PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering7955https://pax-db.org/dataset/7955/1256290770mering@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.Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovary, spleen, and testis) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins.Blattmann Peter P, Stutz Vivienne V, Lizzo Giulia G, Richard Joy J, Gut Philipp P, Aebersold Ruedi RAdd, 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, ratiozebra fish, Danio rerio (Hamilton, Zebra, leopard danio, Danio rerio, Zebra Fish, Protein., Danio frankei, Zebrafishes, Proteins, Gene, Fishes, proteins, Cyprinus rerio Hamilton, danio, Zebra danios, Protein Gene Products, Zebra danio, Gene Proteins, zebra danio, native protein, B. rerio, Danio rerio frankei, 1822), Protein, Zebra Fishes, 1822, D. rerio, Gene Products, Brachydanio rerio, Cyprinus rerio, Brachidanio rerio, zebrafish, D. rerios, Brachydanio rerio frankeithe brain, synganglion, suprasegmental structures, suprasegmental levels of nervous system, encephalon, Encephalon.CDF, visual_system, Herz, Materials, testicle, Mbp1, adult heart, protein, extracted material, DmelCG6383, gonada of female organism genitalia, Polypeptides, circulatory vessel, protein polypeptide chains, POF, peptido, gonad of male genitalia, eye, globe, AGAMOUS-like 61, synganglion, Analysis, protein aggregate, myd, D. rerios, DiA, genitalia of female organism gonada, Mass Spectrum Analysis, Muscle Tissues, l(2)k07135, Man (Taxonomy), peptides, Analyses, heart or heart like organ, Testicle, Zebrafishes, eyes, ovum-producing ovary, visual system, Tissue, crumb, iecur, female organism reproductive system gonad, Mbp-1, Intestine, Fishes, proteins, DIASP, suprasegmental levels of nervous system, cardiac structure, intestinal tract, DIA, Dia, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, reproductive system of female organism gonada, Komplexauge, bowel, scientific observation, data., 38E.16, Zebra Fishes, Medicine, Danio rerio (Hamilton, eye globe, dorsal tube, vertebrate heart, leopard danio, suprasegmental structures, CG6383, gyltl1b-b, gonada of reproductive system of female organism, gonad of female organism reproductive system, Modern, vertebrate eye, Cyprinus rerio Hamilton, Spectrum Analysis, not genetically inherited, Spectroscopy, Eyes, ms(2)04138, Desmoplastic infantile astrocytoma, chambered heart, Experimental, Ovaries, MDDGA6, mKIAA0609, 1822), 1822, Brachydanio rerio, Genetic Materials, cardium, KIAA0609, zusammengesetztes Auge, female reproductive system gonad, Genetic Material, eyeball, fg, gyltl1b, Danio rerio, gonada of genitalia of female organism, POF2, F27C12_24, Encephalon, Orbital part of face, F27C12.24, mdc1d, Spectrometry, expanded, gonad of reproductive system of female organism, lien, male gonad, muscle element, organ system, MDC1D, enr, female organism genitalia gonada, enlarged, orbital part of face, Material, Testicles, DIANA, D. rerio, Cistron, Polypeptide, l(3)S050920, Proteomes, zebrafish, humans, Crbs, zebra fish, the brain, big, compound eye, regio orbitalis, number, adult compound eye, Gene, branchial heart, Coding, far, Spectrum Analyses, protein-containing complex, presence, body system, froggy, Gyltl1a, Biomedical, Human, jecur, gonad of male reproductive system, large, gonad of genitalia of female organism, zebra danio, Investigative, Homo sapiens, Crumbs, camera-type eye plus associated structures, polypeptide chain, DmelCG1768, Medical Research, Mass, HILDA, Gene Products, system, testiculus, Cyprinus rerio, Medical, Man, Mass Spectroscopy, light-detecting organ, Orbital region, CT19912, 0509/20, gonada of female organism reproductive system, anatomical systems, Clinical, Genetic, Research, Tissues, MDDGB6, genitalia of female organism gonad, Medical Coding, 1384/04, LARGE, BPFD#36, cardiac pump, reproductive system of female organism gonad, B. rerio, orchis, great, musculus, Investigational Medicine, ovary - animal, ovary, peptidos, DIA2, testes, female organism genitalia gonad, female reproductive system gonada, Brachydanio rerio frankei, l(3)j1B5, measuring, data, Zebra Fish, gonad of female reproductive system, protein complex, gonada of female reproductive system, Desmoplastic astrocytoma of infancy, Proteins, total expressed protein, bulbus oculi, Hearts, CG1768, DRF2, Muscle, Cistrons, encephalon, Peptide, visual apparatus, l(3)07207, Investigative Medicine, count in organism, MS, native protein, natural protein, Facettenauge, MLPLI, Danio rerio frankei, Protein, heart, CRB, Crb, Dias, connected anatomical system, Brachidanio rerio, l(3)S058104, Library, Mass Spectrum Analyses, Investigational, theoretical mass, Mass Spectrum, ovaries, female organism reproductive system gonada, Zebra, animal ovary, Danio frankei, Experimental Medicine, female gonad, ovarium, gonad of female organism genitalia, muscle, danio, Zebra danios, Protein Gene Products, Zebra danio, Gene Proteins, Livers, orbital region, Modern Man, Peptid, Muscle Tissue, Testes0falseD.rerio - Brain, SC (Blattmannetal,scidata.2019)abundance based on Spectral counting, Interaction consistency score: 11.2, Coverage: 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