PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK2000000ProteomicsChristian von Mering283166https://pax-db.org/dataset/283166/534428800mering@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.Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.Omasits Ulrich U, Quebatte Maxime M, Stekhoven Daniel J DJ, Fortes Claudia C, Roschitzki Bernd B, Robinson Mark D MD, Dehio Christoph C, Ahrens Christian H CHAdd, 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, ratioWhole Transcriptome Shotgun Sequencing, total expressed protein, RNA-seq, Peptidomics, Proteomes.organism, whole body, multi-cellular organism, whole genome, whole organism, animal, body, Koerper, Genomes.biochemical pathways, host organism, Ribonucleic, Haemin, Virulence, Materials, determination, Gene Expression Profile, A4, protein, Profiles, Social Controls, Mendosicutes, 12, 13, Membrane Tissues, protein polypeptide chains, (SP-5-13)-, Symbiosis Island, 7, protohemin IX, protein aggregate, 8, Non Polyadenylated, Formal Social Controls, IKKg, RNA Gene Products, KEY, Key, Ferriprotoporphyrin, me75, Metabacteria, Genomes, catabolism, membrane region, Tissue, Genomic Island, Bodily, proteins, N24)-, Estimated, Signatures, D17Mit170, T1, Pathogenicity Islands, Bacteria Woese et al. 2024, Social, Pathogenicity Factors, Alkaline Hematin D 575, Secretion, Expression Signature, Prokaryotae, Ferrate(2-), Secretions, Symbiosis Islet, Hemine, Transcriptomes, biotransformation, Procaryotae, Membrane Tissue, Genomic Islets, Archaebacteria, PLATEST, ribose nucleic acid, chloro(7, external secretion, Expression Profiles, ribonucleic acids, integral to membrane, RNA-seq, membranous organ component, Tl3, Tl2, INSDC_feature:misc_RNA, chloro(protoporphyrinato)iron(III), Gene Expression, shortened, exocrine gland fluid/secretion, Bodily Secretion, Virulence Factor, DmIKKgamma, Islet, Ferriheme, dIKK, Ribonukleinsaeure, Expression Signatures, Kenny, Pathogenicity, pentosenucleic acids, Genetic Materials, prokaryotes, hemin IX, secretion, Ribonucleic acids, Protohemin IX, Expression Profile, Genetic Material, Transcriptome Profiles, Acid, Anchored Genomic, membrane of organ, Factors, Subcellular, Hematin, IKK-gamma, Symbiosis Islets, Control, 17-tetramethyl-21H, ferriprotoporphyrin IX chloride, whole genome, Protohemin, Controls, Islands, Genomic, Ferrihaem, Symbiosis, organ system, chloro[3, DMDA, DmelCG16910, Material, Hematin D-575, Cistron, Anchored Genomic Islands, short, Regulation, exocrine gland secretion, Proteomes, Platelets, Prokaryota, Genomic Islet, Regulations, localised, exocrine gland fluid, Transcriptome Profile, Peptidomics, exocrine gland fluid or secretion, Rochalimaea henselae, N23, N22, Ferriprotoporphyrin IX Chloride, Gene, Coding, eubacteria, protein-containing complex, Islets, Alkaline Hematin D-575, body system, TYPE, dIKK-gamma, DAGA4, Symbiosis Islands, polypeptide chain, integral component of membrane, Fractions, Island, DmIKK-gamma, Anchored Genomic Island, Gene Products, Pathogenicity Factor, Whole Transcriptome Shotgun Sequencing, system, Low, 18-dipropanoato(2-)]iron(III), Bacteriobiota, dmIKKgamma, Alkaline, MAM, IKK[[gamma]], Panhematin, Medical, SCG3, Bartonella henselae (Regnery et al. 1992) Brenner et al. 1993, anatomical systems, Clinical, Genetic, localized, Tissues, Medical Coding, Profile, 18-dipropanoato(4-)-N21, ligand, stubby, Ferriheme Chloride, Ferriprotoporphyrin IX, Chlorohemin, Monera, Non-Polyadenylated RNA, Bacteria (ex Cavalier-Smith 1987), secreted substance, IKK, bodily secretion, Fraction, 17-tetramethyl-8, Subcellular Fraction, region of membrane, Rochalimaea henselae Regnery et al. 1992, Archaebiota, 12-diethenyl-3, membrane, bacteria, RNA, Transcriptome, cou, degradation, Formal Social Control, protein complex, Proteins, total expressed protein, RNS, Pathogenicity Island, 23H-porphine-2, Factor, Cistrons, LGMD2C, whole transcriptome, IKKgamma, Pathogenicity Islet, Lr, native protein, Genomic Islands, natural protein, Social Control, yeast nucleic acid, Protein, chemical analysis, Gene Expression Signatures, protohemin, whole membrane, Gene Expression Signature, 13-divinylporphyrin-2, connected anatomical system, hemin chloride, ribonucleic acid, Anchored, transmembrane, Pathogenicity Islets, dihydrogen, distinct, DMDA1, biodegradation, Dmikkgamma, not Bacteria Haeckel 1894, Non Polyadenylated RNA, archaea, chlorohemin, Non-Polyadenylated, Chloride, Ribonucleic Acid, Membrane, CG16910, Protein Gene Products, chloroprotoferrihem, Gene Proteins, Virulence., hemine, prokaryote, Gene Expression Profiles, SCARMD2, Bra, regulation, assay, Signature0falseB.henselae - Whole organism, SC (Omasits,genome_res,2013)abundance based on Spectral counting, Interaction consistency score: 8.9, Coverage: 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