Feature-based molecular networking in the GNPS analysis environment.

Autor: Nothias LF; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Petras D; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Schmid R; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Dührkop K; Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany., Rainer J; Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy., Sarvepalli A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Protsyuk I; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Ernst M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark., Tsugawa H; RIKEN Center for Sustainable Resource Science, Yokohama, Japan.; RIKEN Center for Integrative Medical Sciences, Yokohama, Japan., Fleischauer M; Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany., Aicheler F; Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany., Aksenov AA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Alka O; Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany., Allard PM; Department of Phytochemistry and Bioactive Natural Products, University of Geneva, Geneva, Switzerland., Barsch A; Bruker Daltonics, Bremen, Germany., Cachet X; Equipe PNAS, UMR 8038 CiTCoM CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Paris, France., Caraballo-Rodriguez AM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Da Silva RR; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil., Dang T; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Institute of Chemistry, Technische Universität Berlin, Berlin, Germany., Garg N; School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA., Gauglitz JM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Gurevich A; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia., Isaac G; Waters Corporation, Milford, MA, USA., Jarmusch AK; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Kameník Z; Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic., Kang KB; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea., Kessler N; Bruker Daltonics, Bremen, Germany., Koester I; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Korf A; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Le Gouellec A; Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France., Ludwig M; Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany., Martin H C; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama., McCall LI; Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA., McSayles J; Nonlinear Dynamics, Milford, MA, USA., Meyer SW; Bruker Daltonics, Bremen, Germany., Mohimani H; Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA., Morsy M; Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA., Moyne O; Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Neumann S; Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, Germany.; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany., Neuweger H; Bruker Daltonics, Bremen, Germany., Nguyen NH; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Nothias-Esposito M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Paolini J; Laboratoire de Chimie des Produits Naturels, UMR CNRS SPE, Université de Corse Pascal Paoli, Corte, France., Phelan VV; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Denver, Aurora, CO, USA., Pluskal T; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Quinn RA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA., Rogers S; School of Computing Science, University of Glasgow, Glasgow, UK., Shrestha B; Waters Corporation, Milford, MA, USA., Tripathi A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA., van der Hooft JJJ; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands., Vargas F; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Weldon KC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Witting M; Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, München, Germany., Yang H; College of Pharmacy, Kangwon National University, Chuncheon-si, Republic of Korea., Zhang Z; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA., Zubeil F; Bruker Daltonics, Bremen, Germany., Kohlbacher O; Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.; Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.; Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany., Böcker S; Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany., Alexandrov T; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany., Bandeira N; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA., Wang M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu., Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2020 Sep; Vol. 17 (9), pp. 905-908. Date of Electronic Publication: 2020 Aug 24.
DOI: 10.1038/s41592-020-0933-6
Abstrakt: Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.
Databáze: MEDLINE