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interact-072213_HeLa_KH_KL_1_50.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-071813_HeLa_KL_SH_1_200.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022312_HeLa_SILAC_BDP_8_9_50mM_2hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-021712_HeLa_SILAC_BDP_7_8_50mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022312_HeLa_SILAC_BDP_7_10_50mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022712_HeLa_SILAC_BDP_8_9_100mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022212_HeLa_SILAC_BDP_7_8_150mM_4hr.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-071613_HeLa_KH_KL_1_150.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-071613_HeLa_KH_KL_1_100.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022412_HeLa_SILAC_BDP_8_9_150mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-021712_HeLa_SILAC_BDP_7_8_200mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022412_HeLa_SILAC_BDP_7_10_50mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022712_HeLa_SILAC_BDP_8_9_50mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-071613_HeLa_KH_KL_2_200.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-071613_HeLa_KH_KL_1_200.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022212_HeLa_SILAC_BDP_7_8_200mM_4hr.heavy.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022712_HeLa_SILAC_BDP_7_10_100mM_4hr.light.pep.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002378/interact-022312_HeLa_SILAC_BDP_7_10_200mM_4hr.light.pep.xmlprimaryOK200004330Juan ChavezNot availableEpithelial CellCell CultureIntact drug sensitve and resitant HeLa cells cultured in SILAC media were harvested and subjected to in vivo cross-linking with with a protein interaction reporter (PIR) cross-linker. Cells were lysed and protein extracted, reduced with TCEP alkylated with IAA and digested with trypsin. Peptides were fractionated by SCX followed by avidin affinity chromatography. Enriched cross-linked peptide samples were analyzed on a Velos-FTICR mass spectrometer (Thermo) using real-time adaptive MS3 method (ReACT, Weisbrod et al. JPR 2013).PrideJames E. BruceLTQ FTDepartment of Genome Sciences, University of WashingtonPARTIAL26235782 Chavez JD, Schweppe DK, Eng JK, Zheng C, Taipale A, Zhang Y, Takara K, Bruce JE. Quantitative interactome analysis reveals a chemoresistant edgotype. Nat Commun. 2015 Aug 3;6:7928 10.1038/ncomms8928University of Washingtonjimbruce@uw.eduMass SpectrometryChemical cross-linking coupled with mass spectrometry proteomicsCervix CarcinomaChemical cross-linkingMultidrug resistant cancerMass spectrometryProtein interactionshttp://www.ebi.ac.uk/pride/archive/projects/PXD002378SILAC6x(13)Cdimethylated residueiodoacetamide derivatized residueN6monomethylated residuemonohydroxylated residueacetylated residue6x(13)C labeled L-arginineRaw data files were converted to mzXML with tools in the TPP. MS3 spectra in the mzXML files were searched against a human protein database from UniProt using Sequest. Resulting peptide ID's from the Sequest search were mapped back to PIR mass relationships identified in the MS2 spectra to fully identify cross-linked peptides. SILAC quantitative analysis on the MS1 spectra was performed using MassChroQ.ProteomicsHomo Sapiens (human)jdchavez@uw.eduBiomedicalUnited StatesChemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for 'edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype.Quantitative interactome analysis reveals a chemoresistant edgotype.Chavez Juan D JD, Schweppe Devin K DK, Eng Jimmy K JK, Zheng Chunxiang C, Taipale Alex A, Zhang Yiyi Y, Takara Kohji K, Bruce James E JE433scale tissue, BamF, insensitive, single-organism developmental process, determination, AP-2, BamC, neoplasia, topoisomerase II, alpha-Spe, Malignant Epithelial Tumors, protein, Tumor, Epithelial Tumors, alpha-Spc, CG31654, peptide, dmTAF[[II]]230, Polypeptides, Histone H2b, protein polypeptide chains, l(3)04276, Histone H2a, "epithelial carcinoma" EXACT [NCI2004_11_17:C2916], peptido, responsivity, alpha-adaptin, no subtype (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:68453008], Analysis, DmelCG10422, protein aggregate, Carcinomatosis, alpha-spec, relaxing enzyme activity, Mass Spectrum Analysis, treatment, Spindle-Cell Carcinoma, Undifferentiated, peptides, TFIID TAF250, CG4260, Analyses, cel, cell process disease, tumor disease, Moods, plant peltate hair, neoplasm (disease), proteins, alpha-spectrin, epithelial carcinoma, epithelioma malignant, disease management, Histone H5, Histone H4, Histone H7, tumor, type II DNA topoisomerase activity, Histone H1, Histone H3, Tumors, Carcinoma, dTAF[[II]]230, Undifferentiated Carcinoma, epithelioma, functional failure, DNA topoisomerase IV activity, "carcinoma" EXACT [CSP2005:2000-1867], TAF200, ham, neoplastic disease, "carcinoma, TAFII-250, untwisting enzyme activity, TAF250/230, Spectrum Analysis, tumours, Anaplastic, ada, Spectroscopy, alphaSpec, TAFII250, D-Ada, Epitheliomas, cg4260, dAP-2a, failure, spectrin, Carcinomatoses, Carcinomas, l(2)06694, MENE (2L)-A, Spindle Cell, resistant, Spectrometry, common, DNA gyrase activity, alpha, AP-2alpha, Other carcinoma, CG17603, TAF[[II]], human, type I DNA topoisomerase activity, DmelCG4260, Phenotypes, Taf250, SR3-5, malignant epithelial tumor, Spindle-Cell, type I topoisomerase activity, Malignant Epithelial Neoplasm, Anaplastic Carcinomas, Polypeptide, other neoplasm, omega-protein activity, TAF230, alpha-Ada, d230, anon-EST:fe2E2, human being, swivelase activity, l(3)alpha-Spec, Neoplasms, peltate hair, alpha-Spect, number, Gene, dTAFII250, disfunctional, Spectrum Analyses, protein-containing complex, deoxyribonucleic topoisomerase activity, Malignant, EfW1, presence, l(2)SH2 0460, DNA topoisomerase II, NEOPL, fs(3)neo61, DNA topoisomerase (ATP-hydrolysing), Undifferentiated Carcinomas, CG10422, alpha-ada, polypeptide chain, dmTAF1, Taf230, resistance, malignant epithelioma, klo, Gene Products, Mass, Mood, alpha-Sp, Malignant Epithelial, Epithelioma, CG1977, neoplasm, deoxyribonucleate topoisomerase, Mass Spectroscopy, Histone H3.3, TAF250, reactivity, Taf200, dTAF[[II]]250, cell, DNA topoisomerase II activity, Epithelial Neoplasms, dre3, Taf1p, tumour, Alpha-Adaptin, man, malignant epithelial neoplasm, dTAF250, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), scale (sensu Metazoa), peptidos, carcinoma, malignant Epithelioma, TAF, Neoplastic Growth, l(3)dre3, TAF[[II]]250, alpha-Spectrin, DNA topoisomerase type II activity, 3A9, protein complex, malignant, DmelCG1977, Affects, Proteins, malignant epithelial tumour, Phenotypes., DNA topoisomerase I activity, l(3)84Ab, defective, function, BG:DS00004.13, Histone, Cell, Peptide, dTAF230, development, polypeptide, count in organism, neoplastic growth, native protein, epithelial cancer, natural protein, p230, "carcinoma NOS (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:189549006], Protein, chemical analysis, Neoplasm, Spindle-Cell Carcinomas, Malignant Epithelial Neoplasms, TAF[[II]]250/230, TFIID, MENE(2L)-A, scales, topoisomerase, alphaSp, Mass Spectrum Analyses, Anaplastic Carcinoma, Taf[[II]]250, Mass Spectrum, TAF[[II]]230, DNA-gyrase activity, D-alphaAda, scale, mating_type_alpha, FCP-B, TAF[II]250, Epithelial Neoplasm, disease of cellular proliferation, Histone H1(s), Protein Gene Products, Gene Proteins, AP2, DmelCG17603, nicking-closing enzyme activity, l(3)62Bd, Bam-C, BAM, alpha mating type (yeast), Bam, l(2)SH0460, alfa-Spec, Peptid, Malignant Epithelial Tumor, assay, response, quantitative, Epithelial Tumor, NEOPLASMS BENIGN, Neoplasia, Spec, presence or absence in organism, TAF12310042L19Rik, Bru, data, Stars, Raw, SRA1, determination, DmelCG1810, KLK, number, FBN, xpir, presence, male sterility 1., Peptide, ACMICD, polypeptide, peptide, Polypeptides, count in organism, ClvPrd, peptido, Ms1, ECTOL1, chemical analysis, MFS1, Del(8)44H, PIROGI 121, F20L16_130, WMS, tandem MS, Data Base, WMS2, CG1810, Svc, Col4a-1, KLUNKER, peptides, Ly89, PIR-A1, MS1, MALE STERILITY 1 PROTEIN, MS3, MS/MS, MS2, 6M21, human protein, E430039A18Rik, Striated muscle activator of Rho-dependent signaling, PIRP, ATSRA1, TPP, MASS, T6G21.3, CD156a, CD156, OCTD, SSKS, Pirnl, Peptid, peptidos, Polypeptide, assay, PIROGI, quantitative, Pir, PIR, GPHYSD2, STARS, F20L16.130, SGS, presence or absence in organismcount in organism, HeLa Cell, determination, chemical analysis, Cells, HeLa, number, assay, quantitative, HeLa., presence, Cell, presence or absence in organismnumber, chemical analysis., count in organism, assay, quantitative, determination, presence, presence or absence in organismANT-C, Bhlha41, Scx, SCX, DmelCG1810, KLK, Effects, Antp1, bHLHa48, DMANTPE1, protein, 2-(indol-3-yl)ethanoic acid, Antp P1, xpir, Antp P2, protein-containing complex, SCXB, Long Term, SCXA, peptide, period, Polypeptides, protein polypeptide chains, method, IAA, peptido, ClvPrd, polypeptide chain, reduced, scx, subnumerary, Hu, AntP1, tiny, protein aggregate, 3.4, F20L16_130, present in fewer numbers in organism, Effect, ANTC, antp, peptides, Ly89, PIR-A1, Longterm, MS3, 6M21, HeLa, beta-Trypsin, hypoplasia, proteins, Indoleacetic acid, Long-Term, decreased number, xscleraxis, CG1028, BG:DS07700.1, drugs, decreased, (indol-3-yl)acetic acid, method used in an experiment., medicine, bHLHa41, Pirnl, ANT-P, peptidos, Long-Term Effect, AntP, ANTP, Pir, PIR, Avidins, Chromatographies, Long-Term Effects, F20L16.130, TCEP, 2310042L19Rik, small, 1H-indol-3-ylacetic acid, SRA1, protein complex, drug, Longterm Effect, DmAntp, Cell, Peptide, Aus, polypeptide, (Indol-3-yl)acetate, HeLa Cell, native protein, natural protein, BB114693, Protein, Long Term Effects, IES, l(3)84Ba, PIROGI 121, CG1810, Ant, KLUNKER, underdeveloped, PIRP, 3-Indolylessigsaeure, Tripcellim, ATSRA1, beta Trypsin, Longterm Effects, plan specification, Trypure, Indole-3-acetic acid, Ns, heteroauxin, DmelCG1028, Isolation of Nuclei TAgged in specific Cell Types, Cells, Peptid, DRO15DC96Z, Polypeptide, PIROGI, time, Scltype 2, scale tissue, insensitive, single-organism developmental process, methionine aminopeptidase activity, DmelCG1810, KLK, neoplasia, peltate hair, number, Gene, protein, disfunctional, xpir, protein-containing complex, presence, protein polypeptide chains, polypeptide chain, responsivity, resistance, Gene Products, 2, Mood, protein aggregate, neoplasm, F20L16_130, familial adenomatous polyposis, MAP, peptidase M activity, adenomas, treatment, reactivity, rabGAPLP, L-methionine aminopeptidase activity, Ly89, PIR-A1, cell process disease, tumor disease, Moods, plant peltate hair, familial adenomatous polyposis 2, neoplasm (disease), 6M21, HeLa, RabGAP-5, proteins, autosomal recessive multiple colorectal adenomas, drugs, medicine, RUSC3, disease management, Pirnl, scale (sensu Metazoa), tumor, Pir, PIR, F20L16.130, 2310042L19Rik, MUTYH-related attenuated familial adenomatous polyposis, MUTYH-Associated Polyposis, SRA1, functional failure, protein complex, Affects, Arts, drug, Proteins, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, neoplastic disease, defective, function, Cell, development, count in organism, neoplastic growth, native protein, HeLa Cell, natural protein, MUTYH-related attenuated FAP, Protein, failure, scales, PIROGI 121, CG1810, autosomal recessive, MUTYH-associated polyposis, MUTYH-related AFAP, RUTBC3, Industrial, KLUNKER, Industrial Arts, scale, resistant, PIRP, ATSRA1, common, MYH-Associated Polyposis, HeLa., disease of cellular proliferation, RABGAP5, Protein Gene Products, Gene Proteins, Phenotypes, multiple colorectal, Cells, MAP syndrome, MUTYH-related attenuated familial polyposis coli, response, PIROGI, quantitative, other neoplasm, FAP2, presence or absence in organism, colorectal adenomatous polyposis0trueQuantitative cross-linking analysis of chemoresistant HeLa cellsChemoresistance is a common mode of therapy failure for many cancers. Tumors develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. In this project we combine SILAC with PIR cross-linking technology to generate a quantitative protein interaction map of drug senstive and drug resistant HeLa cells.2015-09-152015-06-17PXD002378445441052311009064152499175405499865931173880433303878343235983906327160884019373349615198215275838575748782721519081351750589850765557148046835364921589103064189852915936413885623980332715910022619023888691564546374636013558811345061464796928145943280385833NCBITaxon:61579778118259040816329572633803945264127256314595361235178616722724323074699286745131123869408169NCBITaxon:245309544627912924970361251801424507284812355512744324264281504751029971438865990346941769453475154155405972936329979662877323962891575464784224295486208964317447127057558462821143193382352287230741114817362314896935293725126469039946727360106580240884204399472165999685835521659554440429412826071012832965431280339523218184318329204353152NCBITaxon:61918402357554787931281183657593079721855791908021432138703824261916922591096976106592226155153111795726070461832607052607078853187029455862652817363094317991036989361604882092855664678251249668425286192126385410943433175131971928753555432046NCBITaxon:10359NCBITaxon:13134565860688607699389422829795545351126806379599598704483006418022410023544326420367631076224308185431575412983964271116996328104215745771216979123899342321356223347472697049NCBITaxon:177358331803010239297601011738185833424090699131274414163917018736745101165691569313076749409833422432640817212816120425468761383708127442399011912744201274426992551953883949113702100058999403430531156675060554285321895177311935014219328464587263171450511872366698724642687274924121532395648188229547670911151045800230551480154180066903138475623603142313616859628596398251021691015109823117467349321167627591080772446896776733264837315344685NCBITaxon:9615297223937651097677573578458112111449376083334191107927628086363266689NCBITaxon:26970498333210312983823756124136899759612559292484797492003600943197522833524721966277668960596061572951372211711015151514389922567371233435374726235782