Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-06-22

AUTHORS

Robin Schmid, Daniel Petras, Louis-Félix Nothias, Mingxun Wang, Allegra T. Aron, Annika Jagels, Hiroshi Tsugawa, Johannes Rainer, Mar Garcia-Aloy, Kai Dührkop, Ansgar Korf, Tomáš Pluskal, Zdeněk Kameník, Alan K. Jarmusch, Andrés Mauricio Caraballo-Rodríguez, Kelly C. Weldon, Melissa Nothias-Esposito, Alexander A. Aksenov, Anelize Bauermeister, Andrea Albarracin Orio, Carlismari O. Grundmann, Fernando Vargas, Irina Koester, Julia M. Gauglitz, Emily C. Gentry, Yannick Hövelmann, Svetlana A. Kalinina, Matthew A. Pendergraft, Morgan Panitchpakdi, Richard Tehan, Audrey Le Gouellec, Gajender Aleti, Helena Mannochio Russo, Birgit Arndt, Florian Hübner, Heiko Hayen, Hui Zhi, Manuela Raffatellu, Kimberly A. Prather, Lihini I. Aluwihare, Sebastian Böcker, Kerry L. McPhail, Hans-Ulrich Humpf, Uwe Karst, Pieter C. Dorrestein

ABSTRACT

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. More... »

PAGES

3832

Journal

TITLE

Nature Communications

ISSUE

1

VOLUME

12

Author Affiliations

  • Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
  • CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany
  • Institute of Food Chemistry, University of Münster, Münster, Germany
  • Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
  • Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
  • Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
  • Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
  • Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
  • Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
  • Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA
  • Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil
  • IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
  • School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
  • Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
  • Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
  • Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
  • Department of Psychiatry, University of California San Diego, San Diego, CA, USA
  • NuBBE, Institute of Chemistry, , São Paulo State University (UNESP), Araraquara, SP, Brazil
  • 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
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-021-23953-9

    DOI

    http://dx.doi.org/10.1038/s41467-021-23953-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1139035094

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34158495


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