PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering9606https://pax-db.org/dataset/9606/2304673249mering@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.<h4>Background</h4>The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions including lubrication of food, pre-digestion, and bacterial defense. Consequently, disruptions in saliva secretion and changes in the oral microbiome contribute to conditions such as tooth decay and respiratory tract infections. Here we set out to quantitatively map the saliva proteome in great depth with a rapid and in-depth mass spectrometry-based proteomics workflow.<h4>Methods</h4>We used recent improvements in mass spectrometry (MS)-based proteomics to develop a rapid workflow for mapping the saliva proteome quantitatively and at great depth. Standard clinical cotton swabs were used to collect saliva form eight healthy individuals at two different time points, allowing us to study inter-individual differences and interday changes of the saliva proteome. To accurately identify microbial proteins, we developed a method called "split by taxonomy id" that prevents peptides shared by humans and bacteria or between different bacterial phyla to contribute to protein identification.<h4>Results</h4>Microgram protein amounts retrieved from cotton swabs resulted in more than 3700 quantified human proteins in 100-min gradients or 5500 proteins after simple fractionation. Remarkably, our measurements also quantified more than 2000 microbial proteins from 50 bacterial genera. Co-analysis of the proteomics results with next-generation sequencing data from the Human Microbiome Project as well as a comparison to MALDI-TOF mass spectrometry on microbial cultures revealed strong agreement. The oral microbiome differs between individuals and changes drastically upon eating and tooth brushing.<h4>Conclusion</h4>Rapid shotgun and robust technology can now simultaneously characterize the human and microbiome contributions to the proteome of a body fluid and is therefore a valuable complement to genomic studies. This opens new frontiers for the study of host-pathogen interactions and clinical saliva diagnostics.Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome.Grassl Niklas N, Kulak Nils Alexander NA, Pichler Garwin G, Geyer Philipp Emanuel PE, Jung Jette J, Schubert Sören S, Sinitcyn Pavel P, Cox Juergen J, Mann Matthias MAdd, 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, ratioArt, l(2)01092, dll, DLL, dl, l(2)387, DmelCG3629, Ba., BcDNA:LP01770, 2.7, CG3629, E(Arp), En(Arp)Human, Composition, Microbiome., Microbial Community Composition, Community Composition, Microbiomes, Microbial Community Compositions, Microbial Community, saliva atomaris, saliva molecularis, Microbial Community Structure, Microbial Community Structures, Community Structure, Microbiotas, Salivas, total expressed protein, sailva normalis, Microbial, Proteomes, Human Microbiomes, Microbial Communities, Community, Human Microbiome, MicrobiomePlasma, Fresh, Frozen Plasmas, Fresh Frozen Plasmas, Fresh Frozen, blood plasm, portion of blood plasma, Blood Plasma, Frozen Plasma, Fresh Frozen Plasma, Blood Plasmas, Blood, portion of plasma, Plasmas, plasma.Forms, CPD photolyase activity, Nutrient Intake, Laser Desorption-Ionization Mass Spectrometry, Macronutrient Intake, PhrB photolyase activity, Nucleotide Sequencing, feeding from phloem of other organism, Upper Respiratory Infections, FEZL, fluid, rima oris, Long Term, 5730420M11Rik, Polypeptides, protein polypeptide chains, Lubrications, hierarchy, Method, systematics, Cultural, 2, 3, NUP96, Oral Cavity, Analysis, Work Flow, Nutrient, epithelium, INSL3R, Deep Sequencing, ASD2, adenomas, SET, L-methionine aminopeptidase activity, Macronutrient Intakes, Analyses, Illumina Sequencing, MS-MALD, proteins, procedures, inhibition of homeostatic process, Body Parts and Fluids, adult mouth, Respiratory System Infections, tooth, SUPPRESSOR OF AUXIN RESISTANCE 3, Food, Host Pathogen Interactions, Upper, DmelCG4299, Bacteria Woese et al. 2024, AI047805, Matrix Assisted Laser Desorption Ionization, set, Vestibule Oris, Bacteria <bacteria>, Prokaryotae, eating, Dietary Intakes, Microbial Community Structures, upland cotton, Procaryotae, SIMPLE, sailva normalis., Respiratory Infections, Difference, MYH-associated polyposis, Longterm Effect, Systematics, Salivas, Procedure, Spectrum Analysis, Oral region, DmIKKgamma, Workflows, Cultural Background, Interaction, cavitas oris, Dm1, Cultures, Phyla <beetles>, dIKK, PIG7, anatomische Mund, Next-Generation, dipyrimidine photolyase (photosensitive), prokaryotes, Microbial Communities, LGR8, RUTBC3, Lgr8, Nutrient Intakes, Industrial, HLA-DR-associated protein II, Industrial Arts, Cultural Beliefs, Microbial Community Compositions, DI-2, Complement, Oral part of face, I-2Dm, Host-Pathogen, IKK-gamma, expanded, Spectrometry, Relation, Mouth, Methodological, human, I-2PP1, High Throughput Sequencing, Composition, TAF-IBETA, Individual Difference, feeding on plant sap, multiple colorectal, vestibule of mouth, Complement System, Dental Caries, TAF-Ibeta, oral cavity, Work Flows, humans, Prokaryota, Community, big, Peptidomics, Effects, High-Throughput DNA, protein-containing complex, Complement Protein, dIKK-gamma, deoxyribodipyrimidine photolyase activity, CG7826, Next-Generation Sequencing, Human, large, Host-Pathogen Relations, TOF, Deep, DmIKK-gamma, Host Pathogen Interaction, Gene Products, CG7835, CG42273, Technique, Man, MAP, ZNF312, Backgrounds, Respiratory System, Oral, Longterm, dental element, familial adenomatous polyposis 2, saliva atomaris, F23A5.3, 2pp2a, Cultural Relativisms, Pyrosequencing, Long-Term, Matrix Assisted, man, feeding on or from other organism, CG10574, Sequencing, oral vestibule, Study, Bacteria (ex Cavalier-Smith 1987), 2PP2A, Individual Differences, negative regulation of homeostatic process, dSET, dSet, Customs, Host Pathogen, peptidos, Respiratory Tract, oral fissure, GPR106, Macronutrient, Human Microbiome, MALD-MS, bacteria, cotton, Upper Respiratory Tract Infection, Proteins, Fluids, Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry, Cultural Backgrounds, Intake, Respiratory Tract Infection, Feed, dentine containing tooth, IKKgamma, MS, Teeth, Fluid, native protein, I-2PP2A, Pathogen-Host Interactions, Dm I-2, Long Term Effects, chemical analysis, Dietary Intake, Hemolytic Complement, regulation of homeostatic process, Mass Spectrum Analyses, Next Generation Sequencing, AU020952, RPE, Body Fluid, ensemble, Dmikkgamma, vertebrate tooth, Human Figure, Matrix-Assisted Laser Desorption-Ionization, CG16910, Body, Longterm Effects, p. pigmentosa retinae, ME-IV, plan specification, Gene Proteins, ZFP312, Complement Proteins, Nutritional Intakes, Rima oris, Host, prokaryote, Figures, Microbiotas, High Throughput Nucleotide Sequencing, Relativisms, MAP syndrome, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Relativism, Cultural Relativism, Feed Intake, Interactions, High-Throughput Nucleotide, IPP2A2, feeding from vascular tissue of another organism, Pathogen Interaction, Gossypium purpurascens, methionine aminopeptidase activity, determination, Host Pathogen Relations, Massively-Parallel, Matrix Assisted Laser Desorption Ionization Mass Spectrometry, Human Figures, Cavity, protein, pigmented epithelium, feeding from tissue of other organism, Classifications, Pathogen-Host Interaction, Cavitas Oris, Techniques, Background, feeding from xylem of other organism, hierarchies, High-Throughput RNA Sequencing, peptido, Pathogen Host Interactions, Nutritional Intake, Min, protein aggregate, Effect, Oral Cavity Proper, Host-Pathogen Relation, IKKg, Pathogen Interactions, peptidase M activity, DmelCG42273, Surface Enhanced Laser Desorption Ionization Mass Spectrometry, KEY, Key, Mass Spectrum Analysis, rabGAPLP, Eubacteria, Man (Taxonomy), feeding from plant phloem, peptides, vestibulum oris, TAF-I, TACHD, Differences, mouth cavity, Microbial Community Structure, pigmented retina, Respiratory System Infection, µg, min, RabGAP-5, Parts, mAPC, Mass Spectrometry, MALDI MS, Cavitas oris propria, DNA cyclobutane dipyrimidine photolyase activity, IGAAD, GREAT, Methodological Studies, High Throughput RNA Sequencing, DmelCG10574, Respiratory, RUSC3, Figure, Human Bodies, Great, Body Parts, homeostasis, Dental caries, Micronutrient Intakes, Long-Term Effects, High-Throughput RNA, phapii, PRE, Tooth Decay, Upper Respiratory Tract, Upper Respiratory, Food Intake, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, Modern, Arts, autosomal recessive familial adenomatous polyposis, ug, Dmel_CG7826, StF-IT-1, Maps, High-Throughput DNA Sequencing, Microbial, Laser Desorption Ionization Mass Spectrometry, Spectroscopy, Taxonomies, Ion Torrent Sequencing, positive regulation of homeostatic process, retinal pigment, Massively-Parallel Sequencing, Kenny, cavum oris, Ion Torrent, Individual, retinal pigment layer, Dmel_CG7835, autosomal recessive, Mnb, MNB, Ingestion, Feed Intakes, Respiratory Infection, CG4299, AW124434, Methodological Study, RABGAP5, Host-Pathogen Interaction, Phyala, phr A photolyase activity, DmelCG16910, DNA-photoreactivating enzyme, enlarged, Micronutrient, Polypeptide, i2pp2a, Proteomes, Human Microbiomes, Microbial Community Composition, human being, High Throughput DNA Sequencing, salivation, Procedures, MALDI-MS, Bodies, taxonomy, Gene, eubacteria, Spectrum Analyses, photoreactivating enzyme activity, Illumina, PHAPII, method, Homo sapiens, polypeptide chain, Relations, method used in an experiment, saliva molecularis, Mass, Studies, Phyla <eudicots>, body fluid, Vestibule of the Mouth, stratum pigmentosa retinae, dmIKKgamma, Bacteriobiota, Massively Parallel Sequencing, IKK[[gamma]], valve, familial adenomatous polyposis, Mass Spectroscopy, Nutritional, study, Taxonomy, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Ion Proton Sequencing, Gpr106, PRECOCIOUS, Infections, Upper Respiratory Tract Infections, ipp2a2, Micronutrient Intake, Mouth Cavity Proper, bucca, RXFPR2, Monera, autosomal recessive multiple colorectal adenomas, SELDI-TOF-MS, IKK, taf-ibeta, great, pharyngeal valve, cavity of mouth, Gossypium hirsutum subsp. mexicanum, High-Throughput, RNA Sequencing, Hemolytic, American cotton, Long-Term Effect, fungi, FEZ, F23A5_3, TP53I7, Autoregulation, DYRK1, data, Community Composition, MUTYH-Associated Polyposis, protein complex, igaad, total expressed protein, Peptide, group, MODIFIER OF SNC1, natural protein, DNA Sequencing, Protein, deoxyribonucleic photolyase activity, I2PP2A, Infection, Dyrk1, techniques, buccal cavity, Foods, Microbiome, Mass Spectrum, VSD1, Microbiomes, photolyase activity, Pathogen-Host, Microbial Community, Matrix-Assisted, not Bacteria Haeckel 1894, Dietary, CC1, Community Structure, MYH-Associated Polyposis, LGR8.1, Protein Gene Products, dSET/TAF-Ibeta, 2610030F17Rik, activation of homeostatic process, MALDI, High-Throughput Sequencing, Modern Man, Gossypium lanceolatum, Peptid, sailva normalis, assay, Pathogen Host Interaction, AA407739, Ion Proton, FAP2, methodology, colorectal adenomatous polyposis0falseH.sapiens - Plasma, iBAQ (Grassletal,genomemed2016)abundance based on iBAQ, Interaction consistency score: 2.7, Coverage: 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