PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering8030https://pax-db.org/dataset/8030/2967557145mering@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.Understanding diet- and environmentally induced physiological changes in fish larvae is a major goal for the aquaculture industry. Proteomic analysis of whole fish larvae comprising multiple tissues offers considerable potential but is challenging due to the very large dynamic range of protein abundance. To extend the coverage of the larval phase of the Atlantic salmon (Salmo salar) proteome, we applied a two-step sequential extraction (SE) method, based on differential protein solubility, using a nondenaturing buffer containing 150 mM NaCl followed by a denaturing buffer containing 7 M urea and 2 M thiourea. Extracts prepared using SE and one-step direct extraction were characterized via label-free shotgun proteomics using nanoLC-MS/MS (LTQ-Orbitrap). SE partitioned the proteins into two fractions of approximately equal amounts, but with very distinct protein composition, leading to identification of ∼40% more proteins than direct extraction. This fractionation strategy enabled the most detailed characterization of the salmon larval proteome to date and provides a platform for greater understanding of physiological changes in whole fish larvae. The MS data are available via the ProteomeXchange Consortium PRIDE partner repository, dataset PXD003366.Sequential protein extraction as an efficient method for improved proteome coverage in larvae of Atlantic salmon (Salmo salar).Nuez-Ortín Waldo G WG, Carter Chris G CG, Nichols Peter D PD, Wilson Richard 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, ratioAtlantic Salmons, Procedures, protein complex, Proteins, Atlantic., total expressed protein, Gene, proteins, protein, Methodological, Procedure, protein-containing complex, Methodological Study, 1758, Protein Gene Products, plan specification, Study, Gene Proteins, protein polypeptide chains, method, Techniques, Salmon, native protein, Methodological Studies, natural protein, polypeptide chain, Atlantic salmon, Method, method used in an experiment, Protein, Gene Products, Studies, Salmons, Atlantic Salmon, protein aggregate, Technique, Proteomes, Atlantic, Salmo salar LinnaeusLarvae, Maggot, Tadpoles, Tadpole, Maggots.big, Solubilities, Bioflocs, SOXB2.1, Sectors, GRP1/cytohesin 1, l(3)LG9, Procedures, Peptidomics, fishes, 2310014D11Rik, Sry-rDM33, Tertiary Sectors, Goal, Mbp1, Sry-rDM36, Gene, Carbamide, protein, Basodexan, protein-containing complex, froggy, Gyltl1a, Agnatha, loD, Buffer, CG11633, Oncorhynchus nerka, cytohesin/GRP1, Karbamid, Readability, large, protein polypeptide chains, method, Techniques, AA589508, DM63, halite, Sh3md1, polypeptide chain, C230050L11, Atlantic salmon, Method, Oncorhynchus gorbuscha, GRP1, method used in an experiment, TSK5, Grp1, Harnstoff, Diets, Gene Products, Studies, Sry-rDM23, Atlantic Salmon, CG5893, Carmol, protein aggregate, myd, Technique, Atlantic, Gm5098, Industries, bony fishes, Atlantic Salmons, DM10, Pink Salmon, MDDGB6, MS2, E927b, PTPSTEP, Chinook Salmon, Tissue, l(2)SH2 0323, chlorure de sodium, Mbp-1, Chinook, LARGE, proteins, Fish, EG329070, free, Sockeye Salmon, 1758, Sry-rDM10, Study, cloruro sodico, BPFD#36, salt, Neural-specific protein-tyrosine phosphatase, Methodological Studies, Salmo salmo, l(2)k08110, great, Kochsalz, fish, FISH, Sockeye, Sox70D, GPH, Data Set., DmelCG5893, AI256723, Sox B2-1, data, rock salt, DM33, gyltl1b-b, DM36, protein complex, SH3MD1, Sox70, Proteins, total expressed protein, stepk, Procedure, buffer, ur, Actinopterygi, Oncorhynchus tshawytscha, carbamide, Salmon, common salt, Tertiary, native protein, ray-finned fishes, natural protein, Natriumchlorid, DM23, carbonyldiamide, SOX70D, MDDGA6, Cephalaspidomorphi, mKIAA0609, Protein, proteomic analysis, 3.1.3.48, table salt, Pink, AI413738, NaCl, KIAA0609, l(2)SH0323, tandem MS, Sry-rDM63, SOXDP, CYH1, Hyperotreti, fg, Monorhina, gyltl1b, distinct, Step, CG11628, uree, MS/MS, Dietary, mdc1d, expanded, Biofloc, Striatum-enriched protein-tyrosine phosphatase, Methodological, Understanding, natrii chloridum, Methodological Study, TKS5, Tks5, Aquacultures, DmelCG11628, Osteichthyes, Protein Gene Products, plan specification, Gene Proteins, SOX70, MDC1D, H2NC(O)NH2, Sector, enr, enlarged, STEP, label, Tertiary Sector, Salmons, Proteomes, 1728, Salmo salar Linnaeus0falseSsalar - Larvae, iBAQ (Nuez-ortinetal,proteomics2016)abundance based on iBAQ, Interaction consistency score: 3.6, Coverage: 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