PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering189518https://pax-db.org/dataset/189518/225164180mering@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-based methods for relative proteome quantification have broadly affected life science research. However, important research directions, particularly those involving mathematical modelling and simulation of biological processes, also critically depend on absolutely quantitative data--that is, knowledge of the concentration of the expressed proteins as a function of cellular state. Until now, absolute protein concentration measurements of a considerable fraction of the proteome (73%) have only been derived from genetically altered Saccharomyces cerevisiae cells, a technique that is not directly portable from yeast to other species. Here we present a mass-spectrometry-based strategy to determine the absolute quantity, that is, the average number of protein copies per cell in a cell population, for a large fraction of the proteome in genetically unperturbed cells. Applying the technology to the human pathogen Leptospira interrogans, a spirochete responsible for leptospirosis, we generated an absolute protein abundance scale for 83% of the mass-spectrometry-detectable proteome, from cells at different states. Taking advantage of the unique cellular dimensions of L. interrogans, we used cryo-electron tomography morphological measurements to verify, at the single-cell level, the average absolute abundance values of selected proteins determined by mass spectrometry on a population of cells. Because the strategy is relatively fast and applicable to any cell type, we expect that it will become a cornerstone of quantitative biology and systems biology.Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.Malmström Johan J, Beck Martin M, Schmidt Alexander A, Lange Vinzenz V, Deutsch Eric W EW, Aebersold Ruedi RAdd, 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, ratioStriated muscle activator of Rho-dependent signaling, data, Stars, T6G21.3, STARS, MS1, Ms1, MALE STERILITY 1 PROTEIN, data., male sterility 1human being, wide/broad, Man (Taxonomy), protein complex, Modern, Proteins, total expressed protein, Gene, proteins, Spirochaeta icterohaemorrhagiae, protein, broad, Spirochaeta biflexa, protein-containing complex, man, human, Protein Gene Products, Human, Gene Proteins, wide, protein polypeptide chains, Spirochaeta interrogans, native protein, natural protein, polypeptide chain, Homo sapiens, Spirochaeta icterogenes, Modern Man, Protein, Gene Products, Spirochaeta nodosa., protein aggregate, Proteomes, Man, Leptospira icteroidesorganism, data, Stars, multi-cellular organism, whole organism, MS1, Ms1, MALE STERILITY 1 PROTEIN, data., body, male sterility 1, Koerper, Striated muscle activator of Rho-dependent signaling, whole body, T6G21.3, animal, STARSCane-Cutter Fever, scale tissue, Activity, Laboratory, Leptospiroses, harvest fever, Mbp1, protein, Canicola Fever, dmTAF[[II]]230, School-Age, Techniques, protein polypeptide chains, Method, rice-field worker's disease, Leptospirosis Canicolas, Analysis, Research Activity, protein aggregate, myd, Laboratory Research, WMS, Leptospira icteroides, Priorities, Mass Spectrum Analysis, average, mud fever, Man (Taxonomy), TFIID TAF250, Analyses, Biology, cel, entire life cycle, plant peltate hair, Rice-Field, Swineherd's Disease, Saccharomyes cerevisiae, Mbp-1, beta-particle, proteins, Baker, procedures, Saccharomyces uvarum var. melibiosus, Fast, Leptospira Canicola, e, Methodological Studies, Swineherd's Diseases, e-, Saccharomyces capensis, Fever, Baker's, Mycoderma cerevisiae, infection due to Leptospira, Research Priority, brewer's yeast, GPHYSD2, FAST, Cane Cutter Fever, SGS, Leptospira Infections, dTAF[[II]]230, anatomical protrusion, swineherd's disease, gyltl1b-b, Arts, Modern, TAF200, Research Priorities, FASTK, Positrons, Procedure, TAFII-250, TAF250/230, Spectrum Analysis, canicola fever, ACMICD, Spectroscopy, Baker's Yeasts, TAFII250, Saccharomyces diastaticus, School Age, MDDGA6, mKIAA0609, Fast Electron, Weil disease, Cane-Cutter, KIAA0609, Research and Development, fg, Yeast, Populations, Epistemology, Industrial, gyltl1b, Industrial Arts, Queensland fever, life, mdc1d, expanded, rice-field fever, Spectrometry, MASS, Methodological, Electron, CG17603, Methodological Study, TAF[[II]], cell_type, human, beta(-), Activities, Leptospira Canicola Infection, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, MDC1D, enr, Taf250, enlarged, spine, SR3-5, School-Age Population, cane-cutter fever, Proteomes, Brewer's Yeast, TAF230, Spirochaeta nodosa, Leptospira, big, d230, lifespan, human being, Procedures, Systems., Leptospirosis Canicola, peltate hair, number, e(-), STK10, Brewer's, FBN, Gene, baker's yeast, dTAFII250, Spirochaeta icterohaemorrhagiae, electron, Spectrum Analyses, protein-containing complex, EfW1, presence, Saccharomyces italicus, froggy, Gyltl1a, protrusion, Human, Tomographies, method, large, Leptospira Infection, polypeptide chain, Homo sapiens, dmTAF1, ECTOL1, Taf230, method used in an experiment, yeast, Studies, Gene Products, Mass, Technique, Man, lager beer yeast, Mass Spectroscopy, TAF250, School-Age Populations, japanese autumnal fever, Taf200, dTAF[[II]]250, Infections, Research, Stuttgart Disease, entire lifespan, cell, MDDGB6, Elektron, Sciences, Taf1p, LARGE, Population, man, Leptospira Canicola Infections, S. cerevisiae, OCTD, Study, dTAF250, BPFD#36, Stuttgart disease, cane cutter's fever, S cerevisiae, Candida robusta, Rice-Field Fever, Rice Field Fever, ATP:Fas-activated serine/threonine protein phosphotransferase activity, great, Development and Research, 1883, species, Icterohemorrhagic fever, School Age Population, TAF, Electrons, Positron, data, TAF[[II]]250, Saccharomyces cerevisiae 'var. diastaticus', protein complex, Negatron, Proteins, total expressed protein, l(3)84Ab, swamp fever, Negatrons, function, BG:DS00004.13, Saccaromyces cerevisiae, Cell, Mud, dTAF230, Sccharomyces cerevisiae, count in organism, Priority, MS, native protein, natural protein, p230, Protein, Research Activities, Infection, TAF[[II]]250/230, TFIID, MFS1, techniques, Fevers, scales, Fast Electrons, Mass Spectrum Analyses, WMS2, Saccharomyces oviformis, Taf[[II]]250, Mass Spectrum, TAF[[II]]230, scale, negatron, Canicola, TAF[II]250, Spirochaeta biflexa, School Age Populations, beta, Protein Gene Products, plan specification, Gene Proteins, DmelCG17603, Spirochaeta interrogans, concentration, seven day fever, Spirochaeta icterogenes, Modern Man, SSKS, cardinality, hemorrhagic jaundice, Mud Fever, Baker's Yeast, Baker Yeast, methodology, TAF10falseL.interrogans - Whole organism, Ms1 quantification data, MS1 normalized data (Malmström,nature,2009)abundance based on MS1 normalized data, MS1 quantification data, Interaction consistency score: 1.2, Coverage: 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