Nature Communications (Jun 2021)
Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment
- 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
Affiliations
- Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster
- Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Allegra T. Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Annika Jagels
- Institute of Food Chemistry, University of Münster
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science
- Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck
- Mar Garcia-Aloy
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck
- Kai Dührkop
- Chair for Bioinformatics, Friedrich-Schiller-University
- Ansgar Korf
- Institute of Inorganic and Analytical Chemistry, University of Münster
- Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences
- Zdeněk Kameník
- Institute of Microbiology, Czech Academy of Sciences
- Alan K. Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Andrés Mauricio Caraballo-Rodríguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Kelly C. Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Melissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Alexander A. Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Anelize Bauermeister
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Andrea Albarracin Orio
- IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias
- Carlismari O. Grundmann
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Irina Koester
- Scripps Institution of Oceanography, University of California San Diego
- Julia M. Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Emily C. Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Yannick Hövelmann
- Institute of Food Chemistry, University of Münster
- Svetlana A. Kalinina
- Institute of Food Chemistry, University of Münster
- Matthew A. Pendergraft
- Scripps Institution of Oceanography, University of California San Diego
- Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Richard Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University
- Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG
- Gajender Aleti
- Department of Psychiatry, University of California San Diego
- Helena Mannochio Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- Birgit Arndt
- Institute of Food Chemistry, University of Münster
- Florian Hübner
- Institute of Food Chemistry, University of Münster
- Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster
- Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego
- Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego
- Kimberly A. Prather
- Scripps Institution of Oceanography, University of California San Diego
- Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California San Diego
- Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University
- Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University
- Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster
- Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster
- Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla
- DOI
- https://doi.org/10.1038/s41467-021-23953-9
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 12
Abstract
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.
