PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering246196https://pax-db.org/dataset/246196/1196164352mering@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.Biochemical evidence is vital for accurate genome annotation. The integration of experimental data collected at the proteome level using high resolution mass spectrometry allows for improvements in genome annotation by providing evidence for novel gene models, while validating or modifying others. Here, we report the results of a proteogenomic analysis of a reference strain of Mycobacterium smegmatis (mc(2)155), a fast growing model organism for the pathogenic Mycobacterium tuberculosis-the causative agent for Tuberculosis. By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to a Reference protein, and 63 ORFs not previously annotated to a Reference protein. Further, the translational start site (TSS) was validated for 558 Reference proteome gene models, while upstream translational evidence was identified for 81. In addition, N-terminus derived peptide identifications allowed for downstream TSS modification of a further 24 gene models. We validated the existence of six previously described interrupted coding sequences at the peptide level, and provide evidence for four novel frameshift positions. Analysis of peptide posterior error probability (PEP) scores indicates high-confidence novel peptide identifications and shows that the genome of M. smegmatis mc(2)155 is not yet fully annotated. Data are available via ProteomeXchange with identifier PXD003500.Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry.Potgieter Matthys G MG, Nakedi Kehilwe C KC, Ambler Jon M JM, Nel Andrew J M AJ, Garnett Shaun S, Soares Nelson C NC, Mulder Nicola N, Blackburn Jonathan M JMAdd, 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, ratioBacterium smegmatis, Mass Spectrum Analysis, Spectroscopy, Mass Spectrum, Profiling, Bacillus smegmatis, MS, Mycobacterium smegmatis, Proteogenomic, Mycobacterium paratuberculosis smegmatis, Analyses, Research, Researchs, Proteogenomic Analysis, Mass, Mass., Proteogenomic Profiling, Spectrometry, Proteogenomic Research, Analysis, Spectrum Analyses, Mass Spectrum Analyses, Spectrum Analysis, Mass SpectroscopyKoerper., organism, whole body, multi-cellular organism, whole organism, animal, bodyliquid chromatography tandem mass spectroscopy, protein translation, 70zpep, PEP/X4, PP14, Materials, determination, DmelCG30170, LYP2, b(2)gcn, LYP1, Progress Reports, protein, Reading Frame, DmelCG6143, peptide, Polypeptides, protein polypeptide chains, Rbt, peptido, posterior, Summary Report, Mycobacterium tuberculosis var. hominis, Pop, Tuberculosis, ORFs, Analysis, protein aggregate, animal, Unassigned, Summary Reports, Unassigned Reading Frame, Mass Spectrum Analysis, Koch's Disease, Bacillus tuberculosis, LyP, Bacterium tuberculosis, Koch Disease, Unidentified Reading Frames, LCMSMS, peptides, Genomes, Analyses, Progress Report, Open, X4/PEP, proteins, PEPPER, ecotype, Fast, Bacterium smegmatis, Progress, LYP, Protein Coding, Lymphoid phosphatase, Field Reports, Proteogenomic, PrEP, data., Strains, PAEG, F12B17_170, Protein Coding Regions, fs(2)eo-C, posterior end of organism, FAST, LC-MS2, protein anabolism, protein biosynthetic process, Mycobacterium tuberculosis (Zopf 1883) Lehmann and Neumann 1896 (Approved Lists 1980), CG6143, LC-MS/MS, ben(2)gcn, FASTK, PEPINO, Spectrum Analysis, Ts, Spectroscopy, organism, Investigative Report, 3.1.3.48, protein formation, Genetic Materials, cultivar, Region, Genetic Material, region, 2-(phosphonooxy)-2-propenoic acid, ORF, PEST-domain phosphatase, bcgn, whole organism, F20B18.110, Proteogenomic Analysis, Field, Spectrometry, F20B18_110, INSDC_feature:gene, AI047692, whole genome, 0610025G13Rik, GD, Report, GdA, GdF, protein synthesis, PNBP, Material, Mycobacterium paratuberculosis smegmatis, liquid chromatography-tandem mass spectroscopy, Koerper, Cistron, Polypeptide, Mycobacterium tuberculosis Infection, GdS, Strains and Sprains, PEP, Proteomes, cg10331, active tuberculosis, multi-cellular organism, Open Reading Frame, Researchs, STK10, Proteogenomic Profiling, gcn, Gene, Coding, Spectrum Analyses, protein-containing complex, pep, LC-MS-MS, fs(2)eo6, Unidentified Reading, CG30170, Investigative, polypeptide chain, LC-MSMS, Mass, Unassigned Reading Frames, Gene Products, Sprains, Medical, Mass Spectroscopy, PHOSPHOENOLPYRUVATE, Frame, sORF, Genetic, Clinical, Infections, Research, Medical Coding, Coding Region, Mycobacterium tuberculosis Infections, CG10331, Probabilities, CG10330, Unidentified Reading Frame, INSDC_feature:misc_feature, ATP:Fas-activated serine/threonine protein phosphotransferase activity, PASTICCINO 2, BGCN, site, peptidos, Mycobacterium tuberculosis, species, Investigative Reports, Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP, Profiling, Protein Coding Region, data, Kochs Disease, body, protein complex, Bgcn, Sprain, Proteins, D10Wsu136e, total expressed protein, b(2)cgn, whole body, Cistrons, Peptide, strain, polypeptide, LC/MS/MS, MS, native protein, natural protein, Research Reports, Protein, chemical analysis, Strain, Infection, protein biosynthesis, p100, Proteogenomic Research, Tss, Small Open Reading Frames, Tuberculoses, Mass Spectrum Analyses, Mass Spectrum, F12B17.170, Mycobacterium smegmatis, Ptpn8, Mycobacterium tuberculosis H37Rv, fs(2)eoQS2, Unidentified, Protein Gene Products, Gene Proteins, Bacillus smegmatis, 2-PHOSPHOENOLPYRUVIC ACID, Reports, liquid chromatography tandem mass spectrometry, Small Open Reading Frame, Peptid, assay, PE, AI450383, PTPN8, Summary, Field Report, Mycobacterium tuberculosis typus humanus0falseMsmegmatis strMC2 155 - Whole organism, iBAQ (Potgieteretal,frontmicrobiol2016)abundance based on iBAQ, Interaction consistency score: 11.4, Coverage: 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