PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering511145https://pax-db.org/dataset/511145/1292600129mering@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.Recent advances in mass spectrometry (MS) have led to increased applications of shotgun proteomics to the refinement of genome annotation. The typical "proteo-genomic" workflows rely on the mapping of peptide MS/MS spectra onto databases derived via six-frame translation of the genome sequence. These databases contain a large proportion of spurious protein sequences which make the statistical confidence of the resulting peptide spectrum matches difficult to assess. Here we performed a comprehensive analysis of the Escherichia coli proteome using LTQ-Orbitrap MS and mapped the corresponding MS/MS spectra onto a six-frame translation of the E. coli genome. We hypothesized that the protein-coding part of the E. coli genome approaches complete annotation and that the majority of six frame-specific (novel) peptide spectrum matches can be considered as false positive identifications. We confirm our hypothesis by showing that the posterior error probability distribution of novel hits is almost identical to that of reversed (decoy) hits; this enables us to estimate the sensitivity, specificity, accuracy, and false discovery rate in a typical bacterial proteo-genomic dataset. We use two complementary computational frameworks for processing and statistical assessment of MS/MS data: MaxQuant and Trans-Proteomic Pipeline. We show that MaxQuant achieves a more sensitive six-frame database search with an acceptable false discovery rate and is therefore well suited for global genome reannotation applications, whereas the Trans-Proteomic Pipeline achieves higher specificity and is well suited for high-confidence validation. The use of a small and well-annotated bacterial genome enables us to address genome coverage achieved in state-of-the-art bacterial proteomics: identified peptide sequences mapped to all expressed E. coli proteins but covered 31.7% of the protein-coding genome sequence. Our results show that false discovery rates can be substantially underestimated even in "simple" proteo-genomic experiments obtained by means of high-accuracy MS and point to the necessity of further improvements concerning the coverage of peptide sequences by MS-based methods.Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.Krug Karsten K, Carpy Alejandro A, Behrends Gesa G, Matic Katarina K, Soares Nelson C NC, Macek Boris BAdd, 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, ratioAlkalescens-Dispar Group, Enteroaggregative Escherichia coli, Eschericia coli, Diffusely Adherent Escherichia coli, Bacterium coli, Escherichia/Shigella coli, Bacterium coli commune, Enteroinvasive E. coli, Diffusely Adherent E. coli, Bacillus coli, PIG7, Escherchia coli, total expressed protein, E coli, bacterium E3, TP53I7., Enteroinvasive Escherichia coli, Enterococcus coli, EAggEC, SIMPLE, Enteroaggregative E. coli, Proteomes, E. colil(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, CG18245protein translation, determination, PNT-P1, DmelCG17077, Addresses, Mbp1, bacterium E3, EY3-1, protein, Pnt, CG3629, peptide, Polypeptides, protein polypeptide chains, Techniques, peptido, png, posterior, Method, 10.5, Analysis, Enterococcus coli, D-ets-2, 3520, protein aggregate, methodology., myd, 10.9, Pnt-P1, Mass Spectrum Analysis, AI661365, Art, increased, ART, F, Escherichia/Shigella coli, peptides, Analyses, Genomes, DmelCG2328, proportionality to, hypoplasia, Mbp-1, E coli, proteins, V, procedures, E. coli, Ba, Enteroaggregative Escherichia coli, Eschericia coli, allergic reaction, Methodological Studies, SIMPLE, posterior end of organism, close to, protein anabolism, protein biosynthetic process, dl, Data Set, gyltl1b-b, T5E21.12, Arts, D-Ets-2, ets94F, 0123/09, Procedure, Enteroaggregative E. coli, Spectrum Analysis, results, Spectroscopy, l(2)01092, Diffusely Adherent E. coli, MDDGA6, DmelCG3629, PIG7, mKIAA0609, protein formation, BcDNA:LP01770, VI, IVF, KIAA0609, T5E21_12, fg, Diffusely Adherent Escherichia coli, DLL, 20.35, pntP2, gyltl1b, Pointed-P1, Enteroinvasive E. coli, MS/MS, mdc1d, proportionality, Ets94F, Spectrometry, expanded, rate, whole genome, Methodological, Methodological Study, E(Arp), En(Arp), ptd, MDC1D, PntP2, dll, enr, protein synthesis, enlarged, Specificity and Sensitivity, PntP1, E(E2F)3D, eve2, PNTP2, Polypeptide, AGRT, Proteomes, PNTP1, accessory, CG2328, 14.10, big, 0998/12, Procedures, Peptidomics, ETS2, Ets2, Gene, Coding, 9930121L06Rik, Spectrum Analyses, protein-containing complex, supernumerary, froggy, Gyltl1a, large, DMPOINT1A, pntegfr, 0608/07, polypeptide chain, reduced, l(2)387, sensitive, Escherchia coli, Mass, Gene Products, Studies, Enteroinvasive Escherichia coli, even, tiny, Medical, sensitivity, Technique, Mass Spectroscopy, proportion, Clinical, pointed-RC, MS2, MDDGB6, Medical Coding, TPP, LARGE, EK3-2, Study, BPFD#36, l(3)07825, great, Sensitivity, peptidos, CG17077, 2.7, l(3)j1B7, TP53I7, Alkalescens-Dispar Group, small, data, Bacterium coli, Ets, protein complex, Proteins, total expressed protein, EAggEC, backward, Peptide, near to, polypeptide, MS, native protein, natural protein, Bacillus coli, Protein, chemical analysis, sequence, protein biosynthesis, Eve, EVE, techniques, pnt-P1, pnt-P2, Mass Spectrum Analyses, tandem MS, l(3)s118306, Data Base, Mass Spectrum, underdeveloped, increased number, Specificity, l(2)46Ce, primary structure of sequence macromolecule, l(2)46Cg, Protein Gene Products, l(2)46CFj, present in greater numbers in organism, Gene Proteins, l(2)46CFh, Ets58AB, Bacterium coli commune, Snm1l, l(2)46CFp, approaches, vicinity of, quotient, Peptid, assay, E(eve), POINT, hypothesis, l(2)46CFg, reversed, CG87050falseE.coli - Whole organism, Empai (Krug,mcp,2013)abundance based on MAPPED_BY_AUTHORS, emPAI, Interaction consistency score: 6.0, Coverage: 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