microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.

Autor:	Zuffa S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Schmid R; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Bauermeister A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil., P Gomes PW; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Caraballo-Rodriguez AM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., El Abiead Y; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Aron AT; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA., Gentry EC; Department of Chemistry, Virginia Tech, Blacksburg, VA, USA., Zemlin J; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Center for Microbiome Innovation, University of California San Diego, San Diego, CA, USA., Meehan MJ; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA., Avalon NE; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Cichewicz RH; Department of Chemistry and Biochemistry, College of Arts and Sciences, University of Oklahoma, Norman, OK, USA., Buzun E; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Terrazas MC; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Hsu CY; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Oles R; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Ayala AV; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Zhao J; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA., Chu H; Department of Pathology, School of Medicine, University of California San Diego, San Diego, CA, USA.; Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), Chiba University-University of California San Diego, San Diego, CA, USA., Kuijpers MCM; Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA., Jackrel SL; Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California San Diego, San Diego, CA, USA., Tugizimana F; Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa.; International Research and Development, Omnia Nutriology, Omnia Group (Pty) Ltd, Johannesburg, South Africa., Nephali LP; Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa., Dubery IA; Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg, South Africa., Madala NE; Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, South Africa., Moreira EA; Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil., Costa-Lotufo LV; Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil., Lopes NP; Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil., Rezende-Teixeira P; Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil., Jimenez PC; Department of Marine Science, Institute of Marine Science, Federal University of São Paulo, Santos, Brazil., Rimal B; Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA., Patterson AD; Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, USA., Traxler MF; Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA., Pessotti RC; Plant and Microbial Biology, College of Natural Resources, University of California Berkeley, Berkeley, CA, USA., Alvarado-Villalobos D; Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica., Tamayo-Castillo G; Metabolomics and Chemical Profiling, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.; Escuela de Química, Universidad de Costa Rica, San José, Costa Rica., Chaverri P; Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.; Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica.; Department of Natural Sciences, Bowie State University, Bowie, MD, USA., Escudero-Leyva E; Microbial Biotechnology, Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica., Quiros-Guerrero LM; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland., Bory AJ; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland., Joubert J; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland., Rutz A; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Wolfender JL; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland., Allard PM; School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.; Department of Biology, University of Fribourg, Fribourg, Switzerland., Sichert A; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Pontrelli S; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland., Pullman BS; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA., Bandeira N; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA., Gerwick WH; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Gindro K; Plant Protection, Mycology group, Agroscope, Nyon, Switzerland., Massana-Codina J; Plant Protection, Mycology group, Agroscope, Nyon, Switzerland., Wagner BC; Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany., Forchhammer K; Department of Microbiology and Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany., Petras D; Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tuebingen, Tuebingen, Germany., Aiosa N; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA., Garg N; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA., Liebeke M; Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany.; Department for Metabolomics, Kiel University, Kiel, Germany., Bourceau P; Department of Symbiosis, Metabolic Interactions, Max Planck Institute for Marine Microbiology, Bremen, Germany., Kang KB; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Korea., Gadhavi H; Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK.; King's College London, London, UK., de Carvalho LPS; Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK.; Chemistry Department, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, USA., Silva Dos Santos M; Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK., Pérez-Lorente AI; Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain., Molina-Santiago C; Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain., Romero D; Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Bulevar Louis Pasteur (Campus Universitario de Teatinos), Malaga, Spain., Franke R; Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany., Brönstrup M; Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.; German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig, Germany., Vera Ponce de León A; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway., Pope PB; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., La Rosa SL; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway., La Barbera G; Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark., Roager HM; Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark., Laursen MF; National Food Institute, Technical University of Denmark, Lyngby, Denmark., Hammerle F; Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria., Siewert B; Department of Pharmacognosy, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria., Peintner U; Department of Microbiology, University of Innsbruck, Innsbruck, Austria., Licona-Cassani C; Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico., Rodriguez-Orduña L; Escuela de Ingeniería y Ciencias, Centro de Biotecnología FEMSA, Tecnologico de Monterrey, Monterrey, Mexico., Rampler E; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria., Hildebrand F; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.; Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria., Koellensperger G; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria., Schoeny H; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria., Hohenwallner K; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.; Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria., Panzenboeck L; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.; Vienna Doctoral School in Chemistry (DoSChem), Faculty of Chemistry, University of Vienna, Vienna, Austria., Gregor R; Department of Civil and Environmental Engineering, School of Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA., O'Neill EC; School of Chemistry, University of Nottingham, Nottingham, UK., Roxborough ET; School of Chemistry, University of Nottingham, Nottingham, UK., Odoi J; Faculty of Engineering, University of Nottingham, Nottingham, UK., Bale NJ; Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands., Ding S; Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands., Sinninghe Damsté JS; Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), t Horntje (Texel), the Netherlands., Guan XL; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore., Cui JJ; Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA., Ju KS; Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA.; Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA.; Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.; Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA., Silva DB; Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil., Silva FMR; Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil., da Silva GF; Embrapa Amazônia Ocidental, Manaus, Brazil., Koolen HHF; Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil., Grundmann C; Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil., Clement JA; Baruch S. Blumberg Institute, Doylestown, PA, USA., Mohimani H; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA., Broders K; USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA., McPhail KL; Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA., Ober-Singleton SE; Department of Physics, Study of Heavy-Element-Biomaterials, University of Oregon, Eugene, OR, USA., Rath CM; Emeryville, CA, USA., McDonald D; Department of Pediatrics, University of California San Diego, San Diego, CA, USA., Knight R; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.; Department of Pediatrics, University of California San Diego, San Diego, CA, USA.; Department of Bioengineering, University of California San Diego, San Diego, CA, USA., Wang M; Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA., Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA. pdorrestein@health.ucsd.edu.
Jazyk:	angličtina
Zdroj:	Nature microbiology [Nat Microbiol] 2024 Feb; Vol. 9 (2), pp. 336-345. Date of Electronic Publication: 2024 Feb 05.
DOI:	10.1038/s41564-023-01575-9
Abstrakt:	microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health. (© 2024. The Author(s).)
Databáze:	MEDLINE
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