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Yew Low"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Phospho proteome","Melanoma","Braf","Whole proteome"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD000497"],"sample_protocol":["Not available"],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The raw MS data were processed and analyzed using MaxQuant software version 1.3.0.5. Protein and peptide false discovery rates were set at 1% and a minimum peptide length of 6 amino acids was required. In addition, Andromeda minimum score was set to 60 (~ Mascot score 20 (PMID: 21254760)). Enzyme specificity was set to trypsin/P allowing up to two missed cleavages. The search included cysteine carbamidomethylation as a fixed modification; oxidation of methionine and phosphorylation of STY as variable modifications. Peptide identification was based on a search with an mass deviation of the precursor ion of up to 6 ppm, and the allowed fragment mass deviation were set to 0.05 Da for FTMS and 0.6 Da for ITMS."],"omics_type":["Proteomics","Multiomics"],"labhead":["Teck Yew Low"],"instrument_platform":[""],"labhead_affiliation":["Utrecht Univeristy"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["lowteckyew@gmail.com"],"publication":["25538140 Smit MA, Maddalo G, Greig K, Raaijmakers LM, Possik PA, van Breukelen B, Cappadona S, Heck AJ, Altelaar AM, Peeper DS. ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Mol Syst Biol. 2014 Dec 23;10(12):772 10.15252/msb.20145450"],"submitter_affiliation":["Utrecht Univeristy"],"submitter_country":["Netherlands"],"pubmed_abstract":["Treatment of BRAF mutant melanomas with specific BRAF inhibitors leads to tumor remission. However, most patients eventually relapse due to drug resistance. Therefore, we designed an integrated strategy using (phospho)proteomic and functional genomic platforms to identify drug targets whose inhibition sensitizes melanoma cells to BRAF inhibition. We found many proteins to be induced upon PLX4720 (BRAF inhibitor) treatment that are known to be involved in BRAF inhibitor resistance, including FOXD3 and ErbB3. Several proteins were down-regulated, including Rnd3, a negative regulator of ROCK1 kinase. For our genomic approach, we performed two parallel shRNA screens using a kinome library to identify genes whose inhibition sensitizes to BRAF or ERK inhibitor treatment. By integrating our functional genomic and (phospho)proteomic data, we identified ROCK1 as a potential drug target for BRAF mutant melanoma. ROCK1 silencing increased melanoma cell elimination when combined with BRAF or ERK inhibitor treatment. Translating this to a preclinical setting, a ROCK inhibitor showed augmented melanoma cell death upon BRAF or ERK inhibition in vitro. These data merit exploration of ROCK1 as a target in combination with current BRAF mutant melanoma therapies."],"pubmed_title":["ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma."],"pubmed_authors":["Smit Marjon A MA, Maddalo Gianluca G, Greig Kylie K, Raaijmakers Linsey M LM, Possik Patricia A PA, van Breukelen Bas B, Cappadona Salvatore S, Heck Albert J R AJ, Altelaar A F Maarten AF, Peeper Daniel S DS"],"sample_synonyms":["Not Available, Unavailable."],"name_synonyms":["RAFB1, B-RAF1, determination, Peptidomics, malignant, Naevocarcinoma, AA387315, C87398, NS7, BRAF1, Malignant Melanomas, Malignant, melanoma (disease), 9930012E13Rik., Melanomas, Melanoma, C230098H17, melanoma, Braf-2, Braf2, Malignant Melanoma, chemical analysis, malignant melanoma, AA120551, B-raf, assay, D6Ertd631e, AA473386"],"data_synonyms":["Bru, IPP2A2, E 920, Raw, Aminosaeure, Amino acid, protein, STY, Sty, phosphorylation, 5730420M11Rik, peptide, Polypeptides, L-Isomer Methionine, Methionine, peptido, DmelCG1921, Software Engineering, 2-amino-3-mercaptopropanoic acid, Cystein, protein aggregate, sty, Computer Program, WMS, C79691, Svc, SET, C, F, amino acids, i2pp2a., peptides, TAF-I, cisteina, M, Open, CLK|STY, Computer Programs and Programming, arg, DmelCG4299, Lccp, dSPRY, IGAAD, set, DmelCG10574, ppm, SIAT7C, Half Cystine, GPHYSD2, Racemethionine, SGS, phapii, Zinc Cysteinate, Aminokarbonsaeure, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, Cys, Source Softwares, alpha-amino carboxylic acids, Software Tools, CG1921, Programs, ACMICD, Program, Computer Applications, Computer Applications Software, Computer Applications Softwares, Methionin, Softwares, Hmet, (2R)-2-amino-3-sulfanylpropanoic acid, parent ion, Amino Acid, Acid, Software Applications, HLA-DR-associated protein II, Amino acids, DI-2, Source Software, I-2Dm, MASCOT, L-Cysteine, CG4299, MASS, L-Cystein, I-2PP1, Applications, TAF-IBETA, precursor ion, Biocatalyst, TAF-Ibeta, Acids, Polypeptide, i2pp2a, Liquimeth, Computer Software Applications, CLK, Cysteine Hydrochloride, 2-amino-4-(methylsulfanyl)butanoic acid, False, AW549739, Biocatalysts, Aminocarbonsaeure, L-Zystein, L Isomer, FBN, Gene, Computer, alpha-amino acid, precursor, protein-containing complex, PHAPII, l(3)rQ526, ECTOL1, Gene Products, L-Methionine, UNQ2787/PRO7177, Del(8)44H, Half-Cystine, l(3)j5E11, Pedameth, Application, Open Source Softwares, Software Application, L Cysteine, E-920, ipp2a2, spry, Open Source Software, Argos, 2pp2a, CG4531, Hcys, CG10574, Computer Software Application, OCTD, mKIAA0989, Enzyme, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, 10^[-6], CYSTEINE, taf-ibeta, DmAos, dSET, dSet, FREE CYSTEINE, peptidos, (2R)-2-amino-3-mercaptopropanoic acid, metionina, rlt, CS3-3, Applications Software, Open Source, Computer Software, DL-Methionine, protein complex, Proteins, igaad, Phosphorylations, alpha-amino acids, L-Isomer, Peptide, Tool, group, polypeptide, CLK/STY, Spry, l(3)rJ812, Software Tool, native protein, I-2PP2A, Protein, Dm I-2, I2PP2A, MFS1, l(3)05959, Software, Zystein, Met, WMS2, Col4a-1, ensemble, gil, 2-amino-3-sulfanylpropanoic acid, Engineering, L-2-Amino-3-mercaptopropionic acid, (R)-2-amino-3-mercaptopropanoic acid, Amino, Sry, 2-Amino-3-mercaptopropionic acid, l(3)05845, Protein Gene Products, Computer Programs, DmelCG4531, Gene Proteins, dSET/TAF-Ibeta, Aos, 2610030F17Rik, Applications Softwares, l(3)rJ472, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, E920, Peptid, variable, AA407739"],"description_synonyms":["RAFB1, B-RAF1, C230098H17, Braf-2, determination, Braf2, Peptidomics, chemical analysis, AA387315, C87398, NS7, Cell., AA120551, B-raf, BRAF1, assay, D6Ertd631e, AA473386, 9930012E13Rik"],"pubmed_abstract_synonyms":["Erbb-3, Written Materials, DmErk, extracellular signal-regulated kinase activity, pp44mapk, Materials, Product, Tyro5, Mpk2, Small Hairpin, p42mapk, Tumor, DmelCG9774, SR2-1, ErbB-3, Repeat Associated siRNA, Small, Techniques, relapse, PLX-4720, LeMPK3, Trans Acting, melanoma, p44mpk, MDA-BF-1, Pharmaceutical Product, DRhk, Dp38, Written, AA120551, mitogen-activated protein kinase activity, Relapses, Kinase, Rock-I, SAPK2, malignant melanoma cell, mpk1, SEM, Sem, drug resistance, Rho family GTPase 3, CWH3, treatment, MAP-k, Erk/Map kinase, HFH2, Hfh2, pp42, EK5, Recurrences, DERK-A, Dsor2, E(sina)7, Rho8, sem, Rl, 9930012E13Rik, MP kinase activity, DERK, C230098H17, Repeat-Associated, medicine, Pharmaceutical, erbB3-S, disease management, Therapies, MBP kinase II activity, Malignancies, dERK, D6Ertd631e, AIS1, ATP Phosphotransferases, Materials Translation, ATP, Tumors, ERK-A, Therapy, Relapse, Interfering RNA, B-RAF1, MAP kinase 2 activity, Trans-Acting siRNA, dpERK, dpErk, CG9774, Rhoe, Mapk, Written Materials Translation, ERK-2, Erk1, ERK1, ERK2, mapk1a, Erk2, DmMAPK, Test, Malignant Melanomas, PMK-2, dp-ERK, PMK-1, p85-sErbB3, Short, PMK-3, LCCS2, Melanoma, Benign, p41mapk, Recrudescence, RhoE, mapk1b, MapK, MAPK, Small Scan, pMAPK, pMapK, Genetic Materials, Pharmaceutic, RhoK, Short Interfering RNA, regulator, Hairpin RNA, Scan, erk2, Genetic Material, mapk, Translations, Transphosphorylases, ERKa, RAFB1, drok, DmERKA, rl/MAPK, BcDNA:RE08694, In Vitro, Written Materials Translations, DROK, DRok, l(2R)EMS45-39, Tests, CAPB, AA387315, DmelCG12559, Benign Neoplasms, Rhk, p38, l(2)41Ac, Repeat Associated, Treatments, Malignant Neoplasms, C78273, DpErk, DpERK, ErkA, ERKA, dRok, dROK, CT34260, dpERk, antagonists and inhibitors, Patient, Material, p41, p40, SAPK, ARHE, Cistron, other neoplasm, AA473386, pERK, 9030612K14Rik, GroupII, In Vitro as Topic, Testings, Neoplasms, drug susceptibility/resistance, Benign Neoplasm, Arhe, 12559, NS7, Gene, Malignant, Erbb3r, P160ROCK, EK2-1, Translation, In Vitro Testing, melanoma (disease), Short Hairpin RNA, Hek5, AA407128, Drok, Scan RNA, Small Scan RNA, Gene Products, Prkm1, p42-MAPK, Phosphotransferase, Technique, In Vitro Tests, memB, ERK, Erk, Drugs, PRKM1, 1110055K06Rik, ROCK, PRKM2, scnRNA, In, AI661404, Genetic, Malignancy, Recrudescences, PLX4720, xp42, Naevocarcinoma, Rho-related GTP-binding protein Rho8, PCBC, C87398, inhibiteur, Treatments., Transphosphorylase, p42 mitogen-activated protein kinase activity, CG18732, ATP:protein phosphotransferase (MAPKK-activated) activity, erk, Short Hairpin, Materials Translations, Neoplasias, drugs, inhibidor, Clients, Trans Acting siRNA, rll, DmERK-A, Preparation, STK26, p38-2, myelin basic protein kinase activity, tasiRNA, Cancer, disease remission, Pharmaceuticals, inhibitors, Products, RNA, Trans-Acting, ert1, VAMAS2, ROCK-I, DRT, Malignant Neoplasm, Drug resistance, malignant, Rnd3, drug, Proteins, prkm2, stress-activated kinase activity, prkm1, CT39192, MAP-2 kinase activity, BRAF1, inhibitor, shRNA, Cistrons, Client, Cell, Phosphotransferases, Small Hairpin RNA, Testing, Short Interfering, p180-ErbB3, p38delta, Rock, Melanomas, In Vitro Test, Malignant Melanoma, stress-activated protein kinase activity, Protein, mapk2, ROK, ROCK-1, Rok, mapk1, Neoplasm, Resistance, nuc-ErbB3, MBP kinase I activity, In Vitro Testings, p45-sErbB3, B-raf, Vitro Testing, Library, Xp42, antagonists, C76256, ROCK1, Small Interfering RNA, c-erbB-3, CG12559, Pharmaceutic Preparations, c-erbB3, Kinases, mitogen activated kinase activity, P42MAPK, Su(Raf)2B, dpERK1, response to drug, EY2-2, Cancers, Translatings, 2610017M01Rik, MAPK2, Protein MemB, Drug, Protein Gene Products, Gene Proteins, Preparations, AU018647, D-ERK, Therapeutic, Braf-2, dpMAPK, Braf2, siRNA, ERT1, EPHT3, In Vitro Technique, Treatment, malignant melanoma, Pharmaceutical Products, Genesis, Neoplasia, Her3, ROKalpha/beta, SAP kinase activity, Pharmaceutical Preparation, MAP kinase 1 activity, HER3, Repeat-Associated siRNA"],"pubmed_title_synonyms":["Products, B-RAF1, ROCK-I, CG9774, Product, malignant, drug, NS7, BRAF1, Malignant Melanomas, Naevocarcinoma., DmelCG9774, Malignant, P160ROCK, Rock, melanoma (disease), Melanomas, Melanoma, melanoma, Drok, Malignant Melanoma, Pharmaceutical Product, ROK, ROCK-1, Rok, DRhk, RhoK, Pharmaceutic, AA120551, B-raf, Rock-I, Drugs, 1110055K06Rik, ROCK, ROCK1, RAFB1, drok, DROK, DRok, Pharmaceutic Preparations, AA387315, C87398, Rhk, 9930012E13Rik, Drug, dRok, dROK, Preparations, drugs, C230098H17, Braf-2, medicine, Braf2, Pharmaceutical, malignant melanoma, D6Ertd631e, Preparation, Pharmaceutical Products, ROKalpha/beta, AA473386, Pharmaceutical Preparation, Pharmaceuticals"],"view_count":["692"],"additional_accession":[]},"is_claimable":false,"name":"Proteomics and phosphoproteomics analysis of melanoma BRAF","description":"Proteomics and phosphosproteomics analysis of BRAF mutant cells.","dates":{"publication":"2014-12-19","submission":"2013-10-07"},"accession":"PXD000497","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NEWT:4097","NCBITaxon:6073","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