PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering246200https://pax-db.org/dataset/246200/402674203mering@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.The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of ¹³C-labeled leucine to track bacterial protein biosynthesis through growth phases. A combination of methods allowed observation of real-time bacterial protein production to understand metabolic priorities through the different growth phases. Over 2000 proteins were identified in each experimental culture from exponential and stationary growth phases. Within two hours of the ¹³C-labeled leucine addition, R. pomeroyi significantly assimilated the newly encountered substrate into new proteins. This dataset provides a fundamental baseline for understanding growth phase differences in molecular physiology of a cosmopolitan marine bacterium.Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi.Krayushkina Dasha D, Timmins-Schiffman Emma E, Faux Jessica J, May Damon H DH, Riffle Michael M, Harvey H Rodger HR, Nunn Brook L BLAdd, 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, ratiopostnatal growth, development, growth and development, growth, growth pattern, Peptidomics, non-developmental growth, postnatal development, Silicibacter pomeroyi.DAX-1, Koerper., dss, HHG, multi-cellular organism, whole organism, CHM, DAX1, CMT1E, NROB1, MPP, body, CMTDID, CMT1A, CMT1B, AHX, AHCH, CMT2I, hmsnia, whole body, CMT2J, GAS-3, CMT1, sp110, CMTDI3, P0, organism, DSS, gas-3, HNPP, SRXY2, CMT4E, Sp110, hnpp, GTD, HMSNIA, cmt1e, HMSNIB, animal, cmt1a, AHCprotein translation, Protein Biosynthesis, (RS)-Leucine, Ribosomal Peptide, Procedures, Effects, FON1, postnatal development, Bacterial Protein, L Isomer, Synthesis, Gene, Ribosomal Protein, carbon, SUPERMAN, growth and development, FLORAL ORGAN NUMBER 1, Gene Product, Long Term, L-Leucine, Translation, L-Isomer Leucine, Techniques, Background, Readability, Carbon-12, Method, Cultural, SUP, Studies, Gene Products, Leucin, Effect, Technique, Backgrounds, Genetic Translations, C, Ribosomal, ethnicity, Genetic, mRNA Translation, Ribosomal Protein Biosynthesis, Longterm, L, Bdr, Peptide Biosynthesis, Cultural Relativisms, proteins, procedures, Long-Term, Super protein, (+-)-Leucine, sp, SNAP-25, Study, Mif1, Kohlenstoff, Bacterial Gene Proteins, Methodological Studies, Carbon, Customs, Ribosomal Peptide Biosynthesis, Long-Term Effect, culture, Gene Protein, Genetic Translation, Long-Term Effects, mRNA Translations, protein anabolism, protein biosynthetic process, Data Set, Proteins, Longterm Effect, Synaptosomal-associated 25 kDa protein, Procedure, Cultural Backgrounds, L-Isomer, carbone, carbono, Vitreous, development, Bacterial Gene Product, Cultural Background, native protein, Cultures, Protein, Long Term Effects, protein formation, Silicibacter pomeroyi, GENA70, protein biosynthesis, techniques, Bacterial Gene Products, Bacterial, Ribosomal Protein Synthesis, Cultural Beliefs, function., Biosynthesis, mRNA, growth pattern, Leucine, 6C, non-developmental growth, postnatal growth, Leuzin, FLO10, Methodological, Bacterial Gene Protein, Understanding, HERP, Methodological Study, Longterm Effects, Carbon 12, Protein Gene Products, Gene Proteins, Protein Synthesis, Vitreous Carbon, Protein Translation, protein synthesis, SNAP, carbonium, DL-Leucine, 2-amino-4-methylpentanoic acid, Relativisms, Hleu, Relativism, Cultural Relativism, growth, Leu, methodology, FLORAL DEFECTIVE 100falseRpomeroyi DSS-3 - Whole organism, SC (Krayushkinaetal,scidata2019)abundance based on Spectral counting, Interaction consistency score: 9.3, Coverage: 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