MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v04/MSV000089099/primaryOK2000000celine Henryhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=d6a38000651d43cbb672c7a7fe316b93celine.henry@inrae.frMassIVE121UNIMOD:4 - "Iodoacetamide derivative."UNIMOD:35 - "Oxidation or Hydroxylation."ProteomicsOrbitrap Fusion LumosHomo Sapiens (ncbitaxon:9606)INRAEThanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host-microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes-active ulcerative colitis, or active Crohn's disease either with ileo-colonic or exclusive colonic localization-differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers-Example of Crohn's Disease and Ulcerative Colitis Flare-Ups.Henry Céline C, Bassignani Ariane A, Berland Magali M, Langella Olivier O, Sokol Harry H, Juste Catherine Chost organism, Antemortem Diagnosis, Bowel, CROHNS DIS, Granulomatous Colitis, determination, protein, Enteritis, Diagnosis, dmTAF[[II]]230, Polypeptides, Readability, protein polypeptide chains, unspecified, peptido, diseases, Regional Ileitis, symptoms, Gastritis Associated with Crohn Disease, diseases and disorders, Software Engineering, establishment and maintenance of substrate location, Analysis, Ulcerative Colitis Type, protein aggregate, pediatric ulcerative colitis, Terminal Ileitis, Computer Program, Mass Spectrum Analysis, human disease, TFIID TAF250, peptides, Analyses, pre-mortem, IBD, cel, Open, alimentary tract, Computer Programs and Programming, Community Genomics, proteins, CROHN DIS, Crohn's Enteritis, intestinal tract, Granulomatous, set, Inflammatory Bowel Diseases, paediatric Crohn's disease, g, bowel, digestive tube, Homo sapiens disease, asd, adult alimentary canal, alimentary system, Reference Standard, Diagnose, screening, establishment and maintenance of substance location, Standard Preparation, Standard Preparations, dTAF[[II]]230, Genomics, Standardization, Regional, pediatric, TAF200, Ulcerative Colitis, TAFII-250, TAF250/230, Spectrum Analysis, Source Softwares, Software Tools, Diagnoses, Programs, Spectroscopy, Program, Computer Applications, Menstruation, single organism localization, TAFII250, Postmortem, Screenings, Examinations and Diagnoses, Computer Applications Software, Diseases, Computer Applications Softwares, Softwares, Postmortem Diagnosis, Inflammatory Bowel Disease 1, Diagnoses and Examination, Postmortem Diagnoses, AI747421, Granulomatous Enteritis, Software Applications, Crohn Disease, Standard, Source Software, susceptibility to, Spectrometry, signs, CG17603, TAF[[II]], Phenotypes, Regional Ileitides, living, disease, Applications, Taf250, gastrointestinal system, SR3-5, Crohn's enteritis, Crohn's Disease, autoimmune bowel disorder, Idiopathic Proctocolitis, Polypeptide, Other ulcerative colitis (disorder), Population Genomics, TAF230, Community, establishment and maintenance of cellular component location, Gruppe, Computer Software Applications, other disease, digestive canal, d230, criteria, paediatric, paediatric ulcerative colitis, Gastritis Associated with Crohn's Disease, enteric tract, Gene, dTAFII250, Ulcerative colitis (disorder), Spectrum Analyses, Computer, guidelines, protein-containing complex, EfW1, Inflammatory Bowel Disease, Ileocolitis, Gus, Gur, Gut, polypeptide chain, dmTAF1, Taf230, inflammatory bowel disease, Mass, Gene Products, establishment and maintenance of position, Screening, disease or disorder, left-sided ulcerative colitis, Antemortem, Crohns Disease, Colitis, Mass Spectroscopy, Application, TAF250, Open Source Softwares, Taf200, gut, dTAF[[II]]250, Colitis Gravis, cell, Software Application, Open Source Software, regional enteritis, Taf1p, Diagnoses and Examinations, Population, Computer Software Application, non-neoplastic, dTAF250, Melting, Reference, Tools, grupos, disorder, peptidos, Preparation, TAF, Inflammatory, intestines, Ulcerative colitis, Applications Software, Antemortem Diagnoses, Open Source, TAF[[II]]250, findings, Computer Software, Bowel Diseases, grupo, protein complex, Environmental Genomics, Proteins, disorders, l(3)84Ab, medical condition, BG:DS00004.13, ULCERATVE COLITIS UNSPCF, Regional Enteritis, ulcerative colitis, Examination and Diagnoses, Cell, inflammatory bowel disease (Crohn disease) 1, Peptide, Tool, group, dTAF230, Environmental, gut tube, Ileitis, Software Tool, pediatric Crohn's disease, MS, native protein, Other ulcerative colitis, Period, natural protein, Mass Screenings, p230, Protein, chemical analysis, TAF[[II]]250/230, Crohn disease, condition, TFIID, group., establishment and maintenance of localization, Software, Crohn's associated gastritis, Mass Spectrum Analyses, alimentary canal, Taf[[II]]250, Mass Spectrum, TAF[[II]]230, ensemble, Engineering, Gus-u, Rest, Gus-t, Gus-s, Gus-r, INFLAMM BOWEL DIS, TAF[II]250, UC - ulcerative colitis, single-organism localization, Understanding, Protein Gene Products, Computer Programs, Gene Proteins, Preparations, DmelCG17603, Applications Softwares, localisation, Crohn's disease, Terminal, Standards, psychogenic IBS, Peptid, assay, Crohn's disease of large bowel, groupe, TAF1, Crohn disease-associated Growth failurehost organism, Antemortem Diagnosis, Bowel, CROHNS DIS, Granulomatous Colitis, determination, protein, Enteritis, Diagnosis, dmTAF[[II]]230, Polypeptides, Readability, protein polypeptide chains, unspecified, peptido, diseases, Regional Ileitis, symptoms, Gastritis Associated with Crohn Disease, diseases and disorders, Software Engineering, establishment and maintenance of substrate location, Analysis, Ulcerative Colitis Type, protein aggregate, pediatric ulcerative colitis, Terminal Ileitis, Computer Program, Mass Spectrum Analysis, human disease, TFIID TAF250, peptides, Analyses, pre-mortem, IBD, cel, Open, alimentary tract, Computer Programs and Programming, Community Genomics, proteins, CROHN DIS, Crohn's Enteritis, intestinal tract, Granulomatous, set, Inflammatory Bowel Diseases, paediatric Crohn's disease, g, bowel, digestive tube, Homo sapiens disease, asd, adult alimentary canal, alimentary system, Reference Standard, Diagnose, screening, establishment and maintenance of substance location, Standard Preparation, Standard Preparations, dTAF[[II]]230, Genomics, Standardization, Regional, pediatric, TAF200, Ulcerative Colitis, TAFII-250, TAF250/230, Spectrum Analysis, Source Softwares, Software Tools, Diagnoses, Programs, Spectroscopy, Program, Computer Applications, Menstruation, single organism localization, TAFII250, Postmortem, Screenings, Examinations and Diagnoses, Computer Applications Software, Diseases, Computer Applications Softwares, Softwares, Postmortem Diagnosis, Inflammatory Bowel Disease 1, Diagnoses and Examination, Postmortem Diagnoses, AI747421, Granulomatous Enteritis, Software Applications, Crohn Disease, Standard, Source Software, susceptibility to, Spectrometry, signs, CG17603, TAF[[II]], Phenotypes, Regional Ileitides, living, disease, Applications, Taf250, gastrointestinal system, SR3-5, Crohn's enteritis, Crohn's Disease, autoimmune bowel disorder, Idiopathic Proctocolitis, Polypeptide, Other ulcerative colitis (disorder), Population Genomics, TAF230, Community, establishment and maintenance of cellular component location, Gruppe, Computer Software Applications, other disease, digestive canal, d230, criteria, paediatric, paediatric ulcerative colitis, Gastritis Associated with Crohn's Disease, enteric tract, Gene, dTAFII250, Ulcerative colitis (disorder), Spectrum Analyses, Computer, guidelines, protein-containing complex, EfW1, Inflammatory Bowel Disease, Ileocolitis, Gus, Gur, Gut, polypeptide chain, dmTAF1, Taf230, inflammatory bowel disease, Mass, Gene Products, establishment and maintenance of position, Screening, disease or disorder, left-sided ulcerative colitis, Antemortem, Crohns Disease, Colitis, Mass Spectroscopy, Application, TAF250, Open Source Softwares, Taf200, gut, dTAF[[II]]250, Colitis Gravis, cell, Software Application, Open Source Software, regional enteritis, Taf1p, Diagnoses and Examinations, Population, Computer Software Application, non-neoplastic, dTAF250, Melting, Reference, Tools, grupos, disorder, peptidos, Preparation, TAF, Inflammatory, intestines, Ulcerative colitis, Applications Software, Antemortem Diagnoses, Open Source, TAF[[II]]250, findings, Computer Software, Bowel Diseases, grupo, protein complex, Environmental Genomics, Proteins, disorders, l(3)84Ab, medical condition, BG:DS00004.13, ULCERATVE COLITIS UNSPCF, Regional Enteritis, ulcerative colitis, Examination and Diagnoses, Cell, inflammatory bowel disease (Crohn disease) 1, Peptide, Tool, group, dTAF230, Environmental, gut tube, Ileitis, Software Tool, pediatric Crohn's disease, MS, native protein, Other ulcerative colitis, Period, natural protein, Mass Screenings, p230, Protein, chemical analysis, TAF[[II]]250/230, Crohn disease, condition, TFIID, establishment and maintenance of localization, Software, Crohn's associated gastritis, Mass Spectrum Analyses, alimentary canal, Taf[[II]]250, Mass Spectrum, TAF[[II]]230, ensemble, Engineering, Gus-u, Rest, Gus-t, Gus-s, Gus-r, INFLAMM BOWEL DIS, TAF[II]250, UC - ulcerative colitis, single-organism localization, Understanding, psychogenic IBS., Protein Gene Products, Computer Programs, Gene Proteins, Preparations, DmelCG17603, Applications Softwares, localisation, Crohn's disease, Terminal, Standards, psychogenic IBS, Peptid, assay, Crohn's disease of large bowel, groupe, TAF1, Crohn disease-associated Growth failureMicrobial Community Composition, other disease, Biological Markers, Viral Marker, CROHNS DIS, Surrogate Endpoints, Granulomatous Colitis, Clinical Markers, Laboratory, Clinical Marker, paediatric, paediatric ulcerative colitis, Gastritis Associated with Crohn's Disease, Biochemical, Uros1, Endpoint, Ulcerative colitis (disorder), Serum, UPS, Ups, Enteritis, Normalcies, Inflammatory Bowel Disease, Human, Surrogate End Points, Surrogate Markers, Ileocolitis, Laboratory Markers, unspecified, diseases, Biological, Regional Ileitis, Gastritis Associated with Crohn Disease, disease or disorder, diseases and disorders, left-sided ulcerative colitis, Crohns Disease, Ulcerative Colitis Type, pediatric ulcerative colitis, Colitis, Terminal Ileitis, Normalities, average, Biomarker, human disease, Clinical, malignant fibrohistiocytic tumours, Colitis Gravis, Biological Marker, Microbial Community Structure, T25658, regional enteritis, CROHN DIS, Crohn's Enteritis, non-neoplastic, Granulomatous, Immunologic Markers, Immune, paediatric Crohn's disease, Markers, PBGD, Viral Markers, Microbial Community Structures, disorder, Homo sapiens disease, Immunologic Marker, Biologic, Human Microbiome, Ulcerative colitis, Individual Health, Community Composition, Viral, Surrogate Endpoint, Regional, pediatric, Serum Markers, disorders, End Point, Biochemical Markers, Ulcerative Colitis, medical condition, Normalcy, Regional Enteritis, ULCERATVE COLITIS UNSPCF, Microbial, ulcerative colitis, Biologic Marker, inflammatory bowel disease (Crohn disease) 1, Immune Marker, Ileitis, pediatric Crohn's disease, Other ulcerative colitis, Marker, Surrogate End Point, Diseases, Crohn disease, condition, Individual, Inflammatory Bowel Disease 1, Crohn's associated gastritis, Microbial Communities, Microbiome, Biologic Markers, undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma/high-grade spindle cell sarcoma., Serum Marker, Granulomatous Enteritis, Microbiomes, End Points, Crohn Disease, Microbial Community Compositions, Normality, Microbial Community, Surrogate, susceptibility to, Endpoints, Community Structure, malignant fibrohistiocytic tumors, UC - ulcerative colitis, Immunologic, Laboratory Marker, Surrogate Marker, Composition, Regional Ileitides, disease, Health, Biochemical Marker, Crohn's disease, Crohn's enteritis, Terminal, Microbiotas, Crohn's Disease, Idiopathic Proctocolitis, Crohn's disease of large bowel, Other ulcerative colitis (disorder), Human Microbiomes, Community, Immune Markers, Crohn disease-associated Growth failureMicrobial Community Composition, other disease, Biological Markers, Viral Marker, CROHNS DIS, Surrogate Endpoints, Granulomatous Colitis, Clinical Markers, Laboratory, Clinical Marker, paediatric, paediatric ulcerative colitis, Gastritis Associated with Crohn's Disease, Biochemical, Uros1, Endpoint, Ulcerative colitis (disorder), Serum, UPS, Ups, Enteritis, Normalcies, Inflammatory Bowel Disease, Human, Surrogate End Points, Surrogate Markers, Ileocolitis, Laboratory Markers, unspecified, diseases, Biological, Regional Ileitis, Gastritis Associated with Crohn Disease, disease or disorder, diseases and disorders, left-sided ulcerative colitis, Crohns Disease, Ulcerative Colitis Type, pediatric ulcerative colitis, Colitis, Terminal Ileitis, Normalities, average, Biomarker, human disease, Clinical, malignant fibrohistiocytic tumours, Colitis Gravis, Biological Marker, Microbial Community Structure, T25658, regional enteritis, CROHN DIS, Crohn's Enteritis, non-neoplastic, Granulomatous, Immunologic Markers, Immune, paediatric Crohn's disease, Markers, PBGD, Viral Markers, Microbial Community Structures, disorder, Homo sapiens disease, Immunologic Marker, Biologic, Human Microbiome, Ulcerative colitis, Individual Health, Community Composition, Viral, Surrogate Endpoint, Regional, pediatric, Serum Markers, disorders, End Point, Biochemical Markers, Ulcerative Colitis, medical condition, Normalcy, Regional Enteritis, ULCERATVE COLITIS UNSPCF, Microbial, ulcerative colitis, Biologic Marker, inflammatory bowel disease (Crohn disease) 1, Immune Marker, Ileitis, pediatric Crohn's disease, Other ulcerative colitis, Marker, Surrogate End Point, Diseases, Crohn disease, condition, Individual, Inflammatory Bowel Disease 1, Crohn's associated gastritis, Microbial Communities, Microbiome, Biologic Markers, undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma/high-grade spindle cell sarcoma., Serum Marker, Granulomatous Enteritis, Microbiomes, End Points, Crohn Disease, Microbial Community Compositions, Normality, Microbial Community, Surrogate, susceptibility to, Endpoints, Community Structure, malignant fibrohistiocytic tumors, UC - ulcerative colitis, Immunologic, Laboratory Marker, Surrogate Marker, Composition, Regional Ileitides, disease, Health, Biochemical Marker, Crohn's disease, Crohn's enteritis, Terminal, Microbiotas, Crohn's Disease, Idiopathic Proctocolitis, Crohn's disease of large bowel, Other ulcerative colitis (disorder), Human Microbiomes, Community, Immune Markers, Crohn disease-associated Growth failure0PXD032706falseModern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers. Example of Crohn's Disease and Ulcerative Colitis Flare-upsThanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty fecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host-microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes active ulcerative colitis, or active Crohn's disease either with ileo-colonic or exclusive colonic localization differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising new diagnosis tools of IBDTue Mar 22 12:09:00 GMT 2022MSV00008909935456018