Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment.

Autor: Schmid R; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Petras D; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.; CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany., Nothias LF; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Wang M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Aron AT; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Jagels A; Institute of Food Chemistry, University of Münster, Münster, Germany., Tsugawa H; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.; Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan., Rainer J; Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy., Garcia-Aloy M; Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy., Dührkop K; Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany., Korf A; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Pluskal T; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic., Kameník Z; Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic., Jarmusch AK; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Caraballo-Rodríguez AM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Weldon KC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Nothias-Esposito M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Aksenov AA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA., Bauermeister A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.; Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil., Albarracin Orio A; IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina., Grundmann CO; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.; School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil., Vargas F; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Koester I; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Gauglitz JM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Gentry EC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Hövelmann Y; Institute of Food Chemistry, University of Münster, Münster, Germany., Kalinina SA; Institute of Food Chemistry, University of Münster, Münster, Germany., Pendergraft MA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Panitchpakdi M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA., Tehan R; Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA., Le Gouellec A; Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France., Aleti G; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Mannochio Russo H; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA.; NuBBE, Institute of Chemistry, , São Paulo State University (UNESP), Araraquara, SP, Brazil., Arndt B; Institute of Food Chemistry, University of Münster, Münster, Germany., Hübner F; Institute of Food Chemistry, University of Münster, Münster, Germany., Hayen H; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Zhi H; Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA., Raffatellu M; Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA., Prather KA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Aluwihare LI; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Böcker S; Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany., McPhail KL; Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA., Humpf HU; Institute of Food Chemistry, University of Münster, Münster, Germany., Karst U; Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany., Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA. pdorrestein@ucsd.edu.; Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA. pdorrestein@ucsd.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2021 Jun 22; Vol. 12 (1), pp. 3832. Date of Electronic Publication: 2021 Jun 22.
DOI: 10.1038/s41467-021-23953-9
Abstrakt: Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.
Databáze: MEDLINE