{"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/7227/1621505028"],"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":["Drosophila melanogaster is one of the most widely used model organisms in life sciences. Mapping its proteome is of great significance for understanding the biological characteristics and tissue functions of this species. However, the comprehensive coverage of its proteome remains a challenge. Here, we describe a high-coverage analysis of whole fly through a 1D gel electrophoresis and LC-MS/MS approach. By combining the datasets of two types of SDS-PAGE and two kinds of tagmata, the high-coverage analysis resulted in the identification of 5262 genes, which correspond to 38.23% of the entire coding genes. Moreover, we found that the fly head and body have different molecular weight distributions of their proteomes when the proteins were resolved with SDS-PAGE and image analysis of the stained gel. This phenomenon was further confirmed by both label-free and isobaric tags for relative and absolute quantitation-based quantitative approaches. The consistent results of the two different quantitation methods also demonstrated the stability and accuracy of the LC-MS/MS platform. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD000454 and PXD000455 (http://proteomecentral.proteomexchange.org/dataset/PXD000454; (http://proteomecentral.proteomexchange.org/dataset/PXD000455)."],"pubmed_title":["Qualitative and quantitative analysis of the adult Drosophila melanogaster proteome."],"pubmed_authors":["Xing Xiaohua X, Zhang Chengpu C, Li Ning N, Zhai Linhui L, Zhu Yunping Y, Yang Xiaoming X, Xu Ping P"],"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":["count in organism, fruit fly, Drosophila, determination, Drosophila melangaster, Drosophila melanogasters, chemical analysis, adult stage, Proteomes., number, total expressed protein, assay, Sophophora melanogaster, Adults, melanogaster, presence, adult, D. melanogaster"],"name_synonyms":["Peptidomics., Melanogaster <flies>, organism, whole body, multi-cellular organism, whole organism, Melanogaster <basidiomycete fungi>, animal, body, Koerper"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, big, fruit fly, lifespan, Materials, multi-cellular organism, Molecular Weights, Procedures, determination, Peptidomics, AI461847, Feature, number, IMAGE, Gene, Coding, Gel Electrophoresis, Sophophora melanogaster, melanogaster, SDS polyacrylamide gel electrophoresis of proteins, presence, LC-MS-MS, large, Readability, Sodium Dodecyl Sulfate PAGE, Techniques, Electrophoreses, Method, Drosophila melangaster, LC-MSMS, Polyacrylamide Gel Electrophoresis, Gene Products, Studies, DGS, SDS-PAGE, Pgi, Gpi-1, animal, Medical, Technique, INSL3R, portion of tissue, Polyacrylamide, LCMSMS, Gpr106, Genetic, Clinical, SDS-PAGE electrophoresis, entire lifespan, Molecular, Gpi-1r, Nlk, entire life cycle, Medical Coding, Gpi-1s, gel, cephalic area, Phi, Tissue, Gpi-1t, Weights, Sciences, RXFPR2, Heads, proteins, procedures, free, Study, GREAT, Methodological Studies, DmelCG1106, great, Great, head (volume), Characteristics, species, GPR106, KINDS, SDS PAGE, NK/GPI, LC-MS2, Data Set., close to, Gpi, data, Data Set, body, Proteins, LC-MS/MS, total expressed protein, whole body, Procedure, MF, Cistrons, Amf, D. melanogaster, results, near to, organism, count in organism, LC/MS/MS, Characteristic, native protein, mOC-X, chemical analysis, Weight, Protein, tissue portion, Genetic Materials, simple tissue, NK|GPI, techniques, Genetic Material, NK, LGR8, Lgr8, Org, ORG, whole organism, Sodium Dodecyl Sulfate-PAGE, life, sodium dodecyl sulphate–polyacrylamide gel electrophoresis, expanded, SDS polyacrylamide gel electrophoresis, Gpi1-r, Gpi1-s, Methodological, Understanding, LGR8.1, Features, Gpi1-t, Methodological Study, CG1106, Protein Gene Products, Gene Proteins, Drosophila, enlarged, Material, liquid chromatography-tandem mass spectroscopy, label, approaches, Drosophila melanogasters, Koerper, vicinity of, liquid chromatography tandem mass spectrometry, Cistron, assay, Sodium Dodecyl Sulfate-PAGEs, adult head, Proteomes, Bglap-rs1, methodology, Gpi1s"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"D.melanogaster - Whole organism, SC (Xing,proteomics,2014)","description":"abundance based on Spectral counting, Interaction consistency score: 25.8, Coverage: 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