{"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":["246200"],"full_dataset_link":["https://pax-db.org/dataset/246200/402674203"],"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":["The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of <sup>13</sup>C-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 <sup>13</sup>C-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."],"pubmed_title":["Growth phase proteomics of the heterotrophic marine bacterium Ruegeria pomeroyi."],"pubmed_authors":["Krayushkina Dasha D, Timmins-Schiffman Emma E, Faux Jessica J, May Damon H DH, Riffle Michael M, Harvey H Rodger HR, Nunn Brook L BL"],"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":["postnatal growth, development, growth and development, growth, growth pattern, Peptidomics, non-developmental growth, postnatal development, Silicibacter pomeroyi."],"name_synonyms":["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, AHC"],"pubmed_abstract_synonyms":["protein 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 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