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 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 and Pieter C. Dorrestein ()
Additional contact information
Robin Schmid: University of Münster
Daniel Petras: University of California San Diego, La Jolla
Louis-Félix Nothias: University of California San Diego, La Jolla
Mingxun Wang: University of California San Diego, La Jolla
Allegra T. Aron: University of California San Diego, La Jolla
Annika Jagels: University of Münster
Hiroshi Tsugawa: RIKEN Center for Sustainable Resource Science
Johannes Rainer: Affiliated Institute of the University of Lübeck
Mar Garcia-Aloy: Affiliated Institute of the University of Lübeck
Kai Dührkop: Chair for Bioinformatics, Friedrich-Schiller-University
Ansgar Korf: University of Münster
Tomáš Pluskal: Czech Academy of Sciences
Zdeněk Kameník: Institute of Microbiology, Czech Academy of Sciences
Alan K. Jarmusch: University of California San Diego, La Jolla
Andrés Mauricio Caraballo-Rodríguez: University of California San Diego, La Jolla
Kelly C. Weldon: University of California San Diego, La Jolla
Melissa Nothias-Esposito: University of California San Diego, La Jolla
Alexander A. Aksenov: University of California San Diego, La Jolla
Anelize Bauermeister: University of California San Diego, La Jolla
Andrea Albarracin Orio: IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias
Carlismari O. Grundmann: University of California San Diego, La Jolla
Fernando Vargas: University of California San Diego, La Jolla
Irina Koester: University of California San Diego
Julia M. Gauglitz: University of California San Diego, La Jolla
Emily C. Gentry: University of California San Diego, La Jolla
Yannick Hövelmann: University of Münster
Svetlana A. Kalinina: University of Münster
Matthew A. Pendergraft: University of California San Diego
Morgan Panitchpakdi: University of California San Diego, La Jolla
Richard Tehan: College of Pharmacy, Oregon State University
Audrey Gouellec: Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG
Gajender Aleti: University of California San Diego
Helena Mannochio Russo: University of California San Diego, La Jolla
Birgit Arndt: University of Münster
Florian Hübner: University of Münster
Heiko Hayen: University of Münster
Hui Zhi: University of California San Diego
Manuela Raffatellu: University of California San Diego
Kimberly A. Prather: University of California San Diego
Lihini I. Aluwihare: University of California San Diego
Sebastian Böcker: Chair for Bioinformatics, Friedrich-Schiller-University
Kerry L. McPhail: College of Pharmacy, Oregon State University
Hans-Ulrich Humpf: University of Münster
Uwe Karst: University of Münster
Pieter C. Dorrestein: University of California San Diego, La Jolla

Nature Communications, 2021, vol. 12, issue 1, 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.

Date: 2021
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DOI: 10.1038/s41467-021-23953-9

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