{"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"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["3702"],"full_dataset_link":["https://pax-db.org/dataset/3702/4256979337"],"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":["Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported<sup>1</sup>, advances in mass-spectrometry-based proteomics<sup>2</sup> have enabled increasingly comprehensive identification and quantification of the human proteome<sup>3-6</sup>. However, there have been few comparisons across species<sup>7,8</sup>, in stark contrast with genomics initiatives<sup>9</sup>. Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides from Bacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org."],"pubmed_title":["The proteome landscape of the kingdoms of life."],"pubmed_authors":["Müller Johannes B JB, Geyer Philipp E PE, Colaço Ana R AR, Treit Peter V PV, Strauss Maximilian T MT, Oroshi Mario M, Doll Sophia S, Virreira Winter Sebastian S, Bader Jakob M JM, Köhler Niklas N, Theis Fabian F, Santos Alberto A, Mann Matthias M"],"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":["life., total expressed protein, lifespan, Proteomes, entire lifespan, entire life cycle"],"name_synonyms":["bud, adventitious bud (narrow), primordia, rudiment., future organ, placode"],"pubmed_abstract_synonyms":["scale tissue, FON1, Mbp1, Non-Governmental Organizations, protein, FLORAL ORGAN NUMBER 1, NK/GPI., Photosynthetic Carbon Fixation, peptide, Polypeptides, protein polypeptide chains, peptido, GRP1, Grp1, SUP, 26Fe, Work Flow, protein aggregate, Transfer, Gpi-1, myd, Carbon Fixation, WMS, Divorced, Man (Taxonomy), peptides, Genomes, Nlk, entire life cycle, plant peltate hair, Comparative Genomics, Machine, PTPSTEP, Bdr, Mbp-1, proteins, Divorces, Super protein, inhibition of homeostatic process, Calvin-Benson-Bassham, sp, SNAP-25, l(2)k08110, homeostasis, Calvin, Organizations, GPHYSD2, SGS, GPH, Gpi, Genomics, organisation, gyltl1b-b, Comparative, Modern, Learning, Calvin Benson Cycle, Functional Genomics, results, predicted, ACMICD, Workflows, Iron 56, mOC-X, positive regulation of homeostatic process, MDDGA6, mKIAA0609, 3.1.3.48, GENA70, NK|GPI, KIAA0609, fg, carbohydrate metabolism, Org, ORG, gyltl1b, Iron, Step, CG11628, Nongovernmental, life, administrative structure, mdc1d, expanded, Gpi1-r, Calvin Benson Bassham Cycle, Gpi1-s, Striatum-enriched protein-tyrosine phosphatase, MASS, Gpi1-t, human, Fe, organ system, MDC1D, Health, Eisen, enr, enlarged, STEP, Polypeptide, iron, Proteomes, Work Flows, Bglap-rs1, sulphur metabolism, Gpi1s, FLORAL DEFECTIVE 10, big, lifespan, human being, GRP1/cytohesin 1, conformation, Health Resource, Peptidomics, AI461847, peltate hair, number, FBN, Gene, organization and administration, SUPERMAN, Reductive Pentose Phosphate Cycle, protein-containing complex, body system, froggy, Gyltl1a, Human, CG11633, cytohesin/GRP1, large, Structural, Homo sapiens, polypeptide chain, ECTOL1, Metabolism, Photosynthesis Dark Reactions, Cycle, single-organism carbohydrate metabolic process, Gene Products, Functional, system, Pgi, Non-Governmental, Separated, Man, Resources, study, Transfer Learning, Organization, hierro, multicellular organismal carbohydrate metabolic process, anatomical systems, entire lifespan, Gpi-1r, MDDGB6, Gpi-1s, Phi, Gpi-1t, l(2)SH2 0323, LARGE, man, OCTD, BPFD#36, Mif1, Neural-specific protein-tyrosine phosphatase, Non-Governmental Organization, great, negative regulation of homeostatic process, Calvin-Benson-Bassham Cycle, peptidos, species, organization, Dark Reactions of Photosynthesis, relational structural quality, Autoregulation, data, organizational structure, protein complex, Photosynthetic, Proteins, Photosynthesis Dark Reaction, fer, total expressed protein, stepk, Synaptosomal-associated 25 kDa protein, MF, Amf, Peptide, polypeptide, native protein, Resource, natural protein, Protein, sequence, MFS1, Calvin-Benson Cycle, scales, connected anatomical system, Nongovernmental Organizations, regulation of homeostatic process, l(2)SH0323, WMS2, NK, sulfur metabolism, CYH1, administrative management, Separation, ferrum, scale, Separations, sulphur metabolic process, FLO10, Iron-56, HERP, Carbohydrate, primary structure of sequence macromolecule, DmelCG11628, Protein Gene Products, Gene Proteins, Non Governmental Organizations, activation of homeostatic process, Calvin Cycle, SNAP, Modern Man, SSKS, cardinality, organizational management, Structural Genomics, Peptid, Calvin-Benson, Nongovernmental Organization"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"A.thaliana - Bud, SC (Muelleretal,nature2020)","description":"abundance based on Spectral counting, Interaction consistency score: 14.0, Coverage: 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