Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/Rawfilesdescription.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33793.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33966.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33784.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33745.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33775.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33800.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33975.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33969.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33790.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33960.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33803.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33987.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33787.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33978.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33990.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33769.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33981.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33778.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33972.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33993.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33781.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33963.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33772.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/33984.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/HUMAN.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD004085/MaxQuant_output_DML_MCF7.zipprimaryOK200003930Nikiana SimigdalaNot availableCell CultureWT and LTED MCF7 were isotopically labelled directly using Sep-pak C18 cartridges as described previously (Boersema et al., 2009; Di Palma et al., 2012). The WT cells were labelled with the medium isotope reagent and the LTED cells with the light isotope reagent. After labelling, each sample was eluted using 80% acetonitrile with 2% formic acid. Subsequently, the two labelled samples were pooled at an approximate 1-to-1 ratio and dried down under vacuum. The dried sample was reconstituted in OFFGEL stock solution and run using 12 cm IPG strip pH 3-10. Fractions were desalted (SUM SS18V, The Nest Group Inc) and run through LC-MS/MS using LTQ Velos Orbitrap MS.PrideLesley-Ann MartinLTQ Orbitrap VelosPARTIALThe Institute of Cancer Research The Breast Cancer Now Toby Robins Research CentreNot availableBRFAALesley-Ann.Martin@icr.ac.ukMass SpectrometryShotgun proteomicsBreast CancerLtedMcf7Dimethyl labellinghttp://www.ebi.ac.uk/pride/archive/projects/PXD004085Not availableiodoacetamide derivatized residueRaw data were processed using MaxQuant 1.5.1.0 following the developers’ (Cox and Mann, 2008; Cox et al., 2009, 2011) guidelines. Peak lists were searched against the human Uniprot FASTA database and a common contaminant database by the Andromeda search engine (built in MaxQuant) (Cox et al., 2011). The automatic decoy search option was enabled. Spectra were searched for a match to fully-tryptic peptides with up to two missed cleavage sites. Search parameters were chosen as follows: Carbamidomethylation was set as a fixed modification on all Cysteines. Oxidation of Methionines and N-acetylation were considered as variable modifications. Precursor ion mass tolerance was set to 20 ppm for the first search, fragment ion mass tolerance was set to 0.6 Da. Resulting peptide lists were filtered to an estimated FDR of 1% and protein lists were filtered to an estimated FDR of 5%. The “Re-quantify” and “match between runs” options were enabled with default settings. Light and medium dimethyl labels (+28.0313 Da and +32.0564 Da respectively) were searched at Lysine residues and peptide N-termini.ProteomicsHomo Sapiens (human)Nikiana.Simigdala@icr.ac.ukBiomedicalGreecesodium salt, liquid chromatography tandem mass spectroscopy, d230, ammonium formate, 13C-labeled, MeCN, cadmium salt, nickel formate dihydrate, NCMe, lead formate, aluminum salt, cesium salt, RCB1904, zinc formate, dTAFII250, lead salt, Visible Light, magnesium formate, EfW1, zinc salt, Ly113, formic acid, dmTAF[[II]]230, potassium salt, ammonium tetraformate, dmTAF1, cobalt(II) formate dihydrate, Taf230, 14C-labeled, CH3-C#N, hnu, PH 3, LC-MSMS, light, foton, TAF250, Taf200, proportion, dTAF[[II]]250, LCMSMS, TFIID TAF250, reactivo, cel, thallium (+1) salt, cell, Lichtquant, rubidium salt, Taf1p, labeling, Visible, copper, calcium formate, methanoic acid, Solution, MCF7 cell, dTAF250, Sep-Pak C18, lithium salt, grupos, sample, photon, LC-MS-MS., cromium (+3) salt, TR2, TAF, ammonium (2:1) salt, sodium formate, reagents, MCF-7 cell, MCF 7 cell, gamma, nickel salt, ratio, LC-MS2, dTAF[[II]]230, TAF[[II]]250, Radiation, grupo, 1-(14)C-labeled, nickel formate, 3H-labeled, cobalt (+2) salt, LC-MS/MS, TAF200, strontium formate, l(3)84Ab, Light, BG:DS00004.13, potassium formate, copper (+2) salt, TAFII-250, TAF250/230, acetonitrile, strontium salt, CD258, Cell, group, dTAF230, TAFII250, LC/MS/MS, sodium (4:1:1) salt, LIGHT, magnesium salt, p230, cupric formate, TAF[[II]]250/230, TFIID, Vacuums, reactif, aluminum formate, nickel (+2) salt, ACETONITRILE, cyanomethane, Visible Radiations, Radiations, Taf[[II]]250, ammonium salt, Visible Radiation, lithium formate, TAF[[II]]230, HVEML, HVEM-L, Photoradiation, formate, proportionality, cobaltous formate, Rest, pooled, reagent, cromium (+3), rate, TAF[II]250, ethanenitrile, CG17603, TAF[[II]], sample population, chromic formate, LTg, MCF7, DmelCG17603, light quantum, Photoradiations, Taf250, SR3-5, liquid chromatography-tandem mass spectroscopy, copper salt, ammonium (4:1) salt, calcium salt, quotient, liquid chromatography tandem mass spectrometry, methyl cyanide, lead (+2) salt, groupe, TAF230, Gruppe, TAF1Bru, IPP2A2, cox4, criteria, human being, Raw, Lysine Hydrochloride, cleavage, FBN, Visible Light, protein, precursor, guidelines, protein-containing complex, PHAPII, Ly113, 5730420M11Rik, peptide, CG10664, Polypeptides, protein polypeptide chains, Lysine Acetate, Drug Tolerance, peptido, ClvPrd, template-activating factor I, polypeptide chain, ECTOL1, IV, hnu, 2, Del(8)44H, light, Lysine, DmelCG10664, protein aggregate, foton, WMS, L Lysine, Svc, Search Engines, SET, Coproporphyrinogenase, peptides, TAF-I, K, COXIV, Lichtquant, phosphatase 2A inhibitor I2PP2A, ipp2a2, Acetylations, epsilon-diaminocaproic acid, 2pp2a, proteins, Visible, Estimated, COXA_DROME, man, CG10574, DmelCG4299, OCTD, set, IGAAD, 2PP2A, LYS, Cox4, 10^[-6], DmelCG10574, taf-ibeta, ppm, Lysin, COX, dSET, dSet, photon, peptidos, 1.3.3.3, TR2, GPHYSD2, COX-VA, drug tolerance, SGS, gamma, phapii, data, Radiation, PLATEST, protein complex, immune system tolerance, T5E21.12, acetylation, igaad, StF-IT-1, Light, Search, CD258, Peptide, Engine, ACMICD, polypeptide, LIGHT, Immune Tolerance, native protein, natural protein, I-2PP2A, VA, Acetate, AL024441, Dm I-2, Protein, I2PP2A, lysine, Immunologic Tolerance, IV-1, MFS1, COX IV, L-Lysine, Data Base, WMS2, T5E21_12, parent ion, Visible Radiations, Radiations, Visible Radiation, Col4a-1, HLA-DR-associated protein II, HVEML, DI-2, Va, Coprogen oxidase, HVEM-L, I-2Dm, COX IV-1, tend, Photoradiation, common, CG4299, MASS, alpha, inhibitor of granzyme A-activated DNase, human, LTg, I-2PP1, dSET/TAF-Ibeta, 2610030F17Rik, CG14724, light quantum, TAF-IBETA, Self Tolerance, Photoradiations, precursor ion, Tolerance, SSKS, Peptid, TAF-Ibeta, DmelCG14724, Polypeptide, variable, AA407739, 6-diaminohexanoic acid, i2pp2a, Enisyl, Peptide., Platelets, Cox4a, Immunological Tolerance17 beta Oestradiol, Antemortem Diagnosis, Estradiol Anhydrous, C030036D22Rik, Fanconi syndrome with intestinal malabsorption and galactose intolerance, PNT-P1, DmelCG17077, estrogenes, RCB1904, Activated, Ultracarbon, A4, NTN1R1, EY3-1, Pnt, protein, Diagnosis, dmTAF[[II]]230, peptide, Polypeptides, protein polypeptide chains, oestradiol, png, peptido, symptoms, Line, Phenol, 1-benzoxathiol-3-ylidene)bisphenol S, 3, cancer of the breast, 4, 1-benzoxathiol-3-ylidene)bis-, GSD due to GLUT2 deficiency, D-ets-2, 3520, protein aggregate, 17 beta)-(+-)-Isomer, 1-dioxide, Pnt-P1, Actidose-Aqua, BC, treatment, Phenolsulfonphthalein, TFIID TAF250, peptides, cel, (16 alpha, Progynon Depot, 4'-(1, Estradiol, Sulfonphthal, long, Adsorba, 17 beta-Oestradiol, S, 17-diol (17beta)-, proteins, free, Estradiol 17beta, MCF7 cell, Estradiol-17 alpha, endocrine, cis-estradiol, Kohle-Hevert, cancer of breast, 17beta oestradiol, Sulphonthal, oestrogene, disease management, oestrogens, Estrogene, Diagnose, MCF 7 cell, Estraderm TTS, Activated Charcoal, screening, dTAF[[II]]230, Charcodote, Ovocyclin, Estradiol Valerate, Oestrogene, TAF200, D-Ets-2, ets94F, 0123/09, Estradiol-17beta, TAFII-250, TAF250/230, Estra-1, glycogen storage disease 11, Formocarbine, Diagnoses, TAFII250, Postmortem, photoreceptor DCC, PSP, Examinations and Diagnoses, (9 beta, NOS, breast carcinoma, Bickel-Fanconi glycogenosis, Postmortem Diagnosis, beta-Estradiol, Estradiol Valeriante, alpha-bis(p-hydroxyphenyl)-o-toluenesulfonic acid gamma-sultone, Lines, oestrogen, Diagnoses and Examination, glycogenosis due to GLUT2 deficiency, Postmortem Diagnoses, 17beta-oestradiol, glycogen storage disease due to GLUT2 deficiency, absence, pntP2, Pointed-P1, Estradiol Hemihydrate, estrogenes Hormon, glycogenosis Fanconi EXACT, 4'-(3H-2, Ets94F, signs, CG17603, (17 alpha)-Isomer, TAF[[II]], Fanconi-Bickel syndrome, ptd, MCF7, PntP2, Sodium Salt, DMDA, hepatic glycogenosis with amino aciduria and glucosuria, Taf250, breast cancer, 1-benzoxathiole-3, SR3-5, Estradiol-17 beta, PntP1, Kohle-Compretten, E(E2F)3D, PNTP2, Polypeptide, Fanconi type, Progynova, Carbomix, GSD type XI, carcinoma of the breast, cancer, PNTP1, 17-diol, TAF230, Estradiol Monohydrate, GLUT2 deficiency, 0998/12, d230, CRCR1, CRC18, ETS2, Ets2, dTAFII250, FBS, Fbs, ESTRADIOL, protein-containing complex, EfW1, TYPE, 1-benzoxathiole 1, DAGA4, DMPOINT1A, pntegfr, 0608/07, polypeptide chain, dmTAF1, Taf230, (17beta)-estra-1, resistance, estra-1, Fanconi Bickel syndrome, Antemortem, MAM, 17 beta)-Isomer, SCG3, (17-alpha)-Isomer, alpha-hydroxy-alpha, pseudo-phlorizin diabetes, TAF250, Phenol red, Taf200, Kohle-Tabletten Boxo-Pharm, hormones, dTAF[[II]]250, Igdcc1, pointed-RC, cell, absent from organism, hepatic glycogenosis with Fanconi nephropathy, Monosodium Salt, Estradiol 17 beta, Taf1p, mammary carcinoma, labeling, Diagnoses and Examinations, (-)-Isomer, Oestradiol, estrogenos, EK3-2, Phenol Red, Delestrogen, Liqui-Char, 17beta-diol, dTAF250, l(3)07825, glycogen storage disease type 11, CharcoCaps, 3-bis(p-hydroxyphenyl)-3H-2, CG17077, peptidos, S-dioxide, TAF, l(3)j1B7, 1-dioxido-3H-2, MCF-7 cell, Charcoal, MRMV1, Antemortem Diagnoses, TAF[[II]]250, Ets, findings, 3-diyl)diphenol, 17 alpha)-Isomer, protein complex, carcinoma of breast, Fanconi-Bickel disease, Cell Lines, l(3)84Ab, estrogene, BG:DS00004.13, Cell, Examination and Diagnoses, Peptide, LGMD2C, dTAF230, polypeptide, Electrophoreses., DCC, 17beta-estra-1, estrogens, native protein, Kohle-Pulvis, natural protein, p230, estrogeno, Progynon-Depot, glycogen storage disease XI, Protein, TAF[[II]]250/230, IGDCC1, TFIID, Oestrogen, CharcoAid, glycogen storage disease type XI, pnt-P1, Insta-Char, pnt-P2, glycogenosis, l(3)s118306, 17 beta-Estradiol, (+-)-Isomer, Taf[[II]]250, 5(10)-triene-3, hepatorenal glycogenosis with renal Fanconi syndrome, Estradiol 17 alpha, TAF[[II]]230, GSD type 11, DMDA1, Actidose, Charbon, Vivelle, Estrace, TAF[II]250, FBS1, Fbs1, 17beta-estradiol, Norit, Ets58AB, DmelCG17603, hepatorenal glycogenosis with renal fanconi syndrome, SCARMD2, 17 beta Estradiol, Peptid, Aerodiol, POINT, breast, Sulphental, (8 alpha, oestrogenes, TAF1, CG8705labeling., number, RCB1904, MCF7, count in organism, quantitative, Peptidomics, presence, MCF-7 cell, MCF 7 cell, presence or absence in organism, MCF7 cell393trueQuantitative proteomics on wt-MCF7 versus their LTED derivatives using dimethyl labellingWild type (wt) MCF7 cells, modelling breast cancer at primary diagnosis, were cultured in phenol red-free RPMI supplemented with 10% FBS and 1nM estradiol (E2). Long-term oestrogen deprived (LTED) cell lines, which model resistance to endocrine therapy, were cultured in phenol red-free RPMI in the absence of exogenous E2 and supplemented with 10% dextran charcoal-stripped bovine serum (DCC). Samples were harvested at baseline and at the point of resistance (LTED). To reveal differential protein abundances between wt-MCF7 and MCF7 LTED, the peptides were labelled with chemical labelling and underwent fractionation using OFFGEL electrophoresis.2016-06-012016-05-02PXD0040854466449917558258038804333029535851114512067811080612461962461972842188090320637522995811363350906836351524260275838538791187947398007186801NCBITaxon:1280572307688881114301187263555571468351452627412583649117571508472746707364113546138855821803582329031388869152167786889539978447512951398704351123294126246942229692812397713311809933995232310343043654813583334607925198183659219813143205971293818826826558194762149363295726373719222212502321979116938197912NCBITaxon:12721119577412478186613283882813955843451358672217554372949140816918045416193426683413903634530586112041623264460711210411706127443210859561496367469412831666943694559729452811320810039241065837514633087936944784475174206542208964317447127020896344597413797912838411946694006671454587932993529320101981264690410661145755121659940483392512165972165954550131528269731606212133128312821280339523218108323217825252920435315227794428112353153454349825741948147871720309498019752555536231439841356742951053948824261914548140479NCBITaxon:21571150621551531292439899037122857782996597532059687623193516309800588845586978181780817363094317956606989361604885661409859104782566416242515059071187023482118705320491381693630638632355543204663222618663312994565860688453515126232172192174592161295671713604410016023587002642036945694101676341021076127735113165821504802392547279332160428146100291358430357861746331325291118700215764180969975665457744491566667547604452467675684030191726518130194111929439633664113633672175111764510239870932025NCBITaxon:4055932582359092788396523652649821787074982163472565691569387224982116544872056973474951666905108944835525663661410NCBITaxon:4932871556891758543102459808108944475741755518100058945268087322875351908323311561263730069303911415542193255521872587268723872487298727123598755529NCBITaxon:475154762422314146547730551800664417725564843376771581419198822445299767446982510216998231174673897641041051155744689444474153NCBITaxon:5055796016776744685100036487529600NCBITaxon:58116534911822637082483341475480557841946751299114578458359741276473194439137086326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:582054641498523077479464098609958652283637379196627290587668960596061572951372218759446708756227086266596417110133548330903497412982998603878348106267566430615127936543194747033424947223598596108961588655974649987039202111072878272154078211908503757075298351170828206189257771480418985487350247158779627300251563041190252867463604614796469644375939491146247274612874601134506253256648452659197221963819155263858859652639NCBITaxon:6157505210283071105172375059576131302409720002634196105264110909469407722774694163485689961123869497515NCBITaxon:2NCBITaxon:135231703612506174767927450627249159615384005257313246432136861505962697968666299034694171344346360347515363296440421018194301086731018510976063558633149616128628724620096692729435133813216968583551865368595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719475932118691443906NCBITaxon:102982100071257118348824387279694836419080218787864515970384766425731055347095145122578656870861822607046183260705260707NCBITaxon:7803906NCBITaxon:1502451516658457702921158612184519307920928520131974707856100713370565295076192126385454195NCBITaxon:3055504457391538337991399878168192875NCBITaxon:10239NCBITaxon:7142829126806315327341478281309570547044830064175158592381055524159084128108228233446900815025754122810451930174830085210977970671356225833136185509924NCBITaxon:56938268830640527796179469958334240906151015151034809NCBITaxon:63124067448242813076707087613837047592723708281677285035158199011951953370249240536088817562615835583337602126719285321773572671193501846451772998086167879177437371110490563712153481724073714121532395767690147266470913170475712562745790311333550372885962859634792491308126387121203511082332648373153214693NCBITaxon:9615383235946331858626079914126220029813141313493760833344926701311111497019281239655833325283010184138569591110065812375612750454266625515197887492003750360094129349715300910766204114903524725175014012573983649908515151438992NCBITaxon:1155237453988374744544641521399274356235931179286643235983906288705158059553611945993271602938511497861603293338922853422999810894535936457428412754121536024271831627713512251179948875058NCBITaxon:10407242715502779167971816738713491306274158955210103065027802915954126291586600255158493765327159570210022633889423451287689135588675512930945146479203124216413328038280351928434369093581539858089462108034817939211825902878892950274560990690174934681927256322732189038292867572279011247190400727NCBITaxon:57965374571143112335235621140206411981087135547714245072295337969835552222129163470871410457751262161154293157546139622421392139077020206032818573231143193382935508332923074112922114816402784896160106772526499975744727580240550717629925122968335366581926832140535762294128160783957632066724005402965432823122737777298184318322465962057554992295757575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