{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2919-Bin-cross-6A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2915-Bin-cross-4A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2909-Bin-cross-1A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/230_Bin-hStat3-NCI.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2917-Bin-cross-5A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/229_Bin-hStat-Flag1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2911-Bin-cross-2A.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/228_Bin-pCDH-flag1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/2913-Bin-cross-3A.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/Anti-STAT3-Palmfeldt.tar.gz","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/08/PXD006788/MaxQuant-STAT3-Palmfeldt.tar.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":197,"searchCount":0},"additional":{"labhead_mail":["johan.palmfeldt@clin.au.dk"],"submitter":["Johan Palmfeldt"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry"],"software":["Not available"],"submitter_keywords":["Co-immunoprecipitation","Stat3"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD006788"],"tissue":["Permanent Cell Line Cell","Hela Cell"],"sample_protocol":["Protein identification by mass spectrometry Anti-FLAG® immunoprecipitation from lysates of HeLa cells transfected with pBCMV-STAT3-flag-puro three days earlier was performed according to protocol described above. Interacting proteins were identified and quantified by nano-LC-MS/MS (nanoscale-¬liquid chromatography tandem mass spectrometry), essentially as previously described [1]. Briefly, each gel lane was cut into 1×1 mm pieces and cysteine residues were blocked by reduction and alkylation using tris(2-carboxyethyl)phosphine and iodoacetamide, respectively. In-¬gel digestion was performed using trypsin and resulting peptides were extracted from gel pieces using acetonitrile and trifluoroacetic acid and finally purified on PepClean C-¬18 Spin columns (Thermo Scientific). LC-¬MS/MS was performed on an EASY nanoLC coupled to a Q Exactive Plus Hybrid Quadrupole-¬Orbitrap Mass Spectrometer (Thermo Scientific). Peptide samples were separated on a C-¬18 reverse phase column (PepMap from Thermo Scientific with 25 cm length, 75 μm inner diameter, and 2 μm particle size) and eluted by a 90-¬min linear gradient of acetonitrile (4–40%) containing 0.1% formic acid. The MS was operated in data dependent mode, automatically switching between MS and MS2 acquisition, with mass resolution of 70,000 and 17,500, respectively. Up to 10 most intense ions were fragmented per every full MS scan by higher-¬energy collisional dissociation. Dynamic exclusion of 10 seconds was applied and ions with single charge or unassigned charge states were excluded from fragmentation. 1. Britze, A., Birkler, R. I., Gregersen, N., Ovesen, T. & Palmfeldt, J. Large-scale proteomics differentiates cholesteatoma from surrounding tissues and identifies novel proteins related to the pathogenesis. PLoS One 9, e104103, doi:10.1371/journal.pone.0104103 (2014)."],"repository":["Pride"],"modification":["No PTMs are included in the dataset"],"quantification_method":["Label free"],"data_protocol":["MaxQuant software version 1.5.2.8 was applied for protein identification and label-¬free quantification by means of peptide peak areas [2]. The MS raw files were searched against a database consisting of 20,197 Homo sapiens protein sequences downloaded from UniProt [3]. Carbamidomethylation of cysteines was set as fixed modification,whereas methionine oxidation and protein N-¬terminal acetylation were set as dynamic modifications. The false discovery rate (FDR) was assessed by searching against a reverse decoy database [4] and FDR thresholds of protein and peptide identification were both set to 0.01. 2. Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-1372, doi:10.1038/nbt.1511 (2008). 3. UniProt. Homo sapiens protein sequence database, 2015). 4. Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in largescale protein identifications by mass spectrometry. Nat Methods 4, 207-214, doi:10.1038/nmeth1019 (2007)."],"omics_type":["Proteomics"],"labhead":["Johan Palmfeldt"],"instrument_platform":["Q Exactive"],"labhead_affiliation":["Aarhus University, Denmark"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["johan.palmfeldt@clin.au.dk"],"publication":["30127373 Liu B, Palmfeldt J, Lin L, Colaço A, Clemmensen KKB, Huang J, Xu F, Liu X, Maeda K, Luo Y, Jäättelä M. STAT3 associates with vacuolar H+-ATPase and regulates cytosolic and lysosomal pH. Cell Res. 2018 10.1038/s41422-018-0080-0"],"curator_keywords":["Biological"],"submitter_affiliation":["Aarhus University Hospital"],"submitter_country":["Denmark"],"pubmed_abstract":["Dysregulated intracellular pH is emerging as a hallmark of cancer. In spite of their acidic environment and increased acid production, cancer cells maintain alkaline intracellular pH that promotes cancer progression by inhibiting apoptosis and increasing glycolysis, cell growth, migration, and invasion. Here we identify signal transducer and activator of transcription-3 (STAT3) as a key factor in the preservation of alkaline cytosol. STAT3 associates with the vacuolar H+-ATPase in a coiled-coil domain-dependent manner and increases its activity in living cells and in vitro. Accordingly, STAT3 depletion disrupts intracellular proton equilibrium by decreasing cytosolic pH and increasing lysosomal pH, respectively. This dysregulation can be reverted by reconstitution with wild-type STAT3 or STAT3 mutants unable to activate target genes (Tyr705Phe and DNA-binding mutant) or to regulate mitochondrial respiration (Ser727Ala). Upon cytosolic acidification, STAT3 is transcriptionally inactivated and further recruited to lysosomal membranes to reestablish intracellular proton equilibrium. These data reveal STAT3 as a regulator of intracellular pH and, vice versa, intracellular pH as a regulator of STAT3 localization and activity."],"pubmed_title":["STAT3 associates with vacuolar H+-ATPase and regulates cytosolic and lysosomal pH."],"pubmed_authors":["Liu Bin B, Palmfeldt Johan J, Lin Lin L, Colaço Alexandria A, Clemmensen Knut K B KKB, Huang Jinrong J, Xu Fengping F, Liu Xin X, Maeda Kenji K, Luo Yonglun Y, Jäättelä Marja M"],"sample_synonyms":["liquid chromatography tandem mass spectroscopy, sodium salt, DIWS, Co-Immunoprecipitations, scale tissue, ammonium formate, Size, 13C-labeled, MeCN, cadmium salt, NCMe, ion, Particle, zinc formate, Mbp1, positive regulation by symbiont of host non-apoptotic programmed cell death, lead salt, protein, magnesium formate, zinc salt, Co Immunoprecipitation, l(2)k09905, Alkylations, peptide, Trifluoroacetate, Cut, Polypeptides, protein polypeptide chains, encircling, ammonium tetraformate, peptido, ClvPrd, l(1)7Ba, cobalt(II) formate dihydrate, l(1)7Bb, CH3-C#N, hemolysis by symbiont of host RBCs, pathogenesis, Williams-Beuren syndrome chromosomal region 6 protein, Min, Analysis, protein aggregate, myd, DmelCG42273, Mass Spectrum Analysis, DmelCG8428, modification by symbiont of host biological process, Spin, Divorced, LCMSMS, peptides, stimulation by symbiont of host programmed cell death, Analyses, plant peltate hair, Co-Immunoprecipitation, E430039A18Rik, Tissue, Precipitation, min, Mbp-1, mAPC, proteins, Divorces, copper, SCAN, activation by organism of programmed cell death in other organism during symbiotic interaction, CG11387, AI047805, SPIN, Immune, lithium salt, column, BTKAP1, Diws1t, trifluoro-, n, CT, cholesteatoma, Half Cystine, cytolysis by organism of host cells, Precipitations, GTFII-I, ammonium (2:1) salt, nickel salt, LC-MS2, 6030441I21Rik, ADMIO, Zinc Cysteinate, cobalt (+2) salt, gyltl1b-b, enclosing, aprf, LC-MS/MS, Ct, Dmel_CG7826, BAP135, positive regulation by symbiont of host programmed cell death, Spectrum Analysis, Thermo Scientific, fragmented, doi., Spectroscopy, sodium (4:1:1) salt, enhancement of host programmed cell death, Dm1, magnesium salt, Ionen, wrapping, MDDGA6, mKIAA0609, SRF-Phox1-interacting protein, modulation by symbiont of host system process, Sizes, BAP-135, BcDNA:GH10590, nickel (+2) salt, Acetic acid, Dmel_CG7835, APRF, haemolysis in host, Mnb, MNB, fg, Acid, l(2R)W5, ammonium salt, gyltl1b, MS/MS, cracked, Trifluoroacetic, formate, mdc1d, Spectrometry, cobaltous formate, expanded, perturbation by symbiont of host defense response, stat3, cromium (+3), L-Cysteine, GtfII-I, AW124434, study protocol, beta Trypsin, Aprf, induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, AW109958, MDC1D, regulation of cytolysis of host cells by symbiont, l(2)W5, enr, induction by symbiont of host programmed cell death, Cesium, WBS, enlarged, hemolysis by symbiont of host red blood cells, liquid chromatography-tandem mass spectroscopy, Acetamide, activation by symbiont of host programmed cell death, Cells, copper salt, ammonium (4:1) salt, CG8428, Polypeptide, methyl cyanide, lead (+2) salt, big, Particle Sizes, l(1)VE614, Cysteine Hydrochloride, nickel formate dihydrate, lead formate, Peptidomics, fractured, regulation by symbiont of host system process, peltate hair, modulation by organism of defense response of other organism involved in symbiotic interaction, aluminum salt, cesium salt, Gene, Spectrum Analyses, protein-containing complex, TFII-I, CG7826, froggy, LC-MS-MS, Gyltl1a, DOI, Bruton tyrosine kinase-associated protein 135, formic acid, method, large, potassium salt, polypeptide chain, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, 14C-labeled, method used in an experiment, LC-MSMS, Mass, Immune Precipitations, Gene Products, CG7835, CG42273, IB291, Half-Cystine, AA673430, Separated, Immune Precipitation, Mass Spectroscopy, Cholesteatomas, upregulation by symbiont of host programmed cell death, Cesium Trifluoroacetate, induction of non-apoptotic programmed cell death by other organism, thallium (+1) salt, L Cysteine, MS2, iones, MDDGB6, HIES, HeLa, beta-Trypsin, rubidium salt, blocked, calcium formate, methanoic acid, ions, kf, CD156, hies, BPFD#36, DmelCG11387, primary acquired cholesteatoma (type), great, scale (sensu Metazoa), peptidos, cromium (+3) salt, BTK-associated protein 135, AA553322, 2-iodo-, sodium formate, TCEP, WBSCR6, DYRK1, data, disruption by symbiont of host cell, activation by organism of non-apoptotic programmed cell death in other organism, 1-(14)C-labeled, nickel formate, 3H-labeled, hemolysin activity, protein complex, Proteins, strontium formate, split, potassium formate, copper (+2) salt, acetonitrile, strontium salt, Cell, Peptide, bnch, polypeptide, l(2)k02511, LC/MS/MS, native protein, HeLa Cell, natural protein, cupric formate, Protein, hemorrhaged, modulation by symbiont of host defense response, Xstat3, 25/11, Dyrk1, scales, induction by organism of programmed cell death in other organism involved in symbiotic interaction, mitigation by symbiont of host defense response, aluminum formate, secondary acquired cholesteatoma (type), ACETONITRILE, Mass Spectrum Analyses, tandem MS, cyanomethane, AU020952, torn, Mass Spectrum, Separation, 10^[-9], lithium formate, enhancement of host programmed cell death by organism, scale, Separations, CC1, Tripcellim, ethanenitrile, CD156a, chromic formate, ME-IV, plan specification, Protein Gene Products, incised, l(2)10403, Gene Proteins, Trypure, congenital cholesteatoma (type), activation by organism of host programmed cell death, 1110034C02Rik, Ion, calcium salt, liquid chromatography tandem mass spectrometry, Peptid, cholesteatoma (disease)"],"pubmed_title_synonyms":["Dnahc8, ADMIO, hdhc9, FON1, HIES, aprf, Bdr, stat3, Hst6.7b, SUPERMAN, FLO10, Synaptosomal-associated 25 kDa protein, Super protein, FLORAL ORGAN NUMBER 1, HERP, Aprf, sp, SNAP-25, AW109958, hies, P1-Loop., Mif1, ATPase, 1110034C02Rik, SUP, Xstat3, GENA70, APRF, FLORAL DEFECTIVE 10"],"data_synonyms":["Bru, IPP2A2, cox4, 11alpha, Raw, TalANAc, protein, 5730420M11Rik, peptide, Polypeptides, protein polypeptide chains, L-Isomer Methionine, Techniques, Methionine, ClvPrd, peptido, Method, Software Engineering, Analysis, DmelCG10664, protein aggregate, Computer Program, WMS, Mass Spectrum Analysis, Svc, SET, increased, F, peptides, Analyses, TAF-I, COXIV, M, Open, phosphatase 2A inhibitor I2PP2A, human protein, Computer Programs and Programming, proteins, procedures, COXA_DROME, free, DmelCG4299, set, IGAAD, 13E, Cox4, Methodological Studies, DmelCG10574, 1.3.3.3, GPHYSD2, Racemethionine, COX-VA, SGS, ratio, phapii, wide/broad, T5E21.12, acetylation, 2-Amino-4-(methylthio)butyric acid, StF-IT-1, Procedure, 2-(acetylamino)-2-deoxy-, Spectrum Analysis, Source Softwares, Software Tools, Fsrg1, doi., Programs, ACMICD, Spectroscopy, Program, Computer Applications, RING3, VA, AL024441, Computer Applications Software, FSRG1, Computer Applications Softwares, Methionin, methionine, Softwares, Hmet, COX IV, T5E21_12, Software Applications, HLA-DR-associated protein II, DI-2, Va, Coprogen oxidase, Source Software, I-2Dm, COX IV-1, proportionality, Spectrometry, rate, CG4299, MASS, Methodological, inhibitor of granzyme A-activated DNase, 15S)-, Methodological Study, I-2PP1, Applications, wide, TAF-IBETA, (5Z, TAF-Ibeta, Polypeptide, DmelCG14724, i2pp2a, Liquimeth, Proteomes, Fsrg-1, Cox4a, accessory, Computer Software Applications, NAT, Nat, 2-amino-4-(methylsulfanyl)butanoic acid, D17H6S113E, alpha-L-Talopyranuronic acid, Procedures, False, L Isomer, FBN, alpha-L-N-acetyltalosaminuronic acid, Computer, broad, Spectrum Analyses, protein-containing complex, FSH, supernumerary, PHAPII, DOI, CG10664, polypeptide chain, template-activating factor I, ECTOL1, IV, Mass, Studies, L-Methionine, Del(8)44H, Technique, Pedameth, Application, Mass Spectroscopy, doi, Open Source Softwares, proportion, Coproporphyrinogenase, Software Application, ipp2a2, Open Source Software, Acetylations, 2pp2a, Ring3, CG10574, Computer Software Application, OCTD, Study, 2PP2A, 2-amino-4-(methylthio)butanoic acid, Tools, taf-ibeta, COX, dSET, dSet, peptidos, metionina, Applications Software, Open Source, Computer Software, DL-Methionine, protein complex, igaad, total expressed protein, L-Isomer, Peptide, Tool, polypeptide, Software Tool, native protein, natural protein, I-2PP2A, AW228947, Protein, Dm I-2, I2PP2A, sequence, IV-1, MFS1, mKIAA4005, techniques, Software, Mass Spectrum Analyses, Data Base, Met, WMS2, Mass Spectrum, D6S113E, Col4a-1, increased number, Rnf3, RNF3, Frg-1, Engineering, tend, primary structure of sequence macromolecule, Computer Programs, present in greater numbers in organism, dSET/TAF-Ibeta, 2610030F17Rik, CG14724, Applications Softwares, SSKS, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Peptid, AA407739, alpha-L-2-N-acetylamino-2-desoxytaluronic acid, methodology"],"description_synonyms":["opsonin activity, Dnahc8, ADMIO, hdhc9, membrane bound, HIES, aprf, ligand, Proteins, HeLa, Gene, stat3, Hst6.7b, proteins, B-cell receptor complex, antibodies, Aprf, Cell, P1-Loop, AW109958, hies, Protein Gene Products, Gene Proteins, antibody, immunoglobulin, ATPase, BCR complex, 1110034C02Rik, B cell receptor accessory molecule complex, HeLa Cell, Protein, Cells, B lymphocyte receptor complex, Gene Products, B cell receptor activity, Xstat3, hies., B-lymphocyte receptor complex, immunoglobulin complex, APRF"],"pubmed_abstract_synonyms":["malignant Growth, Dnahc8, nucleocytoplasm, Materials, Activity, FON1, A4, Embden-Meyerhof, FLORAL ORGAN NUMBER 1, type I programmed cell death, Embden Meyerhof Parnas Pathway, dmTAF[[II]]230, Membrane Tissues, Extrinsic Pathway Apoptoses, Programmed, SUP, Impacts, Embden-Meyerhof Pathway, establishment and maintenance of substrate location, Environmental Impacts, IKKg, KEY, Key, increased, oxidative metabolic process, thymus nucleic acid, TFIID TAF250, pre-mortem, cel, non-developmental growth of a unicellular organism, neoplasm (disease), Bdr, Tissue, Pathways, metabolic process resulting in cell growth, Super protein, sp, CA, SNAP-25, Environmental Impact, Intrinsic Pathway Apoptosis, malignant neoplasm, Classic, Classical Apoptosis, cellular growth, Double-Stranded DNA, deoxyribonucleic acids, DNAn, intracellular, cellular suicide, Membrane Tissue, establishment and maintenance of substance location, malignancy, ADMIO, dTAF[[II]]230, Pathway, Caspase-Dependent Apoptosis, aprf, metabolism resulting in cell growth, acid, TAF200, anaerobic glycolysis, Hst6.7b, Double-Stranded, TAFII-250, TAF250/230, Embden-Meyerhof-Parnas, oxidative metabolism, (Deoxyribonucleotide)n+m, Embden-Meyerhof-Parnas Pathway, DmIKKgamma, single organism localization, TAFII250, signaling (initiator) caspase activity, induction of apoptosis, ATP synthase D chain, Intrinsic Pathway, dIKK, Extrinsic Pathway Apoptosis, non-developmental cell growth, organ system cancer, Kenny, GENA70, Genetic Materials, internal to cell, Caspase-Dependent, desoxyribose nucleic acid, regulator, Hydrogen Ions, Hydrogen Ion, Genetic Material, APRF, Acid, Mitochondrial, acidification, acide, IKK-gamma, acids, stat3, acido, Cell Death, CG17603, TAF[[II]], Aprf, Embden-Meyerhof pathway, AW109958, Intrinsic Pathway Apoptoses, living, breathing, DMDA, glycolysis, DmelCG16910, induction of apoptosis by p53, Taf250, Material, SR3-5, ds DNA, Extrinsic Pathway, Cytosols, Cistron, DNA, cancer, Classical, Apoptoses, Embden-Meyerhof Pathways, accessory, TAF230, establishment and maintenance of cellular component location, FLORAL DEFECTIVE 10, d230, DNS, (Deoxyribonucleotide)n, respiration, cell type cancer, caspase-dependent programmed cell death, Caspase Dependent Apoptosis, Gene, dTAFII250, SUPERMAN, apoptotic programmed cell death, EfW1, mitochondrial, supernumerary, activation of apoptosis, dIKK-gamma, TYPE, P1-Loop, Deoxyribonucleic acids, DAGA4, Deoxyribonucleic Acid, dmTAF1, Taf230, DmIKK-gamma, establishment and maintenance of position, dmIKKgamma, Type I, IKK[[gamma]], MAM, neoplasm, SCG3, malignant tumour, TAF250, protoplasm, Taf200, dTAF[[II]]250, Genetic, protoplast, growth of cell, cell, Tissues, HIES, ligand, General activity., Double Stranded, Taf1p, Deoxyribonucleic acid, Proton, apoptosis activator activity, hies, dTAF250, Mif1, ATPase, IKK, Classic Apoptosis, execution phase of apoptotic process, (Deoxyribonucleotide)m, TAF, Saeure, programmed cell death by apoptosis, modifed Embden-Meyerhof pathway, Apoptosis, data, TAF[[II]]250, cell suicide, Embden Meyerhof Pathway, malignant, DNAn+1, apoptotic cell death, l(3)84Ab, BG:DS00004.13, Synaptosomal-associated 25 kDa protein, Cistrons, Cell, LGMD2C, Impact, dTAF230, Environmental, cell expansion, IKKgamma, MT, Ions, p230, malignant neoplasm (disease), Programmed Cell Death, TAF[[II]]250/230, TFIID, Xstat3, establishment and maintenance of localization, ds-DNA, Breathing, Taf[[II]]250, apoptosis signaling, primary cancer, Hydrogen, TAF[[II]]230, apoptosis, DMDA1, hdhc9, Saeuren, Dmikkgamma, increased number, TAF[II]250, FLO10, single-organism localization, Membrane, CG16910, HERP, Embden-Meyerhof-Parnas pathway, malignant tumor, Classic Apoptoses, present in greater numbers in organism, DmelCG17603, 1110034C02Rik, localisation, Ion, malignant neoplastic disease, apoptotic program, SCARMD2, Environments, Desoxyribonukleinsaeure, commitment to apoptosis, General activity, TAF1"],"name_synonyms":["Protein Gene Products, Gene Proteins, ADMIO, 1110034C02Rik, Protein, HIES, aprf, Gene Products, Proteins, Xstat3, Gene, stat3, hies., proteins, Aprf, APRF, AW109958"],"view_count":["197"],"additional_accession":[]},"is_claimable":true,"name":"Mass spectrometry analysis of proteins interacting with STAT3","description":"Mass spectrometry analysis of proteins interacting with STAT3¬Flag was performed. STAT3-Flag was transiently expressed in HeLa cells and the interactome of STAT3-Flag was studied in lysosomal extracts. proteins co-¬immunoprecipitating with STAT3--Flag identified eight subunits of the vacuolar H+-¬ ATPase (V-¬ATPase) as potential STAT3 binding partners. Validation experiments were performed by antibody pull-down of 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