{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["10090"],"full_dataset_link":["https://pax-db.org/dataset/10090/190918057"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["We used high-resolution mass spectrometry to map the cytotoxic T lymphocyte (CTL) proteome and the effect of the metabolic checkpoint kinase mTORC1 on CTLs. The CTL proteome was dominated by metabolic regulators and granzymes, and mTORC1 selectively repressed and promoted expression of a subset of CTL proteins (~10%). These included key CTL effector molecules, signaling proteins and a subset of metabolic enzymes. Proteomic data highlighted the potential for negative control of the production of phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3) by mTORC1 in CTLs. mTORC1 repressed PtdIns(3,4,5)P3 production and determined the requirement for mTORC2 in activation of the kinase Akt. Our unbiased proteomic analysis thus provides comprehensive understanding of CTL identity and the control of CTL function by mTORC1."],"pubmed_title":["The cytotoxic T cell proteome and its shaping by the kinase mTOR."],"pubmed_authors":["Hukelmann Jens L JL, Anderson Karen E KE, Sinclair Linda V LV, Grzes Katarzyna M KM, Murillo Alejandro Brenes AB, Hawkins Phillip T PT, Stephens Len R LR, Lamond Angus I AI, Cantrell Doreen A DA"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"pubmed_title_synonyms":["Cell-Mediated Lympholytic Cells, Mechanistic target of rapamycin, Cytotoxic T Cell, TC2 Cell, 2610315D21Rik, killer T cell, Lympholytic Cell, FKBP12-rapamycin complex-associated protein, CG5092, cytotoxic T cell, Lympholytic Cells, total expressed protein, FRAP1, T-Lymphocyte, FRAP2, killer T lymphocyte, mTOR, l(2)k03905, FRAP/TOR, DmelCG5092, l(2)k17004, Cell, DmTOR, TC2 Cells, TC2, Cytotoxic T-Lymphocytes, TC1, 2.7.11.1, T Lymphocyte, Cell Mediated Lympholytic Cells, Cell-Mediated, Cytotoxic T Lymphocytes, cytotoxic T lymphocyte, RAFT1, TOR, Mammalian target of rapamycin, Cell-Mediated Lympholytic, RAPT1, Cytotoxic T, Cell-Mediated Lympholytic Cell, killer T-lymphocyte, Bx34, Cytotoxic T Lymphocyte, Rapamycin and FKBP12 target 1, Cytotoxic T Cells, killer T-cell, CT24745, Rapamycin target protein 1, AI327068, flat, tor, Tpr, TPR, cytotoxic T-cell, FRAP, DmelCG8274., TC1 Cells, cytotoxic T-lymphocyte, dtor, TC1 Cell, CT16317, Cytotoxic, CG8274, 5092, MTOR, T Cell, Cytotoxic T-Lymphocyte, Frap1, T Lymphocytes, CT24817, Proteomes, Lymphocyte, dTOR, dTor, FK506-binding protein 12-rapamycin complex-associated protein 1"],"name_synonyms":["Thymus-Dependent Lymphocyte., T-cell, Thymus-Dependent Lymphocytes, T-Cells, Thymus-Dependent, T, Lymphocytes, muscle, T-Lymphocyte, T-lymphocyte, Cell, muscle element, T Cells, T cell, T Lymphocyte, T-Cell, musculus, mature T cell, Cells, T Cell, immature T cell, T Lymphocytes, T lymphocyte, Thymus Dependent Lymphocytes, Lymphocyte"],"pubmed_abstract_synonyms":["PRKBA, Akt/PKB, MTORC-2, methionine aminopeptidase activity, Lympholytic Cell, DAKT1/PKB, T-Lymphocyte, killer T lymphocyte, CG10030, neutral molecular compounds, AKT1, ctl, PtdIns, prevention, Readability, T Lymphocyte, 2, Cytotoxic T Lymphocytes, Analysis, prevention and control, molecule, IKKg, peptidase M activity, KEY, Key, mTORC1 Complex, molecula, Mass Spectrum Analysis, adenomas, rabGAPLP, Cytotoxic T, L-methionine aminopeptidase activity, molecules, killer T-lymphocyte, Granzyme, enzymes, reference sample, Analyses, rapamycin and nutrient-sensitive TOR complex, RabGAP-5, killer T-cell, proteins, Granzyme-3, Natural Killer Cell Granule Tryptase 2, Molekuel, mTORC1 Complex., cytotoxic T-cell, PKB|Akt, Phosphatidyl Inositol, RacPK, preventive measures, Inositol Phospholipids, RUSC3, signaling process, Cytotoxic T-Lymphocyte, Cytotoxic T Lymphocyte Proteinase 1, cytolytic T-lymphocyte, single organism signaling, Granzyme Like Protein III, TC2 Cell, preventive therapy, dTORC1, dakt, NK-Tryptase-2, DmelCG33122, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, Lympholytic Cells, l(3)89Bq, Spectrum Analysis, Spectroscopy, DmIKKgamma, PKB/Akt, PKB/AKT, AKT/PKB, Hanukah Factor, dAkt, dAKT, dIKK, Kenny, p-Akt, Cell-Mediated, Phosphoglyceride, TOR complex 1, TOR complex 2, DAkt, activation, autosomal recessive, l(3)04226, Granzyme 3, TORC 2 complex, RUTBC3, DPKB, Cytotoxic T-Lymphocyte Proteinase 1, pAkt, phosphatidylinositols, nutrient sensitive complex, Granzyme C, IKK-gamma, Spectrometry, Cytotoxic T Cells, Granzyme A, Granzyme B, Cytotoxic T Lymphocyte Associated 1 Protein, Granzyme K, dAKT/dPKB, PKB/dAKT, cytotoxic T-lymphocyte, dTOR/dRaptor complex, Granzyme M, RABGAP5, cytolytic T-cell, Phosphoinositides, TC1 Cell, Dakt, DmelCG16910, dPKB, multiple colorectal, Inositide Phospholipids, Biocatalyst, T Cell, Proteomes, RAC-ALPHA, TORC1, TORC2, DRAC-PK85, DmelCG4006, biological signaling, Inositide, Biocatalysts, cytotoxic T cell, Phosphatidylinositol, Gene, Spectrum Analyses, Granzyme-Like Protein III, dIKK-gamma, Dpkb, DmIKK-gamma, Mass, Gene Products, Cell Mediated Lympholytic Cells, Phosphatidyl, dmIKKgamma, TOR, IKK[[gamma]], Inositide Phospholipid, Cell-Mediated Lympholytic, familial adenomatous polyposis, Mass Spectroscopy, MAP, Cell-Mediated Lympholytic Cell, Phospholipid, Cytotoxic Serine Protease B, familial adenomatous polyposis 2, NK Tryptase 2, Complex, autosomal recessive multiple colorectal adenomas, Enzyme, IKK, rapamycin and nutrient-insensitive TOR complex, AKT, Akt, DRAC-PK, Complex 2, Torc2, T Lymphocytes, Lymphocyte, Controlled, Cell-Mediated Lympholytic Cells, data, Controlling, Cytotoxic T Cell, TORC 1 complex, Inositol Phosphoglyceride, MUTYH-Associated Polyposis, akt, killer T cell, Proteins, total expressed protein, enzyme activity, DAkt1, Phosphoglycerides, DAKT1, function, Cell, TC2 Cells, TC2, Cytotoxic T-Lymphocytes, Fragmentin 2, Inositol, TC1, IKKgamma, MS, PKB, native protein, CWS6, Inositol Phosphoglycerides, Protein, PKB-ALPHA, proteomic analysis, Target of Rapamycin Complex 1, D-Akt, CG4006, cytotoxic T lymphocyte, Target of Rapamycin Complex 2, 4632407F12Rik, Mass Spectrum Analyses, mTORC2, CG33122, mTORC1, Dakt1, Mass Spectrum, Phosphoinositide, Phospholipids, akt1, dAkt1, Dmikkgamma, prophylaxis, Cytotoxic T Lymphocyte, DRAC-PK66, Understanding, MYH-Associated Polyposis, CG16910, TC1 Cells, signalling, Cytotoxic T-Lymphocyte Associated 1 Protein, Protein Gene Products, Gene Proteins, Natural Killer Cell Granule Tryptase-2, dAkt/PKB, dakt1, Inositol Phospholipid, signalling process, TOR Complex 1, control, TOR Complex 2, Cytotoxic, PKBalpha, MAP syndrome, dAKT1, RAC, Rac, PI, CTL, FAP2, colorectal adenomatous polyposis"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"M.musculus - T cell, SC (Hukelmannetal,natimmunol2016)","description":"abundance based on Spectral counting, Interaction consistency score: 16.2, Coverage: 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