1392.8 1222.7 1615.1 1221 TRUE FALSE FALSE 1282.377039 1488.463727 1409.512306 1746.287351 1099.282525 1412.298939 1511.104397 1258.076895 1470.641411 1189.278244 1.078281761 1.251568953 1.185182957 1.468358948 0.924327449 1.187526087 1.270606273 1.057849079 1.236583128 1 10.21587057 -10.49649477 2.782135309 1.030587453 1.194902258 0.000333617 0.148585946 0.270686136 4.146442349 0.023445347 0.025627782 3.19E-11 10.49649477 0.164314805 SQS(ph)ADAPGPTER ddPTM_HeLa_Romidepsin_16h_R1 1 SQSADAPGPTER 12 0 Q9NSC5-5;Q9NSC5-2;Q9NSC5;M0R1B8;M0R2U7 Q9NSC5-5 HOMER3 Homer protein homolog 3 1 0 SQS(1)ADAPGPTER 107.69 0.0023559 0 1146.6 1410 1064.7 884.15 1253.6 1068.1 1067 1558.4 1340.4 1137.3 TRUE FALSE FALSE 1132.624798 1429.850017 1083.230657 986.3795831 1189.624114 999.8518571 1157.630953 1603.489845 1220.511267 1107.752782 1.022452678 1.290766352 0.977863179 0.890432955 1.073907584 0.902594761 1.045026446 1.447515972 1.101790297 1 10.11342023 -7.265375001 5.114997809 1.017274145 1.466224183 0.566802161 0.107858911 0.07921625 6.747429942 0.013865657 0.124600046 5.43E-08 7.265375001 0.448950038 SQS(ph)DLSSSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSDLSSSSSR 11 0 J3KP75 J3KP75 PHACTR2 Phosphatase and actin regulator 1 0 S(0.012)QS(0.988)DLSSSSSR 168 0.00046327 10815000 2117.9 2666.3 3260.1 2281.5 1360.6 1546.3 2378.4 622.68 3359.8 3196.2 TRUE FALSE FALSE 2092.08622 2703.836241 3316.840673 2545.297765 1291.163505 1447.49642 2580.421237 640.6962634 3059.291073 3113.162263 0.672013227 0.868517608 1.065424926 0.817592387 0.414743401 0.464960159 0.828874636 0.205802399 0.982695669 1 11.60416506 -8.821688337 6.570771633 0.861193816 0.50310969 0.568584216 0.177905149 0.142637522 11.98327788 0.027880782 0.051147887 1.51E-09 8.821688337 -0.358084126 SQS(ph)ESS(ph)DEVTELDLSHGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5 Q86YS7 C2CD5 C2 domain-containing protein 5 2 0 S(0.155)QS(0.817)ES(0.311)S(0.716)DEVT(0.001)ELDLSHGK 128.09 0.0067794 2791400 939.66 1021.7 1092.4 1076.4 1286.3 1126.6 1006.5 1140.4 1394.3 1215.8 TRUE FALSE FALSE 928.2070625 1036.083519 1111.412764 1200.858433 1220.655311 1054.613896 1091.992085 1173.395675 1269.590316 1184.213341 0.783817434 0.874912893 0.938524103 1.014055822 1.030773146 0.890560729 0.922124458 0.990865104 1.072095941 1 10.2097133 -9.573307996 5.429744572 0.893591584 0.967038006 0 0.083857096 0.31174337 20.39235681 0.014215458 0.02033578 2.67E-10 9.573307996 0.073446422 SQS(ph)ETSLLGR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSETSLLGR 10 0 A0A0C4DFP1;Q96B18 A0A0C4DFP1 DACT3 Dapper homolog 3 1 0 S(0.001)QS(0.97)ET(0.028)SLLGR;S(0.041)QS(0.878)ET(0.074)S(0.007)LLGR ; 171.62 0.00070806 52636000 263.76 168.664 195.32 863.56 8181.5 11194.3 9842.4 13104.4 272.015 320.96 TRUE FALSE FALSE 260.5451917 171.0384562 198.7194627 963.4088704 7763.967526 10479.02036 10678.41321 13483.55514 247.6852971 312.6214129 0.833420812 0.547110496 0.635655315 3.081711075 24.83504714 33.51984197 34.1576513 43.13061928 0.792285131 1 8.288272789 -8.602745408 1.916187702 0.728931055 37.44305745 0.978004134 2.458684291 0.030830014 0.226908085 0.350203624 0.866435907 2.50E-09 8.602745408 36.71412639 up SQS(ph)EYKPDTPQSGLEYSGIQELEDR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSEYKPDTPQSGLEYSGIQELEDR 25 1 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 S(0.21)QS(0.545)EY(0.025)KPDT(0.218)PQS(0.002)GLEYSGIQELEDR 81.38 6.15E-05 5821300 1874.9 1339 1828.3 1495 1822.2 2009.9 1804.4 1887.9 1748.7 1951.6 TRUE FALSE FALSE 1852.047998 1357.850477 1860.120795 1667.858934 1729.206334 1881.473877 1957.665691 1942.523408 1592.291892 1900.897151 0.974302054 0.714320855 0.978548889 0.877406194 0.909679061 0.989782049 1.029864078 1.021898216 0.837652838 1 10.89246476 -7.990758524 4.995562861 0.952665791 1.023607607 0.093203979 0.089999399 0.330202716 23.7806374 0.012548214 0.037307042 1.02E-08 7.990758524 0.070941816 SQS(ph)FNSIDK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSFNSIDK 9 0 Q8IVL0-3;Q8IVL0-2;Q8IVL0;H0YHX7;A0A1B0GTC4;F8VZV4 Q8IVL0-3 NAV3 Neuron navigator 3 1 0 SQS(0.898)FNS(0.102)IDK;S(0.095)QS(0.88)FNS(0.026)IDK ; 118.61 0.014262 28675000 4732.4 5177.8 4942.3 4436 4892.6 4236 3248 3923.3 5519.5 4643.9 TRUE FALSE FALSE 4674.719689 5250.693204 5028.318658 4948.911192 4642.912365 3965.333271 3523.885039 4036.814496 5025.822096 4523.250809 1.03348673 1.160822918 1.111660368 1.09410497 1.026454769 0.876655626 0.779060279 0.892458691 1.111108428 1 12.14314428 -8.217122991 3.635028025 1.041895868 0.83483903 0.742676955 0.059203242 0.105998935 2.914610829 0.009189726 0.024599306 6.07E-09 8.217122991 -0.207056838 SQS(ph)FSHQQPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 0 S(0.191)QS(0.793)FS(0.016)HQQPSR 82.483 0.021207 3548700 1471.8 1539.1 1343.2 1355.7 2166.2 2163.4 1824.8 1872.2 2002.1 1686.8 TRUE FALSE FALSE 1453.861135 1560.76749 1366.577833 1512.452413 2055.650731 2025.165722 1979.798466 1926.369153 1823.027162 1642.976693 0.884894559 0.949963257 0.831769458 0.920556219 1.251174615 1.232619873 1.205007031 1.172487207 1.109587963 1 10.6820963 -8.764182389 24.99985197 0.933681269 1.21582096 0.763538776 0.072160749 19.37412074 176578.3552 0.008575 0.016063769 1.72E-09 8.764182389 0.282139691 SQS(ph)FTHSPSGDPK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSFTHSPSGDPK 13 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 S(0.292)QS(0.639)FT(0.058)HS(0.01)PSGDPK 73.735 0.023066 6272000 4842.1 4890.5 4309.5 4947 6680.4 5854.4 5129 6500.3 6637.1 5855.2 TRUE FALSE FALSE 4783.082623 4959.348587 4384.50504 5518.995416 6339.47426 5480.322734 5564.657132 6688.375925 6043.461153 5703.08106 0.838683963 0.86959111 0.768795848 0.967721721 1.111587613 0.960940705 0.97572822 1.172765362 1.059683545 1 12.47752582 -8.996961039 24.39737723 0.904730019 1.042440282 0.347525884 0.094879159 63.92853648 513216.0319 0.013919797 0.025127315 1.01E-09 8.996961039 0.137710262 SQS(ph)GTLDGESAAWSASGEDSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSGTLDGESAAWSASGEDSR 21 0 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4 P49815 TSC2 Tuberin 1 0 S(0.001)QS(0.773)GT(0.226)LDGESAAWSASGEDSR 369.77 3.10E-301 30125000 2106.2 2198.6 2358.9 2431.9 1989.6 2418.1 2157.1 2312 2544.8 2557.7 TRUE FALSE FALSE 2080.528824 2229.551949 2399.955665 2713.08772 1888.063288 2263.591214 2340.32402 2378.894072 2317.186714 2491.250585 0.835134304 0.894952905 0.963353779 1.089046496 0.75787771 0.90861643 0.939417349 0.954899554 0.930129923 1 11.28265443 SQS(ph)IEQESQEK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSIEQESQEK 11 0 A0A0A0MRN0;Q5VTL8 A0A0A0MRN0 PRPF38B Pre-mRNA-splicing factor 38B 1 0 SQS(0.769)IEQES(0.231)QEK;S(0.367)QS(0.633)IEQESQEK ; 198.37 6.16E-13 108293000 6240.5 5821 5013 5363.8 4476.5 4724.1 4227.2 4366.9 5978.5 6086.3 TRUE FALSE FALSE 6164.438386 5902.948191 5100.249162 5983.987793 4248.047501 4422.245256 4586.258262 4493.249362 5443.767987 5928.177049 1.039853961 0.995744247 0.860340223 1.009414487 0.716585801 0.74597051 0.773637195 0.757947903 0.918287012 1 12.53337282 -9.009941006 1.090724482 1.0166621 0.742452946 0.675089117 0.068114776 0.154897736 0.363406588 0.009800635 0.023754946 9.77E-10 9.009941006 -0.274209154 SQS(ph)LPGADSLLAKPIDK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSLPGADSLLAKPIDK 17 1 H0Y4W2;F2Z2U4;Q9Y4A5-2;Q9Y4A5 H0Y4W2 TRRAP Transformation/transcription domain-associated protein 1 0 S(0.169)QS(0.68)LPGADS(0.151)LLAKPIDK 71.946 0.0036607 0 2191.1 2824.1 1260.6 1658.3 1899.6 1684.9 1121.8 1646.7 1990.8 2288 TRUE FALSE FALSE 2164.39403 2863.857754 1282.540214 1850.040449 1802.656324 1577.240328 1217.085664 1694.344666 1812.737862 2228.55743 0.97120855 1.285072449 0.575502429 0.83015157 0.808889329 0.70774049 0.546131613 0.760287639 0.813413124 1 11.12189442 -9.743288218 24.99997855 1.00842432 0.708137373 0.555210886 0.136972979 124.4925163 171465.9002 0.01877663 0.026524035 1.81E-10 9.743288218 -0.300286946 SQS(ph)LPHSATVTLGGTSDPSTLSSSALSER ddPTM_HeLa_Romidepsin_16h_R1 1 SQSLPHSATVTLGGTSDPSTLSSSALSER 29 0 F8WDP1;A0A0A0MRY0;Q8WUA7-3;Q8WUA7-4;Q8WUA7 F8WDP1 TBC1D22A TBC1 domain family member 22A 1 0 S(0.237)QS(0.685)LPHS(0.05)AT(0.014)VT(0.014)LGGTSDPSTLSSSALSER 77.147 3.15E-06 10299000 1243.2 1217.5 937.85 835.27 1761.2 1485.5 1318 1543.7 1624.4 1417.1 TRUE FALSE FALSE 1228.0474 1234.639997 954.1728858 931.8478475 1671.319392 1390.581344 1429.950887 1588.364524 1479.109596 1380.283538 0.889706619 0.894482882 0.691287594 0.675113353 1.210852224 1.007460646 1.03598344 1.150752349 1.071598375 1 10.43074894 -8.738474991 24.99999677 0.903815376 1.089899242 0.425198732 0.127748742 224.1648057 244034.0926 0.019252072 0.038483513 1.83E-09 8.738474991 0.186083865 SQS(ph)LQDQPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSLQDQPTR 10 0 Q8N4C8-2;Q8N4C8-3;Q8N4C8 Q8N4C8-2 MINK1 Misshapen-like kinase 1 1 0 S(0.155)QS(0.845)LQDQPT(0.001)R 133.88 0.0060805 8527300 1879 2488.9 1202.6 1849.8 1865.1 1889.1 1892.8 2226.9 1655 1691.9 TRUE FALSE FALSE 1856.098025 2523.9388 1223.530749 2063.68258 1769.916987 1768.392607 2053.574385 2291.331838 1506.972655 1647.944194 1.126311214 1.531568125 0.742458848 1.252276981 1.074015124 1.073090104 1.24614316 1.390418344 0.914456121 1 10.68645167 -4.000000015 0.02235917 6.81E-08 2.669982714 0.171817657 0.198796897 3390.214744 5.895976937 253.1239939 486.964676 1.00E-04 4.000000015 2.669982646 SQS(ph)PHYFR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSPHYFR 8 0 Q9UKJ3-2;Q9UKJ3 Q9UKJ3-2 GPATCH8 G patch domain-containing protein 8 1 0 S(0.004)QS(0.996)PHYFR 106.16 0.010827 17556000 2298.3 2220.9 1733.1 1970.7 3988.4 3740.3 3485.1 2848.7 3948.8 3143.7 TRUE FALSE FALSE 2270.287436 2252.165888 1763.263878 2198.561606 3784.857065 3501.306901 3781.124307 2931.12264 3595.609438 3062.026221 0.741433049 0.735514893 0.57584872 0.718008746 1.236062918 1.143460783 1.234843869 0.95724936 1.174258213 1 11.58027092 -8.758898681 24.99848336 0.82802657 1.149511129 0.453930354 0.171166547 45.12867045 444021.4378 0.023968266 0.046218626 1.74E-09 8.758898681 0.321484559 SQS(ph)PVHLR ddPTM_HeLa_Romidepsin_16h_R1 4 SQSPVHLR 8 0 Q96T58;A0A669KB49 Q96T58 SPEN Msx2-interacting protein 1 0 SQS(1)PVHLR;S(0.002)QS(0.998)PVHLR;S(0.005)QS(0.995)PVHLR;SQS(1)PVHLR ;;; 112.13 0.0090849 78073800 12953.8 11744.4 11276.7 11634.6 12513.4 12858.9 11346.7 10821.3 13944.3 12649.5 TRUE FALSE FALSE 12795.9141 11909.73797 11472.96623 12979.84719 11874.7945 12037.25779 12310.48841 11134.39724 12697.08688 12320.86417 1.038556544 0.966631708 0.931181943 1.053485131 0.963795586 0.976981617 0.999157871 0.903702621 1.030535416 1 13.58881583 -4.252373651 0.384027735 1.012970265 3.07E-13 0.300499083 0.037770524 45.0221685 0.65892705 0.009856463 33.5781486 5.59E-05 4.252373651 -1.012970265 SQS(ph)SDTEQQSPT(ph)SGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 S(0.013)QS(0.7)S(0.239)DT(0.048)EQQS(0.262)PT(0.673)S(0.065)GGGK 157.14 0.00021613 5122500 2365.5 2866.4 2706.9 1822.6 2399.4 2500.8 2530.7 1894.9 3207.9 3427.2 TRUE FALSE FALSE 2336.668376 2906.753254 2754.012459 2033.337588 2276.949665 2341.006951 2745.657595 1949.725942 2920.97739 3338.16085 0.699986754 0.870764887 0.825008914 0.609119116 0.682097049 0.701286444 0.82250608 0.584071898 0.875025956 1 11.70483776 -16.52287874 0.229463215 2.57268321 0.685944471 0.447891011 0.093274014 23.67813571 0.304757747 16.7350956 0.062097583 3.00E-17 16.52287874 -1.886738739 SQSAAVT(ph)PSSTTSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 0 S(0.105)QS(0.339)AAVT(0.503)PS(0.04)S(0.011)TTSSTR 145.8 0.00063957 4094600 1919.5 1701.8 2054 1632.7 2094.2 2084.4 2215.6 2258.5 2096 1955 TRUE FALSE FALSE 1896.104396 1725.757985 2089.749008 1821.480456 1987.325159 1951.213567 2403.793009 2323.846134 1908.52851 1904.208818 0.995743942 0.906286101 1.097436893 0.956554995 1.043648753 1.024684661 1.262357881 1.220373581 1.002268497 1 10.89497598 -7.798313685 5.574778992 0.999529613 1.242535171 0.795324899 0.048336694 0.04595933 3.603703587 0.006064735 0.01968592 1.59E-08 7.798313685 0.243005558 SQSAAVTPSS(ph)TTSSTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSAAVTPSSTTSSTR 16 0 Q16186;A0A087WX59 Q16186 ADRM1 Proteasomal ubiquitin receptor ADRM1 1 0 S(0.011)QS(0.011)AAVT(0.116)PS(0.255)S(0.579)T(0.024)T(0.002)S(0.002)STR 163 7.25E-05 40002000 1086.9 1046.6 916.76 814.78 1032.4 1172.8 1304.2 1163.6 880.89 861.88 TRUE FALSE FALSE 1073.652445 1061.334062 932.7158232 908.9886973 979.7127756 1097.861865 1414.978715 1197.26693 802.1009922 839.4882334 1.278936859 1.264263179 1.111052885 1.082789086 1.167035745 1.307775168 1.68552537 1.426186673 0.955464246 1 9.713366294 -4 0.277760725 1.094142919 4.714197565 0.568338511 0.135225932 29.60687715 0.37695594 0.064603456 52.56984832 1.00E-04 4 3.620054646 SQSDLDDQHDYDSVAS(ph)DEDTDQEPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSDLDDQHDYDSVASDEDTDQEPLR 26 0 J3QRU8;A0A0C4DGN6;Q9Y2X7;Q9Y2X7-3;J3QLH1 J3QRU8 GIT1 ARF GTPase-activating protein GIT1 1 0 SQSDLDDQHDYDS(0.28)VAS(0.621)DEDT(0.099)DQEPLR 114.51 3.33E-07 18518000 4564.1 4249.9 3781.7 4544.6 6216.7 6460.8 6022.9 6412.3 5311 4906.1 TRUE FALSE FALSE 4508.470994 4309.730204 3847.518902 5070.068035 5899.438601 6047.975731 6534.484976 6597.829784 4835.970858 4778.638815 0.943463436 0.901874021 0.805149552 1.060985823 1.234543733 1.265627298 1.367436467 1.380692293 1.011997568 1 12.22238401 -8.704311434 2.068038245 0.953980295 1.339983964 0.890085208 0.063402449 0.080541188 0.699962188 0.010409634 0.023597497 1.98E-09 8.704311434 0.386003669 SQSES(ph)SDEVTELDLSHGK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 S(0.011)QS(0.046)ES(0.845)S(0.099)DEVTELDLSHGK;S(0.008)QS(0.04)ES(0.606)S(0.343)DEVT(0.003)ELDLSHGK ; 185.71 4.69E-11 9299100 4624.9 3635.8 5066.7 3749.1 4225.1 4766.9 3349 4057 4944.6 4539.2 TRUE FALSE FALSE 4568.52994 3686.984888 5154.883788 4182.588582 4009.477381 4462.310474 3633.463976 4174.382894 4502.342592 4421.27093 1.033306941 0.833919691 1.165928049 0.946014992 0.90686082 1.009282296 0.821814368 0.944159035 1.018336733 1 12.11024543 -9.016800027 24.64839563 1.011846323 0.920645105 0.198523764 0.086260687 681.0671983 999237.7807 0.011847818 0.019979029 9.62E-10 9.016800027 -0.091201218 SQSES(ph)SDEVTELDLSHGKK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSESSDEVTELDLSHGKK 19 1 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 S(0.124)QS(0.114)ES(0.381)S(0.381)DEVTELDLSHGKK 63.706 0.0068107 12778000 2474.4 2641.4 2639.5 2430.4 2530.7 2414.8 1806 2261.1 2938.1 2791.8 TRUE FALSE FALSE 2444.241061 2678.585699 2685.43939 2711.414283 2401.548936 2260.502073 1959.401595 2326.521361 2675.308977 2719.268634 0.898859727 0.985039016 0.987559433 0.997111595 0.883159871 0.83129046 0.720561982 0.855568785 0.983834015 1 11.40900297 -8.380385864 2.419776335 0.959328301 0.789138549 0.749684028 0.044325459 0.129272082 1.463905828 0.007428687 0.019599516 4.16E-09 8.380385864 -0.170189751 SQSESSDEVT(ph)ELDLSHGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSESSDEVTELDLSHGK 18 0 Q86YS7;Q86YS7-3;Q86YS7-2;Q86YS7-4;Q86YS7-5 Q86YS7 C2CD5 C2 domain-containing protein 5 1 0 S(0.022)QS(0.351)ES(0.036)S(0.186)DEVT(0.404)ELDLSHGK 117.55 0.0011228 7595700 1022 1678.1 1138.7 1266.8 1319.7 1176.7 914.96 1123.2 1178.7 1415.5 TRUE FALSE FALSE 1009.543471 1701.724336 1158.518596 1413.273376 1252.350785 1101.512668 992.6766796 1155.69802 1073.27412 1378.725106 0.7322297 1.234273844 0.840282512 1.025058128 0.908339726 0.798935671 0.719996086 0.838236727 0.778454034 1 10.42911912 -8.218379143 4.635605521 0.90980745 0.776125479 0.180698695 0.136921285 0.329785496 16.48917768 0.020923787 0.054302794 6.05E-09 8.218379143 -0.133681971 SQSEYKPDT(ph)PQSGLEYSGIQELEDR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSEYKPDTPQSGLEYSGIQELEDR 25 1 Q16513-3;Q16513-2;Q16513;Q16513-5;Q16513-4 Q16513-3 PKN2 Serine/threonine-protein kinase N2 1 0 S(0.017)QS(0.048)EY(0.006)KPDT(0.855)PQS(0.073)GLEY(0.001)S(0.001)GIQELEDR 72.899 0.00034079 5939300 2929.2 2558.3 2353.3 2507.1 2834.2 3277.1 2922.8 2786.4 2804.9 2817.8 TRUE FALSE FALSE 2893.497784 2594.315815 2394.258199 2796.982698 2689.560198 3067.703886 3171.062559 2867.020088 2554.022719 2744.59315 1.05425381 0.945246043 0.872354505 1.019088275 0.979948594 1.117726278 1.155385292 1.044606589 0.930565144 1 11.42237659 -8.255316853 24.7034196 1.005060954 1.110853986 0.451316772 0.060357587 341.2043101 1376699.23 0.008736954 0.021643941 5.55E-09 8.255316853 0.105793032 SQSFSHQQPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SQSFSHQQPSR 11 0 B3KNS5;Q8WVR3-2;Q8WVR3-3;Q8WVR3 B3KNS5 C7orf43 Uncharacterized protein C7orf43 1 0 S(0.273)QS(0.026)FS(0.001)HQQPS(0.7)R 110.64 0.014279 3183300 868.25 1080.2 827.83 905.39 1133.9 1180.9 839.99 863.26 1057.9 943.51 TRUE FALSE FALSE 857.667435 1095.407084 842.2380339 1010.075452 1076.032852 1105.444301 911.3387296 888.2370661 963.2787744 918.9974742 0.933264192 1.191958754 0.916474808 1.099105798 1.170876833 1.202880674 0.991666196 0.9665283 1.048184355 1 9.843917086 -10.29418952 24.99556773 0.968485865 1.076903047 0.120481611 0.096022346 710.8990443 542570.2532 0.01604247 0.018346076 5.08E-11 10.29418952 0.108417182 SQSGEDES(ph)MNQPGPIK ddPTM_HeLa_Romidepsin_16h_R1 3 SQSGEDESMNQPGPIK 16 0 A0A0C4DG33;O43933-2;O43933 A0A0C4DG33 PEX1 Peroxisome biogenesis factor 1 1 0 SQSGEDES(1)MNQPGPIK;SQS(0.006)GEDES(0.994)MNQPGPIK;SQS(0.01)GEDES(0.99)MNQPGPIK ;; 133.42 0.0022673 32396900 12444.2 12508.6 12909.7 12890.4 17612.3 18735.4 15201.5 18407.6 13087 13156.3 TRUE FALSE FALSE 12292.5253 12684.6964 13134.38791 14380.8487 16713.47861 17538.26841 16492.71503 18940.19486 11916.46594 12814.49743 0.959267062 0.989870767 1.02496317 1.122232751 1.304263293 1.368627096 1.28703565 1.478028691 0.929920663 1 13.64548928 -8.871032216 1.428757678 0.980434938 1.379617886 0.937055791 0.046749115 0.060974283 0.249599083 0.006592246 0.01541213 1.35E-09 8.871032216 0.399182948 SQSGT(ph)LDGESAAWSASGEDSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSGTLDGESAAWSASGEDSR 21 0 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4 P49815 TSC2 Tuberin 1 0 S(0.001)QS(0.085)GT(0.913)LDGES(0.001)AAWSASGEDSR 329.52 1.60E-193 31498000 1649.1 1713.5 1548.9 1612.2 1662.1 1538.8 1438.4 1929.4 1679.6 1495.4 TRUE FALSE FALSE 1629.000135 1737.622698 1575.857955 1798.61015 1577.276835 1440.475646 1560.57766 1985.224145 1529.372369 1456.549292 1.118396846 1.19297212 1.08191186 1.23484331 1.082885998 0.988964571 1.07142111 1.362963928 1.049996988 1 10.50833881 -11.86399263 0.69491038 0.997465306 1.136093813 0.172736248 0.099295095 0.904144737 0.806774081 0.067884351 0.021472894 1.37E-12 11.86399263 0.138628507 SQSLPNS(ph)LDYTQTSDPGR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSLPNSLDYTQTSDPGR 18 0 H0YNE5;H0YLG5;Q96TC7 H0YNE5 RMDN3 Regulator of microtubule dynamics protein 3 1 0 SQS(0.02)LPNS(0.977)LDYT(0.002)QTSDPGR;S(0.016)QS(0.297)LPNS(0.641)LDYT(0.046)QTSDPGR ; 257.88 1.29E-75 395500000 6782.8 6682.3 5846.7 5090.3 6790.2 7944.6 5823.3 8955.4 6249.6 6479.2 TRUE FALSE FALSE 6700.128625 6776.373595 5948.459361 5678.864437 6443.670756 7436.9657 6317.930957 9214.51037 5690.620124 6310.86945 1.061680752 1.073762284 0.942573667 0.899854526 1.021043266 1.178437576 1.001118944 1.460101566 0.901717294 1 12.62362306 -5.067441181 1.375794937 1.02179631 200 0.714646939 0.083956733 258.9889112 1.364109697 0.010998709 161737.3337 8.56E-06 5.067441181 198.9782037 SQSLPNSLDYT(ph)QTSDPGR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSLPNSLDYTQTSDPGR 18 0 H0YNE5;H0YLG5;Q96TC7 H0YNE5 RMDN3 Regulator of microtubule dynamics protein 3 1 0 S(0.002)QS(0.022)LPNS(0.076)LDYT(0.822)QT(0.062)S(0.017)DPGR 131.84 0.0031771 9200100 1161.7 974.58 1101.7 2482.1 1086.3 1383.1 827.58 1097 1251 1312.3 TRUE FALSE FALSE 1147.540754 988.3001628 1120.874626 2769.092081 1030.862057 1294.724374 897.8746245 1128.739964 1139.107427 1278.206257 0.89777432 0.773193025 0.876912173 2.166389083 0.806491168 1.012922888 0.702448936 0.883065591 0.891176538 1 10.31990494 -7.777546423 23.39579906 1.012333054 0.792757356 0.059875069 0.38652416 252.9020767 367349.6069 0.052839622 0.159409681 1.67E-08 7.777546423 -0.219575698 SQSS(ph)DT(ph)EQQSPTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 S(0.006)QS(0.129)S(0.862)DT(0.972)EQQS(0.03)PT(0.001)SGGGK;S(0.001)QS(0.251)S(0.776)DT(0.869)EQQS(0.081)PT(0.02)S(0.002)GGGK ; 170.48 1.22E-05 85610400 6070.81 5662.5 5638.1 5418.9 5351.8 5521.4 5138.07 4236.56 6281.3 6164.5 TRUE FALSE FALSE 5996.816633 5742.216824 5736.228765 6045.458715 5078.677676 5168.60036 5574.497538 4359.138179 5719.484796 6004.345401 0.998746113 0.956343521 0.955346234 1.00684726 0.845833698 0.860809966 0.928410537 0.725997238 0.952557592 1 12.55179126 -5.391418116 0.331355216 1.005270631 7.89E-17 0.663661182 0.048656876 7.772240402 0.227681059 0.014194926 4.082001399 4.06E-06 5.391418116 -1.005270631 SQSS(ph)DTEQQS(ph)PTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 S(0.13)QS(0.061)S(0.799)DT(0.01)EQQS(0.841)PT(0.147)S(0.012)GGGK 217.67 5.59E-26 85451000 5049.6 4768.4 5414.1 4673.3 4681.7 4176 4684.1 2912.5 5358.4 5145.8 TRUE FALSE FALSE 4988.053533 4835.52966 5508.330139 5213.648935 4442.775379 3909.167077 5081.967337 2996.768592 4879.131284 5012.111374 0.995200059 0.964768996 1.099003938 1.040210112 0.886407952 0.779944176 1.013937432 0.597905427 0.973468249 1 12.29120276 -6.533264011 0.699100193 1.001269222 9.30E-15 0.587584679 0.089550915 3.646617361 0.606075917 0.014044473 3.670359992 2.93E-07 6.533264011 -1.001269222 SQSS(ph)DTEQQSPT(ph)SGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 S(0.004)QS(0.365)S(0.53)DT(0.102)EQQS(0.098)PT(0.826)S(0.076)GGGK 181.32 2.04E-08 16645000 2563.1 2608.7 2671.6 2291 2410.8 2134.5 2398.3 1837.9 2824.4 2588.6 TRUE FALSE FALSE 2531.859951 2645.425347 2718.098077 2555.896199 2287.76788 1998.112339 2602.011542 1891.076737 2571.77859 2521.347799 1.004169259 1.049210802 1.078033772 1.013702354 0.907359104 0.792477872 1.031992311 0.750026132 1.020001521 1 11.29997942 -8.686021091 4.276110073 1.013141715 0.872257727 0.527404846 0.072692237 0.138389011 4.828633668 0.009680517 0.019698963 2.06E-09 8.686021091 -0.140883988 SQSS(ph)DTEQQSPTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 6 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.017)QS(0.257)S(0.724)DT(0.002)EQQSPTSGGGK;S(0.01)QS(0.164)S(0.661)DT(0.164)EQQSPTSGGGK;S(0.064)QS(0.03)S(0.902)DT(0.004)EQQSPTSGGGK;S(0.003)QS(0.195)S(0.49)DT(0.311)EQQS(0.001)PTSGGGK;S(0.01)QS(0.01)S(0.919)DT(0.061)EQQSPTSGGGK;S(0.028)QS(0.165)S(0.779)DT(0.026)EQQS(0.001)PTS(0.001)GGGK ;;;;; 224.36 1.32E-35 320363400 15410.94 16554.32 14001.24 14692.083 13440.5 14337.114 12707.34 11831.72 18420.1 16131.06 TRUE FALSE FALSE 15223.10554 16787.37215 14244.92571 16390.85076 12754.58113 13421.01869 13786.70114 12174.05215 16772.56012 15711.97274 0.968885689 1.068444583 0.906628719 1.043207689 0.811774648 0.854190553 0.877464681 0.774826456 1.06750186 1 13.93957671 -8.754292344 24.99999609 0.98895539 0.834744564 0.720301945 0.053902527 62.08207546 217158.2584 0.006303296 0.012399401 1.76E-09 8.754292344 -0.154210827 SQSSDT(ph)EQQSPTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 SQS(0.004)S(0.018)DT(0.919)EQQS(0.056)PT(0.002)SGGGK;S(0.002)QS(0.116)S(0.032)DT(0.849)EQQSPTSGGGK ; 174.23 2.16E-06 383753000 3990.7 3395.7 3711.4 3460.9 3466.3 3450.9 3368 2298.49 4247.7 4105 TRUE FALSE FALSE 3942.059813 3443.504754 3775.99536 3861.065542 3289.401776 3230.398627 3654.077836 2364.993182 3867.775073 3998.351508 0.985921274 0.861231122 0.944388044 0.965664358 0.822689493 0.807932624 0.913896097 0.591492063 0.967342432 1 11.96518959 -5.87778257 0.326681694 0.998968681 1.13E-11 0.653916121 0.069003495 6.493139566 0.244698066 0.022031261 3.101296027 1.33E-06 5.87778257 -0.998968681 SQSSDTEQQS(ph)PTSGGGK ddPTM_HeLa_Romidepsin_16h_R1 10 SQSSDTEQQSPTSGGGK 17 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 SQSS(0.001)DT(0.397)EQQS(0.6)PT(0.001)SGGGK;SQSSDTEQQS(0.974)PT(0.025)SGGGK;SQSSDT(0.001)EQQS(0.967)PT(0.03)S(0.002)GGGK;SQSSDT(0.001)EQQS(0.998)PTSGGGK;SQSSDT(0.002)EQQS(0.844)PT(0.112)S(0.042)GGGK;SQS(0.002)S(0.006)DT(0.021)EQQS(0.97)PT(0.001)SGGGK;SQSSDTEQQS(0.915)PT(0.079)S(0.006)GGGK;S(0.007)QS(0.043)S(0.029)DT(0.172)EQQS(0.705)PT(0.036)S(0.007)GGGK;SQSS(0.002)DT(0.004)EQQS(0.974)PT(0.019)S(0.002)GGGK;SQSSDT(0.001)EQQS(0.998)PT(0.001)SGGGK ;;;;;;;;; 248.1 4.24E-59 559292480 13052.67 13786.01 15583.61 12573.65 10988.891 12294.202 14946.24 5151.916 17365.12 17008.57 TRUE FALSE FALSE 12893.57904 13980.08981 15854.8362 14027.47457 10428.08689 11508.64217 16215.77325 5300.978561 15811.94018 16566.6849 0.778283592 0.843867672 0.957031313 0.846727916 0.629461292 0.694685886 0.978818234 0.319978233 0.954442019 1 14.01599732 -5.478599052 0.154490198 1.001234966 2.19E-30 0.392502878 0.155036407 38.28989627 0.576500246 0.344576689 8.048879399 3.32E-06 5.478599052 -1.001234966 SQSSEGVSS(ph)LSSS(ph)PSNSLETQSQSLSR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSSEGVSSLSSSPSNSLETQSQSLSR 27 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 2 0 S(0.012)QS(0.012)S(0.024)EGVS(0.352)S(0.568)LS(0.074)S(0.398)S(0.497)PS(0.059)NS(0.003)LETQSQSLSR;S(0.004)QS(0.005)S(0.015)EGVS(0.448)S(0.528)LS(0.036)S(0.271)S(0.534)PS(0.158)NS(0.002)LETQSQSLSR ; 87.578 4.96E-06 23444000 3107.4 2850.1 3021.09 2996.46 2813.39 3292.5 2047.13 2543.77 3272.2 3311.2 TRUE FALSE FALSE 3069.525814 2890.223783 3073.670804 3342.924804 2669.81221 3082.119876 2221.013171 2617.369972 2979.526237 3225.174547 0.951739439 0.896144919 0.953024638 1.036509732 0.827803944 0.955644363 0.688648983 0.811543665 0.923834104 1 11.65516153 -8.022801822 1.24956931 0.969978883 0.74359881 0.492720017 0.069532324 0.282862 0.733007165 0.009561135 0.057334764 9.49E-09 8.022801822 -0.226380073 SQSSEGVSSLSSS(ph)PSNSLETQSQSLSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSSEGVSSLSSSPSNSLETQSQSLSR 27 0 O95155-2;O95155;O95155-4 O95155-2 UBE4B Ubiquitin conjugation factor E4 B 1 0 SQSSEGVSSLSS(0.199)S(0.798)PS(0.002)NSLETQSQSLSR 158.25 1.17E-13 38947000 5933.1 5069.8 5449.6 6004.2 5534.4 5405.4 4366.9 5165.9 6371.3 5784.2 TRUE FALSE FALSE 5860.785095 5141.172777 5544.448002 6698.433855 5251.958916 5060.012385 4737.824377 5315.367166 5801.434971 5633.92565 1.040266674 0.912538272 0.984118064 1.188946087 0.932202383 0.898132616 0.840945492 0.943457102 1.029732256 1 12.45992481 -8.536993913 24.99272088 1.019988247 0.893240468 0.435780463 0.068967396 160.5731954 284314.7856 0.00974296 0.019492697 2.90E-09 8.536993913 -0.126747779 SQSSHS(ph)YDDSTLPLIDR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSSHSYDDSTLPLIDR 17 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22;O60716-25;O60716-27;O60716-29;O60716-26;O60716-28;O60716-30;O60716-31;O60716-32;H0YC95 O60716 CTNND1 Catenin delta-1 1 0 SQSS(0.002)HS(0.987)YDDS(0.007)T(0.003)LPLIDR;SQSS(0.001)HS(0.926)YDDS(0.037)T(0.037)LPLIDR ; 141.07 1.01E-07 1881800 548.65 507.62 529.89 607.3 750.19 886 615.6 581.29 663.55 552.07 TRUE FALSE FALSE 541.9628428 514.7662877 539.1125132 677.5188834 711.905005 829.3874594 667.8890486 598.108709 604.2004261 537.7271418 1.007877045 0.957300176 1.002576346 1.259967799 1.323914955 1.542394636 1.242059395 1.112290347 1.123618987 1 9.070730483 -9.206643615 3.701285914 0.998749751 1.314875222 0.623409312 0.107690454 0.101980568 2.856786857 0.015457012 0.02596666 6.21E-10 9.206643615 0.316125471 SQSST(ph)SPEGQALENR ddPTM_HeLa_Romidepsin_16h_R1 2 SQSSTSPEGQALENR 15 0 O60239-2;O60239 O60239-2 SH3BP5 SH3 domain-binding protein 5 1 0 SQS(0.006)S(0.053)T(0.47)S(0.47)PEGQALENR;SQS(0.001)S(0.009)T(0.495)S(0.495)PEGQALENR ; 176.19 8.09E-07 14736500 2111.1 2190.15 2191.52 2298.57 2838.8 3420.3 2843.9 3372.5 2374.6 2870.3 TRUE FALSE FALSE 2085.369101 2220.982989 2229.662486 2564.341478 2693.925443 3201.753869 3085.460795 3470.077967 2162.209829 2795.729192 0.745912411 0.79441993 0.797524486 0.917235291 0.963585976 1.145230331 1.103633644 1.241206758 0.77339745 1 11.44900891 -8.365257705 1.588818345 0.863839322 1.180698634 0.777194963 0.077638688 0.206111961 0.989658573 0.016034481 0.052398368 4.31E-09 8.365257705 0.316859312 SQSTT(ph)FNPDDMSEPEFK ddPTM_HeLa_Romidepsin_16h_R1 2 SQSTTFNPDDMSEPEFK 17 0 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 SQS(0.001)T(0.085)T(0.848)FNPDDMS(0.066)EPEFK;SQS(0.001)T(0.047)T(0.936)FNPDDMS(0.016)EPEFK ; 169.15 8.94E-06 47870200 6480.7 7778.5 5233.9 5480.8 7462 6912.4 6360.1 6179.1 7302.3 6913.3 TRUE FALSE FALSE 6401.710736 7888.005927 5324.993834 6114.515884 7081.186295 6470.719949 6900.326735 6357.882509 6649.163999 6733.691469 0.950698553 1.171423722 0.790798607 0.908048121 1.051605398 0.960946901 1.024746496 0.944189757 0.987447083 1 12.7171819 -7.805295267 0.002214602 1.941677733 2.98E-05 0.004976012 0.093412913 918664.9951 389.447505 168514.9589 172952.2285 1.57E-08 7.805295267 -1.941647918 SQSTTFNPDDMS(ph)EPEFK ddPTM_HeLa_Romidepsin_16h_R1 1 SQSTTFNPDDMSEPEFK 17 0 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 SQS(0.008)T(0.269)T(0.086)FNPDDMS(0.638)EPEFK 121.29 0.0031881 5151000 2354.3 2445.7 2365.2 2120.2 2415.6 2174.2 2180 2141.3 2702.8 2430.2 TRUE FALSE FALSE 2325.604886 2480.130629 2406.365314 2365.3475 2292.322918 2035.275637 2365.169146 2203.255137 2461.054799 2367.063054 0.982485398 1.047767031 1.016603808 0.999275239 0.968424949 0.85983161 0.999199891 0.930796978 1.039708171 1 11.20888242 -8.517454246 13.60431663 0.998157258 0.933078562 0.470915583 0.038105762 0.483483709 1202.34851 0.00499481 0.010383134 3.04E-09 8.517454246 -0.065078696 SQSTTFNPDDMS(ph)EPEFKR ddPTM_HeLa_Romidepsin_16h_R1 1 SQSTTFNPDDMSEPEFKR 18 1 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 SQS(0.001)T(0.001)T(0.003)FNPDDMS(0.996)EPEFKR 94.339 0.0039279 41898000 3120.6 3474.1 2372.5 3193.6 3212.3 2640.9 2551.9 2768.5 3111.6 3094.9 TRUE FALSE FALSE 3082.564927 3523.008471 2413.792367 3562.859058 3048.364344 2472.155013 2768.658322 2848.60218 2833.290703 3014.494052 1.022581194 1.168689807 0.800728854 1.181909467 1.011235813 0.820089531 0.918448759 0.944968585 0.9398893 1 11.55770017 -8.358683645 8.258535335 1.020318344 0.897164288 0.221979995 0.105804971 0.31258868 23.93577104 0.013280651 0.02977009 4.38E-09 8.358683645 -0.123154056 SQT(ph)DDEEMTGE ddPTM_HeLa_Romidepsin_16h_R1 2 SQTDDEEMTGE 11 0 M0QY77;Q9BQD3 M0QY77 KXD1 KxDL motif-containing protein 1 1 0 S(0.03)QT(0.967)DDEEMT(0.003)GE;S(0.016)QT(0.703)DDEEMT(0.282)GE ; 149.69 0.0058654 8978300 5774.5 6074.7 5354.3 5609.9 6843.1 6577.8 5988.4 6554.8 7068.3 6431 TRUE FALSE FALSE 5704.118173 6160.219786 5447.489345 6258.543033 6493.871072 6157.499809 6497.054547 6744.452796 6436.093545 6263.921693 0.910630505 0.983444572 0.86966115 0.999141327 1.03671013 0.983010343 1.037218354 1.076714098 1.027486271 1 12.61285046 -9.008848056 22.8852717 0.952237245 1.028564972 0.359180164 0.046906624 112.0798484 289896.0868 0.006905224 0.012054782 9.80E-10 9.008848056 0.076327727 SQT(ph)PNNTVTYESER ddPTM_HeLa_Romidepsin_16h_R1 1 SQTPNNTVTYESER 14 0 Q9NVW2-2;Q9NVW2 Q9NVW2-2 RLIM E3 ubiquitin-protein ligase RLIM 1 0 S(0.038)QT(0.962)PNNTVTYESER 132.51 0.00027639 0 886.17 948.02 858.39 1382.5 779.87 713.74 606.33 560.45 1004.3 997.89 TRUE FALSE FALSE 875.3690192 961.3662504 873.3299179 1542.351155 740.0703238 668.1343175 657.8316551 576.6657365 914.4728927 971.9646739 0.900618142 0.989095876 0.898520225 1.586838695 0.761416895 0.687405968 0.676806136 0.593299069 0.940849927 1 9.92476007 -8.538702672 24.99988954 0.997407242 0.666513333 0.462839209 0.193843626 178.7395915 282386.1683 0.027769398 0.05555182 2.89E-09 8.538702672 -0.33089391 SQT(ph)PPGVATPPIPK ddPTM_HeLa_Romidepsin_16h_R1 3 SQTPPGVATPPIPK 14 0 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 S(0.03)QT(0.949)PPGVAT(0.022)PPIPK;S(0.028)QT(0.961)PPGVAT(0.011)PPIPK;SQT(0.999)PPGVAT(0.001)PPIPK ;; 183.75 3.21E-07 173205000 22839.7 22353.1 21018.6 20277.7 17666.4 15228 14343 15610.2 22859.4 22770.1 TRUE FALSE FALSE 22561.32095 22667.78753 21384.41992 22622.30308 16764.81769 14254.97995 15561.29406 16061.85651 20814.79801 22178.52952 1.01725955 1.022059984 0.964194668 1.020009152 0.755903031 0.64273783 0.701637773 0.724207459 0.938511185 1 14.43687609 -8.690780596 4.09255402 1.006994329 0.692131873 0.945793743 0.033843093 0.023716918 0.776016796 0.003654426 0.00744705 2.04E-09 8.690780596 -0.314862457 SQT(ph)VPSPTINNSGQYSR ddPTM_HeLa_Romidepsin_16h_R1 1 SQTVPSPTINNSGQYSR 17 0 Q9P2D1;Q9P2D1-4;Q9P2D1-2;Q9P2D1-3 Q9P2D1 CHD7 Chromodomain-helicase-DNA-binding protein 7 1 0 S(0.061)QT(0.663)VPS(0.017)PT(0.259)INNSGQYSR 154.67 1.77E-06 0 1627.5 1286.1 1078 1134.7 768.38 948.06 857 1010.1 1590.6 1559 TRUE FALSE FALSE 1607.663404 1304.20575 1096.762138 1265.899353 729.1667014 887.4820257 929.7935586 1039.32565 1448.332752 1518.496955 1.058720203 0.858879397 0.72226825 0.833652875 0.480189768 0.584447682 0.61231177 0.684443684 0.953793649 1 10.5684283 -9.670055213 1.145488312 1.030156767 0.607435594 0.784229522 0.084903567 0.124587865 0.327533516 0.015090366 0.024125542 2.14E-10 9.670055213 -0.422721173 SQTTT(ph)ERDS(ph)DTDVEEEELPVENR ddPTM_HeLa_Romidepsin_16h_R1 1 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 2 0 S(0.083)QT(0.136)T(0.141)T(0.774)ERDS(0.718)DT(0.148)DVEEEELPVENR 81.379 0.00038498 21904000 1586.4 1634.2 1263.1 1756.6 1358.8 1387 1433.4 1418 1953.1 1799 TRUE FALSE FALSE 1567.064347 1657.20631 1285.083726 1959.706357 1289.455366 1298.375176 1555.15296 1459.027593 1778.409844 1752.261721 0.894309525 0.945752733 0.733385721 1.118386788 0.735880577 0.740971032 0.887511804 0.832653921 1.014922499 1 10.77500256 -15.51930455 0.085618295 1.433238598 0.705418716 0.260822757 0.10765032 132.7271653 1.070274505 11.67400228 1.642462835 3.02E-16 15.51930455 -0.727819882 SQTTT(ph)ERDSDTDVEEEELPVENR ddPTM_HeLa_Romidepsin_16h_R1 1 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 S(0.004)QT(0.254)T(0.254)T(0.379)ERDS(0.08)DT(0.028)DVEEEELPVENR 83.436 0.00018481 20011000 718.9 722 583.45 497.49 455.49 616.62 583.21 398.91 747.42 800.42 TRUE FALSE FALSE 710.1377703 732.164335 593.6047025 555.0121346 432.2446456 577.219972 632.7478428 410.4518315 680.5688833 779.624973 0.910870989 0.939123759 0.761397753 0.711896301 0.554426372 0.740381583 0.811605406 0.526473427 0.872943924 1 9.606636494 -9.64707154 1.87645481 0.959056836 0.672548574 0.674297517 0.085054588 0.128712984 0.92250074 0.013542366 0.02042011 2.25E-10 9.64707154 -0.286508263 SQTTTERDS(ph)DTDVEEEELPVENR ddPTM_HeLa_Romidepsin_16h_R1 1 SQTTTERDSDTDVEEEELPVENR 23 1 Q14676-3;Q14676;Q14676-2;Q14676-4 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 SQT(0.001)T(0.001)T(0.003)ERDS(0.956)DT(0.04)DVEEEELPVENR 121.48 1.23E-06 24538000 1389.9 1208.1 1349 1193.6 982.27 1158.3 1257.7 949.46 1802.7 1892.6 TRUE FALSE FALSE 1372.959364 1225.107664 1372.478779 1331.609648 932.1410965 1084.288368 1364.529007 976.9311271 1641.461997 1843.429979 0.744785199 0.664580525 0.744524498 0.722354341 0.505655819 0.588190699 0.740212008 0.529952935 0.890439027 1 10.8481769 -11.9857598 0.262646088 1.165477544 0.572691066 0.704877048 0.078931627 1.356468358 0.153233353 0.267134934 0.063802005 1.03E-12 11.9857598 -0.592786478 SQVEEELFSVR ddPTM_HeLa_Romidepsin_16h_R1 3 SQVEEELFSVR 11 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 0 0 ;; ;; 203.03 3.59E-12 10585300 4102.1 3816.25 3750.1 2716.38 4095.6 4375.3 3630.1 4023.6 4494.6 4419.2 FALSE FALSE TRUE 4052.102027 3869.975268 3815.368917 3030.460637 3886.586249 4095.732451 3938.440603 4140.016518 4092.591719 4304.388547 0.941388535 0.899076658 0.886390454 0.70403975 0.902935738 0.9515248 0.914982595 0.96181292 0.950795142 1 12.0715926 -10.70390701 1.17729452 0.983896194 0.885153168 0.205431957 0.068068645 0.413983026 1.19021298 0.016442917 0.015834625 1.98E-11 10.70390701 -0.098743026 SQVIAEKAPEPDLMS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 SQVIAEKAPEPDLMSPTR 18 1 Q9H7D0 Q9H7D0 DOCK5 Dedicator of cytokinesis protein 5 1 0 SQVIAEKAPEPDLMS(0.75)PT(0.25)R 71.905 0.02355 8053800 1348.5 1411.3 1431.9 2370.1 1912.7 1734 1347.7 1677.1 1776 1660.2 TRUE FALSE FALSE 1332.063963 1431.168318 1456.821619 2644.142114 1815.087782 1623.202996 1462.173604 1725.624242 1617.150112 1617.067765 0.823752716 0.885039174 0.900903259 1.63514614 1.122456227 1.003794047 0.904212944 1.067131681 1.000050924 1 10.65916442 SQVNGEAGSYEMT(ph)NQHVK ddPTM_HeLa_Romidepsin_16h_R1 1 SQVNGEAGSYEMTNQHVK 18 0 Q05D32;H0YMH7;Q05D32-2 Q05D32 CTDSPL2 CTD small phosphatase-like protein 2 1 0 S(0.106)QVNGEAGS(0.017)Y(0.036)EMT(0.841)NQHVK 76.176 0.0073624 15495000 1989.5 2466.3 2250.9 1350 2641.7 2767.6 2201.9 2123.9 2285.8 2702.6 TRUE FALSE FALSE 1965.251209 2501.020636 2290.07597 1506.093352 2506.884191 2590.759292 2388.929331 2185.351696 2081.352323 2632.386062 0.746566485 0.950096444 0.869962048 0.572139996 0.952323911 0.984186677 0.907514808 0.830179025 0.790671381 1 11.36215537 -7.218536607 19.27445139 0.87459294 0.830176596 0 0.12469855 6268.226545 2814857.924 0.018782293 4.618824141 6.05E-08 7.218536607 -0.044416344 SQWES(ph)PSPTPSYR ddPTM_HeLa_Romidepsin_16h_R1 1 SQWESPSPTPSYR 13 0 Q92620 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 0 SQWES(0.95)PS(0.045)PT(0.003)PS(0.002)YR 130.2 0.0024961 3626300 2297.8 2355.2 1800.4 1967 2274.6 2410.1 2388.2 2654.8 2502.2 2627.8 TRUE FALSE FALSE 2269.79353 2388.356567 1831.735207 2194.433795 2158.518674 2256.102388 2591.053648 2731.612449 2278.396965 2559.529377 0.886801124 0.933123327 0.715653129 0.857358315 0.843326392 0.881452039 1.012316433 1.06723231 0.890162459 1 11.32166285 -7.611974401 4.273215654 0.910936485 1.056111652 0.379143049 0.074976351 0.211776967 6.886216448 0.01262815 0.054108058 2.44E-08 7.611974401 0.145175168 SRDAT(ph)PPVSPINMEDQER ddPTM_HeLa_Romidepsin_16h_R1 2 SRDATPPVSPINMEDQER 18 1 P17275 P17275 JUNB Transcription factor jun-B 1 0 S(0.023)RDAT(0.854)PPVS(0.123)PINMEDQER;S(0.044)RDAT(0.949)PPVS(0.006)PINMEDQER ; 68.303 0.013664 22364000 1621.23 1204.09 1137.14 1494.61 1038.3 829.06 848.72 877.28 1686.74 1290.17 TRUE FALSE FALSE 1601.469825 1221.041211 1156.931445 1667.423841 985.3116766 776.0857417 920.8102556 902.6627127 1535.87375 1256.651197 1.274394859 0.971662792 0.920646435 1.326878806 0.784077299 0.617582463 0.732749276 0.718308083 1.222195748 1 10.29536855 -8.615393186 6.442526487 1.113847176 0.695082603 0.712605225 0.127273365 0.095834719 5.563588497 0.020599565 0.041482035 2.42E-09 8.615393186 -0.418764573 SRDS(ph)GDENEPIQER ddPTM_HeLa_Romidepsin_16h_R1 3 SRDSGDENEPIQER 14 1 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;Q8WX93-4;Q8WX93-7 Q8WX93-3 PALLD Palladin 1 0 S(0.034)RDS(0.966)GDENEPIQER;S(0.198)RDS(0.802)GDENEPIQER;S(0.187)RDS(0.813)GDENEPIQER ;; 203.05 6.92E-16 71436000 5346.6 4267.56 4809.1 4975.6 5357.3 5160.3 4897.6 4723.35 5373.9 4623.2 TRUE FALSE FALSE 5281.433583 4327.638822 4892.800368 5550.902283 5083.89699 4830.573484 5313.602022 4860.01268 4893.244925 4503.088598 1.172846918 0.961037903 1.086543216 1.232687779 1.128980006 1.072724504 1.179990557 1.079262061 1.086641939 1 12.13669915 -9.499832458 24.76980259 1.072427126 1.139093042 0.23831746 0.068160713 1096.909224 1178943.503 0.012620898 0.019195295 3.16E-10 9.499832458 0.066665916 SREDAGDNDDTEGAIGVR ddPTM_HeLa_Romidepsin_16h_R1 1 SREDAGDNDDTEGAIGVR 18 1 Q9H0S4-2;Q9H0S4 Q9H0S4-2 DDX47 Probable ATP-dependent RNA helicase DDX47 0 0 156.17 7.31E-06 2560600 609.77 614.18 651.38 535.05 705 700.36 456.46 551.9 946.87 728.69 FALSE FALSE TRUE 602.3378887 622.8264422 662.7169957 596.9149985 669.0212193 655.6092563 495.231701 567.8683557 862.1795757 709.7585288 0.84865185 0.877518786 0.933721778 0.841011378 0.942603987 0.923707472 0.697746742 0.800086695 1.214750568 1 9.47118447 -16.52287875 0.098051299 1.451913353 0.745996641 0.442279321 0.097215849 97.50676387 0.715693223 9.287721131 0.64741603 3.00E-17 16.52287875 -0.705916712 SREDS(ph)PELNPPPGIEDNR ddPTM_HeLa_Romidepsin_16h_R1 1 SREDSPELNPPPGIEDNR 18 1 Q03164-2;Q03164;Q03164-3 Q03164-2 KMT2A Histone-lysine N-methyltransferase 2A;MLL cleavage product N320;MLL cleavage product C180 1 0 S(0.232)REDS(0.768)PELNPPPGIEDNR 95.227 0.001488 4794500 863.47 833.92 765.61 793.09 491.99 529.43 822.41 600.66 909.69 950.39 TRUE FALSE FALSE 852.9456955 845.6599476 778.9351209 884.7907974 466.8819144 495.6011317 892.2654849 618.0391494 828.325048 925.6987308 0.921407438 0.913536899 0.841456399 0.955808589 0.504356222 0.535380589 0.963883232 0.667646102 0.894810612 1 9.854398934 -8.786931141 24.83264061 0.947348654 0.679504454 0.497169319 0.122920252 122.6493539 119477.7368 0.018382861 0.033330939 1.63E-09 8.786931141 -0.2678442 SRES(ph)LNVDVVK ddPTM_HeLa_Romidepsin_16h_R1 1 SRESLNVDVVK 11 1 E7EVH7;H0YJU9;H0YJL0;H0YJT3;G5E9S8;G3V2E7;F8W6L3;Q07866-8;Q07866-2;Q07866-3;Q07866;Q07866-5;Q07866-10;H0YGB8;Q07866-6;H0YG16;G3V5R9;Q07866-7;Q07866-4;Q07866-9;G3V3H3 E7EVH7;Q07866-6 KLC1 Kinesin light chain 1 1 0 S(0.108)RES(0.892)LNVDVVK 70.134 0.028949 8413900 2610.4 2949.3 2552.1 2826 3080.9 3569.5 3123.9 3051 3063.5 3031.2 TRUE FALSE FALSE 2578.583441 2990.820323 2596.51823 3152.755417 2923.670177 3341.42047 3389.243988 3139.275871 2789.492887 2952.448987 0.873371039 1.012996443 0.879445586 1.067844163 0.990252563 1.13174537 1.147943285 1.063278616 0.944806464 1 11.52769642 -8.712533372 1.278199057 0.941709305 1.11689621 0.586804263 0.057667084 0.246571748 0.796518964 0.01018953 0.02830779 1.94E-09 8.712533372 0.175186904 SRGGT(ph)S(ph)QVGSPT(ph)LLS(ph)PAVPSK ddPTM_HeLa_Romidepsin_16h_R1 1 SRGGTSQVGSPTLLSPAVPSK 21 1 Q8IY92-2;Q8IY92 Q8IY92-2 SLX4 Structure-specific endonuclease subunit SLX4 4 0 S(0.045)RGGT(0.848)S(0.848)QVGS(0.429)PT(0.834)LLS(0.776)PAVPS(0.221)K 49.188 0.023087 5205400 2512.3 2469.7 2343.7 1666.1 1500.5 1771.9 1811.1 2261.8 2452.9 2890.6 TRUE FALSE FALSE 2481.679121 2504.468501 2384.491115 1858.742321 1423.923886 1658.681309 1964.934789 2327.241614 2233.506481 2815.501795 0.88143404 0.889528291 0.846915146 0.660181544 0.505744265 0.589124579 0.69789861 0.826581471 0.793288956 1 11.45917636 -9.439325336 2.216173513 0.939463916 0.644406167 0.573012847 0.094480967 0.133125684 1.288822444 0.015012953 0.024081529 3.64E-10 9.439325336 -0.295057748 SRIPSPLQPEMQGT(ph)PDDEPSEPEPSPSTLIYR ddPTM_HeLa_Romidepsin_16h_R1 1 SRIPSPLQPEMQGTPDDEPSEPEPSPSTLIYR 32 1 K7EMY4;Q96GY3 K7EMY4 LIN37 Protein lin-37 homolog 1 0 SRIPSPLQPEMQGT(1)PDDEPSEPEPSPSTLIYR 154.71 1.11E-38 0 1609.2 1494.5 1435.1 1601.9 1874.3 1371.9 1415.3 1412.8 1889.6 1658.6 TRUE FALSE FALSE 1589.586451 1515.53961 1460.077314 1787.119215 1778.647477 1284.240018 1535.515547 1453.677139 1720.589443 1615.509333 0.983953741 0.938118759 0.903787607 1.106226488 1.100982483 0.794944351 0.95048386 0.8998259 1.06504457 1 10.65777337 -8.257869804 24.99643526 0.996281657 0.888624627 0.395313726 0.072533015 277.8256235 1945501.128 0.009771204 0.023865299 5.52E-09 8.257869804 -0.10765703 SRKTATNDVVSENANY(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 1 SRKTATNDVVSENANYLR 18 2 K7ENU7;H0Y9S9 K7ENU7 PPIP5K2 1 0 SRKTATNDVVS(0.098)ENANY(0.902)LR 112.84 3.03E-05 0 535.6 297.22 489.16 431.63 456.64 499.64 478.58 536.53 330.33 566.63 TRUE FALSE FALSE 529.0719012 301.404271 497.6736246 481.5370915 433.3359568 467.7146165 519.2305733 552.053649 300.7844575 551.9088709 0.958621847 0.546112387 0.901731519 0.872493842 0.785158528 0.847448992 0.940790411 1.000262323 0.544989351 1 9.108286264 -10.49441852 24.88376723 0.981745047 0.840512562 0 0.17922573 322.0648295 281595.7532 0.019739852 0.021410758 3.20E-11 10.49441852 -0.141232485 SRLGGILLPSGMPR ddPTM_HeLa_Romidepsin_16h_R1 1 SRLGGILLPSGMPR 14 1 K7EMJ7 K7EMJ7 SPIRE1 0 0 77.192 0.022924 7685100 713.5 631.73 1806.7 94.079 9761.6 7768.4 6381.4 5371.2 703.12 379.43 FALSE FALSE TRUE 704.8035876 640.6235115 1838.144856 104.9568566 9263.429126 7272.024311 6923.435957 5526.607198 640.2311862 369.5723539 1.907078763 1.733418381 4.973707682 0.283995422 25.06526538 19.67686228 18.73364142 14.95406012 1.732356816 1 8.529713029 -8.769582667 24.99999989 1.687663636 19.54999974 0.919551107 2.559629998 32.25441899 99021.71249 0.366181651 0.672084869 1.70E-09 8.769582667 17.8623361 VDLTLDWLTETS(ph)EEAK ddPTM_HeLa_Romidepsin_16h_R1 1 VDLTLDWLTETSEEAK 16 0 P49321-4;P49321;P49321-3;E9PPR5 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 VDLTLDWLTET(0.049)S(0.951)EEAK 132.65 0.0017486 6044400 3991.8 3600.1 4300.8 2743 2802.7 2478.7 1809.3 1604.4 3743.5 3962.7 TRUE FALSE FALSE 3943.146406 3650.782302 4375.65362 3060.158566 2659.667761 2320.31907 1962.981897 1650.820783 3408.671984 3859.748483 1.021607088 0.945860156 1.13366289 0.792838855 0.689077999 0.601158101 0.508577672 0.427701647 0.883133188 1 11.91429112 -8.638212669 1.192061789 1.014540648 0.475159517 0.884399509 0.076333891 0.084034157 0.231537621 0.009718334 0.030080989 2.30E-09 8.638212669 -0.539381132 down LGT(ph)SAEGAHLR ddPTM_HeLa_Romidepsin_16h_R1 1 LGTSAEGAHLR 11 0 Q15042-4;Q15042;Q15042-3 Q15042-4 RAB3GAP1 Rab3 GTPase-activating protein catalytic subunit 1 0 LGT(0.855)S(0.145)AEGAHLR 98.407 0.015749 2779000 1642 1549.6 1408.6 1303.4 1034.4 1059.9 682.58 725.32 2035.9 1671.7 TRUE FALSE FALSE 1621.986672 1571.415309 1433.116092 1454.105241 981.6107081 992.1758107 740.5583282 746.3059898 1853.804005 1628.268993 0.996141718 0.965083359 0.880147014 0.893037481 0.602855371 0.60934392 0.45481326 0.458343181 1.138512133 1 10.66912334 -8.637966465 0.876269584 0.999433233 0.431536324 0.931629422 0.061126122 0.073411261 0.101714196 0.006460174 0.025327155 2.30E-09 8.637966465 -0.567896909 down EAIS(ph)DEDEDEALYQK ddPTM_HeLa_Romidepsin_16h_R1 1 EAISDEDEDEALYQK 15 0 Q9C0B7 Q9C0B7 TANGO6 Transport and Golgi organization protein 6 homolog 1 0 EAIS(1)DEDEDEALYQK 192.65 1.59E-12 4332000 1881.9 2135.3 1556 1729.3 1115 983.09 671.39 686.08 1820.8 1975.9 TRUE FALSE FALSE 1858.962679 2165.360809 1583.081527 1929.249803 1058.097389 920.2737218 728.4178498 705.9306423 1657.943088 1924.565833 0.965912751 1.125116518 0.822565537 1.00243378 0.549784981 0.478172119 0.378484247 0.366799945 0.861463432 1 10.91031731 -8.637873312 2.163024543 0.986819203 0.398094268 0.89251579 0.088569216 0.054577542 0.515846258 0.010889669 0.025311607 2.30E-09 8.637873312 -0.588724935 down SRLTPVS(ph)PESSSTEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 SRLTPVS(1)PESSSTEEK 101.62 0.0018895 21805000 1698.9 1696.9 1047 2152.2 1041.9 1108.3 769.82 874.06 1714.9 1607.6 TRUE FALSE FALSE 1678.193153 1720.789003 1065.222596 2401.04749 988.7279551 1037.483207 835.2084916 899.3495471 1561.515049 1565.83432 1.071756527 1.09895982 0.680290745 1.533398176 0.631438424 0.66257534 0.533395188 0.57435805 0.997241553 1 10.61271585 -8.564946404 24.9999474 1.043473197 0.594865321 0.569280852 0.1971339 70.61162321 41962.78467 0.025302701 0.050605436 2.72E-09 8.564946404 -0.448607876 SRLTPVSPES(ph)SSTEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SRLTPVSPESSSTEEK 16 1 Q13501-2;E7EMC7;Q13501 Q13501-2 SQSTM1 Sequestosome-1 1 0 SRLT(0.008)PVS(0.224)PES(0.573)S(0.051)S(0.132)T(0.012)EEK 205.98 5.61E-18 25152000 5970 7500.9 4879 7530.2 3064.1 2676.2 2000.6 1717.8 6277.8 5898.5 TRUE FALSE FALSE 5897.235344 7606.497867 4963.916948 8400.877155 2907.727543 2505.199457 2170.530914 1767.501833 5716.297845 5745.25612 1.026452994 1.323961493 0.864002726 1.462228485 0.506109298 0.43604661 0.377795327 0.307645438 0.99495962 1 12.48815549 -8.617003749 7.249618371 1.053934247 0.390183147 0.801755161 0.171117396 0.071316824 4.726108407 0.02302734 0.04623197 2.42E-09 8.617003749 -0.6637511 SRPFTVAASFQSTSVKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SRPFTVAASFQSTSVKSPK 19 2 Q9UHB6-5;Q9UHB6-4;F8VQE1;Q9UHB6-2;Q9UHB6;F8VS07;Q9UHB6-3 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 SRPFTVAASFQS(0.008)T(0.132)S(0.35)VKS(0.509)PK 80.002 0.008101 21608000 999.06 1015.2 839.33 912.68 1581.9 1741.7 1724 1644.2 1164.2 1086.8 TRUE FALSE FALSE 986.8830724 1029.492012 853.9381866 1018.208356 1501.16974 1630.410991 1870.436517 1691.772333 1060.071036 1058.564779 0.932284062 0.972535675 0.806694312 0.961876284 1.418117974 1.540208991 1.766955177 1.598175535 1.001422924 1 10.04789384 -8.593528682 2.348719894 0.951715428 1.650411276 0.945300008 0.076057361 0.047195501 0.523800776 0.011638365 0.027113725 2.55E-09 8.593528682 0.698695848 SRPTS(ph)EGSDIEST(ph)EPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;D6RFF0;H0YA82 Q4G0J3 LARP7 La-related protein 7 2 0 SRPT(0.015)S(0.956)EGS(0.029)DIES(0.315)T(0.684)EPQK 171.52 8.33E-06 38145000 8572.8 8387.2 8239.4 8818.9 8386 7994.8 6627.5 7276.8 9719.1 9035.8 TRUE FALSE FALSE 8468.311416 8505.275222 8382.803301 9838.582712 7958.031128 7483.958082 7190.439685 7487.342727 8849.799354 8801.048613 0.96219346 0.966393392 0.952477786 1.117887555 0.904213972 0.850348454 0.816998065 0.850733027 1.005539197 1 13.10345971 -8.528443494 24.99771105 0.987414628 0.843816577 0.718437917 0.045407482 60.32117301 270971.694 0.00646276 0.012956467 2.96E-09 8.528443494 -0.143598052 SRPTS(ph)FADELAAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRPTSFADELAAR 13 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;A0A0A0MT65;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 SRPT(0.01)S(0.99)FADELAAR 136.57 0.010001 9190500 1419.4 1335 1530 1279.5 2190.6 1758.5 1395.8 2067.6 1539 1464.4 TRUE FALSE FALSE 1402.099807 1353.794165 1556.629008 1427.44181 2078.805508 1646.137525 1514.359217 2127.422744 1401.347986 1426.354677 0.982995204 0.949128703 1.091333757 1.000762176 1.457425381 1.154087095 1.061698918 1.491510336 0.982468111 1 10.47811705 -8.797231188 22.6439153 0.997042414 1.264996292 0.564510159 0.123930283 34.75649688 21988.7582 0.016927577 0.030685523 1.60E-09 8.797231188 0.267953878 SRPTSEGS(ph)DIESTEPQK ddPTM_HeLa_Romidepsin_16h_R1 3 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;D6RFF0;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 0 S(0.006)RPT(0.029)S(0.029)EGS(0.843)DIES(0.086)T(0.006)EPQK;SRPTSEGS(0.981)DIES(0.007)T(0.012)EPQK;SRPTSEGS(0.857)DIES(0.052)T(0.091)EPQK ;; 141.7 0.00015942 235020000 19935.8 20623.7 18333 19212.9 17383.2 17842.4 17353.7 17624.4 19781.1 19963.7 TRUE FALSE FALSE 19692.8148 20914.04099 18652.07817 21434.3859 16496.07044 16702.32822 18827.72284 18134.33421 18011.82887 19445.0402 1.012742304 1.075546298 0.959220345 1.102306073 0.848343345 0.858950563 0.968253223 0.932594329 0.926294247 1 14.2471146 -8.750762691 24.99999708 1.014069717 0.903687731 0.474276459 0.057049518 122.3991309 286601.7672 0.006922949 0.013735073 1.78E-09 8.750762691 -0.110381986 SRPTSEGSDIES(ph)TEPQK ddPTM_HeLa_Romidepsin_16h_R1 1 SRPTSEGSDIESTEPQK 17 1 Q4G0J3;Q4G0J3-3;D6RFF0;H0YA82 Q4G0J3 LARP7 La-related protein 7 1 0 S(0.001)RPT(0.002)S(0.002)EGS(0.452)DIES(0.54)T(0.003)EPQK 99.881 0.0011981 18539000 5067.6 5124.7 4921.1 4743 4675 4897.8 4344.4 4847.8 5398.5 5150.9 TRUE FALSE FALSE 5005.834142 5196.845661 5006.749681 5291.407976 4436.417305 4584.846387 4713.413228 4988.063444 4915.644639 5017.078875 0.997758709 1.035830967 0.997941194 1.054679049 0.884263017 0.913847779 0.939473615 0.994216668 0.979782212 1 12.2926319 -8.760729154 24.99999994 1.005391302 0.932051763 0.57442352 0.03269439 10.63682844 374390.4378 0.004568161 0.0087204 1.73E-09 8.760729154 -0.073339539 SRPVSRVT(ph)NGT(ph)S(ph)NKK ddPTM_HeLa_Romidepsin_16h_R1 1 SRPVSRVTNGTSNKK 15 3 E9PEZ5;A0A1B0GUL6;Q9UPP5-2;Q9UPP5 E9PEZ5 KIAA1107 Uncharacterized protein KIAA1107 3 0 S(0.001)RPVS(0.007)RVT(0.995)NGT(0.998)S(0.998)NKK 58.817 0.0042437 0 2366.8 2284.4 2264.7 1994.7 2510.7 2834.9 2450.7 2661.5 2101.4 2618.8 TRUE FALSE FALSE 2337.952531 2316.559843 2304.116154 2225.336599 2382.56961 2653.759039 2658.862397 2738.506303 1913.445521 2550.763198 0.916569806 0.908183027 0.903304609 0.87241991 0.934061465 1.040378441 1.042379159 1.073602718 0.750146279 1 11.31671326 -8.218509809 5.209786956 0.942961179 1.05297389 0.419306844 0.070418193 0.127880721 8.632258509 0.006883846 0.017721071 6.05E-09 8.218509809 0.11001271 SRQPS(ph)PLLLLPPPAGLTSDPGPSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SRQPSPLLLLPPPAGLTSDPGPSVR 25 1 I3L2J0 I3L2J0 CIC 1 0 S(0.355)RQPS(0.645)PLLLLPPPAGLTSDPGPSVR 56.832 0.0028047 28596000 2312.7 2274.9 1909.8 2102.1 1598 1402.1 1291 1308.7 2409.7 2207.8 TRUE FALSE FALSE 2284.511923 2306.926102 1943.039268 2345.154693 1516.448097 1312.510335 1400.657508 1346.56517 2194.170397 2150.441038 1.062345762 1.072768823 0.903553845 1.090545917 0.70518004 0.610344721 0.651334997 0.62618093 1.020335065 1 11.07041686 -8.680545382 4.894065138 1.027011915 0.636475494 0.929593557 0.050973755 0.03667184 1.563177726 0.007371171 0.014915198 2.09E-09 8.680545382 -0.390536421 SRS(ph)APPNLWAAQR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSAPPNLWAAQR 13 1 Q92934;F5H3B1;F5H1R6 Q92934 BAD Bcl2-associated agonist of cell death 1 0 S(0.254)RS(0.746)APPNLWAAQR 72.523 0.021475 4698700 782.95 1001.4 739.06 811.57 780.44 996.3 781.47 935.53 1033.2 721.04 TRUE FALSE FALSE 773.4071042 1015.497735 751.9230293 905.407542 740.6112346 932.6396454 847.8480423 962.5980845 940.7880043 702.3072769 1.101237492 1.445945057 1.070646787 1.289190034 1.054540169 1.327965231 1.207232319 1.370622399 1.339567502 1 9.455958573 -10.48419307 9.466716687 1.044454472 1.242740459 0 0.149144687 0.30602961 72.22659938 0.018822436 0.021048105 3.28E-11 10.48419307 0.198285987 SRS(ph)DIDVNAAAGAK ddPTM_HeLa_Romidepsin_16h_R1 3 SRSDIDVNAAAGAK 14 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 0 S(0.236)RS(0.764)DIDVNAAAGAK;S(0.056)RS(0.944)DIDVNAAAGAK;S(0.245)RS(0.755)DIDVNAAAGAK ;; 157.74 0.0012182 249739400 20953.7 20737.5 20502.5 21167.2 20786.7 19708.3 17943.5 20461.3 22397.2 21809.2 TRUE FALSE FALSE 20698.30824 21029.44307 20859.33741 23614.65126 19725.87713 18449.00324 19467.62044 21053.31543 20393.93834 21242.59384 0.97437763 0.989965878 0.981958115 1.11166515 0.928600212 0.868491079 0.916442718 0.991089675 0.960049347 1 14.37467232 -8.558920654 24.99991393 0.996035091 0.920133425 0.374121269 0.048062865 132.4145578 91846.84261 0.006628794 0.013257616 2.76E-09 8.558920654 -0.075901666 SRS(ph)DIDVNAAASAK ddPTM_HeLa_Romidepsin_16h_R1 2 SRSDIDVNAAASAK 14 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 S(0.045)RS(0.955)DIDVNAAASAK;S(0.191)RS(0.809)DIDVNAAASAK ; 174.65 5.75E-06 235350000 23325.5 22218 22084.8 34643 20872.8 19820.3 16907.1 19517.3 23913.8 21731.1 TRUE FALSE FALSE 23041.19983 22530.78559 22469.17668 38648.58666 19807.58313 18553.8468 18343.18865 20082.00228 21774.88983 21166.52289 1.088568016 1.064453794 1.061543117 1.825929883 0.935797685 0.876565645 0.866613224 0.948762458 1.028741941 1 14.36949667 -8.548297104 24.99998109 1.106754508 0.896232448 0.213178525 0.232998575 324.5362314 319193.2271 0.034668185 0.06933811 2.83E-09 8.548297104 -0.21052206 SRS(ph)FSSSAEEHS ddPTM_HeLa_Romidepsin_16h_R1 1 SRSFSSSAEEHS 12 1 Q96EQ0 Q96EQ0 SGTB Small glutamine-rich tetratricopeptide repeat-containing protein beta 1 0 S(0.019)RS(0.934)FS(0.023)S(0.023)S(0.001)AEEHS 138.2 0.015171 6735300 1233.8 1121.6 1155.9 1655.7 2209.8 2439.4 2227.4 2103.2 1796.3 1513.6 TRUE FALSE FALSE 1218.761971 1137.389914 1176.017955 1847.139824 2097.02566 2283.530213 2416.5953 2164.052774 1635.634429 1474.276454 0.826684824 0.771490253 0.797691608 1.25291279 1.422410061 1.548915881 1.639173775 1.467874474 1.109448927 1 10.52579137 -8.954165485 2.258131139 0.894812064 1.543880174 0.878113509 0.108677796 0.06757878 0.694522889 0.016058175 0.031448188 1.11E-09 8.954165485 0.649068111 SRS(ph)FTLDDESLK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSFTLDDESLK 12 1 Q86WR7;Q86WR7-2;X6RHS9 Q86WR7 PROSER2 Proline and serine-rich protein 2 1 0 SRS(0.997)FT(0.002)LDDESLK 137.32 0.00089677 21324000 4886.3 5019.6 4910.3 6642.9 5936.3 5364.5 4487.1 4996 5701.1 4315.4 TRUE FALSE FALSE 4826.743896 5090.266061 4995.761712 7410.983354 5633.34846 5021.725763 4868.234162 5140.551378 5191.179337 4203.285286 1.148326504 1.211020836 1.188537387 1.763140698 1.340225104 1.194714473 1.158197417 1.222984173 1.235029027 1 12.03730166 -10.49429177 1.029451749 1.042567341 1.314543017 0.151314906 0.175249882 0.418241425 0.896373071 0.040146685 0.042433177 3.20E-11 10.49429177 0.271975677 SRS(ph)PESQVIGENTK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPESQVIGENTK 14 1 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 S(0.033)RS(0.402)PES(0.402)QVIGENT(0.163)K 157.07 0.0032104 7488300 2388.7 2132.6 2150.2 1680.6 2184.9 2093 1870.7 2295.7 2368.7 2398.2 TRUE FALSE FALSE 2359.585606 2162.622799 2187.623329 1874.918879 2073.3964 1959.264055 2029.597211 2362.122457 2156.837539 2335.894418 1.010142234 0.925822153 0.936524918 0.802655661 0.887624194 0.838763961 0.868873694 1.011228264 0.923345474 1 11.18975935 -9.969078771 1.837634959 1.005175552 0.88081218 0.271780655 0.058624481 0.186041745 1.250128093 0.008857682 0.011762625 1.07E-10 9.969078771 -0.124363373 SRS(ph)PGSPVGEGTGSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPGSPVGEGTGSPPK 17 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 S(0.452)RS(0.528)PGS(0.011)PVGEGT(0.001)GS(0.008)PPK 69.084 0.012236 20516000 2517.4 2860.1 2555.7 3212.6 2714.4 3211 2108.8 2870.2 2903.1 2640.6 TRUE FALSE FALSE 2486.716961 2900.364563 2600.180886 3584.055928 2575.874039 3005.827463 2287.921419 2953.244709 2643.439465 2571.996831 0.966842933 1.127670348 1.010958044 1.39349158 1.00150747 1.168674637 0.889550637 1.148230306 1.027777108 1 11.32867315 -10.26348699 24.71464041 0.984342495 1.103247364 0.130147802 0.12574377 201.488235 2431959.268 0.01979539 0.023226579 5.45E-11 10.26348699 0.118904869 SRS(ph)PLGFYVHLK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPLGFYVHLK 12 1 Q8IXT5;B9ZVT1 Q8IXT5 RBM12B RNA-binding protein 12B 1 0 S(0.023)RS(0.977)PLGFYVHLK 126.71 0.0016376 6182400 2538.4 2004.5 3752.5 3576.1 3789.5 2984.9 2923 2004.3 2534.2 2087.9 TRUE FALSE FALSE 2507.461004 2032.719404 3817.810688 3989.585508 3596.107674 2794.174523 3171.279547 2062.291258 2307.534805 2033.656057 1.232981849 0.999539424 1.877313853 1.961779867 1.768296887 1.373966121 1.559398177 1.014080651 1.134673091 1 10.98985999 -9.773420671 24.99915147 1.104807259 1.605815817 0.471546061 0.259281318 153.7174957 320733.2008 0.043978397 0.058048023 1.68E-10 9.773420671 0.501008558 SRS(ph)PPPVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPPPVSK 9 1 Q01130-2;Q01130 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 1 0 S(0.016)RS(0.982)PPPVS(0.002)K 71.888 0.029851 8204500 3808.5 4530.1 5116.3 4067.3 3659.6 4533.4 5982.9 1609.8 5557.5 5082.1 TRUE FALSE FALSE 3762.080537 4593.874867 5205.347055 4537.580363 3472.836956 4243.730371 6491.087377 1656.377023 5060.423281 4950.066309 0.760006089 0.928043097 1.051571177 0.916670622 0.701573825 0.857307782 1.311313217 0.334617138 1.022294039 1 12.27323214 -7.229873401 24.171794 0.907245247 0.334615539 0.543023537 0.165207702 5660.788747 4334669.158 0.022647147 4.150990204 5.89E-08 7.229873401 -0.572629709 SRS(ph)PVDLR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPVDLR 8 1 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 1 0 S(0.195)RS(0.805)PVDLR 78.488 0.023262 17939000 3047.9 3063 3037 3020.6 2448.6 2965.2 2518.1 2592.9 3388.2 3087.4 TRUE FALSE FALSE 3010.751022 3106.120994 3089.857711 3369.855984 2323.638805 2775.73329 2731.987351 2667.921471 3085.150906 3007.188903 1.001184535 1.032898529 1.027490394 1.120600033 0.772694659 0.923032566 0.908485446 0.887181204 1.02592521 1 11.55419978 -8.761101869 24.99999995 1.013014109 0.878978558 0.6906058 0.05179837 4.485600982 332204.5138 0.007385721 0.014068437 1.73E-09 8.761101869 -0.134035551 SRSDVDMDPSSAT(ph)AVLGPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSDVDMDPSSATAVLGPAR 20 1 M0QZR4;M0QZH8;M0QYS3;M0QYC1 M0QZR4 ARHGEF1 1 0 S(0.02)RS(0.235)DVDMDPS(0.238)S(0.238)AT(0.269)AVLGPAR 73.273 0.0024668 0 927.25 1327.8 1109.4 1288.1 1369.8 1368.7 982.79 1117.8 1350.2 1447.8 TRUE FALSE FALSE 915.9483203 1346.492803 1128.708642 1437.036183 1299.893995 1281.244487 1066.268158 1150.141779 1229.43473 1410.185947 0.64952308 0.954833514 0.800397028 1.019040209 0.921789071 0.908564214 0.756118837 0.815595831 0.871824551 1 10.46166969 -7.752850129 24.91661399 0.860738347 0.785857335 0.086754614 0.104626158 523.5748835 1518805.254 0.01973973 0.071546295 1.77E-08 7.752850129 -0.074881012 SRSES(ph)DLSQPESDEEGYALSGR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSESDLSQPESDEEGYALSGR 22 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 S(0.273)RS(0.273)ES(0.452)DLS(0.001)QPESDEEGYALSGR 138.96 2.30E-05 10702000 557.54 405.65 517.59 496.09 583.22 658.08 462.71 377.76 648.86 590.9 TRUE FALSE FALSE 550.744488 411.3607513 526.5984368 553.45026 553.4561071 616.0308119 502.0125759 388.6898896 590.8243365 575.5483328 0.956903976 0.714728421 0.914950851 0.961605183 0.961615342 1.070337236 0.872233568 0.675338399 1.026541652 1 9.168793276 -7.349880081 3.400919566 0.95828127 0.662579617 0.45564213 0.090142494 0.175070515 3.267190404 0.012690346 0.114373217 4.47E-08 7.349880081 -0.295701653 SRSESDLSQPES(ph)DEEGYALSGR ddPTM_HeLa_Romidepsin_16h_R1 2 SRSESDLSQPESDEEGYALSGR 22 1 Q15751;H0YNB1 Q15751 HERC1 Probable E3 ubiquitin-protein ligase HERC1 1 0 SRSESDLSQPES(0.99)DEEGYALS(0.01)GR;S(0.001)RS(0.001)ES(0.002)DLS(0.096)QPES(0.886)DEEGY(0.002)ALS(0.013)GR ; 103.42 7.51E-05 9116800 924.18 1082.55 968.35 1188.98 1169.25 1199.63 828.52 964.85 1076.9 997.62 TRUE FALSE FALSE 912.9157387 1097.790167 985.2037255 1326.455462 1109.578809 1122.977515 898.8944681 992.7664125 980.5793669 971.7016886 0.939502061 1.129760481 1.013895249 1.365085064 1.141892437 1.155681345 0.925072457 1.02167818 1.009136218 1 9.924369666 -10.25834966 24.80481351 0.971431528 1.110031625 0.20750458 0.110930707 258.8115583 2077789.433 0.019075188 0.022840652 5.52E-11 10.25834966 0.138600098 SAPAPK(ac)K(ac)GSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SAPAPKKGSKK 11 3 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q5QNW6-2;Q8N257;Q93079;U3KQK0;Q99877;Q99880 P06899;P23527;P33778;P58876;Q16778;Q5QNW6;Q8N257;Q93079;U3KQK0;Q99880 HIST1H2BJ;HIST1H2BO;HIST1H2BB;HIST1H2BD;HIST2H2BE;HIST2H2BF;HIST3H2BB;HIST1H2BH;HIST1H2BN;HIST1H2BL Histone H2B type 1-J;Histone H2B type 1-O;Histone H2B type 1-B;Histone H2B type 1-D;Histone H2B type 2-E;Histone H2B type 2-F;Histone H2B type 3-B;Histone H2B type 1-H;Histone H2B;Histone H2B type 1-N;Histone H2B type 1-L 0 3 ; SAPAPK(1)K(1)GSK(1)K;SAPAPK(1)K(1)GSK(1)K 149.23 0.007725 2738000000 1251.04 1041.17 2206.95 10272.3 54709 79562 79548 76501 0 614.41 FALSE TRUE FALSE 1235.791843 1055.827619 2245.361039 11460.03166 51916.99558 74478.24497 86304.80513 78714.43574 0 598.4475396 2.064996113 1.76427765 3.751976389 19.14960109 86.75279309 124.4524207 144.2144874 131.5310541 0 1 9.225080975 -8.616444978 1.763141121 1.378214203 137.4598774 0.995171809 4.111511571 0.015013589 0.093464817 0.598741099 1.517436802 2.42E-09 8.616444978 136.0816632 up SRSLS(ph)NS(ph)NPDISGTPTSPDDEVR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSLSNSNPDISGTPTSPDDEVR 23 1 Q96N67-2;Q96N67-6;Q96N67;Q96N67-4;Q96N67-3;Q96N67-5;A0A0U1RRC1;A0A0U1RQJ5 Q96N67-2 DOCK7 Dedicator of cytokinesis protein 7 2 0 S(0.026)RS(0.298)LS(0.759)NS(0.917)NPDISGTPTSPDDEVR 104.3 5.00E-05 8850300 2318.4 2406.2 2697.9 1391.1 2373.6 2290.4 2060.3 2306.3 2824.8 2936.5 TRUE FALSE FALSE 2290.142449 2440.074547 2744.855818 1551.945527 2252.466335 2144.050832 2235.301831 2373.029152 2572.142813 2860.209307 0.80069051 0.853110484 0.959669564 0.542598587 0.787518008 0.749613263 0.781516872 0.829669754 0.899284821 1 11.48190501 -12.52755638 0.331884251 1.10998002 0.758808461 0.284856316 0.101548742 2.849227619 0.35783039 0.380028436 0.044889126 2.97E-13 12.52755638 -0.351171559 SRSLSGT(ph)GRSLVGSWLK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSLSGTGRSLVGSWLK 17 2 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 0 SRSLS(0.018)GT(0.87)GRS(0.018)LVGS(0.094)WLK 77.062 0.0042927 0 856.29 777.03 624.29 892.76 952.04 869.67 773.83 910.14 807.53 722.18 TRUE FALSE FALSE 845.8532081 787.9690487 635.1555056 995.9851118 903.4538462 814.1008937 839.5591009 936.4734649 735.3024943 703.4176595 1.20249072 1.120200834 0.90295644 1.415922814 1.284377544 1.157350662 1.193542826 1.331319242 1.045328454 1 9.458237744 -9.254745904 24.99877302 1.087147855 1.265711675 0.535798732 0.10091244 451.3343415 1685642.067 0.017362424 0.028356663 5.56E-10 9.254745904 0.17856382 SRSPGS(ph)PVGEGTGSPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPGSPVGEGTGSPPK 17 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 S(0.416)RS(0.056)PGS(0.498)PVGEGT(0.002)GS(0.028)PPK 155.24 0.00041452 5678200 1172.2 1463.9 1174.4 1842.3 1130.5 1609.4 1097.5 1346.7 1506.2 1058.1 TRUE FALSE FALSE 1157.912776 1484.508823 1194.839939 2055.315394 1072.806367 1506.564534 1190.721623 1385.66464 1371.4817 1030.610409 1.123521328 1.440417066 1.159351709 1.994269974 1.040942685 1.461817696 1.155355711 1.344508679 1.330746989 1 10.00928335 -10.44045341 2.216329824 1.046089174 1.371355777 0.08822797 0.263158973 0.285029907 2.702100821 0.042991761 0.047779641 3.63E-11 10.44045341 0.325266604 SRSPLELEPEAK ddPTM_HeLa_Romidepsin_16h_R1 1 SRSPLELEPEAK 12 1 A0A087WTQ7;A0A087WV56;A0A087WW71;A0A087X0X5;Q92466-3;Q92466-2;Q92466-5;Q92466-4;Q92466 A0A087WTQ7 DDB2 DNA damage-binding protein 2 0 0 119.25 0.0088238 4795300 1951.3 1805.5 1752.3 1602.8 1583.6 1760.6 1302.3 1708.3 1977.4 1680.3 FALSE FALSE TRUE 1927.516805 1830.917876 1782.798046 1788.123277 1502.782983 1648.103342 1412.917329 1757.726965 1800.536392 1636.645564 1.177724028 1.118701518 1.089300021 1.092553768 0.918209181 1.007000769 0.863300742 1.073981444 1.100138253 1 10.67652621 -8.772760174 24.882892 1.089764594 0.961269854 0.486338614 0.065570492 163.4753044 359315.9711 0.011797237 0.021523526 1.69E-09 8.772760174 -0.12849474 SRSS(ph)S(ph)VGSSSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SRSSSVGSSSSYPISPAVSR 20 1 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.082)RS(0.409)S(0.48)S(0.507)VGS(0.303)S(0.079)S(0.069)S(0.061)Y(0.008)PIS(0.001)PAVSR 63.302 0.0036532 0 898.21 842.97 549.95 556.69 603.96 680.74 550.12 594.14 671.2 815.59 TRUE FALSE FALSE 887.262271 854.8373538 559.5216491 621.0571171 573.1376675 637.242911 596.8471791 611.3305035 611.1661909 794.4008542 1.116894911 1.07607809 0.704331631 0.781793113 0.721471615 0.802167958 0.751317393 0.769549152 0.769342313 1 9.633723364 -9.765449953 24.99999975 1.058308586 0.756756472 0.540483454 0.098754853 21.67806104 135130.8 0.007994808 0.010725355 1.72E-10 9.765449953 -0.301552114 SRSSSMT(ph)RS(ph)PPRVSK ddPTM_HeLa_Romidepsin_16h_R1 2 SRSSSMTRSPPRVSK 15 3 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 2 0 S(0.002)RS(0.031)S(0.288)S(0.313)MT(0.711)RS(0.656)PPRVSK;S(0.036)RS(0.043)S(0.028)S(0.027)MT(0.935)RS(0.931)PPRVSK ; 80.746 0.022969 62946000 161.36 177.15 228.94 0 190.83 0 170.23 0 0 117.61 TRUE FALSE FALSE 159.3932823 179.6439223 232.9246047 0 181.091233 0 184.689332 0 0 114.5544752 1.391419077 1.568196458 2.033308643 0 1.580830715 0 1.612240216 0 0 1 6.839890011 -9.258914675 24.9777831 1.282233062 0.709571359 0.11692888 0.739321802 289.1790144 2860944.852 0.086431112 0.139074972 5.51E-10 9.258914675 -0.572661704 SRST(ph)TELDDYSTNK ddPTM_HeLa_Romidepsin_16h_R1 2 SRSTTELDDYSTNK 14 1 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 S(0.001)RS(0.238)T(0.563)T(0.169)ELDDYS(0.023)T(0.007)NK;S(0.008)RS(0.295)T(0.688)T(0.008)ELDDYSTNK ; 172.42 0.00015305 168287000 12522.3 11122.7 10666.7 9033.7 8389.3 8188.1 7398.5 7640.1 12048.3 11774.1 TRUE FALSE FALSE 12369.67339 11279.28566 10852.34944 10078.2189 7961.162716 7664.906836 8026.928405 7861.154239 10970.66987 11468.20718 1.078605678 0.983526499 0.94629869 0.878796375 0.694194183 0.668361385 0.699928792 0.685473685 0.956615947 1 13.48535225 -9.065513771 1.345188127 1.034610982 0.675819568 0.931535474 0.038816666 0.063584082 0.227506153 0.006189444 0.013156747 8.60E-10 9.065513771 -0.358791413 SRT(ph)ASGSSVT(ph)SLDGTR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTASGSSVTSLDGTR 16 1 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 2 0 S(0.027)RT(0.972)AS(0.018)GS(0.093)S(0.163)VT(0.496)S(0.06)LDGT(0.171)R 85.563 0.023323 22995000 3312.8 2802.6 3323.1 3564.5 3956.7 4592 4332.1 5034.9 3709.2 3803.9 TRUE FALSE FALSE 3272.422319 2842.055076 3380.937162 3976.644261 3754.774835 4298.58602 4700.068466 5180.576888 3377.439862 3705.07413 0.883227219 0.767071043 0.912515389 1.073296815 1.013414227 1.160188938 1.268549104 1.398238391 0.911571468 1 11.85528669 -7.856857321 0.885430035 0.929178297 1.461616759 0.855410546 0.069099787 0.354872272 0.346579045 0.013240978 0.149336591 1.39E-08 7.856857321 0.532438461 SRT(ph)GSESSQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTGSESSQTGTSTTSSR 18 1 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.016)RT(0.984)GSESSQTGTSTTSSR 212.55 5.75E-29 27412000 294.13 377.51 299.72 220.71 191.91 256.88 144.47 123.32 300.92 255.55 TRUE FALSE FALSE 290.5450304 382.8245957 304.9365009 246.2295287 182.1161166 240.466197 156.7412782 126.8880696 274.0049615 248.9107742 1.167265786 1.537999297 1.225083574 0.989228086 0.731652204 0.966073879 0.629708693 0.509773312 1.100815995 1 7.959484869 -8.048182387 0.900896456 1.12517743 0.486365585 0.63810261 0.172992977 0.534162721 0.615419114 0.031686619 0.256100529 8.95E-09 8.048182387 -0.638811845 SRT(ph)PPSAPSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.007)RT(0.986)PPSAPSQS(0.006)R 104.55 0.0072888 118340000 2928.1 3120.5 2650 2785.5 2161.2 2032.5 1852.3 1680 3584.3 3205.5 TRUE FALSE FALSE 2892.411191 3164.430481 2696.122138 3107.572616 2050.905899 1902.62981 2009.634316 1728.608149 3263.711231 3122.220648 0.92639551 1.01351917 0.863527099 0.995308457 0.656874107 0.60938352 0.643655443 0.553647017 1.045317291 1 11.60835678 -8.712862209 5.200402397 0.962051123 0.611990922 0.915255262 0.053394396 0.03597466 2.13008517 0.006914515 0.013847282 1.94E-09 8.712862209 -0.350060201 SRT(ph)SVQT(ph)EDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 0 S(0.006)RT(0.569)S(0.425)VQT(1)EDDQLIAGQSAR 126.04 0.0011983 4101400 974.79 937.87 819.14 1328.8 1149.6 1179 811.34 1214.2 1135.2 723.81 TRUE FALSE FALSE 962.9088845 951.0733585 833.3967881 1482.442108 1090.931622 1103.665705 880.2551993 1249.330961 1033.664869 705.0053119 1.365817914 1.34903006 1.182114197 2.10273892 1.547409082 1.565471474 1.248579528 1.772087302 1.466180256 1 9.461490317 -11.15402627 0.406250187 0.964747572 1.602390375 0.127848682 0.277668454 0.838190338 0.331163889 0.221613192 0.109989654 7.01E-12 11.15402627 0.637642803 SRT(ph)SVQTEDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 0 S(0.075)RT(0.904)S(0.021)VQTEDDQLIAGQSAR 139.74 0.0015168 6188700 1047.4 1273.8 1005 1527.9 1097 1068.6 1139.9 996.11 1334.7 1015.5 TRUE FALSE FALSE 1034.633886 1291.73259 1022.491603 1704.562987 1041.015997 1000.319909 1236.723078 1024.930871 1215.321089 989.1171636 1.046017524 1.305944975 1.033741645 1.72331757 1.052469854 1.011326004 1.250330217 1.036207751 1.228692751 1 9.949997612 -10.39783202 6.143312882 1.020090701 1.203997077 0.023650855 0.210596891 0.322418558 14.85178257 0.032943947 0.037482595 4.00E-11 10.39783202 0.183906376 SRTDSLAAT(ph)PPAAK ddPTM_HeLa_Romidepsin_16h_R1 1 SRTDSLAATPPAAK 14 1 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 SRTDS(0.001)LAAT(0.999)PPAAK 72.21 0.028634 27282000 6154.6 6713.9 7334 7438.2 5020 5411.8 5373.1 3650.8 8336.7 7123.9 TRUE FALSE FALSE 6079.585368 6808.41846 7461.645194 8298.239682 4763.810668 5066.003446 5829.49098 3756.430138 7591.044672 6938.820051 0.876169914 0.98120695 1.075347846 1.195915101 0.686544777 0.73009581 0.840127131 0.541364398 1.093996474 1 12.76047464 -8.725679594 24.99895676 0.970521371 0.711758271 0.648652465 0.11550201 105.0846711 73462.18603 0.0168045 0.03360807 1.88E-09 8.725679594 -0.258763099 SRTLTAVHDAILEDLVFPSEIVGK ddPTM_HeLa_Romidepsin_16h_R1 1 SRTLTAVHDAILEDLVFPSEIVGK 24 1 A0A2R8Y623;P62081;B5MCP9 A0A2R8Y623 RPS7 40S ribosomal protein S7 0 0 83.064 9.22E-05 3706200 1902.1 1282.4 1215.7 1833.2 1892.7 2157.8 1534.2 1619.6 2285.6 1612.3 FALSE FALSE TRUE 1878.916474 1300.453661 1236.858749 2045.163209 1796.108456 2019.923544 1664.51491 1666.460571 2081.170212 1570.412214 1.19644795 0.828097011 0.78760133 1.302309796 1.143717835 1.286237796 1.05992229 1.061161239 1.325238172 1 10.61692758 SRTPPSAPSQSR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTPPSAPSQSR 12 1 Q9UQ35;I3L3Q8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 0 0 106.79 0.013965 992390 256.09 598.07 524.41 596.95 262.39 387.98 463.06 302.23 527.94 444.11 FALSE FALSE TRUE 252.9686766 606.4896452 533.5371361 665.9721677 248.9992592 363.1893301 502.3923048 310.9745482 480.7197242 432.5719582 0.584801377 1.402054927 1.233406664 1.539563893 0.57562506 0.839604425 1.161407473 0.718896688 1.111305796 1 8.756796334 -10.27773223 24.95020848 0.803933995 1.06774175 0.032688097 0.311039617 1230.716241 1884663.287 0.054518231 0.062446835 5.28E-11 10.27773223 0.263807755 SRTS(ph)VQT(ph)EDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 2 0 S(0.028)RT(0.18)S(0.792)VQT(0.999)EDDQLIAGQS(0.001)AR 92.39 0.011448 4313100 1522.2 1408.9 1251.8 1579.5 1721.9 2251.3 1527.2 1861.9 1969.8 1676 TRUE FALSE FALSE 1503.646841 1428.734531 1273.587054 1762.129222 1634.025018 2107.449196 1656.92033 1915.771139 1793.616155 1632.457278 0.921094145 0.875204852 0.780165626 1.079433591 1.000960355 1.290967441 1.014985416 1.173550551 1.09872165 1 10.67282952 -8.731688916 2.148199336 0.942965643 1.140626324 0.39653372 0.108662979 0.212941791 2.001390437 0.014528535 0.032098671 1.85E-09 8.731688916 0.197660681 SRTS(ph)VQTEDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 SRTSVQTEDDQLIAGQSAR 19 1 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 0 S(0.091)RT(0.29)S(0.602)VQT(0.017)EDDQLIAGQSAR 98.135 0.00063544 18112000 365.93 440.94 428.13 474.87 581.28 680.93 541.81 557.06 692.36 429.18 TRUE FALSE FALSE 361.4699044 447.1475649 435.5814231 529.7767037 551.6151125 637.4207706 587.8313279 573.1776522 630.4335876 418.0298417 0.864698805 1.069654652 1.041986432 1.267317906 1.319559174 1.524821214 1.406194652 1.371140514 1.508106658 1 8.707462125 -9.187662783 1.239220456 0.939676168 1.431031694 0.234059801 0.190038319 0.093061494 0.281603312 0.012088726 0.024691477 6.49E-10 9.187662783 0.491355526 SRVPSPPPPAEMSS(ph)GPVAES(ph)WCY(ph)T(ph)QIK ddPTM_HeLa_Romidepsin_16h_R1 1 SRVPSPPPPAEMSSGPVAESWCYTQIK 27 1 D6RA79;D6RIS7;D6RD94;D6RFL7;A0A590UJA7;D6RGZ4;D6RDG8;O43791 D6RA79 SPOP Speckle-type POZ protein 4 0 S(0.006)RVPS(0.022)PPPPAEMS(0.419)S(0.826)GPVAES(0.831)WCY(0.947)T(0.949)QIK 40.682 0.0041802 0 0 0 67.126 64.715 65.59 0 53.515 0 0 0 TRUE FALSE FALSE 0 0 68.29429987 72.19765279 62.24269755 0 58.06056276 0 0 0 0 SRVS(ph)VS(ph)PGRTS(ph)VTK ddPTM_HeLa_Romidepsin_16h_R1 1 SRVSVSPGRTSVTK 14 2 M0R088 M0R088 SRRM1 3 0 S(0.021)RVS(0.901)VS(0.905)PGRT(0.248)S(0.826)VT(0.098)K 68.069 0.0042822 0 0 0 71.391 155.59 0 0 0 0 177.66 0 TRUE FALSE FALSE 0 0 72.63353041 173.5800479 0 0 0 0 161.7696446 0 0 SRWDETPASQMGGST(ph)PVLTPGK ddPTM_HeLa_Romidepsin_16h_R1 3 SRWDETPASQMGGSTPVLTPGK 22 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 SRWDETPAS(0.001)QMGGS(0.234)T(0.731)PVLT(0.033)PGK;SRWDETPAS(0.002)QMGGS(0.255)T(0.733)PVLT(0.01)PGK;SRWDETPASQMGGS(0.051)T(0.699)PVLT(0.25)PGK ;; 130.57 6.55E-05 39039000 10484.4 10420.8 9569.3 9691.9 8837 8034.6 6575.7 8735.1 11242.9 11418.3 TRUE FALSE FALSE 10356.6121 10567.5043 9735.849652 10812.52308 8386.014915 7521.21499 7134.239794 8987.836337 10237.30687 11121.65092 0.931211758 0.950174068 0.875396083 0.97220486 0.754026086 0.676267853 0.641473091 0.808138684 0.920484462 1 13.44108334 -8.68922707 4.046376946 0.958283594 0.703730409 0.811744083 0.052106034 0.06292885 2.009052167 0.007793112 0.015901074 2.05E-09 8.68922707 -0.254553186 SS(ph)CLS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 SSCLSSR 7 0 Q6N022;Q9P273;D6RGC5 Q6N022 TENM4;TENM3 Teneurin-4;Teneurin-3 2 0 S(0.421)S(0.579)CLS(0.718)S(0.282)R 47.574 0.02702 5427800 0 64.245 63.435 0 90.999 102.04 66.116 0 131.82 153.45 TRUE FALSE FALSE 0 65.1494428 64.53905957 0 86.35498147 95.51997332 71.73189139 0 120.0296891 149.4633469 0 0.435889094 0.431805261 0 0.577766946 0.639086273 0.479929648 0 0.803071064 1 7.223647923 -12.49576973 1.228156251 1.001828349 0.304622121 0.486357275 0.236225734 0.296388905 0.796693709 0.174169847 0.041872655 3.19E-13 12.49576973 -0.697206228 SS(ph)DEENGPPSS(ph)PDLDR ddPTM_HeLa_Romidepsin_16h_R1 1 SSDEENGPPSSPDLDR 16 0 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 2 0 S(0.369)S(0.631)DEENGPPS(0.123)S(0.877)PDLDR 258.68 4.60E-71 20401000 2581.2 2783.3 3140.3 1958.5 2172.8 1960.4 1962.3 1995.3 2959.2 2610.4 TRUE FALSE FALSE 2549.739342 2822.48337 3194.955604 2184.950985 2061.913908 1835.136767 2128.977713 2053.030857 2694.521741 2542.581432 1.002815214 1.110085732 1.256579461 0.859343562 0.810952948 0.721761256 0.837329215 0.807459235 1.059758286 1 11.31207826 -9.018342969 24.06737845 1.029927796 0.797618385 0.727762012 0.082415291 227.2975977 298232.157 0.013229929 0.022228651 9.59E-10 9.018342969 -0.232309411 SS(ph)DSWEVWGSASTNR ddPTM_HeLa_Romidepsin_16h_R1 1 SSDSWEVWGSASTNR 15 0 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;Q8N6T3-4;E5RHH7 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 S(0.061)S(0.826)DS(0.113)WEVWGSASTNR 136.14 9.22E-07 0 266.94 320.47 545.7 518.48 379.96 483.96 527.71 657.29 331.38 427.41 TRUE FALSE FALSE 263.6864326 324.9815851 555.1976796 578.4290971 360.5692234 453.0365179 572.5336742 676.3076491 301.7405428 416.3058266 0.633395969 0.780631844 1.333629376 1.389433105 0.866116207 1.088230068 1.375271826 1.62454524 0.724804996 1 8.70149994 -9.764136051 24.9906826 0.818575551 1.26139678 0.574644746 0.207395196 48.46442006 449132.224 0.037968877 0.051175647 1.72E-10 9.764136051 0.44282123 SS(ph)GFISELPSEEGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSGFISELPSEEGK 14 0 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 S(0.043)S(0.957)GFISELPSEEGK 108.23 0.0063885 22846000 4840.4 5122.2 4230.8 4238.1 5678 5589.4 4304.1 4804 5153.1 4448.8 TRUE FALSE FALSE 4781.403343 5194.310466 4304.435299 4728.129063 5388.230472 5232.255379 4669.690147 4942.996161 4692.19383 4333.219535 1.103429749 1.19871851 0.99335731 1.091135361 1.243470456 1.207475259 1.077649103 1.140721378 1.082842398 1 12.08122361 -12.16074257 0.294676601 0.939159176 1.155683413 0.175611378 0.072562133 3.221917869 0.400822796 0.245128757 0.045926581 6.91E-13 12.16074257 0.216524238 SS(ph)GGGYGGGPAGGHGGNR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGGGYGGGPAGGHGGNR 18 0 Q9H2U1-3;Q9H2U1-2;Q9H2U1 Q9H2U1-3 DHX36 ATP-dependent RNA helicase DHX36 1 0 S(0.416)S(0.584)GGGYGGGPAGGHGGNR 138.28 0.00031915 648020 380.2 389.71 354.37 373.12 468.28 351.38 304.94 265.27 384.75 503.77 TRUE FALSE FALSE 375.5659762 395.1963476 360.5376612 416.26189 444.3819242 328.927952 330.841596 272.9451689 350.3369964 490.6819828 0.765395897 0.805402198 0.734768493 0.848333349 0.905641413 0.670348543 0.67424851 0.556256758 0.713979744 1 8.938644488 -16.52287875 0.039976936 2.251883319 4.76E-10 0.152887403 0.111897289 335.2623703 1.069889944 52.39743406 17.03629419 3.00E-17 16.52287875 -2.251883318 SS(ph)GSPYGGGYGSGGGSGGYGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 S(0.008)S(0.496)GS(0.496)PYGGGYGSGGGSGGYGSR 309.09 5.45E-170 558690000 11758 10710 10681 9339.3 9362.2 9010.1 8354.8 8737.3 11972 11227 TRUE FALSE FALSE 11614.68897 10860.77566 10866.89832 10419.15381 8884.411999 8434.383689 9064.456503 8990.09999 10901.19434 10935.32092 1.062126028 0.993183075 0.993742973 0.952798174 0.812450962 0.771297317 0.828915454 0.822115789 0.996879233 1 13.41670794 -8.931124055 2.025517948 1.025377689 0.803599589 0.925666436 0.026688897 0.063899696 0.528698912 0.004859898 0.009832405 1.17E-09 8.931124055 -0.221778099 SS(ph)IDSQASLSGPLSGGAPGAGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SSIDSQASLSGPLSGGAPGAGAR 23 0 A6NKD9 A6NKD9 CCDC85C Coiled-coil domain-containing protein 85C 1 0 S(0.146)S(0.854)IDSQASLSGPLSGGAPGAGAR 312.58 1.06E-171 9828000 1868.6 1756.3 1936.9 1494.3 2846.1 3199 3034.4 3890.7 2225.6 1917.2 TRUE FALSE FALSE 1845.824784 1781.025238 1970.610932 1667.077997 2700.852897 2994.594224 3292.14186 4003.271266 2026.536762 1867.390868 0.988451222 0.953750641 1.055275018 0.89273115 1.446324357 1.603624756 1.762963457 2.143777896 1.085223665 1 10.86680822 -8.034502267 0.949656438 0.983422822 2.159676214 0.933418336 0.103801393 0.127343009 0.166514755 0.014864099 0.116376694 9.24E-09 8.034502267 1.176253392 up SS(ph)ITEPEGPGGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSITEPEGPGGPNIQK 16 0 H0YJL1;A0A3B3ISJ2;Q96KQ4 H0YJL1 PPP1R13B Apoptosis-stimulating of p53 protein 1 1 0 S(0.018)S(0.968)IT(0.013)EPEGPGGPNIQK 155.43 8.02E-07 0 516.33 519.68 560.54 907.35 838.44 877.06 819.96 987.97 522.66 496.68 TRUE FALSE FALSE 510.0367714 526.9960687 570.2959636 1012.262076 795.6512781 821.0186966 889.6073819 1016.555353 475.9119806 483.776182 1.054282518 1.0893386 1.178842582 2.092418176 1.64466815 1.69710442 1.838882142 2.101292687 0.983744133 1 8.918195932 -9.37703112 4.840924102 1.035588031 1.848308406 0.892065176 0.141837763 0.051708089 1.860436862 0.02151015 0.033158502 4.20E-10 9.37703112 0.812720375 SS(ph)ITEPEGPNGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 S(0.218)S(0.746)IT(0.036)EPEGPNGPNIQK 255.39 7.17E-72 12790000 1705.8 1868.6 1586.7 1514 1990.4 2079.3 1214.9 1717.8 1639.4 1800.3 TRUE FALSE FALSE 1685.009053 1894.9062 1614.315848 1689.055804 1888.822461 1946.439441 1318.093576 1767.501833 1492.767958 1753.527946 0.960925121 1.080625036 0.920610277 0.963232897 1.077155608 1.110013356 0.751680963 1.007969013 0.851294079 1 10.77604471 -7.765767883 24.99993477 0.996306913 0.879825006 0.194638095 0.094093124 98.07960735 566489.5316 0.010661763 0.033691071 1.71E-08 7.765767883 -0.116481907 SS(ph)LGSHQLPR ddPTM_HeLa_Romidepsin_16h_R1 3 SSLGSHQLPR 10 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 0 S(0.139)S(0.856)LGS(0.005)HQLPR;S(0.124)S(0.875)LGS(0.001)HQLPR;S(0.155)S(0.824)LGS(0.021)HQLPR ;; 160.86 0.00098113 19647100 7124.6 6329 5933.8 5466.5 10058 11228.8 8779.4 8898.9 9212.5 8766.8 TRUE FALSE FALSE 7037.762635 6418.099828 6037.0753 6098.562451 9544.702728 10511.31592 9525.122017 9156.375631 8388.510927 8539.037272 0.824186897 0.751618669 0.706997183 0.714197896 1.117772698 1.230972015 1.115479616 1.072296014 0.982371977 1 13.05985771 -8.664219141 7.960679272 0.871266857 1.142565652 0.656724487 0.105264798 0.153683722 11.16060199 0.018569034 0.037205344 2.17E-09 8.664219141 0.271298795 SS(ph)LSGDEEDELFK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 S(0.18)S(0.81)LS(0.01)GDEEDELFK 233.59 3.51E-41 132600000 4327.7 4056.8 3914.4 3668.7 4704.4 5040.4 4211.5 4794.2 4735.1 4128.9 TRUE FALSE FALSE 4274.952328 4113.911737 3982.52849 4092.892356 4464.316913 4718.334707 4569.224705 4932.912613 4311.580797 4021.630583 1.06298981 1.022946204 0.990277055 1.017719622 1.110076329 1.173239215 1.136162214 1.226595161 1.072097675 1 11.97356485 -8.539438033 2.630311357 1.025722516 1.174877124 0.8224572 0.031577649 0.087205302 1.211201458 0.004851263 0.011329359 2.89E-09 8.539438033 0.149154608 SS(ph)MEMEGIFNHK ddPTM_HeLa_Romidepsin_16h_R1 1 SSMEMEGIFNHK 12 0 E7EPJ7;O75962-4;O75962;O75962-5;O75962-2;E7EWP2 E7EPJ7 TRIO Triple functional domain protein 1 0 S(0.239)S(0.761)MEMEGIFNHK 65.956 0.022205 15374000 3603 2871.4 3592.3 2521.1 3715.4 3018.2 3315.2 3015 4626.7 3894 TRUE FALSE FALSE 3559.08525 2911.823645 3654.822475 2812.601444 3525.789274 2825.346761 3596.793005 3102.234268 4212.876364 3792.833319 0.93837112 0.767717271 0.963612732 0.741556828 0.929592465 0.744917196 0.948312964 0.817920011 1.110746508 1 11.88906026 -10.48396679 4.275671278 0.974260905 0.848487531 0.420025752 0.088941274 0.156889651 5.906084489 0.012322141 0.013630438 3.28E-11 10.48396679 -0.125773375 SS(ph)PAGNSPAPL ddPTM_HeLa_Romidepsin_16h_R1 1 SSPAGNSPAPL 11 0 A0A087WZG9;B4DSP0;Q86TG7-2 A0A087WZG9 PEG10 Retrotransposon-derived protein PEG10 1 0 S(0.088)S(0.905)PAGNS(0.007)PAPL 128.88 0.0060946 4437600 1373 1262.8 1422.6 926.6 1537.2 2064.1 1614.3 1713.8 1429.7 1614.4 TRUE FALSE FALSE 1356.265348 1280.577732 1447.359756 1033.737852 1458.750948 1932.210672 1751.418602 1763.386099 1301.824051 1572.457655 0.862513113 0.814379788 0.920444345 0.657402664 0.927688541 1.228783914 1.113809708 1.121420404 0.827891325 1 10.61880545 -8.32365982 6.982860446 0.901046236 1.150163845 0.649240386 0.096286572 0.14481075 13.93396477 0.015258254 0.034433159 4.75E-09 8.32365982 0.249117609 SS(ph)PELTR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPELTR 7 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.224)S(0.776)PELTR;S(0.119)S(0.881)PELTR ; 132.76 0.01394 198363000 4340.1 4697.3 6275.8 2676.9 3971.5 3923.8 4525.6 1730.13 6177.2 6503 TRUE FALSE FALSE 4287.201192 4763.428713 6385.027666 2986.415773 3768.819535 3673.081843 4910.004351 1780.188582 5624.695761 6334.051123 0.676849793 0.752035091 1.008048016 0.471485897 0.595009333 0.579894569 0.77517599 0.281050555 0.888009214 1 12.6289128 -16.52287875 0.057986796 2.422580201 9.66E-12 0.458651669 0.161574428 210.0039763 0.957886437 44.10002921 8.761163446 3.00E-17 16.52287875 -2.422580201 SS(ph)PGAVAGLSNAPGTPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;U3KPY3;Q9BWG4-2;Q9BWG4 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 0 S(0.45)S(0.54)PGAVAGLS(0.01)NAPGTPR 111.11 0.0019747 33359000 1089.8 690.65 924.57 1398.6 894.2 938.43 808.2 807.98 903.49 859.05 TRUE FALSE FALSE 1076.517098 700.3729888 940.661753 1560.312713 848.5656373 878.4673516 876.8484878 831.3576265 822.6795916 836.7317572 1.286573731 0.837034071 1.124209455 1.864770518 1.01414298 1.0498793 1.047944554 0.993577236 0.983205889 1 9.708621382 SS(ph)PGGQDEGGFMAQGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGGQDEGGFMAQGK 16 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GV30 A0A1B0GTU4 PXN Paxillin 1 0 S(0.04)S(0.96)PGGQDEGGFMAQGK 88.78 0.018552 137550000 5544.6 5113.5 5746.8 4158.2 5397.1 5863.6 4320.1 5197.8 5949.2 5998.6 TRUE FALSE FALSE 5477.020283 5185.487987 5846.820643 4638.990649 5121.665848 5488.934884 4687.049186 5348.190142 5417.088652 5842.755507 0.93740364 0.88750727 1.000695757 0.793973091 0.876583975 0.93944285 0.802198411 0.915354089 0.927146215 1 12.5124332 -10.58316575 0.36671727 1.00602745 0.860739401 0.208500748 0.059636199 0.787516104 0.307972277 0.041749625 0.035657311 2.61E-11 10.58316575 -0.145288049 SS(ph)PGPDTLVVLEFNPASK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGPDTLVVLEFNPASK 18 0 O60303 O60303 KIAA0556 Uncharacterized protein KIAA0556 1 0 S(0.37)S(0.63)PGPDTLVVLEFNPASK 259.29 1.00E-75 11392000 2264.1 2532.6 2583.8 1209.7 3101.8 3501 2473.8 3087.8 2608.3 2558 TRUE FALSE FALSE 2236.504278 2568.254009 2628.769955 1349.571206 2943.503572 3277.297399 2683.92451 3177.140621 2375.007115 2491.542791 0.897638317 1.030788642 1.055077185 0.541660858 1.18139796 1.315368699 1.077213893 1.27517 0.953227504 1 11.28282364 -8.557465112 24.99999713 0.936979851 1.214770593 0.494235083 0.147477921 115.208839 83275.76156 0.020214653 0.040429422 2.77E-09 8.557465112 0.277790742 SS(ph)PGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR 36 1 P40222 P40222 TXLNA Alpha-taxilin 1 0 S(0.486)S(0.514)PGQPEAGPEGAQERPSQAAPAVEAEGPGSSQAPR 88.709 1.90E-13 58595000 364.85 285.79 266.5 282.55 306.36 303.47 303.61 315.95 267.66 329.19 TRUE FALSE FALSE 360.4030679 289.8133591 271.1383207 315.2197604 290.725306 284.0792464 329.3986258 325.0915148 243.7198192 320.6375963 1.12401999 0.903865805 0.845622359 0.98310293 0.906709972 0.885982335 1.027323775 1.013890818 0.760109925 1 8.324799788 -10.25173962 24.70107769 1.058564996 0.936470588 0 0.11223353 438.6618637 1117081.824 0.011885319 0.014459425 5.60E-11 10.25173962 -0.122094407 SS(ph)PQLDPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPQLDPLR 9 0 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.229)S(0.771)PQLDPLR 105.36 0.023464 36280000 5071.3 4669.3 5981 4836.6 7309.2 8032.2 6932.4 6630.5 5290.4 4764.3 TRUE FALSE FALSE 5009.489045 4735.034528 6085.096796 5395.830449 6936.18425 7518.968343 7521.237883 6822.343056 4817.213374 4640.522799 1.079509629 1.020366612 1.311295528 1.162763482 1.494698884 1.620284754 1.620773824 1.470166908 1.038075575 1 12.18007163 -8.995202141 0.95739966 1.034219665 1.599226153 0.869342918 0.086555972 0.124969537 0.223614159 0.014604929 0.038562378 1.01E-09 8.995202141 0.565006489 SS(ph)PQLDPLRK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPQLDPLRK 10 1 Q8ND56-3;Q8ND56-2;Q8ND56 Q8ND56-3 LSM14A Protein LSM14 homolog A 1 0 S(0.18)S(0.82)PQLDPLRK 88.163 0.01236 202780000 4128.3 4472.2 4702.7 2473.3 4085.9 4198.1 3554 3882.9 5187.4 4377.2 TRUE FALSE FALSE 4077.982692 4535.159749 4784.548521 2759.274583 3877.381276 3929.854959 3855.876671 3995.245585 4723.425952 4263.479713 0.956491637 1.063722606 1.122216791 0.647188393 0.909440536 0.921748249 0.904396627 0.937085633 1.10788048 1 12.05781568 -9.299125058 24.99998799 0.996327035 0.871953236 0.43276443 0.097022613 513.523158 340660.4163 0.013859732 0.02117141 5.02E-10 9.299125058 -0.124373799 SS(ph)PSILAVQR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPSILAVQR 10 0 O14646-2;O14646 O14646-2 CHD1 Chromodomain-helicase-DNA-binding protein 1 1 0 S(0.201)S(0.784)PS(0.015)ILAVQR;S(0.214)S(0.741)PS(0.045)ILAVQR ; 129.88 0.0074159 31417000 4766.1 3975.4 5678.7 4316.1 5865 5613.7 5247.1 5495.7 5757 4701.1 TRUE FALSE FALSE 4708.00894 4031.365786 5777.535391 4815.14779 5565.687165 5255.002687 5692.788543 5654.709409 5242.079501 4578.964744 1.028181959 0.880409877 1.261755815 1.05158001 1.215490286 1.14763991 1.243247953 1.234931851 1.144817616 1 12.16080574 -9.751958575 24.99995661 1.003712619 1.187358895 0.5312522 0.082129989 91.37348969 240942.4193 0.010300819 0.014459169 1.77E-10 9.751958575 0.183646276 SS(ph)PSVLIHSLGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSVLIHSLGK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 S(0.302)S(0.694)PS(0.004)VLIHSLGK 126.71 0.0021723 16585000 5305.2 5367.8 5423 4082.3 10075 9196.6 7931 7874.9 7633.4 6647.7 TRUE FALSE FALSE 5240.538182 5443.368029 5517.38504 4554.314734 9560.835155 8608.966941 8604.658942 8102.747807 6950.649586 6474.991796 0.809350552 0.840675664 0.852106877 0.703369962 1.476578729 1.329571869 1.32890654 1.251391208 1.073460756 1 12.66066265 -8.757757036 24.99999956 0.88436562 1.344130281 0.817059586 0.108190366 29.50574069 200315.9743 0.015709927 0.030472482 1.75E-09 8.757757036 0.459764661 SS(ph)PVVNDGVVR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPVVNDGVVR 11 0 H0YAM1;H0Y8R1;F5H5I6;H0YAK1;Q12849-5;Q12849 H0YAM1 GRSF1 G-rich sequence factor 1 1 0 S(0.231)S(0.769)PVVNDGVVR 120.6 0.009762 11017000 2065.1 2158.9 1452.1 1899.4 1951.3 2040.9 1966.8 2159.1 2171.6 1535 TRUE FALSE FALSE 2039.929767 2189.293051 1477.373191 2119.017565 1851.71788 1910.493077 2133.859943 2221.570152 1977.366657 1495.120479 1.364391563 1.464292063 0.988129861 1.417288837 1.238507469 1.277818814 1.427216049 1.485880358 1.322546701 1 10.54604603 -12.29790684 0.75237029 0.970896806 1.330625235 0 0.16969219 0.603110566 0.534175944 0.136893268 0.027185012 5.04E-13 12.29790684 0.359728429 SS(ph)RGQEEISGALPVAS(ph)PASSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSRGQEEISGALPVASPASSR 21 1 H0Y9D5;H0Y8S9;Q9UBK8;Q9UBK8-1 H0Y9D5 MTRR Methionine synthase reductase 2 0 S(0.433)S(0.566)RGQEEISGALPVAS(0.768)PAS(0.204)S(0.027)R 150.26 0.00016293 5713200 2002.3 1789.9 1902 2111.3 2531.5 2844.5 2298.4 2154.2 1872.6 1821.4 TRUE FALSE FALSE 1977.895197 1815.098259 1935.103512 2355.41844 2402.308109 2662.74563 2493.626039 2216.528378 1705.109966 1774.079765 1.114885157 1.023120997 1.09076466 1.327684632 1.354115049 1.500916521 1.405588456 1.249396122 0.96112362 1 10.79285516 -9.226879265 2.704154703 1.052781634 1.386326316 0.847385296 0.070184098 0.080812064 1.170487895 0.011051126 0.018843098 5.93E-10 9.226879265 0.333544681 SS(ph)RGQEEISGALPVASPASSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSRGQEEISGALPVASPASSR 21 1 H0Y9D5;H0Y8S9;Q9UBK8;Q9UBK8-1 H0Y9D5 MTRR Methionine synthase reductase 1 0 S(0.213)S(0.787)RGQEEISGALPVASPASSR 233.34 2.39E-52 50707000 6360.1 5728.4 5526.4 6096.7 7219.4 7549.5 5793.7 6852.5 6984.4 7270.6 TRUE FALSE FALSE 6282.580655 5809.044566 5622.584674 6801.62914 6850.967079 7067.111315 6285.816733 7050.766276 6359.697771 7081.708764 0.887156033 0.820288543 0.793958755 0.960450276 0.96741723 0.997938711 0.887612996 0.995630647 0.898045653 1 12.7898818 -6.489766299 4.206116266 0.930050794 10.21094333 0.067687571 0.068623119 2434.229697 250.9832109 0.010927007 214539.3178 3.24E-07 6.489766299 9.280892532 SS(ph)RSGPS(ph)ETSHRPRT ddPTM_HeLa_Romidepsin_16h_R1 1 SSRSGPSETSHRPRT 15 3 D6RII0;Q8WU39-2 D6RII0 MZB1 2 0 S(0.075)S(0.568)RS(0.334)GPS(0.425)ET(0.25)S(0.188)HRPRT(0.161) 85.976 0.024145 27024000 2101.5 1998.3 2411.9 2093.1 2267.2 2401.9 2832.7 1498.2 2830 2739 TRUE FALSE FALSE 2075.88611 2026.43212 2453.878108 2335.11407 2151.496324 2248.426342 3073.309467 1541.548053 2576.877712 2667.840385 0.778114808 0.759577721 0.919799446 0.875282526 0.806456164 0.842788929 1.151984011 0.577826193 0.965904005 1 11.38145664 -12.46788749 1.223355718 0.999444377 0.842487947 0.149908109 0.136397636 0.661207508 1.780172788 0.0860808 0.021525073 3.40E-13 12.46788749 -0.15695643 SS(ph)SENDVELLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSENDVELLTK 12 0 Q9C0D6 Q9C0D6 FHDC1 FH2 domain-containing protein 1 1 0 S(0.003)S(0.608)S(0.389)ENDVELLTK 158.65 0.00096202 6317600 4143.6 4291.1 4646.3 4622.3 6176.2 6292 5332.7 6325.2 4682.3 4166.6 TRUE FALSE FALSE 4093.096209 4351.510218 4727.166902 5156.752075 5861.005467 5889.961506 5785.659405 6508.209682 4263.503361 4058.351131 1.008561378 1.072236009 1.164799878 1.270652023 1.444183925 1.451318852 1.425618242 1.603658597 1.050550636 1 11.98667798 -9.119986904 0.883093362 0.999201646 1.518264099 0.954725799 0.044327401 0.066156893 0.100954753 0.007025334 0.017604572 7.59E-10 9.119986904 0.519062453 SS(ph)SETILSSLAGSDIVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 0 S(0.16)S(0.681)S(0.16)ETILSSLAGSDIVK 180.7 5.41E-09 7039900 1497.9 1509.5 1722.2 1645.7 2005.5 2024 1708.9 1676.5 1504.4 1369.7 TRUE FALSE FALSE 1479.643019 1530.750781 1752.174169 1835.983577 1903.151851 1894.672932 1854.053923 1725.006882 1369.842696 1334.114997 1.109082067 1.147390431 1.313360672 1.3761809 1.42652759 1.420172127 1.389725719 1.292997146 1.026780075 1 10.38166731 -9.901456492 1.098544881 1.039605899 1.393522704 0.928573976 0.041758942 0.089798433 0.214283302 0.009494885 0.013486816 1.25E-10 9.901456492 0.353916805 SS(ph)SFGSVSTSSNSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSFGSVSTSSNSSK 15 0 E5RG30;E5RJ65;E5RHF1;E5RGS8;E5RH07;E5RGQ6;A0A0C4DGW2;P57768-2;P57768 E5RG30 SNX16 Sorting nexin-16 1 0 S(0.008)S(0.496)S(0.496)FGSVSTSSNSSK 317.77 1.32E-155 10513000 3309.9 3282 3077.7 3355.7 4510 4344.6 3784.6 3983.3 3294.8 2849.5 TRUE FALSE FALSE 3269.557666 3328.204082 3131.266077 3743.701823 4279.837871 4066.994082 4106.06383 4098.550501 3000.104836 2775.469579 1.178019637 1.199149905 1.128193262 1.348853488 1.54202298 1.465335492 1.479412298 1.476705251 1.080935946 1 11.43851617 -9.338947931 0.432798412 1.032127799 1.570425486 0.862663752 0.068658068 0.346525551 0.127181287 0.027437011 0.076089515 4.58E-10 9.338947931 0.538297686 SS(ph)SLIQLTSQNSSPNQQR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLIQLTSQNSSPNQQR 18 0 H7C419;O95639 H7C419 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 0 S(0.005)S(0.497)S(0.497)LIQLTSQNSSPNQQR 336.71 4.96E-211 21400000 1136.8 1362.9 827.69 810.47 997.03 950.07 929.71 830.78 964.83 802.42 TRUE FALSE FALSE 1122.944244 1382.086942 842.0955973 904.1803548 946.1478387 889.3635932 1008.679544 854.8173085 878.5331883 781.5730127 1.436774589 1.768340154 1.077436891 1.156872538 1.210568716 1.137914921 1.29057622 1.093713952 1.124057732 1 9.610236842 SS(ph)SPSASLTENEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPSASLTENEVK 14 0 O96028-5 O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 S(0.019)S(0.756)S(0.225)PSASLTENEVK 219.84 3.33E-25 28960000 2487.1 2355.2 2067 2256 2061.7 1584.2 1631.9 1558.2 2907.4 2265.9 TRUE FALSE FALSE 2456.786269 2388.356567 2102.975268 2516.849335 1956.483756 1482.974733 1770.513545 1603.284059 2647.354862 2207.031591 1.113163164 1.082157853 0.952852363 1.140377575 0.886477458 0.67193181 0.802214863 0.726443638 1.199509274 1 11.10789157 -8.536073104 4.468574341 1.053738093 0.743418279 0.813064817 0.074599966 0.055328585 2.738930153 0.009137029 0.019562681 2.91E-09 8.536073104 -0.310319813 SS(ph)SPTSYWK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-2;Q92614-3;Q92614-4;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 S(0.2)S(0.369)S(0.369)PT(0.057)S(0.005)YWK 128.35 0.0091214 19615000 4540 4807.8 5261.2 3575.4 5679.7 6632.1 5228.5 5584.6 4799.4 4554.4 TRUE FALSE FALSE 4484.664734 4875.484335 5352.768979 3988.804571 5389.843715 6208.330214 5672.608659 5746.18159 4370.129644 4436.076031 1.010953081 1.099053375 1.206645004 0.899174077 1.215002556 1.399509425 1.278744688 1.295329825 0.985134072 1 12.11506838 -8.570680641 5.767777533 1.023684621 1.318585996 0.726554432 0.081126639 0.06891291 5.2827159 0.011615173 0.023685771 2.69E-09 8.570680641 0.294901375 SS(ph)SSERPEPQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSERPEPQQK 12 1 P78362;C9J2M4 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 0 S(0.244)S(0.634)S(0.114)S(0.009)ERPEPQQK 73.415 0.023504 4584600 1531.8 1680.2 1994.6 1677.9 1775.5 1956.2 3303.6 776.64 2581.8 2220 TRUE FALSE FALSE 1513.129832 1703.8539 2029.315176 1871.906693 1684.88961 1831.205133 3584.207702 799.1108531 2350.877342 2162.32408 0.699770144 0.78797342 0.938487989 0.865692016 0.779203092 0.846868955 1.657571931 0.369561094 1.087199353 1 11.07836705 -7.915291947 20.12846835 0.850247383 1.073201549 0.018615145 0.309002191 9.740576311 2309.599892 0.037650789 0.112953382 1.22E-08 7.915291947 0.222954166 SS(ph)SSSS(ph)SDSRTY(ph)S(ph)RK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSSSDSRTYSRK 15 2 C9J713;Q96IZ7-2;Q96IZ7;H7C558;C9J8Q2;C9JVB3;F8WDM0;C9J367 C9J713 RSRC1 Serine/Arginine-related protein 53 4 0 S(0.298)S(0.458)S(0.173)S(0.07)S(0.061)S(0.452)S(0.452)DS(0.063)RT(0.315)Y(0.667)S(0.99)RK 55.782 0.0039619 0 482.58 277.69 242.93 142.23 387.55 322.79 585.41 264.5 491.52 384.23 TRUE FALSE FALSE 476.6981293 281.5993271 247.1580947 158.6753018 367.7718774 302.1647608 635.1347108 272.1528902 447.5572202 374.2476492 1.273750497 0.752441138 0.660413219 0.423984766 0.98269656 0.807392542 1.697097396 0.727199999 1.195885188 1 8.547849444 -10.25831342 24.96239075 1.129271067 0.874048515 0.147330488 0.319410384 456.0466397 3641773.502 0.055827403 0.0668335 5.52E-11 10.25831342 -0.255222552 SS(ph)SVGS(ph)SSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.338)S(0.504)S(0.424)VGS(0.42)S(0.28)S(0.027)S(0.006)YPIS(0.001)PAVS(0.001)R 152.68 1.56E-10 0 1117.7 1412.6 1137.9 1071.3 1094.6 1124.3 929.17 1116.3 1305.9 1569.5 TRUE FALSE FALSE 1104.077042 1432.48662 1157.704672 1195.168747 1038.738477 1052.460859 1008.093677 1148.598379 1189.097033 1528.724164 0.722221228 0.937047149 0.757301219 0.781807978 0.679480643 0.688457005 0.659434645 0.751344426 0.777836225 1 10.5781124 -16.52287875 0.187658099 2.152962259 0.681529107 0.168971144 0.095854887 23.35648548 0.27436718 9.863831248 0.086088069 3.00E-17 16.52287875 -1.471433152 SS(ph)TDFSELEQPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTDFSELEQPR 12 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 S(0.001)S(0.671)T(0.328)DFSELEQPR 240.18 2.29E-39 49842000 2023.7 1806.7 1944.2 2153.8 3639.8 2994.3 2015.8 2633.9 1788.6 1998.7 TRUE FALSE FALSE 1999.034366 1832.13477 1978.037985 2402.83249 3454.047424 2802.973894 2187.022002 2710.107741 1628.623136 1946.773486 1.026844869 0.94111348 1.016059649 1.234264031 1.774242072 1.439804843 1.123408562 1.392102245 0.836575569 1 10.92686932 -9.085749974 4.170452789 1.007885122 1.420030964 0.652109008 0.159303769 0.113589192 3.594225125 0.023028172 0.039547681 8.21E-10 9.085749974 0.412145842 SS(ph)TPEEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPEEVK 8 0 E9PP50;P23528;E9PQB7;G3V1A4;E9PK25;E9PS23;E9PLJ3 E9PP50 CFL1 Cofilin-1 1 0 S(0.319)S(0.589)T(0.092)PEEVK 122.94 0.017032 5521200 1884.7 2356 2156.1 2036.7 1839.3 2313 4213.2 949.05 3746.3 2196.9 TRUE FALSE FALSE 1861.728551 2389.16783 2193.626016 2272.192837 1745.433658 2165.206765 4571.069103 976.5092644 3411.221545 2139.824221 0.870038077 1.116525276 1.025143091 1.061859574 0.815690205 1.011861976 2.136189065 0.456350225 1.594159703 1 11.06327657 -7.967199245 24.99991365 0.958322225 1.365708538 0 0.435310271 224.7492567 171296.1166 0.045871093 0.137612111 1.08E-08 7.967199245 0.407386313 SS(ph)VGPSKPVSQPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSVGPSKPVSQPR 13 1 Q9Y657 Q9Y657 SPIN1 Spindlin-1 1 0 S(0.057)S(0.943)VGPSKPVSQPR 85.469 0.011061 6052800 2349.4 2128 2023.2 2107.1 2074.3 2299 2183.6 2319.9 2777.3 2451.9 TRUE FALSE FALSE 2320.764609 2157.95804 2058.412947 2350.732816 1968.440731 2152.10132 2369.074929 2387.022646 2528.891332 2388.199285 0.97176338 0.903592114 0.861910043 0.984311833 0.824236379 0.901139756 0.991992144 0.999507312 1.058911352 1 11.22170751 -10.43722695 3.616688861 0.98828438 0.921839347 0.297561484 0.058273838 0.262086644 6.210228486 0.009727915 0.010889885 3.65E-11 10.43722695 -0.066445034 SSAS(ph)APDVDDPEAFPALA ddPTM_HeLa_Romidepsin_16h_R1 4 SSASAPDVDDPEAFPALA 18 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 1 0 S(0.02)S(0.026)AS(0.954)APDVDDPEAFPALA;S(0.003)S(0.004)AS(0.993)APDVDDPEAFPALA;S(0.002)S(0.002)AS(0.997)APDVDDPEAFPALA;SS(0.003)AS(0.997)APDVDDPEAFPALA ;;; 188.09 2.19E-14 11923200 7422.1 7778.5 7328 5622.85 7228.5 8239 7421.3 7623.5 8230 8143.2 TRUE FALSE FALSE 7331.63659 7888.005927 7455.540766 6272.990373 6859.602672 7712.55449 8051.665037 7844.073945 7493.888188 7931.63849 0.924353348 0.994498922 0.939974858 0.790882033 0.86484056 0.972378469 1.01513263 0.988960094 0.9448096 1 12.95340321 -7.917180362 0.006785934 1.86473547 4.28E-06 0 0.066972046 26346.6099 35.50117313 4693.201598 5067.044655 1.21E-08 7.917180362 -1.864731194 SSASAPDVDDPEAFPALA ddPTM_HeLa_Romidepsin_16h_R1 1 SSASAPDVDDPEAFPALA 18 0 Q8NC51-2;Q8NC51;Q8NC51-4;Q8NC51-3 Q8NC51-2 SERBP1 Plasminogen activator inhibitor 1 RNA-binding protein 0 0 161.51 3.03E-05 4289000 4449.6 4222.6 4317.7 3346 3748.3 4125.4 3298.2 4021.3 4620.9 4258.7 FALSE FALSE TRUE 4395.366564 4282.045874 4392.847757 3732.880263 3557.010264 3861.800254 3578.349026 4137.649971 4207.595131 4148.05836 1.059620232 1.03230126 1.059013007 0.899910257 0.857512107 0.930989856 0.862656384 0.99749078 1.014352925 1 12.01822048 -9.255241154 24.94910405 1.031350188 0.9053798 0.701690033 0.040154582 204.9886001 825119.6665 0.006098349 0.009941182 5.56E-10 9.255241154 -0.125970388 SSATLWNS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSATLWNSPSR 11 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 SSATLWNS(0.898)PS(0.102)R 139.19 0.0033097 35043000 2777.6 2123 2884.2 2268.3 3577.6 3050 2605.7 2416.6 3108.8 2484.8 TRUE FALSE FALSE 2743.745543 2152.88765 2934.398291 2530.571519 3395.021722 2855.114843 2827.028093 2486.520508 2830.741142 2420.244538 1.133664595 0.88953311 1.212438762 1.045585055 1.402759791 1.179680317 1.168075394 1.027383998 1.169609557 1 11.24093711 SSATLWNSPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SSATLWNSPSR 11 0 Q3KQU3-4;Q3KQU3;C9JIR3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 SSATLWNS(0.087)PS(0.913)R 103.11 0.017742 8970600 2984.1 2100.5 3028.4 1738.9 3151 3184.1 3222.4 3150.7 3423.5 3087.9 TRUE FALSE FALSE 2947.728641 2130.070894 3081.108032 1939.9598 2990.192712 2980.646286 3496.110576 3241.860534 3117.293586 3007.675913 0.980068573 0.708211575 1.024414904 0.645002938 0.994187139 0.991013119 1.162396042 1.077862319 1.036445972 1 11.5544334 -7.914022942 3.731945576 0.945969926 1.119636579 0.257223777 0.131148974 0.256993014 6.922101376 0.018188181 0.060811992 1.22E-08 7.914022942 0.173666652 SSATSGDIWPGLS(ph)AYDNSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSATSGDIWPGLSAYDNSPR 20 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 SSATSGDIWPGLS(0.528)AYDNS(0.472)PR 103.84 0.00023704 6230300 2245.3 2512.2 2824.1 1221.6 2330.5 2347.7 1948.3 2011.5 2747.3 2645.6 TRUE FALSE FALSE 2217.93342 2547.566818 2873.252276 1362.84714 2211.565889 2197.689547 2113.788553 2069.699579 2501.574607 2576.866931 0.860709334 0.988629559 1.115017715 0.528877577 0.858238298 0.852853332 0.820294028 0.803184501 0.970781447 1 11.33140232 -9.282796615 24.99519816 0.949825886 0.784540441 0.478683931 0.108064753 690.8776864 808558.594 0.017178294 0.026255591 5.21E-10 9.282796615 -0.165285445 SSATSGDIWPGLSAYDNS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 SSATSGDIWPGLSAYDNSPR 20 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLSAYDNS(1)PR;SSATSGDIWPGLS(0.264)AY(0.002)DNS(0.735)PR ;;; 310.75 1.40E-169 342064000 8543.9 9435.3 8527.3 4443.55 8257.5 8174.66 6919.84 7651.4 8930.6 9034 TRUE FALSE FALSE 8439.76366 9568.130401 8675.714079 4957.334159 7836.088962 7652.325609 7507.611037 7872.781187 8131.824769 8799.295378 0.959140851 1.087374612 0.985955546 0.563378537 0.890535961 0.869652089 0.853205935 0.894705866 0.924144993 1 13.10317229 -9.460242397 24.99999889 0.990476764 0.818858074 0.452259175 0.097356015 153.7757263 61376.30203 0.014063003 0.021481583 3.47E-10 9.460242397 -0.17161869 SSATVTGEPPSYSSGS(ph)DSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSATVTGEPPSYSSGSDSSK 20 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 SSATVTGEPPS(0.035)YS(0.053)S(0.208)GS(0.424)DS(0.222)S(0.057)K 148.52 2.33E-05 4855900 1345.1 1506.4 1749.2 1520.2 1816.3 1705.5 1684.4 2266 1690.1 1629 TRUE FALSE FALSE 1328.705404 1527.607139 1779.644092 1695.972677 1723.607433 1596.524054 1827.472894 2331.563135 1538.933223 1586.678345 0.837413208 0.962770522 1.121616172 1.068882475 1.08629921 1.006205233 1.151760153 1.469461748 0.969908758 1 10.63179398 -4 0.482667083 0.938496151 14.92863247 0.745599288 0.08033808 35.90210427 0.359955103 0.019928806 508.1884245 1.00E-04 4 13.99013632 SSAWAEGGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 3 SSAWAEGGSPR 11 0 Q8N9B5-2;Q8N9B5 Q8N9B5-2 JMY Junction-mediating and -regulatory protein 1 0 SSAWAEGGS(1)PR;SSAWAEGGS(1)PR;SSAWAEGGS(1)PR ;; 120.03 0.01002 56179900 8070.7 6371.8 7280.2 5795.88 6795.8 6902.6 6146.27 6543.5 7959.7 7537.1 TRUE FALSE FALSE 7972.331204 6461.502368 7406.908827 6466.026916 6448.984967 6461.546137 6668.33402 6732.825849 7247.764497 7341.285055 1.08595854 0.88015958 1.008939003 0.880775895 0.87845451 0.880165542 0.908333346 0.917118161 0.98726101 1 12.84181691 -10.25691326 24.99838435 1.040591534 0.90840409 0.581818664 0.044708679 179.5111368 991464.7234 0.007967407 0.009578744 5.53E-11 10.25691326 -0.132187443 SSDEENGPPS(ph)SPDLDR ddPTM_HeLa_Romidepsin_16h_R1 1 SSDEENGPPSSPDLDR 16 0 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 SSDEENGPPS(0.5)S(0.5)PDLDR 112.03 0.0030165 1649800 581.29 732.39 715.63 706.91 505.59 463.21 526.07 412.69 758.95 844.72 TRUE FALSE FALSE 574.2050139 742.7006056 728.08524 788.6462603 479.7878557 433.6123759 570.7543727 424.630534 691.0676112 822.7740526 0.697889065 0.902678692 0.884915169 0.958521064 0.583134403 0.527012701 0.693695153 0.516096166 0.839923924 1 9.684352487 -8.749785713 24.9096887 0.866415452 0.584322988 0.736929968 0.087744837 121.8368725 260424.3362 0.017649423 0.035062928 1.78E-09 8.749785713 -0.282092465 SSDEENGPPSS(ph)PDLDR ddPTM_HeLa_Romidepsin_16h_R1 2 SSDEENGPPSSPDLDR 16 0 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 1 0 SSDEENGPPS(0.002)S(0.998)PDLDR;SSDEENGPPS(0.008)S(0.992)PDLDR ; 265.43 2.83E-86 131448000 10488.8 9591.1 9365.3 7526.3 6153.1 5523.8 4809.4 5101.4 10467.1 10519.8 TRUE FALSE FALSE 10360.95847 9726.123758 9528.299118 8396.526218 5839.084347 5170.847007 5217.910316 5249.00096 9530.896361 10246.49408 1.011171079 0.949214793 0.929908225 0.819453576 0.569861682 0.504645488 0.509238602 0.512272873 0.930161701 1 13.32284274 -8.920854665 1.443949341 1.001159301 0.497161978 0.977850727 0.031275084 0.0257251 0.107322126 0.003579201 0.008071495 1.20E-09 8.920854665 -0.503997323 SSDGS(ph)LSHEEDLAK ddPTM_HeLa_Romidepsin_16h_R1 1 SSDGSLSHEEDLAK 14 0 A0A2R8Y7R9;Q13136-2;Q13136;E9PJZ7;H0YEF9 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 S(0.009)S(0.009)DGS(0.974)LS(0.007)HEEDLAK 98.508 0.0047499 5471600 3268.9 2726.8 2579 3431.7 5731.9 5922 4233.6 4413.1 4206.2 3425 TRUE FALSE FALSE 3229.057389 2765.187962 2623.886413 3828.489301 5439.379754 5543.603312 4593.201878 4540.786086 3829.986937 3336.018006 0.967937638 0.8288888 0.786532449 1.147622493 1.630500718 1.661742623 1.376851645 1.361139561 1.148071422 1 11.70391136 -8.929001089 4.625152254 0.956818737 1.506045023 0.81022037 0.127971193 0.062722263 2.590742001 0.018111112 0.033353193 1.18E-09 8.929001089 0.549226286 SSDPGPDIGVVEES(ph)PEKGDEISLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSDPGPDIGVVEESPEKGDEISLR 24 1 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 S(0.001)S(0.003)DPGPDIGVVEES(0.996)PEKGDEIS(0.001)LR 61.694 0.00209 6405000 709.92 532.18 602.91 586.33 726.61 719.19 584.35 576.95 1005.5 757.36 TRUE FALSE FALSE 701.267222 539.672044 613.4033956 654.1242334 689.5283803 673.2360801 633.9846744 593.643138 915.5655617 737.683678 0.950634049 0.731576501 0.831526322 0.886727269 0.934720939 0.912635185 0.859426192 0.804739424 1.241135718 1 9.526858505 -10.48428423 13.66381425 0.978235876 0.856827175 0.425782318 0.099354814 1.539740824 544.961134 0.010098674 0.011316364 3.28E-11 10.48428423 -0.121408701 SSDQPLTVPVS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 SSDQPLTVPVSPK 13 0 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 SSDQPLT(0.001)VPVS(0.999)PK;SSDQPLT(0.011)VPVS(0.989)PK;SSDQPLT(0.001)VPVS(0.999)PK;SSDQPLTVPVS(1)PK ;;; 191.89 7.99E-11 989945000 36561.7 35019.7 34117.1 33945.1 33880.6 31539.9 26281.1 26789.8 36387.1 34928 TRUE FALSE FALSE 36116.07194 35512.70826 34710.89381 37869.99218 32151.54656 29524.60218 28513.41598 27564.9206 33132.54664 34020.56552 1.061595285 1.043860021 1.0202915 1.11314999 0.945062084 0.86784572 0.838122928 0.810242868 0.973897586 1 15.0541195 -8.376901535 2.554937777 1.03545627 0.832562914 0.8415495 0.038115085 0.074547734 0.93977733 0.005281424 0.013718259 4.20E-09 8.376901535 -0.202893356 SSDS(ph)EEAFETPESTTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSDSEEAFETPESTTPVK 18 0 E9PGB3;E7EMZ9;E9PBC6;O95359-5;O95359-3;O95359 E9PGB3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 0 S(0.121)S(0.121)DS(0.759)EEAFETPESTTPVK 217.32 5.51E-35 0 795.52 849.99 875.5 866.44 842.79 839.31 668.84 895.67 1251.7 925.75 TRUE FALSE FALSE 785.8238963 861.9561815 890.7377102 966.6218695 799.7792814 785.6807997 725.6512529 921.5847983 1139.744817 901.6988815 0.871492593 0.955924643 0.987843867 1.072000741 0.886969362 0.871333896 0.804760068 1.022053833 1.263997151 1 9.816501922 SSDYQFPSS(ph)PFTDTLK ddPTM_HeLa_Romidepsin_16h_R1 2 SSDYQFPSSPFTDTLK 16 0 Q9UK61-3;Q9UK61 Q9UK61-3 FAM208A Protein FAM208A 1 0 SSDYQFPS(0.239)S(0.761)PFTDTLK;SSDYQFPS(0.207)S(0.705)PFT(0.088)DTLK ; 208.38 2.27E-19 24549000 12542.8 13695.4 13073.7 9584.3 11622.3 11757.7 8521.8 10205.1 13249 13866.6 TRUE FALSE FALSE 12389.92353 13888.2042 13301.24226 10692.48186 11029.17066 11006.42092 9245.641479 10500.36847 12063.97626 13506.34373 0.917341049 1.028272675 0.984814434 0.791663686 0.816591883 0.814907508 0.684540662 0.777439748 0.893208147 1 13.72134956 -9.229698697 5.833013386 0.967799581 0.775066205 0.780224214 0.049810444 0.067211152 7.097340817 0.007671609 0.01263247 5.89E-10 9.229698697 -0.192733376 SSEGGVGVGPGGGDEPPT(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSEGGVGVGPGGGDEPPTSPR 21 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 SSEGGVGVGPGGGDEPPT(0.609)S(0.391)PR 192.72 1.30E-17 4419500 909.71 1032.4 1116 1099 1203.5 1405.2 1112.5 1194.3 1125.4 1165.1 TRUE FALSE FALSE 898.6221046 1046.934154 1135.423512 1226.071551 1142.080904 1315.412255 1206.995722 1228.855186 1024.741405 1134.830534 0.791855768 0.922546691 1.000522525 1.080400566 1.006388945 1.159126597 1.063591158 1.082853474 0.902990689 1 10.14826116 -9.570513932 2.394970637 0.900024388 1.078549916 0.665757781 0.058233746 0.185772294 2.156339846 0.013627788 0.020639026 2.69E-10 9.570513932 0.178525528 SSEGGVGVGPGGGDEPPTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSEGGVGVGPGGGDEPPTSPR 21 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 SSEGGVGVGPGGGDEPPT(0.158)S(0.842)PR;SSEGGVGVGPGGGDEPPT(0.061)S(0.939)PR ; 234.62 3.09E-53 59966000 9652.3 9323.4 8067.9 9165.7 9608.1 9600.6 8471 9319.3 10052.3 8466.2 TRUE FALSE FALSE 9534.654055 9454.65507 8208.318415 10225.48136 9117.762804 8987.152645 9190.526529 9588.939242 9153.197112 8246.246904 1.156241641 1.146540381 0.995400515 1.240016395 1.10568637 1.08984763 1.114510229 1.162824659 1.109983392 1 13.00952194 -12.35979732 0.964719562 0.99619069 1.126424563 0.063690008 0.067597183 0.469379522 0.744941207 0.044204948 0.010236872 4.37E-13 12.35979732 0.130233873 SSEPVKETVQTTQS(ph)PTPVEK ddPTM_HeLa_Romidepsin_16h_R1 4 SSEPVKETVQTTQSPTPVEK 20 1 A0A0A0MT33;Q9UPN6;Q9UPN6-2 A0A0A0MT33 SCAF8 Protein SCAF8 1 0 SSEPVKETVQT(0.008)T(0.212)QS(0.488)PT(0.292)PVEK;SSEPVKETVQTT(0.003)QS(0.996)PT(0.001)PVEK;S(0.002)S(0.002)EPVKET(0.099)VQT(0.099)T(0.12)QS(0.651)PT(0.028)PVEK;SSEPVKETVQT(0.001)T(0.059)QS(0.881)PT(0.059)PVEK ;;; 184.22 7.36E-14 240771000 19401.6 14893.5 17558.7 14105.4 14816.6 12825.5 10792.3 12289.8 18020 16201 TRUE FALSE FALSE 19165.12584 15103.17108 17864.30181 15736.33272 14060.45361 12005.99194 11708.99769 12645.38597 16408.24607 15780.09568 1.214512651 0.95710263 1.132078168 0.997226698 0.891024611 0.760831378 0.742010564 0.801350399 1.0398065 1 13.94581833 -8.694808059 1.624396692 1.093773189 0.760962153 0.771873415 0.070916667 0.147423901 0.78323337 0.013890179 0.034555904 2.02E-09 8.694808059 -0.332811037 SSESGNSVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SSESGNSVKR 10 1 H3BU93;Q9GZU8;H3BNK9 H3BU93 FAM192A Protein FAM192A 0 1 ; SSESGNSVK(1)R;SSESGNSVK(1)R 109.79 0.0043107 1827490 498.03 349.97 591.07 382.85 359.7 241.682 1130.18 0 909.48 435.63 FALSE TRUE FALSE 491.9598188 354.8968868 601.3573254 427.1169184 341.3431668 226.2393002 1226.177461 0 828.133831 424.3122698 1.159428689 0.83640496 1.417251794 1.006609869 0.804462164 0.533190568 2.889799679 0 1.951708423 1 8.728982587 -16.5228316 0.077857212 0.616045093 1.259809399 0 0.767792339 1614.118353 9.671909035 113.1960624 13.2572137 3.00E-17 16.5228316 0.643764307 KFELLPTPPLS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 2 KFELLPTPPLSPSR 14 1 H0YBG3;A0A0B4J1R1;H0YBT0;A0A087WUS5;P01106;P01106-2;P04198 H0YBG3 MYC;MYCN Myc proto-oncogene protein;N-myc proto-oncogene protein 1 0 KFELLPT(0.013)PPLS(0.494)PS(0.494)R;KFELLPT(0.016)PPLS(0.811)PS(0.173)R ; 87.323 0.0067228 21499000 20027.7 17374.6 20940 17876 10298.8 7154.3 5901.2 5515.7 20202.8 17466.1 TRUE FALSE FALSE 19783.59469 17619.20007 21304.45192 19942.90723 9773.213806 6697.163319 6402.447781 5675.288077 18395.81097 17012.3282 1.162897544 1.035672476 1.252294904 1.172262079 0.574478325 0.393665302 0.376341657 0.333598553 1.081322365 1 14.05429297 -8.637584439 3.740645714 1.095929708 0.381472438 0.955253754 0.07472478 0.041240233 1.095975763 0.013666813 0.028518199 2.30E-09 8.637584439 -0.71445727 down ELPTVTTNVQNS(ph)QDKSIEK ddPTM_HeLa_Romidepsin_16h_R1 1 ELPTVTTNVQNSQDKSIEK 19 1 Q96B01-3;Q96B01-2;Q96B01;F5H1Y0;H0YGT5 Q96B01-3 RAD51AP1 RAD51-associated protein 1 1 0 ELPT(0.006)VT(0.025)T(0.006)NVQNS(0.962)QDKSIEK 88.555 0.0016177 16350000 2050.9 1688.2 1636.6 1679 1126.1 897.66 747.46 657.46 1848.1 1640.6 TRUE FALSE FALSE 2025.902842 1711.966524 1665.084336 1873.13388 1068.630915 840.3024231 810.9492337 676.4825678 1682.801307 1597.976975 1.26779226 1.071333661 1.041995199 1.172190782 0.66873987 0.525853899 0.50748493 0.423336868 1.053082324 1 10.64203091 -8.634221249 3.218943602 1.121498285 0.495667513 0.925722614 0.079917591 0.059953247 1.231214074 0.016125194 0.034406156 2.32E-09 8.634221249 -0.625830772 down SSFDWLTGSSTDPLVDHT(ph)SPSSDSLLFAHK ddPTM_HeLa_Romidepsin_16h_R1 1 SSFDWLTGSSTDPLVDHTSPSSDSLLFAHK 30 0 P78527-2;P78527 P78527-2 PRKDC DNA-dependent protein kinase catalytic subunit 1 0 SSFDWLT(0.002)GS(0.015)S(0.014)T(0.014)DPLVDHT(0.419)S(0.419)PS(0.049)S(0.049)DS(0.019)LLFAHK 44.164 0.029182 7937400 833.18 834.38 596.15 515.46 1104.6 1159.1 794.82 875.22 1020.5 794.69 TRUE FALSE FALSE 823.0248817 846.1264235 606.5257407 575.0599105 1048.22814 1085.037251 862.331991 900.5431098 929.2239241 774.0438392 1.063279416 1.093124679 0.783580606 0.742929381 1.35422322 1.401777517 1.114060919 1.163426494 1.200479711 1 9.596271468 -8.736940149 24.99955461 0.997388249 1.258307379 0.44944031 0.149938757 171.023953 174515.7761 0.021095781 0.04217619 1.83E-09 8.736940149 0.26091913 SSFFSDRGS(ph)GSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSFFSDRGSGSR 12 1 A0A2R8Y4A4;A0A2R8YFS5;A0A2R8YFR4;A0A2R8YCW1;A0A2R8Y5G6;O00571;A0A0D9SFB3;A0A2R8Y645;O00571-2;A0A0D9SF53;A0A2U3TZJ9;A0A0D9SG12;A0A2R8YF78;F6S8Q4;A0A2R8YDH3;A0A087WX09;A0A2R8Y650;A0A2R8YCU0;A0A2R8YF89 A0A2R8Y4A4 DDX3X ATP-dependent RNA helicase DDX3X 1 0 SSFFS(0.016)DRGS(0.854)GS(0.129)R;SSFFS(0.004)DRGS(0.918)GS(0.077)R ; 88.706 0.011146 56046000 5750.4 5737.8 5169.2 4245.8 4378.8 5058.8 4452.6 4596.7 5686.8 5187.3 TRUE FALSE FALSE 5680.311913 5818.576899 5259.167758 4736.719373 4155.333496 4735.559007 4830.803733 4729.698262 5178.158365 5052.533198 1.12425029 1.151615768 1.04089722 0.937493963 0.822425768 0.937264303 0.956115189 0.936104341 1.024863798 1 12.30279118 -9.270363152 3.961756564 1.068204682 0.914188224 0.670795898 0.053092313 0.125327699 4.589846303 0.010042644 0.016271009 5.37E-10 9.270363152 -0.154016458 SSFLSS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 SSFLSSPER 9 0 Q4AC94 Q4AC94 C2CD3 C2 domain-containing protein 3 1 0 SSFLS(0.028)S(0.972)PER;SSFLS(0.223)S(0.777)PER ; 120.27 0.01332 16105900 3798.8 2492.6 7679.1 4822.5 7352.6 9206 6786.8 4995.9 4389.8 2688.3 TRUE FALSE FALSE 3752.498764 2527.690888 7812.751514 5380.100141 6977.369386 8617.766311 7363.270623 5140.448484 3997.165294 2618.457578 1.433095115 0.965335818 2.983722776 2.05468295 2.664686815 3.291161324 2.812064126 1.963158971 1.526534295 1 11.35450152 -9.7641873 24.99998752 1.192292923 2.64231943 0.741350245 0.40393465 25.46390484 231665.7482 0.06392093 0.086143599 1.72E-10 9.7641873 1.450026506 SSFSSTSES(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 SSFSSTSESPTR 12 0 Q6ZMT1-2;Q6ZMT1 Q6ZMT1-2 STAC2 SH3 and cysteine-rich domain-containing protein 2 1 0 SSFSS(0.001)T(0.002)S(0.013)ES(0.976)PT(0.009)R 130.69 0.00376 4128500 2336 2835.1 2501.5 2395.3 2621.2 2551.7 2185.5 2290.6 2709.8 2165 TRUE FALSE FALSE 2307.527933 2875.012612 2545.037558 2672.255856 2487.430383 2388.654605 2371.136315 2356.874897 2467.428701 2108.752988 1.094261844 1.363370973 1.206892212 1.267220899 1.179574088 1.13273324 1.124425824 1.117662861 1.170089012 1 11.0421744 -10.56786837 3.657991996 1.037722423 1.197388796 0.218149497 0.083392427 0.13978115 4.009694843 0.014312041 0.015275938 2.70E-11 10.56786837 0.159666372 SSFYSGGWQEGSS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSFYSGGWQEGSSSPR 16 0 D3DPQ1;Q96BR9-2;Q96BR9 D3DPQ1 ZBTB8A Zinc finger and BTB domain-containing protein 8A 1 0 SSFYSGGWQEGS(0.082)S(0.623)S(0.294)PR 138.81 0.00092538 6397900 2640.4 2367.4 2391.6 2344.8 1559.7 1406.3 1229.9 1164.8 2416 2421.7 TRUE FALSE FALSE 2608.217789 2400.728319 2433.224795 2615.916809 1480.102689 1316.441969 1334.367675 1198.50165 2199.906909 2358.783885 1.105746824 1.017782229 1.031559021 1.109010802 0.627485502 0.558101985 0.56570154 0.508101509 0.932644539 1 11.20382753 -8.701515053 5.081971483 1.050710706 0.555353491 0.947828216 0.053819019 0.02680429 1.384934816 0.007077228 0.014234232 1.99E-09 8.701515053 -0.495357215 SSFYVNGLTLGGQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSFYVNGLTLGGQK 14 0 P07737;K7EJ44;I3L3D5 P07737 PFN1 Profilin-1 0 0 146.36 6.83E-06 766940 0 178.75 186.47 159.86 162.21 360.35 150.1 196.97 54.766 59.636 FALSE FALSE TRUE 0 181.2664472 189.7154321 178.3437654 153.9318184 337.324798 162.8494903 202.6690162 49.8675918 58.08664812 0 3.120621572 3.266076427 3.070305675 2.65003789 5.807269121 2.803561498 3.489080929 0.858503519 1 5.860134677 -10.19667423 5.28232373 0.528377664 3.492765514 0.694429977 0.863639771 0.084399592 4.723658747 0.146456292 0.17917214 6.36E-11 10.19667423 2.96438785 SSGAPQDSDSSATCS(ph)ADEVDEAEGGDKNR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGAPQDSDSSATCSADEVDEAEGGDKNR 29 1 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;C9JQE8 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 SSGAPQDS(0.007)DS(0.023)S(0.08)AT(0.196)CS(0.695)ADEVDEAEGGDKNR;SSGAPQDS(0.016)DS(0.01)S(0.042)AT(0.063)CS(0.87)ADEVDEAEGGDKNR ; 100.23 6.84E-09 15453900 1823.67 1626.2 1675.03 30.348 1306.51 1323.49 1183.83 747.79 2287.6 1825.04 TRUE FALSE FALSE 1801.442409 1649.093686 1704.183195 33.85697855 1239.833919 1238.92326 1284.384491 769.4261238 2082.991327 1777.625198 1.013398331 0.927694819 0.958685327 0.019046185 0.697466441 0.696954151 0.722528288 0.432839344 1.171783191 1 10.79573546 -9.481729146 24.99798047 0.99787234 0.540059072 0.608401559 0.200263354 260.8805254 158482.6124 0.028167216 0.043023142 3.30E-10 9.481729146 -0.457813267 SSGDPEQIKEDS(ph)LSEESADAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGDPEQIKEDSLSEESADAR 21 1 Q9BVS4;Q9BVS4-2 Q9BVS4 RIOK2 Serine/threonine-protein kinase RIO2 1 0 SSGDPEQIKEDS(0.778)LS(0.217)EES(0.005)ADAR;SSGDPEQIKEDS(0.717)LS(0.258)EES(0.025)ADAR ; 80.68 0.0011145 60393000 6376.8 6581.9 6406.6 6706.8 7495.7 7232.6 5723.3 6373 7250.8 7239.6 TRUE FALSE FALSE 6299.077109 6674.560161 6518.104186 7482.271772 7113.166459 6770.460202 6209.436959 6557.3927 6602.270288 7051.514148 0.893294259 0.94654283 0.924355259 1.061087252 1.008743131 0.960142752 0.880582075 0.929926901 0.93629115 1 12.78371736 -7.778197437 24.55612297 0.959332843 0.905254498 0.202563108 0.046846876 267.7660224 392368.2943 0.007925892 0.023878296 1.67E-08 7.778197437 -0.054078345 SSGEIVYCGQVFEKS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGEIVYCGQVFEKSPLR 18 1 M0R0P7;M0R3D6;M0R1A7;M0R117;Q02543 M0R0P7 RPL18A 60S ribosomal protein L18a 1 0 SSGEIVYCGQVFEKS(1)PLR;SSGEIVY(0.016)CGQVFEKS(0.984)PLR ; 67.214 0.0098753 77750000 6527.4 6651.2 6244.7 1784.28 6272.8 7114 5497 6840.8 7103.9 7248.9 TRUE FALSE FALSE 6447.841538 6744.835768 6353.386384 1990.586849 5952.675609 6659.438359 5963.915043 7038.727755 6468.509392 7060.572533 0.913217945 0.955281705 0.899840113 0.281929948 0.843086815 0.943186736 0.844678674 0.99690609 0.916145166 1 12.78556946 -9.509337286 24.97999293 0.956164067 0.777104374 0.154348491 0.183134397 866.3957276 1598245.882 0.028634883 0.042581229 3.10E-10 9.509337286 -0.179059693 SSGGREDLES(ph)SGLQR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGGREDLESSGLQR 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 1 0 SSGGREDLES(0.76)S(0.24)GLQR 86.016 0.0079226 31975000 1617.8 1319.9 1662.5 1357.6 1867.3 2030.7 1331.6 2091.3 1236.9 1723.3 TRUE FALSE FALSE 1598.081631 1338.481587 1691.435115 1514.5721 1772.004713 1900.944824 1444.706071 2151.808466 1126.268566 1678.528418 0.952073027 0.797413718 1.007689293 0.902321393 1.055689433 1.132506786 0.860698011 1.281961296 0.670985701 1 10.71298125 -8.64526007 6.920439712 0.959800858 1.072543761 0.222238917 0.144720551 0.269352537 15.32746982 0.015018388 0.030158869 2.26E-09 8.64526007 0.112742903 SSGGREDLESSGLQR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGGREDLESSGLQR 15 1 Q9UK76;J3KT51;Q9UK76-2;Q9UK76-3;J3KSH8 Q9UK76;Q9UK76-3 HN1 "Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed" 0 0 ; ; 128.95 4.33E-05 0 2434.4 2243.5 2202.4 2016.99 3272.5 3182.8 2850.4 3361.5 2233.3 1981.53 FALSE FALSE TRUE 2404.728596 2275.084052 2240.731848 2250.203874 3105.492114 2979.429352 3092.512905 3458.759699 2033.548055 1930.049565 1.245941369 1.178769755 1.160971142 1.165878802 1.60902195 1.543706134 1.602297144 1.792057449 1.053624783 1 10.91442218 -4 0.211422464 1.014745879 5.106146742 0.866446481 0.095411042 13.87424045 0.163254124 0.087796249 19.29589847 1.00E-04 4 4.091400864 SSGNS(ph)PTPVSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGNSPTPVSR 11 0 H0YBT1;O95429-2;O95429 H0YBT1 BAG4 BAG family molecular chaperone regulator 4 1 0 S(0.012)S(0.04)GNS(0.944)PT(0.003)PVSR;S(0.259)S(0.172)GNS(0.558)PT(0.011)PVSR ; 116.79 0.011492 200762000 8224 8210.7 9489.1 6247.5 9257 10929.7 12417.5 5586.3 9958.1 8640 TRUE FALSE FALSE 8123.762725 8326.29045 9654.253805 6969.865345 8784.580747 10231.32744 13472.24214 5747.930777 9067.422595 8415.531554 0.965329721 0.989395666 1.147194772 0.82821451 1.043853343 1.215767225 1.600878335 0.683014583 1.077462848 1 13.03883868 -8.347898933 4.524894601 0.98625814 1.209489047 0.087295313 0.221620374 0.269406584 9.751378834 0.027956671 0.064993856 4.49E-09 8.347898933 0.223230907 SSGNSSSSGS(ph)GSGSTSAGSSSPGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSS(0.001)S(0.001)GS(0.566)GS(0.175)GS(0.025)T(0.175)S(0.054)AGSS(0.002)SPGAR 215.43 2.84E-37 4500900 615.23 788.06 703.7 478.83 589.46 683.91 390.8 694.07 829.7 882.08 TRUE FALSE FALSE 607.7313401 799.1543294 715.9476033 534.1945776 559.3776566 640.2103582 423.9945422 714.1518204 755.489554 859.1634344 0.707352427 0.930154028 0.833307814 0.621761304 0.651072467 0.7451555 0.493496959 0.831217661 0.879331596 1 9.746788784 -16.52287875 0.165869423 2.138848948 0.631575006 0.369155575 0.116560437 37.26107946 0.407124569 13.76529327 0.192795342 3.00E-17 16.52287875 -1.507273941 SSGNSSSSGSGS(ph)GSTSAGSSSPGAR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNS(0.023)S(0.084)S(0.023)S(0.013)GS(0.049)GS(0.538)GS(0.255)T(0.011)S(0.003)AGSSSPGAR 149.41 1.23E-07 6177600 654.15 1047.1 1054.5 424.32 548.53 908.21 516.58 1047.2 1055.9 947.89 TRUE FALSE FALSE 646.1769682 1061.841101 1072.85313 473.3818749 520.5364673 850.1783121 560.4582923 1077.49908 961.4576594 923.2636812 0.699883448 1.150095171 1.162022456 0.512726629 0.563800437 0.920840199 0.607040333 1.16705455 1.04136844 1 9.850598926 -9.255166942 24.98639407 0.901917047 0.744781543 0.169268943 0.226719918 994.8034011 3962820.197 0.035561161 0.058032889 5.56E-10 9.255166942 -0.157135504 SSGNSSSSGSGSGSTS(ph)AGSSSPGARR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGARR 26 1 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSSS(0.001)GS(0.011)GS(0.027)GS(0.022)T(0.07)S(0.74)AGS(0.094)S(0.008)S(0.025)PGARR 67.396 0.0001777 17465000 165.57 63.643 0 136.57 57.111 188.52 176.67 0 0 55.66 TRUE FALSE FALSE 163.5519692 64.53896782 0 152.360866 54.19641256 176.4741804 191.6763454 0 0 54.21394518 3.016787814 1.190449572 0 2.810363007 0.999676603 3.255143669 3.535554271 0 0 1 5.760592091 -12.73421567 1.663853499 1.000185235 2.073693196 0.103552888 1.288584651 0.773801644 3.873132329 0.893072254 0.194265822 1.84E-13 12.73421567 1.073507962 SSGNSSSSGSGSGSTSAGS(ph)SSPGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSSSGSGSGST(0.001)S(0.009)AGS(0.755)S(0.063)S(0.171)PGAR;SSGNSSSSGSGS(0.001)GS(0.002)T(0.002)S(0.002)AGS(0.331)S(0.331)S(0.331)PGAR ; 97.825 1.94E-05 1286770 0 293.82 236.62 42.408 0 0 0 64.457 0 106.72 TRUE FALSE FALSE 0 297.9564057 240.7382718 47.3114125 0 0 0 66.3219616 0 103.947399 0 2.866415211 2.31596244 0.455147632 0 0 0 0.638033873 0 1 6.699709849 -9.005439856 24.69671623 0.873579501 0.148077903 0.202095342 0.888817483 382.9613318 1738645.618 0.147991092 0.262502823 9.88E-10 9.005439856 -0.725501598 SSGNSSSSGSGSGSTSAGS(ph)SSPGARR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGNSSSSGSGSGSTSAGSSSPGARR 26 1 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSSSGSGS(0.001)GS(0.008)T(0.027)S(0.025)AGS(0.409)S(0.265)S(0.265)PGARR 73.296 8.82E-05 13425000 161.96 153.54 156.05 294.09 0 315.1 119.05 192.77 279.02 361.24 TRUE FALSE FALSE 159.9859692 155.7015402 158.7659848 328.0940695 0 294.9661269 129.162104 198.3474958 254.0637524 351.8549327 0.454692984 0.442516292 0.45122569 0.932469717 0 0.838317441 0.367089081 0.563719526 0.722069605 1 8.458836928 -12.23241458 0.813822243 1.023118553 0.502870803 0.206735826 0.255145697 0.548289976 0.608425966 0.18321124 0.042910691 5.86E-13 12.23241458 -0.52024775 SSGNSSSSGSGSGSTSAGSS(ph)SPGAR ddPTM_HeLa_Romidepsin_16h_R1 3 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSSSGSGSGS(0.001)TSAGS(0.005)S(0.608)S(0.385)PGAR;SSGNSSSSGSGSGS(0.005)T(0.015)S(0.015)AGS(0.212)S(0.376)S(0.376)PGAR;SSGNSSSSGSGSGSTSAGS(0.002)S(0.499)S(0.499)PGAR ;; 121.92 7.39E-07 97862810 192.72 657.6 424.5 161.619 271.359 517.11 137.45 310.66 393.051 237.34 TRUE FALSE FALSE 190.3710545 666.8577101 431.8882444 180.3061492 257.5105377 484.0683399 149.1249996 319.648457 357.8955341 231.1738726 0.823497277 2.884658645 1.868239865 0.779959029 1.113925786 2.093957827 0.645077222 1.382718788 1.54816602 1 7.852834543 SSGNSSSSGSGSGSTSAGSSS(ph)PGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGNSSSSGSGSGSTSAGSSSPGAR 25 0 E5RHJ2;E5RG56;Q12797-7;Q12797-6;Q12797-11;Q12797-2;Q12797 E5RHJ2 ASPH Aspartyl/asparaginyl beta-hydroxylase 1 0 SSGNSSSSGSGSGSTSAGS(0.018)S(0.236)S(0.745)PGAR;SSGNSSSSGSGSGSTSAGS(0.013)S(0.375)S(0.611)PGAR ; 243.72 2.77E-71 118509520 412.52 223.45 353.88 161.6 378.97 533.64 384.82 466.73 465.71 423.56 TRUE FALSE FALSE 407.4920476 226.595735 360.039133 180.2849524 359.6297468 499.5421262 417.5066012 480.2340962 424.0557312 412.5558501 0.987725777 0.549248629 0.872703981 0.436995263 0.871711664 1.210847273 1.012000196 1.164046264 1.027874725 1 8.688445629 -8.272583887 24.00211638 0.900576735 1.117268139 0.280761506 0.1989122 561.5872535 1209501.21 0.031476959 0.071056572 5.34E-09 8.272583887 0.216691404 SSGPT(ph)SLFAVTVAPPGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGPTSLFAVTVAPPGAR 18 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;A0A1W2PP22 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 1 0 S(0.022)S(0.003)GPT(0.585)S(0.386)LFAVT(0.003)VAPPGAR;S(0.037)S(0.037)GPT(0.548)S(0.378)LFAVTVAPPGAR ; 170.48 1.84E-11 11730000 2048.83 1664.75 2160.2 1549.51 1643.78 1371.9 1228.24 1489.98 1542.06 1347.13 TRUE FALSE FALSE 2023.858072 1688.186394 2197.797375 1728.671637 1559.891773 1284.240018 1332.566675 1533.090221 1404.134291 1312.131368 1.54242031 1.28659861 1.674982725 1.317453175 1.188822865 0.978743477 1.015574132 1.168396898 1.070117158 1 10.35769645 -8.514910918 3.937785002 1.302700133 1.051910686 0.272806192 0.190530556 0.293792898 10.25601791 0.035176717 0.077754574 3.06E-09 8.514910918 -0.250789447 SSGPTSLFAVTVAPPGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGPTSLFAVTVAPPGAR 18 0 A0A1W2PPS1;Q00839-2;Q00839;A0A1X7SBS1;A0A1W2PP35;A0A1W2PP22 A0A1W2PPS1 HNRNPU Heterogeneous nuclear ribonucleoprotein U 0 0 ; ; 237.32 2.28E-52 3568300 431.5 461.25 314.26 384.7 547.25 281.35 193.581 170.56 552 416.82 FALSE FALSE TRUE 426.240712 467.7434896 319.7295635 429.1808241 519.3217904 263.372643 210.0237653 175.4948845 502.6277375 405.9909563 1.049877357 1.152103224 0.787528782 1.057119173 1.279146204 0.648715541 0.517311438 0.432263039 1.238026931 1 8.665303781 -8.07197453 4.936783413 1.032697373 0.49533472 0.773178208 0.136139398 0.065029092 2.955042821 0.016344426 0.044108299 8.47E-09 8.07197453 -0.537362653 down EVEK(ac)VKLDQK ddPTM_HeLa_Romidepsin_16h_R1 1 EVEKVKLDQK 10 2 M0QXN5;P37198 M0QXN5 NUP62 Nuclear pore glycoprotein p62 0 1 EVEK(0.5)VK(0.5)LDQK 100.25 0.0014743 0 169.48 125.82 216.98 492.53 2828.3 3792 3815.8 4134.8 218.2 281.21 FALSE TRUE FALSE 167.4143126 127.5912973 220.7564459 549.478636 2683.961297 3549.703438 4139.913957 4254.433914 198.6836455 273.9041237 0.611215013 0.465824667 0.805962477 2.006098443 9.798907958 12.9596568 15.11446378 15.53256613 0.725376613 1 8.097527176 -8.587563531 1.735237759 0.728659165 15.02925143 0.99145014 0.579023358 0.021623929 0.129705358 0.088720901 0.231042521 2.58E-09 8.587563531 14.30059227 up SSGPYGGGGQYFAKPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGPYGGGGQYFAKPR 16 1 F8W6I7;P09651-3;P09651-2;P09651;H0YH80 F8W6I7 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1;Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed" 0 0 159.12 1.11E-10 817180 165.19 0 143.22 197.86 351.09 389.57 403.97 525.43 203 0 FALSE FALSE TRUE 163.1766007 0 145.712684 220.7375042 333.1725672 364.6777343 438.2832017 540.6324881 184.8431716 0 0 SSGRNS(ph)PSAASTSSNDSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSGRNSPSAASTSSNDSK 18 1 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 S(0.005)S(0.014)GRNS(0.738)PS(0.244)AASTSSNDSK 117.22 0.0005484 1557300 410.47 417 604.51 430.18 302.05 362.75 946.93 48.893 539.15 508.75 TRUE FALSE FALSE 405.4670338 422.8705369 615.031243 479.9194357 286.6352614 339.5714457 1027.362211 50.30764181 490.9270737 495.5326017 0.81824492 0.853365723 1.241151926 0.968492152 0.578438755 0.6852656 2.073248475 0.101522365 0.990705903 1 8.952836167 SSGS(ph)ETEQVVDFSDR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSETEQVVDFSDR 15 0 O95251-4;O95251;O95251-2 O95251-4 KAT7 Histone acetyltransferase KAT7 1 0 S(0.108)S(0.008)GS(0.775)ET(0.108)EQVVDFSDR 296.95 9.15E-118 23668000 1446.7 1123.6 1196.7 977.78 794.79 813.35 974.96 856.98 1634.5 1233.3 TRUE FALSE FALSE 1429.067064 1139.41807 1217.528062 1090.835524 754.2289005 761.37956 1057.773078 881.7753642 1488.306226 1201.258688 1.189641397 0.948520149 1.013543605 0.908077115 0.627865511 0.63381815 0.880553946 0.734042861 1.23895564 1 10.23033115 -9.154410282 1.914881165 1.079419136 0.725846309 0.720587005 0.104904715 0.142111886 1.019469339 0.017011777 0.031395178 7.01E-10 9.154410282 -0.353572827 SSGS(ph)PEPSPAIAK ddPTM_HeLa_Romidepsin_16h_R1 4 SSGSPEPSPAIAK 13 0 K7ELE9;Q66K64 K7ELE9 DCAF15 DDB1- and CUL4-associated factor 15 1 0 S(0.008)SGS(0.992)PEPSPAIAK;S(0.046)S(0.278)GS(0.546)PEPS(0.131)PAIAK;S(0.127)S(0.002)GS(0.784)PEPS(0.087)PAIAK;S(0.009)S(0.029)GS(0.96)PEPS(0.001)PAIAK ;;; 179.83 6.36E-07 82713000 12281.7 12133.2 11073.3 11908.41 10215.2 11114.6 9783.5 11204.1 12186 11293.2 TRUE FALSE FALSE 12132.00592 12304.01151 11266.02614 13285.31639 9693.880226 10404.41293 10614.51025 11528.27296 11096.05364 10999.80104 1.102929578 1.118566733 1.02420272 1.207777882 0.881277779 0.94587283 0.964972931 1.048043771 1.008750395 1 13.42518981 -8.735343845 24.99999853 1.063482227 0.959382025 0.397323893 0.069393876 205.2693367 196650.8078 0.010375452 0.020745479 1.84E-09 8.735343845 -0.104100201 SSGS(ph)PYGGGYGSGGGS(ph)GGYGSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 2 0 S(0.303)S(0.03)GS(0.667)PY(0.005)GGGYGS(0.109)GGGS(0.885)GGYGS(0.001)R;S(0.193)S(0.25)GS(0.556)PYGGGYGS(0.001)GGGS(0.994)GGYGS(0.005)R ; 129.26 0.0011572 11494700 2434.71 2764.89 2447.94 2158.29 2435.83 2884.9 2510.55 2922.7 3043.22 2738.56 TRUE FALSE FALSE 2405.034818 2803.814194 2490.545369 2407.841645 2311.520506 2700.564201 2723.796054 3007.263713 2771.026781 2667.411816 0.901636112 1.051136602 0.93369361 0.902688378 0.866578041 1.012428671 1.021138183 1.127408859 1.038844757 1 11.38122486 -7.443228583 1.651181474 0.95034679 1.151087172 0.420186886 0.059087432 0.467820173 1.589084798 0.008338861 0.132904064 3.60E-08 7.443228583 0.200740382 SSGS(ph)PYGGGYGSGGGSGGYGSR ddPTM_HeLa_Romidepsin_16h_R1 22 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 SS(0.002)GS(0.998)PYGGGYGSGGGSGGYGSR;S(0.051)S(0.013)GS(0.935)PYGGGYGSGGGSGGYGSR;SSGS(0.999)PYGGGYGSGGGSGGYGSR;SS(0.001)GS(0.999)PYGGGYGSGGGSGGYGSR;S(0.005)S(0.003)GS(0.991)PY(0.001)GGGY(0.001)GSGGGSGGYGSR;SSGS(0.999)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(0.999)PYGGGYGSGGGSGGYGSR;S(0.004)SGS(0.996)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR;S(0.006)S(0.002)GS(0.938)PY(0.052)GGGY(0.001)GSGGGSGGYGSR;S(0.001)SGS(0.999)PYGGGYGSGGGSGGYGSR;S(0.01)S(0.01)GS(0.698)PY(0.28)GGGY(0.001)GS(0.001)GGGSGGYGSR;SS(0.002)GS(0.998)PYGGGYGSGGGSGGYGSR;SSGS(0.999)PYGGGYGSGGGSGGYGSR;S(0.003)S(0.008)GS(0.989)PYGGGYGSGGGSGGYGSR;S(0.018)S(0.001)GS(0.981)PYGGGYGSGGGSGGYGSR;SS(0.002)GS(0.998)PYGGGYGSGGGSGGYGSR;S(0.001)S(0.001)GS(0.998)PYGGGYGSGGGSGGYGSR;SSGS(1)PYGGGYGSGGGSGGYGSR ;;;;;;;;;;;;;;;;;;;;; 306.2 1.61E-149 1428315500 41396.45 41320.04 37864.69 33150.81 37875.74 37416.56 32981.65 35423.17 44841.65 41002.42 TRUE FALSE FALSE 40891.89414 41901.74461 38523.70905 36983.86263 35942.79965 35025.76257 35783.11053 36448.08354 40830.90052 39937.17122 1.023905622 1.049191601 0.964607855 0.926051132 0.899983613 0.877021619 0.895985105 0.912635583 1.022378383 1 15.28544453 -9.321957904 2.133885011 1.014301755 0.896453495 0.917137837 0.017139711 0.068330201 0.607835133 0.002953373 0.004986162 4.76E-10 9.321957904 -0.11784826 LTQYHGGS(ph)LPNVSQLR ddPTM_HeLa_Romidepsin_16h_R1 1 LTQYHGGSLPNVSQLR 16 0 Q6UUV7;Q6UUV7-3;H0YK33 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 0 LT(0.029)QYHGGS(0.971)LPNVSQLR 100.77 0.0053171 13332000 1270.1 1592.2 1597.6 1561.1 844.64 633.83 521.05 553.03 1813.2 1643.9 TRUE FALSE FALSE 1254.619533 1614.615033 1625.405558 1741.601727 801.534869 593.3303086 565.307974 569.0310505 1651.022851 1601.191241 0.783553832 1.008383628 1.015122689 1.087691265 0.500586594 0.370555555 0.353054626 0.355379817 1.031121585 1 10.64492991 -8.631570573 4.958855757 0.925630645 0.37049152 0.911039366 0.090133368 0.056864503 2.256044655 0.01614606 0.032869887 2.34E-09 8.631570573 -0.555139125 down SSGSETEQVVDFS(ph)DRETK ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSETEQVVDFSDRETK 18 1 O95251-4;O95251 O95251-4 KAT7 Histone acetyltransferase KAT7 1 0 SSGSET(0.001)EQVVDFS(0.749)DRET(0.25)K 66.122 0.010549 9583500 2265.9 1845.6 1876.7 1961.5 1545 1596.1 1228.6 1324 2059.3 2138.1 TRUE FALSE FALSE 2238.282339 1871.582405 1909.363176 2188.297859 1466.152885 1494.114361 1332.957253 1362.307851 1875.11105 2082.551854 1.074778683 0.898696665 0.91683824 1.05077713 0.704017469 0.717444014 0.640059574 0.654153148 0.90039105 1 11.0241367 -8.734959376 6.949327829 1.01593378 0.677046809 0.811318981 0.06780987 0.046369468 7.821452648 0.009632842 0.019026791 1.84E-09 8.734959376 -0.338886971 SSGSGSSVADERVDY(ph)VVVDQQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSGSSVADERVDYVVVDQQK 22 1 Q13480-2;B7Z3B9;Q13480 Q13480-2 GAB1 GRB2-associated-binding protein 1 1 0 SSGSGSSVADERVDY(0.999)VVVDQQK 93.029 0.00094252 7554000 1562.7 1436 1196.9 1603.4 1625 983.97 854.58 899.85 1610.8 1137 TRUE FALSE FALSE 1543.653211 1456.216046 1217.731542 1788.792652 1542.070186 921.0974926 927.1680039 925.88574 1466.726014 1107.460576 1.393867416 1.314914569 1.099571008 1.615220163 1.392437997 0.831720345 0.837201815 0.836043973 1.32440472 1 10.11303963 -8.247211216 24.00339506 1.238187506 0.835209926 0.608002482 0.167173029 341.5831109 576260.0942 0.029286972 0.074230557 5.66E-09 8.247211216 -0.40297758 SSGSPYGGGYGS(ph)GGGSGGYGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 1 0 S(0.001)S(0.001)GS(0.114)PY(0.09)GGGY(0.341)GS(0.45)GGGS(0.003)GGYGSR 72.523 0.0034812 12268000 1330.3 1628.5 1551.5 1025.2 1323.6 1331.9 1009.9 1249.9 1725.9 1796 TRUE FALSE FALSE 1314.085792 1651.426066 1578.503207 1143.738448 1256.051753 1246.795889 1095.680881 1286.063884 1571.531181 1749.339661 0.751189618 0.944028254 0.902342319 0.653811534 0.718014792 0.71272373 0.626339701 0.735171055 0.898356801 1 10.77259472 -9.264781778 24.95278527 0.886467119 0.688625589 0.715055755 0.06602944 180.3403736 1346336.85 0.014757421 0.023123179 5.44E-10 9.264781778 -0.197841529 SSGSPYGGGYGSGGGSGGYGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSPYGGGYGSGGGSGGYGSR 22 0 P51991;P51991-2;H7C1J8 P51991 HNRNPA3 Heterogeneous nuclear ribonucleoprotein A3 0 0 185.86 5.06E-21 0 740.93 748.34 656.73 600.66 648.03 603.09 725.44 691.6 965.73 711.35 FALSE FALSE TRUE 731.8992602 758.8751502 668.1601102 670.1111354 614.958611 564.5544954 787.0588555 711.6103548 879.3526901 692.8690245 1.056331333 1.09526494 0.964338261 0.967154125 0.887553909 0.814806948 1.135941755 1.027048879 1.269147067 1 9.43643885 -9.659976903 13.83979766 1.032490786 0.963375185 0.169861134 0.111013612 1.083903346 141.8032769 0.013490358 0.019078227 2.19E-10 9.659976903 -0.069115601 TSS(ph)EASMDAAYLDK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSEASMDAAYLDK 14 0 Q5W0B1 Q5W0B1 RNF219 RING finger protein 219 1 0 T(0.072)S(0.016)S(0.644)EAS(0.257)MDAAY(0.011)LDK 90.689 0.025621 5986700 4408.9 3971.3 3999.6 3150.8 2841.8 2224.6 1572.2 1720.1 4657.4 4016.6 TRUE FALSE FALSE 4355.162631 4027.208066 4069.21136 3515.110321 2696.772342 2082.45524 1705.742629 1769.86838 4240.830479 3912.248153 1.113212266 1.029384617 1.040120974 0.898488589 0.689315257 0.532291194 0.436000622 0.452391646 1.08398811 1 11.93378217 -8.629621065 1.297134716 1.054751395 0.438288785 0.986075567 0.030507517 0.04887345 0.161124521 0.006950889 0.020499006 2.35E-09 8.629621065 -0.61646261 down SSGTAS(ph)SVAFTPLQGLEIVNPQAAEKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSGTASSVAFTPLQGLEIVNPQAAEKK 27 1 E7EVX8;Q8WWY3 E7EVX8 PRPF31 U4/U6 small nuclear ribonucleoprotein Prp31 1 0 S(0.046)S(0.053)GT(0.053)AS(0.616)S(0.19)VAFT(0.042)PLQGLEIVNPQAAEKK 75.887 1.51E-05 10644000 1902.8 1665.8 1756 2434.8 1528 1575.6 1184 1461 1433.1 1800 TRUE FALSE FALSE 1879.607942 1689.251176 1786.562443 2716.323032 1450.020458 1474.924245 1284.56893 1503.27173 1304.919947 1753.235741 1.072079412 0.963504871 1.019008683 1.549319906 0.827053901 0.841258372 0.732684659 0.857427039 0.744292348 1 10.77580428 -8.566646712 24.99997383 1.065036343 0.807922146 0.281158275 0.19061388 105.5811036 60306.84067 0.022988616 0.045977256 2.71E-09 8.566646712 -0.257114198 SSGVVPQS(ph)APPVPTASSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSGVVPQSAPPVPTASSR 18 0 P41162 P41162 ETV3 ETS translocation variant 3 1 0 S(0.173)S(0.082)GVVPQS(0.585)APPVPT(0.087)AS(0.046)S(0.028)R;SSGVVPQS(0.999)APPVPTASSR ; 169.49 4.08E-12 6286600 4302.8 4312.9 4357.5 5047 8535.2 6528.5 4895.7 7461.6 3664.6 3391.5 TRUE FALSE FALSE 4250.355819 4373.617119 4433.34046 5630.557887 8099.616895 6111.34992 5311.540636 7677.489624 3336.828998 3303.388341 1.286665502 1.323979099 1.342058517 1.704479554 2.451911812 1.850024668 1.607906818 2.324125665 1.010123138 1 11.68973087 -9.258253952 2.12670014 1.154985042 2.015810566 0.737118872 0.244362408 0.126593944 1.118080905 0.039523304 0.0685463 5.52E-10 9.258253952 0.860825524 SSHYDELLAAEAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSHYDELLAAEAR 13 0 Q7KZF4;H7C597 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 0 0 ; ; 190.78 4.39E-11 8592700 4218.1 4054.6 4728.1 4105.8 6398.8 6416.1 5218.8 5669.7 5847.8 5019.5 FALSE FALSE TRUE 4166.688175 4111.680765 4810.390597 4580.531914 6072.245359 6006.131917 5662.084742 5833.743824 5324.758122 4889.092666 0.852241604 0.840990557 0.98390252 0.936887931 1.241998418 1.228475778 1.158105425 1.193216047 1.089109674 1 12.25535103 -8.767671615 24.91825913 0.926053832 1.203712027 0.743835748 0.072437783 45.01889938 179999.21 0.009993837 0.018447537 1.71E-09 8.767671615 0.277658196 PEPTK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPTKSAPAPKKGSK 15 3 P58876 P58876 HIST1H2BD Histone H2B type 1-D 0 3 ; PEPTK(1)SAPAPK(1)K(1)GSK;PEPTK(1)SAPAPK(1)K(1)GSK 233.28 3.40E-55 192533000 1955.69 1427.73 2216.17 9329.8 44473 62410 63342 67545 548.28 1255.9 FALSE TRUE FALSE 1931.853298 1447.82962 2254.741509 10408.55537 42203.37686 58422.20242 68722.2679 69499.30801 499.2404636 1223.271537 1.579251409 1.183571739 1.843206059 8.508785711 34.50041596 47.75898127 56.17907866 56.8142934 0.408119088 1 10.25652897 -8.581661229 1.53905417 1.109144628 56.16379949 0.99529198 1.614338682 0.01672222 0.078289124 0.240468955 0.667195878 2.62E-09 8.581661229 55.05465486 up GKLEAIITPPPAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 GKLEAIITPPPAKK 14 2 O75367-2;O75367-3;O75367;D6RCF2 O75367-2 H2AFY Core histone macro-H2A.1;Histone H2A 0 1 GKLEAIITPPPAK(1)K 92.269 0.027605 2155800 1434.1 1413.3 1629.2 2391.3 4072.3 5439.8 4941.7 5907.4 2130.3 1657.9 FALSE TRUE FALSE 1416.620638 1433.196474 1657.555543 2667.793357 3864.475335 5092.214336 5361.447875 6078.321299 1939.760633 1614.827519 0.877258172 0.887522944 1.026459806 1.652060871 2.393119568 3.153410675 3.320136554 3.764068439 1.201218464 1 10.65716436 -8.577041556 1.121610814 0.923987785 3.627110127 0.985489721 0.129133216 0.031252692 0.074505491 0.016516344 0.056573069 2.65E-09 8.577041556 2.703122342 up SSILLDVKPWDDETDMAK ddPTM_HeLa_Romidepsin_16h_R1 1 SSILLDVKPWDDETDMAK 18 1 P24534 P24534 EEF1B2 Elongation factor 1-beta 0 0 90.453 0.008777 21752000 1778.5 2047.6 2379.9 1824.9 2476.2 2201.2 1915.9 2203.1 2520.6 2224.5 FALSE FALSE TRUE 1756.822958 2076.426167 2421.321161 2035.903524 2349.830274 2060.550424 2078.636498 2266.843223 2295.151223 2166.707169 0.810826208 0.958332624 1.117511953 0.939630215 1.084516776 0.951005495 0.959352758 1.046215776 1.059280763 1 11.08128847 -9.998202661 24.97506894 0.90929485 1.012710368 0.022557085 0.083472541 63.03060005 875827.9943 0.013711557 0.017950293 1.00E-10 9.998202661 0.103415518 SSINSVDGES(ph)PNGSSDR ddPTM_HeLa_Romidepsin_16h_R1 2 SSINSVDGESPNGSSDR 17 0 E9PGE5;Q9NUY8-2;Q9NUY8 E9PGE5 TBC1D23 TBC1 domain family member 23 1 0 SSINS(0.003)VDGES(0.997)PNGSSDR;SSINSVDGES(0.999)PNGS(0.001)SDR ; 278.19 1.23E-102 11815000 4548.1 4854.5 3905.8 4076.3 5619.9 5390.8 4885.5 5334.1 4883.1 4819.3 TRUE FALSE FALSE 4492.666008 4922.841778 3973.778811 4547.620986 5333.095532 5046.345278 5300.474248 5488.433768 4446.343306 4694.093891 0.957089081 1.048731 0.846548642 0.968796341 1.136128858 1.075041402 1.129179426 1.169221131 0.947220786 1 12.19663098 -8.763267202 24.99944505 0.973231473 1.123780965 0.699363006 0.052956631 21.82028702 298446.9475 0.007602003 0.014311041 1.72E-09 8.763267202 0.150549492 SSINSVDGESPNGS(ph)SDR ddPTM_HeLa_Romidepsin_16h_R1 1 SSINSVDGESPNGSSDR 17 0 E9PGE5;Q9NUY8-2;Q9NUY8 E9PGE5 TBC1D23 TBC1 domain family member 23 1 0 SSINS(0.02)VDGES(0.223)PNGS(0.721)S(0.036)DR 103.67 0.0027751 9432600 2699.4 2578.2 2613.9 2387.9 3117.9 3133.8 2557.2 2673.7 2947.6 3113.4 TRUE FALSE FALSE 2666.498675 2614.495967 2659.393833 2664.000233 2958.781929 2933.560294 2774.408504 2751.059291 2683.959274 3032.513419 0.879303174 0.862154789 0.876960285 0.878479289 0.975686343 0.96736927 0.914887462 0.907187838 0.885060972 1 11.56629831 -12.37097621 1.121020067 0.999461596 0.906684628 0 0.050088955 0.3810104 0.864158414 0.027141154 0.007180257 4.26E-13 12.37097621 -0.092776968 SSINSVDGESPNGSS(ph)DR ddPTM_HeLa_Romidepsin_16h_R1 1 SSINSVDGESPNGSSDR 17 0 E9PGE5;Q9NUY8-2;Q9NUY8 E9PGE5 TBC1D23 TBC1 domain family member 23 1 0 SSINS(0.004)VDGES(0.129)PNGS(0.209)S(0.658)DR 78.228 0.020562 25266000 986.71 1003.4 1114.9 653 1159.1 1261.6 1027.8 1143.1 1124.8 1066.4 TRUE FALSE FALSE 974.683599 1017.525892 1134.304367 728.5029325 1099.946802 1180.987832 1115.101306 1176.173795 1024.195071 1038.694774 0.93837345 0.979619727 1.092047823 0.701363818 1.058970189 1.136992176 1.073560139 1.132357478 0.986040458 1 10.02055606 -8.534866391 24.99976562 0.96083636 1.10818772 0.38337977 0.094964112 176.8561316 368825.6202 0.01294716 0.025909378 2.92E-09 8.534866391 0.14735136 SSISGSLPSS(ph)GSLQAVSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSISGSLPSSGSLQAVSSR 19 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 0 SSISGSLPS(0.24)S(0.398)GS(0.308)LQAVS(0.033)S(0.02)R 122.01 1.08E-06 0 1049.7 1252.1 1018.7 999.57 1099.8 813.44 1155.1 929.15 1028.4 1228 TRUE FALSE FALSE 1036.905853 1269.727097 1036.430046 1115.144987 1043.673102 761.4638093 1253.214165 956.0334893 936.4173283 1196.096383 0.866908275 1.061559181 0.866510476 0.93232034 0.872566055 0.636624122 1.047753495 0.799294691 0.782894541 1 10.22411793 -8.68535411 4.350919476 0.94001329 0.836347883 0.086087287 0.118397592 0.298618499 10.71194289 0.015462195 0.031437205 2.06E-09 8.68535411 -0.103665407 SSISGSLPSSGS(ph)LQAVSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSISGSLPSSGSLQAVSSR 19 0 A0A1B0GTL5;Q9BXF6 A0A1B0GTL5 RAB11FIP5 Rab11 family-interacting protein 5 1 0 SSIS(0.001)GS(0.008)LPS(0.169)S(0.169)GS(0.62)LQAVS(0.022)S(0.013)R 100.58 0.00041866 0 678 731.43 702.32 568.6 778.97 692.18 634.71 629.97 963.24 793.66 TRUE FALSE FALSE 669.7362752 741.7270907 714.543585 634.3442073 739.2162542 647.9519319 688.6222516 648.197188 877.0854019 773.0405988 0.866366238 0.959493061 0.924328665 0.820583302 0.956245061 0.838186161 0.890797007 0.838503423 1.134591641 1 9.594400374 -16.52287872 0.247726034 1.722137965 0.872118199 0.545646098 0.061114905 28.83941487 0.380203193 10.18291594 0.026521766 3.00E-17 16.52287872 -0.850019766 SSIT(ph)EPEGPNGPNIQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSITEPEGPNGPNIQK 16 0 Q13625-2;Q13625;Q13625-3 Q13625-2 TP53BP2 Apoptosis-stimulating of p53 protein 2 1 0 S(0.013)S(0.013)IT(0.973)EPEGPNGPNIQK 137.81 0.0021858 6023100 1269.2 1461.4 1134.1 1255.3 1904.7 1624.5 1120.4 1361 1514.3 1419.4 TRUE FALSE FALSE 1253.730502 1481.973628 1153.838535 1400.443692 1807.496052 1520.699693 1215.566748 1400.378388 1378.857215 1382.523783 0.906841906 1.07193355 0.834588561 1.012961736 1.307388758 1.099944689 0.879237495 1.012914501 0.997347917 1 10.43308858 -8.998643612 24.99989461 0.955700092 1.074874295 0.176195435 0.114484339 60.34801184 1112235.057 0.017235573 0.031070399 1.00E-09 8.998643612 0.119174202 SSKAS(ph)LGSLEGEAEAEASSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 S(0.213)S(0.213)KAS(0.347)LGS(0.227)LEGEAEAEASSPK 60.104 0.0072113 5087500 1944.9 1946.5 1326.1 1905.5 1544.6 2098 1632.9 1535.7 2297.8 2038.7 TRUE FALSE FALSE 1921.194811 1973.902878 1349.180214 2125.822876 1465.773298 1963.944571 1771.598485 1580.133057 2092.279013 1985.73428 0.967498436 0.9940418 0.679436432 1.070547503 0.738151782 0.989026876 0.892162916 0.795742448 1.053655081 1 10.95545687 SSKASLGS(ph)LEGEAEAEASSPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSKASLGSLEGEAEAEASSPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 S(0.109)S(0.109)KAS(0.109)LGS(0.673)LEGEAEAEASSPK 60.943 0.0066456 4436000 2290.3 2266.2 1828.7 2256.9 2068.9 1943.6 1662.8 1991 2302 2342.6 TRUE FALSE FALSE 2262.384943 2298.103623 1860.527756 2517.853397 1963.316313 1819.410233 1804.03819 2048.606444 2096.103355 2281.738914 0.991517885 1.007172034 0.815399056 1.103480061 0.860447399 0.797378798 0.790641812 0.897826842 0.918642944 1 11.15591801 -8.587251057 8.779047398 0.988430282 0.825472867 0.439313275 0.074691196 0.153243676 19.17427892 0.009471143 0.018977364 2.59E-09 8.587251057 -0.162957416 SSLDVLPSQVYSLVGS(ph)SPLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLDVLPSQVYSLVGSSPLR 20 0 H3BLW0;Q5SQL3;J3KP92;Q86Z02-4;Q86Z02-3;Q86Z02;Q86Z02-2 H3BLW0 HIPK1 Homeodomain-interacting protein kinase 1 1 0 SSLDVLPSQVYS(0.052)LVGS(0.474)S(0.474)PLR 147.84 2.60E-05 5786200 2887.1 2814.3 2806.3 2943.2 3098.5 3081.9 2366.5 2447.1 2639.4 2928.9 TRUE FALSE FALSE 2851.910915 2853.919789 2855.142474 3283.506632 2940.371983 2884.976536 2567.510451 2517.902978 2403.325454 2852.806756 0.999685979 1.000390154 1.000818744 1.15097408 1.030694412 1.011276537 0.899994521 0.882605516 0.842442429 1 11.47816631 -7.743489295 5.010096807 1.013767863 0.887820987 0.288194211 0.070178227 0.10509735 6.933176153 0.006601976 0.024378052 1.81E-08 7.743489295 -0.125946876 SSLET(ph)LEDIEENAPLRR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLETLEDIEENAPLRR 17 1 Q8TDN4-2;Q8TDN4;V9GYB4 Q8TDN4-2 CABLES1 CDK5 and ABL1 enzyme substrate 1 1 0 S(0.304)S(0.304)LET(0.392)LEDIEENAPLRR 95.954 0.0022631 3450100 593.4 524.12 698.87 439.89 447.96 467.12 394.68 307.62 639.52 446.21 TRUE FALSE FALSE 586.1674126 531.4985751 711.0335392 490.7521515 425.0989296 437.2725396 428.2041093 316.5204994 582.3197295 434.6173999 1.348697527 1.222911405 1.635998787 1.129159007 0.978099197 1.006109143 0.985243825 0.728273878 1.339844492 1 8.763602124 -8.780974359 3.657225151 1.212365273 0.928759114 0.474971653 0.17654396 0.224477536 6.390559444 0.03056158 0.060224111 1.66E-09 8.780974359 -0.283606159 SSLFS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLFSPR 7 0 Q7RTP6 Q7RTP6 MICAL3 Protein-methionine sulfoxide oxidase MICAL3 1 0 SSLFS(1)PR 134.77 0.013757 11927000 3237.4 3024.6 4774.4 1888.2 3777.1 4727 3559.7 3984.6 3639.8 3191.2 TRUE FALSE FALSE 3197.941324 3067.180398 4857.496429 2106.522568 3584.340493 4424.959956 3862.060829 4099.888114 3314.247172 3108.292164 1.028841935 0.986773519 1.562754134 0.677710607 1.153154306 1.423598466 1.242502514 1.319016327 1.066259861 1 11.6019064 -7.431590443 0.334657924 0.99778613 1.589979022 0.171680132 0.218446431 6.854626955 0.590687736 0.078330227 1.616106535 3.70E-08 7.431590443 0.592192892 SSLGQS(ph)AS(ph)ETEEDTVSVSKK ddPTM_HeLa_Romidepsin_16h_R1 2 SSLGQSASETEEDTVSVSKK 20 1 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 2 0 S(0.008)S(0.008)LGQS(0.925)AS(0.773)ET(0.235)EEDT(0.045)VS(0.004)VS(0.001)KK;S(0.003)S(0.003)LGQS(0.968)AS(0.844)ET(0.183)EEDTVSVSKK ; 87.49 0.00045357 16706000 4561.9 4387.6 4230.3 4860.8 4581.4 4028.4 4386.1 4917 5533.8 5088 TRUE FALSE FALSE 4506.297808 4449.368748 4303.926597 5422.828567 4347.594062 3770.998241 4758.655225 5059.265637 5038.843068 4955.813027 0.909295364 0.897808034 0.868460245 1.094235908 0.877271608 0.760924236 0.96021686 1.020875003 1.016754071 1 12.27490604 -12.24364977 0.922613871 1.001164682 0.92055133 0.131220616 0.085462352 1.129637303 1.689267805 0.061794527 0.016106722 5.71E-13 12.24364977 -0.080613352 SSLGQS(ph)ASET(ph)EEDTVSVSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLGQSASETEEDTVSVSK 19 0 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 2 0 S(0.002)S(0.002)LGQS(0.994)AS(0.048)ET(0.696)EEDT(0.238)VS(0.018)VS(0.003)K 96.561 0.008978 8413100 2672.5 2410 2960.1 1932.5 2870.5 2814.4 2433 2585.5 3289.4 3218.6 TRUE FALSE FALSE 2639.926542 2443.928043 3011.619299 2155.944743 2724.007674 2634.568923 2639.658959 2660.307363 2995.187826 3134.980308 0.842087121 0.779567271 0.960650149 0.687705992 0.868907427 0.840378141 0.842001767 0.848588221 0.955408816 1 11.61424067 -12.04681787 0.642758349 1.012679747 0.830549796 0.424287687 0.06621796 0.56521705 0.389206515 0.056535405 0.01355014 8.98E-13 12.04681787 -0.182129951 SSLGQS(ph)ASET(ph)EEDTVSVSKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 2 0 S(0.002)S(0.002)LGQS(0.897)AS(0.334)ET(0.759)EEDT(0.005)VSVSKK 72.935 0.00096627 0 1543.1 2072.5 1408 1571.1 1576.9 1942.7 1541.2 1626.4 1943.8 1893.7 TRUE FALSE FALSE 1524.292104 2101.676709 1432.505649 1752.757974 1496.424909 1818.56774 1672.10949 1673.457318 1769.94166 1844.501401 0.82639791 1.139428091 0.776635707 0.950261124 0.811289657 0.985940015 0.906537392 0.90726812 0.959577292 1 10.84901517 SSLGQS(ph)ASETEEDTVSVSK ddPTM_HeLa_Romidepsin_16h_R1 2 SSLGQSASETEEDTVSVSK 19 0 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 SSLGQS(0.779)AS(0.219)ET(0.001)EEDTVSVSK;S(0.038)S(0.07)LGQS(0.446)AS(0.446)ETEEDTVSVSK ; 329.64 2.64E-188 78967000 16446.6 11965.2 13174 8094.2 13033.3 12367.2 14557 13003.3 16752.6 14465 TRUE FALSE FALSE 16246.14251 12133.6464 13403.28794 9030.089488 12368.16207 11576.97583 15793.47122 13379.52997 15254.2055 14089.19721 1.153092136 0.861202112 0.951316653 0.640922925 0.877847182 0.821691659 1.120963173 0.949630399 1.082688053 1 13.78230179 -10.25082354 24.75760671 1.072293509 0.887825529 0.349375067 0.118410266 562.496912 1311822.535 0.021257377 0.025889856 5.61E-11 10.25082354 -0.18446798 SSLGQS(ph)ASETEEDTVSVSKK ddPTM_HeLa_Romidepsin_16h_R1 2 SSLGQSASETEEDTVSVSKK 20 1 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 S(0.001)S(0.001)LGQS(0.931)AS(0.052)ET(0.015)EEDTVSVSKK;S(0.004)S(0.004)LGQS(0.801)AS(0.056)ET(0.134)EEDT(0.001)VSVSKK ; 103.63 0.00016995 46273000 3956.3 3801.5 3914.9 4534.9 4170.7 3573.3 3512.6 3587.7 4038.2 3927.3 TRUE FALSE FALSE 3908.079094 3855.017617 3983.037192 5059.246475 3957.853616 3344.977662 3810.960156 3691.504439 3677.013278 3825.26818 1.021648394 1.007777085 1.041243909 1.322586087 1.034660429 0.874442655 0.996259603 0.965031539 0.961243266 1 11.90134518 -8.385753179 10.97400347 1.038182259 0.950434998 0.193316947 0.098772247 0.717003228 60.43382083 0.014499083 0.032433105 4.11E-09 8.385753179 -0.087747261 SSLGQSAS(ph)ETEEDTVSVSK ddPTM_HeLa_Romidepsin_16h_R1 3 SSLGQSASETEEDTVSVSK 19 0 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 SSLGQS(0.207)AS(0.792)ET(0.002)EEDTVSVSK;SSLGQS(0.225)AS(0.759)ET(0.01)EEDT(0.006)VSVSK;SSLGQS(0.01)AS(0.973)ET(0.006)EEDT(0.01)VSVSK ;; 285.1 3.08E-107 67624200 10210.4 10488.4 9291.63 7620.33 9443.5 9839.5 8889.31 10231.3 10896.8 11046.4 TRUE FALSE FALSE 10085.95172 10636.05597 9453.346922 8501.428409 8961.562956 9210.787706 9644.36777 10527.32652 9922.162916 10759.41294 0.937407252 0.988534973 0.878611777 0.790138687 0.832904454 0.856067869 0.896365613 0.978429454 0.922184414 1 13.39331174 -9.715120169 6.49535526 0.970966692 0.8663559 0.428755278 0.050249954 0.1289224 12.94711591 0.008266436 0.011641956 1.93E-10 9.715120169 -0.104610791 SSLGQSAS(ph)ETEEDTVSVSKK ddPTM_HeLa_Romidepsin_16h_R1 2 SSLGQSASETEEDTVSVSKK 20 1 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 SSLGQS(0.043)AS(0.478)ET(0.478)EEDTVSVSKK;S(0.004)S(0.004)LGQS(0.142)AS(0.621)ET(0.215)EEDT(0.012)VS(0.001)VSKK ; 78.736 0.0014968 218285700 2793.3 3139.1 3204.5 3068.4 2807.9 2799.1 2735.3 3054.8 3010.8 2986.6 TRUE FALSE FALSE 2759.254185 3183.292332 3260.272978 3423.182845 2664.602385 2620.246544 2967.636314 3143.185818 2741.506507 2909.007701 0.948520756 1.094288039 1.120750893 1.176752761 0.915983269 0.900735513 1.020154162 1.08050103 0.942419818 1 11.5063114 -10.276758 24.24336987 0.975690358 1.040841295 0.16282074 0.082079299 952.6458106 1507661.89 0.015189555 0.017406591 5.29E-11 10.276758 0.065150938 SSLGQSASET(ph)EEDTVSVSKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLGQSASETEEDTVSVSKK 20 1 E9PPJ0;Q13435;E9PJ04;H0YCG1 E9PPJ0 SF3B2 Splicing factor 3B subunit 2 1 0 S(0.001)S(0.001)LGQS(0.073)AS(0.294)ET(0.631)EEDTVSVSKK 89.829 0.00070031 239550000 1424 1406.1 1373 1558.4 1233.1 1087.2 924.94 1261.3 1516.4 1551.5 TRUE FALSE FALSE 1406.64374 1425.895113 1396.896489 1738.58954 1170.170306 1017.731429 1003.504381 1297.793725 1380.769386 1511.191806 0.930817474 0.943556673 0.924367432 1.150475759 0.774336058 0.673462776 0.66404832 0.858788223 0.913695654 1 10.56147107 -8.590647592 8.954751152 0.972342852 0.725044343 0.671451393 0.080671068 0.1198185 14.58305884 0.010904167 0.021842174 2.57E-09 8.590647592 -0.247298509 SSLGSLQT(ph)PEAVTTR ddPTM_HeLa_Romidepsin_16h_R1 3 SSLGSLQTPEAVTTR 15 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 S(0.001)SLGS(0.142)LQT(0.858)PEAVTTR;SS(0.002)LGS(0.167)LQT(0.829)PEAVT(0.002)TR;S(0.002)SLGS(0.152)LQT(0.698)PEAVT(0.114)T(0.035)R ;; 142.19 0.0012426 68344000 4882.6 4660.2 4860.1 4880.6 7129.9 7367.4 6093.9 6939.9 5378.3 4665.5 TRUE FALSE FALSE 4823.088993 4725.806418 4944.688002 5444.917936 6766.034598 6896.646917 6611.515714 7140.695057 4897.251378 4544.289637 1.061351581 1.039943929 1.088110221 1.198189018 1.488909189 1.517651265 1.45490632 1.571355619 1.077671489 1 12.14983907 -8.920462561 1.904559645 1.032355435 1.517503795 0.969731943 0.037908346 0.036711673 0.268554806 0.005878671 0.012131793 1.20E-09 8.920462561 0.48514836 SSLNSS(ph)PWSGLMALGNSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLNSSPWSGLMALGNSR 18 0 Q8TCJ2 Q8TCJ2 STT3B Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 1 0 S(0.001)S(0.001)LNS(0.087)S(0.886)PWS(0.01)GLMALGNS(0.016)R 81.656 0.016961 7064000 542.26 773.26 779.73 711.1 804.9 1376.3 565.32 1136.9 711.13 778.54 TRUE FALSE FALSE 535.6507265 784.1459746 793.3008736 793.3207278 763.8229495 1288.358872 613.3382667 1169.794408 647.5247517 758.3134186 0.706371157 1.034065804 1.046138515 1.046164697 1.007265506 1.698979393 0.808818955 1.542626543 0.853901218 1 9.566650442 -9.000039716 0.972078004 0.870427188 1.294623876 0.331458003 0.242166126 0.463000011 0.85557755 0.041221987 0.107435826 1.00E-09 9.000039716 0.424196689 SSLS(ph)GDEEDELFK ddPTM_HeLa_Romidepsin_16h_R1 3 SSLSGDEEDELFK 13 0 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 S(0.006)S(0.003)LS(0.991)GDEEDELFK;S(0.001)SLS(0.999)GDEEDELFK;S(0.005)S(0.005)LS(0.99)GDEEDELFK ;; 152.74 0.00076887 19467800 8425.55 8149.05 8452.77 7895.6 7748.38 6912.27 6732.75 6457.03 9310.85 9861.5 TRUE FALSE FALSE 8322.856156 8263.77254 8599.886916 8808.526422 7352.951255 6470.598255 7304.629617 6643.853976 8478.064257 9605.296808 0.866486098 0.860334949 0.895327556 0.917048853 0.765510052 0.673648965 0.760479323 0.691686484 0.882644693 1 13.22961448 -4.799465397 0.124582679 1.062528008 5.26E-14 0.671631154 0.056819833 24.35995764 0.251189131 0.222264039 4.420461257 1.59E-05 4.799465397 -1.062528008 SSLS(ph)GDEEDELFKGATLK ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSGDEEDELFKGATLK 18 1 Q5T1M5;Q5T1M5-2 Q5T1M5 FKBP15 FK506-binding protein 15 1 0 S(0.051)S(0.051)LS(0.897)GDEEDELFKGATLK 62.002 0.015761 3826500 1569.3 1699.9 1185.8 3252 1595.3 1178.9 1054.9 1225.7 1840.6 1315.2 TRUE FALSE FALSE 1550.172768 1723.831237 1206.438352 3628.011541 1513.885888 1103.572095 1144.50318 1261.163696 1675.972126 1281.030914 1.21009786 1.345659357 0.941771458 2.832103035 1.181771549 0.861471868 0.893423544 0.984491226 1.308299517 1 10.32308958 -5.492590007 13.5170124 1.186904773 1.057257587 0 0.554546128 0 0 0.071662311 0 3.22E-06 5.492590007 -0.129647186 SSLSS(ph)LSPPSSPLDTPFLPASR ddPTM_HeLa_Romidepsin_16h_R1 1 SSLSSLSPPSSPLDTPFLPASR 22 0 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 1 0 SSLS(0.004)S(0.493)LS(0.493)PPS(0.009)S(0.001)PLDTPFLPASR 154.46 4.12E-08 4541000 1656.5 1648.1 1864.6 1459.4 2039.9 2648.3 2185.1 2378.4 1897.3 1816.6 TRUE FALSE FALSE 1636.309941 1671.301995 1897.052581 1628.142695 1935.796291 2479.082177 2370.702339 2447.215252 1727.600736 1769.40447 0.924780042 0.944556218 1.072141849 0.920164226 1.094038318 1.401082804 1.339830649 1.383072832 0.976374122 1 10.78904816 -8.402968688 3.271366634 0.968631382 1.372589376 0.939986809 0.0452567 0.04272126 0.852757192 0.006948823 0.016701665 3.95E-09 8.402968688 0.403957994 SSLSSLS(ph)PPSSPLDTPFLPASR ddPTM_HeLa_Romidepsin_16h_R1 2 SSLSSLSPPSSPLDTPFLPASR 22 0 Q9ULE0;Q9ULE0-2 Q9ULE0 WWC3 Protein WWC3 1 0 S(0.001)S(0.001)LS(0.07)S(0.407)LS(0.459)PPS(0.048)S(0.015)PLDTPFLPASR;SSLS(0.001)S(0.007)LS(0.605)PPS(0.184)S(0.184)PLDT(0.018)PFLPASR ; 116.09 2.78E-06 8160900 1634 1836.7 1630.53 2037.77 2443.67 2330.98 1997.87 2191.38 1647.2 1911.79 TRUE FALSE FALSE 1614.08418 1862.557111 1658.908691 2273.386555 2318.960401 2182.037901 2167.569028 2254.784123 1499.870307 1862.12142 0.866798567 1.000233975 0.890870312 1.220858388 1.245332542 1.171802159 1.164032057 1.210868474 0.805463215 1 10.86273143 -9.257792286 24.95873171 0.938089113 1.201102655 0.847338842 0.061050167 88.97527244 608897.5995 0.008677595 0.014028226 5.52E-10 9.257792286 0.263013542 SSLSTSS(ph)PESAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSLSTSSPESAR 12 0 Q8N7B6;D6RF51;D6RGK2;D6RAM4;D6RC23;D6R9D1;D6REJ6;D6RF67;D6RF08;D6RBZ2;D6RDH3;D6REQ4;D6R9F1;D6RB63;D6RC13;Q8N7B6-2;Q8N7B6-3;Q8N7B6-4;D6R9N9 Q8N7B6 PACRGL PACRG-like protein 1 0 SSLS(0.015)T(0.085)S(0.085)S(0.815)PESAR;SSLS(0.035)T(0.188)S(0.117)S(0.639)PES(0.022)AR ; 126.66 0.0051997 25909900 4725.6 4577.1 4222.4 7175.8 4853.1 5130.5 4347.8 4989.6 5146.8 5493.1 TRUE FALSE FALSE 4668.00257 4641.536534 4295.889101 8005.499759 4605.428198 4802.677608 4717.102023 5133.966204 4686.457318 5350.38847 0.872460494 0.867513931 0.802911625 1.496246451 0.860765199 0.897631571 0.881637296 0.959550177 0.87590973 1 12.38542793 -9.646776831 0.002622506 1.279934716 0.618490115 0 0.188893688 1210438.602 1713.129987 215080.3363 216990.9512 2.26E-10 9.646776831 -0.661444601 SSLVSSS(ph)PASVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSLVSSSPASVR 12 0 S4R3K6;Q86VQ0 S4R3K6 LCA5 Lebercilin 1 0 SSLVS(0.068)S(0.068)S(0.864)PASVR;SSLVS(0.067)S(0.067)S(0.866)PASVR ; 190.66 4.89E-10 21086000 3537.2 3516.6 3812.2 4435.9 13334.7 13497.7 11856.4 14361.1 3698.7 3500.4 TRUE FALSE FALSE 3494.087246 3566.106787 3878.549742 4948.79963 12654.1805 12635.24053 12863.48232 14776.61577 3367.879008 3409.459103 1.024821574 1.045945025 1.137585061 1.451491125 3.711492092 3.705936968 3.772880662 4.334005871 0.987804489 1 11.73532716 -8.787831216 3.39934338 1.030151008 3.909776899 0.985858428 0.16343693 0.018792007 0.452110881 0.02483378 0.049195776 1.63E-09 8.787831216 2.879625891 up SSPAAKPGSTPSRPSSAK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SSPAAKPGSTPSRPSSAKR 19 3 Q15555-2;Q15555;K7EL66;K7ERD8;Q15555-4;Q15555-5;Q15555-3 Q15555-2 MAPRE2 Microtubule-associated protein RP/EB family member 2 0 1 SSPAAKPGSTPSRPSSAK(1)R 60.949 0.009885 1564700 501.61 412.27 407.32 537.24 624.17 471.93 427.43 591.51 729.19 538.19 FALSE TRUE FALSE 495.4961844 418.0739479 414.4092337 599.3582166 592.3162758 441.7751961 463.7358935 608.6244086 663.9694201 524.2077462 0.945228658 0.797534853 0.790543895 1.143360091 1.129926599 0.842748317 0.884641436 1.161036656 1.266615049 1 9.033994862 -9.246487358 24.9649512 0.944906515 1.019025295 0.04252756 0.157840451 1825.510139 3048002.71 0.019367454 0.032029791 5.67E-10 9.246487358 0.07411878 SSPELEDT(ph)ATSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPELEDTATSSK 13 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 S(0.007)S(0.411)PELEDT(0.574)AT(0.008)S(0.001)SK 124.47 0.0080068 6729000 1347 1690.2 2006.9 832.24 1006.2 1638.4 1649.1 1742.2 1826.3 2236.7 TRUE FALSE FALSE 1330.582246 1713.99468 2041.829253 928.4675046 954.8498594 1533.711528 1789.174513 1792.607808 1662.951154 2178.590212 0.610753798 0.786744873 0.937225019 0.426178131 0.43828796 0.703992664 0.821253352 0.822829277 0.76331526 1 11.08917914 -12.3987542 0.888537657 1.020170401 0.684692617 0.098489311 0.172325899 0.654174324 0.830774614 0.155272192 0.031234595 3.99E-13 12.3987542 -0.335477784 SSPEPVALT(ph)ESETEYVIR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPEPVALTESETEYVIR 18 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 1 0 SSPEPVALT(0.597)ES(0.397)ET(0.007)EYVIR 168.68 7.70E-07 1651000 646.28 545.52 677.47 583.11 522.23 602.14 449.19 603.57 735.94 649.22 TRUE FALSE FALSE 638.4028908 553.1998449 689.2610812 650.5319218 495.5786544 563.6651973 487.3441874 621.0333457 670.1156832 632.3531708 1.009566996 0.874827344 1.089993872 1.028747782 0.783705494 0.891377198 0.770683551 0.982098888 1.05971744 1 9.304586722 -8.771811421 24.99984447 1.002452802 0.853261149 0.493089181 0.075952658 119.4158999 287829.6946 0.009886379 0.018062358 1.69E-09 8.771811421 -0.149191653 SSPET(ph)GTTGDVAWQISPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPETGTTGDVAWQISPK 18 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 S(0.223)S(0.223)PET(0.267)GT(0.267)T(0.021)GDVAWQISPK 93.738 0.0097459 9631700 1869.8 1835.2 1893.8 1909.7 2034.8 1879.8 1480.5 1674.4 2115.3 1987.1 TRUE FALSE FALSE 1847.010158 1861.035994 1926.760795 2130.508499 1930.956563 1759.686847 1606.253633 1722.846122 1926.10227 1935.474856 0.954293027 0.961539742 0.995497714 1.100767852 0.997665538 0.909175772 0.829901576 0.890141309 0.995157475 1 10.91847185 -8.084474045 3.693544013 0.988306655 0.860928739 0.660632374 0.0410432 0.122680824 3.127519147 0.006445266 0.018462393 8.23E-09 8.084474045 -0.127377916 SSPETGTTGDVAWQIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPETGTTGDVAWQISPK 18 0 E9PDC2;A0A088AWP5;Q8WUY3-4;Q8WUY3;Q8WUY3-2;Q8WUY3-3;H7BZH9 E9PDC2 PRUNE2 Protein prune homolog 2 1 0 SSPETGTTGDVAWQIS(1)PK;SSPETGTTGDVAWQIS(1)PK ; 219.23 3.96E-35 6000300 2251.8 2101.57 2294.07 2714.5 2947 2964 2242.93 2726.4 2081.55 2399.11 TRUE FALSE FALSE 2224.354195 2131.155958 2333.997326 3028.363262 2796.603593 2774.609966 2433.444418 2805.284082 1895.370955 2336.780776 0.951888264 0.912005088 0.998808853 1.295955227 1.19677619 1.187364255 1.041366158 1.200490911 0.811103452 1 11.19030668 -9.392861596 6.761335627 0.971079847 1.176785321 0.700221549 0.080015148 0.100626922 5.126599656 0.009791609 0.01498393 4.05E-10 9.392861596 0.205705474 SSPGAVAGLSNAPGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPGAVAGLSNAPGTPR 17 0 V9GYB2;U3KPY3;Q9BWG4-2;Q9BWG4 V9GYB2 SSBP4 Single-stranded DNA-binding protein 4 1 0 SSPGAVAGLS(0.005)NAPGT(0.995)PR;SSPGAVAGLSNAPGT(1)PR ; 191.41 5.22E-13 23985000 2623.3 2765.79 2547.1 2278.7 2308.5 2377.2 1670.26 2088.9 2804.2 2517.4 TRUE FALSE FALSE 2591.326211 2804.726864 2591.431207 2542.174016 2190.688631 2225.304592 1812.131843 2149.339026 2553.385329 2451.997585 1.056822497 1.143853844 1.056865318 1.036776721 0.893430175 0.907547628 0.739043078 0.876566534 1.041349039 1 11.25974184 -8.514952759 1.720282488 1.041161651 0.820682569 0.769667673 0.054153361 0.141334819 0.822000693 0.008656973 0.023877882 3.06E-09 8.514952759 -0.220479082 SSPGQTPEEGAQALAEFAALHGPALR ddPTM_HeLa_Romidepsin_16h_R1 1 SSPGQTPEEGAQALAEFAALHGPALR 26 0 Q14166 Q14166 TTLL12 Tubulin--tyrosine ligase-like protein 12 0 0 146.5 3.26E-08 4542300 1714.7 1666.7 1455.1 1236.3 1666.2 1560.1 1214.6 1547.4 1618.7 1538.7 FALSE FALSE TRUE 1693.800577 1690.163846 1480.425405 1379.246823 1581.167597 1460.414645 1317.768094 1592.171578 1473.919418 1498.724352 1.13016151 1.127734959 0.987790318 0.920280518 1.055008944 0.974438457 0.879259813 1.062351176 0.983449302 1 10.54951935 -9.629432555 7.822368277 1.068053348 0.974623414 0.251946363 0.067401399 0.233191814 15.59277148 0.011179753 0.015821493 2.35E-10 9.629432555 -0.093429934 SSPGSVAAS(ph)PSGGGGR ddPTM_HeLa_Romidepsin_16h_R1 2 SSPGSVAASPSGGGGR 16 0 Q9BXB5-2;Q9BXB5 Q9BXB5-2 OSBPL10 Oxysterol-binding protein-related protein 10 1 0 SSPGSVAAS(1)PSGGGGR;SSPGSVAAS(1)PSGGGGR ; 271.41 1.09E-86 26652000 4182.3 4015.9 3973.5 4065.3 3330.7 3142.6 2121.23 2275.93 4183.2 3437 TRUE FALSE FALSE 4131.324519 4072.435946 4042.657101 4535.349114 3160.72195 2941.798002 2301.407223 2341.780444 3809.044115 3347.706245 1.234076175 1.216485452 1.207590154 1.354763167 0.944145549 0.878750341 0.687457935 0.699517901 1.137807154 1 11.70895722 -8.228294718 1.956088693 1.143949384 0.702269763 0.782805428 0.102358374 0.153789755 1.122022263 0.018865793 0.061751812 5.91E-09 8.228294718 -0.441679622 SSPNPFVGS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPNPFVGSPPK 12 0 P98082-3;P98082 P98082-3 DAB2 Disabled homolog 2 1 0 S(0.133)S(0.017)PNPFVGS(0.85)PPK 153.2 0.0014229 223680000 3913.4 4003.3 3981.8 2961 3721.2 2893.2 2566 2452.7 4547.6 4704.3 TRUE FALSE FALSE 3865.701976 4059.658562 4051.101559 3303.364752 3531.293278 2708.333857 2783.955976 2523.665005 4140.851266 4582.081608 0.843656291 0.885985652 0.88411816 0.720931017 0.770674462 0.591070629 0.607574507 0.550768236 0.903705263 1 12.16178744 -6.698905791 0.213727518 1.006191482 1.58E-15 0.886223613 0.049020488 3.480581741 0.112131421 0.048114003 0.969051772 2.00E-07 6.698905791 -1.006191482 SSPNPFVGS(ph)PPKGLSIQNGVK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPNPFVGSPPKGLSIQNGVK 21 1 P98082-3;P98082 P98082-3 DAB2 Disabled homolog 2 1 0 SSPNPFVGS(0.996)PPKGLS(0.004)IQNGVK;SSPNPFVGS(0.927)PPKGLS(0.073)IQNGVK ; 100.41 0.00016813 169947000 4874.8 4685 4270.1 6239.8 3772.7 2951.7 2645.3 3203.1 4907.2 4303.3 TRUE FALSE FALSE 4815.384063 4750.955553 4344.419299 6961.275035 3580.165041 2763.095896 2869.991716 3295.776645 4468.287742 4191.499646 1.148845156 1.133473925 1.03648328 1.660807736 0.854148955 0.659214155 0.684717156 0.786300113 1.066035577 1 12.03325079 -8.534028047 24.99915844 1.117128434 0.715731104 0.569998444 0.18133657 129.2414016 289786.7011 0.026455078 0.052946106 2.92E-09 8.534028047 -0.401397329 SSPNVANQPPS(ph)PGGK ddPTM_HeLa_Romidepsin_16h_R1 2 SSPNVANQPPSPGGK 15 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 SSPNVANQPPS(1)PGGK;SSPNVANQPPS(1)PGGK ; 191.51 1.91E-12 36898000 7351.7 7690.1 6844.5 9286.4 14024.2 16543 14671.7 16499.7 8810.9 7507.4 TRUE FALSE FALSE 7262.094653 7798.36143 6963.625651 10360.13726 13308.49274 15485.95569 15917.91383 16977.09279 8022.831037 7312.356666 0.993126428 1.066463493 0.952309354 1.416798679 1.820000494 2.117779041 2.176851398 2.321699223 1.097160793 1 12.83612073 -8.726485908 1.353773724 0.993565996 2.24631108 0.984517721 0.065620391 0.026946837 0.098357834 0.008396556 0.022326495 1.88E-09 8.726485908 1.252745083 up SSPRPTAEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SSPRPTAEKK 10 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 0 1 SSPRPTAEK(1)K 98.754 0.018135 906360 0 157.56 251.23 191.75 370.02 1010.3 806.2 76.889 197.19 122.3 FALSE TRUE FALSE 0 159.7781338 255.6025528 213.9210372 351.1364987 945.7450906 874.6786079 79.1136619 179.5528325 119.1226284 0 1.341291206 2.145709478 1.795805215 2.947689314 7.939256408 7.342673847 0.664136302 1.50729408 1 6.896303681 -8.647027441 2.41002186 0.752816011 5.504049058 0.440381512 1.947497199 0.161742874 1.900836119 0.279554049 0.627848667 2.25E-09 8.647027441 4.751233047 SSPST(ph)GSLDSGNESK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSTGSLDSGNESK 15 0 A0A0U1RQT1;A0A087X1H5;Q15057 A0A0U1RQT1 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 0 S(0.001)SPS(0.002)T(0.992)GS(0.004)LDSGNESK 264.92 5.22E-84 16729000 1762.1 1670.3 1639.6 835.96 2366.3 2738 2082.1 2619.9 1726.6 1641.3 TRUE FALSE FALSE 1740.622847 1693.814527 1668.13655 932.6176285 2245.538881 2563.050636 2258.953522 2695.702673 1572.168572 1598.658789 1.088801975 1.059522231 1.043460031 0.583375036 1.404639249 1.603250583 1.413030433 1.686227662 0.983429724 1 10.64264633 -8.540743464 24.98993292 1.014970021 1.544037234 0.765300707 0.15382717 85.98559732 120279.9663 0.021349126 0.04270459 2.88E-09 8.540743464 0.529067213 SSPSTGS(ph)LDSGNESK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSTGSLDSGNESK 15 0 A0A0U1RQT1;A0A087X1H5;Q15057 A0A0U1RQT1 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 0 SSPS(0.003)T(0.009)GS(0.576)LDS(0.411)GNES(0.001)K 106.6 0.0055481 20730000 4473 4334.3 4734.3 1176 4781 5101.5 4609.5 5207.7 4995.2 4781.5 TRUE FALSE FALSE 4418.481356 4395.318389 4816.698506 1311.974653 4537.00773 4775.530614 5001.030815 5358.376583 4548.416801 4657.275941 0.948726554 0.943753053 1.034230861 0.281704299 0.974176275 1.025391382 1.073810287 1.150538781 0.976626006 1 12.18527065 -10.86969519 1.14828929 0.986733886 0.917456767 0.010671462 0.226367087 1.932966024 5.35339478 0.056978417 0.050236426 1.35E-11 10.86969519 -0.069277119 SSPSVLIHS(ph)LGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPSVLIHSLGK 12 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 SSPSVLIHS(1)LGK 93.766 0.023393 6414400 961.47 999.78 906.63 1119.7 1189.3 1120.7 1000.7 821.79 1306.6 1143.6 TRUE FALSE FALSE 949.7512338 1013.854929 922.4095148 1249.164982 1128.605583 1049.090887 1085.699433 845.5671971 1189.734424 1113.889107 0.852644332 0.910193773 0.828098155 1.121444652 1.013211796 0.941827046 0.974692567 0.759112547 1.068090545 1 10.1213899 -7.254941925 23.99447083 0.942179623 0.759112399 0.295163021 0.089157019 444.090469 1639902.036 0.012245349 0.152820892 5.56E-08 7.254941925 -0.183067224 SSPYGTLKPEEMS(ph)GPGLAEPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSPYGTLKPEEMSGPGLAEPK 21 1 Q5JSZ5;Q5JSZ5-5;A0A494C0D3;A0A494C065;H0Y412 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 SSPY(0.001)GT(0.003)LKPEEMS(0.996)GPGLAEPK 68.639 0.0078383 36042000 1718.9 1856.7 2039.9 1476.2 1687 1331.3 1437.1 1506.8 1848.9 1762.7 TRUE FALSE FALSE 1697.949386 1882.838671 2075.403604 1646.88519 1600.906095 1246.234227 1559.167238 1550.396881 1683.529753 1716.9048 0.988959543 1.096647101 1.20880529 0.959217535 0.932437311 0.725860995 0.908126786 0.903018549 0.980560922 1 10.74559433 -8.683039709 3.005226415 1.019719077 0.85066809 0.5121088 0.083784996 0.183651029 3.342950266 0.012966779 0.0273968 2.07E-09 8.683039709 -0.169050987 SSQDGDTPAQAS(ph)PPEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SSQDGDTPAQASPPEEK 17 0 E9PNX6;A0A0C4DGE6;E9PNT2;E9PIR1;A0A0G2JRG8;A0A0G2JNY3;Q6ZUM4-2;Q6ZUM4-3;Q6ZUM4 E9PNX6 ARHGAP27 Rho GTPase-activating protein 27 1 0 SSQDGDT(0.002)PAQAS(0.998)PPEEK;SSQDGDTPAQAS(1)PPEEK ; 110.32 0.0019533 4298500 1587.94 1569.4 1749.76 1457.26 1843.83 1847.13 1712.24 1704.29 1535.36 1706 TRUE FALSE FALSE 1568.585576 1591.494054 1780.213839 1625.755258 1749.732475 1729.104354 1857.677623 1753.600942 1398.033556 1661.677874 0.943976929 0.957763282 1.071335104 0.978381721 1.052991378 1.040577347 1.117952915 1.055319427 0.841338492 1 10.69842502 -8.759632835 0.80892395 0.973793516 1.086621716 0.462400341 0.055222163 0.394181037 0.469504657 0.006864656 0.025256052 1.74E-09 8.759632835 0.1128282 SSQLDSGVPSS(ph)PGGR ddPTM_HeLa_Romidepsin_16h_R1 1 SSQLDSGVPSSPGGR 15 0 I3L4X5;Q70CQ4 I3L4X5 USP31 Ubiquitin carboxyl-terminal hydrolase 31 1 0 SSQLDS(0.003)GVPS(0.101)S(0.896)PGGR 162.7 0.00014144 4180300 2091.8 2371.8 2597.9 2310.9 1761.7 1573.1 1294.3 1370.9 2423.8 1896.1 TRUE FALSE FALSE 2066.304337 2405.190263 2643.11536 2578.097131 1671.793875 1472.583987 1404.23781 1410.564829 2207.009257 1846.839049 1.118832926 1.302328031 1.431156311 1.39595117 0.905219042 0.797353721 0.76034661 0.763772474 1.195019815 1 10.85084243 -8.534452633 23.8789838 1.131239119 0.785611425 0.649382938 0.145599772 88.04679048 181655.6552 0.026293755 0.052629083 2.92E-09 8.534452633 -0.345627694 EK(ac)LQEEMLQR ddPTM_HeLa_Romidepsin_16h_R1 1 EKLQEEMLQR 10 1 P08670;B0YJC4 P08670 VIM Vimentin 0 1 EK(1)LQEEMLQR 84.687 0.030539 3484100 289.24 292.98 214.58 232.41 667.96 792.32 797.27 797.53 592.11 328.68 FALSE TRUE FALSE 285.7146316 297.1045801 218.3146749 259.2823377 633.8715087 741.6933091 864.9900939 820.6052723 539.1501986 320.1408462 0.89246541 0.92804334 0.68193321 0.809900832 1.979976989 2.316771877 2.701904815 2.56326327 1.684103122 1 8.322562949 -8.571888507 2.518920998 0.91286254 2.547185411 0.85893469 0.280234389 0.03743409 0.47765011 0.022428946 0.051945115 2.68E-09 8.571888507 1.634322872 up SSQPS(ph)PTAVPASDS(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSQPSPTAVPASDSPPTK 18 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 2 0 S(0.006)S(0.008)QPS(0.98)PT(0.006)AVPAS(0.006)DS(0.94)PPT(0.055)K 134.83 0.012386 8317400 6976.1 7331.7 7035.9 3976.8 4576.9 3967.3 3290.1 2886.6 7420.3 7756.8 TRUE FALSE FALSE 6891.07261 7434.915865 7158.356888 4436.616327 4343.323714 3713.802334 3569.561012 2970.119217 6756.609784 7555.277218 0.912087328 0.984069234 0.947464492 0.587220852 0.574872846 0.49155077 0.472459303 0.393118496 0.894290122 1 12.88326898 -9.142720898 2.092515996 0.962259135 0.47735011 0.9474901 0.052546436 0.049578873 0.424847585 0.008530497 0.015574684 7.20E-10 9.142720898 -0.484909025 QLLLQQQQQQQVSGLKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 QLLLQQQQQQQVSGLKSPK 19 1 Q9H334-8;Q9H334-4;A0A3B3IST0;A0A3B3IUB6;A0A3B3IRS5;C9J0F0;Q9H334;Q9H334-3;Q9H334-7;Q9H334-6;A0A3B3IST6;A0A087WVT2;G5E965;A0A3B3IU15;A0A3B3IU08;A0A3B3IRY1 Q9H334-8 FOXP1 Forkhead box protein P1 1 0 QLLLQQQQQQQVS(0.425)GLKS(0.575)PK;QLLLQQQQQQQVS(0.216)GLKS(0.784)PK ; 92.551 0.001208 45962000 4955.9 4050.5 3901.2 4672.9 2683.7 2141.1 1574.78 1827.17 4246.5 4312.1 TRUE FALSE FALSE 4895.495585 4107.523045 3969.09875 5213.202685 2546.740775 2004.29062 1708.541774 1880.036281 3866.682404 4200.07102 1.165574477 0.97796514 0.945007532 1.241217746 0.606356598 0.477203983 0.406788782 0.447620117 0.9206231 1 12.03619801 -8.626474416 4.697005784 1.070130379 0.454426423 0.886976054 0.098159539 0.045191924 1.688767045 0.014088538 0.028815449 2.36E-09 8.626474416 -0.615703956 down SHILEDDENS(ph)VDISMLK ddPTM_HeLa_Romidepsin_16h_R1 4 SHILEDDENSVDISMLK 17 0 O75717-2;O75717 O75717-2 WDHD1 WD repeat and HMG-box DNA-binding protein 1 1 0 SHILEDDENS(0.979)VDIS(0.021)MLK;SHILEDDENS(0.997)VDIS(0.003)MLK;SHILEDDENS(0.794)VDIS(0.206)MLK;SHILEDDENS(0.994)VDIS(0.006)MLK ;;; 135.81 0.00041625 184086000 28987.8 26072.7 27228.7 30199.9 13616.7 9365.8 7639 8646 26150.6 24363.5 TRUE FALSE FALSE 28634.48554 26439.75215 27702.6041 33691.75453 12921.78899 8767.355607 8287.856469 8896.158369 23811.62484 23730.53276 1.206651609 1.114165974 1.167382308 1.419763934 0.544521656 0.369454647 0.349248647 0.37488237 1.003417204 1 14.53445687 -8.624475394 5.559246054 1.126244317 0.377763116 0.911484205 0.114025443 0.046915565 2.173817143 0.018255 0.03695222 2.37E-09 8.624475394 -0.748481201 down SSQPSPT(ph)AVPASDS(ph)PPTKQEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSQPSPTAVPASDSPPTKQEVK 22 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 2 0 S(0.002)S(0.003)QPS(0.265)PT(0.497)AVPAS(0.296)DS(0.611)PPT(0.326)KQEVK 66.36 0.0048164 24089000 4283.4 4809.2 3840.6 3492 3294.9 3006.8 2426.7 3151.8 5815.5 5726.2 TRUE FALSE FALSE 4231.192273 4876.904044 3907.444032 3895.76147 3126.748958 2814.675184 2632.823837 3242.99236 5295.347115 5577.432499 0.758627249 0.874399474 0.700581142 0.69848653 0.560607225 0.50465428 0.472049431 0.581448966 0.949423792 1 12.44538543 -8.93454389 0.154807441 1.143251433 0.150678392 0.867557133 0.063938125 2.612465522 0.14959984 0.269979575 0.674277276 1.16E-09 8.93454389 -0.992573041 SSQPSPT(ph)AVPASDSPPTK ddPTM_HeLa_Romidepsin_16h_R1 2 SSQPSPTAVPASDSPPTK 18 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 SSQPS(0.305)PT(0.694)AVPASDSPPTK;S(0.003)SQPS(0.09)PT(0.907)AVPASDSPPTK ; 251.41 4.27E-62 35341000 18334.2 16432.5 17360.9 11956 12737.1 10919.2 9509 10005.5 17888.8 18084.2 TRUE FALSE FALSE 18110.73572 16663.83717 17663.05918 13338.40897 12087.07826 10221.49836 10316.69422 10294.99336 16288.78092 17614.36988 1.028179597 0.946036519 1.002764181 0.757245878 0.686205544 0.58029316 0.585697603 0.584465606 0.92474389 1 14.10446525 -8.999408241 1.39289806 1.011826857 0.5824101 0.948725038 0.040795695 0.038671307 0.149100863 0.004548318 0.009918752 1.00E-09 8.999408241 -0.429416757 SSQPSPTAVPASDS(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSQPSPTAVPASDSPPTK 18 0 Q3KQU3-4;Q3KQU3;Q3KQU3-2;C9JIR3;E9PLH3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 SSQPSPTAVPAS(0.004)DS(0.964)PPT(0.032)K 175.52 3.85E-08 5821000 3424.8 3404.1 3883.8 1755.2 2746.6 2663.5 2419.3 2205.4 3642.4 3747.6 TRUE FALSE FALSE 3383.05722 3452.023009 3951.39591 1958.144482 2606.430753 2493.310946 2624.795282 2269.209769 3316.614621 3650.236812 0.926804861 0.945698372 1.082503989 0.536443136 0.71404429 0.683054573 0.719075341 0.621660973 0.90860259 1 11.83377435 -9.263144367 24.99999992 0.970745295 0.663278284 0.85242313 0.066080608 40.63633819 595845.7114 0.009548373 0.015066501 5.46E-10 9.263144367 -0.307467011 SSQQPST(ph)PQQAPPGQPQQGTFVAHK ddPTM_HeLa_Romidepsin_16h_R1 2 SSQQPSTPQQAPPGQPQQGTFVAHK 25 0 E7ERS3;Q86VM9;H3BRH3 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 S(0.007)S(0.007)QQPS(0.259)T(0.727)PQQAPPGQPQQGTFVAHK;S(0.005)S(0.005)QQPS(0.242)T(0.747)PQQAPPGQPQQGTFVAHK ; 104.67 6.29E-06 30389000 4348.2 4206.3 3675.8 4466.3 4310 5251.6 4651.4 4977.2 4619.9 4111.9 TRUE FALSE FALSE 4295.202466 4265.516402 3739.775757 4982.714621 4090.044617 4916.039709 5046.4898 5121.207429 4206.684573 4005.072245 1.072440696 1.065028579 0.933759875 1.244101059 1.02121619 1.227453441 1.260024661 1.278680412 1.050339249 1 11.96761255 -7.933629088 0.595273615 1.02912865 1.368482229 0.594998571 0.075432053 0.899514267 0.342481779 0.013663259 0.179722729 1.17E-08 7.933629088 0.339353579 SSQQQTQPQK(ac)QR ddPTM_HeLa_Romidepsin_16h_R1 1 SSQQQTQPQKQR 12 1 F5H7M9;F5H3E1;F5H2E6;A0A0C4DGG8;Q8IX12-2;Q8IX12 F5H7M9 CCAR1 Cell division cycle and apoptosis regulator protein 1 0 1 SSQQQTQPQK(1)QR 108.37 0.025067 102490 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 SSQSEGIFLGS(ph)ES(ph)DEDSVR ddPTM_HeLa_Romidepsin_16h_R1 1 SSQSEGIFLGSESDEDSVR 19 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 2 0 SSQS(0.002)EGIFLGS(0.632)ES(0.971)DEDS(0.394)VR 91.926 0.0021897 0 902.6 623.68 688.77 758.54 633.17 638.32 637.82 708.45 1015.2 1012 TRUE FALSE FALSE 891.598764 632.4601834 700.7577529 846.2459638 600.8569722 597.5334121 691.9964149 728.947883 924.3979694 985.7080941 0.904526167 0.641630303 0.710918128 0.858515791 0.609568873 0.606197124 0.702029758 0.73951699 0.937800932 1 9.945016662 -10.40160826 3.44416698 0.960440474 0.695902741 0.726196149 0.071184149 0.094884597 2.007238429 0.013570446 0.015318704 3.97E-11 10.40160826 -0.264537733 SSQSEGIFLGS(ph)ESDEDSVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSQSEGIFLGSESDEDSVR 19 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 SSQSEGIFLGS(0.969)ES(0.031)DEDSVR;SSQSEGIFLGS(0.974)ES(0.026)DEDSVR ; 181.49 1.98E-10 19136400 6206.8 5920.4 6252.8 5056.5 4974.7 4654 3583.1 4246.4 6566.8 6274 TRUE FALSE FALSE 6131.149134 6003.747547 6361.627361 5641.156322 4720.822496 4356.62442 3887.448425 4369.262884 5979.448961 6111.000576 1.003297097 0.982449187 1.041012398 0.923115004 0.7725122 0.712915073 0.63613943 0.714983223 0.978472983 1 12.5771929 -8.717465507 1.885010193 1.003027969 0.680979838 0.965793544 0.026391843 0.034840335 0.251247045 0.003546297 0.008212013 1.92E-09 8.717465507 -0.32204813 SSQSEGIFLGSES(ph)DEDS(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 SSQSEGIFLGSESDEDSVR 19 0 Q9BYW2;C9JG86;Q9BYW2-3;Q9BYW2-2;H7BZ93;H7BXT4 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 2 0 SSQS(0.014)EGIFLGS(0.2)ES(0.999)DEDS(0.787)VR 99.991 0.00094251 0 988.93 1035.7 873.02 775.64 905.31 896.05 732.61 709.94 1005.9 1033.3 TRUE FALSE FALSE 976.8765408 1050.280612 888.2145469 865.3231463 859.1086525 838.7952969 794.8378751 730.4809938 915.9297847 1006.454717 0.970611518 1.043544825 0.882518142 0.859773551 0.853598913 0.833415833 0.789740325 0.725796185 0.910055633 1 9.975066548 -8.575515919 0.529978228 0.995987482 0.71645411 0.76572412 0.044622393 0.365016977 0.149707971 0.008441445 0.049979395 2.66E-09 8.575515919 -0.279533372 SSS(ph)APLIHGLSDLSQVFQPYTLR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 1 0 S(0.124)S(0.124)S(0.752)APLIHGLSDLSQVFQPYTLR;S(0.163)S(0.163)S(0.674)APLIHGLSDLSQVFQPYTLR;S(0.106)S(0.106)S(0.788)APLIHGLSDLSQVFQPYTLR ;; 151.18 1.28E-07 59685800 2502.78 2082.95 2315.69 2216.69 5618.64 6143.46 6127.69 6752.14 2555.12 2453.45 TRUE FALSE FALSE 2472.275155 2112.273825 2355.993613 2472.994128 5331.899835 5750.912733 6648.175836 6947.502518 2326.583668 2389.709015 1.034550708 0.883904196 0.985891419 1.034851571 2.231192083 2.406532635 2.782002241 2.907258781 0.973584505 1 11.22261924 -8.607440816 1.99172066 0.993811423 2.740713823 0.971629139 0.135071478 0.036035041 0.287071925 0.020026313 0.048705259 2.47E-09 8.607440816 1.7469024 up SSS(ph)APNVHINTIEPVNIDDLIR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSAPNVHINTIEPVNIDDLIR 22 0 H7C560;A0A2U3TZI2;A0A2R8Y8E0;P15056;A0A2R8Y679;A0A2R8Y492;A0A2R8YDP5 H7C560 BRAF Serine/threonine-protein kinase B-raf 1 0 S(0.131)S(0.131)S(0.738)APNVHINTIEPVNIDDLIR;S(0.05)S(0.05)S(0.9)APNVHINTIEPVNIDDLIR ; 134.15 4.31E-05 79596000 7115.7 6188.5 6971.9 5987.9 6480.6 6386.7 5479.3 5788.5 9087.6 7640.3 TRUE FALSE FALSE 7028.971111 6275.621865 7093.242995 6680.249172 6149.8708 5978.610482 5944.711605 5955.981115 8274.782296 7441.803905 0.944525172 0.843293097 0.953161772 0.897665305 0.82639517 0.803381889 0.798826693 0.800341045 1.111932322 1 12.86143666 -8.72210048 0.259201564 1.012913792 0.700789406 0.754341977 0.049021639 1.233413566 0.130225129 0.028468462 0.12385543 1.90E-09 8.72210048 -0.312124386 SSS(ph)ASSPEMK ddPTM_HeLa_Romidepsin_16h_R1 3 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SS(0.017)S(0.955)AS(0.026)S(0.003)PEMK;SS(0.002)S(0.991)AS(0.007)S(0.001)PEMK;SS(0.002)S(0.996)AS(0.001)S(0.001)PEMK ;; 130.01 0.010145 27740400 23485.2 26183.6 36290 18459.3 10911.6 14083.9 24044.3 4563.9 40449 33898.5 TRUE FALSE FALSE 23198.95335 26552.21341 36921.61223 20593.65112 10354.74034 13183.98424 26086.62224 4695.949246 36831.14013 33017.81208 0.70261934 0.804178464 1.118233157 0.623713378 0.313610736 0.399299148 0.790077252 0.142224725 1.115493057 1 15.0109569 -9.016101537 7.440330281 0.86895642 0.440578448 0.604204889 0.200251678 0.097965609 29.63802227 0.028667976 0.049369928 9.64E-10 9.016101537 -0.428377972 SSS(ph)EITLSECDAEDAGEPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSEITLSECDAEDAGEPR 19 0 O60292 O60292 SIPA1L3 Signal-induced proliferation-associated 1-like protein 3 1 0 S(0.013)S(0.013)S(0.688)EIT(0.285)LSECDAEDAGEPR 145.69 5.89E-05 5246500 642.8 471.41 540.91 193.24 625.47 799.7 653.81 675.66 565.61 594.21 TRUE FALSE FALSE 634.9653064 478.0465224 550.3243116 215.583318 593.5499319 748.6017509 709.3446051 695.2091561 515.020425 578.7723385 1.097089933 0.82596643 0.950847639 0.372483797 1.025532653 1.293430423 1.22560212 1.201178961 0.889849757 1 9.176852162 -8.343573028 5.869891271 0.968604382 1.237677475 0.350372129 0.201461586 0.249755216 14.04270285 0.031314613 0.071076907 4.53E-09 8.343573028 0.269073093 SSS(ph)ETILSSLAGSDIVK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 0 SS(0.041)S(0.955)ET(0.003)ILSSLAGSDIVK;S(0.152)S(0.152)S(0.589)ET(0.009)ILS(0.098)S(0.001)LAGSDIVK ; 309.35 3.32E-158 59862400 4199.9 3790.1 3831.4 4680.2 5941.7 4753 4055.2 4561.6 4633 3722.7 TRUE FALSE FALSE 4148.710003 3843.457127 3898.08391 5221.346745 5638.472877 4449.29864 4399.648587 4693.582699 4218.612876 3625.983717 1.144161234 1.059976389 1.075041758 1.439980748 1.555018808 1.227059741 1.21336689 1.294430164 1.163439553 1 11.82415673 -9.275499673 24.1149781 1.069543918 1.34361191 0.606567018 0.10309661 259.6108426 445260.9282 0.017256027 0.02644805 5.30E-10 9.275499673 0.274067992 SSS(ph)FGSVSTSSNSSK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSFGSVSTSSNSSK 15 0 E5RG30;E5RJ65;E5RHF1;E5RGS8;E5RH07;E5RGQ6;A0A0C4DGW2;P57768-2;P57768 E5RG30 SNX16 Sorting nexin-16 1 0 S(0.273)S(0.273)S(0.455)FGSVSTSSNSSK;SS(0.001)S(0.999)FGSVSTSSNSSK ; 324.84 5.45E-177 24862000 4392 4530.9 4649.6 5180.6 6745.8 6909.3 5568.9 5944.1 5088.6 4554 TRUE FALSE FALSE 4338.468615 4594.686129 4730.524338 5779.605347 6401.536654 6467.818029 6041.922227 6116.083155 4633.462871 4435.686424 0.978082804 1.035845569 1.066469512 1.302978794 1.443189631 1.458132386 1.362116626 1.378835781 1.044587563 1 12.11494166 -9.237485715 2.097549575 0.99275653 1.411684039 0.965998342 0.034611666 0.034311896 0.2946874 0.005160748 0.009047784 5.79E-10 9.237485715 0.418927509 SSS(ph)FSLPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 0 S(0.008)S(0.002)S(0.875)FS(0.115)LPSR 128.03 0.0092821 19867000 2392.4 2632.8 2187.3 2113 1604.2 1038.4 994.88 1228.8 2556.3 2171.7 TRUE FALSE FALSE 2363.240509 2669.864628 2225.369039 2357.315002 1522.331688 972.0495913 1079.385082 1264.353389 2327.658126 2115.278921 1.117224062 1.262180888 1.052045202 1.114422774 0.719683666 0.459537313 0.510280262 0.597724195 1.100402459 1 11.04663219 -8.609551329 3.355531214 1.077603421 0.525752552 0.92533469 0.075673281 0.05291812 1.184676117 0.012815951 0.027448415 2.46E-09 8.609551329 -0.551850869 SSS(ph)FSSWDDSSDSYWK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSFSSWDDSSDSYWK 16 0 Q9NP61;Q9NP61-2 Q9NP61 ARFGAP3 ADP-ribosylation factor GTPase-activating protein 3 1 0 S(0.071)S(0.071)S(0.823)FS(0.032)S(0.004)WDDSSDSYWK 165.34 2.18E-05 5502700 2731.6 2763.6 2669.3 2101.7 3280.2 2834.4 2411 3039.3 2951.6 2920.7 TRUE FALSE FALSE 2698.306209 2802.506033 2715.758047 2344.708443 3112.799154 2653.290988 2615.79028 3127.23735 2687.601504 2844.819793 0.948498114 0.985126032 0.954632716 0.824202801 1.094199064 0.932674539 0.919492435 1.099274322 0.944735238 1 11.47412155 -7.24782572 23.66951551 0.966579734 1.09927451 0.292136658 0.065063355 1058.870642 1840947.776 0.008349686 0.205479228 5.65E-08 7.24782572 0.132694776 SSS(ph)LDALGPTR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSLDALGPTR 11 0 E5RI90;Q9H425-2;Q9H425-3;Q9H425 E5RI90 C1orf198 Uncharacterized protein C1orf198 1 0 S(0.347)S(0.06)S(0.592)LDALGPTR;S(0.026)S(0.004)S(0.97)LDALGPTR ; 148.13 0.0024102 18083300 3134.1 3227.9 3514.6 2720.47 4449.9 5642.6 4858.9 4503.2 3067.9 3051.7 TRUE FALSE FALSE 3095.900384 3273.342461 3575.770139 3035.023542 4222.804998 5282.056071 5271.614845 4633.492987 2793.49934 2972.416394 1.041543301 1.101239539 1.202984261 1.021062711 1.420664011 1.777024269 1.773511563 1.558830383 0.93980754 1 11.53742052 -8.573086604 2.812096908 1.041014246 1.708146922 0.916549704 0.088752355 0.04856373 0.776374683 0.012723389 0.028702755 2.67E-09 8.573086604 0.667132676 SSS(ph)LESLQTAVAEVR ddPTM_HeLa_Romidepsin_16h_R1 4 SSSLESLQTAVAEVR 15 0 R4GN62;A0A087WZG6;A0A087X1S9;Q8TEW8-5;Q8TEW8-2;Q8TEW8 R4GN62 PARD3B Partitioning defective 3 homolog B 1 0 S(0.005)S(0.015)S(0.98)LESLQTAVAEVR;S(0.006)S(0.006)S(0.988)LESLQTAVAEVR;SS(0.08)S(0.92)LESLQTAVAEVR;S(0.002)S(0.089)S(0.909)LESLQTAVAEVR ;;; 252.01 3.91E-58 21433600 4705.1 4026.67 4875.86 5315 5194 5282.8 4685 4604.13 5281.3 5033.2 TRUE FALSE FALSE 4647.752431 4083.357566 4960.722298 5929.545308 4928.930799 4945.246129 5082.943783 4737.343237 4808.927301 4902.436738 0.948049445 0.832924071 1.0118891 1.209509806 1.005404264 1.008732268 1.036819862 0.966324196 0.980925927 1 12.2592833 -9.528634037 24.99060426 0.962106559 1.04763633 0.292539502 0.074097607 174.1672934 756265.3157 0.011924696 0.016893839 2.96E-10 9.528634037 0.085529771 SSS(ph)LGNLK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLGNLK 8 0 Q86W92-2;F5GZP6;Q86W92-3;Q86W92-4;Q86W92;H0YGH8 Q86W92-2 PPFIBP1 Liprin-beta-1 1 0 S(0.001)S(0.025)S(0.974)LGNLK 115.7 0.02037 39841000 4979.4 4985.9 5173.1 3605.4 5705.2 6530.3 5840.5 5869.5 6249.8 6453 TRUE FALSE FALSE 4918.709158 5056.091631 5263.135635 4022.273312 5414.042355 6113.034906 6336.591924 6039.324722 5690.802235 6285.35013 0.782567249 0.804424818 0.837365545 0.639944192 0.861374823 0.972584626 1.008152576 0.960857327 0.905407355 1 12.6177774 -8.244152124 6.050628502 0.861415473 0.984268771 0.329875471 0.090233076 0.227895329 33.46986858 0.016632669 0.041442378 5.70E-09 8.244152124 0.122853298 SSS(ph)LGSTPHEELER ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLGSTPHEELER 14 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 S(0.3)S(0.3)S(0.4)LGSTPHEELER 97.129 0.0052864 4162400 1502.6 1220.3 1454.5 1354.5 1484.4 1522.8 1306.9 1341.3 1754.9 1506.4 TRUE FALSE FALSE 1484.285733 1237.479415 1479.814962 1511.113663 1408.645529 1425.497995 1417.908053 1380.108399 1597.937349 1467.263511 1.01160134 0.843392755 1.008554327 1.029885669 0.960049452 0.971535095 0.96636224 0.940600232 1.089059557 1 10.51891228 SSS(ph)LIQLTSQNSSPNQQR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSLIQLTSQNSSPNQQR 18 0 H7C419;O95639 H7C419 CPSF4 Cleavage and polyadenylation specificity factor subunit 4 1 0 S(0.009)S(0.009)S(0.98)LIQLTSQNSSPNQQR;S(0.013)S(0.015)S(0.915)LIQLT(0.017)S(0.032)QNS(0.006)S(0.002)PNQQR ; 159.64 4.18E-06 27396900 2128.36 2220.66 1800.38 1794.71 2429.8 1676.74 1662.7 1742.65 1778.99 2297.91 TRUE FALSE FALSE 2102.41873 2251.92251 1831.714859 2002.222815 2305.798239 1569.601725 1803.929696 1793.070828 1619.872679 2238.209967 0.93933043 1.006126567 0.818383836 0.894564337 1.030197467 0.701275461 0.805969826 0.801118239 0.723735799 1 11.12812967 -6.930189558 0.255887384 0.998227708 0.53316648 0 0.114467306 7.430326001 0.333425953 0.04810364 1.122166407 1.17E-07 6.930189558 -0.465061228 SSS(ph)LQGMDMASLPPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLQGMDMASLPPR 15 0 Q9C0J8 Q9C0J8 WDR33 pre-mRNA 3 end processing protein WDR33 1 0 S(0.003)S(0.041)S(0.938)LQGMDMAS(0.018)LPPR 60.937 0.0040488 0 1307.8 983.54 1327.4 1205.7 1011.2 846.92 648.93 893.14 1400.8 1361.4 TRUE FALSE FALSE 1291.860031 997.3863019 1350.50284 1345.108707 959.5946907 792.8045453 704.050098 918.9815968 1275.50894 1326.030632 0.974230911 0.752159323 1.018455236 1.014387356 0.72365952 0.597878002 0.530945576 0.693031952 0.961900057 1 10.37289839 -8.609159377 3.513626432 0.972106604 0.604859664 0.784611465 0.082492975 0.074144745 1.806987946 0.012256134 0.02606289 2.46E-09 8.609159377 -0.367246941 SSS(ph)LVDIREEETEGGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLVDIREEETEGGSR 17 1 Q96Q42-3;Q96Q42 Q96Q42-3 ALS2 Alsin 1 0 S(0.021)S(0.021)S(0.959)LVDIREEETEGGSR 77.357 0.0079253 7693500 2514.1 2026.1 2636.4 2882.8 4090.2 5524.5 4820.3 6276.5 3010.7 2334.1 TRUE FALSE FALSE 2483.457182 2054.623489 2682.285436 3216.1229 3881.461831 5171.50228 5229.736162 6458.100625 2741.415452 2273.459746 1.092369103 0.90374307 1.179825348 1.414638155 1.707292966 2.274727885 2.300342538 2.840648768 1.205834173 1 11.15067374 -8.268812573 0.814182883 1.023736659 2.849664396 0.964458457 0.118703846 0.092034464 0.09243503 0.017139655 0.111335851 5.39E-09 8.268812573 1.825927737 up SSS(ph)MS(ph)SIDLVSASDDVHR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSMSSIDLVSASDDVHR 18 0 A0A0A0MRE4;A0A2R8YFA1;A0A2U3TZL3;Q9Y5P4;Q9Y5P4-3 A0A0A0MRE4 COL4A3BP Collagen type IV alpha-3-binding protein 2 0 S(0.086)S(0.107)S(0.803)MS(0.612)S(0.392)IDLVSASDDVHR 113.36 0.0018138 2769900 1581.5 1731.4 2007.7 1972.5 2168.6 2166.9 1766.2 1954.2 2338.6 1995.2 TRUE FALSE FALSE 1562.22407 1755.774695 2042.643176 2200.569731 2057.92825 2028.442083 1916.220984 2010.741694 2129.429759 1943.364416 0.803876029 0.90347167 1.051086023 1.132350532 1.058951287 1.043778545 0.986032762 1.034670429 1.095743928 1 10.92434074 -9.760944103 21.81224027 0.904504579 1.051896476 0.188886255 0.081879781 1.873335235 82470.73455 0.012905163 0.017619 1.73E-10 9.760944103 0.147391897 SSS(ph)MSSIDLVSASDDVHR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSMSSIDLVSASDDVHR 18 0 A0A0A0MRE4;A0A2R8YFA1;A0A2U3TZL3;Q9Y5P4;Q9Y5P4-3 A0A0A0MRE4 COL4A3BP Collagen type IV alpha-3-binding protein 1 0 S(0.073)S(0.073)S(0.433)MS(0.349)S(0.072)IDLVSASDDVHR;S(0.191)S(0.191)S(0.51)MS(0.069)S(0.039)IDLVSASDDVHR;S(0.147)S(0.147)S(0.663)MS(0.036)S(0.008)IDLVSASDDVHR ;; 94.564 0.0013178 18339100 3240.76 3542.59 2848.57 3220.18 3263.55 3201.89 2960.88 3124.03 3709.3 3841.9 TRUE FALSE FALSE 3201.260371 3592.462675 2898.148166 3592.512363 3096.998866 2997.299563 3212.377073 3214.418879 3377.530918 3742.086884 0.855474624 0.960015838 0.774473778 0.960029116 0.827612763 0.800970062 0.858445347 0.85899098 0.902579502 1 11.86962734 -16.52287264 0.211215408 1.719980963 0.836598014 0.179946374 0.063615914 29.13337149 0.362763869 8.629343092 0.046138287 3.00E-17 16.52287264 -0.883382949 SSS(ph)MSSLTGAYTSGIPSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSMSSLTGAYTSGIPSSSR 20 0 A8CG34-2;A8CG34 A8CG34-2 POM121C Nuclear envelope pore membrane protein POM 121C 1 0 S(0.009)S(0.009)S(0.466)MS(0.466)S(0.049)LT(0.001)GAYTSGIPSSSR 84.566 0.0018129 0 1009.9 920.21 702.46 690.5 935.98 1014.3 673.34 876.59 968.77 1046.6 TRUE FALSE FALSE 997.5909504 933.1647405 714.6860216 770.3388589 888.213448 949.4895035 730.5334828 901.9527486 882.1207849 1019.409181 0.97859718 0.915397622 0.701078659 0.755671886 0.871302186 0.931411568 0.71662439 0.884779895 0.865325525 1 9.993517536 -9.983471871 5.953721095 0.988023457 0.810931148 0.365108335 0.079384765 0.084181901 10.52623213 0.01121556 0.014561222 1.04E-10 9.983471871 -0.17709231 SSS(ph)PAELDLKDDLQQTQGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPAELDLKDDLQQTQGK 19 1 H7C1F9;Q2PPJ7-3;Q2PPJ7-2;Q2PPJ7 H7C1F9 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 1 0 S(0.161)S(0.161)S(0.678)PAELDLKDDLQQT(0.001)QGK 66.889 0.00689 5590400 817.55 633.31 828.72 660.57 1281.6 1239.9 1052.8 917.27 888.02 981.42 TRUE FALSE FALSE 807.5853861 642.2257548 843.143524 736.9482115 1216.19517 1160.674392 1142.224806 943.8097602 808.5932671 955.9225669 0.844823016 0.671838679 0.882020734 0.770928773 1.27227373 1.214192898 1.194892605 0.987328674 0.84587737 1 9.900749949 -8.759019719 24.999927 0.890313295 1.172510672 0.663301293 0.111629392 37.619815 388679.31 0.018389532 0.035440482 1.74E-09 8.759019719 0.282197377 SSS(ph)PAGETEGDREPQARPGEGTAPLPPPGQK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPAGETEGDREPQARPGEGTAPLPPPGQK 31 2 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 S(0.197)S(0.197)S(0.536)PAGET(0.07)EGDREPQARPGEGT(0.001)APLPPPGQK 55.271 0.0019194 32997000 1040.9 774.75 824.78 879.71 757.46 508.33 828.88 830.11 1008.7 832.03 TRUE FALSE FALSE 1028.21311 785.6569508 839.1349499 981.4262094 718.8039897 475.8493536 899.2850465 854.1279232 918.4793457 810.4137407 1.268750835 0.969451666 1.035440181 1.211018718 0.886959282 0.587168417 1.109661647 1.053940574 1.133346215 1 9.662514825 -8.747192227 24.95566606 1.114377886 0.900715635 0.270596329 0.154752956 247.2876447 433152.7866 0.024787211 0.049384197 1.79E-09 8.747192227 -0.213662251 SSS(ph)PAPADIAQTVQEDLR ddPTM_HeLa_Romidepsin_16h_R1 29 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 0 SS(0.001)S(0.999)PAPADIAQTVQEDLR;SS(0.01)S(0.989)PAPADIAQTVQEDLR;SSS(1)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;SS(0.004)S(0.996)PAPADIAQTVQEDLR;S(0.001)S(0.029)S(0.97)PAPADIAQTVQEDLR;S(0.009)S(0.009)S(0.983)PAPADIAQTVQEDLR;SSS(0.999)PAPADIAQTVQEDLR;S(0.003)S(0.101)S(0.896)PAPADIAQTVQEDLR;S(0.001)S(0.004)S(0.995)PAPADIAQTVQEDLR;SS(0.002)S(0.997)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;SS(0.104)S(0.895)PAPADIAQTVQEDLR;S(0.184)S(0.184)S(0.632)PAPADIAQTVQEDLR;S(0.005)S(0.15)S(0.845)PAPADIAQTVQEDLR;SS(0.01)S(0.99)PAPADIAQTVQEDLR;S(0.003)S(0.095)S(0.902)PAPADIAQTVQEDLR;SS(0.022)S(0.978)PAPADIAQTVQEDLR;S(0.032)S(0.106)S(0.861)PAPADIAQTVQEDLR;SS(0.093)S(0.907)PAPADIAQTVQEDLR;S(0.001)S(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.015)S(0.015)S(0.969)PAPADIAQTVQEDLR;S(0.019)S(0.222)S(0.759)PAPADIAQTVQEDLR;SS(0.004)S(0.996)PAPADIAQTVQEDLR;S(0.003)S(0.093)S(0.904)PAPADIAQTVQEDLR;SS(0.001)S(0.999)PAPADIAQTVQEDLR;S(0.134)S(0.248)S(0.618)PAPADIAQTVQEDLR;S(0.001)S(0.119)S(0.881)PAPADIAQTVQEDLR;S(0.002)S(0.026)S(0.972)PAPADIAQTVQEDLR ;;;;;;;;;;;;;;;;;;;;;;;;;;;; 333.03 9.08E-211 16644597200 39191.05 42201.87 36207.58 37350.24 38039.52 37356.54 32459.39 37679.1 41875.81 42369.61 TRUE FALSE FALSE 38713.37441 42795.98903 36837.75774 41668.85049 36098.22135 34969.57766 35216.48978 38769.28531 38130.33267 41268.84142 0.938077568 1.037004858 0.892628833 1.009692762 0.874708863 0.847360295 0.853343311 0.939432365 0.923949676 1 15.33276532 -8.746919936 24.95978451 0.971521025 0.874659828 0.461412299 0.046429396 138.6804251 238398.5082 0.006267764 0.012491223 1.79E-09 8.746919936 -0.096861197 LYDSS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 LYDSSPSR 8 0 E9PP00;Q9C0D7;Q9C0D7-2 E9PP00 ZC3H12C Probable ribonuclease ZC3H12C 1 0 LYDS(0.087)S(0.913)PSR 101.46 0.029764 5296600 2613.7 2776.1 2547.5 2078 1876.2 1720.6 1459.2 1050.8 2373 2772 TRUE FALSE FALSE 2581.843219 2815.182009 2591.838169 2318.268137 1780.450513 1610.659213 1583.144412 1081.20324 2160.752937 2699.98304 0.956244236 1.042666553 0.959946092 0.858623222 0.659430258 0.596544196 0.586353465 0.40044816 0.800283892 1 11.39873463 -8.617948444 1.098218374 0.987161474 0.487075225 0.861202009 0.076061175 0.079415057 0.182311605 0.007774631 0.02601175 2.41E-09 8.617948444 -0.500086249 down SSS(ph)PEDPGAEV ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPEDPGAEV 11 0 Q9Y5U2-2;Q9Y5U2 Q9Y5U2-2 TSSC4 Protein TSSC4 1 0 S(0.023)S(0.023)S(0.954)PEDPGAEV 153.1 0.0022638 5945400 3422.2 3096.6 3508.9 2926.7 3604.4 3602.7 2923.8 3161.8 3649.9 3885.3 TRUE FALSE FALSE 3380.48891 3140.194016 3569.970933 3265.098825 3420.454018 3372.499097 3172.147499 3253.281695 3323.443803 3784.359346 0.893279047 0.829782198 0.943348822 0.862787734 0.903839648 0.891167775 0.838225763 0.85966511 0.878205133 1 11.88583337 -12.25547917 0.421762788 1.037288245 0.870454764 0 0.049544297 0.905260479 0.213313937 0.066936422 0.010101918 5.55E-13 12.25547917 -0.166833481 SSS(ph)PFLSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPFLSK 8 0 Q9NYV4-2;J3QSD7;Q9NYV4-3;Q9NYV4 Q9NYV4-2 CDK12 Cyclin-dependent kinase 12 1 0 S(0.003)S(0.09)S(0.907)PFLSK 104.42 0.027283 8495900 3411.5 2954.5 3568.8 2504 2993.4 3198.5 2601 2455.6 3618.7 3434.5 TRUE FALSE FALSE 3369.919326 2996.093529 3630.913467 2793.524262 2840.635628 2994.126173 2821.928875 2526.648912 3295.034409 3345.271195 1.007368052 0.89562052 1.085386881 0.835066606 0.849149579 0.89503242 0.84355758 0.75528971 0.984982746 1 11.70790746 -9.241666015 24.63869769 0.999346991 0.840112607 0.686665308 0.053631381 280.5439394 349573.2838 0.007518421 0.012456156 5.73E-10 9.241666015 -0.159234384 SSS(ph)PGKLLGSGYGGLTGGSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPGKLLGSGYGGLTGGSSR 21 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 S(0.005)S(0.005)S(0.983)PGKLLGS(0.008)GYGGLTGGSSR 141.83 0.00040434 17492000 2040.7 2025.8 1134.6 4311.7 1602.6 1122.7 1346.8 1586.8 1693.3 1384 TRUE FALSE FALSE 2015.827163 2054.319266 1154.347237 4810.239041 1520.813342 1050.963093 1461.197158 1632.711554 1541.847007 1348.04348 1.49537251 1.523926561 0.856313059 3.568311491 1.128163419 0.779621065 1.08393919 1.211171285 1.143766525 1 10.39665132 -5.402804835 15.37529865 1.332964862 0.9877038 0 0.765405524 0 0 0.09743179 0 3.96E-06 5.402804835 -0.345261062 SSS(ph)PIPLTPSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPIPLTPSK 11 0 Q8N5Y2;Q8N5Y2-3;Q8N5Y2-2;A0A3B3IT59;Q8N5Y2-6;Q8N5Y2-4;A0A3B3ITL5;A0A3B3ITF3;A0A3F2YNX2;A0A3B3IRN2 Q8N5Y2 MSL3 Male-specific lethal 3 homolog 1 0 S(0.094)S(0.094)S(0.811)PIPLT(0.001)PSK 114.71 0.012433 12021000 8896.6 8462.9 8416.3 7160.9 5865.3 5537.7 5083.9 5090.7 9471.8 8984.2 TRUE FALSE FALSE 8788.164817 8582.040928 8562.782171 7988.876951 5565.971855 5183.858842 5515.726339 5237.991373 8624.618485 8750.789189 1.004271115 0.980716224 0.978515421 0.912932169 0.636053701 0.592387581 0.630311875 0.598573598 0.985581791 1 13.09519742 -8.821744307 2.820528667 0.997821956 0.606381322 0.993643684 0.014319666 0.015154728 0.245389667 0.002443871 0.00489358 1.51E-09 8.821744307 -0.391440634 SSS(ph)PSASLTENELLWEPTPVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPSASLTENELLWEPTPVK 21 0 O96028-3 O96028-3 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 S(0.131)S(0.131)S(0.733)PS(0.004)ASLTENELLWEPTPVK 150.48 4.27E-06 2202000 1754.3 2064.2 2377.7 1807.6 1544.2 1299.4 1026.8 1074.9 2140.5 2248.9 TRUE FALSE FALSE 1732.917917 2093.259862 2419.082871 2016.603217 1465.393712 1216.372534 1114.016366 1106.000536 1949.048319 2190.473254 0.791115762 0.955619914 1.1043654 0.920624442 0.668984983 0.555301249 0.508573371 0.504913965 0.889784121 1 11.09702688 -8.585747659 2.676302691 0.922194893 0.523482665 0.857168441 0.078148478 0.100845059 1.456783758 0.015365974 0.034800279 2.60E-09 8.585747659 -0.398712228 SSS(ph)PSASLTENEVK ddPTM_HeLa_Romidepsin_16h_R1 3 SSSPSASLTENEVK 14 0 O96028-5 O96028-5 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 SS(0.019)S(0.98)PSASLTENEVK;S(0.165)S(0.028)S(0.638)PS(0.166)AS(0.002)LTENEVK;SS(0.017)S(0.979)PS(0.004)ASLTENEVK ;; 271.04 8.15E-82 45472600 9213.8 8253.6 7724.3 8345.1 7584.2 6411.5 5510 5048.4 9624.3 9016.1 TRUE FALSE FALSE 9101.498662 8369.794397 7858.738201 9309.999727 7197.149973 6001.825842 5978.019262 5194.467489 8763.478503 8781.860422 1.036397554 0.953077593 0.894883068 1.060139797 0.819547297 0.683434438 0.680723557 0.591499664 0.997906831 1 13.10031089 -8.458588019 2.032179498 1.005715091 0.642168163 0.894734282 0.051843681 0.069976724 0.564893404 0.007822289 0.020867113 3.48E-09 8.458588019 -0.363546927 SSS(ph)PTAGPSTEGAEGPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPTAGPSTEGAEGPEEK 19 0 Q8NHM5-2;Q8NHM5-3;Q8NHM5;Q8NHM5-4;A0A0C4DGG3 Q8NHM5-2 KDM2B Lysine-specific demethylase 2B 1 0 S(0.083)S(0.083)S(0.705)PT(0.129)AGPSTEGAEGPEEK 145.69 5.89E-05 8825600 3516.4 3442 3153.1 2707.5 2311.2 2437.1 2457.1 2118.4 4114.6 3726.4 TRUE FALSE FALSE 3473.540764 3490.456566 3207.978383 3020.553889 2193.25084 2281.377175 2665.806013 2179.692562 3746.579871 3629.587591 0.957007009 0.961667539 0.883841016 0.832203057 0.604269985 0.628549971 0.734465265 0.600534498 1.03223294 1 11.82558992 -9.125456775 1.554749367 0.97763463 0.64499887 0.907534715 0.048942973 0.072883547 0.346314082 0.007268167 0.014268545 7.49E-10 9.125456775 -0.33263576 TGQLEGAPAPGPAASPQT(ph)LDHSGATATGGASELK ddPTM_HeLa_Romidepsin_16h_R1 1 TGQLEGAPAPGPAASPQTLDHSGATATGGASELK 34 0 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 0 TGQLEGAPAPGPAAS(0.495)PQT(0.499)LDHS(0.003)GAT(0.001)AT(0.001)GGASELK 101.11 4.74E-13 12746000 3023.8 2760.2 2580.1 2432.7 1726.9 1092.7 842.06 812.72 3073.3 3016.7 TRUE FALSE FALSE 2986.944763 2799.058168 2625.005558 2713.98022 1638.769849 1022.879997 913.5845554 836.2347709 2798.416351 2938.325699 1.016546519 0.952603099 0.893367798 0.923648533 0.557722328 0.348116615 0.310920112 0.28459567 0.95238467 1 11.52077861 -8.612634543 1.49609474 0.999224737 0.285928515 0.98092153 0.040679373 0.032439181 0.143932782 0.005979034 0.016441963 2.44E-09 8.612634543 -0.713296222 down SSS(ph)PTQYGLTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPTQYGLTK 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 0 S(0.001)S(0.166)S(0.809)PT(0.024)QYGLTK 122.46 0.008933 174240000 3561.6 3067.7 3675.8 3513.8 3403.6 3209.1 2408.9 2430.4 3872.2 3372.7 TRUE FALSE FALSE 3518.189849 3110.887161 3739.775757 3920.082089 3229.901591 3004.048867 2613.511906 2500.719789 3525.860734 3285.076768 1.070961228 0.946975484 1.138413505 1.193299994 0.983204296 0.914453171 0.795571029 0.761236332 1.073296298 1 11.68171137 -7.998596271 1.927978087 1.045889527 0.766911217 0.735728634 0.067935421 0.150440214 1.061784586 0.010521441 0.044336576 1.00E-08 7.998596271 -0.27897831 SSS(ph)PTSYWK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPTSYWK 9 0 Q92614;A0A0D9SFK2;Q92614-2;Q92614-3;Q92614-4;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 S(0.032)S(0.181)S(0.698)PT(0.082)S(0.008)YWK 111.27 0.018411 13347000 1811.3 2035.2 2145.8 1771.2 2487.2 2538.3 2211 2400.6 2102.9 2316 TRUE FALSE FALSE 1789.223179 2063.851599 2183.146749 1975.994478 2360.268903 2376.110822 2398.802285 2470.057573 1914.811357 2255.829986 0.793155153 0.914896784 0.967779825 0.875950089 1.046297335 1.053319992 1.063379022 1.094966194 0.848827868 1 11.13944263 -8.704249818 5.801848965 0.904918515 1.065775106 0.678001838 0.055503206 0.133264492 9.165763968 0.011598503 0.023246816 1.98E-09 8.704249818 0.16085659 SSS(ph)PVGLAK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPVGLAK 9 0 B1AKL4;Q9NRA8;Q9NRA8-3;Q9NRA8-2 B1AKL4 EIF4ENIF1 Eukaryotic translation initiation factor 4E transporter 1 0 S(0.002)S(0.021)S(0.976)PVGLAK;SS(0.024)S(0.976)PVGLAK ; 126.39 0.010127 577340000 21733.6 21299.3 20605.6 18134.7 17737.9 18137 16207.6 16739.2 22112 20465.5 TRUE FALSE FALSE 21468.70252 21599.1521 20964.23182 20231.51934 16832.66877 16978.10423 17584.27314 17223.52234 20134.24734 19933.80336 1.076999815 1.083543954 1.051692517 1.014935232 0.844428355 0.851724276 0.88213337 0.864035931 1.010055481 1 14.28292938 -8.818574648 4.962960707 1.042065617 0.861199687 0.917700782 0.026324585 0.051472874 2.588818276 0.005147347 0.009635879 1.52E-09 8.818574648 -0.180865931 SSS(ph)PVQVEEEPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPVQVEEEPVR 13 0 A0A0J9YVR0;Q8IZ21-3;Q8IZ21;Q8IZ21-2 A0A0J9YVR0;Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 S(0.062)S(0.062)S(0.876)PVQVEEEPVR;S(0.018)S(0.018)S(0.964)PVQVEEEPVR ; 269.88 8.07E-80 256028300 6060.2 5281.1 4779.5 5603.1 6358.3 7081.3 6684.1 6772 6284.8 5074.2 TRUE FALSE FALSE 5986.335951 5355.447464 4862.685193 6250.956785 6033.812225 6628.827784 7251.847287 6967.937136 5722.671747 4942.371553 1.211227421 1.083578482 0.983876898 1.264768688 1.220833392 1.341224089 1.467280881 1.409836768 1.157879712 1 12.27098776 -8.426927337 1.043471528 1.093731902 1.454636175 0.753987853 0.076876667 0.258791237 0.503521465 0.01529607 0.065041187 3.74E-09 8.426927337 0.360904272 SSS(ph)PVTELAS(ph)RSPIR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPVTELASRSPIR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 S(0.02)S(0.025)S(0.951)PVT(0.013)ELAS(0.616)RS(0.376)PIR 94.845 0.023517 26890000 3401.4 2975.5 3111.9 2476.6 2772.1 2824.9 2849.8 2817.6 3548.6 3556.1 TRUE FALSE FALSE 3359.942428 3017.389167 3166.061314 2762.956145 2630.629393 2644.398007 3091.861941 2899.122811 3231.204328 3463.712009 0.970040933 0.871143201 0.914065981 0.797686452 0.759482713 0.763457816 0.892644057 0.836998804 0.932873264 1 11.75810327 -9.955785533 1.087486292 0.99066257 0.811519279 0.654456464 0.046677268 0.164265167 0.382448853 0.008879682 0.012274358 1.11E-10 9.955785533 -0.179143291 SSS(ph)PVTELASR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPVTELASR 11 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.063)S(0.063)S(0.874)PVTELASR;S(0.044)S(0.007)S(0.947)PVT(0.002)ELASR ; 178.53 1.21E-05 181884000 8121 8181.5 8465.8 3912.3 6110.6 6843.6 6187.6 6132.5 8650.2 8203.9 TRUE FALSE FALSE 8022.018128 8296.679372 8613.143698 4364.658534 5798.75328 6406.316047 6713.17459 6309.934212 7876.504447 7990.761495 1.003911596 1.038283945 1.077887721 0.546213091 0.725682187 0.801715337 0.840117002 0.789653679 0.985701357 1 12.96411728 -9.281284779 24.99637505 1.010391088 0.748758787 0.763996526 0.077764896 310.2104749 390726.1667 0.012089334 0.018481764 5.23E-10 9.281284779 -0.261632301 SSS(ph)QENLLDEVMK ddPTM_HeLa_Romidepsin_16h_R1 4 SSSQENLLDEVMK 13 0 Q3V6T2;A0A2R8Y7D4;A0A2U3TZV9;A0A2R8Y7B1;H7C2C6;A0A2R8Y820;A0A2R8YCU9;A0A2R8Y885;A0A2R8YDS8;H0Y470;H0Y7U8;A0A2R8Y5D7;Q3V6T2-5;Q3V6T2-4;Q3V6T2-2;Q3V6T2-3;H0Y7K3;A0A2R8Y4Z5;A0A2R8Y4C6 Q3V6T2 CCDC88A Girdin 1 0 S(0.002)S(0.027)S(0.972)QENLLDEVMK;SS(0.004)S(0.996)QENLLDEVMK;SS(0.047)S(0.953)QENLLDEVMK;S(0.001)S(0.033)S(0.966)QENLLDEVMK ;;; 168.93 0.0001565 110796000 18091.7 17250.9 16734 14729.6 19729.2 23414.1 21524.4 23771 20962.7 17008.3 TRUE FALSE FALSE 17871.1914 17493.75862 17025.24825 16432.70566 18722.3453 21918.01458 23352.682 24458.77638 19087.74361 16566.42191 1.078759885 1.055976886 1.027696164 0.991928477 1.130138143 1.323038535 1.409639457 1.476406704 1.152194705 1 14.01597442 -8.18123276 1.771021358 1.035450832 1.453110563 0.921889625 0.046643484 0.052234534 0.308496745 0.005469205 0.019899278 6.59E-09 8.18123276 0.417659731 SSS(ph)QGPLSSIR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSQGPLSSIR 11 0 A0A0U1RQE4 A0A0U1RQE4 1 0 S(0.014)S(0.014)S(0.971)QGPLSSIR 103.97 0.017344 27954000 2456.9 1801.8 1954.1 2398.9 1919.1 1812.4 1426.6 1412.4 2388 2035.9 TRUE FALSE FALSE 2426.954358 1827.165788 1988.110291 2676.272105 1821.161166 1696.593489 1547.775368 1453.265566 2174.411299 1983.007025 1.223875825 0.921411657 1.002573499 1.349602937 0.918383618 0.855566051 0.780519357 0.732859515 1.096522237 1 10.95347407 -8.531189434 24.91298805 1.100850031 0.805108613 0.587906282 0.11723043 105.2201598 315418.3895 0.018905635 0.037861678 2.94E-09 8.531189434 -0.295741418 SSS(ph)QIPEGFGLTSGGSNYSLAR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSQIPEGFGLTSGGSNYSLAR 22 0 Q9Y4E6-2;Q9Y4E6;A2RRE0 Q9Y4E6-2 WDR7 WD repeat-containing protein 7 1 0 S(0.036)S(0.036)S(0.911)QIPEGFGLT(0.013)S(0.004)GGSNYSLAR 105.92 0.00017241 6854400 789.21 739.18 674.42 804.48 978.97 1045.4 957.6 1182.7 794.8 915.92 TRUE FALSE FALSE 779.590805 749.5861954 686.1579972 897.4977628 929.0095079 978.6023139 1038.93852 1216.919559 723.7110974 892.1242664 0.873858984 0.840226215 0.769128274 1.00602326 1.041345408 1.09693498 1.164567044 1.364069563 0.811222298 1 9.801100871 -7.569526062 0.85034886 0.921319315 1.471417074 0.791327505 0.079258638 0.613977383 0.431694733 0.013869029 0.284117183 2.69E-08 7.569526062 0.550097758 SSS(ph)S(ph)S(ph)LFGSKTRPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSLFGSKTRPR 14 2 A0A0A0MQX5;O94779-4;O94779 A0A0A0MQX5 CNTN5 Contactin-5 3 0 SSS(0.999)S(0.865)S(0.782)LFGS(0.192)KT(0.162)RPR 98 0.0010422 0 846.05 792.72 868.6 798.75 849.37 862.62 633.6 776.88 1061.8 618.61 TRUE FALSE FALSE 835.7380172 803.879933 883.7176186 891.1052332 806.0234795 807.501366 687.4179682 799.3577971 966.8299487 602.538423 1.387028586 1.33415547 1.466657702 1.478918521 1.337712997 1.340165764 1.140869929 1.326650329 1.604594681 1 9.234909433 -12.20467868 0.851656374 0.990570781 1.35260456 0 0.206058569 0.315191082 0.395157724 0.074002495 0.0187921 6.24E-13 12.20467868 0.362033779 SSS(ph)S(ph)SSSVHEPKMDALIIPVTMEVPCDSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSSSVHEPKMDALIIPVTMEVPCDSR 29 1 A0A1W2PSA7 A0A1W2PSA7 2 0 S(0.039)S(0.041)S(0.678)S(0.327)S(0.319)S(0.307)S(0.29)VHEPKMDALIIPVTMEVPCDSR 44.317 0.0039175 0 984.06 696.21 868.91 791.46 953.17 818.19 831.87 883.1 850.68 1019.6 TRUE FALSE FALSE 972.0658982 706.0112627 884.0330141 882.9723291 904.5261781 765.9102996 902.529017 908.6511052 774.5930502 993.110645 0.978809263 0.710908967 0.890165681 0.889097638 0.91080101 0.771223532 0.908789994 0.914954552 0.779966516 1 9.955810651 -10.48260921 24.97152449 0.990651203 0.858843557 0 0.091802179 266.9676452 165550.5495 0.010332918 0.011662136 3.29E-11 10.48260921 -0.131807646 SNVSSPATPT(ph)ASSSSSTTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 SNVSSPAT(0.055)PT(0.181)AS(0.181)S(0.181)S(0.08)S(0.08)S(0.08)T(0.08)T(0.08)PT(0.005)R 113.52 0.0004091 17342000 3494.4 3006.3 3146.9 2653.6 2221.2 1229 1098.6 1233.8 3622 3319.8 TRUE FALSE FALSE 3451.808909 3048.62277 3201.670474 2960.421718 2107.843876 1150.470866 1191.915057 1269.498056 3298.039249 3233.551117 1.067497863 0.942809518 0.990140671 0.915532679 0.65186657 0.355791767 0.368608695 0.392601821 1.01994344 1 11.6589037 -8.611798884 1.720446879 1.022676088 0.358954657 0.9829229 0.036786826 0.033929933 0.200761154 0.006473564 0.016634787 2.44E-09 8.611798884 -0.66372143 down SSS(ph)SGSDDYAYTQALLLHQR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSGSDDYAYTQALLLHQR 20 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 0 S(0.135)S(0.135)S(0.593)S(0.135)GSDDYAYTQALLLHQR 136.59 0.00011071 9158300 1390.9 1658 902.02 1016.6 1483.6 1439.1 1207.6 1451.2 1233.7 1091.1 TRUE FALSE FALSE 1373.947176 1681.341368 917.7192797 1134.144075 1407.886356 1347.146154 1310.173514 1493.188182 1123.354782 1062.753065 1.292818832 1.582062121 0.863530118 1.06717554 1.324753983 1.267600348 1.232810855 1.405018938 1.057023329 1 10.0535907 -12.25921971 1.012368209 1.001245604 1.24901998 0.196277241 0.181144118 0.678706263 1.257869385 0.118639405 0.033136098 5.51E-13 12.25921971 0.247774376 SSS(ph)SSASPSSPSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSASPSSPSSR 14 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;Q9NYF8-4;H0YF63 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 S(0.345)S(0.056)S(0.59)S(0.008)SASPSSPSSR 136.3 0.001378 1850800 841.31 786.11 984.02 580.03 652.27 588.26 682.19 301.52 1269.5 985.8 TRUE FALSE FALSE 831.0557901 797.1768772 1001.146455 647.0957977 618.9822279 550.6720845 740.1352016 310.2440055 1155.95274 960.1887739 0.865512921 0.830229325 1.042655864 0.673925602 0.644646391 0.573503981 0.770822594 0.323107303 1.203880708 1 9.907174259 -7.097540831 0.291140579 0.982508888 3.12E-18 0.674620798 0.138119551 3.778311156 0.220712918 0.05447438 1.344756226 7.99E-08 7.097540831 -0.982508888 SSS(ph)T(ph)RSIDTQTPSVQER ddPTM_HeLa_Romidepsin_16h_R1 1 SSSTRSIDTQTPSVQER 17 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 0 S(0.197)S(0.197)S(0.949)T(0.644)RS(0.011)IDTQT(0.001)PSVQER 107.39 0.00092395 0 983.07 852.76 938.57 1009.9 945.46 601.11 609.81 531.31 1343.4 1044.8 TRUE FALSE FALSE 971.0879647 864.7651777 954.9054171 1126.66939 897.2096482 562.701011 661.6072462 546.6826166 1223.242939 1017.655945 0.954239956 0.849761829 0.93833817 1.107122102 0.8816434 0.552938361 0.650128611 0.53719788 1.202020137 1 9.991034174 -8.356750577 4.09898849 0.972467788 0.586580994 0.78563248 0.09878631 0.055744454 1.666432485 0.009620018 0.022620514 4.40E-09 8.356750577 -0.385886794 SSS(ph)TEPPPPVR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSTEPPPPVR 11 0 F5H669;Q8N684-2;Q8N684;Q8N684-3;F5H6M0;F5H047;F5H5B7;F5H1W4;F5H2K8;F5H6P5;F5H6A8;F5GXA3;C9JM38;C9J286;C9J323;J3QT54 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 0 S(0.024)S(0.007)S(0.963)T(0.007)EPPPPVR;S(0.039)S(0.071)S(0.89)TEPPPPVR ; 179.19 1.12E-05 78142000 5791.1 6098.6 5537.9 4490.5 5611.4 5053.3 4590.2 4956 5760.4 5721.9 TRUE FALSE FALSE 5720.515846 6184.456251 5634.284826 5009.712738 5325.029319 4730.410439 4980.091473 5099.394041 5245.175397 5573.244213 1.026424759 1.109668985 1.010952438 0.898886276 0.955463123 0.848771426 0.893571371 0.914977677 0.941135037 1 12.44430166 -9.281333862 5.681822697 1.021782951 0.901538178 0.615661063 0.045528251 0.076691905 8.715762821 0.006081572 0.009573278 5.23E-10 9.281333862 -0.120244773 SSS(ph)TGNLLDKDDLAIPPPDYGAASR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSTGNLLDKDDLAIPPPDYGAASR 25 1 B4DWA1;I3L4C2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-4;Q9UQB8-2;Q9UQB8;Q9UQB8-6;I3L3C6 B4DWA1 BAIAP2 Brain-specific angiogenesis inhibitor 1-associated protein 2 1 0 S(0.138)S(0.138)S(0.69)T(0.035)GNLLDKDDLAIPPPDYGAASR;S(0.17)S(0.17)S(0.466)T(0.195)GNLLDKDDLAIPPPDYGAASR;S(0.119)S(0.119)S(0.633)T(0.129)GNLLDKDDLAIPPPDYGAASR ;; 132.61 7.21E-07 309059000 3610.49 4005.85 4346.34 3483.86 9556 17281 18689.3 20847.8 4924.24 4553.4 TRUE FALSE FALSE 3566.483959 4062.244461 4421.986224 3886.680285 9068.321662 16176.79987 20276.76868 21450.9982 4483.803641 4435.102012 0.804149251 0.915930333 0.997042732 0.876345183 2.044670368 3.647447078 4.571883267 4.836641445 1.010980949 1 12.11475157 -8.242914128 1.547788083 0.898722884 4.825159846 0.995018578 0.109748774 0.019368667 0.086321917 0.01723862 0.064644111 5.72E-09 8.242914128 3.926436962 up SSS(ph)TSDILEPFTVER ddPTM_HeLa_Romidepsin_16h_R1 3 SSSTSDILEPFTVER 15 0 A0A1B0GUI1;Q6GYQ0-3;Q6GYQ0-4;Q6GYQ0;Q6GYQ0-7;Q6GYQ0-5;Q6GYQ0-6;Q6GYQ0-2 A0A1B0GUI1 RALGAPA1 Ral GTPase-activating protein subunit alpha-1 1 0 S(0.003)S(0.003)S(0.994)TSDILEPFTVER;S(0.004)S(0.004)S(0.93)T(0.059)S(0.004)DILEPFTVER;SSS(0.999)T(0.001)SDILEPFTVER ;; 307.43 1.52E-135 191120200 10715.5 11338.9 11473.4 10060.7 11933.1 13108.1 11616.1 14035.8 12811 11803 TRUE FALSE FALSE 10584.89536 11498.52933 11673.08971 11223.96547 11324.10938 12270.53471 12602.77124 14441.90373 11665.15207 11496.35636 0.920717402 1.000189014 1.015372989 0.976306329 0.985017255 1.067341193 1.096240483 1.256215733 1.01468254 1 13.48888907 -5.104248861 0.584276836 0.966216768 4.954181382 0.875149468 0.030791314 8.924361179 0.260011653 0.006296555 40.59380509 7.87E-06 5.104248861 3.987964615 SSS(ph)VGS(ph)SSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 4 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.005)S(0.01)S(0.985)VGS(0.986)S(0.005)S(0.007)S(0.001)YPISPAVSR;S(0.015)S(0.02)S(0.966)VGS(0.633)S(0.136)S(0.185)S(0.04)Y(0.005)PISPAVSR;S(0.18)S(0.24)S(0.58)VGS(0.95)S(0.038)S(0.009)S(0.002)YPISPAVSR;S(0.2)S(0.263)S(0.593)VGS(0.802)S(0.109)S(0.027)S(0.007)YPISPAVSR ;;; 172.42 1.94E-06 123248400 10381.9 10558.1 9737.8 9058.5 8489.8 8727.5 7206.75 9092.65 10624.4 10727.2 TRUE FALSE FALSE 10255.36141 10706.73721 9907.282324 10105.88639 8056.533826 8169.840917 7818.891165 9355.731482 9674.127055 10448.5058 0.98151464 1.024714674 0.948200874 0.967208765 0.771070427 0.781914761 0.74832625 0.895413341 0.925886174 1 13.35100902 -8.807866071 5.589476465 0.989500453 0.794126986 0.77981357 0.045277659 0.048966666 3.496114272 0.005597284 0.010418127 1.56E-09 8.807866071 -0.195373467 SSS(ph)VGSSSSYPIS(ph)PAVSR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 2 0 S(0.007)S(0.01)S(0.982)VGSSSSYPIS(1)PAVSR;S(0.249)S(0.364)S(0.385)VGS(0.003)S(0.001)S(0.002)SYPIS(0.996)PAVS(0.001)R;S(0.013)S(0.018)S(0.968)VGS(0.001)SSS(0.019)YPIS(0.936)PAVS(0.045)R ;; 189.44 1.94E-13 124800400 7358.5 6527.4 7168.4 6707.4 7035.2 8349.2 7180.1 8131.9 8277 6992.8 TRUE FALSE FALSE 7268.811772 6619.292909 7293.162995 7482.941147 6676.167492 7815.713066 7789.977515 8367.183696 7536.68439 6811.126048 1.067196778 0.971835327 1.07077199 1.098634953 0.980185574 1.147492061 1.143713603 1.228458208 1.106525461 1 12.73367762 -4.00000001 0.433604115 1.0257994 5.334196033 0.571535617 0.050700789 30.50920353 0.340189368 0.00986626 116.1950792 1.00E-04 4.00000001 4.308396633 SSS(ph)VGSSSSYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 8 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 S(0.003)S(0.003)S(0.995)VGSSSSYPISPAVSR;S(0.031)S(0.004)S(0.966)VGSSSSYPISPAVSR;SSS(0.999)VGS(0.001)SSSYPISPAVSR;S(0.006)S(0.006)S(0.983)VGS(0.003)SS(0.001)SYPISPAVSR;S(0.002)S(0.073)S(0.923)VGS(0.002)SSSYPISPAVSR;SSS(0.991)VGS(0.007)S(0.002)SSYPISPAVSR;S(0.002)S(0.075)S(0.913)VGS(0.011)SSSYPISPAVSR;S(0.001)S(0.003)S(0.996)VGSSSSYPISPAVSR ;;;;;;; 284.53 9.86E-107 2952996300 17972.48 16078.29 16375.08 16313.3 17387.46 18560.5 15891.55 18444.87 18770.6 19145.5 TRUE FALSE FALSE 17753.4245 16304.64059 16660.0814 18199.5205 16500.11303 17374.54395 17241.37786 18978.54321 17091.71052 18648.09715 0.952023381 0.874332671 0.893393104 0.975945179 0.884814837 0.931705997 0.924564996 1.017720095 0.916539119 1 14.18674081 -11.24205564 1.111141296 0.991179088 0.928542324 0 0.04740949 0.388172163 0.99110279 0.011629532 0.008306937 5.73E-12 11.24205564 -0.062636764 SSS(ph)VLSLEGSEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVLSLEGSEK 12 0 G3V311;A1L390-2;A1L390-3;A1L390;A0A0U1RR71 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 SS(0.003)S(0.989)VLS(0.008)LEGSEK 139.48 0.0021059 7509400 2951.3 3322.7 2493.1 2472.5 2600.2 1915.9 1527.3 2215.3 2647.9 3004.5 TRUE FALSE FALSE 2915.32842 3369.477058 2536.49136 2758.382083 2467.502091 1793.480173 1657.028824 2279.39621 2411.065192 2926.442657 0.996202134 1.151390084 0.866749039 0.942571718 0.843174591 0.612853346 0.566226309 0.778896591 0.823889437 1 11.51493229 -8.584417416 1.711792612 1.001651818 0.640447814 0.645189621 0.100636433 0.116968686 0.681986899 0.011987631 0.031481658 2.60E-09 8.584417416 -0.361204004 SSS(ph)VPHPFQVTLLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVPHPFQVTLLR 14 0 Q5VV41;Q5VV41-2 Q5VV41 ARHGEF16 Rho guanine nucleotide exchange factor 16 1 0 S(0.009)S(0.175)S(0.816)VPHPFQVTLLR 125.39 0.0013472 13785000 1949.1 1761.5 1790.1 1896.7 2532.9 2000.4 1499.2 2249.9 2187.5 1810.3 TRUE FALSE FALSE 1925.34362 1786.298443 1821.25594 2116.005378 2403.636661 1872.580896 1626.542011 2314.997307 1991.844521 1763.268145 1.091917656 1.013061143 1.032886544 1.200047414 1.363171375 1.0619944 0.922458683 1.312901451 1.129632227 1 10.78403617 -9.270337398 23.83992884 1.041032314 1.162741356 0.189783934 0.120403222 431.1361768 1155116.615 0.018237195 0.028128631 5.37E-10 9.270337398 0.121709042 SSS(ph)VTS(ph)IDKESR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVTSIDKESR 12 1 H0Y332;Q5JRH0;Q5T5C0-3;Q5T5C0-2;Q5T5C0 H0Y332 STXBP5 Syntaxin-binding protein 5 2 0 S(0.024)S(0.061)S(0.914)VT(0.003)S(0.998)IDKESR 143.55 0.023132 18486000 5361.9 5475.1 4423.5 4835.1 6177.7 5394.2 4709.6 5490.2 5652.9 5260.4 TRUE FALSE FALSE 5296.5471 5552.178602 4500.489162 5394.157012 5862.428917 5049.528029 5109.633306 5649.050275 5147.290466 5123.73405 1.033727951 1.083619592 0.878361195 1.052778493 1.144171196 0.985517199 0.997247956 1.102526052 1.00459751 1 12.32297988 -9.057886052 24.99940014 1.011039252 1.054257687 0.148676643 0.064760443 495.0118609 213781.1118 0.009453552 0.015676974 8.75E-10 9.057886052 0.043218435 SSS(ph)VTSIDK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVTSIDK 9 0 H0Y332;Q5JRH0;Q5T5C0-3;Q5T5C0-2;Q5T5C0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 0 S(0.002)S(0.015)S(0.982)VTSIDK 141.88 0.0062802 6819700 2262.4 2272.8 2219.4 1451.6 2300.8 2372.3 2446.1 2406.4 2432.1 2428.9 TRUE FALSE FALSE 2234.824999 2304.796538 2258.027726 1619.440822 2183.381591 2220.717686 2653.871673 2476.025387 2214.566885 2365.796828 0.944639443 0.974215753 0.954447017 0.684522358 0.9228948 0.938676416 1.121766519 1.046592572 0.93607653 1 11.20811047 -5.052660678 16.30832313 0.961396549 1.010009216 0 0.106892261 0 0 0.01440862 0 8.86E-06 5.052660678 0.048612666 SSSALDS(ph)PAGPR ddPTM_HeLa_Romidepsin_16h_R1 4 SSSALDSPAGPR 12 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.002)SS(0.004)ALDS(0.994)PAGPR;SSSALDS(1)PAGPR;SSSALDS(1)PAGPR;S(0.004)SSALDS(0.996)PAGPR ;;; 193.15 3.29E-10 157932000 9619.5 9207.2 9569.1 8075.6 14935 18053.8 16003.1 16617.3 10675.9 9729.9 TRUE FALSE FALSE 9502.253834 9336.819203 9735.646171 9009.338869 14172.81122 16900.22045 17362.40291 17098.09536 9721.020766 9477.115795 1.002652499 0.985196278 1.027279436 0.950641425 1.495477266 1.783266218 1.832034481 1.804145452 1.025736202 1 13.21023235 -8.571815652 2.657837206 0.997589321 1.808073429 0.989817727 0.037175398 0.017709216 0.252160806 0.005441178 0.012439393 2.68E-09 8.571815652 0.810484108 SSSAPLIHGLSDLSQVFQPYTLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSAPLIHGLSDLSQVFQPYTLR 23 0 G1UD79;Q7Z309-4;Q7Z309-3;Q7Z309-2;Q7Z309 G1UD79;Q7Z309-2 SPACIA2;FAM122B Protein FAM122B 0 0 151.64 1.22E-07 2785100 599.87 494.5 471.87 627.25 1206.8 1957.4 1994.9 1819.8 590.56 380.06 FALSE FALSE TRUE 592.5585537 501.461584 480.0826994 699.7755963 1145.212493 1832.328457 2164.346756 1872.453042 537.7388345 370.1859864 1.600704985 1.354620657 1.296868917 1.890335188 3.093613845 4.949751002 5.846646917 5.058141341 1.45261802 1 8.532106472 -8.466105377 1.596471218 1.298341267 5.540602643 0.979355565 0.251905649 0.040857068 0.201893419 0.044550225 0.132943174 3.42E-09 8.466105377 4.242261377 up SSSASS(ph)PEMK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSASSPEMK 10 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SSSAS(0.112)S(0.888)PEMK;SSSAS(0.027)S(0.973)PEMK ; 123.96 0.013634 9105100 7936 10325.5 18525.3 6566.4 5801.4 5451.8 13097.1 1812.61 16618.6 12889 TRUE FALSE FALSE 7839.27298 10470.86266 18847.72508 7325.638064 5505.33291 5103.447575 14209.56735 1865.055011 15132.19079 12554.14192 0.62443718 0.834056419 1.501315278 0.583523598 0.438527216 0.406515046 1.131862889 0.148560931 1.205354447 1 13.6158758 -9.042569706 24.99929941 0.87314955 0.558550833 0.297905006 0.334473977 617.5852908 362679.1641 0.048387874 0.080246609 9.07E-10 9.042569706 -0.314598717 SSSASS(ph)PEMKDGLPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSASSPEMKDGLPR 15 1 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 SSS(0.001)AS(0.183)S(0.816)PEMKDGLPR 93.228 0.0041683 0 2210.4 1866.1 1220.1 1522.7 1339.2 1499.9 1128.1 1134.4 1622.9 1444.3 TRUE FALSE FALSE 2183.458795 1892.371005 1241.335329 1698.761739 1270.855627 1404.061231 1223.920786 1167.222074 1477.743759 1406.776878 1.552100286 1.34518205 0.882396738 1.207555914 0.903381088 0.998069596 0.870017702 0.829713718 1.050446437 1 10.45817781 -9.156497069 1.172507447 1.264377516 0.897851605 0.3182371 0.184230019 0.433076248 1.174756812 0.040207467 0.0854709 6.97E-10 9.156497069 -0.366525911 SSSET(ph)ILSSLAGSDIVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSETILSSLAGSDIVK 17 0 Q01850 Q01850 CDR2 Cerebellar degeneration-related protein 2 1 0 S(0.009)S(0.009)S(0.03)ET(0.953)ILSSLAGSDIVK 208.38 1.09E-19 49740000 4598.7 4548.9 4500.1 5211 5660.9 5670.5 4839 4495.7 4815.1 4184 TRUE FALSE FALSE 4542.649276 4612.939534 4578.422353 5813.520338 5372.003149 5308.173351 5250.024539 4625.775986 4384.425396 4075.299077 1.114678749 1.131926626 1.123456774 1.426526061 1.318186236 1.302523631 1.288255031 1.135076445 1.075853652 1 11.99269022 -9.909449064 1.056003941 1.043958592 1.290769961 0.594714144 0.08059842 0.230409144 0.50793202 0.016736239 0.023788181 1.23E-10 9.909449064 0.246811369 SSSFS(ph)LPSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSFSLPSR 9 0 Q14153-2;Q14153 Q14153-2 FAM53B Protein FAM53B 1 0 S(0.001)SS(0.071)FS(0.928)LPSR 130.41 0.0080622 18761000 3313.8 3758.9 3600.4 2842.8 2170.3 1564.6 1517.7 1835.4 3941.4 3370.1 TRUE FALSE FALSE 3273.410131 3811.817893 3663.063452 3171.497912 2059.541492 1464.62711 1646.6134 1888.504403 3588.871313 3282.544316 0.997217346 1.161238821 1.11592201 0.966170631 0.627422296 0.446186546 0.501627165 0.57531726 1.093319988 1 11.68059877 -8.714145737 3.193513361 1.022478312 0.50997954 0.937388043 0.065911699 0.046152693 0.960609456 0.010303139 0.021297949 1.93E-09 8.714145737 -0.512498772 SSSGES(ph)LAQSPDSSK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSGESLAQSPDSSK 15 0 Q9H7U1-2;Q9H7U1;Q9H7U1-3 Q9H7U1-2 CCSER2 Serine-rich coiled-coil domain-containing protein 2 1 0 SSSGES(0.884)LAQS(0.067)PDS(0.038)S(0.011)K;SSSGES(0.516)LAQS(0.483)PDSSK ; 146.84 0.00047943 20213200 7657.9 6834 7258 7185.5 8015.2 8348.1 6838.8 7229.4 8699.3 7318.5 TRUE FALSE FALSE 7564.562569 6930.209231 7384.322445 8016.321319 7606.154435 7814.683352 7419.687501 7438.571283 7921.21282 7128.364315 1.061191914 0.972201886 1.035906993 1.124566726 1.067026614 1.096280017 1.040868167 1.043517272 1.111224465 1 12.79935536 -9.501731986 24.68070575 1.024432595 1.07407125 0.152753289 0.041638581 612.8110544 715222.3797 0.005413489 0.008214613 3.15E-10 9.501731986 0.049638655 SSSISEEKGDS(ph)DDEKPR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSISEEKGDSDDEKPR 17 2 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 S(0.001)S(0.001)S(0.024)IS(0.227)EEKGDS(0.747)DDEKPR;SSSISEEKGDS(1)DDEKPR ; 102.24 0.0026799 71828700 8134.9 8113.7 6799.1 7553.6 7376.3 7321.4 6511.6 6382.3 9214.2 8527.6 TRUE FALSE FALSE 8035.74871 8227.924882 6917.435483 8426.982773 6999.859886 6853.586169 7064.695141 6566.961781 8390.058875 8306.051723 0.9674571 0.990593986 0.832818734 1.01455939 0.84274215 0.825131651 0.850547935 0.790623752 1.010113969 1 13.01994714 -8.199024651 0.369268695 0.997596097 0.727517972 0.647674177 0.051150535 1.405735298 0.215408655 0.016702786 0.15304108 6.32E-09 8.199024651 -0.270078124 SSSLEMT(ph)PYNTPQLSPATTPANKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLEMTPYNTPQLSPATTPANKK 24 1 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08;B0QZ65;A0A0A0MQV8;B4DGD8 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 SSS(0.001)LEMT(0.357)PY(0.285)NT(0.357)PQLSPATTPANKK 139.98 4.55E-07 86231000 5674.9 5361.5 5260.3 5661.6 6232 6898.2 5370.7 6843.4 5814.7 5314.3 TRUE FALSE FALSE 5605.732136 5436.979338 5351.853315 6316.220831 5913.957785 6457.427283 5826.887124 7041.402982 5294.618669 5176.23372 1.082975082 1.050373618 1.033928065 1.22023486 1.142521398 1.247514628 1.125700159 1.360333278 1.022870866 1 12.33768704 -4 0.191480228 0.99367756 2.38794696 0.708809098 0.059436886 20.73277434 0.232725049 0.059859654 8.621583822 1.00E-04 4 1.3942694 SSSLEMTPYNTPQLS(ph)PATTPANKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSLEMTPYNTPQLSPATTPANKK 24 1 Q14C86-4;Q14C86-5;Q14C86-2;Q14C86;Q14C86-6;F8W9S7;Q14C86-3;H0Y4E7;H0Y7I9;C9IZ08;B0QZ65;A0A0A0MQV8;B4DGD8 Q14C86-4 GAPVD1 GTPase-activating protein and VPS9 domain-containing protein 1 1 0 SSSLEMTPYNTPQLS(0.996)PAT(0.003)TPANKK 100.95 1.74E-05 113780000 2326.6 2503.5 2214.5 2574.3 2929.9 3069.5 2642.4 3451.2 2535.3 2555.3 TRUE FALSE FALSE 2298.242504 2538.744339 2253.042444 2871.952678 2780.37627 2873.368856 2866.84539 3551.055027 2308.536418 2488.912938 0.923392084 1.020021352 0.905231521 1.153898409 1.117104672 1.154467403 1.151846393 1.426749395 0.927527992 1 11.28130005 -4 0.381775373 0.960107591 7.343367133 0.816969866 0.064323496 18.01287317 0.218198522 0.017016988 86.21339872 1.00E-04 4 6.383259543 SSSLGNS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 SSSLGNSPER 10 0 Q5SQI0-7;Q5SQI0-6;Q5SQI0-5;Q5SQI0-4;Q5SQI0-3;Q5SQI0-2;Q5SQI0 Q5SQI0-7 ATAT1 Alpha-tubulin N-acetyltransferase 1 1 0 SSSLGNS(1)PER;SSSLGNS(1)PER ; 98.407 0.026303 12587600 3544.4 4121.7 4359.7 2296.17 5118.3 7143.6 8157 3431 4682.8 4025.4 TRUE FALSE FALSE 3501.199489 4179.725401 4435.57875 2561.663979 4857.094052 6687.147015 8849.855376 3530.270572 4263.95864 3920.819528 0.892976447 1.066033611 1.13128868 0.653349118 1.238795619 1.705548283 2.257144282 0.900390989 1.087517191 1 11.93693952 -8.430024461 3.809953161 0.954028952 1.679107905 0.426883125 0.332787016 0.136324162 3.612806032 0.042808741 0.099418218 3.72E-09 8.430024461 0.725078953 SSSMS(ph)SLTGAYTSGIPSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSMSSLTGAYTSGIPSSSR 20 0 A8CG34-2;A8CG34 A8CG34-2 POM121C Nuclear envelope pore membrane protein POM 121C 1 0 S(0.002)S(0.008)S(0.273)MS(0.703)S(0.014)LT(0.001)GAYTSGIPSSSR 117.08 0.00033993 6340400 745.07 871.84 820.49 639.44 582.59 736.29 676.38 886.76 968.4 754.95 TRUE FALSE FALSE 735.9888003 884.1137864 834.7702843 713.3750615 552.8582584 689.2434453 733.8317003 912.4170015 881.7838786 735.3362902 1.000887363 1.202325791 1.135222476 0.970134442 0.75184411 0.937317326 0.997953875 1.240815956 1.199157298 1 9.522260376 -9.042735843 24.92169742 1.029050002 0.965065099 0.044445378 0.139722567 1222.687451 713015.6545 0.02030271 0.033670208 9.06E-10 9.042735843 -0.063984903 SSSNDS(ph)VDEET(ph)AESDTSPVLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSNDSVDEETAESDTSPVLEK 22 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 0 S(0.104)S(0.119)S(0.156)NDS(0.62)VDEET(0.269)AES(0.261)DT(0.241)S(0.229)PVLEK 75.416 0.0029034 3505900 2128.3 2009.6 1927.1 1512 1747.5 1247.9 1199 1347.1 2367.7 2219.2 TRUE FALSE FALSE 2102.359461 2037.891202 1960.640367 1686.824554 1658.318554 1168.163217 1300.84303 1386.076213 2155.926982 2161.544864 0.972618934 0.942793849 0.907055134 0.780379155 0.767191365 0.540429781 0.601811719 0.641243324 0.997400988 1 11.07784707 -8.939815704 0.950065286 0.988142765 0.585061249 0.941462863 0.039877405 0.082369855 0.144355474 0.006657316 0.018482456 1.15E-09 8.939815704 -0.403081516 SSSNDS(ph)VDEETAES(ph)DTSPVLEK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSNDSVDEETAESDTSPVLEK 22 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 0 S(0.035)S(0.041)S(0.17)NDS(0.75)VDEET(0.004)AES(0.923)DT(0.058)S(0.019)PVLEK 90.869 0.0025549 5467800 2881.8 2710.3 2468.5 1703.9 1841.8 1716.4 1751.4 1827 2942 2392.6 TRUE FALSE FALSE 2846.675513 2748.455675 2511.463207 1900.912935 1747.806073 1606.727579 1900.163872 1879.861362 2678.860152 2330.439907 1.221518523 1.179372043 1.077677738 0.815688458 0.749989763 0.689452483 0.815367033 0.806655154 1.149508358 1 11.1863866 -9.244504253 3.476706717 1.11397368 0.765403415 0.884120798 0.063642968 0.086486095 2.229025884 0.014286757 0.023677547 5.70E-10 9.244504253 -0.348570265 SSSNDS(ph)VDEETAESDTSPVLEK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSNDSVDEETAESDTSPVLEK 22 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 S(0.012)S(0.012)S(0.012)NDS(0.941)VDEET(0.023)AESDTSPVLEK;S(0.026)S(0.026)S(0.026)NDS(0.921)VDEETAESDTSPVLEK ; 178.23 8.03E-14 38115000 24304.9 24923 23600.7 17815.3 16907.3 15712.6 14326.9 12501.6 25413 24855 TRUE FALSE FALSE 24008.66253 25273.86665 24011.46028 19875.18881 16044.45739 14708.61557 15543.82653 12863.31407 23139.99763 24209.26352 0.991713875 1.043975032 0.99182944 0.820974533 0.662740417 0.607561463 0.642061107 0.531338513 0.955832366 1 14.56327157 -8.921018588 1.807504458 1.001405642 0.598034579 0.967360931 0.033539366 0.035692246 0.23487088 0.004601836 0.009625124 1.20E-09 8.921018588 -0.403371063 SSSPAPADIAQTVQEDLR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSPAPADIAQTVQEDLR 18 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 0 0 ;; ;; 271.41 5.22E-99 27161000 4725.67 4517.3 4214.03 4368.04 4711.7 4743.39 4088.16 5007.38 4997.09 5207 FALSE FALSE TRUE 4668.071716 4580.894668 4287.373424 4873.093337 4471.244367 4440.302688 4435.408208 5152.26064 4550.137755 5071.721389 0.920411702 0.903222854 0.845348767 0.960836166 0.881602916 0.875502092 0.874537039 1.015880062 0.897158461 1 12.30825978 -11.74851212 0.707716917 0.999415268 0.904785078 0 0.055764376 0.547189309 0.529262676 0.027285856 0.009905234 1.78E-12 11.74851212 -0.09463019 SSSPATEQS(ph)WMENDFDELREEGFR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSPATEQSWMENDFDELREEGFR 24 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 0 S(0.003)S(0.01)S(0.098)PAT(0.205)EQS(0.684)WMENDFDELREEGFR;S(0.003)S(0.007)S(0.048)PAT(0.087)EQS(0.855)WMENDFDELREEGFR ; 64.761 0.0034065 18259800 1535.86 1349.43 1497.32 1394.4 1210.21 1367.3 1362.46 1363.01 1590.6 1397.05 TRUE FALSE FALSE 1517.140348 1368.427311 1523.380227 1555.627089 1148.448468 1279.933943 1478.187318 1402.446544 1448.332752 1360.75444 1.114925885 1.005638689 1.119511487 1.143209269 0.843979218 0.940606112 1.086299831 1.030638963 1.064360115 1 10.41019103 -8.790704928 24.99945195 1.062476944 0.980819541 0.296817034 0.073218565 260.6049447 222615.1756 0.011952928 0.021668905 1.62E-09 8.790704928 -0.081657403 SSSPLPTVQLHPQS(ph)PTAGK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPLPTVQLHPQSPTAGK 19 0 A0A087X2C4;H0YAH0;O60245;O60245-2 A0A087X2C4 PCDH7 Protocadherin-7 1 0 SSSPLPTVQLHPQS(0.954)PT(0.045)AGK 78.428 0.0040933 7908900 1980.1 2746.9 2349.5 1459.3 1882.9 1864.9 1089.1 1525.5 2381.8 2473.4 TRUE FALSE FALSE 1955.96578 2785.57093 2390.392062 1628.031132 1786.808587 1745.738909 1181.608127 1569.637936 2168.765843 2409.140711 0.81189354 1.156250823 0.992217703 0.675772538 0.741678798 0.724631359 0.490468706 0.651534353 0.900223815 1 11.23430294 -9.234768967 9.240521748 0.936717884 0.65580284 0.683752943 0.105855152 0.230309579 76.54889864 0.018389674 0.030282056 5.82E-10 9.234768967 -0.280915045 SSSPLPTVQLHPQS(ph)PTAGKK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPLPTVQLHPQSPTAGKK 20 1 A0A087X2C4;H0YAH0;O60245;O60245-2 A0A087X2C4 PCDH7 Protocadherin-7 1 0 SSSPLPT(0.007)VQLHPQS(0.802)PT(0.19)AGKK 51.827 0.017038 15640000 1351.6 2278.4 1813.1 1255.8 1407.3 1442.2 931.98 1251.8 1543.6 1802.4 TRUE FALSE FALSE 1335.126179 2310.475375 1844.656245 1401.001505 1335.48023 1350.048074 1011.142358 1288.018858 1405.53655 1755.573388 0.760507187 1.3160802 1.050742884 0.798030726 0.760708859 0.769006915 0.575961315 0.733674175 0.800613953 1 10.77772659 -8.890494432 2.595386229 0.933598823 0.698186434 0.395873331 0.154654804 0.28135381 3.843781682 0.026143434 0.051479064 1.29E-09 8.890494432 -0.235412389 SSSPRGEASS(ph)LNGESH ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPRGEASSLNGESH 16 1 Q8IY57-3;Q8IY57;Q8IY57-5 Q8IY57-3 YAF2 YY1-associated factor 2 1 0 S(0.009)S(0.011)S(0.027)PRGEAS(0.376)S(0.574)LNGES(0.003)H 61.015 0.025128 2951600 1176.2 1049.1 960.36 1744.1 1424.5 1473.5 1058 873.05 1597.3 1248.8 TRUE FALSE FALSE 1161.864022 1063.869257 977.0746629 1945.761048 1351.802449 1379.348106 1147.866494 898.3103243 1454.433487 1216.355996 0.955200637 0.874636423 0.80328018 1.599664124 1.111354286 1.134000334 0.943692881 0.738525832 1.195730109 1 10.24834981 SSSS(ph)GSDDYAYTQALLLHQR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSGSDDYAYTQALLLHQR 20 0 F6SS63;Q8N5C8-2;Q8N5C8 F6SS63 TAB3 TGF-beta-activated kinase 1 and MAP3K7-binding protein 3 1 0 S(0.013)S(0.013)S(0.128)S(0.835)GS(0.011)DDYAYTQALLLHQR 159.44 6.67E-08 5031300 294.47 326.48 230.8 245.65 438.51 356.27 375.2 434.52 302.96 341.38 TRUE FALSE FALSE 290.8808864 331.076194 234.8169772 274.0532088 416.1311984 333.5054968 407.0694786 447.0921506 275.8624988 332.5108984 0.87480106 0.995685241 0.706193326 0.824193162 1.251481381 1.002991175 1.224228982 1.344593975 0.829634458 1 8.377257817 -7.785938864 0.932966263 0.924477059 1.396266371 0.583325617 0.128118031 0.62909834 0.668810546 0.020322254 0.248612795 1.64E-08 7.785938864 0.471789312 SSSS(ph)PELQTLQDILGDPGDKADVGR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSPELQTLQDILGDPGDKADVGR 25 1 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 0 S(0.013)S(0.013)S(0.182)S(0.792)PELQTLQDILGDPGDKADVGR 120.72 2.99E-07 7693500 2441.2 2053 2762.5 2764.1 2397.3 2391.9 1886.9 2453.9 2624.4 2437.4 TRUE FALSE FALSE 2411.445715 2081.902188 2810.580154 3083.698247 2274.956835 2239.06531 2047.173239 2524.899725 2389.667091 2374.075997 1.015740742 0.876931569 1.183862757 1.298904606 0.958249373 0.94313127 0.862303162 1.063529444 1.006567226 1 11.2131504 -6.917057719 20.69686786 1.01355474 3.668181428 0.012052485 0.126581113 3071.640375 805404.1665 0.017246728 19362.62627 1.21E-07 6.917057719 2.654626689 SSSS(ph)PLVVVSVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSPLVVVSVK 12 0 Q96B01-3;Q96B01-2;Q96B01 Q96B01-3 RAD51AP1 RAD51-associated protein 1 1 0 SSS(0.025)S(0.974)PLVVVSVK 168.83 0.00018826 13236000 3036.3 3249.2 3150.2 1995.3 2172 2858.4 2178.5 2370.6 2959 3175.4 TRUE FALSE FALSE 2999.292408 3294.942323 3205.02791 2226.005974 2061.154735 2675.757465 2363.541736 2439.189571 2694.339629 3092.90265 0.969733854 1.065323644 1.036252437 0.719714206 0.666414358 0.865128253 0.764182389 0.788640913 0.871136254 1 11.59474571 -9.261678777 24.99999989 0.996028667 0.761553626 0.741845128 0.06707862 6.754151505 705336.0407 0.008508781 0.013515383 5.47E-10 9.261678777 -0.234475041 SSSSGDQSSDSLNSPT(ph)LLAL ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSGDQSSDSLNSPTLLAL 20 0 P15408;P15408-3;P15408-2 P15408 FOSL2 Fos-related antigen 2 1 0 SSSSGDQSSDSLNS(0.393)PT(0.607)LLAL 145.31 7.46E-05 2471100 1357.2 1424.1 1293.7 1255.9 777.89 494 528.32 723.74 1520.6 1489.6 TRUE FALSE FALSE 1340.657924 1444.148517 1316.216306 1401.113067 738.1913706 462.4349943 573.1954876 744.680275 1384.593728 1450.899977 0.924018158 0.995346709 0.907172325 0.965685498 0.508781709 0.318722863 0.395062028 0.51325404 0.954299917 1 10.50273235 -8.707863808 4.093225552 0.962335302 0.408945923 0.959497311 0.052946082 0.029110167 0.999986292 0.007988071 0.016181859 1.96E-09 8.707863808 -0.553389379 SSSSPELQTLQDILGDPGDKADVGRLS(ph)PEVK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSPELQTLQDILGDPGDKADVGRLSPEVK 31 2 P49815;A0A2R8Y5F1;A0A2R8YGD6;A0A2R8Y7C8;A0A2R8YDR3;A0A2R8Y7X5;A0A2R8YDZ2;H3BMQ0;X5D2U8;A0A2R8YGU4;A0A2R8Y6C9;P49815-5;P49815-3;P49815-2;P49815-6;P49815-7;P49815-4;H3BQK4;A0A2R8Y670 P49815 TSC2 Tuberin 1 0 SSSSPELQT(0.004)LQDILGDPGDKADVGRLS(0.996)PEVK 54.732 0.0013212 14283000 1544.3 1893.2 1520.8 1700.2 2066.4 2162.2 1877.7 2552.4 1780 1622.7 TRUE FALSE FALSE 1525.477478 1919.852519 1547.268886 1896.785124 1960.943897 2024.042398 2037.191791 2626.249667 1620.792342 1580.54202 0.965160975 1.214679834 0.978948276 1.200085224 1.240678117 1.280600182 1.288919728 1.661613316 1.025466151 1 10.62620368 -4.000000001 0.310535882 0.973094077 6.789017736 0.823573592 0.084191552 12.68688331 0.162146297 0.028336638 42.05551639 1.00E-04 4.000000001 5.815923659 SSSSPLVVVS(ph)VKSPNQSLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSPLVVVSVKSPNQSLR 19 1 Q96B01-3;Q96B01-2;Q96B01 Q96B01-3 RAD51AP1 RAD51-associated protein 1 1 0 S(0.006)S(0.006)S(0.032)S(0.135)PLVVVS(0.732)VKS(0.069)PNQS(0.021)LR 100.76 0.00019123 0 1057.8 1097.8 931.08 1514.1 840.45 798.95 794.7 633.07 1011.8 1045 TRUE FALSE FALSE 1044.907127 1113.254857 947.2850568 1689.167366 797.5587003 747.8996735 862.2017982 651.3868816 921.3020739 1017.850749 1.026581871 1.09373094 0.930671867 1.659543275 0.783571364 0.734783242 0.847080772 0.639963061 0.905144565 1 9.991310315 -8.56087563 24.99999916 1.059956574 0.752574058 0.400716878 0.206872943 130.0908278 85592.62559 0.027985945 0.055971975 2.75E-09 8.56087563 -0.307382517 SSSSPLVVVSVKS(ph)PNQSLR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSPLVVVSVKSPNQSLR 19 1 Q96B01-3;Q96B01-2;Q96B01 Q96B01-3 RAD51AP1 RAD51-associated protein 1 1 0 SSSSPLVVVS(0.059)VKS(0.616)PNQS(0.324)LR 65.915 0.0075319 17287000 1013.9 1070.8 1013.7 1476.4 874.32 761.29 466.09 487.91 1018.6 1019.3 TRUE FALSE FALSE 1001.542197 1085.874751 1031.343023 1647.108315 829.7001879 712.646026 505.679673 502.0269061 927.4938649 992.8184391 1.008786861 1.093729435 1.038803252 1.659022687 0.835701831 0.717800957 0.509337511 0.505658322 0.9342029 1 9.9553861 -8.225796052 2.579976156 1.058449874 0.531579468 0.577971561 0.204629212 0.164684568 2.141441317 0.029449982 0.085428632 5.95E-09 8.225796052 -0.526870406 SSSSS(ph)QESLNRPFSSK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSQESLNRPFSSK 16 1 E3W994;J3KR49;O75122;A0A0U1RQI6;B3KR06;E7ENG2;O75122-2;E7ERI8;E7EW49;O75122-3 E3W994;E7ERI8 CLASP2 CLIP-associating protein 2 1 0 S(0.003)S(0.003)S(0.026)S(0.026)S(0.942)QESLNRPFSSK 141.34 0.0038815 29953000 4002.1 4572.7 3577.3 3331.9 4026.1 4209 4074.6 4713.1 3621.4 3992.3 TRUE FALSE FALSE 3953.320866 4637.074591 3639.561406 3717.149955 3820.633094 3940.058484 4420.696422 4849.466112 3297.492914 3888.57947 1.016649112 1.192485489 0.935961688 0.955914617 0.982526684 1.013238514 1.136840961 1.247104797 0.84799422 1 11.92502751 -7.530578036 2.404497174 1.010436281 1.250349405 0.490049414 0.083260066 0.187179861 1.841629159 0.009119177 0.07253743 2.95E-08 7.530578036 0.239913125 SSSSS(ph)QESLNRPLSAK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSQESLNRPLSAK 16 1 Q7Z460;H0Y5T1;F8WA11;Q7Z460-2;Q7Z460-5;Q7Z460-3;Q7Z460-4 Q7Z460;Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 S(0.026)S(0.026)S(0.018)S(0.076)S(0.812)QES(0.041)LNRPLSAK 73.76 0.012813 10804000 2024.3 1935.8 2180.6 820 2932.1 2947 2395.1 2465 2351.1 2155.8 TRUE FALSE FALSE 1999.627053 1963.052243 2218.552428 914.8122582 2782.463996 2758.696211 2598.539734 2536.320886 2140.811728 2099.792005 0.952297679 0.934879378 1.056558184 0.435668036 1.325114101 1.313794987 1.237522444 1.207891486 1.019535136 1 11.03603071 SSSSSASPSS(ph)PSSR ddPTM_HeLa_Romidepsin_16h_R1 3 SSSSSASPSSPSSR 14 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;Q9NYF8-4;H0YF63 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 SSSSSAS(0.008)PS(0.063)S(0.66)PS(0.263)S(0.005)R;SSSSS(0.001)AS(0.001)PS(0.043)S(0.949)PS(0.005)S(0.001)R;SSSSSASPS(0.085)S(0.905)PS(0.008)S(0.001)R ;; 185.2 9.16E-08 83699400 2949.37 3806.78 7289.7 2222.95 2428.2 2221.38 4405.82 695.41 6135.3 5498.9 TRUE FALSE FALSE 2913.421944 3860.371949 7416.574171 2479.977938 2304.279893 2079.440987 4780.050241 715.5305912 5586.543402 5356.037785 0.543950969 0.72075144 1.384712817 0.463024728 0.430220993 0.388242404 0.892460142 0.133593268 1.043036593 1 12.38695042 SSSSSASPSSPSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSSASPSSPSSR 14 0 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;Q9NYF8-4;H0YF63 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 SSSSSAS(0.006)PS(0.014)S(0.295)PS(0.158)S(0.527)R 131.08 0.0020598 4980000 1273.3 1560.9 2347 1047.9 846.21 729.84 1809.6 207.92 2238.1 2164.7 TRUE FALSE FALSE 1257.78053 1582.874391 2387.84855 1169.063129 803.0247461 683.2055795 1963.307379 213.9358372 2037.918731 2108.460782 0.596539685 0.750725081 1.132507928 0.554462828 0.38085828 0.32403049 0.931156698 0.10146541 0.966543342 1 11.04197447 -9.019845262 23.43762686 0.822285011 0.462689998 0.436657437 0.240952331 303.1795986 358061.3801 0.037211453 0.062341894 9.55E-10 9.019845262 -0.359595013 SSSSSGVPYS(ph)PAIPNK ddPTM_HeLa_Romidepsin_16h_R1 4 SSSSSGVPYSPAIPNK 16 0 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-4;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 0 S(0.015)SS(0.002)S(0.015)S(0.085)GVPY(0.111)S(0.771)PAIPNK;SSSSSGVPY(0.002)S(0.998)PAIPNK;S(0.265)S(0.007)S(0.006)S(0.003)S(0.014)GVPY(0.003)S(0.702)PAIPNK;S(0.032)S(0.001)SS(0.002)S(0.01)GVPYS(0.954)PAIPNK ;;; 141.82 0.000524 146585000 24754.9 24636.9 22471.7 23179.6 23769.4 21770.2 18271.6 19981.3 25524.1 23376.3 TRUE FALSE FALSE 24453.17776 24983.73892 22862.81051 25859.73442 22556.35882 20379.15448 19823.58925 20559.42739 23241.16057 22768.98036 1.073968943 1.097270872 1.004120964 1.13574407 0.990661789 0.895040277 0.870640184 0.902957755 1.020737873 1 14.47478207 -8.367514768 3.531790673 1.045141929 0.886602974 0.758635416 0.041412339 0.097950685 2.25192408 0.00649048 0.015605765 4.29E-09 8.367514768 -0.158538955 SSSSSGVPYS(ph)PAIPNKR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSSSGVPYSPAIPNKR 17 1 A0A0A0MRE1;B4DJ07;A0A0A0MSB8;Q9UPT5-4;Q9UPT5-2;Q9UPT5-5;Q9UPT5-1;Q9UPT5-6;Q9UPT5 A0A0A0MRE1 EXOC7 Exocyst complex component 7 1 0 SSSSSGVPYS(0.999)PAIPNKR;SSSSSGVPY(0.01)S(0.989)PAIPNKR ; 98.804 0.0010865 89451000 5353.7 5424.7 5031.7 5516.3 5140.7 5499.6 4432.7 4545.4 5681.6 5423.1 TRUE FALSE FALSE 5288.447045 5501.069069 5119.274628 6154.120561 4878.350896 5148.193309 4809.213427 4676.913978 5173.423466 5282.20708 1.001181318 1.041433815 0.969154475 1.16506613 0.923544046 0.974629209 0.910455299 0.885409055 0.979405651 1 12.36692515 SSSSTTTGEK(ac)ITK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSSTTTGEKITK 13 1 A0A3F2YNW7;Q8NFD5;Q8NFD5-2;Q8NFD5-3;A0A1B0GV63;A0A1B0GWJ2;A0A1B0GTJ8;A0A1B0GVK1;H0Y7H8;Q8NFD5-4;H0Y3S9;H0Y2R3 A0A3F2YNW7 ARID1B AT-rich interactive domain-containing protein 1B 0 1 SSSSTTTGEK(1)ITK 182.41 1.79E-06 559920 132.99 180.63 210.93 137.06 0 240.9 319.13 59.19 277.14 201.88 FALSE TRUE FALSE 131.3690667 183.1729139 214.6011482 152.9075221 0 225.5072675 346.2368942 60.90256926 252.3519043 196.6351285 0.668085442 0.931537082 1.091367294 0.777620577 0 1.146831033 1.76080895 0.309723749 1.283351079 1 7.619377269 SSSSVGS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSSVGSPTR 10 0 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 0 SSSS(0.003)VGS(0.996)PT(0.001)R;SSSSVGS(0.997)PT(0.002)R ; 115.29 0.014775 8086600 3336 3514.6 7188.9 3716.1 2870 3413.4 6107.1 1384.35 5840.4 4774.6 TRUE FALSE FALSE 3295.339549 3564.078631 7314.019789 4145.772967 2723.533191 3195.294756 6625.836922 1424.403983 5318.019996 4650.555204 0.708590567 0.766377018 1.572719701 0.89145764 0.585636138 0.687078126 1.424741054 0.306286867 1.143523679 1 12.18318725 -7.209001074 22.88551574 0.900698768 0.306278175 0.261704399 0.315434414 22064.36865 9628682.343 0.04152369 56.77520037 6.18E-08 7.209001074 -0.594420592 SSSSVSSQGSVASSTGS(ph)PASIR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSSVSSQGSVASSTGSPASIR 22 0 A0A087WXK8;Q9H4H8-2;Q9H4H8 A0A087WXK8 FAM83D Protein FAM83D 1 0 SSSSVSSQGSVASSTGS(1)PASIR;SSSSVSSQGSVASST(0.226)GS(0.774)PASIR ; 411.89 0 6889900 4933.5 4000.31 4896.8 4858.8 5601.6 4915 4339.7 3721.73 4753 4605.6 TRUE FALSE FALSE 4873.368604 4056.626469 4982.02675 5420.597317 5315.72945 4600.947362 4708.31401 3829.412386 4327.879776 4485.945848 1.086363672 0.904296799 1.110585575 1.208351037 1.184974057 1.025635957 1.049569961 0.853646592 0.96476416 1 12.13119649 -7.256055633 4.618806151 1.057736836 0.840133238 0.325405555 0.088909037 0.190348833 10.64303555 0.012423602 0.133962987 5.55E-08 7.256055633 -0.217603598 SSST(ph)RSIDTQT(ph)PSVQER ddPTM_HeLa_Romidepsin_16h_R1 1 SSSTRSIDTQTPSVQER 17 1 Q86VQ1;H7C0B2 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 2 0 S(0.006)S(0.002)S(0.097)T(0.882)RS(0.14)IDT(0.058)QT(0.617)PS(0.198)VQER 110.04 0.0026433 5855700 1883.4 1833.3 1705.3 2177.6 1555.5 1095.4 1067.4 1137.5 2216.6 2280.9 TRUE FALSE FALSE 1860.444396 1859.109246 1734.980031 2429.384358 1476.117031 1025.407475 1158.064929 1170.411768 2018.341744 2221.641889 0.83741867 0.836817695 0.780944958 1.093508531 0.664426179 0.461553899 0.521265347 0.526822875 0.908491037 1 11.11741057 -8.557573034 5.533018177 0.912782274 0.512536491 0.824152221 0.085187711 0.058480876 4.721050641 0.013895507 0.028605989 2.77E-09 8.557573034 -0.400245783 LFSLS(ph)NPSLSTTNLSGPSR ddPTM_HeLa_Romidepsin_16h_R1 2 LFSLSNPSLSTTNLSGPSR 19 0 Q6UUV7;Q6UUV7-3 Q6UUV7 CRTC3 CREB-regulated transcription coactivator 3 1 0 LFS(0.002)LS(0.762)NPS(0.208)LS(0.016)T(0.009)T(0.003)NLSGPSR;LFS(0.003)LS(0.782)NPS(0.212)LS(0.002)T(0.001)TNLSGPSR ; 185.96 4.50E-11 83613000 5200.3 4725.5 5579 5035.7 3018.3 2062.67 1861.27 1606.14 5796.1 4720.5 TRUE FALSE FALSE 5136.916743 4792.025713 5676.100155 5617.951328 2864.264888 1930.872044 2019.366227 1652.611127 5277.682299 4597.860729 1.117240614 1.042229418 1.234508935 1.221862005 0.622955991 0.419950094 0.439196911 0.359430445 1.14785606 1 12.16674705 -8.60550701 4.104146999 1.080276155 0.422103038 0.942129533 0.081597212 0.042757339 1.374585374 0.013711092 0.028574989 2.48E-09 8.60550701 -0.658173117 down SSSTSSSTVTSSAGSEQQNQS(ph)SSGSESTDKGSSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSTSSSTVTSSAGSEQQNQSSSGSESTDKGSSR 34 1 Q8N488 Q8N488 RYBP RING1 and YY1-binding protein 1 0 SSSTSSSTVT(0.004)S(0.014)S(0.043)AGS(0.001)EQQNQS(0.304)S(0.304)S(0.304)GS(0.022)ES(0.002)T(0.002)DKGSSR 85.291 6.33E-09 3727600 314.28 143.22 155.8 165.4 234.8 375.42 413.51 427.73 256.67 130.93 TRUE FALSE FALSE 310.4494345 145.2362549 158.5116336 184.5243262 222.8172798 351.4318736 448.6335291 440.1056927 233.7127924 127.5284197 2.434354908 1.138854031 1.242951446 1.446927098 1.747197059 2.755714172 3.517910204 3.451040118 1.832633015 1 6.994674977 -8.097011566 2.279932684 1.595309784 3.499268608 0.810121179 0.386067095 0.142544076 1.426649819 0.081811508 0.279223773 8.00E-09 8.097011566 1.903958824 SSSVGSSS(ph)SYPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 SSSVGSS(0.003)S(0.79)S(0.208)YPISPAVSR 201.4 9.26E-21 6923900 1309.3 1422.6 837.43 903.13 1220.8 1092.9 1012.3 1388.5 1239.3 1492.5 TRUE FALSE FALSE 1293.341748 1442.6274 852.0051179 1007.55414 1158.498021 1023.067217 1098.284737 1428.674057 1128.453904 1453.724635 0.889674507 0.992366343 0.586084254 0.693084588 0.7969171 0.703755851 0.755497094 0.982768003 0.776250108 1 10.5055383 -9.785993352 24.99998553 0.949781028 0.750162462 0.312630908 0.112567415 145.1127681 147748.0406 0.016203909 0.021301531 1.64E-10 9.785993352 -0.199618566 SSSVGSSSS(ph)YPISPAVSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 SSSVGS(0.023)S(0.023)S(0.216)S(0.737)YPISPAVSR 203.05 7.32E-21 5400300 559.79 671.39 482.92 468.1 538.13 539.79 431.88 636.7 599.55 760.54 TRUE FALSE FALSE 552.9670642 680.841846 491.32502 522.2239245 510.6672181 505.2991611 468.5638764 655.12191 545.9247464 740.7810612 0.746464905 0.919086464 0.663252674 0.704963925 0.689363221 0.682116738 0.632526803 0.88436644 0.736958293 1 9.532903405 -12.57328546 0.34650984 1.135546986 0.704727001 0 0.119024782 1.914994015 0.253950752 0.323990168 0.035421314 2.67E-13 12.57328546 -0.430819985 SSSVGSSSSYPIS(ph)PAVSR ddPTM_HeLa_Romidepsin_16h_R1 4 SSSVGSSSSYPISPAVSR 18 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 SSSVGSSS(0.001)SYPIS(0.999)PAVSR;SSSVGSSSS(0.004)YPIS(0.996)PAVSR;SSSVGSSSSYPIS(1)PAVSR;SSSVGSSSSYPIS(1)PAVSR ;;; 303.44 1.57E-143 598570000 3801.46 3048.31 3068.32 3987.35 7103.8 8869 7677.3 8274.5 3305.83 3404.02 TRUE FALSE FALSE 3755.126343 3091.224188 3121.722823 4448.386168 6741.266578 8302.299523 8329.40967 8513.909602 3010.148285 3315.58307 1.132568922 0.932331998 0.941530572 1.341660298 2.033206961 2.504023983 2.512200568 2.567846868 0.907879013 1 11.69504689 -8.675658729 1.939632414 1.043003525 2.538334145 0.987005793 0.078776598 0.0260778 0.198591193 0.012426918 0.029232267 2.11E-09 8.675658729 1.49533062 up SSSVLS(ph)LEGSEK ddPTM_HeLa_Romidepsin_16h_R1 2 SSSVLSLEGSEK 12 0 G3V311;A1L390-2;A1L390-3;A1L390;A0A0U1RR71 G3V311 PLEKHG3 Pleckstrin homology domain-containing family G member 3 1 0 SSSVLS(0.999)LEGS(0.001)EK;SSS(0.001)VLS(0.991)LEGS(0.009)EK ; 150.26 0.0014555 48263500 5831.8 5071.6 4830.4 4582.4 4288.6 3849.7 3304.9 3900 5543.5 5712.5 TRUE FALSE FALSE 5760.719778 5142.998118 4914.471086 5112.238649 4069.736739 3603.716594 3585.618124 4012.840347 5047.675476 5564.088426 1.035339365 0.924319983 0.8832482 0.918791769 0.731429199 0.647674213 0.644421484 0.721203554 0.90718822 1 12.44192963 -8.977796912 0.901741678 1.014371579 0.650641459 0.830542202 0.055927502 0.115744845 0.182193434 0.008210483 0.022826016 1.05E-09 8.977796912 -0.36373012 SSSVS(ph)PSASFR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSVSPSASFR 11 0 Q04727-4;Q04727;Q04727-3;H7C4W5;H7C4P7;Q5JSY7;Q04727-2 Q04727-4 TLE4 Transducin-like enhancer protein 4 1 0 SSS(0.001)VS(0.996)PS(0.003)ASFR;S(0.004)SS(0.014)VS(0.98)PS(0.003)ASFR ; 147.58 0.0024264 87973000 6004.4 6171.8 5933.2 3689.7 8152.9 8131.4 7481.2 8036.1 5839.1 6118.5 TRUE FALSE FALSE 5931.216063 6258.686762 6036.464857 4116.320475 7736.82709 7611.829783 8116.652941 8268.611875 5316.836272 5959.540488 0.995247213 1.050196198 1.012907769 0.690711051 1.298225443 1.277251123 1.361959527 1.387457958 0.892155407 1 12.54098538 -8.611238615 10.57323285 0.984203636 1.334797429 0.76920173 0.103440629 0.134272285 15.0391338 0.013739436 0.027490418 2.45E-09 8.611238615 0.350593793 SSSVT(ph)SIDKESR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSVTSIDKESR 12 1 H0Y332;Q5JRH0;Q5T5C0-3;Q5T5C0-2;Q5T5C0 H0Y332 STXBP5 Syntaxin-binding protein 5 1 0 SSSVT(0.5)S(0.5)IDKESR;SSS(0.001)VT(0.814)S(0.185)IDKESR ; 228.61 7.04E-29 34810000 8155.5 7453.6 7265.7 6954.3 6762.8 5949 4996.3 5111.4 8228.7 7809.1 TRUE FALSE FALSE 8056.097629 7558.531976 7392.156461 7758.388887 6417.669081 5568.8781 5420.685597 5259.290295 7492.704463 7606.218456 1.059146233 0.993730593 0.971856975 1.020006056 0.843739779 0.732148062 0.71266499 0.691446127 0.985076159 1 12.89296366 -8.530841193 1.771629281 1.022893894 0.70126527 0.955593991 0.028337519 0.050946208 0.315605527 0.004680203 0.012578858 2.95E-09 8.530841193 -0.321628624 SSSYADPWT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 SSSYADPWTPPR 12 0 A0A0C4DGA7;O94929-2;O94929-3;O94929;A0A0A0MRD5;O94929-4 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 SSSYADPWT(1)PPR;SSSYADPWT(1)PPR ; 129.74 0.0084532 8683700 2267.39 1772.61 2030.52 2536.2 2518.5 2365.49 1992.53 2009.97 2207.75 1943.99 TRUE FALSE FALSE 2239.754179 1797.56485 2065.860349 2829.447377 2389.971547 2214.342823 2161.775448 2068.125311 2010.283311 1893.48486 1.182874089 0.949342077 1.091036106 1.49430684 1.262207899 1.169453673 1.141691436 1.092232293 1.061684386 1 10.88682817 -9.484334777 24.99955164 1.075717503 1.231918626 0.357755874 0.116061817 582.3363446 377703.0509 0.019696967 0.030084081 3.28E-10 9.484334777 0.156201123 SSSYSKQFTSS(ph)T(ph)S(ph)Y(ph)NRGDS(ph)TFESK ddPTM_HeLa_Romidepsin_16h_R1 1 SSSYSKQFTSSTSYNRGDSTFESK 24 2 P02671-2;P02671 P02671-2 FGA Fibrinogen alpha chain;Fibrinopeptide A;Fibrinogen alpha chain 5 0 S(0.135)S(0.135)S(0.136)Y(0.3)S(0.309)KQFT(0.31)S(0.31)S(0.597)T(0.592)S(0.586)Y(0.578)NRGDS(0.339)T(0.338)FES(0.336)K 44.105 0.0040777 0 197.41 336.96 240.24 0 340.33 379.23 260.71 257.96 309.57 298.78 TRUE FALSE FALSE 195.003891 341.7037317 244.4212764 0 322.9616902 354.9984269 282.8547009 265.4236656 281.8812839 291.0176525 0.670075816 1.174168401 0.839884709 0 1.109766667 1.219851867 0.971950321 0.91205349 0.968605449 1 8.184962856 SST(ph)DFSELEQPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTDFSELEQPR 12 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 S(0.009)S(0.009)T(0.982)DFSELEQPR 103.14 0.028993 55078000 1696.3 1631 1772 1641.8 2830.6 2339.6 1485.9 2779.9 1713.1 1663.9 TRUE FALSE FALSE 1675.624843 1653.961261 1802.840917 1831.632641 2686.14392 2190.107111 1612.112309 2860.332021 1559.876045 1620.671638 1.033907674 1.020540634 1.11240357 1.130168874 1.657426376 1.351357708 0.994718653 1.764905335 0.962487409 1 10.6623761 -8.946994421 7.717599671 1.027499969 1.404043446 0.505124635 0.19419988 0.152106551 19.04655351 0.02649494 0.048119355 1.13E-09 8.946994421 0.376543477 SST(ph)DSLPGPISR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTDSLPGPISR 12 0 Q9HCD5 Q9HCD5 NCOA5 Nuclear receptor coactivator 5 1 0 S(0.075)S(0.075)T(0.846)DS(0.005)LPGPISR 162.93 0.0010753 12955000 1274.7 1674.7 1397.4 1436.9 1616.7 1782.3 1491.1 1645.6 1779.4 1801.7 TRUE FALSE FALSE 1259.163466 1698.276471 1421.721161 1603.041139 1534.193766 1668.416782 1617.753997 1693.21284 1620.246007 1754.891574 0.717516389 0.967738689 0.810147579 0.913470189 0.874238494 0.95072357 0.921854102 0.96485325 0.923274139 1 10.77716618 -8.267747874 19.80578094 0.871219902 0.9434147 0.088133084 0.076639756 57.49200224 180511.0245 0.015245043 0.035106393 5.40E-09 8.267747874 0.072194798 SST(ph)PEMPAVSAFFSLAALAEVAAMENVHR ddPTM_HeLa_Romidepsin_16h_R1 2 SSTPEMPAVSAFFSLAALAEVAAMENVHR 29 0 H7C1Q0;C9JA69;Q8WY36-2;Q8WY36 H7C1Q0 BBX HMG box transcription factor BBX 1 0 S(0.147)S(0.147)T(0.707)PEMPAVSAFFSLAALAEVAAMENVHR;S(0.193)S(0.193)T(0.614)PEMPAVSAFFSLAALAEVAAMENVHR ; 106.67 3.17E-09 37156000 1134.41 840.56 910.56 621.86 595.4 554 474.511 283.775 886.68 740.88 TRUE FALSE FALSE 1120.583375 852.3934257 926.4079148 693.7623791 565.0145163 518.601188 514.8159525 291.9855819 807.3731201 721.6318308 1.552846378 1.181202643 1.283768087 0.961379958 0.782967841 0.718650655 0.713405272 0.40461849 1.118815836 1 9.495119166 -8.805952762 1.275182062 1.265991287 0.596373504 0.750905667 0.156997302 0.215920833 0.698513052 0.035243934 0.091161754 1.56E-09 8.805952762 -0.669617783 SST(ph)PLPTISSSAENTR ddPTM_HeLa_Romidepsin_16h_R1 6 SSTPLPTISSSAENTR 16 0 G5E972;P42167;H0YJH7;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 S(0.007)S(0.083)T(0.91)PLPTISSSAENTR;S(0.011)S(0.096)T(0.893)PLPTISSSAENTR;S(0.006)S(0.006)T(0.989)PLPTISSSAENTR;SS(0.001)T(0.998)PLPTISSSAENTR;S(0.007)S(0.007)T(0.987)PLPTISSSAENTR;S(0.023)S(0.023)T(0.955)PLPTISSSAENTR ;;;;; 213.52 1.28E-25 2529362600 12813.8 15174.4 12412.8 11044.2 9369.92 8893.26 7101.16 8742.43 13633.7 13057.9 TRUE FALSE FALSE 12657.62048 15388.0256 12628.83958 12321.18237 8891.738018 8325.009388 7704.332353 8995.378419 12414.26773 12718.65388 0.995201269 1.209878479 0.99293838 0.968748933 0.699109993 0.65455114 0.605750611 0.707258685 0.976067739 1 13.63465837 -8.762946681 3.156926444 1.015873192 0.652401413 0.871281113 0.067592824 0.064233592 1.325434845 0.010221119 0.020686356 1.73E-09 8.762946681 -0.363471779 SST(ph)PPGESYFGVSSLQLK ddPTM_HeLa_Romidepsin_16h_R1 2 SSTPPGESYFGVSSLQLK 18 0 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 S(0.049)S(0.049)T(0.902)PPGESYFGVSSLQLK;S(0.018)S(0.018)T(0.964)PPGESYFGVSSLQLK ; 151.16 7.39E-05 1749120000 11827.7 10874.5 10889.1 10370.1 10389.8 10003.6 9218.8 9473.9 11494 10290.7 TRUE FALSE FALSE 11683.53944 11027.5915 11078.62022 11569.13975 9859.569736 9364.402245 10001.84464 9748.012349 10465.94785 10023.34613 1.165632643 1.10019063 1.105281617 1.15421932 0.983660507 0.934259091 0.997854859 0.972530752 1.044157083 1 13.29107659 -8.653640767 7.353776678 1.088772231 0.969444361 0.615379044 0.047507898 0.170416385 10.57787915 0.009715118 0.019486449 2.22E-09 8.653640767 -0.119327871 SST(ph)PSDINSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPSDINSPR 11 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-5;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 0 SS(0.003)T(0.997)PS(0.001)DINSPR 155.47 0.0042429 6711300 3472.3 3612.3 3267.5 4143.2 3470.5 2728.9 2070.6 2130.4 3799.6 3891.2 TRUE FALSE FALSE 3429.978272 3663.154054 3324.369467 4622.256278 3293.387435 2554.532097 2246.476712 2192.039763 3459.75426 3790.106063 0.904982134 0.966504365 0.877117793 1.219558556 0.868943344 0.674000161 0.592721332 0.578358422 0.912838375 1 11.88802251 -8.263235832 2.997917776 0.967040849 0.597472149 0.760646425 0.091628256 0.092249843 1.674664304 0.012921355 0.034740269 5.45E-09 8.263235832 -0.3695687 SST(ph)PSPSPLNLSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSTPSPSPLNLSSSR 15 0 P37275-3;P37275-4;P37275-5;P37275;P37275-2 P37275-3 ZEB1 Zinc finger E-box-binding homeobox 1 1 0 SS(0.008)T(0.992)PSPSPLNLSSSR;S(0.001)S(0.009)T(0.989)PS(0.001)PSPLNLSSSR ; 132.86 0.0032854 30028000 3398.7 2655 2961.4 2147.1 2452.44 2347.23 2447.2 2497.69 3506 2927.2 TRUE FALSE FALSE 3357.275337 2692.37716 3012.941925 2395.357804 2327.282835 2197.249578 2655.065107 2569.956719 3192.414579 2851.150922 1.177515827 0.944312396 1.056745857 0.840137148 0.816260836 0.77065355 0.931225733 0.901375195 1.119693298 1 11.47732869 -9.391501749 2.020722814 1.077077073 0.847667452 0.655439201 0.074014402 0.172258302 1.379863366 0.014257256 0.023588306 4.06E-10 9.391501749 -0.229409621 SST(ph)TSMT(ph)S(ph)VPK ddPTM_HeLa_Romidepsin_16h_R1 1 SSTTSMTSVPK 11 0 Q13200;C9JPC0;H7C2Q3 Q13200 PSMD2 26S proteasome non-ATPase regulatory subunit 2 3 0 S(0.058)S(0.451)T(0.511)T(0.362)S(0.326)MT(0.757)S(0.534)VPK 51.875 0.004342 0 1240 1028.7 948.65 626.02 765.19 1035.7 996.55 1186 764.14 986.17 TRUE FALSE FALSE 1224.886403 1043.182066 965.1608553 698.4033779 726.139499 969.5221126 1081.196932 1220.315039 695.7934046 960.5491612 1.275193871 1.086026731 1.004801102 0.727087593 0.755962868 1.009341481 1.125602911 1.270434756 0.724370425 1 9.907715643 -9.783132705 3.94160961 1.131679141 0.966566814 0 0.206481004 0.330599419 11.24161536 0.030751135 0.042156841 1.65E-10 9.783132705 -0.165112327 SSTFPQTDVLSS(ph)SLEAEHR ddPTM_HeLa_Romidepsin_16h_R1 2 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 0 SSTFPQTDVLS(0.009)S(0.983)S(0.009)LEAEHR;SSTFPQTDVLS(0.004)S(0.498)S(0.498)LEAEHR ; 292.35 2.54E-124 33942500 8463.6 7875 7702.8 7012.2 6497.9 5358.8 4585.6 4415.5 9591.7 8264.6 TRUE FALSE FALSE 8360.442388 7985.864457 7836.864003 7822.983557 6166.287916 5016.389975 4975.10075 4543.255526 8733.794329 8049.884501 1.038579173 0.992047085 0.973537447 0.971813143 0.766009489 0.623162975 0.618033805 0.564387666 1.084958962 1 12.97475237 -8.577000585 1.566520378 1.01500134 0.586636938 0.973692675 0.030589234 0.031640916 0.153533672 0.003583931 0.009886579 2.65E-09 8.577000585 -0.428364402 SSTFPQTDVLSSS(ph)LEAEHR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTFPQTDVLSSSLEAEHR 19 0 D4PHA4;Q86WP2-4;Q86WP2-3;Q86WP2;Q86WP2-2 D4PHA4 GPBP1 Vasculin 1 0 SSTFPQTDVLS(0.001)S(0.201)S(0.798)LEAEHR 207.13 5.03E-22 34959000 7551.2 7277.4 6572 6248.1 4826.3 4440.9 3787.6 4027.9 9154.5 7377 TRUE FALSE FALSE 7459.16307 7379.851428 6686.382903 6970.53472 4579.995902 4157.140822 4109.318649 4144.440932 8335.698592 7185.344477 1.038107928 1.027069955 0.930558434 0.97010446 0.637407979 0.578558319 0.571902803 0.576790848 1.160097281 1 12.81084161 -8.749659591 2.9415546 1.012226671 0.575836795 0.936870861 0.054884256 0.026646873 0.473464564 0.004870086 0.010015888 1.78E-09 8.749659591 -0.436389876 SSTLSSSSMSLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 SSTLSSSSMSLSPK 14 0 O15119-3;O15119-2;O15119 O15119-3 TBX3 T-box transcription factor TBX3 1 0 SSTLSSSS(0.003)MS(0.134)LS(0.863)PK;SSTLSSS(0.002)S(0.01)MS(0.06)LS(0.927)PK ; 113.76 0.0068557 25222000 7899.1 7403.1 6764.4 6040.4 7800.8 5959.1 5209.1 5928.5 7733.7 7530.3 TRUE FALSE FALSE 7802.822731 7507.321036 6882.131544 6738.819469 7402.696067 5578.332742 5651.560824 6100.031794 7041.978503 7334.66172 1.063828576 1.023540188 0.938302516 0.918763499 1.009275731 0.76054397 0.770527809 0.831671865 0.96009588 1 12.84051471 -8.527309689 0.866154451 1.027915911 0.767810684 0.674586594 0.057811574 0.261755313 0.340848909 0.009568363 0.042763239 2.97E-09 8.527309689 -0.260105228 SSTPLHS(ph)PSPIR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPLHSPSPIR 12 0 O95817;C9JFK9 O95817 BAG3 BAG family molecular chaperone regulator 3 1 0 S(0.002)STPLHS(0.499)PS(0.499)PIR 135.94 0.002634 9171700 1106.5 1221.4 908.02 1237.8 1719.7 1409.1 1164.6 1128.3 1589.6 1399.7 TRUE FALSE FALSE 1093.013552 1238.594901 923.8237072 1380.92026 1631.937292 1319.063058 1263.521095 1160.94558 1447.422195 1363.335592 0.801720104 0.908503312 0.677620178 1.012898268 1.197018035 0.967526312 0.926786554 0.851547915 1.061677112 1 10.41292502 SSTPLPTISS(ph)SAENTR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTPLPTISSSAENTR 16 0 G5E972;P42167;H0YJH7;P42167-3;P42167-2;P42166 G5E972;P42166 TMPO "Lamina-associated polypeptide 2, isoforms beta/gamma;Thymopoietin;Thymopentin;Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 1 0 SSTPLPTIS(0.039)S(0.68)S(0.279)AENT(0.002)R 163.9 5.27E-05 8992700 1792.5 1669.8 1624 1034.1 1406.4 1606.4 1514.3 1408.5 1862.1 1875.2 TRUE FALSE FALSE 1770.652321 1693.307488 1652.265039 1153.667508 1334.62616 1503.756224 1642.924604 1449.252725 1695.549112 1826.482034 0.969433199 0.927086857 0.904616092 0.631633647 0.730708617 0.823307427 0.899502198 0.793466729 0.928314148 1 10.83485185 -9.592039366 3.066410765 0.981426365 0.781882914 0.586203658 0.070151267 0.122703242 2.344999601 0.011543091 0.016996417 2.56E-10 9.592039366 -0.19954345 SSTPSDINS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSTPSDINSPR 11 0 A0A1B0GWK2;Q674X7-4;Q674X7-3;Q674X7-5;Q674X7-2;Q674X7 A0A1B0GWK2 KAZN Kazrin 1 0 SST(0.002)PSDINS(0.998)PR;SSTPSDINS(1)PR ; 147.96 0.0024151 10864100 3611.5 4277.9 3754.1 3428.3 5511.8 5349.4 4524.2 4584.2 3982.5 3840.5 TRUE FALSE FALSE 3567.481649 4338.124388 3819.438536 3824.696177 5230.512279 5007.590604 4908.485435 4716.836594 3626.295226 3740.723256 0.953687671 1.159702039 1.021042797 1.022448311 1.398262293 1.338669092 1.312175507 1.260942409 0.969410185 1 11.86910152 -8.787122818 10.29410421 0.998992709 1.327192135 0.848958446 0.062916442 0.105093542 41.0314285 0.009953642 0.018204047 1.63E-09 8.787122818 0.328199426 SSTVAS(ph)LDTDSTK ddPTM_HeLa_Romidepsin_16h_R1 1 SSTVASLDTDSTK 13 0 C9IZZ8;C9J6Y2;C9J0J6;C9JZ07;G3V1A3;C9J5T5;C9JBU8;A8MPU2;O14713-2;O14713 C9IZZ8 ITGB1BP1 Integrin beta-1-binding protein 1 1 0 S(0.003)ST(0.148)VAS(0.848)LDTDSTK 236.28 2.42E-41 24460000 3435.6 3328.3 3244 2589.3 3715.8 4150.5 3811 4190.2 3586 3743.3 TRUE FALSE FALSE 3393.725586 3375.155895 3300.460459 2888.687049 3526.16886 3885.296445 4134.706245 4311.436826 3265.259179 3646.048526 0.930795507 0.925702406 0.905215725 0.792278827 0.967120661 1.065618413 1.134023921 1.182495733 0.895561086 1 11.83211805 -8.013701017 2.227284693 0.94508349 1.163757754 0.745145486 0.056657108 0.14853871 1.429030332 0.009378906 0.035321758 9.69E-09 8.013701017 0.218674265 SSTVATLQGT(ph)PDHGDPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTVATLQGTPDHGDPR 17 0 Q8IVT2 Q8IVT2 MISP Mitotic interactor and substrate of PLK1 1 0 SSTVAT(0.01)LQGT(0.99)PDHGDPR 135.55 0.0029129 7790500 1296.7 1148.1 1392.2 1154.7 1667.1 1626.6 1408.3 1351.5 1399.7 1404.2 TRUE FALSE FALSE 1280.895322 1164.262982 1416.430657 1288.211847 1582.021666 1522.66551 1527.920967 1390.60352 1274.507326 1367.718682 0.936519577 0.851244483 1.035615493 0.941869015 1.15668645 1.113288522 1.117131021 1.016732124 0.93184903 1 10.41755581 -8.769648809 24.98477408 0.963133313 1.102995281 0.628263106 0.056480936 93.80532958 285489.9957 0.008375122 0.015368558 1.70E-09 8.769648809 0.139861969 SSTVT(ph)EAPIAVVTSR ddPTM_HeLa_Romidepsin_16h_R1 1 SSTVTEAPIAVVTSR 15 0 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 0 S(0.173)S(0.173)T(0.173)VT(0.482)EAPIAVVTSR 164.92 0.00011176 5373900 2264.3 1955.2 2746.5 3020.9 1949 2281.5 1845 2082.5 2370.5 2151.9 TRUE FALSE FALSE 2236.701841 1982.725357 2794.30168 3370.190672 1849.535257 2135.719513 2001.714254 2142.753852 2158.476543 2095.993328 1.067132138 0.945959766 1.333163443 1.607920515 0.882414668 1.018953393 0.955019383 1.022309481 1.029810789 1 11.03341841 -5.71638698 12.53489041 1.066391118 0.886836805 0 0.208594403 0 0 0.027735324 0 1.92E-06 5.71638698 -0.179554313 ASTSSSSSSSSNQQTEKETNT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 ASTSSSSSSSSNQQTEKETNTPK 23 1 C9J2P0;P51965-3;P51965 C9J2P0 UBE2E1 Ubiquitin-conjugating enzyme E2 E1 1 0 ASTSSS(0.001)S(0.003)S(0.031)S(0.202)S(0.18)S(0.025)NQQT(0.103)EKET(0.128)NT(0.327)PK;ASTSSS(0.001)S(0.002)S(0.007)S(0.024)S(0.024)S(0.024)NQQT(0.297)EKET(0.13)NT(0.489)PK ; 71.882 0.00081947 18948800 2995 2581.1 2946.5 2999.6 1889.19 1394.24 1169.18 1268.52 2934.3 2890.3 TRUE FALSE FALSE 2958.495788 2617.436794 2997.782597 3346.427866 1792.777585 1305.152564 1268.49012 1305.222625 2671.848859 2815.209589 1.050897169 0.929748465 1.064852368 1.188695818 0.636818513 0.463607601 0.450584612 0.463632488 0.949076356 1 11.45902662 -8.602165483 4.508257898 1.029789934 0.469856194 0.93502478 0.069075454 0.034216253 1.297607444 0.009730116 0.020083589 2.50E-09 8.602165483 -0.55993374 down SSVKT(ph)PESIVPIAPELQPSTSR ddPTM_HeLa_Romidepsin_16h_R1 2 SSVKTPESIVPIAPELQPSTSR 22 1 Q14676-3;Q14676;Q14676-2 Q14676-3 MDC1 Mediator of DNA damage checkpoint protein 1 1 0 S(0.25)S(0.25)VKT(0.458)PES(0.042)IVPIAPELQPSTSR;S(0.087)S(0.087)VKT(0.808)PES(0.018)IVPIAPELQPSTSR ; 65.118 0.0037989 76310000 3408.3 2809.6 3077.7 2163.46 3430.5 3802.2 2940 3472.2 3888.7 3271.6 TRUE FALSE FALSE 3366.758329 2849.153623 3131.266077 2413.609425 3255.428784 3559.251691 3189.723527 3572.662629 3540.884933 3186.60336 1.056535109 0.894103627 0.982634399 0.757423862 1.021598365 1.116942176 1.000979151 1.121150713 1.111178434 1 11.63780374 -8.51411709 24.98551974 0.991517566 1.071394665 0.191089293 0.096174211 672.2638582 1917086.719 0.013835471 0.028862181 3.06E-09 8.51411709 0.079877099 SSVSS(ph)VGAR ddPTM_HeLa_Romidepsin_16h_R1 2 SSVSSVGAR 9 0 Q8N4M4;E9PRA3;E9PRP1;E9PS62;Q9BZ68;Q9BZ67-2;Q9BZ67-3;Q9BZ67 Q8N4M4 FRMD8;FRMD8P1 Putative FERM domain-containing protein FRMD8P1;FERM domain-containing protein 8 1 0 SSVS(0.117)S(0.883)VGAR;SSVS(0.134)S(0.866)VGAR ; 121.5 0.0017984 3517000 3948.7 3683.9 3862.7 2892.9 5922.8 6813.2 6438.7 4182.5 4215.5 3859.2 TRUE FALSE FALSE 3900.571726 3735.762041 3929.928673 3227.39071 5620.537415 6377.858509 6985.603017 4303.514039 3838.455122 3758.937428 1.037679344 0.993834591 1.04548925 0.85859123 1.495246336 1.696718456 1.858398324 1.144875147 1.021154301 1 11.87610918 -8.671793268 5.538298097 1.009009577 1.593808422 0.704003974 0.176242656 0.076897374 3.744930294 0.023279749 0.046948835 2.13E-09 8.671793268 0.584798845 SSYHNITDVCELAVGPAGAPATLLNEAGKDALK ddPTM_HeLa_Romidepsin_16h_R1 1 SSYHNITDVCELAVGPAGAPATLLNEAGKDALK 33 1 P16471-2;P16471 P16471-2 PRLR Prolactin receptor 0 0 28.042 0.02939 4740500 1674.7 1133 1039 1420.8 1416 1305.2 864.16 848.25 1875.1 1534 FALSE FALSE TRUE 1654.288112 1148.950404 1057.083359 1585.079581 1343.736236 1221.801932 937.5617288 872.7927754 1707.38636 1494.146459 1.107179355 0.768967725 0.707483094 1.060859577 0.899333682 0.817725682 0.627489844 0.584141381 1.142716867 1 10.54510586 -6.70609608 0.341263895 1.046648352 2.77E-15 0.569939888 0.125231674 5.107562622 0.314679882 0.045407449 2.375582353 1.97E-07 6.70609608 -1.046648352 SSYLES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SSYLESPR 8 0 H0YIQ2;P49750-3;P49750-1;P49750;F8VU51 H0YIQ2 YLPM1 YLP motif-containing protein 1 1 0 SSYLES(1)PR;SSYLES(1)PR ; 114.86 0.020677 31843000 3892 3787.8 4116.8 1843.89 5077.6 6374.5 5390.3 5308.2 4253.6 3952.5 TRUE FALSE FALSE 3844.562807 3841.124748 4188.451177 2057.089238 4818.471125 5967.190023 5848.151947 5461.784392 3873.147363 3849.81348 0.998636123 0.997743077 1.087962105 0.53433478 1.251611578 1.549994579 1.5190741 1.418714029 1.006061042 1 11.91057283 -8.526108906 24.9970023 0.974144419 1.482002418 0.74180521 0.148065381 35.21535962 272518.5317 0.020265714 0.040699205 2.98E-09 8.526108906 0.507857999 SSYLES(ph)PRGPR ddPTM_HeLa_Romidepsin_16h_R1 1 SSYLESPRGPR 11 1 H0YIQ2;P49750-3;P49750-1;P49750;F8VU51 H0YIQ2 YLPM1 YLP motif-containing protein 1 1 0 SSYLES(1)PRGPR 69.314 0.029607 4466200 1453.2 1725.7 1396.4 2511.9 2072.7 2184.2 2355.4 2267.8 1683.1 1707.7 TRUE FALSE FALSE 1435.487839 1749.99445 1420.703756 2802.337697 1966.922385 2044.636669 2555.467617 2333.415215 1532.559321 1663.333708 0.863018547 1.052100635 0.854130322 1.684771783 1.182518202 1.229240206 1.536352931 1.402854523 0.921378142 1 10.69986192 -9.278698801 24.98659582 0.938752885 1.391962469 0.726264203 0.14382195 321.165344 464952.4256 0.021603592 0.033048474 5.26E-10 9.278698801 0.453209584 ST(ph)ALT(ph)WLS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 STALTWLSK 9 0 Q9UNY4-2;Q9UNY4 Q9UNY4-2 TTF2 Transcription termination factor 2 3 0 S(0.098)T(0.903)ALT(0.999)WLS(1)K 71.153 0.0032339 0 784.16 661.59 570.86 436.88 1000.1 777.88 675.33 686.56 1033.6 693.79 TRUE FALSE FALSE 774.6023563 670.9038814 580.7955788 487.3941212 949.0611651 728.1759785 732.6925133 706.4245304 941.1522273 675.7652358 1.146259552 0.992806149 0.859463536 0.721247699 1.404424369 1.077557619 1.084241205 1.045369742 1.392720693 1 9.400378324 -8.748429266 24.99976135 1.025114425 1.142612522 0.106462092 0.188918343 422.8318501 812493.5651 0.02338938 0.046552807 1.78E-09 8.748429266 0.117498098 ST(ph)ELLIR ddPTM_HeLa_Romidepsin_16h_R1 2 STELLIR 7 0 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431;Q16695 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A;HIST3H3 Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1;Histone H3.1t 1 0 S(0.23)T(0.77)ELLIR;S(0.228)T(0.772)ELLIR ; 141.52 0.027115 7586100 4369 3690.7 6077.3 4823.8 9164.9 6576 7194.4 5710.8 4668 3589.8 TRUE FALSE FALSE 4315.748948 3742.657771 6183.072857 5381.550453 8697.180954 6155.814823 7805.492156 5876.032988 4250.482389 3496.536478 1.234292556 1.070390026 1.768342157 1.539108911 2.48737029 1.760546432 2.232349699 1.680529582 1.215626496 1 11.77171084 -9.523277669 1.384945946 1.09956838 2.014179724 0.676295727 0.265252694 0.14918968 0.572055 0.041507294 0.069077869 3.00E-10 9.523277669 0.914611344 ST(ph)ELVLSPDMPR ddPTM_HeLa_Romidepsin_16h_R1 3 STELVLSPDMPR 12 0 Q8TDY2-2;Q8TDY2 Q8TDY2-2 RB1CC1 RB1-inducible coiled-coil protein 1 1 0 S(0.365)T(0.635)ELVLSPDMPR;S(0.151)T(0.849)ELVLSPDMPR;S(0.154)T(0.845)ELVLS(0.001)PDMPR ;; 171.62 0.00029439 129202000 9412.6 8413.3 8561.1 8752.6 12937.7 13925.7 12877 14232.6 9244.1 8320 TRUE FALSE FALSE 9297.875611 8531.742658 8710.102354 9764.616794 12277.44089 13035.89271 13970.77206 14644.39783 8417.284544 8103.845201 1.147341216 1.052801781 1.074811048 1.204936244 1.515014242 1.60860584 1.723968278 1.807092493 1.038677854 1 12.9843909 -8.5929002 1.21268942 1.065229225 1.768467118 0.973832412 0.047927129 0.067041301 0.190124531 0.010046644 0.032015224 2.55E-09 8.5929002 0.703237893 ST(ph)LSPPEASPGPPAAPR ddPTM_HeLa_Romidepsin_16h_R1 1 STLSPPEASPGPPAAPR 17 0 Q6NUJ5-2;Q6NUJ5 Q6NUJ5-2 PWWP2B PWWP domain-containing protein 2B 1 0 S(0.015)T(0.492)LS(0.492)PPEASPGPPAAPR 189.33 6.80E-13 6440000 1777.6 1745.9 1697.4 1474.7 1600.9 1616.8 1389.3 1458.4 1860 1666 TRUE FALSE FALSE 1755.933927 1770.478826 1726.942535 1645.211753 1519.200099 1513.491698 1507.307107 1500.596503 1693.636942 1622.71708 1.082094932 1.091058231 1.064228975 1.01386235 0.936207622 0.932689818 0.928878562 0.924743149 1.043704391 1 10.66419577 -8.840755624 3.112255631 1.046124051 0.929044143 0.855285861 0.024224355 0.106912919 2.086542335 0.005452927 0.010678289 1.44E-09 8.840755624 -0.117079908 ST(ph)PAMMNGQGSTTSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 STPAMMNGQGSTTSSSK 17 0 Q6ZN18-2;Q6ZN18;F5GZR7;A0A669KBC9;A0A669KBL4;G5EA50;Q6ZN18-3 Q6ZN18-2 AEBP2 Zinc finger protein AEBP2 1 0 S(0.428)T(0.572)PAMMNGQGSTTSSSK 84.195 0.013415 3009900 1024.8 866.52 743.22 918.17 570.45 532.23 448.61 562.59 837.67 729.87 TRUE FALSE FALSE 1012.309343 878.7188913 756.1554323 1024.333136 541.3378079 498.2222207 486.7149222 578.867654 762.7466972 710.9078722 1.423966991 1.23605171 1.063647572 1.440880282 0.761473925 0.700825297 0.684638532 0.814265359 1.072919188 1 9.4735188 -8.701717333 9.209463641 1.21139835 0.731837525 0.727657339 0.139603954 0.164584804 23.74151636 0.025563289 0.051129837 1.99E-09 8.701717333 -0.479560825 ST(ph)PFIVPSS(ph)PTEQEGR ddPTM_HeLa_Romidepsin_16h_R1 1 STPFIVPSSPTEQEGR 16 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 S(0.405)T(0.595)PFIVPS(0.359)S(0.639)PT(0.002)EQEGR 149.19 0.0012137 1650300 598.05 409.96 408.59 245.79 295.09 368.07 449.01 355.8 556.58 471.3 TRUE FALSE FALSE 590.7607366 415.7314276 415.7013376 274.2093963 280.0304562 344.5515149 487.1488982 366.0945116 506.7980908 459.0555581 1.286904659 0.90562334 0.905557792 0.59733379 0.610014303 0.750566046 1.061198127 0.797494999 1.104001644 1 8.842524959 -9.943050656 2.651987631 1.134498948 0.77793604 0.529509982 0.143201978 0.176102934 2.516835548 0.028664873 0.038016264 1.14E-10 9.943050656 -0.356562908 ST(ph)PKEDDSSASTSQSTR ddPTM_HeLa_Romidepsin_16h_R1 1 STPKEDDSSASTSQSTR 17 1 E7EX17;P23588-2;P23588;F8VX11 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 S(0.23)T(0.77)PKEDDSSASTSQSTR 182.91 1.52E-08 8204600 1949.4 2038.8 2232.8 2136.3 2241.5 2371.6 1866 1680.6 2459.4 2263 TRUE FALSE FALSE 1925.639963 2067.50228 2271.660947 2383.309058 2127.107891 2220.062414 2024.497993 1729.225509 2239.425104 2204.206934 0.873620318 0.937980118 1.030602396 1.081254678 0.965021867 1.007193281 0.918470023 0.784511419 1.015977706 1 11.10604396 -7.310864549 3.27459454 0.960893672 0.769132389 0.487230208 0.058665755 0.24113222 4.204003856 0.009857878 0.108069207 4.89E-08 7.310864549 -0.191761283 ST(ph)PPYLFPEYPEASK ddPTM_HeLa_Romidepsin_16h_R1 1 STPPYLFPEYPEASK 15 0 Q8TE76-2;Q8TE76-3;Q8TE76 Q8TE76-2 MORC4 MORC family CW-type zinc finger protein 4 1 0 S(0.442)T(0.557)PPY(0.001)LFPEYPEASK 97.417 0.020206 5348400 1276.8 1329.1 1741.1 803.67 1067.1 851.66 739.77 671.24 1490.7 1361.6 TRUE FALSE FALSE 1261.23787 1347.811105 1771.403115 896.5941068 1012.641905 797.2416746 802.6060453 690.6612704 1357.368058 1326.225436 0.950998101 1.016276018 1.335672705 0.676049548 0.763551865 0.601135865 0.605180706 0.520772149 1.023482149 1 10.37311031 -9.067485989 12.94905818 1.004436037 0.63234077 0.756908853 0.120196347 0.667260328 127.5837263 0.018242239 0.030259626 8.56E-10 9.067485989 -0.372095268 ST(ph)SFRQGPEESGLGDGTGPK ddPTM_HeLa_Romidepsin_16h_R1 1 STSFRQGPEESGLGDGTGPK 20 1 Q92614;A0A0D9SFK2;Q92614-2;Q92614-3;Q92614-4;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 S(0.111)T(0.478)S(0.41)FRQGPEES(0.001)GLGDGTGPK 66.52 0.0060026 10557000 1217.6 1090.3 741.66 2635 945.84 904.85 838.58 1014.2 1105 1053.5 TRUE FALSE FALSE 1202.759423 1105.649272 754.5682812 2939.671098 897.5702554 847.0330053 909.8089643 1043.544277 1006.166032 1026.129918 1.172131717 1.077494431 0.735353553 2.864813749 0.874714049 0.825463706 0.886641105 1.01697091 0.980544485 1 10.00299769 ST(ph)TPTSSPFR ddPTM_HeLa_Romidepsin_16h_R1 1 STTPTSSPFR 10 0 E7EPN9;Q9Y520-6;Q9Y520-4;Q9Y520-5;Q9Y520;Q9Y520-7;Q9Y520-2;A0A2R8Y7F4;A0A2R8YET2;H7C5N8;A0A2R8Y424 E7EPN9 PRRC2C Protein PRRC2C 1 0 S(0.163)T(0.273)T(0.273)PT(0.01)S(0.273)S(0.007)PFR 115.7 0.02995 146840000 7031.8 6433.1 8463.1 7897.4 7724.5 6330.3 5557.8 4311.5 6283.4 4917.1 TRUE FALSE FALSE 6946.093717 6523.665351 8610.396705 8810.534546 7330.289941 5925.81426 6029.879393 4436.24645 5721.396967 4789.353033 1.450319838 1.362118287 1.797820425 1.839608499 1.530538653 1.237289091 1.259017523 0.926272592 1.194607482 1 12.22561507 -12.063255 0.854458033 1.001558177 1.440090783 0.18978586 0.259210135 0.658922361 0.877284606 0.178332023 0.054174181 8.64E-13 12.063255 0.438532606 ST(ph)VLGLPQHVQK ddPTM_HeLa_Romidepsin_16h_R1 1 STVLGLPQHVQK 12 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 S(0.43)T(0.57)VLGLPQHVQK 102.52 0.010784 8474400 2347.3 2565.7 2603.4 2511.6 2729.4 2852.3 1954.6 2046.4 1972.7 2476.4 TRUE FALSE FALSE 2318.690205 2601.819992 2648.711085 2802.003009 2590.108533 2670.047235 2120.623675 2105.609355 1796.256771 2412.062771 0.96128933 1.078670101 1.098110346 1.161662558 1.07381473 1.10695595 0.879174332 0.872949651 0.744697357 1 11.23605174 -7.73607826 23.49570935 1.022734035 0.876061485 0.235425403 0.109284124 99.99773838 92639.23566 0.011309579 0.042270507 1.84E-08 7.73607826 -0.146672549 STADS(ph)GGEGLETAPK ddPTM_HeLa_Romidepsin_16h_R1 2 STADSGGEGLETAPK 15 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 STADS(0.984)GGEGLET(0.016)APK;S(0.001)T(0.001)ADS(0.998)GGEGLETAPK ; 208.39 4.27E-19 39963000 12739.5 12588.8 11086.8 10514.9 11992.4 12981.6 11793 13082.9 12369.3 12880.1 TRUE FALSE FALSE 12584.22607 12766.02546 11279.7611 11730.68221 11380.38308 12152.11766 12794.69713 13461.43307 11262.95883 12545.47315 1.003088997 1.017580231 0.899110059 0.935052993 0.90713064 0.968645623 1.01986565 1.07301119 0.89777075 1 13.61487926 STAGDTHLGGEDFDNR ddPTM_HeLa_Romidepsin_16h_R1 6 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 0 ;;;;; ;;;;; 174.39 1.78E-06 440847800 36383.3 33498.9 32180.3 31995.2 45048.4 47903 37829.1 41907.5 42459.8 39203.4 FALSE FALSE TRUE 35939.84635 33970.49839 32740.38462 35694.63557 42749.41205 44842.1529 41042.30281 43120.02739 38662.08915 38184.89002 0.941205967 0.889631956 0.857417282 0.934784297 1.119537389 1.174342859 1.074830981 1.1292432 1.012497067 1 15.22071425 -8.756727801 24.81929269 0.952797022 1.124502695 0.7695028 0.049332138 46.36499119 244234.6957 0.008088276 0.015760148 1.75E-09 8.756727801 0.171705673 STAQQELDGKPAS(ph)PTPVIVASHTANK ddPTM_HeLa_Romidepsin_16h_R1 2 STAQQELDGKPASPTPVIVASHTANK 26 1 H0YAC7;P35606-2;P35606 H0YAC7 COPB2 Coatomer subunit beta 1 0 STAQQELDGKPAS(0.735)PT(0.265)PVIVASHTANK;STAQQELDGKPAS(0.724)PT(0.276)PVIVASHTANK ; 107.58 6.45E-07 258080000 9365.7 10340.5 10712.8 5581.6 10035.5 10573.7 8342.3 9551.9 10156.6 10822.5 TRUE FALSE FALSE 9251.547246 10486.07383 10899.25179 6226.970854 9523.350987 9898.074695 9050.894754 9828.269156 9248.168258 10541.32989 0.877645168 0.994758151 1.03395415 0.590719664 0.903429746 0.938977795 0.858610332 0.932355714 0.877324622 1 13.36376927 STAQQELDGKPAS(ph)PTPVIVASHTANKEEK ddPTM_HeLa_Romidepsin_16h_R1 2 STAQQELDGKPASPTPVIVASHTANKEEK 29 2 H0YAC7;P35606-2;P35606 H0YAC7 COPB2 Coatomer subunit beta 1 0 STAQQELDGKPAS(0.826)PT(0.173)PVIVASHTANKEEK;STAQQELDGKPAS(0.5)PT(0.5)PVIVASHTANKEEK ; 97.295 1.19E-08 268432000 4811.37 4790 4333.61 4698.78 5166.51 4645.88 4167.16 4925.28 5662.1 4875.8 TRUE FALSE FALSE 4752.727172 4857.433746 4409.034664 5242.075052 4902.843716 4349.023262 4521.118466 5067.785206 5155.667595 4749.126013 1.000758278 1.022805824 0.928388645 1.103797844 1.032367577 0.915752341 0.951989577 1.067098492 1.085603452 1 12.21344632 STAYEDYYYHPPPR ddPTM_HeLa_Romidepsin_16h_R1 1 STAYEDYYYHPPPR 14 0 B4DT28;O43390-3;O43390;O43390-4;O43390-2;A0A286YEZ8 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 0 119.17 0.0020138 9546700 3101.8 2978.4 2406.4 2012.7 2344.5 2402 2176.6 2324.8 3088.4 3178.4 FALSE FALSE TRUE 3063.994069 3020.329993 2448.282383 2245.417844 2224.851416 2248.519952 2361.48035 2392.06442 2812.165769 3095.82471 0.989718203 0.975614021 0.790833659 0.725305227 0.718661948 0.726307257 0.762795239 0.772674374 0.908373707 1 11.59610807 -9.719095565 3.225871778 0.995062884 0.741098395 0.918857353 0.031810573 0.022899729 0.490424114 0.002882909 0.004075962 1.91E-10 9.719095565 -0.253964489 STDEYS(ph)EADEEEEEEEGKPSR ddPTM_HeLa_Romidepsin_16h_R1 2 STDEYSEADEEEEEEEGKPSR 21 1 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 1 0 S(0.009)T(0.009)DEY(0.014)S(0.969)EADEEEEEEEGKPSR;S(0.003)T(0.003)DEYS(0.995)EADEEEEEEEGKPSR ; 154.66 2.94E-08 58249000 4371.7 4021.4 4099.3 3856.5 3835.8 3752.6 2658.5 3017.2 4275 4122 TRUE FALSE FALSE 4318.416039 4078.013375 4170.646597 4302.406675 3640.044813 3512.820971 2884.312924 3104.497922 3892.633293 4014.909846 1.075594772 1.015717297 1.038789601 1.071607294 0.906631768 0.874943923 0.718400421 0.77324225 0.969544384 1 11.97115188 -8.247485161 1.488651008 1.037417939 0.743205713 0.86843935 0.042568074 0.093356599 0.382797075 0.00599953 0.023055666 5.66E-09 8.247485161 -0.294212227 STDS(ph)EVSQSPAK ddPTM_HeLa_Romidepsin_16h_R1 1 STDSEVSQSPAK 12 0 H7C3F5;A0A2H2FJL5;B7Z6J7;O75175;A0A0G2JNJ7;H7C148 H7C3F5 CNOT3 CCR4-NOT transcription complex subunit 3 1 0 S(0.096)T(0.096)DS(0.55)EVS(0.192)QS(0.067)PAK 95.428 0.0036285 0 1657.6 1430.1 1560 1373.1 1158.5 948.52 999.06 730.91 1891.7 1738.9 TRUE FALSE FALSE 1637.396534 1450.232985 1587.151146 1531.864283 1099.377422 887.9126332 1083.920131 752.0577277 1722.501614 1693.723127 0.966743919 0.856239702 0.937078274 0.904436066 0.649089219 0.524237178 0.639962999 0.444026367 1.016991258 1 10.72598234 -8.723962762 1.900960453 0.970503208 0.539546074 0.906110842 0.06116941 0.066554555 0.488416709 0.009131048 0.021003836 1.89E-09 8.723962762 -0.430957134 STDS(ph)PVPGSEDDLVAGATLHSPEWSEER ddPTM_HeLa_Romidepsin_16h_R1 1 STDSPVPGSEDDLVAGATLHSPEWSEER 28 0 Q9H694;Q9H694-2 Q9H694 BICC1 Protein bicaudal C homolog 1 1 0 S(0.063)T(0.063)DS(0.857)PVPGS(0.017)EDDLVAGATLHSPEWSEER 159.96 6.30E-14 6959100 1649.1 1700.2 1592.6 2291.5 2144.1 1629.9 1276.6 1130.5 1533.6 1668 TRUE FALSE FALSE 1629.000135 1724.13546 1620.318535 2556.454012 2034.678576 1525.75465 1385.034372 1163.209234 1396.430975 1624.66512 1.002668252 1.061225135 0.997324627 1.573526742 1.252367981 0.939119473 0.852504529 0.715968614 0.859519268 1 10.66592666 -7.769866826 2.609003102 1.064095613 0.752857632 0.306101908 0.189184382 0.299611871 3.978757442 0.027666839 0.127980927 1.70E-08 7.769866826 -0.311237982 STDSEVSQS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 2 STDSEVSQSPAK 12 0 H7C3F5;A0A2H2FJL5;B7Z6J7;O75175;A0A0G2JNJ7;H7C148 H7C3F5 CNOT3 CCR4-NOT transcription complex subunit 3 1 0 S(0.01)T(0.001)DS(0.007)EVS(0.094)QS(0.888)PAK;STDSEVS(0.001)QS(0.999)PAK ; 211.83 5.22E-21 265950000 15486.2 13053.3 13680.4 10839 8921.9 8279.1 8247.3 5646.6 15730.2 14030 TRUE FALSE FALSE 15297.44824 13237.0647 13918.50162 12092.25618 8466.582151 7750.09223 8947.825456 5809.975462 14323.25151 13665.49858 1.119421158 0.9686485 1.018514 0.884874863 0.619558965 0.567128392 0.654774899 0.425156494 1.048132378 1 13.73825048 -8.87153368 1.572266368 1.05128719 0.547511852 0.921631154 0.064204596 0.074293705 0.369913961 0.01083706 0.024374247 1.34E-09 8.87153368 -0.503775338 STEDLS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 STEDLSPQK 9 0 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8 Q96RT1-7 ERBB2IP Protein LAP2 1 0 S(0.001)TEDLS(0.999)PQK 108.7 0.020431 12727000 4786 5891.1 5825.7 4227.6 4811.7 5063.7 3317.6 3440.1 6066.6 5561.7 TRUE FALSE FALSE 4727.666391 5974.03506 5927.093865 4716.415003 4566.140994 4740.145912 3599.396861 3539.633866 5523.988102 5417.206232 0.872713016 1.102788929 1.094123726 0.870636044 0.842895913 0.875016698 0.66443785 0.65340578 1.019711612 1 12.4033333 -7.868624189 1.024271323 0.959959599 0.596864506 0.698823268 0.082305913 0.435974546 0.626985694 0.014301268 0.136687952 1.35E-08 7.868624189 -0.363095094 STETSDFENIES(ph)PLNER ddPTM_HeLa_Romidepsin_16h_R1 2 STETSDFENIESPLNER 17 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 1 0 STETSDFENIES(1)PLNER;STETSDFENIES(1)PLNER ; 188 3.79E-13 119139000 5920.5 5400.4 6175.6 5527.8 6631.4 7159.5 5771.9 6931.5 7120.2 6102 TRUE FALSE FALSE 5848.338669 5476.426973 6283.083727 6166.950245 6292.974913 6702.031056 6262.165042 7132.052016 6483.351479 5943.46916 0.983994114 0.921419263 1.057140797 1.037601118 1.058805008 1.127629483 1.053621189 1.199981328 1.090836228 1 12.53708955 -8.151646192 0.623423057 0.987759969 1.180229667 0.480273696 0.052867218 0.640613073 0.310970536 0.00764912 0.071765781 7.05E-09 8.151646192 0.192469699 STFAGS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 STFAGSPER 9 0 H0YE03;H7C3G7;Q2TBE0-3;Q2TBE0-2;Q2TBE0 H0YE03 CWF19L2 CWF19-like protein 2 1 0 S(0.001)T(0.004)FAGS(0.995)PER 112.85 0.017518 8573700 3750.5 3065.2 3742.3 2055.3 4302.3 4197.7 3326.8 3917.3 4035.7 3346.6 TRUE FALSE FALSE 3704.787463 3108.351966 3807.433162 2292.943456 4082.737577 3929.480517 3609.378309 4030.640895 3674.736884 3259.65485 1.136558205 0.953583158 1.168047949 0.703431364 1.252506098 1.205489752 1.107288494 1.236523829 1.12733926 1 11.6705035 STFREES(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 1 STFREESPLR 10 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 1 0 S(0.005)T(0.005)FREES(0.99)PLR 73.273 0.028663 157330000 3646.4 3307.5 3757.8 4077.7 3647.2 3849.2 2809.1 2962.2 3777.5 3372.3 TRUE FALSE FALSE 3601.956274 3354.063072 3823.202933 4549.18286 3461.069774 3603.248543 3047.704884 3047.906583 3439.630939 3284.68716 1.09659036 1.02112101 1.163947355 1.384966859 1.053698452 1.096983782 0.927852406 0.927913812 1.047171548 1 11.68154026 -7.757646487 24.28735281 1.080794871 0.927883002 0.291300305 0.105782818 76.41995714 489313.8231 0.016111889 0.055938543 1.75E-08 7.757646487 -0.152911868 STFREESPLR ddPTM_HeLa_Romidepsin_16h_R1 1 STFREESPLR 10 1 Q9NYF8-2;Q9NYF8;E9PK91;Q9NYF8-3;A0A1W2PQ43;E9PQN2;E9PKI6;E9PK09;Q9NYF8-4;E9PJA7 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 0 0 109.83 0.020713 6374600 1948.3 1819.9 2138 2303.1 1910.2 2272.2 1973.7 1831.4 2265.8 1628.6 FALSE FALSE TRUE 1924.55337 1845.5206 2175.210993 2569.395258 1812.715366 2127.013753 2141.346029 1884.38867 2063.141173 1586.288737 1.213242788 1.163420351 1.371257919 1.61975257 1.142739858 1.34087427 1.349909369 1.18792287 1.300608852 1 10.63143968 -11.16416679 0.598184574 1.012556935 1.330178237 0.055494328 0.155292699 0.472583166 0.37940853 0.064647031 0.03650404 6.85E-12 11.16416679 0.317621301 STFS(ph)LPEEEEEPEPLVFAEQPSVK ddPTM_HeLa_Romidepsin_16h_R1 2 STFSLPEEEEEPEPLVFAEQPSVK 24 0 H3BR17;Q6Q0C0;Q6Q0C0-2 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 0 S(0.072)T(0.072)FS(0.856)LPEEEEEPEPLVFAEQPSVK;S(0.067)T(0.067)FS(0.866)LPEEEEEPEPLVFAEQPSVK ; 125.98 8.60E-07 9553800 7943.7 7991.4 7432.5 4648.4 7811 7754.9 7113 7880.5 9610.5 8581.6 TRUE FALSE FALSE 7846.879129 8103.903139 7561.859545 5185.869879 7412.375523 7259.386918 7717.178042 8108.509834 8750.91281 8358.648795 0.938773637 0.969523106 0.904674874 0.62041964 0.88679112 0.868488089 0.923256645 0.970074235 1.046929118 1 13.02905403 -9.527827697 14.83343063 0.968591771 0.850539241 0.321202096 0.090653759 0.920230805 2751.239241 0.01407523 0.020076424 2.97E-10 9.527827697 -0.11805253 STFS(ph)PISDIGLAK ddPTM_HeLa_Romidepsin_16h_R1 1 STFSPISDIGLAK 13 0 Q8TEK3-1;Q8TEK3;H7C2S2 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 S(0.288)T(0.03)FS(0.682)PISDIGLAK 153.32 0.00076895 9968200 1962 2130.9 1847 1756.4 1368.7 999.86 1097.1 1149.5 2485.1 2152.3 TRUE FALSE FALSE 1938.086389 2160.898866 1879.14626 1959.483232 1298.850132 935.9721729 1190.287647 1182.758969 2262.826432 2096.382936 0.924490634 1.030774879 0.89637548 0.934697187 0.619567212 0.44647004 0.567781595 0.564190325 1.07939556 1 11.03368656 -8.716487467 3.317898627 0.963574821 0.529356653 0.926423775 0.059484259 0.037468005 0.844497644 0.007246325 0.01489559 1.92E-09 8.716487467 -0.434218167 STFS(ph)TNYR ddPTM_HeLa_Romidepsin_16h_R1 1 STFSTNYR 8 0 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 STFS(0.956)T(0.044)NYR 114.86 0.020677 37070000 2802.1 2937.5 3017.3 1420.1 3182.2 2909.7 2780.5 2990.7 3070.9 2377.6 TRUE FALSE FALSE 2767.946927 2978.854202 3069.814841 1584.298644 3019.80046 2723.779561 3016.675601 3077.231186 2796.231013 2315.829609 1.195229095 1.286301112 1.325578889 0.684117103 1.303982144 1.176157153 1.302632797 1.328781346 1.207442465 1 11.17731339 -16.52287875 0.179207171 0.163883955 1.245389062 0 0.191766275 82.24446783 0.941537569 24.05343323 0.251616642 3.00E-17 16.52287875 1.081505107 STFVLDEFK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 1 STFVLDEFK(1)R 99.788 0.0099254 1549700 334.62 414.05 383.75 247.1 1025.8 626.12 915.76 715.97 739.48 530.93 FALSE TRUE FALSE 330.5415227 419.8790068 390.4290078 275.6708646 973.4495982 586.1129527 993.5446315 736.6854623 673.3390567 517.1363621 0.639176718 0.811930929 0.754982702 0.533071903 1.882384743 1.133381823 1.921243031 1.424547791 1.302053203 1 9.01440094 -8.76298039 25 0.799417721 1.581378386 0.619564473 0.286885783 16.42013149 266392.7546 0.035085205 0.066141412 1.73E-09 8.76298039 0.781960666 STFVLDEFKR ddPTM_HeLa_Romidepsin_16h_R1 1 STFVLDEFKR 10 1 P26641;P26641-2 P26641 EEF1G Elongation factor 1-gamma 0 0 92.611 0.022504 39211000 1608.1 972.98 1330.1 1305 1454.4 1247.9 1156.8 1450.7 1084.9 824.54 FALSE FALSE TRUE 1588.499859 986.677638 1353.249833 1455.89024 1380.176541 1168.163217 1255.058563 1492.673716 987.8638268 803.1183319 1.977915079 1.228558232 1.684994326 1.812796673 1.718522023 1.454534371 1.562731808 1.85859749 1.230035211 1 9.649468761 -12.49987771 1.200853875 0.993694803 1.68183897 0.506207264 0.212144977 0.270566613 0.687852491 0.156055801 0.036428519 3.16E-13 12.49987771 0.688144167 STGGAPTFNVT(ph)VTK ddPTM_HeLa_Romidepsin_16h_R1 1 STGGAPTFNVTVTK 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 1 0 STGGAPT(0.019)FNVT(0.976)VT(0.005)K 108.66 0.01277 21542000 2470.6 2505.9 2417 2160.5 3064.1 2870.8 2563.4 2572.6 2850.8 2856.7 TRUE FALSE FALSE 2440.487377 2541.178126 2459.066871 2410.307175 2907.727543 2687.365145 2781.135132 2647.034122 2595.817308 2782.482522 0.877089921 0.9132773 0.88376723 0.86624342 1.04501197 0.965815643 0.99951576 0.951321024 0.932914147 1 11.44215691 -8.757593172 24.99985067 0.92863598 0.989308887 0.405833317 0.043717373 125.4943169 815684.6128 0.008472262 0.016444501 1.75E-09 8.757593172 0.060672907 STGGAPTFNVTVTK ddPTM_HeLa_Romidepsin_16h_R1 2 STGGAPTFNVTVTK 14 0 P07737;K7EJ44 P07737 PFN1 Profilin-1 0 0 ; ; 296.28 2.57E-115 55836000 5575.2 4391 4463.4 4023.9 4389.8 4612.4 4001.7 4343.4 4747.2 4055.2 FALSE FALSE TRUE 5507.247318 4452.816613 4541.083605 4489.162251 4165.772125 4317.682526 4341.604298 4469.069426 4322.598542 3949.845319 1.394294427 1.127339491 1.14968644 1.136541279 1.054667155 1.09312699 1.099183372 1.131454289 1.0943716 1 11.94758044 -9.385501961 1.907606269 1.186191857 1.09702303 0.031778122 0.096614572 0.770532151 5.501349293 0.024022493 0.040188557 4.12E-10 9.385501961 -0.089168827 STGS(ph)PTQETQAPFIAK ddPTM_HeLa_Romidepsin_16h_R1 2 STGSPTQETQAPFIAK 16 0 H0Y704;O15231-2;O15231-3 H0Y704 ZNF185 Zinc finger protein 185 1 0 S(0.064)T(0.267)GS(0.649)PT(0.021)QETQAPFIAK;S(0.001)TGS(0.824)PT(0.175)QETQAPFIAK ; 181.86 1.78E-08 94923000 6546.6 7528.7 7075.9 6962.6 7697.9 7476.7 6551.3 7347.4 7243.5 6767.8 TRUE FALSE FALSE 6466.807521 7634.689236 7199.053071 7767.648572 7305.047438 6998.963 7107.767258 7559.985427 6595.623218 6591.97158 0.981012652 1.158179938 1.09209407 1.178349827 1.108173382 1.061740469 1.078246041 1.146847394 1.000553952 1 12.68649431 -10.27100285 24.91855884 0.991033749 1.11498066 0.729255667 0.034529489 232.1686234 604936.9912 0.005882353 0.006769682 5.36E-11 10.27100285 0.123946911 STGSAT(ph)SLASQGER ddPTM_HeLa_Romidepsin_16h_R1 1 STGSATSLASQGER 14 0 H0Y2V6;Q5SW79;Q5SW79-3;Q5SW79-2 H0Y2V6 CEP170 Centrosomal protein of 170 kDa 1 0 S(0.012)T(0.001)GS(0.239)AT(0.745)S(0.003)LASQGER 201.3 2.77E-16 10026000 693.37 793.56 996.29 876.29 924.8 973.59 850.65 861.79 1018.4 755.28 TRUE FALSE FALSE 684.9189397 804.7317585 1013.63001 977.6107729 877.6040051 911.3807411 922.9041898 886.724534 927.3117534 735.6577167 0.931029369 1.093894267 1.377855471 1.32889352 1.192951539 1.238865196 1.25452934 1.205349327 1.260520664 1 9.522890862 -9.980276626 4.864802309 0.968897708 1.263706003 0.360309156 0.106925085 0.050323363 3.154605911 0.009707273 0.012609924 1.05E-10 9.980276626 0.294808295 STGTEPPGEVRLADSAASR ddPTM_HeLa_Romidepsin_16h_R1 1 STGTEPPGEVRLADSAASR 19 1 O43586-2 O43586-2 PSTPIP1 Proline-serine-threonine phosphatase-interacting protein 1 0 0 81.565 0.0036897 0 280.45 187.01 308.35 359.4 323.3 206.97 270.79 250.44 275.1 359.51 FALSE FALSE TRUE 277.0317675 189.6427317 313.7167024 400.955519 306.8007946 193.745285 293.7908958 257.6860863 250.494367 350.1698784 0.791135345 0.541573514 0.895898596 1.145031437 0.876148446 0.553289409 0.838995339 0.735888785 0.715350984 1 8.451911178 -12.09654889 0.945934902 0.996161394 0.801521347 0 0.185147541 0.810149661 1.347986827 0.101676238 0.032615737 8.01E-13 12.09654889 -0.194640047 STIDPSS(ph)VMVLVNIIY(ph)FK ddPTM_HeLa_Romidepsin_16h_R1 1 STIDPSSVMVLVNIIYFK 18 0 Q96P15 Q96P15 SERPINB11 Serpin B11 2 0 S(0.029)T(0.029)IDPS(0.272)S(0.673)VMVLVNIIY(0.998)FK 41.136 0.0043033 0 1865.2 2297.1 1472.6 1434.1 2203.1 2070.2 1641.5 2200.2 2166 1759 TRUE FALSE FALSE 1842.466225 2329.438634 1498.229985 1599.91739 2090.667586 1937.920901 1780.928969 2263.859316 1972.267535 1713.300926 1.075389733 1.35962025 0.874469839 0.933821587 1.22025708 1.131103632 1.039472367 1.321343659 1.151150685 1 10.74256286 -4.225729998 1.045241674 1.054185551 199.9999527 0.161456997 0.137678939 1445.333164 2.588333885 0.019919379 688057.6525 5.95E-05 4.225729998 198.9457671 STIFIS(ph)PSSVK ddPTM_HeLa_Romidepsin_16h_R1 1 STIFISPSSVK 11 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 S(0.002)T(0.002)IFIS(0.992)PS(0.003)SVK 182.71 6.33E-06 37461000 6421.5 5344.6 6083.8 4083 4927 5116.8 5003.7 4581.3 6172 5867.3 TRUE FALSE FALSE 6343.232288 5419.841419 6189.685987 4555.095671 4675.556805 4789.852994 5428.714153 4713.852687 5619.960862 5714.8667 1.109952799 0.948375825 1.083084928 0.797060703 0.818139259 0.838139058 0.949928395 0.824840357 0.983393167 1 12.48050413 -9.264148053 24.9896112 1.045952467 0.849473888 0.687117062 0.059646263 99.23604878 915529.8648 0.00960118 0.015087375 5.44E-10 9.264148053 -0.196478579 STIGVMVT(ph)ASHNPEEDNGVK ddPTM_HeLa_Romidepsin_16h_R1 1 STIGVMVTASHNPEEDNGVK 20 0 D6RC77;D6RCQ8;D6RF77;A0A494C163;A0A494C099;A0A494C0G1;H0Y987;O95394;O95394-3;O95394-4 D6RC77 PGM3 Phosphoacetylglucosamine mutase 1 0 S(0.001)T(0.001)IGVMVT(0.629)AS(0.37)HNPEEDNGVK 54.253 0.018704 188490000 1599.5 1456.7 1464.5 871.68 1608.7 1630.8 1601.7 1386.5 1696 1795.7 TRUE FALSE FALSE 1580.004679 1477.207461 1489.989008 972.467743 1526.602036 1526.597143 1737.748358 1426.61619 1544.305512 1749.047455 0.903351521 0.844578263 0.851885982 0.555998489 0.872819106 0.872816308 0.993539857 0.815653221 0.882940887 1 10.77235372 -10.89197694 0.972264571 0.979196816 0.829591021 0.12931647 0.108356758 0.47935009 0.963441712 0.029355284 0.024668227 1.28E-11 10.89197694 -0.149605794 STIGVMVTAS(ph)HNPEEDNGVK ddPTM_HeLa_Romidepsin_16h_R1 6 STIGVMVTASHNPEEDNGVK 20 0 D6RC77;D6RCQ8;D6RF77;A0A494C163;A0A494C099;A0A494C0G1;H0Y987;O95394;O95394-3;O95394-4 D6RC77 PGM3 Phosphoacetylglucosamine mutase 1 0 STIGVMVT(0.116)AS(0.883)HNPEEDNGVK;STIGVMVT(0.014)AS(0.986)HNPEEDNGVK;STIGVMVT(0.011)AS(0.989)HNPEEDNGVK;STIGVMVT(0.018)AS(0.982)HNPEEDNGVK;STIGVMVT(0.001)AS(0.999)HNPEEDNGVK;STIGVMVT(0.063)AS(0.937)HNPEEDNGVK ;;;;; 124.21 7.31E-05 942087000 17144 16954.2 16695.9 17948.8 22896.1 21755.2 19622.6 22478.9 19595.5 17915 TRUE FALSE FALSE 16935.04233 17192.88167 16986.48514 20024.12471 21727.62658 20365.11293 21289.34315 23129.29151 17842.8294 17449.56572 0.970513685 0.985289947 0.97346177 1.147542869 1.245167182 1.167084228 1.220050029 1.325493819 1.022537162 1 14.09090351 -9.099862539 2.856828505 0.984399145 1.232477672 0.897064539 0.039905627 0.056430956 0.89351266 0.005824567 0.010360895 7.95E-10 9.099862539 0.248078527 STKPVVFS(ph)PTLMLTDEEK ddPTM_HeLa_Romidepsin_16h_R1 1 STKPVVFSPTLMLTDEEK 18 1 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 STKPVVFS(0.778)PT(0.046)LMLT(0.176)DEEK 72.359 0.023004 35075000 1352.4 1342.3 1399.9 1188.3 2016.8 2975 2440.3 2538.6 1566 1496.5 TRUE FALSE FALSE 1335.916429 1361.196935 1424.264672 1325.696837 1913.87517 2784.907101 2647.579021 2612.050386 1425.933038 1457.620714 0.916504833 0.933848512 0.977116103 0.909493687 1.313013153 1.910584197 1.816370332 1.791995929 0.978260685 1 10.50939965 -8.465588133 2.931625373 0.956122003 1.838515898 0.984830749 0.049151002 0.023280944 0.393294124 0.007959031 0.01894755 3.42E-09 8.465588133 0.882393895 STKPVVFSPTLMLT(ph)DEEK ddPTM_HeLa_Romidepsin_16h_R1 1 STKPVVFSPTLMLTDEEK 18 1 P40818;P40818-2;A0A075B720 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 ST(0.001)KPVVFS(0.034)PT(0.034)LMLT(0.931)DEEK 70.802 0.012192 26867000 2303 2322.2 2571.6 1732.9 3433.1 3913 2915.2 3344.4 2956 2806.6 TRUE FALSE FALSE 2274.93015 2354.891993 2616.357619 1933.266052 3257.896096 3662.971929 3162.817015 3441.164937 2691.607957 2733.684127 0.832184716 0.861435295 0.957081176 0.707201696 1.191760256 1.339939714 1.15697969 1.258801228 0.984608254 1 11.41663084 -8.630285045 7.163040625 0.903989629 1.245910973 0.780238079 0.090260091 0.082526529 4.971510817 0.013806943 0.027717569 2.34E-09 8.630285045 0.341921344 STLNPQWNES(ph)FTFK ddPTM_HeLa_Romidepsin_16h_R1 2 STLNPQWNESFTFK 14 0 J3KRN5;P17252 J3KRN5 PRKCA Protein kinase C alpha type 1 0 STLNPQWNES(0.917)FT(0.083)FK;STLNPQWNES(0.817)FT(0.183)FK ; 160.63 0.00031959 154062000 6335.8 5783.9 5705.9 5002.6 6685.7 6003.5 5111.8 6179 6428.1 5296.5 TRUE FALSE FALSE 6258.576833 5865.325896 5805.208796 5581.02415 6344.503781 5619.895725 5545.996164 6357.779616 5853.154637 5158.896166 1.213162008 1.136934279 1.125281186 1.081825253 1.229818081 1.089360116 1.075035431 1.232391467 1.134575004 1 12.33284669 -12.48180122 1.206576462 0.999498641 1.15034828 0.060986022 0.069415494 0.320319788 0.829937948 0.040188288 0.009699932 3.30E-13 12.48180122 0.150849639 STLPDADRER ddPTM_HeLa_Romidepsin_16h_R1 2 STLPDADRER 10 1 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 133.99 0.0068954 112266000 7276.4 7077.7 8746.7 8105.8 9382.1 8627.5 7429.1 6783.8 7604.8 6619 FALSE FALSE TRUE 7187.712438 7177.340046 8898.932644 9043.030735 8903.296428 8076.230594 8060.127569 6980.07855 6924.607641 6447.037426 1.114886104 1.113277242 1.380313477 1.402664532 1.380990343 1.252704159 1.250206418 1.082680011 1.074075918 1 12.65442064 -9.904155197 4.912710931 1.056931192 1.29648859 0.577836313 0.090907959 0.116761503 4.764847901 0.016386566 0.021680562 1.25E-10 9.904155197 0.239557397 STLTTLPFPGAEANS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 STLTTLPFPGAEANSPGK 18 0 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 0 STLT(0.012)T(0.176)LPFPGAEANS(0.812)PGK 128.59 0.0015613 7233800 2948.2 3403.4 3492 1717.5 1842.9 2049 1454.3 1465.1 3495.7 3530.2 TRUE FALSE FALSE 2912.266204 3451.313155 3552.776795 1916.085431 1748.849936 1918.075513 1577.828206 1507.490357 3183.035837 3438.484895 0.846962047 1.003730788 1.033239029 0.557247011 0.508610621 0.557825778 0.458873095 0.438417036 0.925708832 1 11.74755729 -9.188887351 5.311012188 0.939829335 0.499680279 0.935807651 0.05988689 0.051051089 2.681055241 0.01149941 0.019202952 6.47E-10 9.188887351 -0.440149056 STLTTLPFPGAEANS(ph)PGKAEAEKPR ddPTM_HeLa_Romidepsin_16h_R1 2 STLTTLPFPGAEANSPGKAEAEKPR 25 2 Q96GV9 Q96GV9 C5orf30 UNC119-binding protein C5orf30 1 0 STLT(0.001)T(0.002)LPFPGAEANS(0.997)PGKAEAEKPR;STLTTLPFPGAEANS(1)PGKAEAEKPR ; 90.518 4.42E-05 83401000 6701.7 6757.9 6871.3 6648.4 4554.1 4475 3496.5 3796 7805.7 6776.5 TRUE FALSE FALSE 6620.017103 6853.037894 6990.892094 7417.11929 4321.687283 4189.061942 3793.492623 3905.831271 7107.538642 6600.445553 1.002965186 1.038268983 1.059154573 1.123730092 0.654756902 0.63466351 0.57473281 0.591752669 1.0768271 1 12.6883477 -8.697905583 6.407563327 1.01679072 0.60794443 0.955069796 0.046042532 0.031713102 2.438105191 0.006721042 0.013471442 2.00E-09 8.697905583 -0.408846291 STNGDTFLGGEDFDQALLR ddPTM_HeLa_Romidepsin_16h_R1 1 STNGDTFLGGEDFDQALLR 19 0 P38646 P38646 HSPA9 "Stress-70 protein, mitochondrial" 0 0 254.72 9.40E-75 10430000 1106.1 1153 950.61 1250.1 1147.9 1191.4 1112.4 858.82 1088.3 1018.1 FALSE FALSE TRUE 1092.618428 1169.231964 967.1549683 1394.642444 1089.31838 1115.273385 1206.887228 883.6686017 990.9597223 991.6496152 1.101819041 1.179077717 0.975299091 1.406386311 1.098491204 1.124664769 1.217050065 0.891109711 0.999304298 1 9.953686645 -11.51530604 0.69791799 1.004417625 1.135880337 0.124076802 0.130276529 0.981573857 0.985694049 0.063193365 0.028476981 3.05E-12 11.51530604 0.131462712 STNT(ph)SQTGLVGTK ddPTM_HeLa_Romidepsin_16h_R1 2 STNTSQTGLVGTK 13 0 Q96R06 Q96R06 SPAG5 Sperm-associated antigen 5 1 0 S(0.009)T(0.009)NT(0.957)S(0.023)QT(0.002)GLVGTK;S(0.054)T(0.013)NT(0.92)S(0.013)QTGLVGTK ; 144.18 0.0015837 12173700 4824.9 4093.9 4160.5 3597.6 3614.6 3451.9 2975.25 3440.6 4717.3 4445.3 TRUE FALSE FALSE 4766.092263 4151.534032 4232.911757 4013.571439 3430.133474 3231.33473 3227.967661 3540.148333 4295.372873 4329.810465 1.100762332 0.958825811 0.977620566 0.926962386 0.792213309 0.746299349 0.7455217 0.817622009 0.992046397 1 12.08008816 -9.053412561 1.209071737 1.043371746 0.759957712 0.860748433 0.043284972 0.115686862 0.334404986 0.008257793 0.018478036 8.84E-10 9.053412561 -0.283414034 STPAEDDS(ph)PGDSQVK ddPTM_HeLa_Romidepsin_16h_R1 1 STPAEDDSPGDSQVK 15 0 Q9UHB6-5;Q9UHB6-4 Q9UHB6-5 LIMA1 LIM domain and actin-binding protein 1 1 0 STPAEDDS(1)PGDSQVK 130.47 0.0019585 10009000 2219.8 2184.7 1965.2 1683.9 2117.2 2788.1 2645.7 2543.1 2509.5 2310.5 TRUE FALSE FALSE 2192.744224 2215.456264 1999.403482 1878.600441 2009.151384 2609.949408 2870.425692 2616.680586 2285.044035 2250.472877 0.974348212 0.984440331 0.888437049 0.83475809 0.89276854 1.159733776 1.275476688 1.162724782 1.015361731 1 11.13601246 -8.129228652 4.79326307 0.962761512 1.218466602 0.782055666 0.06206253 0.086720189 2.998994742 0.009728253 0.025900494 7.43E-09 8.129228652 0.25570509 ASPRPWT(ph)PEDPWSLYGPSPGGR ddPTM_HeLa_Romidepsin_16h_R1 2 ASPRPWTPEDPWSLYGPSPGGR 22 1 Q14934-2;Q14934-9;Q14934-3;Q14934-4;Q14934-5;Q14934-6;Q14934-7;Q14934;Q14934-8;Q14934-10;Q14934-18;Q14934-11;Q14934-12;Q14934-13;Q14934-14;Q14934-15;Q14934-16;Q14934-17 Q14934-2 NFATC4 "Nuclear factor of activated T-cells, cytoplasmic 4" 1 0 AS(0.065)PRPWT(0.85)PEDPWS(0.061)LY(0.022)GPS(0.001)PGGR;AS(0.006)PRPWT(0.993)PEDPWS(0.001)LYGPSPGGR ; 78.583 0.0010787 32588000 2522.7 2497.7 2136.8 2736.1 1607.48 1117.02 1029.94 1117.44 2698.6 2576.6 TRUE FALSE FALSE 2491.952362 2532.862686 2173.990108 3052.460756 1525.444297 1045.646027 1117.423078 1149.771363 2457.230457 2509.659561 0.992944382 1.009245527 0.866249009 1.216284792 0.607829174 0.416648554 0.445248868 0.458138379 0.979109078 1 11.29327596 -8.597416841 5.302208034 0.99980996 0.450572426 0.909856205 0.082627108 0.03681295 1.858226708 0.010780904 0.021963584 2.53E-09 8.597416841 -0.549237534 down STPES(ph)GDSDKESVGSSSTSNEGGR ddPTM_HeLa_Romidepsin_16h_R1 1 STPESGDSDKESVGSSSTSNEGGR 24 1 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 1 0 S(0.004)T(0.004)PES(0.449)GDS(0.374)DKES(0.08)VGS(0.047)S(0.016)S(0.016)T(0.006)S(0.006)NEGGR 50.426 0.014746 3400300 914.26 659.75 796.9 412.42 685.13 585.89 875.69 1061.8 1171 965.56 TRUE FALSE FALSE 903.1166475 669.0379778 810.7697102 460.1059409 650.1652595 548.4535199 950.0710867 1092.521508 1066.262827 940.474612 0.960277541 0.711383348 0.862085696 0.489227391 0.69131612 0.583166747 1.010203864 1.161670388 1.133749719 1 9.877245189 -10.33903663 5.854935364 0.982301687 0.775707584 0.243225071 0.191149608 0.275192804 16.18937137 0.032875456 0.037515642 4.58E-11 10.33903663 -0.206594103 STPESGDS(ph)DKESVGSSSTSNEGGR ddPTM_HeLa_Romidepsin_16h_R1 1 STPESGDSDKESVGSSSTSNEGGR 24 1 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 1 0 S(0.01)T(0.01)PES(0.095)GDS(0.575)DKES(0.067)VGS(0.027)S(0.089)S(0.12)T(0.005)S(0.002)NEGGR 51.568 0.012283 35366000 1442.2 1521.3 1478.5 1608 1557.9 1624.1 1725.5 1785.5 1613.9 1530.9 TRUE FALSE FALSE 1424.621912 1542.716901 1504.232672 1793.924526 1478.39455 1520.325252 1872.063927 1837.160625 1469.548742 1491.126997 0.955399449 1.034597928 1.008789107 1.203066224 0.991461192 1.019581333 1.255469139 1.232061809 0.985528895 1 10.54218742 -4.000000112 0.335347413 0.977500261 4.130824766 0.55659339 0.072097188 25.85483929 0.327225508 0.022381636 51.50224272 1.00E-04 4.000000112 3.153324506 STPFIVPS(ph)SPTEQEGR ddPTM_HeLa_Romidepsin_16h_R1 2 STPFIVPSSPTEQEGR 16 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 STPFIVPS(0.852)S(0.145)PT(0.003)EQEGR;STPFIVPS(0.499)S(0.499)PT(0.002)EQEGR ; 254.72 7.72E-72 968820000 13850.9 14014.2 13219.7 9347.6 13068.9 14830.1 13019 14284.3 15353.1 13739 TRUE FALSE FALSE 13682.0799 14211.49228 13449.78333 10428.41349 12401.94527 13882.50447 14124.83354 14697.59368 13979.88028 13382.0588 1.022419652 1.061981007 1.005060846 0.779283192 0.926759137 1.037396762 1.055505266 1.098305866 1.044673357 1 13.70801247 -7.852190705 2.935829824 0.991664432 1.08153577 0.201747909 0.077111805 0.37463518 6.358864137 0.011545302 0.044771077 1.41E-08 7.852190705 0.089871338 STPFIVPSS(ph)PTEQEGR ddPTM_HeLa_Romidepsin_16h_R1 2 STPFIVPSSPTEQEGR 16 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 STPFIVPS(0.015)S(0.985)PTEQEGR;STPFIVPS(0.115)S(0.787)PT(0.097)EQEGR ; 246.75 2.36E-58 971700000 10334.2 9928.4 9979.3 7068.3 10307.4 10916.4 9386.3 10481.2 10737.9 10180.9 TRUE FALSE FALSE 10208.2428 10068.17228 10152.98553 7885.570103 9781.374916 10218.87727 10183.57209 10784.45699 9777.47533 9916.39875 1.029430447 1.015305307 1.023858135 0.795205024 0.986383783 1.03050286 1.026942577 1.087537649 0.985990537 1 13.27560057 -7.365854428 1.664573914 0.997837865 1.105133078 0.172327627 0.066404072 1.278439903 3.97313508 0.009908836 0.204705277 4.31E-08 7.365854428 0.107295213 STPLSQPSANGVQT(ph)EGLDYDR ddPTM_HeLa_Romidepsin_16h_R1 1 STPLSQPSANGVQTEGLDYDR 21 0 A0A0U1RRM6;Q8N8S7-3;Q8N8S7-2;Q8N8S7 A0A0U1RRM6 ENAH Protein enabled homolog 1 0 S(0.254)T(0.076)PLS(0.002)QPS(0.162)ANGVQT(0.495)EGLDY(0.011)DR 71.529 0.012489 10918000 656.32 550.59 756.24 585.32 807.14 1017.7 713.79 876.52 757.08 917.75 TRUE FALSE FALSE 648.3205194 558.3412205 769.40204 652.9974524 765.9486339 952.6722545 774.4193048 901.8807233 689.3648687 893.9067227 0.72526641 0.624607922 0.860718485 0.730498424 0.856855212 1.065740116 0.866331224 1.008920394 0.771182106 1 9.803980487 -8.437484696 8.724734447 0.835527241 0.968317698 0.333328541 0.110021842 0.526480687 50.02585413 0.019882512 0.044509924 3.65E-09 8.437484696 0.132790457 STPS(ph)PTPVESSDPK ddPTM_HeLa_Romidepsin_16h_R1 2 STPSPTPVESSDPK 14 0 Q9NW07 Q9NW07 ZNF358 Zinc finger protein 358 1 0 S(0.019)T(0.019)PS(0.769)PT(0.185)PVES(0.007)SDPK;S(0.005)T(0.017)PS(0.961)PT(0.017)PVESSDPK ; 170.74 5.16E-05 34853000 14197.8 14294.1 12654.8 12708.7 8347.6 7311.8 7714.9 8363.8 14372.9 13814.3 TRUE FALSE FALSE 14024.75175 14495.33271 12875.05149 14178.13969 7921.590823 6844.599578 8370.203413 8605.793357 13087.35183 13455.40249 1.042313804 1.077287188 0.956868551 1.053713532 0.588729384 0.508687836 0.622070088 0.639579036 0.972646625 1 13.71589793 -8.758715332 24.99390436 1.022071097 0.586282555 0.952626396 0.046679036 9.537053334 87503.46669 0.0064334 0.012416945 1.74E-09 8.758715332 -0.435788541 STS(ph)ATDTHHVEMAR ddPTM_HeLa_Romidepsin_16h_R1 1 STSATDTHHVEMAR 14 0 H3BQP2;H3BNP3;H3BTL2;H3BS02;O14874-2;O14874-3;O14874 H3BQP2 BCKDK "[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial" 1 0 S(0.13)T(0.321)S(0.432)AT(0.114)DT(0.003)HHVEMAR 102.29 0.0027852 26225000 492.65 618.99 454.02 472.95 569.6 629.46 662.06 629.99 627.54 479.36 TRUE FALSE FALSE 486.6453923 627.7041575 461.9220276 527.6347043 540.5311865 589.2395375 718.2953599 648.2177667 571.4112507 466.9061581 1.042276663 1.344390402 0.989325199 1.13006585 1.157686994 1.262008494 1.538414834 1.388325588 1.223824618 1 8.866988806 -6.089267327 0.296823793 1.000389684 2.391875682 0.413897457 0.130509851 6.396767034 0.239992853 0.045085512 3.694902933 8.14E-07 6.089267327 1.391485998 STS(ph)DTDLVTSDSR ddPTM_HeLa_Romidepsin_16h_R1 2 STSDTDLVTSDSR 13 0 Q76N89-2;Q76N89 Q76N89-2 HECW1 E3 ubiquitin-protein ligase HECW1 1 0 S(0.002)T(0.119)S(0.878)DTDLVTSDSR;ST(0.016)S(0.679)DT(0.305)DLVTSDSR ; 231.69 4.28E-41 10352700 2658.3 2628.2 2894.9 3132.9 2525.3 2575 2163.11 1787.76 2982.4 2923.5 TRUE FALSE FALSE 2625.899617 2665.199869 2945.28452 3495.140639 2396.424518 2410.46581 2346.844509 1839.486015 2715.646674 2847.547049 0.922161977 0.935963418 1.034323391 1.227421559 0.841575039 0.846506052 0.824163559 0.645989683 0.953679299 1 11.47550396 -7.647689977 1.157923502 0.979177218 0.624408883 0.564784654 0.095848349 0.55174561 0.92443129 0.015063616 0.199420276 2.25E-08 7.647689977 -0.354768335 STS(ph)FGVPNANSIK ddPTM_HeLa_Romidepsin_16h_R1 1 STSFGVPNANSIK 13 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6;P53814-2;H7BZZ8;A0A096LNK9;B5MCI0 A0A087WVP4 SMTN Smoothelin 1 0 S(0.001)T(0.001)S(0.999)FGVPNANSIK 139.19 0.0012233 17998000 1876.4 1483.2 1756 1582 3837.4 3995.4 2998 3820.1 1671.1 1262.6 TRUE FALSE FALSE 1853.529715 1504.080529 1786.562443 1764.918284 3641.563159 3740.106835 3252.650045 3930.628566 1521.632631 1229.79747 1.507182898 1.223031081 1.452728996 1.43512922 2.961108026 3.04123803 2.644866431 3.196159256 1.237303432 1 10.26420503 -8.785888186 4.979207925 1.267328056 2.953382518 0.951155991 0.183479842 0.034488669 2.168470208 0.034206804 0.065151162 1.64E-09 8.785888186 1.686054462 up STS(ph)LSALVR ddPTM_HeLa_Romidepsin_16h_R1 2 STSLSALVR 9 0 Q5VZ89-5;Q5VZ89-3;Q5VZ89;Q5VZ89-7;X6RAE7;X6R5W5;A0A0A0MRX3 Q5VZ89-5 DENND4C DENN domain-containing protein 4C 1 0 S(0.004)T(0.046)S(0.949)LS(0.001)ALVR;S(0.002)T(0.025)S(0.85)LS(0.123)ALVR ; 120.63 0.013118 50144000 4882.3 4666 4715.3 4604.4 6668 6335.6 6038 6459.1 5179.1 4582.6 TRUE FALSE FALSE 4822.79265 4731.68807 4797.367819 5136.782392 6327.707078 5930.775607 6550.867569 6645.983868 4715.868325 4463.543391 1.080485217 1.060074397 1.074789108 1.150830616 1.417642112 1.328714675 1.467638375 1.488947969 1.056530185 1 12.12397374 -8.824102517 1.276189657 1.038265273 1.454946627 0.930900469 0.047753762 0.079154654 0.25662921 0.008094311 0.020646762 1.50E-09 8.824102517 0.416681354 STS(ph)LVEGR ddPTM_HeLa_Romidepsin_16h_R1 2 STSLVEGR 8 0 M0QY76;P26651 M0QY76 ZFP36 Tristetraprolin 1 0 S(0.004)T(0.14)S(0.856)LVEGR;S(0.001)T(0.041)S(0.958)LVEGR ; 133.99 0.0094209 9913900 3365.5 5054.1 2076.6 2942.9 8533.3 5933.8 3385.6 5248.1 3130.5 3507.2 TRUE FALSE FALSE 3324.479991 5125.251752 2112.742352 3283.171945 8097.813859 5554.64933 3673.172779 5399.945493 2850.50024 3416.082438 0.973184943 1.500330231 0.61846937 0.961092715 2.370497201 1.626029064 1.075258822 1.580742149 0.834435436 1 11.73812708 STS(ph)PIIGSPPVR ddPTM_HeLa_Romidepsin_16h_R1 2 STSPIIGSPPVR 12 0 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 1 0 S(0.067)T(0.067)S(0.866)PIIGSPPVR;S(0.132)T(0.132)S(0.733)PIIGS(0.003)PPVR ; 184.87 4.60E-07 43846000 4347.6 4012.7 4152.2 3513.8 4706.9 5843.8 5329.2 5954.1 4645.9 4404.2 TRUE FALSE FALSE 4294.609779 4069.190896 4224.467299 3920.082089 4466.689329 5470.40004 5781.862115 6126.372489 4230.359068 4289.778249 1.001126289 0.948578379 0.984775215 0.913819284 1.041240146 1.275217441 1.347823076 1.428132676 0.986148659 1 12.06668736 -8.158653149 2.205569739 0.988470627 1.389732934 0.965075321 0.032707615 0.042747939 0.399104379 0.005121981 0.01678946 6.94E-09 8.158653149 0.401262307 STS(ph)PTFNK ddPTM_HeLa_Romidepsin_16h_R1 4 STSPTFNK 8 0 Q9BX63 Q9BX63 BRIP1 Fanconi anemia group J protein 1 0 S(0.046)T(0.076)S(0.87)PT(0.009)FNK;S(0.046)T(0.079)S(0.873)PT(0.001)FNK;S(0.005)T(0.06)S(0.928)PT(0.008)FNK;S(0.096)T(0.096)S(0.785)PT(0.023)FNK ;;; 123.35 0.016701 91633000 22586.2 21948.1 21925.3 21718.8 17383.1 16924.6 14920.1 11663.5 23573.9 21591.8 TRUE FALSE FALSE 22310.91071 22257.08593 22306.90065 24230.02985 16495.97554 15843.17268 16187.41292 12000.96497 21465.39134 21030.84192 1.060866264 1.058306938 1.060675589 1.152118871 0.784370669 0.753330406 0.769698759 0.57063645 1.020662483 1 14.36021899 -8.634250961 5.205148109 1.041880049 0.714918292 0.870183327 0.064442418 0.056760473 2.377650649 0.009553256 0.019385678 2.32E-09 8.634250961 -0.326961756 AGS(ph)ISPGSPPYPQSR ddPTM_HeLa_Romidepsin_16h_R1 1 AGSISPGSPPYPQSR 15 0 Q63HR2-5;Q63HR2-6;Q63HR2;Q63HR2-4 Q63HR2-5 TNS2 Tensin-2 1 0 AGS(0.982)IS(0.014)PGS(0.004)PPYPQSR 150.9 0.00047553 6618100 1818.9 1645.1 1561.3 1453.8 1013.7 815.43 560.49 565.58 1750 1495.4 TRUE FALSE FALSE 1796.730547 1668.259761 1588.473772 1621.895196 961.9671064 763.3266547 608.0980066 581.944165 1593.475617 1456.549292 1.233552861 1.145350706 1.090573302 1.113518921 0.660442535 0.524065103 0.417492226 0.399536197 1.09400734 1 10.50833881 -8.59638291 2.128039288 1.117776381 0.43523794 0.955830331 0.065545482 0.062865491 0.571723272 0.014219764 0.034055875 2.53E-09 8.59638291 -0.682538441 down STS(ph)QGSINSPVYSR ddPTM_HeLa_Romidepsin_16h_R1 2 STSQGSINSPVYSR 14 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 S(0.33)T(0.052)S(0.617)QGSINSPVYSR;S(0.074)T(0.13)S(0.796)QGSINSPVYSR ; 233.28 6.87E-43 128512000 4470.7 4041 3272.5 3646.7 4439.8 3925.5 3424.3 3773 4136.1 3576 TRUE FALSE FALSE 4416.209389 4097.889304 3329.45649 4068.348612 4213.220439 3674.673219 3715.159957 3882.165802 3766.156857 3483.095004 1.267898057 1.176508048 0.955890231 1.168026886 1.20961973 1.055002294 1.066626076 1.114573618 1.081267336 1 11.76615411 STS(ph)STSSGSNSNALVPVSWK ddPTM_HeLa_Romidepsin_16h_R1 1 STSSTSSGSNSNALVPVSWK 20 0 H0Y9X0;A0A286YEZ9;A0A2C9F2R7;O94915 H0Y9X0 FRYL Protein furry homolog-like 1 0 S(0.101)T(0.101)S(0.616)S(0.141)T(0.033)S(0.008)SGSNSNALVPVSWK 120.99 0.00018803 8325900 2161.4 2327.6 1790.8 2004 3016.9 3046.9 2586 3226.3 2788.6 2377.4 TRUE FALSE FALSE 2135.056025 2360.368014 1821.968123 2235.711909 2862.936335 2852.212923 2805.654775 3319.6479 2539.180632 2315.634805 0.922017591 1.019317903 0.786811512 0.965485535 1.236350537 1.231719664 1.211613666 1.433580067 1.0965376 1 11.17719203 -8.737288534 4.44562024 0.951677314 1.275713271 0.730646567 0.093292142 0.068516043 3.140196261 0.011895074 0.023653405 1.83E-09 8.737288534 0.324035957 STS(ph)TPNVHMVSTTLPVDSR ddPTM_HeLa_Romidepsin_16h_R1 3 STSTPNVHMVSTTLPVDSR 19 0 H7C155;P04049;P04049-2 H7C155 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 0 S(0.137)T(0.137)S(0.556)T(0.169)PNVHMVSTTLPVDSR;S(0.014)T(0.014)S(0.485)T(0.485)PNVHMVS(0.001)TTLPVDSR;S(0.138)T(0.138)S(0.394)T(0.331)PNVHMVSTTLPVDSR ;; 114.21 0.0011289 95448000 4629.77 4366.35 4833.08 3503.44 4587.58 4196.4 3436.02 3658.6 5547 4809.87 TRUE FALSE FALSE 4573.340582 4427.81959 4917.19773 3908.524217 4353.458674 3928.263583 3727.875453 3764.455819 5050.862427 4684.908884 0.976185598 0.94512395 1.049582362 0.834279666 0.929251514 0.838493059 0.795719948 0.803528075 1.078113268 1 12.19380527 -8.530567641 0.725114684 0.990962278 0.778414472 0.708034812 0.052614286 0.315032803 0.26829071 0.007548606 0.038953827 2.95E-09 8.530567641 -0.212547806 STS(ph)VPENPK ddPTM_HeLa_Romidepsin_16h_R1 1 STSVPENPK 9 0 A0A494C0P1;P04150-7;P04150-5;P04150-2;P04150-6;P04150-10;P04150;P04150-3;D6RDA9;Q3MSN4;P04150-9;P04150-8;P04150-13;P04150-12;P04150-11 A0A494C0P1 NR3C1 Glucocorticoid receptor 1 0 ST(0.002)S(0.998)VPENPK 117.52 0.014876 37714000 8581.9 14911 5365.4 5821.6 7261.4 4602.7 2979.3 4849.6 8909.5 8515.1 TRUE FALSE FALSE 8477.300502 15120.91745 5458.782536 6494.720783 6890.823662 4308.602325 3232.361668 4989.915525 8112.612006 8293.876474 1.022115597 1.82314235 0.658170224 0.783074212 0.830832685 0.519491982 0.389728697 0.601638515 0.978144783 1 13.01783085 -8.776533002 1.18630236 1.05982693 0.491431815 0.449587037 0.281416561 0.351302812 0.974468421 0.0453354 0.125107717 1.67E-09 8.776533002 -0.568395115 STSAPQMS(ph)PGSSDNQSS(ph)SPQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 2 0 STSAPQMS(0.849)PGS(0.148)S(0.002)DNQS(0.004)S(0.86)S(0.136)PQPAQQK 138.78 1.31E-06 4895200 3049.2 3306.4 2613.9 2559.3 2709 2533.8 2120.3 2354.2 3421.3 2755.1 TRUE FALSE FALSE 3012.035178 3352.947586 2659.393833 2855.218308 2570.749621 2371.898357 2300.398229 2422.315063 3115.290359 2683.522105 1.12241862 1.249457785 0.99100873 1.063981662 0.957975944 0.883875096 0.85723096 0.902662608 1.160896105 1 11.38991206 -8.583050854 1.914192825 1.07162638 0.875656678 0.630381896 0.074160139 0.198418776 1.452613833 0.01194726 0.029958053 2.61E-09 8.583050854 -0.195969702 STSAPQMS(ph)PGSSDNQSSS(ph)PQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 2 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 2 0 STSAPQMS(0.968)PGS(0.031)SDNQSS(0.312)S(0.687)PQPAQQK;STSAPQMS(0.882)PGS(0.052)S(0.065)DNQSS(0.31)S(0.69)PQPAQQK ; 170.59 2.71E-14 113783000 17797.3 17242 15767.4 15593.8 16276.6 14860.1 13056 13219 18009.4 16934.3 TRUE FALSE FALSE 17580.37966 17484.73333 16041.82498 17396.82853 15445.94437 13910.58757 14164.97631 13601.47091 16398.59416 16494.34444 1.065842885 1.06004415 0.972565174 1.054714759 0.936438815 0.843354982 0.858777768 0.824614216 0.994194963 1 14.00968382 -8.495796753 2.610233838 1.031002921 0.842588021 0.874786046 0.030814917 0.071165333 0.961900204 0.004904383 0.011778288 3.19E-09 8.495796753 -0.188414899 STSAPQMSPGS(ph)SDNQSSSPQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 2 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 STSAPQMS(0.001)PGS(0.325)S(0.325)DNQS(0.325)S(0.019)S(0.006)PQPAQQK;STSAPQMS(0.011)PGS(0.494)S(0.494)DNQSSSPQPAQQK ; 116.04 5.70E-07 180164000 13413.2 13964.3 12624.2 13132.4 12574.9 12340.9 11108.3 11266.9 14905.4 14200.2 TRUE FALSE FALSE 13249.71476 14160.88978 12843.91891 14650.82988 11933.15593 11552.35632 12051.83872 11592.88998 13572.22369 13831.27676 0.957953123 1.023830991 0.928614121 1.059253613 0.862766044 0.835234268 0.871346799 0.838164848 0.981270488 1 13.75564672 -8.665935405 7.862919753 0.983887518 0.850676664 0.793611213 0.034852889 0.078940745 5.732769276 0.004721254 0.009460486 2.16E-09 8.665935405 -0.133210854 STSAPQMSPGSS(ph)DNQSSSPQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 S(0.001)T(0.001)S(0.001)APQMS(0.134)PGS(0.17)S(0.218)DNQS(0.218)S(0.218)S(0.041)PQPAQQK 57.826 0.0021044 1330800 555.92 594.2 379.77 297.5 401.76 548.88 730.22 480.23 454.87 702.26 TRUE FALSE FALSE 549.1442332 602.5651632 386.3797375 331.8983498 381.256688 513.8083394 792.2448686 494.1246974 414.185288 684.015184 0.802824624 0.880923666 0.564870118 0.485220734 0.557380446 0.751165108 1.158227021 0.722388492 0.605520605 1 9.417884541 -11.35976558 0.747490861 0.981307475 0.730099933 0 0.214801611 0.71830226 0.85266036 0.084664227 0.045787029 4.37E-12 11.35976558 -0.251207542 STSAPQMSPGSSDNQS(ph)SSPQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 STSAPQMSPGS(0.002)S(0.002)DNQS(0.332)S(0.332)S(0.332)PQPAQQK 83.905 3.86E-05 5045400 1141.7 1224.3 1256.3 1557.4 1326 1220.7 1160.3 1171.5 1421.9 1819.8 TRUE FALSE FALSE 1127.784521 1241.535728 1278.165375 1737.473916 1258.329272 1142.70121 1258.855853 1205.395504 1294.721703 1772.521334 0.636260055 0.700434857 0.721100136 0.980227365 0.70990924 0.644675575 0.71020632 0.680045696 0.730440688 1 10.79158728 -12.39642155 1.068928315 1.003399972 0.720023744 0.01561217 0.122030365 0.327124192 0.655850794 0.070862315 0.017235287 4.01E-13 12.39642155 -0.283376228 STSAPQMSPGSSDNQSS(ph)SPQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 1 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 STSAPQMSPGSSDNQS(0.005)S(0.497)S(0.497)PQPAQQK 164.13 2.53E-11 10625000 5846.9 4945.9 4964.4 5033.4 4802.5 3908.2 3408.7 3768.6 5314.4 5242.4 TRUE FALSE FALSE 5775.635734 5015.52851 5050.8033 5615.385391 4557.410504 3658.478633 3698.234893 3877.638495 4839.066754 5106.201692 1.131102154 0.982242538 0.989150763 1.099718681 0.892524577 0.716477502 0.724263379 0.759397832 0.947684217 1 12.31803481 -8.507465061 3.072622486 1.052917119 0.733573995 0.830507933 0.05804542 0.068899886 1.320093612 0.008923734 0.020553334 3.11E-09 8.507465061 -0.319343124 STSAPQMSPGSSDNQSSS(ph)PQPAQQK ddPTM_HeLa_Romidepsin_16h_R1 2 STSAPQMSPGSSDNQSSSPQPAQQK 25 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 STSAPQMS(0.001)PGS(0.042)S(0.179)DNQS(0.039)S(0.167)S(0.572)PQPAQQK;STSAPQMSPGSSDNQS(0.001)S(0.243)S(0.755)PQPAQQK ; 141.12 1.88E-07 36691000 14617.5 13204.6 12418.3 12860.9 12100.1 10531.3 9529.5 9824.8 14731 14181.5 TRUE FALSE FALSE 14439.33629 13390.49471 12634.4353 14347.93777 11482.58675 9858.383918 10338.93549 10109.06509 13413.42247 13813.06259 1.045339236 0.969408096 0.914672993 1.038722418 0.831284639 0.713700083 0.748489731 0.731848207 0.971067957 1 13.7537456 -8.601229975 3.24831433 1.009988102 0.735135394 0.893399322 0.040118689 0.052940284 1.120545587 0.006265919 0.013545031 2.50E-09 8.601229975 -0.274852708 STSIQSFK(ac)DK ddPTM_HeLa_Romidepsin_16h_R1 1 STSIQSFKDK 10 1 P13797;A0A0A0MSQ0;P13797-3;P13797-2 P13797 PLS3 Plastin-3 0 1 STSIQSFK(1)DK 123.51 0.013958 753550 329.89 71.767 216.19 266.44 393.87 450.36 316.94 257.99 344.24 385.75 FALSE TRUE FALSE 325.8691738 72.77733771 219.9526963 297.2470464 373.7693442 421.5834495 343.8608757 265.4545336 313.4503122 375.7281594 0.867300376 0.193696788 0.585403811 0.791122622 0.994786616 1.122043794 0.915185267 0.706506891 0.834247592 1 8.553545434 -7.249182238 21.06188751 0.868419614 0.706505945 0 0.253433805 725.6701129 1246718.145 0.038068186 0.715759081 5.63E-08 7.249182238 -0.161913669 STSPVT(ph)DPSIPIR ddPTM_HeLa_Romidepsin_16h_R1 1 STSPVTDPSIPIR 13 0 A0A087WU18;Q99607 A0A087WU18 ELF4 ETS-related transcription factor Elf-4 1 0 STS(0.005)PVT(0.995)DPSIPIR 224.25 3.55E-31 34702000 5057.8 5477.9 4780.7 4211.5 2567.5 2487.4 2129.2 2377.8 5639.7 4564.6 TRUE FALSE FALSE 4996.153588 5555.01802 4863.906078 4698.453446 2436.470894 2328.463168 2310.054195 2446.597891 5135.271107 4446.011034 1.123738459 1.249438649 1.093993254 1.056779529 0.548012786 0.523719611 0.519579051 0.550290558 1.155028871 1 12.11829581 -8.763161911 5.930274885 1.079475205 0.530555083 0.947956137 0.066067484 0.03005529 3.805352666 0.011481159 0.022057851 1.73E-09 8.763161911 -0.548920122 STSQGSINS(ph)PVYSR ddPTM_HeLa_Romidepsin_16h_R1 2 STSQGSINSPVYSR 14 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 STSQGS(0.443)INS(0.557)PVYSR;S(0.001)TS(0.013)QGS(0.186)INS(0.8)PVYSR ; 240.5 1.32E-43 158578000 5871.8 6200.9 6396.3 5998.7 8566.3 8601.5 7888.8 7541.2 6642.1 6567.6 TRUE FALSE FALSE 5800.232243 6288.196433 6507.624918 6692.297919 8129.129746 8051.89191 8558.874475 7759.392724 6048.013941 6396.972805 0.906715164 0.982995649 1.017297574 1.046166386 1.2707776 1.258703477 1.337956989 1.212978851 0.945449375 1 12.64317363 -8.894719769 1.879027915 0.959638053 1.283063232 0.917201855 0.042521159 0.070450929 0.502884597 0.007434145 0.015601456 1.27E-09 8.894719769 0.323425179 STSS(ph)TSSGSNSNALVPVSWK ddPTM_HeLa_Romidepsin_16h_R1 1 STSSTSSGSNSNALVPVSWK 20 0 H0Y9X0;A0A286YEZ9;A0A2C9F2R7;O94915 H0Y9X0 FRYL Protein furry homolog-like 1 0 S(0.054)T(0.054)S(0.245)S(0.352)T(0.077)S(0.171)S(0.006)GS(0.038)NSNALVPVSWK 134.08 0.00034626 10559000 3263.4 3379.8 2716 2543.4 4260.5 3674.5 3289.2 4230.4 4040.2 3358 TRUE FALSE FALSE 3223.624426 3427.380913 2763.270841 2837.479875 4043.070787 3439.711309 3568.584566 4352.79995 3678.834393 3270.758676 0.9855892 1.047885599 0.844840942 0.867529572 1.23612629 1.051655487 1.091057128 1.330822718 1.12476485 1 11.6754096 -4.000000033 0.611230812 0.985544473 23.82166681 0.443115888 0.106108083 97.19832086 0.667095024 0.016563934 2982.43778 1.00E-04 4.000000033 22.83612234 STST(ph)PNVHMVSTTLPVDSR ddPTM_HeLa_Romidepsin_16h_R1 2 STSTPNVHMVSTTLPVDSR 19 0 H7C155;P04049;P04049-2 H7C155 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 0 S(0.003)T(0.003)S(0.125)T(0.851)PNVHMVS(0.018)TTLPVDSR;S(0.037)T(0.037)S(0.199)T(0.6)PNVHMVS(0.123)T(0.003)T(0.001)LPVDSR ; 137.27 7.07E-05 18285000 2447.4 2225.23 2129.39 2442.39 2551.4 2330.6 1780.97 2043.98 3497.4 2588 TRUE FALSE FALSE 2417.570147 2256.556846 2166.45114 2724.790624 2421.192537 2181.682182 1932.245547 2103.119336 3184.583785 2520.763387 0.959062703 0.895187886 0.859442481 1.08093867 0.960499724 0.865484715 0.7665319 0.834318424 1.263341018 1 11.29964499 -8.115076647 3.121099383 0.971004278 0.801962519 0.348875234 0.109274021 0.135500345 2.489048773 0.008552198 0.025273921 7.67E-09 8.115076647 -0.169041759 STST(ph)PTSPGPR ddPTM_HeLa_Romidepsin_16h_R1 3 STSTPTSPGPR 11 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 STS(0.023)T(0.973)PT(0.004)SPGPR;STS(0.027)T(0.968)PT(0.005)SPGPR;S(0.001)T(0.001)S(0.03)T(0.962)PT(0.005)SPGPR ;; 152.69 0.0046953 28712800 10125.3 9393.3 8760 9638.2 12500.9 14310.9 12622.9 11691.8 11120.9 9912.3 TRUE FALSE FALSE 10001.88895 9525.539124 8912.464125 10752.61403 11862.93243 13396.47968 13695.08881 12030.08379 10126.21885 9654.777017 1.035952351 0.986614099 0.923114445 1.113709205 1.228711176 1.387549361 1.418478002 1.246023991 1.048829904 1 13.23702722 -8.715424468 2.150829868 1.008650131 1.354851066 0.882694791 0.05606157 0.067484716 0.635248836 0.008042262 0.01792032 1.93E-09 8.715424468 0.346200935 STSTLEIQPSRAS(ph)PTSDIESVER ddPTM_HeLa_Romidepsin_16h_R1 1 STSTLEIQPSRASPTSDIESVER 23 1 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 0 STSTLEIQPS(0.07)RAS(0.777)PT(0.126)S(0.026)DIESVER 65.581 0.0011976 5262100 846.71 799.78 773.08 713.72 706.58 497.59 577.19 446.56 776.81 778.77 TRUE FALSE FALSE 836.3899728 811.0393238 786.5351331 796.2436646 670.520586 465.7956049 626.2165042 459.480509 707.330168 758.5374431 1.102635052 1.06921462 1.036910096 1.04970911 0.883965046 0.614070682 0.825557802 0.605745324 0.932492093 1 9.567076587 -8.532739474 3.073378251 1.050463869 0.696758196 0.819603446 0.07290055 0.063981624 1.236394076 0.009278042 0.021044894 2.93E-09 8.532739474 -0.353705673 STSTPNVHMVS(ph)TTLPVDSR ddPTM_HeLa_Romidepsin_16h_R1 1 STSTPNVHMVSTTLPVDSR 19 0 H7C155;P04049;P04049-2 H7C155 RAF1 RAF proto-oncogene serine/threonine-protein kinase 1 0 S(0.005)T(0.005)S(0.131)T(0.01)PNVHMVS(0.815)T(0.033)T(0.002)LPVDSR 91.202 0.0050218 15161000 1406.3 1216.6 1448.4 1281.3 1460 1341.2 1184.7 1426 2213.8 1826.1 TRUE FALSE FALSE 1389.159475 1233.727327 1473.608794 1429.449935 1385.490752 1255.501649 1285.328388 1467.25906 2015.792183 1778.657659 0.781015654 0.693628322 0.828494897 0.803667827 0.778953018 0.705870319 0.72263956 0.824924939 1.133322185 1 10.79657314 -12.05396877 0.613362121 1.022095537 0.760943458 0.764640077 0.063641511 0.337881499 0.207736782 0.047468144 0.010862699 8.83E-13 12.05396877 -0.261152079 STSTPT(ph)SPGPR ddPTM_HeLa_Romidepsin_16h_R1 1 STSTPTSPGPR 11 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BRB0;A0A0C4DGL7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 S(0.003)T(0.091)S(0.193)T(0.193)PT(0.503)S(0.017)PGPR 111.5 0.028655 33613000 979.83 5649.3 1004.9 1776.2 942.22 764.87 799.49 830.8 1520.8 1455.3 TRUE FALSE FALSE 967.8874551 5728.830994 1022.389863 1981.572601 894.1349975 715.9972755 867.3986606 854.8378872 1384.775839 1417.491096 0.682817308 4.041528733 0.72126722 1.397943597 0.630787029 0.505115889 0.611925297 0.603064026 0.976920309 1 10.46912396 -8.679118395 7.511310743 1.135811555 0.578108361 0.118248741 0.945578671 0.55225152 43.23455819 0.141502231 0.283582442 2.09E-09 8.679118395 -0.557703194 STSYGYS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 STSYGYSR 8 0 Q13242 Q13242 SRSF9 Serine/arginine-rich splicing factor 9 1 0 STSYGYS(1)R;STSYGYS(1)R ; 136.52 0.0092372 636990000 7386.5 7515 7197.7 2275.65 8792.8 9886.1 9723.9 8860.9 7978 7660.7 TRUE FALSE FALSE 7296.470497 7620.796367 7322.972949 2538.77136 8344.070606 9254.410116 10549.84782 9117.276161 7264.427699 7461.67391 0.977859738 1.021325303 0.981411549 0.340241532 1.118257204 1.240259254 1.413871465 1.22188081 0.973565421 1 12.8652836 -8.38377478 4.064489354 0.944349749 1.303416819 0.431694025 0.202445965 0.184520643 5.184141275 0.029183005 0.068133975 4.13E-09 8.38377478 0.35906707 STT(ph)PPPAEPVSLPQEPPK ddPTM_HeLa_Romidepsin_16h_R1 3 STTPPPAEPVSLPQEPPK 18 0 Q9UN86-2;Q9UN86 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 S(0.166)T(0.166)T(0.668)PPPAEPVSLPQEPPK;S(0.021)T(0.021)T(0.958)PPPAEPVSLPQEPPK;S(0.102)T(0.102)T(0.795)PPPAEPVSLPQEPPK ;; 185.86 2.09E-10 91805000 27485.8 27764.6 27105.3 19636.2 29820.2 30832.2 28186.4 31043.3 29925.9 27482.3 TRUE FALSE FALSE 27150.7925 28155.47077 27577.05638 21906.62984 28298.36392 28862.12193 30580.55211 31941.48891 27249.25255 26768.30588 1.014288787 1.051821168 1.030212988 0.81837939 1.057159315 1.078219968 1.142416418 1.193257767 1.017967019 1 14.70823822 -7.923210298 1.783127896 1.000499679 1.182781674 0.543705738 0.06330537 0.226320016 1.331590215 0.009049783 0.044919299 1.19E-08 7.923210298 0.182281995 STT(ph)PPPAEPVSLPQEPPKPR ddPTM_HeLa_Romidepsin_16h_R1 3 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 1 0 S(0.163)T(0.163)T(0.674)PPPAEPVSLPQEPPKPR;S(0.134)T(0.134)T(0.732)PPPAEPVSLPQEPPKPR;S(0.164)T(0.164)T(0.671)PPPAEPVSLPQEPPKPR ;; 259.81 1.51E-80 3460680000 23346.6 23702.9 21238.7 17984.4 22473.7 22495.9 20575.4 21068.8 26229.4 24451.7 TRUE FALSE FALSE 23062.04266 24036.59005 21608.35066 20063.84095 21326.78323 21058.48459 22323.07396 21678.39249 23883.37677 23816.44131 0.96832446 1.009243561 0.907287129 0.842436562 0.895464732 0.884199462 0.937296789 0.910228031 1.002810473 1 14.53967024 -9.690350307 6.117570382 0.986381272 0.894171908 0.787371138 0.025061706 0.077278913 5.059525453 0.004157067 0.005876532 2.04E-10 9.690350307 -0.092209364 STT(ph)SVSEEDVSSR ddPTM_HeLa_Romidepsin_16h_R1 2 STTSVSEEDVSSR 13 0 Q96IZ0 Q96IZ0 PAWR PRKC apoptosis WT1 regulator protein 1 0 STT(0.495)S(0.495)VS(0.01)EEDVSSR;S(0.008)T(0.008)T(0.643)S(0.333)VS(0.008)EEDVSSR ; 226.42 2.45E-31 49935000 4391.7 5247.4 3678 3655.7 4300.6 3652.5 2739.6 3656.7 4343.4 4069.7 TRUE FALSE FALSE 4338.172271 5321.273035 3742.014047 4078.389235 4081.124334 3419.117038 2972.301556 3762.500845 3954.915426 3963.968607 1.094401268 1.342410489 0.944006983 1.02886517 1.02955516 0.86254897 0.749829741 0.949175238 0.997716132 1 11.95272982 -8.284051507 3.348662308 1.060162963 0.838730374 0.428164038 0.110897092 0.175760623 4.102699395 0.015974951 0.041055183 5.20E-09 8.284051507 -0.221432588 STTPPPAEPVSLPQEPPKPR ddPTM_HeLa_Romidepsin_16h_R1 2 STTPPPAEPVSLPQEPPKPR 20 1 Q9UN86-2 Q9UN86-2 G3BP2 Ras GTPase-activating protein-binding protein 2 0 0 ; ; 88.781 0.0020499 12259400 3058.26 3057.1 2697.45 2665.2 3237.4 2816.8 2392.54 2977.1 3068.7 3239.79 FALSE FALSE TRUE 3020.984751 3100.137934 2744.397986 2973.362964 3072.183398 2636.815571 2595.762288 3063.237691 2794.227786 3155.619789 0.957334835 0.98241808 0.869685884 0.942243731 0.973559428 0.835593559 0.822583981 0.970724579 0.885476697 1 11.62370767 -9.704248034 0.380594579 0.997741991 0.873183185 1.26E-05 0.061487012 1.02522777 0.347713388 0.025229736 0.049426024 1.98E-10 9.704248034 -0.124558806 STTTGHLIYK ddPTM_HeLa_Romidepsin_16h_R1 2 STTTGHLIYK 10 0 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01;A6PW80;Q5JR01;A0A2R8Y488;A0A2U3TZH3;Q05639;A0A2R8Y660;A0A2R8YDN5 Q5VTE0;A0A2R8Y488 EEF1A1P5;EEF1A1;EEF1A2 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha;Elongation factor 1-alpha 2 0 0 ; ; 135.43 0.0026998 19433800 10580.6 9097.6 8919.4 8827.5 22772.1 21947.3 14654.9 13525.1 19403.8 14049.5 FALSE FALSE TRUE 10451.63958 9225.676252 9074.638415 9848.177085 21609.95476 20544.93836 15899.68684 13916.42743 17668.27553 13684.49196 0.763757953 0.674170168 0.663133015 0.719659678 1.579156524 1.501330003 1.161876296 1.016948782 1.291116658 1 13.74025426 -8.772142127 24.99995637 0.838663209 1.317224384 0.494168077 0.229169653 116.985159 273259.3731 0.030537369 0.055760346 1.69E-09 8.772142127 0.478561175 STVNEK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 2 STVNEKPK 8 1 A0A590UJS4;Q6KC79-2;Q6KC79-3;Q6KC79 A0A590UJS4;Q6KC79 NIPBL Nipped-B-like protein 0 1 ; STVNEK(1)PK;STVNEK(1)PK 146.79 0.015406 8333800 8995.5 8168.9 10949.4 8058.7 5884.9 6342.7 6212.5 3439.8 10014.7 7368.1 FALSE TRUE FALSE 8885.859386 8283.901989 11139.96971 8990.484811 5584.571593 5937.42194 6740.189595 3539.325186 9118.96015 7176.6757 1.238158133 1.154281221 1.552246497 1.252736669 0.778155768 0.827322034 0.939179904 0.493170562 1.270638459 1 12.80910001 -8.753172134 24.8329519 1.163982653 0.777141798 0.627193088 0.176607792 112.6382237 338336.9907 0.028147348 0.05553659 1.77E-09 8.753172134 -0.386840855 STVTGERQS(ph)GDGQESTEPVENK ddPTM_HeLa_Romidepsin_16h_R1 3 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 0 STVT(0.001)GERQS(0.99)GDGQES(0.006)T(0.002)EPVENK;STVT(0.001)GERQS(0.797)GDGQES(0.148)T(0.054)EPVENK;S(0.004)T(0.005)VT(0.094)GERQS(0.896)GDGQESTEPVENK ;; 88.471 0.00025292 257624000 10703.2 9625.7 8583.6 8890.3 9915.4 9891.3 9565.2 10453.3 10451.1 9402.6 TRUE FALSE FALSE 10572.74528 9761.210857 8732.993957 9918.238316 9409.380139 9259.277853 10377.66785 10755.74974 9516.327441 9158.319097 1.15444168 1.065829958 0.953558602 1.08297584 1.027413441 1.011023721 1.133141108 1.174424 1.039091054 1 13.16086712 -12.7171867 1.631677743 1.000093972 1.083920949 0.083887539 0.065321079 0.575102457 2.769358405 0.050905549 0.011207733 1.92E-13 12.7171867 0.083826977 STVTGERQSGDGQES(ph)TEPVENK ddPTM_HeLa_Romidepsin_16h_R1 1 STVTGERQSGDGQESTEPVENK 22 1 O15234;J3KSY7 O15234 CASC3 Protein CASC3 1 0 STVTGERQS(0.001)GDGQES(0.741)T(0.258)EPVENK 90.755 0.00021948 44082000 1479.8 1240.9 1347.2 1441.9 1251.9 1404.7 1478.5 1377.8 1614.6 1481.3 TRUE FALSE FALSE 1461.763628 1258.369423 1370.647451 1608.619262 1188.010872 1314.944203 1604.083753 1417.664469 1470.186132 1442.815612 1.013132666 0.872162328 0.949981023 1.114916728 0.823397572 0.9113737 1.111773216 0.982568013 1.018970213 1 10.49467122 SVAAEGALLPQT(ph)PPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 SVAAEGALLPQTPPSPR 17 0 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 2 0 S(0.043)VAAEGALLPQT(0.988)PPS(0.968)PR 95.365 0.0023569 0 1119.5 1323.9 1109.5 1206.9 1432.1 1306.7 930.38 1257.9 1119.5 1145.5 TRUE FALSE FALSE 1105.855103 1342.537899 1128.810382 1346.447457 1359.014593 1223.206087 1009.406454 1294.295352 1019.369116 1115.739745 0.991140728 1.203271556 1.011714772 1.206775561 1.218039063 1.096318467 0.904697048 1.160033384 0.913626247 1 10.12378483 -10.29972532 24.18066493 0.995816432 1.109234411 0.31759387 0.09543756 380.7355311 240464.0696 0.015550669 0.017783093 5.02E-11 10.29972532 0.113417979 SVAAEGALLPQTPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 SVAAEGALLPQTPPSPR 17 0 H7C2H2;Q86X27-3;Q86X27 H7C2H2 RALGPS2 Ras-specific guanine nucleotide-releasing factor RalGPS2 1 0 SVAAEGALLPQT(0.126)PPS(0.874)PR;SVAAEGALLPQT(0.117)PPS(0.883)PR ; 134.4 0.0015956 35143000 4201.5 4716.3 4587.1 5018.5 4907.9 4462.5 3853.9 3928.8 4509 4229.1 TRUE FALSE FALSE 4150.290502 4782.696195 4666.936551 5598.762583 4657.431549 4177.360652 4181.25017 4042.473629 4105.703747 4119.227372 1.007541009 1.161066327 1.132964056 1.359177845 1.130656584 1.014112666 1.015056901 0.981366956 0.996716951 1 12.00815805 -10.27983026 21.53287569 1.003560991 1.116737371 0.20737333 0.1002351 165.2605577 193493.5806 0.018381539 0.021054716 5.25E-11 10.27983026 0.11317638 SVAEGLS(ph)GSLVQEPFQLATEKR ddPTM_HeLa_Romidepsin_16h_R1 1 SVAEGLSGSLVQEPFQLATEKR 22 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 SVAEGLS(0.499)GS(0.499)LVQEPFQLAT(0.001)EKR 96.455 0.00010931 11235000 938.81 1402.6 1001.8 1557.7 1072.9 1297 1099.9 1266.6 1067.4 768.13 TRUE FALSE FALSE 927.3674226 1422.34584 1019.235909 1737.808603 1018.145909 1214.125886 1193.325479 1303.247073 971.9290706 748.1738719 1.239507897 1.901089965 1.362298186 2.322733617 1.360841307 1.622785734 1.594984165 1.741904017 1.299068448 1 9.547229774 -10.43771651 3.628441064 1.099011479 1.691260891 0.432746369 0.271255051 0.133691421 3.188564622 0.044289872 0.049576733 3.65E-11 10.43771651 0.592249412 SVAEGLSGS(ph)LVQEPFQLATEKR ddPTM_HeLa_Romidepsin_16h_R1 1 SVAEGLSGSLVQEPFQLATEKR 22 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 SVAEGLS(0.13)GS(0.87)LVQEPFQLATEKR 102.46 6.38E-05 8834300 1327.3 1357.9 1195.8 1561.2 1326.4 1544.9 1393.5 1380 1546.5 1407.5 TRUE FALSE FALSE 1311.122357 1377.016552 1216.612397 1741.71329 1258.708859 1446.185876 1511.863855 1419.928123 1408.177167 1370.932947 0.956372345 1.004437565 0.887433919 1.270458408 0.918140352 1.054891765 1.102799271 1.035738565 1.027167061 1 10.42094229 SVAK(ac)LQDER ddPTM_HeLa_Romidepsin_16h_R1 1 SVAKLQDER 9 1 O14818;O14818-4;Q8TAA3-5;Q8TAA3;A0A087WYS6 O14818;Q8TAA3-5 PSMA7;PSMA8 Proteasome subunit alpha type-7;Proteasome subunit alpha type-7-like 0 1 SVAK(1)LQDER 99.013 0.0042417 0 161.82 164.34 467.26 383.64 629.45 961.8 876.95 641.6 268.04 148.06 FALSE TRUE FALSE 159.8476756 166.6535828 475.3924643 427.9982619 597.3268177 900.3440841 951.4381111 660.1636837 244.0658311 144.2133799 1.108410855 1.155604168 3.29645186 2.967812434 4.141965318 6.243138362 6.597432999 4.577686789 1.692393808 1 7.172061211 -9.008979674 0.883428483 1.015856453 6.006953669 0.86354081 0.731922879 0.124950299 0.188905561 0.121296706 0.332727032 9.80E-10 9.008979674 4.991097216 SVAS(ph)NQSEMEFSSLQDMPK ddPTM_HeLa_Romidepsin_16h_R1 2 SVASNQSEMEFSSLQDMPK 19 0 G3V119;H0YB24;Q8N163-2;Q8N163;A0A087X2B6 G3V119 CCAR2 Cell cycle and apoptosis regulator protein 2 1 0 S(0.374)VAS(0.609)NQS(0.017)EMEFSSLQDMPK;S(0.073)VAS(0.806)NQS(0.121)EMEFSSLQDMPK ; 70.316 0.0043624 28585000 7675.7 6406.2 6277.3 6394.1 7054.8 6662 7887.2 7309.7 9252.5 7796.1 TRUE FALSE FALSE 7582.145616 6496.386652 6386.553773 7133.415927 6694.767231 6236.319701 8557.138571 7521.194637 8424.933227 7593.556198 0.998497334 0.85551308 0.841049122 0.93940385 0.881637938 0.821264706 1.126894744 0.990470662 1.109484543 1 12.89055997 -10.35479451 12.75823816 0.999321241 0.92227233 0.220098128 0.090476146 1.42644063 191.4434472 0.01469285 0.016796228 4.42E-11 10.35479451 -0.077048911 SVASPLALPS(ph)PHK ddPTM_HeLa_Romidepsin_16h_R1 1 SVASPLALPSPHK 13 0 Q9BX66-11;Q9BX66;A0A3B3IRW8 Q9BX66-11 SORBS1 Sorbin and SH3 domain-containing protein 1 1 0 SVASPLALPS(1)PHK 87.308 0.026354 5098000 500.83 507.16 475.45 706.4 555.33 481.57 452.05 615.51 569.8 318.82 TRUE FALSE FALSE 494.7256913 514.2998118 483.7250078 788.0772917 526.9894379 450.7992312 490.4471157 633.3188107 518.8356609 310.5370104 1.593129562 1.656162694 1.557704852 2.537788622 1.697026184 1.451676341 1.579351572 2.039431016 1.670769163 1 8.278621412 -11.57851095 0.53406599 0.965961243 1.806750965 0.109279934 0.354774662 0.612295053 0.345881891 0.241043137 0.085465711 2.64E-12 11.57851095 0.840789722 SVAVS(ph)DEEEVEEEAER ddPTM_HeLa_Romidepsin_16h_R1 2 SVAVSDEEEVEEEAER 16 0 Q9Y6X9-2;Q9Y6X9 Q9Y6X9-2 MORC2 MORC family CW-type zinc finger protein 2 1 0 S(0.106)VAVS(0.894)DEEEVEEEAER;S(0.002)VAVS(0.998)DEEEVEEEAER ; 135.57 0.0013584 55134000 8399.5 8606.8 7453.4 7653.1 7601.7 8419.2 6194.1 7396.9 8691.6 8187.8 TRUE FALSE FALSE 8297.123663 8727.966756 7583.1233 8537.987431 7213.756883 7881.240292 6720.226699 7610.917631 7914.201527 7975.079776 1.040381275 1.094404947 0.950852344 1.070583326 0.904537269 0.988233411 0.842653226 0.954337492 0.99236644 1 12.96128324 -8.750764539 24.99936162 1.023325877 0.921440755 0.487802917 0.051349832 131.0094721 306808.3804 0.006823314 0.013537753 1.78E-09 8.750764539 -0.101885123 SVDISLGDS(ph)PRR ddPTM_HeLa_Romidepsin_16h_R1 2 SVDISLGDSPRR 12 1 H0YDE2;A0A1B0GTN9;E9PKC0;Q6IQ23-3;Q6IQ23;Q6IQ23-2 H0YDE2 PLEKHA7 Pleckstrin homology domain-containing family A member 7 1 0 SVDISLGDS(1)PRR;SVDISLGDS(1)PRR ; 105.17 0.00075757 4713500 2779.5 3136.1 2787.7 3142.4 3101 2617.4 2080.29 2253.7 3168.7 2776.7 TRUE FALSE FALSE 2745.622385 3180.250098 2836.218749 3505.739073 2942.744399 2450.156587 2256.989781 2318.907254 2885.283536 2704.560934 1.015182298 1.175884063 1.048679922 1.296232239 1.088067332 0.905935066 0.834512454 0.857406178 1.06682142 1 11.40117869 -8.111140211 4.156958978 1.050113686 0.850407414 0.545991187 0.090836198 0.17154904 5.016878552 0.014657446 0.040210375 7.74E-09 8.111140211 -0.199706273 SVDVILDDDLVDK ddPTM_HeLa_Romidepsin_16h_R1 3 SVDVILDDDLVDK 13 0 P25205;P25205-2;J3KQ69;A0A499FHX9 P25205 MCM3 DNA replication licensing factor MCM3 0 0 ;; ;; 205.46 1.49E-15 6953300 4919.53 4541.75 4702.73 3700.75 4065.66 4057.39 3536.51 3831.21 5249.58 4544.51 FALSE FALSE TRUE 4859.568876 4605.688876 4784.579043 4128.648128 3858.174199 3798.135874 3836.901071 3942.060017 4780.044417 4426.442975 1.097849651 1.040494343 1.080908321 0.932723668 0.871619542 0.858055982 0.866813623 0.890570609 1.079883881 1 12.11193212 -9.071066379 3.336716831 1.049125474 0.87160641 0.910748059 0.02788329 0.073680841 1.600933556 0.005898903 0.010417685 8.49E-10 9.071066379 -0.177519064 SVDYNMPRS(ph)PVEMDEDFDVIFDPYAPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVDYNMPRSPVEMDEDFDVIFDPYAPK 27 1 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 0 S(0.01)VDY(0.177)NMPRS(0.808)PVEMDEDFDVIFDPY(0.005)APK 47.018 0.019774 5832500 1460.5 1347.7 1197.4 2995.2 1669.2 2124 1836.5 1845.5 1497.6 1448.7 TRUE FALSE FALSE 1442.698864 1366.672956 1218.240245 3341.519117 1584.014495 1988.283255 1992.492264 1898.896631 1363.650905 1411.062565 1.022420196 0.968541714 0.86334956 2.368087142 1.122568577 1.409068105 1.41205097 1.345721074 0.96640003 1 10.46256624 SVEAAAELSAK ddPTM_HeLa_Romidepsin_16h_R1 1 SVEAAAELSAK 11 0 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 0 0 172.27 0.0041969 3062800 2976.2 2776.3 2853.4 2503.7 3214.3 3387.6 2360.8 2684.4 2851.4 2858.7 FALSE FALSE TRUE 2939.92493 2815.384824 2903.06223 2793.189574 3050.262277 3171.143293 2561.326293 2762.068879 2596.363643 2784.430562 1.055844225 1.011116909 1.042605361 1.00314571 1.095470765 1.138883956 0.919874364 0.991969028 0.932457673 1 11.4431666 -7.720347218 24.99999786 1.036271635 0.955921677 0.244183211 0.055568853 135.0828055 82181.1335 0.006474594 0.024225186 1.90E-08 7.720347218 -0.080349958 SVEAAAELSAK(ac)DLK ddPTM_HeLa_Romidepsin_16h_R1 2 SVEAAAELSAKDLK 14 1 P20962;F5H7R9;F5GXR3 P20962 PTMS Parathymosin 0 1 ; SVEAAAELSAK(1)DLK;SVEAAAELSAK(1)DLK 230.14 5.04E-33 2059110 853.72 851.37 959.36 756.95 900.81 777.92 880.18 690.7 830.36 825.18 FALSE TRUE FALSE 843.3145323 863.3556092 976.0572584 844.4721206 854.8383043 728.2134226 954.9424672 710.6843148 756.0905219 803.7417046 1.049235752 1.074170476 1.214391704 1.050676002 1.063573408 0.906029161 1.188121086 0.884219782 0.940713313 1 9.650588132 -7.205491655 22.29352882 1.044766155 0.884215625 0.233527238 0.090926153 18782.96824 7483513.1 0.011330269 18.97246451 6.23E-08 7.205491655 -0.160550529 SVEDEMDS(ph)PGEEPFYTGQGR ddPTM_HeLa_Romidepsin_16h_R1 4 SVEDEMDSPGEEPFYTGQGR 20 0 A0A590UJA3;S4R3W2;A0A590UJU2;A0A590UK38;A0A590UK73;B1AKN7;B1AKN5;A0A590UK09;B1AKN8;Q12857-2;Q12857-3;Q12857;Q12857-4 A0A590UJA3 NFIA Nuclear factor 1;Nuclear factor 1 A-type 1 0 SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(0.987)PGEEPFY(0.012)T(0.001)GQGR;SVEDEMDS(1)PGEEPFYTGQGR;SVEDEMDS(1)PGEEPFYTGQGR ;;; 181.72 1.01E-15 161656100 15304.6 14983.8 14790.8 12686.9 14784.3 13802.1 11016.8 11579.7 16027.1 15002.4 TRUE FALSE FALSE 15118.06165 15194.74233 15048.22767 14153.81907 14029.802 12920.19035 11952.56672 11914.74035 14593.59604 14612.63549 1.034588296 1.039835856 1.029809283 0.968601392 0.960114417 0.884179337 0.817961054 0.815372447 0.998697056 1 13.83492878 -8.217098236 1.11815335 1.019268777 0.799426293 0.957450136 0.016829464 0.08974386 0.190979116 0.003002012 0.015379167 6.07E-09 8.217098236 -0.219842484 SVEST(ph)SPEPSK ddPTM_HeLa_Romidepsin_16h_R1 3 SVESTSPEPSK 11 0 P18583-6;P18583-10;P18583-3;P18583-4;P18583-7;P18583;P18583-5;P18583-9;P18583-2;P18583-8 P18583-6 SON Protein SON 1 0 SVEST(0.5)S(0.5)PEPSK;SVES(0.005)T(0.927)S(0.067)PEPSK;SVES(0.002)T(0.499)S(0.499)PEPSK ;; 202.18 8.27E-13 793790000 23626.1 21810.7 19949.6 19332.3 20477.6 21390.8 19618.4 19399.8 21938.5 21617.4 TRUE FALSE FALSE 23338.13601 22117.75161 20296.81442 21567.59149 19432.55166 20023.99692 21284.78641 19961.10261 19976.26561 21055.77683 1.108395866 1.050436267 0.963954671 1.024307565 0.922908322 0.950997775 1.01087633 0.948010741 0.948730877 1 14.36192848 -9.765717213 24.24117744 1.052560869 0.971466185 0.172185049 0.049390432 56.02490842 317476.3512 0.00768566 0.01030457 1.72E-10 9.765717213 -0.081094684 SVFEEEVR ddPTM_HeLa_Romidepsin_16h_R1 1 SVFEEEVR 8 0 Q03252 Q03252 LMNB2 Lamin-B2 0 0 166.68 0.01908 2117700 1658.1 1568.4 1614.1 1254.1 1649.7 1677.8 1373.9 1248.4 1713.5 1637.1 FALSE FALSE TRUE 1637.890439 1590.479976 1642.192733 1399.104943 1565.509653 1570.593995 1490.599032 1284.520484 1560.240268 1594.567906 1.027168823 0.99743634 1.029866917 0.87741948 0.981776723 0.984965262 0.934798089 0.805560227 0.978472138 1 10.63894982 -5.758343653 0.538740906 1.008905207 8.74E-21 0.601613584 0.042392019 7.565287177 0.428525165 0.007835141 6.921110791 1.74E-06 5.758343653 -1.008905207 SVFGT(ph)PTLETANK ddPTM_HeLa_Romidepsin_16h_R1 2 SVFGTPTLETANK 13 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 S(0.128)VFGT(0.865)PT(0.007)LETANK;SVFGT(0.999)PT(0.001)LETANK ; 225.72 2.80E-31 124541000 6210.5 5851.2 6801.7 4816.8 7844.6 9960.3 8303.3 8268.8 6469.1 6001.1 TRUE FALSE FALSE 6134.804037 5933.573347 6920.080735 5373.74108 7444.26079 9323.868975 9008.582095 8508.044682 5890.487494 5845.190557 1.049547312 1.0151206 1.183893094 0.919344036 1.273570248 1.59513516 1.541195622 1.45556327 1.007749437 1 12.51303434 -8.506636474 3.710397133 1.030561033 1.527210052 0.909023049 0.071115859 0.04323268 1.283573528 0.009782603 0.021907754 3.11E-09 8.506636474 0.49664902 SVFWASS(ph)PYRR ddPTM_HeLa_Romidepsin_16h_R1 1 SVFWASSPYRR 11 1 O15027;O15027-5;F1T0I1;O15027-2;O15027-3;O15027-4 O15027;O15027-4 SEC16A Protein transport protein Sec16A 1 0 SVFWAS(0.121)S(0.877)PY(0.002)RR 91.123 0.0031887 0 1580.3 1282.1 1856.9 2082.3 2346.7 2633.5 1654.4 1639.5 1474.2 1259.8 TRUE FALSE FALSE 1561.038696 1300.149437 1889.218566 2323.065324 2226.939142 2465.227849 1794.924695 1686.936346 1342.34386 1227.070214 1.272167377 1.059555861 1.539617329 1.893180436 1.814842473 2.009035685 1.462772606 1.374767577 1.093942175 1 10.26100209 -9.63316444 4.070089175 1.12714357 1.719758406 0.696652257 0.188328184 0.104098372 3.179750996 0.033244837 0.047606311 2.33E-10 9.63316444 0.592614837 SIQDLTVTGTEPGQVSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SIQDLTVTGTEPGQVSSR 18 0 Q9UG54;O43318-4;O43318-3;O43318-2;O43318 Q9UG54 DKFZp586F0420;MAP3K7 Mitogen-activated protein kinase kinase kinase 7 1 0 SIQDLTVT(0.009)GT(0.022)EPGQVS(0.208)S(0.762)R 208.87 4.56E-22 23897000 5028.5 5745.4 4577.9 4710.6 3219 1910.1 1626.1 2210.6 4689.5 4818.4 TRUE FALSE FALSE 4967.210708 5826.283892 4657.576429 5255.261736 3054.722418 1788.050775 1764.220893 2274.560223 4270.059375 4693.217273 1.058380727 1.241426414 0.992405882 1.119756753 0.650880247 0.380986149 0.375908634 0.484648396 0.909836286 1 12.19636154 -8.585982205 3.294169044 1.048957056 0.416211305 0.913949352 0.089239551 0.043474865 0.955944621 0.011928772 0.025916647 2.59E-09 8.585982205 -0.63274575 down SVGDES(ph)WEQTQEGDVGALYHEQLALK ddPTM_HeLa_Romidepsin_16h_R1 1 SVGDESWEQTQEGDVGALYHEQLALK 26 0 O75691 O75691 UTP20 Small subunit processome component 20 homolog 1 0 S(0.007)VGDES(0.989)WEQT(0.004)QEGDVGALYHEQLALK 93.384 5.63E-06 4110100 994.57 1050.1 1035.1 710.16 647.06 817.61 729.57 688.06 1216.3 1057.9 TRUE FALSE FALSE 982.4477983 1064.883335 1053.115481 792.2720406 614.0381137 765.3673597 791.5396576 707.9679305 1107.511082 1030.415605 0.953448097 1.033450318 1.022029825 0.76888591 0.595913057 0.742775396 0.768175145 0.687070272 1.074819787 1 10.00901063 -9.160928823 4.43206144 0.985367571 0.704618479 0.879166476 0.05612857 0.054658061 1.825805559 0.007555662 0.012744574 6.90E-10 9.160928823 -0.280749092 SVGDGETVEFDVVEGEK ddPTM_HeLa_Romidepsin_16h_R1 2 SVGDGETVEFDVVEGEK 17 0 H0Y449;P67809;A0A0D9SEI8;Q9Y2T7;P16989-2;P16989;P16989-3 H0Y449;P16989-2 YBX1;YBX3;YBX2 Nuclease-sensitive element-binding protein 1;Y-box-binding protein 2;Y-box-binding protein 3 0 0 ; ; 348.24 1.14E-228 37811000 10115.8 9864.4 10185.6 7525.1 9937.4 9695.5 7936.5 9109.4 11137.6 10735.4 FALSE FALSE TRUE 9992.504739 10003.27128 10362.8761 8395.187469 9430.257396 9075.988841 8610.626112 9372.966117 10141.42516 10456.49276 0.955626802 0.956656454 0.99104703 0.802868386 0.901856637 0.86797639 0.823471723 0.896377622 0.969868712 1 13.35211141 -9.27469437 24.99862883 0.977296579 0.859497612 0.782024356 0.030637129 261.9590606 494048.2359 0.004760385 0.007297846 5.31E-10 9.27469437 -0.117798966 SVGGDS(ph)DTEDMR ddPTM_HeLa_Romidepsin_16h_R1 1 SVGGDSDTEDMR 12 0 Q9UK61-3;Q9UK61;Q9UK61-2;A0A087X0F1;Q9UK61-4 Q9UK61-3 FAM208A Protein FAM208A 1 0 SVGGDS(0.681)DT(0.319)EDMR 110.64 0.014379 20653000 4393.6 4598.2 4246.3 3843.6 4021 3451.9 3263.7 3543.7 4090.6 3749.7 TRUE FALSE FALSE 4340.049113 4662.93358 4320.20507 4288.015117 3815.793366 3231.33473 3540.918597 3646.231368 3724.726491 3652.282253 1.18831153 1.27671775 1.182878203 1.174064549 1.044769572 0.884743978 0.969508475 0.998343259 1.019835334 1 11.83458255 -8.50789748 5.776413017 1.119615152 0.953658067 0.50868019 0.082268451 0.14533 17.06372139 0.014875229 0.032128426 3.11E-09 8.50789748 -0.165957085 SVGGS(ph)GGGSFGDNLVTR ddPTM_HeLa_Romidepsin_16h_R1 1 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 S(0.339)VGGS(0.463)GGGS(0.198)FGDNLVTR 166.52 4.93E-06 76206000 709.23 737.54 616.72 613.51 1061.3 894.58 743.62 904.34 883.83 917.36 TRUE FALSE FALSE 700.585632 747.9231075 627.4537529 684.4469129 1007.137901 837.4192251 806.7830642 930.5056511 804.7780312 893.526855 0.784067796 0.837046031 0.702221483 0.766005979 1.127149 0.937206555 0.902919772 1.04138521 0.900675818 1 9.80336728 -8.772003992 24.9998818 0.866006432 0.9904363 0.39465887 0.09762851 264.2258536 625259.018 0.018031169 0.032930302 1.69E-09 8.772003992 0.124429867 SVGGSGGGS(ph)FGDNLVTR ddPTM_HeLa_Romidepsin_16h_R1 4 SVGGSGGGSFGDNLVTR 17 0 P02545;P02545-3;P02545-5;P02545-4;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 SVGGSGGGS(0.995)FGDNLVT(0.005)R;SVGGSGGGS(1)FGDNLVTR;SVGGSGGGS(0.998)FGDNLVT(0.002)R;SVGGS(0.025)GGGS(0.974)FGDNLVTR ;;; 218.64 3.40E-27 308356000 5193.2 5069.6 5008.5 5197.2 5889.8 7350.5 6863.5 7414.8 6118 4878.41 TRUE FALSE FALSE 5129.903281 5140.969962 5095.670842 5798.124718 5589.221528 6880.826773 7446.485519 7629.335539 5570.790757 4751.668205 1.079600481 1.081929491 1.072396182 1.220229289 1.176265111 1.448086541 1.567130784 1.60561201 1.172386311 1 12.21421839 -8.078386003 0.695934922 1.035480944 1.74190123 0.915390003 0.060272892 0.171125477 0.104455196 0.007924859 0.076790225 8.35E-09 8.078386003 0.706420285 SVIEPLPVT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 SVIEPLPVTPTR 12 0 H0YCM0;E9PM17;B3KNX7;Q13153;Q13153-2 H0YCM0 PAK1 Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase PAK 1 1 0 S(0.338)VIEPLPVT(0.657)PT(0.005)R;SVIEPLPVT(0.5)PT(0.5)R ; 133.98 0.0060385 14676000 3563.9 3860.7 4261.3 5681.5 4863.1 4809.6 3651.9 3909.5 4005.5 3994.5 TRUE FALSE FALSE 3520.461816 3915.051036 4335.466139 6338.421762 4614.91786 4502.282082 3962.092295 4022.615214 3647.238048 3890.722314 0.904835023 1.006253009 1.114308807 1.629111833 1.186133959 1.157184121 1.018343633 1.033899335 0.937419264 1 11.9258223 -9.716313181 3.840028612 0.956392726 1.204995968 0.336208989 0.159900685 0.199142235 6.12391137 0.026867406 0.037826573 1.92E-10 9.716313181 0.248603242 SVKPQILSVFGDIALAIGGEFKK ddPTM_HeLa_Romidepsin_16h_R1 1 SVKPQILSVFGDIALAIGGEFKK 23 2 Q14974;J3KTM9;Q14974-2 Q14974 KPNB1 Importin subunit beta-1 0 0 110.44 2.50E-05 13970000 638.08 769.23 615.34 698.84 656.16 4577.8 2310.5 2893.3 1084 1199.6 FALSE FALSE TRUE 630.3028355 780.0592401 626.0497346 779.6431689 622.6737067 4285.293354 2506.753812 2977.013071 987.0443251 1168.434219 0.539442294 0.667610746 0.535802294 0.667254653 0.532912933 3.667552083 2.145395754 2.547865359 0.844758146 1 10.1903608 -8.275188755 24.99353829 0.726757092 2.722783537 0.863726164 0.382271176 191.1896592 347543.2095 0.05367769 0.12060948 5.31E-09 8.275188755 1.996026445 SVLNNLK(ac)GDK ddPTM_HeLa_Romidepsin_16h_R1 2 SVLNNLKGDK 10 1 E9PER7;P29083 E9PER7 GTF2E1 General transcription factor IIE subunit 1 0 1 ; SVLNNLK(1)GDK;SVLNNLK(1)GDK 157.97 0.0097583 2238500 993.67 810.22 658.02 543.28 985.45 1182.75 1115.2 1300.15 966.23 1011.01 FALSE TRUE FALSE 981.5587678 821.6262984 669.4725621 606.0965898 935.1588093 1107.176092 1209.92506 1337.767789 879.8079688 984.7438145 0.996765609 0.834355379 0.679844394 0.615486567 0.949646797 1.124329065 1.228669876 1.358493213 0.893438431 1 9.94360464 -7.930269997 2.106460643 0.929708548 1.317353973 0.607889122 0.136873258 0.234387701 2.003138749 0.024014484 0.103599062 1.17E-08 7.930269997 0.387645426 SVNEILGLAESS(ph)PNEPK ddPTM_HeLa_Romidepsin_16h_R1 4 SVNEILGLAESSPNEPK 17 0 Q9H8G2;Q9H8G2-2 Q9H8G2 CAAP1 Caspase activity and apoptosis inhibitor 1 1 0 SVNEILGLAES(0.031)S(0.969)PNEPK;SVNEILGLAES(0.096)S(0.904)PNEPK;SVNEILGLAES(0.163)S(0.837)PNEPK;SVNEILGLAES(0.393)S(0.607)PNEPK ;;; 222.96 1.59E-35 143603300 20438.3 19410.8 19757.2 18195.8 21970.6 23839.4 21572.5 23829.4 20535.5 19164.7 TRUE FALSE FALSE 20189.19014 19684.06575 20101.06578 20299.68401 20849.3583 22316.13928 23404.86761 24518.86609 18698.75345 18666.79833 1.081556129 1.054496085 1.076835214 1.087475401 1.116922031 1.195499029 1.25382335 1.313501419 1.001711869 1 14.18818688 -4 0.284999535 1.020167115 3.471930244 0.96488788 0.018560292 7.632406025 0.097429001 0.010202566 9.502509381 1.00E-04 4 2.451763129 SVNELIYK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 SVNELIYKR 9 1 P18124;A8MUD9 P18124 RPL7 60S ribosomal protein L7 0 1 SVNELIYK(1)R 114.4 0.0015437 1466300 229.54 232.24 284.05 278.21 695.94 557.74 633.74 560.41 578.84 443.81 FALSE TRUE FALSE 226.7422782 235.5094808 288.9937711 310.3779492 660.4235849 522.102214 687.5698598 576.6245792 527.0671007 432.2797522 0.524526715 0.544808031 0.668534137 0.718002515 1.527768954 1.207787807 1.590566887 1.333915309 1.219273163 1 8.755821452 -8.766341845 24.99883038 0.738517816 1.412748008 0.66617645 0.219364017 49.96107742 254764.9229 0.031372215 0.058194409 1.71E-09 8.766341845 0.674230193 SVNFSLT(ph)PNEIK ddPTM_HeLa_Romidepsin_16h_R1 1 SVNFSLTPNEIK 12 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 SVNFS(0.028)LT(0.972)PNEIK 180.3 2.75E-06 128490000 4018 3740.5 4420 3021.5 3974.4 4390 4206.3 4215 4269 3691.2 TRUE FALSE FALSE 3969.027071 3793.158857 4496.928246 3370.860047 3771.571537 4109.493168 4563.583017 4336.954375 3887.169948 3595.302092 1.103948144 1.055032028 1.25077897 0.937573522 1.049027715 1.143017489 1.269318377 1.206283718 1.081180343 1 11.81189728 -4 0.266398729 1.034815415 2.512457356 0.304245005 0.085470769 39.54267612 0.500329477 0.041265835 27.08877298 1.00E-04 4 1.477641941 SVNFSLTPNEIK ddPTM_HeLa_Romidepsin_16h_R1 1 SVNFSLTPNEIK 12 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 0 0 119.39 9.50E-06 0 170.76 71.415 0 0 79.843 70.181 65.31 76.415 0 60.665 FALSE FALSE TRUE 168.6787114 72.42038224 0 0 75.76831377 65.6966606 70.85742977 78.62594746 0 59.08891455 2.854659164 1.225617069 0 0 1.282276284 1.111827169 1.199166211 1.330637871 0 1 5.884815592 -10.00830365 24.89036181 1.884460074 0.816275363 0 0.85574754 382.3818175 1146199.561 0.13550256 0.173463863 9.81E-11 10.00830365 -1.068184711 SVNGGPGS(ph)PDLAR ddPTM_HeLa_Romidepsin_16h_R1 2 SVNGGPGSPDLAR 13 0 A0A087X2C4;H0YAH0;O60245;O60245-2 A0A087X2C4 PCDH7 Protocadherin-7 1 0 S(0.142)VNGGPGS(0.858)PDLAR;SVNGGPGS(1)PDLAR ; 169.15 0.0001102 86375000 4237.5 7195.5 4745 4044.5 4982.4 4666.4 2188.57 3700.1 5205.7 5177.8 TRUE FALSE FALSE 4185.85172 7296.798438 4827.584735 4512.14412 4728.129536 4368.2321 2374.467081 3807.156556 4740.089154 5043.28001 0.829985984 1.446835873 0.957231152 0.894684434 0.937510812 0.866149032 0.470818015 0.754896922 0.939882209 1 12.30014661 -7.922877053 5.352241684 0.958675758 0.615742882 0.424443181 0.173940564 0.155869086 7.808766651 0.024826979 0.077176204 1.19E-08 7.922877053 -0.342932876 SVNGT(ph)T(ph)SDCLVS(ph)LVTSVTNVDLPPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVNGTTSDCLVSLVTSVTNVDLPPK 25 0 Q13705 Q13705 ACVR2B Activin receptor type-2B 3 0 S(0.133)VNGT(0.756)T(0.756)S(0.327)DCLVS(0.303)LVT(0.254)S(0.254)VT(0.215)NVDLPPK 40.137 0.030308 10433000 902.19 836.24 716.46 659.36 939.7 908.66 807.45 1044.9 820 1053.8 TRUE FALSE FALSE 891.1937613 848.0126087 728.9296858 735.5983056 891.7436025 850.5995586 876.0347828 1075.132533 746.6571463 1026.422124 0.868252681 0.826183096 0.710165602 0.716662559 0.868788368 0.828703453 0.853483925 1.047456507 0.727436723 1 10.00340846 -11.54066639 0.855649615 0.987934843 0.83185494 0 0.120120461 0.483124659 0.725201086 0.038363327 0.019506474 2.88E-12 11.54066639 -0.156079903 SVPGTTSS(ph)PLVGDISPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPGTTSSPLVGDISPK 17 0 Q9UQR0;H0Y6S1;B4DRC2;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 0 SVPGTTS(0.02)S(0.757)PLVGDIS(0.223)PK 254.72 1.76E-72 41248000 3847.6 3487.4 3348.3 4080.1 4760.5 4468.6 4279.8 4541.2 3649.4 3651 TRUE FALSE FALSE 3800.703971 3536.495709 3406.575757 4551.860359 4517.553921 4183.070882 4643.326105 4672.592457 3322.988524 3556.146494 1.068770361 0.994474135 0.957940221 1.279997989 1.270350906 1.176293184 1.305718455 1.313948249 0.934435218 1 11.79609904 -9.25368226 24.99257009 1.024763265 1.266182728 0.869282005 0.053126965 159.3317155 513348.7324 0.007467525 0.012233312 5.58E-10 9.25368226 0.241419462 SVPGTTSSPLVGDIS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPGTTSSPLVGDISPK 17 0 Q9UQR0;H0Y6S1;B4DRC2;Q9UQR0-2 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 0 SVPGTTS(0.001)S(0.001)PLVGDIS(0.998)PK 116.61 0.0021579 102560000 3522.4 3275.8 2660.8 3037.8 2931.1 2528.6 2215.1 2338.4 3704.7 2746.5 TRUE FALSE FALSE 3479.467634 3321.916798 2707.110108 3389.044729 2781.51503 2367.030621 2403.250539 2406.057915 3373.342353 2675.145534 1.300664801 1.241770497 1.011948723 1.266863685 1.039762134 0.884823121 0.898362541 0.89941197 1.260993957 1 11.38540166 -8.451607583 3.785166726 1.150898303 0.896626879 0.615243968 0.099803717 0.164247636 4.524561238 0.01828135 0.042137776 3.54E-09 8.451607583 -0.254271424 SVPHLQK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPHLQK 7 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 91.9 0.020134 9527400 3779.4 4851.9 6347.4 6365.2 6840.1 7758.2 7869.6 2084.4 6012.1 3643.4 FALSE FALSE TRUE 3733.335219 4920.205176 6457.873834 7101.174373 6491.024173 7262.476058 8538.043628 2144.708825 5474.362718 3548.743943 1.052015947 1.386463846 1.819763257 2.001038815 1.829104685 2.046491991 2.405933977 0.604357164 1.542619813 1 11.79309277 -9.978358958 2.335282019 1.02233124 1.840789178 0.217705467 0.468122974 0.196072048 2.147399839 0.068924745 0.090575267 1.05E-10 9.978358958 0.818457938 SVPHLQK(ac)VFDR ddPTM_HeLa_Romidepsin_16h_R1 1 SVPHLQKVFDR 11 1 P07355;P07355-2;H0YN42;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 1 SVPHLQK(1)VFDR 108.56 0.0082592 919420 290.21 422.97 783.61 310.71 682.62 722.78 440.71 337.74 328.67 256.6 FALSE TRUE FALSE 286.6728089 428.9245828 797.2484033 346.6357521 647.7833542 676.5966907 478.1438964 347.511974 299.272932 249.933495 1.14699636 1.716154863 3.189842175 1.386911955 2.591822893 2.707106907 1.913084504 1.390417775 1.197410263 1 7.965400448 -10.1227912 3.731963132 1.069271136 2.203268067 0.445520438 0.535074492 0.143676834 3.587121674 0.085535201 0.106064261 7.54E-11 10.1227912 1.133996931 SVPNT(ph)PLRPNQQSVVNSSFSELFVK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPNTPLRPNQQSVVNSSFSELFVK 25 1 H0YJ97;Q15643-2;Q15643 H0YJ97 TRIP11 Thyroid receptor-interacting protein 11 1 0 S(0.191)VPNT(0.743)PLRPNQQS(0.052)VVNS(0.011)S(0.001)FSELFVK 52.272 0.013987 46350000 840.06 951.49 693.54 840.61 689.36 616.35 777.25 690.19 835.83 799.5 TRUE FALSE FALSE 829.8210256 964.8851012 705.6107728 937.8052834 654.1793868 576.9672242 843.2695956 710.1595587 761.0712714 778.7288747 1.065609678 1.239051398 0.906105829 1.204277013 0.840060524 0.74090899 1.082879578 0.911947125 0.977325095 1 9.604977311 -8.73491894 24.99996543 1.049467424 0.896512638 0.31399154 0.12277746 224.1860797 211331.9897 0.016800923 0.033594048 1.84E-09 8.73491894 -0.152954786 SVPT(ph)STVFYPSDGVATEK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPTSTVFYPSDGVATEK 18 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 1 0 SVPT(0.944)S(0.028)T(0.028)VFYPSDGVATEK 176.49 1.59E-09 4221900 1620.5 1323.8 1540.6 1293.9 2065.1 1841.1 1715.6 1115.2 998.06 1391.9 TRUE FALSE FALSE 1600.748723 1342.436491 1567.413497 1443.506806 1959.710241 1723.459652 1861.323021 1147.466553 908.7910139 1355.738237 1.180721085 0.990188559 1.156132839 1.06473858 1.44549308 1.271233343 1.372922125 0.846377657 0.670329263 1 10.40486294 SVPTS(ph)TVFYPSDGVATEK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPTSTVFYPSDGVATEK 18 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 1 0 SVPT(0.001)S(0.834)T(0.162)VFY(0.002)PSDGVATEK 147.92 6.50E-05 6939000 2613 2363.5 3413.6 1596.8 2286.6 3129.4 2648.5 2132.8 2643.3 2491.8 TRUE FALSE FALSE 2581.151751 2396.773415 3473.012276 1781.429529 2169.90627 2929.44144 2873.463524 2194.509203 2406.876628 2427.062677 1.063487884 0.987520198 1.430952859 0.733985795 0.894046244 1.206990437 1.183926378 0.904183161 0.99168293 1 11.24499565 -12.21828518 0.990823236 1.000532702 1.055210624 0.013135198 0.183734648 3.033426393 5.417753897 0.114159454 0.032943723 6.05E-13 12.21828518 0.054677922 SVPTSTVFYPSDGVATEK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPTSTVFYPSDGVATEK 18 0 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 143.76 1.16E-10 0 868.12 580.39 656.57 397.06 901.26 735.31 688.82 842.56 730.35 692.92 FALSE FALSE TRUE 857.5390195 588.5607457 667.9973254 442.9699454 855.2653391 688.3260641 747.3283536 866.9381443 665.0256668 674.9178385 1.270582833 0.872047992 0.98974614 0.65633166 1.267214008 1.019866456 1.107287896 1.284509158 0.985343147 1 9.398568075 -7.280737681 3.599607611 1.072427528 1.304610979 0.110066882 0.176928753 0.495469106 11.56499115 0.026353908 0.299707886 5.24E-08 7.280737681 0.232183452 SVPVNNLPERS(ph)PTDSPR ddPTM_HeLa_Romidepsin_16h_R1 1 SVPVNNLPERSPTDSPR 17 1 P49454 P49454 CENPF Centromere protein F 1 0 SVPVNNLPERS(0.862)PT(0.137)DS(0.001)PR 134.04 0.00061046 17409000 2741.6 2884.5 2665.9 2688.2 2988.3 2716.6 2050.9 2208.3 2868.9 2699.7 TRUE FALSE FALSE 2708.184325 2925.108067 2712.298871 2999.022332 2835.7959 2543.018027 2225.103395 2272.193676 2612.298399 2629.561405 1.029899633 1.1123939 1.03146436 1.140502871 1.078429237 0.967088284 0.846188034 0.86409607 0.993435025 1 11.36060647 -7.918672245 3.510046495 1.036567924 0.854962921 0.734745953 0.046994643 0.103367612 2.507763725 0.0073948 0.025096885 1.21E-08 7.918672245 -0.181605003 SVPVT(ph)PARPPPHNK ddPTM_HeLa_Romidepsin_16h_R1 1 SVPVTPARPPPHNK 14 1 Q99618;F5GX58;F8WDL1;J3KMY0 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 S(0.006)VPVT(0.994)PARPPPHNK 59.155 0.023924 6674600 1578.7 1539.1 1305.3 1323.8 1762.5 2345.2 1222.2 1453.6 1378.9 1468.2 TRUE FALSE FALSE 1559.458197 1560.76749 1328.018199 1476.863985 1672.553048 2195.349289 1326.013637 1495.657623 1255.56773 1430.055952 1.09048754 1.091403093 0.92864772 1.032731609 1.169571754 1.535149226 0.927245983 1.045873499 0.877985039 1 10.48185588 -8.750288895 8.283274095 1.037610515 1.17857804 0.188875863 0.158892189 0.209701666 95.17621976 0.021828738 0.042433569 1.78E-09 8.750288895 0.140967526 SVPVTVDDDDDDNDPENR ddPTM_HeLa_Romidepsin_16h_R1 1 SVPVTVDDDDDDNDPENR 18 0 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LP59 P46100-4 ATRX Transcriptional regulator ATRX 0 0 283.05 1.90E-105 9013600 1650.9 1426.1 1493.4 1405.2 1024.1 1153.5 925.9 1101.5 1884.9 1501.1 FALSE FALSE TRUE 1630.778196 1446.176673 1519.392001 1567.675836 971.8363556 1079.795073 1004.545923 1133.370165 1716.309823 1462.101206 1.115366152 0.989108461 1.039183878 1.072207471 0.664684737 0.738522798 0.687056354 0.775165331 1.173865268 1 10.51382746 -8.764470325 24.99995301 1.050132985 0.715847602 0.895475217 0.058214174 16.05261317 132407.3459 0.00766017 0.014329683 1.72E-09 8.764470325 -0.334285383 SVQEGENPDDGVRGS(ph)PPEDYR ddPTM_HeLa_Romidepsin_16h_R1 1 SVQEGENPDDGVRGSPPEDYR 21 1 H7C5M1;Q5TCT4;A2A2V2;P42696-2;P42696 H7C5M1 RBM34 RNA-binding protein 34 1 0 SVQEGENPDDGVRGS(0.992)PPEDY(0.008)R 84.113 0.0008234 13188000 875.82 1159.8 1047.9 1120.2 1037.7 1029.4 1211.1 970.21 1146.1 1047.2 TRUE FALSE FALSE 865.145169 1176.127695 1066.13826 1249.722795 984.7422968 963.6246622 1313.970804 998.2814956 1043.589946 1019.993593 0.848186866 1.15307361 1.045240154 1.225226122 0.965439689 0.944735995 1.288214762 0.978713496 1.023133824 1 9.994344375 -10.25828709 24.9978849 0.928310464 1.087338008 0.195298422 0.115326703 252.8128796 2004825.347 0.018953828 0.022694249 5.52E-11 10.25828709 0.159027544 SVS(ph)EINSDDELSGK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSEINSDDELSGK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 S(0.002)VS(0.994)EINS(0.004)DDELSGK 238.07 3.19E-43 24453000 5700.2 6292.6 4519.8 3709.7 5230.7 5355.5 5865.7 6642.3 6746 6609.2 TRUE FALSE FALSE 5630.72377 6381.187388 4598.465223 4138.632969 4963.757861 5013.300834 6363.932412 6834.484471 6142.620864 6437.492031 0.87467662 0.991253637 0.714325579 0.642895238 0.771070137 0.778766142 0.988573249 1.061668805 0.954194713 1 12.65228303 -11.46024917 0.695703589 0.991720757 0.838884057 0.137378883 0.125584529 0.927136164 0.93741203 0.068168075 0.032236329 3.47E-12 11.46024917 -0.1528367 (ac)MEDMNEYS(ph)NIEEFAEGSK ddPTM_HeLa_Romidepsin_16h_R1 2 MEDMNEYSNIEEFAEGSK 18 0 O14979-3;O14979-2;A0A087WU03 O14979-3 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 0 MEDMNEY(0.363)S(0.637)NIEEFAEGSK;MEDMNEY(0.059)S(0.941)NIEEFAEGSK ; 73.296 0.0027368 3375200 2231.2 1945.44 2459.5 2446.3 1446.94 1041.26 803.21 1011.62 2242.4 2144.2 TRUE FALSE FALSE 2204.005276 1972.827955 2502.306566 2729.152716 1373.097253 974.7268465 871.4346374 1040.889629 2041.834128 2088.493375 1.055308723 0.94461777 1.198139576 1.306756703 0.657458275 0.466712922 0.41725516 0.498392593 0.977658896 1 11.02824685 -8.578480624 5.379798652 1.051290202 0.471011229 0.877976291 0.105639741 0.049926213 3.033960594 0.016052418 0.032823258 2.64E-09 8.578480624 -0.580278973 down SVS(ph)FGGFGWIDK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSFGGFGWIDK 12 0 Q684P5-2;Q684P5 Q684P5-2 RAP1GAP2 Rap1 GTPase-activating protein 2 1 0 S(0.323)VS(0.677)FGGFGWIDK 129.54 0.0041704 9873200 781.78 625.92 705.8 738.66 1250.7 1365.8 1311.4 1653.8 631.41 607.78 TRUE FALSE FALSE 772.2513647 634.7317182 718.0841529 824.0673447 1186.872112 1278.529788 1422.790283 1701.650094 574.9351082 591.989788 1.304501159 1.072200452 1.213000912 1.392029662 2.004886125 2.159715951 2.403403424 2.874458527 0.971190922 1 9.209428479 -8.152636791 0.696674474 1.116791431 3.029398798 0.958892237 0.12895945 0.190968381 0.12207474 0.026231371 0.228154098 7.04E-09 8.152636791 1.912607367 up SVS(ph)GSPEPAAK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 S(0.006)VS(0.896)GS(0.098)PEPAAK;S(0.023)VS(0.582)GS(0.395)PEPAAK ; 152.38 0.0022851 99977400 10526.7 10779.4 10782.4 9099.5 9206.7 8909.8 10184.8 6558.2 12875.3 11391.1 TRUE FALSE FALSE 10398.39653 10931.15268 10970.06315 10151.627 8736.847744 8340.492535 11049.89666 6747.95117 11723.70092 11095.15758 0.937201338 0.985218335 0.988725313 0.914960146 0.787446927 0.751723666 0.99592066 0.608188854 1.05665024 1 13.43764254 -8.901899305 3.489256518 0.971778709 0.798214093 0.514884086 0.093503289 0.152331897 3.650102597 0.012222368 0.023109026 1.25E-09 8.901899305 -0.173564616 SVS(ph)PQNSDSSGFADVNGWHLR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSPQNSDSSGFADVNGWHLR 21 0 S4R3E2;Q9UKB3 S4R3E2 DNAJC12 DnaJ homolog subfamily C member 12 1 0 S(0.133)VS(0.866)PQNSDSSGFADVNGWHLR 214 1.18E-32 7252400 854.56 896.19 1054.4 1092.1 1264.7 1541.9 1506.5 1336.9 1179.9 1108.5 TRUE FALSE FALSE 844.144294 908.8065863 1072.75139 1218.37374 1200.15764 1443.377566 1634.462072 1375.581092 1074.366789 1079.70101 0.781831531 0.841720604 0.993563384 1.128436233 1.111564802 1.336830801 1.513809895 1.274038904 0.995059538 1 10.07641614 -8.690475859 1.072877903 0.892562049 1.408795516 0.804703171 0.094657035 0.174752023 0.386298128 0.017940814 0.057044497 2.04E-09 8.690475859 0.516233468 SVS(ph)PSPVPLLFQPDQNAPPIR ddPTM_HeLa_Romidepsin_16h_R1 3 SVSPSPVPLLFQPDQNAPPIR 21 0 Q02241-3;Q02241-2 Q02241-3 KIF23 Kinesin-like protein KIF23 1 0 S(0.189)VS(0.654)PS(0.156)PVPLLFQPDQNAPPIR;S(0.125)VS(0.626)PS(0.249)PVPLLFQPDQNAPPIR;S(0.068)VS(0.921)PS(0.011)PVPLLFQPDQNAPPIR ;; 125.51 2.29E-11 46085000 4645.6 4231.58 4595.1 3198.2 3245.95 3395.7 2939.1 3629.84 4695.9 4249.94 TRUE FALSE FALSE 4588.97764 4291.152294 4675.075788 3567.990932 3080.297059 3178.725729 3188.747081 3734.863693 4275.886943 4139.525946 1.108575644 1.036628916 1.129374679 0.861932255 0.744118312 0.767896076 0.770316969 0.902244301 1.032941211 1 12.01524985 -9.111648973 4.564695562 1.05618214 0.793178504 0.851233782 0.053157855 0.069033939 2.317135197 0.008977134 0.015222922 7.73E-10 9.111648973 -0.263003636 SVS(ph)PSPVPLSSNYIAQISNGQQLMSQPQLHR ddPTM_HeLa_Romidepsin_16h_R1 3 SVSPSPVPLSSNYIAQISNGQQLMSQPQLHR 31 0 Q02241;H7BYN4 Q02241 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 0 S(0.218)VS(0.641)PS(0.13)PVPLS(0.002)S(0.002)NY(0.006)IAQISNGQQLMSQPQLHR;S(0.192)VS(0.577)PS(0.219)PVPLS(0.004)S(0.004)NY(0.004)IAQISNGQQLMSQPQLHR;S(0.154)VS(0.423)PS(0.406)PVPLS(0.005)S(0.005)NY(0.006)IAQIS(0.001)NGQQLMSQPQLHR ;; 78.901 4.29E-07 30221000 4272.4 4042.4 3908.7 2544.81 3452.7 3610.4 2836.48 2811.83 5817.5 4841.1 TRUE FALSE FALSE 4220.326345 4099.309013 3976.729284 2839.052906 3276.495835 3379.707092 3077.41054 2893.185865 5297.16823 4715.327524 0.895022949 0.869358277 0.843362261 0.602090288 0.694860711 0.716749171 0.652639827 0.6135705 1.123393487 1 12.20314227 -9.729824276 0.617204426 0.975417788 0.634193567 0.82914349 0.068410714 0.179812128 0.141930684 0.013607217 0.024391906 1.86E-10 9.729824276 -0.341224221 SVS(ph)PTFLNPSDENLK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSPTFLNPSDENLK 15 0 Q9UKA4 Q9UKA4 AKAP11 A-kinase anchor protein 11 1 0 S(0.01)VS(0.495)PT(0.495)FLNPSDENLK;S(0.015)VS(0.804)PT(0.181)FLNPSDENLK ; 244.05 2.99E-57 168774000 4816.7 3698.2 3964.8 4304.7 6679.2 7212.6 6137.3 7462.6 3959.1 3712.7 TRUE FALSE FALSE 4757.992208 3750.263357 4033.805681 4802.429668 6338.3355 6751.738138 6658.602109 7678.518557 3604.98818 3616.243519 1.315727822 1.037060512 1.115468485 1.328016115 1.752740231 1.867058483 1.841303572 2.123341118 0.996887561 1 11.82027612 -8.738618285 1.821998048 1.138700704 1.944704238 0.918533826 0.113945858 0.083917813 0.56540813 0.021004921 0.048580614 1.83E-09 8.738618285 0.806003534 SVS(ph)PVQDLDDDTPPS(ph)PAHSDMPYDAR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSPVQDLDDDTPPSPAHSDMPYDAR 26 0 G3V3A7;O00409-2;O00409 G3V3A7 FOXN3 Forkhead box protein N3 2 0 S(0.076)VS(0.909)PVQDLDDDT(0.015)PPS(0.951)PAHS(0.042)DMPY(0.007)DAR 84.596 5.83E-05 7432400 1083.9 1081.9 1108.4 1177 877.17 576.41 657.04 615.06 1195.1 1028.4 TRUE FALSE FALSE 1070.68901 1097.131017 1127.691237 1313.090278 832.4047417 539.5792613 712.8489612 632.8557907 1088.207263 1001.68202 1.068891114 1.095288719 1.125797623 1.310885343 0.831006972 0.538673202 0.711651949 0.631793102 1.08637995 1 9.968208888 -8.5335328 8.186296166 1.064177238 0.643396413 0.845740831 0.092769859 0.044645793 21.27576706 0.014255225 0.029179399 2.93E-09 8.5335328 -0.420780825 SVS(ph)SDSLGPPRPAPAR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSDSLGPPRPAPAR 16 1 Q9P1Y5;Q9P1Y5-2 Q9P1Y5 CAMSAP3 Calmodulin-regulated spectrin-associated protein 3 1 0 S(0.157)VS(0.684)S(0.131)DS(0.027)LGPPRPAPAR 65.105 0.019289 6785900 284.44 225.58 356.84 560.97 971.38 1430.7 1448.4 1226.6 291.65 434.42 TRUE FALSE FALSE 280.9731359 228.7557212 363.0506505 625.8319908 921.8068539 1339.282887 1571.42706 1262.089736 265.5640935 423.1337058 0.664029199 0.540622782 0.858004563 1.479040744 2.178523812 3.165152927 3.713783701 2.982720872 0.627612714 1 8.724969802 -8.610151509 1.490469541 0.810363665 3.40408323 0.959623397 0.228109495 0.055314093 0.243420845 0.036925041 0.101946178 2.45E-09 8.610151509 2.593719565 up SVS(ph)SPTSSNTPTPTK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSPTSSNTPTPTK 15 0 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 0 S(0.223)VS(0.298)S(0.298)PT(0.097)S(0.039)S(0.012)NT(0.032)PTPTK 86.539 0.020561 27100000 923.22 859.21 1381.6 945.55 1024.3 1117.8 983.96 1157 970.3 1095.4 TRUE FALSE FALSE 911.9674395 871.3059809 1405.646168 1054.87894 972.0261488 1046.376188 1067.537538 1190.47597 883.5139378 1066.94135 0.854749363 0.81663906 1.317454018 0.988694402 0.911039907 0.980725124 1.000558782 1.11578389 0.828081073 1 10.05926516 SVS(ph)TTNIAGHFNDESPLGLR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF5;V9GYG5;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 S(0.169)VS(0.636)T(0.169)T(0.026)NIAGHFNDESPLGLR;S(0.135)VS(0.644)T(0.174)T(0.048)NIAGHFNDESPLGLR ; 122.68 8.79E-05 57532000 1649.29 1721.99 1674.18 1949.34 1702.39 1860.55 1686.45 1584.32 2467.57 1950.79 TRUE FALSE FALSE 1629.187819 1746.23222 1703.318401 2174.731863 1615.510686 1741.66686 1829.697021 1630.1598 2246.864359 1900.108195 0.857418448 0.919017257 0.896432322 1.144530542 0.850220367 0.916614572 0.962943598 0.857929987 1.182492852 1 10.89186585 -8.117608146 0.006397953 1.834332074 3.81E-07 0.042946802 0.109701031 35221.47149 48.49195573 6723.103665 7184.431711 7.63E-09 8.117608146 -1.834331692 SVS(ph)VDESRPELIFR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSVDESRPELIFR 14 1 Q96BY7 Q96BY7 ATG2B Autophagy-related protein 2 homolog B 1 0 S(0.197)VS(0.803)VDESRPELIFR 88.108 0.00784 4120400 1052.9 1437.5 774.93 1211.9 1999.6 1291 1082.7 1251.7 1107.1 1096 TRUE FALSE FALSE 1040.06685 1457.737163 788.4173316 1352.02558 1897.55295 1208.509267 1174.664511 1287.915965 1008.078203 1067.525762 0.974277986 1.365528791 0.738546422 1.266503937 1.77752427 1.13206567 1.100361746 1.20644954 0.944312764 1 10.06005517 -9.033513097 23.9105815 1.004778401 1.307853646 0.295689149 0.225932977 341.237212 243461.912 0.032969535 0.054703568 9.26E-10 9.033513097 0.303075246 SVS(ph)VDSGEQR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSVDSGEQR 10 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 S(0.018)VS(0.965)VDS(0.017)GEQR 126.71 0.0087421 8807400 3779.4 3318 3113.4 2570.8 3179.7 2892.4 2765.9 3005.2 3949 3489.1 TRUE FALSE FALSE 3733.335219 3364.710891 3167.587421 2868.047992 3017.428044 2707.584975 3000.835477 3092.150721 3595.79155 3398.452679 1.09853971 0.990071426 0.932067538 0.843927594 0.887882907 0.796711101 0.883000518 0.909870171 1.05806727 1 11.73066232 -9.70395717 2.172510562 1.046215068 0.863456319 0.825708734 0.037776785 0.105219694 1.017354326 0.007716835 0.011230276 1.98E-10 9.70395717 -0.182758749 SVS(ph)VVTGSEQK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSVVTGSEQK 11 0 Q9UPN4-2;Q9UPN4;I3L2J8;Q9UPN4-3 Q9UPN4-2 CEP131 Centrosomal protein of 131 kDa 1 0 S(0.002)VS(0.941)VVT(0.053)GS(0.004)EQK 94.402 0.027246 8731600 1698.5 2535.7 1551.7 1640.4 3383 1962 1309.2 2844 1471.8 1847.9 TRUE FALSE FALSE 1677.798029 2571.397651 1578.706688 1830.070766 3210.352886 1836.634532 1420.403415 2926.286653 1340.158522 1799.891292 0.932166313 1.428640531 0.877112243 1.016767387 1.783637101 1.020414144 0.789160669 1.625812996 0.74457748 1 10.81369406 -10.30624385 24.94319341 0.967967393 1.196605025 0.174860194 0.310861527 690.8167871 384584.0571 0.049274711 0.056347902 4.94E-11 10.30624385 0.228637631 SVSEINS(ph)DDELSGK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSEINSDDELSGK 14 0 F8WF45;A0A2R8Y7M0;P82094;P82094-2 F8WF45 TMF1 TATA element modulatory factor 1 0 S(0.002)VS(0.027)EINS(0.91)DDELS(0.062)GK;S(0.005)VS(0.196)EINS(0.79)DDELS(0.01)GK ; 204.23 8.49E-17 186625000 10809.2 10740.7 10943.5 9339.5 12911.2 13565.3 12463.6 13164.3 12143 11148.6 TRUE FALSE FALSE 10677.45331 10891.90786 11133.96703 10419.37693 12252.29329 12698.52111 13522.25787 13545.18825 11056.89967 10858.95776 0.983285279 1.00303437 1.025325567 0.959519059 1.128312086 1.169405148 1.245262959 1.247374614 1.018228444 1 13.40659802 -8.389413221 1.56559054 0.992799293 1.244285459 0.931482816 0.027279459 0.058515751 0.273637468 0.003603497 0.011629226 4.08E-09 8.389413221 0.251486167 SVSENS(ph)LVAMDFSGQTGR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSENSLVAMDFSGQTGR 18 0 A0A2R8YCL1;Q13322-3;Q13322-2;Q13322-4;Q13322 A0A2R8YCL1 GRB10 Growth factor receptor-bound protein 10 1 0 S(0.003)VS(0.429)ENS(0.568)LVAMDFSGQTGR;S(0.001)VS(0.153)ENS(0.845)LVAMDFS(0.001)GQTGR ; 104.78 0.0023322 34641800 5297.9 5491.4 4924.5 4637.5 3493.2 2817.2 2259.4 2728.3 5478.3 5547.5 TRUE FALSE FALSE 5233.327157 5568.708073 5010.208857 5173.70957 3314.928969 2637.190012 2451.31338 2807.239056 4988.307127 5403.37515 0.968529301 1.030598083 0.927236906 0.957495903 0.613492285 0.488063468 0.45366337 0.519534361 0.923183564 1 12.39964513 -8.680048634 2.632580654 0.984960083 0.485357231 0.974359879 0.036056596 0.023346905 0.327984375 0.004510474 0.00976742 2.09E-09 8.680048634 -0.499602851 SVSGS(ph)PEPAAK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSGSPEPAAK 11 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2 A9Z1X7 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 S(0.025)VS(0.001)GS(0.974)PEPAAK 158.04 0.0016782 6481100 5514.4 5542.2 5634 4637.6 4552.8 5334.1 5622.4 2835.6 7163.1 6752.4 TRUE FALSE FALSE 5447.188372 5620.223237 5732.057407 5173.821133 4320.453627 4993.268225 6099.966516 2917.643612 6522.414396 6576.971675 0.828221352 0.854530552 0.871534452 0.78665705 0.656906224 0.759204764 0.927473436 0.443615049 0.991704803 1 12.68320774 -6.365365333 0.071042755 1.289409713 7.71E-11 0.515974365 0.109954372 85.16391718 0.750834111 3.501684957 12.57347678 4.31E-07 6.365365333 -1.289409712 SVSGS(ph)PESDELQELR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSGSPESDELQELR 15 0 Q7Z2Z1;Q7Z2Z1-2 Q7Z2Z1 TICRR Treslin 1 0 SVS(0.012)GS(0.704)PES(0.283)DELQELR 85.28 0.022692 6391100 907.59 879.24 981.63 746.22 987.38 932.41 731.91 861.92 953.39 864.58 TRUE FALSE FALSE 896.527944 891.6179638 998.7148584 832.5014675 936.9903142 872.8320102 794.0784171 886.8582953 868.1164106 842.118087 1.064610721 1.058780209 1.185955834 0.988580438 1.112659054 1.036472228 0.942953761 1.053128188 1.030872539 1 9.717878741 -6.866835367 20.15795326 1.040608511 7.107952445 0 0.064208848 7399.394727 1161359.536 0.008683875 76609.12831 1.36E-07 6.866835367 6.067343934 VKGEYDVT(ph)VPK ddPTM_HeLa_Romidepsin_16h_R1 1 VKGEYDVTVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VKGEY(0.253)DVT(0.747)VPK 117.53 0.001537 0 1771.3 1879.5 1378 1480.3 1318 816.78 816.84 778.05 1741.3 1756.9 TRUE FALSE FALSE 1749.710714 1905.95965 1401.983512 1651.459251 1250.737542 764.590394 886.2223692 800.5616492 1585.553767 1711.255485 1.022471939 1.113778549 0.819271888 0.965057097 0.730888843 0.446800844 0.517878468 0.467821232 0.926544155 1 10.74083945 -8.577874138 1.574045219 1.008408465 0.464877598 0.892223757 0.077063549 0.072882785 0.357227413 0.010517933 0.02892233 2.64E-09 8.577874138 -0.543530867 down SVSPTT(ph)EMVSNESVDYR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSPTTEMVSNESVDYR 17 0 P08581;P08581-2 P08581 MET Hepatocyte growth factor receptor 1 0 S(0.001)VS(0.036)PT(0.05)T(0.897)EMVS(0.016)NESVDYR;S(0.001)VS(0.123)PT(0.167)T(0.505)EMVS(0.203)NES(0.001)VDYR ; 103.43 0.006958 19172100 2751.7 3993.7 3798.8 2606.6 2281.18 3033.9 1400.73 2627.5 3741.1 4128.1 TRUE FALSE FALSE 2718.161222 4049.923413 3864.91652 2907.987356 2164.762872 2840.043581 1519.707971 2703.522567 3406.486646 4020.851367 0.676016339 1.007230321 0.96121845 0.723226772 0.538384206 0.706328915 0.377956764 0.672375654 0.847205314 1 11.97328529 -8.976057042 3.937948029 0.865277195 0.570862198 0.601574772 0.123051854 0.15165141 5.245581221 0.022623686 0.041242632 1.06E-09 8.976057042 -0.294414998 SVSPTTEMVS(ph)NESVDYR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSPTTEMVSNESVDYR 17 0 P08581;P08581-2 P08581 MET Hepatocyte growth factor receptor 1 0 SVSPTTEMVS(0.994)NES(0.006)VDYR;SVSPTTEMVS(0.999)NESVDYR ; 142.57 0.00040349 11734200 2097.52 3510 2660.5 2248.7 2594 3590.5 1798.2 2956.5 2616.4 3065.7 TRUE FALSE FALSE 2071.954619 3559.413872 2706.804886 2508.705274 2461.6185 3361.078638 1950.939063 3042.041663 2382.382631 2986.052672 0.693877452 1.19201309 0.906482632 0.840140999 0.824372096 1.125592549 0.653350519 1.018750169 0.797836774 1 11.5440239 SVSS(ph)PTSSNTPT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSPTSSNTPTPTK 15 0 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 2 0 S(0.006)VS(0.104)S(0.616)PT(0.023)S(0.177)S(0.083)NT(0.363)PT(0.576)PT(0.053)K 107.63 0.021551 3158600 1589.1 1529.5 1447.1 1801.4 2349.6 2305 1952.3 1482.3 1483.9 1431.2 TRUE FALSE FALSE 1569.731438 1551.032341 1472.286168 2009.686344 2229.691144 2157.717939 2118.128313 1525.188012 1351.176268 1394.017218 1.126048816 1.112634996 1.05614633 1.44165102 1.59947174 1.547841671 1.519442003 1.094095534 0.969267991 1 10.44503266 -9.251817382 7.065734891 1.06544549 1.460485919 0.669140784 0.135812223 0.066282696 20.64260899 0.020188689 0.032617399 5.60E-10 9.251817382 0.395040428 SVSS(ph)YGNIR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSSYGNIR 9 0 Q8N122;Q8N122-3 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 0 SVS(0.019)S(0.981)YGNIR;SVS(0.015)S(0.985)YGNIR ; 184.71 4.42E-05 111313000 6570.5 5465.1 6277.3 3646.7 5999.5 6012.6 4207.8 5616.9 6151.7 5988.3 TRUE FALSE FALSE 6490.416219 5542.037821 6386.553773 4068.348612 5693.323128 5628.414265 4565.210427 5779.416139 5601.476545 5832.723103 1.112759187 0.950163024 1.094952334 0.697504157 0.976100361 0.964971963 0.78268938 0.990860707 0.960353585 1 12.50995387 -9.309499478 24.98992771 1.04807216 0.88667414 0.324128585 0.098769664 282.2599146 146766.6987 0.014149621 0.021613931 4.90E-10 9.309499478 -0.16139802 SVSSNVASVS(ph)PIPAGSK ddPTM_HeLa_Romidepsin_16h_R1 4 SVSSNVASVSPIPAGSK 17 0 Q9Y6G9;E9PHI6 Q9Y6G9 DYNC1LI1 Cytoplasmic dynein 1 light intermediate chain 1 1 0 S(0.001)VS(0.015)S(0.012)NVAS(0.227)VS(0.744)PIPAGSK;SVSSNVASVS(0.995)PIPAGS(0.005)K;S(0.002)VS(0.018)S(0.015)NVAS(0.162)VS(0.734)PIPAGS(0.07)K;SVSSNVAS(0.004)VS(0.993)PIPAGS(0.003)K ;;; 232.37 3.00E-46 204471000 19365.1 19341.8 20028.6 17356.6 27175 31257.1 26846.8 27587.5 21662.9 20653 TRUE FALSE FALSE 19129.07071 19614.09437 20377.18938 19363.45176 25788.15835 29259.87219 29127.16652 28385.70079 19725.31597 20116.43208 0.950917669 0.975028489 1.012962403 0.962568893 1.281944941 1.454525935 1.447929056 1.411070346 0.980557382 1 14.29608683 -8.618160783 2.9647435 0.97734438 1.435711793 0.986454397 0.024479284 0.022412656 0.395527726 0.004205112 0.009167509 2.41E-09 8.618160783 0.458367413 SVSSPTSSNT(ph)PTPTK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSPTSSNTPTPTK 15 0 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 0 SVSSPTS(0.003)S(0.039)NT(0.458)PT(0.458)PT(0.042)K 109.07 0.009616 10122000 5601.7 5696.1 5659.9 3788.1 4969.9 4271 3485 3516.1 6114 5392.7 TRUE FALSE FALSE 5533.424326 5776.289845 5758.408185 4226.097946 4716.267458 3998.096884 3781.015813 3617.832806 5567.148527 5252.596877 1.053464497 1.099701725 1.096297378 0.804573061 0.897892522 0.761165758 0.719837426 0.688770315 1.059884978 1 12.35881515 -8.703102426 1.137445131 1.036022365 0.709323076 0.841968191 0.06154599 0.149307794 0.375501428 0.010325672 0.031154857 1.98E-09 8.703102426 -0.32669929 SVSSPTSSNTPT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 SVSSPTSSNTPTPTK 15 0 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 0 SVS(0.001)S(0.001)PTSS(0.004)NT(0.266)PT(0.714)PT(0.014)K;SVSSPTS(0.004)S(0.078)NT(0.279)PT(0.594)PT(0.045)K ; 130.95 0.0038736 37592000 7927.31 7571.7 9157.8 5847.7 6635.5 6723.6 5299 6371.8 8454.4 8042.3 TRUE FALSE FALSE 7830.688897 7678.294591 9317.187667 6523.838588 6296.865675 6293.983659 5749.096928 6556.15798 7698.21729 7833.359887 0.999659024 0.980204497 1.189424181 0.832827635 0.803852468 0.803484552 0.73392478 0.836953501 0.982747812 1 12.93541553 -9.060206144 11.00785641 1.011038811 0.794266383 0.76640724 0.062820887 0.296656163 53.75310987 0.008823264 0.014647624 8.71E-10 9.060206144 -0.216772429 SVSSS(ph)SYR ddPTM_HeLa_Romidepsin_16h_R1 2 SVSSSSYR 8 0 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 SVS(0.021)S(0.131)S(0.847)S(0.001)YR;SVS(0.259)S(0.259)S(0.479)S(0.002)YR ; 112.11 0.021682 136598000 5368.7 5331.1 6393.1 3165.9 6163.9 6979.3 7305.7 3242.8 8001.1 6315.7 TRUE FALSE FALSE 5303.264219 5406.151366 6504.369224 3531.956254 5849.333182 6533.345255 7926.245976 3336.625302 7285.461577 6151.617204 0.862092689 0.878817909 1.057342973 0.574150851 0.950861048 1.062053284 1.288481665 0.542398071 1.184316471 1 12.58675002 -12.54068909 1.321123361 0.999720649 0.908807575 0.075134215 0.218299417 1.709407163 5.370119565 0.137493384 0.033133129 2.88E-13 12.54068909 -0.090913074 SVSSS(ph)SYRR ddPTM_HeLa_Romidepsin_16h_R1 3 SVSSSSYRR 9 1 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 SVSS(0.001)S(0.546)S(0.453)YRR;SVS(0.001)S(0.003)S(0.498)S(0.498)YRR;SVSS(0.002)S(0.499)S(0.499)YRR ;; 89.561 0.012327 12127800 1330.2 1164.55 2049.25 1210.15 1177.39 1955.45 3070.29 699.83 2177.51 1365.3 TRUE FALSE FALSE 1313.987011 1180.944565 2084.916337 1350.073237 1117.303395 1830.503056 3331.080356 720.0784769 1982.748052 1329.829309 0.988086969 0.888042215 1.567807479 1.015222952 0.840185569 1.376494745 2.504893172 0.541481882 1.49097936 1 10.37702536 -8.005793652 24.99632206 1.026057259 1.627564028 0.078431077 0.501473953 263.3128068 1136065.134 0.058512181 0.167964283 9.87E-09 8.005793652 0.601506768 SVSSVLSS(ph)LTPAK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSVLSSLTPAK 13 0 H0Y4T7;E7ESY4;Q13330-3;Q13330;F8W9Y9 H0Y4T7 MTA1 Metastasis-associated protein MTA1 1 0 S(0.009)VS(0.25)S(0.25)VLS(0.012)S(0.31)LT(0.17)PAK 186.51 6.59E-08 46796000 4478.9 4364.9 5265.7 4593.1 3542.7 2564.5 2317.6 2315.3 4538.2 4730.4 TRUE FALSE FALSE 4424.309444 4426.349177 5357.3473 5124.175833 3361.902799 2400.636727 2514.456886 2382.289553 4132.292026 4607.503526 0.960240056 0.960682754 1.162744048 1.112137148 0.729658215 0.521027648 0.545730865 0.517045628 0.896861392 1 12.16976955 -8.545237997 3.706522092 1.001919341 0.536304581 0.896772766 0.074722286 0.051034548 1.514010545 0.011054792 0.024111073 2.85E-09 8.545237997 -0.46561476 SVSSVLSSLT(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 1 SVSSVLSSLTPAK 13 0 H0Y4T7;E7ESY4;Q13330-3;Q13330;F8W9Y9 H0Y4T7 MTA1 Metastasis-associated protein MTA1 1 0 SVSSVLSS(0.001)LT(0.999)PAK 251.24 6.25E-53 46729000 4775.7 4586.4 5015.6 4568.6 2970.5 2593.4 2134.1 2247.7 4812.7 4421.3 TRUE FALSE FALSE 4717.491931 4650.96746 5102.894414 5096.843028 2818.904301 2427.69011 2315.370401 2312.733653 4382.240058 4306.433989 1.095452048 1.080004354 1.184946623 1.183541427 0.654579707 0.563735591 0.537653754 0.537041473 1.01760298 1 12.072278 -8.661934644 4.995440883 1.068970001 0.556066135 0.944696157 0.061784558 0.041471069 1.692915927 0.010870667 0.022037965 2.18E-09 8.661934644 -0.512903866 SVST(ph)PSEAGSQDSGDGAVGSR ddPTM_HeLa_Romidepsin_16h_R1 4 SVSTPSEAGSQDSGDGAVGSR 21 0 E7EQL5;Q13409-2;E7EV09;Q13409-3;Q13409-6;E7EQU2;E9PGG1;E7ETL8;E7ESD3;E7EMU4;Q13409;Q13409-7;Q13409-5;E7ET01;E7ERR6;E7EUM4;E7ERH4 E7EQL5 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 1 0 SVS(0.04)T(0.96)PSEAGSQDSGDGAVGSR;S(0.005)VS(0.053)T(0.681)PS(0.261)EAGSQDSGDGAVGSR;S(0.005)VS(0.142)T(0.848)PS(0.006)EAGSQDSGDGAVGSR;S(0.005)VS(0.13)T(0.57)PS(0.29)EAGS(0.004)QDSGDGAVGSR ;;; 188.54 2.28E-17 62422300 8723 7697.6 8057.5 8087.2 11828.5 14929.4 12220.6 14259.3 9730 9158.1 TRUE FALSE FALSE 8616.680721 7805.967015 8197.737408 9022.280115 11224.84751 13975.45952 13258.61746 14671.87035 8859.724431 8920.171242 0.965977052 0.87509161 0.919011215 1.011446963 1.258366819 1.566725475 1.486363557 1.644796938 0.993223582 1 13.12285569 -8.515581458 2.100255508 0.968396509 1.568391417 0.964521844 0.052183727 0.042528512 0.371159699 0.00817364 0.020706871 3.05E-09 8.515581458 0.599994907 SVST(ph)TNIAGHFNDESPLGLR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF5;V9GYG5;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 S(0.024)VS(0.112)T(0.717)T(0.147)NIAGHFNDESPLGLR 153.88 1.38E-06 42884000 1554.8 1280.3 1260.4 1355.2 1238.1 1298.2 1520 1135 1610.3 1231 TRUE FALSE FALSE 1535.8495 1298.324097 1282.336733 1511.8946 1174.915137 1215.24921 1649.108762 1167.839434 1466.270735 1199.018443 1.280922332 1.082822458 1.069488748 1.260943574 0.979897469 1.013536712 1.375382316 0.973996223 1.222892562 1 10.22763813 -8.75587876 24.99398666 1.134347446 1.101239859 0.040666187 0.135654927 806.4572852 3624848.432 0.021683931 0.042400048 1.75E-09 8.75587876 -0.033107587 SVSTTNIAGHFNDES(ph)PLGLR ddPTM_HeLa_Romidepsin_16h_R1 1 SVSTTNIAGHFNDESPLGLR 20 0 V9GYM8;A0A5F9ZI21;Q92974-3;Q92974-2;Q92974;V9GYF5;V9GYG5;V9GZ14 V9GYM8 ARHGEF2 Rho guanine nucleotide exchange factor 2 1 0 SVSTTNIAGHFNDES(1)PLGLR 137.86 9.34E-05 20714000 1292.1 1210.8 1391 1143.7 1505.1 1399.3 1464.2 1335.1 1536.5 1564.4 TRUE FALSE FALSE 1276.351388 1227.845674 1415.209772 1275.939975 1428.289131 1309.889246 1588.569111 1373.729012 1399.071592 1523.756662 0.837634656 0.805801677 0.928763632 0.837364657 0.937347259 0.859644639 1.042534645 0.901540939 0.918172584 1 10.57341681 -6.921404236 15.90448653 0.913302962 0.692664034 0 0.071404579 28924567.64 90540653.04 0.011369258 217849088.4 1.20E-07 6.921404236 -0.220638928 SVTEQGAELSNEER ddPTM_HeLa_Romidepsin_16h_R1 3 SVTEQGAELSNEER 14 0 P63104;E7EX29;E7ESK7;E5RGE1;E5RIR4;E9PD24;E7EVZ2 P63104 YWHAZ 14-3-3 protein zeta/delta 0 0 ;; ;; 237.76 3.49E-42 289422070 2658.92 2726.16 2005.96 2324.843 3083.07 3039.45 2788.78 2638.24 3127.75 2656 FALSE FALSE TRUE 2626.51206 2764.538952 2040.872892 2593.652286 2925.729433 2845.238954 3025.658904 2714.573312 2847.996206 2586.996737 1.015274593 1.068628697 0.788896585 1.002572693 1.130936654 1.099823171 1.169564252 1.049314548 1.100888983 1 11.33706252 -8.780336876 9.529845251 0.99396727 1.115614318 0.324838433 0.082105335 0.198198308 92.4736567 0.010811603 0.019937106 1.66E-09 8.780336876 0.121647049 SVTMT(ph)DGLTADK ddPTM_HeLa_Romidepsin_16h_R1 1 SVTMTDGLTADK 12 0 H0Y5X5;Q8N5H7-3;Q8N5H7-6;Q8N5H7-5;Q8N5H7-2;Q8N5H7-4;Q8N5H7;Q5JU32 H0Y5X5 SH2D3C SH2 domain-containing protein 3C 1 0 SVTMT(0.561)DGLT(0.439)ADK 141.2 0.0045881 6185200 1203.8 1478.9 1264.6 1106.1 1019.8 1295.2 1281.1 1108.5 1207.5 1581.4 TRUE FALSE FALSE 1189.127623 1499.719993 1286.609833 1233.992486 967.7558006 1212.4409 1389.916602 1140.572699 1099.498176 1540.315 0.772002884 0.973644997 0.835290075 0.801129955 0.628284345 0.78713828 0.902358675 0.740480161 0.713813847 1 10.5890097 -9.402013198 3.184345086 0.895616853 0.77170142 0.126744988 0.1027533 0.30013116 5.760058491 0.016830792 0.026409614 3.96E-10 9.402013198 -0.123915433 SVTS(ph)SPVEK ddPTM_HeLa_Romidepsin_16h_R1 1 SVTSSPVEK 9 0 G8JLP4;Q9Y4F3-3;Q9Y4F3-4;Q9Y4F3-5;Q9Y4F3;F8VVB8 G8JLP4 KIAA0430 Meiosis arrest female protein 1 1 0 SVT(0.018)S(0.957)S(0.025)PVEK 147.3 8.36E-06 0 4648.1 4851.6 4215.5 3337.6 4060.1 4719.7 4532.1 4090.6 5310.5 5449.3 TRUE FALSE FALSE 4591.447169 4919.900952 4288.869009 3723.509016 3852.897947 4418.126402 4917.056461 4208.955057 4835.51558 5307.7264 0.865049707 0.926931907 0.808042594 0.701526178 0.725903646 0.83239528 0.926395991 0.792986439 0.911033315 1 12.37387829 -11.31521998 0.511489057 1.001761367 0.804024788 0.385104272 0.0705573 0.587534901 0.336572166 0.051274381 0.023250628 4.84E-12 11.31521998 -0.19773658 SVVDMDLDDT(ph)DDGDDNAPLFYQPGKR ddPTM_HeLa_Romidepsin_16h_R1 1 SVVDMDLDDTDDGDDNAPLFYQPGKR 26 1 E7EMW7;O95071-2;O95071;E7ET84 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 0 S(0.483)VVDMDLDDT(0.516)DDGDDNAPLFYQPGKR 58.357 0.0028217 8204300 1642.3 1589 1447.8 1199.6 1076.1 1349.5 835.41 1262.3 1482.1 1461.8 TRUE FALSE FALSE 1622.283016 1611.369984 1472.998352 1338.303396 1021.182602 1263.271305 906.3697045 1298.822659 1349.537264 1423.822225 1.139385934 1.131721331 1.034538108 0.939937144 0.717212151 0.88723949 0.63657505 0.912208446 0.947827081 1 10.47555331 -9.043316937 2.632451435 1.071880615 0.784463254 0.636294906 0.092269816 0.114825774 1.582177554 0.013191823 0.024257725 9.05E-10 9.043316937 -0.287417361 SVVS(ph)FDKVK ddPTM_HeLa_Romidepsin_16h_R1 1 SVVSFDKVK 9 1 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 SVVS(1)FDKVK 72.34 0.029431 144780000 7645.5 6140.3 8060.8 7209.9 10449 10554 9413.6 8996.6 7721.3 7934.8 TRUE FALSE FALSE 7552.313705 6226.743305 8201.094843 8043.542562 9915.748539 9879.633461 10213.19095 9256.902427 7030.68759 7728.652752 0.977183728 0.805669954 1.061128648 1.04074317 1.282985387 1.278312505 1.321471061 1.197738173 0.909691225 1 12.91600123 -8.862518542 2.698945008 0.978071499 1.278087738 0.812755561 0.071793373 0.084017604 1.241018159 0.010152426 0.02011083 1.37E-09 8.862518542 0.300016239 SVVS(ph)FDKVKEPR ddPTM_HeLa_Romidepsin_16h_R1 1 SVVSFDKVKEPR 12 2 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 1 0 S(0.006)VVS(0.994)FDKVKEPR 88.78 0.027306 82375000 5199.5 4783.4 3649 7308.9 5669.2 5001.4 4360.9 5873.8 4753.7 5003.4 TRUE FALSE FALSE 5136.126494 4850.740831 3712.509314 8153.989407 5379.879569 4681.826681 4731.314737 6043.749136 4328.517166 4873.410947 1.053907941 0.995348204 0.761788685 1.673158594 1.103924875 0.960687849 0.970842555 1.240147651 0.888190471 1 12.25071617 SVVSDLEADDVKGSVPLS(ph)SSPPATHFPDETEITNPVPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 SVVSDLEADDVKGS(0.001)VPLS(0.294)S(0.294)S(0.294)PPAT(0.093)HFPDET(0.011)EIT(0.013)NPVPK 57.851 0.0004107 432290000 3512 3044.4 3233.6 2292.5 3001.4 2915.3 2705.2 3136.9 4146.5 3125.9 TRUE FALSE FALSE 3469.194393 3087.259143 3289.879452 2557.569637 2848.227358 2729.021739 2934.97962 3227.661252 3775.626655 3044.688667 1.139425003 1.013981881 1.080530659 0.840010233 0.935474089 0.8963221 0.963967072 1.060095663 1.240069862 1 11.572079 -9.288237977 24.87615123 1.063799314 0.937965032 0.441351157 0.083994109 515.2956599 478328.4047 0.011242908 0.01717682 5.15E-10 9.288237977 -0.125834282 SVVSDLEADDVKGSVPLSS(ph)SPPATHFPDETEITNPVPK ddPTM_HeLa_Romidepsin_16h_R1 1 SVVSDLEADDVKGSVPLSSSPPATHFPDETEITNPVPK 38 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 SVVSDLEADDVKGSVPLS(0.08)S(0.37)S(0.37)PPAT(0.08)HFPDET(0.018)EIT(0.08)NPVPK 87.357 8.20E-10 18842000 3712.5 3063.8 3081.7 3172.4 3183.4 3176.3 2437.1 3169.7 4198.1 3576.6 TRUE FALSE FALSE 3667.250622 3106.932257 3135.335696 3539.207815 3020.939219 2973.344681 2644.107213 3261.410269 3822.611422 3483.679416 1.052694632 0.891853665 0.900006953 1.015939583 0.867169121 0.853506975 0.758998432 0.936197014 1.097291388 1 11.76639615 -9.243300635 0.667711083 1.023597371 0.835932097 0.514791399 0.068326659 0.431151173 0.372007909 0.014287395 0.037497859 5.71E-10 9.243300635 -0.187665274 SVVTSIFGVK ddPTM_HeLa_Romidepsin_16h_R1 1 SVVTSIFGVK 10 0 J3KR24;A0A0A0MSX9;P41252 J3KR24 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 0 133.13 0.015749 251780 164.73 160.09 44.235 114.93 107.32 186.03 106.36 51.542 191.3 0 FALSE FALSE TRUE 162.7222074 162.3437512 45.00489162 128.2187474 101.8430599 174.1432834 115.3942157 53.03328645 174.1896489 0 0 SWAS(ph)PVYTEADGTFSR ddPTM_HeLa_Romidepsin_16h_R1 1 SWASPVYTEADGTFSR 16 0 E9PMS6;Q8WWI1-3;E9PMP7;E9PJ10;E9PK58;E9PLU6 E9PMS6 LMO7 LIM domain only protein 7 1 0 S(0.232)WAS(0.767)PVYTEADGTFSR 139.21 0.00087205 105140000 1967.5 2019.5 1926.6 1681.8 2474.5 2621.1 2204.5 2380.6 2424.2 2196.7 TRUE FALSE FALSE 1943.519353 2047.930574 1960.131665 1876.257629 2348.217031 2453.620169 2391.750175 2449.478905 2207.37348 2139.629417 0.908343911 0.957142652 0.916108018 0.876907755 1.09748773 1.146750063 1.117833843 1.144814558 1.031661587 1 11.06314523 -8.642203672 5.802210709 0.947595055 1.132350499 0.808876675 0.042709764 0.066713104 3.141135795 0.006350488 0.012814976 2.28E-09 8.642203672 0.184755444 SWDSS(ph)SPVDRPEPEAAS(ph)PTTR ddPTM_HeLa_Romidepsin_16h_R1 1 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 0 S(0.008)WDS(0.04)S(0.529)S(0.529)PVDRPEPEAAS(0.834)PT(0.048)T(0.014)R 67.418 0.015033 36805000 1103.3 979.92 719.86 1125.4 1134.8 1287.7 800.79 1036.4 1167.2 1150.9 TRUE FALSE FALSE 1089.852555 993.7153395 732.3888613 1255.524043 1076.886921 1205.420126 868.8090826 1066.386599 1062.802709 1120.999452 0.972215065 0.886454795 0.65333561 1.120004154 0.960648928 1.075308399 0.775030783 0.951281998 0.948084949 1 10.13056986 -10.43164103 4.903240231 0.9880874 0.917510906 0.03663107 0.127178151 0.520168461 20.19207292 0.021563718 0.02434376 3.70E-11 10.43164103 -0.070576494 SWDSS(ph)SPVDRPEPEAASPTTR ddPTM_HeLa_Romidepsin_16h_R1 2 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 1 0 S(0.002)WDS(0.076)S(0.461)S(0.461)PVDRPEPEAASPTTR;S(0.002)WDS(0.136)S(0.431)S(0.431)PVDRPEPEAASPTTR ; 70.569 0.0023743 232800000 2258.73 2133.72 2100.4 2094.2 1529 1793.49 1395.11 1622.46 2526.1 2071.8 TRUE FALSE FALSE 2231.19973 2163.758566 2136.956581 2336.341258 1450.969425 1678.891777 1513.610609 1669.40332 2300.159289 2017.974337 1.105663084 1.072242856 1.058961227 1.157765594 0.719022734 0.831968844 0.750064349 0.827266873 1.139835749 1 10.97869211 -8.757279711 24.99998338 1.060417683 0.783357228 0.876547925 0.05582278 28.67034862 172309.0626 0.008224345 0.015987922 1.75E-09 8.757279711 -0.277060455 SWDSSS(ph)PVDRPEPEAAS(ph)PTTR ddPTM_HeLa_Romidepsin_16h_R1 1 SWDSSSPVDRPEPEAASPTTR 21 1 C9J0I9;Q86WB0-2;Q86WB0 C9J0I9 ZC3HC1 Nuclear-interacting partner of ALK 2 0 S(0.01)WDS(0.109)S(0.439)S(0.491)PVDRPEPEAAS(0.793)PT(0.12)T(0.04)R 69.726 0.013267 34199000 2305.3 2269 2286.2 1985.3 2042.2 2067.1 1544.5 1642.5 2530.1 2304.9 TRUE FALSE FALSE 2277.202117 2300.943042 2325.990352 2214.849727 1937.978914 1935.018981 1675.689791 1690.023146 2303.801519 2245.018366 1.014335629 1.024910565 1.036067405 0.986561964 0.863235216 0.861916771 0.746403601 0.752788116 1.026183819 1 11.13251153 -8.355770654 1.169056555 1.011678682 0.744617498 0.945137098 0.025541688 0.082870769 0.204416492 0.00395029 0.016462273 4.41E-09 8.355770654 -0.267061184 SWEDS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 SWEDSPER 8 0 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IRI3;Q9UDY2-5;A0A3B3IRV6;A0A3B3ISF1;A0A3B3ISZ5;A0A3B3IU26;B1AN86 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 SWEDS(1)PER 109.83 0.022759 53872000 3076 2464.3 2931 2471.7 3264.5 3094.2 2416.1 2745 3788.4 2888.8 TRUE FALSE FALSE 3038.508529 2498.99248 2982.012826 2757.489584 3097.900383 2896.490606 2621.323474 2824.422244 3449.556016 2813.74856 1.079879195 0.888136387 1.059800747 0.980005685 1.100986928 1.02940634 0.931612551 1.003793404 1.22596456 1 11.4582777 -7.785575388 24.07099604 1.029317221 0.967703006 0.094022917 0.085510634 185.6062849 185106.7975 0.008180557 0.024563849 1.64E-08 7.785575388 -0.061614215 SWS(ph)LATFR ddPTM_HeLa_Romidepsin_16h_R1 1 SWSLATFR 8 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 S(0.001)WS(0.999)LATFR 106.18 0.025815 4350600 1558.7 1833.5 1360.7 1933.3 1741.9 1816.4 1765 1723.9 2132 1757.9 TRUE FALSE FALSE 1539.701965 1859.312061 1384.382413 2156.837242 1653.004343 1700.337902 1914.919056 1773.778327 1941.30858 1712.229505 0.899238076 1.085901193 0.808526199 1.259665972 0.965410501 0.993054902 1.11837756 1.035946596 1.133789936 1 10.74166038 -9.2773451 24.99799218 0.953533388 1.066344994 0.09766541 0.115200504 869.6601187 1366785.709 0.014586032 0.022324126 5.28E-10 9.2773451 0.112811607 SWSTATS(ph)PLGGERPFR ddPTM_HeLa_Romidepsin_16h_R1 2 SWSTATSPLGGERPFR 16 1 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;D6RD46;Q6NVB9;D6RJ93 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 SWST(0.023)AT(0.026)S(0.95)PLGGERPFR;SWSTAT(0.009)S(0.991)PLGGERPFR ; 214.89 3.28E-25 23941000 4430.5 4633.6 3988.9 4301.7 5136.2 4564.5 4266.5 4814.7 4713.1 4287.3 TRUE FALSE FALSE 4376.499362 4698.831942 4058.325131 4799.082794 4874.080548 4272.843181 4628.896404 4954.005748 4291.548532 4175.915328 1.048033549 1.125222035 0.971840857 1.149228952 1.167188548 1.023211163 1.108474679 1.186328112 1.027690505 1 12.02787674 -4 0.082418795 0.910724918 1.545736519 0.341029822 0.058330218 128.009003 0.773504539 0.891143328 9.283636824 1.00E-04 4 0.635011601 SWSYNGYYS(ph)DLSTAR ddPTM_HeLa_Romidepsin_16h_R1 2 SWSYNGYYSDLSTAR 15 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 0 SWSYNGYYS(0.999)DLS(0.001)TAR;SWSYNGYYS(1)DLSTAR ; 277.34 1.92E-99 16215800 3107.4 3145.55 3418.3 2372.97 3717.5 3475 2659.04 3061.9 3504.3 3567.5 TRUE FALSE FALSE 3069.525814 3189.833135 3477.794078 2647.343957 3527.782103 3252.958715 2884.898791 3150.491246 3190.866631 3474.815836 0.883363596 0.917986243 1.000857093 0.761865976 1.015242899 0.936152841 0.830230702 0.906664236 0.918283668 1 11.7627208 -12.38653162 0.904971917 1.00523388 0.905334283 0.027337215 0.074312657 0.829515085 1.109790086 0.058879796 0.012288974 4.11E-13 12.38653162 -0.099899597 SWVIGS(ph)PEILR ddPTM_HeLa_Romidepsin_16h_R1 2 SWVIGSPEILR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 S(0.305)WVIGS(0.695)PEILR;S(0.003)WVIGS(0.997)PEILR ; 148.13 0.0024102 89073000 7518.4 6834.8 7497 6045.9 6480.3 5544.5 5095.9 5701.7 7580.5 7441.9 TRUE FALSE FALSE 7426.762849 6931.020494 7627.48214 6744.955405 6149.58611 5190.224344 5528.745619 5866.669694 6902.481094 7248.558365 1.024584817 0.956192962 1.052275743 0.930523708 0.848387472 0.716035394 0.76273727 0.809356757 0.95225571 1 12.82347838 -8.752892899 2.100788811 1.009469563 0.763619326 0.875680691 0.038433755 0.057302499 0.515312563 0.004815662 0.010580435 1.77E-09 8.752892899 -0.245850237 SYEDDDDMDLQPNK ddPTM_HeLa_Romidepsin_16h_R1 1 SYEDDDDMDLQPNK 14 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 0 0 152.54 0.00026142 0 1883.4 1873.1 1980.8 1282 1517 1502.1 1332.9 1470.1 1706 1730.3 FALSE FALSE TRUE 1860.444396 1899.469551 2015.274993 1430.230872 1439.581829 1406.120658 1446.116493 1512.635024 1553.411087 1685.346557 1.103894264 1.127049831 1.195762964 0.848627166 0.854175554 0.834321376 0.858052895 0.897521651 0.921716119 1 10.71882957 -9.238571466 24.62008947 1.067399658 0.856924735 0.692945316 0.070263971 268.289849 288846.8166 0.009867855 0.016356791 5.77E-10 9.238571466 -0.210474922 SYELPDGQVITIGNER ddPTM_HeLa_Romidepsin_16h_R1 6 SYELPDGQVITIGNER 16 0 P60709;A0A2R8Y793;P63267-2;Q6S8J3;A5A3E0;Q562R1;A0A2R8YEA7;Q9BYX7;P63261;P63267;P68133;P68032;P62736 P60709;P63261;P63267 ACTB;ACTG2;POTEE;POTEF;ACTBL2;POTEKP;ACTG1;ACTA1;ACTC1;ACTA2 "Actin, cytoplasmic 1;Actin, cytoplasmic 1, N-terminally processed;Actin, gamma-enteric smooth muscle;POTE ankyrin domain family member E;POTE ankyrin domain family member F;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" 0 0 ;;;;; ;;;;; 312.91 9.45E-157 453343970 9919.85 8853.311 8500.18 8458.98 9123.45 10189.49 8771.95 9645.82 9119.36 9002.952 FALSE FALSE TRUE 9798.943053 8977.948145 8648.122067 9437.047068 8657.846302 9538.414474 9517.039214 9924.906583 8303.701602 8769.054009 1.117445855 1.023821741 0.986209237 1.076176183 0.987318164 1.087735857 1.085298278 1.131810407 0.946932428 1 13.0982055 SYESSEDCSEAAGS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 SYESSEDCSEAAGSPAR 17 0 Q6P6C2-3;Q6P6C2;K7ER58 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 0 SYESSEDCSEAAGS(1)PAR;SYESSEDCSEAAGS(1)PAR ; 229.02 4.25E-36 15283600 1277.77 1154.48 1073.91 293.298 1518.77 1551.8 1183.77 1249.48 1538.8 1368.53 TRUE FALSE FALSE 1262.196048 1170.7328 1092.600953 327.2104948 1441.2615 1452.644988 1284.319394 1285.631732 1401.165874 1332.975393 0.946901236 0.87828538 0.81967076 0.24547377 1.081236388 1.089776297 0.963498202 0.96448272 1.051156594 1 10.38043443 -10.37688303 2.377900698 0.978788761 0.857867472 0.070627565 0.225524456 0.757942596 8.105669355 0.042601061 0.048425898 4.20E-11 10.37688303 -0.120921289 SYETLVDFDNHLDDIR ddPTM_HeLa_Romidepsin_16h_R1 2 SYETLVDFDNHLDDIR 16 0 M0R1B0;O43402 M0R1B0 EMC8 ER membrane protein complex subunit 8 0 0 ; ; 153.22 0.00012621 8043500 3206.2 3010.6 2952.2 2038.41 3226.5 3832.8 3212.1 3396 3721.5 3543.7 FALSE FALSE TRUE 3167.121601 3052.983306 3003.581803 2274.100555 3061.839665 3587.89645 3484.935694 3494.257902 3388.639719 3451.634163 0.917571635 0.884503734 0.870191237 0.658847505 0.887069579 1.039477616 1.009648048 1.012348858 0.981749386 1 11.75306385 -8.256882234 24.4415197 0.91983977 1.019407166 0.263761874 0.091496423 420.4908096 2255220.72 0.015121396 0.037125799 5.54E-09 8.256882234 0.099567396 SYHY(ph)S(ph)MHYSALPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SYHYSMHYSALPGSR 15 0 Q15784 Q15784 NEUROD2 Neurogenic differentiation factor 2 2 0 SYHY(0.512)S(0.75)MHY(0.428)S(0.309)ALPGSR 98.337 0.020841 36065000 0 0 0 0 0 0 60.413 0 0 68.921 TRUE FALSE FALSE 0 0 0 0 0 0 65.54447871 0 0 67.13042248 0 0 0 0 0 0 0.976375186 0 0 1 6.068894817 -12.24586133 0.92000955 1.013586729 0.125845659 0 0.419858958 0.358369612 0.531834388 0.215842636 0.055938925 5.68E-13 12.24586133 -0.88774107 SYHY(ph)SMHYS(ph)ALPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 SYHYSMHYSALPGSR 15 0 Q15784 Q15784 NEUROD2 Neurogenic differentiation factor 2 2 0 SYHY(0.446)S(0.402)MHY(0.446)S(0.706)ALPGSR 99.844 0.018436 41598000 0 0 0 0 0 114.4 0 0 56.917 0 TRUE FALSE FALSE 0 0 0 0 0 107.0902092 0 0 51.82620097 0 0 SYNPFDDDGEDEGARPAPWR ddPTM_HeLa_Romidepsin_16h_R1 2 SYNPFDDDGEDEGARPAPWR 20 1 O95721 O95721 SNAP29 Synaptosomal-associated protein 29 0 0 ; ; 96.805 0.0011129 13956500 3848.8 2167.9 2530.8 2232.7 4827.8 4004.3 4621.7 3962.6 4207.4 3421.4 FALSE FALSE TRUE 3801.889345 2198.419753 2574.847512 2490.855279 4581.419351 3748.438153 5014.267083 4077.251579 3831.079606 3332.511535 1.140848068 0.659688565 0.772644741 0.747440857 1.374764739 1.124808756 1.504651081 1.223477109 1.149607306 1 11.70239415 -8.739877211 24.99892987 0.989727498 1.308040441 0.493622358 0.186303739 203.7606581 236236.6671 0.029463932 0.058885305 1.82E-09 8.739877211 0.318312943 SYQNSPSSDDGIRPLPEY(ph)STEK ddPTM_HeLa_Romidepsin_16h_R1 1 SYQNSPSSDDGIRPLPEYSTEK 22 1 Q15648 Q15648 MED1 Mediator of RNA polymerase II transcription subunit 1 1 0 SYQNS(0.012)PS(0.214)S(0.214)DDGIRPLPEY(0.348)S(0.122)T(0.089)EK 61.276 0.023101 7973000 1276.4 1467.6 1304.3 1038 1270.6 1444.5 1252.7 1429.8 1396.9 1556 TRUE FALSE FALSE 1260.842746 1488.260911 1327.000794 1158.018444 1205.756541 1352.201112 1359.104307 1471.169007 1271.957765 1515.574896 0.831923747 0.981977806 0.875575861 0.764078666 0.795577008 0.892203424 0.89675826 0.970700301 0.83925761 1 10.56564943 -12.43798274 0.965873291 1.006554178 0.87042019 0 0.081553414 0.591768566 0.906971156 0.060135516 0.012383273 3.65E-13 12.43798274 -0.136133987 SYS(ph)AGNASQLEQLSR ddPTM_HeLa_Romidepsin_16h_R1 3 SYSAGNASQLEQLSR 15 0 Q14678-2;Q14678 Q14678-2 KANK1 KN motif and ankyrin repeat domain-containing protein 1 1 0 S(0.228)YS(0.772)AGNASQLEQLSR;S(0.287)YS(0.713)AGNASQLEQLSR;S(0.073)Y(0.001)S(0.925)AGNAS(0.002)QLEQLSR ;; 141.22 0.00070534 132192000 4534 4168.35 4301.2 3354.81 3615.74 3288.88 2705.45 3081.65 5366 4869.4 TRUE FALSE FALSE 4478.737864 4227.032141 4376.060582 3742.708917 3431.215296 3078.731182 2935.250855 3170.812681 4886.051521 4742.892286 0.944305203 0.891235113 0.922656539 0.789119527 0.723443648 0.649125259 0.618873607 0.668539889 1.030183952 1 12.21155139 -9.016266906 0.764936311 0.978226153 0.617087574 0.955098501 0.030734104 0.086361796 0.095880057 0.005368559 0.016025318 9.63E-10 9.016266906 -0.36113858 SYS(ph)PDGKESPSDK ddPTM_HeLa_Romidepsin_16h_R1 1 SYSPDGKESPSDK 13 1 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2 D6REM6 MATR3 Matrin-3 1 0 S(0.004)YS(0.995)PDGKES(0.001)PSDK 121.13 0.00065768 0 789.06 872.94 600.46 881.08 795.77 632.28 711.5 619.51 886.23 901.55 TRUE FALSE FALSE 779.4426332 885.2292722 610.9107544 982.9546152 755.1588875 591.8793486 771.9347922 637.4345444 806.9633692 878.127601 0.887618875 1.008087288 0.695697019 1.119375606 0.859964869 0.674024308 0.879069046 0.725901957 0.918959122 1 9.778286783 -4 0.156999962 1.005541469 0.043164933 0.232724075 0.120780729 64.75499278 0.647260345 0.215843132 14.41142963 1.00E-04 4 -0.962376536 SYS(ph)PDGKESPSDKK ddPTM_HeLa_Romidepsin_16h_R1 1 SYSPDGKESPSDKK 14 2 D6REM6;A0A0R4J2E8;A8MXP9;P43243;B3KM87;P43243-2 D6REM6 MATR3 Matrin-3 1 0 S(0.1)YS(0.9)PDGKESPSDKK 85.576 0.023447 850660000 2714.6 2758.8 2374.3 3689.9 2308.9 2271.7 2122.8 1942.1 2945.9 2827.1 TRUE FALSE FALSE 2681.513411 2797.638459 2415.623696 4116.5436 2191.068217 2126.545702 2303.110579 1998.291599 2682.411326 2753.651534 0.973802741 1.015974034 0.877243785 1.494939918 0.79569553 0.77226391 0.836384179 0.7256879 0.974128822 1 11.42713029 -8.573823122 24.99999302 1.017535493 0.783937807 0.398309265 0.160618595 85.21503129 41817.32427 0.021887915 0.043775838 2.67E-09 8.573823122 -0.233597686 SYS(ph)PSFQR ddPTM_HeLa_Romidepsin_16h_R1 1 SYSPSFQR 8 0 Q9P227-2;Q9P227 Q9P227-2 ARHGAP23 Rho GTPase-activating protein 23 1 0 S(0.059)YS(0.771)PS(0.17)FQR 119.75 0.018891 25416000 4029.5 4037.7 3844.2 2592.2 2986.5 3381 2583.9 2840.7 4117.3 3904 TRUE FALSE FALSE 3980.386904 4094.542847 3911.106688 2891.922361 2834.087761 3164.965012 2803.376402 2922.891173 3749.038376 3802.573517 1.046761328 1.076782034 1.028542031 0.760517147 0.745307815 0.832321847 0.737231348 0.768661318 0.98592134 1 11.89276043 -9.262551746 24.97194404 1.02805587 0.769276628 0.938667676 0.033075719 16.65557129 373908.2758 0.005096419 0.008064317 5.46E-10 9.262551746 -0.258779242 SYS(ph)SPDITQAIQEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 SYSSPDITQAIQEEEK 16 0 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 SYS(0.791)S(0.209)PDITQAIQEEEK;S(0.009)YS(0.491)S(0.491)PDIT(0.009)QAIQEEEK ; 205.12 1.07E-18 125088000 7672.3 8209 8025.1 7360.8 8172.2 9449 7885.9 8652 9160.2 8137.6 TRUE FALSE FALSE 7578.787057 8324.566517 8164.773499 8211.89033 7755.142139 8845.239395 8555.728149 8902.331969 8340.88877 7926.183979 0.956170974 1.050261581 1.030101436 1.036045889 0.978420657 1.115951815 1.079425884 1.123154849 1.052320864 1 12.95241074 -7.813721817 0.472417758 0.98165727 1.176905802 0.389340839 0.040590194 1.398038756 0.29158079 0.008585206 0.137963076 1.54E-08 7.813721817 0.195248532 SYS(ph)SPDITQAIQEEEKR ddPTM_HeLa_Romidepsin_16h_R1 4 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 S(0.008)YS(0.983)S(0.008)PDITQAIQEEEKR;S(0.054)YS(0.89)S(0.054)PDITQAIQEEEKR;S(0.413)Y(0.001)S(0.561)S(0.026)PDITQAIQEEEKR;S(0.058)YS(0.937)S(0.005)PDITQAIQEEEKR ;;; 210.71 6.00E-27 675924800 10792.7 11038.98 10981.22 10545.7 11178.1 11676 10098 11191.6 11922.3 11272.5 TRUE FALSE FALSE 10661.15442 11194.38705 11172.34353 11765.04345 10607.63985 10929.94128 10955.72387 11515.41129 10855.93963 10979.63882 0.97099318 1.01955877 1.017551097 1.071532829 0.966119197 0.995473663 0.997821881 1.048796911 0.988733764 1 13.42254298 -10.24709922 24.38013087 0.986302335 1.015348529 0.194176307 0.028020843 723.6888992 1230364.469 0.004770277 0.005828356 5.66E-11 10.24709922 0.029046194 SYSEDDIHR ddPTM_HeLa_Romidepsin_16h_R1 2 SYSEDDIHR 9 0 Q9Y5A9;A0A024R7W5;A0A087X0Q1;A0A087WY31;Q9Y5A9-2;Q9BYJ9;Q7Z739 Q9Y5A9 YTHDF2;YTHDF3;YTHDF1 YTH domain-containing family protein 2;YTH domain-containing family protein 1;YTH domain-containing family protein 3 0 0 ; ; 176.38 8.72E-05 18269400 12420.1 11359.2 11118.9 7525.7 12216.6 12295.9 10113.5 10551.1 14373.7 12243.7 FALSE FALSE TRUE 12268.71904 11519.11512 11312.41979 8395.856843 11593.14132 11510.23167 10972.54044 10856.37943 13088.08027 11925.60691 1.028771042 0.965914373 0.948582313 0.704019251 0.972121705 0.965169468 0.920082351 0.910341882 1.097477082 1 13.54177507 -9.823118759 2.779536144 1.012744661 0.899449804 0.387919352 0.076008562 0.222254496 3.511675835 0.011684335 0.016078048 1.50E-10 9.823118759 -0.113294856 SYSLS(ph)ELSVLQAK ddPTM_HeLa_Romidepsin_16h_R1 1 SYSLSELSVLQAK 13 0 Q9P0V3;Q9P0V3-2 Q9P0V3 SH3BP4 SH3 domain-binding protein 4 1 0 S(0.036)YS(0.066)LS(0.888)ELS(0.01)VLQAK 209.67 4.08E-23 138290000 5264.2 5179.1 4540.4 3976.2 4174.7 3772.6 3897.5 3632.7 5506.1 4464.4 TRUE FALSE FALSE 5200.037906 5252.011506 4619.423757 4435.946953 3961.649481 3531.543036 4228.553553 3737.806443 5013.620626 4348.414244 1.195846949 1.20779926 1.062323757 1.0201298 0.911056136 0.812145034 0.97243577 0.859579201 1.152976774 1 12.08627367 -8.93743197 2.164936926 1.103379101 0.886046259 0.717926877 0.069070526 0.178930957 1.692267047 0.013876984 0.027605126 1.15E-09 8.93743197 -0.217332843 SYSS(ph)PDITQAIQEEEKR ddPTM_HeLa_Romidepsin_16h_R1 2 SYSSPDITQAIQEEEKR 17 1 P40818;P40818-2 P40818 USP8 Ubiquitin carboxyl-terminal hydrolase 8 1 0 S(0.001)YS(0.305)S(0.694)PDITQAIQEEEKR;S(0.055)Y(0.002)S(0.181)S(0.761)PDIT(0.001)QAIQEEEKR ; 151.11 0.00015218 369412000 6482.8 6765.7 6344.6 5636.1 6832.6 7235.6 6603.3 7092.6 6964.5 6493.4 TRUE FALSE FALSE 6403.78514 6860.947702 6455.025102 6287.772401 6483.906926 6773.268512 7164.184137 7297.813191 6341.577677 6324.700532 1.012504087 1.084786176 1.020605651 0.994161284 1.025172163 1.070923197 1.132730965 1.153859088 1.00266845 1 12.62678146 -7.909271875 1.720952528 1.012878313 1.155913923 0.80264961 0.024341403 0.129063503 0.697493962 0.003834689 0.020052197 1.23E-08 7.909271875 0.143035609 SYSSGGEDGYVR ddPTM_HeLa_Romidepsin_16h_R1 2 SYSSGGEDGYVR 12 0 Q13347 Q13347 EIF3I Eukaryotic translation initiation factor 3 subunit I 0 0 ; ; 187.16 2.42E-07 21189200 3590.4 4125.5 3302.7 2517.1 3535.8 3446 3549.9 3396.8 5011.4 7374.6 FALSE FALSE TRUE 3546.638824 4183.578897 3360.182108 2808.138945 3355.354932 3225.811721 3851.428417 3495.081049 4563.167833 7183.006829 0.493754065 0.582427248 0.467796034 0.390941985 0.467124007 0.44908933 0.5361861 0.486576323 0.635272657 1 12.81037217 -12.21688537 0.545412329 1.091648827 0.466519572 0.449532415 0.121301244 0.216139618 0.092265535 0.070058624 0.012056945 6.07E-13 12.21688537 -0.625129255 SYSSSSSS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 3 SYSSSSSSPER 11 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 SYSSSSSS(1)PER;SYSSS(0.002)S(0.011)S(0.095)S(0.892)PER;SYSSSSS(0.026)S(0.974)PER ;; 175.74 4.46E-05 45808000 10322.3 10913.3 13134.8 8936.2 10152.8 11124.9 13776.1 5011.6 13702.6 13334.5 TRUE FALSE FALSE 10196.48784 11066.93772 13363.40568 9969.44549 9634.664731 10414.05479 14946.24159 5156.602739 12477.00514 12988.06777 0.785065802 0.852085 1.028898672 0.767584961 0.741808936 0.801817097 1.150767139 0.397026165 0.960651373 1 13.6648992 -16.52287875 0.268435033 2.257274206 0.807267922 0.119430424 0.184701136 74.08532779 0.993843633 49.75883309 0.087882613 3.00E-17 16.52287875 -1.450006284 SYSVGAS(ph)GSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 SYSVGASGSSSR 12 0 F5H669;Q8N684-2;Q8N684;Q8N684-3 F5H669 CPSF7 Cleavage and polyadenylation specificity factor subunit 7 1 0 SYSVGAS(0.944)GS(0.054)S(0.001)SR;SYSVGAS(0.676)GS(0.317)S(0.008)SR ; 119.21 0.0077638 10681000 2284.4 2099.11 2405.4 1712.71 1857.35 2085.66 1506.88 2067.51 2043.08 2423.5 TRUE FALSE FALSE 2256.556854 2128.661326 2447.264978 1910.741589 1762.562499 1952.393057 1634.87435 2127.33014 1860.341808 2360.537121 0.95595059 0.901769901 1.03674073 0.80945204 0.746678577 0.827096952 0.69258574 0.901205968 0.78810106 1 11.20489945 -9.181443664 6.054793588 0.975434644 0.786970817 0.373030006 0.084099448 0.090254413 5.476997523 0.008250167 0.013755029 6.59E-10 9.181443664 -0.188463827 T(ph)AAPSPSLLYK ddPTM_HeLa_Romidepsin_16h_R1 2 TAAPSPSLLYK 11 0 Q9BTC0;Q9BTC0-1;Q9BTC0-2;Q9BTC0-3 Q9BTC0 DIDO1 Death-inducer obliterator 1 1 0 T(0.98)AAPS(0.013)PS(0.006)LLYK;T(0.943)AAPS(0.048)PS(0.009)LLYK ; 137.4 0.0075087 122652000 13669 12078 12592.3 9244.7 12674.7 13925.7 13357.7 13443 13671.5 12046.9 TRUE FALSE FALSE 13502.39697 12248.0344 12811.4637 10313.61571 12027.86276 13035.89271 14492.3027 13831.952 12448.6868 11733.9198 1.150714953 1.043814395 1.091831538 0.878957406 1.025050705 1.110958054 1.235077702 1.178800625 1.060914597 1 13.51839742 -7.938872367 4.188311118 1.054989234 1.205392802 0.481402289 0.068833908 0.175360034 6.235206201 0.011585248 0.037114617 1.15E-08 7.938872367 0.150403568 T(ph)AATSVPAYEPLDSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 TAATSVPAYEPLDSLDR 17 0 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 T(0.539)AAT(0.176)S(0.128)VPAYEPLDS(0.156)LDR 90.853 0.017978 2681600 731.53 672.21 613.69 682.64 812.81 764.14 632.44 793.06 831.8 886.21 TRUE FALSE FALSE 722.613831 681.67339 624.371017 761.5700487 771.3292727 715.3139201 686.1594378 816.0059399 757.4017247 863.1861364 0.83714717 0.789717723 0.723332999 0.882277896 0.893583945 0.828690233 0.794914803 0.945341805 0.877448899 1 9.753527884 -12.00145549 0.846451955 0.998233899 0.834271029 0.184100104 0.068845729 0.373976352 0.496909792 0.036891489 0.011931785 9.97E-13 12.00145549 -0.16396287 T(ph)ACNMT(ph)Y(ph)GSFGGVK ddPTM_HeLa_Romidepsin_16h_R1 1 TACNMTYGSFGGVK 14 0 A0A5F9ZGY2;A0A5F9ZHP5;A0A5F9ZH74;A0A5F9ZH37;A0A5F9ZHE7;A0A5F9ZH14;A0A5F9ZGX9;Q3SYG4-7;Q3SYG4-3;Q3SYG4;F8WCG5;Q3SYG4-5;Q3SYG4-6;Q3SYG4-2;Q3SYG4-4 A0A5F9ZGY2 BBS9 Protein PTHB1 3 0 T(0.89)ACNMT(0.891)Y(0.869)GS(0.35)FGGVK 58.723 0.024433 7839400 1875.2 1391.7 1642.5 1306.7 1717 1438.1 1521.7 1476.5 1769.4 1867.6 TRUE FALSE FALSE 1852.344341 1411.292389 1671.087024 1457.786802 1629.375083 1346.210051 1650.95316 1519.220198 1611.140432 1819.079483 1.018286644 0.775827776 0.918644314 0.801387084 0.895714068 0.740050154 0.907576154 0.835158778 0.885689959 1 10.82899287 -10.27366243 24.95963509 1.008635365 0.841786414 0.399718711 0.066935606 276.5279075 564672.2446 0.008225926 0.009443388 5.33E-11 10.27366243 -0.166848951 T(ph)ALSST(ph)ES(ph)CT(ph)MK ddPTM_HeLa_Romidepsin_16h_R1 1 TALSSTESCTMK 12 0 Q96T23-3;Q96T23-2;Q96T23;H0YER1;H0YCN2 Q96T23-3 RSF1 Remodeling and spacing factor 1 4 0 T(0.564)ALS(0.429)S(0.429)T(0.642)ES(0.936)CT(1)MK 50.149 0.0042922 0 861.05 760.06 473.92 793.93 910.49 935.12 668.26 930.46 924.76 927.59 TRUE FALSE FALSE 850.5551914 770.7601446 482.1683788 885.7279222 864.0242978 875.36885 725.0219877 957.3813921 842.0471495 903.4910781 0.941409619 0.853091041 0.53367254 0.980339423 0.956317465 0.968873818 0.802467235 1.059646758 0.931992767 1 9.819366544 -10.53995361 2.864613906 0.977093221 0.874186569 0.062458497 0.136393985 0.44257191 7.443882208 0.025117089 0.027033394 2.88E-11 10.53995361 -0.102906651 T(ph)APSPLVEAK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 T(0.843)APS(0.157)PLVEAK 127.87 0.017035 27424000 5636.6 4966.9 6087 5255.1 5785.3 5670.8 4425.8 5387.3 5816.8 5252.2 TRUE FALSE FALSE 5567.898951 5036.824149 6192.941682 5862.719388 5490.054553 5308.454182 4801.727342 5543.173026 5296.53084 5115.747087 1.088384327 0.984572549 1.210564474 1.146014314 1.073167704 1.037669394 0.938617031 1.08355103 1.035338681 1 12.32072923 -6.938734201 21.40991725 1.052207917 1.726024341 0.007188648 0.075049 2756.778781 1150415.933 0.01066663 191580.7789 1.15E-07 6.938734201 0.673816424 T(ph)AQQNGDTPEAQGLDITTYGESNLVAEPQK ddPTM_HeLa_Romidepsin_16h_R1 1 TAQQNGDTPEAQGLDITTYGESNLVAEPQK 30 0 Q15003;E9PHA2;Q15003-2 Q15003 NCAPH Condensin complex subunit 2 1 0 T(0.526)AQQNGDT(0.344)PEAQGLDIT(0.06)T(0.06)Y(0.01)GESNLVAEPQK 51.296 0.01135 5216800 1652.5 1916 1627.5 1900.9 2230.1 2147.9 1815.9 1983 1800.4 1876.2 TRUE FALSE FALSE 1632.358694 1942.973498 1655.825955 2120.691002 2116.289675 2010.656122 1970.142501 2040.374976 1639.367715 1827.456054 0.893241012 1.06321216 0.906082503 1.160460739 1.158052294 1.100248686 1.078079277 1.116511104 0.897076409 1 10.835621 -9.259325969 24.99912046 0.955668962 1.120913145 0.718346903 0.053426968 85.80969894 1015025.581 0.008650002 0.013887129 5.50E-10 9.259325969 0.165244183 T(ph)AS(ph)PPPPPKR ddPTM_HeLa_Romidepsin_16h_R1 5 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 2 0 T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR;T(1)AS(1)PPPPPKR ;;;; 93.442 0.0015749 16748900 18178.6 16629.2 15402 14604.9 17486.8 16256.5 15319.6 15911.3 18367.5 17215.3 TRUE FALSE FALSE 17957.03223 16863.30631 15670.06535 16293.58726 16594.38334 15217.76212 16620.84644 16371.66836 16724.6648 16768.04402 1.070907985 1.005681181 0.934519573 0.971704704 0.989643355 0.907545453 0.991221541 0.976361246 0.997412982 1 14.03342679 -9.967575987 6.424232968 1.033759808 0.962742976 0.443051206 0.030809772 0.113999784 14.25095567 0.005542361 0.007254622 1.08E-10 9.967575987 -0.071016832 T(ph)ASEGDGGAAAGAAAAGAR ddPTM_HeLa_Romidepsin_16h_R1 2 TASEGDGGAAAGAAAAGAR 19 0 Q9Y4H2 Q9Y4H2 IRS2 Insulin receptor substrate 2 1 0 T(0.926)AS(0.074)EGDGGAAAGAAAAGAR;T(0.926)AS(0.074)EGDGGAAAGAAAAGAR ; 300.56 2.50E-143 240120000 3132.9 3906.6 3694 3297.4 3371.1 3195.5 2345.83 2958.3 3653.3 3259.2 TRUE FALSE FALSE 3094.71501 3961.597217 3758.29252 3678.660903 3199.060188 2991.317863 2545.084742 3043.893743 3326.539698 3174.525514 0.974859076 1.247933652 1.183891106 1.158806532 1.007728611 0.942288178 0.801721306 0.958849985 1.047885639 1 11.63232526 -8.157419055 3.16043374 1.037526156 0.879663081 0.367620187 0.09974727 0.282285808 5.348188506 0.016806091 0.048172435 6.96E-09 8.157419055 -0.157863075 T(ph)ASELLLDR ddPTM_HeLa_Romidepsin_16h_R1 1 TASELLLDR 9 0 Q92508 Q92508 PIEZO1 Piezo-type mechanosensitive ion channel component 1 1 0 T(0.5)AS(0.5)ELLLDR 125.72 0.0216 2426400 981.27 1734.2 1334.6 806.58 1316.8 1594.7 771.3 1941 1233.5 1332.6 TRUE FALSE FALSE 969.3099038 1758.614113 1357.828153 899.8405747 1249.598782 1492.803817 836.8142027 1997.159773 1123.172671 1297.97886 0.746784045 1.354886561 1.046109606 0.693262889 0.962726606 1.150098713 0.644705572 1.538668952 0.865324317 1 10.34205117 -7.244149447 24.04513503 0.920076122 1.538669808 0.42749375 0.206485591 1525.831651 2121920.767 0.02847581 1.075517473 5.70E-08 7.244149447 0.618593685 T(ph)ASELLLDRR ddPTM_HeLa_Romidepsin_16h_R1 3 TASELLLDRR 10 1 Q92508 Q92508 PIEZO1 Piezo-type mechanosensitive ion channel component 1 1 0 T(0.997)AS(0.003)ELLLDRR;T(0.995)AS(0.005)ELLLDRR;T(0.994)AS(0.006)ELLLDRR ;; 125.54 0.0038177 8520600 3367.35 7048.3 4583.1 3300.93 5470.1 7037.1 2951.46 7371.5 4730 4562.7 TRUE FALSE FALSE 3326.307443 7147.526152 4662.866933 3682.599058 5190.940385 6587.452021 3202.156939 7584.782722 4306.936953 4444.160396 0.74846701 1.608296172 1.049212116 0.828637747 1.168036237 1.482271438 0.720531361 1.706685188 0.969122752 1 12.11769517 -4 0.269361781 0.901393045 4.522319786 0.13030358 0.314901122 59.498706 0.754251735 0.14597855 101.3826811 1.00E-04 4 3.620926741 T(ph)ASGSSVTSLDGTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASGSSVTSLDGTR 14 0 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 1 0 T(0.971)AS(0.013)GS(0.013)S(0.004)VTSLDGTR 230.69 1.39E-33 93246000 3150.9 2599.1 3177 2566.3 3833.9 4328.5 4352.5 4534 2912.8 2864.4 TRUE FALSE FALSE 3112.495619 2635.690198 3232.294352 2863.027681 3638.241777 4051.92282 4722.201241 4665.184137 2652.271873 2789.982475 1.115596835 0.944697761 1.158535719 1.026181242 1.304037502 1.452311208 1.692555879 1.672119513 0.950641051 1 11.44604034 -8.244390436 1.294853441 1.049923934 1.711244824 0.928555732 0.072532827 0.082303007 0.247886297 0.01017621 0.044017205 5.70E-09 8.244390436 0.66132089 T(ph)ASLTSAASVDGNR ddPTM_HeLa_Romidepsin_16h_R1 1 TASLTSAASVDGNR 14 0 G3V578;H0YJT9;A0A0A0MS87;Q9UN36-4;Q9UN36-5;Q9UN36-2;Q9UN36-3;Q9UN36-6;Q9UN36 G3V578 NDRG2 Protein NDRG2 1 0 T(0.992)AS(0.002)LT(0.001)S(0.002)AAS(0.004)VDGNR 188.63 1.22E-10 5147900 431.76 494.29 571.06 739.49 779.17 1049.9 752.41 806.33 709.09 542.27 TRUE FALSE FALSE 426.497543 501.2486276 580.9990598 824.9933132 739.4060474 982.8147784 816.3196866 829.6598864 645.6672145 528.1817472 0.807482548 0.949007856 1.099998368 1.561949684 1.399908367 1.860751121 1.545528014 1.57078485 1.222433789 1 9.044890636 -9.340348972 1.887084619 0.907082451 1.613260186 0.774315094 0.152346717 0.080864765 0.56303049 0.019688655 0.033621507 4.57E-10 9.340348972 0.706177735 T(ph)ASNPKVENEDEPVR ddPTM_HeLa_Romidepsin_16h_R1 1 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 T(0.851)AS(0.149)NPKVENEDEPVR 111.73 0.017403 7908400 724.5 583.09 920.08 952.43 868.11 1089 898.68 1273.1 1089.5 830.62 TRUE FALSE FALSE 715.6695153 591.2987563 936.0936064 1062.554438 823.8071073 1019.416415 975.0138568 1309.93514 992.0523913 809.0403727 0.884590608 0.730864338 1.157041896 1.313351563 1.01825216 1.260031574 1.205148581 1.619122091 1.226208759 1 9.660067887 -4 0.367608154 0.934807422 9.34035875 0.48984041 0.167965306 26.63424435 0.328054075 0.039958796 159.7322915 1.00E-04 4 8.405551328 T(ph)ASPPPPPK ddPTM_HeLa_Romidepsin_16h_R1 1 TASPPPPPK 9 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 T(0.986)AS(0.014)PPPPPK 120.45 0.027271 733680000 8504.6 7564.5 6801.3 6726 7501.9 7607.2 6453.1 7266.7 7773.2 7355.4 TRUE FALSE FALSE 8400.942664 7670.99323 6919.673773 7503.691767 7119.05005 7121.124471 7001.226153 7476.9505 7077.945524 7164.305648 1.172610868 1.070723892 0.965854071 1.047371809 0.993683184 0.993972734 0.977237223 1.04363924 0.987945779 1 12.80661117 -9.874762966 6.870693231 1.083501289 1.003730639 0.131810304 0.054687349 0.240464569 13.70793391 0.010877881 0.014339136 1.33E-10 9.874762966 -0.07977065 T(ph)ASPPPPPKR ddPTM_HeLa_Romidepsin_16h_R1 1 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 T(0.979)AS(0.021)PPPPPKR 75.788 0.029568 4611500 2490.4 2360.3 2210 2373.9 2643.4 2663.7 2475.6 2624.3 2239.9 2395.1 TRUE FALSE FALSE 2460.046047 2393.528365 2248.464123 2648.381488 2508.497434 2493.498167 2685.877402 2700.22998 2039.557734 2332.874957 1.054512605 1.025999425 0.96381682 1.135243653 1.075281565 1.068852044 1.151316488 1.157468801 0.874267919 1 11.18789326 -4 0.25958051 1.011615474 2.083929599 0.509660594 0.059201234 23.88523802 0.300692537 0.019904068 11.46602825 1.00E-04 4 1.072314125 T(ph)ASPSTSSIDSATDTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASPSTSSIDSATDTR 16 0 Q96P50-4;Q96P50-1;Q96P50 Q96P50-4 ACAP3 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3" 1 0 T(0.832)AS(0.165)PS(0.002)T(0.001)SSIDSATDTR 257.48 1.13E-71 6692100 1596.1 1190.8 1279.8 1454.2 1894.4 2021.3 1527.1 1953.8 1690.8 1548.3 TRUE FALSE FALSE 1576.646119 1207.564114 1302.074382 1622.341446 1797.721699 1892.145453 1656.811836 2010.33012 1539.570613 1508.074943 1.045469343 0.800732165 0.863401642 1.075769778 1.192063901 1.254676011 1.098626991 1.333043911 1.020884685 1 10.55849241 -8.865834491 3.432387734 0.99054776 1.215263916 0.64302559 0.092969682 0.143475859 3.318744597 0.014768795 0.028299902 1.36E-09 8.865834491 0.224716156 T(ph)ATPPGYKPGSPPS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 2 0 T(0.846)AT(0.155)PPGYKPGS(0.291)PPS(0.709)FR 123.43 0.009229 9566600 3161.3 3039 2716.3 2613.7 1727.4 1990.7 1360.7 1717.1 2911.2 2526.4 TRUE FALSE FALSE 3122.76886 3081.783122 2763.576062 2915.908292 1639.244332 1863.500695 1476.277824 1766.781579 2650.814981 2460.763764 1.269024238 1.25236854 1.123056225 1.184960676 0.666152662 0.757285491 0.599926676 0.71798098 1.077232614 1 11.26489045 -8.759697611 24.99997929 1.143729543 0.684374896 0.883491465 0.082835705 15.13915995 217289.2513 0.016629649 0.031927835 1.74E-09 8.759697611 -0.459354647 T(ph)AVPSPVEAAAASDPAAAR ddPTM_HeLa_Romidepsin_16h_R1 2 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;J3KNC2;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 0 T(0.783)AVPS(0.217)PVEAAAASDPAAAR;T(0.784)AVPS(0.216)PVEAAAASDPAAAR ; 182.28 3.52E-10 29325000 6909.6 7055.6 6391.2 6614.5 6158.7 6748.1 5876.6 6800.5 6632.9 6446.9 TRUE FALSE FALSE 6825.383138 7154.928922 6502.436155 7379.299612 5844.398558 6316.918188 6375.758257 6997.261738 6039.636812 6279.408609 1.086946807 1.139427193 1.035517285 1.175158374 0.93072436 1.005973426 1.015343746 1.114318589 0.961816182 1 12.61641298 -7.242592632 22.22817098 1.045971274 1.114318871 0.082051276 0.072268085 1801.241873 2124255.278 0.009462499 0.358125786 5.72E-08 7.242592632 0.068347597 T(ph)DLQGSASPSK ddPTM_HeLa_Romidepsin_16h_R1 1 TDLQGSASPSK 11 0 B4DF77;Q6VY07;Q6VY07-2 B4DF77 PACS1 Phosphofurin acidic cluster sorting protein 1 1 0 T(0.973)DLQGSAS(0.026)PS(0.001)K 147.58 0.005006 9322500 5634.8 5954.9 5860.2 2745 5045.8 4986.3 4169.4 3737.1 5641.4 5473.9 TRUE FALSE FALSE 5566.12089 6038.733239 5962.194323 3062.389816 4788.293998 4667.691523 4523.548732 3845.227092 5136.819055 5331.687289 1.043969871 1.132612044 1.118256567 0.574375362 0.898082303 0.875462357 0.84842724 0.721202667 0.963450926 1 12.38037645 -9.285609228 24.9925732 1.038106266 0.798590061 0.646966155 0.09847243 389.3006818 402550.9961 0.014571686 0.022265577 5.18E-10 9.285609228 -0.239516205 T(ph)DSQTIGDFATR ddPTM_HeLa_Romidepsin_16h_R1 1 TDSQTIGDFATR 12 0 Q13480-2 Q13480-2 GAB1 GRB2-associated-binding protein 1 1 0 T(0.991)DS(0.004)QT(0.004)IGDFATR 148.85 0.0030353 6384500 1210.6 1908.1 1293.2 1489.1 1167.1 894.41 615.77 917.18 1305.6 1434.7 TRUE FALSE FALSE 1195.844742 1934.962282 1315.707604 1661.276748 1107.538532 837.2600876 668.0734884 943.7171562 1188.823866 1397.426287 0.855747994 1.384661431 0.941522008 1.18881172 0.79255596 0.599144367 0.478074224 0.675325178 0.850723846 1 10.44855647 -8.444051794 3.499937701 0.985313118 0.575526539 0.602663891 0.161880999 0.137563929 3.215071846 0.023719331 0.055387048 3.60E-09 8.444051794 -0.409786579 T(ph)DSVIIADQTPTPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TDSVIIADQTPTPTR 15 0 K7ELQ4;P17544-4;P17544-2;P17544;K7ESA4;P17544-5;P17544-3;P17544-1 K7ELQ4 ATF7 Cyclic AMP-dependent transcription factor ATF-7 2 0 T(0.999)DS(0.001)VIIADQT(0.004)PT(0.044)PT(0.952)R 149.74 0.0094631 4412600 1299.6 1373.9 1491.9 1646.3 874.89 994.76 732.88 1530.5 1303.8 1309.1 TRUE FALSE FALSE 1283.759975 1393.2418 1517.865894 1836.652952 830.2410986 931.1980464 795.1308089 1574.782603 1187.184863 1275.089393 1.00679998 1.092662058 1.190399592 1.440411129 0.651123837 0.730300206 0.623588286 1.235037019 0.931060104 1 10.31638268 T(ph)DSVIIADQTPTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TDSVIIADQTPTPTR 15 0 K7ELQ4;P17544-4;P17544-2;P17544;K7ESA4;P17544-5;P17544-3;P17544-1 K7ELQ4 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 0 T(0.998)DS(0.002)VIIADQTPTPTR 138.28 0.0020981 4657200 1459.9 1862.6 1104.6 1074.8 1329.7 998.21 774.77 1061.2 1006.7 1494.5 TRUE FALSE FALSE 1442.106177 1888.821732 1123.8251 1199.073433 1261.840447 934.4276026 840.5789445 1091.904148 916.6582307 1455.672675 0.990680256 1.297559379 0.77203146 0.823724629 0.866843535 0.641921511 0.577450521 0.750102799 0.629714528 1 10.50747027 -8.895378388 1.074948037 1.012336091 0.65302936 0.280535841 0.174552412 0.262245732 0.594927993 0.020617729 0.054938227 1.27E-09 8.895378388 -0.359306731 T(ph)DYNASVSVPDSSGPER ddPTM_HeLa_Romidepsin_16h_R1 1 TDYNASVSVPDSSGPER 17 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 T(0.982)DYNAS(0.017)VSVPDSSGPER 189.04 7.03E-13 5529300 1753.6 2036.7 1738.1 1820.6 1884.6 1872.2 1752.9 1923.5 2202.6 2004.7 TRUE FALSE FALSE 1732.226449 2065.372716 1768.350901 2031.106338 1788.42183 1752.572462 1901.791282 1979.153438 2005.593939 1952.617605 0.887130406 1.057745618 0.905630932 1.040196674 0.915909918 0.897550272 0.973970161 1.013589877 1.027130931 1 10.93119373 -7.517586571 24.41870952 0.951904331 1.003684979 0.005321078 0.061363758 284.8759893 1314425.593 0.008288945 0.033132447 3.04E-08 7.517586571 0.051780649 T(ph)EEARPSPAPGPGTPTGT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 2 0 T(0.788)EEARPS(0.025)PAPGPGT(0.297)PT(0.187)GT(0.6)PT(0.103)R 63.042 0.01231 23290000 1478.2 1561.5 1679.8 2207.1 3663.2 3475.2 3169.1 3498.9 1860.9 1527.7 TRUE FALSE FALSE 1460.18313 1583.482838 1709.036214 2462.295287 3476.253235 3253.145936 3438.283275 3600.135151 1694.456443 1488.010134 0.981299184 1.064161327 1.148538021 1.654757068 2.33617578 2.1862391 2.310658508 2.419429189 1.138739855 1 10.53916864 -9.041009433 1.806125548 0.99632111 2.327652001 0.979384568 0.085014619 0.024819352 0.160469657 0.010702923 0.02107392 9.10E-10 9.041009433 1.331330891 up T(ph)EESPASDEAGEKEAK ddPTM_HeLa_Romidepsin_16h_R1 1 TEESPASDEAGEKEAK 16 1 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 1 0 T(0.559)EES(0.433)PAS(0.007)DEAGEKEAK 91.547 0.0062297 7672900 2849.8 2884.5 2933.1 2143.7 3278.8 3358.4 3783.3 3503.1 2682.8 2711.2 TRUE FALSE FALSE 2815.065541 2925.108067 2984.149375 2391.56468 3111.470601 3143.809079 4104.653408 3604.456672 2442.843649 2640.762633 1.066004762 1.107675499 1.130033172 0.905634096 1.178246981 1.190492867 1.554343944 1.364930201 0.925052338 1 11.36673891 -8.049473189 1.994157927 1.04104619 1.461702922 0.749030642 0.094201514 0.105284074 0.798946107 0.011739872 0.045510229 8.92E-09 8.049473189 0.420656731 T(ph)EGAEATPGAQKR ddPTM_HeLa_Romidepsin_16h_R1 1 TEGAEATPGAQKR 13 1 H3BM18;X6RHM1;Q16666-3;Q16666-2;Q16666 H3BM18 IFI16 Gamma-interferon-inducible protein 16 1 0 T(0.63)EGAEAT(0.37)PGAQKR 110.64 0.0017212 0 623.86 762.14 783.52 633.87 940.64 1237.2 1145.1 346.34 641.8 755.89 TRUE FALSE FALSE 616.2561544 772.8694269 797.1568369 707.1610318 892.6356308 1158.146913 1242.364765 356.3608015 584.3958006 736.2518688 0.837018119 1.049735097 1.082723006 0.960487928 1.21240525 1.573030863 1.687418149 0.484020233 0.793744404 1 9.524055581 -8.698874205 3.947816694 0.946570068 1.305734065 0.16122329 0.310027879 0.243691922 7.604295426 0.04236766 0.086321243 2.00E-09 8.698874205 0.359163997 T(ph)EMDSRT(ph)KS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TEMDSRTKSK 10 2 Q5JPT2;Q96B97-2;Q96B97;Q96B97-3;Q5VSN0 Q5JPT2 SH3KBP1 SH3 domain-containing kinase-binding protein 1 3 0 T(0.995)EMDS(0.018)RT(0.987)KS(1)K 61.48 0.0036569 0 928.7 958.49 1004.6 636.51 1043.1 1207.5 789.04 1057.7 801.51 968.37 TRUE FALSE FALSE 917.3806472 971.9836474 1022.084642 710.1062811 989.8667147 1130.344647 856.0610379 1088.302881 729.8209382 943.2116078 0.972613822 1.030504332 1.08362178 0.752859989 1.049464093 1.198399848 0.907602314 1.153826853 0.773761616 1 9.881437663 -8.538271702 24.98585974 0.980489156 1.077912858 0.190014173 0.125466168 310.0194399 503222.6375 0.014320964 0.028648624 2.90E-09 8.538271702 0.097423702 T(ph)ESVPSDINNPVDR ddPTM_HeLa_Romidepsin_16h_R1 3 TESVPSDINNPVDR 14 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 T(0.495)ES(0.495)VPS(0.01)DINNPVDR;T(0.858)ES(0.141)VPS(0.001)DINNPVDR;T(0.559)ES(0.367)VPS(0.073)DINNPVDR ;; 206.67 9.02E-17 108111600 6369.6 6159.2 5830.7 6437.8 6327.1 6030.9 4830.7 5363.3 6681.9 6142.2 TRUE FALSE FALSE 6291.964865 6245.909379 5932.180888 7182.168727 6004.204477 5645.544954 5241.019537 5518.478624 6084.254129 5982.624759 1.05170642 1.044008212 0.991568271 1.200504631 1.003607065 0.94365687 0.876040158 0.922417642 1.016987422 1 12.54656286 -8.204999688 3.144953384 1.036741485 0.902644638 0.527050172 0.05732812 0.161336935 3.164086044 0.008264166 0.022985626 6.24E-09 8.204999688 -0.134096847 T(ph)ETPIVSK ddPTM_HeLa_Romidepsin_16h_R1 1 TETPIVSK 8 0 O95292 O95292 VAPB Vesicle-associated membrane protein-associated protein B/C 1 0 T(0.986)ET(0.011)PIVS(0.003)K 128.86 0.025399 16288000 3782.1 5367.1 4705.7 2207.3 4460.4 8052.1 3179.2 6569 4809.1 4643.7 TRUE FALSE FALSE 3736.00231 5442.658175 4787.600735 2462.518412 4232.769144 7537.596797 3449.241169 6759.063651 4378.962051 4523.056005 0.825990725 1.203314345 1.058488051 0.544436861 0.935820635 1.66648319 0.76259086 1.494357718 0.968142346 1 12.14308214 -8.469714001 24.99919406 0.920572007 1.261266099 0.283101112 0.269289558 324.9268519 152787.2144 0.035545562 0.079481722 3.39E-09 8.469714001 0.340694092 T(ph)ETPPPLASLNVSK ddPTM_HeLa_Romidepsin_16h_R1 2 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 0 T(0.698)ET(0.302)PPPLASLNVSK;T(0.99)ET(0.01)PPPLASLNVSK ; 180.85 5.86E-07 123939000 6299.2 6173.7 6645.7 6152.7 5835.7 5780.4 4572.6 5338.7 6338.9 6088 TRUE FALSE FALSE 6222.422927 6260.613511 6761.365621 6864.104123 5537.882453 5411.051095 4960.99653 5493.166861 5771.932908 5929.832882 1.049342039 1.055782454 1.140228697 1.157554396 0.933901943 0.912513253 0.836616584 0.926361159 0.973371935 1 12.53377573 -8.562677215 10.6606987 1.044770524 0.892420481 0.644248311 0.058092448 0.272221252 71.62214595 0.00900636 0.018037323 2.74E-09 8.562677215 -0.152350043 T(ph)FHRNWDWES(ph)EY(ph)TLFMS(ph)ALK ddPTM_HeLa_Romidepsin_16h_R1 1 TFHRNWDWESEYTLFMSALK 20 1 Q6ZXV5-2;Q6ZXV5 Q6ZXV5-2 TMTC3 Transmembrane and TPR repeat-containing protein 3 4 0 T(1)FHRNWDWES(0.998)EY(0.871)T(0.454)LFMS(0.677)ALK 48.907 0.017496 100060000 1908.4 1801 1675.4 204.98 1874.2 2078.4 1807.2 1920.2 1923.6 1881.1 TRUE FALSE FALSE 1885.139687 1826.354525 1704.559634 228.6807521 1778.55258 1945.596948 1960.703523 1975.757957 1751.548398 1832.228751 1.028877909 0.996793945 0.930320318 0.124810154 0.970704438 1.061874478 1.070119395 1.078335855 0.955966005 1 10.83938392 -9.523664679 24.98373371 1.01041189 0.853768121 0.05349503 0.262526155 59.99717226 1907198.016 0.042400129 0.060265481 2.99E-10 9.523664679 -0.156643769 T(ph)FNTSTGGLLLPSDTKR ddPTM_HeLa_Romidepsin_16h_R1 1 TFNTSTGGLLLPSDTKR 17 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 1 0 T(0.536)FNT(0.449)S(0.011)T(0.004)GGLLLPSDTKR 73.208 0.011293 21511000 1572 1110.1 1147.7 1014 1158.1 1314.8 1095.6 1133.7 1522.9 1300.5 TRUE FALSE FALSE 1552.839859 1125.728017 1167.675237 1131.243451 1098.997836 1230.788523 1188.660237 1166.501821 1386.68801 1266.712823 1.225881535 0.888700262 0.921815281 0.893054393 0.867598256 0.971639745 0.938381783 0.920888934 1.094713802 1 10.30687377 -10.24294734 24.80193258 1.106666282 0.915335583 0.701783204 0.057438406 431.641211 578927.8962 0.014358254 0.01756666 5.72E-11 10.24294734 -0.191330698 T(ph)FPASNYTVSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TFPASNYTVSSR 12 0 O95835;O95835-2;Q6PJG3 O95835 LATS1 Serine/threonine-protein kinase LATS1 1 0 T(1)FPASNYTVSSR 181.71 2.19E-06 13200000 330.21 247.15 383.38 425.6 274.13 269.22 250.43 282.81 328.48 276.29 TRUE FALSE FALSE 326.1852735 250.6293842 390.0525681 474.8098745 260.1401232 252.0177109 271.7015179 290.9926611 299.0999261 269.111946 1.212080245 0.931320173 1.449406368 1.764358222 0.966661373 0.936479092 1.009622657 1.081307112 1.111433107 1 8.072062624 T(ph)FPPMT(ph)S(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 TFPPMTSSK 9 0 O15146 O15146 MUSK "Muscle, skeletal receptor tyrosine-protein kinase" 3 0 T(0.999)FPPMT(0.922)S(0.922)S(0.158)K 48.284 0.0043187 0 721.48 659.24 648.75 680.09 609.49 589.93 408.8 714.36 937.92 714.02 TRUE FALSE FALSE 712.6863243 668.520798 660.0412216 758.7252057 578.385451 552.2353769 443.5234618 735.0288795 854.0300861 695.4696575 1.024755454 0.961250848 0.949058258 1.090953714 0.831647283 0.794046686 0.637732296 1.056881306 1.227990433 1 9.441843763 -8.68122621 7.202462765 1.007366825 0.811693299 0.395228543 0.123469426 0.14315057 10.82920503 0.013305049 0.026673873 2.08E-09 8.68122621 -0.195673526 T(ph)FPSQHAT(ph)LSAFAAVY(ph)VSLLK ddPTM_HeLa_Romidepsin_16h_R1 1 TFPSQHATLSAFAAVYVSLLK 21 0 H0YBY4 H0YBY4 LPPR3 3 0 T(0.843)FPS(0.219)QHAT(0.471)LS(0.472)AFAAVY(0.926)VS(0.07)LLK 44.382 0.0041853 0 1179.9 1431.4 1166.3 390.62 1192 1265 794.77 1468.9 1280.3 1119.8 TRUE FALSE FALSE 1165.518925 1451.551287 1186.598962 435.7853223 1131.167792 1184.170583 862.277744 1511.400304 1165.786761 1090.707435 1.068589878 1.330834687 1.087916819 0.399543735 1.037095518 1.085690392 0.790567403 1.385706429 1.068835441 1 10.09104846 T(ph)FSPTYGLLR ddPTM_HeLa_Romidepsin_16h_R1 1 TFSPTYGLLR 10 0 O15061;H0YL34;A0A075B7B1;O15061-2 O15061 SYNM Synemin 1 0 T(0.989)FS(0.008)PT(0.003)YGLLR 121.61 0.022442 25202000 1677.5 1073 2954.7 2246.8 3390.6 2476.1 1958.3 1164.2 1210.8 977.41 TRUE FALSE FALSE 1657.053985 1088.105722 3006.125314 2506.585588 3217.56503 2317.885201 2124.637953 1197.88429 1102.503015 952.0167473 1.740572306 1.142948089 3.157639109 2.632921737 3.379735744 2.434710532 2.231723296 1.258259683 1.15807103 1 9.894843143 -9.773900708 24.99963778 1.343978558 2.543821003 0.539878817 0.565334203 144.253008 289396.4781 0.097319321 0.128395831 1.68E-10 9.773900708 1.199842445 T(ph)FWSPELK ddPTM_HeLa_Romidepsin_16h_R1 1 TFWSPELK 8 0 X6RM00;G8JLD3;X6RLX0;Q8IUD2-5;Q8IUD2-4;Q8IUD2-2;Q8IUD2-3;Q8IUD2;K7EPP6;O15083 X6RM00 ERC1;ERC2 ELKS/Rab6-interacting/CAST family member 1;ERC protein 2 1 0 T(0.998)FWS(0.002)PELK 137.95 0.018842 70403000 3850.3 3967.8 4190.1 2157.7 3794.2 3987.4 3722.5 3533.5 4177.6 4404.5 TRUE FALSE FALSE 3803.371063 4023.658793 4263.026933 2407.183426 3600.567816 3732.618009 4038.689057 3635.736248 3803.944993 4290.070455 0.886552121 0.937900399 0.993696252 0.561105803 0.839279414 0.870059839 0.9414039 0.847477049 0.886685902 1 12.06678563 -11.38407891 0.465432007 1.005666502 0.841972713 0.075813219 0.113307276 1.334425076 0.618654244 0.095649562 0.038945527 4.13E-12 11.38407891 -0.163693789 T(ph)GAIVDVPVGEELLGR ddPTM_HeLa_Romidepsin_16h_R1 2 TGAIVDVPVGEELLGR 16 0 P25705-2;P25705;K7EK77;K7EQH4;K7EJP1;K7ERX7 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 1 0 T(1)GAIVDVPVGEELLGR;T(1)GAIVDVPVGEELLGR ; 123.63 7.31E-05 1009500 1447.73 1483.47 1305.8 1291.72 1786 1822.71 1588.7 1718.78 1758.53 1401.39 TRUE FALSE FALSE 1430.08451 1504.35433 1328.526901 1441.074744 1694.853756 1706.244714 1723.644138 1768.510188 1601.242672 1364.981686 1.047695017 1.102105871 0.97329284 1.055746578 1.241667762 1.250012899 1.262759901 1.295629242 1.173087294 1 10.41466588 -8.76554182 3.816740094 1.026391122 1.26576216 0.745412314 0.056922225 0.044328368 1.408825046 0.005229241 0.010344222 1.72E-09 8.76554182 0.239371038 T(ph)GKVEE ddPTM_HeLa_Romidepsin_16h_R1 1 TGKVEE 6 1 Q96KT7;P0C7Q5 Q96KT7 SLC35G5;SLC35G4 Solute carrier family 35 member G5;Putative solute carrier family 35 member G4 1 0 T(1)GKVEE 81.297 0.026806 8145000 219.7 0 185.38 0 0 0 0 136 170.37 150.16 TRUE FALSE FALSE 217.0222119 0 188.6064611 0 0 0 0 139.9349454 155.1316805 146.2588216 1.483823058 0 1.289539045 0 0 0 0 0.956762429 1.060665462 1 7.192379833 -9.808090539 1.204113142 1.213642662 0.194475618 0.346200503 0.481883221 0.28591273 0.827607225 0.088659567 0.130688778 1.56E-10 9.808090539 -1.019167044 T(ph)GRDTPENGETAIGAENSEK ddPTM_HeLa_Romidepsin_16h_R1 2 TGRDTPENGETAIGAENSEK 20 1 Q8N3X1-2;Q8N3X1 Q8N3X1-2 FNBP4 Formin-binding protein 4 1 0 T(0.587)GRDT(0.413)PENGETAIGAENSEK;T(0.725)GRDT(0.274)PENGET(0.002)AIGAENSEK ; 90.836 0.00086735 77436000 8695.5 7710.4 7924.9 5158.8 7187.3 7015.4 6381.7 6856.5 8530.2 9103.1 TRUE FALSE FALSE 8589.515901 7818.947214 8062.82956 5755.284729 6820.505261 6567.138581 6923.761439 7054.88201 7767.237548 8866.60015 0.968749662 0.881842767 0.909348502 0.649097132 0.769235687 0.740660284 0.780881208 0.795669354 0.876010806 1 13.1141653 -9.729695399 1.501364507 0.985498929 0.751895558 0.647142825 0.061368724 0.109206201 0.49887618 0.008495398 0.012669862 1.86E-10 9.729695399 -0.233603371 T(ph)GSESSQT(ph)GTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 2 0 T(0.993)GS(0.007)ES(0.312)S(0.194)QT(0.409)GT(0.068)S(0.013)T(0.004)TSSR 171.15 0.00020324 86722000 17726 17076 16609 10194 11694 10501 8715.7 9195.6 16460 16221 TRUE FALSE FALSE 17509.94869 17316.39638 16898.07268 11372.67824 11097.21154 9830.01999 9456.01134 9461.660178 14987.77638 15799.57608 1.108254336 1.09600386 1.069526966 0.719809075 0.702374006 0.622169857 0.598497788 0.598855319 0.948618893 1 13.94759823 -9.160333709 2.896636933 1.058942831 0.630893449 0.932823352 0.053399501 0.046995904 0.763838717 0.008444784 0.014677296 6.91E-10 9.160333709 -0.428049382 T(ph)GSESSQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 T(0.832)GS(0.167)ES(0.002)SQTGTSTTSSR;T(0.913)GS(0.086)ES(0.001)SQTGTSTTSSR ; 228.76 4.30E-35 3262570 422.588 454.58 328.34 291.7 345.63 505.07 377.87 245.199 365.36 581.55 TRUE FALSE FALSE 417.4373349 460.9795892 334.05462 325.4277265 327.9912114 472.797657 409.9662684 252.2934462 332.6812865 566.4412472 0.736947277 0.813817128 0.589742752 0.574512764 0.579038361 0.834680842 0.723757796 0.445400909 0.587318258 1 9.145782513 -11.82839846 0.356019994 1.086586981 0.620298568 0 0.166650716 1.137145581 0.243932502 0.211169017 0.051966617 1.48E-12 11.82839846 -0.466288413 T(ph)GSGQGPSSTGQPGR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSGQGPSSTGQPGR 15 0 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 T(0.779)GS(0.033)GQGPS(0.022)S(0.05)T(0.115)GQPGR 152.69 0.00097754 6162300 527.95 696.42 687.07 561.59 482.44 589.41 486.48 510.62 565.04 477.6 TRUE FALSE FALSE 521.5151423 706.224219 699.0281651 626.5236782 457.8192866 551.7486032 527.8015991 525.3939841 514.5014072 465.1918831 1.121075327 1.5181353 1.502666298 1.346806986 0.984151494 1.186066703 1.134589012 1.129413481 1.105998247 1 8.861682114 -10.4952764 9.666337623 1.053165963 1.25710374 0.222542835 0.15905413 0.391249167 130.2721798 0.030592813 0.033687712 3.20E-11 10.4952764 0.203937777 T(ph)GSGSPFAGNS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSGSPFAGNSPAR 14 0 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 2 0 T(0.529)GS(0.11)GS(0.361)PFAGNS(1)PAR 137.27 0.0052981 75955000 4874.1 5205.8 4878.4 3168.7 4210.3 4068.3 3658.8 4275.1 4822.5 5655.9 TRUE FALSE FALSE 4814.692594 5279.087389 4963.306506 3535.080003 3995.43268 3808.34876 3969.578381 4398.793274 4391.163522 5508.958903 0.873975043 0.958273148 0.900951812 0.641696565 0.725260934 0.691300993 0.720567797 0.798479958 0.797094986 1 12.42756398 -9.375361734 5.211091043 0.939582466 0.715557204 0.672311305 0.064849699 0.07809847 3.085414777 0.008970912 0.013798768 4.21E-10 9.375361734 -0.224025261 T(ph)GSGSPFAGNSPAR ddPTM_HeLa_Romidepsin_16h_R1 2 TGSGSPFAGNSPAR 14 0 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 0 T(0.779)GS(0.198)GS(0.017)PFAGNS(0.007)PAR;T(0.557)GS(0.147)GS(0.063)PFAGNS(0.233)PAR ; 154.13 0.0012681 115193000 6635.8 6550 6991.3 5559.9 6464.7 6233.9 5713.5 5322.6 7177.6 6487.8 TRUE FALSE FALSE 6554.920317 6642.211072 7112.980644 6202.761798 6134.782236 5835.573909 6198.804547 5476.601033 6535.617479 6319.246021 1.037294686 1.051108162 1.125605906 0.981566753 0.97080921 0.923460471 0.980940531 0.866654189 1.034240075 1 12.62553672 -8.725428131 2.323781443 1.028691222 0.931398156 0.590229495 0.043447324 0.192216413 2.114918523 0.006770499 0.014719695 1.88E-09 8.725428131 -0.097293066 T(ph)GSNISGASSDISLDEQYK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 T(0.401)GS(0.401)NIS(0.198)GASSDISLDEQYK 197.84 5.47E-20 0 1034.8 1048 996.76 580.6 964.54 1046.7 1191.8 1070.4 1019.6 1187.5 TRUE FALSE FALSE 1022.18746 1062.753772 1014.10819 647.7317038 915.3159246 979.8192481 1293.031462 1101.370335 928.4044224 1156.648579 0.883749376 0.918821664 0.876764307 0.560007349 0.791351791 0.847119225 1.117912118 0.952208264 0.802667672 1 10.17573489 -7.770606264 24.9677418 0.893511192 1.035060203 0.188214619 0.125758212 253.230943 689729.7082 0.019720578 0.060373406 1.70E-08 7.770606264 0.14154901 T(ph)GSPGPELLFHEGQQK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSPGPELLFHEGQQK 16 0 A6NHN7;A6NHB5;Q14202-2;Q14202;A6NL54;Q14202-3 A6NHN7 ZMYM3 Zinc finger MYM-type protein 3 1 0 T(0.5)GS(0.5)PGPELLFHEGQQK 123.42 0.0055161 5489700 1550.5 1746.1 1407.4 1285.4 1720.9 1668.3 1494.4 1560.7 1686.9 1594.3 TRUE FALSE FALSE 1531.60191 1770.681642 1431.895207 1434.023996 1633.076051 1561.701014 1621.334299 1605.856392 1536.019439 1552.879856 0.986297751 1.140256688 0.922090142 0.923461007 1.051643529 1.005680515 1.044082253 1.034115026 0.989142485 1 10.6007305 T(ph)GSPGSPGAGGVQSTAK ddPTM_HeLa_Romidepsin_16h_R1 2 TGSPGSPGAGGVQSTAK 17 0 J3KRZ2;O43237-2;O43237;J3KRI4 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 T(0.754)GS(0.12)PGS(0.126)PGAGGVQSTAK;T(0.961)GS(0.008)PGS(0.03)PGAGGVQSTAK ; 185.99 2.19E-09 23390100 2275.57 2430.21 2839.11 2348.86 3601.2 3034.1 2550.02 2837.5 3021.17 2629.42 TRUE FALSE FALSE 2247.834478 2464.42256 2888.523519 2620.446245 3417.417326 2840.230802 2766.618635 2919.598586 2750.948989 2561.107289 0.877680715 0.962248856 1.127841669 1.023169258 1.334351489 1.108985482 1.080243161 1.139975119 1.074124852 1 11.32255198 -9.7717762 4.047818153 0.941006605 1.13770897 0.400323976 0.090100216 0.121447923 4.469654025 0.013704983 0.018856209 1.69E-10 9.7717762 0.196702365 T(ph)GSYGALAEITASK ddPTM_HeLa_Romidepsin_16h_R1 2 TGSYGALAEITASK 14 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 T(1)GSYGALAEITASK;T(0.472)GS(0.472)YGALAEIT(0.055)AS(0.002)K ; 196.97 1.63E-11 234879000 8611.3 7107.9 8307.3 8037.7 8264.7 7797.2 5934.6 7100.8 7602.3 8021.2 TRUE FALSE FALSE 8506.342163 7207.965203 8451.885072 8967.056693 7842.921519 7298.984084 6438.684776 7306.250445 6922.331248 7812.808068 1.088768864 0.922583166 1.081798631 1.147737998 1.00385437 0.934233123 0.824119154 0.935163181 0.886023461 1 12.93162546 -8.209840353 2.930171162 1.043513009 0.880792438 0.311742466 0.079474923 0.154879607 2.624120392 0.009239656 0.026081103 6.17E-09 8.209840353 -0.162720571 T(ph)HS(ph)RMAIFELVSKQR ddPTM_HeLa_Romidepsin_16h_R1 1 THSRMAIFELVSKQR 15 2 Q9H5L6 Q9H5L6 THAP9 DNA transposase THAP9 2 0 T(1)HS(1)RMAIFELVSKQR 82.489 0.0012807 0 411.07 675.53 500.85 371.69 573.77 546.81 498.68 525.6 532.92 618.02 TRUE FALSE FALSE 406.0597207 685.0401291 509.5670842 414.6665467 544.4883759 511.8706057 541.0378668 540.8074067 485.2543005 601.9637513 0.674558426 1.138008938 0.846507922 0.68885634 0.904520205 0.8503346 0.898788117 0.89840527 0.806118806 1 9.233532804 -12.7615806 1.720514823 1.000198657 0.832527131 0 0.137146933 0.521511737 2.791008185 0.096880115 0.020691767 1.73E-13 12.7615806 -0.167671526 T(ph)IDDLEETLASAK ddPTM_HeLa_Romidepsin_16h_R1 2 TIDDLEETLASAK 13 0 Q5TCU3;P07951-3;P07951-2 Q5TCU3 TPM2 Tropomyosin beta chain 1 0 T(1)IDDLEETLASAK;T(1)IDDLEETLASAK ; 198.29 8.72E-16 5259600 2170.19 2542.66 2277.11 1204.44 1578.89 1782.22 1652.26 1618.39 2279 2108.37 TRUE FALSE FALSE 2143.73889 2578.455634 2316.742144 1343.70302 1498.313352 1668.341894 1792.602923 1665.215561 2075.160532 2053.594243 1.043896036 1.255581838 1.128140163 0.654317679 0.729605352 0.81240094 0.872909986 0.810878569 1.010501728 1 11.00393544 -9.267749014 24.9902963 1.049929013 0.780847435 0.742910806 0.090278707 243.9253414 966103.5674 0.015474424 0.023994506 5.40E-10 9.267749014 -0.269081577 T(ph)IDS(ph)WMS(ph)IMVPKR ddPTM_HeLa_Romidepsin_16h_R1 1 TIDSWMSIMVPKR 13 1 P07093-2;P07093;P07093-3 P07093-2 SERPINE2 Glia-derived nexin 3 0 T(1)IDS(1)WMS(1)IMVPKR 53.136 0.0042141 0 536.84 605.11 640.43 553.49 660.19 636.18 501.78 590.74 697.99 548.95 TRUE FALSE FALSE 530.2967876 613.6287545 651.5764155 617.487118 626.4980408 595.5301512 544.4011807 607.8321299 635.5600263 534.6881999 0.991786966 1.147638483 1.218610053 1.154854583 1.171707251 1.113789591 1.018165691 1.136797352 1.188655419 1 9.062554028 -10.26300687 24.83432424 0.99612162 1.136992932 0.00369624 0.077498547 60.82719675 963707.4917 0.008715237 0.010250572 5.46E-11 10.26300687 0.140871312 T(ph)IGFFYT(ph)LFLHCLVFLVLYK ddPTM_HeLa_Romidepsin_16h_R1 1 TIGFFYTLFLHCLVFLVLYK 20 0 P39880-9;Q13948-9;Q13948-10;Q13948-2;Q13948 P39880-9 CUX1 Protein CASP 2 0 T(0.857)IGFFY(0.16)T(0.982)LFLHCLVFLVLYK 51.503 0.0040368 0 376.01 424.29 353.24 278.33 306.24 380.52 356.49 290.77 421.38 397.7 TRUE FALSE FALSE 371.4270455 430.2631658 359.387994 310.5118242 290.6114301 356.2060001 386.7702517 299.1829712 383.6907174 387.3676967 0.958848785 1.110735793 0.927769654 0.801594523 0.750221127 0.919555252 0.99845768 0.772348788 0.99050778 1 8.59755984 -9.520778168 24.97255592 0.991190263 0.856206509 0.49254367 0.078045582 61.96568068 736676.7481 0.012357972 0.017638592 3.01E-10 9.520778168 -0.134983753 T(ph)ISDGTISASK ddPTM_HeLa_Romidepsin_16h_R1 2 TISDGTISASK 11 0 A0A075B6Q2;S4R347;Q5T0N5-3;Q5T0N5-4;Q5T0N5-2;Q5T0N5-5;Q5T0N5 A0A075B6Q2 FNBP1L Formin-binding protein 1-like 1 0 T(0.964)IS(0.036)DGTISASK;T(0.979)IS(0.016)DGT(0.005)ISASK ; 210.95 8.48E-19 115595000 10704 10819 10913 11245.9 12794.3 11415.4 10031.3 11468 11088.9 9620.1 TRUE FALSE FALSE 10573.53553 10971.31017 11102.93619 12546.20387 12141.35913 10685.99278 10883.35837 11799.80849 10097.08101 9370.168415 1.128425345 1.170876518 1.184923866 1.338951801 1.295746095 1.140426971 1.161490156 1.25929524 1.077577325 1 13.19385926 -10.89086191 0.63936281 1.014362852 1.232093422 0.592099583 0.061371654 0.296443863 0.275456534 0.025090727 0.018427638 1.29E-11 10.89086191 0.217730569 T(ph)ITVPVSGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TITVPVSGSPK 11 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 T(0.945)IT(0.001)VPVS(0.019)GS(0.035)PK 139.31 0.0067847 24386000 7289.4 6576 6568.1 6164.7 6368.8 6843.4 5271 6385.6 6691.6 5968.6 TRUE FALSE FALSE 7200.553989 6668.577101 6682.415025 6877.49162 6043.776371 6406.128826 5718.718608 6570.357261 6093.086537 5813.534912 1.238584458 1.147077845 1.14945814 1.18301373 1.039604382 1.101933492 0.983690422 1.130182817 1.048086341 1 12.50519994 -8.739539996 24.9921328 1.125618871 1.060846938 0.158092345 0.071955224 471.2007191 537743.6484 0.01399209 0.027965857 1.82E-09 8.739539996 -0.064771933 T(ph)IWTPPWS(ph)Y(ph)RLSPHPS(ph)SLKK ddPTM_HeLa_Romidepsin_16h_R1 1 TIWTPPWSYRLSPHPSSLKK 20 2 J3QR11 J3QR11 IRX3 4 0 T(0.861)IWT(0.388)PPWS(0.865)Y(0.851)RLS(0.055)PHPS(0.49)S(0.49)LKK 40.844 0.004316 0 542.38 542.11 562 860.59 748.29 639.01 596.89 714.12 758.56 732.83 TRUE FALSE FALSE 535.7692639 549.7418388 571.7813743 960.095465 710.101969 598.1793233 647.5898217 734.7819355 690.7124938 713.790971 0.750596863 0.770172027 0.801048763 1.345065298 0.994831818 0.838031507 0.907254151 1.029407719 0.967667737 1 9.479357842 T(ph)KFS(ph)S(ph)PVDMLS(ph)ILLAK ddPTM_HeLa_Romidepsin_16h_R1 1 TKFSSPVDMLSILLAK 16 1 A0A087X1N7;P20929-4;P20929;P20929-3;P20929-2 A0A087X1N7 NEB Nebulin 4 0 T(1)KFS(1)S(1)PVDMLS(1)ILLAK 71.531 0.0022445 0 1764 1938.6 1686 1978.1 1349.9 1120.2 869.16 909.78 1921.5 2122.1 TRUE FALSE FALSE 1742.499689 1965.891662 1715.344123 2206.817229 1281.009566 1048.622835 942.9864287 936.1030489 1749.636228 2066.967536 0.843022282 0.951099438 0.829884404 1.067659356 0.619753113 0.507324289 0.456217339 0.452887156 0.846474943 1 11.01330001 -8.590190608 4.38438692 0.926702412 0.481564459 0.889416338 0.072710135 0.050914583 1.931919909 0.011492773 0.023888347 2.57E-09 8.590190608 -0.445137953 T(ph)KSPTDDEVTPSAVVR ddPTM_HeLa_Romidepsin_16h_R1 2 TKSPTDDEVTPSAVVR 16 1 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 T(0.984)KS(0.015)PTDDEVTPSAVVR;T(0.996)KS(0.003)PTDDEVTPSAVVR ; 80.596 0.013201 86331000 3189.8 3399 3325 3532.3 3128.2 2886.8 2449.4 2640 4011.4 3622.2 TRUE FALSE FALSE 3150.921491 3446.851211 3382.87023 3940.721146 2968.556281 2702.342797 2657.451975 2716.384235 3652.610337 3528.094722 0.893094358 0.976972412 0.958837701 1.116954463 0.841404927 0.765949616 0.753225802 0.769929508 1.035292594 1 11.78467358 -8.531822274 24.99357845 0.962563244 0.768991242 0.750155807 0.059861363 84.13034457 235110.1702 0.00915775 0.018335956 2.94E-09 8.531822274 -0.193572002 T(ph)KSSDDLLAGMAGGVTVTNGVK ddPTM_HeLa_Romidepsin_16h_R1 2 TKSSDDLLAGMAGGVTVTNGVK 22 1 F8WAN1;Q69YQ0-2;Q69YQ0;C9J8U1 F8WAN1 SPECC1L-ADORA2A;SPECC1L Cytospin-A 1 0 T(0.333)KS(0.333)S(0.333)DDLLAGMAGGVTVTNGVK;T(0.333)KS(0.333)S(0.333)DDLLAGMAGGVTVTNGVK ; 118.57 4.01E-05 101409000 6366 6354.2 6654.4 6761.9 5601.1 6086.2 6537.4 6680.8 6712.7 6449.1 TRUE FALSE FALSE 6288.408743 6443.654594 6770.217041 7543.742694 5315.254966 5697.311462 7092.686593 6874.098407 6112.2993 6281.551452 1.001091656 1.025806227 1.077793773 1.200936226 0.846169136 0.906991132 1.129129746 1.094331306 0.973055677 1 12.61690521 T(ph)LDELSQGTTTVK ddPTM_HeLa_Romidepsin_16h_R1 2 TLDELSQGTTTVK 13 0 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 1 0 T(0.996)LDELS(0.003)QGTTTVK;T(1)LDELSQGTTTVK ; 149.32 0.0015852 7407600 1577.99 1415.41 1306.29 1720.44 1573.54 1840.27 1619.71 1751.72 1586.02 1371.53 TRUE FALSE FALSE 1558.756851 1435.336179 1329.025429 1919.365368 1493.236382 1722.682686 1757.288127 1802.403254 1444.162399 1335.897453 1.166823732 1.074435898 0.994855875 1.436761006 1.1177777 1.289532129 1.315436393 1.349207793 1.081042857 1 10.38359355 -4.000000001 0.117828162 0.929244274 2.281566481 0.483341437 0.105760005 56.42942611 0.459222254 0.481271803 12.54918237 1.00E-04 4.000000001 1.352322207 T(ph)LDPLVNTSSLIMR ddPTM_HeLa_Romidepsin_16h_R1 1 TLDPLVNTSSLIMR 14 0 J3KNS1;Q9UPW5 J3KNS1 AGTPBP1 Cytosolic carboxypeptidase 1 1 0 T(0.554)LDPLVNT(0.36)S(0.084)S(0.002)LIMR 98.04 0.029193 1751600 547.17 549.92 380.16 363.15 418.7 440.15 389.83 401 395.28 375.68 TRUE FALSE FALSE 540.5008816 557.6617882 386.7765253 405.1391117 397.3321766 412.0258355 422.9421505 412.6023023 359.9251668 365.9197794 1.477102119 1.524000121 1.056998137 1.107180137 1.085845037 1.126000448 1.155832984 1.127575839 0.983617686 1 8.515383591 T(ph)LGTPTQPGSTPR ddPTM_HeLa_Romidepsin_16h_R1 2 TLGTPTQPGSTPR 13 0 Q8NFH5-2;Q8NFH5;Q8NFH5-3 Q8NFH5-2 NUP35 Nucleoporin NUP53 1 0 T(0.669)LGT(0.303)PT(0.017)QPGS(0.005)T(0.005)PR;T(0.657)LGT(0.283)PT(0.06)QPGS(0.001)TPR ; 123.95 0.0082676 80980000 7565.9 7043.3 6556.3 6331.4 7310.4 6833.1 6496.5 6461.5 7028.7 7071.8 TRUE FALSE FALSE 7473.683901 7142.455762 6670.409651 7063.466258 6937.323009 6396.486963 7048.312548 6648.453308 6400.035468 6888.073617 1.085018006 1.036930811 0.968399878 1.025463236 1.007149952 0.928632201 1.023263243 0.96521229 0.929147368 1 12.74988485 -9.814188249 8.560516173 1.041103621 0.988160032 0 0.048592205 0.275911269 40.96194247 0.006514542 0.008585299 1.53E-10 9.814188249 -0.052943589 T(ph)LRDSPNVEAAHLAR ddPTM_HeLa_Romidepsin_16h_R1 1 TLRDSPNVEAAHLAR 15 1 Q9UHF7;Q9UHF7-3;Q9UHF7-2;E5RFF3;H0YC29;E5RJ97 Q9UHF7 TRPS1 Zinc finger transcription factor Trps1 1 0 T(0.765)LRDS(0.235)PNVEAAHLAR 94.639 0.0031518 4501700 1236.6 1425 1250.3 1596.7 706.13 760.17 634.12 641.25 1437.4 1342.7 TRUE FALSE FALSE 1221.527844 1445.061187 1272.060947 1781.317967 670.0935512 711.5975903 687.982137 659.803557 1308.835344 1307.81646 0.934020851 1.104941887 0.972660144 1.362055014 0.512375835 0.544111205 0.526054043 0.504507763 1.000779072 1 10.35294437 -8.729856645 24.99979585 1.004353095 0.52366469 0.824544929 0.120403441 65.05558265 51495.47819 0.017202783 0.034403106 1.86E-09 8.729856645 -0.480688405 T(ph)LSDPPSPLPHGPPNK ddPTM_HeLa_Romidepsin_16h_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 0 T(0.467)LS(0.467)DPPS(0.066)PLPHGPPNK 81.643 0.017125 4103900 3182 2335 2396.2 2642.9 4257.9 4221.8 4386.4 3448.7 3766.2 3133.6 TRUE FALSE FALSE 3143.21656 2367.872191 2437.904856 2948.484533 4040.603475 3952.040605 4758.980707 3548.482693 3429.341639 3052.18862 1.029823825 0.775794843 0.798739907 0.966023041 1.323838064 1.294821879 1.55920269 1.162602688 1.123568058 1 11.57562841 -8.745922576 6.241830729 0.973286943 1.350649136 0.664738284 0.13355414 0.074465753 10.53174247 0.019066968 0.037286639 1.80E-09 8.745922576 0.377362193 T(ph)LSFDTSK ddPTM_HeLa_Romidepsin_16h_R1 2 TLSFDTSK 8 0 Q7L804;Q7L804-2 Q7L804 RAB11FIP2 Rab11 family-interacting protein 2 1 0 T(0.994)LS(0.006)FDTSK;T(0.999)LS(0.001)FDTSK ; 132.01 0.020209 89599000 11809.5 13594 12007.9 13154.9 14577.5 13462.2 10617.8 12904.9 14007.2 13072.6 TRUE FALSE FALSE 11665.56127 13785.37669 12216.89246 14675.93143 13833.55578 12602.00887 11519.67567 13278.28292 12754.36095 12732.97197 0.916169556 1.082651931 0.959469046 1.15259277 1.086435737 0.989714648 0.904712246 1.042826683 1.001679811 1 13.63628157 -10.266381 24.9332434 0.960413402 1.02877437 0.121238171 0.069788198 559.3968349 2822467.911 0.012479288 0.014511023 5.42E-11 10.266381 0.068360967 T(ph)LSPTPS(ph)AEGYQDVR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSPTPSAEGYQDVR 15 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 2 0 T(1)LSPT(0.001)PS(0.999)AEGYQDVR;T(0.597)LS(0.403)PT(0.483)PS(0.517)AEGYQDVR ; 231.21 1.42E-36 52726000 4031.1 4444 4059.4 3349.9 4697.8 3967.6 3103.6 3531 4227 4360.7 TRUE FALSE FALSE 3981.967403 4506.562749 4130.052154 3737.2312 4458.053736 3714.083165 3367.219707 3633.163914 3848.926533 4247.408385 0.937505189 1.061014704 0.972369921 0.879885064 1.049593854 0.874435144 0.792770415 0.855383703 0.906182355 1 12.05236711 -8.053187164 5.888394315 0.974418195 0.825702244 0.552032738 0.055475518 0.097131153 7.672209049 0.007080961 0.018810327 8.85E-09 8.053187164 -0.148715952 T(ph)LSPTPSAEGYQDVR ddPTM_HeLa_Romidepsin_16h_R1 3 TLSPTPSAEGYQDVR 15 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 T(0.988)LS(0.012)PTPSAEGYQDVR;T(0.997)LS(0.003)PTPSAEGYQDVR;T(0.648)LS(0.11)PT(0.071)PS(0.171)AEGYQDVR ;; 263.15 4.09E-71 670840000 7795.2 7343.1 6645.1 6074.2 8276.1 7993.2 6817.9 7180.2 7349.7 6540.1 TRUE FALSE FALSE 7700.189104 7446.476355 6760.755178 6776.527584 7853.739735 7482.460317 7397.012256 7387.947759 6692.324424 6370.187259 1.208785361 1.168957215 1.061311843 1.063787815 1.232889932 1.174606022 1.161192278 1.159769322 1.050569497 1 12.63712007 -12.42457039 1.095640543 0.997976768 1.156846884 0.470948067 0.053666347 0.333727389 0.701938573 0.041434357 0.009904953 3.76E-13 12.42457039 0.158870117 T(ph)LSSSAQEDIIR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSSSAQEDIIR 12 0 Q9H788;Q9H788-2 Q9H788 SH2D4A SH2 domain-containing protein 4A 1 0 T(0.932)LS(0.023)S(0.023)S(0.023)AQEDIIR;T(0.756)LS(0.112)S(0.112)S(0.021)AQEDIIR ; 198.29 2.74E-14 144912000 11477.7 14186.2 8297.2 6642.8 8409.4 8090.3 7614.2 9965.7 12306.3 11283.5 TRUE FALSE FALSE 11337.80538 14385.9137 8441.609285 7410.871791 7980.236938 7573.35594 8260.949958 10254.04181 11205.59371 10990.35304 1.031614301 1.308958287 0.76809264 0.674306982 0.726112883 0.689091234 0.751654649 0.933003859 1.019584509 1 13.42395011 -9.568359605 24.13675413 1.037452281 0.746588329 0.681348533 0.109177697 41.81666472 22191.94283 0.016914544 0.023920786 2.70E-10 9.568359605 -0.290863952 T(ph)LT(ph)RTSQET(ph)ADVK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTRTSQETADVK 13 1 H3BNN5;H3BV11;H3BRI8;H3BM93;H3BVG0;Q8N1F7 H3BNN5 NUP93 Nuclear pore complex protein Nup93 3 0 T(0.997)LT(0.44)RT(0.309)S(0.316)QET(0.939)ADVK 61.398 0.02682 10775000 765.37 885.76 908.72 329.95 919.76 789.36 1044.4 935.36 1262.8 1117.9 TRUE FALSE FALSE 756.041376 898.2297525 924.5358904 368.1003715 872.8212151 738.9224435 1133.11131 962.4231658 1149.852005 1088.856797 0.694344177 0.824929187 0.849088597 0.338061325 0.801594128 0.678622245 1.040643098 0.88388406 1.056017659 1 10.08859851 -12.37412189 0.994075121 1.006156497 0.757119062 0.26322944 0.173805937 0.738363838 1.252924248 0.135386453 0.031637566 4.23E-13 12.37412189 -0.249037435 T(ph)LTPPLRR ddPTM_HeLa_Romidepsin_16h_R1 1 TLTPPLRR 8 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 T(0.982)LT(0.018)PPLRR 75.738 0.028659 63365000 2635.5 2797.8 2419.4 2956.7 2865.4 2721.9 2713 2419.5 2857.4 2623.5 TRUE FALSE FALSE 2603.377512 2837.187502 2461.508642 3298.567566 2719.167946 2547.979375 2943.442152 2489.504415 2601.826988 2555.341092 1.018798438 1.110296982 0.963279873 1.290852159 1.064111541 0.997119086 1.151878378 0.97423566 1.01819166 1 11.31930016 -10.36783893 1.561165748 1.005867029 1.083881147 0.091234916 0.091425716 0.548596617 2.569529613 0.016713252 0.019013365 4.29E-11 10.36783893 0.078014119 T(ph)MDPGY(ph)PKPIT(ph)VWK ddPTM_HeLa_Romidepsin_16h_R1 1 TMDPGYPKPITVWK 14 1 P51512 P51512 MMP16 Matrix metalloproteinase-16 3 0 T(1)MDPGY(1)PKPIT(1)VWK 53.947 0.026887 12380000 5566.5 5884.2 5678.9 2769 4991.4 4897.5 4077 4958.9 5672.5 6289.1 TRUE FALSE FALSE 5498.653357 5967.037922 5777.738872 3089.164809 4736.670233 4584.565556 4423.300278 5102.377948 5165.137393 6125.708275 0.897635524 0.974097631 0.943195238 0.504295123 0.7732445 0.748413955 0.722087974 0.832944978 0.843190234 1 12.58066095 -9.417222064 13.13185106 0.952309178 0.721503666 0.585303422 0.089803103 0.423553039 51.08013206 0.012690649 0.019385517 3.83E-10 9.417222064 -0.230805511 T(ph)MT(ph)TMPESLNS(ph)PVSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TMTTMPESLNSPVSGK 16 0 J3KP55;F8VXJ2;P56177-2;P56177 J3KP55 DLX1 Homeobox protein DLX-1 3 0 T(0.858)MT(0.562)T(0.571)MPES(0.019)LNS(0.945)PVS(0.046)GK 57.164 0.0040276 0 286.86 323.47 379.89 413.79 221.14 267.17 290.02 353.1 338.06 399.83 TRUE FALSE FALSE 283.36364 328.0238192 386.5018261 461.6343467 209.8544006 250.0986993 314.6542916 363.3163914 307.8230669 389.442359 0.727613814 0.842291065 0.992449376 1.185372716 0.538858693 0.642196961 0.807961138 0.932914417 0.790420096 1 8.605266002 -8.737595851 24.99999865 0.895669462 0.729710997 0.262096621 0.154222856 323.4278283 339113.3203 0.025100598 0.050179524 1.83E-09 8.737595851 -0.165958465 T(ph)NNNQILEVKSPIK ddPTM_HeLa_Romidepsin_16h_R1 1 TNNNQILEVKSPIK 14 1 P42568-2;P42568;A0A0D9SF09;B1APT5 P42568-2 MLLT3 Protein AF-9 1 0 T(0.735)NNNQILEVKS(0.265)PIK 79.089 0.020516 75103000 4410.7 4109.9 4238.5 3719.7 3010.4 2970.4 2749 2684.5 4481.2 4765.9 TRUE FALSE FALSE 4356.940692 4167.75928 4312.269315 4149.789216 2856.768055 2780.601027 2982.499991 2762.171772 4080.390249 4642.081231 0.938574849 0.897821273 0.928951714 0.893950151 0.615406735 0.598998787 0.642491986 0.595028746 0.879000182 1 12.18055605 -8.823253877 3.412099777 0.959431401 0.610361252 0.93695988 0.039038925 0.036629449 0.862679283 0.005865988 0.011429616 1.50E-09 8.823253877 -0.349070149 T(ph)PASTPVSGTPQAS(ph)PMIER ddPTM_HeLa_Romidepsin_16h_R1 1 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 0 T(0.897)PAS(0.043)T(0.059)PVSGT(0.001)PQAS(0.999)PMIER 144.3 0.00010906 35479000 2023.8 1470.5 1895.2 1515.9 1819.5 1526.6 1220.3 1753.5 1634.7 1528.7 TRUE FALSE FALSE 1999.133147 1491.201738 1928.185161 1691.175491 1726.644126 1429.055187 1323.952252 1804.234756 1488.488338 1488.984154 1.342615462 1.001489327 1.294966878 1.135791463 1.159612157 0.959751777 0.889164769 1.211721932 0.999667011 1 10.54011268 -8.274269301 22.22205369 1.161055893 1.007108034 0.101291813 0.136749169 223.73883 387528.3263 0.0216556 0.048815134 5.32E-09 8.274269301 -0.153947859 T(ph)PDSTFSETFK ddPTM_HeLa_Romidepsin_16h_R1 2 TPDSTFSETFK 11 0 B7Z1S6;Q9NZI5-3;Q9NZI5 B7Z1S6 GRHL1 Grainyhead-like protein 1 homolog 1 0 T(1)PDSTFSETFK;T(1)PDSTFSETFK ; 111.94 0.028244 10824600 376.19 481.52 552 779.88 2438.97 2763.6 1817.84 2266 760.44 673.61 TRUE FALSE FALSE 371.6048516 488.2988512 561.6073284 870.053395 2314.50026 2587.014879 1972.247284 2331.563135 692.4243418 656.1095151 0.566376257 0.74423376 0.855965834 1.326079526 3.527612703 3.94296199 3.00597269 3.553618841 1.055348727 1 9.357792833 -8.825622846 3.780217618 0.799790711 3.522109091 0.961423571 0.254606724 0.03068515 0.879139495 0.040495278 0.07782909 1.49E-09 8.825622846 2.72231838 up T(ph)PEDGDYSYEIIEK ddPTM_HeLa_Romidepsin_16h_R1 1 TPEDGDYSYEIIEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(1)PEDGDYSYEIIEK 165.78 0.00020082 7499500 2212.7 2296.6 2428 1138.8 2314.1 2695.9 2335.8 2492.7 2633.3 2817.4 TRUE FALSE FALSE 2185.730761 2328.931595 2470.258322 1270.473414 2196.002842 2523.640691 2534.202794 2564.822342 2397.771053 2744.203542 0.79649003 0.848673052 0.900173141 0.462966174 0.800233222 0.919625914 0.923474792 0.934632691 0.873758457 1 11.42217178 -12.25021365 0.844904531 1.007076414 0.818932934 0.07092916 0.135619438 0.894837219 1.079031752 0.110558804 0.026212533 5.62E-13 12.25021365 -0.18814348 T(ph)PEEGGYSYDISEK ddPTM_HeLa_Romidepsin_16h_R1 2 TPEEGGYSYDISEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(1)PEEGGYSYDISEK;T(1)PEEGGYSYDISEK ; 195.87 3.02E-11 149084000 5442.7 4478.8 4982.8 2819.93 4318.3 4644.7 4077.2 4304.7 4317.5 4684.6 TRUE FALSE FALSE 5376.362279 4541.852664 5069.523544 3145.983575 4097.921037 4347.91866 4423.517266 4429.249703 3931.331987 4562.893417 1.178279172 0.995388726 1.111032645 0.689471195 0.898097033 0.952886308 0.969454437 0.970710753 0.861587512 1 12.15573324 T(ph)PEGISEEQR ddPTM_HeLa_Romidepsin_16h_R1 2 TPEGISEEQR 10 0 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;A0A1W2PQ63;E9PGF6 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 T(1)PEGISEEQR;T(1)PEGISEEQR ; 122.69 0.021506 11316700 1270.94 1338.88 1252.57 1043.91 1322.19 1113.62 1157.1 1142.5 1522.77 1621.73 TRUE FALSE FALSE 1255.449294 1357.728788 1274.370455 1164.611786 1254.713711 1042.463276 1255.384045 1175.556435 1386.569637 1579.597221 0.794790772 0.859541135 0.806769244 0.737284018 0.794325094 0.659955122 0.794749464 0.744212777 0.877799492 1 10.62534102 -14.88433173 0.186186482 1.523591335 0.711470036 0.560956527 0.057728972 8.477941492 0.171337837 1.740715743 0.058718683 1.31E-15 14.88433173 -0.812121299 T(ph)PELPEPSVK ddPTM_HeLa_Romidepsin_16h_R1 2 TPELPEPSVK 10 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 T(1)PELPEPSVK;T(1)PELPEPSVK ; 154.15 0.0071627 194537000 12164.5 11789.4 10204.5 9400.5 11115.3 11198.3 9938.8 11141.2 11705.5 11051.7 TRUE FALSE FALSE 12016.2344 11955.37148 10382.10504 10487.43004 10548.04476 10482.76477 10783.00142 11463.55304 10658.53076 10764.57524 1.116275759 1.110621758 0.96446955 0.974253959 0.979884903 0.973820568 1.001711743 1.064933152 0.990148754 1 13.39400377 -9.749332643 24.99862576 1.060620726 0.991222398 0.292456061 0.046061997 224.5501754 463661.7721 0.00849274 0.011959596 1.78E-10 9.749332643 -0.069398327 T(ph)PENLITEIR ddPTM_HeLa_Romidepsin_16h_R1 2 TPENLITEIR 10 0 Q5VY60;Q7Z4H7-3;Q7Z4H7;Q5SYF9 Q5VY60 HAUS6 HAUS augmin-like complex subunit 6 1 0 T(1)PENLITEIR;T(1)PENLITEIR ; 169.09 0.0021812 22711000 557.76 622.61 792.34 467.66 758.09 901.95 881.55 919.17 684.08 640.53 TRUE FALSE FALSE 550.9618066 631.3751199 806.1303453 521.7330496 719.4018385 844.3183059 956.428835 945.7647337 622.8941715 623.8889383 0.883108792 1.011999222 1.292105527 0.836259497 1.153092793 1.353315076 1.533011368 1.51591842 0.998405539 1 9.28514542 -8.235417473 1.661720385 0.969370303 1.536096625 0.753093251 0.119227091 0.133448172 0.691528979 0.018291569 0.06572543 5.82E-09 8.235417473 0.566726322 T(ph)PETLLPFAEAEAFLKK ddPTM_HeLa_Romidepsin_16h_R1 1 TPETLLPFAEAEAFLKK 17 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 1 0 T(0.993)PET(0.007)LLPFAEAEAFLKK 134.83 0.00063152 9056400 495.67 625.45 599.8 308.2 504.87 487.58 604.54 624.79 568.88 626.65 TRUE FALSE FALSE 489.6285834 634.2551015 610.2392674 343.8355341 479.1046 456.4252116 655.8896125 642.8673129 517.997948 610.3695427 0.80218384 1.039132947 0.999786563 0.563323544 0.784941853 0.747785038 1.074577885 1.053242778 0.848662838 1 9.253539164 -12.55956783 1.288564985 1.001053071 0.870240271 0 0.162115995 1.022968114 3.003515241 0.118675781 0.027020647 2.76E-13 12.55956783 -0.1308128 T(ph)PFNTDLGENSGIGK ddPTM_HeLa_Romidepsin_16h_R1 1 TPFNTDLGENSGIGK 15 0 Q6P0N0 Q6P0N0 MIS18BP1 Mis18-binding protein 1 1 0 T(0.71)PFNT(0.28)DLGENS(0.01)GIGK 91.701 0.030202 8265500 2290.9 2011 2576.5 2046.7 1891.9 1686.2 1248.9 1223.1 2711.6 2524.7 TRUE FALSE FALSE 2262.97763 2039.310911 2621.342902 2283.349084 1795.349283 1578.457262 1354.981535 1258.488469 2469.067705 2459.10793 0.920243313 0.8292889 1.065973099 0.928527397 0.730081531 0.641882059 0.551005313 0.51176626 1.004050158 1 11.26391934 -8.451404461 1.526594803 0.959102992 0.536303695 0.889088081 0.062822545 0.094885984 0.42605914 0.009869232 0.030630028 3.54E-09 8.451404461 -0.422799297 T(ph)PGTPGTPSYPR ddPTM_HeLa_Romidepsin_16h_R1 1 TPGTPGTPSYPR 12 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 T(0.999)PGTPGTPSYPR 110.64 0.021529 63793000 1081.6 720.45 894.64 747.07 1146.4 738.9 887.29 989.39 1094 861.59 TRUE FALSE FALSE 1068.417043 730.592514 910.2108339 833.4497485 1087.89493 691.6866747 962.6563905 1018.016439 996.1499 839.2057676 1.273128813 0.870576135 1.084609841 0.993141111 1.29633872 0.824215826 1.147104116 1.213071309 1.187015078 1 9.712880783 -10.29344822 24.9771006 1.128977467 1.062791433 0.066630331 0.149737255 2000.656155 1561142.278 0.02727774 0.031195085 5.09E-11 10.29344822 -0.066186034 T(ph)PKEEAQSLEDLAGFK ddPTM_HeLa_Romidepsin_16h_R1 1 TPKEEAQSLEDLAGFK 16 1 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 T(0.998)PKEEAQS(0.002)LEDLAGFK 72.359 0.0038775 0 1292.5 1166.2 1162.4 1013.6 873.05 1068.3 918.57 974.01 1511.6 1284 TRUE FALSE FALSE 1276.746513 1182.617794 1182.631084 1130.797201 828.4950007 1000.039078 996.5933129 1002.191443 1376.39871 1250.641495 1.020873302 0.945608953 0.945619579 0.904173743 0.662456031 0.7996209 0.796865702 0.801341909 1.100554168 1 10.28845257 -9.166115294 1.931376668 1.003855616 0.770922907 0.787237335 0.057580561 0.095317587 0.695043921 0.007561715 0.01386096 6.82E-10 9.166115294 -0.232932709 T(ph)PLCNLLVK ddPTM_HeLa_Romidepsin_16h_R1 1 TPLCNLLVK 9 0 H7C3M5;A0A1B0GW05;Q2PZI1-2;Q2PZI1 H7C3M5 DPY19L1 Probable C-mannosyltransferase DPY19L1 1 0 T(1)PLCNLLVK 135.77 0.014012 258180000 3915 2730.1 3686.3 3007.5 3910.9 3653.3 2842.8 2785.7 3437.9 2813.4 TRUE FALSE FALSE 3867.282474 2768.534419 3750.458505 3355.241301 3711.312179 3419.86592 3084.267361 2866.299834 3130.405614 2740.307462 1.4112586 1.010300653 1.368626899 1.224403227 1.354341522 1.247986209 1.125518725 1.045977458 1.142355614 1 11.42012206 -4.079197317 20.97129058 1.201020252 0.006031143 0 0.144400666 0 0 0.022938822 0 8.33E-05 4.079197317 -1.194989109 T(ph)PLGASLDEQSSSTLK ddPTM_HeLa_Romidepsin_16h_R1 1 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 T(1)PLGASLDEQSSSTLK 214.82 1.04E-25 20241000 1953.6 2301.7 1869.7 2098.5 1478.9 2398.2 2126.3 1998.6 2755.1 2178.6 TRUE FALSE FALSE 1929.788772 2334.103393 1902.241344 2341.138444 1403.426214 2244.96276 2306.907869 2056.426338 2508.676956 2121.999658 0.909419926 1.099954651 0.896438101 1.103269944 0.66136967 1.057946806 1.087138662 0.969098336 1.182223073 1 11.05120871 T(ph)PMYGSQTPLQDGSR ddPTM_HeLa_Romidepsin_16h_R1 2 TPMYGSQTPLQDGSR 15 0 O00267-2;O00267 O00267-2 SUPT5H Transcription elongation factor SPT5 1 0 T(0.987)PMY(0.001)GS(0.007)QT(0.006)PLQDGSR;T(0.676)PMY(0.037)GS(0.071)QT(0.216)PLQDGS(0.001)R ; 105.2 0.015011 20396300 1740.49 1739.38 1353.26 1418.42 1803.51 1874.98 1376.41 1482.61 1479.23 1487.05 TRUE FALSE FALSE 1719.276238 1763.867037 1376.812923 1582.424394 1711.470155 1755.174829 1493.322231 1525.506981 1346.923964 1448.416227 1.187004265 1.217790166 0.950564415 1.092520482 1.181614872 1.211788985 1.031003522 1.053224172 0.9299288 1 10.50026053 -12.53568232 1.323418923 1.000591676 1.124084948 0.302616917 0.086290741 0.541130077 1.710333997 0.058986456 0.014355002 2.91E-13 12.53568232 0.123493272 T(ph)PPAPSPFDLPELK ddPTM_HeLa_Romidepsin_16h_R1 1 TPPAPSPFDLPELK 14 0 O95239 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 T(1)PPAPSPFDLPELK 135.86 0.0029418 5129600 2519 2430.5 2346.6 1485.2 2316.5 2318 1887.7 2062.2 2682.2 2450.6 TRUE FALSE FALSE 2488.297459 2464.716643 2387.441589 1656.925812 2198.280361 2169.887281 2048.041191 2121.866503 2442.297314 2386.933059 1.042466378 1.03258725 1.000213047 0.694165178 0.920964395 0.909069181 0.858022048 0.888950989 1.023194725 1 11.22094239 -9.489827455 24.90736265 1.021308506 0.859797434 0.65943943 0.059572396 280.1736425 211138.3965 0.008738496 0.013342116 3.24E-10 9.489827455 -0.161511072 T(ph)PPMMPGS(ph)QR ddPTM_HeLa_Romidepsin_16h_R1 1 TPPMMPGSQR 10 0 Q96RT1-7;Q96RT1-6;Q96RT1-4;Q96RT1-5;Q96RT1-3;Q96RT1-9;Q96RT1-2;Q96RT1;Q96RT1-8;H0YA04 Q96RT1-7 ERBB2IP Protein LAP2 2 0 T(1)PPMMPGS(1)QR 57.55 0.024672 2170000 416.88 449.61 471.18 760.48 484 378.93 379.53 464.84 651.16 749.37 TRUE FALSE FALSE 411.7989062 455.9396214 479.3806902 848.4102758 459.2996739 354.7175959 411.7672687 478.289412 592.9186187 729.9012594 0.564184403 0.624659316 0.656774713 1.16236308 0.62926275 0.485980249 0.564141058 0.655279609 0.812327162 1 9.5115575 -12.39399954 1.061062294 1.00453419 0.663342107 0.189280489 0.182595112 0.517739304 1.020679745 0.134521313 0.032593575 4.04E-13 12.39399954 -0.341192082 T(ph)PPTDT(ph)TMYMELPNAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPPTDTTMYMELPNAK 16 0 A0A5F9ZHH1;A0A376A8X2;B0L653;B0L652;A0A0G2JPC4;A0A0G2JN68;Q8NHK3;Q8N109 A0A5F9ZHH1 KIR2DL5B;KIR2DL5A Killer cell immunoglobulin-like receptor 2DL5B;Killer cell immunoglobulin-like receptor 2DL5A 2 0 T(0.591)PPT(0.466)DT(0.834)T(0.044)MY(0.065)MELPNAK 43.184 0.0042168 0 600.56 525.62 648.49 613.27 634.69 618.92 340.81 542.02 753.77 658.82 TRUE FALSE FALSE 593.2401437 533.0196922 659.7766964 684.1791629 602.2994009 579.3730095 369.7583929 557.7024935 686.3509233 641.7037614 0.92447665 0.830632021 1.028163985 1.066191604 0.938594157 0.902866781 0.576213535 0.869096501 1.06957597 1 9.32576363 -7.934664255 7.078695072 0.963006404 0.723484031 0.528408919 0.094973654 0.115275693 10.22131369 0.01181796 0.035875261 1.16E-08 7.934664255 -0.239522373 T(ph)PPTPPSSIVAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPPTPPSSIVAK 12 0 Q96QT6;Q96QT6-4 Q96QT6 PHF12 PHD finger protein 12 1 0 T(1)PPTPPSSIVAK 116.52 0.01775 9629600 1894.1 1696.9 1492.9 1902.3 1703.7 1840.9 1563.3 1491.6 1875.9 1868.2 TRUE FALSE FALSE 1871.013981 1720.789003 1518.883298 2122.252877 1616.753832 1723.272431 1696.086663 1534.757093 1708.114806 1819.663895 1.028219544 0.945663102 0.834705411 1.166288391 0.888490362 0.947027875 0.932087881 0.843428887 0.938697971 1 10.82945628 -4.869905343 0.360002646 1.009271437 5.50E-18 0.122423372 0.085985082 30.92313022 0.69488948 0.022224699 19.54662254 1.35E-05 4.869905343 -1.009271437 T(ph)PQAPASANLVGPR ddPTM_HeLa_Romidepsin_16h_R1 3 TPQAPASANLVGPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 T(1)PQAPASANLVGPR;T(1)PQAPASANLVGPR;T(1)PQAPASANLVGPR ;; 132.56 0.0036761 26101000 708.44 795.67 1069.02 845.62 1026.88 1166.19 1138.02 828.12 1174.39 1173.52 TRUE FALSE FALSE 699.8052608 806.8714631 1087.625845 943.3945632 974.4744818 1091.674223 1234.68339 852.0803456 1069.349617 1143.031781 0.612236048 0.705904662 0.951527213 0.825344123 0.852534897 0.955069002 1.080182905 0.74545639 0.935537957 1 10.1586498 -8.425875968 3.304496778 0.815452976 0.9416141 0.062484706 0.133571376 0.477061806 9.817985763 0.024472573 0.058121513 3.75E-09 8.425875968 0.126161124 T(ph)PQSPTLPPAK ddPTM_HeLa_Romidepsin_16h_R1 2 TPQSPTLPPAK 11 0 P78310-7;P78310-2;P78310-6;P78310 P78310-7 CXADR Coxsackievirus and adenovirus receptor 1 0 T(1)PQSPTLPPAK;T(0.731)PQS(0.005)PT(0.264)LPPAK ; 174.23 0.00026129 83349000 4888.8 8546.5 6506.6 5773 8427.5 9727.2 5236.1 8474.4 6557 6380.4 TRUE FALSE FALSE 4829.213425 8666.817851 6619.844644 6440.501423 7997.413228 9105.663313 5680.854203 8719.593394 5970.525498 6214.636288 0.777070966 1.39458167 1.065202264 1.036344063 1.286867462 1.465196496 0.914108878 1.403073807 0.96072002 1 12.60145424 -10.26890839 24.99795222 0.894727955 1.210147812 0.393015601 0.176155729 415.2013553 1389631.118 0.029955497 0.034612406 5.38E-11 10.26890839 0.315419857 T(ph)PSASNDDQQE ddPTM_HeLa_Romidepsin_16h_R1 2 TPSASNDDQQE 11 0 O43765 O43765 SGTA Small glutamine-rich tetratricopeptide repeat-containing protein alpha 1 0 T(0.498)PS(0.498)AS(0.004)NDDQQE;T(0.495)PS(0.495)AS(0.009)NDDQQE ; 163.9 0.0016824 27937000 5276 4945.9 5005.3 4693 5257.6 4998.5 5054.7 4178.7 5306.9 5083.7 TRUE FALSE FALSE 5211.694083 5015.52851 5092.415147 5235.626741 4989.285053 4679.111982 5484.046092 4299.604092 4832.237573 4951.624741 1.052522022 1.012905616 1.028433174 1.057355316 1.007605647 0.944964982 1.107524576 0.868321877 0.975889294 1 12.27368627 -7.240424911 24.45610205 1.024550483 0.868321668 0.529433178 0.04299484 2093.381818 2436177.31 0.00527506 0.303935766 5.75E-08 7.240424911 -0.156228815 T(ph)PSDDEEDNLFAPPK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSDDEEDNLFAPPK 15 0 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 T(0.698)PS(0.302)DDEEDNLFAPPK 169.94 4.69E-05 36502000 5143.8 5142.2 4843.7 5533.1 5228.6 5228.5 4507.7 4849.8 4814.8 5602.9 TRUE FALSE FALSE 5081.105387 5214.592027 4928.002567 6172.863056 4961.765031 4894.415724 4890.583925 4990.121311 4384.152229 5457.33585 0.931059683 0.955519721 0.903005185 1.131112914 0.909191805 0.896850745 0.896148608 0.914387798 0.80335027 1 12.41398112 -8.560729575 24.9999992 0.972536336 0.902028711 0.060142958 0.078475029 169.7596436 112123.5119 0.008333451 0.016666924 2.75E-09 8.560729575 -0.070507625 T(ph)PSPAAEDAREPEAK ddPTM_HeLa_Romidepsin_16h_R1 2 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 0 T(0.804)PS(0.196)PAAEDAREPEAK;T(0.903)PS(0.097)PAAEDAREPEAK ; 147.1 0.0020276 15317600 3438.9 3353.9 3510 2521.29 2537.87 2742.19 2131.53 2673.43 3557.1 3247.7 TRUE FALSE FALSE 3396.985364 3401.116292 3571.090078 2812.813413 2408.353024 2566.972909 2312.582105 2750.781479 3238.944067 3163.324286 1.073865673 1.075171555 1.128904202 0.889195403 0.761336115 0.811479531 0.731060712 0.869585673 1.023905163 1 11.62722574 -9.043688609 4.332497077 1.045476658 0.79227449 0.875384164 0.047626678 0.058302436 2.390068751 0.007727896 0.013442614 9.04E-10 9.043688609 -0.253202168 T(ph)PSPPPPIPEDIALGKK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSPPPPIPEDIALGKK 17 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 T(0.5)PS(0.5)PPPPIPEDIALGKK 102.37 0.0012143 13738000 2144.7 2058.7 1956.9 2650.7 1682.6 1848.3 1663.4 1815.7 2315.5 2223 TRUE FALSE FALSE 2118.559571 2087.682433 1990.959024 2957.186406 1596.730643 1730.199595 1804.689154 1868.234415 2108.395881 2165.24614 0.978438217 0.96417788 0.919507019 1.365750689 0.737436088 0.799077557 0.833479909 0.862827732 0.973744205 1 11.08031532 T(ph)PSPSQPK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSPSQPK 8 0 Q9NTI5-2;Q9NTI5 Q9NTI5-2 PDS5B Sister chromatid cohesion protein PDS5 homolog B 1 0 T(0.999)PS(0.001)PSQPK 131.11 0.021699 45889000 6549.2 6752 8330.2 6216.1 4256 4619.6 5840.7 2696.9 8393.8 7931.9 TRUE FALSE FALSE 6469.375831 6847.054833 8475.183637 6934.83473 4038.800439 4324.422469 6336.808912 2774.930546 7643.037505 7725.828095 0.837369891 0.886255137 1.096993556 0.897617012 0.522766024 0.559735787 0.820210964 0.359175808 0.98928392 1 12.91547386 -8.800181989 7.117071345 0.931847679 0.583292446 0.691727995 0.125586557 0.092173714 12.98321375 0.018340287 0.033737413 1.58E-09 8.800181989 -0.348555233 T(ph)PSSDVLVFDYTK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSSDVLVFDYTK 13 0 E9PC52;Q16576;Q16576-2;Q5JP01;H0YF10;Q09028-4;Q09028-2;Q09028-3;Q09028 E9PC52;Q09028-3 RBBP7;RBBP4 Histone-binding protein RBBP7;Histone-binding protein RBBP4 1 0 T(0.496)PS(0.164)S(0.34)DVLVFDYTK 124.42 0.008033 3615200 1414.6 1383.9 1233.6 1114.2 1449.8 1638.4 1207.4 1330.7 1454.9 1677.7 TRUE FALSE FALSE 1397.358311 1403.382581 1255.070291 1243.029046 1375.811296 1533.711528 1309.956526 1369.201705 1324.7701 1634.113112 0.85511725 0.858803818 0.768043706 0.760675034 0.841931495 0.938558975 0.801631488 0.837886738 0.810696696 1 10.67429213 -11.80147629 0.646137154 1.0041598 0.828444191 0 0.074471276 0.408228446 0.317358779 0.037331836 0.011905232 1.58E-12 11.80147629 -0.17571561 T(ph)PSSEEISPTK ddPTM_HeLa_Romidepsin_16h_R1 3 TPSSEEISPTK 11 0 J3QLT3;E7ENF8;A0A1W2PRI7;Q15311 J3QLT3 RALBP1 RalA-binding protein 1 1 0 T(0.936)PS(0.064)SEEISPTK;T(0.763)PS(0.234)S(0.002)EEISPTK;T(0.921)PS(0.071)S(0.007)EEISPTK ;; 151.13 0.0047904 72197000 7565.1 8027 8414.8 6622.2 10111.2 11334.6 9861.7 10665.9 8459.2 9004.8 TRUE FALSE FALSE 7472.893651 8140.004317 8561.256064 7387.889922 9595.187734 10610.35564 10699.35255 10974.50099 7702.587966 8770.853998 0.852014371 0.928074315 0.976102905 0.842322757 1.093985573 1.209728909 1.219875802 1.251246571 0.878202735 1 13.09850161 -8.511477621 3.226197429 0.926782455 1.224207638 0.886166181 0.05064292 0.074261414 1.588999214 0.009247087 0.021066822 3.08E-09 8.511477621 0.297425183 T(ph)PSSEEISPTKFPGLYR ddPTM_HeLa_Romidepsin_16h_R1 1 TPSSEEISPTKFPGLYR 17 1 J3QLT3;E7ENF8;A0A1W2PRI7;Q15311 J3QLT3 RALBP1 RalA-binding protein 1 1 0 T(0.542)PS(0.158)S(0.3)EEISPTKFPGLYR 103.77 0.011691 43357000 1085.7 867.43 609.85 1031.8 909.18 1158.5 720.63 1058.3 1137 1002.1 TRUE FALSE FALSE 1072.467071 879.6417023 620.4641834 1151.101571 862.781152 1084.475589 781.8402942 1088.920241 1035.303872 976.0652975 1.098765701 0.901211942 0.63567897 1.179328446 0.883937944 1.111068687 0.801012285 1.115622329 1.060691201 1 9.930833855 -10.25766049 24.79715545 1.046639359 0.942100314 0.08939667 0.154558023 531.3719433 3486873.865 0.024386913 0.029263523 5.53E-11 10.25766049 -0.104539045 T(ph)PSSSSTLAYSPR ddPTM_HeLa_Romidepsin_16h_R1 3 TPSSSSTLAYSPR 13 0 H3BR17;Q6Q0C0;A0A087WUB0 H3BR17 TRAF7 E3 ubiquitin-protein ligase TRAF7 1 0 T(0.95)PS(0.048)S(0.001)S(0.001)STLAYSPR;T(0.772)PS(0.196)S(0.005)S(0.025)S(0.001)T(0.001)LAYSPR;T(0.94)PS(0.058)S(0.001)SSTLAYSPR ;; 153.81 0.0015866 56802600 1662.97 1422.18 1322.26 740.3 1601.57 1630.93 1445.37 1698.53 1675.34 1506.87 TRUE FALSE FALSE 1642.701082 1442.201487 1345.273381 825.8969692 1519.835907 1526.718837 1568.139692 1747.674286 1525.493394 1467.7213 1.11921867 0.98261263 0.916572772 0.562706945 1.035507154 1.040196689 1.068417888 1.190739881 1.03936176 1 10.51936233 -10.06685362 7.97181407 1.056160609 0.960355683 0.05331876 0.156279916 0.714287227 78.30102859 0.027517114 0.033792677 8.57E-11 10.06685362 -0.095804926 T(ph)PTAPAVNLAGAR ddPTM_HeLa_Romidepsin_16h_R1 1 TPTAPAVNLAGAR 13 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 T(1)PTAPAVNLAGAR 123.95 0.0082676 35723000 320.28 267.09 318.07 185.49 335.95 353.12 255.34 358.52 307.88 236.15 TRUE FALSE FALSE 316.3763042 270.8501 323.6058749 206.9372266 318.8052179 330.5567716 277.0285732 368.8932105 280.3424417 230.014789 1.375460707 1.177533415 1.406891602 0.899669223 1.386020522 1.437110949 1.204394615 1.603780401 1.218801813 1 7.845582813 -15.02456965 0.309903142 9.00E-12 1.33220892 0.106416864 0.190979683 17.92896792 0.556587695 11.1498963 0.070385712 9.45E-16 15.02456965 1.33220892 T(ph)PTDPGLDSALEPSGDPHGK ddPTM_HeLa_Romidepsin_16h_R1 1 TPTDPGLDSALEPSGDPHGK 20 0 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 T(0.818)PT(0.182)DPGLDSALEPSGDPHGK 144.4 2.99E-05 2878500 1050.7 1625.7 1153.5 967.5 1636 1967.8 1393.1 1572.1 1622.4 1434.6 TRUE FALSE FALSE 1037.893664 1648.586647 1173.576184 1079.366902 1552.508815 1842.063931 1511.429879 1617.586233 1477.288481 1397.328885 0.742769777 1.179812902 0.839871126 0.772450147 1.111054693 1.318275139 1.081656506 1.157627421 1.057223175 1 10.44845591 -8.616568639 5.960385156 0.89142688 1.181506495 0.398396857 0.138215269 0.136840464 7.157980346 0.020689417 0.041776678 2.42E-09 8.616568639 0.290079615 T(ph)PTPEPAEVETR ddPTM_HeLa_Romidepsin_16h_R1 1 TPTPEPAEVETR 12 0 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 0 T(0.985)PT(0.015)PEPAEVETR 116.9 0.017503 101260000 1868.2 1447.1 1820.2 1590.4 1627.8 1398.9 1317.7 1223.7 1767.1 1654.6 TRUE FALSE FALSE 1845.42966 1467.472312 1851.879817 1774.289531 1544.727292 1309.514805 1429.625405 1259.105829 1609.04615 1611.613253 1.145082206 0.910561084 1.149084505 1.100940022 0.958497511 0.812549042 0.88707722 0.781270461 0.998407122 1 10.65428986 -8.487909126 3.293405499 1.065432243 0.833942094 0.645002044 0.073539239 0.116748667 2.566611502 0.011306148 0.026039066 3.25E-09 8.487909126 -0.231490149 T(ph)PTPEPAEVETRK ddPTM_HeLa_Romidepsin_16h_R1 3 TPTPEPAEVETRK 13 1 F8W6G1;Q9UHY1 F8W6G1 NRBP1 Nuclear receptor-binding protein 1 0 T(0.84)PT(0.16)PEPAEVETRK;T(0.797)PT(0.203)PEPAEVETRK;T(0.853)PT(0.147)PEPAEVETRK ;; 84.195 0.0027706 14216000 10868.3 10359.8 8980.4 11530 9491.5 9096.8 7611.7 8151.9 10613.6 10226 TRUE FALSE FALSE 10735.83298 10505.64554 9136.700095 12863.15285 9007.113337 8515.543839 8258.237608 8387.762365 9664.293034 9960.327046 1.077859485 1.054749055 0.917309246 1.291438804 0.904298955 0.854946208 0.829113097 0.842117164 0.970278686 1 13.2819774 -8.538826545 24.99993106 1.047195171 0.847240575 0.520163089 0.092779539 130.8205922 205075.0998 0.012271365 0.024548133 2.89E-09 8.538826545 -0.199954596 T(ph)PTPEPFDSETR ddPTM_HeLa_Romidepsin_16h_R1 1 TPTPEPFDSETR 12 0 Q9NSY0;H0YCB1;Q9NSY0-2;Q9NSY0-4 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 0 T(0.833)PT(0.167)PEPFDSETR 150.51 0.0029973 5395200 469.54 569.4 605.01 506.24 530.77 449.62 439.66 558.52 727.56 555.76 TRUE FALSE FALSE 463.8170659 577.4160281 615.5399453 564.7738507 503.6828263 420.8907331 477.0047094 574.679895 662.4852114 541.3212751 0.85682401 1.066678985 1.137106509 1.043324689 0.930469297 0.777524831 0.881185964 1.061624439 1.223829991 1 9.08034128 -7.23576951 22.88363633 0.94811346 1.06162484 0 0.134081321 5287.893541 4713708.076 0.015818655 1.299543546 5.81E-08 7.23576951 0.11351138 TPLALAGS(ph)PTPK ddPTM_HeLa_Romidepsin_16h_R1 1 TPLALAGSPTPK 12 0 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785 B9EGQ5 WIZ Protein Wiz 1 0 T(0.294)PLALAGS(0.68)PT(0.026)PK 135.81 0.0026525 63500000 5601.6 4957.1 5571.5 4421.7 4164.8 3314.2 2492.1 2662.4 5969.7 5777.2 TRUE FALSE FALSE 5533.325545 5026.886184 5668.46962 4932.957759 3952.254715 3102.433316 2703.778912 2739.432343 5435.755081 5627.107511 0.983333895 0.893333951 1.00735051 0.876641818 0.702359908 0.551337132 0.480491781 0.486827795 0.965994531 1 12.45817781 -8.577451157 1.303567481 0.986843424 0.473640095 0.974889653 0.032859482 0.043198822 0.142631264 0.00501698 0.015430337 2.65E-09 8.577451157 -0.51320333 down T(ph)QES(ph)FAS(ph)AS(ph)S(ph)TEPSPAGR ddPTM_HeLa_Romidepsin_16h_R1 1 TQESFASASSTEPSPAGR 18 0 F5H5P5 F5H5P5 CHFR 5 0 T(1)QES(1)FAS(0.998)AS(0.975)S(0.5)T(0.446)EPS(0.082)PAGR 46.131 0.030371 2615000 1648.3 1593.1 1751 1782.1 1490.4 1394.5 1435.3 1047.5 1502.7 1675.4 TRUE FALSE FALSE 1628.209886 1615.527704 1781.47542 1988.154787 1414.339327 1305.395951 1557.214346 1077.80776 1368.294748 1631.872866 0.997755352 0.989983801 1.091675373 1.218327008 0.866697005 0.799937285 0.954249794 0.660472873 0.838481218 1 10.67231295 -8.544420945 24.94861109 1.020524784 0.822071941 0.448455645 0.111029563 137.8376987 159633.0524 0.013399165 0.026800079 2.85E-09 8.544420945 -0.198452843 T(ph)QLSPSIK ddPTM_HeLa_Romidepsin_16h_R1 1 TQLSPSIK 8 0 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 T(0.684)QLS(0.315)PS(0.001)IK 128.03 0.026753 35540000 6715 6540.9 6737.5 3749.4 5353.2 5543 4776.5 4756.1 7320.9 7780.7 TRUE FALSE FALSE 6633.154997 6632.982962 6854.763361 4182.923269 5080.006228 5188.820189 5182.215791 4893.71025 6666.100368 7578.556292 0.875253114 0.875230414 0.904494616 0.551941967 0.670313188 0.684671326 0.683799868 0.6457312 0.879600297 1 12.88770733 -9.340258366 6.294081331 0.932063097 0.653095119 0.860436439 0.051803996 0.069705891 4.546624215 0.009671032 0.01484286 4.57E-10 9.340258366 -0.278967978 T(ph)QPTSLPKQPAPTTIGGLNK ddPTM_HeLa_Romidepsin_16h_R1 1 TQPTSLPKQPAPTTIGGLNK 20 1 E7EVA0;P27816;P27816-6;P27816-5;P27816-4;B5MEG9;H7C4C5 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 T(0.364)QPT(0.317)S(0.317)LPKQPAPT(0.001)T(0.001)IGGLNK 55.846 0.019072 13787000 1688.3 2055.1 1717.1 1022.7 2232.9 1950 1808.1 2093.2 1641.8 1821.3 TRUE FALSE FALSE 1667.72235 2084.031752 1746.985405 1140.949386 2118.946781 1825.401293 1961.679969 2153.763439 1494.953296 1773.982363 0.940100863 1.174775914 0.984781721 0.643157119 1.194457636 1.028985029 1.10580579 1.214083907 0.842710349 1 10.79277595 ADYDT(ph)LSLR ddPTM_HeLa_Romidepsin_16h_R1 1 ADYDTLSLR 9 0 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71;E9PQ15 E9PKC4 PKP3 Plakophilin-3 1 0 ADY(0.478)DT(0.522)LSLR 141.91 0.012951 5601200 3059.6 3142.9 2853 3114.5 1881 1708 1063.1 889.83 3846.8 3548.9 TRUE FALSE FALSE 3022.308418 3187.145829 2902.655268 3474.613144 1785.005551 1598.864312 1153.399687 915.5758271 3502.732574 3456.699066 0.874333681 0.922020045 0.839718822 1.005182423 0.516390208 0.462540789 0.333670842 0.264869984 1.013317187 1 11.7551793 -8.575402314 2.24574395 0.934980531 0.343176374 0.923188604 0.077836884 0.058343139 0.589817085 0.011778226 0.028097755 2.66E-09 8.575402314 -0.591804157 down T(ph)QS(ph)S(ph)GS(ph)GQGS(ph)EAPEK ddPTM_HeLa_Romidepsin_16h_R1 1 TQSSGSGQGSEAPEK 15 0 Q9HC10-3;Q9HC10-5;Q9HC10;A0A2U3TZT7;Q9HC10-4;Q9HC10-2 Q9HC10-3;A0A2U3TZT7 OTOF Otoferlin 5 0 T(1)QS(1)S(1)GS(1)GQGS(1)EAPEK 56.087 0.0040003 0 589.86 533.75 421.45 514.78 616.09 369.42 533.62 579.99 757.08 585.13 TRUE FALSE FALSE 582.6705594 541.2641465 428.7851605 574.3012857 584.6486284 345.8152542 578.9456695 596.7710956 689.3648687 569.9282382 1.022357764 0.949705788 0.752349387 1.007672979 1.025828498 0.606769819 1.015822047 1.047098662 1.209564332 1 9.154636465 -10.00508554 24.87780753 1.009266994 0.905198872 0.168866939 0.144991248 336.2106023 1644708.305 0.020462647 0.026474872 9.88E-11 10.00508554 -0.104068122 T(ph)QSASPPPKER ddPTM_HeLa_Romidepsin_16h_R1 1 TQSASPPPKER 11 1 Q9UN81 Q9UN81 L1RE1 LINE-1 retrotransposable element ORF1 protein 1 0 T(0.96)QS(0.024)AS(0.016)PPPKER 84.169 0.025432 23069000 3374.9 3916 4414.6 4109.1 3465.4 3627.4 5099 1335.8 5207.6 4111.1 TRUE FALSE FALSE 3333.765421 3971.129551 4491.434261 4584.213476 3288.547707 3395.620847 5532.108933 1374.449265 4741.819213 4004.293029 0.832547817 0.991718019 1.121654741 1.144824677 0.821255508 0.847995095 1.38154448 0.343243927 1.184183869 1 11.96733184 -7.232635507 24.59206616 0.964004766 0.343242742 0.535970995 0.182632924 5354.691528 4571626.145 0.023037764 3.250115603 5.85E-08 7.232635507 -0.620762024 T(ph)QSPEFEAQSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TQSPEFEAQSSK 12 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 T(0.918)QS(0.014)PEFEAQS(0.065)S(0.004)K 175.66 3.68E-05 15136000 3431.5 3364.5 3738.7 2169.8 3050 5351.4 5227.4 6276.1 4136.3 4127.7 TRUE FALSE FALSE 3389.675558 3411.865519 3803.770505 2420.682485 2894.347119 5009.462811 5671.415226 6457.689051 3766.338968 4020.461759 0.843106031 0.848625288 0.946102894 0.602090663 0.719904153 1.245991906 1.410637774 1.606205814 0.936792636 1 11.97314549 -7.96852273 2.741671977 0.883900417 1.519484562 0.824723731 0.124567653 0.093199084 1.399799871 0.019980737 0.070949497 1.08E-08 7.96852273 0.635584145 T(ph)QSSLTVSEVLTR ddPTM_HeLa_Romidepsin_16h_R1 2 TQSSLTVSEVLTR 13 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 T(0.624)QS(0.017)S(0.123)LT(0.026)VS(0.21)EVLTR;T(0.474)QS(0.217)S(0.217)LT(0.067)VS(0.025)EVLTR ; 167.92 0.00026621 83689700 2025.58 2880.3 2510.7 2110.65 3496.3 3156.9 2805.3 3178.6 2789.5 2688.1 TRUE FALSE FALSE 2000.891452 2920.848939 2554.39768 2354.693284 3317.870765 2955.184278 3043.582112 3270.567776 2540.000134 2618.262774 0.764205744 1.115567531 0.975607836 0.89933421 1.267203123 1.128681318 1.162443335 1.249136568 0.970108943 1 11.35439418 -8.919703719 1.071579793 0.901485059 1.208326336 0.480673765 0.108971358 0.310150816 0.699794457 0.020966564 0.054913913 1.20E-09 8.919703719 0.306841277 T(ph)QT(ph)VTISDNANAVK ddPTM_HeLa_Romidepsin_16h_R1 1 TQTVTISDNANAVK 14 0 P11171;Q4VB86;P11171-4;P11171-3;P11171-2;A0A2R8YD30;A0A3B3ITP0;A0A2R8Y7Y3;A0A2U3TZH6;P11171-5;P11171-6;A0A2R8Y783 P11171 EPB41 Protein 4.1 2 0 T(0.989)QT(0.989)VT(0.023)ISDNANAVK 65.234 0.0192 44309000 1127.8 1102.9 1291.3 1117.3 1449.4 1423.9 1182.6 1097.3 1496.8 1336 TRUE FALSE FALSE 1114.05394 1118.426655 1313.774535 1246.487483 1375.43171 1332.917385 1283.050014 1129.048644 1362.922459 1301.290527 0.856114693 0.859474984 1.009593559 0.95788562 1.056975119 1.024304225 0.985982751 0.867637642 1.047362161 1 10.34572738 -9.73205937 24.99824134 0.924712204 0.98783112 0.060236124 0.071836064 315.1762153 268170.0556 0.011705981 0.016553348 1.85E-10 9.73205937 0.063118916 T(ph)QTPPVS(ph)PAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 2 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 T(0.996)QT(0.014)PPVS(0.808)PAPQPT(0.182)EER;T(0.988)QT(0.021)PPVS(0.597)PAPQPT(0.394)EER ; 127.29 0.0095334 118020300 2662.9 2666.3 2706.6 3540 3318.1 3421.6 3096.6 3553.3 2847.7 3104.9 TRUE FALSE FALSE 2630.443551 2703.836241 2753.707238 3949.311456 3148.764975 3202.970803 3359.625127 3656.109129 2592.99458 3024.23425 0.869788294 0.894056484 0.910546938 1.305888079 1.041177606 1.059101425 1.110901091 1.208937148 0.857405335 1 11.56235418 -9.295892686 24.93372066 0.931001258 1.13273315 0.678470132 0.081103573 315.4744612 228306.7287 0.012951294 0.019784055 5.06E-10 9.295892686 0.201731892 T(ph)QTPPVSPAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 1 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 T(0.615)QT(0.384)PPVSPAPQPTEER 186.96 2.15E-09 140670000 2580.3 2560.2 2675.2 1678.8 2260.2 2570.9 1848.4 2037.5 2508.8 2556.5 TRUE FALSE FALSE 2548.850311 2596.242563 2721.760734 1872.910755 2144.85356 2406.627787 2005.40305 2096.451848 2284.406645 2490.081761 1.023601052 1.04263346 1.093040709 0.752148296 0.861358688 0.966485448 0.805356306 0.841920888 0.917402264 1 11.2819774 -9.266724836 24.99998731 1.01987443 0.850833851 0.630412441 0.06492555 189.0478689 894188.0721 0.008608076 0.013392519 5.41E-10 9.266724836 -0.169040579 T(ph)RRSFVY(ph)REK ddPTM_HeLa_Romidepsin_16h_R1 1 TRRSFVYREK 10 3 A0A0C4DGY7 A0A0C4DGY7 MYCBP2 2 0 T(0.933)RRS(0.067)FVY(1)REK 70.977 0.0027393 0 959.14 965.15 1081.5 1076.9 857.7 800.93 782.95 731.96 1062.3 985.67 TRUE FALSE FALSE 947.4496328 978.737407 1100.323054 1201.416245 813.9283685 749.7531579 849.4537535 753.1381078 967.2852274 960.0621513 0.98686281 1.019452132 1.146095648 1.251394239 0.847787164 0.780942314 0.884790378 0.784468075 1.007523551 1 9.906983994 -8.556424826 24.99998785 1.025581762 0.822009972 0.638364441 0.086642629 109.545648 81637.75121 0.013680148 0.0273604 2.78E-09 8.556424826 -0.20357179 T(ph)RS(ph)MLLFANVS(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 1 TRSMLLFANVSAR 13 1 A6NGN9 A6NGN9 IGLON5 IgLON family member 5 3 0 T(1)RS(1)MLLFANVS(1)AR 52.79 0.027385 1087300 426.24 548.54 568.47 411.12 389.64 438.48 441.17 578.07 573.49 503.78 TRUE FALSE FALSE 421.0448229 556.2623605 578.3639819 458.6556288 369.7552169 410.4625431 478.6429688 594.7955434 522.1956181 490.691723 0.858063838 1.133628986 1.178670752 0.934712381 0.753538728 0.836497793 0.975445369 1.212157278 1.064203029 1 8.938673126 -11.20213293 0.003322756 6.55E-08 1.912119241 0 0.14981933 190277.3912 313.4382548 90756.5934 89608.10455 6.28E-12 11.20213293 1.912119175 T(ph)RS(ph)RS(ph)PESQVIGENTK ddPTM_HeLa_Romidepsin_16h_R1 1 TRSRSPESQVIGENTK 16 2 O95218-2 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 3 0 T(1)RS(0.998)RS(0.996)PES(0.007)QVIGENTK 70.451 0.014405 4548200 1947.6 1532.7 1694.5 1246.9 2183.6 1969.5 1470.5 1791.1 1907.4 1734.8 TRUE FALSE FALSE 1923.861902 1554.277391 1723.992062 1391.072445 2072.162744 1843.655306 1595.404233 1842.922653 1736.797367 1689.729646 1.138561963 0.919837913 1.020276863 0.823251488 1.22632798 1.091094845 0.944177216 1.090661253 1.027855179 1 10.72257672 -12.97424812 2.340922822 0.99925164 1.052050358 0 0.111367267 1.180663778 11.7461375 0.090999897 0.016668408 1.06E-13 12.97424812 0.052798718 T(ph)RSNPEGAEDR ddPTM_HeLa_Romidepsin_16h_R1 2 TRSNPEGAEDR 11 1 M0QXG9;M0R3F4;M0R2A4;M0R2K3;M0R193;M0R0I0;J3KQS6;Q9NWV8-3;Q9NWV8;M0R3H9;M0R2I2 M0QXG9 BABAM1 BRISC and BRCA1-A complex member 1 1 0 T(0.994)RS(0.006)NPEGAEDR;T(1)RSNPEGAEDR ; 107.55 0.0085623 69014000 2958.3 3130.5 3798.1 3221.1 2416.9 3022.4 4279.3 1027.64 4411.8 3315.8 TRUE FALSE FALSE 2922.243102 3174.571261 3864.204337 3593.538738 2293.556574 2829.278394 4642.783635 1057.373142 4017.197558 3229.655038 0.90481586 0.982944378 1.196475875 1.112669525 0.710155279 0.876031143 1.437547844 0.327395071 1.243847256 1 11.65716436 -7.231720985 24.65251803 0.985207224 0.327393791 0.503321863 0.20655448 6217.977238 5157952.569 0.024792871 3.962136214 5.87E-08 7.231720985 -0.657813434 T(ph)RSPDVISSASTALSQDIPEIASEALSR ddPTM_HeLa_Romidepsin_16h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 T(0.271)RS(0.271)PDVIS(0.09)S(0.268)AS(0.026)T(0.07)ALS(0.003)QDIPEIASEALSR 47.695 0.019511 4653400 302.54 374.49 235.39 283.25 271.18 356.63 258.15 351.77 469.73 282.51 TRUE FALSE FALSE 298.8525261 379.76208 239.4868642 316.0006977 257.3406727 333.842494 280.0772546 361.9479099 427.7161723 275.1703495 1.086063694 1.380098113 0.870322201 1.148382078 0.935204949 1.213221172 1.017832245 1.315359415 1.554368678 1 8.104181213 T(ph)RTFSATVR ddPTM_HeLa_Romidepsin_16h_R1 1 TRTFSATVR 9 1 H3BTK3;I3L3X8;H3BSW7;H3BUY4;H3BPY5;H3BNU9;Q9Y2V2 H3BTK3 CARHSP1 Calcium-regulated heat stable protein 1 1 0 T(0.972)RT(0.019)FS(0.009)ATVR 92.943 0.020279 11479000 1520.5 2053.8 1225.4 3347.8 1550 1646.7 1690 1386.3 1604.5 1351.8 TRUE FALSE FALSE 1501.967561 2082.71345 1246.727573 3734.888388 1470.897716 1541.481184 1833.548558 1426.410403 1460.989501 1316.680041 1.140723269 1.581791616 0.946872083 2.836595278 1.117126158 1.170733311 1.39255438 1.083338669 1.109601008 1 10.36268909 -10.43443131 2.078152562 1.050981736 1.460005773 0.095098728 0.504090705 0.496184704 4.138034663 0.091371367 0.101694755 3.68E-11 10.43443131 0.409024038 T(ph)RTPASINATPANINLADLTR ddPTM_HeLa_Romidepsin_16h_R1 1 TRTPASINATPANINLADLTR 21 1 Q7KZ85;Q7KZ85-2 Q7KZ85 SUPT6H Transcription elongation factor SPT6 1 0 T(0.744)RT(0.256)PAS(0.001)INATPANINLADLTR 90.896 0.004546 8545200 1890.4 1802.6 1660.8 1399 1377.5 1900.7 1572.3 1581.9 1484.8 1643.9 TRUE FALSE FALSE 1867.359078 1827.97705 1689.705527 1560.758962 1307.201035 1779.251404 1705.851123 1627.669781 1351.995769 1601.191241 1.166231135 1.141635679 1.055280271 0.974748626 0.816392821 1.111204807 1.065363761 1.016536775 0.844368702 1 10.64492991 -9.448346752 5.184275817 1.085995676 0.997711457 0 0.112510709 0.325450241 15.93105614 0.015153079 0.023153604 3.56E-10 9.448346752 -0.088284219 T(ph)S(ph)S(ph)STTPNRKDSS(ph)SQTMPVEDK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSSTTPNRKDSSSQTMPVEDK 22 2 F6VD24;Q9BTG3;Q5SYW2;F5H2X7;Q9ULV3-5;Q9ULV3-3;Q9ULV3-4;Q9ULV3 F6VD24 CIZ1 Cip1-interacting zinc finger protein 4 0 T(0.467)S(0.467)S(0.467)S(0.491)T(0.491)T(0.513)PNRKDS(0.158)S(0.667)S(0.139)QT(0.139)MPVEDK 52.784 0.0037185 0 1156.6 1183.7 947.25 962.42 1136 1125 881.96 1128.7 1156.4 1319 TRUE FALSE FALSE 1142.502914 1200.36416 963.7364889 1073.699529 1078.025681 1053.116131 956.8736604 1161.357154 1052.968688 1284.73219 0.889292666 0.934330259 0.750145825 0.835738014 0.839105371 0.819716466 0.744803989 0.903968285 0.819601701 1 10.32725194 -11.03172861 0.43960225 1.005123564 0.808820021 0 0.075645338 0.465364549 0.220551191 0.037365238 0.0212723 9.30E-12 11.03172861 -0.196303543 T(ph)S(ph)S(ph)TLSEDQMS(ph)RLAKQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSTLSEDQMSRLAKQK 17 2 K7ENH3 K7ENH3 PIK3C3 4 0 T(0.851)S(0.851)S(0.851)T(0.232)LS(0.217)EDQMS(0.999)RLAKQK 42.242 0.030385 13461000 3264.9 2889 2853.7 2871.2 2946.5 3539.9 2724.1 2811.5 3110.4 3049.3 TRUE FALSE FALSE 3225.106143 2929.671418 2903.367451 3203.181653 2796.12911 3313.711815 2955.484986 2892.846317 2832.198034 2970.078746 1.085865534 0.9863952 0.97753888 1.078483746 0.941432652 1.115698302 0.995086406 0.973996504 0.953576749 1 11.53628547 -10.23186294 24.87913988 1.040547627 1.012082122 0 0.059153206 1634.070923 1374549.61 0.009051794 0.011085065 5.86E-11 10.23186294 -0.028465505 T(ph)SAFSFLVEQMWAPLWSRSMR ddPTM_HeLa_Romidepsin_16h_R1 1 TSAFSFLVEQMWAPLWSRSMR 21 1 A0A3B3ITA6;A0A3B3ITU9;A0A3B3IRX9;P35218 A0A3B3ITA6 CA5A "Carbonic anhydrase 5A, mitochondrial" 1 0 T(0.346)S(0.346)AFS(0.307)FLVEQMWAPLWSRSMR 51.827 0.027168 6969600 140.89 0 0 0 67.052 199.8 0 145.9 155.35 160.14 TRUE FALSE FALSE 139.1727785 0 0 0 63.63008623 187.0334248 0 150.1213863 141.4551069 155.9795397 0.892250219 0 0 0 0.407938672 1.199089478 0 0.962442809 0.906882449 1 7.285212989 -10.38249718 6.972583399 0.95250972 0.35905465 0.297238903 0.399133572 0.219476396 11.7160729 0.067746254 0.077217567 4.14E-11 10.38249718 -0.59345507 T(ph)SDIFGSPVTATSR ddPTM_HeLa_Romidepsin_16h_R1 2 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BU16;H3BMV3;Q9H910-2;H3BMT0;H3BTV5 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 0 T(0.593)S(0.008)DIFGS(0.393)PVT(0.006)ATSR;T(0.519)S(0.039)DIFGS(0.432)PVT(0.011)ATSR ; 223.36 2.02E-32 593283000 9277.3 9194.5 8331.7 7811.5 10104.7 11212.9 9441.1 9176.1 8657.9 8611.9 TRUE FALSE FALSE 9164.224699 9323.940412 8476.709744 8714.702384 9589.019453 10496.43188 10243.0268 9441.595976 7883.51574 8388.161597 1.092518855 1.111559464 1.010556323 1.038928767 1.14316103 1.251338778 1.22112893 1.125585847 0.939838324 1 13.03413894 -4 0.124819307 0.965121956 1.763857969 0.566204482 0.061516634 53.80129311 0.457610999 0.243259683 7.544267347 1.00E-04 4 0.798736013 T(ph)SDPNPAAPDSESVIVAMER ddPTM_HeLa_Romidepsin_16h_R1 1 TSDPNPAAPDSESVIVAMER 20 0 P42858 P42858 HTT Huntingtin 1 0 T(0.488)S(0.488)DPNPAAPDS(0.023)ES(0.002)VIVAMER 75.319 0.016222 3192700 827.2 480.72 720.66 589.73 746.95 888.59 640.01 526.98 588.05 732.8 TRUE FALSE FALSE 817.1177682 487.4875888 733.202785 657.9173574 708.8303542 831.8119668 694.3724334 542.2273349 535.4533352 713.7617504 1.144804646 0.682983627 1.027237428 0.921760457 0.993090977 1.165391626 0.972835029 0.759675528 0.750184967 1 9.479298781 T(ph)SDSDQQAYLVQR ddPTM_HeLa_Romidepsin_16h_R1 4 TSDSDQQAYLVQR 13 0 Q96CV9-3;Q96CV9-2;Q96CV9 Q96CV9-3 OPTN Optineurin 1 0 T(0.998)S(0.002)DSDQQAYLVQR;T(0.998)S(0.002)DSDQQAYLVQR;T(0.6)S(0.392)DS(0.007)DQQAYLVQR;T(0.918)S(0.082)DSDQQAYLVQR ;;; 207.08 1.73E-16 40258000 5191.69 4937.49 4783.96 5166.13 7723.2 9182.8 8442 10167.5 5755.88 5090.42 TRUE FALSE FALSE 5128.411685 5007.000114 4867.222817 5763.462258 7329.056285 8596.048716 9159.063269 10461.68057 5241.059677 4958.170155 1.034335556 1.009848383 0.981657076 1.162417198 1.478177645 1.73371394 1.847266831 2.10998821 1.057055227 1 12.27559207 -8.328633946 1.023875128 1.007436371 2.064994999 0.981475137 0.054140768 0.053560781 0.096400513 0.008400718 0.040747271 4.69E-09 8.328633946 1.057558628 up T(ph)SDVGGYYYEK ddPTM_HeLa_Romidepsin_16h_R1 1 TSDVGGYYYEK 11 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.873)S(0.127)DVGGYYYEK 151.7 0.0047556 48693000 3000.1 2621.4 3073.1 2269.9 2773.8 2835.8 2695.3 2396.8 2705.1 2472.1 TRUE FALSE FALSE 2963.533627 2658.304138 3126.586016 2532.356518 2632.242636 2654.601532 2924.238715 2466.147626 2463.149081 2407.874486 1.230767486 1.104004446 1.298483802 1.051697891 1.093180999 1.102466739 1.21444815 1.024201071 1.022955763 1 11.23354448 -12.54605058 1.322466262 1.000290607 1.15192359 0.274482498 0.081545914 0.410891137 1.291173263 0.055309377 0.013226572 2.84E-13 12.54605058 0.151632983 T(ph)SETSISPPGSSIGSPNR ddPTM_HeLa_Romidepsin_16h_R1 1 TSETSISPPGSSIGSPNR 18 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 T(0.974)S(0.008)ET(0.008)S(0.008)IS(0.001)PPGSSIGSPNR 241.64 5.86E-50 12807000 1368.5 1363.3 1159.4 1145.3 1095 1110.6 913.87 1153.5 1574 1475.4 TRUE FALSE FALSE 1351.820196 1382.492573 1179.578871 1277.724975 1039.118064 1039.636244 991.494095 1186.874703 1433.217498 1437.068895 0.940678766 0.962022473 0.82082277 0.889118802 0.723081592 0.723442173 0.689941935 0.825899653 0.997319963 1 10.48891351 -9.360684838 0.841871032 0.978090605 0.729816453 0.800131803 0.050015077 0.171543483 0.241257391 0.009324838 0.019908429 4.36E-10 9.360684838 -0.248274152 T(ph)SFSVGS(ph)DDELGPIR ddPTM_HeLa_Romidepsin_16h_R1 2 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 2 0 T(0.997)S(0.003)FS(0.043)VGS(0.957)DDELGPIR;T(0.983)S(0.017)FS(0.003)VGS(0.996)DDELGPIR ; 115.26 0.016151 5508500 3109.4 2212.5 2538.5 2373.9 2838.7 3063.9 2790.9 2886.6 3037.8 2798.7 TRUE FALSE FALSE 3071.501437 2243.647633 2582.681528 2648.381488 2693.830546 2868.126678 3027.958976 2970.119217 2766.09156 2725.989371 1.1267474 0.8230581 0.947429053 0.971530379 0.98820288 1.052141549 1.110774315 1.089556419 1.014711059 1 11.41256422 -7.930484208 4.439181772 1.023211854 1.099101486 0.15742822 0.078304215 0.391591155 15.00922838 0.013291082 0.042330002 1.17E-08 7.930484208 0.075889632 T(ph)SGETTQTHTEPTGDSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSGETTQTHTEPTGDSK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 T(0.446)S(0.446)GET(0.053)T(0.053)QT(0.002)HTEPTGDSK 77.66 0.01588 4615700 3963 3537.5 4340.6 1532.8 2681.5 3334.7 2555.4 3168.3 5337.3 4868 TRUE FALSE FALSE 3914.697432 3587.301018 4416.146322 1710.029548 2544.653049 3121.623432 2772.455612 3259.969762 4859.91852 4741.528658 0.82561927 0.756570565 0.931376069 0.360649417 0.536673557 0.658358023 0.584717675 0.687535602 1.024968712 1 12.21113654 -10.14070875 0.632700758 0.96081785 0.578768037 0.602896968 0.127862751 0.351919263 0.302937396 0.03675397 0.047812097 7.23E-11 10.14070875 -0.382049813 T(ph)SLAGDTSNSSSPASTGAK ddPTM_HeLa_Romidepsin_16h_R1 1 TSLAGDTSNSSSPASTGAK 19 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5;H0Y4F5;H0Y6T5;H0Y314 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 T(0.606)S(0.394)LAGDTSNSSSPASTGAK 219.23 1.20E-34 0 1041 1033.9 743.26 898.84 798.49 1047.3 520.78 808.6 959.09 929.78 TRUE FALSE FALSE 1028.311892 1048.455271 756.1961285 1002.76811 757.7400757 980.38091 565.0150402 831.9955652 873.3065883 905.6241816 1.135473094 1.157715632 0.83499993 1.107267375 0.836704774 1.082547187 0.623895708 0.918698487 0.964314565 1 9.822768671 -8.294295512 0.778147282 1.064171266 0.777026018 0.238203908 0.138918059 0.788038702 0.716337667 0.022227112 0.145328532 5.08E-09 8.294295512 -0.287145247 T(ph)SLSFQDPK ddPTM_HeLa_Romidepsin_16h_R1 1 TSLSFQDPK 9 0 P48681 P48681 NES Nestin 1 0 T(0.957)S(0.003)LS(0.04)FQDPK 119.03 0.028932 45412000 8040.8 7170.5 7639.1 4808.9 8636.3 10258 7733.4 8989.5 7518.3 7307.5 TRUE FALSE FALSE 7942.795637 7271.446487 7772.055331 5364.927645 8195.557385 9602.546906 8390.274803 9249.596999 6845.844418 7117.650097 1.115929489 1.021607748 1.091941192 0.753749843 1.151441455 1.349117585 1.178798436 1.299529602 0.961812442 1 12.7971853 -8.523675823 24.99986556 1.034147349 1.263474558 0.582030602 0.105362028 16.24843061 509622.9824 0.015005308 0.030225053 2.99E-09 8.523675823 0.229327209 T(ph)SPASLDFPESQK ddPTM_HeLa_Romidepsin_16h_R1 2 TSPASLDFPESQK 13 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 T(0.847)S(0.152)PASLDFPESQK;T(0.988)S(0.012)PASLDFPESQK ; 177.42 3.47E-05 3465900 3407.1 3521.3 3206.6 4061.5 2467.9 2786.5 2525.18 2676.2 3898.9 3447 TRUE FALSE FALSE 3365.572955 3570.872954 3262.409528 4531.10974 2341.953854 2608.451643 2739.668726 2753.631625 3550.172619 3357.446443 1.002420444 1.063568106 0.971693691 1.349570222 0.697540197 0.776915339 0.815997745 0.82015653 1.057402606 1 11.71314867 T(ph)SPDPSPVSAAPSK ddPTM_HeLa_Romidepsin_16h_R1 2 TSPDPSPVSAAPSK 14 0 Q13469-5;Q13469-3;Q13469-4;Q13469-2;Q13469 Q13469-5 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 0 T(0.5)S(0.5)PDPSPVSAAPSK;T(0.611)S(0.389)PDPSPVSAAPSK ; 133.04 0.0035701 20975400 13491.9 13126 12219.8 14016 15618.1 15024 12962 14697.4 13763.7 12788 TRUE FALSE FALSE 13327.45553 13310.78817 12432.48049 15636.59587 14821.05008 14064.01489 14062.99196 15122.64608 12532.6402 12455.76592 1.069982819 1.068644695 0.998130551 1.255370081 1.189894718 1.129116827 1.129034702 1.214108083 1.006171783 1 13.60452612 -9.271686492 24.95610866 1.034742298 1.177812195 0.768342492 0.042407647 284.8205355 693659.1639 0.007092122 0.010910293 5.35E-10 9.271686492 0.143069896 T(ph)SPDSLR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPDSLR 7 0 Q9BRL6-2;Q9BRL6 Q9BRL6-2 SRSF8 Serine/arginine-rich splicing factor 8 1 0 T(0.949)S(0.051)PDSLR 148.99 0.024053 24861000 6737.1 5801 7577 4033.2 4907.7 4722.3 4873.5 3178.3 6580.2 6459.1 TRUE FALSE FALSE 6654.985634 5882.66663 7708.874507 4499.537561 4657.241756 4420.560271 5287.454968 3270.259096 5991.650432 6291.291651 1.057809112 0.935049105 1.225324613 0.715200917 0.740267979 0.702647487 0.840440288 0.519807263 0.952372067 1 12.61914053 -9.236160555 24.19774281 1.033107592 0.713247017 0.713861563 0.104513507 191.6332273 183437.7827 0.01372771 0.022757752 5.81E-10 9.236160555 -0.319860575 T(ph)SPDTLR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPDTLR 7 0 Q01130-2;Q01130;J3QL05;J3KP15 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 1 0 T(0.949)S(0.051)PDTLR 148.99 0.024053 1148400000 3623.5 3681 4229.5 2581.5 5092.8 5147.1 5172.5 3640.2 4514.5 4407.5 TRUE FALSE FALSE 3579.335388 3732.821215 4303.112673 2879.985176 4832.895412 4818.216922 5611.852021 3745.523444 4110.711813 4292.992515 0.833762318 0.86951496 1.002357367 0.670857256 1.125763764 1.122344589 1.307212161 0.872473789 0.957539944 1 12.06776794 -8.635189415 20.47687052 0.906067365 1.122500915 0.382971641 0.133896647 1.965820943 347.7242064 0.018730941 0.037461903 2.32E-09 8.635189415 0.216433551 T(ph)SPENVQDR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPENVQDR 9 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 T(0.988)S(0.012)PENVQDR;T(0.989)S(0.011)PENVQDR ; 187.85 6.42E-07 186617000 7026.6 6625.2 7087.6 5291.2 6165.8 7509.1 7069.8 5364.5 7446 6681 TRUE FALSE FALSE 6940.957096 6718.46974 7210.956705 5902.99344 5851.136218 7029.292745 7670.308636 5519.713344 6780.011111 6507.426657 1.066620872 1.032431112 1.108111867 0.9071164 0.899147471 1.080195462 1.178700743 0.848217527 1.04188821 1 12.66787143 -9.275618502 24.93853709 1.037573535 0.99434313 0.101955741 0.093090279 2129.082375 3744667.938 0.014355031 0.021989667 5.30E-10 9.275618502 -0.043230405 T(ph)SPGRVDLPGSSTTLTK ddPTM_HeLa_Romidepsin_16h_R1 3 TSPGRVDLPGSSTTLTK 17 1 O94875-12;O94875-11;O94875-9;H7BZX1;O94875-4;O94875-10;O94875-8;O94875-5;O94875-3;H7BXR3;O94875-2;O94875-7;O94875;H7BZK1;H7C1R7 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 T(0.848)S(0.152)PGRVDLPGSSTTLTK;T(0.583)S(0.417)PGRVDLPGSSTTLTK;T(0.596)S(0.404)PGRVDLPGSSTTLTK ;; 152.59 0.00035763 119734100 11067.5 10708.3 8820.5 10166.5 9007.2 7755.6 6801.2 7513.5 10848.7 9861.5 TRUE FALSE FALSE 10932.60505 10859.05173 8974.017102 11341.99856 8547.528974 7260.04219 7378.893758 7730.891268 9878.365101 9605.296808 1.138185032 1.130527452 0.934277959 1.180806673 0.889876611 0.755837361 0.768210905 0.804857093 1.028428928 1 13.22961448 -8.559916359 4.900127415 1.068299156 0.781039772 0.787832269 0.068921117 0.067957817 3.897414453 0.010871898 0.022624684 2.75E-09 8.559916359 -0.287259384 T(ph)SPINLGLNVNDLLK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPINLGLNVNDLLK 15 0 P50616 P50616 TOB1 Protein Tob1 1 0 T(0.646)S(0.354)PINLGLNVNDLLK 288.41 7.50E-116 19879000 2214.9 2082.2 2511.2 1616.2 2200.2 1884.7 1716.5 1917.2 2226.4 2247 TRUE FALSE FALSE 2187.903947 2111.513266 2554.906383 1803.072648 2087.915584 1764.273753 1862.299467 1972.671157 2027.265208 2188.622616 0.999671634 0.964768092 1.16735812 0.823838991 0.953986114 0.806111451 0.850900221 0.90132997 0.926274449 1 11.0958075 -9.221011492 24.99742093 1.008073608 0.867749875 0.516887638 0.069749211 285.0851825 176274.4019 0.008944471 0.014832647 6.01E-10 9.221011492 -0.140323733 T(ph)SPKPAVVETVTTAK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPKPAVVETVTTAK 15 1 P56192;H0YI94;H0YIP0 P56192 MARS "Methionine--tRNA ligase, cytoplasmic" 1 0 T(0.943)S(0.057)PKPAVVETVTTAK 74.744 0.022574 17718000 4720.5 2984.3 4349.6 2139.8 3596.6 4119.9 3851.2 4050.5 4308 4252.2 TRUE FALSE FALSE 4662.96473 3026.313054 4425.302963 2387.213744 3413.052081 3856.651686 4178.320832 4167.694827 3922.68169 4141.727231 1.125850272 0.730688644 1.068467988 0.576381208 0.824064911 0.931169889 1.008835348 1.00626975 0.947112514 1 12.01601683 -10.27838183 24.94930283 1.059429296 0.878713553 0.165018528 0.144506763 798.9777434 1176563.883 0.024138066 0.027640568 5.27E-11 10.27838183 -0.180715743 T(ph)SPLKDNPSPEPQLDDIKR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 1 0 T(0.775)S(0.225)PLKDNPSPEPQLDDIKR;T(0.5)S(0.5)PLKDNPSPEPQLDDIKR ; 125.98 0.0040676 25731000 2624.4 2414.2 2455.1 2288.64 2905.8 2862.9 2569.5 2949.9 3074.7 2571.6 TRUE FALSE FALSE 2592.412803 2448.187171 2497.829986 2553.263325 2757.506183 2679.96993 2787.753266 3035.250702 2799.691131 2504.789461 1.034982318 0.977402376 0.997221533 1.01935247 1.100893399 1.069938201 1.112969097 1.211778774 1.117735113 1 11.29047363 -5.000779734 0.478354181 1.010492879 2.989493897 0.631846304 0.0417781 8.599777438 0.228970905 0.005475166 15.20001023 9.98E-06 5.000779734 1.979001018 T(ph)SPLNSSGSSQGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPLNSSGSSQGR 13 0 H0YJL4;G3XAH6;P51003 H0YJL4 PAPOLA Poly(A) polymerase alpha 1 0 T(0.99)S(0.01)PLNSSGSSQGR;T(0.984)S(0.016)PLNSSGSSQGR ; 188.92 2.42E-10 28252000 5515.5 5205.1 5949.2 3091.2 5103.3 5549 5288.6 5249.4 5883.1 5833.5 TRUE FALSE FALSE 5448.274965 5278.377534 6052.74333 3448.619089 4842.859558 5194.436809 5737.813552 5401.283107 5356.900802 5681.944829 0.958875021 0.928973739 1.065259082 0.606943431 0.852324284 0.914200501 1.009832676 0.950604638 0.942793526 1 12.47216911 T(ph)SPLVSQNNEQGSTLR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPLVSQNNEQGSTLR 16 0 A0A1W2PNZ9;Q15652-3;Q15652;H7BXU7 A0A1W2PNZ9 JMJD1C Probable JmjC domain-containing histone demethylation protein 2C 1 0 T(0.895)S(0.105)PLVSQNNEQGSTLR 158.91 0.00033524 13655000 1252.2 1065.2 1148.8 857.29 961.33 596.6 687.38 780.22 1210 1285.6 TRUE FALSE FALSE 1236.937705 1080.195914 1168.794382 956.4139035 912.2697429 558.4791854 745.76604 802.7944347 1101.774569 1252.199927 0.987811673 0.862638538 0.933392789 0.763786903 0.728533618 0.445998417 0.595564673 0.641107237 0.879871134 1 10.29024921 -9.016517243 1.012066962 0.990847295 0.5585256 0.813667132 0.074709478 0.116898159 0.235114233 0.011028851 0.027721148 9.63E-10 9.016517243 -0.432321694 T(ph)SPPGGELS(ph)PGAGR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPPGGELSPGAGR 14 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 2 0 T(0.985)S(0.015)PPGGELS(1)PGAGR 121.95 0.016275 19629000 4652.4 3674.5 4132.9 2977.9 2814.4 2682.8 1811.8 2002 4364.7 3902.4 TRUE FALSE FALSE 4595.694759 3726.229707 4204.831391 3322.218809 2670.770666 2511.377738 1965.694247 2059.924711 3974.3103 3801.015085 1.209070381 0.980324893 1.106239069 0.874034629 0.702646689 0.660712384 0.517149815 0.541940683 1.045591825 1 11.89216904 -8.778579658 1.186400607 1.096324983 0.541528364 0.911766391 0.068657357 0.11347347 0.314865597 0.014306133 0.039411935 1.67E-09 8.778579658 -0.554796619 T(ph)SPPGGELSPGAGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPPGGELSPGAGR 14 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 1 0 T(0.99)S(0.01)PPGGELSPGAGR;T(0.974)S(0.026)PPGGELSPGAGR ; 115.37 0.0098511 149981000 6168.5 7070.9 5760.6 5650.2 4588.5 3885.7 3684.6 3658.5 6179.4 6060.7 TRUE FALSE FALSE 6093.315949 7170.444316 5860.860827 6303.502709 4354.331723 3637.416311 3997.569832 3764.352925 5626.698987 5903.24214 1.032198206 1.21466207 0.992820672 1.067803515 0.737616994 0.616172643 0.677182087 0.637675507 0.953154022 1 12.5272918 -8.668718009 4.080013111 1.033813714 0.651111592 0.880377041 0.068388359 0.05219992 1.618529262 0.009655326 0.019801823 2.14E-09 8.668718009 -0.382702122 T(ph)SPPLLDR ddPTM_HeLa_Romidepsin_16h_R1 3 TSPPLLDR 8 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 T(0.931)S(0.069)PPLLDR;T(0.989)S(0.011)PPLLDR;T(0.924)S(0.076)PPLLDR ;; 140.17 0.0021667 2657041000 22886.6 23892.5 21604.4 13910.3 17708.9 19468.6 15592.5 18923.7 24062.3 23919.3 TRUE FALSE FALSE 22607.64932 24228.85924 21980.41552 15518.67434 16805.14875 18224.61929 16916.92656 19471.2274 21910.10762 23297.87314 0.970373956 1.039960133 0.943451593 0.666098328 0.721316862 0.782243906 0.726114631 0.835751285 0.940433811 1 14.50791064 -9.382418513 5.206877716 0.989629253 0.74655141 0.857343479 0.047614904 0.053946743 2.094169014 0.006706861 0.010311269 4.15E-10 9.382418513 -0.243077844 T(ph)SPQELSEELSR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPQELSEELSR 12 0 Q96PU5-9;Q96PU5-4;A0A1B0GVY1;Q96PU5-2;Q96PU5-6;Q96PU5-5;Q96PU5-7;Q96PU5;K7ERN1;Q96PU5-3 Q96PU5-9 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 0 T(0.916)S(0.084)PQELSEELSR;T(0.865)S(0.135)PQELSEELSR ; 170 0.00032782 20765200 1693.98 1779.03 1859.12 1553.72 1990.67 1944.14 1880.59 1722.55 1824.14 1784.34 TRUE FALSE FALSE 1673.33312 1804.075231 1891.477204 1733.368417 1889.078682 1819.915728 2040.327268 1772.389267 1660.98435 1737.98259 0.962802004 1.038028368 1.088317694 0.997345098 1.086937633 1.04714267 1.173963007 1.019796905 0.955696771 1 10.76319791 -10.0660221 4.129446295 0.982631751 1.070059897 0.460143831 0.046086448 0.149921441 5.018333329 0.00730234 0.009143 8.59E-11 10.0660221 0.087428146 T(ph)SPQELSEELSRR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPQELSEELSRR 13 1 Q96PU5-9;Q96PU5-4;A0A1B0GVY1;Q96PU5-2;Q96PU5-6;Q96PU5-5;Q96PU5-7;Q96PU5;K7ERN1;Q96PU5-3 Q96PU5-9 NEDD4L E3 ubiquitin-protein ligase NEDD4-like 1 0 T(0.985)S(0.015)PQELSEELSRR 119.92 0.0020274 2669000 1028.1 1268.7 1191.5 999.8 1211.2 1120.6 804.75 921.82 1447.2 1034.9 TRUE FALSE FALSE 1015.569122 1286.560792 1212.237558 1115.40158 1149.387944 1048.997277 873.1054449 948.4914073 1317.758807 1008.013149 1.007495907 1.276333343 1.202600937 1.106534753 1.140250944 1.040658327 0.866164738 0.940951424 1.307283351 1 9.977298743 -7.813051467 7.052093271 1.056716784 0.903872031 0.196066467 0.122629494 0.211113509 23.00681475 0.01581505 0.048719865 1.54E-08 7.813051467 -0.152844753 T(ph)SPQVLGSILK ddPTM_HeLa_Romidepsin_16h_R1 2 TSPQVLGSILK 11 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 T(0.984)S(0.016)PQVLGSILK;T(0.998)S(0.002)PQVLGSILK ; 182.72 1.30E-05 226189000 11033.1 9556.6 11946.9 10648.3 11572.6 9513.6 8085.5 6921.9 9839.2 8386.2 TRUE FALSE FALSE 10898.62433 9691.138066 12154.83078 11879.50655 10982.00704 8905.711664 8772.282168 7122.174256 8959.157309 8168.325315 1.334254442 1.186429004 1.488044405 1.454338079 1.344462496 1.090273871 1.073938883 0.871925882 1.096816907 1 12.99582461 -7.513275423 1.712166557 1.22025004 0.850012494 0.380970257 0.151870117 0.665186517 2.713138463 0.027737644 0.341600431 3.07E-08 7.513275423 -0.370237546 T(ph)SPS(ph)GGTWSSVVSGVPRLSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSGGTWSSVVSGVPRLSPK 21 1 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4 Q99700 ATXN2 Ataxin-2 2 0 T(0.662)S(0.311)PS(0.347)GGT(0.103)WS(0.233)S(0.064)VVS(0.028)GVPRLS(0.253)PK 61.039 0.016432 37770000 2260.8 2082.3 2347.6 2985.7 2058.9 2401.2 1891.2 1923.3 2449.2 2102.4 TRUE FALSE FALSE 2233.2445 2111.614674 2388.458993 3330.920682 1953.82665 2247.77107 2051.838481 1978.947651 2230.137418 2047.779345 1.090568916 1.031172953 1.166365409 1.626601367 0.954119718 1.097662732 1.001982214 0.966387153 1.089051622 1 10.99984455 -6.253216931 14.33459426 1.07876593 1.119853895 0 0.187331284 0 0 0.024591106 0 5.58E-07 6.253216931 0.041087965 T(ph)SPSGGTWSSVVSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSGGTWSSVVSGAK 16 0 F8WB06;F8VRK6 F8WB06 ATXN2 1 0 T(0.929)S(0.067)PS(0.003)GGT(0.001)WSSVVSGAK 103.66 0.0095549 32984000 3265 3153.1 3050.8 2830.9 2774.9 2743.3 1920.4 2392.2 3332.6 3229.1 TRUE FALSE FALSE 3225.204924 3197.489425 3103.897894 3158.221978 2633.286498 2568.011984 2083.518728 2461.414533 3034.523909 3145.207516 1.025434699 1.016622721 0.986865852 1.00413787 0.837237761 0.816484118 0.662442372 0.782592093 0.964808806 1 11.61893949 -8.511121659 1.50971782 1.012485092 0.728055016 0.886736299 0.040121657 0.071535803 0.317621305 0.005085325 0.015100316 3.08E-09 8.511121659 -0.284430076 T(ph)SPSGGTWSSVVSGVPR ddPTM_HeLa_Romidepsin_16h_R1 3 TSPSGGTWSSVVSGVPR 17 0 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4 Q99700 ATXN2 Ataxin-2 1 0 T(0.985)S(0.015)PSGGTWSSVVSGVPR;T(0.913)S(0.037)PS(0.045)GGT(0.004)WSSVVSGVPR;T(0.988)S(0.012)PSGGTWSSVVSGVPR ;; 227.63 1.43E-35 174317000 5154.4 5281.7 5755.4 4011.22 5551.6 4620.7 4379.96 4547.9 6252.4 5872.7 TRUE FALSE FALSE 5091.57619 5356.055911 5855.570323 4475.01613 5268.281136 4325.452183 4751.993693 4679.486311 5693.169685 5720.126407 0.890116027 0.936352718 1.023678483 0.782328188 0.921007817 0.756181223 0.830749769 0.818073934 0.99528739 1 12.48183131 -9.252746472 24.99332363 0.950875791 0.824053421 0.64152393 0.054237319 387.6705249 1114606.628 0.008830877 0.01449586 5.59E-10 9.252746472 -0.126822371 T(ph)SPSSPAPLPHQEATPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSSPAPLPHQEATPR 17 0 P04920-2;P04920-3;P04920 P04920-2 SLC4A2 Anion exchange protein 2 1 0 T(0.26)S(0.26)PS(0.26)S(0.219)PAPLPHQEATPR 79.467 0.014506 2590500 2844.8 2939.4 2985.6 2497.2 3302.9 3443.7 2985.9 3010.2 3471.2 2576.6 TRUE FALSE FALSE 2810.126483 2980.78095 3037.563116 2785.938014 3134.340688 3223.658684 3239.522271 3097.295388 3160.727178 2509.659561 1.119724176 1.187723226 1.210348672 1.110086028 1.248910704 1.28450039 1.290821402 1.234149618 1.259424676 1 11.29327596 -10.36015912 0.223673946 0.937568738 1.339621516 0 0.090122289 0.599752636 0.127088852 0.090381025 0.092467246 4.36E-11 10.36015912 0.402052778 T(ph)SPSVTPTPAR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPSVTPTPAR 11 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 0 T(0.985)S(0.015)PSVTPTPAR;T(0.903)S(0.095)PS(0.002)VTPTPAR ; 136.81 0.0077322 22144000 7349.4 7161.2 6572.3 5135.2 7425.1 7146.1 6318.1 6407.6 6939.9 6729.2 TRUE FALSE FALSE 7259.822686 7262.015562 6686.688125 5728.955986 7046.16944 6689.487273 6854.759256 6592.993796 6319.177963 6554.374414 1.107630146 1.107964712 1.020187085 0.874066024 1.075033099 1.02061415 1.045829674 1.005892154 0.96411611 1 12.67824237 -9.538360044 24.75362839 1.056890208 1.005001764 0.070308119 0.064020847 341.4079387 545887.7909 0.010212571 0.014445817 2.89E-10 9.538360044 -0.051888444 T(ph)SPTPPESATTVK ddPTM_HeLa_Romidepsin_16h_R1 4 TSPTPPESATTVK 13 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 0 T(0.665)S(0.334)PT(0.001)PPESATTVK;T(0.946)S(0.054)PTPPESATTVK;T(0.613)S(0.385)PT(0.002)PPESATTVK;T(0.5)S(0.5)PTPPESATTVK ;;; 158.11 0.0011583 394273000 12674.4 12764.1 11757.5 15087.9 14498 14804 12770.5 13691.7 13569.4 12843.7 TRUE FALSE FALSE 12519.91954 12943.79333 11962.13436 16832.43399 13758.11296 13858.07218 13855.22595 14087.84774 12355.71888 12510.01882 1.000791423 1.034674169 0.956204345 1.34551628 1.099767567 1.1077579 1.107530384 1.126125223 0.98766589 1 13.61079634 T(ph)SPTVATQTGASATSTR ddPTM_HeLa_Romidepsin_16h_R1 4 TSPTVATQTGASATSTR 17 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 0 T(0.803)S(0.146)PT(0.016)VAT(0.021)QT(0.007)GAS(0.001)AT(0.001)S(0.001)T(0.004)R;T(0.978)S(0.022)PTVATQTGASATSTR;T(0.837)S(0.159)PT(0.004)VATQTGASATSTR;T(0.987)S(0.013)PTVATQTGASATSTR ;;; 254.68 3.63E-72 153644400 9152.8 8819.5 8120.7 7157.25 5159.1 4830.9 4836.13 5001.9 10218.9 8769.7 TRUE FALSE FALSE 9041.242153 8943.661152 8262.037377 7984.804921 4895.811876 4522.221081 5246.910761 5146.622085 9304.89599 8541.86193 1.05846269 1.047038834 0.967240801 0.934785061 0.573155117 0.529418658 0.614258437 0.602517592 1.089328775 1 13.06033486 -8.834650816 3.415048374 1.02392681 0.574778355 0.967714752 0.039305724 0.029209764 0.682172132 0.00601291 0.011660536 1.46E-09 8.834650816 -0.449148455 T(ph)SPYILR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 0 T(0.926)S(0.074)PYILR 136.27 0.0281 78437000 6090.4 5463.5 6099.6 4950.1 5125.5 4584.9 3928.1 3606.6 6402.1 6259.7 TRUE FALSE FALSE 6016.167862 5540.415296 6205.760979 5522.453853 4863.926609 4291.939687 4261.752716 3710.951281 5829.480142 6097.072092 0.986730642 0.908700966 1.017826407 0.905755053 0.797747925 0.703934548 0.698983488 0.608644809 0.956111401 1 12.57390089 -8.522322347 1.01691346 0.99131979 0.632476137 0.934814696 0.035339184 0.085899245 0.162153264 0.005234249 0.020506328 3.00E-09 8.522322347 -0.358843653 T(ph)SSAVWNSPPLQGAR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSAVWNSPPLQGAR 15 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 T(0.975)S(0.021)S(0.002)AVWNS(0.002)PPLQGAR;T(0.814)S(0.028)S(0.154)AVWNS(0.004)PPLQGAR ; 144.51 0.00099375 47008000 6083.7 4684.3 5072 3967.6 5193.2 5734.3 5958.8 5149.6 6741.1 5055.3 TRUE FALSE FALSE 6009.549524 4750.245698 5160.276032 4426.35258 4928.171626 5367.896737 6464.940323 5298.595551 6138.159133 4923.962577 1.220470186 0.964720106 1.047992537 0.89894115 1.000854809 1.090157907 1.312954805 1.076083636 1.246589314 1 12.26560408 -7.971262615 24.14127815 1.0686788 1.196278751 0.18085473 0.114941731 198.3899056 166657.3446 0.016763538 0.050289291 1.07E-08 7.971262615 0.127599951 T(ph)SSEDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 4 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 0 T(0.743)S(0.128)S(0.128)EDNLYLAVLR;T(0.809)S(0.124)S(0.067)EDNLYLAVLR;T(0.855)S(0.012)S(0.133)EDNLYLAVLR;T(0.767)S(0.117)S(0.117)EDNLYLAVLR ;;; 244.23 2.84E-52 2104725800 10753.9 10668.6 10144.9 10315.8 10661.02 10683.2 8341.64 9854.59 11494.5 10515.74 TRUE FALSE FALSE 10622.82733 10818.79283 10321.46773 11508.56133 10116.94837 10000.578 9050.178693 10139.71701 10466.40313 10242.53956 1.03712827 1.056260781 1.007705918 1.123604285 0.987738276 0.9763768 0.88358738 0.989961225 1.021856257 1 13.32228584 -8.242534807 2.798518292 1.027328169 0.937969189 0.456098043 0.04300985 0.188335716 2.925620203 0.0060567 0.016885118 5.72E-09 8.242534807 -0.08935898 T(ph)SSESIYSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSESIYSR 9 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;A0A494C1P1;A0A494C1G0;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 T(0.982)S(0.017)S(0.001)ESIYSR 120.63 0.027063 8122000 973.36 1011.7 956.66 871.38 815.76 1004.2 955.25 1215.3 1260.5 1020.7 TRUE FALSE FALSE 961.4963139 1025.942739 973.310266 972.1330556 774.1287232 940.0348609 1036.388911 1250.462788 1147.757723 994.1820669 0.967122971 1.031946535 0.979006058 0.977821958 0.778658909 0.945535926 1.042453838 1.257780471 1.154474378 1 9.95736627 -7.307359329 2.856050763 0.970236582 1.293527946 0.474150142 0.087407691 0.181519151 2.174034348 0.009484763 0.128188843 4.93E-08 7.307359329 0.323291364 T(ph)SSFTEQLDEGTPNR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSFTEQLDEGTPNR 15 0 Q86W71;C9J0Y3;C9JHJ5;Q13439-3;Q13439-4;Q13439;Q13439-5;E7EVX2 Q86W71;Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 T(0.349)S(0.349)S(0.255)FT(0.046)EQLDEGTPNR;T(0.456)S(0.069)S(0.456)FT(0.018)EQLDEGTPNR ; 238.12 2.86E-45 55629600 3724.58 3110.08 2852.21 2157.36 3766.88 3197.54 2820.74 3276.37 3643.48 3462.95 TRUE FALSE FALSE 3679.183386 3153.863788 2901.851519 2406.804114 3574.642057 2993.227514 3060.333585 3371.166597 3317.598024 3372.98206 1.090780597 0.935037226 0.860322251 0.713553785 1.059786857 0.887412818 0.907307994 0.999461763 0.983580098 1 11.71980893 -10.11653441 5.147187788 1.042570911 0.902035326 0.258884141 0.089243554 0.189203978 7.320176571 0.014771698 0.018208395 7.65E-11 10.11653441 -0.140535585 T(ph)SSIADEGTYTLDSILR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSIADEGTYTLDSILR 17 0 E7ERV5;A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3 E7ERV5 MYO5A Unconventional myosin-Va 1 0 T(0.783)S(0.108)S(0.108)IADEGTYTLDSILR 352.77 3.65E-256 28603000 2566.3 2183.6 2543.5 2682.7 2852.7 2615.3 2111.8 2790.6 2677.1 2625.7 TRUE FALSE FALSE 2535.020949 2214.340778 2587.768551 2992.886396 2707.116074 2448.19077 2291.176239 2871.341608 2437.653471 2557.483935 0.991216763 0.865827835 1.011841566 1.170246411 1.058507558 0.957265356 0.895871214 1.122721268 0.953145174 1 11.32050946 -9.525958225 24.99959831 0.983739401 1.03537838 0.166549541 0.081900232 196.9635002 1598965.796 0.013100088 0.018584062 2.98E-10 9.525958225 0.05163898 T(ph)SSKES(ph)SPIPS(ph)PTSDRK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSKESSPIPSPTSDRK 17 2 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 0 T(0.684)S(0.29)S(0.277)KES(0.714)S(0.036)PIPS(0.842)PT(0.125)S(0.033)DRK 60.761 0.020951 5727200 1302.9 1138.6 1132.5 888.83 1068.5 1251.4 1232.4 1423.1 1210.5 1384.8 TRUE FALSE FALSE 1287.019754 1154.629241 1152.210687 991.6007067 1013.970458 1171.439579 1337.080025 1464.275153 1102.229848 1348.822696 0.954180084 0.856027441 0.854234356 0.735160158 0.751744807 0.868490412 0.991294133 1.085594984 0.817179197 1 10.397485 -10.42796885 2.715739978 0.981814182 0.870215236 0 0.11028908 0.344907737 4.810537712 0.019284241 0.02156364 3.73E-11 10.42796885 -0.111598946 T(ph)SSLDTLAAPYLAGHWPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 0 T(0.462)S(0.462)S(0.076)LDTLAAPYLAGHWPR 239.43 1.02E-49 27572000 2496.7 2590.2 2336.7 1800.5 2234.6 1870 2148.2 2065.8 2554.9 2057.1 TRUE FALSE FALSE 2466.26926 2626.664904 2377.369283 2008.682282 2120.560024 1750.513035 2330.668054 2125.570664 2326.383345 2003.656245 1.230884422 1.3109359 1.186515546 1.002508432 1.058345227 0.873659361 1.163207541 1.060845975 1.161069096 1 10.9684193 -9.253893597 24.6390433 1.135436587 1.031717317 0.294839179 0.103054422 785.745761 2565674.728 0.019412339 0.031770854 5.57E-10 9.253893597 -0.103719271 T(ph)SSTNEDEDLNPEQKIER ddPTM_HeLa_Romidepsin_16h_R1 1 TSSTNEDEDLNPEQKIER 18 1 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 T(0.443)S(0.099)S(0.443)T(0.016)NEDEDLNPEQKIER 161.59 3.28E-11 0 874.3 758.96 551.14 1720.8 701.46 556.2 460.43 425.21 934.46 764.57 TRUE FALSE FALSE 863.6436953 769.6446588 560.7323605 1919.766993 665.6618787 520.6606151 499.5389127 437.5127805 850.8795572 744.7063612 1.159710378 1.033487424 0.752957662 2.577884509 0.893858188 0.699148876 0.670786418 0.587497037 1.142570551 1 9.540527871 -8.526809153 24.9999762 1.164519205 0.678007341 0.247622594 0.471212943 143.3655445 911898.7292 0.067379625 0.135231506 2.97E-09 8.526809153 -0.486511864 T(ph)STSLGSAFGVQLDS(ph)RK ddPTM_HeLa_Romidepsin_16h_R1 1 TSTSLGSAFGVQLDSRK 17 1 Q70Z35-4;Q70Z35 Q70Z35-4 PREX2 "Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 2 protein" 2 0 T(0.25)S(0.25)T(0.25)S(0.25)LGS(0.002)AFGVQLDS(1)RK 95.618 0.0046161 4678100 9192.3 8981.6 8804.1 7829.4 9603.8 9963 8605.3 9159.6 10504 9762.1 TRUE FALSE FALSE 9080.260712 9108.043201 8957.331667 8734.672066 9113.682249 9326.396454 9336.233967 9424.618575 9564.495932 9508.479235 0.954964562 0.957886427 0.942036202 0.91861925 0.958479482 0.980850483 0.981885088 0.991180434 1.005891236 1 13.2149989 -12.20277188 0.93315482 1.000094422 0.959864329 0.406661662 0.020110957 0.555424415 0.866307905 0.014980297 0.004164978 6.27E-13 12.20277188 -0.040230093 T(ph)SVAGTVR ddPTM_HeLa_Romidepsin_16h_R1 1 TSVAGTVR 8 0 Q96EB6;B0QZ35;E9PC49 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 T(0.989)S(0.011)VAGTVR 150.81 0.013963 5605300 2954.5 2764.8 3045.2 2620.2 2994.5 3274.2 2355.3 2305.2 3039.4 3123.6 TRUE FALSE FALSE 2918.489418 2803.722927 3098.200429 2923.159852 2841.679491 3064.989187 2555.359123 2371.897325 2767.548452 3042.448422 0.959256826 0.921535073 1.018324717 0.960791917 0.934010736 1.007408758 0.8399022 0.779601491 0.90964515 1 11.57101709 -7.636881237 4.216808042 0.975421207 0.792230484 0.74010767 0.036635875 0.058524778 1.797532666 0.004314504 0.018242458 2.31E-08 7.636881237 -0.183190723 T(ph)SVQTEDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 TSVQTEDDQLIAGQSAR 17 0 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 0 T(0.868)S(0.131)VQTEDDQLIAGQSAR 324.79 3.32E-180 22813000 1529.1 2011.7 1434.3 784.21 1756.5 1907.9 1817.6 1957.8 1883.7 1769.6 TRUE FALSE FALSE 1510.462741 2040.020765 1459.26339 874.88405 1666.859251 1785.991347 1971.986899 2014.445854 1715.217154 1723.625537 0.876328825 1.183563786 0.846624373 0.507583597 0.967065766 1.036182923 1.144092412 1.168725927 0.995121688 1 10.75123066 -7.997221377 2.525106619 0.920297299 1.158426997 0.273272168 0.161542859 0.315155708 3.963046175 0.023927915 0.085693113 1.01E-08 7.997221377 0.238129697 T(ph)SVSPAPDK ddPTM_HeLa_Romidepsin_16h_R1 1 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 0 T(0.98)S(0.002)VS(0.018)PAPDK 128.51 0.018643 22382000 6582.4 6592.2 7781.8 7298.4 5124.2 3960.4 3955.5 2121.6 6663.9 6805.7 TRUE FALSE FALSE 6502.171177 6685.005165 7917.238965 8142.275348 4862.692953 3707.343222 4291.480071 2182.985149 6067.864094 6628.886933 0.980884309 1.00846571 1.194354202 1.228302041 0.733561004 0.559270849 0.647390748 0.329313981 0.915366962 1 12.69455093 -8.536032568 4.228878199 1.023962444 0.536821218 0.805289783 0.120036775 0.070666148 2.987011256 0.017559085 0.03785026 2.91E-09 8.536032568 -0.487141226 T(ph)T(ph)AGLT(ph)VPGATPSRPTPGAASR ddPTM_HeLa_Romidepsin_16h_R1 1 TTAGLTVPGATPSRPTPGAASR 22 1 A0A0C4DGY1;A0A3B3IU58;Q7Z410 A0A0C4DGY1 TMPRSS9 Transmembrane protease serine 9;Serase-1;Serase-2;Serase-3 3 0 T(0.973)T(0.973)AGLT(0.97)VPGAT(0.054)PS(0.024)RPT(0.004)PGAAS(0.002)R 41.53 0.021739 594150 0 116 128.02 47.967 136.95 59.091 0 0 0 138.8 TRUE FALSE FALSE 0 117.633051 130.2481344 53.51317023 129.9609305 55.31527581 0 0 0 135.193956 0 0.870105843 0.963416844 0.395825167 0.96129246 0.409154946 0 0 0 1 7.078886845 -7.861536218 3.964024843 0.594998034 4.44E-11 0.305665379 0.355250853 0.230103515 6.648947682 0.057573645 0.195131119 1.38E-08 7.861536218 -0.594998034 T(ph)T(ph)DMAPS(ph)KET(ph)EMALAK ddPTM_HeLa_Romidepsin_16h_R1 1 TTDMAPSKETEMALAK 16 1 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;H7C456 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 4 0 T(1)T(1)DMAPS(1)KET(1)EMALAK 44.601 0.0042843 0 281.19 349.51 440.88 462.21 1168.2 952.36 754.23 721.97 840.76 625.4 TRUE FALSE FALSE 277.7627481 354.430411 448.5533315 515.652895 1108.582395 891.5072696 818.2942774 742.8590629 765.5603199 609.1520178 0.455982645 0.5818423 0.736356966 0.846509377 1.819878064 1.46352182 1.343333443 1.219497007 1.256763989 1 9.250658497 -8.888753117 6.552141919 0.724584791 1.450597766 0.598057841 0.256004661 0.099383393 5.399229466 0.037267643 0.068031788 1.29E-09 8.888753117 0.726012975 T(ph)T(ph)EGEEET(ph)ESR ddPTM_HeLa_Romidepsin_16h_R1 1 TTEGEEETESR 11 0 Q8WXH0-12;Q8WXH0-5;A0A0C4DGK3;Q8WXH0-6;Q8WXH0-11;Q8WXH0-10;Q8WXH0-4;Q8WXH0-3;Q8WXH0-13;Q8WXH0-7;Q8WXH0;Q8WXH0-2 Q8WXH0-12 SYNE2 Nesprin-2 3 0 T(1)T(1)EGEEET(0.975)ES(0.025)R 66.326 0.0035745 0 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 T(ph)T(ph)VLRLLETKY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TTVLRLLETKYK 12 2 Q96NH3;Q96NH3-4 Q96NH3 TBC1D32 Protein broad-minded 3 0 T(1)T(1)VLRLLET(0.006)KY(0.994)K 54.005 0.028602 94161000 2498.5 2171.5 2308 2537.9 2768.2 2841.9 2384.3 2321.4 2787.7 2304.3 TRUE FALSE FALSE 2468.047321 2202.070434 2348.169772 2831.343939 2626.928424 2660.311762 2586.822382 2388.566046 2538.36113 2244.433954 1.099630184 0.981125076 1.046219145 1.26149577 1.170419125 1.185292959 1.152550013 1.064217569 1.130958265 1 11.13213593 -9.356168143 9.98836103 1.042069451 1.167177156 0.471081718 0.060627252 0.281832341 28.16363259 0.009145764 0.013973666 4.40E-10 9.356168143 0.125107705 T(ph)T(ph)VY(ph)VIER ddPTM_HeLa_Romidepsin_16h_R1 1 TTVYVIER 8 0 A0A2R8YEW2 A0A2R8YEW2 3 0 T(1)T(1)VY(1)VIER 70.256 0.0031746 0 943.56 884.48 1321.9 984 1019.1 1174.2 964.13 1121.8 1140.2 1321.9 TRUE FALSE FALSE 932.0595278 896.9317327 1344.907115 1097.77471 967.0915242 1099.17241 1046.023178 1154.257513 1038.217656 1287.556847 0.723897768 0.696615248 1.04454193 0.852602906 0.751105884 0.85368845 0.812409316 0.896471108 0.806347043 1 10.33042042 -12.53798984 1.325362259 0.999170888 0.817192465 0 0.110592775 0.416666921 1.320346471 0.06704841 0.016280677 2.90E-13 12.53798984 -0.181978422 T(ph)T(ph)Y(ph)T(ph)S(ph)GVGDTQ ddPTM_HeLa_Romidepsin_16h_R1 1 TTYTSGVGDTQ 11 0 H0YMT3 H0YMT3 WDR73 5 0 T(0.999)T(0.999)Y(0.999)T(0.999)S(0.996)GVGDT(0.008)Q 41.448 0.0043572 0 1077.8 999.56 919.07 694.32 1192.4 961.08 760.78 911.56 1243.5 896.53 TRUE FALSE FALSE 1064.663359 1013.631832 935.0660278 774.6005453 1131.547379 899.6700897 825.4006342 937.9345504 1132.278246 873.2380214 1.219213242 1.160773818 1.070803154 0.887043998 1.295806356 1.030269031 0.945218387 1.074088081 1.296643318 1 9.770231137 -9.531757595 24.18041786 1.110946121 1.046320929 0.1146815 0.126435589 335.2776395 913081.325 0.019883172 0.028146203 2.94E-10 9.531757595 -0.064625192 T(ph)TAPTEGKSPLK ddPTM_HeLa_Romidepsin_16h_R1 1 TTAPTEGKSPLK 12 1 A0A494C001;A0A499FJY3;A0A087WWP4;Q96T37-4;Q96T37-2;Q96T37-3;Q96T37 A0A494C001 RBM15 Putative RNA-binding protein 15 1 0 T(0.705)T(0.002)APT(0.184)EGKS(0.11)PLK 128.36 0.019424 7190100 1991.5 1513.2 1825.6 1163.8 1635.9 1510.2 1198.7 1492.5 1948.3 2014.3 TRUE FALSE FALSE 1967.226832 1534.502869 1857.373802 1298.364032 1552.413919 1413.703094 1300.517548 1535.683133 1774.039168 1961.968196 1.002680286 0.782124233 0.946689047 0.661766095 0.791253356 0.720553522 0.662863726 0.782725804 0.90421403 1 10.93808594 -9.79608979 0.954982503 1.00578117 0.71999898 0.597127321 0.078223678 0.167103731 0.303660832 0.013012825 0.020034913 1.60E-10 9.79608979 -0.28578219 T(ph)TCEACNIT(ph)FS(ph)RHET(ph)YMVHK ddPTM_HeLa_Romidepsin_16h_R1 1 TTCEACNITFSRHETYMVHK 20 1 E7ET52;Q8WW38-2;Q8WW38 E7ET52 ZFPM2 Zinc finger protein ZFPM2 4 0 T(0.923)T(0.176)CEACNIT(0.91)FS(0.99)RHET(0.523)Y(0.478)MVHK 51.193 0.0041119 0 0 120.05 121.01 0 122.79 210.73 169.27 118.96 136.36 162.24 TRUE FALSE FALSE 0 121.7400671 123.1161283 0 116.5235681 197.2650331 183.6477896 122.4019199 124.1636201 158.0249814 0 0.770384948 0.779092819 0 0.737374351 1.248315496 1.162144035 0.774573228 0.785721466 1 7.304008835 -8.516094156 24.61325852 0.518705712 1.058577763 0.314093305 0.331599408 266.2072832 965749.7562 0.060853701 0.12559632 3.05E-09 8.516094156 0.539872051 T(ph)TKSPSDSGYSYETIGK ddPTM_HeLa_Romidepsin_16h_R1 1 TTKSPSDSGYSYETIGK 17 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.383)T(0.096)KS(0.383)PS(0.122)DS(0.015)GYSYETIGK 100.95 0.0016973 383390000 3507 3104.1 3275 3492.6 3575.3 2989.3 2872.5 3213.9 3637.5 3448 TRUE FALSE FALSE 3464.255335 3147.799601 3332.000001 3896.430845 3392.8391 2798.293378 3116.490078 3306.889126 3312.15289 3358.420463 1.031513288 0.937285738 0.992133069 1.160197446 1.01024846 0.833217106 0.927963045 0.984656079 0.986223413 1 11.71356715 -8.409097977 9.639638608 1.018688118 0.916779597 0.347877857 0.063750969 0.316383737 24.96634647 0.008936164 0.019998504 3.90E-09 8.409097977 -0.10190852 T(ph)TPNSGDVQVTEDAVR ddPTM_HeLa_Romidepsin_16h_R1 2 TTPNSGDVQVTEDAVR 16 0 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 T(0.993)T(0.007)PNSGDVQVTEDAVR;T(0.997)T(0.003)PNSGDVQVTEDAVR ; 242.09 3.80E-47 51238000 4092.7 4157.7 4113.8 2866.7 4497 5404.3 5351 4844.5 4820.3 4546 TRUE FALSE FALSE 4042.816598 4216.23221 4185.398963 3198.161342 4267.501309 5058.982672 5805.513806 4984.667964 4389.160295 4427.894265 0.913033681 0.952198033 0.945234622 0.722275906 0.963776697 1.142525627 1.311122954 1.12574232 0.991252282 1 12.11240506 -8.188194507 3.58124963 0.938075333 1.218383107 0.676293757 0.085122093 0.108781788 2.713431188 0.012399367 0.033913736 6.48E-09 8.188194507 0.280307773 T(ph)TPNSGDVQVTEDAVRR ddPTM_HeLa_Romidepsin_16h_R1 1 TTPNSGDVQVTEDAVRR 17 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 T(0.798)T(0.158)PNS(0.045)GDVQVTEDAVRR 85.397 0.0055015 11474000 1468.7 1741.1 1455.2 1348.3 1925.2 2067.5 1763 2176.3 1864.2 1814.9 TRUE FALSE FALSE 1450.798919 1765.611252 1480.527146 1504.19679 1826.94986 1935.393423 1912.749176 2239.267807 1697.461283 1767.748636 0.820704307 0.9987909 0.837521305 0.850911017 1.033489616 1.094835195 1.082025542 1.266734286 0.960239057 1 10.78769743 -7.885617745 1.008625915 0.91079724 1.256161936 0.696817349 0.071802038 0.428236672 0.598231701 0.013344462 0.125705803 1.30E-08 7.885617745 0.345364696 T(ph)TPSYVAFTDTER ddPTM_HeLa_Romidepsin_16h_R1 1 TTPSYVAFTDTER 13 0 P11142;E9PKE3;P11142-2;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;E9PI65;P54652;A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P17066;P48741 P11142;P54652;A0A0G2JIW1;P17066 HSPA8;HSPA2;HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;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 1 0 T(0.646)T(0.007)PS(0.347)YVAFTDTER 228.93 1.17E-31 17874000 1198.1 1385.3 1288.4 846.77 1186.3 1189.9 1162.5 1348.6 1604.9 1252.7 TRUE FALSE FALSE 1183.497096 1404.80229 1310.824062 944.6775316 1125.758684 1113.86923 1261.242721 1387.619613 1461.353724 1220.154673 0.969956615 1.151331319 1.074309749 0.774227688 0.922636047 0.912891828 1.033674458 1.137248944 1.197679078 1 10.25284833 -7.377888646 3.486982384 0.979982439 1.140140993 0.088112656 0.116913002 0.3206563 6.237329363 0.013336958 0.108760333 4.19E-08 7.377888646 0.160158554 YFDSGDY(ph)NMAK ddPTM_HeLa_Romidepsin_16h_R1 1 YFDSGDYNMAK 11 0 O43768-2;O43768;A6NMQ3;Q5T5H1;O43768-9;O43768-3;O43768-4;H3BMD8;O43768-6;O43768-5;H3BQ52;O43768-7;P56211;H3BTD3;P56211-2 O43768-2;P56211;H3BTD3 ENSA;ARPP19 Alpha-endosulfine;cAMP-regulated phosphoprotein 19 1 0 Y(0.172)FDS(0.08)GDY(0.747)NMAK 85.862 0.0025101 0 2250.1 2327.5 2154.4 2424.9 1436 1183.7 819.55 731.06 2387.9 2055.2 TRUE FALSE FALSE 2222.674916 2360.266606 2191.896428 2705.278347 1362.715562 1108.06539 889.1625565 752.2120677 2174.320243 2001.805608 1.110335043 1.179068835 1.09495968 1.351419107 0.680743203 0.553532963 0.444180271 0.37576679 1.086179515 1 10.96708617 -8.568378296 4.73911151 1.085933087 0.476488882 0.898116131 0.103810889 0.051006943 2.548360741 0.016776986 0.034882285 2.70E-09 8.568378296 -0.609444205 down T(ph)TPTQPSEQK ddPTM_HeLa_Romidepsin_16h_R1 2 TTPTQPSEQK 10 0 O95104-2;O95104-3;O95104 O95104-2 SCAF4 "Splicing factor, arginine/serine-rich 15" 1 0 T(0.991)T(0.009)PTQPSEQK;T(0.988)T(0.012)PTQPSEQK ; 174.4 0.00066769 81696000 12443.6 12343.3 13963.8 10151.6 15131.2 17999.4 19042.3 10274.3 14061.1 13676.8 TRUE FALSE FALSE 12291.93262 12517.0693 14206.83408 11325.37576 14358.9984 16849.29643 20659.75249 10571.57066 12803.44 13321.47476 0.922715603 0.939615885 1.066461059 0.850159307 1.077883542 1.264822156 1.550860761 0.793573598 0.961112807 1 13.70146619 -8.465477243 4.198277083 0.961933478 1.234167959 0.26902235 0.179748917 0.184989736 6.594708861 0.023329496 0.052936996 3.42E-09 8.465477243 0.272234481 T(ph)TQIYT(ph)Y(ph)FVYK ddPTM_HeLa_Romidepsin_16h_R1 1 TTQIYTYFVYK 11 0 Q9UGP8 Q9UGP8 SEC63 Translocation protein SEC63 homolog 3 0 T(0.809)T(0.193)QIY(0.006)T(1)Y(0.938)FVY(0.054)K 67.519 0.0032374 0 1324.3 1532.4 1456.2 1170.5 1813.3 1739.8 1378.8 1555.4 1723 1568.5 TRUE FALSE FALSE 1308.158922 1553.973167 1481.54455 1305.838717 1720.760535 1628.632395 1495.915238 1600.403045 1568.890565 1527.750144 0.856264964 1.017164471 0.969755792 0.854746257 1.126336359 1.066033213 0.97916223 1.047555486 1.026928762 1 10.5771929 -8.759910554 24.99997038 0.935931026 1.050175514 0.334779487 0.06645885 33.57482613 549012.2279 0.010421019 0.019984198 1.74E-09 8.759910554 0.114244488 T(ph)TRTPEEGGYSYDISEK ddPTM_HeLa_Romidepsin_16h_R1 1 TTRTPEEGGYSYDISEK 17 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.479)T(0.479)RT(0.043)PEEGGYSYDISEK 100.47 0.0017298 330010000 4795.2 4620.8 4437.3 4501.4 4517.5 4661.1 4332.1 4679.3 5403.2 4708.6 TRUE FALSE FALSE 4736.754258 4685.851744 4514.529345 5021.873048 4286.955118 4363.270753 4700.068466 4814.688163 4919.924259 4586.269893 1.03281193 1.021713038 0.984357539 1.094979834 0.934736773 0.951376795 1.024812882 1.049804803 1.072750705 1 12.16310554 -8.729147285 24.99995167 1.018746693 0.989884621 0.139960292 0.044500764 367.7972524 284740.6336 0.005938773 0.011876849 1.87E-09 8.729147285 -0.028862073 T(ph)TSPLEEEEREIK ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPLEEEEREIK 13 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 T(0.466)T(0.267)S(0.267)PLEEEEREIK 179.59 2.78E-06 2798400 2177.7 1606.6 1573 2815.6 2116.8 1856 1820.8 1987.3 2071.5 2017.2 TRUE FALSE FALSE 2151.157355 1629.217757 1600.377405 3141.15292 2008.771797 1737.40759 1975.458707 2044.79939 1886.219852 1964.792853 1.094851985 0.829205865 0.814527294 1.598719638 1.022383502 0.884270109 1.005428487 1.040720087 0.960009524 1 10.9401615 -8.515943932 24.98983663 1.053990583 0.975278156 0.023682077 0.20772381 1107.204679 3989849.682 0.029503673 0.06087192 3.05E-09 8.515943932 -0.078712427 T(ph)TSPPLSIPTTHLIHQPAGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPPLSIPTTHLIHQPAGSR 21 0 Q5T5U3;A0A087WW76;A0A452Q6Z5;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 T(0.35)T(0.346)S(0.297)PPLS(0.007)IPTTHLIHQPAGSR 98.067 0.0004281 10829000 814.65 691.42 627.78 513.28 751.8 672.61 602.61 804.65 1025.9 825.2 TRUE FALSE FALSE 804.7207325 701.1538289 638.7062476 572.6278487 713.4328406 629.6323917 653.7956784 827.9312782 934.1409346 803.761185 1.001193822 0.872340991 0.794646792 0.71243531 0.887617932 0.783357549 0.813420318 1.030071237 1.16221205 1 9.650623099 -10.17589879 3.536594253 1.001020587 0.830285553 0.499257556 0.093312229 0.143322612 3.418419518 0.012768472 0.01564398 6.67E-11 10.17589879 -0.170735034 T(ph)TSPSSDTDLLDR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPSSDTDLLDR 13 0 Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3;K7ENU0;K7ERZ4;K7EJ43 Q96QT6 PHF12 PHD finger protein 12 1 0 T(0.867)T(0.009)S(0.124)PSSDTDLLDR 234.87 6.17E-41 40885000 3582.3 3315.8 3041.7 2605 2448.1 2821.6 2363.5 2852.5 3614.4 3100.2 TRUE FALSE FALSE 3538.63755 3362.479919 3094.639513 2906.202357 2323.164322 2641.308866 2564.255631 2935.032587 3291.119012 3019.656357 1.171867634 1.113530654 1.024831685 0.962428175 0.769347253 0.874705117 0.849187897 0.971975695 1.089898526 1 11.56016866 -9.193087532 2.43785272 1.084591478 0.866394459 0.716246263 0.063476929 0.147912777 1.720666022 0.012472113 0.021814131 6.41E-10 9.193087532 -0.218197018 T(ph)TTLSGTAPAAGVVPSR ddPTM_HeLa_Romidepsin_16h_R1 1 TTTLSGTAPAAGVVPSR 17 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 T(0.916)T(0.079)T(0.005)LSGTAPAAGVVPSR 195.6 2.03E-13 11777000 900.5 850.21 782.18 848.65 985.18 884.3 763.9 797.53 844.56 796.5 TRUE FALSE FALSE 889.5243596 862.1792787 795.7935148 946.774906 934.9025884 827.7960839 828.7856469 820.6052723 769.0204384 775.8068152 1.146579718 1.111332437 1.02576247 1.220374567 1.205071379 1.067013163 1.068288691 1.057744346 0.991252491 1 9.599553639 -12.37929955 1.001314897 0.997112087 1.115972782 0.373280602 0.060243256 0.551437386 0.950279385 0.04850367 0.01133053 4.18E-13 12.37929955 0.118860695 T(ph)VEDFNKFCT(ph)FVLAY(ph)AGYIPYPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVEDFNKFCTFVLAYAGYIPYPK 23 1 Q86YI8 Q86YI8 PHF13 PHD finger protein 13 3 0 T(0.998)VEDFNKFCT(0.985)FVLAY(0.338)AGY(0.339)IPY(0.339)PK 45.047 0.019915 16322000 504.22 377.17 559.59 165.52 401.3 491.4 306.26 403.48 632.18 864.59 TRUE FALSE FALSE 498.0743727 382.4798092 569.3294292 184.6582012 380.8201635 460.0011259 332.2737168 415.1540572 575.6362375 842.1278272 0.59144747 0.454182604 0.676060582 0.219275738 0.452211827 0.546236701 0.394564466 0.492982234 0.683549716 1 9.717895427 -11.69350703 0.447032035 1.068858254 0.42967104 0.472929597 0.144011189 0.430308199 0.158100765 0.122178052 0.035411363 2.03E-12 11.69350703 -0.639187214 T(ph)VFSPTLPAAR ddPTM_HeLa_Romidepsin_16h_R1 4 TVFSPTLPAAR 11 0 Q7Z2W4-2;Q7Z2W4;C9J6P4;Q7Z2W4-3 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 T(0.974)VFS(0.014)PT(0.013)LPAAR;T(0.936)VFS(0.06)PT(0.004)LPAAR;T(0.975)VFS(0.012)PT(0.012)LPAAR;T(0.947)VFS(0.046)PT(0.007)LPAAR ;;; 171.67 0.00054685 725580000 15127.2 14927.1 13162.1 12364.7 15457.7 14380.8 12558.1 13406.5 14596.1 13771.6 TRUE FALSE FALSE 14942.82387 15137.24411 13391.18083 13794.36479 14668.83589 13461.91329 13624.7847 13794.39593 13290.58826 13413.81185 1.113987883 1.128481917 0.998312857 1.028370231 1.093562073 1.003585964 1.015728031 1.028372552 0.990813679 1 13.71143165 T(ph)VFYY(ph)YGSDKDK ddPTM_HeLa_Romidepsin_16h_R1 1 TVFYYYGSDKDK 12 1 O75563 O75563 SKAP2 Src kinase-associated phosphoprotein 2 2 0 T(0.89)VFY(0.17)Y(0.47)Y(0.47)GSDKDK 72.928 0.0040715 0 587 640.59 638.62 772.63 727.4 472.76 548.4 562.41 669.2 664.38 TRUE FALSE FALSE 579.8454182 649.6082428 649.7349132 861.9651159 690.2780637 442.5521618 594.9810823 578.682446 609.345076 647.1193118 0.896040974 1.00384617 1.004041915 1.332003388 1.066693655 0.68388032 0.919430268 0.894243821 0.941627092 1 9.337887922 -8.283238636 24.86484512 0.994007391 0.841209304 0.308839711 0.12875664 890.6396683 1015886.774 0.020245284 0.045308671 5.21E-09 8.283238636 -0.152798087 T(ph)VGTPIASVPGSTNTGTVPGSEKDSDSMETEEK ddPTM_HeLa_Romidepsin_16h_R1 1 TVGTPIASVPGSTNTGTVPGSEKDSDSMETEEK 33 1 A0A087WW66;Q99460-2;Q99460;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 1 0 T(0.501)VGT(0.452)PIAS(0.005)VPGS(0.005)T(0.015)NT(0.015)GT(0.005)VPGSEKDSDSMETEEK 54.748 0.00074359 13343000 3332.1 3937.2 3562.5 3696.2 3563.1 3458.8 3020.4 3509.5 3626.5 3536.8 TRUE FALSE FALSE 3291.487084 3992.628005 3624.503818 4123.572035 3381.261711 3237.793843 3276.952701 3611.041845 3302.136757 3444.913426 0.955462932 1.158992262 1.052132048 1.197003096 0.981522986 0.939876694 0.951243847 1.048224265 0.958554352 1 11.75025201 -6.895990145 17.35105204 1.005961914 3.74434156 0 0.086509222 532.7763825 90671.46316 0.01224944 1157.514964 1.27E-07 6.895990145 2.738379646 T(ph)VIIEQSWGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVIIEQSWGSPK 12 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JL19;C9JCQ4;C9JL25 P10809;C9JL25 HSPD1 "60 kDa heat shock protein, mitochondrial" 1 0 T(0.995)VIIEQS(0.004)WGS(0.001)PK 244.73 7.48E-50 385210000 6969.1 5985.8 7124.8 5673.9 6064.3 5958.1 5749.9 5503.5 6306.4 5395.2 TRUE FALSE FALSE 6884.157929 6070.06825 7248.804155 6329.943015 5754.816142 5577.396639 6238.296362 5662.735089 5742.339789 5255.031926 1.310012579 1.15509636 1.379402496 1.204548917 1.095105838 1.061344007 1.187109127 1.077583385 1.092731666 1 12.35948381 -8.751420068 24.52417882 1.173580596 1.107991434 0.126010654 0.104148982 459.38598 1124423.129 0.02010286 0.03982218 1.77E-09 8.751420068 -0.065589162 T(ph)VSASSTGDLPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVSASSTGDLPK 12 0 P78362;H7C5L6;P78362-2 P78362 SRPK2 SRSF protein kinase 2;SRSF protein kinase 2 N-terminal;SRSF protein kinase 2 C-terminal 1 0 T(0.959)VS(0.009)AS(0.009)S(0.021)T(0.003)GDLPK 139.19 0.0044325 16459000 2354.6 2544.8 1925.6 2439.1 2915.6 3136 3147 2824 2847.3 2368.1 TRUE FALSE FALSE 2325.90123 2580.625761 1959.11426 2721.120218 2766.806052 2935.619721 3414.306101 2905.707984 2592.630357 2306.576421 1.008378135 1.118812166 0.849360222 1.179722551 1.199529323 1.272717303 1.48024842 1.25974928 1.124016674 1 11.17153738 -8.651793798 1.394403865 1.004376508 1.361841136 0.656699238 0.097002436 0.142825418 0.550224158 0.012647669 0.0350664 2.23E-09 8.651793798 0.357464628 T(ph)VSDNSLSNSR ddPTM_HeLa_Romidepsin_16h_R1 3 TVSDNSLSNSR 11 0 H0Y7W6;B7ZL14;Q96RU3-4;Q96RU3-3;Q96RU3-5;Q96RU3-2;Q96RU3 H0Y7W6 FNBP1 Formin-binding protein 1 1 0 T(0.941)VS(0.014)DNS(0.044)LSNSR;T(0.992)VS(0.007)DNS(0.001)LSNSR;T(0.911)VS(0.081)DNS(0.008)LSNSR ;; 185.57 4.90E-06 399970000 5512.3 4643.59 4971.31 4820 7218.4 8251.2 8051.9 7890.9 5426.7 4778 TRUE FALSE FALSE 5445.113967 4708.962582 5057.833565 5377.311079 6850.018112 7723.97495 8735.828185 8119.210742 4941.322361 4653.866871 1.17001928 1.011838695 1.086802374 1.155450129 1.471898166 1.659689708 1.87711175 1.744616029 1.06176702 1 12.18421423 -8.512218892 1.524819769 1.074613295 1.810183901 0.964452021 0.059532042 0.061471013 0.278699729 0.011400708 0.03362493 3.07E-09 8.512218892 0.735570606 T(ph)VSEPNLK ddPTM_HeLa_Romidepsin_16h_R1 2 TVSEPNLK 8 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;C9JF80;H0YI41;C9JAH2;F8VWY3;C9JEB6 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 0 T(0.999)VS(0.001)EPNLK;T(0.94)VS(0.06)EPNLK ; 150.27 0.014258 197263000 12113.5 11086.1 10347.4 10291 8566.8 7126.6 5686.8 5958.9 10464.5 9858.9 TRUE FALSE FALSE 11965.856 11242.17041 10527.49216 11480.89384 8129.604229 6671.23326 6169.83665 6131.31137 9528.528911 9602.764357 1.246084519 1.170722303 1.096298083 1.195582169 0.846589995 0.694720084 0.642506306 0.638494411 0.992269367 1 13.22923406 -8.535946091 2.715233343 1.126963606 0.656635753 0.872929198 0.078890283 0.081397397 1.207188235 0.014547172 0.033790045 2.91E-09 8.535946091 -0.470327853 T(ph)VSFSVY(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 TVSFSVYLK 9 0 A0A5F9ZGY2;A0A5F9ZHP5;A0A5F9ZH74;A0A5F9ZH37;A0A5F9ZHE7;A0A5F9ZH14;A0A5F9ZGX9;Q3SYG4-7;Q3SYG4-3;Q3SYG4;H7BZ69 A0A5F9ZGY2 BBS9 Protein PTHB1 2 0 T(0.499)VS(0.499)FS(0.006)VY(0.995)LK 68.787 0.0043542 0 905.42 840.32 764.41 831.72 837.95 839.71 878.66 894.42 705.53 851.12 TRUE FALSE FALSE 894.3843928 852.150047 777.7142354 927.8873798 795.1862847 786.055241 953.2933585 920.2986315 642.4256298 829.0077797 1.078861278 1.027915621 0.938126583 1.119274635 0.95920244 0.948188015 1.149920884 1.110120621 0.774933174 1 9.69524183 -7.739802977 24.9998494 1.025752569 1.130020828 0.171452539 0.096984895 204.792752 236624.9175 0.007938925 0.029649881 1.82E-08 7.739802977 0.10426826 T(ph)VSLYEQGMVQMTVKDY(ph)MR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSLYEQGMVQMTVKDYMR 19 1 A0A087WUB1;B8ZZ49;E7ERG9;E7EQ43;Q6ZRS4-2;Q6ZRS4;Q6ZRS4-4 A0A087WUB1 CCDC129 Coiled-coil domain-containing protein 129 2 0 T(0.456)VS(0.457)LY(0.086)EQGMVQMT(0.049)VKDY(0.952)MR 42.913 0.004236 0 454.31 327.94 351.32 440.92 715.02 837.8 531.83 618.72 437.84 628.55 TRUE FALSE FALSE 448.772695 332.5567479 357.4345772 491.901245 678.5298613 784.2672839 577.0036269 636.621687 398.6784938 612.2201804 0.733024996 0.543197952 0.58383338 0.803471138 1.108310185 1.281021614 0.942477307 1.039857403 0.651201164 1 9.25790679 -8.76160274 24.99771701 0.814853919 1.095607069 0.522523808 0.160047173 3.904221712 597567.7225 0.027915436 0.053029079 1.73E-09 8.76160274 0.28075315 T(ph)VSQQS(ph)FDGVSLDSSGPEDR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSQQSFDGVSLDSSGPEDR 20 0 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 2 0 T(0.994)VS(0.006)QQS(0.868)FDGVS(0.125)LDS(0.007)S(0.001)GPEDR 191.89 4.62E-17 10194000 1641.7 1761.3 1842.8 1727.8 1316.9 1489.9 1301.1 1274.3 1759.6 1630.4 TRUE FALSE FALSE 1621.690329 1786.095628 1874.873161 1927.576366 1249.693679 1394.700198 1411.615402 1311.16986 1602.216969 1588.041973 1.021188581 1.12471563 1.1806194 1.213806939 0.786939955 0.878251471 0.88890308 0.825651892 1.008926084 1 10.63303333 -8.741051306 24.99058711 1.046753258 0.850456669 0.67960996 0.079420375 150.8040315 184846.5255 0.013362676 0.02669952 1.82E-09 8.741051306 -0.196296589 T(ph)VSSPIPYTPSPSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 T(0.857)VS(0.132)S(0.011)PIPYTPSPSSSR 225.33 1.02E-34 21166000 2032.4 2217.8 1895.7 1084.7 1961.4 1650.7 1372.5 1282.6 2106.1 2327.7 TRUE FALSE FALSE 2007.628327 2249.022247 1928.693863 1210.118118 1861.302439 1545.225597 1489.080116 1319.710007 1917.725141 2267.226018 0.885499862 0.991970906 0.850684426 0.533743927 0.82096025 0.681548988 0.656785033 0.582081361 0.845846477 1 11.1467125 -9.472690884 5.388695883 0.947063573 0.666473217 0.716446131 0.082480235 0.07742977 5.140932271 0.012166221 0.018470346 3.37E-10 9.472690884 -0.280590356 T(ph)WSY(ph)T(ph)Y(ph)LEK ddPTM_HeLa_Romidepsin_16h_R1 1 TWSYTYLEK 9 0 Q6N022;Q9P273;H0YCJ4 Q6N022 TENM4;TENM3 Teneurin-4;Teneurin-3 4 0 T(0.846)WS(0.176)Y(0.982)T(0.996)Y(0.999)LEK 64.82 0.0030333 0 1327.2 527.84 713.1 31.022 734.54 655.33 1070.7 731.37 1446.8 919.7 TRUE FALSE FALSE 1311.023576 535.2709454 725.5112064 34.6089096 697.0536829 613.456528 1161.645231 752.531037 1317.394584 895.8060614 1.463512732 0.597529944 0.80989763 0.038634378 0.778130125 0.68480953 1.296759736 0.84006022 1.470624772 1 9.807042618 -10.25268683 24.64615136 1.218881014 0.720988301 0.41162637 0.317828144 467.7306753 1317075.036 0.056754183 0.068934799 5.59E-11 10.25268683 -0.497892713 T(ph)Y(ph)S(ph)IPY(ph)SES(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TYSIPYSESK 10 0 Q6ZP01 Q6ZP01 RBM44 RNA-binding protein 44 5 0 T(1)Y(1)S(1)IPY(0.977)S(0.056)ES(0.967)K 55.335 0.0039694 0 800.33 574.31 895.58 530.09 905.24 643.04 734.6 518.53 610.49 615.56 TRUE FALSE FALSE 790.5752701 582.3951513 911.1671942 591.3814999 859.0422249 601.9518193 796.9969057 533.5328474 555.8862454 599.5676625 1.318575566 0.97135851 1.519707034 0.986346558 1.432769441 1.00397646 1.32928601 0.889862614 0.927145142 1 9.227778764 -6.300988454 14.42735588 1.162151939 1.175077559 0 0.223936084 0 0 0.026035807 0 5.00E-07 6.300988454 0.01292562 T(ph)Y(ph)VDEVNSELVNIYT(ph)FNHTVTR ddPTM_HeLa_Romidepsin_16h_R1 1 TYVDEVNSELVNIYTFNHTVTR 22 0 E9PMC3;F5H8L4;C9JBG5;Q8NBJ9;Q8NBJ9-2 E9PMC3 SIDT2 SID1 transmembrane family member 2 3 0 T(0.984)Y(0.974)VDEVNS(0.042)ELVNIYT(0.539)FNHT(0.257)VT(0.203)R 52.96 0.0077372 4629800 754.69 590.12 996.32 650.61 1551.1 1433.3 1304 1406 1186.4 1036.9 TRUE FALSE FALSE 745.491548 598.4277248 1013.660532 725.8365894 1471.941579 1341.716756 1414.761727 1446.680392 1080.285413 1009.961189 0.738138808 0.592525467 1.003662857 0.718677705 1.457423905 1.328483481 1.400808015 1.432411867 1.06963062 1 9.980084138 -8.756754345 24.99999852 0.850568428 1.399048183 0.784693044 0.141379362 41.1402352 219527.3729 0.02100763 0.040938041 1.75E-09 8.756754345 0.548479755 T(ph)YLEVVR ddPTM_HeLa_Romidepsin_16h_R1 1 TYLEVVR 7 0 O94874;O94874-2 O94874 UFL1 E3 UFM1-protein ligase 1 1 0 T(0.647)Y(0.353)LEVVR 80.377 0.012625 4560700 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 T(ph)YSAPAINAIQGGSFESPKK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSAPAINAIQGGSFESPKK 20 1 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 T(0.845)Y(0.002)S(0.153)APAINAIQGGSFESPKK 66.853 0.0044811 23715000 1653.9 1685.9 1752.6 878.42 1353.2 1452 927.53 1029.6 1538.1 1352.6 TRUE FALSE FALSE 1633.741631 1709.634144 1783.103268 979.9870535 1284.141155 1359.221886 1006.314375 1059.389852 1400.528484 1317.459257 1.240069947 1.297675154 1.353440919 0.743846194 0.974710336 1.03169937 0.763829598 0.804115836 1.063052596 1 10.36354263 -9.251826955 24.96713272 1.149370056 0.873602408 0.60253792 0.130598834 489.6644876 1271845.356 0.023285915 0.0382849 5.60E-10 9.251826955 -0.275767649 T(ph)YVENS(ph)KS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 TYVENSKSPK 10 1 O95171-3;O95171-2;O95171 O95171-3 SCEL Sciellin 3 0 T(0.998)Y(0.002)VENS(1)KS(1)PK 104.87 0.001174 0 147.75 158.26 0 148.83 142.03 281.85 0 0 165.37 111.62 TRUE FALSE FALSE 145.9491662 160.4879884 0 166.0384249 134.7816791 263.8406946 0 0 150.578893 108.7200963 1.342430435 1.476157526 0 1.527210061 1.239712654 2.42678864 0 0 1.385014345 1 6.764474829 -7.630147003 24.99966335 1.204214814 4.56E-08 0.449710028 0.567261925 5.260950524 1201.064723 0.07365158 0.275579059 2.34E-08 7.630147003 -1.204214768 TAAAASEK(ac)NR ddPTM_HeLa_Romidepsin_16h_R1 1 TAAAASEKNR 10 1 K7EN09;Q9UNZ5 K7EN09 C19orf53 Leydig cell tumor 10 kDa protein homolog 0 1 TAAAASEK(1)NR 117.7 0.015444 477780 0 132.95 215.2 166.3 0 153.55 356.99 0 193.69 0 FALSE TRUE FALSE 0 134.8216736 218.9454657 185.5283885 0 143.7386506 387.3127217 0 176.3658813 0 0 TAADVVS(ph)PGANSVDSR ddPTM_HeLa_Romidepsin_16h_R1 3 TAADVVSPGANSVDSR 16 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 0 TAADVVS(0.91)PGANS(0.082)VDS(0.008)R;T(0.073)AADVVS(0.859)PGANS(0.067)VDSR;T(0.078)AADVVS(0.921)PGANS(0.001)VDSR ;; 270.78 1.28E-86 78458000 15124.6 14462.5 12898.4 12134.4 13723.6 14235.8 11596.6 12180.4 15510.5 14598.3 TRUE FALSE FALSE 14940.25556 14666.10345 13122.89124 13537.43642 13023.23348 13326.17832 12581.61491 12532.82066 14123.20203 14219.03406 1.050722257 1.031441615 0.922910177 0.95206442 0.91590142 0.937207005 0.884843152 0.881411536 0.9932603 1 13.79553584 -9.747400908 7.814123201 1.025222904 0.916758908 0.800679515 0.025127337 0.05192747 17.37626457 0.004469774 0.006200015 1.79E-10 9.747400908 -0.108463996 TAAILHGGS(ph)PDFVGNGK ddPTM_HeLa_Romidepsin_16h_R1 1 TAAILHGGSPDFVGNGK 17 0 H0YME5;Q9P2K8-3;Q9P2K8-2;Q9P2K8 H0YME5 EIF2AK4 Eukaryotic translation initiation factor 2-alpha kinase 4 1 0 TAAILHGGS(1)PDFVGNGK 195.5 1.02E-13 18210000 7152.3 7357.5 6756.9 6697.6 7451.9 7073.6 5902.7 7195.9 7105.2 7168.1 TRUE FALSE FALSE 7065.125017 7461.079078 6874.50101 7472.008025 7071.601736 6621.619789 6404.075191 7404.102013 6469.693117 6981.871729 1.011924208 1.068635943 0.984621499 1.070201275 1.012851856 0.948401811 0.917243318 1.060475228 0.926641647 1 12.76939814 -8.284383224 21.09198155 1.014365905 0.969560469 0.084385265 0.051291326 127.050699 116796.2752 0.005791262 0.01296731 5.20E-09 8.284383224 -0.044805436 TAAKGEAAAERPGEAAVAS(ph)SPSK ddPTM_HeLa_Romidepsin_16h_R1 1 TAAKGEAAAERPGEAAVASSPSK 23 2 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 TAAKGEAAAERPGEAAVAS(0.803)S(0.187)PS(0.01)K 59.574 0.0034066 31185000 4762.8 5151.5 4206.3 6833.8 4597.8 4476.3 3831.2 4049.3 4957.1 4529 TRUE FALSE FALSE 4704.749162 5224.022952 4279.508887 7623.95611 4363.157109 4190.278877 4156.622032 4166.460107 4513.724561 4411.335927 1.066513464 1.184226964 0.9701163 1.728264688 0.989078406 0.949888865 0.942259239 0.944489419 1.023210346 1 12.10699991 -8.539763866 24.99954462 1.094334995 0.949261246 0.146144695 0.209805086 455.2621238 674043.8141 0.030892424 0.061795945 2.89E-09 8.539763866 -0.145073749 TADGIVSHLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TADGIVSHLKK 11 1 P30101 P30101 PDIA3 Protein disulfide-isomerase A3 0 1 ; TADGIVSHLK(1)K;TADGIVSHLK(1)K 112.94 6.00E-06 3037200 3603.2 3343.1 4148 3559 10715.3 8396.7 8017.4 7413.6 9246.1 6585.6 FALSE TRUE FALSE 3559.282812 3390.16425 4220.1942 3970.508326 10168.45826 7860.177969 8698.397756 7628.100819 8419.105659 6414.505163 0.554880341 0.52851532 0.657914226 0.61898903 1.58522879 1.225375578 1.356051252 1.189195523 1.312510544 1 12.64712226 -8.769256112 24.99999752 0.741469381 1.332070034 0.557252489 0.243215056 82.2781743 263148.1856 0.031721285 0.058268779 1.70E-09 8.769256112 0.590600653 TADSSSS(ph)EDEEEYVVEK ddPTM_HeLa_Romidepsin_16h_R1 1 TADSSSSEDEEEYVVEK 17 0 P45973;F8VNY3 P45973 CBX5 Chromobox protein homolog 5 1 0 TADS(0.189)S(0.012)S(0.004)S(0.794)EDEEEYVVEK 335.1 3.72E-204 92488000 981.51 830.77 847.14 894.69 940.27 855.71 882.63 768.52 969.36 792.18 TRUE FALSE FALSE 969.5469786 842.4656019 861.8841163 998.1382674 892.2845133 801.0328927 957.6005702 790.7559137 882.6580138 771.5990494 1.256542474 1.091843753 1.11701034 1.293597067 1.156409555 1.038146552 1.241059811 1.024827486 1.143933516 1 9.591707556 -12.56192962 1.335615861 0.999988903 1.16649731 0.006452535 0.096446947 0.401230992 1.282552104 0.060040471 0.014130503 2.74E-13 12.56192962 0.166508407 TADSVS(ph)PLEPPTKDK ddPTM_HeLa_Romidepsin_16h_R1 2 TADSVSPLEPPTKDK 15 1 Q9UMZ2-6;Q9UMZ2-9;Q9UMZ2-4;Q9UMZ2-8;Q9UMZ2-3;Q9UMZ2-7;Q9UMZ2-5;Q9UMZ2 Q9UMZ2-6 SYNRG Synergin gamma 1 0 T(0.03)ADS(0.107)VS(0.863)PLEPPTKDK;TADS(0.003)VS(0.996)PLEPPTKDK ; 102.5 0.002593 27058000 5744.9 4248.7 4290.6 4136.1 6816.9 6479.7 7207.4 7756.5 6227.7 5166.6 TRUE FALSE FALSE 5674.878949 4308.51331 4365.276093 4614.335343 6469.008156 6065.668082 7819.596376 7980.92209 5670.678914 5032.370987 1.127674999 0.856159715 0.867439246 0.916930678 1.285479185 1.205330072 1.553859283 1.585916879 1.126840396 1 12.29702257 -7.94888442 1.290568932 1.024241799 1.633305233 0.780377735 0.11655027 0.213360142 0.581381549 0.018838707 0.122664584 1.12E-08 7.94888442 0.609063434 TAEK(ac)TSLSFK ddPTM_HeLa_Romidepsin_16h_R1 2 TAEKTSLSFK 10 1 H0Y612;Q9UPN9-2;Q9UPN9 H0Y612 TRIM33 E3 ubiquitin-protein ligase TRIM33 0 1 ; TAEK(1)TSLSFK;TAEK(1)TSLSFK 188.91 1.07E-07 55329000 9520.2 10484.4 10789.1 7685.6 6520.4 5546.1 5454.2 3947.7 9997.2 7875.8 FALSE TRUE FALSE 9404.164141 10631.99966 10976.87976 8574.245234 6187.639657 5191.722109 5917.479612 4061.920471 9103.025394 7671.185581 1.225907527 1.385965643 1.430923505 1.117721002 0.806608 0.676782233 0.771390491 0.529503612 1.186651698 1 12.90523385 -8.679021346 3.133591313 1.161664021 0.677590927 0.781713584 0.136067401 0.121683167 2.39599412 0.025153145 0.052907703 2.09E-09 8.679021346 -0.484073093 TAENATSGETLEENEAGD ddPTM_HeLa_Romidepsin_16h_R1 2 TAENATSGETLEENEAGD 18 0 Q9UQ80;Q9UQ80-2 Q9UQ80 PA2G4 Proliferation-associated protein 2G4 0 0 ; ; 143.55 0.0010599 286310000 16836.3 15930.5 15586.5 14954.6 16205.7 15872 14883.5 15436.9 18217.7 15652.9 FALSE FALSE TRUE 16631.0927 16154.77 15857.77649 16683.72122 15378.66266 14857.83042 16147.70412 15883.54235 16588.26328 15246.2354 1.090832738 1.05959075 1.040110957 1.09428464 1.008685899 0.974524532 1.059127299 1.041800938 1.088023558 1 13.89616544 TAEPS(ph)PGQDGTSR ddPTM_HeLa_Romidepsin_16h_R1 1 TAEPSPGQDGTSR 13 0 Q9Y2D5-6;Q9Y2D5-4;C9JZH4;B1ALY0;Q8IXS6-2 Q9Y2D5-6;B1ALY0 AKAP2;PALM2;PALM2-AKAP2 A-kinase anchor protein 2;Paralemmin-2 1 0 TAEPS(0.999)PGQDGTSR 98.253 0.014238 6893500 2169.7 2388.4 2344.6 2097.5 1927.9 2549.6 2200.8 2794.1 2560.1 1987.5 TRUE FALSE FALSE 2143.254862 2422.023958 2385.406779 2340.022819 1829.512069 2386.688788 2387.735897 2874.942875 2331.118244 1935.864463 1.10713064 1.251133023 1.232217867 1.208774097 0.945062066 1.232880108 1.233421008 1.485095124 1.204174305 1 10.91876223 -4 0.165357851 0.989377502 2.417254324 0.242042279 0.123073294 42.51037193 0.439053651 0.185376991 14.9836694 1.00E-04 4 1.427876822 TAFYNEDDS(ph)EEEQR ddPTM_HeLa_Romidepsin_16h_R1 4 TAFYNEDDSEEEQR 14 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 0 TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR;TAFYNEDDS(1)EEEQR ;;; 260.08 5.82E-68 162918000 15793.8 15338.6 16287.2 9495.5 9939.9 10202.7 7958.1 7867.6 15779.3 15892.3 TRUE FALSE FALSE 15601.29909 15554.53721 16570.67188 10593.41439 9432.629812 9550.780398 8634.060815 8095.236593 14367.95989 15479.41575 1.007873898 1.004852991 1.070497243 0.684354924 0.60936601 0.616998765 0.557776918 0.522967838 0.928197815 1 13.9180634 -9.132805811 3.589535471 1.008490301 0.583058933 0.956988863 0.04317537 0.028763906 0.674598023 0.005627437 0.009676429 7.37E-10 9.132805811 -0.425431368 TAGS(ph)MPLGGRAS(ph)LT(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 TAGSMPLGGRASLTPQK 17 1 A0A087WX19;A0A087WX45;Q6IPM2-4;Q6IPM2;C9JE72 A0A087WX19 IQCE IQ domain-containing protein E 3 0 T(0.074)AGS(0.926)MPLGGRAS(1)LT(1)PQK 61.962 0.0036973 0 175.43 240.6 225.01 237.97 263.88 264.83 380.97 439.98 326.38 337.05 TRUE FALSE FALSE 173.2917917 243.9871731 228.9262047 265.4852111 250.4132189 247.9082177 413.3295823 452.7101271 297.1877554 328.2933924 0.527856471 0.74319855 0.697321999 0.808682773 0.762772644 0.75514227 1.259024981 1.378980319 0.905250493 1 8.358841903 -7.716207832 4.377248068 0.76369809 1.347553693 0.771499064 0.118837313 0.096038868 3.865710276 0.024044111 0.094793236 1.92E-08 7.716207832 0.583855602 TAHNSEAADLEESFNEHELEPSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 TAHNSEAADLEESFNEHELEPSSPK 25 0 A0A0D9SGE8;Q5JRC6;Q8IWS0-2 A0A0D9SGE8 PHF6 PHD finger protein 6 1 0 TAHNSEAADLEES(0.019)FNEHELEPS(0.291)S(0.69)PK 70.637 0.00026955 3606300 1907.6 1857.5 1977.1 1819.2 2092.9 2343.8 1790.7 1736.4 2465 2177.5 TRUE FALSE FALSE 1884.349437 1883.649934 2011.510596 2029.544464 1986.091503 2194.038744 1942.802013 1786.639994 2244.524226 2120.928236 0.888455067 0.888125257 0.948410494 0.956913312 0.936425603 1.034470996 0.916014969 0.842385878 1.05827448 1 11.05048009 -12.5284022 1.313141873 0.99963687 0.925453494 0.350958504 0.052118898 0.531667734 1.654345103 0.034585558 0.008448675 2.96E-13 12.5284022 -0.074183375 TAHNSEADLEES(ph)FNEHELEPSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 2 0 TAHNS(0.001)EADLEES(0.999)FNEHELEPS(0.386)S(0.614)PK 67.083 0.00047216 4022400 1809.4 1773.5 1826.4 1693.1 1788 2042.7 1645 1324.5 2441.2 2107.1 TRUE FALSE FALSE 1787.346337 1798.46738 1858.187726 1888.864188 1696.751688 1912.178063 1784.726259 1362.822318 2222.852958 2052.357238 0.870874867 0.876293535 0.905391952 0.920338893 0.826733113 0.931698452 0.869598248 0.664027827 1.08307312 1 11.00306616 -14.22044394 0.023013756 2.003864276 1.95E-18 0.549084072 0.069810018 830.3277825 2.456992905 130.729964 87.03011559 6.02E-15 14.22044394 -2.003864276 TAHNSEADLEESFNEHELEPSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TAHNSEADLEESFNEHELEPSSPK 24 0 Q8IWS0-5;Q8IWS0 Q8IWS0-5 PHF6 PHD finger protein 6 1 0 TAHNSEADLEES(0.072)FNEHELEPS(0.127)S(0.801)PK;TAHNSEADLEES(0.001)FNEHELEPS(0.116)S(0.884)PK ; 90.964 2.55E-05 32185000 7735.8 7096.4 7661.7 7277.6 8990.8 9883.7 8240.6 7703.8 10887 9481.6 TRUE FALSE FALSE 7641.513094 7196.303305 7795.048675 8119.070354 8531.965927 9252.163468 8940.556358 7926.697298 9913.239453 9235.266665 0.827427444 0.779219872 0.844052365 0.87913762 0.92384619 1.001829596 0.968088598 0.858307354 1.073411284 1 13.1729379 -6.958407548 14.31507057 0.908656753 0.659982055 0.026308631 0.087366412 8747471.475 93937171.79 0.012259403 55399620.03 1.10E-07 6.958407548 -0.248674697 TAIT(ph)TPNFK ddPTM_HeLa_Romidepsin_16h_R1 1 TAITTPNFK 9 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6;Q9BXS6-7;H0YMD2 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 TAIT(0.871)T(0.129)PNFK 147.73 0.011535 52596000 4937.8 5257.8 5637.7 3928.6 5550.2 7332.6 7323.6 6689.3 5782.5 5164.5 TRUE FALSE FALSE 4877.616194 5331.819446 5735.821804 4382.843217 5266.952583 6864.070525 7945.666401 6882.844342 5265.298717 5030.325545 0.969642253 1.059935266 1.140248628 0.87128421 1.047040104 1.364538033 1.579553118 1.368270161 1.046711325 1 12.29643605 -8.213714621 3.266306762 0.995891621 1.473111246 0.845809802 0.082376004 0.05805215 1.247313606 0.01086797 0.029775955 6.11E-09 8.213714621 0.477219625 TALALHYLLT(ph)YK ddPTM_HeLa_Romidepsin_16h_R1 1 TALALHYLLTYK 12 0 Q8IZT6;Q8IZT6-2;Q5VYL4 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 0 TALALHYLLT(0.998)Y(0.002)K 108.9 0.023173 34600000 5983.8 5692.2 5468.5 4549.9 6101.2 5785.1 5417.4 5799.2 6338.2 5736.2 TRUE FALSE FALSE 5910.867144 5772.334941 5563.676949 5075.980846 5789.832997 5415.450781 5877.553821 5966.990702 5771.295518 5587.172697 1.057935286 1.033140598 0.995794698 0.908506166 1.036272425 0.969264971 1.051972821 1.067980359 1.03295456 1 12.4479027 -16.52281141 17.11824082 1.023330239 1.019165358 0 0.046140488 0 0 0 0.006337168 3.00E-17 16.52281141 -0.004164881 TALAT(ph)SPITVGDLGIVR ddPTM_HeLa_Romidepsin_16h_R1 1 TALATSPITVGDLGIVR 17 0 P13994 P13994 CCDC130 Coiled-coil domain-containing protein 130 1 0 T(0.007)ALAT(0.879)S(0.114)PITVGDLGIVR 146.27 0.00029969 8920500 1317.9 1352.8 1356.9 1223.8 2205 2446.9 2070.7 2320.4 1229.1 1192.6 TRUE FALSE FALSE 1301.836928 1371.844754 1380.516275 1365.301514 2092.470622 2290.550987 2246.585206 2387.537113 1119.166218 1161.61608 1.120711869 1.18097948 1.188444529 1.175346603 1.801344401 1.971865771 1.934016966 2.055358181 0.963456203 1 10.18191761 -8.725744058 2.417611401 1.078477899 1.984256233 0.968988707 0.073861703 0.035961779 0.428395194 0.012082607 0.026033264 1.88E-09 8.725744058 0.905778335 TALIHDGLAR ddPTM_HeLa_Romidepsin_16h_R1 2 TALIHDGLAR 10 0 P25398 P25398 RPS12 40S ribosomal protein S12 0 0 ; ; 115.23 0.0069288 68076000 11043.8 10525.1 11551.2 9221.8 11924 11790.5 9853.4 10370.7 11669.6 9697.7 FALSE FALSE TRUE 10909.19392 10673.27263 11752.24379 10288.06791 11315.47379 11037.1251 10690.34755 10670.75984 10625.84175 9445.752356 1.15493118 1.129954739 1.244182925 1.089174003 1.197943092 1.16847496 1.131762421 1.129688715 1.12493334 1 13.20545 -12.1009685 0.676415501 0.988920736 1.158642586 0.191640139 0.055311681 0.365212954 0.276273717 0.035286718 0.008261636 7.93E-13 12.1009685 0.169721851 TALINS(ph)TGEEVAMR ddPTM_HeLa_Romidepsin_16h_R1 1 TALINSTGEEVAMR 14 0 P02545;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8 P02545 LMNA Prelamin-A/C;Lamin-A/C 1 0 TALINS(0.973)T(0.027)GEEVAMR 98.408 0.015743 10244000 2957.8 2570 2548.8 2078.7 2814.2 3052.2 2541.5 2770.4 3078.5 2811.2 TRUE FALSE FALSE 2921.749196 2606.180527 2593.160795 2319.049075 2670.580873 2857.174271 2757.374947 2850.557153 2803.15125 2738.164619 1.067046581 0.951798336 0.947043424 0.846935593 0.975317866 1.043463293 1.007015768 1.041046668 1.023733646 1 11.41899347 -13.34261014 23.28666864 0.999999606 1.007032666 0 0.063194572 190.9888278 613376.3228 0.123918751 0.010105655 4.54E-14 13.34261014 0.007033061 TALLDAAGVASLLTTAEVVVTEIPKEEK ddPTM_HeLa_Romidepsin_16h_R1 2 TALLDAAGVASLLTTAEVVVTEIPKEEK 28 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 182.21 9.46E-24 86179100 254.94 64.102 386.6 312.06 301 402.54 325.81 181.36 132.59 410.53 FALSE FALSE TRUE 251.8326932 65.00442964 393.3286108 348.1418455 285.6388468 376.8189931 353.4842933 186.6073655 120.7308183 399.8643714 0.629795279 0.162566196 0.983655056 0.870649826 0.714339329 0.942367013 0.884010476 0.46667665 0.301929421 1 8.64336693 -12.34715059 1.179106637 0.99352135 0.712278363 0 0.318531725 0.664360445 1.708253397 0.143965283 0.041315512 4.50E-13 12.34715059 -0.281242986 TALPT(ph)SGSSAGELELLAGEVPAR ddPTM_HeLa_Romidepsin_16h_R1 1 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 1 0 T(0.01)ALPT(0.798)S(0.077)GS(0.038)S(0.077)AGELELLAGEVPAR 181.54 7.45E-15 2018400 1080.1 1136.5 933.93 864.64 1149.2 1193.5 1116.6 1158.2 1020.2 1086.2 TRUE FALSE FALSE 1066.935326 1152.499677 950.1846599 964.6137451 1090.552036 1117.239202 1211.443976 1191.71069 928.9507569 1057.980367 1.008464201 1.089339379 0.898111807 0.911750137 1.030786647 1.05601128 1.145053362 1.126401516 0.878041583 1 10.04709714 -8.009378486 2.225695902 0.996669325 1.137612298 0.486968694 0.064115144 0.188657235 1.81295292 0.007661423 0.029004447 9.79E-09 8.009378486 0.140942973 TALPTSGSS(ph)AGELELLAGEVPAR ddPTM_HeLa_Romidepsin_16h_R1 3 TALPTSGSSAGELELLAGEVPAR 23 0 Q9Y6I3-3;Q9Y6I3;Q9Y6I3-1 Q9Y6I3-3 EPN1 Epsin-1 1 0 TALPTSGS(0.01)S(0.99)AGELELLAGEVPAR;TALPTSGS(0.034)S(0.966)AGELELLAGEVPAR;TALPT(0.011)S(0.173)GS(0.254)S(0.562)AGELELLAGEVPAR ;; 201.48 6.36E-26 18148300 4605.4 5294.18 4271.68 4015.45 4539.97 4668.8 4637.53 5285.2 5739.49 5060.9 TRUE FALSE FALSE 4549.267613 5368.711605 4346.026799 4479.735222 4308.27839 4370.478748 5031.441682 5438.118923 5226.13564 4929.417088 0.922881455 1.08911693 0.881651262 0.908775854 0.873993479 0.886611676 1.020697091 1.103197158 1.060193436 1 12.26720134 -7.49908777 4.463878967 0.951413935 1.090588289 0.301100238 0.071554311 0.17017372 8.024399712 0.009181953 0.049609832 3.17E-08 7.49908777 0.139174355 TAMPS(ph)PGVSQNK ddPTM_HeLa_Romidepsin_16h_R1 2 TAMPSPGVSQNK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 T(0.055)AMPS(0.933)PGVS(0.012)QNK;T(0.001)AMPS(0.997)PGVS(0.002)QNK ; 122.55 0.0091905 37247000 13605.1 13154.5 12817.6 8179.7 12068.3 10809.2 9147.7 10425.6 13612.9 12152.4 TRUE FALSE FALSE 13439.27581 13339.6894 13040.68495 9125.475401 11452.40962 10118.52701 9924.70541 10727.24829 12395.32813 11836.6789 1.135392446 1.126979072 1.101718232 0.77094897 0.967535718 0.854845104 0.838470444 0.9062718 1.047196451 1 13.53097673 -9.274377232 24.90275089 1.073866709 0.870837076 0.764087258 0.059528881 322.6507977 621036.3578 0.010738393 0.016466884 5.32E-10 9.274377232 -0.203029634 TAMPSPGVS(ph)QNK ddPTM_HeLa_Romidepsin_16h_R1 1 TAMPSPGVSQNK 12 0 Q86UU0-3;Q86UU0-4;Q86UU0-2;Q86UU0;A0A087WZX0 Q86UU0-3 BCL9L B-cell CLL/lymphoma 9-like protein 1 0 T(0.001)AMPS(0.321)PGVS(0.678)QNK 117.95 0.011241 7573500 4412.4 4585.9 4415.1 3503.9 3843.6 3673.4 3056.6 3458.8 4875.2 4934.1 TRUE FALSE FALSE 4358.619972 4650.460421 4491.942963 3909.037404 3647.44675 3438.681595 3316.227528 3558.874921 4439.149902 4805.911371 0.906928912 0.96765422 0.934670371 0.813381085 0.758950065 0.715510822 0.690030937 0.740520298 0.923685345 1 12.23059433 -9.034870603 1.508449586 0.957201755 0.713317029 0.935191715 0.027564628 0.083646928 0.377333111 0.00592155 0.012300905 9.23E-10 9.034870603 -0.243884726 TANQASDTFSGIGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TANQASDTFSGIGKK 15 1 Q15847 Q15847 ADIRF Adipogenesis regulatory factor 0 1 ; TANQASDTFSGIGK(1)K;TANQASDTFSGIGK(1)K 250.81 1.19E-56 1764760 977.05 1159.71 1149.05 999.28 1642 1436.89 1448.35 1404.59 1421.53 1357.03 FALSE TRUE FALSE 965.1413388 1176.036428 1169.048733 1114.821455 1558.202613 1345.077366 1571.372813 1445.229596 1294.384797 1321.774165 0.730186264 0.889740819 0.884454216 0.843428087 1.178872045 1.017630244 1.188836077 1.093401304 0.97927833 1 10.36825999 -8.766357446 24.99995675 0.870217012 1.117334679 0.647952241 0.083103099 68.14693415 346412.6029 0.015645273 0.029016368 1.71E-09 8.766357446 0.247117667 TANSPGS(ph)GARPDPVR ddPTM_HeLa_Romidepsin_16h_R1 1 TANSPGSGARPDPVR 15 1 A0A3B3ISR7;E9PIF2;Q13206 A0A3B3ISR7 DDX10 Probable ATP-dependent RNA helicase DDX10 1 0 T(0.006)ANS(0.104)PGS(0.89)GARPDPVR 110.35 0.027782 16522000 1969.9 1904.9 1685.1 1362.4 1571.1 1724 1356.6 1413.8 1921.6 1762.5 TRUE FALSE FALSE 1945.890101 1931.717232 1714.428459 1519.927098 1490.920904 1613.841964 1471.82957 1454.706072 1749.727283 1716.709996 1.133499604 1.125243773 0.998670983 0.885372079 0.868475694 0.940078387 0.857354809 0.847380207 1.019232886 1 10.74543063 -9.403276787 3.22960803 1.069376601 0.880690965 0.797831967 0.045188834 0.107730931 2.119833629 0.009257541 0.014506074 3.95E-10 9.403276787 -0.188685636 TAPAAAVS(ph)PMQR ddPTM_HeLa_Romidepsin_16h_R1 1 TAPAAAVSPMQR 12 0 Q5M775-4;Q5M775;J3KSG2 Q5M775-4 SPECC1 Cytospin-B 1 0 TAPAAAVS(1)PMQR 103.43 0.019166 24763000 4261.5 4677 4532 4418.7 6017.5 6813.9 5606 5405.3 4446.6 3782.8 TRUE FALSE FALSE 4209.559199 4742.842929 4610.877559 4929.610885 5710.404521 6378.513781 6082.1735 5561.693827 4048.884959 3684.522311 1.142497953 1.287234146 1.251418005 1.337924015 1.549835783 1.73116438 1.650735967 1.509474868 1.098890064 1 11.84726187 -9.329693691 0.570958921 1.03608156 1.682706724 0.880387215 0.080603416 0.194167043 0.123250899 0.021107448 0.054905415 4.68E-10 9.329693691 0.646625164 TAPAAPAEDAVAAAAAAPS(ph)EPSEPSRPSPQPK ddPTM_HeLa_Romidepsin_16h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPK 32 1 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 0 TAPAAPAEDAVAAAAAAPS(0.376)EPS(0.376)EPS(0.219)RPS(0.029)PQPK 137.4 9.09E-16 10718000 6397.1 5973.1 5840 3580.3 6809.8 6063.4 4888.9 5521.9 6749.7 6210.5 TRUE FALSE FALSE 6319.129685 6057.189459 5941.64275 3994.271132 6462.270495 5675.968309 5304.163044 5681.667464 6145.989927 6049.150315 1.044630957 1.001328971 0.982227659 0.66030284 1.068293919 0.93830836 0.876844312 0.939250501 1.016008796 1 12.5625168 -9.508529645 24.95280401 1.018830982 0.89874885 0.26283899 0.095195434 644.5400067 1120843.649 0.013929499 0.020789252 3.10E-10 9.508529645 -0.120082133 TAPAAPAEDAVAAAAAAPSEPS(ph)EPSRPSPQPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 0 TAPAAPAEDAVAAAAAAPS(0.102)EPS(0.468)EPS(0.14)RPS(0.291)PQPKPR 88.708 7.97E-12 61493000 5275.4 5300.2 3772.3 3811.9 4090.7 4506.7 3211.6 4178.8 5591 5337.6 TRUE FALSE FALSE 5211.101396 5374.816355 3837.955299 4252.649814 3881.936314 4218.736415 3484.393224 4299.706985 5090.926957 5198.928383 1.002341447 1.033831582 0.738220459 0.817985843 0.74668009 0.811462691 0.670213738 0.827037164 0.979226214 1 12.34399857 -9.761272263 24.99999915 1.003591029 0.767324633 0.867379192 0.045062969 0.964321357 144241.6208 0.006286499 0.008572136 1.73E-10 9.761272263 -0.236266396 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPK ddPTM_HeLa_Romidepsin_16h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPK 32 1 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 0 TAPAAPAEDAVAAAAAAPS(0.007)EPS(0.129)EPS(0.432)RPS(0.432)PQPK 83.293 1.38E-08 10500000 4343.8 3948 3844 2796.1 4329.9 4037.2 3463.5 3568.7 4538.5 4654.3 TRUE FALSE FALSE 4290.856095 4003.580048 3910.903208 3119.398238 4108.929046 3779.235949 3757.689604 3671.954704 4132.565193 4533.380615 0.946502502 0.883133447 0.862690239 0.688095376 0.906371954 0.833646294 0.828893473 0.80998156 0.911585756 1 12.14637158 -10.17677351 1.34247351 0.980956319 0.818894357 0.513328248 0.056523907 0.177291047 0.613068425 0.009989876 0.012292984 6.66E-11 10.17677351 -0.162061962 TAPAAPAEDAVAAAAAAPSEPSEPS(ph)RPSPQPKPR ddPTM_HeLa_Romidepsin_16h_R1 1 TAPAAPAEDAVAAAAAAPSEPSEPSRPSPQPKPR 34 2 Q53GA4 Q53GA4 PHLDA2 Pleckstrin homology-like domain family A member 2 1 0 TAPAAPAEDAVAAAAAAPS(0.002)EPS(0.009)EPS(0.494)RPS(0.494)PQPKPR 92.363 5.33E-12 52112000 5902.1 5877.2 4785.3 5090.2 5349.5 5328.6 4050.9 5067 6580.9 6048.9 TRUE FALSE FALSE 5830.162935 5959.939376 4868.586139 5678.752874 5076.495053 4988.119657 4394.983345 5213.605651 5992.287822 5891.748706 0.989547115 1.011573927 0.826339748 0.963848453 0.861627898 0.84662804 0.745955669 0.884899528 1.017064393 1 12.52448018 -9.135251328 0.674276582 0.999851033 0.808781081 0.624460841 0.054735322 0.333995463 0.288448396 0.010617763 0.030593838 7.32E-10 9.135251328 -0.191069952 TAPPALPTGYDS(ph)EEEEESRPMSYDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TAPPALPTGYDSEEEEESRPMSYDEK 26 1 H0Y6K2;A0A140T9E9;A0A0G2JK44;P25440-4;P25440-3;P25440;P25440-2;A0A0G2JHN8;A0A140T9I1 H0Y6K2 BRD2 Bromodomain-containing protein 2 1 0 TAPPALPT(0.164)GY(0.141)DS(0.548)EEEEES(0.141)RPMS(0.005)Y(0.002)DEK 59.212 0.0047564 110220000 1545.7 1279 1531.8 1408.5 2033.8 2382.6 2025.4 1911.3 1381.1 1588.7 TRUE FALSE FALSE 1526.860414 1297.005796 1558.460336 1571.357397 1930.007597 2230.359549 2197.437425 1966.60045 1257.570957 1547.425345 0.986710227 0.83817019 1.007131195 1.015465723 1.247237938 1.441335801 1.420060381 1.270885511 0.812686028 1 10.59565409 -8.660967457 2.724440909 0.98102265 1.380526867 0.851658994 0.08255006 0.059643139 0.894092457 0.009363434 0.020326729 2.18E-09 8.660967457 0.399504217 TAPPAS(ph)PEAR ddPTM_HeLa_Romidepsin_16h_R1 4 TAPPASPEAR 10 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 T(0.093)APPAS(0.907)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR;TAPPAS(1)PEAR ;;; 139.31 1.41E-05 478306000 13273.8 13378.3 12033.7 10781.9 11169.9 12148 10292.1 10064.1 12810.3 13217 TRUE FALSE FALSE 13112.01382 13566.64006 12243.1415 12028.55401 10599.85832 11371.78201 11166.31072 10355.28885 11664.51468 12873.62043 1.018517975 1.053832535 0.951025515 0.934356739 0.823378192 0.883339855 0.86737921 0.80438047 0.90607881 1 13.65213022 -9.140969243 1.733332254 1.011727304 0.848184089 0.675770491 0.044841715 0.087175917 0.513419586 0.004560209 0.00864512 7.23E-10 9.140969243 -0.163543215 TAPS(ph)PLVEAK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 T(0.024)APS(0.976)PLVEAK 124.39 0.0097148 27966000 6779.6 6399.3 6786.9 6123.1 6804.9 6700.2 5512.2 6649.9 6698.3 6584.6 TRUE FALSE FALSE 6696.967628 6489.389513 6905.023148 6831.081632 6457.62056 6272.078844 5980.40613 6842.304365 6099.187272 6413.531143 1.044193515 1.011827863 1.076633604 1.065104617 1.006874437 0.977944709 0.932466998 1.066854469 0.950987395 1 12.64690317 -8.524586294 24.97747591 1.028332442 0.987423718 0.088867708 0.045181291 69.41415036 1015366.037 0.005622809 0.011310376 2.99E-09 8.524586294 -0.040908723 TAPSS(ph)PLTSPSDTR ddPTM_HeLa_Romidepsin_16h_R1 2 TAPSSPLTSPSDTR 14 0 A0A087WVA8;Q8IWB9;Q8IWB9-2 A0A087WVA8 TEX2 Testis-expressed sequence 2 protein 1 0 TAPS(0.121)S(0.846)PLT(0.027)S(0.005)PS(0.002)DTR;TAPS(0.004)S(0.995)PLTSPSDTR ; 198.37 1.84E-16 16099400 4261.8 4656.6 4111.1 3599.3 4314.3 5268.1 4205.3 5616.4 4305 3885.9 TRUE FALSE FALSE 4209.855542 4722.155737 4182.651971 4015.468001 4094.125172 4931.485412 4562.498077 5778.901673 3919.950018 3784.943758 1.112263698 1.247615827 1.105076386 1.060905593 1.081687189 1.302921715 1.20543352 1.52681309 1.035669291 1 11.88605615 -4 0.431855484 1.05931979 9.612748723 0.720289133 0.079579879 28.77307107 0.32189551 0.018898435 216.4349671 1.00E-04 4 8.553428934 TAPTALGITLSS(ph)SPTSTPELR ddPTM_HeLa_Romidepsin_16h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 TAPTALGITLSS(0.472)S(0.472)PT(0.055)STPELR 197.51 8.58E-19 122930000 2429.9 2303.2 2449.1 2446.3 2656.5 2421.3 2164.4 2276.4 2623.3 2510.6 TRUE FALSE FALSE 2400.283444 2335.62451 2491.725558 2729.152716 2520.928892 2266.586744 2348.244082 2342.264042 2388.665478 2445.37425 0.981560775 0.955119451 1.018954689 1.116047049 1.030896965 0.926887467 0.96028004 0.95783459 0.976809778 1 11.25583956 -8.257520268 24.96687578 1.002332108 0.949528633 0.300918592 0.042471009 410.8642534 2617416.294 0.006520826 0.016023374 5.53E-09 8.257520268 -0.052803474 TAPTALGITLSSS(ph)PT(ph)STPELR ddPTM_HeLa_Romidepsin_16h_R1 1 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 2 0 TAPTALGIT(0.016)LS(0.046)S(0.18)S(0.76)PT(0.474)S(0.143)T(0.38)PELR 77.037 0.0018991 0 409.03 498.69 460.92 517.27 579.35 588.48 351.84 398.45 563.94 485.71 TRUE FALSE FALSE 404.044585 505.7105709 468.9421193 577.0791912 549.7836076 550.8780272 381.7252808 409.9785221 513.499794 473.0911842 0.854052239 1.068949471 0.991229883 1.219805421 1.162109179 1.164422517 0.806874644 0.866595142 1.085413999 1 8.885974467 -13.30198038 5.277596842 1.001490683 0.976486348 0 0.141737435 2.089415427 114.7809671 0.162747652 0.022047553 4.99E-14 13.30198038 -0.025004335 TAPTALGITLSSS(ph)PTSTPELR ddPTM_HeLa_Romidepsin_16h_R1 4 TAPTALGITLSSSPTSTPELR 21 0 F5H1U9;O75970-5;O75970-3;O75970-2;O75970 F5H1U9 MPDZ Multiple PDZ domain protein 1 0 TAPTALGITLS(0.002)S(0.324)S(0.476)PT(0.152)S(0.037)T(0.009)PELR;TAPTALGITLSS(0.229)S(0.762)PT(0.008)STPELR;TAPTALGITLSS(0.225)S(0.765)PT(0.007)S(0.002)TPELR;TAPTALGITLS(0.012)S(0.152)S(0.425)PT(0.13)S(0.13)T(0.152)PELR ;;; 225.17 5.72E-42 146433400 5136.54 4989.36 5395.2 5006.97 5893.13 5624.65 4986.5 5627.67 5541.44 5332.74 TRUE FALSE FALSE 5073.933875 5059.600341 5489.101193 5585.89943 5592.381586 5265.253018 5410.053186 5790.497752 5045.799728 5194.194646 0.97684708 0.974087551 1.056776183 1.075412034 1.076659996 1.013680344 1.041557653 1.114801841 0.97143062 1 12.34268436 -9.752170899 23.25776491 0.987637752 1.061089773 0.706698944 0.025876347 37.89340231 95086.54244 0.004076376 0.005712679 1.77E-10 9.752170899 0.073452021 TAPTLS(ph)PEHWK ddPTM_HeLa_Romidepsin_16h_R1 3 TAPTLSPEHWK 11 0 Q96JM3 Q96JM3 CHAMP1 Chromosome alignment-maintaining phosphoprotein 1 1 0 TAPT(0.203)LS(0.797)PEHWK;T(0.004)APT(0.144)LS(0.853)PEHWK;T(0.027)APT(0.416)LS(0.557)PEHWK ;; 127.17 0.0068489 165455000 11475.6 11502.6 11227 10012.2 9900 8823.4 7679.3 8193.6 12032.6 10804.7 TRUE FALSE FALSE 11335.73097 11664.5339 11422.40123 11169.85767 9394.766058 8259.613216 8331.57955 8430.668889 10956.37412 10523.99234 1.077132196 1.10837537 1.085367688 1.061370753 0.892699819 0.784836491 0.791674802 0.801090368 1.041085338 1 13.36139448 -8.583877299 2.990324335 1.049096433 0.794293834 0.942888439 0.030087789 0.059914814 1.084294031 0.006241765 0.013822316 2.61E-09 8.583877299 -0.254802599 TAPTSTIAPGVVMAS(ph)SPALPTQPAEEAAR ddPTM_HeLa_Romidepsin_16h_R1 2 TAPTSTIAPGVVMASSPALPTQPAEEAAR 29 0 C9JBT4;C9J896;P16220;P16220-1;H7C1R5 C9JBT4 CREB1 Cyclic AMP-responsive element-binding protein 1 1 0 TAPTSTIAPGVVMAS(0.487)S(0.487)PALPT(0.027)QPAEEAAR;TAPTSTIAPGVVMAS(0.598)S(0.397)PALPT(0.005)QPAEEAAR ; 94.949 2.91E-08 57366000 5892.1 5406 4682.4 6015.7 7091.1 6862 6461.3 7450.5 6218.3 6254.7 TRUE FALSE FALSE 5820.284819 5482.10581 4763.895208 6711.263539 6729.214706 6423.540346 7010.122661 7666.068463 5662.119674 6092.201992 0.955366356 0.899856212 0.781966063 1.101615401 1.104561982 1.05438729 1.150671411 1.25834115 0.929404455 1 12.57274806 -7.819196057 0.790573251 0.963260634 1.291622179 0.625669982 0.080385706 0.771663629 0.548798241 0.014098257 0.187531361 1.52E-08 7.819196057 0.328361545 TAQALSS(ph)GSGSQETKIPISLVLR ddPTM_HeLa_Romidepsin_16h_R1 2 TAQALSSGSGSQETKIPISLVLR 23 1 C9JIG9;O95747 C9JIG9 OXSR1 Serine/threonine-protein kinase OSR1 1 0 T(0.011)AQALS(0.239)S(0.655)GS(0.031)GS(0.052)QET(0.012)KIPISLVLR;T(0.001)AQALS(0.064)S(0.833)GS(0.018)GS(0.084)QETKIPISLVLR ; 97.589 2.06E-05 57005000 2355.63 2057.49 1819.93 2872.02 2168.85 2152.09 2251.13 2086.43 2224.99 2206.05 TRUE FALSE FALSE 2326.918675 2086.455398 1851.605118 3204.096466 2058.165491 2014.578395 2442.340926 2146.79756 2025.981322 2148.736503 1.082924161 0.971015011 0.861718091 1.491153737 0.957849177 0.937564188 1.136640497 0.999097636 0.942870994 1 11.06927286 -12.54562194 1.017459548 0.99596164 1.058880051 0.032508554 0.164935271 3.037962721 4.999100151 0.152691808 0.027779635 2.85E-13 12.54562194 0.06291841 TAQALSSGS(ph)GSQETK ddPTM_HeLa_Romidepsin_16h_R1 4 TAQALSSGSGSQETK 15 0 C9JIG9;O95747 C9JIG9 OXSR1 Serine/threonine-protein kinase OSR1 1 0 T(0.002)AQALS(0.018)S(0.003)GS(0.974)GS(0.003)QETK;T(0.332)AQALS(0.004)S(0.032)GS(0.45)GS(0.184)QETK;TAQALS(0.007)S(0.134)GS(0.841)GS(0.017)QETK;TAQALS(0.003)S(0.01)GS(0.961)GS(0.025)QETK ;;; 189.52 2.47E-12 12640000 5499.2 6322.6 4821.33 4317.8 5768.8 5637.9 4683.56 5420.3 5514.9 5507.5 TRUE FALSE FALSE 5432.173635 6411.609729 4905.243226 4817.044352 5474.39661 5277.656385 5081.381469 5577.127829 5021.633532 5364.414356 1.012631254 1.1952115 0.914404239 0.897962766 1.020502192 0.983827131 0.94723881 1.039652692 0.936100979 1 12.38920496 TAQAS(ph)PNTELDFGGAAGSDVDQEEIVDER ddPTM_HeLa_Romidepsin_16h_R1 1 TAQASPNTELDFGGAAGSDVDQEEIVDER 29 0 D6RA38;Q9UBS8-2;Q9UBS8 D6RA38 RNF14 E3 ubiquitin-protein ligase RNF14 1 0 T(0.278)AQAS(0.716)PNT(0.006)ELDFGGAAGSDVDQEEIVDER 139.05 8.50E-11 7054900 3183.8 3241.3 3050.4 3331 3520.7 3289.8 3177.1 3378 3466.8 3091.3 TRUE FALSE FALSE 3144.994621 3286.931106 3103.490932 3716.145893 3341.025541 3079.592397 3446.962795 3475.7371 3156.720725 3010.98758 1.044506009 1.091645521 1.030721931 1.234195025 1.1096112 1.022784822 1.144794757 1.154351191 1.048400447 1 11.55602104 -10.2595122 0.764325668 1.010384073 1.12360181 0.324566857 0.057068997 0.420395251 0.50745979 0.014165718 0.016887656 5.50E-11 10.2595122 0.113217738 TAQVPS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 3 TAQVPSPPR 9 0 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 TAQVPS(1)PPR;TAQVPS(1)PPR;TAQVPS(1)PPR ;; 132.14 0.01175 1381584000 8680.3 8431.9 7722.1 5655.6 8527.5 8335.4 6798.1 8269.5 9239.9 8152.5 TRUE FALSE FALSE 8574.501165 8550.60451 7856.499911 6309.527082 8092.309855 7802.794841 7375.530444 8508.764935 8413.460202 7940.696875 1.079817213 1.076807822 0.989396779 0.794581028 1.019093158 0.98263351 0.928826596 1.071538817 1.059536755 1 12.95504991 -9.530966504 22.41258405 1.041269988 0.955227548 0.280182123 0.070461509 56.67325646 157049.8773 0.011166876 0.015817058 2.94E-10 9.530966504 -0.08604244 TAQVPS(ph)PPRGK ddPTM_HeLa_Romidepsin_16h_R1 1 TAQVPSPPRGK 11 1 S4R3H4;E7EQT4;Q9UKV3;G3V3B0;Q9UKV3-3;Q9UKV3-2;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 TAQVPS(1)PPRGK 68.132 0.030555 142770000 1421.4 1429.6 1171.5 2782.5 1833.9 1992.8 1919.3 1922.6 2068.1 1767.5 TRUE FALSE FALSE 1404.07543 1449.725946 1191.889466 3104.225742 1740.30924 1865.466511 2082.325294 1978.227398 1883.123956 1721.580095 0.81557369 0.842090328 0.692322982 1.803125948 1.010879043 1.083578113 1.209543082 1.149076597 1.093834647 1 10.74951759 TAS(ph)DT(ph)DS(ph)SYCIPT(ph)AGMSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 TASDTDSSYCIPTAGMSPSR 20 0 Q13480-2;B7Z3B9;Q13480 Q13480-2 GAB1 GRB2-associated-binding protein 1 4 0 T(0.156)AS(0.811)DT(0.534)DS(0.538)S(0.538)Y(0.515)CIPT(0.764)AGMS(0.132)PS(0.011)R 43.523 0.0043236 0 680.95 667.71 735.61 479.34 463.34 720.7 607.46 504.35 627.23 562.99 TRUE FALSE FALSE 672.6503195 677.1100389 748.4129835 534.7635462 439.6940308 674.649596 659.0576372 518.9425715 571.1289779 548.3634386 1.226650561 1.234783341 1.364811967 0.975199126 0.801829589 1.230296457 1.201862835 0.946347869 1.041515421 1 9.098988574 TAS(ph)EINFDK ddPTM_HeLa_Romidepsin_16h_R1 1 TASEINFDK 9 0 Q9Y4K4 Q9Y4K4 MAP4K5 Mitogen-activated protein kinase kinase kinase kinase 5 1 0 T(0.003)AS(0.997)EINFDK 113.61 0.017087 7081000 1570 1441.4 1443.5 1033.2 1940.7 1503.7 1285.3 1522.7 1512.1 1615.4 TRUE FALSE FALSE 1550.864236 1461.692067 1468.623512 1152.663445 1841.658837 1407.618423 1394.47335 1566.756922 1376.853989 1573.431675 0.985657185 0.928983502 0.933388806 0.732579281 1.17047271 0.894616808 0.886262411 0.995757837 0.875064364 1 10.61969882 -10.31835578 4.015521133 0.993820587 0.932291096 0 0.108795486 0.468411473 15.26316801 0.016678326 0.019213309 4.80E-11 10.31835578 -0.061529491 TAS(ph)ELLLDR ddPTM_HeLa_Romidepsin_16h_R1 2 TASELLLDR 9 0 Q92508 Q92508 PIEZO1 Piezo-type mechanosensitive ion channel component 1 1 0 T(0.004)AS(0.996)ELLLDR;T(0.06)AS(0.94)ELLLDR ; 147.62 8.80E-06 2876000 1487.71 3026.2 2371.7 1547.21 2320.9 3749.2 1567.95 3671.8 2179.49 2924.7 TRUE FALSE FALSE 1469.577218 3068.802923 2412.978444 1726.1057 2202.455813 3509.63822 1701.131634 3778.03774 1984.550956 2848.715872 0.515873567 1.077258337 0.847040755 0.605924135 0.773139868 1.232007114 0.597157354 1.326224836 0.696647558 1 11.47609602 -8.332041013 24.9915512 0.783192883 1.006334725 0.197306409 0.238477516 229.6610708 81294.60546 0.036425153 0.081449127 4.66E-09 8.332041013 0.223141841 TAS(ph)FSESR ddPTM_HeLa_Romidepsin_16h_R1 2 TASFSESR 8 0 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 0 T(0.022)AS(0.899)FS(0.078)ES(0.001)R;T(0.001)AS(0.854)FS(0.012)ES(0.133)R ; 122.94 0.017032 4325100000 29937 28992 29587 19733 22944.1 21938.1 18531.5 18071.4 28639 27154 TRUE FALSE FALSE 29572.11633 29400.15014 30101.94932 22014.62231 21773.17696 20536.32621 20105.56515 18594.26745 26077.45611 26448.53517 1.118100346 1.111598429 1.138132949 0.832356959 0.823228085 0.776463652 0.760176888 0.703035814 0.985969769 1 14.6909002 -9.13265161 4.115236391 1.067642521 0.77177342 0.88039849 0.054055677 0.06652407 1.911144191 0.009466918 0.016110407 7.37E-10 9.13265161 -0.295869101 TAS(ph)FSESRADEVAPAK ddPTM_HeLa_Romidepsin_16h_R1 1 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 0 T(0.11)AS(0.351)FS(0.304)ES(0.235)RADEVAPAK 64.2 0.020582 88711000 4116.7 4007.7 3238.6 5468.4 3602.3 3286.4 2946.8 3499.1 4426.7 4153.4 TRUE FALSE FALSE 4066.524077 4064.120506 3294.966474 6100.682138 3418.461189 3076.409646 3197.101118 3600.340938 4030.764865 4045.494069 1.005198378 1.004604243 0.814478137 1.508019054 0.845004623 0.760453382 0.790286937 0.889963222 0.996359109 1 11.98210019 -8.551226158 24.99974766 1.024939597 0.809820573 0.303580637 0.170042167 198.0892525 174695.3208 0.02294829 0.045897216 2.81E-09 8.551226158 -0.215119024 TAS(ph)FSESRADEVAPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 TASFSESRADEVAPAKK 17 2 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 0 T(0.113)AS(0.433)FS(0.433)ES(0.021)RADEVAPAKK 66.777 0.013399 122660000 4880.9 4859.1 3549.2 8834.3 3890.8 3376.5 3353.3 3356.5 5472.9 4178 TRUE FALSE FALSE 4821.409713 4927.506537 3610.972337 9855.763333 3692.237957 3160.752547 3638.129218 3453.615032 4983.390117 4069.454958 1.184780213 1.210851721 0.88733562 2.421887804 0.907305277 0.776701691 0.894008966 0.848667713 1.224584169 1 11.99061986 -8.548825339 24.99958308 1.186272852 0.844677516 0.198936119 0.407424801 336.473569 324191.559 0.058891157 0.117784946 2.83E-09 8.548825339 -0.341595336 TAS(ph)LPGYGR ddPTM_HeLa_Romidepsin_16h_R1 4 TASLPGYGR 9 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;O14639-4 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 T(0.347)AS(0.653)LPGYGR;T(0.079)AS(0.921)LPGYGR;T(0.08)AS(0.92)LPGYGR;T(0.376)AS(0.619)LPGY(0.005)GR ;;; 122.94 0.011896 384028000 9307 8500.4 7856.4 8702.7 11844.3 11353.6 10135 11084.5 9149.1 8027.8 TRUE FALSE FALSE 9193.562704 8620.068854 7993.137346 9708.947121 11239.84117 10628.1416 10995.86665 11405.21252 8330.781582 7819.236599 1.175762184 1.102418215 1.022240118 1.241674555 1.43746017 1.359230082 1.406258336 1.458609466 1.065421346 1 12.93281205 -8.983169262 3.334445647 1.083121718 1.410125876 0.905996957 0.051803395 0.0732405 1.709780043 0.010969198 0.020169522 1.04E-09 8.983169262 0.327004157 TAS(ph)NPKVENEDEPVR ddPTM_HeLa_Romidepsin_16h_R1 1 TASNPKVENEDEPVR 15 1 Q9UBF8-2 Q9UBF8-2 PI4KB Phosphatidylinositol 4-kinase beta 1 0 T(0.409)AS(0.591)NPKVENEDEPVR 60.307 0.030209 33193000 3455.3 3275.2 2881.6 3620.5 3543.4 4000.3 3589.2 3585.8 4092.2 3697.7 TRUE FALSE FALSE 3413.185475 3321.308352 2931.753039 4039.119245 3362.567076 3744.69374 3894.066558 3689.549466 3726.183383 3601.633221 0.947677141 0.922167291 0.814006552 1.121468789 0.933622851 1.039721013 1.081194647 1.024410105 1.034581578 1 11.81443555 -8.145128557 5.566156722 0.967186097 1.054342711 0.191511926 0.076218461 0.264127468 11.10405776 0.01003929 0.026230771 7.16E-09 8.145128557 0.087156614 TAS(ph)PPPPPK ddPTM_HeLa_Romidepsin_16h_R1 2 TASPPPPPK 9 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 T(0.087)AS(0.913)PPPPPK;T(0.005)AS(0.995)PPPPPK ; 107.24 0.0034604 736370000 10646 11334.7 10568.8 9446.7 10156.2 10711.3 9861.9 9551.3 11835.4 10894.8 TRUE FALSE FALSE 10516.24246 11494.2702 10752.74553 10538.9719 9637.891216 10026.8825 10699.56954 9827.651796 10776.81218 10611.75153 0.990999689 1.08316428 1.013286591 0.993141601 0.908228127 0.944884779 1.008275544 0.926110244 1.015554516 1 13.37337518 -8.974443515 21.93282233 1.004716078 0.951063994 0.466406313 0.035106085 50.36245455 43220.27915 0.005293743 0.009595137 1.06E-09 8.974443515 -0.053652085 TAS(ph)PPPPPKR ddPTM_HeLa_Romidepsin_16h_R1 5 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 T(0.321)AS(0.679)PPPPPKR;T(0.491)AS(0.509)PPPPPKR;T(0.011)AS(0.989)PPPPPKR;T(0.008)AS(0.992)PPPPPKR;T(0.157)AS(0.843)PPPPPKR ;;;; 112.64 0.0048764 748382600 31506.6 31351.6 28317 30879.6 29059.1 29294.4 25376.3 27905.2 33402.7 32964.7 TRUE FALSE FALSE 31122.58544 31792.96865 28809.84551 34450.04464 27576.10569 27422.58238 27531.76229 28712.59293 30415.07885 32108.27234 0.969301154 0.990179986 0.897271744 1.072933613 0.858847384 0.854065958 0.857466325 0.894242849 0.947266129 1 14.97065742 -8.731214919 24.99319581 0.983667265 0.864671322 0.62605627 0.042832301 86.43533732 71474.7047 0.005485183 0.010969294 1.86E-09 8.731214919 -0.118995943 TAS(ph)PSTSSIDSATDTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASPSTSSIDSATDTR 16 0 Q96P50-4;Q96P50-1;Q96P50 Q96P50-4 ACAP3 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3" 1 0 T(0.033)AS(0.924)PS(0.041)T(0.002)SSIDSATDTR 171.81 8.93E-06 10259000 1516.3 1491.9 1573.8 1476.8 2059.8 2397.6 1848.8 1856.9 1635.5 1566.5 TRUE FALSE FALSE 1497.818752 1512.903007 1601.191329 1647.554565 1954.68072 2244.401098 2005.837026 1910.626472 1489.216784 1525.802104 0.981659907 0.991546022 1.049409569 1.079795709 1.281084037 1.470964742 1.314611522 1.252211192 0.976022238 1 10.57535214 -8.815264008 2.375385035 0.995712335 1.348805738 0.894360701 0.054187341 0.06225091 0.716237367 0.008184744 0.016937237 1.53E-09 8.815264008 0.353093403 TAS(ph)RPDDIPDSPSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 T(0.005)AS(0.704)RPDDIPDS(0.274)PS(0.013)S(0.004)PK 117.2 0.019431 5136700 1202 1392.7 1307.2 1240.8 1358.3 1303.2 1184.7 1079.1 1474.1 1163 TRUE FALSE FALSE 1187.349562 1412.306467 1329.951268 1384.267134 1288.980882 1219.929726 1285.328388 1110.322056 1342.252804 1132.785092 1.048168421 1.246755873 1.174054352 1.222003312 1.137886516 1.076929538 1.134662168 0.980170081 1.184913902 1 10.14565847 -10.46826366 9.418715436 1.021158582 1.141430924 0 0.087257802 0.372238873 62.21320079 0.012315462 0.013962633 3.40E-11 10.46826366 0.120272342 TASESIS(ph)NLSEAGSIKKGER ddPTM_HeLa_Romidepsin_16h_R1 1 TASESISNLSEAGSIKKGER 20 2 J3KP58;P30622-2;P30622-1;P30622;F5H1T5;F5H6A0 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 0 T(0.003)AS(0.008)ES(0.072)IS(0.336)NLS(0.262)EAGS(0.32)IKKGER 56.799 0.029786 9276300 1412.3 1195.9 1000.5 2705 1266.4 985.96 853.5 855.71 1393.8 1209.6 TRUE FALSE FALSE 1395.086344 1212.735912 1017.913283 3017.764827 1201.770882 922.960338 925.9962687 880.4686188 1269.135037 1178.174418 1.184108502 1.029334786 0.863975034 2.561390557 1.020027989 0.783381751 0.78595856 0.747316022 1.077204714 1 10.20233742 -8.365813288 5.190960665 1.179598223 0.77641401 0.179395757 0.456844374 0.350859779 14.18120369 0.065642573 0.149823835 4.31E-09 8.365813288 -0.403184213 TASESISNLSEAGS(ph)IK ddPTM_HeLa_Romidepsin_16h_R1 4 TASESISNLSEAGSIK 16 0 J3KP58;P30622-2;P30622-1;P30622;F5H1T5;F5H6A0 J3KP58 CLIP1 CAP-Gly domain-containing linker protein 1 1 0 TASESISNLSEAGS(1)IK;TASESISNLSEAGS(1)IK;TASESISNLS(0.001)EAGS(0.999)IK;TASESISNLSEAGS(1)IK ;;; 266.44 2.53E-86 250122000 25759.2 25602.6 22832.7 15848.3 17338.2 17420.3 14190.5 14920.5 26642 25573.3 TRUE FALSE FALSE 25445.23696 25963.03407 23230.09357 17680.75501 16453.36696 16307.19905 15395.84072 15352.20113 24259.07279 24908.90198 1.02153186 1.042319493 0.932602071 0.709816716 0.66054164 0.654673541 0.618085885 0.616333917 0.973911769 1 14.60437381 -9.258178296 2.188699748 1.013296518 0.636892293 0.98502083 0.02140484 0.022681721 0.212358022 0.003143856 0.005429824 5.52E-10 9.258178296 -0.376404225 TASETRS(ph)EGSEY(ph)EEIPK ddPTM_HeLa_Romidepsin_16h_R1 1 TASETRSEGSEYEEIPK 17 1 P48634 P48634 PRRC2A Protein PRRC2A 2 0 T(0.002)AS(0.013)ET(0.552)RS(0.458)EGS(0.286)EY(0.689)EEIPK 126.07 0.0054993 18370000 5913.6 5198.2 4747.4 4278.3 4508.5 4091 3721.9 4143.4 5368.4 5565.5 TRUE FALSE FALSE 5841.522769 5271.380396 4830.026506 4772.977176 4278.414421 3829.598303 4038.038093 4263.282742 4888.236859 5420.907508 1.0775913 0.972416591 0.890999616 0.880475671 0.789243206 0.706449667 0.744900755 0.786451851 0.901737735 1 12.40431868 -9.302966848 1.069947311 1.03640329 0.745710336 0.763169523 0.054991524 0.105131304 0.238344213 0.007605497 0.015318378 4.98E-10 9.302966848 -0.290692953 TASFS(ph)ESRADEVAPAK ddPTM_HeLa_Romidepsin_16h_R1 1 TASFSESRADEVAPAK 16 1 P53396;P53396-2;P53396-3 P53396 ACLY ATP-citrate synthase 1 0 T(0.071)AS(0.293)FS(0.436)ES(0.2)RADEVAPAK 64.2 0.020582 91899000 4128.3 3825.6 3034 4993.5 2888.8 2509 2473.2 2665.1 3504.4 3249.8 TRUE FALSE FALSE 4077.982692 3879.456897 3086.805497 5570.871965 2741.373756 2348.682997 2683.273546 2742.210464 3190.957687 3165.369728 1.288311648 1.225593606 0.975180078 1.759943528 0.866051676 0.741993258 0.847696723 0.866316007 1.008083719 1 11.62815831 -8.555603495 24.99999687 1.177970623 0.818645575 0.423326724 0.21535707 143.5582971 109670.5077 0.030941399 0.061883099 2.78E-09 8.555603495 -0.359325048 TASGS(ph)SVTS(ph)LDGTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASGSSVTSLDGTR 14 0 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 2 0 T(0.011)AS(0.303)GS(0.679)S(0.006)VT(0.004)S(0.993)LDGT(0.002)R 135.81 0.014624 6085000 3341 2700.9 3093 2775.6 4232.1 4424.8 4431.3 5039 3629.7 3029.5 TRUE FALSE FALSE 3300.278607 2738.923341 3146.832368 3096.527932 4016.120145 4142.06956 4807.694511 5184.795515 3305.050541 2950.793153 1.118437801 0.928199029 1.066436109 1.049388341 1.361030725 1.403713966 1.629288893 1.757085382 1.120054972 1 11.52688708 -8.094514873 0.962973711 1.042073434 1.795292399 0.928535842 0.071266904 0.142776397 0.19971985 0.011685984 0.082370627 8.04E-09 8.094514873 0.753218965 TASGSSVT(ph)SLDGTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASGSSVTSLDGTR 14 0 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 1 0 TASGS(0.001)S(0.007)VT(0.496)S(0.496)LDGTR 175.88 1.84E-05 0 1377.4 1576.6 1420.9 1187.7 1782.4 1733.9 1803.2 2155.4 1697.5 1578.9 TRUE FALSE FALSE 1360.611719 1598.795416 1445.630168 1325.027462 1691.437477 1623.109386 1956.363763 2217.763098 1545.671349 1537.87995 0.884732075 1.039610027 0.940014965 0.861593561 1.099850139 1.055420084 1.272117347 1.442091171 1.005066324 1 10.58672717 -7.456530957 0.970803551 0.947854502 1.621271374 0.855340937 0.064108597 0.383840255 0.338076889 0.010212575 0.250119977 3.50E-08 7.456530957 0.673416872 TASGSSVTS(ph)LDGTR ddPTM_HeLa_Romidepsin_16h_R1 2 TASGSSVTSLDGTR 14 0 Q92597-3;Q92597-2;Q92597;E5RJY1;E7ESM1 Q92597-3 NDRG1 Protein NDRG1 1 0 TASGSS(0.003)VT(0.059)S(0.938)LDGTR;TASGSSVT(0.023)S(0.977)LDGTR ; 214.61 4.69E-24 38972700 4081.5 3768.24 3612.01 3304.73 6276.2 6307.1 5785.51 6382.1 5215.8 4114.7 TRUE FALSE FALSE 4031.753108 3821.289382 3674.875519 3686.838432 5955.902094 5904.096665 6276.931075 6566.755994 4749.285785 4007.799501 1.005976748 0.953463211 0.916930979 0.919915887 1.486077857 1.473151704 1.566178915 1.638494139 1.185010823 1 11.96859462 -8.722276341 6.102358214 0.986306926 1.543284454 0.913758776 0.081908445 0.026363985 2.533357043 0.008464939 0.016850475 1.90E-09 8.722276341 0.556977528 TASPLEHILQTLFGK ddPTM_HeLa_Romidepsin_16h_R1 1 TASPLEHILQTLFGK 15 0 Q9BTC0 Q9BTC0 DIDO1 Death-inducer obliterator 1 0 0 78.985 0.015602 12078000 836.84 715.99 732.78 735.05 1048.1 1309.9 1024.3 1208.1 798.08 743.47 FALSE FALSE TRUE 826.6402722 726.069726 745.5337285 820.0399395 994.611546 1226.201618 1111.304016 1243.054467 726.697726 724.1545422 1.141524666 1.002644717 1.029522961 1.13241013 1.373479676 1.6932872 1.534622724 1.71655965 1.003511935 1 9.500153806 -8.588276195 2.179240496 1.060425446 1.640742157 0.945425428 0.064717566 0.054131429 0.515929762 0.010548678 0.025199242 2.58E-09 8.588276195 0.580316712 TASPPPPPKR ddPTM_HeLa_Romidepsin_16h_R1 2 TASPPPPPKR 10 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 0 0 ; ; 100.02 0.015796 4834100 2264.13 2102.03 1989.31 1804.61 1783.73 1966.69 1837.45 1883.34 2196.64 2017.12 FALSE FALSE TRUE 2236.533913 2131.622434 2023.933106 2013.267499 1692.699602 1841.024856 1993.522957 1937.831471 2000.167017 1964.714932 1.138350341 1.084952529 1.030140848 1.024712271 0.861549721 0.937044264 1.0146627 0.986316865 1.018044391 1 10.94010429 -9.085941458 3.083056781 1.066562937 0.953167119 0.445230845 0.053097103 0.204860951 3.77163057 0.010046722 0.017803743 8.20E-10 9.085941458 -0.113395817 TASPSTS(ph)SIDSATDTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASPSTSSIDSATDTR 16 0 Q96P50-4;Q96P50-1;Q96P50 Q96P50-4 ACAP3 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3" 1 0 TASPST(0.002)S(0.74)S(0.257)IDS(0.001)ATDTR 220.52 9.02E-35 5770700 1260.9 1199.6 1241.6 1363.6 1296.1 1435.8 1547.6 1605.1 1540.3 1288.6 TRUE FALSE FALSE 1245.531666 1216.488 1263.209527 1521.265848 1229.955181 1344.057014 1679.053105 1651.541036 1402.53171 1255.121986 0.992359053 0.969218939 1.006443629 1.212046211 0.979948717 1.070857676 1.33776089 1.315841053 1.117446532 1 10.29361187 -7.337940282 0.678664722 0.997815547 1.571463396 0.595963439 0.084966757 1.05714013 0.357146381 0.01262947 0.456240881 4.59E-08 7.337940282 0.573647848 TASPSTSSIDS(ph)ATDTR ddPTM_HeLa_Romidepsin_16h_R1 1 TASPSTSSIDSATDTR 16 0 Q96P50-4;Q96P50-1;Q96P50 Q96P50-4 ACAP3 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3" 1 0 TASPS(0.002)T(0.012)S(0.096)S(0.324)IDS(0.52)AT(0.046)DTR 150.9 0.00028232 3903900 442.89 350.38 235.94 210.4 285.77 458.16 362.75 379.62 423.43 479.11 TRUE FALSE FALSE 437.4918863 355.3126588 240.0464367 234.727438 271.1860905 428.8850546 393.5619759 390.6037058 385.5573603 466.6626531 0.937490676 0.761390817 0.514389646 0.502991693 0.581118049 0.919047307 0.843354345 0.83701514 0.826201449 1 8.866236203 -10.24061873 3.372789197 0.972766947 0.69796783 0.313402238 0.140748568 0.176823818 4.158946527 0.025661056 0.030672932 5.75E-11 10.24061873 -0.274799117 TASRPDDIPDS(ph)PSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 T(0.125)AS(0.407)RPDDIPDS(0.466)PS(0.002)S(0.001)PK 160.03 0.00091165 3719300 1579.6 1387 1300.3 1484 1054.2 1179 1142.3 986.49 1259.4 1147.7 TRUE FALSE FALSE 1560.347228 1406.526222 1322.931176 1655.587062 1000.40024 1103.665705 1239.326933 1015.032532 1146.75611 1117.882589 1.395806003 1.25820568 1.183425871 1.481002638 0.894906362 0.987282311 1.108637836 0.907995654 1.02582876 1 10.12655295 -8.726632666 24.99930451 1.215292758 0.985170432 0.405269901 0.1475276 184.3251984 132387.5734 0.025489058 0.05097632 1.88E-09 8.726632666 -0.230122326 TASRPDDIPDSPS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 TASRPDDIPDSPSSPK 16 1 Q5VZK9;Q5VZK9-2;A0A0U1RQQ1 Q5VZK9 LRRC16A Leucine-rich repeat-containing protein 16A 1 0 TASRPDDIPDS(0.002)PS(0.499)S(0.499)PK 109.77 0.0011743 28934000 3046 3514.9 3251.6 3543.1 3784.8 3457.5 2452.9 3021.9 3129.3 3149.7 TRUE FALSE FALSE 3008.87418 3564.382854 3308.192734 3952.769893 3591.647533 3236.576909 2661.249265 3109.333909 2849.407571 3067.87034 0.98076967 1.161842731 1.078335251 1.288440988 1.170729899 1.054991427 0.867458194 1.013515424 0.92879009 1 11.58302179 -5.842091898 11.87631882 1.034087411 1.063386761 0 0.120566971 0 0 0.016838867 0 1.44E-06 5.842091898 0.02929935 TASTPT(ph)PPQTGGGLEPQANGETPQVAVIVRPDDR ddPTM_HeLa_Romidepsin_16h_R1 1 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6;C9JSU8;C9J556;C9JF13;C9K073;C9J2Z7;C9J6B6;C9JWW9;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 T(0.011)AS(0.054)T(0.135)PT(0.675)PPQT(0.089)GGGLEPQANGET(0.037)PQVAVIVRPDDR 44.763 0.012795 87916000 506.77 529.77 340.18 564.94 578.06 426.18 319.64 412.23 505.26 349.07 TRUE FALSE FALSE 500.5932923 537.228116 346.1006902 630.2610209 548.5594412 398.9484734 346.7902136 424.1572247 460.0682802 340.0011111 1.472328401 1.580077531 1.01793988 1.853702827 1.613404849 1.173374029 1.019967883 1.247517172 1.353137579 1 8.409395651 -12.33741766 1.050085567 0.99902521 1.378884611 0.013397443 0.275901297 0.643638477 1.265402794 0.180802229 0.047042374 4.60E-13 12.33741766 0.379859401 TASTPTPPQT(ph)GGGLEPQANGETPQVAVIVRPDDR ddPTM_HeLa_Romidepsin_16h_R1 2 TASTPTPPQTGGGLEPQANGETPQVAVIVRPDDR 34 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6;C9JSU8;C9J556;C9JF13;C9K073;C9J2Z7;C9J6B6;C9JWW9;C9JWH7 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 T(0.005)AS(0.019)T(0.051)PT(0.265)PPQT(0.651)GGGLEPQANGET(0.008)PQVAVIVRPDDR;TAS(0.001)T(0.002)PT(0.354)PPQT(0.419)GGGLEPQANGET(0.225)PQVAVIVRPDDR ; 79.67 2.64E-08 249831000 2971.68 3595.64 3071.11 2861.84 2622.37 2454.61 1863.76 2204.48 3397.68 3045.29 TRUE FALSE FALSE 2935.460021 3646.259514 3124.561381 3192.739406 2488.540673 2297.768343 2022.067728 2268.263151 3093.782991 2966.172927 0.989645612 1.229280829 1.053398254 1.076383436 0.838973565 0.774657581 0.68170932 0.764710355 1.043021789 1 11.53438699 -8.560422504 3.043370974 1.024374245 0.737402158 0.79519842 0.073883295 0.101371789 1.91431593 0.011958604 0.026735636 2.75E-09 8.560422504 -0.286972087 TATDS(ph)DERIDDEIDTEVEETQEEK ddPTM_HeLa_Romidepsin_16h_R1 1 TATDSDERIDDEIDTEVEETQEEK 24 1 A0A0C4DGZ1;Q8N5P1 A0A0C4DGZ1 ZC3H8 Zinc finger CCCH domain-containing protein 8 1 0 T(0.058)AT(0.203)DS(0.635)DERIDDEIDT(0.103)EVEET(0.001)QEEK 60.8 0.0023634 18511000 1066.1 1115.5 996.97 934.91 951.45 1105.3 734.77 611.83 1233.7 1417.3 TRUE FALSE FALSE 1053.105963 1131.204038 1014.321845 1043.008693 902.8939562 1034.674897 797.1813455 629.5323357 1123.354782 1380.478342 0.762855839 0.819429037 0.734761143 0.755541512 0.654044275 0.749504622 0.577467477 0.456024783 0.813743141 1 10.43095254 -8.137600912 0.092765015 1.285678205 1.29E-15 0.689520743 0.077627642 12.30990755 0.258936358 1.086187455 2.71129471 7.28E-09 8.137600912 -1.285678205 TATESFAS(ph)DPILYRPVAVALDTK ddPTM_HeLa_Romidepsin_16h_R1 1 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 1 0 T(0.012)AT(0.037)ES(0.362)FAS(0.587)DPILY(0.002)RPVAVALDTK 63.125 0.0021052 33645000 2297.6 2140.6 2449.8 2017.1 2406.5 2087.7 2027.3 2700.9 2313 2438.5 TRUE FALSE FALSE 2269.595967 2170.735423 2492.437741 2250.326593 2283.687325 1954.302708 2199.498811 2779.04628 2106.119487 2375.147418 0.955560042 0.913937133 1.049382334 0.947447125 0.961492877 0.822813225 0.926047282 1.170052123 0.886732112 1 11.21380134 TATESFASDPILYRPVAVALDTK ddPTM_HeLa_Romidepsin_16h_R1 3 TATESFASDPILYRPVAVALDTK 23 1 P14618;P14618-3;P14618-2;H3BTN5;H3BQ34;H3BT25;H3BUW1;H3BTJ2 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ;; ;; 91.964 4.06E-05 82427510 4616.17 4265.16 4483.27 4172.99 4376.86 4910.83 3856.94 4507.29 4443.89 4537.99 FALSE FALSE TRUE 4559.906344 4325.205034 4561.299434 4655.490738 4153.492502 4597.043812 4184.548387 4637.701325 4046.417348 4420.092366 1.031631461 0.978532727 1.031946633 1.053256437 0.939684549 1.040033427 0.946710621 1.049231767 0.915459908 1 12.1098608 TATPPGYKPGS(ph)PPSFR ddPTM_HeLa_Romidepsin_16h_R1 1 TATPPGYKPGSPPSFR 16 1 P54259 P54259 ATN1 Atrophin-1 1 0 T(0.004)AT(0.004)PPGY(0.023)KPGS(0.755)PPS(0.214)FR 70.02 0.015169 48902000 2220.9 2679.5 2112.5 2251.5 2138.9 1594.8 1310 1554.3 2422.6 2117.9 TRUE FALSE FALSE 2193.830817 2717.222071 2149.267176 2511.829024 2029.743952 1492.897427 1421.271367 1599.271218 2205.916588 2062.876653 1.063481335 1.317200458 1.041878667 1.217634133 0.983938593 0.723696894 0.688975449 0.775262649 1.069340033 1 11.01044184 -8.338349502 3.875941721 1.068179348 0.723144947 0.750805759 0.097440059 0.099412961 2.85285554 0.015163062 0.036294756 4.59E-09 8.338349502 -0.345034401 TATPQQAQEVHEK ddPTM_HeLa_Romidepsin_16h_R1 2 TATPQQAQEVHEK 13 0 P60174;P60174-3;U3KPZ0;P60174-4 P60174 TPI1 Triosephosphate isomerase 0 0 ; ; 146.59 0.0003593 6833800 6452.3 5410.5 4625.5 2524.05 5186.8 5895 4935.8 6192.1 5953 4941 FALSE FALSE TRUE 6373.656886 5486.669161 4706.004887 2815.892537 4922.098241 5518.328525 5355.046729 6371.258644 5420.54877 4812.632108 1.324359881 1.140055803 0.977844303 0.585104465 1.022745585 1.146634191 1.112706438 1.323861559 1.126316878 1 12.23261043 -9.821104967 7.123430733 1.156879382 1.017129456 0.084310266 0.190259136 0.444629585 43.50930612 0.035411063 0.046772818 1.51E-10 9.821104967 -0.139749926 TATSLPVVNFGS(ph)PLRR ddPTM_HeLa_Romidepsin_16h_R1 2 TATSLPVVNFGSPLRR 16 1 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 TATSLPVVNFGS(1)PLRR;TATSLPVVNFGS(1)PLRR ; 108.47 0.0010355 145606000 8331 6839.2 7044.2 9382.8 9083.9 8562.1 7262.9 7086.1 7579.6 7164 TRUE FALSE FALSE 8229.458568 6935.482437 7166.801346 10467.68348 8620.314686 8015.009443 7879.810545 7291.125123 6901.661593 6977.878247 1.179364024 0.993924255 1.027074577 1.500124123 1.235377629 1.148631312 1.129255952 1.044891422 0.989077388 1 12.76857271 -12.75317294 0.421863986 0.91907192 1.17356969 0.194636493 0.134229742 4.516477179 0.792093234 0.531773374 0.042938116 1.77E-13 12.75317294 0.25449777 TAVAPSAVNLADPRT(ph)PTAPAVNLAGAR ddPTM_HeLa_Romidepsin_16h_R1 2 TAVAPSAVNLADPRTPTAPAVNLAGAR 27 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 TAVAPS(0.002)AVNLADPRT(0.628)PT(0.37)APAVNLAGAR;TAVAPSAVNLADPRT(0.75)PT(0.25)APAVNLAGAR ; 101.92 1.97E-08 142443000 2123.9 2320.7 1807.08 2039.87 2333.6 2892.5 2502.2 3075.1 2477.7 2190.48 TRUE FALSE FALSE 2098.01309 2353.370876 1838.531469 2275.729367 2214.507684 2707.678585 2714.736806 3164.073167 2256.088306 2133.571014 0.98333408 1.103019707 0.86171562 1.066629305 1.037934838 1.269082945 1.272391117 1.482994073 1.057423583 1 11.05905441 -7.795738099 0.949958853 0.991562569 1.525179812 0.828512102 0.070564368 0.250450539 0.281118365 0.009567792 0.11292418 1.60E-08 7.795738099 0.533617243 TAVETAVLLLR ddPTM_HeLa_Romidepsin_16h_R1 1 TAVETAVLLLR 11 0 B4DUR8;P49368-2;P49368 B4DUR8 CCT3 T-complex protein 1 subunit gamma 0 0 128.28 0.022225 368710 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 TAVIPINGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TAVIPINGSPR 11 0 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 0 TAVIPINGS(1)PR 110.51 0.014336 51617000 4170.3 4305.5 3994.8 3065.5 4363.9 3971.5 3557 3817.2 3914.4 4055.2 TRUE FALSE FALSE 4119.47078 4366.112942 4064.327818 3419.947534 4141.193899 3717.733967 3859.131491 3927.644659 3564.28626 3949.845319 1.042944836 1.105388335 1.028984046 0.865843408 1.048444575 0.941235331 0.977033575 0.99437936 0.902386289 1 11.94758044 TAVPPLSEGDGYS(ph)S(ph)ENTSR ddPTM_HeLa_Romidepsin_16h_R1 1 TAVPPLSEGDGYSSENTSR 19 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 2 0 T(0.211)AVPPLS(0.255)EGDGY(0.084)S(0.349)S(0.881)ENT(0.192)S(0.028)R 127.49 0.0093209 5349500 2475.4 2658 2333.6 1987.4 2123.6 1973.6 1699.6 2078.7 2668.4 2575.5 TRUE FALSE FALSE 2445.228873 2695.419394 2374.215329 2217.192539 2015.224768 1847.49333 1843.963982 2138.843905 2429.731621 2508.588139 0.974743058 1.074476656 0.946434886 0.883840797 0.803330262 0.736467378 0.735060472 0.852608633 0.968565379 1 11.29265991 -9.015752761 1.824306851 0.994126447 0.771023927 0.847207597 0.042573682 0.088917053 0.588656707 0.006446855 0.012820075 9.64E-10 9.015752761 -0.22310252 TAVPPLSEGDGYS(ph)SENTSR ddPTM_HeLa_Romidepsin_16h_R1 1 TAVPPLSEGDGYSSENTSR 19 0 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 TAVPPLS(0.011)EGDGYS(0.845)S(0.141)ENT(0.002)S(0.001)R 126.43 0.00090375 9547400 4409.8 4182.8 3781.5 7125.7 3915.7 3762.9 2973.9 3390.1 4488.2 3920.4 TRUE FALSE FALSE 4356.051661 4241.685568 3847.315421 7949.606961 3715.867218 3522.462834 3226.502992 3488.187195 4086.764151 3818.547443 1.140761435 1.110811279 1.007533749 2.081840564 0.973110135 0.922461456 0.844955586 0.913485362 1.070240507 1 11.89880823 -8.53751515 24.99996172 1.146151098 0.898602483 0.181458357 0.304433704 383.6388966 655279.2856 0.04507405 0.090175644 2.90E-09 8.53751515 -0.247548615 TAVPS(ph)PVEAAAASDPAAAR ddPTM_HeLa_Romidepsin_16h_R1 1 TAVPSPVEAAAASDPAAAR 19 0 Q147X3;J3KNC2;Q147X3-2 Q147X3 NAA30 N-alpha-acetyltransferase 30 1 0 T(0.018)AVPS(0.982)PVEAAAASDPAAAR 182.28 1.71E-10 26977000 3996.4 3505.3 3643.6 3598 3626.9 3616.5 3323.2 3085.2 3597.8 3714.5 TRUE FALSE FALSE 3947.69034 3554.647705 3707.01533 4014.017689 3441.805759 3385.417322 3605.472525 3174.465394 3276.003757 3617.996755 1.091126004 0.982490573 1.024604382 1.109458621 0.951301505 0.935715964 0.996538352 0.877409685 0.905474488 1 11.8209754 -8.649093421 8.582104519 1.041552467 0.942835269 0.23506043 0.061900967 0.168119159 12.08201777 0.007071303 0.01416127 2.24E-09 8.649093421 -0.098717198 TAVSVTQGGHS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 TAVSVTQGGHSR 12 0 P40425 P40425 PBX2 Pre-B-cell leukemia transcription factor 2 1 0 TAVSVTQGGHS(1)R;TAVSVTQGGHS(1)R ; 134.88 0.0011701 3811500 3150 3190.4 2836.3 2667.85 3875.1 3880.1 2804.2 2528.7 4386.4 4188.4 TRUE FALSE FALSE 3111.606588 3235.314535 2885.664612 2976.31937 3677.339187 3632.174132 3042.388678 2601.863945 3994.069398 4079.584764 0.762726299 0.79304996 0.707342727 0.729564292 0.901400363 0.89032937 0.745759398 0.63777666 0.979038218 1 11.9942066 -12.1923097 0.747312519 1.013933584 0.773873909 0.571580804 0.075365151 0.488453006 0.449049752 0.071595689 0.016314252 6.42E-13 12.1923097 -0.240059675 TCVS(ph)LTT(ph)QRLPVS(ph)RIK ddPTM_HeLa_Romidepsin_16h_R1 1 TCVSLTTQRLPVSRIK 16 2 Q9UBD3;P47992 Q9UBD3 XCL2;XCL1 Cytokine SCM-1 beta;Lymphotactin 3 0 T(0.102)CVS(0.897)LT(0.471)T(0.535)QRLPVS(0.996)RIK 47.532 0.026667 31115000 2867.8 3191.3 2722.7 1312.8 2930.7 2791.2 2478.7 2858.1 3270.2 2845.1 TRUE FALSE FALSE 2832.846151 3236.227205 2770.087451 1464.592113 2781.135443 2612.851328 2689.240716 2940.794614 2977.705122 2771.183892 1.022251233 1.167813949 0.999604342 0.528507732 1.003591083 0.942864649 0.970430264 1.061205149 1.074524549 1 11.43628673 -9.499178764 24.99952721 1.025509129 0.898239755 0.209461894 0.143134812 1099.909503 1160222.713 0.021587229 0.032851235 3.17E-10 9.499178764 -0.127269374 TDAEAT(ph)DTEATET ddPTM_HeLa_Romidepsin_16h_R1 1 TDAEATDTEATET 13 0 Q9Y3D3 Q9Y3D3 MRPS16 "28S ribosomal protein S16, mitochondrial" 1 0 TDAEAT(0.896)DT(0.103)EATET 157.68 0.0012071 9031900 3506.1 3257 3541.3 3693.4 3920.6 3747 3169.6 3872.7 3103.1 3088.4 TRUE FALSE FALSE 3463.366305 3302.852131 3602.934841 4120.448286 3720.517152 3507.578793 3438.825745 3984.750464 2825.550964 3008.162923 1.151322715 1.097963181 1.197719317 1.369755692 1.236807064 1.16602022 1.143164726 1.324645828 0.939294525 1 11.55466699 -11.23908047 0.407556198 0.983005991 1.243067251 0.640049255 0.07515332 0.677035821 0.259458081 0.073668668 0.033587754 5.77E-12 11.23908047 0.26006126 TDALTSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 2 TDALTSSPGR 10 0 P49736;F8WDM3;C9J013;C9JZ21 P49736 MCM2 DNA replication licensing factor MCM2 1 0 TDALT(0.001)S(0.004)S(0.995)PGR;TDALTS(0.003)S(0.997)PGR ; 120.63 0.011433 223910000 17486 16363.4 17875.6 13302 16894.1 17174.7 13532.9 15331.6 17139.5 18774.5 TRUE FALSE FALSE 17272.87391 16593.76437 18186.71732 14840.03983 16031.93104 16077.2921 14682.38419 15775.19566 15606.50019 18286.73578 0.944557526 0.907420798 0.994530546 0.811519344 0.876697253 0.879177798 0.802898033 0.862657822 0.853432804 1 14.15850995 -9.413628267 0.345160077 0.99922799 0.807029851 0.145685174 0.060131013 0.744846132 0.187208492 0.021388415 0.054788431 3.86E-10 9.413628267 -0.192198139 TDANESSSS(ph)PEIR ddPTM_HeLa_Romidepsin_16h_R1 2 TDANESSSSPEIR 13 0 Q96JM7-2;Q96JM7 Q96JM7-2 L3MBTL3 Lethal(3)malignant brain tumor-like protein 3 1 0 TDANES(0.002)S(0.008)S(0.028)S(0.962)PEIR;TDANES(0.032)S(0.014)S(0.032)S(0.922)PEIR ; 191.01 9.09E-11 19300700 5347.2 5144.3 5865 7287.9 7289 6076.5 4711.5 5530 5295.7 5262 TRUE FALSE FALSE 5282.02627 5216.72159 5967.077865 8130.561289 6917.015131 5688.231261 5111.694692 5690.001825 4822.039329 5125.292481 1.030580457 1.017838808 1.164241433 1.58636045 1.349584469 1.109835445 0.997346924 1.110180901 0.94083203 1 12.32341862 -9.679962786 4.643791585 1.015011462 1.231017908 0.341147783 0.152113685 0.211179536 8.309619877 0.025963142 0.036790578 2.09E-10 9.679962786 0.216006446 TDASSAS(ph)SFLDSDELER ddPTM_HeLa_Romidepsin_16h_R1 2 TDASSASSFLDSDELER 17 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;Q14498-3;A0A0U1RQW2;A0A0U1RQH7 Q14498-2 RBM39 RNA-binding protein 39 1 0 TDAS(0.012)S(0.181)AS(0.75)S(0.057)FLDS(0.001)DELER;TDASS(0.004)AS(0.96)S(0.036)FLDSDELER ; 187.78 3.87E-13 3048700 612.13 697.33 556.45 712.94 866.23 493.55 567.03 657.16 755.89 573.49 TRUE FALSE FALSE 604.6691241 707.14703 566.1347788 795.3734773 822.0230508 462.0137479 615.193514 676.1738878 688.2813052 558.5906471 1.082490599 1.265948568 1.013505653 1.423893295 1.471601888 0.827106129 1.101331569 1.210499838 1.232174776 1 9.125647608 -10.67289791 1.364246411 1.0238765 1.185036262 0 0.189385561 0.578625848 2.220742903 0.039156977 0.038837749 2.12E-11 10.67289791 0.161159762 TDASSASS(ph)FLDSDELER ddPTM_HeLa_Romidepsin_16h_R1 3 TDASSASSFLDSDELER 17 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;Q14498-3;A0A0U1RQW2;A0A0U1RQH7 Q14498-2 RBM39 RNA-binding protein 39 1 0 TDASSAS(0.06)S(0.94)FLDSDELER;TDASSAS(0.017)S(0.983)FLDSDELER;TDAS(0.001)S(0.001)AS(0.199)S(0.798)FLDS(0.001)DELER ;; 389.47 0 23900100 4588.24 4529 4269.71 4104.38 3683.01 3385.71 2601.74 3430.03 4688.77 4464.1 TRUE FALSE FALSE 4532.316766 4592.759381 4344.022511 4578.947727 3495.052256 3169.374058 2822.731731 3529.272506 4269.394668 4348.122038 1.042361904 1.056262759 0.999057173 1.053086295 0.803807305 0.728906417 0.649184109 0.811677427 0.981893937 1 12.08617672 -8.645633524 3.677096569 1.0239917 0.726630265 0.903890915 0.044092026 0.043901149 1.133808495 0.006008966 0.012532891 2.26E-09 8.645633524 -0.297361435 TDASSASSFLDS(ph)DELER ddPTM_HeLa_Romidepsin_16h_R1 4 TDASSASSFLDSDELER 17 0 Q14498-2;Q14498;G3XAC6;H0Y4X3;Q14498-3;A0A0U1RQW2;A0A0U1RQH7 Q14498-2 RBM39 RNA-binding protein 39 1 0 TDASSASSFLDS(1)DELER;TDASSASSFLDS(1)DELER;TDASSASS(0.003)FLDS(0.997)DELER;TDASSASS(0.001)FLDS(0.998)DELER ;;; 316.96 7.41E-159 18238300 4034.21 4397.61 4177.38 3885.13 4119.82 3776.34 3537.13 3433.81 4900.33 4420.16 TRUE FALSE FALSE 3985.039497 4459.519669 4250.085547 4334.347011 3909.570212 3535.044062 3837.573734 3533.161875 4462.032212 4305.323606 0.925607425 1.035815209 0.987169824 1.006741283 0.908078131 0.821086725 0.891355467 0.820649549 1.036398798 1 12.07190597 -8.534717589 4.419030515 0.974265666 0.850224128 0.745665516 0.03926602 0.088473714 4.250499088 0.0057879 0.012422493 2.92E-09 8.534717589 -0.124041539 TDDEVVQREEEAIQLDGLNASQIR ddPTM_HeLa_Romidepsin_16h_R1 1 TDDEVVQREEEAIQLDGLNASQIR 24 1 P14625;Q96GW1;A0A1W2PRR1 P14625 HSP90B1 Endoplasmin 0 0 145.73 4.09E-07 5496500 861.88 701.25 1042.5 716.74 874.92 879.71 822.15 969.87 878.94 856.98 FALSE FALSE TRUE 851.375075 711.1222159 1060.644275 799.6128512 830.2695676 823.4993701 891.9834005 997.9316582 800.3254051 834.7155361 1.019958343 0.851933605 1.270665549 0.95794653 0.994673672 0.986562888 1.068607642 1.195535024 0.958800179 1 9.705140813 -7.339294714 2.702980647 1.011177447 1.215515167 0.250674735 0.099797867 0.377157234 4.01857801 0.012384533 0.157120356 4.58E-08 7.339294714 0.204337721 TDDIPVWDQEFLK ddPTM_HeLa_Romidepsin_16h_R1 1 TDDIPVWDQEFLK 13 0 E5RJR5;P63208;E5RGM3;E7ERH2;F8W8N3;P63208-2 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 0 169.23 0.0011087 4729100 1432 1281.6 1482 1166.9 1778.2 1692.8 1626.9 1746.3 1347.8 1245.1 FALSE FALSE TRUE 1414.546233 1299.642398 1507.793588 1301.822468 1687.451819 1584.635543 1765.088845 1796.826435 1227.249392 1212.752123 1.166393533 1.071647185 1.24328258 1.073444807 1.391423513 1.306644213 1.455440739 1.481610629 1.011954026 1 10.24406899 -4 0.191205767 0.998179946 3.37965161 0.817531525 0.073906805 15.52794057 0.174171862 0.076885814 11.0084594 1.00E-04 4 2.381471664 TDEIVALK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 TDEIVALKR 9 1 Q9UQ88-2;Q9UQ88-3;Q5QPR3;Q5QPR4;Q9UQ88;Q9UQ88-4;A0A0D9SEN2;A0A0D9SER5;A0A0D9SEI3;P21127-8;P21127-2;P21127-3;P21127;P21127-9;P21127-6;P21127-10;P21127-5;Q9UQ88-5;Q9UQ88-10;Q9UQ88-9;P21127-12;P21127-4 Q9UQ88-2 CDK11A;CDK11B Cyclin-dependent kinase 11A;Cyclin-dependent kinase 11B 0 1 ; TDEIVALK(1)R;TDEIVALK(1)R 140.35 0.0037143 2635400 1802.73 1290.32 1843.55 1557.23 1903.84 1905.69 1538 1459.26 1679.85 1642.61 FALSE TRUE FALSE 1780.757633 1308.485159 1875.636214 1737.28426 1806.679941 1783.922559 1668.637682 1501.481386 1529.600009 1599.934755 1.113018907 0.817836574 1.172320439 1.085846941 1.12922101 1.114997067 1.04294108 0.938464135 0.956038991 1 10.64379736 -12.69497394 1.558582449 0.999843006 1.063345967 0.060070416 0.100175935 1.07762008 4.699595979 0.070172267 0.015348676 2.02E-13 12.69497394 0.063502961 TDESSPVLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TDESSPVLSPR 11 0 Q8NA72-3;Q8NA72 Q8NA72-3 POC5 Centrosomal protein POC5 1 0 TDESSPVLS(1)PR 147.33 0.0024338 8017200 1680.3 1403.9 1269.4 1633.6 2033.1 2198.5 1791 2400.6 1513.8 1633.4 TRUE FALSE FALSE 1659.819857 1423.664141 1291.493375 1822.484518 1929.34332 2058.022945 1943.127495 2470.057573 1378.401937 1590.964033 1.043279309 0.8948437 0.811767801 1.145522137 1.212688207 1.29356975 1.221352247 1.552554001 0.866394154 1 10.63568551 -8.14657117 0.888366234 0.997832718 1.469579256 0.731780895 0.111625059 0.367970892 0.431758777 0.017665673 0.12511399 7.14E-09 8.14657117 0.471746538 TDEVPAGGS(ph)RS(ph)EAEDEDDEDYVPYVPLR ddPTM_HeLa_Romidepsin_16h_R1 1 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 D6RD33;D6RGI7;A0A499FJW5;Q9UJV9 D6RD33 DDX41 Probable ATP-dependent RNA helicase DDX41 2 0 T(0.004)DEVPAGGS(0.9)RS(0.9)EAEDEDDEDY(0.163)VPY(0.033)VPLR 57.688 0.0060916 4133100 406.43 517.27 416.13 382.84 507.13 577.2 423.33 618.87 500.47 496.95 TRUE FALSE FALSE 401.4762748 524.5521406 423.3725681 427.1057621 481.2492637 540.3187828 459.2876396 636.776027 455.7067097 484.0391674 0.829429315 1.083697717 0.874665929 0.882378516 0.994236203 1.116270788 0.948864618 1.315546489 0.941466601 1 8.918979982 -4.000000001 0.71396741 0.928461565 49.80775032 0.571247838 0.089010189 165.6060377 0.776451887 0.015688484 12968.62897 1.00E-04 4.000000001 48.87928876 TDEVPAGGSRS(ph)EAEDEDDEDYVPYVPLR ddPTM_HeLa_Romidepsin_16h_R1 3 TDEVPAGGSRSEAEDEDDEDYVPYVPLR 28 1 D6RD33;D6RGI7;A0A499FJW5;Q9UJV9 D6RD33 DDX41 Probable ATP-dependent RNA helicase DDX41 1 0 T(0.001)DEVPAGGS(0.101)RS(0.898)EAEDEDDEDYVPYVPLR;TDEVPAGGS(0.173)RS(0.827)EAEDEDDEDYVPYVPLR;T(0.017)DEVPAGGS(0.164)RS(0.819)EAEDEDDEDYVPYVPLR ;; 120.33 1.97E-10 75172600 5123.4 5153.7 4665.8 4891.4 5948.8 5595.5 5703.8 6309.7 5337 5547 TRUE FALSE FALSE 5060.95403 5226.253924 4747.006292 5456.966683 5645.210538 5237.965609 6188.28063 6492.261214 4859.645353 5402.88814 0.936712717 0.967307445 0.878605325 1.010009192 1.04485053 0.969475116 1.145365306 1.201627916 0.89945326 1 12.3995151 -7.437870493 1.055890519 0.965918095 1.296447676 0.744424857 0.049135062 0.500180434 0.533130339 0.007055939 0.171766689 3.65E-08 7.437870493 0.330529581 TDFK(ac)EEPEPGFKR ddPTM_HeLa_Romidepsin_16h_R1 1 TDFKEEPEPGFKR 13 2 P47897;P47897-2;A0A1B0GVU9;B4DDN1;H7C0R3;A0A0U1RRC8;A0A0U1RQX5 P47897 QARS Glutamine--tRNA ligase 0 1 TDFK(1)EEPEPGFKR 105.95 0.00861 794530 375.79 238.52 311.75 180.83 840.69 737.04 774.43 1035.5 713.45 662.41 FALSE TRUE FALSE 371.2097269 241.8778908 317.175878 201.7384154 797.7864523 689.9455227 840.2100649 1065.460559 649.6372451 645.2004927 0.575340117 0.374887951 0.49159274 0.312675545 1.236493867 1.069350582 1.302246471 1.651363523 1.006876548 1 9.33360373 -8.638257079 7.787879749 0.703725047 1.306315377 0.619550316 0.260415591 0.15474665 9.956853169 0.043364473 0.086933135 2.30E-09 8.638257079 0.60259033 TDGALLVNAMFFKPHWDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TDGALLVNAMFFKPHWDEK 19 1 P50454;E9PPV6;E9PR70;E9PK86;E9PMI5 P50454 SERPINH1 Serpin H1 0 0 99.813 0.0003636 7535500 4554.7 3915.1 4411.4 4305.6 3759.7 3730.7 3231.1 3689.7 4501.7 3828.2 FALSE FALSE TRUE 4499.185564 3970.216881 4488.178567 4803.43373 3567.82848 3492.32031 3505.549553 3796.455648 4099.056677 3728.742812 1.206622658 1.064760183 1.203670726 1.288218033 0.956844883 0.936594581 0.94014249 1.018159696 1.09931333 1 11.86447358 TDGEPGPQGWS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TDGEPGPQGWSPR 13 0 Q9H773 Q9H773 DCTPP1 dCTP pyrophosphatase 1 1 0 TDGEPGPQGWS(1)PR 108.06 0.0080254 10499000 1527.7 1564.6 1343.3 1370.3 1552.9 1954.8 1518.7 1488.7 1954.8 1641.9 TRUE FALSE FALSE 1509.079805 1586.62648 1366.679573 1528.740533 1473.649718 1829.894589 1647.69834 1531.773186 1779.957792 1599.243201 0.94362121 0.992110818 0.854578948 0.95591498 0.921466927 1.144225336 1.030298793 0.957811285 1.113000068 1 10.64317363 -8.295957921 24.99536762 0.960769261 1.042730619 0.169226985 0.075167329 563.7084552 408187.9912 0.00841293 0.018812808 5.06E-09 8.295957921 0.081961359 TDGFAEAIHS(ph)PQVAGVPR ddPTM_HeLa_Romidepsin_16h_R1 3 TDGFAEAIHSPQVAGVPR 18 0 P12270 P12270 TPR Nucleoprotein TPR 1 0 TDGFAEAIHS(1)PQVAGVPR;T(0.066)DGFAEAIHS(0.934)PQVAGVPR;TDGFAEAIHS(1)PQVAGVPR ;; 151.41 3.36E-05 47985300 7503.7 11939.1 5810.06 7840.7 9860 8541.1 6532 8098.7 7159.4 7400 TRUE FALSE FALSE 7412.242018 12107.17896 5911.181657 8747.278626 9356.807407 7995.351275 7086.827917 8333.023107 6519.045333 7207.746933 1.028371568 1.67974529 0.820115039 1.213594027 1.298159812 1.109271919 0.983223743 1.156120378 0.904449808 1 12.81533264 -10.48418796 24.99987586 1.012516563 1.175470388 0.154746757 0.212279822 722.8280632 467056.2577 0.033883179 0.038080199 3.28E-11 10.48418796 0.162953825 TDGS(ph)IS(ph)GDRQPVTVADYISR ddPTM_HeLa_Romidepsin_16h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 2 0 T(0.027)DGS(0.955)IS(0.969)GDRQPVT(0.028)VADY(0.002)IS(0.019)R 99.011 0.011358 15880000 1614.4 1608.7 1486.4 1448.2 2030.5 1975.2 1666.5 1993.3 1794.9 2022.2 TRUE FALSE FALSE 1594.723072 1631.347321 1512.270168 1615.647698 1926.876008 1848.991095 1808.052468 2050.972991 1634.359649 1969.662952 0.809642619 0.82823679 0.767781191 0.820266074 0.978277022 0.938734768 0.917950183 1.041281194 0.829766152 1 10.94373306 -6.282848343 0.862766165 0.889065646 1.646716608 0.318273175 0.073634317 13.73143402 2.150442069 0.014881112 14.7393842 5.21E-07 6.282848343 0.757650962 TDGSIS(ph)GDRQPVTVADYISR ddPTM_HeLa_Romidepsin_16h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 TDGS(0.003)IS(0.988)GDRQPVT(0.009)VADY(0.001)ISR 96.866 0.0064191 44045000 1661.8 1942.2 1866.9 2014 2260 2098.9 1799.6 2117.3 2080.5 1453.9 TRUE FALSE FALSE 1641.545342 1969.542343 1899.392611 2246.868156 2144.663767 1964.787064 1952.457979 2178.560735 1894.414869 1416.127468 1.159179085 1.390794534 1.341258223 1.586628468 1.514456724 1.387436589 1.378730392 1.538393106 1.337743185 1 10.46773542 -10.35575224 0.980635584 1.042380097 1.471817846 0.497754576 0.118533846 0.123978614 0.237811289 0.017542003 0.019866211 4.41E-11 10.35575224 0.429437749 TDGSISGDRQPVTVADY(ph)ISR ddPTM_HeLa_Romidepsin_16h_R1 1 TDGSISGDRQPVTVADYISR 20 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 TDGSIS(0.011)GDRQPVT(0.001)VADY(0.987)ISR 118.61 0.00073324 9224200 1411.2 1535.9 1395.6 1557.9 1590.9 1597.4 1375.8 1405.2 1206.1 1316.7 TRUE FALSE FALSE 1393.999752 1557.522441 1419.889833 1738.031728 1509.710437 1495.331295 1492.660418 1445.857245 1098.223395 1282.491944 1.086946205 1.214450077 1.107133529 1.355198944 1.177169528 1.165957652 1.163875083 1.127381152 0.856319917 1 10.32473405 -10.66700498 1.043325198 1.021564679 1.191722692 0.548602908 0.084046639 0.241901434 0.54656824 0.015672669 0.015147866 2.15E-11 10.66700498 0.170158013 TDLEKDIISDTSGDFR ddPTM_HeLa_Romidepsin_16h_R1 3 TDLEKDIISDTSGDFR 16 1 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33;H0YKS4;H0YNA0;H0YN52 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 ;; ;; 155.37 0.00027365 122880300 12531.6 14912.3 13597.1 13827.5 15895.8 15572.6 14169.3 14486 14646.7 13818.4 FALSE FALSE TRUE 12378.86004 15122.23575 13833.75182 15426.30061 15084.57801 14577.56112 15372.83999 14905.12955 13336.66247 13459.39598 0.919718839 1.123544903 1.027813718 1.146136174 1.120747026 1.083076918 1.142164181 1.107414447 0.990881202 1 13.71632605 -10.25525279 24.99468422 0.962089451 1.106639624 0.735218116 0.037599936 188.5744583 761866.9027 0.006987186 0.008442433 5.56E-11 10.25525279 0.144550173 TDLEKDIISDTSGDFRK ddPTM_HeLa_Romidepsin_16h_R1 1 TDLEKDIISDTSGDFRK 17 2 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33;H0YKS4;H0YNA0;H0YN52 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 102.15 0.0032821 18414000 1279.8 1353.8 1711.8 1136.5 1527.9 1563 1343.9 1400.4 1556.6 1462.1 FALSE FALSE TRUE 1264.201305 1372.858832 1741.593161 1267.907477 1449.925562 1463.129344 1458.050832 1440.918365 1417.373797 1424.114431 0.88771048 0.964008792 1.222930632 0.89031292 1.018124337 1.027395912 1.023829827 1.011799567 0.995266789 1 10.47584936 -9.977466395 24.99999957 0.945863042 1.030407564 0.145935216 0.081236921 290.8558575 322690.649 0.013110832 0.017230395 1.05E-10 9.977466395 0.084544522 TDLETS(ph)PGAAPR ddPTM_HeLa_Romidepsin_16h_R1 2 TDLETSPGAAPR 12 0 Q6F5E8;Q6F5E8-2 Q6F5E8 RLTPR Leucine-rich repeat-containing protein 16C 1 0 TDLET(0.047)S(0.952)PGAAPR;TDLET(0.048)S(0.952)PGAAPR ; 142.76 0.0016153 42325000 8505 8340.3 7675.3 11322 17148.4 19232.4 15854.7 17375.5 8702.8 7723.4 TRUE FALSE FALSE 8401.337789 8457.714962 7808.885377 12631.10291 16273.25316 18003.51171 17201.39782 17878.23268 7924.399771 7522.744955 1.116791522 1.124285751 1.038036704 1.679055051 2.163206816 2.393210433 2.286585273 2.376557066 1.053392056 1 12.87704346 -8.953779227 1.905991657 1.056890313 2.345774101 0.990173421 0.058276704 0.023784339 0.173514938 0.010160657 0.02061541 1.11E-09 8.953779227 1.288883788 up TDLQGS(ph)ASPSKVEGVHTPR ddPTM_HeLa_Romidepsin_16h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 B4DF77;Q6VY07;Q6VY07-2 B4DF77 PACS1 Phosphofurin acidic cluster sorting protein 1 1 0 T(0.007)DLQGS(0.699)AS(0.127)PS(0.162)KVEGVHT(0.005)PR 69.024 0.0062645 32332000 1592.4 1817 1753.4 1473 1730.1 1707.9 1561.4 1367.4 1890.4 1780.7 TRUE FALSE FALSE 1572.991216 1842.579774 1783.917191 1643.315191 1641.806541 1598.770702 1694.025277 1406.963562 1721.317889 1734.437157 0.906917388 1.062350265 1.028528006 0.947463091 0.94659327 0.921780703 0.976700291 0.811193162 0.992436009 1 10.76025185 -6.574257104 1.690071812 0.965678413 4.12E-11 0.506843608 0.047033978 7.039854892 3.464590515 0.007647732 19.59542705 2.67E-07 6.574257104 -0.965678413 TDLQGSAS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 TDLQGSASPSK 11 0 B4DF77;Q6VY07;Q6VY07-2 B4DF77 PACS1 Phosphofurin acidic cluster sorting protein 1 1 0 T(0.003)DLQGS(0.004)AS(0.497)PS(0.497)K 147.52 0.0024281 8522300 4093.9 4303.2 4751.8 2328.5 4434.1 4022.4 2978.3 2913.4 4433.6 4313.8 TRUE FALSE FALSE 4044.001972 4363.780563 4834.503086 2597.732126 4207.811331 3765.381622 3231.276728 2997.694632 4037.047712 4201.726854 0.962461891 1.038568359 1.150599088 0.618253451 1.00144809 0.896150976 0.769035408 0.713443481 0.960806795 1 12.03676666 -9.269940202 24.9914078 0.998417831 0.814534925 0.500470503 0.109496565 463.1080346 1361480.64 0.016320657 0.025177462 5.37E-10 9.269940202 -0.183882906 TDLQGSAS(ph)PSKVEGVHTPR ddPTM_HeLa_Romidepsin_16h_R1 1 TDLQGSASPSKVEGVHTPR 19 1 B4DF77;Q6VY07;Q6VY07-2 B4DF77 PACS1 Phosphofurin acidic cluster sorting protein 1 1 0 T(0.003)DLQGS(0.277)AS(0.691)PS(0.024)KVEGVHT(0.006)PR 63.522 0.010032 13612000 1070.9 1089.2 809.89 672.4 1003 927.15 908.83 987.31 1241.1 1204.7 TRUE FALSE FALSE 1057.847459 1104.533786 823.9857957 750.1460517 951.8131673 867.9081072 986.0259975 1015.876257 1130.092908 1173.40172 0.901521994 0.941309159 0.702219693 0.639291761 0.811157126 0.739651299 0.840314089 0.865753168 0.963091231 1 10.1964813 -9.776623225 23.49361207 0.951283146 0.764798916 0.654284212 0.065903273 58.7146745 90847.5547 0.011950702 0.015747197 1.67E-10 9.776623225 -0.186484229 TDLT(ph)Y(ph)RILR ddPTM_HeLa_Romidepsin_16h_R1 1 TDLTYRILR 9 1 P24347 P24347 MMP11 Stromelysin-3 2 0 TDLT(1)Y(1)RILR 101.6 0.02587 5146000 1702.8 1761.7 1623.6 1905.2 1724.7 1342.8 1262.8 1479.8 1685 1797.3 TRUE FALSE FALSE 1682.045619 1786.501259 1651.858077 2125.488188 1636.682123 1256.999414 1370.0622 1522.615678 1534.28938 1750.605887 0.960836263 1.020504542 0.94359221 1.214144317 0.934923237 0.71803678 0.782621726 0.869764971 0.876433349 1 10.77363861 -8.447581374 6.153638195 0.998638525 0.792712973 0.535123804 0.088397902 0.122404844 7.951797323 0.01113783 0.025021818 3.57E-09 8.447581374 -0.205925551 TDNSSLSS(ph)PLNPK ddPTM_HeLa_Romidepsin_16h_R1 3 TDNSSLSSPLNPK 13 0 Q9UIG0-2;Q9UIG0 Q9UIG0-2 BAZ1B Tyrosine-protein kinase BAZ1B 1 0 TDNSSLS(0.1)S(0.899)PLNPK;TDNSSLS(0.205)S(0.794)PLNPK;TDNSS(0.002)LS(0.225)S(0.773)PLNPK ;; 187.63 1.33E-10 99617000 13042.6 11771.2 11094.3 8149.8 13529.3 16945.5 14796.7 13365.3 13917.5 12805.8 TRUE FALSE FALSE 12883.63177 11936.91526 11287.39164 9092.118222 12838.84934 15862.73724 16053.53133 13752.00387 12672.68394 12473.10347 1.032913084 0.957012446 0.904938507 0.72893793 1.029322764 1.271755444 1.287051885 1.102532654 1.016000867 1 13.60653285 -8.34578635 5.333489483 0.980436309 1.226356683 0.604318247 0.097935392 0.130132317 6.18703011 0.015169225 0.034662225 4.51E-09 8.34578635 0.245920374 TDPASNTK(ac)LIAMK ddPTM_HeLa_Romidepsin_16h_R1 2 TDPASNTKLIAMK 13 1 E7EWM1;Q15596 E7EWM1 NCOA2 Nuclear receptor coactivator 2 0 1 ; TDPASNTK(1)LIAMK;TDPASNTK(1)LIAMK 158.42 1.71E-05 10875300 2116.24 1807.22 1980.5 1807.14 1378 910.78 936.22 861.47 2212.96 2329.46 FALSE TRUE FALSE 2090.446453 1832.662091 2014.969772 2016.09003 1307.675518 852.5840974 1015.742503 886.3952753 2015.027315 2268.940293 0.921331627 0.807717196 0.888066459 0.888560195 0.576337562 0.375763126 0.447672645 0.390664875 0.88809182 1 11.14780293 -8.670072741 2.16215995 0.94316424 0.405359478 0.939252101 0.056917128 0.053772333 0.509624892 0.009881209 0.022548467 2.14E-09 8.670072741 -0.537804762 down TDPVPEEGEDVAATISAT(ph)ETLSEEEQEELRR ddPTM_HeLa_Romidepsin_16h_R1 1 TDPVPEEGEDVAATISATETLSEEEQEELRR 31 1 H0YC42;P55327-2;P55327;P55327-3;E5RFR7;H0YC44;P55327-8;P55327-4;P55327-7;P55327-5;P55327-6 H0YC42 TPD52 Tumor protein D52 1 0 TDPVPEEGEDVAAT(0.178)IS(0.215)AT(0.225)ET(0.205)LS(0.178)EEEQEELRR 44.107 0.014279 1313000 299.9 321.79 499.97 339.48 402.41 428.11 286.42 329.06 336.59 421.22 TRUE FALSE FALSE 296.2447034 326.3201681 508.6717681 378.7322749 381.8735161 400.7551527 310.7485077 338.5808319 306.4845474 410.2766437 0.722060853 0.795366183 1.239826288 0.923114393 0.930770791 0.97679251 0.757412133 0.825250077 0.747019242 1 8.680453216 -7.747698478 24.9626826 0.901496137 0.791331083 0.104076379 0.141700007 505.3848163 918100.9662 0.021609492 0.079985883 1.79E-08 7.747698478 -0.110165054 TDQEAPNASQPT(ph)PPPLPK ddPTM_HeLa_Romidepsin_16h_R1 4 TDQEAPNASQPTPPPLPK 18 0 Q9H792 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 T(0.001)DQEAPNAS(0.002)QPT(0.998)PPPLPK;TDQEAPNAS(0.002)QPT(0.998)PPPLPK;TDQEAPNAS(0.022)QPT(0.978)PPPLPK;TDQEAPNAS(0.14)QPT(0.86)PPPLPK ;;; 150.61 8.41E-05 27750400 8791.2 8531.8 8608.4 8768.57 10868.8 12862.5 10077.1 11076.9 9239.3 8787.59 TRUE FALSE FALSE 8684.049473 8651.910904 8758.225591 9782.433321 10314.12458 12040.62776 10933.04862 11397.39263 8412.913868 8559.287145 1.014576252 1.010821434 1.023242408 1.142902809 1.205021447 1.406732542 1.277331679 1.331581992 0.982898894 1 13.06327493 -8.825652599 1.502683147 1.007044848 1.333756057 0.936000236 0.037631835 0.058420553 0.265602554 0.005298526 0.012487578 1.49E-09 8.825652599 0.326711209 TDS(ph)ASADPDNLK ddPTM_HeLa_Romidepsin_16h_R1 2 TDSASADPDNLK 12 0 Q96Q15;H3BR09;E9PNP6;I3L0W2 Q96Q15 SMG1 Serine/threonine-protein kinase SMG1 1 0 T(0.014)DS(0.976)AS(0.011)ADPDNLK;T(0.162)DS(0.836)AS(0.002)ADPDNLK ; 161.48 0.00067052 3477200 2977.7 4115.5 2848.7 2612.3 3539.4 3106.9 2388.9 3217.9 2782.3 3261.1 TRUE FALSE FALSE 2941.406647 4173.438117 2898.280429 2914.346417 3358.771211 2908.379117 2591.813106 3311.004859 2533.44412 3176.376152 0.92602592 1.31389921 0.912448743 0.917506705 1.057422374 0.915628055 0.815965422 1.042384372 0.797589454 1 11.63316605 -8.130787086 11.87644322 0.988765505 0.91337763 0.042695139 0.137138855 1.193673747 107.7618051 0.01691356 0.043149849 7.40E-09 8.130787086 -0.075387874 TDSREDEIS(ph)PPPPNPVVK ddPTM_HeLa_Romidepsin_16h_R1 8 TDSREDEISPPPPNPVVK 18 1 K7EPB2;P10644-2;P10644;K7EMU2;K7EMZ6;K7EIE5;K7EID3;K7EJ40;K7EK41 K7EPB2 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 1 0 TDS(0.001)REDEIS(0.999)PPPPNPVVK;TDS(0.002)REDEIS(0.998)PPPPNPVVK;TDS(0.001)REDEIS(0.999)PPPPNPVVK;T(0.002)DS(0.007)REDEIS(0.991)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;TDSREDEIS(1)PPPPNPVVK;T(0.008)DS(0.008)REDEIS(0.984)PPPPNPVVK ;;;;;;; 194.67 3.60E-20 3599006000 38373.8 38874.2 33507.6 38377.3 38966.2 40066.8 33423.5 38208.7 40250.1 38200.3 TRUE FALSE FALSE 37906.08537 39421.47201 34090.78572 42814.664 36977.60941 37506.66079 36262.49126 39314.20845 36650.03025 37207.8507 1.018765789 1.059493394 0.916225611 1.150688986 0.993812024 1.008030834 0.974592474 1.056610573 0.98500799 1 15.18331944 TDSVIIADQTPT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 2 TDSVIIADQTPTPTR 15 0 K7ELQ4;P17544-4;P17544-2;P17544;K7ESA4;P17544-5;P17544-3;P17544-1 K7ELQ4 ATF7 Cyclic AMP-dependent transcription factor ATF-7 1 0 TDSVIIADQT(0.055)PT(0.918)PT(0.027)R;T(0.003)DS(0.001)VIIADQTPT(0.933)PT(0.063)R ; 147.07 0.00098868 17664500 2936.8 2868.5 2765.1 3005 2391.7 2320.08 1786.6 2258.43 2871.7 2846.9 TRUE FALSE FALSE 2901.005152 2908.882818 2813.225406 3352.452239 2269.642624 2171.834376 1938.353759 2323.774109 2614.84796 2772.937128 1.046184972 1.049025883 1.014529099 1.208989633 0.818497687 0.78322525 0.699025499 0.83801904 0.942988549 1 11.43719919 -8.610160407 7.681049975 1.035500809 0.771720247 0.762063994 0.071104996 0.074206932 5.640216581 0.009113325 0.018281446 2.45E-09 8.610160407 -0.263780562 TDTALT(ph)NTYSALPPMPS(ph)FTMANN ddPTM_HeLa_Romidepsin_16h_R1 1 TDTALTNTYSALPPMPSFTMANN 23 0 A0A1W2PRS6 A0A1W2PRS6 2 0 T(0.016)DT(0.062)ALT(0.287)NT(0.287)Y(0.259)S(0.085)ALPPMPS(0.502)FT(0.502)MANN 41.257 0.0042227 0 956.37 1028.3 988.36 1031.7 1076.5 1386.3 983.46 1119.2 1005.9 1125.6 TRUE FALSE FALSE 944.7133946 1042.776434 1005.561991 1150.990008 1021.562188 1297.719904 1066.995068 1151.582286 915.9297847 1096.35675 0.861684296 0.951128759 0.917185023 1.049831643 0.931778993 1.183665722 0.973218862 1.050371867 0.835430424 1 10.09850161 -8.997531819 1.480991964 0.9332567 1.049265097 0.375930232 0.07640752 0.367417636 1.603234887 0.012150408 0.025932248 1.01E-09 8.997531819 0.116008396 TDTAVQAT(ph)GSVPSTPIAHR ddPTM_HeLa_Romidepsin_16h_R1 1 TDTAVQATGSVPSTPIAHR 19 0 I3L533;I3L2R9;Q9NXR1;Q9NXR1-1;I3L2R3;I3L522 I3L533 NDE1 Nuclear distribution protein nudE homolog 1 1 0 TDTAVQAT(0.803)GS(0.196)VPSTPIAHR 95.51 0.0018396 4146300 1166.2 1397.8 1228.9 1307.5 1419.7 1798.9 1493.8 1506.4 1469.9 1248.5 TRUE FALSE FALSE 1151.985906 1417.478265 1250.288489 1458.679302 1347.247411 1683.956096 1620.683335 1549.985307 1338.428463 1216.06379 0.947307136 1.165628215 1.028143835 1.199508869 1.107875609 1.384759673 1.332728882 1.274592106 1.100623564 1 10.24800319 -8.953814889 0.692772712 0.976417442 1.348067717 0.63571686 0.083018807 0.256757369 0.225993742 0.014397377 0.048571658 1.11E-09 8.953814889 0.371650275 TDTAVQATGS(ph)VPSTPIAHR ddPTM_HeLa_Romidepsin_16h_R1 1 TDTAVQATGSVPSTPIAHR 19 0 I3L533;I3L2R9;Q9NXR1;Q9NXR1-1;I3L2R3;I3L522 I3L533 NDE1 Nuclear distribution protein nudE homolog 1 1 0 TDTAVQAT(0.055)GS(0.941)VPS(0.002)T(0.002)PIAHR 76.668 0.0045659 10548000 1893.7 1929 1543.2 1430.1 2654.7 2490.2 2175.6 2267.2 2024 1784 TRUE FALSE FALSE 1870.618856 1956.156513 1570.058749 1595.454891 2519.220753 2331.084257 2360.39541 2332.797855 1842.968371 1737.651423 1.07652135 1.125747366 0.90355219 0.918167401 1.449784876 1.341514314 1.358382572 1.342500472 1.060608789 1 10.76292299 -8.758621535 24.99996173 1.026022594 1.369746004 0.862688509 0.070053631 21.14435145 187589.6045 0.010836726 0.020931134 1.74E-09 8.758621535 0.34372341 TDTESELDLIS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TDTESELDLISR 12 0 A0A494C1T2;V9GZ78;V9GYY3;A0A384N5Y3;F5H2F4;P11586 A0A494C1T2 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 1 0 TDTESELDLIS(1)R 143.76 0.0015278 1248000 721.58 758.92 724.29 577.96 641.8 614.11 518.28 533.7 582.98 901.92 TRUE FALSE FALSE 712.7851054 769.6040957 736.8959636 644.7864546 609.0465511 574.8703529 562.3026903 549.1417675 530.8368087 878.4879884 0.811377179 0.876055343 0.838823038 0.733972989 0.69328956 0.654386128 0.640080112 0.625098777 0.604261886 1 9.77887875 -6.842821775 0.09870104 1.200427927 2.68E-11 0 0.124713404 12.15282217 0.17180916 0.46233168 2.135605495 1.44E-07 6.842821775 -1.200427927 TDTESELDLISR ddPTM_HeLa_Romidepsin_16h_R1 1 TDTESELDLISR 12 0 A0A494C1T2;V9GZ78;V9GYY3;A0A384N5Y3;F5H2F4;P11586 A0A494C1T2 MTHFD1 "C-1-tetrahydrofolate synthase, cytoplasmic;Methylenetetrahydrofolate dehydrogenase;Methenyltetrahydrofolate cyclohydrolase;Formyltetrahydrofolate synthetase;C-1-tetrahydrofolate synthase, cytoplasmic, N-terminally processed" 0 0 260.98 9.33E-63 6354300 2028.5 2137.1 1769.4 1738.1 2032.1 1924.2 1685.9 1873.1 2012.2 2024.6 FALSE FALSE TRUE 2003.775862 2167.18615 1800.195665 1939.0673 1928.394354 1801.24983 1829.100304 1927.295193 1832.223792 1972.0006 1.016113211 1.098978443 0.912877848 0.983299549 0.977887306 0.913412415 0.927535369 0.977329922 0.929119287 1 10.94544428 -9.72892006 24.99995572 1.014674406 0.94905282 0.31150604 0.045265904 135.8023457 104400.8529 0.005669554 0.008017654 1.87E-10 9.72892006 -0.065621586 TDTGIVTVEQS(ph)PSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TDTGIVTVEQSPSSSK 16 0 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 TDTGIVT(0.001)VEQS(0.513)PS(0.143)S(0.04)S(0.303)K 141.1 0.00061948 46090000 5005.4 4807.3 5084.2 4447.4 5172.3 4608.1 3122.9 4010.6 5179.8 5169.6 TRUE FALSE FALSE 4944.39226 4874.977296 5172.688368 4961.629314 4908.33823 4313.657282 3388.159048 4126.640383 4716.505715 5035.293047 0.98194727 0.968161585 1.02728646 0.985370517 0.974787005 0.856684455 0.672882197 0.819543241 0.936689418 1 12.29786003 -8.091174264 2.881723611 0.991250579 0.746423526 0.839341488 0.0414098 0.054121582 0.864480194 0.0047123 0.014576627 8.11E-09 8.091174264 -0.244827053 TDTGIVTVEQSPS(ph)SSK ddPTM_HeLa_Romidepsin_16h_R1 1 TDTGIVTVEQSPSSSK 16 0 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 TDTGIVTVEQS(0.198)PS(0.739)S(0.058)S(0.005)K 303.44 1.15E-137 46974000 6246.6 6611.9 6024.9 5241.3 6416.9 5719.3 4338.1 4670 5931.2 6329.4 TRUE FALSE FALSE 6170.464037 6704.982502 6129.760857 5847.323767 6089.421648 5353.855188 4706.578106 4805.119082 5400.698617 6164.961276 1.000892586 1.087595234 0.994290245 0.948476966 0.987746942 0.868432898 0.763440011 0.779424049 0.876031231 1 12.58987612 -8.076934645 1.631576883 1.004653191 0.75931222 0.726858035 0.052180825 0.090216087 0.442468528 0.004856794 0.021110886 8.38E-09 8.076934645 -0.245340971 TDTS(ph)PVLETAGTVAAMAATPSAR ddPTM_HeLa_Romidepsin_16h_R1 1 TDTSPVLETAGTVAAMAATPSAR 23 0 Q8WWH5 Q8WWH5 TRUB1 Probable tRNA pseudouridine synthase 1 1 0 T(0.134)DT(0.174)S(0.659)PVLET(0.029)AGT(0.003)VAAMAATPSAR 98.804 3.64E-05 0 988.17 1278 1023.2 671 1001.5 984.28 1066.5 1037.8 1216.7 1112.3 TRUE FALSE FALSE 976.125804 1295.991718 1041.008367 748.5841771 950.3897179 921.3876846 1157.088483 1067.827106 1107.875305 1083.402286 0.900981858 1.196223909 0.960869642 0.690956801 0.877226983 0.850457579 1.0680137 0.985623826 1.022589041 1 10.08135332 -12.60798842 1.178267958 1.00299136 0.9357069 0.04304926 0.12684714 1.983160568 4.556242305 0.11726102 0.022304213 2.47E-13 12.60798842 -0.067284459 TDVSNFDEEFTGEAPT(ph)LSPPRDAR ddPTM_HeLa_Romidepsin_16h_R1 1 TDVSNFDEEFTGEAPTLSPPRDAR 24 1 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 TDVSNFDEEFT(0.168)GEAPT(0.698)LS(0.134)PPRDAR 59.943 0.0038768 27002000 559.68 620.09 447.6 533.89 476.99 660.06 522.64 681.68 666.62 634.23 TRUE FALSE FALSE 552.8584049 628.8196433 455.3902902 595.6208738 452.6474204 617.8842962 567.0330286 701.4033353 606.9958376 617.7526132 0.894951139 1.017914987 0.737172584 0.964173783 0.732732506 1.000213165 0.917896609 1.135411361 0.982587244 1 9.270885398 -7.259705982 24.05834886 0.927860638 1.135411474 0.298903478 0.09923792 88.77628364 1231966.216 0.013078246 0.111779498 5.50E-08 7.259705982 0.207550835 TDVSNFDEEFTGEAPTLS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 TDVSNFDEEFTGEAPTLSPPR 21 0 Q16512;Q16512-2 Q16512 PKN1 Serine/threonine-protein kinase N1 1 0 TDVSNFDEEFTGEAPT(0.037)LS(0.963)PPR 164.48 2.68E-09 11248000 5224.1 5093.5 5124.9 4345.3 5534.7 6023.1 5190.3 4556.4 5433.2 5745.5 TRUE FALSE FALSE 5160.42666 5165.206427 5214.096735 4847.724031 5252.243606 5638.243349 5631.163952 4688.232245 4947.240984 5596.231082 0.922125371 0.922979475 0.931715767 0.866248009 0.938532296 1.007507243 1.006242214 0.837748152 0.884030861 1 12.45023982 -12.24539312 0.928506148 1.000880238 0.932086463 0 0.061154902 0.763935939 1.159142169 0.03577118 0.009359899 5.68E-13 12.24539312 -0.068793775 TDYIPLLDVDEKTGNSES(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TDYIPLLDVDEKTGNSESK 19 1 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;H7C456;A0A0J9YW37;A0A0J9YVV8;P27816-7 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 TDYIPLLDVDEKT(0.097)GNS(0.302)ES(0.601)K 78.234 0.0036463 26360000 2418.3 2506.9 1922.2 4424.5 3216.6 4027.2 3188.4 3600.7 2321 1907.3 TRUE FALSE FALSE 2388.824829 2542.192204 1955.655085 4936.081508 3052.444899 3769.874917 3459.222616 3704.880574 2113.403947 1857.748071 1.285871247 1.368426776 1.052701986 2.65702416 1.64308872 2.02927134 1.862051518 1.994285787 1.137616009 1 10.85933916 -9.288205021 24.98982581 1.154033949 2.005087611 0.735680916 0.259775894 277.5661727 259149.7283 0.038721085 0.059157523 5.15E-10 9.288205021 0.851053661 TDYNAS(ph)VSVPDSSGPER ddPTM_HeLa_Romidepsin_16h_R1 1 TDYNASVSVPDSSGPER 17 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 T(0.019)DYNAS(0.711)VS(0.145)VPDS(0.094)S(0.031)GPER 137.85 0.0010457 7551100 729.62 701.89 669.46 2728.1 634.72 647.28 560.31 654.21 1014 745.93 TRUE FALSE FALSE 720.7271108 711.7712258 681.1116705 3043.535758 602.3278699 605.920897 607.9027174 673.1385342 923.3053004 726.5506311 0.991984701 0.979658121 0.937459334 4.189020872 0.829023944 0.833969267 0.836696978 0.926485375 1.270806549 1 9.504919528 TDYNASVS(ph)VPDSSGPER ddPTM_HeLa_Romidepsin_16h_R1 1 TDYNASVSVPDSSGPER 17 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 1 0 TDYNAS(0.242)VS(0.751)VPDS(0.002)S(0.004)GPER 122.97 8.85E-06 0 1399.1 1435.1 1176.1 2226.9 1131 1191.4 807.22 1245.6 1690.8 1360.3 TRUE FALSE FALSE 1382.047231 1455.303375 1196.569527 2484.384656 1073.28085 1115.273385 875.7852467 1281.639471 1539.570613 1324.95921 1.043086625 1.098375984 0.903099143 1.875065011 0.81004822 0.841741675 0.660990346 0.967304851 1.161975857 1 10.37173223 TDYNASVSVPDSSGPER ddPTM_HeLa_Romidepsin_16h_R1 3 TDYNASVSVPDSSGPER 17 0 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 ;; ;; 164.7 5.36E-07 27022090 8706.2 4802.8 6026.5 3041.69 5299.2 4014.831 6755.8 6013.381 8144.5 7133.2 FALSE FALSE TRUE 8600.085486 4870.413944 6131.388705 3393.384509 5028.76205 3758.296256 7329.637483 6187.368692 7416.035522 6947.878436 1.237800224 0.700992971 0.88248359 0.488405855 0.723783828 0.540927175 1.054946132 0.890540724 1.067381301 1 12.7623568 -10.25409012 24.95409279 1.112294551 0.751414891 0.478083045 0.166081265 355.2375935 1206194.116 0.029732013 0.036017498 5.57E-11 10.25409012 -0.36087966 TEADAEK(ac)TFEEK ddPTM_HeLa_Romidepsin_16h_R1 2 TEADAEKTFEEK 12 1 P19338;H7BY16 P19338 NCL Nucleolin 0 1 ; TEADAEK(1)TFEEK;TEADAEK(1)TFEEK 257.54 1.14E-65 4087700 1706.99 1559.44 1317.71 1348.66 3483.8 3039.6 2648.4 3075.8 3632.9 3090.2 FALSE TRUE FALSE 1686.184549 1581.393837 1340.64419 1504.598415 3306.008686 2845.37937 2873.35503 3164.79342 3307.964325 3009.916159 0.560209807 0.525394647 0.445409147 0.499880507 1.098372351 0.945335092 0.954629591 1.051455673 1.099022083 1 11.55550759 -8.745363821 24.98208362 0.718054844 1.003524512 0.366741403 0.206317296 263.4599499 409425.5667 0.034036778 0.067901539 1.80E-09 8.745363821 0.285469669 TEAELSQDLET(ph)SPTAKPQIK ddPTM_HeLa_Romidepsin_16h_R1 1 TEAELSQDLETSPTAKPQIK 20 1 Q5VT06;H0Y7F7 Q5VT06 CEP350 Centrosome-associated protein 350 1 0 TEAELS(0.001)QDLET(0.593)S(0.406)PTAKPQIK 92.565 0.00077058 18869000 3122.2 3022 2608.3 2304.1 3382.6 3650.2 2900.7 3299.5 3196.8 2789 TRUE FALSE FALSE 3084.145425 3064.543795 2653.696367 2570.510883 3209.9733 3416.964 3147.085386 3394.965827 2910.870201 2716.541378 1.135320614 1.128104957 0.9768658 0.946243964 1.181639759 1.257836169 1.158489766 1.249738309 1.071535381 1 11.40755531 -8.588989634 8.506546819 1.056227971 1.216359155 0.634952443 0.062775399 0.16881379 19.6433356 0.010866879 0.021780802 2.58E-09 8.588989634 0.160131185 TEAELSQDLETS(ph)PTAKPQIK ddPTM_HeLa_Romidepsin_16h_R1 1 TEAELSQDLETSPTAKPQIK 20 1 Q5VT06;H0Y7F7 Q5VT06 CEP350 Centrosome-associated protein 350 1 0 T(0.002)EAELS(0.073)QDLET(0.33)S(0.583)PT(0.012)AKPQIK 61.903 0.0078453 13310000 2017.5 1882.8 1890.7 1600.3 2317.3 2432.6 2025.1 2441.8 2223.3 2395.1 TRUE FALSE FALSE 1992.909934 1909.306108 1923.60684 1785.334216 2199.039534 2277.164711 2197.111943 2512.44963 2024.44248 2332.874957 0.854272077 0.818434825 0.824564915 0.765293575 0.942630692 0.976119489 0.941804419 1.076975696 0.86778868 1 11.18789326 -6.944791026 1.080177635 0.903019886 1.2638356 0.398477961 0.07101373 3.447212521 2.028535891 0.013544815 1.669640809 1.14E-07 6.944791026 0.360815715 TEAPAPASSTPQEPWPGPT(ph)APSPTSRPPWAVDPAFAER ddPTM_HeLa_Romidepsin_16h_R1 1 TEAPAPASSTPQEPWPGPTAPSPTSRPPWAVDPAFAER 38 1 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 1 0 TEAPAPASST(0.001)PQEPWPGPT(0.539)APS(0.26)PT(0.1)S(0.1)RPPWAVDPAFAER 75.186 1.95E-06 12553000 2356.7 2462 2271.7 2697.8 2703.7 3116.8 2274.9 2898.3 3127.5 2525.7 TRUE FALSE FALSE 2327.975634 2496.660101 2311.237986 3009.73233 2565.7201 2917.646539 2468.129949 2982.157738 2847.768567 2460.08195 0.946300034 1.014868672 0.939496339 1.223427671 1.042940907 1.185995669 1.003271435 1.21221886 1.157590936 1 11.26449066 -9.277256288 24.98765764 0.975258278 1.124209539 0.272941154 0.089544325 422.3551217 667238.0312 0.00940991 0.014403639 5.28E-10 9.277256288 0.148951261 TEAPAPASSTPQEPWPGPTAPS(ph)PTSRPPWAVDPAFAER ddPTM_HeLa_Romidepsin_16h_R1 1 TEAPAPASSTPQEPWPGPTAPSPTSRPPWAVDPAFAER 38 1 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 1 0 TEAPAPASSTPQEPWPGPT(0.031)APS(0.916)PT(0.023)S(0.031)RPPWAVDPAFAER 124.98 1.14E-22 9553600 1466.6 1713.6 1533.4 1563.5 2331.4 2047.8 1720.2 2002.4 1751.4 1520 TRUE FALSE FALSE 1448.724515 1737.724106 1560.088184 1744.279226 2212.419958 1916.952189 1866.313745 2060.336285 1594.750398 1480.510181 0.9785306 1.173733304 1.053750392 1.178160913 1.494363218 1.294791629 1.260588255 1.39163939 1.077162736 1 10.5318787 -9.31346646 1.2040261 0.995467452 1.350251237 0.701506186 0.08839649 0.150785161 0.431808984 0.014321174 0.027515317 4.86E-10 9.31346646 0.354783784 TEARS(ph)S(ph)DEENGPPS(ph)SPDLDR ddPTM_HeLa_Romidepsin_16h_R1 1 TEARSSDEENGPPSSPDLDR 20 1 Q96B36-3;Q96B36;Q96B36-2 Q96B36-3 AKT1S1 Proline-rich AKT1 substrate 1 3 0 T(0.586)EARS(0.741)S(0.673)DEENGPPS(0.586)S(0.413)PDLDR 52.144 0.030198 10564000 1665.9 1561.8 1501.7 1720.1 1492.9 1567.7 1352.5 1172.1 1486.5 1676 TRUE FALSE FALSE 1645.59537 1583.787061 1527.836459 1918.986055 1416.711742 1467.52903 1467.381316 1206.012864 1353.543717 1632.457278 1.008048046 0.970185917 0.935912063 1.175519924 0.867840011 0.898969332 0.898878847 0.738771471 0.829144955 1 10.67282952 -6.805171578 0.676361115 1.004290472 0.41173123 0.334379528 0.09136222 2.672498313 0.555815018 0.011509825 1.401439643 1.57E-07 6.805171578 -0.592559243 TEATQGLDYVPSAGT(ph)ISPTSSLEEDKGFK ddPTM_HeLa_Romidepsin_16h_R1 1 TEATQGLDYVPSAGTISPTSSLEEDKGFK 29 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 TEATQGLDY(0.001)VPS(0.165)AGT(0.495)IS(0.325)PT(0.011)S(0.003)SLEEDKGFK 147.17 2.26E-11 15087000 822.05 920.44 778.12 1187.9 1595.9 1825.7 1500.8 1918.2 959.03 1068.2 TRUE FALSE FALSE 812.0305384 933.3979785 791.6628522 1325.250587 1514.455268 1709.043662 1628.277915 1973.700091 873.2519549 1040.44801 0.780462388 0.8971116 0.760886507 1.273730715 1.455579955 1.642603615 1.564977682 1.896971373 0.839303787 1 10.02298916 -8.832865025 1.614471852 0.883454212 1.69095391 0.914393387 0.113885636 0.08263164 0.43511087 0.019509026 0.044485559 1.47E-09 8.832865025 0.807499698 TEATQGLDYVPSAGTISPT(ph)SSLEEDKGFK ddPTM_HeLa_Romidepsin_16h_R1 1 TEATQGLDYVPSAGTISPTSSLEEDKGFK 29 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 TEATQGLDY(0.003)VPS(0.061)AGT(0.061)IS(0.222)PT(0.319)S(0.319)S(0.014)LEEDKGFK 77.873 2.24E-06 7037400 1764.3 1625.9 1474.7 1893 2553.3 3005.2 2639.4 3863 2107.9 1792.9 TRUE FALSE FALSE 1742.796033 1648.789463 1500.366535 2111.877567 2422.995573 2813.177419 2863.59057 3974.76981 1919.364145 1746.3202 0.997981947 0.944150714 0.859158896 1.209330092 1.387486427 1.610917299 1.639785516 2.276083052 1.099090616 1 10.7701024 -7.213049405 0.58295445 0.977371318 3.093193025 0.926572662 0.112486475 0.629542893 0.13887415 0.020231182 0.906376552 6.12E-08 7.213049405 2.115821707 up TEDEEFLIQHLLQAPS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 TEDEEFLIQHLLQAPSPPR 19 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 1 0 TEDEEFLIQHLLQAPS(1)PPR;TEDEEFLIQHLLQAPS(1)PPR ; 128.09 0.00038399 25527000 6894.8 5928.9 5462.9 3031.9 3920 3781.7 3464 3106.9 6501.7 6347.9 TRUE FALSE FALSE 6810.763526 6012.36721 5557.979483 3382.462544 3719.947772 3540.061575 3758.232074 3196.79325 5920.171668 6182.980643 1.10153402 0.972405957 0.89891588 0.547060186 0.601643121 0.572549354 0.607835006 0.517031095 0.957494776 1 12.59408677 -9.434016545 2.274034322 1.04486785 0.569061404 0.943076043 0.051298821 0.04416708 0.449595379 0.008130153 0.01302738 3.68E-10 9.434016545 -0.475806446 TEDEEFLIQHLLQAPSPPR ddPTM_HeLa_Romidepsin_16h_R1 2 TEDEEFLIQHLLQAPSPPR 19 0 Q9ULL5;Q9ULL5-2 Q9ULL5 PRR12 Proline-rich protein 12 0 0 ; ; 132.5 0.00043704 7638200 5552.9 5514.7 5143.9 3129.9 3560.8 3826.2 3288.5 3590.5 6089.6 5616.4 FALSE FALSE TRUE 5485.219119 5592.336091 5233.427422 3491.793765 3379.079089 3581.718168 3567.825108 3694.385453 5544.930924 5470.485118 1.002693363 1.022274254 0.956666056 0.638296913 0.617692767 0.654735017 0.652195378 0.6753305 1.01360863 1 12.41745306 -9.300371767 4.442994842 1.002006186 0.645284143 0.990306831 0.017420661 0.013467904 0.618993019 0.002636648 0.004163781 5.01E-10 9.300371767 -0.356722044 TEDFQTPS(ph)PVLR ddPTM_HeLa_Romidepsin_16h_R1 1 TEDFQTPSPVLR 12 0 Q5VT06;H0Y7F7 Q5VT06 CEP350 Centrosome-associated protein 350 1 0 TEDFQT(0.006)PS(0.994)PVLR 123.95 0.0061693 3501200 1594.6 1388.8 1626.3 1420.1 1888.1 1706.3 1555.6 1527.2 1484.9 1589.4 TRUE FALSE FALSE 1575.164402 1408.351563 1654.605069 1584.298644 1791.743212 1597.272937 1687.732625 1571.387122 1352.086825 1548.107159 1.017477629 0.909724856 1.068792338 1.023377894 1.157376737 1.03175864 1.090191086 1.015037695 0.873380642 1 10.59628962 TEDGDWEWS(ph)DDEMDEK ddPTM_HeLa_Romidepsin_16h_R1 2 TEDGDWEWSDDEMDEK 16 0 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 0 TEDGDWEWS(1)DDEMDEK;TEDGDWEWS(1)DDEMDEK ; 152.11 0.00038006 38279000 14917.8 13085.9 15134 7674.4 12790.9 12462.6 10939.8 11935.6 14580.4 14290.1 TRUE FALSE FALSE 14735.97612 13270.12364 15397.40092 8561.750237 12138.13264 11666.28008 11869.02634 12280.93775 13276.29251 13918.84114 1.058707113 0.953392851 1.106227219 0.615119474 0.872064888 0.838164612 0.852730929 0.88232473 0.953836054 1 13.76475148 -9.285536004 24.99999731 1.027022299 0.819120763 0.595971093 0.082880503 357.5050051 370906.6071 0.011546152 0.017642354 5.18E-10 9.285536004 -0.207901536 TEDGDWEWS(ph)DDEMDEKSEEGK ddPTM_HeLa_Romidepsin_16h_R1 1 TEDGDWEWSDDEMDEKSEEGK 21 1 Q9UEW8-2;Q9UEW8 Q9UEW8-2 STK39 STE20/SPS1-related proline-alanine-rich protein kinase 1 0 T(0.002)EDGDWEWS(0.997)DDEMDEKS(0.001)EEGK 58.123 0.025258 89800000 2033.2 2167.9 1981.2 2325 1692.8 1899.1 1455.4 2174.8 2147.9 2325.1 TRUE FALSE FALSE 2008.418576 2198.419753 2015.681955 2593.827439 1606.410099 1777.753639 1579.02164 2237.724407 1955.786444 2264.693567 0.886838999 0.970736079 0.890046223 1.14533263 0.709327797 0.784986395 0.697234126 0.988091475 0.863598711 1 11.14510014 -8.733292627 24.99999175 0.955046519 0.78722428 0.369511212 0.104992701 164.7922553 146368.0379 0.01401334 0.028022256 1.85E-09 8.733292627 -0.167822238 TEDGGEFEEGAS(ph)ENNAK ddPTM_HeLa_Romidepsin_16h_R1 2 TEDGGEFEEGASENNAK 17 0 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 TEDGGEFEEGAS(1)ENNAK;TEDGGEFEEGAS(1)ENNAK ; 292.44 8.71E-120 6404600 3193.5 3326.8 2899.2 3187.51 3834.3 3928.5 3319 3474.3 3221.2 3397.9 TRUE FALSE FALSE 3154.576394 3373.634778 2949.65936 3556.064904 3638.621363 3677.481529 3600.915777 3574.823389 2933.087804 3309.622068 0.953153058 1.019341396 0.891237519 1.074462531 1.099406908 1.111148479 1.088014191 1.080130394 0.886230435 1 11.69245077 -9.092624997 7.543388722 0.975243932 1.09437084 0.714756438 0.043113123 0.098952626 7.134305926 0.004861104 0.008093087 8.08E-10 9.092624997 0.119126908 TEDGGWEWS(ph)DDEFDEESEEGK ddPTM_HeLa_Romidepsin_16h_R1 2 TEDGGWEWSDDEFDEESEEGK 21 0 C9JIG9;O95747 C9JIG9 OXSR1 Serine/threonine-protein kinase OSR1 1 0 TEDGGWEWS(1)DDEFDEESEEGK;TEDGGWEWS(1)DDEFDEESEEGK ; 162.11 1.01E-08 25877700 11334.1 10551.7 13623.2 8132.5 12038.4 12658.9 10707 11510.1 12826.2 12616.5 TRUE FALSE FALSE 11195.95563 10700.24711 13860.30608 9072.817915 11424.03553 11850.03714 11616.45231 11843.12658 11678.99255 12288.72151 0.911075706 0.870737212 1.127888371 0.738304461 0.929635806 0.964301871 0.945293805 0.963739521 0.950383043 1 13.58504721 -12.36406836 1.040695047 1.0007905 0.929628509 0.02413892 0.09193667 1.151204816 2.192439321 0.061115396 0.015173666 4.32E-13 12.36406836 -0.071161991 TEDGGWEWS(ph)DDEFDEESEEGKAAISQLR ddPTM_HeLa_Romidepsin_16h_R1 1 TEDGGWEWSDDEFDEESEEGKAAISQLR 28 1 C9JIG9;O95747 C9JIG9 OXSR1 Serine/threonine-protein kinase OSR1 1 0 TEDGGWEWS(1)DDEFDEESEEGKAAISQLR 105.71 5.81E-09 5048500 2582.6 2865.8 2521.1 2885 2657.9 2588.2 2295.5 2545.7 2980.3 2756 TRUE FALSE FALSE 2551.122278 2906.144808 2564.978688 3218.577274 2522.257445 2422.822373 2490.479713 2619.355813 2713.734504 2684.398723 0.950351472 1.082605495 0.955513302 1.198993744 0.939598661 0.902556819 0.927760728 0.975770027 1.01092825 1 11.39038326 -8.55965411 24.99999919 0.999887478 0.932347377 0.226905401 0.073365122 236.4345419 160727.9918 0.010760109 0.021520251 2.76E-09 8.55965411 -0.0675401 TEDS(ph)IRDYEDGMEVDTTPTVAGQFEDADVDH ddPTM_HeLa_Romidepsin_16h_R1 2 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH 31 1 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 1 0 T(0.015)EDS(0.528)IRDY(0.449)EDGMEVDT(0.003)T(0.003)PT(0.001)VAGQFEDADVDH;T(0.023)EDS(0.492)IRDY(0.296)EDGMEVDT(0.075)T(0.101)PT(0.013)VAGQFEDADVDH ; 67.138 9.94E-05 7873800 1225.51 1172.99 1200.72 1384.41 1132.39 1248.75 959.43 1008.63 1226.28 927.56 TRUE FALSE FALSE 1210.573013 1189.503384 1221.618028 1544.481998 1074.599913 1168.958905 1040.92396 1037.813118 1116.598446 903.4618575 1.339927085 1.31660609 1.352152299 1.709515444 1.189424771 1.29386636 1.152150422 1.148707175 1.235910998 1 9.819319884 -12.15516023 0.850385801 0.994833739 1.317766152 0.120933433 0.166817215 0.551916797 0.703263153 0.113515369 0.03068286 7.00E-13 12.15516023 0.322932413 TEDSIRDYEDGMEVDT(ph)TPTVAGQFEDADVDH ddPTM_HeLa_Romidepsin_16h_R1 2 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH 31 1 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 1 0 TEDSIRDYEDGMEVDT(0.497)T(0.497)PT(0.005)VAGQFEDADVDH;TEDSIRDYEDGMEVDT(0.424)T(0.424)PT(0.152)VAGQFEDADVDH ; 95.287 1.54E-11 23927000 2134.9 1962.14 2324.9 2656.9 2240.2 2149.8 2202.6 2243.7 2401.3 1929.49 TRUE FALSE FALSE 2108.879018 1989.763058 2365.363909 2964.103279 2125.874235 2012.434718 2389.688789 2308.61792 2186.521714 1879.361572 1.12212522 1.058744144 1.258599699 1.577186276 1.1311683 1.070807634 1.271542861 1.228405409 1.163438556 1 10.87602694 -9.761544624 22.23285824 1.05936212 1.257447144 0.278918684 0.131283115 0.606423069 127967.4716 0.021390242 0.029138476 1.73E-10 9.761544624 0.198085024 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH ddPTM_HeLa_Romidepsin_16h_R1 4 TEDSIRDYEDGMEVDTTPTVAGQFEDADVDH 31 1 P54105;E9PMI6;J3KN38 P54105 CLNS1A Methylosome subunit pICln 0 0 ;;; ;;; 90.397 8.47E-11 79306000 4688.1 4115.4 3856.19 4801.22 4570.53 4367.76 4164.32 4803.97 5346.2 4583.02 FALSE FALSE TRUE 4630.959634 4173.336709 3923.305369 5356.359647 4337.278799 4088.674232 4518.037237 4942.965293 4868.022482 4463.95248 1.037412395 0.934897208 0.878886007 1.199914128 0.971622977 0.915931397 1.01211589 1.10730688 1.090518437 1 12.12410595 TEEARPSPAPGPGT(ph)PT(ph)GTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 2 0 TEEARPS(0.001)PAPGPGT(0.999)PT(0.895)GT(0.093)PT(0.012)R 172.99 1.28E-10 6738000 1365.5 1151.8 1284.7 1710.2 2860 3221 2597.6 2857.7 1416 1512.8 TRUE FALSE FALSE 1348.856761 1168.015071 1307.059665 1907.941371 2714.043528 3015.188495 2818.240079 2940.383041 1289.349414 1473.497238 0.915411801 0.792682226 0.887045887 1.294838783 1.841906084 2.046280385 1.912619859 1.9955131 0.875026692 1 10.52502864 -8.862364615 2.380926646 0.93945406 1.97878964 0.981051685 0.069163812 0.030172857 0.347810601 0.011753356 0.0237798 1.37E-09 8.862364615 1.03933558 TEEARPSPAPGPGT(ph)PTGTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 TEEARPS(0.001)PAPGPGT(0.67)PT(0.109)GT(0.188)PT(0.031)R 68.49 0.0039478 74988000 402.18 531.27 487.54 646.18 553.89 733.9 639.75 986.73 561.88 778.53 TRUE FALSE FALSE 397.2780755 538.749233 496.0254292 720.894372 525.6229265 687.0061586 694.090349 1015.279476 511.6240455 758.3036784 0.523903664 0.710466332 0.654125047 0.950667117 0.69315624 0.905977616 0.915319771 1.338882436 0.674695455 1 9.566631911 -5.407878911 0.874506464 0.763308952 15.57565478 0.627829391 0.135973597 33.21880215 1.199973001 0.029099513 893.711512 3.91E-06 5.407878911 14.81234583 TEEARPSPAPGPGTPT(ph)GT(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 2 0 TEEARPSPAPGPGT(0.106)PT(0.865)GT(0.848)PT(0.181)R 72.302 0.005 13808000 1021.8 1397.2 1397.3 1281.8 3013.7 3208.6 2581 2603.9 1307 1456.1 TRUE FALSE FALSE 1009.345909 1416.869818 1421.61942 1430.007747 2859.899643 3003.580815 2800.230076 2679.239738 1190.098647 1418.270312 0.711673861 0.999012534 1.002361403 1.00827588 2.016470076 2.117777401 1.974398006 1.889089629 0.839119762 1 10.46991681 -8.788461262 4.847589976 0.887847943 2.012581926 0.963972362 0.101607401 0.030941321 1.778087921 0.020038395 0.038190915 1.63E-09 8.788461262 1.124733983 TEEARPSPAPGPGTPT(ph)GTPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEARPSPAPGPGTPTGTPTR 21 1 Q4KMP7 Q4KMP7 TBC1D10B TBC1 domain family member 10B 1 0 TEEARPSPAPGPGT(0.098)PT(0.717)GT(0.151)PT(0.034)R 114.71 0.00010171 78790000 961.78 853.14 795.85 572.15 1029.8 1068.8 971.41 873.49 909.63 873.33 TRUE FALSE FALSE 950.0574554 865.1505273 809.7014354 638.304675 977.2454633 1000.507129 1053.921541 898.763055 828.2704146 850.6407607 1.116872714 1.017057455 0.951872368 0.750381012 1.148834512 1.176180564 1.238973712 1.056571818 0.97370177 1 9.732406177 -8.55864924 24.99998835 1.022595739 1.164931404 0.378594923 0.104054441 176.2080316 123151.1145 0.016405924 0.032811928 2.76E-09 8.55864924 0.142335665 TEEGEIDYS(ph)AEEGENRR ddPTM_HeLa_Romidepsin_16h_R1 1 TEEGEIDYSAEEGENRR 17 1 B7WPG3;V9GYK2;Q8WVV9-2;Q8WVV9-5;Q8WVV9;C9IYN3;Q8WVV9-3;Q8WVV9-4 B7WPG3 HNRNPLL Heterogeneous nuclear ribonucleoprotein L-like 1 0 TEEGEIDY(0.001)S(0.999)AEEGENRR 81.807 0.0010129 0 980.62 999.9 903.06 991.78 1445.7 1254.3 777.27 811.42 1008.7 933.34 TRUE FALSE FALSE 968.6678263 1013.976618 918.7773805 1106.45427 1371.920534 1174.154278 843.2912944 834.8971575 918.4793457 909.0916923 1.065533691 1.115373319 1.010654248 1.217098649 1.509111288 1.291568593 0.927619625 0.918386082 1.01032641 1 9.828282004 -9.262703834 24.88796813 1.038024146 1.184425125 0.140170755 0.162602586 166.7137557 3281394.809 0.026664009 0.042165509 5.46E-10 9.262703834 0.146400979 TEEGPTLS(ph)YGR ddPTM_HeLa_Romidepsin_16h_R1 2 TEEGPTLSYGR 11 0 D6REM6;A0A0R4J2E8;A8MXP9;P43243;D6R991 D6REM6 MATR3 Matrin-3 1 0 TEEGPT(0.001)LS(0.999)YGR;TEEGPT(0.002)LS(0.998)YGR ; 105.36 0.016707 6920800 2811.7 2699.6 2692.2 2548.6 2474.4 2581.1 2263.7 2055.96 2760 2906.4 TRUE FALSE FALSE 2777.429919 2737.60504 2739.056612 2843.281124 2348.122135 2416.17604 2455.978621 2115.445959 2513.138687 2830.891309 0.981114997 0.967047032 0.967559794 1.004376648 0.829463896 0.853503641 0.867563729 0.747272052 0.887755273 1 11.46704064 -8.089538211 0.599155995 0.994009338 0.736197127 0.624788249 0.050169869 0.495640096 0.210671297 0.007012106 0.073322058 8.14E-09 8.089538211 -0.257812211 TEEK(ac)EIAAR ddPTM_HeLa_Romidepsin_16h_R1 2 TEEKEIAAR 9 1 Q04727-4;Q04727;Q04727-3;H7C4W5;H7C4P7;Q5JSY7;H7C4E4;Q04727-2 Q04727-4 TLE4 Transducin-like enhancer protein 4 0 1 ; TEEK(1)EIAAR;TEEK(1)EIAAR 137.95 0.013397 3471700 1727.17 1786.19 2070.05 1571.12 1640.6 2000.74 1779.35 1787.1 1873.13 2050.72 FALSE TRUE FALSE 1706.118588 1811.33603 2106.078352 1752.780287 1556.87406 1872.899171 1930.487945 1838.806919 1705.592561 1997.441999 0.854151754 0.906827848 1.054387739 0.877512482 0.779433927 0.937648839 0.966480101 0.920580883 0.853888405 1 10.9639379 TEELIES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TEELIESPK 9 0 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 TEELIES(1)PK;TEELIES(1)PK ; 109.16 0.020013 22480000 13803.1 12541.1 12863.6 3573.5 11216.6 11099.3 9845.6 9886.4 12929.9 13124.7 TRUE FALSE FALSE 13634.86251 12717.65393 13087.48556 3986.684884 10644.17505 10390.09055 10681.88502 10172.44739 11773.41736 12783.7184 1.066580323 0.99483214 1.023762035 0.311856438 0.832635288 0.812759654 0.835585131 0.795734626 0.920969705 1 13.64201991 -9.451772874 24.9999188 1.028611069 0.729115292 0.468980937 0.149191027 93.78384921 32972.9913 0.021468871 0.032794237 3.53E-10 9.451772874 -0.299495778 TEELIES(ph)PKLESS(ph)EGEIIQTVDR ddPTM_HeLa_Romidepsin_16h_R1 2 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 2 0 TEELIES(1)PKLES(0.12)S(0.88)EGEIIQTVDR;TEELIES(1)PKLES(0.288)S(0.711)EGEIIQT(0.001)VDR ; 78.221 0.0010567 21552700 4007.8 4069.9 4023.4 3778.4 3095 3455.9 2420.66 3095.6 4185.6 3942.2 TRUE FALSE FALSE 3958.951392 4127.196159 4093.425589 4215.276386 2937.050601 3235.079143 2626.2708 3185.166302 3811.229453 3839.781076 1.031035706 1.074851945 1.066057025 1.097790812 0.764900535 0.84251656 0.683963681 0.829517683 0.992564258 1 11.90680834 -8.753664595 24.99957743 1.029492731 0.777798202 0.863566727 0.05111714 46.9611792 151000.9519 0.007336464 0.014456383 1.76E-09 8.753664595 -0.25169453 TEELIES(ph)PKLESSEGEIIQTVDR ddPTM_HeLa_Romidepsin_16h_R1 3 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 TEELIES(0.999)PKLESSEGEIIQTVDR;TEELIES(0.999)PKLESSEGEIIQTVDR;T(0.017)EELIES(0.975)PKLES(0.007)S(0.001)EGEIIQTVDR ;; 92.289 4.07E-05 321082000 4923.71 5294.9 4776.03 4389.67 4529.91 4118.98 3609.61 4110.6 5349.1 4827.34 TRUE FALSE FALSE 4863.697929 5369.441741 4859.154799 4897.224299 4298.731789 3855.790471 3916.210183 4229.533726 4870.663099 4701.925011 1.034405678 1.14196669 1.03343945 1.041536028 0.91424933 0.82004508 0.832895075 0.899532365 1.035887022 1 12.19903581 -8.611027604 3.486181754 1.030160979 0.850300129 0.819096021 0.041926786 0.084297736 2.021945021 0.006795066 0.014456086 2.45E-09 8.611027604 -0.17986085 TEELIESPKLESS(ph)EGEIIQTVDR ddPTM_HeLa_Romidepsin_16h_R1 2 TEELIESPKLESSEGEIIQTVDR 23 1 F8VXG7;Q99590-2;Q99590;A0A0A0MTP7 F8VXG7 SCAF11 Protein SCAF11 1 0 TEELIES(0.001)PKLES(0.239)S(0.76)EGEIIQTVDR;TEELIES(0.113)PKLES(0.207)S(0.68)EGEIIQTVDR ; 106.1 7.79E-06 11525200 2584 2493.33 2144.18 3654.3 2200.68 1589.98 1513.47 1796.91 2834.4 2562 TRUE FALSE FALSE 2552.505214 2528.431165 2181.498553 4076.82736 2088.371088 1488.385409 1642.024104 1848.900756 2580.884165 2495.438871 1.022868259 1.013221039 0.874194347 1.633711572 0.836875274 0.596442344 0.658010149 0.740912061 1.034240588 1 11.28507785 -8.527181526 24.99999834 1.046660227 0.673118377 0.486742932 0.197254374 81.39716729 472933.2159 0.027397658 0.054972094 2.97E-09 8.527181526 -0.37354185 TEES(ph)PASDEAGEK ddPTM_HeLa_Romidepsin_16h_R1 2 TEESPASDEAGEK 13 0 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 1 0 TEES(1)PASDEAGEK;TEES(0.99)PAS(0.01)DEAGEK ; 173.59 4.21E-05 25435000 7325.7 6951.5 8455.8 2909.96 8064.5 9805.5 7797.1 8663 8559.8 9374.9 TRUE FALSE FALSE 7236.411551 7049.363399 8602.969652 3246.423267 7652.938472 9178.960196 8459.385479 8913.650237 7794.19005 9131.338747 0.7924809 0.771996702 0.942136733 0.355525445 0.838095999 1.005215166 0.926412404 0.976160285 0.853564879 1 13.15661067 -8.271750083 22.75723449 0.847261142 0.964977591 0.134805845 0.169161248 431.2571418 951851.6853 0.026658412 0.060357231 5.35E-09 8.271750083 0.117716449 TEES(ph)PASDEAGEKEAK ddPTM_HeLa_Romidepsin_16h_R1 2 TEESPASDEAGEKEAK 16 1 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 1 0 T(0.042)EES(0.906)PAS(0.052)DEAGEKEAK;T(0.002)EES(0.998)PASDEAGEKEAK ; 111.64 0.008316 27152300 4372.2 3775.2 3728.6 3089 4028.3 4183.9 3964.7 4404.4 4437.9 4200.3 TRUE FALSE FALSE 4318.909945 3828.347365 3793.494719 3446.164714 3822.720819 3916.562293 4301.461519 4531.834365 4040.963109 4091.1756 1.055664769 0.935757283 0.927238302 0.842340943 0.934381995 0.957319528 1.051399876 1.10770957 0.987726635 1 11.99829975 -10.25913562 24.93291014 1.026286141 0.960812428 0.084488128 0.070233184 303.149083 3280905.09 0.01273674 0.015221043 5.51E-11 10.25913562 -0.065473713 TEESPASDEAGEKEAKS(ph)D ddPTM_HeLa_Romidepsin_16h_R1 1 TEESPASDEAGEKEAKSD 18 2 A6NEL0;P05114;A6NL93 A6NEL0 HMGN1 Non-histone chromosomal protein HMG-14 1 0 TEESPASDEAGEKEAKS(1)D 78.428 0.013393 39648000 3042 3400.6 2845.4 2527.7 3023.9 3245.7 3231.7 3260.1 3629.6 3508.2 TRUE FALSE FALSE 3004.922934 3448.473736 2894.922993 2819.964567 2869.579099 3038.310245 3506.200517 3354.42585 3304.959486 3417.056458 0.879389314 1.009194252 0.847197882 0.825261333 0.839781003 0.889160095 1.026087968 0.981671181 0.967194873 1 11.73853837 -12.43596526 1.005346107 1.00354412 0.908051153 0.140599817 0.068456778 0.833547226 1.412791826 0.060423945 0.013002924 3.66E-13 12.43596526 -0.095492967 TEFLDLDNSPLSPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TEFLDLDNSPLSPPSPR 17 0 Q8NCF5 Q8NCF5 NFATC2IP NFATC2-interacting protein 1 0 TEFLDLDNSPLSPPS(1)PR;TEFLDLDNSPLSPPS(1)PR ; 200.73 5.14E-19 115131000 10209.4 9850 9958.9 7022.6 8720.2 9560.3 8218.9 9127.9 9610.7 10166.1 TRUE FALSE FALSE 10084.96391 9988.668559 10132.23048 7834.586054 8275.175654 8949.427684 8917.013161 9392.001385 8751.094922 9901.983256 1.018479192 1.008754337 1.023252637 0.791213826 0.835708912 0.903801537 0.900527998 0.948496997 0.883771937 1 13.27350179 -9.282490766 24.97649775 1.00994093 0.876627012 0.469616086 0.056314886 310.7915271 368738.8183 0.006294823 0.009621649 5.22E-10 9.282490766 -0.133313918 TEFLHSQNS(ph)LSPR ddPTM_HeLa_Romidepsin_16h_R1 2 TEFLHSQNSLSPR 13 0 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 0 TEFLHS(0.001)QNS(0.675)LS(0.324)PR;TEFLHS(0.195)QNS(0.483)LS(0.321)PR ; 82.663 0.014843 22446700 5542.1 4825.6 4572 4443.9 8416.3 8096.5 6490.1 7807.2 6323.6 5838.2 TRUE FALSE FALSE 5474.550753 4893.534923 4651.573742 4957.724627 7986.784805 7579.15978 7041.368932 8033.089014 5758.001378 5686.522722 0.962723798 0.860549612 0.817999676 0.871837654 1.404511192 1.33282854 1.238255657 1.41265399 1.012569836 1 12.47333101 -8.760258627 25 0.951223709 1.338273781 0.880237255 0.076485629 9.126122526 193218.6425 0.012414004 0.023762185 1.74E-09 8.760258627 0.387050072 TEFLHSQNSLS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TEFLHSQNSLSPR 13 0 Q96FS4;F6RY50 Q96FS4 SIPA1 Signal-induced proliferation-associated protein 1 1 0 TEFLHS(0.002)QNS(0.163)LS(0.835)PR;TEFLHSQNS(0.003)LS(0.997)PR ; 203.85 2.08E-16 17732400 2599.69 2337.68 2469.35 2493.18 4218.4 4518.3 3680.8 4711.4 3064.11 2705.24 TRUE FALSE FALSE 2568.003978 2370.58992 2512.328001 2781.453202 4003.119307 4229.595212 3993.44706 4847.716926 2790.048327 2634.957475 0.974590293 0.899669138 0.953460549 1.055596999 1.519234881 1.605185379 1.51556414 1.83977046 1.058858958 1 11.36356396 -8.735449903 2.860222535 0.976956301 1.635046361 0.931412732 0.084446713 0.042093378 0.704573288 0.01137994 0.023660045 1.84E-09 8.735449903 0.65809006 TEFLSFMNTELAAFTK ddPTM_HeLa_Romidepsin_16h_R1 1 TEFLSFMNTELAAFTK 16 0 P31949 P31949 S100A11 "Protein S100-A11;Protein S100-A11, N-terminally processed" 0 0 120.55 0.0071477 4845800 2708.4 2733.1 2880.8 2787.7 2798.7 2978.2 2398.3 2771.5 3079.2 2522.3 FALSE FALSE TRUE 2675.388979 2771.576654 2930.939116 3110.026991 2655.871896 2787.902632 2602.011542 2851.68898 2803.78864 2456.770282 1.088986218 1.128138301 1.193004953 1.265900607 1.081042015 1.134783603 1.059118779 1.1607471 1.141249819 1 11.26254725 -11.06075619 0.870547743 1.014880839 1.145246556 0.062937288 0.067981532 0.33009953 0.537895297 0.018402644 0.013434288 8.69E-12 11.06075619 0.130365717 TEFSPAAFEQEQLGS(ph)PQVR ddPTM_HeLa_Romidepsin_16h_R1 2 TEFSPAAFEQEQLGSPQVR 19 0 Q92585 Q92585 MAML1 Mastermind-like protein 1 1 0 TEFSPAAFEQEQLGS(1)PQVR;TEFSPAAFEQEQLGS(1)PQVR ; 221.9 1.08E-35 4293100 3358.6 3740.2 3141.9 2675.79 2939.4 3149.9 2273.5 3321.7 3213.6 2719.9 TRUE FALSE FALSE 3317.664091 3792.854634 3196.583452 2985.17743 2789.39145 2948.631556 2466.611033 3417.808149 2926.167567 2649.236606 1.252309471 1.431678328 1.206605497 1.126806652 1.05290386 1.113011782 0.931064831 1.29011057 1.104532363 1 11.37136098 -6.936438868 20.11142202 1.133547796 4.261886929 0.109431675 0.132276397 627.8799847 209708.3307 0.020668472 4801.569559 1.16E-07 6.936438868 3.128339134 TEGTDS(ph)PLSR ddPTM_HeLa_Romidepsin_16h_R1 1 TEGTDSPLSR 10 0 Q155Q3;Q155Q3-2 Q155Q3 DIXDC1 Dixin 1 0 T(0.001)EGT(0.16)DS(0.839)PLSR 96.756 0.028744 7287600 1005.6 1334.9 1401.1 1330.4 1737.4 1680.6 1331.3 1316.6 1523 1187.8 TRUE FALSE FALSE 993.3433604 1353.692757 1425.485558 1484.227108 1648.733995 1573.215084 1444.380589 1354.693744 1386.779066 1156.940785 0.858594816 1.170062267 1.232116264 1.282889433 1.42508071 1.359806055 1.248448156 1.170927468 1.198660367 1 10.17609931 -10.03002846 2.781315829 0.933472384 1.2947157 0.486555154 0.112035188 0.088294084 1.367936636 0.014939717 0.019194385 9.33E-11 10.03002846 0.361243317 TEIIILATR ddPTM_HeLa_Romidepsin_16h_R1 1 TEIIILATR 9 0 E9PPU1;E9PL09;P23396;P23396-2;E9PQ96;E9PJH4;F2Z2S8;E9PK82;H0YCJ7;H0YEU2;H0YF32 E9PPU1 RPS3 40S ribosomal protein S3 0 0 123.21 0.011718 2064400 1354.5 1026 1683.8 1336.4 1624.3 1680.7 1363.8 1191.8 1264.6 924.82 FALSE FALSE TRUE 1337.990833 1040.444055 1713.105833 1490.920856 1541.40591 1573.308694 1479.641138 1226.282853 1151.491009 900.7930431 1.485347654 1.155031184 1.901775159 1.655120305 1.711165424 1.746581755 1.642598319 1.361336949 1.278308062 1 9.815051875 -11.64460666 0.42230578 0.921969465 1.66180523 0.436613143 0.205340166 0.730827789 0.245062404 0.233840238 0.07043147 2.27E-12 11.64460666 0.739835765 TEIKEEEDQPSTSATQS(ph)SPAPGQSK ddPTM_HeLa_Romidepsin_16h_R1 2 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 0 TEIKEEEDQPS(0.081)T(0.081)S(0.081)AT(0.094)QS(0.314)S(0.314)PAPGQS(0.034)K;TEIKEEEDQPS(0.003)T(0.064)S(0.064)AT(0.064)QS(0.401)S(0.401)PAPGQS(0.002)K ; 86.211 3.36E-05 67081000 9601.7 9106.9 8829.7 5997.7 7168.1 7099.7 5627.7 5972.8 9813.6 10000.7 TRUE FALSE FALSE 9484.670787 9235.107177 8983.377225 6691.182294 6802.285109 6646.052083 6105.716698 6145.613544 8935.847037 9740.880372 0.973697492 0.94807726 0.922234632 0.686917613 0.698323442 0.68228454 0.626813641 0.630909457 0.917355177 1 13.24983645 -9.307209302 1.836124934 0.98612487 0.653905362 0.948975124 0.033169919 0.037746476 0.248460823 0.004237181 0.007372727 4.93E-10 9.307209302 -0.332219507 TEIKEEEDQPSTSATQSS(ph)PAPGQSK ddPTM_HeLa_Romidepsin_16h_R1 1 TEIKEEEDQPSTSATQSSPAPGQSK 25 1 A0A669KB12;Q09472 A0A669KB12 EP300 Histone acetyltransferase p300 1 0 TEIKEEEDQPS(0.066)T(0.148)S(0.148)AT(0.148)QS(0.148)S(0.339)PAPGQS(0.001)K 46.878 0.020362 57507000 3016.8 3218.7 3054.3 2090.7 2599.1 2243.5 1902.1 2173 3553.8 3696.9 TRUE FALSE FALSE 2980.030081 3264.012943 3107.45881 2332.436571 2466.458228 2100.147591 2063.664327 2235.872327 3235.939227 3600.854005 0.82758981 0.906455229 0.862978284 0.647745387 0.684964796 0.583235973 0.573104137 0.620928347 0.898658824 1 11.81412339 -8.935859313 0.2896578 0.996457385 0.438649627 0.831793459 0.060442769 0.862939778 0.123349779 0.043752585 0.167149802 1.16E-09 8.935859313 -0.557807759 TEIMS(ph)PLYQDEAPK ddPTM_HeLa_Romidepsin_16h_R1 4 TEIMSPLYQDEAPK 14 0 Q8IY81 Q8IY81 FTSJ3 pre-rRNA processing protein FTSJ3 1 0 T(0.001)EIMS(0.994)PLY(0.005)QDEAPK;TEIMS(1)PLYQDEAPK;TEIMS(1)PLYQDEAPK;T(0.022)EIMS(0.882)PLY(0.096)QDEAPK ;;; 146.84 0.00085104 109187000 14733.2 14849.1 14765.6 10370.5 20267.2 26223.1 22635.7 23247.2 16446.9 17097.2 TRUE FALSE FALSE 14553.62609 15058.14602 15022.58907 11569.586 19232.88916 24547.52854 24558.37579 23919.82105 14975.84807 16653.01228 0.873933547 0.904229563 0.902094397 0.694744339 1.154919533 1.474059355 1.474710724 1.436366025 0.899287638 1 14.02349554 -8.449066365 3.645745425 0.917182501 1.4595788 0.9115877 0.080675446 0.055834183 1.422736742 0.013018324 0.030170625 3.56E-09 8.449066365 0.542396299 TEK(ac)EESTEVLK ddPTM_HeLa_Romidepsin_16h_R1 2 TEKEESTEVLK 11 1 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;E7ES10;B7Z574;E7EVY3;P20810-4;P20810-8;P20810;H0YA91;E9PDE4;E9PCH5;P20810-2;H0Y9H6;H0Y7F0;P20810-3 P20810-6;P20810-3 CAST Calpastatin 0 1 ; TEK(1)EESTEVLK;TEK(1)EESTEVLK 185.99 2.28E-05 1444930 354.92 228.83 146.669 169.45 361.31 407.59 444.22 536.46 505.78 446.91 FALSE TRUE FALSE 350.5940985 232.0514747 149.2217124 189.0426063 342.8710025 381.5463144 481.9520357 551.9816237 460.5417701 435.2992138 0.805409446 0.533084985 0.342802623 0.434281984 0.787667406 0.876515055 1.107174147 1.268051047 1.057988977 1 8.765863604 -11.5307661 1.173293719 0.970651886 0.757296559 0.1176558 0.271515445 0.838917297 2.334386524 0.095696454 0.058546223 2.95E-12 11.5307661 -0.213355327 TEKEPDATPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TEKEPDATPPSPR 13 1 A0A494C0S2;A0A090HNM7;A0A1W2PS85;R4GMW8;P28715 A0A494C0S2 ERCC5-201;BIVM-ERCC5;ERCC5 DNA repair protein complementing XP-G cells 1 0 TEKEPDATPPS(1)PR;TEKEPDATPPS(1)PR ; 77.726 0.016639 34024000 5960.5 5394.5 5052.8 4625.4 6672.2 6910 5167.7 5639.3 6827.8 5861.8 TRUE FALSE FALSE 5887.851133 5470.443913 5140.741864 5160.210511 6331.692737 6468.473301 5606.644309 5802.464248 6217.104467 5709.509591 1.031235878 0.958128509 0.900382385 0.903792249 1.108973133 1.132929755 0.981983517 1.016280673 1.088903411 1 12.47915112 -6.862671794 17.45369281 1.008440079 2.977097937 0 0.076504015 13046864.42 457338.0158 0.010344331 1028030580 1.37E-07 6.862671794 1.968657858 TEKGESSSPS(ph)PSAEK ddPTM_HeLa_Romidepsin_16h_R1 1 TEKGESSSPSPSAEK 15 1 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 TEKGES(0.001)S(0.001)S(0.012)PS(0.856)PS(0.129)AEK 67.396 0.020763 2519900 1120.5 1137.8 1004.8 1077.9 882.9 1209 1124.2 627.35 1312.1 1096.4 TRUE FALSE FALSE 1106.842915 1153.817978 1022.288123 1202.53187 837.8423184 1131.748802 1219.68952 645.5013825 1194.74249 1067.91537 1.036451901 1.080439528 0.957274473 1.126055401 0.784558723 1.059773868 1.142121889 0.604449941 1.118761396 1 10.06058161 -7.250662585 24.79724322 1.018581797 0.604449677 0.617402049 0.100777913 638.8708903 1470002.052 0.011928165 0.232032434 5.61E-08 7.250662585 -0.41413212 TEKGESSSPSPS(ph)AEK ddPTM_HeLa_Romidepsin_16h_R1 1 TEKGESSSPSPSAEK 15 1 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 TEKGESSSPS(0.076)PS(0.924)AEK 80.459 0.011398 4308000 1226.4 1267.2 1248.9 1312.3 1441.6 1417.4 1343.7 1007.8 2025.7 1474.7 TRUE FALSE FALSE 1211.452165 1285.039675 1270.636581 1464.034301 1368.029773 1326.832714 1457.833844 1036.959103 1844.516319 1436.387081 0.843402298 0.894633272 0.884605965 1.01924775 0.952410245 0.923729217 1.014931047 0.721921769 1.28413597 1 10.48822887 TELESTIFGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TELESTIFGSPR 12 0 Q9UQK1 Q9UQK1 PPP1R3C Protein phosphatase 1 regulatory subunit 3C 1 0 TELESTIFGS(1)PR;TELESTIFGS(1)PR ; 187.62 6.85E-10 26881000 3719.3 3625.4 2921.9 2803 3101.4 2486.4 2198.37 2431.6 4095.9 3336.1 TRUE FALSE FALSE 3673.967741 3676.438476 2972.754444 3127.096049 2943.123985 2327.527064 2385.099493 2501.95451 3729.552446 3249.427641 1.130650732 1.131411092 0.914854791 0.96235288 0.90573612 0.71628832 0.734006033 0.769967756 1.147756731 1 11.66596991 -8.736196241 1.067362351 1.064252588 0.727959222 0.827060849 0.064883302 0.172589807 0.379921292 0.011756556 0.035991487 1.84E-09 8.736196241 -0.336293366 TELGSQT(ph)PESSR ddPTM_HeLa_Romidepsin_16h_R1 3 TELGSQTPESSR 12 0 H0YID1;F8VUX5;H0YIQ8;F8VXI8;F8VX10;Q9H9L4-4;Q9H9L4 H0YID1 KANSL2 KAT8 regulatory NSL complex subunit 2 1 0 T(0.044)ELGS(0.005)QT(0.95)PESSR;TELGS(0.001)QT(0.975)PES(0.022)S(0.003)R;TELGSQT(0.999)PES(0.001)SR ;; 170.26 0.00031457 16985600 4606.4 3979.55 4049.38 4715.14 4147.9 3874.35 3836.34 3886.98 4584.5 4129.8 TRUE FALSE FALSE 4550.255425 4035.574209 4119.85776 5260.326672 3936.217185 3626.791539 4162.198624 3999.443634 4174.450838 4022.507201 1.131198827 1.003248474 1.024201463 1.30772337 0.978548201 0.901624623 1.034727451 0.99426637 1.037773366 1 11.97387929 -8.582477573 24.99999977 1.073616348 0.975550954 0.24659362 0.090297634 90.03070357 37764.76866 0.013653894 0.027307791 2.62E-09 8.582477573 -0.098065394 TELHGK(ac)MISVEK ddPTM_HeLa_Romidepsin_16h_R1 1 TELHGKMISVEK 12 1 Q15424-2;Q15424;Q15424-4;Q15424-3 Q15424-2 SAFB Scaffold attachment factor B1 0 1 TELHGK(1)MISVEK 68.171 0.014994 1094700 886.88 731.19 708.65 629.25 1089.4 1197.3 1071.5 1045 1520.9 741.39 FALSE TRUE FALSE 876.0703654 741.483712 720.983756 702.0068457 1033.803853 1120.796394 1162.513183 1075.235426 1384.866895 722.1285809 1.213177803 1.026802887 0.998414652 0.972135523 1.431606337 1.552073168 1.609842366 1.48898057 1.917756659 1 9.496111933 -8.633030904 4.590485326 1.080753976 1.547142108 0.213194296 0.274887798 0.062369144 2.239058279 0.014598627 0.029878789 2.33E-09 8.633030904 0.466388132 TEMDKS(ph)PFNSPSPQDSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 T(0.226)EMDKS(0.774)PFNSPSPQDSPR 189.8 5.79E-16 0 3910.7 3939.8 3112.9 3567.2 3280.8 2654.6 1761.7 2275.3 3921.8 3516.2 TRUE FALSE FALSE 3863.034884 3995.264608 3167.078719 3979.656448 3113.368534 2484.979627 1911.338754 2341.132216 3571.024386 3424.848617 1.127943251 1.166552176 0.924735389 1.161994848 0.90905289 0.725573567 0.558079777 0.683572466 1.042680943 1 11.74182451 -8.321531363 2.245496118 1.065727017 0.624033699 0.848152113 0.078697792 0.084586608 0.823793763 0.011825559 0.03349531 4.77E-09 8.321531363 -0.441693318 TEMDKSPFNSPSPQDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TEMDKSPFNSPSPQDSPR 18 1 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 TEMDKSPFNS(0.001)PS(0.005)PQDS(0.995)PR 72.513 0.022819 48444000 3241.5 3128.8 3060.5 3006.9 1765.5 1625.9 1692.4 1368.9 3495.2 3230.2 TRUE FALSE FALSE 3201.991351 3172.847329 3113.766719 3354.571926 1675.399947 1522.010237 1836.152414 1408.506962 3182.580558 3146.278938 1.017707398 1.008444385 0.989666454 1.066202963 0.532502038 0.483749301 0.583594923 0.4476739 1.011537953 1 11.61943087 -8.756277969 24.99995358 1.010620538 0.514993075 0.977177402 0.037706654 11.3996508 55215.0306 0.004837811 0.009446051 1.75E-09 8.756277969 -0.495627463 TENNDHINLK ddPTM_HeLa_Romidepsin_16h_R1 1 TENNDHINLK 10 0 P61956-2;P61956 P61956-2 SUMO2 Small ubiquitin-related modifier 2 0 0 103.31 0.010465 9345400 4014.1 3836.5 3588 3508.9 3716.5 3660.9 3532.7 2662.1 4683.2 4002.2 FALSE FALSE TRUE 3965.174605 3890.510348 3650.447635 3914.615528 3526.833137 3426.980305 3832.76745 2739.123663 4264.322863 3898.222267 1.017175095 0.998021683 0.93643907 1.004205317 0.90472859 0.879113624 0.98320906 0.702659694 1.093914757 1 11.92860064 -5.926077949 0.489586048 1.00519106 2.37E-17 0.655246176 0.05943608 5.606180354 0.337874855 0.009838909 4.366949927 1.19E-06 5.926077949 -1.00519106 TEPAAEAEAASGPS(ph)ES(ph)PSPPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_HeLa_Romidepsin_16h_R1 1 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 2 0 TEPAAEAEAAS(0.034)GPS(0.654)ES(0.597)PS(0.597)PPAAEELPGS(0.118)HAEPPVPAQGEAPGEQAR 75.851 8.31E-08 5667500 1105.8 1205.9 1284 1229.4 955.34 1145.8 955.96 1040.7 1239.3 1419.9 TRUE FALSE FALSE 1092.322084 1222.876692 1306.347481 1371.549013 906.5854349 1072.587078 1037.159219 1070.811013 1128.453904 1383.010793 0.789814577 0.884213412 0.944567814 0.991712443 0.655515806 0.77554498 0.749928506 0.774260778 0.815940056 1 10.4335967 -8.761734884 25 0.906394262 0.742230265 0.570477638 0.070340435 5.615716832 475162.9137 0.012978416 0.024637632 1.73E-09 8.761734884 -0.164163997 TEPAAEAEAASGPSES(ph)PSPPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_HeLa_Romidepsin_16h_R1 2 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 0 TEPAAEAEAAS(0.009)GPS(0.091)ES(0.447)PS(0.447)PPAAEELPGS(0.007)HAEPPVPAQGEAPGEQAR;TEPAAEAEAAS(0.03)GPS(0.276)ES(0.303)PS(0.303)PPAAEELPGS(0.089)HAEPPVPAQGEAPGEQAR ; 83.221 2.12E-10 90808700 5354.3 5529.2 5631.7 5511.5 5700.4 5529.5 4637.3 5050 6462.9 6013.7 TRUE FALSE FALSE 5289.039732 5607.040223 5729.717376 6148.765562 5409.487317 5176.182796 5031.192146 5196.113782 5884.842037 5857.463207 0.902957397 0.957247195 0.978190929 1.049731828 0.923520494 0.883690194 0.858937046 0.887092859 1.004674179 1 12.51606027 -8.397577238 3.840673538 0.962017349 0.874985027 0.563135826 0.039410301 0.182056974 4.699513999 0.006832728 0.016015807 4.00E-09 8.397577238 -0.087032322 TEPAAEAEAASGPSESPS(ph)PPAAEELPGSHAEPPVPAQGEAPGEQAR ddPTM_HeLa_Romidepsin_16h_R1 1 TEPAAEAEAASGPSESPSPPAAEELPGSHAEPPVPAQGEAPGEQAR 46 0 P55884;P55884-2 P55884 EIF3B Eukaryotic translation initiation factor 3 subunit B 1 0 TEPAAEAEAAS(0.002)GPS(0.078)ES(0.235)PS(0.656)PPAAEELPGS(0.029)HAEPPVPAQGEAPGEQAR 70.555 4.31E-07 71651000 1474.7 1576.7 1472.7 1379.7 1734.9 1465.3 1250.8 1651.6 1682.5 1933.9 TRUE FALSE FALSE 1456.725789 1598.896824 1498.331726 1539.227406 1646.361579 1371.672059 1357.042921 1699.38644 1532.012986 1883.656999 0.773349814 0.848825887 0.795437665 0.817148454 0.874024082 0.728196301 0.720429952 0.902174037 0.813318447 1 10.87932057 -12.33873029 0.783328671 1.016922638 0.802271106 0 0.079733704 0.393948254 0.377204621 0.055112032 0.010722103 4.58E-13 12.33873029 -0.214651531 TEPSK(ac)FPFPTK ddPTM_HeLa_Romidepsin_16h_R1 1 TEPSKFPFPTK 11 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3 Q9UHB7 AFF4 AF4/FMR2 family member 4 0 1 TEPSK(1)FPFPTK 93.058 0.015441 0 153.74 196.12 135.66 0 152.48 0 201.81 219.1 140.39 317.72 FALSE TRUE FALSE 151.8661577 198.8809825 138.0211054 0 144.6983766 0 218.9517364 225.4393128 127.8331668 309.4655886 0.490736816 0.642659442 0.445998232 0 0.467575013 0 0.707515615 0.728479421 0.413077161 1 8.273635186 -11.88115244 0.52921467 1.056997315 0.394657963 0 0.299460269 0.807031241 0.387072773 0.260743692 0.066094978 1.31E-12 11.88115244 -0.662339353 TEPSLVVPGIDLPKEPPT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TEPSLVVPGIDLPKEPPTPK 20 1 A0A669KB77;P11137-3;P11137;E7EV03 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 TEPSLVVPGIDLPKEPPT(1)PK;TEPSLVVPGIDLPKEPPT(1)PK ; 84.025 0.0017924 10386500 2104.7 2257.31 1868.02 2378.08 3627.1 4013.3 2640.11 3249.8 2367.88 1722.97 TRUE FALSE FALSE 2079.047107 2289.088469 1900.532105 2653.044799 3441.995552 3756.863082 2864.360878 3343.827836 2156.090882 1678.206991 1.238850224 1.364008422 1.132477766 1.580880555 2.050995837 2.238617228 1.706798323 1.992500242 1.284758611 1 10.71270495 -9.035417984 2.581602928 1.138040839 1.994180857 0.842211674 0.160092992 0.077904698 1.034477783 0.026382633 0.048807968 9.22E-10 9.035417984 0.856140018 TEPT(ph)SPTPSAFK ddPTM_HeLa_Romidepsin_16h_R1 2 TEPTSPTPSAFK 12 0 Q86XN7-2;Q86XN7 Q86XN7-2 PROSER1 Proline and serine-rich protein 1 1 0 TEPT(0.62)S(0.37)PT(0.009)PSAFK;TEPT(0.874)S(0.126)PTPSAFK ; 168.98 0.0003804 74985000 14010.3 13246.9 13306 11279.2 11788.7 10555.2 9479.3 9882.8 14582.7 13594.1 TRUE FALSE FALSE 13839.53707 13433.39021 13537.58535 12583.35417 11187.07865 9880.756785 10284.47151 10168.74323 13278.38679 13240.92332 1.045209366 1.01453576 1.022404935 0.95033812 0.844886597 0.746228684 0.776718606 0.767978409 1.00282937 1 13.69271611 -8.747346918 1.81627503 1.021639261 0.763253671 0.980019217 0.016034581 0.037102018 0.248471223 0.002977108 0.006856696 1.79E-09 8.747346918 -0.25838559 TEQEEDEELLTESSK ddPTM_HeLa_Romidepsin_16h_R1 1 TEQEEDEELLTESSK 15 0 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 0 211.82 1.53E-24 1460400 511.74 566.36 640.58 605.96 641.63 442.74 364.25 449.74 663.26 707.54 FALSE FALSE TRUE 505.502716 574.3332309 651.7290262 676.0239463 608.8852268 414.4503429 395.1893859 462.7525173 603.9363644 689.1580088 0.733507715 0.833383961 0.945688823 0.980941871 0.883520498 0.601386529 0.573437994 0.671475208 0.87633947 1 9.428690989 -8.26259742 24.6062082 0.882572292 0.611233702 0.737960957 0.075685896 45.61409771 969233.744 0.015558409 0.036716536 5.46E-09 8.26259742 -0.27133859 TEQELPRPQS(ph)PSDLDS(ph)LDGR ddPTM_HeLa_Romidepsin_16h_R1 1 TEQELPRPQSPSDLDSLDGR 20 1 P54259 P54259 ATN1 Atrophin-1 2 0 TEQELPRPQS(0.89)PS(0.335)DLDS(0.775)LDGR 68.959 0.019179 10892000 1503.6 1572.9 1682.7 1229.9 1100.7 1395.9 812.89 1110.7 1576.5 1729.5 TRUE FALSE FALSE 1485.273545 1595.043327 1711.986688 1372.106825 1044.527172 1306.706495 881.9368563 1142.836352 1435.493892 1684.567341 0.881694373 0.946856376 1.016276789 0.814515865 0.620056644 0.775692644 0.523539092 0.678415356 0.852143964 1 10.71816239 -8.960906318 3.517660838 0.947564891 0.64992701 0.769896994 0.074458381 0.07745579 2.012412364 0.010856694 0.020078392 1.09E-09 8.960906318 -0.297637881 NLSGS(ph)TLYPVSNIPR ddPTM_HeLa_Romidepsin_16h_R1 1 NLSGSTLYPVSNIPR 15 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 0 NLS(0.006)GS(0.976)T(0.018)LYPVSNIPR 114.58 0.0039252 31651000 2298.9 2228.4 2160.4 2338.9 1608 1383.3 857.81 1121.2 2339.5 2421.9 TRUE FALSE FALSE 2270.880123 2259.771474 2198.000856 2609.334623 1525.93776 1294.911594 930.67236 1153.640153 2130.249261 2358.978689 0.962653937 0.957944845 0.931759522 1.106128951 0.646863733 0.548928907 0.394523428 0.489042211 0.90303879 1 11.20394667 -8.565256341 3.256953494 0.983283337 0.476426455 0.922433923 0.065926719 0.039976046 0.870757671 0.008700373 0.019153791 2.72E-09 8.565256341 -0.506856881 down TES(ph)FHSYR ddPTM_HeLa_Romidepsin_16h_R1 1 TESFHSYR 8 0 Q9Y597-3;Q9Y597-2;Q9Y597 Q9Y597-3 KCTD3 BTB/POZ domain-containing protein KCTD3 1 0 T(0.005)ES(0.993)FHS(0.002)YR 85.355 0.020725 4172200 6258.8 7167.9 6002.1 6435.8 4682.1 3736.9 3212.7 3444.7 6270.6 6343.7 TRUE FALSE FALSE 6182.515338 7268.809884 6106.564033 7179.937477 4443.154966 3498.12415 3485.586658 3544.36696 5709.741831 6178.889759 1.000586769 1.176394169 0.988294705 1.162010937 0.719086298 0.566141214 0.564112129 0.573625214 0.924072455 1 12.59313192 -8.590273375 4.544742052 1.023566125 0.576620891 0.892137241 0.075356302 0.044426304 1.799684382 0.010227768 0.021170967 2.57E-09 8.590273375 -0.446945234 TES(ph)GEETDLISPPQEEVK ddPTM_HeLa_Romidepsin_16h_R1 2 TESGEETDLISPPQEEVK 18 0 A0A5F9UY30;A0A5H1ZRP2;O43493;O43493-5;O43493-3;O43493-7 A0A5F9UY30 TGOLN2 Trans-Golgi network integral membrane protein 2 1 0 T(0.161)ES(0.839)GEETDLISPPQEEVK;T(0.006)ES(0.994)GEETDLISPPQEEVK ; 215.49 6.52E-29 8973800 2970.66 3819.63 3353.85 2017.15 3023.7 2947.81 1638.59 2348.38 3176.5 3147.14 TRUE FALSE FALSE 2934.452453 3873.402851 3412.222352 2250.382374 2869.389306 2759.454455 1777.771794 2416.32667 2892.385884 3065.376849 0.957289298 1.263597607 1.113149384 0.734129109 0.936064128 0.900200723 0.579952117 0.788264148 0.943566167 1 11.58184873 -8.266123232 1.003074547 1.005088864 0.68124269 0.444926453 0.135724924 0.495611273 0.829182732 0.021957291 0.117383151 5.42E-09 8.266123232 -0.323846174 TES(ph)PATAAETASEELDNR ddPTM_HeLa_Romidepsin_16h_R1 6 TESPATAAETASEELDNR 18 0 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4 1 0 TES(0.967)PAT(0.033)AAETASEELDNR;T(0.134)ES(0.866)PATAAETASEELDNR;T(0.281)ES(0.365)PAT(0.054)AAET(0.051)AS(0.25)EELDNR;T(0.01)ES(0.99)PATAAETASEELDNR;TES(0.998)PAT(0.002)AAETASEELDNR;T(0.019)ES(0.971)PAT(0.01)AAETASEELDNR ;;;;; 358.85 1.31E-263 1139994400 18249.71 17927.49 17028.38 16682.54 17965.63 15796.25 14467.53 17012.03 19570.6 18381.38 TRUE FALSE FALSE 18027.27551 18179.87367 17324.75181 18611.45377 17048.77686 14786.92061 15696.40164 17504.24625 17820.15652 17903.8291 1.006894973 1.015418187 0.967656232 1.03952365 0.952241935 0.825908275 0.876706405 0.97768171 0.995326554 1 14.12798055 -8.513673991 7.57836621 1.003405849 0.891116282 0.625651935 0.038435605 0.061726432 23.54494674 0.005122001 0.010867716 3.06E-09 8.513673991 -0.112289568 TES(ph)VPSDINNPVDR ddPTM_HeLa_Romidepsin_16h_R1 1 TESVPSDINNPVDR 14 0 A0A2R8Y4X0;A0A0A0MQW1;A0A2R8Y5H9;Q8IVT5-4;Q8IVT5-3;Q8IVT5-2;Q8IVT5;A8MY87 A0A2R8Y4X0 KSR1 Kinase suppressor of Ras 1 1 0 T(0.167)ES(0.56)VPS(0.273)DINNPVDR 147.1 0.0006175 4375800 735.27 892.16 851.52 637.12 769.36 840.85 745.72 671.81 983.2 968.79 TRUE FALSE FALSE 726.3082464 904.7198519 866.3403484 710.7868121 730.0966883 787.1223987 809.0614382 691.2477624 895.2601295 943.6206961 0.7697036 0.958774914 0.918102318 0.753254793 0.773718393 0.834151266 0.857401116 0.732548327 0.948749994 1 9.882063251 -12.46572244 0.938572617 1.011902044 0.823598246 0.415523559 0.07016567 0.486297858 0.683293873 0.068167782 0.013045001 3.42E-13 12.46572244 -0.188303798 TESPAT(ph)AAETASEELDNR ddPTM_HeLa_Romidepsin_16h_R1 1 TESPATAAETASEELDNR 18 0 Q9NTJ3;C9JWF0;C9IYK2;C9JJ64;C9JR83;Q9NTJ3-2 Q9NTJ3 SMC4 Structural maintenance of chromosomes protein 4 1 0 T(0.014)ES(0.404)PAT(0.582)AAETASEELDNR 130.64 2.98E-08 0 702.91 664.53 636.8 692.86 778.94 975.03 746.92 391.81 689.2 862.01 TRUE FALSE FALSE 694.3426626 673.8852708 647.8832369 772.9717332 739.1877852 912.7287298 810.3633662 403.1464042 627.5562259 839.6148559 0.826977581 0.802612372 0.77164337 0.920626556 0.880389121 1.087080253 0.965160824 0.480156349 0.747433447 1 9.713583883 -12.26866105 0.996945359 1.000031443 0.853521642 0 0.167894226 0.952668613 1.697348204 0.098368977 0.026734553 5.39E-13 12.26866105 -0.146509801 TESQSLLQQSSS(ph)PFR ddPTM_HeLa_Romidepsin_16h_R1 1 TESQSLLQQSSSPFR 15 0 E7EWN3;Q9C0A6;Q9C0A6-2;Q9C0A6-3 E7EWN3 SETD5 SET domain-containing protein 5 1 0 TESQSLLQQSS(0.038)S(0.962)PFR 130.95 0.0018776 5962700 854.93 807.8 1065.5 1309 917.31 821.89 771.9 730.52 1041.2 1020.2 TRUE FALSE FALSE 844.5097843 819.1722296 1084.044581 1460.352739 870.4962477 769.3738815 837.4651667 751.6564436 948.0724643 993.6950569 0.849868155 0.824369834 1.090922787 1.469618601 0.876019501 0.774255518 0.842778839 0.756425664 0.954087934 1 9.956659378 -8.527592205 24.99658752 0.974265801 0.80111942 0.249753274 0.173911163 189.9655715 1007431.482 0.027713942 0.05559091 2.97E-09 8.527592205 -0.173146381 TESSPSEASQHSMQS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 3 TESSPSEASQHSMQSPQK 18 0 Q9UQR0 Q9UQR0 SCML2 Sex comb on midleg-like protein 2 1 0 TESSPSEASQHS(0.033)MQS(0.967)PQK;TESSPSEASQHS(0.03)MQS(0.97)PQK;TESSPSEASQHS(0.327)MQS(0.673)PQK ;; 81.526 0.0037691 4987000 1553.63 1803.94 1352.32 2469.48 2850.12 2065.14 1378.51 1337.2 2112.42 2115.71 TRUE FALSE FALSE 1534.69376 1829.335915 1375.856562 2755.012897 2704.667741 1933.184219 1495.600605 1375.889772 1923.479865 2060.743549 0.744728164 0.887706729 0.667650549 1.336902352 1.312471774 0.938100337 0.725757752 0.667666665 0.933391186 1 11.00894926 -7.227731194 0.002936056 1.78832543 0.000193716 0 0.230746663 1500910.04 689.8067537 205629.7401 214555.1836 5.92E-08 7.227731194 -1.788131714 TEST(ph)PITAVK ddPTM_HeLa_Romidepsin_16h_R1 1 TESTPITAVK 10 0 Q9Y678 Q9Y678 COPG1 Coatomer subunit gamma-1 1 0 T(0.002)ES(0.022)T(0.922)PIT(0.054)AVK 117.52 0.027601 14490000 2218.4 1747.3 1991.6 993.59 2153.9 2594.6 2163.9 2423.3 1985.6 2168.7 TRUE FALSE FALSE 2191.361288 1771.898535 2026.262963 1108.473551 2043.978446 2428.813434 2347.701612 2493.414362 1808.002963 2112.356861 1.037401079 0.838825374 0.95924273 0.524756764 0.967629326 1.149812079 1.111413348 1.180394472 0.855917386 1 11.04463787 -8.269388255 9.01051222 0.9589473 1.143742887 0.321651713 0.149632952 0.189443185 170.4769951 0.022765106 0.053245344 5.38E-09 8.269388255 0.184795587 TET(ph)PPPLASLNVSK ddPTM_HeLa_Romidepsin_16h_R1 3 TETPPPLASLNVSK 14 0 K7ELG9;Q3MHD2;Q3MHD2-2 K7ELG9 LSM12 Protein LSM12 homolog 1 0 TET(1)PPPLASLNVSK;T(0.096)ET(0.901)PPPLAS(0.002)LNVSK;T(0.219)ET(0.781)PPPLASLNVSK ;; 203.11 2.14E-16 127854500 5294.7 5059.9 5441.2 5439.7 5293.5 5539.3 4433.6 4861.1 5883.9 5352.9 TRUE FALSE FALSE 5230.16616 5131.133405 5535.901804 6068.663709 5023.352942 5185.356607 4810.189873 5001.748259 5357.629248 5213.830886 1.003133065 0.984138826 1.061772413 1.163954843 0.963466797 0.994538703 0.922582642 0.959323071 1.027580174 1 12.34812807 -8.057038118 2.285439715 1.015286249 0.942588951 0.268161494 0.054161652 0.37404961 3.779389983 0.008129507 0.028820141 8.77E-09 8.057038118 -0.072697298 TET(ph)QEKNTLPTK ddPTM_HeLa_Romidepsin_16h_R1 1 TETQEKNTLPTK 12 1 P63313;CON__P21752 P63313 TMSB10 Thymosin beta-10 1 0 T(0.083)ET(0.912)QEKNT(0.005)LPTK 132.51 0.013311 11652000 1028.1 1089.4 1103.1 976.97 978.35 1043.6 751.83 787.34 888.31 1053.1 TRUE FALSE FALSE 1015.569122 1104.736602 1122.298993 1089.931868 928.4211488 976.9173281 815.6904214 810.1204407 808.8573288 1025.74031 0.990084051 1.077013929 1.094135603 1.062580711 0.905123002 0.9524022 0.795221182 0.789790976 0.788559561 1 10.00244981 -7.911338659 1.346047582 1.012108251 0.76669383 0.436469661 0.085982817 0.219507442 0.653874537 0.007975837 0.052899987 1.23E-08 7.911338659 -0.245414421 TETDS(ph)VGTPQSNGGMR ddPTM_HeLa_Romidepsin_16h_R1 1 TETDSVGTPQSNGGMR 16 0 Q9H0H5;F8VRD2;H0YIK5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 0 TET(0.004)DS(0.943)VGT(0.022)PQS(0.03)NGGMR 99.238 0.007912 6805100 1911 2116 1889.2 813.86 1801.9 2496.3 2219 2123.9 2466.8 1722.3 TRUE FALSE FALSE 1887.707997 2145.789104 1922.080734 907.9623225 1709.942319 2336.794486 2407.481805 2185.351696 2246.16323 1677.554398 1.125273791 1.27911745 1.145763581 0.541241657 1.01930663 1.392976877 1.435114002 1.302700943 1.338951054 1 10.71214383 -8.260166035 24.69198499 1.041871898 1.38274897 0.322166296 0.206019009 74.38246729 1442356.06 0.027115847 0.065160667 5.49E-09 8.260166035 0.340877072 TETQEK(ac)NPLPSK ddPTM_HeLa_Romidepsin_16h_R1 2 TETQEKNPLPSK 12 1 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 1 ; TETQEK(1)NPLPSK;TETQEK(1)NPLPSK 219.43 1.23E-21 20463700 3596.7 3856 3865 2555.5 7272.4 6434.3 5888.2 6346.7 8086.6 6075.2 FALSE TRUE FALSE 3552.862037 3910.284869 3932.268704 2850.978934 6901.262291 6023.168996 6388.343561 6530.331751 7363.314243 5917.365428 0.600412815 0.660815175 0.664530314 0.481798694 1.166272791 1.017880181 1.079592538 1.103587708 1.244356856 1 12.53073928 -8.736563256 24.99909669 0.761545966 1.085676694 0.35997225 0.206203308 178.7555131 179638.3438 0.027546981 0.055075394 1.83E-09 8.736563256 0.324130728 TETQEK(ac)NTLPTK ddPTM_HeLa_Romidepsin_16h_R1 2 TETQEKNTLPTK 12 1 P63313;CON__P21752 P63313 TMSB10 Thymosin beta-10 0 1 ; TETQEK(1)NTLPTK;TETQEK(1)NTLPTK 204.32 3.08E-14 3187500 1748.71 1396.95 1557.1 1305.78 1181.79 1367.84 1226.6 1328.7 1680.75 1807.14 FALSE TRUE FALSE 1727.39605 1416.616299 1584.200672 1456.760427 1121.478846 1280.439439 1330.787373 1367.143838 1530.41951 1760.190242 0.98136895 0.804808631 0.900016734 0.82761533 0.637135021 0.727443777 0.756047467 0.776702316 0.869462558 1 10.78151565 -9.763526701 0.854593369 0.997626171 0.729590707 0.580591926 0.069418753 0.172847416 0.252760389 0.01188915 0.019119713 1.72E-10 9.763526701 -0.268035464 TETQEKNPLPSK(ac)ETIEQEK ddPTM_HeLa_Romidepsin_16h_R1 1 TETQEKNPLPSKETIEQEK 19 2 P62328 P62328 TMSB4X Thymosin beta-4;Hematopoietic system regulatory peptide 0 1 TETQEK(0.061)NPLPSK(0.939)ETIEQEK 156.06 3.98E-16 3225800 414.42 521.75 413.93 427.21 999.04 577.5 717.15 812.79 924.13 713.9 FALSE TRUE FALSE 409.3688896 529.0952102 421.134278 476.6060303 948.0552609 540.5996138 778.0647031 836.3067963 841.4734983 695.3527751 0.588721156 0.760901846 0.605641184 0.685416162 1.363416233 0.777446547 1.118949591 1.202708648 1.21013898 1 9.441601279 -8.784313012 24.9999673 0.773320842 1.09171151 0.303271093 0.223140534 194.2120414 212265.4643 0.03077646 0.055814034 1.64E-09 8.784313012 0.318390668 TETVVDDWDEEFDR ddPTM_HeLa_Romidepsin_16h_R1 2 TETVVDDWDEEFDR 14 0 Q9P275;K7EKN3;K7EKL7;K7EIH0 Q9P275 USP36 Ubiquitin carboxyl-terminal hydrolase 36 0 0 ; ; 210.35 8.37E-23 3473800 864.16 885.11 1042.25 687.9 728.12 710.58 585.29 673.36 767.25 950.51 FALSE FALSE TRUE 853.6272855 897.5706018 1060.389924 767.4382347 690.9613194 665.1762313 635.004518 692.8426092 698.6252384 925.8156132 0.922027317 0.969491753 1.145357573 0.828932051 0.746327141 0.718475927 0.685886594 0.748359176 0.754605159 1 9.854581083 -9.001535424 4.595322028 0.976049461 0.725852285 0.585652603 0.091942816 0.067276228 3.712760799 0.009589327 0.017072392 9.96E-10 9.001535424 -0.250197176 TEVSETARPSS(ph)PDTR ddPTM_HeLa_Romidepsin_16h_R1 1 TEVSETARPSSPDTR 15 1 O75132 O75132 ZBED4 Zinc finger BED domain-containing protein 4 1 0 TEVSET(0.002)ARPS(0.102)S(0.895)PDT(0.001)R 158.31 0.0020793 9285800 1611.9 1850.4 1865.8 2084.7 1858.5 2574.1 1756.2 2717 1750.4 1660.1 TRUE FALSE FALSE 1592.253543 1876.44998 1898.273466 2325.742823 1763.65381 2409.623318 1905.371584 2795.612108 1593.83984 1616.970363 0.984714117 1.160472711 1.173969239 1.438333612 1.090714988 1.49020871 1.178359003 1.72891982 0.985695147 1 10.65907752 -4 0.212630047 0.938801085 4.263001999 0.617147768 0.146730309 22.02176314 0.259760304 0.111254266 25.07338247 1.00E-04 4 3.324200914 TFIAIK(ac)PDGVQR ddPTM_HeLa_Romidepsin_16h_R1 2 TFIAIKPDGVQR 12 1 Q32Q12;P22392-2;P22392;J3KPD9;E7ERL0;F6XY72;E5RHP0;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 1 ; TFIAIK(1)PDGVQR;TFIAIK(1)PDGVQR 177.44 1.83E-05 2150200 573.11 489.56 613.64 535.28 1181.61 1083.41 1080.18 1244.85 1757.73 1087.18 FALSE TRUE FALSE 566.1247149 496.4520385 624.3201468 597.1715922 1121.308033 1014.183598 1171.930462 1280.867771 1600.514226 1058.934907 0.534617106 0.468822054 0.589573677 0.563936072 1.058901756 0.95773932 1.1067068 1.209581214 1.511437782 1 10.04839819 -8.740007851 21.46884754 0.719760524 1.075946496 0.187914805 0.296113667 40.1312215 40199.46617 0.032674829 0.065252819 1.82E-09 8.740007851 0.356185972 TFIAIKPDGVQR ddPTM_HeLa_Romidepsin_16h_R1 3 TFIAIKPDGVQR 12 1 Q32Q12;P22392-2;P22392;J3KPD9;E7ERL0;F6XY72;E5RHP0;C9K028;P15531;P15531-2 Q32Q12;P15531 NME1-NME2;NME2;NME1 Nucleoside diphosphate kinase;Nucleoside diphosphate kinase B;Nucleoside diphosphate kinase A 0 0 ;; ;; 128.36 0.0013 92425000 7568.8 6691.7 6958.5 6358.2 6378.1 6335.7 6027.3 5933.9 7199.1 6164 FALSE FALSE TRUE 7476.548554 6785.905928 7079.609774 7093.365 6052.601757 5930.869218 6539.258712 6105.588034 6555.194466 6003.858391 1.245290623 1.130257492 1.179176675 1.181467739 1.008118673 0.987842955 1.089176041 1.016944044 1.091830293 1 12.55167423 -8.749707773 24.99565698 1.129111899 1.027375991 0.411847652 0.065320759 282.30453 601481.9481 0.014076909 0.027966275 1.78E-09 8.749707773 -0.101735907 TFLEGDWTS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 TFLEGDWTSPSK 12 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 TFLEGDWT(0.069)S(0.928)PS(0.003)K 207.34 2.32E-15 108660000 5753.5 5268.8 5334.6 4578.9 3535 3369 2803.3 2765.1 6292.7 5681 TRUE FALSE FALSE 5683.374129 5342.974305 5427.446475 5108.333962 3354.595759 3153.731773 3041.412232 2845.103806 5729.865152 5533.406801 1.027102169 0.965584946 0.980850798 0.923180627 0.606244196 0.569943958 0.549645515 0.51416856 1.03550405 1 12.43395228 -8.782400094 2.423188198 1.006753598 0.54399935 0.987280569 0.024036114 0.022111157 0.265063154 0.003838548 0.008038127 1.65E-09 8.782400094 -0.462754248 TFLVWVNEEDHLR ddPTM_HeLa_Romidepsin_16h_R1 3 TFLVWVNEEDHLR 13 0 P12277;H0YJG0 P12277 CKB Creatine kinase B-type 0 0 ;; ;; 159.58 0.00022524 51199000 5823.11 4964.16 4796.45 5399.51 6234.84 6383.46 5299.35 6819.94 5102.42 4986.02 FALSE FALSE TRUE 5752.135696 5034.045575 4879.9302 6023.826752 5916.652849 5975.577508 5749.476657 7017.264204 4646.046776 4856.482482 1.184424265 1.036562078 1.004828128 1.240368265 1.21830005 1.230433247 1.183876742 1.444927317 0.956669111 1 12.24569604 -4 0.230242183 1.045700246 2.841572707 0.652949728 0.083818425 27.84154562 0.338770925 0.05893522 19.04684046 1.00E-04 4 1.795872461 TFNLEK(ac)QNHTPR ddPTM_HeLa_Romidepsin_16h_R1 2 TFNLEKQNHTPR 12 1 Q15233;C9JYS8;C9IZL7;C9JJ13;C9J4X2 Q15233 NONO Non-POU domain-containing octamer-binding protein 0 1 ; TFNLEK(1)QNHTPR;TFNLEK(1)QNHTPR 116.51 0.0055929 5884200 3090.7 3564.6 2268.39 2429.6 2475.6 2030.06 2251.4 1821.05 4115 2661.5 FALSE TRUE FALSE 3053.02936 3614.782532 2307.870376 2710.521784 2349.260894 1900.345718 2442.63386 1873.739209 3746.944094 2592.353846 1.177705491 1.39440167 0.890260556 1.045583259 0.90622694 0.733057997 0.942245544 0.722794541 1.445382967 1 11.34004694 -8.827503646 1.439044099 1.102810667 0.808931959 0.471148609 0.1710455 0.280491209 1.166515418 0.022188958 0.053224457 1.49E-09 8.827503646 -0.293878708 TFNTSTGGLLLPSDTK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 TFNTSTGGLLLPSDTKR 17 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 1 ; TFNTSTGGLLLPSDTK(1)R;TFNTSTGGLLLPSDTK(1)R 215.93 3.23E-29 656610 0 0 0 0 158.06 0 180.79 175 153.74 87.772 FALSE TRUE FALSE 0 0 0 0 149.9936084 0 196.1462981 180.0633489 139.9891094 85.49167079 0 0 0 0 1.754482127 0 2.294332258 2.106209263 1.637459042 1 6.417711964 -7.75390568 24.99858297 0.464605855 2.200271661 0.493285331 0.665056547 90.75643179 301143.4455 0.083571994 0.300776243 1.76E-08 7.75390568 1.735665806 TFNTSTGGLLLPSDTKR ddPTM_HeLa_Romidepsin_16h_R1 1 TFNTSTGGLLLPSDTKR 17 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 0 93.495 0.012607 718330 229.74 0 248.14 286.97 230.16 191.61 153.85 244.71 189.97 246.97 FALSE FALSE TRUE 226.9398405 0 252.4587726 320.1508216 218.4140764 179.3667394 166.9180152 251.7902978 172.9786074 240.5536838 0.943406216 0 1.049490362 1.330891369 0.907963964 0.745641208 0.693890913 1.046711461 0.719085256 1 7.910215083 -10.49935026 24.93968241 0.975032356 0.821251912 0 0.33655623 599.4829163 635447.533 0.058097501 0.06244929 3.17E-11 10.49935026 -0.153780444 TFPSAS(ph)NTQATPDLLK ddPTM_HeLa_Romidepsin_16h_R1 1 TFPSASNTQATPDLLK 16 0 Q0VF96 Q0VF96 CGNL1 Cingulin-like protein 1 1 0 T(0.02)FPS(0.02)AS(0.48)NT(0.48)QATPDLLK 87.824 0.0031521 0 784.72 973.07 903.27 904.29 827.21 750.9 689.26 1116.7 1028.1 905.04 TRUE FALSE FALSE 775.1555308 986.768905 918.9910354 1008.848265 784.994387 702.9199134 747.8057272 1149.009953 936.1441611 881.5269303 0.879332785 1.119386001 1.042499104 1.144432722 0.890493937 0.797389041 0.848307297 1.303431481 1.061957529 1 9.783860834 -12.58807086 0.005221509 5.17E-07 1.917827928 0 0.153571575 107023.9172 122.0462785 23015.54715 21820.65524 2.58E-13 12.58807086 1.917827411 TFS(ph)DESNVL ddPTM_HeLa_Romidepsin_16h_R1 2 TFSDESNVL 9 0 H7C113;Q8NB49 H7C113 ATP11C Phospholipid-transporting ATPase IG 1 0 T(0.229)FS(0.771)DESNVL;T(0.371)FS(0.629)DESNVL ; 145.72 0.0058499 3725400 1712.89 2707.6 2057.18 1616.3 2344.5 2572.3 1712.99 2527.6 2060.06 1940.53 TRUE FALSE FALSE 1692.012638 2745.717664 2092.984355 1803.184211 2224.851416 2407.938332 1858.491328 2600.732118 1875.803074 1890.114751 0.895190431 1.45267247 1.107331898 0.954007798 1.177098594 1.273964097 0.983269046 1.375965198 0.992428144 1 10.88425811 -10.36348448 21.3464615 0.950504138 1.17211766 0.318630513 0.150123953 9.46523114 1974.626947 0.024513188 0.028031633 4.33E-11 10.36348448 0.221613522 TFS(ph)DGLATR ddPTM_HeLa_Romidepsin_16h_R1 2 TFSDGLATR 9 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 T(0.032)FS(0.966)DGLAT(0.002)R;T(0.112)FS(0.888)DGLATR ; 111.5 0.018281 22396000 6263.2 7407.2 5754.5 5555.5 7886.5 4708.8 3319.3 4860.7 5693.7 5306.7 TRUE FALSE FALSE 6186.861709 7511.478756 5854.654659 6197.853049 7484.022476 4407.922877 3601.241259 5001.336686 5184.441212 5168.831169 1.196955657 1.453225789 1.132684444 1.199082123 1.447913896 0.852789099 0.696722555 0.967595288 1.003020033 1 12.33562236 -8.080043383 11.72332133 1.154345396 0.81783317 0.499330294 0.16236312 0.59075765 85.24384083 0.024388663 0.062232993 8.32E-09 8.080043383 -0.336512226 TFS(ph)LDAVPPDHSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TFSLDAVPPDHSPR 14 0 Q9BST9-3;Q9BST9-2;Q9BST9 Q9BST9-3 RTKN Rhotekin 1 0 T(0.212)FS(0.788)LDAVPPDHSPR 75.877 0.018499 3049200 964.97 1043.8 970.44 1456 983.6 901.97 827.23 944.26 1196 979.37 TRUE FALSE FALSE 953.2085745 1058.494644 987.3301011 1624.349571 933.4032217 844.337028 897.4948956 971.5806733 1089.026765 953.9258262 0.999248105 1.109619443 1.035017686 1.7028049 0.978486163 0.885118114 0.940843482 1.018507568 1.141626251 1 9.897733282 -5.695554741 12.19767218 1.041399179 0.760751207 0 0.222419788 0 0 0.028792731 0 2.02E-06 5.695554741 -0.280647972 TFS(ph)LTEVR ddPTM_HeLa_Romidepsin_16h_R1 4 TFSLTEVR 8 0 O95239;O95239-2 O95239 KIF4A Chromosome-associated kinesin KIF4A 1 0 T(0.001)FS(0.987)LT(0.012)EVR;TFS(0.988)LT(0.012)EVR;TFS(0.987)LT(0.013)EVR;TFS(0.998)LT(0.002)EVR ;;; 133.99 0.0094209 183970000 16966.4 15515.3 15417.1 12292 11053.5 10381 9290.8 10653.8 15936.5 14716.2 TRUE FALSE FALSE 16759.60699 15733.7248 15685.42816 13713.25888 10489.39865 9717.687603 10079.96032 10962.05089 14511.09953 14333.871 1.169231046 1.097660555 1.094291148 0.956703104 0.73179106 0.677952774 0.703226666 0.764765561 1.012364317 1 13.80714066 -8.889478355 2.620581185 1.084176988 0.710107157 0.920046611 0.049416485 0.068405725 0.952579863 0.010154582 0.019974584 1.29E-09 8.889478355 -0.374069831 TFSVWYVPEVTGTHK ddPTM_HeLa_Romidepsin_16h_R1 2 TFSVWYVPEVTGTHK 15 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 ; ; 120.21 0.001663 11056630 4566.23 4572.31 4490.55 4268.01 5222.89 5590.38 4079.12 4777.1 5116.81 4561.12 FALSE FALSE TRUE 4510.575032 4636.6791 4568.706139 4761.497398 4956.346434 5233.17276 4425.600351 4915.317851 4659.149698 4442.621445 1.015295831 1.043680889 1.028380697 1.07177653 1.115635553 1.177947035 0.996168682 1.106400334 1.048738848 1 12.1171955 -9.431098599 1.3591621 1.008195201 1.096730633 0.338270416 0.044823973 0.27545194 1.008940474 0.007183941 0.012557873 3.71E-10 9.431098599 0.088535431 TFVEESIYNEFLER ddPTM_HeLa_Romidepsin_16h_R1 1 TFVEESIYNEFLER 14 0 P30837 P30837 ALDH1B1 "Aldehyde dehydrogenase X, mitochondrial" 0 0 208.08 2.01E-16 2535400 695.39 787.62 840.45 714.21 949.08 820.59 786.01 833.16 826.93 633.72 FALSE FALSE TRUE 686.9143192 798.708135 855.0776797 796.7903207 900.6449061 768.1569473 852.7736698 857.2661701 752.9673097 617.255863 1.112851834 1.293966057 1.385288874 1.290859056 1.45911114 1.24447088 1.381556208 1.38883439 1.219862548 1 9.269724825 -10.34261125 1.370652522 1.03685113 1.360567209 0.61630466 0.082363803 0.098379037 0.356475264 0.011724831 0.013453523 4.54E-11 10.34261125 0.323716079 TFVLAGSADS(ph)PELGK ddPTM_HeLa_Romidepsin_16h_R1 1 TFVLAGSADSPELGK 15 0 O15061 O15061 SYNM Synemin 1 0 T(0.002)FVLAGS(0.003)ADS(0.995)PELGK 137.17 0.0011354 28887000 2693.3 2079.2 2447.1 2380.9 3606.5 3925.3 3755.2 3080.3 2703 2943.6 TRUE FALSE FALSE 2660.473024 2108.471032 2489.690749 2656.19086 3422.446847 3674.485998 4074.166594 3169.423621 2461.23691 2867.124848 0.927923674 0.735395612 0.868357983 0.926430135 1.19368602 1.281592604 1.420993787 1.105436208 0.858433811 1 11.48538901 -8.665989893 3.56775368 0.934866554 1.279132949 0.744378099 0.102751463 0.100063353 2.47731787 0.015681317 0.032605106 2.16E-09 8.665989893 0.344266394 TFVQEDIYDEFVER ddPTM_HeLa_Romidepsin_16h_R1 2 TFVQEDIYDEFVER 14 0 P05091;P05091-2;S4R3S4 P05091 ALDH2 "Aldehyde dehydrogenase, mitochondrial" 0 0 ; ; 195.1 1.97E-10 2285700 1441.4 1549.46 1300.33 1380.91 1283.76 1367.73 1258.53 1528.04 1399.71 1268.84 FALSE FALSE TRUE 1423.831662 1571.273339 1322.961698 1540.577312 1218.244937 1280.336467 1365.429507 1572.251427 1274.516432 1235.875354 1.152083548 1.271384961 1.070465314 1.246547483 0.98573447 1.035975402 1.104827847 1.272176374 1.031266161 1 10.27131753 -12.16666418 0.989464029 1.002477679 1.137051247 0.221514276 0.093823416 0.619738269 1.120679948 0.056118047 0.017251309 6.81E-13 12.16666418 0.134573568 TFY(ph)LY(ph)VS(ph)QKEEKK ddPTM_HeLa_Romidepsin_16h_R1 1 TFYLYVSQKEEKK 13 2 B5MC67;Q7Z6J6-2;Q7Z6J6;A0A087WVP2;H0Y5N1 B5MC67 FRMD5 FERM domain-containing protein 5 3 0 T(0.335)FY(0.704)LY(0.962)VS(1)QKEEKK 55.213 0.0043155 0 511.24 525.53 514.9 355.99 708.05 613.32 406.16 640.46 805.03 575.81 TRUE FALSE FALSE 505.0088102 532.9284251 523.8616185 397.1512388 671.9155664 574.1308314 440.6592203 658.9906996 733.0261006 560.8503732 0.900434116 0.950214978 0.934048801 0.708123339 1.198029989 1.023679147 0.785698363 1.174984864 1.306990484 1 9.131472122 -7.228508288 23.27674541 0.947021575 1.174985961 0.082421804 0.169325832 6536.244684 4619831.951 0.016308366 3.043246643 5.91E-08 7.228508288 0.227964386 TGAAGK(ac)FK ddPTM_HeLa_Romidepsin_16h_R1 2 TGAAGKFK 8 1 P39748-2;P39748 P39748-2 FEN1 Flap endonuclease 1 0 1 ; TGAAGK(1)FK;TGAAGK(1)FK 117.04 0.0082258 21515000 2170.52 1811.18 8470.1 8955 26943 34995 26607 9524.6 2351.62 938.28 FALSE TRUE FALSE 2144.064867 1836.67784 8617.518537 9990.419235 25567.99817 32758.93244 28866.99792 9800.179274 2141.285217 913.9033503 2.346052092 2.009706868 9.429354356 10.93159275 27.97669815 35.84507315 31.58648877 10.72343073 2.343010578 1 9.835897791 -9.027511853 1.780638991 1.914532381 27.7055534 0.732442631 6.550994389 0.120817643 0.760628241 0.999505412 1.987876801 9.39E-10 9.027511853 25.79102102 TGADTTAAGPLFQQRPYPS(ph)PGAVLR ddPTM_HeLa_Romidepsin_16h_R1 2 TGADTTAAGPLFQQRPYPSPGAVLR 25 1 O60828-5;O60828-4;O60828-2;O60828;H7C053 O60828-5 PQBP1 Polyglutamine-binding protein 1 1 0 TGADTTAAGPLFQQRPY(0.016)PS(0.984)PGAVLR;TGADT(0.001)T(0.001)AAGPLFQQRPY(0.005)PS(0.993)PGAVLR ; 87.237 2.77E-05 149026000 1214.24 1317.64 1074.81 1036.39 1303.38 1325.86 1006.2 1619.9 1390.81 1182.93 TRUE FALSE FALSE 1199.440376 1336.189771 1093.516617 1156.222288 1236.863655 1241.141825 1091.666603 1666.769251 1266.41247 1152.197308 1.041002585 1.159688329 0.949070623 1.003493308 1.073482507 1.07719556 0.947464983 1.446600542 1.099128128 1 10.17017208 -7.254730248 24.91741146 1.027202712 1.446600742 0.782106591 0.064282277 222.193834 825195.3253 0.007905562 0.102916356 5.56E-08 7.254730248 0.41939803 TGDLGIPPNPEDRS(ph)PS(ph)PEPIYNSEGK ddPTM_HeLa_Romidepsin_16h_R1 9 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-4;Q15637-3;Q15637-2;Q15637;Q15637-7;Q15637-5 Q15637-6 SF1 Splicing factor 1 2 0 T(0.069)GDLGIPPNPEDRS(0.941)PS(0.973)PEPIY(0.009)NS(0.008)EGK;T(0.007)GDLGIPPNPEDRS(0.99)PS(0.98)PEPIY(0.019)NS(0.004)EGK;T(0.003)GDLGIPPNPEDRS(0.989)PS(0.989)PEPIY(0.013)NS(0.007)EGK;T(0.033)GDLGIPPNPEDRS(0.985)PS(0.957)PEPIY(0.011)NS(0.014)EGK;T(0.007)GDLGIPPNPEDRS(0.982)PS(0.927)PEPIY(0.051)NS(0.033)EGK;T(0.001)GDLGIPPNPEDRS(0.989)PS(0.9)PEPIY(0.079)NS(0.031)EGK;T(0.001)GDLGIPPNPEDRS(0.999)PS(0.995)PEPIY(0.004)NS(0.001)EGK;TGDLGIPPNPEDRS(0.994)PS(0.972)PEPIY(0.014)NS(0.019)EGK;T(0.02)GDLGIPPNPEDRS(0.976)PS(0.974)PEPIY(0.024)NS(0.006)EGK ;;;;;;;; 76.421 0.00026993 377342700 57358.8 55349.8 55834.75 48506.9 53194.95 53972.3 47187.42 52929.15 61632.8 60447.4 TRUE FALSE FALSE 56659.68888 56129.01594 56806.5304 54115.49601 50480.2132 50523.64422 51195.51828 54460.57145 56120.20801 58876.96783 0.96234047 0.953327218 0.96483451 0.919128447 0.857384731 0.858122388 0.86953388 0.924989405 0.953177619 1 15.84541575 -9.167769233 1.90576355 0.979496072 0.875354233 0.756223189 0.023337358 0.11149861 0.791590349 0.003926745 0.007210689 6.80E-10 9.167769233 -0.104141839 TGDLGIPPNPEDRS(ph)PSPEPIYNSEGK ddPTM_HeLa_Romidepsin_16h_R1 2 TGDLGIPPNPEDRSPSPEPIYNSEGK 26 1 Q15637-6;Q15637-4;Q15637-3;Q15637-2;Q15637;Q15637-7;Q15637-5 Q15637-6 SF1 Splicing factor 1 1 0 T(0.024)GDLGIPPNPEDRS(0.513)PS(0.453)PEPIY(0.005)NS(0.006)EGK;TGDLGIPPNPEDRS(0.433)PS(0.433)PEPIY(0.057)NS(0.076)EGK ; 55.061 0.0029749 10030800 5103.9 5088.5 4087.8 5061.1 5785.9 6359.1 6035.5 7228.9 5018.8 4847.1 TRUE FALSE FALSE 5041.691704 5160.136037 4158.946444 5646.288195 5490.623933 5952.774033 6548.155219 7438.056816 4569.905958 4721.171643 1.06788994 1.092977851 0.880914052 1.195950629 1.162979097 1.260867955 1.386976733 1.575468417 0.967960139 1 12.20492922 -7.134651253 0.57588436 1.025024537 2.024331558 0.871453075 0.070709149 0.941152316 0.19080055 0.012476942 0.64559757 7.33E-08 7.134651253 0.999307021 TGEDEDEEDNDALLKENES(ph)PDVR ddPTM_HeLa_Romidepsin_16h_R1 1 TGEDEDEEDNDALLKENESPDVR 23 1 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 0 TGEDEDEEDNDALLKENES(1)PDVR 72.082 0.00054241 9408600 593.12 575.58 672.49 289.19 479.86 537.72 458.65 553.53 759.9 511.58 TRUE FALSE FALSE 585.8908253 583.6830303 684.1944064 322.6275085 455.3709536 503.3614274 497.6077196 569.5455172 691.9326408 498.2890779 1.175805072 1.171374321 1.373087304 0.64747056 0.913869025 1.010179532 0.998632604 1.14300221 1.388616912 1 8.960839141 -9.270092918 24.99917975 1.112937501 0.947896826 0.311229088 0.17312781 791.4865259 2286520.343 0.024515125 0.037809671 5.37E-10 9.270092918 -0.165040675 TGEDEDEEDNDALLKENES(ph)PDVRR ddPTM_HeLa_Romidepsin_16h_R1 1 TGEDEDEEDNDALLKENESPDVRR 24 2 A0A087WWS1;Q96FV9 A0A087WWS1 THOC1 THO complex subunit 1 1 0 TGEDEDEEDNDALLKENES(1)PDVRR 59.918 0.0026252 17005000 2758.9 2800.8 2532.5 1487.4 2737.1 2735.6 2235.8 2739.7 2994.3 3132.3 TRUE FALSE FALSE 2725.273466 2840.229736 2576.5771 1659.380186 2597.415573 2560.803989 2425.708796 2818.968897 2726.482309 3050.922394 0.89326214 0.930941325 0.844523972 0.543894591 0.851354193 0.839354024 0.79507391 0.923972665 0.893658362 1 11.57502977 -10.51005754 0.819341127 0.973199641 0.798812104 0.230368209 0.101983563 0.456792654 0.642029013 0.026724269 0.02736471 3.09E-11 10.51005754 -0.174387536 TGFGGK(ac)FGVQSER ddPTM_HeLa_Romidepsin_16h_R1 2 TGFGGKFGVQSER 13 1 Q14247 Q14247 CTTN Src substrate cortactin 0 1 ; TGFGGK(1)FGVQSER;TGFGGK(1)FGVQSER 139.78 0.00038129 8850200 975.13 1246.91 1417.67 1201.52 1172.51 1278.49 1244.87 1252.52 1330.79 980.31 FALSE TRUE FALSE 963.2447405 1264.464032 1442.343952 1340.445396 1112.672439 1196.798615 1350.609227 1288.75969 1211.760809 954.8414049 1.008800766 1.324266025 1.510558659 1.403840878 1.165295549 1.253400417 1.4144854 1.34971073 1.269070238 1 9.899117317 -10.25192553 5.630827924 1.003584005 1.347709748 0.431148053 0.121221433 0.059881823 7.164052991 0.015616094 0.018625092 5.60E-11 10.25192553 0.344125744 TGGPAYGPS(ph)SDVSTASETESEKREEPNR ddPTM_HeLa_Romidepsin_16h_R1 1 TGGPAYGPSSDVSTASETESEKREEPNR 28 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 TGGPAY(0.006)GPS(0.231)S(0.231)DVS(0.231)T(0.231)AS(0.068)ET(0.002)ESEKREEPNR 59.561 0.0022558 9339400 1009.9 925.59 982.92 1421 1505 1098.5 1018.1 1312 1042.8 1103 TRUE FALSE FALSE 997.5909504 938.6204803 1000.02731 1585.302706 1428.194234 1028.309395 1104.577389 1349.96065 949.5293563 1074.343901 0.928558304 0.873668552 0.930826069 1.475600787 1.32936412 0.957151052 1.02814135 1.256544249 0.883822541 1 10.06924016 TGGPAYGPSSDVS(ph)TASETESEKREEPNR ddPTM_HeLa_Romidepsin_16h_R1 1 TGGPAYGPSSDVSTASETESEKREEPNR 28 2 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 TGGPAY(0.001)GPS(0.036)S(0.036)DVS(0.491)T(0.183)AS(0.183)ET(0.063)ES(0.009)EKREEPNR 43.884 0.019779 14025000 2349.8 2240.8 1852.8 2694.6 2462.8 2649.1 2092.6 1845 1988.6 2402.4 TRUE FALSE FALSE 2321.159734 2272.346041 1885.047207 3006.16233 2337.114126 2479.83106 2270.345392 1898.382164 1810.734635 2339.985302 0.991954835 0.971094152 0.80558079 1.284692826 0.998772994 1.05976352 0.970239168 0.811279525 0.773823081 1 11.19228375 -7.288342258 3.637344818 1.005165154 0.794809466 0.119503974 0.132670487 0.278739417 6.689896986 0.014173798 0.151545128 5.15E-08 7.288342258 -0.210355687 TGGPAYGPSSDVSTAS(ph)ETESEKR ddPTM_HeLa_Romidepsin_16h_R1 1 TGGPAYGPSSDVSTASETESEKR 23 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 TGGPAYGPSSDVS(0.001)T(0.014)AS(0.973)ET(0.009)ES(0.002)EKR 115.34 2.18E-06 17702000 2143.7 2202.6 2240.1 1247.7 2498.2 2205.5 1419.5 2615.5 1722.2 2138.2 TRUE FALSE FALSE 2117.57176 2233.608261 2279.088001 1391.964945 2370.707532 2064.575668 1540.072295 2691.175366 1568.162119 2082.649256 1.016768308 1.072484123 1.094321569 0.668362635 1.138313389 0.991321828 0.739477514 1.292188475 0.752965058 1 11.02420418 TGGSGS(ph)PPLR ddPTM_HeLa_Romidepsin_16h_R1 1 TGGSGSPPLR 10 0 Q8N2Y8 Q8N2Y8 RUSC2 Iporin 1 0 T(0.064)GGS(0.028)GS(0.908)PPLR 93.561 0.0040237 0 5223.2 4974.3 4430.1 3838 3432.5 2869.1 2447.5 2774 5360.2 5172.6 TRUE FALSE FALSE 5159.537629 5044.328326 4507.204032 4281.767618 3257.326717 2685.77377 2655.390589 2854.261313 4880.770287 5038.215106 1.024080457 1.00121337 0.894603334 0.849858041 0.646523947 0.533080409 0.527049864 0.566522321 0.968749881 1 12.298697 -8.881974256 1.204230025 1.01077039 0.526137165 0.97747932 0.029803397 0.038102397 0.109566614 0.004411874 0.011126017 1.31E-09 8.881974256 -0.484633225 TGIVAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TGIVAKK 7 1 Q9BQ61 Q9BQ61 C19orf43 Uncharacterized protein C19orf43 0 1 ; TGIVAK(1)K;TGIVAK(1)K 87.323 0.028014 14561700 14347 14592.1 12070.5 11596.6 13796.4 14144 15976.5 9548.5 15463.4 13823.4 FALSE TRUE FALSE 14172.13325 14797.52797 12280.58199 12937.45346 13092.31823 13240.24405 17333.54351 9824.770782 14080.31478 13464.26608 1.052573766 1.099022248 0.912086995 0.960873276 0.972375186 0.983361735 1.28737381 0.729692263 1.045754347 1 13.71684797 -9.7681876 24.98700101 1.031084853 0.988239719 0.061056201 0.130157738 561.4098459 2078760.281 0.019346441 0.025753928 1.71E-10 9.7681876 -0.042845134 TGKEYIPGQPPLSQSSDS(ph)SPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TGKEYIPGQPPLSQSSDSSPTR 22 1 P07814;V9GYZ6 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 1 0 TGKEYIPGQPPLS(0.166)QS(0.166)S(0.166)DS(0.222)S(0.222)PT(0.059)R 60.621 0.0049028 8511900 2008.6 2051.1 966.06 8477.8 1606.7 1505.9 1365 1724.9 2326.8 1486.9 TRUE FALSE FALSE 1984.118411 2079.97544 982.8738691 9458.043125 1524.704104 1409.67785 1480.943066 1774.80726 2118.68518 1448.270124 1.36999195 1.436179208 0.678653694 6.530579462 1.052776052 0.973352848 1.022559978 1.225467011 1.462907469 1 10.500115 TGLFEWDNDFEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 TGLFEWDNDFEDIR 14 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 0 0 158.06 0.00033623 0 549.12 649.91 404.82 396.96 576.92 666.33 342.55 527.99 633.58 571.93 FALSE FALSE TRUE 542.4271142 659.05945 411.8657223 442.858383 547.4776196 623.7536635 371.6461884 543.2665576 576.911018 557.0711762 0.973712404 1.183079431 0.739341291 0.794976301 0.98277858 1.119701916 0.667143095 0.975219291 1.035614555 1 9.12171786 -9.749849401 24.99957243 1.001901552 0.881912829 0.243752579 0.135718318 311.2248539 671310.1265 0.02068506 0.029113878 1.78E-10 9.749849401 -0.119988723 TGLLFS(ph)PDVDEKLPK ddPTM_HeLa_Romidepsin_16h_R1 1 TGLLFSPDVDEKLPK 15 1 Q6P4F7-3;Q6P4F7;H3BQ41;H3BR51;Q6P4F7-2 Q6P4F7-3 ARHGAP11A Rho GTPase-activating protein 11A 1 0 T(0.008)GLLFS(0.992)PDVDEKLPK 77.505 0.013245 16502000 4360.8 4003.9 3655.3 3620.7 3367.6 3733.5 2576.6 3226.8 4266.9 3300.7 TRUE FALSE FALSE 4307.648892 4060.267009 3718.918963 4039.34237 3195.738806 3494.941399 2795.45634 3320.162367 3885.257777 3214.947338 1.339881634 1.26293422 1.156758905 1.256425672 0.994025242 1.087091337 0.869518547 1.032726828 1.208498109 1 11.65057939 -8.745316023 24.43818407 1.178456639 0.99333531 0.504901881 0.099079101 187.6450704 284411.6077 0.020340329 0.040572098 1.80E-09 8.745316023 -0.185121329 TGLSLWDT(ph)SPSYIDK ddPTM_HeLa_Romidepsin_16h_R1 1 TGLSLWDTSPSYIDK 15 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 0 TGLSLWDT(0.791)S(0.206)PS(0.002)YIDK 196.11 1.26E-12 15012000 2049.1 2003.1 1948.1 1879.2 1876 2102.8 1774.9 1733.5 2410.2 1911 TRUE FALSE FALSE 2024.124781 2031.299694 1982.005863 2096.481946 1780.26072 1968.437866 1925.659962 1783.656087 2194.625676 1861.351945 1.087448715 1.091303394 1.064820583 1.126322162 0.956434233 1.05753126 1.034549091 0.958258374 1.179049283 1 10.86213515 -7.25864756 3.081690647 1.048298715 0.943828652 0.170676273 0.061403149 0.44604459 6.290118444 0.006983542 0.113370094 5.51E-08 7.25864756 -0.104470063 TGLSLWDTSPS(ph)YIDK ddPTM_HeLa_Romidepsin_16h_R1 1 TGLSLWDTSPSYIDK 15 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 0 TGLSLWDT(0.023)S(0.039)PS(0.746)Y(0.191)IDK 135.8 0.0012808 13163000 4027.6 3362 3741.9 3556 3676.9 4388.7 3411.9 3383.9 3790.8 3657.6 TRUE FALSE FALSE 3978.510062 3409.330324 3807.0262 3967.161451 3489.254073 4108.276234 3701.706701 3481.807808 3451.741354 3562.575025 1.116751236 0.95698485 1.068616429 1.113565728 0.979419114 1.153176061 1.039053683 0.977328978 0.968889449 1 11.79870468 -7.302374936 4.664687635 1.05538303 0.974939285 0.065622602 0.065566222 0.281304797 13.72345773 0.008574596 0.063928131 4.98E-08 7.302374936 -0.080443745 TGLYNYYDDEK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 1 TGLYNYYDDEKEK 13 1 P50454;E9PPV6;E9PR70;E9PKH2 P50454 SERPINH1 Serpin H1 0 1 TGLYNYYDDEK(1)EK 189.3 9.33E-10 484100 211.57 234.45 0 124.18 147.65 211.79 223.72 68.586 263.38 209.68 FALSE TRUE FALSE 208.9913035 237.7505933 0 138.5382759 140.1148695 198.2573025 242.7227712 70.5704277 239.8226332 204.2324834 1.023300995 1.164117428 0 0.678336147 0.68605575 0.97074324 1.188463104 0.345539684 1.174262924 1 7.674068536 TGLYNYYDDEKEK ddPTM_HeLa_Romidepsin_16h_R1 1 TGLYNYYDDEKEK 13 1 P50454;E9PPV6;E9PR70;E9PKH2 P50454 SERPINH1 Serpin H1 0 0 104.55 0.011474 41352000 2154 2100.1 2180.4 2299.4 1919.1 2009.8 1627.9 1950.6 2724.6 2095.5 FALSE FALSE TRUE 2127.746219 2129.665263 2218.348947 2565.267447 1821.161166 1881.380266 1766.173785 2007.037533 2480.904952 2041.058608 1.042471887 1.043412107 1.086861954 1.256831841 0.892263044 0.9217669 0.865322426 0.983331652 1.215499125 1 10.99510189 TGNESGS(ph)NLSDSGSVK ddPTM_HeLa_Romidepsin_16h_R1 1 TGNESGSNLSDSGSVK 16 0 Q9UDT6-2;Q9UDT6 Q9UDT6-2 CLIP2 CAP-Gly domain-containing linker protein 2 1 0 TGNES(0.001)GS(0.408)NLS(0.312)DS(0.279)GSVK 133.78 1.72E-06 0 3447 2961.1 3379.9 2964.9 3724.9 3277.4 2709.3 3068.2 3339.9 3578.2 TRUE FALSE FALSE 3404.986638 3002.786444 3438.725742 3307.715688 3534.804453 3067.984717 2939.427874 3156.973526 3041.170979 3485.237848 0.976973965 0.86157289 0.986654539 0.949064549 1.014221872 0.880279869 0.843393766 0.905812936 0.872586352 1 11.7670414 -4.000000001 0.177546158 1.008741832 0.410462558 0 0.062337997 42.05876195 0.453114765 0.064048783 6.802831972 1.00E-04 4.000000001 -0.598279274 APAGQEEPGT(ph)PPSS(ph)PLSAEQLDR ddPTM_HeLa_Romidepsin_16h_R1 1 APAGQEEPGTPPSSPLSAEQLDR 23 0 P13051;Q68DM5;F5GYA2;P13051-2 P13051 UNG;DKFZp781L1143 Uracil-DNA glycosylase 2 0 APAGQEEPGT(1)PPS(0.275)S(0.709)PLS(0.015)AEQLDR 103.04 3.09E-05 4290700 355.71 401.78 575.03 369.04 317.32 141.71 199.48 169.74 462.37 494.04 TRUE FALSE FALSE 351.3744697 407.4362694 585.0381559 411.7101412 301.1259763 132.6551883 216.4238262 174.6511591 421.0144692 481.2047696 0.730197396 0.846700397 1.215777966 0.855582004 0.625775128 0.275673054 0.449754117 0.362945611 0.87491749 1 8.910507132 -8.564947025 2.952071062 0.895237195 0.373927154 0.79358949 0.127649815 0.105970567 1.875235858 0.022309497 0.050049732 2.72E-09 8.564947025 -0.521310042 down SNVSSPAT(ph)PTASSSSST(ph)TPTR ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 SNVS(0.03)S(0.119)PAT(0.844)PT(0.008)AS(0.077)S(0.059)S(0.045)S(0.192)S(0.144)T(0.308)T(0.044)PT(0.13)R 124.45 0.0032045 4898000 1305 1288.6 1199.3 1322.9 821.26 489.08 414.16 400.2 1280.3 1367.2 TRUE FALSE FALSE 1289.094158 1306.740945 1220.173313 1475.859922 779.3480377 457.8293664 449.3387401 411.7791556 1165.786761 1331.679947 0.968021003 0.981272525 0.916266192 1.10826924 0.585236745 0.343798348 0.337422472 0.309217809 0.875425634 1 10.37903167 -8.562630245 3.340435951 0.986024014 0.338212859 0.955221503 0.063176819 0.026607022 0.613047775 0.007516398 0.016498013 2.74E-09 8.562630245 -0.647811156 down TGQPAQPAPSAQQPPRPPAS(ph)PDEPSVAASSVGSSR ddPTM_HeLa_Romidepsin_16h_R1 3 TGQPAQPAPSAQQPPRPPASPDEPSVAASSVGSSR 35 1 O94964-2 O94964-2 SOGA1 Protein SOGA1;N-terminal form;C-terminal 80 kDa form 1 0 TGQPAQPAPS(0.251)AQQPPRPPAS(0.454)PDEPS(0.046)VAAS(0.054)S(0.059)VGS(0.065)S(0.071)R;TGQPAQPAPS(0.005)AQQPPRPPAS(0.795)PDEPS(0.077)VAAS(0.045)S(0.054)VGS(0.011)S(0.013)R;TGQPAQPAPS(0.331)AQQPPRPPAS(0.392)PDEPS(0.039)VAAS(0.044)S(0.051)VGS(0.071)S(0.071)R ;; 53.091 0.002331 31527000 3909.12 3275.89 3162.15 2842.38 3003.47 2167.77 1893.24 2048.04 3744.13 3580.79 TRUE FALSE FALSE 3861.474142 3322.008065 3217.185894 3171.029349 2850.191718 2029.256493 2054.051758 2107.296806 3409.245635 3487.76056 1.107150011 0.952475954 0.922421663 0.9091878 0.817198219 0.581822192 0.588931414 0.604197671 0.977488442 1 11.76808528 -8.661395276 0.888730756 1.045406976 0.551479183 0.912256791 0.053445773 0.129782066 0.18695379 0.010261275 0.03880825 2.18E-09 8.661395276 -0.493927793 TGS(ph)EPALSPAVVR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSEPALSPAVVR 13 0 O75815;O75815-2;O75815-3 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 0 T(0.227)GS(0.773)EPALSPAVVR 139.19 0.0012233 6097600 1287.9 1406.7 1210.7 1258.5 1199.8 984.9 861.87 926.07 1344.5 1517.5 TRUE FALSE FALSE 1272.202579 1426.50356 1231.771726 1404.013691 1138.569729 921.9680686 935.0772163 952.8643744 1224.244553 1478.075131 0.860715773 0.965108965 0.833362053 0.949893319 0.770305721 0.623762655 0.632631723 0.644665724 0.828269502 1 10.52950389 -8.533285956 2.602231595 0.928369704 0.632722421 0.820221862 0.056605194 0.081583743 1.106909767 0.008918184 0.020957871 2.93E-09 8.533285956 -0.295647283 TGS(ph)ESSQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 T(0.47)GS(0.53)ESSQTGTSTTSSR;T(0.049)GS(0.949)ES(0.002)SQTGTSTTSSR ; 220.72 8.85E-35 4552500 1190.05 1099.79 925.5 593.74 518.606 496.656 782.49 721.19 1145.94 1130.41 TRUE FALSE FALSE 1175.545213 1115.272872 941.6079393 662.3910124 492.1396006 464.9212845 848.9546811 742.0564948 1043.444256 1101.041785 1.067666304 1.012925111 0.855197279 0.601603882 0.446976316 0.422255804 0.771046742 0.673958523 0.947688153 1 10.10465351 -9.441431942 2.430295048 1.031615884 0.574131086 0.804095951 0.099090963 0.089840946 1.044379018 0.016477875 0.026136747 3.62E-10 9.441431942 -0.457484798 TGS(ph)NISGASSDISLDEQYK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 T(0.144)GS(0.756)NIS(0.1)GASSDISLDEQYK 182.98 1.47E-10 10149000 1163.4 1031.7 908.29 589.91 874.22 1214 1048 1374.3 1090.2 1259.3 TRUE FALSE FALSE 1149.220033 1046.2243 924.0984064 658.1181698 829.6052912 1136.429318 1137.017094 1414.063202 992.6897815 1226.583204 0.936927906 0.852958279 0.753392353 0.536545884 0.67635468 0.926499983 0.926979181 1.152847354 0.80931304 1 10.26042939 -10.33475311 2.294535767 0.974715977 0.81709458 0.016697204 0.163673353 0.428035542 4.261336422 0.030461733 0.035145045 4.63E-11 10.33475311 -0.157621398 TGS(ph)PGSPGAGGVQSTAK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSPGSPGAGGVQSTAK 17 0 J3KRZ2;O43237-2;O43237;J3KRI4 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 T(0.085)GS(0.521)PGS(0.393)PGAGGVQSTAK 216.71 7.49E-27 18532000 4031.1 3791.5 3994.7 3767.4 4736.3 4285.7 3596.2 3682.5 4083 3922.8 TRUE FALSE FALSE 3981.967403 3844.876837 4064.226078 4203.004514 4494.588937 4011.857601 3901.661138 3789.047327 3717.806254 3820.88509 1.042158376 1.006279107 1.063687073 1.100008091 1.17632141 1.049981223 1.021140664 0.991667438 0.973022262 1 11.89969116 -10.78066334 0.698884052 1.007918338 1.066124826 0.230375713 0.050170889 0.827229021 0.897957611 0.017885188 0.014742904 1.66E-11 10.78066334 0.058206488 TGS(ph)SSSILSASSESSEK ddPTM_HeLa_Romidepsin_16h_R1 2 TGSSSSILSASSESSEK 17 0 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 T(0.029)GS(0.969)S(0.002)SSILSASSESSEK;T(0.217)GS(0.724)S(0.058)S(0.001)SILSASSESSEK ; 216.71 3.72E-31 5475700 2415.89 2096.35 2442.77 2361.04 2821 2869.09 2705.24 2401.72 2621.37 2336.08 TRUE FALSE FALSE 2386.444203 2125.86247 2485.285387 2634.034554 2677.033843 2685.764409 2935.023018 2471.209979 2386.908102 2275.388305 1.048807449 0.934285575 1.092246709 1.1576198 1.176517361 1.180354317 1.289899843 1.086060772 1.049011326 1 11.15189705 -9.368228274 2.664488617 1.016944916 1.187101608 0.665937263 0.056218334 0.117912358 1.628935613 0.008309968 0.013401709 4.28E-10 9.368228274 0.170156692 TGS(ph)YGALAEITASK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSYGALAEITASK 14 0 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4;H0YHI8 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 T(0.047)GS(0.953)YGALAEITASK 115.26 0.004789 215900000 3562.8 3482.1 3206.5 3225.8 3452.7 3287.6 3169.7 2771.3 3314.6 3621.4 TRUE FALSE FALSE 3519.375223 3531.121095 3262.307787 3598.782174 3276.495835 3077.53297 3438.934239 2851.483193 3018.133874 3527.315506 0.997748916 1.001078891 0.924869857 1.020260923 0.928892193 0.872485879 0.974943759 0.808400379 0.855646134 1 11.78435491 -4.799611516 0.337566508 1.002505192 9.52E-15 0.188959243 0.062164926 14.75887977 0.309268962 0.011823915 8.592739248 1.59E-05 4.799611516 -1.002505192 TGSEPALS(ph)PAVVR ddPTM_HeLa_Romidepsin_16h_R1 4 TGSEPALSPAVVR 13 0 O75815;O75815-2;O75815-3 O75815 BCAR3 Breast cancer anti-estrogen resistance protein 3 1 0 T(0.001)GSEPALS(0.999)PAVVR;TGSEPALS(1)PAVVR;TGSEPALS(1)PAVVR;TGSEPALS(1)PAVVR ;;; 172.58 5.77E-05 214307000 14351.7 16112.7 13096.4 12725.7 10910.9 9020.7 7070.9 8568.2 15281.6 14730 TRUE FALSE FALSE 14176.77596 16339.53501 13324.33735 14197.10531 10354.07606 8444.306383 7671.50207 8816.107349 13914.77542 14347.31248 0.988113696 1.138856844 0.928699181 0.989530641 0.721673559 0.588563635 0.534699588 0.614477963 0.969852399 1 13.8084929 -8.618059121 2.247508542 1.003070929 0.572543034 0.926281459 0.054618864 0.051556791 0.525131287 0.007669117 0.017832682 2.41E-09 8.618059121 -0.430527895 ENQPENSQT(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 2 ENQPENSQTPTK 12 0 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 0 ENQPENS(0.001)QT(0.971)PT(0.028)K;ENQPENSQT(0.5)PT(0.5)K ; 217.19 3.91E-21 10021100 5049.3 5153.8 6147.2 4260.3 3827.5 2738.5 2825.7 1385.65 6284.1 5586.8 TRUE FALSE FALSE 4987.757189 5226.355332 6254.189437 4752.895931 3632.168393 2563.518688 3065.714887 1425.741597 5722.034357 5441.654131 0.916588425 0.960435045 1.149317705 0.873428523 0.667475055 0.471091809 0.563379225 0.262005185 1.051524816 1 12.40982955 -8.559548516 1.764185838 0.973969412 0.427736618 0.879084276 0.094622305 0.087851197 0.542432744 0.01380202 0.036398991 2.76E-09 8.559548516 -0.546232794 down TGSESS(ph)QTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 TGS(0.001)ES(0.08)S(0.919)QT(0.001)GTSTTSSR 257.37 5.56E-72 34874000 421.53 467.89 513.24 410.66 373.61 356.01 405.3 171.85 437.72 415.28 TRUE FALSE FALSE 416.3922302 474.4769677 522.1727269 458.1424414 354.5432876 333.26211 439.7261719 176.8222086 398.5692269 404.4909657 1.029422819 1.173022411 1.290937922 1.132639491 0.876517197 0.823904953 1.087109995 0.437147486 0.985360022 1 8.65996367 -7.258252376 24.82602937 1.032983814 0.437147243 0.659674698 0.130604922 137.0533705 1067556.289 0.018956589 0.18024295 5.52E-08 7.258252376 -0.595836571 TGSGSPFAGNS(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 1 TGSGSPFAGNSPAR 14 0 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 0 TGSGSPFAGNS(1)PAR 146.27 0.00061783 77575000 2004 1809.2 1971.8 1261 1419.5 1173.6 787.71 1275.5 2139.9 2161.3 TRUE FALSE FALSE 1979.574477 1834.669965 2006.118352 1406.802753 1347.057618 1098.610748 854.6180677 1312.40458 1948.501985 2105.149114 0.940348816 0.871515444 0.952957839 0.668267508 0.639887032 0.521868375 0.405965574 0.623425947 0.925588582 1 11.03970671 -9.031787158 1.110243323 0.970793509 0.500216685 0.884682308 0.067105853 0.094965343 0.231055105 0.010523473 0.024884758 9.29E-10 9.031787158 -0.470576824 TGSGSPFAGNS(ph)PAREGEQDAASLKDVFK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSGSPFAGNSPAREGEQDAASLKDVFK 28 2 M0QY97;Q9UPT8 M0QY97 ZC3H4 Zinc finger CCCH domain-containing protein 4 1 0 T(0.001)GS(0.003)GS(0.043)PFAGNS(0.951)PAREGEQDAAS(0.001)LKDVFK 54.263 0.0031547 23764000 1465.1 1136.2 1176.6 1822 933.19 772.76 683.12 761.74 1416.6 1243.6 TRUE FALSE FALSE 1447.242798 1152.195453 1197.078229 2032.668213 885.5658321 723.38313 741.1441957 783.7797451 1289.895748 1211.291093 1.194793561 0.951212686 0.988266352 1.67810052 0.731092499 0.597200074 0.611862995 0.647061429 1.064893283 1 10.24232989 -8.545301337 24.99669546 1.114153941 0.625710527 0.61053398 0.195921981 117.5576719 131052.775 0.027838999 0.055680871 2.85E-09 8.545301337 -0.488443414 TGSKDSS(ph)T(ph)QT(ph)DK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSKDSSTQTDK 12 1 Q8IY63-2;Q8IY63 Q8IY63-2 AMOTL1 Angiomotin-like protein 1 3 0 T(0.004)GS(0.004)KDS(0.589)S(0.701)T(0.701)QT(1)DK 81.278 0.0034394 0 1745.7 1453.5 1338 1395.5 1465.6 1247.3 1049.1 1373.6 1779.2 1562.5 TRUE FALSE FALSE 1724.422737 1473.962411 1361.287329 1556.854276 1390.804963 1167.601555 1138.210528 1413.342949 1620.063896 1521.906025 1.133067817 0.968497652 0.894462146 1.022963475 0.913857321 0.767196881 0.747884895 0.928666374 1.06449667 1 10.57166356 -8.981855535 0.860432154 1.05740956 0.806654362 0.571213042 0.075674871 0.331267557 0.471901215 0.01557787 0.044474163 1.04E-09 8.981855535 -0.250755198 TGSNIS(ph)GASSDISLDEQYK ddPTM_HeLa_Romidepsin_16h_R1 3 TGSNISGASSDISLDEQYK 19 0 P22059 P22059 OSBP Oxysterol-binding protein 1 1 0 T(0.017)GS(0.017)NIS(0.959)GAS(0.005)S(0.002)DISLDEQYK;TGSNIS(0.939)GAS(0.02)S(0.039)DIS(0.001)LDEQYK;T(0.288)GS(0.288)NIS(0.393)GAS(0.028)S(0.001)DIS(0.002)LDEQYK ;; 270.73 1.26E-90 42147500 6389 6043.36 6353.6 4271.73 7336.7 8134.8 6884.9 8393.2 7041.4 6637.1 TRUE FALSE FALSE 6311.128411 6128.438581 6464.181743 4765.647522 6962.280822 7615.012534 7469.703234 8636.044 6411.599548 6464.667185 0.976249547 0.947989804 0.999924908 0.737183738 1.076974363 1.177943476 1.155466016 1.335883774 0.991791126 1 12.65836038 -8.338028249 3.069060381 0.968973944 1.223111995 0.66063278 0.088546589 0.125871846 2.302305696 0.01242669 0.031377916 4.59E-09 8.338028249 0.254138051 TGSPGS(ph)PGAGGVQSTAK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSPGSPGAGGVQSTAK 17 0 J3KRZ2;O43237-2;O43237;J3KRI4 J3KRZ2 DYNC1LI2 Cytoplasmic dynein 1 light intermediate chain 2 1 0 TGSPGS(0.996)PGAGGVQS(0.004)TAK 181.86 4.45E-09 4297500 1873.5 1745.4 1982.5 1938.7 1919.6 2002.9 2019.6 1882.9 2041.4 1940.3 TRUE FALSE FALSE 1850.665061 1769.971787 2017.004581 2162.861616 1821.635649 1874.921154 2191.144774 1937.378741 1858.812071 1889.890726 0.97924448 0.936547157 1.067259896 1.144437393 0.963884114 0.992079133 1.159402892 1.025127386 0.983555316 1 10.8840871 -9.73908632 24.99550526 0.98590105 1.059835293 0.31998286 0.059002472 238.6731115 266887.234 0.009125958 0.012900386 1.82E-10 9.73908632 0.073934242 TGSS(ph)PTQGIVNK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSSPTQGIVNK 12 0 E9PFH7;A0A087WYG2;A0A669KB35;Q9UPT6 E9PFH7 MAPK8IP3 C-Jun-amino-terminal kinase-interacting protein 3 1 0 T(0.004)GS(0.028)S(0.96)PT(0.008)QGIVNK 99.732 0.0032301 0 1086.9 1073.4 1251.3 843.99 1442.2 1657.4 1559.6 1611.2 1383.6 1434.2 TRUE FALSE FALSE 1073.652445 1088.511353 1273.078352 941.5760949 1368.599152 1551.497489 1692.072385 1657.81753 1259.847351 1396.939277 0.768574885 0.779211646 0.911334066 0.674027934 0.979712701 1.110640609 1.21127125 1.186749887 0.901862644 1 10.4480536 -8.286230434 2.683544275 0.866429628 1.188708659 0.725231357 0.090108293 0.143293604 2.030184765 0.016352211 0.044600754 5.17E-09 8.286230434 0.322279031 TGSSS(ph)PPGGPPKPGSQLDSMLGSLQSDLNK ddPTM_HeLa_Romidepsin_16h_R1 2 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 A0A1B0GTU4;F5GZ78;P49023;P49023-2;P49023-3;P49023-4 A0A1B0GTU4 PXN Paxillin 1 0 T(0.064)GS(0.072)S(0.186)S(0.471)PPGGPPKPGS(0.149)QLDS(0.045)MLGS(0.012)LQSDLNK;T(0.019)GS(0.008)S(0.213)S(0.671)PPGGPPKPGS(0.057)QLDS(0.019)MLGS(0.013)LQSDLNK ; 56.374 0.0022226 221390000 4833.6 4599 4807.4 4663.8 4871.6 4415.9 4316 4630.5 5591 4835.4 TRUE FALSE FALSE 4774.686224 4663.744843 4891.07078 5203.0505 4622.984074 4133.738242 4682.600932 4764.476212 5090.926957 4709.775611 1.013782103 0.990226548 1.038493377 1.104734265 0.981572044 0.877693246 0.994230154 1.011614269 1.080927708 1 12.20144261 -8.529592558 24.99657915 1.015269332 0.958675694 0.281586656 0.049337235 176.0841243 655587.5989 0.006563871 0.013152085 2.95E-09 8.529592558 -0.056593638 TGSSSPPGGPPKPGS(ph)QLDSMLGSLQSDLNK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 A0A1B0GTU4;F5GZ78;P49023;P49023-2;P49023-3;P49023-4 A0A1B0GTU4 PXN Paxillin 1 0 T(0.009)GS(0.033)S(0.132)S(0.124)PPGGPPKPGS(0.545)QLDS(0.123)MLGS(0.031)LQS(0.004)DLNK 42.347 0.017967 35846000 3190.2 3127.7 3051.4 2715.9 3047.4 2793.3 2592 2830.1 3392.3 2977.7 TRUE FALSE FALSE 3151.316615 3171.731843 3104.508337 3029.925137 2891.879807 2614.817145 2812.164415 2911.984478 3088.884192 2900.338925 1.086533918 1.093572829 1.070395018 1.044679679 0.997083404 0.901555719 0.96959855 1.004015239 1.065008012 1 11.50200578 -8.613577554 3.731613687 1.048890102 0.958073208 0.628640305 0.034825604 0.153530076 4.141270108 0.006473544 0.013621892 2.43E-09 8.613577554 -0.090816894 TGSSSPPGGPPKPGSQLDS(ph)MLGSLQSDLNK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSSSPPGGPPKPGSQLDSMLGSLQSDLNK 30 1 A0A1B0GTU4;F5GZ78;P49023;P49023-2;P49023-3;P49023-4 A0A1B0GTU4 PXN Paxillin 1 0 T(0.005)GS(0.005)S(0.016)S(0.019)PPGGPPKPGS(0.403)QLDS(0.53)MLGS(0.02)LQS(0.001)DLNK 63.291 0.00075052 260520000 3998.7 4014.1 4345.7 4443.8 4414.8 4494.9 4024.6 4116.7 4381.6 3974 TRUE FALSE FALSE 3949.962306 4070.610605 4421.335086 4957.613065 4189.496282 4207.690397 4366.449424 4235.810219 3989.698722 3870.754907 1.020463037 1.051632228 1.142241034 1.280787129 1.082346049 1.087046454 1.128061458 1.094311141 1.030728842 1 11.91839924 -9.915306332 3.282472332 1.010292394 1.137279496 0.507515296 0.053699555 0.140973972 3.058169306 0.009067345 0.012067651 1.22E-10 9.915306332 0.126987102 TGST(ph)SSKEDDYESDAATIVQK ddPTM_HeLa_Romidepsin_16h_R1 1 TGSTSSKEDDYESDAATIVQK 21 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 T(0.115)GS(0.047)T(0.624)S(0.153)S(0.054)KEDDY(0.005)ES(0.001)DAATIVQK 63.639 0.0071312 22473000 2036.3 1834.9 1588.8 1690 2188.1 2565.4 1984.1 2647.7 1672.3 1671.8 TRUE FALSE FALSE 2011.480792 1860.73177 1616.452398 1885.405752 2076.433092 2401.479219 2152.629404 2724.307022 1522.7253 1628.366395 1.235275303 1.142698459 0.992683466 1.157851057 1.275163316 1.474778175 1.321956417 1.673030732 0.935124493 1 10.66920964 -4 0.326545166 1.080279787 6.71975722 0.76237012 0.106228594 20.97984817 0.26676017 0.03657033 72.13347753 1.00E-04 4 5.639477433 TGSVQTPPDLES(ph)SEEVDAAEGAPEVVGPK ddPTM_HeLa_Romidepsin_16h_R1 2 TGSVQTPPDLESSEEVDAAEGAPEVVGPK 29 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 TGSVQT(0.002)PPDLES(0.499)S(0.499)EEVDAAEGAPEVVGPK;TGSVQT(0.001)PPDLES(0.499)S(0.499)EEVDAAEGAPEVVGPK ; 73.299 2.55E-05 23945000 10195.9 9668.8 9715.4 8344.3 6285.8 5979.8 5240.9 5683.6 11160.8 10029.9 TRUE FALSE FALSE 10071.62845 9804.91762 9884.492462 9309.107227 5965.01217 5597.710079 5686.061915 5848.045999 10162.5501 9769.321752 1.030944492 1.003643638 1.011789018 0.952891865 0.61058611 0.572988609 0.582032413 0.598613307 1.040251345 1 13.25404269 -8.786018747 3.7683505 1.01278265 0.583311252 0.995613186 0.013572679 0.010613781 0.322319138 0.00222936 0.004366696 1.64E-09 8.786018747 -0.429471399 TGT(ph)PSDPRR ddPTM_HeLa_Romidepsin_16h_R1 1 TGTPSDPRR 9 1 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 T(0.309)GT(0.684)PS(0.007)DPRR 77.288 0.027809 1974200 1270.1 1355.3 1631.4 1633 1304.4 1294 1873.4 623.49 1914.5 1695.6 TRUE FALSE FALSE 1254.619533 1374.379949 1659.793833 1821.815143 1237.831601 1211.317576 2032.526549 641.5296994 1743.262325 1651.548068 0.759662741 0.832176778 1.004992749 1.103095441 0.749497774 0.733443731 1.230679621 0.388441434 1.055532297 1 10.68960324 -7.234171005 24.32688933 0.900979896 0.388440399 0.491129544 0.164250522 4592.098498 4096654.581 0.022000379 2.54383907 5.83E-08 7.234171005 -0.512539497 TGTIVVEGHELHDEDIR ddPTM_HeLa_Romidepsin_16h_R1 4 TGTIVVEGHELHDEDIR 17 0 J3KR24;A0A0A0MSX9;P41252 J3KR24 IARS "Isoleucine--tRNA ligase, cytoplasmic" 0 0 ;;; ;;; 115.58 0.00080842 17491000 11036.8 11124.8 10779.2 10496.3 11184.4 10696.6 10068.7 10287 11701.4 9853.2 FALSE FALSE TRUE 10902.27924 11281.41523 10966.80745 11709.93159 10613.61833 10013.12178 10923.93513 10584.63811 10654.79748 9597.212444 1.135983943 1.175488747 1.142707585 1.220138833 1.105906366 1.043336473 1.13824042 1.102886716 1.110197106 1 13.22839971 -12.06660946 0.853633988 1.000190129 1.133421598 0.138720857 0.054914008 0.371730911 0.493274192 0.030593228 0.009248675 8.58E-13 12.06660946 0.133231469 TGVAVNKPAEFTVDAK ddPTM_HeLa_Romidepsin_16h_R1 2 TGVAVNKPAEFTVDAK 16 1 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 112.96 0.0015784 2889000 1454.03 956.52 1198.62 907.87 1442.63 1490.61 939.84 1005.2 1267.49 1214.14 FALSE FALSE TRUE 1436.307723 969.9859137 1219.481478 1012.842201 1369.007208 1395.364832 1019.669986 1034.283876 1154.12252 1182.596468 1.214537471 0.820217158 1.031189853 0.856456305 1.157628359 1.179916286 0.862229859 0.874587321 0.975922516 1 10.20774216 -10.27470207 24.97747683 1.101309356 0.978234458 0.072205389 0.133591639 1145.277492 2156882.601 0.024173748 0.027730303 5.31E-11 10.27470207 -0.123074898 TGVAVNKPAEFTVDAK(ac)HGGK ddPTM_HeLa_Romidepsin_16h_R1 2 TGVAVNKPAEFTVDAKHGGK 20 2 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 1 ; TGVAVNKPAEFTVDAK(1)HGGK;TGVAVNKPAEFTVDAK(1)HGGK 81.639 0.00099285 6686400 6250.1 5131.7 5565.1 3638.6 6647.4 7146.7 5499.5 6149.9 6016.3 5429.4 FALSE TRUE FALSE 6173.921377 5203.944207 5661.958231 4059.312052 6308.158373 6690.048935 5966.627393 6327.837654 5478.18706 5288.343405 1.167458484 0.984040522 1.070648745 0.767596153 1.192842047 1.265055694 1.128260201 1.196563303 1.035898511 1 12.36860015 -8.586730327 24.99999468 1.04992472 1.196335908 0.406052754 0.105042757 61.57921239 24109.78465 0.016628306 0.033256616 2.59E-09 8.586730327 0.146411188 TGVLLPSSPEAEVPGKLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TGVLLPSSPEAEVPGKLSPK 20 1 O60285 O60285 NUAK1 NUAK family SNF1-like kinase 1 1 0 TGVLLPS(0.001)S(0.001)PEAEVPGKLS(0.998)PK;TGVLLPS(0.265)S(0.265)PEAEVPGKLS(0.471)PK ; 63.979 0.0061077 19119800 5410 4754 5561.7 6240.9 1993.7 1663.93 1382.89 1660.39 5144.3 5490.8 TRUE FALSE FALSE 5344.060839 4820.926937 5658.499055 6962.502222 1891.954049 1557.610243 1500.352642 1708.430765 4684.180924 5348.148224 0.999235738 0.901419844 1.058029587 1.30185289 0.353758716 0.291242908 0.280536847 0.319443421 0.875850991 1 12.38482374 -8.7100938 9.108881478 1.015052758 0.305402146 0.910076979 0.109551347 0.061317908 10.17029545 0.014336295 0.028653962 1.95E-09 8.7100938 -0.709650612 TGVPST(ph)ASVGK ddPTM_HeLa_Romidepsin_16h_R1 1 TGVPSTASVGK 11 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 T(0.001)GVPS(0.14)T(0.739)AS(0.12)VGK 123.26 0.017704 40255000 7143.1 6819.7 6765.3 5251.8 4442 3332.2 2815.6 3637.8 6049 5900.4 TRUE FALSE FALSE 7056.03715 6915.707916 6883.047209 5859.037826 4215.308165 3119.283174 3054.756994 3743.054004 5507.96229 5747.106757 1.227754668 1.203337298 1.197654315 1.019476073 0.733466132 0.542757131 0.531529537 0.651293627 0.95838872 1 12.48862013 -8.709139032 2.412377025 1.125145988 0.573335093 0.885748489 0.087378896 0.073815612 0.874374168 0.015037826 0.032689544 1.95E-09 8.709139032 -0.551810895 TGVPSTAS(ph)VGK ddPTM_HeLa_Romidepsin_16h_R1 1 TGVPSTASVGK 11 0 E9PHV5;P28290-3;P28290;P28290-2;E7EUL7;H7BZ26 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 TGVPS(0.058)T(0.026)AS(0.916)VGK 108.32 0.015342 38353000 8470.6 8071.9 7843.9 5835.1 5258.3 4170.2 3804.2 4398.6 7708.7 7223.3 TRUE FALSE FALSE 8367.357069 8185.53642 7980.419789 6509.781717 4989.94933 3903.737679 4127.328653 4525.866551 7019.214565 7035.637625 1.189281983 1.163439173 1.134285223 0.925258244 0.709239105 0.55485201 0.586631784 0.643277382 0.997665733 1 12.78046546 -8.826312235 2.119129218 1.101236549 0.595746677 0.924889278 0.064089261 0.07019909 0.641988043 0.012350817 0.026055612 1.49E-09 8.826312235 -0.505489873 TGVSPGDVS(ph)DSATSDSTK ddPTM_HeLa_Romidepsin_16h_R1 2 TGVSPGDVSDSATSDSTK 18 0 Q5T5U3;A0A087WW76;A0A452Q6Z5 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 TGVSPGDVS(0.697)DS(0.302)ATSDSTK;TGVSPGDVS(0.943)DS(0.056)AT(0.001)SDSTK ; 238.45 1.84E-49 12556600 5415.5 5448.9 5401.1 4623.3 4248.6 3178.6 2383.2 3450.5 5983.1 5522.6 TRUE FALSE FALSE 5349.493803 5525.609757 5495.10388 5157.867699 4031.778088 2975.497718 2585.628949 3550.334774 5447.956551 5379.122056 0.994491991 1.027232641 1.021561478 0.958867943 0.749523444 0.553156758 0.480678617 0.660021233 1.012796604 1 12.39315501 -8.585147473 2.228037498 1.001798665 0.554692926 0.954492433 0.043358314 0.039764594 0.396192553 0.006051306 0.014385062 2.60E-09 8.585147473 -0.447105739 TGVT(ph)STSDS(ph)EEEGDDQEGEKK ddPTM_HeLa_Romidepsin_16h_R1 1 TGVTSTSDSEEEGDDQEGEKK 21 1 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 2 0 T(0.001)GVT(0.343)S(0.297)T(0.262)S(0.262)DS(0.835)EEEGDDQEGEKK 88.551 0.00014173 0 1234.2 1313.6 1209.2 1247.3 1421 1193.2 1019.3 1003.4 1245.1 1343.1 TRUE FALSE FALSE 1219.157096 1332.092895 1230.245619 1391.518695 1348.481068 1116.958371 1105.879317 1032.431796 1133.735138 1308.206068 0.93193047 1.018259223 0.940406598 1.063684635 1.030786434 0.853809196 0.845340305 0.789196611 0.866633449 1 10.3533741 -8.132679602 4.835204951 0.97976908 0.824504639 0.612108613 0.054822799 0.096840976 3.386373758 0.006595081 0.017526197 7.37E-09 8.132679602 -0.155264442 TGVTST(ph)SDSEEEGDDQEGEKKR ddPTM_HeLa_Romidepsin_16h_R1 1 TGVTSTSDSEEEGDDQEGEKKR 22 2 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 1 0 T(0.001)GVT(0.013)S(0.051)T(0.458)S(0.458)DS(0.018)EEEGDDQEGEKKR 61.096 0.0037573 4939200 2253.1 2284.4 2007.3 2281.8 1747.4 2047.9 1938.7 1754.2 2611.6 2128 TRUE FALSE FALSE 2225.638351 2316.559843 2042.236214 2545.632452 1658.223658 1917.045799 2103.37313 1804.955009 2378.011955 2072.714253 1.073779633 1.117645541 0.985295591 1.228163722 0.800025211 0.924896327 1.014791656 0.870817097 1.147293676 1 11.01730552 -8.743569679 24.99999596 1.050506051 0.912234255 0.492195093 0.08818585 189.5040492 265117.8912 0.011681062 0.023323441 1.80E-09 8.743569679 -0.138271796 TGVTSTS(ph)DS(ph)EEEGDDQEGEK ddPTM_HeLa_Romidepsin_16h_R1 1 TGVTSTSDSEEEGDDQEGEK 20 0 O75475;O75475-3;O75475-2 O75475 PSIP1 PC4 and SFRS1-interacting protein 2 0 T(0.002)GVT(0.003)S(0.02)T(0.142)S(0.863)DS(0.969)EEEGDDQEGEK 130.52 0.0015917 18624000 2779.7 2709.1 3092.2 2319 3091.7 2730.2 2591.2 2788.2 3542.1 3028.6 TRUE FALSE FALSE 2745.819947 2747.238781 3146.018444 2587.133691 2933.919012 2555.749031 2811.296463 2868.872168 3225.285705 2949.916535 0.930812758 0.931293733 1.066477104 0.877019285 0.994576957 0.866380116 0.953008816 0.972526556 1.093348122 1 11.52645842 TGYES(ph)GEYEMLGEGLGVK ddPTM_HeLa_Romidepsin_16h_R1 1 TGYESGEYEMLGEGLGVK 18 0 H0YHL1;F8VX93;F8VRV7;F8VW18;F8W1I6;Q13561;Q13561-3;Q13561-2 H0YHL1 DCTN2 Dynactin subunit 2 1 0 T(0.002)GYES(0.998)GEYEMLGEGLGVK 155.1 9.80E-06 7488200 2122.2 2257.2 2054.9 2037.9 2983.6 3613.5 2935.3 3612.1 2397.2 2091.5 TRUE FALSE FALSE 2096.33381 2288.976921 2090.664673 2273.531587 2831.335759 3382.609012 3184.624309 3716.610415 2182.788428 2037.162528 1.029045931 1.123610359 1.026263071 1.116028572 1.389842842 1.660451223 1.56326472 1.824405448 1.071484674 1 10.99234537 -8.542663997 1.37770156 1.020905194 1.712810574 0.944954194 0.067755844 0.058980973 0.217523148 0.009553074 0.029217913 2.87E-09 8.542663997 0.691905379 TGYESGEY(ph)EMLGEGLGVK ddPTM_HeLa_Romidepsin_16h_R1 1 TGYESGEYEMLGEGLGVK 18 0 H0YHL1;F8VX93;F8VRV7;F8VW18;F8W1I6;Q13561;Q13561-3;Q13561-2 H0YHL1 DCTN2 Dynactin subunit 2 1 0 TGYES(0.03)GEY(0.97)EMLGEGLGVK 145.14 0.0011235 9067500 1890.6 1659.2 1478.5 1680.1 2229.2 2778.9 2654.5 2240 1914.2 1587 TRUE FALSE FALSE 1867.55664 1682.558261 1504.232672 1874.361067 2115.435606 2601.337258 2879.973164 2304.810866 1742.989158 1545.769511 1.208172775 1.088492333 0.973128698 1.212574743 1.368532366 1.682875254 1.863132338 1.49104433 1.12758671 1 10.5941095 -8.532862852 1.989079675 1.092700695 1.703736238 0.85282681 0.107981494 0.092876368 0.728402478 0.01761682 0.045018693 2.93E-09 8.532862852 0.611035543 THAVS(ph)VSETDDYAEIIDEEDTYTMPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 H0YBP1;E7ESA6;Q05397-2;Q05397-7;Q05397;Q05397-5;H0YB33;H0YB99;Q05397-4;Q05397-3 H0YBP1 PTK2 Focal adhesion kinase 1 1 0 T(0.03)HAVS(0.863)VS(0.095)ET(0.012)DDY(0.001)AEIIDEEDTYTMPSTR 70.154 4.72E-05 2729700 906.42 1052.6 968.07 1107.5 1068.1 1215.5 1184.9 1388 1266.5 1065.5 TRUE FALSE FALSE 895.3722044 1067.41853 984.9188523 1235.554361 1013.590871 1137.833473 1285.545376 1428.15959 1153.221068 1037.818156 0.862744787 1.028521735 0.94902835 1.190530685 0.976655559 1.096370752 1.238700025 1.376117368 1.111197623 1 10.01933797 -5.754194985 0.432726362 0.939691604 2.895563013 0.595271096 0.092262735 5.845622078 0.273342344 0.019016648 7.86938241 1.76E-06 5.754194985 1.955871409 THAVSVSETDDY(ph)AEIIDEEDTYTMPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 THAVSVSETDDYAEIIDEEDTYTMPSTR 28 0 H0YBP1;E7ESA6;Q05397-2;Q05397-7;Q05397;Q05397-5;H0YB33;H0YB99;Q05397-4;Q05397-3 H0YBP1 PTK2 Focal adhesion kinase 1 1 0 THAVSVS(0.005)ET(0.105)DDY(0.889)AEIIDEEDTYTMPSTR 62.069 0.00052215 3073000 531.81 518.49 362.54 520.08 520.37 457.11 325.73 370.18 766.07 665.15 TRUE FALSE FALSE 525.3280952 525.7893158 368.8498566 580.2140966 493.8135771 427.9021463 353.3974981 380.8905743 697.5507805 647.8693071 0.810855043 0.811566947 0.569327567 0.895572749 0.762211717 0.660476027 0.545476525 0.58791267 1.076684407 1 9.339559001 -8.285845143 0.084892834 1.34721013 1.73E-14 0.719949427 0.091960647 19.98118833 0.407763376 2.102673686 4.618261822 5.18E-09 8.285845143 -1.34721013 THDHQLES(ph)SLSPVEVFAK ddPTM_HeLa_Romidepsin_16h_R1 1 THDHQLESSLSPVEVFAK 18 0 Q5JW53;Q9H410-4;Q9H410 Q5JW53 DSN1 Kinetochore-associated protein DSN1 homolog 1 0 THDHQLES(0.556)S(0.183)LS(0.261)PVEVFAK 70.959 0.0094762 9092600 1542.1 1467 1436.7 1483 1732.6 1671.9 1319.4 1341.9 1945.4 1370.9 TRUE FALSE FALSE 1523.304292 1487.652465 1461.705161 1654.471438 1644.178957 1565.070986 1431.469803 1380.725759 1771.398552 1335.28382 1.140809369 1.114109556 1.094677505 1.239041028 1.231332943 1.172088632 1.072034111 1.03403167 1.326608265 1 10.38293071 -12.14193436 0.635370737 0.985986779 1.143497437 0 0.119034999 0.81209092 0.518308422 0.071268571 0.015033192 7.21E-13 12.14193436 0.157510658 THEVVGSSLLFVHDHT(ph)GLAK ddPTM_HeLa_Romidepsin_16h_R1 1 THEVVGSSLLFVHDHTGLAK 20 0 Q96DU7 Q96DU7 ITPKC Inositol-trisphosphate 3-kinase C 1 0 THEVVGSSLLFVHDHT(1)GLAK 55.988 0.026026 6594700 2168.4 1400.9 1543.1 1872.7 1656.7 1719.2 1782.7 1957.4 1911.3 1864 TRUE FALSE FALSE 2141.970707 1420.621907 1569.957008 2089.230385 1572.152417 1609.348668 1934.122494 2014.034281 1740.348541 1815.573011 1.179776684 0.782464764 0.864717088 1.150727827 0.865926298 0.886413633 1.065295905 1.109310542 0.958567092 1 10.82620923 -10.29067553 24.99529836 1.084894537 0.961832592 0.0644544 0.125217592 934.7248239 799134.9452 0.022001133 0.025161284 5.12E-11 10.29067553 -0.123061945 THFDYQFGYR ddPTM_HeLa_Romidepsin_16h_R1 1 THFDYQFGYR 10 0 Q6PKG0;A0A0B4J210;Q6PKG0-3;E5RH50 Q6PKG0 LARP1 La-related protein 1 0 0 92.239 0.016572 6601100 1775.2 1528.8 1583 1195.1 1632 1408.7 1403.5 1229.5 1428.8 1450.2 FALSE FALSE TRUE 1753.56318 1550.322487 1610.551451 1333.283085 1548.71295 1318.688616 1522.713255 1265.073643 1301.00455 1412.523595 1.241439921 1.097555108 1.14019437 0.943901461 1.096415632 0.933569266 1.078009076 0.895612397 0.921049782 1 10.46405925 -9.2704893 24.82687832 1.117198232 0.99725097 0.115169422 0.101068169 648.6561024 1779474.178 0.015671922 0.024154146 5.36E-10 9.2704893 -0.119947262 THGFTLES(ph)CRS(ph)MIALMDTDGSGK ddPTM_HeLa_Romidepsin_16h_R1 1 THGFTLESCRSMIALMDTDGSGK 23 1 A0A669KBE1;A0A669KB98;H3BUZ3;H3BV08;A0A669KAU6;H3BS77;A0A669KBA3;A0A669KAB9;A0A669KB08;H3BMH1;F8W8F5;P20807-5;P20807-4;P20807-2;P20807-3;P20807 A0A669KBE1 CAPN3 Calpain-3 2 0 T(0.028)HGFT(0.08)LES(0.896)CRS(0.99)MIALMDT(0.004)DGS(0.001)GK 50.232 0.0037475 0 578.26 743.77 826.88 695.63 867.5 991.92 761.16 809.71 846.32 789.61 TRUE FALSE FALSE 571.2119447 754.2408136 841.2714995 776.0620136 823.2282379 928.5395133 825.8129114 833.1376813 770.6230196 769.0958184 0.742705826 0.980685105 1.093844849 1.009057643 1.070384493 1.207313174 1.073745159 1.08326903 1.00198571 1 9.587019538 -9.959752405 4.305247233 0.877552262 1.088451901 0.454583087 0.08383285 0.138533435 5.707989767 0.017294088 0.022651087 1.10E-10 9.959752405 0.21089964 THILLFLPK ddPTM_HeLa_Romidepsin_16h_R1 1 THILLFLPK 9 0 P07237;H7BZ94;I3L398;I3L312;I3L4M2 P07237 P4HB Protein disulfide-isomerase 0 0 80.239 0.01695 0 166.99 62.918 471.81 379.15 340.15 581.68 488.04 281.27 129.1 120.39 FALSE FALSE TRUE 164.9546616 63.80376126 480.0216551 422.989107 322.7908762 544.5125253 529.4941054 289.4081037 117.5529727 117.2622504 1.40671581 0.54411169 4.093573621 3.607206116 2.752726261 4.643544902 4.515469415 2.468041527 1.002479248 1 6.873594839 -9.758352286 24.99998308 1.148830433 3.716392592 0.789202581 0.679346723 26.57239111 215187.9234 0.104194171 0.143783834 1.74E-10 9.758352286 2.567562159 THINIVVIGHVDSGK ddPTM_HeLa_Romidepsin_16h_R1 2 THINIVVIGHVDSGK 15 0 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01;A6PW80;Q5JR01;A0A2R8Y488;A0A2U3TZH3;Q05639;A0A2R8Y660;A0A2R8YDN5 Q5VTE0;A0A2R8Y488 EEF1A1P5;EEF1A1;EEF1A2 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha;Elongation factor 1-alpha 2 0 0 ; ; 95.236 0.0066403 3383700 5095.7 4123.5 3379.7 3751.1 5858 6311.5 4837.1 5697.6 6304.4 5264.3 FALSE FALSE TRUE 5033.591648 4181.550741 3438.522261 4184.819831 5559.044401 5908.215519 5247.963153 5862.451067 5740.518674 5127.532727 0.981679087 0.815509323 0.670599769 0.816146879 1.084155811 1.152253108 1.023487013 1.143327869 1.119547935 1 12.32404908 -8.6271552 9.097903096 0.938892144 1.10133552 0.367518893 0.122843409 0.29197872 23.221115 0.018982114 0.038003533 2.36E-09 8.6271552 0.162443376 THNDIIHNENMR ddPTM_HeLa_Romidepsin_16h_R1 1 THNDIIHNENMR 12 0 E7EQR4;P15311 E7EQR4 EZR Ezrin 0 0 64.827 0.025736 1973000 355.74 414.43 419.44 524.45 759.29 579.21 492.2 825.27 516.82 502.3 FALSE FALSE TRUE 351.404104 420.2643564 426.7401773 585.0893766 720.540598 542.2003503 534.0074557 849.1478854 470.5943248 489.2501736 0.718250341 0.858996847 0.872233063 1.195889972 1.472744696 1.108227201 1.091481382 1.7356108 0.961868488 1 8.934428553 -9.176359267 3.490103189 0.862201766 1.317705516 0.587246829 0.185872175 0.140023522 3.271684263 0.029271597 0.049842029 6.66E-10 9.176359267 0.455503749 THS(ph)DASDDEAFTTSK ddPTM_HeLa_Romidepsin_16h_R1 2 THSDASDDEAFTTSK 15 0 H0YK04;Q13017-2;Q13017 H0YK04 ARHGAP5 Rho GTPase-activating protein 5 1 0 T(0.001)HS(0.931)DAS(0.069)DDEAFTTSK;THS(0.906)DAS(0.094)DDEAFTTSK ; 241.41 2.75E-46 11232700 3324.8 3128.6 2765 3482.5 2905.7 2523 2541.6 2709.2 3816.1 3291.5 TRUE FALSE FALSE 3284.276059 3172.644513 2813.123665 3885.163036 2757.411286 2361.788443 2757.483441 2787.586428 3474.778458 3205.986356 1.024419849 0.98960013 0.87745965 1.211846404 0.86008204 0.736680753 0.860104547 0.869494165 1.083840688 1 11.64655257 -8.546637035 24.99924967 1.012305305 0.821308744 0.557942412 0.086556262 116.8354261 122937.5894 0.011005095 0.022011013 2.84E-09 8.546637035 -0.190996561 THT(ph)T(ph)MSGVAHR ddPTM_HeLa_Romidepsin_16h_R1 1 THTTMSGVAHR 11 0 E7ENC1;F8WBI9;E9PEC3;E7ETT4;E7EUY3;E7ETT1;E9PDR0;C9JQS9;E7EX59;P05166;P05166-2 E7ENC1 PCCB "Propionyl-CoA carboxylase beta chain, mitochondrial" 2 0 T(0.125)HT(0.621)T(0.882)MS(0.372)GVAHR 84.507 0.025493 3769200 198.37 180.57 256.42 324.66 363.55 262.64 200.4 218.74 248.22 213.48 TRUE FALSE FALSE 195.9521901 183.1120692 260.8828825 362.1987168 344.9966869 245.8581516 217.421971 225.0688968 226.0185815 207.9337588 0.942377954 0.880626937 1.254644191 1.741894721 1.659166308 1.182386896 1.045630937 1.082406715 1.086973961 1 7.699980194 -9.650527769 5.39374436 0.965724275 1.349045135 0.389695004 0.216081331 0.167438065 7.357847433 0.036834757 0.052260641 2.24E-10 9.650527769 0.383320859 THTDS(ph)SEKELEPEAAEEALENGPK ddPTM_HeLa_Romidepsin_16h_R1 1 THTDSSEKELEPEAAEEALENGPK 24 1 Q9H3P7 Q9H3P7 ACBD3 Golgi resident protein GCP60 1 0 T(0.022)HT(0.022)DS(0.478)S(0.478)EKELEPEAAEEALENGPK 73.981 0.00016776 0 1178.3 1381.2 1123.3 686.15 1284 1347.2 926.61 1331 1548.4 1449.4 TRUE FALSE FALSE 1163.938426 1400.64457 1142.850565 765.4858914 1218.472689 1261.118268 1005.31623 1369.510385 1409.907226 1411.744379 0.824468256 0.992137522 0.809530806 0.54222698 0.863097248 0.893304968 0.71210925 0.970083823 0.998698664 1 10.46326317 -12.21584409 0.454276767 1.043626152 0.807939598 0.252007896 0.121140663 2.087043049 0.59032377 0.227989107 0.036452185 6.08E-13 12.21584409 -0.235686554 THTGEK(ac)PYR ddPTM_HeLa_Romidepsin_16h_R1 1 THTGEKPYR 9 1 Q8N8E2-2;Q8N8E2;Q9NX65;Q9UJW8-2;Q8WXB4;Q9UJW8-3;P52747-3;Q9UJW8;A0A087X2B0;P17017;M0QZI7;E7EN86;A0A1W2PQ54;G5E9B8;A0A0A0MP75;O94892;P52747;F5H032;Q9UJW8-4;P52747-2;Q99612;Q86UD4;Q86TJ5;Q7Z3I7;Q15937;Q9BSK1;Q9NX65-2;Q499Z4;Q9BSK1-2;Q9NX65-3;Q9HCG1 Q8N8E2-2 ZNF513;ZSCAN32;ZNF180;ZNF606;ZNF143;ZNF79;ZNF14;ZNF160;ZNF432;KLF6;ZNF329;ZNF554;ZNF572;ZNF577;ZNF672 Zinc finger protein 513;Zinc finger and SCAN domain-containing protein 32;Zinc finger protein 180;Zinc finger protein 606;Zinc finger protein 143;Zinc finger protein 14;Zinc finger protein 432;Krueppel-like factor 6;Zinc finger protein 329;Zinc finger protein 554;Zinc finger protein 572;Zinc finger protein 79;Zinc finger protein 577;Zinc finger protein 672;Zinc finger protein 160 0 1 THTGEK(1)PYR 140.11 0.0054341 2342700 420.84 441.11 242.39 299.09 251.79 362.13 319.4 203.14 491.5 343.25 FALSE TRUE FALSE 415.7106402 447.3199582 246.6086963 333.6721931 238.9402167 338.9910617 346.529828 209.0175354 447.539009 334.3323155 1.243405501 1.33795011 0.737615495 0.99802555 0.714678796 1.013934478 1.036483199 0.625178978 1.338605299 1 8.385138998 -9.751939551 24.99415419 1.13487874 0.870039621 0.518880845 0.167072585 159.0344682 418420.3906 0.025891289 0.036340429 1.77E-10 9.751939551 -0.264839119 THVADFAPEVAWVTR ddPTM_HeLa_Romidepsin_16h_R1 1 THVADFAPEVAWVTR 15 0 P07814 P07814 EPRS Bifunctional glutamate/proline--tRNA ligase;Glutamate--tRNA ligase;Proline--tRNA ligase 0 0 103.6 0.0030994 8908100 2073.4 1969 2080.1 1915.3 2327.2 2561.5 1872.5 2190.7 2398.1 2129.2 FALSE FALSE TRUE 2048.128603 1996.719634 2116.303268 2136.755998 2208.4343 2397.828417 2031.550103 2254.084448 2183.60793 2073.883077 0.987581521 0.962792771 1.020454476 1.030316521 1.064878886 1.156202316 0.979587579 1.086890806 1.052907926 1 11.01811884 -9.11496498 1.982472996 0.992110266 1.070541895 0.30964475 0.045947156 0.229846452 1.773061914 0.006196885 0.011561495 7.67E-10 9.11496498 0.078431629 TIAATPIQTLPQSQS(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 2 TIAATPIQTLPQSQSTPK 18 0 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 0 TIAATPIQTLPQSQS(0.672)T(0.328)PK;TIAATPIQTLPQSQS(0.669)T(0.33)PK ; 156 6.53E-06 43527000 9532.3 9934.9 9086 10367 9983.5 10494.6 8848.8 9654.1 9533.1 8779.6 TRUE FALSE FALSE 9416.116661 10074.76378 9244.138019 11565.68132 9474.004741 9824.02893 9600.416851 9933.426152 8680.43566 8551.504726 1.101106409 1.178127605 1.080995487 1.352473242 1.107875753 1.148807051 1.122658194 1.161599797 1.015076988 1 13.06196258 -11.10028974 0.696287681 1.01036957 1.167517892 0.434696903 0.070110076 0.404175497 0.433715456 0.026955747 0.017330174 7.94E-12 11.10028974 0.157148322 TIAPALVSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TIAPALVSKK 10 1 P06733;K7EM90;A0A2R8Y879;A0A2R8YEM5;K7ERS8;A0A2R8Y6I8 P06733 ENO1 Alpha-enolase;Enolase 0 1 ; TIAPALVSK(1)K;TIAPALVSK(1)K 164.97 0.0019364 6563200 5368.9 3475.7 7735.1 4843.9 8567 8489.8 7162.2 4798.2 4250.3 2577.7 FALSE TRUE FALSE 5303.461782 3524.630996 7869.726171 5403.974509 8129.794022 7947.32918 7770.557089 4937.028347 3870.142523 2510.730982 2.112317815 1.403826623 3.134436236 2.152351067 3.23801876 3.165344768 3.094938145 1.966370902 1.541440541 1 11.29389174 -10.9129709 0.359372969 0.880173257 2.966779091 0.516521166 0.547064925 0.618493448 0.218138504 0.515089356 0.320022026 1.22E-11 10.9129709 2.086605834 TIAQDYGVLK ddPTM_HeLa_Romidepsin_16h_R1 1 TIAQDYGVLK 10 0 Q06830;A0A0A0MSI0 Q06830 PRDX1 Peroxiredoxin-1 0 0 140.49 3.30E-05 0 2054.6 1806.5 2552.4 1126.4 2087.6 1960.8 1874.5 1803.5 2067.9 1636.1 FALSE FALSE TRUE 2029.557745 1831.931954 2596.823451 1256.639668 1981.061982 1835.511208 2033.719983 1855.681427 1882.941845 1593.593886 1.273572748 1.149560105 1.62953904 0.788557034 1.243141053 1.151806131 1.276184604 1.164463194 1.181569446 1 10.6380683 -12.37212657 1.070404136 0.998778827 1.213587289 0.022655728 0.200502474 0.776518071 1.577255833 0.126158504 0.031838497 4.24E-13 12.37212657 0.214808462 TIASDS(ph)EEEAGKELSDK ddPTM_HeLa_Romidepsin_16h_R1 1 TIASDSEEEAGKELSDK 17 1 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 T(0.013)IAS(0.193)DS(0.793)EEEAGKELS(0.001)DK 65.467 0.014956 6287000 2217.2 2108 2013.2 1790.8 1994 2242.4 2000.5 2162.1 2416.6 2437.3 TRUE FALSE FALSE 2190.175914 2137.676479 2048.238902 1997.860722 1892.238739 2099.117877 2170.42242 2224.656952 2200.453244 2373.978595 0.9225761 0.900461564 0.862787435 0.841566443 0.797074895 0.884219378 0.914255261 0.937100679 0.926905259 1 11.21309121 -11.03416628 0.719776817 0.990146085 0.871565625 0.37564554 0.042137356 0.313962533 0.359738247 0.015428711 0.010610653 9.24E-12 11.03416628 -0.118580459 TICTFDSSGFESMS(ph)PIKETVSSR ddPTM_HeLa_Romidepsin_16h_R1 2 TICTFDSSGFESMSPIKETVSSR 23 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 TICTFDSSGFES(0.474)MS(0.517)PIKET(0.008)VSSR;TICTFDS(0.001)SGFES(0.119)MS(0.879)PIKET(0.001)VSSR ; 86.546 0.00024014 57272000 2407.33 2145.43 2634.45 457.64 4436.4 4227.4 3177.3 3401.4 2918.2 2752.2 TRUE FALSE FALSE 2377.988536 2175.63342 2680.301497 510.5544901 4209.993954 3957.282783 3447.179783 3499.814142 2657.188883 2680.697447 0.887078301 0.811592305 0.999852296 0.190455842 1.570484561 1.476213881 1.285926462 1.305561038 0.99123043 1 11.38839269 TIEDAIAVLSVAEEAADRHPER ddPTM_HeLa_Romidepsin_16h_R1 1 TIEDAIAVLSVAEEAADRHPER 22 1 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 0 0 66.777 0.0020305 2860900 597.12 617.45 420.46 608.72 790.63 687.6 510.47 568.62 753.95 750.33 FALSE FALSE TRUE 589.8420718 626.1424773 427.7779299 679.1030705 750.2812009 643.6645791 553.8293091 585.0721226 686.5148237 730.8363184 0.807078216 0.856747895 0.58532659 0.929213633 1.026606344 0.880723307 0.757802117 0.800551516 0.939355101 1 9.513404519 -12.23947324 0.935095073 1.001641269 0.831556079 0.196483474 0.110180492 0.689368835 1.066204106 0.079827028 0.021197986 5.76E-13 12.23947324 -0.17008519 TIEGS(ph)SPADNR ddPTM_HeLa_Romidepsin_16h_R1 1 TIEGSSPADNR 11 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 0 TIEGS(0.5)S(0.5)PADNR 132.03 0.004703 5924000 2640.4 3013.2 3125 2198.9 2880.9 3677.5 2640.5 2939.9 3424.6 3187.7 TRUE FALSE FALSE 2608.217789 3055.619909 3179.389314 2453.147164 2733.876923 3442.519619 2864.784004 3024.961368 3118.295199 3104.883094 0.840037357 0.984133642 1.023996465 0.790093247 0.880508811 1.108743716 0.922670489 0.974259344 1.004319681 1 11.60032323 TIEGSS(ph)PADNR ddPTM_HeLa_Romidepsin_16h_R1 1 TIEGSSPADNR 11 0 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 0 TIEGS(0.14)S(0.86)PADNR 176.87 1.44E-05 4315800 3111.2 3223.2 3666.3 2265.3 3505.1 3668.9 3574.6 2861.7 3439.7 3632.8 TRUE FALSE FALSE 3073.279498 3268.576294 3730.110414 2527.224645 3326.221668 3434.469131 3878.226435 2944.498774 3132.044617 3538.419332 0.86854587 0.923739101 1.054174213 0.71422418 0.940030379 0.970622419 1.096033587 0.832150884 0.885153602 1 11.78888931 -8.274382033 5.510557599 0.927250708 0.979615203 0.03666509 0.103674234 0.462008453 50.32850074 0.014641518 0.034998696 5.32E-09 8.274382033 0.052364495 TIEGSS(ph)PADNRYSEYAEEFSK ddPTM_HeLa_Romidepsin_16h_R1 1 TIEGSSPADNRYSEYAEEFSK 21 1 Q9Y217 Q9Y217 MTMR6 Myotubularin-related protein 6 1 0 T(0.006)IEGS(0.155)S(0.579)PADNRY(0.168)S(0.042)EY(0.048)AEEFS(0.002)K 53.998 0.013527 6258200 1987.9 1600.9 1563.7 2011 2014.4 1749.6 1506.9 1612 2060.9 1686.1 TRUE FALSE FALSE 1963.67071 1623.437512 1590.915543 2243.521282 1911.597651 1637.806207 1634.896048 1658.640677 1876.567942 1642.294879 1.195687045 0.988517673 0.968714914 1.366089191 1.163979548 0.997266829 0.995494822 1.009953022 1.142649817 1 10.68149748 -8.236680191 23.14761131 1.102069087 1.000363821 0.177444156 0.111879959 522.281168 488282.6446 0.017475922 0.044521581 5.80E-09 8.236680191 -0.101705265 TIET(ph)SPSLSR ddPTM_HeLa_Romidepsin_16h_R1 1 TIETSPSLSR 10 0 H3BP78;F8W7R3;Q9NVI1-2;Q9NVI1-1;Q9NVI1 H3BP78 FANCI Fanconi anemia group I protein 1 0 T(0.002)IET(0.495)S(0.495)PS(0.007)LSR 115.7 0.02995 16783000 3871.5 4266.5 4139.1 3290.6 4187.1 4633.6 3576.7 4346.9 4301.6 3846.5 TRUE FALSE FALSE 3824.312669 4326.563899 4211.139299 3671.074655 3973.416663 4337.527914 3880.504809 4472.670693 3916.854122 3746.567375 1.020751073 1.154807445 1.123999351 0.979850163 1.060548567 1.157733861 1.035749373 1.193804954 1.045451404 1 11.87135368 -4 0.0941658 0.929702876 1.510289478 0.189964172 0.06359147 117.8842355 0.799245605 0.624068498 8.878204706 1.00E-04 4 0.580586602 TIGGGDDS(ph)FNTFFSETGAGK ddPTM_HeLa_Romidepsin_16h_R1 4 TIGGGDDSFNTFFSETGAGK 20 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q6PEY2;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;F8W0F6;F8VXZ7;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A;TUBA3E Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 1 0 TIGGGDDS(0.995)FNT(0.005)FFSETGAGK;TIGGGDDS(0.898)FNT(0.092)FFS(0.003)ET(0.006)GAGK;T(0.313)IGGGDDS(0.479)FNT(0.208)FFSETGAGK;TIGGGDDS(0.98)FNT(0.02)FFSETGAGK ;;; 226.23 7.21E-42 413522000 14005.7 11669.2 13570.4 11094.4 10713.2 10462.5 6642.8 9553.5 12692.2 13294.7 TRUE FALSE FALSE 13834.99314 11833.4793 13806.58712 12377.18673 10166.46543 9793.980016 7207.039266 9829.91545 11556.97784 12949.30178 1.068396843 0.913831456 1.06620321 0.95581885 0.785097575 0.756332672 0.556558136 0.759107759 0.892478841 1 13.66058669 -8.631368533 1.536828809 1.026296772 0.665377467 0.739078066 0.078293327 0.101007931 0.475163744 0.009689769 0.025899631 2.34E-09 8.631368533 -0.360919304 TIGGGDDSFNT(ph)FFSETGAGK ddPTM_HeLa_Romidepsin_16h_R1 2 TIGGGDDSFNTFFSETGAGK 20 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q6PEY2;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;F8W0F6;F8VXZ7;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A;TUBA3E Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 1 0 TIGGGDDS(0.189)FNT(0.807)FFS(0.004)ETGAGK;TIGGGDDS(0.119)FNT(0.872)FFS(0.009)ETGAGK ; 253.73 1.36E-79 71911000 7792 6966.6 8608.8 5720.5 6492.5 5492.9 4454.9 5759.7 8083.9 7089.3 TRUE FALSE FALSE 7697.028107 7064.675978 8758.632553 6381.931126 6161.163498 5141.921418 4833.299095 5926.347832 7360.855738 6905.118964 1.114684359 1.023107062 1.268426018 0.924231886 0.892260297 0.74465356 0.699958845 0.858254269 1.065999844 1 12.75345055 -8.736640086 2.140574172 1.067002013 0.767098746 0.722079392 0.085993824 0.128468491 1.199107945 0.013282956 0.029295686 1.83E-09 8.736640086 -0.299903267 TIGGGDDSFNTFFS(ph)ETGAGK ddPTM_HeLa_Romidepsin_16h_R1 1 TIGGGDDSFNTFFSETGAGK 20 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q6PEY2;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;F8W0F6;F8VXZ7;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A;TUBA3E Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 1 0 TIGGGDDSFNT(0.259)FFS(0.601)ET(0.14)GAGK 135.79 0.00029037 3630400 1469.3 1545.8 1322.9 1216.8 1791.9 1632.2 1288.4 1323.6 1374.7 1450.6 TRUE FALSE FALSE 1451.391606 1567.561813 1345.92452 1357.492141 1700.452656 1527.907688 1397.836664 1361.896278 1251.743389 1412.913203 1.027233381 1.109453723 0.952588253 0.960775325 1.203508222 1.081388216 0.989329466 0.963892386 0.885930846 1 10.46445713 -11.47660238 0.828547073 1.002212324 1.038523307 0.0863636 0.083298976 1.767559278 2.515194792 0.031767126 0.016663964 3.34E-12 11.47660238 0.036310983 TIGGGDDSFNTFFSETGAGK ddPTM_HeLa_Romidepsin_16h_R1 5 TIGGGDDSFNTFFSETGAGK 20 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;F8VVB9;A0A1W2PQM2;F8VQQ4;Q6PEY2;F8VX09;F8VWV9;F8VRZ4;F8VS66;F8VRK0;F8W0F6;F8VXZ7;Q71U36-2;Q71U36;P68363;P68363-2 Q9BQE3;Q71U36-2 TUBA1C;TUBA1B;TUBA1A;TUBA3E Tubulin alpha-1C chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain 0 0 ;;;; ;;;; 205.26 3.45E-23 64590820 6194.18 5508.96 6452.89 6052.18 6150.02 5894 5177.611 6515.61 7394.08 5995.17 FALSE FALSE TRUE 6118.682952 5586.515283 6565.199844 6751.961528 5836.161531 5517.392422 5617.397149 6704.128895 6732.734966 5839.414619 1.047824714 0.956690978 1.12429075 1.156273697 0.999442908 0.944853685 0.961979499 1.148082356 1.152981147 1 12.51160804 -7.240743245 23.41758764 1.024549859 1.148082644 0.131649703 0.077743261 2408.381245 2724973.737 0.00940657 0.469718388 5.74E-08 7.240743245 0.123532785 TIIFVETK ddPTM_HeLa_Romidepsin_16h_R1 2 TIIFVETK 8 0 A0A1X7SBZ2;A0A5H1ZRQ2;Q92841;Q92841-1;Q92841-3;Q92841-2 A0A1X7SBZ2 DDX17 Probable ATP-dependent RNA helicase DDX17 0 0 ; ; 111.04 0.019669 1756510 2486.1 2366.2 2035.44 2056.6 2177.06 2142.7 1661.78 1947.34 2368.11 2192.02 FALSE FALSE TRUE 2455.798457 2399.511426 2070.865979 2294.393769 2065.956504 2005.788385 1802.931552 2003.683211 2156.300311 2135.071004 1.150218635 1.123855563 0.969928389 1.074621764 0.967628945 0.939448094 0.844436343 0.938462096 1.009943138 1 11.06006833 -8.524707743 1.267345049 1.072002588 0.888512056 0.560043239 0.058258224 0.275697464 0.84789849 0.010864882 0.035741273 2.99E-09 8.524707743 -0.183490532 TIISYIDEQFER ddPTM_HeLa_Romidepsin_16h_R1 1 TIISYIDEQFER 12 0 B5MCX3;Q15019;Q15019-3;Q15019-2;C9J2Q4;C9IY94;C9J938;H7C310;C9JB25;C9IZU3;C9JQJ4 B5MCX3 Sep-02 Septin-2 0 0 139.32 0.00017393 0 690.74 399.01 545.06 482.29 610.91 367.04 487.83 469.53 734.74 549.83 FALSE FALSE TRUE 682.3209952 404.6272733 554.5465407 538.054639 579.7329831 343.5873286 529.266268 483.1151098 669.0230142 535.5453373 1.274067661 0.755542519 1.035480102 1.004685508 1.082509626 0.641565344 0.988275373 0.902099367 1.249236932 1 9.064864903 -10.26518557 24.99985253 1.129420838 0.922422673 0.391296452 0.144459274 316.9528892 2115148.902 0.026303614 0.030693504 5.43E-11 10.26518557 -0.206998165 TILALRIMEK ddPTM_HeLa_Romidepsin_16h_R1 1 TILALRIMEK 10 1 Q08AF3 Q08AF3 SLFN5 Schlafen family member 5 0 0 66.27 0.026241 0 157.84 0 259.62 143.51 264.23 122.26 215.57 67.882 114.73 125.06 FALSE FALSE TRUE 155.9161854 0 264.1385772 160.1033014 250.7453571 114.4479806 233.8805104 69.84605857 104.4682615 121.8109232 1.279985253 0 2.168430961 1.31435915 2.058480066 0.939554332 1.920029044 0.573397334 0.857626383 1 6.9284997 TIMQVSS(ph)GSRGSSGEAT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TIMQVSSGSRGSSGEATR 18 1 K7EJ87 K7EJ87 POLR2E 2 0 T(0.15)IMQVS(0.383)S(0.465)GS(0.003)RGSS(0.13)GEAT(0.87)R 81.696 0.011325 51210000 0 0 0 131.21 68.385 0 0 0 0 135.93 TRUE FALSE FALSE 0 0 0 146.3811176 64.89505827 0 0 0 0 132.398519 0 0 0 1.105609932 0.490149427 0 0 0 0 1 7.048743174 -12.34786034 1.032244437 1.007490993 0.19944996 0 0.455457776 0.435811366 0.819131945 0.260059799 0.065554194 4.49E-13 12.34786034 -0.808041033 TIPVKS(ph)PNLSEIK ddPTM_HeLa_Romidepsin_16h_R1 1 TIPVKSPNLSEIK 13 1 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 T(0.004)IPVKS(0.822)PNLS(0.174)EIK 70.784 0.023117 22120000 2930.2 2898.3 3255 3296.4 4063.3 4303.7 3506.4 4193.3 3365.4 2882.1 TRUE FALSE FALSE 2894.485595 2939.102343 3311.65191 3677.545278 3855.934639 4028.70746 3804.233528 4314.62652 3064.390195 2807.222627 1.031085162 1.046978717 1.179689804 1.310029794 1.373576361 1.435122181 1.355159186 1.536973405 1.091609253 1 11.45492777 -9.292982961 1.031626767 1.009791595 1.441854822 0.926168097 0.049081125 0.064893208 0.136793335 0.006802694 0.013983632 5.09E-10 9.292982961 0.432063227 TIPWLEDRVPQK ddPTM_HeLa_Romidepsin_16h_R1 2 TIPWLEDRVPQK 12 1 O43707;O43707-2;K7EJH8 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 128.88 0.005015 21483000 3436 3078.2 3357.9 4152 3747.2 3771.5 3347.8 3527.1 3446.8 3233.4 FALSE FALSE TRUE 3394.12071 3121.53498 3416.342841 4632.073776 3555.966401 3530.513322 3632.162048 3629.151074 3138.509575 3149.395802 1.077705352 0.991153598 1.08476135 1.47078172 1.129094793 1.1210129 1.153288528 1.15233248 0.996543392 1 11.62085936 -9.508122979 24.89583528 1.034477896 1.201923526 0.453690618 0.097638761 493.2545371 832216.841 0.014971009 0.022361578 3.10E-10 9.508122979 0.16744563 TIQEVLEEQS(ph)EDEDR ddPTM_HeLa_Romidepsin_16h_R1 2 TIQEVLEEQSEDEDR 15 0 M0R0Q7;P18858-2;P18858-3;P18858 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 TIQEVLEEQS(1)EDEDR;TIQEVLEEQS(1)EDEDR ; 207.85 6.90E-19 39512000 4901.3 4853.6 4851.6 2575.46 4239.3 4183.5 3707.8 3643.6 4554.1 4788.6 TRUE FALSE FALSE 4841.56107 4921.929108 4936.040063 2873.246803 4022.952702 3916.187852 4022.740439 3749.021817 4146.76989 4664.191482 1.038027939 1.0552588 1.058284181 0.61602248 0.86251877 0.839628447 0.862473261 0.803788145 0.889065105 1 12.1874113 -9.292919827 24.99985009 1.024554345 0.806550732 0.628434262 0.080551112 254.8735802 202404.3283 0.010092458 0.015417318 5.09E-10 9.292919827 -0.218003612 TIQEVLEEQS(ph)EDEDREAK ddPTM_HeLa_Romidepsin_16h_R1 3 TIQEVLEEQSEDEDREAK 18 1 M0R0Q7;P18858-2;P18858-3;P18858 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK;TIQEVLEEQS(1)EDEDREAK ;; 134.34 0.00047087 292041000 7613.5 7225.3 6822.1 5990.1 6711.1 6566.9 5422.1 6736.9 7606 6829.8 TRUE FALSE FALSE 7520.703734 7327.017963 6940.835789 6682.703546 6368.607524 6147.296284 5882.653039 6931.821572 6925.70031 6652.360811 1.130531543 1.1014162 1.043364301 1.004561198 0.957345476 0.9240774 0.884295546 1.042009261 1.041089097 1 12.6996507 -9.024772862 1.998669639 1.066124522 0.943672246 0.532779683 0.049287173 0.22744521 1.806228221 0.009550876 0.018531965 9.45E-10 9.024772862 -0.122452275 TIQGDEEDLR ddPTM_HeLa_Romidepsin_16h_R1 1 TIQGDEEDLR 10 0 M0R213;M0R0Y2;P54920 M0R213 NAPA Alpha-soluble NSF attachment protein 0 0 157.97 0.028835 9378100 2046.9 2642.3 1802.9 2100.6 2485 3136.8 2678.5 2862.1 2539.6 2355.3 FALSE FALSE TRUE 2021.951595 2679.498369 1834.278718 2343.481256 2358.181177 2936.368604 2906.011723 2944.910348 2312.451815 2294.108966 0.881366851 1.167990888 0.799560415 1.021521336 1.027929018 1.279960388 1.266727852 1.283683727 1.007995631 1 11.1637182 -8.368419541 2.343514812 0.954071491 1.284136499 0.67052567 0.092465078 0.120603144 1.280919423 0.013125812 0.035316419 4.28E-09 8.368419541 0.330065008 TIQNSSVSPT(ph)SSSSSSSSTGETQTQSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 TIQNSSVSPTSSSSSSSSTGETQTQSSSR 29 0 Q7Z417 Q7Z417 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2 1 0 TIQNSS(0.001)VS(0.098)PT(0.715)S(0.152)S(0.033)S(0.001)SSSSSTGETQTQSSSR;TIQNSSVS(0.141)PT(0.785)S(0.047)S(0.02)S(0.005)S(0.001)SSSSTGETQTQSSSR ; 173.24 2.10E-18 18450200 3388.4 3235.3 2905.8 2947.1 3382.1 3212.5 2556.5 2691 3438.2 3126.3 TRUE FALSE FALSE 3347.100877 3280.846638 2956.37423 3287.857569 3209.498817 3007.231618 2773.649046 2768.859839 3130.678781 3045.078275 1.099183855 1.077426043 0.970869699 1.079728424 1.053995506 0.987571204 0.910862971 0.909290202 1.028111102 1 11.5722636 -7.941713153 2.585432497 1.047226903 0.906932871 0.681476904 0.036445706 0.143579683 1.901481129 0.006431412 0.024168709 1.14E-08 7.941713153 -0.140294032 TIS(ph)AQDTLAYATALLNEK ddPTM_HeLa_Romidepsin_16h_R1 1 TISAQDTLAYATALLNEK 18 0 Q9UPU5;A0A0U1RQI9 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 T(0.055)IS(0.668)AQDT(0.278)LAYATALLNEK 201.22 9.47E-21 274300000 4047.8 4687.5 4926.2 3190.3 3543.4 3741.9 2685.9 3505.8 5155.2 4545 TRUE FALSE FALSE 3998.463857 4753.490748 5011.938445 3559.177497 3362.567076 3502.804666 2914.040279 3607.234792 4694.106001 4426.920245 0.903215697 1.073769231 1.132150156 0.803985005 0.759572545 0.791250909 0.658254524 0.8148407 1.060354771 1 12.11208767 -9.070674468 7.582997484 0.976102146 0.7550762 0.729645449 0.078213396 0.138949558 13.37682344 0.012261506 0.020438954 8.50E-10 9.070674468 -0.221025946 TIS(ph)DGTISASK ddPTM_HeLa_Romidepsin_16h_R1 2 TISDGTISASK 11 0 A0A075B6Q2;S4R347;Q5T0N5-3;Q5T0N5-4;Q5T0N5-2;Q5T0N5-5;Q5T0N5 A0A075B6Q2 FNBP1L Formin-binding protein 1-like 1 0 T(0.335)IS(0.659)DGT(0.006)ISASK;T(0.347)IS(0.648)DGT(0.005)ISASK ; 202.05 4.08E-13 120773000 10946 9674.2 10321.7 9375.5 11479.1 10828.6 9482.2 9969 9682.3 8630 TRUE FALSE FALSE 10812.58594 9810.393642 10501.34486 10459.53942 10893.27869 10136.68741 10287.61783 10257.43729 8816.290838 8405.791356 1.286325759 1.167099352 1.249298777 1.244325368 1.29592542 1.205917085 1.223872613 1.220282166 1.048835317 1 13.03716793 -12.35096148 0.872473204 0.986574852 1.239528319 0.830528523 0.03810123 0.188831946 0.234876182 0.032947544 0.006991365 4.46E-13 12.35096148 0.252953467 TIS(ph)ETIER ddPTM_HeLa_Romidepsin_16h_R1 1 TISETIER 8 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 1 0 T(0.008)IS(0.991)ET(0.001)IER 112.3 0.021613 4295800 2114.5 2268.6 2305.7 2034.4 2247.2 2280.5 2014.4 2087.1 2188.7 2153.8 TRUE FALSE FALSE 2088.727661 2300.53741 2345.829741 2269.6269 2132.516999 2134.78341 2185.503086 2147.486946 1992.93719 2097.843966 0.995654441 1.096619886 1.118209829 1.081885468 1.016527937 1.01760829 1.041785338 1.02366381 0.949993051 1 11.03469166 -10.28971954 23.83579022 0.997947922 1.056343021 0.461580831 0.035744599 316.4190081 266691.0192 0.006128931 0.00700946 5.13E-11 10.28971954 0.058395099 TIS(ph)PAESTALLQGR ddPTM_HeLa_Romidepsin_16h_R1 1 TISPAESTALLQGR 14 0 H0Y8J2;Q03188;Q03188-2 H0Y8J2 CENPC Centromere protein C 1 0 T(0.01)IS(0.771)PAES(0.11)T(0.11)ALLQGR 91.712 0.017643 7373200 621.1 741.18 727.84 687.25 779.7 680.72 586.36 629.22 862.95 781.86 TRUE FALSE FALSE 613.5297943 751.6143515 740.5077499 766.7130786 739.9089995 637.2241889 636.1654038 647.425488 785.7655907 761.5471645 0.805635978 0.986957061 0.972372802 1.006783446 0.971586573 0.836749473 0.835359165 0.850144966 1.03180161 1 9.572789579 -8.243672422 23.64711142 0.928474241 0.84021197 0.342153163 0.066598989 542.1993178 721642.3989 0.011789376 0.029968903 5.71E-09 8.243672422 -0.088262271 TIS(ph)QEFLTPGK ddPTM_HeLa_Romidepsin_16h_R1 2 TISQEFLTPGK 11 0 E7ETM8;E7EUA0;Q0ZGT2-4;Q0ZGT2-2;Q0ZGT2;Q0ZGT2-3;H7BXY5 E7ETM8 NEXN Nexilin 1 0 T(0.37)IS(0.58)QEFLT(0.05)PGK;T(0.036)IS(0.962)QEFLT(0.002)PGK ; 145.71 0.0024814 40938000 6107.6 5856.1 6186.5 3685.7 5589.4 5152.6 4523.6 6086.3 5982.3 6568.9 TRUE FALSE FALSE 6033.158222 5938.54233 6294.173437 4111.857976 5304.152061 4823.365489 4907.834471 6262.397488 5447.228105 6398.239031 0.942940424 0.928152621 0.983735276 0.642654636 0.829001861 0.753858283 0.767060194 0.978768917 0.851363645 1 12.64345918 -9.296543553 24.94109365 0.969016923 0.792441756 0.391244111 0.088313252 321.2076327 228213.3026 0.01171924 0.017901869 5.05E-10 9.296543553 -0.176575167 TISET(ph)IER ddPTM_HeLa_Romidepsin_16h_R1 1 TISETIER 8 0 P26639;P26639-2 P26639 TARS "Threonine--tRNA ligase, cytoplasmic" 1 0 TIS(0.143)ET(0.857)IER 145.72 0.016728 4779300 2433.8 2569.8 2264.2 1940.8 2688.1 2733.6 2370.3 2297.9 2502.1 2394.4 TRUE FALSE FALSE 2404.135909 2605.977712 2303.607451 2165.204428 2550.916226 2558.931782 2571.633223 2364.386111 2278.305909 2332.193143 1.030847688 1.117393609 0.987743 0.928398419 1.093784292 1.09722121 1.102667346 1.013803732 0.976894181 1 11.18747156 -4.000000688 0.060917819 0.929852045 1.277488785 0.144169405 0.056544971 492.6517648 2.262971415 2.6321514 15.23094722 1.00E-04 4.000000688 0.34763674 TISHVIIGLK ddPTM_HeLa_Romidepsin_16h_R1 1 TISHVIIGLK 10 0 Q9Y265;E7ETR0;Q9Y265-2 Q9Y265 RUVBL1 RuvB-like 1 0 0 74.173 0.023532 0 3432.2 3054.5 3456 3418 3548.6 3581.8 3447.9 3591.8 3481.7 2526.9 FALSE FALSE TRUE 3390.367026 3097.501331 3516.15023 3813.205242 3367.5017 3352.93454 3740.76454 3695.723066 3170.288032 2461.250774 1.377497597 1.258507001 1.428602996 1.549295701 1.368207473 1.362288872 1.519863226 1.501562988 1.288080055 1 11.26517594 -13.79515112 0.226931391 0.405332772 1.506690035 0.417389462 0.116084495 3.913982581 0.148641258 1.255087726 0.067384667 1.60E-14 13.79515112 1.101357263 TISIDENMEPS(ph)PTGDFYPSPS(ph)SPAAGSR ddPTM_HeLa_Romidepsin_16h_R1 2 TISIDENMEPSPTGDFYPSPSSPAAGSR 28 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 2 0 T(0.001)IS(0.003)IDENMEPS(0.806)PT(0.19)GDFY(0.001)PS(0.007)PS(0.539)S(0.452)PAAGS(0.002)R;TIS(0.001)IDENMEPS(0.615)PT(0.337)GDFY(0.062)PS(0.254)PS(0.573)S(0.155)PAAGS(0.003)R ; 121.98 3.56E-10 19957600 3619.8 3965.3 3897 4220.5 2910.6 2833.1 2448.1 2587.4 4051 4556.2 TRUE FALSE FALSE 3575.680485 4021.123597 3964.82565 4708.494068 2762.061221 2652.074053 2656.041553 2662.262337 3688.668414 4437.829267 0.805727366 0.906101464 0.893415544 1.060990359 0.622390149 0.597606148 0.598500166 0.599901929 0.831187545 1 12.11563845 -8.701162754 9.048094608 0.914169099 0.602492426 0.827921628 0.069604674 0.116026282 16.18563167 0.012197663 0.024398159 1.99E-09 8.701162754 -0.311676673 TISIDENMEPSPTGDFYPSPS(ph)SPAAGSR ddPTM_HeLa_Romidepsin_16h_R1 4 TISIDENMEPSPTGDFYPSPSSPAAGSR 28 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 TISIDENMEPSPTGDFYPS(0.006)PS(0.495)S(0.495)PAAGS(0.004)R;TISIDENMEPSPTGDFYPS(0.001)PS(0.835)S(0.163)PAAGSR;TISIDENMEPSPTGDFYPS(0.016)PS(0.49)S(0.49)PAAGS(0.004)R;TISIDENMEPSPTGDFYPS(0.021)PS(0.489)S(0.489)PAAGS(0.001)R ;;; 173.98 1.05E-18 65257000 11774.2 11737.9 10528.4 10402.2 7864.5 6651.4 6111.2 6004.2 12301.4 10941.1 TRUE FALSE FALSE 11630.69152 11903.14646 10711.64239 11604.95131 7463.145219 6226.397006 6630.285175 6177.922054 11201.13197 10656.84864 1.091381881 1.116948064 1.005141646 1.088966513 0.700314461 0.584262498 0.622161898 0.579713784 1.051073572 1 13.37949326 -8.672692323 4.073839152 1.050299499 0.604152614 0.967668126 0.039397022 0.032337198 1.007215156 0.006979089 0.014300209 2.12E-09 8.672692323 -0.446146886 TISINS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 T(0.019)IS(0.001)INS(0.98)PK 112.83 0.021417 117530000 6714.5 6415.1 6562.2 5878.5 7498.1 8778 7329.4 7639.1 7229.9 6245.2 TRUE FALSE FALSE 6632.661091 6505.411946 6676.412338 6558.199829 7115.443978 8217.11413 7951.959053 7860.125306 6583.239636 6082.948804 1.090369376 1.069450386 1.097561816 1.078128395 1.169735963 1.350843874 1.307253983 1.29215707 1.082244788 1 12.57055515 -8.539430312 2.201269053 1.051188988 1.317572578 0.915580874 0.033200672 0.071901701 0.693545423 0.006377882 0.015656398 2.89E-09 8.539430312 0.26638359 TISQEFLT(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 1 TISQEFLTPGK 11 0 E7ETM8;E7EUA0;Q0ZGT2-4;Q0ZGT2-2;Q0ZGT2;Q0ZGT2-3;H7BXY5 E7ETM8 NEXN Nexilin 1 0 T(0.091)IS(0.062)QEFLT(0.847)PGK 126.71 0.014554 40724000 4552.7 5291.3 5070.6 2472.8 4392.7 4734.8 4092.3 4386.4 5152.8 4984.5 TRUE FALSE FALSE 4497.209941 5365.79106 5158.851666 2758.716771 4168.524128 4432.261561 4439.89986 4513.313563 4691.920663 4855.001971 0.926304452 1.105208832 1.062584876 0.568221555 0.858604003 0.91292683 0.914500115 0.929621366 0.966409631 1 12.24525617 TITGNSAAVIT(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 2 TITGNSAAVITPFK 14 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 TITGNSAAVIT(1)PFK;TITGNS(0.039)AAVIT(0.961)PFK ; 138.91 0.0022615 45016000 3602 3286.3 3817.9 2869.8 3445.2 3396.5 3350.9 3143.9 3172.8 3262.5 TRUE FALSE FALSE 3558.097439 3332.564618 3884.348948 3201.619779 3269.378588 3179.474612 3635.525362 3234.863786 2889.016822 3177.73978 1.119694401 1.048721685 1.222362187 1.007514775 1.028837732 1.000545933 1.144060123 1.017976301 0.909142039 1 11.63378527 -6.981336881 16.90683888 1.064203999 0.922395436 0.001214481 0.084494411 12767878.53 263248488.2 0.00995106 46429161.46 1.04E-07 6.981336881 -0.141808563 TITLVKS(ph)PISVPGGSALISNLGK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 T(0.002)IT(0.002)LVKS(0.91)PIS(0.085)VPGGS(0.002)ALISNLGK 69.525 0.00070258 20896000 3379.8 3031.2 2682.1 3669.5 3406.5 3139.8 2552.6 2799.5 3033.8 2892.7 TRUE FALSE FALSE 3338.605698 3073.873313 2728.780825 4093.784856 3232.653594 2939.176913 2769.41778 2880.499116 2762.44933 2817.547237 1.184933354 1.090974899 0.968495147 1.452960505 1.147328979 1.043168638 0.982917959 1.022342794 0.980444726 1 11.46022408 -8.053265181 4.848212149 1.111719983 1.004166504 0.114194061 0.132124478 0.367754567 18.60755043 0.019166131 0.052578995 8.85E-09 8.053265181 -0.107553479 TITLVKSPIS(ph)VPGGSALISNLGK ddPTM_HeLa_Romidepsin_16h_R1 1 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 0 T(0.017)IT(0.017)LVKS(0.424)PIS(0.518)VPGGS(0.022)ALIS(0.002)NLGK 53.525 0.0092654 72367000 4267.4 3825.3 4373.2 4742.7 4178.7 4366.4 4084.7 4310.6 4578 4276.1 TRUE FALSE FALSE 4215.387287 3879.152674 4449.313712 5291.073289 3965.445346 4087.401132 4431.654316 4435.32041 4168.532214 4165.006306 1.012096256 0.931367779 1.068260979 1.270363812 0.952086277 0.981367333 1.064021034 1.064901247 1.000846555 1 12.02410296 TITVALADGGRPDNTGR ddPTM_HeLa_Romidepsin_16h_R1 1 TITVALADGGRPDNTGR 17 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 0 0 97.2 0.0097959 1824500 424.53 355.71 391.66 308.75 575.44 359.13 273.68 511.75 364.08 271.56 FALSE FALSE TRUE 419.3556651 360.7176947 398.476678 344.4491277 546.0731495 336.182752 296.9263724 526.5566788 331.5157729 264.5048321 1.585436689 1.363747089 1.506500562 1.302241343 2.064511054 1.270989076 1.122574473 1.990726123 1.253344865 1 8.047150268 -12.37395717 0.713947354 0.934422482 1.518897757 0.206471953 0.29559089 0.891302173 0.664072489 0.325914346 0.055332326 4.23E-13 12.37395717 0.584475275 TITVPVS(ph)GSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TITVPVSGSPK 11 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 TITVPVS(0.817)GS(0.183)PK 129.74 0.0057137 19631000 3970.1 3118.8 3328.6 2951.3 3546 3274.8 2867.5 3060.7 3546.5 3602 TRUE FALSE FALSE 3921.710894 3162.706548 3386.532887 3292.543192 3365.034388 3065.550849 3111.065378 3149.256526 3229.292158 3508.419521 1.117799873 0.901461906 0.96525882 0.938469066 0.959131132 0.87376975 0.886742694 0.897628264 0.920440711 1 11.77660555 -10.24958178 24.89083965 1.055627718 0.91887524 0.289359354 0.057630641 348.7962904 732175.1137 0.008673796 0.010576247 5.63E-11 10.24958178 -0.136752478 TIVITSHPGQIVK ddPTM_HeLa_Romidepsin_16h_R1 2 TIVITSHPGQIVK 13 0 P31689;P31689-2 P31689 DNAJA1 DnaJ homolog subfamily A member 1 0 0 ; ; 168.98 2.64E-33 0 6697.4 6144.4 6671.4 6554.9 7277.7 7548.2 6339.9 6116.4 6648.5 5947.3 FALSE FALSE TRUE 6615.769513 6230.901024 6787.512918 7312.80838 6906.291812 7065.894381 6878.410948 6293.368384 6053.841509 5792.788289 1.142069964 1.075630718 1.17171776 1.262398696 1.192222375 1.219774317 1.187409345 1.08641436 1.04506521 1 12.50004222 -11.7213961 0.417386472 0.974025859 1.189982283 0.568036435 0.052136949 0.764494944 0.239922418 0.071210011 0.019700633 1.90E-12 11.7213961 0.215956424 TIVLVPS(ph)PLGQQQDMIFEAR ddPTM_HeLa_Romidepsin_16h_R1 2 TIVLVPSPLGQQQDMIFEAR 20 0 Q96R06;F5GZT2 Q96R06 SPAG5 Sperm-associated antigen 5 1 0 TIVLVPS(1)PLGQQQDMIFEAR;T(0.002)IVLVPS(0.998)PLGQQQDMIFEAR ; 101.5 0.00088712 15632000 11173.7 11201.3 10677.1 9627.1 10874.9 12926.4 11267.9 11373.4 11670.6 10785.6 TRUE FALSE FALSE 11037.51065 11358.9922 10862.93045 10740.2306 10319.91327 12100.44476 12224.99514 11702.47138 10626.75231 10505.38856 1.0506523 1.081253885 1.034034142 1.022354437 0.982344748 1.151832195 1.163688052 1.11394941 1.011552524 1 13.3588419 -8.249797917 24.98525953 1.027102798 1.145209714 0.784687186 0.028106371 280.3098956 601608.8841 0.004470029 0.011287898 5.63E-09 8.249797917 0.118106916 TKDGVVEITGK ddPTM_HeLa_Romidepsin_16h_R1 1 TKDGVVEITGK 11 1 P04792 P04792 HSPB1 Heat shock protein beta-1 0 0 92.247 0.013173 1019400 611.87 457.8 510.06 415.84 377.7 581.21 512.34 470.43 505.17 475.41 FALSE FALSE TRUE 604.4122931 464.2449204 518.9373803 463.9213774 358.4245596 544.0725568 555.8581468 484.0411498 459.98633 463.0587797 1.305260411 1.002561534 1.120672803 1.001862826 0.774036851 1.174953549 1.200405156 1.045312541 0.993364882 1 8.855051527 TKDGVVEITGK(ac)HEER ddPTM_HeLa_Romidepsin_16h_R1 2 TKDGVVEITGKHEER 15 2 P04792 P04792 HSPB1 Heat shock protein beta-1 0 1 ; TKDGVVEITGK(1)HEER;TKDGVVEITGK(1)HEER 143.93 1.55E-07 3768900 3864.9 3799.5 3052.33 3212.82 3990.2 3963.5 3460.2 3444.4 4576.3 3470.9 FALSE TRUE FALSE 3817.793112 3852.989461 3105.454523 3584.301365 3786.565205 3710.245142 3754.109302 3544.05828 4166.984266 3380.725518 1.129282189 1.139693075 0.918576355 1.060216615 1.120045146 1.097470091 1.110444868 1.048312932 1.23257101 1 11.72311717 -12.55816449 1.350496602 1.000299129 1.083930641 0 0.094173163 0.574211369 1.887390483 0.043215404 0.010350688 2.77E-13 12.55816449 0.083631513 TKDQPDGSSLS(ph)PAQSPSQSQPPAASSLR ddPTM_HeLa_Romidepsin_16h_R1 2 TKDQPDGSSLSPAQSPSQSQPPAASSLR 28 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 T(0.002)KDQPDGS(0.006)S(0.084)LS(0.908)PAQS(0.001)PSQSQPPAASSLR;TKDQPDGSSLS(1)PAQSPSQSQPPAASSLR ; 148.3 2.11E-11 25604000 5250.2 4529.6 5018.8 4027.6 4967.8 5355 4444.2 4998.5 5154 5263.5 TRUE FALSE FALSE 5186.208543 4593.367828 5106.150109 4493.290062 4714.274629 5012.832782 4821.690237 5143.123711 4693.013332 5126.753511 1.011597014 0.895960342 0.995981199 0.876439652 0.919543844 0.977779168 0.940495818 1.003193093 0.915396717 1 12.32382982 -10.29011727 24.88761771 1.005476372 0.943785344 0 0.047971045 505.9119147 439045.2531 0.006197252 0.007087449 5.13E-11 10.29011727 -0.061691028 TKDS(ph)GSISLQETR ddPTM_HeLa_Romidepsin_16h_R1 1 TKDSGSISLQETR 13 1 Q9H2G2-2;Q9H2G2 Q9H2G2-2 SLK STE20-like serine/threonine-protein kinase 1 0 T(0.001)KDS(0.488)GS(0.488)IS(0.023)LQETR 138.73 0.0084234 24416000 1673.6 1786.8 1316.8 1519.3 1871.5 1258.3 750.19 1151 1578 1312.9 TRUE FALSE FALSE 1653.201519 1811.954617 1339.718352 1694.968615 1775.990371 1177.898691 813.9111199 1184.302369 1436.859728 1278.790669 1.292785098 1.416928244 1.047644767 1.325446499 1.388804606 0.921103602 0.636469392 0.926111206 1.123608236 1 10.32056441 -8.042809378 6.521025066 1.184043802 0.779472401 0.597169478 0.150412202 0.122891294 14.36165491 0.024395406 0.064570139 9.06E-09 8.042809378 -0.4045714 TKEEQHS(ph)MLGS(ph)GFK ddPTM_HeLa_Romidepsin_16h_R1 1 TKEEQHSMLGSGFK 14 1 P53990-5 P53990-5 2 0 TKEEQHS(1)MLGS(1)GFK 71.933 0.0028913 0 488.57 298.88 446.59 257.07 376.59 479.15 359.31 401.42 555.78 499.86 TRUE FALSE FALSE 482.6151209 303.0876405 454.3627116 286.793643 357.371207 448.5338614 389.8297824 413.0344544 506.0696448 486.8735651 0.991253491 0.622518169 0.933225265 0.58905158 0.734012345 0.921253265 0.800679705 0.848340275 1.039427237 1 8.927403361 -10.34146249 11.08555446 0.995988837 0.781780904 0.496135489 0.106718124 0.431826072 58.6577231 0.016992158 0.019419179 4.56E-11 10.34146249 -0.214207932 TKEGVMYVGAK(ac)TK ddPTM_HeLa_Romidepsin_16h_R1 2 TKEGVMYVGAKTK 13 2 F8W754;O76070 F8W754 SNCG Gamma-synuclein 0 1 ; TKEGVMYVGAK(1)TK;TK(0.001)EGVMYVGAK(0.999)TK 111.43 0.00074829 2507900 2201.67 2134.32 2221.22 2590.5 2368.02 2147.71 2000.57 1714.94 2242.6 1883.79 FALSE TRUE FALSE 2174.835199 2164.367013 2259.879402 2890.025799 2247.171103 2010.478262 2170.498366 1764.559083 2042.016239 1834.848864 1.185293918 1.179588714 1.23164335 1.575075667 1.224717276 1.095718727 1.182930326 0.961691787 1.112907051 1 10.84144552 -11.75457688 0.758908481 1.005459835 1.214838387 0.12234894 0.148775368 0.763242391 0.856291241 0.085809814 0.03278804 1.76E-12 11.75457688 0.209378552 TKEVYELLDS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 TKEVYELLDSPGK 13 1 E9PBS1;P22234;P22234-2 E9PBS1 PAICS Multifunctional protein ADE2;Phosphoribosylaminoimidazole-succinocarboxamide synthase;Phosphoribosylaminoimidazole carboxylase 1 0 TKEVYELLDS(1)PGK;TKEVYELLDS(1)PGK ; 180.56 3.79E-06 218550000 4890.2 4170.6 5486.6 3798.6 6337.6 7907.8 6719 6896.7 4698.9 4524.9 TRUE FALSE FALSE 4830.596361 4229.313816 5582.091971 4237.812005 6014.168623 7402.517101 7289.711692 7096.245133 4278.618615 4407.342446 1.096033817 0.959606354 1.266543737 0.961534543 1.36457938 1.679587459 1.653992578 1.610096157 0.970793322 1 12.10569328 -8.521164303 3.08047721 1.052473068 1.646068122 0.900677317 0.090364101 0.050685086 0.982063932 0.012295476 0.028073158 3.01E-09 8.521164303 0.593595054 TKEYVSNDAAQS(ph)DDEEKLQSQPTDTDGGR ddPTM_HeLa_Romidepsin_16h_R1 2 TKEYVSNDAAQSDDEEKLQSQPTDTDGGR 29 2 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 T(0.001)KEY(0.001)VS(0.001)NDAAQS(0.987)DDEEKLQS(0.01)QPTDTDGGR;T(0.002)KEY(0.001)VS(0.001)NDAAQS(0.929)DDEEKLQS(0.062)QPT(0.003)DTDGGR ; 63.563 0.00032967 64514000 3133.3 3182.1 2968.1 3897.9 4010.6 3711.1 3045.4 3856.3 3909.2 3165.6 TRUE FALSE FALSE 3095.110134 3226.897687 3019.758535 4348.593538 3805.924116 3473.972687 3304.0762 3967.875956 3559.551361 3083.357256 1.003811715 1.046553292 0.979373548 1.410343719 1.234344191 1.126685103 1.071583967 1.286868704 1.154440133 1 11.59028634 -9.302975467 24.97273724 1.004385084 1.212338443 0.460949843 0.098657623 255.1403381 153397.3614 0.013201431 0.020165651 4.98E-10 9.302975467 0.207953359 TKFAS(ph)DDEHDEHDENGATGPVK ddPTM_HeLa_Romidepsin_16h_R1 1 TKFASDDEHDEHDENGATGPVK 22 1 P05455 P05455 SSB Lupus La protein 1 0 T(0.231)KFAS(0.768)DDEHDEHDENGATGPVK 56.688 0.0059364 10863000 2741.1 2609.4 2462.6 2942 2649.7 3137.5 2398.3 3177.2 3041.5 2635.8 TRUE FALSE FALSE 2707.690419 2646.135202 2505.46052 3282.167883 2514.475922 2937.023876 2602.011542 3269.127269 2769.460622 2567.321536 1.054675225 1.03069879 0.975904453 1.278440521 0.979416051 1.144003131 1.013512139 1.273361059 1.078735399 1 11.32604828 TKPLASVTNANTSSTQAAPVAVTTPTVSSGQATPTS(ph)PIKK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPLASVTNANTSSTQAAPVAVTTPTVSSGQATPTSPIKK 40 2 O14974-5;O14974-4;O14974-3;O14974-2;O14974;F8VZN8;H0YIS4;A0A3B3ISH4 O14974-5 PPP1R12A Protein phosphatase 1 regulatory subunit 12A 1 0 TKPLASVTNANTS(0.001)S(0.005)T(0.005)QAAPVAVT(0.081)T(0.081)PT(0.081)VS(0.066)S(0.066)GQAT(0.054)PT(0.251)S(0.309)PIKK 77.308 5.11E-08 13557000 2099.7 2182.9 2454.6 1073.2 2024.3 1880.1 1803.1 1442.9 2526.8 2292.1 TRUE FALSE FALSE 2074.108049 2213.630923 2497.321283 1197.288434 1920.992417 1759.967678 1956.255269 1484.648035 2300.79668 2232.550912 0.929030571 0.991525395 1.118595446 0.53628718 0.860447306 0.788321408 0.876242176 0.665000752 1.030568516 1 11.12447736 -9.275770148 24.99718296 0.978282683 0.761328173 0.61285879 0.104486937 461.1380371 804362.2389 0.015115289 0.023154445 5.30E-10 9.275770148 -0.21695451 TKPLATTQPAKTS(ph)TSK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPLATTQPAKTSTSK 16 2 E7EVA0;P27816;P27816-6;P27816-5;P27816-4;B5MEG9;H7C4C5 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 TKPLATTQPAKT(0.307)S(0.49)T(0.154)S(0.049)K 100.46 0.0048961 10279000 1217.9 1287.6 1611.6 1621.7 1613.1 1836.2 1538.2 1729.8 1603.1 1532.1 TRUE FALSE FALSE 1203.055766 1305.726867 1639.649222 1809.208584 1530.777488 1718.872746 1668.85467 1779.849034 1459.714721 1492.295821 0.806177803 0.874978572 1.098742755 1.212365912 1.025786889 1.151831106 1.118313572 1.19269183 0.97816713 1 10.54331784 -9.701830294 5.392900286 0.903396052 1.134592094 0.707095922 0.068947235 0.096539681 5.633247372 0.013469268 0.019004303 1.99E-10 9.701830294 0.231196042 TKPLT(ph)PSIGAK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPLTPSIGAK 11 1 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YF61;A0A2R8Y7Y0;A0A2R8YCQ1;A0A2R8YD28 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 T(0.002)KPLT(0.986)PS(0.012)IGAK 88.73 0.019719 30796000 6091.6 6205.9 5979.1 5794 5806.8 6353.6 5565.6 5914 6737.7 6480.4 TRUE FALSE FALSE 6017.353236 6293.266823 6083.163727 6463.929542 5510.457328 5947.625465 6038.341925 6085.112259 6135.063237 6312.038274 0.953313807 0.997026087 0.963739994 1.024063743 0.873007591 0.942267015 0.956638991 0.964048695 0.9719623 1 12.62389024 -8.778100816 24.99999647 0.980727162 0.93619946 0.40863193 0.029758075 213.5625397 320444.0573 0.004587176 0.008330759 1.67E-09 8.778100816 -0.044527701 AEESIEDIY(ph)ANIPDLPK ddPTM_HeLa_Romidepsin_16h_R1 3 AEESIEDIYANIPDLPK 17 0 S4R313;Q9NP74-2;Q9NP74 S4R313 PALMD Palmdelphin 1 0 AEESIEDIY(1)ANIPDLPK;AEESIEDIY(1)ANIPDLPK;AEESIEDIY(1)ANIPDLPK ;; 160.69 0.0015781 20171700 28322.2 25714.8 24713.8 27865.3 16548.7 9875.3 7994 6951 32001.7 26777.7 TRUE FALSE FALSE 27976.99813 26076.81363 25143.93332 31087.2171 15704.15809 9244.300201 8673.01016 7152.116218 29139.3878 26082.01149 1.072654927 0.999800711 0.964033519 1.191902592 0.602106862 0.354432027 0.332528423 0.274216435 1.117221646 1 14.67076752 -8.553128431 3.344655928 1.035926622 0.329839916 0.95526945 0.072256939 0.03253333 0.756096704 0.010005048 0.022078607 2.80E-09 8.553128431 -0.706086706 down TKPTQAAGPS(ph)S(ph)PQKPPTPEETK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPTQAAGPSSPQKPPTPEETK 22 2 P18887;F5H8D7 P18887 XRCC1 DNA repair protein XRCC1 2 0 T(0.006)KPT(0.014)QAAGPS(0.785)S(0.914)PQKPPT(0.275)PEET(0.006)K 64.377 0.0026977 25312000 1614.7 1480.6 1517.9 1302 1327 1283.5 1292.1 1490.5 1452.9 1643.5 TRUE FALSE FALSE 1595.019415 1501.443926 1544.318413 1452.543366 1259.278238 1201.488492 1401.850942 1533.625266 1322.948985 1600.801633 0.996387924 0.93793253 0.964715665 0.907384985 0.786654769 0.750554264 0.875718086 0.958035795 0.826429058 1 10.64457883 -9.210432969 2.005756636 0.993121504 0.839391173 0.16578761 0.076155359 0.168168186 1.320225237 0.009032028 0.01613336 6.16E-10 9.210432969 -0.153730331 TKPTQAAGPSS(ph)PQKPPT(ph)PEETK ddPTM_HeLa_Romidepsin_16h_R1 1 TKPTQAAGPSSPQKPPTPEETK 22 2 P18887;F5H8D7 P18887 XRCC1 DNA repair protein XRCC1 2 0 TKPTQAAGPS(0.315)S(0.692)PQKPPT(0.987)PEET(0.005)K 84.905 0.00055033 57948000 4481.4 4132 4133.7 3378.2 4057.1 4237.7 4103.8 3913.8 4861.8 4865.1 TRUE FALSE FALSE 4426.778973 4190.170404 4205.645314 3768.803379 3850.051048 3966.924647 4452.37667 4027.039628 4426.948431 4738.704001 0.934175034 0.884243963 0.887509605 0.795323654 0.8124692 0.837132821 0.939576869 0.849818775 0.934210795 1 12.21027683 -10.53165987 0.85441939 0.984768474 0.850507219 0.550869586 0.04121536 0.232193068 0.353247779 0.010645576 0.010814599 2.94E-11 10.53165987 -0.134261255 TKPTQAAGPSS(ph)PQKPPTPEETK ddPTM_HeLa_Romidepsin_16h_R1 2 TKPTQAAGPSSPQKPPTPEETK 22 2 P18887;F5H8D7 P18887 XRCC1 DNA repair protein XRCC1 1 0 TKPTQAAGPS(0.025)S(0.975)PQKPPTPEETK;TKPTQAAGPS(0.316)S(0.681)PQKPPT(0.003)PEETK ; 143.93 1.27E-05 198925000 9612.5 8575.1 8269.7 7764.7 6990.4 7059.3 6242.1 7068.4 8868.1 8731.8 TRUE FALSE FALSE 9495.339153 8695.820483 8413.63066 8662.491148 6633.653803 6608.233513 6772.303818 7272.913002 8074.914925 8504.946577 1.116449006 1.022442693 0.989263199 1.018523875 0.779975952 0.776987069 0.796278231 0.855139175 0.949437466 1 13.05408646 -8.803616235 5.235802336 1.046831386 0.799316951 0.80780562 0.049858048 0.054660896 3.474222793 0.007866411 0.014751652 1.57E-09 8.803616235 -0.247514435 TKPYIQVDIGGGQTK ddPTM_HeLa_Romidepsin_16h_R1 2 TKPYIQVDIGGGQTK 15 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 ; ; 200.69 3.40E-18 7922000 9960 8421.8 9359.1 8815.1 10105.8 11224.9 9654.3 11307.3 9264.3 9830.1 FALSE FALSE TRUE 9838.603689 8540.362321 9521.99121 9834.343338 9590.063316 10507.66512 10474.336 11634.45889 8435.677805 9574.712585 1.027561256 0.89197062 0.994493686 1.027116297 1.001603258 1.097439221 1.093958269 1.215123565 0.881037183 1 13.22501347 -7.229501183 0.866115246 1.001730306 1.334369588 0.646372622 0.055354104 0.950464519 0.502729836 0.006581814 0.303965876 5.90E-08 7.229501183 0.332639283 TKQDSASKK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 TKQDSASKKK 10 3 Q8IUR5-2 Q8IUR5-2 0 1 TKQDSASK(0.129)K(0.871)K 52.725 0.027945 827040 898.5 894.67 748.6 812.29 844.56 829.5 993.25 660.8 1173.2 1086.6 FALSE TRUE FALSE 887.5487364 907.2651877 761.629069 906.2107917 801.4589517 776.4976271 1077.61663 679.9192054 1068.266054 1058.369975 0.838599693 0.857228766 0.719624599 0.856232521 0.757257831 0.733673144 1.018185186 0.642421102 1.009350301 1 10.04762832 -11.82606727 0.50511039 1.021077786 0.796502719 0.42256596 0.095566653 0.896350166 0.399050553 0.095479825 0.025114638 1.49E-12 11.82606727 -0.224575067 TKSPT(ph)DDEVTPSAVVR ddPTM_HeLa_Romidepsin_16h_R1 1 TKSPTDDEVTPSAVVR 16 1 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 T(0.315)KS(0.316)PT(0.342)DDEVT(0.006)PS(0.021)AVVR 165.16 0.00010535 15647000 1612.3 1767.7 1565.3 1623.8 1067.8 1114.3 1075.2 1337.4 1920.4 2133 TRUE FALSE FALSE 1592.648667 1792.585727 1592.54339 1811.551396 1013.306181 1043.099826 1166.527461 1376.095559 1748.634614 2077.584353 0.766586765 0.862822116 0.766536092 0.871950828 0.487732871 0.502073394 0.561482599 0.66235364 0.841667205 1 11.02069134 -9.122206076 0.136924652 1.169235823 0.226918008 0.553710526 0.109649411 5.429191575 0.300458995 0.656696028 1.350307909 7.55E-10 9.122206076 -0.942317815 TKT(ph)KY(ph)T(ph)GNPT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TKTKYTGNPTK 11 2 Q9UHG3-2;Q9UHG3 Q9UHG3-2 PCYOX1 Prenylcysteine oxidase 1 4 0 T(0.378)KT(0.623)KY(1)T(1)GNPT(1)K 52.254 0.022431 6947600 2281.4 2083.9 2411.5 2336.4 2393.8 2979.9 2481.3 3002.4 2343.7 2169.3 TRUE FALSE FALSE 2253.593419 2113.237199 2453.471146 2606.545561 2271.635454 2789.494007 2692.06156 3089.269707 2134.073602 2112.941273 1.066566993 1.000140054 1.161163908 1.233610036 1.075105817 1.320194765 1.274082529 1.462070785 1.01000138 1 11.04503695 -4 0.257740127 1.001134165 3.980113985 0.826227103 0.06252 12.605751 0.158450326 0.029948258 16.65058094 1.00E-04 4 2.97897982 TKVGDGDLS(ph)AEEIPENEVSLR ddPTM_HeLa_Romidepsin_16h_R1 1 TKVGDGDLSAEEIPENEVSLR 21 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 T(0.003)KVGDGDLS(0.997)AEEIPENEVSLR 66.36 0.0029957 4490700 1907.2 2456.4 2475.6 2518.9 2597.9 2745.2 2454.6 2825.1 2564.9 2366.2 TRUE FALSE FALSE 1883.954313 2490.981264 2518.68678 2810.14707 2465.319469 2569.79058 2663.093663 2906.839811 2335.48892 2304.725783 0.817431005 1.080814595 1.092835772 1.219297797 1.069680171 1.115009256 1.155492633 1.261251917 1.013347851 1 11.17037939 -10.06226346 4.05005959 0.914017039 1.147076845 0.600300558 0.074584165 0.109814024 3.584067471 0.014201258 0.017815642 8.66E-11 10.06226346 0.233059806 TKVSRHHS(ph)ET(ph)NFGVK ddPTM_HeLa_Romidepsin_16h_R1 1 TKVSRHHSETNFGVK 15 2 A0A0J9YW69;A0A0J9YY72;A0A1W2PQQ1;Q5HYW2-2;Q5HYW2 A0A0J9YW69 NHSL2 NHS-like protein 2 2 0 T(0.045)KVS(0.051)RHHS(0.904)ET(1)NFGVK 99.568 0.0011504 0 708.51 729.86 744.57 627.37 494.23 836.86 620.21 738.51 625.9 667.82 TRUE FALSE FALSE 699.8744076 740.1349882 757.5289285 699.9094713 469.0075989 783.3873468 672.8906219 759.8776217 569.9179364 650.4699401 1.075951961 1.137846567 1.164587142 1.076005866 0.721028859 1.204340583 1.034468436 1.168197906 0.876163372 1 9.345338578 TLAGDVHIVR ddPTM_HeLa_Romidepsin_16h_R1 2 TLAGDVHIVR 10 0 Q9UBQ0;F8VXU5;Q9UBQ0-2 Q9UBQ0 VPS29 Vacuolar protein sorting-associated protein 29 0 0 ; ; 95.483 0.0051992 2436200 3335 2652.95 2938.4 2489.68 3506.7 3573.3 3198.7 3231.2 3229 2866.33 FALSE FALSE TRUE 3294.351737 2690.2983 2989.541619 2777.548516 3327.740014 3344.977662 3470.397498 3324.689674 2940.190153 2791.862333 1.179983589 0.963621403 1.070805528 0.994873022 1.191942731 1.198116978 1.243040338 1.190850148 1.053128629 1 11.44701209 -8.646777843 6.993208939 1.070169994 1.210593579 0.621960448 0.059974205 0.164570098 9.488434626 0.011370833 0.022828888 2.26E-09 8.646777843 0.140423585 TLAYIITELDEREREEFYR ddPTM_HeLa_Romidepsin_16h_R1 1 TLAYIITELDEREREEFYR 19 2 G3V2V6;H0YJH8;G3V2S6;Q9Y5K8 G3V2V6 ATP6V1D V-type proton ATPase subunit D 0 0 51.888 0.022738 939520 516.91 339.83 341.1 913.25 853.74 739.88 710.69 833.23 567.16 499.03 FALSE FALSE TRUE 510.6097021 344.6141357 347.0367024 1018.844262 810.1704621 692.6040559 771.0559909 857.3381954 516.4317891 486.0651287 1.050496471 0.708987573 0.71397161 2.096106472 1.666794045 1.424920273 1.586322378 1.76383399 1.062474468 1 8.925005826 -9.26904046 24.99679304 0.974700033 1.682887125 0.795092848 0.201520594 221.2010352 727437.3887 0.032058697 0.049548195 5.38E-10 9.26904046 0.708187091 TLDFDPLLS(ph)PASPK ddPTM_HeLa_Romidepsin_16h_R1 1 TLDFDPLLSPASPK 14 0 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 0 TLDFDPLLS(0.72)PAS(0.28)PK 127.78 0.0027298 59368000 7580.5 6968.9 7213.7 7108.5 6241.3 5131.3 4153 3921.1 6985.3 6794.7 TRUE FALSE FALSE 7488.10595 7067.008357 7339.251422 7930.418216 5922.783172 4803.426491 4505.755716 4034.550842 6360.517273 6618.172714 1.131446137 1.067818666 1.10895435 1.198279126 0.89492726 0.725793463 0.680815674 0.609617037 0.961068492 1 12.69221723 -8.383074358 2.483102045 1.076170695 0.660297124 0.874043614 0.068862858 0.071994573 0.85807203 0.010283471 0.026849131 4.14E-09 8.383074358 -0.415873571 TLDFDPLLS(ph)PASPKR ddPTM_HeLa_Romidepsin_16h_R1 1 TLDFDPLLSPASPKR 15 1 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 0 T(0.002)LDFDPLLS(0.813)PAS(0.185)PKR 67.252 0.01677 17483000 5056.9 4779 4635.1 5366.3 3852.7 2953.7 2696.2 3004.7 5576.4 4782.5 TRUE FALSE FALSE 4995.264558 4846.278887 4715.771971 5986.776855 3656.082343 2764.968103 2925.215161 3091.636254 5077.632818 4658.249961 1.072347899 1.040364714 1.012348416 1.285198713 0.784861777 0.593563704 0.627964404 0.663690502 1.090030132 1 12.18557234 -8.557693313 6.935208194 1.049368577 0.637568529 0.868378719 0.080359269 0.047454716 6.89486938 0.011405456 0.023114981 2.77E-09 8.557693313 -0.411800048 TLDFDPLLSPAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 TLDFDPLLSPASPK 14 0 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 0 TLDFDPLLS(0.227)PAS(0.773)PK 214.89 4.46E-24 60947000 8401.4 8103.6 8003.9 7835.1 7284 5323.1 4400.6 5204.8 7965.8 7991.9 TRUE FALSE FALSE 8299.000505 8217.682694 8143.204522 8741.031127 6912.2703 4982.97109 4774.386854 5355.392676 7253.318897 7784.269286 1.066124539 1.055678111 1.046110331 1.122909654 0.88797934 0.640133442 0.613337833 0.687976286 0.931791878 1 12.9263459 -8.422627469 3.134376822 1.040652984 0.642428618 0.920556051 0.051078885 0.039041534 0.728590663 0.00615271 0.014778334 3.78E-09 8.422627469 -0.398224366 TLDFDPLLSPAS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 1 TLDFDPLLSPASPKR 15 1 Q53H80 Q53H80 AKIRIN2 Akirin-2 1 0 TLDFDPLLS(0.046)PAS(0.954)PKR 98.077 0.0027413 20525000 5552 4910.2 4861.3 5663.5 4905.2 3481.9 3243.8 2704.8 5211.1 5248.3 TRUE FALSE FALSE 5484.330088 4979.325924 4945.908887 6318.340518 4654.86934 3259.417827 3519.328291 2783.059121 4745.006165 5111.948409 1.072845352 0.974056373 0.967519327 1.235994578 0.910586134 0.637607731 0.688451449 0.54442238 0.928218711 1 12.31965756 -8.358382957 3.481277558 1.03818872 0.626220108 0.811191525 0.087293845 0.065124898 1.476823986 0.011155982 0.027017819 4.38E-09 8.358382957 -0.411968612 TLDGFK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TLDGFKK 7 1 P07237;H7BZ94;H0Y3Z3;I3L0S0 P07237 P4HB Protein disulfide-isomerase 0 1 ; TLDGFK(1)K;TLDGFK(1)K 87.616 0.027476 4108000 3172.6 3124.2 4606.9 3495.4 9416.5 9305.2 11442.2 3657.3 10587.1 7172 FALSE TRUE FALSE 3133.931131 3168.18257 4687.081162 3899.554594 8935.940867 8710.627751 12414.10018 3763.118205 9640.16326 6985.670406 0.448622816 0.453525916 0.670956528 0.558221955 1.279181574 1.24692796 1.777080718 0.538691061 1.379991139 1 12.77018286 -8.754608797 24.98463128 0.692662627 1.253546739 0.24246283 0.385742345 127.8226994 467540.4436 0.049224709 0.096718606 1.76E-09 8.754608797 0.560884112 TLDPLVNT(ph)SSLIMR ddPTM_HeLa_Romidepsin_16h_R1 1 TLDPLVNTSSLIMR 14 0 J3KNS1;Q9UPW5 J3KNS1 AGTPBP1 Cytosolic carboxypeptidase 1 1 0 T(0.156)LDPLVNT(0.687)S(0.156)SLIMR 106.4 0.017978 2443400 405.47 348.54 386.35 281.72 433.54 478.31 377.9 461.57 533.83 461.79 TRUE FALSE FALSE 400.5279757 353.4467553 393.0742597 314.2937919 411.414836 447.7475347 409.9988166 474.9247997 486.0829078 449.7926292 0.890472519 0.785799349 0.873901069 0.698752651 0.914676696 0.99545325 0.911528535 1.055875016 1.080682244 1 8.81311621 -5.504008106 1.175577649 0.911590321 9.264110056 0.158063776 0.103171114 142.8239453 4.21069522 0.015221156 3060.758783 3.13E-06 5.504008106 8.352519735 TLDS(ph)DEERPR ddPTM_HeLa_Romidepsin_16h_R1 2 TLDSDEERPR 10 1 Q9BW71;Q9BW71-2 Q9BW71 HIRIP3 HIRA-interacting protein 3 1 0 T(0.108)LDS(0.892)DEERPR;T(0.007)LDS(0.993)DEERPR ; 98.407 0.0097169 25504300 6298.9 5790.6 6258.9 3784.6 5067 4805.4 4415.3 4736.1 5803.2 6356.1 TRUE FALSE FALSE 6222.126584 5872.120219 6367.833529 4222.193259 4808.412082 4498.350449 4790.335472 4873.131581 5284.147258 6190.967606 1.005032974 0.948497972 1.028568381 0.681992465 0.776681835 0.726598932 0.773761999 0.787135694 0.853525264 1 12.5959492 -9.267030382 24.99161038 0.999324789 0.750864195 0.777026949 0.057068123 74.30692161 332149.4741 0.004761719 0.007399397 5.41E-10 9.267030382 -0.248460594 TLEAEFNS(ph)PSPPTPEPGEGPR ddPTM_HeLa_Romidepsin_16h_R1 1 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 TLEAEFNS(0.928)PS(0.071)PPT(0.001)PEPGEGPR 161.31 3.00E-08 5956800 937.05 899.37 896.09 1083.8 1114.8 1180 1217.6 1066.1 1211.4 1024.1 TRUE FALSE FALSE 925.6288742 912.0313545 911.6860706 1209.114055 1057.907596 1104.601808 1321.022914 1096.945921 1103.04935 997.4937344 0.927954575 0.914322891 0.913976739 1.21215203 1.060565655 1.10737719 1.324342067 1.099702067 1.105820831 1 9.962163969 -9.262779461 24.99937189 0.956872819 1.161372333 0.540065602 0.08634275 56.90444339 1061560.173 0.011256623 0.01779279 5.46E-10 9.262779461 0.204499514 TLEAEFNSPS(ph)PPTPEPGEGPR ddPTM_HeLa_Romidepsin_16h_R1 1 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 T(0.013)LEAEFNS(0.127)PS(0.858)PPT(0.002)PEPGEGPR 114.78 0.00018569 8127300 2197 2585.9 2577.6 2386.4 2737 3077.8 2750.8 3090.1 2816.4 2269.8 TRUE FALSE FALSE 2170.222119 2622.304368 2622.462047 2662.326796 2597.320677 2881.138513 2984.452883 3179.507168 2564.49413 2210.830269 0.981632172 1.186117453 1.186188774 1.204220348 1.174816861 1.303192992 1.34992402 1.438150731 1.159968798 1 11.11037255 -8.406378302 0.368144439 0.970889359 1.54279916 0.683999234 0.075448106 0.683723698 0.11585071 0.021402756 0.155415415 3.92E-09 8.406378302 0.571909801 TLEAEFNSPSPPT(ph)PEPGEGPR ddPTM_HeLa_Romidepsin_16h_R1 3 TLEAEFNSPSPPTPEPGEGPR 21 0 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 TLEAEFNSPS(0.001)PPT(0.999)PEPGEGPR;TLEAEFNS(0.436)PS(0.005)PPT(0.56)PEPGEGPR;TLEAEFNSPS(0.004)PPT(0.996)PEPGEGPR ;; 138.77 9.34E-05 30871300 6609.1 7000.3 5561.4 6396.7 7155 7499.3 5798.4 6064.2 6551.5 6335.5 TRUE FALSE FALSE 6528.545747 7098.850407 5658.193834 7136.316551 6789.853651 7020.118933 6290.915951 6239.658059 5965.517431 6170.902797 1.057956342 1.150374692 0.91691508 1.156446113 1.100301508 1.137616191 1.019448233 1.011141848 0.966717128 1 12.59126585 -11.74520824 0.674739643 0.999270251 1.071758472 0.174705481 0.071091276 1.178553202 1.029127251 0.044406686 0.015562859 1.80E-12 11.74520824 0.072488221 TLEEDEEELFK ddPTM_HeLa_Romidepsin_16h_R1 4 TLEEDEEELFK 11 0 C9JJ34;C9JDM3;F6WQW2;P43487-2;P43487 C9JJ34 RANBP1 Ran-specific GTPase-activating protein 0 0 ;;; ;;; 256.47 3.83E-60 53034000 10321.3 10278.4 9731.1 9663.3 10360.3 10350.1 8353.1 9055.1 11201.2 10724.2 FALSE FALSE TRUE 10195.50003 10423.09958 9900.465713 10780.61621 9831.575231 9688.762013 9062.612106 9317.095032 10199.33662 10445.58374 0.976058426 0.997847497 0.947813541 1.032074079 0.941218363 0.927546249 0.867602265 0.891964994 0.97642572 1 13.3506055 -8.222140539 1.804675107 0.98833807 0.88059473 0.756621869 0.023815089 0.115286642 0.710364737 0.003218272 0.011105104 6.00E-09 8.222140539 -0.10774334 TLEEMLLER ddPTM_HeLa_Romidepsin_16h_R1 1 TLEEMLLER 9 0 A0A1B0GTU1;A0A494C0C4 A0A1B0GTU1 0 0 80.219 0.028456 4105100 1375.1 1323 1395.9 1524.8 1338.1 1575 2047.7 1178.7 1767.1 1710.1 FALSE FALSE TRUE 1358.339752 1341.625229 1420.195054 1701.10455 1269.811764 1474.362583 2221.631587 1212.803825 1609.04615 1665.671355 0.815490852 0.805456145 0.852626209 1.021272621 0.762342319 0.885146147 1.333775465 0.728117117 0.966004575 1 10.70188806 TLEEVVMAEEEDEGTDRPGS(ph)PA ddPTM_HeLa_Romidepsin_16h_R1 2 TLEEVVMAEEEDEGTDRPGSPA 22 1 F8WC89;A6NKF1 F8WC89 SAC3D1 SAC3 domain-containing protein 1 1 0 TLEEVVMAEEEDEGT(0.042)DRPGS(0.958)PA;TLEEVVMAEEEDEGT(0.035)DRPGS(0.965)PA ; 140.21 5.30E-05 28727000 4522.6 4296.7 4290.9 4485.4 4766.5 4615.8 4511.1 4740 5033 4240.1 TRUE FALSE FALSE 4467.476812 4357.189055 4365.581315 5004.023052 4523.247719 4320.865277 4894.272721 4877.144422 4582.835875 4129.941591 1.081728812 1.055024377 1.05705643 1.211644994 1.095232855 1.046229149 1.185070688 1.180923341 1.109661184 1 12.01190566 -4.000001502 0.043641741 0.713035917 1.763952479 0.207156997 0.058664533 331.5100306 1.109865889 7.015980509 24.94112737 1.00E-04 4.000001502 1.050916562 TLEGELHDLR ddPTM_HeLa_Romidepsin_16h_R1 5 TLEGELHDLR 10 0 P02545;P02545-3;P02545-2;P02545-6;Q3BDU5;P02545-5;P02545-4;Q5TCI8;H0YAB0 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ;;;; ;;;; 169.99 0.00043624 239634000 22017.2 20395.27 21146.36 18824.07 24027.55 24642.8 20796.48 22782.04 21351.19 20624.67 FALSE FALSE TRUE 21748.8459 20682.39515 21514.40353 21000.59754 22801.33446 23068.20461 22562.93249 23441.20238 19441.48609 20088.8381 1.08263334 1.029546609 1.07096306 1.04538637 1.13502505 1.148309549 1.123157665 1.166876963 0.967775538 1 14.2941065 -4 0.117619346 0.971056963 1.57597159 0.77975836 0.029621196 36.45985631 0.296300926 0.13954619 3.619734365 1.00E-04 4 0.604914627 TLENQS(ph)HETLER ddPTM_HeLa_Romidepsin_16h_R1 1 TLENQSHETLER 12 0 P48681 P48681 NES Nestin 1 0 TLENQS(0.992)HET(0.007)LER 81.594 0.019002 5770800 1551.5 1113.8 1035.9 1260.2 1772.4 1804.6 1353.5 1295 1541.1 1421.9 TRUE FALSE FALSE 1532.589721 1129.480106 1053.929405 1405.910253 1681.947814 1689.291884 1468.466256 1332.468782 1403.260156 1384.958833 1.106595867 0.815533342 0.760982478 1.015127829 1.214438851 1.219741586 1.060295961 0.96209992 1.013214345 1 10.43562738 -7.248210665 21.48497798 1.036715163 0.962099558 0.008034874 0.140655597 1255.434615 2038694.952 0.020880958 0.440525438 5.65E-08 7.248210665 -0.074615605 TLEPVRPPVVPNDYVPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 3 TLEPVRPPVVPNDYVPSPTR 20 1 H7C3Q7;H0Y6B5;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9 H7C3Q7 ABI2 Abl interactor 2 1 0 TLEPVRPPVVPNDYVPS(0.622)PT(0.378)R;TLEPVRPPVVPNDY(0.002)VPS(0.499)PT(0.499)R;TLEPVRPPVVPNDYVPS(0.5)PT(0.5)R ;; 92.147 0.00053769 94216000 3213.25 3112.89 3011.39 3859.19 4326.14 3904.74 3678.41 3597.08 3198.82 2931.33 TRUE FALSE FALSE 3174.085673 3156.713347 3063.80198 4305.407706 4105.360933 3655.239716 3990.854054 3701.155835 2912.709528 2855.173624 1.111696202 1.105611694 1.073070287 1.507932011 1.43786735 1.280216266 1.397762301 1.296297992 1.020151455 1 11.47936276 -9.278240959 23.8499309 1.060277005 1.382004081 0.846309853 0.068585263 132.8899543 188637.6141 0.011515145 0.01762448 5.27E-10 9.278240959 0.321727076 TLEPVRPPVVPNDYVPSPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TLEPVRPPVVPNDYVPSPTR 20 1 H7C3Q7;H0Y6B5;B7Z836;E7EW77;E7EP65;A0A0C4DG21;F8WAL6;Q9NYB9-3;Q9NYB9-2;Q9NYB9-4;Q9NYB9 H7C3Q7 ABI2 Abl interactor 2 1 0 TLEPVRPPVVPNDYVPS(0.27)PT(0.73)R 80.477 0.0024352 26507000 1049.3 1005.8 848.23 1348.7 1477.2 1631.2 1194.8 1215.8 933.88 849.19 TRUE FALSE FALSE 1036.510728 1019.959679 862.9930873 1504.64304 1401.812972 1526.971584 1296.286282 1250.977255 850.3514339 827.1279214 1.253144406 1.233134141 1.043361087 1.819117697 1.694795854 1.846112971 1.567213787 1.512435045 1.028077292 1 9.69196666 -9.264185013 24.99859882 1.12770952 1.690397156 0.848656209 0.121605792 78.27894834 712718.5347 0.021328895 0.033501274 5.44E-10 9.264185013 0.562687637 TLEVVS(ph)PS(ph)QSVTGSAGHTPYYQS(ph)PTDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLEVVSPSQSVTGSAGHTPYYQSPTDEK 28 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 3 0 T(0.011)LEVVS(0.401)PS(0.401)QS(0.401)VT(0.39)GS(0.359)AGHT(0.033)PY(0.09)Y(0.091)QS(0.72)PT(0.102)DEK 55.049 0.0044566 9512100 2157.8 1859.3 1801.1 1858.7 2647.9 2792.4 2331.4 2039.9 2656.8 2593.6 TRUE FALSE FALSE 2131.499904 1885.475274 1832.44739 2073.611639 2512.767782 2613.974652 2529.429058 2098.921288 2419.169154 2526.217898 0.843751406 0.746362883 0.725371866 0.820836414 0.99467579 1.034738395 1.001271133 0.830855204 0.957624897 1 11.30276337 -6.969003032 14.22524062 0.908249057 0.617243983 0.036839808 0.106972224 2266917.524 31790944.54 0.016980565 15376694.2 1.07E-07 6.969003032 -0.291005074 TLEVVS(ph)PSQSVTGSAGHTPYYQS(ph)PTDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLEVVSPSQSVTGSAGHTPYYQSPTDEK 28 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 T(0.013)LEVVS(0.838)PS(0.025)QS(0.011)VT(0.005)GS(0.099)AGHT(0.012)PY(0.005)Y(0.004)QS(0.783)PT(0.205)DEK 73.128 0.00040884 15033000 997.03 1092.9 1030.5 721.93 2098.8 2022.7 1602 1437.8 2010.4 1746.5 TRUE FALSE FALSE 984.8778149 1108.285875 1048.43542 805.4029434 1991.690404 1893.455998 1738.07384 1479.400475 1830.584789 1701.125678 0.578956527 0.651501467 0.616318614 0.473452934 1.170807325 1.113060618 1.021719831 0.869659716 1.076102026 1 10.73227402 -8.742105199 24.99995666 0.748184477 1.047180218 0.394933309 0.188036874 227.6164862 294316.8488 0.030399943 0.060727457 1.81E-09 8.742105199 0.298995741 TLEVVSPS(ph)QS(ph)VTGSAGHTPYYQS(ph)PTDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLEVVSPSQSVTGSAGHTPYYQSPTDEK 28 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 3 0 T(0.009)LEVVS(0.257)PS(0.54)QS(0.579)VT(0.362)GS(0.355)AGHT(0.134)PY(0.091)Y(0.075)QS(0.462)PT(0.137)DEK 65.141 0.00054122 8753000 1724.4 1293.8 1440.2 1052.2 1988.3 1674.1 1533.1 1699.2 2074.4 1628 TRUE FALSE FALSE 1703.38235 1312.01415 1465.266077 1173.860315 1886.829632 1567.130413 1663.321476 1748.363671 1888.860469 1585.704325 1.074211833 0.827401508 0.924047474 0.74027692 1.189900035 0.988286648 1.04894806 1.10257861 1.191180751 1 10.63090807 -7.4051231 1.148755356 0.998032564 1.131622612 0.06581247 0.134426784 3.149418479 3.997090608 0.018762778 0.472239262 3.93E-08 7.4051231 0.133590048 TLFLGIPDENFEDHS(ph)APPSPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 1 0 TLFLGIPDENFEDHS(0.651)APPS(0.349)PEEK 83.436 0.000142 5554800 3857.6 3698.9 4037.3 2893.3 2944.4 3046.8 2823.8 3000.3 3717.8 3872.7 TRUE FALSE FALSE 3810.582087 3750.973211 4107.567513 3227.836959 2794.136281 2852.119313 3063.653502 3087.108947 3385.270657 3772.086696 1.010205331 0.994402704 1.088937727 0.855716536 0.740740207 0.756111814 0.812190638 0.8184088 0.897453036 1 11.88114712 -9.072436623 4.768604656 1.009340949 0.783297489 0.81338068 0.049082347 0.043291599 1.848892036 0.005056886 0.008619114 8.46E-10 9.072436623 -0.226043461 TLFLGIPDENFEDHSAPPS(ph)PEEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLFLGIPDENFEDHSAPPSPEEK 23 0 Q99683-2;Q99683 Q99683-2 MAP3K5 Mitogen-activated protein kinase kinase kinase 5 1 0 TLFLGIPDENFEDHS(0.429)APPS(0.571)PEEK 62.398 0.002693 7071500 3136.7 3408.6 3769 2160.9 2633.1 2733.5 2170.3 2872.3 3846 3340.9 TRUE FALSE FALSE 3098.468694 3456.58636 3834.597864 2410.753425 2498.723082 2558.838172 2354.645228 2955.405469 3502.004128 3254.102936 0.95217292 1.062224038 1.178388619 0.740835023 0.767868482 0.786342111 0.72359273 0.908208968 1.076181115 1 11.66804417 -9.234830179 24.98377868 0.998253976 0.781019162 0.713707682 0.081259411 354.9871368 333303.1428 0.011914341 0.019754206 5.82E-10 9.234830179 -0.217234814 TLFPLIEAK ddPTM_HeLa_Romidepsin_16h_R1 1 TLFPLIEAK 9 0 P13010 P13010 XRCC5 X-ray repair cross-complementing protein 5 0 0 97.431 0.0093998 0 0 0 126.23 61.76 0 0 0 129.21 0 0 FALSE FALSE TRUE 0 0 128.4269802 68.90098179 0 0 0 132.9484875 0 0 0 TLFREGIT(ph)GLY(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TLFREGITGLYR 12 1 O43772 O43772 SLC25A20 Mitochondrial carnitine/acylcarnitine carrier protein 2 0 TLFREGIT(1)GLY(1)R 66.784 0.024423 5548200 2672.4 2775.9 2915 2780.6 3088.7 3126.7 2440.6 2636.5 3222.2 3036.7 TRUE FALSE FALSE 2639.827761 2814.979193 2965.734352 3102.106055 2931.072113 2926.913961 2647.904503 2712.782968 2933.998362 2957.806096 0.892495206 0.951711877 1.002680452 1.048786146 0.99096155 0.989555727 0.895225859 0.917160517 0.991950881 1 11.53031176 -4.841873411 13.68071891 0.958313777 0.925029245 0 0.050113999 0 0 0.007801844 0 1.44E-05 4.841873411 -0.033284532 TLHPAVHAGILAR ddPTM_HeLa_Romidepsin_16h_R1 2 TLHPAVHAGILAR 13 0 P31939-2;P31939;C9JLK0 P31939-2 ATIC Bifunctional purine biosynthesis protein PURH;Phosphoribosylaminoimidazolecarboxamide formyltransferase;IMP cyclohydrolase 0 0 ; ; 126.71 0.00038365 7249500 3877.4 4340.5 4313.5 4645.8 4655.7 4779.1 4141.4 3988.7 4482.4 3873.2 FALSE FALSE TRUE 3830.140757 4401.605673 4388.574658 5182.969255 4418.102256 4473.730934 4493.170413 4104.106741 4081.482918 3772.573706 1.015259358 1.166738152 1.163284007 1.373855002 1.171110918 1.185856469 1.191009312 1.087879803 1.081882883 1 11.88133337 -10.20247262 2.687163281 1.005517096 1.200878447 0.500806734 0.071613716 0.127382827 1.779046629 0.011637042 0.014102254 6.27E-11 10.20247262 0.195361351 TLHPDLGTDKDK(ac)EQWK ddPTM_HeLa_Romidepsin_16h_R1 2 TLHPDLGTDKDKEQWK 16 2 P00338;P00338-3;P00338-5;P00338-2;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 1 ; TLHPDLGTDK(0.212)DK(0.788)EQWK;TLHPDLGTDK(0.248)DK(0.752)EQWK 54.898 0.02397 5366300 2162.51 1878.03 1890.08 1290.02 4866.4 4083 3654.3 3651.1 5619.6 4090.1 FALSE TRUE FALSE 2136.152496 1904.468956 1922.97605 1439.178182 4618.049449 3822.109477 3964.696151 3756.738818 5116.968901 3983.838612 0.536204577 0.478048722 0.482694265 0.361254138 1.159195916 0.959403693 0.995194971 0.94299473 1.284431775 1 11.95994349 -12.59420943 1.42988483 0.997957561 0.711222622 0.214492385 0.273186681 0.723083721 2.68214289 0.194033903 0.046399271 2.55E-13 12.59420943 -0.286734939 TLHS(ph)PPLQLQQR ddPTM_HeLa_Romidepsin_16h_R1 1 TLHSPPLQLQQR 12 0 A0A2R8YGT1;F8W9A8;B7WPL9;Q6PFW1-7;Q6PFW1-4;Q6PFW1-3;Q6PFW1-2;Q6PFW1 A0A2R8YGT1 PPIP5K1 Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1 1 0 T(0.001)LHS(0.999)PPLQLQQR 94.532 0.0093744 9705300 1300.8 1515.6 1503.9 2070.8 1992.7 2017.9 1639.3 1590 1660 1555.1 TRUE FALSE FALSE 1284.945349 1536.936657 1530.074749 2310.235639 1891.005083 1888.962702 1778.542101 1636.004141 1511.525442 1514.698278 0.848317693 1.014681722 1.010151507 1.525211769 1.248436808 1.247088433 1.17418903 1.080085827 0.997905302 1 10.56481473 -9.493572993 17.61221683 0.936632412 1.251507884 0.59687321 0.114877112 9.391297655 5643.612374 0.018520537 0.028192338 3.21E-10 9.493572993 0.314875472 TLHSDDEGTVLDDSR ddPTM_HeLa_Romidepsin_16h_R1 2 TLHSDDEGTVLDDSR 15 0 E9PMH2;O00170 E9PMH2 AIP AH receptor-interacting protein 0 0 ; ; 210.37 8.25E-26 21340000 4159.3 4497.4 4261.6 4546.4 4374.3 4302.8 3132.4 3908.5 5161.1 4568.8 FALSE FALSE TRUE 4108.604852 4560.714515 4335.77136 5072.076159 4151.063148 4027.864967 3398.465978 4021.586281 4699.47829 4450.101917 0.923260844 1.024856194 0.974308328 1.139766292 0.932801816 0.905117465 0.763682729 0.903706557 1.056038351 1 12.11962266 -8.150497191 2.825908827 0.980753256 0.835015459 0.478657921 0.07011823 0.189649517 2.904205866 0.009758146 0.029079742 7.07E-09 8.150497191 -0.145737797 TLK(ac)IPAMTIAK ddPTM_HeLa_Romidepsin_16h_R1 1 TLKIPAMTIAK 11 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 TLK(1)IPAMTIAK 118.9 0.0046505 1318500 569.32 709.34 1527.6 1043.4 1598.8 2239.8 1673.4 927.31 621.42 329.53 FALSE TRUE FALSE 562.3809089 719.3261071 1554.187237 1164.042817 1517.20727 2096.684009 1815.538554 954.1402518 565.8386388 320.9687631 1.752135951 2.241109385 4.842175987 3.626654526 4.726962385 6.532361556 5.656433781 2.972688814 1.762908743 1 8.32628909 -9.840519879 1.058701938 1.243587799 5.039347439 0.693066327 0.980974822 0.169990466 0.378450849 0.186551876 0.275177084 1.44E-10 9.840519879 3.79575964 TLK(ac)MIQPSASGSLVGR ddPTM_HeLa_Romidepsin_16h_R1 2 TLKMIQPSASGSLVGR 16 1 C9K0U5;H7C608;E2QRF9;O75496 C9K0U5 GMNN Geminin 0 1 ; TLK(1)MIQPSASGSLVGR;TLK(1)MIQPSASGSLVGR 109.48 0.004663 1548040 157.84 132.833 275.34 136.73 192.216 0 0 0 436.03 122.34 FALSE TRUE FALSE 155.9161854 134.7030265 280.1321772 152.5393659 182.4065003 0 0 0 397.0303847 119.1615892 1.30844332 1.130423213 2.350859695 1.280105166 1.530749141 0 0 0 3.331865474 1 6.896775459 -8.254216114 24.70179742 1.272880377 5.56E-08 0.462998049 0.745924269 207.5126707 709639.7112 0.055776077 0.138998321 5.57E-09 8.254216114 -1.272880322 TLLDIS(ph)GYRQQR ddPTM_HeLa_Romidepsin_16h_R1 1 TLLDISGYRQQR 12 1 G3V2R1;Q9UPU9-2;Q9UPU9-3;Q9UPU9 G3V2R1 SAMD4A Protein Smaug homolog 1 1 0 TLLDIS(0.948)GY(0.052)RQQR 138.4 0.014982 12500000 1575.2 1441.3 1343.6 1604.7 1935.1 1770.5 1200.8 1634.5 1754.7 1371.8 TRUE FALSE FALSE 1556.000857 1461.590659 1366.984794 1790.242964 1836.344626 1657.370764 1302.795922 1681.791679 1597.755237 1336.160438 1.164531453 1.093873623 1.023069352 1.339841319 1.374344408 1.240398022 0.975029558 1.258674954 1.195780979 1 10.38387753 -9.274424369 24.93906406 1.077415197 1.230813157 0.273120711 0.113841529 761.2218194 1462005.495 0.018631678 0.028568397 5.32E-10 9.274424369 0.15339796 TLLEQLDDDQ ddPTM_HeLa_Romidepsin_16h_R1 1 TLLEQLDDDQ 10 0 O75400-2;O75400-3;O75400 O75400-2 PRPF40A Pre-mRNA-processing factor 40 homolog A 0 0 214.96 1.14E-17 13181000 8505.4 8265 7952.6 7378.6 8667.9 7799.1 7282.4 7758.8 8281.3 8095.2 FALSE FALSE TRUE 8401.732913 8381.354887 8091.011667 8231.748449 8225.544719 7300.76268 7900.966874 7983.288637 7540.599787 7884.885537 1.065549129 1.062964687 1.026141931 1.043990862 1.043204074 0.925918664 1.002039514 1.012479966 0.956335986 1 12.9448741 -8.315783165 24.99900827 1.035420903 0.982335157 0.24505312 0.037249635 245.9878932 113157.763 0.00472383 0.010562806 4.83E-09 8.315783165 -0.053085745 TLLIK(ac)TVETR ddPTM_HeLa_Romidepsin_16h_R1 1 TLLIKTVETR 10 1 P08670 P08670 VIM Vimentin 0 1 TLLIK(1)TVETR 109.16 0.021974 1294400 288.26 421.85 488.94 332.21 384.79 376.88 240.6 363.06 487.56 318.74 FALSE TRUE FALSE 284.7465762 427.7888154 497.4497956 370.6216833 365.1527305 352.7985843 261.036558 373.5645683 443.9514125 310.4590889 0.917179063 1.37792331 1.602303857 1.193785902 1.176170206 1.136377053 0.840808233 1.203265041 1.429983622 1 8.278259358 -10.27984099 24.6860068 0.960890105 1.213128699 0 0.234191007 695.5763414 933122.193 0.033649104 0.038517797 5.25E-11 10.27984099 0.252238594 TLLISSLS(ph)PALPAEHLEDR ddPTM_HeLa_Romidepsin_16h_R1 2 TLLISSLSPALPAEHLEDR 19 0 Q8NDT2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 TLLIS(0.001)S(0.008)LS(0.99)PALPAEHLEDR;TLLIS(0.004)S(0.037)LS(0.959)PALPAEHLEDR ; 91.733 0.0014656 22341400 3774.3 3488.5 3335.7 2858.8 3638.6 4435.1 3953.7 4658.6 4343.8 3292.5 TRUE FALSE FALSE 3728.29738 3537.611195 3393.756459 3189.347907 3452.908665 4151.711424 4289.527179 4793.389241 3955.279649 3206.960375 1.162564218 1.103104117 1.058247082 0.994508049 1.076692026 1.294593926 1.337567877 1.494683027 1.233342226 1 11.64699081 -7.944556715 1.659602814 1.071786879 1.456805234 0.761767439 0.07532285 0.136208476 0.681476446 0.010719906 0.054922137 1.14E-08 7.944556715 0.385018355 TLLLS(ph)SDDEF ddPTM_HeLa_Romidepsin_16h_R1 1 TLLLSSDDEF 10 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 0 TLLLS(0.581)S(0.419)DDEF 101.11 0.023779 791300 1076.5 1019.4 1125 531.8 960.94 1338.9 971.09 1715.3 1012.5 844.43 TRUE FALSE FALSE 1063.379204 1033.75114 1144.580153 593.2892182 911.899646 1253.348611 1053.57436 1764.929499 921.9394641 822.4915869 1.292875479 1.256853148 1.391601047 0.721331656 1.108703919 1.523843686 1.280954574 2.14583289 1.12091051 1 9.683857112 -4.576999204 0.949795773 1.144031338 199.9935024 0.673484771 0.203415885 158.5246545 0.912992874 0.032477321 67644.79254 2.65E-05 4.576999204 198.8494711 TLLLSS(ph)DDEF ddPTM_HeLa_Romidepsin_16h_R1 1 TLLLSSDDEF 10 0 A0A0J9YYJ3;Q9Y519 A0A0J9YYJ3 TMEM184B Transmembrane protein 184B 1 0 TLLLS(0.14)S(0.86)DDEF 98.048 0.026833 882340 956.08 1080.3 945.05 772.7 1129.2 1318.4 986.56 1420 1080.4 815.26 TRUE FALSE FALSE 944.4269292 1095.508492 961.4981988 862.0432097 1071.57271 1234.158495 1070.358382 1461.08546 983.7663181 794.0794277 1.189335596 1.379595609 1.210833785 1.085588141 1.349452804 1.554200313 1.347923576 1.839973948 1.23887647 1 9.63313951 -4 0.224278651 1.027863057 4.745541875 0.629722884 0.1392052 18.82799316 0.226916263 0.089888151 25.74310916 1.00E-04 4 3.717678818 TLLSES(ph)SSQSSKSPSLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 T(0.004)LLS(0.023)ES(0.258)S(0.258)S(0.075)QS(0.019)S(0.019)KS(0.231)PS(0.11)LS(0.002)SK 56.906 0.016945 161870000 3411.6 3413.6 3130.6 3603.1 3096.3 2848.1 2211.5 2955.9 3888.9 3100 TRUE FALSE FALSE 3370.018107 3461.65675 3185.08678 4019.707375 2938.284257 2666.115602 2399.344755 3041.424303 3541.067044 3019.461553 1.116099029 1.146448362 1.05485257 1.331266289 0.973115307 0.882977165 0.794626695 1.007273731 1.17274785 1 11.56007559 -8.528312073 24.99985523 1.083863334 0.892112627 0.50379381 0.102366221 103.1708408 474709.4795 0.015032992 0.030141022 2.96E-09 8.528312073 -0.191750707 TLLSESSSQSSKS(ph)PSLSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TLLSESSSQSSKSPSLSSK 19 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 T(0.001)LLSES(0.001)S(0.003)S(0.007)QS(0.228)S(0.228)KS(0.483)PS(0.047)LS(0.003)S(0.001)K 83.727 0.0025572 188680000 4742.9 3721.2 4608 4894.3 3907.6 3360.4 3159.2 3343.3 4563.6 4286.5 TRUE FALSE FALSE 4685.09171 3773.587151 4688.200307 5460.201994 3708.180591 3145.681285 3427.542369 3440.033111 4155.420186 4175.136112 1.122141072 0.903823744 1.122885621 1.307790177 0.888158012 0.753432032 0.820941468 0.823933165 0.995277777 1 12.02760752 -8.536289912 24.98423017 1.068493927 0.804787593 0.607159135 0.10175085 116.4336655 216908.657 0.014911349 0.02983492 2.91E-09 8.536289912 -0.263706335 TLLTGDGGGEAT(ph)GSPLAQGK ddPTM_HeLa_Romidepsin_16h_R1 1 TLLTGDGGGEATGSPLAQGK 20 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;H0Y2S9;H0Y7E2 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 TLLTGDGGGEAT(0.974)GS(0.026)PLAQGK 222.96 2.46E-41 37255000 4874.5 5459.5 5167.6 4446.4 6148.7 8014.8 7351.6 7811.5 5888.9 5080.8 TRUE FALSE FALSE 4815.087719 5536.358984 5257.53991 4960.513689 5834.908895 7502.680147 7976.044721 8037.513428 5362.182035 4948.800084 0.972980851 1.118727548 1.062386805 1.002366959 1.179055285 1.516060463 1.611712857 1.624133788 1.083531754 1 12.27286305 -8.316667908 1.898421763 1.003492825 1.626079555 0.959676729 0.049859551 0.041597337 0.286909995 0.007234739 0.022246775 4.82E-09 8.316667908 0.62258673 TLLTGDGGGEATGS(ph)PLAQGK ddPTM_HeLa_Romidepsin_16h_R1 1 TLLTGDGGGEATGSPLAQGK 20 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;H0Y2S9;H0Y7E2 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 TLLTGDGGGEAT(0.164)GS(0.836)PLAQGK 294.39 2.68E-129 37445000 3093.4 2709.3 2649 2428.9 2832.7 3850.8 3617.3 3801.4 2943.7 2750.3 TRUE FALSE FALSE 3055.696451 2747.441597 2695.104734 2709.740846 2688.136749 3604.746308 3924.553372 3911.387511 2680.408099 2678.84681 1.14067607 1.025606088 1.006069001 1.011532588 1.003467887 1.345633612 1.465015975 1.460101226 1.000582822 1 11.38739637 -8.124940656 3.56236965 1.052251636 1.454533705 0.938053707 0.0469108 0.055535616 1.274512694 0.00893478 0.025259719 7.50E-09 8.124940656 0.402282069 TLNAEGTDALGPNVDGT(ph)SVSPGDTEPMIR ddPTM_HeLa_Romidepsin_16h_R1 1 TLNAEGTDALGPNVDGTSVSPGDTEPMIR 29 0 Q5M775-4;Q5M775;Q5M775-5;Q5M775-3;Q5M775-2 Q5M775-4 SPECC1 Cytospin-B 1 0 TLNAEGT(0.017)DALGPNVDGT(0.61)S(0.172)VS(0.138)PGDT(0.063)EPMIR 54.097 0.0033862 4249500 992.46 1133.1 1035.1 1169.7 1353.3 1400.1 1107.5 1211.6 1090.5 1119.5 TRUE FALSE FALSE 980.3635158 1149.051812 1053.115481 1304.946218 1284.236051 1310.638129 1201.571022 1246.655734 992.9629488 1090.415229 0.899073573 1.053774545 0.965793079 1.196742473 1.177749556 1.201962421 1.101938959 1.14328533 0.910628284 1 10.0906619 -9.268111465 24.43763166 0.961268215 1.163704844 0.807221351 0.048471628 134.7943472 493706.2768 0.008347056 0.012933775 5.39E-10 9.268111465 0.202436629 TLNAETPKS(ph)SPLPAK ddPTM_HeLa_Romidepsin_16h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 0 TLNAET(0.003)PKS(0.854)S(0.143)PLPAK 87.668 0.0068896 231370000 4131.3 3810.5 3112.2 4147 2879.6 2392.5 2184.6 2148.2 4269.7 3849.3 TRUE FALSE FALSE 4080.946127 3864.144319 3166.366535 4626.495652 2732.643267 2239.626971 2370.159869 2210.354778 3887.807338 3749.294631 1.088457037 1.030632345 0.844523263 1.233964281 0.728841965 0.597346219 0.63216154 0.589538832 1.036943671 1 11.87240349 -8.597713673 5.870041504 1.036918665 0.617019639 0.829252032 0.090552687 0.055972992 3.306658304 0.012550057 0.025407847 2.53E-09 8.597713673 -0.419899026 TLNAETPKSS(ph)PLPAK ddPTM_HeLa_Romidepsin_16h_R1 1 TLNAETPKSSPLPAK 15 1 Q7L2J0 Q7L2J0 MEPCE 7SK snRNA methylphosphate capping enzyme 1 0 TLNAETPKS(0.079)S(0.921)PLPAK 185.27 7.89E-08 37290000 4222.9 4780.7 3691.7 3971.3 2770.4 2225.9 2100.6 2646.7 3773.8 4143.9 TRUE FALSE FALSE 4171.429671 4848.00282 3755.95249 4430.480392 2629.01615 2083.672174 2279.024912 2723.278089 3436.261876 4036.240881 1.033493737 1.201118309 0.930557071 1.097674921 0.651352639 0.516240788 0.564640461 0.674706532 0.851352032 1 11.97879656 -8.697019248 5.346337291 1.02961998 0.585239501 0.82042036 0.095724515 0.045626608 2.507957311 0.010799519 0.021716897 2.01E-09 8.697019248 -0.444380479 TLPSTSSS(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 TLPSTSSSGSK 11 0 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 1 0 TLPST(0.001)S(0.001)S(0.031)S(0.836)GS(0.131)K;TLPST(0.002)S(0.002)S(0.041)S(0.938)GS(0.017)K ; 128.36 0.0063234 12795500 7133.1 7158.4 7427.5 6203.7 6904.9 8332.1 8017.2 5564.9 8603.2 7882.2 TRUE FALSE FALSE 7046.159034 7259.176143 7556.772522 6921.000983 6552.517187 7799.705701 8698.180768 5725.911602 7833.708245 7677.419308 0.917777023 0.945522949 0.984285503 0.901474924 0.853479135 1.01592806 1.132956325 0.74581202 1.020356963 1 12.90640573 -12.47403219 1.18841368 1.000296192 0.941473585 0.079643932 0.096335474 1.33251933 3.339785003 0.064595444 0.015540152 3.36E-13 12.47403219 -0.058822608 TLPSTSSSGSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 TLPSTSSSGSKR 12 1 A0A286YEX4;P08651-4;P08651-5;P08651-3;P08651-6;P08651-2;P08651 A0A286YEX4 NFIC Nuclear factor 1 C-type 0 1 ; TLPSTSSSGSK(1)R;TLPSTSSSGSK(1)R 158.47 0.00038432 6604400 304.18 364.15 336.614 1818.11 1970.92 1881.61 1965.15 1755.66 374.19 451.19 FALSE TRUE FALSE 300.4725372 369.2765133 342.4726255 2028.328433 1870.336598 1761.381194 2132.069792 1806.457252 340.7215092 439.4680188 0.683718779 0.840280743 0.779289074 4.61541761 4.255910597 4.007984924 4.851478836 4.110554523 0.775304447 1 8.77961437 -9.263261116 24.99985388 0.841043771 4.368856406 0.982510807 0.236976032 14.2065845 194958.4815 0.036013437 0.056798411 5.45E-10 9.263261116 3.527812635 TLQEVTEMDSVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 TLQEVTEMDSVKR 13 1 A0A075B730;P58107 A0A075B730 EPPK1 Epiplakin 0 1 ; TLQEVTEMDSVK(1)R;TLQEVTEMDSVK(1)R 117.7 0.0008885 1639630 132.25 73.942 0 69.116 356.896 410.63 556.91 571.25 272.73 438.93 FALSE TRUE FALSE 130.6380861 74.98295742 0 77.10751712 338.6822654 384.3920682 604.2139215 587.7782175 248.3363457 427.5265353 0.3055672 0.175387844 0 0.180357266 0.792190045 0.899106924 1.413278175 1.37483447 0.580867678 1 8.739870156 -8.004623957 1.923571521 0.540136624 1.42082277 0.618728301 0.296101811 0.26600115 1.868232999 0.058772842 0.24623148 9.89E-09 8.004623957 0.880686146 TLQRLS(ph)SGFDDIDLPSAVK ddPTM_HeLa_Romidepsin_16h_R1 2 TLQRLSSGFDDIDLPSAVK 19 1 E9PKC4;Q9Y446;Q9Y446-2 E9PKC4 PKP3 Plakophilin-3 1 0 T(0.255)LQRLS(0.372)S(0.372)GFDDIDLPSAVK;T(0.013)LQRLS(0.494)S(0.494)GFDDIDLPSAVK ; 121.92 0.0003214 62048000 6652.9 6366.3 6221.8 8226.9 3520.8 3196.9 2923.6 2753.4 6729.4 6525.8 TRUE FALSE FALSE 6571.811896 6455.924939 6330.087819 9178.132887 3341.120438 2992.628408 3171.930511 2833.065285 6127.50561 6356.258775 1.033911949 1.015680004 0.995882648 1.44395205 0.525642608 0.470816012 0.49902476 0.445712704 0.964011351 1 12.63396215 -8.645898926 8.835505887 1.041162224 0.479041817 0.8263583 0.132124719 0.076528622 5.6178655 0.017871664 0.03578386 2.26E-09 8.645898926 -0.562120407 TLQTDSIDSFETQRT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TLQTDSIDSFETQRTPR 17 1 A0A3B3IS71;P06400 A0A3B3IS71 RB1 Retinoblastoma-associated protein 1 0 TLQTDSIDSFET(0.004)QRT(0.996)PR;TLQTDSIDSFETQRT(1)PR ; 152.94 4.43E-05 70211000 4447.2 4172.2 4207.1 4237.9 4219.4 4592.4 3082.1 3306.2 4821.3 4720 TRUE FALSE FALSE 4392.995816 4230.936341 4280.322811 4727.905938 4004.068273 4298.960461 3343.893497 3401.859681 4390.070853 4597.37372 0.95554464 0.920294194 0.931036516 1.02839278 0.870946875 0.935090494 0.727348634 0.739957177 0.954908415 1 12.16659423 -7.819407308 1.353594473 0.971014144 0.698239473 0.763169551 0.046437471 0.18406854 0.530435632 0.006672525 0.051903248 1.52E-08 7.819407308 -0.272774671 TLS(ph)DESIYNSQR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSDESIYNSQR 12 0 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 T(0.299)LS(0.701)DESIYNSQR 142.12 0.0017118 131150000 1058.8 1423.7 861.85 907.94 919.31 856.15 758.8 1138.2 1516.2 1627.4 TRUE FALSE FALSE 1045.894938 1443.742886 876.8501377 1012.920295 872.3941803 801.4447781 823.2524531 1171.132021 1380.587275 1585.119913 0.659820705 0.910809885 0.553175902 0.639018087 0.550364785 0.505605141 0.519362886 0.73882866 0.870967088 1 10.63037627 -13.37973754 0.22142543 1.427859 0.535572827 0.554106167 0.112652027 5.397283879 0.235997737 1.349807681 0.110083719 4.17E-14 13.37973754 -0.892286173 TLS(ph)GSGSGSGSSYSGSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSGSGSGSGSSYSGSSSR 19 0 E7ERS3;Q86VM9 E7ERS3 ZC3H18 Zinc finger CCCH domain-containing protein 18 1 0 T(0.004)LS(0.992)GS(0.004)GSGSGSSYSGSSSR 168.08 1.92E-07 1601500 497.85 415.97 507.22 272.9 373.22 291.84 483.27 546.65 304.57 524.66 TRUE FALSE FALSE 491.7820127 421.8260366 516.0479513 304.453982 354.1731907 273.1923659 524.3189417 562.4664553 277.3284964 511.0292576 0.962336315 0.825444004 1.009820756 0.595766245 0.693058539 0.534592417 1.026005721 1.100654115 0.542686142 1 8.997262081 -9.998943215 1.314299406 0.985460974 0.797552649 0 0.223799481 0.548943887 1.855896606 0.034114172 0.045445611 1.00E-10 9.998943215 -0.187908325 TLS(ph)LSYNALGAPALAR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSLSYNALGAPALAR 16 0 Q96HA7-2;Q96HA7 Q96HA7-2 TONSL Tonsoku-like protein 1 0 T(0.291)LS(0.354)LS(0.354)YNALGAPALAR 82.55 0.021576 24787000 3109.9 3053.6 3140.2 2418.4 2991.4 2950.2 3293.7 3440.4 3514.4 3430.9 TRUE FALSE FALSE 3071.995343 3096.588661 3194.853864 2698.026787 2838.737696 2761.691741 3573.466796 3539.942546 3200.063262 3341.764723 0.919273377 0.926632758 0.95603794 0.807365871 0.849472638 0.826417169 1.069335244 1.059303344 0.957596817 1 11.70639445 -7.726958842 24.98719813 0.931860871 1.064319617 0.468256829 0.062873781 160.1746667 116072.5561 0.010376758 0.038822762 1.88E-08 7.726958842 0.132458746 TLS(ph)MIEEEIR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSMIEEEIR 10 0 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5;C9JVY5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 T(0.001)LS(0.999)MIEEEIR;T(0.001)LS(0.999)MIEEEIR ; 119.03 0.017135 153855000 9845.2 8994.7 8987.4 9158.9 10302.8 8861.7 7824.1 8129.3 9621.4 8631.7 TRUE FALSE FALSE 9725.202916 9121.327623 9143.821927 10217.89511 9777.009671 8295.46597 8488.678859 8364.50847 8760.837887 8407.44719 1.156736724 1.084910487 1.087586008 1.215338602 1.162898731 0.986680711 1.009661871 0.994892776 1.042033056 1 13.0374521 -8.236613952 24.63664117 1.093486494 0.998336774 0.404885525 0.059529924 730.5250025 724968.5544 0.010815902 0.027561715 5.80E-09 8.236613952 -0.09514972 TLS(ph)PEFNER ddPTM_HeLa_Romidepsin_16h_R1 1 TLSPEFNER 9 0 Q9BSJ8;Q9BSJ8-2 Q9BSJ8 ESYT1 Extended synaptotagmin-1 1 0 T(0.23)LS(0.77)PEFNER 94.82 0.003618 0 2792 3107 2349.5 2292.6 2198.9 3007 2040.6 2879.5 2883.9 2635.7 TRUE FALSE FALSE 2757.97003 3150.740428 2390.392062 2557.681199 2086.681928 2814.862405 2213.928513 2962.813789 2625.956761 2567.224134 1.074300445 1.227294643 0.931119348 0.996282781 0.812816419 1.096461492 0.862382245 1.154092372 1.022877873 1 11.32599354 TLS(ph)PTPASATAPTSQGIPTS(ph)DEESTPKK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSPTPASATAPTSQGIPTSDEESTPKK 28 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 2 0 T(0.2)LS(0.743)PT(0.051)PAS(0.004)AT(0.003)APT(0.014)S(0.013)QGIPT(0.295)S(0.597)DEES(0.038)T(0.042)PKK 59.386 0.00089032 8878700 1804 1721.8 1623.6 1686.9 1196.3 1708.2 1613.1 1313 2208.1 1862.1 TRUE FALSE FALSE 1782.012154 1746.039546 1651.858077 1881.947315 1135.248347 1599.051533 1750.116674 1350.989583 2010.602006 1813.722374 0.982516498 0.962682917 0.910755748 1.037615978 0.625921786 0.881640739 0.964930851 0.744871212 1.108550038 1 10.82473792 -8.808113273 24.99999989 0.985247944 0.821331519 0.492227001 0.096186569 78.21194886 41892.48281 0.012281057 0.022261355 1.56E-09 8.808113273 -0.163916425 TLS(ph)PTPSAEGYQDVR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSPTPSAEGYQDVR 15 0 F8W8M4;A0A0A0MRL6;A0A3B3IS55;O14639-3;O14639-5;O14639-2;O14639-6;O14639;J3QSX6;A0A494C1P1;A0A494C1G0;O14639-4;H0Y7N6;F6XFR5 F8W8M4 ABLIM1 Actin-binding LIM protein 1 1 0 T(0.006)LS(0.994)PTPSAEGYQDVR;T(0.193)LS(0.355)PT(0.355)PS(0.096)AEGYQDVR ; 163.62 0.0001055 562060000 3755 3507.25 3674.02 4579.67 3775.55 3853.25 3853.41 3749.57 3940.34 3536.52 TRUE FALSE FALSE 3709.232616 3556.625158 3737.964777 5109.192993 3582.869595 3607.039761 4180.718549 3858.057892 3587.906122 3444.640701 1.076812631 1.032509764 1.085153751 1.483229584 1.040128683 1.047145428 1.213687845 1.120017508 1.041590817 1 11.75013779 -9.51083862 24.89488341 1.038043324 1.179098612 0.253238656 0.11700448 596.6721734 1233716.81 0.017892294 0.026444029 3.08E-10 9.51083862 0.141055288 TLS(ph)TSDDVEDRENEK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSTSDDVEDRENEK 15 1 Q96A65;Q96A65-2 Q96A65 EXOC4 Exocyst complex component 4 1 0 T(0.026)LS(0.444)T(0.444)S(0.086)DDVEDRENEK 76.526 0.013959 4433900 1446.6 2061.7 1388.3 1472.2 1832 1529.5 1322.9 1536.5 1691.7 1766.5 TRUE FALSE FALSE 1428.968283 2090.724667 1412.462779 1642.422691 1738.506204 1431.769886 1435.267093 1580.956203 1540.390115 1720.606075 0.830502869 1.21510943 0.820910027 0.954560555 1.010403386 0.832131135 0.834163678 0.918836813 0.895260186 1 10.74870112 -8.241318839 24.5970433 0.9412035 0.858955852 0.1326922 0.108260987 1263.187036 1544223.217 0.015647714 0.039839781 5.74E-09 8.241318839 -0.082247648 TLSASTQDLS(ph)PH ddPTM_HeLa_Romidepsin_16h_R1 2 TLSASTQDLSPH 12 0 Q6P597;Q6P597-3;Q6P597-2 Q6P597 KLC3 Kinesin light chain 3 1 0 TLSASTQDLS(1)PH;TLSASTQDLS(1)PH ; 151.16 0.0014456 25313000 2028.8 1773.46 1724.2 2084 7081.1 13542.2 12394.5 14179.3 2303.7 1987.04 TRUE FALSE FALSE 2004.072205 1798.426816 1754.208978 2324.961886 6719.725044 12676.89713 13447.28852 14589.55567 2097.651302 1935.416414 1.035473395 0.929219574 0.906372895 1.201272175 3.471978947 6.549958464 6.948007892 7.538199824 1.08382428 1 10.91842829 -8.4135645 1.851864608 0.989188034 7.291673694 0.996526676 0.158578501 0.013294613 0.088215773 0.023734689 0.068270566 3.86E-09 8.4135645 6.302485659 up TLSDVEDQKELAS(ph)PVSPELR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 TLS(0.004)DVEDQKELAS(0.984)PVS(0.011)PELR 67.097 0.0039567 18230000 1379.9 1705.5 1430.9 1370 1634.1 1648 1463.2 1992.3 1515.1 1659.9 TRUE FALSE FALSE 1363.081248 1729.510074 1455.804214 1528.405846 1550.705779 1542.698119 1587.484171 2049.944057 1379.585661 1616.775559 0.843086253 1.069727993 0.900436802 0.945342004 0.959134848 0.954181989 0.981882836 1.267921231 0.853294481 1 10.6589037 -7.216456021 2.611516646 0.938142434 1.358951739 0.705873332 0.0629491 0.26563152 2.093368341 0.009582643 0.255278722 6.07E-08 7.216456021 0.420809305 TLSDVEDQKELASPVS(ph)PELR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSDVEDQKELASPVSPELR 20 1 Q5T4S7-3;Q5T4S7-4;Q5T4S7;Q5T4S7-2;Q5T4S7-5 Q5T4S7-3 UBR4 E3 ubiquitin-protein ligase UBR4 1 0 TLSDVEDQKELAS(0.032)PVS(0.968)PELR;TLSDVEDQKELASPVS(1)PELR ; 120.33 7.31E-05 75473000 3460.5 3423.2 3726.9 3806.4 4198.3 5570.2 4502.3 5663.9 3812.3 3279.1 TRUE FALSE FALSE 3418.322095 3471.391899 3791.765131 4246.513878 3984.045085 5214.282197 4884.72525 5827.77601 3471.31834 3193.908509 1.070262998 1.086878941 1.187186521 1.329566537 1.247388607 1.632570934 1.529387969 1.824653397 1.08685591 1 11.64110727 -7.463335048 0.389171162 1.004359892 2.293522697 0.918170772 0.075058491 0.740729824 0.085407827 0.018581839 0.432399033 3.44E-08 7.463335048 1.289162805 SNVS(ph)SPATPTASSSSSTTPT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 SNVSSPATPTASSSSSTTPTR 21 0 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 S(0.056)NVS(0.362)S(0.321)PAT(0.252)PT(0.007)AS(0.015)S(0.012)S(0.026)S(0.055)S(0.042)T(0.033)T(0.402)PT(0.417)R 115.84 0.00072904 5216300 3545 3345.8 3296.1 3079.2 2531.4 1576.9 1332.3 1570.8 3519.9 3539.6 TRUE FALSE FALSE 3501.792176 3392.90226 3353.467238 3435.231592 2402.213212 1476.141179 1445.465529 1616.24862 3205.071328 3447.640682 1.015706827 0.984122933 0.97268467 0.996400701 0.696770178 0.42815981 0.419262232 0.468798453 0.929641927 1 11.75139371 -8.546721212 2.354375855 1.003861713 0.433320013 0.982111865 0.032990306 0.018210364 0.201684002 0.00362183 0.008670808 2.84E-09 8.546721212 -0.5705417 down TLSNAEDYLDDEDS(ph)D ddPTM_HeLa_Romidepsin_16h_R1 4 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 1 0 TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D;TLSNAEDYLDDEDS(1)D ;;; 315.21 3.77E-155 370369200 14415.68 14200.28 13229.88 13202.9 14844.62 15231.15 14483.82 15503.19 14904.9 14096.07 TRUE FALSE FALSE 14239.97615 14400.19191 13460.14051 14729.48142 14087.04365 14257.92867 15714.07531 15951.75034 13571.76841 13729.85207 1.037154375 1.04882353 0.980355829 1.072807001 1.02601569 1.038461929 1.144518909 1.161829731 0.988486136 1 13.74502846 -7.764355054 3.466451409 1.022398125 1.159728088 0.796820462 0.026271159 0.067513118 1.676261236 0.003532512 0.014069066 1.72E-08 7.764355054 0.137329963 TLSNAEDYLDDEDSD ddPTM_HeLa_Romidepsin_16h_R1 2 TLSNAEDYLDDEDSD 15 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 0 0 ; ; 234.67 2.59E-44 32331000 12001.4 11030.8 11216.8 12118.5 16850.5 17637.1 15044.7 15179.2 11433.8 9926.5 FALSE FALSE TRUE 11855.12232 11186.09189 11412.0237 13519.69799 15990.55611 16510.14623 16322.59644 15618.3862 10411.13229 9668.608099 1.226145708 1.156949561 1.180317123 1.398308614 1.653863301 1.707603211 1.688205404 1.615370697 1.076797424 1 13.2390925 -9.046338781 1.641875825 1.112266034 1.683369254 0.948032698 0.059521922 0.081634807 0.4358062 0.014280661 0.028741736 8.99E-10 9.046338781 0.57110322 TLSPSSGYSSQSGT(ph)PTLPPK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSPSSGYSSQSGTPTLPPK 20 0 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 TLSPSSGYSSQSGT(0.988)PT(0.012)LPPK 241.79 5.59E-54 11359000 10098 10032 9534.9 11055 8355.2 8064.2 8130.3 7797.3 11615 10618 TRUE FALSE FALSE 9974.921692 10173.23076 9700.850935 12333.23112 7928.802966 7548.923646 8820.887479 8022.902573 10576.12531 10342.14283 0.964492742 0.983667595 0.937992358 1.192521832 0.766649919 0.729918719 0.852907142 0.775748576 1.022624178 1 13.33624751 -8.713701312 24.99999818 0.992189223 0.782749497 0.709943168 0.072745432 50.46797398 26429.36537 0.009745724 0.019491411 1.93E-09 8.713701312 -0.209439727 TLSPT(ph)PASATAPTSQGIPTS(ph)DEESTPKK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSPTPASATAPTSQGIPTSDEESTPKK 28 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 2 0 T(0.2)LS(0.29)PT(0.51)PASATAPT(0.004)S(0.002)QGIPT(0.119)S(0.874)DEES(0.001)TPKK 102.55 1.30E-08 11763000 3482.9 2892.2 2914.9 2638.5 2588.8 2591.2 2528.5 2681.6 3721.6 3502 TRUE FALSE FALSE 3440.449075 2932.916468 2965.632612 2943.575785 2456.683876 2425.630683 2743.270727 2759.187865 3388.730775 3411.017535 1.008628375 0.859836233 0.869427548 0.8629612 0.720220242 0.711116451 0.804238236 0.808904626 0.993466243 1 11.73598646 -9.76442509 1.000989753 1.00724126 0.767126819 0.820446187 0.043806297 0.134619084 0.268937124 0.008913377 0.01385707 1.72E-10 9.76442509 -0.240114441 TLSPT(ph)PASATAPTSQGIPTSDEESTPKK ddPTM_HeLa_Romidepsin_16h_R1 2 TLSPTPASATAPTSQGIPTSDEESTPKK 28 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 T(0.02)LS(0.383)PT(0.593)PAS(0.003)ATAPTSQGIPTSDEESTPKK;T(0.106)LS(0.106)PT(0.782)PAS(0.005)ATAPTSQGIPTSDEESTPKK ; 137.36 1.11E-10 26711000 7452.1 7014.9 6315 5944.6 5216.6 4962.6 4818.4 4463.6 7607 8018.9 TRUE FALSE FALSE 7361.270939 7113.655946 6424.909926 6631.942622 4950.377436 4645.505876 5227.674776 4592.747224 6926.610868 7810.567822 0.942475772 0.910773212 0.822591913 0.849098654 0.633805064 0.59477185 0.669307904 0.588017072 0.88682552 1 12.93121172 -9.121782538 0.738186195 0.980072353 0.589522879 0.879693546 0.050709167 0.119124224 0.124633555 0.008261642 0.022903972 7.55E-10 9.121782538 -0.390549474 TLSPTPASATAPTSQGIPT(ph)S(ph)DEESTPKK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSPTPASATAPTSQGIPTSDEESTPKK 28 1 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 2 0 TLSPTPASAT(0.001)APT(0.001)S(0.001)QGIPT(0.499)S(0.499)DEES(0.499)T(0.499)PKK 57.694 0.0010756 0 1214.7 1333 1122.1 829.35 620.54 621.59 460.64 486.06 1243 854.79 TRUE FALSE FALSE 1199.894769 1351.766009 1141.62968 925.2433492 588.8715282 581.8724051 499.7667501 500.1233792 1131.822967 832.5824326 1.441172336 1.62358219 1.37119117 1.111293384 0.707283153 0.69887663 0.600260984 0.600689325 1.359412501 1 9.701449308 -8.805318556 2.949636863 1.262354702 0.637472272 0.804483057 0.161380286 0.126541927 2.24909019 0.033395954 0.066906845 1.57E-09 8.805318556 -0.624882431 TLSQGESQTS(ph)EHELFLDTK ddPTM_HeLa_Romidepsin_16h_R1 1 TLSQGESQTSEHELFLDTK 19 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5;H7C1I7;Q5VZL5-3 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 0 TLSQGESQT(0.013)S(0.987)EHELFLDTK 113.08 0.0003403 8434400 2006.7 1893.2 1740.7 1737.1 1873.2 1671.9 1357.2 1146.6 2272.7 2058.6 TRUE FALSE FALSE 1982.241569 1919.852519 1770.996153 1937.951675 1777.603614 1565.070986 1472.480534 1179.775062 2069.42402 2005.117275 0.988591337 0.957476424 0.88323819 0.966502907 0.886533489 0.780538378 0.734361303 0.588382074 1.032071313 1 10.9694709 -6.595897689 0.435693878 0.998066337 3.28E-14 0.948295675 0.030419539 1.070486792 0.090161165 0.006443894 0.626505942 2.54E-07 6.595897689 -0.998066337 TLSQPEAS(ph)ETEEQR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSQPEASETEEQR 14 0 Q9P209 Q9P209 CEP72 Centrosomal protein of 72 kDa 1 0 TLS(0.01)QPEAS(0.77)ET(0.219)EEQR 88.163 0.021122 17744000 1402.2 1491.2 1517.2 1644 1947.3 1570.2 1547.7 1529.9 1686.3 1596.6 TRUE FALSE FALSE 1385.109447 1512.193153 1543.60623 1834.087015 1847.922015 1469.869288 1679.161599 1574.165243 1535.473105 1555.120102 0.890676833 0.972396377 0.992596152 1.179386089 1.188282508 0.945180559 1.079763291 1.012246733 0.987366251 1 10.60281029 -9.483900146 7.048719985 0.950185576 1.080249045 0.377074995 0.072306259 0.183578862 26.91805301 0.012089702 0.018300045 3.28E-10 9.483900146 0.130063468 TLSS(ph)PSNRPSGETSVPPPPAVGR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 T(0.008)LS(0.103)S(0.365)PS(0.088)NRPS(0.259)GET(0.088)S(0.088)VPPPPAVGR 57.798 0.0040727 50307000 1403.6 1400.4 1312.1 1069.2 1310.9 1037.4 1220.8 1066.1 1596.7 1344.7 TRUE FALSE FALSE 1386.492383 1420.114868 1334.93655 1192.825935 1243.999881 971.1134881 1324.494722 1096.945921 1453.887153 1309.7645 1.058581434 1.084252068 1.01921876 0.910717869 0.949788974 0.741441296 1.011246466 0.837513859 1.110037074 1 10.35509172 -9.171231384 2.335716085 1.033738445 0.884698884 0.55434121 0.072884251 0.182056939 1.940909762 0.010230206 0.018153214 6.74E-10 9.171231384 -0.149039561 TLSSFFT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSSFFTPR 9 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135;F5GZ28 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 TLSSFFT(1)PR;TLSSFFT(1)PR ; 128.51 0.018643 80497000 5873.6 5712 5316.5 4621.7 7308.6 7939.8 5669 5825.2 5885.6 5408.5 TRUE FALSE FALSE 5802.010304 5792.413686 5409.031452 5156.0827 6935.61487 7432.472405 6150.524719 5993.742971 5359.177195 5267.98639 1.101371544 1.099549858 1.026773999 0.978757787 1.316558995 1.4108754 1.167528589 1.137767361 1.017310372 1 12.3630359 -8.75909526 24.99999971 1.047213676 1.262613949 0.647379125 0.07963602 32.65861626 348295.9193 0.012561797 0.02420307 1.74E-09 8.75909526 0.215400274 TLSSPS(ph)NRPSGETSVPPPPAVGR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 T(0.001)LS(0.026)S(0.131)PS(0.323)NRPS(0.238)GET(0.141)S(0.141)VPPPPAVGR 93.215 3.72E-05 130750000 782.72 771.96 730.91 838.61 878.79 891.62 714.73 774.49 793.73 969.08 TRUE FALSE FALSE 773.1799076 782.8276731 743.6311819 935.574034 833.9420671 834.6483596 775.4391484 796.8986462 722.7368009 943.9031619 0.819130541 0.82935168 0.787825713 0.991175866 0.883503839 0.884252107 0.82152405 0.844258901 0.765689564 1 9.882495046 -12.35571789 1.055600299 1.000787024 0.856741634 0 0.089248993 0.358547831 0.70887151 0.038581351 0.009832285 4.41E-13 12.35571789 -0.144045391 TLSSPSNRPS(ph)GETSVPPPPAVGR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSSPSNRPSGETSVPPPPAVGR 23 1 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 TLS(0.01)S(0.038)PS(0.038)NRPS(0.552)GET(0.18)S(0.18)VPPPPAVGR 87.228 7.16E-05 122820000 838.77 652.7 582.99 761.73 644.26 949.8 590.01 560.09 611.32 682.14 TRUE FALSE FALSE 828.5467486 661.8887277 593.1366964 849.8048066 611.3810081 889.1108453 640.1254347 576.2953205 556.6420081 664.4179045 1.247026522 0.996193395 0.892716305 1.279021533 0.920175396 1.338180141 0.963437966 0.86736874 0.837788995 1 9.375947141 -7.534692723 24.93822423 1.105432119 0.891385922 0.083713952 0.167087004 197.3122641 416508.7893 0.020205262 0.075716522 2.92E-08 7.534692723 -0.214046196 TLSSS(ph)SMDLSR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 0 TLS(0.016)S(0.084)S(0.45)S(0.45)MDLSR 98.754 0.028135 31862000 6207.5 5755.2 6288 4145.6 6990.6 5819.6 4682.1 5468.7 5630 5469.6 TRUE FALSE FALSE 6131.840602 5836.221857 6397.440002 4624.933778 6633.843596 5447.746342 5079.797457 5626.928206 5126.438699 5327.499004 1.150979212 1.095489995 1.200833637 0.868124757 1.245207853 1.022571067 0.953505098 1.05620446 0.962259908 1 12.3792427 -8.017161493 24.8463529 1.081089291 1.000650569 0.067143249 0.108500834 1146.305066 1659623.576 0.014198765 0.03719934 9.61E-09 8.017161493 -0.080438723 TLSSSS(ph)MDLSR ddPTM_HeLa_Romidepsin_16h_R1 1 TLSSSSMDLSR 11 0 Q9H0B6;Q9H0B6-2 Q9H0B6 KLC2 Kinesin light chain 2 1 0 TLS(0.002)S(0.018)S(0.183)S(0.798)MDLSR 110.84 0.01955 16249000 8437 7330.8 8948.5 6071.6 8783.4 7362.7 5884 7339.2 7782.3 7827.6 TRUE FALSE FALSE 8334.166599 7434.003195 9104.244889 6773.62696 8335.150323 6892.247232 6383.786813 7551.548173 7086.231597 7624.237824 1.093114721 0.975048702 1.194118691 0.888433325 1.093243747 0.903991637 0.837301637 0.990465978 0.929434753 1 12.89637741 -8.246939678 23.5580853 1.042042289 0.903257895 0.232742584 0.091019284 295.3429277 479849.6354 0.010967332 0.027795662 5.66E-09 8.246939678 -0.138784393 TLSVAAAFNEDEDS(ph)EPEEMPPEAK ddPTM_HeLa_Romidepsin_16h_R1 5 TLSVAAAFNEDEDSEPEEMPPEAK 24 0 Q8WW12 Q8WW12 PCNP PEST proteolytic signal-containing nuclear protein 1 0 TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK;TLSVAAAFNEDEDS(1)EPEEMPPEAK ;;;; 108.5 2.47E-06 348524000 33790.1 32674.7 29674.3 30760.3 32646.8 31208 27675.17 31815.1 36419.4 33335 TRUE FALSE FALSE 33378.25326 33134.69528 30190.76874 34316.95062 30980.71197 29213.90952 30025.89825 32735.61972 33161.95765 32468.95189 1.028005258 1.020504 0.929835026 1.056915872 0.954164214 0.899749078 0.924757237 1.00821301 1.021343644 1 14.98677319 -8.594595805 8.402331555 1.009857657 0.939765695 0.374168374 0.039754618 0.189582361 19.88682897 0.005488263 0.011000026 2.54E-09 8.594595805 -0.070091962 TLSYLLPAIVHINHQPFLER ddPTM_HeLa_Romidepsin_16h_R1 1 TLSYLLPAIVHINHQPFLER 20 0 P17844;J3KTA4;J3QRQ7;J3QRN5 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 0 93.381 0.00050586 1307900 513.43 582 647.54 515.04 470.13 716.71 458.22 474.95 639.79 247.9 FALSE FALSE TRUE 507.1721177 590.1934113 658.8101621 574.5913481 446.1375118 670.9145441 497.1411954 488.6919289 582.56558 241.4595223 2.100443639 2.444274741 2.728449704 2.379659095 1.847669985 2.778579771 2.058900766 2.02390829 2.412684224 1 7.915637549 -11.74803891 0.691065198 0.999554265 2.326940125 0 0.512697587 0.271192863 0.249174355 0.188484926 0.067143532 1.79E-12 11.74803891 1.32738586 TLTAEEAEEEWER ddPTM_HeLa_Romidepsin_16h_R1 1 TLTAEEAEEEWER 13 0 P35269;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 0 153.34 0.0078227 2341200 408.12 298.76 516.07 371.97 357.14 333.15 361.95 394.63 361.05 457.97 FALSE FALSE TRUE 403.1456765 302.9659511 525.0519819 414.9789216 338.9138131 311.8627902 392.694024 406.0479964 328.7567837 446.0718734 0.90376843 0.679186403 1.177056912 0.930296094 0.759774004 0.699131258 0.880338007 0.910274825 0.737004064 1 8.801132373 -8.836363147 7.10896888 0.947999222 0.80946253 0.043098372 0.142791954 0.265042255 20.91208521 0.018618962 0.033988621 1.46E-09 8.836363147 -0.138536692 TLTAEEAEEEWERR ddPTM_HeLa_Romidepsin_16h_R1 4 TLTAEEAEEEWERR 14 1 P35269;M0R0R9 P35269 GTF2F1 General transcription factor IIF subunit 1 0 0 ;;; ;;; 246.25 9.51E-55 22059700 5862.4 5471.5 5195.4 6797.3 6697.7 6305.7 5977.6 6932.8 6353.1 4886.49 FALSE FALSE TRUE 5790.946814 5548.527921 5285.823758 7583.235808 6355.891376 5902.786121 6485.337195 7133.38963 5784.862824 4759.538285 1.216703484 1.165770205 1.1105749 1.593271312 1.33540083 1.240201416 1.362597968 1.498756644 1.215425211 1 12.21660591 -11.74117898 0.051351513 5.42E-10 2.244134516 0.364508367 0.134678829 47.57959628 0.83749641 21.17140409 15.38076922 1.81E-12 11.74117898 2.244134515 TLTAVHDAILEDLVFPSEIVGK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTAVHDAILEDLVFPSEIVGK 22 0 A0A2R8Y623;P62081;B5MCP9 A0A2R8Y623 RPS7 40S ribosomal protein S7 0 0 100.46 0.00011215 1804900 2140.9 1933.7 1984.2 1887.9 2569.8 2382.9 2068.2 2253.5 2494.1 2204.3 FALSE FALSE TRUE 2114.805887 1960.922679 2018.734169 2106.187881 2438.653517 2230.64038 2243.872856 2318.701467 2271.021449 2147.031968 0.984990405 0.913317877 0.940244113 0.980976488 1.135825434 1.038941391 1.045104539 1.079956657 1.057749248 1 11.06812796 -8.794339855 24.77485175 0.980979235 1.07025213 0.540125049 0.043029903 93.70917227 70564.96623 0.005674165 0.010285797 1.61E-09 8.794339855 0.089272895 TLTDEVNS(ph)PDSDRR ddPTM_HeLa_Romidepsin_16h_R1 3 TLTDEVNSPDSDRR 14 1 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 1 0 TLTDEVNS(0.866)PDS(0.134)DRR;TLTDEVNS(0.999)PDS(0.001)DRR;TLTDEVNS(0.99)PDS(0.01)DRR ;; 174.68 4.54E-06 292450000 20566.3 19775 19205.5 17039.5 20052.6 18746.5 18144.5 17930.8 21012.4 19147.1 TRUE FALSE FALSE 20315.63003 20053.39297 19539.76367 19009.68716 19029.241 17548.65915 19685.69338 18449.59941 19132.99832 18649.65558 1.089330038 1.07526881 1.047727857 1.019304999 1.020353481 0.940964249 1.05555265 0.989272929 1.025916979 1 14.18686137 -8.957096636 2.289823159 1.04649943 1.000450976 0.281607551 0.035064508 0.387239472 4.092184912 0.006581741 0.012840797 1.10E-09 8.957096636 -0.046048453 TLTDGVLDINHEQENT(ph)PSTSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTDGVLDINHEQENTPSTSGK 22 0 A0A2R8Y7R9;Q13136-2;Q13136;E9PJZ7 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 TLTDGVLDINHEQENT(0.993)PS(0.005)T(0.002)S(0.001)GK 104.33 0.00014428 4588500 1491.7 1249.8 1358.2 1328.2 2135.1 2604 2276.5 2504.7 1223.6 1460.2 TRUE FALSE FALSE 1473.518587 1267.394717 1381.838901 1481.772733 2026.13788 2437.612804 2469.865853 2577.169543 1114.158151 1422.263793 1.036037473 0.891110864 0.971577078 1.041841 1.424586556 1.713896406 1.736573668 1.81201937 0.783369552 1 10.47397336 -8.541933126 2.015131281 1.000964792 1.767279581 0.951133021 0.081916607 0.031293097 0.252425573 0.007533061 0.019038977 2.87E-09 8.541933126 0.766314789 TLTEPS(ph)VDFNHSDDFTPISTVQK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 TLT(0.002)EPS(0.79)VDFNHS(0.208)DDFTPISTVQK 122.19 1.56E-06 53445000 2364.2 2536.9 2318.9 2482.4 2656.3 2415.3 1667.7 2062.5 2451.5 2274 TRUE FALSE FALSE 2335.384221 2572.614545 2359.259482 2769.426768 2520.739099 2260.970125 1809.354396 2122.175183 2232.2317 2214.921152 1.054387069 1.161492608 1.065166351 1.250350048 1.138071708 1.020790344 0.816893366 0.95812674 1.007815424 1 11.11303963 -7.909726662 5.950430968 1.064032405 0.889713763 0.476848243 0.081964172 0.159359515 8.456277016 0.012750583 0.039280726 1.23E-08 7.909726662 -0.174318642 TLTEPSVDFNHS(ph)DDFTPISTVQK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTEPSVDFNHSDDFTPISTVQK 23 0 Q6R327-3;Q6R327 Q6R327-3 RICTOR Rapamycin-insensitive companion of mTOR 1 0 T(0.08)LT(0.08)EPS(0.291)VDFNHS(0.548)DDFT(0.001)PISTVQK 80.277 0.0001926 76374000 3458.6 3063.3 3278.8 3034.9 3451.3 3143.9 2353 3226.8 3146.9 3285.5 TRUE FALSE FALSE 3416.445253 3106.425218 3335.866139 3385.809418 3275.167282 2943.014936 2552.863761 3320.162367 2865.433382 3200.142236 1.067591688 0.970714733 1.042411834 1.058018415 1.023444285 0.91965129 0.797734467 1.037504624 0.895408132 1 11.64392031 -8.248145668 4.953923665 1.030434572 0.904611406 0.195564994 0.073599469 0.118282717 8.693449353 0.008029713 0.020122897 5.65E-09 8.248145668 -0.125823167 TLTS(ph)PGDLDIYSGDK ddPTM_HeLa_Romidepsin_16h_R1 1 TLTSPGDLDIYSGDK 15 0 H7BZ08;Q96M89-2;Q96M89 H7BZ08 CCDC138 Coiled-coil domain-containing protein 138 1 0 TLTS(1)PGDLDIYSGDK 214.58 1.01E-25 4216500 1363.2 1211.8 1405.8 1279.3 1848.6 1687.7 1199.8 1231.9 1734.9 1608.4 TRUE FALSE FALSE 1346.584794 1228.859752 1430.267359 1427.218685 1754.259044 1579.861417 1301.710982 1267.543083 1579.726199 1566.613536 0.859551359 0.784405167 0.912967574 0.911021546 1.11977779 1.008456381 0.830907529 0.809097492 1.008370069 1 10.61343361 -12.49665047 1.301826512 0.99894449 0.903728361 0.150488367 0.094063534 0.820588786 2.53146366 0.067120623 0.017084623 3.19E-13 12.49665047 -0.095216129 TLTTGSSAYLWKPPS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TLTTGSSAYLWKPPSR 16 1 Q9BQS8-3;Q9BQS8-2;Q9BQS8;Q9BQS8-4 Q9BQS8-3 FYCO1 FYVE and coiled-coil domain-containing protein 1 1 0 TLTTGSSAYLWKPPS(1)R 169.02 6.92E-08 0 1107.9 819.28 833.33 954.99 920.12 729.6 631.28 799.76 707.17 679.65 TRUE FALSE FALSE 1094.396489 830.8138453 847.8337591 1065.410437 873.162843 682.9809147 684.9009074 822.8997938 643.9189441 661.992595 1.653185393 1.255019847 1.280729974 1.609399327 1.318991858 1.031704765 1.034605089 1.243064953 0.972698107 1 9.370671269 -8.276521374 19.79385052 1.332594553 1.09627307 0.135826361 0.213999215 74.17426238 97349.39048 0.037015234 0.083371182 5.29E-09 8.276521374 -0.236321483 TLVITSTPAS(ph)PNR ddPTM_HeLa_Romidepsin_16h_R1 1 TLVITSTPASPNR 13 0 E9PK89;Q8TBN0 E9PK89 RAB3IL1 Guanine nucleotide exchange factor for Rab-3A 1 0 TLVIT(0.006)S(0.003)T(0.011)PAS(0.981)PNR 113.76 0.0060529 12858000 986.27 1141.7 783.19 677.34 1012 1229 832.58 1124.5 991.57 963.58 TRUE FALSE FALSE 974.2489619 1157.772883 796.8210934 755.6572378 960.3538637 1150.470866 903.2993244 1157.035633 902.8814958 938.5460527 1.038040658 1.233581324 0.8489952 0.805136025 1.023235739 1.225801188 0.962445393 1.232795802 0.962000206 1 9.874283727 -8.492345706 24.29404482 1.005176361 1.12288417 0.216346638 0.129600014 711.7205587 566290.0268 0.018148308 0.040523351 3.22E-09 8.492345706 0.117707809 TLVLLMGK ddPTM_HeLa_Romidepsin_16h_R1 2 TLVLLMGK 8 0 P07737;K7EJ44;CON__P02584 P07737 PFN1 Profilin-1 0 0 ; ; 116.88 0.0050704 14649400 1641.82 984.65 11490.8 5197.2 6059.2 8114.9 5624.1 1396.53 1362.3 337.035 FALSE FALSE TRUE 1621.808866 998.5119285 11690.79255 5798.124718 5749.976414 7596.38408 6101.810914 1436.936392 1240.452476 328.2787821 4.940340207 3.041658441 35.61239163 17.6621976 17.51552865 23.14003979 18.58728388 4.377183268 3.778655654 1 8.358777696 -9.88216518 18.09970639 2.920238802 19.43572044 0.551315773 7.198775961 0.757602681 115.0343791 1.114421043 1.464646051 1.31E-10 9.88216518 16.51548164 AAVVVSK(ac)SGSLK ddPTM_HeLa_Romidepsin_16h_R1 2 AAVVVSKSGSLK 12 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 ; AAVVVSK(1)SGSLK;AAVVVSK(1)SGSLK 205.56 2.43E-14 1330630 653.37 584.26 457.87 924.29 2833.6 4090.7 3805.2 4344.7 702.01 638.55 FALSE TRUE FALSE 645.4064751 592.4852276 465.8390353 1031.160759 2688.990818 3829.317472 4128.413593 4470.40704 639.2204674 621.9603789 1.03769709 0.952609278 0.748985066 1.657920333 4.323411763 6.156851146 6.63774371 7.187607428 1.027751106 1 9.280678868 -8.552244179 1.667037558 0.97766497 6.875003546 0.99425954 0.193512272 0.019013383 0.104406983 0.030831028 0.083965485 2.80E-09 8.552244179 5.897338576 up TLWLFDIDRDPEER ddPTM_HeLa_Romidepsin_16h_R1 1 TLWLFDIDRDPEER 14 1 P15848 P15848 ARSB Arylsulfatase B 0 0 132.06 0.0021196 4002400 1380.3 1491.1 1661.2 1808.8 1885.5 1607.2 1335 1575.7 1514.9 1466.3 FALSE FALSE TRUE 1363.476373 1512.091745 1690.112489 2017.941967 1789.275899 1504.505107 1448.394867 1621.290393 1379.40355 1428.205315 0.954678126 1.058735554 1.183382019 1.41292148 1.2528142 1.053423546 1.014136309 1.135194203 0.965830008 1 10.47998768 -9.940065084 3.508407506 0.979227277 1.176270722 0.438758 0.103191609 0.182510035 4.608783318 0.018920644 0.024972025 1.15E-10 9.940065084 0.197043445 S(ph)LSSPPSSK ddPTM_HeLa_Romidepsin_16h_R1 2 SLSSPPSSK 9 0 Q5VW31;O00712;O00712-4;A0A1B0GW37;U3KQE8;A0A0A0MRX8;A0A1B0GU97;A0A2R8Y7V8;Q5VW30;Q5VW27;A0A1B0GWI9;A0A1B0GWJ4;A0A1B0GWB8;A0A1B0GVN4;Q5VW26;O00712-5;O00712-6 Q5VW31 NFIB Nuclear factor 1 B-type;Nuclear factor 1 1 0 S(0.578)LS(0.211)S(0.211)PPSSK;S(0.707)LS(0.143)S(0.143)PPS(0.007)SK ; 123.96 0.011374 91041000 23956.2 30318.9 18283.8 18757.3 18322.2 11992 9392.4 10221.5 24470 23368.1 TRUE FALSE FALSE 23664.21262 30745.73027 18602.02187 20926.10728 17387.14976 11225.7499 10190.19022 10517.24298 22281.34191 22760.99339 1.039682768 1.350807926 0.817276362 0.919384621 0.763901182 0.493201228 0.447704107 0.462073109 0.978926602 1 14.4742759 -8.54613184 1.232734708 1.036927288 0.428571822 0.809079264 0.121537277 0.145208669 0.422626226 0.018673906 0.061419309 2.84E-09 8.54613184 -0.608355466 down TMFAQVES(ph)DDEEAK ddPTM_HeLa_Romidepsin_16h_R1 2 TMFAQVESDDEEAK 14 0 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 0 TMFAQVES(1)DDEEAK;TMFAQVES(1)DDEEAK ; 165.78 0.00013413 5720600 3614.75 3531.11 3307.1 1697.98 3629.7 3739.96 3249.58 3781.3 3259.42 3498.12 TRUE FALSE FALSE 3570.692037 3580.821059 3364.658688 1894.308437 3444.462865 3500.988626 3525.599244 3890.70595 2967.889312 3407.238338 1.047972487 1.050945283 0.987503178 0.555965932 1.010925131 1.027515037 1.034738076 1.141894274 0.871054214 1 11.73438715 -9.52137153 24.95235938 1.025114035 0.946488156 0 0.153216054 139.2030916 2304560.487 0.023261198 0.033165764 3.01E-10 9.52137153 -0.078625879 TMFAQVES(ph)DDEEAKNEPEWK ddPTM_HeLa_Romidepsin_16h_R1 1 TMFAQVESDDEEAKNEPEWK 20 1 Q9NW82 Q9NW82 WDR70 WD repeat-containing protein 70 1 0 T(0.182)MFAQVES(0.818)DDEEAKNEPEWK 63.443 0.019377 69832000 1876.1 1870 1827.9 1813.8 2096.7 2294.9 2252.6 2553.2 1981.9 1554.6 TRUE FALSE FALSE 1853.233372 1896.325909 1859.713833 2023.52009 1989.697575 2148.263296 2443.935788 2627.072814 1804.6339 1514.211268 1.223893529 1.252352264 1.228173289 1.336352551 1.314015829 1.41873419 1.613999208 1.7349447 1.19179796 1 10.56435079 -4 0.189921594 1.000013598 4.261661214 0.898110248 0.064510447 9.310561882 0.104068634 0.064346339 8.960887678 1.00E-04 4 3.261647616 TMIIS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 1 TMIISPER 8 0 O75533;B4DGZ4;A0A494C1M2;O75533-2 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 TMIIS(1)PER 102.05 0.0054431 4022400 5598.4 6349.2 6386 2643.5 4055.2 4754 3742.7 4360.4 5776.3 6806.1 TRUE FALSE FALSE 5530.164547 6438.584204 6497.145651 2949.153908 3848.248012 4450.234743 4060.604845 4486.561294 5259.653261 6629.276541 0.834203327 0.971234819 0.980068581 0.444868138 0.580492907 0.671300211 0.612526091 0.676779927 0.793397776 1 12.69463572 -9.272949762 24.99274793 0.928200117 0.6012345 0.777600204 0.085046527 251.7822974 546699.6652 0.01341505 0.02059982 5.33E-10 9.272949762 -0.326965617 TMLEDLGMDDEGDDDPVPLPNVNAAILK ddPTM_HeLa_Romidepsin_16h_R1 2 TMLEDLGMDDEGDDDPVPLPNVNAAILK 28 0 E5RJR5;P63208;E5RGM3;E7ERH2;F8W8N3;P63208-2;E5RI56 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 0 ; ; 105.65 4.75E-09 17257600 14484.4 13801.4 14391.5 11694.9 16797.3 17932.9 16424.2 18691.2 15197 14297.8 FALSE FALSE TRUE 14307.85856 13995.69647 14641.97802 13047.11936 15940.0711 16787.04557 17819.27114 19232.00038 13837.74226 13926.34109 1.027395384 1.004980158 1.05138729 0.936866279 1.144598642 1.205416803 1.279537175 1.380980133 0.993638039 1 13.76552864 -8.057976489 1.166609634 1.010516814 1.374177942 0.914659146 0.040141529 0.113366633 0.251570068 0.005764186 0.035196664 8.75E-09 8.057976489 0.363661128 TMLEDLGMDDEGDDDPVPLPNVNAAILKK ddPTM_HeLa_Romidepsin_16h_R1 1 TMLEDLGMDDEGDDDPVPLPNVNAAILKK 29 1 E5RJR5;P63208;E5RGM3;E7ERH2;F8W8N3;P63208-2;E5RI56 E5RJR5 SKP1 S-phase kinase-associated protein 1 0 0 84.404 2.19E-08 0 1081.1 1073.2 879.16 1337.9 1168.1 1109.6 789.88 943.3 1012.5 971.24 FALSE FALSE TRUE 1067.923137 1088.308538 894.461411 1492.594293 1108.487498 1038.700141 856.9723875 970.5928972 921.9394641 946.0070448 1.128874402 1.150423291 0.945512421 1.577783486 1.171753957 1.097983516 0.905883727 1.02598908 0.974558772 1 9.885707117 -7.813108765 9.454628674 1.107159694 0.966156274 0.118454615 0.170437144 0.566195707 98.73174234 0.023872917 0.072109006 1.54E-08 7.813108765 -0.141003419 TMQAVNK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TMQAVNKK 8 1 Q9UQN3-2;Q9UQN3;A0A087WW88 Q9UQN3-2 CHMP2B Charged multivesicular body protein 2b 0 1 ; TMQAVNK(1)K;TMQAVNK(1)K 88.948 0.0084541 6238500 1335.89 690.88 1088.4 625.04 1471.22 1325.45 1879.64 1295.21 1614.28 1126.17 FALSE TRUE FALSE 1319.607659 700.6062268 1107.343145 697.3100657 1396.138154 1240.758023 2039.296575 1332.684858 1469.894754 1096.911941 1.203020598 0.638707813 1.00950961 0.635702867 1.272789639 1.13113731 1.859125148 1.214942429 1.340029859 1 10.099232 -7.915832904 7.25829131 1.037073466 1.535417693 0.373982795 0.265473493 0.161016219 11.74050198 0.033774326 0.102547287 1.21E-08 7.915832904 0.498344227 TNATSPGVNSST(ph)SPQSTDK ddPTM_HeLa_Romidepsin_16h_R1 2 TNATSPGVNSSTSPQSTDK 19 0 B7ZM87;O75044 B7ZM87 SRGAP2 SLIT-ROBO Rho GTPase-activating protein 2 1 0 TNATSPGVNS(0.007)S(0.007)T(0.948)S(0.039)PQSTDK;TNATSPGVNS(0.189)S(0.189)T(0.594)S(0.027)PQSTDK ; 256.79 1.49E-75 23378000 8389.6 8376.5 8348.4 8414 10823.9 11805.5 9532.8 10924.2 9558.3 8492.3 TRUE FALSE FALSE 8287.344328 8494.424587 8493.7004 9386.866269 10271.51599 11051.16665 10342.51579 11240.27449 8703.381709 8271.668822 1.001895084 1.026929967 1.026842416 1.134821337 1.241770701 1.336026247 1.250354193 1.358888361 1.052191752 1 13.01396271 -8.907556238 1.42662782 1.001997288 1.314151182 0.944507015 0.0316738 0.045440783 0.185117417 0.003871473 0.008847037 1.24E-09 8.907556238 0.312153893 TNEK(ac)VELQELNDR ddPTM_HeLa_Romidepsin_16h_R1 2 TNEKVELQELNDR 13 1 P08670;B0YJC4;A0A1B0GTT5;P17661 P08670 VIM;DES Vimentin;Desmin 0 1 ; TNEK(1)VELQELNDR;TNEK(1)VELQELNDR 296.28 3.04E-113 8728800 927.01 1011.37 1093.18 1135.81 1734.85 1736.1 1954.82 1810.66 2268.19 1567.65 FALSE TRUE FALSE 915.7112456 1025.608093 1112.206339 1267.137696 1646.314131 1625.168813 2120.862362 1863.04859 2065.317406 1526.922227 0.599710469 0.671683256 0.728397504 0.829863941 1.078191215 1.064342888 1.388978642 1.220133257 1.352601573 1 10.57641087 -8.406018528 1.404440608 0.787076705 1.290487062 0.344500934 0.214917329 0.232037386 0.866029499 0.026088229 0.089209926 3.93E-09 8.406018528 0.503410357 TNEKVELQELNDR ddPTM_HeLa_Romidepsin_16h_R1 1 TNEKVELQELNDR 13 1 P08670;B0YJC4;A0A1B0GTT5;P17661 P08670 VIM;DES Vimentin;Desmin 0 0 127.78 0.00018126 0 2353 1949 1524.9 3525.3 2354.2 1800.3 1934.7 1947.8 2422 1947.4 FALSE FALSE TRUE 2324.320731 1976.438073 1551.440245 3932.911773 2234.056389 1685.26664 2099.03337 2004.15652 2205.370254 1896.806267 1.225386467 1.041982045 0.817922353 2.073438833 1.177798929 0.888475892 1.106614527 1.056595265 1.162675542 1 10.88935662 -6.088735915 14.36206659 1.135182247 1.193750342 0 0.329621707 0 0 0.041972267 0 8.15E-07 6.088735915 0.058568096 TNIDESAMPPPPPQGVK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 TNIDESAMPPPPPQGVKR 18 1 O60216;E5RFZ5 O60216 RAD21 Double-strand-break repair protein rad21 homolog 0 1 TNIDESAMPPPPPQGVK(1)R 82.483 0.0071844 1091700 231.18 192.74 152.27 108.42 208.79 132.12 152.27 179.25 293.16 166.98 FALSE TRUE FALSE 228.3622892 195.4533988 154.9201955 120.9560305 198.1346672 123.6779584 165.20381 184.4363159 266.9390354 162.6418355 1.404080866 1.201741226 0.952523654 0.74369568 1.21822695 0.760431398 1.015752248 1.134002917 1.641269201 1 7.345554592 -9.762472421 24.86597873 1.196966995 0.964182018 0.326953868 0.215736255 27.93143518 672337.5914 0.031204943 0.042344372 1.73E-10 9.762472421 -0.232784977 TNLQPLESTQS(ph)QDF ddPTM_HeLa_Romidepsin_16h_R1 3 TNLQPLESTQSQDF 14 0 Q9Y248 Q9Y248 GINS2 DNA replication complex GINS protein PSF2 1 0 TNLQPLESTQS(1)QDF;TNLQPLESTQS(1)QDF;TNLQPLES(0.001)T(0.017)QS(0.982)QDF ;; 147.39 0.00061738 20476400 13840.1 13138.1 12888.4 11505.7 10242.6 8929.3 7241.8 8679.2 13875.5 12504.9 TRUE FALSE FALSE 13671.41154 13323.05852 13112.7172 12836.04317 9719.881902 8358.746548 7856.918311 8930.318958 12634.44053 12180.0209 1.122445655 1.093845292 1.07657592 1.053860521 0.798018492 0.686267012 0.645066078 0.733194059 1.037308609 1 13.57222899 -8.651031718 2.826051776 1.064832725 0.686725318 0.955832337 0.037215784 0.050921887 0.818758771 0.007713194 0.016706249 2.23E-09 8.651031718 -0.378107407 TNLSGRQS(ph)PSFK ddPTM_HeLa_Romidepsin_16h_R1 1 TNLSGRQSPSFK 12 1 Q6IN85-4;Q6IN85-2;Q6IN85 Q6IN85-4 SMEK1 Serine/threonine-protein phosphatase 4 regulatory subunit 3A 1 0 TNLS(0.002)GRQS(0.998)PSFK 131.35 0.023271 21801000 3339.2 3321 2253.1 4310.7 2101 1680.8 1392.8 1613.3 2975.8 2810.6 TRUE FALSE FALSE 3298.500546 3367.753125 2292.31426 4809.123416 1993.77813 1573.402305 1511.104397 1659.97829 2709.636995 2737.580207 1.204896404 1.230193408 0.837350538 1.756705942 0.728299439 0.574741993 0.551985434 0.606366997 0.989792733 1 11.41868552 -8.541318501 24.99997562 1.134268722 0.587859 0.584737056 0.230321782 121.51174 164740.8679 0.031069315 0.062146626 2.88E-09 8.541318501 -0.546409722 TNPPLIQEK(ac)PAK ddPTM_HeLa_Romidepsin_16h_R1 2 TNPPLIQEKPAK 12 1 H0Y3P2;D3DQV9;P78344-2;P78344;E9PKF8 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 1 ; TNPPLIQEK(1)PAK;TNPPLIQEK(1)PAK 166.04 0.0011869 1342490 755.28 580.76 699.36 582.07 1074.36 1172.11 743.87 1096.12 1360.03 1093.89 FALSE TRUE FALSE 746.0743569 588.9359545 711.5320674 649.3716721 1019.5314 1097.215954 807.0542992 1127.834503 1238.385511 1065.47058 0.700229899 0.55274727 0.66781015 0.60946936 0.956883671 1.029794698 0.757462772 1.058531811 1.162289728 1 10.05727504 TNS(ph)MGSATGPLPGTK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSMGSATGPLPGTK 15 0 O15014 O15014 ZNF609 Zinc finger protein 609 1 0 T(0.189)NS(0.73)MGS(0.078)AT(0.002)GPLPGTK 96.208 0.014908 52009000 6217.8 6503.3 6314.5 5768.4 3414.6 3062.9 2938 3332.1 6688.9 7186.3 TRUE FALSE FALSE 6142.015062 6594.853628 6424.401224 6435.369549 3240.34022 2867.190575 3187.553647 3428.509056 6090.628031 6999.59889 0.877481004 0.942175935 0.917824196 0.919391189 0.462932272 0.409622126 0.455390901 0.489815075 0.870139579 1 12.77305654 -8.763191966 6.103678118 0.938088021 0.448985197 0.970564103 0.039769995 0.020576775 2.924555328 0.007192439 0.013800441 1.73E-09 8.763191966 -0.489102824 TNS(ph)PGFQK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSPGFQK 8 0 A0A087X0H9;Q5T8P6-3;Q5T8P6-5;Q5T8P6-4;Q5T8P6-2;Q5T8P6 A0A087X0H9 RBM26 RNA-binding protein 26 1 0 T(0.389)NS(0.611)PGFQK 106.4 0.025629 40088000 6362 6727.8 7266.2 5721.5 6207 7397.8 7420.1 3171.2 7956 6668.3 TRUE FALSE FALSE 6284.457497 6822.514145 7392.665163 6383.04675 5890.233628 6925.104455 8050.363109 3262.953669 7244.395434 6495.056605 0.967575478 1.050416426 1.138198728 0.982754599 0.906879491 1.066211563 1.239460038 0.502374939 1.115370639 1 12.66512638 -7.244489683 24.62555057 1.011876363 0.502374443 0.726517279 0.098425837 1134.369179 1648050.447 0.012820486 0.486430098 5.70E-08 7.244489683 -0.50950192 TNS(ph)TGGSSGSSVGGGSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSTGGSSGSSVGGGSGK 18 0 X6RM00;G8JLD3;X6RLX0;Q8IUD2-5;Q8IUD2-4;Q8IUD2-2;Q8IUD2-3;Q8IUD2;K7EKH8;K7EIZ7 X6RM00 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 0 T(0.045)NS(0.633)T(0.188)GGS(0.121)S(0.013)GSSVGGGSGK 251.38 2.10E-62 10037000 1176.2 1469 2297.7 1282.1 1203.1 1112.5 3157.1 678.33 2037.8 1717.1 TRUE FALSE FALSE 1161.864022 1489.680621 2337.690505 1430.342434 1141.701318 1041.41484 3425.263995 697.9564083 1855.534064 1672.489494 0.694691372 0.890696549 1.397731054 0.85521759 0.682635868 0.622673472 2.048003295 0.41731587 1.109444376 1 10.70778143 -9.978293475 24.95417447 0.852503625 1.023653679 0 0.444409607 730.1336235 839371.9801 0.067238897 0.088365511 1.05E-10 9.978293475 0.171150053 TNSEQVDEDADVDTAMAALDDQPAEAQPPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TNSEQVDEDADVDTAMAALDDQPAEAQPPSPR 32 0 Q9Y2K6 Q9Y2K6 USP20 Ubiquitin carboxyl-terminal hydrolase 20 1 0 TNSEQVDEDADVDT(0.001)AMAALDDQPAEAQPPS(0.999)PR;TNSEQVDEDADVDTAMAALDDQPAEAQPPS(1)PR ; 87.16 2.72E-09 15711700 2454.8 2441.8 2622.5 2595.4 4352.8 5781 5169.8 6110 2943.7 2630.9 TRUE FALSE FALSE 2424.879953 2476.175724 2668.143512 2895.49236 4130.660373 5411.612757 5608.922683 6286.78321 2680.408099 2562.548839 0.946276581 0.966294061 1.041206892 1.129926703 1.611934302 2.111808632 2.18880616 2.453332056 1.045992981 1 11.32336379 -8.438058287 1.281578859 0.971433726 2.371782675 0.989231295 0.058146895 0.027345196 0.084458359 0.007943611 0.028167575 3.65E-09 8.438058287 1.400348949 up TNSGISSASGGSTEPT(ph)TPDSERPAQALLR ddPTM_HeLa_Romidepsin_16h_R1 2 TNSGISSASGGSTEPTTPDSERPAQALLR 29 1 A2A2F0;Q86X10-4;Q86X10-2;Q86X10-3;Q86X10;A0A0J9YW54 A2A2F0 RALGAPB Ral GTPase-activating protein subunit beta 1 0 TNSGISSASGGS(0.001)T(0.001)EPT(0.369)T(0.369)PDS(0.26)ERPAQALLR;TNSGIS(0.001)S(0.002)AS(0.004)GGS(0.004)T(0.004)EPT(0.54)T(0.41)PDS(0.036)ERPAQALLR ; 80.171 1.78E-06 25449000 5130.2 6423.1 2842.6 2383.7 2675.5 3659.5 4117.9 5724 7248.8 7037.8 TRUE FALSE FALSE 5067.671149 6513.52457 2892.074261 2659.31461 2538.959251 3425.66976 4467.674323 5889.614909 6600.449173 6854.956941 0.73927104 0.950191901 0.421895321 0.387940381 0.370382961 0.499736146 0.651743601 0.859176062 0.962872448 1 12.74293189 -9.764246065 24.99999687 0.878936374 0.521928465 0.600836009 0.151093163 45.5459327 405692.5457 0.027587912 0.037169487 1.72E-10 9.764246065 -0.35700791 TNSS(ph)SSSPVVLK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSSSSSPVVLK 12 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 T(0.069)NS(0.045)S(0.85)S(0.032)S(0.001)S(0.003)PVVLK 141.59 0.0017912 52962000 4009.9 4344.2 4114.8 3871.6 4368.7 4407.7 3970.1 4467.7 5031.4 4611.6 TRUE FALSE FALSE 3961.025796 4405.357762 4186.416368 4319.252608 4145.748937 4126.062195 4307.320195 4596.965851 4581.378983 4491.789967 0.881836823 0.980757737 0.932015165 0.961588284 0.92296144 0.918578612 0.95893179 1.023415138 1.019945059 1 12.13307475 -7.295193012 3.595024915 0.943075976 1.02992401 0.194009647 0.039776015 0.289278767 6.652749952 0.006092122 0.063593303 5.07E-08 7.295193012 0.086848034 TNSSSS(ph)SPVVLK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSSSSSPVVLK 12 0 E9PMC9;Q7Z589-6;Q7Z589;Q7Z589-5;Q7Z589-4;Q7Z589-7;Q7Z589-2 E9PMC9 C11orf30;EMSY Protein EMSY 1 0 TNS(0.007)S(0.144)S(0.144)S(0.387)S(0.317)PVVLK 165.78 0.00026424 45813000 2916.1 2645.6 2977 2871.4 2617.9 2835.1 1967 2419.3 3111.9 2544.1 TRUE FALSE FALSE 2880.557452 2682.844826 3028.813436 3203.404778 2484.298794 2653.94626 2134.076931 2489.298628 2833.56387 2478.003915 1.162450727 1.082663675 1.22227952 1.292735963 1.002540302 1.071001641 0.861208055 1.004557988 1.143486438 1 11.27496275 -8.00841751 2.420572944 1.102727815 0.935223235 0.367529463 0.094833261 0.297719887 3.417573544 0.015415604 0.055747656 9.81E-09 8.00841751 -0.16750458 TNST(ph)GGSSGSSVGGGSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TNSTGGSSGSSVGGGSGK 18 0 X6RM00;G8JLD3;X6RLX0;Q8IUD2-5;Q8IUD2-4;Q8IUD2-2;Q8IUD2-3;Q8IUD2;K7EKH8;K7EIZ7 X6RM00 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 0 TNS(0.091)T(0.801)GGS(0.101)S(0.003)GS(0.001)S(0.003)VGGGSGK 209.43 3.06E-28 10152000 523.63 618.26 1062.9 602.43 814.85 531.38 1456.9 351.28 914.42 589.44 TRUE FALSE FALSE 517.2477962 626.9638805 1081.399329 672.0857911 773.2651639 497.426533 1580.64905 361.4437326 832.631985 574.1262638 0.900930385 1.092031353 1.883556626 1.170623665 1.346855583 0.866406162 2.753138376 0.62955443 1.450259355 1 9.165224244 -9.981907077 23.8576553 0.955494134 1.460959209 0.053374498 0.569219446 179.4613969 236639.6721 0.079433194 0.104382052 1.04E-10 9.981907077 0.505465075 TNSTFNQVVLK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 TNSTFNQVVLKR 12 1 G3V203;H0YHA7;J3QQ67;Q07020-2;Q07020;F8VYV2;A0A075B7A0 G3V203 RPL18 60S ribosomal protein L18 0 1 ; TNSTFNQVVLK(1)R;TNSTFNQVVLK(1)R 117.86 0.0037125 2398300 183.75 252.508 319.94 184.97 394.11 551.35 51.275 433.81 609.07 515.26 FALSE TRUE FALSE 181.5103843 256.0628143 325.5084215 206.3571017 373.9970961 516.1205144 55.63029722 446.3616079 554.5932538 501.8734709 0.361665629 0.510213887 0.648586627 0.41117356 0.745201964 1.02838772 0.110845264 0.889390721 1.105045965 1 8.971179877 -12.50241048 1.257815662 0.999381509 0.560751156 0.333887231 0.255481811 0.44692429 1.268354474 0.16712886 0.04073443 3.14E-13 12.50241048 -0.438630353 TNT(ph)PQGVLPSSQLK ddPTM_HeLa_Romidepsin_16h_R1 2 TNTPQGVLPSSQLK 14 0 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YF61 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 T(0.077)NT(0.923)PQGVLPSS(0.001)QLK;T(0.104)NT(0.491)PQGVLPS(0.32)S(0.086)QLK ; 110.6 0.011073 39401000 8196.5 7988 7639 6468.5 7016.3 7306.6 5995.3 6770.3 8788.5 8455.6 TRUE FALSE FALSE 8096.597905 8100.455274 7771.953591 7216.418405 6658.23203 6839.731841 6504.540632 6966.187949 8002.434549 8235.922293 0.983083329 0.983551688 0.94366524 0.876212542 0.808437937 0.830475519 0.789776834 0.845829732 0.971650079 1 13.0077145 -9.23670277 1.546199976 0.991967014 0.815228216 0.953804429 0.016604622 0.043466055 0.20331553 0.002335994 0.00434946 5.80E-10 9.23670277 -0.176738797 TNT(ph)PVKEDWNVR ddPTM_HeLa_Romidepsin_16h_R1 2 TNTPVKEDWNVR 12 1 A0A494C1K3;P78347-2;P78347-4;P78347-3;P78347;A0A494C0Q7 A0A494C1K3 GTF2I General transcription factor II-I 1 0 T(0.273)NT(0.727)PVKEDWNVR;T(0.386)NT(0.614)PVKEDWNVR ; 153.32 0.0060154 136391000 5222.4 5149.1 5789.6 5260.6 4034.4 3606.5 2946.76 2714.64 5430.1 5163.7 TRUE FALSE FALSE 5158.74738 5221.589165 5890.365559 5868.855324 3828.509514 3376.056289 3197.057721 2793.183825 4944.418256 5029.54633 1.02568841 1.038182934 1.171152461 1.166875686 0.761203747 0.671244694 0.635655288 0.555355025 0.983074403 1 12.29621256 -8.58459025 4.328841522 1.037113394 0.633210606 0.89373729 0.069670035 0.055544219 2.105574749 0.011359959 0.023700942 2.60E-09 8.58459025 -0.403902787 TNTPQGVLPS(ph)SQLK ddPTM_HeLa_Romidepsin_16h_R1 1 TNTPQGVLPSSQLK 14 0 A0A2R8Y7W5;A0A2R8Y4Z0;Q14004-2;Q14004;A0A2R8YF61 A0A2R8Y7W5 CDK13 Cyclin-dependent kinase 13 1 0 TNTPQGVLPS(0.943)S(0.057)QLK 144.7 0.00061847 19921000 2836 2660.5 2471.7 2074.4 1907 2173.6 1894.3 2178 2612.6 2325.1 TRUE FALSE FALSE 2801.433741 2697.954589 2514.718902 2314.251888 1809.678674 2034.713975 2055.201795 2241.016994 2378.922513 2264.693567 1.237003444 1.191311102 1.110401398 1.021883014 0.79908324 0.898450018 0.907496637 0.989545352 1.05043903 1 11.14510014 -9.015458664 3.927714357 1.120955754 0.898938309 0.648983835 0.075664317 0.136678991 4.728423523 0.015368624 0.027406022 9.65E-10 9.015458664 -0.222017445 TNYNDRYDEIR ddPTM_HeLa_Romidepsin_16h_R1 4 TNYNDRYDEIR 11 1 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 0 ;;; ;;; 125.72 0.0085281 65511300 10539.6 11533 11981.3 13232.5 12237.2 13040.3 10785 12440.1 13138.1 12282 FALSE FALSE TRUE 10411.1393 11695.36188 12189.8295 14762.50391 11612.69002 12207.06692 11701.07763 12800.03467 11962.99543 11962.91187 0.870284711 0.977635044 1.018968428 1.234022625 0.970724364 1.020409333 0.978112834 1.069976508 1.000006985 1 13.54628098 -9.809067914 3.511847003 0.938500825 1.05009121 0.225590164 0.077289371 0.229992089 5.844756652 0.013467908 0.018398208 1.55E-10 9.809067914 0.111590385 TNYNDRYDEIRR ddPTM_HeLa_Romidepsin_16h_R1 2 TNYNDRYDEIRR 12 2 P62424;Q5T8U2 P62424 RPL7A 60S ribosomal protein L7a 0 0 ; ; 69.346 0.023812 33402000 2791 3232.2 2593.7 3547.1 3676.8 3336.2 2766.7 3183.3 3205.3 2796.9 FALSE FALSE TRUE 2756.982218 3277.702996 2638.84226 3957.232392 3489.159176 3123.027587 3001.703429 3275.403763 2918.60994 2724.236135 1.012020281 1.203164056 0.968654012 1.452602563 1.280784412 1.146386522 1.101851411 1.202320064 1.071349837 1 11.41163605 -9.993876434 1.313458061 1.003171697 1.212488411 0.288428638 0.118339788 0.313172061 1.058194813 0.021649624 0.02890911 1.01E-10 9.993876434 0.209316714 TPAAAAAMNLAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TPAAAAAMNLASPR 14 0 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 TPAAAAAMNLAS(1)PR;TPAAAAAMNLAS(1)PR ; 89.136 0.027608 26178700 5624.6 5390.5 5691.5 4689.8 5168.5 5183 4938.6 4609.2 5389.3 5174.5 TRUE FALSE FALSE 5556.045212 5466.3876 5790.55817 5232.056742 4904.732159 4851.823027 5358.084561 4742.55993 4907.26751 5040.065744 1.102375543 1.084586567 1.148905285 1.038092955 0.973148448 0.962650742 1.063098148 0.940971839 0.973651488 1 12.29922684 -8.909975101 5.51603876 1.061055196 0.989581145 0.302909131 0.054921522 0.222684269 10.83349799 0.008459127 0.015510326 1.23E-09 8.909975101 -0.071474051 TPAAPAS(ph)PAAVPSEGSGGSTTGWR ddPTM_HeLa_Romidepsin_16h_R1 2 TPAAPASPAAVPSEGSGGSTTGWR 24 0 P07199 P07199 CENPB Major centromere autoantigen B 1 0 TPAAPAS(1)PAAVPSEGSGGSTTGWR;TPAAPAS(1)PAAVPSEGSGGSTTGWR ; 178.1 7.68E-18 42539000 6088.7 6063.4 6043.1 6205.2 6031.4 6279.5 5686.7 6850.7 6798.5 6639.6 TRUE FALSE FALSE 6014.488582 6148.760704 6148.277621 6922.67442 5723.595152 5878.260216 6169.728156 7048.914196 6190.425133 6467.102235 0.930012912 0.950775244 0.950700545 1.070444562 0.885032422 0.908948089 0.954017415 1.089964862 0.957217763 1 12.6589037 -7.259455333 24.07837636 0.961098134 1.089964938 0.405888011 0.048188976 88.06735758 1068641.885 0.006890603 0.060127358 5.50E-08 7.259455333 0.128866804 TPADTGFAFPDWAYKPES(ph)SPGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 0 TPADTGFAFPDWAYKPES(0.469)S(0.469)PGS(0.061)R 79.332 0.00018309 42865000 983.36 919.92 1004.7 984.3 621.73 457.86 517.75 649.48 1121.5 937.73 TRUE FALSE FALSE 971.3744301 932.8706579 1022.186382 1098.109397 590.0007981 428.6042237 561.7276721 668.2716791 1021.190231 913.3676394 1.063508699 1.021352868 1.119140134 1.2022644 0.645962012 0.469257071 0.615007197 0.731656838 1.118049498 1 9.835051866 -8.69685644 7.265979216 1.047955499 0.601255759 0.877937164 0.08543695 0.058552355 5.487202294 0.01239351 0.024817414 2.01E-09 8.69685644 -0.44669974 TPADTGFAFPDWAYKPESS(ph)PGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TPADTGFAFPDWAYKPESSPGSR 23 1 P50548 P50548 ERF ETS domain-containing transcription factor ERF 1 0 TPADTGFAFPDWAY(0.001)KPES(0.431)S(0.509)PGS(0.059)R 97.784 1.98E-05 59570000 1279.5 1192.5 1042 1051.5 898.01 547.59 486.89 758.74 1122.2 839.96 TRUE FALSE FALSE 1263.904962 1209.288046 1060.135573 1173.079377 852.1811988 512.6007663 528.2464244 780.6929448 1021.827621 818.1377181 1.544855999 1.478098393 1.295791099 1.433840968 1.041610941 0.626545819 0.64566932 0.954231699 1.248967746 1 9.676199904 -8.495839464 4.121441452 1.295332845 0.738184949 0.717257514 0.165675838 0.126286164 4.817242454 0.033824634 0.075470258 3.19E-09 8.495839464 -0.557147896 TPAPPEPGS(ph)PAPGEGPSGR ddPTM_HeLa_Romidepsin_16h_R1 2 TPAPPEPGSPAPGEGPSGR 19 0 P0C1Z6-2;P0C1Z6 P0C1Z6-2 TFPT TCF3 fusion partner 1 0 TPAPPEPGS(1)PAPGEGPSGR;TPAPPEPGS(0.997)PAPGEGPS(0.003)GR ; 201.22 4.53E-21 79526000 3143.6 3324.2 2892.4 2400.6 2646.7 2348.2 2049.56 2216.9 3155.4 3140.4 TRUE FALSE FALSE 3105.284594 3370.998175 2942.741009 2678.168667 2511.629023 2198.157598 2223.649575 2281.042504 2873.173121 3058.811955 1.015193036 1.102061266 0.962053585 0.875558454 0.821112595 0.718631165 0.726965112 0.745728256 0.939310152 1 11.5787557 -8.911424424 1.440144778 1.014629323 0.73081972 0.893053364 0.041633774 0.072873941 0.302575651 0.005687203 0.012914547 1.23E-09 8.911424424 -0.283809603 TPAQFDADELR ddPTM_HeLa_Romidepsin_16h_R1 1 TPAQFDADELR 11 0 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 0 144.7 0.025546 48535000 2688.8 2346.7 2500.7 3032.9 3193.6 3258 2645.7 2598.4 2373.7 2323.3 FALSE FALSE TRUE 2656.027871 2379.736904 2544.223635 3383.578168 3030.618675 3049.824315 2870.425692 2673.580604 2161.390327 2262.940331 1.173706542 1.05161275 1.124299921 1.495213162 1.339239322 1.347726351 1.268449571 1.181463147 0.955124754 1 11.14398283 -9.433130625 7.622616851 1.082296432 1.324724683 0.671832599 0.092618376 0.150738851 11.40605625 0.014884363 0.022745709 3.69E-10 9.433130625 0.242428251 TPAS(ph)KSPSEGQTATTSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TPASKSPSEGQTATTSPR 18 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 T(0.021)PAS(0.563)KS(0.415)PSEGQTATTSPR 101.04 0.0007284 12974000 1110.6 1332.5 1511.9 1425.2 1244.4 1352.9 1227 1467.1 1439.7 1442.5 TRUE FALSE FALSE 1097.06358 1351.25897 1538.213985 1589.98833 1180.893625 1266.454056 1331.221349 1509.548224 1310.929626 1405.023642 0.780815032 0.961733973 1.094795802 1.131645249 0.84047954 0.90137562 0.947472562 1.074393468 0.933030297 1 10.45637869 -10.01296597 24.60194811 0.895168539 0.993666228 0.152771952 0.097672787 789.0166762 1497100.439 0.01943655 0.024430383 9.71E-11 10.01296597 0.098497689 TPAS(ph)PHFR ddPTM_HeLa_Romidepsin_16h_R1 2 TPASPHFR 8 0 P29590-2 P29590-2 PML Protein PML 1 0 T(0.001)PAS(0.999)PHFR;TPAS(1)PHFR ; 110.38 0.0093519 12493800 2102.25 2233.02 2011.28 2588 2129.66 2244.5 1789.93 2009.1 2507.98 2239.9 TRUE FALSE FALSE 2076.626968 2264.456514 2046.285485 2887.236737 2020.975503 2101.083694 1941.96661 2067.230139 2283.659987 2181.707075 0.951835832 1.037928758 0.93792861 1.32338423 0.926327611 0.963045735 0.890113357 0.947528732 1.046730798 1 11.0912417 TPASGLQTPTSTPAPGS(ph)ATR ddPTM_HeLa_Romidepsin_16h_R1 1 TPASGLQTPTSTPAPGSATR 20 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 0 TPASGLQTPTSTPAPGS(0.958)AT(0.042)R 195.09 7.06E-21 0 456.09 688.83 248.4 693.01 812.56 745.23 585.7 793.87 701.15 638.19 TRUE FALSE FALSE 450.5309997 698.5273668 252.7232978 773.1390769 771.0920311 697.6122081 635.4493434 816.8393759 638.4373879 621.6097318 0.724781123 1.123739432 0.406562647 1.243769261 1.240476125 1.122267192 1.022264149 1.314071087 1.027071095 1 9.27986528 TPASKS(ph)PSEGQTATTSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TPASKSPSEGQTATTSPR 18 1 P25054-2;P25054-3;P25054 P25054-2 APC Adenomatous polyposis coli protein 1 0 T(0.026)PAS(0.412)KS(0.54)PS(0.018)EGQT(0.003)ATTSPR 91.565 0.0021203 11669000 1351.6 1514 1364.6 1386.5 1613.4 1477.6 1397.5 1381 1478 1621.3 TRUE FALSE FALSE 1335.126179 1535.314132 1388.350291 1546.813654 1531.062178 1383.186129 1516.203615 1420.957056 1345.803978 1579.178392 0.845456211 0.972223366 0.879159883 0.979505331 0.969530855 0.875889726 0.960121809 0.899807813 0.852217827 1 10.62495844 -12.68704434 1.569874213 0.999857514 0.912921459 0 0.064233815 0.39150106 1.743183932 0.034790399 0.007782197 2.06E-13 12.68704434 -0.086936055 TPASTPVSGT(ph)PQAS(ph)PMIER ddPTM_HeLa_Romidepsin_16h_R1 1 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 2 0 T(0.024)PAS(0.228)T(0.019)PVS(0.149)GT(0.58)PQAS(0.999)PMIER 99.011 0.0023751 40881000 997.61 1085.6 928.42 985.78 996.17 1059.5 912.32 886.96 1173.6 1143.9 TRUE FALSE FALSE 985.4507456 1100.883105 944.5787606 1099.760522 945.3317277 991.8013694 989.812438 912.6227882 1068.630277 1114.181313 0.884461742 0.988064593 0.847778319 0.987057052 0.848454122 0.890161554 0.888376449 0.819097195 0.959117034 1 10.12176831 -16.52287875 0.143277742 1.376565843 0.850810235 0.371188127 0.05013008 50.48955 0.499978599 5.435661566 0.126986371 3.00E-17 16.52287875 -0.525755608 TPASTPVSGT(ph)PQASPMIER ddPTM_HeLa_Romidepsin_16h_R1 3 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 0 TPAST(0.006)PVS(0.013)GT(0.98)PQASPMIER;T(0.037)PAS(0.003)T(0.006)PVS(0.058)GT(0.828)PQAS(0.068)PMIER;TPASTPVS(0.002)GT(0.579)PQAS(0.418)PMIER ;; 146.15 0.0001389 182240800 3336.14 3584.9 3117.44 2965.3 3608.67 4461.89 3651.24 3765.5 3856.4 3501.12 TRUE FALSE FALSE 3295.477842 3635.368316 3171.697735 3308.161938 3424.506104 4176.789629 3961.376234 3874.448802 3511.473925 3410.160398 0.966370334 1.066040272 0.93007289 0.970089835 1.004206754 1.224807382 1.16163927 1.136148553 1.029709315 1 11.73562388 -8.322146783 6.476175137 0.985599714 1.172650765 0.799348507 0.040922014 0.061811605 5.339576384 0.005314699 0.012042616 4.76E-09 8.322146783 0.187051051 TPASTPVSGTPQAS(ph)PMIER ddPTM_HeLa_Romidepsin_16h_R1 1 TPASTPVSGTPQASPMIER 19 0 Q9UHR4 Q9UHR4 BAIAP2L1 Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 1 1 0 T(0.048)PAS(0.013)T(0.048)PVS(0.081)GT(0.396)PQAS(0.414)PMIER 86.411 0.0075538 8237500 1079.4 1052 833.48 813.88 958.09 1149.4 1025.2 1006.4 875.02 1292.6 TRUE FALSE FALSE 1066.243858 1066.810084 847.9863698 907.984635 909.1950922 1075.95705 1112.280462 1035.518596 796.7560197 1259.018066 0.846885273 0.847335009 0.673529946 0.721184755 0.722146184 0.854600167 0.883450756 0.822481126 0.632839227 1 10.29808327 -11.3969409 0.714587506 0.989045585 0.787418137 0 0.128215399 0.353730475 0.382184487 0.03372404 0.017173361 4.01E-12 11.3969409 -0.201627448 TPAVEGLTEAEEEELRAELTK ddPTM_HeLa_Romidepsin_16h_R1 1 TPAVEGLTEAEEEELRAELTK 21 1 O43399;O43399-5;O43399-7;A0A087WYR3;O43399-2;O43399-4;O43399-3;A0A087WZ51;O43399-6 O43399 TPD52L2 Tumor protein D54 0 0 65.287 0.011458 1923500 635.85 571.17 332.49 338.22 604.05 680.83 478.64 665.96 607.03 486.37 FALSE FALSE TRUE 628.1000156 579.2109463 338.276849 377.3265878 573.2230745 637.3271603 519.2956697 685.2285019 552.7357165 473.7340373 1.325849456 1.222650054 0.714064902 0.796494569 1.210010321 1.345326935 1.096175552 1.446441353 1.166763781 1 8.887933522 -4.017340212 0.938263772 1.113385512 199.6856364 0.21293458 0.199052007 1672.907855 3.026972133 0.034840972 712645.0636 9.61E-05 4.017340212 198.5722509 TPDDFLNSVDEMDTGDT(ph)INQSTLPSQQNR ddPTM_HeLa_Romidepsin_16h_R1 1 TPDDFLNSVDEMDTGDTINQSTLPSQQNR 29 0 P46937-6;P46937-7;P46937;P46937-9;P46937-5;P46937-3;P46937-2;P46937-8;H0YCI3;P46937-4 P46937-6 YAP1 Transcriptional coactivator YAP1 1 0 TPDDFLNS(0.11)VDEMDT(0.017)GDT(0.831)INQS(0.03)T(0.011)LPS(0.002)QQNR 54.3 0.0030651 4753100 438.12 461.2 435.27 396.76 461.82 516.5 332.87 301.63 429.79 529.93 TRUE FALSE FALSE 432.7800249 467.6927857 442.8456918 442.635258 438.2516021 483.4973169 361.1439695 310.3571882 391.348506 516.1623422 0.838457186 0.906096295 0.857958157 0.857550468 0.849057683 0.936715598 0.699671285 0.601278247 0.758188798 1 9.01168108 -6.637830399 0.725767525 0.914753334 5.64E-28 0.543947183 0.074746274 2.698677561 0.532348507 0.011936016 2.495524856 2.30E-07 6.637830399 -0.914753334 TPDELY(ph)FEEGDIIYIT(ph)DMS(ph)DT(ph)NWWK ddPTM_HeLa_Romidepsin_16h_R1 1 TPDELYFEEGDIIYITDMSDTNWWK 25 0 Q92882 Q92882 OSTF1 Osteoclast-stimulating factor 1 4 0 T(0.055)PDELY(0.782)FEEGDIIY(0.279)IT(0.885)DMS(0.999)DT(0.999)NWWK 48.18 0.003736 0 792.24 772.46 821.81 573.62 1028.6 866.53 685.05 723.3 941.68 711.16 TRUE FALSE FALSE 782.5838742 783.3347122 836.1132583 639.9446434 976.1067038 811.1615296 743.2381299 744.2275443 857.4537823 692.6839607 1.129784893 1.130868847 1.207063114 0.923862367 1.409166025 1.171041305 1.072983023 1.074411401 1.237871571 1 9.436053458 -12.00344266 0.568587445 0.984944381 1.14673604 0 0.13719229 1.450075372 0.767657409 0.120546969 0.027734214 9.92E-13 12.00344266 0.161791658 TPDGGHSSQEIKSET(ph)S(ph)SNPSSPEICPNK ddPTM_HeLa_Romidepsin_16h_R1 1 TPDGGHSSQEIKSETSSNPSSPEICPNK 28 1 Q684P5-2;Q684P5;A0A1B0GV05;Q684P5-3 Q684P5-2 RAP1GAP2 Rap1 GTPase-activating protein 2 2 0 TPDGGHSS(0.007)QEIKS(0.021)ET(0.415)S(0.415)S(0.381)NPS(0.381)S(0.381)PEICPNK 50.029 0.0035433 0 1086.5 823.69 783.98 552.38 739.31 891.65 729.03 769.06 957.14 1041.6 TRUE FALSE FALSE 1073.25732 835.2859294 797.624843 616.2487746 701.580252 834.6764427 790.95379 791.3115377 871.5310012 1014.539082 1.057876763 0.823315675 0.7861943 0.607417482 0.691526097 0.822714923 0.779618848 0.779971469 0.859041329 1 9.986608726 -10.09962596 2.963080858 1.027598448 0.742449105 0.597555799 0.079385525 0.080191027 1.357015614 0.010993764 0.013780199 7.95E-11 10.09962596 -0.285149343 TPDSEDKLFS(ph)PVIAR ddPTM_HeLa_Romidepsin_16h_R1 1 TPDSEDKLFSPVIAR 15 1 Q5VZ89-5;Q5VZ89-3;Q5VZ89;Q5VZ89-7;X6RAE7;X6R5W5 Q5VZ89-5 DENND4C DENN domain-containing protein 4C 1 0 TPDS(0.001)EDKLFS(0.999)PVIAR 65.809 0.022343 16258000 1838.4 1787.8 1844.4 1875.7 2505.2 3043.4 2412 3133.4 2649.9 2006.2 TRUE FALSE FALSE 1815.992874 1812.968695 1876.501008 2092.577259 2377.350296 2848.936562 2616.87522 3224.059985 2412.886307 1954.078635 0.929334593 0.92778697 0.960299639 1.070876689 1.216609329 1.457943663 1.33918624 1.649913124 1.234794887 1 10.93227281 -8.447169729 1.13647744 0.959300667 1.531353715 0.77410996 0.1111337 0.100590708 0.239004858 0.01055424 0.040803614 3.57E-09 8.447169729 0.572053048 TPDVLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 TPDVLKK 7 1 P31948-3;P31948;P31948-2 P31948-3 STIP1 Stress-induced-phosphoprotein 1 0 1 TPDVLK(1)K 87.616 0.027476 3445900 1621.6 1723.6 2096.7 1336.7 3307.1 2917.8 4398.8 1481.2 3411.9 2640.8 FALSE TRUE FALSE 1601.835315 1747.864886 2133.192184 1491.255543 3138.326347 2731.361997 4772.433962 1524.056185 3106.731119 2572.191635 0.622751156 0.679523587 0.829328637 0.579760669 1.220098185 1.061881222 1.855395958 0.59251269 1.207814797 1 11.32878242 -8.742248377 24.59697993 0.791337759 1.221924636 0.212661944 0.335736161 185.9657331 238349.5096 0.043144147 0.086173457 1.81E-09 8.742248377 0.430586877 TPEAS(ph)PEPK ddPTM_HeLa_Romidepsin_16h_R1 1 TPEASPEPK 9 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 1 0 T(0.499)PEAS(0.501)PEPK 101.39 0.027068 12508000 6075 6003.4 5653 6057.4 5442.5 5035.8 4969.2 3960.4 6898 6543.9 TRUE FALSE FALSE 6000.955563 6087.916023 5751.388094 6757.785089 5164.748916 4714.028632 5391.283724 4074.987926 6281.025604 6373.888535 0.941490509 0.955133744 0.902335845 1.060229568 0.810297966 0.739584416 0.845839034 0.639325257 0.985430726 1 12.63795807 -6.114537746 0.377487039 0.982815212 1.12E-19 0.705800412 0.066641484 5.031097023 0.256686342 0.017852414 2.70050212 7.68E-07 6.114537746 -0.982815212 TPEDGDYS(ph)YEIIEK ddPTM_HeLa_Romidepsin_16h_R1 2 TPEDGDYSYEIIEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.05)PEDGDYS(0.949)Y(0.001)EIIEK;T(0.022)PEDGDYS(0.978)YEIIEK ; 209.53 8.91E-24 53337000 7854.7 7154.2 6602.4 6262 6093.2 6970.7 5006.7 5153.9 7855.1 7322.2 TRUE FALSE FALSE 7758.963895 7254.917015 6717.312002 6986.041904 5782.241267 6525.294767 5431.968973 5303.019965 7152.520183 7131.968188 1.087913419 1.017239116 0.941859501 0.979539128 0.810749728 0.914936045 0.761636736 0.743556312 1.002881672 1 12.80008455 -8.538956077 0.69638969 1.041923854 0.736080843 0.798522416 0.04973091 0.304143766 0.235722228 0.01005197 0.052973596 2.89E-09 8.538956077 -0.305843012 TPEDGDYSYEIIEK ddPTM_HeLa_Romidepsin_16h_R1 1 TPEDGDYSYEIIEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 0 0 182.71 2.05E-06 3054000 769.96 938.84 843.87 728.95 765.53 840.81 724.01 762.23 865.85 769.93 FALSE FALSE TRUE 760.5754314 952.0570142 858.5572034 813.2346288 726.4621475 787.0849546 785.5073913 784.2839225 788.4062074 749.9271076 1.014199145 1.269532738 1.144854206 1.084418233 0.968710346 1.049548612 1.047444989 1.045813539 1.051310453 1 9.550606563 -10.48460171 24.99761769 1.006264227 1.086059859 0.126262577 0.075766104 593.4645277 387577.9432 0.013611355 0.015276233 3.28E-11 10.48460171 0.079795631 TPEELDDS(ph)DFETEDFDVR ddPTM_HeLa_Romidepsin_16h_R1 8 TPEELDDSDFETEDFDVR 18 0 G3XAM7;P35221-3;P35221;P35221-2 G3XAM7 CTNNA1 Catenin alpha-1 1 0 TPEELDDS(0.999)DFET(0.001)EDFDVR;TPEELDDS(1)DFETEDFDVR;T(0.001)PEELDDS(0.999)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR;TPEELDDS(1)DFETEDFDVR ;;;;;;; 216.72 4.83E-29 1635898100 9380.5 8289.879 8397.31 8423.23 8106.91 8703.16 6946.85 7733.07 9319.86 8878.76 TRUE FALSE FALSE 9266.166858 8406.584134 8543.461658 9397.163485 7693.184132 8147.056164 7536.915266 7956.81418 8486.26838 8648.088535 1.071469935 0.972074245 0.987901734 1.086617401 0.889582027 0.94206438 0.871512269 0.920066226 0.981288333 1 13.07816558 -8.749271978 24.999552 1.028879479 0.905946498 0.639094825 0.040137218 100.0553266 205575.795 0.005944728 0.01181959 1.78E-09 8.749271978 -0.122932981 TPESQPDT(ph)PPGTPLVSQDEKR ddPTM_HeLa_Romidepsin_16h_R1 1 TPESQPDTPPGTPLVSQDEKR 21 1 A0A0D9SEV0;M0R000;M0QYI1;A0A0D9SFD6;M0R3C8;A0A0D9SFL2;M0QYH2;Q96T60-2;Q96T60 A0A0D9SEV0 PNKP Bifunctional polynucleotide phosphatase/kinase;Polynucleotide 3-phosphatase;Polynucleotide 5-hydroxyl-kinase 1 0 TPES(0.001)QPDT(0.994)PPGT(0.005)PLVSQDEKR 131.37 2.91E-12 0 2578 2223.6 2421.8 1535 2135.4 2355.8 2189.9 2584.7 2401.9 3109.5 TRUE FALSE FALSE 2546.578344 2254.903899 2463.950413 1712.483922 2026.42257 2205.271983 2375.910051 2659.484217 2187.068048 3028.714742 0.840811553 0.74450851 0.813530036 0.565416049 0.669070131 0.728121388 0.784461481 0.878090029 0.72211094 1 11.56448999 -11.01969171 0.710418826 0.980496264 0.729191051 0 0.114073228 0.308094651 0.344865837 0.031873224 0.022041884 9.56E-12 11.01969171 -0.251305213 TPETLLPFAEAEAFLKK ddPTM_HeLa_Romidepsin_16h_R1 1 TPETLLPFAEAEAFLKK 17 1 Q3KQU3-4;Q3KQU3;Q3KQU3-2;Q3KQU3-3 Q3KQU3-4 MAP7D1 MAP7 domain-containing protein 1 0 0 138.81 0.00057576 5266100 2251.9 2312.8 2109.5 1229.5 1848.4 2470.5 2330.3 2265.3 2297.8 2539.1 FALSE FALSE TRUE 2224.452977 2345.359659 2146.214963 1371.660575 1754.069251 2312.643023 2528.235624 2330.842881 2092.279013 2473.133816 0.899447075 0.948335122 0.867811903 0.554624487 0.709249633 0.935106304 1.022280156 0.942465331 0.846003156 1 11.27212459 -10.99820541 0.789221295 0.982724871 0.846022733 0.012552113 0.134205887 0.836080208 1.136690877 0.047068875 0.034537996 1.00E-11 10.99820541 -0.136702138 TPGDFSYAY(ph)QKPEETTRSPDEEDYDYESYEK ddPTM_HeLa_Romidepsin_16h_R1 1 TPGDFSYAYQKPEETTRSPDEEDYDYESYEK 31 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.002)PGDFS(0.013)Y(0.087)AY(0.665)QKPEET(0.139)T(0.046)RS(0.046)PDEEDYDYESYEK 58.462 0.00051606 175100000 1401.7 1604.7 1568.5 1312.7 1454.7 1850.3 1639 1517.2 1741.8 1846.2 TRUE FALSE FALSE 1384.615541 1627.291009 1595.799085 1464.48055 1380.461231 1732.071802 1778.216619 1561.097788 1586.009046 1798.235458 0.769985674 0.904937672 0.887424991 0.814398662 0.767675459 0.963206344 0.98886751 0.868127576 0.881980743 1 10.81236622 -6.893211662 15.4337528 0.887643659 0.000365144 0.004647548 0.079064362 14062332.48 16363602.36 0.013875072 430168152.2 1.28E-07 6.893211662 -0.887278515 TPGDFSYAYQKPEET(ph)TRSPDEEDYDYESYEK ddPTM_HeLa_Romidepsin_16h_R1 2 TPGDFSYAYQKPEETTRSPDEEDYDYESYEK 31 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 TPGDFSY(0.012)AY(0.032)QKPEET(0.63)T(0.163)RS(0.163)PDEEDYDYESYEK;TPGDFS(0.001)Y(0.005)AY(0.005)QKPEET(0.758)T(0.115)RS(0.115)PDEEDYDYESYEK ; 82.157 1.54E-08 176699000 4632.2 4280.5 4170.7 3802.8 4494.1 4519.3 4452 4714.1 4526.1 4712.6 TRUE FALSE FALSE 4575.740965 4340.760991 4243.289284 4242.497629 4264.749307 4230.531315 4830.152769 4850.495046 4121.27428 4590.165973 0.99685741 0.945665367 0.924430469 0.924258002 0.929105687 0.921651056 1.052282815 1.056714523 0.897848641 1 12.1643306 -14.25470866 12.89917254 0.989578776 0.982861727 0 0.057322756 0 0 0 0.007244571 5.56E-15 14.25470866 -0.006717049 TPGNGDGGSTSET(ph)PQPPR ddPTM_HeLa_Romidepsin_16h_R1 1 TPGNGDGGSTSETPQPPR 18 0 H0YMJ0;B3KTM8;Q9UBU8-2;H0YNE0;H0YLJ3;Q9UBU8;H0YNI8;H0YNX3;H0YLV1;H0YMT8;H0YM21;Q9UBU8-3 H0YMJ0 MORF4L1 Mortality factor 4-like protein 1 1 0 TPGNGDGGS(0.074)T(0.074)S(0.114)ET(0.739)PQPPR 152.86 3.84E-10 0 476.73 437.98 465.21 475.97 376.89 452.67 509.25 392.16 388.81 402.05 TRUE FALSE FALSE 470.9194314 444.1458939 473.3067849 531.0038909 357.6558969 423.7458479 552.5056823 403.5065309 354.0338598 391.604683 1.202537793 1.134169006 1.208634129 1.355969205 0.913308529 1.082075538 1.410876086 1.030392506 0.904059311 1 8.613254207 -12.30337575 0.89463711 0.993703749 1.172621216 0.251902508 0.141648033 0.875915478 1.185624684 0.10745995 0.025034519 4.97E-13 12.30337575 0.178917467 TPGPPGLTTTPAPPDK(ac)LGGK ddPTM_HeLa_Romidepsin_16h_R1 2 TPGPPGLTTTPAPPDKLGGK 20 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 0 1 ; TPGPPGLTTTPAPPDK(1)LGGK;TPGPPGLTTTPAPPDK(1)LGGK 169.15 1.69E-16 1680580 0 139.96 164.6 520.675 1362.88 1452.28 1599.76 1501.4 256.03 58.504 FALSE TRUE FALSE 0 141.9303606 167.464794 580.8778933 1293.327148 1359.483995 1735.643574 1544.84064 233.1300356 56.98405765 0 2.490702951 2.938800796 10.19369131 22.6962979 23.85726905 30.4584062 27.11004979 4.091144878 1 5.83248645 -8.839758351 1.327965842 0.57346354 28.33644851 0.974299512 1.845375738 0.030814214 0.108537271 0.217625069 0.537702983 1.45E-09 8.839758351 27.76298497 TPGPPGLTTTPAPPDK(ac)LGGK(ac)QR ddPTM_HeLa_Romidepsin_16h_R1 1 TPGPPGLTTTPAPPDKLGGKQR 22 2 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 0 2 TPGPPGLTTTPAPPDK(1)LGGK(1)QR 67.415 0.013727 1421800 0 0 0 0 0 244.31 65.674 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 228.6993795 71.25234792 0 0 0 0 TPGT(ph)PGTPSYPR ddPTM_HeLa_Romidepsin_16h_R1 2 TPGTPGTPSYPR 12 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 TPGT(0.915)PGT(0.085)PS(0.001)YPR;T(0.039)PGT(0.942)PGT(0.007)PS(0.012)YPR ; 155.47 0.0026621 183437000 2228.4 2591.8 1884.91 2403.8 3543 3007.5 2412.5 2637.1 1929.9 1663.1 TRUE FALSE FALSE 2201.239404 2628.287428 1917.716068 2681.738666 3362.187489 2815.330456 2617.41769 2713.400328 1757.28491 1619.892422 1.358879993 1.622507391 1.183853966 1.655504174 2.075562206 1.737973718 1.615797231 1.675049707 1.08481581 1 10.66168229 -10.52654934 0.392224606 0.985339049 1.794774273 0.657093249 0.186411726 0.466588203 0.200899053 0.13241796 0.120092003 2.97E-11 10.52654934 0.809435224 TPHDILEDINAS(ph)PEMR ddPTM_HeLa_Romidepsin_16h_R1 2 TPHDILEDINASPEMR 16 0 Q9Y6Q9-2;Q9Y6Q9-3;Q9Y6Q9-5;Q9Y6Q9;Q9Y6Q9-4 Q9Y6Q9-2 NCOA3 Nuclear receptor coactivator 3 1 0 TPHDILEDINAS(1)PEMR;TPHDILEDINAS(1)PEMR ; 147.28 9.17E-05 45759000 1664.31 1700.16 1876.52 1724.83 2034.83 1897.93 1976.13 2422.6 1946.25 1957.65 TRUE FALSE FALSE 1644.02475 1724.094897 1909.180043 1924.26296 1930.985032 1776.658398 2143.982433 2492.694109 1772.172526 1906.789971 0.862194985 0.904187102 1.001253454 1.009163563 1.012688897 0.931753589 1.124393596 1.307272509 0.92940101 1 10.89693023 -4.00000134 0.691104922 0.938971914 46.0621549 0.818897301 0.051644207 92.34466415 0.473622351 0.010917529 6438.566384 1.00E-04 4.00000134 45.12318299 TPHPVLT(ph)PVAANQAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPHPVLTPVAANQAK 15 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;A0A494C104;H0Y837 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 T(0.009)PHPVLT(0.991)PVAANQAK 140.89 0.00055585 17520000 3970.3 3221.5 3390.8 3879.5 5119.4 5617.3 4997.3 5653.7 4044 3749.8 TRUE FALSE FALSE 3921.908456 3266.852362 3449.815452 4328.066044 4858.137915 5258.372659 5421.770537 5817.280889 3682.294512 3652.379655 1.073795395 0.894444902 0.944539116 1.184998946 1.330129497 1.439711409 1.484448784 1.592737185 1.008190511 1 11.83462102 -8.649455339 1.461552784 1.016974543 1.522535508 0.930797257 0.062302098 0.083933824 0.356622868 0.010912298 0.029533614 2.24E-09 8.649455339 0.505560965 TPHS(ph)PPLAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPHSPPLAK 9 0 Q8IZW8 Q8IZW8 TNS4 Tensin-4 1 0 T(0.002)PHS(0.998)PPLAK 75.566 0.029995 46167000 10550 10341 10119 14607 7450.3 4344.6 3878.4 3562.2 10997 10826 TRUE FALSE FALSE 10421.41254 10486.58087 10295.11695 16295.93007 7070.08339 4066.994082 4207.831199 3665.266637 10013.40078 10544.73896 0.98830446 0.994484634 0.976327341 1.545408581 0.670484439 0.385689404 0.399045554 0.347591975 0.949611064 1 13.36423576 -8.528127731 24.99812056 1.030496962 0.404349953 0.777722329 0.167992807 48.52490871 231098.0316 0.02363182 0.047387739 2.96E-09 8.528127731 -0.626147009 TPHVQAVQGPLGS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 3 TPHVQAVQGPLGSPPK 16 0 Q15149 Q15149 PLEC Plectin 1 0 TPHVQAVQGPLGS(1)PPK;TPHVQAVQGPLGS(1)PPK;TPHVQAVQGPLGS(1)PPK ;; 108.34 0.0035186 450265000 15755.9 15056.3 15040.6 12096.5 11537.4 10906.1 9150.5 9834.8 16812.2 16071.4 TRUE FALSE FALSE 15563.86103 15268.26299 15302.37533 13495.15425 10948.60343 10209.23541 9927.743242 10119.35442 15308.47473 15653.86271 0.994250513 0.97536712 0.977546285 0.862097394 0.699418644 0.652186339 0.634204057 0.646444562 0.977935926 1 13.93423108 -8.884231169 1.651327959 0.995983345 0.639232422 0.995980924 0.00984104 0.012250274 0.067348338 0.001310851 0.002875971 1.31E-09 8.884231169 -0.356750923 TPHVQAVQGPLGS(ph)PPKR ddPTM_HeLa_Romidepsin_16h_R1 2 TPHVQAVQGPLGSPPKR 17 1 Q15149 Q15149 PLEC Plectin 1 0 TPHVQAVQGPLGS(1)PPKR;TPHVQAVQGPLGS(1)PPKR ; 83.065 0.0046495 174486000 5231.8 5101.5 5390.2 4240.1 4237.1 3956.3 3636.3 3996 5845 5369 TRUE FALSE FALSE 5168.032809 5173.319051 5484.01417 4730.360312 4020.864976 3703.505198 3945.167231 4111.617955 5322.208561 5229.512606 0.988243685 0.989254533 1.048666402 0.904550896 0.768879488 0.708193187 0.754404383 0.786233492 1.017725544 1 12.35246078 -8.884990336 2.912494293 0.997320416 0.748349407 0.953914103 0.026269902 0.035602133 0.60891261 0.003728297 0.007238525 1.30E-09 8.884990336 -0.248971009 IPSLGWS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 IPSLGWSPSK 10 0 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 IPSLGWS(0.991)PS(0.009)K;IPSLGWS(0.997)PS(0.003)K ; 160.72 0.0023638 109643000 14799.2 14832.8 17005.5 12105.5 10273.5 8557.6 5419.5 6364 14151.1 13745.8 TRUE FALSE FALSE 14618.82166 15041.61655 17301.47359 13505.19487 9749.204959 8010.796978 5879.832195 6548.132299 12885.39017 13388.68213 1.09187906 1.123457589 1.292246199 1.00870233 0.728167632 0.598326026 0.439164373 0.489079674 0.962409149 1 13.70872634 -8.538731478 1.950442808 1.07178645 0.487893828 0.894036514 0.089797115 0.080608254 0.608191552 0.014441337 0.037039358 2.89E-09 8.538731478 -0.583892623 down TPKDS(ph)PGIPPSAGAHQLFR ddPTM_HeLa_Romidepsin_16h_R1 1 TPKDSPGIPPSAGAHQLFR 19 1 Q5SVM6;E9PGT3;Q15418-3;Q15418-4;Q15418;Q15418-2 Q5SVM6 RPS6KA1 Ribosomal protein S6 kinase;Ribosomal protein S6 kinase alpha-1 1 0 T(0.153)PKDS(0.836)PGIPPS(0.012)AGAHQLFR 89.502 0.0013006 40329000 2132.9 1556.4 1949.7 1725.8 2453.6 2404.1 3079.1 2969.6 2435.1 2151.7 TRUE FALSE FALSE 2106.903394 1578.31104 1983.633711 1925.345116 2328.383636 2250.485769 3340.638677 3055.520691 2217.298557 2095.798524 1.005298635 0.753083382 0.946481109 0.918668991 1.110976847 1.073808261 1.593969382 1.457926731 1.057973146 1 11.03328432 -7.840193009 4.306805763 0.98250315 1.528116351 0.835749459 0.096740984 0.055867769 1.923288302 0.013557016 0.045384805 1.44E-08 7.840193009 0.5456132 VPLAPITDPQQLQLS(ph)PLK ddPTM_HeLa_Romidepsin_16h_R1 2 VPLAPITDPQQLQLSPLK 18 0 A0A286YFD6;P31350;P31350-2 A0A286YFD6 RRM2 Ribonucleoside-diphosphate reductase subunit M2 1 0 VPLAPITDPQQLQLS(1)PLK;VPLAPITDPQQLQLS(1)PLK ; 249.41 4.35E-62 1104010000 11242.2 13194.5 10655.7 8411.2 8837.6 4747.6 3887.62 3894.18 11326.6 11849.6 TRUE FALSE FALSE 11105.17574 13380.25252 10841.15799 9383.74252 8386.584294 4444.243682 4217.834346 4006.851954 10313.52053 11541.74568 0.962174704 1.15929192 0.939299677 0.813026277 0.726630488 0.385058188 0.365441629 0.347161691 0.893584109 1 13.49457383 -8.522418694 1.300063143 0.994594961 0.327930204 0.933037092 0.072202154 0.069983489 0.227224402 0.010256037 0.033207234 3.00E-09 8.522418694 -0.666664757 down TPLDLFAHFGPEPGDHSDPLPPS(ph)APSPTR ddPTM_HeLa_Romidepsin_16h_R1 1 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 F8WCX2;Q8N1G0-2;Q8N1G0 F8WCX2 ZNF687 Zinc finger protein 687 1 0 TPLDLFAHFGPEPGDHS(0.04)DPLPPS(0.476)APS(0.347)PT(0.137)R 81.178 1.21E-06 10129000 328.27 497.49 432.56 204.33 434.31 513.07 415.4 424.26 593.76 541.52 TRUE FALSE FALSE 324.268919 504.4936773 440.0885253 227.955596 412.1455401 480.2864829 450.6840656 436.5352937 540.6526185 527.4512323 0.614784646 0.956474545 0.834368181 0.432183266 0.781390799 0.910579886 0.854456371 0.827631574 1.025028638 1 9.042893899 -12.59128837 1.380204649 1.000096655 0.757544405 0.286625244 0.145457436 0.484094047 1.653117789 0.108494189 0.025142907 2.56E-13 12.59128837 -0.242552249 TPLDLFAHFGPEPGDHSDPLPPSAPS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 1 TPLDLFAHFGPEPGDHSDPLPPSAPSPTR 29 0 F8WCX2;Q8N1G0-2;Q8N1G0 F8WCX2 ZNF687 Zinc finger protein 687 1 0 TPLDLFAHFGPEPGDHS(0.001)DPLPPS(0.23)APS(0.54)PT(0.23)R 79.27 1.17E-06 11142000 1340 1318.6 1461.2 1003 1656.8 1572.2 1302.1 1346.6 1622.7 1246.4 TRUE FALSE FALSE 1323.667565 1337.163285 1486.631573 1118.971579 1572.247314 1471.741494 1412.700341 1385.561746 1477.561648 1214.018348 1.090319241 1.101435812 1.224554452 0.921708952 1.29507706 1.212289333 1.163656499 1.141302146 1.217083457 1 10.24557451 -10.73330339 0.273267996 0.970095052 1.203183991 0 0.112772893 1.534699209 0.388444232 0.141921356 0.105012577 1.85E-11 10.73330339 0.233088938 TPLGAS(ph)LDEQSSSTLK ddPTM_HeLa_Romidepsin_16h_R1 3 TPLGASLDEQSSSTLK 16 0 E9PHV5;P28290-3;P28290 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 T(0.001)PLGAS(0.999)LDEQSSSTLK;T(0.017)PLGAS(0.841)LDEQS(0.106)S(0.028)S(0.008)TLK;TPLGAS(0.973)LDEQS(0.022)S(0.006)STLK ;; 200.33 2.32E-18 93503000 5733.3 6261.6 5556 6924.5 4344.62 6838.6 5649.7 5861 7296.1 5913.4 TRUE FALSE FALSE 5663.420334 6349.750969 5652.699849 7725.143271 4122.897829 6401.635531 6129.585377 6030.578788 6643.518543 5759.769016 0.983272128 1.10243153 0.981410858 1.341224492 0.715809578 1.111439628 1.064206804 1.047017471 1.15343489 1 12.49179524 -10.29684325 23.72645449 0.99210072 1.050181271 0 0.153002751 941.0425023 630651.0089 0.022520683 0.025754228 5.05E-11 10.29684325 0.058080551 TPLHEIALSIK ddPTM_HeLa_Romidepsin_16h_R1 2 TPLHEIALSIK 11 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 ; ; 83.081 0.012085 1399730 2463.3 1649.8 2474.02 2261.65 2886.5 2804.4 2110.83 1918.18 2335.4 1815.33 FALSE FALSE TRUE 2433.276352 1673.025928 2517.07928 2523.152614 2739.191134 2625.207891 2290.123848 1973.679512 2126.515975 1768.167465 1.37615718 0.94619201 1.423552537 1.426987355 1.549169515 1.484705461 1.295196237 1.116228836 1.202666612 1 10.7880392 -13.12087531 0.373335708 0.73918052 1.364534084 0.168871747 0.179722857 4.175208385 0.467866302 1.139045362 0.060793626 7.57E-14 13.12087531 0.625353564 TPLVSVLLEGPPHSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TPLVSVLLEGPPHSGK 16 0 I3L0N3;P46459-2;P46459 I3L0N3 NSF Vesicle-fusing ATPase 0 0 92.269 0.0052415 0 49.445 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 48.84234532 0 0 0 0 0 0 0 0 0 0 TPLYLQPDAYGS(ph)LDR ddPTM_HeLa_Romidepsin_16h_R1 3 TPLYLQPDAYGSLDR 15 0 Q8WUF5 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR;TPLYLQPDAYGS(1)LDR ;; 186.17 6.59E-09 219605000 5911.3 5008.7 5134.9 6253.7 4905.7 3940.5 3479.62 3862.8 4876 5199.7 TRUE FALSE FALSE 5839.250802 5079.21261 5224.270781 6976.782219 4655.343823 3688.714767 3775.178836 3974.564024 4439.878348 5064.611044 1.152951481 1.002883058 1.03152458 1.377555385 0.919190789 0.728331304 0.745403507 0.784771819 0.876647448 1 12.30623576 -8.524179085 24.99708849 1.086403396 0.764037088 0.574816401 0.123572087 19.42636548 373443.7229 0.015897692 0.031996209 2.99E-09 8.524179085 -0.322366308 TPPGALLGAPPPLVPAPRPS(ph)SPPR ddPTM_HeLa_Romidepsin_16h_R1 1 TPPGALLGAPPPLVPAPRPSSPPR 24 1 J3KNZ9;Q9HAH7 J3KNZ9 FBRS Probable fibrosin-1 1 0 TPPGALLGAPPPLVPAPRPS(0.5)S(0.5)PPR 90.017 3.12E-05 19894000 1369.7 1778.7 1547.1 794.17 1385.9 1385.6 1333.8 1406.1 1745 1659.5 TRUE FALSE FALSE 1353.00557 1803.740585 1574.026627 885.9956721 1315.172351 1297.064632 1447.092939 1446.783285 1588.92283 1616.385951 0.837056007 1.115909591 0.973793806 0.548133737 0.813649952 0.802447356 0.895264487 0.895072915 0.983009552 1 10.658556 TPPGALLGAPPPLVPAPRPS(ph)SPPRGPGPAR ddPTM_HeLa_Romidepsin_16h_R1 1 TPPGALLGAPPPLVPAPRPSSPPRGPGPAR 30 2 J3KNZ9;Q9HAH7 J3KNZ9 FBRS Probable fibrosin-1 1 0 TPPGALLGAPPPLVPAPRPS(0.5)S(0.5)PPRGPGPAR 49.942 0.0071295 10885000 1360.6 1449.9 1243.2 1574.9 1364.2 1335.7 932.19 1297.8 1501.8 1129.9 TRUE FALSE FALSE 1344.016484 1470.31173 1264.837375 1756.997348 1294.579783 1250.353081 1011.370195 1335.349795 1367.475247 1100.545035 1.221228065 1.335985065 1.149282705 1.596479283 1.176307868 1.136121686 0.918972112 1.213353159 1.242543652 1 10.10400247 -5.736831404 16.04388513 1.154293118 1.172875659 0 0.1800887 0 0 0.025249429 0 1.83E-06 5.736831404 0.018582541 TPPKSY(ph)ST(ph)ARRSR ddPTM_HeLa_Romidepsin_16h_R1 1 TPPKSYSTARRSR 13 3 Q5T757;Q05519-2;Q05519;Q5T760 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 2 0 T(0.308)PPKS(0.224)Y(0.499)S(0.286)T(0.682)ARRS(0.001)R 50.467 0.026073 12950000 4150.2 4020.5 3562.8 218.74 3114.7 2973 2369.7 2385.5 4463.7 4662.2 TRUE FALSE FALSE 4099.615766 4077.100705 3624.809039 244.031748 2955.745236 2783.034895 2570.982259 2454.520679 4064.455492 4541.075372 0.902785228 0.897827138 0.798227015 0.053738757 0.650891032 0.612858116 0.566161547 0.540515292 0.895042509 1 12.14881827 -9.508793524 22.34652132 0.943801773 0.49771847 0.637235402 0.158014148 73.45692917 116540.9118 0.02383653 0.035491459 3.10E-10 9.508793524 -0.446083303 TPPTAALSAPPPLIS(ph)TLGGRPVSPR ddPTM_HeLa_Romidepsin_16h_R1 2 TPPTAALSAPPPLISTLGGRPVSPR 25 1 A0A2R8Y568;A0A024RDL5;A0A2R8Y522;A0A087WVB5;Q75MD7;A0A2R8Y8C6;Q8WXX7-5;Q8WXX7-2;Q8WXX7 A0A2R8Y568 AUTS2 Autism susceptibility gene 2 protein 1 0 TPPTAALSAPPPLIS(0.671)T(0.229)LGGRPVS(0.1)PR;TPPTAALSAPPPLIS(0.785)T(0.204)LGGRPVS(0.012)PR ; 83.436 4.96E-05 61321000 1665.8 1564.81 1589.37 1644.04 1139.05 1372.1 863.45 1197.6 1893.05 1507.5 TRUE FALSE FALSE 1645.496589 1586.839436 1617.032318 1834.13164 1080.920028 1284.427238 936.7914214 1232.250666 1723.730867 1468.334933 1.120654799 1.080706725 1.101269392 1.24912348 0.736153587 0.874750855 0.637995733 0.839216339 1.173935747 1 10.51996537 -8.744353726 24.99995494 1.075980446 0.769792484 0.772771189 0.090742735 94.19621477 137828.4681 0.012870986 0.025690512 1.80E-09 8.744353726 -0.306187962 TPQEAIMDGTEIAVS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TPQEAIMDGTEIAVSPR 17 0 Q06587 Q06587 RING1 E3 ubiquitin-protein ligase RING1 1 0 TPQEAIMDGTEIAVS(1)PR 128.44 0.0028435 14611000 1305.9 1579.8 1164.8 1514.9 1512 1374.8 1350.4 1513 1239 1156.9 TRUE FALSE FALSE 1289.983189 1602.040466 1185.072855 1690.059866 1434.836998 1286.954717 1465.102942 1556.776268 1128.180737 1126.843571 1.144775745 1.421706177 1.051674683 1.49981764 1.273324031 1.142088174 1.300183078 1.381537161 1.001186647 1 10.13807154 -10.87225677 0.764548468 1.020471285 1.295927421 0.450323814 0.126400893 0.358840976 0.459756156 0.038495503 0.030542294 1.34E-11 10.87225677 0.275456137 TPQGPVSATVEVS(ph)SPTGFAQSQVLEDVSQAAR ddPTM_HeLa_Romidepsin_16h_R1 1 TPQGPVSATVEVSSPTGFAQSQVLEDVSQAAR 32 0 O15061;H0YL34;A0A075B7B1;O15061-2 O15061 SYNM Synemin 1 0 TPQGPVSAT(0.001)VEVS(0.537)S(0.337)PT(0.125)GFAQSQVLEDVSQAAR 126.62 1.18E-15 7131700 849.79 835.23 897.23 983.95 1436.1 1324 1130.6 1417.9 1081.7 1195.4 TRUE FALSE FALSE 839.4324326 846.9883899 912.8459118 1097.718929 1362.810458 1239.400673 1226.633136 1458.924699 984.9500428 1164.343336 0.720949231 0.727438689 0.784000633 0.942779415 1.170454123 1.064463234 1.053497794 1.253002147 0.845927496 1 10.18530082 -8.922129388 4.1236766 0.846683461 1.123492925 0.720980968 0.092517382 0.136748296 4.512805355 0.018978995 0.035217763 1.20E-09 8.922129388 0.276809464 TPQNVPAS(ph)PGGDR ddPTM_HeLa_Romidepsin_16h_R1 3 TPQNVPASPGGDR 13 0 H0YLX2;A0A669KBM4;Q2KHR2-2;Q2KHR2 H0YLX2 RFX7 DNA-binding protein RFX7 1 0 TPQNVPAS(1)PGGDR;TPQNVPAS(1)PGGDR;TPQNVPAS(1)PGGDR ;; 110.84 0.0065968 19250100 3436.61 3862.5 3736.13 3635.8 3469.5 3034.23 2588.7 2810.35 3583.7 3677.5 TRUE FALSE FALSE 3394.723275 3916.876376 3801.155775 4056.188303 3292.438469 2840.352496 2808.584113 2891.663043 3263.164896 3581.95802 0.947728381 1.093501475 1.061194954 1.132394149 0.919172824 0.792960855 0.784091856 0.807285576 0.911000318 1 11.80653271 -8.415719042 3.862545863 1.00227868 0.794726502 0.71221663 0.064262347 0.108429753 2.866526039 0.0097456 0.022700231 3.84E-09 8.415719042 -0.207552178 TPS(ph)GEFLER ddPTM_HeLa_Romidepsin_16h_R1 1 TPSGEFLER 9 0 B3KT28;B1ANM7;Q9UNN5-2;Q9UNN5 B3KT28 FAF1 FAS-associated factor 1 1 0 T(0.326)PS(0.674)GEFLER 108.31 0.02078 4854200 1134.6 1376.6 1213.1 1154.3 1485.6 1490.5 1377.6 1624 1361 1234.1 TRUE FALSE FALSE 1120.771059 1395.979811 1234.213497 1287.765597 1409.784288 1395.26186 1494.61331 1670.987878 1239.268751 1202.037904 0.932392444 1.161344252 1.026767536 1.071318627 1.17282848 1.160746974 1.243399484 1.390129107 1.030973106 1 10.23126667 -6.024910548 0.330086878 0.963927522 2.216917097 0.790938073 0.058363417 4.142875696 0.170803458 0.020641531 2.458438643 9.44E-07 6.024910548 1.252989575 TPS(ph)IQPSLLPHAAPFAK ddPTM_HeLa_Romidepsin_16h_R1 2 TPSIQPSLLPHAAPFAK 17 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3;H0YF36 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 T(0.143)PS(0.857)IQPSLLPHAAPFAK;T(0.208)PS(0.79)IQPS(0.001)LLPHAAPFAK ; 118.37 0.00092898 23147500 3359.3 3554.1 2483.5 2967.8 6770.4 5109 2752.5 4649 3739 3384.6 TRUE FALSE FALSE 3318.355559 3604.134713 2526.724276 3310.951 6424.881224 4782.551389 2986.297281 4783.51148 3404.574476 3296.667604 1.006578751 1.093266033 0.766447995 1.004332677 1.948901738 1.450722961 0.905853316 1.451014192 1.032732105 1 11.68679272 -8.941382978 24.99998941 0.990467066 1.411206597 0.44733701 0.247089693 58.70730202 25038.07388 0.035805043 0.064902153 1.14E-09 8.941382978 0.420739531 TPS(ph)PAAEDAREPEAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSPAAEDAREPEAK 15 1 Q92797 Q92797 SYMPK Symplekin 1 0 T(0.444)PS(0.556)PAAEDAREPEAK 172.09 9.94E-05 6667200 1641 1900.1 1747.9 1144.5 1345.7 1497.4 1272.8 1307.7 1842.4 1650.6 TRUE FALSE FALSE 1620.998861 1926.849658 1778.321466 1276.832475 1277.023908 1401.720973 1380.9116 1345.536236 1677.61113 1607.717174 1.008261208 1.198500388 1.106115861 0.794189734 0.794308805 0.871870373 0.858926945 0.83692347 1.043474037 1 10.65079792 -9.254481134 24.99056697 1.028660248 0.832986889 0.764775054 0.064423256 270.0051148 969723.9452 0.011068368 0.018104438 5.57E-10 9.254481134 -0.195673359 TPS(ph)PPPPIPEDIALGKK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSPPPPIPEDIALGKK 17 1 Q5T200;Q5T200-2 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 T(0.037)PS(0.963)PPPPIPEDIALGKK 115.56 0.00063021 14297000 2119.5 1942.1 1698.7 2156.7 1788.5 1830.7 1780.9 1662.1 1874.3 1829.6 TRUE FALSE FALSE 2093.666719 1969.440935 1728.265161 2406.067802 1697.226171 1713.724178 1932.169602 1710.190241 1706.657914 1782.066728 1.174853155 1.105144327 0.969809454 1.350155841 0.952392043 0.961649837 1.084229659 0.959666781 0.957684629 1 10.79933564 TPSNTPSAEADWS(ph)PGLELHPDYK ddPTM_HeLa_Romidepsin_16h_R1 4 TPSNTPSAEADWSPGLELHPDYK 23 0 Q9Y3Z3-3;Q9Y3Z3-4;Q9Y3Z3;A0A2R8Y7R5;A0A2R8Y755;A0A2R8Y586;A0A2R8YF51;A0A2R8Y5D2;A0A2R8YCS7 Q9Y3Z3-3 SAMHD1 Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 1 0 TPSNT(0.004)PS(0.014)AEADWS(0.982)PGLELHPDYK;TPS(0.001)NT(0.005)PS(0.009)AEADWS(0.985)PGLELHPDYK;T(0.001)PS(0.001)NT(0.002)PS(0.008)AEADWS(0.988)PGLELHPDYK;TPSNT(0.001)PS(0.001)AEADWS(0.998)PGLELHPDYK ;;; 106.63 8.30E-06 193984000 16913 16417.4 16411.1 13655.3 20016.4 21893.9 20503.5 22709 18992.4 16612.4 TRUE FALSE FALSE 16706.85785 16648.52459 16696.72831 15234.19004 18994.88842 20494.95045 22245.06678 23366.04909 17293.67218 16180.80745 1.032510763 1.028905673 1.031884741 0.941497517 1.173914743 1.266620996 1.374781008 1.444059523 1.068776835 1 13.98199598 -8.190486597 1.418007299 1.013268961 1.427744373 0.931909821 0.042420437 0.068073394 0.248314232 0.005662944 0.024120606 6.45E-09 8.190486597 0.414475412 TPSPKEEDEEPES(ph)PPEK ddPTM_HeLa_Romidepsin_16h_R1 1 TPSPKEEDEEPESPPEK 17 1 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 T(0.017)PS(0.358)PKEEDEEPES(0.625)PPEK 61.767 0.020231 118380000 2707.7 2666.5 2355.9 2569 2845.7 2492.8 2136.4 2559.6 2813.3 3171.2 TRUE FALSE FALSE 2674.697511 2704.039057 2396.903451 2866.039868 2700.47331 2333.518125 2317.865763 2633.657988 2561.671402 3088.811767 0.865930886 0.875430185 0.775995312 0.9278778 0.874275778 0.75547437 0.750406932 0.852644378 0.829338786 1 11.59283624 -16.52287875 0.12182786 1.60121461 0.741993696 0 0.074524623 41.28742535 0.362097065 6.021342716 0.233487106 3.00E-17 16.52287875 -0.859220914 TPSPKEEDEEPES(ph)PPEKK ddPTM_HeLa_Romidepsin_16h_R1 2 TPSPKEEDEEPESPPEKK 18 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 TPSPKEEDEEPES(1)PPEKK;TPSPKEEDEEPES(1)PPEKK ; 80.109 0.012239 11204900 1687.39 1563.98 1691.02 2171.16 1765.01 1736.25 1408.97 1751.41 1755.89 1812.67 TRUE FALSE FALSE 1666.823442 1585.997751 1720.451494 2422.199735 1674.934954 1625.309228 1528.647877 1802.084285 1598.838801 1765.576572 0.944067489 0.898288852 0.974441732 1.371902965 0.948661746 0.92055437 0.865806616 1.020677502 0.905561858 1 10.78592368 -6.915264352 20.17549482 0.982782541 2.964243007 0.007437547 0.136052097 3006.234221 804736.1038 0.017935294 33730.89953 1.22E-07 6.915264352 1.981460465 SNVSSPAT(ph)PT(ph)ASSSSSTTPTRK ddPTM_HeLa_Romidepsin_16h_R1 2 SNVSSPATPTASSSSSTTPTRK 22 1 A6NNK5;Q12888;Q12888-3;Q12888-2;H7BZY0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 2 0 SNVS(0.003)S(0.021)PAT(0.959)PT(0.387)AS(0.07)S(0.195)S(0.165)S(0.06)S(0.051)T(0.044)T(0.037)PT(0.009)RK;S(0.006)NVS(0.02)S(0.068)PAT(0.88)PT(0.183)AS(0.069)S(0.181)S(0.154)S(0.131)S(0.111)T(0.095)T(0.082)PT(0.02)RK ; 68.074 0.0013378 37262000 8164.5 6725.9 7658.5 6616.8 5720.4 3477.9 3444.4 2481.45 8365 7595.4 TRUE FALSE FALSE 8064.987934 6820.587397 7791.79298 7381.865549 5428.466642 3255.673414 3736.96725 2553.246841 7616.813449 7398.070413 1.090147496 0.9219414 1.05321963 0.997809582 0.733767907 0.440070617 0.505127289 0.345123349 1.02956758 1 12.85293332 -8.511839229 1.934231913 1.034864456 0.421887027 0.956450387 0.056052158 0.047222898 0.348503351 0.008751267 0.022944541 3.08E-09 8.511839229 -0.61297743 down TPSSS(ph)PPITPPASETK ddPTM_HeLa_Romidepsin_16h_R1 2 TPSSSPPITPPASETK 16 0 F5GZ90;Q9NZJ0 F5GZ90 DTL Denticleless protein homolog 1 0 T(0.016)PS(0.001)S(0.209)S(0.773)PPITPPASETK;T(0.11)PS(0.15)S(0.033)S(0.707)PPIT(0.001)PPASETK ; 153.24 0.00026968 33011000 6202.2 6535.1 5050.4 4712.5 3401.84 3788.9 3573 3801.2 6108.9 5560.2 TRUE FALSE FALSE 6126.605201 6627.101309 5138.300093 5257.381423 3228.231411 3546.801518 3876.490531 3911.181725 5562.504684 5415.745202 1.131258021 1.223673024 0.94877065 0.970758636 0.596082587 0.654905537 0.715781557 0.722187174 1.027098668 1 12.40294415 -8.916471104 3.211538561 1.068549813 0.674036076 0.845010157 0.079692877 0.076078756 1.579515006 0.013331222 0.025284869 1.21E-09 8.916471104 -0.394513737 TPT(ph)PEPFDSETR ddPTM_HeLa_Romidepsin_16h_R1 1 TPTPEPFDSETR 12 0 Q9NSY0;H0YCB1;Q9NSY0-2;Q9NSY0-4 Q9NSY0 NRBP2 Nuclear receptor-binding protein 2 1 0 T(0.318)PT(0.682)PEPFDSETR 117.27 0.017267 5814700 624.2 581.22 734.59 774.89 536.13 689.84 615.99 779.72 751.28 653.5 TRUE FALSE FALSE 616.5920103 589.4024304 747.3752308 864.4864278 508.7692855 645.7614504 668.3121752 802.279968 684.0836352 636.5219758 0.968689274 0.925973419 1.174154639 1.358140741 0.799295711 1.014515563 1.049943601 1.260412049 1.074721158 1 9.314066514 -7.259211141 2.936992627 1.009428772 1.303739804 0.150115907 0.143493113 0.485212991 5.926731393 0.01959383 0.336658053 5.51E-08 7.259211141 0.294311032 TPT(ph)SSPASSPLVAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 T(0.092)PT(0.524)S(0.342)S(0.041)PASSPLVAK 126.32 0.0062417 52725000 3583.8 3782.5 4001.9 3336.2 2618.3 1870.3 1200.9 2074.3 3197.3 3316.4 TRUE FALSE FALSE 3540.119267 3835.750134 4071.551391 3721.947141 2484.678381 1750.793866 1302.904416 2134.316598 2911.32548 3230.23945 1.095930912 1.187450712 1.260448785 1.152220199 0.76919325 0.542001264 0.403346079 0.66073015 0.901272344 1 11.6574254 -8.532284603 3.021783192 1.082476216 0.525933211 0.838574618 0.111754211 0.072366276 1.347453059 0.016334991 0.037181218 2.94E-09 8.532284603 -0.556543004 TPTGEGLLDS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 4 TPTGEGLLDSPSK 13 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425;A0A0J9YWY6 O95425-2 SVIL Supervillin 1 0 TPTGEGLLDS(0.975)PS(0.025)K;TPTGEGLLDS(0.766)PS(0.234)K;TPTGEGLLDS(0.731)PS(0.269)K;TPTGEGLLDS(0.979)PS(0.021)K ;;; 185.27 1.72E-07 176617000 12877 12543.3 12476.4 10866.5 9378.7 7995.9 6769.2 6644.7 13902.8 12504.9 TRUE FALSE FALSE 12720.05017 12719.88491 12693.54651 12122.93586 8900.069942 7484.987796 7344.175679 6836.953911 12659.29875 12180.0209 1.044337303 1.044323734 1.042161308 0.995313223 0.730710564 0.614529963 0.602969054 0.561325302 1.03934951 1 13.57222899 -8.63828512 2.303036714 1.026108107 0.592723853 0.990365862 0.019701618 0.024583483 0.263595215 0.003758921 0.008581992 2.30E-09 8.63828512 -0.433384254 TPTIS(ph)LAGAS(ph)MMEIK ddPTM_HeLa_Romidepsin_16h_R1 1 TPTISLAGASMMEIK 15 0 D6RH05;A0A2R8YFM9;Q9ULG3-2;Q9ULG3 D6RH05 KIAA1257 Uncharacterized protein KIAA1257 2 0 T(0.321)PT(0.486)IS(0.553)LAGAS(0.64)MMEIK 55.196 0.026415 57803000 1619 1709.8 1749.9 1288.4 1885.1 1822.6 1997.4 1933.5 1787.6 2134.8 TRUE FALSE FALSE 1599.267005 1733.870609 1780.356275 1437.37087 1788.896313 1706.141742 2167.059106 1989.442772 1627.712579 2079.337588 0.769123308 0.833857195 0.856213193 0.691263832 0.860320288 0.820521762 1.042187242 0.95676757 0.782803422 1 11.02190829 -7.761748826 24.99999632 0.862007192 0.999477425 0.352907204 0.083243094 9.098777151 735430.6001 0.014786381 0.048853301 1.73E-08 7.761748826 0.137470233 TPTSS(ph)PASSPLVAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 T(0.023)PT(0.001)S(0.023)S(0.953)PASSPLVAK 139.48 0.0010344 36938000 3557.7 4033 3248.5 3441.1 3061.3 2526.2 1975.2 2536.1 3707.3 3843.2 TRUE FALSE FALSE 3514.337384 4089.77668 3305.03878 3838.976173 2905.070438 2364.783973 2142.973439 2609.478052 3375.709803 3743.35311 0.938820699 1.092543653 0.882908634 1.025544762 0.776061021 0.631728801 0.572474297 0.69709642 0.901787703 1 11.87011543 -8.543506022 2.941157833 0.976743594 0.629260711 0.848756972 0.06475745 0.060352075 1.060991564 0.008396066 0.01908529 2.86E-09 8.543506022 -0.347482883 TPTSSPAS(ph)SPLVAK ddPTM_HeLa_Romidepsin_16h_R1 1 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 T(0.028)PT(0.018)S(0.012)S(0.336)PAS(0.598)S(0.009)PLVAK 145.81 0.00061802 19015000 2368.3 2633.3 2644.5 2700.3 1921 1566.6 1193.4 1579.4 2746.4 2775 TRUE FALSE FALSE 2339.434249 2670.371667 2690.526413 3012.521391 1822.964202 1466.499316 1294.767366 1625.097447 2500.755106 2702.9051 0.865525855 0.987963531 0.995420229 1.11454945 0.674446247 0.542564116 0.479028053 0.60124103 0.925210103 1 11.40029514 -8.584150135 5.02970856 0.954906432 0.544523582 0.894761261 0.069086834 0.053361625 2.708565509 0.011798507 0.024222009 2.61E-09 8.584150135 -0.410382849 TPTSSPASSPLVAKK(ac)PLTTTPR ddPTM_HeLa_Romidepsin_16h_R1 2 TPTSSPASSPLVAKKPLTTTPR 22 2 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 0 1 ; TPTSSPASSPLVAK(0.054)K(0.946)PLTTTPR;TPTSSPASSPLVAK(0.215)K(0.785)PLTTTPR 150.13 4.26E-16 1419720 214.741 123.88 0 228.303 453.36 142.214 400.77 440.26 184.31 201.964 FALSE TRUE FALSE 212.1236541 125.6239859 0 254.7004671 430.2233475 133.1269844 434.8113938 452.9982285 167.824852 196.7169462 1.07831917 0.638602766 0 1.294756105 2.187017214 0.676743854 2.2103403 2.302792095 0.853128595 1 7.619977434 -7.350104965 0.745349409 0.958639837 3.1604677 0.458693146 0.541571741 1.746845857 0.73742942 0.089281194 3.121792891 4.47E-08 7.350104965 2.201827862 TPVDES(ph)DDEIQHDEIPTGK ddPTM_HeLa_Romidepsin_16h_R1 2 TPVDESDDEIQHDEIPTGK 19 0 Q86TC9;A0A087WX60;Q86TC9-2 Q86TC9 MYPN Myopalladin 1 0 T(0.131)PVDES(0.869)DDEIQHDEIPTGK;T(0.067)PVDES(0.933)DDEIQHDEIPTGK ; 100.9 0.00054405 214932000 10240.2 9541.4 9456.8 10259.9 8129.4 7316 6647.4 6831.4 11081.8 10483 TRUE FALSE FALSE 10115.3885 9675.72408 9621.391637 11446.19791 7714.526383 6848.531211 7212.02999 7029.055781 10090.61605 10210.65015 0.990670364 0.947610969 0.942289815 1.121005788 0.755537235 0.670724304 0.706324268 0.688404331 0.988244226 1 13.31778711 -8.629684755 5.873684034 0.994514084 0.694094185 0.903623112 0.047188606 0.04120415 2.000850984 0.006404565 0.012928137 2.35E-09 8.629684755 -0.300419899 TPVEPEVAIHR ddPTM_HeLa_Romidepsin_16h_R1 2 TPVEPEVAIHR 11 0 P60866;P60866-2;E5RIP1;E5RJX2 P60866 RPS20 40S ribosomal protein S20 0 0 ; ; 182.28 3.24E-06 24864000 8242.7 8387 7966.2 6884.1 8110.8 8780.3 7718.7 8653.4 9580.4 8850.1 FALSE FALSE TRUE 8142.234802 8505.072406 8104.848369 7680.072033 7696.87561 8219.267167 8374.326185 8903.772476 8723.505029 8620.173126 0.944555832 0.986647516 0.940218746 0.890941739 0.89289107 0.953492122 0.971480046 1.032899496 1.011987219 1 13.07350113 -12.24990893 0.699137451 1.004860555 0.948174389 0.222896747 0.039757742 1.308884671 0.993307669 0.044506876 0.008836389 5.62E-13 12.24990893 -0.056686167 TPVQYSQQQNS(ph)PQK ddPTM_HeLa_Romidepsin_16h_R1 1 TPVQYSQQQNSPQK 14 0 P46013 P46013 MKI67 Antigen KI-67 1 0 TPVQYSQQQNS(1)PQK 103.39 0.0011971 0 5505.5 5643.2 5884.6 3759.4 2827.6 2924.2 3094.8 3038.4 6173.4 5856.5 TRUE FALSE FALSE 5438.396848 5722.645118 5987.018995 4194.079517 2683.297021 2737.353057 3357.672235 3126.31131 5621.235642 5704.347286 0.953377587 1.0032077 1.049553734 0.735242668 0.470395102 0.479871389 0.588616377 0.548057675 0.985430122 1 12.4778461 -9.024604558 3.415154851 0.983953907 0.525441797 0.965882663 0.042180137 0.032819878 0.79666072 0.006969086 0.012529581 9.45E-10 9.024604558 -0.458512111 TPVS(ph)PVKFSPGDFWGR ddPTM_HeLa_Romidepsin_16h_R1 1 TPVSPVKFSPGDFWGR 16 1 P23443-3;P23443-5;P23443-2;P23443 P23443-3 RPS6KB1 Ribosomal protein S6 kinase beta-1 1 0 T(0.374)PVS(0.623)PVKFS(0.003)PGDFWGR 144.41 0.0020984 10693000 696.84 913.02 694.84 1022.1 881.87 842.64 672.53 904.39 617.74 841.29 TRUE FALSE FALSE 688.346646 925.8735195 706.9333987 1140.280011 836.8648832 788.7980235 729.6546814 930.5570978 562.4877872 819.4331645 0.840027809 1.129895103 0.86271026 1.391547304 1.021272899 0.962614229 0.890438309 1.135610734 0.686435223 1 9.678482473 -10.26007253 24.99478589 0.924457577 1.050417288 0.219810991 0.163957313 185.8660916 3398831.92 0.024680286 0.029359931 5.49E-11 10.26007253 0.12595971 TQASS(ph)SFQDSSQPAGK ddPTM_HeLa_Romidepsin_16h_R1 1 TQASSSFQDSSQPAGK 16 0 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 TQASS(0.5)S(0.5)FQDSSQPAGK 234.36 1.05E-45 4629400 2279.7 2292.5 2074.2 1807.1 2433.7 2808.4 2921.7 2946 2654.8 2372.7 TRUE FALSE FALSE 2251.91414 2324.773875 2110.300581 2016.045405 2309.499208 2628.952304 3169.869125 3031.237862 2417.348039 2311.056912 0.974408777 1.005935364 0.913132243 0.872347796 0.999325978 1.137554117 1.371610153 1.311624065 1.045992432 1 11.17433707 -7.990247905 2.563285 0.974948106 1.345090119 0.896315482 0.049971176 0.058294548 0.757489738 0.006948771 0.024885466 1.02E-08 7.990247905 0.370142013 TQASS(ph)SPAALKPPAGR ddPTM_HeLa_Romidepsin_16h_R1 1 TQASSSPAALKPPAGR 16 1 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 0 T(0.001)QAS(0.038)S(0.481)S(0.481)PAALKPPAGR 85.054 0.0067291 9798600 3751.4 3185.2 2765.9 1690.1 3896.9 3134.5 2883.2 3010.1 3918.9 3341.6 TRUE FALSE FALSE 3705.676494 3230.041329 2814.039329 1885.517314 3698.026652 2934.215566 3128.098936 3097.192494 3568.383769 3254.78475 1.13853197 0.992397832 0.864585386 0.579306301 1.136181633 0.90150833 0.961077053 0.951581359 1.096350156 1 11.66834642 -9.967937558 4.94693271 1.065615391 0.899216644 0.267571458 0.133033489 0.206199676 12.60829571 0.022145225 0.028927289 1.08E-10 9.967937558 -0.166398747 TQASSS(ph)FQDSSQPAGK ddPTM_HeLa_Romidepsin_16h_R1 1 TQASSSFQDSSQPAGK 16 0 P46087;P46087-4;P46087-2 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 1 0 TQASS(0.08)S(0.919)FQDSSQPAGK 210.2 9.31E-26 4300700 1207.9 1107.6 1007 1151.2 1049 1352.3 1443.6 1456.8 906.63 1142.9 TRUE FALSE FALSE 1193.17765 1123.192822 1024.526413 1284.307161 995.4656156 1265.892394 1566.219348 1498.95021 825.5387421 1113.207293 1.071837795 1.008970053 0.920337496 1.153699916 0.894232028 1.137157834 1.406943125 1.346514902 0.741585819 1 10.12050655 -7.890796846 4.033474589 1.024762238 1.37591235 0.646899648 0.114493752 0.062699164 1.856323038 0.009295447 0.030820855 1.29E-08 7.890796846 0.351150112 TQDPS(ph)SPGTTPPQAR ddPTM_HeLa_Romidepsin_16h_R1 1 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 TQDPS(0.929)S(0.067)PGT(0.003)TPPQAR 124.5 0.0029534 1903100 2353.6 2268 2033.9 1806.5 1778.2 1432.4 1191.3 1848.7 2299.4 2122.7 TRUE FALSE FALSE 2324.913418 2299.928964 2069.299176 2015.37603 1687.451819 1340.874263 1292.488992 1902.189218 2093.735905 2067.551948 1.124476423 1.112392347 1.000845071 0.974764398 0.816159333 0.648532321 0.625130118 0.920020036 1.012664232 1 11.01370786 -8.789434815 2.003439604 1.061043063 0.719868189 0.740426761 0.084434556 0.116897677 0.955571415 0.013322694 0.02906708 1.62E-09 8.789434815 -0.341174874 TQDPSS(ph)PGTTPPQAR ddPTM_HeLa_Romidepsin_16h_R1 1 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 TQDPS(0.282)S(0.469)PGT(0.245)T(0.004)PPQAR 144.4 0.00048177 112440000 5387 5410.7 5309.2 5235.3 4608.1 4675.3 3428.9 3520.4 5744.4 6266.4 TRUE FALSE FALSE 5321.341172 5486.871977 5401.604399 5840.630019 4372.931462 4376.563419 3720.15068 3622.25722 5230.606477 6103.598025 0.871836768 0.898956968 0.884986917 0.956915904 0.716451418 0.71704647 0.609501259 0.593462611 0.856970996 1 12.57544424 -6.539535347 0.310503477 0.968420822 2.45E-14 0.78968864 0.061821696 3.087398984 0.152523479 0.023171094 1.230553341 2.89E-07 6.539535347 -0.968420822 TQDPSSPGT(ph)TPPQAR ddPTM_HeLa_Romidepsin_16h_R1 2 TQDPSSPGTTPPQAR 15 0 Q13112 Q13112 CHAF1B Chromatin assembly factor 1 subunit B 1 0 TQDPSS(0.003)PGT(0.892)T(0.105)PPQAR;TQDPS(0.001)S(0.03)PGT(0.756)T(0.213)PPQAR ; 187.75 6.12E-12 129090200 6134.4 5098.8 5672 5221.5 4612.5 4257.4 3595.1 3986.8 6130 5934.4 TRUE FALSE FALSE 6059.631573 5170.58104 5770.718781 5825.234398 4377.106913 3985.36588 3900.467704 4102.151768 5581.717447 5780.223433 1.04833864 0.894529615 0.99835566 1.007787063 0.757255661 0.689483015 0.674795317 0.709687405 0.965657731 1 12.49690955 -8.696837348 3.526025445 1.010582748 0.693364792 0.909803522 0.042769948 0.045563793 1.138366969 0.00660601 0.013601479 2.01E-09 8.696837348 -0.317217956 TQEISRPNS(ph)PSEGEGESSDSR ddPTM_HeLa_Romidepsin_16h_R1 1 TQEISRPNSPSEGEGESSDSR 21 1 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 T(0.002)QEIS(0.018)RPNS(0.788)PS(0.121)EGEGES(0.034)S(0.034)DS(0.003)R 48.84 0.025098 3913700 695.11 876.98 730.23 710.71 692.65 916.31 859.07 703.82 932.43 878.38 TRUE FALSE FALSE 686.637732 889.3261475 742.9393468 792.8856342 657.3014859 857.7607483 932.0393844 724.1839213 849.0311255 855.559561 0.802559825 1.039467254 0.8683666 0.926745104 0.768270867 1.002572804 1.089391583 0.846444776 0.992369397 1 9.740724483 TQKPNPAVPPPLS(ph)SSPLYSR ddPTM_HeLa_Romidepsin_16h_R1 1 TQKPNPAVPPPLSSSPLYSR 20 1 H7C1T0;H0Y770;A0A2R8Y5T1;A0A2R8Y842;A0A2R8YEW8;A0A5F9UWT1;A0A2R8Y5K9;A0A2R8Y721;A0A2R8Y6V4;A0A2R8Y6H3;A0A2R8Y7U0;O75140-9;O75140-4;O75140-8;O75140-1;O75140-5;O75140-6;O75140 H7C1T0 DEPDC5 DEP domain-containing protein 5 1 0 TQKPNPAVPPPLS(0.479)S(0.479)S(0.04)PLYS(0.001)R 103.51 0.00021305 13295000 2141.6 2048.1 2284.6 1972.1 2058.4 1733.2 1351.2 1631.6 1800.8 1914.8 TRUE FALSE FALSE 2115.497355 2076.933206 2324.362505 2200.123481 1953.352167 1622.454114 1465.970894 1678.807772 1639.731938 1865.05322 1.134282568 1.11360533 1.246271409 1.179657212 1.047343929 0.869923762 0.786020945 0.900139339 0.879187747 1 10.86500108 -8.280271539 3.64095836 1.092131171 0.840254647 0.552093518 0.097199987 0.115883596 3.341755962 0.012699113 0.032139947 5.24E-09 8.280271539 -0.251876524 TQLEELEDELQATEDAK ddPTM_HeLa_Romidepsin_16h_R1 2 TQLEELEDELQATEDAK 17 0 P35579;P35749-4;P35749-3;P35749;P35749-2;P35579-2;P35580;P35580-5;P35580-2;P35580-3;P35580-4 P35579;P35749-4;P35579-2;P35580 MYH9;MYH11;MYH10 Myosin-9;Myosin-11;Myosin-10 0 0 ; ; 177.39 8.27E-08 21182100 2361.66 2008.31 2803 1629.97 2472.49 2410.61 2309.05 2472.92 2932.43 2495.86 FALSE FALSE TRUE 2332.87518 2036.583041 2851.785039 1818.434801 2346.309609 2256.579801 2505.180649 2544.470039 2670.146116 2431.017197 0.959629238 0.837749335 1.173083038 0.74801396 0.965155496 0.9282451 1.030507169 1.046668876 1.098365787 1 11.24734438 -7.652405984 6.45841246 0.963534226 1.04216392 0.066373795 0.112698141 0.387732969 20.33059202 0.013089086 0.050098468 2.23E-08 7.652405984 0.078629695 TQLWASEPGT(ph)PPLPTSLPSQNPILK ddPTM_HeLa_Romidepsin_16h_R1 2 TQLWASEPGTPPLPTSLPSQNPILK 25 0 Q9BXP5-5;Q9BXP5-4;Q9BXP5-2;Q9BXP5-3;Q9BXP5;H7C3A1 Q9BXP5-5 SRRT Serrate RNA effector molecule homolog 1 0 T(0.001)QLWAS(0.041)EPGT(0.959)PPLPTSLPSQNPILK;T(0.003)QLWAS(0.034)EPGT(0.963)PPLPTSLPSQNPILK ; 119.35 8.44E-07 445830000 7452 7071.2 7117.6 7099.3 7500.4 7379.3 6828.5 7583 7610.5 7763.7 TRUE FALSE FALSE 7361.172158 7170.748539 7241.478842 7920.154469 7117.6266 6907.786546 7408.51262 7802.402141 6929.797819 7561.997955 0.97344276 0.948261105 0.957614494 1.047362683 0.94123625 0.913486963 0.979703071 1.031791094 0.916397738 1 12.88455174 -11.96202251 0.896868434 0.999201608 0.972562289 0 0.045991557 1.322186646 2.021215837 0.021209253 0.007542423 1.09E-12 11.96202251 -0.026639318 TQMAEVLPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TQMAEVLPSPR 11 0 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 TQMAEVLPS(1)PR;TQMAEVLPS(1)PR ; 100.73 0.02596 106644000 10603.5 9355.9 9791 8702 10938.4 11895 9288.1 9737.3 11242.8 9463.1 TRUE FALSE FALSE 10474.26046 9487.612606 9961.408248 9708.166184 10380.17263 11134.94789 10077.03098 10019.03341 10237.21581 9217.247298 1.136376201 1.029332544 1.080735704 1.0532609 1.126168399 1.208055673 1.093279876 1.086987588 1.11065869 1 13.17012024 -12.45909849 0.947034795 0.993429967 1.1045859 0 0.057463747 0.553124911 0.797875893 0.045851924 0.008949598 3.47E-13 12.45909849 0.111155933 TQPDGTSVPGEPAS(ph)PISQR ddPTM_HeLa_Romidepsin_16h_R1 2 TQPDGTSVPGEPASPISQR 19 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 TQPDGTSVPGEPAS(0.997)PIS(0.003)QR;TQPDGTSVPGEPAS(0.996)PIS(0.004)QR ; 234.62 1.77E-49 705639700 3857.94 3695.93 3429.48 3344.28 3390.8 3428.24 2782.36 3071.03 3976.3 3581.97 TRUE FALSE FALSE 3810.917943 3747.9614 3489.168661 3730.961389 3217.754823 3209.186528 3018.693589 3159.885408 3620.649769 3488.909903 1.092294742 1.074249982 1.000074166 1.069377397 0.922280859 0.919824993 0.865225435 0.905694184 1.037759607 1 11.76856063 -8.681415695 4.779092155 1.045135587 0.898158505 0.83561886 0.031014028 0.078886632 3.252620613 0.005940338 0.012030473 2.08E-09 8.681415695 -0.146977082 TQPSSGVDSAVGTLPAT(ph)SPQSTSVQAK ddPTM_HeLa_Romidepsin_16h_R1 2 TQPSSGVDSAVGTLPATSPQSTSVQAK 27 0 Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 Q13428 TCOF1 Treacle protein 1 0 TQPSSGVDSAVGTLPAT(0.47)S(0.47)PQS(0.022)T(0.032)S(0.006)VQAK;TQPSSGVDSAVGTLPAT(0.476)S(0.476)PQS(0.022)T(0.02)S(0.006)VQAK ; 148.87 5.44E-11 58242000 10787.3 10537.1 9246 11027.4 10618.7 10295 9033.1 9309.1 11060.8 11787 TRUE FALSE FALSE 10655.82024 10685.44157 9406.922751 12302.43987 10076.78812 9637.182726 9800.371289 9578.444121 10071.49435 11480.77204 0.928144919 0.930725001 0.819363255 1.07156904 0.877709973 0.839419395 0.853633471 0.834303136 0.877248874 1 13.48693204 -4 0.104858347 1.048253619 0.412877587 0.108207861 0.072365386 87.44678907 0.648428382 0.428666392 8.048045241 1.00E-04 4 -0.635376033 TQQLHPVLQKPS(ph)VFGNDSDDDDETSVSESLQR ddPTM_HeLa_Romidepsin_16h_R1 1 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 0 T(0.002)QQLHPVLQKPS(0.496)VFGNDS(0.496)DDDDET(0.004)S(0.002)VSESLQR 53.522 0.0020677 51352000 1422.9 1406.4 1203.6 654.19 1136 975.6 1133.1 1124.3 1598.3 1932.5 TRUE FALSE FALSE 1405.557147 1426.199336 1224.548153 729.8305259 1078.025681 913.2623086 1229.345486 1156.829847 1455.344045 1882.293371 0.746725866 0.757692376 0.650561794 0.387734737 0.572719268 0.485185956 0.653110458 0.614585305 0.773175992 1 10.87827579 -10.85147847 0.500455982 0.989850961 0.541388479 0.573953126 0.105209319 0.280804873 0.171730313 0.048598366 0.034011 1.41E-11 10.85147847 -0.448462482 TQQLHPVLQKPSVFGNDS(ph)DDDDETSVSESLQR ddPTM_HeLa_Romidepsin_16h_R1 1 TQQLHPVLQKPSVFGNDSDDDDETSVSESLQR 32 1 Q9H0G5 Q9H0G5 NSRP1 Nuclear speckle splicing regulatory protein 1 1 0 TQQLHPVLQKPS(0.22)VFGNDS(0.742)DDDDET(0.027)S(0.011)VS(0.001)ESLQR 68.412 1.16E-05 33468000 1078.5 1199.2 1084.7 523.53 1144.7 946.5 614.7 743.9 975.62 1076.4 TRUE FALSE FALSE 1065.354827 1216.082369 1103.578748 584.0630019 1086.281688 886.0217047 666.9126027 765.4235728 888.3581037 1048.434973 1.016138201 1.159902522 1.052596276 0.557080808 1.036098295 0.845089803 0.636102972 0.730062992 0.847318267 1 10.03402167 -9.295756823 24.82689905 1.024724714 0.773921939 0.453901945 0.13890538 357.2533918 258453.4025 0.0191146 0.029198876 5.06E-10 9.295756823 -0.250802775 TQRLS(ph)AETWDLLR ddPTM_HeLa_Romidepsin_16h_R1 2 TQRLSAETWDLLR 13 1 A0A0A0MSK4;A0A0A0MRC4;Q86YR5-4;Q86YR5 A0A0A0MSK4 GPSM1 G-protein-signaling modulator 1 1 0 T(0.102)QRLS(0.894)AET(0.004)WDLLR;T(0.457)QRLS(0.542)AET(0.001)WDLLR ; 86.411 0.010382 4242600 1660.32 1783.83 1815.31 2025.9 2161.4 2081.23 1968.1 1716.72 1589.35 1984.38 TRUE FALSE FALSE 1640.083381 1808.942806 1846.904709 2260.14409 2051.095693 1948.24612 2135.270365 1766.390585 1447.194555 1932.825522 0.848541869 0.935905898 0.955546524 1.169347189 1.061190299 1.007978267 1.104740361 0.913890346 0.748745574 1 10.91649569 -9.499293335 23.3129721 0.927926743 1.053512131 0.40443348 0.090185749 267.9511659 264855.9274 0.012218516 0.018579447 3.17E-10 9.499293335 0.125585387 TQRSLSAELEIPAVKESDAGK ddPTM_HeLa_Romidepsin_16h_R1 1 TQRSLSAELEIPAVKESDAGK 21 2 Q96LA5 Q96LA5 FCRL2 Fc receptor-like protein 2 0 0 45.257 0.02926 13577000 2894.3 3297.2 2171.9 4511.1 3098.4 2990.8 3033 3019.8 3044.4 2943.5 FALSE FALSE TRUE 2859.023158 3343.618068 2209.701008 5032.694607 2940.277086 2799.697532 3290.622944 3107.173149 2772.101239 2867.027446 0.997208158 1.166231622 0.770728935 1.755370223 1.025548985 0.976515777 1.147747277 1.083761215 0.966890374 1 11.48534 TQS(ph)PEFEAQSSK ddPTM_HeLa_Romidepsin_16h_R1 2 TQSPEFEAQSSK 12 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 T(0.37)QS(0.625)PEFEAQS(0.005)SK;T(0.277)QS(0.463)PEFEAQS(0.064)S(0.197)K ; 188.92 6.01E-10 46161000 5774.5 6937 7165.1 4464.3 5813.6 8224.5 8426.2 9360 7091.1 6580.8 TRUE FALSE FALSE 5704.118173 7034.659268 7289.80556 4980.483371 5516.910298 7698.980993 9141.921218 9630.816832 6456.854256 6409.829867 0.88990165 1.097479873 1.137285343 0.777007108 0.860695278 1.201120958 1.426234613 1.502507404 1.007336293 1 12.64607035 -7.935520316 2.707162651 0.955277578 1.476570075 0.784996436 0.104032265 0.089967254 1.311188961 0.015500076 0.057316796 1.16E-08 7.935520316 0.521292496 TQSRPGGPPNPPGPS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 3 TQSRPGGPPNPPGPSPK 17 1 B9EGQ5;A0A669KBG4;M0QXA7;A0A669KBH9;A0A2R8YFV2;A0A669KAV7;O95785-4;O95785-3;O95785;O95785-2 B9EGQ5 WIZ Protein Wiz 1 0 TQSRPGGPPNPPGPS(1)PK;T(0.002)QS(0.002)RPGGPPNPPGPS(0.995)PK;TQSRPGGPPNPPGPS(1)PK ;; 67.56 0.013031 29891800 7471.6 7621 7512.28 7287.3 6364.5 6290.1 5174.34 5929.19 8457.9 7884.5 TRUE FALSE FALSE 7380.533265 7728.288638 7643.028082 8129.891914 6039.695816 5888.18291 5613.84831 6100.741758 7701.404241 7679.659553 0.961049538 1.006332193 0.995230066 1.058626604 0.786453589 0.766724471 0.731002237 0.794402631 1.002831465 1 12.90682664 -8.703046958 7.230307055 0.989103248 0.764936553 0.938005953 0.029371014 0.041431634 4.225426705 0.004467556 0.008939524 1.98E-09 8.703046958 -0.224166695 TQSS(ph)PAAPGGMK ddPTM_HeLa_Romidepsin_16h_R1 2 TQSSPAAPGGMK 12 0 Q9UQL6-2;Q9UQL6;Q9UQL6-3 Q9UQL6-2 HDAC5 Histone deacetylase 5 1 0 T(0.002)QS(0.334)S(0.664)PAAPGGMK;T(0.013)QS(0.195)S(0.792)PAAPGGMK ; 95.273 0.029451 4499900 4194.1 3709.2 3794.8 4416.1 8548.4 6899.4 5650.7 6540.9 3458.8 3812.33 TRUE FALSE FALSE 4142.980696 3761.418215 3860.846902 4926.71026 8112.14325 6458.550607 6130.670317 6730.150622 3149.436265 3713.285117 1.115718445 1.012962403 1.039738878 1.326779416 2.184627087 1.739309103 1.651009853 1.812451888 0.848153634 1 11.85848038 -8.958010475 5.449770658 1.055761966 1.823955262 0.875897733 0.148917242 0.044853176 3.229492507 0.020012102 0.036398937 1.10E-09 8.958010475 0.768193296 TQSSLT(ph)VSEVLTR ddPTM_HeLa_Romidepsin_16h_R1 1 TQSSLTVSEVLTR 13 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 T(0.258)QS(0.166)S(0.166)LT(0.404)VS(0.005)EVLTR 174.21 6.75E-05 82662000 1926 2029.9 1729.2 1654.7 2629.2 2621.5 2113.9 2647.1 1897.4 1787.3 TRUE FALSE FALSE 1902.525171 2058.476985 1759.296001 1846.0242 2495.022113 2453.994611 2293.454613 2723.689662 1727.691792 1740.865688 1.092861548 1.182444458 1.010586866 1.060405873 1.433207702 1.409640403 1.317421917 1.564560483 0.99243256 1 10.76558918 -8.763117718 24.54977208 1.054684366 1.421539617 0.852614568 0.076286522 9.55981795 139840.1469 0.011092426 0.020897571 1.73E-09 8.763117718 0.366855251 TQT(ph)PPLGQTPQLGLK ddPTM_HeLa_Romidepsin_16h_R1 1 TQTPPLGQTPQLGLK 15 0 H0Y3P2;D3DQV9;P78344-2;P78344;E9PKF8 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 1 0 T(0.222)QT(0.777)PPLGQT(0.001)PQLGLK 116.87 0.007786 334040000 3885.7 3784.9 3431.2 2801.9 3318.3 3242.3 2423.6 2979.3 3486.6 2916.4 TRUE FALSE FALSE 3838.339594 3838.183922 3490.918597 3125.868861 3148.954769 3035.127494 2629.460524 3065.501345 3174.749764 2840.631508 1.351227565 1.351172763 1.228923423 1.10041336 1.108540393 1.068469277 0.92566055 1.079161918 1.117621119 1 11.47199598 -8.541994834 1.491625534 1.188790672 1.008385369 0.348412689 0.106497182 0.518199296 2.257206508 0.023428889 0.068291733 2.87E-09 8.541994834 -0.180405303 TQT(ph)PPVSPAPQPT(ph)EER ddPTM_HeLa_Romidepsin_16h_R1 1 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 T(0.001)QT(0.999)PPVS(0.003)PAPQPT(0.997)EER 139.39 0.01683 26364000 2322.6 2446.4 2695.4 1413.7 2661.1 2908 2678.1 3065.4 2480.7 2151.2 TRUE FALSE FALSE 2294.291258 2480.840483 2742.312306 1577.158646 2525.294137 2722.188185 2905.577747 3154.092513 2258.819979 2095.311514 1.094964277 1.183996015 1.308785013 0.752708433 1.205211788 1.299180655 1.386704425 1.505309588 1.078035397 1 11.03294903 -8.120249463 1.834049214 1.060594686 1.454416644 0.530802805 0.13913319 0.202973865 1.288007397 0.020181523 0.076502546 7.58E-09 8.120249463 0.393821958 TQT(ph)PPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 1 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 T(0.405)QT(0.592)PPVS(0.253)PAPQPT(0.739)EERLPS(0.005)S(0.002)PVY(0.004)EDAASFK 70.054 8.92E-06 0 1136.7 869.41 940.89 1053.7 1115.2 808.28 948.58 1143.5 1115.1 1140.4 TRUE FALSE FALSE 1122.845463 881.6495768 957.2657958 1175.533752 1058.287183 756.6335166 1029.152362 1176.585368 1015.362663 1110.772244 1.010869213 0.79372669 0.861802049 1.058303139 0.952749034 0.681177911 0.926519696 1.059249882 0.914105181 1 10.11734732 -10.3758092 24.59657732 1.005133897 0.903050899 0.058321296 0.110792014 24.85359351 5302.463225 0.018297371 0.020923787 4.21E-11 10.3758092 -0.102082997 TQT(ph)PPVSPAPQPTEER ddPTM_HeLa_Romidepsin_16h_R1 4 TQTPPVSPAPQPTEER 16 0 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 TQT(0.547)PPVS(0.452)PAPQPTEER;T(0.008)QT(0.991)PPVS(0.002)PAPQPTEER;T(0.427)QT(0.568)PPVS(0.004)PAPQPT(0.001)EER;T(0.015)QT(0.982)PPVS(0.002)PAPQPT(0.001)EER ;;; 135.09 0.0029344 483619000 5571.2 5206.3 6079.4 3813.18 5703.9 5633.1 5242.72 4986.04 6071 6558.4 TRUE FALSE FALSE 5503.296072 5279.594428 6185.209407 4254.077813 5412.808699 5273.16309 5688.036506 5130.303201 5527.994555 6388.011823 0.861503739 0.826484762 0.968252655 0.665947079 0.847338554 0.825477979 0.890423603 0.803114231 0.86537012 1 12.64115127 -11.93418083 0.445599118 1.029801571 0.824316407 0.110129707 0.081929016 1.070613184 0.342028026 0.098934125 0.021923845 1.16E-12 11.93418083 -0.205485164 TQTESS(ph)TPPGIPGGSR ddPTM_HeLa_Romidepsin_16h_R1 2 TQTESSTPPGIPGGSR 16 0 E9PER6;Q6A1A2;O15530-4;O15530-5;O15530;H3BQ10;O15530-3 E9PER6 PDPK1;PDPK2P Putative 3-phosphoinositide-dependent protein kinase 2;3-phosphoinositide-dependent protein kinase 1 1 0 TQT(0.006)ES(0.003)S(0.495)T(0.495)PPGIPGGSR;TQTES(0.004)S(0.498)T(0.498)PPGIPGGSR ; 238.64 4.79E-46 32005000 4268.1 3854.2 3396.8 4025.7 6780.8 10677.8 9173 9810.2 3995.1 3906.5 TRUE FALSE FALSE 4216.078756 3908.459529 3455.919879 4491.170375 6434.750473 9995.523041 9952.154391 10094.04266 3637.76825 3805.008567 1.108033972 1.027188102 0.908255479 1.180331213 1.691126409 2.62693838 2.6155406 2.652830469 0.956047322 1 11.89368399 -8.46281408 2.0820027 1.041002848 2.666096247 0.989918895 0.072379682 0.022204684 0.188380468 0.011296981 0.029759451 3.44E-09 8.46281408 1.6250934 up TQTGDSS(ph)SISSFSYR ddPTM_HeLa_Romidepsin_16h_R1 2 TQTGDSSSISSFSYR 15 0 Q4V328-4;Q4V328;A0A087WXA6;A0A087WT45;Q4V328-2;Q4V328-3 Q4V328-4 GRIPAP1 GRIP1-associated protein 1 1 0 TQTGDS(0.201)S(0.376)S(0.376)IS(0.046)S(0.001)FSYR;TQTGDS(0.014)S(0.464)S(0.464)IS(0.048)S(0.011)FSYR ; 223.68 1.27E-34 65344000 3698.8 4189.1 3470.1 2915.3 4059.7 3583.2 3441.8 4037.4 4082 3471.6 TRUE FALSE FALSE 3653.717603 4248.07426 3530.495635 3252.380703 3852.51836 3354.245084 3734.146406 4154.215799 3716.895696 3381.407332 1.080531638 1.256303617 1.044090607 0.961842329 1.139323951 0.991967177 1.104317238 1.228546399 1.099215602 1 11.7234081 -11.69931451 1.002795626 1.007629241 1.095086669 0.003539552 0.09251977 0.71920435 1.451185873 0.034842435 0.017290747 2.00E-12 11.69931451 0.087457428 TQTPPVS(ph)PAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 T(0.007)QT(0.019)PPVS(0.627)PAPQPT(0.543)EERLPS(0.335)S(0.334)PVY(0.132)EDAAS(0.003)FK;T(0.131)QT(0.309)PPVS(0.38)PAPQPT(0.503)EERLPS(0.297)S(0.319)PVY(0.059)EDAAS(0.001)FK ; 55.691 0.0020004 72489000 7794.3 7258.1 6841.2 7110 9008.9 8511.7 7261.4 8378 7581.1 7580.1 TRUE FALSE FALSE 7699.300074 7360.279722 6960.268216 7932.091654 8549.142216 7967.82984 7878.183135 8620.404212 6903.027429 7383.167909 1.042817957 0.99689995 0.942721106 1.074347997 1.157923309 1.079188492 1.067046454 1.167575263 0.93496823 1 12.85002425 -9.008502199 24.6905354 1.013120768 1.112106684 0.638527179 0.045465462 182.4259113 529770.876 0.005805628 0.010164915 9.81E-10 9.008502199 0.098985916 TQTPPVSPAPQPT(ph)EERLPS(ph)SPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 2 0 T(0.023)QT(0.093)PPVS(0.19)PAPQPT(0.527)EERLPS(0.472)S(0.471)PVY(0.224)EDAAS(0.001)FK;T(0.032)QT(0.199)PPVS(0.425)PAPQPT(0.565)EERLPS(0.359)S(0.358)PVY(0.058)EDAAS(0.005)FK ; 56.021 0.0019409 29518900 3792.5 3800.8 4043.2 4047.8 4509.8 4683.9 3723.2 4668.9 4112.5 3707 TRUE FALSE FALSE 3746.275551 3854.307762 4113.5702 4515.825681 4279.648078 4384.613907 4039.448515 4803.987255 3744.6677 3610.691606 1.037550686 1.067470774 1.139274867 1.250681635 1.185271008 1.214341845 1.118746477 1.330489496 1.037105383 1 11.81805949 -9.745283119 1.632810245 1.016661013 1.213334929 0.738952645 0.051720541 0.120077616 0.65132134 0.008233895 0.012088014 1.80E-10 9.745283119 0.196673916 TQTPPVSPAPQPT(ph)EERLPSSPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 5 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 T(0.066)QT(0.077)PPVS(0.065)PAPQPT(0.791)EERLPS(0.001)SPVYEDAASFK;TQTPPVS(0.001)PAPQPT(0.326)EERLPS(0.326)S(0.326)PVY(0.02)EDAASFK;TQTPPVS(0.021)PAPQPT(0.346)EERLPS(0.204)S(0.204)PVY(0.223)EDAAS(0.002)FK;T(0.09)QT(0.094)PPVS(0.259)PAPQPT(0.547)EERLPS(0.003)S(0.004)PVY(0.002)EDAASFK;T(0.017)QT(0.047)PPVS(0.214)PAPQPT(0.659)EERLPS(0.023)S(0.028)PVY(0.012)EDAAS(0.001)FK ;;;; 101.73 3.40E-09 162265000 16974.2 14858.2 14277.1 17421 15974.3 13698.49 12891.25 12281.47 16711.5 15033.6 TRUE FALSE FALSE 16767.31192 15067.37413 14525.58694 19435.29799 15159.07186 12823.2007 13986.23245 12636.81496 15216.78159 14643.0249 1.145071598 1.028979615 0.991979938 1.327273437 1.035241828 0.875720746 0.955146395 0.86299211 1.039182934 1 13.83792599 -8.363127552 5.142755327 1.080133677 0.904497591 0.444476531 0.094637105 0.174185577 7.043473238 0.014230669 0.032517936 4.33E-09 8.363127552 -0.175636086 TQTPPVSPAPQPTEERLPS(ph)SPVYEDAASFK ddPTM_HeLa_Romidepsin_16h_R1 5 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 TQTPPVS(0.006)PAPQPT(0.033)EERLPS(0.422)S(0.422)PVY(0.116)EDAASFK;TQTPPVSPAPQPT(0.001)EERLPS(0.479)S(0.479)PVY(0.041)EDAASFK;TQTPPVS(0.001)PAPQPT(0.015)EERLPS(0.468)S(0.468)PVY(0.048)EDAAS(0.001)FK;TQTPPVS(0.001)PAPQPT(0.087)EERLPS(0.393)S(0.393)PVY(0.126)EDAAS(0.001)FK;TQTPPVS(0.001)PAPQPT(0.051)EERLPS(0.452)S(0.452)PVY(0.045)EDAASFK ;;;; 104.72 1.61E-09 1225790000 15459 16025.6 13955.6 18595.8 21019.5 21407.8 19790.8 22462.9 16844.1 15291.5 TRUE FALSE FALSE 15270.57976 16251.20882 14198.49136 20745.93389 19946.79648 20039.91067 21471.83006 23112.82857 15337.52151 14894.22463 1.025268528 1.091108079 0.953288387 1.392884451 1.339230271 1.345481969 1.441621205 1.551798039 1.029763005 1 13.8624654 -9.254345995 24.35160429 1.015434794 1.407743435 0.904899859 0.06389024 83.77231268 287590.1546 0.00971727 0.015884439 5.57E-10 9.254345995 0.392308641 TQTPPVSPAPQPTEERLPSSPVY(ph)EDAASFK ddPTM_HeLa_Romidepsin_16h_R1 2 TQTPPVSPAPQPTEERLPSSPVYEDAASFK 30 1 Q14247;Q14247-3;Q14247-2;H0YEV2;H0YCD9 Q14247 CTTN Src substrate cortactin 1 0 TQTPPVSPAPQPT(0.002)EERLPS(0.251)S(0.251)PVY(0.438)EDAAS(0.057)FK;TQTPPVSPAPQPTEERLPS(0.071)S(0.071)PVY(0.858)EDAASFK ; 89.186 1.42E-07 10628200 5113.6 4537.7 4616.1 6564.3 3684.8 2990 2711.76 2214.98 5911 4685.4 TRUE FALSE FALSE 5051.273476 4601.58186 4696.441284 7323.295252 3496.750906 2798.94865 2942.096827 2279.066952 5382.305356 4563.672633 1.106843957 1.008306737 1.029092501 1.604693378 0.766214229 0.613310567 0.644677448 0.499393172 1.179380247 1 12.15597959 -8.535060361 24.99994896 1.085155538 0.608028723 0.678785417 0.175710338 104.8504365 215180.7782 0.024760358 0.04954727 2.92E-09 8.535060361 -0.477126814 TQTPQLHFLDT(ph)DDEVSPTSWGDSR ddPTM_HeLa_Romidepsin_16h_R1 1 TQTPQLHFLDTDDEVSPTSWGDSR 24 0 Q86US8 Q86US8 SMG6 Telomerase-binding protein EST1A 1 0 TQTPQLHFLDT(0.618)DDEVS(0.13)PT(0.049)S(0.049)WGDS(0.153)R 50.58 0.029315 2243800 606.85 682.24 715.51 823.67 871.23 1043.7 840.72 903.51 915 700.59 TRUE FALSE FALSE 599.4534788 691.8445926 727.9631514 918.9066009 826.7678821 977.0109384 912.1307358 929.6516363 833.1601083 682.3885708 0.878463539 1.013857239 1.066786846 1.346603153 1.211579322 1.431751615 1.336673524 1.362349365 1.220946751 1 9.414449673 -9.405991353 1.679589822 0.943144733 1.348264866 0.634306842 0.107307014 0.083427872 0.463667361 0.01109191 0.018792912 3.93E-10 9.405991353 0.405120133 TQVAGGQLSFK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 2 TQVAGGQLSFKGK 13 1 P46060;B0QYT5;B0QYT4;B0QYT6 P46060 RANGAP1 Ran GTPase-activating protein 1 0 1 ; TQVAGGQLSFK(1)GK;TQVAGGQLSFK(1)GK 184.21 1.24E-06 1479460 869.07 865.17 813.61 759.32 804.19 698.76 1089.96 663.96 1013.23 728.86 FALSE TRUE FALSE 858.4774406 877.349886 827.7705408 847.1161511 763.1491835 654.1114911 1182.541175 683.170635 922.6041711 709.9241121 1.209252406 1.235836156 1.165998628 1.193248879 1.074972903 0.921382272 1.665728991 0.962315018 1.299581399 1 9.471521005 -12.2425757 0.879886988 0.994971524 1.185692641 0 0.212453931 1.072501526 1.431664029 0.136229684 0.033952152 5.72E-13 12.2425757 0.190721117 TQVLS(ph)PDSLFTAK ddPTM_HeLa_Romidepsin_16h_R1 1 TQVLSPDSLFTAK 13 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-1;H0Y948;H0Y8L4 A8MQ02 MLLT4 Afadin 1 0 T(0.011)QVLS(0.538)PDS(0.447)LFT(0.004)AK 181.75 4.72E-07 7573000 2249.4 1980.3 2142 2400.8 4031.7 4984.1 4246 4284.5 2318.1 2405.7 TRUE FALSE FALSE 2221.983448 2008.178715 2179.280611 2678.391792 3825.947305 4665.632095 4606.655134 4408.465248 2110.76333 2343.199567 0.948268973 0.857024192 0.930044816 1.143048945 1.632787646 1.991137315 1.965967901 1.881387019 0.900803909 1 11.19426412 -8.692377084 2.154124581 0.961278254 1.949453567 0.985983748 0.054181738 0.02544258 0.239823284 0.008617027 0.019438939 2.03E-09 8.692377084 0.988175313 TRDDGDEEGLLT(ph)HS(ph)EEELEHSQDTDADDGALQ ddPTM_HeLa_Romidepsin_16h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9-2;Q9UKM9 Q9UKM9-2 RALY RNA-binding protein Raly 2 0 TRDDGDEEGLLT(0.657)HS(0.657)EEELEHS(0.343)QDT(0.343)DADDGALQ 42.057 0.026377 75942000 972.39 982.09 996.16 1119 1109.6 1526.3 1181.8 1201.1 1240 1191.8 TRUE FALSE FALSE 960.5381367 995.9158888 1013.497747 1248.384045 1052.972972 1428.774356 1282.182063 1235.851933 1129.091294 1160.836864 0.827453164 0.85792924 0.873075088 1.075417299 0.907080921 1.230814079 1.104532516 1.064621543 0.972652859 1 10.18094952 -8.276942064 24.77719245 0.920020883 1.130443691 0.575252636 0.079491197 404.509189 646506.699 0.013110764 0.029411612 5.29E-09 8.276942064 0.210422808 TRDDGDEEGLLTHS(ph)EEELEHSQDT(ph)DADDGALQ ddPTM_HeLa_Romidepsin_16h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9-2;Q9UKM9 Q9UKM9-2 RALY RNA-binding protein Raly 2 0 TRDDGDEEGLLT(0.108)HS(0.815)EEELEHS(0.351)QDT(0.725)DADDGALQ 52.402 0.0048486 24152000 1499.7 1152.5 1102.8 1175.3 1221.8 1265.4 1155.4 773.02 1132 1046.7 TRUE FALSE FALSE 1481.42108 1168.724925 1121.993771 1311.193716 1159.446987 1184.545024 1253.539647 795.3861141 1030.751085 1019.506583 1.453076522 1.146363294 1.100526264 1.286106179 1.137262874 1.161880701 1.229555226 0.780167708 1.011029357 1 9.993655376 -7.259169273 24.17906808 1.202876677 0.78016747 0.429630148 0.129560186 109.9005284 1170428.276 0.022847828 0.20276854 5.51E-08 7.259169273 -0.422709207 TRDDGDEEGLLTHS(ph)EEELEHSQDTDADDGALQ ddPTM_HeLa_Romidepsin_16h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9-2;Q9UKM9 Q9UKM9-2 RALY RNA-binding protein Raly 1 0 TRDDGDEEGLLT(0.026)HS(0.371)EEELEHS(0.301)QDT(0.301)DADDGALQ 44.264 0.0096507 6574500 694.52 630.81 723.98 597.66 1057.6 825.71 702.38 675.68 803.78 761.99 TRUE FALSE FALSE 686.0549231 639.6905597 736.5805682 666.7642613 1003.626726 772.9497959 762.0401397 695.2297348 731.8879037 742.19339 0.924361403 0.86189202 0.992437521 0.898369981 1.352244225 1.041439881 1.026740672 0.936723156 0.986114823 1 9.535651342 TRDDGDEEGLLTHSEEELEHS(ph)QDTDADDGALQ ddPTM_HeLa_Romidepsin_16h_R1 1 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9-2;Q9UKM9 Q9UKM9-2 RALY RNA-binding protein Raly 1 0 TRDDGDEEGLLTHS(0.001)EEELEHS(0.5)QDT(0.5)DADDGALQ 81.534 1.59E-08 16092000 684.53 729.49 575.62 838.04 931.97 1009.6 966.35 755.49 688.74 673.88 TRUE FALSE FALSE 676.1866851 739.7597794 585.6384246 934.9381279 884.4080932 945.0898183 1048.431745 777.3489112 627.1373694 656.3725005 1.030187408 1.127042615 0.892234858 1.424401734 1.347417956 1.43986809 1.597312112 1.184310602 0.955459543 1 9.358370986 -9.251428616 24.7523188 1.0165511 1.40914056 0.762205004 0.110814621 201.614208 498505.1626 0.014968086 0.024627057 5.60E-10 9.251428616 0.392589461 TRDDGDEEGLLTHSEEELEHSQDT(ph)DADDGALQ ddPTM_HeLa_Romidepsin_16h_R1 2 TRDDGDEEGLLTHSEEELEHSQDTDADDGALQ 32 1 Q9UKM9-2;Q9UKM9 Q9UKM9-2 RALY RNA-binding protein Raly 1 0 TRDDGDEEGLLT(0.019)HS(0.267)EEELEHS(0.267)QDT(0.447)DADDGALQ;TRDDGDEEGLLT(0.03)HS(0.301)EEELEHS(0.301)QDT(0.368)DADDGALQ ; 46.847 0.0060043 258125000 2364.8 2673.6 2267.1 2382 2926.3 2730.1 2532.7 3261.8 2605.8 2746.8 TRUE FALSE FALSE 2335.976908 2711.239011 2306.557924 2657.418048 2776.959991 2555.655421 2747.827475 3356.175037 2372.730722 2675.43774 0.873119517 1.013381463 0.862123566 0.993264769 1.037946034 0.955228889 1.027057155 1.254439596 0.886857013 1 11.38555924 -4.000000067 0.857934675 0.945145432 115.8625966 0.715450199 0.057481479 295.9688036 0.749293664 0.009715396 66451.58112 1.00E-04 4.000000067 114.9174511 TRDELEVIHLIEEHR ddPTM_HeLa_Romidepsin_16h_R1 1 TRDELEVIHLIEEHR 15 1 P10155-3;P10155-5;P10155-4;P10155 P10155-3 TROVE2 60 kDa SS-A/Ro ribonucleoprotein 0 0 106.76 0.0010588 8370100 2377.7 2098.4 1955.6 2134.2 2232.1 1985.5 2003.9 2275.4 2292.1 1908.2 FALSE FALSE TRUE 2348.719678 2127.94133 1989.636398 2380.966246 2118.187608 1858.632958 2174.111216 2341.235109 2087.088835 1858.624689 1.263686903 1.144901035 1.070488523 1.281036597 1.139653218 1.000004449 1.169741922 1.259659964 1.122921076 1 10.86001976 -12.55149384 1.324652212 1.000139987 1.172836463 0.122113504 0.091067067 0.400154978 1.259611389 0.061570145 0.014617964 2.81E-13 12.55149384 0.172696477 TREEEEDSTIEASDQVS(ph)DDTVEMPLPK ddPTM_HeLa_Romidepsin_16h_R1 1 TREEEEDSTIEASDQVSDDTVEMPLPK 27 1 P12270 P12270 TPR Nucleoprotein TPR 1 0 TREEEEDSTIEAS(0.023)DQVS(0.722)DDT(0.254)VEMPLPK 53.496 0.0032556 0 623.55 708.37 636.2 691.76 743.6 891.26 546.15 777.16 711.92 680.17 TRUE FALSE FALSE 615.9499328 718.3424515 647.2727941 771.744546 705.6513172 834.3113624 592.5399674 799.6458984 648.2440922 662.4990853 0.929737031 1.08429199 0.977016887 1.164899036 1.065135534 1.259339644 0.894401186 1.207014343 0.978482999 1 9.371774653 -9.670340834 1.435351439 0.969180203 1.108535136 0.24969094 0.100395586 0.361288855 1.504382293 0.016167711 0.02492745 2.14E-10 9.670340834 0.139354933 TREEIQEVR ddPTM_HeLa_Romidepsin_16h_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 0 ; ; 148.91 0.0061915 14684600 5388.6 5044.1 5482.4 5881 5665.1 6922.8 5055.2 5330 5138.9 5182.3 FALSE FALSE TRUE 5322.921671 5115.110972 5577.818872 6560.988891 5375.988808 6480.455422 5484.588562 5484.215141 4679.263913 5047.663099 1.054531883 1.013362198 1.105029944 1.29980721 1.065045092 1.283852606 1.086559949 1.08648597 0.927015893 1 12.30139991 -9.58123209 4.940518891 1.026096689 1.164878117 0.466125584 0.08143541 0.135443931 6.813408233 0.01121231 0.016075158 2.62E-10 9.58123209 0.138781428 TRLQQELDDLLVDLDHQR ddPTM_HeLa_Romidepsin_16h_R1 1 TRLQQELDDLLVDLDHQR 18 1 P35579 P35579 MYH9 Myosin-9 0 0 127.2 0.00060607 1594200 3487.5 3463.6 2642 7274 3811.2 3655.7 3429.8 3293.7 3783.2 3450.5 FALSE FALSE TRUE 3444.993009 3512.360652 2687.982902 8115.054105 3616.700242 3422.112568 3721.127126 3388.998013 3444.821117 3360.855513 1.025034547 1.045079337 0.799791271 2.414579881 1.076124882 1.018226626 1.107196401 1.008373612 1.024983402 1 11.71461281 TRLS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 TRLSPPR 7 1 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 0 TRLS(1)PPR;T(0.039)RLS(0.961)PPR ; 65.157 0.019642 23417000 9424.8 9343.8 9810 9851.9 10034.9 10337.9 8866.3 10200.8 10885.1 10138.9 TRUE FALSE FALSE 9309.926912 9475.342262 9980.738935 10991.02303 9522.781608 9677.341554 9619.403301 10495.94405 9911.509394 9875.489916 0.942730638 0.959480729 1.0106576 1.112959775 0.964284475 0.979935338 0.974068465 1.062827682 1.003647361 1 13.26963661 -9.708847829 7.426136139 0.971206192 1.015893913 0.162504224 0.044921668 0.307476568 36.24491229 0.007344245 0.0103665 1.96E-10 9.708847829 0.044687721 TRLS(ph)TASEETVQNR ddPTM_HeLa_Romidepsin_16h_R1 1 TRLSTASEETVQNR 14 1 O43379;O43379-4;H7C3R4;O43379-3;O43379-2 O43379 WDR62 WD repeat-containing protein 62 1 0 T(0.004)RLS(0.495)T(0.495)AS(0.002)EET(0.004)VQNR 111.7 0.0019323 8688700 568.19 428.46 752.5 511.73 958.4 923.87 922.74 715.93 1146.6 505.43 TRUE FALSE FALSE 561.2646817 434.4918711 765.5969468 570.8986304 909.4892717 864.8376887 1001.117513 736.644305 1044.045224 492.2988557 1.140089349 0.882577455 1.555146712 1.159658658 1.847433243 1.756733087 2.033556448 1.496335603 2.120754928 1 8.943390576 -9.050970761 1.12792217 1.058213947 1.820575505 0.091490574 0.397166953 0.177875598 0.44687548 0.032493409 0.075233774 8.89E-10 9.050970761 0.762361559 TRNEMTAEEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 TRNEMTAEEKR 11 2 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 1 TRNEMTAEEK(1)R 53.034 0.02804 218490 0 0 0 0 0 0 0 0 55.647 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 50.66979295 0 0 TRNS(ph)GIWESPELDR ddPTM_HeLa_Romidepsin_16h_R1 3 TRNSGIWESPELDR 14 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 T(0.004)RNS(0.995)GIWESPELDR;TRNS(1)GIWESPELDR;T(0.002)RNS(0.998)GIWESPELDR ;; 126.43 0.0011091 19181800 2447.09 2509.08 1833.11 2161.1 2084.15 1944.58 1865.04 2095.81 2738.85 2910.54 TRUE FALSE FALSE 2417.263926 2544.402894 1865.014511 2410.97655 1977.788048 1820.327614 2023.456451 2156.448956 2493.880396 2834.923751 0.852673348 0.897520751 0.657871137 0.850455519 0.697651232 0.642108139 0.71376045 0.760672648 0.879699285 1 11.46909422 -10.54300233 0.370486322 1.010072291 0.682547937 0.565317938 0.073873172 0.415145316 0.165063986 0.048675265 0.043226511 2.86E-11 10.54300233 -0.327524353 TRPAANPIQFTLNK ddPTM_HeLa_Romidepsin_16h_R1 2 TRPAANPIQFTLNK 14 1 P23921;E9PL69 P23921 RRM1 Ribonucleoside-diphosphate reductase large subunit 0 0 ; ; 150.26 8.71E-07 1070670 1167.61 1177.19 1298.12 984.07 1444.59 1422.12 913.6 1220.73 1035.11 845.31 FALSE FALSE TRUE 1153.37872 1193.762512 1320.713234 1097.852804 1370.867182 1331.251122 991.2011612 1256.049897 942.5271691 823.3487243 1.400838656 1.449886878 1.604075157 1.333399532 1.664989744 1.616873971 1.203865546 1.525538158 1.144748442 1 9.685359795 -11.79860469 0.580965367 0.972798575 1.491381004 0.577657441 0.137076126 0.427333531 0.262718735 0.11099364 0.032782795 1.59E-12 11.79860469 0.518582429 TRPGS(ph)FQSLSDALSDTPAK ddPTM_HeLa_Romidepsin_16h_R1 2 TRPGSFQSLSDALSDTPAK 19 1 G3V4K3;Q9H9C1-2;Q9H9C1 G3V4K3 VIPAS39 Spermatogenesis-defective protein 39 homolog 1 0 T(0.001)RPGS(0.635)FQS(0.182)LS(0.182)DALSDTPAK;T(0.007)RPGS(0.662)FQS(0.222)LS(0.083)DALS(0.007)DT(0.019)PAK ; 125.51 0.0053156 30533000 3109.1 2946.9 3060.8 2579.91 3715.5 4012.8 3609.5 3591.6 3221.8 2917.5 TRUE FALSE FALSE 3071.205093 2988.386536 3114.07194 2878.211333 3525.884171 3756.395031 3916.09084 3695.517279 2933.634139 2841.702929 1.080762194 1.051618206 1.095847109 1.012847368 1.24076452 1.321881676 1.378078897 1.300458694 1.032350746 1 11.47254003 -8.603335963 3.034196299 1.04304153 1.33514759 0.936613217 0.034241794 0.049976592 0.925697428 0.006042303 0.013210273 2.49E-09 8.603335963 0.292106059 TRRS(ph)FVY(ph)REK ddPTM_HeLa_Romidepsin_16h_R1 1 TRRSFVYREK 10 3 A0A0C4DGY7 A0A0C4DGY7 MYCBP2 2 0 T(0.009)RRS(0.991)FVY(1)REK 85.963 0.0016642 0 949.76 886.56 851.4 806.86 862.5 701.3 709.05 819.31 880.52 939.6 TRUE FALSE FALSE 938.1839598 899.041015 866.2182599 900.1529496 818.4834066 656.4891933 769.2766893 843.0154422 801.7640859 915.1890565 1.02512585 0.982355513 0.94649106 0.983570491 0.894332598 0.717326315 0.840565874 0.921138027 0.876063891 1 9.837925991 -8.667041562 3.091999284 1.003299309 0.824982643 0.444749753 0.064978956 0.10085759 1.928696815 0.007603787 0.01610549 2.15E-09 8.667041562 -0.178316667 TRSPDVIS(ph)SASTALSQDIPEIASEALSR ddPTM_HeLa_Romidepsin_16h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 1 0 T(0.15)RS(0.116)PDVIS(0.25)S(0.25)AS(0.116)T(0.116)ALS(0.004)QDIPEIASEALSR 46.194 0.015509 16943000 592.96 575.36 497.17 610.84 644.27 743.46 629.17 642.96 810.03 742 TRUE FALSE FALSE 585.7327754 583.4599332 505.8230353 681.4681949 611.3904978 695.9553054 682.6116841 661.5630332 737.578888 722.722733 0.810452956 0.807308123 0.699885326 0.942917891 0.84595443 0.962963075 0.944500087 0.915375984 1.020555815 1 9.497298464 TRSPDVISSASTALSQDIPEIASEALSR ddPTM_HeLa_Romidepsin_16h_R1 1 TRSPDVISSASTALSQDIPEIASEALSR 28 1 Q6P2E9-2;Q6P2E9 Q6P2E9-2 EDC4 Enhancer of mRNA-decapping protein 4 0 0 65.744 0.00050729 12236000 1813.6 1897 1688.7 1647.3 2107.5 2249 2186.7 2900.6 2199.8 2139.3 FALSE FALSE TRUE 1791.495146 1923.706016 1718.091115 1837.768577 1999.946411 2105.296158 2372.438243 2984.524285 2003.044378 2083.720678 0.859757819 0.92320724 0.824530434 0.881964937 0.959795827 1.010354306 1.13855867 1.432305355 0.961282575 1 11.02494618 -7.167078946 1.152370614 0.919850017 1.757086108 0.915024705 0.048742349 0.494835135 0.462717575 0.009592911 0.523427361 6.81E-08 7.167078946 0.837236091 TRTPISTYS(ph)DS(ph)YRAPT(ph)S(ph)IKEVYK ddPTM_HeLa_Romidepsin_16h_R1 1 TRTPISTYSDSYRAPTSIKEVYK 23 3 Q8NCR6 Q8NCR6 SMRP1 Spermatid-specific manchette-related protein 1 4 0 T(0.094)RT(0.094)PIS(0.086)T(0.086)Y(0.087)S(0.6)DS(0.496)Y(0.465)RAPT(0.901)S(0.901)IKEVY(0.19)K 46.027 0.01623 16834000 913.99 783.94 909 180.96 589.69 469.96 637.08 528.86 980.73 885.74 TRUE FALSE FALSE 902.8499383 794.9763279 924.8207637 201.8834466 559.5959189 439.9310727 691.1935593 544.1617297 893.0110525 862.7283471 1.046505475 0.921467726 1.071972153 0.234005811 0.648635136 0.509930008 0.801171726 0.63074516 1.03510109 1 9.75276255 -9.289259003 24.995446 1.016792882 0.579622213 0.722206893 0.139427394 277.9770567 249756.7212 0.020298832 0.031010966 5.14E-10 9.289259003 -0.43717067 TS(ph)DPNPAAPDSESVIVAMER ddPTM_HeLa_Romidepsin_16h_R1 1 TSDPNPAAPDSESVIVAMER 20 0 P42858 P42858 HTT Huntingtin 1 0 T(0.47)S(0.529)DPNPAAPDSESVIVAMER 64.723 0.020459 2879600 547.31 603.73 653.44 371.08 555.16 639.08 436.14 563.45 543.91 530.51 TRUE FALSE FALSE 540.6391752 612.2293268 664.8128491 413.9860156 526.8281136 598.2448505 473.1857207 579.7525368 495.2613274 516.7272737 1.046275671 1.184821003 1.286583625 0.801169276 1.01954772 1.15775745 0.915735911 1.121970073 0.95845788 1 9.013259223 -11.30280588 1.524432715 1.010209851 1.063941669 0.055833435 0.131338503 1.139074837 5.325673749 0.032706188 0.024688088 4.98E-12 11.30280588 0.053731818 TS(ph)IETNIR ddPTM_HeLa_Romidepsin_16h_R1 2 TSIETNIR 8 0 A0A0C4DG88;P14859-4;P14859-5;P14859-3;P14859;P14859-2;P14859-6;A0A0A0MT46;H0YLC5;Q9UKI9-3;Q9UKI9;Q9UKI9-2 A0A0C4DG88 POU2F1;POU2F3 "POU domain protein;POU domain, class 2, transcription factor 1;POU domain, class 2, transcription factor 3" 1 0 T(0.183)S(0.817)IETNIR;T(0.223)S(0.776)IETNIR ; 125.68 0.014844 12738800 5254.2 4353 5286.3 4818.7 5499.2 6939.6 4852 5538.1 6178.6 5349.9 TRUE FALSE FALSE 5190.159789 4414.281648 5378.305834 5375.860767 5218.555304 6496.181957 5264.128759 5698.336186 5625.970541 5210.908827 0.996018154 0.847123179 1.03212434 1.031655119 1.001467398 1.246650474 1.010213177 1.093539798 1.079652461 1 12.3473193 -8.48159264 24.99769725 0.991468072 1.109128494 0.323219146 0.07804672 399.6898349 242002.1509 0.009825721 0.021968848 3.30E-09 8.48159264 0.117660422 TS(ph)LADSSIFDSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSLADSSIFDSK 12 0 Q9H8V3-2;Q9H8V3-4;Q9H8V3;Q9H8V3-3;C9J0L6;C9JDV9;C9JTI2;C9J1C4;C9JDB4 Q9H8V3-2 ECT2 Protein ECT2 1 0 T(0.017)S(0.979)LADS(0.003)S(0.001)IFDSK 107.93 0.0023264 0 3653.9 3378.5 4072.2 2304 2409.4 2828.9 2254.8 2420.9 4298.2 3846.2 TRUE FALSE FALSE 3609.364861 3426.062612 4143.074933 2570.399321 2286.439327 2648.14242 2446.322656 2490.944922 3913.758227 3746.27517 0.963454284 0.914525083 1.105918478 0.686121335 0.610323381 0.706873441 0.653001327 0.664912429 1.044706555 1 11.87124116 -9.204819896 7.928466135 0.98441801 0.662038679 0.908172975 0.054083598 0.061692509 7.931900047 0.007071071 0.011734891 6.24E-10 9.204819896 -0.322379331 TS(ph)MSLMRT(ph)TSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSMSLMRTTSR 11 1 A0A087WTN8 A0A087WTN8 ANKRD11 2 0 T(0.424)S(0.574)MS(0.351)LMRT(0.65)TSR 66.538 0.020584 23004000 1885.8 1503.1 1697.1 263.83 1769.3 1813.6 1653.8 1805.7 1687.8 1600.5 TRUE FALSE FALSE 1862.815144 1524.260681 1726.637314 294.335266 1679.006019 1697.716813 1794.273731 1857.945081 1536.838941 1558.918779 1.194940473 0.977767862 1.107586448 0.188807313 1.07703239 1.089034808 1.150973197 1.191816473 0.985836441 1 10.60633005 TS(ph)PDPSPVSAAPSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPDPSPVSAAPSK 14 0 Q13469-5;Q13469-3;Q13469-4;Q13469-2;Q13469 Q13469-5 NFATC2 "Nuclear factor of activated T-cells, cytoplasmic 2" 1 0 T(0.177)S(0.822)PDPS(0.001)PVS(0.001)AAPSK 87.863 0.021667 6011600 3184.5 3259.5 2890.4 3073.3 3630.9 3679.6 3736.1 3602.9 3462.6 3549 TRUE FALSE FALSE 3145.686089 3305.387327 2940.7062 3428.649406 3445.601624 3444.485435 4053.444241 3707.144227 3152.896384 3456.796468 0.910000377 0.956199579 0.850702732 0.991857472 0.996761497 0.996438601 1.17260136 1.072421897 0.912086208 1 11.75521995 -7.912062504 4.191781686 0.95431298 1.121659576 0.65521265 0.050229775 0.103707577 3.38055503 0.007487879 0.024335762 1.22E-08 7.912062504 0.167346596 TS(ph)PDTLRR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPDTLRR 8 1 Q01130-2;Q01130;J3QL05;J3KP15 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 1 0 T(0.323)S(0.677)PDTLRR 92.239 0.011663 3973200 544.23 680.77 564.43 658.37 651.32 804.34 858.72 494.45 606.11 630.17 TRUE FALSE FALSE 537.5967154 690.3538979 574.2536674 734.4938371 618.08071 752.9452699 931.6596554 508.7561306 551.8980036 613.7980926 0.875852698 1.124724737 0.935574213 1.196637536 1.006977241 1.226698615 1.517860135 0.82886561 0.89915236 1 9.261620352 -9.190933349 0.99756847 0.947116604 1.199544562 0.203779809 0.177425743 0.509123158 1.000277801 0.029521825 0.065904815 6.44E-10 9.190933349 0.252427958 TS(ph)PINEDIR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPINEDIR 9 0 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 T(0.225)S(0.775)PINEDIR;T(0.224)S(0.776)PINEDIR ; 168.85 0.0018083 74371000 11350.4 10637.1 11145.7 6735.4 12881.7 13769.1 12487.2 12823.7 11453.2 11007.7 TRUE FALSE FALSE 11212.05696 10786.84937 11339.68623 7514.178639 12224.29878 12889.29895 13547.86246 13194.73353 10428.79711 10721.71837 1.045733209 1.00607468 1.057637017 0.700837159 1.140143619 1.202167275 1.263590592 1.23065474 0.972679635 1 13.38824852 -8.531623729 24.99997079 1.000430735 1.224594994 0.592763911 0.098966523 110.5799044 316123.0267 0.014073778 0.028182307 2.94E-09 8.531623729 0.224164259 TS(ph)PLKDNPS(ph)PEPQLDDIKR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPLKDNPSPEPQLDDIKR 19 2 Q96JC9-2;Q96JC9 Q96JC9-2 EAF1 ELL-associated factor 1 2 0 T(0.451)S(0.549)PLKDNPS(1)PEPQLDDIKR 88.329 0.0044029 48702000 1825.2 1506.5 1546.3 1612.7 1923.1 1875.7 1852.1 2022.9 1631.7 1709.1 TRUE FALSE FALSE 1802.95376 1527.708547 1573.212703 1799.167962 1824.957031 1755.848824 2009.417328 2081.42942 1485.756665 1664.697336 1.083051989 0.917709492 0.945044285 1.080777823 1.096269569 1.054755592 1.207076677 1.250335046 0.892508586 1 10.70104418 -7.562549944 1.008097291 1.025943517 1.321791307 0.617843205 0.069047692 0.618028028 0.665370435 0.009519185 0.174902837 2.74E-08 7.562549944 0.29584779 TS(ph)PSGGTWSSVVSGAK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSGGTWSSVVSGAK 16 0 F8WB06;F8VRK6 F8WB06 ATXN2 1 0 T(0.163)S(0.834)PS(0.003)GGTWSSVVSGAK 184.48 9.20E-09 23881000 3570.5 3199.5 3061.3 3002.8 3039.1 2759 2302.2 2706.1 3332.3 3177.9 TRUE FALSE FALSE 3526.981373 3244.542645 3114.580642 3349.997865 2884.003387 2582.708804 2497.748811 2784.396734 3034.250742 3095.3377 1.139449622 1.048203123 1.006216751 1.082272175 0.931724957 0.834386763 0.806939033 0.899545382 0.980264849 1 11.5958811 -8.571185417 2.986216876 1.062164929 0.844258747 0.748056413 0.050463181 0.09735806 1.762585194 0.008642189 0.019275998 2.68E-09 8.571185417 -0.217906183 TS(ph)PSGGTWSSVVSGVPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSGGTWSSVVSGVPR 17 0 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4 Q99700 ATXN2 Ataxin-2 1 0 T(0.162)S(0.611)PS(0.223)GGT(0.002)WS(0.001)SVVSGVPR 81.651 0.017095 78522000 892.04 1052.5 943.37 1088.8 1070.7 1057.1 757.66 900.95 1407.9 1104.2 TRUE FALSE FALSE 881.1674734 1067.317123 959.7889591 1214.692179 1016.058184 989.5547216 822.0156215 927.0175668 1281.973898 1075.512725 0.819299905 0.992379818 0.892401305 1.129407538 0.944719816 0.920077186 0.764301158 0.861930822 1.191965347 1 10.07080888 -7.851890065 6.654114396 0.935144836 0.813914162 0.17148916 0.114618632 0.234249949 14.17202536 0.013241579 0.04060179 1.41E-08 7.851890065 -0.121230674 TS(ph)PTPGDFPK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPTPGDFPK 10 0 Q9UPU7;C9JW56;Q9UPU7-2 Q9UPU7 TBC1D2B TBC1 domain family member 2B 1 0 T(0.116)S(0.861)PT(0.023)PGDFPK 104.82 0.021399 11671000 5073.5 4088.6 4261.8 3904.1 4733.8 4399 3795.3 4152.3 4217.2 4649.6 TRUE FALSE FALSE 5011.662231 4146.159418 4335.974841 4355.510411 4492.216522 4117.918097 4117.672687 4272.440249 3840.00307 4528.802722 1.106619683 0.915508949 0.957421886 0.961735514 0.991921441 0.909273013 0.909218825 0.943392881 0.847906899 1 12.14491398 -10.25161183 24.8602288 1.050348184 0.942114929 0 0.072563156 348.6827869 882045.3422 0.007701569 0.009367237 5.60E-11 10.25161183 -0.108233255 TS(ph)PYILR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPYILR 7 0 P49454 P49454 CENPF Centromere protein F 1 0 T(0.225)S(0.775)PYILR 115.49 0.028149 20106000 3893 3746.4 3365.7 3383 2973.6 3046.5 2431.9 2486.4 4087 3828.5 TRUE FALSE FALSE 3845.550619 3799.141918 3424.278597 3774.158377 2821.846096 2851.838482 2638.465525 2558.340061 3721.448484 3729.035018 1.03124551 1.018800279 0.918274723 1.012100546 0.756722874 0.764765809 0.70754646 0.686059543 0.99796555 1 11.86458663 -8.727782974 4.361477123 1.007843432 0.724623592 0.931258236 0.035596346 0.037653338 1.592853726 0.005581601 0.011168221 1.87E-09 8.727782974 -0.283219841 TS(ph)RDT(ph)SPSSGSAVSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSRDTSPSSGSAVSSSK 17 1 F8WF16;B7Z8L1;F8W6A0;F8W0Q9;Q8NEY8-7;Q8NEY8-5;Q8NEY8-6;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-3;Q8NEY8 F8WF16 PPHLN1 Periphilin-1 2 0 T(0.448)S(0.553)RDT(0.949)S(0.05)PSSGSAVSSSK 90.397 0.0083047 16178000 3859.6 3162.1 4045.8 2390.7 4614.9 5289 4752.8 4513.6 4679.7 4198.7 TRUE FALSE FALSE 3812.557711 3206.616127 4116.215452 2667.123983 4379.384432 4951.049969 5156.502713 4644.193895 4261.135911 4089.617169 0.93225296 0.784087115 1.006503856 0.652169597 1.070854374 1.210638983 1.26087663 1.135606025 1.041940049 1 11.99775008 -8.524492909 24.99999205 0.932448996 1.196977943 0.577120907 0.114297663 29.13619111 451258.5116 0.016005029 0.032197068 2.99E-09 8.524492909 0.264528947 TS(ph)SEDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 0 T(0.001)S(0.499)S(0.499)EDNLYLAVLR;T(0.091)S(0.899)S(0.01)EDNLYLAVLR ; 222.56 2.14E-31 9946600 4239.5 3557.2 3265.3 2902.1 3664.4 3409 3089.7 3686.7 4137.2 4002.5 TRUE FALSE FALSE 4187.827343 3607.278355 3322.131177 3237.654457 3477.391994 3191.175902 3352.139041 3793.368848 3767.15847 3898.514473 1.074211055 0.925295617 0.852153096 0.830484144 0.891978731 0.818562025 0.859850352 0.97302931 0.966306139 1 11.92870878 -10.07139706 4.001589923 1.034721433 0.868082321 0.624410152 0.048437937 0.086230573 2.662546354 0.007876608 0.009859703 8.48E-11 10.07139706 -0.166639112 TS(ph)SGTSLSAMHSSGSSGK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSGTSLSAMHSSGSSGK 18 0 A6NNK5;Q12888;Q12888-3;Q12888-2;M0R142 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 T(0.355)S(0.422)S(0.089)GT(0.023)S(0.023)LS(0.089)AMHSSGSSGK 66.636 0.0030151 0 689.81 895.26 694.35 616.07 1698.9 1734.4 1321.1 1105.8 1427.2 1229.7 TRUE FALSE FALSE 681.4023304 907.8634938 706.4348705 687.3029121 1612.198794 1623.577438 1433.314201 1137.794578 1299.547658 1197.752217 0.568900914 0.75797271 0.589800512 0.573827293 1.346020296 1.355520294 1.196670047 0.949941534 1.084988731 1 10.22611377 -8.757019146 24.9982017 0.757349813 1.221189101 0.566050861 0.192690805 67.36438281 380967.9107 0.030696311 0.059747675 1.75E-09 8.757019146 0.463839289 TS(ph)SLTQFPPSQSEER ddPTM_HeLa_Romidepsin_16h_R1 1 TSSLTQFPPSQSEER 15 0 B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4 B7Z7F3 RANBP3 Ran-binding protein 3 1 0 T(0.21)S(0.72)S(0.07)LTQFPPSQSEER 212.43 1.40E-25 15471000 2710.7 2404.1 2803 2321.7 2203.4 1956.3 1769.3 2275.5 2794.4 2299.1 TRUE FALSE FALSE 2677.660946 2437.944983 2851.785039 2590.145878 2090.952276 1831.298744 1919.584298 2341.338002 2544.461865 2239.369051 1.195721154 1.088674947 1.273477026 1.15664092 0.933723843 0.817774428 0.857198726 1.045534679 1.136240525 1 11.12887659 -8.686339657 5.64145617 1.113249094 0.898879091 0.604216509 0.088662739 0.137871635 7.61656269 0.015492596 0.031174193 2.06E-09 8.686339657 -0.214370002 TS(ph)TGSASSSAAVAASSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSTGSASSSAAVAASSK 17 0 Q9UDT6-2;Q9UDT6 Q9UDT6-2 CLIP2 CAP-Gly domain-containing linker protein 2 1 0 T(0.333)S(0.613)T(0.053)GS(0.001)ASSSAAVAASSK 273.44 1.15E-87 8086200 1248.2 1274.6 1295.1 1065.7 2473.6 3349.6 2935 2743.6 1370.8 1041.7 TRUE FALSE FALSE 1232.986458 1292.543852 1317.640672 1188.921248 2347.362962 3135.57137 3184.298827 2822.981737 1248.192215 1014.636484 1.2152002 1.273898458 1.298633248 1.171770646 2.313501435 3.090339664 3.13836421 2.782259245 1.230186608 1 9.986747227 -8.609562137 2.554382327 1.131926239 3.014850032 0.973501939 0.135097288 0.0319315 0.420237861 0.022462158 0.050759789 2.46E-09 8.609562137 1.882923793 up TS(ph)TSSSSVQAR ddPTM_HeLa_Romidepsin_16h_R1 1 TSTSSSSVQAR 11 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 T(0.388)S(0.599)T(0.012)S(0.001)SSSVQAR 108.98 0.015037 1890300 481.58 712.83 1017.1 697.17 875.88 1071.5 1553.4 429.07 922.71 858.78 TRUE FALSE FALSE 475.7103177 722.8652395 1034.802199 777.7800757 831.1805752 1003.034608 1685.345757 441.4844635 840.1805066 836.4687718 0.568712585 0.864186762 1.237107987 0.929837553 0.993677951 1.199129773 2.014834043 0.527795512 1.004437386 1 9.70816787 -9.01103283 0.934717428 0.805148812 1.287986418 0.089354533 0.375291208 0.659047877 1.122709517 0.064965877 0.171836112 9.75E-10 9.01103283 0.482837607 TS(ph)VAGTVR ddPTM_HeLa_Romidepsin_16h_R1 1 TSVAGTVR 8 0 Q96EB6;B0QZ35;E9PC49 Q96EB6 SIRT1 NAD-dependent protein deacetylase sirtuin-1;SirtT1 75 kDa fragment 1 0 T(0.223)S(0.777)VAGTVR 117.53 0.019702 5698100 3118.8 2814.3 3255.9 2700.5 3635 3286.2 2502.5 2794.3 3027.8 3401.1 TRUE FALSE FALSE 3080.786866 2853.919789 3312.567574 3012.744516 3449.492386 3076.222426 2715.062288 2875.148662 2756.985985 3312.738932 0.929981785 0.861498551 0.999948273 0.90944218 1.041281084 0.92860394 0.819582329 0.867906805 0.832237626 1 11.6938088 TS(ph)VQTEDDQLIAGQSAR ddPTM_HeLa_Romidepsin_16h_R1 1 TSVQTEDDQLIAGQSAR 17 0 G3XAM7;P35221-3;P35221;P35221-2;A0A0A0MTJ6;A0A0A0MRI5;P26232-4;P26232-6;P26232-3;P26232-2;P26232-5;P26232 G3XAM7 CTNNA1;CTNNA2 Catenin alpha-1;Catenin alpha-2 1 0 T(0.152)S(0.847)VQT(0.002)EDDQLIAGQSAR 222.96 1.59E-35 23499000 1874.9 2190.6 1676.7 1142.3 2470.4 2901.7 2282.2 2046.1 2096.5 2247.6 TRUE FALSE FALSE 1852.047998 2221.439324 1705.88226 1274.378101 2344.32627 2716.290735 2476.050011 2105.300675 1908.983789 2189.207028 0.84599034 1.014723275 0.779223819 0.582118586 1.07085636 1.24076467 1.131025974 0.961672719 0.871997835 1 11.09619268 -8.544832721 24.99857125 0.896058894 1.12025325 0.43786696 0.134151621 192.6856039 219406.6123 0.020790064 0.041582463 2.85E-09 8.544832721 0.224194356 TSADAQEPASPVVSPQQS(ph)PPT(ph)SPHTWR ddPTM_HeLa_Romidepsin_16h_R1 1 TSADAQEPASPVVSPQQSPPTSPHTWR 27 0 E9PMG1;H0YDT0;Q96D71-2;Q96D71-4;Q96D71-3;Q96D71;F2Z3L2 E9PMG1 REPS1 RalBP1-associated Eps domain-containing protein 1 2 0 TSADAQEPAS(0.011)PVVS(0.293)PQQS(0.696)PPT(0.493)S(0.451)PHT(0.055)WR 62.455 0.0020457 11657000 2695.5 2604.8 2566 1574.9 2760.7 2789.7 2403.9 3002.6 3395.8 2919.4 TRUE FALSE FALSE 2662.646209 2641.470443 2610.660154 1756.997348 2619.811177 2611.447173 2608.087206 3089.475494 3092.071143 2843.553567 0.936379831 0.928932893 0.918097758 0.617887902 0.921315922 0.918374531 0.917192922 1.086484014 1.087396833 1 11.47347927 -10.8806383 0.969734986 0.985768005 0.892981358 0.159981925 0.113008038 0.785883858 1.571168134 0.029697262 0.025106481 1.32E-11 10.8806383 -0.092786647 TSASEGNPYVSSTLSVPAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TSASEGNPYVSSTLSVPASPR 21 0 E9PFQ4;Q86SQ0-2;Q86SQ0-3;Q86SQ0;G5E9V3;E9PDY7;A0A1W2PQ63 E9PFQ4 PHLDB2 Pleckstrin homology-like domain family B member 2 1 0 TSASEGNPYVSSTLSVPAS(1)PR;TSASEGNPYVSSTLSVPAS(1)PR ; 375.11 0 167782000 6376.7 5456.4 5438.1 5889.1 5336.9 5550.9 4421.5 4863.6 5914.9 6082 TRUE FALSE FALSE 6298.978328 5533.215342 5532.747849 6570.025451 5064.538078 5196.215405 4797.0621 5004.320593 5385.85653 5923.988763 1.063300182 0.934035422 0.933956506 1.109054341 0.854920271 0.877148086 0.80976894 0.844755247 0.909160491 1 12.53235319 -8.7028595 9.878268095 1.019519821 0.845746657 0.536721616 0.062832754 0.169608828 27.33802552 0.007983821 0.015967029 1.98E-09 8.7028595 -0.173773164 TSAVS(ph)SPLLDQQR ddPTM_HeLa_Romidepsin_16h_R1 1 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 T(0.001)SAVS(0.5)S(0.5)PLLDQQR 217.46 1.08E-23 151850000 6408.2 5006.3 5412.9 4889.7 5533.6 5822.1 5324.3 5309.3 6002.3 5311.3 TRUE FALSE FALSE 6330.094394 5076.778823 5507.109254 5455.070121 5251.199743 5450.0866 5776.545909 5462.916219 5465.439255 5173.31166 1.223605847 0.981340224 1.064523001 1.054463848 1.015055749 1.053500535 1.116605047 1.055980497 1.056468199 1 12.33687239 TSAVSS(ph)PLLDQQR ddPTM_HeLa_Romidepsin_16h_R1 1 TSAVSSPLLDQQR 13 0 Q5T200;Q5T200-2;A0A087WX14 Q5T200 ZC3H13 Zinc finger CCCH domain-containing protein 13 1 0 TSAVS(0.031)S(0.969)PLLDQQR 148.89 0.0007683 159950000 3791.3 3692.1 4239.2 3623.8 3739.6 4007.2 2964.7 3788.8 4340.6 3934.8 TRUE FALSE FALSE 3745.090177 3744.077481 4312.981498 4042.800806 3548.754258 3751.152853 3216.521544 3898.42295 3952.365865 3832.573329 0.977173783 0.976909549 1.125348722 1.054852826 0.92594556 0.978755664 0.83925897 1.017181569 1.031256424 1 11.90409768 -8.736484892 24.98126275 1.003389998 0.935817108 0.28114899 0.061305556 271.6703519 271960.6474 0.008815701 0.0176255 1.83E-09 8.736484892 -0.067572891 TSDDEVGS(ph)PKEESR ddPTM_HeLa_Romidepsin_16h_R1 2 TSDDEVGSPKEESR 14 1 Q6ULP2-7;Q6ULP2-8;Q6ULP2-6;Q6ULP2;Q6ULP2-9;B8ZZI9 Q6ULP2-7 AFTPH Aftiphilin 1 0 TSDDEVGS(0.999)PKEES(0.001)R;TSDDEVGS(0.996)PKEES(0.004)R ; 166.79 0.00058194 28326000 3972.4 4018 3763.7 3458.1 5772.4 5918.6 5405.9 6020.7 4228.5 3865 TRUE FALSE FALSE 3923.982861 4074.565509 3829.20562 3857.941793 5477.812888 5540.420561 5865.077011 6194.899455 3850.29237 3764.586743 1.042340934 1.082340716 1.017164932 1.02479822 1.455090097 1.471720786 1.557960385 1.645572244 1.022766278 1 11.87827579 -8.699694633 3.470414364 1.024212722 1.54766855 0.965903497 0.046332125 0.031265006 0.759724037 0.007426008 0.015297666 2.00E-09 8.699694633 0.523455828 TSDIFGS(ph)PVTATSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSDIFGSPVTATSR 14 0 A6NGP5;Q9H910;Q9H910-3;H3BU16;H3BMV3;Q9H910-2;H3BMT0;H3BTV5 A6NGP5 HN1L Hematological and neurological expressed 1-like protein 1 0 TSDIFGS(0.956)PVT(0.043)ATSR 222.56 1.08E-32 546540000 3377.7 3873.9 3163 3197.2 3796.9 3822 2992.1 3575.3 3485.7 2810.4 TRUE FALSE FALSE 3336.531293 3928.436866 3218.050688 3566.875307 3603.130025 3577.786535 3246.248899 3678.745665 3173.930262 2737.385403 1.218875241 1.435105507 1.175592843 1.303022696 1.316266983 1.307008699 1.185893991 1.343890291 1.159475118 1 11.41858285 -11.58921299 0.684194941 1.004025984 1.290593686 0.443254852 0.086547574 0.283310912 0.267817707 0.040517524 0.016782867 2.58E-12 11.58921299 0.286567702 TSDS(ph)TPDPQRVPLR ddPTM_HeLa_Romidepsin_16h_R1 1 TSDSTPDPQRVPLR 14 1 P52948-6;P52948-2;P52948-5;P52948;H7C3P6 P52948-6 NUP98 Nuclear pore complex protein Nup98-Nup96;Nuclear pore complex protein Nup98;Nuclear pore complex protein Nup96 1 0 T(0.011)S(0.07)DS(0.459)T(0.459)PDPQRVPLR 70.529 0.020805 9078100 2706.8 2881.8 2778.8 3419.6 2923.7 2971.6 2156.3 2548.2 2949 2805 TRUE FALSE FALSE 2673.80848 2922.370056 2827.163848 3814.990242 2774.492679 2781.72435 2339.456068 2621.928147 2685.234054 2732.125696 0.978655003 1.06963236 1.034785425 1.396345069 1.015506967 1.01815387 0.856276881 0.959666003 0.982836938 1 11.41580814 -7.846541474 6.952007464 1.031365556 0.908675178 0.172521503 0.121031042 0.314107162 21.13243968 0.017736343 0.054216755 1.42E-08 7.846541474 -0.122690378 TSEIYVHR ddPTM_HeLa_Romidepsin_16h_R1 1 TSEIYVHR 8 0 G3V529;Q9GZR7-2;Q9GZR7;A0A1W2PRR2;F5GYL3;A0A087WXU8 G3V529 DDX24 ATP-dependent RNA helicase DDX24 0 0 92.47 0.0024356 0 771.6 831.63 1013 959.11 1363 1200.1 1120.6 840.9 1167.9 844.74 FALSE FALSE TRUE 762.1954424 843.337709 1030.63084 1070.006811 1293.441024 1123.417483 1215.783736 865.2301148 1063.440099 822.793533 0.926350794 1.024968811 1.252599588 1.300456029 1.572011655 1.36536985 1.477629183 1.051576222 1.292475033 1 9.684386644 -9.664852834 2.116063248 0.964441262 1.372822418 0.367033326 0.163984061 0.124882497 1.142104154 0.020030626 0.029641697 2.16E-10 9.664852834 0.408381156 TSETDDGVVGKS(ph)SDGEDEQQVPK ddPTM_HeLa_Romidepsin_16h_R1 1 TSETDDGVVGKSSDGEDEQQVPK 23 1 Q16649 Q16649 NFIL3 Nuclear factor interleukin-3-regulated protein 1 0 TSET(0.003)DDGVVGKS(0.81)S(0.187)DGEDEQQVPK 75.611 0.00032139 8210800 1994.1 1503.1 1527.3 2950.2 3355.2 3549.2 3376.6 4257.6 1709.1 2001.1 TRUE FALSE FALSE 1969.795142 1524.260681 1553.882016 3291.316005 3183.971624 3322.417575 3663.40832 4380.786939 1556.233815 1949.111134 1.010612021 0.782028616 0.797225971 1.688624085 1.633550581 1.704580882 1.879527676 2.247581917 0.798432572 1 10.92860064 -9.156692432 4.24036602 0.97111126 1.83569355 0.869606007 0.183300378 0.066543595 2.059594842 0.028001583 0.047367813 6.97E-10 9.156692432 0.86458229 TSETSIS(ph)PPGSSIGSPNR ddPTM_HeLa_Romidepsin_16h_R1 1 TSETSISPPGSSIGSPNR 18 0 A0A0C4DGA7;O94929-2;O94929-3;O94929 A0A0C4DGA7 ABLIM3 Actin-binding LIM protein 3 1 0 TSET(0.015)S(0.228)IS(0.74)PPGS(0.016)S(0.001)IGSPNR 137.27 0.00089328 10778000 1443.7 1421.4 1662.6 1450.4 1521 1632.8 1371.2 1449.4 1360.3 1470.2 TRUE FALSE FALSE 1426.103629 1441.410507 1691.536856 1618.102072 1443.377694 1528.46935 1487.669694 1491.336102 1238.631361 1432.003992 0.995879646 1.006568777 1.181237528 1.129956398 1.007942507 1.067363889 1.038872588 1.041432922 0.864963623 1 10.4838198 -9.963117471 24.99996983 0.998221046 1.07634833 0.396725785 0.062470273 132.1280066 89559.70956 0.007669162 0.010079241 1.09E-10 9.963117471 0.078127285 TSEVYS(ph)DDEEEEEDDKSSEK ddPTM_HeLa_Romidepsin_16h_R1 2 TSEVYSDDEEEEEDDKSSEK 20 1 Q92541 Q92541 RTF1 RNA polymerase-associated protein RTF1 homolog 1 0 T(0.001)S(0.002)EVYS(0.997)DDEEEEEDDKSSEK;T(0.015)S(0.004)EVY(0.003)S(0.977)DDEEEEEDDKSSEK ; 127.58 0.00011388 29828700 3165.5 3019.3 3027 2199.68 4762.9 5916 5396.4 5961.7 3510.1 3478.4 TRUE FALSE FALSE 3126.917668 3061.805785 3079.683665 2454.017351 4519.83144 5537.986693 5854.770081 6134.192383 3196.147865 3388.030667 0.922930745 0.903712536 0.908989312 0.724319699 1.334058598 1.634573957 1.728074701 1.81054807 0.943364503 1 11.72623122 -8.437960361 2.621501073 0.938746212 1.73761636 0.943630785 0.090065057 0.047637557 0.63660388 0.013697245 0.034008497 3.65E-09 8.437960361 0.798870148 TSFSVGS(ph)DDELGPIR ddPTM_HeLa_Romidepsin_16h_R1 2 TSFSVGSDDELGPIR 15 0 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 0 TSFSVGS(1)DDELGPIR;TSFS(0.13)VGS(0.87)DDELGPIR ; 198.81 5.14E-18 331280000 2479.2 2213.33 2548.3 2298.9 2586.8 2658.8 1951.17 2593.4 2889.3 2459.3 TRUE FALSE FALSE 2448.982557 2244.489318 2592.652093 2564.709635 2454.785943 2488.911261 2116.902331 2668.435937 2630.873772 2395.407031 1.022365938 0.936997048 1.082343025 1.07067801 1.024788652 1.039034798 0.883733872 1.113980172 1.098299261 1 11.22605511 -6.914182672 20.21542067 1.010755931 6.719569635 0.168498767 0.062610919 508.3101445 119650.8693 0.007061592 98.30937724 1.22E-07 6.914182672 5.708813704 TSFSVGS(ph)DDELGPIRK ddPTM_HeLa_Romidepsin_16h_R1 2 TSFSVGSDDELGPIRK 16 1 Q9NRY4 Q9NRY4 ARHGAP35 Rho GTPase-activating protein 35 1 0 TSFSVGS(1)DDELGPIRK;TSFS(0.004)VGS(0.996)DDELGPIRK ; 146.27 0.00047353 30465000 2527.1 2344.2 2001.75 1882.83 2268.8 2537.9 2118.74 2628.1 3125 2439.8 TRUE FALSE FALSE 2496.298733 2377.201709 2036.589619 2100.531664 2153.01467 2375.736381 2298.705723 2704.139927 2845.492173 2376.413644 1.050447905 1.000331619 0.857001315 0.883908266 0.905993229 0.999715006 0.967300339 1.137907928 1.197389259 1 11.21457026 -9.987835342 24.95657299 1.023905109 0.952905333 0.193589759 0.091736562 309.6028534 635167.9787 0.012192586 0.01601827 1.03E-10 9.987835342 -0.070999777 TSGAPGS(ph)PQTPPER ddPTM_HeLa_Romidepsin_16h_R1 1 TSGAPGSPQTPPER 14 0 K7EIM4;K7ESM2;K7ELS4;K7EJA3;K7ERG7;Q96MH2 K7EIM4 HEXIM2 Protein HEXIM2 1 0 TSGAPGS(0.917)PQT(0.083)PPER 166.64 8.94E-05 13790000 5748.6 4580.1 4498.2 3512.7 3018 3617.6 3478 3745.7 5232.2 5306.1 TRUE FALSE FALSE 5678.533852 4644.578768 4576.489284 3918.854902 2863.980198 3386.447035 3773.421233 3854.07592 4764.218928 5168.246757 1.098735049 0.898675893 0.885501312 0.758256153 0.554149276 0.655240973 0.730116306 0.745722118 0.921824973 1 12.33545924 -9.556615127 1.450575648 1.044292167 0.675238516 0.772405549 0.07481617 0.106442268 0.4493428 0.01234312 0.020048745 2.78E-10 9.556615127 -0.369053651 TSGAPGSPQT(ph)PPER ddPTM_HeLa_Romidepsin_16h_R1 1 TSGAPGSPQTPPER 14 0 K7EIM4;K7ESM2;K7ELS4;K7EJA3;K7ERG7;Q96MH2 K7EIM4 HEXIM2 Protein HEXIM2 1 0 TSGAPGS(0.058)PQT(0.942)PPER 191.63 8.36E-11 12849000 3406.4 3428.9 2840.5 2019.5 2157.9 2335.4 2223.6 2211.9 3751.3 3644.9 TRUE FALSE FALSE 3364.881487 3477.172144 2889.937711 2253.004092 2047.774311 2186.175477 2412.472528 2275.897837 3415.774333 3550.204973 0.947799215 0.97942856 0.81401996 0.634612398 0.57680453 0.615788523 0.679530491 0.641060968 0.9621344 1 11.79368661 -9.49040315 2.398060219 0.97567897 0.626929181 0.97020063 0.028322394 0.038400931 0.439908706 0.005396812 0.008418939 3.23E-10 9.49040315 -0.348749789 TSGETTQT(ph)HTEPTGDSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSGETTQTHTEPTGDSK 17 0 P46013;P46013-2 P46013 MKI67 Antigen KI-67 1 0 T(0.098)S(0.117)GET(0.232)T(0.232)QT(0.317)HT(0.005)EPTGDSK 69.485 0.024461 4660000 4915.8 4417.2 4793.8 2052.3 3356.1 4070.9 3661.4 3482.5 5727.3 5836.1 TRUE FALSE FALSE 4855.884339 4479.385458 4877.234078 2289.596582 3184.825694 3810.782628 3972.399225 3583.260643 5215.035944 5684.477281 0.85423586 0.788003054 0.857991656 0.402780497 0.560267116 0.670384002 0.698815217 0.630358864 0.917416974 1 12.47281198 -10.05357206 0.87216224 0.953989711 0.609320549 0.644773079 0.10200268 0.242646092 0.368170545 0.023879777 0.032029105 8.84E-11 10.05357206 -0.344669162 TSIAIDTIINQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSIAIDTIINQK 12 0 P25705-2;P25705;P25705-3;K7EK77;K7ENJ4 P25705-2 ATP5A1 "ATP synthase subunit alpha, mitochondrial" 0 0 183 1.69E-05 479550 0 141.43 277.91 121.89 270.8 219.74 123.75 223.53 248.29 285.52 FALSE FALSE TRUE 0 143.4210553 282.746907 135.9834953 256.9800655 205.6993232 134.2613219 229.9974879 226.0823205 278.1021492 0 0.515713581 1.016701625 0.488969595 0.924049189 0.739653842 0.482777002 0.827025208 0.812947045 1 8.119471084 -9.922003041 24.99998932 0.513556762 0.73355934 0.050970246 0.289473154 77.74391798 24915.3509 0.064010925 0.084126838 1.20E-10 9.922003041 0.220002579 TSIDAYDNFDNISLAQR ddPTM_HeLa_Romidepsin_16h_R1 1 TSIDAYDNFDNISLAQR 17 0 A0A087WVQ6;Q00610-2;Q00610;J3KS13;K7EJJ5 A0A087WVQ6 CLTC Clathrin heavy chain;Clathrin heavy chain 1 0 0 134.88 0.015442 8159500 537.16 543.82 474.27 629.47 437.84 447.65 422.59 524.66 536.55 640.81 FALSE FALSE TRUE 530.6128873 551.4759122 482.5244704 702.2522831 415.495391 419.0466097 458.4847841 539.8402093 488.5596242 624.1616638 0.850120919 0.883546594 0.773076109 1.125112809 0.665685535 0.671375116 0.734560949 0.864904464 0.782745325 1 9.285775939 -16.52287875 0.065291531 1.722174599 0.528338467 0 0.137329779 240.2581163 1.224876175 27.09803237 4.424187979 3.00E-17 16.52287875 -1.193836132 TSISDPPES(ph)PPLLPPREPVR ddPTM_HeLa_Romidepsin_16h_R1 1 TSISDPPESPPLLPPREPVR 20 1 G5E9C8;Q07889 G5E9C8 SOS1 Son of sevenless homolog 1 1 0 T(0.003)S(0.003)IS(0.03)DPPES(0.964)PPLLPPREPVR 73.672 0.0027242 5799400 1556.4 1605 1505 1398.5 1831.3 1765.7 1372.7 1550.6 1783.8 1649.6 TRUE FALSE FALSE 1537.429998 1627.595232 1531.193894 1560.20115 1737.841927 1652.877469 1489.297104 1595.464165 1624.25246 1606.743154 0.956861085 1.012977854 0.952979877 0.971033327 1.081592863 1.028712937 0.926904278 0.992980216 1.01089739 1 10.64992361 TSKAETPT(ph)ESVSEPEVATK ddPTM_HeLa_Romidepsin_16h_R1 2 TSKAETPTESVSEPEVATK 19 1 M0R0Q7;P18858-2;P18858-3;P18858;B4E135 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 T(0.014)S(0.015)KAET(0.041)PT(0.884)ES(0.045)VSEPEVATK;T(0.068)S(0.068)KAET(0.068)PT(0.723)ES(0.036)VS(0.036)EPEVATK ; 72.317 0.0022731 8072800 4071.9 3260.5 2996.4 5882.2 3531.2 2835.5 2879.9 2877.4 4421.1 3511.5 TRUE FALSE FALSE 4022.270117 3306.401405 3048.551085 6562.327641 3350.989687 2654.320701 3124.518634 2960.653029 4025.665743 3420.270724 1.176009282 0.966707513 0.89131865 1.918657373 0.97974399 0.776055732 0.913529626 0.865619499 1.177002076 1 11.73989481 -8.526426192 24.99996641 1.125092869 0.861245224 0.221490514 0.272107744 141.4446383 996804.331 0.039200637 0.078699905 2.98E-09 8.526426192 -0.263847644 TSKEPPSS(ph)PLQPQK ddPTM_HeLa_Romidepsin_16h_R1 1 TSKEPPSSPLQPQK 14 1 Q92615;A0A087X183;H0Y4V9 Q92615 LARP4B La-related protein 4B 1 0 TSKEPPS(0.054)S(0.946)PLQPQK 86.772 0.0087367 42236000 6374.2 5773.4 5524.9 6122.2 7154 6857.9 5882.3 6257.5 6850.2 6317.4 TRUE FALSE FALSE 6296.508799 5854.678077 5621.058567 6830.07757 6788.904685 6419.702323 6381.942415 6438.55089 6237.500955 6153.273037 1.023277979 0.9514738 0.913507093 1.10999098 1.103299763 1.043298791 1.037162235 1.046361969 1.013688311 1 12.58713829 -9.235703866 24.99944086 0.999214084 1.066894552 0.529832317 0.039317963 632.6616874 614567.2743 0.00646142 0.010712591 5.81E-10 9.235703866 0.067680468 TSLAGDTSNSSS(ph)PASTGAK ddPTM_HeLa_Romidepsin_16h_R1 3 TSLAGDTSNSSSPASTGAK 19 0 H3BQK9;H3BPE1;Q9UPN3-2;Q9UPN3-3;A0A590UJG2;Q9UPN3;Q9UPN3-4;H0Y390;Q9UPN3-5;H0Y4F5;H0Y6T5;H0Y314 H3BQK9 MACF1 "Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5" 1 0 TSLAGDT(0.002)S(0.01)NS(0.006)S(0.047)S(0.935)PAS(0.001)TGAK;TSLAGDTSNSS(0.065)S(0.93)PAS(0.005)TGAK;TSLAGDTSNSS(0.078)S(0.915)PAS(0.007)T(0.001)GAK ;; 336.47 2.50E-211 46706200 8936.74 8736.9 8499.83 9286.04 12115.2 14272.3 12181 12734.5 9591.8 8050.3 TRUE FALSE FALSE 8827.815575 8859.898308 8647.765976 10359.73564 11496.91614 13360.34609 13215.65384 13102.95267 8733.885385 7841.152045 1.12583145 1.129923034 1.102869314 1.321200708 1.46622793 1.703875402 1.685422468 1.671049431 1.113852318 1 12.93684992 -8.803634743 1.120738721 1.061244289 1.711623851 0.97061871 0.045023719 0.063700721 0.156920312 0.009052354 0.025313918 1.57E-09 8.803634743 0.650379561 TSLDIEEYS(ph)DTEVQK ddPTM_HeLa_Romidepsin_16h_R1 3 TSLDIEEYSDTEVQK 15 0 P51580 P51580 TPMT Thiopurine S-methyltransferase 1 0 TSLDIEEYS(0.996)DT(0.004)EVQK;TSLDIEEYS(1)DTEVQK;TSLDIEEYS(0.799)DT(0.201)EVQK ;; 277.41 1.91E-99 92832000 13449.5 13911.7 13896.5 13113.4 18216.4 19558.3 16685.2 20464.9 14763.5 13844.8 TRUE FALSE FALSE 13285.57232 14107.54928 14138.36275 14629.63301 17286.74913 18308.58775 18102.44047 21057.01959 13443.01558 13485.1101 0.985203103 1.046157515 1.048442515 1.084873086 1.28191383 1.357689156 1.342402126 1.561501496 0.996878445 1 13.71907968 -8.285881374 0.680462736 0.989584068 1.560923702 0.947200035 0.043666281 0.166048335 0.107735623 0.007685486 0.056653591 5.18E-09 8.285881374 0.571339634 TSLEASMEAS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TSLEASMEASPK 12 0 A0A0A0MRP0;Q8IWC1-2;Q8IWC1-4;Q8IWC1;Q8IWC1-3 A0A0A0MRP0 MAP7D3 MAP7 domain-containing protein 3 1 0 TSLEAS(0.002)MEAS(0.998)PK;TSLEAS(0.109)MEAS(0.891)PK ; 105.25 0.017938 166373000 16834.8 17140.9 16198.9 14267.9 12505.4 11341.5 9213.6 10168.5 17465.3 16132.9 TRUE FALSE FALSE 16629.61098 17382.21004 16480.83506 15917.62173 11867.20277 10616.81475 9996.202954 10462.7095 15903.15983 15713.76493 1.058283044 1.106177298 1.048815171 1.012973135 0.755210659 0.675637875 0.636143088 0.665830853 1.012052802 1 13.93974126 -8.679180751 2.716000698 1.037535247 0.659591245 0.973265797 0.029280898 0.036828096 0.55006317 0.005481271 0.011803194 2.09E-09 8.679180751 -0.377944003 TSLPTVGPSGLYS(ph)PSTNR ddPTM_HeLa_Romidepsin_16h_R1 2 TSLPTVGPSGLYSPSTNR 18 0 Q6VMQ6-2;Q6VMQ6-5;Q6VMQ6;Q6VMQ6-4 Q6VMQ6-2 ATF7IP Activating transcription factor 7-interacting protein 1 1 0 TSLPTVGPS(0.347)GLY(0.018)S(0.622)PS(0.005)T(0.008)NR;TSLPTVGPSGLYS(0.983)PS(0.001)T(0.016)NR ; 226.79 2.06E-38 30105000 3488.3 3336.7 3302.1 3086.3 3421.3 3265.7 2646.47 2821 3967.4 3484 TRUE FALSE FALSE 3445.783258 3383.67415 3359.571665 3443.152527 3246.698294 3057.03231 2871.261096 2902.621184 3612.545807 3393.485178 1.015411318 0.997108864 0.990006288 1.014636089 0.956744504 0.900853297 0.846109809 0.855351072 1.064553289 1 11.728552 -8.237811122 1.594367444 1.00601108 0.847197175 0.907581944 0.021090343 0.042027225 0.199462029 0.001553783 0.005732779 5.78E-09 8.237811122 -0.158813905 TSLQGLTGTPLVAGS(ph)PIR ddPTM_HeLa_Romidepsin_16h_R1 1 TSLQGLTGTPLVAGSPIR 18 0 Q96A47 Q96A47 ISL2 Insulin gene enhancer protein ISL-2 1 0 TSLQGLTGTPLVAGS(1)PIR 120.4 2.62E-06 0 724.13 886.01 760.32 580.42 1151.5 1168 1100.4 1122.5 1136.6 919.17 TRUE FALSE FALSE 715.304025 898.483272 773.5530507 647.5308914 1092.734658 1093.36857 1193.867949 1154.977766 1034.939649 895.2898309 0.798963643 1.003566936 0.864025284 0.723263986 1.220537328 1.22124538 1.333498837 1.290060187 1.155982804 1 9.806210989 -8.651399255 6.441681856 0.8966576 1.275381803 0.669409981 0.117189999 0.076005494 4.055853354 0.014552593 0.029262745 2.23E-09 8.651399255 0.378724203 TSLS(ph)FQDPK ddPTM_HeLa_Romidepsin_16h_R1 2 TSLSFQDPK 9 0 P48681 P48681 NES Nestin 1 0 T(0.127)S(0.005)LS(0.869)FQDPK;TSLS(0.999)FQDPK ; 107.11 0.021869 44654000 14952.3 14384.6 14698.4 9203.8 17143.8 18972 15085.4 16354 13787.6 13553 TRUE FALSE FALSE 14770.05562 14587.10678 14954.21949 10267.98666 16268.88791 17759.75043 16366.7535 16827.17719 12554.40252 13200.89111 1.118868075 1.10500925 1.132818941 0.777825268 1.232408311 1.345344817 1.23982187 1.274700098 0.951026898 1 13.6883477 -8.545250119 24.99687126 1.048692929 1.283098053 0.594515249 0.10308745 125.6164838 140358.3239 0.014258664 0.028518867 2.85E-09 8.545250119 0.234405124 TSLSPT(ph)SK ddPTM_HeLa_Romidepsin_16h_R1 1 TSLSPTSK 8 0 Q8NDI1-3;Q8NDI1-2;Q8NDI1;H7C0Q4 Q8NDI1-3 EHBP1 EH domain-binding protein 1 1 0 T(0.003)SLS(0.07)PT(0.927)SK 140.11 0.018517 24068000 3433.2 3150.3 4707.1 3389.9 3837.3 3861.7 4105.4 1834.2 3991.4 3940.1 TRUE FALSE FALSE 3391.354838 3194.650006 4789.025101 3781.856188 3641.468262 3614.949833 4454.112574 1887.269683 3634.399187 3837.735634 0.883686413 0.832430973 1.2478778 0.985439475 0.948858548 0.941948633 1.160609536 0.491766464 0.947016557 1 11.90603962 -7.246657186 24.7440193 0.970240094 0.491766074 0.608721295 0.119465361 1274.508096 2133369.721 0.016312216 0.49233758 5.67E-08 7.246657186 -0.47847402 TSMPS(ph)GDESIDEK ddPTM_HeLa_Romidepsin_16h_R1 1 TSMPSGDESIDEK 13 0 Q03468 Q03468 ERCC6 DNA excision repair protein ERCC-6 1 0 T(0.022)S(0.011)MPS(0.965)GDES(0.001)IDEK 93.228 0.026657 7649400 4530.4 5248 3542.4 2821 4162.5 4160.3 4893.6 4148.4 5657 4589.8 TRUE FALSE FALSE 4475.181742 5321.881482 3604.053986 3147.177293 3950.072093 3894.470257 5309.262262 4268.427409 5151.023752 4470.556334 1.001034638 1.190429352 0.806175723 0.703978892 0.883575063 0.871137721 1.187606612 0.954786628 1.152210903 1 12.12623866 -9.730939918 24.99998827 1.014747953 0.903094611 0.250578877 0.135730415 315.6780646 258756.5233 0.021292401 0.030109944 1.86E-10 9.730939918 -0.111653342 TSNSLTEDS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 TSNSLTEDSK 10 0 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0;H7C3N7 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 TSNS(0.245)LT(0.023)EDS(0.732)K;TSNS(0.012)LT(0.034)EDS(0.954)K ; 123.67 0.010014 43516000 5270.4 5202.8 6400.4 4471 5244.8 6476.8 9095.2 2514.2 7251.6 5996.9 TRUE FALSE FALSE 5206.162338 5276.045155 6511.796277 4987.958057 4977.138285 6062.953383 9867.746061 2586.94441 6602.998734 5841.099673 0.891298322 0.903262305 1.114823688 0.85394161 0.852089258 1.037981497 1.689364437 0.442886538 1.130437606 1 12.51202429 -7.998481676 24.99978887 0.944033668 1.140512221 0.005606154 0.295969916 96.31545455 1585735.094 0.035103074 0.104213065 1.00E-08 7.998481676 0.196478554 TSNTLEKDLDLLASVPS(ph)PSSSGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSNTLEKDLDLLASVPSPSSSGSR 24 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 0 TSNTLEKDLDLLAS(0.023)VPS(0.531)PS(0.094)S(0.125)S(0.116)GS(0.11)R 79.407 0.00011946 16594000 2767 1939.4 1708.6 6070.1 3853.5 3554 3953.7 4219.2 2327.9 1795.4 TRUE FALSE FALSE 2733.27474 1966.702924 1738.337466 6771.953523 3656.841516 3326.91087 4289.527179 4341.275895 2119.686794 1748.755249 1.562983008 1.124630176 0.994042744 3.872442142 2.091111102 1.902445109 2.452903104 2.482494847 1.212111755 1 10.77211267 -9.313805012 24.99998517 1.241234871 2.491705965 0.640588223 0.515072432 174.777529 83440.48794 0.079424346 0.121322758 4.86E-10 9.313805012 1.250471095 TSNTLEKDLDLLASVPSPSSSGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TSNTLEKDLDLLASVPSPSSSGSR 24 1 A0A087WV97;Q8WU79-3;Q8WU79-2;Q8WU79 A0A087WV97 SMAP2 Stromal membrane-associated protein 2 1 0 TSNTLEKDLDLLAS(0.22)VPS(0.168)PS(0.12)S(0.054)S(0.072)GS(0.365)R 58.903 0.0029434 20629000 1480.1 1369.2 1046.7 3687.6 2324.5 2647.8 2183.2 2642.5 1666.9 1279.8 TRUE FALSE FALSE 1462.059972 1388.475634 1064.917374 4113.977663 2205.872091 2478.614125 2368.640954 2718.956568 1517.808289 1246.550612 1.172884565 1.1138542 0.854291326 3.300289314 1.76958085 1.988378252 1.900156265 2.181184256 1.21760663 1 10.28372574 -9.302684209 24.99998098 1.07114111 2.170938668 0.671222632 0.403607743 215.0761672 130364.8684 0.057553278 0.087914586 4.98E-10 9.302684209 1.099797558 TSPDTLRR ddPTM_HeLa_Romidepsin_16h_R1 2 TSPDTLRR 8 1 Q01130-2;Q01130;J3QL05;J3KP15 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 0 0 ; ; 104.06 0.017806 6768300 6022.9 5820.7 6763.1 5940.7 7217.4 8339.3 8384.8 3697.8 7526.4 6194.5 FALSE FALSE TRUE 5949.490578 5902.643967 6880.808919 6627.591686 6849.069146 7806.445644 9097.004703 3804.790009 6853.219934 6033.565997 0.986065385 0.978301053 1.140421588 1.0984535 1.135161056 1.293836124 1.507732692 0.63060386 1.135849005 1 12.55879521 -9.7193155 5.199527177 0.991964231 1.158517458 0.044997935 0.210782068 0.289379382 18.09497683 0.0301764 0.04237038 1.91E-10 9.7193155 0.166553227 TSPS(ph)SPAPLPHQEATPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSSPAPLPHQEATPR 17 0 P04920-2;P04920-3;P04920 P04920-2 SLC4A2 Anion exchange protein 2 1 0 T(0.059)S(0.365)PS(0.46)S(0.116)PAPLPHQEATPR 106.39 0.0010223 3154100 468.16 706.42 586.53 466.29 674.4 778.48 488.23 884.93 922.89 1021 TRUE FALSE FALSE 462.4538858 716.3649993 596.7383086 520.2046438 639.9828515 728.7376404 529.700244 910.5340534 840.344407 994.4742728 0.465023479 0.720345432 0.600054044 0.523095125 0.643538872 0.73278682 0.532643487 0.915593373 0.845013722 1 9.957790239 -12.47700761 1.193937185 1.001772484 0.620456334 0.401952017 0.130930303 0.274968818 0.696035953 0.086677489 0.020853959 3.33E-13 12.47700761 -0.38131615 TSPSGGTWSSVVSGVPRLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 TSPSGGTWSSVVSGVPRLSPK 21 1 Q99700;H0YH87;A0A5F9ZHW5;A0A5F9ZHX3;A0A2R8Y5A6;A0A2R8Y7E6;A0A5F9ZI57;V9GY86;F8VQP2;A0A5F9ZHH4;A0A2R8YDM9;A0A2R8Y7P6;Q99700-5;Q99700-2;Q99700-4 Q99700 ATXN2 Ataxin-2 1 0 TSPSGGTWSSVVSGVPRLS(1)PK 95.223 0.00028442 52233000 1337.3 1446.5 908.05 1489.2 1283.5 925.96 849.97 887.58 1375.6 1038.5 TRUE FALSE FALSE 1321.000473 1466.863865 923.8542293 1661.388311 1217.998206 866.7941444 922.1664306 913.2607269 1252.562891 1011.51962 1.305956352 1.450158589 0.91333298 1.642467707 1.204127118 0.85692272 0.911664403 0.902860121 1.238298166 1 9.982308589 -8.264672316 23.70218821 1.195066024 0.892600594 0.386124116 0.199663252 129.9087464 952433.8317 0.030457367 0.070930759 5.44E-09 8.264672316 -0.30246543 TSQEELLAEVVQGQS(ph)RTPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSQEELLAEVVQGQSRTPR 19 1 Q6PJT7;Q6PJT7-5;H0YJA2;Q6PJT7-2;Q6PJT7-9;Q6PJT7-3;Q6PJT7-11;Q6PJT7-4;Q6PJT7-10;G3V256;G3V5I6;A0A087WTC9 Q6PJT7 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 0 TSQEELLAEVVQGQS(0.5)RT(0.5)PR 81.312 0.003036 3005700 1145 1258.4 1023.6 1065.8 1300.1 965.42 853.11 1013.2 982.29 1054.9 TRUE FALSE FALSE 1131.0443 1276.115788 1041.415329 1189.032811 1233.751046 903.7327778 925.5731421 1042.515343 894.4315222 1027.493546 1.100779955 1.241969639 1.013549265 1.157216817 1.200738487 0.879550807 0.90080677 1.014619846 0.870498434 1 10.00491362 -8.242748647 24.98278553 1.078215341 0.928573898 0.299805353 0.10611392 704.7376895 941979.7701 0.012947069 0.032947243 5.72E-09 8.242748647 -0.149641442 TSQEELLAEVVQGQSRT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 TSQEELLAEVVQGQSRTPR 19 1 Q6PJT7;Q6PJT7-5;H0YJA2;Q6PJT7-2;Q6PJT7-9;Q6PJT7-3;Q6PJT7-11;Q6PJT7-4;Q6PJT7-10;G3V256;G3V5I6;A0A087WTC9 Q6PJT7 ZC3H14 Zinc finger CCCH domain-containing protein 14 1 0 TSQEELLAEVVQGQS(0.266)RT(0.734)PR 74.278 0.0069768 2417300 983.4 1040.8 753.7 1147.6 1017.4 1007.3 993.68 923.03 1098.3 1066.6 TRUE FALSE FALSE 971.4139425 1055.45241 766.8178323 1280.290912 965.4782816 942.9367809 1078.083154 949.7364167 1000.065297 1038.889578 0.935050233 1.015942822 0.738112932 1.232364766 0.929336767 0.90763908 1.037726412 0.91418418 0.962629059 1 10.02082661 TSQLGDS(ph)PFYPGK ddPTM_HeLa_Romidepsin_16h_R1 2 TSQLGDSPFYPGK 13 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 1 0 T(0.019)S(0.004)QLGDS(0.964)PFY(0.013)PGK;TSQLGDS(0.998)PFY(0.002)PGK ; 156.96 0.00062426 86614000 10240.2 9221.4 9698.5 8826.6 11974 13118 11253.1 11999.1 10536.5 9956.3 TRUE FALSE FALSE 10115.3885 9351.219111 9867.298324 9847.173022 11362.9221 12279.80214 12208.93803 12346.27503 9594.089051 9697.633891 1.043077994 0.964278423 1.017495446 1.015420167 1.171721084 1.266267862 1.258960502 1.27312241 0.98932267 1 13.24341707 -8.596936467 2.580023339 1.014863487 1.265141911 0.966852236 0.02199145 0.038337952 0.514459634 0.003595257 0.008161489 2.53E-09 8.596936467 0.250278424 TSQVGAASAPAKES(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 7 TSQVGAASAPAKESPR 16 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR;TSQVGAAS(0.002)APAKES(0.998)PR;TSQVGAASAPAKES(1)PR;TSQVGAASAPAKES(1)PR ;;;;;; 208.4 1.46E-18 2827014300 47556.5 52858.2 44711.9 44359.9 36047.3 30995.8 28461.5 29355.7 49978.8 49029.2 TRUE FALSE FALSE 46976.86309 53602.33913 45490.09186 49489.00036 34207.67177 29015.26841 30879.0191 30205.06086 45508.57095 47755.41432 0.983697111 1.122434804 0.952564071 1.036301351 0.71630981 0.607580707 0.64660771 0.632495002 0.952951024 1 15.54337669 -8.670030696 4.094847329 1.002613878 0.634970584 0.930699372 0.048071868 0.036277497 1.133846963 0.006458333 0.013236951 2.14E-09 8.670030696 -0.367643294 TSQVGAASAPAKES(ph)PRK ddPTM_HeLa_Romidepsin_16h_R1 1 TSQVGAASAPAKESPRK 17 2 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;A0A2R8Y857;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 TSQVGAASAPAKES(1)PRK 76.158 0.0085247 78607000 4380.2 4808.6 4603.1 5198.9 3521.5 2894.6 2865.1 2727.2 4818.3 4643.9 TRUE FALSE FALSE 4326.812438 4876.295597 4683.215025 5800.02128 3341.784714 2709.644402 3108.461522 2806.107229 4387.33918 4523.250809 0.956571417 1.078051119 1.035364879 1.282268334 0.738801551 0.599048011 0.687218475 0.620374007 0.969952666 1 12.14314428 -8.560747699 12.25181546 1.010846712 0.645396556 0.806134888 0.093833507 0.310010519 99.80355144 0.01386213 0.02774293 2.75E-09 8.560747699 -0.365450156 TSRDT(ph)SPSSGSAVSSSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSRDTSPSSGSAVSSSK 17 1 F8WF16;B7Z8L1;F8W6A0;F8W0Q9;Q8NEY8-7;Q8NEY8-5;Q8NEY8-6;Q8NEY8-9;Q8NEY8-8;Q8NEY8-2;Q8NEY8-3;Q8NEY8 F8WF16 PPHLN1 Periphilin-1 1 0 T(0.082)S(0.092)RDT(0.409)S(0.409)PS(0.003)S(0.003)GS(0.001)AVSSSK 64.295 0.024554 1509900 806.32 661.77 513.85 3503.2 812.2 526.74 758.37 659.21 814.1 619.69 TRUE FALSE FALSE 796.4922617 671.0864154 522.7933437 3908.256467 770.7504033 493.083014 822.7859289 678.2832013 741.284857 603.5903645 1.31959075 1.111824268 0.866139313 6.475014674 1.276942855 0.816916642 1.363152855 1.123747563 1.22812573 1 9.237425965 TSRPENAIIYNNNEDFQVGQAK ddPTM_HeLa_Romidepsin_16h_R1 1 TSRPENAIIYNNNEDFQVGQAK 22 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 60.561 0.015204 13613000 1201.1 1011.9 1159.1 968.5 1137.7 1233.7 1119.1 1109 1045.2 1126.9 FALSE FALSE TRUE 1186.460531 1026.145555 1179.273649 1080.482527 1079.638924 1154.870552 1214.156326 1141.087165 951.7146942 1097.622976 1.080936312 0.934879806 1.074388634 0.984384029 0.983615456 1.052155956 1.106168833 1.039598469 0.867068853 1 10.10016687 -8.002609442 24.89312976 1.026260764 1.074453346 0.063222377 0.067439526 144.4083615 1377663.933 0.006698745 0.019628668 9.94E-09 8.002609442 0.048192582 ADY(ph)DTLSLR ddPTM_HeLa_Romidepsin_16h_R1 2 ADYDTLSLR 9 0 E9PKC4;Q9Y446;Q9Y446-2;E9PJR7;E9PRW6;E9PK71;E9PQ15 E9PKC4 PKP3 Plakophilin-3 1 0 ADY(0.998)DT(0.002)LSLR;ADY(1)DTLSLR ; 204.62 2.66E-10 11563500 4474.5 4704.8 4156.3 4075.1 3080.5 2320.1 1715.39 1572.16 5301.6 4461 TRUE FALSE FALSE 4419.963073 4771.034298 4228.638658 4546.282236 2923.29059 2171.853098 1861.095184 1617.647969 4827.411618 4345.102577 1.017228706 1.0980257 0.973196509 1.046300324 0.672778269 0.499839315 0.428320195 0.372292239 1.111000611 1 12.08517452 -8.510345197 1.992210829 1.017324868 0.415862083 0.961366085 0.055104052 0.035832079 0.280682922 0.00664801 0.017241427 3.09E-09 8.510345197 -0.601462785 down TSS(ph)EDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 4 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 1 0 T(0.318)S(0.047)S(0.635)EDNLYLAVLR;T(0.014)S(0.002)S(0.983)EDNLYLAVLR;T(0.321)S(0.048)S(0.631)EDNLYLAVLR;T(0.191)S(0.191)S(0.618)EDNLYLAVLR ;;; 255.39 9.01E-66 2300840200 10258.75 10931.41 9471.01 9361.45 8986.97 9295.71 8782.67 8706.17 10258.98 9611.1 TRUE FALSE FALSE 10133.71241 11085.30268 9635.848956 10443.8649 8528.331386 8701.744132 9528.669771 8958.069293 9341.391135 9361.402236 1.082499411 1.18414981 1.029316839 1.115630397 0.911010036 0.929534263 1.017867786 0.956915328 0.997862382 1 13.19250893 -8.756501207 24.99988474 1.055953067 0.956670307 0.469177789 0.058721119 103.9512838 526254.9767 0.009207841 0.017957352 1.75E-09 8.756501207 -0.09928276 TSS(ph)FAEPGGGGGGGGGGPGGSASGPGGTGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSFAEPGGGGGGGGGGPGGSASGPGGTGGGK 32 0 P49840 P49840 GSK3A Glycogen synthase kinase-3 alpha 1 0 T(0.273)S(0.273)S(0.454)FAEPGGGGGGGGGGPGGSASGPGGTGGGK 100.33 7.27E-13 8021300 5027 4666.9 5485.2 5490.3 5128.6 6332.4 5551.2 7171.4 5816.6 6005 TRUE FALSE FALSE 4965.72899 4732.600741 5580.667605 6125.114319 4866.868405 5927.780077 6022.718789 7378.893144 5296.348728 5848.989234 0.848989251 0.809131382 0.954125129 1.047209026 0.832087085 1.013470848 1.029702492 1.26156723 0.905515212 1 12.51397162 -6.639852641 0.987411974 0.922685566 2.031302985 0.66848374 0.073120877 2.900881991 0.918556238 0.012691173 4.598051246 2.29E-07 6.639852641 1.108617419 TSS(ph)FTEQLDEGTPNR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSFTEQLDEGTPNR 15 0 Q86W71;C9J0Y3;C9JHJ5;Q13439-3;Q13439-4;Q13439;Q13439-5;E7EVX2 Q86W71;Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 T(0.176)S(0.176)S(0.538)FT(0.111)EQLDEGTPNR;T(0.001)SS(0.988)FT(0.011)EQLDEGTPNR ; 290.37 2.82E-116 60604000 5257.15 4677.25 5627.55 4252.4 4908.67 4899.91 4109.1 5499.63 5514.76 5088.5 TRUE FALSE FALSE 5193.073834 4743.096448 5725.495147 4744.082496 4658.162253 4586.821565 4458.126851 5658.753117 5021.506054 4956.300036 1.047772289 0.956983317 1.155195429 0.957182265 0.939846704 0.925452763 0.899486879 1.141729329 1.013156188 1 12.27504781 TSS(ph)IADEGTYTLDSILR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSIADEGTYTLDSILR 17 0 E7ERV5;A0A087WY00;G3V394;F8WE88;F8W6H6;Q9Y4I1-2;Q9Y4I1;Q9Y4I1-3 E7ERV5 MYO5A Unconventional myosin-Va 1 0 T(0.363)S(0.071)S(0.567)IADEGTYTLDSILR 158.65 4.33E-05 20744000 2034.4 1877 2150.2 2258.9 2377.5 2300.5 1863.9 2364.6 2278.8 2554.9 TRUE FALSE FALSE 2009.60395 1903.424455 2187.623329 2520.084646 2256.167303 2153.505475 2022.219619 2433.01597 2074.978421 2488.52333 0.807548769 0.764881097 0.879084919 1.012682749 0.906628954 0.865374838 0.812618309 0.97769466 0.833819155 1 11.2810742 -12.51057597 1.300288184 0.999060761 0.869386398 0 0.087863143 0.458665943 1.403864252 0.051475894 0.012807089 3.09E-13 12.51057597 -0.129674362 TSS(ph)KES(ph)SPIPSPT(ph)SDR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSKESSPIPSPTSDR 16 1 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 3 0 T(0.258)S(0.08)S(0.619)KES(0.522)S(0.522)PIPS(0.073)PT(0.823)S(0.104)DR 115.53 0.0061805 27076000 1836.7 2178.8 1870.4 1614.1 1930.4 1799.5 1488.6 2127.4 2387 2200.1 TRUE FALSE FALSE 1814.313594 2209.473204 1902.953527 1800.729837 1831.884485 1684.517758 1615.041647 2188.952963 2173.500742 2142.941085 0.846646512 1.031047106 0.888010194 0.840307673 0.854845939 0.786077494 0.753656579 1.021471368 1.014260615 1 11.06537647 -9.524094611 24.98714102 0.93456752 0.844598745 0.276636828 0.08412691 51.3080604 1054417.787 0.01369794 0.019461886 2.99E-10 9.524094611 -0.089968776 TSS(ph)KES(ph)SPIPSPTSDRK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSKESSPIPSPTSDRK 17 2 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 0 T(0.112)S(0.133)S(0.756)KES(0.786)S(0.212)PIPSPTSDRK 76.817 0.0027369 0 4406.7 4273.6 3471 2451.1 3637.5 3438.1 2942.5 3399.9 4636.8 4589.5 TRUE FALSE FALSE 4352.989445 4333.763853 3531.411299 2734.507715 3451.864802 3218.416506 3192.435877 3498.270742 4222.072995 4470.264128 0.973765603 0.96946483 0.78997822 0.611710547 0.772183634 0.719961151 0.714149273 0.782564663 0.944479537 1 12.12614436 -9.698709707 3.524442148 0.986998438 0.720903342 0.870328369 0.045897088 0.048440196 1.218030478 0.00664144 0.009419052 2.00E-10 9.698709707 -0.266095096 TSS(ph)KESS(ph)PIPSPTSDRK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSKESSPIPSPTSDRK 17 2 A0A087WUZ3;Q01082 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 2 0 T(0.015)S(0.025)S(0.959)KES(0.016)S(0.986)PIPSPTSDRK 115.74 0.0021055 11316000 1965.8 1743.3 1866.8 1734.9 1719.6 1417.4 1325.8 1751.5 2316 1850.7 TRUE FALSE FALSE 1941.840073 1767.842223 1899.290871 1935.497301 1631.842395 1326.832714 1438.413419 1802.176889 2108.851159 1802.618547 1.077232938 0.980707885 1.05362883 1.073714294 0.90526218 0.736058506 0.797957738 0.999754991 1.169882093 1 10.81587842 -8.604903266 4.695285784 1.036076134 0.83688517 0.595072098 0.080171954 0.096732461 3.868940436 0.009900636 0.020339227 2.48E-09 8.604903266 -0.199190964 TSS(ph)LDTITGPYLTGQWPR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSLDTITGPYLTGQWPR 18 0 Q86VQ1;H7C0Q2;H7C2L5 Q86VQ1 GLCCI1 Glucocorticoid-induced transcript 1 protein 1 0 TSS(1)LDTITGPYLTGQWPR;TS(0.074)S(0.926)LDTITGPYLTGQWPR ; 293.42 4.13E-124 163796000 2124.8 2037.2 2034.56 2107.97 1732.88 1821.73 1357.15 1801.09 2189.95 2014.81 TRUE FALSE FALSE 2098.90212 2065.879755 2069.970663 2351.70341 1644.444667 1705.327332 1472.426287 1853.201698 1994.075387 1962.464946 1.069523369 1.052696386 1.054780962 1.198341614 0.837948556 0.868972124 0.750294312 0.944323465 1.016107519 1 10.93845117 -8.73052141 24.99994473 1.047424063 0.844562812 0.702502977 0.067863469 88.11895551 71251.71869 0.009668119 0.019334673 1.86E-09 8.73052141 -0.202861251 TSS(ph)LDTLAAPYLAGHWPR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSLDTLAAPYLAGHWPR 18 0 Q6P1L5;Q6P1L5-2 Q6P1L5 FAM117B Protein FAM117B 1 0 T(0.022)S(0.004)S(0.974)LDTLAAPYLAGHWPR 173.19 1.52E-07 8817100 850.76 849.63 1061.8 772.92 632.64 1006.7 712.12 808.35 1086.9 959.02 TRUE FALSE FALSE 840.3906099 861.5911134 1080.280184 862.2886471 600.3540201 942.375119 772.607455 831.7383319 989.6849418 934.1045221 0.899675133 0.922371205 1.156487479 0.923117945 0.6427054 1.008854038 0.827110282 0.890412488 1.059501285 1 9.86744018 -8.989399963 24.99867254 0.96592838 0.844314651 0.29834452 0.11075051 249.9140273 589382.3996 0.015445431 0.027978265 1.02E-09 8.989399963 -0.121613728 TSS(ph)LTQFPPSQSEER ddPTM_HeLa_Romidepsin_16h_R1 6 TSSLTQFPPSQSEER 15 0 B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4 B7Z7F3 RANBP3 Ran-binding protein 3 1 0 T(0.013)S(0.013)S(0.971)LT(0.004)QFPPSQSEER;T(0.004)S(0.036)S(0.96)LTQFPPSQSEER;T(0.011)S(0.011)S(0.946)LT(0.033)QFPPSQSEER;T(0.129)S(0.02)S(0.849)LT(0.002)QFPPSQSEER;T(0.005)S(0.005)S(0.987)LT(0.002)QFPPSQSEER;T(0.045)S(0.076)S(0.879)LT(0.001)QFPPSQSEER ;;;;; 225.29 1.00E-34 44367300 10580.2 9921.15 10110.79 9386.97 8463.59 8498.04 7367.04 8617.47 12161.8 10565.31 TRUE FALSE FALSE 10451.24445 10060.82021 10286.76406 10472.33564 8031.66142 7955.04267 7992.796194 8866.802898 11074.01815 10290.82172 1.015588914 0.97764984 0.999605701 1.017638428 0.780468425 0.773023077 0.776691736 0.861622438 1.076106306 1 13.32907057 -8.761703304 24.99997186 1.005052881 0.794652247 0.906068652 0.034059835 1.09201997 103456.6616 0.003624166 0.006880701 1.73E-09 8.761703304 -0.210400635 TSS(ph)PHSETQGWK ddPTM_HeLa_Romidepsin_16h_R1 2 TSSPHSETQGWK 12 0 H7C1N2;J3KR05;O75128-2;O75128-3;O75128;O75128-7;O75128-6 H7C1N2 COBL Protein cordon-bleu 1 0 TS(0.001)S(0.999)PHSETQGWK;T(0.012)S(0.017)S(0.955)PHS(0.005)ET(0.011)QGWK ; 225.79 3.45E-29 12932800 2194.3 1972.29 1799.43 2149.3 2672.8 2423.2 2200.5 2274.8 2393.24 2298.1 TRUE FALSE FALSE 2167.555028 2000.05595 1830.748324 2397.812179 2536.397042 2268.365341 2387.410415 2340.617749 2179.18262 2238.395031 0.968352323 0.893522333 0.817884377 1.071219399 1.133132002 1.013389196 1.066572425 1.045667863 0.973546935 1 11.12824895 TSS(ph)PLFNK ddPTM_HeLa_Romidepsin_16h_R1 2 TSSPLFNK 8 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 T(0.318)S(0.047)S(0.634)PLFNK;T(0.035)S(0.064)S(0.901)PLFNK ; 136.99 0.0092027 213270000 19805.9 19446.4 17929.4 18173.6 18291.9 16606.2 14557.3 14549.8 19321.7 18067.9 TRUE FALSE FALSE 19564.49807 19720.16693 18241.45369 20274.91714 17358.39609 15545.11741 15793.7967 14970.77551 17593.51876 17598.49335 1.111714377 1.120559956 1.036534965 1.152082552 0.986356942 0.883320924 0.897451639 0.850685068 0.999717328 1 14.1031643 -8.421495273 3.43512002 1.064712604 0.879101215 0.754141019 0.049071398 0.104487973 2.293143095 0.00801974 0.018958475 3.79E-09 8.421495273 -0.18561139 TSS(ph)PSSTGSVSLGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSPSSTGSVSLGR 14 0 D6RAL0;F5GYR0;Q6H8Q1-4;Q6H8Q1-6;Q6H8Q1-8;Q6H8Q1-3;Q6H8Q1-7;Q6H8Q1-2;Q6H8Q1-5;Q6H8Q1;Q6H8Q1-9 D6RAL0 ABLIM2 Actin-binding LIM protein 2 1 0 T(0.042)S(0.006)S(0.864)PS(0.015)S(0.015)T(0.015)GS(0.042)VSLGR;T(0.05)S(0.084)S(0.843)PS(0.018)S(0.002)T(0.002)GS(0.001)VSLGR ; 194.86 2.08E-11 28090000 3099.6 2720.2 2895.7 2929.3 6548.5 7453.2 7905.7 7635.4 2977.79 3072.8 TRUE FALSE FALSE 3061.820883 2758.495047 2946.098444 3267.999449 6214.305609 6976.964574 8577.209961 7856.318252 2711.449004 2992.968213 1.023004812 0.921658651 0.984340038 1.091892468 2.076301907 2.331118835 2.865787189 2.624925389 0.905939793 1 11.54736124 -8.558253682 1.707631339 0.993860936 2.696421671 0.973119352 0.123597483 0.035526787 0.205172075 0.016973953 0.045486958 2.77E-09 8.558253682 1.702560736 up TSS(ph)TDEVLSLEEK ddPTM_HeLa_Romidepsin_16h_R1 3 TSSTDEVLSLEEK 13 0 K7ENH8;A0A0A0MRB7;P15923-2;K7EMM4 K7ENH8 TCF3 Transcription factor E2-alpha 1 0 T(0.002)SS(0.994)T(0.003)DEVLSLEEK;TSS(0.998)T(0.002)DEVLSLEEK;TSS(0.997)T(0.003)DEVLSLEEK ;; 335.2 4.22E-195 63630000 17909.1 17860.7 17564.5 12923.4 11611.6 10534 8309.7 9488.9 20572.6 16851.3 TRUE FALSE FALSE 17690.817 18112.1434 17870.20275 14417.66431 11019.01672 9860.911397 9015.525711 9763.44635 18732.53513 16413.5008 1.077821071 1.103490573 1.088750229 0.878402755 0.671338605 0.600780511 0.549275004 0.594842409 1.141288221 1 14.00259536 -8.836273848 2.068694567 1.047383039 0.580909335 0.960749643 0.045465382 0.042730585 0.372092818 0.00684565 0.014451623 1.46E-09 8.836273848 -0.466473704 TSS(ph)TLDSEGTFNSYR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSTLDSEGTFNSYR 15 0 Q92609;Q92609-2;C9JNM0;C9JED7;F2Z3C3;C9K0P2;C9J397;C9JWX0;C9JW04;C9JDR8 Q92609 TBC1D5 TBC1 domain family member 5 1 0 T(0.001)S(0.004)S(0.992)T(0.004)LDSEGTFNSYR;T(0.071)S(0.071)S(0.429)T(0.429)LDSEGTFNSYR ; 141.06 0.00072217 7624600 1350.99 1529.96 1698.58 1659.95 2180.3 2383.4 1871.79 2074.74 2534.3 1850.52 TRUE FALSE FALSE 1334.523614 1551.498817 1728.143072 1851.881229 2069.031155 2231.108432 2030.779796 2134.769329 2307.625861 1802.443224 0.740397033 0.860775417 0.958778091 1.027428329 1.14790365 1.237824528 1.1266817 1.184375353 1.280276588 1 10.8157381 -9.076690307 1.636469394 0.874255611 1.18033352 0.213355853 0.144218929 0.172703786 0.912779898 0.016224294 0.03218476 8.38E-10 9.076690307 0.306077908 TLSEVDY(ph)APAGPAR ddPTM_HeLa_Romidepsin_16h_R1 2 TLSEVDYAPAGPAR 14 0 O15357;A0A0A0MTP6;O15357-2;H0YFZ4 O15357 INPPL1 "Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2" 1 0 TLSEVDY(1)APAGPAR;TLSEVDY(1)APAGPAR ; 257.09 4.98E-66 67179000 4113 3373 3447.5 4330 2592.9 1698.03 1334.79 1162.91 4537.5 3462.5 TRUE FALSE FALSE 4062.869174 3420.485183 3507.502291 4830.654973 2460.574638 1589.531363 1448.167029 1196.556966 4131.654636 3372.543751 1.204689835 1.014215214 1.040016839 1.432347608 0.729590131 0.471315268 0.429399034 0.354793608 1.225085556 1 11.71962144 -8.507552339 3.937866155 1.108768106 0.431991688 0.865253629 0.130046966 0.060400408 2.091552373 0.019375145 0.0430603 3.11E-09 8.507552339 -0.676776418 down TSS(ph)TNEDEDLNPEQKIER ddPTM_HeLa_Romidepsin_16h_R1 1 TSSTNEDEDLNPEQKIER 18 1 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2;B4DZP2 B4DGI9 TCF12 Transcription factor 12 1 0 T(0.166)S(0.166)S(0.628)T(0.04)NEDEDLNPEQKIER 61.616 0.016249 5576900 916.46 703.44 750.12 1095.6 778.1 729.52 980.64 848.57 2082.5 887.72 TRUE FALSE FALSE 905.289833 713.3430468 763.1755239 1222.278427 738.3906535 682.9060264 1063.935537 873.1220341 1896.235984 864.6569064 1.046993121 0.825001271 0.882633931 1.413599334 0.853969532 0.789800002 1.230471334 1.009790158 2.19305018 1 9.755983978 -7.716103682 24.99997771 1.002072295 1.120130198 0 0.415544114 282.4439748 155747.406 0.023011091 0.086098989 1.92E-08 7.716103682 0.118057903 TSS(ph)VPEYVYNLHLVENDFVGGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSVPEYVYNLHLVENDFVGGR 22 0 Q99959-2;Q99959 Q99959-2 PKP2 Plakophilin-2 1 0 T(0.051)S(0.051)S(0.897)VPEY(0.001)VYNLHLVENDFVGGR;T(0.142)S(0.142)S(0.715)VPEYVYNLHLVENDFVGGR ; 143.25 6.49E-06 20750000 1359.96 1266.28 1265.93 1797.25 5240.4 6464.5 5769.4 5288.7 1087.99 1409.03 TRUE FALSE FALSE 1343.384284 1284.106723 1287.962981 2005.056501 4972.962833 6051.439313 6259.452692 5441.72019 990.6774495 1372.423197 0.978841138 0.935649241 0.938459058 1.460960806 3.623490803 4.409309989 4.560876487 3.96504533 0.721845456 1 10.4225097 -8.733499151 2.667531424 0.982056896 4.324627992 0.988511001 0.167477629 0.01603479 0.232928397 0.021122441 0.044470538 1.85E-09 8.733499151 3.342571097 up TSS(ph)VVTLEVAK ddPTM_HeLa_Romidepsin_16h_R1 2 TSSVVTLEVAK 11 0 A8MQ02;J3KN01;P55196;P55196-5;P55196-3;P55196-1;Q5TIG5;P55196-2;P55196-6 A8MQ02 MLLT4 Afadin 1 0 T(0.001)S(0.003)S(0.99)VVT(0.006)LEVAK;T(0.007)S(0.039)S(0.559)VVT(0.394)LEVAK ; 184.87 3.35E-06 14419900 5657.9 5452.8 6118.2 5926.4 6585.8 6379.8 5603.6 5608 5858.4 5463.8 TRUE FALSE FALSE 5588.939339 5529.564662 6224.684705 6611.638253 6249.702051 5972.15137 6079.569644 5770.258632 5334.410031 5321.849688 1.050187372 1.039030598 1.169646846 1.242357195 1.174347721 1.122194673 1.14237906 1.0842581 1.002360146 1 12.37771205 -9.796973421 5.85134251 1.025030186 1.158619268 0.721434001 0.04048583 0.079036551 7.16043793 0.007159297 0.009576985 1.60E-10 9.796973421 0.133589083 TSSAFVGK(ac)TPEASPEPK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSAFVGKTPEASPEPK 17 1 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 1 TSSAFVGK(1)TPEASPEPK 264.92 1.21E-74 726760 146.35 295.21 236.83 283.64 281.69 188.95 178.48 233.6 407.58 245.74 FALSE TRUE FALSE 144.5662299 299.3659741 240.9519268 316.4357914 267.3143082 176.8767048 193.6400867 240.3588474 371.125024 239.3556394 0.603980881 1.250716193 1.006669103 1.322031903 1.116808064 0.738970284 0.809005742 1.004191287 1.550517151 1 7.903011987 -10.26358757 24.98692422 0.812990977 1.028410104 0 0.299837184 260.4210427 3029113.372 0.038433543 0.045105498 5.45E-11 10.26358757 0.215419128 TSSAVST(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSAVSTPSK 10 0 U3KPZ7;Q9P2N5 U3KPZ7 RBM27 RNA-binding protein 27 1 0 TSSAVS(0.005)T(0.856)PS(0.138)K 120.86 0.023297 8480700 4417.2 4799.9 7803.1 4389.6 4469.7 5452.3 7893.5 1411.7 7234.2 6507.1 TRUE FALSE FALSE 4363.361467 4867.473118 7938.909682 4897.146206 4241.59453 5103.915626 8563.973693 1452.545312 6587.155034 6338.044604 0.688439691 0.767977101 1.25258028 0.772658842 0.669227624 0.805282377 1.351201234 0.229178777 1.039303988 1 12.6298221 TSSEDNLYLAVLR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSEDNLYLAVLR 13 0 Q15149-4 Q15149-4 PLEC Plectin 0 0 158.06 0.0057398 3020000 504.14 397.79 484.5 445.97 576.41 607.8 290.73 523.19 723.47 351.42 FALSE FALSE TRUE 497.9953478 403.3900981 492.9325193 497.5351498 546.9936468 568.9635416 315.4245989 538.3276772 658.7610312 342.2900577 1.454892821 1.178503696 1.440101774 1.453548353 1.598041294 1.662226316 0.921512594 1.572723674 1.924569576 1 8.419075578 -12.4552593 0.60045505 0.910582505 1.416509136 0 0.355908096 1.174668948 0.544694076 0.34007932 0.044915469 3.51E-13 12.4552593 0.505926631 TSSESIISVPAS(ph)STSGSPSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSESIISVPASSTSGSPSR 20 0 D6RAL0;F5GYR0;Q6H8Q1-4;Q6H8Q1-6;Q6H8Q1-8;Q6H8Q1-3;Q6H8Q1-7;Q6H8Q1-2;Q6H8Q1-5;Q6H8Q1;Q6H8Q1-9 D6RAL0 ABLIM2 Actin-binding LIM protein 2 1 0 TSSES(0.004)IIS(0.058)VPAS(0.187)S(0.187)T(0.187)S(0.187)GS(0.187)PS(0.003)R 147.49 2.74E-05 5126900 621.45 625.2 543.05 853.15 1465.6 1853.8 1319.4 1767.1 788.08 498.66 TRUE FALSE FALSE 613.8755284 634.001582 552.5015575 951.7952172 1390.804963 1735.348163 1431.469803 1818.22825 717.592151 485.7047413 1.263886218 1.305323025 1.137525559 1.959616895 2.863478251 3.572845837 2.947201625 3.743484664 1.477424637 1 8.923935759 -8.843779195 1.714173396 1.136439413 3.395991976 0.943025626 0.239144902 0.046621479 0.277281649 0.032138941 0.071289707 1.43E-09 8.843779195 2.259552563 up TSSESIISVPASSTSGS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSESIISVPASSTSGSPSR 20 0 D6RAL0;F5GYR0;Q6H8Q1-4;Q6H8Q1-6;Q6H8Q1-8;Q6H8Q1-3;Q6H8Q1-7;Q6H8Q1-2;Q6H8Q1-5;Q6H8Q1;Q6H8Q1-9 D6RAL0 ABLIM2 Actin-binding LIM protein 2 1 0 TSSESIISVPAS(0.003)S(0.003)T(0.01)S(0.034)GS(0.824)PS(0.125)R 185.2 1.36E-13 4437800 563.57 481.33 561.22 736.43 1368.8 1840.6 1596.4 1656.2 677.72 647.03 TRUE FALSE FALSE 556.7009921 488.1061764 570.9877987 821.5795016 1298.945028 1722.9916 1731.998176 1704.119534 617.1030258 630.2200673 0.883343805 0.774501165 0.906013357 1.303639069 2.061097537 2.733952296 2.748243456 2.704007096 0.97918657 1 9.299711883 -8.660488938 1.798309155 0.924454852 2.753765049 0.992054302 0.072112948 0.023772334 0.154979603 0.013102676 0.031983818 2.19E-09 8.660488938 1.829310197 up TSSGDPPS(ph)PLVK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSGDPPSPLVK 12 0 Q99618;F5GX58;F8WDL1 Q99618 CDCA3 Cell division cycle-associated protein 3 1 0 TSSGDPPS(1)PLVK 92.906 0.024544 33537000 5261.7 5397.3 5050.7 3718.6 4279.1 5266.9 3849.4 4037.3 5841 4975.1 TRUE FALSE FALSE 5197.568377 5473.283331 5138.605315 4148.562029 4060.721559 4930.362088 4176.36794 4154.112906 5318.566331 4845.846185 1.072582203 1.129479377 1.06041445 0.856106833 0.837979871 1.017440897 0.861844925 0.857252324 1.09755162 1 12.2425329 -9.265583356 24.88594159 1.045582741 0.889396678 0.704733441 0.058911572 172.029256 1033091.984 0.009466243 0.014784543 5.43E-10 9.265583356 -0.156186063 TSSISGPLS(ph)PAYTGQVPYNYNQLEGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSISGPLSPAYTGQVPYNYNQLEGR 26 0 Q01082-3 Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 T(0.012)S(0.012)S(0.011)IS(0.155)GPLS(0.629)PAY(0.142)T(0.037)GQVPY(0.001)NYNQLEGR;T(0.006)S(0.006)S(0.014)IS(0.082)GPLS(0.848)PAY(0.028)T(0.013)GQVPY(0.003)NY(0.001)NQLEGR ; 55.668 0.0025927 18374900 3538.8 3040.4 3129.8 3538.77 4432.4 4957.7 4451.1 4842.8 3943.76 3389.5 TRUE FALSE FALSE 3495.667744 3083.202831 3184.272856 3947.939238 4206.198088 4640.91897 4829.176323 4982.918777 3591.020228 3301.440301 1.058831124 0.933896285 0.964510203 1.195823301 1.274049416 1.405725546 1.462748341 1.509316638 1.08771321 1 11.68887984 -8.629169044 1.287701012 1.015660839 1.483587308 0.933725065 0.052139391 0.077306281 0.250919311 0.008289847 0.024571166 2.35E-09 8.629169044 0.467926469 TSSLAPVVGTTTTTPS(ph)PSAIK ddPTM_HeLa_Romidepsin_16h_R1 1 TSSLAPVVGTTTTTPSPSAIK 21 0 Q92733 Q92733 PRCC Proline-rich protein PRCC 1 0 TSSLAPVVGTTT(0.001)T(0.007)T(0.336)PS(0.641)PS(0.015)AIK 217.26 1.13E-40 0 3143.1 3563.5 2910.3 2934.1 4018.1 3731.5 2882.9 3271.3 3268.2 3131.9 TRUE FALSE FALSE 3104.790688 3613.667047 2960.952551 3273.354447 3813.041363 3493.069193 3127.773454 3365.949904 2975.884007 3050.532787 1.017786369 1.184601937 0.970634561 1.073043523 1.249959148 1.145068563 1.025320386 1.103397387 0.975529265 1 11.57484552 -10.4216633 9.170763296 1.007819967 1.104601825 0.310476735 0.074499989 0.365705112 30.70950583 0.012692316 0.014488558 3.79E-11 10.4216633 0.096781858 TSSPRS(ph)PPSSSEIFTPAHEENVR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSPRSPPSSSEIFTPAHEENVR 23 1 I3L3A7;I3L2L5;I3L317;I3L4Q0;C9JLW8 I3L3A7 FAM195B Protein FAM195B 1 0 T(0.222)S(0.222)S(0.222)PRS(0.285)PPS(0.023)S(0.023)S(0.005)EIFTPAHEENVR;T(0.138)S(0.138)S(0.138)PRS(0.559)PPS(0.014)S(0.01)S(0.003)EIFTPAHEENVR ; 89.659 4.33E-05 12094700 3873.9 3763.86 2973.5 4423.8 3848.7 3338.22 3377.41 3285.67 4658.8 3824.61 TRUE FALSE FALSE 3826.683417 3816.84772 3025.25252 4935.300571 3652.286478 3124.918516 3664.287121 3380.735678 4242.10526 3725.246081 1.027229701 1.02458942 0.812094679 1.324825384 0.980414823 0.838848883 0.98363626 0.907520095 1.138744976 1 11.86312001 -8.515420318 24.9500128 1.022331737 0.916076289 0.183575061 0.126642605 485.3218761 1623502.558 0.016275333 0.033705286 3.05E-09 8.515420318 -0.106255447 TSSS(ph)SPANS(ph)DVEIDGIGR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSSSPANSDVEIDGIGR 18 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 2 0 T(0.345)S(0.007)S(0.051)S(0.413)S(0.193)PANS(0.991)DVEIDGIGR 131.9 0.01574 14484000 2253 2005.1 1674.8 1919.3 1874.4 2209.7 2000.2 1952.9 2228.5 2193.9 TRUE FALSE FALSE 2225.539569 2033.32785 1703.949191 2141.218497 1778.742374 2068.507301 2170.096938 2009.40408 2029.177379 2136.902162 1.041479394 0.951530625 0.797392235 1.002019903 0.832392987 0.967993453 1.015534065 0.940335087 0.949588341 1 11.06130514 -10.1361872 5.406652533 1.019365861 0.927017978 0.152572526 0.068523915 0.207185193 8.363446345 0.010568458 0.013001328 7.31E-11 10.1361872 -0.092347882 TSSS(ph)SPANSDVEIDGIGR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSSSPANSDVEIDGIGR 18 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 TSS(0.004)S(0.498)S(0.498)PANSDVEIDGIGR 308.24 3.61E-164 20238000 1858.5 1970.7 2108.8 1558 2012.9 1793.1 2232.4 2248.7 2223 2076.5 TRUE FALSE FALSE 1835.847887 1998.443566 2145.502779 1738.143291 1910.174202 1678.526697 2422.02 2313.762587 2024.169312 2022.552231 0.907688741 0.988080078 1.060789802 0.859381164 0.944437515 0.829905241 1.197506776 1.143981625 1.000799525 1 10.98196124 -7.745576091 24.99998713 0.950694057 1.170744348 0.637796278 0.066865186 113.1307316 178287.1801 0.009184667 0.034134668 1.80E-08 7.745576091 0.22005029 TSSSS(ph)PANS(ph)DVEIDGIGR ddPTM_HeLa_Romidepsin_16h_R1 1 TSSSSPANSDVEIDGIGR 18 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 2 0 T(0.022)S(0.027)S(0.03)S(0.136)S(0.822)PANS(0.962)DVEIDGIGR 105.01 0.017132 19026000 2367 2235.6 2569.5 2107.9 1879.9 2479.3 2641.1 2968.4 2823.2 2738.5 TRUE FALSE FALSE 2338.150094 2267.072835 2614.22107 2351.625316 1783.961688 2320.880732 2865.434968 3054.285971 2570.685921 2667.353375 0.876580552 0.849933442 0.980080515 0.881632459 0.668813403 0.870106208 1.074261474 1.145062367 0.963759037 1 11.38119325 -7.643120313 4.584319161 0.90930942 1.128173514 0.486281217 0.090380507 0.155954957 5.370348872 0.014261472 0.058341916 2.27E-08 7.643120313 0.218864094 TSSSS(ph)PANSDVEIDGIGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSSSPANSDVEIDGIGR 18 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 T(0.052)S(0.014)S(0.032)S(0.15)S(0.747)PANS(0.005)DVEIDGIGR;TSSS(0.148)S(0.844)PANS(0.007)DVEIDGIGR ; 144.4 9.65E-05 34742000 3971.1 3944 3923.5 3741.6 3817.8 4678.6 4518.6 4216.2 4598.1 4613.4 TRUE FALSE FALSE 3922.698706 3999.523736 3991.786872 4174.221397 3622.96342 4379.652559 4902.409771 4338.189095 4186.83442 4493.543203 0.87296339 0.89006015 0.888338376 0.928937635 0.806259839 0.974654601 1.090989794 0.965427258 0.931744557 1 12.13363776 -7.999612112 24.99968233 0.921155178 1.029361973 0.428563942 0.056428782 12.49263484 804896.3776 0.009338106 0.027647461 1.00E-08 7.999612112 0.108206795 TSSSSPANS(ph)DVEIDGIGR ddPTM_HeLa_Romidepsin_16h_R1 2 TSSSSPANSDVEIDGIGR 18 0 O60293-2;O60293 O60293-2 ZFC3H1 Zinc finger C3H1 domain-containing protein 1 0 T(0.004)SS(0.003)SSPANS(0.992)DVEIDGIGR;TSSS(0.013)S(0.002)PANS(0.985)DVEIDGIGR ; 163.15 1.92E-06 4015800 841.9 1121.46 998.74 803.37 790.55 707.06 501.21 544.78 909.96 889.55 TRUE FALSE FALSE 831.638599 1137.247943 1016.122651 896.2594194 750.2052836 661.8811479 543.7827649 560.5423498 828.5708986 866.4393628 0.959834738 1.312553414 1.172756796 1.034416784 0.86584857 0.76390937 0.627606256 0.646949312 0.956294155 1 9.758954977 -8.316644621 1.785957765 1.026932589 0.642691687 0.719540325 0.109274477 0.181419226 1.10302158 0.018544397 0.05897215 4.82E-09 8.316644621 -0.384240902 T(ph)PTSSPASSPLVAK ddPTM_HeLa_Romidepsin_16h_R1 2 TPTSSPASSPLVAK 14 0 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 T(0.745)PT(0.074)S(0.157)S(0.023)PAS(0.001)SPLVAK;T(0.338)PT(0.247)S(0.207)S(0.207)PASSPLVAK ; 229.75 3.81E-33 86637000 9510.5 9906 8717.3 9344.9 7104.4 4587.1 3777.6 4117.2 9983.7 9344.5 TRUE FALSE FALSE 9394.582368 10045.45693 8869.02095 10425.40131 6741.835958 4293.999114 4098.46925 4236.324686 9090.732867 9101.728543 1.032175627 1.103686721 0.974432594 1.145430921 0.740720395 0.47177842 0.450295703 0.465441775 0.998791913 1 13.15192484 -8.488972717 3.005305554 1.027413653 0.461850389 0.957892141 0.054531801 0.033964956 0.613611593 0.007624117 0.017825078 3.24E-09 8.488972717 -0.565563264 down TSSVLGMS(ph)VESAPAVEEEKGEELEQK ddPTM_HeLa_Romidepsin_16h_R1 4 TSSVLGMSVESAPAVEEEKGEELEQK 26 1 A6NNK5;Q12888;Q12888-3;Q12888-2;C9JXV0 A6NNK5 TP53BP1 Tumor suppressor p53-binding protein 1 1 0 T(0.001)S(0.001)S(0.002)VLGMS(0.815)VES(0.182)APAVEEEKGEELEQK;T(0.128)S(0.076)S(0.378)VLGMS(0.405)VES(0.014)APAVEEEKGEELEQK;T(0.001)S(0.001)S(0.004)VLGMS(0.497)VES(0.497)APAVEEEKGEELEQK;T(0.08)S(0.025)S(0.191)VLGMS(0.351)VES(0.351)APAVEEEKGEELEQK ;;; 117.01 6.45E-07 55790100 8766.2 8163.3 8830 6469.1 8805.4 8636.6 7014.4 7316.1 8989.5 8873.9 TRUE FALSE FALSE 8659.354183 8278.223152 8983.682446 7217.08778 8356.027581 8084.749133 7610.202961 7527.779811 8185.456605 8643.354799 1.001851062 0.957755796 1.039374485 0.834986871 0.966757443 0.935371661 0.880468653 0.87093264 0.947023094 1 13.07737567 -9.271738929 24.99501997 0.999601494 0.902674974 0.538594951 0.041666148 334.724748 812311.0707 0.005540892 0.00852245 5.35E-10 9.271738929 -0.09692652 TSSVSSISQVS(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 3 TSSVSSISQVSPER 14 0 P42356 P42356 PI4KA Phosphatidylinositol 4-kinase alpha 1 0 TSSVSSISQVS(1)PER;TSSVSSISQVS(1)PER;TSSVSSISQVS(1)PER ;; 274.38 1.60E-82 41757200 2392.21 2593.98 2278.92 2436.06 2829.96 2876.34 2668 3061.15 2906.19 2592.53 TRUE FALSE FALSE 2363.052824 2630.498119 2318.583647 2717.728719 2685.536581 2692.551157 2894.619853 3149.719546 2646.253088 2525.175697 0.935797389 1.041708948 0.918187059 1.076253317 1.063504842 1.066282699 1.146304337 1.247326889 1.047948106 1 11.30216806 -6.704338057 0.492646293 0.970365474 1.61748732 0.722775064 0.04772255 2.072271563 0.229064553 0.008848183 0.875697899 1.98E-07 6.704338057 0.647121846 TST(ph)PEDFIR ddPTM_HeLa_Romidepsin_16h_R1 1 TSTPEDFIR 9 0 Q9Y490 Q9Y490 TLN1 Talin-1 1 0 T(0.007)S(0.383)T(0.61)PEDFIR 164.66 0.0055824 1685700 1569 1598.4 1448.3 1340.3 1567.4 1424.3 1302.7 1373.2 1702.6 1506.8 TRUE FALSE FALSE 1549.876425 1620.902317 1473.507054 1495.271792 1487.409729 1333.291827 1413.351305 1412.931375 1550.315192 1467.653119 1.056023664 1.10441786 1.003988637 1.018818257 1.013461362 0.908451602 0.963000921 0.962714798 1.056322623 1 10.51929531 -8.416171613 5.227366833 1.030711858 0.946955927 0.624856896 0.032493737 0.134827754 5.443450515 0.005149 0.011682583 3.84E-09 8.416171613 -0.083755931 TST(ph)PVIMEGVQEETDTR ddPTM_HeLa_Romidepsin_16h_R1 2 TSTPVIMEGVQEETDTR 17 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 T(0.009)S(0.013)T(0.978)PVIMEGVQEETDTR;T(0.003)S(0.005)T(0.993)PVIMEGVQEETDTR ; 162.7 5.03E-05 24708000 6299.6 6761.8 5415.4 4571.4 5251.6 4491.4 3974.9 4766.3 6187.8 6257.2 TRUE FALSE FALSE 6222.818052 6856.992798 5509.652765 5099.966777 4983.591256 4204.414035 4312.527907 4904.205371 5634.34767 6094.637042 1.021031771 1.125086326 0.904016552 0.836795816 0.817701074 0.689854704 0.707593886 0.804675543 0.924476328 1 12.57332459 -9.173161778 1.56953249 1.018242737 0.742266255 0.785346421 0.061134664 0.103270136 0.498458255 0.008652723 0.016548647 6.71E-10 9.173161778 -0.275976482 TSTGAPAAIK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TSTGAPAAIKK 11 1 P40121-2;P40121;E7ENU9;B8ZZL6 P40121-2 CAPG Macrophage-capping protein 0 1 ; TSTGAPAAIK(1)K;TSTGAPAAIK(1)K 140.16 0.00087186 12411300 10017.4 9095.8 13192 12844.8 14219.4 10991.6 15261.2 8546.6 15197.9 7935.4 FALSE TRUE FALSE 9895.304076 9223.850911 13421.60123 14329.97621 13493.73096 10289.27223 16557.48595 8793.882387 13838.56176 7729.237164 1.280243298 1.193371443 1.736471652 1.853996185 1.745803715 1.331214454 2.142188886 1.1377426 1.790417536 1 12.91611032 -9.799533265 5.982710315 1.13872615 1.678329161 0.119216658 0.336549303 0.112029996 10.42286193 0.04060881 0.054214604 1.59E-10 9.799533265 0.539603011 TSTGS(ph)ASSSAAVAASSK ddPTM_HeLa_Romidepsin_16h_R1 1 TSTGSASSSAAVAASSK 17 0 Q9UDT6-2;Q9UDT6 Q9UDT6-2 CLIP2 CAP-Gly domain-containing linker protein 2 1 0 T(0.002)ST(0.001)GS(0.988)AS(0.008)SS(0.001)AAVAASSK 142.94 0.00023374 1383500 486.81 597.96 271.64 524.73 673.22 947.59 923.26 1075.9 670.31 423.69 TRUE FALSE FALSE 480.8765725 606.3780966 276.3677803 585.4017515 638.8630713 887.0420572 1001.681681 1107.029469 610.3557948 412.6824727 1.165245932 1.469357525 0.669686256 1.418528264 1.548074157 2.149454159 2.427245516 2.682521169 1.478996166 1 8.688888356 -8.220634876 1.133587606 1.084905265 2.693174876 0.848335665 0.234956318 0.119944677 0.263984395 0.029983783 0.150907979 6.02E-09 8.220634876 1.60826961 up TSTPS(ph)PQPSKR ddPTM_HeLa_Romidepsin_16h_R1 1 TSTPSPQPSKR 11 1 Q8IY18 Q8IY18 SMC5 Structural maintenance of chromosomes protein 5 1 0 T(0.01)ST(0.001)PS(0.987)PQPS(0.002)KR 112.02 0.021027 1576700 926.34 1003.4 848.88 985.35 825.53 678.17 702.88 517.44 1106.6 764.04 TRUE FALSE FALSE 915.0494118 1017.525892 863.6544003 1099.280803 783.4001236 634.8371257 762.5826097 532.41131 1007.622924 744.1901307 1.229590899 1.367292913 1.160529231 1.477150473 1.052688139 0.853057706 1.024714758 0.715423772 1.353985874 1 9.539527448 -8.44315248 5.038325501 1.16350804 0.885569139 0.503684657 0.160641292 0.188878742 8.428495852 0.02441382 0.055253492 3.60E-09 8.44315248 -0.277938901 TSTS(ph)PPPEK ddPTM_HeLa_Romidepsin_16h_R1 3 TSTSPPPEK 9 0 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 T(0.08)S(0.008)T(0.018)S(0.894)PPPEK;T(0.003)S(0.005)T(0.437)S(0.556)PPPEK;T(0.021)ST(0.089)S(0.89)PPPEK ;; 104.05 0.024656 223233000 18222.4 18563.5 27219.5 12008.9 15650.5 17700.3 25856.4 7178.3 25106.3 23001.1 TRUE FALSE FALSE 18000.29838 18824.83744 27693.24398 13397.42552 14851.79658 16569.30796 28052.64197 7385.992785 22860.72965 22403.52811 0.803458201 0.840262183 1.236110841 0.598005165 0.66292222 0.73958476 1.252152868 0.329679895 1.020407569 1 14.45143833 -9.196879435 24.99999892 0.921176656 0.744538747 0.204309419 0.243636347 350.2634433 135634.6323 0.034698044 0.057540193 6.36E-10 9.196879435 -0.176637909 TSTTGVATTQS(ph)PTPR ddPTM_HeLa_Romidepsin_16h_R1 4 TSTTGVATTQSPTPR 15 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2 E9PMS6 LMO7 LIM domain only protein 7 1 0 TSTTGVATTQS(0.919)PT(0.081)PR;TSTTGVATTQS(0.698)PT(0.302)PR;TSTTGVATTQS(0.54)PT(0.46)PR;TSTTGVATTQS(0.5)PT(0.5)PR ;;; 227.91 5.59E-35 546084000 16413.9 15507.1 15793.8 14693 15553.6 13891.8 14080.1 12230.8 17328.8 15714.7 TRUE FALSE FALSE 16213.84107 15725.40936 16068.68446 16391.87379 14759.84175 13004.15881 15276.06334 12584.6789 15778.86873 15306.42983 1.059283011 1.02737278 1.049799636 1.070914248 0.964290296 0.849587981 0.998016096 0.82218251 1.030865388 1 13.9018502 -8.532671726 5.244777083 1.03284135 0.901001477 0.671626365 0.046770925 0.081378406 6.806945522 0.006515551 0.013757817 2.93E-09 8.532671726 -0.131839874 TSTTLSS(ph)EEK ddPTM_HeLa_Romidepsin_16h_R1 1 TSTTLSSEEK 10 0 O96028;O96028-4;O96028-2 O96028 WHSC1 Histone-lysine N-methyltransferase NSD2 1 0 TSTTLS(0.204)S(0.796)EEK 178.46 5.05E-05 3016300 2237.3 1726.1 1964.6 1871.2 1729 2185.9 1456.8 1716.7 2320.7 2258.9 TRUE FALSE FALSE 2210.030927 1750.400081 1998.793039 2087.556948 1640.762678 2046.228045 1580.540556 1766.370006 2113.13078 2200.213452 1.004462056 0.795559212 0.908454149 0.948797466 0.745728864 0.930013423 0.718357827 0.802817565 0.960420807 1 11.10342778 -9.429128414 0.462798472 1.014008979 0.7699693 0.426196753 0.076362915 0.602818357 0.260049942 0.023964437 0.06030566 3.72E-10 9.429128414 -0.244039678 TSVLFSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TSVLFSKK 8 1 A0A5F9ZH11;P55201-3;P55201;P55201-2 A0A5F9ZH11 BRPF1 Peregrin 0 1 ; TSVLFSK(1)K;TSVLFSK(1)K 149.94 0.0023492 5961100 283.04 216.85 4202.9 993.81 4849.7 10284.9 6891.1 1001.28 439.73 92.462 FALSE TRUE FALSE 279.5901996 219.90282 4276.049711 1108.718988 4602.201712 9627.728083 7476.429862 1030.250457 400.3994475 90.05982391 3.104494185 2.441741616 47.48010296 12.31091668 51.10160683 106.9036965 83.01626116 11.43962327 4.445927497 1 6.492811752 -9.127341427 1.059565447 2.090498993 68.2113968 0.475037724 26.17990019 0.284848492 0.630918397 4.41844511 10.0122342 7.46E-10 9.127341427 66.12089781 TSVLGGGEDGIEPVS(ph)PPEGMTEPGHSR ddPTM_HeLa_Romidepsin_16h_R1 3 TSVLGGGEDGIEPVSPPEGMTEPGHSR 27 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;C9JE98;Q9Y618-5;Q9Y618-2 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 TSVLGGGEDGIEPVS(0.818)PPEGMT(0.13)EPGHS(0.052)R;TSVLGGGEDGIEPVS(0.998)PPEGMT(0.002)EPGHSR;TSVLGGGEDGIEPVS(0.834)PPEGMT(0.129)EPGHS(0.038)R ;; 85.242 9.44E-07 118377000 3983.5 3827 3643.03 3144.5 3674.48 3508.48 3072.8 3366.5 4709.7 4352.8 TRUE FALSE FALSE 3934.94757 3880.876606 3706.435409 3508.081885 3486.957574 3284.299451 3333.803555 3463.904366 4288.452636 4239.713629 0.928116358 0.91536291 0.87421834 0.827433688 0.822451203 0.774651247 0.786327532 0.817013758 1.011495825 1 12.04975111 -9.783431602 0.465455541 0.991013055 0.77408363 0.950312628 0.017974245 0.144818169 0.070334739 0.006716984 0.012139051 1.65E-10 9.783431602 -0.216929424 TSVPS(ph)PEQPQPYR ddPTM_HeLa_Romidepsin_16h_R1 1 TSVPSPEQPQPYR 13 0 Q8TEH3 Q8TEH3 DENND1A DENN domain-containing protein 1A 1 0 T(0.42)S(0.008)VPS(0.568)PEQPQPY(0.004)R 161.87 0.0003564 9478400 1968.9 1681.1 2011.6 1562.5 1671.6 2152.5 1343.9 1815.4 2043.3 2035.6 TRUE FALSE FALSE 1944.902289 1704.76657 2046.611054 1743.163602 1586.292014 2014.962197 1458.050832 1867.925735 1860.54213 1982.714819 0.980928912 0.859814308 1.032226639 0.879180195 0.800060604 1.016264254 0.735381013 0.942105096 0.938381109 1 10.95326147 -9.636976669 0.560386339 0.998478326 0.86063805 0.139721274 0.086280637 0.763220246 0.49754418 0.021378815 0.042502718 2.31E-10 9.636976669 -0.137840276 TSVS(ph)PAPDK ddPTM_HeLa_Romidepsin_16h_R1 1 TSVSPAPDK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 0 T(0.015)SVS(0.985)PAPDK 125.68 0.010489 21078000 6136.6 6205.2 6647.9 5867.4 4900.4 4061.5 4132.7 2190.4 6073.5 5614.3 TRUE FALSE FALSE 6061.804759 6292.556968 6763.603911 6545.816395 4650.314302 3801.983258 4483.731435 2253.775768 5530.270949 5468.439677 1.108507201 1.150704285 1.236843471 1.197017208 0.850391442 0.695259248 0.819928846 0.412142385 1.011306931 1 12.41691353 -8.48263653 2.835199235 1.08494787 0.657532773 0.755377454 0.120740952 0.111935642 1.783930504 0.018302466 0.043454905 3.29E-09 8.48263653 -0.427415097 REDFQDISVPVQEDELSKVEESS(ph)EISPEPK ddPTM_HeLa_Romidepsin_16h_R1 1 REDFQDISVPVQEDELSKVEESSEISPEPK 30 2 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 REDFQDIS(0.003)VPVQEDELS(0.177)KVEES(0.228)S(0.296)EIS(0.296)PEPK 42.353 0.020046 5636300 1304 961.12 1116.5 1109 601.91 573.51 466.58 337.18 1315.8 1438.7 TRUE FALSE FALSE 1288.106346 974.6506726 1135.932214 1237.227798 571.1922867 536.8645619 506.2112936 346.9357713 1198.111553 1401.322367 0.919207726 0.695522098 0.810614489 0.8829002 0.407609484 0.383112819 0.361238289 0.247577417 0.854986391 1 10.45257316 -8.487321263 0.488598365 0.981701289 0.103266666 0.839911242 0.1054062 0.399132602 0.129870658 0.024595625 0.165743749 3.26E-09 8.487321263 -0.878434623 down DVTGS(ph)PPAK ddPTM_HeLa_Romidepsin_16h_R1 1 DVTGSPPAK 9 0 O75362 O75362 ZNF217 Zinc finger protein 217 1 0 DVT(0.427)GS(0.573)PPAK 125.23 0.010723 21628000 7808.6 7649 7515.1 7687 5471 4408.8 3090.1 2836.2 8060.1 7628.4 TRUE FALSE FALSE 7713.42578 7756.682823 7645.897163 8575.807108 5191.794455 4127.091909 3352.573017 2918.260972 7339.184469 7430.213068 1.038116365 1.043938142 1.029027982 1.15418051 0.698740993 0.555447316 0.451208194 0.392756028 0.987748857 1 12.85918787 -8.475761128 2.379709703 1.02990238 0.45346241 0.942588758 0.064050866 0.045724811 0.509201688 0.00904368 0.022556036 3.34E-09 8.475761128 -0.576439969 down TSVSSVSAS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 4 TSVSSVSASPSR 12 0 P12036-2;P12036 P12036-2 NEFH Neurofilament heavy polypeptide 1 0 T(0.002)SVSSVSAS(0.865)PS(0.132)R;TSVSSVSAS(0.956)PS(0.044)R;TSVSSVSAS(0.956)PS(0.043)R;T(0.052)S(0.001)VSSVSAS(0.895)PS(0.051)R ;;; 168.82 0.00018842 104927000 8820.8 8971.6 9386.4 6214.3 7764.6 7596.3 7418.7 5524.84 9752.6 8615.6 TRUE FALSE FALSE 8713.288697 9097.90242 9549.766355 6932.826605 7368.343488 7110.920946 8048.844193 5684.692529 8880.30303 8391.76547 1.038314134 1.084146411 1.137992522 0.826146373 0.878044497 0.847368885 0.959135979 0.67741318 1.058216303 1 13.03475864 -9.244412515 24.98132959 1.032732219 0.847159771 0.677932499 0.076304132 419.8497217 615991.9069 0.010981389 0.018180605 5.70E-10 9.244412515 -0.185572448 TSY(ph)NHRS(ph)WISTTS(ph)SYNR ddPTM_HeLa_Romidepsin_16h_R1 1 TSYNHRSWISTTSSYNR 17 1 Q8WXI7 Q8WXI7 MUC16 Mucin-16 3 0 T(0.195)S(0.23)Y(0.575)NHRS(0.892)WIS(0.103)T(0.003)T(0.003)S(0.534)S(0.448)Y(0.017)NR 69.979 0.014757 10662000 2315.9 2310.9 2052.2 1373.5 2000.1 2058.4 1721.8 1923.4 2208.9 2662 TRUE FALSE FALSE 2287.67292 2343.432911 2087.91768 1532.310533 1898.027434 1926.874883 1868.049649 1979.050544 2011.330452 2592.840856 0.882303638 0.903809004 0.805262566 0.590977471 0.732026198 0.743152006 0.720464445 0.763274977 0.775724606 1 11.34031794 -9.693681114 2.539906884 0.942467048 0.71247174 0.5270305 0.074292232 0.102014462 1.346329424 0.010204861 0.014732929 2.02E-10 9.693681114 -0.229995307 TT(ph)PNSGDVQVTEDAVRR ddPTM_HeLa_Romidepsin_16h_R1 1 TTPNSGDVQVTEDAVRR 17 1 P35269;M0QXD6 P35269 GTF2F1 General transcription factor IIF subunit 1 1 0 T(0.437)T(0.561)PNS(0.002)GDVQVTEDAVRR 139.11 0.00034921 11677000 1976.3 1635.6 1383.2 1328.2 1886.7 2156.2 2069.4 1817 1509.8 1639.9 TRUE FALSE FALSE 1952.212095 1658.62602 1407.274016 1481.772733 1790.414659 2018.425779 2245.174784 1869.572028 1374.759707 1597.295162 1.222198716 1.038396697 0.881035672 0.927676217 1.120904077 1.263652346 1.405610458 1.17046121 0.860679817 1 10.64141522 -8.285702392 3.789843803 1.070856308 1.296546558 0.449611795 0.125907505 0.186798032 5.927913789 0.018876761 0.04714836 5.18E-09 8.285702392 0.22569025 TT(ph)SPPEVSGYSYEK ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPPEVSGYSYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.017)T(0.492)S(0.492)PPEVSGYSYEK 126.56 0.0061395 682740000 5216.1 4860.4 5084.5 4964.7 5148.5 4878.5 4123.4 4710.1 5568.4 5337 TRUE FALSE FALSE 5152.524167 4928.824839 5172.99359 5538.741974 4885.752833 4566.779595 4473.641493 4846.379312 5070.348358 5198.343971 0.991185692 0.948152886 0.995123374 1.065482008 0.939867169 0.878506621 0.860589741 0.932292926 0.975377618 1 12.34383638 -8.52799478 7.382840041 0.996377762 0.890780223 0.68545512 0.032212142 0.050970952 18.20446497 0.004445128 0.00921361 2.96E-09 8.52799478 -0.105597539 TTAGS(ph)VDWTDQLGLR ddPTM_HeLa_Romidepsin_16h_R1 1 TTAGSVDWTDQLGLR 15 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 T(0.001)T(0.001)AGS(0.98)VDWT(0.017)DQLGLR 95.195 0.011677 13603000 1112.7 759.15 832.54 616.4 944.39 847.31 740.86 908.01 813.86 745.63 TRUE FALSE FALSE 1099.137984 769.8373336 847.0300095 687.6710682 896.1942543 793.1696256 803.7886299 934.2818367 741.0663233 726.2584251 1.513425451 1.060004686 1.166292851 0.946868283 1.2339881 1.092131393 1.106752916 1.286431667 1.020389296 1 9.504339185 TTAS(ph)PSVR ddPTM_HeLa_Romidepsin_16h_R1 1 TTASPSVR 8 0 Q9Y3P9;Q9Y3P9-2 Q9Y3P9 RABGAP1 Rab GTPase-activating protein 1 1 0 T(0.001)T(0.001)AS(0.499)PS(0.499)VR 104.42 0.027283 20439000 3217.4 3821.3 5385.3 3780 5179.8 7225.1 10283 1397.1 5953.8 4824.1 TRUE FALSE FALSE 3178.185091 3875.096362 5479.028887 4217.061385 4915.455478 6763.439428 11156.43776 1437.522884 5421.277216 4698.769187 0.676386723 0.824704557 1.166056188 0.897482132 1.046115543 1.43940661 2.374331941 0.30593605 1.15376538 1 12.19806719 -8.384274137 3.263638835 0.87372312 1.473004576 0.106889185 0.489668684 0.265342868 5.27604331 0.063861491 0.154879356 4.13E-09 8.384274137 0.599281455 TTGFYSGFSEVAEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 TTGFYSGFSEVAEKR 15 1 H7C5R6;Q4LE39-2;Q4LE39;H0Y7Y8;Q4LE39-4;Q4LE39-3 H7C5R6 ARID4B AT-rich interactive domain-containing protein 4B 0 1 TTGFYSGFSEVAEK(1)R 89.189 0.022098 323520 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 TTGIVMDSGDGVTHTVPIYEGYALPHAILR ddPTM_HeLa_Romidepsin_16h_R1 3 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 0 ;; ;; 86.641 1.03E-07 273440000 4079.8 3892.9 3862.3 4231.9 5367 5755.4 4506.9 4880.4 4311.5 4277 FALSE FALSE TRUE 4030.073828 3947.704348 3929.521711 4721.21219 5093.101963 5387.648515 4889.715974 5021.606674 3925.868642 4165.882923 0.967399685 0.947627291 0.943262637 1.133304098 1.222574435 1.293278907 1.173752615 1.205412338 0.942385735 1 12.02440658 -9.061921333 3.196548266 0.978187883 1.223688203 0.925990245 0.035190621 0.050519017 1.019331535 0.005486301 0.009771954 8.67E-10 9.061921333 0.24550032 TTGMSQS(ph)TELLPDATDEEVAPPKPPLPGIR ddPTM_HeLa_Romidepsin_16h_R1 1 TTGMSQSTELLPDATDEEVAPPKPPLPGIR 30 1 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 0 T(0.048)T(0.048)GMS(0.131)QS(0.367)T(0.367)ELLPDAT(0.039)DEEVAPPKPPLPGIR 48.626 0.025643 7411600 951.03 995.02 747 589.22 856.83 1000.8 664.77 1042.5 1019.4 862.73 TRUE FALSE FALSE 939.4384806 1009.027918 760.0012216 657.3483888 813.1027678 936.8521099 721.2355472 1072.663093 928.2223109 840.3161502 1.117958378 1.200771778 0.904422962 0.782263186 0.967615305 1.114880524 0.858290712 1.276499437 1.104610819 1 9.714788402 -9.733356601 24.99970964 1.068139243 0.974316672 0.132483224 0.138706802 402.8307271 358605.4805 0.021582668 0.030518889 1.85E-10 9.733356601 -0.093822571 TTGQVVAMK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 TTGQVVAMKK 10 1 A0A087WZZ9;A0A024QZP7;P06493-2;P06493;E5RIU6 A0A087WZZ9 CDK1;CDC2 Cyclin-dependent kinase 1 0 1 TTGQVVAMK(1)K 106.4 0.0027403 13713000 2245.9 1843.4 3484 2219.2 2142.8 2694.4 2141.1 1438.7 2423.5 1060.5 FALSE TRUE FALSE 2218.526107 1869.351434 3544.637559 2475.794346 2033.44492 2522.236536 2322.964981 1480.326515 2206.73609 1032.948057 2.147761537 1.809724527 3.431573867 2.396823663 1.968583905 2.441784481 2.248869113 1.433108378 2.136347588 1 10.01255199 -11.88516221 0.692310222 0.976351919 2.280472646 0.051285419 0.597259814 0.498882316 0.437851439 0.353955137 0.109029875 1.30E-12 11.88516221 1.304120727 TTHLAGALS(ph)PGEAWPFESV ddPTM_HeLa_Romidepsin_16h_R1 1 TTHLAGALSPGEAWPFESV 19 0 Q9Y3X0 Q9Y3X0 CCDC9 Coiled-coil domain-containing protein 9 1 0 T(0.001)T(0.001)HLAGALS(0.999)PGEAWPFESV 88.311 0.0044618 41340000 840.53 1155.3 804.8 699.61 849.53 1168.2 837.37 1337.2 1011.3 1042.5 TRUE FALSE FALSE 830.2852971 1171.564344 818.8072064 780.5022 806.1753141 1093.55579 908.4961869 1375.889772 920.8467952 1015.4157 0.817680185 1.153778048 0.806376351 0.768652878 0.793936232 1.076953794 0.894703703 1.355001476 0.906866809 1 9.987854756 TTHLAGALS(ph)PGGGQSAPAFPESGPSLR ddPTM_HeLa_Romidepsin_16h_R1 1 TTHLAGALSPGGGQSAPAFPESGPSLR 27 0 A0A2R8Y4Z8 A0A2R8Y4Z8 1 0 TTHLAGALS(0.966)PGGGQS(0.033)APAFPESGPSLR 80.632 2.93E-06 11224000 843.98 944.49 757.23 841.19 1143.6 1067.1 1162.6 1137.4 1319 997.71 TRUE FALSE FALSE 833.6932471 957.786555 770.4092705 938.4523457 1085.237825 998.9157539 1261.351215 1170.308874 1201.025337 971.7893504 0.857895023 0.985590709 0.792773938 0.965695236 1.116741837 1.027913872 1.297967728 1.204282465 1.235890614 1 9.924499812 -8.203396766 1.142810875 0.926206135 1.25775257 0.342221123 0.126060837 0.257414124 0.574025635 0.013222061 0.067496029 6.26E-09 8.203396766 0.331546435 TTHS(ph)PYEER ddPTM_HeLa_Romidepsin_16h_R1 1 TTHSPYEER 9 0 Q8NDT2;Q8NDT2-2 Q8NDT2 RBM15B Putative RNA-binding protein 15B 1 0 T(0.001)T(0.041)HS(0.958)PYEER 98.156 0.012769 8851900 949.73 774.97 1097.6 824.13 813.23 935.11 1344.7 423.98 1343.1 1414.9 TRUE FALSE FALSE 938.1543255 785.880048 1116.703268 919.4197882 771.7278385 875.3594889 1458.918784 436.2471924 1222.969772 1378.140694 0.680739151 0.570246602 0.810296998 0.667145083 0.559977542 0.635174255 1.05861382 0.316547646 0.887405602 1 10.42850746 -12.09543867 0.678229804 1.022928992 0.670073894 0.267302839 0.181893838 0.757342032 0.578122047 0.152117409 0.035945112 8.03E-13 12.09543867 -0.352855098 TTIFS(ph)PEGR ddPTM_HeLa_Romidepsin_16h_R1 2 TTIFSPEGR 9 0 H0YLS6;H0YLC2;H0YMI6;H0YMA1;H0YMZ1;H0YL69;P25789 H0YLS6 PSMA4 Proteasome subunit alpha type;Proteasome subunit alpha type-4 1 0 T(0.004)T(0.007)IFS(0.989)PEGR;T(0.024)T(0.002)IFS(0.974)PEGR ; 144.77 0.0059729 54397000 7291.7 6516.1 7192.7 5179.8 7153.2 7467.2 6456.4 7218 7945.6 7299.3 TRUE FALSE FALSE 7202.825956 6607.833827 7317.885926 5778.712848 6788.145512 6990.070019 7004.806455 7426.841442 7234.925636 7109.663134 1.01310369 0.929415881 1.029287294 0.812796997 0.954777376 0.983178793 0.985251526 1.044612284 1.017618627 1 12.79556549 -10.28353076 23.88036349 1.006187857 0.960894323 0.114752487 0.059961718 743.9348932 804176.9656 0.009982703 0.011421573 5.21E-11 10.28353076 -0.045293534 TTIPEEEEEEEEAAGVVVEEELFHQQGT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 1 0 TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR;TTIPEEEEEEEEAAGVVVEEELFHQQGT(1)PR ; 93.993 3.27E-08 88859000 6803.4 7257.4 6747.5 5788.8 5716.9 5500.9 3848.6 3824 7985 7409.3 TRUE FALSE FALSE 6720.477544 7359.569868 6864.937407 6458.128293 5425.14526 5149.410243 4175.499988 3934.641407 7270.801601 7216.805318 0.93122611 1.019782237 0.951243259 0.894873564 0.751737787 0.713530436 0.578580106 0.545205424 1.00748202 1 12.81714462 -8.321656398 0.897002297 0.973838756 0.521316132 0.963318562 0.032542468 0.106623649 0.139314371 0.005945167 0.032947585 4.77E-09 8.321656398 -0.452522624 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ddPTM_HeLa_Romidepsin_16h_R1 1 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR 30 0 P20700 P20700 LMNB1 Lamin-B1 0 0 122.35 3.15E-11 2724700 260.43 370.75 358.43 261.47 290.93 253.01 237.59 361.38 242.46 297.19 FALSE FALSE TRUE 257.255779 375.9694282 364.6683238 291.7023917 276.0827565 236.8434776 257.7708887 371.8359601 220.7737703 289.468961 0.888716283 1.298824672 1.259783856 1.007715614 0.953755994 0.818199909 0.890495782 1.284545185 0.762685469 1 8.17726485 TTKPPYPGS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 2 TTKPPYPGSPVK 12 1 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 TT(0.001)KPPYPGS(0.999)PVK;TTKPPYPGS(1)PVK ; 156.72 0.0076797 297724000 17519.6 16277.3 20477.4 17630.5 16200.7 14155.5 11336.7 10713.1 17253.6 15895.4 TRUE FALSE FALSE 17306.06438 16506.45226 20833.80056 19669.02136 15373.91783 13251.00923 12299.63902 11023.06665 15710.3948 15482.43522 1.117786972 1.066140567 1.345641061 1.270408763 0.992990935 0.855873708 0.79442535 0.711972406 1.014723755 1 13.91834479 -8.223525725 2.379160084 1.095686128 0.762478664 0.667568372 0.108512548 0.168985403 1.852958967 0.018073921 0.054149779 5.98E-09 8.223525725 -0.333207464 TTKPPYPGS(ph)PVKYR ddPTM_HeLa_Romidepsin_16h_R1 1 TTKPPYPGSPVKYR 14 2 Q96T17-2;Q96T17;Q96T17-5;Q96T17-4 Q96T17-2 MAP7D2 MAP7 domain-containing protein 2 1 0 T(0.001)TKPPYPGS(0.998)PVKY(0.001)R 88.781 0.018492 22432000 2261.9 2454.8 1397.8 3584.7 1654.2 1546.6 1181.5 1201.8 2067.5 1849.9 TRUE FALSE FALSE 2234.331093 2489.358739 1422.128123 3999.179881 1569.780001 1447.777251 1281.856581 1236.572187 1882.577622 1801.839331 1.240027928 1.381565324 0.789264669 2.219498604 0.871209754 0.803499639 0.711415584 0.686283269 1.044808818 1 10.81525466 -8.539828001 24.99942523 1.195060491 0.749142905 0.31176584 0.363304737 243.9957642 359882.2338 0.050840398 0.101699137 2.89E-09 8.539828001 -0.445917587 TTKT(ph)PEDGDYSYEIIEK ddPTM_HeLa_Romidepsin_16h_R1 1 TTKTPEDGDYSYEIIEK 17 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.41)T(0.125)KT(0.464)PEDGDY(0.001)SYEIIEK 65.298 0.02244 143000000 4102.7 3617.8 3729.5 3845.9 4304.6 4827.7 4325.2 4724.4 4685.4 4381.8 TRUE FALSE FALSE 4052.694714 3668.731483 3794.410383 4290.581054 4084.920199 4519.225551 4692.58238 4861.09306 4266.326089 4267.960204 0.949562442 0.859598335 0.889045399 1.005300155 0.957113001 1.058872467 1.09949066 1.13897338 0.99961712 1 12.05933101 -7.998785925 1.6531208 0.960022992 1.132995349 0.693751761 0.045946279 0.207957835 1.040759689 0.007622579 0.036277331 1.00E-08 7.998785925 0.172972357 TTPATGEQS(ph)PGAR ddPTM_HeLa_Romidepsin_16h_R1 2 TTPATGEQSPGAR 13 0 O00308-4;O00308-2;O00308 O00308-4 WWP2 NEDD4-like E3 ubiquitin-protein ligase WWP2 1 0 TTPATGEQS(1)PGAR;TTPATGEQS(1)PGAR ; 139.64 0.0011743 141206000 4320.6 4501.6 3611.8 4015.9 3608.2 3617.1 3112.2 3781.8 3800.8 3612.1 TRUE FALSE FALSE 4267.938865 4564.973643 3674.661864 4480.237253 3424.06009 3385.978984 3376.55019 3891.220416 3460.846929 3518.257121 1.213083273 1.297509956 1.044455177 1.273425193 0.973226223 0.962402368 0.959722406 1.10600797 0.983682207 1 11.78064521 -8.691157396 24.99999231 1.125495567 0.994727916 0.269470469 0.108022077 56.20021353 19989.83073 0.016846817 0.033693631 2.04E-09 8.691157396 -0.130767651 TTPES(ph)PPYSSGSYDSIK ddPTM_HeLa_Romidepsin_16h_R1 3 TTPESPPYSSGSYDSIK 17 0 A0A087WTU5;Q96MY1-2;Q96MY1;A0A087X0N3 A0A087WTU5 NOL4L Nucleolar protein 4-like 1 0 TTPES(0.806)PPY(0.119)S(0.055)S(0.017)GS(0.002)YDSIK;T(0.174)T(0.174)PES(0.646)PPY(0.001)S(0.005)S(0.001)GSYDSIK;TTPES(0.997)PPYS(0.001)S(0.002)GSYDSIK ;; 161.26 2.85E-05 209553900 11514.5 11317.8 10978.4 9066.9 11948.1 11460.2 9819.1 11299.3 12240.5 11442.4 TRUE FALSE FALSE 11374.15685 11477.13229 11169.47445 10115.25764 11338.34387 10727.93021 10653.13411 11626.22742 11145.67902 11145.1248 1.020549976 1.029789481 1.00218478 0.907594829 1.017336645 0.962567078 0.955855973 1.043167091 1.000049728 1 13.44412515 -9.504749492 24.93051322 1.011696247 0.975255209 0.188037149 0.034894576 838.9016012 1153621.344 0.00498871 0.007522906 3.13E-10 9.504749492 -0.036441038 TTPPESAPQNGPSPMAALMS(ph)VADTLGTAHSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 TTPPESAPQNGPS(0.159)PMAALMS(0.553)VADT(0.176)LGT(0.039)AHS(0.072)PK 72.228 4.16E-07 0 1959.7 1633.1 1772.7 1254.2 1469.5 1531.7 1065 981.59 1899.5 1776.5 TRUE FALSE FALSE 1935.814423 1656.090825 1803.5531 1399.216505 1394.505932 1433.829313 1155.461073 1009.990758 1729.603963 1730.346274 1.118743948 0.957086365 1.042307616 0.808633813 0.805911483 0.828637213 0.667762916 0.583692856 0.999571004 1 10.75684506 -8.432847444 0.632574043 1.057076095 0.570570751 0.843328119 0.064316417 0.335416324 0.196035072 0.014109659 0.090539388 3.69E-09 8.432847444 -0.486505344 TTPPESAPQNGPSPMAALMSVADTLGTAHS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 TTPPESAPQNGPSPMAALMSVADTLGTAHSPK 32 0 Q9H1B7 Q9H1B7 IRF2BPL Interferon regulatory factor 2-binding protein-like 1 0 TTPPESAPQNGPS(0.047)PMAALMS(0.161)VADT(0.117)LGT(0.228)AHS(0.447)PK;TTPPESAPQNGPS(0.019)PMAALMS(0.127)VADT(0.095)LGT(0.211)AHS(0.547)PK ; 47.167 0.0061189 26074000 2024.85 2040.63 2018.44 1539.1 1554.49 1536.76 1416.6 1338.72 2117.31 2070.44 TRUE FALSE FALSE 2000.170349 2069.358043 2053.570102 1717.057984 1475.158575 1438.565996 1536.925969 1377.453751 1927.932491 2016.64967 0.991828367 1.026136603 1.018307806 0.851440887 0.731489756 0.713344522 0.762118474 0.683040674 0.956007639 1 10.97774477 -9.009901378 2.580738519 1.000393266 0.723388837 0.960265113 0.026449606 0.031053256 0.415125184 0.003402534 0.006365057 9.77E-10 9.009901378 -0.277004429 TTPQQGASGPGRS(ph)PVGQAR ddPTM_HeLa_Romidepsin_16h_R1 2 TTPQQGASGPGRSPVGQAR 19 1 A0A2R8YFR7;A0A2R8YF49;Q12774;H0Y895 A0A2R8YFR7 ARHGEF5 Rho guanine nucleotide exchange factor 5 1 0 TTPQQGASGPGRS(1)PVGQAR;TTPQQGAS(0.023)GPGRS(0.977)PVGQAR ; 95.9 0.00086459 7011300 974.72 1070.65 863.38 907.38 926.1 932.18 777.5 649.9 1009.77 1094.04 TRUE FALSE FALSE 962.8397377 1085.722639 878.4067667 1012.295545 878.8376612 872.6167065 843.5408306 668.7038311 919.4536422 1065.616683 0.903551674 1.018867906 0.824317769 0.949962178 0.824722131 0.818884239 0.791598747 0.627527554 0.862837132 1 10.05747286 -5.933130984 0.333823535 0.970108576 9.25E-16 0.675290532 0.061825638 5.058988476 0.201199984 0.017149219 2.387926937 1.17E-06 5.933130984 -0.970108576 TTPS(ph)YVAFTDTER ddPTM_HeLa_Romidepsin_16h_R1 1 TTPSYVAFTDTER 13 0 P11142;E9PKE3;P11142-2;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;E9PI65;P54652;A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P17066;P48741 P11142;P54652;A0A0G2JIW1;P17066 HSPA8;HSPA2;HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;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 1 0 T(0.263)T(0.063)PS(0.674)YVAFTDTER 157.09 0.00061733 6200800 663.17 785.1 791.13 710.86 629.13 786.03 801.22 710.13 1033.4 859.11 TRUE FALSE FALSE 655.087029 796.1526584 804.8992858 793.0529779 597.0231485 735.8052198 869.2756068 730.6764912 940.9701158 836.7901984 0.782856958 0.951436405 0.961888998 0.947732155 0.713468143 0.879318641 1.03882145 0.873189591 1.124499448 1 9.708722143 TTPSYVAFT(ph)DTER ddPTM_HeLa_Romidepsin_16h_R1 1 TTPSYVAFTDTER 13 0 P11142;E9PKE3;P11142-2;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;E9PI65;P54652;A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P17066;P48741 P11142;P54652;A0A0G2JIW1;P17066 HSPA8;HSPA2;HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;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 1 0 TTPSYVAFT(1)DTER 117.27 0.011135 6070100 1174.8 1366.2 945.36 812.09 1260 1007.4 1031.3 951.03 1352.9 1114.5 TRUE FALSE FALSE 1160.481086 1385.433399 961.8135942 905.9876668 1195.697498 943.0303912 1118.898596 978.5465526 1231.893236 1085.545129 1.069030715 1.276255922 0.886018986 0.834592356 1.101471939 0.868715971 1.030725086 0.901433322 1.134815313 1 10.08420399 TTPSYVAFTDTER ddPTM_HeLa_Romidepsin_16h_R1 5 TTPSYVAFTDTER 13 0 P11142;E9PKE3;P11142-2;E9PNE6;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;E9PI65;P54652;A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;Q53FA3;P34931;P17066;P48741 P11142;P54652;A0A0G2JIW1;P17066 HSPA8;HSPA2;HSPA1B;HSPA1A;HSPA1L;HSPA6;HSPA7 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2;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 0 ;;;; ;;;; 255.52 9.04E-65 202386300 6744.72 7614.04 6380 5748.28 7969.45 8163.92 7245.41 7218.35 7292.41 7151.04 FALSE FALSE TRUE 6662.512758 7721.230655 6491.041224 6412.92318 7562.739228 7642.27186 7860.834945 7427.201569 6640.158585 6965.25495 0.956535375 1.108535253 0.931917248 0.920701859 1.085780676 1.097199157 1.128578207 1.066321566 0.953325992 1 12.76596045 -8.659820049 7.286401598 0.982208656 1.098712137 0.552812643 0.051065489 0.130252576 8.265726967 0.00725342 0.014548973 2.19E-09 8.659820049 0.116503481 TTQIINITMTK ddPTM_HeLa_Romidepsin_16h_R1 1 TTQIINITMTK 11 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 0 0 118.48 0.012291 434980 195.04 167.96 59.246 0 164.26 238.01 166.06 129.35 198.73 154.21 FALSE FALSE TRUE 192.6627775 170.3245453 60.27715178 0 155.8771993 222.8019291 180.1651323 133.0925382 180.9550911 150.203602 1.282677479 1.133957795 0.401302971 0 1.037772711 1.483332798 1.199472782 0.886080869 1.204732035 1 7.2307756 -9.925457276 24.99999813 1.137448581 0.844987655 0.138183991 0.390815815 74.74895453 25067.10512 0.070178669 0.092232839 1.19E-10 9.925457276 -0.292460926 TTQIINITMTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TTQIINITMTKK 12 1 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 0 1 ; TTQIINITMTK(1)K;TTQIINITMTK(1)K 132.59 0.00035992 845850 487.22 374.34 451.73 410.2 339.22 345.03 341.93 356.92 456.66 406.85 FALSE TRUE FALSE 481.2815752 379.6099683 459.5921712 457.629254 321.9083376 322.9836965 370.9735257 367.2469171 415.8151859 396.2799783 1.214498843 0.957933757 1.159766317 1.154812958 0.812325515 0.81503915 0.936139967 0.926735988 1.049296479 1 8.630376268 -8.762323861 24.99938251 1.099921221 0.872992911 0.628337357 0.081452576 13.46812963 380687.1432 0.014457361 0.027347346 1.73E-09 8.762323861 -0.22692831 TTQPSINESES(ph)DPFEVVRDDFK ddPTM_HeLa_Romidepsin_16h_R1 1 TTQPSINESESDPFEVVRDDFK 22 1 Q76FK4-2;Q76FK4-4;Q76FK4;F8WE42;F5H101;F5GWN9 Q76FK4-2 NOL8 Nucleolar protein 8 1 0 TTQPS(0.01)INES(0.439)ES(0.551)DPFEVVRDDFK 63.184 0.003575 4014100 703.22 691.11 723.96 956.41 679.48 654.8 578.72 402.2 765.82 756.88 TRUE FALSE FALSE 694.6488842 700.8394647 736.5602201 1066.994624 644.8036001 612.9603933 627.8764624 413.8370224 697.3231412 737.2161485 0.942259452 0.950656692 0.999110263 1.447329425 0.874646603 0.831452749 0.851685715 0.561351 0.945886959 1 9.525943863 -7.27101468 1.138677265 0.999362688 0.378709614 0.449360029 0.154206848 1.207699471 1.266733742 0.023200603 0.889468971 5.36E-08 7.27101468 -0.620653074 TTQS(ph)MQDFPVVDSEEEAEEEFQK ddPTM_HeLa_Romidepsin_16h_R1 1 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 T(0.028)T(0.028)QS(0.662)MQDFPVVDS(0.281)EEEAEEEFQK 67.251 0.0006949 21713000 1044.3 848.28 1035.9 548.34 911.78 1231.2 1068.3 1192.7 1038.8 1082.1 TRUE FALSE FALSE 1031.57167 860.2221081 1053.929405 611.7416508 865.2484643 1152.530294 1159.041375 1227.208893 945.8871263 1053.986886 0.978732927 0.816160162 0.999945463 0.58040727 0.820929061 1.093495857 1.099673431 1.1643493 0.897437282 1 10.0416412 -5.200954906 12.605088 0.964885703 1.045393846 0 0.165034461 0 0 0.021957206 0 6.30E-06 5.200954906 0.080508143 TTQSMQDFPVVDS(ph)EEEAEEEFQK ddPTM_HeLa_Romidepsin_16h_R1 3 TTQSMQDFPVVDSEEEAEEEFQK 23 0 Q9UBB9 Q9UBB9 TFIP11 Tuftelin-interacting protein 11 1 0 T(0.006)T(0.006)QS(0.014)MQDFPVVDS(0.974)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK;TTQSMQDFPVVDS(1)EEEAEEEFQK ;; 141.12 7.77E-07 62388000 9830.1 8734.6 10389.6 7475.9 11198.3 11486.7 10339.4 11091.1 11045.2 11046.4 TRUE FALSE FALSE 9710.28696 8857.565928 10570.42663 8340.298733 10626.80896 10752.73694 11217.62838 11412.00348 10057.28965 10759.41294 0.902492266 0.823238775 0.982435259 0.775162993 0.987675538 0.999379521 1.042587402 1.060652988 0.934743346 1 13.39331174 -8.166324169 2.294206787 0.932612074 1.047888766 0.391092154 0.06862672 0.306448518 3.102771241 0.010883665 0.034774088 6.82E-09 8.166324169 0.115276692 TTRT(ph)PEEGGYSYDISEK ddPTM_HeLa_Romidepsin_16h_R1 1 TTRTPEEGGYSYDISEK 17 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.043)T(0.009)RT(0.948)PEEGGYSYDISEK 144.08 0.00070369 128970000 6662.9 5945.2 6039.3 6454.9 5823.9 6405.3 5501.2 5369.5 6865.8 5915.4 TRUE FALSE FALSE 6581.690012 6028.896682 6144.411483 7201.245909 5526.684651 5996.022002 5968.471791 5524.858011 6251.705652 5761.717055 1.142313992 1.046371528 1.066420205 1.249843725 0.959207923 1.04066582 1.035884222 0.958890893 1.085042114 1 12.4922831 -7.357543074 0.972992542 1.074416912 0.923155772 0.20004135 0.074070579 2.622579265 2.091513768 0.012597558 0.399548385 4.39E-08 7.357543074 -0.151261141 TTS(ph)PLEEEER ddPTM_HeLa_Romidepsin_16h_R1 2 TTSPLEEEER 10 0 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 T(0.034)T(0.065)S(0.901)PLEEEER;T(0.004)T(0.06)S(0.936)PLEEEER ; 201.09 2.20E-12 126082000 7508.9 7366.5 7592.1 4253.5 7044.5 7407.9 6215.5 7365 6968.8 7676.9 TRUE FALSE FALSE 7417.378639 7470.20578 7724.237316 4745.309683 6684.992878 6934.559098 6743.444415 7578.094655 6345.493074 7477.453031 0.991965928 0.999030786 1.033003789 0.634615779 0.894020043 0.927395875 0.901837081 1.013459345 0.848616908 1 12.86833123 TTS(ph)PLEEEEREIK ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPLEEEEREIK 13 1 S4R3H4;E7EQT4;Q9UKV3;Q9UKV3-5 S4R3H4;Q9UKV3-5 ACIN1 Apoptotic chromatin condensation inducer in the nucleus 1 0 TTS(1)PLEEEEREIK 167.84 0.00086007 26312000 3972.1 3861.7 3050.4 5067.1 3974.3 4081.2 3480.5 4133.4 4078.7 3482 TRUE FALSE FALSE 3923.686517 3916.065114 3103.490932 5652.981943 3771.476641 3820.424491 3776.133583 4252.993408 3713.890857 3391.537138 1.156905072 1.154657889 0.915069128 1.666790518 1.112025753 1.126458103 1.11339886 1.254001721 1.095046495 1 11.72772358 -11.77995944 0.427541258 0.971035043 1.205085452 0.089567011 0.181320744 2.328320325 0.743345702 0.238200193 0.062104588 1.66E-12 11.77995944 0.234050409 TTS(ph)PPEVSGYSYEK ddPTM_HeLa_Romidepsin_16h_R1 2 TTSPPEVSGYSYEK 14 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 T(0.181)T(0.038)S(0.781)PPEVSGYSYEK;T(0.348)T(0.061)S(0.591)PPEVSGYSYEK ; 171.36 8.41E-05 730359000 5726.9 5562.3 4778.7 5198.1 5439.8 5566.8 4950.3 4789.4 5624.5 5461.4 TRUE FALSE FALSE 5657.09834 5640.606205 4861.871269 5799.12878 5162.186707 5211.099446 5370.778358 4927.973733 5121.430633 5319.512041 1.063461892 1.060361582 0.913969408 1.090161792 0.970424856 0.979619823 1.00963741 0.926395823 0.962763237 1 12.3770782 -4.746854112 0.457351145 1.028168303 3.37E-11 0.110690803 0.052788373 42.35106132 0.897831062 0.010289892 38.009025 1.79E-05 4.746854112 -1.028168303 TTS(ph)PPLSIPTTHLIHQPAGSR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPPLSIPTTHLIHQPAGSR 21 0 Q5T5U3;A0A087WW76;A0A452Q6Z5;E7ESW5;A0A1B0GV73;Q5T5U3-3 Q5T5U3 ARHGAP21 Rho GTPase-activating protein 21 1 0 T(0.183)T(0.183)S(0.633)PPLS(0.001)IPTTHLIHQPAGSR 99.097 0.00020845 15002000 866.24 1095.9 975.35 698.52 1234.1 1298 853.69 1003 1046.3 1153.3 TRUE FALSE FALSE 855.6819337 1111.328109 992.3255576 779.286169 1171.119272 1215.061989 926.2024073 1032.020223 952.7163075 1123.3371 0.761732105 0.98930954 0.883372905 0.693724234 1.042535916 1.08165393 0.824509764 0.918709284 0.848112564 1 10.13357521 TTS(ph)PSSDTDLLDR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSPSSDTDLLDR 13 0 Q96QT6;C9J9G2;Q96QT6-2;Q96QT6-5;Q96QT6-3;K7ENU0;K7ERZ4;K7EJ43 Q96QT6 PHF12 PHD finger protein 12 1 0 T(0.3)T(0.002)S(0.697)PSSDTDLLDR 274.59 9.17E-81 41077000 3601.3 3280.4 2932.9 2809.4 3305.7 3010.4 3274.5 2662.3 3534.5 2978 TRUE FALSE FALSE 3557.40597 3326.581557 2983.945894 3134.236047 3136.997794 2818.045156 3552.635948 2739.32945 3218.365468 2900.631131 1.226424806 1.146847499 1.028722978 1.080535892 1.081488012 0.971528274 1.224780328 0.944390833 1.109539725 1 11.50215113 -9.760641459 24.99961584 1.112904724 1.061485068 0.112845828 0.087808178 56.69691556 1776316.636 0.016830254 0.023022982 1.74E-10 9.760641459 -0.051419656 TTSESSS(ph)SPSASLK ddPTM_HeLa_Romidepsin_16h_R1 2 TTSESSSSPSASLK 14 0 Q96CB8;A0A087WXN4 Q96CB8 INTS12 Integrator complex subunit 12 1 0 T(0.001)TS(0.001)ES(0.011)S(0.068)S(0.458)S(0.458)PS(0.003)ASLK;TTSES(0.211)S(0.211)S(0.565)S(0.012)PS(0.001)ASLK ; 146.67 5.35E-05 11475000 4656.7 4850.4 5492.4 3556.6 5584.1 7225.4 6188.7 6505.7 5044.9 5376.4 TRUE FALSE FALSE 4599.942349 4918.684059 5587.992918 3967.830826 5299.12254 6763.720259 6714.368024 6693.932165 4593.671509 5236.720353 0.878401373 0.939268039 1.067078733 0.757693854 1.011916273 1.291594701 1.282170437 1.278268022 0.877203898 1 12.35444785 -8.326164385 4.190388467 0.938246631 1.285701097 0.809458466 0.078605068 0.070008508 2.450119105 0.011273207 0.026773897 4.72E-09 8.326164385 0.347454466 TTSIS(ph)PALAR ddPTM_HeLa_Romidepsin_16h_R1 3 TTSISPALAR 10 0 Q9UKE5-6;Q9UKE5-2;Q9UKE5-4;Q9UKE5;Q9UKE5-8;Q9UKE5-5;Q9UKE5-7;Q9UKE5-3 Q9UKE5-6 TNIK TRAF2 and NCK-interacting protein kinase 1 0 T(0.128)T(0.001)S(0.003)IS(0.868)PALAR;T(0.009)TS(0.004)IS(0.987)PALAR;T(0.016)TS(0.004)IS(0.979)PALAR ;; 131.42 0.0067711 130412000 7865.8 7462.5 6822.6 6822.8 8555.9 7971 7212.3 7287.1 7807.4 6867.8 TRUE FALSE FALSE 7769.928604 7567.557271 6941.344491 7611.684238 8119.260497 7461.678825 7824.912582 7497.940741 7109.08659 6689.373566 1.161533068 1.13128041 1.037667342 1.137876987 1.213754983 1.115452553 1.169752669 1.120873377 1.062743248 1 12.7076554 -12.3854424 0.77447015 0.985689907 1.138372792 0.420249833 0.046735431 0.482812572 0.437748278 0.048406151 0.008697142 4.12E-13 12.3854424 0.152682885 TTSS(ph)SDLTTSSSSSGPR ddPTM_HeLa_Romidepsin_16h_R1 1 TTSSSDLTTSSSSSGPR 17 0 Q5QP82;A0A0A0MQT4 Q5QP82 DCAF10 DDB1- and CUL4-associated factor 10 1 0 T(0.035)T(0.002)S(0.111)S(0.67)S(0.154)DLT(0.001)T(0.001)S(0.016)S(0.005)S(0.002)S(0.002)S(0.001)GPR 105.63 0.0025327 7238100 991.05 911.15 1330 925.86 1121.1 1125.8 1278.9 730.13 1424.1 1322.7 TRUE FALSE FALSE 978.9707014 923.9771936 1353.148092 1032.91229 1063.886084 1053.865013 1387.529734 751.2551596 1296.724929 1288.336063 0.759872155 0.71718647 1.050306772 0.801741346 0.82578305 0.818004745 1.07699363 0.583120492 1.006511396 1 10.33129326 -12.47954563 1.235659696 0.999499085 0.831309236 0.202334796 0.13767522 0.62236407 1.7082739 0.087644036 0.021743988 3.31E-13 12.47954563 -0.168189849 TTSVSLTIGSS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 TTSVSLTIGSSSPK 14 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-2;Q8WX93-9;D6R9Z5;D6RBH5;D6RBB1;H0Y952;Q8WX93-6 Q8WX93-3 PALLD Palladin 1 0 TTSVSLTIGS(0.002)S(0.499)S(0.499)PK;TTSVSLT(0.001)IGS(0.095)S(0.549)S(0.355)PK ; 234.04 6.29E-43 74551000 9608.2 9331.9 9249.8 8694.9 9463.9 9049.3 7558.4 7559.5 10322.8 8982.7 TRUE FALSE FALSE 9491.091563 9463.274733 9410.788889 9700.245249 8980.921868 8471.078935 8200.410307 7778.222206 9399.502914 8749.328159 1.08477947 1.08160016 1.075601317 1.108684584 1.026469885 0.968197647 0.937261714 0.88900794 1.074311392 1 13.09495652 -8.01178731 1.757281023 1.051926924 0.903636893 0.79634458 0.031530444 0.183141502 1.053795266 0.006221247 0.027665127 9.73E-09 8.01178731 -0.148290031 TTT(ph)PPDSGVLFEGLGISTRPR ddPTM_HeLa_Romidepsin_16h_R1 1 TTTPPDSGVLFEGLGISTRPR 21 1 Q9NS56-2;Q9NS56 Q9NS56-2 TOPORS E3 ubiquitin-protein ligase Topors 1 0 T(0.25)T(0.25)T(0.329)PPDS(0.171)GVLFEGLGISTRPR 121.51 6.68E-05 25486000 1053 800.69 948.48 904.99 1268 1490.8 1193.4 1456.1 1233.2 1045.1 TRUE FALSE FALSE 1040.165631 811.9621348 964.9878965 1009.629202 1203.289228 1395.542691 1294.767366 1498.229956 1122.899503 1017.948151 1.021825748 0.797645866 0.947973524 0.991827728 1.1820732 1.370936908 1.271938423 1.471813623 1.103100882 1 9.991448365 -8.526092816 2.339689103 0.985607575 1.365675765 0.811277183 0.085546002 0.091304766 0.994333054 0.011970446 0.029076956 2.98E-09 8.526092816 0.38006819 AQS(ph)SPAAPASLSAPEPASQAR ddPTM_HeLa_Romidepsin_16h_R1 2 AQSSPAAPASLSAPEPASQAR 21 0 J3KPH8;Q8WUI4-3;Q8WUI4-4;Q8WUI4;Q8WUI4-7;Q8WUI4-6;Q8WUI4-5;Q8WUI4-8;Q8WUI4-10;H0YI15 J3KPH8 HDAC7 Histone deacetylase;Histone deacetylase 7 1 0 AQS(0.5)S(0.5)PAAPASLSAPEPASQAR;AQS(0.963)S(0.037)PAAPASLSAPEPASQAR ; 273.01 1.44E-95 81684500 6252.2 5825.4 5198.6 5378.7 4509.9 3416 2408.57 2585.17 6221.9 6121.1 TRUE FALSE FALSE 6175.995782 5907.410134 5289.079452 6000.610602 4279.742974 3197.728625 2613.153876 2659.967815 5665.397681 5962.07294 1.035880615 0.990831577 0.88712089 1.006463802 0.717828013 0.536345103 0.438296194 0.446148151 0.950239579 1 12.54159831 -8.465295305 1.441678376 1.009480894 0.430828878 0.956159472 0.048526986 0.050040853 0.199893285 0.00681498 0.021669155 3.43E-09 8.465295305 -0.578652016 down TTTAAAVASTGPS(ph)SR ddPTM_HeLa_Romidepsin_16h_R1 1 TTTAAAVASTGPSSR 15 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 TTTAAAVASTGPS(0.878)S(0.122)R 130.02 0.0020339 5140500 1920 2067.6 1638.2 1365.5 1543.5 1592.5 1640.8 1568.7 2155 2070.4 TRUE FALSE FALSE 1896.598301 2096.707727 1666.712184 1523.385535 1464.729435 1490.74439 1780.169511 1614.08786 1962.251403 2016.61071 0.940488064 1.039718631 0.826491784 0.755418747 0.726332271 0.739232606 0.882753177 0.800396354 0.973044224 1 10.97771689 -9.631442537 5.304398461 0.975903564 0.782106167 0.812365689 0.047259925 0.072621652 3.145072836 0.008085478 0.011489262 2.34E-10 9.631442537 -0.193797397 TTTAAAVASTGPSS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TTTAAAVASTGPSSR 15 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 TTTAAAVAS(0.023)T(0.197)GPS(0.197)S(0.584)R 84.195 0.024528 1998800 1518.1 1513.5 1289.6 1639.8 1057.9 1566.8 1357.2 1213.6 1807.6 1576.3 TRUE FALSE FALSE 1499.596813 1534.807093 1312.044947 1829.401391 1003.911415 1466.686537 1472.480534 1248.713601 1645.923729 1535.347499 0.976714923 0.999648024 0.85455895 1.191522696 0.653865927 0.955279855 0.959053592 0.813310083 1.072020328 1 10.58434951 -8.763328404 24.99997661 0.99108883 0.861347306 0.334249975 0.113775825 50.56322608 669184.4774 0.014726632 0.027708154 1.72E-09 8.763328404 -0.129741524 TTTAAAVASTGPSSRS(ph)PSTLLPK ddPTM_HeLa_Romidepsin_16h_R1 1 TTTAAAVASTGPSSRSPSTLLPK 23 1 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;B5MEG9;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 TTTAAAVAS(0.002)T(0.002)GPS(0.004)S(0.014)RS(0.876)PS(0.051)T(0.051)LLPK 90.744 4.65E-05 284270000 2779.1 2577.5 2050 4866.7 2585.4 2612.4 2583 2467.3 2778.9 2749.2 TRUE FALSE FALSE 2745.22726 2613.786113 2085.67939 5429.410753 2453.457391 2445.476071 2802.399956 2538.687433 2530.348224 2677.775388 1.025189518 0.976103569 0.778885115 2.027582589 0.916229719 0.91324914 1.046540337 0.948058394 0.944944164 1 11.38681924 -6.096570029 17.91475994 1.045812969 1.110003091 0 0.331149756 0 0 0.040495356 0 8.01E-07 6.096570029 0.064190122 TTTTNTQVEGDDEAAFLER ddPTM_HeLa_Romidepsin_16h_R1 2 TTTTNTQVEGDDEAAFLER 19 0 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;C9JEK3;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 0 0 ; ; 176.19 2.56E-08 9691100 2495.32 2115.75 1719.46 1514.88 1822.93 1861.5 1551.58 1885.87 2312.26 2084.79 FALSE FALSE TRUE 2464.90608 2145.535584 1749.38648 1690.037553 1729.89908 1742.556158 1683.371166 1940.434673 2105.445674 2030.626855 1.213864612 1.056587811 0.861500711 0.832273812 0.85190397 0.858137059 0.828990891 0.955584069 1.036845184 1 10.98770944 -9.810524223 4.42835271 1.102335356 0.859901155 0.735149938 0.062067157 0.09532763 3.947142697 0.013682227 0.018455422 1.55E-10 9.810524223 -0.242434201 TTVVYPATEK(ac)HLQK ddPTM_HeLa_Romidepsin_16h_R1 1 TTVVYPATEKHLQK 14 1 Q96C86;A0A3B3ITF0 Q96C86 DCPS m7GpppX diphosphatase 0 1 TTVVYPATEK(1)HLQK 89.231 0.028654 597070 335.87 481.87 282.16 281.26 514.02 433.77 422.87 308.91 334.79 299.51 FALSE TRUE FALSE 331.7762873 488.6537785 287.0708764 313.7806046 487.7876413 406.0534969 458.7885672 317.8478235 304.8455439 291.728687 1.137276867 1.675028203 0.984033759 1.075590501 1.672059222 1.391887445 1.572654962 1.089532287 1.04496252 1 8.18848345 -10.62220899 0.480132799 0.991459501 1.397015906 0.21112476 0.239172818 0.828819151 0.480014382 0.118416646 0.101144588 2.39E-11 10.62220899 0.405556406 TTYDS(ph)AEEENKENLYAGK ddPTM_HeLa_Romidepsin_16h_R1 2 TTYDSAEEENKENLYAGK 18 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 0 T(0.014)T(0.004)Y(0.02)DS(0.962)AEEENKENLYAGK;T(0.006)T(0.006)Y(0.204)DS(0.785)AEEENKENLYAGK ; 80.362 0.0049086 67146000 5377.3 5304 5274.6 4419.4 3785 4382.4 3762.1 3702.2 5481.7 5078.6 TRUE FALSE FALSE 5311.759399 5378.669851 5366.4022 4930.391822 3591.837326 4102.378784 4081.65268 3809.317316 4991.403023 4946.65724 1.073807855 1.087334252 1.084854264 0.996711836 0.726114051 0.829323437 0.825133516 0.770079092 1.009045661 1 12.27223822 -8.863282472 5.378070816 1.043635807 0.794104581 0.909421414 0.039498604 0.049592314 2.208832544 0.006580409 0.012127826 1.37E-09 8.863282472 -0.249531226 TTYLVLDEADR ddPTM_HeLa_Romidepsin_16h_R1 1 TTYLVLDEADR 11 0 P17844;J3KTA4;P17844-2;J3QSF1;J3KRZ1 P17844 DDX5 Probable ATP-dependent RNA helicase DDX5 0 0 169.99 0.0036163 22711000 2579.1 2563.6 2913.3 2299.7 2458.9 2184.9 2164.6 1991.8 2991.4 2559.2 FALSE FALSE TRUE 2547.664937 2599.690428 2964.004764 2565.602134 2333.413158 2045.291941 2348.46107 2049.42959 2723.841692 2492.711615 1.0220456 1.042916642 1.189068461 1.029241457 0.936094309 0.82050885 0.942131074 0.822168749 1.092722349 1 11.28350027 -8.594883325 3.619965019 1.029283433 0.870033406 0.653094538 0.063909273 0.128855105 3.376496808 0.009400645 0.020021601 2.54E-09 8.594883325 -0.159250027 TVAISDAAQLPHDYCTTPGGTLFSTT(ph)PGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 0 TVAISDAAQLPHDY(0.034)CT(0.288)T(0.074)PGGT(0.033)LFS(0.052)T(0.052)T(0.321)PGGT(0.146)R 63.167 0.0004084 22794000 1076.6 1418.4 1272.7 274.7 2338.2 2673.2 2801.2 2532.4 1683.7 1204 TRUE FALSE FALSE 1063.477985 1438.368272 1294.85081 306.4621065 2218.872929 2502.391147 3039.133858 2605.670999 1533.105655 1172.719906 0.906847389 1.226523285 1.104143285 0.261325918 1.892074072 2.133835312 2.59152577 2.221903955 1.307307607 1 10.19564276 -8.580941456 5.742147125 0.947119742 2.294813699 0.821016381 0.288809073 0.050143169 3.38062153 0.037439654 0.076134552 2.62E-09 8.580941456 1.347693957 up TVAISDAAQLPHDYCTTPGGTLFSTTPGGT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 TVAISDAAQLPHDYCTTPGGTLFSTTPGGTR 31 0 Q13542 Q13542 EIF4EBP2 Eukaryotic translation initiation factor 4E-binding protein 2 1 0 TVAISDAAQLPHDY(0.011)CT(0.005)T(0.012)PGGT(0.068)LFS(0.084)T(0.106)T(0.287)PGGT(0.428)R 59.305 0.00086257 15842000 1021.6 793.61 968.78 104.59 1903.5 2436.2 2424.7 2389.4 1234.5 1168.3 TRUE FALSE FALSE 1009.148346 804.7824624 985.6412095 116.6831879 1806.357292 2280.534682 2630.653957 2458.533519 1124.083228 1137.947398 0.886814582 0.707222903 0.866157093 0.102538297 1.587382067 2.004077418 2.311753569 2.160498389 0.987816511 1 10.15221815 -8.498599932 4.022111293 0.863579291 2.147167567 0.844390027 0.269262631 0.065344679 2.353833412 0.039877 0.089002826 3.17E-09 8.498599932 1.283588276 up PEPSK(ac)SAPAPK ddPTM_HeLa_Romidepsin_16h_R1 1 PEPSKSAPAPK 11 1 P33778;U3KQK0;Q99877 P33778;U3KQK0 HIST1H2BB;HIST1H2BN Histone H2B type 1-B;Histone H2B;Histone H2B type 1-N 0 1 PEPSK(1)SAPAPK 104.07 0.010753 17232000 1140 1223.3 1371.9 4962.9 13737 19456 20821 21676 0 1058.7 FALSE TRUE FALSE 1126.105242 1240.52165 1395.777344 5536.733849 13035.94963 18212.82439 22589.53522 22303.16086 0 1031.194821 1.092039271 1.202994452 1.353553485 5.369241325 12.64159726 17.66186565 21.90617597 21.62846477 0 1 10.01010121 -8.549202706 1.230084369 0.972208088 22.11871046 0.995068237 0.608398897 0.018064432 0.052366081 0.080709965 0.265107349 2.82E-09 8.549202706 21.14650237 up (ac)SETAPAAPAAAPPAEK(ac)APVKK ddPTM_HeLa_Romidepsin_16h_R1 2 SETAPAAPAAAPPAEKAPVKK 21 2 P16403 P16403 HIST1H1C Histone H1.2 0 1 ; SETAPAAPAAAPPAEK(0.988)APVK(0.012)K;SETAPAAPAAAPPAEK(0.837)APVK(0.163)K 54.812 0.0003343 2576500 377.14 1034.46 530.57 855.01 1215.28 1557.53 1370.44 1666.14 766.64 843.02 FALSE TRUE FALSE 372.5432726 1049.023155 539.8043483 953.8702791 1153.259727 1458.00886 1486.845139 1714.347132 698.0697983 821.1182189 0.453702359 1.277554353 0.657401499 1.161672287 1.404499012 1.77563818 1.810756485 2.087820113 0.850145305 1 9.681446136 -8.541639097 0.955551129 0.763456039 2.030912748 0.815835335 0.215971659 0.210245292 0.346017983 0.042650386 0.172487841 2.87E-09 8.541639097 1.267456709 up GSTSSSPYVAASHT(ph)PPINGSDSILGTR ddPTM_HeLa_Romidepsin_16h_R1 1 GSTSSSPYVAASHTPPINGSDSILGTR 27 0 B4DGI9;Q99081;Q99081-3;F5GY10;Q99081-4;Q99081-2 B4DGI9 TCF12 Transcription factor 12 1 0 GSTSSSPYVAAS(0.012)HT(0.946)PPINGS(0.025)DS(0.012)ILGT(0.005)R 58.054 0.0027438 11537000 1438.1 1633.9 1365.8 1468.8 1236.8 771.28 652.48 634.21 1950.2 1437.5 TRUE FALSE FALSE 1420.571884 1656.902087 1389.571176 1638.629567 1173.681481 721.9976972 707.9016349 652.5598657 1775.769228 1400.153543 1.01458293 1.183371706 0.992441996 1.170321338 0.838251981 0.515656087 0.505588575 0.466063075 1.268267496 1 10.45136933 -8.386650039 2.983605244 1.030634277 0.489999243 0.869227089 0.103291813 0.049915911 0.845198168 0.010339095 0.02556331 4.11E-09 8.386650039 -0.540635034 down TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK ddPTM_HeLa_Romidepsin_16h_R1 3 TVAQQHDEDGIEEEDDDDDEIDDDDTISDWNLRK 34 1 Q92973-3;Q92973-2;Q92973 Q92973-3 TNPO1 Transportin-1 0 0 ;; ;; 155.42 1.76E-19 27184600 5961.6 6360.1 5267.3 8130.4 5361.8 5422.8 3972.13 5493.5 6382.7 5964.7 FALSE FALSE TRUE 5888.937726 6449.637655 5358.975147 9070.475103 5088.167338 5076.300581 4309.522623 5652.445755 5811.815326 5809.736234 1.013632545 1.110142938 0.922412814 1.561254201 0.875800059 0.873757495 0.741775952 0.972926399 1.000357863 1 12.50425695 -8.559547492 24.9999276 1.049928455 0.854723995 0.270854675 0.17739754 188.7503611 128685.0941 0.024759573 0.04951925 2.76E-09 8.559547492 -0.195204459 TVAT(ph)PLNQVANPNSAIFGGAR ddPTM_HeLa_Romidepsin_16h_R1 2 TVATPLNQVANPNSAIFGGAR 21 0 Q15056;Q15056-2 Q15056 EIF4H Eukaryotic translation initiation factor 4H 1 0 T(0.006)VAT(0.993)PLNQVANPNS(0.001)AIFGGAR;T(0.004)VAT(0.996)PLNQVANPNSAIFGGAR ; 184.97 2.04E-13 32436000 2158.42 2208.13 2606.13 1924.01 2668.99 3207.32 2035.84 2534.55 2717.42 2433.04 TRUE FALSE FALSE 2132.112347 2239.216112 2651.488599 2146.473089 2532.781481 3002.382603 2208.764199 2607.883205 2474.367149 2369.82927 0.899690275 0.944884993 1.118852161 0.905750096 1.068761161 1.266919369 0.932035158 1.100451935 1.044111988 1 11.21056741 -9.119056188 1.109949768 0.954272685 1.086758628 0.130667446 0.102484006 0.528114763 1.284198922 0.016910424 0.037700079 7.60E-10 9.119056188 0.132485943 TVAT(ph)PLNQVANPNSAIFGGARPR ddPTM_HeLa_Romidepsin_16h_R1 1 TVATPLNQVANPNSAIFGGARPR 23 1 Q15056;Q15056-2 Q15056 EIF4H Eukaryotic translation initiation factor 4H 1 0 T(0.045)VAT(0.955)PLNQVANPNSAIFGGARPR 116.69 3.51E-06 51016000 1184.7 1316.3 959.64 1334.6 1570.8 1853.8 1084.8 1260.1 1197.2 1037.6 TRUE FALSE FALSE 1170.260421 1334.830906 976.3421317 1488.912731 1490.636215 1735.348163 1176.942885 1296.559005 1090.119434 1010.643002 1.1579365 1.320773906 0.966060349 1.473233108 1.474938441 1.717073347 1.164548591 1.282905044 1.078639471 1 9.981057757 -9.253012821 24.90521183 1.091457583 1.427480901 0.492255419 0.161091142 393.1680493 1162031.899 0.025376385 0.041635037 5.58E-10 9.253012821 0.336023318 TVDLK(ac)PDWGK ddPTM_HeLa_Romidepsin_16h_R1 1 TVDLKPDWGK 10 1 P31948-3;P31948;P31948-2;F5GXD8;F5H783 P31948-3 STIP1 Stress-induced-phosphoprotein 1 0 1 TVDLK(1)PDWGK 117.02 0.015558 414080 351.63 314.15 317.44 216.88 992.6 597 622.62 727.08 689.57 500.47 FALSE TRUE FALSE 347.3441983 318.5726119 322.96491 241.9566861 941.9439181 558.8536267 675.5053273 748.1169127 627.8931321 487.4677173 0.712548105 0.653525558 0.662535997 0.496354276 1.932320613 1.146442332 1.385743719 1.534700425 1.288071209 1 8.929162869 -8.769914861 24.99999727 0.803732814 1.466414838 0.608374036 0.273682653 86.47443555 255072.7952 0.035519998 0.065137875 1.70E-09 8.769914861 0.662682024 TVDVAAEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 TVDVAAEKK 9 1 F8VZQ9;P82979;H0YHG0 F8VZQ9 SARNP SAP domain-containing ribonucleoprotein 0 1 ; TVDVAAEK(1)K;TVDVAAEK(1)K 119.68 0.0012965 13705300 9465.9 8801 7572.5 5665.2 7334.5 6793 8508.6 7061.8 9338.1 8887.1 FALSE TRUE FALSE 9350.52597 8924.900709 7704.296186 6320.23708 6960.193096 6358.949223 9231.320272 7266.122041 8502.876948 8656.211861 1.080209926 1.031040004 0.890030918 0.730138908 0.804069171 0.734611089 1.066438809 0.839411299 0.982286141 1 13.07952009 -9.692815841 3.969160104 1.038867397 0.838244402 0.487116608 0.09081263 0.13489723 4.212980602 0.014698311 0.020818499 2.03E-10 9.692815841 -0.200622995 TVEDEDQDS(ph)EEEKDNDSYIK ddPTM_HeLa_Romidepsin_16h_R1 1 TVEDEDQDSEEEKDNDSYIK 20 1 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 0 TVEDEDQDS(0.584)EEEKDNDS(0.208)Y(0.208)IK 49.306 0.026786 109220000 1629.5 1824.8 1859.7 1378.9 1662.8 1815.8 1698 1441.7 1942 2008.1 TRUE FALSE FALSE 1609.639027 1850.489582 1892.067298 1538.334906 1577.941111 1699.77624 1842.228078 1483.413315 1768.302656 1955.929273 0.822953595 0.946092279 0.967349548 0.786498227 0.806747531 0.869037682 0.941868453 0.758418689 0.904072903 1 10.93363849 -9.263917427 24.99223621 0.920445056 0.839186968 0.353951012 0.063832535 286.9733184 2894261.306 0.012356001 0.019440347 5.45E-10 9.263917427 -0.081258088 TVEDEDQDS(ph)EEEKDNDSYIKER ddPTM_HeLa_Romidepsin_16h_R1 1 TVEDEDQDSEEEKDNDSYIKER 22 2 Q9Y5T5-4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5 Q9Y5T5-4 USP16 Ubiquitin carboxyl-terminal hydrolase 16 1 0 TVEDEDQDS(1)EEEKDNDSYIKER 80.752 0.0015362 6177800 1185.9 1177.1 1071.8 1590.5 1101.5 1272 988.7 893.93 1566.1 1170.7 TRUE FALSE FALSE 1171.445795 1193.671245 1090.454229 1774.401094 1045.286345 1190.723305 1072.680153 919.7944542 1426.024094 1140.285045 1.027327158 1.046818293 0.956299685 1.5561031 0.916688638 1.044233028 0.940712288 0.80663555 1.250585632 1 10.15517879 -7.38639698 1.78980414 1.046217573 0.761281658 0.170722499 0.181433188 0.939350465 3.637570225 0.023341772 0.41322843 4.11E-08 7.38639698 -0.284935915 TVEIVHIDIADR ddPTM_HeLa_Romidepsin_16h_R1 2 TVEIVHIDIADR 12 0 B3KYB6;B3KYB7;A0A0A0MSW4;P48739;P48739-2;P48739-3 B3KYB6 PITPNB Phosphatidylinositol transfer protein beta isoform 0 0 ; ; 97.69 0.0084853 6670400 6621.4 5196.2 5926.6 5306.7 7132.5 6648.5 6905.9 5624.8 7708.5 6559 FALSE FALSE TRUE 6540.69583 5269.35224 6029.749987 5920.285623 6768.50191 6223.682307 7492.486974 5787.544714 7019.032454 6388.596234 1.023807984 0.824805958 0.943830188 0.926695851 1.059466221 0.974186203 1.172790813 0.905918061 1.098681494 1 12.64128325 -6.951875852 16.01974415 0.999057578 0.356312638 0.090378213 0.091454542 6926074.593 60040955.42 0.011487257 136758165.3 1.12E-07 6.951875852 -0.64274494 TVFPGAVPVLPAS(ph)PPPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVFPGAVPVLPASPPPK 17 0 M0R2S2;M0R165;Q9UBC2-4;Q9UBC2-3;Q9UBC2;Q9UBC2-2 M0R2S2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 0 TVFPGAVPVLPAS(1)PPPK 114.29 0.0020807 35816000 3899.3 3912.8 4094.5 2439.8 5445.3 6721.1 6074.7 5945.3 4616.1 4383 TRUE FALSE FALSE 3851.773832 3967.884501 4165.763055 2721.901156 5167.406022 6291.643401 6590.684866 6117.317875 4203.224455 4269.129028 0.902238795 0.929436537 0.975787573 0.637577627 1.210412238 1.473753396 1.543800813 1.432919416 0.984562525 1 12.05972605 -8.481929543 4.002077501 0.931881004 1.480960444 0.860347498 0.104345515 0.059025892 2.006033742 0.015027963 0.033927589 3.30E-09 8.481929543 0.54907944 TVFPGAVPVLPAS(ph)PPPKDSLR ddPTM_HeLa_Romidepsin_16h_R1 2 TVFPGAVPVLPASPPPKDSLR 21 1 M0R2S2;M0R165;Q9UBC2-4;Q9UBC2-3;Q9UBC2;Q9UBC2-2 M0R2S2 EPS15L1 Epidermal growth factor receptor substrate 15-like 1 1 0 TVFPGAVPVLPAS(1)PPPKDSLR;TVFPGAVPVLPAS(1)PPPKDSLR ; 147.28 6.88E-06 833260000 14767.5 13488.1 11973 13073.5 17238.1 20463.7 18136.9 20043.9 14831.9 13207.6 TRUE FALSE FALSE 14587.50803 13677.98583 12181.38504 14585.11958 16358.37543 19156.13561 19677.44783 20623.83862 13505.29772 12864.46465 1.133938211 1.063237857 0.946901824 1.133752549 1.271593951 1.489073672 1.529597101 1.60316338 1.049814204 1 13.6511038 -8.42741861 1.572060608 1.056187725 1.571974474 0.949827853 0.050537153 0.075805777 0.360113893 0.009764446 0.030390474 3.74E-09 8.42741861 0.515786749 SKLNTITPVVGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SKLNTITPVVGKK 13 2 Q9HCK8-2;Q9HCK8;A0A2R8Y840;A0A2R8YFT4;A0A2R8Y808;A0A2R8Y4P3 Q9HCK8-2 CHD8 Chromodomain-helicase-DNA-binding protein 8 0 1 ; SKLNTITPVVGK(1)K;SKLNTITPVVGK(1)K 102.52 0.011216 2328300 1615.41 1693.04 1633.12 3298.6 4639.7 6175.7 6380.4 6991.1 1784.88 1584.59 FALSE TRUE FALSE 1595.720762 1716.874662 1661.543769 3679.999652 4402.918796 5781.092701 6922.351017 7193.376448 1625.235862 1543.422123 1.033884857 1.112381788 1.0765323 2.384311846 2.852699031 3.745632911 4.485066601 4.660666929 1.053008012 1 10.59191698 -8.534970697 0.893826166 0.989574717 4.805376517 0.986669582 0.165264369 0.048339773 0.067962557 0.027110449 0.116923607 2.92E-09 8.534970697 3.815801801 up TVGLFLQGGK ddPTM_HeLa_Romidepsin_16h_R1 2 TVGLFLQGGK 10 0 P43304-2;P43304 P43304-2 GPD2 "Glycerol-3-phosphate dehydrogenase, mitochondrial" 0 0 ; ; 123.35 0.00047354 271690 63.228 73.755 395 333.35 279.98 348.53 203.634 89.646 0 0 FALSE FALSE TRUE 62.45735282 74.79332483 401.8748093 371.8934955 265.6915759 326.2600578 220.9306669 92.23976557 0 0 0 TVGT(ph)PIASVPGSTNTGTVPGSEK ddPTM_HeLa_Romidepsin_16h_R1 1 TVGTPIASVPGSTNTGTVPGSEK 23 0 A0A087WW66;Q99460-2;Q99460;H7BZR6 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 1 0 T(0.233)VGT(0.665)PIAS(0.083)VPGS(0.005)T(0.005)NT(0.007)GTVPGSEK 71.097 0.0012287 6474900 3381.8 3654.5 4076.7 2479 3158.1 3669.9 2659.7 3653.7 4159.5 4101.5 TRUE FALSE FALSE 3340.581321 3705.948147 4147.653253 2765.633644 2996.930373 3435.405234 2885.614852 3759.414045 3787.463902 3994.942439 0.836202617 0.927659961 1.038226036 0.692283728 0.750181115 0.859938607 0.722317004 0.941043357 0.948064699 1 11.963959 -9.258686885 24.998338 0.929021932 0.790540456 0.460886871 0.083275611 211.2942148 1918987.271 0.013898232 0.022393459 5.51E-10 9.258686885 -0.138481476 TVIES(ph)SPESPVTITEPYR ddPTM_HeLa_Romidepsin_16h_R1 1 TVIESSPESPVTITEPYR 18 0 Q8TEQ6 Q8TEQ6 GEMIN5 Gem-associated protein 5 1 0 T(0.005)VIES(0.437)S(0.437)PES(0.119)PVT(0.001)ITEPYR 165.45 5.31E-07 3303600 974.69 1080.2 1094 1220.9 1090.2 1001.9 624.25 1059.7 1181.3 1072.1 TRUE FALSE FALSE 962.8101034 1095.407084 1113.040611 1362.066203 1034.563026 937.8818235 677.2737794 1090.360748 1075.641569 1044.246687 0.922014036 1.048992635 1.065878996 1.304352907 0.990726653 0.898142014 0.648576421 1.044160121 1.030064622 1 10.02824685 -8.146125706 4.15724319 1.004564043 0.832722993 0.244065679 0.135266347 0.270895505 7.913235845 0.019747957 0.053538799 7.14E-09 8.146125706 -0.17184105 TVIIEQS(ph)WGSPK ddPTM_HeLa_Romidepsin_16h_R1 1 TVIIEQSWGSPK 12 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JL19;C9JCQ4;C9JL25 P10809;C9JL25 HSPD1 "60 kDa heat shock protein, mitochondrial" 1 0 TVIIEQS(0.741)WGS(0.259)PK 167.22 0.00022834 383640000 6507.2 6107.4 6580.5 5696.6 5805.4 6885.6 6134.5 5781.2 6667.9 6147.9 TRUE FALSE FALSE 6427.887743 6193.380138 6695.030842 6355.267695 5509.128775 6445.632382 6655.564277 5948.469901 6071.506324 5988.176672 1.073429876 1.034268105 1.118041636 1.061302637 0.920001042 1.076393155 1.111450888 0.993369138 1.013915697 1 12.54790107 -12.47454643 1.210286651 0.999964961 1.052002203 0.079507695 0.055096699 0.875179601 2.290900456 0.037773706 0.009249164 3.35E-13 12.47454643 0.052037242 TVIIEQSWGSPK ddPTM_HeLa_Romidepsin_16h_R1 2 TVIIEQSWGSPK 12 0 P10809;E7EXB4;E7ESH4;P10809-2;C9JL19;C9JCQ4;C9JL25 P10809;C9JL25 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 298.58 3.87E-131 4274100 1714.26 1906.6 1390.6 1798.24 1472.61 1994.46 1409.02 1543.24 1859.32 1328.03 FALSE FALSE TRUE 1693.36594 1933.441165 1414.80281 2006.16097 1397.457217 1867.020443 1528.702124 1587.891215 1693.017762 1293.527589 1.309106937 1.494704234 1.093755419 1.550922444 1.080345892 1.443355718 1.181808673 1.227566561 1.308837768 1 10.33709511 -12.09781534 0.86430015 0.999435596 1.298283488 0 0.178664596 0.486669765 0.657718212 0.09124643 0.026885251 7.98E-13 12.09781534 0.298847892 TVKEEAEK(ac)PER ddPTM_HeLa_Romidepsin_16h_R1 1 TVKEEAEKPER 11 2 K7ELL7;P14314-2;P14314 K7ELL7 PRKCSH Glucosidase 2 subunit beta 0 1 TVKEEAEK(1)PER 107.09 0.00060645 0 817.56 870.67 1198.3 741.56 2332.4 2179.8 2877.5 763.48 2677.2 1586.4 FALSE TRUE FALSE 807.5952643 882.9273151 1219.155909 827.3026563 2213.368925 2040.517815 3121.914778 785.5700892 2437.744527 1545.185099 0.522652765 0.571405533 0.789003149 0.53540683 1.432429633 1.320565294 2.020414758 0.508398696 1.577639163 1 10.59356396 -8.75353528 24.99561356 0.738658433 1.370457641 0.197605699 0.454157003 134.9378844 426718.8153 0.052375488 0.103253328 1.76E-09 8.75353528 0.631799208 LPSANQGS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 2 LPSANQGSPFK 11 0 E5RFP7;E5RIE3;E5RFE4;Q56NI9 E5RFP7 ESCO2 N-acetyltransferase ESCO2 1 0 LPS(0.186)ANQGS(0.814)PFK;LPSANQGS(1)PFK ; 161.87 0.0011142 83270000 5952.8 6224.2 5736.9 5384.5 4969.4 3403.7 2333.59 2466.3 5743.5 6067.1 TRUE FALSE FALSE 5880.244984 6311.824451 5836.748338 6007.081225 4715.792975 3186.214555 2531.805076 2537.658499 5229.786975 5909.475867 0.995053557 1.068085325 0.987693066 1.016516754 0.798005285 0.539170415 0.42843141 0.429421924 0.884983219 1 12.52881446 -8.349453114 1.836421586 1.005135353 0.426018078 0.962926384 0.046391057 0.024647622 0.159326881 0.003928975 0.011958512 4.47E-09 8.349453114 -0.579117276 down TVKQEQINTEPLEDTVLS(ph)PTK ddPTM_HeLa_Romidepsin_16h_R1 1 TVKQEQINTEPLEDTVLSPTK 21 1 O15446;O15446-2 O15446 CD3EAP DNA-directed RNA polymerase I subunit RPA34 1 0 TVKQEQINTEPLEDT(0.048)VLS(0.476)PT(0.476)K 99.859 0.00017273 13193000 5421.8 4588.4 3566.3 14022 4294.1 3514.5 3656.5 2925.6 5427.3 4479.5 TRUE FALSE FALSE 5355.717016 4652.995616 3628.369956 15643.28962 4074.956054 3289.934793 3967.083019 3010.24762 4941.868695 4363.121944 1.227496523 1.066437215 0.831599484 3.585343205 0.933954197 0.754032281 0.909230379 0.689929747 1.132645101 1 12.09114508 -8.53995014 24.99992035 1.279248008 0.804731557 0.124407064 0.754491395 497.0242958 727856.8626 0.110258886 0.220557142 2.88E-09 8.53995014 -0.474516451 TVLEGSTAST(ph)SPADHSALPNQSLTVR ddPTM_HeLa_Romidepsin_16h_R1 1 TVLEGSTASTSPADHSALPNQSLTVR 26 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 T(0.001)VLEGS(0.041)T(0.119)AS(0.155)T(0.473)S(0.18)PADHS(0.031)ALPNQSLTVR 54.56 0.007973 22299000 896.56 821.29 822.81 760.39 923.55 978.01 737.87 927.41 824.7 1004.7 TRUE FALSE FALSE 885.6323819 832.8521422 837.1306629 848.3098695 876.4177973 915.5183174 800.5446594 954.2431451 750.9367665 978.5977492 0.90500145 0.851066889 0.855438983 0.866862682 0.895585339 0.935541001 0.818052831 0.975112753 0.767359998 1 9.934572154 -11.68193419 0.776695281 0.99589805 0.884114212 0 0.082890723 0.354436806 0.425511075 0.020867536 0.008719693 2.08E-12 11.68193419 -0.111783839 TVLELQYVLDKLGDDEVR ddPTM_HeLa_Romidepsin_16h_R1 1 TVLELQYVLDKLGDDEVR 18 1 E9PLA9;Q14444-2;Q14444;G3V153 E9PLA9 CAPRIN1 Caprin-1 0 0 188.58 2.38E-14 3121500 900.58 839.71 580.33 873.33 666.34 682.78 701.85 697.12 804.04 615.37 FALSE FALSE TRUE 889.6033846 851.5314594 590.4304002 974.3085237 632.3341833 639.1525616 761.4651215 717.2900673 732.1246486 599.3825987 1.484199552 1.420680983 0.9850643 1.625520203 1.054975878 1.066351547 1.270415796 1.196714868 1.221464638 1 9.22733339 -7.189575175 17.41898154 1.235620124 1.196698117 0.003295622 0.207135633 19698.45128 4765551.081 0.032171834 55.68188815 6.46E-08 7.189575175 -0.038922007 TVLLSTK(ac)SMK ddPTM_HeLa_Romidepsin_16h_R1 1 TVLLSTKSMK 10 1 Q9HCI7-2;Q9HCI7 Q9HCI7-2 MSL2 E3 ubiquitin-protein ligase MSL2 0 1 TVLLSTK(1)SMK 88.134 0.024771 334550 394.95 290.86 360.05 336.25 496.68 420.38 448.63 361.94 336.67 474.75 FALSE TRUE FALSE 390.1361975 294.9547347 366.3165192 375.1288071 471.3325662 393.5190747 486.736621 372.4121629 306.557392 462.4159266 0.843691091 0.637855917 0.79217972 0.81123678 1.019282726 0.85100675 1.052594846 0.805361886 0.662947304 1 8.853047278 -6.33003294 16.63998467 0.894674253 0.867917968 0 0.14183177 0 0 0.017277354 0 4.68E-07 6.33003294 -0.026756286 TVLPT(ph)VPESPEEEVK ddPTM_HeLa_Romidepsin_16h_R1 1 TVLPTVPESPEEEVK 15 0 E9PBY7;E9PQ61;O75152;A0A1W2PPR9 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 TVLPT(0.807)VPES(0.193)PEEEVK 224.34 2.39E-34 15975000 5290.8 5355 5213.6 3949.4 4923.9 4558.6 4420.3 4840.8 5374.7 5288.3 TRUE FALSE FALSE 5226.313695 5430.387831 5304.340521 4406.04821 4672.615009 4267.320172 4795.760172 4980.86091 4893.973371 5150.909204 1.014639064 1.054258116 1.02978723 0.855392327 0.907143734 0.828459599 0.931051195 0.966986742 0.950118353 1 12.33061139 -9.268723959 24.98988319 1.012952213 0.896319739 0.625721412 0.043249981 240.9656617 826636.5021 0.005960533 0.009221583 5.39E-10 9.268723959 -0.116632474 TVLPTVPES(ph)PEEEVK ddPTM_HeLa_Romidepsin_16h_R1 3 TVLPTVPESPEEEVK 15 0 E9PBY7;E9PQ61;O75152;A0A1W2PPR9 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 TVLPTVPES(1)PEEEVK;TVLPT(0.007)VPES(0.993)PEEEVK;TVLPT(0.001)VPES(0.999)PEEEVK ;; 213.83 1.15E-25 128570000 13094.1 13024.4 12124.3 9710.6 12606.4 12624.3 11356.9 11922.4 13716.3 13392.1 TRUE FALSE FALSE 12934.50407 13207.75785 12335.31836 10833.38526 11963.04837 11817.64797 12321.5548 12267.35583 12489.47977 13044.17131 0.991592625 1.012540968 0.945657494 0.830515408 0.917118311 0.90597154 0.944602344 0.940447311 0.957475908 1 13.67111767 -9.567350411 5.451565921 0.996759603 0.90810841 0.59097339 0.032194491 0.083720525 5.873099763 0.00468871 0.006717178 2.71E-10 9.567350411 -0.088651193 TVLPTVPES(ph)PEEEVKASQLSVQQNK ddPTM_HeLa_Romidepsin_16h_R1 1 TVLPTVPESPEEEVKASQLSVQQNK 25 1 E9PBY7;E9PQ61;O75152;A0A1W2PPR9 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 TVLPT(0.006)VPES(0.994)PEEEVKASQLSVQQNK 102.45 1.05E-07 0 1564 1321.6 931.27 2468.5 1207.3 1125.9 1181.8 1305.8 1165.6 1356.4 TRUE FALSE FALSE 1544.937366 1340.205519 947.4783637 2753.919585 1145.686976 1053.958624 1282.182063 1343.581263 1061.345817 1321.160532 1.169378988 1.014415347 0.717156122 2.084470068 0.86718226 0.797752126 0.970496795 1.016970481 0.803343568 1 10.36759006 TVLS(ph)LFDEEEDKMEDQNIIQAPQK ddPTM_HeLa_Romidepsin_16h_R1 1 TVLSLFDEEEDKMEDQNIIQAPQK 24 1 A0A0A0MR88;A0A096LPC5;J3KP36;Q9Y4E1-3;Q9Y4E1-6;Q9Y4E1-2;Q9Y4E1-1;Q9Y4E1;Q9Y4E1-5;B1AP61;F8W7U3;Q641Q2;E7ESD2;Q641Q2-2;A0A087WYF6 A0A0A0MR88;F8W7U3 FAM21C;FAM21A WASH complex subunit FAM21C;WASH complex subunit FAM21A 1 0 T(0.309)VLS(0.691)LFDEEEDKMEDQNIIQAPQK 59.661 0.0080142 55465000 4148.7 3589.8 4693.9 4127.4 3616.8 3077 2957 3634.5 4210.8 4060.9 TRUE FALSE FALSE 4098.134049 3640.337299 4775.595361 4604.629408 3432.2212 2880.389631 3208.167506 3739.658523 3834.175502 3955.397233 1.036086595 0.920346829 1.207361759 1.164138299 0.867731102 0.728217537 0.811086047 0.945457132 0.96935283 1 11.94960687 -8.599808277 7.546149894 1.034204961 0.821872746 0.544405359 0.094565539 0.136621223 11.44919087 0.013671474 0.027442429 2.51E-09 8.599808277 -0.212332216 TVMDGGLES(ph)DGPNMTENGLEDESRPQR ddPTM_HeLa_Romidepsin_16h_R1 3 TVMDGGLESDGPNMTENGLEDESRPQR 27 1 P51116 P51116 FXR2 Fragile X mental retardation syndrome-related protein 2 1 0 T(0.004)VMDGGLES(0.954)DGPNMT(0.042)ENGLEDESRPQR;T(0.001)VMDGGLES(0.952)DGPNMT(0.047)ENGLEDESRPQR;T(0.005)VMDGGLES(0.971)DGPNMT(0.025)ENGLEDESRPQR ;; 91.883 1.54E-07 91551000 2668.24 2155.04 2997.91 1904.53 3039.63 3306.95 2583.35 3383.23 2656.01 3315.27 TRUE FALSE FALSE 2635.718465 2185.37871 3050.087366 2124.74072 2884.506339 3095.646568 2802.779685 3481.118422 2418.449814 3229.138807 0.816229534 0.676768278 0.944551333 0.6579899 0.893274186 0.958660111 0.867965068 1.07803307 0.748945759 1 11.65693374 -4.95221224 1.392196358 0.878357166 142.2445515 0.212197549 0.116959884 1442.259628 4.976565425 0.017787123 649490.9692 1.12E-05 4.95221224 141.3661943 TVNSGGSSEPSPT(ph)EVDVSR ddPTM_HeLa_Romidepsin_16h_R1 1 TVNSGGSSEPSPTEVDVSR 19 0 Q6PIJ6-2;Q6PIJ6 Q6PIJ6-2 FBXO38 F-box only protein 38 1 0 TVNS(0.002)GGSSEPS(0.007)PT(0.99)EVDVS(0.001)R 218.38 1.41E-34 0 4001.1 3449.4 2932.5 3065.3 3691.1 3045.9 2935.4 3195.7 3748.8 3772 TRUE FALSE FALSE 3952.333054 3497.960744 2983.538932 3419.724409 3502.729394 2851.27682 3184.732803 3288.162538 3413.497939 3674.002896 1.075756652 0.952084373 0.812067659 0.930789797 0.953382317 0.776068202 0.866829149 0.894980932 0.929095059 1 11.84313705 -10.0117717 5.06382352 1.035175812 0.874102305 0.452243853 0.06139482 0.08311946 6.213618654 0.009073348 0.011558998 9.73E-11 10.0117717 -0.161073508 TVPST(ph)PTLVVPHR ddPTM_HeLa_Romidepsin_16h_R1 2 TVPSTPTLVVPHR 13 0 P12270 P12270 TPR Nucleoprotein TPR 1 0 T(0.001)VPS(0.139)T(0.86)PTLVVPHR;T(0.016)VPS(0.132)T(0.852)PT(0.001)LVVPHR ; 103.3 0.0081233 60388000 8910.1 14514.9 7861.6 6375.7 14140.6 11224.2 7397.8 10032.6 8643.6 8908.3 TRUE FALSE FALSE 8801.500274 14719.24114 7998.42785 7112.888433 13418.95242 10507.00984 8026.168947 10322.87745 7870.494768 8676.861082 1.014364549 1.696378564 0.921811214 0.819753637 1.546521523 1.210922907 0.925008349 1.189701824 0.907067048 1 13.08295752 -10.47025816 24.99920592 1.006335984 1.180894733 0.120444728 0.259481262 605.5308101 287679.803 0.042867304 0.048974525 3.39E-11 10.47025816 0.174558749 TVPVEAVTS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 TVPVEAVTSK 10 0 Q14247;Q14247-3;Q14247-2 Q14247 CTTN Src substrate cortactin 1 0 TVPVEAVT(0.165)S(0.835)K 106.62 0.020251 4607300 1951.9 2631.5 1971.3 1415.9 2403.7 2549.3 2653.9 2832.7 3101.2 2801.5 TRUE FALSE FALSE 1928.109492 2668.546326 2005.60965 1579.61302 2281.03022 2386.407957 2879.3222 2914.659705 2823.820905 2728.716626 0.706599386 0.977949231 0.735001074 0.578884962 0.835935178 0.874553237 1.055192823 1.068143052 1.034853117 1 11.41400686 -7.79818807 3.534505752 0.83503549 1.06929946 0.301484291 0.134075099 0.22409523 5.711528168 0.020618342 0.077760291 1.59E-08 7.79818807 0.23426397 TVQSLEIDLDS(ph)MR ddPTM_HeLa_Romidepsin_16h_R1 2 TVQSLEIDLDSMR 13 0 P05783;F8VZY9;CON__H-INV:HIT000015463 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 TVQSLEIDLDS(1)MR;TVQSLEIDLDS(1)MR ; 148.94 0.0010587 34707000 10475.8 9397.9 9682.7 9365.9 11299.3 12695.3 10994 11488.1 10758.4 9356.3 TRUE FALSE FALSE 10348.11692 9530.203883 9851.223332 10448.82943 10722.65456 11884.1113 11927.83009 11820.49005 9796.141759 9113.221977 1.135505856 1.045755706 1.080981387 1.146557107 1.176604124 1.304051556 1.308848848 1.297070353 1.074937249 1 13.15374549 -4 0.182796621 1.001063537 2.526997579 0.826791582 0.044590819 17.24931813 0.188891756 0.061970305 7.389447815 1.00E-04 4 1.525934042 TVS(ph)DNSLSNSR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSDNSLSNSR 11 0 H0Y7W6;B7ZL14;Q96RU3-4;Q96RU3-3;Q96RU3-5;Q96RU3-2;Q96RU3 H0Y7W6 FNBP1 Formin-binding protein 1 1 0 TVS(0.61)DNS(0.39)LSNSR 116.71 0.011525 129080000 1763.1 1608.6 1879.2 1432.9 2373.2 2584.4 2758.5 2640.7 1983.2 2050.9 TRUE FALSE FALSE 1741.610659 1631.245913 1911.906688 1598.57864 2252.086748 2419.265181 2992.806921 2717.104488 1805.817625 1997.617322 0.871843991 0.816595799 0.957093567 0.80024268 1.127386473 1.211075392 1.49818831 1.360172671 0.903985766 1 10.96406452 -8.232935503 1.790256846 0.921571877 1.425759748 0.866122837 0.082617501 0.098469483 0.597060626 0.012826651 0.044017021 5.85E-09 8.232935503 0.504187871 TVS(ph)QQS(ph)FDGVSLDSSGPEDR ddPTM_HeLa_Romidepsin_16h_R1 2 TVSQQSFDGVSLDSSGPEDR 20 0 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 2 0 T(0.007)VS(0.819)QQS(0.993)FDGVS(0.163)LDS(0.017)S(0.001)GPEDR;T(0.047)VS(0.948)QQS(0.937)FDGVS(0.015)LDS(0.046)S(0.007)GPEDR ; 101.61 0.00032864 10921000 2412.32 2263.03 2479.94 2528.67 2106.75 2056.18 1777.49 2027.85 2801.04 2935.85 TRUE FALSE FALSE 2382.917716 2294.888996 2523.102315 2821.046723 1999.234686 1924.796734 1928.469956 2086.52264 2550.507967 2859.576194 0.833311496 0.802527662 0.882334355 0.986526161 0.699136708 0.673105595 0.674390128 0.729661495 0.89191817 1 11.48158563 -5.38659265 0.082282121 1.191477279 6.89E-11 0.515327638 0.080933328 66.84515018 0.537995487 1.507049425 9.381710806 4.11E-06 5.38659265 -1.191477279 TVS(ph)SPIPYTPSPSSSR ddPTM_HeLa_Romidepsin_16h_R1 4 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 T(0.025)VS(0.391)S(0.058)PIPY(0.002)T(0.025)PS(0.159)PS(0.024)S(0.206)S(0.11)R;T(0.001)VS(0.5)S(0.5)PIPYTPSPSSSR;T(0.258)VS(0.566)S(0.174)PIPYT(0.001)PSPSS(0.001)SR;T(0.118)VS(0.814)S(0.068)PIPYTPSPSSSR ;;; 236.12 8.15E-46 47531700 6007.86 5823.01 6456.28 4453.93 6673 7120.7 5779.2 6118.7 6751.5 7465.6 TRUE FALSE FALSE 5934.633891 5904.986488 6568.648845 4968.914343 6332.45191 6665.710251 6270.085104 6295.734931 6147.628931 7271.642636 0.816133876 0.81205675 0.903323936 0.683327632 0.870842013 0.91667187 0.862265298 0.865792675 0.845425063 1 12.82806558 -12.26248986 0.90903875 1.003596896 0.840246508 0.008557956 0.077406507 0.417543169 0.598020102 0.046358152 0.011610774 5.46E-13 12.26248986 -0.163350388 TVSGPGTPEPRPAT(ph)PGASSVEQLR ddPTM_HeLa_Romidepsin_16h_R1 3 TVSGPGTPEPRPATPGASSVEQLR 24 1 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 0 TVSGPGTPEPRPAT(0.912)PGAS(0.035)S(0.052)VEQLR;TVSGPGT(0.024)PEPRPAT(0.943)PGAS(0.016)S(0.016)VEQLR;TVSGPGT(0.006)PEPRPAT(0.901)PGAS(0.047)S(0.047)VEQLR ;; 94.957 2.81E-05 39850400 3199.16 3160.12 3007.99 2931.08 3210.17 3489.2 2837.99 3239.1 2942.67 2814.56 TRUE FALSE FALSE 3160.167407 3204.608252 3060.342804 3269.985261 3046.343046 3266.251381 3079.0488 3332.818248 2679.470225 2741.437325 1.152741074 1.168951857 1.116327839 1.192799569 1.111221117 1.191437554 1.123151265 1.215719293 0.977396127 1 11.42071678 -12.24405536 0.53229393 0.968939324 1.162531025 0.800719464 0.033886618 0.455566745 0.180896792 0.045233158 0.007416956 5.70E-13 12.24405536 0.193591701 TVSGPGTPEPRPAT(ph)PGASSVEQLRK ddPTM_HeLa_Romidepsin_16h_R1 1 TVSGPGTPEPRPATPGASSVEQLRK 25 2 Q9H3U1 Q9H3U1 UNC45A Protein unc-45 homolog A 1 0 TVSGPGTPEPRPAT(0.956)PGAS(0.022)S(0.022)VEQLRK 60.176 0.024197 9425900 945.82 843.32 600.08 976.13 683.69 788.28 623.01 811.16 943.42 888.06 TRUE FALSE FALSE 934.291982 855.1922811 610.5241407 1088.994743 648.7987481 737.9114521 675.9284538 834.6296348 859.0381524 864.9880732 1.080121231 0.988675229 0.705817987 1.25897082 0.750066698 0.853088586 0.781430952 0.964903056 0.993121384 1 9.75653643 -9.227424376 0.729354946 1.035358961 0.847039395 0.114555074 0.150069366 0.828316155 0.857800729 0.029106454 0.074055428 5.92E-10 9.227424376 -0.188319566 TVSLGAGAKDELHIVEAEAMNY(ph)EGSPIK ddPTM_HeLa_Romidepsin_16h_R1 2 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 TVSLGAGAKDELHIVEAEAMNY(0.783)EGS(0.217)PIK;TVSLGAGAKDELHIVEAEAMNY(0.953)EGS(0.047)PIK ; 84.125 3.12E-08 4771100 2080.41 2214.92 2884.93 2017.87 2458.32 2608.21 2213.11 2414.22 2557.23 2470.13 TRUE FALSE FALSE 2055.053163 2246.101702 2935.140996 2251.185624 2332.862757 2441.553799 2401.091508 2484.071647 2328.504944 2405.955667 0.854152548 0.933559056 1.21994808 0.935672114 0.96962001 1.014795839 0.997978284 1.032467755 0.967808749 1 11.23239434 -9.947514305 24.9999938 0.929164657 1.024292462 0.232153483 0.078810564 113.8598127 54233.36497 0.013873432 0.018233261 1.13E-10 9.947514305 0.095127805 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIK ddPTM_HeLa_Romidepsin_16h_R1 4 TVSLGAGAKDELHIVEAEAMNYEGSPIK 28 1 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 TVSLGAGAKDELHIVEAEAMNY(0.083)EGS(0.917)PIK;TVSLGAGAKDELHIVEAEAMNY(0.039)EGS(0.961)PIK;TVSLGAGAKDELHIVEAEAMNY(0.265)EGS(0.735)PIK;TVSLGAGAKDELHIVEAEAMNY(0.271)EGS(0.729)PIK ;;; 80.418 1.69E-06 496877900 24624.4 22471.6 24476 21174.3 25196.5 26953.1 24470 24452.1 26498.8 25848.2 TRUE FALSE FALSE 24324.26834 22787.95577 24901.99451 23622.57219 23910.62858 25230.8839 26548.48119 25159.58293 24128.68096 25176.66004 0.966143575 0.905122274 0.98909047 0.938272676 0.949714082 1.002153735 1.054487813 0.999321709 0.958374976 1 14.61979929 -8.009668162 7.771695504 0.972595004 1.027393772 0.423237297 0.030073259 0.114393182 51.01057579 0.004570416 0.012676819 9.78E-09 8.009668162 0.054798768 TVSLGAGAKDELHIVEAEAMNYEGS(ph)PIKVTLATLK ddPTM_HeLa_Romidepsin_16h_R1 5 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 1 0 TVSLGAGAKDELHIVEAEAMNY(0.458)EGS(0.536)PIKVT(0.004)LAT(0.002)LK;TVSLGAGAKDELHIVEAEAMNY(0.452)EGS(0.521)PIKVT(0.017)LAT(0.01)LK;TVSLGAGAKDELHIVEAEAMNY(0.383)EGS(0.433)PIKVT(0.08)LAT(0.103)LK;TVSLGAGAKDELHIVEAEAMNY(0.434)EGS(0.499)PIKVT(0.028)LAT(0.038)LK;TVSLGAGAKDELHIVEAEAMNY(0.471)EGS(0.528)PIKVTLATLK ;;;; 75.261 3.03E-06 692928200 21351.9 20295.7 17868.6 26900 22598.2 21635.3 19176.43 21310.3 23932.8 20041.2 TRUE FALSE FALSE 21091.65483 20581.4234 18179.59549 30010.30457 21444.92953 20252.87415 20805.27549 21926.87991 21792.19043 19520.52673 1.080485948 1.054347748 0.931306605 1.537371659 1.098583548 1.037516786 1.065815271 1.123272963 1.116373073 1 14.25270436 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK ddPTM_HeLa_Romidepsin_16h_R1 3 TVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLK 35 2 P06748;P06748-2;P06748-3 P06748 NPM1 Nucleophosmin 0 0 ;; ;; 76.208 1.33E-06 34918900 4519.43 4110.56 3612.1 6143.8 4548 4855.78 3487.1 4250.38 5100.12 3781.49 FALSE FALSE TRUE 4464.345449 4168.428572 3674.967085 6854.175063 4315.898589 4545.511329 3783.294187 4373.358039 4643.952494 3683.246345 1.212068114 1.131726792 0.997752184 1.860905957 1.171764847 1.23410462 1.027162952 1.187365066 1.260831359 1 11.84676218 -11.92827472 0.555467782 0.979572776 1.240274452 0 0.238573258 1.782825225 0.930495522 0.233419004 0.057749247 1.18E-12 11.92827472 0.260701676 TVSLPLS(ph)SPNIK ddPTM_HeLa_Romidepsin_16h_R1 2 TVSLPLSSPNIK 12 0 H0Y785;H0Y472;H0Y4P6;Q8IWZ3;Q8IWZ3-4;Q8IWZ3-6;A0A0A0MQZ8;H0Y7Y3 H0Y785 ANKHD1 Ankyrin repeat and KH domain-containing protein 1 1 0 TVSLPLS(0.5)S(0.5)PNIK;TVSLPLS(0.5)S(0.5)PNIK ; 236.08 6.88E-39 159562000 16138.8 15471.1 15683.8 15986.3 20113.8 16810.5 13759.4 13594.1 15729.7 14252 TRUE FALSE FALSE 15942.0941 15688.90255 15956.76996 17834.71122 19087.31773 15736.3633 14928.12309 13987.42384 14322.79624 13881.73099 1.148422637 1.130183445 1.149479843 1.284761334 1.374995507 1.133602381 1.07537908 1.007613809 1.031773073 1 13.76089986 -11.80543397 0.649928951 0.99656272 1.172717277 0.267131196 0.097263737 0.841350555 0.661564119 0.077354878 0.024678031 1.57E-12 11.80543397 0.176154556 TVSLTPSPT(ph)TQVETPDLVDHDNTSPLFR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSLTPSPTTQVETPDLVDHDNTSPLFR 28 0 Q05209-2;Q05209-3;Q05209;H3BM04 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 TVSLT(0.001)PS(0.006)PT(0.496)T(0.496)QVETPDLVDHDNTSPLFR 164.31 2.10E-14 69132000 5274.3 5192 4505.1 4348.2 4456.6 4019 3368.9 3870.4 5834.4 5669 TRUE FALSE FALSE 5210.014803 5265.093112 4583.509376 4850.959343 4229.163072 3762.198871 3655.054282 3982.383918 5312.556651 5521.718563 0.943549503 0.953524352 0.830087467 0.878523468 0.765914275 0.68134564 0.66194143 0.721221821 0.962120143 1 12.43090164 -8.974823453 0.633407837 0.982148999 0.653753415 0.9145434 0.034856996 0.159372521 0.115398699 0.007377131 0.025720286 1.06E-09 8.974823453 -0.328395583 TVSPGSVS(ph)PIHGQGQVVENLK ddPTM_HeLa_Romidepsin_16h_R1 2 TVSPGSVSPIHGQGQVVENLK 21 0 A0A087WVF7;Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3 A0A087WVF7 ITSN2 Intersectin-2 1 0 T(0.016)VS(0.003)PGS(0.178)VS(0.802)PIHGQGQVVENLK;T(0.003)VS(0.004)PGS(0.21)VS(0.783)PIHGQGQVVENLK ; 84.947 0.00085398 39606000 3986.6 3555.1 3553.2 3771.6 3759.1 3762.7 3164 3406.6 4445.9 3934.8 TRUE FALSE FALSE 3938.009786 3605.148791 3615.041956 4207.690138 3567.2591 3522.275614 3432.750081 3505.164596 4048.247569 3832.573329 1.027510617 0.940660095 0.943241432 1.097875964 0.930773868 0.919036718 0.8956776 0.914572089 1.056274002 1 11.90409768 -8.546440678 24.99072433 1.007061512 0.911112262 0.52818637 0.044645618 127.1086605 134816.0422 0.006013665 0.012027814 2.84E-09 8.546440678 -0.09594925 TVSQQS(ph)FDGVSLDSSGPEDR ddPTM_HeLa_Romidepsin_16h_R1 2 TVSQQSFDGVSLDSSGPEDR 20 0 H7C1J4;Q6BDS2 H7C1J4 UHRF1BP1 UHRF1-binding protein 1 1 0 TVS(0.001)QQS(0.671)FDGVS(0.287)LDS(0.031)S(0.011)GPEDR;TVS(0.004)QQS(0.988)FDGVS(0.008)LDSSGPEDR ; 142.23 7.96E-05 25437000 2084.59 2192.48 2240.15 1093.99 2321 2284.3 1757.8 2203.16 2459.6 2253.96 TRUE FALSE FALSE 2059.182215 2223.345791 2279.138871 1220.482271 2202.550709 2138.340602 1907.107488 2266.904959 2239.607216 2195.401794 0.937952324 1.01272842 1.038142028 0.555926607 1.003256313 0.97400877 0.868682668 1.032569512 1.020135458 1 11.10026929 TVSS(ph)PIPYTPSPSSSR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSSPIPYTPSPSSSR 16 0 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 T(0.041)VS(0.114)S(0.845)PIPYTPSPSSSR 212.55 7.13E-26 7971600 1521.1 1783 1605 1072.2 1551.3 1433.8 1232.1 1376.4 1917.3 1967.4 TRUE FALSE FALSE 1502.560248 1808.101121 1632.934352 1196.172809 1472.131372 1342.184807 1336.754543 1416.223962 1745.811886 1916.286664 0.784099935 0.943544176 0.852134695 0.624213919 0.768220851 0.700409199 0.697575456 0.739045983 0.911039 1 10.90409768 -16.52287875 0.107373622 1.836107398 0.591829787 0.575673285 0.074812073 49.45982981 0.391812547 9.111418213 0.503068541 3.00E-17 16.52287875 -1.244277611 TVSS(ph)PPT(ph)SPRPGSAATVSASTSNIIPPR ddPTM_HeLa_Romidepsin_16h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 2 0 T(0.009)VS(0.066)S(0.548)PPT(0.558)S(0.555)PRPGS(0.013)AAT(0.003)VS(0.018)AS(0.053)T(0.123)S(0.053)NIIPPR;T(0.023)VS(0.24)S(0.625)PPT(0.503)S(0.503)PRPGS(0.096)AAT(0.004)VS(0.001)AS(0.001)T(0.002)S(0.002)NIIPPR ; 55.62 0.0034895 411440000 3735.6 3086 3075.5 2453.4 2889.5 3736.3 2874.1 3047.5 4048.1 3513.5 TRUE FALSE FALSE 3690.06907 3129.444789 3129.027787 2737.073652 2742.038033 3497.562488 3118.225982 3135.674604 3686.027797 3422.218763 1.078268026 0.914449077 0.914327226 0.799795057 0.80124569 1.022016046 0.911170851 0.916269479 1.077087133 1 11.74071627 -10.16646001 5.270237985 1.036810244 0.894149395 0.554969472 0.063193657 0.140960772 6.176916204 0.011261301 0.013830046 6.82E-11 10.16646001 -0.142660848 TVSS(ph)PPTSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSSPPTSPR 10 0 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 0 TVS(0.142)S(0.857)PPT(0.001)SPR 126.03 0.0090282 10128000 3095.2 2730.6 3722.7 2838.1 3240.4 3566.4 2723.9 2966.7 3454 3250.1 TRUE FALSE FALSE 3057.474512 2769.041458 3787.492032 3166.254476 3075.030296 3338.51855 2955.267998 3052.536784 3145.065589 3165.661933 0.965824708 0.874711677 1.196429724 1.000187178 0.971370399 1.054603625 0.933538723 0.96426493 0.993493827 1 11.62829148 -7.694529919 24.99999718 0.994991523 0.94890157 0.065551605 0.077803148 137.3284629 51307.65048 0.010247918 0.038344192 2.02E-08 7.694529919 -0.046089953 TVSS(ph)PPTSPRPGSAATVSASTSNIIPPR ddPTM_HeLa_Romidepsin_16h_R1 2 TVSSPPTSPRPGSAATVSASTSNIIPPR 28 1 O76094-2;O76094 O76094-2 SRP72 Signal recognition particle subunit SRP72 1 0 T(0.026)VS(0.092)S(0.338)PPT(0.329)S(0.211)PRPGS(0.001)AAT(0.001)VSAS(0.001)T(0.001)SNIIPPR;T(0.101)VS(0.104)S(0.512)PPT(0.133)S(0.133)PRPGS(0.002)AAT(0.002)VS(0.002)AS(0.001)T(0.005)S(0.005)NIIPPR ; 66.884 8.23E-05 236220000 1468.93 1287.82 1047.77 1333.69 1074.89 1364.87 988.26 1190.32 1350 1294.92 TRUE FALSE FALSE 1451.026116 1305.949964 1066.005997 1487.897513 1020.034352 1277.659212 1072.20278 1224.760031 1229.252619 1261.277792 1.150441343 1.035418186 0.845179392 1.17967471 0.808730923 1.012987956 0.850092491 0.971047012 0.974608946 1 10.30067034 -9.320214485 0.959844375 1.068085253 0.924534704 0.084873933 0.112334937 0.59704407 1.090921947 0.020059597 0.041698956 4.78E-10 9.320214485 -0.143550549 TVSSPIPYTPSPSSSRPISPGLS(ph)YASHTVGFTPPTSLTR ddPTM_HeLa_Romidepsin_16h_R1 1 TVSSPIPYTPSPSSSRPISPGLSYASHTVGFTPPTSLTR 39 1 Q16204 Q16204 CCDC6 Coiled-coil domain-containing protein 6 1 0 TVSSPIPY(0.001)T(0.001)PS(0.003)PS(0.002)S(0.031)S(0.139)RPIS(0.139)PGLS(0.501)Y(0.127)AS(0.034)HT(0.012)VGFT(0.005)PPT(0.002)S(0.002)LT(0.002)R 65.758 3.48E-05 29615000 1300.8 1258.7 1328.7 995.34 2696.5 2918.1 2237.6 2731.6 2061.9 1249.7 TRUE FALSE FALSE 1284.945349 1276.420012 1351.825466 1110.425894 2558.887543 2731.642828 2427.661688 2810.634536 1877.4785 1217.232614 1.055628427 1.048624558 1.110572828 0.912254471 2.102217369 2.244141996 1.99441065 2.309036502 1.54241554 1 10.24938918 -8.756146904 25 1.028642993 2.156284007 0.882804744 0.186104132 12.43920602 58758.26281 0.011745891 0.02294693 1.75E-09 8.756146904 1.127641013 TVSTSS(ph)QPEENVDR ddPTM_HeLa_Romidepsin_16h_R1 2 TVSTSSQPEENVDR 14 0 P42684-2;P42684-3;P42684-4;P42684-10;P42684-6;P42684;P42684-7;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 TVS(0.002)T(0.043)S(0.424)S(0.531)QPEENVDR;TVSTS(0.001)S(0.999)QPEENVDR ; 199.31 1.68E-16 11956200 2268.8 1949.86 2000.54 2030.61 2378.8 1779.04 1758.67 2052.04 2447.6 2442.5 TRUE FALSE FALSE 2241.146993 1977.31018 2035.35856 2265.398683 2257.400959 1665.365086 1908.051386 2111.41254 2228.680526 2379.043498 0.942036997 0.831136624 0.855536505 0.95223088 0.948869141 0.700014559 0.80202459 0.887504807 0.93679688 1 11.21616593 -10.02036432 0.282107061 1.020697475 0.789451375 0.291060593 0.071760068 1.234047218 0.311740335 0.078252846 0.109958922 9.54E-11 10.02036432 -0.2312461 TVTDVSTIDGNAAELVSGRPVS(ph)DTTEPSSPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 TVTDVSTIDGNAAELVSGRPVSDTTEPSSPEGK 33 1 B1ALY0;Q8IXS6-2;C9JA33;Q8IXS6 B1ALY0 PALM2-AKAP2;PALM2 Paralemmin-2 1 0 TVTDVS(0.001)T(0.001)IDGNAAELVS(0.009)GRPVS(0.307)DT(0.307)T(0.307)EPS(0.053)S(0.017)PEGK 74.733 4.51E-06 13749000 3902.2 3332.9 3672.5 1913.5 3087.6 3380.2 3128.4 3306 4063.2 4159.9 TRUE FALSE FALSE 3854.638485 3379.820654 3736.418322 2134.747873 2930.028251 3164.216129 3394.126218 3401.653894 3699.777216 4051.825198 0.951333855 0.834147696 0.92215684 0.526860802 0.723137872 0.780935992 0.837678343 0.839536191 0.913113729 1 11.98435622 -9.990894946 1.428094361 0.980773392 0.755257703 0.42912671 0.097002576 0.230199513 0.921285269 0.017777093 0.023651268 1.02E-10 9.990894946 -0.225515689 TVTDVSTIDGNAAELVSGRPVSDTTEPS(ph)SPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 TVTDVSTIDGNAAELVSGRPVSDTTEPSSPEGK 33 1 B1ALY0;Q8IXS6-2;C9JA33;Q8IXS6 B1ALY0 PALM2-AKAP2;PALM2 Paralemmin-2 1 0 TVTDVSTIDGNAAELVS(0.024)GRPVS(0.1)DT(0.145)T(0.145)EPS(0.508)S(0.078)PEGK 74.973 4.08E-07 0 1388.3 1116.2 1206.5 597.42 1272.3 987.1 1078.8 1085.6 1360.1 1088.4 TRUE FALSE FALSE 1371.378866 1131.913893 1227.498626 666.4965113 1207.369783 924.0274957 1170.433245 1117.010123 1238.44925 1060.123211 1.293603282 1.067719187 1.157882983 0.628697216 1.138895716 0.871622738 1.104053975 1.053660661 1.168212559 1 10.05001623 SAFMAPVPTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 SAFMAPVPTKK 11 1 A0A1W2PQJ7;Q7Z5J4-3;Q7Z5J4-2;Q7Z5J4 A0A1W2PQJ7 RAI1 Retinoic acid-induced protein 1 0 1 ; SAFMAPVPTK(1)K;SAFMAPVPTK(1)K 130.94 0.00078957 3618900 706 830.11 474.91 705.63 2743.5 4531.7 4102 4123.3 971.85 744.15 FALSE TRUE FALSE 697.3950004 841.7963104 483.1756093 787.2182607 2603.488958 4242.138995 4450.423778 4242.60118 884.925302 724.8168757 0.962167168 1.161391709 0.666617494 1.086092622 3.591926519 5.852704507 6.140066445 5.853342164 1.220895003 1 9.501472735 -8.525101228 2.238653643 0.961895452 6.026103101 0.99260201 0.19172774 0.01637032 0.162930605 0.0277847 0.068456832 2.98E-09 8.525101228 5.064207649 up TVTNAVVTVPAYFNDSQR ddPTM_HeLa_Romidepsin_16h_R1 4 TVTNAVVTVPAYFNDSQR 18 0 P11142;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PI65 P11142 HSPA8 Heat shock cognate 71 kDa protein 0 0 ;;; ;;; 174.94 7.81E-33 24000780 3239.74 3229.129 3507.01 3347.57 3234.74 3130.51 3033.09 3635.99 3506.84 3414.93 FALSE FALSE TRUE 3200.252803 3274.588763 3568.048038 3734.631794 3069.659147 2930.480514 3290.720589 3741.191634 3193.179447 3326.209626 0.962132025 0.984480574 1.072706906 1.122789064 0.922870021 0.881027008 0.989330487 1.124761231 0.960005474 1 11.69966338 -6.401758242 20.56701046 0.993522207 1.007159702 0 0.077524653 0 0 0.010138586 0 3.96E-07 6.401758242 0.013637496 QSPLPPQK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 QSPLPPQKK 9 1 Q01105;B2REB7 Q01105 SET Protein SET 0 1 QSPLPPQK(1)K 134.25 4.52E-07 0 573.22 668.11 659 1218.5 5472 9790.6 9010.1 10435 907.84 580.41 FALSE TRUE FALSE 566.2333742 677.5156701 670.4696186 1359.388703 5192.743421 9165.012258 9775.417669 10736.92026 826.6405167 565.3308645 1.001596427 1.198440971 1.185977382 2.404589575 9.18531739 16.21176701 17.29149828 18.9922768 1.462224281 1 9.142951654 -8.477149983 1.629759394 0.989822797 18.32132422 0.996503864 0.430698004 0.012901778 0.06666977 0.058705311 0.171586902 3.33E-09 8.477149983 17.33150142 up SPEAKPLPGK(ac)LPK ddPTM_HeLa_Romidepsin_16h_R1 2 SPEAKPLPGKLPK 13 2 P46087;P46087-4;P46087-2;F5GWB7;F5H709;P46087-3;F5H359;F5H5X6 P46087 NOP2 Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase 0 1 ; SPEAKPLPGK(1)LPK;SPEAKPLPGK(1)LPK 111.31 0.0045373 8547400 3462 4135.4 3335.2 5194.7 9005.5 11117 11398 12882.7 4188.1 4239 FALSE TRUE FALSE 3419.803812 4193.61827 3393.247757 5795.335656 8545.915731 10406.65958 12366.14584 13255.4406 3813.505847 4128.870169 0.82826625 1.015681796 0.821834453 1.403612954 2.069795218 2.52046181 2.995043518 3.210428049 0.923619705 1 12.01153134 -8.452161829 1.077261351 0.906759208 3.194245663 0.986163914 0.104839625 0.046629588 0.098340635 0.018464582 0.074280445 3.53E-09 8.452161829 2.287486455 up PEK(ac)DQLKNK(ac)FMK ddPTM_HeLa_Romidepsin_16h_R1 2 PEKDQLKNKFMK 12 3 Q9Y6R1-3;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1;Q9Y6R1-5 Q9Y6R1-3 SLC4A4 Electrogenic sodium bicarbonate cotransporter 1 0 2 ; PEK(1)DQLK(0.039)NK(0.961)FMK;PEK(1)DQLK(0.011)NK(0.989)FMK 129.16 0.0011261 80037000 224.67 0 222.55 1452.86 8567 11851.4 13551.8 15046.3 189.947 308.973 FALSE TRUE FALSE 221.9316356 0 226.4233894 1620.846509 8129.794022 11094.13379 14702.88955 15481.64095 172.9576646 300.9458369 0.737447103 0 0.752372559 5.385841272 27.01414349 36.86422083 48.85560041 51.44327999 0.574713598 1 8.233360049 -8.438592674 1.272617342 0.531701054 50.99471672 0.988678126 2.173731492 0.031288552 0.095189823 0.325293461 1.159045558 3.64E-09 8.438592674 50.46301567 up TVVTGIEMFHK ddPTM_HeLa_Romidepsin_16h_R1 1 TVVTGIEMFHK 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 0 59.542 0.027818 1537800 1330.9 1070.2 1023.4 1105.3 1407.5 1280.7 1203.6 1314.4 1307.3 969.2 FALSE FALSE TRUE 1314.678479 1085.266304 1041.211848 1233.099987 1335.670023 1198.867403 1305.833754 1352.43009 1190.371814 944.0200443 1.39263831 1.149622098 1.102955233 1.30622225 1.414874643 1.269959691 1.383269097 1.432628574 1.260960316 1 9.882673682 -14.97825447 0.318984371 1.45E-13 1.334385631 0.092302975 0.132006793 11.36515079 0.371089574 7.291205576 0.044515352 1.05E-15 14.97825447 1.334385631 PEPAK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPAKSAPAPKKGSK 15 3 P06899;Q16778 P06899;Q16778 HIST1H2BJ;HIST2H2BE Histone H2B type 1-J;Histone H2B type 2-E 0 3 ; PEPAK(1)SAPAPK(1)K(1)GSK;PEPAK(1)SAPAPK(1)K(1)GSK 176.43 6.10E-09 1095090000 1582.21 1514.5 1963.47 12589.8 65320 99872 110244 124679 0 2969 FALSE TRUE FALSE 1562.925416 1535.821171 1997.643372 14045.49191 61986.47666 93490.50152 119608.1226 128286.3902 0 2891.864952 0.540455879 0.531083296 0.690780311 4.856897589 21.43477572 32.32879234 41.3602034 44.36112761 0 1 11.49778447 -8.411196543 1.270967952 0.552860821 43.99218093 0.993701497 1.384847588 0.023938449 0.072140029 0.210706085 0.772476456 3.88E-09 8.411196543 43.43932011 up TVY(ph)LQSALSSST(ph)S(ph)AEK ddPTM_HeLa_Romidepsin_16h_R1 1 TVYLQSALSSSTSAEK 16 0 B7ZB74;O14681-3;O14681 B7ZB74 EI24 Etoposide-induced protein 2.4 homolog 3 0 T(0.003)VY(0.997)LQS(0.001)ALS(0.021)S(0.106)S(0.196)T(0.703)S(0.974)AEK 86.497 0.0022203 0 397.78 479.64 321.72 363.44 589.86 457.04 455.99 555.25 680.99 630.48 TRUE FALSE FALSE 392.9317044 486.3923845 327.3194016 405.4626428 559.7572431 427.836619 494.7217792 571.3152827 620.0805488 614.1000387 0.639849666 0.792040961 0.533006646 0.660255035 0.911508236 0.6966888 0.80560454 0.930329338 1.009738658 1 9.262329884 -12.43329841 1.146234961 1.000957784 0.734192068 0.436236071 0.116464383 0.391758524 0.915287837 0.083340037 0.020576147 3.69E-13 12.43329841 -0.266765716 TWDDDS(ph)DPESETDPDAQAK ddPTM_HeLa_Romidepsin_16h_R1 2 TWDDDSDPESETDPDAQAK 19 0 K7EL01;Q5XUX1;Q5XUX1-2 K7EL01 FBXW9 F-box/WD repeat-containing protein 9 1 0 T(0.007)WDDDS(0.992)DPES(0.001)ETDPDAQAK;T(0.001)WDDDS(0.998)DPESETDPDAQAK ; 174.04 2.22E-08 56264000 13771.4 13453 12236.1 12299.9 14752.2 15270 14899.2 16373.6 14235.5 12887.3 TRUE FALSE FALSE 13603.54888 13642.39169 12449.06419 13722.07231 13999.34019 14294.29628 16164.73768 16847.34428 12962.24123 12552.48609 1.083733436 1.086827868 0.991760843 1.093175664 1.115264346 1.138762169 1.287771806 1.342151998 1.032643345 1 13.61568551 -7.414404045 0.699766633 1.039399466 1.517418842 0.902892736 0.034051869 0.588934422 0.22715783 0.00690668 0.212645826 3.85E-08 7.414404045 0.478019376 TWDHFWLNEGHTVYLER ddPTM_HeLa_Romidepsin_16h_R1 1 TWDHFWLNEGHTVYLER 17 0 P09960-3;P09960-2;P09960-4;P09960 P09960-3 LTA4H Leukotriene A-4 hydrolase 0 0 66.738 0.013869 8500700 2659.5 2490.9 2840.7 1579.9 3040.7 3200.2 3011.4 2696.7 3240.7 2693.9 FALSE FALSE TRUE 2627.084991 2525.966956 2890.141192 1762.575472 2885.521733 2995.717548 3267.188241 2774.72476 2950.843676 2623.91209 1.001209225 0.962672098 1.101462661 0.671735718 1.099702137 1.141698901 1.245159186 1.057476266 1.124597004 1 11.35750367 -8.537201579 24.99121986 0.981299009 1.151630372 0.294093766 0.122314114 188.6977297 329248.7178 0.015352105 0.030715079 2.90E-09 8.537201579 0.170331363 TWTTPEVTS(ph)PPPSPR ddPTM_HeLa_Romidepsin_16h_R1 1 TWTTPEVTSPPPSPR 15 0 Q5T1S5;Q7Z6M1-2;Q7Z6M1 Q5T1S5 RABEPK Rab9 effector protein with kelch motifs 1 0 TWTTPEVT(0.038)S(0.852)PPPS(0.11)PR 110.93 0.0041653 6857400 1701.3 1677.4 1776.5 1314.3 1561.6 1646 1758.6 1742.5 2101.1 1697.4 TRUE FALSE FALSE 1680.563901 1701.014481 1807.419237 1466.26555 1481.905725 1540.825912 1907.97544 1792.916488 1913.172354 1653.301303 1.016489794 1.028859336 1.093218298 0.886871345 0.896331311 0.931969212 1.154039761 1.084446304 1.157183116 1 10.69113395 -7.753443347 24.99974564 0.99489009 1.11924306 0.250783979 0.080880529 144.0030048 450217.379 0.009096788 0.032856482 1.76E-08 7.753443347 0.12435297 TYAGGTAS(ph)ATK ddPTM_HeLa_Romidepsin_16h_R1 1 TYAGGTASATK 11 0 P20810-6;P20810-7;P20810-10;P20810-9;P20810-5;A0A0C4DGB5;F8W7E0;H0YA91;E9PSG1;H0Y944;D6RGF7;D6RBR1;E7EN75 P20810-6 CAST Calpastatin 1 0 T(0.074)YAGGT(0.159)AS(0.53)AT(0.237)K 125.82 0.0074483 11710000 2232.9 2715.4 2810.3 2366.6 2556.3 3070.3 3309.6 1389.9 3232.8 3079.6 TRUE FALSE FALSE 2205.684556 2753.627472 2859.212093 2640.237427 2425.842472 2874.117739 3590.717341 1430.114564 2943.650271 2999.591548 0.735328301 0.918000811 0.953200476 0.880198982 0.808724266 0.958169702 1.197068762 0.476769767 0.981350369 1 11.55055035 -12.72591635 1.648890534 0.999892333 0.857692818 0.074745906 0.173552737 0.785815399 3.864302289 0.119099587 0.026075175 1.88E-13 12.72591635 -0.142199515 TYEDMTLEELEDHEDEFNEEDER ddPTM_HeLa_Romidepsin_16h_R1 1 TYEDMTLEELEDHEDEFNEEDER 23 0 Q9H2J4 Q9H2J4 PDCL3 Phosducin-like protein 3 0 0 145.44 3.53E-06 4691400 433.68 589.59 453.66 589.7 584.97 533.9 437.44 602.6 525.48 489.39 FALSE FALSE TRUE 428.3941413 597.8902635 461.555762 657.8838886 555.1167981 499.7855131 474.5961427 620.0352803 478.4797527 476.6755773 0.898712168 1.254291791 0.968280701 1.38015019 1.164558926 1.048481477 0.995637631 1.300749 1.003784913 1 8.8968639 -10.27063299 24.99285083 0.952169633 1.149752234 0.318554263 0.127192607 522.2202642 1419654.55 0.02084275 0.024013337 5.36E-11 10.27063299 0.197582602 TYFPHFDLHPGS(ph)AQLR ddPTM_HeLa_Romidepsin_16h_R1 1 TYFPHFDLHPGSAQLR 16 0 P02008 P02008 HBZ Hemoglobin subunit zeta 1 0 TYFPHFDLHPGS(1)AQLR 85.909 0.0033081 0 1090.6 1133.4 1115.3 1119 1292.7 1082.8 1183.6 1156.3 1425.5 1128.4 TRUE FALSE FALSE 1077.307348 1149.356035 1134.711329 1248.384045 1226.728695 1013.612575 1284.134954 1189.755716 1297.99971 1099.084005 0.980186539 1.045739934 1.032415469 1.135840426 1.116137337 0.922233942 1.16836834 1.082497526 1.180983167 1 10.10208594 -9.883931063 1.859202087 0.990857163 1.080743583 0 0.086784856 0.304478576 2.129179107 0.010422977 0.014310121 1.31E-10 9.883931063 0.08988642 TYGGDT(ph)GSPEISFTK ddPTM_HeLa_Romidepsin_16h_R1 1 TYGGDTGSPEISFTK 15 0 H0Y9X0;A0A286YEZ9;A0A2C9F2R7;O94915 H0Y9X0 FRYL Protein furry homolog-like 1 0 T(0.345)YGGDT(0.651)GS(0.001)PEIS(0.002)FT(0.001)K 219.95 1.10E-26 40975000 3349.8 3852.3 4085.1 3156.8 4264.1 5350.9 3907.4 4646.2 3606.5 3463.4 TRUE FALSE FALSE 3308.971349 3906.532781 4156.199452 3521.804069 4046.487065 5008.994759 4239.294458 4780.630467 3283.925607 3373.420369 0.980895052 1.158033199 1.232043148 1.043986128 1.199520553 1.484841559 1.25667542 1.417146381 0.973470617 1 11.71999639 -8.834991989 0.516758854 0.983457806 1.436913225 0.704529324 0.092810848 0.494753485 0.215074804 0.02339824 0.104332534 1.46E-09 8.834991989 0.453455419 TYGGDTGS(ph)PEISFTK ddPTM_HeLa_Romidepsin_16h_R1 1 TYGGDTGSPEISFTK 15 0 H0Y9X0;A0A286YEZ9;A0A2C9F2R7;O94915 H0Y9X0 FRYL Protein furry homolog-like 1 0 T(0.001)Y(0.001)GGDT(0.299)GS(0.665)PEIS(0.034)FTK 108.66 0.0048109 41633000 2420.3 2392.6 2952 2526.2 2711.5 3418.6 2750.2 3659.7 3015.5 2750.9 TRUE FALSE FALSE 2390.800453 2426.283086 3003.378322 2818.29113 2573.122037 3200.162493 2983.801919 3765.587645 2745.786128 2679.431221 0.89227909 0.905521689 1.120901443 1.051824398 0.960323973 1.194343959 1.113595264 1.405368279 1.024764549 1 11.38771107 -4 0.445148029 0.951202407 10.48419209 0.709503706 0.078155671 27.8614381 0.303679976 0.017154092 242.7673743 1.00E-04 4 9.532989683 TYS(ph)FEQPWPNAR ddPTM_HeLa_Romidepsin_16h_R1 2 TYSFEQPWPNAR 12 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 T(0.374)YS(0.626)FEQPWPNAR;T(0.073)YS(0.927)FEQPWPNAR ; 154.23 0.0014115 16897600 2307.16 2366.74 2398.64 2442.69 2114.41 1861.23 1702.53 1724.84 2596.75 2969.4 TRUE FALSE FALSE 2279.039446 2400.059028 2440.387323 2725.125311 2006.503768 1742.30341 1847.142856 1774.745524 2364.490176 2892.25456 0.787980241 0.829822887 0.843766436 0.94221489 0.693750749 0.602403203 0.638651549 0.613620097 0.81752492 1 11.49797882 -6.048885156 0.123453807 1.080542681 2.60E-15 0.569526742 0.085365127 22.85909948 0.324149025 0.417675844 4.134530419 8.94E-07 6.048885156 -1.080542681 TYS(ph)LSS(ph)S(ph)FS(ph)SSSST(ph)RK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSLSSSFSSSSSTRK 16 1 O60563 O60563 CCNT1 Cyclin-T1 5 0 T(0.197)Y(0.165)S(0.612)LS(0.146)S(0.778)S(0.631)FS(0.356)S(0.356)S(0.356)S(0.343)S(0.343)T(0.716)RK 42.425 0.023849 1953500 560.16 489.52 582.07 466.53 438.57 639.74 552.29 544.43 540.87 727.92 TRUE FALSE FALSE 553.3325545 496.4114754 592.2006842 520.4723937 416.1881364 598.8626787 599.2014988 560.1822231 492.4932326 709.0085335 0.780431445 0.700148802 0.835251843 0.734084809 0.587000179 0.844648055 0.845125934 0.790092357 0.694622433 1 9.469659181 -11.96380842 0.696988944 1.007995693 0.76138884 0 0.119629669 0.43519804 0.375781984 0.059772759 0.016941628 1.09E-12 11.96380842 -0.246606854 TYS(ph)SPGSFK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSSPGSFK 9 0 Q8N3Z6 Q8N3Z6 ZCCHC7 Zinc finger CCHC domain-containing protein 7 1 0 T(0.039)YS(0.896)S(0.065)PGSFK 132.88 0.0070338 32796000 9322.8 9409.8 8879.4 5823 9495.4 8726.9 8425.3 7755.6 9773.8 9423.1 TRUE FALSE FALSE 9209.170128 9542.271411 9033.942232 6496.282658 9010.814306 8169.279255 9140.944772 7979.99605 8899.606849 9178.286504 1.003364857 1.039657174 0.984273288 0.707788175 0.981753435 0.890065837 0.995931514 0.869442902 0.969637072 1 13.16400913 -9.49732574 24.99599974 1.004844524 0.894737892 0.353561933 0.074766877 607.7403389 594493.6912 0.010564411 0.016094675 3.18E-10 9.49732574 -0.110106632 TYSAPAINAIQGGS(ph)FESPKKEK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSAPAINAIQGGSFESPKKEK 22 2 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 TYSAPAINAIQGGS(0.599)FES(0.401)PKKEK 60.669 0.0048636 25110000 3946.5 3507.7 3871.9 4287.3 2999.9 2780.4 2236.1 2514.5 3903 4094.6 TRUE FALSE FALSE 3898.39854 3557.081493 3939.288795 4783.017798 2846.803909 2602.741413 2426.034278 2587.25309 3553.905905 3988.221702 0.977477892 0.891896629 0.987730645 1.199285836 0.713802823 0.652607003 0.608299754 0.648723487 0.891100388 1 11.96152989 -8.608636198 6.912098532 0.99366837 0.641718648 0.808133939 0.080661762 0.059602555 4.007689137 0.010503377 0.021116133 2.46E-09 8.608636198 -0.351949722 TYSAPAINAIQGGSFES(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSAPAINAIQGGSFESPKK 20 1 Q9H4L5-7;Q9H4L5-5;Q9H4L5-3;Q9H4L5 Q9H4L5-7 OSBPL3 Oxysterol-binding protein-related protein 3 1 0 TYSAPAINAIQGGS(0.19)FES(0.81)PKK 102.21 0.00018406 28291000 2244.1 2173.1 2395.3 1877.1 1843.3 1887.2 1262.8 1462.2 2383.7 2072.6 TRUE FALSE FALSE 2216.748046 2203.692959 2436.989192 2094.139134 1749.229523 1766.614011 1370.0622 1504.50645 2170.495902 2018.753553 1.098077595 1.09161069 1.207175184 1.037342637 0.866489879 0.875101375 0.678667388 0.745265041 1.075166356 1 10.97924908 -8.3793851 1.477313042 1.064167235 0.722923707 0.831023853 0.066152133 0.144583222 0.597418755 0.011411973 0.038630115 4.17E-09 8.3793851 -0.341243528 TYSLGSALRPS(ph)TSR ddPTM_HeLa_Romidepsin_16h_R1 2 TYSLGSALRPSTSR 14 1 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 1 0 TYSLGS(0.002)ALRPS(0.902)T(0.087)S(0.009)R;TYSLGS(0.071)ALRPS(0.826)T(0.092)S(0.011)R ; 171.36 0.00030359 165611000 6132.4 4891.5 5517.3 4545.2 7328.7 7574.6 5028.8 6567.9 4604.4 5048.9 TRUE FALSE FALSE 6057.65595 4960.362665 5613.326292 5070.73741 6954.689092 7090.607506 5455.946146 6757.931824 4192.570932 4917.72885 1.231799502 1.008669412 1.141446888 1.031113663 1.414207514 1.441845966 1.109444281 1.37419773 0.85254211 1 12.26377648 -8.764144103 24.99999327 1.101379105 1.326455488 0.511419294 0.132186778 49.73876491 459746.2992 0.017779199 0.033314142 1.72E-09 8.764144103 0.225076383 TYSLGSALRPSTSR ddPTM_HeLa_Romidepsin_16h_R1 1 TYSLGSALRPSTSR 14 1 P08670;B0YJC4;A0A1B0GTT5;A0A1B0GVG8 P08670 VIM Vimentin 0 0 72.705 0.026849 2573400 214.41 336.98 265.56 224.31 298.1 207.57 267.03 361.26 350.69 202.82 FALSE FALSE TRUE 211.7966884 341.7240133 270.1819604 250.2457776 282.8868446 194.3069469 289.7115215 371.7124881 319.3234081 197.5507072 1.072113036 1.72980405 1.367658786 1.266741999 1.431970802 0.983580113 1.466517259 1.881605454 1.616412377 1 7.6260792 -4.000000001 0.096508559 0.701306662 3.24430379 0 0.316216829 105.2568587 0.728595502 2.352776655 35.58707765 1.00E-04 4.000000001 2.542997128 TYSLMPSAPHPVKEASPGFSWSPKTASATPAPLKNDATASCGFSER ddPTM_HeLa_Romidepsin_16h_R1 1 TYSLMPSAPHPVKEASPGFSWSPKTASATPAPLKNDATASCGFSER 46 3 Q8NFU7 Q8NFU7 TET1 Methylcytosine dioxygenase TET1 0 0 20.352 0.028558 1740200 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 TYSS(ph)PGSFK ddPTM_HeLa_Romidepsin_16h_R1 1 TYSSPGSFK 9 0 Q8N3Z6 Q8N3Z6 ZCCHC7 Zinc finger CCHC domain-containing protein 7 1 0 T(0.192)YS(0.346)S(0.46)PGS(0.002)FK 121.5 0.012633 31188000 6493.3 6613.3 6097.6 3380.4 6685.9 6413.3 6111.1 5143.3 7214.9 6789.9 TRUE FALSE FALSE 6414.157162 6706.402211 6203.72617 3771.257753 6344.693574 6003.510828 6630.176681 5292.113271 6569.581274 6613.497419 0.969858572 1.014047755 0.938040159 0.57023652 0.959355266 0.907766413 1.002522003 0.800198887 0.993359619 1 12.6911977 -9.513651766 24.97090519 0.986944902 0.85490789 0.283030082 0.109891838 465.7828997 1260545.626 0.016673044 0.024344722 3.06E-10 9.513651766 -0.132037013 TYSVEYLPK ddPTM_HeLa_Romidepsin_16h_R1 2 TYSVEYLPK 9 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 ; ; 130.75 0.019663 862750 653.69 451.36 564.91 468.98 686.56 638.18 584.83 516.29 431.04 537.03 FALSE FALSE TRUE 645.7225748 457.7142579 574.7420216 523.2056742 651.5222813 597.4023576 634.5054456 531.2280366 392.4867028 523.0778832 1.234467363 0.875040358 1.098769495 1.000244306 1.245555016 1.142090646 1.21302289 1.015581147 0.750340849 1 9.030881961 -8.762711438 24.9986441 1.085758024 1.157418744 0.045132299 0.150023372 76.3395198 1500274.016 0.017928199 0.033863082 1.73E-09 8.762711438 0.071660721 TYT(ph)HEVVTLWYR ddPTM_HeLa_Romidepsin_16h_R1 1 TYTHEVVTLWYR 12 0 G3V5T9;P24941;Q00526;K7EJ83 G3V5T9 CDK2;CDK3 Cyclin-dependent kinase 2;Cyclin-dependent kinase 3 1 0 T(0.025)Y(0.001)T(0.974)HEVVTLWYR 83.869 0.030351 4471100 1542 1301.5 1847.1 1623.6 1808.7 1019.9 1001.3 938.85 1338 1467.4 TRUE FALSE FALSE 1523.205511 1319.822551 1879.248001 1811.328271 1716.39529 954.7316816 1086.350397 966.0141435 1218.325929 1429.276736 1.065717696 0.923419879 1.314824451 1.267304102 1.200883808 0.667982384 0.76007002 0.67587621 0.852407304 1 10.48106956 -8.252844072 24.91235007 1.073226225 0.707185557 0.617864137 0.139379963 312.0695899 904489.6289 0.01901824 0.047657535 5.59E-09 8.252844072 -0.366040668 TYTAYVDLEKDFAAEVVHPGDLK ddPTM_HeLa_Romidepsin_16h_R1 1 TYTAYVDLEKDFAAEVVHPGDLK 23 1 P54577;A0A0C4DGZ5 P54577 YARS "Tyrosine--tRNA ligase, cytoplasmic;Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed;Tyrosine--tRNA ligase" 0 0 101.49 1.29E-05 1397000 1286 1132.5 1026.3 1243.4 1270.5 1084 916.79 1200.5 1122.2 1471.6 FALSE FALSE TRUE 1270.325737 1148.443365 1044.162321 1387.167758 1205.661644 1014.735898 994.6621197 1235.234573 1021.827621 1433.36762 0.88625257 0.801220391 0.728467915 0.96776831 0.841139166 0.707938344 0.693933717 0.861770949 0.712885939 1 10.48519295 -11.14299919 0.278860295 1.053127726 0.748967504 0 0.119252932 1.328914706 0.279548036 0.156316429 0.07948376 7.19E-12 11.14299919 -0.304160222 VAAAAGSGPS(ph)PPGS(ph)PGHDR ddPTM_HeLa_Romidepsin_16h_R1 1 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 2 0 VAAAAGSGPS(1)PPGS(1)PGHDR 111.35 0.0034693 6521100 791.72 686.2 955.72 518.97 1108.3 1619.4 781.99 1253.4 703.19 796 TRUE FALSE FALSE 782.0702121 695.8603416 972.3539057 578.9757532 1051.739315 1515.925566 848.4122111 1289.665151 640.2949252 775.3198052 1.00870661 0.897513951 1.254132681 0.746757337 1.356523216 1.955226161 1.094273879 1.663397662 0.825846213 1 9.598647708 -8.562882759 7.477284766 1.001333494 1.545184092 0.582995367 0.235796415 0.10310454 15.81646918 0.029286958 0.059056368 2.74E-09 8.562882759 0.543850599 VAAAAGSGPS(ph)PPGSPGHDR ddPTM_HeLa_Romidepsin_16h_R1 1 VAAAAGSGPSPPGSPGHDR 19 0 Q9BTU6 Q9BTU6 PI4K2A Phosphatidylinositol 4-kinase type 2-alpha 1 0 VAAAAGSGPS(1)PPGSPGHDR 124.1 0.00037148 4213900 1551.1 1400.9 2092.4 1378.7 3151.6 4434.7 2745.2 3580.9 1685.9 2034.5 TRUE FALSE FALSE 1532.194597 1420.621907 2128.817344 1538.111781 2990.762092 4151.336982 2978.377219 3684.507692 1535.108882 1981.643397 0.773193905 0.716890793 1.074268634 0.776179904 1.509233244 2.094896079 1.502983445 1.859319239 0.774664546 1 10.95248165 -8.630076892 4.132695764 0.883982939 1.7908315 0.865703525 0.17399165 0.056069691 1.744770183 0.02463676 0.050942995 2.34E-09 8.630076892 0.906848561 VAAAPDEDLDGDDEDDAEDENNIDNR ddPTM_HeLa_Romidepsin_16h_R1 2 VAAAPDEDLDGDDEDDAEDENNIDNR 26 0 Q9BXV9 Q9BXV9 C14orf142 Uncharacterized protein C14orf142 0 0 ; ; 156.23 1.08E-10 32105000 4107.5 3297.2 3399.6 3802.1 4421.7 3891.1 3690.3 4325.6 3997.3 3736.5 FALSE FALSE TRUE 4057.43621 3343.618068 3458.768612 4241.716691 4196.044149 3642.471268 4003.75399 4450.754411 3639.771477 3639.425191 1.114856329 0.918721472 0.950361233 1.165490831 1.152941448 1.000836966 1.100106137 1.222927846 1.000095148 1 11.82949489 -9.24285658 24.97998762 1.036213258 1.121155234 0.377428161 0.076307779 1072.839978 1442168.523 0.012755793 0.021129793 5.72E-10 9.24285658 0.084941976 VAAAVDLIIK ddPTM_HeLa_Romidepsin_16h_R1 1 VAAAVDLIIK 10 0 A0A0U1RQF0;P49327 A0A0U1RQF0 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 0 116.52 0.00063618 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 VAADLQLS(ph)TPQK ddPTM_HeLa_Romidepsin_16h_R1 2 VAADLQLSTPQK 12 0 Q9H582-2;Q9H582 Q9H582-2 ZNF644 Zinc finger protein 644 1 0 VAADLQLS(0.787)T(0.213)PQK;VAADLQLS(0.866)T(0.134)PQK ; 121.73 0.0069607 11111700 6987.9 5550.4 6618.8 4559.1 3487.6 3300.6 3131.5 3066.3 7339.5 6433.8 TRUE FALSE FALSE 6902.728787 5628.538677 6733.997438 5086.244593 3309.614758 3089.702312 3397.489532 3155.018553 6683.036738 6266.648949 1.101502389 0.898173605 1.074577097 0.81163707 0.528131508 0.493038997 0.542154118 0.503461831 1.066445048 1 12.61347846 -8.945783267 2.444846479 1.037862753 0.5106578 0.949468795 0.055500421 0.045460588 0.549478298 0.009177416 0.017802485 1.13E-09 8.945783267 -0.527204953 VAAETQSPS(ph)LFGSTK ddPTM_HeLa_Romidepsin_16h_R1 4 VAAETQSPSLFGSTK 15 0 Q9UKX7;Q9UKX7-2 Q9UKX7 NUP50 Nuclear pore complex protein Nup50 1 0 VAAET(0.005)QS(0.002)PS(0.994)LFGSTK;VAAETQS(0.005)PS(0.989)LFGS(0.006)TK;VAAETQS(0.001)PS(0.999)LFGSTK;VAAETQS(0.087)PS(0.913)LFGSTK ;;; 220.25 1.85E-34 97528000 12302.6 11940.2 13434.7 8622.5 15665.2 19562.6 15812.9 17582.6 14673.6 13300.3 TRUE FALSE FALSE 12152.65118 12108.29445 13668.52532 9619.47402 14865.74639 18312.613 17156.04733 18091.32479 13361.15647 12954.75629 0.938084122 0.934660149 1.055097063 0.742543804 1.147512625 1.413582208 1.324304908 1.396500589 1.031370731 1 13.66119425 -8.48355817 4.55239951 0.958915223 1.365835363 0.83814682 0.084086121 0.054552484 2.575079874 0.010991851 0.024557266 3.28E-09 8.48355817 0.406920141 VAAGLQIK ddPTM_HeLa_Romidepsin_16h_R1 1 VAAGLQIK 8 0 Q14974;J3QR48 Q14974 KPNB1 Importin subunit beta-1 0 0 124.89 0.015523 2067700 1587.5 1574.6 4196.5 2601.1 2391.9 2942 2046.7 1257.2 1229.6 944.74 FALSE FALSE TRUE 1568.150939 1596.76726 4269.538322 2901.851421 2269.832418 2754.015695 2220.546647 1293.575098 1119.621496 920.1955186 1.704149724 1.735247812 4.639816469 3.153516141 2.466684929 2.992859277 2.413124822 1.405761137 1.21672131 1 9.84579662 -9.98126208 24.98695844 1.35289305 2.859022601 0.456552998 0.775051325 166.0958435 221487.7935 0.129489044 0.170167934 1.04E-10 9.98126208 1.506129552 VAAILNHAHYLENLHFTIDGVDTHYFVKPGPSEGDLAILGLSGGR ddPTM_HeLa_Romidepsin_16h_R1 1 VAAILNHAHYLENLHFTIDGVDTHYFVKPGPSEGDLAILGLSGGR 45 1 Q6N022 Q6N022 TENM4 Teneurin-4 0 0 26.184 0.028744 8038900 1205.7 1492.6 1418.6 1315.2 2036.5 1868.8 1452.8 1851.5 1360.8 1307.9 FALSE FALSE TRUE 1191.004465 1513.612862 1443.290138 1467.269612 1932.569806 1749.389711 1576.200796 1905.070231 1239.08664 1273.920569 0.934912657 1.188153248 1.132951436 1.151774802 1.517025356 1.373232958 1.237283417 1.495438787 0.972656121 1 10.31505961 -9.42481257 0.965741002 0.970448676 1.392172191 0.739923182 0.100467561 0.180959606 0.336020985 0.018568553 0.03592936 3.76E-10 9.42481257 0.421723515 VACET(ph)VAK ddPTM_HeLa_Romidepsin_16h_R1 1 VACETVAK 8 0 P31153 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 1 0 VACET(1)VAK 75.38 0.0028108 0 1344.3 2729.3 1955.7 263.23 762.51 1694.7 1238.4 1222.5 2045.8 1643.2 TRUE FALSE FALSE 1327.915155 2767.723157 1989.738138 293.6658911 723.5962694 1586.414139 1343.589665 1257.871109 1862.818524 1600.509427 0.829682807 1.729276385 1.243190514 0.183482763 0.452103722 0.991193249 0.839476258 0.785919213 1.163891004 1 10.64431546 -9.294587499 24.9984662 1.013203796 0.668849614 0.35264561 0.324268257 823.6515945 621149.8791 0.053894606 0.08232857 5.07E-10 9.294587499 -0.344354181 VADAKGDS(ph)ES(ph)EEDEDLEVPVPSR ddPTM_HeLa_Romidepsin_16h_R1 3 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 2 0 VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR;VADAKGDS(1)ES(1)EEDEDLEVPVPSR ;; 87.352 0.00037147 404255000 17310.7 17627.2 16761 17606.8 18435.6 18188 16046.4 19564.1 18372.4 16224.5 TRUE FALSE FALSE 17099.71053 17875.35618 17052.71817 19642.58106 17494.76254 17025.8455 17409.38082 20130.15637 16729.12653 15802.98515 1.082055723 1.131137947 1.079082086 1.242966495 1.107054292 1.077381605 1.101651406 1.273819862 1.05860547 1 13.94790949 -16.52287874 0.067563872 0.461406345 1.333692266 0.365586889 0.062865757 150.2244807 0.790583875 12.70954238 1.953042429 3.00E-17 16.52287874 0.872285921 VADAKGDS(ph)ESEEDEDLEVPVPSR ddPTM_HeLa_Romidepsin_16h_R1 2 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 0 VADAKGDS(0.877)ES(0.123)EEDEDLEVPVPSR;VADAKGDS(0.964)ES(0.036)EEDEDLEVPVPSR ; 79.029 0.00018737 36622000 3791.3 3489.4 3287.7 3703.7 3070.3 4153.1 3467.3 3520 4287.4 3935 TRUE FALSE FALSE 3745.090177 3538.523865 3344.921039 4131.93922 2913.611134 3887.730314 3761.812375 3621.845646 3903.924206 3832.768133 0.977124117 0.923229306 0.872716774 1.07805614 0.760184554 1.014340075 0.981487073 0.944968629 1.018565191 1 11.90417101 -10.45444964 3.681843809 0.990526599 0.939820779 0.101823581 0.080255574 0.452391626 11.42941493 0.013067786 0.014561794 3.51E-11 10.45444964 -0.05070582 VADAKGDSES(ph)EEDEDLEVPVPSR ddPTM_HeLa_Romidepsin_16h_R1 1 VADAKGDSESEEDEDLEVPVPSR 23 1 P13861;P13861-2 P13861 PRKAR2A cAMP-dependent protein kinase type II-alpha regulatory subunit 1 0 VADAKGDS(0.057)ES(0.942)EEDEDLEVPVPSR 75.82 0.0003083 22735000 996.47 698.32 794.38 950.84 889.63 954.72 731.15 743.17 1124.8 1010.4 TRUE FALSE FALSE 984.3246404 708.1509673 808.2058507 1060.780595 844.2288614 893.7164732 793.2538628 764.6724514 1024.195071 984.1496623 1.000177796 0.719556176 0.821222505 1.077865121 0.857825688 0.908110329 0.806029706 0.776987973 1.040690365 1 9.942733917 -4 0.125919616 1.06577162 0.177169909 0.297190365 0.097777208 78.92748916 0.675777335 0.390337595 12.43779392 1.00E-04 4 -0.888601711 VADNS(ph)FDAK ddPTM_HeLa_Romidepsin_16h_R1 1 VADNSFDAK 9 0 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 0 VADNS(1)FDAK 100.02 0.028314 144550000 3911.6 4087.5 3902.8 2964.4 3277.6 3144.1 2934.8 2966.4 3712.7 3605.3 TRUE FALSE FALSE 3863.923915 4145.043932 3970.726597 3307.157876 3110.331842 2943.202157 3184.081839 3052.228104 3380.626813 3511.633786 1.100320862 1.180374773 1.13073482 0.941771858 0.885722154 0.838129012 0.906723774 0.869176084 0.962693441 1 11.77792668 -9.05155052 4.026387004 1.066120962 0.87701573 0.711823794 0.060294188 0.104633797 3.501022741 0.009897917 0.017272629 8.88E-10 9.05155052 -0.189105232 VADPDHDHTGFLTEY(ph)VATR ddPTM_HeLa_Romidepsin_16h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482-2;P28482 P28482-2 MAPK1 Mitogen-activated protein kinase 1 1 0 VADPDHDHTGFLT(0.008)EY(0.988)VAT(0.004)R 77.027 0.0028894 6115400 3305.1 3701.7 3127.2 3428 3102.6 3777 3801.4 3815.7 3655.8 2907.2 TRUE FALSE FALSE 3264.81617 3753.81263 3181.627604 3824.361489 2944.262745 3535.66189 4124.290821 3926.101259 3328.816092 2831.670525 1.152964704 1.325653037 1.123586793 1.350567255 1.039761766 1.248613445 1.456486828 1.386496496 1.175566176 1 11.4674377 -4.000000001 0.073877249 0.724243341 2.45039589 0.334739764 0.117906293 112.3755366 0.61600185 2.432010047 20.11143666 1.00E-04 4.000000001 1.726152549 VADPDHDHTGFLTEYVATR ddPTM_HeLa_Romidepsin_16h_R1 1 VADPDHDHTGFLTEYVATR 19 0 P28482-2;P28482 P28482-2 MAPK1 Mitogen-activated protein kinase 1 0 0 76.526 0.0041895 5817500 2654.4 2823.2 2731.1 3094.9 3494.2 3277.8 2564.9 2923.6 3184.5 2758.5 FALSE FALSE TRUE 2622.047152 2862.945084 2778.63365 3452.7469 3315.877935 3068.359159 2782.762542 3008.189753 2899.670344 2686.833772 0.975887373 1.065546039 1.034166564 1.285061598 1.234120983 1.141998136 1.035703277 1.119603968 1.079214641 1 11.39169135 -9.45826047 7.478592437 0.996579332 1.159502747 0.436448759 0.071135834 0.166139755 17.11760894 0.011050595 0.01686069 3.48E-10 9.45826047 0.162923415 VAEIEHAEK ddPTM_HeLa_Romidepsin_16h_R1 1 VAEIEHAEK 9 0 F8VQ14;F5GWF6;P78371;P78371-2 F8VQ14 CCT2 T-complex protein 1 subunit beta 0 0 88.134 0.020386 6355300 6405 7139.2 7527.5 4051 6716.8 7158.5 8276.5 2599.2 8208.6 7282.6 FALSE FALSE TRUE 6326.933396 7239.705845 7658.51298 4519.395681 6374.016632 6701.094953 8979.505703 2674.403751 7474.402257 7093.397002 0.89194689 1.020626062 1.079667891 0.637127131 0.898584505 0.944694756 1.265896396 0.37702722 1.053712665 1 12.79226098 VAEKLDEIYVAGLVAHSDLDER ddPTM_HeLa_Romidepsin_16h_R1 2 VAEKLDEIYVAGLVAHSDLDER 22 1 O60506-2;O60506;O60506-4;O60506-3;F6UXX1 O60506-2 SYNCRIP Heterogeneous nuclear ribonucleoprotein Q 0 0 ; ; 139.44 2.28E-05 29630000 22486.3 21539.8 20142.2 23363.2 20040 19304.7 18050.5 19379.7 24930 21633.3 FALSE FALSE TRUE 22212.22833 21843.03787 20492.76654 26064.56311 19017.28402 18071.19197 19583.70902 19940.42104 22700.19836 21071.26375 1.054147895 1.036626855 0.972545681 1.236971993 0.902522234 0.857622599 0.92940363 0.946332469 1.077305976 1 14.36298922 VAETANEEEVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VAETANEEEVKK 12 1 D6R9I9;P61221 D6R9I9 ABCE1 ATP-binding cassette sub-family E member 1 0 1 VAETANEEEVK(1)K 234.3 1.08E-40 1034400 258.32 136.24 155.32 189.42 381.08 235.91 267.18 195.34 290.32 514.83 FALSE TRUE FALSE 255.1714965 138.1579903 158.0232794 211.3216316 361.6320656 220.8361124 289.8742625 200.9918547 264.3530521 501.4546424 0.508862567 0.275514431 0.315129757 0.421417241 0.721166054 0.440391002 0.578066764 0.400817617 0.52717241 1 8.969975402 -11.88178674 0.790203716 0.993167009 0.459632076 0.149319469 0.185936261 0.264551346 0.312399537 0.079857058 0.027696724 1.31E-12 11.88178674 -0.533534932 VAFITGGGS(ph)GIGFR ddPTM_HeLa_Romidepsin_16h_R1 1 VAFITGGGSGIGFR 14 0 G3V0I9;A0A0J9YXZ6;A0A0J9YY83;A0A0J9YWI0;Q4VXZ8;Q9NUI1-2;Q9NUI1 G3V0I9 DECR2 "Peroxisomal 2,4-dienoyl-CoA reductase" 1 0 VAFIT(0.007)GGGS(0.993)GIGFR 77.644 0.016863 7123800 2349.9 1661 1583.1 1141 1228.2 1561 1728.1 1652.6 2314.5 1762 TRUE FALSE FALSE 2321.258515 1684.383602 1610.653191 1272.927789 1165.520371 1461.257138 1874.884771 1700.415374 2107.485323 1716.222986 1.352538996 0.981447991 0.938487134 0.74170303 0.679119427 0.851437808 1.092448234 0.990789302 1.22797873 1 10.7450213 -10.01728896 4.410408946 1.167175949 0.878663974 0.502456246 0.137265182 0.166750371 7.922216729 0.029341157 0.037385947 9.61E-11 10.01728896 -0.288511975 VAFQFPTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VAFQFPTKK 9 1 Q96GN5-5;Q96GN5-2;Q96GN5;C9IZR6;Q96GN5-4 Q96GN5-5 CDCA7L Cell division cycle-associated 7-like protein 0 1 ; VAFQFPTK(1)K;VAFQFPTK(1)K 182.76 1.60E-05 1316400 725.67 646.59 485.1 491.76 1304.3 1425.19 1288.2 1274.25 711.15 751.72 FALSE TRUE FALSE 716.8252549 655.692711 493.542962 548.619605 1237.736704 1334.124959 1397.619676 1311.118413 647.5429629 732.190206 0.979015082 0.895522373 0.674063867 0.749285637 1.690457881 1.822101617 1.908820501 1.790680075 0.88439173 1 9.516074666 -8.681881473 5.429177796 0.941060466 1.829444835 0.939894743 0.115623758 0.042292619 2.130237612 0.019605719 0.039516133 2.08E-09 8.681881473 0.888384369 VAFSEITSPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 VAFSEITSPSKR 12 1 Q13415 Q13415 ORC1 Origin recognition complex subunit 1 0 1 VAFSEITSPSK(1)R 92.866 0.019435 0 0 153.99 0 0 141.41 173.89 166.01 0 0 0 FALSE TRUE FALSE 0 156.1578753 0 0 134.19332 162.7789902 180.1108853 0 0 0 0 VAFT(ph)QSPSAAPTR ddPTM_HeLa_Romidepsin_16h_R1 1 VAFTQSPSAAPTR 13 0 P08174-6 P08174-6 1 0 VAFT(0.5)QS(0.5)PSAAPTR 72.898 0.0030521 0 2861 2580.1 2529.8 1920.5 2662.9 2986.5 2389.9 2699 2798.2 3061.5 TRUE FALSE FALSE 2826.129032 2616.422716 2573.830108 2142.557246 2527.002276 2795.672288 2592.898046 2777.091307 2547.921984 2981.961789 0.947741531 0.87741658 0.863133162 0.718505936 0.847429463 0.937527871 0.86952759 0.931296745 0.85444488 1 11.54204606 -10.40234029 1.642038016 0.981469482 0.858116795 0.087878522 0.069465516 0.236305841 1.230105841 0.011762295 0.013209345 3.96E-11 10.40234029 -0.123352687 VAGGAAPSKPAS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 VAGGAAPSKPASAK 14 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 1 0 VAGGAAPS(0.01)KPAS(0.99)AK 81.606 0.012204 99295000 2592.1 3035 2760.3 2522.1 3680 4787.2 3984.8 3650.1 3155.7 3250.3 TRUE FALSE FALSE 2560.506488 3077.72681 2808.341864 2813.717069 3492.195868 4481.31337 4323.268813 3755.709885 2873.446288 3165.856737 0.808787858 0.972162377 0.887071683 0.88876955 1.103080827 1.415513632 1.365592056 1.186317069 0.907636235 1 11.62838026 -8.519542659 3.42694158 0.910125771 1.324501425 0.862555 0.073591448 0.072105439 1.780559642 0.013048594 0.029293862 3.02E-09 8.519542659 0.414375654 VAGGAAPSKPASAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VAGGAAPSKPASAKK 15 2 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 1 VAGGAAPSKPASAK(1)K 132.24 3.87E-05 19038000 2147.4 2496.6 2781.8 2543.6 2898.4 3200 2338.1 2502.7 2392.7 1622.3 FALSE TRUE FALSE 2121.226663 2531.7472 2830.216062 2837.703 2750.483833 2995.530328 2536.698156 2575.111676 2178.690919 1580.152412 1.342419027 1.602217091 1.791103213 1.795841324 1.740644644 1.895722403 1.605350304 1.629660314 1.378785301 1 10.625848 -10.61961802 0.822647253 1.070360681 1.758512507 0.716152528 0.136200522 0.123199936 0.17683846 0.029861552 0.02857486 2.40E-11 10.61961802 0.688151826 VAGPADAPMDS(ph)GAEEEK ddPTM_HeLa_Romidepsin_16h_R1 2 VAGPADAPMDSGAEEEK 17 0 Q8TEK3-1;Q8TEK3 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 VAGPADAPMDS(1)GAEEEK;VAGPADAPMDS(1)GAEEEK ; 90.614 0.012217 15327300 4701.2 4894 4511.2 3085.6 3214.7 3171.9 2220.34 2747.4 4867.8 4509 TRUE FALSE FALSE 4643.899966 4962.89786 4589.715544 3442.37159 3050.641863 2969.225827 2408.935624 2826.891684 4432.411776 4391.85553 1.057389054 1.130023023 1.045051576 0.783808021 0.694613437 0.676075478 0.548500653 0.64366682 1.009234422 1 12.10061488 -9.028660816 2.072850592 1.039320667 0.628816905 0.938651244 0.049462651 0.059536428 0.508387023 0.008558754 0.016458142 9.36E-10 9.028660816 -0.410503762 VAGPADAPMDS(ph)GAEEEKAGAATVK ddPTM_HeLa_Romidepsin_16h_R1 3 VAGPADAPMDSGAEEEKAGAATVK 24 1 Q8TEK3-1;Q8TEK3 Q8TEK3-1 DOT1L "Histone-lysine N-methyltransferase, H3 lysine-79 specific" 1 0 VAGPADAPMDS(1)GAEEEKAGAATVK;VAGPADAPMDS(1)GAEEEKAGAATVK;VAGPADAPMDS(1)GAEEEKAGAATVK ;; 86.439 0.00015778 55734000 8651.6 8789.4 7647.3 8535.8 6194.6 5641.9 5130.7 5613.2 8715.7 8127.3 TRUE FALSE FALSE 8546.150971 8913.137404 7780.398049 9522.749358 5878.466447 5281.400798 5566.50153 5775.609086 7936.145963 7916.151574 1.079584049 1.125943247 0.98285107 1.202951872 0.742591446 0.66716772 0.703182787 0.729598092 1.002525771 1 12.95058352 -8.672391524 6.916666147 1.051324089 0.702403502 0.878556947 0.064599932 0.053607616 3.512755671 0.009143123 0.018346548 2.13E-09 8.672391524 -0.348920587 VAIDVGYR ddPTM_HeLa_Romidepsin_16h_R1 1 VAIDVGYR 8 0 E9PEF9;E9PCX2;P15121 E9PEF9 AKR1B1 Aldose reductase 0 0 121.99 0.013007 4029200 4029.8 3084.5 3765.5 2921.6 5510.6 4936.5 3179.9 3789.5 3430.6 3070.9 FALSE FALSE TRUE 3980.683248 3127.923672 3831.036948 3259.409139 5229.373519 4621.073582 3450.000627 3899.143204 3123.758544 2991.117575 1.330834762 1.045737452 1.280804533 1.089696094 1.74830089 1.544932108 1.15341525 1.303574034 1.044344953 1 11.54646891 -8.826781448 24.99999993 1.156880616 1.42494882 0.41713623 0.175264402 53.65662243 20528.60024 0.028828953 0.052256934 1.49E-09 8.826781448 0.268068204 VAIEHLDK ddPTM_HeLa_Romidepsin_16h_R1 1 VAIEHLDK 8 0 E7ENZ3;B7ZAR1;E9PCA1;P48643-2;P48643 E7ENZ3 CCT5 T-complex protein 1 subunit epsilon 0 0 99.442 0.014716 21871000 11739 10638 11313 9170.9 11437 10638 8923.2 9308.4 11808 11548 FALSE FALSE TRUE 11595.92055 10787.76204 11509.89802 10231.28261 10853.32721 9958.266133 9681.136385 9577.723868 10751.86291 11247.9813 1.030933485 0.95908428 1.023285665 0.909610564 0.964913341 0.885338077 0.860699901 0.851506027 0.955892673 1 13.45737848 -8.435277057 0.664206616 1.014051719 0.830155645 0.706283805 0.033366056 0.304271634 0.200548316 0.005149716 0.031872004 3.67E-09 8.435277057 -0.183896073 VALEK(ac)SVSQK ddPTM_HeLa_Romidepsin_16h_R1 1 VALEKSVSQK 10 1 Q13573;G3V3A4 Q13573 SNW1 SNW domain-containing protein 1 0 1 VALEK(1)SVSQK 157.66 0.018188 542100 218.7 130.64 163.75 0 139.33 0 156.14 0 235.82 121.72 FALSE TRUE FALSE 216.0344003 132.4791533 166.6000001 0 132.2194702 0 169.4025277 0 214.7276686 118.5576969 1.822187897 1.117423473 1.40522298 0 1.11523312 0 1.428861493 0 1.811165992 1 6.889445516 -9.290492877 23.74390671 1.374653397 0.565354352 0.445726894 0.51041017 294.1045677 240355.4762 0.075823239 0.115837997 5.12E-10 9.290492877 -0.809299045 VALSDDET(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 VALSDDETK 9 0 H0YD46;Q15054-3;Q15054-2;Q15054 H0YD46 POLD3 DNA polymerase delta subunit 3 1 0 VALS(0.475)DDET(0.525)K 131.52 0.015465 8319200 4406 4583.5 4576.1 1988.3 3753 3485.1 3464.8 3943.8 4541 4292.1 TRUE FALSE FALSE 4352.297977 4648.026633 4655.745101 2218.196601 3561.470406 3262.413358 3759.100026 4057.907631 4134.841587 4180.590623 1.041072511 1.111810998 1.113657261 0.530594072 0.851906041 0.7803714 0.899179174 0.970654148 0.989056801 1 12.02949106 -9.315641308 24.99996747 1.034716404 0.812752649 0.532190102 0.114062842 197.7027742 91187.46504 0.017120092 0.026151382 4.83E-10 9.315641308 -0.221963755 VALSSET(ph)EVALAR ddPTM_HeLa_Romidepsin_16h_R1 2 VALSSETEVALAR 13 0 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 VALS(0.008)S(0.183)ET(0.809)EVALAR;VALS(0.267)S(0.267)ET(0.466)EVALAR ; 200.93 6.62E-16 9914100 3208.3 3585.3 3063.5 3006.2 3337.9 3844 3032.3 3285.5 3640.4 3663.4 TRUE FALSE FALSE 3169.196006 3635.773948 3116.818932 3353.790989 3167.554508 3598.380806 3289.863486 3380.560759 3314.793506 3568.22434 0.888171736 1.018930875 0.873492986 0.939904745 0.887711704 1.008451393 0.921988971 0.947407012 0.928975645 1 11.80099061 -12.59919413 1.389805728 1.00006727 0.930175796 0 0.050827758 0.481040775 1.664501747 0.031282132 0.00720381 2.52E-13 12.59919413 -0.069891474 VALVNDS(ph)LSDVTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 VALVNDSLSDVTSTTSSR 18 0 Q7Z2W4-2;Q7Z2W4 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 VALVNDS(0.596)LS(0.403)DVTSTTSSR 147.49 6.88E-05 5158900 2225.5 2076.2 1955.5 1988.9 1539.7 1415.7 1192.3 1568.4 1801.4 1747.2 TRUE FALSE FALSE 2198.37475 2105.428798 1989.534657 2218.865976 1461.123364 1325.241339 1293.573932 1613.779179 1640.278272 1701.807492 1.291788149 1.237172129 1.169071512 1.303829009 0.858571472 0.778725764 0.760117662 0.948273637 0.963844783 1 10.73285213 -8.68148023 7.147629163 1.162040038 0.823200129 0.659526969 0.114205589 0.116072452 8.711543956 0.01878747 0.037667774 2.08E-09 8.68148023 -0.338839909 VALVNDSLS(ph)DVTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 1 VALVNDSLSDVTSTTSSR 18 0 Q7Z2W4-2;Q7Z2W4 Q7Z2W4-2 ZC3HAV1 Zinc finger CCCH-type antiviral protein 1 1 0 VALVNDS(0.003)LS(0.652)DVT(0.265)S(0.071)T(0.008)TSSR 204.81 5.24E-21 6252700 1743 2242.6 1898.5 1788.7 1650 1513.9 1125.8 1358.4 2105.3 1912 TRUE FALSE FALSE 1721.755646 2274.171382 1931.542596 1995.51791 1565.794343 1417.166676 1221.425424 1397.703161 1916.996695 1862.325964 0.92451895 1.221145721 1.037166765 1.071519137 0.840773513 0.760965966 0.65586017 0.75051478 1.029356156 1 10.8628899 -8.471629352 2.714571354 0.997415961 0.713634844 0.736787667 0.085074511 0.13072276 1.896349277 0.013776538 0.033243443 3.38E-09 8.471629352 -0.283781117 VALVYGQMNEPPGAR ddPTM_HeLa_Romidepsin_16h_R1 1 VALVYGQMNEPPGAR 15 0 H0YH81;P06576;F8W0P7 H0YH81 ATP5B "ATP synthase subunit beta;ATP synthase subunit beta, mitochondrial" 0 0 106.26 0.0018164 0 176.77 64.37 255.04 0 235.75 204.83 188.72 113.69 59.338 198.39 FALSE FALSE TRUE 174.6154592 65.27620255 259.4788642 0 223.7187978 191.7420241 204.7498721 116.9794408 54.03066067 193.2357992 0.903639284 0.337805949 1.342809486 0 1.157750265 0.992269677 1.05958561 0.605371475 0.279609994 1 7.594218585 -10.50592194 17.74016319 0.95749346 0.795738192 0 0.433480487 14.05264355 14706.28115 0.060742611 0.065233463 3.12E-11 10.50592194 -0.161755268 VAMANIQPQMLVAGAT(ph)SIAR ddPTM_HeLa_Romidepsin_16h_R1 1 VAMANIQPQMLVAGATSIAR 20 0 P18206-2;P18206 P18206-2 VCL Vinculin 1 0 VAMANIQPQMLVAGAT(0.626)S(0.374)IAR 89.913 0.0015565 10246000 1066.8 934.51 957.92 928.8 1510.7 1236.2 868.59 1169.3 991.45 1080 TRUE FALSE FALSE 1053.797431 947.6660563 974.5921958 1036.192226 1433.603342 1157.21081 942.3680129 1203.131851 902.7722289 1051.941444 1.001764344 0.900873391 0.926470006 0.985028427 1.362816675 1.100071507 0.895836948 1.143725116 0.858196275 1 10.03883868 -8.914691416 24.35526582 0.98529372 1.115694292 0.330644532 0.117331442 22.18040731 6328.781128 0.016361024 0.029656877 1.22E-09 8.914691416 0.130400572 VANPSGNLTETYVQDR ddPTM_HeLa_Romidepsin_16h_R1 1 VANPSGNLTETYVQDR 16 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 137.93 2.28E-07 0 800.08 1078 941.4 912.83 1071.8 1043.6 828.15 1020.5 1156.6 991.18 FALSE FALSE TRUE 790.3283172 1093.176112 957.7846721 1018.3757 1017.102047 976.9173281 898.4930403 1050.026557 1053.150799 965.4290007 0.818629145 1.132321602 0.992081936 1.054842665 1.053523403 1.011899712 0.930667133 1.087626906 1.090863024 1 9.915026355 -10.2627991 24.99969269 0.914352653 1.031996342 0.002483176 0.086060625 108.3665438 1992406.57 0.01375864 0.016203107 5.46E-11 10.2627991 0.117643688 VAPAPAVVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VAPAPAVVKK 10 1 P62424;Q5T8U3 P62424 RPL7A 60S ribosomal protein L7a 0 1 ; VAPAPAVVK(1)K;VAPAPAVVK(1)K 133.12 0.0017518 4745500 3763.9 4790.2 3386.4 2800.6 3878.7 4045.5 3900 3238.6 5265.3 4122.6 FALSE TRUE FALSE 3718.024139 4857.636561 3445.338871 3124.418549 3680.755466 3787.005606 4231.265903 3332.303781 4794.358381 4015.494258 0.925919426 1.2097232 0.858011156 0.778090653 0.916638209 0.94309825 1.053734766 0.829861424 1.193964696 1 11.97136186 VAPEEHPVLLT(ph)EAPLNPK ddPTM_HeLa_Romidepsin_16h_R1 2 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" 1 0 VAPEEHPVLLT(1)EAPLNPK;VAPEEHPVLLT(1)EAPLNPK ; 148.06 4.78E-05 27238000 5822.6 5837.1 5087 4560.9 10208.1 6882.3 6052.6 6301.6 6118.8 5414 TRUE FALSE FALSE 5751.631912 5919.274847 5175.537101 5088.252718 9687.142565 6442.543242 6566.707693 6483.926854 5571.519203 5273.3435 1.090699271 1.122489906 0.981452678 0.964900678 1.837002002 1.221718866 1.245264545 1.229566565 1.056543956 1 12.36450226 VAPEEHPVLLTEAPLNPK ddPTM_HeLa_Romidepsin_16h_R1 3 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 0 ;; ;; 154.88 2.28E-15 166141600 6575.79 5622.94 5912.79 6257.19 6471.52 7569.7 6528.25 6968.56 6407.96 6246.21 FALSE FALSE TRUE 6495.641742 5702.099897 6015.69963 6980.675749 6141.254186 7086.0206 7082.759392 7170.184289 5834.816009 6083.932564 1.067671555 0.937239168 0.988784732 1.14739532 1.009421804 1.164710576 1.16417454 1.17854434 0.959053367 1 12.57078845 -8.259861879 1.060287543 1.02438405 1.190110529 0.591392269 0.057183795 0.357959063 0.682161953 0.008707774 0.044477408 5.50E-09 8.259861879 0.165726479 VAPGPSSGSTPGQVPGSS(ph)ALSSPRR ddPTM_HeLa_Romidepsin_16h_R1 1 VAPGPSSGSTPGQVPGSSALSSPRR 25 1 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-5 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 VAPGPSSGSTPGQVPGS(0.188)S(0.297)ALS(0.297)S(0.219)PRR 76.557 8.95E-05 15289000 1058.9 1035.7 939.53 1112.4 865.55 1120.8 824.32 688.75 1146 1195.6 TRUE FALSE FALSE 1045.99372 1050.280612 955.8821255 1241.020922 821.3777537 1049.184497 894.3377202 708.6778946 1043.49889 1164.53814 0.898204777 0.901885972 0.820825092 1.065676494 0.705324906 0.900944728 0.767976325 0.608548463 0.896062442 1 10.18554217 -5.928697367 0.335476373 0.962461323 8.43E-32 0.492518306 0.091542516 8.397343174 0.335040941 0.027849316 3.958226448 1.18E-06 5.928697367 -0.962461323 VAPGPSSGSTPGQVPGSSALSS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VAPGPSSGSTPGQVPGSSALSSPR 24 0 Q8NEY1-2;Q8NEY1-3;Q8NEY1;A0A0A0MRJ3;Q8NEY1-7;Q8NEY1-4;Q8NEY1-5 Q8NEY1-2 NAV1 Neuron navigator 1 1 0 VAPGPSSGSTPGQVPGSS(0.001)ALS(0.24)S(0.759)PR 166.59 5.82E-14 6414200 869.58 750.51 758.68 485.62 585.18 681.91 640.14 494.65 826.1 630.93 TRUE FALSE FALSE 858.9812245 761.0756995 771.8845071 541.7696693 555.316081 638.3381518 694.5134756 508.9619173 752.211547 614.5383476 1.397766678 1.238451111 1.256039611 0.881588059 0.903631292 1.03872794 1.130138548 0.828202047 1.224027028 1 9.263359228 -9.26626652 24.72630584 1.201857354 0.967742301 0.544687142 0.120958237 326.6797303 1673366.65 0.025766902 0.040170474 5.42E-10 9.26626652 -0.234115053 VAPSK(ac)LEALQK ddPTM_HeLa_Romidepsin_16h_R1 2 VAPSKLEALQK 11 1 A0A5H1ZRP4;Q8WX92;Q8WX92-2 A0A5H1ZRP4 NELFB Negative elongation factor B 0 1 ; VAPSK(1)LEALQK;VAPSK(1)LEALQK 132.76 0.0060555 1473610 575.09 552.65 463.18 662.17 577.7 613.57 632.68 475.66 715.44 518.96 FALSE TRUE FALSE 568.0805819 560.4302212 471.2414536 738.733211 548.2178133 574.3648572 686.4198234 489.4224716 651.4492545 505.4773444 1.12384974 1.108714817 0.932270178 1.46145662 1.084554668 1.136282098 1.357963578 0.968238195 1.288780322 1 8.981502621 ELFDDPSY(ph)VNVQNLDK ddPTM_HeLa_Romidepsin_16h_R1 5 ELFDDPSYVNVQNLDK 16 0 Q5T188;H0Y539;X6R6D0;P29353-5;P29353-3;P29353-2;P29353-7;P29353;P29353-6 Q5T188 SHC1 SHC-transforming protein 1 1 0 ELFDDPS(0.358)Y(0.642)VNVQNLDK;ELFDDPS(0.014)Y(0.986)VNVQNLDK;ELFDDPS(0.161)Y(0.839)VNVQNLDK;ELFDDPS(0.109)Y(0.891)VNVQNLDK;ELFDDPS(0.123)Y(0.877)VNVQNLDK ;;;; 257.2 2.83E-70 272360000 26988.5 27917.4 25855.5 27569.3 23820.7 14936.17 11616.44 12203.75 30340.2 27322.3 TRUE FALSE FALSE 26659.55378 28310.42189 26305.50413 30756.99218 22605.04079 13981.79694 12603.14012 12556.84625 27626.49652 26612.46271 1.001769512 1.063803159 0.988465608 1.155736413 0.849415593 0.525385309 0.473580377 0.471840821 1.03810372 1 14.6998144 -8.347300793 2.923979745 1.014758761 0.477470121 0.956441366 0.05233862 0.035477339 0.58623307 0.007195069 0.018299204 4.49E-09 8.347300793 -0.53728864 down VAPVINNGSPTILGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 VAPVINNGSPTILGKR 16 1 H0Y4T7;E7ESY4;Q13330-3;Q13330;F8W9Y9 H0Y4T7 MTA1 Metastasis-associated protein MTA1 0 1 VAPVINNGSPTILGK(1)R 133.88 1.07E-15 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 VAQGATEK(ac)SPEDK ddPTM_HeLa_Romidepsin_16h_R1 2 VAQGATEKSPEDK 13 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 0 1 ; VAQGATEK(1)SPEDK;VAQGATEK(1)SPEDK 148.13 0.00017497 1582400 474.04 447.25 360.68 236.39 623.3 418.07 457.42 552.63 460.65 661.02 FALSE TRUE FALSE 468.2622181 453.5463972 366.9574841 263.722524 591.4906751 391.3566763 496.2732434 568.6194771 419.4483103 643.8466051 0.727288479 0.704432381 0.569945514 0.409604589 0.918682603 0.607841485 0.770794222 0.883159859 0.651472427 1 9.3305732 -11.81915046 0.756206044 0.995813236 0.69069713 0 0.17521778 0.507798917 0.554786386 0.084875038 0.03027253 1.52E-12 11.81915046 -0.305116106 VAQGATEKS(ph)PEDK ddPTM_HeLa_Romidepsin_16h_R1 1 VAQGATEKSPEDK 13 1 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 VAQGATEKS(1)PEDK 139.3 0.0080082 6487100 809.33 759.91 1054.4 559.54 663.03 746.37 894.29 347.3 893.28 530.29 TRUE FALSE FALSE 799.4655747 770.6080329 1072.75139 624.2366475 629.193105 698.6793658 970.2509703 357.3485776 813.3827995 516.5129894 1.547813107 1.491943182 2.076910769 1.208559437 1.218155435 1.352684986 1.878463834 0.691848191 1.574757685 1 9.01266082 -12.28044997 1.019512381 1.001366149 1.457674124 0 0.399008821 0.691524666 1.293662311 0.225223478 0.061568708 5.24E-13 12.28044997 0.456307975 VAQGATEKS(ph)PEDKVQIAANEETQER ddPTM_HeLa_Romidepsin_16h_R1 1 VAQGATEKSPEDKVQIAANEETQER 25 2 P49321-4;P49321;P49321-3 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 VAQGAT(0.298)EKS(0.702)PEDKVQIAANEETQER 60.171 0.0036775 0 530.49 416.66 409.76 623.51 390.07 467.31 411.43 521.97 470.46 427.59 TRUE FALSE FALSE 524.0241838 422.5257504 416.8917009 695.6031599 370.1632723 437.4503992 446.3768539 537.0723784 428.3808793 416.4811502 1.25821825 1.014513503 1.000985761 1.670191219 0.888787577 1.050348615 1.071781649 1.289547866 1.028572071 1 8.702107391 -6.145752659 16.22601879 1.129734459 1.15136725 0 0.214190316 0 0 0.026954718 0 7.15E-07 6.145752659 0.02163279 VAQILK(ac)EPK ddPTM_HeLa_Romidepsin_16h_R1 2 VAQILKEPK 9 1 A0A494C0K9;H7C0C1;P48047 A0A494C0K9 ATP5O "ATP synthase subunit O, mitochondrial" 0 1 ; VAQILK(1)EPK;VAQILK(1)EPK 125.56 0.0068747 1349310 594.6 515.7 1245.69 427.81 1834.59 2142.7 1394.32 1018.68 994.5 554.51 FALSE TRUE FALSE 587.3527865 522.9600381 1267.370712 477.2754051 1740.964027 2005.788385 1512.753506 1048.153899 905.5494292 540.1037503 1.087481407 0.968258483 2.34653196 0.883673562 3.223388147 3.71370942 2.800857252 1.94065288 1.676621258 1 9.077092756 -8.761516633 24.99999999 1.135100935 2.967885188 0.620817773 0.598082228 0.853575764 276341.417 0.084062916 0.159765136 1.73E-09 8.761516633 1.832784253 VAS(ph)DTEEADR ddPTM_HeLa_Romidepsin_16h_R1 3 VASDTEEADR 10 0 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 VAS(0.944)DT(0.056)EEADR;VAS(0.941)DT(0.059)EEADR;VAS(0.774)DT(0.226)EEADR ;; 163.9 0.0018206 39292600 5783.4 5765.4 5683.1 3897.15 6568.4 6454.9 6680.4 5453.4 6518.4 6107 TRUE FALSE FALSE 5712.909696 5846.565453 5782.011972 4347.75682 6233.190038 6042.452722 7247.833009 5611.185525 5935.377978 5948.33926 0.960420959 0.982890383 0.972038029 0.730919443 1.047887447 1.015821805 1.218463287 0.943319686 0.997821025 1 12.53827122 -8.548253068 24.99997678 0.961577133 1.06791582 0.231576711 0.09872206 254.485822 250730.37 0.013699595 0.027399916 2.83E-09 8.548253068 0.106338687 VAS(ph)DTEEADRTSSK ddPTM_HeLa_Romidepsin_16h_R1 2 VASDTEEADRTSSK 14 1 A0A590UJ84;B1AKN3;Q9P2R6;Q9P2R6-2;D6RA28 A0A590UJ84 RERE Arginine-glutamic acid dipeptide repeats protein 1 0 VAS(0.962)DT(0.038)EEADRTSSK;VAS(0.962)DT(0.038)EEADRTSSK ; 164.92 0.00078933 11900000 4005.7 2745.52 3137.27 4250 3756.6 4032.4 3256.5 3705.1 3470.5 3184.5 TRUE FALSE FALSE 3956.876988 2784.171503 3191.872868 4741.404997 3564.886684 3774.742654 3533.107029 3812.301223 3160.089788 3101.766231 1.275685107 0.897608425 1.029050106 1.528614552 1.149308626 1.216965552 1.139062961 1.229074321 1.018803337 1 11.59887424 VAS(ph)ETHSEGSEYEELPK ddPTM_HeLa_Romidepsin_16h_R1 1 VASETHSEGSEYEELPK 17 0 Q5JSZ5;A0A494C0D3 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 VAS(0.83)ET(0.159)HS(0.011)EGSEYEELPK 107.18 0.00098103 7758900 5106.8 5248.8 4642.2 4957.9 3328.9 3851.3 3421.3 3336.6 6228.2 6023.7 TRUE FALSE FALSE 5044.556357 5322.692744 4722.995544 5531.155726 3159.013811 3605.21436 3711.905137 3433.139257 5671.134193 5867.203406 0.859788899 0.907194173 0.804982411 0.942724386 0.538419004 0.614468957 0.632653222 0.585140657 0.966582169 1 12.51845729 -8.765308419 24.99991062 0.919855843 0.597083385 0.887620512 0.055897522 27.54454613 177981.4475 0.010163002 0.018936743 1.72E-09 8.765308419 -0.322772458 VAS(ph)LTLHNK ddPTM_HeLa_Romidepsin_16h_R1 1 VASLTLHNK 9 0 Q9P0K7-3;Q9P0K7;Q9P0K7-2;Q9P0K7-4 Q9P0K7-3 RAI14 Ankycorbin 1 0 VAS(0.943)LT(0.057)LHNK 75.819 0.029728 8191900 3998.6 3821.3 3809.9 3681.3 1920.3 1854.7 1473 1629 4349.8 3640.9 TRUE FALSE FALSE 3949.863525 3875.096362 3876.209711 4106.949227 1822.299925 1736.190656 1598.116583 1676.132545 3960.742994 3546.308893 1.11379568 1.092712586 1.093026532 1.15809123 0.513858206 0.489576827 0.45064224 0.472641441 1.116863509 1 11.79210249 -8.754007678 24.99999999 1.068032346 0.480026633 0.977626646 0.045393133 21.8010606 73337.41798 0.00820812 0.016158758 1.76E-09 8.754007678 -0.588005713 VAS(ph)SPAPPEGPSHPR ddPTM_HeLa_Romidepsin_16h_R1 2 VASSPAPPEGPSHPR 15 0 H7BYJ3;O14578;O14578-4;O14578-3 H7BYJ3 CIT Citron Rho-interacting kinase 1 0 VAS(0.562)S(0.438)PAPPEGPSHPR;VAS(0.5)S(0.5)PAPPEGPSHPR ; 94.61 0.0051024 25626000 4994.1 4345 4809.7 4474.4 4637.1 4941.1 3855.1 4561.6 5332.8 4607.6 TRUE FALSE FALSE 4933.229988 4406.169024 4893.410811 4991.751181 4400.451484 4625.379657 4182.552098 4693.582699 4855.821012 4487.893888 1.099230533 0.98178993 1.090357957 1.112270322 0.980515938 1.030634808 0.931963233 1.045831924 1.081982135 1 12.13182285 -8.716412372 24.99975183 1.050240783 0.994959644 0.272499547 0.049104088 166.0638061 92200.61657 0.0076808 0.015361546 1.92E-09 8.716412372 -0.055281139 VASEAPLEHKPQVEAS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 VASEAPLEHKPQVEASSPR 19 1 Q8TD19 Q8TD19 NEK9 Serine/threonine-protein kinase Nek9 1 0 VASEAPLEHKPQVEAS(0.5)S(0.5)PR 53.255 0.022935 8919800 973.08 1053.5 1003 1039.7 950.92 969.23 924.78 872.45 1118.1 1101.6 TRUE FALSE FALSE 961.2197267 1068.331201 1020.456794 1159.915006 902.391004 907.299331 1003.33079 897.6929643 1018.094336 1072.980273 0.895841005 0.995667141 0.95104898 1.081021744 0.841013602 0.845588082 0.935087825 0.836635106 0.948847207 1 10.06740784 VASETHS(ph)EGSEYEELPK ddPTM_HeLa_Romidepsin_16h_R1 1 VASETHSEGSEYEELPK 17 0 Q5JSZ5;A0A494C0D3 Q5JSZ5 PRRC2B Protein PRRC2B 1 0 VAS(0.016)ET(0.079)HS(0.904)EGSEYEELPK 188.59 3.57E-13 4489000 1736.4 1484.3 1441.9 1809.5 1640.7 1279.1 957.85 1202.7 1862.8 1739.7 TRUE FALSE FALSE 1715.236089 1505.196014 1466.995665 2018.722904 1556.968957 1197.369638 1039.209755 1237.498227 1696.186503 1694.502343 1.012235891 0.88828205 0.865738351 1.191336744 0.918835529 0.706620232 0.613283162 0.730301868 1.000993896 1 10.72664592 -8.302564505 3.613398295 0.997621823 0.670753334 0.716868466 0.086981137 0.085196967 2.321991446 0.012027094 0.029913953 4.98E-09 8.302564505 -0.326868489 VASPSQGQVGS(ph)SSPKR ddPTM_HeLa_Romidepsin_16h_R1 1 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 VASPSQGQVGS(0.437)S(0.281)S(0.281)PKR 79.383 0.0076665 5364900 976.99 920.28 812.85 832.04 698 992.4 981.32 1630.5 821.73 1119.9 TRUE FALSE FALSE 965.0820701 933.235726 826.9973133 928.2443797 662.3784554 928.9888428 1064.673296 1677.675945 748.2324107 1090.804837 0.884743116 0.855547844 0.758153325 0.850972006 0.607238282 0.851654496 0.976043799 1.538016599 0.685945263 1 10.09117729 -7.264897747 3.428495911 0.889070911 1.617751691 0.734580196 0.124227898 0.127448194 2.529004715 0.017728375 0.240233761 5.43E-08 7.264897747 0.72868078 VASPSQGQVGSSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 VASPSQGQVGSSSPK 15 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 VASPSQGQVGSS(0.104)S(0.896)PK;VASPSQGQVGSS(0.087)S(0.913)PK ; 183.06 2.51E-08 12634300 4915.4 5136.3 4860.3 4413.8 5273.9 5049.7 4635 5206.5 5119.5 5382.2 TRUE FALSE FALSE 4855.489214 5208.608966 4944.891483 4924.144324 5004.753203 4727.040467 5028.696784 5357.141863 4661.599098 5242.369668 0.926201226 0.99356003 0.943255016 0.939297424 0.954673844 0.901699187 0.959241164 1.02189319 0.889216021 1 12.35600337 -12.53362482 1.263413339 1.000287614 0.950407915 0 0.046867285 0.526702812 1.491504949 0.022814883 0.005313114 2.93E-13 12.53362482 -0.0498797 VASPSQGQVGSSS(ph)PKR ddPTM_HeLa_Romidepsin_16h_R1 2 VASPSQGQVGSSSPKR 16 1 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 VASPSQGQVGS(0.01)S(0.031)S(0.958)PKR;VASPSQGQVGS(0.117)S(0.327)S(0.556)PKR ; 105.91 0.0012161 44343000 3423.9 3867.3 3458 3868.9 3874 3601.4 3764.8 3609.1 3781.2 3663 TRUE FALSE FALSE 3382.16819 3921.743951 3518.185039 4316.240422 3676.295324 3371.282163 4084.582018 3713.523614 3443.000002 3567.834732 0.947961003 1.099194398 0.986084083 1.209764674 1.030399556 0.944909845 1.144834984 1.040833977 0.965011067 1 11.80083307 -10.26415264 24.98053332 0.975426028 1.06477145 0.261532191 0.072386298 238.8089316 2198668.935 0.011809522 0.013826343 5.44E-11 10.26415264 0.089345422 VATLNS(ph)EEESDPPTYKDAFPPLPEK ddPTM_HeLa_Romidepsin_16h_R1 1 VATLNSEEESDPPTYKDAFPPLPEK 25 1 A0A024R4E5;Q00341-2;Q00341;C9JT62;C9JHS7;C9JK79;C9JHZ8;C9JES8;C9JZI8;C9J5E5;C9JIZ1;C9JQ82;C9JBS3;C9JEJ8;C9JHN6 A0A024R4E5 HDLBP Vigilin 1 0 VAT(0.01)LNS(0.364)EEES(0.364)DPPT(0.139)Y(0.124)KDAFPPLPEK 59.918 0.0020422 26694000 2402.2 2157.7 1508.1 2653.4 1992 1631.3 1715.1 1934.6 1838.5 2108.4 TRUE FALSE FALSE 2372.921062 2188.076157 1534.347848 2960.198593 1890.340807 1527.065195 1860.780551 1990.574599 1674.059955 2053.623464 1.155480108 1.065470957 0.747141759 1.441451485 0.92049046 0.743595514 0.906096265 0.969298722 0.815173757 1 11.00395597 -8.541910975 24.99915539 1.074707778 0.868929304 0.123685681 0.186685043 240.6521532 316099.6914 0.023230466 0.046466303 2.87E-09 8.541910975 -0.205778474 VATLNSEEES(ph)DPPTYK ddPTM_HeLa_Romidepsin_16h_R1 4 VATLNSEEESDPPTYK 16 0 A0A024R4E5;Q00341-2;Q00341;C9JT62;C9JHS7;C9JK79;C9JHZ8;C9JES8;C9JZI8;C9J5E5;C9JIZ1;C9JQ82;C9JBS3;C9JEJ8;C9JHN6;C9JMQ6 A0A024R4E5 HDLBP Vigilin 1 0 VATLNSEEES(0.999)DPPTYK;VATLNS(0.002)EEES(0.998)DPPTYK;VATLNS(0.255)EEES(0.745)DPPTYK;VATLNSEEES(1)DPPTYK ;;; 264.85 2.99E-86 195545000 21449.2 20435.2 19905.8 15646.8 19292.6 18632.8 17663.2 17622.7 20708.8 20190.6 TRUE FALSE FALSE 21187.7689 20722.88728 20252.2521 17455.95664 18308.02663 17442.22421 19163.51177 18132.58502 18856.55306 19666.0453 1.077378221 1.053739426 1.029808067 0.88761906 0.930946021 0.886920779 0.97444664 0.92202498 0.958838077 1 14.26341925 -9.304915455 8.232095471 1.038671511 0.922160366 0.632942386 0.038619089 0.13358408 23.68639692 0.005597307 0.008586231 4.96E-10 9.304915455 -0.116511145 VATLNSEEESDPPT(ph)YKDAFPPLPEK ddPTM_HeLa_Romidepsin_16h_R1 1 VATLNSEEESDPPTYKDAFPPLPEK 25 1 A0A024R4E5;Q00341-2;Q00341;C9JT62;C9JHS7;C9JK79;C9JHZ8;C9JES8;C9JZI8;C9J5E5;C9JIZ1;C9JQ82;C9JBS3;C9JEJ8;C9JHN6 A0A024R4E5 HDLBP Vigilin 1 0 VAT(0.002)LNS(0.042)EEES(0.025)DPPT(0.49)Y(0.442)KDAFPPLPEK 47.728 0.027533 19627000 2534 2261.9 1708.3 3188.7 2328.6 2136.9 1980.2 2066.2 2635.7 2280.1 TRUE FALSE FALSE 2503.114633 2293.743088 1738.032245 3557.392497 2209.762853 2000.358987 2148.398139 2125.982237 2399.956391 2220.862673 1.127091136 1.032816263 0.782593298 1.601806604 0.995002023 0.900712597 0.967370997 0.957277666 1.080641509 1 11.11690447 -8.531871632 24.99875024 1.07903011 0.944930666 0.12118019 0.193513627 360.6835273 1002639.241 0.027072366 0.054203843 2.94E-09 8.531871632 -0.134099445 VATTPGS(ph)PSLGR ddPTM_HeLa_Romidepsin_16h_R1 2 VATTPGSPSLGR 12 0 A0A087WWW7;E9PGF5;E9PF55;A0A494C067;A0A2R8Y4T1;Q9HBL0;H0Y4U1 A0A087WWW7 TNS1 Tensin-1 1 0 VAT(0.003)T(0.039)PGS(0.874)PS(0.084)LGR;VAT(0.003)T(0.033)PGS(0.482)PS(0.482)LGR ; 134.18 0.002896 31809000 5787.1 6126 5722.1 5724.7 4959.3 4541.4 3865.6 4485.7 6340.9 6140.5 TRUE FALSE FALSE 5716.564599 6212.241989 5821.69075 6386.61675 4706.208415 4251.219197 4193.943968 4615.486652 5773.754023 5980.968925 0.955792393 1.03866816 0.973369169 1.067823095 0.78686388 0.710791052 0.701214807 0.771695474 0.965354292 1 12.54616351 -8.636316554 5.170221458 0.988359802 0.728988184 0.918159153 0.037807514 0.041354344 1.714480762 0.005512629 0.011188047 2.31E-09 8.636316554 -0.259371618 SEDVTPMEVTAEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 SEDVTPMEVTAEKR 14 1 O94916-2;O94916;O94916-4;O94916-5 O94916-2 NFAT5 Nuclear factor of activated T-cells 5 0 1 ; SEDVTPMEVTAEK(1)R;SEDVTPMEVTAEK(1)R 147.24 3.89E-07 1996260 352.61 263.1 290.12 299.767 1520.06 2445.87 2354.9 2855.61 484.08 420.22 FALSE TRUE FALSE 348.3122537 266.8039287 295.1694169 334.427471 1442.485666 2289.586801 2554.925147 2938.23257 440.7826724 409.3026238 0.850989545 0.651850033 0.721152027 0.817066521 3.524252184 5.593872767 6.242142118 7.178631162 1.076911426 1 8.677024105 -8.406336184 1.671327651 0.858207768 6.707320463 0.984184499 0.313681849 0.03048649 0.163752623 0.046476178 0.142045579 3.92E-09 8.406336184 5.849112696 up VAVATPAKK ddPTM_HeLa_Romidepsin_16h_R1 1 VAVATPAKK 9 1 P19338;C9JYW2;C9JLB1;C9J1H7;C9JWL1 P19338;C9JWL1 NCL Nucleolin 0 0 111.74 0.0007494 0 2500.3 2604.6 3298.7 2595.2 2999.6 4196.6 4289.6 1508.9 3035 2356.1 FALSE FALSE TRUE 2469.825382 2641.267627 3356.11249 2895.269235 2846.519219 3928.450804 4653.958517 1552.557641 2763.541999 2294.888182 1.076229073 1.150935217 1.462429636 1.261616691 1.240373819 1.711826674 2.027967442 0.676528666 1.204216406 1 11.16420815 -9.793171156 0.850860131 1.018904153 1.469772244 0.124868215 0.335681967 0.565461494 0.819724244 0.065979375 0.104201162 1.61E-10 9.793171156 0.45086809 VAVEELS(ph)PGGQPR ddPTM_HeLa_Romidepsin_16h_R1 1 VAVEELSPGGQPR 13 0 Q9H611-2;Q9H611;Q9H611-3 Q9H611-2 PIF1 ATP-dependent DNA helicase PIF1 1 0 VAVEELS(1)PGGQPR 131.08 0.0022825 3908600 1448.9 1429.8 1617 1133.4 1025.2 1026.6 705.59 950.42 1574.3 1341.9 TRUE FALSE FALSE 1431.240249 1449.928762 1645.143207 1264.449041 972.8802185 961.0035732 765.522797 977.9189032 1433.490665 1307.037245 1.09502637 1.109324748 1.258681199 0.967416228 0.744340089 0.735253396 0.585693178 0.748195132 1.096748139 1 10.35208454 -8.791945473 3.101920037 1.067987072 0.688105079 0.853679306 0.078891483 0.077931611 1.541365308 0.012866663 0.025748175 1.61E-09 8.791945473 -0.379881993 VAVEEVDEEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VAVEEVDEEGK 11 0 P02545;P02545-3;P02545-2;P02545-6;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 180.09 0.00010131 31195000 6399.7 5654.1 5264.3 2647.7 5914.5 7082.2 5626.6 6858.8 6191 5662.9 FALSE FALSE TRUE 6321.697995 5733.698568 5355.922933 2953.839532 5612.660995 6629.670277 6104.523264 7057.248557 5637.261454 5515.777042 1.146111953 1.039508763 0.971018751 0.53552555 1.017564878 1.201946748 1.106738582 1.279465885 1.022024895 1 12.42934843 -8.265071807 22.08341944 1.016671565 1.187119238 0.260722746 0.163210977 88.54330767 538318.2317 0.025817596 0.06007608 5.43E-09 8.265071807 0.170447673 VAVEEVDEEGKFVR ddPTM_HeLa_Romidepsin_16h_R1 2 VAVEEVDEEGKFVR 14 1 P02545;P02545-3;P02545-2;P02545-6;P02545-5;P02545-4;Q5TCI8;A0A0C4DGC5 P02545 LMNA Prelamin-A/C;Lamin-A/C 0 0 ; ; 221.09 1.43E-32 41856000 3964.2 3769.5 3219.3 4167.3 4464.4 4310.6 3806.5 3997.1 4176.4 3562.4 FALSE FALSE TRUE 3915.882806 3822.56712 3275.330566 4649.142834 4236.565009 4035.166572 4129.824015 4112.749782 3802.852324 3469.848334 1.128545812 1.101652508 0.943940556 1.339869177 1.220965472 1.16292304 1.190203034 1.185282291 1.095970762 1 11.76065689 -9.263810107 24.9997066 1.058005827 1.215101142 0.606217442 0.066731499 129.5851295 1366495.829 0.011329407 0.017805644 5.45E-10 9.263810107 0.157095315 VAVLLLAGGQGTR ddPTM_HeLa_Romidepsin_16h_R1 1 VAVLLLAGGQGTR 13 0 Q16222-2;Q3KQV9;Q16222-3;Q16222 Q16222-2 UAP1;UAP1L1 UDP-N-acetylhexosamine pyrophosphorylase;UDP-N-acetylgalactosamine pyrophosphorylase;UDP-N-acetylglucosamine pyrophosphorylase;UDP-N-acetylhexosamine pyrophosphorylase-like protein 1 0 0 154.84 0.00069898 715780 296.05 168.43 378.15 235.61 257.81 241.75 211.17 192.17 348.53 351.2 FALSE FALSE TRUE 292.4416287 170.801162 384.7315421 262.8523368 244.6529937 226.3029552 229.1067745 197.7301358 317.3566039 342.0757734 0.85490307 0.499307976 1.124696842 0.768403837 0.715201171 0.661557973 0.669754459 0.578030224 0.927737737 1 8.418172122 -6.498793452 0.108143542 1.162546974 3.43E-13 0.358258055 0.148741256 41.12784956 0.577959827 1.175194103 7.287765176 3.17E-07 6.498793452 -1.162546974 VAVNDAHLLQYNHR ddPTM_HeLa_Romidepsin_16h_R1 1 VAVNDAHLLQYNHR 14 0 P17931 P17931 LGALS3 Galectin-3 0 0 149.41 0.0002347 10797000 3083.3 2777.1 2752.6 2736.3 3619.3 3210.5 2284.7 2787.5 2582.3 2477.9 FALSE FALSE TRUE 3045.719554 2816.196087 2800.507848 3052.683881 3434.593616 3005.359411 2478.762361 2868.151915 2351.332621 2413.523801 1.261938893 1.16683999 1.160339851 1.264824436 1.423061838 1.245216397 1.027030419 1.188366949 0.974232208 1 11.23692534 -12.34654907 0.863973272 0.987293025 1.220274702 0.476475625 0.095780665 0.574778856 0.699326599 0.091809173 0.019419223 4.50E-13 12.34654907 0.232981678 VAVPTGPTPLDS(ph)TPPGGAPHPLTGQEEAR ddPTM_HeLa_Romidepsin_16h_R1 2 VAVPTGPTPLDSTPPGGAPHPLTGQEEAR 29 0 A0A0A0MR08;E7ESU0;O94966-2;O94966-4;O94966-3;O94966;O94966-7;O94966-6;O94966-5 A0A0A0MR08 USP19 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 19 1 0 VAVPT(0.025)GPT(0.051)PLDS(0.867)T(0.057)PPGGAPHPLTGQEEAR;VAVPT(0.027)GPT(0.02)PLDS(0.476)T(0.476)PPGGAPHPLTGQEEAR ; 70.145 4.39E-05 11478500 2107.18 2003.84 1718.36 1786.11 2234.8 2518 2044.47 2268.27 2250.85 2216.4 TRUE FALSE FALSE 2081.49688 2032.050112 1748.267335 1992.628442 2120.749817 2357.107926 2218.127231 2333.898814 2049.528339 2158.817608 0.96418376 0.9412792 0.809826327 0.923018431 0.98236637 1.091851353 1.027473197 1.081100508 0.949375404 1 11.07602564 -8.383874885 5.043453646 0.960765798 1.062302079 0.521475248 0.0536712 0.191335988 7.083911124 0.008908068 0.020330203 4.13E-09 8.383874885 0.10153628 VAVPTGPTPLDST(ph)PPGGAPHPLTGQEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 VAVPTGPTPLDSTPPGGAPHPLTGQEEAR 29 0 A0A0A0MR08;E7ESU0;O94966-2;O94966-4;O94966-3;O94966;O94966-7;O94966-6;O94966-5 A0A0A0MR08 USP19 Ubiquitin carboxyl-terminal hydrolase;Ubiquitin carboxyl-terminal hydrolase 19 1 0 VAVPT(0.001)GPT(0.012)PLDS(0.246)T(0.741)PPGGAPHPLTGQEEAR 77.646 3.15E-06 22013000 1902.5 1826.8 1690.2 1886.5 1863.5 2085.6 2122.3 1918 1722.7 1767.7 TRUE FALSE FALSE 1879.311598 1852.517738 1719.617222 2104.626006 1768.398641 1952.336891 2302.568109 1973.494304 1568.617397 1721.774899 1.091496687 1.07593492 0.99874683 1.222358397 1.027078884 1.133909486 1.337322382 1.146197627 0.911046733 1 10.74968083 -4 0.175868215 0.998230444 2.012919627 0.454629767 0.086182177 38.75222193 0.415225005 0.102619851 10.50137896 1.00E-04 4 1.014689183 VAVT(ph)SSSS(ph)SSSS(ph)SSSIPS(ph)AEKVPTTK ddPTM_HeLa_Romidepsin_16h_R1 1 VAVTSSSSSSSSSSSIPSAEKVPTTK 26 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 4 0 VAVT(0.272)S(0.272)S(0.273)S(0.216)S(0.276)S(0.276)S(0.276)S(0.276)S(0.588)S(0.123)S(0.123)S(0.028)IPS(0.308)AEKVPT(0.346)T(0.346)K 46.578 0.0040807 0 672.85 607.24 639.95 1041.4 701.49 554.78 642.66 678.22 453.41 710.43 TRUE FALSE FALSE 664.6490454 615.7887407 651.0880613 1161.811568 665.6903477 519.3313485 697.2475244 697.8432256 412.855874 691.9729262 0.960513078 0.889902939 0.940915514 1.678984139 0.962017909 0.75050819 1.00762255 1.008483424 0.596635877 1 9.434571783 -6.381169982 3.990405292 1.003482897 2.560855621 0 0.265750394 157703.7028 7274.858149 0.031736748 2232999.808 4.16E-07 6.381169982 1.557372724 VAVTSSSSSSSSSSSIPS(ph)AEKVPTTK ddPTM_HeLa_Romidepsin_16h_R1 1 VAVTSSSSSSSSSSSIPSAEKVPTTK 26 1 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 VAVTSSSSSSSSSS(0.001)SIPS(0.992)AEKVPT(0.005)T(0.002)K 108.99 5.84E-07 10271000 2948.3 2193 2329.4 2148 3317.8 3563.2 2894.3 3110.8 2562.2 2496.7 TRUE FALSE FALSE 2912.364986 2223.873112 2369.94223 2396.361867 3148.480286 3335.52302 3140.14177 3200.80609 2333.030415 2431.835374 1.197599565 0.914483413 0.974548794 0.985412866 1.29469302 1.371607246 1.291264122 1.316210021 0.959370211 1 11.24782985 -8.69743776 6.872780527 1.064063102 1.322810718 0.745408192 0.085669781 0.116285967 10.02377098 0.014955943 0.029958928 2.01E-09 8.69743776 0.258747616 VAVVAGYGDVGK ddPTM_HeLa_Romidepsin_16h_R1 2 VAVVAGYGDVGK 12 0 P23526-2;P23526 P23526-2 AHCY Adenosylhomocysteinase 0 0 ; ; 142.98 0.0012585 2942000 2448.7 2318.89 2640.54 2586.31 2342.63 2665.52 2028.11 2490.54 2730.94 2530.32 FALSE FALSE TRUE 2418.854303 2351.535394 2686.497491 2885.351331 2223.07685 2495.201875 2200.377613 2562.599845 2486.677887 2464.581922 0.981446095 0.95413156 1.090041872 1.170726485 0.90200972 1.012423995 0.892799543 1.039770609 1.008965401 1 11.26712722 -6.920756095 21.04809702 0.99668279 3.046701943 0.018058231 0.078239544 1674.298769 667646.5836 0.010370019 81635.93053 1.20E-07 6.920756095 2.050019153 VAYEGSDS(ph)EKGEGAEPLKVPVWEPQDWQQQLVNIR ddPTM_HeLa_Romidepsin_16h_R1 1 VAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIR 35 2 P78549-3;P78549-2;P78549;H3BRL9;A0A494C106;H3BPD5 P78549-3 NTHL1 Endonuclease III-like protein 1 1 0 VAY(0.012)EGS(0.071)DS(0.917)EKGEGAEPLKVPVWEPQDWQQQLVNIR 44.443 0.0079906 17908000 1574.4 1622 1215 1602.8 1778 1719.9 1433.2 1545.1 1523.5 1252.4 TRUE FALSE FALSE 1555.210607 1644.834559 1236.146565 1788.123277 1687.262025 1610.003941 1554.935972 1589.805031 1387.234344 1219.862467 1.274906515 1.348377053 1.013349126 1.465840064 1.383157586 1.319824147 1.274681379 1.303265797 1.13720553 1 10.25250279 -12.53922475 0.361919563 0.856431923 1.326277399 0.365308295 0.116576738 2.001898459 0.293836608 0.380786445 0.042347167 2.89E-13 12.53922475 0.469845476 VAYVSFGPHAGK ddPTM_HeLa_Romidepsin_16h_R1 2 VAYVSFGPHAGK 12 0 P50914;E7EPB3 P50914 RPL14 60S ribosomal protein L14 0 0 ; ; 127.83 0.00072045 2079200 1197.37 1090.24 1888.82 1292.11 4197.4 4366.1 2911.7 1971.69 1940.25 1277.94 FALSE FALSE TRUE 1182.775994 1105.588427 1921.69412 1441.509838 3983.191015 4087.120301 3159.019725 2028.737739 1766.709181 1244.738935 0.950220131 0.888209083 1.543853146 1.158082067 3.200021229 3.283516075 2.537897416 1.629849989 1.419341142 1 10.28162747 -8.806959276 8.238664296 1.025187247 2.697100752 0.704514346 0.471864194 0.091035206 14.73866835 0.068084287 0.12425208 1.56E-09 8.806959276 1.671913505 VCAKPWAPDMTLPGIS(ph)PPPEK ddPTM_HeLa_Romidepsin_16h_R1 1 VCAKPWAPDMTLPGISPPPEK 21 1 Q96FF9;B5MBX0 Q96FF9 CDCA5 Sororin 1 0 VCAKPWAPDMT(0.074)LPGIS(0.926)PPPEK 62.678 0.016188 12441000 2861.9 2648.4 2269.8 593.11 3476.2 3834.2 3108 2950.5 2803.1 2821.9 TRUE FALSE FALSE 2827.018062 2685.684245 2309.304917 661.6881689 3298.796543 3589.206994 3371.993442 3035.868062 2552.383716 2748.586631 1.028535186 0.977114643 0.840179054 0.240737607 1.200179214 1.305837318 1.226809955 1.104519693 0.928616798 1 11.42447424 -8.567315446 24.99999988 0.938918852 1.220367207 0.337741577 0.230499662 144.8052222 81466.59576 0.03532682 0.070653666 2.71E-09 8.567315446 0.281448355 VDAAPGIPPAVESIQDS(ph)PLPK ddPTM_HeLa_Romidepsin_16h_R1 1 VDAAPGIPPAVESIQDSPLPK 21 0 Q15814 Q15814 TBCC Tubulin-specific chaperone C 1 0 VDAAPGIPPAVES(0.001)IQDS(0.999)PLPK 94.295 0.00035005 5493500 4893.5 4616.9 5072.8 3856.7 6591 7995.8 6362.4 8119.3 5192.3 4573.1 TRUE FALSE FALSE 4833.85614 4681.896839 5161.089956 4302.6298 6254.636676 7484.894185 6902.822097 8354.219135 4727.887684 4454.290203 1.085213563 1.051098295 1.158678425 0.965951836 1.404182573 1.680378656 1.549701924 1.87554442 1.061423362 1 12.12097984 -8.522873491 2.61066265 1.04665638 1.69050559 0.909329818 0.09197036 0.05389198 0.734420105 0.012810888 0.030269559 3.00E-09 8.522873491 0.64384921 VDDDFTAQDYR ddPTM_HeLa_Romidepsin_16h_R1 1 VDDDFTAQDYR 11 0 Q8IUI8-2;Q8IUI8 Q8IUI8-2 CRLF3 Cytokine receptor-like factor 3 0 0 125.68 0.00050959 0 1605.5 1579.3 1674.5 1263.2 1951.6 1673.3 1666.1 1640 1778.5 1588.2 FALSE FALSE TRUE 1585.931548 1601.533427 1703.64397 1409.257128 1852.00257 1566.38153 1807.618492 1687.450813 1619.426506 1546.938335 1.025206702 1.035292352 1.101300505 0.910997611 1.197205168 1.012568824 1.168513606 1.09083263 1.046859121 1 10.59519997 -7.76924273 0.322944212 1.002740166 1.193409052 0.161036669 0.072868021 5.141913052 0.491567947 0.027252872 0.367605769 1.70E-08 7.76924273 0.190668886 VDDDS(ph)LGEFPVTNSR ddPTM_HeLa_Romidepsin_16h_R1 2 VDDDSLGEFPVTNSR 15 0 J3KMZ8;Q92785;Q92785-2 J3KMZ8 DPF2 Zinc finger protein ubi-d4 1 0 VDDDS(1)LGEFPVTNSR;VDDDS(0.987)LGEFPVT(0.013)NSR ; 201.75 3.69E-18 76755000 5682.9 5861.7 5774.7 7076.3 4531.9 3293.6 3127.1 3097.2 5651.8 5440 TRUE FALSE FALSE 5613.634629 5944.221166 5875.206231 7894.495101 4300.620232 3083.14959 3392.715796 3186.812595 5146.288853 5298.668016 1.059442602 1.1218331 1.108808141 1.489901816 0.81164176 0.581872573 0.640295974 0.601436547 0.971241987 1 12.37141402 -8.528914458 24.99917534 1.075275631 0.625385414 0.734086991 0.139512095 65.048161 269421.0953 0.020677958 0.041446378 2.96E-09 8.528914458 -0.449890217 VDDKPS(ph)SPGDSSK ddPTM_HeLa_Romidepsin_16h_R1 2 VDDKPSSPGDSSK 13 1 C9JM54;C9J6K3;Q9HC52 C9JM54 CBX8 Chromobox protein homolog 8 1 0 VDDKPS(0.916)S(0.082)PGDS(0.001)SK;VDDKPS(0.752)S(0.248)PGDSSK ; 106.35 0.0033338 139088000 11659.9 11922.4 14588.4 14407.5 14482.3 15935.9 23816 5651.4 17142.3 15124.9 TRUE FALSE FALSE 11517.78465 12090.24386 14842.30498 16073.36294 13743.21419 14917.64742 25838.93045 5814.914343 15609.04975 14731.95292 0.781823341 0.820681679 1.007490661 1.09105446 0.932884748 1.01260488 1.753937892 0.394714426 1.059537038 1 13.84666107 -9.578175367 5.168647383 0.888651873 1.068195282 0.024732487 0.316787653 0.419376487 23.65078977 0.045741819 0.06549445 2.64E-10 9.578175367 0.179543409 VDDLSS(ph)SPTSSPER ddPTM_HeLa_Romidepsin_16h_R1 1 VDDLSSSPTSSPER 14 0 Q96JK2-2;Q96JK2-3;Q96JK2 Q96JK2-2 DCAF5 DDB1- and CUL4-associated factor 5 1 0 VDDLS(0.052)S(0.451)S(0.451)PT(0.023)S(0.023)SPER 151.74 0.00061562 2902300 1800.3 1747 1577.6 1951.3 1102.8 1033 1014.1 1144.1 1810.8 1708.8 TRUE FALSE FALSE 1778.357251 1771.594312 1605.057466 2176.918487 1046.520001 966.9946339 1100.237629 1177.202728 1648.837513 1664.40513 1.068464173 1.064400896 0.964343018 1.307925846 0.628765186 0.580985132 0.661039556 0.707281363 0.990646738 1 10.70079092 -8.73673934 24.99337242 1.047314753 0.641159639 0.825701962 0.094622208 66.00612749 66789.68816 0.01274662 0.025484382 1.83E-09 8.73673934 -0.406155114 VDDS(ph)PSTSGGSSDGDQR ddPTM_HeLa_Romidepsin_16h_R1 2 VDDSPSTSGGSSDGDQR 17 0 F8WF15;F8W8F0;C9J180;Q96LR5 F8WF15 UBE2E2 Ubiquitin-conjugating enzyme E2 E2 1 0 VDDS(0.729)PS(0.27)TSGGSSDGDQR;VDDS(1)PSTSGGSSDGDQR ; 217.32 6.20E-27 12400900 3273.8 3261.5 3736.8 2240.36 4162.5 4180.3 3378.4 3419.1 3299.5 3800.2 TRUE FALSE FALSE 3233.897666 3307.415483 3801.837436 2499.400964 3950.072093 3913.192321 3665.361212 3518.026264 3004.384456 3701.470256 0.873679225 0.893541013 1.02711549 0.675245454 1.067162997 1.057199451 0.990244675 0.950440236 0.811673267 1 11.85388272 VDDSPSTSGGS(ph)SDGDQR ddPTM_HeLa_Romidepsin_16h_R1 1 VDDSPSTSGGSSDGDQR 17 0 F8WF15;F8W8F0;C9J180;Q96LR5 F8WF15 UBE2E2 Ubiquitin-conjugating enzyme E2 E2 1 0 VDDS(0.034)PS(0.005)T(0.009)S(0.009)GGS(0.472)S(0.472)DGDQR 130.95 0.0019743 10337000 1323.9 1335.8 1045 1096.8 1248 1153.6 1086.3 1246.5 1261.1 1307.7 TRUE FALSE FALSE 1307.763798 1354.605427 1063.187787 1223.617177 1184.309903 1079.888683 1178.570295 1282.565511 1148.304058 1273.725765 1.026723203 1.063498489 0.83470698 0.960659829 0.929799754 0.847818826 0.925293597 1.00694007 0.901531624 1 10.31483898 -9.774526857 24.99886727 1.016787827 0.91723768 0.272461704 0.061344478 140.0031646 267424.4943 0.007709732 0.010166744 1.68E-10 9.774526857 -0.099550147 VDDSPSTSGGSS(ph)DGDQR ddPTM_HeLa_Romidepsin_16h_R1 1 VDDSPSTSGGSSDGDQR 17 0 F8WF15;F8W8F0;C9J180;Q96LR5 F8WF15 UBE2E2 Ubiquitin-conjugating enzyme E2 E2 1 0 VDDSPSTSGGS(0.042)S(0.958)DGDQR 270.79 2.90E-87 11248000 3930.6 3621.1 3725 2623.5 4774.5 4304.7 3487.6 3796.5 3950.9 3647.5 TRUE FALSE FALSE 3882.692335 3672.077941 3789.832062 2926.841414 4530.839449 4029.643563 3783.836657 3906.345738 3597.521609 3552.737424 1.09287343 1.033591145 1.066735762 0.823827113 1.275309405 1.134236247 1.065048216 1.099531227 1.012605543 1 11.79471535 -16.52286884 0.032811215 0.591717978 1.352776447 0.089615719 0.103163417 2070.841359 5.447982301 99.7367804 39.56836319 3.00E-17 16.52286884 0.761058468 VDDSS(ph)EDKTEFTVK ddPTM_HeLa_Romidepsin_16h_R1 1 VDDSSEDKTEFTVK 14 1 P49588;P49588-2 P49588 AARS "Alanine--tRNA ligase, cytoplasmic" 1 0 VDDS(0.167)S(0.833)EDKTEFTVK 169.4 1.07E-05 0 1470.2 1590.2 1614 1494 1650.9 1589.5 1279.7 1788 1516.5 1564.2 TRUE FALSE FALSE 1452.280637 1612.586877 1642.090993 1666.743309 1566.648413 1487.93608 1388.397686 1839.732959 1380.860442 1523.561859 0.953214094 1.058432166 1.077797389 1.093978101 1.028280148 0.976616782 0.911284093 1.207521013 0.906336972 1 10.57323236 -10.25585539 24.78700104 0.977906655 1.044218678 0.231170851 0.076934337 582.6135094 2586195.862 0.0120002 0.014465961 5.55E-11 10.25585539 0.066312022 VDDSSGS(ph)IGRR ddPTM_HeLa_Romidepsin_16h_R1 1 VDDSSGSIGRR 11 1 P41250 P41250 GARS Glycine--tRNA ligase 1 0 VDDS(0.013)S(0.041)GS(0.946)IGRR 70.68 0.02291 3589000 1724.3 1427.6 1505.7 1821.2 1789.9 1570.6 1535.4 1278 1690.2 1647.1 TRUE FALSE FALSE 1703.283568 1447.69779 1531.906077 2031.775713 1698.554724 1470.243729 1665.816838 1314.976914 1539.024279 1604.308105 1.061693551 0.902381398 0.954870248 1.266449822 1.05874596 0.91643477 1.038339726 0.8196536 0.959307177 1 10.64773552 -6.563917348 1.384852861 1.029753049 3.71E-12 0.248657689 0.099739891 7.736609401 3.185054763 0.014043479 17.89764969 2.73E-07 6.563917348 -1.029753049 VDDSSGSIGRR ddPTM_HeLa_Romidepsin_16h_R1 2 VDDSSGSIGRR 11 1 P41250 P41250 GARS Glycine--tRNA ligase 0 0 ; ; 155.53 0.0013215 2413760 1111.28 1295.78 1020.06 1785.36 1197.51 1338.95 1505.24 886.11 1544.76 1243.11 FALSE FALSE TRUE 1097.735292 1314.022025 1037.813716 1991.791724 1136.396596 1253.395416 1633.095048 911.7481948 1406.592797 1210.813823 0.906609481 1.085238705 0.857120803 1.645002465 0.938539497 1.035167746 1.34875818 0.753004448 1.161692054 1 10.24176134 VDDSTGTVIS(ph)DVEEDAGELSR ddPTM_HeLa_Romidepsin_16h_R1 3 VDDSTGTVISDVEEDAGELSR 21 0 S4R403;Q9Y2D8-2;Q9Y2D8-3;Q9Y2D8 S4R403 SSX2IP Afadin- and alpha-actinin-binding protein 1 0 VDDSTGTVIS(1)DVEEDAGELSR;VDDS(0.001)T(0.202)GT(0.003)VIS(0.794)DVEEDAGELSR;VDDSTGTVIS(1)DVEEDAGELSR ;; 251.74 4.15E-67 12677000 1598.03 2006.5 1931.63 1960.35 1962.2 2003.29 1713.78 1756.43 2046.51 1970.1 TRUE FALSE FALSE 1578.552596 2034.74756 1965.24921 2187.014891 1862.061612 1875.286234 1859.34843 1807.249531 1863.46502 1918.916518 0.82262703 1.060362731 1.024145236 1.139713411 0.97037135 0.977263063 0.968957437 0.941807272 0.971102704 1 10.90607623 -10.24343442 24.97804196 0.916240538 1.012627384 0.21488535 0.068782226 924.7881002 1282948.028 0.014086717 0.017233385 5.71E-11 10.24343442 0.096386846 VDEDEDDLEEEHITK ddPTM_HeLa_Romidepsin_16h_R1 1 VDEDEDDLEEEHITK 15 0 F5GXJ8;F6WZM0;F5H235;C9K0E8;B4DMS8;Q96FC9-4;Q96FC9-3;Q96FC9-2;Q96FC9;A8MPP1 F5GXJ8 DDX11;DDX11L8 Probable ATP-dependent RNA helicase DDX11;Putative ATP-dependent RNA helicase DDX11-like protein 8 0 0 104.95 0.0028726 1364500 1635.6 1513.7 1241.7 1150.8 1170.5 1056.7 883.35 1059.8 1677.6 1407.3 FALSE FALSE TRUE 1615.664678 1535.009908 1263.311268 1283.860911 1110.765017 989.1802803 958.381727 1090.463641 1527.551254 1370.738143 1.17868222 1.119841828 0.921628448 0.93662011 0.810340781 0.721640589 0.699171999 0.795530238 1.114400487 1 10.42073728 -9.05769518 1.224928944 1.087136399 0.734252318 0.861104594 0.060782844 0.149526112 0.443637545 0.013424045 0.029784687 8.76E-10 9.05769518 -0.352884081 VDEGAGDSAAVASGGAQTLALAGS(ph)PAPSGHPK ddPTM_HeLa_Romidepsin_16h_R1 1 VDEGAGDSAAVASGGAQTLALAGSPAPSGHPK 32 0 Q9NZT2-2;Q9NZT2;A0A0A0MRN5 Q9NZT2-2 OGFR Opioid growth factor receptor 1 0 VDEGAGDSAAVASGGAQT(0.018)LALAGS(0.973)PAPS(0.008)GHPK 112.71 2.49E-14 8829900 1268.9 1333.2 1089.2 1006.1 1975.9 2508.9 1655.9 1806.9 2081.5 1620 TRUE FALSE FALSE 1253.434159 1351.968825 1108.157069 1122.430016 1875.06245 2348.589387 1796.552105 1859.179801 1895.325427 1577.912166 0.79436244 0.85680867 0.702293253 0.711338717 1.188318646 1.488415792 1.138562807 1.178253036 1.201160285 1 10.62380119 -8.639332353 6.072895564 0.86865913 1.267899135 0.561353081 0.16134466 0.100164581 4.959304656 0.020530281 0.041371003 2.29E-09 8.639332353 0.399240005 VDGIPNDS(ph)SDSEMEDK ddPTM_HeLa_Romidepsin_16h_R1 1 VDGIPNDSSDSEMEDK 16 0 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 0 VDGIPNDS(0.333)S(0.333)DS(0.333)EMEDK 94.45 0.012783 7563300 2321.1 2345.9 2763.6 1578.5 2390.5 2513.8 1790.1 2072.2 2516 2304.2 TRUE FALSE FALSE 2292.80954 2378.925642 2811.699299 1761.013597 2268.503865 2353.176293 1942.151049 2132.155838 2290.962659 2244.336552 1.021597914 1.059968319 1.252797535 0.784647737 1.010768132 1.048495285 0.865356422 0.950016091 1.020775007 1 11.13207332 -9.229674782 24.99990651 1.031523447 0.939026207 0.292788729 0.09873716 918.6394484 723003.7521 0.014650736 0.02429405 5.89E-10 9.229674782 -0.092497241 VDGIPNDSSDS(ph)EMEDKTTANLAALK ddPTM_HeLa_Romidepsin_16h_R1 2 VDGIPNDSSDSEMEDKTTANLAALK 25 1 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 0 VDGIPNDS(0.178)S(0.178)DS(0.638)EMEDKT(0.003)T(0.003)ANLAALK;VDGIPNDS(0.301)S(0.301)DS(0.388)EMEDKT(0.006)T(0.003)ANLAALK ; 66.853 0.0012654 52025000 6337.3 5098.8 6947.4 4530.3 5658.9 6093.3 4715.5 5726.2 6449.4 5239.6 TRUE FALSE FALSE 6260.05855 5170.58104 7068.316583 5054.114602 5370.105217 5703.957795 5116.034452 5891.878563 5872.549511 5103.474437 1.226626806 1.0131492 1.385000879 0.99032819 1.052244953 1.117661677 1.002461072 1.1544838 1.15069637 1 12.31726405 VDGIPNDSSDSEMEDKTT(ph)ANLAALK ddPTM_HeLa_Romidepsin_16h_R1 1 VDGIPNDSSDSEMEDKTTANLAALK 25 1 Q9H6S0 Q9H6S0 YTHDC2 Probable ATP-dependent RNA helicase YTHDC2 1 0 VDGIPNDS(0.099)S(0.099)DS(0.273)EMEDKT(0.23)T(0.298)ANLAALK 47.931 0.026417 29389000 4100.9 4397.7 4389.1 3287.7 4319.2 4591.4 3337.5 4351.6 4615 3775.4 TRUE FALSE FALSE 4050.916653 4459.610936 4465.490444 3667.839343 4098.775107 4298.024358 3620.987167 4477.50668 4202.222842 3677.314564 1.101596446 1.212735777 1.214334637 0.997423331 1.114610957 1.168794315 0.984682464 1.217602303 1.142742283 1 11.84443688 -11.66162124 0.929333717 1.008852236 1.122524625 0 0.08988357 0.527432675 0.917356366 0.032315214 0.015720787 2.18E-12 11.66162124 0.113672389 VDHGAEIITQS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 6 VDHGAEIITQSPGR 14 0 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 1 0 VDHGAEIIT(0.03)QS(0.97)PGR;VDHGAEIIT(0.359)QS(0.641)PGR;VDHGAEIITQS(1)PGR;VDHGAEIIT(0.006)QS(0.994)PGR;VDHGAEIIT(0.097)QS(0.903)PGR;VDHGAEIIT(0.177)QS(0.823)PGR ;;;;; 169.6 2.60E-05 735786800 24722.8 22632.4 22795.5 21645.9 33454.5 35227.6 32157 34008.6 25683.2 23938.3 TRUE FALSE FALSE 24421.469 22951.01952 23192.24612 24148.70081 31747.19203 32976.67005 34888.41478 34992.58518 23386.03027 23316.37952 1.047395415 0.984330329 0.994676129 1.035696849 1.36158326 1.414313489 1.49630498 1.500772672 1.002987203 1 14.50905617 -8.672082916 2.648348311 1.016055392 1.469753389 0.981377707 0.029440936 0.02917297 0.414261517 0.005127392 0.01113323 2.13E-09 8.672082916 0.453697998 VDHGAEIITQS(ph)PGRS(ph)SVAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VDHGAEIITQSPGRSSVASPR 21 1 A0A669KB77;P11137-3;P11137;P11137-2;P11137-4 A0A669KB77;P11137-4 MAP2 Microtubule-associated protein 2 3 0 VDHGAEIIT(0.428)QS(0.596)PGRS(0.536)S(0.536)VAS(0.903)PR 58.319 0.012395 4992900 671.1 716.86 676.59 731.53 1409 1276.6 1195.4 1466.4 936.49 1000.7 TRUE FALSE FALSE 662.9203751 726.9519739 688.3657651 816.1129406 1337.093472 1195.02938 1296.937246 1508.82797 852.7279889 974.7016697 0.680126438 0.745819974 0.706232262 0.837295109 1.371797663 1.226046304 1.330599184 1.547989521 0.874860499 1 9.928816906 -8.764868386 13.75024155 0.824201857 1.356169418 0.853973338 0.113615969 0.127594455 504.4885552 0.021916819 0.041247567 1.72E-09 8.764868386 0.531967561 VDIDAPDVDVHGPDWHLK ddPTM_HeLa_Romidepsin_16h_R1 1 VDIDAPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 54.974 0.025677 10038000 2485.9 2182.3 2118.9 1924.9 2344.9 2060.9 1946.1 2180.9 2301.7 2193.1 FALSE FALSE TRUE 2455.600895 2213.022477 2155.778566 2147.465995 2225.231003 1929.215141 2111.401685 2244.000901 2095.830187 2136.122946 1.14955972 1.035999581 1.00920154 1.005310111 1.041714854 0.903138626 0.988427042 1.050501754 0.981137435 1 11.06077897 -9.879750443 3.592636899 1.071419574 0.996670042 0.047589559 0.057914761 0.276201196 6.920163604 0.010857417 0.014540934 1.32E-10 9.879750443 -0.074749532 VDIDAPDVEVHDPDWHLK ddPTM_HeLa_Romidepsin_16h_R1 1 VDIDAPDVEVHDPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 171.81 8.37E-08 5160200 7067.1 6237.3 6658.5 5814.5 5785.2 5949.4 5619.7 5279.9 6934.2 6402.3 FALSE FALSE TRUE 6980.963467 6325.108873 6774.388399 6486.799848 5489.959656 5569.252541 6097.037178 5432.665576 6313.987785 6235.967323 1.119467615 1.014294743 1.086341228 1.040223515 0.880370177 0.893085588 0.977721156 0.871182496 1.012511365 1 12.60639765 -8.810837299 6.62389719 1.056078371 0.909932479 0.707328857 0.043763474 0.092999068 9.299569817 0.007671558 0.014106308 1.55E-09 8.810837299 -0.146145892 VDIDT(ph)PDIDIHGPEGK ddPTM_HeLa_Romidepsin_16h_R1 4 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK;VDIDT(1)PDIDIHGPEGK ;;; 184.92 1.60E-08 205905000 21271.1 31719.9 16026.71 15166.99 22400 16035.4 10307.7 13642.91 18925.6 22236.8 TRUE FALSE FALSE 21011.83965 32166.45358 16305.64816 16920.66875 21256.84441 15010.78969 11183.23578 14037.64608 17232.84694 21659.08473 0.970116693 1.485125248 0.752831819 0.781227321 0.981428564 0.6930482 0.516330026 0.648118157 0.795640589 1 14.40268466 -8.310839882 0.920794015 1.010678761 0.541334066 0.392082171 0.198768165 0.510555807 0.707623838 0.030313857 0.166168465 4.89E-09 8.310839882 -0.469344695 VDIDT(ph)PDINIEGSEGK ddPTM_HeLa_Romidepsin_16h_R1 5 VDIDTPDINIEGSEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDIDT(1)PDINIEGSEGK;VDIDT(0.999)PDINIEGS(0.001)EGK;VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK;VDIDT(1)PDINIEGSEGK ;;;; 221.34 1.72E-34 138431000 17909.5 26268.2 12921.3 14474.5 18286.3 10935.2 7777.4 8838.9 14809.1 16938.2 TRUE FALSE FALSE 17691.21213 26638.00441 13146.18981 16148.10979 17353.08188 10236.47601 8438.012162 9094.639626 13484.53701 16498.14312 1.072315351 1.614606214 0.79682845 0.978783471 1.051820302 0.620462311 0.511452234 0.551252317 0.817336648 1 14.01001604 -8.21383618 3.443007232 1.059659245 0.535908729 0.52738174 0.211647948 0.131411602 3.173761012 0.027855697 0.075485524 6.11E-09 8.21383618 -0.523750516 VDIDTPDIDIHGPEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VDIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 ; ; 92.575 0.0049878 13438000 4746 4721.8 5321.6 3552 4677.4 4732.2 3797.8 4609.8 5304.8 4930.5 FALSE FALSE TRUE 4688.153927 4788.273624 5414.220216 3962.698953 4438.694824 4429.827692 4120.385037 4743.17729 4830.325402 4802.404899 0.976209633 0.997057459 1.127397695 0.825148865 0.924265013 0.922418618 0.857983682 0.987667094 1.005813859 1 12.22954133 -9.24090148 24.99812011 0.998686289 0.903173182 0.491764662 0.057629317 610.0859663 742578.9761 0.008201463 0.013589963 5.74E-10 9.24090148 -0.095513106 VDIDVPDVDVQGPDWHLK ddPTM_HeLa_Romidepsin_16h_R1 1 VDIDVPDVDVQGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 83.253 0.005194 22851000 3096.1 3223.6 3003.6 2893.4 3105.3 3110.9 2427.7 2927.4 3226.3 3298.5 FALSE FALSE TRUE 3058.363542 3268.981925 3055.876398 3227.948522 2946.824954 2912.12353 2633.908777 3012.0997 2937.731648 3212.804494 0.951929552 1.017485481 0.951155417 1.004713647 0.917212659 0.906411683 0.819816077 0.937529721 0.914382326 1 11.64961748 -8.504516041 2.522058848 0.979645422 0.88038692 0.472060678 0.04030471 0.138556857 1.749963984 0.004939409 0.011904971 3.13E-09 8.504516041 -0.099258502 VDIDVPDVNLEAPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VDIDVPDVNLEAPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 184.21 5.53E-11 0 2650.7 2591.8 2203.6 1998.8 1858.5 2030.1 1724.3 2069.4 2266.4 2349.9 FALSE FALSE TRUE 2618.392249 2628.287428 2241.952734 2229.910661 1763.65381 1900.383162 1870.761999 2129.274824 2063.687508 2288.849259 1.143977585 1.148300797 0.979510872 0.974249681 0.770541705 0.830278864 0.817337355 0.930281807 0.901626658 1 11.16040674 -9.139833571 2.034034913 1.073969363 0.837177562 0.536426915 0.08276732 0.141371725 1.145133703 0.011695077 0.021482992 7.25E-10 9.139833571 -0.236791801 VDIEAPDVS(ph)LEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VDIEAPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDIEAPDVS(1)LEGPEGK 175.26 2.08E-06 4301400 2697.8 3461.7 2504.3 2138.5 2147.4 2062 1711.1 1767.4 2779 2889.7 TRUE FALSE FALSE 2664.918176 3510.433903 2547.886291 2385.763432 2037.810165 1930.244855 1856.440791 1818.536931 2530.43928 2814.625177 0.946811034 1.24721186 0.905231116 0.847630957 0.724007652 0.685791085 0.659569454 0.646102701 0.899032418 1 11.4587271 -8.94780358 1.726273249 0.995174384 0.665900428 0.740691231 0.09043698 0.133600589 0.798574186 0.013714462 0.028648347 1.13E-09 8.94780358 -0.329273956 VDIEGPDVNIEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VDIEGPDVNIEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 ; ; 146.79 0.003099 10458900 7344.3 7496.9 7766.5 6171.7 7843.1 7120.9 5945.8 6251.5 8005.8 7864.2 FALSE FALSE TRUE 7254.784847 7602.441555 7901.672675 6885.300993 7442.83734 6665.897472 6450.836104 6432.377289 7289.741197 7659.88695 0.947113827 0.99250049 1.031565182 0.898877625 0.971664124 0.870234445 0.842158134 0.839748332 0.951677387 1 12.90310738 -8.202598697 1.211052609 0.977826572 0.828272275 0.727399277 0.033762182 0.211414196 0.540014626 0.005284011 0.025546883 6.27E-09 8.202598697 -0.149554297 VDIETPNLEGTLT(ph)GPR ddPTM_HeLa_Romidepsin_16h_R1 1 VDIETPNLEGTLTGPR 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDIET(0.085)PNLEGT(0.227)LT(0.688)GPR 95.073 0.018189 1999200 563.84 728.62 688.03 2378.6 582.1 441.38 476.4 847.04 832.84 622.31 TRUE FALSE FALSE 556.9677012 738.8775315 700.0048735 2653.624924 552.3932649 413.1772425 516.8654041 871.547766 758.3487045 606.1422965 0.918872853 1.218983621 1.15485238 4.377891032 0.91132605 0.681650571 0.85271298 1.437860006 1.251106727 1 9.243512707 -9.504167127 24.92931925 0.98977358 1.638137535 0.066562725 0.986526129 1478.306933 1969537.363 0.153329002 0.231716865 3.13E-10 9.504167127 0.648363954 VDINAPDVDVR ddPTM_HeLa_Romidepsin_16h_R1 1 VDINAPDVDVR 11 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 121.61 0.0014322 0 1182 1232 1287.9 1002.9 1161.3 1010.2 889.35 1126.6 1523.2 1491.6 FALSE FALSE TRUE 1167.593329 1249.344128 1310.315359 1118.860017 1102.034528 945.6514803 964.8913668 1159.196394 1386.961177 1452.848017 0.803658274 0.859927614 0.90189431 0.770114977 0.758533938 0.65089498 0.664137856 0.797878636 0.954649875 1 10.50466807 -16.52287875 0.080106606 1.827511802 0.509631378 0.699706756 0.059677423 71.41893124 0.43906688 10.51001397 1.160679112 3.00E-17 16.52287875 -1.317880425 VDINT(ph)PDVDVHGPDWHLK ddPTM_HeLa_Romidepsin_16h_R1 2 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDINT(1)PDVDVHGPDWHLK;VDINT(1)PDVDVHGPDWHLK ; 150.63 1.21E-05 217260000 15355.8 24412.9 9946.7 13450.1 15755.4 10449.6 7176.4 9859.9 14234.3 12262.1 TRUE FALSE FALSE 15168.6376 24756.58545 10119.81814 15005.26385 14951.34315 9781.904285 7785.963237 10145.18065 12961.14856 11943.52887 1.270029801 2.072803248 0.847305537 1.25635095 1.251836313 0.819012905 0.651898054 0.849429072 1.085202597 1 13.54394154 -8.197375293 4.893183774 1.198547209 0.750652159 0.323686067 0.311886619 0.220328713 10.61824821 0.045101618 0.117922742 6.35E-09 8.197375293 -0.44789505 VDINTPDVDVHGPDWHLK ddPTM_HeLa_Romidepsin_16h_R1 1 VDINTPDVDVHGPDWHLK 18 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 131.18 0.00058783 13173000 4174.4 4227.7 4293.6 4574.3 3961.8 3844.4 3357 4107 4124.4 4148.8 FALSE FALSE TRUE 4123.520807 4287.217672 4368.328307 5103.202089 3759.614562 3598.755247 3642.143496 4225.829565 3755.503334 4041.013578 1.020417459 1.060926322 1.080998176 1.262852002 0.930364249 0.890557574 0.901294546 1.045735057 0.929346873 1 11.98050148 VDLKS(ph)PQVDIK ddPTM_HeLa_Romidepsin_16h_R1 1 VDLKSPQVDIK 11 1 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 VDLKS(1)PQVDIK 136.6 0.025013 25019000 2059.8 2303 1429.9 1767.2 1813.3 1626.5 1273.4 1301.8 1573.2 1910.3 TRUE FALSE FALSE 2034.694365 2335.421694 1454.78681 1971.531979 1720.760535 1522.571899 1381.562564 1339.465529 1432.489052 1860.670131 1.09352772 1.255150849 0.781861753 1.059581678 0.924806878 0.818292224 0.742508057 0.719883394 0.769878029 1 10.86160659 -8.244117494 0.879865829 1.050543127 0.685066323 0.333358322 0.139457852 0.431264976 0.518745569 0.017526976 0.109458864 5.70E-09 8.244117494 -0.365476804 VDLNSNGFICDYELHELFK ddPTM_HeLa_Romidepsin_16h_R1 1 VDLNSNGFICDYELHELFK 19 0 P13797;U3KQI3 P13797 PLS3 Plastin-3 0 0 136.49 0.00028866 16429000 2153.3 2092.3 1971.1 142.52 2122.6 1995.4 1854.5 2093.3 2440.8 2140.8 FALSE FALSE TRUE 2127.054751 2121.755454 2005.406169 158.998833 2014.275801 1867.90038 2012.021184 2153.866333 2222.488735 2085.181707 1.020081245 1.017539837 0.961741685 0.076251788 0.965995335 0.895797413 0.964914078 1.032939396 1.065848951 1 11.02595739 -9.499960283 24.995866 1.009365854 0.783619759 0.167454094 0.253909773 1115.250733 1216342.362 0.038544374 0.058620241 3.16E-10 9.499960283 -0.225746095 VQTTPS(ph)KPGGDR ddPTM_HeLa_Romidepsin_16h_R1 3 VQTTPSKPGGDR 12 1 Q12834 Q12834 CDC20 Cell division cycle protein 20 homolog 1 0 VQT(0.058)T(0.1)PS(0.841)KPGGDR;VQT(0.001)T(0.009)PS(0.99)KPGGDR;VQTT(0.023)PS(0.977)KPGGDR ;; 106.55 0.0045746 331023000 19408.3 18836.3 17947.5 19007.3 15060.1 10975.1 7838.1 6734.3 20112.5 17862.1 TRUE FALSE FALSE 19171.74417 19101.47793 18259.86871 21205.01346 14291.5269 10273.82653 8503.868018 6929.146346 18313.58763 17398.04007 1.101948501 1.097909756 1.049535961 1.218816222 0.821444648 0.590516316 0.488783103 0.398271663 1.052623603 1 14.08663717 -8.326967159 2.113750005 1.064012696 0.456497431 0.935783975 0.06971214 0.05900599 0.507797653 0.010887656 0.031510944 4.71E-09 8.326967159 -0.607515265 down VDLTLLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 VDLTLLSPK 9 0 E7EVA0;P27816-4;B5MEG9 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 VDLT(0.003)LLS(0.997)PK;VDLT(0.001)LLS(0.999)PK ; 113.61 0.017087 172290000 12853.7 11471.4 12152.1 11102.2 11577.7 11442.2 11872 10972 12633.2 10831 TRUE FALSE FALSE 12697.03416 11632.89467 12363.6022 12385.8886 10986.84677 10711.08035 12880.40738 11289.45751 11503.25495 10549.60906 1.203554946 1.102684906 1.17194885 1.174061383 1.041445868 1.015305903 1.220936938 1.070130414 1.090396325 1 13.36490192 -12.54609669 1.320188176 1.000196031 1.13407246 0.115136827 0.070885712 0.397354453 1.243501825 0.04719895 0.011266388 2.84E-13 12.54609669 0.133876429 VDLYQQAS(ph)PPDALR ddPTM_HeLa_Romidepsin_16h_R1 2 VDLYQQASPPDALR 14 0 P48634;P48634-2;P48634-3;P48634-4 P48634 PRRC2A Protein PRRC2A 1 0 VDLYQQAS(1)PPDALR;VDLYQQAS(1)PPDALR ; 164.63 0.00013311 34234000 5804.2 5830.4 5922.4 5043.3 4823.7 4974.1 3784.1 4129.8 6146.3 6741 TRUE FALSE FALSE 5733.456178 5912.480524 6025.476888 5626.430075 4577.528589 4656.271063 4105.52136 4249.289247 5596.559534 6565.867848 0.873221379 0.900487287 0.917696948 0.856921005 0.697170381 0.70916308 0.625282362 0.647178613 0.852371638 1 12.68077 -6.855019471 0.241817453 0.994359808 0.18029271 0.776550444 0.057384152 3.158769473 0.127072123 0.035341421 0.794865339 1.40E-07 6.855019471 -0.814067098 VDNDENEHQLS(ph)LR ddPTM_HeLa_Romidepsin_16h_R1 2 VDNDENEHQLSLR 13 0 P06748;P06748-2;P06748-3;E5RGW4 P06748 NPM1 Nucleophosmin 1 0 VDNDENEHQLS(1)LR;VDNDENEHQLS(1)LR ; 103.67 0.0044407 11544800 3659 3747 4376.2 3367.1 4281.1 3678.7 3938.3 3506.6 4644.9 4577.3 TRUE FALSE FALSE 3614.402701 3799.750364 4452.365925 3756.419945 4062.619492 3443.642942 4272.819104 3608.057939 4229.448511 4458.381086 0.810698464 0.852271327 0.998650819 0.842552458 0.911231995 0.772397621 0.958379067 0.809275356 0.948651187 1 12.12230422 -12.48426985 1.209786381 1.000447081 0.866780443 0.266955366 0.067838449 0.404137874 1.052736685 0.045026976 0.01085514 3.28E-13 12.48426985 -0.133666637 VDNDENEHQLSLR ddPTM_HeLa_Romidepsin_16h_R1 5 VDNDENEHQLSLR 13 0 P06748;P06748-2;P06748-3;E5RGW4 P06748 NPM1 Nucleophosmin 0 0 ;;;; ;;;; 168 5.98E-05 434823100 14497 12914.3 12411.4 11450.2 14565.2 14950.7 12743.1 14119.6 14484.1 14408.1 FALSE FALSE TRUE 14320.30499 13096.10785 12627.41521 12774.126 13821.88349 13995.39852 13825.4986 14528.12835 13188.60582 14033.77548 1.020417136 0.933184934 0.899787461 0.910241582 0.984901284 0.997265386 0.985158884 1.035225935 0.939776031 1 13.77661557 -10.27568829 24.49860436 1.009641426 0.962101961 0 0.044870983 704.7427855 1211684.353 0.007291501 0.00835893 5.30E-11 10.27568829 -0.047539466 VDNLTYRT(ph)SPDTLR ddPTM_HeLa_Romidepsin_16h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130-2;Q01130;J3QL05;J3KP15 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 1 0 VDNLT(0.013)Y(0.001)RT(0.955)S(0.029)PDT(0.001)LR 73.735 0.026738 35743000 2152.3 2212.3 1851.5 3792.2 2401 2384.9 2292.8 2282.3 1898.2 1993.1 TRUE FALSE FALSE 2126.06694 2243.444817 1883.724581 4230.672007 2278.468011 2232.512587 2487.550375 2348.33475 1728.420238 1941.318975 1.095166208 1.155629161 0.970332339 2.179277111 1.173670087 1.149997819 1.281371278 1.209659402 0.890332944 1 10.92282147 VDNLTYRTS(ph)PDTLR ddPTM_HeLa_Romidepsin_16h_R1 1 VDNLTYRTSPDTLR 14 1 Q01130-2;Q01130;J3QL05;J3KP15 Q01130-2 SRSF2 Serine/arginine-rich splicing factor 2 1 0 VDNLT(0.002)Y(0.001)RT(0.079)S(0.687)PDT(0.231)LR 68.033 0.022905 35194000 1683.3 1294.4 894.52 2211.3 1506.5 1545.8 1563 1493.3 1138.8 1254.3 TRUE FALSE FALSE 1662.783292 1312.622597 910.0887454 2466.98091 1429.617683 1447.028369 1695.761181 1536.506279 1036.942876 1221.713105 1.361025993 1.07441149 0.744928365 2.019280058 1.170174632 1.184425675 1.388019146 1.257665382 0.848761359 1 10.25468982 VDPSLMEDS(ph)DDGPSLPTK ddPTM_HeLa_Romidepsin_16h_R1 1 VDPSLMEDSDDGPSLPTK 18 0 Q5T092;A0A0A0MR06;Q5T091;O15258 Q5T092 RER1 Protein RER1 1 0 VDPS(0.001)LMEDS(0.999)DDGPSLPTK 124.04 0.0021925 6119300 1048.1 938.01 895.5 861.05 758.33 923.44 764.85 996.85 834.31 1121.6 TRUE FALSE FALSE 1035.325354 951.2153294 911.0858019 960.6086524 719.6295904 864.4351643 829.8163399 1025.692282 759.687224 1092.46067 0.947700345 0.870708992 0.833975837 0.879307309 0.658723568 0.791273487 0.759584635 0.93888257 0.695390914 1 10.09336563 -10.07647129 0.95736749 0.984850008 0.79237767 0 0.114595815 0.248935269 0.450179226 0.014240282 0.018694389 8.39E-11 10.07647129 -0.192472338 VDS(ph)EGDFS(ph)ENDDAAGDFR ddPTM_HeLa_Romidepsin_16h_R1 1 VDSEGDFSENDDAAGDFR 18 0 M0QYL4;O43823 M0QYL4 AKAP8 A-kinase anchor protein 8 2 0 VDS(1)EGDFS(1)ENDDAAGDFR 102.5 0.019039 13447000 1463.9 1463.9 1473.8 828.37 1237.4 1329.9 1027.3 1129.2 1586.5 1421 TRUE FALSE FALSE 1446.057424 1484.508823 1499.450871 924.150037 1174.250861 1244.923682 1114.558836 1161.87162 1444.599467 1384.082215 1.044777115 1.072558267 1.083353904 0.667698802 0.848396755 0.8994579 0.805269242 0.839452749 1.04372374 1 10.43471393 -9.278852768 24.97247656 1.030597341 0.818552784 0.790508433 0.060547543 295.0110143 423073.2682 0.009359022 0.014316764 5.26E-10 9.278852768 -0.212044557 VDS(ph)LVSLSEEDLESDQR ddPTM_HeLa_Romidepsin_16h_R1 2 VDSLVSLSEEDLESDQR 17 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;H0YMW2;H0YLH1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 VDS(0.98)LVS(0.016)LS(0.004)EEDLESDQR;VDS(0.995)LVS(0.005)LSEEDLESDQR ; 217.32 6.20E-27 4519600 1056.83 1035.14 1228.61 652.22 1607.69 1690.24 1517.11 1631.36 949.75 1029.18 TRUE FALSE FALSE 1043.948949 1049.712728 1249.993442 727.6327452 1525.64358 1582.239119 1645.973286 1678.560828 864.8019813 1002.441755 1.041406091 1.04715583 1.246948698 0.725860372 1.521927406 1.578385089 1.641964011 1.674472177 0.86269549 1 9.969302699 -8.637509111 6.511552597 1.023521131 1.618645928 0.840841212 0.131407708 0.053369382 2.851300893 0.016083874 0.032348957 2.30E-09 8.637509111 0.595124797 VDS(ph)PTVNTTLR ddPTM_HeLa_Romidepsin_16h_R1 2 VDSPTVNTTLR 11 0 Q9H0B6;Q9H0B6-2;A8MZ87 Q9H0B6 KLC2 Kinesin light chain 2 1 0 VDS(0.711)PT(0.287)VNT(0.002)TLR;VDS(0.996)PT(0.004)VNTTLR ; 147.7 0.0024229 56278000 5890.5 4091.8 5351.8 3441.5 7555.3 7736.7 7537.7 7326.6 5984.9 5433.7 TRUE FALSE FALSE 5818.70432 4149.404468 5444.945834 3839.422423 7169.724848 7242.349839 8177.95205 7538.583612 5449.595555 5292.531691 1.099417946 0.784011265 1.028797965 0.725441556 1.354687183 1.368409348 1.545187167 1.424381383 1.029676509 1 12.36974229 -8.604699489 7.388044186 1.004783614 1.440572952 0.776513049 0.123956492 0.089056112 6.828752767 0.018625284 0.037394549 2.48E-09 8.604699489 0.435789338 VDS(ph)PTVTTTLK ddPTM_HeLa_Romidepsin_16h_R1 2 VDSPTVTTTLK 11 0 E7EVH7;H0YJU9;H0YJL0;H0YJT3;G5E9S8;G3V2E7;F8W6L3;Q07866-8;Q07866-2;Q07866-3;Q07866;Q07866-5;Q07866-10;Q07866-6;H0YG16;G3V5R9;Q07866-7;Q07866-4;Q07866-9;G3V3H3 E7EVH7;Q07866-6 KLC1 Kinesin light chain 1 1 0 VDS(0.997)PT(0.003)VTTTLK;VDS(0.993)PT(0.007)VTTTLK ; 137.95 0.0035383 294460000 8852.2 8199.8 8371.9 7152.9 8650 10229.4 8979.6 9600.7 8441.6 9311.9 TRUE FALSE FALSE 8744.305982 8315.237 8517.609408 7979.951953 8208.558222 9575.774354 9742.327 9878.481107 7686.562154 9069.975496 0.964093672 0.916787152 0.939099495 0.879820674 0.905025402 1.055766287 1.074129363 1.089140882 0.84747331 1 13.14688294 -8.112334003 5.702753097 0.961884082 1.07776561 0.576542263 0.052221051 0.130793042 5.702735208 0.006701125 0.017529858 7.72E-09 8.112334003 0.115881528 VDSETNIEASKLPT(ph)SEPEADAEIEPK ddPTM_HeLa_Romidepsin_16h_R1 1 VDSETNIEASKLPTSEPEADAEIEPK 26 1 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 VDS(0.001)ET(0.002)NIEAS(0.008)KLPT(0.495)S(0.495)EPEADAEIEPK 48.374 0.023009 18579000 3703.4 3505.5 3015.5 3705.9 3629.3 3115.3 2678.6 2763 4249.9 3839.1 TRUE FALSE FALSE 3658.261536 3554.850521 3067.983513 4134.393595 3444.083278 2916.242384 2906.120217 2842.943046 3869.7783 3739.359629 0.978312305 0.950657565 0.820456928 1.105642143 0.921035584 0.779877485 0.77717056 0.760275375 1.034877274 1 11.86857551 -8.339497611 3.669578956 0.980321241 0.77090699 0.652248305 0.068095557 0.101230489 2.61337293 0.009110928 0.022034729 4.58E-09 8.339497611 -0.20941425 VDSETNIEASKLPTS(ph)EPEADAEIEPK ddPTM_HeLa_Romidepsin_16h_R1 1 VDSETNIEASKLPTSEPEADAEIEPK 26 1 Q9BYW2;H7C3H4;A0A1W2PPX9 Q9BYW2 SETD2 Histone-lysine N-methyltransferase SETD2 1 0 VDSETNIEASKLPT(0.2)S(0.799)EPEADAEIEPK 79.845 2.71E-05 16116000 4469.2 4026.7 3594.5 4232.8 3411.7 3094.9 3224.2 2997 4625.9 3708 TRUE FALSE FALSE 4414.727671 4083.387988 3657.060765 4722.216252 3237.588218 2897.145878 3498.063468 3083.713467 4212.147918 3611.665625 1.222352269 1.130610752 1.012569032 1.307489879 0.896425238 0.802163372 0.968545771 0.853820311 1.166261873 1 11.81844862 -8.631454359 10.15535695 1.114465244 0.878484113 0.637692171 0.094809292 0.190702612 16.60363613 0.015640502 0.031296775 2.34E-09 8.631454359 -0.235981131 VDSLVS(ph)LSEEDLESDQR ddPTM_HeLa_Romidepsin_16h_R1 2 VDSLVSLSEEDLESDQR 17 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;H0YMW2;H0YLH1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 VDSLVS(0.996)LS(0.004)EEDLESDQR;VDSLVS(1)LSEEDLESDQR ; 244.18 7.49E-59 10471100 3415.7 3909.2 3604.5 2969.3 6213.4 6877.1 5758 7093.8 4125.7 4098.1 TRUE FALSE FALSE 3374.068135 3964.23382 3667.23481 3312.624437 5896.307013 6437.675505 6247.084376 7299.047911 3756.687059 3991.630771 0.845285631 0.993136401 0.91873097 0.829892499 1.477167441 1.612793335 1.56504565 1.828587945 0.941140921 1 11.96276256 -8.653793076 4.044486553 0.923942802 1.643722488 0.942321589 0.085496181 0.039567796 1.189512045 0.013670228 0.028161731 2.22E-09 8.653793076 0.719779687 VDSLVSLS(ph)EEDLESDQR ddPTM_HeLa_Romidepsin_16h_R1 2 VDSLVSLSEEDLESDQR 17 0 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;H0YMW2;H0YLH1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 VDSLVSLS(1)EEDLESDQR;VDSLVSLS(1)EEDLESDQR ; 375.27 0 41951000 6850.1 6968.7 6919.2 5749.6 11464.3 13114.6 11147.7 13208 7252.5 6658.4 TRUE FALSE FALSE 6766.608346 7066.805542 7039.625774 6414.395805 10879.23399 12276.61939 12094.58536 13590.15264 6603.818236 6485.413808 1.043357995 1.08964605 1.085455143 0.98904958 1.677492649 1.892958529 1.864890309 2.095495067 1.018257035 1 12.66298291 -8.635862378 2.963889557 1.028117926 1.934438425 0.971141473 0.072292649 0.028889327 0.508614253 0.010748653 0.023240916 2.31E-09 8.635862378 0.906320499 VDSLVSLS(ph)EEDLESDQREHR ddPTM_HeLa_Romidepsin_16h_R1 2 VDSLVSLSEEDLESDQREHR 20 1 Q12802-4;Q12802;Q12802-2;A0A087WTD7;A8MYJ1;A0A087WY36;H0YMW2;H0YLH1 Q12802-4 AKAP13 A-kinase anchor protein 13 1 0 VDSLVS(0.007)LS(0.992)EEDLESDQREHR;VDSLVS(0.13)LS(0.869)EEDLESDQREHR ; 119.46 6.67E-05 5039700 1137.07 1095.27 865.22 1565.23 1252.09 1535.42 1493.35 1738.05 1148.3 978.04 TRUE FALSE FALSE 1123.210953 1110.68924 880.2787912 1746.209257 1188.191175 1437.311617 1620.195112 1788.337735 1045.593172 952.6303798 1.179062706 1.165918349 0.924050723 1.833039649 1.247274074 1.50878205 1.70075944 1.877262968 1.097585374 1 9.895772747 -4 0.224852227 0.992705046 5.989735596 0.636413147 0.200056168 20.65348451 0.249156637 0.131445582 38.08684241 1.00E-04 4 4.99703055 VDVDVPDVNIEGPDAK ddPTM_HeLa_Romidepsin_16h_R1 1 VDVDVPDVNIEGPDAK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 158.52 0.0017409 9688900 4092.6 3495.8 3513.8 2668.4 2983.1 2993.5 2568.2 2618 3645 3918.8 FALSE FALSE TRUE 4042.717817 3545.013964 3574.956215 2976.932963 2830.861276 2802.225011 2786.342844 2693.747699 3318.982071 3816.989011 1.059137924 0.92874618 0.936590649 0.779916566 0.74164774 0.734145423 0.729984508 0.70572582 0.869528851 1 11.89821932 -9.387158947 1.246324744 1.02671149 0.721104973 0.780846679 0.056485992 0.063557451 0.19550861 0.005399623 0.009865097 4.10E-10 9.387158947 -0.305606516 VDVEVPDVS(ph)LEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VDVEVPDVS(1)LEGPEGK 98.552 0.0062482 10632000 5566 6436.6 4352.3 9434.4 4611.8 3370.5 3168.6 3032.2 5453.5 5476.3 TRUE FALSE FALSE 5498.159451 6527.214624 4428.049956 10525.24972 4376.442637 3155.135928 3437.740805 3119.931923 4965.725301 5334.024937 1.030771231 1.223694059 0.830151716 1.973228443 0.820476599 0.591511282 0.644492826 0.584911387 0.930952772 1 12.38100885 -8.528579103 24.99999542 1.08965309 0.626602133 0.402329762 0.300997251 123.3357337 540911.5104 0.0418204 0.083838948 2.96E-09 8.528579103 -0.463050957 VDVEVPDVSLEGPEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VDVEVPDVSLEGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 ; ; 233.37 1.20E-44 12966400 8810.9 8448.7 8084.6 7310.8 8016.9 7472.8 6333.2 7721.9 8953.6 7611 FALSE FALSE TRUE 8703.509362 8567.64102 8225.309072 8156.109094 7607.767678 6995.312197 6871.14185 7945.320993 8152.767591 7413.265123 1.174045339 1.155717606 1.10953931 1.100204695 1.026237097 0.943620939 0.926871188 1.071770787 1.099753949 1 12.85589339 -8.579737227 3.633731373 1.093540743 0.975864143 0.496219836 0.056763772 0.209014328 5.648176307 0.011311927 0.02425333 2.63E-09 8.579737227 -0.1176766 VDVIAGSSK(ac)MK ddPTM_HeLa_Romidepsin_16h_R1 1 VDVIAGSSKMK 11 1 O60885;O60885-2;O60885-3 O60885 BRD4 Bromodomain-containing protein 4 0 1 VDVIAGSSK(1)MK 94.767 0.017267 1518300 609.02 517.97 715.3 724.07 1142.4 1338.6 1089.6 1094.8 634.41 639.66 FALSE TRUE FALSE 601.59703 525.2619953 727.7494964 807.7903803 1084.099065 1253.06778 1182.150597 1126.476311 577.6667807 623.041541 0.965580929 0.843060953 1.168059348 1.296527321 1.740010888 2.011210646 1.897386481 1.808027614 0.927172175 1 9.283184547 -8.896629924 1.64746204 0.977058822 1.915526951 0.962765024 0.08273335 0.044760015 0.244661313 0.012608372 0.02748727 1.27E-09 8.896629924 0.93846813 VDY(ph)VVVDQQK ddPTM_HeLa_Romidepsin_16h_R1 1 VDYVVVDQQK 10 0 Q13480-2;B7Z3B9;Q13480 Q13480-2 GAB1 GRB2-associated-binding protein 1 1 0 VDY(1)VVVDQQK 127.76 0.00023636 0 1495.2 1837.2 2063.8 1668.8 2142.7 1630.3 1088.9 1083.9 1751 1777.8 TRUE FALSE FALSE 1476.975927 1863.06415 2099.719573 1861.754508 2033.350023 1526.129092 1181.391139 1115.260936 1594.386175 1731.6125 0.852948294 1.075912856 1.212580513 1.075156542 1.174252336 0.88133407 0.68224914 0.644059186 0.92075229 1 10.7579004 -7.844588996 3.535966002 0.988204882 0.65589843 0.625201215 0.111801102 0.147032175 3.559656618 0.019209048 0.068851902 1.43E-08 7.844588996 -0.332306451 VEADVSLPS(ph)MQGDLK ddPTM_HeLa_Romidepsin_16h_R1 1 VEADVSLPSMQGDLK 15 0 Q8IVF2;Q8IVF2-3 Q8IVF2 AHNAK2 Protein AHNAK2 1 0 VEADVS(0.317)LPS(0.683)MQGDLK 108.23 0.0014036 0 1688.3 1726.8 1624.7 1212.8 1216.3 1106.4 748.23 1043.3 1724.8 1879.1 TRUE FALSE FALSE 1667.72235 1751.109936 1652.977222 1353.029642 1154.227672 1035.704611 811.7846375 1073.486239 1570.529568 1830.280711 0.911183918 0.956743916 0.903127707 0.739247064 0.630628769 0.565872002 0.443530128 0.586514535 0.858081254 1 10.83784922 -8.931553329 1.147255465 0.960492762 0.511756871 0.919770666 0.051794196 0.071365914 0.185669271 0.007486699 0.018691878 1.17E-09 8.931553329 -0.44873589 VEAIVIS(ph)DEETDVSDEQPQGPER ddPTM_HeLa_Romidepsin_16h_R1 1 VEAIVISDEETDVSDEQPQGPER 23 0 A0A6E1W9L1;Q9H5J0 A0A6E1W9L1 ZBTB3 Zinc finger and BTB domain-containing protein 3 1 0 VEAIVIS(0.607)DEET(0.393)DVSDEQPQGPER 104.03 1.10E-05 2076500 2813.9 2637.7 2717.9 2265.5 2925 3128 2745.2 3098 3348.1 3118.4 TRUE FALSE FALSE 2779.603104 2674.83361 2765.203909 2527.447769 2775.726335 2928.130895 2978.377219 3187.635742 3048.637551 3037.383518 0.915130766 0.880637428 0.910390108 0.83211348 0.913854414 0.964030679 0.980573313 1.04946765 1.003705173 1 11.56861337 -7.388701079 1.726697283 0.937234834 1.069552101 0.36381087 0.049784436 0.769465962 2.721925475 0.00839311 0.153380422 4.09E-08 7.388701079 0.132317267 VEAK(ac)FINYVK ddPTM_HeLa_Romidepsin_16h_R1 2 VEAKFINYVK 10 1 P06748;P06748-2 P06748 NPM1 Nucleophosmin 0 1 ; VEAK(1)FINYVK;VEAK(1)FINYVK 157.95 0.0085819 19679600 2653.54 2586.02 2600.26 2428.63 2609.02 1845.41 1714.27 2065.24 2252.76 2045.68 FALSE TRUE FALSE 2621.197634 2622.426057 2645.516435 2709.439628 2475.871974 1727.494257 1859.880051 2124.994461 2051.267503 1992.532939 1.315510315 1.316126829 1.327715283 1.359796656 1.242575179 0.86698404 0.933424996 1.066478962 1.029477337 1 10.96038786 -8.267817798 24.66634578 1.200412816 0.953408897 0.483651896 0.12651548 364.6071497 1409995.958 0.022948318 0.052514603 5.40E-09 8.267817798 -0.247003919 VEAKEESEES(ph)DEDMGFGLFD ddPTM_HeLa_Romidepsin_16h_R1 2 VEAKEESEESDEDMGFGLFD 20 1 F8VWS0;P05388-2;Q8NHW5;P05388;F8W1K8 F8VWS0 RPLP0;RPLP0P6 60S acidic ribosomal protein P0;60S acidic ribosomal protein P0-like 1 0 VEAKEES(0.001)EES(0.999)DEDMGFGLFD;VEAKEESEES(1)DEDMGFGLFD ; 95.122 0.0012559 31409000 10409.3 7727.1 7633.5 9900.4 7500.4 6705.8 5758.6 6376.8 9603.8 8475.4 TRUE FALSE FALSE 10282.42745 7835.882317 7766.357865 11045.13083 7117.6266 6277.321022 6247.73534 6561.302647 8744.812075 8255.207886 1.245568566 0.949204723 0.940782833 1.337959138 0.862198348 0.760407383 0.756823502 0.794807682 1.059308523 1 13.01108883 -8.56924851 9.636890503 1.104064247 0.776194616 0.605899169 0.117977505 0.19520071 38.91983973 0.019190822 0.038449334 2.70E-09 8.56924851 -0.327869631 VEANS(ph)PLPK ddPTM_HeLa_Romidepsin_16h_R1 2 VEANSPLPK 9 0 Q9H7C4-2;Q9H7C4 Q9H7C4-2 SYNC Syncoilin 1 0 VEANS(1)PLPK;VEANS(1)PLPK ; 111.52 0.018265 66011000 14760.9 14439.8 14190.8 12673.7 11901.9 9702.6 7694.6 8394.7 14372 14512.5 TRUE FALSE FALSE 14580.98847 14643.08388 14437.78492 14139.09283 11294.50163 9082.635174 8348.179132 8637.5874 13086.53232 14135.46316 1.031518268 1.035911149 1.021387468 1.000256777 0.799018858 0.642542453 0.590584054 0.611057968 0.925794378 1 13.78703153 -8.517333604 1.937844639 1.018648355 0.601874782 0.966158938 0.032661803 0.021455797 0.159113651 0.002711983 0.0070777 3.04E-09 8.517333604 -0.416773573 VEAPETNIDKT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 VEAPETNIDKTPK 13 1 E9PBY7;E9PQ61;O75152 E9PBY7 ZC3H11A Zinc finger CCCH domain-containing protein 11A 1 0 VEAPETNIDKT(1)PK 96.247 0.0088792 13400000 6424.6 6351 6988.2 5316.5 4928.3 4339.5 4174.5 3502.8 7570.5 7186.4 TRUE FALSE FALSE 6346.294504 6440.409545 7109.82669 5931.218745 4676.790461 4062.219955 4529.081926 3604.147991 6893.375519 6999.696292 0.906652837 0.920098427 1.015733597 0.847353728 0.668141912 0.580342316 0.647039777 0.514900624 0.984810659 1 12.77307661 -8.788015172 2.22799183 0.955821961 0.588209668 0.936133755 0.045089231 0.057187739 0.579066243 0.007501515 0.015948942 1.63E-09 8.788015172 -0.367612293 VEAPEYIPISDDPKAS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 2 VEAPEYIPISDDPKASAK 18 1 Q1ED39;H3BPL4 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 0 VEAPEYIPIS(0.008)DDPKAS(0.992)AK;VEAPEYIPISDDPKAS(1)AK ; 100.47 0.00074417 28394000 6662.9 6715.5 6961.1 5229.2 7031.6 8227.7 6696.8 7475.6 7028.6 6173.5 TRUE FALSE FALSE 6581.690012 6810.040985 7082.255025 5833.824708 6672.751213 7701.976524 7265.626025 7691.894691 6399.944413 6013.11158 1.094556441 1.13253195 1.17780203 0.97018401 1.109700215 1.280863729 1.208297223 1.279187088 1.064331557 1 12.55389601 -4 0.178382043 0.998287183 2.193041078 0.542670076 0.068242116 30.34524974 0.327794645 0.091141784 9.86121892 1.00E-04 4 1.194753894 VEAPSLDVHMDS(ph)PDINIEGPDVK ddPTM_HeLa_Romidepsin_16h_R1 1 VEAPSLDVHMDSPDINIEGPDVK 23 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VEAPS(0.001)LDVHMDS(0.999)PDINIEGPDVK 66.732 0.00072162 21032000 2853.4 3455.5 2599.4 2536.7 4054.2 4433.2 3179.2 3925.8 3597.8 2780.5 TRUE FALSE FALSE 2818.621663 3504.14662 2644.641467 2830.00519 3847.299046 4149.932827 3449.241169 4039.386829 3276.003757 2708.262209 1.040749176 1.293872731 0.976508647 1.044952435 1.420578492 1.532323131 1.273599416 1.491505075 1.209633154 1 11.40315171 -8.761059475 8.09122349 1.040436134 1.426364088 0.647439744 0.117213086 0.041714001 22.27373838 0.015086895 0.028807705 1.73E-09 8.761059475 0.385927954 VEEAEPEEFVVEK ddPTM_HeLa_Romidepsin_16h_R1 2 VEEAEPEEFVVEK 13 0 S4R2Y4;Q13185;C9JMM0;B8ZZ43 S4R2Y4 CBX3 Chromobox protein homolog 3 0 0 ; ; 208.74 2.01E-16 10352400 6107.7 5507.6 5122.8 4251.9 4941.8 4121.6 3876.8 3843.2 6092.7 5713.6 FALSE FALSE TRUE 6033.257003 5585.136137 5211.960185 4743.524684 4689.601506 3858.243062 4206.095295 3954.396928 5547.753653 5565.159848 1.084112077 1.003589527 0.936533779 0.852360905 0.842671484 0.693285219 0.755790563 0.710563045 0.996872292 1 12.44220741 -9.069123216 1.008536441 1.040255368 0.720947433 0.92048794 0.036632694 0.103358932 0.206804217 0.007323874 0.017733717 8.53E-10 9.069123216 -0.319307935 VEEAPVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VEEAPVKK 8 1 Q8NFC6;H0Y9Y2 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 0 1 ; VEEAPVK(1)K;VEEAPVK(1)K 139.19 0.0033855 28954000 14463.5 14645.1 11277 12674.3 14344.7 13506.8 15530.4 14731.6 17160.7 14685.8 FALSE TRUE FALSE 14287.2133 14851.2741 11473.27145 14139.7622 13612.63643 12643.75907 16849.55179 15157.8356 15625.80401 14304.2608 0.998808222 1.038241284 0.802087687 0.988500028 0.951649066 0.883915586 1.177939358 1.059672766 1.092388082 1 13.80415733 -7.752723708 24.99998778 0.977717981 1.118806067 0.350284587 0.080738999 145.2113165 416513.9041 0.009811201 0.035587494 1.77E-08 7.752723708 0.141088086 VEEAS(ph)PGRPSSVDTLLSPTALIDSILR ddPTM_HeLa_Romidepsin_16h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 1 0 VEEAS(0.377)PGRPS(0.311)S(0.311)VDTLLSPTALIDSILR 80.68 2.56E-06 133060000 1216.8 1589.8 1348.8 645.14 968.67 669.31 761.85 958.33 1476.4 1359.1 TRUE FALSE FALSE 1201.969174 1612.181246 1372.275298 719.7341223 919.2351553 626.5432511 826.56152 986.0577666 1344.347086 1323.790386 0.907975452 1.21785236 1.036625823 0.543691909 0.694396307 0.47329491 0.624390031 0.744874549 1.015528667 1 10.37045898 -9.263061482 24.99998213 0.984655573 0.613001347 0.791246549 0.106121244 56.75355769 874690.9467 0.016944329 0.026741736 5.46E-10 9.263061482 -0.371654226 VEEASPGRPSSVDTLLSPTALIDSILR ddPTM_HeLa_Romidepsin_16h_R1 1 VEEASPGRPSSVDTLLSPTALIDSILR 27 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 0 0 152.66 2.53E-11 74250000 258.68 215.16 163.38 165.03 242.79 143.75 180.6 119.59 387.94 279.02 FALSE FALSE TRUE 255.5271087 218.1890281 166.2235604 184.1115451 230.3995203 134.5648389 195.9401595 123.050148 353.2416748 271.7710202 0.94022942 0.802841407 0.611630925 0.677450984 0.847770745 0.4951405 0.720975177 0.45277141 1.299776829 1 8.086247815 -10.07583639 1.868396689 0.976515372 0.640839053 0.627968782 0.146854843 0.135361322 0.917940422 0.017772219 0.022624071 8.40E-11 10.07583639 -0.33567632 VEEEEAGFPSS(ph)PDLGSEGSR ddPTM_HeLa_Romidepsin_16h_R1 1 VEEEEAGFPSSPDLGSEGSR 20 0 Q9BRR0 Q9BRR0 ZKSCAN3 Zinc finger protein with KRAB and SCAN domains 3 1 0 VEEEEAGFPS(0.438)S(0.562)PDLGSEGSR 159.54 2.12E-11 0 416.79 693.51 600.79 639.11 796.55 814.87 570.51 800.43 498.76 673.03 TRUE FALSE FALSE 411.7100032 703.273252 611.2464979 713.0069053 755.8990812 762.8024369 618.9691052 823.5891792 454.1496564 655.5445836 0.62804272 1.072807662 0.932425518 1.087655856 1.153085694 1.163616413 0.944205964 1.256343504 0.692782257 1 9.356550091 -9.717698686 1.648255444 0.829707684 1.111398929 0.499809181 0.135827186 0.287413289 1.589345619 0.028204939 0.041865513 1.92E-10 9.717698686 0.281691244 VEEEQEADEEDVS(ph)EEEAESKEGTNK ddPTM_HeLa_Romidepsin_16h_R1 1 VEEEQEADEEDVSEEEAESKEGTNK 25 1 Q9H3N1 Q9H3N1 TMX1 Thioredoxin-related transmembrane protein 1 1 0 VEEEQEADEEDVS(0.98)EEEAES(0.019)KEGT(0.001)NK 77.543 8.36E-05 8973300 1130.3 1520.9 1279.2 865.27 1392 1596.3 872.13 1741 1478.5 1799.5 TRUE FALSE FALSE 1116.523469 1542.31127 1301.463939 965.3165886 1320.961046 1494.301582 946.2087004 1791.373088 1346.259257 1752.748731 0.637012853 0.879938603 0.74252739 0.550744423 0.753651121 0.852547519 0.539842753 1.022036449 0.768084571 1 10.77540347 -12.44854489 1.09858014 1.004907057 0.731866809 0.024182489 0.157702628 0.460669205 0.965209147 0.099507614 0.02299172 3.56E-13 12.44854489 -0.273040248 VEEESTGDPFGFDS(ph)DDESLPVSSK ddPTM_HeLa_Romidepsin_16h_R1 3 VEEESTGDPFGFDSDDESLPVSSK 24 0 Q7Z5K2;Q7Z5K2-2;Q7Z5K2-3 Q7Z5K2 WAPAL Wings apart-like protein homolog 1 0 VEEESTGDPFGFDS(0.942)DDES(0.057)LPVS(0.001)SK;VEEESTGDPFGFDS(0.794)DDES(0.205)LPVS(0.001)SK;VEEESTGDPFGFDS(0.696)DDES(0.286)LPVS(0.013)S(0.005)K ;; 137.9 7.86E-07 44879900 17562.4 16756.9 18028.6 17392.6 18853.8 18557.7 15582.3 18175.1 19259.2 17373.4 TRUE FALSE FALSE 17348.34271 16992.80408 18342.38022 19403.61425 17891.62023 17371.92286 16905.86017 18700.96784 17536.60892 16922.03656 1.025192367 1.004181974 1.083934558 1.146647697 1.057297103 1.026585825 0.999044064 1.105125129 1.036317872 1 14.04661559 -9.767058998 24.95915044 1.01165021 1.06752172 0.303497576 0.039239248 125.3163237 556584.4757 0.006540639 0.008729066 1.71E-10 9.767058998 0.05587151 VEELALQS(ph)MIS(ph)S(ph)RR ddPTM_HeLa_Romidepsin_16h_R1 1 VEELALQSMISSRR 14 1 O75971;H3BQA0 O75971 SNAPC5 snRNA-activating protein complex subunit 5 3 0 VEELALQS(1)MIS(1)S(1)RR 40.278 0.0042866 0 0 148.27 123.69 0 0 0 0 68.523 130.47 67.06 TRUE FALSE FALSE 0 150.357349 125.8427726 0 0 0 0 70.50560489 118.8004364 65.31777153 0 2.301936294 1.92662379 0 0 0 0 1.079424531 1.81880725 1 6.029403666 VEENIQKQS(ph)QQT(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 VEENIQKQSQQTK 13 1 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 2 0 VEENIQKQS(1)QQT(1)K 40.577 0.02867 9825800 1788.7 1693.8 1766.3 938.35 1664.5 1872.3 1782.1 1790.3 2032.7 1372.3 TRUE FALSE FALSE 1766.898636 1717.645361 1797.041711 1046.846442 1579.554354 1752.666073 1933.47153 1842.099506 1850.890221 1336.647448 1.32188831 1.285039943 1.344439563 0.78318815 1.181728478 1.311240354 1.446508226 1.378149121 1.38472581 1 10.38440328 -12.36776196 1.021623131 0.995695233 1.255288313 0 0.20882007 0.700339387 1.273582923 0.134919272 0.032708926 4.29E-13 12.36776196 0.25959308 VEENPDADS(ph)DFDAK ddPTM_HeLa_Romidepsin_16h_R1 2 VEENPDADSDFDAK 14 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 0 VEENPDADS(1)DFDAK;VEENPDADS(1)DFDAK ; 232.73 7.29E-43 71117000 13456.7 13323.8 13490.9 7674.4 9550.4 9061.4 8142 8263.5 13085.8 12799.7 TRUE FALSE FALSE 13292.68456 13511.37281 13725.70346 8561.750237 9063.007451 8482.405784 8833.581277 8502.591335 11915.37327 12467.16195 1.066215761 1.083756902 1.100948517 0.686744126 0.726950327 0.680379851 0.708547889 0.681998948 0.955740635 1 13.60584546 -9.256570655 24.99885704 1.041585385 0.698318957 0.94682318 0.040809641 60.68538495 311593.6958 0.005833702 0.009474003 5.54E-10 9.256570655 -0.343266428 YSEEGLS(ph)PSKR ddPTM_HeLa_Romidepsin_16h_R1 2 YSEEGLSPSKR 11 1 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 YSEEGLS(0.758)PS(0.242)KR;YSEEGLS(0.776)PS(0.224)KR ; 168.85 0.00064312 22022000 6800 5797.1 5581.2 6598.8 5228.3 4816 3765.9 3092.3 6475.8 6723.6 TRUE FALSE FALSE 6717.118984 5878.711726 5678.338445 7361.784304 4961.480342 4508.273143 4085.775452 3181.770822 5896.588229 6548.919903 1.025683484 0.897661265 0.867064879 1.124121903 0.757602844 0.688399493 0.623885391 0.485846654 0.900390952 1 12.67704127 -8.180618516 1.011395791 1.001829887 0.492167887 0.774296919 0.088920871 0.196597118 0.32368972 0.012813812 0.07606059 6.60E-09 8.180618516 -0.509661999 down VEESSWLIEDGK ddPTM_HeLa_Romidepsin_16h_R1 1 VEESSWLIEDGK 12 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 0 227.94 2.12E-28 5578000 1494.1 1464.2 1295.3 1010.1 1341.9 1624.8 1090 1555.9 1483.2 1207 FALSE FALSE TRUE 1475.889335 1484.813046 1317.844153 1126.892515 1273.417836 1520.980524 1182.584573 1600.917512 1350.538877 1175.641966 1.255390142 1.262980643 1.120957053 0.95853376 1.083168067 1.293744667 1.005905375 1.361738997 1.148767156 1 10.19923305 -12.5319115 1.317959164 1.000819816 1.170086856 0.030018478 0.13013567 0.559004967 1.752176975 0.083233798 0.020293759 2.94E-13 12.5319115 0.169267039 VEET(ph)SPLGNAR ddPTM_HeLa_Romidepsin_16h_R1 2 VEETSPLGNAR 11 0 P30414;A0A087WYW3 P30414 NKTR NK-tumor recognition protein;Putative peptidyl-prolyl cis-trans isomerase 1 0 VEET(0.854)S(0.146)PLGNAR;VEET(0.867)S(0.133)PLGNAR ; 158.08 0.0034507 34879000 10357.7 9980.3 9769.4 6064 10147.8 9767.6 9188.7 10067.9 9917.5 10296.5 TRUE FALSE FALSE 10231.45637 10120.80293 9939.432309 6765.148212 9629.919899 9143.481883 9969.187949 10359.1988 9030.453961 10028.99545 1.020187558 1.009154205 0.99106958 0.674558908 0.960207825 0.91170466 0.994036542 1.032924869 0.900434546 1 13.29188949 -9.49753005 24.99754905 1.009311033 0.912593807 0.090997598 0.095968792 893.2883005 880915.4492 0.013606778 0.020730817 3.18E-10 9.49753005 -0.096717226 VEETVKHDWDR ddPTM_HeLa_Romidepsin_16h_R1 4 VEETVKHDWDR 11 1 E2QRB9;E9PIR7;F8W809;A0A087WSW9;A0A182DWI3;A0A087WSY9;Q16881-7;Q16881-5;Q16881-2;Q16881-4;Q16881-3;Q16881-6;Q16881;E9PKD3;A0A0B4J225 E2QRB9 TXNRD1 "Thioredoxin reductase 1, cytoplasmic" 0 0 ;;; ;;; 88.134 0.014917 72834200 12723.4 12187.8 10088.3 16174.7 11193.2 10462.9 8409.5 9930.4 12111.1 11638.1 FALSE FALSE TRUE 12568.32231 12359.38017 10263.88263 18044.89492 10621.96924 9794.354457 9123.80272 10217.72046 11027.85288 11335.74048 1.108734125 1.090301969 0.90544439 1.591858507 0.937033558 0.864024231 0.804870465 0.901372122 0.972839216 1 13.46859101 -8.534143579 24.99999202 1.084893326 0.859727264 0.296932151 0.177295877 214.5475375 476143.3252 0.024549475 0.049131507 2.92E-09 8.534143579 -0.225166062 VEFATLQEALAHALTEK ddPTM_HeLa_Romidepsin_16h_R1 1 VEFATLQEALAHALTEK 17 0 A0A087WY61;Q14980-2;Q14980;Q14980-4;Q14980-3 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 0 0 187.78 1.81E-13 968850 927.54 783.1 754.47 717.19 701.73 530.73 720.94 839.14 737.62 991.32 FALSE FALSE TRUE 916.2347857 794.1245024 767.6012339 800.1148823 665.9180996 496.8180659 782.1766256 863.419192 671.6454198 965.5653635 0.948910162 0.8224451 0.794975941 0.828649113 0.689666515 0.514535923 0.810071131 0.894211024 0.695598087 1 9.915230115 -10.03257042 0.975981219 0.986272629 0.730558927 0.011286993 0.132312337 0.274199782 0.514867499 0.020705561 0.027788068 9.28E-11 10.03257042 -0.255713701 VEGDNIY(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 VEGDNIYVR 9 0 O43491;H0Y5B0;E9PMV8;E9PPC9;Q6ZSX4 O43491 EPB41L2 Band 4.1-like protein 2 1 0 VEGDNIY(1)VR 101.46 0.0018265 0 4490.9 4348.9 4556.8 4367.1 5254.9 5054.2 4189.9 4520.1 6015 5757.7 TRUE FALSE FALSE 4436.163183 4410.123928 4636.109193 4872.04465 4986.722844 4731.252932 4545.790001 4650.881962 5477.003335 5608.114124 0.79102584 0.7863827 0.826678825 0.868749198 0.889197818 0.843644196 0.810573733 0.829313002 0.976621234 1 12.45329999 -12.32750507 1.010678304 1.00169049 0.82975528 0.804895685 0.030925661 0.204762135 0.368768923 0.025572388 0.006497539 4.70E-13 12.32750507 -0.17193521 VEGQATDEK(ac)KEPK ddPTM_HeLa_Romidepsin_16h_R1 1 VEGQATDEKKEPK 13 2 F8VXC8;Q8TAQ2-2;Q8TAQ2-3;Q8TAQ2 F8VXC8 SMARCC2 SWI/SNF complex subunit SMARCC2 0 1 VEGQATDEK(0.678)K(0.322)EPK 89.992 0.028785 3297400 1828.8 2750.9 1578.2 1310.4 1819.9 1654.3 1667.7 1629.9 2579.7 2350 FALSE TRUE FALSE 1806.509882 2789.627242 1605.667909 1461.914614 1727.023712 1548.595569 1809.354396 1677.058585 2348.965171 2288.946661 0.78923197 1.218738422 0.701487691 0.638684439 0.754505879 0.676553803 0.790474687 0.732677005 1.026221017 1 11.16046813 VEIAGPGFINVHLR ddPTM_HeLa_Romidepsin_16h_R1 1 VEIAGPGFINVHLR 14 0 P54136-2;P54136 P54136-2 RARS "Arginine--tRNA ligase, cytoplasmic" 0 0 103.97 0.0025052 253100 0 0 0 0 0 0 127.1 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 137.8958708 0 0 0 0 VEILANDQGNR ddPTM_HeLa_Romidepsin_16h_R1 3 VEILANDQGNR 11 0 P17066;P48741 P17066 HSPA6;HSPA7 Heat shock 70 kDa protein 6;Putative heat shock 70 kDa protein 7 0 0 ;; ;; 172.56 0.0039689 25251100 5721.8 5777 4695.3 5331.1 6205.9 6929.2 5293.2 5709 5553.5 4848.1 FALSE FALSE TRUE 5652.060501 5858.328758 4777.019727 5947.506866 5889.189766 6486.446483 5742.804276 5874.180908 5056.781051 4722.145663 1.196926335 1.24060738 1.011620578 1.259492462 1.247142758 1.373622702 1.216142975 1.24396436 1.070865113 1 12.20522683 -16.52287875 0.131790771 0.180387345 1.331713683 0.493931784 0.081101566 42.49450246 0.395849075 9.080259691 0.27754052 3.00E-17 16.52287875 1.151326338 VEKEEAGGGIS(ph)EEEAAQYDR ddPTM_HeLa_Romidepsin_16h_R1 2 VEKEEAGGGISEEEAAQYDR 20 1 A0A590UK93;A0A590UKC5;B3KNJ4;Q9UBE0-2;Q9UBE0-3;Q9UBE0;M0R375;M0QZS6 A0A590UK93 SAE1 "SUMO-activating enzyme subunit 1;SUMO-activating enzyme subunit 1, N-terminally processed" 1 0 VEKEEAGGGIS(1)EEEAAQYDR;VEKEEAGGGIS(1)EEEAAQYDR ; 89.392 0.00064211 8525900 2004.49 2216.91 1927.44 1805.83 2287.57 2200.03 1500.13 1972.13 2470.8 2482.4 TRUE FALSE FALSE 1980.058505 2248.119717 1960.986285 2014.628561 2170.826767 2059.455183 1627.551005 2029.19047 2249.80546 2417.90689 0.81891429 0.929779276 0.811026385 0.833211804 0.897812391 0.851751236 0.673123937 0.83923433 0.930476467 1 11.23954297 -16.52287875 0.185578219 1.755070621 0.788250006 0.41966797 0.064221786 31.31288848 0.36559828 8.56419637 0.078131856 3.00E-17 16.52287875 -0.966820615 VELQELNDR ddPTM_HeLa_Romidepsin_16h_R1 1 VELQELNDR 9 0 P08670;B0YJC4;A0A1B0GTT5;P17661 P08670 VIM;DES Vimentin;Desmin 0 0 187.5 3.27E-06 147120000 4099.1 3401.9 3702.5 2485.1 4011.1 4025.8 2947.9 3357.1 3600.1 3564.4 FALSE FALSE TRUE 4049.138593 3449.792037 3766.940459 2772.438955 3806.3986 3768.564373 3198.294552 3454.232392 3278.098039 3471.796374 1.166294954 0.993661974 1.085011923 0.798560358 1.096377261 1.085479667 0.921221814 0.994940953 0.944208037 1 11.76146662 -9.744979885 2.38459832 1.076759756 0.988736677 0 0.10200859 0.447905925 5.22925016 0.016733503 0.023838473 1.80E-10 9.744979885 -0.088023079 VELS(ph)PGPPKPAGR ddPTM_HeLa_Romidepsin_16h_R1 3 VELSPGPPKPAGR 13 1 A0A087WXE2;Q8IZ73-2;Q8IZ73 A0A087WXE2 RPUSD2 RNA pseudouridylate synthase domain-containing protein 2 1 0 VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR;VELS(1)PGPPKPAGR ;; 82.578 0.013143 209988000 19571.6 19083.8 17205.8 15733.9 19342.3 19892.2 18260.6 18906.7 20773.3 19309.8 TRUE FALSE FALSE 19333.05381 19352.46224 17505.25973 17553.12755 18355.19025 18621.15262 19811.65491 19453.73553 18915.28402 18808.12861 1.027909486 1.028941403 0.930728415 0.933273475 0.975917947 0.990058767 1.053355989 1.034325952 1.005697292 1 14.19906869 -7.761829348 24.9999946 0.999071285 1.043840979 0.256838135 0.03401045 13.37983244 858026.8734 0.005556864 0.018310945 1.73E-08 7.761829348 0.044769695 VEMY(ph)S(ph)GSDDDDDFNKLPK ddPTM_HeLa_Romidepsin_16h_R1 3 VEMYSGSDDDDDFNKLPK 18 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 2 0 VEMY(0.667)S(0.667)GS(0.667)DDDDDFNKLPK;VEMY(0.884)S(0.898)GS(0.218)DDDDDFNKLPK;VEMY(0.871)S(0.887)GS(0.242)DDDDDFNKLPK ;; 61.097 0.0041908 109637000 16020.7 15813.8 15877.1 14287.9 16701.2 17770.3 15679.4 18944.2 16769.6 16937.8 TRUE FALSE FALSE 15825.43355 16036.42709 16153.43427 15939.93422 15848.87544 16634.83518 17011.20784 19492.32054 15269.68498 16497.75351 0.959247787 0.972037016 0.979129325 0.966188167 0.960668701 1.008309111 1.031122682 1.181513624 0.925561469 1 14.00998197 -7.018335587 1.392074791 0.977568784 1.374761498 0.900570427 0.02116861 0.412006655 0.455464119 0.002586274 0.268156723 9.59E-08 7.018335587 0.397192714 VENMSSNQDGNDS(ph)DEFM ddPTM_HeLa_Romidepsin_16h_R1 3 VENMSSNQDGNDSDEFM 17 0 Q86WR0-2;Q86WR0 Q86WR0-2 CCDC25 Coiled-coil domain-containing protein 25 1 0 VENMSSNQDGNDS(1)DEFM;VENMS(0.001)S(0.007)NQDGNDS(0.992)DEFM;VENMSSNQDGNDS(1)DEFM ;; 131.79 0.0014723 160721000 7622.8 6796.4 6982.7 7092.9 7326.6 7999.5 6569.9 7469.7 7397.4 7067.9 TRUE FALSE FALSE 7529.890382 6892.079898 7104.230964 7913.014471 6952.696263 7488.357767 7127.947142 7685.823984 6735.758017 6884.274939 1.093781182 1.001133737 1.0319505 1.149433243 1.009938784 1.087748214 1.035395478 1.116431876 0.978426643 1 12.749089 -12.49736323 1.13860317 0.99852461 1.066427685 0.301524446 0.045618948 0.592469865 1.324870319 0.033023881 0.007326743 3.18E-13 12.49736323 0.067903075 VENSPQVDGS(ph)PPGLEGLLGGIGEK ddPTM_HeLa_Romidepsin_16h_R1 1 VENSPQVDGSPPGLEGLLGGIGEK 24 0 E7EXA6;A0A0D9SF58;Q8WVB6;Q8WVB6-2;Q8WVB6-3 E7EXA6 CHTF18 Chromosome transmission fidelity protein 18 homolog 1 0 VENS(0.025)PQVDGS(0.975)PPGLEGLLGGIGEK 60.941 0.0026324 7301100 0 143.36 0 0 138.24 0 0 170.02 0 145.47 TRUE FALSE FALSE 0 145.3782258 0 0 131.185097 0 0 174.9392605 0 141.6906684 0 1.026025408 0 0 0.925855587 0 0 1.234656187 0 1 7.146600937 -12.54510326 1.283984764 1.003290065 0.336389589 0 0.559899687 0.544154171 1.594049547 0.318876684 0.074096416 2.85E-13 12.54510326 -0.666900476 VEPEVLSTDTQT(ph)SPEPGTR ddPTM_HeLa_Romidepsin_16h_R1 2 VEPEVLSTDTQTSPEPGTR 19 0 P29375-2;P29375 P29375-2 KDM5A Lysine-specific demethylase 5A 1 0 VEPEVLSTDT(0.009)QT(0.958)S(0.033)PEPGTR;VEPEVLSTDT(0.001)QT(0.806)S(0.188)PEPGT(0.005)R ; 213.36 9.31E-29 11281600 3373.5 3201.3 3477.8 2062.49 3621.6 3483.3 2646 3302.3 3438.3 3046.4 TRUE FALSE FALSE 3332.382484 3246.367985 3538.32965 2300.964798 3436.776238 3260.728372 2870.751174 3397.84684 3130.769837 2967.254089 1.123052622 1.09406471 1.192459272 0.775452566 1.158234561 1.098904332 0.967477367 1.14511489 1.055106756 1 11.53491276 -12.63240137 1.481404477 1.000330413 1.073657988 0.011176848 0.115209036 1.054289626 4.187140734 0.074901759 0.017398345 2.33E-13 12.63240137 0.073327574 VEPGLGADNS(ph)VVR ddPTM_HeLa_Romidepsin_16h_R1 2 VEPGLGADNSVVR 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 VEPGLGADNS(1)VVR;VEPGLGADNS(1)VVR ; 100.18 0.012632 10605300 3000.4 2399.5 2350.8 2563.33 2182.6 2554.9 2559 2680.2 3187.8 3455.4 TRUE FALSE FALSE 2963.829971 2433.280224 2391.714688 2859.714275 2071.213778 2391.650136 2776.361396 2757.747358 2902.675184 3365.62821 0.880617164 0.722979507 0.710629499 0.849682168 0.615401835 0.710610319 0.824916248 0.81938562 0.862446772 1 11.7166601 -10.72915572 1.043233727 0.971475558 0.746990922 0.447393442 0.077912236 0.202614026 0.461259064 0.017771639 0.016610122 1.87E-11 10.72915572 -0.224484636 VEPLGEDNS(ph)GALY(ph)WY(ph)FYGTRMY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 VEPLGEDNSGALYWYFYGTRMYK 23 1 A0A087WT21;Q9BXF3-2;Q9BXF3-3;Q9BXF3 A0A087WT21 CECR2 Cat eye syndrome critical region protein 2 4 0 VEPLGEDNS(0.957)GALY(0.828)WY(0.828)FY(0.301)GT(0.135)RMY(0.952)K 41.136 0.018611 16697000 289.33 317.33 338.96 420.39 426.21 161.43 287.5 357.37 416.22 435.63 TRUE FALSE FALSE 285.8035347 321.7973801 344.8594566 468.9974698 404.4589133 151.115144 311.9202428 367.7099371 378.9922408 424.3122698 0.673568867 0.758397536 0.812749197 1.105312062 0.953210506 0.356141349 0.735119545 0.866602178 0.893191802 1 8.728982587 -12.48924082 1.223314945 1.000439029 0.771704524 0.099219881 0.186594694 0.706142245 1.885233768 0.135487991 0.032777551 3.24E-13 12.48924082 -0.228734505 VEPRNISQDK ddPTM_HeLa_Romidepsin_16h_R1 1 VEPRNISQDK 10 1 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 0 0 113.26 0.0239 1820400 945.74 828.96 579.92 748.12 1183.3 1328 914.57 804.27 1266.4 1095.3 FALSE FALSE TRUE 934.2129571 840.6301206 590.0132643 834.6211544 1122.911785 1243.145086 992.253553 827.5402835 1153.130012 1066.843948 0.875679108 0.787959778 0.553045518 0.782327308 1.052554863 1.165254851 0.930083125 0.775690095 1.080879743 1 10.05913345 -7.257150867 21.52788544 0.915284046 0.775689708 0.057503543 0.168172737 164.48833 825457.9196 0.024066814 0.239888291 5.53E-08 7.257150867 -0.139594339 VEPSSQSPGRS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VEPSSQSPGRSPR 13 1 X6RM00;G8JLD3;X6RLX0;Q8IUD2-5;Q8IUD2-4;Q8IUD2-2;Q8IUD2-3;Q8IUD2;K7EKH8;K7EIZ7 X6RM00 ERC1 ELKS/Rab6-interacting/CAST family member 1 1 0 VEPSSQSPGRS(1)PR 123.63 0.001509 141240000 4589.6 4501.7 4046.4 3698.5 4613.7 5552.8 4403.6 4714.9 4488.9 3828.7 TRUE FALSE FALSE 4533.66019 4565.075051 4116.825895 4126.137972 4378.245673 5197.994001 4777.641674 4851.318193 4087.401541 3729.229822 1.215709518 1.224133472 1.103934617 1.106431668 1.174034823 1.393851881 1.281133613 1.30089011 1.096044421 1 11.86466199 -16.52287875 0.079705642 0.226199486 1.477650848 0.534963129 0.075800995 98.61907654 0.603558909 13.72084054 1.531188918 3.00E-17 16.52287875 1.251451362 VEPTLVTENS(ph)GNK ddPTM_HeLa_Romidepsin_16h_R1 1 VEPTLVTENSGNK 13 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 VEPTLVTENS(1)GNK 141.82 0.00093338 5646600 1145.6 1418.3 1162.7 1056.5 1197.4 1188 947.05 925.08 1365.8 1296.3 TRUE FALSE FALSE 1131.636987 1438.266865 1182.936306 1178.657501 1136.29221 1112.090634 1027.492403 951.8457303 1243.639427 1262.621939 0.896259562 1.139111257 0.936888762 0.933499937 0.899946512 0.880778798 0.81377677 0.7538644 0.984965799 1 10.30220701 -7.734305106 0.834615726 0.964584265 0.709228701 0.61325887 0.062292104 0.818910358 0.628106341 0.011078528 0.164845476 1.84E-08 7.734305106 -0.255355563 VEQALSEVASS(ph)LQSSAPK ddPTM_HeLa_Romidepsin_16h_R1 1 VEQALSEVASSLQSSAPK 18 0 H0YK02;H0YJS2;A0A0C4DGK5;Q86TV6;Q86TV6-2 H0YK02 TTC7B Tetratricopeptide repeat protein 7B 1 0 VEQALSEVAS(0.226)S(0.758)LQS(0.012)S(0.004)APK 106.31 0.00026147 0 1077.5 751.89 679.98 794.26 1004.7 1002 754.1 812 951.24 817.6 TRUE FALSE FALSE 1064.367016 762.4751272 691.8147667 886.0960783 953.4264099 937.9754338 818.1532352 835.4939389 866.158712 796.3586341 1.336542319 0.95745195 0.868722629 1.112684713 1.197232464 1.177830432 1.027367822 1.049142815 1.08764905 1 9.637274474 -10.22688313 24.99892183 1.158922848 1.059812963 0.089739713 0.120686637 1256.689196 909124.7004 0.026162992 0.032042399 5.93E-11 10.22688313 -0.099109884 VEQATKPS(ph)FESGR ddPTM_HeLa_Romidepsin_16h_R1 1 VEQATKPSFESGR 13 1 P38159;P38159-2;H0Y6E7;H3BT71 P38159 RBMX "RNA-binding motif protein, X chromosome;RNA-binding motif protein, X chromosome, N-terminally processed" 1 0 VEQAT(0.02)KPS(0.899)FES(0.081)GR 151.49 0.0050797 35462000 2243 2137 1922.5 1583.5 2670.1 2072.4 2079.3 2476.5 2216.4 1968.9 TRUE FALSE FALSE 2215.661453 2167.084742 1955.960306 1766.591721 2533.834833 1939.980328 2255.91569 2548.15362 2018.159633 1917.747694 1.155345648 1.130015564 1.019925776 0.921180469 1.321255576 1.011593097 1.17633602 1.328722036 1.052359306 1 10.90519721 -4.00000028 0.782888753 1.073563787 58.56779477 0.355091864 0.104141382 377.9735447 1.334351325 0.016939757 38504.0168 1.00E-04 4.00000028 57.49423098 VEQMPQAS(ph)PGLAPR ddPTM_HeLa_Romidepsin_16h_R1 1 VEQMPQASPGLAPR 14 0 Q8N3F8;H0Y6J8 Q8N3F8 MICALL1 MICAL-like protein 1 1 0 VEQMPQAS(1)PGLAPR 90.853 0.025411 35671000 4021.3 4501.2 3227.2 3456 3287 3183.5 2573.7 2654.9 3605.5 3492.7 TRUE FALSE FALSE 3972.286849 4564.568012 3283.368062 3855.598981 3119.252125 2980.084624 2792.310014 2731.715343 3283.01505 3401.95915 1.167646839 1.341746861 0.965140355 1.133346642 0.916898759 0.875990714 0.820794692 0.802982994 0.965036588 1 11.7321501 -8.53462592 1.84707237 1.098209674 0.821776105 0.551277334 0.107663144 0.205282266 1.385494674 0.016730808 0.044014737 2.92E-09 8.53462592 -0.276433569 VERPPSPFS(ph)MAPQASLPPVPPR ddPTM_HeLa_Romidepsin_16h_R1 1 VERPPSPFSMAPQASLPPVPPR 22 1 A0A1B0GW38;A0A0U1RQX8;P22681 A0A1B0GW38 CBL E3 ubiquitin-protein ligase CBL 1 0 VERPPS(0.196)PFS(0.803)MAPQAS(0.001)LPPVPPR 66.448 0.0056385 39532000 710.63 809.63 645.03 691.15 903.15 942.78 723.37 973.67 928.94 722.59 TRUE FALSE FALSE 701.9685682 821.0279924 656.2564766 771.064015 857.0588854 882.5394007 784.8130297 1001.841605 845.8532798 703.8170076 0.997373693 1.166536164 0.932424863 1.095546153 1.217729717 1.253933041 1.115081081 1.42344046 1.201808525 1 9.459056567 -4 0.276389193 0.9837849 3.834441537 0.395742821 0.107010898 20.0626303 0.255282161 0.03513665 27.86515894 1.00E-04 4 2.850656637 VESGYFS(ph)LEK ddPTM_HeLa_Romidepsin_16h_R1 2 VESGYFSLEK 10 0 A0A494BZV2;Q6WCQ1;Q6WCQ1-2;J3KSW8;Q6WCQ1-3;A0A1W2PPU9 A0A494BZV2 MPRIP Myosin phosphatase Rho-interacting protein 1 0 VES(0.044)GYFS(0.956)LEK;VESGYFS(1)LEK ; 158.3 0.0027783 59446000 7406.1 6104.4 6131.3 5495.1 7890.1 8068.3 7303.8 7338.7 6647.4 6294 TRUE FALSE FALSE 7315.831605 6190.337903 6238.012705 6130.469317 7487.438755 7552.761669 7924.18459 7551.033706 6052.839895 6130.480973 1.193353611 1.009763823 1.017540505 0.999998099 1.221346056 1.232001486 1.292587747 1.231719622 0.987335239 1 12.58178455 -8.64391054 6.053824167 1.074978293 1.251177554 0.690735745 0.065681356 0.134637519 6.641314773 0.012167019 0.024514951 2.27E-09 8.64391054 0.176199262 VESLES(ph)LYFTPIPAR ddPTM_HeLa_Romidepsin_16h_R1 1 VESLESLYFTPIPAR 15 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 VES(0.234)LES(0.748)LYFT(0.018)PIPAR 209.22 1.87E-20 5544400 444.11 446.72 393.14 342.72 658.13 620.02 629.09 554.76 259.78 361.17 TRUE FALSE FALSE 438.6970165 453.0089359 399.9824368 382.3468989 624.5431703 580.402723 682.5248889 570.8111053 236.5446262 351.7867513 1.247053833 1.287737341 1.13700256 1.08687123 1.77534591 1.649870897 1.940166553 1.622605465 0.672409138 1 8.45855734 -8.76003236 24.99999326 1.13346961 1.753857523 0.763101812 0.18234251 10.30759058 183139.2344 0.018870756 0.036168194 1.74E-09 8.76003236 0.620387914 VESLESLYFT(ph)PIPAR ddPTM_HeLa_Romidepsin_16h_R1 2 VESLESLYFTPIPAR 15 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 VESLESLYFT(1)PIPAR;VES(0.001)LES(0.009)LY(0.001)FT(0.99)PIPAR ; 172.85 1.07E-05 9139800 2401 2188.3 2378.9 1293.97 2426.1 2202.2 2173.4 2306.45 2562.2 2250.92 TRUE FALSE FALSE 2371.735688 2219.106945 2420.303757 1443.5849 2302.287064 2061.486527 2358.008542 2373.183492 2333.030415 2192.440774 1.081778681 1.012162778 1.103931192 0.658437353 1.050102284 0.94027011 1.075517556 1.082439042 1.064124716 1 11.09832216 VET(ph)GVLKPGMVVTFAPVNVTTEVK ddPTM_HeLa_Romidepsin_16h_R1 1 VETGVLKPGMVVTFAPVNVTTEVK 24 1 Q5VTE0;P68104;A0A087WVQ9 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1 1 0 VET(0.975)GVLKPGMVVT(0.024)FAPVNVT(0.001)TEVK 52.669 0.014352 14642000 1227.4 1110.3 1151.7 1164.2 1159.3 1309 981.26 1077.2 1222.3 1168.6 TRUE FALSE FALSE 1212.439977 1125.930833 1171.744855 1298.810282 1100.136595 1225.359125 1064.6082 1108.367082 1112.974427 1138.239604 1.065188712 0.989186134 1.029436027 1.141069312 0.966524615 1.076538824 0.935311156 0.973755507 0.977803288 1 10.15258857 -7.750979266 24.99991134 1.034069244 0.954533307 0.262154109 0.050877209 189.4562477 452795.4537 0.006440666 0.023592421 1.77E-08 7.750979266 -0.079535937 VET(ph)LSPESALQGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VETLSPESALQGSPR 15 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 2 0 VET(0.598)LS(0.402)PESALQGS(1)PR 154.31 0.0019649 59474000 4957.5 4333.3 4007.4 3008.2 3325.3 2854 2379.8 2404.9 4750.9 3789.6 TRUE FALSE FALSE 4897.076083 4394.304311 4077.147116 3356.022238 3155.597533 2671.638611 2581.940153 2474.481987 4325.967605 3691.145646 1.326708982 1.190498759 1.104574977 0.909208837 0.854910057 0.723796584 0.699495604 0.670383189 1.171985075 1 11.84985295 -8.904348438 1.321927576 1.161526298 0.696317065 0.868631333 0.079071454 0.170470118 0.594186213 0.020478531 0.048499123 1.25E-09 8.904348438 -0.465209233 VET(ph)PSHPGGVSEEFWER ddPTM_HeLa_Romidepsin_16h_R1 2 VETPSHPGGVSEEFWER 17 0 Q92620;H3BQT9 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 0 VET(0.929)PS(0.071)HPGGVSEEFWER;VET(0.915)PS(0.085)HPGGVSEEFWER ; 76.573 0.016948 6553500 1471.29 1403.42 1445.59 1123.6 1768.22 1531.59 970.92 1414.28 1471.35 1575.04 TRUE FALSE FALSE 1453.357352 1423.177384 1470.749888 1253.515919 1677.981135 1433.726342 1053.389921 1455.19996 1339.748771 1534.120234 0.947355572 0.92768308 0.958692712 0.817091054 1.093774203 0.934559307 0.686641045 0.948556657 0.873301024 1 10.58319584 -4 0.168965642 1.004791634 0.35076383 0.009490636 0.103016881 74.65349567 0.781237384 0.141261792 12.38774046 1.00E-04 4 -0.654027804 VETFSGVYK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VETFSGVYKK 10 1 A0A2R8Y623;P62081 A0A2R8Y623 RPS7 40S ribosomal protein S7 0 1 VETFSGVYK(1)K 160.36 0.0034168 2071800 329.91 542.05 352.34 263.52 1156.4 801.67 704.52 626.33 1199.9 637.54 FALSE TRUE FALSE 325.88893 549.6809941 358.4723299 293.9894223 1097.384593 750.4458743 764.3619112 644.4518704 1092.577939 620.9766189 0.524800645 0.885187908 0.577271863 0.473430743 1.767191484 1.208492963 1.230902884 1.037803761 1.759451009 1 9.278395139 -8.774470453 24.99190975 0.744094651 1.29804074 0.191578872 0.395711386 138.0736009 264807.1676 0.038794016 0.070631352 1.68E-09 8.774470453 0.553946089 VETGVLKPGMVVTFAPVNVTTEVK ddPTM_HeLa_Romidepsin_16h_R1 4 VETGVLKPGMVVTFAPVNVTTEVK 24 1 Q5VTE0;P68104;A0A087WVQ9 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1 0 0 ;;; ;;; 161.02 1.13E-26 2250790 899.871 614.13 619.5 651.093 933.531 578.813 566.39 796.73 852.41 579.447 FALSE FALSE TRUE 888.9030261 622.7757383 630.2821376 726.3754361 885.8894296 541.8287173 614.4991525 819.7821255 776.1683147 564.3928834 1.574972067 1.103443641 1.116743595 1.287003181 1.56963253 0.960020463 1.088779059 1.452502591 1.37522697 1 9.140555986 -8.211914585 24.99781621 1.270907537 1.159268852 0.060465398 0.211823046 1214.645543 613095.1086 0.036456557 0.092946234 6.14E-09 8.211914585 -0.111638685 VETLS(ph)PESALQGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VETLSPESALQGSPR 15 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 2 0 VET(0.179)LS(0.819)PES(0.002)ALQGS(1)PR 140.68 0.0078005 3202000 1601 1604.4 1378 938.05 834.87 872.52 907.68 1030.3 1580.9 1318.9 TRUE FALSE FALSE 1581.486396 1626.986785 1401.983512 1046.511755 792.2634686 816.7687879 984.7783165 1060.110105 1439.500345 1284.634788 1.2310786 1.26649753 1.091347926 0.814637564 0.616722726 0.635798435 0.76658232 0.825222947 1.120552205 1 10.32714255 -9.195354778 3.361785694 1.126317214 0.710683447 0.844335762 0.088780352 0.094843853 2.122679039 0.017925246 0.030402011 6.38E-10 9.195354778 -0.415633767 VETLSPESALQGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 VETLSPESALQGSPR 15 0 Q99958 Q99958 FOXC2 Forkhead box protein C2 1 0 VETLSPESALQGS(1)PR;VETLSPESALQGS(1)PR;VETLSPESALQGS(1)PR;VET(0.01)LSPES(0.001)ALQGS(0.989)PR ;;; 188.92 2.64E-12 111116000 6259.5 6563.5 6125.7 4761.06 4218.09 4108.15 3518.8 3704.28 7026.1 6497 TRUE FALSE FALSE 6183.206806 6655.901125 6232.315239 5311.556159 4002.825127 3845.652473 3817.686784 3811.457497 6397.668019 6328.207003 0.977086686 1.051783091 0.98484693 0.839346146 0.632537009 0.60770017 0.603280958 0.60229659 1.010976413 1 12.62758108 -8.922706586 2.197753335 0.994725527 0.602763089 0.987424306 0.02092539 0.024966645 0.24383987 0.003518771 0.007027761 1.19E-09 8.922706586 -0.391962438 VETPSHPGGVS(ph)EEFWER ddPTM_HeLa_Romidepsin_16h_R1 1 VETPSHPGGVSEEFWER 17 0 Q92620;H3BQT9 Q92620 DHX38 Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 1 0 VET(0.328)PS(0.237)HPGGVS(0.435)EEFWER 85.734 0.0030315 0 711.7 531.11 759.17 651.82 730.9 705.5 648.03 431.62 764.33 698.36 TRUE FALSE FALSE 703.0255267 538.5869805 772.3830354 727.1864953 693.5994456 660.4208269 703.073652 444.1082437 695.9664105 680.2165065 1.033532 0.791787578 1.135495872 1.069051527 1.019674529 0.970897972 1.03360275 0.652892483 1.023154251 1 9.409850206 -7.259212716 24.80867272 1.010866906 0.652892344 0.619555261 0.083599264 85.0722403 947772.0468 0.010717851 0.095038209 5.51E-08 7.259212716 -0.357974562 VETSEGLNS(ph)DLEMHADK ddPTM_HeLa_Romidepsin_16h_R1 1 VETSEGLNSDLEMHADK 17 0 P49454 P49454 CENPF Centromere protein F 1 0 VETS(0.001)EGLNS(0.998)DLEMHADK 99.881 0.00098523 3924600 3682.2 4048.7 3054 3607.4 3027.8 2699.7 1906.3 2506.8 3927.7 3749 TRUE FALSE FALSE 3637.31993 4105.697705 3107.153589 4024.504561 2873.280068 2527.197883 2068.221074 2579.330303 3576.396675 3651.60044 0.996089246 1.124355683 0.850901855 1.102120735 0.786855001 0.692079521 0.566387563 0.706356116 0.979405259 1 11.8343132 -8.524107584 2.980849584 1.002841548 0.647687127 0.800995904 0.079818664 0.072777303 1.313329058 0.010362334 0.023765085 2.99E-09 8.524107584 -0.355154421 VEVAAPAHRGT(ph)PDTDLEVQR ddPTM_HeLa_Romidepsin_16h_R1 1 VEVAAPAHRGTPDTDLEVQR 20 1 P0C7T5 P0C7T5 ATXN1L Ataxin-1-like 1 0 VEVAAPAHRGT(0.795)PDT(0.205)DLEVQR 49.555 0.018424 4505000 3639.9 4191.5 3398 3979.9 3648.1 3318.8 3166.5 2895.8 4075 3814.6 TRUE FALSE FALSE 3595.535499 4250.508047 3457.140765 4440.074764 3461.923844 3106.739391 3435.462431 2979.585404 3710.521794 3715.496142 0.967713425 1.143994741 0.930465443 1.195015307 0.931752776 0.836157345 0.92463087 0.801934732 0.998661189 1 11.85933916 -8.525333569 24.99966185 1.008569927 0.865059131 0.481168531 0.083313712 56.11739432 571494.0497 0.011516964 0.023146472 2.98E-09 8.525333569 -0.143510796 VEVERDNLAEDIMR ddPTM_HeLa_Romidepsin_16h_R1 2 VEVERDNLAEDIMR 14 1 P08670;B0YJC4 P08670 VIM Vimentin 0 0 ; ; 91.093 0.025547 83228000 4118.9 3561.3 2894.7 7229.4 4267.4 3731.8 3178.4 3274.6 4540.7 3209.3 FALSE FALSE TRUE 4068.697263 3611.436075 2945.081039 8065.297243 4049.618654 3493.350024 3448.373217 3369.345385 4134.56842 3125.921923 1.301599132 1.155318707 0.942147984 2.580133938 1.295495778 1.117542315 1.103153982 1.077872534 1.322671686 1 11.61006603 -11.82832059 0.621470966 0.989735586 1.34228304 0.001607857 0.446693846 1.941272592 1.36856044 0.35358019 0.106207587 1.48E-12 11.82832059 0.352547455 VEVGKDQEFTVDTR ddPTM_HeLa_Romidepsin_16h_R1 1 VEVGKDQEFTVDTR 14 1 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 105.95 0.0084882 20257000 2463.6 2171.4 2465 2257.6 2792.1 3081.7 2731 2676.5 2852.1 2593.5 FALSE FALSE TRUE 2433.572696 2201.969026 2507.902291 2518.634334 2649.608718 2884.789316 2962.971072 2753.940305 2597.001033 2526.120496 0.963363664 0.871680124 0.99278807 0.997036499 1.048884534 1.14198405 1.172933388 1.090185646 1.028059048 1 11.30270774 -8.533478394 2.036419859 0.973713915 1.140407148 0.734822275 0.043030326 0.119359785 0.981971855 0.006277894 0.01589415 2.93E-09 8.533478394 0.166693233 VEVNTNS(ph)GEIIHK ddPTM_HeLa_Romidepsin_16h_R1 2 VEVNTNSGEIIHK 13 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 0 VEVNT(0.309)NS(0.691)GEIIHK;VEVNT(0.037)NS(0.963)GEIIHK ; 83.106 0.0029248 0 4745.9 3807 4022 2966.2 4032.5 3975.5 3546.7 3865.3 4697.8 4105.9 TRUE FALSE FALSE 4688.055145 3860.595046 4092.001223 3309.166 3826.706478 3721.47838 3847.956609 3977.136357 4277.617002 3999.228126 1.172239992 0.965335041 1.023197751 0.827451172 0.956861263 0.930549162 0.962174822 0.994475992 1.069610652 1 11.96550586 -10.11137093 6.939032922 1.08126675 0.947729466 0.48112351 0.061632852 0.192508114 10.69629404 0.012929281 0.01587311 7.74E-11 10.11137093 -0.133537284 VEVS(ph)EDEPASK ddPTM_HeLa_Romidepsin_16h_R1 1 VEVSEDEPASK 11 0 O75683 O75683 SURF6 Surfeit locus protein 6 1 0 VEVS(0.991)EDEPAS(0.009)K 98.407 0.020962 13698000 2799.2 3044.7 2974 1781.6 3043.9 3303.2 2267 2849.6 3236 3342.3 TRUE FALSE FALSE 2765.082274 3087.563367 3025.761222 1987.596975 2888.558425 3092.136181 2459.558923 2932.04868 2946.564055 3255.466564 0.849365896 0.948424229 0.929440116 0.610541357 0.88729476 0.949828886 0.755516567 0.900653907 0.905112677 1 11.66864861 -12.75316187 0.369099548 1.083598014 0.838323843 0.106727647 0.101858596 4.129820888 0.557561686 0.422107333 0.03601934 1.77E-13 12.75316187 -0.245274171 VEVTEFEDIK ddPTM_HeLa_Romidepsin_16h_R1 2 VEVTEFEDIK 10 0 Q01105;A0A0C4DFV9;Q01105-3;Q01105-4;A0A087X027;P0DME0;Q01105-2 Q01105;Q01105-2 SET;SETSIP Protein SET;Protein SETSIP 0 0 ; ; 176.83 0.00060796 65571000 8355.7 7924.3 6990.2 6286.4 7580.8 6707.1 6415.8 6520.7 7134.9 7179.1 FALSE FALSE TRUE 8253.857514 8035.858503 7111.861499 7013.263146 7193.923488 6278.537956 6960.757892 6709.366167 6496.736674 6992.585947 1.180372694 1.149196959 1.017057431 1.002957018 1.028793002 0.897884989 0.995448314 0.959497133 0.929089284 1 12.77161037 -9.562206925 4.886462199 1.092377012 0.97898413 0.197176075 0.075216503 0.175674573 9.874305498 0.012224272 0.017638199 2.74E-10 9.562206925 -0.113392882 VEY(ph)S(ph)LLIYVSVPGS(ph)KK ddPTM_HeLa_Romidepsin_16h_R1 1 VEYSLLIYVSVPGSKK 16 1 Q9H3M7-2;Q9H3M7 Q9H3M7-2 TXNIP Thioredoxin-interacting protein 3 0 VEY(0.995)S(0.99)LLIY(0.041)VS(0.045)VPGS(0.928)KK 44.457 0.02813 8998000 2899.9 1945.5 2144.9 2432.4 3295.3 3349.2 2833.3 3593.4 2157.1 2092.1 TRUE FALSE FALSE 2864.554903 1972.8888 2182.231085 2713.645533 3127.128545 3135.196929 3073.960431 3697.36936 1964.163573 2037.74694 1.405746144 0.968171641 1.07090387 1.331689171 1.534601026 1.538560489 1.508509408 1.814439902 0.963889841 1 10.99275918 -4 0.236060469 1.099305183 5.061618634 0.708229898 0.152393482 26.45145433 0.32457951 0.113667832 41.28600896 1.00E-04 4 3.962313451 VFDDES(ph)DEKEDEEYADEK ddPTM_HeLa_Romidepsin_16h_R1 1 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 VFDDES(0.553)DEKEDEEY(0.447)ADEK 81.651 0.0045485 81488000 2837.1 2943.1 3290.7 1825.1 3096.7 3488.9 3281.1 4118.6 2742.2 3315.5 TRUE FALSE FALSE 2802.520334 2984.533039 3347.973253 2036.126649 2938.663844 3265.97055 3559.796552 4237.765193 2496.930764 3229.362832 0.867824546 0.924186347 1.036728738 0.630504144 0.909982556 1.011335895 1.102321646 1.312260472 0.773196105 1 11.65703383 -7.465059739 1.582442758 0.919150903 1.369176503 0.578557365 0.114321147 0.402882087 1.259920388 0.015829121 0.246650287 3.43E-08 7.465059739 0.4500256 VFDDESDEKEDEEY(ph)ADEK ddPTM_HeLa_Romidepsin_16h_R1 1 VFDDESDEKEDEEYADEK 18 1 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 VFDDES(0.005)DEKEDEEY(0.995)ADEK 86.777 0.015777 87483000 7197.7 5846.1 7699.7 4266.7 6759.5 7867.7 7715.4 8183.7 6595.2 7012.6 TRUE FALSE FALSE 7109.971664 5928.401549 7833.710049 4760.035929 6414.537492 7364.979362 8370.745883 8420.482448 6005.308794 6830.411641 1.040928723 0.86794206 1.146886961 0.696888589 0.939114336 1.078262885 1.225511188 1.232792823 0.879201593 1 12.73775681 -7.892973576 3.220174109 0.98881489 1.232611279 0.453187151 0.119437857 0.175703412 3.566286029 0.015865276 0.05667639 1.28E-08 7.892973576 0.243796389 VFDDESDEKEDEEY(ph)ADEKGLEAADK ddPTM_HeLa_Romidepsin_16h_R1 2 VFDDESDEKEDEEYADEKGLEAADK 25 2 O43719 O43719 HTATSF1 HIV Tat-specific factor 1 1 0 VFDDES(0.255)DEKEDEEY(0.745)ADEKGLEAADK;VFDDES(0.315)DEKEDEEY(0.685)ADEKGLEAADK ; 52.227 0.011196 104661000 4193.2 3047.5 3523.8 3043 4439.9 4270.9 4191.9 4574.1 4276.2 3997.8 TRUE FALSE FALSE 4142.091666 3090.402785 3585.130261 3394.845978 4213.315335 3998.003274 4547.959881 4706.444367 3893.725962 3893.93658 1.06372859 0.793644869 0.920695596 0.87182878 1.082019506 1.026725318 1.167959413 1.208659738 0.999945911 1 11.92701367 -7.739607997 1.648617121 0.994431008 1.223441906 0.501679783 0.08550745 0.378475174 1.717010898 0.013997528 0.103198253 1.82E-08 7.739607997 0.229010898 VFDKDGNGYISAAELR ddPTM_HeLa_Romidepsin_16h_R1 2 VFDKDGNGYISAAELR 16 1 P0DP25;P0DP24;P0DP23;E7EMB3;G3V361;A0A590UJI2;Q96HY3 P0DP25 CALM2;CALM1 0 0 ; ; 113.52 0.003409 95432000 3977.6 3618.5 4470.2 3675.4 4988.4 5310.8 4673.5 4146.9 4525.1 4206.4 FALSE FALSE TRUE 3929.119481 3669.441338 4548.001956 4100.367041 4733.823334 4971.45702 5070.466973 4266.884009 4120.363723 4097.117122 0.958996134 0.895615436 1.110049291 1.000793221 1.155403469 1.213403687 1.237569448 1.041435693 1.005673892 1 12.00039342 -8.938287415 1.471750148 0.977983135 1.175672995 0.56465231 0.070528579 0.191334834 0.828737546 0.010617556 0.023514313 1.15E-09 8.938287415 0.19768986 VFDLQFSTDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VFDLQFSTDSPR 12 0 Q15003;E9PHA2;C9JZP1;C9J470 Q15003 NCAPH Condensin complex subunit 2 1 0 VFDLQFST(0.001)DS(0.999)PR 201.76 9.10E-15 25700000 3103.1 3247.3 3063.1 2539.2 4301.7 4126.8 3765.6 4468 3439.2 3296.9 TRUE FALSE FALSE 3065.278224 3293.015575 3116.411971 2832.794251 4082.168197 3863.110799 4085.44997 4597.274531 3131.589338 3211.246063 0.954544798 1.025463484 0.970468133 0.882147987 1.271210028 1.202994328 1.27223199 1.431617024 0.97519445 1 11.6489175 -8.748637815 24.64140556 0.975249522 1.286384886 0.862425931 0.063820393 52.0280177 100146.6504 0.009131711 0.018164932 1.78E-09 8.748637815 0.311135364 VFEEDALSWEDKLNR ddPTM_HeLa_Romidepsin_16h_R1 1 VFEEDALSWEDKLNR 15 1 Q14204 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 157.5 0.00039456 7540600 776.51 777.09 666.15 1027 623.93 784.54 768.21 973.48 848.34 989.42 FALSE FALSE TRUE 767.0455974 788.0298934 677.7440613 1145.746572 592.0885239 734.410426 833.4617382 1001.646108 772.4623457 963.7147258 0.79592599 0.817700376 0.70326212 1.188885613 0.614381526 0.762062057 0.864842796 1.039359554 0.801546687 1 9.91246234 -12.36843056 1.075396648 1.000612453 0.840379154 0 0.166325941 0.845441705 1.738942707 0.102450827 0.026113583 4.28E-13 12.36843056 -0.1602333 VFEVSLADLQNDEVAFR ddPTM_HeLa_Romidepsin_16h_R1 1 VFEVSLADLQNDEVAFR 17 0 D6RAT0;P61247;D6RG13;H0Y8L7;D6RB09;E9PFI5;D6RGE0;D6RI02;D6RED7;D6RAS7 D6RAT0 RPS3A 40S ribosomal protein S3a 0 0 201.09 5.00E-18 6038100 1846.8 2175.3 1899.4 1746.5 2094 1698.3 1754.9 1893.6 2125.5 1723.4 FALSE FALSE TRUE 1824.290491 2205.92393 1932.45826 1948.438548 1987.135366 1589.784111 1903.961162 1948.388328 1935.389957 1678.62582 1.086776142 1.314124866 1.151214427 1.160734289 1.183786966 0.94707474 1.134237982 1.160704372 1.152960912 1 10.71306496 -11.00077198 1.584102191 1.023389723 1.143544468 0.021153398 0.094845395 0.335412358 1.727382104 0.020112189 0.017529254 9.98E-12 11.00077198 0.120154746 VFLLGEEVAQYDGAYK ddPTM_HeLa_Romidepsin_16h_R1 1 VFLLGEEVAQYDGAYK 16 0 P11177-3;P11177-2;P11177;F8WF02;C9J634 P11177-3 PDHB "Pyruvate dehydrogenase E1 component subunit beta, mitochondrial" 0 0 136.38 0.012721 3545600 420.97 456.21 467.23 520.05 552.09 558.69 456.81 443.4 636.56 361.71 FALSE FALSE TRUE 415.8390557 462.6325364 475.3619422 580.1806279 523.9147872 522.9915121 495.61143 456.2290794 579.6244793 352.3127221 1.180312347 1.313130374 1.349261359 1.646777399 1.487073144 1.484452531 1.406737251 1.294954882 1.645198833 1 8.460712761 -10.35418059 0.934571712 1.049406531 1.462698512 0 0.208936435 0.169662273 0.297558977 0.022768253 0.025766338 4.42E-11 10.35418059 0.413291981 VFNTTPDDLDLHVIYDVSHNIAK ddPTM_HeLa_Romidepsin_16h_R1 1 VFNTTPDDLDLHVIYDVSHNIAK 23 0 Q9Y3I0 Q9Y3I0 RTCB tRNA-splicing ligase RtcB homolog 0 0 46.35 0.026531 5766800 2798.3 2531 2807 3286.7 2986.2 3079.2 2812.3 3248.9 3370.7 2939.3 FALSE FALSE TRUE 2764.193243 2566.631484 2855.854658 3666.723718 2833.803071 2882.449058 3051.176692 3342.901796 3069.21615 2862.936562 0.965509778 0.896503093 0.997526349 1.280756188 0.989823913 1.006815553 1.065750716 1.167647876 1.072051749 1 11.48327999 -9.497353645 24.9173254 0.975302719 1.093652775 0.303613962 0.087096634 634.8811954 619765.0855 0.012293616 0.018731779 3.18E-10 9.497353645 0.118350055 VFPLS(ph)PASNLR ddPTM_HeLa_Romidepsin_16h_R1 2 VFPLSPASNLR 11 0 Q5VWN6;A0A2R8YH03;J3KPH3 Q5VWN6 FAM208B Protein FAM208B 1 0 VFPLS(0.993)PAS(0.007)NLR;VFPLS(0.769)PAS(0.231)NLR ; 110.98 0.014124 21325900 3693.1 3557.8 3393.7 3705.43 3896.2 4337.8 3685.8 3402.2 4242.1 4123.5 TRUE FALSE FALSE 3648.087077 3607.886802 3452.765925 4133.869251 3697.362375 4060.62858 3998.87176 3500.637289 3862.675951 4016.370876 0.908304335 0.898295231 0.859673081 1.029254862 0.920572948 1.011019327 0.995643053 0.871592141 0.961732886 1 11.97167678 VFS(ph)GLVSTGLK ddPTM_HeLa_Romidepsin_16h_R1 2 VFSGLVSTGLK 11 0 P13639 P13639 EEF2 Elongation factor 2 1 0 VFS(0.981)GLVS(0.006)T(0.013)GLK;VFS(0.999)GLVS(0.001)TGLK ; 111.79 0.013755 22792800 3125.2 3219.53 3326.3 2849.8 3209.8 3734.7 2825.5 2998.1 3554.2 3248.67 TRUE FALSE FALSE 3087.10886 3264.854628 3384.192856 3179.307285 3045.991929 3496.064723 3065.497899 3084.845293 3236.30345 3164.269085 0.975615151 1.031787923 1.069502234 1.004752503 0.962621018 1.10485696 0.968785466 0.974899798 1.02276493 1 11.62765657 -10.26279706 24.99361009 0.988484932 1.017774457 0.01316532 0.044020995 230.5161699 4243529.876 0.007064443 0.008322284 5.46E-11 10.26279706 0.029289525 VFS(ph)LSEADSHGGHWV ddPTM_HeLa_Romidepsin_16h_R1 2 VFSLSEADSHGGHWV 15 0 H7BXG1 H7BXG1 CLEC16A 1 0 VFS(0.979)LS(0.021)EADSHGGHWV;VFS(0.801)LS(0.198)EADSHGGHWV ; 188.39 1.17E-12 5267600 1894.02 1936.55 1767.97 1991.97 3265.8 4107.7 3192.4 3382.6 2738.4 2033.21 TRUE FALSE FALSE 1870.934956 1963.812802 1798.740776 2222.290944 3099.13404 3845.231227 3463.562376 3480.470194 2493.470646 1980.386911 0.944732035 0.991630873 0.908277451 1.122149885 1.564913413 1.941656555 1.748932169 1.757469803 1.259082572 1 10.9515666 -8.714972971 2.516427879 0.970975807 1.808418852 0.914129274 0.109058407 0.026995452 0.34814845 0.008572928 0.018415555 1.93E-09 8.714972971 0.837443046 VFSGLVST(ph)GLK ddPTM_HeLa_Romidepsin_16h_R1 1 VFSGLVSTGLK 11 0 P13639 P13639 EEF2 Elongation factor 2 1 0 VFS(0.025)GLVS(0.194)T(0.78)GLK 142.97 0.0053971 20540000 3080.1 2818.9 3176.4 2009.5 2641.7 2962.7 3080.2 2739.2 3110.9 3013.6 TRUE FALSE FALSE 3042.558556 2858.584548 3231.68391 2241.847845 2506.884191 2773.393032 3341.832111 2818.45443 2832.653313 2935.306238 1.036538715 0.973862458 1.100969932 0.763752625 0.854045196 0.944839416 1.138495217 0.960190931 0.965028206 1 11.51929531 VFTCS(ph)S(ph)T(ph)LTQDKKIHT(ph)GEK ddPTM_HeLa_Romidepsin_16h_R1 1 VFTCSSTLTQDKKIHTGEK 19 2 A0A087WV98;Q86V71 A0A087WV98 ZNF429 Zinc finger protein 429 4 0 VFT(0.285)CS(0.894)S(0.826)T(0.914)LT(0.09)QDKKIHT(0.991)GEK 44.045 0.0236 11583000 2059.3 1920.3 1723.7 1669.4 1885.6 2011.7 1886.1 1745.2 2123.3 1998.4 TRUE FALSE FALSE 2034.20046 1947.334034 1753.700275 1862.423883 1789.370796 1883.158862 2046.305287 1795.694609 1933.38673 1946.48128 1.045065514 1.0004381 0.90095923 0.956815718 0.919284873 0.967468263 1.05128434 0.922533716 0.993272707 1 10.92665275 -9.986986962 24.91412459 1.021358353 0.956303696 0.312967292 0.040653486 183.8459505 351980.9836 0.006643591 0.008728634 1.03E-10 9.986986962 -0.065054658 VFTTVGSAEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 VFTTVGSAEKR 11 1 A0A0U1RQF0;P49327 A0A0U1RQF0 FASN Fatty acid synthase;[Acyl-carrier-protein] S-acetyltransferase;[Acyl-carrier-protein] S-malonyltransferase;3-oxoacyl-[acyl-carrier-protein] synthase;3-oxoacyl-[acyl-carrier-protein] reductase;3-hydroxyacyl-[acyl-carrier-protein] dehydratase;Enoyl-[acyl-carrier-protein] reductase;Oleoyl-[acyl-carrier-protein] hydrolase 0 1 ; VFTTVGSAEK(1)R;VFTTVGSAEK(1)R 181.87 1.36E-05 13683500 2092.06 1936.38 2809 2676.2 2954.9 3250.3 2115.88 2400 2460.6 1908.1 FALSE TRUE FALSE 2066.561168 1963.640408 2857.889467 2985.634836 2804.100427 3042.61632 2295.602794 2469.440213 2240.517773 1858.527287 1.111934801 1.056557212 1.537717249 1.606451978 1.508775495 1.63711146 1.235173038 1.328708075 1.205533967 1 10.85994415 -9.766391744 24.99515137 1.054612418 1.479514737 0.68727362 0.125175291 46.16128076 232981.3005 0.020023396 0.026778136 1.71E-10 9.766391744 0.424902319 VFVGGLS(ph)PDTSEEQIK ddPTM_HeLa_Romidepsin_16h_R1 2 VFVGGLSPDTSEEQIK 16 0 O14979-3;O14979-2;A0A087WUK2;O14979 O14979-3 HNRNPDL Heterogeneous nuclear ribonucleoprotein D-like 1 0 VFVGGLS(0.599)PDT(0.167)S(0.234)EEQIK;VFVGGLS(0.605)PDT(0.351)S(0.044)EEQIK ; 100.18 0.0054566 21481000 3631 4299.4 4347.8 2920.6 4539.7 4582 4040 4256.8 4016.6 4281 TRUE FALSE FALSE 3586.743975 4359.927066 4423.471635 3258.293514 4308.022169 4289.224988 4383.157499 4379.963792 3657.345236 4169.779003 0.860176036 1.045601473 1.060840786 0.781406763 1.033153595 1.028645639 1.051172615 1.050406698 0.877107692 1 12.02575521 -8.563568603 24.99945267 0.941354354 1.041971234 0.281928884 0.080757637 160.6454739 98698.39052 0.012334585 0.024669188 2.73E-09 8.563568603 0.10061688 VGDDVEFEVSSDRR ddPTM_HeLa_Romidepsin_16h_R1 3 VGDDVEFEVSSDRR 14 1 O75534-2;O75534;O75534-3;O75534-4;E9PLD4 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 0 ;; ;; 179.67 2.17E-07 34414700 7211.5 6590.7 6170.1 6819.3 5503.2 5744.5 4151.35 4345.17 7883.4 6398.5 FALSE FALSE TRUE 7123.603464 6683.484048 6277.488002 7607.779552 5222.351169 5377.44499 4503.965565 4470.890638 7178.28896 6232.266048 1.143019796 1.072400311 1.007256101 1.220708406 0.837953824 0.862839447 0.72268506 0.717378014 1.151794372 1 12.60554111 -8.617501865 5.99008516 1.073785076 0.776878096 0.806265958 0.075262935 0.075581538 3.95655944 0.011680251 0.023578721 2.41E-09 8.617501865 -0.29690698 VGDGDLS(ph)AEEIPENEVSLRR ddPTM_HeLa_Romidepsin_16h_R1 1 VGDGDLSAEEIPENEVSLRR 20 1 Q14684-2;Q14684 Q14684-2 RRP1B Ribosomal RNA processing protein 1 homolog B 1 0 VGDGDLS(0.998)AEEIPENEVS(0.002)LRR 65.425 0.0039348 36165000 483.42 590.1 529.72 621.14 504.16 573.72 496.37 675.01 423.42 537.15 TRUE FALSE FALSE 477.5278911 598.4074433 538.9395544 692.9591294 478.4308339 537.0611436 538.5316554 694.5403494 385.5482547 523.1947656 0.912715345 1.143756556 1.030093552 1.324476419 0.914441171 1.026503281 1.029313921 1.327498658 0.736911529 1 9.031204297 -10.25984829 24.99155024 0.958782246 1.104349194 0.312841861 0.143569335 154.821405 2431808.632 0.020273828 0.024123002 5.50E-11 10.25984829 0.145566949 VGDSTPVSEKPVSAAVDANASES(ph)P ddPTM_HeLa_Romidepsin_16h_R1 1 VGDSTPVSEKPVSAAVDANASESP 24 1 Q9H8Y8-2;Q9H8Y8;Q9H8Y8-3 Q9H8Y8-2 GORASP2 Golgi reassembly-stacking protein 2 1 0 VGDSTPVSEKPVSAAVDANAS(0.017)ES(0.983)P 128.33 9.33E-07 123610000 4007.2 3796.3 3451.5 3459.8 3695.6 3772.3 3016.8 3104.1 3897 3892.8 TRUE FALSE FALSE 3958.358705 3849.744411 3511.57191 3859.838355 3506.999742 3531.262205 3273.046917 3193.912236 3548.44256 3791.664495 1.043963333 1.015317789 0.926129386 1.017979929 0.924923539 0.931322434 0.863221659 0.842350962 0.935853519 1 11.8886156 -7.917162557 0.573363844 1.020154276 0.78721263 0.604825728 0.040292652 0.647793569 0.223302619 0.006348858 0.086737087 1.21E-08 7.917162557 -0.232941646 VGDVT(ph)PQVK ddPTM_HeLa_Romidepsin_16h_R1 1 VGDVTPQVK 9 0 E7ETY2;Q13428-6;Q13428-7;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 VGDVT(1)PQVK 125.72 0.0216 87808000 11249 10445 10159 11940 10308 10960 8797.3 8853.9 10006 9525.4 TRUE FALSE FALSE 11111.89286 10592.04498 10335.81313 13320.55898 9781.944296 10259.69137 9544.542442 9110.073627 9111.0383 9277.928735 1.197669564 1.141638968 1.114021613 1.435725512 1.054324147 1.105817006 1.028736339 0.981908127 0.982012102 1 13.17958705 -7.668949274 1.971879134 1.123928893 0.980071225 0.152358906 0.119713029 0.660283014 4.45087598 0.018080963 0.127863571 2.14E-08 7.668949274 -0.143857668 VGEDEDGS(ph)DEEVVHNEDIHFEPIVSLPEVEVK ddPTM_HeLa_Romidepsin_16h_R1 1 VGEDEDGSDEEVVHNEDIHFEPIVSLPEVEVK 32 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 VGEDEDGS(0.996)DEEVVHNEDIHFEPIVS(0.004)LPEVEVK 50.479 0.0046136 47675000 3545.9 2976.3 3478.6 3223.7 3626.4 3779.8 2838.1 3644.2 3847 3304.5 TRUE FALSE FALSE 3502.681207 3018.20043 3539.143574 3596.439362 3441.331276 3538.282979 3079.168143 3749.639177 3502.914685 3218.648614 1.088245915 0.937722874 1.099574386 1.11737558 1.069185142 1.099307008 0.956664897 1.164973139 1.088318455 1 11.65223937 -16.52287875 0.305055459 0.395258074 1.071159356 0 0.071545015 73.9876747 1.001016505 27.55991264 0.025217163 3.00E-17 16.52287875 0.675901282 VGEEEHVYS(ph)FPNK ddPTM_HeLa_Romidepsin_16h_R1 2 VGEEEHVYSFPNK 13 0 A0A1B0GTU4;F5GZ78;P49023;A0A1B0GU60;P49023-2;P49023-3;F5H836 A0A1B0GTU4 PXN Paxillin 1 0 VGEEEHVY(0.017)S(0.983)FPNK;VGEEEHVY(0.211)S(0.789)FPNK ; 217.19 1.18E-23 40012000 8877.6 6267.8 8148.2 9808.8 8123.2 6883.8 5692.7 5442.9 10834.7 9220.1 TRUE FALSE FALSE 8769.396397 6356.038253 8290.016003 10942.93961 7708.642792 6443.947396 6176.237796 5600.381724 9865.617296 8980.560473 0.976486537 0.707755187 0.923106751 1.218514105 0.8583699 0.717544013 0.687734114 0.623611604 1.098552515 1 13.13258977 -8.341849237 3.23168899 0.975545821 0.671511016 0.549489632 0.125056142 0.142840732 2.880710043 0.017389397 0.043229895 4.55E-09 8.341849237 -0.304034805 VGELKDDDFER ddPTM_HeLa_Romidepsin_16h_R1 2 VGELKDDDFER 11 1 P36507;A0A1B0GUL7 P36507 MAP2K2 Dual specificity mitogen-activated protein kinase kinase 2 0 0 ; ; 99.973 0.021841 31050000 8076.1 7209.5 7274.6 7217.1 8962.3 8363.4 7569.3 8578.8 8235.3 7469 FALSE FALSE TRUE 7977.665387 7310.99553 7401.211361 8051.575059 8504.920388 7829.005732 8212.236153 8827.014043 7498.714142 7274.954303 1.096593196 1.004954152 1.017355031 1.106752665 1.169068565 1.07615875 1.128836802 1.213342885 1.030757559 1 12.82872247 -9.079598555 4.412281445 1.04135322 1.140497453 0.635117572 0.041540996 0.149027319 5.322010158 0.007432526 0.012723177 8.33E-10 9.079598555 0.099144234 VGEVIVTK ddPTM_HeLa_Romidepsin_16h_R1 2 VGEVIVTK 8 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 ; ; 124.98 0.015623 6386500 7902.2 7074.7 8537.4 6236.3 7760.6 8535.6 7741.5 7348.7 8044.5 7832.5 FALSE FALSE TRUE 7805.884947 7174.297812 8685.989866 6957.370349 7364.547623 7990.202707 8399.062817 7561.32304 7324.979772 7629.010521 1.023184452 0.940396896 1.13854737 0.911962348 0.965334574 1.047344565 1.100937375 0.99112762 0.960148076 1 12.89728024 -8.073234752 11.93280962 1.0053532 1.053045008 0.107408948 0.063875605 1.606467733 259.3915807 0.008036844 0.020507563 8.45E-09 8.073234752 0.047691808 VGFQYEGTYK ddPTM_HeLa_Romidepsin_16h_R1 1 VGFQYEGTYK 10 0 P11413;P11413-3;P11413-2 P11413 G6PD Glucose-6-phosphate 1-dehydrogenase 0 0 147.4 0.024348 1014900 365.58 162.99 480.61 414.95 442.89 475.6 214.98 430.11 493.62 467.94 FALSE FALSE TRUE 361.1241703 165.2845775 488.9748154 462.9284714 420.2876706 445.2106949 233.2403958 442.5545542 449.4693909 455.7828513 0.792316274 0.362638869 1.072824074 1.015677685 0.922122606 0.976804401 0.511735786 0.970976756 0.986148096 1 8.832202835 -12.22994175 1.149622045 0.993090048 0.824895497 0.084474204 0.215676993 0.960407253 2.401919636 0.116582587 0.037979067 5.89E-13 12.22994175 -0.168194551 VGGPLAVLGPS(ph)RSSEDLAGPLPSSVSSSSTTSSKPK ddPTM_HeLa_Romidepsin_16h_R1 1 VGGPLAVLGPSRSSEDLAGPLPSSVSSSSTTSSKPK 36 2 Q9NRF2-2;Q9NRF2-3;Q9NRF2 Q9NRF2-2 SH2B1 SH2B adapter protein 1 1 0 VGGPLAVLGPS(0.28)RS(0.28)S(0.28)EDLAGPLPS(0.109)S(0.035)VS(0.012)S(0.001)S(0.001)S(0.002)TTSSKPK 60.762 0.00040553 32378000 989.13 851.08 1062.3 1566.3 790.8 1034.8 775.23 668.92 1024.6 915.67 TRUE FALSE FALSE 977.0741031 863.0615266 1080.788886 1747.402976 750.4425251 968.6796197 841.0780169 688.2741448 932.9572098 891.8807614 1.095520999 0.967687121 1.211808722 1.959233847 0.841415756 1.086108885 0.943038636 0.771710945 1.046055987 1 9.800707034 -7.453245232 1.614048577 1.108301938 0.71859074 0.142393609 0.289919305 1.237249029 4.01272911 0.042254511 0.668708594 3.52E-08 7.453245232 -0.389711198 VGGS(ph)DEEASGIPSR ddPTM_HeLa_Romidepsin_16h_R1 1 VGGSDEEASGIPSR 14 0 H7C446;A8MV53;A0A0A6YYI3;A0A0B4J1V8;Q9NQ55-2;Q9NQ55;Q9NQ55-3 H7C446 PPAN;PPAN-P2RY11 Suppressor of SWI4 1 homolog 1 0 VGGS(0.997)DEEAS(0.002)GIPS(0.001)R 101.72 0.0094358 416330000 1033.8 1040.7 765.72 929.22 833.72 707.43 879.54 536.83 1233.9 1158.7 TRUE FALSE FALSE 1021.199648 1055.351002 779.0470354 1036.660789 791.1721574 662.2275061 954.2481056 552.3623291 1123.536894 1128.596807 0.9048401 0.935100113 0.690279319 0.918539537 0.701022856 0.586770671 0.845517283 0.489423969 0.995516633 1 10.14031446 -6.29055112 0.18570077 1.040416246 1.58E-11 0.631720379 0.10279148 10.76998377 0.253558312 0.133490577 2.751314967 5.12E-07 6.29055112 -1.040416246 VGGS(ph)SVDLHR ddPTM_HeLa_Romidepsin_16h_R1 4 VGGSSVDLHR 10 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 VGGS(0.714)S(0.286)VDLHR;VGGS(0.918)S(0.082)VDLHR;VGGS(0.514)S(0.486)VDLHR;VGGS(0.994)S(0.006)VDLHR ;;; 130.69 0.0029665 104672000 21053.2 20021.3 20889.7 20658.9 28968.3 27837.6 22231.3 26012.8 22034.5 18784 TRUE FALSE FALSE 20796.5955 20303.16039 21253.27647 23047.57922 27489.93956 26058.8672 24119.62607 26765.43933 20063.67913 18295.98897 1.136675122 1.109705544 1.161635837 1.259706663 1.502511813 1.424293994 1.318301301 1.462912957 1.096616267 1 14.15923978 -9.235548034 1.502120401 1.067390476 1.420575833 0.863511135 0.060763742 0.111298808 0.491757907 0.011757228 0.02206359 5.81E-10 9.235548034 0.353185357 VGGSS(ph)VDLHR ddPTM_HeLa_Romidepsin_16h_R1 2 VGGSSVDLHR 10 0 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-11;O60716-10;O60716-8;O60716-9;O60716-7;O60716-6;O60716-4;A0A669KB05;O60716-13;O60716-21;O60716-14;O60716-12;O60716-18;O60716-17;O60716-19;A0A669KB62;O60716-16;O60716-15;O60716-23;O60716-24;O60716-20;O60716-22 O60716 CTNND1 Catenin delta-1 1 0 VGGS(0.205)S(0.795)VDLHR;VGGS(0.4)S(0.6)VDLHR ; 142.89 0.0017932 43250000 11457.6 11340.2 9667.8 10258 13743 13773.1 11136.4 12149 11430.6 9982.1 TRUE FALSE FALSE 11317.95036 11499.84763 9836.064004 11444.07823 13041.64343 12893.04336 12082.32554 12500.51215 10408.21851 9722.763603 1.164067217 1.182775608 1.011653107 1.177039646 1.341351488 1.326067761 1.242684285 1.28569537 1.070500007 1 13.24715073 -4 0.038438276 0.339843691 2.566407266 0.597598545 0.073833639 351.7170159 1.041441795 17.09916794 52.37585612 1.00E-04 4 2.226563575 VGGTSDVEVNEK ddPTM_HeLa_Romidepsin_16h_R1 1 VGGTSDVEVNEK 12 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 163.12 0.0051003 13030000 2525.6 2529 2332.1 2412.8 2574.5 2266 2217.3 2143.4 2243.3 2326.2 FALSE FALSE TRUE 2494.817016 2564.603328 2372.689222 2691.779289 2443.113658 2121.209913 2405.637407 2205.415897 2042.65363 2265.764989 1.101092579 1.131892911 1.047191229 1.18802228 1.078273197 0.936200323 1.061732977 0.973364805 0.901529347 1 11.14578251 -8.293503662 24.83148318 1.067748305 0.997562706 0.154312097 0.078046684 733.7199856 568212.0868 0.009524741 0.021299563 5.09E-09 8.293503662 -0.0701856 VGGTSDVEVNEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VGGTSDVEVNEKK 13 1 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 ; VGGTSDVEVNEK(1)K;VGGTSDVEVNEK(1)K 213.63 2.00E-22 8408000 1455.74 1477.07 1605.65 1675.87 3996.1 3625.7 3946.9 3822.8 4010.4 2875.8 FALSE TRUE FALSE 1437.996881 1497.86423 1633.595665 1869.641975 3792.164105 3394.029471 4282.149587 3933.406687 3651.69978 2801.086301 0.513371145 0.534744049 0.583200762 0.667470322 1.353819089 1.211683292 1.528746039 1.404243305 1.303672714 1 11.45177072 -8.757286335 24.51213155 0.723226457 1.373993369 0.606438253 0.238205228 36.97059057 218204.1728 0.031926546 0.062041152 1.75E-09 8.757286335 0.650766912 VGIDT(ph)PDIDIHGPEGK ddPTM_HeLa_Romidepsin_16h_R1 5 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VGIDT(1)PDIDIHGPEGK;VGIDT(1)PDIDIHGPEGK;VGIDT(1)PDIDIHGPEGK;VGIDT(1)PDIDIHGPEGK;VGIDT(1)PDIDIHGPEGK ;;;; 165.3 1.64E-05 195803300 20512.9 31730.4 15054.9 18915.2 18767.1 11463.7 7861 11101.3 17797.4 20540.8 TRUE FALSE FALSE 20262.88088 32177.1014 15316.92422 21102.26442 17809.34486 10731.20657 8528.713144 11422.4986 16205.55597 20007.14705 1.012782124 1.608280347 0.765572631 1.054736308 0.890149146 0.536368656 0.426283324 0.57092091 0.809988347 1 14.28822784 -8.351572503 2.492563163 1.039549309 0.487680794 0.547605989 0.21575395 0.152341817 1.831624386 0.028747701 0.07658024 4.45E-09 8.351572503 -0.551868515 VGIDTPDIDIHGPEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VGIDTPDIDIHGPEGK 16 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 94.487 0.0043274 4769100 8372.3 7530.8 8140.1 7466.9 8065.8 7305.3 6561.1 6645.1 8265.3 8320.3 FALSE FALSE TRUE 8270.255187 7636.8188 8281.775026 8330.258111 7654.172128 6838.514907 7118.39967 6837.365484 7526.030867 8104.137407 1.020497898 0.942335799 1.021919374 1.027901884 0.944477092 0.843830079 0.878366113 0.843688247 0.928665259 1 12.98444292 -8.46421458 3.259454857 1.006300378 0.85791989 0.739693996 0.034876195 0.059010884 1.234421412 0.003593635 0.008398743 3.43E-09 8.46421458 -0.148380488 VGINYQPPTVVPGGDLAK ddPTM_HeLa_Romidepsin_16h_R1 1 VGINYQPPTVVPGGDLAK 18 0 Q9BQE3;F5H5D3;P0DPH7;P0DPH8;P0DPH7-2;A0A1W2PQM2;Q9NY65;C9J2C0;Q9NY65-2;Q6PEY2;V9GZ17;Q71U36-2;Q71U36;P68363;P68363-2;P68366-2;P68366 Q9BQE3;Q71U36-2;P68366-2 TUBA1C;TUBA8;TUBA3E;TUBA1A;TUBA1B;TUBA4A Tubulin alpha-1C chain;Tubulin alpha-8 chain;Tubulin alpha-3E chain;Tubulin alpha-1A chain;Tubulin alpha-1B chain;Tubulin alpha-4A chain 0 0 134.61 2.41E-08 415890 237.71 81.607 164.12 212.82 0 201.02 136.55 0 228.51 157.47 FALSE FALSE TRUE 234.8126991 82.75586549 166.9764398 237.4272497 0 188.1754708 148.1485536 0 208.0714933 153.3789067 1.530932148 0.539551802 1.088653214 1.547978499 0 1.226866685 0.965899137 0 1.356584799 1 7.260956281 -7.502146096 0.492517377 1.212814473 1.26E-19 0.24591648 0.469771908 3.941067529 0.74459397 0.102770876 2.634058218 3.15E-08 7.502146096 -1.212814473 VGK(ac)FPFAANSR ddPTM_HeLa_Romidepsin_16h_R1 1 VGKFPFAANSR 11 1 E9PEX6;P09622-2;P09622-3;P09622 E9PEX6 DLD "Dihydrolipoyl dehydrogenase;Dihydrolipoyl dehydrogenase, mitochondrial" 0 1 VGK(1)FPFAANSR 140.78 0.0040068 1093700 124.66 146.15 416.29 239.46 340.5 525.67 283.56 176.56 224.79 117.73 FALSE TRUE FALSE 123.140596 148.2075035 423.5353528 267.1474919 323.1230144 492.0813835 307.6455793 181.668485 204.6842194 114.6713576 1.073856615 1.292454425 3.693471165 2.329679332 2.81781799 4.291231862 2.68284588 1.584253372 1.784963775 1 6.841361273 -9.857445344 6.479623412 1.044310625 2.919991879 0.534793386 0.72466444 0.099426357 5.711949545 0.108263955 0.142903571 1.39E-10 9.857445344 1.875681255 VGKEDSSSAEFLEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 VGKEDSSSAEFLEKR 15 2 H0YK42;Q13596-2;Q13596;Q13596-3 H0YK42 SNX1 Sorting nexin-1 0 1 VGKEDSSSAEFLEK(1)R 113.43 0.0027301 971020 121.22 156.53 58.656 219.23 149.95 306.02 422.56 360.82 53.493 163.11 FALSE TRUE FALSE 119.742524 158.7336334 59.67688307 244.5784041 142.297492 286.4663096 458.4522359 371.2597574 48.7084521 158.8723787 0.753702595 0.999126687 0.375627806 1.539464608 0.89567169 1.803122179 2.885663573 2.336842694 0.306588549 1 7.311724511 -8.054232302 2.571326824 0.897669189 2.619159507 0.799707585 0.357543576 0.072289008 0.932032196 0.040737646 0.136543703 8.83E-09 8.054232302 1.721490319 VGLQVVAVK ddPTM_HeLa_Romidepsin_16h_R1 1 VGLQVVAVK 9 0 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 0 151.27 0.027575 23924000 3072.7 2569.8 3710.5 3096.7 3151.6 3157.8 3057.8 2655.2 3028.8 2228.8 FALSE FALSE TRUE 3035.248751 2605.977712 3775.079696 3454.755024 2990.762092 2956.026771 3317.529456 2732.024023 2757.896542 2170.895455 1.398155192 1.200416034 1.738950481 1.591396314 1.377662883 1.361662426 1.528184809 1.258477932 1.270395834 1 11.08407454 -11.9346306 0.574991226 0.963435617 1.454195657 0.289718737 0.168353357 0.585560606 0.32949342 0.146778406 0.036899475 1.16E-12 11.9346306 0.49076004 VGLQVVAVK(ac)APGFGDNRK ddPTM_HeLa_Romidepsin_16h_R1 1 VGLQVVAVKAPGFGDNRK 18 2 P10809 P10809 HSPD1 "60 kDa heat shock protein, mitochondrial" 0 1 VGLQVVAVK(1)APGFGDNRK 117.2 2.74E-07 0 0 0 0 0 0 54.434 0 190.71 0 0 FALSE TRUE FALSE 0 0 0 0 0 50.95584308 0 196.227893 0 0 0 VGLSPDS(ph)PAGDR ddPTM_HeLa_Romidepsin_16h_R1 1 VGLSPDSPAGDR 12 0 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 0 VGLS(0.001)PDS(0.999)PAGDR 131.79 0.0033636 2832100 1391.8 1343.5 1555.3 1297.4 1541.5 1547.4 1360.2 1332.9 1574.1 1620.8 TRUE FALSE FALSE 1374.836206 1362.413828 1582.369344 1447.411492 1462.831503 1448.526134 1475.735354 1371.465359 1433.308554 1578.691382 0.870870787 0.863002005 1.002329753 0.916842588 0.926610178 0.917548642 0.934783942 0.86873557 0.907909278 1 10.62451345 -10.73250781 0.009660229 1.863193129 1.05E-06 0.04702908 0.045668797 1733.817181 12.40511923 1205.362038 1186.123162 1.85E-11 10.73250781 -1.863192081 VGLSPDS(ph)PAGDRNSVGSEGSVGSIR ddPTM_HeLa_Romidepsin_16h_R1 1 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 0 VGLS(0.01)PDS(0.882)PAGDRNS(0.087)VGS(0.016)EGS(0.004)VGSIR 62.707 0.0013532 21257000 1565.9 1182.8 1147 1129 1322.8 972.1 928.76 1268.4 1298.3 1044.4 TRUE FALSE FALSE 1546.814208 1199.451489 1166.963054 1259.540292 1255.29258 909.9859473 1007.648851 1305.099153 1182.176796 1017.266337 1.520559711 1.179092874 1.147155873 1.238161773 1.233986159 0.894540509 0.990545754 1.282947351 1.162111389 1 9.990481735 -8.354887659 11.56418094 1.237191744 1.049525743 0.163643144 0.153514735 1.02483515 122.9527847 0.030001258 0.06710379 4.42E-09 8.354887659 -0.187666 VGLSPDSPAGDRNS(ph)VGSEGSVGSIR ddPTM_HeLa_Romidepsin_16h_R1 1 VGLSPDSPAGDRNSVGSEGSVGSIR 25 1 Q8WXE0-2;Q8WXE0 Q8WXE0-2 CASKIN2 Caskin-2 1 0 VGLS(0.005)PDS(0.189)PAGDRNS(0.371)VGS(0.371)EGS(0.061)VGS(0.004)IR 48.852 0.016378 26085000 1245.6 1099.2 902.31 958.41 1153.5 1147.8 885.03 895.84 1120.8 1113.4 TRUE FALSE FALSE 1230.418148 1114.674566 918.014327 1069.225874 1094.632591 1074.459284 960.2044261 921.759717 1020.552841 1084.473707 1.134576283 1.027848401 0.846506762 0.985939877 1.00936757 0.990765638 0.885410517 0.84996041 0.941058168 1 10.08277936 -9.969622072 13.25019487 1.064479559 0.935384465 0.253646627 0.072865882 1.00630045 437.6205699 0.011896115 0.015627561 1.07E-10 9.969622072 -0.129095094 VGLVEDSPSTAGDGDDSPVVSLTVPSTS(ph)PPSSSGLSR ddPTM_HeLa_Romidepsin_16h_R1 2 VGLVEDSPSTAGDGDDSPVVSLTVPSTSPPSSSGLSR 37 0 B4DF77;Q6VY07;Q6VY07-2 B4DF77 PACS1 Phosphofurin acidic cluster sorting protein 1 1 0 VGLVEDSPSTAGDGDDSPVVS(0.025)LT(0.001)VPS(0.024)T(0.071)S(0.665)PPS(0.125)S(0.042)S(0.042)GLS(0.004)R;VGLVEDSPSTAGDGDDS(0.013)PVVS(0.024)LT(0.003)VPS(0.124)T(0.255)S(0.556)PPS(0.005)S(0.002)S(0.01)GLS(0.008)R ; 109.8 2.97E-23 9279400 2979.3 2613.4 2449.5 2581.8 3162.4 3477.9 2632.3 3396.8 3407.6 2950.2 TRUE FALSE FALSE 2942.987146 2650.191514 2492.13252 2880.319864 3001.010927 3255.673414 2855.887496 3495.081049 3102.815722 2873.553379 1.024163034 0.922269805 0.867265087 1.002354745 1.044355379 1.132978228 0.993852252 1.21629237 1.079783568 1 11.48862013 -4.00000009 0.692014622 0.996104666 24.62030444 0.443028159 0.070429823 185.3271392 0.94706364 0.0113304 6775.058712 1.00E-04 4.00000009 23.62419977 VGMVETNS(ph)QDRPVDDVK ddPTM_HeLa_Romidepsin_16h_R1 1 VGMVETNSQDRPVDDVK 17 1 Q9Y3C6 Q9Y3C6 PPIL1 Peptidyl-prolyl cis-trans isomerase-like 1 1 0 VGMVET(0.001)NS(0.999)QDRPVDDVK 105.63 0.0092983 6364500 1512.9 1548.8 1179.1 1489.8 1519.8 1979.1 1804.2 1570.5 1560.9 1448.1 TRUE FALSE FALSE 1494.460193 1570.604047 1199.621741 1662.057686 1442.238935 1852.641897 1957.448703 1615.93994 1421.289195 1410.478153 1.059541539 1.113525965 0.850507141 1.178364714 1.022517741 1.313485 1.38779087 1.145668181 1.007664806 1 10.4619686 -8.262815515 24.96099536 1.032863309 1.292862313 0.578945489 0.097245801 55.85098879 1013062.975 0.012635829 0.029788344 5.46E-09 8.262815515 0.259999005 VGNES(ph)PVQELK ddPTM_HeLa_Romidepsin_16h_R1 4 VGNESPVQELK 11 0 Q5JSH3-2;Q5JSH3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK;VGNES(1)PVQELK ;;; 193.15 9.26E-09 885311000 23785.4 23425.5 22517.5 18824.4 25655.5 23884.4 23644.3 24794.6 23974.4 23582.9 TRUE FALSE FALSE 23495.4944 23755.2848 22909.40764 21000.9657 24346.2041 22358.26392 25652.64625 25511.99263 21830.06962 22970.21286 1.022867944 1.034177826 0.997352867 0.914269529 1.059903287 0.973359022 1.116778778 1.110655473 0.950364272 1 14.48747661 -7.751499323 24.99890289 1.006330609 1.113717193 0.564419057 0.040930442 102.0373718 256615.1879 0.004833874 0.017659311 1.77E-08 7.751499323 0.107386585 VGNES(ph)PVQELKQDVSK ddPTM_HeLa_Romidepsin_16h_R1 2 VGNESPVQELKQDVSK 16 1 Q5JSH3-2;Q5JSH3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 VGNES(1)PVQELKQDVSK;VGNES(0.998)PVQELKQDVS(0.002)K ; 96.379 0.0029008 36012000 5426.4 5302.5 3708.6 7309.1 5428 5214.5 4819.7 5106.1 5154.8 4680.6 TRUE FALSE FALSE 5360.26095 5377.148734 3773.146627 8154.212532 5150.988905 4881.310279 5229.085198 5253.836947 4693.741778 4558.997337 1.17575435 1.179458626 0.827626416 1.788597783 1.129851264 1.070698208 1.146981411 1.15241062 1.029555718 1 12.15450085 -12.09469532 0.514374126 0.970259446 1.194365509 0.084016516 0.225872507 2.735358366 1.095104068 0.302480498 0.058701443 8.04E-13 12.09469532 0.224106063 VGPAT(ph)PSAQVGK ddPTM_HeLa_Romidepsin_16h_R1 2 VGPATPSAQVGK 12 0 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 VGPAT(0.981)PS(0.019)AQVGK;VGPAT(0.899)PS(0.101)AQVGK ; 136.01 0.0054111 163774000 15119.4 14552.6 15149.7 8913.9 13163.4 15024.3 12620.6 13601.5 14541 13991.4 TRUE FALSE FALSE 14935.11894 14757.47188 15413.37417 9944.567059 12491.62258 14064.29572 13692.59345 13995.03794 13240.41654 13627.90141 1.095922144 1.082886604 1.131015973 0.729721089 0.916621144 1.032022121 1.004747029 1.026940064 0.971566798 1 13.7342758 VGRPTASK(ac)ASK ddPTM_HeLa_Romidepsin_16h_R1 2 VGRPTASKASK 11 2 Q9H1E3;Q9H1E3-2 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 1 ; VGRPTASK(1)ASK;VGRPTASK(1)ASK 106.79 0.010421 27317000 954.11 711.29 2984.7 3097.2 10111.4 16293.6 12669.4 6593.7 936.96 490.5 FALSE TRUE FALSE 942.4809403 721.3035593 3036.647451 3455.312837 9595.377527 15252.49155 13745.53852 6784.478306 853.1559509 477.7567393 1.972721393 1.509771605 6.356053618 7.232368594 20.0842327 31.92522531 28.77099869 14.20069619 1.78575388 1 8.900132414 -8.801921749 2.136313137 1.817781744 25.58482884 0.83531944 4.512183069 0.080336528 0.747354718 0.665404663 1.418630129 1.58E-09 8.801921749 23.7670471 VGS(ph)AQPSPPDDLDAGGLAQR ddPTM_HeLa_Romidepsin_16h_R1 2 VGSAQPSPPDDLDAGGLAQR 20 0 Q8N3D4;E9PIH6;A0A0U1RQH4;H0YDZ9 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 VGS(0.981)AQPS(0.019)PPDDLDAGGLAQR;VGS(0.861)AQPS(0.139)PPDDLDAGGLAQR ; 136.33 0.0002728 16472400 2706.3 2686.5 3140 3157.5 3020.3 3503.2 2887.6 3171.9 3446.1 2840.17 TRUE FALSE FALSE 2673.314575 2724.320618 3194.650383 3522.585006 2866.162821 3279.356826 3132.872672 3263.673922 3137.872185 2766.381974 0.966357719 0.984795536 1.154811741 1.273354526 1.036069078 1.185431678 1.13248015 1.179762575 1.134287389 1 11.43378466 -9.758682033 7.690833221 0.983602462 1.159938935 0.432807929 0.072995557 0.048369716 19.47341869 0.00830455 0.011374817 1.74E-10 9.758682033 0.176336472 VGS(ph)ESEDEDLLSELELADR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSESEDEDLLSELELADR 19 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 VGS(0.865)ES(0.135)EDEDLLSELELADR 148.36 3.43E-11 0 0 0 0 0 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 0 0 0 0 0 0 0 VGS(ph)LDNVGHLPAGGAVK ddPTM_HeLa_Romidepsin_16h_R1 4 VGSLDNVGHLPAGGAVK 17 0 E7EVA0;P27816;P27816-6;P27816-2;P27816-5;P27816-4;H7C4C5;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK;VGS(1)LDNVGHLPAGGAVK ;;; 210.98 1.97E-26 807502000 30175.8 30778.8 29871.5 30675.6 37597.7 40516.5 38199 41406 31616.4 29040.7 TRUE FALSE FALSE 29808.00574 31212.10475 30391.40093 34222.45721 35678.94907 37927.62641 41443.62211 42604.01728 28788.55 28286.21843 1.053799603 1.103438582 1.074424317 1.209863287 1.261354506 1.340851783 1.465152446 1.506175786 1.01775888 1 14.7878117 -8.042124908 0.472435576 1.011907725 1.684363679 0.985044962 0.021438324 0.18386521 0.04369291 0.005123837 0.060478787 9.08E-09 8.042124908 0.672455954 VGS(ph)PATVTFQQNK ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPATVTFQQNK 13 0 E7ETD6;E9PE19;A0A2R8Y7Q1;Q12830-4;Q12830;F5GXF5;Q12830-2;J3QQK4 E7ETD6 BPTF Nucleosome-remodeling factor subunit BPTF 1 0 VGS(0.99)PAT(0.009)VT(0.001)FQQNK 100.02 0.012727 9987300 2070.1 1906.2 2128 1824 2036.1 2078.1 1838.8 2115.9 1881.2 1651.7 TRUE FALSE FALSE 2044.868825 1933.035534 2165.036947 2034.899462 1932.190219 1945.316117 1994.987626 2177.120228 1712.94076 1608.788596 1.271061238 1.201547263 1.345756026 1.264864425 1.201021827 1.209180698 1.240055798 1.353266821 1.064739497 1 10.65175904 -12.22889251 0.681833919 0.974064902 1.261292647 0.733501993 0.054556284 0.326532194 0.235780965 0.055248028 0.011039397 5.90E-13 12.22889251 0.287227745 VGS(ph)PGDAGLSIIGPR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPGDAGLSIIGPR 15 0 Q5TAT6-9;Q5TAT6-4;Q5TAT6-3;Q5TAT6-8;Q5TAT6-7;Q5TAT6-2;Q5TAT6-5;Q5TAT6-6;Q5TAT6 Q5TAT6-9 COL13A1 Collagen alpha-1(XIII) chain 1 0 VGS(0.975)PGDAGLS(0.025)IIGPR 81.017 0.029908 1917700 725.18 561.21 640.8 574.58 647.54 557.67 543.74 532.17 684.68 639.86 TRUE FALSE FALSE 716.3412272 569.1107291 651.9528552 641.0156431 614.4936175 522.0366868 589.925262 547.5674993 623.440506 623.236345 1.149389366 0.913153948 1.046076437 1.028527377 0.985972051 0.837622342 0.946551444 0.878587239 1.000327582 1 9.283635559 -8.570923388 2.46717921 1.055251213 0.893283322 0.410031129 0.065349778 0.191521927 2.342298811 0.011221755 0.026142782 2.69E-09 8.570923388 -0.161967891 VGS(ph)PLDYSLVDLPSTNGQS(ph)PGK ddPTM_HeLa_Romidepsin_16h_R1 2 VGSPLDYSLVDLPSTNGQSPGK 22 0 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 2 0 VGS(0.976)PLDYS(0.024)LVDLPSTNGQS(1)PGK;VGS(0.999)PLDYS(0.001)LVDLPS(0.003)T(0.007)NGQS(0.99)PGK ; 162.52 4.62E-08 11801200 3361.7 3409.6 3452.1 1957.12 2601.18 2299 1697.99 2189.87 3423.9 3007.2 TRUE FALSE FALSE 3320.726307 3457.600438 3512.182352 2183.411423 2468.432078 2152.10132 1842.217228 2253.230433 3117.657809 2929.07251 1.133712564 1.180442077 1.199076615 0.745427577 0.842735053 0.734738151 0.628942173 0.769264136 1.064383964 1 11.51622819 -9.248837665 24.59161994 1.084677824 0.742763116 0.858617848 0.074811675 215.2225738 419996.0427 0.013603934 0.022458136 5.64E-10 9.248837665 -0.341914708 VGS(ph)PLDYSLVDLPSTNGQS(ph)PGKAIENLIGKPTEK ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPLDYSLVDLPSTNGQSPGKAIENLIGKPTEK 34 2 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 2 0 VGS(0.925)PLDY(0.029)S(0.046)LVDLPS(0.288)T(0.26)NGQS(0.452)PGKAIENLIGKPTEK 56.574 0.00063331 3067700 776.98 468.54 456.16 1015.1 489.49 534.44 321.67 460.47 710.19 573.76 TRUE FALSE FALSE 767.5098689 475.1361184 464.0992734 1132.470638 464.5094988 500.2910088 348.9926418 473.7929729 646.6688277 558.8536325 1.373364731 0.850197781 0.830448702 2.026417245 0.831182749 0.895209371 0.624479509 0.847794387 1.157134516 1 9.126326671 -8.559443978 24.99997339 1.187600016 0.787773833 0.272451876 0.325184873 176.2422899 120497.79 0.047180372 0.094360945 2.76E-09 8.559443978 -0.399826183 VGS(ph)PLTLTDAQTR ddPTM_HeLa_Romidepsin_16h_R1 2 VGSPLTLTDAQTR 13 0 A0A0D9SF60;Q99569-2;Q99569 A0A0D9SF60 PKP4 Plakophilin-4 1 0 VGS(1)PLTLTDAQTR;VGS(0.996)PLT(0.004)LTDAQTR ; 206.45 1.08E-16 96836000 4318.1 4838.1 4514.4 3673.9 4182.5 4187.1 3644.7 3946.6 4209.1 4285.4 TRUE FALSE FALSE 4265.469336 4906.210899 4592.971238 4098.693604 3969.051418 3919.557823 3954.280727 4060.788644 3832.627554 4174.06469 1.021898234 1.175403656 1.100359381 0.981943 0.950884021 0.939026612 0.947345339 0.972861933 0.918200325 1 12.02723724 -9.015654833 15.35506259 1.032156104 0.953094765 0.31128799 0.063184891 4.677054823 4589.136132 0.009068208 0.015452753 9.65E-10 9.015654833 -0.079061338 VGS(ph)PQPSSSGGEK ddPTM_HeLa_Romidepsin_16h_R1 2 VGSPQPSSSGGEK 13 0 V9GYB6;O94761 V9GYB6 RECQL4 ATP-dependent DNA helicase Q4 1 0 VGS(0.999)PQPS(0.001)SSGGEK;VGS(0.994)PQPS(0.005)S(0.001)SGGEK ; 134.37 0.0017555 37077000 5743.6 5773.7 6886.7 5712.7 5204.8 7070.5 7602 3783.5 6551.6 6180.4 TRUE FALSE FALSE 5673.594794 5854.9823 7006.560125 6373.229253 4939.179634 6618.717869 8247.71369 3892.969603 5965.608487 6019.832317 0.942483859 0.972615513 1.163912839 1.058705445 0.820484587 1.099485421 1.370090271 0.646690705 0.990992468 1 12.55550759 -9.923140084 24.99985857 0.972023833 1.040141834 0.014268889 0.182515679 112.9601891 36737.67677 0.027374646 0.035977912 1.19E-10 9.923140084 0.068118001 VGS(ph)PSGDAASSTPPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPSGDAASSTPPSTR 17 0 F8WEJ1;C9JF34;C9J222;F8WB78;F8WDE4;Q9H980;Q6PIY2;Q9NP87-2;Q9NP87;Q9NP87-3 F8WEJ1 POLM DNA-directed DNA/RNA polymerase mu 1 0 VGS(0.653)PS(0.087)GDAAS(0.087)S(0.087)T(0.087)PPSTR 82.578 0.016157 19434000 1135.7 1195.6 1376.4 1086.4 1374.8 1557.5 1482.7 1393.2 1260.5 1423.4 TRUE FALSE FALSE 1121.857652 1212.431688 1400.355665 1212.01468 1304.638826 1457.980777 1608.640501 1433.510044 1147.757723 1386.419863 0.80917598 0.874505423 1.010051646 0.874204642 0.941012792 1.051615615 1.160283796 1.03396531 0.827857241 1 10.43714851 -8.227994995 3.006505426 0.910906107 1.098621129 0.592242623 0.067967772 0.16692805 3.021950527 0.011753459 0.032490407 5.92E-09 8.227994995 0.187715021 VGSES(ph)EDEDLLSELELADR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSESEDEDLLSELELADR 19 0 Q5SXM2 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 VGS(0.001)ES(0.999)EDEDLLSELELADR 205.78 1.96E-21 3893900 0 0 150.16 152.05 175.44 130.12 157.08 58.112 0 59.635 TRUE FALSE FALSE 0 0 152.7734718 169.6307364 166.4866421 121.8057519 170.4223713 59.79337903 0 58.0856741 0 0 2.630140291 2.920354098 2.866225532 2.097001607 2.933982844 1.029399761 0 1 5.860110485 -9.755971643 24.99760321 0.474999968 2.465858255 0.745139204 0.613592723 55.55612349 253992.5034 0.101131517 0.140680539 1.75E-10 9.755971643 1.990858287 VGSGS(ph)LDNLGR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSGSLDNLGR 11 0 A0A2R8Y7R9;Q13136-2;Q13136;H0YDW2 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 VGS(0.003)GS(0.997)LDNLGR 139.19 0.0033097 18949000 2894.8 2629.1 2707 2825.5 3137.5 3434.6 3396.4 3838.5 3636 3219.6 TRUE FALSE FALSE 2859.517064 2666.112539 2754.114199 3152.197604 2977.381667 3215.140145 3684.890131 3949.560941 3310.787053 3135.954328 0.911849079 0.850175819 0.878237982 1.005179692 0.949434002 1.025250947 1.175045854 1.259444663 1.055751043 1 11.61468883 -7.709960479 1.537947796 0.944730458 1.28218982 0.773975736 0.05785842 0.176994383 0.659323033 0.00826165 0.069926278 1.95E-08 7.709960479 0.337459363 VGSLPLEKGS(ph)PVTTTK ddPTM_HeLa_Romidepsin_16h_R1 1 VGSLPLEKGSPVTTTK 16 1 Q7Z2K8-2;Q7Z2K8 Q7Z2K8-2 GPRIN1 G protein-regulated inducer of neurite outgrowth 1 1 0 VGSLPLEKGS(0.696)PVT(0.262)T(0.021)T(0.021)K 127.2 0.015193 10030000 826.36 814.86 779.11 639.52 1253.8 1820.8 1073.6 1388.2 647.52 593.64 TRUE FALSE FALSE 816.2880065 826.3316205 792.6700827 713.4643114 1189.813907 1704.456756 1164.791557 1428.365377 589.6041895 578.2171472 1.411732617 1.429102586 1.370886503 1.233903759 2.057728508 2.947779679 2.014453502 2.470292318 1.019693367 1 9.175467583 -8.654543318 3.654414005 1.234061592 2.442182736 0.831005501 0.253806336 0.069749608 1.786919419 0.03871387 0.080576116 2.22E-09 8.654543318 1.208121144 up VGSPQPS(ph)SSGGEK ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPQPSSSGGEK 13 0 V9GYB6;O94761 V9GYB6 RECQL4 ATP-dependent DNA helicase Q4 1 0 VGS(0.221)PQPS(0.599)S(0.176)S(0.004)GGEK 149.82 0.00076843 25142000 5244.3 5242.2 6511.9 5039 5188.3 6341.8 6795.7 3525.1 6323.5 6002.5 TRUE FALSE FALSE 5180.380454 5315.999829 6625.236888 5621.632889 4923.521691 5936.579447 7372.926588 3627.093207 5757.910323 5846.554185 0.886057033 0.909253496 1.133186605 0.961529255 0.842123674 1.015398004 1.261072138 0.620381355 0.984838272 1 12.51337087 VGSPS(ph)GDAASSTPPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPSGDAASSTPPSTR 17 0 F8WEJ1;C9JF34;C9J222;F8WB78;F8WDE4;Q9H980;Q6PIY2;Q9NP87-2;Q9NP87;Q9NP87-3 F8WEJ1 POLM DNA-directed DNA/RNA polymerase mu 1 0 VGS(0.337)PS(0.448)GDAAS(0.107)S(0.107)T(0.002)PPSTR 94.339 0.006498 18320000 997.09 1251.5 894.1 1037.3 1243.5 1395.1 1405.6 1335.9 1378.8 1142.7 TRUE FALSE FALSE 984.9370836 1269.11865 909.6614354 1157.237507 1180.039555 1305.957612 1524.991629 1374.552159 1255.476675 1113.012489 0.884929049 1.140255534 0.817296701 1.03973452 1.060221306 1.173353961 1.370147814 1.234983589 1.12799873 1 10.12025407 -8.284283577 1.441558096 0.954047844 1.309111238 0.54415943 0.104179151 0.171303542 0.659503485 0.013103606 0.049643545 5.20E-09 8.284283577 0.355063394 VGSPSGDAAS(ph)STPPSTR ddPTM_HeLa_Romidepsin_16h_R1 1 VGSPSGDAASSTPPSTR 17 0 F8WEJ1;C9JF34;C9J222;F8WB78;F8WDE4;Q9H980;Q6PIY2;Q9NP87-2;Q9NP87;Q9NP87-3 F8WEJ1 POLM DNA-directed DNA/RNA polymerase mu 1 0 VGS(0.235)PS(0.04)GDAAS(0.504)S(0.087)T(0.133)PPS(0.001)T(0.001)R 78.69 0.020094 6550600 791.92 686.04 1287.7 626.42 1017.7 1038 895.97 879.16 1197.5 1039.1 TRUE FALSE FALSE 782.2677744 695.6980891 1310.111878 698.8496278 965.7629714 971.67515 972.0736694 904.5971075 1090.392601 1012.104032 0.772912418 0.687378043 1.294443888 0.690491892 0.954213145 0.960054618 0.960448371 0.89377878 1.077352294 1 9.983141874 VGT(ph)PLATEDSGR ddPTM_HeLa_Romidepsin_16h_R1 1 VGTPLATEDSGR 12 0 F5GX28;A0A0C4DFL8;O94953 F5GX28 KDM4B Lysine-specific demethylase 4B 1 0 VGT(0.999)PLAT(0.001)EDSGR 115.37 0.018486 3624500 1360 1309.4 1112.7 1013.1 1375.2 1744.8 1500.9 2288.3 1283.8 975.14 TRUE FALSE FALSE 1343.423797 1327.833768 1132.066077 1130.239389 1305.018412 1633.312911 1628.386409 2354.50835 1168.973713 949.8057222 1.414419565 1.398005652 1.191892247 1.189969025 1.373984576 1.719628418 1.714441565 2.478936792 1.230750337 1 9.891488638 -4 0.496226139 1.192527436 40.12802831 0.889692212 0.132492866 26.71197545 0.258970439 0.034610055 1089.002481 1.00E-04 4 38.93550087 up VGTASVLQPVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VGTASVLQPVKK 12 1 Q2TAL8 Q2TAL8 QRICH1 Glutamine-rich protein 1 0 1 ; VGTASVLQPVK(1)K;VGTASVLQPVK(1)K 125.72 0.0025127 1451910 1523.15 1837.31 1638.24 1461.37 2470.2 2351.28 2450.9 1610.98 3340.5 2483.82 FALSE TRUE FALSE 1504.585262 1863.175698 1666.75288 1630.340475 2344.136476 2201.040796 2659.079385 1657.591165 3041.717314 2419.289998 0.621911909 0.770133262 0.688942988 0.673892124 0.968935712 0.909787912 1.099115603 0.685156044 1.257276852 1 11.240368 -6.965856633 16.3232509 0.827787252 0.170492672 0.011188323 0.200762222 1036068.157 13644096.39 0.024941631 19489843.43 1.08E-07 6.965856633 -0.65729458 VGTEGLVDS(ph)FSQGLER ddPTM_HeLa_Romidepsin_16h_R1 2 VGTEGLVDSFSQGLER 16 0 T1ECW5;O75170-6;O75170-2;O75170-4;O75170-3;O75170-5;O75170 T1ECW5 PPP6R2 Serine/threonine-protein phosphatase 6 regulatory subunit 2 1 0 VGTEGLVDS(0.984)FS(0.016)QGLER;VGTEGLVDS(0.994)FS(0.006)QGLER ; 147.53 0.00030058 12009700 2768.7 2742.6 3015.4 1794.45 2852.4 2835.6 2190.68 2604.6 2841.7 3179.8 TRUE FALSE FALSE 2734.954019 2781.210395 3067.881772 2001.932752 2706.831384 2654.414311 2376.756305 2679.959992 2587.531235 3097.188338 0.883044142 0.8979791 0.990537687 0.646371009 0.873964089 0.857040006 0.767391597 0.865288029 0.835445234 1 11.5967434 -9.303000131 24.99998382 0.942234642 0.807142034 0.356000071 0.07765274 341.3392036 205324.4307 0.01133916 0.017320939 4.98E-10 9.303000131 -0.135092608 VGVNGFGR ddPTM_HeLa_Romidepsin_16h_R1 2 VGVNGFGR 8 0 P04406 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ; ; 114.72 0.016911 3769300 3668.3 3404.6 3258.1 4422.7 4811.3 4268.2 3848.2 3669.2 4030.5 3143.8 FALSE FALSE TRUE 3623.589349 3452.530048 3314.805864 4934.073383 4565.761408 3995.475795 4175.066012 3775.362513 3670.001985 3062.123623 1.183358282 1.127495318 1.082518628 1.611324032 1.491044115 1.304805516 1.363454428 1.232922957 1.198515291 1 11.58031681 -9.289739914 24.55668042 1.092226935 1.398330956 0.618619041 0.109877678 284.4416175 246812.209 0.018274845 0.027919018 5.13E-10 9.289739914 0.306104021 VGVSSKPDSS(ph)PVLSPGNK ddPTM_HeLa_Romidepsin_16h_R1 3 VGVSSKPDSSPVLSPGNK 18 1 Q8N4C8-2;Q8N4C8-3;Q8N4C8;Q8N4C8-5;Q8N4C8-4 Q8N4C8-2 MINK1 Misshapen-like kinase 1 1 0 VGVSSKPDS(0.086)S(0.914)PVLSPGNK;VGVSSKPDS(0.033)S(0.967)PVLSPGNK;VGVSSKPDS(0.147)S(0.844)PVLS(0.009)PGNK ;; 257.72 8.73E-75 149109000 14304.3 14450.6 13593.4 15345.8 14622.4 14130.9 13794.9 13898.4 15521.9 13654.7 TRUE FALSE FALSE 14129.95369 14654.03593 13829.98742 17120.1536 13876.16436 13227.9811 14966.63846 14300.52828 14133.58239 13299.94893 1.062406613 1.101811444 1.039852672 1.287234537 1.043324635 0.994588864 1.125315484 1.075231819 1.062679448 1 13.69913309 -11.19252661 0.767375316 1.007403222 1.096235223 0.083232525 0.075849015 0.703763977 0.897679673 0.027685334 0.017371962 6.42E-12 11.19252661 0.088832001 VHAAPAAPSATALPAS(ph)PVAR ddPTM_HeLa_Romidepsin_16h_R1 1 VHAAPAAPSATALPASPVAR 20 0 H0Y5X5;Q8N5H7-3;Q8N5H7-6;Q8N5H7-5;Q8N5H7-2;Q8N5H7-4;Q8N5H7 H0Y5X5 SH2D3C SH2 domain-containing protein 3C 1 0 VHAAPAAPS(0.003)AT(0.008)ALPAS(0.989)PVAR 97.776 0.00087799 3182200 621 644.77 785.06 455.31 2301.3 2699.4 2546.9 2857.6 727.24 852.94 TRUE FALSE FALSE 613.4310131 653.847089 798.72364 507.9550845 2183.856074 2526.917052 2763.233622 2940.280147 662.193833 830.7804958 0.73837917 0.787027491 0.961413567 0.611419126 2.62868 3.041618171 3.326069445 3.539178113 0.797074361 1 9.698323536 -8.635465627 3.37637565 0.854531523 3.263463654 0.97602603 0.179665843 0.028044759 0.627269016 0.029787027 0.063061871 2.31E-09 8.635465627 2.40893213 up VHAELADVLTEAVVDSILAIK ddPTM_HeLa_Romidepsin_16h_R1 1 VHAELADVLTEAVVDSILAIK 21 0 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 0 123.42 6.91E-05 4299500 1391.3 1117.3 1083.4 1171.2 1514.4 1329.1 977.04 791.82 1280.2 1193.1 FALSE FALSE TRUE 1374.3423 1133.029379 1102.256123 1306.619655 1437.114517 1244.174799 1060.029753 814.7300624 1165.695706 1162.10309 1.18263372 0.974981814 0.948501155 1.124357784 1.236649768 1.070623433 0.91216499 0.701082434 1.003091478 1 10.18252234 -7.454791627 2.341213282 1.082932226 0.680741577 0.620319144 0.088822389 0.211880011 1.801483689 0.014192372 0.144830147 3.51E-08 7.454791627 -0.40219065 VHAELADVLTEAVVDSILAIKK ddPTM_HeLa_Romidepsin_16h_R1 1 VHAELADVLTEAVVDSILAIKK 22 1 P40227;P40227-2 P40227 CCT6A T-complex protein 1 subunit zeta 0 0 73.252 0.0013406 10111000 1041.4 1142.5 792.52 915.22 847.93 1138.9 1083.1 825.33 572.68 381.39 FALSE FALSE TRUE 1028.707016 1158.584145 806.3134782 1021.042043 804.656968 1066.127966 1175.098487 849.2096214 521.4580665 371.4814328 2.769201703 3.118821138 2.170535071 2.748568172 2.166075871 2.869936076 3.163276501 2.286008253 1.403725787 1 8.537146294 -12.18898158 0.767780913 0.910194646 2.679866205 0.717033947 0.362412387 0.268782931 0.26422461 0.293737823 0.068950622 6.47E-13 12.18898158 1.769671559 VHDRS(ph)EEEEEEEEEEEEEQPR ddPTM_HeLa_Romidepsin_16h_R1 3 VHDRSEEEEEEEEEEEEEQPR 21 1 V9GYQ9;Q5TAQ8;V9GY54;Q5TAQ9-2;Q5TAQ9 V9GYQ9 DCAF8 DDB1- and CUL4-associated factor 8 1 0 VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR;VHDRS(1)EEEEEEEEEEEEEQPR ;; 147.06 7.10E-06 83394200 2211.16 2189.75 2318.04 2100.67 2068.58 1774.37 1643.48 1613.8 2104.2 1673.91 TRUE FALSE FALSE 2184.209531 2220.577358 2358.384514 2343.559349 1963.012644 1660.993484 1783.07715 1660.492757 1915.995082 1630.421577 1.339659363 1.361965144 1.446487551 1.43739471 1.20399084 1.018750921 1.09362951 1.018443806 1.175153168 1 10.67102933 -8.307317523 6.461939302 1.225498406 1.048657345 0.345964138 0.13525306 0.310425294 33.94049593 0.026966824 0.061445135 4.93E-09 8.307317523 -0.176841061 VHELNEEIGK ddPTM_HeLa_Romidepsin_16h_R1 2 VHELNEEIGK 10 0 Q9NQ29-3;Q9NQ29;B8ZZ09;B8ZZ10;A8MYV2;Q96HJ9-2;A0A0A6YYJ8;Q9NQ29-2;Q9Y383-3;Q9Y383-2;Q9Y383 Q9NQ29-3 LUC7L;LUC7L2 Putative RNA-binding protein Luc7-like 1;Putative RNA-binding protein Luc7-like 2 0 0 ; ; 129.89 0.0034674 18547000 15701.2 14492.5 13496.7 13802.9 14037 13705.8 12379.5 12351.3 15165.3 14422.5 FALSE FALSE TRUE 15509.82774 14696.5258 13731.6044 15398.85624 13320.63951 12830.04361 13431.01442 12708.66538 13808.87759 14047.80137 1.104075102 1.046179783 0.977491355 1.096175539 0.948236607 0.913313285 0.956093702 0.904672912 0.982992087 1 13.77805673 -8.648581741 6.151861979 1.046882691 0.928537179 0.578098132 0.042947329 0.112706228 5.686005222 0.006816248 0.013724252 2.25E-09 8.648581741 -0.118345512 VHELQGNAPS(ph)DPDAVSAEEALK ddPTM_HeLa_Romidepsin_16h_R1 1 VHELQGNAPSDPDAVSAEEALK 22 0 F5H2T0;O95163 F5H2T0 IKBKAP Elongator complex protein 1 1 0 VHELQGNAPS(0.999)DPDAVS(0.001)AEEALK 66.925 0.0021091 5918300 1027.1 1258.5 876.38 1096.6 945.46 1148.9 910.34 1042.7 1279 1078.3 TRUE FALSE FALSE 1014.58131 1276.217196 891.6330263 1223.394052 897.2096482 1075.488998 987.6642569 1072.868879 1164.603037 1050.285611 0.966005151 1.215114425 0.84894339 1.164820349 0.854253014 1.023996699 0.940376834 1.021502026 1.108844132 1 10.03656599 VHFEESSKLEDLLR ddPTM_HeLa_Romidepsin_16h_R1 2 VHFEESSKLEDLLR 14 1 B1AHC9;P12956-2;P12956 B1AHC9 XRCC6 X-ray repair cross-complementing protein 6 0 0 ; ; 74.392 0.019019 18783600 9635.5 8438.9 9280.4 9342.2 11063 10608.9 9907.1 9481.2 11066.2 9785.9 FALSE FALSE TRUE 9518.05882 8557.703056 9441.921469 10422.38912 10498.41383 9931.025529 10748.60883 9755.523563 10076.41136 9531.660907 0.998572957 0.897818663 0.990585121 1.093449423 1.101425442 1.041898744 1.127674277 1.023486217 1.057151682 1 13.21851191 -9.267491929 23.81695248 0.98948507 1.079711156 0.486930572 0.045527572 145.0405426 570738.5581 0.006072243 0.009433802 5.40E-10 9.267491929 0.090226086 VHGLPTTS(ph)PSGMNMAELAQQVVK ddPTM_HeLa_Romidepsin_16h_R1 2 VHGLPTTSPSGMNMAELAQQVVK 23 0 B0QYS6;B0QYS7;P19484;B1AKB5;P19484-2 B0QYS6 TFEB Transcription factor EB 1 0 VHGLPT(0.016)T(0.285)S(0.35)PS(0.35)GMNMAELAQQVVK;VHGLPT(0.056)T(0.281)S(0.331)PS(0.331)GMNMAELAQQVVK ; 78.794 0.00014133 228088000 8560.8 7640.2 7158.4 7861.6 6769.1 5341.1 4750.8 5244.3 8835.3 7601.9 TRUE FALSE FALSE 8456.457677 7747.758936 7282.988949 8770.595182 6423.647568 4999.820948 5154.332833 5396.035546 8045.04864 7404.401542 1.142085235 1.046372066 0.983602646 1.184511014 0.867544464 0.675249839 0.696117411 0.728760524 1.086522468 1 12.85416742 -8.528276975 4.07736467 1.067102552 0.705101883 0.891348468 0.058811748 0.055949272 2.153398099 0.010017299 0.021824465 2.96E-09 8.528276975 -0.362000669 VHGS(ph)PLELK ddPTM_HeLa_Romidepsin_16h_R1 1 VHGSPLELK 9 0 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3;D6RD46 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 VHGS(1)PLELK 78.548 0.027018 15690000 5889.8 5704.8 6022.8 3855.5 6981.7 7987.8 7820 7106.5 6066.8 5635.8 TRUE FALSE FALSE 5818.012852 5785.112324 6127.624308 4301.291051 6625.397797 7477.405359 8484.230605 7312.115365 5524.170213 5489.381104 1.059866812 1.053873327 1.1162687 0.783565755 1.206948046 1.362158177 1.545571431 1.332047316 1.006337529 1 12.42242779 -8.386685225 3.074922739 1.022592338 1.431715084 0.765347702 0.100877676 0.084686552 1.514810638 0.013492979 0.033121301 4.11E-09 8.386685225 0.409122747 VHIDIGADGR ddPTM_HeLa_Romidepsin_16h_R1 5 VHIDIGADGR 10 0 P31942-4;P31942-3;P31942;P31942-5;P31942-2;P31942-6 P31942-4 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 0 0 ;;;; ;;;; 131.12 2.70E-06 31521300 16450 14202.9 18764.9 16948.1 19605.6 16274.8 14309.9 13128.2 14621.2 12887.8 FALSE FALSE TRUE 16249.50107 14402.8488 19091.49521 18907.71907 18605.05307 15234.8928 15525.38255 13508.04375 13313.44325 12552.9731 1.294474301 1.147365543 1.520874383 1.506234333 1.482123233 1.213648168 1.236789279 1.076083223 1.06058088 1 13.61574148 -11.91641521 0.664472647 0.989265466 1.324135825 0.370736045 0.145277119 0.671290104 0.530013599 0.121488253 0.034897563 1.21E-12 11.91641521 0.334870359 VHIEIGPDGR ddPTM_HeLa_Romidepsin_16h_R1 6 VHIEIGPDGR 10 0 P31943;E9PCY7;G8JLB6;H0YB39;H0YBD7;H0YBG7;P52597;P55795 P31943;P55795 HNRNPH1;HNRNPF;HNRNPH2 "Heterogeneous nuclear ribonucleoprotein H;Heterogeneous nuclear ribonucleoprotein H, N-terminally processed;Heterogeneous nuclear ribonucleoprotein F;Heterogeneous nuclear ribonucleoprotein F, N-terminally processed;Heterogeneous nuclear ribonucleoprotein H2" 0 0 ;;;;; ;;;;; 176.6 2.86E-05 130309000 24763.1 21443.7 25146.3 22640 23818.9 23317 19034.5 18981.5 21511.1 19120.9 FALSE FALSE TRUE 24461.27781 21745.58497 25583.9608 25257.74332 22603.33265 21827.11895 20651.28995 19530.69975 19587.09334 18624.13626 1.313418108 1.167602334 1.373699185 1.35618334 1.213658037 1.171980201 1.108845514 1.048676807 1.051704791 1 14.1848859 -6.166451343 15.17725741 1.177428854 1.190603632 0 0.126085443 0 0 0.020023895 0 6.82E-07 6.166451343 0.013174778 VHLVGIDIFTGK ddPTM_HeLa_Romidepsin_16h_R1 3 VHLVGIDIFTGK 12 0 I3L397;I3L504;P63241;P63241-2;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4;Q6IS14 I3L397 EIF5A;EIF5A2;EIF5AL1 Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-2;Eukaryotic translation initiation factor 5A-1-like 0 0 ;; ;; 138.75 0.00072045 21402800 7412.89 6475.89 6817.78 5643.23 6829.82 7281.03 6482.88 6812.61 7711.77 6253.16 FALSE FALSE TRUE 7322.538845 6567.057749 6936.440601 6295.726805 6481.2688 6815.795681 7033.535665 7009.722122 7022.009977 6090.702002 1.202248746 1.078210319 1.138857327 1.033661933 1.064125087 1.119049279 1.15479885 1.15088903 1.152906508 1 12.5723928 -12.59793497 1.404477656 1.000235013 1.126093624 0 0.066101469 0.324835577 1.153089316 0.038137502 0.008897518 2.52E-13 12.59793497 0.125858611 VHLVGIDIFTGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VHLVGIDIFTGKK 13 1 I3L397;I3L504;P63241;P63241-2;F8WCJ1;C9J7B5;C9J4W5;Q9GZV4;Q6IS14 I3L397 EIF5A;EIF5A2;EIF5AL1 Eukaryotic translation initiation factor 5A;Eukaryotic translation initiation factor 5A-1;Eukaryotic translation initiation factor 5A-2;Eukaryotic translation initiation factor 5A-1-like 0 1 VHLVGIDIFTGK(1)K 104.59 0.0028036 272270 68.79 196.05 0 158.55 151.97 197.66 153.38 225.22 367.09 302.41 FALSE TRUE FALSE 67.95156102 198.809997 0 176.882297 144.2144038 185.0301639 166.4080934 231.7363854 334.256551 294.5533446 0.230693565 0.674954132 0 0.600510231 0.489603688 0.628172001 0.564950616 0.786738258 1.134791226 1 8.202385124 -12.49799377 1.23767283 1.000688115 0.466973373 0.497015958 0.22380932 0.339980692 0.930052822 0.153513345 0.037066536 3.18E-13 12.49799377 -0.533714742 VHPAVVIR ddPTM_HeLa_Romidepsin_16h_R1 1 VHPAVVIR 8 0 C9JD32;J3KT29;P62829;J3QQT9;J3KTJ3 C9JD32 RPL23 60S ribosomal protein L23 0 0 71.296 0.021993 725890 545.35 652.12 996.79 785.75 1048.5 1068.3 726.82 497.22 540.85 473.88 FALSE FALSE TRUE 538.7030644 661.3005625 1014.138712 876.6021121 994.9911325 1000.039078 788.5560727 511.6062762 492.4750214 461.5685293 1.167113939 1.432724548 2.197157405 1.899180851 2.155673685 2.166610187 1.708426859 1.108408056 1.066959704 1 8.850401051 -10.03303247 3.161768155 1.079474337 1.891982587 0.579928118 0.303162091 0.128598043 2.610021095 0.052170195 0.066726469 9.27E-11 10.03303247 0.81250825 VHS(ph)PPASLVPR ddPTM_HeLa_Romidepsin_16h_R1 2 VHSPPASLVPR 11 0 Q9BTE3;Q9BTE3-2;Q9BTE3-3 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 0 VHS(1)PPASLVPR;VHS(1)PPASLVPR ; 111.31 0.0058563 31088000 4160.8 4090.4 3878.7 3192.2 3634.4 4312.2 3044.1 3350.6 4548.2 4279.2 TRUE FALSE FALSE 4110.086569 4147.984759 3946.207146 3561.297184 3448.923006 4036.664337 3302.665778 3447.544325 4141.397601 4168.025767 0.986099127 0.995191726 0.94678089 0.854432622 0.827471613 0.968483537 0.792381325 0.827140838 0.993611324 1 12.02514848 -9.415023762 2.748241993 0.993270332 0.854756889 0.703685846 0.043093707 0.112320932 1.648592072 0.006592418 0.010428107 3.85E-10 9.415023762 -0.138513443 VHSAVITVPAYFNDSQR ddPTM_HeLa_Romidepsin_16h_R1 1 VHSAVITVPAYFNDSQR 17 0 P54652 P54652 HSPA2 Heat shock-related 70 kDa protein 2 0 0 67.646 0.016447 159390000 1818.9 1864.6 2219.2 2130.2 2574.1 2865.8 2519.7 2535.2 2460.2 1785.5 FALSE FALSE TRUE 1796.730547 1890.849888 2257.824245 2376.503747 2442.734072 2682.684629 2733.723255 2608.552012 2240.15355 1739.112453 1.033130747 1.087249927 1.298262365 1.366503784 1.404586614 1.542559611 1.571907125 1.499932916 1.28810161 1 10.76413551 -9.377556657 0.855592678 1.005539291 1.544603373 0.76357363 0.096500407 0.059460009 0.086469219 0.007136478 0.014945996 4.19E-10 9.377556657 0.539064082 VHSEAIS(ph)PAPEEK ddPTM_HeLa_Romidepsin_16h_R1 1 VHSEAISPAPEEK 13 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 VHS(0.002)EAIS(0.998)PAPEEK 108.23 0.0079263 12483000 3020.8 2979.3 2745.2 3224.4 3101.6 3332.9 3264.9 3066.3 3273.5 3241.3 TRUE FALSE FALSE 2983.981328 3021.242664 2792.979054 3597.220299 2943.313778 3119.938446 3542.220525 3155.018553 2980.709961 3157.090559 0.945168114 0.956970542 0.884668654 1.139409919 0.932286776 0.988232168 1.121988888 0.999343698 0.944131917 1 11.62437993 -9.275548394 24.99261519 0.965793508 1.032571796 0.307125267 0.064234575 948.8295774 1680747.62 0.009639388 0.014766105 5.30E-10 9.275548394 0.066778288 VHVGDEDFVHLR ddPTM_HeLa_Romidepsin_16h_R1 3 VHVGDEDFVHLR 12 0 P04080 P04080 CSTB Cystatin-B 0 0 ;; ;; 189.17 2.23E-10 23758200 7603.2 7015.1 6758.15 4360.75 7639.8 8169 5915.89 7902.02 7080.4 7240.1 FALSE FALSE TRUE 7510.529274 7113.858762 6875.772766 4864.960433 7249.912498 7647.027264 6418.385549 8130.652481 6447.111291 7052.001158 1.065020993 1.008771638 0.975010158 0.689869489 1.028064564 1.084376916 0.910150949 1.152956771 0.914224366 1 12.783817 -6.766992758 0.004866525 1.970766825 1.93E-07 0 0.124393541 161681.097 107.840508 20969.12984 22732.41429 1.71E-07 6.766992758 -1.970766632 VHVIFNYK ddPTM_HeLa_Romidepsin_16h_R1 1 VHVIFNYK 8 0 P27797;K7EJB9 P27797 CALR Calreticulin 0 0 92.467 0.0065776 0 0 165.47 853.68 213.28 437.84 455.74 292.76 150.37 213.73 0 FALSE FALSE TRUE 0 167.799491 868.5379423 237.9404371 415.495391 426.6196848 317.6270271 154.7207187 194.6134535 0 0 VHVQFFDDS(ph)PTR ddPTM_HeLa_Romidepsin_16h_R1 4 VHVQFFDDSPTR 12 0 A0A087WWJ1;P52701-2;P52701;F8WAX8;C9J7Y7;A0A494C0M1;C9JH55;C9J8Y8 A0A087WWJ1 MSH6 DNA mismatch repair protein Msh6 1 0 VHVQFFDDS(0.93)PT(0.07)R;VHVQFFDDS(0.993)PT(0.007)R;VHVQFFDDS(0.764)PT(0.236)R;VHVQFFDDS(0.764)PT(0.236)R ;;; 120.21 0.0005394 83256400 12380.3 11668.2 12242.2 9985.72 11915.5 12307.4 10575.5 11313.1 12577.5 12360.8 TRUE FALSE FALSE 12229.40414 11832.46523 12455.27036 11140.31593 11307.40757 11520.99686 11473.78271 11640.4267 11452.5369 12039.66463 1.015759534 0.982790267 1.034519709 0.925301183 0.939179613 0.956920081 0.952998531 0.966839779 0.95123388 1 13.55550759 -9.259013607 24.99980545 1.007236178 0.948489766 0.487016033 0.023781871 74.41157497 766877.3697 0.00235301 0.003788392 5.51E-10 9.259013607 -0.058746412 VIDFDENTALDDAEEESFRK ddPTM_HeLa_Romidepsin_16h_R1 2 VIDFDENTALDDAEEESFRK 20 1 Q14257;Q14257-2;H0YL43 Q14257 RCN2 Reticulocalbin-2 0 0 ; ; 136.33 0.00017606 8926400 1562.45 2038.52 1515.29 1835 1979.69 1726.47 1351.73 1693.24 1982.73 1863.6 FALSE FALSE TRUE 1543.406258 2067.218338 1541.662987 2047.171334 1878.659032 1616.154139 1466.545912 1742.231228 1805.389663 1815.183403 0.850275656 1.138848193 0.849315272 1.127804127 1.034969265 0.890353083 0.807932636 0.959810025 0.994604545 1 10.82589961 -8.028944305 22.70872201 0.959241909 0.875189212 0.129239168 0.102449816 373.7460841 293230.0813 0.015111312 0.038643726 9.36E-09 8.028944305 -0.084052697 VIEEEWQQVDR ddPTM_HeLa_Romidepsin_16h_R1 2 VIEEEWQQVDR 11 0 P42166 P42166 TMPO "Lamina-associated polypeptide 2, isoform alpha;Thymopoietin;Thymopentin" 0 0 ; ; 172.21 0.0023943 10330000 1657.68 1477.09 1689.28 1470.68 1023.97 1111.4 1251.73 1418.63 1879.03 1505.89 FALSE FALSE TRUE 1637.475559 1497.884512 1718.68121 1640.726941 971.7129899 1040.385127 1358.051915 1459.675821 1710.964851 1466.766761 1.116384419 1.021215201 1.171748131 1.11860112 0.662486372 0.709305088 0.9258813 0.995165598 1.166487336 1 10.51842376 -8.777986869 24.99415264 1.06713702 0.822407223 0.613036265 0.105557207 136.0492885 205495.3475 0.016085401 0.02921638 1.67E-09 8.777986869 -0.244729797 VIET(ph)PENDFK ddPTM_HeLa_Romidepsin_16h_R1 2 VIETPENDFK 10 0 Q9H0G5;A0A024QZ33 Q9H0G5 NSRP1;CCDC55 Nuclear speckle splicing regulatory protein 1 1 0 VIET(1)PENDFK;VIET(1)PENDFK ; 145.23 0.0083901 92724000 10180.6 10737.4 10645.2 8150.7 7689.3 6951.9 6576.7 6822.4 10705 9417.5 TRUE FALSE FALSE 10056.51493 10888.5614 10830.47524 9093.122284 7296.886328 6507.696026 7135.324734 7019.79538 9747.517989 9172.831992 1.096336981 1.187044678 1.180712265 0.99131024 0.795488932 0.709453311 0.777875877 0.765281146 1.06265088 1 13.1631515 -8.800703333 3.311925445 1.069260901 0.753705502 0.879029279 0.059512466 0.077532314 1.750358195 0.011053717 0.02183754 1.58E-09 8.800703333 -0.315555399 VIFLEDDDVAAVVDGR ddPTM_HeLa_Romidepsin_16h_R1 1 VIFLEDDDVAAVVDGR 16 0 A0A6I8PRN4;A0A6I8PTT9;Q06210-2;Q06210 A0A6I8PRN4 GFPT1 Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 0 0 173.19 6.30E-05 2802700 879.18 571.04 731.32 715.28 768.3 699.26 592.4 543.82 865.32 629.64 FALSE FALSE TRUE 868.464216 579.0791161 744.0483178 797.9840391 729.0907841 654.5795428 642.7184412 559.5545737 787.923612 613.281862 1.416093105 0.944229973 1.213224072 1.301170128 1.188834742 1.067338826 1.047998451 0.912393808 1.284765881 1 9.260406473 -7.683991406 1.382876159 1.189659394 0.906408872 0.313116678 0.132170695 0.802495099 2.219971379 0.025234116 0.254471423 2.07E-08 7.683991406 -0.283250522 VIGAK(ac)K(ac)DQYFLDKK ddPTM_HeLa_Romidepsin_16h_R1 2 VIGAKKDQYFLDKK 14 3 Q9UQE7 Q9UQE7 SMC3 Structural maintenance of chromosomes protein 3 0 2 ; VIGAK(1)K(1)DQYFLDKK;VIGAK(1)K(1)DQYFLDKK 141.59 8.28E-07 1937080 369.52 613.27 612.82 487.13 600.2 364.39 260.9 452.58 441.68 583.057 FALSE TRUE FALSE 365.0161481 621.9036312 623.485875 543.4542626 569.5695543 341.106655 283.0608395 465.6746882 402.1750346 567.9090951 0.64273693 1.095076019 1.097862106 0.956938826 1.002923812 0.600636014 0.498426318 0.819981036 0.708167976 1 9.149516207 -8.248790917 24.52965856 0.888029691 0.625555611 0.382017051 0.162630621 614.5239922 1191767.154 0.027004517 0.068316371 5.64E-09 8.248790917 -0.262474081 VIGQDHDFSES(ph)SEEEAPAEASSGALR ddPTM_HeLa_Romidepsin_16h_R1 2 VIGQDHDFSESSEEEAPAEASSGALR 26 0 P23497;E9PHV6;P23497-7;P23497-5;P23497-2;P23497-3;P23497-4;P23497-6;H7C1G8;H7C4B4 P23497 SP100 Nuclear autoantigen Sp-100 1 0 VIGQDHDFS(0.003)ES(0.907)S(0.09)EEEAPAEASSGALR;VIGQDHDFS(0.015)ES(0.807)S(0.173)EEEAPAEAS(0.004)S(0.001)GALR ; 140.17 1.15E-07 8207200 1917.41 1703.99 1997.62 1616.66 1257.69 1176.37 1010.21 1289.63 2181.44 1982.4 TRUE FALSE FALSE 1894.039869 1727.978816 2032.387738 1803.585836 1193.505386 1101.203754 1096.017212 1326.943409 1986.326543 1930.896962 0.980911932 0.894909904 1.052561466 0.934066328 0.618109309 0.570306844 0.567620766 0.687216063 1.028706649 1 10.91505546 -8.78671763 4.31689138 0.98634777 0.601249613 0.931455131 0.049480525 0.032188191 1.362286453 0.006620654 0.012775811 1.63E-09 8.78671763 -0.385098157 VIHDNFGIVEGLMTTVHAITAT(ph)QK ddPTM_HeLa_Romidepsin_16h_R1 2 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 VIHDNFGIVEGLMT(0.001)T(0.001)VHAIT(0.366)AT(0.631)QK;VIHDNFGIVEGLMT(0.006)T(0.006)VHAIT(0.453)AT(0.535)QK ; 76.294 0.00011341 6122600 1392.65 1502.06 1832.35 1839.99 1851.96 2110.75 1598.37 1687.75 1660.51 1110.83 TRUE FALSE FALSE 1375.675846 1523.20604 1864.241283 2052.738301 1757.447571 1975.879887 1734.135508 1736.582383 1511.989827 1081.970476 1.271454144 1.407807397 1.723005686 1.897222102 1.624302704 1.826186509 1.602756772 1.605018271 1.397440928 1 10.07944542 -10.29058397 1.028213721 1.081942849 1.723708909 0.67423921 0.146583762 0.124947302 0.260183812 0.026190499 0.030688242 5.12E-11 10.29058397 0.64176606 VIHDNFGIVEGLMTTVHAITATQK ddPTM_HeLa_Romidepsin_16h_R1 1 VIHDNFGIVEGLMTTVHAITATQK 24 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 63.376 0.0013 5647500 732.94 691.92 485.62 748.62 688.13 883.78 638.07 697.33 776.28 479.61 FALSE FALSE TRUE 724.0066454 701.6608679 494.0720124 835.1789668 653.0121583 827.3093103 692.2676499 717.5061433 706.8475726 467.1496631 1.54983874 1.50200444 1.057631101 1.787818836 1.397864988 1.770972722 1.481896926 1.535923495 1.513107315 1 8.867741017 -14.32787373 0.287795197 4.00E-12 1.566369162 0 0.25147445 8.021008429 0.325276432 4.903455672 0.090153883 4.70E-15 14.32787373 1.566369162 VIHGK(ac)LLDMVGK ddPTM_HeLa_Romidepsin_16h_R1 2 VIHGKLLDMVGK 12 1 Q15382 Q15382 RHEB GTP-binding protein Rheb 0 1 ; VIHGK(1)LLDMVGK;VIHGK(1)LLDMVGK 60.255 0.020758 1904580 1604.94 1438.85 1648.47 1185.56 1620.94 1462.23 1066.82 1501.9 1674.66 1465.31 FALSE TRUE FALSE 1585.378374 1459.106168 1677.160929 1322.640025 1538.217383 1368.798222 1157.435664 1545.355107 1524.874215 1427.241035 1.110799322 1.022326385 1.175106999 0.926711041 1.077755856 0.959051897 0.810960192 1.08275692 1.068406932 1 10.47901328 -8.163413055 5.195362259 1.052306324 0.933382756 0.223680659 0.087368356 0.225269946 9.431575632 0.011773337 0.030884834 6.86E-09 8.163413055 -0.118923568 VIILMLTNQTVHR ddPTM_HeLa_Romidepsin_16h_R1 1 VIILMLTNQTVHR 13 0 G3V198;Q12769;E9PR16;Q12769-2 G3V198 NUP160 Nuclear pore complex protein Nup160 0 0 73.219 0.013658 352360 0 0 0 0 180.02 0 0 118.74 0 67.078 FALSE FALSE TRUE 0 0 0 0 170.8329077 0 0 122.1755546 0 65.33530389 0 0 0 0 2.614710539 0 0 1.869977597 0 1 6.029790857 -7.247897341 23.88096913 0.490980711 1.869979315 0.224445086 0.803539905 1522.898893 2685499.315 0.110233494 2.745787328 5.65E-08 7.247897341 1.378998605 VIILSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 VIILSLDR 8 0 H0Y3P2;D3DQV9;P78344-2;P78344;E9PKF8 H0Y3P2 EIF4G2 Eukaryotic translation initiation factor 4 gamma 2 0 0 95.62 0.017907 0 0 0 0 0 0 0 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 0 0 0 0 0 0 VIIS(ph)APSADAPMFVMGVNHEK ddPTM_HeLa_Romidepsin_16h_R1 1 VIISAPSADAPMFVMGVNHEK 21 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 1 0 VIIS(0.5)APS(0.5)ADAPMFVMGVNHEK 51.398 0.014349 10674000 1501.2 1392.3 1508.7 978.02 1366.8 1430.9 1273.9 1059.2 1261.4 1318.2 TRUE FALSE FALSE 1482.902797 1411.900836 1534.958291 1091.103274 1297.047096 1339.470108 1382.105034 1089.846281 1148.577225 1283.952974 1.15495102 1.099651517 1.195494167 0.849800029 1.010198288 1.043239227 1.076445214 0.848821026 0.894563312 1 10.32637665 -9.267707343 24.99130106 1.085777427 0.978633005 0.18265903 0.104461718 575.6914223 2295363.669 0.014478486 0.022457753 5.40E-10 9.267707343 -0.107144423 VIISAPSADAPMFVMGVNHEK ddPTM_HeLa_Romidepsin_16h_R1 5 VIISAPSADAPMFVMGVNHEK 21 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 ;;;; ;;;; 159.01 6.75E-24 128079390 8096.59 7424.06 7884.42 7283.23 8619.23 8346.35 7512.58 7289.62 8590.41 7688.06 FALSE FALSE TRUE 7997.905647 7528.576112 8021.645023 8125.351321 8179.35853 7813.045172 8150.698358 7500.533654 7822.062215 7488.323093 1.068050289 1.005375438 1.071220475 1.085069544 1.092281734 1.043363791 1.088454419 1.001630613 1.044567938 1 12.87042697 -12.59025554 0.557792285 0.981947247 1.060986581 0.076161918 0.033540357 1.495711895 0.534024374 0.065872675 0.00686346 2.57E-13 12.59025554 0.079039333 VIKPGGPYVGK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 VIKPGGPYVGKR 12 2 O00472 O00472 ELL2 RNA polymerase II elongation factor ELL2 0 1 ; VIKPGGPYVGK(1)R;VIKPGGPYVGK(1)R 127.51 0.0034108 16003300 4223.8 4160.2 3484 4735.4 6695.4 5866.1 5334 5056.5 3731.4 3854.6 FALSE TRUE FALSE 4172.318701 4218.767405 3544.637559 5282.929229 6353.708754 5491.275142 5787.069827 5202.80185 3397.654239 3754.456936 1.111297525 1.123669142 0.944114587 1.407108756 1.692310995 1.462601712 1.541386657 1.38576682 0.904965564 1 11.87438853 -9.133122943 4.670766586 1.053553927 1.520970158 0.854133042 0.099494066 0.057574038 1.950494892 0.01327471 0.022414621 7.36E-10 9.133122943 0.467416231 VILAS(ph)PETSSAK ddPTM_HeLa_Romidepsin_16h_R1 1 VILASPETSSAK 12 0 C9JKS0;P49116;P49116-2 C9JKS0 NR2C2 Nuclear receptor subfamily 2 group C member 2 1 0 VILAS(0.602)PET(0.371)S(0.02)S(0.006)AK 125.36 0.0056644 14807000 3153.2 3181 2691.9 2687.6 2906.1 2728.9 2945.8 3116 3796.3 3175.1 TRUE FALSE FALSE 3114.767586 3225.782201 2738.75139 2998.352958 2757.790873 2554.532097 3196.016178 3206.156544 3456.74942 3092.610444 1.007164543 1.043061278 0.88557917 0.969521707 0.891735614 0.826011599 1.033436392 1.036715293 1.117744857 1 11.5946094 -9.770033614 24.98598102 1.006453639 0.938622936 0.27800783 0.07143377 220.3560074 640639.059 0.010151172 0.013457536 1.70E-10 9.770033614 -0.067830703 VILHLK ddPTM_HeLa_Romidepsin_16h_R1 2 VILHLK 6 0 P08238;Q58FF7;Q58FF6;P07900-2;P07900;G3V2J8;Q14568 P08238;P07900-2 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 0 ; ; 74.849 0.018828 65621000 22234 20476.2 24608 15077.4 23839 25791 22736 22801 21439 18696.6 FALSE FALSE TRUE 21963.00346 20764.46448 25036.29192 16820.71993 22622.40687 24143.03834 24667.19527 23460.71096 19521.44215 18210.85964 1.206038808 1.140224289 1.374800115 0.923664246 1.24224816 1.325749515 1.354532173 1.288281357 1.071967086 1 14.15251141 -16.52287871 0.068041048 0.13606057 1.567613828 0.3641192 0.117105514 174.7397098 0.925609651 24.39572539 3.70153842 3.00E-17 16.52287871 1.431553258 VILHLKEDQTEYLEER ddPTM_HeLa_Romidepsin_16h_R1 3 VILHLKEDQTEYLEER 16 1 P08238;Q58FF7;Q58FF6;P07900-2;P07900;G3V2J8 P08238;P07900-2 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 0 ;; ;; 138.21 0.00040226 85462900 8742.9 7889.84 7187.46 10139.4 9102.5 8735.7 7979.61 8681.6 9586.4 8509.9 FALSE FALSE TRUE 8636.338172 8000.913375 7312.554726 11311.76514 8637.965459 8177.516963 8657.397874 8932.788399 8728.968374 8288.811571 1.041927193 0.96526665 0.882219925 1.364702894 1.042123516 0.986572911 1.044467931 1.077692299 1.053102523 1 13.01694955 VINAAHSFYNGTTTLPISDEDRT(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VINAAHSFYNGTTTLPISDEDRTPR 25 1 P49915-2;P49915 P49915-2 GMPS GMP synthase [glutamine-hydrolyzing] 1 0 VINAAHS(0.01)FY(0.041)NGT(0.007)T(0.007)T(0.007)LPIS(0.109)DEDRT(0.819)PR 45.985 0.015565 30601000 1870 2083.4 1535.7 2827.3 1439.7 1333.5 1299.4 1275.2 2220.5 2003.8 TRUE FALSE FALSE 1847.207721 2112.73016 1562.428214 3154.205729 1366.226737 1248.293654 1409.771004 1312.0959 2021.892919 1951.740987 0.946441015 1.082484906 0.800530513 1.616098524 0.700004122 0.639579566 0.722314596 0.672269481 1.035943259 1 10.93054589 -8.571019302 24.99999219 1.01464799 0.680359136 0.45552997 0.205182799 83.50576441 43365.26315 0.027642034 0.055284079 2.69E-09 8.571019302 -0.334288854 PEPSK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 PEPSKSAPAPKKGSK 15 3 P33778;U3KQK0;Q99877 P33778;U3KQK0 HIST1H2BB;HIST1H2BN Histone H2B type 1-B;Histone H2B;Histone H2B type 1-N 0 3 ; PEPSK(1)SAPAPK(1)K(1)GSK;PEPSK(1)SAPAPK(1)K(1)GSK 161.49 1.10E-06 38371000 448.72 399.26 395.94 3033.3 18162.4 29753 32169 37087 0 755.91 FALSE TRUE FALSE 443.250828 404.8807928 402.8311696 3384.024418 17235.50495 27851.87932 34901.43406 38160.05383 0 736.2713492 0.602021019 0.549907032 0.547123245 4.596164745 23.40917513 37.82828077 47.40295014 51.82879094 0 1 9.524093752 -8.387815779 1.314458805 0.55363592 50.99398179 0.994552846 1.498225634 0.021866375 0.070499875 0.228444124 0.835430791 4.09E-09 8.387815779 50.44034587 up VIPEDAS(ph)ESEEK ddPTM_HeLa_Romidepsin_16h_R1 1 VIPEDASESEEK 12 0 Q9H2P0;A0A669KBJ7;A0A2R8Y6X0 Q9H2P0 ADNP Activity-dependent neuroprotector homeobox protein 1 0 VIPEDAS(0.842)ES(0.158)EEK 106.29 0.012509 2793000 1964.8 1681.5 1787.7 1128.4 1338.3 1216.7 917.61 992.36 1654.4 1688.8 TRUE FALSE FALSE 1940.852262 1705.172201 1818.814169 1258.870917 1270.001557 1138.956797 995.5517705 1021.072371 1506.42632 1644.924733 1.179903386 1.036626277 1.105712701 0.765306091 0.772072747 0.692406634 0.605226337 0.62074109 0.915802584 1 10.68380586 -9.045770465 1.561001521 1.087461959 0.648430117 0.816776043 0.08373582 0.099539805 0.480349298 0.012979911 0.026518462 9.00E-10 9.045770465 -0.439031842 VIPEDAS(ph)ESEEKLDQK ddPTM_HeLa_Romidepsin_16h_R1 1 VIPEDASESEEKLDQK 16 1 Q9H2P0;A0A669KBJ7;A0A2R8Y6X0 Q9H2P0 ADNP Activity-dependent neuroprotector homeobox protein 1 0 VIPEDAS(0.979)ES(0.021)EEKLDQK 72.676 0.013496 22402000 3444.5 3427.7 3477.3 2501.8 2747.8 2380 2018.8 2109.3 3519.6 3491.5 TRUE FALSE FALSE 3402.517109 3475.955251 3537.820948 2791.069887 2607.569513 2227.925681 2190.276822 2170.329268 3204.798161 3400.790327 1.000507759 1.022102193 1.040293758 0.820712134 0.766753978 0.655119977 0.644049357 0.638183792 0.942368642 1 11.73165435 -8.844192503 1.527952111 1.005653333 0.645554887 0.949100762 0.035847818 0.045100946 0.212082701 0.004582767 0.010599764 1.43E-09 8.844192503 -0.360098446 VIQAQTAFSANPANPAILSEASAPIPHDGNLY(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VIQAQTAFSANPANPAILSEASAPIPHDGNLYPR 34 0 B4DHN5;E9PBU7;O00560-2;O00560;G5EA09 B4DHN5 SDCBP Syntenin-1 1 0 VIQAQTAFSANPANPAILS(0.008)EAS(0.089)APIPHDGNLY(0.902)PR 68.011 3.54E-05 0 1355.9 1310.8 1096.1 990.79 1143.2 1025.5 954.52 898.51 1334.8 1062.3 TRUE FALSE FALSE 1339.373769 1329.253477 1115.177161 1105.349802 1084.858238 959.9738596 1035.596905 924.5069692 1215.412145 1034.701293 1.294454524 1.284673641 1.077776909 1.068279135 1.048474807 0.927778738 1.000865576 0.893501318 1.174650262 1 10.01499862 -8.723422983 1.330565655 1.151304064 0.942476322 0.55863774 0.086239033 0.387619811 1.364100135 0.019829545 0.053360699 1.89E-09 8.723422983 -0.208827742 VIQLMPS(ph)PIMHPLILNPR ddPTM_HeLa_Romidepsin_16h_R1 1 VIQLMPSPIMHPLILNPR 18 0 P41212 P41212 ETV6 Transcription factor ETV6 1 0 VIQLMPS(1)PIMHPLILNPR 67.846 0.0071289 14525000 1734.7 1705.6 1500.3 1756.8 1585.3 1366.2 1045.1 1075.2 1730.3 1473 TRUE FALSE FALSE 1713.556809 1729.611482 1526.412092 1959.929482 1504.396225 1278.904229 1133.870768 1106.309216 1575.537634 1434.731248 1.194339924 1.205529945 1.063901058 1.366060358 1.048556117 0.891389402 0.790301856 0.771091602 1.098141298 1 10.4865648 -8.175530341 2.627386139 1.120408709 0.788021907 0.705306451 0.097082064 0.145789707 1.94629297 0.016424815 0.049269569 6.68E-09 8.175530341 -0.332386801 VISFIENTS(ph)TPVDR ddPTM_HeLa_Romidepsin_16h_R1 1 VISFIENTSTPVDR 14 0 E9PGE5;Q9NUY8-2;Q9NUY8 E9PGE5 TBC1D23 TBC1 domain family member 23 1 0 VISFIENT(0.069)S(0.862)T(0.069)PVDR 228.17 3.80E-33 14609000 1451 1769.2 1992.1 1717.4 2917.2 2891.6 2397.7 3056.4 1500.8 1367.5 TRUE FALSE FALSE 1433.314654 1794.106844 2026.771665 1915.973869 2768.324398 2706.836092 2601.360578 3144.832112 1366.564689 1331.972153 1.076084549 1.34695522 1.521632161 1.438448893 2.078365071 2.032201714 1.953014237 2.361034429 1.025970916 1 10.37934821 -9.059342919 0.599661303 1.00380728 2.272734621 0.920153524 0.131840803 0.155935514 0.102433847 0.028354244 0.093536098 8.72E-10 9.059342919 1.268927341 up VISFIENTST(ph)PVDR ddPTM_HeLa_Romidepsin_16h_R1 1 VISFIENTSTPVDR 14 0 E9PGE5;Q9NUY8-2;Q9NUY8 E9PGE5 TBC1D23 TBC1 domain family member 23 1 0 VISFIENT(0.067)S(0.192)T(0.741)PVDR 193.51 6.00E-11 14948000 2912.6 2788.8 3337.2 2786.3 3717.4 4385.9 3565.8 4350 2917.2 2787.7 TRUE FALSE FALSE 2877.100111 2828.0608 3395.282566 3108.465116 3527.687206 4105.655145 3868.678963 4475.860387 2656.278326 2715.275152 1.059597996 1.041537465 1.250437755 1.144806674 1.299200637 1.5120586 1.4247834 1.648400304 0.978272248 1 11.40688269 -8.032714475 0.44907606 1.008714757 1.812265867 0.917426254 0.063315881 0.468270445 0.098981827 0.014928518 0.177576068 9.27E-09 8.032714475 0.80355111 VISGTTLGYLS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 VISGTTLGYLSPK 13 0 E5RJ67;H0YBY0;E5RJN7;E7EPX0;E7EVJ4;Q9NUL3-4;Q9NUL3-6;Q9NUL3-8;Q9NUL3-3;Q9NUL3-7;Q9NUL3-2;Q9NUL3 E5RJ67 STAU2 Double-stranded RNA-binding protein Staufen homolog 2 1 0 VISGTTLGYLS(1)PK 152.16 0.00076878 32647000 2526.5 2239.7 2326.3 2504.9 2912.6 3469.9 3053.4 2728.6 2243.9 1959.1 TRUE FALSE FALSE 2495.706046 2271.230555 2366.788276 2794.528324 2763.959154 3248.184589 3312.75572 2807.547736 2043.199964 1908.2023 1.307883366 1.19024621 1.240323563 1.464482212 1.448462332 1.702222343 1.736061067 1.471305079 1.070745992 1 10.89799841 -8.498703915 0.168182271 0.877771937 2.110585751 0.78373946 0.108931281 3.803917191 0.190717244 0.323291669 1.152687804 3.17E-09 8.498703915 1.232813814 VISRPPPSVS(ph)PPK ddPTM_HeLa_Romidepsin_16h_R1 2 VISRPPPSVSPPK 13 1 Q8NHM5-2;Q8NHM5-3;Q8NHM5;Q8NHM5-4;A0A0C4DGG3 Q8NHM5-2 KDM2B Lysine-specific demethylase 2B 1 0 VISRPPPS(0.001)VS(0.999)PPK;VISRPPPS(0.209)VS(0.791)PPK ; 88.427 0.0089493 106450000 7393.2 6623.1 6111.8 7176.8 5711.1 5856 5115 5856.8 7949.6 7692.4 TRUE FALSE FALSE 7303.088835 6716.340176 6218.173315 8006.615384 5419.641256 5481.820499 5549.467972 6026.257267 7238.567866 7492.550339 0.974713349 0.896402409 0.829914119 1.068610156 0.723337316 0.731636125 0.740664756 0.804299871 0.966102 1 12.87124116 -8.953666405 0.626010539 0.991025667 0.725669076 0.520853031 0.082026005 0.468667242 0.328460935 0.017061819 0.061185554 1.11E-09 8.953666405 -0.26535659 VISSIEQK(ac)TER ddPTM_HeLa_Romidepsin_16h_R1 1 VISSIEQKTER 11 1 P31946-2;P31946;Q4VY20;Q4VY19;A0A0J9YWE8;A0A0J9YWZ2 P31946-2 YWHAB "14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed" 0 1 VISSIEQK(1)TER 101.93 0.00246 0 74.605 65.029 63.976 61.128 71.923 120.01 0 170.92 0 103.88 FALSE TRUE FALSE 73.69568556 65.94447997 65.08947544 68.19590698 68.25250093 112.3417483 0 175.8653005 0 101.1811826 0.728353669 0.651746483 0.643296251 0.673997923 0.674557256 1.11030278 0 1.738122603 0 1 6.660797197 -12.13423797 0.936846948 0.997033266 0.7483702 0 0.517136966 1.390239835 2.238090676 0.225728412 0.068620822 7.34E-13 12.13423797 -0.248663066 VITEEEK(ac)NFK ddPTM_HeLa_Romidepsin_16h_R1 1 VITEEEKNFK 10 1 H3BUK8;J3KS98;P26373-2;P26373 H3BUK8 RPL13 60S ribosomal protein L13 0 1 VITEEEK(1)NFK 107.57 0.025973 591100 229.17 251.81 311.38 431.2 581.26 417.58 277.07 452.78 607.02 448.94 FALSE TRUE FALSE 226.3767879 255.3549878 316.7994383 481.0573729 551.5961332 390.8979857 300.6043189 465.8804749 552.7266109 437.2764741 0.517697158 0.583966902 0.724483152 1.10012178 1.26143565 0.893937838 0.687446814 1.065413994 1.26402092 1 8.772401922 -9.274487838 24.18455562 0.746087853 0.992660472 0.087690991 0.245686991 622.6423133 1154029.405 0.036848868 0.056521962 5.32E-10 9.274487838 0.246572619 VKAPVHFVEPLS(ph)PTGVAGHR ddPTM_HeLa_Romidepsin_16h_R1 1 VKAPVHFVEPLSPTGVAGHR 20 1 Q5T5Y3-2;Q5T5Y3;Q5T5Y3-3 Q5T5Y3-2 CAMSAP1 Calmodulin-regulated spectrin-associated protein 1 1 0 VKAPVHFVEPLS(0.964)PT(0.036)GVAGHR 79.455 0.0015178 9526700 2483.1 2392.9 2045.2 2528.5 2617.5 2500.3 2495.3 2564 2699.5 2384.6 TRUE FALSE FALSE 2452.835022 2426.587309 2080.795848 2820.857067 2483.919208 2340.538899 2707.25072 2638.185295 2458.049959 2322.647748 1.056051235 1.044750462 0.895872329 1.214500593 1.069434317 1.007702912 1.165588162 1.135852519 1.05829649 1 11.18155466 -9.253063455 24.99416501 1.01989866 1.112331153 0.382470388 0.067670437 584.8065276 1745090.889 0.009980231 0.016381673 5.58E-10 9.253063455 0.092432493 VKAQT(ph)PPGPS(ph)LSGSKSPCPQEK ddPTM_HeLa_Romidepsin_16h_R1 1 VKAQTPPGPSLSGSKSPCPQEK 22 2 Q9UQ35;Q9UQ35-2 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 2 0 VKAQT(0.999)PPGPS(0.871)LS(0.053)GS(0.027)KS(0.049)PCPQEK 62.717 0.0049667 53741000 7324.9 6653 5865.5 597.14 6470.6 5258.7 5379.7 5361.6 7391.9 6588.1 TRUE FALSE FALSE 7235.621301 6746.661109 5967.586567 666.1841364 6140.381137 4922.686042 5836.651584 5516.729437 6730.749951 6416.940212 1.127581224 1.051382884 0.929973846 0.103816479 0.956901722 0.767139147 0.909569264 0.859713392 1.048903329 1 12.64766983 -9.514489685 24.9199163 1.057904015 0.722941039 0.338149621 0.224025532 330.2846687 981120.128 0.03422198 0.049791245 3.06E-10 9.514489685 -0.334962976 VKAQT(ph)PPGPSLSGSK ddPTM_HeLa_Romidepsin_16h_R1 2 VKAQTPPGPSLSGSK 15 1 Q9UQ35;Q9UQ35-2;I3L4D8 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 VKAQT(0.99)PPGPS(0.01)LSGSK;VKAQT(0.706)PPGPS(0.17)LS(0.081)GS(0.044)K ; 111.81 0.0024599 158821000 14441.9 13508.1 12498 11947.1 13519.2 13118.6 13163.4 13799.5 15305.2 13592.1 TRUE FALSE FALSE 14265.87657 13698.26739 12715.52245 13328.47991 12829.26478 12280.3638 14281.49887 14198.76676 13936.26458 13238.97528 1.077566523 1.034692421 0.960461227 1.006760692 0.969052703 0.927591716 1.078746547 1.072497414 1.052669431 1 13.69250384 -9.957734483 24.99679678 1.037655021 1.000943144 0.13604111 0.047412768 265.1977966 156843.4424 0.008610814 0.011316824 1.10E-10 9.957734483 -0.036711876 VKEEIIEAFVQELR ddPTM_HeLa_Romidepsin_16h_R1 1 VKEEIIEAFVQELR 14 1 P50552 P50552 VASP Vasodilator-stimulated phosphoprotein 0 0 102.63 0.010258 2043900 1032.5 1084.9 1006.2 1244.5 1159.6 1225.3 786.31 940.57 983.05 1172.7 FALSE FALSE TRUE 1019.915493 1100.173251 1023.712489 1388.394946 1100.421285 1147.007284 853.0991518 967.783909 895.1235459 1142.233085 0.892913632 0.963177538 0.896237819 1.215509307 0.963394687 1.004179707 0.746869586 0.847273575 0.783661021 1 10.15764136 -7.764397225 24.99987983 0.968540396 0.79707156 0.283730816 0.106525449 57.29863751 484312.3397 0.012838412 0.041123683 1.72E-08 7.764397225 -0.171468836 VKEEPPS(ph)PPQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VKEEPPSPPQSPR 13 1 E9PMQ6;Q00613-2;Q00613 E9PMQ6 HSF1 Heat shock factor protein 1 2 0 VKEEPPS(1)PPQS(1)PR 81.992 0.002913 0 3167 3595.1 3271.4 2050.9 2991 3458.7 2537 3611.1 3577.8 3814.1 TRUE FALSE FALSE 3128.399386 3645.711912 3328.337345 2288.034708 2838.358109 3237.700232 2752.492717 3715.581481 3257.792607 3715.009132 0.842097361 0.981346689 0.895916329 0.61588939 0.764024531 0.871518782 0.740911427 1.000154064 0.876927214 1 11.85915004 -12.12337347 0.388014944 1.046724424 0.81388548 0.083615565 0.112848894 2.409447298 0.516168754 0.234512209 0.041353784 7.53E-13 12.12337347 -0.232838944 VKEPS(ph)VQEATSTSDILK ddPTM_HeLa_Romidepsin_16h_R1 1 VKEPSVQEATSTSDILK 17 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 VKEPS(0.999)VQEAT(0.001)STSDILK 111.45 0.00073369 20862000 2620.1 2680.1 2644.7 2911.5 2995.9 3023.4 2771.9 2661.8 3002.4 2863.4 TRUE FALSE FALSE 2588.165213 2717.830518 2690.729894 3248.141329 2843.008044 2830.214498 3007.345117 2738.814983 2733.857824 2789.008455 0.927987582 0.974479125 0.964762186 1.16462226 1.019361572 1.014774442 1.07828469 0.982003112 0.980225721 1 11.44553659 -9.415055281 21.64343762 0.965800447 1.050949885 0.416682803 0.048593848 7.624145995 1522.493041 0.007603896 0.011615138 3.85E-10 9.415055281 0.085149438 VKEPSVQEAT(ph)STSDILK ddPTM_HeLa_Romidepsin_16h_R1 2 VKEPSVQEATSTSDILK 17 1 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 VKEPS(0.013)VQEAT(0.943)S(0.033)T(0.009)S(0.002)DILK;VKEPS(0.038)VQEAT(0.435)S(0.109)T(0.165)S(0.253)DILK ; 121.32 0.0012627 28163700 9450.8 8209.6 9831.4 9752.6 9201 9623.3 9089.5 9409.4 8424.9 8977.3 TRUE FALSE FALSE 9335.610014 8325.174964 10002.51139 10880.2415 8731.438636 9008.402188 9861.561903 9681.646143 7671.355843 8744.068452 1.06765061 0.952093983 1.143919612 1.244299671 0.998555613 1.030230063 1.127800172 1.107224423 0.87732111 1 13.09408898 -11.23480342 0.381823979 0.99269973 1.100805289 0.270444663 0.085802713 1.933812622 0.659162495 0.086272872 0.039172238 5.82E-12 11.23480342 0.10810556 VKESSIIAPAPAEDVDT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 2 VKESSIIAPAPAEDVDTPPR 20 1 Q15910-5;Q15910-3;Q15910-4;Q15910;Q15910-2 Q15910-5 EZH2 Histone-lysine N-methyltransferase EZH2 1 0 VKESSIIAPAPAEDVDT(1)PPR;VKESSIIAPAPAEDVDT(1)PPR ; 118.15 4.62E-07 209810000 10554.8 8967.7 8393 9462.3 9205.3 8167.1 7915.2 7868.4 10523.5 10010.9 TRUE FALSE FALSE 10426.15404 9093.947516 8539.076644 10556.37565 8735.519191 7645.248668 8587.51689 8096.05974 9582.251803 9750.815375 1.069259712 0.932634571 0.875729497 1.082614658 0.895875766 0.784062499 0.880697312 0.830295665 0.982712874 1 13.25130715 -8.724705811 0.68156462 1.027801517 0.813155774 0.443299816 0.070006302 0.529358658 0.418910569 0.014125196 0.061163498 1.88E-09 8.724705811 -0.214645743 VKGDVDISLPK ddPTM_HeLa_Romidepsin_16h_R1 1 VKGDVDISLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 98.156 0.0037022 0 1808.3 2043.2 1562.6 1863.6 1745.9 1844 1732.4 2144.2 1890.9 2261.9 FALSE FALSE TRUE 1786.259744 2071.964223 1589.796398 2079.078201 1656.800208 1726.174351 1879.550013 2206.239044 1721.773168 2203.135512 0.810780696 0.940461543 0.721606269 0.943690567 0.752019201 0.783508024 0.853125013 1.001408689 0.781510333 1 11.10534252 -12.36528176 0.892264396 1.008281533 0.844185074 0 0.108506356 0.614406173 0.802183509 0.070625314 0.015003434 4.31E-13 12.36528176 -0.164096459 VKGDVDVSLPK ddPTM_HeLa_Romidepsin_16h_R1 1 VKGDVDVSLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 96.82 0.0038115 0 4097.9 3492.6 3222.4 4277.6 3610.7 3286.3 3005.7 3116.2 4316 3562.8 FALSE FALSE TRUE 4047.953219 3541.768914 3278.48452 4772.196239 3426.432506 3076.316036 3261.004083 3206.36233 3929.96615 3470.237942 1.166477137 1.0206127 0.944743437 1.375178394 0.98737682 0.886485621 0.939706192 0.923960369 1.132477431 1 11.76081887 -8.530183168 24.99888703 1.086922062 0.922002051 0.366665364 0.111911501 161.2439406 551845.4477 0.016667472 0.03338896 2.95E-09 8.530183168 -0.164920011 VKGDVDVSVPK ddPTM_HeLa_Romidepsin_16h_R1 2 VKGDVDVSVPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 ; ; 121.02 0.0028835 2974800 8804.7 8132.7 7738.9 6877.9 7726.6 6532 6844.3 6739.1 8925.2 8827.6 FALSE FALSE TRUE 8697.38493 8247.192364 7873.592308 7673.155159 7332.28277 6114.626281 7425.654671 6934.085226 8126.907758 8598.257679 1.01152876 0.95917018 0.91571951 0.892408142 0.852763786 0.711147131 0.863623184 0.806452363 0.945180764 1 13.06982863 -9.284162526 0.994565808 1.00598731 0.799459112 0.75228739 0.043412083 0.139042063 0.272396343 0.006790256 0.01424945 5.20E-10 9.284162526 -0.206528198 VKGDVDVTLPK ddPTM_HeLa_Romidepsin_16h_R1 1 VKGDVDVTLPK 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 86.463 0.02077 0 1399.7 1264.7 1421.3 1339.3 1286.7 1316.1 1130.7 936.57 1495.7 1534.9 FALSE FALSE TRUE 1382.639918 1282.50448 1446.03713 1494.156168 1221.034898 1232.005458 1226.74163 963.6681753 1361.920846 1495.023077 0.924828479 0.857849287 0.967233986 0.999420137 0.816733144 0.824071198 0.820550297 0.644584147 0.910969782 1 10.54595204 -6.027620934 0.391588716 0.969092636 1.00E-11 0.71535831 0.054851786 4.849988561 0.245242414 0.014217023 2.721898642 9.38E-07 6.027620934 -0.969092636 PTS(ph)SPAKGPPQK ddPTM_HeLa_Romidepsin_16h_R1 1 PTSSPAKGPPQK 12 1 E7ETY2;Q13428-6;Q13428-7;A0A3B3IS06;H0Y8Y7;Q13428-5;Q13428;Q13428-3;Q13428-4;Q13428-2;Q13428-8;A0A6I8PRA0 E7ETY2;Q13428 TCOF1 Treacle protein 1 0 PTS(0.5)S(0.5)PAKGPPQK 163.51 0.0030475 12038000 4024.8 3901 4094.9 3333 2111.6 2234.9 2409.7 1088.3 4031.6 4846.5 TRUE FALSE FALSE 3975.74419 3955.91838 4166.170017 3718.377142 2003.837173 2092.097103 2614.379858 1119.788243 3671.003599 4720.587231 0.842213902 0.838014041 0.882553338 0.787693768 0.424488962 0.443185773 0.553825134 0.237213759 0.777658249 1 12.20475062 -8.140731907 0.393266253 0.966167583 0.083448374 0.78033624 0.109833344 0.843964887 0.142602032 0.031365795 0.315567942 7.23E-09 8.140731907 -0.882719209 down VKGGVDVTLPR ddPTM_HeLa_Romidepsin_16h_R1 1 VKGGVDVTLPR 11 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 0 0 95.618 0.010238 825060 654.28 594.64 540.52 879.85 630.05 559.77 463.91 425.31 570.85 592.56 FALSE FALSE TRUE 646.3053837 603.0113575 549.9275239 981.5823968 597.8961975 524.0025036 503.3145038 437.6156738 519.7917463 577.1652058 1.119792699 1.044781202 0.952807824 1.700695723 1.035918644 0.907889974 0.872045818 0.758215619 0.90059439 1 9.17284052 -8.173696988 3.207270862 1.097454992 0.830883969 0.250912469 0.211202066 0.28724129 5.669847177 0.029226562 0.082613836 6.70E-09 8.173696988 -0.266571023 VKPPPSPT(ph)TEGPSLQPDLAPEEAAGTQRPK ddPTM_HeLa_Romidepsin_16h_R1 2 VKPPPSPTTEGPSLQPDLAPEEAAGTQRPK 30 2 Q9Y2D5-6;Q9Y2D5-4;Q9Y2D5-5;Q9Y2D5-7;Q9Y2D5 Q9Y2D5-6 AKAP2 A-kinase anchor protein 2 1 0 VKPPPS(0.019)PT(0.472)T(0.472)EGPS(0.037)LQPDLAPEEAAGTQRPK;VKPPPS(0.029)PT(0.477)T(0.477)EGPS(0.018)LQPDLAPEEAAGTQRPK ; 133.53 4.43E-11 354770000 5731.3 5501.4 5568.6 5998.6 5815.3 5838 5198.1 5477.3 5699.6 5899.9 TRUE FALSE FALSE 5661.444711 5578.848854 5665.519147 6692.186356 5518.523541 5464.970641 5639.626484 5635.777034 5189.813501 5746.619747 0.985178237 0.970805291 0.985887251 1.164543097 0.960307761 0.950988734 0.981381531 0.980711667 0.903107171 1 12.48849787 VKPYVNGT(ph)SPVYSR ddPTM_HeLa_Romidepsin_16h_R1 1 VKPYVNGTSPVYSR 14 1 E9PDR5;E7EPI0;Q9P2D0-2;Q9P2D0 E9PDR5 IBTK Inhibitor of Bruton tyrosine kinase 1 0 VKPYVNGT(0.5)S(0.5)PVYSR 80.508 0.019109 19467000 3626.8 3297.7 3333.6 2913 3455.1 2793.3 2099.4 2561.7 3603.7 3635.5 TRUE FALSE FALSE 3582.595167 3344.125107 3391.61991 3249.814766 3278.773354 2614.817145 2277.722984 2635.818748 3281.376046 3541.049186 1.011732675 0.944388211 0.957800847 0.917754766 0.925932734 0.738430055 0.64323393 0.744360953 0.92666774 1 11.78996117 -8.36895148 1.213683064 0.997002332 0.673322642 0.856394302 0.045181831 0.100877113 0.271643605 0.006136751 0.024412617 4.28E-09 8.36895148 -0.32367969 VKS(ph)PGGPGSHVR ddPTM_HeLa_Romidepsin_16h_R1 1 VKSPGGPGSHVR 12 1 O75382-3;O75382-2;O75382;A0A1W2PPI7;O75382-4 O75382-3 TRIM3 Tripartite motif-containing protein 3 1 0 VKS(1)PGGPGSHVR 64.52 0.026971 6257800 1622.8 1958.8 1965.7 2069.1 3043 3417.6 3952.5 1690.1 2288.1 1713.2 TRUE FALSE FALSE 1603.020689 1986.376038 1999.912184 2308.339077 2887.704355 3199.22639 4288.225251 1739.000377 2083.446605 1668.690817 0.960645719 1.190379918 1.198491754 1.383323414 1.730520912 1.917207404 2.569814137 1.042134564 1.248551609 1 10.70450095 -9.022200114 1.240387025 0.993542914 1.916686792 0.44109519 0.360732146 0.224702124 0.684659708 0.052760083 0.11907292 9.50E-10 9.022200114 0.923143877 VLAET(ph)PDSFEK ddPTM_HeLa_Romidepsin_16h_R1 1 VLAETPDSFEK 11 0 Q99567;J3KMX1 Q99567 NUP88 Nuclear pore complex protein Nup88 1 0 VLAET(0.952)PDS(0.048)FEK 137.4 0.0075087 35604000 5265.4 5420.3 4902.7 4215.8 4809.9 3953.4 4086.5 3861.3 5719 5060.2 TRUE FALSE FALSE 5201.22328 5496.607126 4988.029437 4703.250632 4564.432855 3700.790499 4433.607208 3973.020623 5207.478317 4928.735275 1.055285583 1.115216545 1.0120303 0.954251014 0.926086024 0.750860067 0.899542572 0.806093329 1.056554679 1 12.26700178 -8.764249552 1.715484371 1.033447264 0.827430688 0.796350852 0.049230067 0.124350139 0.741645375 0.007684454 0.017874612 1.72E-09 8.764249552 -0.206016576 VLAGDKNFITAEELR ddPTM_HeLa_Romidepsin_16h_R1 2 VLAGDKNFITAEELR 15 1 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 ; ; 133.04 0.0017908 41838000 3439.7 3294.3 3756.8 3825.7 4347.9 4007.8 3594.8 3874.7 3689.6 3510.5 FALSE FALSE TRUE 3397.775613 3340.677242 3822.185528 4268.045434 4126.010439 3751.714515 3900.142222 3986.808331 3359.592935 3419.296704 0.993705989 0.977007125 1.11782798 1.248223189 1.206683946 1.097218182 1.140627024 1.165973203 0.982539167 1 11.7394839 -9.642037444 4.333383374 0.995558901 1.169074052 0.837182493 0.038154344 0.065741749 2.187732672 0.006278275 0.008957381 2.28E-10 9.642037444 0.173515151 VLAGDKNFITAEELRR ddPTM_HeLa_Romidepsin_16h_R1 1 VLAGDKNFITAEELRR 16 2 O43707;O43707-2;O43707-3;F5GXS2;H7C144 O43707 ACTN4 Alpha-actinin-4 0 0 96.371 0.0025634 13935000 2224.1 2104.6 1666.8 4206.7 2404.5 1654.9 2257.1 2125 2464.7 1877.2 FALSE FALSE TRUE 2196.991814 2134.228614 1695.809955 4693.098447 2281.789393 1549.157231 2448.818018 2186.483522 2244.251059 1828.430073 1.201572784 1.167246506 0.927467766 2.566736631 1.247950045 0.847260857 1.339300886 1.195825618 1.227419682 1 10.83638974 VLAGETLS(ph)VNDPPDVLDR ddPTM_HeLa_Romidepsin_16h_R1 2 VLAGETLSVNDPPDVLDR 18 0 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906;K7EKJ9;K7EQR9 Q12906-4 ILF3 Interleukin enhancer-binding factor 3 1 0 VLAGET(0.002)LS(0.998)VNDPPDVLDR;VLAGET(0.25)LS(0.75)VNDPPDVLDR ; 154.39 7.56E-06 10724400 3571.1 3300.7 3320 3188.6 2764.8 2739.2 2306.9 2762 3273.8 3260.8 TRUE FALSE FALSE 3527.57406 3347.167341 3377.783207 3557.280935 2623.701939 2564.17396 2502.848028 2841.914112 2980.983129 3176.083946 1.110667766 1.053866144 1.063505646 1.120021069 0.826080791 0.80733822 0.788029558 0.894785579 0.938571895 1 11.63303333 -8.751898373 24.99858967 1.058782711 0.824576377 0.786425025 0.055640954 57.80563327 151456.6727 0.007361594 0.01457322 1.77E-09 8.751898373 -0.234206334 VLAPILPDNFST(ph)PTGSR ddPTM_HeLa_Romidepsin_16h_R1 2 VLAPILPDNFSTPTGSR 17 0 Q9NQS7-2;Q9NQS7 Q9NQS7-2 INCENP Inner centromere protein 1 0 VLAPILPDNFS(0.03)T(0.931)PT(0.039)GS(0.001)R;VLAPILPDNFS(0.006)T(0.965)PT(0.029)GSR ; 246.38 1.17E-58 178138000 7450.3 6572 6850.2 6954.3 6379.1 6938 5680.4 6014.9 7468.5 6741.3 TRUE FALSE FALSE 7359.492878 6664.520789 6969.424857 7758.388887 6053.550723 6494.684191 6162.893034 6188.931642 6800.498655 6566.160054 1.120821426 1.014979948 1.061415622 1.181571698 0.921931642 0.989114511 0.93858404 0.942549617 1.035688835 1 12.6808342 -8.723272945 24.99999971 1.063022662 0.950302639 0.564549679 0.051897038 115.7967794 75849.40422 0.008676672 0.017353089 1.89E-09 8.723272945 -0.112720022 VLATVTKPVGGDK ddPTM_HeLa_Romidepsin_16h_R1 1 VLATVTKPVGGDK 13 1 Q02878;F8VZA3;F8VWR1;F8VU16;F8VZ45;U3KQR5 Q02878 RPL6 60S ribosomal protein L6 0 0 100.02 0.003718 0 1121.8 1125.6 1040.9 1141.5 998.93 1202.7 1025.8 1011 1142.6 1092.7 FALSE FALSE TRUE 1108.12707 1141.446226 1059.016428 1273.485601 947.9508746 1125.851352 1112.931426 1040.25169 1040.402994 1064.311496 1.041167998 1.072473829 0.995024888 1.196534666 0.890670521 1.057821282 1.045682049 0.977394018 0.97753618 1 10.05570474 -7.248135333 22.2530193 1.028802847 0.97739386 0.043962523 0.074162227 1244.247233 2081013.061 0.008952953 0.199707931 5.65E-08 7.248135333 -0.051408986 VLDNYLTSPLPEEVDETSAEDEGVSQR ddPTM_HeLa_Romidepsin_16h_R1 1 VLDNYLTSPLPEEVDETSAEDEGVSQR 27 0 O00299 O00299 CLIC1 Chloride intracellular channel protein 1 0 0 166.78 9.38E-18 4401200 2328.4 2486.8 2368.1 1968.1 2330.2 2072.4 2119.6 2137.6 2458.7 2353.1 FALSE FALSE TRUE 2300.020565 2521.809236 2409.315787 2195.660982 2211.281199 1939.980328 2299.638771 2199.448083 2238.787714 2291.966123 1.003514207 1.100282073 1.051200436 0.957981429 0.964796633 0.846426267 1.003347627 0.959633767 0.976797908 1 11.16237 -9.094397892 5.386242462 1.013986354 0.94308802 0.387334829 0.04926154 0.209128367 9.405954799 0.007469789 0.01257364 8.05E-10 9.094397892 -0.070898334 VLDPFTIKPLDR ddPTM_HeLa_Romidepsin_16h_R1 1 VLDPFTIKPLDR 12 1 P29401;P29401-2;A0A0B4J1R6 P29401 TKT Transketolase 0 0 190.36 5.79E-10 37034000 8758.9 6578.4 9003.1 5510.1 9095 9787.2 8283.7 6621.4 7374.9 6459.2 FALSE FALSE TRUE 8652.143158 6671.010888 9159.795179 6147.203688 8630.848212 9161.829507 8987.317271 6812.979762 6715.270473 6291.389053 1.375235752 1.060339908 1.455925727 0.97708211 1.371850976 1.456249078 1.42851081 1.082905493 1.067374854 1 12.61916286 -12.43725945 0.983016878 0.986899807 1.28805813 0.243045146 0.168823858 0.607224828 0.972737879 0.137545829 0.028869261 3.65E-13 12.43725945 0.301158323 VLDSVEAGDT(ph)TPPTK ddPTM_HeLa_Romidepsin_16h_R1 1 VLDSVEAGDTTPPTK 15 0 Q8IZ21-3 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 VLDSVEAGDT(0.499)T(0.499)PPT(0.001)K 221.85 3.26E-34 27958000 5437.6 5455.4 5361 5036 5455.6 5228.8 4668.9 5071.9 5696.2 5388.7 TRUE FALSE FALSE 5371.32444 5532.201264 5454.305956 5618.286015 5177.180374 4894.696555 5065.476249 5218.647424 5186.717606 5248.700797 1.023362666 1.054013456 1.039172581 1.07041461 0.98637369 0.93255393 0.965091447 0.994274131 0.988190755 1 12.35774464 -8.530055326 24.99695814 1.021226088 0.963314795 0.539693782 0.026964628 111.4513397 388198.7306 0.004083706 0.008181086 2.95E-09 8.530055326 -0.057911293 VLDSVEAGDTT(ph)PPTK ddPTM_HeLa_Romidepsin_16h_R1 3 VLDSVEAGDTTPPTK 15 0 Q8IZ21-3 Q8IZ21-3 PHACTR4 Phosphatase and actin regulator 4 1 0 VLDSVEAGDT(0.019)T(0.981)PPTK;VLDSVEAGDT(0.076)T(0.918)PPT(0.005)K;VLDSVEAGDT(0.061)T(0.936)PPT(0.003)K ;; 192.39 3.42E-12 72592000 16293.2 16371.5 16088.7 14258 16711.5 15563.1 15449.2 15289.6 17595.5 16442.5 TRUE FALSE FALSE 16094.61221 16601.97841 16368.71707 15906.57705 15858.6498 14568.66814 16761.45466 15731.98045 16021.71441 16015.32148 1.00495093 1.03663098 1.022066094 0.993209975 0.990217388 0.909670665 1.046588711 0.982308127 1.000399176 1 13.96716514 -8.91684149 3.397278825 1.006862844 0.981690984 0.152138354 0.032709104 0.411485334 9.503302594 0.004736309 0.008933138 1.21E-09 8.91684149 -0.02517186 VLDTSSLTQS(ph)APAS(ph)PTNK ddPTM_HeLa_Romidepsin_16h_R1 1 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 2 0 VLDTSSLT(0.003)QS(0.997)APAS(0.701)PT(0.299)NK 180.39 5.04E-09 15509000 3828.5 3562.6 3494.3 2916.6 3345.2 2763.7 1984.9 2614.4 3884.9 3660.9 TRUE FALSE FALSE 3781.836769 3612.754376 3555.116826 3253.831015 3174.481961 2587.108489 2153.497356 2690.043539 3537.424814 3565.78929 1.060588964 1.013171021 0.997006984 0.912513542 0.89026067 0.725535997 0.603932869 0.754403393 0.992045386 1 11.80000574 -8.529369337 1.163070818 1.026897331 0.662945364 0.899193932 0.045544004 0.099369103 0.253817472 0.00714522 0.024939221 2.96E-09 8.529369337 -0.363951966 VLDTSSLTQSAPAS(ph)PTNK ddPTM_HeLa_Romidepsin_16h_R1 3 VLDTSSLTQSAPASPTNK 18 0 Q8N122;Q8N122-3;I3L436 Q8N122 RPTOR Regulatory-associated protein of mTOR 1 0 VLDTSSLTQSAPAS(0.952)PT(0.047)NK;VLDTSSLTQSAPAS(0.998)PT(0.001)NK;VLDTSSLTQS(0.019)APAS(0.975)PT(0.005)NK ;; 238.05 2.03E-49 218312000 14903.5 14845.6 14621.8 14445.9 13048.6 12413.9 10729.4 13055.6 16131.5 13897.8 TRUE FALSE FALSE 14721.85041 15054.59675 14876.2863 16116.20293 12382.68125 11620.69185 11640.75497 13433.34319 14688.65824 13536.73315 1.087548247 1.11212924 1.0989569 1.190553344 0.914746646 0.858456152 0.859938276 0.992362266 1.085096239 1 13.72459199 -8.622829178 9.385881245 1.06226362 0.897174635 0.680125357 0.061063464 0.158557564 13.53139807 0.009963435 0.019944255 2.38E-09 8.622829178 -0.165088985 VLDWICRRLEGEDS(ph)AR ddPTM_HeLa_Romidepsin_16h_R1 1 VLDWICRRLEGEDSAR 16 2 H0YML5;Q16822-3;Q16822 H0YML5 PCK2 "Phosphoenolpyruvate carboxykinase [GTP], mitochondrial" 1 0 VLDWICRRLEGEDS(1)AR 96.135 0.019738 9346900 1566.1 1334.9 1243.1 1504.4 1555.4 1409.8 1189.1 1433 1670.4 1443.5 TRUE FALSE FALSE 1547.011771 1353.692757 1264.735634 1678.345806 1476.022134 1319.71833 1290.102124 1474.461594 1520.99524 1405.997662 1.100294697 0.962798726 0.899528974 1.19370455 1.049804117 0.938634797 0.917570604 1.048694201 1.081790732 1 10.45737848 -8.269367752 23.59547284 1.041900885 0.96322694 0.142790549 0.081476609 384.2507055 1143564.937 0.011861123 0.027011906 5.38E-09 8.269367752 -0.078673945 VLEDSDLK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VLEDSDLKK 9 1 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 1 ; VLEDSDLK(1)K;VLEDSDLK(1)K 116.52 0.0014445 4070600 2696.06 2638.52 3270.2 2108.03 7855.5 6615.4 6467.5 7271.5 7202.7 5104.9 FALSE TRUE FALSE 2663.199384 2675.665154 3327.116459 2351.770347 7454.604522 6192.69729 7016.849289 7481.88938 6558.472473 4972.273962 0.535609945 0.538117001 0.669133778 0.472976824 1.499234471 1.245445713 1.411195228 1.504721871 1.319008671 1 12.27969007 -8.753197918 24.99997637 0.726852341 1.402745319 0.629879938 0.246933606 79.19889169 240243.1826 0.031905511 0.062955922 1.77E-09 8.753197918 0.675892978 VLEEEEQRR ddPTM_HeLa_Romidepsin_16h_R1 2 VLEEEEQRR 9 1 E7EX44;Q05682-3;Q05682-6;Q05682-2;Q05682;E9PGZ1;Q05682-5;Q05682-4;C9J813 E7EX44;E9PGZ1 CALD1 Caldesmon 0 0 ; ; 105.1 0.015294 7519500 3886.4 3613.4 3753 3414 3207.1 3236 3088.8 2853 3768.3 4011.8 FALSE FALSE TRUE 3839.031062 3664.26954 3818.319391 3808.742743 3043.42972 3029.230044 3351.162595 2935.547054 3431.25381 3907.572858 0.982459241 0.937735437 0.977158848 0.974708056 0.778854248 0.775220362 0.857607194 0.751245635 0.878103604 1 11.93205706 -8.773118738 10.32386803 0.984791429 0.79435741 0.755444903 0.045230452 0.049039769 40.35717463 0.004401478 0.008178019 1.69E-09 8.773118738 -0.190434019 VLEEGGFFEEK ddPTM_HeLa_Romidepsin_16h_R1 1 VLEEGGFFEEK 11 0 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 0 0 128.51 0.00037386 0 1489 1423.6 1367 913.47 1586.4 1560.8 1285.2 1592.2 1412.9 1521.6 FALSE FALSE TRUE 1470.851495 1443.641478 1390.792062 1019.089699 1505.440088 1461.069917 1394.364856 1638.267795 1286.526685 1482.068613 0.992431445 0.97407196 0.938412736 0.687613037 1.015769496 0.985831496 0.940823417 1.105392679 0.868061488 1 10.53339652 -7.253991858 23.59891167 0.968217186 1.105392823 0.143084189 0.097268094 603.5388033 1912321.613 0.012967034 0.174877583 5.57E-08 7.253991858 0.137175637 VLEEGS(ph)VEAR ddPTM_HeLa_Romidepsin_16h_R1 1 VLEEGSVEAR 10 0 Q96CT7 Q96CT7 CCDC124 Coiled-coil domain-containing protein 124 1 0 VLEEGS(1)VEAR 124.39 0.0097148 2902500 931.74 1186.1 640.05 646.14 1014.2 1025.4 888.82 1107.1 1092.1 1202.1 TRUE FALSE FALSE 920.3835945 1202.797947 651.1898018 720.849747 962.4415895 959.8802493 964.3163486 1139.132192 994.4198408 1170.869269 0.786068624 1.027269209 0.556159273 0.615653486 0.82198894 0.819801386 0.823590109 0.972894432 0.849300488 1 10.19336429 -12.21186558 0.65065115 1.021803433 0.792785663 0.066685894 0.140532366 1.156308604 0.752393569 0.151596605 0.029781352 6.14E-13 12.21186558 -0.22901777 VLENGEDHGVAGSPAS(ph)PASIEEER ddPTM_HeLa_Romidepsin_16h_R1 1 VLENGEDHGVAGSPASPASIEEER 24 0 H0Y7I6;E9PI60;Q9ULD4 H0Y7I6 BRPF3 Bromodomain and PHD finger-containing protein 3 1 0 VLENGEDHGVAGS(0.332)PAS(0.436)PAS(0.231)IEEER 85.291 7.28E-05 2312900 757.47 623.84 703.36 469.83 360.39 619.93 490.75 553.62 875.33 752.13 TRUE FALSE FALSE 748.2376643 632.6224359 715.6016858 524.1539552 341.9979535 580.3184737 532.4342928 569.6381212 797.0382925 732.5895542 1.021359996 0.863542801 0.976811206 0.715481066 0.46683433 0.792146804 0.726783899 0.7775679 1.08797387 1 9.51686132 -9.259487277 4.461912431 0.995792659 0.687799643 0.693101925 0.09799972 0.082471641 4.347296863 0.01440087 0.023339229 5.50E-10 9.259487277 -0.307993016 VLES(ph)PENK ddPTM_HeLa_Romidepsin_16h_R1 1 VLESPENK 8 0 Q8N3D4 Q8N3D4 EHBP1L1 EH domain-binding protein 1-like protein 1 1 0 VLES(1)PENK 102.52 0.028873 35590000 7008.2 7076.8 7118.7 6697.9 7935.7 9268.9 9021.3 8006.8 8014.8 6909.2 TRUE FALSE FALSE 6922.781363 7176.427376 7242.597987 7472.342713 7530.711617 8676.647204 9787.568997 8238.464125 7297.936215 6729.697988 1.028691239 1.066381788 1.076214416 1.110353351 1.119026683 1.289307071 1.454384582 1.224195222 1.084437404 1 12.71632605 -8.470706937 1.14340664 1.021345885 1.358168813 0.756818748 0.065015609 0.148722488 0.360484546 0.009387051 0.035232761 3.38E-09 8.470706937 0.336822927 VLETAEDIQER ddPTM_HeLa_Romidepsin_16h_R1 1 VLETAEDIQER 11 0 A0A0D9SF54;A0A0D9SGF6;Q13813-3;Q13813;Q13813-2;A0A1B0GTB7;A0A0D9SFF6 A0A0D9SF54 SPTAN1 "Spectrin alpha chain, non-erythrocytic 1" 0 0 232.88 1.00E-35 6670700 2152.4 2136.9 1906.3 1887.5 2141.5 2114.2 1900.2 2007.6 2131.1 2125.1 FALSE FALSE TRUE 2126.165721 2166.983334 1939.478352 2105.741631 2032.211264 1979.109443 2061.602941 2065.686739 1940.489079 2069.889596 1.027187984 1.04690769 0.936996039 1.017320748 0.981796937 0.956142515 0.995996571 0.997969526 0.937484339 1 11.0153381 -9.777062556 24.99998115 1.015752664 0.982269251 0.038569944 0.034455079 218.9677167 350387.9121 0.003895291 0.005129185 1.67E-10 9.777062556 -0.033483414 VLGAGGAGPAPAT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 VLGAGGAGPAPATPSR 16 0 B7WPE2;Q32P44;H7C355;G3V195 B7WPE2 EML3 Echinoderm microtubule-associated protein-like 3 1 0 VLGAGGAGPAPAT(0.996)PS(0.004)R 151.22 0.00057891 15232000 824.07 960.9 896.4 918.89 1124.9 916.95 666.6 1001.5 868.52 929.59 TRUE FALSE FALSE 814.0259179 974.4275754 912.001466 1025.136385 1067.492155 858.3598543 723.2209874 1030.476822 790.837396 905.4391178 0.899039926 1.07619337 1.007247697 1.13219803 1.178977288 0.948003944 0.798751648 1.138096203 0.873429677 1 9.822473827 -10.25636081 24.73911103 0.95232441 1.034753196 0.17813075 0.108631693 659.3615907 3211932.401 0.018630285 0.022442718 5.54E-11 10.25636081 0.082428786 VLGEK(ac)GK ddPTM_HeLa_Romidepsin_16h_R1 1 VLGEKGK 7 1 P14618;B4DNK4;P14618-3;P14618-2;H3BTN5;H3BQ34;H3BR70 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 1 VLGEK(1)GK 108.46 0.028072 5085300 4211.5 4401.8 4732.8 4610.8 3892.1 4001.5 5496.7 2201.9 6806.4 4407.6 FALSE TRUE FALSE 4160.168618 4463.768656 4815.172399 5143.92239 3693.471614 3745.817064 5963.589561 2265.608502 6197.618537 4293.089917 0.969038315 1.039756619 1.121609957 1.198186502 0.860329433 0.872522388 1.389113593 0.527733764 1.443626539 1 12.06780067 -7.224741733 23.7468443 1.016327492 0.527731514 0.359290451 0.203415378 6649.686986 4302827.062 0.019486247 5.82734634 5.96E-08 7.224741733 -0.488595978 VLGILAMIDEGETDWK ddPTM_HeLa_Romidepsin_16h_R1 1 VLGILAMIDEGETDWK 16 0 Q5SQT6;Q15181 Q5SQT6 PPA1 Inorganic pyrophosphatase 0 0 92.866 0.025826 3214700 569.45 644.92 508.18 514.26 663.8 612.67 562.25 657.1 588.67 500.87 FALSE FALSE TRUE 562.5093244 653.9992007 517.0246597 573.7211609 629.923809 573.5223643 610.007501 676.1121518 536.0178808 487.8573252 1.153020146 1.34055423 1.059786608 1.17600194 1.291204982 1.175594451 1.25038094 1.385880906 1.098718525 1 8.93031548 -16.52287871 0.054496247 0.016351126 1.682373522 0.45539914 0.08668755 181.9524418 0.782509865 25.19661235 5.50202963 3.00E-17 16.52287871 1.666022396 VLGS(ph)EGEEEDEALS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 5 VLGSEGEEEDEALSPAK 17 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135;F5GZ28;M0QY71;M0R1G7 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 2 0 VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK;VLGS(1)EGEEEDEALS(1)PAK ;;;; 214.54 1.24E-25 227062300 38025.6 36367.1 36343.1 27169 26887.6 24982.2 20338.2 21740.8 37776.5 35534 TRUE FALSE FALSE 37562.12936 36879.07699 36975.63641 30310.40761 25515.42544 23385.91805 22065.7262 22369.83575 34397.67523 34610.82156 1.085271244 1.065536018 1.06832588 0.87574944 0.737209471 0.675682258 0.637538354 0.646324899 0.993841628 1 15.07893557 -8.869822789 1.797058604 1.04622602 0.652821186 0.96709018 0.032192595 0.048243039 0.315295866 0.005998422 0.012918223 1.35E-09 8.869822789 -0.393404834 VLGS(ph)EGEEEDEALSPAK ddPTM_HeLa_Romidepsin_16h_R1 4 VLGSEGEEEDEALSPAK 17 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135;F5GZ28;M0QY71;M0R1G7 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK;VLGS(1)EGEEEDEALSPAK ;;; 192.4 2.16E-13 287093000 18955.8 18089.1 17207.6 17536.3 21076.3 21636.8 19005.3 22242.9 19051 18132.7 TRUE FALSE FALSE 18724.75942 18343.75882 17507.09106 19563.92952 20000.69776 20254.27831 20619.60971 22886.46322 17347.03085 17661.60984 1.060195508 1.038623262 0.99125115 1.107709302 1.132439112 1.146796837 1.167481894 1.295831095 0.982188544 1 14.10832923 -4 0.318849666 1.016048645 3.632024238 0.8870017 0.031293275 12.04454476 0.153609411 0.010807678 18.60630617 1.00E-04 4 2.615975593 VLGSEGEEEDEALS(ph)PAK ddPTM_HeLa_Romidepsin_16h_R1 6 VLGSEGEEEDEALSPAK 17 0 M0R0Q7;P18858-2;P18858-3;P18858;B4E135;F5GZ28;M0QY71;M0R1G7 M0R0Q7 LIG1 DNA ligase;DNA ligase 1 1 0 VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK;VLGSEGEEEDEALS(1)PAK ;;;;; 197.94 4.97E-15 106415400 22641.81 20528.57 21646.86 16991.13 15469.09 13405.21 10597.19 11765.36 21912.96 20147.38 TRUE FALSE FALSE 22365.84291 20817.57175 22023.61452 18955.7244 14679.64461 12548.66034 11497.31505 12105.77213 19953.00998 19623.94816 1.139721871 1.060824844 1.122282547 0.965948556 0.748047462 0.639456456 0.58588185 0.616887694 1.01676838 1 14.26032771 -8.701652558 1.928661775 1.071563811 0.608397664 0.958802609 0.042061373 0.057766061 0.435886446 0.008552313 0.019841764 1.99E-09 8.701652558 -0.463166147 VLGSS(ph)T(ph)S(ph)ATNS(ph)TSVSSRK ddPTM_HeLa_Romidepsin_16h_R1 1 VLGSSTSATNSTSVSSRK 18 1 A0A0U1RQC1;H0YMA4;A0A0U1RQM0;Q15004-2;Q15004 A0A0U1RQC1 KIAA0101 PCNA-associated factor 4 0 VLGS(0.296)S(0.843)T(0.805)S(0.805)AT(0.169)NS(0.18)T(0.197)S(0.192)VS(0.263)S(0.25)RK 46.592 0.0042589 0 1294.3 1111 1384.2 475.55 1114.8 1250.3 924.86 918.46 1834.4 1391.4 TRUE FALSE FALSE 1278.524574 1126.640687 1408.29142 530.5353285 1057.907596 1170.409865 1003.417585 945.034191 1670.32667 1355.251227 0.94338566 0.83131501 1.039136798 0.391466407 0.780598884 0.863610998 0.740392309 0.69731292 1.232484897 1 10.4043446 -9.333094088 24.99999687 0.96417309 0.711365556 0.508109929 0.151104548 91.60377096 31959.77372 0.018669805 0.028518601 4.64E-10 9.333094088 -0.252807535 VLGSSNSDS(ph)DLFSR ddPTM_HeLa_Romidepsin_16h_R1 1 VLGSSNSDSDLFSR 14 0 Q8IWY7;Q6IQ55-2;Q6IQ55 Q8IWY7 TTBK2 Tau-tubulin kinase 2 1 0 VLGS(0.001)S(0.012)NS(0.058)DS(0.927)DLFS(0.002)R 123.1 0.0036786 2500600 706.56 648.83 570.47 638.03 626.91 910.83 677 699.86 725.96 728.99 TRUE FALSE FALSE 697.9481749 657.9642458 580.398791 711.8020306 594.9164434 852.6309026 734.5043631 720.1093449 661.0283194 710.0507347 0.982955359 0.92664399 0.817404676 1.002466438 0.837850613 1.200802789 1.034439269 1.014166044 0.930959278 1 9.471778302 -8.259944442 24.99596498 0.965246323 1.078266348 0.386225905 0.080438911 132.0214851 2207417.835 0.01145002 0.027573438 5.50E-09 8.259944442 0.113020025 VLGTS(ph)PEAIDSAENR ddPTM_HeLa_Romidepsin_16h_R1 3 VLGTSPEAIDSAENR 15 0 P27708;F8VPD4 P27708 CAD CAD protein;Glutamine-dependent carbamoyl-phosphate synthase;Aspartate carbamoyltransferase;Dihydroorotase 1 0 VLGT(0.16)S(0.84)PEAIDSAENR;VLGT(0.04)S(0.96)PEAIDSAENR;VLGT(0.049)S(0.951)PEAIDSAENR ;; 180.85 3.82E-08 9938600 4387.6 4275.8 4043.6 4025.7 3602.8 3881.8 3488.8 3883 4500.7 4233.2 TRUE FALSE FALSE 4334.122244 4335.994825 4113.977162 4491.170375 3418.935672 3633.765508 3785.138585 3995.348479 4098.14612 4123.220854 1.051149671 1.051603826 0.997758138 1.089238373 0.829190527 0.881292959 0.918005297 0.96898726 0.993918654 1 12.00955602 -8.76408846 24.99999999 1.028872022 0.899409027 0.69508457 0.04257505 29.62573175 279589.0643 0.006236972 0.01168693 1.72E-09 8.76408846 -0.129462995 VLIAAHGNSLR ddPTM_HeLa_Romidepsin_16h_R1 2 VLIAAHGNSLR 11 0 P18669;P15259 P18669 PGAM1;PGAM2 Phosphoglycerate mutase 1;Phosphoglycerate mutase 2 0 0 ; ; 123.51 0.0013527 4362900 1193.34 1065.93 1906.8 1381.33 3288.2 2933.1 1845.64 1507 1432.59 728.86 FALSE FALSE TRUE 1178.795113 1080.936191 1939.987054 1541.045874 3120.390884 2745.684376 2002.408616 1550.602667 1304.455562 709.9241121 1.660452283 1.522608082 2.732668212 2.170719162 4.395386536 3.867574476 2.820595302 2.184180874 1.837457751 1 9.471521005 -9.646989567 1.178002153 1.275225077 3.254335853 0.555766689 0.670216662 0.215448528 0.599501489 0.123134319 0.198299682 2.25E-10 9.646989567 1.979110776 VLIEGSINSVR ddPTM_HeLa_Romidepsin_16h_R1 1 VLIEGSINSVR 11 0 F8WDD7;H7C0A3;F8WCF6;A0A0A6YYG9;P59998;P59998-3;P59998-2 F8WDD7 ARPC4;ARPC4-TTLL3 Actin-related protein 2/3 complex subunit 4 0 0 167.93 0.0076717 1251600 212.27 229 376.33 225.42 196.97 316.78 161.79 284.29 265.98 201.54 FALSE FALSE TRUE 209.6827716 232.223868 382.8798658 251.484121 186.9178859 296.5387804 175.5324386 292.5154826 242.1900826 196.3039617 1.06815354 1.182981056 1.950443905 1.281095495 0.952186009 1.510610268 0.894186938 1.490115024 1.233750356 1 7.616945479 -9.999440335 24.99985411 1.037098524 1.333642318 0.121976855 0.286120487 23.55728096 1052220.383 0.043940673 0.057462435 1.00E-10 9.999440335 0.296543794 VLIIGSGGR ddPTM_HeLa_Romidepsin_16h_R1 1 VLIIGSGGR 9 0 C9JZG2;C9JKQ7;C9JBJ1;C9JTV6;F8WD69;P22102-2;P22102 C9JZG2 GART Trifunctional purine biosynthetic protein adenosine-3;Phosphoribosylamine--glycine ligase;Phosphoribosylformylglycinamidine cyclo-ligase;Phosphoribosylglycinamide formyltransferase 0 0 153.04 0.024741 819580 808.66 760.69 911.12 929.24 1136.3 1122.1 794.04 709.39 860.74 751.26 FALSE FALSE TRUE 798.8037409 771.3990138 926.9776614 1036.683101 1078.310371 1050.401431 861.4857378 729.9150804 783.7532586 731.7421569 1.091646468 1.054195124 1.266809152 1.416732781 1.473620675 1.435480273 1.177307785 0.997503114 1.071078455 1 9.515191567 -9.72494515 4.124701383 1.044408396 1.313026722 0.441660239 0.132169839 0.148875676 5.476396065 0.022686702 0.031812187 1.88E-10 9.72494515 0.268618326 VLISVGS(ph)YK ddPTM_HeLa_Romidepsin_16h_R1 1 VLISVGSYK 9 0 Q8TEV9-2;Q8TEV9 Q8TEV9-2 SMCR8 Smith-Magenis syndrome chromosomal region candidate gene 8 protein 1 0 VLIS(0.001)VGS(0.999)YK 149.33 0.0053851 25907000 5194.9 5606.8 5296.1 5132.4 4895.8 4687.5 3385.4 4149.6 4957.4 4225.7 TRUE FALSE FALSE 5131.582561 5685.732678 5388.276399 5725.832237 4645.949057 4387.983878 3672.955791 4269.662129 4513.997728 4115.915705 1.246765709 1.381401633 1.309131864 1.391144194 1.128776532 1.066101493 0.892378769 1.037354124 1.09671773 1 12.00699772 -8.107705707 2.922098517 1.17629061 0.966666043 0.372877612 0.127205161 0.310692316 5.0662477 0.023375494 0.071024646 7.80E-09 8.107705707 -0.209624567 VLLGETGK(ac)EK ddPTM_HeLa_Romidepsin_16h_R1 1 VLLGETGKEK 10 1 M0QZC5;P62280;M0R1H6 M0QZC5 RPS11 40S ribosomal protein S11 0 1 VLLGETGK(1)EK 124.92 0.013125 1365500 923.52 650.43 869.99 1127.7 3085.6 2289.5 2415.9 1697.1 2601 1665.1 FALSE TRUE FALSE 912.263783 659.5867706 885.131811 1258.08998 2928.130318 2143.208339 2621.106486 1746.202911 2368.360046 1621.840462 0.562486758 0.406690292 0.545757633 0.77571747 1.805436716 1.321466808 1.6161309 1.076679829 1.460291626 1 10.6634162 -8.817320726 9.747999792 0.734075366 1.456436833 0.489121416 0.328861773 0.183975907 30.74708449 0.039908838 0.072494311 1.52E-09 8.817320726 0.722361467 VLLGSLMDSS(ph)REK ddPTM_HeLa_Romidepsin_16h_R1 1 VLLGSLMDSSREK 13 1 M0QZ23;M0R2B3;Q9H6X5-2;Q9H6X5 M0QZ23 C19orf44 Uncharacterized protein C19orf44 1 0 VLLGSLMDS(0.003)S(0.997)REK 64.945 0.029098 182430000 783.24 632.95 526.47 881.31 759.24 655.15 692.2 867.97 848.82 825.71 TRUE FALSE FALSE 773.6935696 641.8606867 535.6329895 983.2112089 720.4931497 613.2880294 750.9954507 893.0833425 772.8994133 804.2579352 0.961996812 0.798078152 0.665996524 1.222507315 0.895848357 0.762551419 0.933774375 1.11044393 0.961009372 1 9.651514455 -10.49609578 15.19202839 0.983240541 0.907441406 0.03308286 0.152750958 8.75767269 4968.849622 0.026209256 0.028620267 3.19E-11 10.49609578 -0.075799134 VLLPEYGGTK ddPTM_HeLa_Romidepsin_16h_R1 1 VLLPEYGGTK 10 0 P61604;B8ZZL8;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 0 117.53 0.029471 643080 1262.9 1108.9 1222.4 1006.4 874.97 1346.6 1049.5 1210.8 1131.8 957.29 FALSE FALSE TRUE 1247.507289 1124.511123 1243.675359 1122.764703 830.3170159 1260.556606 1138.644504 1245.832588 1030.568973 932.4194678 1.337924971 1.206014205 1.333815308 1.204141207 0.890497297 1.351920085 1.221171954 1.336128889 1.105263252 1 9.864835316 -12.47466679 1.203267202 0.999483005 1.239676124 0.221897179 0.131959518 0.457830548 1.181841753 0.091038584 0.022156904 3.35E-13 12.47466679 0.240193119 VLLQAS(ph)QDENFGNTTPR ddPTM_HeLa_Romidepsin_16h_R1 2 VLLQASQDENFGNTTPR 17 0 G3V1T4;P57740 G3V1T4 NUP107 Nuclear pore complex protein Nup107 1 0 VLLQAS(1)QDENFGNTTPR;VLLQAS(0.998)QDENFGNT(0.002)TPR ; 190.18 2.99E-13 40962000 3832.9 4537.1 3940.3 3858.3 4192.4 4649.6 3719.3 4110.3 3880.5 3869.1 TRUE FALSE FALSE 3786.183141 4600.973413 4008.879269 4304.4148 3978.446184 4352.505566 4035.217249 4229.225046 3533.418361 3768.580224 1.004670968 1.220877131 1.063763813 1.142184734 1.055688335 1.154945711 1.070752647 1.122232988 0.937599348 1 11.87980539 -10.39916216 13.14603201 1.002060848 1.114558938 0.597691661 0.050873644 0.344146948 35.23666082 0.007001739 0.008004382 3.99E-11 10.39916216 0.11249809 VLLS(ph)DSNLHDA ddPTM_HeLa_Romidepsin_16h_R1 1 VLLSDSNLHDA 11 0 H3BV90;Q6FI81-3;Q6FI81;Q6FI81-2 H3BV90 CIAPIN1 Anamorsin 1 0 VLLS(0.921)DS(0.079)NLHDA 116.84 0.011469 7501200 3043.3 3056.2 2642.3 2902.9 3153.7 2973.4 2742.8 2789.3 3145.6 2853.9 TRUE FALSE FALSE 3006.207089 3099.225264 2688.288123 3238.546957 2992.754921 2783.409336 2975.773364 2870.003995 2864.249658 2779.755267 1.081464662 1.114927383 0.967095253 1.165047512 1.076625326 1.001314529 1.070516315 1.032466429 1.030396342 1 11.44074216 -12.34003281 1.058515422 0.9999178 1.06514042 0.107599309 0.053311279 0.704070162 1.409449058 0.034092641 0.008907564 4.57E-13 12.34003281 0.06522262 VLLSDS(ph)NLHDA ddPTM_HeLa_Romidepsin_16h_R1 1 VLLSDSNLHDA 11 0 H3BV90;Q6FI81-3;Q6FI81;Q6FI81-2 H3BV90 CIAPIN1 Anamorsin 1 0 VLLS(0.228)DS(0.772)NLHDA 96.756 0.0035493 0 2118.7 2006.3 1662 1735.8 1824.3 1601.8 1616.9 2123.3 1871 2002.5 TRUE FALSE FALSE 2092.876469 2034.544744 1690.926413 1936.501363 1731.199164 1499.45015 1754.239446 2184.734335 1703.653074 1950.474761 1.073008742 1.043102318 0.866930681 0.992835899 0.887578347 0.768761626 0.899391 1.120103874 0.873455585 1 10.92960962 -9.774256767 24.91202924 1.03608662 0.916153236 0.065887739 0.100937757 203.1441605 394832.4206 0.014168679 0.018688604 1.68E-10 9.774256767 -0.119933385 VLNNMEIGTSLFDEEGAK ddPTM_HeLa_Romidepsin_16h_R1 2 VLNNMEIGTSLFDEEGAK 18 0 P00558;P00558-2 P00558 PGK1 Phosphoglycerate kinase 1 0 0 ; ; 127.3 0.0038809 23829000 2428.8 2431.4 2321.7 1780.48 2624.4 2718.4 1967.09 2425 2699.8 2417.6 FALSE FALSE TRUE 2399.196851 2465.629313 2362.108215 1986.347475 2490.467075 2544.703013 2134.174576 2495.163549 2458.323126 2354.790403 1.01885792 1.047069544 1.003107627 0.843534725 1.057617303 1.080649475 0.906311905 1.059611737 1.043966853 1 11.20138294 -13.16030719 3.435676937 0.999845775 1.004763184 0 0.071528024 6.076090232 132.6392681 0.061468036 0.00951169 6.91E-14 13.16030719 0.004917409 VLNSYWVGEDSTYK ddPTM_HeLa_Romidepsin_16h_R1 1 VLNSYWVGEDSTYK 14 0 P61313;E7EX53;A0A2R8Y738;A0A2R8YEM3;E7EQV9;E7ENU7 P61313 RPL15 60S ribosomal protein L15;Ribosomal protein L15 0 0 131.32 0.00013256 0 869.07 809.98 806.79 806.11 880.69 776.01 657.7 745.08 878.01 773.01 FALSE FALSE TRUE 858.4774406 821.3829197 820.8318415 899.3162311 835.745103 726.4254655 713.5650216 766.6377143 799.4785866 752.9270888 1.140186684 1.090919602 1.090187687 1.194426717 1.109994733 0.964801873 0.947721276 1.018209765 1.061827365 1 9.556366355 -8.255841887 24.29270549 1.083759242 0.973991991 0.526636334 0.051418561 268.5734233 1165580.501 0.009630444 0.023795061 5.55E-09 8.255841887 -0.109767251 VLNTGS(ph)DVEEAVADALK ddPTM_HeLa_Romidepsin_16h_R1 1 VLNTGSDVEEAVADALK 17 0 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 0 VLNTGS(1)DVEEAVADALK 223.93 1.40E-35 5218100 1585.9 1564 1689.6 1253.6 1330.3 1383.5 1155.1 1649.2 1451.2 1685.8 TRUE FALSE FALSE 1566.570441 1586.018033 1719.006779 1398.54713 1262.409827 1295.098815 1253.214165 1696.917 1321.401037 1642.002673 0.954060835 0.96590466 1.046896456 0.851732554 0.768823247 0.788731247 0.763222975 1.033443506 0.804749626 1 10.68124076 -9.144505268 5.963635328 0.981120663 0.827636095 0.240085654 0.094009519 0.145665744 6.65933431 0.010823117 0.018085565 7.17E-10 9.144505268 -0.153484568 VLNTGS(ph)DVEEAVADALKKPAR ddPTM_HeLa_Romidepsin_16h_R1 2 VLNTGSDVEEAVADALKKPAR 21 2 E3W994;J3KR49;O75122 E3W994 CLASP2 CLIP-associating protein 2 1 0 VLNT(0.345)GS(0.655)DVEEAVADALKKPAR;VLNT(0.346)GS(0.654)DVEEAVADALKKPAR ; 115.38 6.62E-05 34510000 8755.5 8506.7 7622 9529.7 9031.8 8470.9 6914.6 8291.4 9908 7960.7 TRUE FALSE FALSE 8648.784598 8626.457546 7754.657713 10631.56875 8570.873544 7929.636829 7501.925951 8531.298577 9021.803665 7753.879866 1.115413799 1.11253433 1.000100317 1.371128898 1.10536579 1.02266697 0.967506085 1.100261898 1.163521208 1 12.92070267 -6.859797807 19.44461196 1.072498712 15.90349126 0 0.112247107 4307.679709 597930.6397 0.015064218 2379.626953 1.38E-07 6.859797807 14.83099255 VLPAFRES(ph)PSGR ddPTM_HeLa_Romidepsin_16h_R1 2 VLPAFRESPSGR 12 1 O43166-3;O43166-2;O43166;F5GYF8 O43166-3 SIPA1L1 Signal-induced proliferation-associated 1-like protein 1 1 0 VLPAFRES(0.966)PS(0.034)GR;VLPAFRES(0.743)PS(0.257)GR ; 75.483 0.021744 39598000 4914.6 5031.7 4331.4 4592 4039.5 3653.4 2840.6 3038.36 5300.9 5356.7 TRUE FALSE FALSE 4854.698965 5102.536405 4406.7862 5122.948646 3833.349242 3419.959531 3081.880493 3126.270153 4826.774228 5217.532162 0.930458848 0.977959742 0.844611219 0.981871982 0.734705436 0.655474547 0.590677814 0.599185603 0.925106751 1 12.34915187 -8.535275543 1.550971883 0.961566376 0.593710631 0.90296803 0.048551894 0.077507128 0.365636571 0.007358594 0.021092515 2.92E-09 8.535275543 -0.367855745 VLPIT(ph)VPKSPAFALK ddPTM_HeLa_Romidepsin_16h_R1 1 VLPITVPKSPAFALK 15 1 Q9ULW0;Q9ULW0-2 Q9ULW0 TPX2 Targeting protein for Xklp2 1 0 VLPIT(0.994)VPKS(0.006)PAFALK 73.219 0.024252 36485000 4080.6 3583.6 3065.9 12061 4520.4 4262.7 3426.2 3875.5 4733 3260.7 TRUE FALSE FALSE 4030.864078 3634.050015 3119.260703 13455.54957 4289.70712 3990.327227 3717.221342 3987.631478 4309.668626 3175.986544 1.26916913 1.144227145 0.982139143 4.236651945 1.350669173 1.256405584 1.170414701 1.255556792 1.356954309 1 11.63298908 VLPPPAGYVPIRT(ph)PAR ddPTM_HeLa_Romidepsin_16h_R1 2 VLPPPAGYVPIRTPAR 16 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 VLPPPAGYVPIRT(1)PAR;VLPPPAGY(0.001)VPIRT(0.999)PAR ; 180.32 1.25E-08 78343000 3042 2718.61 3337.67 3483.14 3165.8 2851.35 2408.59 3160.54 3452.98 3052.04 TRUE FALSE FALSE 3004.922934 2756.882663 3395.760746 3885.877035 3004.237413 2669.157937 2613.175574 3251.985238 3144.136821 2972.747561 1.010823446 0.927385392 1.142297042 1.30716684 1.010592844 0.897875747 0.879043888 1.093932523 1.057653486 1 11.53758124 -6.926783718 19.81848118 1.015261305 3.316604834 0.021523756 0.11978111 987.2946329 285720.4182 0.016577203 6922.696036 1.18E-07 6.926783718 2.301343529 VLPPPAGYVPIRT(ph)PARK ddPTM_HeLa_Romidepsin_16h_R1 1 VLPPPAGYVPIRTPARK 17 2 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 VLPPPAGYVPIRT(1)PARK 57.53 0.021198 21271000 3660.2 3135.8 3752 3768.6 2755.2 2933.3 2432.1 2895.6 3683.7 3313.9 TRUE FALSE FALSE 3615.588075 3179.945875 3817.301986 4204.343264 2614.591863 2745.871597 2638.682513 2979.379617 3354.220646 3227.8044 1.12013853 0.98517304 1.182631136 1.302539665 0.810021779 0.850693306 0.817485258 0.923035986 1.039164779 1 11.65633744 -8.722125927 24.99998657 1.077944507 0.847991744 0.633773726 0.093477197 91.46646531 58164.44252 0.01450129 0.02900225 1.90E-09 8.722125927 -0.229952763 VLPS(ph)ITTEILK ddPTM_HeLa_Romidepsin_16h_R1 1 VLPSITTEILK 11 0 P35232;C9JZ20;E7ESE2;E9PCW0;C9JW96;P35232-2 P35232 PHB Prohibitin 1 0 VLPS(0.973)IT(0.025)T(0.001)EILK 121.21 0.0094877 4780600 2057 1876.8 1430.2 1324.5 2032.5 1760.5 1759.3 1516.7 1657.6 1737.1 TRUE FALSE FALSE 2031.928493 1903.22164 1455.092031 1477.644922 1928.773941 1648.009732 1908.734898 1560.583322 1509.340104 1691.969892 1.200924734 1.124855501 0.859998773 0.873328142 1.139957602 0.974018356 1.128113986 0.922346981 0.892060853 1 10.72448818 VLPSEQESTK(ac)KPYR ddPTM_HeLa_Romidepsin_16h_R1 2 VLPSEQESTKKPYR 14 2 Q96T23-3;Q96T23-2;Q96T23 Q96T23-3 RSF1 Remodeling and spacing factor 1 0 1 ; VLPSEQESTK(0.993)K(0.007)PYR;VLPSEQESTK(0.991)K(0.009)PYR 145.61 1.10E-06 8742200 2089.82 2277.6 2530.2 1887.94 3814.5 3772.9 2883.7 3436.2 2100.57 2198.35 FALSE TRUE FALSE 2064.34847 2309.664113 2574.23707 2106.232506 3619.831831 3531.823866 3128.641406 3535.621026 1912.689758 2141.23655 0.964091739 1.078659017 1.202219843 0.983652416 1.690533365 1.649431898 1.46113768 1.651205247 0.893264109 1 11.06422847 -8.764975781 24.99998969 1.008919218 1.604821057 0.903006281 0.095113409 18.60140876 131500.8304 0.013737471 0.025636129 1.72E-09 8.764975781 0.595901839 VLQATVVAVGS(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 VLQATVVAVGSGSK 14 0 P61604;B8ZZL8;S4R3N1 P61604 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 1 0 VLQATVVAVGS(0.768)GS(0.232)K 149.6 8.47E-05 0 2473 2373.7 2639.6 5756.4 2202.7 2727.2 2088.4 2251 2499 2373 TRUE FALSE FALSE 2442.858125 2407.117011 2685.541131 6421.982053 2090.288 2552.940722 2265.788644 2316.129134 2275.483181 2311.349118 1.056897076 1.041433764 1.161893333 2.778456099 0.904358404 1.104524064 0.980288363 1.002068063 0.984482683 1 11.17451947 -9.515334889 24.93668553 1.032185092 1.361930188 0.088166768 0.506096271 689.9655212 2280725.882 0.078864583 0.1143345 3.05E-10 9.515334889 0.329745096 VLQATVVAVGSGSK ddPTM_HeLa_Romidepsin_16h_R1 2 VLQATVVAVGSGSK 14 0 P61604;B8ZZL8;S4R3N1 P61604 HSPE1;HSPE1-MOB4 "10 kDa heat shock protein, mitochondrial" 0 0 ; ; 234.82 1.36E-42 9664000 3413.7 2762 3005.8 3033.6 3352.5 3219.2 2763.9 3070.9 2830.1 3016.2 FALSE FALSE TRUE 3372.092511 2800.883508 3058.114688 3384.359106 3181.409415 3013.503509 2998.665597 3159.751646 2576.968768 2937.838689 1.147814046 0.953382335 1.040940301 1.151989426 1.082908135 1.025755267 1.020704645 1.075536127 0.877164828 1 11.52053947 -8.257907332 24.09946218 1.067204336 1.038669278 0 0.083700894 646.1947303 4409033.953 0.010016764 0.024331383 5.52E-09 8.257907332 -0.028535057 VLS(ph)PEELEDR ddPTM_HeLa_Romidepsin_16h_R1 2 VLSPEELEDR 10 0 A0A494C179;A0A0A0MRH8;A0A494C1P7;A0A0A0MSH9;A0A494C1F7;Q86WJ1-5;Q86WJ1-3;Q86WJ1-4;Q86WJ1-2;Q86WJ1 A0A494C179 CHD1L Chromodomain-helicase-DNA-binding protein 1-like 1 0 VLS(1)PEELEDR;VLS(1)PEELEDR ; 120.57 0.011468 6251300 2216.5 1987.4 2543 2172.68 2674.4 2838.2 2132.85 2583.6 2539.5 2355.89 TRUE FALSE FALSE 2189.484445 2015.378669 2587.259848 2423.895484 2537.915388 2656.84818 2314.014226 2658.35239 2312.36076 2294.683638 0.954155252 0.87828171 1.127501763 1.05630922 1.105997945 1.157827657 1.008424075 1.158483176 1.007703511 1 11.16407955 -9.742732435 24.99966779 0.970240984 1.098735946 0.624951926 0.053760918 124.5529768 166450.3572 0.008047106 0.01136887 1.81E-10 9.742732435 0.128494962 SSS(ph)PTLTPSQEGSPVFAGFEGR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSPTLTPSQEGSPVFAGFEGR 22 0 P0C860 P0C860 MSL3P1 Putative male-specific lethal-3 protein-like 2 1 0 S(0.007)S(0.007)S(0.927)PT(0.057)LT(0.001)PSQEGSPVFAGFEGR 218.79 5.54E-41 0 730.93 735.48 503.87 659.11 479.98 588.49 280.94 343.59 794.34 727.49 TRUE FALSE FALSE 722.021144 745.8341067 512.639646 735.3193994 455.4848295 550.8873883 304.8030366 353.5312346 723.2922409 708.5897049 1.018955171 1.052561308 0.723464711 1.037722386 0.642804752 0.777441987 0.430154481 0.498922341 1.020749012 1 9.468806695 -8.090564582 0.605988947 1.013031611 0.325050199 0.7465845 0.113837107 0.511734513 0.223711046 0.019603627 0.203532241 8.12E-09 8.090564582 -0.687981412 down VLS(ph)PLRS(ph)PPLIGSESAYESFLSADDK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPLRSPPLIGSESAYESFLSADDK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VLS(0.363)PLRS(0.679)PPLIGS(0.409)ES(0.413)AY(0.126)ES(0.01)FLSADDK 62.193 0.0055327 2922600 412.07 395.47 225.82 221.61 394.89 349.75 349.22 548.76 327.18 412.56 TRUE FALSE FALSE 407.0475323 401.037437 229.7503024 247.2335909 374.7372898 327.4021038 378.8827381 564.6375048 297.9162014 401.8416317 1.012955105 0.997998727 0.571743404 0.615251311 0.932549692 0.814754067 0.942865816 1.405124458 0.741377144 1 8.650483228 -9.951210959 24.99966997 1.00608521 0.863417917 0 0.228849424 217.8505031 111626.8048 0.034622398 0.04550274 1.12E-10 9.951210959 -0.142667293 VLS(ph)PLRS(ph)PPLIGSESAYESFLSADDKASGR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPLRSPPLIGSESAYESFLSADDKASGR 30 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VLS(0.999)PLRS(0.998)PPLIGS(0.003)ESAYESFLSADDKASGR 121.97 2.15E-11 25820000 1679.9 1867.6 1391 2319.6 1963.3 2267.2 1980.8 2175.6 1462.7 1352.9 TRUE FALSE FALSE 1659.424733 1893.892122 1415.209772 2587.803066 1863.105475 2122.333237 2149.049103 2238.547553 1331.872449 1317.751463 1.259285062 1.437214964 1.073958035 1.963802082 1.41385195 1.610571718 1.630845545 1.698763095 1.01071597 1 10.36386258 -9.988197587 0.344854524 0.981763871 1.748584064 0.608786865 0.192071843 0.627288016 0.205242045 0.122531828 0.182255 1.03E-10 9.988197587 0.766820193 VLS(ph)PLRSPPLIGS(ph)ESAYESFLSADDK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPLRSPPLIGSESAYESFLSADDK 26 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VLS(0.921)PLRS(0.217)PPLIGS(0.683)ES(0.17)AY(0.007)ES(0.001)FLSADDK 71.002 0.0008138 9161500 449.27 366.47 531.18 501.28 564.5 634.56 408.76 568.74 598.8 550.41 TRUE FALSE FALSE 443.7941244 371.6291743 540.4249651 559.2403522 535.6914586 594.0136639 443.4800642 585.1955946 545.2418283 536.1102689 0.827803812 0.693195404 1.008048151 1.043144265 0.999218798 1.108006503 0.827218 1.091558264 1.017032987 1 9.066385959 -9.594265556 25 0.897173712 1.009672342 0.241109386 0.110568082 57.78733555 20236.27513 0.018055014 0.025533647 2.55E-10 9.594265556 0.11249863 VLS(ph)PPGRR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPPGRR 8 1 H0YBI6;H0YBQ0;Q86VQ6 H0YBI6 TXNRD3 Thioredoxin reductase 3 1 0 VLS(1)PPGRR 67.704 0.026591 3709900 980.07 831.61 1014.1 953.74 744.03 1006.3 838.71 924.68 977.93 832.95 TRUE FALSE FALSE 968.1245299 843.3174274 1031.749985 1064.015906 706.0593727 942.0006777 909.9500065 951.4341569 890.4614915 811.3098389 1.193285824 1.039451745 1.271708952 1.311479111 0.870270936 1.161086224 1.121581377 1.172713692 1.097560326 1 9.664109174 -12.43084216 1.085718956 0.997592018 1.144813639 0.068167984 0.119450777 0.738809865 1.515997418 0.084964022 0.019933427 3.71E-13 12.43084216 0.14722162 VLS(ph)PPHIK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPPHIK 8 0 A0A0D9SG79;Q9NZ09-2;Q9NZ09;Q9NZ09-3;Q9NZ09-4 A0A0D9SG79 UBAP1 Ubiquitin-associated protein 1 1 0 VLS(1)PPHIK 74.841 0.029993 37259000 10613 9277 9589.1 9313.3 12750 14092 11702 13178 11231 9868.6 TRUE FALSE FALSE 10483.64467 9407.60185 9755.994263 10390.14757 12099.31992 13191.56668 12695.96759 13559.28464 10226.47123 9612.212349 1.090658872 0.978713485 1.014958254 1.080931963 1.258744552 1.372375703 1.320816387 1.410630992 1.063904007 1 13.2306528 -8.668462623 2.285163884 1.035934221 1.363721747 0.945335081 0.036470719 0.056220311 0.595326702 0.006519031 0.01466755 2.15E-09 8.668462623 0.327787526 VLS(ph)PTAAKPSPFEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 0 VLS(0.658)PT(0.337)AAKPS(0.005)PFEGK 63.998 0.024932 247870000 5932.7 5339.6 5335.6 5395.4 5241.7 5544.6 5172.5 5728.3 5738.3 5298.6 TRUE FALSE FALSE 5860.38997 5414.771029 5428.46388 6019.241534 4974.19649 5190.317954 5611.852021 5894.039323 5225.052076 5160.941608 1.135527277 1.049182773 1.051835942 1.166306847 0.963815689 1.005692052 1.087369795 1.142047279 1.012422242 1 12.33341859 -7.373342908 3.876266052 1.06005802 1.142239629 0.171022458 0.059505623 0.382157652 9.039455811 0.009212257 0.068226109 4.23E-08 7.373342908 0.082181608 VLS(ph)RNSADDEELTNDSLTLSQSK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSRNSADDEELTNDSLTLSQSK 23 1 A0A0U1RRH6;O94880 A0A0U1RRH6 PHF14 PHD finger protein 14 1 0 VLS(0.539)RNS(0.461)ADDEELTNDSLTLSQSK 98.151 1.84E-05 7491700 1916.3 1703 1482.4 1939.5 1746.3 1732.8 1746.3 1530.6 2051.6 1849.2 TRUE FALSE FALSE 1892.943399 1726.974879 1508.20055 2163.754116 1657.179795 1622.079672 1894.630678 1574.885496 1868.099758 1801.157517 1.050959386 0.958813908 0.837350723 1.201313097 0.92006378 0.900576244 1.051896161 0.874374107 1.037166233 1 10.81470864 -4 0.327923644 1.018641291 6.17E-10 0.081529887 0.098016791 97.60603043 1.240269511 0.030165083 60.95908442 1.00E-04 4 -1.01864129 VLS(ph)STSEEDEPGVVK ddPTM_HeLa_Romidepsin_16h_R1 2 VLSSTSEEDEPGVVK 15 0 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 0 VLS(0.494)S(0.494)T(0.012)S(0.001)EEDEPGVVK;VLS(0.252)S(0.252)T(0.252)S(0.245)EEDEPGVVK ; 255.39 1.66E-70 81166700 5959.8 6766.1 5553.6 6193 7340.1 5117.2 3617.7 4433 5120.2 5389.3 TRUE FALSE FALSE 5887.159665 6861.353333 5650.258078 6909.063799 6965.507307 4790.227435 3924.987348 4561.261861 4662.236488 5249.285209 1.121516441 1.307102407 1.076386185 1.316191352 1.326943961 0.912548517 0.74771844 0.868930088 0.88816597 1 12.35790527 -8.028217396 10.98816735 1.114960889 0.813660962 0.498607675 0.139976965 0.504334143 196.3007922 0.01969102 0.051270288 9.37E-09 8.028217396 -0.301299927 VLS(ph)TSTDLEAAVADALKKPVR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 0 VLS(0.25)T(0.25)S(0.25)T(0.25)DLEAAVADALKKPVR 111.35 8.10E-05 18229000 4883.6 6530.8 4652.2 5442.4 4577 4285.5 3220.5 4263.5 4548.3 4472 TRUE FALSE FALSE 4824.076805 6622.740774 4733.169589 6071.675895 4343.418611 4011.670381 3494.04919 4386.857646 4141.488657 4355.816795 1.107502228 1.520436025 1.086631925 1.393923615 0.997153649 0.920991531 0.802157059 1.007126298 0.95079496 1 12.08872756 -8.528514957 24.9924368 1.118723199 0.909260533 0.299996185 0.173708317 168.6441535 747811.6471 0.026190765 0.052506848 2.96E-09 8.528514957 -0.209462666 VLSEDEEDVDFDIIHNANDTFTVK ddPTM_HeLa_Romidepsin_16h_R1 2 VLSEDEEDVDFDIIHNANDTFTVK 24 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 ; ; 180.04 2.84E-18 7657500 1911.09 1917.09 1881.38 1864.13 2288.9 2606.2 2228.43 2574.9 2243.55 2135.12 FALSE FALSE TRUE 1887.7969 1944.078843 1914.12463 2079.669482 2172.088892 2439.672231 2417.712789 2649.400669 2042.881269 2079.649275 0.907747726 0.934810916 0.920407423 1.000009717 1.044449619 1.173117151 1.162557946 1.273965135 0.982320093 1 11.02212453 -8.287702036 1.197561104 0.950655262 1.23996073 0.913146849 0.034480156 0.13022868 0.332562488 0.006606491 0.029122516 5.16E-09 8.287702036 0.289305468 VLSGALK(ac)LDSK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSGALKLDSK 11 1 H0YCS9;H0Y5L2;Q9NTX5-3;Q9NTX5-6;Q9NTX5-2;Q9NTX5 H0YCS9 ECHDC1 Ethylmalonyl-CoA decarboxylase 0 1 VLSGALK(1)LDSK 92.943 0.015672 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 VLSPLRS(ph)PPLIGSESAYESFLSADDKASGR ddPTM_HeLa_Romidepsin_16h_R1 3 VLSPLRSPPLIGSESAYESFLSADDKASGR 30 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 1 0 VLS(0.003)PLRS(0.996)PPLIGSESAYESFLSADDKASGR;VLS(0.037)PLRS(0.925)PPLIGS(0.031)ES(0.004)AY(0.004)ESFLSADDKASGR;VLS(0.061)PLRS(0.335)PPLIGS(0.152)ES(0.152)AY(0.291)ES(0.01)FLSADDKASGR ;; 123.03 2.72E-11 290156000 2516.96 2315.57 1906.62 6945.7 2528.86 2454.54 2360.52 2451.67 2461.7 2176.72 TRUE FALSE FALSE 2486.282323 2348.168655 1939.803921 7748.794515 2399.802838 2297.702816 2561.02251 2522.605203 2241.519387 2120.168501 1.172681474 1.107538695 0.91492913 3.654801263 1.131892506 1.083735946 1.207933478 1.189813547 1.057236435 1 11.04996321 VLSPT(ph)AAKPSPFEGK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSPTAAKPSPFEGK 15 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 0 VLS(0.349)PT(0.453)AAKPS(0.198)PFEGK 69.878 0.027928 297400000 4136.1 3843.3 3573.5 3967.5 3458 3876.1 3257.6 2946.7 3476.5 3168.9 TRUE FALSE FALSE 4085.687622 3897.406078 3635.695268 4426.241018 3281.525356 3628.42972 3534.300463 3031.958115 3165.553133 3086.571521 1.3236977 1.262697479 1.177907346 1.434031574 1.063161937 1.175553424 1.145057044 0.982306127 1.025588784 1 11.59178951 -6.850334346 1.425008456 1.181630759 0.652590878 0.18183538 0.127223871 5.516630067 4.537086902 0.02157474 5.542603154 1.41E-07 6.850334346 -0.529039882 VLSQSTPGT(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 2 VLSQSTPGTPSK 12 0 Q6MZP7;Q6MZP7-3 Q6MZP7 LIN54 Protein lin-54 homolog 1 0 VLSQSTPGT(0.768)PS(0.232)K;VLSQST(0.002)PGT(0.995)PS(0.003)K ; 149.3 0.0030251 18798700 7832.6 8302.5 7878.8 6509 5335.6 5490.9 3962.9 3805.4 7414.8 7118.2 TRUE FALSE FALSE 7737.133258 8419.382813 8015.927209 7261.601206 5063.304422 5140.049211 4299.508627 3915.503245 6751.601717 6933.268138 1.115943175 1.214345478 1.156154219 1.047356176 0.730291159 0.741360223 0.620127268 0.564741355 0.973797866 1 12.75931984 -8.696094166 2.734018387 1.079575031 0.645970607 0.877959388 0.077347818 0.075122067 1.139946234 0.012924373 0.027575953 2.01E-09 8.696094166 -0.433604424 VLSS(ph)TSEEDEPGVVK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSSTSEEDEPGVVK 15 0 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 0 VLS(0.177)S(0.771)T(0.052)SEEDEPGVVK 281.6 9.96E-100 3772500 1776.3 2400 1725 2043 2439.2 1566.1 1210.3 1445 1741.9 1705.4 TRUE FALSE FALSE 1754.649772 2433.787263 1755.022901 2279.221273 2314.718522 1466.031264 1313.102852 1486.808795 1586.100101 1661.093462 1.056322123 1.465171779 1.056546752 1.37212103 1.393490839 0.882570004 0.790505099 0.89507835 0.954853015 1 10.69791753 -8.030272614 24.58065545 1.111957235 0.841228082 0.373510364 0.179042258 515.1335566 418276.4466 0.027383195 0.069930047 9.33E-09 8.030272614 -0.270729152 VLSSAAS(ph)LPGSELPSSRPEGSQGGELSR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 0 VLS(0.006)S(0.013)AAS(0.438)LPGS(0.051)ELPS(0.127)S(0.326)RPEGS(0.038)QGGELS(0.001)R 47.854 0.012969 28059000 601.2 488.1 541.64 653.12 661.73 665.5 650.26 788.66 573.22 597.9 TRUE FALSE FALSE 593.8723432 494.9714846 551.067017 728.6368074 627.9594488 622.9766978 705.4930682 811.4786328 521.9497675 582.3664718 1.019757098 0.849931287 0.94625471 1.251165448 1.078289152 1.069733111 1.211424597 1.393415782 0.896256555 1 9.185783488 -4 0.469815188 0.997962049 11.28315943 0.650406522 0.095121237 39.10734522 0.404126475 0.018855513 393.4938071 1.00E-04 4 10.28519738 VLSSAASLPGSELPSSRPEGS(ph)QGGELSR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSSAASLPGSELPSSRPEGSQGGELSR 28 1 O15027;O15027-5;A0A0C4DH09;Q8N9G1 O15027 SEC16A Protein transport protein Sec16A 1 0 VLSSAASLPGS(0.003)ELPS(0.051)S(0.126)RPEGS(0.477)QGGELS(0.343)R 50.498 0.0089245 17614000 944.91 1341.5 1368.3 748.19 1079.1 1336.7 729.98 1215.1 948.98 989 TRUE FALSE FALSE 933.3930735 1360.385672 1392.114688 834.6992481 1024.0295 1251.289184 791.984483 1250.257001 864.100852 963.3056374 0.968948003 1.412205659 1.4451433 0.86649472 1.063036964 1.298953453 0.822152858 1.297881952 0.897016293 1 9.911849798 VLSST(ph)SEEDEPGVVK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSSTSEEDEPGVVK 15 0 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 0 VLS(0.123)S(0.121)T(0.668)S(0.088)EEDEPGVVK 124.2 0.0022568 5681100 2384.7 2849.1 2686.2 2579 2702.3 2506.1 2136.3 2421.2 2835.8 2845.4 TRUE FALSE FALSE 2355.634359 2889.209705 2732.952184 2877.196115 2564.391547 2345.968298 2317.757269 2491.253602 2582.158946 2771.476098 0.849956585 1.04248047 0.986099857 1.038145744 0.925280052 0.846468891 0.836289828 0.898890524 0.931690859 1 11.43643885 -8.368567602 4.790069092 0.94955747 0.858543663 0.40213242 0.057472404 0.254355785 9.168491814 0.010670298 0.024518265 4.28E-09 8.368567602 -0.091013807 VLSSTS(ph)EEDEPGVVK ddPTM_HeLa_Romidepsin_16h_R1 2 VLSSTSEEDEPGVVK 15 0 Q8NI08-4;Q8NI08-3;Q8NI08-7;Q8NI08-2;Q8NI08 Q8NI08-4 NCOA7 Nuclear receptor coactivator 7 1 0 VLSST(0.021)S(0.979)EEDEPGVVK;VLS(0.002)S(0.018)T(0.143)S(0.837)EEDEPGVVK ; 266.77 2.08E-84 23304000 7737.9 7018.3 6941.2 7405.2 7296.4 6176.6 5163.3 5977 8044.7 6914.5 TRUE FALSE FALSE 7643.587499 7117.103812 7062.008674 8261.424067 6924.037481 5781.935194 5601.870573 6149.935065 7325.161884 6734.860293 1.134928887 1.056755968 1.048575377 1.22666599 1.028089252 0.858508557 0.83177235 0.913149612 1.087648676 1 12.7174323 -8.32831544 4.414629639 1.075122727 0.863500266 0.724089984 0.061264663 0.102298262 3.932717935 0.010230716 0.024060571 4.70E-09 8.32831544 -0.211622461 VLST(ph)SPTISK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSPTISK 10 0 A0A087WX19;A0A087WX45;Q6IPM2-4;Q6IPM2;H7C427;Q6IPM2-2;Q6IPM2-3 A0A087WX19 IQCE IQ domain-containing protein E 1 0 VLS(0.072)T(0.855)S(0.072)PTISK 138.25 0.010743 16793000 2666.1 2288 2356.1 2343.1 2573.5 2390 2539.1 2591.3 2460.2 2263.7 TRUE FALSE FALSE 2633.604548 2320.210524 2397.106932 2614.020247 2442.164692 2237.286713 2754.771091 2666.275177 2240.15355 2204.888748 1.194438745 1.052302764 1.087178178 1.185556527 1.107613568 1.014693696 1.24939233 1.209256104 1.015993915 1 11.10649015 -12.47855008 1.136107712 0.997536803 1.139583059 0.352330851 0.070144988 0.472845948 1.060855702 0.05458775 0.012453704 3.32E-13 12.47855008 0.142046256 VLSTS(ph)TDLEAAVADALK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 0 VLS(0.001)T(0.005)S(0.941)T(0.054)DLEAAVADALK 163.9 1.35E-05 149530000 4581.2 5261.6 5607.9 3740.7 5498.1 4681.1 3869.1 4287.4 5068.1 5340.7 TRUE FALSE FALSE 4525.362572 5335.672943 5705.503147 4173.217335 5217.511441 4381.992818 4197.741257 4411.449155 4614.796443 5201.947844 0.869936168 1.025706736 1.096801298 0.802241287 1.002991879 0.842375385 0.80695566 0.848037944 0.887128549 1 12.34483622 -8.15870703 6.211928264 0.949271147 0.827389411 0.322845665 0.08109813 0.230422205 11.81592158 0.011795335 0.030547589 6.94E-09 8.15870703 -0.121881735 VLSTS(ph)TDLEAAVADALKKPVR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 0 VLS(0.04)T(0.147)S(0.555)T(0.258)DLEAAVADALKKPVR 75.743 0.0040059 22910000 1386.6 1042.1 1139.3 1087.5 1210.3 1050.2 1042 987.57 1046.8 966.71 TRUE FALSE FALSE 1369.699586 1056.770711 1159.129039 1213.241867 1148.533875 983.0956094 1130.507454 1016.14378 953.1715862 941.5947348 1.454659351 1.122320115 1.231027528 1.288496868 1.219775167 1.044075092 1.200630603 1.079173175 1.012294941 1 9.878962443 -8.298358771 20.98174317 1.219434149 1.117226779 0.042043693 0.132090751 182.7571129 103862.6935 0.024398822 0.054562652 5.03E-09 8.298358771 -0.10220737 VLSTST(ph)DLEAAVADALK ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSTDLEAAVADALK 17 0 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 1 0 VLS(0.11)T(0.11)S(0.331)T(0.449)DLEAAVADALK 114.56 0.0015699 1599700 1198.4 941.43 1076.3 719.71 1039.1 984.3 724.01 957.1 933.91 1105.3 TRUE FALSE FALSE 1183.79344 954.6834763 1095.03255 802.9262565 986.0708496 921.4064067 785.5073913 984.7921784 850.3787506 1076.584147 1.099582827 0.886770885 1.017136053 0.745809103 0.915925478 0.855861021 0.72962935 0.914737767 0.789886005 1 10.07224537 -9.666374503 1.405274799 1.0442528 0.83372757 0.018932386 0.113312438 0.206022725 0.821466074 0.013765158 0.021326268 2.16E-10 9.666374503 -0.21052523 VLSTSTDLEAAVADALKKPVR ddPTM_HeLa_Romidepsin_16h_R1 1 VLSTSTDLEAAVADALKKPVR 21 2 Q7Z460 Q7Z460 CLASP1 CLIP-associating protein 1 0 0 199.61 1.75E-24 3830100 2991.9 3170.8 3010.7 3393.7 2745.3 2545.4 2606.2 2736.4 3170.3 3017.9 FALSE FALSE TRUE 2955.433572 3215.438606 3063.099971 3786.095562 2605.197097 2382.757155 2827.570563 2815.573417 2886.740428 2939.494523 1.005422378 1.093874671 1.042049899 1.288009055 0.886273839 0.810600985 0.961924079 0.957842716 0.982053345 1 11.52135237 VLT(ph)NHIHT(ph)GHHSS(ph)MFWMR ddPTM_HeLa_Romidepsin_16h_R1 1 VLTNHIHTGHHSSMFWMR 18 0 G3V5L5;G3V2X6;C9JSX3;H0YJX6;O14744-3;O14744-5;O14744-2;O14744 G3V5L5 PRMT5 "Protein arginine N-methyltransferase 5;Protein arginine N-methyltransferase 5, N-terminally processed" 3 0 VLT(1)NHIHT(0.996)GHHS(0.479)S(0.525)MFWMR 50.827 0.019258 27673000 7729.7 8258.1 7292.4 6866.9 7571.2 8300 6422 6646 8416.7 7247.2 TRUE FALSE FALSE 7635.487443 8374.357749 7419.321163 7660.883288 7184.813412 7769.656787 6967.48452 6838.291524 7663.889272 7058.916699 1.081679777 1.186351689 1.051056625 1.085277474 1.017835132 1.10068685 0.987047279 0.968745179 1.085703317 1 12.78523108 -7.631282692 6.814974169 1.055899282 0.973471663 0.320241129 0.051071106 0.222371988 12.28534157 0.00794289 0.030299467 2.34E-08 7.631282692 -0.082427619 VLT(ph)PEEQLADK ddPTM_HeLa_Romidepsin_16h_R1 2 VLTPEEQLADK 11 0 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 VLT(1)PEEQLADK;VLT(1)PEEQLADK ; 154.23 0.0046017 98943000 8162.9 9028.1 9700.5 3526.5 8006.1 9982.6 8967 8953.1 7855 7933.5 TRUE FALSE FALSE 8063.407435 9155.197829 9869.333133 3934.250523 7597.518842 9344.744077 9728.656756 9212.143823 7152.429127 7727.386526 1.043484418 1.184772859 1.277189008 0.509130805 0.983193841 1.209302012 1.258984098 1.192142232 0.925594844 1 12.91576485 -8.241531072 9.364620367 1.011854427 1.224309415 0.229129213 0.191022183 0.442580247 196.4175723 0.026428019 0.066089254 5.73E-09 8.241531072 0.212454989 VLT(ph)PEEQLADKLR ddPTM_HeLa_Romidepsin_16h_R1 1 VLTPEEQLADKLR 13 1 O75822;O75822-2;O75822-3 O75822 EIF3J Eukaryotic translation initiation factor 3 subunit J 1 0 VLT(1)PEEQLADKLR 75.877 0.027034 72609000 5192.3 5487.7 5026.8 3399.6 5880 6119.1 5632.5 6057 5593.6 5313.2 TRUE FALSE FALSE 5129.01425 5564.955985 5114.289345 3792.677748 5579.921659 5728.109258 6110.924409 6232.249739 5093.294407 5175.162298 0.991082783 1.075320089 0.988237479 0.732861605 1.078211916 1.106846303 1.180817926 1.204261698 0.984180614 1 12.33738839 -8.210584507 2.445723564 0.984271408 1.183149803 0.502441259 0.088600486 0.196995216 2.284885082 0.012772857 0.038260359 6.16E-09 8.210584507 0.198878395 VLT(ph)PELYAELR ddPTM_HeLa_Romidepsin_16h_R1 2 VLTPELYAELR 11 0 P12277;G3V4N7;G3V461 P12277 CKB Creatine kinase B-type 1 0 VLT(1)PELYAELR;VLT(1)PELYAELR ; 145.29 0.0051447 12639100 2190.11 2058.33 2227.72 2295 2777.13 3270.49 2910.89 3485.13 2408.08 1859.94 TRUE FALSE FALSE 2163.416097 2087.307224 2266.492532 2560.358698 2635.402693 3061.516244 3158.140924 3585.966738 2192.695294 1811.618491 1.194189675 1.15217814 1.251087105 1.413299054 1.454722783 1.68993431 1.743270418 1.979427101 1.210351575 1 10.82306345 -4 0.226081938 0.99048576 6.696162211 0.942879122 0.070167342 4.508511474 0.054499656 0.032188117 9.562715451 1.00E-04 4 5.705676451 VLT(ph)PPQAAGDGILATTANQR ddPTM_HeLa_Romidepsin_16h_R1 2 VLTPPQAAGDGILATTANQR 20 0 Q96QT6;C9J9G2;Q96QT6-4;Q96QT6-2;Q96QT6-5;Q96QT6-3;K7EPF7 Q96QT6 PHF12 PHD finger protein 12 1 0 VLT(1)PPQAAGDGILATTANQR;VLT(1)PPQAAGDGILATTANQR ; 151.58 2.27E-05 37037000 5806.6 5050.9 4747.7 5404.4 5797.5 5737.8 4728.1 5455.1 6300.5 5551.9 TRUE FALSE FALSE 5735.826926 5122.006703 4830.331727 6029.282156 5501.631942 5371.173098 5129.704696 5612.934712 5736.9675 5407.660838 1.060685405 0.947176026 0.893238661 1.11495198 1.017377403 0.993252584 0.948599561 1.037959828 1.060896323 1 12.40078895 -10.27631972 24.56021568 1.028656995 0.993272624 0.110579224 0.058649505 1341.909079 2214834.34 0.010205858 0.011695378 5.29E-11 10.27631972 -0.03538437 VLTANSNPS(ph)SPSAAK ddPTM_HeLa_Romidepsin_16h_R1 2 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 0 VLTANS(0.014)NPS(0.97)S(0.015)PS(0.002)AAK;VLTANSNPS(0.983)S(0.016)PSAAK ; 292.16 2.08E-116 107777000 12873 12871.2 12049.3 10652.9 9745.7 9831.9 9360.1 9497.5 13102.5 12264.5 TRUE FALSE FALSE 12716.09892 13052.40109 12259.01301 11884.63842 9248.340563 9203.673321 10155.14666 9772.295178 11930.57958 11945.86652 1.064476897 1.092629075 1.026213794 0.994874537 0.774187502 0.770448364 0.850097114 0.818048248 0.998720316 1 13.54422389 -8.838734369 4.709912372 1.035423119 0.804161635 0.913854495 0.034161312 0.047274465 1.929496629 0.00578677 0.01081604 1.45E-09 8.838734369 -0.231261484 VLTANSNPSS(ph)PSAAK ddPTM_HeLa_Romidepsin_16h_R1 2 VLTANSNPSSPSAAK 15 0 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 0 VLTANS(0.001)NPS(0.272)S(0.675)PS(0.052)AAK;VLTANS(0.01)NPS(0.071)S(0.918)PSAAK ; 115.83 0.0038429 150117000 9995.4 9225.7 8416.3 8140.4 7500.8 6753.3 6995.7 6431.2 9705.3 9394.9 TRUE FALSE FALSE 9873.57222 9355.579647 8562.782171 9081.63135 7118.006187 6321.785925 7589.914583 6617.276625 8837.233661 9150.819144 1.078982336 1.022376194 0.935739417 0.992439169 0.777854537 0.690843719 0.829424608 0.723134893 0.96573143 1 13.15968518 -8.791537791 2.845553165 1.028661083 0.749995681 0.838260155 0.051824306 0.069271479 1.147842158 0.007974459 0.016164292 1.62E-09 8.791537791 -0.278665402 VLTANSNPSS(ph)PSAAKR ddPTM_HeLa_Romidepsin_16h_R1 2 VLTANSNPSSPSAAKR 16 1 Q9NV56 Q9NV56 MRGBP MRG/MORF4L-binding protein 1 0 VLTANSNPS(0.31)S(0.69)PSAAKR;VLTANSNPS(0.165)S(0.832)PS(0.003)AAKR ; 112.44 0.00089365 106849000 5923.6 5713.1 5081.6 6462.8 4882.9 4174.8 3854.2 3589.9 5789 4965 TRUE FALSE FALSE 5851.400885 5793.529172 5170.043116 7210.059344 4633.707392 3908.043754 4181.575652 3693.768093 5271.217341 4836.008584 1.20996495 1.197998116 1.069072361 1.490911196 0.958167735 0.808113486 0.864674985 0.763805115 1.08999338 1 12.23960109 -8.528293166 24.99393972 1.135389274 0.828394698 0.612033191 0.129060301 87.50759336 403950.3266 0.020467351 0.041039403 2.96E-09 8.528293166 -0.306994575 (ac)ALVDK(ac)HK ddPTM_HeLa_Romidepsin_16h_R1 1 ALVDKHK 7 1 P56545 P56545 CTBP2 C-terminal-binding protein 2 0 1 ALVDK(1)HK 43.246 0.0075489 13455000 1298.8 979.19 1019.4 1129.6 2958.7 4192.5 4212.8 4970.6 1423 1039.3 FALSE TRUE FALSE 1282.969726 992.9750625 1037.142229 1260.209667 2807.706499 3924.612781 4570.635127 5114.416469 1295.723316 1012.298836 1.267382398 0.980910999 1.024541561 1.24489886 2.773594514 3.876931041 4.515104595 5.052279313 1.279981039 1 9.983419529 -8.362671037 1.373423351 1.091507382 4.875746896 0.985492375 0.18452272 0.036178643 0.127514444 0.029258199 0.10612361 4.34E-09 8.362671037 3.784239514 up VLTEDEMGHPEIGDAIAR ddPTM_HeLa_Romidepsin_16h_R1 1 VLTEDEMGHPEIGDAIAR 18 0 A0A087WTP2;A0A087X1D8;A0A087WVN4;P14324-2;P14324 A0A087WTP2 FDPS Farnesyl pyrophosphate synthase 0 0 91.14 0.024372 12684000 1818.5 1653.4 1615.9 1549.6 1878.7 1853.4 1556.1 1717.7 2176.9 2129.9 FALSE FALSE TRUE 1796.335423 1676.676609 1644.024062 1728.772043 1782.822929 1734.973722 1688.275095 1767.398939 1982.192612 2074.564891 0.865885387 0.808206393 0.792466926 0.833317893 0.859371975 0.83630728 0.813797198 0.851937169 0.955473902 1 11.01859307 -11.64252016 0.655060342 1.000088427 0.827240065 0.846875492 0.024574371 0.178922795 0.151880541 0.015519571 0.005904289 2.28E-12 11.64252016 -0.172848362 VLTEIIASR ddPTM_HeLa_Romidepsin_16h_R1 1 VLTEIIASR 9 0 P08758;D6RBL5;E9PHT9 P08758 ANXA5 Annexin A5;Annexin 0 0 131.22 0.021966 958390 399.97 542.98 437.42 392.46 393.05 421.71 387.69 376.59 384.84 391.35 FALSE FALSE TRUE 395.0950118 550.6240867 445.0331116 437.8380718 372.9911918 394.764092 420.6203789 387.4860375 350.4189466 381.1826706 1.036497832 1.444515003 1.167506149 1.148630579 0.978510359 1.035629693 1.103461441 1.016536342 0.919294012 1 8.574338722 -10.49668224 24.98050711 1.016101883 1.128539977 0.205362102 0.124783092 400.1975989 381625.8369 0.022079119 0.023825242 3.19E-11 10.49668224 0.112438094 VLTLS(ph)DDLER ddPTM_HeLa_Romidepsin_16h_R1 2 VLTLSDDLER 10 0 P55010 P55010 EIF5 Eukaryotic translation initiation factor 5 1 0 VLT(0.012)LS(0.988)DDLER;VLT(0.023)LS(0.977)DDLER ; 177.57 5.56E-05 6639100 3412.3 3661.4 2955.2 2553.36 3603.9 3534.2 3153.7 3050.6 3696.6 3468.2 TRUE FALSE FALSE 3370.709575 3712.945285 3006.634016 2848.591497 3419.979535 3308.376026 3421.575199 3138.864298 3365.966838 3378.095664 0.997813535 1.099123783 0.89003815 0.84325365 1.012398663 0.97936126 1.01287102 0.929181589 0.996409567 1 11.72199447 -9.737575569 24.99964757 1.006450417 0.947690827 0.294647927 0.057286588 296.8088287 310935.4364 0.009216392 0.013030161 1.83E-10 9.737575569 -0.05875959 VMDS(ph)DEDDDY ddPTM_HeLa_Romidepsin_16h_R1 2 VMDSDEDDDY 10 0 O14737;K7EQA1 O14737 PDCD5 Programmed cell death protein 5 1 0 VMDS(1)DEDDDY;VMDS(1)DEDDDY ; 201.61 2.84E-12 134075000 6067.5 6209.5 6120.6 5446.9 6189.8 6150.1 4922.6 5227.4 6366.1 6285.6 TRUE FALSE FALSE 5993.546976 6296.917504 6227.126476 6076.696206 5873.911409 5757.128459 5340.725521 5378.646572 5796.700072 6122.299206 0.978969955 1.028521686 1.017122206 0.992551328 0.959429001 0.940353985 0.872339842 0.878533765 0.946817507 1 12.57985784 -8.050488357 1.40454772 0.995263493 0.867361421 0.809274444 0.022198726 0.118637905 0.410908729 0.002730113 0.014016024 8.90E-09 8.050488357 -0.127902073 VMECTACIIIK ddPTM_HeLa_Romidepsin_16h_R1 1 VMECTACIIIK 11 0 Q9NZJ4-2;Q9NZJ4 Q9NZJ4-2 SACS Sacsin 0 0 114.93 0.0037396 0 744.64 628.79 667.16 765.5 869.65 663.9 571.93 661.34 832.54 849.26 FALSE FALSE TRUE 735.5640413 637.6421221 678.7716399 854.0107118 825.2685154 621.4789326 620.5097199 680.4748295 758.0755373 827.1961028 0.889225709 0.77084759 0.820569195 1.032416266 0.997669733 0.751307859 0.750136174 0.822628186 0.916439928 1 9.692085578 -16.52287875 0.04639853 1.666197352 0.499545751 0.174321717 0.093029272 491.8209002 1.813135438 43.17759084 11.76150058 3.00E-17 16.52287875 -1.1666516 VMEK(ac)PSPLLVGR ddPTM_HeLa_Romidepsin_16h_R1 1 VMEKPSPLLVGR 12 1 Q9UN86-2;Q9UN86;D6R9X5;D6RB17;E5RJU8;E5RIZ6;D6RAC7;D6RGJ4;E5RH42;D6RBW8;E5RH00;E5RIF8;E5RI46;D6RBR0;D6REX8;D6RBM9;D6R9A4;Q13283-2;D6RE13;Q13283 Q9UN86-2;Q13283 G3BP2;G3BP1 Ras GTPase-activating protein-binding protein 2;Ras GTPase-activating protein-binding protein 1 0 1 VMEK(1)PSPLLVGR 93.345 0.018236 1302700 198.79 286.49 269.42 109.52 386.94 418.74 315.21 407.6 205.78 288.24 FALSE TRUE FALSE 196.367071 290.5232137 274.1091421 122.1832177 367.1930079 391.9838654 341.9839295 419.3932629 187.3745214 280.7514832 0.699433779 1.034805624 0.976340851 0.435200613 1.307893386 1.396195172 1.218101951 1.493823855 0.667403496 1 8.133149834 -8.618716917 10.446837 0.853029483 1.353824022 0.676941198 0.18502371 0.16910761 17.0485889 0.026616378 0.053256122 2.41E-09 8.618716917 0.500794539 VMFENPDFQVDEESEEFR ddPTM_HeLa_Romidepsin_16h_R1 1 VMFENPDFQVDEESEEFR 18 0 Q9BSC4-2;Q9BSC4-4;Q9BSC4 Q9BSC4-2 NOL10 Nucleolar protein 10 0 0 92.265 0.0033844 0 262.77 386.77 347.12 882.09 292.28 328.24 410.37 646.99 405.29 269.95 FALSE FALSE TRUE 259.5672582 392.2149582 353.161478 984.0813962 277.363861 307.2665233 445.2268176 665.7096349 369.0398473 262.9366601 0.9871855 1.491670877 1.343142785 3.742655725 1.054869492 1.168595217 1.693285438 2.531825097 1.403531357 1 8.038571494 -9.868203674 2.24488614 0.999660683 1.93625515 0.191581669 0.740655934 0.309174041 3.177370429 0.120917604 0.165521473 1.35E-10 9.868203674 0.936594468 VMHSSPSS(ph)PSSDGK ddPTM_HeLa_Romidepsin_16h_R1 1 VMHSSPSSPSSDGK 14 0 H7C428;A0A0A0MSB4;Q6ZN50;Q969R2-5;Q969R2-4;Q969R2-6;Q969R2-3;Q969R2-2;Q969R2 H7C428 OSBP2 Oxysterol-binding protein;Oxysterol-binding protein 2 1 0 VMHSSPS(0.181)S(0.818)PS(0.001)SDGK 79.837 0.011012 1708300 1076.6 721.33 1047.2 799.38 1224.1 948.96 1107.3 895.03 1156.8 1123.5 TRUE FALSE FALSE 1063.477985 731.4849027 1065.426077 891.8080768 1161.629609 888.3245186 1201.354034 920.9262809 1053.332911 1094.311308 0.971823993 0.668443154 0.973604192 0.814949156 1.061516591 0.811765822 1.097817436 0.841557859 0.962553254 1 10.0958075 -10.49624103 24.66942626 0.987569501 0.900317262 0.089521237 0.119787389 402.3892098 372661.2211 0.019231525 0.020776575 3.19E-11 10.49624103 -0.087252239 VMITTS(ph)RDPS(ph)S(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 VMITTSRDPSSR 12 1 E7ENR5;B8ZZ47;H0Y714;Q96G21 E7ENR5 IMP4 U3 small nucleolar ribonucleoprotein protein IMP4 3 0 VMIT(0.17)T(0.205)S(0.625)RDPS(1)S(1)R 58.814 0.023339 138170000 4909.9 1807.5 2969.4 2333.1 3195.2 2192.9 3870.7 2439.3 4585.2 3901.3 TRUE FALSE FALSE 4850.05625 1832.946032 3021.081161 2602.864 3032.137021 2052.780767 4199.477161 2509.877297 4175.088228 3799.943664 1.276349515 0.48236137 0.795033145 0.684974365 0.797942625 0.540213474 1.105141953 0.660503818 1.098723717 1 11.89176231 -10.27111429 24.99828043 1.130498383 0.735454528 0.534345461 0.171399049 390.4108397 1008751.653 0.030232316 0.034799524 5.36E-11 10.27111429 -0.395043855 VMRERT(ph)GY(ph)TKT(ph)YQAHAK ddPTM_HeLa_Romidepsin_16h_R1 1 VMRERTGYTKTYQAHAK 17 3 K7ES09;Q96MN2 K7ES09 NLRP4 "NACHT, LRR and PYD domains-containing protein 4" 3 0 VMRERT(0.972)GY(0.843)T(0.191)KT(0.525)Y(0.469)QAHAK 44.807 0.026715 2846600 2436.5 773.82 1277.2 878.75 1592.8 921.1 1913.5 1298.2 1857.8 1448.4 TRUE FALSE FALSE 2406.803001 784.7138583 1299.42913 980.3552096 1511.513472 862.2446827 2076.032642 1335.761369 1691.633715 1410.770359 1.706020392 0.556230752 0.921077709 0.694907717 1.071410001 0.611187127 1.471559584 0.946831183 1.199085098 1 10.46226745 -10.25968022 24.99751096 1.333398514 0.907298254 0.281597095 0.295153871 166.895125 2371561.091 0.058204973 0.069339299 5.50E-11 10.25968022 -0.42610026 VMS(ph)PENFPTASVEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VMSPENFPTASVEGK 15 0 H3BTW3;Q3L8U1;Q3L8U1-2;Q3L8U1-3;H3BRU9;H3BSP3 H3BTW3 CHD9 Chromodomain-helicase-DNA-binding protein 9 1 0 VMS(1)PENFPTASVEGK;VMS(1)PENFPTASVEGK ; 138.42 0.0013808 17180900 6121.5 6601.1 6444.9 5205.8 5934.2 6097.2 5046.7 5198.6 6821.5 7172.2 TRUE FALSE FALSE 6046.888803 6694.030459 6557.070781 5807.71909 5631.35563 5707.608598 5475.366572 5349.013289 6211.367955 6985.86521 0.865589103 0.958224967 0.93861971 0.83135287 0.806107112 0.817022434 0.783777873 0.765690881 0.889133668 1 12.77022309 -4 0.079515116 1.127958115 0.152078495 0.610251678 0.046833679 69.89546736 0.40917935 0.782670286 7.541055638 1.00E-04 4 -0.97587962 VMS(ph)PENFPTASVEGKEEK ddPTM_HeLa_Romidepsin_16h_R1 1 VMSPENFPTASVEGKEEK 18 1 H3BTW3;Q3L8U1;Q3L8U1-2;Q3L8U1-3;H3BRU9;H3BSP3 H3BTW3 CHD9 Chromodomain-helicase-DNA-binding protein 9 1 0 VMS(0.999)PENFPT(0.001)ASVEGKEEK 74.428 0.0022936 0 973.35 799.72 983.83 1634.7 1139.9 1027.4 827.51 919.74 1469.5 1308.8 TRUE FALSE FALSE 961.4864358 810.9784792 1000.953148 1823.711705 1081.726649 961.7524558 897.7986787 946.3512258 1338.06424 1274.797187 0.754226982 0.636162746 0.785186192 1.430589684 0.848548036 0.754435659 0.704267853 0.742354341 1.049629112 1 10.31605203 -12.48146128 1.272977718 0.998373047 0.828772195 0.114802043 0.209595654 1.007787585 2.965584842 0.144608807 0.036847942 3.30E-13 12.48146128 -0.169600852 VMTIPYQPMPASS(ph)PVICAGGQDR ddPTM_HeLa_Romidepsin_16h_R1 1 VMTIPYQPMPASSPVICAGGQDR 23 0 Q15365 Q15365 PCBP1 Poly(rC)-binding protein 1 1 0 VMTIPYQPMPAS(0.044)S(0.956)PVICAGGQDR 79.163 0.00013747 24696000 1562.5 1724.4 1337.6 129.09 1522.3 1564.1 1333.3 1513.3 1498.7 1482.8 TRUE FALSE FALSE 1543.455649 1748.676148 1360.880367 144.0159932 1444.611351 1464.159058 1446.550469 1557.084948 1364.652518 1444.276642 1.068670367 1.210762604 0.942257409 0.099714964 1.000231748 1.013766349 1.00157437 1.078107132 0.944869202 1 10.49613139 -9.522155698 24.99846456 1.048127974 0.831886449 0.125801777 0.269585761 43.44267872 1501992.576 0.042517941 0.06054511 3.00E-10 9.522155698 -0.216241524 VNASASS(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 2 VNASASSLK 9 0 Q16658 Q16658 FSCN1 Fascin 1 0 VNASAS(0.181)S(0.819)LK;VNASAS(0.093)S(0.907)LK ; 159.09 0.0038036 57064000 10551.5 14456 12245.6 10432.8 11829.6 13582.3 11852.4 10474 10978 9818.7 TRUE FALSE FALSE 10422.89426 14659.51195 12458.72953 11639.08942 11225.89137 12714.43486 12859.14256 10777.04866 9996.100185 9563.608759 1.089849504 1.532843126 1.302722628 1.217018567 1.173813322 1.329459954 1.344591031 1.126880965 1.045222618 1 13.2233394 -10.48103231 14.19170234 1.039618688 1.288306252 0.536312965 0.105222401 1.761617339 597.3375832 0.018155352 0.020458058 3.30E-11 10.48103231 0.248687564 VNASASS(ph)LKK ddPTM_HeLa_Romidepsin_16h_R1 1 VNASASSLKK 10 1 Q16658 Q16658 FSCN1 Fascin 1 0 VNAS(0.001)AS(0.3)S(0.699)LKK 140.63 0.007288 7108900 2609.8 2647.2 2731.8 2436.6 3064.5 2884.7 2606.4 2108.5 2878.7 2564 TRUE FALSE FALSE 2577.990754 2684.467351 2779.345833 2718.331157 2908.10713 2700.37698 2827.787551 2169.506121 2621.221862 2497.38691 1.032275273 1.074910475 1.112901578 1.088470171 1.164459987 1.081280986 1.132298539 0.868710456 1.04958581 1 11.28620363 -10.44259956 1.848656763 1.011733981 1.083197485 0.061985419 0.075946194 0.44223545 2.93733008 0.01360324 0.015069438 3.61E-11 10.44259956 0.071463505 VVNGAAASQPPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 0 1 VVNGAAASQPPSK(1)R 154.36 1.75E-06 2295200 254.8 268.9 282.11 426.64 1081 1630.5 1536 2106.1 367.26 328.28 FALSE TRUE FALSE 251.6943996 272.6855813 287.0200062 475.9701242 1025.832536 1526.316312 1666.467802 2167.036681 334.4113458 319.7512383 0.787156919 0.852805396 0.897635324 1.488563818 3.208220684 4.773449261 5.211763403 6.777258135 1.045848478 1 8.320806136 -8.297953573 1.043702797 0.85883497 6.493180332 0.981331382 0.289237369 0.053321234 0.099287538 0.044566925 0.220396445 5.04E-09 8.297953573 5.634345362 up VNDAEPGS(ph)PEAPQGK ddPTM_HeLa_Romidepsin_16h_R1 2 VNDAEPGSPEAPQGK 15 0 Q8N8A6 Q8N8A6 DDX51 ATP-dependent RNA helicase DDX51 1 0 VNDAEPGS(1)PEAPQGK;VNDAEPGS(1)PEAPQGK ; 212.92 1.31E-25 375460000 23846.7 21956.3 21887.8 20192.7 19706.7 19197.4 18020 20597.3 22112.4 21311.3 TRUE FALSE FALSE 23556.04725 22265.40137 22268.74798 22527.47498 18700.99356 17970.7481 19550.61835 21193.25038 20134.61156 20757.62935 1.134813945 1.072637004 1.072798227 1.085262416 0.900921451 0.865741834 0.941852175 1.020986068 0.969986082 1 14.34135407 -8.763958613 24.99995719 1.068003739 0.928292746 0.523552041 0.056987382 38.3980596 381054.3695 0.00911356 0.017090365 1.72E-09 8.763958613 -0.139710993 VNEK(ac)TVGVIVSR ddPTM_HeLa_Romidepsin_16h_R1 2 VNEKTVGVIVSR 12 1 Q9UGU0-2;Q9UGU0 Q9UGU0-2 TCF20 Transcription factor 20 0 1 ; VNEK(1)TVGVIVSR;VNEK(1)TVGVIVSR 126.5 5.35E-09 0 773.58 786.77 606.03 453.51 587.32 590.04 670.92 599.49 895.54 888.67 FALSE TRUE FALSE 764.1513094 797.8461687 616.5776979 505.94696 557.3468688 552.3383483 727.9079281 616.8352973 815.4406595 865.5822253 0.8828177 0.921745093 0.712327125 0.584516347 0.643898237 0.638111935 0.840946021 0.712624727 0.942071863 1 9.757527064 -9.757382295 4.165539366 0.942693137 0.684157794 0.7635674 0.067797154 0.08424873 3.354612427 0.012707799 0.017579653 1.75E-10 9.757382295 -0.258535343 VNFAMNVGK ddPTM_HeLa_Romidepsin_16h_R1 2 VNFAMNVGK 9 0 P14618;B4DNK4;P14618-3;P14618-2;H3BR70 P14618 PKM Pyruvate kinase PKM;Pyruvate kinase 0 0 ; ; 145.34 0.0060345 3972200 1350.36 995.56 2012.23 705.51 1697.23 1859.8 1742.13 1185.92 1319.89 1021.51 FALSE FALSE TRUE 1333.901293 1009.57552 2047.252019 787.0843857 1610.61402 1740.964782 1890.106479 1220.232724 1201.835733 994.9710229 1.340643358 1.014678314 2.05759964 0.791062622 1.6187547 1.749764307 1.899659824 1.226400263 1.207910286 1 9.9585107 -10.79304863 0.192267313 0.790605901 1.779949151 0.166675779 0.36528867 3.431018987 0.5347781 1.347791437 0.995072773 1.61E-11 10.79304863 0.989343251 VNGDAS(ph)PAAAESGAK ddPTM_HeLa_Romidepsin_16h_R1 3 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 VNGDAS(0.982)PAAAES(0.018)GAK;VNGDAS(1)PAAAESGAK;VNGDAS(1)PAAAESGAK ;; 241.66 1.89E-46 290920000 12933 14490.5 13642.6 8010.3 13411.2 15494.2 12644.9 13239.2 13222.5 12891.9 TRUE FALSE FALSE 12775.36762 14694.49764 13880.04373 8936.488576 12726.77642 14504.17063 13718.95749 13622.25536 12039.84648 12556.96658 1.017392819 1.170226706 1.105365985 0.711675747 1.013523158 1.155069621 1.092537549 1.084836475 0.958818072 1 13.61620037 -8.31911471 9.047313415 1.005757662 1.108900336 0.171981088 0.113515859 0.629363921 95.22733961 0.016171889 0.03626105 4.80E-09 8.31911471 0.103142673 VNGDASPAAAES(ph)GAK ddPTM_HeLa_Romidepsin_16h_R1 1 VNGDASPAAAESGAK 15 0 P29966 P29966 MARCKS Myristoylated alanine-rich C-kinase substrate 1 0 VNGDAS(0.148)PAAAES(0.852)GAK 193.3 1.40E-12 265320000 3824.5 3725.6 3456.6 1973.9 3327.5 4076.5 2842 2920.2 3691.5 3305.8 TRUE FALSE FALSE 3777.885523 3778.049095 3516.760673 2202.131605 3157.685258 3816.024806 3083.399409 3004.69138 3361.322994 3219.914839 1.173287404 1.173338204 1.092190585 0.683909891 0.980673532 1.185132215 0.957602782 0.933158648 1.043916738 1 11.65280682 -9.439332239 25 1.092984147 0.956047019 0.265163113 0.123138359 112.8405125 33764.44512 0.02056992 0.031421073 3.64E-10 9.439332239 -0.136937128 VNGDDHHEEDMDMS(ph)D ddPTM_HeLa_Romidepsin_16h_R1 1 VNGDDHHEEDMDMSD 15 0 Q5T757;Q05519-2;Q05519 Q5T757 SRSF11 Serine/arginine-rich splicing factor 11 1 0 VNGDDHHEEDMDMS(1)D 57.197 0.025686 108530000 3706.2 4147.4 3713 3551.8 3707.7 3596.5 3770.6 4313.8 4395 4272.2 TRUE FALSE FALSE 3661.027409 4205.787206 3777.623207 3962.475828 3518.482234 3366.695257 4090.87467 4438.612997 4001.900193 4161.207628 0.879799264 1.010713135 0.907818966 0.952241797 0.845543541 0.809066876 0.983097945 1.06666463 0.961716057 1 12.02278656 VNGTTVS(ph)SPSTSLQR ddPTM_HeLa_Romidepsin_16h_R1 3 VNGTTVSSPSTSLQR 15 0 A0A075B6G3;H0Y304;A0A087WTU7;A0A5H1ZRP8;A0A5H1ZRP7;A0A087WV90;A0A5H1ZRQ1;A0A5H1ZRP9;A0A5H1ZRQ8;P11532;P11532-11;P11532-4;P11532-2;P11532-3;P11532-14;P11532-8;P11532-12;P11532-17;P11532-6;P11532-5;P11532-7;P11532-15;P11532-9;P11532-16;P11532-13;A0A5H1ZRR9 A0A075B6G3 DMD Dystrophin 1 0 VNGTTVS(0.485)S(0.485)PS(0.026)T(0.002)S(0.002)LQR;VNGT(0.002)T(0.006)VS(0.495)S(0.495)PSTSLQR;VNGTTVS(0.5)S(0.5)PS(0.001)TSLQR ;; 150.12 0.00047628 70736000 6302.9 6878.8 5956.9 6166.6 7431.9 8278.5 6457.6 7416.9 6822 6147.8 TRUE FALSE FALSE 6226.07783 6975.639927 6060.577346 6879.611307 7052.622411 7749.530568 7006.108383 7631.4963 6211.823234 5988.07927 1.039745392 1.164921106 1.012107067 1.148884475 1.177777062 1.294159649 1.170009291 1.274448109 1.037364897 1 12.5478776 -9.006549633 0.462544656 1.005409492 1.285385533 0.709776186 0.054077113 0.476619886 0.174617139 0.015049021 0.057717196 9.85E-10 9.006549633 0.279976041 VNGTTVSS(ph)PSTSLQR ddPTM_HeLa_Romidepsin_16h_R1 1 VNGTTVSSPSTSLQR 15 0 A0A075B6G3;H0Y304;A0A087WTU7;A0A5H1ZRP8;A0A5H1ZRP7;A0A087WV90;A0A5H1ZRQ1;A0A5H1ZRP9;A0A5H1ZRQ8;P11532;P11532-11;P11532-4;P11532-2;P11532-3;P11532-14;P11532-8;P11532-12;P11532-17;P11532-6;P11532-5;P11532-7;P11532-15;P11532-9;P11532-16;P11532-13;A0A5H1ZRR9 A0A075B6G3 DMD Dystrophin 1 0 VNGT(0.001)T(0.003)VS(0.219)S(0.744)PS(0.033)TSLQR 163.62 3.32E-05 0 2420.8 2768.9 2314.8 2459.4 3057.8 2956.3 2670.1 2728.3 2941.2 2743.8 TRUE FALSE FALSE 2391.294358 2807.880647 2355.088123 2743.7674 2901.749056 2767.401971 2896.898227 2807.239056 2678.131706 2672.51568 0.894772807 1.050650766 0.881225184 1.026660917 1.08577438 1.035504484 1.0839593 1.050410696 1.0021014 1 11.3839827 -9.036579248 8.379925266 0.953420909 1.062513995 0.460260867 0.049521145 0.19814619 42.56887643 0.007798535 0.013092565 9.19E-10 9.036579248 0.109093086 VNHEPEPAGGAT(ph)PGATLPK ddPTM_HeLa_Romidepsin_16h_R1 1 VNHEPEPAGGATPGATLPK 19 0 O00499-6;O00499-11;O00499-2;O00499;O00499-7;O00499-8;O00499-4;O00499-3;O00499-5;O00499-9;O00499-10 O00499-6;O00499-9 BIN1 Myc box-dependent-interacting protein 1 1 0 VNHEPEPAGGAT(0.999)PGAT(0.001)LPK 95.666 0.0018071 9271400 5239.5 5083.2 5363 3966.5 5780.6 6671.6 4282.1 5821.6 4796.8 4448.4 TRUE FALSE FALSE 5175.638959 5154.761423 5456.340765 4425.125393 5485.594412 6245.306292 4645.821467 5990.038811 4367.762194 4332.829927 1.194516989 1.189698537 1.259301855 1.021301428 1.266053481 1.441391976 1.072237209 1.382477252 1.008062229 1 12.08109389 -16.52287874 0.129332577 0.188987604 1.334808252 0.415417345 0.11390946 60.29117317 0.553705329 12.54643744 0.406502534 3.00E-17 16.52287874 1.145820648 VNHEPEPAGGATPGAT(ph)LPKSPSQLR ddPTM_HeLa_Romidepsin_16h_R1 1 VNHEPEPAGGATPGATLPKSPSQLR 25 1 O00499-6;O00499-11;O00499-2;O00499 O00499-6 BIN1 Myc box-dependent-interacting protein 1 1 0 VNHEPEPAGGAT(0.014)PGAT(0.914)LPKS(0.054)PS(0.019)QLR 88.413 3.12E-05 6879700 1135.8 1339.1 1530.4 1894.3 1771.3 1743.5 1748 2024.1 1690 1493.1 TRUE FALSE FALSE 1121.956433 1357.951885 1557.03597 2113.327879 1680.903951 1632.095977 1896.475076 2082.66414 1538.842167 1454.309047 0.771470435 0.933743683 1.07063624 1.453149098 1.155809321 1.122248384 1.304038561 1.43206435 1.058125968 1 10.50611817 -9.562633087 3.33310156 0.892377321 1.277355998 0.636149824 0.123521093 0.109077221 2.515386881 0.020649891 0.030533257 2.74E-10 9.562633087 0.384978677 VNHEPEPAGGATPGATLPKS(ph)PSQLR ddPTM_HeLa_Romidepsin_16h_R1 2 VNHEPEPAGGATPGATLPKSPSQLR 25 1 O00499-6;O00499-11;O00499-2;O00499 O00499-6 BIN1 Myc box-dependent-interacting protein 1 1 0 VNHEPEPAGGATPGAT(0.001)LPKS(0.499)PS(0.499)QLR;VNHEPEPAGGAT(0.005)PGAT(0.273)LPKS(0.675)PS(0.047)QLR ; 87.772 2.46E-05 110993000 4592.5 4408 4162.1 6553.8 4409.6 4338 3273.94 3562.4 5586.9 5022.5 TRUE FALSE FALSE 4536.524844 4470.05594 4234.539605 7311.581193 4184.561658 4060.8158 3552.028382 3665.472423 5087.193671 4892.014726 0.927332622 0.913745397 0.865602383 1.494595091 0.855386153 0.830090674 0.726087017 0.749276654 1.039897457 1 12.25621303 -8.53271049 24.99986324 0.992862877 0.777327124 0.330998144 0.169394155 209.1182205 531738.4632 0.024188612 0.048422428 2.93E-09 8.53271049 -0.215535753 VNIFGVESGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VNIFGVESGKK 11 1 H0YMF9;H0YL19;H0YN81;Q9GZS3 H0YMF9 WDR61 "WD repeat-containing protein 61;WD repeat-containing protein 61, N-terminally processed" 0 1 VNIFGVESGK(1)K 96.015 0.0082461 0 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 VNLEESSGVENS(ph)PAGAR ddPTM_HeLa_Romidepsin_16h_R1 2 VNLEESSGVENSPAGAR 17 0 Q8WVM8-2;Q8WVM8-3;Q8WVM8 Q8WVM8-2 SCFD1 Sec1 family domain-containing protein 1 1 0 VNLEES(0.001)SGVENS(0.999)PAGAR;VNLEESSGVENS(1)PAGAR ; 177.07 8.39E-09 7006300 2772.3 3055 2950.7 2036.86 2776.6 2352.6 2276.11 2483.21 3418.9 2963.1 TRUE FALSE FALSE 2738.510141 3098.00837 3002.055696 2272.371337 2634.899741 2202.276453 2469.442727 2555.057763 3113.105021 2886.118235 0.94885584 1.073416998 1.040170725 0.787345199 0.912956271 0.763058293 0.855627707 0.885292131 1.078647778 1 11.49491469 -9.261990742 24.99986467 0.988490575 0.841360058 0.689164684 0.060019519 23.92249123 1084699.247 0.008264628 0.013104868 5.47E-10 9.261990742 -0.147130517 VNLEESSGVENS(ph)PAGARPK ddPTM_HeLa_Romidepsin_16h_R1 3 VNLEESSGVENSPAGARPK 19 1 Q8WVM8-2;Q8WVM8-3;Q8WVM8 Q8WVM8-2 SCFD1 Sec1 family domain-containing protein 1 1 0 VNLEES(0.001)S(0.004)GVENS(0.996)PAGARPK;VNLEES(0.379)S(0.042)GVENS(0.579)PAGARPK;VNLEES(0.042)S(0.127)GVENS(0.83)PAGARPK ;; 219.96 1.24E-29 163792000 8411.5 8927.7 7508 7444.2 7198.8 7638.5 6531.3 6882.8 8294.9 8569.2 TRUE FALSE FALSE 8308.977403 9053.384395 7638.673591 8304.93343 6831.418374 7150.424502 7086.068459 7081.942959 7552.983369 8346.570949 0.995495929 1.084683093 0.915187044 0.995011422 0.818470054 0.856690076 0.848979599 0.848485324 0.904920526 1 13.0269679 -8.768099073 24.98898825 0.997988377 0.844538911 0.653956868 0.048903288 48.02720046 180211.7514 0.005417754 0.009986249 1.71E-09 8.768099073 -0.153449465 VNLFPGLS(ph)PSALK ddPTM_HeLa_Romidepsin_16h_R1 1 VNLFPGLSPSALK 13 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 VNLFPGLS(0.934)PS(0.066)ALK 88.706 0.023941 133740000 6093.3 6278.1 6133.5 6598.8 8772.6 9492.5 7397.9 8669.4 6804.3 6459.2 TRUE FALSE FALSE 6019.032516 6366.483257 6240.250995 7361.784304 8324.901487 8885.959886 8026.277441 8920.235411 6195.706366 6291.389053 0.956709634 1.011936029 0.991871738 1.170136554 1.323221536 1.412400316 1.275756017 1.417848322 0.984791485 1 12.61916286 -8.990384525 1.956428828 0.981023597 1.362810251 0.95095004 0.039484477 0.045497578 0.348012759 0.005867561 0.011623856 1.02E-09 8.990384525 0.381786654 ES(ph)RSPQQSAALPR ddPTM_HeLa_Romidepsin_16h_R1 1 ESRSPQQSAALPR 13 1 A0A0A6YYG7;Q6IBW4-2;Q6IBW4;Q6IBW4-4;E5RJN3 A0A0A6YYG7 NCAPH2 Condensin-2 complex subunit H2 1 0 ES(0.815)RS(0.185)PQQS(0.001)AALPR 90.793 0.008061 32296000 2105.4 1956.5 2012.6 1602.8 1420.3 1461.8 1135.4 766.94 2258.1 2230.1 TRUE FALSE FALSE 2079.738575 1984.043658 2047.628459 1788.123277 1347.816791 1368.395698 1231.840848 789.1301989 2056.12988 2172.161681 0.957451093 0.913395939 0.94266853 0.8231999 0.620495612 0.629969541 0.567103664 0.36329257 0.946582337 1 11.08491578 -8.087784654 0.51427081 0.992790692 0.256608897 0.945207187 0.048003395 0.296508048 0.087670377 0.010212914 0.112719321 8.17E-09 8.087784654 -0.736181794 down SPLDPMT(ph)SPGSGLILQANFVHSQR ddPTM_HeLa_Romidepsin_16h_R1 1 SPLDPMTSPGSGLILQANFVHSQR 24 0 Q08499;Q08499-2;A0A1B0GW84;A0A087WSZ7;Q08499-10;Q08499-11;Q08499-6;Q08499-9;A0A1W2PQN6;Q08499-12;Q08499-7 Q08499 PDE4D "cAMP-specific 3,5-cyclic phosphodiesterase 4D" 1 0 S(0.014)PLDPMT(0.523)S(0.46)PGS(0.002)GLILQANFVHSQR 87.659 4.95E-05 30618000 1968.6 1963.5 1724.8 1775.5 1381 1580.8 1001.5 896.13 2011 2044.1 TRUE FALSE FALSE 1944.605946 1991.142205 1754.81942 1980.791664 1310.522417 1479.791982 1086.567385 922.0581077 1831.131123 1990.993987 0.976701064 1.000074444 0.881378563 0.994875764 0.658225201 0.743242818 0.545741168 0.463114461 0.919707008 1 10.95927315 -8.034416204 0.661493309 0.994194297 0.361576209 0.872321782 0.068573186 0.285535678 0.149602461 0.010467355 0.112081636 9.24E-09 8.034416204 -0.632618088 down LAVLSSS(ph)LTHWK ddPTM_HeLa_Romidepsin_16h_R1 1 LAVLSSSLTHWK 12 0 F5GX19;F5H3Y3;Q6IAA8 F5GX19 LAMTOR1 Ragulator complex protein LAMTOR1 1 0 LAVLS(0.014)S(0.074)S(0.854)LT(0.059)HWK 82.202 0.018449 4085200 3972.1 4507.2 4413 2740.9 3364.3 2710.9 1518.2 2311.5 4691.3 5279.6 TRUE FALSE FALSE 3923.686517 4570.65248 4489.806414 3057.815754 3192.607217 2537.682239 1647.15587 2378.379606 4271.698378 5142.435231 0.763001641 0.888810899 0.873089541 0.594624068 0.620835669 0.493478697 0.320306586 0.462500644 0.830676165 1 12.328236 -7.831760453 0.28283865 0.969937587 3.42E-16 0.80806074 0.091366331 1.830879577 0.143414807 0.054380255 0.596664557 1.47E-08 7.831760453 -0.969937587 down VNPHKVS(ph)PASSVDSNIPSSQGYKK ddPTM_HeLa_Romidepsin_16h_R1 1 VNPHKVSPASSVDSNIPSSQGYKK 24 2 Q9UHB7;Q9UHB7-2 Q9UHB7 AFF4 AF4/FMR2 family member 4 1 0 VNPHKVS(0.34)PAS(0.266)S(0.266)VDS(0.115)NIPS(0.009)S(0.003)QGY(0.001)KK 50.132 0.015335 15199000 1390.7 1484 1516.7 1355.6 1952.9 1853.4 1337.7 1690.3 2016.9 1413.8 TRUE FALSE FALSE 1373.749613 1504.891791 1543.097527 1512.34085 1853.236226 1734.973722 1451.324205 1739.206164 1836.503413 1377.069272 0.997589331 1.092822141 1.120566378 1.098231498 1.345782862 1.25990301 1.053922438 1.262976525 1.333631829 1 10.42738542 -9.656751742 1.146012854 0.997640427 1.212517546 0 0.131040794 0.226746778 0.596681546 0.013913291 0.022404422 2.20E-10 9.656751742 0.214877119 VNPTVFFDIAVDGEPLGR ddPTM_HeLa_Romidepsin_16h_R1 1 VNPTVFFDIAVDGEPLGR 18 0 F8WE65;C9J5S7;P62937;E5RIZ5 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 0 157.8 5.46E-05 5158400 837.38 784.49 679.07 766.62 742.01 687.61 630.91 733.98 838.58 683.16 FALSE FALSE TRUE 827.1736905 795.5340708 690.8889285 855.2602115 704.1424609 643.6739402 684.4994797 755.2165533 763.5753045 665.4114047 1.243101162 1.195552203 1.038288379 1.285310419 1.05820618 0.967332293 1.028686125 1.134961842 1.147523621 1 9.378102783 -8.544331815 24.99966584 1.130212622 1.037263693 0.223597474 0.09015674 366.9480377 427609.7521 0.016305592 0.032613502 2.86E-09 8.544331815 -0.092948928 VNPVTSLSENYT(ph)CSDSEESSEKDK ddPTM_HeLa_Romidepsin_16h_R1 1 VNPVTSLSENYTCSDSEESSEKDK 24 1 Q14432 Q14432 PDE3A "cGMP-inhibited 3,5-cyclic phosphodiesterase A" 1 0 VNPVTS(0.001)LS(0.035)ENY(0.126)T(0.414)CS(0.414)DS(0.007)EES(0.001)S(0.001)EKDK 67.877 0.0008635 6828000 1516.4 1283.5 1538.9 591.85 1034.5 930.23 723.34 809.18 1544.6 1554.9 TRUE FALSE FALSE 1497.917534 1301.569147 1565.683909 660.2824817 981.7056047 870.7913052 784.7804815 832.5923466 1406.447107 1514.503474 0.989048595 0.85940321 1.033793541 0.435972907 0.64820294 0.574968179 0.518176746 0.549746079 0.928652282 1 10.56462917 -9.266810286 24.99979275 0.985042465 0.551252686 0.903789335 0.067770974 82.55498844 384265.8824 0.009507831 0.014787301 5.41E-10 9.266810286 -0.433789779 VNPVTSLSENYT(ph)CSDSEESSEKDKLAIPK ddPTM_HeLa_Romidepsin_16h_R1 1 VNPVTSLSENYTCSDSEESSEKDKLAIPK 29 2 Q14432 Q14432 PDE3A "cGMP-inhibited 3,5-cyclic phosphodiesterase A" 1 0 VNPVTSLS(0.005)ENY(0.099)T(0.346)CS(0.346)DS(0.117)EES(0.008)S(0.08)EKDKLAIPK 78.653 1.14E-06 25724000 2084.8 1629.7 1711.6 186.19 1122.1 1220.7 1003.5 1007.1 2321.8 1425.6 TRUE FALSE FALSE 2059.389656 1652.642959 1741.38968 207.7181639 1064.83505 1142.70121 1088.737265 1036.23885 2114.132393 1388.562706 1.483108862 1.190182447 1.254095096 0.14959221 0.766861334 0.822938139 0.784074972 0.746267234 1.522532892 1 10.43937661 -9.314521604 24.98926988 1.232249566 0.676837245 0.653017718 0.229595138 182.3726514 85854.27881 0.038020004 0.058076543 4.85E-10 9.314521604 -0.555412321 VNQPASFAVQLNGAR ddPTM_HeLa_Romidepsin_16h_R1 1 VNQPASFAVQLNGAR 15 0 Q14315-2;Q14315 Q14315-2 FLNC Filamin-C 0 0 130.15 0.0004503 552400 419.34 393.46 445.38 202.92 920.89 817.87 836.42 325.44 1025.1 600.8 FALSE FALSE TRUE 414.2289228 398.9991402 453.1316521 226.3825652 873.893547 765.6107466 907.4654939 334.8560929 933.4124886 585.1911294 0.707852361 0.681827048 0.774331034 0.386852353 1.493347221 1.308308872 1.550716421 0.572216625 1.595055772 1 9.19276409 -8.746255146 24.9920419 0.806802713 1.259485161 0.176397843 0.384151079 203.4759113 334903.4067 0.04186936 0.083482768 1.79E-09 8.746255146 0.452682448 VNQSALEAVTPS(ph)PSFQQR ddPTM_HeLa_Romidepsin_16h_R1 2 VNQSALEAVTPSPSFQQR 18 0 Q9UKG1 Q9UKG1 APPL1 DCC-interacting protein 13-alpha 1 0 VNQSALEAVT(0.002)PS(0.994)PS(0.004)FQQR;VNQSALEAVT(0.001)PS(0.979)PS(0.021)FQQR ; 259.55 9.48E-76 212182000 6095.5 5409.2 4973.3 5199.6 5449.4 4946.9 3557.2 4117.8 5653 5062.3 TRUE FALSE FALSE 6021.205701 5485.35086 5059.8582 5800.802217 5171.296783 4630.809055 3859.348479 4236.942046 5147.381522 4930.780716 1.221146518 1.112471062 1.0261779 1.176447007 1.048778496 0.939163455 0.782705357 0.859284217 1.043928298 1 12.26760038 -8.137373957 2.229849411 1.105498039 0.821036829 0.725047508 0.06714829 0.151449958 1.445838164 0.01289809 0.04287383 7.29E-09 8.137373957 -0.28446121 VNS(ph)NGKES(ph)PGSSEFFQEAVSHGK ddPTM_HeLa_Romidepsin_16h_R1 1 VNSNGKESPGSSEFFQEAVSHGK 23 1 Q8N108-17;Q8N108;Q8N108-13;Q8N108-12 Q8N108-17 MIER1 Mesoderm induction early response protein 1 2 0 VNS(0.961)NGKES(0.961)PGS(0.034)S(0.034)EFFQEAVS(0.011)HGK 46.569 0.020475 6818900 2172.4 1833.2 2178.4 1576.5 1923.9 2066.6 1496.6 1651.3 2199.5 2051.4 TRUE FALSE FALSE 2145.921953 1859.007838 2216.314138 1758.782348 1825.716204 1934.55093 1623.721167 1699.07776 2002.771211 1998.104332 1.07397893 0.93038577 1.109208414 0.880225481 0.913724161 0.968193151 0.812630822 0.850344866 1.002335653 1 10.9644162 -8.596245606 0.732027631 1.033394644 0.833482208 0.502578173 0.063667167 0.476060488 0.425782421 0.011513887 0.054634411 2.53E-09 8.596245606 -0.199912435 VNS(ph)PGTLAR ddPTM_HeLa_Romidepsin_16h_R1 1 VNSPGTLAR 9 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6;P53814-2 A0A087WVP4 SMTN Smoothelin 1 0 VNS(0.775)PGT(0.225)LAR 168.85 0.0029615 5071900 3791 2912.3 2834.9 3523.6 8631 11711 9700.7 10639 3594.3 2990.7 TRUE FALSE FALSE 3744.793834 2953.299436 2884.240245 3931.015211 8190.527863 10962.7049 10524.67722 10946.82268 3272.816806 2913.001183 1.285544907 1.013833929 0.990126699 1.349472576 2.811714568 3.763371247 3.613001353 3.757919064 1.123520589 1 11.50829057 -8.640368445 2.386575699 1.114019711 3.702104572 0.992311667 0.10413431 0.021982596 0.253189637 0.02053715 0.046403259 2.29E-09 8.640368445 2.58808486 up VNSGDT(ph)EVGSSLLR ddPTM_HeLa_Romidepsin_16h_R1 2 VNSGDTEVGSSLLR 14 0 A0A499FJI4;O75592-2;O75592 A0A499FJI4 MYCBP2 E3 ubiquitin-protein ligase MYCBP2 1 0 VNS(0.039)GDT(0.943)EVGS(0.017)S(0.001)LLR;VNS(0.26)GDT(0.74)EVGSSLLR ; 216 7.28E-24 176979000 3702.6 3702.2 3903.7 3137.4 5177.8 4731.2 4021.9 4890.7 3808.6 3496.1 TRUE FALSE FALSE 3657.471287 3754.319669 3971.642261 3500.16095 4913.557545 4428.891589 4363.520086 5032.204688 3467.949277 3405.270818 1.074061795 1.102502523 1.166321997 1.027865664 1.4429271 1.300598932 1.281401779 1.477769304 1.018406307 1 11.73355382 -8.272777412 0.385892355 1.009488698 1.553812938 0.726004562 0.08772256 1.065139727 0.185410457 0.027975641 0.239820438 5.34E-09 8.272777412 0.54432424 VNSPGT(ph)LAR ddPTM_HeLa_Romidepsin_16h_R1 2 VNSPGTLAR 9 0 A0A087WVP4;A0A087X1R1;P53814-5;P53814;P53814-6;P53814-2 A0A087WVP4 SMTN Smoothelin 1 0 VNS(0.004)PGT(0.996)LAR;VNS(0.12)PGT(0.88)LAR ; 121.61 0.025953 82980000 4302.8 4140.4 4125.3 5223.3 12370.1 15058 13259.7 14139.3 5010.4 4725.8 TRUE FALSE FALSE 4250.355819 4198.68866 4197.099116 5827.242522 11738.80764 14095.8424 14385.97859 14548.39834 4562.257275 4603.023035 0.923383565 0.91215895 0.911813624 1.265959887 2.550238734 3.062301077 3.125332739 3.160618191 0.991143699 1 12.16836595 -8.701255166 2.25905284 0.95260172 3.119466359 0.997991622 0.044110617 0.011470186 0.119044701 0.008796223 0.019500724 1.99E-09 8.701255166 2.166864638 up VNTLIRPDGEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VNTLIRPDGEKK 12 2 K7EMA7;H7BY10;K7EJV9;K7ERT8;A8MUS3;P62750 K7EMA7 RPL23A 60S ribosomal protein L23a 0 1 VNTLIRPDGEK(1)K 99.669 0.0149 7864900 2013.8 2454.8 2135.3 1935.9 4972 4265.7 4579.4 4507.9 5317.8 4414.8 FALSE TRUE FALSE 1989.255031 2489.358739 2172.464001 2159.737867 4718.260287 3993.135537 4968.374122 4638.328974 4842.162649 4300.10286 0.462606383 0.578906789 0.505212101 0.502252606 1.097243587 0.928613958 1.155408204 1.078655354 1.126057401 1 12.07015545 -8.746155399 24.99190203 0.691044755 1.061699073 0.422007868 0.211581833 203.2678144 332375.6023 0.034227596 0.068250845 1.79E-09 8.746155399 0.370654318 VNVTVDYIRPAS(ph)PATETVPAFSER ddPTM_HeLa_Romidepsin_16h_R1 1 VNVTVDYIRPASPATETVPAFSER 24 1 Q7KZF4 Q7KZF4 SND1 Staphylococcal nuclease domain-containing protein 1 1 0 VNVT(0.01)VDY(0.087)IRPAS(0.803)PAT(0.054)ET(0.039)VPAFS(0.007)ER 51.094 0.013305 54278000 1637.6 1337.3 1438.2 1642.9 1663.2 1817.6 1469.2 1483.7 1854 1484.3 TRUE FALSE FALSE 1617.640301 1356.126545 1463.231268 1832.859828 1578.320698 1701.461226 1593.993811 1526.628519 1688.173597 1445.737672 1.118903057 0.938017021 1.012100117 1.267767911 1.091706143 1.17688102 1.102547054 1.055951262 1.167690121 1 10.49759008 VPAAFPTKVPVPGPGS(ph)GGNGPER ddPTM_HeLa_Romidepsin_16h_R1 1 VPAAFPTKVPVPGPGSGGNGPER 23 1 J3KPS2;A0A494C1T9;Q6ZRV2 J3KPS2 FAM83H Protein FAM83H 1 0 VPAAFPT(0.002)KVPVPGPGS(0.998)GGNGPER 74.525 0.00038943 15793000 991.59 990.62 854.89 978.78 668.69 585.63 439.59 519.53 1073.3 1015.9 TRUE FALSE FALSE 979.5041197 1004.565974 869.7690018 1091.951149 634.5642541 548.210133 476.9287636 534.5617809 977.3013599 989.5067715 0.989891275 1.015218898 0.878992471 1.103530749 0.641293493 0.55402363 0.481986357 0.540230543 0.987665156 1 9.95056577 -8.635838221 4.52807539 0.993510618 0.531741139 0.938563957 0.05578587 0.03285745 1.155521989 0.007578717 0.015520434 2.31E-09 8.635838221 -0.461769479 VPAEDET(ph)QSIDS(ph)EDSFVPGR ddPTM_HeLa_Romidepsin_16h_R1 1 VPAEDETQSIDSEDSFVPGR 20 0 J3KSI3;Q8WZ73-2;Q8WZ73 J3KSI3 RFFL E3 ubiquitin-protein ligase rififylin 2 0 VPAEDET(0.42)QS(0.329)IDS(0.925)EDS(0.325)FVPGR 87.49 0.0013816 0 64.464 73.136 213.09 185.8 211.11 159.35 156.04 171.41 183.73 160.17 TRUE FALSE FALSE 63.67828797 74.16561053 216.7987421 207.2830702 200.3362689 149.1680493 169.2940337 176.3694779 167.2967286 156.0087603 0.408171232 0.475393884 1.389657489 1.328663017 1.284134741 0.956151751 1.085157227 1.130510092 1.072354708 1 7.285483232 -9.760096682 24.99999912 0.694331592 1.189860449 0.494545515 0.224351111 24.86797839 463016.8379 0.042408335 0.058118177 1.74E-10 9.760096682 0.495528857 VPAPFS(ph)PPPSKPR ddPTM_HeLa_Romidepsin_16h_R1 1 VPAPFSPPPSKPR 13 1 Q9P206;Q9P206-3;Q9P206-2 Q9P206 KIAA1522 Uncharacterized protein KIAA1522 1 0 VPAPFS(1)PPPSKPR 109.55 0.0026431 30176000 3506.4 4031.2 3534.3 3482.3 3144.7 2669.7 2135.2 1770 3727.8 3760 TRUE FALSE FALSE 3463.662648 4087.951339 3595.813009 3884.939911 2984.214225 2499.114786 2316.563835 1821.212157 3394.376232 3662.314658 0.945757798 1.116220675 0.981841634 1.060788128 0.814843754 0.682386692 0.632540907 0.497284457 0.926839048 1 11.83854003 -8.267738574 1.570156378 0.991938418 0.556865506 0.889031155 0.063970782 0.092489471 0.426573458 0.009359938 0.033860111 5.40E-09 8.267738574 -0.435072913 VPAQANGTPT(ph)TK ddPTM_HeLa_Romidepsin_16h_R1 2 VPAQANGTPTTK 12 0 I3L1L3;Q9BQG0;Q9BQG0-2 I3L1L3 MYBBP1A Myb-binding protein 1A 1 0 VPAQANGT(0.221)PT(0.619)T(0.16)K;VPAQANGT(0.108)PT(0.705)T(0.187)K ; 164.13 0.00081888 9529500 3915.7 3871.6 3536.6 2502.2 3225.5 4142 3102.5 3567.3 3551.2 3314.8 TRUE FALSE FALSE 3867.973942 3926.104486 3598.153039 2791.516137 3060.890699 3877.339568 3366.026273 3670.514197 3233.571778 3228.681018 1.198004362 1.216008786 1.114434352 0.864599544 0.948031311 1.200905121 1.042539122 1.13684634 1.001514786 1 11.6567292 VPDEEENEES(ph)DNEKETEK ddPTM_HeLa_Romidepsin_16h_R1 4 VPDEEENEESDNEKETEK 18 1 P11388;P11388-2;P11388-3;P11388-4 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 VPDEEENEES(0.999)DNEKET(0.001)EK;VPDEEENEES(0.999)DNEKET(0.001)EK;VPDEEENEES(0.995)DNEKET(0.005)EK;VPDEEENEES(0.985)DNEKET(0.015)EK ;;; 72.864 0.0075776 416727000 11991.3 10878.3 13321 6369.2 9126.4 9456.6 8717.2 9916.9 14287.2 15175.8 TRUE FALSE FALSE 11845.14542 11031.44499 13552.84642 7105.636872 8660.645753 8852.35378 9457.63875 10203.82986 13009.31705 14781.53053 0.801347695 0.74629924 0.916877071 0.480710496 0.585909946 0.598879376 0.639828111 0.690309426 0.880106226 1 13.85150804 -10.55263502 0.400968902 1.002408149 0.590915617 0.581506281 0.101330919 0.447251942 0.198577612 0.064980748 0.057634586 2.80E-11 10.55263502 -0.411492532 VPEASSEPFDTSS(ph)PQAGR ddPTM_HeLa_Romidepsin_16h_R1 2 VPEASSEPFDTSSPQAGR 18 0 Q9H4I2;H0Y6F5 Q9H4I2 ZHX3 Zinc fingers and homeoboxes protein 3 1 0 VPEASSEPFDT(0.009)S(0.177)S(0.814)PQAGR;VPEASSEPFDT(0.156)S(0.264)S(0.58)PQAGR ; 127.2 0.00079173 48164600 3659.7 3815.5 2855.3 3382.3 2833.6 2798 2399.42 2745.6 4480.9 4646.1 TRUE FALSE FALSE 3615.094169 3869.214709 2904.995299 3773.37744 2688.990818 2619.21683 2603.226675 2825.039604 4080.117081 4525.393652 0.798846343 0.855000693 0.641932066 0.833823028 0.594200422 0.578782098 0.575248669 0.624263837 0.901604898 1 12.14382758 -9.782740574 0.156044829 1.158478589 0.34716969 0.751277826 0.073399989 1.598252012 0.167163661 0.319079565 0.466577597 1.65E-10 9.782740574 -0.811308899 VPEPEGQTS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 VPEPEGQTSPK 11 0 Q504Q3-2;Q504Q3-3;Q504Q3 Q504Q3-2 PAN2 PAB-dependent poly(A)-specific ribonuclease subunit PAN2 1 0 VPEPEGQT(0.353)S(0.647)PK;VPEPEGQT(0.15)S(0.85)PK ; 132.14 0.00010966 19504000 7590.7 6982.9 6947.5 7072.1 6403 6022.3 5304.6 6076.6 7565.7 6827.6 TRUE FALSE FALSE 7498.181629 7081.205449 7068.418323 7889.809477 6076.231017 5637.494466 5755.172592 6252.416834 6889.004843 6650.217968 1.127509153 1.064808023 1.06288521 1.186398629 0.913689002 0.847715743 0.865411122 0.940182241 1.035906624 1 12.69918591 -8.619648988 7.445891371 1.069939244 0.882318848 0.752171759 0.052821229 0.100768006 6.750716226 0.009045564 0.018150845 2.40E-09 8.619648988 -0.187620397 VPFS(ph)PGPAPPPHMGELDQER ddPTM_HeLa_Romidepsin_16h_R1 1 VPFSPGPAPPPHMGELDQER 20 0 C9JHW1;E7ESB6;I1E4Y6;Q6Y7W6-4;Q6Y7W6-5;Q6Y7W6;Q6Y7W6-3 C9JHW1 GIGYF2 PERQ amino acid-rich with GYF domain-containing protein 2 1 0 VPFS(1)PGPAPPPHMGELDQER 66.702 0.0033147 15867000 1181.9 1128.1 1183.5 819.88 1133.1 1488.7 1288.7 1338 1022.7 1209.5 TRUE FALSE FALSE 1167.494548 1143.981421 1204.098321 914.6783833 1075.273679 1393.576875 1398.162146 1376.712919 931.2271506 1178.077016 0.991017168 0.971058264 1.022087949 0.776416458 0.912736319 1.182925103 1.186817269 1.168610287 0.790463729 1 10.20221814 -8.251078387 24.54124243 0.974130167 1.180187553 0.599200898 0.089466512 273.923775 648819.0989 0.010299111 0.025921365 5.61E-09 8.251078387 0.206057386 VPGEDGTLPPTQGS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 2 VPGEDGTLPPTQGSPLR 17 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 VPGEDGTLPPT(0.002)QGS(0.998)PLR;VPGEDGTLPPT(0.388)QGS(0.612)PLR ; 181.86 4.46E-09 94451000 1865.58 1445.44 1527.13 1650.62 1829.72 1816.03 1518.21 1875.46 1764.72 1891.87 TRUE FALSE FALSE 1842.841593 1465.788942 1553.709057 1841.472451 1736.342561 1699.991544 1647.16672 1929.723476 1606.879023 1842.718945 1.000066559 0.795449 0.843161168 0.999323557 0.942272052 0.922545214 0.893878431 1.047215302 0.872015251 1 10.84762033 VPGGS(ph)PLGVSLVYSDKK ddPTM_HeLa_Romidepsin_16h_R1 1 VPGGSPLGVSLVYSDKK 17 1 I3L2J0;A0A0A0MQR4;Q96RK0 I3L2J0 CIC Protein capicua homolog 1 0 VPGGS(0.984)PLGVS(0.014)LVY(0.002)S(0.001)DKK 53.059 0.026806 26649000 2360.2 1956.6 2170.1 1999.7 2282.2 2300 1528.2 2094.9 2100.2 2249.1 TRUE FALSE FALSE 2331.432975 1984.145066 2207.86968 2230.914723 2165.730818 2153.037423 1658.00527 2155.512626 1912.352852 2190.668058 1.064256616 0.905726022 1.007852227 1.018371868 0.988616605 0.982822302 0.756849156 0.983952187 0.872954186 1 11.09715518 -7.953372882 11.5831987 1.015220926 0.870048373 0.144946304 0.07837451 0.445136408 108.7685768 0.008574131 0.025738143 1.11E-08 7.953372882 -0.145172552 VPGPAEGPAEPAAEAS(ph)DEAERR ddPTM_HeLa_Romidepsin_16h_R1 2 VPGPAEGPAEPAAEASDEAERR 22 1 H0YFQ2;Q24JP5-4;Q24JP5;Q24JP5-2 H0YFQ2 TMEM132A Transmembrane protein 132A 1 0 VPGPAEGPAEPAAEAS(1)DEAERR;VPGPAEGPAEPAAEAS(1)DEAERR ; 83.059 0.00041199 6427300 1134.06 1501.79 1450.05 1153.36 1051.05 1321.58 710.28 967.76 1633.29 1229.84 TRUE FALSE FALSE 1120.237641 1522.932239 1475.287512 1286.71691 997.4109965 1237.135303 770.6111655 995.7606087 1487.204452 1197.88858 0.935176827 1.271347156 1.231573234 1.074154084 0.832640876 1.032763251 0.643307882 0.831263129 1.241521521 1 10.22627801 -7.770780617 24.90671331 1.010184553 0.737285498 0.39278355 0.151740842 130.9967009 349282.7728 0.020062541 0.061393535 1.70E-08 7.770780617 -0.272899054 VPGPGPS(ph)PSAPQR ddPTM_HeLa_Romidepsin_16h_R1 1 VPGPGPSPSAPQR 13 0 A0A0C4DFP1;Q96B18 A0A0C4DFP1 DACT3 Dapper homolog 3 1 0 VPGPGPS(0.881)PS(0.119)APQR 99.991 0.012745 7610300 727.78 548.13 654.47 514.02 905.44 958.08 886.66 759.69 646.91 801.51 TRUE FALSE FALSE 718.9095374 555.8465885 665.8607758 573.4534109 859.2320181 896.8617801 961.9728783 781.6704316 589.0487494 780.6866547 0.920868229 0.711997042 0.852916816 0.734550037 1.100610614 1.148811466 1.232213811 1.001260143 0.754526475 1 9.608599798 -8.569235826 15.47670871 0.917472658 1.135708685 0.528128237 0.118652211 2.05284837 684.8816788 0.017372647 0.034747153 2.70E-09 8.569235826 0.218236028 VPGVENSDS(ph)PAQR ddPTM_HeLa_Romidepsin_16h_R1 1 VPGVENSDSPAQR 13 0 Q9BZL4-5;Q9BZL4-4;Q9BZL4;K7EL81;Q9BZL4-3 Q9BZL4-5 PPP1R12C Protein phosphatase 1 regulatory subunit 12C 1 0 VPGVENS(0.026)DS(0.974)PAQR 91.845 0.020751 3729000 1304.4 1567.6 1220.8 1757.1 1114 1451.4 1114.9 1403 1486.5 1622.2 TRUE FALSE FALSE 1288.501471 1589.668714 1242.047512 1960.264169 1057.148423 1358.660224 1209.599578 1443.593591 1353.543717 1580.05501 0.815478868 1.006084411 0.786078652 1.24063033 0.669057986 0.859881596 0.7655427 0.91363502 0.856643413 1 10.62575907 VPIVINPNAY(ph)DNLAIYK ddPTM_HeLa_Romidepsin_16h_R1 2 VPIVINPNAYDNLAIYK 17 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 VPIVINPNAY(0.993)DNLAIY(0.007)K;VPIVINPNAY(1)DNLAIYK ; 215.53 4.96E-25 18613200 4711.9 4529.6 5372.6 4612.5 4454.2 4487.2 3714.9 3889.4 5673.5 5288.2 TRUE FALSE FALSE 4654.46955 4593.367828 5466.107849 5145.818952 4226.885553 4200.482402 4030.443513 4001.933653 5166.04795 5150.811802 0.903638054 0.891775511 1.061212884 0.999030668 0.82062512 0.815499103 0.782487046 0.776952024 1.002958009 1 12.33058411 -8.679423133 5.527851768 0.959780918 0.7957066 0.753951784 0.049248616 0.096375178 4.905119178 0.008232703 0.016589932 2.09E-09 8.679423133 -0.164074318 VPKPEPIPEPKEPS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 2 VPKPEPIPEPKEPSPEK 17 2 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 VPKPEPIPEPKEPS(1)PEK;VPKPEPIPEPKEPS(1)PEK ; 74.047 0.0096213 1885350000 11541.6 10581.9 10997.6 11864.8 11187 11425.9 10211.6 12457.1 12457.9 12593.1 TRUE FALSE FALSE 11400.92654 10730.87227 11189.00861 13236.664 10616.08565 10695.82187 11078.97305 12817.52653 11343.63422 12265.92945 0.92947922 0.874851948 0.912202264 1.079140725 0.86549378 0.871994406 0.903231434 1.044969857 0.92480837 1 13.58236894 -12.08493134 0.918690958 0.99898309 0.93229061 0 0.072174526 0.967007266 1.510260389 0.04103909 0.012993634 8.22E-13 12.08493134 -0.06669248 VPKPEPIPEPKEPS(ph)PEKNSK ddPTM_HeLa_Romidepsin_16h_R1 2 VPKPEPIPEPKEPSPEKNSK 20 3 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 VPKPEPIPEPKEPS(0.998)PEKNS(0.002)K;VPKPEPIPEPKEPS(0.972)PEKNS(0.028)K ; 69.024 0.0070543 113109000 5848.4 5230.2 4270.6 10351.4 5536.4 5323.1 5004 5419.6 5888 5417.9 TRUE FALSE FALSE 5777.117451 5303.830893 4344.928002 11548.27757 5253.856849 4982.97109 5429.039635 5576.407575 5361.362533 5277.142177 1.094743567 1.005057418 0.823348672 2.188358241 0.995587512 0.944255607 1.028784037 1.056709747 1.015959463 1 12.36554114 SSSTS(ph)ESGDSDNMR ddPTM_HeLa_Romidepsin_16h_R1 1 SSSTSESGDSDNMR 14 0 O75179-4;O75179-6;O75179-2;O75179;H0YM23;O75179-7 O75179-4 ANKRD17 Ankyrin repeat domain-containing protein 17 1 0 SS(0.001)S(0.006)T(0.03)S(0.962)ESGDSDNMR 110.51 0.0074107 2489400 908.19 1054.5 1091.9 1013.1 923.38 973.28 534.42 499.51 1096.1 1165.5 TRUE FALSE FALSE 897.120631 1069.345279 1110.904061 1130.239389 876.256473 911.0905491 579.8136215 513.9625338 998.0620708 1135.220142 0.790261376 0.941971728 0.978580295 0.995612522 0.771882422 0.802567287 0.510749942 0.452742613 0.879179318 1 10.14875638 -7.797887512 1.417908096 0.911531108 0.405649729 0.843561345 0.072952274 0.196786985 0.630856709 0.013818761 0.106588048 1.59E-08 7.797887512 -0.505881379 down VPLSNENSQVPQS(ph)PEDWRK ddPTM_HeLa_Romidepsin_16h_R1 2 VPLSNENSQVPQSPEDWRK 19 1 Q8IZT6;Q8IZT6-2 Q8IZT6 ASPM Abnormal spindle-like microcephaly-associated protein 1 0 VPLS(0.002)NENS(0.01)QVPQS(0.987)PEDWRK;VPLSNENSQVPQS(1)PEDWRK ; 108.99 0.00025726 23767000 1135.57 1176.52 1134.74 954.47 915.52 654.83 752.4 761.55 1163.98 1097.86 TRUE FALSE FALSE 1121.729236 1193.083079 1154.489674 1064.830312 868.7975981 612.9884764 816.3088372 783.5842477 1059.870714 1069.337439 1.048994635 1.115721788 1.079630837 0.995785122 0.812463462 0.573241387 0.763378151 0.732775473 0.991147111 1 10.06250146 -8.67336709 3.06728843 1.035826415 0.69603965 0.880523136 0.05868681 0.060884818 1.148916963 0.008720066 0.018443202 2.12E-09 8.67336709 -0.339786765 VPLVAEK(ac)PLKEPK ddPTM_HeLa_Romidepsin_16h_R1 1 VPLVAEKPLKEPK 13 2 P41250 P41250 GARS Glycine--tRNA ligase 0 1 VPLVAEK(0.855)PLK(0.145)EPK 101.32 0.012127 1293600 475.81 544.51 591.88 464.8 1421.8 1038.6 1046.4 1297.3 1224.8 1024.2 FALSE TRUE FALSE 470.0106447 552.1756261 602.1814231 518.5423629 1349.240241 972.2368119 1135.28119 1334.835329 1115.25082 997.5911364 0.47114557 0.553508954 0.603635499 0.519794477 1.352498224 0.974584453 1.138022531 1.338058529 1.117943795 1 9.962304837 -8.760765355 24.9999986 0.701428776 1.180149892 0.545006714 0.218807227 11.89715619 441240.6237 0.035023881 0.066849235 1.73E-09 8.760765355 0.478721116 VPPELLGGS(ph)PPWK ddPTM_HeLa_Romidepsin_16h_R1 1 VPPELLGGSPPWK 13 0 E7EVA0 E7EVA0 MAP4 Microtubule-associated protein 1 0 VPPELLGGS(1)PPWK 115.06 0.0058088 176910000 7077 7810.9 6622.2 5724.8 5546.1 5192.3 4779.9 4638.1 7301.5 6977.4 TRUE FALSE FALSE 6990.742802 7920.862055 6737.456613 6386.728312 5263.061822 4860.528787 5185.904587 4772.296106 6648.435553 6796.126142 1.028636411 1.165496621 0.99136721 0.939760119 0.774420856 0.715191079 0.763067736 0.702208288 0.978268416 1 12.73049692 -8.840671659 2.132876344 1.026040759 0.728905566 0.884037832 0.050571698 0.07493258 0.693751847 0.007795788 0.016303035 1.44E-09 8.840671659 -0.297135193 VPPFTFHVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VPPFTFHVKK 10 1 Q6NZI2-3;Q6NZI2-2;Q6NZI2 Q6NZI2-3 PTRF Polymerase I and transcript release factor 0 1 VPPFTFHVK(1)K 93.178 0.0080204 304780 224.06 151.34 264.43 215.25 312.56 260.35 148.67 0 172.22 0 FALSE TRUE FALSE 221.3290705 153.4705685 269.0322932 240.1382178 296.6088969 243.7144752 161.2980261 0 156.8162119 0 0 VPQALNFS(ph)PEESDSTFSK ddPTM_HeLa_Romidepsin_16h_R1 4 VPQALNFSPEESDSTFSK 18 0 Q9NYZ3 Q9NYZ3 GTSE1 G2 and S phase-expressed protein 1 1 0 VPQALNFS(0.979)PEES(0.019)DS(0.001)T(0.001)FSK;VPQALNFS(0.994)PEES(0.006)DSTFSK;VPQALNFS(0.971)PEES(0.029)DSTFSK;VPQALNFS(0.995)PEES(0.005)DSTFSK ;;; 200.9 9.86E-21 42923700 6534.53 6665.39 6533.14 4715.86 7177.57 7762.52 7113.66 7712.38 7232.54 7956.89 TRUE FALSE FALSE 6454.884635 6759.225535 6646.846561 5261.129922 6811.27182 7266.520024 7717.894103 7935.525547 6585.643508 7750.168851 0.832870194 0.872139132 0.857638935 0.678840684 0.878854635 0.937595059 0.995835607 1.023916472 0.849741939 1 12.92001203 -4.982920171 14.92198806 0.905422333 1.116798175 0 0.09797738 0 0 0.014491732 0 1.04E-05 4.982920171 0.211375842 VPS(ph)PPDEHQEAENAVSSGNR ddPTM_HeLa_Romidepsin_16h_R1 2 VPSPPDEHQEAENAVSSGNR 20 0 Q9BXS6-4;Q9BXS6-6;Q9BXS6-3;Q9BXS6-5;Q9BXS6-2;Q9BXS6;Q9BXS6-7 Q9BXS6-4 NUSAP1 Nucleolar and spindle-associated protein 1 1 0 VPS(1)PPDEHQEAENAVSSGNR;VPS(1)PPDEHQEAENAVSSGNR ; 107.02 0.00019248 14558300 1186.91 1278.9 1229.91 1241.64 1563.44 1801.06 1677.63 2038.15 1552.44 1748.58 TRUE FALSE FALSE 1172.443484 1296.904388 1251.316068 1385.204259 1483.651823 1685.978079 1820.12785 2097.120655 1413.585878 1703.15164 0.688396416 0.761473234 0.734706199 0.813318219 0.87112139 0.989916599 1.068682205 1.231317638 0.829982396 1 10.73399118 -7.703690529 1.218941629 0.829701355 1.261656097 0.745683051 0.081446268 0.472494697 0.952227192 0.01897868 0.209870515 1.98E-08 7.703690529 0.431954742 VPS(ph)SDEEVVEEPQSR ddPTM_HeLa_Romidepsin_16h_R1 2 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 VPS(0.982)S(0.018)DEEVVEEPQSR;VPS(0.977)S(0.023)DEEVVEEPQSR ; 196.97 3.65E-13 34605000 0 107.35 55.009 198.379 52.893 117.76 0 78.817 65.156 103.79 TRUE FALSE FALSE 0 108.8612761 55.96640857 221.3165134 50.19367284 110.2355161 0 81.09744554 59.32828417 101.0935208 0 1.076837321 0.553610242 2.189225497 0.496507317 1.09043107 0 0.802202207 0.586865347 1 6.659546727 -10.20113968 24.9982116 0.527774418 0.88293131 0.074632832 0.577577425 553.7344301 229559.6496 0.10417613 0.127589165 6.29E-11 10.20113968 0.355156892 VPS(ph)VESLFR ddPTM_HeLa_Romidepsin_16h_R1 1 VPSVESLFR 9 0 Q86W71;Q13439-3;Q13439-4;Q13439;Q13439-5;E7EVX2 Q86W71;Q13439-3 GOLGA4 Golgin subfamily A member 4 1 0 VPS(0.997)VES(0.003)LFR 115.91 0.015783 81133000 1218.6 1089.5 1127.4 1046.6 1179.1 1219.9 1041.8 1260.9 1199 1058.9 TRUE FALSE FALSE 1203.747234 1104.83801 1147.021924 1167.612816 1118.926127 1141.952327 1130.290466 1297.382152 1091.758437 1031.389625 1.167112025 1.071213034 1.11211311 1.132077333 1.084872389 1.107197803 1.095890862 1.257897229 1.058531529 1 10.01037372 -12.42912975 1.039838555 0.996478992 1.126894749 0.340531307 0.053066499 0.384716069 0.710951961 0.038510294 0.00866917 3.72E-13 12.42912975 0.130415757 VPSGETPPS(ph)PSQEGEEGSGLSRPGEAGLGGQER ddPTM_HeLa_Romidepsin_16h_R1 1 VPSGETPPSPSQEGEEGSGLSRPGEAGLGGQER 33 1 Q9P2Y4 Q9P2Y4 ZNF219 Zinc finger protein 219 1 0 VPS(0.006)GET(0.054)PPS(0.75)PS(0.186)QEGEEGS(0.002)GLS(0.002)RPGEAGLGGQER 63.203 0.00018852 0 360.3 288.95 304.32 172.04 157.27 302.26 0 442.83 493.24 394.61 TRUE FALSE FALSE 355.908525 293.0178457 309.6165619 191.9320743 149.243925 282.9465615 0 455.6425874 449.1233791 384.3579753 0.925981892 0.762356617 0.805542182 0.499357595 0.388294076 0.736153741 0 1.185464116 1.168502823 1 8.586306794 -9.755606522 1.197049989 0.970455034 0.531546064 0.309074806 0.290063908 0.353798641 1.015120643 0.046500516 0.070495022 1.76E-10 9.755606522 -0.43890897 VPSPLEGSEGDGDT(ph)D ddPTM_HeLa_Romidepsin_16h_R1 3 VPSPLEGSEGDGDTD 15 0 F5H168;F5H1S9;Q9Y606-2;Q9Y606 F5H168 PUS1 "tRNA pseudouridine synthase;tRNA pseudouridine synthase A, mitochondrial" 1 0 VPSPLEGSEGDGDT(1)D;VPSPLEGSEGDGDT(1)D;VPSPLEGSEGDGDT(1)D ;; 205.96 3.34E-18 15880900 3282.9 2851.03 3168.8 3534.66 2506.93 3147.82 2740.54 2439.84 3406.32 2974.1 TRUE FALSE FALSE 3242.886752 2891.166875 3223.951635 3943.35402 2378.992007 2946.684461 2973.321399 2510.432921 3101.650208 2896.832453 1.119459549 0.998044216 1.112923059 1.361264099 0.821239076 1.017209144 1.026404339 0.866613089 1.070704039 1 11.50026053 -6.190118867 0.756732015 1.066325413 0.105514523 0.189994531 0.126566509 15.13352038 1.843130892 0.020291114 18.05094664 6.45E-07 6.190118867 -0.96081089 VPSPLEGSEGDGDTD ddPTM_HeLa_Romidepsin_16h_R1 1 VPSPLEGSEGDGDTD 15 0 F5H168;F5H1S9;Q9Y606-2;Q9Y606 F5H168 PUS1 "tRNA pseudouridine synthase;tRNA pseudouridine synthase A, mitochondrial" 0 0 139.43 0.0091034 3970700 1600.5 1437.1 1458.3 1222.4 1207.3 1464.4 1313.6 1251.1 1541.8 1327.1 FALSE FALSE TRUE 1580.99249 1457.331532 1483.6811 1363.73964 1145.686976 1370.829566 1425.177151 1287.298605 1403.897546 1292.621751 1.223089809 1.127423031 1.147807624 1.055018329 0.886328097 1.060503249 1.10254771 0.9958819 1.08608535 1 10.33608446 -9.00630269 24.88078576 1.112425167 1.015011274 0.315970218 0.073289946 365.7637502 1443917.409 0.014524943 0.025678562 9.86E-10 9.00630269 -0.097413893 VPSS(ph)DEEVVEEPQSR ddPTM_HeLa_Romidepsin_16h_R1 2 VPSSDEEVVEEPQSR 15 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 VPS(0.035)S(0.965)DEEVVEEPQSR;VPS(0.037)S(0.963)DEEVVEEPQSR ; 258.42 1.09E-70 43254000 555.86 477.62 403.81 348.79 668.96 532.44 182.48 700.64 507.92 419.04 TRUE FALSE FALSE 549.0849645 484.3439469 410.8381437 389.1187409 634.820475 498.4188024 197.9798466 720.911913 462.4903631 408.1532804 1.345291073 1.186671699 1.006578076 0.953364237 1.555348212 1.221155939 0.48506249 1.766277395 1.133129109 1 8.672967242 -12.68555243 1.57037262 1.000421434 1.194798104 0.015868035 0.330583624 1.097700762 4.894457598 0.217898955 0.048892198 2.06E-13 12.68555243 0.19437667 VPTANVSVVDLTCR ddPTM_HeLa_Romidepsin_16h_R1 1 VPTANVSVVDLTCR 14 0 P04406;P04406-2;E7EUT5 P04406 GAPDH Glyceraldehyde-3-phosphate dehydrogenase 0 0 132.06 0.0010254 3653100 335.59 207.4 292.03 184.91 305.73 396.08 336.3 196.09 319.77 213.77 FALSE FALSE TRUE 331.4997 210.3197826 297.1126596 206.2901642 290.1274573 370.7717663 364.8653136 201.7635548 291.1689703 208.2162246 1.592093511 1.010102758 1.426942882 0.990749711 1.393395053 1.780705452 1.752338533 0.969009765 1.398397127 1 7.70193868 -12.53837504 1.258677947 0.996814612 1.396892165 0 0.309053272 0.602142441 1.686328037 0.209476198 0.048216929 2.89E-13 12.53837504 0.400077553 VPTISINK ddPTM_HeLa_Romidepsin_16h_R1 1 VPTISINK 8 0 Q01518-2;Q01518;P40123-3;B7Z385;A0A087X0J3;A0A087WZ15;E9PDI2;P40123-2;P40123 Q01518-2;B7Z385 CAP1;CAP2 Adenylyl cyclase-associated protein 1;Adenylyl cyclase-associated protein 2;Adenylyl cyclase-associated protein 0 0 116.25 0.016089 1903300 1388.4 1127 1500.5 1379.8 1626.4 1517.2 1462.7 1461.5 1235.4 1211 FALSE FALSE TRUE 1371.477647 1142.865936 1526.615573 1539.338968 1543.398739 1420.255817 1586.941701 1503.786197 1124.90273 1179.538045 1.162724384 0.968909769 1.294248693 1.305035454 1.308477285 1.204078005 1.345392552 1.274894186 0.953680752 1 10.20400624 -10.20574792 0.289031087 0.980458631 1.352768369 0.653726435 0.085392187 0.802071101 0.223683501 0.094647912 0.112864069 6.23E-11 10.20574792 0.372309738 (ac)MS(ph)TRES(ph)FNPES(ph)Y(ph)ELDK ddPTM_HeLa_Romidepsin_16h_R1 1 MSTRESFNPESYELDK 16 1 Q5T5U6;P49903-2;P49903-4;P49903 Q5T5U6 SEPHS1 "Selenide, water dikinase 1" 4 0 MS(0.684)T(0.684)RES(0.737)FNPES(0.952)Y(0.943)ELDK 45.879 0.0042614 0 180.97 188.78 181.47 191.96 293.15 218.06 145.34 0 206.84 201.34 TRUE FALSE FALSE 178.764268 191.4376498 184.6284092 214.1553184 278.1894616 204.1266698 157.685176 0 188.3397124 196.1091578 0.911554922 0.976179042 0.941457356 1.092020999 1.418543962 1.040882905 0.804068396 0 0.960382037 1 7.615513097 -7.33083744 3.441158463 1.002614835 1.12E-17 0.826100218 0.142274589 0.088360646 1.724736407 0.021585947 0.203889624 4.67E-08 7.33083744 -1.002614835 down VPTTPAS(ph)PVKNWGGFR ddPTM_HeLa_Romidepsin_16h_R1 1 VPTTPASPVKNWGGFR 16 1 Q6IE81-2;Q6IE81 Q6IE81-2 JADE1 Protein Jade-1 1 0 VPT(0.044)T(0.044)PAS(0.911)PVKNWGGFR 66.893 0.017138 14833000 2371.3 2234.1 1822.4 2716 772.92 673.01 527.71 844.01 2280.9 2164.4 TRUE FALSE FALSE 2342.397684 2265.551718 1854.118108 3030.036699 733.4750082 630.006833 572.5336742 868.4300977 2076.890591 2108.168576 1.111105492 1.074653965 0.879492337 1.437283875 0.347920473 0.298840823 0.271578697 0.411935795 0.985163433 1 11.04177452 -8.740591372 24.77283793 1.065173628 0.325802885 0.871922496 0.140487643 49.8557993 59241.28895 0.018473161 0.036913595 1.82E-09 8.740591372 -0.739370743 VPVHDVTDASK ddPTM_HeLa_Romidepsin_16h_R1 1 VPVHDVTDASK 11 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 106.16 0.0076445 7926000 2235.6 2419.7 2219.9 2349.8 2393.8 2554.4 2483.7 2835.2 2733.8 2576.3 FALSE FALSE TRUE 2208.351647 2453.7646 2258.536428 2621.494932 2271.635454 2391.182084 2694.665416 2917.232039 2489.282081 2509.367355 0.880043188 0.977841923 0.900042166 1.044683604 0.905262217 0.952902364 1.073842541 1.162536858 0.991995882 1 11.29310797 -7.585260183 2.539625104 0.946128219 1.159704799 0.64874613 0.049147944 0.150089081 1.748247635 0.00769089 0.050488261 2.60E-08 7.585260183 0.21357658 VPVLIS(ph)PTLK ddPTM_HeLa_Romidepsin_16h_R1 2 VPVLISPTLK 10 0 P42684-2;P42684-3;P42684-4;P42684-10;P42684-6;P42684;P42684-7;P42684-5 P42684-2 ABL2 Abelson tyrosine-protein kinase 2 1 0 VPVLIS(0.975)PT(0.025)LK;VPVLIS(0.968)PT(0.032)LK ; 158.08 0.0028159 49083000 8406.3 8093 7776.3 7556.9 8932.5 10060.3 8931.3 9749.5 8036.4 8015.3 TRUE FALSE FALSE 8303.840782 8206.933466 7911.643239 8430.664334 8476.641193 9417.479298 9689.924399 10031.5864 7317.604256 7807.061351 1.063632065 1.051219287 1.013395807 1.079876788 1.085765926 1.206277097 1.241174363 1.284937565 0.937305848 1 12.93056389 -8.16583061 1.069518371 1.03102058 1.293783134 0.885373768 0.036081198 0.118704205 0.222597319 0.004263754 0.024417982 6.83E-09 8.16583061 0.262762554 VQAGPGS(ph)PRR ddPTM_HeLa_Romidepsin_16h_R1 1 VQAGPGSPRR 10 1 I3L4F6;I3L0U5;Q6PK04 I3L4F6 CCDC137 Coiled-coil domain-containing protein 137 1 0 VQAGPGS(1)PRR 69.229 0.025941 2135900 812.61 1004.5 1072.2 1092.5 606.56 815.43 666.27 241.88 1171 893.16 TRUE FALSE FALSE 802.7055968 1018.641377 1090.861191 1218.81999 575.6049798 763.3266547 722.8629572 248.8784162 1066.262827 869.9555744 0.922697228 1.170911949 1.253927469 1.401014059 0.661648706 0.877431764 0.830919392 0.286081753 1.225652043 1 9.764797919 -7.214236922 1.189227947 1.014892876 1.27E-15 0.566763527 0.204521349 1.078779571 1.159931137 0.03025535 1.38537067 6.11E-08 7.214236922 -1.014892876 VQAYEEPSVAS(ph)SPNGK ddPTM_HeLa_Romidepsin_16h_R1 3 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 0 VQAYEEPSVAS(0.985)S(0.015)PNGK;VQAYEEPS(0.001)VAS(0.891)S(0.109)PNGK;VQAYEEPSVAS(0.887)S(0.113)PNGK ;; 151.38 0.00027975 293017000 22454.2 21825.4 20683.4 16708.2 20655.3 20533.5 18424.9 19520.9 22265.7 21860 TRUE FALSE FALSE 22180.51957 22132.65855 21043.3859 18640.0807 19601.18297 19221.47562 19989.91055 20085.70644 20274.20003 21292.07405 1.041726584 1.039478752 0.988320154 0.875446922 0.920585891 0.902752619 0.938842806 0.94334194 0.952194698 1 14.37802887 -9.455757337 5.025328852 1.021516936 0.917348422 0.674457556 0.030279343 0.067450693 3.303933785 0.003758832 0.005735472 3.50E-10 9.455757337 -0.104168514 VQAYEEPSVAS(ph)SPNGKESDLR ddPTM_HeLa_Romidepsin_16h_R1 2 VQAYEEPSVASSPNGKESDLR 21 1 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 0 VQAYEEPS(0.117)VAS(0.44)S(0.44)PNGKES(0.003)DLR;VQAYEEPS(0.059)VAS(0.441)S(0.441)PNGKES(0.059)DLR ; 77.838 0.0013555 40432000 4282.2 3471.2 3188.9 4999.6 3380.1 2803.6 3402.5 3018.7 4536.3 3706.8 TRUE FALSE FALSE 4230.006899 3520.067645 3244.401467 5577.677276 3207.600884 2624.459008 3691.508265 3106.041322 4130.561967 3610.496802 1.171585832 0.974953819 0.898602504 1.544850358 0.88840984 0.726896921 1.022437761 0.860280868 1.14404255 1 11.81798165 -8.566908484 24.99999941 1.093011611 0.872212373 0.310007764 0.178086111 132.7344874 75365.88804 0.025052941 0.050105904 2.71E-09 8.566908484 -0.220799237 VQAYEEPSVASS(ph)PNGK ddPTM_HeLa_Romidepsin_16h_R1 2 VQAYEEPSVASSPNGK 16 0 Q99575 Q99575 POP1 Ribonucleases P/MRP protein subunit POP1 1 0 VQAYEEPSVAS(0.066)S(0.934)PNGK;VQAYEEPSVAS(0.037)S(0.963)PNGK ; 302.15 1.47E-137 216602000 12597.9 12815.1 11861.1 10664 12212 12098.5 10138.1 11429.7 12975.1 12126.5 TRUE FALSE FALSE 12444.35195 12995.51131 12067.53747 11897.02186 11588.77607 11325.4449 10999.22996 11760.40034 11814.57456 11811.45178 1.053583605 1.10024674 1.021681136 1.00724467 0.981147473 0.958852909 0.931234379 0.995677801 1.000264386 1 13.52789868 -8.799603994 1.921596835 1.032263786 0.959641462 0.52889637 0.030687566 0.222480938 1.671297672 0.00526543 0.011559039 1.59E-09 8.799603994 -0.072622324 VQDLSAGGQGSLT(ph)DSGPER ddPTM_HeLa_Romidepsin_16h_R1 1 VQDLSAGGQGSLTDSGPER 19 0 P40222 P40222 TXLNA Alpha-taxilin 1 0 VQDLSAGGQGS(0.433)LT(0.565)DS(0.001)GPER 97.713 0.0037904 4952900 1345.7 1470.4 1434.6 1327.5 1020.9 1012.1 1064.1 1030.3 1473.8 1591 TRUE FALSE FALSE 1329.298091 1491.10033 1459.568611 1480.991796 968.7996635 947.4300764 1154.484627 1060.110105 1341.979637 1549.665591 0.857796739 0.962207807 0.941860373 0.955684765 0.625166919 0.611377114 0.744989522 0.684089594 0.865980148 1 10.59774121 -8.7644496 24.99994476 0.93590977 0.66808827 0.859083958 0.052388624 23.95678602 198963.9603 0.009211106 0.01723496 1.72E-09 8.7644496 -0.267821499 VQDT(ph)SNTGLGEDIIHQLSK ddPTM_HeLa_Romidepsin_16h_R1 2 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 0 VQDT(0.44)S(0.27)NT(0.29)GLGEDIIHQLSK;VQDT(0.494)S(0.494)NT(0.012)GLGEDIIHQLSK ; 155.39 2.53E-06 95807000 10276.1 9804.3 10732.9 8427 9193.4 9384.5 6459 8283.9 10219.1 9380 TRUE FALSE FALSE 10150.85094 9942.325193 10919.70162 9401.36939 8724.226493 8784.860737 7007.627299 8523.581577 9305.078102 9136.306248 1.11104539 1.088221533 1.19519873 1.029012068 0.95489646 0.961533086 0.767008801 0.932935187 1.018472657 1 13.1573953 -8.394490932 1.604750508 1.067063291 0.859017334 0.611319292 0.068679514 0.214245532 1.05572428 0.011174804 0.035349913 4.03E-09 8.394490932 -0.208045958 VQDTS(ph)NTGLGEDIIHQLSK ddPTM_HeLa_Romidepsin_16h_R1 2 VQDTSNTGLGEDIIHQLSK 19 0 Q8IWA0 Q8IWA0 WDR75 WD repeat-containing protein 75 1 0 VQDT(0.177)S(0.818)NT(0.005)GLGEDIIHQLSK;VQDT(0.17)S(0.809)NT(0.021)GLGEDIIHQLSK ; 122.59 0.00036673 66018000 6751.4 7111.8 7950.5 6303.3 6798.7 6910.2 5028.1 6330 8095.8 7917.3 TRUE FALSE FALSE 6669.11134 7211.920107 8088.875117 7032.117204 6451.73697 6468.660522 5455.186688 6513.148563 7371.691372 7711.607405 0.864814686 0.935203224 1.048922059 0.911887345 0.836626741 0.838821297 0.707399431 0.844590268 0.955921507 1 12.91281589 -8.610188227 2.068191075 0.94319189 0.787292093 0.612511056 0.057571142 0.202872388 1.745062211 0.010327522 0.02475342 2.45E-09 8.610188227 -0.155899797 VQEHEDS(ph)GDS(ph)EVENEAK ddPTM_HeLa_Romidepsin_16h_R1 2 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 2 0 VQEHEDS(1)GDS(1)EVENEAK;VQEHEDS(1)GDS(1)EVENEAK ; 163.44 0.00016457 125827000 5914.5 5086.2 4741.55 5082.3 4653.1 4059.81 3527.92 4487.2 5779.5 5389.7 TRUE FALSE FALSE 5842.411799 5157.803657 4824.074689 5669.939439 4415.634944 3800.401243 3827.581437 4617.030052 5262.567045 5249.674817 1.112909276 0.982499647 0.918928287 1.080055363 0.841125422 0.723930791 0.729108291 0.879488771 1.002455815 1 12.35801234 -8.647306607 4.307911382 1.039059132 0.773914627 0.728280811 0.066384546 0.082348427 2.702601719 0.010721182 0.02199704 2.25E-09 8.647306607 -0.265144505 VQEHEDS(ph)GDSEVENEAK ddPTM_HeLa_Romidepsin_16h_R1 1 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 1 0 VQEHEDS(0.998)GDS(0.002)EVENEAK 140.8 0.00057524 11555000 1675.5 1393 1411 1103.4 1240.6 1172.6 1376.5 1185.4 1707.6 1644.9 TRUE FALSE FALSE 1655.078362 1412.610691 1435.557863 1230.9803 1177.287553 1097.674644 1493.419876 1219.697679 1554.867979 1602.165261 1.033025994 0.881688503 0.896011103 0.768322925 0.73481031 0.685119489 0.932125987 0.761280817 0.970479149 1 10.64580725 -9.811653553 1.465609541 1.015854521 0.779560079 0.663860855 0.066793413 0.146184469 0.632926344 0.011563188 0.016649458 1.54E-10 9.811653553 -0.236294442 VQEHEDSGDS(ph)EVENEAK ddPTM_HeLa_Romidepsin_16h_R1 2 VQEHEDSGDSEVENEAK 17 0 Q9Y5J1 Q9Y5J1 UTP18 U3 small nucleolar RNA-associated protein 18 homolog 1 0 VQEHEDS(0.021)GDS(0.979)EVENEAK;VQEHEDS(0.263)GDS(0.737)EVENEAK ; 269.85 3.52E-87 43497000 7636 6776 6373 6028.9 5772.7 6250.9 7007.6 5858.2 9142.7 7800.9 TRUE FALSE FALSE 7542.929495 6871.392706 6483.919392 6725.989785 5478.097578 5851.487664 7602.825369 6027.697774 8324.954014 7598.231493 0.992721728 0.904341058 0.85334586 0.885204641 0.720970081 0.770111791 1.000604598 0.793302728 1.09564364 1 12.89144795 -10.02151915 1.708346674 0.998340722 0.835134621 0.549041423 0.076475357 0.204920326 1.172769818 0.012471981 0.016257044 9.52E-11 10.02151915 -0.163206101 VQEKPDSPGGS(ph)TQIQR ddPTM_HeLa_Romidepsin_16h_R1 1 VQEKPDSPGGSTQIQR 16 1 M0R300;M0R0P8;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 1 0 VQEKPDS(0.172)PGGS(0.414)T(0.414)QIQR 70.134 0.015097 10119000 3021.4 2828.6 2647.8 3071.3 3283.6 3750.4 2726.6 3832.4 3051 3129.8 TRUE FALSE FALSE 2984.574015 2868.421105 2693.883848 3426.418157 3116.025639 3510.761544 2958.197336 3943.284447 2778.110919 3048.487345 0.979034412 0.940932594 0.883678869 1.123973227 1.022154691 1.151640518 0.970382029 1.293521672 0.911308004 1 11.57387784 -9.238145729 24.91332058 0.978122415 1.101621879 0.452410313 0.088663527 629.8917903 673690.469 0.011770155 0.019510544 5.78E-10 9.238145729 0.123499464 VQESTKGPDEAK(ac)IK ddPTM_HeLa_Romidepsin_16h_R1 2 VQESTKGPDEAKIK 14 2 B4DT28;O43390-3;O43390;O43390-4;O43390-2 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 1 ; VQESTKGPDEAK(1)IK;VQESTKGPDEAK(1)IK 163.62 1.87E-06 30175000 9412.8 9031.8 8628 11027.7 10499.5 10861.4 11050.6 10921.1 9961.9 8209.8 FALSE TRUE FALSE 9298.073173 9158.949917 8778.166721 12302.77456 9963.671336 10167.39159 11989.23769 11237.0848 9070.882714 7996.508212 1.162766663 1.145368663 1.097749979 1.538518343 1.246002764 1.271478916 1.49930912 1.405248954 1.134355455 1 12.96515445 -8.416372023 0.190336152 0.936142171 1.722869804 0.55124309 0.113603394 4.139698484 0.234937148 0.198595587 0.848307098 3.83E-09 8.416372023 0.786727633 VQEVS(ph)AVLY(ph)Y(ph)LDQT(ph)EHPYK ddPTM_HeLa_Romidepsin_16h_R1 1 VQEVSAVLYYLDQTEHPYK 19 0 M0R127;P21817-3;P21817-2;P21817 M0R127 RYR1 Ryanodine receptor 1 4 0 VQEVS(0.999)AVLY(0.999)Y(0.999)LDQT(0.965)EHPY(0.038)K 47.754 0.018107 6374600 910.14 687.3 768.76 834.07 871.71 914.74 754.94 786.32 1003.3 964.35 TRUE FALSE FALSE 899.0468636 696.9758274 782.1399453 930.5090978 827.2233859 856.2910662 819.0645848 809.0709286 913.5623352 939.296048 0.957149629 0.742019333 0.832687359 0.990645175 0.88068441 0.911630649 0.87199833 0.861358813 0.972603193 1 9.875436129 -10.49161818 17.33865879 0.981098098 0.8735671 0.410636834 0.058960736 8.000312852 4438.031454 0.010569806 0.01163652 3.22E-11 10.49161818 -0.107530998 VQGEAVSNIQENTQTPTVQEES(ph)EEEEVDETGVEVK ddPTM_HeLa_Romidepsin_16h_R1 3 VQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVK 35 0 F8VZJ2;F8W0W4;H0YHX9;Q13765;E9PAV3-2;E9PAV3 F8VZJ2 NACA "Nascent polypeptide-associated complex subunit alpha;Nascent polypeptide-associated complex subunit alpha, muscle-specific form" 1 0 VQGEAVSNIQENTQT(0.025)PT(0.199)VQEES(0.703)EEEEVDET(0.073)GVEVK;VQGEAVSNIQENT(0.013)QT(0.157)PT(0.157)VQEES(0.672)EEEEVDET(0.002)GVEVK;VQGEAVS(0.001)NIQENT(0.034)QT(0.13)PT(0.115)VQEES(0.527)EEEEVDET(0.193)GVEVK ;; 94.203 9.92E-13 77413900 10059.7 9445.7 9493.3 5474.2 9587.6 9638.6 7665.1 8931.4 10856.5 10099.8 TRUE FALSE FALSE 9937.088507 9578.676813 9658.526904 6107.152761 9098.308996 9022.724567 8316.173403 9189.815968 9885.467449 9837.40574 1.010133034 0.973699476 0.981816463 0.620809279 0.924868734 0.917185364 0.845362448 0.934170676 1.004885608 1 13.26406219 -9.489874589 24.99978577 1.001405009 0.850861581 0.4292003 0.084040749 439.8330879 333162.595 0.01219948 0.018626972 3.24E-10 9.489874589 -0.150543428 VQGLLENGDSVT(ph)SPEK ddPTM_HeLa_Romidepsin_16h_R1 1 VQGLLENGDSVTSPEK 16 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 0 VQGLLENGDSVT(0.5)S(0.5)PEK 315.47 1.06E-172 0 5948 5548.3 5949.3 3037 3621.7 3078.1 2371.6 2540.6 5627.5 5620.3 TRUE FALSE FALSE 5875.503488 5626.409113 6052.845071 3388.15223 3436.871135 2881.419344 2573.043645 2614.108253 5124.162306 5474.283796 1.073291723 1.027789081 1.105687118 0.618921553 0.627821148 0.526355493 0.470023795 0.477525161 0.936042503 1 12.41845451 -9.165951179 3.786785518 1.039976757 0.530590057 0.941031565 0.060798549 0.037276766 0.987001238 0.008963449 0.015229346 6.82E-10 9.165951179 -0.5093867 VQGLLENGDSVTS(ph)PEK ddPTM_HeLa_Romidepsin_16h_R1 1 VQGLLENGDSVTSPEK 16 0 P41229-4;P41229-3;P41229-2;P41229-5;P41229 P41229-4 KDM5C Lysine-specific demethylase 5C 1 0 VQGLLENGDSVT(0.042)S(0.958)PEK 172.26 8.03E-06 23165000 6396.7 6925.3 7582.5 3853.8 4395.5 4470.1 3159.4 3504.7 6718 7272.1 TRUE FALSE FALSE 6318.73456 7022.794555 7714.470232 4299.394489 4171.181233 4184.475037 3427.759357 3606.102965 6117.125254 7083.169794 0.89207724 0.99147624 1.089126825 0.606987354 0.588886241 0.590763056 0.483930141 0.509108643 0.863614093 1 12.79017941 -9.165574822 5.374663812 0.960801711 0.549748906 0.906691518 0.066093022 0.050659036 2.264553835 0.010361897 0.017344606 6.83E-10 9.165574822 -0.411052805 VQIPVSRPDPEPVSDNEEDS(ph)Y(ph)DEEIHDPR ddPTM_HeLa_Romidepsin_16h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0YKB1 G3V1L9 TJP1 Tight junction protein ZO-1 2 0 VQIPVS(0.005)RPDPEPVS(0.075)DNEEDS(0.962)Y(0.957)DEEIHDPR 63.372 0.00039074 10643000 1118.7 1045.1 1109.5 1063.7 1325.4 1092.6 880.89 929.59 1126.5 1100 TRUE FALSE FALSE 1105.064854 1059.812945 1128.810382 1186.689999 1257.759892 1022.786386 955.7127746 956.48622 1025.743019 1071.421841 1.031400342 0.989164962 1.053562974 1.107584289 1.173916607 0.954606623 0.892004193 0.89272608 0.957366164 1 10.0653109 -8.007650625 21.09121744 1.033643118 0.900099812 0.523293756 0.058816689 29.01720346 80003.48179 0.0083386 0.02346095 9.83E-09 8.007650625 -0.133543305 VQIPVSRPDPEPVSDNEEDS(ph)YDEEIHDPR ddPTM_HeLa_Romidepsin_16h_R1 1 VQIPVSRPDPEPVSDNEEDSYDEEIHDPR 29 1 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2;H0YKB1 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 VQIPVSRPDPEPVS(0.198)DNEEDS(0.419)Y(0.382)DEEIHDPR 46.695 0.012796 8382400 834.13 799.58 944.46 956.34 752.01 763.94 719.25 1017.3 1211 1143.5 TRUE FALSE FALSE 823.9633027 810.8365082 960.8979301 1066.916531 713.6321236 715.1266995 780.343077 1046.73397 1102.685127 1113.791705 0.739782222 0.727996541 0.862726779 0.957913877 0.640723144 0.642065025 0.700618503 0.93979329 0.990028137 1 10.12126374 -12.304736 0.794572792 1.016669422 0.769504726 0.398546503 0.106747465 0.652876817 0.659418775 0.104853813 0.021712914 4.96E-13 12.304736 -0.247164696 VQIS(ph)PDSGGLPER ddPTM_HeLa_Romidepsin_16h_R1 2 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QXW7;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 0 VQIS(0.768)PDS(0.232)GGLPER;VQIS(0.755)PDS(0.245)GGLPER ; 130.66 0.0023852 40557000 3427.1 3618.6 3617.7 3260.3 3543 3447.5 3152.9 3312.3 3770 3051.2 TRUE FALSE FALSE 3385.329187 3669.542746 3680.664551 3637.271226 3362.187489 3227.215876 3420.707247 3408.136175 3432.801758 2971.929384 1.139101489 1.234734165 1.238476449 1.223875387 1.13131473 1.085899246 1.151005561 1.146775624 1.155075143 1 11.53718412 -11.65106633 0.8524708 1.009886243 1.169734143 0.099816115 0.065442183 0.294618946 0.431093998 0.024935476 0.011508774 2.23E-12 11.65106633 0.159847899 VQISPDS(ph)GGLPER ddPTM_HeLa_Romidepsin_16h_R1 1 VQISPDSGGLPER 13 0 A0A087WTP3;Q92945;M0QXW7;M0QYH3 A0A087WTP3 KHSRP Far upstream element-binding protein 2 1 0 VQIS(0.219)PDS(0.781)GGLPER 126.07 0.0034949 53782000 2987.1 2864.8 2798.6 2957.7 2725.3 2908.2 2854.6 3041.3 3056.6 2443.2 TRUE FALSE FALSE 2950.692076 2905.13073 2847.308459 3299.68319 2586.217772 2722.375406 3097.069653 3129.295217 2783.210041 2379.725312 1.239929693 1.220784061 1.196486185 1.386581541 1.086771552 1.143987246 1.301439976 1.314981692 1.169550967 1 11.21657934 -12.23434244 0.628943497 0.969481928 1.238172976 0.205416029 0.096370126 0.647933983 0.383682443 0.098284996 0.018237657 5.83E-13 12.23434244 0.268691048 VQIVSK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VQIVSKK 7 1 E7EVA0;P27816;P27816-6;P27816-2;P27816-4;H0Y2V1;F8W9U4 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 0 1 ; VQIVSK(1)K;VQIVSK(1)K 127.02 0.0035754 9252000 8740.1 9034.6 9011.2 8179.9 12087.9 13085.8 12845 11641.5 10232.4 7784.1 FALSE TRUE FALSE 8633.572299 9161.789336 9168.036156 9125.698526 11471.00936 12249.65961 13936.05398 11978.32844 9317.188516 7581.86796 1.138713091 1.208381547 1.209205463 1.2036214 1.512952932 1.615651931 1.838076587 1.579865081 1.228877707 1 12.88833762 -8.699037667 0.723589575 1.061594364 1.781026348 0.834359125 0.10224888 0.182251085 0.164559315 0.017067767 0.072821044 2.00E-09 8.699037667 0.719431983 VQMTS(ph)PSSTGS(ph)PMFK ddPTM_HeLa_Romidepsin_16h_R1 1 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 2 0 VQMT(0.394)S(0.481)PS(0.275)S(0.244)T(0.219)GS(0.387)PMFK 60.631 0.02094 5198100 2169.6 2315.1 2316.6 1990.7 2622 2726.4 2396.3 2610.2 2477.3 2830.5 TRUE FALSE FALSE 2143.156081 2347.692039 2356.919451 2220.874101 2488.189556 2552.191839 2599.841662 2685.722019 2255.724083 2756.963202 0.777361148 0.851550009 0.854896957 0.805550868 0.902510978 0.925725754 0.9430092 0.974159545 0.818191582 1 11.4288643 -8.024236609 1.936076053 0.879633485 0.96199984 0.286856177 0.060243097 0.612448527 4.363157345 0.012859502 0.052367807 9.46E-09 8.024236609 0.082366355 VQMTSPS(ph)S(ph)TGSPMFK ddPTM_HeLa_Romidepsin_16h_R1 1 VQMTSPSSTGSPMFK 15 0 P49790-3;P49790;P49790-2 P49790-3 NUP153 Nuclear pore complex protein Nup153 2 0 VQMT(0.014)S(0.017)PS(0.617)S(0.698)T(0.614)GS(0.04)PMFK 70.68 0.012894 6446400 1754.1 1910 1412.5 1473.3 2215 2527 2110.9 1999.3 1870.8 1559.4 TRUE FALSE FALSE 1732.720355 1936.88903 1437.08397 1643.649878 2101.960285 2365.532856 2290.199793 2057.146591 1703.470962 1518.886563 1.140783253 1.275203216 0.946143053 1.082141299 1.383882336 1.557412458 1.507814901 1.35437803 1.121526126 1 10.56879841 -8.691804714 3.873659331 1.075666468 1.475363223 0.770214201 0.09589067 0.078615935 2.330244653 0.015011703 0.030704434 2.03E-09 8.691804714 0.399696755 VQNHLPASGPTQPPVVS(ph)STNEGSPSPPEPTGK ddPTM_HeLa_Romidepsin_16h_R1 2 VQNHLPASGPTQPPVVSSTNEGSPSPPEPTGK 32 0 H3BQC4;O43294-2;O43294 H3BQC4 TGFB1I1 Transforming growth factor beta-1-induced transcript 1 protein 1 0 VQNHLPASGPTQPPVVS(0.325)S(0.325)T(0.325)NEGS(0.022)PS(0.002)PPEPTGK;VQNHLPAS(0.002)GPT(0.004)QPPVVS(0.237)S(0.237)T(0.237)NEGS(0.237)PS(0.045)PPEPT(0.002)GK ; 141.7 4.68E-16 33614000 10534.7 8901.6 9620 8591 8193.4 8182.4 6435.9 6740.2 11101.1 11088.9 TRUE FALSE FALSE 10406.29902 9026.916958 9787.432065 9584.331842 7775.260224 7659.571047 6982.565185 6935.217053 10108.18981 10800.80878 0.963474054 0.835763057 0.906175849 0.887371681 0.719877593 0.709166434 0.6464854 0.642101642 0.935873416 1 13.39885173 -8.583513199 0.454920597 0.99650378 0.551504171 0.889265521 0.042416435 0.322110256 0.093592803 0.010530237 0.064228978 2.61E-09 8.583513199 -0.44499961 VQNS(ph)PPVGR ddPTM_HeLa_Romidepsin_16h_R1 1 VQNSPPVGR 9 0 E9PGB3;E7EMZ9;E9PBC6;O95359-5;O95359-3;O95359;D6RAA5;Q4VXL8;O95359-6;O95359-1;H0YA73;H0Y8P9 E9PGB3 TACC2 Transforming acidic coiled-coil-containing protein 2 1 0 VQNS(1)PPVGR 119.03 0.014023 8266900 3594.6 3672.8 3228.7 3247.6 2725 2622.1 2662.9 2817.1 3731.1 3776.8 TRUE FALSE FALSE 3550.787633 3724.505775 3284.894169 3623.102792 2585.933082 2454.556272 2889.08666 2898.608344 3397.381071 3678.678192 0.965234643 1.012457622 0.892955023 0.984892563 0.702951698 0.667238651 0.785359988 0.787948332 0.923533099 1 11.84497176 -8.764988225 24.99996723 0.97813651 0.734506741 0.841694165 0.048029431 22.40659767 157845.5816 0.006752549 0.01260018 1.72E-09 8.764988225 -0.24362977 VQQEIDS(ph)DESPVAR ddPTM_HeLa_Romidepsin_16h_R1 1 VQQEIDSDESPVAR 14 0 A0A087WU78;A0A087WWC4;Q6T4R5-4;Q6T4R5-3;Q6T4R5-2;Q6T4R5 A0A087WU78 NHS Nance-Horan syndrome protein 1 0 VQQEIDS(0.974)DES(0.026)PVAR 157.37 0.00047152 6692300 1267.4 1392.2 1065.1 853.46 1013.9 1357.7 872.65 1212.3 1355.9 1325.9 TRUE FALSE FALSE 1251.952441 1411.799428 1083.637619 952.1410609 962.1568996 1270.947352 946.7728692 1247.375988 1234.624908 1291.452927 0.969413918 1.093186905 0.839084101 0.737263466 0.745018947 0.984122089 0.733106759 0.965870271 0.955996833 1 10.33477934 -9.672567912 8.590075522 0.993129493 0.827075362 0.464552379 0.08923176 0.172887965 14.99204922 0.012945637 0.018310324 2.13E-10 9.672567912 -0.166054132 VQRPEDASGGS(ph)SPSGTSK ddPTM_HeLa_Romidepsin_16h_R1 1 VQRPEDASGGSSPSGTSK 18 1 H0YJL6;H0YJN0;G3V314;Q9UI08-4;Q9UI08-3;Q9UI08-5;Q9UI08;Q9UI08-2 H0YJL6 EVL Ena/VASP-like protein 1 0 VQRPEDAS(0.03)GGS(0.567)S(0.386)PS(0.016)GTSK 83.251 0.0041017 3080100 1410.1 1222.9 1025.5 1441.3 1734.5 1989 1293.6 1312.6 1513.1 1310.1 TRUE FALSE FALSE 1392.913159 1240.116018 1043.348397 1607.949888 1645.981993 1861.909319 1403.478352 1350.57801 1377.764546 1276.063413 1.091570485 0.97182946 0.817630524 1.260086192 1.289890436 1.45910407 1.099850005 1.058394118 1.079699122 1 10.31748431 -9.217639369 24.94273648 1.022465376 1.24171224 0.472972139 0.125190108 346.5158925 197330.1851 0.019502177 0.03234055 6.06E-10 9.217639369 0.219246864 VQS(ph)PEPPAPER ddPTM_HeLa_Romidepsin_16h_R1 1 VQSPEPPAPER 11 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 VQS(1)PEPPAPER 132.14 0.0046522 16899000 1959.8 2304.3 1924.2 1487.3 2027 3045.5 1889.6 2523.2 1935.1 1916.9 TRUE FALSE FALSE 1935.913204 2336.739996 1957.689894 1659.268624 1923.554626 2850.902379 2050.102577 2596.204811 1762.019809 1867.098662 1.036856404 1.25153536 1.048519789 0.88868824 1.030237269 1.526915764 1.098015128 1.390502208 0.943720782 1 10.86658245 -8.297629609 23.28296714 1.029021103 1.314431393 0.532608737 0.132491408 141.489452 91026.86718 0.017468185 0.039062069 5.04E-09 8.297629609 0.28541029 VQS(ph)PKPITGGLGAFTK ddPTM_HeLa_Romidepsin_16h_R1 1 VQSPKPITGGLGAFTK 16 1 Q9ULM3 Q9ULM3 YEATS2 YEATS domain-containing protein 2 1 0 VQS(0.996)PKPIT(0.004)GGLGAFTK 67.214 0.016936 19028000 1769.6 1675.4 1792.5 1658.5 1219.7 1163.1 823.87 1129.5 1933.3 1294.3 TRUE FALSE FALSE 1748.031435 1698.986325 1823.697711 1850.263573 1157.454158 1088.781664 893.8494972 1162.1803 1760.380806 1260.673899 1.386584933 1.347681051 1.446605432 1.467678179 0.918123361 0.863650516 0.709025147 0.921872263 1.396380782 1 10.29997942 -8.608384063 6.61667088 1.240007881 0.830732956 0.687241285 0.153078037 0.138018897 8.776970846 0.028869252 0.058109889 2.46E-09 8.608384063 -0.409274924 VQS(ph)SPNLLAAGR ddPTM_HeLa_Romidepsin_16h_R1 2 VQSSPNLLAAGR 12 0 O94875-12;O94875-11;O94875-9;C9J4Z9;C9IZT7;C9JWC3;C9JN77;C9JI79;C9J372;C9JZ60;C9JDX2;C9JBB0;C9JEA9;C9JG84;C9J9D3 O94875-12 SORBS2 Sorbin and SH3 domain-containing protein 2 1 0 VQS(0.5)S(0.5)PNLLAAGR;VQS(0.988)S(0.012)PNLLAAGR ; 123.95 0.0061693 65595000 3431.7 3232.1 4073.1 3061.6 2540.1 2595.7 2506.7 2498.6 3871.2 3215.6 TRUE FALSE FALSE 3389.87312 3277.601589 4143.990597 3415.596597 2410.469219 2429.843147 2719.619035 2570.893049 3524.950176 3132.058248 1.082314839 1.046468912 1.323088611 1.090527802 0.769611874 0.77579756 0.868316877 0.820831812 1.125442088 1 11.61289533 -8.763843589 24.99940798 1.067322524 0.810556322 0.720322327 0.089917265 31.60187391 328607.2375 0.01441123 0.027044112 1.72E-09 8.763843589 -0.256766202 VQSGMGLILQGYES(ph)GS(ph)EEEGEIHEK ddPTM_HeLa_Romidepsin_16h_R1 2 VQSGMGLILQGYESGSEEEGEIHEK 25 0 Q13523 Q13523 PRPF4B Serine/threonine-protein kinase PRP4 homolog 2 0 VQSGMGLILQGY(0.381)ES(0.81)GS(0.81)EEEGEIHEK;VQSGMGLILQGY(0.237)ES(0.882)GS(0.882)EEEGEIHEK ; 75.404 0.00053485 45742000 7218.5 6564.7 6555.1 6440.7 7022.1 6333.9 5783.3 6261.1 7385.4 7214.9 TRUE FALSE FALSE 7130.518145 6657.118019 6669.188766 7185.404038 6663.736034 5929.184232 6274.533358 6442.25505 6724.831327 7027.455858 1.014665661 0.947301293 0.949018948 1.022475869 0.94824303 0.843717037 0.892859875 0.916726505 0.956936829 1 12.77878677 -8.505397607 4.828272031 0.998044711 0.885839289 0.624657055 0.032218498 0.074434278 4.638828974 0.004530646 0.009908099 3.12E-09 8.505397607 -0.112205422 VQSLEGEKLS(ph)PKS(ph)DISPLTPR ddPTM_HeLa_Romidepsin_16h_R1 1 VQSLEGEKLSPKSDISPLTPR 21 2 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VQS(0.001)LEGEKLS(0.79)PKS(0.798)DIS(0.368)PLT(0.043)PR 58.479 0.022235 38279000 2166.6 2124.3 1837.7 1951.6 1617.6 1897.2 1537.8 1773.4 2364.2 2132.3 TRUE FALSE FALSE 2140.192646 2154.205951 1869.684398 2177.253175 1535.047836 1775.975043 1668.420694 1824.710531 2152.740031 2076.902539 1.030473316 1.03722053 0.900227316 1.048317451 0.739104415 0.855107551 0.803321611 0.878573018 1.036514709 1 11.0202178 -8.769359812 24.99714977 1.009234662 0.820482063 0.762180491 0.051927033 57.74072412 182232.0833 0.007071296 0.012985864 1.70E-09 8.769359812 -0.1887526 VQT(ph)PEVDVK ddPTM_HeLa_Romidepsin_16h_R1 3 VQTPEVDVK 9 0 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VQT(1)PEVDVK;VQT(1)PEVDVK;VQT(1)PEVDVK ;; 132.56 0.014565 98932000 22065.1 25957.5 19425.5 20370 18478 18044.4 14248.9 14992.7 22770.9 21405.2 TRUE FALSE FALSE 21796.16207 26322.93037 19763.59268 22725.27524 17534.99871 16891.42108 15459.20121 15426.49012 20734.21367 20849.08982 1.045425113 1.26254578 0.947935514 1.089988841 0.841043847 0.810175467 0.741480868 0.739911922 0.994490112 1 14.34769678 -8.610295702 3.28759903 1.04033601 0.7662922 0.723886826 0.083056341 0.10214171 2.19997365 0.012144711 0.026090282 2.45E-09 8.610295702 -0.27404381 VQT(ph)TPPPAVQGQK ddPTM_HeLa_Romidepsin_16h_R1 1 VQTTPPPAVQGQK 13 0 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 VQT(0.759)T(0.241)PPPAVQGQK 110.64 0.01369 16658000 6686.7 6811.9 6091.5 6194.6 6097.4 6755.6 5511.4 5967 6912.3 5852.7 TRUE FALSE FALSE 6605.199928 6907.798107 6197.520002 6910.848798 5786.226925 6323.938963 5979.538178 6139.645731 6294.046576 5700.64601 1.158675686 1.21175707 1.087160997 1.212292218 1.015012494 1.109337249 1.048922906 1.077008767 1.104093565 1 12.4769097 -5.898375833 14.83490824 1.091017863 0.520285695 0 0.07100265 0 0 0.010882885 0 1.26E-06 5.898375833 -0.570732168 VQTT(ph)PPPAVQGQK ddPTM_HeLa_Romidepsin_16h_R1 1 VQTTPPPAVQGQK 13 0 Q2M2I8-2;Q2M2I8;E9PG46 Q2M2I8-2 AAK1 AP2-associated protein kinase 1 1 0 VQT(0.139)T(0.861)PPPAVQGQK 146.36 0.0015843 17730000 5152.2 5346.3 5202.4 5632.4 5284.6 5297 4596.3 5043.4 5353.5 5529.2 TRUE FALSE FALSE 5089.403005 5421.565352 5292.94559 6283.644589 5014.907142 4958.538795 4986.709607 5189.322822 4874.669552 5385.550587 0.945010714 1.006687295 0.982804916 1.166759923 0.93117817 0.920711581 0.925942395 0.963564029 0.905138569 1 12.39487813 NVSGISFT(ph)ENMGSSQQK ddPTM_HeLa_Romidepsin_16h_R1 1 NVSGISFTENMGSSQQK 17 0 P49792 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 NVS(0.001)GIS(0.057)FT(0.927)ENMGS(0.013)S(0.002)QQK 99.5 0.00061763 0 1625.8 1379 1295.5 1402 1115.8 1270.8 774.75 756.7 1472.9 1752 TRUE FALSE FALSE 1605.984124 1398.413598 1318.047634 1564.105837 1058.856562 1189.599981 840.5572457 778.5939206 1341.160135 1706.482787 0.941107719 0.819471259 0.772376753 0.916567016 0.62049062 0.697106347 0.492567081 0.456256533 0.785920693 1 10.73681015 -7.314490167 0.31391695 1.005642376 3.06E-16 0.714903999 0.093327362 1.472951714 0.107482619 0.025911556 0.563539625 4.85E-08 7.314490167 -1.005642376 down VQVAALQAS(ph)PPLDQDDR ddPTM_HeLa_Romidepsin_16h_R1 5 VQVAALQASPPLDQDDR 17 0 Q9UDY2-7;A0A2R8YDH4;A0A1B0GTW1;A0A3B3ITE1;Q9UDY2-3;Q9UDY2;Q9UDY2-6;Q9UDY2-2;Q9UDY2-4;A0A3B3IU51;A0A3B3IRI3;Q9UDY2-5;A0A3B3IRV6;A0A3B3ISF1;A0A3B3ISZ5;A0A3B3IU26;B1AN86;U3KQJ2 Q9UDY2-7 TJP2 Tight junction protein ZO-2 1 0 VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR;VQVAALQAS(1)PPLDQDDR ;;;; 171.29 1.90E-08 34186000 9868.7 8810.4 9846.5 6624.88 9008.5 9933.9 7356.75 7909.37 9803.1 10317.4 TRUE FALSE FALSE 9748.416489 8934.433042 10017.8742 7390.879797 8548.76263 9299.15585 7981.632161 8138.215142 8926.286184 10049.35246 0.970054193 0.889055596 0.996867633 0.735458312 0.850677958 0.925348761 0.794243429 0.809824829 0.888244911 1 13.29481492 -9.734595097 0.958227616 0.989498354 0.829697459 0.329230443 0.069517966 0.274105185 0.502396571 0.0117288 0.018723496 1.84E-10 9.734595097 -0.159800896 VQVEYK(ac)GETK ddPTM_HeLa_Romidepsin_16h_R1 1 VQVEYKGETK 10 1 P11142;E9PKE3;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 1 VQVEYK(1)GETK 149.96 0.015123 1552000 805.39 416 896.93 610.38 1652.9 1134 1167.1 1057.2 1386.1 865.09 FALSE TRUE FALSE 795.5735969 421.8564589 912.5406904 680.9550075 1568.546345 1061.54106 1266.233445 1087.788414 1262.123744 842.6148371 0.94417231 0.500651591 1.082986734 0.808145047 1.861522342 1.259817669 1.502742877 1.290967553 1.49786556 1 9.718729509 -8.781069763 24.99997925 0.932376839 1.464836673 0.436912278 0.279294351 116.4296795 148276.9723 0.029919206 0.054287402 1.66E-09 8.781069763 0.532459833 VQVEYKGETK ddPTM_HeLa_Romidepsin_16h_R1 1 VQVEYKGETK 10 1 P11142;E9PKE3;P11142-2;E9PN89;E9PQQ4;E9PQK7;E9PK54;E9PLF4;E9PPY6;E9PN25;P54652 P11142;P54652 HSPA8;HSPA2 Heat shock cognate 71 kDa protein;Heat shock-related 70 kDa protein 2 0 0 84.821 0.019275 2041500 1097.9 1234.9 1238.5 1754.1 1824.9 1619.2 1218.5 1456.6 1238 1020.8 FALSE FALSE TRUE 1084.518373 1252.284955 1260.055573 1956.917295 1731.768543 1515.738346 1321.99936 1498.744423 1127.270179 994.2794688 1.090758088 1.259489906 1.267305232 1.968176309 1.741732177 1.524459061 1.329605409 1.507367365 1.133755865 1 9.957507607 -9.734725872 2.004162118 1.046882593 1.596010074 0.629775558 0.175538604 0.145026403 1.193424939 0.030804366 0.044604608 1.84E-10 9.734725872 0.549127481 VREEEIEVDSR ddPTM_HeLa_Romidepsin_16h_R1 2 VREEEIEVDSR 11 1 A0A0A0MRM9;Q14978;Q14978-3;Q14978-2 A0A0A0MRM9 NOLC1 Nucleolar and coiled-body phosphoprotein 1 0 0 ; ; 150.09 0.0026781 72428000 8972.4 9127.1 7351.3 7448.6 8623.4 8079.7 6583.3 7869.3 8937.3 8355.1 FALSE FALSE TRUE 8863.040938 9255.591553 7479.246293 8309.842179 8183.31572 7563.433246 7142.485338 8096.98578 8137.925504 8138.033298 1.089088802 1.137325348 0.919048377 1.021111843 1.005564296 0.929393254 0.877667254 0.994956089 0.999986754 1 12.99046447 -8.759458038 1.035072666 1.045385968 0.928623052 0.311460538 0.060826017 0.456193429 0.942333602 0.010599093 0.032470776 1.74E-09 8.759458038 -0.116762916 VREEGDEEGEGDEAEDEEQRGPELK ddPTM_HeLa_Romidepsin_16h_R1 2 VREEGDEEGEGDEAEDEEQRGPELK 25 2 Q7KZ85;Q7KZ85-3 Q7KZ85 SUPT6H Transcription elongation factor SPT6 0 0 ; ; 174.2 2.44E-15 9561200 2540.3 2383.7 2489 2764 2366.8 3056.6 2804.8 2911.7 2928.2 2745.4 FALSE FALSE TRUE 2509.337847 2417.257791 2532.320001 3083.586685 2246.013364 2861.293125 3043.039642 2995.945446 2666.294458 2674.074112 0.938395026 0.903960657 0.946989461 1.153141819 0.839921883 1.070012649 1.137978797 1.120367394 0.997090711 1 11.38482374 -8.013853351 20.23164969 0.969206969 1.122879279 0.430348649 0.076293352 33.4441663 48846.61154 0.010070154 0.02704258 9.69E-09 8.013853351 0.15367231 VREEYPDR ddPTM_HeLa_Romidepsin_16h_R1 2 VREEYPDR 8 1 A0A0B4J269;Q13509;Q13509-2;G3V2A3 A0A0B4J269 TUBB3 Tubulin beta-3 chain 0 0 ; ; 134.77 0.01066 12600700 3006.6 2829.3 3551.3 4047.6 5429.1 6493.8 5296.4 3440.5 3354.8 2552 FALSE FALSE TRUE 2969.954403 2869.13096 3613.108887 4515.602557 5152.032768 6078.867138 5746.276084 3540.045439 3054.738286 2485.698672 1.194816748 1.154255337 1.453558682 1.816633129 2.07266988 2.445536624 2.311734784 1.424165157 1.22892542 1 11.2794357 -9.329005708 1.498961832 1.091589137 2.111266205 0.721307631 0.258823956 0.134866387 0.594819423 0.041797449 0.075046593 4.69E-10 9.329005708 1.019677068 VRELELELDR ddPTM_HeLa_Romidepsin_16h_R1 2 VRELELELDR 10 1 O94992 O94992 HEXIM1 Protein HEXIM1 0 0 ; ; 160.77 4.74E-05 3227200 2434.45 2313.33 2535 2571.2 3017 3270 2848.1 2963 2448.4 2123.72 FALSE FALSE TRUE 2404.777987 2345.89712 2579.120612 2868.494242 2863.031232 3061.057553 3090.017543 3048.72973 2229.408972 2068.545448 1.162545396 1.134080531 1.24682811 1.386720434 1.384079443 1.479811602 1.493811773 1.473851944 1.077766492 1 11.01440094 -9.324809692 0.39602002 1.017699251 1.574531493 0.948520621 0.039349107 0.2222713 0.068529684 0.017443792 0.049287143 4.73E-10 9.324809692 0.556832241 VRGEVAPDAK ddPTM_HeLa_Romidepsin_16h_R1 1 VRGEVAPDAK 10 1 P09382;F8WEI7 P09382 LGALS1 Galectin-1 0 0 88.338 0.015533 1079900 1478 1421.5 1633.6 1378.9 1319.7 1867.8 1656 1345.6 1920.4 1484.1 FALSE FALSE TRUE 1459.985568 1441.511914 1662.032123 1538.334906 1252.350785 1748.453608 1796.660599 1384.532813 1748.634614 1445.542868 1.009991194 0.99721146 1.149763289 1.064191827 0.866353266 1.209548085 1.242896796 0.957794365 1.209673302 1 10.49739568 -8.855340972 0.508972872 1.001496603 1.126177536 0 0.125269269 2.048176932 0.867857669 0.026808087 0.117559785 1.40E-09 8.855340972 0.124680933 VRGGAPDPSPGATATPGAPAQPS(ph)SPDAR ddPTM_HeLa_Romidepsin_16h_R1 2 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 0 VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.5)S(0.5)PDAR ; 129.57 2.14E-10 23572500 3430.54 3979.9 2940.2 3328.85 2836.45 3035.43 2484.1 2796.03 3578.2 3245.64 TRUE FALSE FALSE 3388.727259 4035.929137 2991.372948 3713.7473 2691.695372 2841.475819 2695.099392 2876.928717 3258.15683 3161.317805 1.071935018 1.276660363 0.9462424 1.174746586 0.851447257 0.898826374 0.852524029 0.910040968 1.030632487 1 11.62631036 -8.741683609 24.99960406 1.056472529 0.877847533 0.542487166 0.090295564 162.1477488 205186.1087 0.012968807 0.025909469 1.81E-09 8.741683609 -0.178624996 VRGGAPDPSPGATATPGAPAQPSS(ph)PDAR ddPTM_HeLa_Romidepsin_16h_R1 2 VRGGAPDPSPGATATPGAPAQPSSPDAR 28 1 O95365 O95365 ZBTB7A Zinc finger and BTB domain-containing protein 7A 1 0 VRGGAPDPSPGATATPGAPAQPS(0.085)S(0.915)PDAR;VRGGAPDPSPGATATPGAPAQPS(0.403)S(0.597)PDAR ; 121.66 9.44E-11 22823000 2822.43 3029.12 2643.49 2358.84 2277.77 2883.18 2535.69 2138.4 2673.83 2981.68 TRUE FALSE FALSE 2788.029138 3071.764031 2689.498835 2631.580179 2161.526897 2698.954103 2751.071445 2200.27123 2434.675948 2904.215524 0.959993883 1.057691485 0.926067233 0.906124273 0.744272207 0.929322938 0.947268349 0.757612929 0.838324817 1 11.50393281 -9.326046913 2.694495157 0.986105481 0.857180609 0.263751115 0.081474706 0.188137998 2.682603351 0.010058272 0.016460757 4.72E-10 9.326046913 -0.128924872 VRK(ac)MPVSYLGSK ddPTM_HeLa_Romidepsin_16h_R1 2 VRKMPVSYLGSK 12 2 Q9H0W5 Q9H0W5 CCDC8 Coiled-coil domain-containing protein 8 0 1 ; VRK(1)MPVSYLGSK;VRK(1)MPVSYLGSK 81.95 0.012252 1960190 0 0 128.02 203.868 1478.32 1377.78 845.15 816.29 0 0 FALSE TRUE FALSE 0 0 130.2481344 227.4401774 1402.875814 1289.744305 916.9370199 839.9080633 0 0 0 VRPAS(ph)TGGLSLLPPPPGGK ddPTM_HeLa_Romidepsin_16h_R1 1 VRPASTGGLSLLPPPPGGK 19 1 D6RB24;Q9NVZ3-4;Q9NVZ3;Q9NVZ3-2 D6RB24 NECAP2 Adaptin ear-binding coat-associated protein 2 1 0 VRPAS(0.764)T(0.226)GGLS(0.011)LLPPPPGGK 124.77 0.0058901 21062000 2363.2 2477.7 2340 2545.4 2867.5 3636.2 3230.7 3319.5 2264.8 2323.1 TRUE FALSE FALSE 2334.396409 2512.581126 2380.726718 2839.711124 2721.160775 3403.858555 3505.115577 3415.544495 2062.230616 2262.745527 1.031665462 1.110412592 1.052140725 1.254984748 1.202592489 1.504304622 1.549054251 1.509469118 0.911384241 1 11.14385863 -8.534356735 0.772682731 1.014824447 1.597758293 0.918087606 0.063558902 0.12630522 0.12556911 0.009020156 0.044033833 2.92E-09 8.534356735 0.582933846 VRPAST(ph)GGLSLLPPPPGGK ddPTM_HeLa_Romidepsin_16h_R1 1 VRPASTGGLSLLPPPPGGK 19 1 D6RB24;Q9NVZ3-4;Q9NVZ3;Q9NVZ3-2 D6RB24 NECAP2 Adaptin ear-binding coat-associated protein 2 1 0 VRPAS(0.382)T(0.56)GGLS(0.058)LLPPPPGGK 77.53 0.0055907 40720000 1818.9 1919.7 1906 2907.6 2701.5 3171.5 2551.7 2984.9 2394.6 2151.7 TRUE FALSE FALSE 1796.730547 1946.725587 1939.17313 3243.790393 2563.632374 2968.851386 2768.441334 3071.263372 2180.420979 2095.798524 0.85730118 0.928870578 0.925266961 1.547758697 1.22322463 1.416572897 1.320948222 1.465438274 1.04037719 1 11.03328432 -9.274339568 24.99562489 0.930061452 1.382365214 0.849610353 0.09322206 191.7724544 371580.8648 0.013508506 0.020713557 5.32E-10 9.274339568 0.452303763 VRS(ph)LETENR ddPTM_HeLa_Romidepsin_16h_R1 1 VRSLETENR 9 1 P05783;F8VZY9 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 VRS(0.994)LET(0.006)ENR 77.124 0.024992 4581100 975.01 1010.8 848.41 847.36 989.25 996.05 922.77 1058.7 1084.4 917.53 TRUE FALSE FALSE 963.1262031 1025.030069 863.1762202 945.3357501 938.7648811 932.4056196 1001.150061 1089.331814 987.4085481 893.6924383 1.077693132 1.14696066 0.96585378 1.057786448 1.050433953 1.043318237 1.120240049 1.218911303 1.104863939 1 9.803634607 -7.387654541 1.880768912 1.042556068 1.249849269 0.498145088 0.049155146 0.350596789 1.548772726 0.006946384 0.115640398 4.10E-08 7.387654541 0.207293201 VRVELSNGEK ddPTM_HeLa_Romidepsin_16h_R1 2 VRVELSNGEK 10 1 P84103-2;P84103 P84103-2 SRSF3 Serine/arginine-rich splicing factor 3 0 0 ; ; 152.64 0.0015882 10739500 5768.9 5461 5497.5 4832.2 5807 6893.8 5556.8 5522.3 6664 5564.9 FALSE FALSE TRUE 5698.586428 5537.880101 5593.181681 5390.9217 5510.647121 6453.308429 6028.794453 5682.079038 6067.95515 5420.323096 1.051337038 1.021688192 1.031890827 0.994575712 1.016663956 1.190576339 1.112257396 1.048291575 1.119482186 1 12.40416314 -8.293524522 24.85343395 1.022436099 1.116563342 0.386052923 0.046704987 304.4184933 235804.4934 0.005217304 0.011667018 5.09E-09 8.293524522 0.094127243 VRVELSNGEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 VRVELSNGEKR 11 2 P84103-2;P84103 P84103-2 SRSF3 Serine/arginine-rich splicing factor 3 0 1 ; VRVELSNGEK(1)R;VRVELSNGEK(1)R 132.03 0.002437 2856000 1156.78 999.77 1078.03 1315.4 2033.3 1591.77 1356.86 1345.38 1853.96 1326.6 FALSE TRUE FALSE 1142.68072 1013.844788 1096.79266 1467.492737 1929.533114 1490.061034 1472.111655 1384.306448 1688.137174 1292.134741 0.884335576 0.784627761 0.848822205 1.13571185 1.493290949 1.153177751 1.139286491 1.071332891 1.30647147 1 10.3355408 -9.121558881 5.202034578 0.923432306 1.216409919 0.314103458 0.169625289 0.132129865 5.110728264 0.019237398 0.032346274 7.56E-10 9.121558881 0.292977613 VRVS(ph)PQDANPLMANGTLTR ddPTM_HeLa_Romidepsin_16h_R1 1 VRVSPQDANPLMANGTLTR 19 1 O60716;O60716-5;O60716-2;O60716-3;C9JZR2;O60716-8;O60716-7;O60716-6;O60716-4;A0A669KB05;A0A669KB62 O60716 CTNND1 Catenin delta-1 1 0 VRVS(1)PQDANPLMANGTLTR 102.84 0.0043862 23530000 2921 2323.8 2409.6 2497.5 1954 2134.4 2209.5 2024.3 2806.9 2855.6 TRUE FALSE FALSE 2885.397728 2356.514517 2451.538077 2786.272701 1854.280089 1998.018728 2397.174875 2082.869927 2555.843834 2781.4111 1.037386285 0.847237043 0.881400839 1.00174789 0.666668832 0.718347147 0.861855651 0.748853676 0.91890186 1 11.44160128 -9.454704846 0.807835403 1.01788248 0.761719444 0.44380085 0.089609145 0.300678646 0.391134833 0.017098998 0.034635696 3.51E-10 9.454704846 -0.256163037 VRYDS(ph)SNQVK ddPTM_HeLa_Romidepsin_16h_R1 1 VRYDSSNQVK 10 1 A0A087WZ12;A0A087WT34;A0A087X1H1;A0A0A0MTS6;K7EIE8;O95983-2;O95983 A0A087WZ12 MBD3 Methyl-CpG-binding domain protein 3 1 0 VRYDS(0.764)S(0.236)NQVK 94.547 0.011825 24686000 3646.4 3414 3355.3 3092.9 4089.6 3892 2981.8 2807.9 3919.4 3774.8 TRUE FALSE FALSE 3601.956274 3462.062382 3413.697589 3450.515651 3880.892452 3643.313761 3235.074018 2889.142156 3568.839048 3676.730152 0.979662941 0.941614489 0.928460194 0.938473999 1.055528225 0.990911383 0.879878012 0.785791189 0.970655691 1 11.84420758 -7.530426328 2.787268905 0.983273804 0.789115089 0.738117253 0.035851737 0.110788219 1.561288954 0.00536218 0.036738586 2.95E-08 7.530426328 -0.194158715 VS(ph)DSESEGPQK ddPTM_HeLa_Romidepsin_16h_R1 1 VSDSESEGPQK 11 0 Q96ST2-3;Q96ST2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 VS(0.937)DS(0.062)ESEGPQK 140.14 0.0031352 6079400 1862.8 1388.2 1907.6 1308.2 1760.4 2062.1 2288.8 1974.7 2196.6 2505.3 TRUE FALSE FALSE 1840.095477 1407.743116 1940.800978 1459.460239 1670.560219 1930.338465 2483.210615 2031.834829 2000.130595 2440.211945 0.75407199 0.576893789 0.795341151 0.598087491 0.684596362 0.791053609 1.017620875 0.832646866 0.819654456 1 11.25279074 -12.02001766 0.928901735 0.992926163 0.756566362 0.131894745 0.129504035 0.487727039 0.79462009 0.071682321 0.024679469 9.55E-13 12.02001766 -0.2363598 VS(ph)EAKPS(ph)QY(ph)Y(ph)ELQVLK ddPTM_HeLa_Romidepsin_16h_R1 1 VSEAKPSQYYELQVLK 16 1 F5GYN0;A6NE01 F5GYN0 FAM186A Protein FAM186A 4 0 VS(1)EAKPS(1)QY(1)Y(1)ELQVLK 55.66 0.0040023 0 545.65 720.16 735.39 777.12 543.48 661.73 653.27 721.59 920.95 871.87 TRUE FALSE FALSE 538.9994079 730.2984314 748.1891545 866.9742709 515.7441876 619.4475886 708.7587375 742.4680682 838.5779254 849.2186917 0.634700358 0.859965093 0.881032367 1.020908135 0.607316104 0.729432353 0.834600963 0.874295485 0.987469934 1 9.729992316 -12.63933759 1.479414715 0.99952955 0.782519991 0.274250889 0.11797921 0.428933523 1.693187841 0.090548962 0.020749401 2.29E-13 12.63933759 -0.217009559 VS(ph)EGGPAEIAGLQIGDK ddPTM_HeLa_Romidepsin_16h_R1 2 VSEGGPAEIAGLQIGDK 17 0 O14907 O14907 TAX1BP3 Tax1-binding protein 3 1 0 VS(1)EGGPAEIAGLQIGDK;VS(1)EGGPAEIAGLQIGDK ; 188.9 3.46E-13 11562000 5404.96 3496.92 4372.56 2902.13 3359.16 3114.24 3491.49 3466.17 5286.15 4469.88 TRUE FALSE FALSE 5339.082269 3546.149732 4448.662573 3237.687926 3187.72953 2915.250115 3788.057073 3566.45816 4813.343505 4353.751873 1.226317536 0.814504325 1.021799749 0.743654673 0.732179881 0.669594915 0.870067285 0.819168906 1.105562201 1 12.08804347 -9.734330911 1.44065486 1.101624139 0.770272529 0.606638288 0.107541094 0.201569548 0.845988733 0.021805613 0.032605062 1.84E-10 9.734330911 -0.33135161 VS(ph)GRTSPPLLDR ddPTM_HeLa_Romidepsin_16h_R1 1 VSGRTSPPLLDR 12 1 Q9UQ35 Q9UQ35 SRRM2 Serine/arginine repetitive matrix protein 2 1 0 VS(0.56)GRT(0.22)S(0.22)PPLLDR 70.728 0.02579 326540000 2493.1 2391.2 1649.2 3610.4 2169.6 1741.9 1856.8 1809.5 2494.3 2182.3 TRUE FALSE FALSE 2462.713138 2424.863376 1677.903634 4027.851435 2058.877216 1630.598212 2014.516546 1861.855028 2271.203561 2125.603531 1.158594772 1.140788176 0.789377515 1.894921313 0.968608297 0.767122461 0.947738614 0.875918298 1.068498206 1 11.05365681 -8.530840755 24.99994666 1.122473205 0.871317143 0.200842297 0.272745294 255.0143657 800719.32 0.038232438 0.076572527 2.95E-09 8.530840755 -0.251156062 VS(ph)LSEIGFGK ddPTM_HeLa_Romidepsin_16h_R1 1 VSLSEIGFGK 10 0 H0YBX5;E5RJM2;E5RGN0;A0A087WZU2;Q00536;Q00536-3;Q00536-2 H0YBX5 CDK16 Cyclin-dependent kinase 16 1 0 VS(1)LSEIGFGK 126.19 0.0089578 5614000 1531.3 1834.6 1625.7 2273.9 1813.3 1599.3 1329.5 1770.2 1631.6 1867.3 TRUE FALSE FALSE 1512.635927 1860.427547 1653.994627 2536.819017 1720.760535 1497.109892 1442.427697 1821.417944 1485.66561 1818.787277 0.831672811 1.022894525 0.909394214 1.394785992 0.94610324 0.823136334 0.793071139 1.001446385 0.816844074 1 10.8287611 -6.93639462 20.36784095 0.944017721 2.135579374 0.008200161 0.167314803 1113.258618 727432.1544 0.022607587 61613.64341 1.16E-07 6.93639462 1.191561653 VS(ph)PAHS(ph)PPENGLDK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPAHSPPENGLDK 14 0 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 2 0 VS(1)PAHS(1)PPENGLDK 81.51 0.0018113 0 3310.6 3506.1 3788.8 2753.8 2554.4 2898.7 2224.9 2919.4 3478.6 3267.5 TRUE FALSE FALSE 3270.249134 3555.458968 3854.742475 3072.207313 2424.039436 2713.482425 2413.88295 3003.868233 3167.465304 3182.609879 1.027536914 1.117151993 1.211189125 0.965310682 0.761651452 0.85259662 0.758460208 0.943838028 0.99524146 1 11.63599461 -8.938810665 5.840290287 1.038449695 0.827755477 0.663023919 0.079354625 0.104817941 7.079422676 0.012142353 0.022157945 1.15E-09 8.938810665 -0.210694218 DSFEMEEVQST(ph)EGEAPHVPATYQLGLTK ddPTM_HeLa_Romidepsin_16h_R1 1 DSFEMEEVQSTEGEAPHVPATYQLGLTK 28 0 E9PHV5;P28290-3;P28290;P28290-2 E9PHV5 SSFA2 Sperm-specific antigen 2 1 0 DS(0.003)FEMEEVQS(0.035)T(0.911)EGEAPHVPAT(0.035)Y(0.015)QLGLTK 56.452 0.0015318 5382000 901.99 1113 881.8 833.47 882.11 835.16 478.66 459.46 1205.9 1239.3 TRUE FALSE FALSE 890.9961989 1128.668843 897.1473591 929.839723 837.0926351 781.7959714 519.3173685 472.7537502 1098.041284 1207.102807 0.738127849 0.935022963 0.743223654 0.770306984 0.693472528 0.647663121 0.430218011 0.391643319 0.909650178 1 10.23733284 -7.267417581 0.292080431 0.934238419 2.77E-36 0.859835666 0.071170322 2.77710405 0.176324571 0.045010749 0.928401317 5.40E-08 7.267417581 -0.934238419 down VS(ph)PENLVDK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPENLVDK 9 0 E7EVK1;A0A088AWL3;O75376;O75376-2;J3KS29;J3QKP0 E7EVK1 NCOR1 Nuclear receptor corepressor 1 1 0 VS(1)PENLVDK 122.18 0.012287 110160000 2102.2 1809.4 1822.6 1542.2 1568.7 1546.2 1262.4 1500.5 2014 1893.3 TRUE FALSE FALSE 2076.577578 1834.872781 1854.321588 1720.51642 1488.643385 1447.40281 1369.628224 1543.9146 1833.862796 1844.111793 1.126058401 0.994989993 1.00553643 0.932978373 0.8072414 0.784878019 0.742703468 0.837213127 0.994442312 1 10.8487104 -9.025773457 1.377357818 1.056437514 0.778615311 0.85149564 0.04505654 0.11519254 0.433348374 0.0087472 0.018861064 9.42E-10 9.025773457 -0.277822203 VS(ph)PFGLR ddPTM_HeLa_Romidepsin_16h_R1 1 VSPFGLR 7 0 J3KNZ9;H3BRE6 J3KNZ9 FBRS 1 0 VS(1)PFGLR 112.41 0.028708 20941000 1714.2 2236.9 1703.9 1560.7 1786.3 1540.9 1339.4 1918.7 2189.4 2298.2 TRUE FALSE FALSE 1693.306671 2268.391137 1733.555665 1741.155477 1695.138445 1442.441463 1453.168603 1974.214557 1993.574581 2238.492433 0.756449585 1.013356625 0.774429987 0.777825045 0.757267892 0.644380764 0.64917289 0.881939348 0.890588037 1 11.12831173 -16.52287875 0.165258432 1.906738669 0.702570389 0.316387048 0.101317419 41.6019205 0.453498211 12.22149326 0.173507804 3.00E-17 16.52287875 -1.20416828 VS(ph)PGLPSPNLENGAPAVGPVQPR ddPTM_HeLa_Romidepsin_16h_R1 2 VSPGLPSPNLENGAPAVGPVQPR 23 0 C9JRJ5;Q9UGP4 C9JRJ5 LIMD1 LIM domain-containing protein 1 1 0 VS(0.988)PGLPS(0.012)PNLENGAPAVGPVQPR;VS(0.993)PGLPS(0.007)PNLENGAPAVGPVQPR ; 163.15 5.93E-10 25609400 9889.2 8980.6 9519.3 9261.4 7678.2 8499.8 6289 7237.5 9896.3 9580.1 TRUE FALSE FALSE 9768.666627 9107.029123 9684.979423 10332.24664 7286.352803 7956.690212 6823.187503 7446.905644 9011.150142 9331.207621 1.046881285 0.975975403 1.037912757 1.107278614 0.780858502 0.852696729 0.731222343 0.798064511 0.965700315 1 13.18784809 -8.750446785 24.99096921 1.025442742 0.790888887 0.856764726 0.046376898 51.56916514 117238.46 0.00613125 0.012169152 1.78E-09 8.750446785 -0.234553855 VS(ph)PPAPGSAPET(ph)PEDK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPPAPGSAPETPEDK 16 0 M0R300;M0R0P8;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 2 0 VS(0.79)PPAPGS(0.21)APET(1)PEDK 103.67 0.0014156 0 1270.4 1122.3 1083 1339.4 1512.6 1201.4 1162.4 1733.6 1694 1628.4 TRUE FALSE FALSE 1254.915876 1138.099769 1101.849161 1494.26773 1435.406378 1124.634417 1261.134227 1783.758981 1542.484397 1586.093933 0.791198964 0.717548781 0.694693509 0.942105445 0.904994558 0.709059151 0.795119507 1.124623797 0.972505074 1 10.6312625 -12.27072066 1.055606778 0.997704282 0.825740867 0.187142928 0.124315881 0.625265029 1.273178921 0.077266818 0.022120331 5.36E-13 12.27072066 -0.171963415 VS(ph)PPAPGSAPETPEDK ddPTM_HeLa_Romidepsin_16h_R1 2 VSPPAPGSAPETPEDK 16 0 M0R300;M0R0P8;Q13459-2;Q13459 M0R300 MYO9B Unconventional myosin-IXb 1 0 VS(1)PPAPGSAPETPEDK;VS(1)PPAPGSAPETPEDK ; 163.8 5.47E-05 11347500 2684.5 2979.1 2762.8 2182.92 2293.7 3154.3 2850.1 2886.3 2716.5 2929.8 TRUE FALSE FALSE 2651.780281 3021.039848 2810.885375 2435.319481 2176.64393 2952.75041 3092.187423 2969.810537 2473.529436 2853.683374 0.92924825 1.058645775 0.985002541 0.853395126 0.762748927 1.034715497 1.083577615 1.04069378 0.866784822 1 11.47860956 -8.019882973 24.75687769 0.951858399 1.06138847 0.305022963 0.083034006 688.1772244 856871.8221 0.011886387 0.030780384 9.55E-09 8.019882973 0.109530072 VS(ph)PPASPGP ddPTM_HeLa_Romidepsin_16h_R1 1 VSPPASPGP 9 0 A0A0C4DGU2;Q9Y4U1 A0A0C4DGU2 MMACHC Methylmalonic aciduria and homocystinuria type C protein 1 0 VS(1)PPASPGP 157.34 0.0067909 9883100 8018.8 8288.7 7705.4 7583.5 5350 5227 4210 4588.5 8285.7 7615.6 TRUE FALSE FALSE 7921.063781 8405.388536 7839.509255 8460.339951 5076.969536 4893.011569 4567.597295 4721.261008 7544.60624 7417.745614 1.067853253 1.133145968 1.056858736 1.14055407 0.684435649 0.659635936 0.615766236 0.636481925 1.017102316 1 12.85676508 -8.713107388 6.904221387 1.049986769 0.644315128 0.951694853 0.04626839 0.036732196 4.046463549 0.007735399 0.015448122 1.94E-09 8.713107388 -0.405671641 VS(ph)PPASPTLEVELGSAELPLQGAVGPELPPGGGHGR ddPTM_HeLa_Romidepsin_16h_R1 1 VSPPASPTLEVELGSAELPLQGAVGPELPPGGGHGR 36 0 Q7Z6J0 Q7Z6J0 SH3RF1 E3 ubiquitin-protein ligase SH3RF1 1 0 VS(0.998)PPAS(0.002)PT(0.001)LEVELGSAELPLQGAVGPELPPGGGHGR 124.96 2.66E-22 28061000 970.01 936.07 934.66 965.54 933.41 764.21 726.39 906.24 1232 1234.5 TRUE FALSE FALSE 958.187145 949.248018 950.9273652 1077.180278 885.7746047 715.3794474 788.0895485 932.4606246 1121.806834 1202.427512 0.796877263 0.78944303 0.79083966 0.895838017 0.736655304 0.594946007 0.655415433 0.775481778 0.932951736 1 10.23173421 -16.52287875 0.098732984 1.874504449 0.551172457 0.628018489 0.070741419 53.26484818 0.393274697 9.577054473 0.656211383 3.00E-17 16.52287875 -1.323331991 VS(ph)PSFSAELK ddPTM_HeLa_Romidepsin_16h_R1 2 VSPSFSAELK 10 0 Q13416 Q13416 ORC2 Origin recognition complex subunit 2 1 0 VS(0.999)PS(0.001)FSAELK;VS(0.997)PS(0.003)FSAELK ; 147.58 0.00391 16932600 4511.5 4430.8 5014.1 4920.2 4994.3 4977.4 3956.9 4290.2 5075.4 4279.7 TRUE FALSE FALSE 4456.512103 4493.176919 5101.368307 5489.096674 4739.422235 4659.360204 4292.998987 4414.330168 4621.443512 4168.512777 1.069089227 1.077884886 1.223786175 1.316799772 1.136957589 1.117751211 1.029863459 1.058970046 1.108655235 1 12.02531704 -10.45582118 1.471308367 1.024072156 1.144631333 0.149742871 0.082564725 0.371097929 1.577363904 0.017656137 0.019352926 3.50E-11 10.45582118 0.120559177 VS(ph)PSTSYTPSR ddPTM_HeLa_Romidepsin_16h_R1 1 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 0 VS(1)PSTSYTPSR 137.4 0.0036395 93653000 1090 867.94 762.22 1071.5 957.94 832.04 863.08 1115.5 877.41 951.85 TRUE FALSE FALSE 1076.714661 880.1588821 775.4861194 1195.391872 909.0527472 778.8753293 936.3899937 1147.775233 798.9322521 927.1207998 1.161353149 0.949346495 0.836445606 1.28935935 0.980511652 0.840101235 1.009997828 1.237999657 0.861734795 1 9.856613518 -10.24978675 24.69215651 1.076194545 1.014911589 0 0.158762558 1949.599962 4131247.085 0.024577364 0.029954567 5.63E-11 10.24978675 -0.061282956 VS(ph)PTGAAGR ddPTM_HeLa_Romidepsin_16h_R1 2 VSPTGAAGR 9 0 A0A0G2JMS7;A0A0G2JNZ2;A0A669KB89;Q14160-2;Q14160;H0YCG0;A0A0G2JPP5;Q14160-3 A0A0G2JMS7 SCRIB Protein scribble homolog 1 0 VS(0.731)PT(0.269)GAAGR;VS(0.814)PT(0.186)GAAGR ; 105.17 0.02364 16743700 3831.4 3739.8 4471.7 3342.7 3987.4 5453 5023.1 3183.8 4940.7 4520.3 TRUE FALSE FALSE 3784.701423 3792.449003 4549.528063 3729.198702 3783.908099 5104.570899 5449.761989 3275.91823 4498.791418 4402.861954 0.859600292 0.861359961 1.033311539 0.846994237 0.859420109 1.159375641 1.237777165 0.744042912 1.021787979 1 12.1042259 -8.268696115 24.8738838 0.923417857 1.066136433 0.136438283 0.136885578 624.7877519 2141585.509 0.018418585 0.041962898 5.39E-09 8.268696115 0.142718576 VS(ph)SGYVPPPVATPFSSK ddPTM_HeLa_Romidepsin_16h_R1 1 VSSGYVPPPVATPFSSK 17 0 Q15942;Q15942-2;H7C3R3 Q15942 ZYX Zyxin 1 0 VS(0.797)S(0.134)GY(0.069)VPPPVATPFSSK 120.77 0.0022963 27718000 6067 5597.3 5964.2 4486.2 6369.5 7043.4 5285.5 6029.6 6838.5 6258.1 TRUE FALSE FALSE 5993.05307 5676.098936 6068.004399 5004.915552 6044.440647 6593.349472 5734.450238 6204.056963 6226.847433 6095.51366 0.983190819 0.931192883 0.995486966 0.821081837 0.991621213 1.081672495 0.94076571 1.017807081 1.021545973 1 12.57353208 -8.521407037 24.99998105 0.973602061 1.011232948 0.111258113 0.062127209 119.951005 2037616.185 0.008863313 0.017927456 3.01E-09 8.521407037 0.037630888 VS(ph)SPSPELGTTPASIFR ddPTM_HeLa_Romidepsin_16h_R1 2 VSSPSPELGTTPASIFR 17 0 A0A5E8;Q99501 A0A5E8 GAS2L1 GAS2-like protein 1 1 0 VS(0.591)S(0.406)PS(0.002)PELGTTPASIFR;VS(0.895)S(0.104)PS(0.002)PELGTTPASIFR ; 169.98 3.18E-06 28195000 1405.8 1197.63 1311.93 1555.59 1220.61 1463.88 1203.38 1262.65 1337.88 1474.29 TRUE FALSE FALSE 1388.665569 1214.490267 1334.763591 1735.454635 1158.317717 1370.342792 1305.595067 1299.182786 1218.216662 1435.987733 0.967045565 0.845752536 0.929509048 1.208544192 0.806634827 0.954285862 0.909196532 0.904731117 0.848347541 1 10.48782771 -4 0.132147928 1.011134314 0.662114976 0 0.110296944 180.6866185 1.603436331 0.318907556 11.83055694 1.00E-04 4 -0.349019338 VS(ph)SPTVNTTLR ddPTM_HeLa_Romidepsin_16h_R1 2 VSSPTVNTTLR 11 0 Q9NSK0-5;Q9NSK0;Q9NSK0-3 Q9NSK0-5 KLC4 Kinesin light chain 4 1 0 VS(0.905)S(0.093)PT(0.002)VNTTLR;VS(0.499)S(0.499)PT(0.002)VNTTLR ; 137.4 0.0036395 61780000 4206.2 4208 3771.4 3560.8 3950.8 4171.8 4207.3 3810.9 4510.5 4061 TRUE FALSE FALSE 4154.933217 4267.240334 3837.039635 3972.51645 3749.175934 3905.235444 4564.667957 3921.162379 4107.069583 3955.494635 1.050420643 1.078813329 0.97005305 1.004303334 0.947839974 0.987293829 1.154006864 0.991320363 1.0383201 1 11.9496424 -10.75602456 0.001990633 7.98E-05 2.044469163 0 0.057534624 204725.359 294.495815 151482.0648 150960.5176 1.75E-11 10.75602456 2.044389395 VS(ph)SQAEDTSSSFDNLFIDR ddPTM_HeLa_Romidepsin_16h_R1 1 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 0 VS(0.448)S(0.448)QAEDT(0.057)S(0.047)SSFDNLFIDR 174.72 3.72E-08 3086500 397.55 429.95 545.95 359.99 439.07 687.18 402.42 916.36 379.89 442.76 TRUE FALSE FALSE 392.7045077 436.0028474 555.4520307 401.6137376 416.6626195 643.2714158 436.6015448 942.8734308 345.9116869 431.2570314 0.910604301 1.011004611 1.287983709 0.931263048 0.966158437 1.491619542 1.012392872 2.186337525 0.802100979 1 8.752404169 -4.696764293 0.973479097 0.992940144 199.9999999 0.741711871 0.198758593 99.71431572 0.689441835 0.026947427 43543.29294 2.01E-05 4.696764293 199.0070598 up VS(ph)SSGLTDSLFILK ddPTM_HeLa_Romidepsin_16h_R1 1 VSSSGLTDSLFILK 14 0 Q6P3S1 Q6P3S1 DENND1B DENN domain-containing protein 1B 1 0 VS(0.734)S(0.216)S(0.045)GLTDS(0.005)LFILK 113.54 0.0050022 4032100 980.4 815.56 781.35 864.25 861.86 655.17 783 796.33 835.68 725.31 TRUE FALSE FALSE 968.4505077 827.0414751 794.949069 964.1786514 817.8760682 613.3067515 849.5080005 819.3705521 760.9346878 706.4663416 1.370837435 1.170673571 1.125246911 1.364790641 1.157699978 0.86813301 1.202474839 1.159815413 1.077099704 1 9.464477017 -8.50655564 24.88701155 1.189512367 1.076631473 0.112802908 0.135227762 1366.97335 2084154.818 0.023720702 0.051739847 3.11E-09 8.50655564 -0.112880894 VSAEAEVAPVS(ph)PEVT(ph)QEVVEEHCASPEDK ddPTM_HeLa_Romidepsin_16h_R1 1 VSAEAEVAPVSPEVTQEVVEEHCASPEDK 29 0 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VS(0.001)AEAEVAPVS(0.934)PEVT(0.751)QEVVEEHCAS(0.314)PEDK 55.789 0.0031691 2876000 1097.5 876.13 1183.9 136.88 1075.9 1185.7 893.39 745.78 988.66 1153 TRUE FALSE FALSE 1084.123248 888.4641811 1204.505283 152.7067096 1020.992808 1109.937597 969.2745243 767.3579677 900.2317735 1123.044894 0.965342752 0.791120806 1.072535292 0.135975606 0.909129113 0.988328786 0.863077273 0.683283431 0.801599098 1 10.13319989 -9.993595142 1.584338803 0.985216279 0.761256669 0.058465666 0.246083672 0.525451147 2.594961519 0.04223489 0.055844141 1.01E-10 9.993595142 -0.22395961 VSAGEPGSHPS(ph)PAPR ddPTM_HeLa_Romidepsin_16h_R1 3 VSAGEPGSHPSPAPR 15 0 A0A1B0GV68;C9JME2;Q9Y4F1;Q9Y4F1-2 A0A1B0GV68 FARP1 "FERM, RhoGEF and pleckstrin domain-containing protein 1" 1 0 VSAGEPGS(0.169)HPS(0.831)PAPR;VSAGEPGS(0.025)HPS(0.975)PAPR;VSAGEPGSHPS(1)PAPR ;; 197.7 1.59E-13 62104000 5858.9 7692.5 6242.1 4908.59 8684.1 9475.1 5190.28 6803.6 7438.8 7318.5 TRUE FALSE FALSE 5787.489473 7800.795217 6350.741132 5476.144271 8240.917972 8869.671689 5631.142254 7000.451432 6773.455097 7128.364315 0.81189586 1.094331725 0.890911414 0.768218911 1.156074186 1.244278673 0.789962747 0.982055788 0.950211689 1 12.79935536 -8.753321216 24.99986208 0.913744889 1.039382506 0.158208788 0.139481114 282.4595489 869826.5354 0.021372255 0.042159175 1.76E-09 8.753321216 0.125637618 VSALEEDMDDVES(ph)S(ph)EEEEEEDEKLER ddPTM_HeLa_Romidepsin_16h_R1 4 VSALEEDMDDVESSEEEEEEDEKLER 26 1 Q8NAV1 Q8NAV1 PRPF38A Pre-mRNA-splicing factor 38A 2 0 VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VSALEEDMDDVES(1)S(1)EEEEEEDEKLER;VS(0.046)ALEEDMDDVES(0.977)S(0.977)EEEEEEDEKLER ;;; 117.01 1.05E-06 136845800 7356.17 7207.25 6990.9 6325.74 7962.73 8798.83 7632.99 8719.86 7856.95 7578.84 TRUE FALSE FALSE 7266.510171 7308.713855 7112.573682 7057.151822 7556.362175 8236.61316 8281.33598 8972.155391 7154.204714 7381.940644 0.984363126 0.990080279 0.963510007 0.956002244 1.023628141 1.115778839 1.121837248 1.215419606 0.969149585 1 12.84978442 -8.00655023 1.373887429 0.987161361 1.194131891 0.920288221 0.023321202 0.101010271 0.327888869 0.003516486 0.019642301 9.85E-09 8.00655023 0.20697053 VSAS(ph)SPTTK ddPTM_HeLa_Romidepsin_16h_R1 1 VSASSPTTK 9 0 Q9BVI0;Q5JWZ0;Q5JXL1 Q9BVI0 PHF20 PHD finger protein 20 1 0 VS(0.005)AS(0.497)S(0.497)PT(0.001)TK 148.91 0.0054389 8060300 3410.5 4462.6 6035.6 2868.6 1971.7 1851.6 2572.1 606.02 6493.3 5625.2 TRUE FALSE FALSE 3368.931514 4525.4246 6140.647086 3200.281029 1871.076792 1733.288736 2790.57411 623.5542326 5912.522985 5479.056493 0.614874389 0.825949615 1.120749 0.584093454 0.341496167 0.316348031 0.509316543 0.113806863 1.079113346 1 12.41971176 -8.962611248 4.013052925 0.836041562 0.337310452 0.722142347 0.173115138 0.110335262 3.883589037 0.027992292 0.051304799 1.09E-09 8.962611248 -0.498731111 VSASS(ph)PSLAVASQSDSK ddPTM_HeLa_Romidepsin_16h_R1 4 VSASSPSLAVASQSDSK 17 0 A0A494C0P1;P04150-7;P04150-5;P04150-2;P04150-6;P04150-10;P04150;P04150-3;D6RDA9;Q3MSN4;P04150-9;P04150-8 A0A494C0P1 NR3C1 Glucocorticoid receptor 1 0 VSAS(0.081)S(0.917)PS(0.002)LAVASQSDSK;VSAS(0.006)S(0.992)PS(0.002)LAVASQSDSK;VSAS(0.037)S(0.947)PS(0.016)LAVASQSDSK;VSAS(0.028)S(0.485)PS(0.485)LAVAS(0.002)QSDSK ;;; 278.72 1.15E-102 59749000 16472.6 15429.8 16228.3 14830.4 16299 17213.9 13040.1 15379.8 16105.1 15788.5 TRUE FALSE FALSE 16271.82562 15647.02113 16510.74675 16545.16063 15467.20121 16113.98735 14147.72577 15824.79025 14664.61952 15378.31249 1.058102157 1.01747322 1.073638396 1.075876214 1.005780135 1.047838464 0.919979079 1.029032948 0.953590943 1 13.90860958 -7.790351644 24.99999693 1.033579043 0.974505893 0.197155886 0.043246648 166.6416697 144092.3824 0.005063961 0.015195485 1.62E-08 7.790351644 -0.05907315 VSAVPTNMAAK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VSAVPTNMAAKK 12 1 Q96KR1 Q96KR1 ZFR Zinc finger RNA-binding protein 0 1 ; VSAVPTNMAAK(1)K;VSAVPTNMAAK(1)K 140.78 0.00011224 1990690 2082.9 1916.38 2996.4 1638.41 3078.7 3009.3 3105.9 2288.9 2681.5 1632.02 FALSE TRUE FALSE 2057.512814 1943.358848 3048.551085 1827.850673 2921.582451 2817.015442 3369.715068 2355.12571 2441.659924 1589.619885 1.294342649 1.222530535 1.917786204 1.149866512 1.837912622 1.772131482 2.119824431 1.48156533 1.536002378 1 10.63446611 -9.781888095 0.383454888 1.007415022 1.910749466 0.256257685 0.302390952 0.638161319 0.225957109 0.121820284 0.221823413 1.65E-10 9.781888095 0.903334443 VSDQNS(ph)PVLPK ddPTM_HeLa_Romidepsin_16h_R1 4 VSDQNSPVLPK 11 0 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 VSDQNS(1)PVLPK;VS(0.002)DQNS(0.998)PVLPK;VSDQNS(1)PVLPK;VSDQNS(1)PVLPK ;;; 146.67 0.002453 770575000 45847.6 42441.2 45676.5 40223.3 38096.8 33781.6 30918.1 34308.2 45798.5 42461.5 TRUE FALSE FALSE 45288.79182 43038.68833 46471.48032 44874.1072 36152.57814 31623.06479 33544.28264 35300.85364 41702.16746 41358.34411 1.095033972 1.040628905 1.1236301 1.085007347 0.874130213 0.764611482 0.811064451 0.853536436 1.008313276 1 15.3358908 -8.649362038 4.299432068 1.054538627 0.811274431 0.88499683 0.041509385 0.059718452 1.956388242 0.00712893 0.014622885 2.24E-09 8.649362038 -0.243264195 VSDQNS(ph)PVLPKK ddPTM_HeLa_Romidepsin_16h_R1 1 VSDQNSPVLPKK 12 1 Q9UPU5 Q9UPU5 USP24 Ubiquitin carboxyl-terminal hydrolase 24 1 0 VS(0.003)DQNS(0.997)PVLPKK 65.956 0.024072 30714000 5589.2 5555.8 4600.4 6412.9 3969.5 3281.9 3445.9 3850.6 5256.7 4404 TRUE FALSE FALSE 5521.076681 5634.014698 4680.468032 7154.389672 3766.921603 3072.197182 3738.59466 3962.011036 4786.527586 4289.583445 1.287089236 1.313417671 1.091124136 1.667851847 0.878155572 0.716199421 0.871551914 0.92363538 1.115849044 1 12.06662184 -8.556391555 24.9998763 1.186706779 0.83333818 0.52267481 0.181654757 131.2229069 97889.15465 0.028416939 0.05683411 2.78E-09 8.556391555 -0.3533686 VSDS(ph)LTDLALK ddPTM_HeLa_Romidepsin_16h_R1 1 VSDSLTDLALK 11 0 Q8N3C0 Q8N3C0 ASCC3 Activating signal cointegrator 1 complex subunit 3 1 0 VS(0.031)DS(0.93)LT(0.039)DLALK 107.53 0.015707 2111700 2086.4 2468.5 2120.9 2154 2097.6 2233.1 1834.8 2719 2497.3 1880.1 TRUE FALSE FALSE 2060.970154 2503.251608 2157.813375 2403.055615 1990.551645 2090.412117 1990.647866 2797.669975 2273.935233 1831.254731 1.125441545 1.366959804 1.178325079 1.31224541 1.086987851 1.141519026 1.087040395 1.527733924 1.241736169 1 10.83861677 -10.94376811 1.213928413 1.029904623 1.225987004 0.024436084 0.147873929 0.356190981 1.09833042 0.031068708 0.026649291 1.14E-11 10.94376811 0.196082381 VSDS(ph)PSHIATK ddPTM_HeLa_Romidepsin_16h_R1 1 VSDSPSHIATK 11 0 Q9P2D3 Q9P2D3 HEATR5B HEAT repeat-containing protein 5B 1 0 VS(0.253)DS(0.331)PS(0.331)HIAT(0.085)K 121.21 0.0094877 6835300 1959.2 1929.8 1821.8 2093.5 3180.4 3236.2 2913.8 3371.4 2846.4 2285.8 TRUE FALSE FALSE 1935.320517 1956.967775 1853.507665 2335.56032 3018.09232 3029.417264 3161.298099 3468.94614 2591.810855 2226.414586 0.869254329 0.878977252 0.83250787 1.049023095 1.355584148 1.360670777 1.419905402 1.558086333 1.1641187 1 11.12050655 -8.77823683 2.424676117 0.923536858 1.438926043 0.838954874 0.099275955 0.060101707 0.721409418 0.011617559 0.024374073 1.67E-09 8.77823683 0.515389186 VSDSESEGPQKGPASDS(ph)ETEDASR ddPTM_HeLa_Romidepsin_16h_R1 1 VSDSESEGPQKGPASDSETEDASR 24 1 Q96ST2-3;Q96ST2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 VSDSESEGPQKGPAS(0.395)DS(0.558)ET(0.046)EDAS(0.001)R 79.029 0.00012301 9812100 2960.4 1646.3 1657.4 3924.2 1553.7 1036 1759.4 1217.9 2494.9 2541.5 TRUE FALSE FALSE 2924.317506 1669.476655 1686.246352 4377.934468 1474.408891 969.8029435 1908.843392 1253.138015 2271.749895 2475.471464 1.181317397 0.674407554 0.681181899 1.768525524 0.595607307 0.391764946 0.771102968 0.506221959 0.917703932 1 11.2734876 -8.569703159 24.99999838 1.067115778 0.563807504 0.366977585 0.30181069 87.35393254 46638.76356 0.041497987 0.082996 2.69E-09 8.569703159 -0.503308274 VSEEAESQQQWDTSKGEQVS(ph)QNGLPAEQGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 VSEEAESQQQWDTSKGEQVSQNGLPAEQGSPR 32 1 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 VSEEAESQQQWDT(0.123)S(0.101)KGEQVS(0.653)QNGLPAEQGS(0.123)PR 76.611 1.01E-06 5177800 821.7 467.66 371.05 473.76 591.35 514.22 477.94 408.53 523.2 463.67 TRUE FALSE FALSE 811.6848043 474.2437298 377.5079696 528.5383603 561.1712029 481.3630016 518.5362117 420.350171 476.4036816 451.6237866 1.797258755 1.05008581 0.83589036 1.170306738 1.242563433 1.065849532 1.148159657 0.930752949 1.054868445 1 8.818977663 VSEEAESQQQWDTSKGEQVSQNGLPAEQGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 VSEEAESQQQWDTSKGEQVSQNGLPAEQGSPR 32 1 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 1 0 VSEEAESQQQWDTSKGEQVS(0.018)QNGLPAEQGS(0.981)PR;VSEEAESQQQWDTSKGEQVS(0.001)QNGLPAEQGS(0.999)PR ; 138.33 6.86E-16 25853000 2772.7 2497.1 2249.6 2584.4 2686 2901.7 2588.4 2606.6 2843.4 2599.1 TRUE FALSE FALSE 2738.905266 2532.254239 2288.753344 2883.220488 2548.923397 2716.290735 2808.258631 2682.017858 2589.079183 2531.575007 1.081897735 1.000268304 0.90408277 1.138903836 1.006852805 1.072964746 1.109293078 1.059426583 1.022714782 1 11.30581951 -8.095320021 5.825282572 1.032147636 1.085980628 0.160093204 0.058575842 0.352437583 17.38742053 0.008476758 0.022185274 8.03E-09 8.095320021 0.053832992 VSEEQTQPPS(ph)PAGAGMSTAMGR ddPTM_HeLa_Romidepsin_16h_R1 3 VSEEQTQPPSPAGAGMSTAMGR 22 0 H3BM18;X6RHM1;Q16666-3;Q16666-2;Q16666 H3BM18 IFI16 Gamma-interferon-inducible protein 16 1 0 VSEEQT(0.02)QPPS(0.944)PAGAGMS(0.027)T(0.009)AMGR;VSEEQTQPPS(0.596)PAGAGMS(0.202)T(0.202)AMGR;VSEEQT(0.012)QPPS(0.939)PAGAGMS(0.041)T(0.009)AMGR ;; 97.08 0.00026009 383993000 13116.8 13653.7 12437.4 12329.3 11517.3 10945.2 9461.8 10749.7 14919.1 13726 TRUE FALSE FALSE 12956.9274 13845.91715 12653.86773 13754.87168 10929.5292 10245.83704 10265.48506 11060.72561 13584.69833 13369.39654 0.96914826 1.035642641 0.946480097 1.02883265 0.817503555 0.76636496 0.767834586 0.827316744 1.016104077 1 13.70664673 -8.688590761 5.483198083 0.988672993 0.787167767 0.911863474 0.031103246 0.038645292 2.07568431 0.004096973 0.008246959 2.05E-09 8.688590761 -0.201505226 VSEFNVS(ph)SEGSGEK ddPTM_HeLa_Romidepsin_16h_R1 1 VSEFNVSSEGSGEK 14 0 Q9BVJ6-3;Q9BVJ6 Q9BVJ6-3 UTP14A U3 small nucleolar RNA-associated protein 14 homolog A 1 0 VSEFNVS(0.821)S(0.176)EGS(0.003)GEK 159.64 0.00036577 4538500 1112.9 1183 1250.9 805.63 977.82 1088 841.68 834.71 1540.7 1334.4 TRUE FALSE FALSE 1099.335547 1199.654305 1272.67139 898.7807312 927.9181967 1018.480311 913.1722782 858.8610169 1402.895933 1299.732096 0.845817034 0.923001216 0.979179782 0.6915123 0.713930355 0.783607879 0.702585003 0.660798498 1.079373155 1 10.34399857 -9.256886628 24.97751026 0.928505702 0.714301401 0.773287263 0.067550509 154.2826954 846431.6917 0.009943446 0.016131771 5.53E-10 9.256886628 -0.214204301 VSESEGKLEGQAT(ph)AVTPNK ddPTM_HeLa_Romidepsin_16h_R1 1 VSESEGKLEGQATAVTPNK 19 1 Q9BXB4 Q9BXB4 OSBPL11 Oxysterol-binding protein-related protein 11 1 0 VSESEGKLEGQAT(0.926)AVT(0.073)PNK 70.167 0.008756 6465100 1675.5 1532.5 2337.3 989.24 1906.9 1887 1747.7 1759.2 1772.4 1780.7 TRUE FALSE FALSE 1655.078362 1554.074575 2377.979726 1103.620583 1809.583777 1766.42679 1896.149594 1810.099676 1613.872105 1734.437157 0.954245217 0.896010887 1.371038274 0.636298974 1.043326228 1.018443812 1.093236262 1.043623673 0.930487506 1 10.76025185 -8.558797862 24.99946131 0.976662729 1.051744702 0.054987217 0.168511142 450.6887544 313674.676 0.022231013 0.044462121 2.76E-09 8.558797862 0.075081973 VSFELFADKVPK ddPTM_HeLa_Romidepsin_16h_R1 1 VSFELFADKVPK 12 1 F8WE65;C9J5S7;P62937 F8WE65 PPIA "Peptidyl-prolyl cis-trans isomerase;Peptidyl-prolyl cis-trans isomerase A;Peptidyl-prolyl cis-trans isomerase A, N-terminally processed" 0 0 110.31 0.012005 22695000 2014.7 1594.3 1803.3 2501.2 2121.5 1925.7 1746.2 1715.2 1772.8 1704.7 FALSE FALSE TRUE 1990.144061 1616.744597 1834.68568 2790.400512 2013.231939 1802.653985 1894.522184 1764.826606 1614.236328 1660.411648 1.198584739 0.973701069 1.104958329 1.680547421 1.21248965 1.085666911 1.140995479 1.062884983 0.972190438 1 10.69732524 -12.35087809 0.511331533 0.955433664 1.196479889 0.161392307 0.179991694 2.844932775 0.966220364 0.347668334 0.048689987 4.46E-13 12.35087809 0.241046225 VSGAGFS(ph)PSSK ddPTM_HeLa_Romidepsin_16h_R1 2 VSGAGFSPSSK 11 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 VSGAGFS(0.999)PS(0.001)SK;VSGAGFS(0.998)PS(0.001)S(0.001)K ; 162.93 0.00095878 172921000 11859.7 11540.4 10447.9 9453 12987.1 12610.1 10894.5 11437.8 11547.8 11823.6 TRUE FALSE FALSE 11715.14941 11702.86605 10629.74132 10546.00034 12324.31983 11804.35531 11819.87856 11768.7347 10514.93585 11516.42117 1.017256077 1.016189481 0.923007344 0.915735903 1.070151885 1.02500205 1.026349973 1.021909022 0.913038495 1 13.49140484 VSGAQEMVSSAKDTVATQLSEAVDATR ddPTM_HeLa_Romidepsin_16h_R1 1 VSGAQEMVSSAKDTVATQLSEAVDATR 27 1 K7EL96;K7ERZ3;O60664-4;O60664-3;O60664 K7EL96 PLIN3 Perilipin-3 0 0 59.674 0.0092404 1779600 1611.1 1459.2 1640.8 1288.4 890.25 1010.2 904.41 915.58 1395.3 1579 FALSE FALSE TRUE 1591.463294 1479.742656 1669.357436 1437.37087 844.8172205 945.6514803 981.2305628 942.0708628 1270.500873 1537.977352 1.034776807 0.962135531 1.085423939 0.934585199 0.549304071 0.614866974 0.638000658 0.61253884 0.826085554 1 10.58681854 -8.848107967 4.717478782 1.016116921 0.607154258 0.864582061 0.071121952 0.024921706 0.981680026 0.005352151 0.009979715 1.42E-09 8.848107967 -0.408962663 VSGEEELHTGPPAPQGPLSVPQGLPTQSLAS(ph)PPAR ddPTM_HeLa_Romidepsin_16h_R1 2 VSGEEELHTGPPAPQGPLSVPQGLPTQSLASPPAR 35 0 Q9UPN7 Q9UPN7 PPP6R1 Serine/threonine-protein phosphatase 6 regulatory subunit 1 1 0 VSGEEELHTGPPAPQGPLS(0.005)VPQGLPT(0.067)QS(0.051)LAS(0.877)PPAR;VSGEEELHTGPPAPQGPLS(0.001)VPQGLPT(0.026)QS(0.026)LAS(0.947)PPAR ; 109.39 1.01E-14 27835000 3623.99 3564.17 3896.53 3432.58 5331.1 6180.4 4624.6 5425.3 4271.12 3923.89 TRUE FALSE FALSE 3579.819416 3614.346479 3964.34747 3829.47105 5059.034074 5785.492386 5017.413409 5582.272496 3889.10033 3821.946772 0.936648161 0.945682055 1.037258682 1.001968703 1.323679888 1.513755353 1.312789975 1.460583527 1.017570511 1 11.90009197 -8.714077603 3.333720961 0.97291336 1.418864081 0.929475294 0.0561544 0.039417728 0.895515168 0.007843975 0.016132348 1.93E-09 8.714077603 0.445950721 VSGGT(ph)PIKIEDPNQFVPLNTNPNEVLEK ddPTM_HeLa_Romidepsin_16h_R1 2 VSGGTPIKIEDPNQFVPLNTNPNEVLEK 28 1 Q9UEY8-2;Q9UEY8 Q9UEY8-2 ADD3 Gamma-adducin 1 0 VS(0.117)GGT(0.881)PIKIEDPNQFVPLNT(0.001)NPNEVLEK;VS(0.011)GGT(0.989)PIKIEDPNQFVPLNTNPNEVLEK ; 64.545 0.0004587 22631800 4433.9 3832.7 4979.8 4870.3 7442.1 8046.5 6505.1 6619.6 4618.7 4991.6 TRUE FALSE FALSE 4379.857921 3886.656851 5066.47133 5433.427001 7062.301867 7532.354619 7057.643032 6811.127682 4205.591904 4861.917512 0.900849903 0.799408226 1.042072663 1.117548166 1.452575419 1.549255947 1.451617189 1.400913871 0.86500684 1 12.2473097 -8.921131984 2.180332831 0.94327999 1.477240285 0.924053312 0.073207588 0.061436356 0.590566046 0.011739269 0.023499868 1.20E-09 8.921131984 0.533960294 VSGS(ph)PEQAVEENLSSYSLDR ddPTM_HeLa_Romidepsin_16h_R1 1 VSGSPEQAVEENLSSYSLDR 20 0 A0A494BZT8;Q9Y6A5;E7EMT0;C9JA91 A0A494BZT8 TACC3 Transforming acidic coiled-coil-containing protein 3 1 0 VS(0.111)GS(0.889)PEQAVEENLSSYSLDR 178.56 5.69E-13 9938900 1993.7 1732 1872.9 1143.3 2298.2 3150 1963 2309.2 2146.9 2234.3 TRUE FALSE FALSE 1969.400018 1756.383141 1905.497039 1275.493725 2180.914278 2948.725166 2129.737171 2376.013059 1954.875887 2176.252564 0.904950119 0.807067695 0.87558635 0.586096369 1.002142083 1.354955401 0.978625922 1.091791044 0.898276202 1 11.08763028 -8.517107578 24.99914231 0.907324922 1.13432006 0.440442703 0.140588818 225.369057 976236.287 0.021397128 0.043921348 3.04E-09 8.517107578 0.226995138 VSGS(ph)PEQAVEENLSSYSLDRR ddPTM_HeLa_Romidepsin_16h_R1 2 VSGSPEQAVEENLSSYSLDRR 21 1 A0A494BZT8;Q9Y6A5;E7EMT0;C9JA91 A0A494BZT8 TACC3 Transforming acidic coiled-coil-containing protein 3 1 0 VS(0.047)GS(0.801)PEQAVEENLS(0.15)SYS(0.002)LDRR;VS(0.065)GS(0.934)PEQAVEENLSSYSLDRR ; 130.72 7.26E-05 42032000 1544.12 1765.31 1567.7 1418.27 2035.2 2781.6 2165.2 2588.8 1765.44 1724.07 TRUE FALSE FALSE 1525.299672 1790.162081 1594.985161 1582.257051 1931.33615 2603.864737 2349.112034 2663.702844 1607.534625 1679.278413 0.908306603 1.066030544 0.949803885 0.942224374 1.150098837 1.550585488 1.398881815 1.586218713 0.957277014 1 10.71362572 -8.432163239 2.967058626 0.963796415 1.503157678 0.936871661 0.062614412 0.044298992 0.750403849 0.009211165 0.022268922 3.70E-09 8.432163239 0.539361263 (ac)AT(ph)PPKR ddPTM_HeLa_Romidepsin_16h_R1 1 ATPPKR 6 1 D6R9C6;D6RG38;D6RCP9;D6RFG8;Q9UBK9;P27707 D6R9C6 DCK;UXT Protein UXT;Deoxycytidine kinase 1 0 AT(1)PPKR 43.124 0.027984 14093000 18102 18273 18886 17669 12939 14140 11996 6145.3 20398 18400 TRUE FALSE FALSE 17881.36586 18530.24777 19214.70291 19711.97292 12278.67455 13236.49963 13014.93994 6323.10456 18573.55179 17921.96535 0.997734652 1.033940609 1.072131462 1.099877861 0.685118753 0.738562952 0.726200486 0.352813123 1.036356863 1 14.12944123 -7.245410934 0.653817986 1.012978369 1.71E-14 0.824244925 0.095682461 0.964348723 0.278107153 0.016756616 0.730433436 5.68E-08 7.245410934 -1.012978369 down VSGTLDTPEKTVDS(ph)QGPTPVCTPTFLER ddPTM_HeLa_Romidepsin_16h_R1 1 VSGTLDTPEKTVDSQGPTPVCTPTFLER 28 1 H7BZL0;Q9BYG3;C9J808 H7BZL0 NIFK MKI67 FHA domain-interacting nucleolar phosphoprotein 1 0 VSGTLDT(0.011)PEKT(0.07)VDS(0.663)QGPT(0.236)PVCT(0.015)PT(0.005)FLER 49.141 0.011 9640700 947.97 873.96 1217.3 143.61 461.08 408.2 246.47 337.54 1253.1 1193.8 TRUE FALSE FALSE 936.415777 886.2636318 1238.486596 160.2148639 437.5493671 382.1173374 267.4051556 347.3061873 1141.019598 1162.784904 0.805321581 0.762190521 1.065103779 0.137785469 0.376294331 0.328622548 0.22996958 0.298684809 0.981281743 1 10.18336853 -9.260367011 24.9999997 0.903178683 0.280497581 0.908333545 0.102903648 22.58924502 526618.471 0.016840931 0.026917525 5.49E-10 9.260367011 -0.622681102 VSHLLGINVTDFTR ddPTM_HeLa_Romidepsin_16h_R1 1 VSHLLGINVTDFTR 14 0 P35579;P35579-2 P35579;P35579-2 MYH9 Myosin-9 0 0 88.706 0.0095605 7658200 945.22 1007.1 1123.3 1321.5 1186.2 1238.3 1155.9 1358.8 1051.7 814.22 FALSE FALSE TRUE 933.6992951 1021.27798 1142.850565 1474.298048 1125.663788 1159.176626 1254.082117 1398.114734 957.633318 793.066447 1.177327951 1.287758402 1.441052726 1.858984267 1.41938143 1.46163872 1.581307748 1.762922564 1.20750704 1 9.631297937 -10.02752852 1.132154513 1.062386674 1.602242375 0.701400025 0.137854374 0.158894762 0.398112266 0.026820045 0.035622038 9.39E-11 10.02752852 0.539855701 VSIGNITLS(ph)PAISR ddPTM_HeLa_Romidepsin_16h_R1 1 VSIGNITLSPAISR 14 0 Q0JRZ9-3;Q0JRZ9 Q0JRZ9-3 FCHO2 F-BAR domain only protein 2 1 0 VSIGNIT(0.001)LS(0.999)PAISR 185.74 6.80E-08 50977000 1798.7 1674.6 1627.8 1018.7 1547 1491.2 1234.5 1572.9 1643.8 1582.4 TRUE FALSE FALSE 1776.776753 1698.175063 1656.131176 1136.486887 1468.050817 1395.917133 1339.358399 1618.40938 1496.774411 1541.28902 1.152786226 1.101788854 1.074510462 0.737361308 0.952482499 0.905681618 0.868985883 1.050036274 0.971118584 1 10.5899217 -9.395444998 14.5219404 1.076946706 0.903939413 0.441866071 0.087271433 0.641329894 71.52385745 0.013462382 0.020564212 4.02E-10 9.395444998 -0.173007293 VSILESLDKWER ddPTM_HeLa_Romidepsin_16h_R1 2 VSILESLDKWER 12 1 K7EPB2;P10644-2;P10644;K7EM13 K7EPB2 PRKAR1A "cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP-dependent protein kinase type I-alpha regulatory subunit, N-terminally processed" 0 0 ; ; 129.74 0.0046643 12977300 4088.8 3589.8 4474.9 4422.8 4815.4 4262.8 3269.7 3287.2 3720.7 3058.6 FALSE FALSE TRUE 4038.964133 3640.337299 4552.783757 4934.184946 4569.652169 3990.420838 3547.428236 3382.309946 3387.911273 2979.137131 1.355749653 1.221943515 1.528222286 1.656246332 1.533884467 1.339455239 1.190756948 1.135332077 1.137212261 1 11.54067882 -11.95598443 0.672982595 0.985442284 1.384785714 0.350682528 0.160964865 0.636787298 0.508917924 0.139454918 0.038695847 1.11E-12 11.95598443 0.399343431 VSLDVNHFAPDELTVK ddPTM_HeLa_Romidepsin_16h_R1 1 VSLDVNHFAPDELTVK 16 0 P04792;F8WE04 P04792 HSPB1 Heat shock protein beta-1 0 0 91.657 0.0066535 334780 386.24 229.83 250.98 273.45 256.88 177.47 301.76 301.88 333.12 338.31 FALSE FALSE TRUE 381.5323583 233.0655528 255.3482016 305.0675756 243.770455 166.1302398 327.3914869 310.6144215 303.3249129 329.5206574 1.157840487 0.707286622 0.774908024 0.925791961 0.739772908 0.504157284 0.993538582 0.942625036 0.920503483 1 8.364225099 -10.26214551 24.99975878 1.074535787 0.796246537 0.326529167 0.144992644 43.18462884 1528886.523 0.024324714 0.028715674 5.47E-11 10.26214551 -0.27828925 VSLEPHQGPGT(ph)PESK ddPTM_HeLa_Romidepsin_16h_R1 1 VSLEPHQGPGTPESK 15 0 A0A087WY61;Q14980-2;Q14980;Q14980-5;H0YFY6 A0A087WY61 NUMA1 Nuclear mitotic apparatus protein 1 1 0 VSLEPHQGPGT(0.999)PES(0.001)K 201.57 7.79E-18 27555000 3304.1 3400.9 2838.2 2436.2 3161.2 3399.4 2204.7 1763.8 4815.9 4440.2 TRUE FALSE FALSE 3263.828358 3448.777959 2887.59768 2717.884907 2999.872168 3182.189311 2391.967163 1814.83277 4385.153842 4324.842964 0.754669796 0.797434263 0.667676886 0.628435513 0.693637247 0.735793031 0.553076073 0.41962975 1.013945218 1 12.07843203 -11.15235009 0.075097098 1.64463116 1.98E-18 0.857214417 0.06563855 7.952754392 0.319238747 3.868687787 2.976998891 7.04E-12 11.15235009 -1.64463116 VSLLGPVT(ph)TPEHQLLK ddPTM_HeLa_Romidepsin_16h_R1 2 VSLLGPVTTPEHQLLK 16 0 Q9H0H5 Q9H0H5 RACGAP1 Rac GTPase-activating protein 1 1 0 VSLLGPVT(0.5)T(0.5)PEHQLLK;VSLLGPVT(0.632)T(0.368)PEHQLLK ; 162.15 6.84E-05 60030000 6558.9 6286.3 7099.7 5579.1 4765.4 4133.5 4572 4614.7 8100.3 6943.4 TRUE FALSE FALSE 6478.957604 6374.798696 7223.2673 6224.181792 4522.203856 3869.38269 4960.345566 4748.219064 7375.78888 6763.009467 0.957999192 0.942597926 1.068055181 0.920327233 0.668667385 0.57213918 0.733452406 0.70208671 1.090607505 1 12.72344966 -8.815715682 4.201472224 0.982476022 0.664897192 0.87597351 0.06061511 0.045050793 1.631870003 0.007369717 0.014049406 1.53E-09 8.815715682 -0.31757883 SEEIS(ph)ESESEETNAPK ddPTM_HeLa_Romidepsin_16h_R1 1 SEEISESESEETNAPK 16 0 P54259 P54259 ATN1 Atrophin-1 1 0 SEEIS(1)ESESEETNAPK 164.7 3.51E-05 13008000 3815.9 3284.7 3735.9 3131.7 3159.5 2539.7 2189.5 1990.6 4183 4431.5 TRUE FALSE FALSE 3769.390343 3330.942093 3800.921772 3493.801889 2998.258925 2377.421367 2375.476075 2048.19487 3808.862003 4316.368991 0.873278061 0.771700033 0.880583143 0.809430773 0.694625258 0.550791967 0.550341289 0.474518021 0.882422706 1 12.07560249 -7.219315306 0.266970422 0.996681271 2.68E-16 0.893931062 0.0539864 1.675142528 0.090594641 0.029358877 0.552390414 6.04E-08 7.219315306 -0.996681271 down RPS(ph)ASSPNNNTAAK ddPTM_HeLa_Romidepsin_16h_R1 1 RPSASSPNNNTAAK 14 1 O75151;E7ET14;A0A087WW48 O75151 PHF2 Lysine-specific demethylase PHF2 1 0 RPS(0.549)AS(0.113)S(0.338)PNNNTAAK 77.795 0.011861 2066100 2099.3 1979.4 2273.8 1665.3 1480.9 1512 1661.4 567.09 2800.7 2293 TRUE FALSE FALSE 2073.712924 2007.266045 2313.374535 1857.849821 1405.324147 1415.38808 1802.519275 583.4978544 2550.198378 2233.427529 0.928489014 0.898737935 1.035795657 0.83183797 0.629223079 0.633729128 0.807064143 0.261256677 1.141831711 1 11.12504373 -7.207232569 0.429777078 0.981118768 1.21E-18 0.725189375 0.126684909 1.989879543 0.23929489 0.027534947 1.005468966 6.21E-08 7.207232569 -0.981118768 down VSMPDVELNLKS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 VSMPDVELNLKSPK 14 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VS(0.02)MPDVELNLKS(0.98)PK 133.87 0.0060241 73999000 4817.2 6228.3 4892.5 4814.6 6090.5 5411 4791.6 5432.7 5441.9 4673 TRUE FALSE FALSE 4758.486114 6315.982171 4977.65191 5371.286705 5779.679058 5065.254563 5198.598384 5589.886603 4955.162835 4551.594786 1.045454689 1.387641578 1.093606119 1.180088948 1.269814061 1.112852703 1.142148769 1.228116048 1.088665197 1 12.15215641 -10.48813545 22.19944196 1.020053213 1.195514777 0.422940924 0.083012017 65.01939005 41545.45991 0.013022435 0.01444765 3.25E-11 10.48813545 0.175461564 VSNS(ph)PEPQKAVEQEDELSDVSQGGSK ddPTM_HeLa_Romidepsin_16h_R1 1 VSNSPEPQKAVEQEDELSDVSQGGSK 26 1 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 VS(0.121)NS(0.878)PEPQKAVEQEDELSDVSQGGSK 97.068 2.98E-06 14702000 2555.5 2452.7 2278.9 3838.6 3169.6 2752.9 2741.3 2342.3 2940.4 2429.9 TRUE FALSE FALSE 2524.352583 2487.229175 2318.563299 4282.436993 3007.843485 2576.998575 2974.145954 2410.070755 2677.40326 2366.770848 1.066580901 1.050895644 0.97963151 1.80940077 1.270863839 1.088824707 1.256626072 1.01829493 1.131247354 1 11.20870431 VSNSPEPQKAVEQEDELS(ph)DVSQGGSK ddPTM_HeLa_Romidepsin_16h_R1 1 VSNSPEPQKAVEQEDELSDVSQGGSK 26 1 O60271;O60271-3;D6RHI8 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 VS(0.036)NS(0.324)PEPQKAVEQEDELS(0.622)DVS(0.017)QGGSK 53.551 0.005822 12731000 1228.4 1141.3 1249.4 1749 1511.6 1648.3 1473.2 1311.8 1611.9 1503.6 TRUE FALSE FALSE 1213.427788 1157.367251 1271.145283 1951.227609 1434.457411 1542.97895 1598.333571 1349.754863 1467.727627 1464.536255 0.828540628 0.790261933 0.86795071 1.332317723 0.979461865 1.053561456 1.091358145 0.921626118 1.0021791 1 10.51622819 VSPAS(ph)PAGS(ph)PSADFAVHGESLGDR ddPTM_HeLa_Romidepsin_16h_R1 2 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-4;Q96C92-3;Q96C92-2;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 2 0 VS(0.007)PAS(0.969)PAGS(0.992)PS(0.032)ADFAVHGESLGDR;VS(0.027)PAS(0.973)PAGS(0.994)PS(0.006)ADFAVHGESLGDR ; 99.446 9.50E-05 26235000 4057.2 3854.8 3564.3 3163.5 3788.6 3958.4 2847.3 3217.5 3924.3 4417.9 TRUE FALSE FALSE 4007.749286 3909.067976 3626.335146 3529.278755 3595.253605 3705.471015 3089.149591 3310.593286 3573.300779 4303.122321 0.931358439 0.908425948 0.842721837 0.82016696 0.835498816 0.861112174 0.71788561 0.769346776 0.830397212 1 12.07116814 -8.694615433 0.224985197 1.027498836 0.637072383 0.349111235 0.061508118 1.360535828 0.11342788 0.039402688 0.1575161 2.02E-09 8.694615433 -0.390426453 VSPAS(ph)PAGSPSADFAVHGESLGDR ddPTM_HeLa_Romidepsin_16h_R1 2 VSPASPAGSPSADFAVHGESLGDR 24 0 A0A0A0MRP9;Q96C92-4;Q96C92-3;Q96C92-2;Q96C92 A0A0A0MRP9 SDCCAG3 Serologically defined colon cancer antigen 3 1 0 VS(0.064)PAS(0.839)PAGS(0.097)PSADFAVHGESLGDR;VS(0.035)PAS(0.954)PAGS(0.011)PSADFAVHGESLGDR ; 113.87 1.66E-06 21761900 2773.96 2369.23 2243.65 1954.37 2970.9 2976.3 2661.8 2636.1 3131.3 2822.68 TRUE FALSE FALSE 2740.149909 2402.584082 2282.699787 2180.343455 2819.283887 2786.124036 2887.893226 2712.371394 2851.228686 2749.346367 0.996655038 0.873874646 0.830269992 0.793040659 1.025437872 1.013376877 1.050392654 0.986551359 1.037056924 1 11.42487296 VSPASESPFS(ph)EEESR ddPTM_HeLa_Romidepsin_16h_R1 1 VSPASESPFSEEESR 15 0 E9PPC2;E9PJ11;E9PI48;E9PRH8;E9PLB9;E9PN31;E9PL66;E9PNN9;A0A0C4DG86;Q9NX95-4;Q9NX95-3;Q9NX95 E9PPC2 SYBU Syntabulin 1 0 VSPASES(0.001)PFS(0.998)EEES(0.001)R 141.06 0.00072217 4409100 751.12 862.24 834.11 665.42 920.05 725.23 468.77 670.84 696.71 698.9 TRUE FALSE FALSE 741.9650605 874.3786374 848.6273347 742.3589913 873.0964153 678.8901436 508.5873121 690.249697 634.3945127 680.7424772 1.089935013 1.284448476 1.246620217 1.090513691 1.282564912 0.997278951 0.747106768 1.013965956 0.931915568 1 9.410965324 -7.996928451 24.92455285 1.096901822 0.878450417 0.367338577 0.128209015 80.38136274 652236.6551 0.018112083 0.053923449 1.01E-08 7.996928451 -0.218451405 VSPLNLSSVT(ph)P ddPTM_HeLa_Romidepsin_16h_R1 1 VSPLNLSSVTP 11 0 Q9UJX2-3;Q9UJX2 Q9UJX2-3 CDC23 Cell division cycle protein 23 homolog 1 0 VSPLNLSSVT(1)P 134.75 0.0085102 9233500 3017.4 2241.1 2676.8 2030.1 2465.4 1951.4 1908.5 2017 2292.3 2239.3 TRUE FALSE FALSE 2980.622768 2272.650265 2723.388581 2264.829714 2339.581438 1826.711838 2070.607942 2075.358713 2087.270947 2181.122663 1.366554398 1.041963528 1.2486178 1.038377966 1.072650098 0.837509907 0.949331267 0.951509398 0.956970913 1 11.09085519 -8.717185848 1.652678758 1.169971517 0.919281735 0.269687379 0.125706883 0.311863447 1.71966317 0.022560983 0.054881777 1.92E-09 8.717185848 -0.250689781 VSPS(ph)KSPSLSPS(ph)PPSPLEK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPSKSPSLSPSPPSPLEK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VS(0.219)PS(0.314)KS(0.105)PS(0.305)LS(0.128)PS(0.896)PPS(0.032)PLEK 78.451 0.019157 21976000 2883.3 2526.5 2570.7 2551.9 2192.9 2556.9 2124.5 2260.5 3128.5 2947.1 TRUE FALSE FALSE 2848.157231 2562.068133 2615.441955 2846.962685 2080.98813 2393.522342 2304.954977 2325.904001 2848.679125 2870.533917 0.992204695 0.892540624 0.911134315 0.991788555 0.724948107 0.83382479 0.802970821 0.810268775 0.992386506 1 11.48710339 -9.227265338 0.680609244 0.999153272 0.787768219 0.642684098 0.056043108 0.30522533 0.273412701 0.01144222 0.030172564 5.93E-10 9.227265338 -0.211385053 VSPSKS(ph)PSLSPSPPS(ph)PLEK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPSKSPSLSPSPPSPLEK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VS(0.055)PS(0.379)KS(0.453)PS(0.108)LS(0.004)PS(0.001)PPS(0.999)PLEK 97.839 0.0035396 41722000 3692.6 3452.3 3116.5 3598.4 4026 3984.8 3588.1 4654.9 3519 3633.5 TRUE FALSE FALSE 3647.593171 3500.90157 3170.741375 4014.463939 3820.538197 3730.18414 3892.873124 4789.582187 3204.251827 3539.101146 1.030655248 0.989206419 0.895917139 1.13431738 1.079522183 1.053991956 1.099960969 1.353332948 0.905385773 1 11.78916728 -4.000000011 0.771552395 1.01264233 69.33872558 0.714075918 0.066259809 145.7495722 0.539501923 0.009005575 17368.72434 1.00E-04 4.000000011 68.32608325 VSPSKSPS(ph)LSPSPPS(ph)PLEK ddPTM_HeLa_Romidepsin_16h_R1 1 VSPSKSPSLSPSPPSPLEK 19 1 P46821 P46821 MAP1B Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 2 0 VS(0.038)PS(0.229)KS(0.276)PS(0.403)LS(0.046)PS(0.009)PPS(0.999)PLEK 98.766 0.0030344 30689000 2383.9 2357.3 2241.7 2638.9 2996.3 2839.2 2375.2 2800.3 2543.7 2287.6 TRUE FALSE FALSE 2354.84411 2390.486131 2280.715848 2944.022034 2843.38763 2657.784283 2576.949429 2881.322262 2316.185101 2228.167822 1.05685222 1.072848332 1.023583514 1.321274818 1.276110175 1.192811536 1.156532916 1.293135209 1.039502087 1 11.12164218 -9.273901396 24.90966192 1.031488263 1.241391588 0.824128884 0.048267317 229.9023746 459538.7766 0.007960376 0.012214758 5.32E-10 9.273901396 0.209903324 VSPSTSYT(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 VSPSTSYTPSR 11 0 Q9BTE3;Q9BTE3-2 Q9BTE3 MCMBP Mini-chromosome maintenance complex-binding protein 1 0 VSPSTSYT(0.999)PS(0.001)R 160.72 0.0026476 60148000 1484.9 1341.5 1527.3 1095.7 1583.4 1579.1 1168.8 1197.1 1597.6 1342.2 TRUE FALSE FALSE 1466.801468 1360.385672 1553.882016 1222.389989 1502.59319 1478.200606 1268.077843 1231.7362 1454.706655 1307.329451 1.121983037 1.040583666 1.188592527 0.935028266 1.149360774 1.130702445 0.969975734 0.942177352 1.112731496 1 10.35240703 -7.630223088 6.645567922 1.068496332 0.949329502 0.317535066 0.072827659 0.195613756 10.54623447 0.010192244 0.038975033 2.34E-08 7.630223088 -0.11916683 VSQGSAESLS(ph)PSFR ddPTM_HeLa_Romidepsin_16h_R1 2 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 VSQGS(0.006)AES(0.204)LS(0.532)PS(0.257)FR;VSQGSAES(0.01)LS(0.985)PS(0.004)FR ; 173.19 6.02E-06 0 2173.9 2351.8 2093.5 2295.1 4312.6 4684.7 3991.5 4812.1 2678.1 2141.22 TRUE FALSE FALSE 2147.403671 2384.908702 2129.936489 2560.470261 4092.511929 4385.362789 4330.53791 4951.330521 2438.564029 2085.590796 1.029638065 1.143517083 1.021262893 1.227695417 1.962279436 2.102695696 2.076408238 2.374066155 1.169243762 1 11.02624041 -8.751314663 2.240960684 1.025048359 2.177201998 0.96562243 0.09604087 0.030357528 0.310896772 0.012445064 0.026925127 1.77E-09 8.751314663 1.152153639 up VSQGSAESLSPS(ph)FR ddPTM_HeLa_Romidepsin_16h_R1 1 VSQGSAESLSPSFR 14 0 Q86YV5 Q86YV5 SGK223 Tyrosine-protein kinase SgK223 1 0 VSQGSAES(0.133)LS(0.209)PS(0.658)FR 110.6 0.0053671 29346000 1090.2 917.67 938.32 1125.9 2347.1 2290.6 1698.5 2310.8 1192.9 1029.6 TRUE FALSE FALSE 1076.912223 930.5889823 954.651066 1256.081856 2227.318729 2144.238053 1842.770548 2377.659352 1086.204036 1002.850844 1.073850842 0.92794356 0.951937242 1.252511142 2.220987042 2.138142543 1.837532031 2.370900286 1.083116241 1 9.969891331 -8.846509822 4.245760271 1.023617244 2.121651839 0.939911068 0.136299215 0.034042263 1.144852456 0.018947665 0.035690747 1.42E-09 8.846509822 1.098034595 up VSQLLAVTGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VSQLLAVTGKK 11 1 J3KS23;Q13951 J3KS23 CBFB Core-binding factor subunit beta 0 1 ; VSQLLAVTGK(1)K;VSQLLAVTGK(1)K 155.99 0.0016823 1377110 843.62 875.18 1222.67 1050.87 1027.82 819.25 643.4 843.06 1149.61 729.31 FALSE TRUE FALSE 833.337635 887.500807 1243.950058 1172.376534 975.3665101 766.902569 698.0503799 867.452611 1046.786002 710.3624211 1.173116159 1.249363396 1.751148458 1.650392108 1.373054769 1.079593383 0.982667944 1.221140907 1.473594283 1 9.472411453 -10.65849826 1.56884215 1.055985323 1.333113756 0 0.257878109 0.428940323 2.176703259 0.052607697 0.053029687 2.20E-11 10.65849826 0.277128433 VSQSALNPHQS(ph)PDFKR ddPTM_HeLa_Romidepsin_16h_R1 2 VSQSALNPHQSPDFKR 16 1 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 0 VSQSALNPHQS(1)PDFKR;VSQSALNPHQS(1)PDFKR ; 74.742 0.009799 29651000 3268.4 3561.5 3291.3 3403.2 3220.1 2562.64 2546.3 2529.85 4357.6 3553.2 TRUE FALSE FALSE 3228.563484 3611.63889 3348.583696 3796.693997 3055.766281 2398.895575 2762.582658 2603.047218 3967.845342 3460.887352 0.932871589 1.043558638 0.967550618 1.097029059 0.882943006 0.693144656 0.79822958 0.752132894 1.146482084 1 11.75692627 -8.49598984 5.625623469 0.982308883 0.75650316 0.737810222 0.072644074 0.059517804 5.702858083 0.00755903 0.016568729 3.19E-09 8.49598984 -0.225805724 VSS(ph)PAPMEGGEEEEELLGPK ddPTM_HeLa_Romidepsin_16h_R1 1 VSSPAPMEGGEEEEELLGPK 20 0 O14497-2;O14497;H0Y488;A0A1B0GTU5;O14497-3 O14497-2 ARID1A AT-rich interactive domain-containing protein 1A 1 0 VS(0.035)S(0.965)PAPMEGGEEEEELLGPK 173.45 3.85E-11 17313000 8678.2 8788.2 8870 5086.2 6653.5 7667 5842.9 6478.1 8224.3 8088.3 TRUE FALSE FALSE 8572.42676 8911.92051 9024.378629 5674.290375 6313.947067 7177.103444 6339.19578 6665.533603 7488.69801 7878.1648 1.088124833 1.131217833 1.145492492 0.720255354 0.80144897 0.911012098 0.804653868 0.846076945 0.950563767 1 12.94364388 -9.26327951 24.99999642 1.057899906 0.820414257 0.758182112 0.069527993 62.88973112 854420.121 0.010578434 0.016679188 5.45E-10 9.26327951 -0.237485649 VSS(ph)PLSPLS(ph)PGIKSPTIPR ddPTM_HeLa_Romidepsin_16h_R1 1 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 2 0 VS(0.162)S(0.716)PLS(0.142)PLS(0.466)PGIKS(0.287)PT(0.227)IPR 73.11 0.0027077 0 1506 1496 1319.9 1498.7 1863.9 1696.8 1250.8 1651.8 1632.3 1185.4 TRUE FALSE FALSE 1487.644293 1517.060727 1342.872306 1671.986746 1768.778228 1588.379956 1357.042921 1699.592227 1486.303 1154.603137 1.288446432 1.313923961 1.163059637 1.448105147 1.531936101 1.375693435 1.175332785 1.472014212 1.287284741 1 10.17318133 -12.09833432 0.348760345 0.882793204 1.387775386 0.168069744 0.139977267 1.411012627 0.248273749 0.27877398 0.051595267 7.97E-13 12.09833432 0.504982182 VSS(ph)PVFGATSSIK ddPTM_HeLa_Romidepsin_16h_R1 1 VSSPVFGATSSIK 13 0 F6Q6H0;I6L8A6;Q99708-3;Q99708;Q99708-2 F6Q6H0 RBBP8 DNA endonuclease RBBP8 1 0 VS(0.035)S(0.965)PVFGATSSIK 99.941 0.012774 39789000 3434.4 3150.1 3981.6 4141.3 2079.7 2041 1537.3 1526.8 3476.6 3236.5 TRUE FALSE FALSE 3392.540212 3194.44719 4050.898078 4620.136591 1973.565149 1910.586687 1667.878224 1570.975549 3165.644189 3152.415263 1.076171738 1.013333246 1.285014105 1.46558629 0.626048596 0.606070751 0.529079479 0.498340294 1.004196441 1 11.62224188 -8.618160009 8.54843675 1.082268426 0.55514449 0.785906217 0.145743237 0.10185622 8.145095857 0.022710455 0.045492269 2.41E-09 8.618160009 -0.527123936 VSS(ph)QAEDTSSSFDNLFIDR ddPTM_HeLa_Romidepsin_16h_R1 1 VSSQAEDTSSSFDNLFIDR 19 0 H8Y6P7;P0CAP2-3;P0CAP2;Q9BZD3 H8Y6P7 GCOM1;POLR2M;GCOM2 DNA-directed RNA polymerase II subunit GRINL1A;Putative GRINL1B complex locus protein 2 1 0 VS(0.031)S(0.969)QAEDTSSSFDNLFIDR 201.52 4.37E-21 3347700 933.87 640.94 885.73 657.13 1002.8 759.61 599.54 978.87 835.82 877.59 TRUE FALSE FALSE 922.4876332 649.9631701 901.1457591 733.1104625 951.623374 711.0733725 650.4649126 1007.192059 761.0621659 854.7900853 1.079197863 0.760377526 1.054230477 0.857649703 1.113283121 0.831868999 0.760964503 1.178291696 0.890349782 1 9.739426364 VSSPLSPLS(ph)PGIK ddPTM_HeLa_Romidepsin_16h_R1 1 VSSPLSPLSPGIK 13 0 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 VSS(0.004)PLS(0.179)PLS(0.817)PGIK 133.15 0.0018909 9784900 1743.3 2275.2 1839.8 1717.5 1981.7 1650.7 1644.4 1459.7 2316 2093.9 TRUE FALSE FALSE 1722.051989 2307.230325 1871.820947 1916.085431 1880.566454 1545.225597 1784.075295 1501.934116 2108.851159 2039.500176 0.844350008 1.131272432 0.917784156 0.93948775 0.92207222 0.757649161 0.87476104 0.736422646 1.034003911 1 10.99399992 -8.349507482 5.365749294 0.941407421 0.798532596 0.473373289 0.083398157 0.183727896 8.568019925 0.012371925 0.028235827 4.47E-09 8.349507482 -0.142874825 VSSPLSPLSPGIKS(ph)PTIPR ddPTM_HeLa_Romidepsin_16h_R1 3 VSSPLSPLSPGIKSPTIPR 19 1 Q9P2B4 Q9P2B4 CTTNBP2NL CTTNBP2 N-terminal-like protein 1 0 VSSPLSPLS(0.008)PGIKS(0.983)PT(0.009)IPR;VSSPLSPLSPGIKS(0.912)PT(0.088)IPR;VSSPLS(0.012)PLS(0.001)PGIKS(0.907)PT(0.081)IPR ;; 297.63 1.11E-142 1272822000 8847.7 7929.7 8046.4 9153.9 9672.7 8541.2 7903.5 8887.3 8535.7 9125 TRUE FALSE FALSE 8739.860829 8041.334525 8186.444217 10212.31699 9179.066025 7995.444885 8574.823093 9144.440004 7772.245614 8887.931185 0.98334029 0.904747613 0.921074213 1.149009457 1.032756199 0.899584472 0.964771544 1.028860352 0.874471849 1 13.11763193 -7.237379183 21.43817175 0.987052131 1.028860677 0.008132732 0.077748903 3040.50518 2708851.158 0.009445421 0.558053826 5.79E-08 7.237379183 0.041808546 VSSQS(ph)FSEIER ddPTM_HeLa_Romidepsin_16h_R1 1 VSSQSFSEIER 11 0 Q8N6H7;E9PQP3;A0A0D9SF70;G5E9L0;Q8N6H7-2;E9PIY6 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 0 VS(0.016)S(0.002)QS(0.812)FS(0.17)EIER 115.12 0.012249 6611100 1949.1 2084.7 1441.8 1298.1 1173.3 1676.7 1154 1612.4 2487.2 2636.7 TRUE FALSE FALSE 1925.34362 2114.048461 1466.893924 1448.19243 1113.422123 1569.564281 1252.020731 1659.05225 2264.738603 2568.198154 0.749686552 0.823164076 0.571176302 0.56389435 0.43354214 0.611153886 0.487509396 0.645998537 0.88183951 1 11.32654081 -10.68177969 0.427048203 1.000139992 0.514147371 0.755740641 0.085230971 0.287056559 0.138771196 0.051394116 0.040694038 2.08E-11 10.68177969 -0.485992621 VSSVFK(ac)DEATVR ddPTM_HeLa_Romidepsin_16h_R1 1 VSSVFKDEATVR 12 1 P46060 P46060 RANGAP1 Ran GTPase-activating protein 1 0 1 VSSVFK(1)DEATVR 142.1 0.00087166 460870 0 0 0 0 151.43 106.91 60.838 0 163.3 0 FALSE TRUE FALSE 0 0 0 0 143.701962 100.078796 66.0055782 0 148.694039 0 0 VSTAVLSITAK ddPTM_HeLa_Romidepsin_16h_R1 1 VSTAVLSITAK 11 0 A0A087WW66;Q99460-2;Q99460 A0A087WW66 PSMD1 26S proteasome non-ATPase regulatory subunit 1 0 0 150.1 0.011253 262040 124.15 107.14 297.1 0 300.79 120.24 251.3 148.94 211.07 225.44 FALSE FALSE TRUE 122.636812 108.6483197 302.2709009 0 285.4395639 112.5570521 272.6454157 153.2493439 192.1913706 219.5830363 0.558498571 0.494793776 1.376567635 0 1.299916281 0.512594479 1.241650632 0.69791067 0.875256002 1 7.778622794 -7.763501905 24.99958141 0.772783382 0.969780557 0.039108941 0.405026909 142.7510839 1730379.501 0.05144556 0.166426053 1.72E-08 7.763501905 0.196997175 VSVGAPDLSLEASEGS(ph)IKLPK ddPTM_HeLa_Romidepsin_16h_R1 2 VSVGAPDLSLEASEGSIKLPK 21 1 Q09666 Q09666 AHNAK Neuroblast differentiation-associated protein AHNAK 1 0 VSVGAPDLS(0.001)LEAS(0.047)EGS(0.952)IKLPK;VSVGAPDLS(0.001)LEAS(0.099)EGS(0.9)IKLPK ; 65.387 0.0036514 89776000 6664.1 7998 7129.4 6958.7 5657.3 6381.1 4784.6 5532.4 6649.8 6508.5 TRUE FALSE FALSE 6582.875386 8110.596054 7253.484216 7763.297636 5368.586871 5973.368304 5191.003805 5692.471265 6055.025233 6339.408232 1.038405344 1.279393243 1.144189481 1.224609199 0.846859308 0.942259606 0.818846746 0.897949944 0.95514045 1 12.63013246 -8.731306594 24.99782494 1.063738675 0.877060834 0.527047605 0.102149326 162.4489756 134765.2028 0.016099946 0.032196674 1.86E-09 8.731306594 -0.186677841 VSVS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 1 VSVSPGR 7 0 A9Z1X7;Q8IYB3;E9PCT1;Q8IYB3-2;M0R088 A9Z1X7;M0R088 SRRM1 Serine/arginine repetitive matrix protein 1 1 0 VS(0.021)VS(0.979)PGR 136.99 0.0222 54451000 19957 20662 17081 14515 18244 17958 16234 11601 21617 20548 TRUE FALSE FALSE 19713.75641 20952.88018 17378.28764 16193.2926 17312.9406 16810.54176 17612.91555 11936.65663 19683.52138 20014.16 0.984990447 1.046902802 0.868299626 0.809091793 0.865034586 0.839932416 0.880022722 0.596410573 0.983479765 1 14.28873345 -5.820666348 0.291951295 1.009772718 2.28E-16 0.696515922 0.067662413 7.255475279 0.234975461 0.028607326 3.088517204 1.51E-06 5.820666348 -1.009772718 VSVTPPEESQNSDT(ph)PPRPDR ddPTM_HeLa_Romidepsin_16h_R1 1 VSVTPPEESQNSDTPPRPDR 20 1 Q05209-2;Q05209-3;Q05209;H3BM04 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 VS(0.001)VT(0.004)PPEES(0.015)QNS(0.254)DT(0.726)PPRPDR 58.516 0.015772 9782100 2243.1 1842.5 2574 1807.5 1894.6 1858.9 1296.6 1757.2 2321.3 2127.7 TRUE FALSE FALSE 2215.760234 1868.438763 2618.79939 2016.491655 1797.911492 1740.122289 1406.733172 1808.04181 2113.677114 2072.422047 1.069164574 0.901572518 1.263641927 0.973012064 0.867541192 0.839656329 0.678787013 0.872429345 1.019906692 1 11.01710212 -8.67093918 2.399461922 1.039515871 0.789278921 0.569778207 0.097588215 0.1510554 1.763854411 0.013791808 0.030616475 2.13E-09 8.67093918 -0.25023695 VSVTPPEESQNSDT(ph)PPRPDRLPLDEK ddPTM_HeLa_Romidepsin_16h_R1 1 VSVTPPEESQNSDTPPRPDRLPLDEK 26 2 Q05209-2;Q05209-3;Q05209;H3BM04 Q05209-2 PTPN12 Tyrosine-protein phosphatase non-receptor type 12 1 0 VS(0.001)VT(0.002)PPEES(0.202)QNS(0.157)DT(0.637)PPRPDRLPLDEK 51.398 0.0079719 7228600 4072 4337.3 3996.1 3915.5 3682.1 3537 2697.9 3155.4 4719.4 4587.7 TRUE FALSE FALSE 4022.368898 4398.360623 4065.650444 4368.228533 3494.188697 3310.997115 2927.059559 3246.696521 4297.285044 4468.510893 0.900158687 0.984301198 0.909844586 0.977557991 0.781958192 0.740962078 0.655041384 0.726572364 0.961681676 1 12.12557843 -8.581741243 2.458557884 0.952928939 0.70145096 0.900008248 0.037844649 0.073684882 0.895866744 0.006709456 0.015547013 2.62E-09 8.581741243 -0.251477979 VT(ph)NDISPESSPGVGR ddPTM_HeLa_Romidepsin_16h_R1 1 VTNDISPESSPGVGR 15 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154;E9PGW9;E5RGQ4;Q15154-3 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 VT(0.977)NDIS(0.002)PES(0.021)SPGVGR 185.86 1.74E-08 20266000 3336.5 3511.8 2971.2 2895.1 3678.5 3058.4 2944.7 3398.1 3753.9 3175.3 TRUE FALSE FALSE 3295.833455 3561.239213 3022.91249 3229.845084 3490.772419 2862.978111 3194.822744 3496.418662 3418.141782 3092.805248 1.065645325 1.15145925 0.9774015 1.044309235 1.128675147 0.925689748 1.032985425 1.130500753 1.105191406 1 11.59470028 -12.26492515 1.102307778 1.001308667 1.054556036 0 0.073698679 0.986191347 2.22316549 0.038118183 0.011448865 5.43E-13 12.26492515 0.05324737 VT(ph)S(ph)SITIYPSDSS(ph)S(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VTSSITIYPSDSSSPR 16 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 4 0 VT(0.704)S(0.731)S(0.208)IT(0.216)IY(0.046)PS(0.09)DS(0.005)S(1)S(1)PR 61.186 0.026039 10514000 609.32 838.29 751.99 649.07 473.61 394.07 432.22 655.9 618.21 727.18 TRUE FALSE FALSE 601.8933735 850.0914686 765.0780705 724.1185274 449.4399144 368.8901988 468.932756 674.8774317 562.9157493 708.2877588 0.849786497 1.200206354 1.080179717 1.022350758 0.634544236 0.520819673 0.662065312 0.952829444 0.794755722 1 9.468191798 -8.760200896 24.99957446 0.968432372 0.678118607 0.492260731 0.147212863 22.47276514 453608.527 0.021848952 0.04183539 1.74E-09 8.760200896 -0.290313765 VTAEADSS(ph)SPTGILATSESK ddPTM_HeLa_Romidepsin_16h_R1 1 VTAEADSSSPTGILATSESK 20 0 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 VTAEADS(0.002)S(0.911)S(0.086)PTGILATSESK 276.62 6.62E-111 49019000 2963.4 3454.3 3564.8 3254.9 3767.2 3766 3371.4 3816.9 3370.7 3023.5 TRUE FALSE FALSE 2927.280941 3502.929726 3626.843849 3631.246853 3574.945727 3525.364754 3657.766632 3927.335979 3069.21615 2944.949034 0.994000544 1.189470407 1.231547238 1.233042342 1.213924481 1.197088545 1.242047516 1.333583683 1.042196695 1 11.52402695 -10.18567099 3.34824575 0.996303907 1.236886629 0.882286803 0.037413131 0.048045395 1.04577557 0.005924677 0.007234087 6.52E-11 10.18567099 0.240582722 VTAEADSSS(ph)PTGILATSESK ddPTM_HeLa_Romidepsin_16h_R1 3 VTAEADSSSPTGILATSESK 20 0 A0MZ66-4;A0MZ66;A0MZ66-3;A0MZ66-7;A0MZ66-8;A0MZ66-5;A0MZ66-6 A0MZ66-4 KIAA1598 Shootin-1 1 0 VTAEADS(0.004)S(0.024)S(0.905)PT(0.064)GILAT(0.003)S(0.001)ESK;VTAEADS(0.001)S(0.022)S(0.9)PT(0.072)GILAT(0.004)S(0.001)ESK;VTAEADS(0.002)S(0.013)S(0.759)PT(0.222)GILAT(0.004)SESK ;; 157.5 8.87E-08 71609000 8155.2 8412.8 8368.1 7464.7 9583.3 9683.8 9011.3 9698.7 9478.7 9034.5 TRUE FALSE FALSE 8055.801286 8531.235619 8513.74327 8327.803736 9094.228441 9065.036433 9776.719597 9979.316582 8630.901332 8799.782388 0.915454602 0.969482567 0.967494751 0.946364736 1.033460606 1.030143251 1.111018337 1.134041291 0.980808496 1 13.10325213 -7.954487633 1.00547725 0.959283487 1.153956896 0.848956029 0.025756884 0.280172084 0.405120275 0.005370217 0.045084281 1.11E-08 7.954487633 0.194673409 VTDK(ac)LTPIHDR ddPTM_HeLa_Romidepsin_16h_R1 1 VTDKLTPIHDR 11 1 I3L3X7;A0A087X2I4;P28072 I3L3X7 PSMB6 Proteasome subunit beta type;Proteasome subunit beta type-6 0 1 VTDK(1)LTPIHDR 96.745 0.01935 1283500 689.83 751.14 546.62 834.08 1359.9 1200.6 1119.4 1240.7 1533.1 1064.7 FALSE TRUE FALSE 681.4220866 761.7145686 556.1336918 930.5202541 1290.499229 1123.885535 1214.481808 1276.597697 1395.975696 1037.038941 0.657084377 0.734509129 0.53627079 0.897285741 1.244407686 1.083744776 1.171105308 1.231002663 1.346116951 1 10.01825435 -8.875714183 5.012405815 0.800737393 1.173273516 0.339805837 0.21217384 0.125448548 5.022026469 0.024506596 0.045289302 1.33E-09 8.875714183 0.372536123 VTEGLVDVILYHQPDDK ddPTM_HeLa_Romidepsin_16h_R1 2 VTEGLVDVILYHQPDDK 17 0 B4DT28;O43390-3;O43390 B4DT28 HNRNPR Heterogeneous nuclear ribonucleoprotein R 0 0 ; ; 146.3 6.79E-05 22363000 9422.2 9297.6 9122.5 6289.9 7907.9 8364.4 7895.7 8524.6 10702.4 9602.9 FALSE FALSE TRUE 9307.358602 9428.491857 9281.273286 7017.167833 7504.330355 7829.941835 8566.360561 8771.245851 9745.150539 9353.415274 0.995075951 1.008026649 0.992287097 0.750225199 0.802309118 0.837121159 0.915853761 0.937758626 1.041881522 1 13.19127753 -9.345537101 9.332432694 0.998343417 0.849255162 0.703066763 0.051434122 0.190035194 19.99429862 0.007997575 0.012222011 4.51E-10 9.345537101 -0.149088255 VTENLASLT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 VTENLASLTPK 11 0 Q96DF8 Q96DF8 DGCR14 Protein DGCR14 1 0 VTENLAS(0.001)LT(0.999)PK 113.53 0.026756 23892000 4461.9 4191.8 3709.3 3670.5 4092 4323.2 3914.1 4669.2 4284.4 4028.6 TRUE FALSE FALSE 4407.516647 4250.81227 3773.858811 4094.90048 3883.169971 4046.961472 4246.563556 4804.295935 3901.192534 3923.936391 1.123238556 1.083303052 0.961753309 1.043569536 0.989610836 1.031352466 1.082220284 1.224356222 0.994203816 1 11.93808594 -7.280900601 3.000095126 1.046992868 1.249263868 0.583553307 0.047960805 0.247877278 3.327324135 0.008026258 0.116672152 5.24E-08 7.280900601 0.202270999 VTFFEPGS(ph)GDENGTSNKEDEFR ddPTM_HeLa_Romidepsin_16h_R1 2 VTFFEPGSGDENGTSNKEDEFR 22 1 Q5JW30;O95793-2;O95793-3;O95793 Q5JW30 STAU1 Double-stranded RNA-binding protein Staufen homolog 1 1 0 VT(0.008)FFEPGS(0.87)GDENGT(0.094)S(0.029)NKEDEFR;VT(0.002)FFEPGS(0.977)GDENGT(0.01)S(0.011)NKEDEFR ; 47.507 0.025533 17561800 1695.86 1866.69 1621.78 1312.54 3699.5 5224.6 4098.9 5402 2035.6 2171 TRUE FALSE FALSE 1675.190206 1892.969311 1650.006401 1464.30205 3510.70071 4890.764922 4447.060464 5558.298347 1853.530838 2114.597107 0.792203016 0.895191479 0.780293511 0.692473306 1.660222034 2.312858986 2.103029674 2.628537762 0.876540894 1 11.0461671 -8.517673041 2.809227265 0.875779855 2.324847113 0.950588739 0.154657397 0.042204041 0.669556675 0.02358112 0.054953629 3.04E-09 8.517673041 1.449067258 up VTFGEDLS(ph)PEVFDESLPANTPLRK ddPTM_HeLa_Romidepsin_16h_R1 2 VTFGEDLSPEVFDESLPANTPLRK 24 1 E9PEI0;Q69YH5 E9PEI0 CDCA2 Cell division cycle-associated protein 2 1 0 VT(0.003)FGEDLS(0.997)PEVFDESLPANTPLRK;VT(0.011)FGEDLS(0.989)PEVFDESLPANTPLRK ; 105.68 3.69E-06 35663000 2278.6 2187.8 2418.6 2271.6 3569.6 4261.5 3373.1 3859 2216.9 2583.2 TRUE FALSE FALSE 2250.827547 2218.599906 2460.694718 2534.25308 3387.429992 3989.203903 3659.61103 3970.654077 2018.614912 2516.088092 0.894574222 0.881765592 0.977984327 1.007219536 1.346308185 1.585478631 1.45448446 1.578106144 0.802283083 1 11.29696672 -8.67222021 2.436441068 0.944974609 1.531354844 0.947712044 0.066062571 0.038637521 0.46518014 0.008346982 0.018450834 2.13E-09 8.67222021 0.586380235 VTFLIGDSMS(ph)PDSDTELR ddPTM_HeLa_Romidepsin_16h_R1 1 VTFLIGDSMSPDSDTELR 18 0 A0A087WX11;J3KNG8;Q8TF40-3;Q8TF40 A0A087WX11 FNIP1 Folliculin-interacting protein 1 1 0 VTFLIGDS(0.143)MS(0.857)PDSDTELR 122.55 0.002206 17034000 2177.2 2042.4 2364.4 1868.2 2928.9 3043.2 2944 3010.2 2773.8 2416.9 TRUE FALSE FALSE 2150.663449 2071.152961 2405.55139 2084.210074 2779.427304 2848.749341 3194.063287 3097.295388 2525.704381 2354.10859 0.913578693 0.879803493 1.021852348 0.885350015 1.180670814 1.210118069 1.356803718 1.315697756 1.072892046 1 11.20096515 -8.449292567 1.774150143 0.951574335 1.321917117 0.821206953 0.070068799 0.086807881 0.531067436 0.008927371 0.025508395 3.55E-09 8.449292567 0.370342782 VTGGAASK(ac)LSK ddPTM_HeLa_Romidepsin_16h_R1 2 VTGGAASKLSK 11 1 F2Z388;P42766 F2Z388 RPL35 60S ribosomal protein L35 0 1 ; VTGGAASK(1)LSK;VTGGAASK(1)LSK 172.61 0.0020618 25987000 5875.6 6543.3 6118.4 6451.7 6489.5 6678.3 4988 5079 5745.9 5125.3 FALSE TRUE FALSE 5803.985927 6635.416749 6224.888185 7197.67591 6158.316599 6251.578183 5411.680595 5225.952852 5231.972313 4992.143967 1.162623908 1.329171753 1.246936832 1.441800549 1.233601563 1.252283232 1.084039369 1.046835365 1.048041152 1 12.28544382 -11.31507118 0.946340184 1.023611723 1.23368079 0.356772608 0.107667609 0.385105735 0.720936934 0.038462334 0.024548491 4.84E-12 11.31507118 0.210069067 VTGMNLCTVIMVRETTMK ddPTM_HeLa_Romidepsin_16h_R1 1 VTGMNLCTVIMVRETTMK 18 1 F5H5G4 F5H5G4 WBP11 0 0 88.187 0.00085464 0 2468.8 2630.1 2358.1 2312.2 2417.8 2571.4 1852.9 2325 2382.1 2437 FALSE FALSE TRUE 2438.709316 2667.126617 2399.141741 2579.547443 2294.410644 2407.095839 2010.28528 2392.270207 2169.03901 2373.686389 1.027393226 1.123622156 1.010723975 1.086726307 0.966602267 1.014074922 0.84690433 1.007829096 0.913784997 1 11.21291362 -7.90750421 10.4781874 1.023296823 0.927459028 0.231634713 0.065546191 0.289738354 30.62822351 0.007285098 0.021899343 1.24E-08 7.90750421 -0.095837796 VTGTEGSSSTLVDYTSTS(ph)STGGSPVRK ddPTM_HeLa_Romidepsin_16h_R1 1 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 VTGTEGSSSTLVDYT(0.009)S(0.075)T(0.192)S(0.499)S(0.101)T(0.101)GGS(0.022)PVRK 78.025 2.72E-06 77769000 1266.2 1207.8 1326.7 1082.9 1489.5 1492.5 1264.3 1093.9 1552.7 1221.4 TRUE FALSE FALSE 1250.767067 1224.80344 1349.790657 1208.109993 1413.485257 1397.134067 1371.68961 1125.550271 1413.822623 1189.667852 1.051358213 1.029533948 1.134594547 1.015501925 1.188134364 1.174390032 1.153002166 0.946104637 1.188417944 1 10.21634312 -10.22040502 0.679499793 1.012439252 1.112472262 0 0.090642752 0.672554371 0.658922913 0.019277083 0.023613894 6.02E-11 10.22040502 0.10003301 VTGTEGSSSTLVDYTSTSSTGGS(ph)PVRK ddPTM_HeLa_Romidepsin_16h_R1 1 VTGTEGSSSTLVDYTSTSSTGGSPVRK 27 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 VTGTEGSSSTLVDYT(0.004)S(0.031)T(0.079)S(0.206)S(0.147)T(0.147)GGS(0.386)PVRK 83.479 1.36E-06 98219000 2804.4 3159.7 2889.1 3058.8 3399 3464.1 2775.6 3481.6 3289.5 3383.2 TRUE FALSE FALSE 2770.218894 3204.18234 2939.383574 3412.472848 3225.536347 3242.75519 3011.359395 3582.334603 2995.278881 3295.303976 0.840656557 0.972348033 0.891991633 1.035556317 0.978828166 0.984053433 0.913833569 1.087102929 0.908953742 1 11.68619584 -9.266361777 24.9442844 0.924936024 0.993046578 0.303282631 0.057911754 537.1180853 2721846.333 0.010832306 0.016875158 5.42E-10 9.266361777 0.068110554 VTHAVVTVPAYFNDAQR ddPTM_HeLa_Romidepsin_16h_R1 1 VTHAVVTVPAYFNDAQR 17 0 P11021 P11021 HSPA5 78 kDa glucose-regulated protein 0 0 119.54 0.00032845 3253000 1112.3 1108.4 891.62 924.86 975.38 1332.8 1025.8 1065.5 957.45 972.66 FALSE FALSE TRUE 1098.74286 1124.004084 907.1382721 1031.796665 925.602719 1247.638381 1112.931426 1096.328561 871.813274 947.390153 1.159757526 1.18642154 0.957512878 1.089093719 0.977002681 1.316921416 1.174734003 1.157209158 0.920226235 1 9.887814867 -16.52287875 0.268688013 0.074173295 1.14242876 0.294687168 0.100935958 59.56836234 0.799223671 29.51309467 0.051882673 3.00E-17 16.52287875 1.068255466 VTIADDYS(ph)DPFDAK ddPTM_HeLa_Romidepsin_16h_R1 1 VTIADDYSDPFDAK 14 0 Q15464;Q15464-2 Q15464 SHB SH2 domain-containing adapter protein B 1 0 VTIADDY(0.332)S(0.668)DPFDAK 119.77 0.0004553 0 1414.5 1267 1999.3 1424.5 1210.3 1376 972.38 1120 1788.7 1439.8 TRUE FALSE FALSE 1397.25953 1284.836859 2034.096978 1589.207392 1148.533875 1288.078041 1054.973933 1152.405433 1628.714192 1402.393788 0.996338932 0.916174095 1.450446369 1.133210519 0.818981005 0.918485272 0.752266547 0.821741684 1.161381493 1 10.4536758 -8.746124162 24.78194565 1.03750446 0.828941016 0.412482613 0.150630888 212.5345689 343905.5224 0.022246673 0.044356483 1.79E-09 8.746124162 -0.208563444 VTKNEEPS(ph)EEEIDAPKPK ddPTM_HeLa_Romidepsin_16h_R1 1 VTKNEEPSEEEIDAPKPK 18 2 Q9NR30;Q9NR30-2 Q9NR30 DDX21 Nucleolar RNA helicase 2 1 0 VT(0.003)KNEEPS(0.997)EEEIDAPKPK 52.769 0.029001 328560000 7434 6843.8 6005.9 7334.1 5185.4 4552 4885 5112.7 7405.6 6909.8 TRUE FALSE FALSE 7343.391549 6940.147196 6110.43017 8182.10315 4920.769689 4261.141891 5299.931778 5260.627908 6743.224588 6730.2824 1.091097091 1.031182168 0.907901007 1.215714685 0.731138665 0.633129732 0.787475393 0.781635539 1.001922979 1 12.71645133 -8.739514541 24.92808217 1.042567166 0.730052898 0.766253284 0.083316953 78.79090676 89583.17108 0.011606169 0.023196591 1.82E-09 8.739514541 -0.312514268 VTLDWAK(ac)PK ddPTM_HeLa_Romidepsin_16h_R1 1 VTLDWAKPK 9 1 P19338;H7BY16 P19338 NCL Nucleolin 0 1 VTLDWAK(1)PK 101.65 0.0045051 0 353.39 414.53 356.69 71.755 489.01 437.83 410.01 248.32 318.83 247.36 FALSE TRUE FALSE 349.0827468 420.3657642 362.8980398 80.05165072 464.053995 409.854076 444.8362392 255.5047474 290.3130463 240.9335515 1.448875611 1.744737342 1.506216289 0.332256135 1.926066303 1.701108349 1.846302586 1.060478069 1.204950678 1 7.912491502 -12.12703409 0.681563093 0.964106357 1.46131435 0.077250826 0.445127673 1.456791187 1.107800144 0.416407874 0.094974946 7.46E-13 12.12703409 0.497207993 VTLELGGK ddPTM_HeLa_Romidepsin_16h_R1 1 VTLELGGK 8 0 P30837;H0Y2X5;H0YMG7;O94788-4;O94788-2;O94788-3;P00352;P47895;O94788;P05091;P05091-2 P30837;P05091 ALDH1B1;ALDH1A3;ALDH1A2;ALDH1A1;ALDH2 "Aldehyde dehydrogenase X, mitochondrial;Retinal dehydrogenase 2;Retinal dehydrogenase 1;Aldehyde dehydrogenase family 1 member A3;Aldehyde dehydrogenase, mitochondrial" 0 0 110.12 0.022731 879250 1805.3 1310.8 1894.4 1774.4 2083.6 1542.1 1437.1 1453.1 1517.2 1321.2 FALSE FALSE TRUE 1783.296309 1329.253477 1927.371237 1979.564477 1977.266117 1443.564787 1559.167238 1495.143156 1381.497832 1286.875034 1.385757174 1.032931281 1.497714376 1.538272501 1.536486501 1.121759883 1.2115918 1.161840207 1.073529128 1 10.32965625 -12.38365347 0.837098313 0.975348708 1.320250101 0.286796793 0.17122251 0.744687004 0.821228641 0.175568625 0.034070142 4.13E-13 12.38365347 0.344901393 VTLLEGDHVR ddPTM_HeLa_Romidepsin_16h_R1 2 VTLLEGDHVR 10 0 O75534-2;O75534;O75534-3;O75534-4;E9PLT0 O75534-2 CSDE1 Cold shock domain-containing protein E1 0 0 ; ; 149.33 0.0017746 7626000 5421.8 4829.3 6516 4321.9 4909.5 4412.8 3860.9 4104.9 5563.8 5899.9 FALSE FALSE TRUE 5355.717016 4897.287012 6629.408247 4821.618413 4658.949895 4130.836322 4188.84475 4223.668805 5066.159793 5746.619747 0.931976928 0.852203074 1.153618742 0.839035577 0.810728759 0.718828895 0.728923251 0.734983171 0.881589528 1 12.48849787 -8.853522063 2.556630739 0.969576027 0.737237494 0.607117397 0.080966191 0.121857687 1.619085277 0.011049736 0.022166151 1.40E-09 8.853522063 -0.232338533 VTLSVLSR ddPTM_HeLa_Romidepsin_16h_R1 2 VTLSVLSR 8 0 O00625 O00625 PIR Pirin 0 0 ; ; 121.62 0.013206 1069860 510.51 354.91 600.61 433.51 594.99 521.61 458.45 148.89 189.94 148.61 FALSE FALSE TRUE 504.2877078 359.9064323 611.0633651 483.6344659 564.6254401 488.2808044 497.3907316 153.1978972 172.9512907 144.7490908 3.483874787 2.486415841 4.221535084 3.341191736 3.900718388 3.373290995 3.436226983 1.058368632 1.194835075 1 7.177410476 -12.25751569 0.789553527 0.863842863 3.246408047 0.493273492 0.831648961 0.472738224 0.481409439 0.719218909 0.158126309 5.53E-13 12.25751569 2.382565184 VTLT(ph)SEEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 1 0 VTLT(0.785)S(0.215)EEEAR 144.77 0.008453 4746600 4072.1 3429.8 3492.7 4116.1 3992.7 4145.9 3477 3133.9 4057.6 3921 TRUE FALSE FALSE 4022.467679 3478.084814 3553.488978 4592.022849 3788.93762 3880.99037 3772.336293 3224.574452 3694.678094 3819.131855 1.053241373 0.910700376 0.930444173 1.202373477 0.992093953 1.01619701 0.987747068 0.844321321 0.967413076 1 11.89902901 -7.20679669 2.237165301 1.020662183 0.782849347 0.282863724 0.076433226 0.677083918 3.418913033 0.01024092 0.333650477 6.21E-08 7.20679669 -0.237812836 VTLTSEEEAR ddPTM_HeLa_Romidepsin_16h_R1 2 VTLTSEEEAR 10 0 P00338;P00338-3;P00338-4 P00338 LDHA L-lactate dehydrogenase A chain 0 0 ; ; 179.81 0.00043522 137678000 4097 4203.2 3894.2 3564.5 3661 3766.5 3344.5 3392.7 4511.1 3448 FALSE FALSE TRUE 4047.064188 4262.37276 3961.976917 3976.644261 3474.165509 3525.832806 3628.581747 3490.862422 4107.615918 3358.420463 1.205049884 1.269159954 1.179714381 1.184081715 1.034464132 1.049848536 1.08044296 1.039435788 1.223079708 1 11.71356715 -8.740162871 24.97972568 1.125805015 1.053061823 0.272199424 0.077274612 442.6362429 519675.2403 0.014730926 0.029438198 1.82E-09 8.740162871 -0.072743192 VTLYNTDQDGSDS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 4 VTLYNTDQDGSDSPR 15 0 Q9UPW0-2;Q9UPW0;C9JXI1;C9JVP0 Q9UPW0-2 FOXJ3 Forkhead box protein J3 1 0 VTLYNTDQDGS(0.009)DS(0.991)PR;VTLYNTDQDGS(0.007)DS(0.993)PR;VTLYNTDQDGSDS(1)PR;VTLYNTDQDGS(0.001)DS(0.999)PR ;;; 284.24 4.22E-100 146999000 10026.7 10328.5 10884.2 10649.9 9865.3 9244.2 7643.8 9247.7 10293.8 9774.6 TRUE FALSE FALSE 9904.490724 10473.90489 11073.63494 11881.29155 9361.836928 8653.525454 8293.064181 9515.267609 9373.096747 9520.654483 1.040316161 1.100124462 1.163116985 1.247949032 0.983318631 0.90892128 0.871060303 0.999434191 0.984501303 1 13.21684504 -8.526519243 24.99994552 1.055075427 0.925128937 0.416419532 0.08236616 100.1760146 687926.2341 0.013361956 0.026824938 2.97E-09 8.526519243 -0.12994649 VTMLFLGLHNVR ddPTM_HeLa_Romidepsin_16h_R1 2 VTMLFLGLHNVR 12 0 P14868-2;P14868;H7BZ35 P14868-2 DARS "Aspartate--tRNA ligase, cytoplasmic" 0 0 ; ; 74.962 0.014772 378620 0 0 0 0 0 63.908 0 0 0 0 FALSE FALSE TRUE 0 0 0 0 0 59.82448505 0 0 0 0 0 VTNDIS(ph)PESS(ph)PGVGR ddPTM_HeLa_Romidepsin_16h_R1 2 VTNDISPESSPGVGR 15 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154;E9PGW9;E5RGQ4;Q15154-3 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 2 0 VTNDIS(1)PES(0.066)S(0.934)PGVGR;VTNDIS(1)PES(0.124)S(0.876)PGVGR ; 133.9 0.015153 107320000 9501 9131.2 8291.4 8379.1 8614.8 8363 7745.2 7411.3 10424.8 9441.7 TRUE FALSE FALSE 9385.198158 9259.749273 8435.708339 9347.930967 8175.15461 7828.63129 8403.077095 7625.734272 9492.379779 9196.403273 1.020529209 1.006888128 0.91728343 1.016476843 0.888951296 0.851270987 0.913735169 0.829208338 1.032183942 1 13.16685402 -8.764626751 0.864369206 1.009244782 0.853789773 0.728835405 0.037651458 0.237603166 0.329421298 0.006141713 0.021381199 1.72E-09 8.764626751 -0.155455009 VTNDISPES(ph)SPGVGR ddPTM_HeLa_Romidepsin_16h_R1 2 VTNDISPESSPGVGR 15 0 A0A5H1ZRS1;A0A4W8VX11;Q15154-5;E7EV93;Q15154-4;Q15154-2;Q15154;E9PGW9;E5RGQ4;Q15154-3 A0A5H1ZRS1 PCM1 Pericentriolar material 1 protein 1 0 VT(0.127)NDIS(0.195)PES(0.62)S(0.058)PGVGR;VT(0.001)NDIS(0.021)PES(0.769)S(0.209)PGVGR ; 149.59 0.0004768 198587000 3630.1 4372.1 3453 3273.8 4111 3745.4 3840 4065 4459.9 4344.2 TRUE FALSE FALSE 3585.854945 4433.650539 3513.098017 3652.33216 3901.20033 3506.081028 4166.169504 4182.614361 4060.995374 4231.337058 0.847451975 1.047813133 0.83025719 0.863162662 0.921978154 0.828598852 0.984598827 0.988485272 0.959742823 1 12.0468979 -12.59878964 1.381854992 1.000212633 0.904582249 0.099463327 0.071999456 0.56727043 1.936481976 0.050369623 0.011538491 2.52E-13 12.59878964 -0.095630384 VTNGAFTGEIS(ph)PGMIK ddPTM_HeLa_Romidepsin_16h_R1 1 VTNGAFTGEISPGMIK 16 0 P60174;P60174-3 P60174 TPI1 Triosephosphate isomerase 1 0 VTNGAFT(0.024)GEIS(0.976)PGMIK 93.738 0.013508 13777000 1739.8 1728.5 1433.9 1378.9 1541.2 1753.5 1525 1765 1841.4 1580.5 TRUE FALSE FALSE 1718.594648 1752.833868 1458.856428 1538.334906 1462.546813 1641.457009 1654.533462 1816.06749 1676.700572 1539.438382 1.116377679 1.13861905 0.947654966 0.999283196 0.950052194 1.06627003 1.07476433 1.179694823 1.089163809 1 10.58818841 -7.242729862 2.119101837 1.043598576 1.220644727 0.317659872 0.062170175 0.808095541 3.822807036 0.009983898 0.27619058 5.72E-08 7.242729862 0.177046151 VTPDIEES(ph)LLEPENEK ddPTM_HeLa_Romidepsin_16h_R1 1 VTPDIEESLLEPENEK 16 0 Q14151 Q14151 SAFB2 Scaffold attachment factor B2 1 0 VTPDIEES(1)LLEPENEK 167.18 1.81E-05 4094900 2550.8 2051.3 3517.1 2645.2 2616.7 2657.4 1258.2 1843.2 1878.3 2097 TRUE FALSE FALSE 2519.709868 2080.178255 3578.31365 2951.05047 2483.160035 2487.600716 1365.071477 1896.530084 1710.300144 2042.519638 1.233628222 1.018437334 1.751911504 1.44480886 1.215733738 1.217907858 0.668327223 0.928524773 0.837348201 1 10.99613423 -7.770653838 24.98688285 1.188974975 0.798425988 0.309191447 0.246613681 161.202677 437138.5779 0.034242046 0.104816337 1.70E-08 7.770653838 -0.390548987 VTPRPQQTSAS(ph)SPSSVNSR ddPTM_HeLa_Romidepsin_16h_R1 1 VTPRPQQTSASSPSSVNSR 19 1 H0YC63;Q9ULD2-5;Q9ULD2-2;Q9ULD2 H0YC63 MTUS1 Microtubule-associated tumor suppressor 1 1 0 VT(0.001)PRPQQT(0.001)S(0.002)AS(0.294)S(0.294)PS(0.294)S(0.108)VNS(0.005)R 63.125 0.010448 3558700 356.33 386.56 374.86 474.6 513.51 492.7 408.96 218.59 646.77 377.59 TRUE FALSE FALSE 351.9869129 392.0020018 381.3842811 529.4754851 487.3036685 461.2180601 443.6970522 224.9145568 588.9212713 367.7801574 0.957057921 1.065859574 1.036989825 1.439652125 1.324986296 1.254059119 1.206419224 0.611546198 1.601286148 1 8.522699835 -9.502334511 24.20690822 0.988749277 1.188604784 0 0.283107975 679.0587187 800123.5959 0.031066498 0.047084988 3.15E-10 9.502334511 0.199855507 VTPRPQQTSASSPS(ph)SVNSR ddPTM_HeLa_Romidepsin_16h_R1 1 VTPRPQQTSASSPSSVNSR 19 1 H0YC63;Q9ULD2-5;Q9ULD2-2;Q9ULD2 H0YC63 MTUS1 Microtubule-associated tumor suppressor 1 1 0 VTPRPQQT(0.001)S(0.003)AS(0.136)S(0.092)PS(0.574)S(0.168)VNS(0.026)R 82.216 0.0028568 4086400 765.53 453.94 410.01 613.04 698.37 613.39 460.08 362.97 520.8 456.34 TRUE FALSE FALSE 756.1994259 460.3305792 417.1460521 683.9225692 662.7295729 574.1963586 499.1591837 373.4719643 474.2183436 444.484221 1.701296447 1.035651115 0.938494624 1.538688072 1.491008098 1.291826192 1.123007657 0.840236721 1.066895789 1 8.795988395 -7.406474606 2.243703603 1.312825334 0.794096249 0.184306756 0.24693086 0.59941422 4.304514884 0.042869361 0.539234866 3.92E-08 7.406474606 -0.518729085 VTQGAAS(ph)PGHGIQEK ddPTM_HeLa_Romidepsin_16h_R1 1 VTQGAASPGHGIQEK 15 0 G5E9C0;Q9HB58-2;Q9HB58-5;Q9HB58-3;Q9HB58-7;Q9HB58;Q9HB58-6;Q9HB58-4 G5E9C0 SP110 Sp110 nuclear body protein 1 0 VTQGAAS(1)PGHGIQEK 215.15 9.10E-26 6609400 1783 1469.8 1836.3 1446.6 1457.7 1739.4 1443.2 1484.3 1848.1 1764 TRUE FALSE FALSE 1761.26811 1490.491883 1868.260031 1613.862698 1383.30813 1628.257954 1565.785372 1527.245879 1682.801307 1718.171026 1.025083117 0.867487497 1.087353938 0.939291068 0.805105027 0.947669312 0.91130938 0.888878846 0.97941432 1 10.74665793 -9.005379235 24.99072531 1.004568544 0.8913914 0.37926385 0.061428552 160.6102283 746165.5555 0.008415114 0.014931356 9.88E-10 9.005379235 -0.113177144 VTQHES(ph)DNENEIQIQNK ddPTM_HeLa_Romidepsin_16h_R1 2 VTQHESDNENEIQIQNK 17 0 Q5VZL5-2;Q5VZL5-4;Q5VZL5 Q5VZL5-2 ZMYM4 Zinc finger MYM-type protein 4 1 0 VT(0.049)QHES(0.951)DNENEIQIQNK;VT(0.032)QHES(0.968)DNENEIQIQNK ; 137.12 0.00048679 97082000 9341.9 9704.5 9354.9 9096.4 8061.6 7270.3 6762.4 8074.8 9515.9 9304.3 TRUE FALSE FALSE 9228.03733 9841.120206 9517.71811 10148.16857 7650.18647 6805.751294 7336.798087 8308.431598 8664.774071 9062.572945 1.018257992 1.085907972 1.050222511 1.119788898 0.844151712 0.750973408 0.809571204 0.916785073 0.956105305 1 13.14570499 -8.669941458 7.098803228 1.025515219 0.82058048 0.756401912 0.057539297 0.081533412 5.406447892 0.008054606 0.016157702 2.14E-09 8.669941458 -0.204934738 VTQSDLYK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VTQSDLYKK 9 1 O43399;O43399-5;O43399-7;A0A087WYR3 O43399 TPD52L2 Tumor protein D54 0 1 VTQSDLYK(1)K 130.41 0.0023251 840930 656.08 412.35 469.41 79.898 715.63 731.53 808.2 690.31 918.85 589.02 FALSE TRUE FALSE 648.0834446 418.1550741 477.5798841 89.13618269 679.1087307 684.7875939 876.8484878 710.2830307 836.6657547 573.7171755 1.129621828 0.728852285 0.832430864 0.15536607 1.183699495 1.193597862 1.52836367 1.238036895 1.458324398 1 9.164195899 -8.297882131 3.208312243 0.952886789 1.356251264 0.244129998 0.328634869 0.278031675 5.802125554 0.04477952 0.114999867 5.04E-09 8.297882131 0.403364475 VTRS(ph)PPTQVAISSDSAR ddPTM_HeLa_Romidepsin_16h_R1 1 VTRSPPTQVAISSDSAR 17 1 H0YM82;Q6ZUT6-3;Q6ZUT6-4;Q6ZUT6 H0YM82 C15orf52 Uncharacterized protein C15orf52 1 0 VTRS(0.676)PPT(0.321)QVAIS(0.002)S(0.002)DSAR 125.39 0.014351 13845000 4244.6 4028.5 3578.1 5114.1 3979.6 3720.2 3201.9 3235.2 4437.3 4072.5 TRUE FALSE FALSE 4192.865183 4085.213329 3640.37533 5705.416305 3776.506162 3482.491226 3473.869306 3328.805408 4040.416775 3966.695863 1.057017056 1.029878133 0.917734925 1.438329658 0.952053369 0.877932503 0.875758925 0.839188464 1.018584967 1 11.95372207 -8.526833716 24.99994715 1.050442612 0.873698652 0.338224563 0.131645851 109.286842 690817.7055 0.018519178 0.03716873 2.97E-09 8.526833716 -0.17674396 VTRSPPTQVAISS(ph)DSAR ddPTM_HeLa_Romidepsin_16h_R1 1 VTRSPPTQVAISSDSAR 17 1 H0YM82;Q6ZUT6-3;Q6ZUT6-4;Q6ZUT6 H0YM82 C15orf52 Uncharacterized protein C15orf52 1 0 VTRS(0.017)PPT(0.001)QVAIS(0.109)S(0.724)DS(0.148)AR 132.25 1.48E-06 0 1543 1383.3 1190.3 1324.5 1143.6 1439.8 1218.8 941.26 1474.3 1421.1 TRUE FALSE FALSE 1524.193323 1402.774134 1211.016672 1477.644922 1085.237825 1347.801427 1322.324842 968.493873 1342.434916 1384.179617 1.101152844 1.013433601 0.874898501 1.067523971 0.784029624 0.973718591 0.955313043 0.699688004 0.969841557 1 10.43481545 -5.680369533 0.353533543 1.045471792 1.77E-10 0.3869082 0.092528502 11.43235328 0.41916547 0.027215309 6.482597057 2.09E-06 5.680369533 -1.045471792 VTS(ph)PTTYVLDEDEPR ddPTM_HeLa_Romidepsin_16h_R1 4 VTSPTTYVLDEDEPR 15 0 J3KNS1;Q9UPW5;Q9UPW5-2;Q9UPW5-3 J3KNS1 AGTPBP1 Cytosolic carboxypeptidase 1 1 0 VT(0.005)S(0.995)PTTYVLDEDEPR;VT(0.063)S(0.935)PT(0.002)TYVLDEDEPR;VT(0.065)S(0.934)PTTYVLDEDEPR;VT(0.069)S(0.928)PT(0.002)T(0.001)YVLDEDEPR ;;; 266.85 2.06E-84 20637300 3000.43 3106.34 3264.57 3286.25 4966.1 6173.8 4647.7 6127.9 3658.27 2893.69 TRUE FALSE FALSE 2963.859605 3150.071136 3321.388471 3666.221687 4712.661386 5779.314105 5042.475522 6305.201118 3331.065169 2818.511517 1.051569095 1.117636425 1.178419337 1.300765197 1.672039074 2.050484474 1.789056207 2.237067715 1.181852602 1 11.46071775 -8.690417065 0.994860256 1.025661136 2.089659448 0.92390913 0.116488518 0.081680746 0.152841001 0.016012115 0.053846785 2.04E-09 8.690417065 1.063998313 up VTSATMLLGLLVS(ph)CMSLL ddPTM_HeLa_Romidepsin_16h_R1 1 VTSATMLLGLLVSCMSLL 18 0 Q8IVL8 Q8IVL8 CPO Carboxypeptidase O 1 0 VTSATMLLGLLVS(0.5)CMS(0.5)LL 56.036 0.019167 16117000 5465.7 5329.4 4997.6 5893.7 7095.4 6347.7 5405 5544.2 5588.9 5157.8 TRUE FALSE FALSE 5399.081946 5404.427433 5084.581132 6575.157325 6733.295261 5942.102456 5864.100565 5704.61268 5089.014786 5023.799612 1.074700896 1.075764929 1.012098715 1.30880167 1.340279426 1.1827905 1.167264027 1.13551756 1.012981245 1 12.2945632 -9.271874797 24.99659839 1.038272087 1.227460751 0.702473452 0.062401308 328.4022947 786641.029 0.010607753 0.01631148 5.35E-10 9.271874797 0.189188663 VTSFSTPPT(ph)PER ddPTM_HeLa_Romidepsin_16h_R1 2 VTSFSTPPTPER 12 0 B0QY16;Q6ICG6-3;Q6ICG6;Q6ICG6-2 B0QY16 KIAA0930 Uncharacterized protein KIAA0930 1 0 VTSFSTPPT(1)PER;VTSFST(0.001)PPT(0.998)PER ; 162.93 0.0010753 44344000 3772.6 4043.1 3589.1 2922.53 4287.3 4985 3559.4 4477.5 4051.5 3071.8 TRUE FALSE FALSE 3726.6181 4100.018868 3651.56678 3260.44667 4068.503083 4666.474588 3861.735347 4607.049398 3689.123693 2991.994193 1.245529857 1.370329821 1.220445811 1.089723595 1.35979645 1.559653625 1.290689453 1.539792226 1.23299828 1 11.54689166 -8.809291122 0.044162951 3.98E-13 2.66301758 0.388167204 0.131050476 68.43558021 0.919394419 23.44117346 32.10499464 1.55E-09 8.809291122 2.66301758 VTSGGVSES(ph)PSGFSK ddPTM_HeLa_Romidepsin_16h_R1 2 VTSGGVSESPSGFSK 15 0 E7EPP6;O14757-2;O14757-3;O14757 E7EPP6 CHEK1 Serine/threonine-protein kinase Chk1 1 0 VTSGGVS(0.004)ES(0.663)PS(0.333)GFS(0.001)K;VTSGGVS(0.001)ES(0.731)PS(0.267)GFS(0.001)K ; 202.32 3.41E-18 43643000 6403.8 5482.5 6293.5 5162.5 6175.1 6041.8 5534.6 5503.4 6299.8 5043.8 TRUE FALSE FALSE 6325.748022 5559.682779 6403.035728 5759.41254 5859.961605 5655.748479 6004.708786 5662.632196 5736.33011 4912.761349 1.287615574 1.131681835 1.303347603 1.17233713 1.192804044 1.151236154 1.222267552 1.152637345 1.167638666 1 12.26231844 -12.45535868 1.151652347 0.998318214 1.208953588 0.165308194 0.073790715 0.231325247 0.541756674 0.039346587 0.00943819 3.50E-13 12.45535868 0.210635374 VTSLANLIS(ph)PVR ddPTM_HeLa_Romidepsin_16h_R1 1 VTSLANLISPVR 12 0 Q7Z628;Q7Z628-2 Q7Z628 NET1 Neuroepithelial cell-transforming gene 1 protein 1 0 VTSLANLIS(1)PVR 108.36 0.011499 10285000 1161.1 1176.2 1235 1299.9 1325.7 1572.7 1257.4 1551.5 1042.9 1134 TRUE FALSE FALSE 1146.948067 1192.758574 1256.494657 1450.200554 1258.044582 1472.209546 1364.203525 1596.390205 949.620412 1104.538517 1.038395719 1.079870513 1.137574325 1.31294702 1.138977558 1.332872981 1.235089138 1.445300622 0.859744045 1 10.10922801 -8.659161555 0.384284592 0.992188153 1.451329934 0.774743188 0.079159656 0.674236561 0.141849277 0.022383659 0.124914575 2.19E-09 8.659161555 0.459141781 VTSSITIYPSDSS(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 2 VTSSITIYPSDSSSPR 16 0 Q86V48-2;Q86V48-3;Q86V48 Q86V48-2 LUZP1 Leucine zipper protein 1 1 0 VTSSITIYPSDS(0.039)S(0.928)S(0.033)PR;VTSSITIYPSDS(0.128)S(0.436)S(0.436)PR ; 304.86 8.05E-138 121707000 4468.5 3943.5 4501.5 4294.6 8581 11712.9 9806.1 10892.6 5023.8 4678.5 TRUE FALSE FALSE 4414.036203 3999.016697 4579.846719 4791.161859 8143.07955 10964.48349 10639.02989 11207.7602 4574.458746 4556.951896 0.968637876 0.877563948 1.005024153 1.051396189 1.78695754 2.406100337 2.334681193 2.459486177 1.00384179 1 12.15385343 -8.571062085 2.184754772 0.974583854 2.407096295 0.992861455 0.054308881 0.017149528 0.16384176 0.008220604 0.01983123 2.68E-09 8.571062085 1.432512441 up VTSSMSSPS(ph)MQPK ddPTM_HeLa_Romidepsin_16h_R1 1 VTSSMSSPSMQPK 13 0 A0A2R8Y7R9;Q13136-2;Q13136 A0A2R8Y7R9 PPFIA1 Liprin-alpha-1 1 0 VTS(0.005)S(0.033)MS(0.249)S(0.249)PS(0.463)MQPK 84.213 0.024524 18746000 3893.9 4318.8 3490.6 3909 3637.8 3992.5 3405.8 3630.6 4257.7 3813.4 TRUE FALSE FALSE 3846.439649 4379.60018 3551.352429 4360.976972 3452.149491 3737.392135 3695.088567 3735.645683 3876.880648 3714.327318 1.035568306 1.179109918 0.956122637 1.174096034 0.929414453 1.006209689 0.994820394 1.005739495 1.043763868 1 11.85888524 VTSSVPLPSGSTSS(ph)PGR ddPTM_HeLa_Romidepsin_16h_R1 4 VTSSVPLPSGSTSSPGR 17 0 Q15036-2;Q15036 Q15036-2 SNX17 Sorting nexin-17 1 0 VTSSVPLPS(0.002)GST(0.004)S(0.188)S(0.805)PGR;VTSSVPLPS(0.073)GS(0.028)T(0.028)S(0.028)S(0.844)PGR;VTSSVPLPS(0.004)GS(0.026)T(0.026)S(0.123)S(0.821)PGR;VTSS(0.002)VPLPS(0.053)GS(0.053)T(0.053)S(0.21)S(0.628)PGR ;;; 204.07 3.13E-19 280417800 10696.9 10021.6 10170 9533.1 10326.7 9910.9 9697.43 9650.45 11859.7 11563.2 TRUE FALSE FALSE 10566.52207 10162.68435 10347.00458 10635.36188 9799.689965 9277.625476 10521.12946 9929.670545 10798.93873 11262.7864 0.9381801 0.902324166 0.918689587 0.944292247 0.87009463 0.823741581 0.934149782 0.881635343 0.958815905 1 13.45927617 -10.97738394 0.322233045 1.01567083 0.87449785 0.510721561 0.033172762 0.727237636 0.210366111 0.041038449 0.023945978 1.05E-11 10.97738394 -0.141172981 VTTEIQLPS(ph)QSPVEEQS(ph)PASLSSLR ddPTM_HeLa_Romidepsin_16h_R1 1 VTTEIQLPSQSPVEEQSPASLSSLR 25 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 2 0 VT(0.001)T(0.003)EIQLPS(0.496)QS(0.5)PVEEQS(0.974)PAS(0.013)LS(0.01)S(0.003)LR 62.57 0.00089307 0 1044.4 1082.1 1091.8 1035.8 1302 1477 1425.3 1352.3 1140.7 1224.2 TRUE FALSE FALSE 1031.670451 1097.333832 1110.802321 1155.56407 1235.554082 1382.624467 1546.364946 1391.426667 1038.672935 1192.395108 0.865208558 0.920277033 0.931572357 0.969111717 1.036195196 1.159535508 1.296856165 1.166917457 0.871081178 1 10.21964665 -8.360557997 1.686035396 0.933822371 1.235957666 0.873107895 0.0484287 0.111160545 0.603426046 0.008660977 0.027399595 4.36E-09 8.360557997 0.302135296 VTTEIQLPSQS(ph)PVEEQSPASLSSLR ddPTM_HeLa_Romidepsin_16h_R1 3 VTTEIQLPSQSPVEEQSPASLSSLR 25 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424 E9PMS6 LMO7 LIM domain only protein 7 1 0 VTTEIQLPS(0.39)QS(0.608)PVEEQS(0.001)PASLSSLR;VTTEIQLPS(0.128)QS(0.87)PVEEQS(0.002)PASLSSLR;VT(0.058)T(0.052)EIQLPS(0.332)QS(0.556)PVEEQS(0.001)PASLSSLR ;; 109.92 1.50E-06 105208000 7862.3 8279.6 7199.5 8054.2 8331.9 7706.8 6529 6535.1 8112.8 7781 TRUE FALSE FALSE 7766.471263 8396.160426 7324.804277 8985.4645 7906.692052 7214.360353 7083.573097 6724.182808 7387.170849 7578.848498 1.024756104 1.107841175 0.966479839 1.185597588 1.0432577 0.951907187 0.93465031 0.887230139 0.974708869 1 12.88776295 -8.059270665 3.040091006 1.030861751 0.91305001 0.426691576 0.062913568 0.201666959 3.65229839 0.008759413 0.02727276 8.72E-09 8.059270665 -0.11781174 VTVDTGVIPASEEKAET(ph)PTAAEDDNEGDKK ddPTM_HeLa_Romidepsin_16h_R1 1 VTVDTGVIPASEEKAETPTAAEDDNEGDKK 30 2 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 VTVDT(0.001)GVIPAS(0.061)EEKAET(0.743)PT(0.195)AAEDDNEGDKK 58.47 0.00048495 34985000 1481.4 1492.2 1693.2 1391.6 1626.2 1833.5 1623.3 1792.8 1733.7 1613.6 TRUE FALSE FALSE 1463.344127 1513.207231 1722.669436 1552.50334 1543.208946 1716.345267 1761.183061 1844.671839 1578.63353 1571.678439 0.931070943 0.962796965 1.096069904 0.987799604 0.98188593 1.092046073 1.120574678 1.173695454 1.004425263 1 10.61809036 -7.394088778 0.585838446 0.970596084 1.297532769 0.667517126 0.043444109 1.333582156 0.339934276 0.008884927 0.284985245 4.04E-08 7.394088778 0.326936685 VTVEST(ph)PDLEK ddPTM_HeLa_Romidepsin_16h_R1 2 VTVESTPDLEK 11 0 A0A087WZ40;Q14244-5;Q14244-3;Q14244-6;Q14244;Q14244-7;Q14244-2;Q14244-4 A0A087WZ40 MAP7 Ensconsin 1 0 VTVES(0.073)T(0.927)PDLEK;VTVES(0.041)T(0.959)PDLEK ; 166.29 0.0011465 13020500 5264.7 5004.5 5732.8 11623.2 5054 6769.6 4856.2 5114.6 5191.1 5363.5 TRUE FALSE FALSE 5200.531811 5074.953482 5832.576979 12967.12907 4796.075521 6337.044408 5268.685507 5262.582881 4726.795015 5224.155497 0.99547799 0.971439974 1.116463126 2.482148374 0.918057574 1.213027524 1.008523868 1.007355712 0.904796003 1 12.35098212 -9.512513018 24.97605751 0.998114888 1.331277932 0.14079532 0.415663718 799.9324427 1927426.72 0.063369237 0.092975063 3.07E-10 9.512513018 0.333163044 VTVLFAGQHIAK ddPTM_HeLa_Romidepsin_16h_R1 2 VTVLFAGQHIAK 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98 Q60FE5 FLNA Filamin-A 0 0 ; ; 124.39 0.0010312 12843600 4430.8 3670.7 5768.4 4358.1 5468.7 6033.8 4468.1 4223.2 3466.5 2705.8 FALSE FALSE TRUE 4376.795705 3722.376211 5868.796582 4862.004027 5189.611832 5648.259653 4847.620302 4345.391629 3156.447558 2635.502926 1.66070607 1.412396918 2.22682226 1.844810711 1.969116324 2.143143002 1.839353034 1.648790288 1.197664221 1 11.36386258 -11.51477519 0.442426504 0.919008993 1.949681009 0.675803861 0.214228999 0.476417107 0.187887839 0.214660841 0.075074503 3.06E-12 11.51477519 1.030672016 VTYVVLDEADR ddPTM_HeLa_Romidepsin_16h_R1 1 VTYVVLDEADR 11 0 Q7L014;A0A0C4DG89 Q7L014 DDX46 Probable ATP-dependent RNA helicase DDX46 0 0 152.54 0.023198 4349200 1882.5 1799.6 1903.6 1810.3 2144.2 2173.3 1667.1 2093.7 1975.1 1687.3 FALSE FALSE TRUE 1859.555366 1824.934816 1936.731359 2019.615404 2034.773473 2034.433144 1808.703432 2154.277906 1798.442109 1643.463703 1.13148551 1.110419909 1.178444864 1.228877401 1.238100646 1.237893566 1.100543583 1.310815628 1.094299866 1 10.68252388 -11.19048094 0.298571053 0.957821014 1.243671967 0.547590011 0.058877481 0.783345464 0.178752049 0.087440442 0.04198171 6.45E-12 11.19048094 0.285850953 VVDNS(ph)PPPALPPK ddPTM_HeLa_Romidepsin_16h_R1 2 VVDNSPPPALPPK 13 0 Q13905-2;Q13905;Q13905-4;Q13905-3 Q13905-2 RAPGEF1 Rap guanine nucleotide exchange factor 1 1 0 VVDNS(1)PPPALPPK;VVDNS(1)PPPALPPK ; 111.07 0.0065541 40247000 14354.1 13431 13675.7 13163.8 13261.8 14201.5 10920.5 13805.9 14512.2 12829 TRUE FALSE FALSE 14179.14671 13620.08197 13913.71982 14685.86049 12585.00086 13294.06998 11848.087 14205.35193 13214.19249 12495.70073 1.134722015 1.089981448 1.113480558 1.175273065 1.007146468 1.063891515 0.948173076 1.136819154 1.057499117 1 13.60914419 -6.939531684 20.89943195 1.066993542 2.418522338 0.099263175 0.064256489 552.7784006 357548.0906 0.00980077 29711.56033 1.15E-07 6.939531684 1.351528796 VVDRDSEEAEIIR ddPTM_HeLa_Romidepsin_16h_R1 4 VVDRDSEEAEIIR 13 1 P09874 P09874 PARP1 Poly [ADP-ribose] polymerase 1 0 0 ;;; ;;; 158.86 0.00059277 23329300 44859.2 40248.3 42158.7 25880 40178 42654.4 36027.9 39145.3 42801.2 44512.8 FALSE FALSE TRUE 44312.43882 40814.91662 42892.45449 28872.36737 38127.56674 39928.9215 39088.10893 40277.90749 38972.95347 43356.35104 1.022051851 0.94138265 0.989300378 0.665931673 0.879399807 0.920947463 0.901554397 0.92899671 0.898898375 1 15.40395572 -9.484968289 24.9999272 1.003613477 0.862381176 0.285794106 0.079671313 367.9765712 242661.309 0.011042792 0.016865472 3.27E-10 9.484968289 -0.141232301 VVDVEEQQLEES(ph)GPHDLTETSYLPR ddPTM_HeLa_Romidepsin_16h_R1 2 VVDVEEQQLEESGPHDLTETSYLPR 25 0 P38398-8;P38398-4;P38398;P38398-7;K7EPC7;H0Y8B8;B7ZA85;E7EUM2;A0A2R8Y7V5;P38398-6;P38398-5;P38398-3 P38398-8 BRCA1 Breast cancer type 1 susceptibility protein 1 0 VVDVEEQQLEES(1)GPHDLTETSYLPR;VVDVEEQQLEES(1)GPHDLTETSYLPR ; 141.82 2.14E-07 16421000 5321.3 4824.4 4440.1 4788.5 3627.1 3376 2788.1 2711.3 5292 5283.2 TRUE FALSE FALSE 5256.441949 4892.31803 4517.378078 5342.168901 3441.995552 3160.284496 3024.921144 2789.747188 4818.670266 5145.941702 1.02147328 0.950713847 0.877852556 1.038132418 0.668875738 0.614131422 0.587826547 0.542125688 0.936402032 1 12.3292194 -8.67708754 4.097888145 0.996460117 0.590144419 0.923472764 0.051809482 0.038630315 1.225556237 0.007625412 0.015599284 2.10E-09 8.67708754 -0.406315699 VVDYSQFQES(ph)DDADEDYGR ddPTM_HeLa_Romidepsin_16h_R1 12 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 VVDYS(0.002)QFQES(0.998)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR;VVDYSQFQES(1)DDADEDYGR ;;;;;;;;;;; 261.66 2.48E-76 2895041700 39006.9 38939.29 37941.46 27654.93 38562.22 36476.2 30632.78 36365.69 42043.87 40455.44 TRUE FALSE FALSE 38531.4689 39487.47835 38601.8152 30852.52313 36594.24602 34145.48854 33234.72757 37417.87386 38283.36097 39404.40184 0.977846817 1.002108305 0.979632056 0.782971488 0.928684216 0.866539954 0.843426775 0.949586141 0.971550364 1 15.26606918 -9.410324196 8.936865806 0.990215496 0.875223844 0.626211503 0.043275765 0.147699669 10.82497324 0.005949052 0.009090211 3.89E-10 9.410324196 -0.114991652 VVDYSQFQES(ph)DDADEDYGRDSGPPTK ddPTM_HeLa_Romidepsin_16h_R1 6 VVDYSQFQESDDADEDYGRDSGPPTK 26 1 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 VVDY(0.013)S(0.059)QFQES(0.927)DDADEDYGRDSGPPTK;VVDYSQFQES(1)DDADEDYGRDSGPPTK;VVDY(0.052)S(0.148)QFQES(0.723)DDADEDY(0.051)GRDS(0.024)GPPT(0.002)K;VVDY(0.001)S(0.004)QFQES(0.995)DDADEDYGRDSGPPTK;VVDYS(0.004)QFQES(0.976)DDADEDY(0.011)GRDS(0.009)GPPTK;VVDYSQFQES(0.998)DDADEDY(0.001)GRDS(0.001)GPPTK ;;;;; 160.36 4.63E-11 766174600 19701.9 21203.7 17636.9 19573.88 19268 18747.37 15673.1 17992.1 20482.1 20492.2 TRUE FALSE FALSE 19461.76566 21502.20625 17943.86285 21837.1041 18284.68206 17549.47356 17004.37272 18512.67303 18650.12968 19959.80969 0.975047657 1.077275113 0.898999696 1.094053723 0.91607497 0.879240526 0.851930604 0.927497472 0.934384143 1 14.28481034 -8.53928216 24.89791223 0.994964948 0.885270976 0.442752894 0.057293967 129.017417 195828.4735 0.006941035 0.013884929 2.89E-09 8.53928216 -0.109693973 VVDYSQFQES(ph)DDADEDYGRDSGPPTKK ddPTM_HeLa_Romidepsin_16h_R1 2 VVDYSQFQESDDADEDYGRDSGPPTKK 27 2 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 1 0 VVDY(0.008)S(0.021)QFQES(0.967)DDADEDY(0.002)GRDS(0.001)GPPT(0.001)KK;VVDY(0.001)S(0.135)QFQES(0.863)DDADEDYGRDSGPPTKK ; 59.818 0.0010848 956060000 5002.8 5121.5 3972.7 6833.4 4951.5 3982.8 3614.6 4118.8 5322.6 4442.3 TRUE FALSE FALSE 4941.823949 5193.600611 4041.843177 7623.50986 4698.806478 3728.311934 3921.624034 4237.97098 4846.533325 4326.888406 1.142119576 1.200308426 0.934122353 1.761891952 1.085955088 0.861661218 0.90633815 0.97945003 1.120096677 1 12.0791142 -8.334696275 6.541252362 1.123644138 0.915453253 0.208042852 0.217419144 0.342988451 25.32010201 0.031678381 0.071569039 4.63E-09 8.334696275 -0.208190884 VVDYSQFQESDDADEDYGR ddPTM_HeLa_Romidepsin_16h_R1 2 VVDYSQFQESDDADEDYGR 19 0 Q9H1E3 Q9H1E3 NUCKS1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 0 0 ; ; 222.88 1.89E-37 16648400 3149 3182.6 3261.5 2472.56 2587.41 3063.9 2874.3 3362.2 4203.4 3770.5 FALSE FALSE TRUE 3110.618777 3227.404726 3318.265039 2758.449021 2455.364813 2868.126678 3118.44297 3459.479952 3827.437376 3672.541866 0.846993415 0.878793175 0.903533618 0.751100769 0.668573675 0.780965005 0.849123872 0.941985164 1.042176649 1 11.84256322 -11.86025559 0.441660913 1.028311753 0.807475968 0.516786136 0.074995892 1.127161122 0.368409504 0.110973945 0.02667048 1.38E-12 11.86025559 -0.220835785 VVEAVNS(ph)DSDSEFGIPK ddPTM_HeLa_Romidepsin_16h_R1 1 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 VVEAVNS(0.82)DS(0.138)DS(0.042)EFGIPK 91.789 0.0081191 5271900 2158.2 1478.3 1713.4 1216.6 1418.5 1515.3 1897 1793.5 2309.6 1895.1 TRUE FALSE FALSE 2131.895028 1499.111546 1743.221008 1357.269016 1346.108652 1418.47722 2058.131133 1845.392093 2103.023592 1845.865029 1.154957158 0.812145809 0.944392456 0.735302417 0.729256273 0.768462048 1.114995463 0.999743786 1.139316016 1 10.85008135 -10.25719875 24.74333861 1.073174214 0.869434744 0.411972415 0.122652288 271.7340179 1585522.632 0.022579648 0.027133591 5.53E-11 10.25719875 -0.20373947 VVEAVNSDSDS(ph)EFGIPK ddPTM_HeLa_Romidepsin_16h_R1 1 VVEAVNSDSDSEFGIPK 17 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 VVEAVNS(0.381)DS(0.045)DS(0.574)EFGIPK 96.666 0.0015654 0 986.19 637.39 821.98 589.36 752.54 776.8 807.51 1052.6 956.56 944.5 TRUE FALSE FALSE 974.169937 646.3631932 836.2862171 657.5045762 714.1350757 727.164987 876.0998792 1083.05532 871.0028779 919.9617538 1.058924388 0.702597897 0.909044548 0.714708599 0.776266049 0.790429585 0.952322067 1.177282986 0.946781618 1 9.845430074 -10.29132923 24.89853886 1.027825415 0.854258675 0.182749984 0.133380794 638.1475176 531581.0908 0.022527191 0.025762724 5.11E-11 10.29132923 -0.17356674 VVESPDFS(ph)KDEDYLGK ddPTM_HeLa_Romidepsin_16h_R1 1 VVESPDFSKDEDYLGK 16 1 Q9Y6Y8 Q9Y6Y8 SEC23IP SEC23-interacting protein 1 0 VVES(0.267)PDFS(0.732)KDEDY(0.001)LGK 66.246 0.01766 82302000 2126.6 1804.4 1828.9 1962.4 5321.9 5935.9 4722 5445.5 1886.6 2134.8 TRUE FALSE FALSE 2100.680181 1829.802391 1860.731237 2189.301921 5050.303584 5556.615147 5123.086562 5603.056951 1717.857771 2079.337588 1.010264131 0.879992937 0.894867312 1.05288431 2.428804064 2.67230063 2.463807027 2.694635533 0.826156263 1 11.02190829 -8.747246845 4.64480684 0.98426613 2.586799073 0.98740267 0.089805222 0.012030105 0.640820874 0.010770538 0.021232557 1.79E-09 8.747246845 1.602532943 up VVFPPGS(ph)PIPLRR ddPTM_HeLa_Romidepsin_16h_R1 1 VVFPPGSPIPLRR 13 1 A0A1B0GTU4;A0A1B0GV30 A0A1B0GTU4 1 0 VVFPPGS(1)PIPLRR 94.007 0.0055075 11375000 1167.5 953.79 792.47 1268.8 1245.2 1032.3 738.7 744.8 1020.1 1094 TRUE FALSE FALSE 1153.270061 967.2174807 806.2626079 1415.504626 1181.652798 966.3393616 801.4451596 766.3496129 928.8597011 1065.577722 1.082295582 0.907693039 0.756643641 1.328391722 1.10893159 0.906868961 0.752122668 0.71918697 0.871695871 1 10.05742011 -7.907136665 3.05887735 1.033846207 0.730509022 0.339734055 0.147072989 0.179708692 3.327229342 0.01955517 0.070446712 1.24E-08 7.907136665 -0.303337185 VVFVFGPDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VVFVFGPDKK 10 1 P30041 P30041 PRDX6 Peroxiredoxin-6 0 1 ; VVFVFGPDK(1)K;VVFVFGPDK(1)K 105.78 0.0064531 864640 0 0 577.91 138.68 1141.76 932.09 597.65 402.87 272.25 210.4 FALSE TRUE FALSE 0 0 587.9682811 154.7148341 1083.491727 872.5324572 648.4143761 414.5264078 247.8992781 204.9337777 0 0 2.869064767 0.754950384 5.287033397 4.257631256 3.164019048 2.022733453 1.209655533 1 7.679013982 -9.266648954 1.493506273 0.506028665 3.551192552 0.509447735 1.195913453 0.21003815 0.917707392 0.191737087 0.354957001 5.41E-10 9.266648954 3.045163887 VVGQT(ph)TPESFEK ddPTM_HeLa_Romidepsin_16h_R1 1 VVGQTTPESFEK 12 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 VVGQT(0.913)T(0.031)PES(0.056)FEK 168.76 0.00039199 23297000 3056.1 2436.3 2811.7 2425.7 2963.6 3064.5 3027 2873.6 3002.2 2818.1 TRUE FALSE FALSE 3018.851078 2470.598295 2860.636459 2706.170847 2812.356433 2868.68834 3284.113304 2956.743082 2733.675713 2744.885356 1.099809532 0.9000734 1.042169741 0.985895765 1.024580654 1.045103153 1.196448259 1.077182723 0.995916171 1 11.42253018 -7.882908702 7.208711132 1.030629361 1.136058554 0.401725138 0.057699231 0.184163779 10.80762967 0.008533419 0.025952326 1.31E-08 7.882908702 0.105429193 VVGQTTPES(ph)FEK ddPTM_HeLa_Romidepsin_16h_R1 1 VVGQTTPESFEK 12 0 Q02952-3;Q02952-2;Q02952 Q02952-3 AKAP12 A-kinase anchor protein 12 1 0 VVGQT(0.009)T(0.095)PES(0.896)FEK 171.62 0.00011866 19365000 4184.6 4133.2 4048.7 3495.6 4402 4778.1 3861.2 4262.8 3790.6 3900.4 TRUE FALSE FALSE 4133.596486 4191.387298 4119.165925 3899.777719 4177.349514 4472.794831 4189.170232 4386.137392 3451.559242 3799.067046 1.088055682 1.103267525 1.084257234 1.026509317 1.099572464 1.177340325 1.102683944 1.154530136 0.90852812 1 11.89142946 -16.52287874 0.074199374 0.622415295 1.23546284 0.628403276 0.045171394 101.1879517 0.580405174 6.4879344 0.836387099 3.00E-17 16.52287874 0.613047546 VVIIGAGKPAAVVLQTK ddPTM_HeLa_Romidepsin_16h_R1 2 VVIIGAGKPAAVVLQTK 17 1 F5H6X6;Q14697;Q14697-2;E9PKU7 F5H6X6 GANAB Neutral alpha-glucosidase AB 0 0 ; ; 74.783 0.017109 722150 201.93 255.63 210.911 217.924 234.15 52.667 320.5 307.08 288.48 62.734 FALSE FALSE TRUE 199.4687995 259.2287658 214.5818175 243.1213982 222.2004518 49.30174867 347.723262 315.9648753 262.6776263 61.10416164 3.264406125 4.2424077 3.511738182 3.978802617 3.636420922 0.806847641 5.690664149 5.170922354 4.298850017 1 5.933198736 -12.21063925 0.359860378 1.06E-10 4.030457408 0 1.59895716 2.040996334 0.357604315 3.283108725 0.532201753 6.16E-13 12.21063925 4.030457408 VVINVPIFK ddPTM_HeLa_Romidepsin_16h_R1 1 VVINVPIFK 9 0 A0A0C4DGB2;B4E2I4;E1CEI4;A0A2R8YEL6;P48506 A0A0C4DGB2 GCLC Glutamate--cysteine ligase catalytic subunit 0 0 113.89 0.014112 217850 63.507 0 101.86 0 156.71 63.384 0 117.17 121.94 148.1 FALSE FALSE TRUE 62.73295226 0 103.6328306 0 148.7125039 59.33396696 0 120.5601291 111.033381 144.2523407 0.434883427 0 0.718413511 0 1.030919174 0.411320653 0 0.835758564 0.769716321 1 7.172450918 -11.99326373 0.843770545 0.9940188 0.41957691 0.204106702 0.348172968 0.567922416 0.751069149 0.195511105 0.063637081 1.02E-12 11.99326373 -0.57444189 VVKPKS(ph)PEPEATLTFPFLDK ddPTM_HeLa_Romidepsin_16h_R1 1 VVKPKSPEPEATLTFPFLDK 20 2 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 VVKPKS(0.814)PEPEAT(0.168)LT(0.019)FPFLDK 57.735 0.011301 181240000 6942.9 5952.4 5747.6 10216 7080 5719.5 5815.6 6270.1 6769.7 5735.4 TRUE FALSE FALSE 6858.277264 6036.198043 5847.634567 11397.22199 6718.681181 5354.042409 6309.576919 6451.515451 6164.201077 5586.393481 1.227675295 1.08051788 1.046763818 2.040175298 1.202686707 0.958407679 1.12945444 1.154862341 1.103431238 1 12.44770148 -12.03179668 0.620395264 0.982360703 1.239660748 0.056599727 0.284641654 2.056482314 1.313210797 0.284958242 0.067589 9.29E-13 12.03179668 0.257300045 VVKPKSPEPEAT(ph)LTFPFLDK ddPTM_HeLa_Romidepsin_16h_R1 1 VVKPKSPEPEATLTFPFLDK 20 2 Q9UPQ0-6;E9PDJ9;Q9UPQ0;Q9UPQ0-4;Q9UPQ0-2;Q9UPQ0-10;Q9UPQ0-9;Q9UPQ0-5;E7EPK0;Q9UPQ0-8;H0Y8P3;G5EA03;Q9UPQ0-3 Q9UPQ0-6 LIMCH1 LIM and calponin homology domains-containing protein 1 1 0 VVKPKS(0.004)PEPEAT(0.924)LT(0.073)FPFLDK 71.376 0.0025453 93592000 10563 9462.9 8748.2 15697 10089 9052.4 9393.1 9393 10853 9166.6 TRUE FALSE FALSE 10434.25409 9596.118955 8900.458751 17511.961 9574.120683 8473.980855 10190.94968 9664.771635 9882.280498 8928.450411 1.168652298 1.07477989 0.996864892 1.961366216 1.072316051 0.94909872 1.141401835 1.082469095 1.106830418 1 13.12419409 -11.831437 0.637265879 0.995391191 1.190457775 0.030520617 0.271954569 2.065023953 1.537759115 0.210131878 0.064148796 1.47E-12 11.831437 0.195066584 VVLASAS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 VVLASASPR 9 0 O95671;O95671-2 O95671 ASMTL N-acetylserotonin O-methyltransferase-like protein 1 0 VVLAS(0.003)AS(0.997)PR;VVLAS(0.011)AS(0.989)PR ; 117.53 0.00059658 0 3084.9 3413.6 3875.1 4172.7 6709.6 8873.1 7439.4 6948.5 3650.4 3072.1 TRUE FALSE FALSE 3047.300052 3461.65675 3942.54449 4655.167207 6367.184075 8306.137547 8071.30245 7149.543885 3323.899081 2992.286399 1.018385156 1.156860102 1.317569231 1.555722476 2.127865861 2.775849781 2.697369628 2.389324727 1.110822508 1 11.54703255 -8.835329775 1.270123806 1.022035454 2.663243464 0.961995647 0.131816398 0.051546581 0.165506989 0.020760399 0.052652373 1.46E-09 8.835329775 1.64120801 up VVLDDKDYFLFR ddPTM_HeLa_Romidepsin_16h_R1 3 VVLDDKDYFLFR 12 1 P61604;B8ZZ54 P61604 HSPE1 "10 kDa heat shock protein, mitochondrial" 0 0 ;; ;; 187.42 7.95E-10 871945420 8943.25 8326.67 9686.29 8706.45 8714.79 9026.18 8343.48 7864.97 8720.44 7774.69 FALSE FALSE TRUE 8834.246229 8443.893079 9854.875814 9713.130714 8270.041747 8449.436229 9052.174983 8092.530498 7940.462006 7572.702433 1.166590964 1.11504356 1.301368422 1.28265052 1.092085926 1.115775551 1.195369165 1.068644988 1.048563848 1 12.88659252 -12.02100393 0.745509244 0.995950082 1.171476099 0.36686962 0.074089381 0.550725793 0.542844223 0.056108591 0.015796719 9.53E-13 12.02100393 0.175526017 VVLGDGVQLPPGDY(ph)STTPGGTLFSTT(ph)PGGTR ddPTM_HeLa_Romidepsin_16h_R1 3 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 VVLGDGVQLPPGDY(0.369)S(0.225)T(0.108)T(0.298)PGGT(0.01)LFS(0.117)T(0.257)T(0.573)PGGT(0.042)R;VVLGDGVQLPPGDY(0.538)S(0.155)T(0.137)T(0.172)PGGT(0.05)LFS(0.054)T(0.245)T(0.565)PGGT(0.083)R;VVLGDGVQLPPGDY(0.299)S(0.293)T(0.312)T(0.312)PGGT(0.199)LFS(0.177)T(0.177)T(0.201)PGGT(0.03)R ;; 79.126 4.49E-08 152108000 21591.2 20459.5 19787.1 17809.9 19456.5 18968 16622 17898.4 22266.4 21409.5 TRUE FALSE FALSE 21328.03815 20747.52938 20131.48618 19869.16444 18463.5622 17756.00602 18033.87227 18416.26196 20274.83742 20853.2781 1.022766687 0.994928916 0.965387124 0.952807723 0.885403346 0.851473132 0.864797955 0.883135106 0.972261403 1 14.34798657 -9.027406216 1.209507089 1.010056659 0.862806396 0.908911866 0.017859968 0.067443681 0.195251994 0.002484917 0.005653641 9.39E-10 9.027406216 -0.147250263 VVLGDGVQLPPGDYS(ph)TTPGGTLFST(ph)TPGGTRIIYDRK ddPTM_HeLa_Romidepsin_16h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTRIIYDRK 37 2 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 VVLGDGVQLPPGDY(0.278)S(0.299)T(0.299)T(0.115)PGGT(0.128)LFS(0.128)T(0.348)T(0.348)PGGT(0.029)RIIY(0.028)DRK 43.24 0.014858 20878000 1380.3 1209.2 949.22 2607 1299.4 1067.2 1329.6 1160.2 1501 1091.2 TRUE FALSE FALSE 1363.476373 1226.223149 965.7407759 2908.433606 1233.086769 999.0093642 1442.536191 1193.768557 1366.746801 1062.850467 1.282848731 1.153711823 0.908632782 2.736446657 1.16016957 0.939934069 1.357233436 1.123176396 1.285925766 1 10.05372292 -11.51029093 0.607898291 1.005864748 1.361210508 0.015464442 0.497299422 1.813910902 1.376374615 0.307403734 0.126541444 3.09E-12 11.51029093 0.35534576 VVLGDGVQLPPGDYST(ph)TPGGTLFSTT(ph)PGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 VVLGDGVQLPPGDY(0.214)S(0.3)T(0.317)T(0.3)PGGT(0.079)LFS(0.168)T(0.14)T(0.391)PGGT(0.091)R 45.809 0.0076862 12643000 814.5 960.65 1064.8 1053.5 867.77 957.76 827.66 800.16 1161.2 766.66 TRUE FALSE FALSE 804.5725607 974.1740559 1083.332397 1175.310627 823.4844588 896.562227 897.9614197 823.3113672 1057.339364 746.7420627 1.07744374 1.304565665 1.450745112 1.573917803 1.102769617 1.200631747 1.202505476 1.102537822 1.415936528 1 9.544466188 -10.35336374 3.858107199 1.033142935 1.282500769 0 0.184324813 0.187088315 5.021380388 0.026114783 0.029808165 4.43E-11 10.35336374 0.249357833 VVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR ddPTM_HeLa_Romidepsin_16h_R1 1 VVLGDGVQLPPGDYSTTPGGTLFSTTPGGTR 31 0 Q13541 Q13541 EIF4EBP1 Eukaryotic translation initiation factor 4E-binding protein 1 2 0 VVLGDGVQLPPGDY(0.115)S(0.035)T(0.091)T(0.758)PGGT(0.01)LFS(0.31)T(0.208)T(0.44)PGGT(0.032)R 74.052 3.26E-06 91191000 14612 15995 13929 12339 14897 13196 11927 13228 15437 15201 TRUE FALSE FALSE 14433.90332 16220.17803 14171.4284 13765.69324 14136.7505 12352.81819 12940.07908 13610.73131 14056.27606 14806.07583 0.974863528 1.095508237 0.957136014 0.929732726 0.954793874 0.83430737 0.873970877 0.919266622 0.949358643 1 13.8539017 -8.841335373 1.424698153 0.995301423 0.879488375 0.539185128 0.04547345 0.219180732 0.892732759 0.006808444 0.016253408 1.44E-09 8.841335373 -0.115813048 VVLIGGKPDR ddPTM_HeLa_Romidepsin_16h_R1 4 VVLIGGKPDR 10 1 P61978-3;P61978;P61978-2;Q5T6W2 P61978-3 HNRNPK Heterogeneous nuclear ribonucleoprotein K 0 0 ;;; ;;; 161.27 0.0014499 63615600 16833 17406.8 17051.3 17106.4 15393.6 14368.8 14194.2 14233.5 16979.2 16131.2 FALSE FALSE TRUE 16627.83292 17651.85339 17348.07072 19084.32246 14608.00715 13450.68005 15399.85499 14645.32387 15460.53783 15712.1091 1.058281407 1.123455373 1.104121071 1.214625124 0.929729234 0.856070943 0.980126532 0.932104263 0.983988701 1 13.93958923 -8.572571138 24.99999741 1.05495209 0.922568375 0.529724184 0.069640626 77.67150368 39075.82917 0.010785274 0.021570552 2.68E-09 8.572571138 -0.132383715 VVNANQNAS(ph)PNVPGKR ddPTM_HeLa_Romidepsin_16h_R1 1 VVNANQNASPNVPGKR 16 1 Q8IWI9-3;Q8IWI9;H3BP52;H3BTF4 Q8IWI9-3 MGA MAX gene-associated protein 1 0 VVNANQNAS(1)PNVPGKR 90.755 0.0035634 9285800 2523.2 2321.1 2004.3 1860.7 2003 2411.9 2566.9 2369 2263.1 1969.8 TRUE FALSE FALSE 2492.446268 2353.776507 2039.184001 2075.842889 1900.779436 2257.787374 2784.932422 2437.543277 2060.682668 1918.624312 1.299079894 1.226804274 1.062836527 1.081943388 0.99069913 1.176774087 1.451525661 1.270464083 1.074041778 1 10.90585653 -12.52277566 1.279999499 1.000058863 1.201935783 0.191615063 0.126625191 0.555567864 1.630455999 0.097242076 0.023356525 3.00E-13 12.52277566 0.201876919 VVNGAAAS(ph)QPPSKR ddPTM_HeLa_Romidepsin_16h_R1 1 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 VVNGAAAS(0.721)QPPS(0.279)KR 76.051 0.012983 4491500 2242.3 1860.7 2021.6 1974.1 1537.3 1873.5 1275.9 1428.6 2074.2 1721.7 TRUE FALSE FALSE 2214.969985 1886.894983 2056.7851 2202.35473 1458.845845 1753.789396 1384.274914 1469.934287 1888.678357 1676.969986 1.320816713 1.12518113 1.226488916 1.313294066 0.869929609 1.045808459 0.82546195 0.876541798 1.12624458 1 10.71164115 -8.746558029 24.99955871 1.169192987 0.908892497 0.635411318 0.103786787 168.6650565 283343.1996 0.019977071 0.039822803 1.79E-09 8.746558029 -0.26030049 VVNGAAASQPPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 VVNGAAASQPPSK 13 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 VVNGAAASQPPS(1)K 125.33 0.0036726 4258200 3263.9 3237.3 3034.6 1444.1 2639.6 2491.6 1987.6 2247 3158.6 3130.1 TRUE FALSE FALSE 3224.118331 3282.874794 3087.41594 1611.073637 2504.891362 2332.394801 2156.426694 2312.0134 2876.086905 3048.779551 1.057511138 1.076783264 1.01267274 0.528432315 0.821604619 0.76502573 0.707308173 0.758340628 0.943356795 1 11.57401612 -9.359444789 8.163066614 1.032023116 0.7245611 0.783465005 0.079166735 0.09100752 6.849542267 0.010798311 0.016509261 4.37E-10 9.359444789 -0.307462016 VVNGAAASQPPS(ph)KR ddPTM_HeLa_Romidepsin_16h_R1 2 VVNGAAASQPPSKR 14 1 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 VVNGAAAS(0.001)QPPS(0.999)KR;VVNGAAAS(0.044)QPPS(0.956)KR ; 113.52 0.00062153 14963000 3728.75 3059.61 3445.6 3045.67 3059.76 2866.66 2316 2813.52 3274.76 3470.51 TRUE FALSE FALSE 3683.302561 3102.68327 3505.569223 3397.824696 2903.60903 2683.489678 2512.720982 2894.924762 2981.857264 3380.34565 1.089623057 0.917859767 1.037044606 1.005170787 0.858968085 0.793850676 0.743332559 0.856399038 0.882116083 1 11.72295506 -8.686944214 2.398648123 1.032044939 0.792839443 0.586329929 0.068199219 0.09281134 1.08470411 0.008128385 0.017895446 2.06E-09 8.686944214 -0.239205496 RPDDVPLSLSPSK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 RPDDVPLSLSPSKR 14 2 F8WDB4;Q9UFC0 F8WDB4 LRWD1 Leucine-rich repeat and WD repeat-containing protein 1 0 1 ; RPDDVPLSLSPSK(1)R;RPDDVPLSLSPSK(1)R 130.21 0.00034877 1872960 411.55 267.78 371.04 447.42 715.65 835.89 912.87 998.56 430.31 479.45 FALSE TRUE FALSE 406.5338703 271.5498139 377.4977956 499.1528056 679.12771 782.4793267 990.409155 1027.451758 391.8219959 466.9938199 0.870533727 0.581484813 0.808357155 1.068863836 1.45425417 1.675566771 2.120818548 2.200139947 0.839030367 1 8.867259647 -8.265024912 1.170723429 0.895790115 2.226899889 0.942691247 0.129640744 0.104415091 0.251407074 0.023315178 0.107769152 5.43E-09 8.265024912 1.331109774 up VVPEDGS(ph)PEKR ddPTM_HeLa_Romidepsin_16h_R1 4 VVPEDGSPEKR 11 1 Q02040 Q02040 AKAP17A A-kinase anchor protein 17A 1 0 VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR;VVPEDGS(1)PEKR ;;; 84.297 0.013749 447724000 19826.4 18933.1 17311.1 18739.4 18783.3 20609.6 18182.3 21581.7 20412.6 18646.2 TRUE FALSE FALSE 19584.74821 19199.64068 17612.39243 20906.1376 17824.71811 19292.71307 19726.70411 22206.13244 18586.84593 18161.76904 1.078350252 1.057145955 0.969750931 1.151106897 0.981441735 1.062270588 1.086166445 1.222685543 1.023405038 1 14.14861711 -7.15695057 1.696365275 1.039481863 1.322322838 0.551055154 0.049669674 0.727932586 1.642262909 0.007032986 0.361195952 6.97E-08 7.15695057 0.282840975 VVPGQFDDADS(ph)SDSENR ddPTM_HeLa_Romidepsin_16h_R1 3 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 0 VVPGQFDDADS(0.495)S(0.495)DS(0.009)ENR;VVPGQFDDADS(0.684)S(0.307)DS(0.009)ENR;VVPGQFDDADS(0.5)S(0.5)DSENR ;; 177.44 8.10E-09 83738600 7504.6 8290.3 8442.7 5229 7365.2 8455.1 6849.8 7073.9 7651.4 7765.4 TRUE FALSE FALSE 7413.131049 8407.011061 8589.641652 5833.601583 6989.326361 7914.846398 7431.621841 7278.572136 6967.039621 7563.653789 0.980099203 1.111501306 1.135647121 0.771267663 0.924067462 1.046431608 0.982543893 0.962309003 0.921120905 1 12.88486761 -9.295152651 24.99911927 1.011243896 0.945161023 0.199763591 0.087964435 1056.782648 783624.1151 0.013491306 0.020608932 5.07E-10 9.295152651 -0.066082872 VVPGQFDDADS(ph)SDSENRDLK ddPTM_HeLa_Romidepsin_16h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 0 VVPGQFDDADS(0.558)S(0.412)DS(0.03)ENRDLK 78.758 0.00186 85737000 3522.4 3360.4 2917.1 3269.9 3534.8 3298.2 3054.5 3220.1 3098.3 3071.2 TRUE FALSE FALSE 3479.467634 3407.707799 2967.870902 3647.981223 3354.405966 3087.455664 3313.949154 3313.268513 2821.180288 2991.409781 1.163153125 1.139164491 0.992131175 1.219485624 1.121346192 1.03210723 1.107821862 1.10759433 0.94309389 1 11.54660984 -12.48507054 1.222496334 0.999886213 1.11445232 0.415042258 0.063165027 0.433295801 1.156877484 0.041539934 0.010108322 3.27E-13 12.48507054 0.114566107 VVPGQFDDADSS(ph)DSENR ddPTM_HeLa_Romidepsin_16h_R1 1 VVPGQFDDADSSDSENR 17 0 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 0 VVPGQFDDADS(0.225)S(0.747)DS(0.029)ENR 165.24 5.84E-06 5902600 2089.8 2431.3 2653.7 1848.7 2317.2 2600.4 1902.2 2474.5 2669.1 2608.7 TRUE FALSE FALSE 2064.328714 2465.527905 2699.886535 2062.455392 2198.944637 2434.242832 2063.772821 2546.095753 2430.369011 2540.925598 0.812431783 0.970326682 1.062560249 0.811694523 0.865410872 0.958014211 0.812213007 1.002034753 0.95648964 1 11.31113842 VVPGQFDDADSS(ph)DSENRDLK ddPTM_HeLa_Romidepsin_16h_R1 2 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 0 VVPGQFDDADS(0.29)S(0.703)DS(0.008)ENRDLK;VVPGQFDDADS(0.286)S(0.714)DSENRDLK ; 126.32 0.00010453 83989000 4480.5 4644.9 4220.5 5169 4795.5 5062.1 4173.7 4316.8 5197.9 4722.9 TRUE FALSE FALSE 4425.889943 4710.291024 4293.956032 5766.664101 4550.767741 4738.648147 4528.213974 4441.699797 4732.986806 4600.198377 0.962108496 1.023932152 0.933428448 1.25356857 0.989254673 1.030096478 0.984351891 0.965545273 1.028865805 1 12.16748036 VVPGQFDDADSSDS(ph)ENRDLK ddPTM_HeLa_Romidepsin_16h_R1 1 VVPGQFDDADSSDSENRDLK 20 1 E9PFQ8;Q9BRS2 E9PFQ8 RIOK1 Serine/threonine-protein kinase RIO1 1 0 VVPGQFDDADS(0.124)S(0.326)DS(0.55)ENRDLK 82.216 0.0014358 15738000 2266.3 2171.2 1993.2 2139.3 1961.6 2101.3 2157.4 1918.4 2141.6 1854.7 TRUE FALSE FALSE 2238.677464 2201.766211 2027.89081 2386.655932 1861.492232 1967.033712 2340.649502 1973.905877 1950.049932 1806.514627 1.239224654 1.218792352 1.122543255 1.321138449 1.03043297 1.08885568 1.295671492 1.092659782 1.079454273 1 10.81899322 -12.4019256 1.10704706 0.999163426 1.181845483 0.243490389 0.092353112 0.427165653 0.929645525 0.060558442 0.015131171 3.96E-13 12.4019256 0.182682057 VVPQQITHT(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 VVPQQITHTSPR 12 0 H7BXF5;A0A2R8YDB8;Q9H0E3;Q9H0E3-3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 0 VVPQQIT(0.141)HT(0.43)S(0.43)PR 85.976 0.0016723 0 4332.6 4108.1 4470.9 4033 5145.2 5826.9 4883.8 4579.7 5571.8 4755.8 TRUE FALSE FALSE 4279.792605 4165.93394 4548.714139 4499.314436 4882.621245 5454.579895 5298.62985 4712.206394 5073.444253 4632.24363 0.923913539 0.899333945 0.981967811 0.971303497 1.054051046 1.177524399 1.143858198 1.01726221 1.095245557 1 12.17749542 -8.638218003 3.105441401 0.959310638 1.116438794 0.460706782 0.063419133 0.113269454 2.176597805 0.007503754 0.016077284 2.30E-09 8.638218003 0.157128156 VVPQQITHTS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 VVPQQITHTSPR 12 0 H7BXF5;A0A2R8YDB8;Q9H0E3;Q9H0E3-3 H7BXF5 SAP130 Histone deacetylase complex subunit SAP130 1 0 VVPQQIT(0.007)HT(0.234)S(0.759)PR 103.11 0.014066 9701800 1488.3 1985.8 1630.6 1550.5 2004.2 1690 1676.3 1604 1676.2 1686.5 TRUE FALSE FALSE 1470.160027 2013.756145 1658.979909 1729.776105 1901.918195 1582.014454 1818.68488 1650.409209 1526.276474 1642.684487 0.894974074 1.225893445 1.009919995 1.053017861 1.157811016 0.963066533 1.107141934 1.004702499 0.929135501 1 10.68183969 -10.30155254 24.99311365 0.950404423 1.071370016 0.385238322 0.07674694 411.5038424 256392.4344 0.01293895 0.014796349 4.99E-11 10.30155254 0.120965593 VVPS(ph)PLQFCAATPK ddPTM_HeLa_Romidepsin_16h_R1 1 VVPSPLQFCAATPK 14 0 Q9Y2F5 Q9Y2F5 ICE1 Little elongation complex subunit 1 1 0 VVPS(1)PLQFCAATPK 171.15 4.78E-05 10294000 5198.1 4897.7 4802.5 352.59 3602.7 4365.1 3548.3 3925.2 4906 4583.5 TRUE FALSE FALSE 5134.743558 4966.649949 4886.085498 393.3581148 3418.840775 4086.184198 3849.692513 4038.769469 4467.195073 4464.420009 1.150147958 1.112496122 1.094450228 0.088109567 0.765797297 0.915277727 0.862305183 0.904657147 1.000621596 1 12.12425705 VVQFEPSKGAIGKAYK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 VVQFEPSKGAIGKAYKK 17 3 H7C443 H7C443 GARS 0 1 VVQFEPSKGAIGK(0.1)AYK(0.9)K 62.378 0.010433 4276100 166.94 164.15 140.56 824.43 3239.3 4328.4 3750.7 5197.2 246.36 184.74 FALSE TRUE FALSE 164.9052711 166.460908 143.0063878 919.7544757 3073.986434 4051.829209 4069.284364 5347.572782 224.3249446 179.9404282 0.916443696 0.925088985 0.794742956 5.111438741 17.08335622 22.51761458 22.61461977 29.71857318 1.246662281 1 7.491375551 -8.620904046 1.466829846 0.830324331 25.87875323 0.975701642 1.697270242 0.038215756 0.162940575 0.244217237 0.674470255 2.39E-09 8.620904046 25.0484289 VVS(ph)ETNDTK ddPTM_HeLa_Romidepsin_16h_R1 1 VVSETNDTK 9 0 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 1 0 VVS(0.775)ET(0.203)NDT(0.022)K 107.11 0.021869 10337000 3648.8 4311 3906.3 3064.3 3480.1 3766.4 3991 1965.8 4223.9 4093.9 TRUE FALSE FALSE 3604.327022 4371.690371 3974.287513 3418.608784 3302.497511 3525.739195 4329.99544 2022.677321 3846.103805 3987.539888 0.903897421 1.096337716 0.996676554 0.85732278 0.828204257 0.884189073 1.085881411 0.507249427 0.964530491 1 11.96128324 -9.243627804 14.88487617 0.969216353 0.849263686 0.232773051 0.140299677 6.597738201 5510.522158 0.019802519 0.032617777 5.71E-10 9.243627804 -0.119952668 VVSDADDS(ph)DSDAVSDK ddPTM_HeLa_Romidepsin_16h_R1 2 VVSDADDSDSDAVSDK 16 0 Q96ST2-3;Q96ST2;Q96ST2-2 Q96ST2-3 IWS1 Protein IWS1 homolog 1 0 VVS(0.001)DADDS(0.921)DS(0.078)DAVSDK;VVSDADDS(0.889)DS(0.111)DAVSDK ; 268.17 2.03E-86 11868900 5432.7 5659.2 4709.9 4257.3 4986.6 5204.5 4465.1 5120 5723.9 5091.6 TRUE FALSE FALSE 5366.484163 5738.870366 4791.873834 4749.549057 4732.115194 4871.949247 4844.365483 5268.139122 5211.940048 4959.319498 1.082100914 1.15718908 0.966236161 0.957701769 0.954186395 0.982382613 0.976820607 1.062270564 1.050938551 1 12.27592646 VVSETNDTK(ac)VLR ddPTM_HeLa_Romidepsin_16h_R1 1 VVSETNDTKVLR 12 1 P05783 P05783 KRT18 "Keratin, type I cytoskeletal 18" 0 1 VVSETNDTK(1)VLR 144.7 5.60E-18 0 124.73 0 185 134.6 156.78 244.16 49.455 199.42 257.87 0 FALSE TRUE FALSE 123.2097428 0 188.2198474 150.1630853 148.7789316 228.558964 53.65570647 205.1899031 234.8054614 0 0 VVSQSQPGS(ph)R ddPTM_HeLa_Romidepsin_16h_R1 2 VVSQSQPGSR 10 0 Q7Z460-4 Q7Z460-4 CLASP1 CLIP-associating protein 1 1 0 VVSQSQPGS(1)R;VVSQSQPGS(1)R ; 118.61 0.012699 12896400 3179.5 3052.3 3729.6 3383.2 2813.6 3474.1 3988.6 1507.48 4321.4 3790.9 TRUE FALSE FALSE 3140.747031 3095.27036 3794.512124 3774.381502 2670.011493 3252.116222 4327.391584 1551.096555 3934.883161 3692.411872 0.850594988 0.838278737 1.027651371 1.022199482 0.72310771 0.880756626 1.17196882 0.420076798 1.065667455 1 11.85034777 -7.243216809 24.6061628 0.929909863 0.420076258 0.610891019 0.126442233 1647.814914 2225024.707 0.016324721 0.71264625 5.71E-08 7.243216809 -0.509833605 VVSSVS(ph)SSPR ddPTM_HeLa_Romidepsin_16h_R1 1 VVSSVSSSPR 10 0 P29375-2;P29375 P29375-2 KDM5A Lysine-specific demethylase 5A 1 0 VVS(0.009)S(0.251)VS(0.479)S(0.223)S(0.038)PR 97.163 0.028142 70603000 3406 2998.4 2960.1 2474.6 3099.9 3473.6 2884.7 3551.5 3211.4 3162.4 TRUE FALSE FALSE 3364.486362 3040.611554 3011.619299 2760.724895 2941.700536 3251.648171 3129.726346 3654.257049 2924.164341 3080.240392 1.09228045 0.987134498 0.977722163 0.896269298 0.955023038 1.055647533 1.016065614 1.1863545 0.949329912 1 11.58882723 -7.260602253 24.14935946 1.019940516 1.186354579 0.440598578 0.058544024 36.99605725 1066951.307 0.009106106 0.073061214 5.49E-08 7.260602253 0.166414063 VVT(ph)SENEAGK ddPTM_HeLa_Romidepsin_16h_R1 1 VVTSENEAGK 10 0 P49321-4;P49321;P49321-3;E9PPR5 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 VVT(0.949)S(0.051)ENEAGK 123.96 0.020413 9808500 6135.9 5358.7 5221.2 3869.9 5490.2 5387.9 5114.2 3324.7 5965.8 5787.6 TRUE FALSE FALSE 6061.113291 5434.139919 5312.072796 4317.356046 5210.014607 5043.630579 5548.60002 3420.894949 5432.203906 5637.237318 1.075192146 0.963972175 0.942318461 0.765863809 0.92421417 0.894698998 0.984276465 0.60683891 0.963628742 1 12.46077259 -9.718909705 2.149913519 1.034465462 0.852220529 0.354296513 0.101900661 0.21499259 2.037025997 0.01567939 0.022712194 1.91E-10 9.718909705 -0.182244933 VVTDTDETELAR ddPTM_HeLa_Romidepsin_16h_R1 1 VVTDTDETELAR 12 0 P05198 P05198 EIF2S1 Eukaryotic translation initiation factor 2 subunit 1 0 0 199.33 9.43E-13 0 1146.2 1089 1338.1 898.57 1390.7 1085.7 1180.3 1428.3 1082.7 1224.6 FALSE FALSE TRUE 1132.229674 1104.330971 1361.389069 1002.466891 1319.72739 1016.327274 1280.554653 1469.625607 985.8606003 1192.784715 0.949232212 0.925842657 1.14135355 0.840442436 1.10642547 0.852062624 1.073584056 1.232096277 0.826520149 1 10.22011796 -7.40927673 3.609071842 0.976350906 1.229857882 0.39934308 0.102768877 0.155932241 3.30971125 0.010861508 0.080587744 3.90E-08 7.40927673 0.253506976 VVTS(ph)ENEAGK ddPTM_HeLa_Romidepsin_16h_R1 1 VVTSENEAGK 10 0 P49321-4;P49321;P49321-3;E9PPR5 P49321-4 NASP Nuclear autoantigenic sperm protein 1 0 VVT(0.067)S(0.933)ENEAGK 147.91 0.0038878 18272000 4484.9 3952.6 4139.3 2902 3974.5 4577.1 4269.2 2158.9 4579.2 4440.9 TRUE FALSE FALSE 4430.236314 4008.244807 4211.34278 3237.542894 3771.666434 4284.638082 4631.825741 2221.364365 4169.624883 4325.524778 1.024207822 0.926649369 0.973602741 0.748474014 0.871955804 0.990547576 1.07081244 0.513547946 0.963958155 1 12.07865946 -9.759476666 1.784238309 1.010253507 0.864575493 0.160836358 0.143506333 0.431905588 2.807295642 0.023017757 0.033321198 1.74E-10 9.759476666 -0.145678013 VVTSGEQEAILRGNAADAESFR ddPTM_HeLa_Romidepsin_16h_R1 1 VVTSGEQEAILRGNAADAESFR 22 1 Q5VZN3;Q6P088;Q8TF39-2;Q8TF39 Q5VZN3 ZNF483 Zinc finger protein 483 0 0 78.529 0.025833 5926200 2592.4 2539.3 2530.2 2668 2924.5 2572.7 2017.7 2764.8 2978.4 2259.7 FALSE FALSE TRUE 2560.802832 2575.048332 2574.23707 2976.486713 2775.251852 2408.312773 2189.083388 2844.795126 2712.004444 2200.992668 1.163476312 1.169948619 1.169580029 1.352338314 1.260909176 1.09419391 0.994589132 1.292505499 1.232173321 1 11.10393862 -11.84616239 0.670388133 0.996086753 1.187451547 0 0.118404284 0.708915875 0.587716581 0.07226782 0.022618312 1.43E-12 11.84616239 0.191364793 VVTVHLEK ddPTM_HeLa_Romidepsin_16h_R1 2 VVTVHLEK 8 0 Q9Y266 Q9Y266 NUDC Nuclear migration protein nudC 0 0 ; ; 120.87 0.000548 13147600 14010.7 12756.9 16455.3 12167.5 15260.4 16342 14497 13890.3 14849.1 12755.5 FALSE FALSE TRUE 13839.9322 12936.49197 16741.69759 13574.3636 14481.60484 15297.79894 15728.37482 14292.19392 13520.95931 12424.11027 1.113957611 1.041240917 1.347516822 1.09258235 1.165604983 1.231299353 1.265955829 1.150359551 1.08828391 1 13.60085492 -10.83364721 0.356915194 0.984006784 1.225667147 0.336757482 0.082267851 0.760651837 0.272481782 0.072441653 0.04858037 1.47E-11 10.83364721 0.241660362 VVTVVTTK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 VVTVVTTKK 9 1 Q7L014;A0A0C4DG89;D6RJA6 Q7L014 DDX46 Probable ATP-dependent RNA helicase DDX46 0 1 ; VVTVVTTK(1)K;VVTVVTTK(1)K 211.45 2.35E-20 20684400 9109.7 9467.4 9368.2 10346.5 12770.7 12820 13979.9 11302.3 9059.2 7172.1 FALSE TRUE FALSE 8998.667472 9600.682306 9531.249591 11542.81101 12118.96352 12000.84337 15167.35236 11629.31422 8248.922463 6985.767808 1.288142939 1.374320271 1.364381104 1.652332475 1.734807663 1.717898978 2.171178999 1.664715252 1.180818299 1 12.77020298 -9.289260361 0.364225457 1.016979942 2.067934803 0.798840903 0.144094015 0.43693322 0.11349061 0.061254701 0.178332082 5.14E-10 9.289260361 1.050954861 VVVDPVVTEQPSTSS(ph)AAK ddPTM_HeLa_Romidepsin_16h_R1 2 VVVDPVVTEQPSTSSAAK 18 0 Q8WWQ0 Q8WWQ0 PHIP PH-interacting protein 1 0 VVVDPVVTEQPSTS(0.02)S(0.979)AAK;VVVDPVVTEQPS(0.017)T(0.009)S(0.189)S(0.785)AAK ; 291.68 6.05E-124 12236400 8656.5 7538.9 7890.2 6714.7 5148 5463.4 4719.6 4649.2 8181.9 7483.8 TRUE FALSE FALSE 8550.991248 7645.032832 8027.525621 7491.085208 4885.27835 5114.306372 5120.482706 4783.717267 7450.090372 7289.369797 1.17307689 1.048792014 1.101264697 1.027672545 0.670192141 0.701611595 0.702458902 0.656259375 1.022048624 1 12.83157838 -8.802760085 4.754193787 1.081140087 0.683649095 0.938754602 0.047471081 0.043902892 2.218046122 0.009723952 0.018409566 1.57E-09 8.802760085 -0.397490992 VVVISSSEDS(ph)DAENSSSR ddPTM_HeLa_Romidepsin_16h_R1 2 VVVISSSEDSDAENSSSR 18 0 P29590-12;P29590-11;P29590-5;P29590 P29590-12;P29590-5 PML Protein PML 1 0 VVVISSSEDS(1)DAENSSSR;VVVIS(0.001)S(0.015)S(0.284)EDS(0.7)DAENSSSR ; 300.56 2.53E-143 8691600 3108.9 2884.4 3361.7 3832.2 4381.4 4455.7 3853.9 3537.2 3765.8 2854.7 TRUE FALSE FALSE 3071.007531 2925.006659 3420.208978 4275.296995 4157.800809 4170.99515 4181.25017 3639.543301 3428.977416 2780.534482 1.104466623 1.051958419 1.230054509 1.537581002 1.495324311 1.500069564 1.503757711 1.308936582 1.233208017 1 11.44114651 -9.497811944 2.951532986 1.050961605 1.473772607 0.802033333 0.086185614 0.057734321 1.015789014 0.010990942 0.016801426 3.18E-10 9.497811944 0.422811002 VVVPATEEEAEVDEFPTDGEMSAQEEDR ddPTM_HeLa_Romidepsin_16h_R1 1 VVVPATEEEAEVDEFPTDGEMSAQEEDR 28 0 B3KXD6;B5MCF9;O00541 B3KXD6 PES1 Pescadillo homolog 0 0 113.13 1.07E-08 3697600 3420.6 4077.9 3410.2 2362.3 3406.6 3504.3 3164.6 3280.4 3613.1 4030.3 FALSE FALSE TRUE 3378.908412 4135.308783 3469.5531 2635.440241 3232.74849 3280.38654 3433.401045 3375.313198 3289.935287 3925.592225 0.860738512 1.05342291 0.883829216 0.671348446 0.823505934 0.835641185 0.874619891 0.859822673 0.83807362 1 11.9386946 -9.519941304 24.99489339 0.942638433 0.81418795 0.368050739 0.077388426 96.19181027 818504.8737 0.012431486 0.017775634 3.02E-10 9.519941304 -0.128450483 (ac)PEPTK(ac)SAPAPK(ac)K(ac)GSK ddPTM_HeLa_Romidepsin_16h_R1 1 PEPTKSAPAPKKGSK 15 3 P58876 P58876 HIST1H2BD Histone H2B type 1-D 0 3 PEPTK(1)SAPAPK(1)K(1)GSK 53.001 1.03E-05 5801700 1797.9 1779.4 1827.4 510.05 4111.9 7356.1 8503.8 9988.6 1737.1 1589.2 FALSE TRUE FALSE 1775.986503 1804.45044 1859.20513 569.0243809 3902.054399 6886.068951 9226.11256 10277.60438 1581.729425 1547.912355 1.147343063 1.165731661 1.20110491 0.367607623 2.520849703 4.448616828 5.960358499 6.639655242 1.02184689 1 10.59610807 -8.153136022 1.576129252 1.040214723 6.519109718 0.977777803 0.323745603 0.038645317 0.177070663 0.046706011 0.190594756 7.03E-09 8.153136022 5.478894995 up VVVTMEHSAK ddPTM_HeLa_Romidepsin_16h_R1 1 VVVTMEHSAK 10 0 P55809;E9PDW2;P55809-2 P55809 OXCT1 "Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial" 0 0 101.38 0.0028257 1001000 454.32 455.32 811.57 571.58 679.36 667.52 618.09 354.71 447.08 221.47 FALSE FALSE TRUE 448.7825731 461.7300069 825.6950354 637.668769 644.6897242 624.8676263 670.5905492 364.9729742 407.0920451 215.7161775 2.080430769 2.14045146 3.827691762 2.956054462 2.988601651 2.896711937 3.108670648 1.691912857 1.887165116 1 7.752990564 -10.91113979 0.748281273 1.167072106 2.899172344 0.449316198 0.589166923 0.267007067 0.3291918 0.182739745 0.139957432 1.23E-11 10.91113979 1.732100238 VWDLFPEADKVR ddPTM_HeLa_Romidepsin_16h_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 0 112.94 0.0018392 0 1611.3 1256.7 2188.7 2530.2 2005.2 1716.6 1576.8 1412.1 1746.5 1135.9 FALSE FALSE TRUE 1591.660856 1274.391856 2226.793405 2822.753629 1902.867162 1606.9148 1710.733353 1452.956886 1590.288666 1106.389154 1.438608513 1.151847748 2.012667421 2.55132077 1.719889565 1.452395655 1.54623113 1.313242163 1.437368271 1 10.1116432 -10.83144735 0.790762662 1.085806364 1.725351479 0.192341192 0.380835487 0.496123856 0.675008576 0.121900048 0.100557456 1.47E-11 10.83144735 0.639545115 VWDYETGDFER ddPTM_HeLa_Romidepsin_16h_R1 3 VWDYETGDFER 11 0 P43034 P43034 PAFAH1B1 Platelet-activating factor acetylhydrolase IB subunit alpha 0 0 ;; ;; 218.94 5.86E-19 52263000 6830.6 7030.4 6808.9 5752.8 6940.8 5994.2 5777.9 6604.6 7638.7 7171.4 FALSE FALSE TRUE 6747.34602 7129.374156 6927.406048 6417.965804 6586.585076 5611.189965 6268.674682 6795.693681 6955.475541 6985.085994 0.965964632 1.020656605 0.991742414 0.918809848 0.942949748 0.803310077 0.897437009 0.972886187 0.995760903 1 12.77006216 -9.032502146 2.067035723 0.987402463 0.894967277 0.502649495 0.04312979 0.206518504 1.75240715 0.006676104 0.012822341 9.28E-10 9.032502146 -0.092435186 VWGSPGGEGTGDLDEFDF ddPTM_HeLa_Romidepsin_16h_R1 2 VWGSPGGEGTGDLDEFDF 18 0 B4E321;Q13438-8;Q13438-6;Q13438-5;Q13438-3;Q13438-2;Q13438-7;Q13438-4;Q13438 B4E321 OS9 Protein OS-9 0 0 ; ; 160.91 3.42E-05 24336000 5876.7 5482.3 5470.9 5715.7 8970.2 12061.7 10285.6 12692.7 6048.6 5595.6 FALSE FALSE TRUE 5805.07252 5559.479963 5566.11872 6376.576127 8512.417222 11290.9963 11159.25861 13059.94325 5507.598067 5450.225505 1.06510685 1.02004586 1.02126393 1.169965558 1.561846792 2.071656721 2.047485668 2.396220713 1.01052664 1 12.41210021 -8.42633524 1.344884284 1.025425824 2.265482418 0.979904723 0.072840857 0.039306829 0.134335771 0.010545251 0.036486932 3.75E-09 8.42633524 1.240056595 up VWQVTIGTR ddPTM_HeLa_Romidepsin_16h_R1 1 VWQVTIGTR 9 0 D6RF23;H0YAF8;D6RAC2;J3KPE3;P63244;D6RHJ5;H0Y8R5;D6RHH4 D6RF23 GNB2L1 "Guanine nucleotide-binding protein subunit beta-2-like 1;Guanine nucleotide-binding protein subunit beta-2-like 1, N-terminally processed" 0 0 116.37 0.013066 3163300 272.88 307.48 173.21 285.38 331.41 363.38 319.39 324.48 229.06 176.71 FALSE FALSE TRUE 269.5540336 311.8087115 176.2246474 318.3769784 314.496911 340.1611908 346.5189786 333.8683169 208.5722999 172.1190487 1.566090654 1.811587467 1.02385325 1.849748652 1.827205724 1.976313449 2.013251765 1.939752278 1.211790917 1 7.427262962 -10.8191486 0.093991922 1.39E-18 2.901823029 0.635065754 0.228087199 5.665862586 0.381648537 6.170833139 5.132105828 1.52E-11 10.8191486 2.901823029 VWS(ph)PLVTEEGK ddPTM_HeLa_Romidepsin_16h_R1 2 VWSPLVTEEGK 11 0 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 0 VWS(0.999)PLVT(0.001)EEGK;VWS(0.968)PLVT(0.032)EEGK ; 150.51 0.00234 45909000 7728.1 7767.9 8607.9 5824.1 11284.2 12455 10823 11224.7 7591.7 8379.5 TRUE FALSE FALSE 7633.906945 7877.2567 8757.716889 6497.509845 10708.32517 11659.1657 11742.30535 11549.46898 6912.679338 8161.799382 0.935321562 0.965137261 1.073013006 0.796087914 1.312005437 1.428504323 1.438690759 1.415064062 0.846955312 1 12.99467153 -8.619797965 5.379006797 0.966748689 1.419707205 0.897827851 0.076636209 0.039158767 1.774204395 0.009237618 0.018740091 2.40E-09 8.619797965 0.452958516 VWS(ph)PLVTEEGKR ddPTM_HeLa_Romidepsin_16h_R1 1 VWSPLVTEEGKR 12 1 O00151 O00151 PDLIM1 PDZ and LIM domain protein 1 1 0 VWS(1)PLVTEEGKR 58.817 0.030368 110870000 2356.4 2595.4 2888.6 2159.2 3810.1 4589.7 3982.3 3989.8 2597.6 2378.3 TRUE FALSE FALSE 2327.67929 2631.938109 2938.874871 2408.856863 3615.65638 4296.432983 4320.556463 4105.238568 2365.26415 2316.511423 1.004820985 1.136164529 1.268664096 1.039864012 1.560819577 1.854699675 1.865113385 1.772164181 1.021045753 1 11.17773808 -8.624557997 2.259274208 1.032800339 1.83933114 0.934591111 0.090097974 0.052849989 0.544417859 0.014802829 0.03424049 2.37E-09 8.624557997 0.806530801 VY(ph)DIWSLGVILYIMVCGSMPYDDS(ph)NIKKMLR ddPTM_HeLa_Romidepsin_16h_R1 1 VYDIWSLGVILYIMVCGSMPYDDSNIKKMLR 31 2 Q9BXA7 Q9BXA7 TSSK1B Testis-specific serine/threonine-protein kinase 1 2 0 VY(0.983)DIWS(0.017)LGVILY(0.014)IMVCGS(0.013)MPY(0.046)DDS(0.928)NIKKMLR 45.187 0.0092927 5456500 2497.4 1995.3 2149.8 1854.7 1773.7 2352.9 1681.9 2300.8 2520.4 2306.9 TRUE FALSE FALSE 2466.960728 2023.389886 2187.216367 2069.149141 1683.18147 2202.557284 1824.760544 2367.370018 2294.969112 2246.966405 1.097907259 0.900498504 0.973408575 0.920863407 0.749090626 0.980235965 0.812099611 1.053584963 1.021363339 1 11.13376284 -10.24955945 24.25611676 1.046233983 0.907886266 0.321444018 0.084140448 385.7872482 787690.0728 0.013627912 0.016615928 5.63E-11 10.24955945 -0.138347717 VY(ph)S(ph)QRS(ph)RVVLS(ph)TS(ph)TQR ddPTM_HeLa_Romidepsin_16h_R1 1 VYSQRSRVVLSTSTQR 16 2 Q8N5H3-2 Q8N5H3-2 5 0 VY(0.999)S(0.999)QRS(0.977)RVVLS(0.804)T(0.285)S(0.491)T(0.443)QR 40.844 0.0042709 0 585.09 508.93 621.84 591.15 641.62 630.35 612.87 758.37 729.79 724.73 TRUE FALSE FALSE 577.958698 516.0947299 632.6628644 659.5015444 608.8757372 590.0726694 664.9271625 780.3122394 664.5157546 705.9014101 0.818752718 0.731114462 0.896248195 0.934268632 0.862550674 0.835913714 0.941954716 1.105412496 0.941371904 1 9.463322893 -7.30854258 3.302205532 0.89173469 1.124092201 0.4703233 0.071690231 0.250790855 4.478072459 0.012538286 0.137339078 4.91E-08 7.30854258 0.232357511 VYEDSGIPLPAES(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 2 VYEDSGIPLPAESPK 15 0 F8W038;H0YIS7;Q8IXM2;Q8IXM2-3;F8W1H0;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 0 VYEDSGIPLPAES(1)PK;VYEDS(0.001)GIPLPAES(0.999)PK ; 193.54 1.33E-12 197364000 22354 21473 22405 13170 12096.1 12341.7 10752.2 12620.3 20927 21547 TRUE FALSE FALSE 22081.54085 21775.29746 22794.94963 14692.77737 11478.79088 11553.1052 11665.4916 12985.44847 19055.23671 20987.20583 1.052142959 1.03755105 1.086135515 0.700082588 0.546942312 0.550483246 0.555838242 0.618731649 0.907945386 1 14.35722248 -9.119737192 3.514221189 1.030599406 0.569303971 0.947227114 0.050433273 0.026527981 0.602087378 0.005584749 0.009654443 7.59E-10 9.119737192 -0.461295435 VYEDSGIPLPAES(ph)PKK ddPTM_HeLa_Romidepsin_16h_R1 1 VYEDSGIPLPAESPKK 16 1 F8W038;H0YIS7;Q8IXM2;Q8IXM2-3;F8W1H0;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 0 VYEDSGIPLPAES(1)PKK 78.088 0.0081824 10869000 1589.7 1499.5 1980.2 1113.3 1168.8 1126.6 885.66 1278.3 1764.3 1833 TRUE FALSE FALSE 1570.324125 1520.61 2014.66455 1242.024984 1109.151775 1054.613896 960.8879383 1315.285594 1606.496589 1785.378396 0.879546951 0.851701804 1.128424403 0.695664845 0.621241848 0.59069489 0.53819848 0.736698504 0.899807342 1 10.80201416 -9.083625198 5.920534552 0.945719745 0.618363045 0.775365578 0.085533562 0.079752329 4.484567573 0.013000016 0.021813982 8.25E-10 9.083625198 -0.3273567 VYEDSGIPLPAES(ph)PKKGPK ddPTM_HeLa_Romidepsin_16h_R1 2 VYEDSGIPLPAESPKKGPK 19 2 F8W038;H0YIS7;Q8IXM2;Q8IXM2-3;F8W1H0;Q8IXM2-2 F8W038;Q8IXM2-2 C17orf49;RNASEK-C17orf49;BAP18 Chromatin complexes subunit BAP18 1 0 VYEDSGIPLPAES(1)PKKGPK;VYEDS(0.009)GIPLPAES(0.991)PKKGPK ; 81.428 0.0030043 76073000 18536 15459.3 15333.8 21976 11731.3 10660.9 9954.4 10141.1 18885.3 14683.8 TRUE FALSE FALSE 18310.0761 15676.93643 15600.67836 24516.96852 11132.60799 9979.702896 10799.92649 10434.51673 17196.15147 14302.31276 1.280217851 1.096111985 1.090780115 1.714196084 0.778378167 0.69776847 0.755117488 0.72956849 1.20233362 1 13.80396084 -8.559705379 24.99999513 1.168533143 0.731551309 0.611803248 0.187818621 96.55554631 65547.00524 0.028478565 0.056957248 2.76E-09 8.559705379 -0.436981834 VYFHPMT(ph)NAATMGLS(ph)PEDFLTFVK ddPTM_HeLa_Romidepsin_16h_R1 1 VYFHPMTNAATMGLSPEDFLTFVK 24 0 A6NEY8 A6NEY8 PRORSD1P Putative prolyl-tRNA synthetase associated domain-containing protein 1 2 0 VY(0.034)FHPMT(0.606)NAAT(0.361)MGLS(0.931)PEDFLT(0.068)FVK 40.849 0.021727 55003000 3063.3 5008.7 4308.9 3162 3076.1 4541.8 4607.7 2398.6 3871.1 3034.8 TRUE FALSE FALSE 3025.963321 5079.21261 4383.894597 3527.605318 2919.115138 4251.593638 4999.077923 2467.999707 3524.859121 2955.955459 1.023683666 1.718298087 1.48307194 1.193389199 0.987536916 1.438314514 1.691188515 0.834924525 1.192460161 1 11.52940882 -10.46761377 24.98679371 1.010448341 1.341987776 0.154897531 0.270333451 291.5846606 131834.0657 0.043541183 0.04976554 3.41E-11 10.46761377 0.331539435 VYFQS(ph)PPGAAGEGPGGADDEGPVRR ddPTM_HeLa_Romidepsin_16h_R1 2 VYFQSPPGAAGEGPGGADDEGPVRR 25 1 Q96C90 Q96C90 PPP1R14B Protein phosphatase 1 regulatory subunit 14B 1 0 VY(0.025)FQS(0.975)PPGAAGEGPGGADDEGPVRR;VY(0.068)FQS(0.932)PPGAAGEGPGGADDEGPVRR ; 55.302 0.0026972 185108000 1823.03 1795.29 1773.57 1808.69 2274.32 3015.3 2731 2867.9 2066.25 1717.67 TRUE FALSE FALSE 1800.810209 1820.56414 1804.438242 2017.819248 2158.252964 2822.632061 2962.971072 2950.878162 1881.439425 1673.044686 1.076367072 1.088174246 1.078535593 1.206076123 1.290015134 1.687122935 1.77100534 1.763777254 1.124560175 1 10.70826026 -8.407395543 1.214642948 1.042804158 1.813570817 0.972705797 0.048440367 0.048480474 0.132130308 0.007197449 0.027467907 3.91E-09 8.407395543 0.770766659 VYNVTQHAVGIVVNK ddPTM_HeLa_Romidepsin_16h_R1 2 VYNVTQHAVGIVVNK 15 0 G3V1B3;M0R181;P46778 G3V1B3 RPL21 60S ribosomal protein L21 0 0 ; ; 106.58 0.0021461 746180 924.57 1027.77 763.28 1032.27 1125.81 1163.84 1063.19 1091.61 1344 1157.7 FALSE FALSE TRUE 913.3009852 1042.238973 776.5645682 1151.625914 1068.355715 1089.47438 1153.497332 1123.194013 1223.789274 1127.622787 0.809934843 0.924279808 0.688674065 1.021286487 0.947440693 0.966169177 1.0229461 0.996072468 1.085282497 1 10.13906882 VYREELK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 VYREELKR 8 2 P04083;Q5T3N1 P04083 ANXA1 Annexin A1;Annexin 0 1 ; VYREELK(1)R;VYREELK(1)R 95.358 0.01909 4284500 801.66 854.1 1132.79 1169.09 2966.1 2197.72 2439.33 1000.37 1757.62 1016.41 FALSE TRUE FALSE 791.8890596 866.1240422 1152.505735 1304.265687 2814.728849 2057.292785 2646.526629 1029.314128 1600.414065 990.0035217 0.799885094 0.874869658 1.164143066 1.317435401 2.84315034 2.078066128 2.673249712 1.039707542 1.616574113 1 9.951289847 -8.94683318 5.561358812 0.929864674 2.188823206 0.489078484 0.505466329 0.087905923 5.884584891 0.06225463 0.11354975 1.13E-09 8.94683318 1.258958532 VYS(ph)SSEFLAVQPTPTFAER ddPTM_HeLa_Romidepsin_16h_R1 1 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 0 VYS(0.618)S(0.382)S(0.001)EFLAVQPTPTFAER 207.21 1.16E-21 20241000 1435.5 1524.2 1201.6 1527.7 2543.9 3561.8 2846.6 4023.9 1361.2 1288.9 TRUE FALSE FALSE 1418.003574 1545.657728 1222.513344 1704.339862 2414.07529 3334.212475 3088.390133 4140.325198 1239.450863 1255.414192 1.129510549 1.231193448 0.973792834 1.35759168 1.922931336 2.655866483 2.46005673 3.29797546 0.987284412 1 10.29394771 -8.380483368 1.063625103 1.057704037 3.045979667 0.945634679 0.184809077 0.085020609 0.170301143 0.027396326 0.120714889 4.16E-09 8.380483368 1.98827563 up VYSSS(ph)EFLAVQPTPTFAER ddPTM_HeLa_Romidepsin_16h_R1 1 VYSSSEFLAVQPTPTFAER 19 0 O60307;V9GYV0 O60307 MAST3 Microtubule-associated serine/threonine-protein kinase 3 1 0 VYS(0.066)S(0.241)S(0.548)EFLAVQPT(0.125)PT(0.02)FAER 67.902 0.017847 14483000 794.88 861.35 1005.8 1165.3 2036.1 2247.2 1830.4 2725.9 1052.1 1034.2 TRUE FALSE FALSE 785.1916968 873.4761079 1023.305527 1300.037469 1932.190219 2103.611173 1985.87413 2804.769616 957.997541 1007.331335 0.779477089 0.867118968 1.015857932 1.290575825 1.918127782 2.088301137 1.971420983 2.784356565 0.951025256 1 9.976322582 -8.62202613 0.990236808 0.881093274 2.427853763 0.91592886 0.186357435 0.113934039 0.207853225 0.030999874 0.111930732 2.39E-09 8.62202613 1.546760489 up VYTLSVSGDR ddPTM_HeLa_Romidepsin_16h_R1 1 VYTLSVSGDR 10 0 J3QT28;O43684-2;O43684 J3QT28 BUB3 Mitotic checkpoint protein BUB3 0 0 123.35 0.026764 969690 191.14 145.84 114.57 138.79 59.781 150.45 130.15 0 0 140.09 FALSE FALSE TRUE 188.8103122 147.8931393 116.5640428 154.8375528 56.7301525 140.8367306 141.2049378 0 0 136.4504416 1.383728114 1.083859734 0.854259183 1.134753036 0.415756459 1.032145656 1.034844124 0 0 1 7.092233253 -7.403969589 0.503076549 1.166021806 1.70E-17 0 0.468788041 2.887242458 0.535641078 0.063830492 1.925375773 3.94E-08 7.403969589 -1.166021806 VYYTAGYNS(ph)PVK ddPTM_HeLa_Romidepsin_16h_R1 1 VYYTAGYNSPVK 12 0 Q9Y5Z4-2;Q9Y5Z4 Q9Y5Z4-2 HEBP2 Heme-binding protein 2 1 0 VYYTAGYNS(1)PVK 165.64 0.0002678 18281000 2896.1 2266.9 2758.2 2446.3 2840.2 2690.9 1986.3 2430.5 2641.1 1944 TRUE FALSE FALSE 2860.801219 2298.813478 2806.205314 2729.152716 2695.253996 2518.960174 2155.016272 2500.822683 2404.873401 1893.4946 1.510857871 1.21405864 1.482024461 1.441331133 1.423428404 1.3303234 1.13811588 1.320744555 1.270071434 1 10.88683559 -12.46122493 1.156739522 0.996886334 1.369237158 0.211698141 0.136663535 0.286407684 0.6762659 0.086502524 0.020654575 3.46E-13 12.46122493 0.372350824 WAAHGAS(ph)PEDFSLTLGAR ddPTM_HeLa_Romidepsin_16h_R1 1 WAAHGASPEDFSLTLGAR 18 0 Q86UU1-2;Q86UU1;Q86UU1-3 Q86UU1-2 PHLDB1 Pleckstrin homology-like domain family B member 1 1 0 WAAHGAS(1)PEDFSLTLGAR 102.07 0.00025451 0 2166.4 1823.5 2192.8 1805.2 2300.7 1972.9 1547.8 1858 2495.8 1921.7 TRUE FALSE FALSE 2139.995084 1849.171281 2230.964764 2013.925718 2183.286694 1846.838057 1679.270093 1911.758299 2272.569397 1871.773957 1.143297819 0.987924463 1.191898603 1.07594494 1.166426472 0.986677932 0.897154321 1.021361736 1.214125984 1 10.8701905 -8.021297949 21.71550571 1.078792929 0.954922533 0.355579589 0.08072998 113.5859618 115815.1331 0.010572072 0.027365598 9.52E-09 8.021297949 -0.123870396 WADPQISES(ph)NFSPK ddPTM_HeLa_Romidepsin_16h_R1 1 WADPQISESNFSPK 14 0 D6RAW2;Q9BW91-2;Q9BW91 D6RAW2 NUDT9 "ADP-ribose pyrophosphatase, mitochondrial" 1 0 WADPQIS(0.091)ES(0.888)NFS(0.021)PK 101.72 0.0094358 20250000 5584.5 6080.5 5766.7 5311.8 7365.7 8261.3 7303.6 7753.8 5875.4 6275.8 TRUE FALSE FALSE 5516.433966 6166.101439 5867.066994 5925.975309 6989.800844 7733.429592 7923.967602 7978.14397 5349.889509 6112.753811 0.902446612 1.008727266 0.959807507 0.969444459 1.143478219 1.265130223 1.296300791 1.305163633 0.875201206 1 12.57760675 -8.525729443 1.881558516 0.956968342 1.29915635 0.938867068 0.038846833 0.058878325 0.411924176 0.006001122 0.015762 2.98E-09 8.525729443 0.342188007 WAEYHADIYDK ddPTM_HeLa_Romidepsin_16h_R1 1 WAEYHADIYDK 11 0 Q9NRX4-2;Q9NRX4 Q9NRX4-2 PHPT1 14 kDa phosphohistidine phosphatase 0 0 96.64 0.011105 33439000 5547.5 4451.5 5386.3 3246.1 6750.9 5833.1 4913.5 5155.1 5782.7 4700.1 FALSE FALSE TRUE 5479.884936 4514.168334 5480.046292 3621.429355 6406.376382 5460.383735 5330.852567 5304.254685 5265.480829 4577.990724 1.197006562 0.986058864 1.197041808 0.791052139 1.399386055 1.192746789 1.164452461 1.158642515 1.150172892 1 12.16049882 -16.01140519 0.325472045 1.44E-08 1.151415217 0 0.156624599 59.79444766 1.099524662 39.07455043 0.052498953 9.74E-17 16.01140519 1.151415203 WAHDKFS(ph)GEEGEIEDDESGTENR ddPTM_HeLa_Romidepsin_16h_R1 1 WAHDKFSGEEGEIEDDESGTENR 23 1 Q9Y2W1 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 1 0 WAHDKFS(0.999)GEEGEIEDDES(0.001)GTENR 59.537 0.0029339 17414000 5201.2 5421.1 5061.7 3313.1 5063.9 5290.8 4886.2 4845.1 5607.8 5095.9 TRUE FALSE FALSE 5137.805774 5497.418388 5149.796765 3696.176211 4805.470287 4952.734955 5301.233706 4985.285324 5106.224323 4963.507783 1.035115889 1.107567194 1.037531719 0.744670175 0.968160119 0.997829594 1.068041784 1.00438753 1.028753161 1 12.27714434 WASLADS(ph)YSDPGLTEDGLGR ddPTM_HeLa_Romidepsin_16h_R1 1 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 WASLADS(0.431)Y(0.002)S(0.431)DPGLT(0.136)EDGLGR 122.16 0.0001993 4050900 918.95 1074.2 1266.5 1037.9 922.44 1040.8 881.81 1150.1 925.78 1051.2 TRUE FALSE FALSE 907.7494839 1089.322616 1288.542901 1157.906881 875.3644447 974.296239 956.7109194 1183.376329 842.9759181 1023.889672 0.886569626 1.063906244 1.258478268 1.130890283 0.854940203 0.951563694 0.93438868 1.15576547 0.823307375 1 9.999844553 -10.24543228 24.1436127 0.946435656 1.045386914 0.214793779 0.12010502 840.4575479 1267668.373 0.020686719 0.025287744 5.68E-11 10.24543228 0.098951258 WASLADSYS(ph)DPGLTEDGLGR ddPTM_HeLa_Romidepsin_16h_R1 1 WASLADSYSDPGLTEDGLGR 20 0 J3KQR7;Q9Y4F5-3;Q9Y4F5-2;Q9Y4F5 J3KQR7 CEP170B Centrosomal protein of 170 kDa protein B 1 0 WASLADS(0.026)Y(0.001)S(0.928)DPGLT(0.046)EDGLGR 135.57 0.00029759 3775700 1152.6 1304.3 1282.8 1226.3 1325.9 1555.4 1173.3 1562.3 1492.2 1402.7 TRUE FALSE FALSE 1138.551668 1322.66197 1305.126596 1368.090576 1258.234375 1456.01496 1272.960073 1607.502686 1358.733895 1366.257652 0.833335986 0.968091171 0.955256568 1.001341565 0.920934916 1.06569574 0.931713042 1.176573601 0.994493164 1 10.41601386 -4 0.6142671 0.929618512 15.79849921 0.422872713 0.065751569 122.9371339 0.834990745 0.013106587 2470.275142 1.00E-04 4 14.8688807 WCNEHLK ddPTM_HeLa_Romidepsin_16h_R1 1 WCNEHLK 7 0 Q60FE5;P21333-2;P21333;A0A087WWY3;F8WE98;Q14315-2;Q14315;O75369-8;O75369-2;O75369-9;O75369;O75369-6;O75369-3;O75369-5;O75369-4 Q60FE5;Q14315-2;O75369-8 FLNA;FLNC;FLNB Filamin-A;Filamin-C;Filamin-B 0 0 83.005 0.0033793 0 3810.1 2770.5 6710.4 320.19 6612.2 7868 5773.8 3105.1 3472.3 1928.1 FALSE FALSE TRUE 3763.661036 2809.503172 6827.191697 357.2118743 6274.75476 7365.260193 6264.226428 3194.941169 3161.728791 1878.007684 2.004071159 1.496001958 3.635337467 0.190207888 3.341176298 3.921847741 3.33557018 1.701239668 1.683554768 1 10.87498725 -10.38294584 0.26164577 0.759586689 3.247823865 0.189377598 1.070463382 1.736209266 0.442768221 1.573540627 1.589679648 4.14E-11 10.38294584 2.488237177 WDAADDIHR ddPTM_HeLa_Romidepsin_16h_R1 2 WDAADDIHR 9 0 Q9HD15;R4GMW4 Q9HD15 SRA1 Steroid receptor RNA activator 1 0 0 ; ; 103.26 0.011873 14638700 17126.2 16196.8 15578.7 15305.8 18220.1 17182.2 15613.7 15766.3 17132.9 15929.7 FALSE FALSE TRUE 16917.45929 16424.81898 15849.84074 17075.52861 17290.26031 16084.31287 16939.92729 16222.47302 15600.49051 15515.8441 1.090334447 1.058583656 1.021526166 1.100522054 1.114361565 1.036637954 1.091782515 1.045542409 1.005455483 1 13.92145456 -12.39417518 0.959972091 0.997104016 1.07169462 0.471276923 0.028363233 0.42923879 0.662304604 0.02342515 0.00512867 4.03E-13 12.39417518 0.074590604 WDDPYYDIAR ddPTM_HeLa_Romidepsin_16h_R1 1 WDDPYYDIAR 10 0 E9PNR6;H0YE29;Q07960 E9PNR6 ARHGAP1 Rho GTPase-activating protein 1 0 0 196.79 1.27E-07 14078000 4166.3 2993.8 4364.3 4012.2 4284.4 3865.3 3399.8 3310.1 3926.9 3184.4 FALSE FALSE TRUE 4115.519533 3035.946795 4440.258811 4476.109442 4065.751081 3618.319805 3688.578927 3405.872521 3575.668229 3101.668829 1.326872648 0.978810751 1.431570892 1.443129389 1.310826947 1.166571934 1.189223973 1.098077425 1.152820764 1 11.59882894 -12.43028305 0.969340969 0.988061071 1.252752554 0.142472101 0.144332707 0.616935675 0.957815232 0.121720893 0.025461774 3.71E-13 12.43028305 0.264691483 WDGS(ph)EEDEDNSK ddPTM_HeLa_Romidepsin_16h_R1 6 WDGSEEDEDNSK 12 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK;WDGS(0.999)EEDEDNS(0.001)K;WDGS(1)EEDEDNSK;WDGS(1)EEDEDNSK ;;;;; 175.88 1.22E-05 65878100 17363.47 16853.85 16225.17 15110.23 18203.97 19112 17635.23 19218.19 17621.05 16902.62 TRUE FALSE FALSE 17151.83735 17091.11894 16507.56228 16857.34589 17274.95348 17890.80488 19133.166 19774.23801 16044.97916 16463.4875 1.041810695 1.03812263 1.002677123 1.023923145 1.049288827 1.086695932 1.162157532 1.201096548 0.974579606 1 14.00698236 -7.797809885 1.200439121 1.020307973 1.220970699 0.921060542 0.019349012 0.126789805 0.263547577 0.002692706 0.02486989 1.59E-08 7.797809885 0.200662726 WDGS(ph)EEDEDNSKK ddPTM_HeLa_Romidepsin_16h_R1 5 WDGSEEDEDNSKK 13 1 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 1 0 WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK;WDGS(1)EEDEDNSKK ;;;; 226.23 1.90E-31 421340000 17355.6 16571.1 16119.2 15696.4 18499.1 19636.3 17185.1 18963.1 18177.2 18911.8 TRUE FALSE FALSE 17144.06327 16804.38838 16399.74791 17511.29162 17555.0219 18381.6038 18644.80197 19511.76738 16551.38571 18420.46871 0.930707223 0.912267144 0.890300251 0.950643108 0.953017112 0.997890124 1.012178477 1.059243806 0.898532278 1 14.16902215 -7.708198169 1.410600796 0.954315458 1.061129965 0.558850587 0.034839605 0.466285066 1.385919948 0.005962177 0.055716738 1.96E-08 7.708198169 0.106814507 WDGSEEDEDNSK ddPTM_HeLa_Romidepsin_16h_R1 1 WDGSEEDEDNSK 12 0 A0A087WUT6;O60841 A0A087WUT6 EIF5B Eukaryotic translation initiation factor 5B 0 0 142.08 0.00032016 0 648.55 661.49 578.17 844.3 610.33 599.8 599.23 967.79 653.51 806.34 FALSE FALSE TRUE 640.6452231 670.8024736 588.2328063 941.9219386 579.1825826 561.4747158 650.1285812 995.7914767 595.0584289 785.3911706 0.815702095 0.854099841 0.748967939 1.199302938 0.737444734 0.714898177 0.827776789 1.267892375 0.757658669 1 9.617267569 -12.53425096 1.319519329 0.999449887 0.877514143 0 0.195233411 1.098932288 3.451086544 0.118073606 0.028714803 2.92E-13 12.53425096 -0.121935745 WDKDDFES(ph)EEEDVK ddPTM_HeLa_Romidepsin_16h_R1 1 WDKDDFESEEEDVK 14 1 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-4 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 WDKDDFES(1)EEEDVK 87.676 0.0081299 109530000 2955.9 2832.6 2799.7 1589.1 2781.2 3058.5 2797.7 3430.4 3161 3027.4 TRUE FALSE FALSE 2919.872354 2872.477417 2848.427604 1772.839219 2639.264986 2863.071721 3035.336568 3529.653212 2878.272243 2948.747712 0.990207586 0.974134683 0.965978742 0.601217667 0.895046048 0.970944957 1.02936462 1.197000746 0.976099865 1 11.52588668 -9.660598545 4.869248973 0.993584799 0.929142481 0.017531454 0.139139143 0.62387697 24.683871 0.022857308 0.03245064 2.18E-10 9.660598545 -0.064442318 WDKDDFES(ph)EEEDVKSTQPISSVGKPASVIK ddPTM_HeLa_Romidepsin_16h_R1 1 WDKDDFESEEEDVKSTQPISSVGKPASVIK 30 3 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-4 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 WDKDDFES(0.361)EEEDVKS(0.303)T(0.303)QPIS(0.017)S(0.017)VGKPASVIK 47.919 0.018631 76346000 2132.1 2353.7 2071.3 2954 2778.6 2812.2 2083.1 2837.3 2659.1 2295 TRUE FALSE FALSE 2106.113145 2386.83545 2107.350108 3295.555379 2636.797674 2632.509496 2260.038462 2919.392799 2421.263436 2235.375569 0.942174181 1.067755899 0.942727538 1.474273686 1.179577029 1.177658704 1.011032997 1.305996558 1.083157331 1 11.12630153 -9.334459458 24.99999941 0.978598527 1.211887721 0.453782169 0.119253715 84.8230437 29040.65569 0.016935952 0.025870096 4.63E-10 9.334459458 0.233289194 WDKDDFESEEEDVKS(ph)TQPISSVGKPASVIK ddPTM_HeLa_Romidepsin_16h_R1 1 WDKDDFESEEEDVKSTQPISSVGKPASVIK 30 3 A0A2R8Y880;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-4 A0A2R8Y880 RBBP6 E3 ubiquitin-protein ligase RBBP6 1 0 WDKDDFES(0.267)EEEDVKS(0.533)T(0.182)QPIS(0.008)S(0.01)VGKPASVIK 46.412 0.022059 46268000 1097.4 1016.6 981.92 1110.6 1315 1149.9 1117.6 1236.9 965.5 918.62 TRUE FALSE FALSE 1084.024467 1030.911721 999.0099057 1239.012798 1247.890643 1076.425101 1212.528916 1272.68775 879.1432619 894.75412 1.211533362 1.152173204 1.116518922 1.384752269 1.394674375 1.203040117 1.355153208 1.422388253 0.982552907 1 9.805347471 -12.2009764 0.046478222 8.10E-18 2.174381527 0.745336225 0.077734426 58.26271274 0.715921992 20.09212818 13.64048233 6.30E-13 12.2009764 2.174381527 WDQTADQTPGAT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 4 WDQTADQTPGATPK 14 0 O75533 O75533 SF3B1 Splicing factor 3B subunit 1 1 0 WDQT(0.269)ADQT(0.25)PGAT(0.481)PK;WDQTADQT(0.24)PGAT(0.759)PK;WDQTADQT(0.004)PGAT(0.996)PK;WDQTADQT(0.001)PGAT(0.999)PK ;;; 203.92 1.86E-16 236892000 24292.1 22534.6 23402 22408.9 21465.6 22434.7 18922.4 23151.6 24903.9 22952.1 TRUE FALSE FALSE 23996.01854 22851.84269 23809.30199 24999.92246 20370.13033 21001.19507 20529.66818 23821.45502 22676.43281 22355.80113 1.07336876 1.022188494 1.06501672 1.118274505 0.911178723 0.939406955 0.91831503 1.065560338 1.014342214 1 14.44836163 -8.747748209 24.99993845 1.042172547 0.954364656 0.424945346 0.050982173 186.0930483 339802.1311 0.007598848 0.01513099 1.79E-09 8.747748209 -0.087807892 WDS(ph)YENLSADGEVLHTQGPVDGSLYAK ddPTM_HeLa_Romidepsin_16h_R1 1 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 0 WDS(0.54)Y(0.028)ENLS(0.34)ADGEVLHT(0.091)QGPVDGSLYAK 54.375 0.0039826 136380000 1464.7 1265.4 1259.5 867.41 1164.9 1573.4 1029.7 1122.1 1668.2 1299.6 TRUE FALSE FALSE 1446.847673 1283.214334 1281.421069 967.7040255 1105.450806 1472.864818 1117.162692 1154.566193 1518.992014 1265.836205 1.142997544 1.013728577 1.012311912 0.764478075 0.873296878 1.163550871 0.88254917 0.912097623 1.199990969 1 10.30587502 -9.638506582 3.165983418 1.066059105 0.926116361 0.335777239 0.109482234 0.258921333 5.190100147 0.017469252 0.025303295 2.30E-10 9.638506582 -0.139942744 WDSYENLS(ph)ADGEVLHTQGPVDGSLYAK ddPTM_HeLa_Romidepsin_16h_R1 1 WDSYENLSADGEVLHTQGPVDGSLYAK 27 0 Q68CZ2;E9PCX8;C9JHU5;Q68CZ2-3 Q68CZ2 TNS3 Tensin-3 1 0 WDS(0.28)Y(0.053)ENLS(0.587)ADGEVLHT(0.081)QGPVDGSLYAK 53.551 0.0055953 147210000 1040.8 999.1 903.9 1019.3 1036.4 831.05 926.34 1054.8 1128.2 961.79 TRUE FALSE FALSE 1028.114329 1013.165356 919.6320003 1137.156262 983.5086407 777.9485871 1005.023296 1085.318974 1027.290966 936.8025571 1.097471737 1.081514294 0.981671104 1.213869724 1.049856913 0.830429615 1.072822964 1.158535452 1.096592829 1 9.871601204 -7.318480594 4.83708724 1.04290106 1.160218559 0.115988573 0.093676536 0.280888572 13.13712763 0.012720231 0.086819639 4.80E-08 7.318480594 0.117317499 WDVDDWDNENSSAR ddPTM_HeLa_Romidepsin_16h_R1 4 WDVDDWDNENSSAR 14 0 A0A087WUZ3;Q01082;Q01082-2;F8W6C1 A0A087WUZ3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 ;;; ;;; 320.07 8.55E-173 48383500 10863 8903.49 9622 7896.3 9502 9478.5 8908.4 9991.3 11694.6 10243.3 FALSE FALSE TRUE 10730.59758 9028.833566 9789.466874 8809.307359 9017.077483 8872.85444 9665.079274 10280.3825 10648.60569 9977.177589 1.075514341 0.904948668 0.98118599 0.882945831 0.90377037 0.889315075 0.968718777 1.030389848 1.067296396 1 13.28441604 -10.25804017 24.98625789 1.03565955 0.934990758 0.522584358 0.047859847 199.6281789 1467389.55 0.008641549 0.010364665 5.52E-11 10.25804017 -0.100668792 WEADTLDKEGLSES(ph)VR ddPTM_HeLa_Romidepsin_16h_R1 1 WEADTLDKEGLSESVR 16 1 Q6PHR2-3;Q6PHR2;Q6PHR2-4 Q6PHR2-3 ULK3 Serine/threonine-protein kinase ULK3 1 0 WEADTLDKEGLS(0.002)ES(0.998)VR 88.57 0.0050309 9517600 2506.2 2138.4 1838 2389.1 2469.3 2178.5 1809.9 2651.9 2146.9 2242.8 TRUE FALSE FALSE 2475.65347 2168.504451 1869.989619 2665.338983 2343.282407 2039.300881 1963.632861 2728.628542 1954.875887 2184.531733 1.133265053 0.992663287 0.856013942 1.220096254 1.072670345 0.933518543 0.898880447 1.249067936 0.89487182 1 11.09310835 WEDRWEWLR ddPTM_HeLa_Romidepsin_16h_R1 1 WEDRWEWLR 9 1 A0A087WUZ3;Q01082;Q01082-2;Q01082-3 A0A087WUZ3;Q01082-3 SPTBN1 "Spectrin beta chain, non-erythrocytic 1" 0 0 128.12 0.010516 8700600 2403.9 2053.7 2701.1 1987.6 2387.7 2368.2 2529.1 2655.6 2296.7 2256.2 FALSE FALSE TRUE 2374.600342 2082.612043 2748.111512 2217.415664 2265.846759 2216.879663 2743.921691 2732.435596 2091.2774 2197.583599 1.08055063 0.947682738 1.250515118 1.009024487 1.031062828 1.008780583 1.248608559 1.243381866 0.951625868 1 11.10170233 -7.755907476 24.9983999 1.043382029 1.245995317 0.516171254 0.08141763 73.18662931 330716.0881 0.010124084 0.035830485 1.75E-08 7.755907476 0.202613288 WEGGDSNS(ph)DDYDLESDMSNGWDPNEMFK ddPTM_HeLa_Romidepsin_16h_R1 1 WEGGDSNSDDYDLESDMSNGWDPNEMFK 28 0 Q8WWM7-6;Q8WWM7-8;Q8WWM7-5;Q8WWM7-4;Q8WWM7-9;Q8WWM7-2;Q8WWM7;Q8WWM7-3;H3BUF6;H3BSK9;Q8WWM7-7 Q8WWM7-6 ATXN2L Ataxin-2-like protein 1 0 WEGGDS(0.367)NS(0.486)DDY(0.023)DLES(0.037)DMS(0.086)NGWDPNEMFK 66.593 6.26E-05 3141400 1862.8 2062.5 1670.4 1731.1 1821.3 1836.5 1413.5 1354.9 2071.7 1875 TRUE FALSE FALSE 1840.095477 2091.535929 1699.472611 1931.257927 1728.352265 1719.153577 1533.562655 1394.101894 1886.401963 1826.28723 1.00756083 1.145239311 0.930561515 1.05747765 0.946374829 0.941338005 0.839716026 0.763353032 1.032916363 1 10.83469797 -7.613577341 1.033729114 1.012683274 0.707328261 0.726990204 0.054077616 0.420940504 0.507376477 0.007695078 0.122822556 2.43E-08 7.613577341 -0.305355013 WEWLVNQHR ddPTM_HeLa_Romidepsin_16h_R1 1 WEWLVNQHR 9 0 Q9BWJ5 Q9BWJ5 SF3B5 Splicing factor 3B subunit 5 0 0 128.86 7.09E-05 0 3620.2 3250.5 4546 3989 5111.8 4663.1 3920.3 2755.4 3525 1982.9 FALSE FALSE TRUE 3576.07561 3296.260624 4625.121223 4450.226949 4850.925771 4365.142959 4253.290184 2835.123152 3209.715171 1931.383972 1.851561192 1.706683224 2.394718652 2.304164792 2.511631991 2.260111414 2.202198136 1.467923102 1.661873153 1 10.91541929 -11.45640062 0.53246071 0.972994019 2.198320677 0.407564505 0.351313405 0.395010011 0.232948333 0.221510475 0.088913623 3.50E-12 11.45640062 1.225326658 WFSDLT(ph)NHKRIHT(ph)GEKPY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 WFSDLTNHKRIHTGEKPYK 19 3 A8MUV8 A8MUV8 ZNF727 Putative zinc finger protein 727 3 0 WFS(0.104)DLT(0.9)NHKRIHT(0.998)GEKPY(0.998)K 41.912 0.0042055 0 164.42 140.41 0 0 126.66 111.66 194.72 122.81 0 152.76 TRUE FALSE FALSE 162.4159858 142.3866957 0 0 120.1960676 104.5252864 211.2595119 126.3633136 0 148.7912732 1.091569299 0.95695596 0 0 0.807816648 0.702496081 1.419838055 0.849265625 0 1 7.217146103 -9.976890744 24.99922258 1.042242325 0.634389815 0 0.509235052 309.8228088 335160.7564 0.06779593 0.089098698 1.05E-10 9.976890744 -0.40785251 WGDEHIPGSPYR ddPTM_HeLa_Romidepsin_16h_R1 2 WGDEHIPGSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 ; ; 94.538 0.010461 107282000 16380 14324 24030 23693 28991 27696 21976 15634.8 15534.5 9871.6 FALSE FALSE TRUE 16180.35426 14525.65365 24448.23207 26432.49614 27511.48109 25926.31498 23842.64089 16087.16827 14145.05541 9615.134409 1.682800632 1.51070729 2.5426823 2.749051133 2.861268488 2.696406923 2.479699178 1.673109037 1.471124044 1 13.23109131 -10.22409718 0.883531982 1.204355745 2.547805806 0.635949459 0.381343571 0.226612763 0.354327804 0.092678967 0.112644133 5.97E-11 10.22409718 1.343450061 WGDIEFPPPFGR ddPTM_HeLa_Romidepsin_16h_R1 1 WGDIEFPPPFGR 12 0 P53396;P53396-2 P53396 ACLY ATP-citrate synthase 0 0 109.79 0.0038222 0 4654.5 4414.4 3409.6 3080.3 4025.3 4250.4 4142.1 4970.2 5101.2 5583.1 FALSE FALSE TRUE 4597.769164 4476.546039 3468.942658 3436.458779 3819.873921 3978.813158 4493.929871 5114.004895 4644.935896 5438.050257 0.845481183 0.823189531 0.637901912 0.63192847 0.702434465 0.731661711 0.826386234 0.940411481 0.854154647 1 12.40887377 -11.02502701 0.824695049 0.97473502 0.746968857 0.305667197 0.096694612 0.331203058 0.488331234 0.031569622 0.0231245 9.44E-12 11.02502701 -0.227766163 WGDYDSHDIER ddPTM_HeLa_Romidepsin_16h_R1 4 WGDYDSHDIER 11 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 ;;; ;;; 199.03 2.71E-13 58338000 22481 21401.6 23262.5 21884.2 22368.7 22059.8 22247.5 22986 25371.7 22589.8 FALSE FALSE TRUE 22206.99292 21702.89229 23667.37405 24414.55417 21227.14177 20650.24997 24137.20209 23651.06364 23102.39161 22002.91374 1.009275098 0.986364467 1.075647268 1.109605503 0.964742307 0.938523426 1.09700026 1.074905984 1.049969649 1 14.42540697 -9.780143449 24.97408969 1.00315113 1.040506635 0.068475577 0.053894688 434.175763 579718.9981 0.00869309 0.011435903 1.66E-10 9.780143449 0.037355505 WGEAS(ph)NDEDDPKDK ddPTM_HeLa_Romidepsin_16h_R1 2 WGEASNDEDDPKDK 14 1 Q5SXM2;A0A1B0GUB4 Q5SXM2 SNAPC4 snRNA-activating protein complex subunit 4 1 0 WGEAS(1)NDEDDPKDK;WGEAS(1)NDEDDPKDK ; 147.75 0.0016905 5811000 3592.4 3786.2 3755.3 2282.8 4659.9 5325.6 4660.4 5278.4 3675.9 3802.3 TRUE FALSE FALSE 3548.614447 3839.502223 3820.659421 2546.748077 4422.087915 4985.311348 5056.25426 5431.122176 3347.118298 3703.515698 0.958174539 1.036718226 1.031630411 0.687656887 1.194024347 1.346102394 1.365257953 1.466477428 0.903767817 1 11.85467974 -8.512969029 4.949635299 0.968995636 1.376466534 0.800461509 0.101998852 0.061100477 4.231465046 0.014034344 0.030407124 3.07E-09 8.512969029 0.407470898 WGQPPSPT(ph)PVPRPPDADPNTPSPKPLEGRPER ddPTM_HeLa_Romidepsin_16h_R1 1 WGQPPSPTPVPRPPDADPNTPSPKPLEGRPER 32 3 Q14839-2;A0A2R8Y8C1;A0A0C4DGG9;A0A2R8Y521;A0A2R8Y212;F5GWX5;A0A2R8YFD8;A0A2U3TZM0;A0A2R8YFK9;A0A2R8Y5J0;A0A2R8Y425;A0A2R8Y445;A0A2R8YER1;A0A2R8YDJ9;A0A2R8YD40;A0A2R8Y5Z7;Q14839;A0A2R8Y685;A0A2R8Y8B3 Q14839-2 CHD4 Chromodomain-helicase-DNA-binding protein 4 1 0 WGQPPS(0.013)PT(0.904)PVPRPPDADPNT(0.039)PS(0.044)PKPLEGRPER 40.849 0.02193 32852000 1373.3 1276.3 1306.7 1072.3 844.24 1124.5 1144.4 1055.5 1157.8 1428.5 TRUE FALSE FALSE 1356.561691 1294.267785 1329.442565 1196.284371 801.1552825 1052.648079 1241.605307 1086.039227 1054.243468 1391.387364 0.974970541 0.930199467 0.955479832 0.859778091 0.575796003 0.756545665 0.89235057 0.780544121 0.757692283 1 10.44230841 -9.125554621 3.466178881 0.9806463 0.758271145 0.308276262 0.103480055 0.117295899 2.59943173 0.011833251 0.020449193 7.49E-10 9.125554621 -0.222375155 WGRDDIENIAR ddPTM_HeLa_Romidepsin_16h_R1 1 WGRDDIENIAR 11 1 O60264 O60264 SMARCA5 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 0 0 152.69 0.0025907 7371100 3519.6 3571 3566.5 2964.5 3051.1 2611 2382.4 2742.5 3695.1 3398 FALSE FALSE TRUE 3476.701761 3621.272632 3628.573436 3307.269438 2895.390982 2444.165527 2584.760997 2821.849911 3364.601001 3309.71947 1.050452098 1.0941328 1.096338668 0.999259746 0.87481462 0.738481176 0.780960749 0.852594891 1.016581928 1 11.69249322 -8.6743586 2.812691976 1.036040907 0.790774239 0.890681762 0.040506715 0.068562387 1.09562881 0.006751188 0.014477623 2.12E-09 8.6743586 -0.245266668 WGSDFSPASTVS(ph)APVSR ddPTM_HeLa_Romidepsin_16h_R1 1 WGSDFSPASTVSAPVSR 17 0 A0A1B0GV45 A0A1B0GV45 1 0 WGSDFSPAS(0.007)T(0.163)VS(0.83)APVSR 160.03 3.55E-05 3723000 639.32 742.85 671.29 674.09 770.14 754.72 601.19 672.67 770.72 828.31 TRUE FALSE FALSE 631.5277219 753.3078618 682.9735209 752.0314575 730.836882 706.4958277 652.2550636 692.1326452 701.7848729 806.7903868 0.782765551 0.933709516 0.846531555 0.93212744 0.905857202 0.875686968 0.808456663 0.8578841 0.869847837 1 9.656050084 -12.56600983 1.34098417 1.000029851 0.859594638 0 0.060917313 0.290686004 0.936539156 0.036821317 0.008642924 2.72E-13 12.56600983 -0.140435213 WIDNPTVDDR ddPTM_HeLa_Romidepsin_16h_R1 3 WIDNPTVDDR 10 0 P18206-2;P18206 P18206-2 VCL Vinculin 0 0 ;; ;; 231.38 3.43E-38 0 6616.2 6245.9 6940.9 5103.9 10136.7 11539.5 8442.1 10168.8 6657.7 6076.9 FALSE FALSE TRUE 6535.55921 6333.829944 7061.703453 5694.036933 9619.386374 10802.16319 9159.171763 10463.01818 6062.218637 5919.021262 1.104162144 1.07008062 1.193052557 0.961989606 1.625165031 1.824991449 1.547413222 1.767693969 1.024192746 1 12.53114292 -8.715796567 6.192687543 1.058583379 1.69701427 0.921998904 0.090191167 0.035444499 3.225152655 0.012598127 0.025145609 1.92E-09 8.715796567 0.638430891 WIEIMS(ph)S(ph)TNTMPVS(ph)SCT(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 WIEIMSSTNTMPVSSCTPK 19 0 A0A182DWE8;Q6ZTR5-6;Q6ZTR5 A0A182DWE8 CXorf22 Uncharacterized protein CXorf22 4 0 WIEIMS(0.92)S(0.841)T(0.268)NT(0.351)MPVS(0.407)S(0.403)CT(0.81)PK 44.567 0.026493 7773700 554.72 568.89 608.46 473.5 602.5 664.62 523.79 547 682.53 645.18 TRUE FALSE FALSE 547.9588593 576.8988484 619.0499911 528.2482979 571.7521768 622.152927 568.2807095 562.826582 621.4828074 628.4181306 0.871965388 0.918017511 0.985092506 0.840600028 0.909827627 0.990030199 0.904303491 0.895624354 0.98896384 1 9.295580994 -12.50231797 1.237134369 1.000227557 0.911534054 0.353217839 0.043134245 0.410433951 1.119655463 0.030864306 0.007398298 3.15E-13 12.50231797 -0.088693503 WIPLSSDAQAPLAQPES(ph)PTASAGDEPR ddPTM_HeLa_Romidepsin_16h_R1 1 WIPLSSDAQAPLAQPESPTASAGDEPR 27 0 Q6GQQ9-2;Q6GQQ9 Q6GQQ9-2 OTUD7B OTU domain-containing protein 7B 1 0 WIPLS(0.001)S(0.003)DAQAPLAQPES(0.87)PT(0.111)AS(0.016)AGDEPR 69.803 9.13E-05 3131200 486.46 498.62 686.68 520.05 474.53 509.73 754.76 626.1 760.29 611.65 TRUE FALSE FALSE 480.5308384 505.6395854 698.6313774 580.1806279 450.3129634 477.1598981 818.8692956 644.2152157 692.2877582 595.7592448 0.806585618 0.848731413 1.172674001 0.973850818 0.755863996 0.800927392 1.374497001 1.08133482 1.162026044 1 9.218585624 -7.765617275 24.99981397 0.909389357 1.227915928 0.344328693 0.154293197 63.43662316 379605.3312 0.019406548 0.061419124 1.72E-08 7.765617275 0.318526571 WISIMTER ddPTM_HeLa_Romidepsin_16h_R1 1 WISIMTER 8 0 P07355;P07355-2;H0YN42;H0YMU9;H0YMD0;A6NMY6;H0YN28;H0YM50;H0YNP5;H0YL33 P07355 ANXA2;ANXA2P2 Annexin A2;Annexin;Putative annexin A2-like protein 0 0 113.7 0.0056216 4488400 298.44 432.81 716.66 464.68 735.88 786.96 594.25 576.23 463.5 354.72 FALSE FALSE TRUE 294.8024985 438.9031105 729.1331667 518.408488 698.3252977 736.6757958 644.7255802 592.9023059 422.0433991 345.5043233 0.853252705 1.270325958 2.110344553 1.500439946 2.021176728 2.132175334 1.866042005 1.716048877 1.221528562 1 8.432559953 -9.938982098 4.042245008 0.934367048 1.88722614 0.792372401 0.202512777 0.054911291 1.837799286 0.029492544 0.038876556 1.15E-10 9.938982098 0.952859092 WIY(ph)IT(ph)KGY(ph)EDK ddPTM_HeLa_Romidepsin_16h_R1 1 WIYITKGYEDK 11 1 A8MSG4;A6PVS8-2;A6PVS8 A8MSG4 LRRIQ3 Leucine-rich repeat and IQ domain-containing protein 3 3 0 WIY(1)IT(1)KGY(1)EDK 66.692 0.0036749 0 581.25 769.1 579.38 653.41 702.3 656.33 609.57 705.08 742.36 816.15 TRUE FALSE FALSE 574.1655014 779.92741 589.4638659 728.9603386 666.4590104 614.3926312 661.3468606 725.4803774 675.9614623 794.9463053 0.722269539 0.981107032 0.741514064 0.916993178 0.838369844 0.77287312 0.831939033 0.912615572 0.850323422 1 9.634713607 -12.58997048 1.378484993 1.000055008 0.824966827 0.013655495 0.090004583 0.342167745 1.165635865 0.05529082 0.012825513 2.57E-13 12.58997048 -0.175088182 WKDTDEADLVLAK ddPTM_HeLa_Romidepsin_16h_R1 2 WKDTDEADLVLAK 13 1 P45973 P45973 CBX5 Chromobox protein homolog 5 0 0 ; ; 146.96 0.00016027 14551000 8159.5 7075.6 7218.7 7831.7 8185.4 7189.6 6926.6 7358.7 8096.4 7347.1 FALSE FALSE TRUE 8060.048876 7175.210483 7344.338445 8737.238003 7767.668494 6730.207763 7514.945231 7571.612374 7372.237706 7156.221283 1.126299559 1.002653523 1.02628722 1.220928987 1.085442748 0.940469488 1.050127565 1.05804615 1.030185822 1 12.80498228 WKEPGSGGPQNLS(ph)GPGGR ddPTM_HeLa_Romidepsin_16h_R1 2 WKEPGSGGPQNLSGPGGR 18 1 Q9H0W8-2;Q9H0W8;M0QZH1;M0QX70;M0QYR7;M0R2N0;M0QZC7 Q9H0W8-2 SMG9 Protein SMG9 1 0 WKEPGSGGPQNLS(1)GPGGR;WKEPGSGGPQNLS(1)GPGGR ; 102.19 0.00069654 52897400 3671.1 3298.3 3353.5 3246.6 3151.6 3313.8 2664.46 3429 3444.8 3428.1 TRUE FALSE FALSE 3626.355221 3344.733554 3411.866261 3621.987168 2990.762092 3102.058875 2890.779166 3528.212705 3136.68846 3339.037468 1.086048077 1.001705907 1.021811313 1.0847399 0.895695877 0.929027872 0.86575224 1.05665562 0.939399001 1 11.70521657 -8.758302942 24.99996173 1.039524042 0.931155346 0.287066457 0.062313634 54.57749709 435019.3063 0.007968614 0.015410862 1.74E-09 8.758302942 -0.108368695 WLAES(ph)PVGLPPEEEDKLTR ddPTM_HeLa_Romidepsin_16h_R1 4 WLAESPVGLPPEEEDKLTR 19 1 E9PGC8;P78559;P78559-2 E9PGC8 MAP1A Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 1 0 WLAES(0.999)PVGLPPEEEDKLT(0.001)R;WLAES(1)PVGLPPEEEDKLTR;WLAES(1)PVGLPPEEEDKLTR;WLAES(1)PVGLPPEEEDKLTR ;;; 97.589 0.00069146 114696900 7721 7513.7 7561.6 9093.6 13735.5 16659.2 15501.5 18377.7 8288 7776.5 TRUE FALSE FALSE 7626.893482 7619.478066 7693.206476 10145.04482 13034.52618 15594.73089 16818.19702 18909.42975 7546.700522 7574.465409 1.006921686 1.005942684 1.015676495 1.339374368 1.720850975 2.058855648 2.220380729 2.496470541 0.99633441 1 12.88692835 -8.459920358 0.985808924 0.993273366 2.449734269 0.990860839 0.053418583 0.038420615 0.066246697 0.008760479 0.037739719 3.47E-09 8.459920358 1.456460903 up WLDDLLAS(ph)PPPSGGGAR ddPTM_HeLa_Romidepsin_16h_R1 4 WLDDLLASPPPSGGGAR 17 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 WLDDLLAS(0.999)PPPS(0.001)GGGAR;WLDDLLAS(0.975)PPPS(0.025)GGGAR;WLDDLLAS(0.943)PPPS(0.057)GGGAR;WLDDLLAS(0.998)PPPS(0.002)GGGAR ;;; 127.3 0.0020084 240618000 4806.04 4701.06 4171.47 4762.14 5167.63 5236.83 4467.34 5204.43 5856.91 4607.82 TRUE FALSE FALSE 4747.462136 4767.241646 4244.072686 5312.761033 4903.906558 4902.213464 4846.795748 5355.011971 5333.053301 4488.108172 1.057786924 1.062194017 0.945626202 1.183741753 1.092644466 1.092267226 1.079919548 1.193155727 1.188263094 1 12.13189173 -9.254895201 24.99997335 1.025586802 1.121667631 0.194300259 0.069499839 336.5102003 1285530.957 0.007078057 0.01155583 5.56E-10 9.254895201 0.096080829 WLDES(ph)DAEMELR ddPTM_HeLa_Romidepsin_16h_R1 4 WLDESDAEMELR 12 0 H3BPZ1;H3BS72;Q9P035 H3BPZ1 HACD3 Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 1 0 WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR;WLDES(1)DAEMELR ;;; 123.21 0.0088649 43756900 10646.74 17156 13153.1 5186.31 9365.45 14174.4 6600.72 13436.4 12108.5 15283.2 TRUE FALSE FALSE 10516.97344 17397.52262 13382.02419 5785.975565 8887.496139 13268.70159 7161.384992 13825.16103 11025.48543 14886.14026 0.706494313 1.168706079 0.898958626 0.388682053 0.5970316 0.891346001 0.481077356 0.928727044 0.74065441 1 13.86168211 WLDGAS(ph)FDNER ddPTM_HeLa_Romidepsin_16h_R1 1 WLDGASFDNER 11 0 E7EMW7;O95071-2;O95071 E7EMW7 UBR5 E3 ubiquitin-protein ligase UBR5 1 0 WLDGAS(1)FDNER 101.56 0.018458 2014300 1207.3 1304.8 1125.8 924.02 1335.1 1655.8 1162.4 1290.5 1469.1 1327.9 TRUE FALSE FALSE 1192.584963 1323.169009 1145.394077 1030.85954 1266.964865 1549.999724 1261.134227 1327.838581 1337.700017 1293.400967 0.922053558 1.023015324 0.885567667 0.797014667 0.979560784 1.198390726 0.975052795 1.026625629 1.034250052 1 10.33695388 -8.505982764 24.89957906 0.94797831 1.062767655 0.299408534 0.08398249 684.1771811 1008270.28 0.011743111 0.02567144 3.12E-09 8.505982764 0.114789345 WLEASEEER ddPTM_HeLa_Romidepsin_16h_R1 2 WLEASEEER 9 0 Q14137-2;Q14137 Q14137-2 BOP1 Ribosome biogenesis protein BOP1 0 0 ; ; 180.87 0.0011167 14835200 3051.2 3070.2 3056 2991 3104.1 3401.7 3091.6 3221.4 3337 3189.5 FALSE FALSE TRUE 3014.010801 3113.422356 3109.188398 3336.833493 2945.686194 3184.342348 3354.200427 3314.606126 3038.530362 3106.63633 0.970184624 1.002184364 1.000821489 1.074098523 0.94819151 1.025012911 1.079688792 1.066943721 0.978077264 1 11.60113765 -7.013613477 0.514872732 0.987876076 1.171338296 0.417732905 0.033172445 3.408090589 0.508172172 0.006677964 0.397395302 9.69E-08 7.013613477 0.18346222 WLNSGRGDEASEEGQNGS(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 WLNSGRGDEASEEGQNGSSPK 21 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 WLNSGRGDEAS(0.003)EEGQNGS(0.498)S(0.498)PK 73.057 0.0020163 45628000 2444.7 2263.3 2075.2 3475.2 2754.4 2333 2230.8 2339.1 2641.6 2255.9 TRUE FALSE FALSE 2414.903056 2295.162797 2111.317985 3877.018975 2613.83269 2183.928829 2420.284096 2406.778168 2405.32868 2197.291393 1.099036324 1.044541841 0.960873006 1.764453722 1.189570349 0.99391862 1.101485267 1.095338641 1.094678971 1 11.10151049 WLNSGRGDEASEEGQNGSS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 WLNSGRGDEASEEGQNGSSPK 21 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;H0Y9H2 E7EV99 ADD1 Alpha-adducin 1 0 WLNSGRGDEASEEGQNGS(0.158)S(0.842)PK 91.065 0.0003925 35527000 2361.8 2243.2 1849.8 3206.9 2157.9 2271.3 1810 2431.4 2462.3 1893.3 TRUE FALSE FALSE 2333.013473 2274.779828 1881.994993 3577.696867 2047.774311 2126.17126 1963.741355 2501.748723 2242.065721 1844.111793 1.26511499 1.233536837 1.020542789 1.940065066 1.110439355 1.152951393 1.064871101 1.356614459 1.215797073 1 10.8487104 -12.11669652 0.659825767 0.978570136 1.26975139 0.032825101 0.253719334 1.430416511 1.012040637 0.235191566 0.052850778 7.64E-13 12.11669652 0.291181254 WLPADLAFAVR ddPTM_HeLa_Romidepsin_16h_R1 1 WLPADLAFAVR 11 0 X6R3N0;Q5K4L6-3;Q5K4L6-2;Q5K4L6 X6R3N0 SLC27A3 Long-chain fatty acid transport protein 3 0 0 71.451 0.020276 1599900 554.53 616.26 553.14 352.25 1437.6 1317.6 1081.9 1067.1 1095.5 942.5 FALSE FALSE TRUE 547.7711751 624.9357245 562.7671697 392.9788024 1364.233908 1233.409612 1173.796559 1097.974855 997.5157363 918.0137141 0.596691712 0.6807477 0.613026974 0.428075089 1.486071381 1.343563384 1.278626388 1.196033172 1.086602216 1 9.842371896 -8.751151532 24.99971775 0.754161968 1.323933827 0.692382876 0.192996623 102.7691968 249729.9388 0.030557615 0.060576199 1.77E-09 8.751151532 0.569771859 WLREAEEES(ph)DHN ddPTM_HeLa_Romidepsin_16h_R1 1 WLREAEEESDHN 12 1 Q04637-9;Q04637;E7EX73;E9PGM1;Q04637-3;Q04637-8;E7EUU4;Q04637-7;Q04637-4;Q04637-5;Q04637-6 Q04637-9 EIF4G1 Eukaryotic translation initiation factor 4 gamma 1 1 0 WLREAEEES(1)DHN 74.475 0.022602 7928800 3451.4 3376.5 1672.9 8850.9 2206.1 2676.8 2031.6 2296.3 4328 3013.6 TRUE FALSE FALSE 3409.333009 3424.034456 1702.016123 9874.282703 2093.514485 2505.761119 2204.164053 2362.739818 3940.89284 2935.306238 1.16149142 1.166499908 0.579842778 3.363970197 0.713218423 0.853662588 0.750914513 0.804938097 1.3425832 1 11.51929531 WLY(ph)S(ph)LY(ph)DAET(ph)LMDRIK ddPTM_HeLa_Romidepsin_16h_R1 1 WLYSLYDAETLMDRIK 16 1 J3QT87;A0A1W2PPJ5;Q96SW2-2;Q96SW2 J3QT87 CRBN Protein cereblon 4 0 WLY(1)S(1)LY(1)DAET(1)LMDRIK 42.309 0.025668 2815800 1527.7 1908.9 959.64 293.9 1011.8 1027.8 948.47 1622.7 1651.7 1707.6 TRUE FALSE FALSE 1509.079805 1935.773544 976.3421317 327.8821008 960.1640705 962.1268971 1029.033018 1669.650264 1503.967815 1663.236306 0.907315334 1.163859602 0.58701348 0.197135007 0.577286623 0.578466748 0.618693215 1.003856312 0.904241815 1 10.69977744 -9.74073266 24.08791166 0.970581341 0.57540595 0.503128604 0.193728043 99.10702024 115289.6969 0.03033083 0.042862011 1.82E-10 9.74073266 -0.395175391 WLYDETLEDR ddPTM_HeLa_Romidepsin_16h_R1 1 WLYDETLEDR 10 0 Q9H5Q4 Q9H5Q4 TFB2M "Dimethyladenosine transferase 2, mitochondrial" 0 0 112.11 0.003589 0 517.1 445.03 564.94 520.79 622.8 538.45 620.6 521.33 610.49 436.14 FALSE FALSE TRUE 510.7973863 451.295144 574.7725437 581.0061902 591.016192 504.0447828 673.3137485 536.413861 555.8862454 424.8090199 1.202416527 1.062348309 1.353013982 1.36768798 1.391251514 1.186520905 1.584979878 1.262717682 1.308555655 1 8.730670589 -10.4533701 0.277493238 0.955085803 1.446909709 0.151349875 0.148372705 0.828485843 0.227109762 0.150945322 0.143565109 3.52E-11 10.4533701 0.491823907 WMDEAQSLDTADR ddPTM_HeLa_Romidepsin_16h_R1 2 WMDEAQSLDTADR 13 0 Q6N069-3;Q6N069-2;Q6N069 Q6N069-3 NAA16 "N-alpha-acetyltransferase 16, NatA auxiliary subunit" 0 0 ; ; 135.8 0.003952 18845200 1938.98 2132.3 1967.31 2083.05 1900.9 2056.6 1776.84 1892.06 2453.3 2155.16 FALSE FALSE TRUE 1915.346966 2162.318575 2001.550205 2323.902042 1803.88998 1925.189897 1927.764745 1946.803771 2233.870704 2099.168633 0.912431206 1.030083311 0.953496624 1.107058293 0.85933543 0.917120172 0.918346776 0.927416569 1.064169247 1 11.03560235 WNSVS(ph)PASAGK ddPTM_HeLa_Romidepsin_16h_R1 1 WNSVSPASAGK 11 0 E5RJU9;Q86UE4;H0YBE0;H0YB56 E5RJU9 MTDH Protein LYRIC 1 0 WNS(0.007)VS(0.937)PAS(0.056)AGK 107.53 0.015707 7940200 1140.8 1637.9 1251.2 1056.3 1210.7 1797.7 880.47 1644.4 1430.7 1562.4 TRUE FALSE FALSE 1126.895491 1660.958399 1272.976611 1178.434376 1148.913461 1682.832772 955.2570998 1691.97812 1302.734609 1521.808623 0.740497507 1.091437106 0.836489288 0.77436437 0.754965798 1.105811037 0.627711715 1.111820563 0.85604365 1 10.57157123 -12.69414114 1.575278443 0.999964066 0.854815969 0 0.16891087 0.725085955 3.244772661 0.108213369 0.023975517 2.02E-13 12.69414114 -0.145148097 WPTETDVSS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 WPTETDVSSAK 11 0 E7EVA0;P27816;P27816-6;P27816-2 E7EVA0 MAP4 Microtubule-associated protein;Microtubule-associated protein 4 1 0 WPTETDVS(0.36)S(0.64)AK 119.74 0.010151 4290900 1482.6 1611.3 1865.8 1533.6 1513.8 1627.8 1121.5 1489 2047.7 1987.5 TRUE FALSE FALSE 1464.529501 1633.983924 1898.273466 1710.922048 1436.545137 1523.788833 1216.760182 1532.081866 1864.548583 1935.864463 0.756524813 0.844059052 0.980581803 0.883802601 0.742069068 0.787136115 0.628535832 0.791420006 0.963160706 1 10.91876223 -16.52287875 0.199462888 1.940384086 0.753357689 0.446269766 0.084466402 39.19529612 0.475187729 14.4624152 0.09847517 3.00E-17 16.52287875 -1.187026397 WQELS(ph)PETSGK ddPTM_HeLa_Romidepsin_16h_R1 1 WQELSPETSGK 11 0 Q9NWF9-3;Q9NWF9;Q9NWF9-1 Q9NWF9-3 RNF216 E3 ubiquitin-protein ligase RNF216 1 0 WQELS(0.995)PET(0.005)SGK 125.53 0.0075769 9162200 2795 2721.1 2530.8 1533.9 2193.9 2307 2213.4 2031 2880.9 2885.7 TRUE FALSE FALSE 2760.933465 2759.407717 2574.847512 1711.256735 2081.937096 2159.590146 2401.406141 2089.763781 2623.225089 2810.729098 0.982283731 0.981740901 0.91607815 0.608830192 0.740710692 0.768338061 0.854371253 0.743495267 0.933289904 1 11.4567287 -9.468844232 5.864002987 0.98905761 0.750485165 0.778000304 0.058982939 0.068579836 5.274176334 0.008850581 0.013458662 3.40E-10 9.468844232 -0.238572445 SSIISK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 SSIISKK 7 1 P46100-4;P46100;P46100-2;P46100-5;P46100-3;A0A096LNL9;P46100-6;A0A096LNW1 P46100-4 ATRX Transcriptional regulator ATRX 0 1 SSIISK(1)K 89.296 0.0244 1263900 177.57 229.09 238.53 438.98 1029.4 2434.4 2983.6 3861.3 291.12 239.09 FALSE TRUE FALSE 175.4057085 232.315135 242.6815146 489.7369331 976.8658768 2278.849697 3237.02691 3973.020623 265.0814981 232.8784073 0.753207266 0.99758126 1.042095389 2.1029727 4.194746469 9.785577473 13.9000732 17.0604938 1.138282854 1 7.863433068 -8.002519444 1.089155317 0.86163784 18.04664822 0.998572621 0.219275128 0.01628335 0.029663606 0.033190409 0.236980202 9.94E-09 8.002519444 17.18501038 up WQPDT(ph)EEEYEDSSGNVVNKK ddPTM_HeLa_Romidepsin_16h_R1 1 WQPDTEEEYEDSSGNVVNKK 20 1 Q12874 Q12874 SF3A3 Splicing factor 3A subunit 3 1 0 WQPDT(0.84)EEEY(0.13)EDS(0.025)S(0.006)GNVVNKK 90.872 0.00065606 17465000 2394.1 1999.9 1951.7 2181.7 2167.7 2221.3 1880.5 2322.2 2286.1 2222.2 TRUE FALSE FALSE 2364.919788 2028.054645 1985.66852 2433.958419 2057.07418 2079.366099 2040.229623 2389.389193 2081.62549 2164.466924 1.092610731 0.936976501 0.917393792 1.124507098 0.950383745 0.960682779 0.942601433 1.10391578 0.961726635 1 11.07979604 -10.26320606 24.98884001 1.043732844 0.98865201 0 0.074084046 261.9730672 3705466.533 0.012027801 0.014137595 5.45E-11 10.26320606 -0.055080834 WQRPS(ph)SPPPFLPAASEEAEPAEGLR ddPTM_HeLa_Romidepsin_16h_R1 1 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3;Q4KMQ1 H3BLU1 TPRN Taperin 1 0 WQRPS(0.5)S(0.5)PPPFLPAASEEAEPAEGLR 96.777 8.71E-06 83628000 580.28 627.79 775.64 553.57 1059.3 1553.1 1235.5 1566.6 561.01 443.96 TRUE FALSE FALSE 573.2073242 636.6280441 789.1396888 617.576368 1005.239968 1453.861922 1340.443339 1611.927099 510.8318605 432.4258552 1.325562099 1.472224744 1.824913287 1.428167073 2.324652784 3.362106833 3.09982237 3.727638114 1.181316645 1 8.756308976 -8.282701 0.602199916 1.127245145 4.117216905 0.930523942 0.248113758 0.244071769 0.117119619 0.050543789 0.405064477 5.22E-09 8.282701 2.98997176 up WQRPS(ph)SPPPFLPAASEEAEPAEGLRVPGLAK ddPTM_HeLa_Romidepsin_16h_R1 1 WQRPSSPPPFLPAASEEAEPAEGLRVPGLAK 31 2 H3BLU1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3;Q4KMQ1 H3BLU1 TPRN Taperin 1 0 WQRPS(0.541)S(0.456)PPPFLPAAS(0.003)EEAEPAEGLRVPGLAK 44.365 0.029274 10017000 1359.3 1390.1 1149.3 1437.4 2340.7 2405.4 2465.4 2727.9 1433.2 1450.9 TRUE FALSE FALSE 1342.732329 1409.669864 1169.303084 1603.598951 2221.245345 2251.702703 2674.811014 2806.827483 1305.011002 1413.205409 0.950132458 0.997498209 0.827411979 1.134724606 1.571778123 1.593330091 1.892726279 1.986142612 0.923440424 1 10.46475546 -8.492650747 1.212178835 0.963222891 1.932261764 0.948904918 0.092563687 0.074206005 0.205720458 0.014522716 0.050913189 3.22E-09 8.492650747 0.969038873 WQRPSS(ph)PPPFLPAASEEAEPAEGLR ddPTM_HeLa_Romidepsin_16h_R1 1 WQRPSSPPPFLPAASEEAEPAEGLR 25 1 H3BLU1;Q4KMQ1-2;Q4KMQ1-4;Q4KMQ1-3;Q4KMQ1 H3BLU1 TPRN Taperin 1 0 WQRPS(0.078)S(0.922)PPPFLPAASEEAEPAEGLR 79.416 7.28E-05 107010000 692.71 788.79 684.77 737.86 1131.1 1457.9 1196.6 1547.9 773.27 695.76 TRUE FALSE FALSE 684.2669841 799.8946063 696.6881346 823.1748449 1073.375746 1364.744895 1298.239174 1592.686044 704.1067945 677.6840549 1.009713862 1.180335586 1.028042684 1.21468823 1.583888153 2.013836515 1.915699749 2.350189639 1.038989761 1 9.404469017 -8.434226797 1.000283921 1.009396402 2.240308135 0.955114513 0.100086898 0.077436812 0.136953904 0.014903176 0.065246557 3.68E-09 8.434226797 1.230911732 up WS(ph)DQGPAQTSR ddPTM_HeLa_Romidepsin_16h_R1 2 WSDQGPAQTSR 11 0 Q9C0C2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 WS(1)DQGPAQTSR;WS(1)DQGPAQTSR ; 118.73 0.010611 31067000 3506.6 4263.6 3345.6 4054.1 5021.9 5083.1 3549.2 4132.8 4299.1 3714.6 TRUE FALSE FALSE 3463.86021 4323.623073 3403.828765 4522.854117 4765.613704 4758.306315 3850.668959 4252.376048 3914.577729 3618.094157 0.957371495 1.195000154 0.940779487 1.250065344 1.317161328 1.315141649 1.064281026 1.175308288 1.081944681 1 11.82101424 -9.256657535 24.77159018 0.996250589 1.225692059 0.458493713 0.098489351 198.1229148 1026343.239 0.014723691 0.02389754 5.54E-10 9.256657535 0.22944147 WS(ph)PAYSFSSDSPLDSSPK ddPTM_HeLa_Romidepsin_16h_R1 1 WSPAYSFSSDSPLDSSPK 18 0 E7ET49;Q8NCG7-2;Q8NCG7-4;Q8NCG7 E7ET49 DAGLB Sn1-specific diacylglycerol lipase beta 1 0 WS(0.534)PAY(0.014)S(0.395)FS(0.014)S(0.022)DS(0.022)PLDSSPK 106.31 0.00026147 0 3074 2924.4 3022.1 1403.9 2829.9 3700.3 2872.9 3414.3 3031.8 2476.6 TRUE FALSE FALSE 3036.532906 2965.56978 3074.698383 1566.225524 2685.479643 3463.862772 3116.924054 3513.087384 2760.628215 2412.257575 1.258792982 1.229375259 1.274614459 0.649277896 1.113264052 1.435942334 1.292119087 1.456348368 1.14441685 1 11.23616825 -8.269281325 23.05462706 1.10790645 1.384534851 0.379498031 0.174642274 183.5829975 539720.9956 0.026868268 0.061252761 5.38E-09 8.269281325 0.276628401 WS(ph)PPQNYK ddPTM_HeLa_Romidepsin_16h_R1 1 WSPPQNYK 8 0 Q96K21-3;H3BRM1;H3BRF9;Q96K21-2;Q96K21 Q96K21-3 ZFYVE19 Abscission/NoCut checkpoint regulator 1 0 WS(1)PPQNYK 109.44 0.023086 101550000 6031.9 5933 5744.2 4195 6443.7 6779.9 6440 6610.5 6713 6040.5 TRUE FALSE FALSE 5958.380883 6016.52493 5844.175391 4680.045638 6114.853944 6346.686271 6987.013439 6801.764388 6112.572467 5883.566939 1.012715746 1.022598195 0.993304819 0.795443595 1.039310678 1.078714041 1.187547199 1.156061358 1.038922907 1 12.52247535 -8.055156629 2.461589318 0.991978261 1.171068052 0.553962708 0.067055336 0.168855933 1.989833381 0.009580358 0.032753548 8.81E-09 8.055156629 0.179089791 WSTELVPEGLQS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 WSTELVPEGLQSPR 14 0 H3BV44;H3BRD5;B2RTY4-5;B2RTY4-2;B2RTY4;B2RTY4-4;H3BMM1 H3BV44 MYO9A Unconventional myosin-IXa 1 0 WSTELVPEGLQS(1)PR 84.62 0.027559 3680400 1333.7 1433.6 1308.7 1240.6 1507.4 1532.1 1160.9 1464.8 1358.6 1199.9 TRUE FALSE FALSE 1317.444351 1453.782258 1331.477375 1384.044009 1430.471753 1434.203755 1259.506817 1507.181677 1237.083413 1168.726425 1.127247851 1.243902959 1.139254958 1.184232665 1.223957739 1.22715096 1.077674629 1.289593223 1.058488442 1 10.19072155 -11.34798001 0.558169302 0.997665238 1.199395493 0.547459694 0.059078095 0.369974337 0.248867408 0.033661644 0.015432798 4.49E-12 11.34798001 0.201730255 WT(ph)VQEKPEAVLT(ph)S(ph)Y(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 WTVQEKPEAVLTSYPR 16 1 Q53TS8-4 Q53TS8-4 4 0 WT(1)VQEKPEAVLT(1)S(1)Y(1)PR 49.433 0.027257 4402400 2753.2 3188.9 3341 2651.3 3165.1 3069.8 2751.2 2978.3 3347.6 3314 TRUE FALSE FALSE 2719.642939 3233.793418 3399.148704 2957.855781 3003.573136 2873.649687 2984.886859 3064.472412 3048.182272 3227.901802 0.842542031 1.001825215 1.053052079 0.916340075 0.930503256 0.890253131 0.92471427 0.949369776 0.944323111 1 11.65638097 -7.217650968 18.44087703 0.935129918 0.949370882 0 0.058065424 6461.101285 2719194.379 0.009956636 2.259114132 6.06E-08 7.217650968 0.014240964 WTDGSLS(ph)PPAKEPLASDSR ddPTM_HeLa_Romidepsin_16h_R1 1 WTDGSLSPPAKEPLASDSR 19 1 O15085;O15085-2 O15085 ARHGEF11 Rho guanine nucleotide exchange factor 11 1 0 WT(0.286)DGS(0.167)LS(0.546)PPAKEPLASDSR 55.536 0.018376 40747000 1711.4 2013.4 1914.4 1769.6 2206 1482.9 1634.9 1723.6 1830.1 1998.8 TRUE FALSE FALSE 1690.540799 2041.744698 1947.719329 1974.209478 2093.419588 1388.147476 1773.768365 1773.469647 1666.411272 1946.870888 0.868337397 1.048731434 1.000435797 1.014042323 1.07527397 0.713014656 0.911086799 0.910933364 0.855943392 1 10.9269415 -8.269969354 24.99932425 0.963629483 0.851619122 0.336149674 0.084775281 645.9664024 1893174.082 0.012559688 0.028514031 5.37E-09 8.269969354 -0.112010361 WTPVGPAPSTSQSQK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 1 WTPVGPAPSTSQSQKR 16 1 Q9UHB7;Q9UHB7-2;Q9UHB7-3;C9JCE0 Q9UHB7 AFF4 AF4/FMR2 family member 4 0 1 WTPVGPAPSTSQSQK(1)R 122.52 2.99E-05 597870 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 WVWDQEEER ddPTM_HeLa_Romidepsin_16h_R1 1 WVWDQEEER 9 0 E9PMS6;Q8WWI1-3;Q8WWI1;J3KP06;F8WD26;Q8WWI1-4;Q8WWI1-2;E9PMT2;Q8WWI1-5;A0A0A0MTE2;E9PMP7;H0Y424;H0YDG6;H0YDQ3;U3KQE6 E9PMS6 LMO7 LIM domain only protein 7 0 0 214.96 5.87E-17 12402000 1941.3 1748.2 1786.7 1487.4 1946.5 1919.3 1592.2 1475.2 2389.7 1782.7 FALSE FALSE TRUE 1917.638689 1772.811205 1817.796764 1659.380186 1847.162842 1796.662924 1727.441428 1517.882585 2175.959247 1736.385197 1.104385532 1.020978069 1.046885661 0.955652115 1.063797851 1.03471449 0.994849202 0.874162362 1.253154686 1 10.76187131 -7.208575984 1.812901814 1.041995752 0.803465102 0.337570501 0.076599329 0.597413834 1.760950728 0.006676071 0.252744823 6.19E-08 7.208575984 -0.238530651 Y(ph)ESDVRNT(ph)VTYT(ph)SLKTK ddPTM_HeLa_Romidepsin_16h_R1 1 YESDVRNTVTYTSLKTK 17 2 A0A0C4DG51;Q9NP80-3;Q9NP80-2;Q9NP80 A0A0C4DG51 PNPLA8 Calcium-independent phospholipase A2-gamma 3 0 Y(0.478)ES(0.51)DVRNT(0.958)VT(0.055)Y(0.039)T(0.465)S(0.417)LKT(0.078)K 56.708 0.018183 7709600 2191.1 1702.2 1607.7 418.3 1728.5 1679 1513.2 1526.8 1758.4 2122.2 TRUE FALSE FALSE 2164.39403 1726.163616 1635.681344 466.6658142 1640.288195 1571.717319 1641.73117 1570.975549 1601.1243 2067.064938 1.047085648 0.83507953 0.791306221 0.225762532 0.793534913 0.760361849 0.794232992 0.760002998 0.774588292 1 11.013368 -9.959204407 2.418319278 1.021781364 0.67788321 0.262666518 0.178317216 0.182097167 2.150626662 0.027329329 0.036129155 1.10E-10 9.959204407 -0.343898154 Y(ph)FPVIFGKASEFMQVIFGTDVK ddPTM_HeLa_Romidepsin_16h_R1 1 YFPVIFGKASEFMQVIFGTDVK 22 1 A0A075B7A9;P43362 A0A075B7A9 MAGEA9 Melanoma-associated antigen 9 1 0 Y(0.538)FPVIFGKAS(0.462)EFMQVIFGTDVK 46.362 0.027714 1325500 602.43 771.38 608.43 753.87 592.86 505.51 608.77 628.78 591.82 579.92 TRUE FALSE FALSE 595.0873514 782.2395079 619.0194689 841.0359965 562.6041419 473.2095425 660.4789086 646.9727572 538.886137 564.8535948 1.053524943 1.384853553 1.095893652 1.488945108 0.996017636 0.837756096 1.169292211 1.145381322 0.954027985 1 9.141733172 -10.49778459 21.37890476 1.023613329 1.156453602 0.146506667 0.173025888 82.86997028 70604.27634 0.030333563 0.032772777 3.18E-11 10.49778459 0.132840274 Y(ph)HHRDPQLLQSLRKNEIMK ddPTM_HeLa_Romidepsin_16h_R1 1 YHHRDPQLLQSLRKNEIMK 19 3 D6RGC4 D6RGC4 Mar-01 1 0 Y(0.897)HHRDPQLLQS(0.103)LRKNEIMK 41.202 0.0043536 0 208.23 145.1 146.37 117.31 183.62 342.92 274.41 173.29 171.65 238.15 TRUE FALSE FALSE 205.6920127 147.1427216 148.9175085 130.8739342 174.2491862 321.0085187 297.7183786 178.3038727 156.2971941 231.9628287 0.886745578 0.634337503 0.641988673 0.564202182 0.751194436 1.383879135 1.283474513 0.768674334 0.67380276 1 7.857749826 -8.276066135 24.66835976 0.857252251 1.159155865 0.347458656 0.215983347 674.9938588 1138391.484 0.033542157 0.075315057 5.30E-09 8.276066135 0.301903614 Y(ph)IKDDFRFK ddPTM_HeLa_Romidepsin_16h_R1 1 YIKDDFRFK 9 2 B4E1Q4;O14730-2;O14730 B4E1Q4 RIOK3 Serine/threonine-protein kinase RIO3 1 0 Y(1)IKDDFRFK 49.536 0.0042055 0 2099.4 2094.6 1737.3 2280.3 2204.1 2330.6 1748.8 2460.3 2362.6 2560.2 TRUE FALSE FALSE 2073.811705 2124.087834 1767.536978 2543.959015 2091.616552 2181.682182 1897.343028 2531.484899 2151.283139 2493.685635 0.831625156 0.85178653 0.708805053 1.020160272 0.838765129 0.874882604 0.760858948 1.015157991 0.862692197 1 11.28406389 -12.27881087 0.974904903 1.001127368 0.857628532 0 0.100657422 0.590206751 0.99346605 0.059481174 0.015603436 5.26E-13 12.27881087 -0.143498836 Y(ph)ILDGISALRK ddPTM_HeLa_Romidepsin_16h_R1 1 YILDGISALRK 11 1 C9J5B0;B5MCZ3;B5MC14;P05231 C9J5B0 IL6 Interleukin-6 1 0 Y(1)ILDGISALRK 114.89 0.0031366 19830000 6086.7 5437.4 5087 5872.7 5822.6 5400.3 5311.1 5727.6 5653.6 5018.5 TRUE FALSE FALSE 6012.512959 5513.94786 5175.537101 6551.729206 5525.450995 5055.238259 5762.224701 5893.319069 5147.927856 4888.118647 1.230025986 1.128030692 1.058799402 1.340337598 1.130383977 1.034188943 1.178822594 1.205641576 1.053151167 1 12.25506359 -12.46130618 1.148586628 0.998290158 1.166574876 0.29291295 0.083691824 0.44349527 1.02943366 0.060388092 0.014314079 3.46E-13 12.46130618 0.168284718 Y(ph)LLSLEEERPALMDDR ddPTM_HeLa_Romidepsin_16h_R1 1 YLLSLEEERPALMDDR 16 1 Q86TB9;Q86TB9-4;Q86TB9-2 Q86TB9 PATL1 Protein PAT1 homolog 1 1 0 Y(1)LLSLEEERPALMDDR 82.489 0.0036758 0 686.27 1017.7 936.81 873 1040.2 922.52 979.99 849.38 1065.8 939.17 TRUE FALSE FALSE 677.9054773 1032.027207 953.1147851 973.9403676 987.1147125 863.5739493 1063.230326 873.9554702 970.4721787 914.770228 0.741066397 1.128181893 1.041917146 1.064683062 1.07908487 0.944033729 1.162292228 0.955382503 1.06089174 1 9.837265603 -10.24845683 24.94675663 0.877725796 1.05456682 0.161102238 0.103498348 604.2174209 1161041.34 0.018159656 0.022167241 5.64E-11 10.24845683 0.176841024 Y(ph)LLVY(ph)S(ph)QK ddPTM_HeLa_Romidepsin_16h_R1 1 YLLVYSQK 8 0 H3BV75;Q8N5Y8-2;Q8N5Y8;Q8N5Y8-3 H3BV75 PARP16 Mono [ADP-ribose] polymerase PARP16 3 0 Y(1)LLVY(1)S(1)QK 64.654 0.027954 7129900 4124.5 3514.5 3895.9 3220.3 3420.2 3510.1 3662.1 3937.9 4260.1 4476.6 TRUE FALSE FALSE 4074.229008 3563.977223 3963.706505 3592.646238 3245.654431 3285.815938 3973.158683 4051.836924 3879.065986 4360.297287 0.934392483 0.817370236 0.909045013 0.82394525 0.744365399 0.753576126 0.911212796 0.929257034 0.889633374 1 12.09021079 -10.54568047 0.931598735 0.984776146 0.832647782 0.254227489 0.068206183 0.300248666 0.537219806 0.01601137 0.016303124 2.85E-11 10.54568047 -0.152128364 Y(ph)LPNPS(ph)LNAFKDLNEK ddPTM_HeLa_Romidepsin_16h_R1 1 YLPNPSLNAFKDLNEK 16 1 E7EMT5;P04798 E7EMT5 CYP1A1 Cytochrome P450;Cytochrome P450 1A1 2 0 Y(1)LPNPS(1)LNAFKDLNEK 53.995 0.0043195 0 1007 878.23 1020.5 938.04 1191.3 947.01 756.3 1072.5 969.56 975.7 TRUE FALSE FALSE 994.7262967 890.593745 1038.261374 1046.500598 1130.503516 886.4991173 820.5401031 1103.531095 882.8401253 950.3511733 1.046693396 0.937120688 1.09250286 1.101172522 1.189563971 0.932812146 0.863407261 1.161182441 0.928961999 1 9.892316906 -12.59974574 0.637827203 0.990631172 1.038255451 0.061669365 0.100964143 6.578352634 3.210289245 0.192045007 0.021172736 2.51E-13 12.59974574 0.047624279 Y(ph)LSGLLE ddPTM_HeLa_Romidepsin_16h_R1 1 YLSGLLE 7 0 A0A1W2PR96 A0A1W2PR96 1 0 Y(0.555)LS(0.445)GLLE 43.066 0.028048 6744700 979.5 1300.1 1079.1 955.99 969.86 898.57 990.91 1164.4 1402.8 1269.1 TRUE FALSE FALSE 967.5614772 1318.402842 1097.881283 1066.526062 920.3644252 841.154277 1075.077871 1198.090077 1277.330055 1236.128599 0.78273529 1.066557996 0.888161057 0.862795394 0.744553945 0.680474732 0.869713614 0.969227698 1.033331043 1 10.27161312 -9.072727473 3.629622334 0.909253278 0.809633774 0.220573137 0.107334223 0.382956707 9.761706416 0.017901673 0.031305139 8.46E-10 9.072727473 -0.099619504 Y(ph)LTQLPDGLTNS(ph)NS(ph)GKK ddPTM_HeLa_Romidepsin_16h_R1 1 YLTQLPDGLTNSNSGKK 17 1 I3L3E8 I3L3E8 MED11 3 0 Y(0.773)LT(0.15)QLPDGLT(0.134)NS(0.973)NS(0.971)GKK 44.294 0.026908 5784900 1193.6 992.71 928.67 832.66 990.52 1082.1 829.3 1080.3 1116.4 969.54 TRUE FALSE FALSE 1179.051944 1006.685397 944.8331118 928.936067 939.9700683 1012.957302 899.7407213 1111.556776 1016.546388 944.351211 1.248531193 1.066007419 1.000510298 0.983676471 0.995360685 1.072648915 0.9527607 1.177058665 1.076449499 1 9.883179698 -10.00505046 24.28118239 1.119462337 1.025708805 0.150082401 0.081568618 224.8586318 1081065.871 0.017043018 0.022039774 9.88E-11 10.00505046 -0.093753532 Y(ph)MCFHNMSDDTWS(ph)AK ddPTM_HeLa_Romidepsin_16h_R1 1 YMCFHNMSDDTWSAK 15 0 C9J1P7;Q9Y2T6 C9J1P7 GPR55 G-protein coupled receptor 55 2 0 Y(0.991)MCFHNMS(0.009)DDT(0.209)WS(0.791)AK 76.282 0.0040015 0 1263.8 1231.2 1372.4 1173.6 1394.5 1521.9 1227.7 1153.9 1340.9 1163.7 TRUE FALSE FALSE 1248.396319 1248.532866 1396.286046 1309.297154 1323.333461 1424.655502 1331.980807 1187.286276 1220.966546 1133.466906 1.101396355 1.101516823 1.231871913 1.155126053 1.167509571 1.256900836 1.175138683 1.047482083 1.077196466 1 10.14652655 -10.96539648 0.619015431 1.009463515 1.175354659 0.400538182 0.05930182 0.356679465 0.312037795 0.023713554 0.016171161 1.08E-11 10.96539648 0.165891145 Y(ph)MSESSKVIHLTS(ph)FTDIS(ph)ECLK ddPTM_HeLa_Romidepsin_16h_R1 1 YMSESSKVIHLTSFTDISECLK 22 1 G3V112;A0A087WV61;Q8NE09-3;Q8NE09 G3V112 RGS22 Regulator of G-protein signaling 22 3 0 Y(0.579)MS(0.324)ES(0.088)S(0.058)KVIHLT(0.144)S(0.702)FT(0.291)DIS(0.815)ECLK 44.641 0.0040944 0 1450.3 1162.4 1101.8 336.68 1289.5 1331.9 1364 1113.9 1148.9 1356.2 TRUE FALSE FALSE 1432.623186 1178.764298 1120.976367 375.6085257 1223.692003 1246.795889 1479.858126 1146.128939 1046.139507 1320.965728 1.084527142 0.892350401 0.848603671 0.284343884 0.926361659 0.943851806 1.120285026 0.86764472 0.791950528 1 10.36737732 -10.09268153 3.826497814 1.039605329 0.831493679 0.025944979 0.21710125 0.321365424 8.655988036 0.035640438 0.044449496 8.08E-11 10.09268153 -0.20811165 Y(ph)MSIMS(ph)NK ddPTM_HeLa_Romidepsin_16h_R1 1 YMSIMSNK 8 0 A6NIJ9 A6NIJ9 OR6C70 Olfactory receptor 6C70 2 0 Y(0.999)MS(0.04)IMS(0.961)NK 73.233 0.0292 305300 0 0 0 551.98 0 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 615.8025247 0 0 0 0 0 0 0 Y(ph)QS(ph)T(ph)SANS(ph)LK ddPTM_HeLa_Romidepsin_16h_R1 1 YQSTSANSLK 10 0 C9IYK1;P57773-2;P57773 C9IYK1 GJA9 Gap junction protein;Gap junction alpha-9 protein 4 0 Y(0.966)QS(0.898)T(0.917)S(0.219)ANS(1)LK 62.298 0.0034195 0 1740.1 1597.3 1583.1 1089.5 1263.4 1726 1267.7 1395.5 2011.1 1654.4 TRUE FALSE FALSE 1718.890992 1619.786831 1610.653191 1215.473116 1198.923984 1615.71417 1375.378406 1435.876591 1831.222179 1611.41845 1.066694373 1.005193177 0.999525103 0.7542877 0.744017784 1.002665801 0.85352033 0.891063765 1.13640388 1 10.65411546 -9.409555688 6.110920966 1.029154252 0.852484705 0.607077118 0.077391496 0.127646754 6.077691144 0.01113593 0.01705074 3.89E-10 9.409555688 -0.176669547 Y(ph)RSPEPDPYLSYR ddPTM_HeLa_Romidepsin_16h_R1 1 YRSPEPDPYLSYR 13 1 H3BRT8;H3BQR7;H3BV35;H3BRK0;H3BUL5;H3BVF8;H3BQG1;P49761-2;P49761-3;P49761-1;P49761 H3BRT8 CLK3 Dual specificity protein kinase CLK3 1 0 Y(0.991)RS(0.009)PEPDPYLSYR 106.54 0.01667 129860000 2279.6 2334.2 2439.4 2199.5 2623.8 3267.5 2413.1 2827.2 2150.3 2228.7 TRUE FALSE FALSE 2251.815358 2367.060929 2481.856734 2453.816539 2489.897695 3058.717295 2618.068654 2909.000571 1957.971782 2170.798053 1.037321438 1.090410472 1.143292316 1.130375318 1.146996466 1.409028947 1.20603971 1.34006043 0.901959434 1 11.0840098 -8.866774645 0.522103866 1.006697579 1.352490215 0.766408244 0.069398259 0.37975117 0.171193215 0.014227731 0.061059643 1.36E-09 8.866774645 0.345792636 Y(ph)S(ph)FRVPEEERMQQRR ddPTM_HeLa_Romidepsin_16h_R1 1 YSFRVPEEERMQQRR 15 3 H0Y7V8;A0A0A0MRJ1;H0Y5V1;A0A0A0MRJ0;Q5VT25-3;Q5VT25-4;Q5VT25-5;Q5VT25;Q5VT25-2;Q5VT25-6;H0Y6R0 H0Y7V8 CDC42BPA Non-specific serine/threonine protein kinase;Serine/threonine-protein kinase MRCK alpha 2 0 Y(1)S(1)FRVPEEERMQQRR 44.614 0.0042697 0 468.86 338.14 345.39 138.29 345.5 385.06 310.14 358.12 438.03 445.57 TRUE FALSE FALSE 463.145354 342.9003438 351.4013681 154.2797405 327.8678458 360.4559087 336.4832839 368.4816372 398.8514997 433.9940272 1.06716988 0.790103832 0.809691715 0.355488165 0.755466263 0.830554999 0.775317776 0.849047715 0.91902532 1 8.761531378 -10.13061222 3.154047859 1.032048596 0.723166867 0.418477196 0.13788825 0.152330593 2.866618759 0.023229396 0.02882476 7.40E-11 10.13061222 -0.308881729 Y(ph)S(ph)ST(ph)LT(ph)THK ddPTM_HeLa_Romidepsin_16h_R1 1 YSSTLTTHK 9 0 A0A087X1I5;Q68DY1-2;Q68DY1 A0A087X1I5 ZNF626 Zinc finger protein 626 4 0 Y(0.951)S(0.795)S(0.342)T(0.859)LT(0.527)T(0.527)HK 49.418 0.0041369 0 386.33 378.93 296.72 404.32 358.04 329.54 334.43 412.17 376.55 608.09 TRUE FALSE FALSE 381.6212614 384.2645865 301.8842871 451.0693808 339.7678828 308.4834575 362.8364759 424.0954887 342.8704249 592.2917341 0.644312995 0.648775872 0.509688503 0.761566226 0.573649543 0.520830259 0.612597568 0.716024662 0.578887743 1 9.210164142 -12.06938381 0.578124904 1.044269496 0.609605171 0 0.149676562 0.360136206 0.191303159 0.081979784 0.017621036 8.52E-13 12.06938381 -0.434664325 Y(ph)S(ph)YLT(ph)EPGMTSCTVK ddPTM_HeLa_Romidepsin_16h_R1 1 YSYLTEPGMTSCTVK 15 0 Q12955-7 Q12955-7 3 0 Y(0.904)S(0.921)Y(0.536)LT(0.629)EPGMT(0.004)S(0.004)CT(0.001)VK 45.829 0.0042886 0 257.26 321.38 235.88 301.92 248.98 278.89 216.17 486.62 215.97 320.62 TRUE FALSE FALSE 254.1244162 325.9043961 239.9853925 336.829411 236.2736215 261.0698291 234.5314744 500.6995819 196.6531023 312.2902462 0.813744327 1.043594541 0.768469062 1.07857807 0.756583417 0.835984576 0.751004802 1.603314827 0.629712598 1 8.2867437 -7.254084123 24.81279233 0.897220848 1.603315198 0.704733979 0.143140915 284.0445594 958192.091 0.015941595 0.219400405 5.57E-08 7.254084123 0.70609435 Y(ph)SLIDGT(ph)FIISNPSEAK ddPTM_HeLa_Romidepsin_16h_R1 1 YSLIDGTFIISNPSEAK 17 0 A0A0A0MQX5;O94779-4;O94779;A0A087WTT8;O94779-2 A0A0A0MQX5 CNTN5 Contactin-5 2 0 Y(0.693)S(0.308)LIDGT(0.924)FIIS(0.076)NPSEAK 76.548 0.0022058 0 1173 1315.7 1217.2 593.01 1125.8 1112.2 889.45 1045.6 1253.2 1286.9 TRUE FALSE FALSE 1158.703025 1334.222459 1238.384855 661.5766064 1068.346225 1041.134009 964.9998608 1075.852786 1141.110653 1253.466152 0.924399133 1.064426396 0.987968325 0.527797743 0.852313581 0.830604007 0.769865113 0.858302224 0.910364154 1 10.29170732 Y(ph)VLGMQELFR ddPTM_HeLa_Romidepsin_16h_R1 1 YVLGMQELFR 10 0 D6RGZ2;Q96J01-2;Q96J01 D6RGZ2 THOC3 THO complex subunit 3 1 0 Y(1)VLGMQELFR 71.379 0.0043564 0 0 0 146.98 136.91 60.412 65.677 0 0 121.91 128.51 TRUE FALSE FALSE 0 0 149.5381252 152.7401784 57.32895021 61.48045166 0 0 111.0060643 125.1712917 0 0 1.194667909 1.220249279 0.458003984 0.491170546 0 0 0.886833257 1 6.967759905 -7.807658136 3.866606131 0.574498161 2.17E-13 0.26748989 0.418982838 0.296063803 9.056111751 0.071714946 0.257500787 1.56E-08 7.807658136 -0.574498161 Y(ph)Y(ph)S(ph)QPRSYR ddPTM_HeLa_Romidepsin_16h_R1 1 YYSQPRSYR 9 1 A0A1W2PNU3 A0A1W2PNU3 3 0 Y(1)Y(1)S(1)QPRSYR 62.408 0.023575 1908800 712.37 740.15 679.75 812.51 734.54 750.52 673.15 707.4 750.77 634.02 TRUE FALSE FALSE 703.6873604 750.5698511 691.5807636 906.4562292 697.0536829 702.5641942 730.3273442 727.8675029 683.6192509 617.548069 1.13948597 1.215403122 1.119881671 1.467831048 1.128744009 1.137667219 1.182624286 1.178641047 1.106989537 1 9.270407628 -11.30448717 0.687633187 1.00994387 1.206860636 0.243953352 0.099142333 0.477413388 0.487091213 0.042913292 0.02311623 4.96E-12 11.30448717 0.196916766 YAALS(ph)DQGLDIK ddPTM_HeLa_Romidepsin_16h_R1 1 YAALSDQGLDIK 12 0 Q8WX93-3;Q8WX93;Q8WX93-8;Q8WX93-5;Q8WX93-4;Q8WX93-7 Q8WX93-3 PALLD Palladin 1 0 Y(0.014)AALS(0.986)DQGLDIK 147.52 0.001486 8306000 2085.6 2078.4 1886.8 1953.4 2224.6 1885.2 1833.4 2032 2404.4 2229 TRUE FALSE FALSE 2060.179905 2107.65977 1919.638963 2179.261299 2111.070361 1764.741804 1989.12895 2090.792714 2189.344442 2171.090259 0.948914904 0.970784039 0.884182016 1.003763565 0.97235495 0.812836683 0.916188971 0.963015105 1.008407842 1 11.08420399 -12.08004192 0.156766311 1.062990482 0.890181903 0.261765933 0.050213947 13.17339505 0.666157221 0.562691646 0.18862715 8.32E-13 12.08004192 -0.172808579 YAALSVDGEDENEGEDYAE ddPTM_HeLa_Romidepsin_16h_R1 4 YAALSVDGEDENEGEDYAE 19 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 0 0 ;;; ;;; 198.81 6.00E-20 167082290 19122.98 19772.34 18733.3 19129.54 16341.27 16482.28 14440.92 15871.31 21302.06 20407.5 FALSE FALSE TRUE 18889.90176 20050.69552 19059.34523 21341.38742 15507.31401 15429.1155 15667.53138 16330.52131 19396.7504 19877.31021 0.950324846 1.008722775 0.958849313 1.073655701 0.780151532 0.776217473 0.788211847 0.821565953 0.9758237 1 14.27883492 -8.74605049 24.99999971 0.983272971 0.790204915 0.890106421 0.034811408 58.64203875 95266.35264 0.005114498 0.010199037 1.79E-09 8.74605049 -0.193068056 YACGLWGLS(ph)PASR ddPTM_HeLa_Romidepsin_16h_R1 1 YACGLWGLSPASR 13 0 Q15637-6;H7C0N4;H7C561 Q15637-6 SF1 Splicing factor 1 1 0 YACGLWGLS(0.971)PAS(0.029)R 97.957 0.014539 5967700 568.55 598.44 593.66 352.49 725.34 700.25 645.17 621.67 681.74 614.8 TRUE FALSE FALSE 561.6202939 606.864854 603.9924033 393.2465523 688.3231932 655.506285 699.9707237 639.6570406 620.763467 598.8274074 0.937866716 1.013421975 1.008625183 0.656694312 1.14945172 1.094649772 1.168902283 1.06818264 1.036631689 1 9.225996443 SSGS(ph)SPAMETR ddPTM_HeLa_Romidepsin_16h_R1 1 SSGSSPAMETR 11 0 Q6P0Q8;Q6P0Q8-2;A0A669KBJ4;E7ERL6 Q6P0Q8 MAST2 Microtubule-associated serine/threonine-protein kinase 2 1 0 S(0.001)S(0.012)GS(0.888)S(0.099)PAMETR 105.13 0.003574 0 1387.7 1381.2 1542.9 1365.3 1157.4 1046 1151.8 490.88 1754.5 1528.8 TRUE FALSE FALSE 1370.786179 1400.64457 1569.753527 1523.16241 1098.333559 979.1639758 1249.633863 505.0828383 1597.573126 1489.081556 0.920558161 0.94060971 1.054175657 1.022887164 0.737591272 0.657562356 0.839197731 0.33919085 1.072858044 1 10.54020706 -7.083323716 0.631562044 0.970900028 9.88E-12 0.741135486 0.109941195 1.508264553 0.353570226 0.018361242 1.111263579 8.25E-08 7.083323716 -0.970900028 down YADSPGAS(ph)SPEQPKR ddPTM_HeLa_Romidepsin_16h_R1 2 YADSPGASSPEQPKR 15 1 A0A0U1RRL5;P32519-2;P32519 A0A0U1RRL5 ELF1 ETS-related transcription factor Elf-1 1 0 YADSPGAS(0.609)S(0.391)PEQPKR;YADSPGAS(0.5)S(0.5)PEQPKR ; 80.361 0.0092075 11896800 5196.5 4658.6 4637.5 4150.3 3597.8 3133.8 3437.4 2582.8 5518.7 5633.1 TRUE FALSE FALSE 5133.163059 4724.183893 4718.213742 4630.177214 3414.190841 2933.560294 3729.37267 2657.529243 5025.09365 5486.75125 0.935556001 0.861016598 0.859928495 0.843883202 0.622260913 0.534662528 0.679705075 0.484353878 0.915859572 1 12.42173646 -8.902551672 0.612749959 0.980120068 0.508942741 0.868300646 0.061825108 0.205305365 0.134881954 0.012488373 0.047789872 1.25E-09 8.902551672 -0.471177327 SDHTLTS(ph)PGGGGK ddPTM_HeLa_Romidepsin_16h_R1 1 SDHTLTSPGGGGK 13 0 C9J0Q5;Q9Y618-4;Q9Y618;C9J7T7;A0A384DVL6;H7C2R5 C9J0Q5 NCOR2 Nuclear receptor corepressor 2 1 0 S(0.002)DHT(0.126)LT(0.228)S(0.644)PGGGGK 129.54 0.002656 2444700 1838.3 1914 1870.6 1777.8 2291.1 1787 1790.9 866.41 2456 2337.8 TRUE FALSE FALSE 1815.894093 1940.945342 1903.157008 1983.357601 2174.176618 1672.816467 1943.019001 891.4782064 2236.329209 2277.063619 0.797471831 0.852389598 0.835794394 0.871015454 0.95481593 0.734637563 0.85330027 0.391503425 0.982110992 1 11.15295888 -7.043561874 1.716788438 0.887929597 2.64E-22 0.767761806 0.079586172 0.740691501 1.339730869 0.01306883 1.281727314 9.05E-08 7.043561874 -0.887929597 down YAELLEEHR ddPTM_HeLa_Romidepsin_16h_R1 4 YAELLEEHR 9 0 P40222 P40222 TXLNA Alpha-taxilin 0 0 ;;; ;;; 157.34 0.00194 15819200 18404.8 16847.2 19221.1 13991.6 17855.7 17616.4 15679.6 15296.3 20164.2 17304.1 FALSE FALSE TRUE 18180.47522 17084.37532 19555.63518 15609.37462 16944.457 16490.76889 17011.42483 15738.87431 18360.66345 16854.53699 1.078669514 1.013636586 1.160259412 0.926123016 1.005335063 0.9784172 1.009308345 0.933806388 1.089360299 1 14.04084938 -9.191399919 24.99999114 1.044351502 0.975112867 0.448216415 0.050743074 154.5414055 55162.03144 0.00757939 0.012568997 6.44E-10 9.191399919 -0.069238635 YAEYS(ph)FTSLPVPESNLR ddPTM_HeLa_Romidepsin_16h_R1 1 YAEYSFTSLPVPESNLR 17 0 Q5UIP0-2;Q5UIP0 Q5UIP0-2 RIF1 Telomere-associated protein RIF1 1 0 YAEY(0.002)S(0.949)FT(0.025)S(0.025)LPVPESNLR 84.195 0.014519 3348100 376.6 353.11 558.87 356.32 423.47 430.96 374.35 489.22 414.26 404.73 TRUE FALSE FALSE 372.0098543 358.0810918 568.5968979 397.5193949 401.8587457 403.4230469 406.1472797 503.3748088 377.2075481 394.2150563 0.943672365 0.908339461 1.442352059 1.008382071 1.019389644 1.023357785 1.03026831 1.276904068 0.956857284 1 8.622839068 YAHVVLR ddPTM_HeLa_Romidepsin_16h_R1 4 YAHVVLR 7 0 P62269 P62269 RPS18 40S ribosomal protein S18 0 0 ;;; ;;; 118.06 0.0025389 27581400 15024.2 12996.4 14874.2 12881.1 15302.7 16117 12257.5 13576.1 13856.6 12083.1 FALSE FALSE TRUE 14841.07927 13179.36366 15133.07921 14370.47339 14521.74612 15087.17572 13298.65174 13968.90303 12617.23099 11769.17932 1.261012248 1.119820108 1.285822809 1.221025952 1.233879247 1.281922495 1.129955741 1.186905446 1.072056993 1 13.5227261 -12.35455941 0.866313489 0.98713081 1.218257288 0.594697685 0.057984494 0.303706272 0.37049879 0.048318763 0.010127723 4.42E-13 12.35455941 0.231126478 YALTGDEVK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 YALTGDEVKK 10 1 P62701;C9JEH7;Q8TD47;P22090 P62701 RPS4X;RPS4Y1;RPS4Y2 "40S ribosomal protein S4, X isoform;40S ribosomal protein S4, Y isoform 2;40S ribosomal protein S4, Y isoform 1" 0 1 YALTGDEVK(1)K 163.77 0.0028726 3078300 1023.6 1318.4 1147.7 560.83 2319.7 2261.4 2068.1 2083.9 2295.4 1638.3 FALSE TRUE FALSE 1011.123969 1336.96047 1167.675237 625.6758034 2201.317053 2116.903838 2243.764362 2144.194359 2090.093675 1595.73673 0.633640845 0.837832736 0.731746795 0.392092124 1.379498893 1.326599682 1.40609934 1.343701827 1.309798563 1 10.64000694 -8.733608831 24.89837963 0.788752706 1.364314601 0.583988095 0.225165732 89.40324832 79983.49235 0.027094289 0.054178951 1.85E-09 8.733608831 0.575561896 YALYDASFETK ddPTM_HeLa_Romidepsin_16h_R1 1 YALYDASFETK 11 0 F6RFD5;P60981;P60981-2 F6RFD5 DSTN Destrin 0 0 199.11 5.84E-12 9579100 1502.6 1193.6 997.93 864.59 1170.9 1096.9 1112.2 1301.1 1302.6 1297.9 FALSE FALSE TRUE 1484.285733 1210.403532 1015.298553 964.5579638 1111.144604 1026.81163 1206.67024 1338.745276 1186.092194 1264.180371 1.174109144 0.957461103 0.803127921 0.762990777 0.878944674 0.812235068 0.954507971 1.058982805 0.938230193 1 10.3039866 -10.0298436 6.043963417 1.081813647 0.873846686 0.315434548 0.098888017 0.121567305 14.15932018 0.017048429 0.021345603 9.34E-11 10.0298436 -0.207966961 YAPDK(ac)TSTVLTR ddPTM_HeLa_Romidepsin_16h_R1 1 YAPDKTSTVLTR 12 1 Q9NR12-2;Q9NR12 Q9NR12-2 PDLIM7 PDZ and LIM domain protein 7 0 1 YAPDK(1)TSTVLTR 107.03 0.027393 996950 374.31 297.01 413.24 107.94 463.16 517.74 463.09 369.01 355.36 267.3 FALSE TRUE FALSE 369.7477657 301.1913146 420.4322689 120.4205307 439.5232169 484.6580849 502.424853 379.6867221 323.5757116 260.3555075 1.420164948 1.156846335 1.61483916 0.462523462 1.688165621 1.861524228 1.929764643 1.458339506 1.242822611 1 8.024339115 -4 0.155360252 1.000460749 3.987517603 0.222547867 0.368499666 68.30652392 0.678123234 0.724410708 46.57024004 1.00E-04 4 2.987056854 YASGSSAS(ph)LGGPESAVA ddPTM_HeLa_Romidepsin_16h_R1 1 YASGSSASLGGPESAVA 17 0 Q15149;Q15149-7;Q15149-8;Q15149-9;Q15149-5;Q15149-6;Q15149-3;Q15149-2;H0YDN1;Q15149-4 Q15149;Q15149-3;Q15149-4 PLEC Plectin 1 0 YASGSS(0.002)AS(0.997)LGGPESAVA 113.25 0.0020461 5539100 1622.9 1901 1350 1643.1 1555 1519.7 871.85 1216 1535 1469.4 TRUE FALSE FALSE 1603.119471 1927.762328 1373.496184 1833.082953 1475.642547 1422.596075 945.9049172 1251.183041 1397.705756 1431.224776 1.120103213 1.346931915 0.959664901 1.28077922 1.031034798 0.993971107 0.660905913 0.874204431 0.976580184 1 10.48303455 -7.931364704 4.313427584 1.086602917 0.769408047 0.504015919 0.130173255 0.124922078 4.561616042 0.017523698 0.056075293 1.17E-08 7.931364704 -0.31719487 YATVSS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 YATVSSPSK 9 0 Q01804-5;Q01804-3;Q01804 Q01804-5 OTUD4 OTU domain-containing protein 4 1 0 YATVS(0.326)S(0.654)PS(0.02)K 112.85 0.017518 10133000 5104.1 4810.4 6601.5 4179.9 4600.8 4711.4 3819.5 2992.8 5772.1 5210.1 TRUE FALSE FALSE 5041.889266 4878.120937 6716.396338 4663.199705 4366.004008 4410.356745 4143.928235 3079.391946 5255.82892 5074.740851 0.993526451 0.961255181 1.323495433 0.918904008 0.860340289 0.86908019 0.816579281 0.606807724 1.0356842 1 12.30911844 -7.349304672 0.767821807 1.012842614 0.430627658 0.593345025 0.110670987 1.301211485 0.587757467 0.018085752 0.630557966 4.47E-08 7.349304672 -0.582214956 YDEFHDYLER ddPTM_HeLa_Romidepsin_16h_R1 4 YDEFHDYLER 10 0 Q96K76-2;Q96K76-4;Q96K76 Q96K76-2 USP47 Ubiquitin carboxyl-terminal hydrolase 47 0 0 ;;; ;;; 127.83 0.0038705 28787800 20841.8 18675.1 19083.8 15765.2 18771 18556.5 16654.9 16784.2 21632.7 19224 FALSE FALSE TRUE 20587.77213 18938.00855 19415.94553 17588.0466 17813.04583 17370.79954 18069.56679 17269.82435 19697.81713 18724.55771 1.099506458 1.011399513 1.03692412 0.939303714 0.951319978 0.927701461 0.965019685 0.9223088 1.051977699 1 14.19264402 -9.287297028 4.573463323 1.044683478 0.941835166 0.76623096 0.027240741 0.102746988 5.485206849 0.006017718 0.009553498 5.16E-10 9.287297028 -0.102848312 YDEIFYNLAPADGKLS(ph)GSK ddPTM_HeLa_Romidepsin_16h_R1 2 YDEIFYNLAPADGKLSGSK 19 1 Q9NZN4-2;Q9NZN4 Q9NZN4-2 EHD2 EH domain-containing protein 2 1 0 YDEIFYNLAPADGKLS(0.856)GS(0.144)K;YDEIFYNLAPADGKLS(0.682)GS(0.318)K ; 98.21 0.00062772 168507000 7494.7 6997.2 7271.2 5330.6 7161.3 6344 4511.9 5893.7 7780.1 6945.7 TRUE FALSE FALSE 7403.351714 7095.706765 7397.752186 5946.949053 6795.832139 5938.638874 4895.140673 6064.224911 7084.22837 6765.249713 1.094320539 1.048846246 1.093492849 0.87904354 1.004520517 0.877815177 0.723571321 0.896378577 1.047149576 1 12.72392747 -8.484100073 1.055089544 1.04723633 0.803968717 0.645952153 0.067256473 0.263133014 0.53429477 0.011052813 0.043726414 3.28E-09 8.484100073 -0.243267613 YDERPGPS(ph)PLPHR ddPTM_HeLa_Romidepsin_16h_R1 1 YDERPGPSPLPHR 13 1 P08621;P08621-4 P08621 SNRNP70 U1 small nuclear ribonucleoprotein 70 kDa 1 0 Y(0.015)DERPGPS(0.985)PLPHR 80.387 0.014722 176110000 2430.6 2486.5 2193.2 2232.6 2991.2 2955.7 2655.7 2849.5 2659.1 2613.6 TRUE FALSE FALSE 2400.974912 2521.505012 2231.371726 2490.743717 2838.547902 2766.840309 2881.275092 2931.945787 2421.263436 2545.698295 0.943149829 0.990496406 0.876526386 0.978412768 1.115037044 1.086868901 1.131821118 1.151725557 0.951119558 1 11.31384573 -8.769805418 5.317605915 0.965857254 1.120691265 0.835736176 0.03568686 0.058615058 4.88319086 0.005726833 0.010994954 1.70E-09 8.769805418 0.15483401 YDHQAEEDLR ddPTM_HeLa_Romidepsin_16h_R1 2 YDHQAEEDLR 10 0 Q15417-3;Q15417 Q15417-3 CNN3 Calponin-3 0 0 ; ; 136.81 0.002571 20590000 12019 11690.4 12398.4 6671.2 14653.1 14891.2 12723.2 14549.6 12426.6 12582.6 FALSE FALSE TRUE 11872.50781 11854.97776 12614.18895 7442.555533 13905.29763 13939.70038 13803.90829 14970.56972 11315.13377 12255.70224 0.968733376 0.967303018 1.029250606 0.607272875 1.134598194 1.137405275 1.126325364 1.221518721 0.923254625 1 13.58116553 -8.560614664 24.99995872 0.959742097 1.154507654 0.47771833 0.117359808 120.6848669 79953.02651 0.016315183 0.032630412 2.75E-09 8.560614664 0.194765558 YDIDLPNK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 YDIDLPNKK 9 1 E5RGN3;E5RIM7;O00244 E5RGN3 ATOX1 Copper transport protein ATOX1 0 1 ; YDIDLPNK(1)K;YDIDLPNK(1)K 95.502 0.011375 1137080 848.97 910.6 1000.93 442.05 2271.22 2400.5 2048.54 2401.2 2521.8 1876.55 FALSE TRUE FALSE 838.6224271 923.4194507 1018.350767 493.1619009 2155.311168 2247.115797 2222.542936 2470.674934 2296.243892 1827.79696 0.458815965 0.505208987 0.557146548 0.26981219 1.179185224 1.229412153 1.215968176 1.351722859 1.256290464 1 10.8358901 -8.627200531 8.269763068 0.673621941 1.251141635 0.524682142 0.266340917 0.148973968 10.6608524 0.038072476 0.076282182 2.36E-09 8.627200531 0.577519693 YDLDFKSPDDPSR ddPTM_HeLa_Romidepsin_16h_R1 1 YDLDFKSPDDPSR 13 1 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 90.697 0.024951 15364000 5474.2 4708.7 4261.2 5301.3 5720.5 5037.1 4520.8 5096.4 4685.5 4116.9 FALSE FALSE TRUE 5407.478345 4774.989202 4335.364399 5914.261249 5428.561539 4715.245566 4904.796639 5243.856293 4266.417145 4009.942345 1.348517729 1.190787496 1.081153799 1.474899323 1.353775459 1.175888619 1.223158893 1.307713638 1.063959723 1 11.96936578 -12.40915111 0.977907442 0.989305105 1.272631386 0.440619757 0.106266544 0.426344727 0.683678336 0.08962212 0.019543103 3.90E-13 12.40915111 0.283326281 YDSDGDKS(ph)DDLVVDVSNEDPATPR ddPTM_HeLa_Romidepsin_16h_R1 2 YDSDGDKSDDLVVDVSNEDPATPR 24 1 H0YKH0;H0YLW9;H0YLI3;H0YNT2;H0YKT5;H0YKN8;H0YL70;Q04726-2;Q04726-7;Q04726-3;Q04726-6;Q04726-5;Q04726-4;Q04726;A0A0D9SES8 H0YKH0 TLE3 Transducin-like enhancer protein 3 1 0 Y(0.005)DS(0.025)DGDKS(0.968)DDLVVDVS(0.001)NEDPATPR;Y(0.005)DS(0.044)DGDKS(0.951)DDLVVDVSNEDPATPR ; 98.76 9.62E-06 23725900 3940.6 3883.4 3939.9 3098.1 3139.9 2715.3 2348.55 2473.6 4360.9 4190.5 TRUE FALSE FALSE 3892.570451 3938.070607 4008.472307 3456.316899 2979.659186 2541.801093 2548.035778 2545.169713 3970.850182 4081.630206 0.953680332 0.964827877 0.982076304 0.846798148 0.730016938 0.622741641 0.62426914 0.623566954 0.972858878 1 11.99492977 -8.791074721 1.509774383 0.978184535 0.618400917 0.989130588 0.016286797 0.032743105 0.15033204 0.003251579 0.007824535 1.62E-09 8.791074721 -0.359783619 YDYEEVEAEGANK ddPTM_HeLa_Romidepsin_16h_R1 2 YDYEEVEAEGANK 13 0 A0A3B3ITK7;P36871;P36871-2;P36871-3 A0A3B3ITK7 PGM1 Phosphoglucomutase-1 0 0 ; ; 281.83 1.11E-93 9806800 3695 3658.7 3180.6 4086.7 4001.3 3504.2 3296 3505.9 4440.1 4094.8 FALSE FALSE TRUE 3649.963919 3710.207275 3235.957009 4559.223483 3797.09873 3280.292929 3575.962158 3607.337685 4042.966336 3988.416506 0.915141113 0.930245693 0.811338787 1.143116191 0.952031646 0.822454958 0.896586942 0.904453605 1.013677065 1 11.96160036 -16.52287875 0.226012412 1.433252756 0.91038153 0.13734704 0.085453404 85.38500955 1.092920791 16.38719539 0.065095658 3.00E-17 16.52287875 -0.522871226 YEAQGDK(ac)AK ddPTM_HeLa_Romidepsin_16h_R1 1 YEAQGDKAK 9 1 O75351;K7EKZ3;K7EL71 O75351 VPS4B Vacuolar protein sorting-associated protein 4B 0 1 YEAQGDK(1)AK 118.18 0.0018798 0 651.64 576.57 659.49 694.72 639.2 676.16 1073.2 490.06 794.5 718.6 FALSE TRUE FALSE 643.697561 584.6869676 670.9681468 775.0467952 606.5792388 632.9555582 1164.357581 504.2391129 723.4379301 699.9306684 0.919659032 0.835349834 0.958620871 1.107319382 0.866627605 0.904311794 1.663532738 0.720412943 1.033585129 1 9.451068213 YEDDGIS(ph)DDEIEGK ddPTM_HeLa_Romidepsin_16h_R1 2 YEDDGISDDEIEGK 14 0 I3VM54;Q9Y2K7-3;Q9Y2K7 I3VM54 KDM2A Lysine-specific demethylase 2A 1 0 YEDDGIS(1)DDEIEGK;YEDDGIS(1)DDEIEGK ; 127.07 0.0028731 23130000 8907.8 8741.8 9830.2 5724.2 8217.1 8463.9 6980.3 7705 10175.7 9512.4 TRUE FALSE FALSE 8799.228307 8864.86729 10001.29051 6386.058937 7797.750725 7923.084106 7573.206508 7927.932019 9265.559906 9265.266477 0.949700511 0.956784925 1.079439057 0.689247196 0.841611058 0.855138287 0.817376006 0.855661522 1.00003167 1 13.17761675 -9.267490574 24.99937734 0.980910591 0.816179309 0.726372116 0.056418643 210.7920936 870847.6363 0.00838784 0.013018139 5.40E-10 9.267490574 -0.164731283 YEDKPEPEVDALGS(ph)PPALLK ddPTM_HeLa_Romidepsin_16h_R1 2 YEDKPEPEVDALGSPPALLK 20 1 Q68DQ2 Q68DQ2 CRYBG3 Very large A-kinase anchor protein 1 0 YEDKPEPEVDALGS(1)PPALLK;Y(0.001)EDKPEPEVDALGS(0.999)PPALLK ; 112.86 0.0001145 13188900 5168.9 4544.8 5043.5 4288.8 5791.9 5073.6 3949.2 4824.7 5689.4 4377.4 TRUE FALSE FALSE 5105.899459 4608.781814 5131.280002 4784.691235 5496.31773 4749.413334 4284.644949 4964.295082 5180.525815 4263.674517 1.197534999 1.080941286 1.203487738 1.12219899 1.289103497 1.113924929 1.004918394 1.164323182 1.215037826 1 12.05788159 -12.42217008 1.071179091 0.997314326 1.149402181 0 0.098012583 0.466242155 0.929355873 0.054890274 0.012871852 3.78E-13 12.42217008 0.152087856 YEDSDKPFVDS(ph)PASR ddPTM_HeLa_Romidepsin_16h_R1 1 YEDSDKPFVDSPASR 15 1 E9PQ01;E9PKN0;O94913 E9PQ01;O94913 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 1 0 YEDS(0.002)DKPFVDS(0.958)PAS(0.04)R 60.618 0.029765 10198000 1566.8 1519.4 1389.5 1571.1 2263.7 2695.6 2115.4 2134.4 1885.8 1774.3 TRUE FALSE FALSE 1547.703239 1540.790153 1413.683665 1752.757974 2148.174942 2523.35986 2295.082023 2196.155496 1717.129325 1728.20343 0.895556167 0.891556009 0.818007672 1.014208133 1.243010461 1.460105804 1.328016125 1.270773717 0.993592129 1 10.75505733 -8.732832409 2.999514739 0.934530412 1.350493766 0.891686436 0.067768468 0.062208295 1.147287575 0.010924336 0.022580116 1.85E-09 8.732832409 0.415963354 YEEEEEQSR ddPTM_HeLa_Romidepsin_16h_R1 1 YEEEEEQSR 9 0 Q9Y5B9 Q9Y5B9 SUPT16H FACT complex subunit SPT16 0 0 189.38 2.70E-06 8613700 2425.3 2306.2 2806.2 2018.2 2292.2 2262.6 2490 893.15 2581.1 2890.7 FALSE FALSE TRUE 2395.739511 2338.666744 2855.040734 2251.55378 2175.220481 2118.027162 2701.500538 918.9918861 2350.239952 2815.599197 0.850880876 0.830610673 1.014008221 0.799671268 0.772560414 0.752247395 0.959476242 0.326393006 0.834721062 1 11.45922626 -7.257643773 24.77714435 0.89784461 0.326392757 0.751053837 0.092179958 129.245885 843657.1651 0.014198474 0.142257282 5.53E-08 7.257643773 -0.571451853 YEEIDNAPEER ddPTM_HeLa_Romidepsin_16h_R1 1 YEEIDNAPEER 11 0 P49411 P49411 TUFM "Elongation factor Tu, mitochondrial" 0 0 152.69 0.023152 13765000 1403 1666.2 1445.7 1591.2 1496.3 1933.1 1450.8 1449.8 1611.5 1718.8 FALSE FALSE TRUE 1385.899696 1689.656807 1470.861802 1775.182031 1419.938228 1809.581149 1574.030916 1491.747676 1467.363404 1674.145328 0.827825203 1.009265312 0.878574743 1.060351214 0.848157089 1.080898485 0.940199688 0.891050287 0.876485081 1 10.70920905 YEEIVK ddPTM_HeLa_Romidepsin_16h_R1 1 YEEIVK 6 0 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 0 129.96 0.025163 2486200 2830.1 2793 2545.1 2759.2 2734.6 3222.2 2370.7 2490.8 3162.1 2938.4 FALSE FALSE TRUE 2795.605653 2832.319927 2589.396398 3078.231686 2595.043158 3016.311819 2572.067199 2562.867368 2879.273856 2862.059944 0.976780957 0.989608877 0.904731714 1.075530124 0.906704684 1.053895403 0.898676914 0.895462505 1.006014518 1 11.48283817 -7.689273857 12.41312867 0.986602399 0.896807221 0.340417891 0.051175653 0.5521439 93.0309672 0.006005345 0.0224799 2.05E-08 7.689273857 -0.089795178 YEEVSVSGFEEFHR ddPTM_HeLa_Romidepsin_16h_R1 2 YEEVSVSGFEEFHR 14 0 I3L0K2;I3L3M7;I3L2R6;Q9BRA2 I3L0K2 TXNDC17 Thioredoxin domain-containing protein 17 0 0 ; ; 187.63 3.04E-11 15311300 5456.7 4964.7 4640.5 4768.6 6280.1 7229.6 5593.5 6133.6 6024.1 5491.5 FALSE FALSE TRUE 5390.191642 5034.593177 4721.265956 5319.967969 5959.603063 6767.651892 6068.61175 6311.066039 5485.289408 5348.830038 1.007732832 0.941251291 0.882672645 0.994604041 1.114188153 1.265258354 1.134568066 1.179896537 1.025512003 1 12.38500765 -8.632746323 3.570702422 0.987777526 1.187989932 0.798989437 0.049531558 0.083223753 2.051814898 0.007558135 0.015891333 2.33E-09 8.632746323 0.200212406 YELEPS(ph)PLTQFILER ddPTM_HeLa_Romidepsin_16h_R1 1 YELEPSPLTQFILER 15 0 C9JAV7;G5E9X1;B3KQH5;Q9UL03-3;Q9UL03 C9JAV7 INTS6 Integrator complex subunit 6 1 0 YELEPS(0.663)PLT(0.337)QFILER 84.734 0.0098985 14331000 4376.9 4288 4007.5 3569.6 4944.2 4405.6 4077.7 4578.8 4645.5 4598.4 TRUE FALSE FALSE 4323.552659 4348.366577 4077.248856 3982.333947 4691.879025 4124.096378 4424.059736 4711.280354 4229.994845 4478.932905 0.965308646 0.970848787 0.91031702 0.889125609 1.047543941 0.920776548 0.987748607 1.051875626 0.94442023 1 12.12893934 -7.301862485 4.043849187 0.971152144 1.056112701 0.246111787 0.045216591 0.238293205 7.642639704 0.00617889 0.053701396 4.99E-08 7.301862485 0.084960558 YELISETGGSHDKR ddPTM_HeLa_Romidepsin_16h_R1 1 YELISETGGSHDKR 14 1 Q12906-4;Q12906-6;Q12906-7;Q12906-5;Q12906-2;Q12906-3;Q12906;Q96SI9-2;Q96SI9 Q12906-4 ILF3;STRBP Interleukin enhancer-binding factor 3;Spermatid perinuclear RNA-binding protein 0 0 62.162 0.017087 6708600 2167.6 1967.8 1956 1896.5 2917 2581.3 2357.6 2439.5 3204.2 2493.3 FALSE FALSE TRUE 2141.180457 1995.50274 1990.043359 2115.782253 2768.134605 2416.363261 2557.854485 2510.083084 2917.608327 2428.523707 0.881679867 0.821693745 0.819445721 0.871221577 1.13984253 0.994992659 1.053254896 1.033583933 1.201391742 1 11.24586385 -8.772902563 24.99828973 0.917676252 1.050947839 0.223505554 0.109967018 167.6485796 365598.8442 0.01184824 0.021613292 1.69E-09 8.772902563 0.133271587 YEPQS(ph)PGYEPR ddPTM_HeLa_Romidepsin_16h_R1 3 YEPQSPGYEPR 11 0 H3BS42;Q9H5H4 H3BS42 ZNF768 Zinc finger protein 768 1 0 YEPQS(1)PGYEPR;YEPQS(1)PGYEPR;YEPQS(1)PGYEPR ;; 171.36 0.0002817 101650000 6010.6 6960.2 6509.7 3589.42 5731 8186.8 7332.4 7479.9 7583.7 6163.8 TRUE FALSE FALSE 5937.340495 7058.185878 6622.998598 4004.445629 5438.525685 7663.689902 7955.213873 7696.319105 6905.394878 6003.663587 0.988952897 1.175646466 1.103159513 0.667000336 0.905867826 1.276502221 1.3250599 1.281937103 1.150196839 1 12.55162742 -8.237237615 12.26126259 0.986578755 1.297648175 0.495012094 0.136522549 0.864765022 435.9529601 0.018327349 0.046340983 5.79E-09 8.237237615 0.31106942 YESGPDGGEEDGTGS(ph)LKR ddPTM_HeLa_Romidepsin_16h_R1 1 YESGPDGGEEDGTGSLKR 18 1 Q07866-6;G3V5R9;G3V3H3 Q07866-6 KLC1 Kinesin light chain 1 1 0 YESGPDGGEEDGT(0.116)GS(0.884)LKR 50.237 0.02722 12525000 3055.6 3318.7 2744.8 3050.3 3051.3 3769.1 3391.2 3147.4 3344.5 3285 TRUE FALSE FALSE 3018.357172 3365.420746 2792.572093 3402.990038 2895.580775 3528.266674 3679.248443 3238.465053 3045.359544 3199.655226 0.943338253 1.051807307 0.872772813 1.063548976 0.904966495 1.102702143 1.14988903 1.012129378 0.951777404 1 11.64370074 -8.241775324 24.51810803 0.97399047 1.094405092 0.415679637 0.06411832 426.5236129 531809.4548 0.008030028 0.020437923 5.73E-09 8.241775324 0.120414622 YESLTDPS(ph)KLDSGK ddPTM_HeLa_Romidepsin_16h_R1 1 YESLTDPSKLDSGK 14 1 P08238;Q58FF7;Q58FF8;P07900-2;P07900;G3V2J8 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB3P;HSP90AB2P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha 1 0 YESLT(0.006)DPS(0.992)KLDS(0.002)GK 118.51 0.00060022 0 923.99 869.62 863.69 647.8 856.21 886.25 919.01 938.01 963.06 1106.9 TRUE FALSE FALSE 912.7280545 881.8625332 878.7221621 722.701684 812.5144087 829.6214852 997.0706865 965.1498394 876.9215016 1078.142578 0.846574537 0.817946115 0.815033354 0.670321067 0.753624265 0.76949144 0.924804109 0.895196849 0.813363204 1 10.07433226 -11.59126095 0.673120122 0.996607111 0.802759215 0.024434271 0.087258284 0.447984966 0.409146571 0.043223346 0.017653557 2.56E-12 11.59126095 -0.193847896 YESLTDPSK ddPTM_HeLa_Romidepsin_16h_R1 1 YESLTDPSK 9 0 P08238;Q58FF7;Q58FF6;Q58FF8;P07900-2;P07900;G3V2J8 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB3P;HSP90AB4P;HSP90AB2P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 4;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha 0 0 169.44 0.017083 9598500 8615.3 7909.4 8743.2 6602.5 8899.6 10140 8859.5 9253.7 9377.7 8625.9 FALSE FALSE TRUE 8510.29341 8020.748741 8895.371728 7365.912116 8445.420203 9492.086725 9612.025709 9521.44121 8538.935025 8401.797874 1.012913371 0.954646715 1.058746219 0.876706656 1.005192023 1.129768517 1.144043912 1.133262351 1.016322358 1 13.03648236 -8.262096481 5.443091631 0.996106082 1.137660535 0.684196963 0.045488092 0.071203377 7.728587872 0.00609919 0.014868154 5.47E-09 8.262096481 0.141554452 YESLTDPSK(ac)LDSGK ddPTM_HeLa_Romidepsin_16h_R1 1 YESLTDPSKLDSGK 14 1 P08238;Q58FF7;Q58FF8;P07900-2;P07900;G3V2J8 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB3P;HSP90AB2P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha 0 1 YESLTDPSK(1)LDSGK 185.59 1.54E-08 412650 349.37 258.06 337.34 299.34 856.95 736.25 653.28 617.01 648.11 629.99 FALSE TRUE FALSE 345.1117441 261.6929755 343.2112612 333.9510992 813.2166438 689.2060011 708.7695869 634.8622109 590.1414184 613.622769 0.562416784 0.426472075 0.559319632 0.544228663 1.325271298 1.123175403 1.155057509 1.034613191 0.961733248 1 9.261208206 -8.760636832 24.99994474 0.722903224 1.156613237 0.610031954 0.187238967 15.31515038 477049.6369 0.034287827 0.065490343 1.74E-09 8.760636832 0.433710013 YESLTDPSKLDSGK ddPTM_HeLa_Romidepsin_16h_R1 3 YESLTDPSKLDSGK 14 1 P08238;Q58FF7;Q58FF8;P07900-2;P07900;G3V2J8 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB3P;HSP90AB2P;HSP90AA1 Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta-3;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha 0 0 ;; ;; 103.13 0.0099891 72680370 9197.6 8516.1 7981 8379.3 9326.9 10039.2 8050.3 9852.6 9588.1 8914.2 FALSE FALSE TRUE 9085.496113 8635.989879 8119.905957 9348.154092 8850.91349 9397.72752 8734.092281 10137.66944 8730.516322 8682.607799 1.046401764 0.994630885 0.93519207 1.076652811 1.019384233 1.08236232 1.00592961 1.167583481 1.005517757 1 13.0839127 -4.573363147 1.294212298 1.019644487 199.9644021 0.524951483 0.041602923 1023.537296 1.662823988 0.005917307 604636.3839 2.67E-05 4.573363147 198.9447577 YESQEPLAGQES(ph)PLPLATR ddPTM_HeLa_Romidepsin_16h_R1 5 YESQEPLAGQESPLPLATR 19 0 Q9C0C2;Q9C0C2-2 Q9C0C2 TNKS1BP1 182 kDa tankyrase-1-binding protein 1 0 YESQEPLAGQES(0.957)PLPLAT(0.043)R;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR;YESQEPLAGQES(1)PLPLATR ;;;; 227.89 7.43E-39 427458700 17163.61 17417.9 16878.3 14192.69 19107.5 18693.7 16517.2 18050.6 18688.5 17386.13 TRUE FALSE FALSE 16954.41332 17663.10965 17172.05973 15833.7156 18132.37298 17499.2329 17920.17056 18572.86563 17016.95375 16934.43584 1.001179696 1.043029117 1.014031994 0.935001068 1.070739713 1.033351986 1.05820889 1.096751366 1.004872788 1 14.0476723 -7.655440014 0.835354657 1.002071121 1.115719356 0.459890819 0.031653267 0.923124556 0.666946065 0.004886412 0.084769974 2.21E-08 7.655440014 0.113648235 YESSS(ph)YTDQFSR ddPTM_HeLa_Romidepsin_16h_R1 1 YESSSYTDQFSR 12 0 G3V1L9;Q07157;A0A087X0K9;G5E9E7;Q07157-2 G3V1L9 TJP1 Tight junction protein ZO-1 1 0 YESS(0.041)S(0.941)YT(0.017)DQFSR 137.95 0.0023341 4156800 1515.8 1560.9 1083.9 1596.3 1145.7 1479.2 912.55 984.11 1517.4 1475.6 TRUE FALSE FALSE 1497.324847 1582.874391 1102.764825 1780.871717 1087.230654 1384.683894 990.0619742 1012.58367 1381.679944 1437.263699 1.041788537 1.101311048 0.767266873 1.239070964 0.756458717 0.96341673 0.688852 0.704521843 0.961326682 1 10.48910907 -7.865018431 0.899728614 1.019007379 0.623611465 0.402009074 0.136017303 0.660667649 0.676344021 0.01900479 0.208092432 1.36E-08 7.865018431 -0.395395913 YET(ph)LQMALSYIMALT(ph)R ddPTM_HeLa_Romidepsin_16h_R1 1 YETLQMALSYIMALTR 16 0 Q8N100 Q8N100 ATOH7 Protein atonal homolog 7 2 0 Y(0.333)ET(0.666)LQMALS(0.084)Y(0.013)IMALT(0.903)R 43.932 0.025897 3983200 3032.4 3562.9 3532.2 2485.4 3557.4 3779 2789.5 2807 3665.7 3609.7 TRUE FALSE FALSE 2995.439942 3613.0586 3593.676459 2772.773642 3375.852604 3537.534096 3026.44006 2888.216116 3337.830611 3515.919474 0.851964889 1.027628371 1.02211569 0.788634001 0.960162094 1.006147644 0.860781961 0.821468221 0.949347855 1 11.77968631 -7.57629396 7.713612872 0.93832249 0.8310116 0.257008848 0.073459543 0.243461624 30.01580035 0.011229403 0.042725747 2.65E-08 7.57629396 -0.10731089 YETLVGTIGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 YETLVGTIGKK 11 1 H3BSB3;H3BNT4;Q99547 H3BSB3 MPHOSPH6 M-phase phosphoprotein 6 0 1 YETLVGTIGK(1)K 94.297 0.016254 182890 0 0 0 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 0 0 0 0 0 0 0 0 0 YETPSDAIEVIS(ph)PASS(ph)PAPPQEK ddPTM_HeLa_Romidepsin_16h_R1 2 YETPSDAIEVISPASSPAPPQEK 23 0 E7EVK1;A0A088AWL3;O75376;O75376-2 E7EVK1 NCOR1 Nuclear receptor corepressor 1 2 0 YETPSDAIEVIS(0.99)PAS(0.237)S(0.772)PAPPQEK;YETPSDAIEVIS(0.927)PAS(0.517)S(0.555)PAPPQEK ; 91.767 0.00050015 8584300 4096.2 4198.8 3986.2 3154.5 3327.5 3038.7 2617.8 2717.5 4158.3 3944.4 TRUE FALSE FALSE 4046.273939 4257.910817 4055.578139 3519.238132 3157.685258 2844.536877 2840.155867 2796.126575 3786.371233 3841.923919 1.053189502 1.108275673 1.055611257 0.916009324 0.821902079 0.740393859 0.739253542 0.727793323 0.985540399 1 11.90761323 -8.810732361 1.806092039 1.035296571 0.737043775 0.938166241 0.034591344 0.063162839 0.41831341 0.005909968 0.013137459 1.55E-09 8.810732361 -0.298252796 YEYDPDIS(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 4 YEYDPDISPPR 11 0 Q9BRD0;H7C462 Q9BRD0 BUD13 BUD13 homolog 1 0 YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR;YEYDPDIS(1)PPR ;;; 187.78 1.90E-08 117056000 7659.6 7945.9 6979.71 5041.04 6272.42 6883.85 5561.1 6787.43 8043.5 7940.84 TRUE FALSE FALSE 7566.241849 8057.762589 7101.188925 5623.908764 5952.315002 6443.994202 6033.459695 6983.813578 7324.069215 7734.535832 0.97824123 1.041790065 0.918114426 0.727116518 0.76957624 0.833145562 0.780067457 0.902938939 0.946930672 1 12.917099 -9.484899141 5.168092638 0.993053698 0.801949666 0.775797436 0.048165888 0.06115199 4.10553511 0.006838161 0.010324992 3.27E-10 9.484899141 -0.191104032 YFAES(ph)DEEEDDVDFAMFN ddPTM_HeLa_Romidepsin_16h_R1 2 YFAESDEEEDDVDFAMFN 18 0 Q02880;Q02880-2 Q02880 TOP2B DNA topoisomerase 2-beta 1 0 YFAES(1)DEEEDDVDFAMFN;YFAES(1)DEEEDDVDFAMFN ; 175.66 4.36E-08 2058160 1806.79 1948.38 1954 1529.8 1996.75 2239.95 1371.64 1999.47 2377.6 1995.52 TRUE FALSE FALSE 1784.768149 1975.809345 1988.00855 1706.682674 1894.848397 2096.824424 1488.147067 2057.32151 2164.941501 1943.676103 0.918243603 1.0165322 1.022808557 0.878069485 0.974878682 1.078793129 0.765635316 1.058469313 1.113838617 1 10.92457211 YFDDEFTAQSIT(ph)ITPPDR ddPTM_HeLa_Romidepsin_16h_R1 1 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 0 YFDDEFTAQS(0.003)IT(0.498)IT(0.498)PPDR 156.83 1.24E-05 3627300 2444.8 2344.5 3341.6 1674.2 2628.3 3099.9 1934.7 2598 3123.2 3181.9 TRUE FALSE FALSE 2415.001837 2377.505933 3399.759146 1867.778881 2494.168043 2901.826394 2099.03337 2673.169031 2843.85317 3099.233779 0.77922545 0.767127007 1.096967634 0.602658274 0.80476925 0.936304455 0.677274939 0.862525779 0.917598791 1 11.59769587 -12.35256152 0.836361249 1.013059051 0.812549457 0.149138947 0.130545938 0.841142398 0.941099923 0.114079012 0.023166446 4.44E-13 12.35256152 -0.200509593 YFDDEFTAQSITIT(ph)PPDR ddPTM_HeLa_Romidepsin_16h_R1 3 YFDDEFTAQSITITPPDR 18 0 P31751;P31751-2;M0R0P9;M0R283 P31751 AKT2 RAC-beta serine/threonine-protein kinase 1 0 YFDDEFTAQSIT(0.001)IT(0.999)PPDR;YFDDEFTAQSIT(0.001)IT(0.999)PPDR;YFDDEFTAQSITIT(1)PPDR ;; 287.48 2.20E-123 16050300 5018.75 5239.8 5418.9 3220.38 4656 4323 3624.94 4484.1 5097 5458.3 TRUE FALSE FALSE 4957.579545 5313.566042 5513.213681 3592.735488 4418.386946 4046.774252 3932.842313 4613.840359 4641.111554 5316.492579 0.932490636 0.999449536 1.037002046 0.675771749 0.831071779 0.761173686 0.739743779 0.86783538 0.872964927 1 12.37625906 -9.268065909 24.99920447 0.974855359 0.775487686 0.697948355 0.063497448 185.2850661 699004.7035 0.008314884 0.012883825 5.39E-10 9.268065909 -0.199367673 YFDEHYEYR ddPTM_HeLa_Romidepsin_16h_R1 2 YFDEHYEYR 9 0 P33552 P33552 CKS2 Cyclin-dependent kinases regulatory subunit 2 0 0 ; ; 185.81 1.18E-05 93257000 14535.8 14387.5 14423.4 6994.6 16672.9 17694.3 15098.8 15400.8 15453.7 14675 FALSE FALSE TRUE 14358.63208 14590.0476 14674.43323 7803.348563 15822.0197 16563.69134 16381.2917 15846.39785 14071.48237 14293.74138 1.004539798 1.020729787 1.026633464 0.545927644 1.106919404 1.158807263 1.146046459 1.108624917 0.984450606 1 13.80309597 -8.548654237 24.99999595 0.971236017 1.137684599 0.312808488 0.137796012 233.6759838 226644.6743 0.019857689 0.039716469 2.83E-09 8.548654237 0.166448582 YFDNKDDDSDT(ph)ETSNDLPK ddPTM_HeLa_Romidepsin_16h_R1 2 YFDNKDDDSDTETSNDLPK 19 1 C9J3R1;C9IZP0;J3KR59;J3KR68;Q9UID6 C9J3R1 ZNF639 Zinc finger protein 639 1 0 YFDNKDDDS(0.006)DT(0.784)ET(0.171)S(0.038)NDLPK;YFDNKDDDS(0.26)DT(0.401)ET(0.26)S(0.079)NDLPK ; 94.281 0.0015218 62224000 8796.2 7769.2 7718.3 6683 5801.6 5131.4 4754.5 4884.9 8313.1 7586 TRUE FALSE FALSE 8688.988531 7878.575002 7852.633774 7455.719904 5505.522703 4803.520101 5158.347111 5026.236874 7569.555515 7388.914626 1.175949239 1.066269594 1.062758764 1.009041284 0.74510574 0.6500982 0.698119734 0.680240215 1.024447554 1 12.85114674 -8.772310795 2.599933533 1.081840263 0.677268182 0.939066644 0.045643256 0.063131217 0.872202749 0.009978761 0.020718675 1.69E-09 8.772310795 -0.404572081 YFDPANGK(ac)FSK ddPTM_HeLa_Romidepsin_16h_R1 2 YFDPANGKFSK 11 1 P13639 P13639 EEF2 Elongation factor 2 0 1 ; YFDPANGK(1)FSK;YFDPANGK(1)FSK 141.1 0.0039484 1049290 1211.6 1276.91 1173.04 1167.2 1325.31 1270.17 1219.85 1263.28 1307.38 1232.3 FALSE TRUE FALSE 1196.832553 1294.886372 1193.456269 1302.157156 1257.674485 1189.010236 1323.464029 1299.831014 1190.444658 1200.284668 0.99712392 1.078816056 0.994311017 1.084873606 1.047813505 0.990606868 1.102625122 1.082935613 0.991801936 1 10.22916089 -4 0.16928545 0.984491624 1.403717288 0.350819598 0.035625728 43.56366565 0.456406703 0.052586303 4.644776897 1.00E-04 4 0.419225664 YFDRVDENNPEYLR ddPTM_HeLa_Romidepsin_16h_R1 2 YFDRVDENNPEYLR 14 1 E7EV99;E7ENY0;P35611-5;P35611-2;P35611-6;P35611-4;P35611;P35611-3;A0A0A0MSR2;D6RJE2;D6RAH3;D6RF25 E7EV99 ADD1 Alpha-adducin 0 0 ; ; 116.98 0.0052085 9306400 1978.83 1511.65 1929.38 1729.29 1836.3 2052.23 1952.46 1985.17 2356.9 1779.91 FALSE FALSE TRUE 1954.711259 1532.931048 1962.96005 1929.238646 1742.586759 1921.099126 2118.301904 2042.607762 2146.092961 1733.667682 1.127500547 0.884212738 1.132258547 1.112807643 1.005144629 1.108112672 1.221861563 1.178200288 1.237891773 1 10.75961167 -7.930411991 4.239659218 1.054335158 1.198466701 0.218956078 0.091657199 0.16630713 5.862072473 0.010510563 0.033761999 1.17E-08 7.930411991 0.144131543 TGSES(ph)SQTGTSTTSSR ddPTM_HeLa_Romidepsin_16h_R1 2 TGSESSQTGTSTTSSR 16 0 E7EX17;P23588-2;P23588 E7EX17 EIF4B Eukaryotic translation initiation factor 4B 1 0 T(0.014)GS(0.288)ES(0.346)S(0.346)QT(0.005)GTS(0.001)TTSSR;T(0.03)GS(0.061)ES(0.848)S(0.061)QTGTSTTSSR ; 293.42 3.03E-119 594368000 3536.6 3393.9 3447 2906.6 2568.05 2593.43 2417.2 1803.81 4509.5 4110.2 TRUE FALSE FALSE 3493.494559 3441.679413 3506.993589 3242.674768 2436.992826 2427.718193 2622.516908 1856.000396 4106.159026 4003.416411 0.872628325 0.859685593 0.876000203 0.809976888 0.60872829 0.60641161 0.65506973 0.463604133 1.025663734 1 11.96701597 -7.003064379 0.244548795 1.00525204 1.11E-20 0.909240534 0.052950928 2.505369373 0.108804265 0.039045075 0.779194709 9.93E-08 7.003064379 -1.00525204 down YFEADPPGQVAAS(ph)PDPTT ddPTM_HeLa_Romidepsin_16h_R1 1 YFEADPPGQVAASPDPTT 18 0 H0Y8X4;O43598 H0Y8X4 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 0 YFEADPPGQVAAS(0.969)PDPT(0.015)T(0.015) 164.82 8.47E-07 33749000 8427.3 8082.1 7562.5 7773.9 8483.9 8293.2 7376.3 8849.8 8024.2 8048.4 TRUE FALSE FALSE 8324.584826 8195.880016 7694.12214 8672.754895 8050.934925 7763.291285 8002.842738 9105.855 7306.495455 7839.301408 1.061903911 1.045486018 0.981480586 1.106317316 1.026996477 0.990303967 1.020861722 1.1615646 0.932034001 1 12.93650938 -13.24132907 0.006397137 1.44E-05 2.031694806 0.204792167 0.055573918 22257.93838 24.33034097 4029.511505 3702.8202 5.74E-14 13.24132907 2.031680409 YFEADPPGQVAASPDPT(ph)T ddPTM_HeLa_Romidepsin_16h_R1 1 YFEADPPGQVAASPDPTT 18 0 H0Y8X4;O43598 H0Y8X4 DNPH1 2-deoxynucleoside 5-phosphate N-hydrolase 1 1 0 YFEADPPGQVAAS(0.255)PDPT(0.372)T(0.372) 172.93 3.41E-07 37540000 10616 10577 9875.5 9776.5 11912 10523 9223.7 10619 10305 9922.7 TRUE FALSE FALSE 10486.60811 10725.90328 10047.37893 10906.90493 11304.08619 9850.614261 10007.16085 10926.24401 9383.294991 9664.906824 1.085019059 1.10977824 1.039573285 1.128505958 1.169601156 1.019214612 1.035412036 1.130506916 0.970862437 1 13.23854011 -12.04522434 0.681924394 0.99500785 1.089398654 0.436037144 0.046432186 0.744719101 0.589694496 0.039623553 0.010005845 9.01E-13 12.04522434 0.094390804 YFEGEFTGLPPALT(ph)PPAPHSLLTAR ddPTM_HeLa_Romidepsin_16h_R1 2 YFEGEFTGLPPALTPPAPHSLLTAR 25 0 Q6P5Z2 Q6P5Z2 PKN3 Serine/threonine-protein kinase N3 1 0 YFEGEFTGLPPALT(0.92)PPAPHS(0.044)LLT(0.036)AR;YFEGEFTGLPPALT(0.986)PPAPHS(0.008)LLT(0.006)AR ; 85.191 8.03E-05 67093000 2340.1 2634.5 1968.24 2624 1772.19 1673.57 1260.19 1351.39 2457.2 1998.16 TRUE FALSE FALSE 2311.577961 2671.58856 2002.496392 2927.399226 1681.748531 1566.634278 1367.230507 1390.490338 2237.421878 1946.247515 1.187710167 1.372686947 1.028901194 1.504124837 0.864097972 0.804951203 0.702495698 0.714446815 1.149608084 1 10.92647948 -8.538528902 24.99634594 1.137314687 0.753102102 0.655300532 0.1516552 129.2449265 206428.7366 0.023384934 0.046781167 2.89E-09 8.538528902 -0.384212585 YFEQLLEEEREK ddPTM_HeLa_Romidepsin_16h_R1 1 YFEQLLEEEREK 12 1 O15460-2;O15460 O15460-2 P4HA2 Prolyl 4-hydroxylase subunit alpha-2 0 0 139.78 0.0023456 6211200 1561 1417.3 1493.6 1698.6 1947.5 1814.1 1298.7 1708.8 1599.5 1245.7 FALSE FALSE TRUE 1541.973932 1437.252787 1519.595481 1895.000124 1848.111808 1698.184865 1409.011546 1758.241432 1456.436714 1213.336534 1.270854283 1.184545875 1.252410554 1.561809169 1.523165054 1.399599218 1.161270188 1.449096258 1.200356762 1 10.24476404 -11.43119255 0.400720653 0.960490105 1.401980962 0.386167716 0.132523972 0.797746146 0.269838691 0.148299141 0.055416988 3.71E-12 11.43119255 0.441490858 YFGTDAVPDGS(ph)DEEEVAYTG ddPTM_HeLa_Romidepsin_16h_R1 2 YFGTDAVPDGSDEEEVAYTG 20 0 Q9NWZ5;Q9NWZ5-4 Q9NWZ5 UCKL1 Uridine-cytidine kinase-like 1 1 0 YFGTDAVPDGS(0.999)DEEEVAYT(0.001)G;YFGTDAVPDGS(1)DEEEVAYTG ; 134.88 0.00032004 51180000 14693.5 14211.2 14052 11485.2 13933.9 13809.9 11296.5 12345.8 15334.6 14982.7 TRUE FALSE FALSE 14514.40997 14411.26565 14296.56917 12813.17286 13222.80109 12927.49196 12256.02443 12703.00624 13963.03497 14593.44729 0.994584054 0.987516202 0.979656751 0.878008644 0.906077969 0.885842234 0.839830657 0.870459597 0.956801686 1 13.8330331 -9.296380292 2.629573357 0.996708069 0.873869689 0.87117932 0.020450033 0.052389206 0.7152659 0.00262598 0.004361466 5.05E-10 9.296380292 -0.12283838 YFLHDDRDDGVDYWAK ddPTM_HeLa_Romidepsin_16h_R1 2 YFLHDDRDDGVDYWAK 16 1 Q9NYF8-2;Q9NYF8;Q9NYF8-4;H0YF14 Q9NYF8-2 BCLAF1 Bcl-2-associated transcription factor 1 0 0 ; ; 141.59 0.00063154 99383000 7228.3 7873.8 7453.8 6300.4 7581.4 7509.6 6930.7 6987.9 8361.5 7382 FALSE FALSE TRUE 7140.198699 7984.647563 7583.530262 7028.881892 7194.492868 7029.760796 7519.393485 7190.083861 7613.626498 7190.214576 0.993043897 1.110488078 1.054701523 0.977562188 1.000595016 0.977684424 1.045781514 0.999981821 1.058887244 1 12.81181911 -6.595042814 20.6872366 1.00846854 1.010904359 0 0.043389279 0 0 0.005483922 0 2.54E-07 6.595042814 0.002435819 YFQINQDEEEEEDED ddPTM_HeLa_Romidepsin_16h_R1 6 YFQINQDEEEEEDED 15 0 K7ERI7;P35268 K7ERI7 RPL22 60S ribosomal protein L22 0 0 ;;;;; ;;;;; 217.02 5.87E-25 777850300 43523.2 41394.3 37694.3 36867.2 39014.3 40000.7 37788.2 38663.9 45056.6 40811.9 FALSE FALSE TRUE 42992.7225 41977.05004 38350.35348 41129.95913 37023.25469 37444.78437 40997.92876 39782.57894 41026.62485 39751.60095 1.081534365 1.055983886 0.964749911 1.034674281 0.931365122 0.941969216 1.031352896 1.000779289 1.032074781 1 15.27872534 -9.764163487 24.99887872 1.040889257 0.984274256 0.373760049 0.036917168 70.86959518 650364.2834 0.007037078 0.009481983 1.72E-10 9.764163487 -0.056615002 YFQISQDEDES(ph)ESED ddPTM_HeLa_Romidepsin_16h_R1 2 YFQISQDEDESESED 15 0 C9JYQ9;H0Y8C2;Q6P5R6 C9JYQ9 RPL22L1 60S ribosomal protein L22-like 1 1 0 YFQISQDEDES(0.958)ES(0.042)ED;YFQISQDEDES(0.943)ES(0.057)ED ; 146.79 0.00047948 4196500 4389.8 4297.6 3629.5 4054.3 3271.4 3184.9 2766.2 3176.9 4316.9 4997.2 TRUE FALSE FALSE 4336.295429 4358.101726 3692.669925 4523.077242 3104.448251 2981.395169 3001.160959 3268.818589 3930.785652 4867.372024 0.890890486 0.895370583 0.758657836 0.929264749 0.637807884 0.612526668 0.616587543 0.671577717 0.807578634 1 12.24892733 -9.004661124 0.416902404 0.980707642 0.55123849 0.595391723 0.086327041 0.51346941 0.151279929 0.023414295 0.091172556 9.89E-10 9.004661124 -0.429469152 YFQS(ph)PSR ddPTM_HeLa_Romidepsin_16h_R1 1 YFQSPSR 7 0 Q16629-4;Q16629;H7BZZ6 Q16629-4 SRSF7 Serine/arginine-rich splicing factor 7 1 0 YFQS(0.979)PS(0.021)R 131.62 0.024284 4238900 6786.2 7066.5 11897 5970.7 7395.4 9910.4 8534.7 6637.9 7651.4 5132 TRUE FALSE FALSE 6703.487184 7165.982372 12104.06229 6661.060427 7017.985142 9277.157424 9259.637205 6829.957164 6967.039621 4998.6699 1.341054184 1.433577835 2.421456615 1.332566575 1.403970513 1.855925198 1.852420222 1.36635491 1.393778697 1 12.28732854 -10.66332021 1.143470307 1.093615846 1.687537967 0.247099424 0.328117593 0.309489491 0.835518387 0.071977223 0.070503987 2.17E-11 10.66332021 0.593922121 YFY(ph)FY(ph)NT(ph)GLQNQR ddPTM_HeLa_Romidepsin_16h_R1 1 YFYFYNTGLQNQR 13 0 A0A499FJL1;P48147 A0A499FJL1 PREP Prolyl endopeptidase 3 0 YFY(1)FY(1)NT(1)GLQNQR 98 0.010917 26897000 12276 12275 11326 11290 10932 11669 10551 11070 13002 11885 TRUE FALSE FALSE 12126.37539 12447.80777 11523.12428 12595.40292 10374.09925 10923.38856 11447.20168 11390.29298 11839.06856 11576.22599 1.047524073 1.075290668 0.995412865 1.088040518 0.896155557 0.943605332 0.988854372 0.983938375 1.022705376 1 13.49887737 -8.761452746 25 1.029216019 0.955008622 0.554663536 0.036787498 0.245205301 457549.5255 0.005631493 0.0107113 1.73E-09 8.761452746 -0.074207397 YGEHEAS(ph)PDNGQNEFSDIIK ddPTM_HeLa_Romidepsin_16h_R1 1 YGEHEASPDNGQNEFSDIIK 20 0 Q5SYY2;P46939 Q5SYY2 UTRN Utrophin 1 0 Y(0.004)GEHEAS(0.995)PDNGQNEFS(0.001)DIIK 63.376 0.0037977 0 2150.8 1840.4 2173.1 1982.7 1976.4 2309.7 2149.8 1967 2659.7 2267.7 TRUE FALSE FALSE 2124.585222 1866.3092 2210.921894 2211.949103 1875.536933 2162.117624 2332.403958 2023.912042 2421.809771 2208.784827 0.961879671 0.844948397 1.000967531 1.001432587 0.849126139 0.978872001 1.055967032 0.916301134 1.096444407 1 11.10903717 -11.59762032 1.168073973 0.994754444 0.95337904 0.154417129 0.070930246 0.906976285 2.493913747 0.020547867 0.011996549 2.53E-12 11.59762032 -0.041375404 YGEYFPGTGDLR ddPTM_HeLa_Romidepsin_16h_R1 1 YGEYFPGTGDLR 12 0 Q13547;Q5TEE2;Q92769;Q92769-3 Q13547;Q92769 HDAC1;HDAC2 Histone deacetylase 1;Histone deacetylase 2 0 0 147.73 0.015093 10374000 1723.9 1316.6 1584.4 1335 1957.5 2084.9 1851.1 1772.5 1745.6 1606.8 FALSE FALSE TRUE 1702.888444 1335.135129 1611.975817 1489.358981 1857.601471 1951.681619 2008.332388 1823.784491 1589.469164 1565.055104 1.08806932 0.853091451 1.029980231 0.951633573 1.186924004 1.247036998 1.283234298 1.165316471 1.015599489 1 10.61199774 -8.635552094 5.267518995 1.020515165 1.233786231 0.73038139 0.067492969 0.095911664 4.067333707 0.010538132 0.021367636 2.31E-09 8.635552094 0.213271067 YGFIEGHVVIPR ddPTM_HeLa_Romidepsin_16h_R1 1 YGFIEGHVVIPR 12 0 P16070;P16070-17;H0Y2P0;P16070-8;P16070-5;P16070-7;P16070-3;H0YD13;P16070-6;P16070-4;P16070-13;P16070-16;P16070-10;P16070-11;P16070-14;P16070-12;P16070-18;P16070-9;H0YDX6;H0Y5E4;P16070-15;H0YCV9;H0YDW7;H0YD17 P16070 CD44 CD44 antigen 0 0 103.31 0.0025929 333180 238.66 168.61 214.64 216.11 388.44 386.76 49.733 223.97 260.53 301.49 FALSE FALSE TRUE 235.7511201 170.983696 218.3757192 241.097655 368.6164573 362.0472842 53.95731978 230.4502186 237.2275443 293.6572463 0.802810498 0.582256008 0.743641514 0.821017217 1.255260893 1.232890687 0.183742511 0.784759176 0.80783821 1 8.197989428 -12.00463793 0.978964989 0.991772749 0.804376434 0.002927869 0.293027628 1.318375296 2.420517309 0.154640953 0.056646326 9.89E-13 12.00463793 -0.187396314 YGGDEIPFS(ph)PYR ddPTM_HeLa_Romidepsin_16h_R1 2 YGGDEIPFSPYR 12 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 YGGDEIPFS(1)PYR;YGGDEIPFS(1)PYR ; 138.02 0.0023232 60297000 6016.2 5410.9 6007.5 4930.6 6577.1 6822.1 5613.5 6357.6 5627.1 5547.8 TRUE FALSE FALSE 5942.87224 5487.074792 6112.058017 5500.699171 6241.446044 6386.189827 6090.31055 6541.547125 5123.798083 5403.667356 1.099784988 1.015435339 1.131094424 1.01795666 1.155038908 1.181825121 1.127069849 1.210575466 0.948207531 1 12.39972315 -4 0.118381325 0.969179281 1.666304514 0.643319372 0.049716211 48.16065227 0.393358854 0.209936049 5.550245979 1.00E-04 4 0.697125233 YGGISTAS(ph)VDFEQPTR ddPTM_HeLa_Romidepsin_16h_R1 1 YGGISTASVDFEQPTR 16 0 P98175-5;P98175-4;P98175-3;P98175-2;P98175 P98175-5 RBM10 RNA-binding protein 10 1 0 YGGISTAS(0.991)VDFEQPT(0.009)R 157.07 0.00020311 4477200 576.47 470.87 514.18 540.03 610.42 694.1 589.97 544.4 515.85 525.45 TRUE FALSE FALSE 569.4437619 477.4989202 523.1290872 602.4708095 579.2679896 649.7492501 640.0820371 560.1513551 469.711084 511.7987333 1.112632222 0.932981833 1.0221383 1.177163542 1.131827713 1.269540559 1.250651859 1.094475853 0.917765234 1 8.999432766 -9.21932665 5.740341759 1.041473089 1.191219561 0.578086483 0.075453807 0.130256289 11.38219882 0.010854518 0.017966363 6.03E-10 9.21932665 0.149746472 YGGPNHIVGS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 1 YGGPNHIVGSPFK 13 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;A0A0A0MT44 O75369-8 FLNB Filamin-B 1 0 YGGPNHIVGS(1)PFK 80.632 0.016503 13615000 3061 2675.7 6249.5 5827.6 5716.6 7919.5 6505.8 4403.5 3215.3 2109.6 TRUE FALSE FALSE 3023.691355 2713.368575 6358.269926 6501.414532 5424.86057 7413.469509 7058.40249 4530.908325 2927.715515 2054.792288 1.471531391 1.320507475 3.094361393 3.164025177 2.64010168 3.607892415 3.435092944 2.205044447 1.424823099 1 11.00477685 -9.7706398 7.110573552 1.233910597 3.060924785 0.823833736 0.389001815 0.039231504 10.12203017 0.062506773 0.084566167 1.70E-10 9.7706398 1.827014188 YGGPYHIGGS(ph)PFK ddPTM_HeLa_Romidepsin_16h_R1 1 YGGPYHIGGSPFK 13 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 1 0 YGGPYHIGGS(1)PFK 102.73 0.011143 19373000 2250.9 2173.1 2374.2 1832.9 1933.2 2041.4 1973.8 1833.8 2218.8 2515 TRUE FALSE FALSE 2223.465165 2203.692959 2415.521955 2044.828522 1834.54159 1910.961128 2141.454523 1886.85811 2020.344971 2449.659937 0.907662787 0.899591378 0.986064195 0.834739749 0.748896433 0.780092412 0.874184408 0.770253079 0.824745076 1 11.25836577 -9.136084919 4.548449343 0.951986023 0.797581021 0.502125477 0.058240412 0.099550071 3.268906462 0.007553583 0.012768177 7.31E-10 9.136084919 -0.154405003 YGGSVGSQPPPVAPEPGPVPSS(ph)PSQEPPTKR ddPTM_HeLa_Romidepsin_16h_R1 2 YGGSVGSQPPPVAPEPGPVPSSPSQEPPTKR 31 1 A0A087WTZ5;E9PJ81;E9PRQ7;Q04323;Q04323-2;E9PS08 A0A087WTZ5 UBXN1 UBX domain-containing protein 1 1 0 YGGSVGSQPPPVAPEPGPVPS(0.4)S(0.541)PS(0.055)QEPPT(0.004)KR;YGGSVGSQPPPVAPEPGPVPS(0.2)S(0.705)PS(0.082)QEPPT(0.013)KR ; 100.77 6.50E-13 147282000 8648.1 8910 8386.4 8925.3 11503.2 11961 9791.1 10902.1 9521.3 8810.8 TRUE FALSE FALSE 8542.693631 9035.435214 8532.361774 9957.285181 10916.14878 11196.7307 10622.75579 11217.53506 8669.691081 8581.894146 0.995432184 1.052848597 0.99422827 1.160266605 1.271997603 1.304692241 1.237810163 1.307116456 1.010230485 1 13.06708039 -9.041653605 2.260274527 1.001519965 1.281356984 0.96072981 0.025701414 0.036344253 0.368420512 0.003740462 0.007041757 9.09E-10 9.041653605 0.279837018 YGLQDS(ph)DEEEEEHPSK ddPTM_HeLa_Romidepsin_16h_R1 2 YGLQDSDEEEEEHPSK 16 0 P52948-6;P52948-2;P52948-5;P52948;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 0 YGLQDS(1)DEEEEEHPSK;YGLQDS(0.998)DEEEEEHPS(0.002)K ; 135.57 0.0013584 48769200 7724.4 6836.9 6798.4 5814.4 11163.1 12229.9 8861.6 10178.6 10775.7 8383.9 TRUE FALSE FALSE 7630.252042 6933.150058 6916.7233 6486.688286 10593.40535 11448.44886 9614.304083 10473.10173 9811.894404 8166.085069 0.93438312 0.849017614 0.847006031 0.794344932 1.29724406 1.401950722 1.17734557 1.282511956 1.201542027 1 12.99542888 -8.747377748 24.99949345 0.937208869 1.289746779 0.687062129 0.116395641 81.75687666 145350.7892 0.013292116 0.026479482 1.79E-09 8.747377748 0.352537911 YGLQDSDEEEEEHPS(ph)K ddPTM_HeLa_Romidepsin_16h_R1 2 YGLQDSDEEEEEHPSK 16 0 P52948-6;P52948-2;P52948-5;P52948;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 0 YGLQDS(0.004)DEEEEEHPS(0.996)K;YGLQDS(0.351)DEEEEEHPS(0.649)K ; 136.6 0.00051141 74284000 12727.8 11027.9 11898 9921.7 19044.1 20897.6 14914.7 17798.2 18906.2 15955.1 TRUE FALSE FALSE 12572.66868 11183.15107 12105.0797 11068.89364 18072.20851 19562.3108 16181.55425 18313.16284 17215.18212 15540.5842 0.809021625 0.719609438 0.778933375 0.712257242 1.162904063 1.258788637 1.041244913 1.178408907 1.107756433 1 13.92375312 -8.741127293 24.92533934 0.868611094 1.158862513 0.587149406 0.125264569 134.5563088 165115.7243 0.01816535 0.036295422 1.81E-09 8.741127293 0.290251419 YGPADVEDTTGSGATDS(ph)KDDDDIDLFGSDDEEESEEAKR ddPTM_HeLa_Romidepsin_16h_R1 1 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 0 Y(0.001)GPADVEDT(0.05)T(0.05)GS(0.068)GAT(0.196)DS(0.539)KDDDDIDLFGS(0.097)DDEEESEEAKR 46.259 0.0051077 24467000 840.79 768.75 848.99 613.77 818.94 689.4 557.17 656.18 663.62 600.95 TRUE FALSE FALSE 830.5421281 779.5724827 863.7663148 684.7369753 777.1464359 645.3495649 604.4960059 675.165533 604.2641651 585.3372324 1.418912179 1.331834778 1.47567294 1.169816197 1.327690078 1.102526081 1.032731172 1.153464184 1.032335091 1 9.193124239 -8.149754302 7.205892845 1.238994869 1.087407304 0.184776456 0.147277226 0.444149385 25.60199064 0.025965645 0.06679682 7.08E-09 8.149754302 -0.151587565 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAK ddPTM_HeLa_Romidepsin_16h_R1 3 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAK 38 1 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 0 YGPADVEDTTGS(0.001)GAT(0.001)DS(0.004)KDDDDIDLFGS(0.992)DDEEES(0.001)EEAK;YGPADVEDT(0.018)T(0.018)GS(0.068)GAT(0.06)DS(0.06)KDDDDIDLFGS(0.666)DDEEES(0.11)EEAK;YGPADVEDTTGS(0.001)GAT(0.002)DS(0.004)KDDDDIDLFGS(0.993)DDEEESEEAK ;; 85.469 2.35E-09 262956300 21581.2 18361.8 17685.8 16141.5 17159.3 16711.8 16458.8 16418.2 22442.2 20468 TRUE FALSE FALSE 21318.16003 18620.2979 17993.61393 18007.85618 16283.59689 15643.96991 17856.81006 16893.23471 20434.91342 19936.23841 1.06931707 0.933992538 0.902558124 0.903272514 0.816783816 0.784700182 0.895696053 0.847363197 1.025013496 1 14.28310561 -9.788329869 1.512460243 1.032503634 0.845855385 0.80770422 0.038048452 0.122070859 0.564860057 0.007709885 0.011186689 1.63E-10 9.788329869 -0.186648249 YGPADVEDTTGSGATDSKDDDDIDLFGS(ph)DDEEESEEAKR ddPTM_HeLa_Romidepsin_16h_R1 2 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 1 0 YGPADVEDT(0.009)T(0.009)GS(0.033)GAT(0.019)DS(0.07)KDDDDIDLFGS(0.86)DDEEESEEAKR;YGPADVEDT(0.065)T(0.065)GS(0.17)GAT(0.184)DS(0.157)KDDDDIDLFGS(0.35)DDEEES(0.008)EEAKR ; 71.05 5.99E-06 414160000 6309.8 6108.7 5609.3 5599 5160.1 6243 5235.5 5317.8 6660.8 6731.4 TRUE FALSE FALSE 6232.893731 6194.698439 5706.927514 6246.382724 4896.760842 5844.092448 5680.203239 5471.662153 6065.041366 6556.517258 0.95064094 0.944815394 0.870420574 0.952698282 0.746853955 0.891340969 0.866344588 0.834537901 0.925040098 1 12.67871396 -9.830678374 0.585559608 0.989720153 0.839788301 0.444440449 0.051515389 0.363132292 0.264091652 0.012538512 0.020967042 1.48E-10 9.830678374 -0.149931852 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR ddPTM_HeLa_Romidepsin_16h_R1 1 YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR 39 2 P24534;C9JZW3 P24534 EEF1B2 Elongation factor 1-beta 0 0 101.82 6.28E-19 24677000 3937.3 4213.5 4061.1 3325.6 4103.7 4097.8 3718.3 4332 4485.1 4306.7 FALSE FALSE TRUE 3889.310673 4272.817764 4131.781742 3710.121519 3894.272876 3835.963805 4034.132309 4457.339585 4083.941423 4194.811313 0.92717178 1.018595938 0.984974397 0.884454924 0.928354719 0.914454434 0.961695773 1.062584048 0.973569755 1 12.0343902 YGPLS(ph)EPGSAR ddPTM_HeLa_Romidepsin_16h_R1 2 YGPLSEPGSAR 11 0 Q9H1Z4 Q9H1Z4 WDR13 WD repeat-containing protein 13 1 0 YGPLS(0.998)EPGS(0.002)AR;YGPLS(0.999)EPGS(0.001)AR ; 126.66 0.0070768 74808000 5373.7 5395.5 4477.7 2940.4 4722.1 4469.2 4040.2 4971.3 5617.3 5542.4 TRUE FALSE FALSE 5308.203277 5471.457991 4555.63249 3280.382883 4481.113616 4183.632544 4383.374487 5115.136722 5114.874619 5398.407649 0.983290559 1.013531831 0.843884491 0.607657498 0.830080629 0.774975292 0.811975451 0.947526948 0.947478396 1 12.39831821 -9.665394146 4.773373899 0.993388772 0.790372121 0.562566337 0.079773429 0.1047896 4.087680187 0.012072231 0.017134977 2.16E-10 9.665394146 -0.203016651 YGQCWVFAAVACT(ph)VLR ddPTM_HeLa_Romidepsin_16h_R1 1 YGQCWVFAAVACTVLR 16 0 P21980-2;P21980 P21980-2 TGM2 Protein-glutamine gamma-glutamyltransferase 2 1 0 YGQCWVFAAVACT(1)VLR 88.78 0.027776 532600000 2803.4 3005.4 2940.9 2604.5 2823.5 2667.4 2676.4 2421.9 3003.9 2938 TRUE FALSE FALSE 2769.231083 3047.7101 2992.085131 2905.644545 2679.406259 2496.961749 2903.733349 2491.973855 2735.223661 2861.670336 0.967697448 1.0650109 1.045572962 1.015366623 0.9363085 0.872553948 1.014698763 0.870810947 0.955813682 1 11.48264177 -8.689781042 6.119305764 0.998020224 0.925405987 0.413719284 0.04853421 0.182801497 11.86902291 0.006898741 0.013852206 2.04E-09 8.689781042 -0.072614237 YGS(ph)FEEAEASYPILNR ddPTM_HeLa_Romidepsin_16h_R1 2 YGSFEEAEASYPILNR 16 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 YGS(0.98)FEEAEAS(0.02)Y(0.001)PILNR;YGS(1)FEEAEASYPILNR ; 202.92 1.64E-18 12627300 2433.46 2338.1 2197.46 1775.67 2112.08 2708.01 2555.77 2770.03 2862.32 2401.2 TRUE FALSE FALSE 2403.800054 2371.015833 2235.70587 1980.98132 2004.292676 2534.976901 2772.85704 2850.176448 2606.30693 2338.816478 1.027784812 1.013767372 0.955913339 0.847001609 0.856968768 1.083871661 1.185581283 1.218640485 1.114370005 1 11.19156295 -7.909078275 3.551724546 0.986765745 1.202944831 0.587847949 0.075932915 0.123183344 3.019508048 0.010533017 0.035865859 1.23E-08 7.909078275 0.216179086 YGS(ph)IVDDER ddPTM_HeLa_Romidepsin_16h_R1 2 YGSIVDDER 9 0 Q13576 Q13576 IQGAP2 Ras GTPase-activating-like protein IQGAP2 1 0 YGS(1)IVDDER;Y(0.002)GS(0.998)IVDDER ; 129.88 0.0083368 10027200 5723.6 5556.3 5251.4 4365.5 4520.4 5429.4 4144.5 5296.9 6003.3 5834.3 TRUE FALSE FALSE 5653.838562 5634.521737 5342.798414 4870.25965 4289.70712 5082.478863 4496.533727 5450.157444 5466.349812 5682.724045 0.994916965 0.991517746 0.940182626 0.857029061 0.754868103 0.894373688 0.791263783 0.959074803 0.961924206 1 12.47236694 -9.431619974 2.537775155 0.997015779 0.844322073 0.596012886 0.052789967 0.119574059 1.510129805 0.007465114 0.011830343 3.70E-10 9.431619974 -0.152693706 YGVIILDEAHER ddPTM_HeLa_Romidepsin_16h_R1 2 YGVIILDEAHER 12 0 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 0 ; ; 187.31 3.30E-10 21113400 7938.5 6942.7 7685.1 7472.4 7351.4 7101.6 6868.4 7604.5 8805.5 7682 FALSE FALSE TRUE 7841.742509 7040.439513 7818.855942 8336.394047 6976.230626 6647.830679 7451.801725 7824.52421 8017.914026 7482.420533 1.048022157 0.940930743 1.044963446 1.114130649 0.932349444 0.888459911 0.995907901 1.04572099 1.07156688 1 12.86928934 -8.688094607 24.9999984 1.023972452 0.962263033 0.249768031 0.057725687 50.94788739 17364.4738 0.008237204 0.016474407 2.05E-09 8.688094607 -0.061709419 YGVYEDENYEVGS(ph)DDEEIPFK ddPTM_HeLa_Romidepsin_16h_R1 2 YGVYEDENYEVGSDDEEIPFK 21 0 O15541 O15541 RNF113A RING finger protein 113A 1 0 YGVYEDENY(0.001)EVGS(0.999)DDEEIPFK;YGVYEDENY(0.008)EVGS(0.992)DDEEIPFK ; 103.99 0.00015678 77276000 11487 11140.6 10884 9593.3 12772.9 12406.2 10942 11696 11821.8 10779 TRUE FALSE FALSE 11346.99203 11297.43766 11073.43145 10702.52248 12121.05125 11613.48386 11871.41321 12034.40531 10764.4286 10498.96003 1.080772953 1.076053022 1.054716984 1.019388821 1.154500181 1.106155641 1.130722774 1.146247369 1.025285226 1 13.35795881 -4.000000031 0.042984023 0.764229694 1.634313114 0.63433642 0.031371668 277.8675587 0.916761789 4.918909506 17.16106879 1.00E-04 4.000000031 0.87008342 YHEEFEK ddPTM_HeLa_Romidepsin_16h_R1 2 YHEEFEK 7 0 C9J9W2;Q14847;Q14847-2;Q14847-3 C9J9W2 LASP1 LIM and SH3 domain protein 1 0 0 ; ; 120.62 0.012734 56663000 16884.8 16185.3 15836.3 12747.5 17554.1 17900.6 16524 10769.8 18268.7 17004.3 FALSE FALSE TRUE 16679.00156 16413.15708 16111.92416 14221.42593 16658.24877 16756.80943 17927.54815 11081.40717 16634.70172 16562.52583 1.007032486 0.990981523 0.972793903 0.858650792 1.005779489 1.011730312 1.082416313 0.66906505 1.004357782 1 14.01563508 -7.25194351 24.93341065 0.995559629 0.66906487 0.77444293 0.052366065 436.1864739 1145276.038 0.007173188 0.12406118 5.60E-08 7.25194351 -0.326494759 YHGHS(ph)MSDPGVSYR ddPTM_HeLa_Romidepsin_16h_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 0 YHGHS(0.757)MS(0.243)DPGVSYR 74.428 0.01441 23211000 2312.7 2679.6 2073.8 1467.7 2649.5 2910.5 2037.2 1834.9 3016.9 2564.6 TRUE FALSE FALSE 2284.511923 2717.323479 2109.893619 1637.40238 2514.286128 2724.528443 2210.239717 1887.989937 2747.060908 2497.971322 0.914546898 1.08781212 0.844642851 0.655492865 1.006531222 1.090696446 0.884813888 0.755809292 1.099716752 1 11.2865412 -16.52287869 0.103384969 1.31574914 0.839484656 0.158629765 0.13145727 250.5121889 1.922961397 16.98439061 1.03559018 3.00E-17 16.52287869 -0.476264484 YHPGYFGK ddPTM_HeLa_Romidepsin_16h_R1 1 YHPGYFGK 8 0 E9PLL6;P46776 E9PLL6 RPL27A 60S ribosomal protein L27a 0 0 98.418 0.015228 24595000 7027.9 6777.5 6849 5091.8 7526.3 7949.3 6246.2 6941.6 7113.7 6220.9 FALSE FALSE TRUE 6942.241252 6872.913823 6968.203972 5680.537874 7142.204827 7441.365385 6776.752072 7142.444244 6477.432855 6059.280121 1.145720467 1.134278938 1.150005254 0.937493854 1.178721677 1.228093971 1.118408777 1.17876119 1.069010299 1 12.56493069 -16.52287875 0.232542272 0.224100865 1.152024956 0.196720563 0.075151187 41.8219109 0.54079589 14.80043828 0.051696522 3.00E-17 16.52287875 0.927924091 YHSDFNR ddPTM_HeLa_Romidepsin_16h_R1 2 YHSDFNR 7 0 Q15424-2;Q15424;Q15424-4;Q15424-3;K7EII0 Q15424-2 SAFB Scaffold attachment factor B1 0 0 ; ; 134.06 0.0064667 1597500 187.469 0 252.31 123.47 59.911 285.38 283.95 206.36 239.4 247.91 FALSE FALSE TRUE 185.1840557 0 256.7013497 137.7461823 56.85351811 267.145139 308.0687059 212.330701 217.9874644 241.4692625 0.766905294 0 1.063080854 0.570450172 0.235448262 1.106331863 1.275809197 0.879328072 0.902754505 1 7.915695744 -8.094562271 24.92528273 0.766417104 1.106316412 0.210109915 0.338989435 69.27098682 18252.81035 0.049774359 0.12690028 8.04E-09 8.094562271 0.339899307 YHTINGHNAEVR ddPTM_HeLa_Romidepsin_16h_R1 1 YHTINGHNAEVR 12 0 P22626;P22626-2;A0A087WUI2 P22626 HNRNPA2B1 Heterogeneous nuclear ribonucleoproteins A2/B1 0 0 108.68 0.0043162 2449400 550.43 516.08 708.96 412.83 815.17 693.89 604.49 511.53 769.77 556.11 FALSE FALSE TRUE 543.7211474 523.3453878 721.2991514 460.563347 773.5688331 649.5526684 655.8353655 526.3303135 700.9198433 541.662182 1.003801198 0.9661841 1.331640228 0.850277834 1.4281389 1.199184086 1.210783007 0.971694778 1.294016578 1 9.081249557 -9.798618578 24.99850229 0.999174302 1.166524778 0.017505966 0.18020651 177.4767689 119330.8784 0.022669209 0.0297936 1.59E-10 9.798618578 0.167350477 YHVLVNLGK ddPTM_HeLa_Romidepsin_16h_R1 2 YHVLVNLGK 9 0 O75643;A0A494C1A5;O75643-2 O75643 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa helicase 0 0 ; ; 87.181 0.007983 2623900 3912.1 3355 5516.9 3690.8 4472.8 4572.2 3513.2 3374.1 3336.5 2544.4 FALSE FALSE TRUE 3864.41782 3402.231778 5612.91933 4117.547662 4244.536326 4280.051176 3811.61112 3471.72426 3038.075084 2478.296121 1.559304309 1.372810839 2.26482997 1.661442967 1.712683278 1.727013628 1.537996645 1.400851266 1.225872509 1 11.27513286 -11.70742353 0.639591156 0.993176203 1.684987973 0.44577157 0.240370436 0.457322471 0.360525184 0.160427729 0.056086929 1.96E-12 11.70742353 0.69181177 YHYLGGR ddPTM_HeLa_Romidepsin_16h_R1 2 YHYLGGR 7 0 Q8NCW5-2;Q8NCW5 Q8NCW5-2 APOA1BP NAD(P)H-hydrate epimerase 0 0 ; ; 92.692 0.019763 6742800 3143 2899.8 3255.8 3596.4 3869.7 4253 4178.6 1986.04 3222.5 2235.9 FALSE FALSE TRUE 3104.691907 2940.623461 3312.465833 4012.23269 3672.214769 3981.247026 4533.53018 2043.502934 2934.271529 2177.810996 1.42560209 1.350265687 1.521007029 1.842323644 1.686195348 1.82809575 2.081691289 0.938328872 1.347349028 1 11.08866304 -11.01754617 0.451972066 0.992620978 1.710456421 0.236040401 0.304665006 0.656804129 0.327903146 0.192345621 0.111802634 9.60E-12 11.01754617 0.717835444 YIASVQGSTPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 YIASVQGSTPSPR 13 0 P49792;F8WBP7 P49792 RANBP2 E3 SUMO-protein ligase RanBP2 1 0 YIASVQGST(0.002)PS(0.997)PR;YIASVQGSTPS(1)PR ; 154.23 0.00076909 20805300 2417.3 2406.23 2411.5 2481.94 2544.9 2731.6 2809.53 3017.4 2755.78 2518.39 TRUE FALSE FALSE 2387.837018 2440.104969 2453.471146 2768.913581 2415.024257 2557.059576 3048.171408 3104.703708 2509.296135 2452.961865 0.973450526 0.994758624 1.000207619 1.12880417 0.984533959 1.042437558 1.242649326 1.265695873 1.022965816 1 11.26030909 -7.788216879 3.433310212 0.999685814 1.264574819 0.828666575 0.042695454 0.061525414 1.482204412 0.006232653 0.024123885 1.63E-08 7.788216879 0.264889005 YIDLEPDTPLS(ph)PEELKEK ddPTM_HeLa_Romidepsin_16h_R1 2 YIDLEPDTPLSPEELKEK 18 1 Q5VTI5;A0A1B0GUN5;Q9Y2H5 Q5VTI5 PLEKHA6 Pleckstrin homology domain-containing family A member 6 1 0 YIDLEPDTPLS(1)PEELKEK;YIDLEPDT(0.12)PLS(0.88)PEELKEK ; 99.93 0.00075892 25648000 17216.4 16994.9 16129.3 16354.1 17653.9 17047.9 14483.8 15851.7 17819.6 16283.4 TRUE FALSE FALSE 17006.55989 17234.15465 16410.0237 18245.03799 16752.95561 15958.59421 15714.05361 16310.34393 16225.77035 15860.35492 1.072268558 1.086618473 1.034656777 1.150354963 1.056278733 1.006194016 0.99077566 1.028371938 1.023039549 1 13.95313744 -8.255571188 23.29267213 1.049157521 1.006680041 0.227079182 0.040325777 284.961122 1131083.775 0.006684295 0.016502572 5.55E-09 8.255571188 -0.04247748 YIDQEELNK ddPTM_HeLa_Romidepsin_16h_R1 1 YIDQEELNK 9 0 P08238;Q58FF8;P07900-2;P07900;Q14568 P08238;Q58FF8;P07900-2 HSP90AB1;HSP90AB2P;HSP90AA1;HSP90AA2P Heat shock protein HSP 90-beta;Putative heat shock protein HSP 90-beta 2;Heat shock protein HSP 90-alpha;Heat shock protein HSP 90-alpha A2 0 0 163.32 0.013432 1805700 1917.1 1475.4 1694.3 1622.7 1589.4 1745.3 1331.2 1301.3 1547.4 1812.9 FALSE FALSE TRUE 1893.733648 1496.17072 1723.788581 1810.324209 1508.286987 1633.780963 1444.272095 1338.951062 1408.996668 1765.800597 1.072450452 0.847304459 0.97620795 1.025214406 0.854166088 0.925235254 0.817913471 0.758268552 0.797936455 1 10.78610672 -6.718940893 0.367904445 1.031622982 0.420142828 0.101508784 0.096398297 3.990314831 0.277790575 0.019758909 1.170101572 1.91E-07 6.718940893 -0.611480154 YIEDDTREK ddPTM_HeLa_Romidepsin_16h_R1 1 YIEDDTREK 9 1 A0A5F9ZHW7 A0A5F9ZHW7 0 0 104.75 0.0025138 0 1912.8 1961.6 1740.1 1723.8 2134.2 2375.6 1892 2132.7 1920.5 2297.5 FALSE FALSE TRUE 1889.486058 1989.215456 1770.385711 1923.113867 2025.28381 2223.806827 2052.706433 2194.40631 1748.72567 2237.810619 0.844345827 0.888911439 0.79112401 0.859372929 0.905029136 0.993742191 0.917283355 0.980604119 0.781444889 1 11.12787223 -8.291782367 21.50145945 0.905210474 0.959217213 0.167940706 0.068408916 225.5414758 159821.5443 0.010958056 0.024509979 5.11E-09 8.291782367 0.054006739 YIEIDS(ph)DEEPR ddPTM_HeLa_Romidepsin_16h_R1 3 YIEIDSDEEPR 11 0 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 0 YIEIDS(1)DEEPR;YIEIDS(1)DEEPR;YIEIDS(1)DEEPR ;; 171.49 3.19E-05 40573000 7038.7 7837.4 7316.51 3347.27 6466.45 6732.3 5557.01 6298.5 6387.02 6359.82 TRUE FALSE FALSE 6952.909617 7947.735123 7443.850787 3734.297107 6136.442927 6302.127758 6029.022291 6480.73716 5815.748935 6194.59096 1.12241626 1.283012095 1.201669462 0.602831911 0.990613096 1.01735979 0.973272058 1.046192913 0.938843093 1 12.59679331 YIEIDS(ph)DEEPRGELLSLR ddPTM_HeLa_Romidepsin_16h_R1 8 YIEIDSDEEPRGELLSLR 18 1 E7EW05;Q9NVU7-2;Q9NVU7 E7EW05 SDAD1 Protein SDA1 homolog 1 0 YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;YIEIDS(1)DEEPRGELLSLR;Y(0.001)IEIDS(0.999)DEEPRGELLSLR;Y(0.002)IEIDS(0.997)DEEPRGELLS(0.001)LR;Y(0.003)IEIDS(0.996)DEEPRGELLSLR;Y(0.011)IEIDS(0.988)DEEPRGELLS(0.001)LR ;;;;;;; 193.64 6.58E-14 132811900 9523.51 9162.83 8461.31 8545 9351.42 9586.71 8692.57 9000.43 10096.5 9493.47 TRUE FALSE FALSE 9407.433797 9291.824561 8608.575551 9533.013105 8874.182142 8974.150171 9430.916679 9260.843242 9193.443753 9246.828281 1.017368714 1.004866131 0.930976037 1.030949512 0.959700113 0.970511174 1.019908275 1.001515651 0.99422672 1 13.17474288 -9.970442156 24.99953264 1.008355373 0.985733072 0.089998027 0.027784863 306.8021259 259487.2253 0.004225924 0.005553932 1.07E-10 9.970442156 -0.022622301 YIES(ph)PDVEK ddPTM_HeLa_Romidepsin_16h_R1 2 YIESPDVEK 9 0 Q15545 Q15545 TAF7 Transcription initiation factor TFIID subunit 7 1 0 Y(0.014)IES(0.986)PDVEK;Y(0.169)IES(0.831)PDVEK ; 120.06 0.013439 12829600 5280.8 4540.6 5154.8 4604.7 4646.9 5677.4 4600.3 5275.7 4957.2 5346.1 TRUE FALSE FALSE 5216.435578 4604.522686 5244.517132 5137.11708 4409.751353 5314.632463 4991.049367 5428.344056 4513.815616 5207.207551 1.001772164 0.884259489 1.007164988 0.98653972 0.846855308 1.020630042 0.958488656 1.042467388 0.866839966 1 12.3462942 YIFTANK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 YIFTANKK 8 1 F8VRB8;H0YHC1;A0A3B3IS46;A0A3B3IRX3;Q71F56 F8VRB8 MED13L Mediator of RNA polymerase II transcription subunit 13-like 0 1 ; YIFTANK(1)K;YIFTANK(1)K 107.01 0.003679 1331470 597.2 570.54 1222.84 1055.33 1962.94 2524.4 1596.23 676.63 491.92 305.73 FALSE TRUE FALSE 589.9210967 578.5720771 1244.123017 1177.35222 1862.763847 2363.098987 1731.813736 696.2072215 447.9214432 297.7870905 1.981016355 1.942905168 4.177894398 3.953671121 6.255354602 7.935532004 5.81561052 2.337936209 1.50416676 1 8.218137402 -9.565141974 1.216872227 1.41111811 5.67824963 0.617414142 1.372624034 0.202711589 0.600972105 0.248504425 0.41545094 2.72E-10 9.565141974 4.267131519 YIHLENLLAR ddPTM_HeLa_Romidepsin_16h_R1 1 YIHLENLLAR 10 0 Q2TAY7 Q2TAY7 SMU1 "WD40 repeat-containing protein SMU1;WD40 repeat-containing protein SMU1, N-terminally processed" 0 0 106.88 0.0021266 514510 65.775 101.66 113.63 109.25 175.87 140.96 182.44 0 115.95 76.507 FALSE FALSE TRUE 64.973309 103.0911721 115.6076825 121.881999 166.8946976 131.9531109 197.936449 0 105.5791416 74.51933711 0.871898644 1.383415046 1.551378299 1.63557546 2.239615972 1.770723091 2.656175655 0 1.416801943 1 6.219542936 -9.934863988 1.8620425 0.937558296 1.741239066 0.098044919 0.662802056 0.333664816 2.319879629 0.102868124 0.13839959 1.16E-10 9.934863988 0.80368077 YIHPDDELVLEDELQR ddPTM_HeLa_Romidepsin_16h_R1 2 YIHPDDELVLEDELQR 16 0 C9IZD2;C9J8Z7;C9JLE1;F8W8R3;A0A087WWF6;P49005 C9IZD2 POLD2 DNA polymerase delta subunit 2 0 0 ; ; 204.17 6.17E-19 4184600 3480.7 3271 2990.5 2884.7 3632.8 3134.9 2590.3 3501.8 3493.2 3174.4 FALSE FALSE TRUE 3438.27589 3317.049224 3042.548398 3218.242587 3447.40466 2934.590007 2810.320017 3603.119058 3180.759443 3091.92863 1.112016576 1.072809117 0.98402931 1.040852805 1.114969028 0.949113113 0.908921373 1.165330604 1.028729904 1 11.5942913 -8.252884763 24.95576402 1.052922508 0.997901671 0.060405623 0.073719502 1160.202838 3384566.334 0.010589449 0.026496597 5.59E-09 8.252884763 -0.055020836 YINENLIVNTDELGR ddPTM_HeLa_Romidepsin_16h_R1 1 YINENLIVNTDELGR 15 0 P17987;F5H7Y1;F5H136;E7ERF2 P17987 TCP1 T-complex protein 1 subunit alpha 0 0 186.51 4.66E-08 4311400 651.09 779.06 675.96 796.29 711.62 891.68 616.84 937.87 711.8 760.9 FALSE FALSE TRUE 643.1542646 790.0276271 687.7248002 888.3607965 675.303376 834.7045258 669.2343742 965.0057887 648.1348253 741.1317083 0.867800227 1.065974669 0.927938709 1.198654418 0.911178632 1.126256665 0.902989802 1.302070574 0.874520437 1 9.53358614 -9.700023983 1.648065119 0.940634553 1.067472243 0.207668595 0.127002568 0.458087115 2.531572177 0.020165277 0.03016223 2.00E-10 9.700023983 0.126837689 YIQHTYR ddPTM_HeLa_Romidepsin_16h_R1 1 YIQHTYR 7 0 J3KRY1;J3KTF8;J3QQX2;P52565-2;P52565 J3KRY1 ARHGDIA Rho GDP-dissociation inhibitor 1 0 0 124.83 0.010722 5635100 1164.3 1068.5 3769.5 2552.4 3397.9 3438.8 2911.4 430.39 1374.8 645.22 FALSE FALSE TRUE 1150.109064 1083.542371 3835.106566 2847.520497 3224.492484 3219.071778 3158.694243 442.8426556 1251.834445 628.4570914 1.830051852 1.724131028 6.102415931 4.53097043 5.1308077 5.122182282 5.026109637 0.704650583 1.991917128 1 9.295670436 -9.853854635 7.389876596 1.415070648 4.525259526 0.497961788 1.37024271 0.124735124 8.638782499 0.211094068 0.278152891 1.40E-10 9.853854635 3.110188878 YIQPWESEFIDSQR ddPTM_HeLa_Romidepsin_16h_R1 2 YIQPWESEFIDSQR 14 0 Q6P2Q9 Q6P2Q9 PRPF8 Pre-mRNA-processing-splicing factor 8 0 0 ; ; 176.99 4.62E-06 3289400 1901.72 1808.75 1810.42 1527.02 1900.33 1867.29 1589.46 2316.8 2263.31 2019.65 FALSE FALSE TRUE 1878.541105 1834.21363 1841.929601 1703.581237 1803.349069 1747.976195 1724.468693 2383.832953 2060.873885 1967.179202 0.954941524 0.932408002 0.936330355 0.866002058 0.916718247 0.888569884 0.876620031 1.211802641 1.047628952 1 10.94191267 -11.38765283 0.867204489 0.99462298 0.938273562 0.06976245 0.094842955 1.218896894 1.917533905 0.033111629 0.019153642 4.10E-12 11.38765283 -0.056349419 YIQSSDSIS(ph)SDEEELR ddPTM_HeLa_Romidepsin_16h_R1 1 YIQSSDSISSDEEELR 16 0 Q96NL0-2;Q96NL0-4;Q96NL0-5;Q96NL0 Q96NL0-2 RUNDC3B RUN domain-containing protein 3B 1 0 YIQSSDSIS(0.5)S(0.5)DEEELR 97.904 0.0067263 29952000 283.18 334.01 299.28 321.42 1328.8 1428.5 1087 1785.7 423.84 475.98 TRUE FALSE FALSE 279.7284932 338.7122015 304.4888429 358.5840927 1260.986378 1337.22346 1179.329753 1837.366412 385.9306889 463.613971 0.603365107 0.730591015 0.656772362 0.773454027 2.719905906 2.884346771 2.543775267 3.963138575 0.83243973 1 8.856780232 -8.722091925 4.33282679 0.781638823 3.028266791 0.908052541 0.353621172 0.043901201 1.791530838 0.051077364 0.102521306 1.90E-09 8.722091925 2.246627968 up YIS(ph)PDQLADLYK ddPTM_HeLa_Romidepsin_16h_R1 1 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 1 0 YIS(1)PDQLADLYK 108.17 0.01159 6536800 2671.2 2370.8 2285.9 2351.1 2821.6 2668.2 2575.7 2200.2 2602 2415.1 TRUE FALSE FALSE 2638.642387 2404.176185 2325.685131 2622.945244 2677.603223 2497.710631 2794.479894 2263.859316 2369.270603 2352.355354 1.12170229 1.022029338 0.988662332 1.115029343 1.138264769 1.061791377 1.187949724 0.962379817 1.007190771 1 11.1998903 KDPSGASNPSADS(ph)PLHR ddPTM_HeLa_Romidepsin_16h_R1 1 KDPSGASNPSADSPLHR 17 1 P55317-2;P55317 P55317-2 FOXA1 Hepatocyte nuclear factor 3-alpha 1 0 KDPSGAS(0.002)NPS(0.196)ADS(0.801)PLHR 81.884 0.0050045 3540100 998.99 868.92 1109.2 917.06 1124 940.92 875.98 478.99 1300.2 1119.1 TRUE FALSE FALSE 986.8139256 881.1526786 1128.505161 1023.094792 1066.638086 880.7982487 950.3857193 492.8488199 1183.906856 1090.025621 0.905312597 0.808377952 1.035301501 0.938597013 0.97854405 0.808052794 0.87189301 0.452144253 1.086127549 1 10.09014633 -7.001466735 1.382988168 0.945903438 3.76E-19 0.759477386 0.083158549 0.749917419 0.792263543 0.010411065 1.169082089 9.97E-08 7.001466735 -0.945903438 down YISENESPRPS(ph)QK ddPTM_HeLa_Romidepsin_16h_R1 1 YISENESPRPSQK 13 1 O94782 O94782 USP1 Ubiquitin carboxyl-terminal hydrolase 1 1 0 YISENES(0.055)PRPS(0.945)QK 120.6 0.00071005 0 2371.7 2230.5 2130.1 2015.5 1571.6 1510.5 1445.9 1394 2521 2388.2 TRUE FALSE FALSE 2342.792808 2261.901038 2167.173497 2248.541593 1491.395388 1413.983925 1568.71471 1434.333191 2295.515446 2326.15422 1.007152831 0.972377935 0.931655124 0.966634789 0.641142094 0.607863362 0.674381215 0.616611392 0.986828572 1 11.18373103 -8.773915038 5.111161866 0.993692023 0.633485957 0.974650303 0.027011453 0.020271953 1.4592035 0.00444737 0.008531537 1.68E-09 8.773915038 -0.360206066 YISPDQLADLYK ddPTM_HeLa_Romidepsin_16h_R1 2 YISPDQLADLYK 12 0 P06733;A0A2R8Y6G6;P06733-2 P06733 ENO1 Alpha-enolase 0 0 ; ; 188.06 6.68E-09 69993490 3597.74 3019.7 4035.19 2596.6 5081.65 4383.65 3994.69 3182.1 3483.68 2621.2 FALSE FALSE TRUE 3553.889361 3062.211416 4105.420789 2896.831109 4822.314438 4103.548913 4333.998869 3274.169043 3172.090936 2553.100846 1.391989418 1.199408719 1.608013563 1.134632466 1.888806878 1.607280386 1.697543156 1.282428404 1.242446392 1 11.31803481 -11.90348166 0.243946687 0.761504838 1.636530121 0.312166118 0.222970716 2.907770585 0.305669643 0.819393968 0.221504828 1.25E-12 11.90348166 0.875025283 YITDWQNVFR ddPTM_HeLa_Romidepsin_16h_R1 1 YITDWQNVFR 10 0 A0A024QZ42;O75340-2;O75340 A0A024QZ42 PDCD6 Programmed cell death protein 6 0 0 195.57 2.32E-07 19838000 2271.2 1626.3 2205.1 1882.7 2300.5 2311.8 2321.2 2012.8 2182.7 1477.4 FALSE FALSE TRUE 2243.517741 1649.195094 2243.478841 2100.386632 2183.096901 2164.083441 2518.36267 2071.037192 1987.473845 1439.016935 1.559062778 1.146056766 1.559035746 1.459598272 1.517075197 1.503862386 1.750057702 1.439202793 1.381133048 1 10.49086786 -14.41027527 0.27863758 5.61E-16 1.558854416 0.204209158 0.182304028 6.678312534 0.250736408 3.957009324 0.071704147 3.89E-15 14.41027527 1.558854416 YK(ac)AEDEVQR ddPTM_HeLa_Romidepsin_16h_R1 2 YKAEDEVQR 9 1 A0A0G2JIW1;P0DMV9;P0DMV8;P0DMV8-2;V9GZ37;Q53FA3;P34931 A0A0G2JIW1 HSPA1B;HSPA1A;HSPA1L Heat shock 70 kDa protein 1B;Heat shock 70 kDa protein 1A;Heat shock 70 kDa protein 1-like 0 1 ; YK(1)AEDEVQR;YK(1)AEDEVQR 169.41 0.0040201 17654500 5241.4 5604.9 5869.9 3461.6 19463.5 17691 16920.1 15537.8 14901.7 12535.2 FALSE TRUE FALSE 5177.515801 5683.805929 5972.063147 3861.846479 18470.20497 16560.6022 18357.29287 15987.36173 13568.85463 12209.5337 0.424055163 0.46552195 0.489131141 0.316297622 1.512769073 1.356366476 1.50352121 1.309416242 1.111332748 1 13.57572048 -8.749850261 24.99964773 0.654177043 1.42186494 0.714952762 0.242981683 104.7641876 225992.3053 0.03964371 0.07875472 1.78E-09 8.749850261 0.767687897 YK(ac)PESEELTAER ddPTM_HeLa_Romidepsin_16h_R1 1 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 1 YK(1)PESEELTAER 181.31 1.17E-05 1252000 259.94 157.36 209.22 99.806 355.98 404.6 350.98 303.36 381.11 364.28 FALSE TRUE FALSE 256.7717513 159.5753182 212.8613863 111.3460393 337.8130123 378.7473658 380.7922324 312.137243 347.0225671 354.8159531 0.723675892 0.449741103 0.599920563 0.313813509 0.952079548 1.067447398 1.073210573 0.879715921 0.978035413 1 8.470927067 -6.231076537 14.74881168 0.820158815 0.918242301 0 0.255893245 0 0 0.036649812 0 5.87E-07 6.231076537 0.098083486 YKDDDDDQLFYTR ddPTM_HeLa_Romidepsin_16h_R1 1 YKDDDDDQLFYTR 13 1 H7C2V1;O60568 H7C2V1 PLOD3 "Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3" 0 0 125.03 0.004263 27822000 2724.6 2521.9 2624.1 2491 2245.7 2042.4 1939.2 2208.5 2633 2546.4 FALSE FALSE TRUE 2691.391527 2557.403374 2669.77136 2779.021141 2131.093549 1911.897232 2103.9156 2272.399463 2397.497886 2480.244161 1.085131686 1.031109523 1.076414734 1.120462729 0.859227322 0.770850411 0.848269551 0.916199904 0.966637851 1 11.27626643 -8.707785537 8.124122941 1.048354265 0.842024413 0.773517382 0.05244473 0.087414536 11.71506981 0.007497471 0.014988361 1.96E-09 8.707785537 -0.206329852 YKDLDEDELLGNLS(ph)ETELK ddPTM_HeLa_Romidepsin_16h_R1 3 YKDLDEDELLGNLSETELK 19 1 Q9NYL9;H0YNU8 Q9NYL9 TMOD3 Tropomodulin-3 1 0 YKDLDEDELLGNLS(0.627)ET(0.373)ELK;YKDLDEDELLGNLS(0.631)ET(0.369)ELK;YKDLDEDELLGNLS(0.829)ET(0.171)ELK ;; 114.66 0.00030374 220603700 13247.7 15314.3 13574.9 10496.92 12001.8 11970.3 10655.9 11706.6 13572.4 14597.9 TRUE FALSE FALSE 13086.23194 15529.89512 13811.16544 11710.62328 11389.30336 11205.43646 11561.01188 12045.312 12358.45055 14218.64445 0.92035721 1.092220511 0.971341923 0.823610388 0.801011897 0.788080502 0.81308819 0.84714911 0.869172205 1 13.79549631 -9.249774615 5.628552138 0.974036721 0.811478982 0.666236963 0.055220975 0.070441315 8.314159877 0.007662463 0.012428484 5.63E-10 9.249774615 -0.162557739 YKDNPFSLGES(ph)FGSR ddPTM_HeLa_Romidepsin_16h_R1 2 YKDNPFSLGESFGSR 15 1 Q8N6H7;E9PQP3;A0A0D9SF70;G5E9L0;Q8N6H7-2;E9PMU9;H0YDN9;Q8N6H7-3 Q8N6H7 ARFGAP2 ADP-ribosylation factor GTPase-activating protein 2 1 0 YKDNPFS(0.029)LGES(0.95)FGS(0.021)R;YKDNPFSLGES(0.954)FGS(0.046)R ; 79.462 0.012021 32057000 7449.2 7799.5 6837.3 7239.7 5614.5 4424.2 3392.5 4260.2 6181.7 6484.7 TRUE FALSE FALSE 7358.406285 7909.301566 6956.300338 8076.788178 5327.971114 4141.507898 3680.658865 4383.462166 5628.79327 6316.226559 1.165000371 1.252219421 1.101338002 1.2787363 0.843537049 0.655693373 0.582730659 0.694000148 0.891163928 1 12.62484721 -8.525439928 3.890649426 1.108624212 0.646131396 0.787950848 0.110204014 0.06859588 2.328279175 0.015142012 0.033258018 2.98E-09 8.525439928 -0.462492817 YKLDEDEDEDDADLSK ddPTM_HeLa_Romidepsin_16h_R1 2 YKLDEDEDEDDADLSK 16 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 0 0 ; ; 122.96 0.0030953 29367000 6228.3 5351.8 5817 3746.3 6058.8 5353.1 5861.4 5739 5237 6277.7 FALSE FALSE TRUE 6152.387084 5427.142781 5918.242445 4179.464833 5749.596828 5011.054186 6359.26717 5905.04891 4768.589604 6114.604449 1.006179081 0.887570541 0.967886393 0.683521701 0.940305604 0.819522216 1.040012845 0.965728684 0.77986886 1 12.57804346 -10.26417951 23.78450855 1.002917903 0.898649718 0 0.115518852 134.9822591 1171652.679 0.015027172 0.017604487 5.44E-11 10.26417951 -0.104268184 YKLDEDEDEDDADLSKYNLDAS(ph)EEEDSNK ddPTM_HeLa_Romidepsin_16h_R1 1 YKLDEDEDEDDADLSKYNLDASEEEDSNK 29 2 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 Y(0.002)KLDEDEDEDDADLS(0.176)KY(0.055)NLDAS(0.761)EEEDS(0.007)NK 48.831 0.0099009 6053300 748.6 772.95 808.91 656.75 1017.6 711.44 846.31 929.48 1043.6 854.13 TRUE FALSE FALSE 739.4757753 783.8316104 822.9887392 732.6865251 965.6680748 665.9812801 918.1955503 956.3730373 950.2578023 831.9395795 0.888857549 0.942173722 0.989240997 0.8806968 1.160743038 0.800516403 1.103680571 1.149570306 1.142219731 1 9.700334945 -7.571527578 13.25539956 0.95164609 1.138109427 0.221014721 0.107623838 0.73716882 200.1962419 0.011499423 0.043052695 2.68E-08 7.571527578 0.186463337 YKPESEELTAER ddPTM_HeLa_Romidepsin_16h_R1 2 YKPESEELTAER 12 1 P07237;H7BZ94;H0Y3Z3;I3L398 P07237 P4HB Protein disulfide-isomerase 0 0 ; ; 118.73 0.0090092 66263000 7052 6175.6 5848.6 5030.9 6785.5 8210.5 6966.8 8106.4 6850.4 6912.4 FALSE FALSE TRUE 6966.047512 6262.540259 5950.39243 5612.596329 6439.210615 7685.875548 7558.559818 8340.945894 6237.683067 6732.814852 1.034641181 0.93015186 0.883789702 0.833618101 0.956392052 1.141554568 1.122644835 1.238849735 0.926459914 1 12.71699408 -8.184886052 4.581017209 0.982396754 1.16881305 0.666489475 0.069837654 0.13985606 5.461864545 0.011569057 0.030578222 6.53E-09 8.184886052 0.186416296 YKPLNTT(ph)PNATK ddPTM_HeLa_Romidepsin_16h_R1 1 YKPLNTTPNATK 12 1 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 1 0 Y(0.003)KPLNT(0.001)T(0.754)PNAT(0.242)K 78.69 0.028174 26199000 2720.2 2614.4 2634 2673.4 3727.1 4000.7 3182.9 3362.2 2876.8 2592.6 TRUE FALSE FALSE 2687.045156 2651.205592 2679.843665 2982.511087 3536.892179 3745.068182 3453.255447 3459.479952 2619.491803 2525.243878 1.064073525 1.049881009 1.061221725 1.181078435 1.400614099 1.483052078 1.367493839 1.369958752 1.037322306 1 11.30220701 -8.948808882 2.275637062 1.034219665 1.412478288 0.959187482 0.03524537 0.045590999 0.476275514 0.006339357 0.012428344 1.13E-09 8.948808882 0.378258624 YKPLNTTPNATK(ac)EIK ddPTM_HeLa_Romidepsin_16h_R1 1 YKPLNTTPNATKEIK 15 2 Q96QC0 Q96QC0 PPP1R10 Serine/threonine-protein phosphatase 1 regulatory subunit 10 0 1 YKPLNTTPNATK(1)EIK 151.44 4.53E-07 1949800 859.62 804.99 537.73 514.11 664.15 549.82 857.01 418.84 1129.4 665.99 FALSE TRUE FALSE 849.1426208 816.3226703 547.0889651 573.5538172 630.2559472 514.6882765 929.804408 430.9584746 1028.383635 648.6874838 1.309016502 1.258422107 0.843378327 0.884175865 0.971586416 0.793430256 1.433362646 0.66435454 1.585329856 1 9.341379793 -9.762185541 24.99999972 1.158439084 0.947882696 0.283890552 0.244025629 25.6292456 858712.2033 0.033428024 0.045414246 1.73E-10 9.762185541 -0.210556388 YLAEFATGNDRK ddPTM_HeLa_Romidepsin_16h_R1 1 YLAEFATGNDRK 12 1 P62258;P62258-2;K7EM20 P62258 YWHAE 14-3-3 protein epsilon 0 0 87.641 0.020784 45202000 1445.2 1462 1292.8 1480.9 1578.2 1469.7 1382.4 1194.9 1533.6 1500.1 FALSE FALSE TRUE 1427.585347 1482.582074 1315.300642 1652.128626 1497.658565 1375.790913 1499.821021 1229.472546 1396.430975 1461.127186 0.977043861 1.014683793 0.900195859 1.130721981 1.02500219 0.941595589 1.026482182 0.841454843 0.955721712 1 10.51286605 -7.254126577 24.45992966 0.995250562 0.841454743 0.386706639 0.058669886 484.9899821 1622144.463 0.007282875 0.09909247 5.57E-08 7.254126577 -0.153795818 YLAEKYEWDVAEAR ddPTM_HeLa_Romidepsin_16h_R1 2 YLAEKYEWDVAEAR 14 1 P13639 P13639 EEF2 Elongation factor 2 0 0 ; ; 120.57 0.0047013 50901000 6017.2 5773.3 5218.8 10771.8 5856.5 5844.7 4936 5917.1 6527.5 5632.8 FALSE FALSE TRUE 5943.860052 5854.576669 5309.631025 12017.2862 5557.620951 5471.242533 5355.263717 6088.301953 5943.664052 5486.459044 1.083369074 1.067095666 0.967770101 2.190353761 1.012970462 0.997226533 0.976087432 1.109696054 1.083333349 1 12.42165962 YLAEVAAGDDK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 3 YLAEVAAGDDKK 12 1 P63104;E7EX29;B0AZS6;P63104-2;B7Z2E6;H0YB80 P63104 YWHAZ 14-3-3 protein zeta/delta 0 1 ;; YLAEVAAGDDK(1)K;YLAEVAAGDDK(1)K;YLAEVAAGDDK(1)K 201.09 1.01E-14 6150980 2678.35 2378.18 2536.01 2034.52 5706.92 4337.15 4926.56 3615.09 6178.47 4892.35 FALSE TRUE FALSE 2645.70524 2411.66008 2580.14819 2269.760775 5415.674577 4060.020113 5345.021883 3719.686925 5625.852169 4765.246042 0.555208528 0.506093507 0.541451201 0.476315547 1.136494219 0.852006397 1.121667556 0.780586541 1.180600565 1 12.21833499 -8.749634338 24.99983875 0.721101633 0.974709827 0.228959581 0.235664609 279.7921751 592519.4722 0.034719069 0.068994443 1.78E-09 8.749634338 0.253608194 YLAEVAAGDDKK ddPTM_HeLa_Romidepsin_16h_R1 3 YLAEVAAGDDKK 12 1 P63104;E7EX29;B0AZS6;P63104-2;B7Z2E6;H0YB80 P63104 YWHAZ 14-3-3 protein zeta/delta 0 0 ;; ;; 110.64 0.0036961 55662970 5779.48 6015.14 4943.86 4439.82 6309.12 5797.37 5528.37 5282.46 6707.3 5869.92 FALSE FALSE TRUE 5709.037475 6099.821299 5029.905809 4953.172878 5987.142064 5426.936767 5997.94961 5435.299646 6107.382289 5717.418632 0.998534101 1.066883797 0.879751184 0.866330279 1.047175736 0.949193529 1.04906602 0.950656231 1.068206245 1 12.48114821 -9.777256989 24.99999564 1.004356617 0.960831088 0.212626736 0.062468743 412.939642 652655.6791 0.009519638 0.012533775 1.67E-10 9.777256989 -0.043525528 YLAEVASGEK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 YLAEVASGEKK 11 1 Q04917;A2IDB2 Q04917 YWHAH 14-3-3 protein eta 0 1 YLAEVASGEK(1)K 119.27 0.0042019 355110 195.19 248.76 117.76 161.24 395.47 308.22 413.89 187.07 388.61 309.1 FALSE TRUE FALSE 192.8109492 252.2620498 119.8095634 179.8833275 375.2876902 288.5257367 449.0458063 192.4825753 353.8517483 301.0695374 0.640419987 0.83788633 0.397946482 0.597480997 1.246514986 0.958335869 1.491501964 0.639329296 1.175315681 1 8.233952932 -8.757566151 24.99994886 0.776319458 1.104063158 0.218482963 0.285351539 106.9580213 690356.0996 0.038753612 0.075229683 1.75E-09 8.757566151 0.3277437 YLAEVATGDDK(ac)KR ddPTM_HeLa_Romidepsin_16h_R1 1 YLAEVATGDDKKR 13 2 P31947-2;P31947 P31947-2 SFN 14-3-3 protein sigma 0 1 YLAEVATGDDK(0.991)K(0.009)R 141.58 8.90E-05 3390000 612.19 673.86 843.19 391.26 1395.4 1120.3 891.39 1039.3 1565.3 1027.2 FALSE TRUE FALSE 604.7283928 683.3466188 857.8653682 436.4993221 1324.187531 1048.716446 967.1046444 1069.370506 1425.295648 1000.513196 0.604418208 0.682996108 0.857425341 0.436275427 1.323508312 1.048178525 0.966608585 1.068821991 1.424564567 1 9.96652448 -8.748987664 24.99999356 0.778125808 1.088295592 0.17815148 0.264878671 196.1514936 393821.8084 0.02914178 0.057959388 1.78E-09 8.748987664 0.310169784 YLAEVATGEK(ac)R ddPTM_HeLa_Romidepsin_16h_R1 2 YLAEVATGEKR 11 1 P61981 P61981 YWHAG "14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed" 0 1 ; YLAEVATGEK(1)R;YLAEVATGEK(1)R 177.78 2.24E-05 4181100 603.69 615.19 636.22 486.67 1910.49 1487.94 1336.99 1361.35 1384.97 1142.85 FALSE TRUE FALSE 596.3319941 623.850661 647.2931422 542.9410753 1812.990566 1392.865436 1450.553897 1400.738514 1261.094814 1113.158592 0.535711621 0.560432867 0.581492293 0.487748178 1.628690268 1.25127313 1.303097247 1.258345867 1.132897705 1 10.12044343 -8.76397416 24.99999993 0.722369875 1.348470722 0.674592108 0.219025712 32.26622563 318239.7945 0.034151101 0.064046894 1.72E-09 8.76397416 0.626100847 YLAIAPPIIK ddPTM_HeLa_Romidepsin_16h_R1 1 YLAIAPPIIK 10 0 Q16531;F5GY55 Q16531 DDB1 DNA damage-binding protein 1 0 0 120.65 0.00014605 0 283.91 249.77 148.45 155.9 126.64 174.84 290.18 187.63 194.64 229.26 FALSE FALSE TRUE 280.4495957 253.2862686 151.03371 173.9258915 120.1770882 163.6682883 314.827882 193.058778 177.2309109 223.3037922 1.255910583 1.134267655 0.676359808 0.778875674 0.538177552 0.732940031 1.409863572 0.864556648 0.793676226 1 7.802863941 -9.782609886 24.65179876 1.125229895 0.839189859 0.121382219 0.245179601 217.5909685 253370.7207 0.039079695 0.051390747 1.65E-10 9.782609886 -0.286040036 YLDEDTIYHLQPSGR ddPTM_HeLa_Romidepsin_16h_R1 1 YLDEDTIYHLQPSGR 15 0 P31153;P31153-2 P31153 MAT2A S-adenosylmethionine synthase isoform type-2 0 0 158.31 0.00014721 23057000 2488.3 2330.8 1782.9 2142.3 2650.6 2685.5 1849.6 2368.5 2662.8 2239.2 FALSE FALSE TRUE 2457.971643 2363.613064 1813.930627 2390.002806 2515.329991 2513.905217 2006.704978 2437.028811 2424.632499 2181.025261 1.126979905 1.083716501 0.831687124 1.095816196 1.153278706 1.152625447 0.920074157 1.117377618 1.111693909 1 11.09079076 YLEES(ph)DEDDLF ddPTM_HeLa_Romidepsin_16h_R1 4 YLEESDEDDLF 11 0 P11388;P11388-2;P11388-3;P11388-4;J3QR57 P11388 TOP2A DNA topoisomerase 2-alpha 1 0 YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF;YLEES(1)DEDDLF ;;; 166.66 0.00053584 42987800 18477.4 15955.4 16291 13396.3 13449.6 12791.5 11811.4 12731.1 19355.8 18094.1 TRUE FALSE FALSE 18252.19034 16180.02054 16574.53802 14945.24324 12763.21672 11974.16443 12814.66002 13099.45429 17624.56877 17624.01267 1.035643283 0.918066779 0.940452003 0.848004567 0.724194709 0.679423276 0.727113641 0.743273086 1.000031553 1 14.10525482 -9.202621543 1.139790803 1.014275749 0.707605773 0.937188744 0.031933999 0.075285399 0.193059373 0.00581186 0.012149027 6.27E-10 9.202621543 -0.306669977 YLGS(ph)PITTVPK ddPTM_HeLa_Romidepsin_16h_R1 2 YLGSPITTVPK 11 0 A0A3B3IT42;D6RJC2;P30307-4;P30307-3;P30307-2;P30307 A0A3B3IT42 CDC25C M-phase inducer phosphatase 3 1 0 YLGS(0.786)PIT(0.214)TVPK;YLGS(0.846)PIT(0.131)T(0.023)VPK ; 140.39 0.0030894 97400000 6614.1 6714.3 7787.9 6327.9 9214.5 9992.5 8686 9491.7 7318.9 6265.8 TRUE FALSE FALSE 6533.484805 6808.824092 7923.445133 7059.561572 8744.249681 9354.011499 9423.788623 9766.327364 6664.279253 6103.013613 1.070534202 1.115649501 1.298284034 1.156733709 1.432775713 1.532687307 1.544120531 1.600246695 1.091965327 1 12.57530609 -8.717814914 0.520010803 1.013772083 1.688774853 0.914358211 0.062731285 0.212823874 0.08920193 0.013466025 0.068195184 1.92E-09 8.717814914 0.67500277 YLHDESGLNR ddPTM_HeLa_Romidepsin_16h_R1 1 YLHDESGLNR 10 0 B5MCX3;Q15019;Q15019-3;Q15019-2;C9J2Q4;C9IY94;C9J938;H7C310;C9JB25 B5MCX3 Sep-02 Septin-2 0 0 85.807 0.022138 1610700 1294.2 887.39 1119 1207 1485.4 1413.5 1045.6 1256.3 1276.9 1063.3 FALSE FALSE TRUE 1278.425793 899.8826997 1138.475726 1346.559019 1409.594495 1323.181912 1134.413238 1292.649058 1162.690866 1035.675313 1.234388594 0.868884957 1.099259306 1.300174874 1.361039003 1.277603024 1.095336757 1.248121919 1.122640321 1 10.01635607 -9.275686085 20.9683684 1.090734316 1.254489168 0.426890724 0.108867541 94.88647946 139654.3906 0.019782754 0.03036282 5.30E-10 9.275686085 0.163754852 YLHDESGLNRR ddPTM_HeLa_Romidepsin_16h_R1 1 YLHDESGLNRR 11 1 B5MCX3;Q15019;Q15019-3;Q15019-2;C9J2Q4;C9IY94;C9J938;H7C310;C9JB25 B5MCX3 Sep-02 Septin-2 0 0 72.325 0.015486 1809700 707.14 447.01 549.89 603.05 835.91 755.15 520.92 627.44 643.06 664.77 FALSE FALSE TRUE 698.5211057 453.3030185 559.4606048 672.7774784 793.2503935 706.8983521 565.1669318 645.5939865 585.543103 647.4991796 1.078798441 0.700082769 0.864032917 1.039039893 1.225098685 1.09173629 0.872845788 0.997057613 0.904314818 1 9.338734555 YLKSNS(ph)RS(ph)QQNRHSFMESS(ph)QSK ddPTM_HeLa_Romidepsin_16h_R1 1 YLKSNSRSQQNRHSFMESSQSK 22 3 A0A1B0GTX4;A0A096LNR9;A0A1B0GUM4;A0A669KBC2;O76039;O76039-1 A0A1B0GTX4 CDKL5 Cyclin-dependent kinase-like 5 3 0 Y(0.469)LKS(0.488)NS(0.331)RS(0.723)QQNRHS(0.046)FMES(0.41)S(0.473)QS(0.06)K 47.397 0.0041574 0 386.35 360.2 443.85 341.67 289.93 507.04 315.68 455.49 484.59 555.53 TRUE FALSE FALSE 381.6410176 365.2709051 451.5750231 381.175493 275.1337902 474.6417804 342.4938513 468.6688845 441.2470567 541.0972505 0.705309475 0.675055925 0.834554274 0.70444914 0.508473828 0.87718387 0.632961729 0.866145382 0.815467194 1 9.0797441 -12.20033845 0.739913238 1.018764077 0.71910116 0.208256158 0.120662907 0.504884379 0.451318531 0.092156292 0.020586843 6.30E-13 12.20033845 -0.299662917 YLLGDAPVS(ph)PSSQK ddPTM_HeLa_Romidepsin_16h_R1 3 YLLGDAPVSPSSQK 14 0 Q9NYB0;A0A590UJT3;H3BMI8 Q9NYB0 TERF2IP Telomeric repeat-binding factor 2-interacting protein 1 1 0 Y(0.338)LLGDAPVS(0.656)PS(0.005)S(0.001)QK;YLLGDAPVS(0.555)PS(0.394)S(0.051)QK;Y(0.005)LLGDAPVS(0.981)PS(0.014)SQK ;; 241.3 7.13E-44 602642000 16413.4 15463.9 15172.9 14731.2 19907.7 20335.2 20410.2 21514 17733.8 15461.9 TRUE FALSE FALSE 16213.34717 15681.60119 15436.97796 16434.49066 18891.73578 19035.84635 22143.84188 22136.47365 16147.64451 15060.19761 1.076569351 1.041261317 1.025018287 1.091253321 1.254414867 1.263983836 1.470355334 1.469866082 1.072206682 1 13.87845308 -8.174671343 0.878317914 1.033017998 1.529383869 0.946215636 0.039265365 0.13226267 0.153036631 0.006771989 0.046600292 6.69E-09 8.174671343 0.496365871 YLLSQS(ph)SPAPLTAAEEELR ddPTM_HeLa_Romidepsin_16h_R1 4 YLLSQSSPAPLTAAEEELR 19 0 F8VS81;Q12792-4;Q12792;Q12792-3 F8VS81 TWF1 Twinfilin-1 1 0 YLLSQS(0.5)S(0.5)PAPLT(0.001)AAEEELR;YLLS(0.008)QS(0.496)S(0.496)PAPLTAAEEELR;YLLSQS(0.5)S(0.5)PAPLT(0.001)AAEEELR;YLLSQS(0.499)S(0.499)PAPLT(0.001)AAEEELR ;;; 272.32 8.11E-91 79152500 8844.21 9112.3 8928.1 8056.41 8808.28 9212.64 7812.11 10023.88 9704.04 8412.99 TRUE FALSE FALSE 8736.413367 9240.583199 9083.489835 8987.930031 8358.760603 8623.982036 8475.670428 10313.90515 8836.086358 8194.419307 1.066141851 1.12766785 1.108497075 1.096835504 1.020055271 1.052421375 1.034322276 1.258649914 1.078305372 1 13.000426 -16.52287875 0.1205779 0.68087695 1.138120129 0.064876167 0.067091015 94.46442455 0.821788814 7.247682767 0.289650481 3.00E-17 16.52287875 0.457243178 YLPHSAGR ddPTM_HeLa_Romidepsin_16h_R1 2 YLPHSAGR 8 0 M0R0F0;M0R0R2;P46782 M0R0F0 RPS5 "40S ribosomal protein S5;40S ribosomal protein S5, N-terminally processed" 0 0 ; ; 134.81 0.0043799 17348600 7601.5 7443 10801.9 10232.6 10285.6 11866.3 11955.6 3769.5 8775.1 5884.8 FALSE FALSE TRUE 7508.849994 7547.782749 10989.90254 11415.74136 9760.687451 11108.08173 12971.10837 3878.564535 7990.233078 5731.912048 1.310007888 1.316800168 1.917318767 1.991611396 1.702867624 1.937936527 2.262963608 0.676661558 1.393990873 1 12.48480076 -10.0928159 1.598327475 1.126866699 1.786827628 0.228628741 0.413224729 0.29141455 1.43689945 0.070502301 0.089449717 8.08E-11 10.0928159 0.659960929 YLQLAEELIRPER ddPTM_HeLa_Romidepsin_16h_R1 1 YLQLAEELIRPER 13 1 Q14566 Q14566 MCM6 DNA replication licensing factor MCM6 0 0 163.71 0.00029088 4667600 1683.2 1435.3 1622 1781.3 1550.1 1504.1 1485.1 1470 1850.9 1539.4 FALSE FALSE TRUE 1662.684511 1455.506191 1650.23023 1987.262287 1470.992613 1407.992864 1611.244357 1512.532131 1685.350868 1499.406166 1.10889534 0.970721759 1.100589198 1.325366223 0.981050129 0.939033663 1.074588323 1.008754109 1.12401223 1 10.55017552 YLREDTVQS(ph)VKPWLT(ph)EIMNNY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 YLREDTVQSVKPWLTEIMNNYK 22 2 H7C0X5;Q9H3G5 H7C0X5 CPVL Probable serine carboxypeptidase CPVL 3 0 Y(0.013)LREDT(0.175)VQS(0.819)VKPWLT(0.994)EIMNNY(0.999)K 42.64 0.020365 28728000 1344.7 1461 1299.3 1856.1 1344.5 1170.3 905.06 1155.1 1545.6 1211.4 TRUE FALSE FALSE 1328.310279 1481.567996 1321.913771 2070.711015 1275.885148 1095.521607 981.9357738 1188.520996 1407.357665 1179.927653 1.125755698 1.255643083 1.120334597 1.75494744 1.081324897 0.928465066 0.832199984 1.00728294 1.192749116 1 10.20448269 -8.296854346 5.170815895 1.135916929 0.912429342 0.23903846 0.209000068 0.268721021 19.26372296 0.032321466 0.075856897 5.05E-09 8.296854346 -0.223487587 YLS(ph)FTPPEK ddPTM_HeLa_Romidepsin_16h_R1 2 YLSFTPPEK 9 0 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 YLS(0.965)FT(0.035)PPEK;YLS(0.954)FT(0.046)PPEK ; 140.78 0.0063722 467580000 12413.8 11322.5 14734 7692 11864.3 11187.1 9135.2 10516.1 12569.6 12563.4 TRUE FALSE FALSE 12262.49583 11481.89845 14990.43909 8581.385232 11258.8205 10472.28041 9911.14366 10820.36676 11445.34349 12237.00106 1.002083417 0.938293492 1.225009218 0.701265383 0.920063702 0.855788143 0.809932402 0.88423354 0.935306244 1 13.57896242 -9.244712731 24.99897436 1.01058417 0.838868555 0.500155459 0.092608845 509.8416287 761989.1641 0.012199005 0.020191995 5.69E-10 9.244712731 -0.171715616 YLS(ph)FTPPEKDGFPSGTPALNAK ddPTM_HeLa_Romidepsin_16h_R1 1 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 Y(0.012)LS(0.721)FT(0.242)PPEKDGFPS(0.015)GT(0.011)PALNAK 46.66 0.027455 555130000 883.94 866.58 845.53 965.25 976.76 702.3 607.32 810.04 1018.6 888.06 TRUE FALSE FALSE 873.1661993 878.779736 860.246095 1076.856747 926.9122924 657.4252966 658.9057456 833.4772294 927.4938649 864.9880732 1.009454611 1.015944339 0.994517869 1.24493826 1.07158968 0.760039724 0.76175125 0.963570777 1.072262027 1 9.75653643 -8.264359049 24.99145797 1.027049115 0.821783646 0.561455389 0.090136769 152.1196613 1302103.19 0.012983455 0.030272571 5.44E-09 8.264359049 -0.205265469 YLSFT(ph)PPEKDGFPSGTPALNAK ddPTM_HeLa_Romidepsin_16h_R1 1 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 Y(0.006)LS(0.278)FT(0.71)PPEKDGFPS(0.004)GT(0.002)PALNAK 54.875 0.012995 607250000 1620.2 1572.3 1610 1806 1558.8 1674.7 1174.2 1434.1 1878.7 1459.1 TRUE FALSE FALSE 1600.452379 1594.434881 1638.021375 2014.818217 1479.248619 1567.692075 1273.936519 1475.593421 1710.664367 1421.192372 1.126133528 1.121899408 1.15256837 1.417695632 1.040850379 1.103082247 0.8963857 1.038278456 1.203682486 1 10.47288613 -7.781222151 24.44795731 1.09842333 0.967332099 0.190436435 0.118471622 230.7357817 285148.973 0.017438233 0.052425404 1.65E-08 7.781222151 -0.131091231 YLSFTPPEKDGFPSGT(ph)PALNAK ddPTM_HeLa_Romidepsin_16h_R1 1 YLSFTPPEKDGFPSGTPALNAK 22 1 Q13177 Q13177 PAK2 Serine/threonine-protein kinase PAK 2;PAK-2p27;PAK-2p34 1 0 YLS(0.001)FT(0.169)PPEKDGFPS(0.348)GT(0.481)PALNAK 74.519 0.0015975 33585000 2449.6 2597.3 1884.1 2716.3 1935.4 1900.7 1750.1 2056.5 2025.9 2341.4 TRUE FALSE FALSE 2419.743333 2633.864858 1916.89197 3030.371387 1836.629316 1779.251404 1898.75345 2116.001583 1844.69843 2280.57009 1.061025637 1.15491511 0.840531926 1.32877801 0.805337807 0.780178347 0.832578423 0.927838873 0.808876008 1 11.15517879 YLSPGWGS(ph)ASEEEPSR ddPTM_HeLa_Romidepsin_16h_R1 1 YLSPGWGSASEEEPSR 16 0 H0YMC6;Q9BRS8-2;Q9BRS8 H0YMC6 LARP6 La-related protein 6 1 0 YLSPGWGS(0.997)AS(0.003)EEEPSR 202.32 1.80E-18 11617000 1198 1101 1283.1 1775.5 1968.4 1901.2 2023.7 2085.6 1349.5 1262.6 TRUE FALSE FALSE 1183.398315 1116.499907 1305.431817 1980.791664 1867.945203 1779.719456 2195.593027 2145.943545 1228.79734 1229.79747 0.962270898 0.907872991 1.061501466 1.610664937 1.518904737 1.447164675 1.785328951 1.744956871 0.999186752 1 10.26420503 -9.295062254 3.941411697 0.97643584 1.619649344 0.918284545 0.095009866 0.046420233 1.597132604 0.015362885 0.02455691 5.07E-10 9.295062254 0.643213505 YLTAEAFGFK ddPTM_HeLa_Romidepsin_16h_R1 1 YLTAEAFGFK 10 0 Q16658 Q16658 FSCN1 Fascin 0 0 114.89 0.030311 357480 0 0 70.351 138.11 69.921 56.133 0 139.79 131.62 65.593 FALSE FALSE TRUE 0 0 71.57542964 154.078928 66.35267046 52.54628246 0 143.8346031 119.8475776 63.8888844 0 0 1.120311151 2.411670347 1.038563611 0.822463609 0 2.25132438 1.875875259 1 5.997493043 -9.622080609 7.877139378 0.476150885 1.246958831 0.069993871 0.826559955 0.301844222 21.31162652 0.118108237 0.167152529 2.39E-10 9.622080609 0.770807945 YLTNQK(ac)NSNSK ddPTM_HeLa_Romidepsin_16h_R1 2 YLTNQKNSNSK 11 1 B1AK63;Q9HAF1-2;Q9HAF1;Q9HAF1-4;Q9HAF1-3 B1AK63 MEAF6 Chromatin modification-related protein MEAF6 0 1 ; YLTNQK(1)NSNSK;YLTNQK(1)NSNSK 259.35 1.85E-64 22248000 8170.2 7503.1 7277.8 6066.4 2689.9 2038.22 2090.5 1788.12 7892 6937.4 FALSE TRUE FALSE 8070.61846 7608.728839 7404.467056 6767.825711 2552.624366 1907.98432 2268.067018 1839.856431 7186.119754 6757.165348 1.194379306 1.126023776 1.09579486 1.001577638 0.377765562 0.282364604 0.335653621 0.272282286 1.063481413 1 12.72220244 -8.769567552 3.694194609 1.096164528 0.302249538 0.983641961 0.048423159 0.029077277 0.853138568 0.011145535 0.022072343 1.70E-09 8.769567552 -0.79391499 down ILHRDMK(ac)PQNILLAK ddPTM_HeLa_Romidepsin_16h_R1 2 ILHRDMKPQNILLAK 15 2 C9JDA4;Q9NRP7-2;Q9NRP7 C9JDA4 STK36 Serine/threonine-protein kinase 36 0 1 ; ILHRDMK(1)PQNILLAK;ILHRDMK(1)PQNILLAK 56.648 0.018027 7725500 382.92 277.62 387.63 1998.25 5505.9 9642.8 11305.5 17335.9 502.99 761 FALSE TRUE FALSE 378.2528238 281.5283416 394.3765375 2229.297067 5224.913378 9026.656201 12265.78889 17837.48691 458.0013146 741.2291103 0.510304869 0.379812851 0.532057541 3.007568154 7.048985671 12.17795696 16.54790498 24.06474148 0.617894398 1 9.533775731 -7.747538194 0.775855203 0.579390642 29.17289239 0.991836542 0.715971118 0.094265149 0.060691947 0.130914912 2.008474303 1.79E-08 7.747538194 28.59350175 up GQQQVFK(ac)GLNDK ddPTM_HeLa_Romidepsin_16h_R1 2 GQQQVFKGLNDK 12 1 H0YFD6;P40939;A0A2R8YG21;A0A2R8Y4F5 H0YFD6 HADHA "Trifunctional enzyme subunit alpha, mitochondrial;Long-chain enoyl-CoA hydratase;Long chain 3-hydroxyacyl-CoA dehydrogenase" 0 1 ; GQQQVFK(1)GLNDK;GQQQVFK(1)GLNDK 246.08 6.18E-52 2299400 1102.48 1156.18 1099.57 879.04 1409.17 1245.21 1417.03 1395.23 806.18 735.16 FALSE TRUE FALSE 1089.04255 1172.456732 1118.707555 980.6787408 1337.254797 1165.6451 1537.392493 1435.598779 734.0732417 716.0604372 1.520880771 1.637371193 1.562308845 1.369547443 1.867516661 1.627858543 2.147014991 2.004856998 1.025155425 1 9.483937549 -4.000000028 0.061302702 2.80E-11 5.088983986 0.822010502 0.15108466 87.53189768 0.404435398 6.804846819 39.80044423 1.00E-04 4.000000028 5.088983986 YLVDGTKPNAGSEEIS(ph)SEDDELVEEK ddPTM_HeLa_Romidepsin_16h_R1 1 YLVDGTKPNAGSEEISSEDDELVEEK 26 1 Q9NY61 Q9NY61 AATF Protein AATF 1 0 YLVDGT(0.015)KPNAGS(0.067)EEIS(0.459)S(0.459)EDDELVEEK 54.311 0.0038173 0 754.02 783.35 715.09 466.76 642.15 817.85 698.76 722.92 758.03 834.08 TRUE FALSE FALSE 744.8297142 794.3780219 727.5358415 520.7289874 609.3786893 765.5920245 758.112657 743.8365496 690.2298983 812.4104814 0.916814506 0.977803758 0.895527394 0.640967835 0.750087183 0.942370934 0.933164545 0.915592015 0.849607328 1 9.666065043 -9.5243419 19.73051143 0.959747895 0.83543334 0.184451804 0.094039203 3.415620881 46051.0851 0.015129911 0.021563737 2.99E-10 9.5243419 -0.124314555 YMAENPTAGVVQEEEEDNLEYDS(ph)DGNPIAPTKK ddPTM_HeLa_Romidepsin_16h_R1 1 YMAENPTAGVVQEEEEDNLEYDSDGNPIAPTKK 33 1 J3KRE3;A0A0A0MSJ0;Q86XP3-2;Q86XP3 J3KRE3 DDX42 ATP-dependent RNA helicase DDX42 1 0 Y(0.01)MAENPT(0.059)AGVVQEEEEDNLEY(0.448)DS(0.483)DGNPIAPTKK 51.236 0.0027042 5754100 1842.9 2026.1 2174.2 1750.1 1797.1 1734.7 1703.7 1654 2165.5 2053.8 TRUE FALSE FALSE 1820.438026 2054.623489 2212.041039 1952.454796 1705.387281 1623.858268 1848.412235 1701.85588 1971.812256 2000.44198 0.910017908 1.027084769 1.105776154 0.976011709 0.852505245 0.811749746 0.924001923 0.850739935 0.985688301 1 10.96610307 -8.763944049 24.85184418 0.975829198 0.860910146 0.585841388 0.055764979 45.62700766 452728.007 0.009664971 0.018132788 1.72E-09 8.763944049 -0.114919052 YMIGVTYGGDDIPLSPYR ddPTM_HeLa_Romidepsin_16h_R1 1 YMIGVTYGGDDIPLSPYR 18 0 O75369-8;O75369-2;O75369-9;O75369;E7EN95;O75369-7;O75369-6;O75369-3;O75369-5;O75369-4 O75369-8 FLNB Filamin-B 0 0 101.39 0.001223 0 571.21 464.38 574.61 514.19 586.2 415.24 613.28 553.12 605.67 484.06 FALSE FALSE TRUE 564.2478728 470.9175538 584.610846 573.6430671 556.2840266 388.7075041 665.3719879 569.1236545 551.4973583 471.4840514 1.196748588 0.99879848 1.239937691 1.216675443 1.179857569 0.824434046 1.411229046 1.207089938 1.169705225 1 8.88106516 -12.50818872 0.729496082 0.973354133 1.161790071 0 0.155933929 1.63388635 1.181820604 0.201784122 0.028426497 3.10E-13 12.50818872 0.188435938 YMLTHQELAS(ph)DGEIETK ddPTM_HeLa_Romidepsin_16h_R1 5 YMLTHQELASDGEIETK 17 0 Q02241;A0A2U3TZL8;H7BYN4;Q02241-3;Q02241-2 Q02241;Q02241-3 KIF23 Kinesin-like protein KIF23;Kinesin-like protein 1 0 YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLTHQELAS(1)DGEIETK;YMLT(0.001)HQELAS(0.985)DGEIET(0.014)K;YMLTHQELAS(0.999)DGEIET(0.001)K ;;;; 132.14 0.00058697 213826000 23828.8 23389.8 21490.9 16760.8 16077.7 15859.4 12948.4 16320 24600.6 25538.2 TRUE FALSE FALSE 23538.36542 23719.08222 21864.9401 18698.76256 15257.19497 14846.03552 14048.23677 16792.19345 22400.26072 24874.71388 0.946276831 0.953541911 0.879002677 0.751717694 0.613361627 0.596832414 0.564759733 0.675070818 0.900523352 1 14.60239231 -9.181167098 1.406712115 0.974493556 0.600370659 0.940738907 0.038436055 0.04992431 0.194033678 0.005326324 0.010463763 6.59E-10 9.181167098 -0.374122897 YNAPTSHVTPS(ph)VK ddPTM_HeLa_Romidepsin_16h_R1 1 YNAPTSHVTPSVK 13 0 O60271;A0A087X2D8;O60271-3;O60271-9;O60271-4;O60271-2;O60271-5 O60271 SPAG9 C-Jun-amino-terminal kinase-interacting protein 4 1 0 YNAPT(0.002)S(0.007)HVT(0.355)PS(0.635)VK 101.2 0.012036 6320100 1444 1169.1 1238.8 1089.4 1944.3 2691.7 1789.4 2326.4 1365.3 1187.1 TRUE FALSE FALSE 1426.399973 1185.55862 1260.360794 1215.361554 1845.075116 2519.709057 1941.391591 2393.710714 1243.184149 1156.258971 1.233633648 1.025340041 1.090033311 1.051115351 1.59572826 2.179190926 1.679028349 2.070220231 1.075177949 1 10.17524884 -8.587429881 3.55610348 1.100718741 1.944457758 0.897967972 0.136415481 0.053266625 1.36259427 0.020394516 0.043710874 2.59E-09 8.587429881 0.843739017 YNDWS(ph)DDDDDSNESK ddPTM_HeLa_Romidepsin_16h_R1 2 YNDWSDDDDDSNESK 15 0 Q9UH62;H3BV87 Q9UH62 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 0 YNDWS(0.962)DDDDDS(0.037)NESK;Y(0.002)NDWS(0.998)DDDDDSNESK ; 125.61 0.0027687 329550000 2134.57 2141.18 2353.3 2150.2 2260.53 2626.4 2136 2302.4 2415.9 2299.6 TRUE FALSE FALSE 2108.55304 2171.323588 2394.258199 2398.816241 2145.166719 2458.581516 2317.431787 2369.016311 2199.815853 2239.85606 0.941378813 0.96940318 1.068933956 1.070968927 0.957725256 1.097651568 1.034634246 1.057664532 0.982123759 1 11.12919031 -9.771163138 24.9528047 0.971325697 1.04653252 0.49378607 0.037018466 129.2842459 331764.6729 0.00623156 0.008245137 1.69E-10 9.771163138 0.075206823 YNDWSDDDDDS(ph)NESK ddPTM_HeLa_Romidepsin_16h_R1 1 YNDWSDDDDDSNESK 15 0 Q9UH62;H3BV87 Q9UH62 ARMCX3 Armadillo repeat-containing X-linked protein 3 1 0 YNDWS(0.312)DDDDDS(0.677)NES(0.011)K 153.22 4.33E-05 0 974.44 1266.5 768.9 1036.7 954.13 1181.6 792.43 1021.3 993.32 986.94 TRUE FALSE FALSE 962.5631505 1284.32982 782.282382 1156.568132 905.4371858 1106.099573 859.7389844 1050.849704 904.4749714 961.2991565 1.001314881 1.336035522 0.813776208 1.203130289 0.941889088 1.150629922 0.894351127 1.093155754 0.940888136 1 9.908841658 YNEDLELEDAIHTAILTLK ddPTM_HeLa_Romidepsin_16h_R1 1 YNEDLELEDAIHTAILTLK 19 0 A0A024RA52;P25787;C9JCK5 A0A024RA52 PSMA2 Proteasome subunit alpha type;Proteasome subunit alpha type-2 0 0 57.009 0.021324 36204000 884.77 790.25 937.44 977.43 929.72 800.42 712.88 877.95 864.99 695.61 FALSE FALSE TRUE 873.9860829 801.3751602 953.75575 1090.445056 882.2729191 749.2757452 773.4320094 903.3520981 787.623128 677.5379519 1.289944099 1.182775309 1.40767871 1.609422841 1.302174906 1.105880111 1.141533116 1.333286343 1.162478243 1 9.40415795 -12.04380238 0.702725308 0.986819309 1.299020827 0.237804868 0.14408903 0.692828927 0.589104942 0.123442574 0.032063943 9.04E-13 12.04380238 0.312201518 YNGLIHR ddPTM_HeLa_Romidepsin_16h_R1 1 YNGLIHR 7 0 H0YMF4;H0YKD8;P46779-4;P46779-5;P46779;P46779-2;P46779-3;H0YLP6 H0YMF4 RPL28 60S ribosomal protein L28 0 0 85.359 0.024371 6825600 5675.8 5132.9 7019.3 5919.5 7826.8 7614.1 5508.2 4627.6 4915.2 4212.2 FALSE FALSE TRUE 5606.621166 5205.161101 7141.467972 6603.940442 7427.36919 7127.583583 5976.066371 4761.492305 4475.572202 4102.766437 1.366546513 1.268695448 1.740646971 1.609631097 1.810331956 1.737262818 1.45659434 1.160556512 1.090866924 1 12.00238131 -11.06657446 0.606399956 1.029675998 1.585031533 0.509965734 0.194343358 0.408282988 0.341028353 0.094435993 0.058524561 8.58E-12 11.06657446 0.555355535 YNLDAS(ph)EEEDSNK ddPTM_HeLa_Romidepsin_16h_R1 3 YNLDASEEEDSNK 13 0 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 YNLDAS(1)EEEDSNK;Y(0.003)NLDAS(0.997)EEEDSNK;Y(0.003)NLDAS(0.833)EEEDS(0.164)NK ;; 244.57 1.33E-52 74572000 14257.1 12237.6 15716 7003.4 13866.8 14410.9 11903.5 13332.8 14174.9 15733.6 TRUE FALSE FALSE 14083.32898 12409.88125 15989.53039 7813.16606 13159.12545 13490.09 12914.58299 13718.56353 12907.06144 15324.8388 0.918987088 0.809788697 1.04337348 0.509836753 0.858679535 0.880276143 0.842722273 0.89518485 0.842231465 1 13.90358428 -10.60867201 0.816627141 0.982824948 0.823993421 0.041956817 0.132808605 0.589958128 0.83443993 0.032803624 0.031567332 2.46E-11 10.60867201 -0.158831527 YNLDAS(ph)EEEDSNKK ddPTM_HeLa_Romidepsin_16h_R1 3 YNLDASEEEDSNKK 14 1 O95218-2;O95218 O95218-2 ZRANB2 Zinc finger Ran-binding domain-containing protein 2 1 0 YNLDAS(0.973)EEEDS(0.027)NKK;Y(0.038)NLDAS(0.961)EEEDS(0.001)NKK;YNLDAS(0.999)EEEDS(0.001)NKK ;; 206.49 7.20E-17 122459000 9977.8 8429.6 9750.2 5909.9 8594.3 9730 8229.7 8433.6 9417.6 10359.2 TRUE FALSE FALSE 9856.186736 8548.27213 9919.898141 6593.230445 8155.700801 9108.284402 8928.730513 8677.61291 8575.266269 10090.06649 0.976820792 0.847196809 0.983135062 0.65343776 0.808290095 0.902698155 0.88490304 0.860015434 0.849872127 1 13.30064806 -10.13367104 1.365915691 0.992798084 0.837772063 0.117110387 0.090950916 0.278569821 0.999572818 0.014959078 0.018741414 7.35E-11 10.13367104 -0.155026021 YNQQRVHELENCNGLSMIHQVLIKQK ddPTM_HeLa_Romidepsin_16h_R1 1 YNQQRVHELENCNGLSMIHQVLIKQK 26 2 Q99698-2;Q99698 Q99698-2 LYST Lysosomal-trafficking regulator 0 0 43.349 0.014313 6229300 3312.9 2667.5 2904.5 3724.8 2924.6 2173.8 1950.1 2186.9 3502.2 3055.3 FALSE FALSE TRUE 3272.521101 2705.053135 2955.051604 4155.478902 2775.346749 2034.901196 2115.741445 2250.174501 3188.954461 2975.922866 1.099665969 0.908979586 0.992986626 1.396366468 0.932600364 0.683788286 0.710953053 0.756126621 1.071585053 1 11.53912142 -8.420208652 4.678268359 1.057584645 0.720440042 0.628908714 0.1230584 0.115230134 4.076255756 0.017671115 0.040352296 3.80E-09 8.420208652 -0.337144602 YNSNLAT(ph)PIAIK ddPTM_HeLa_Romidepsin_16h_R1 1 YNSNLATPIAIK 12 0 Q8IX90 Q8IX90 SKA3 Spindle and kinetochore-associated protein 3 1 0 YNS(0.01)NLAT(0.99)PIAIK 105.19 0.026919 7327800 2524.6 2317.9 2561.5 2491.9 3544.6 3445.4 2894.7 3184 2381.1 2145.5 TRUE FALSE FALSE 2493.829204 2350.531457 2606.081833 2780.025203 3363.705835 3225.25006 3140.575746 3276.124016 2168.128452 2089.759601 1.193356979 1.124785576 1.247072549 1.330308616 1.609613773 1.543359369 1.502840683 1.567703776 1.037501372 1 11.02912127 -9.299704545 0.586088821 1.058965318 1.605321833 0.905892112 0.066516206 0.213147414 0.141769449 0.019497604 0.051603235 5.02E-10 9.299704545 0.546356515 YNTEGRVS(ph)PSPSQESLSSSK ddPTM_HeLa_Romidepsin_16h_R1 2 YNTEGRVSPSPSQESLSSSK 20 1 Q5JSH3-2;Q5JSH3;Q5JSH3-4;H7BY83;Q5JSH3-3 Q5JSH3-2 WDR44 WD repeat-containing protein 44 1 0 YNT(0.021)EGRVS(0.962)PS(0.012)PS(0.005)QESLSSSK;Y(0.001)NT(0.001)EGRVS(0.912)PS(0.07)PS(0.014)QES(0.002)LSSSK ; 98.015 0.00031529 102157000 4842.9 4221.6 4874.2 5328.7 6327.7 5742.1 5301.6 5875.5 4798.1 4531.5 TRUE FALSE FALSE 4783.872872 4281.031796 4959.033406 5944.829366 6004.773857 5375.198342 5751.917772 6045.498322 4368.945919 4413.770977 1.083851631 0.969926129 1.123536639 1.346882155 1.360463397 1.217824479 1.303175403 1.36969008 0.989844272 1 12.10779606 -9.408875305 3.804730922 1.035674189 1.314775906 0.888210917 0.051581202 0.062116092 1.603914229 0.008417991 0.013045189 3.90E-10 9.408875305 0.279101717 YPDIAS(ph)PTFR ddPTM_HeLa_Romidepsin_16h_R1 1 YPDIASPTFR 10 0 Q8IVL0-3;Q8IVL0-2;Q8IVL0;H0YHA8;A0A2R8YFX5 Q8IVL0-3 NAV3 Neuron navigator 3 1 0 YPDIAS(0.706)PT(0.294)FR 105.36 0.021057 9465500 2394.1 1842.4 1998.8 1555.1 2068.3 1869.6 1380.3 1715.2 2374.1 2495.7 TRUE FALSE FALSE 2364.919788 1868.337356 2033.588276 1734.907979 1962.746933 1750.138594 1497.542648 1764.826606 2161.75455 2430.861354 0.972873169 0.768590669 0.836571066 0.713700918 0.807428581 0.719966439 0.616054324 0.726008747 0.8892957 1 11.2472519 -9.91696834 0.746213875 1.000791351 0.69674136 0.689460055 0.064301926 0.159586419 0.180798501 0.012503801 0.018686648 1.21E-10 9.91696834 -0.30404999 YPDLYPQEDEDEEEER ddPTM_HeLa_Romidepsin_16h_R1 1 YPDLYPQEDEDEEEER 16 0 Q8N4Q1;Q8N4Q1-2 Q8N4Q1 CHCHD4 Mitochondrial intermembrane space import and assembly protein 40 0 0 160.87 0.0012152 2320200 581.21 660.05 404.2 409.84 624.85 762.61 516.53 614.39 636.17 630.2 FALSE FALSE TRUE 574.125989 669.3422012 411.2349314 457.2276292 592.9615729 713.8816822 560.4040453 632.1664053 579.2693619 613.8273132 0.935321672 1.090440563 0.669952155 0.744879902 0.966007149 1.163000842 0.912966942 1.029876631 0.943700858 1 9.261689032 -5.966769564 13.68048337 0.954912301 1.006626461 0 0.140367088 0 0 0.01845678 0 1.08E-06 5.966769564 0.05171416 YPDVAS(ph)PTLR ddPTM_HeLa_Romidepsin_16h_R1 2 YPDVASPTLR 10 0 A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-4;Q8IVL1-8;Q8IVL1-9;Q8IVL1-10;Q8IVL1-13;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;Q8IVL1-5;E9PNV5 A0A0A0MTL4 NAV2 Neuron navigator 2 1 0 YPDVAS(0.697)PT(0.302)LR;YPDVAS(0.62)PT(0.38)LR ; 132.56 0.0063428 76664000 6035.1 5943.6 5688.7 4470.7 3912.4 3832.9 3263 3700 5963.8 6045.7 TRUE FALSE FALSE 5961.54188 6027.274157 5787.709437 4987.623369 3712.735629 3587.99006 3540.159139 3807.053662 5430.382791 5888.631842 1.01238149 1.023544062 0.982861485 0.846991882 0.630492061 0.609307927 0.60118534 0.64650903 0.922180727 1 12.52371676 -8.94926904 2.139943017 1.007022338 0.612871143 0.968132935 0.031239768 0.018447927 0.170158952 0.002579599 0.005114699 1.12E-09 8.94926904 -0.394151195 YPDVAS(ph)PTLRR ddPTM_HeLa_Romidepsin_16h_R1 1 YPDVASPTLRR 11 1 A0A0A0MTL4;A0A0A0MTE8;Q8IVL1-4;Q8IVL1-8;Q8IVL1-9;Q8IVL1-10;Q8IVL1-13;Q8IVL1-12;Q8IVL1-11;Q8IVL1-3;Q8IVL1-2;Q8IVL1;Q8IVL1-5;E9PNV5 A0A0A0MTL4 NAV2 Neuron navigator 2 1 0 YPDVAS(0.834)PT(0.166)LRR 118.73 0.0031496 14473000 6124.9 5411.2 5751.4 5385.6 4502.3 3904.4 3927 3920.2 6076.3 5396.7 TRUE FALSE FALSE 6050.247363 5487.379016 5851.500704 6008.308412 4272.530831 3654.921441 4260.559282 4033.624802 5532.82051 5256.492956 1.15100456 1.043923974 1.113194815 1.143026056 0.81281015 0.695315579 0.810532672 0.76736045 1.052568805 1 12.35988486 -8.685954758 5.529661764 1.078514585 0.763054698 0.89878374 0.05147905 0.057959251 3.092507824 0.009586095 0.019299963 2.06E-09 8.685954758 -0.315459887 YPGGS(ph)PIPADPR ddPTM_HeLa_Romidepsin_16h_R1 1 YPGGSPIPADPR 12 0 Q9BY89 Q9BY89 KIAA1671 Uncharacterized protein KIAA1671 1 0 Y(0.002)PGGS(0.998)PIPADPR 89.356 0.0293 16424000 1972.8 2018.6 1610.4 2113.5 2137.7 1923.5 2153.1 1927.7 2196.3 1815.6 TRUE FALSE FALSE 1948.754755 2047.017904 1638.428336 2357.872814 2028.605192 1800.594558 2335.98426 1983.474958 1999.857427 1768.43045 1.101968559 1.157533735 0.926487291 1.333313851 1.14712184 1.01818794 1.320936461 1.121601903 1.13086575 1 10.78825377 -16.52287623 0.057522318 0.380581854 1.418636305 0.04938221 0.119549283 334.778527 1.515456139 29.95703252 6.026611265 3.00E-17 16.52287623 1.038054451 YPIEHGIITNWDDMEK ddPTM_HeLa_Romidepsin_16h_R1 2 YPIEHGIITNWDDMEK 16 0 P63267;P68133;P68032;P62736;A6NL76;F8WB63;B8ZZJ2;C9JFL5;F6UVQ4;F6QUT6 P63267 ACTG2;ACTA1;ACTC1;ACTA2 "Actin, gamma-enteric smooth muscle;Actin, alpha skeletal muscle;Actin, alpha cardiac muscle 1;Actin, aortic smooth muscle" 0 0 ; ; 88.706 0.0065443 1183900 393.12 265.137 300.11 194.38 297.98 785.35 526.05 514.74 257.051 186.74 FALSE FALSE TRUE 388.3285022 268.8696056 305.3332887 216.8551302 282.7729687 735.1686696 570.7326739 529.6331898 234.0597148 181.8884679 2.134981435 1.478211394 1.678684153 1.192242327 1.554650341 4.041865205 3.13781671 2.911856898 1.286830977 1 7.506910266 -8.276549271 24.41294868 1.528657012 3.341243255 0.82713926 0.395109763 207.7096462 335594.8087 0.070553494 0.158380673 5.29E-09 8.276549271 1.812586243 YPLFEGQETGK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 1 YPLFEGQETGKK 12 1 P41250 P41250 GARS Glycine--tRNA ligase 0 1 YPLFEGQETGK(1)K 129.84 0.0014883 380590 209.56 140.19 126.24 0 156.04 286.68 249.4 260.84 372.91 262.14 FALSE TRUE FALSE 207.0058021 142.1635985 128.4371542 0 148.0766965 268.3620732 270.5840298 268.3869939 339.5559956 255.329565 0.81073965 0.556784713 0.503024999 0 0.579943402 1.051041908 1.059744216 1.05113951 1.329873396 1 7.996216789 -10.95388255 1.415913577 0.949908441 0.682189004 0.188375413 0.330997979 0.635261061 2.641195196 0.080181416 0.070229202 1.11E-11 10.95388255 -0.267719437 YPSSISS(ph)SPQK ddPTM_HeLa_Romidepsin_16h_R1 2 YPSSISSSPQK 11 0 F8W726;Q14157-4;Q14157-1;Q14157-3;Q14157;Q14157-5 F8W726 UBAP2L Ubiquitin-associated protein 2-like 1 0 YPSSISS(0.5)S(0.5)PQK;YPSSISS(0.5)S(0.5)PQK ; 182.41 6.75E-06 117122000 9722.2 8835.8 12957.8 7639 8724.4 8015.7 6997.4 7113.3 10069.9 9547 TRUE FALSE FALSE 9603.702087 8960.190624 13183.32507 8522.257123 8279.161313 7503.522639 7591.758981 7319.112113 9169.222923 9298.967564 1.032770791 0.963568328 1.417719223 0.916473476 0.890331239 0.806919971 0.816408803 0.787088681 0.986047414 1 13.18285483 -8.849172996 3.368693079 1.042183821 0.819367603 0.453841849 0.127524606 0.183716686 4.140510271 0.01859665 0.035926397 1.42E-09 8.849172996 -0.222816217 YQDEVFGGFVTEPQEES(ph)EEEVEEPEER ddPTM_HeLa_Romidepsin_16h_R1 10 YQDEVFGGFVTEPQEESEEEVEEPEER 27 0 Q13283 Q13283 G3BP1 Ras GTPase-activating protein-binding protein 1 1 0 YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVT(0.004)EPQEES(0.996)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVT(0.157)EPQEES(0.842)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER;YQDEVFGGFVTEPQEES(1)EEEVEEPEER ;;;;;;;;; 187.17 1.05E-25 1373287300 40852.4 39462.6 39381.04 33900.45 39970.28 40523.01 35713.15 38131.15 46349.21 40868.38 TRUE FALSE FALSE 40354.47524 40018.15552 40066.45048 37820.17954 37930.44746 37933.72044 38746.62407 39234.41466 42203.62057 39806.6136 1.013763081 1.005314241 1.00652748 0.950097889 0.952867979 0.952950201 0.973371522 0.985625531 1.0602163 1 15.28072052 -9.271578613 24.68799956 1.006558521 0.962440504 0.630727847 0.019916572 193.3608945 470813.2527 0.00177096 0.002723979 5.35E-10 9.271578613 -0.044118017 YQEDS(ph)DPERSDY(ph)EEQQLQKEEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 YQEDSDPERSDYEEQQLQKEEEAR 24 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 2 0 Y(0.041)QEDS(0.752)DPERS(0.468)DY(0.739)EEQQLQKEEEAR 57.981 0.0038053 5347600 1418.4 1189.3 1300.6 1470.1 1615.9 2222.8 1283 1801.9 1587.4 1465.2 TRUE FALSE FALSE 1401.111995 1206.042997 1323.236397 1640.079879 1533.434593 2080.770254 1391.977988 1854.035134 1445.418968 1427.133893 0.981766324 0.845080481 0.927198495 1.149212339 1.074485443 1.458006333 0.975366078 1.299131878 1.012812446 1 10.47890498 -8.967305322 2.144093234 0.974408944 1.209966375 0.458031149 0.12860804 0.217725793 2.010868952 0.018239074 0.035846015 1.08E-09 8.967305322 0.235557431 YQEDSDPERS(ph)DYEEQQLQKEEEAR ddPTM_HeLa_Romidepsin_16h_R1 1 YQEDSDPERSDYEEQQLQKEEEAR 24 2 Q6P6C2-3;Q6P6C2;Q6P6C2-1 Q6P6C2-3 ALKBH5 RNA demethylase ALKBH5 1 0 Y(0.003)QEDS(0.035)DPERS(0.797)DY(0.165)EEQQLQKEEEAR 45.511 0.025276 18127000 2726.9 2470.5 2325.6 2428.8 2747.5 3368.8 3059.5 3457.3 3142.8 3134.4 TRUE FALSE FALSE 2693.663494 2505.279764 2366.076092 2709.629284 2607.284823 3153.544552 3319.373854 3557.331521 2861.700097 3052.967836 0.882309817 0.820604703 0.775008523 0.887539414 0.854016473 1.032943916 1.087261325 1.165204389 0.937350228 1 11.57599668 -7.923264778 2.367427502 0.911297099 1.137848417 0.686596891 0.066102165 0.183023786 2.010374188 0.012194446 0.049161311 1.19E-08 7.923264778 0.226551318 YQEQGGEAS(ph)PQR ddPTM_HeLa_Romidepsin_16h_R1 2 YQEQGGEASPQR 12 0 H0Y5J4;Q9UJU6-5;Q9UJU6 H0Y5J4 DBNL Drebrin-like protein 1 0 YQEQGGEAS(1)PQR;YQEQGGEAS(1)PQR ; 170.26 0.00015247 125118000 6928.4 6554.8 7056.6 4949 7446.9 7550.1 7062.5 6320 7238.6 6370.8 TRUE FALSE FALSE 6843.953996 6647.078646 7179.417163 5521.226666 7066.856905 7067.672977 7662.388574 6502.859229 6591.161487 6205.285698 1.10292327 1.07119623 1.156984144 0.88976188 1.138844728 1.138976241 1.234816404 1.047954848 1.062185016 1 12.59928192 -16.52287875 0.112868582 0.667369314 1.164089756 0.093585238 0.08578192 129.3726383 1.067608535 10.03169283 0.483696778 3.00E-17 16.52287875 0.496720442 YQEQGGEAS(ph)PQRTWEQQQEVVSR ddPTM_HeLa_Romidepsin_16h_R1 2 YQEQGGEASPQRTWEQQQEVVSR 23 1 H0Y5J4;Q9UJU6-5;Q9UJU6 H0Y5J4 DBNL Drebrin-like protein 1 0 Y(0.009)QEQGGEAS(0.751)PQRT(0.24)WEQQQEVVSR;Y(0.003)QEQGGEAS(0.932)PQRT(0.065)WEQQQEVVSR ; 61.437 0.0027287 43252000 1129.42 1213.68 778.59 1577.61 1150.4 1195.38 998.34 957.67 1323.24 1066.5 TRUE FALSE FALSE 1115.654195 1230.766219 792.1410323 1760.020691 1091.690795 1118.999076 1083.138975 985.3786705 1204.8861 1038.792176 1.073991719 1.184805052 0.762559683 1.69429529 1.050923197 1.07721169 1.042690732 0.948581144 1.159891389 1 10.02069134 -11.15636799 0.793239973 1.009973528 1.114830719 0 0.22932291 1.673547921 2.278855074 0.076915319 0.050422224 6.98E-12 11.15636799 0.10485719 YQEQGGEAS(ph)PQSR ddPTM_HeLa_Romidepsin_16h_R1 1 YQEQGGEASPQSR 13 0 B4DDD6;Q9UJU6-4;Q9UJU6-6;Q9UJU6-2;Q9UJU6-3 B4DDD6 DBNL Drebrin-like protein 1 0 YQEQGGEAS(0.989)PQS(0.011)R 166.79 0.00014627 25268000 2497.2 2460.6 2307.7 2017 2946 3064.5 2892.8 2392.9 2470.3 2325.1 TRUE FALSE FALSE 2466.763166 2495.240391 2347.86455 2250.21503 2795.654627 2868.68834 3138.51436 2462.134786 2249.350181 2264.693567 1.089226022 1.10180045 1.03672505 0.993606845 1.234451613 1.266700441 1.385845046 1.087182311 0.993224962 1 11.14510014 -8.705958969 6.643787231 1.044667124 1.257382676 0.636817042 0.076471623 0.096600114 8.836464829 0.010667444 0.021343717 1.97E-09 8.705958969 0.212715552 YQEVWTSS(ph)TSPR ddPTM_HeLa_Romidepsin_16h_R1 1 YQEVWTSSTSPR 12 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 YQEVWT(0.008)S(0.054)S(0.417)T(0.417)S(0.104)PR 89.189 0.029524 6158100 1315.8 1478 1116.6 1530.7 2205.2 2428.7 2139.6 2209 1774 1329.2 TRUE FALSE FALSE 1299.762523 1498.807323 1136.033955 1707.686736 2092.660415 2273.513908 2321.337571 2272.91393 1615.328997 1294.667192 1.00393563 1.157677689 0.877471802 1.319015996 1.616369386 1.756060493 1.792999455 1.75559707 1.247678945 1 10.33836557 -8.858754367 2.044233508 1.006710541 1.766048246 0.900835101 0.104938585 0.038780767 0.329235938 0.010071195 0.021078883 1.38E-09 8.858754367 0.759337706 YQEVWTSST(ph)SPR ddPTM_HeLa_Romidepsin_16h_R1 1 YQEVWTSSTSPR 12 0 Q9H792;H0YN99;H3BUZ5 Q9H792 PEAK1 Pseudopodium-enriched atypical kinase 1 1 0 YQEVWT(0.005)S(0.036)S(0.036)T(0.873)S(0.049)PR 116.9 0.017503 4200500 1358.9 1223.1 1099.4 1393.3 1496.6 1780.3 1500.9 1522.5 1350.6 1236.9 TRUE FALSE FALSE 1342.337204 1240.318834 1118.534596 1554.399902 1420.222917 1666.544576 1628.386409 1566.551135 1229.798953 1204.76516 1.114189926 1.029510875 0.928425417 1.290209871 1.178837972 1.383294132 1.35162143 1.300295848 1.020778982 1 10.23453624 -9.240456789 22.49842235 1.044516795 1.301474086 0.811529152 0.067438214 86.36245114 92601.11733 0.011287257 0.018697318 5.75E-10 9.240456789 0.25695729 YQPLASTAS(ph)DNDFVTPEPR ddPTM_HeLa_Romidepsin_16h_R1 3 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 0 YQPLAS(0.01)T(0.01)AS(0.98)DNDFVTPEPR;YQPLAS(0.002)T(0.036)AS(0.962)DNDFVTPEPR;YQPLAST(0.003)AS(0.993)DNDFVT(0.004)PEPR ;; 164.69 4.47E-07 98177900 7405.6 6807.5 6625.3 7080.1 7195.9 5988.5 5072.2 5196.9 6996.3 6526.4 TRUE FALSE FALSE 7315.337699 6903.336164 6740.610567 7898.734475 6828.666371 5605.854177 5503.032541 5347.264102 6370.533405 6356.843187 1.150781525 1.08596924 1.060370748 1.242556131 1.074222876 0.881861328 0.865686376 0.84118232 1.002153619 1 12.63409478 -8.248538922 4.704877097 1.086799924 0.859704977 0.707477808 0.066492804 0.091622908 5.661542155 0.010803205 0.027186607 5.64E-09 8.248538922 -0.227094946 YQPLASTASDNDFVT(ph)PEPR ddPTM_HeLa_Romidepsin_16h_R1 3 YQPLASTASDNDFVTPEPR 19 0 Q15021 Q15021 NCAPD2 Condensin complex subunit 1 1 0 YQPLASTASDNDFVT(1)PEPR;YQPLAST(0.006)AS(0.002)DNDFVT(0.992)PEPR;YQPLAS(0.004)T(0.001)AS(0.482)DNDFVT(0.513)PEPR ;; 277.64 5.02E-106 96435400 7092 6040.1 7513.6 7041.5 8450.9 8871 7814 8194.7 7559 6166.06 TRUE FALSE FALSE 7005.559976 6125.132686 7644.371056 7855.671361 8019.619038 8304.17173 8477.720965 8431.800715 6882.904108 6005.864872 1.166453146 1.019858558 1.27281769 1.308000018 1.335297948 1.382677084 1.411573711 1.40392781 1.146030464 1 12.5521563 -9.109888811 0.307472987 1.004085837 1.533042341 0.773971521 0.069146651 0.693618093 0.121062268 0.039909882 0.132700841 7.76E-10 9.109888811 0.528956504 YQQETSVSQLPGRPKS(ph)PLSK ddPTM_HeLa_Romidepsin_16h_R1 2 YQQETSVSQLPGRPKSPLSK 20 2 Q9HCD6;Q9HCD6-2 Q9HCD6 TANC2 Protein TANC2 1 0 YQQETSVSQLPGRPKS(0.833)PLS(0.167)K;YQQETSVSQLPGRPKS(0.877)PLS(0.123)K ; 81.316 0.0015416 83596000 6470.4 5873.2 5600.7 8725.1 6957.1 5620 5191.7 5629.6 6968.3 6518.2 TRUE FALSE FALSE 6391.536276 5955.883064 5698.177834 9733.937115 6602.053226 5260.900138 5632.682868 5792.483594 6345.037796 6348.856224 1.006722479 0.938103314 0.897512502 1.533179642 1.039880727 0.828637467 0.887196476 0.912366478 0.999398564 1 12.63228099 -8.271660895 23.27280548 1.032996712 0.877179779 0.187636837 0.168580497 390.1861443 888395.9201 0.024241974 0.054873224 5.35E-09 8.271660895 -0.155816933 YQQIT(ph)PVNQSR ddPTM_HeLa_Romidepsin_16h_R1 1 YQQITPVNQSR 11 0 Q9NYL2 Q9NYL2 ZAK Mitogen-activated protein kinase kinase kinase MLT 1 0 Y(0.016)QQIT(0.983)PVNQSR 126.34 0.014887 4541700 1211.9 1546.2 1459.3 1025.9 1062.1 1045.6 829.93 698.8 1294.4 1417.7 TRUE FALSE FALSE 1197.128897 1567.967444 1484.698504 1144.519385 1007.897074 978.7895345 900.4242335 719.0186755 1178.625622 1380.86795 0.866939447 1.135494125 1.07519224 0.828840575 0.729901128 0.708821966 0.652071209 0.520700532 0.853539705 1 10.43135965 -8.673755301 1.604627539 0.962131762 0.620294443 0.740252694 0.093391018 0.162804013 0.841687228 0.015510321 0.039369413 2.12E-09 8.673755301 -0.341837319 YQT(ph)QPVTLGEVEQVQSGK ddPTM_HeLa_Romidepsin_16h_R1 1 YQTQPVTLGEVEQVQSGK 18 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 YQT(0.999)QPVT(0.001)LGEVEQVQSGK 199.41 5.69E-20 0 1748.4 1049.1 1381.1 1715.9 2970.9 1196 571.28 1465.1 889.21 1195.4 TRUE FALSE FALSE 1727.089828 1063.869257 1405.137466 1914.300432 2819.283887 1119.57946 619.8045089 1507.490357 809.6768305 1164.343336 1.483316626 0.913707516 1.20680681 1.644103052 2.421350989 0.961554402 0.532321086 1.294712917 0.695393537 1 10.18530082 -6.905278495 20.75404523 1.253448242 5.122983629 0 0.516520487 18480.33469 4066381.594 0.068308485 14376.79042 1.24E-07 6.905278495 3.869535387 YQTQPVT(ph)LGEVEQVQSGK ddPTM_HeLa_Romidepsin_16h_R1 1 YQTQPVTLGEVEQVQSGK 18 0 O95425-2;O95425-3;A0A6I8PIX7;O95425-4;O95425 O95425-2 SVIL Supervillin 1 0 YQT(0.444)QPVT(0.556)LGEVEQVQSGK 165.66 1.07E-06 7802900 2774.9 1770.6 2408.3 2471.9 5074.9 2211.8 920.21 2272.7 1487.7 1881.5 TRUE FALSE FALSE 2741.078451 1795.526553 2450.215451 2757.712709 4815.908916 2070.473118 998.3726144 2338.456989 1354.636386 1832.618359 1.49571701 0.979760213 1.337002568 1.504793781 2.627884247 1.129789576 0.544779337 1.276019624 0.739180844 1 10.83969066 -12.45860946 0.996984245 0.982286685 1.373740331 0.117464586 0.509250992 1.531327288 2.513155936 0.457669995 0.094220556 3.48E-13 12.45860946 0.391453646 YQVSDGSLT(ph)VTSVSR ddPTM_HeLa_Romidepsin_16h_R1 1 YQVSDGSLTVTSVSR 15 0 H0YDP1;Q9UPX0;Q9UPX0-2 H0YDP1 IGSF9B Protein turtle homolog B 1 0 YQVS(0.203)DGS(0.203)LT(0.482)VT(0.112)SVSR 152.16 0.00097859 53571000 0 0 0 0 62.114 0 0 0 0 0 TRUE FALSE FALSE 0 0 0 0 58.9440908 0 0 0 0 0 0 YQYGGLNSGRPVT(ph)PPR ddPTM_HeLa_Romidepsin_16h_R1 1 YQYGGLNSGRPVTPPR 16 1 P62140 P62140 PPP1CB Serine/threonine-protein phosphatase PP1-beta catalytic subunit 1 0 YQYGGLNS(0.01)GRPVT(0.99)PPR 116 0.012517 12920000 1537.8 1491.6 1339.1 1223.6 1314.1 1601.2 1313 1181.8 1519 1075.6 TRUE FALSE FALSE 1519.056702 1512.598784 1362.406474 1365.078389 1247.036573 1498.888488 1424.526187 1215.993518 1383.136836 1047.655757 1.449957863 1.443793702 1.300433339 1.302983714 1.190311383 1.43070706 1.359727351 1.160680415 1.320220718 1 10.03294903 -12.40259503 1.119792285 0.999336961 1.3409562 0.019537959 0.134863328 0.259368132 0.57997436 0.069054379 0.017434546 3.96E-13 12.40259503 0.341619239 YRDLDEDEILGALTEEELR ddPTM_HeLa_Romidepsin_16h_R1 1 YRDLDEDEILGALTEEELR 19 1 P28289 P28289 TMOD1 Tropomodulin-1 0 0 150.23 3.40E-05 1100400 471.48 544.62 702.59 448.5 485.14 404.89 532.09 484.97 460.48 580.54 FALSE FALSE TRUE 465.7334204 552.2871747 714.8182842 500.3576803 460.3814955 379.0188357 577.2857113 499.0018418 419.2935155 565.4574871 0.823640028 0.976708572 1.264141515 0.884872323 0.814175258 0.670287058 1.020917973 0.882474551 0.741512006 1 9.143274752 -9.009338447 24.93798016 0.94943028 0.847113545 0.113713766 0.150069543 842.9734679 2251138.577 0.022127161 0.038581633 9.79E-10 9.009338447 -0.102316735 YREPPPT(ph)PPGYLGISLADLK ddPTM_HeLa_Romidepsin_16h_R1 2 YREPPPTPPGYLGISLADLK 20 1 E9PCH4;Q8TEU7;Q8TEU7-4;A0A5F9ZHG7 E9PCH4 RAPGEF6 Rap guanine nucleotide exchange factor 6 1 0 Y(0.069)REPPPT(0.848)PPGY(0.083)LGISLADLK;Y(0.074)REPPPT(0.924)PPGY(0.002)LGISLADLK ; 70.907 0.0047882 27638000 5892.1 5714.6 5311.6 5943.1 5860.9 5935.2 4908.9 5488.3 5324.3 5231.2 TRUE FALSE FALSE 5820.284819 5795.050289 5404.04617 6630.269185 5561.796403 5555.959875 5325.861843 5647.095301 4848.081273 5095.29267 1.142286655 1.137334136 1.060595832 1.301253846 1.091555827 1.090410352 1.045251409 1.108296553 0.951482395 1 12.3149493 -12.27075704 0.913006432 0.997154696 1.122859355 0.404222387 0.069043469 0.586415281 0.845865338 0.050347129 0.012521744 5.36E-13 12.27075704 0.125704659 YRGMGSLDAMEK ddPTM_HeLa_Romidepsin_16h_R1 1 YRGMGSLDAMEK 12 1 A0A3B3IRL5;C9J381;P20839-2;P20839-4;P20839;P20839-3;P20839-7;P20839-5;P20839-6 A0A3B3IRL5 IMPDH1 Inosine-5-monophosphate dehydrogenase;Inosine-5-monophosphate dehydrogenase 1 0 0 53.327 0.027723 3421100 0 0 112.68 122.01 3193 5001.6 3370 4556 133.04 62.571 FALSE FALSE TRUE 0 0 114.6411481 136.1173703 3030.049295 4682.013902 3656.247716 4687.820672 121.1405692 60.9453964 0 0 1.881046886 2.233431536 49.71744339 76.82309376 59.99218861 76.918372 1.987690233 1 5.929445344 -8.661171789 3.058336853 0.471026571 69.74019482 0.978436761 4.776995663 0.021288093 0.398280208 0.618978362 1.316533492 2.18E-09 8.661171789 69.26916825 YRPAS(ph)ASVSALIGGR ddPTM_HeLa_Romidepsin_16h_R1 1 YRPASASVSALIGGR 15 1 P46108-2 P46108-2 CRK Adapter molecule crk 1 0 YRPAS(0.942)AS(0.029)VS(0.029)ALIGGR 116.87 0.024939 15465000 1092.4 1108 1156 1483.5 1872.8 1644.4 1413.4 1748.9 985.77 866.38 TRUE FALSE FALSE 1079.085409 1123.598453 1176.119695 1655.02925 1777.224028 1539.328147 1533.454161 1799.501662 897.6002623 843.8713227 1.278732171 1.331480787 1.393719236 1.961234143 2.106036762 1.824126624 1.817165863 2.132436088 1.063669588 1 9.720879217 -9.544051711 1.215877801 1.123455288 1.97960193 0.891609259 0.133006583 0.110927714 0.327980146 0.027120678 0.045860152 2.86E-10 9.544051711 0.856146642 YRPEAPGPSVSLS(ph)PMPPSEVK ddPTM_HeLa_Romidepsin_16h_R1 1 YRPEAPGPSVSLSPMPPSEVK 21 1 Q9BWG6-2;Q9BWG6 Q9BWG6-2 SCNM1 Sodium channel modifier 1 1 0 YRPEAPGPSVS(0.002)LS(0.995)PMPPS(0.002)EVK 72.968 0.0059973 8871200 1503.8 1670 1448.1 1648.6 1752.6 2406.3 1691.8 1949.6 1633.6 2031.2 TRUE FALSE FALSE 1485.471107 1693.510304 1473.303573 1839.218889 1663.158282 2252.545196 1835.50145 2006.0086 1487.486725 1978.429131 0.75083362 0.855987347 0.744683522 0.929635972 0.840645872 1.13855238 0.927756987 1.013940084 0.751852417 1 10.95013967 -8.287424022 24.93809695 0.868426345 1.01685056 0.43605453 0.093526481 693.357588 665430.7332 0.015689732 0.035095872 5.16E-09 8.287424022 0.148424215 YRPGTVALR ddPTM_HeLa_Romidepsin_16h_R1 1 YRPGTVALR 9 1 K7EMV3;K7EP01;A0A590UJJ6;B4DEB1;K7EK07;K7ES00;P84243;Q6NXT2;Q5TEC6;Q71DI3;P68431;Q16695 K7EMV3;Q5TEC6 H3F3B;H3F3A;H3F3C;HIST2H3PS2;HIST2H3A;HIST1H3A;HIST3H3 Histone H3;Histone H3.3;Histone H3.3C;Histone H3.2;Histone H3.1;Histone H3.1t 0 0 108.57 0.023389 15079000 1646.6 1998.1 4200.4 2637.7 4124.9 4233 3913.1 3517.6 2620.5 1204.8 FALSE FALSE TRUE 1626.530606 2026.229304 4273.5062 2942.683285 3914.390961 3962.524961 4245.478616 3619.376206 2386.115917 1173.499122 1.38605183 1.726656003 3.641678224 2.507614389 3.33565734 3.37667484 3.617794454 3.084259832 2.033334215 1 10.19660105 -9.895774981 3.839741606 1.194507606 3.25098403 0.799230005 0.415949959 0.04906502 1.379038781 0.054644955 0.072783247 1.27E-10 9.895774981 2.056476424 up YRS(ph)DIHTEAVQAALAK ddPTM_HeLa_Romidepsin_16h_R1 2 YRSDIHTEAVQAALAK 16 1 Q9P265 Q9P265 DIP2B Disco-interacting protein 2 homolog B 1 0 Y(0.054)RS(0.754)DIHT(0.192)EAVQAALAK;Y(0.416)RS(0.584)DIHTEAVQAALAK ; 125.67 0.00090521 57085000 15834.2 11300.5 12227.7 9413.9 12295.6 9775.2 11900.9 11731.4 15439.4 12334.7 TRUE FALSE FALSE 15641.20668 11459.58874 12440.51799 10502.37941 11668.10965 9150.596268 12911.76215 12070.82955 14058.4614 12014.24272 1.301888687 0.95383363 1.035480828 0.874160749 0.971189773 0.761645697 1.07470462 1.004709979 1.170149607 1 13.55245809 -10.17488585 12.54106366 1.142548953 0.951611319 0.431322647 0.106746973 0.954710264 136.4852807 0.022410134 0.027449357 6.69E-11 10.17488585 -0.190937634 YRS(ph)PYSGPK ddPTM_HeLa_Romidepsin_16h_R1 1 YRSPYSGPK 9 1 Q14498-2;Q14498;G3XAC6;Q5QP22;Q5QP23 Q14498-2 RBM39 RNA-binding protein 39 1 0 Y(0.001)RS(0.999)PYSGPK 76.24 0.025812 603000000 5128.4 5243.7 4257.4 4766.4 4827.9 4294.1 4171.4 4199.7 5357.1 5006.7 TRUE FALSE FALSE 5065.893088 5317.520946 4331.498261 5317.513595 4581.514248 4019.720869 4525.718612 4321.211693 4877.947559 4876.625212 1.038811241 1.09041001 0.888216353 1.090408502 0.939484592 0.82428333 0.928043148 0.886106991 1.00027116 1 12.25166738 -8.539867511 8.998513129 1.01834079 0.883864059 0.536618005 0.058232596 0.108347616 50.10613641 0.007707887 0.01561527 2.88E-09 8.539867511 -0.134476731 YRSDS(ph)QDEVEK ddPTM_HeLa_Romidepsin_16h_R1 2 YRSDSQDEVEK 11 1 H7C5V5;H0YF01;H0YBZ4;Q15390-2;Q15390 H7C5V5 MTFR1 Mitochondrial fission regulator 1 1 0 YRS(0.207)DS(0.793)QDEVEK;Y(0.002)RS(0.24)DS(0.759)QDEVEK ; 127.03 0.001219 3769000 3652.4 3771.5 3659.7 4268.9 4917.9 5034.3 4306.9 4052.2 5146.9 4683.4 TRUE FALSE FALSE 3607.883144 3824.595276 3723.395543 4762.490304 4666.921212 4712.624477 4672.727978 4169.444014 4686.548373 4561.724593 0.790903324 0.838409947 0.816225414 1.044010923 1.023060712 1.033079569 1.024333645 0.91400608 1.027363287 1 12.15536363 -9.250412056 24.93818316 0.88724036 1.010885932 0.344111043 0.077693069 678.1323946 1533589.761 0.013628437 0.022463839 5.62E-10 9.250412056 0.123645571 YRVRSLNGSLS(ph)VQMSGR ddPTM_HeLa_Romidepsin_16h_R1 1 YRVRSLNGSLSVQMSGR 17 2 M0QZD8 M0QZD8 1 0 YRVRSLNGS(0.002)LS(0.932)VQMS(0.066)GR 66.777 0.02597 20853000 1324.6 2282.1 1625.6 79065 0 2963.3 1168.9 1582 969.16 1376.9 TRUE FALSE FALSE 1308.455266 2314.227464 1653.892886 88206.86731 0 2773.954694 1268.186337 1627.772674 882.4759023 1341.12794 0.975637914 1.725582918 1.233210373 65.7706582 0 2.068374397 0.945611749 1.213734071 0.658010229 1 10.38923116 -9.450283722 24.99999939 1.063059925 14.00059928 0.110094274 18.3114326 264.5011316 91087.21833 2.791319529 4.263810374 3.55E-10 9.450283722 12.93753936 YS(ph)DGSIALDIFGPQK ddPTM_HeLa_Romidepsin_16h_R1 1 YSDGSIALDIFGPQK 15 0 Q12923-2;Q12923-3;Q12923;Q12923-4 Q12923-2 PTPN13 Tyrosine-protein phosphatase non-receptor type 13 1 0 YS(0.881)DGS(0.119)IALDIFGPQK 141.85 0.00063886 7075900 1133.6 987.88 1010.5 850 1008.3 1391.8 977.6 1275.6 1200.8 1087.1 TRUE FALSE FALSE 1119.783247 1001.787401 1028.087329 948.2809994 956.8426885 1302.868472 1060.63732 1312.507473 1093.397441 1058.856985 1.057539651 0.946102651 0.970940687 0.895570424 0.903656208 1.230448011 1.001681374 1.239551225 1.03262051 1 10.04829203 -8.259595872 24.99987829 0.99994495 1.141672317 0.501419905 0.080839058 131.5485338 1783915.14 0.011686871 0.028194083 5.50E-09 8.259595872 0.141727367 YS(ph)GAYGASVSDEELK ddPTM_HeLa_Romidepsin_16h_R1 3 YSGAYGASVSDEELK 15 0 A0A286YEX5;C9JRZ6;F8WAR4;Q9NX63 A0A286YEX5 CHCHD3 MICOS complex subunit MIC19 1 0 YS(0.987)GAYGAS(0.013)VSDEELK;YS(1)GAYGASVSDEELK;YS(1)GAYGASVSDEELK ;; 270.99 1.04E-84 318070300 16490.5 16659.4 18055.3 11686.6 16929.5 20267.9 15347.2 17033.7 16560.5 16843.1 TRUE FALSE FALSE 16289.50744 16893.93147 18369.54492 13037.85968 16065.52444 18972.8466 16650.79078 17526.54323 15079.2874 16405.51383 0.992928817 1.029771554 1.119717743 0.79472425 0.979275907 1.156492067 1.014950885 1.068332477 0.919159714 1 14.00189316 -8.306904633 24.9835522 0.992065388 1.073427859 0.221472141 0.085175176 528.7317889 290541.6595 0.011228969 0.02510882 4.93E-09 8.306904633 0.081362471 YS(ph)GAYGASVSDEELKR ddPTM_HeLa_Romidepsin_16h_R1 2 YSGAYGASVSDEELKR 16 1 A0A286YEX5;C9JRZ6;F8WAR4;Q9NX63 A0A286YEX5 CHCHD3 MICOS complex subunit MIC19 1 0 YS(1)GAYGASVSDEELKR;YS(1)GAYGASVSDEELKR ; 222.45 1.14E-34 14569300 2973.7 2994 3302.2 2171.89 3286.8 3563.1 3032.4 3431.2 3330 3247.5 TRUE FALSE FALSE 2937.455401 3036.149611 3359.673406 2423.014141 3119.062331 3335.429409 3289.97198 3530.476358 3032.15646 3163.129482 0.928654808 0.959856252 1.062135908 0.766018007 0.986068496 1.054471348 1.040100318 1.116133999 0.958593847 1 11.6271369 -8.284506837 4.1158424 0.95770261 1.069134948 0.357282993 0.073320541 0.195150895 7.765115457 0.010345207 0.025463395 5.19E-09 8.284506837 0.111432338 YS(ph)GSYNDYLR ddPTM_HeLa_Romidepsin_16h_R1 1 YSGSYNDYLR 10 0 Q96PK6 Q96PK6 RBM14 RNA-binding protein 14 1 0 Y(0.031)S(0.968)GSYNDYLR 118.76 0.012601 5253700 1246.6 701.91 1231.8 1033.5 1118.8 1138.9 831.18 1024.3 1395.6 1251.1 TRUE FALSE FALSE 1231.40596 711.7915074 1253.238962 1152.998133 1061.703461 1066.127966 901.7804085 1053.936504 1270.774041 1218.596242 1.010511864 0.584107749 1.028428383 0.946169119 0.871251219 0.87488204 0.740015747 0.864877527 1.042817955 1 10.25100448 YS(ph)PPAISPLVSEK ddPTM_HeLa_Romidepsin_16h_R1 1 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 0 Y(0.001)S(0.997)PPAIS(0.002)PLVSEK 108.23 0.0079263 31637000 4041.6 3336.7 3290.8 2025.3 3021.4 3302.7 2877.5 3190.8 3540.4 4044.7 TRUE FALSE FALSE 3992.339425 3383.67415 3348.074994 2259.474715 2867.206684 3091.668129 3121.914778 3283.120764 3223.737757 3939.618111 1.013382341 0.858883794 0.849847599 0.57352633 0.727787974 0.784763406 0.792440965 0.833360156 0.818286866 1 11.94384007 -9.952875959 1.94540211 1.006898923 0.748470094 0.408744801 0.092066827 0.122148052 0.925478466 0.012391111 0.016526945 1.11E-10 9.952875959 -0.258428829 YSDEQLNSGRQS(ph)PSQNER ddPTM_HeLa_Romidepsin_16h_R1 1 YSDEQLNSGRQSPSQNER 18 1 P25054-2;P25054-3;P25054;A0A2Q2SV78;E9PFT7 P25054-2 APC Adenomatous polyposis coli protein 1 0 YSDEQLNS(0.004)GRQS(0.984)PS(0.012)QNER 98.552 0.016349 7541700 1576.7 1142.7 1374.6 1319.8 1508 1630.1 1689.7 1608 1500 1594.8 TRUE FALSE FALSE 1557.482574 1158.786961 1398.524336 1472.401486 1431.041133 1525.941871 1833.223076 1654.524943 1365.836243 1553.366866 1.00264954 0.745984085 0.90031812 0.94787749 0.921251228 0.982344805 1.180161053 1.06512182 0.879274737 1 10.60118288 -7.837310028 6.91698826 0.964857692 1.121855855 0.412503853 0.084280745 0.169307614 12.52272951 0.012399625 0.037973937 1.45E-08 7.837310028 0.156998164 YSDFEWLKNELER ddPTM_HeLa_Romidepsin_16h_R1 1 YSDFEWLKNELER 13 1 A0A087X0R6;Q9UMY4-3;Q9UMY4;Q9UMY4-1 A0A087X0R6 SNX12 Sorting nexin-12 0 0 100.02 0.014488 7834700 2239.5 2188.1 1775.5 2158.6 2081.4 1827.5 1834.5 1893.6 2223.2 1987 FALSE FALSE TRUE 2212.204113 2218.904129 1806.401833 2408.187489 1975.178391 1710.728648 1990.322384 1948.388328 2024.351424 1935.377454 1.143034972 1.146496837 0.933358932 1.244298617 1.020564949 0.883925068 1.028389775 1.006722655 1.045972412 1 10.91839924 -8.526535729 24.99988914 1.077836237 0.974166008 0.250366173 0.087616169 124.2676457 849519.4653 0.013157996 0.026414516 2.97E-09 8.526535729 -0.103670229 YSEEGLS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 YSEEGLSPSK 10 0 J3KPG5;F8VU39;Q9UIF9-2;Q9UIF9-3;Q9UIF9;A0A0C4DGI9 J3KPG5 BAZ2A Bromodomain adjacent to zinc finger domain protein 2A 1 0 Y(0.003)S(0.001)EEGLS(0.987)PS(0.009)K 119.03 0.012435 42983000 5850 5146.6 5518 4023.4 3746.9 3764.6 3318.2 2821 6164.7 6144 TRUE FALSE FALSE 5778.69795 5219.05397 5614.038475 4488.604439 3555.681711 3524.05421 3600.047825 2902.621184 5613.313792 5984.377994 0.965630506 0.872113021 0.93811562 0.75005363 0.594160615 0.588875605 0.60157427 0.485033062 0.937994525 1 12.54698559 -9.041714428 0.97891314 0.983812202 0.536140655 0.941491731 0.044051444 0.073965736 0.139018003 0.007107217 0.017859029 9.08E-10 9.041714428 -0.447671548 NIDDAS(ph)QMDLFHRDSDDDQTEEQLDESEAR ddPTM_HeLa_Romidepsin_16h_R1 1 NIDDASQMDLFHRDSDDDQTEEQLDESEAR 30 1 E7ESG2;Q9HAW4-2;Q9HAW4-3;Q9HAW4 E7ESG2 CLSPN Claspin 1 0 NIDDAS(0.603)QMDLFHRDS(0.396)DDDQT(0.001)EEQLDESEAR 92.613 5.77E-08 11078000 1253.6 1405.5 1494.2 1139.7 1127.1 1174 698.35 800.96 1446.9 1694.9 TRUE FALSE FALSE 1238.320641 1425.286666 1520.205924 1271.477476 1069.579881 1098.985189 757.6678316 824.1345139 1317.48564 1650.866254 0.750103552 0.863356836 0.920853474 0.77018806 0.647890087 0.665702135 0.458951675 0.499213375 0.798057164 1 10.68900753 -6.967911717 0.251372639 0.952279299 1.73E-23 0.743643675 0.083321553 4.45643228 0.198180686 0.062161471 1.350979366 1.08E-07 6.967911717 -0.952279299 down YSHS(ph)YLSDSDTEAK ddPTM_HeLa_Romidepsin_16h_R1 1 YSHSYLSDSDTEAK 14 0 Q92614;A0A0D9SFK2;Q92614-2;Q92614-3;Q92614-4;Q92614-5 Q92614 MYO18A Unconventional myosin-XVIIIa 1 0 YSHS(0.687)YLS(0.312)DSDTEAK 277.82 1.47E-96 19490000 2466.7 2301.6 2463.9 1842.9 2970.6 2585.5 2888.9 2456.6 2353.6 2358.1 TRUE FALSE FALSE 2436.634912 2334.001985 2506.783146 2055.984769 2818.999197 2420.294894 3134.283094 2527.677845 2143.088121 2296.836222 1.060865763 1.016181286 1.091407007 0.895137733 1.227340099 1.053751622 1.364608875 1.100504172 0.933060921 1 11.16543227 -8.739325601 24.99407718 1.025236446 1.18978396 0.469895634 0.094994116 156.5155913 176900.798 0.011796173 0.02357703 1.82E-09 8.739325601 0.164547514 YSISLS(ph)PPEQQK ddPTM_HeLa_Romidepsin_16h_R1 1 YSISLSPPEQQK 12 0 A0A0U1RQT1;A0A087X1H5;Q15057;H7C3K3 A0A0U1RQT1 ACAP2 "Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2" 1 0 YS(0.001)IS(0.002)LS(0.997)PPEQQK 129.71 0.0041099 5165300 951.42 693.99 971.29 708.97 1041.3 1276.5 1251.6 1081.8 1067.7 1180.7 TRUE FALSE FALSE 939.8237271 703.7600094 988.194895 790.9444472 988.1585754 1194.93577 1357.910873 1113.100176 972.2022379 1150.025244 0.817220085 0.611951793 0.859281047 0.687762683 0.859249465 1.039051774 1.180766144 0.96789195 0.845374693 1 10.16744981 -8.204317172 4.59330128 0.863803077 1.080095839 0.449841567 0.117796363 0.200014914 8.8867711 0.019815652 0.051924296 6.25E-09 8.204317172 0.216292761 YSKMMAFLEK ddPTM_HeLa_Romidepsin_16h_R1 1 YSKMMAFLEK 10 1 Q6PI26-2;Q6PI26 Q6PI26-2 SHQ1 Protein SHQ1 homolog 0 0 53.775 0.0043369 0 846.97 756.93 914.15 1048 1074.4 712.47 653.93 794.12 751.09 823.04 FALSE FALSE TRUE 836.6468039 767.5860804 930.0603973 1169.174691 1019.569359 666.9454664 709.4747979 817.0966093 683.9106293 801.6573022 1.043646458 0.957499019 1.160172052 1.458447005 1.271826947 0.831958325 0.885010086 1.019259236 0.853120938 1 9.646841825 -8.229898986 24.986871 1.075107519 0.909369303 0.20474316 0.167715857 974.46661 771989.7604 0.024347017 0.062066598 5.89E-09 8.229898986 -0.165738215 YSLS(ph)PSK ddPTM_HeLa_Romidepsin_16h_R1 1 YSLSPSK 7 0 Q99666;O14715;J3KQ37;F8W705;Q99666-2;P49792;J3KNE0;A6NKT7;F8VYC4;A0A286YES2;A0A1W2PNU4;P0DJD0;P0DJD1;Q7Z3J3 Q99666;P49792;Q7Z3J3 RGPD5;RGPD8;RANBP2;RGPD3;RGPD1;RGPD2;RGPD4 RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 8;E3 SUMO-protein ligase RanBP2;RanBP2-like and GRIP domain-containing protein 3;RANBP2-like and GRIP domain-containing protein 1;RANBP2-like and GRIP domain-containing protein 2;RanBP2-like and GRIP domain-containing protein 4 1 0 YS(0.002)LS(0.996)PS(0.002)K 123.21 0.024857 95829000 5077.7 3821.7 12720 7681.8 6668.7 9648.3 7553.1 5160.3 6504.6 3328.4 TRUE FALSE FALSE 5015.811039 3875.501993 12941.38626 8570.00586 6328.371355 9031.804768 8194.660125 5309.605139 5922.812285 3241.927688 1.547169315 1.19543135 3.991879989 2.643490751 1.952039639 2.785936528 2.527712187 1.637792588 1.826941516 1 11.6626362 YSPDEMNNS(ph)PNFEEK ddPTM_HeLa_Romidepsin_16h_R1 2 YSPDEMNNSPNFEEK 15 0 Q14687-2;Q14687-3;Q14687;H7C3B5;H0Y613 Q14687-2 GSE1 Genetic suppressor element 1 1 0 YSPDEMNNS(1)PNFEEK;YSPDEMNNS(1)PNFEEK ; 128.85 5.63E-05 5978400 4191 4475 4590.4 4479.9 3029.3 2561.1 2231.6 2533.6 4638 4907.8 TRUE FALSE FALSE 4139.91848 4537.999167 4670.293986 4997.887117 2874.703517 2397.453976 2421.152048 2606.905719 4223.165664 4780.294648 0.866038348 0.949313693 0.976988728 1.045518631 0.60136534 0.501528494 0.506485944 0.545344149 0.883453003 1 12.22288383 -8.665006152 5.168207031 0.946152505 0.52307447 0.938917036 0.052032423 0.04217432 1.81735959 0.009171876 0.018558246 2.16E-09 8.665006152 -0.423078035 YSPPAIS(ph)PLVSEK ddPTM_HeLa_Romidepsin_16h_R1 2 YSPPAISPLVSEK 13 0 Q14694;Q14694-3;Q14694-2 Q14694 USP10 Ubiquitin carboxyl-terminal hydrolase 10 1 0 YSPPAIS(0.984)PLVS(0.015)EK;Y(0.006)S(0.071)PPAIS(0.921)PLVS(0.002)EK ; 164.93 0.00018907 67333000 4538.4 4679.1 3872.9 3719.1 5530 5982.8 5239.2 5116.8 4430.8 4581.2 TRUE FALSE FALSE 4483.084235 4744.972493 3940.3062 4149.119841 5247.783465 5600.518389 5684.217517 5264.846535 4034.498151 4462.179764 1.004684812 1.063375468 0.88304515 0.929841481 1.176058282 1.255108195 1.273865648 1.179882213 0.904154105 1 12.12353292 -8.630645448 4.843932003 0.993202095 1.236409019 0.817908722 0.058876772 0.062021206 2.393384243 0.007680877 0.015663416 2.34E-09 8.630645448 0.243206924 YSPT(ph)SPTYSPT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 2 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 0 YS(0.009)PT(0.59)S(0.399)PT(0.001)YS(0.005)PT(0.697)S(0.298)PK;YS(0.016)PT(0.931)S(0.053)PTYS(0.001)PT(0.979)S(0.02)PK ; 144.8 0.012278 67789000 6438.5 5947.7 5914 4199.7 5424.4 6142.9 5832.9 6059.3 6316 6110.6 TRUE FALSE FALSE 6360.025086 6031.431877 6016.930689 4685.289074 5147.572627 5750.388515 6328.34638 6234.616286 5751.081141 5951.845731 1.068580298 1.013371675 1.010935256 0.787199347 0.864869968 0.966152144 1.063257797 1.047509725 0.966268516 1 12.53912142 -9.50182555 24.93822646 1.030925423 0.943969075 0.130316261 0.079459985 958.4990443 1135376.173 0.013058532 0.019816913 3.15E-10 9.50182555 -0.086956348 YSPT(ph)SPTYSPTTPK ddPTM_HeLa_Romidepsin_16h_R1 1 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 0 YS(0.009)PT(0.603)S(0.373)PT(0.014)YSPTTPK 203.85 1.88E-16 140590000 4858 4729 4606.7 4168.7 5453 6089 5120.4 6049.3 5449.3 5035.9 TRUE FALSE FALSE 4798.788827 4795.574986 4686.877681 4650.704708 5174.713062 5699.932551 5555.326648 6224.326951 4961.90096 4905.066592 0.978333064 0.977677855 0.955517646 0.948143032 1.05497305 1.162049983 1.132569058 1.268958705 1.01158687 1 12.26005701 -8.241402289 1.635009299 0.982792353 1.207788379 0.876061943 0.035375883 0.093598004 0.468919489 0.00502991 0.018165375 5.74E-09 8.241402289 0.224996026 YSPTS(ph)PTYSPT(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 1 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 2 0 YS(0.039)PT(0.058)S(0.54)PT(0.358)Y(0.005)S(0.237)PT(0.69)T(0.073)PK 98 0.0038789 0 3161.4 2917 2872.5 2437.9 2706.9 3080.4 2749.2 3279.4 3022.9 2742.1 TRUE FALSE FALSE 3122.867641 2958.065603 2922.494658 2719.781469 2568.756792 2883.572382 2982.716979 3374.284265 2752.524253 2670.859847 1.169236808 1.107533069 1.094214907 1.018316806 0.961771467 1.079641968 1.116762822 1.263370023 1.030576073 1 11.38308856 -12.60654254 1.427669133 1.000341801 1.104379717 0.1643444 0.076675468 0.585372961 2.152696051 0.05740239 0.013421407 2.47E-13 12.60654254 0.104037916 YSPTS(ph)PTYSPTTPK ddPTM_HeLa_Romidepsin_16h_R1 3 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 0 YSPT(0.006)S(0.983)PT(0.008)Y(0.001)SPTTPK;YS(0.002)PT(0.1)S(0.866)PT(0.03)YS(0.002)PTTPK;YS(0.001)PT(0.006)S(0.969)PT(0.019)YS(0.004)PT(0.001)TPK ;; 147.7 0.00061725 166430000 11362.7 11012.9 11300.5 9964.2 13336.1 13695 12428.7 13637.6 11564.7 10995 TRUE FALSE FALSE 11224.20704 11167.9399 11497.18046 11116.30769 12655.50905 12819.9337 13484.39347 14032.18244 10530.32427 10709.34831 1.048075636 1.042821614 1.073564901 1.038000386 1.181725412 1.197078788 1.259123625 1.310274167 0.983283386 1 13.38658307 -7.899838607 0.534373415 1.017361682 1.409767282 0.940273228 0.026544885 0.353055403 0.102164486 0.005323894 0.075843791 1.26E-08 7.899838607 0.3924056 YSPTSPTYS(ph)PTSPK ddPTM_HeLa_Romidepsin_16h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 0 YSPT(0.031)S(0.06)PT(0.205)YS(0.703)PTSPK 254.94 1.31E-67 93451000 5538.5 4997.1 5131.2 5633.7 4998.9 5496.1 4777.6 5287.1 5547 4946.2 TRUE FALSE FALSE 5470.994632 5067.449305 5220.506384 6285.094901 4743.78748 5144.916948 5183.409225 5440.073897 5050.862427 4817.697011 1.135603717 1.051840598 1.083610358 1.304584927 0.984658742 1.067920406 1.075910173 1.12918556 1.048397692 1 12.23412795 -12.40688094 1.013545391 0.996990579 1.10508411 0.129176987 0.079588179 0.741739845 1.300503106 0.060324035 0.013688261 3.92E-13 12.40688094 0.108093531 YSPTSPTYSPT(ph)SPK ddPTM_HeLa_Romidepsin_16h_R1 1 YSPTSPTYSPTSPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 0 YSPTSPTYS(0.006)PT(0.993)S(0.001)PK 237.07 8.16E-43 21225000 3136.3 2405.8 2643.7 2852.6 3550.7 3938.8 3296.2 3606.2 2913 2685.3 TRUE FALSE FALSE 3098.073569 2439.668916 2689.71249 3182.431034 3369.49453 3687.123392 3576.179146 3710.539707 2652.453984 2615.535519 1.184489198 0.932760767 1.028360147 1.216741662 1.288261813 1.409701136 1.367283724 1.418653916 1.014115069 1 11.35289065 -8.81585633 1.872357788 1.071951164 1.392200762 0.835657545 0.070398173 0.130240475 0.927870107 0.013408191 0.029392612 1.53E-09 8.81585633 0.320249597 YSPTSPTYSPT(ph)TPK ddPTM_HeLa_Romidepsin_16h_R1 2 YSPTSPTYSPTTPK 14 0 P24928 P24928 POLR2A DNA-directed RNA polymerase II subunit RPB1 1 0 YSPTSPTYS(0.001)PT(0.917)T(0.082)PK;YSPTSPT(0.007)YS(0.016)PT(0.699)T(0.277)PK ; 168.83 0.00014291 17735600 6547.9 6598.1 6815.3 7172.3 11022 11862.4 10308.1 11823.3 7099.6 6127.5 TRUE FALSE FALSE 6468.091676 6690.988225 6933.917438 8001.595073 10459.50621 11104.43092 11183.66976 12165.38853 6464.593995 5968.306667 1.083739834 1.121086532 1.161789738 1.340680954 1.752508173 1.860566413 1.873843015 2.038331676 1.083153791 1 12.54310595 -8.820837892 1.095340877 1.040338757 1.973967193 0.982339151 0.050724469 0.042672708 0.100248816 0.008593419 0.024039075 1.51E-09 8.820837892 0.933628437 YSQSAPGSPVS(ph)AQPVIMAVPPRPSSLVAK ddPTM_HeLa_Romidepsin_16h_R1 2 YSQSAPGSPVSAQPVIMAVPPRPSSLVAK 29 1 P85037-2;P85037 P85037-2 FOXK1 Forkhead box protein K1 1 0 YSQSAPGS(0.039)PVS(0.959)AQPVIMAVPPRPS(0.001)S(0.001)LVAK;YS(0.001)QS(0.005)APGS(0.265)PVS(0.715)AQPVIMAVPPRPS(0.007)S(0.007)LVAK ; 65.056 0.00055161 63549000 6675.5 6233.2 7529.3 5186.3 4430.4 4658.8 4542.8 4399 7328 6118.4 TRUE FALSE FALSE 6594.136438 6320.951153 7660.344308 5785.964408 4204.300156 4361.117716 4928.665319 4526.278125 6672.565327 5959.443086 1.106502125 1.060661384 1.285412781 0.970890119 0.705485411 0.731799541 0.827034548 0.759513609 1.119662564 1 12.5409618 -8.904194671 4.85050371 1.0708045 0.761157998 0.8107835 0.080127795 0.078465852 3.137972495 0.01269312 0.023419951 1.25E-09 8.904194671 -0.309646502 YSS(ph)YQGSR ddPTM_HeLa_Romidepsin_16h_R1 2 YSSYQGSR 8 0 Q5VWV2;Q8TEW0-4;Q8TEW0-11;Q8TEW0-2;Q8TEW0;Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6 Q5VWV2 PARD3 Partitioning defective 3 homolog 1 0 YS(0.155)S(0.844)YQGSR;YS(0.046)S(0.954)YQGSR ; 103.31 0.0035558 2109100 2493.3 2358.9 2623 2634 3031.7 3578.8 3221.8 1762.49 2726.6 3030.1 TRUE FALSE FALSE 2462.910701 2392.108656 2668.652215 2938.555473 2876.981036 3350.12623 3495.459612 1813.484867 2482.726067 2951.377565 0.834495298 0.810505807 0.904205631 0.995655557 0.974792609 1.135105948 1.184348507 0.614453701 0.841209236 1 11.52717278 -9.249220798 7.6973872 0.90851142 1.000548571 0.079564683 0.151539956 0.351737598 142.3531751 0.02275798 0.036890114 5.63E-10 9.249220798 0.092037151 YSSEVAT(ph)ESPLDFTK ddPTM_HeLa_Romidepsin_16h_R1 2 YSSEVATESPLDFTK 15 0 Q8WTT2 Q8WTT2 NOC3L Nucleolar complex protein 3 homolog 1 0 YSS(0.012)EVAT(0.849)ES(0.139)PLDFTK;YSSEVAT(0.765)ES(0.077)PLDFT(0.158)K ; 228.11 1.08E-34 20607000 6500.4 6739.5 5989.5 5798.9 5670.4 6697.8 5030.7 6049.7 6680.4 6169.8 TRUE FALSE FALSE 6421.170624 6834.378858 6093.744735 6469.396103 5381.018329 6269.832196 5458.007532 6224.738525 6082.888293 6009.507707 1.068501937 1.137261019 1.014017293 1.0765268 0.895417494 1.043318771 0.908228727 1.03581505 1.012210748 1 12.5530311 -8.785189109 24.99973062 1.043077677 0.971420479 0.313202806 0.057770579 232.4176384 244649.686 0.008381072 0.015198217 1.64E-09 8.785189109 -0.071657198 SDKNQQGFS(ph)PK ddPTM_HeLa_Romidepsin_16h_R1 1 SDKNQQGFSPK 11 1 D6RCT7;C9JKA9;Q9NS87-4;Q9NS87-2;Q9NS87 D6RCT7 KIF15 Kinesin-like protein;Kinesin-like protein KIF15 1 0 SDKNQQGFS(1)PK 100.18 0.0070521 12220000 5896.8 5193 5581.7 5422.1 4957 4941 4829.7 2257.7 6825.3 6402.9 TRUE FALSE FALSE 5824.927533 5266.10719 5678.847147 6049.028714 4704.025793 4625.286046 5239.934597 2323.022987 6214.828074 6236.551735 0.93399811 0.844394052 0.910574848 0.969931618 0.7542671 0.741641574 0.840197407 0.372485163 0.996516719 1 12.60653285 -6.865843038 0.509237745 0.963995859 1.18E-25 0.743497259 0.090070438 2.121295045 0.27889111 0.01729309 1.330745342 1.36E-07 6.865843038 -0.963995859 down YSSSS(ph)IPEPFGSR ddPTM_HeLa_Romidepsin_16h_R1 2 YSSSSIPEPFGSR 13 0 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 YSS(0.007)S(0.176)S(0.813)IPEPFGS(0.004)R;YSSS(0.041)S(0.958)IPEPFGSR ; 103.14 0.010906 8321200 2388.1 2581.1 2345.2 2039.23 2273.3 2078.43 1711.69 1932.38 2817.8 2297.1 TRUE FALSE FALSE 2358.992919 2617.436794 2386.017222 2275.015367 2157.285018 1945.625031 1857.080906 1988.290367 2565.768911 2237.421011 1.054335732 1.169845452 1.066414059 1.01680254 0.964183767 0.869583785 0.830009594 0.888652764 1.146752845 1 11.12762104 -8.473377196 2.035183518 1.041760381 0.855616929 0.727547089 0.056606992 0.139497812 1.132673158 0.008030829 0.021189075 3.36E-09 8.473377196 -0.186143453 YSSSSIPEPFGS(ph)RGSPR ddPTM_HeLa_Romidepsin_16h_R1 1 YSSSSIPEPFGSRGSPR 17 1 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 YSSSSIPEPFGS(0.862)RGS(0.138)PR 173.19 1.04E-05 21116000 2529.8 2604.5 2499 3074.1 1857.8 1776.1 1228.8 1218.4 2673.2 2714.3 TRUE FALSE FALSE 2498.965825 2641.166219 2542.494047 3429.541906 1762.989534 1662.612942 1333.174241 1253.652482 2434.102297 2643.782095 0.945223825 0.999010556 0.961688201 1.297210505 0.666843738 0.628876694 0.504267823 0.474189036 0.920689455 1 11.36838756 -8.577917199 8.018616488 0.994815916 0.551314654 0.812798321 0.10715907 0.076554247 9.848098683 0.015056092 0.030225651 2.64E-09 8.577917199 -0.443501262 YSSSSIPEPFGSRGS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 1 YSSSSIPEPFGSRGSPR 17 1 Q8WUF5;K7EN03 Q8WUF5 PPP1R13L RelA-associated inhibitor 1 0 YSSSSIPEPFGS(0.083)RGS(0.917)PR 191.93 1.55E-12 27889000 3114.2 2820 2549.1 3342.1 2045.5 1485.5 1229.9 1473.5 3066.2 2637.6 TRUE FALSE FALSE 3076.242933 2859.700034 2593.466016 3728.529327 1941.110502 1390.581344 1334.367675 1516.133398 2791.951393 2569.074772 1.197412768 1.113124486 1.009494175 1.45131211 0.755567928 0.541277101 0.519396201 0.590147634 1.086753653 1 11.32703316 -8.557266947 7.403350463 1.112711447 0.563017505 0.830108922 0.122139996 0.061312797 10.45174568 0.018631277 0.037653254 2.77E-09 8.557266947 -0.549693942 YSVGSLS(ph)PVSASVLK ddPTM_HeLa_Romidepsin_16h_R1 1 YSVGSLSPVSASVLK 15 0 Q9UBU7 Q9UBU7 DBF4 Protein DBF4 homolog A 1 0 YS(0.001)VGS(0.001)LS(0.978)PVS(0.019)ASVLK 144.18 0.00048198 16577000 1315.2 1199.6 1502.7 1439.5 1230.5 1065.7 820.15 980.26 1699.9 1268.3 TRUE FALSE FALSE 1299.169837 1216.488 1528.853863 1605.941763 1167.702993 997.6052094 889.8135205 1008.622277 1547.856687 1235.349383 1.051661865 0.984731945 1.237588235 1.299989934 0.945241087 0.807549041 0.720293006 0.81646722 1.252970785 1 10.27070341 -8.365264548 3.570255497 1.058236633 0.77315549 0.599006058 0.120804283 0.137782216 3.234403609 0.016509432 0.039649764 4.31E-09 8.365264548 -0.285081143 YSVGSLS(ph)PVSASVLKK ddPTM_HeLa_Romidepsin_16h_R1 1 YSVGSLSPVSASVLKK 16 1 Q9UBU7 Q9UBU7 DBF4 Protein DBF4 homolog A 1 0 YSVGS(0.016)LS(0.979)PVS(0.003)AS(0.001)VLKK 91.622 0.0033734 10916000 1670.9 1560.7 1576.4 2105.5 1250.4 1169.6 1031.5 956.89 1687.3 1386.2 TRUE FALSE FALSE 1650.534428 1582.671576 1603.836581 2348.947817 1186.587422 1094.866335 1119.115584 984.5761024 1536.383662 1350.186324 1.222449375 1.172187532 1.18786315 1.739721233 0.878832351 0.810900181 0.828860109 0.729214987 1.137904921 1 10.3989428 -8.54578965 24.99835271 1.165640181 0.802126165 0.530803616 0.191741156 169.5298756 184975.351 0.030036075 0.060074895 2.85E-09 8.54578965 -0.363514016 YSVLNNDDYFADVS(ph)PLR ddPTM_HeLa_Romidepsin_16h_R1 5 YSVLNNDDYFADVSPLR 17 0 Q1ED39;H3BMC9 Q1ED39 KNOP1 Lysine-rich nucleolar protein 1 1 0 YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR;YSVLNNDDYFADVS(1)PLR ;;;; 266.39 5.79E-87 157616000 8743.27 8813.07 9044.62 6868.64 8864.32 10057.25 8224.01 9052 9593.32 10210.45 TRUE FALSE FALSE 8636.703662 8937.140631 9202.037817 7662.824475 8411.940673 9414.624183 8922.557204 9313.905338 8735.269432 9945.181037 0.868431015 0.898640316 0.925276049 0.770506283 0.845830824 0.946651866 0.897173935 0.936524464 0.878341923 1 13.27978192 -12.27996039 0.824648514 1.006246831 0.883780895 0 0.061037825 0.545201134 0.611014842 0.043811719 0.009737408 5.25E-13 12.27996039 -0.122465936 YT(ph)AGSAS(ph)PT(ph)PTFKT(ph)RK ddPTM_HeLa_Romidepsin_16h_R1 1 YTAGSASPTPTFKTRK 16 2 H7C0G8;H7C070;Q2LD37-2;Q2LD37-6;Q2LD37-7;Q2LD37-4;Q2LD37 H7C0G8 KIAA1109 Uncharacterized protein KIAA1109 4 0 Y(0.415)T(0.593)AGS(0.405)AS(0.588)PT(0.93)PT(0.186)FKT(0.882)RK 46.415 0.0287 35531000 3524.1 1714.8 2163.3 2070.5 2970 2188.8 3835.9 2627.9 4359.5 3409.6 TRUE FALSE FALSE 3481.146914 1738.940999 2200.951329 2309.900952 2818.429817 2048.942744 4161.72125 2703.93414 3969.575401 3321.0181 1.048216784 0.523616839 0.662733915 0.695540007 0.848664395 0.616962233 1.253146211 0.814188318 1.195288698 1 11.69740987 -10.33091349 24.99903925 1.022769204 0.78159838 0.334537658 0.193401355 162.7939411 58577.9214 0.03185199 0.036424135 4.67E-11 10.33091349 -0.241170824 YTGEDFDEDLR ddPTM_HeLa_Romidepsin_16h_R1 2 YTGEDFDEDLR 11 0 Q14204;A0A2R8YFZ7;A0A2R8Y706;A0A2R8Y6H2 Q14204 DYNC1H1 Cytoplasmic dynein 1 heavy chain 1 0 0 ; ; 221.68 4.24E-26 41988000 4108.9 4474.7 5063.9 4744.6 4708.6 4728.9 4096.5 4678.2 4984.1 4102.5 FALSE FALSE TRUE 4058.819146 4537.694944 5152.035055 5293.192976 4468.302572 4426.738552 4444.456608 4813.556336 4538.309613 3995.916459 1.015741742 1.135583036 1.289325017 1.32465056 1.118217215 1.107815591 1.112249631 1.204618862 1.13573686 1 11.96431071 -10.17984602 3.59305626 1.006854192 1.189203716 0.351151262 0.079633492 0.13176542 3.259657558 0.012639497 0.015470365 6.61E-11 10.17984602 0.182349525 YTLENKEEGSLS(ph)DTEADAVSGQLPDPTTNPSAGK ddPTM_HeLa_Romidepsin_16h_R1 1 YTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 34 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 0 YTLENKEEGS(0.034)LS(0.931)DT(0.034)EADAVSGQLPDPTTNPSAGK 82.151 1.09E-08 43873000 4446.7 4130.9 4510.4 3999.5 4799.3 4825.7 4020.6 4562.8 5222.1 4641.8 TRUE FALSE FALSE 4392.50191 4189.054919 4588.90162 4461.941008 4554.373812 4517.353344 4362.109664 4694.817419 4755.022297 4521.205367 0.971533375 0.926534979 1.014973054 0.986891912 1.007336195 0.99914801 0.96481122 1.038399506 1.051715618 1 12.14249174 YTLENKEEGSLSDT(ph)EADAVSGQLPDPTTNPSAGK ddPTM_HeLa_Romidepsin_16h_R1 1 YTLENKEEGSLSDTEADAVSGQLPDPTTNPSAGK 34 1 Q8N1G4 Q8N1G4 LRRC47 Leucine-rich repeat-containing protein 47 1 0 YTLENKEEGSLS(0.077)DT(0.908)EADAVS(0.015)GQLPDPTTNPSAGK 91.123 4.39E-12 41815000 6458.8 7090.6 5779.1 5652.3 7018.2 7620.2 6887.7 6964.5 7076.6 6740.6 TRUE FALSE FALSE 6380.077661 7190.421653 5879.682811 6305.845521 6660.035065 7133.293813 7472.741066 7166.006819 6443.651172 6565.47824 0.971761299 1.095186274 0.895545244 0.960454866 1.014402123 1.086485029 1.138186861 1.091467606 0.981444296 1 12.68068439 -8.260476134 2.805892552 0.98624212 1.114296594 0.569532346 0.047451258 0.141841645 2.220088261 0.006582796 0.018074167 5.49E-09 8.260476134 0.128054474 YTQVGPDHNR ddPTM_HeLa_Romidepsin_16h_R1 1 YTQVGPDHNR 10 0 Q08211 Q08211 DHX9 ATP-dependent RNA helicase A 0 0 88.155 0.01949 2681100 2264.6 2354.3 2222.5 2242.5 1705.8 2250.7 2268.9 1242.6 2202.3 2036.3 FALSE FALSE TRUE 2236.998184 2387.443897 2261.18168 2501.788401 1618.746661 2106.887534 2461.620309 1278.552671 2005.320772 1983.396632 1.127862248 1.203714808 1.140055218 1.261365659 0.816148739 1.062262333 1.241113486 0.644627832 1.011053835 1 10.9537575 -7.248022449 24.53060406 1.082650798 0.644627456 0.531111013 0.126665545 1090.550588 1993845.356 0.017240922 0.443253809 5.65E-08 7.248022449 -0.438023342 YTVPLPSPVQDS(ph)ENLSGESGTFYEGTDDK ddPTM_HeLa_Romidepsin_16h_R1 1 YTVPLPSPVQDSENLSGESGTFYEGTDDK 29 0 A0A669KB77;P11137-3;P11137 A0A669KB77 MAP2 Microtubule-associated protein 2 1 0 Y(0.003)T(0.004)VPLPS(0.361)PVQDS(0.566)ENLS(0.065)GESGTFYEGTDDK 74.525 6.08E-06 0 1451 1309.7 1664.2 1690.1 1984.4 2597.3 1802.9 2166.1 1830.2 1430.8 TRUE FALSE FALSE 1433.314654 1328.137991 1693.164703 1885.517314 1883.128663 2431.340912 1956.038281 2228.772686 1666.502328 1393.62761 1.02847751 0.953007806 1.21493338 1.352956343 1.351242362 1.744613048 1.40355879 1.599259853 1.195801745 1 10.4446294 -9.13969434 1.166248303 1.006812857 1.558218752 0.77927755 0.115383841 0.110488715 0.296580808 0.015311494 0.032961056 7.25E-10 9.13969434 0.551405895 YTYLEK(ac)AIK ddPTM_HeLa_Romidepsin_16h_R1 1 YTYLEKAIK 9 1 Q93009;A0A669KBL1;Q93009-3 Q93009 USP7 Ubiquitin carboxyl-terminal hydrolase 7 0 1 YTYLEK(1)AIK 102.06 0.025103 190430 0 0 163.93 0 0 0 0 0 0 0 FALSE TRUE FALSE 0 0 166.7831329 0 0 0 0 0 0 0 0 YVAEIEK(ac)EKEENEK ddPTM_HeLa_Romidepsin_16h_R1 1 YVAEIEKEKEENEK 14 2 O14818;O14818-2;H0Y586 O14818 PSMA7 Proteasome subunit alpha type-7 0 1 YVAEIEK(0.999)EK(0.001)EENEK 110.55 2.64E-05 0 0 0 0 0 0 62.369 0 176.86 130.61 0 FALSE TRUE FALSE 0 0 0 0 0 58.38382219 0 181.9771651 118.9279145 0 0 YVASVLGLTPS(ph)PR ddPTM_HeLa_Romidepsin_16h_R1 2 YVASVLGLTPSPR 13 0 Q99666;O14715;F8W705;Q99666-2;C9J1W9;C9JF75 Q99666 RGPD5;RGPD8;RGPD6 RANBP2-like and GRIP domain-containing protein 5/6;RANBP2-like and GRIP domain-containing protein 8 1 0 YVASVLGLT(0.027)PS(0.973)PR;YVASVLGLT(0.021)PS(0.979)PR ; 137.95 0.0013607 24576000 3381.9 2939.3 2889.9 3302.9 2708.3 2883 2372.5 2419.7 3572.2 2800.6 TRUE FALSE FALSE 3340.680102 2980.679543 2940.197497 3684.796839 2570.085345 2698.785604 2574.020091 2489.710202 3252.693485 2727.840008 1.224661304 1.09268855 1.07784822 1.350811201 0.942168653 0.989348934 0.943611093 0.912703895 1.192406254 1 11.41354332 YVASYLLAALGGNS(ph)SPSAK ddPTM_HeLa_Romidepsin_16h_R1 1 YVASYLLAALGGNSSPSAK 19 0 P05387 P05387 RPLP2 60S acidic ribosomal protein P2 1 0 YVASYLLAALGGNS(0.973)S(0.027)PSAK 193.54 4.87E-15 205090000 8168.7 8033.9 8180.2 7246.7 9524.1 9385.4 9087.5 8997.5 9149.3 7659.5 TRUE FALSE FALSE 8069.136742 8147.001455 8322.57295 8084.597551 9038.049638 8785.70323 9859.392023 9257.828467 8330.963693 7460.505086 1.081580489 1.092017412 1.115550871 1.083652844 1.211452782 1.177628475 1.321544843 1.240911756 1.11667556 1 12.86505759 -4.809590221 0.177368003 0.980642892 2.054509627 0.673439636 0.050832758 10.24794238 0.142374187 0.049497878 2.80427402 1.55E-05 4.809590221 1.073866735 YVATLGVEVHPLVFHTNR ddPTM_HeLa_Romidepsin_16h_R1 1 YVATLGVEVHPLVFHTNR 18 0 F5H018;B5MDF5;J3KQE5;P62826;H0YFC6 F5H018 RAN GTP-binding nuclear protein Ran 0 0 71.08 0.0083428 594570 67.934 188.89 115.58 154.84 147.35 156.29 121.43 152.73 0 0 FALSE FALSE TRUE 67.10599428 191.5491984 117.5916214 172.7433293 139.8301797 146.3035734 131.7442612 157.1490016 0 0 0 YVDEENS(ph)DGETSNHR ddPTM_HeLa_Romidepsin_16h_R1 2 YVDEENSDGETSNHR 15 0 A0A494C108;Q8N9T8;F8WFC1;H0YFD2;H0YH26 A0A494C108 KRI1 Protein KRI1 homolog 1 0 YVDEENS(1)DGETSNHR;YVDEENS(1)DGETSNHR ; 223.76 5.27E-35 29188000 8883.4 8137.8 7506.3 7912.6 13087 13999.5 11271.2 11312.2 14235.1 11191.6 TRUE FALSE FALSE 8775.125704 8252.364162 7636.944003 8827.492042 12419.12156 13104.97713 12228.57545 11639.50066 12961.877 10900.84062 0.804995322 0.757039246 0.700583035 0.809799203 1.139281088 1.202198765 1.121801141 1.06776175 1.189071326 1 13.41215177 -8.753816763 24.98003906 0.869787551 1.136937792 0.469176075 0.133159809 100.6921126 329974.8124 0.017068651 0.033619493 1.76E-09 8.753816763 0.267150241 YVGFGNT(ph)PPPQK ddPTM_HeLa_Romidepsin_16h_R1 1 YVGFGNTPPPQK 12 0 F8VWH9;Q8N6T3-5;Q8N6T3;Q8N6T3-2;Q8N6T3-4;E5RHT6;E5RHC5;F8W1U7;Q8N6T3-3 F8VWH9 ARFGAP1 ADP-ribosylation factor GTPase-activating protein 1 1 0 YVGFGNT(1)PPPQK 122.34 0.01391 16420000 3952.1 3820.5 3989.6 2740.4 4370.1 4933.7 4468.9 4843.1 3584.3 3512.9 TRUE FALSE FALSE 3903.930285 3874.285099 4059.037314 3057.257942 4147.07749 4618.452493 4848.488254 4983.227457 3263.711231 3421.634352 1.140954843 1.132290801 1.186286113 0.893508081 1.212016558 1.349779672 1.417009463 1.456388072 0.953845705 1 11.74046988 -8.324076082 2.551151563 1.072434397 1.423429989 0.758917838 0.089402965 0.105704567 1.337172595 0.012806978 0.03451879 4.74E-09 8.324076082 0.350995592 YVIS(ph)DEEEEDDD ddPTM_HeLa_Romidepsin_16h_R1 1 YVISDEEEEDDD 12 0 Q8WVC0-2;Q8WVC0 Q8WVC0-2 LEO1 RNA polymerase-associated protein LEO1 1 0 YVIS(1)DEEEEDDD 118.28 0.0080549 2183700 1948.3 1837 1473.1 1592.9 1722.4 1554.8 2048.7 1557.8 1765.3 1865.8 TRUE FALSE FALSE 1924.55337 1862.861334 1498.738688 1777.078593 1634.499501 1455.453298 2222.716527 1602.872485 1607.407147 1817.326247 1.059002682 1.025056088 0.82469435 0.977853369 0.89939795 0.800876177 1.223069622 0.881994902 0.88449014 1 10.82760172 -9.94501064 24.99997426 1.028608516 0.940608491 0.016720446 0.119070945 136.6619403 62130.57361 0.016982447 0.022319307 1.13E-10 9.94501064 -0.088000025 YVLGQLVGLNS(ph)PNSILK ddPTM_HeLa_Romidepsin_16h_R1 1 YVLGQLVGLNSPNSILK 17 0 P33981-2;P33981 P33981-2 TTK Dual specificity protein kinase TTK 1 0 Y(0.385)VLGQLVGLNS(0.579)PNS(0.036)ILK 136.26 0.001299 51606000 4260.5 3820.5 4342.4 4127.9 4241.4 4285.9 3473.6 3570.7 4197.7 4147.8 TRUE FALSE FALSE 4208.571387 3874.285099 4417.97765 4605.18722 4024.945531 4012.044822 3768.647497 3674.012571 3822.247199 4040.039558 1.041715391 0.95897207 1.093548117 1.139886666 0.996263891 0.993070678 0.932824405 0.909400148 0.946091528 1 11.9801537 -7.84273004 1.923316115 1.028899137 0.910121484 0.363812617 0.054924323 0.276680668 1.903490641 0.007390992 0.038849322 1.44E-08 7.84273004 -0.118777653 YWEEETVPTTAGAS(ph)PGPPR ddPTM_HeLa_Romidepsin_16h_R1 1 YWEEETVPTTAGASPGPPR 19 0 O15213 O15213 WDR46 WD repeat-containing protein 46 1 0 YWEEETVPTTAGAS(1)PGPPR 185.63 1.09E-15 0 706.33 346.15 652.98 532.81 750.32 683.39 543.9 528.92 757.77 639.46 TRUE FALSE FALSE 697.7209783 351.0231088 664.344843 594.4159991 712.0283706 639.7235845 590.0988524 544.2234657 689.9931533 622.846737 1.120212946 0.563578627 1.066626513 0.954353557 1.143183914 1.027096309 0.947422243 0.873767868 1.10780568 1 9.282733395 YWGPAS(ph)PTHK ddPTM_HeLa_Romidepsin_16h_R1 2 YWGPASPTHK 10 0 A0A3B3ISQ4;Q9H6S3-2;Q9H6S3;Q9H6S3-3 A0A3B3ISQ4 EPS8L2 Epidermal growth factor receptor kinase substrate 8-like protein 2 1 0 Y(0.003)WGPAS(0.499)PT(0.499)HK;YWGPAS(0.938)PT(0.062)HK ; 113.44 0.015927 87005000 7053.2 6353.7 7432.4 6187 8718.5 8669.7 7411.3 8933.8 8038.4 6664.3 TRUE FALSE FALSE 6967.232885 6443.147555 7561.757804 6902.370051 8273.562412 8115.73415 8040.815637 9192.285408 7319.425371 6491.160525 1.07334164 0.99260333 1.164931567 1.063349154 1.274589094 1.250274757 1.238733137 1.416123569 1.127598885 1 12.66426072 -4.000000968 0.239045675 0.998638921 3.402906933 0.726695113 0.067076685 12.83849358 0.158167614 0.032080127 12.36624036 1.00E-04 4.000000968 2.404268012 YWPQEAGEYAVHVLCNSEDIR ddPTM_HeLa_Romidepsin_16h_R1 1 YWPQEAGEYAVHVLCNSEDIR 21 0 Q60FE5;P21333-2;P21333;A0A087WWY3 Q60FE5 FLNA Filamin-A 0 0 106 0.00015373 17615000 705.24 577.8 824.97 239.19 703.96 773.84 614.75 818.27 732.96 554.36 FALSE FALSE TRUE 696.6442636 585.9342836 839.3282568 266.8462732 668.0342944 724.3941215 666.9668497 841.9453514 667.4022219 539.9576473 1.29018316 1.085148597 1.554433502 0.494198526 1.23719758 1.341575816 1.235220675 1.559280354 1.236026983 1 9.076702441 -7.036847941 1.031628782 1.130569668 1.913163306 0.1866769 0.261074215 3.421546247 2.09631277 0.038306692 3.276747512 9.19E-08 7.036847941 0.782593638 YY(ph)RAPEVILGMGY(ph)K ddPTM_HeLa_Romidepsin_16h_R1 1 YYRAPEVILGMGYK 14 1 A0A1W2PPZ3;A0A286YFI3;A0A286YEN5;A0A1W2PRF2;A0A286YEQ7;A0A286YEX7;A0A286YFC0;A0A286YFJ6;A0A1P0B7D2;A0A286YFJ4;A0A286YFD7;A0A286YES9;A0A286YF85;D6RCB1;A0A286YF97;A0A286YFA6;A0A286YF62;F8W9R5;D6RJF9;A0A286YEQ0;A0A286YEW9;A0A286YFN2;A0A286YF83;A0A286YEY0;J3KNK1;A0A286YEV3;P45983-4;A0A286YEV8;A0A286YES0;A0A286YFB6;D7R525;A0A286YFM6;A0A286YF35;A0A286YF19;A0A286YFE2;A0A286YF02;P53779;P45983-3;P45984-5;P45984-3;P45983;P45983-5;P53779-3;P45984-2;P45984;P53779-2;P45983-2;P45984-4 A0A1W2PPZ3 MAPK10;MAPK9;MAPK8 Mitogen-activated protein kinase 8;Mitogen-activated protein kinase 10;Mitogen-activated protein kinase 9 2 0 Y(0.274)Y(0.726)RAPEVILGMGY(0.999)K 43.305 0.02962 3353400 1573.7 1777.8 1456.6 1454.8 1618.4 1641.5 1638.4 1936.8 1626.6 1392.1 TRUE FALSE FALSE 1554.519139 1802.827915 1481.951512 1623.010821 1535.807009 1536.613448 1777.565655 1992.838252 1481.112822 1355.933041 1.146457157 1.329584766 1.092938565 1.196969741 1.132656969 1.133251717 1.310953861 1.469717303 1.092320031 1 10.40507022 -4 0.102661449 0.899478225 2.194903447 0.482130344 0.095434278 70.47999634 0.513621162 0.728964567 12.934073 1.00E-04 4 1.295425222 YY(ph)RGS(ph)ALQKRLR ddPTM_HeLa_Romidepsin_16h_R1 1 YYRGSALQKRLR 12 3 P49756 P49756 RBM25 RNA-binding protein 25 2 0 Y(0.003)Y(0.997)RGS(1)ALQKRLR 89.886 0.014751 178880000 1132.7 1271.1 1497 1389.9 1787.4 1564.1 1475.1 1098.3 1409.1 1091.3 TRUE FALSE FALSE 1118.894217 1288.994579 1523.054657 1550.606778 1696.182308 1464.159058 1600.394957 1130.077578 1283.066567 1062.947869 1.0526332 1.212660204 1.432859223 1.458779704 1.595734239 1.377451426 1.505619423 1.063154282 1.207083249 1 10.05385513 -10.02331716 2.234639805 1.022522289 1.421389458 0.486695202 0.143516681 0.128208049 1.268520922 0.021569601 0.027911856 9.48E-11 10.02331716 0.398867169 YYDDIY(ph)FDS(ph)DSEDEDR ddPTM_HeLa_Romidepsin_16h_R1 1 YYDDIYFDSDSEDEDR 16 0 G3V2W9;A0A087X060;Q56P03 G3V2W9 EAPP E2F-associated phosphoprotein 2 0 YYDDIY(0.975)FDS(0.947)DS(0.078)EDEDR 129.17 0.0048644 2311200 1537.3 1395.5 1416.9 843.6 1646.6 1924.6 1447.3 1890.9 1719.9 1532.5 TRUE FALSE FALSE 1518.562796 1415.145886 1441.56055 941.1410013 1562.567858 1801.624271 1570.233626 1945.610208 1566.067836 1492.685429 1.017336116 0.948053661 0.96574973 0.630501901 1.046816581 1.206968485 1.051952136 1.30342949 1.049161334 1 10.54369445 -8.515073393 24.99614235 0.970721766 1.166065661 0.428087429 0.126108984 317.7871308 1017692.029 0.018233563 0.037825473 3.05E-09 8.515073393 0.195343895 YYDILK(ac)K ddPTM_HeLa_Romidepsin_16h_R1 2 YYDILKK 7 1 O43143 O43143 DHX15 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 0 1 ; YYDILK(1)K;YYDILK(1)K 103.92 0.0087847 1118320 1307.49 1105.61 1149.21 1104.19 1714.15 1398.91 1320.77 1573.27 1772.13 1410.14 FALSE TRUE FALSE 1291.553809 1121.174807 1169.211518 1231.861643 1626.670529 1309.524166 1432.956171 1618.790085 1613.626254 1373.50436 0.940334699 0.816287767 0.851261599 0.896874942 1.184321344 0.953418281 1.043284763 1.178583871 1.174824268 1 10.42364577 -6.325313375 0.675418627 0.952153063 1.790716732 0.217915553 0.115437322 8.088420699 1.022558178 0.016330133 7.010954791 4.73E-07 6.325313375 0.838563669 YYDSRPGGYGYGYGR ddPTM_HeLa_Romidepsin_16h_R1 2 YYDSRPGGYGYGYGR 15 1 P98179 P98179 RBM3 RNA-binding protein 3 0 0 ; ; 138.89 0.0010838 141532000 5257.1 4644.8 4662.9 3754.4 5159 5054.1 4292.8 3979.1 4619.2 3937.1 FALSE FALSE TRUE 5193.024443 4710.189616 4744.055819 4188.501393 4895.716979 4731.159321 4657.430325 4094.228981 4206.047183 3834.813574 1.354179113 1.228270821 1.237102072 1.092230773 1.276650581 1.233739067 1.21451284 1.067647462 1.096806168 1 11.90494073 -12.55433222 1.339104607 1.00060608 1.231044624 0.348377269 0.084276306 0.291513711 0.940545793 0.060156856 0.014374541 2.79E-13 12.55433222 0.230438544 YYEDLDEVSS(ph)TSSVSQSLESEDAR ddPTM_HeLa_Romidepsin_16h_R1 2 YYEDLDEVSSTSSVSQSLESEDAR 24 0 A0A494C1F2;P35658-2;P35658-4;P35658;P35658-3;P35658-5;A0A0A0MSW3 A0A494C1F2 NUP214 Nuclear pore complex protein Nup214 1 0 YYEDLDEVS(0.034)S(0.888)T(0.077)S(0.001)SVSQSLESEDAR;YYEDLDEVS(0.176)S(0.782)T(0.04)S(0.001)SVSQSLESEDAR ; 156.61 4.34E-10 6327700 2407.79 2687.2 2864.8 2381.26 2814.2 2126.47 1788.84 2086.93 3031.2 2480.3 TRUE FALSE FALSE 2378.442929 2725.030472 2914.660642 2656.592485 2670.580873 1990.59543 1940.784025 2147.312027 2760.08188 2415.861448 0.984511314 1.12797465 1.20646846 1.099646044 1.105436272 0.823969202 0.803350716 0.888839063 1.142483515 1 11.238322 -8.250463625 24.68291469 1.034112867 0.835182742 0.624679513 0.082027032 395.5852877 889613.0199 0.012908273 0.032553684 5.62E-09 8.250463625 -0.198930125 YYGGGS(ph)EGGRAPK ddPTM_HeLa_Romidepsin_16h_R1 1 YYGGGSEGGRAPK 13 1 P14866 P14866 HNRNPL Heterogeneous nuclear ribonucleoprotein L 1 0 YYGGGS(1)EGGRAPK 149.41 0.0050776 2191300 677.62 910.05 1035.3 709.34 810.92 754.31 673.08 740.55 960.89 652.21 TRUE FALSE FALSE 669.3609068 922.8617078 1053.318962 791.3572283 769.5357264 706.1120254 730.2513984 761.9766459 874.9455918 635.2654902 1.05367113 1.45271815 1.658076786 1.24571103 1.211360822 1.11152272 1.149521593 1.199461733 1.377291235 1 9.311215839 -10.39422981 6.952246909 1.023568898 1.286632356 0.006284691 0.188624288 0.209872297 11.0016826 0.028803523 0.032820591 4.03E-11 10.39422981 0.263063458 YYITIIDAPGHR ddPTM_HeLa_Romidepsin_16h_R1 3 YYITIIDAPGHR 12 0 A0A2R8Y488;A0A2U3TZH3;Q05639;A0A2R8Y660;A0A2R8YDN5 A0A2R8Y488 EEF1A2 Elongation factor 1-alpha 2 0 0 ;; ;; 118.77 0.0013198 8552400 4123.22 3763.52 4334.01 3790.67 4179.74 3982.34 3795.61 3962.33 4445.34 4395.48 FALSE FALSE TRUE 4072.964609 3816.502933 4409.441626 4228.965101 3966.432271 3727.881326 4118.009019 4076.973767 4047.737657 4281.284796 0.951341666 0.891438695 1.029934199 0.987779441 0.926458402 0.870738926 0.961862902 0.952278104 0.945449287 1 12.06382809 -16.5228787 0.1667073 1.221267827 0.930763149 0 0.045878301 76.73123283 0.841039885 5.498152531 0.075591075 3.00E-17 16.5228787 -0.290504678 YYK(ac)VDENGK ddPTM_HeLa_Romidepsin_16h_R1 2 YYKVDENGK 9 1 P62979;A0A2R8Y422 P62979 RPS27A Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a 0 1 ; YYK(1)VDENGK;YYK(1)VDENGK 145.9 0.018996 4118000 2669.5 2668.2 2465.1 2046.63 3744.9 3158.9 3611.4 3140.7 4200.2 3285.9 FALSE TRUE FALSE 2636.963107 2705.76299 2508.004031 2283.27099 3553.783779 2957.056485 3918.152226 3231.571199 3824.523592 3200.531844 0.823914035 0.845410426 0.783621021 0.713403616 1.110372885 0.923926594 1.224219104 1.009698187 1.194965018 1 11.64409595 -8.730787843 24.9998821 0.885141387 1.06805694 0.259754175 0.143062028 174.5346579 142352.5485 0.017156488 0.034309782 1.86E-09 8.730787843 0.182915554 YYLHDDR ddPTM_HeLa_Romidepsin_16h_R1 4 YYLHDDR 7 0 Q9Y2W1;A0A3B3ITZ9 Q9Y2W1 THRAP3 Thyroid hormone receptor-associated protein 3 0 0 ;;; ;;; 91.626 0.020262 28290500 13183.5 14110.4 15157.1 9750.1 13822.1 16234.3 12871.7 11803.8 12885.7 11508.8 FALSE FALSE TRUE 13022.81443 14309.04658 15420.90297 10877.45244 13116.70666 15196.98062 13965.02188 12145.32433 11733.17072 11209.79972 1.1617348 1.27647656 1.375662666 0.970352077 1.170110706 1.355687078 1.245786921 1.083455961 1.046688702 1 13.45247288 -11.56349104 0.77608274 1.009678976 1.211453907 0.279705175 0.11554856 0.540323089 0.664927012 0.055140115 0.025674094 2.73E-12 11.56349104 0.201774931 YYS(ph)DSDDELTVEQR ddPTM_HeLa_Romidepsin_16h_R1 2 YYSDSDDELTVEQR 14 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 Y(0.006)YS(0.731)DS(0.262)DDELT(0.001)VEQR;YYS(0.48)DS(0.48)DDELT(0.04)VEQR ; 198.38 5.23E-14 11117000 1363.02 1191.5 1045.37 885.42 1481.6 1465.45 1376.09 1510.09 1310.06 1271.85 TRUE FALSE FALSE 1346.406988 1208.273968 1063.564226 987.7964264 1405.988423 1371.812475 1492.97505 1553.782072 1192.884952 1238.807154 1.086857615 0.975352753 0.858538977 0.797377076 1.134953426 1.107365638 1.20517148 1.254256619 0.962930307 1 10.2747359 -8.043348494 1.730695193 1.007996048 1.237447081 0.537659592 0.094320696 0.298114836 1.662078622 0.01569782 0.067875262 9.05E-09 8.043348494 0.229451033 YYSDS(ph)DDELTVEQR ddPTM_HeLa_Romidepsin_16h_R1 1 YYSDSDDELTVEQR 14 0 Q8NFC6 Q8NFC6 BOD1L1 Biorientation of chromosomes in cell division protein 1-like 1 1 0 YYS(0.017)DS(0.891)DDELT(0.092)VEQR 263.83 4.53E-77 0 1823.4 1538.4 1353.6 1657.5 1712.8 1823.4 1406.5 1556.9 1774.4 1915.8 TRUE FALSE FALSE 1801.175699 1560.057636 1377.15884 1849.147949 1625.389425 1706.890625 1525.968075 1601.946445 1615.69322 1866.02724 0.965246198 0.836031545 0.738016472 0.990954424 0.87104271 0.914719029 0.817763022 0.858479668 0.865846535 1 10.86575433 -10.35993952 4.643027872 0.98487379 0.862237108 0.154380589 0.072147331 0.14845535 5.266522649 0.010591133 0.012061578 4.37E-11 10.35993952 -0.122636682 YYTVFDRDNNR ddPTM_HeLa_Romidepsin_16h_R1 1 YYTVFDRDNNR 11 1 H7C1V0;H7C469;A0A1B0GW44;A0A1B0GVP3;A0A1B0GV23;A0A1B0GVD5;A0A1B0GWE8;P07339 H7C1V0 CTSD Cathepsin D;Cathepsin D light chain;Cathepsin D heavy chain 0 0 106.62 0.018358 29565000 1761.8 1459.3 1789 2002.4 2308.6 2347.4 1472.1 1258.5 1662 1175 FALSE FALSE TRUE 1740.326504 1479.844064 1820.136795 2233.92691 2190.783527 2197.408716 1597.140137 1294.912712 1513.346557 1144.473331 1.520635263 1.293034992 1.59037065 1.951925702 1.914228553 1.920017406 1.39552412 1.131448569 1.322308277 1 10.16046813 -11.7462932 0.505311229 0.949162848 1.649221411 0.266751007 0.275061195 0.863923639 0.401001374 0.284303107 0.081729226 1.79E-12 11.7462932 0.700058563 YYVTIIDAPGHR ddPTM_HeLa_Romidepsin_16h_R1 3 YYVTIIDAPGHR 12 0 Q5VTE0;P68104;A0A087WVQ9;A0A087WV01;A6PW80;Q5JR01 Q5VTE0 EEF1A1P5;EEF1A1 Putative elongation factor 1-alpha-like 3;Elongation factor 1-alpha 1;Elongation factor 1-alpha 0 0 ;; ;; 136.96 0.00016076 444203000 15838.3 14015.9 14110.5 13267.8 14100.2 13472.7 13459.5 13382.3 16741.1 14911.6 FALSE FALSE TRUE 15645.25671 14213.21621 14356.08733 14801.88546 13380.61418 12611.83795 14602.74959 13769.49574 15243.73409 14524.19448 1.077185845 0.978588949 0.988425716 1.0191192 0.921263771 0.86833304 1.005408569 0.948038513 1.049540758 1 13.82617053 -9.26504318 1.202081409 1.033662989 0.939406393 0.442360811 0.043259052 0.333300851 0.950192466 0.008303017 0.016402133 5.43E-10 9.26504318 -0.094256597