PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimaryOK200ProteomicsChristian von Mering208964https://pax-db.org/dataset/208964/1231515390mering@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.Biofilms are surface-associated bacteria that are embedded in a matrix of self-produced polymeric substances (EPSs). The EPS is composed of nucleic acids, polysaccharides, lipids, and proteins. While polysaccharide components have been well studied, the protein content of the matrix is largely unknown. Here we conducted a comprehensive proteomic study to identify proteins associated with the biofilm matrix of Pseudomonas aeruginosa PAO1 (the matrix proteome). This analysis revealed that approximately 30% of the identified matrix proteins were outer membrane proteins, which are also typically found in outer membrane vesicles (OMVs). Electron microscopic inspection confirmed the presence of large amounts of OMVs within the biofilm matrix, supporting previous notions that OMVs are abundant constituents of P. aeruginosa biofilms. Our results demonstrate that while some proteins associated with the P. aeruginosa matrix are derived from secreted proteins and lysed cells, the large majority of the matrix proteins originate from OMVs. Furthermore, we demonstrate that the protein content of planktonic and biofilm OMVs is surprisingly different and may reflect the different physiological states of planktonic and sessile cells.Identification of proteins associated with the Pseudomonas aeruginosa biofilm extracellular matrix.Toyofuku Masanori M, Roschitzki Bernd B, Riedel Katharina K, Eberl Leo LAdd, 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, ratioBiofilm.matrisome, Peudomonas aeruginosa, Proteins, Pseudomonas pyocyanea, Matrix, Gene, proteins, proteinaceous extracellular matrix., Bacterium pyocyaneum, Matrices, Bacillus pyocyaneus, Protein Gene Products, Gene Proteins, Pseudomonas polycolor, Micrococcus pyocyaneus, native protein, Bacterium aeruginosum, Extracellular, Protein, Gene Products, probable synonym or variety: "Pseudomonas polycolor" Clara 1930, Bacillus aeruginosus, Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (Approved Lists 1980), Extracellular Matrices, Biofilmtotal expressed protein, organism, whole body, multi-cellular organism, whole organism, Biofilm, animal, body, Koerper, Proteomes.Integral Membrane Proteins, big, lipids, EPS, determination, 14-3-3-e, 143E_DROME, EPS Matrix, Surface Proteins, e(-), number, D14-3-3epsilon, Mbp1, glycans, Matrix, Gene, Glykan, eubacteria, protein, Membrane-Associated Proteins, electron, Integral, protein-containing complex, composed of, presence, froggy, Gyltl1a, surface, polisacarido, protein polypeptide chains, large, acides nucleiques, eps, polypeptide chain, Biofilm Matrices, Membrane-Associated Protein, Gene Products, Pseudomonas aeruginosa str. PAO1, Cell., Bacteriobiota, protein aggregate, myd, D14-3-3e, Polysaccharide, integumentum commune, Cell Membrane, study, CG31196, Eubacteria, Extracellular Polymeric Substances, l(3)j2B10, Glycans, anon-WO02059370.52, MDDGB6, Surface, Elektron, par-5, Glycane, beta-particle, Mbp-1, composition, proteins, LARGE, EK3-5, Monera, Fast, Bacteria Woese et al. 2024, Bacteria (ex Cavalier-Smith 1987), BPFD#36, Pseudomonas aeruginosa PA01, e, Bacteria <bacteria>, acidos nucleicos, e-, Prokaryotae, Extracellular, great, Glycan, PAR-5, Surface Protein, Membrane Associated Proteins, Procaryotae, fungi, associated, 14-3-3-epsilon, Membrane Protein, Par-5, Electrons, Positron, bacteria, EPS Matrices, CT24092, external covering of organism, 14-3-3e, gyltl1b-b, acide nucleique, protein complex, Negatron, Proteins, total expressed protein, Cell Surface, Cell Surface Protein, Negatrons, organism surface, Positrons, compositionality, anon-WO0172774.141, Exopolymers, Cell, results, Glykane, Extracellular Polymeric Substance, count in organism, 14-3-3omicron, native protein, natural protein, nucleic acids, Nucleic Acid, MDDGA6, mKIAA0609, DmelCG31196, Lipid, Protein, chemical analysis, Fast Electron, Membrane Proteins, 14-3-30epsilon, prokaryotes, NA, Biofilm, Pseudomonas sp. PAO1, Fast Electrons, KIAA0609, 14-3-3 epsilon, Biofilm Matrix, Cell Surface Proteins, Membrane Associated Protein, fg, Acid, Exopolymer, polisacaridos, Cell Membrane Protein, gyltl1b, d14-3-3epsilon, Nukleinsaeure, negatron, body surface, not Bacteria Haeckel 1894, content, Membrane-Associated, mdc1d, expanded, Cell Membrane Proteins, SR3-9, acido nucleico, Electron, Membrane, 14-3-3EPSILON, Nucleic, Polymeric Substance, beta, beta(-), 14-3-3, polysaccharides, Protein Gene Products, Su(Raf)3B, Gene Proteins, MDC1D, Integral Membrane Protein, enr, enlarged, integumentary system, prokaryote, Nukleinsaeuren, 1433epsilon, structure, PAR5, Pseudomonas aeruginosa str. PA01, Acids, assay, dermal system, Proteomes, Prokaryota, Integral MembranefalseP.aeruginosa - Whole organism, Biofilm, SC (Toyofuku,j_proteome_res,2012)abundance based on Spectral counting, biofilm, Interaction consistency score: 7.2, Coverage: 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