PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2001000ProteomicsChristian von Mering511145https://pax-db.org/dataset/511145/3645765292mering@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 describe a proteomic approach combining the multi-enzyme digestion FASP-sample processing strategy and the 'Total Protein Approach' applied to absolute quantification of proteins in Escherichia coli. Consecutive digestion of whole cell lysates with LysC and trypsin allowed the generation of two populations of peptides at a yield of 76%. Subsequent two 4-hour LC-MS/MS analyses allowed the identification of 19,000 unique peptides per sample. Notably, only 1.2 and 2.4% of the identified peptides were found to be incompletely cleaved by the LysC and trypsin, respectively. The analysis resulted in the identification of 2200 proteins per sample. We show high reproducibility of the approach, allowing the accurate estimation of cellular protein concentrations. Quantitative analysis of the DNA content per sample enabled the calculation of the protein content per bacterial cell and, as a result, estimation of protein copy numbers. The accuracy of these estimations was confirmed by analyzing protein complexes with known subunit stoichiometry and cellular abundances. In stationary culture, a single bacterium contains about 6500 copies of ribosomes, 300 molecules of RNA polymerase and 10 DNA polymerase assembles. The here presented experimental and computational workflow offers an easy way to analyze proteomes quantitatively.<h4>Biological significance</h4>We demonstrate a proteomic workflow for in-depth analysis of small proteomes with minimal fractionation extent and mass spectrometry measuring time. For the first time we provide the quantitative picture of the Escherichia coli proteome at protein copy number.Multi-enzyme digestion FASP and the 'Total Protein Approach'-based absolute quantification of the Escherichia coli proteome.Wiśniewski Jacek R JR, Rakus Dariusz D, Rakus Dariusz DAdd, 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, ratioCPC complex, cytidine-3'-phosphate-5'-cytidine., CpC, CPC, chromosomal passenger complexAlkalescens-Dispar Group, Diffusely Adherent Escherichia coli, Bacterium coli, Escherichia/Shigella coli, Enteroinvasive E. coli, Biocatalysts, protein complex, Proteins, total expressed protein, Gene, E coli, bacterium E3, proteins, protein, EAggEC, protein-containing complex, Enteroaggregative E. coli, E. coli, Protein Gene Products, Enteroaggregative Escherichia coli, Eschericia coli, Gene Proteins, protein polypeptide chains, Enzyme, native protein, Bacterium coli commune, natural protein, polypeptide chain, Diffusely Adherent E. coli, Bacillus coli, Escherchia coli, Protein, Proteomes., Biocatalyst, Gene Products, Enteroinvasive Escherichia coli, Enterococcus coli, protein aggregatePeptidomics., CPC complex, organism, multi-cellular organism, whole organism, chromosomal passenger complex, body, Koerper, whole body, CpC, CPC, animal, cytidine-3'-phosphate-5'-cytidineliquid chromatography tandem mass spectroscopy, extent, Ribonucleic, determination, bacterium E3, protein, neutral molecular compounds, composed of, Long Term, dmTAF[[II]]230, Polypeptides, protein polypeptide chains, Background, peptido, Cultural, Enterococcus coli, Analysis, protein aggregate, Work Flow, Effect, molecule, Non Polyadenylated, RNA Gene Products, molecula, Mass Spectrum Analysis, ethnicity, thymus nucleic acid, LCMSMS, molecules, Escherichia/Shigella coli, TFIID TAF250, peptides, Analyses, cel, hypoplasia, E coli, composition, proteins, Molekuel, E. coli, Enteroaggregative Escherichia coli, Eschericia coli, h, scientific observation, sample, Double-Stranded DNA, deoxyribonucleic acids, DNAn, Long-Term Effects, LC-MS2, dTAF[[II]]230, ribose nucleic acid, completeness, LC-MS/MS, ribonucleic acids, TAF200, Longterm Effect, Double-Stranded, TAFII-250, TAF250/230, Enteroaggregative E. coli, Spectrum Analysis, (Deoxyribonucleotide)n+m, Spectroscopy, TAFII250, Cultural Background, Workflows, Cultures, Diffusely Adherent E. coli, Ribonukleinsaeure, pentosenucleic acids, Ribonucleic acids, desoxyribose nucleic acid, Acid, Diffusely Adherent Escherichia coli, Enteroinvasive E. coli, Cultural Beliefs, content, Spectrometry, CG17603, TAF[[II]], beta Trypsin, Taf250, SR3-5, liquid chromatography-tandem mass spectroscopy, ds DNA, Biocatalyst, Polypeptide, DNA, Proteomes, Work Flows, TAF230, d230, DNS, (Deoxyribonucleotide)n, Effects, Biocatalysts, number, Gene, dTAFII250, Spectrum Analyses, protein-containing complex, EfW1, presence, Deoxyribonucleic acids, LC-MS-MS, polypeptide chain, Deoxyribonucleic Acid, reduced, dmTAF1, Taf230, Escherchia coli, LC-MSMS, Gene Products, Mass, Enteroinvasive Escherichia coli, tiny, Mass Spectroscopy, Backgrounds, TAF250, Taf200, dTAF[[II]]250, Longterm, cell, beta-Trypsin, Double Stranded, Taf1p, Cultural Relativisms, Deoxyribonucleic acid, Long-Term, Non-Polyadenylated RNA, dTAF250, Enzyme, Customs, peptidos, Long-Term Effect, (Deoxyribonucleotide)m, culture, TAF, Alkalescens-Dispar Group, small, measuring, RNA, Bacterium coli, TAF[[II]]250, protein complex, DNAn+1, Proteins, total expressed protein, l(3)84Ab, RNS, BG:DS00004.13, EAggEC, compositionality, Cultural Backgrounds, Cell, Peptide, dTAF230, count in organism, LC/MS/MS, MS, native protein, natural protein, Bacillus coli, p230, yeast nucleic acid, Protein, chemical analysis, Long Term Effects, TAF[[II]]250/230, TFIID, ds-DNA, Mass Spectrum Analyses, Taf[[II]]250, ribonucleic acid, Mass Spectrum, Ribosome, TAF[[II]]230, PRSS, underdeveloped, Non Polyadenylated RNA, Tripcellim, Non-Polyadenylated, TAF[II]250, Ribonucleic Acid, cardinality., sample population, Longterm Effects, Protein Gene Products, Gene Proteins, Trypure, DmelCG17603, Bacterium coli commune, structure, Desoxyribonukleinsaeure, liquid chromatography tandem mass spectrometry, Relativisms, Peptid, assay, Relativism, Cultural Relativism, TAF11falseE.coli - Whole organism, Cpc (Wisniewski,j_proteomics,2014)abundance based on MAPPED_BY_AUTHORS, cpc, Interaction consistency score: 12.7, Coverage: 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