PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering4565https://pax-db.org/dataset/4565/3866569555mering@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.Protein abundance in cereal grains is determined by the relative rates of protein synthesis and protein degradation during grain development but quantitation of these rates is lacking. Through combining in vivo stable isotope labelling and in-depth quantitative proteomics, we have measured the turnover of 1400 different types of proteins during wheat grain development. We demonstrate that there is a spatiotemporal pattern to protein turnover rates which explain part of the variation in protein abundances that is not attributable to differences in wheat gene expression. We show that c. 20% of total grain adenosine triphosphate (ATP) production is used for grain proteome biogenesis and maintenance, and nearly half of this budget is invested exclusively in storage protein synthesis. We calculate that 25% of newly synthesized storage proteins are turned over during grain development rather than stored. This approach to measure protein turnover rates at proteome scale reveals how different functional categories of grain proteins accumulate, calculates the costs of protein turnover during wheat grain development and identifies the most and the least stable proteins in the developing wheat grain.Protein turnover in the developing Triticum aestivum grain.Cao Hui H, Duncan Owen O, Millar A Harvey AHAdd, 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, ratioLFQ.Triticum durum, protein complex, Durum, Triticum vulgare, Triticum aestivum8, Triticum spelta, Proteins, Triticum sativum, Triticum aestivam, Gene, Triticum turgidum subsp. durum, proteins, protein, protein-containing complex, Triticum aestivum subsp. aestivum, wheat, Tricum aestivum, common wheat, Protein Gene Products, Gene Proteins, protein polypeptide chains, grain., bread wheat, Durum Wheats, native protein, natural protein, polypeptide chain, Protein, Canadian hard winter wheat, Gene Products, Durum Wheat, Triticum turgidum, protein aggregate, Wheat, Triticum aestivum内胚乳、胚乳 (Japanese, LFQ., albumen (exact), Endosperms, exact), albumen, endosperma (Spanishprotein translation, Striadyne, scale tissue, single-organism developmental process, Magnesium Adenosine Triphosphate, Grain Protein, Peptidomics, Adenosine Triphosphate, P62, postnatal development, peltate hair, Degradation, number, ATP-MgCl2, Gene, growth and development, protein, sci, IB, protein-containing complex, Triticum aestivum subsp. aestivum, presence, Adenylpyrophosphate, protein polypeptide chains, grain., polypeptide chain, ATP-synbeta, Gene Products, HOW, How, protein aggregate, l(3)j5D5, Wheat, H4atp, 24B, Chromium Adenosine Triphosphate, pheromone catabolism, pattern, Gene Expressions, l(3)s2612, DmelCG11154, distribution, Triticum aestivum8, Triticum spelta, plant peltate hair, beta-ATPase, ATP MgCl2, Triticum aestivam, stru, proteins, labeling, l(3)S053606, Protein Degradations, wheat, Maintenances, Budget, Expressions, CG10293, Protein Degradation, Tricum aestivum, retention, common wheat, Budgetary Control, l(3)j5B5, bread wheat, ATPsyn b, Chromium Salt, ATPasebeta, CrATP, MnATP, Cr(H2O)4 ATP, ATPase beta, DmelCG10293, Durum Wheat, Triticum turgidum, Expression, ATPB, ATP, Chromium Ammonium Salt, ATPsyn-&bgr, Triticum durum, protein anabolism, 0904/17, Degradations, protein biosynthetic process, ATPsyn-b, protein complex, clone 2.39, Triticum vulgare, Proteins, Magnesium Chloride, total expressed protein, Triticum turgidum subsp. durum, qkr, Protein Digestion, Adenosine 5'-(tetrahydrogen triphosphate), grain, l(3)S090417, Digestions, ATP-syn-B, development, Isotope, count in organism, Atriphos, ML-1, native protein, Budgetary Controls, natural protein, Proteolyses, Digestion, SZ1, KH93F, Protein, Canadian hard winter wheat, Manganese Salt, protein formation, Magnesium Salt, protein biosynthesis, Adenosine 5'-triphosphate, scales, CG11154, who, pheromone catabolic process, ADENOSINE-5'-TRIPHOSPHATE, Manganese Adenosine Triphosphate, scale, storage, Durum, Protein Digestions, postnatal growth, Triticum sativum, Control, Who/How, Controls, Adenosine triphosphate, Protein Gene Products, Gene Proteins, CaATP, Durum Wheats, multicellular organismal protein catabolic process, Budgetary, protein synthesis, ATPIB, MgATP, qkr[93F], anon-EST:Liang-2.39, sequestering, growth, Proteomes, Calcium Salt, Triticum aestivum0falseTaestivum - Endosperm, LFQ (Caoetal,newphytol2022)abundance based on LFQ, Interaction consistency score: 2.0, Coverage: 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