PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4896https://pax-db.org/dataset/4896/2189306272mering@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.Mass spectrometry (MS)-based proteomics typically employs multistep sample-preparation workflows that are subject to sample contamination and loss. We report an in-StageTip method for performing sample processing, from cell lysis through elution of purified peptides, in a single, enclosed volume. This robust and scalable method largely eliminates contamination or loss. Peptides can be eluted in several fractions or in one step for single-run proteome analysis. In one day, we obtained the largest proteome coverage to date for budding and fission yeast, and found that protein copy numbers in these cells were highly correlated (R(2) = 0.78). Applying the in-StageTip method to quadruplicate measurements of a human cell line, we obtained copy-number estimates for 9,667 human proteins and observed excellent quantitative reproducibility between replicates (R(2) = 0.97). The in-StageTip method is straightforward and generally applicable in biological or clinical applications.Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells.Kulak Nils A NA, Pichler Garwin G, Paron Igor I, Nagaraj Nagarjuna N, Mann Matthias MAdd, 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, rationumber, Eukaryotic Cell, count in organism, Eukaryotic., presence, sample population, sample, Cell, cardinality, Cells, EukaryoticKoerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyCG1849, human being, GRP1/cytohesin 1, Procedures, determination, Peptidomics, Fission, leg, number, Gene, Progress Reports, protein, Spectrum Analyses, Schizosaccharomyces pombe, Schizosaccharomyces malidevorans, protein-containing complex, presence, Human, CG11633, l(1)AA33, cytohesin/GRP1, Polypeptides, method, Techniques, protein polypeptide chains, Fission Yeast, Investigative, peptido, polypeptide chain, Homo sapiens, Method, Summary Report, method used in an experiment, GRP1, Grp1, Mass, Studies, Gene Products, Line, 1, 2, Analysis, protein aggregate, Summary Reports, Technique, fission yeast, Man, Mass Spectroscopy, Mass Spectrum Analysis, Schizosaccharomyces pombeP, Man (Taxonomy), peptides, Analyses, Progress Report, Runt, PTPSTEP, l(2)SH2 0323, proteins, man, Study, Progress, Field Reports, Neural-specific protein-tyrosine phosphatase, Methodological Studies, method used in an experiment., l(1)B2/13.1, RUN, Run, l(2)k08110, sample, peptidos, Investigative Reports, degree of contamination, GPH, LB5, l(1)LB9, protein complex, Modern, Proteins, DmelCG1849, Cell Lines, total expressed protein, stepk, budding, Procedure, Rnt, S pombe, Spectrum Analysis, Peptide, Cell, AA33, Spectroscopy, lLB5, count in organism, MS, native protein, Investigative Report, natural protein, Research Reports, chemical analysis, Protein, 3.1.3.48, l(2)SH0323, Mass Spectrum Analyses, Lines, CYH1, Mass Spectrum, Yeast, Step, CG11628, Field, Spectrometry, Striatum-enriched protein-tyrosine phosphatase, l(1)19Ea, Methodological, Methodological Study, sample population, human, DmelCG11628, plan specification, Protein Gene Products, P235, Gene Proteins, Report, Fission Yeasts, Reports, STEP, Modern Man, cardinality, Peptid, Polypeptide, assay, Summary, Proteomes, Field Report0falseS.pombe - Whole organism, SC (Kulaketal,natmethods2014)abundance based on Spectral counting, Interaction consistency score: 15.4, Coverage: 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