PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering3702https://pax-db.org/dataset/3702/1928073589mering@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.We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.Baerenfaller Katja K, Grossmann Jonas J, Grobei Monica A MA, Hull Roger R, Hirsch-Hoffmann Matthias M, Yalovsky Shaul S, Zimmermann Philip P, Grossniklaus Ueli U, Gruissem Wilhelm W, Baginsky Sacha SAdd, 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, ratiothale cress, mouse-ear cress, scale tissue, Materials, Genetic, scale, Genomes, Peptidomics, Arbisopsis thaliana, Cresses, A., plant peltate hair, peltate hair, Arabidopsis thaliana, Mouse-ear Cress, thaliana, total expressed protein, Gene, A. thaliana, INSDC_feature:gene, whole genome, Mouse-ear Cresses, Cistrons, Mouse-ear, Arabis thaliana, thale-cress, Arabidopsis, Arabidopsis thalianas, Material, A. thalianas, Proteomes., thalianas, Arabidopsis thaliana (thale cress), Genetic Materials, Cress, Cistron, Mouse ear, scales, Arabidopses, Genetic Materialorganism, whole body, multi-cellular organism, Sciences., whole organism, animal, body, KoerperIPP2A2, Biological Markers, Viral Marker, Materials, Surrogate Endpoints, Activity, Systems., methionine aminopeptidase activity, determination, Clinical Markers, Laboratory, Peptidomics, A., Clinical Marker, Pflanze, number, Biochemical, Gene, Endpoint, protein, Serum, protein-containing complex, presence, Arabis thaliana, PHAPII, element, viridiplantae, Cardaminopsis, Surrogate End Points, 5730420M11Rik, Polypeptides, Surrogate Markers, protein polypeptide chains, Laboratory Markers, Arabidopsis thalianas, peptido, polypeptide chain, Biological, A. thalianas, thalianas, Gene Products, 2, protein aggregate, familial adenomatous polyposis, MAP, peptidase M activity, Catalogs, adenomas, organ, plantae, Biomarker, rabGAPLP, SET, L-methionine aminopeptidase activity, Genetic, Clinical, peptides, Genomes, Biology, Cresses, TAF-I, familial adenomatous polyposis 2, Biological Marker, Mouse-ear Cress, ipp2a2, RabGAP-5, 2pp2a, proteins, Mouse-ear, high grade, CG10574, autosomal recessive multiple colorectal adenomas, DmelCG4299, IGAAD, set, thale-cress, Immunologic Markers, Immune, Markers, 2PP2A, DmelCG10574, taf-ibeta, RUSC3, anatomical unit, Viral Markers, body organ, dSET, dSet, Cress, peptidos, Mouse ear, Arabidopses, Immunologic Marker, Biologic, phapii, Viral, MUTYH-Associated Polyposis, Surrogate Endpoint, Arbisopsis thaliana, protein complex, Arabidopsis thaliana, Proteins, Serum Markers, MYH-associated polyposis, igaad, autosomal recessive familial adenomatous polyposis, total expressed protein, Maps, End Point, StF-IT-1, A. thaliana, Biochemical Markers, Cistrons, Biologic Marker, INSDC_feature:misc_RNA, Cell, Peptide, Immune Marker, group, count in organism, native protein, natural protein, I-2PP2A, Marker, Surrogate End Point, Protein, chemical analysis, Dm I-2, I2PP2A, Arabidopsis thaliana (thale cress), Genetic Materials, Genetic Material, Data Base, autosomal recessive, Biologic Markers, thale cress, mouse-ear cress, RUTBC3, Serum Marker, HLA-DR-associated protein II, End Points, ensemble, DI-2, Surrogate, I-2Dm, Endpoints, Plant, thaliana, INSDC_feature:gene, Immunologic, CG4299, whole genome, MYH-Associated Polyposis, Laboratory Marker, Mouse-ear Cresses, Surrogate Marker, RABGAP5, Protein Gene Products, I-2PP1, Gene Proteins, dSET/TAF-Ibeta, Arabidopsis, 2610030F17Rik, TAF-IBETA, Material, Biochemical Marker, multiple colorectal, MAP syndrome, Peptid, Cistron, TAF-Ibeta, Polypeptide, assay, AA407739, i2pp2a, Proteomes, General activity, FAP2, colorectal adenomatous polyposis, Immune Markers0falseA.thaliana - Whole organism, SC (Baerenfaller,science,2008)abundance based on Spectral counting, Interaction consistency score: 13.5, Coverage: 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