PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/1935546345mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.Knowledge of the identity and quantity of expressed proteins of a cell type is a prerequisite for a complete understanding of its molecular functions. Mass-spectrometry-based proteomics has allowed the identification of the entire protein complement of yeast and the close-to-complete set of proteins expressed in mammalian cell lines. Using recent technological advances, we here characterized the proteome of murine platelets, key actors in mediating hemostasis and thrombosis. We accurately measured the absolute protein concentrations of 13 platelet proteins using SILAC-protein epitope signature tags and used them as reference points to estimate the copy numbers of all proteins of the platelet proteome. To distinguish contaminants such as plasma or erythrocyte proteins from true platelet proteins, we monitored protein abundance profiles across multiple purification steps. In total, we absolutely quantified 4,400 platelet proteins, with estimated copy numbers ranging from less than 10 to about a million per cell. Stoichiometries derived from our data correspond well with previous studies. Our study provides a close-to-complete reference map of platelet proteins that will be useful to the community, for instance, for interpreting mouse models of human platelet diseases.Copy number analysis of the murine platelet proteome spanning the complete abundance range.Zeiler Marlis M, Moser Markus M, Mann Matthias MAdd, 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, ratiocount in organism, Thrombocytes, anucleate thrombocyte, determination, cardinality, chemical analysis, Blood, Proteomes., thrombocyte, number, Blood Platelet, blood platelet, Platelet, total expressed protein, assay, enucleate thrombocyte, platelet, Thrombocyte, presence, PlateletsThrombocytes, anucleate thrombocyte, musculus, Blood, thrombocyte, Blood Platelet, Blood., blood platelet, Platelet, muscle, enucleate thrombocyte, platelet, Thrombocyte, Platelets, muscle elementAntigenic Determinants, IPP2A2, Thrombus, methionine aminopeptidase activity, Laboratory, Blood, Mus domesticus, RBC, protein, House Mouse, clot, 5730420M11Rik, Thromboses, dmTAF[[II]]230, Readability, protein polypeptide chains, epitope function, Thrombocytes, diseases, 2, diseases and disorders, protein aggregate, WMS, IKKg, peptidase M activity, KEY, Key, adenomas, SET, Fresh Frozen Plasmas, Fresh Frozen, rabGAPLP, L-methionine aminopeptidase activity, human disease, Man (Taxonomy), TFIID TAF250, antigenic determinant, TAF-I, cel, thrombus, red blood corpuscle, Saccharomyes cerevisiae, RabGAP-5, Swiss Mice, proteins, purification, Saccharomyces uvarum var. melibiosus, Estimated, DmelCG4299, isolation and purification, IGAAD, set, DmelCG10574, anucleate thrombocyte, Saccharomyces capensis, RUSC3, blood, Red, Homo sapiens disease, house mouse, brewer's yeast, GPHYSD2, blood clot, epitope role, plasma, SGS, Blood Clot, phapii, Epitope, dTAF[[II]]230, Frozen Plasma, PLATEST, Modern, Blood Platelet, MYH-associated polyposis, mouse, TAF200, Blood Clots, autosomal recessive familial adenomatous polyposis, StF-IT-1, Maps, Red Blood Cell, TAFII-250, TAF250/230, Plasmas, mice C57BL/6xCBA/CaJ hybrid, ACMICD, DmIKKgamma, TAFII250, dIKK, Kenny, Diseases, Red Blood Corpuscle, autosomal recessive, Antigenic Determinant, Mus musculus, Yeast, Blood Cell, RUTBC3, Epistemology, portion of blood plasma, HLA-DR-associated protein II, Complement, DI-2, mice, I-2Dm, red blood cell, IKK-gamma, Swiss Mouse, thrombosis, MASS, CG4299, CG17603, TAF[[II]], cell_type, human, RABGAP5, domesticus, I-2PP1, Red Blood Corpuscles, disease, blood plasm, TAF-IBETA, DmelCG16910, Taf250, Red Blood Cells, SR3-5, Atherothrombosis, multiple colorectal, Erythrocyte, Complement System, Platelet, blood platelet, medical condition., TAF-Ibeta, Mouse, Blood Corpuscles, platelet, i2pp2a, Proteomes, Platelets, TAF230, Fresh, other disease, d230, human being, Fresh Frozen Plasma, Peptidomics, FBN, Gene, baker's yeast, dTAFII250, Antigenic Specificity, protein-containing complex, Complement Protein, EfW1, blood Clots, Saccharomyces italicus, dIKK-gamma, PHAPII, Human, Determinant, polypeptide chain, Homo sapiens, dmTAF1, isolation, House, ECTOL1, Taf230, DmIKK-gamma, yeast, Gene Products, thrombocyte, Mus musculus domesticus, disease or disorder, dmIKKgamma, IKK[[gamma]], Blood Corpuscle, Mice, Man, familial adenomatous polyposis, lager beer yeast, MAP, TAF250, study, Taf200, Blood Plasma, dTAF[[II]]250, cell, Swiss, familial adenomatous polyposis 2, ipp2a2, 2pp2a, Antigenic, Taf1p, man, CG10574, OCTD, autosomal recessive multiple colorectal adenomas, non-neoplastic, dTAF250, Candida robusta, 2PP2A, IKK, taf-ibeta, Blood Plasmas, dSET, dSet, disorder, Hemolytic, TAF, Thrombocyte, data, TAF[[II]]250, MUTYH-Associated Polyposis, protein complex, Proteins, igaad, disorders, total expressed protein, l(3)84Ab, BG:DS00004.13, Saccaromyces cerevisiae, Cell, group, Mus muscaris, dTAF230, Sccharomyces cerevisiae, Frozen Plasmas, IKKgamma, native protein, natural protein, Hemostases, I-2PP2A, Mus, p230, Protein, Dm I-2, I2PP2A, TAF[[II]]250/230, TFIID, condition, MFS1, Hemolytic Complement, Determinants, WMS2, Saccharomyces oviformis, Taf[[II]]250, Plasma, Blood Cells, TAF[[II]]230, thrombotic disorder, ensemble, Dmikkgamma, Specificity, portion of plasma, House Mice, TAF[II]250, Understanding, enucleate thrombocyte, MYH-Associated Polyposis, CG16910, Laboratory Mice, Protein Gene Products, Gene Proteins, Complement Proteins, dSET/TAF-Ibeta, 2610030F17Rik, DmelCG17603, Clots, Modern Man, SSKS, MAP syndrome, AA407739, Laboratory Mouse, FAP2, TAF1, colorectal adenomatous polyposis0falseM.musculus - Platelet, SC (Zeileretal,molcellproteomics2014)abundance based on Spectral counting, Interaction consistency score: 15.1, Coverage: 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