{"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":["7227"],"full_dataset_link":["https://pax-db.org/dataset/7227/1963625303"],"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":["Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism."],"pubmed_title":["A high-quality catalog of the Drosophila melanogaster proteome."],"pubmed_authors":["Brunner Erich E, Ahrens Christian H CH, Mohanty Sonali S, Baetschmann Hansruedi H, Loevenich Sandra S, Potthast Frank F, Deutsch Eric W EW, Panse Christian C, de Lichtenberg Ulrik U, Rinner Oliver O, Lee Hookeun H, Pedrioli Patrick G A PG, Malmstrom Johan J, Koehler Katja K, Schrimpf Sabine S, Krijgsveld Jeroen J, Kregenow Floyd F, Heck Albert J R AJ, Hafen Ernst E, Schlapbach Ralph R, Aebersold Ruedi R"],"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":["total expressed protein, fruit fly, Drosophila, Sophophora melanogaster, melanogaster, D. melanogaster, Drosophila melangaster, Catalogs, Drosophila melanogasters, Proteomes."],"name_synonyms":["NAT, Nat, Fsrg1., D6S113E, 11alpha, multi-cellular organism, D17H6S113E, alpha-L-Talopyranuronic acid, whole organism, body, TalANAc, RNF3, Rnf3, Frg-1, Melanogaster <flies>, whole body, alpha-L-N-acetyltalosaminuronic acid, Ring3, 15S)-, 2-(acetylamino)-2-deoxy-, FSH, 13E, organism, RING3, AW228947, (5Z, Koerper, FSRG1, mKIAA4005, Melanogaster <basidiomycete fungi>, animal, Fsrg-1, alpha-L-2-N-acetylamino-2-desoxytaluronic acid"],"pubmed_abstract_synonyms":["fruit fly, multi-cellular organism, Materials, GRP1/cytohesin 1, determination, Peptidomics, P62, STK10, number, Eukaryotes, Gene, Sophophora melanogaster, sci, melanogaster, presence, CG11633, cytohesin/GRP1, peptide, Polypeptides, Readability, peptido, Method, Drosophila melangaster, GRP1, Grp1, Gene Products, HOW, How, Data Collection Method, animal, l(3)j5D5, 24B, l(3)s2612, Genetic, peptides, pre-mortem, Biology, Data Collection, Genomes, Dual Data, PTPSTEP, Melanogaster <flies>, stru, l(2)SH2 0323, Sciences, proteins, l(3)S053606, Eucarya, CG10293, Fast, l(3)j5B5, Neural-specific protein-tyrosine phosphatase, ATP:Fas-activated serine/threonine protein phosphotransferase activity, l(2)k08110, sample, DmelCG10293, peptidos, species, statistical analysis, FAST, GPH, 0904/17, data, Data Collection Methods, Eukaryote, clone 2.39, body, Proteins, total expressed protein, whole body, stepk, Eukaryotas, FASTK, qkr, l(3)S090417, Cistrons, D. melanogaster, Peptide, predicted, polypeptide, organism, count in organism, native protein, SZ1, KH93F, Protein, Systems, chemical analysis, 3.1.3.48, Genetic Materials, Collection, l(2)SH0323, Library, Genetic Material, Methods, who, CYH1, Koerper., whole organism, distinct, Collection Methods, Step, CG11628, Eukarya, Striatum-enriched protein-tyrosine phosphatase, INSDC_feature:gene, Who/How, whole genome, Understanding, sample population, DmelCG11628, Protein Gene Products, Gene Proteins, living, Drosophila, STEP, Data, Material, Drosophila melanogasters, data collection, Koerper, qkr[93F], anon-EST:Liang-2.39, Peptid, Cistron, Polypeptide, assay, Dual Data Collection, Feedbacks, Collection Method, Melanogaster <basidiomycete fungi>, Proteomes"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"D.melanogaster - Whole organism, SC (Brunner,nat_biotechnol,2007)","description":"abundance based on Spectral counting, Interaction consistency score: 20.4, Coverage: 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