PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering4932https://pax-db.org/dataset/4932/2521601554mering@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.Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities.System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap.Nagaraj Nagarjuna N, Kulak Nils Alexander NA, Cox Juergen J, Neuhauser Nadin N, Mayr Korbinian K, Hoerning Ole O, Vorm Ole O, 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, ratiol(2)k04204, OG12X, determination, kop, Liquid Chromatography, CG18076, total expressed protein, baker's yeast, 6330543G17Rik, CG18637, body system, Saccharomyces italicus, Saccaromyces cerevisiae, shortstop/kakapo, l(2)k05821, Sccharomyces cerevisiae, l(2)k15606, DmelCG18076, chemical analysis, yeast, High Performance Liquid Chromatography, system, connected anatomical system, lager beer yeast, Shot, Saccharomyces oviformis, Yeast, l(2)k05434, anatomical systems, l(2)k10821, Grv, l(2)k03010, High-Performance Liquid Chromatography., Su(Mir)1, Saccharomyes cerevisiae, kak, Saccharomyces uvarum var. melibiosus, SHOT, High-Performance Liquid Chromatographies, OG12, HPLC, organ system, High Pressure, Candida robusta, High-Performance, Saccharomyces capensis, grv, Chromatography, Ultra Performance Liquid Chromatography, Liquid, High-Performance Liquid, l(2)CA4, High Speed Liquid, High Performance Liquid, assay, UPLC, brewer's yeast, Og12x, Proteomes, Prx3, 42/4l(3)Ca, multi-cellular organism, body, mCRY, titin, whole body, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, ingensin, kettin, organism, large multicatalytic protease, CFU-MC, HEL-S-66, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, animal, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, whole organism, AFCP, colony forming unit mast cell, D-Titin, CG18857, MIC10, ket, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, multicatalytic proteinase (complex), Koerper, proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245Heat Shock Stress, cox4, Materials, Product, Lysine Hydrochloride, Laboratory, 26S protease, Long Term, l(1)AA33, dmTAF[[II]]230, protein polypeptide chains, large multicatalytic protease, Lysine Acetate, Bio Informatics, Biological, B1, l(2)SH1330, DmelCG1915, 1, 2, Biological Product, Research Activity, multicatalytic endopeptidase complex, myd, Laboratory Research, L Lysine, Priorities, average, Biologic Drugs, TFIID TAF250, Genomes, cel, K, COXIV, Saccharomyes cerevisiae, HardwareType, Mbp-1, Weights, proteins, Saccharomyces uvarum var. melibiosus, COXA_DROME, Computational, allergic reaction, Biological Medicine, LYS, Cox4, l(1)B2/13.1, Lysin, sample, polyhedral organelle, Medicine, Birth Place, 1.3.3.3, AHUS2, COX-VA, Biologic Drug, Computational Molecular Biologies, multicatalytic proteinase, LC-MS2, dTAF[[II]]230, Communities, l(1)LB9, Heat Shock Response, protein biosynthetic process, anatomical protrusion, Biologic Products, titin, Biologies, Liquid Chromatography, TAF200, Longterm Effect, Research Priorities, threonine endopeptidase activity, Heat Stresses, Computational Molecular, l(2)br3, mKIAA0609, AL024441, Computational Molecular Biology, Neighborhood, protein formation, numerical data, prosome, tricorn proteinase, Research and Development, fg, Industrial, whole organism, Industrial Arts, instrument, Coprogen oxidase, Biological Medicines, Biological Drug, expanded, Biologics, alpha, Activities, TLX, MDC1D, enr, Taf250, protein synthesis, Material, liquid chromatography-tandem mass spectroscopy, multicatalytic proteinase (complex), Koerper, Arrangement, Residence Characteristic, CG18242, alkaline protease, TAF230, CG18245, big, multi-cellular organism, Biologic Pharmaceuticals, Peptidomics, Effects, Mypt1, protein-containing complex, Mbh1, SLS, Sls, DmelCG4482, body system, Saccharomyces italicus, CG10664, large, sensitive, IV, yeast, LC-MSMS, Gene Products, system, Titin, Lysine, lager beer yeast, CFU-Mast, Heat Stress Response, Biologicals, anatomical systems, dTAF[[II]]250, Longterm, cell, MDDGB6, colony forming unit mast cell, Long-Term, Living Arrangement, dTAF250, l(3)dre8, Living, COX, KZ, species, Development and Research, Mcp, MCP, Biologic, LB5, Pharmaceuticals, Products, Place of Birth, use, CG4482, body, Biologic Medicines, Proteins, whole body, BG:DS00004.13, Rnt, Saccaromyces cerevisiae, Cell, dTAF230, lLB5, Sccharomyces cerevisiae, native protein, Acetate, chemical analysis, Long Term Effects, Biopharmaceutical, TAF[[II]]250/230, L-Lysine, Saccharomyces oviformis, Taf[[II]]250, Specificity, D-Titin, Longterm Effects, Gene Proteins, br3, CG14724, Heat-Stress Responses, Stress, liquid chromatography tandem mass spectrometry, NIP, Enisyl, Heat-Stress Response, proteasome endopeptidase complex, liquid chromatography tandem mass spectroscopy, protein translation, Heat-Shock Reaction, l(3)Ca, Activity, determination, mCRY, leg, instrument configuration, Mbp1, nip, d-titin, protein, Measure, Molecular Biologies, Living Arrangements, Heat, DmelCG10664, Community., protein aggregate, animal, Effect, Ket, Shock, LCMSMS, Heat-Stress Reaction, Biology, Natural, epsilon-diaminocaproic acid, 35Bb, Biological Drugs, ket, Bio-Informatic, Saccharomyces capensis, RUN, Run, Bio-Informatics, Medicines, Research Priority, brewer's yeast, TRA2.10, Long-Term Effects, M110, protein anabolism, gyltl1b-b, statistics and numerical data, Arts, LC-MS/MS, Heat-Shock Responses, MBSP, 0020/01, TAFII-250, TAF250/230, AA33, organism, TAFII250, l35Bb, CFU-MC, Heat Shock Stresses, VA, MDDGA6, Biopharmaceuticals, Genetic Materials, Biologic Product, median, COX IV, KIAA0609, Genetic Material, Yeast, gyltl1b, Bioinformatic, Va, COX IV-1, mdc1d, Heat-Stress Reactions, MIC10, CG17603, TAF[[II]], l(2)SH2 1330, organ system, CG1915, enlarged, Specificity and Sensitivity, spine, SR3-5, tricorn protease, Cistron, Measures and Weights, DmelCG14724, BG:DS01219.1, Residential Selection, Proteomes, Cox4a, CG1849, d230, mol, Goal, baker's yeast, Gene, dTAFII250, EfW1, froggy, LC-MS-MS, hardware, Gyltl1a, protrusion, ingensin, polypeptide chain, dmTAF1, utilization, Taf230, HEL-S-66, Crry, anon-CREST, sensitivity, l(2)br23, l(3)j1D7, TAF250, Drugs, study, Taf200, Coproporphyrinogenase, Genetic, Research, AFCP, Runt, Natural Product, Measures, Taf1p, LARGE, CG18857, BPFD#36, lens neutral proteinase, Domiciles, Candida robusta, Heat Shock Reaction, great, Sensitivity, l(3)rL182, Long-Term Effect, TAF, Molecular Biology, TAF[[II]]250, Encyclopedias, protein complex, l(2)35Bb, DmelCG1849, total expressed protein, l(3)84Ab, l(3)62Ca, Cistrons, Bioinformatics, kettin, Neighborhoods, LC/MS/MS, Priority, Heat Stress, natural protein, p230, Systems, Protein, Research Activities, TFIID, Heat Stress Reaction, protein biosynthesis, IV-1, connected anatomical system, D-titin, TAF[[II]]230, Heat-Shock Reactions, Scales, tend, TAF[II]250, l(1)19Ea, CG15268, Heat Shock, Heat Shocks, sample population, sam, sal, Protein Gene Products, Drug, P235, DmelCG17603, CT41299, l(3)S002001, Natural Products, assay, Domicile, TAF10falseS.cerevisiae - Whole organism, Intensity (Nagaraj,mcp,2012)abundance based on MAPPED_BY_AUTHORS, intensity, Interaction consistency score: 11.4, Coverage: 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