Feature-based molecular networking in the GNPS analysis environment

Louis-Félix Nothias; Daniel Petras; Robin Schmid; Kai Dührkop; Johannes Rainer; Abinesh Sarvepalli; Ivan Protsyuk; Madeleine Ernst; Hiroshi Tsugawa; Markus Fleischauer; Fabian Aicheler; Alexander A Aksenov; Oliver Alka; Pierre-Marie Allard; Aiko Barsch; Xavier Cachet; Andres Mauricio Caraballo-Rodriguez; Ricardo R Da Silva; Tam Dang; Neha Garg; Julia M Gauglitz; Alexey Gurevich; Giorgis Isaac; Alan K Jarmusch; Zdeněk Kameník; Kyo Bin Kang; Nikolas Kessler; Irina Koester; Ansgar Korf; Audrey Le Gouellec; Marcus Ludwig; Christian Martin H; Laura-Isobel McCall; Jonathan McSayles; Sven W Meyer; Hosein Mohimani; Mustafa Morsy; Oriane Moyne; Steffen Neumann; Heiko Neuweger; Ngoc Hung Nguyen; Melissa Nothias-Esposito; Julien Paolini; Vanessa V Phelan; Tomáš Pluskal; Robert A Quinn; Simon Rogers; Bindesh Shrestha; Anupriya Tripathi; Justin J J van der Hooft; Fernando Vargas; Kelly C Weldon; Michael Witting; Heejung Yang; Zheng Zhang; Florian Zubeil; Oliver Kohlbacher; Sebastian Böcker; Theodore Alexandrov; Nuno Bandeira; Mingxun Wang; Pieter C Dorrestein

doi:10.1038/s41592-020-0933-6

Feature-based molecular networking in the GNPS analysis environment

Nat Methods. 2020 Sep;17(9):905-908. doi: 10.1038/s41592-020-0933-6. Epub 2020 Aug 24.

Authors

Louis-Félix Nothias^#^{1

2}, Daniel Petras^#^{1

2

3}, Robin Schmid^#⁴, Kai Dührkop⁵, Johannes Rainer⁶, Abinesh Sarvepalli^{1

2}, Ivan Protsyuk⁷, Madeleine Ernst^{1

2

8}, Hiroshi Tsugawa^{9

10}, Markus Fleischauer⁵, Fabian Aicheler^{11

12}, Alexander A Aksenov^{1

2}, Oliver Alka^{11

12}, Pierre-Marie Allard¹³, Aiko Barsch¹⁴, Xavier Cachet¹⁵, Andres Mauricio Caraballo-Rodriguez^{1

2}, Ricardo R Da Silva^{2

16}, Tam Dang^{2

17}, Neha Garg¹⁸, Julia M Gauglitz^{1

2}, Alexey Gurevich¹⁹, Giorgis Isaac²⁰, Alan K Jarmusch^{1

2}, Zdeněk Kameník²¹, Kyo Bin Kang^{1

2

22}, Nikolas Kessler¹⁴, Irina Koester^{1

2

3}, Ansgar Korf⁴, Audrey Le Gouellec²³, Marcus Ludwig⁵, Christian Martin H²⁴, Laura-Isobel McCall²⁵, Jonathan McSayles²⁶, Sven W Meyer¹⁴, Hosein Mohimani²⁷, Mustafa Morsy²⁸, Oriane Moyne^{23

29}, Steffen Neumann^{30

31}, Heiko Neuweger¹⁴, Ngoc Hung Nguyen^{1

2}, Melissa Nothias-Esposito^{1

2}, Julien Paolini³², Vanessa V Phelan³³, Tomáš Pluskal³⁴, Robert A Quinn³⁵, Simon Rogers³⁶, Bindesh Shrestha²⁰, Anupriya Tripathi^{1

29

37}, Justin J J van der Hooft^{1

2

38}, Fernando Vargas^{1

2}, Kelly C Weldon^{1

2

39}, Michael Witting⁴⁰, Heejung Yang⁴¹, Zheng Zhang^{1

2}, Florian Zubeil¹⁴, Oliver Kohlbacher^{11

12

42

43}, Sebastian Böcker⁵, Theodore Alexandrov^{1

2

7}, Nuno Bandeira^{1

2

44}, Mingxun Wang^{45

46

47}, Pieter C Dorrestein^{48

49

50

51}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
² Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
³ Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁴ Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
⁵ Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.
⁶ Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
⁷ Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
⁸ Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark.
⁹ RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
¹⁰ RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
¹¹ Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.
¹² Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.
¹³ Department of Phytochemistry and Bioactive Natural Products, University of Geneva, Geneva, Switzerland.
¹⁴ Bruker Daltonics, Bremen, Germany.
¹⁵ Equipe PNAS, UMR 8038 CiTCoM CNRS, Faculté de Pharmacie de Paris, Université Paris Descartes, Paris, France.
¹⁶ Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
¹⁷ Institute of Chemistry, Technische Universität Berlin, Berlin, Germany.
¹⁸ School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA.
¹⁹ Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
²⁰ Waters Corporation, Milford, MA, USA.
²¹ Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
²² College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea.
²³ Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France.
²⁴ Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.
²⁵ Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.
²⁶ Nonlinear Dynamics, Milford, MA, USA.
²⁷ Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
²⁸ Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA.
²⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
³⁰ Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, Germany.
³¹ German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
³² Laboratoire de Chimie des Produits Naturels, UMR CNRS SPE, Université de Corse Pascal Paoli, Corte, France.
³³ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Denver, Aurora, CO, USA.
³⁴ Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
³⁵ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
³⁶ School of Computing Science, University of Glasgow, Glasgow, UK.
³⁷ Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
³⁸ Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
³⁹ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁴⁰ Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, München, Germany.
⁴¹ College of Pharmacy, Kangwon National University, Chuncheon-si, Republic of Korea.
⁴² Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.
⁴³ Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany.
⁴⁴ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
⁴⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.
⁴⁶ Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.
⁴⁷ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. miw023@ucsd.edu.
⁴⁸ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
⁴⁹ Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
⁵⁰ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
⁵¹ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.

^# Contributed equally.

Abstract

Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biological Products / chemistry*
Computational Biology / methods
Databases, Factual
Mass Spectrometry*
Metabolomics / methods
Software

Substances

Biological Products

Abstract

Publication types

MeSH terms

Substances

Grants and funding