New Results
Ion Identity Molecular Networking in the GNPS Environment
View ORCID ProfileRobin Schmid, View ORCID ProfileDaniel Petras, View ORCID ProfileLouis-Félix Nothias, View ORCID ProfileMingxun Wang, View ORCID ProfileAllegra 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 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 W. 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
doi: https://doi.org/10.1101/2020.05.11.088948
Robin Schmid
1Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
Daniel Petras
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
3Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, US
Louis-Félix Nothias
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Mingxun Wang
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Allegra T. Aron
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Annika Jagels
4Institute of Food Chemistry, University of Münster, Münster, Germany
Hiroshi Tsugawa
5RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
6RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
Johannes Rainer
7Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
Mar Garcia-Aloy
7Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
Kai Dührkop
8Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
Ansgar Korf
1Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
Tomáš Pluskal
9Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
Zdeněk Kameník
10Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
Alan K. Jarmusch
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Andrés Mauricio Caraballo-Rodríguez
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Kelly Weldon
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Melissa Nothias-Esposito
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Alexander A. Aksenov
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
11Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA
Anelize Bauermeister
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
12Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, SP, Brazil
Andrea Albarracin Orio
13IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias. Córdoba, Argentina
Carlismari O. Grundmann
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
14School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
Fernando Vargas
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Irina Koester
3Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, US
Julia M. Gauglitz
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Emily C. Gentry
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Yannick Hövelmann
4Institute of Food Chemistry, University of Münster, Münster, Germany
Svetlana A. Kalinina
4Institute of Food Chemistry, University of Münster, Münster, Germany
Matthew A. Pendergraft
3Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, US
Morgan W. Panitchpakdi
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
Richard Tehan
15Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
Audrey Le Gouellec
16Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France
Gajender Aleti
17Department of Psychiatry, University of California San Diego, San Diego, CA, USA
Helena Mannochio Russo
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
18NuBBE, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
Birgit Arndt
4Institute of Food Chemistry, University of Münster, Münster, Germany
Florian Hübner
4Institute of Food Chemistry, University of Münster, Münster, Germany
Heiko Hayen
1Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
Hui Zhi
19Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
Manuela Raffatellu
19Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
20Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
Kimberly A. Prather
3Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, US
Lihini I. Aluwihare
3Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, US
Sebastian Böcker
8Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
Kerry L. McPhail
15Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
Hans-Ulrich Humpf
4Institute of Food Chemistry, University of Münster, Münster, Germany
Uwe Karst
1Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
Pieter C. Dorrestein
2Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA
11Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, CA, USA

Abstract
Molecular networking connects tandem 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. To connect ion species of the same molecule, we developed Ion Identity Molecular Networking. These new relationships improve network connectivity, are shown to reveal novel ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral libraries.
Competing Interest Statement
MW is the founder of Ometa Labs LLC. AA is a consultant for Ometa Labs LLC. SB and KD are co-founders of Bright Giant GmbH. AK is an employee of Bruker Daltonics GmbH.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted May 13, 2020.
Ion Identity Molecular Networking 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 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 W. 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
bioRxiv 2020.05.11.088948; doi: https://doi.org/10.1101/2020.05.11.088948
Ion Identity Molecular Networking 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 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 W. 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
bioRxiv 2020.05.11.088948; doi: https://doi.org/10.1101/2020.05.11.088948
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