Feature-Based Molecular Networking in the GNPS Analysis Environment

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

doi:10.1038/s41592-020-0933-6

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Feature-Based Molecular Networking in the GNPS Analysis Environment

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Author(s): Louis Felix Nothias ¹ ^, ² , Daniel Petras ¹ ^, ² ^, ³ , Robin Schmid ⁴ , Kai Dührkop ⁵ , Johannes Rainer ⁶ , Abinesh Sarvepalli ¹ ^, ² , Ivan Protsyuk ⁷ , Madeleine Ernst ¹ ^, ² ^, ⁸ , Hiroshi Tsugawa ⁹ ^, ¹⁰ , Markus Fleischauer ⁵ , Fabian Aicheler ¹¹ ^, ¹² , Alexander Aksenov ¹ ^, ² , Oliver Alka ¹¹ ^, ¹² , Pierre-Marie Allard ¹³ , Aiko Barsch ¹⁴ , Xavier Cachet ¹⁵ , Mauricio Caraballo ¹ ^, ² , Ricardo R. Da Silva ² ^, ¹⁶ , Tam Dang ² ^, ¹⁷ , Neha Garg ¹⁸ , Julia M. Gauglitz ¹ ^, ² , Alexey Gurevich ¹⁹ , Giorgis Isaac ²⁰ , Alan K. Jarmusch ¹ ^, ² , Zdeněk Kameník ²¹ , Kyo Bin Kang ¹ ^, ² ^, ²² , Nikolas Kessler ¹⁴ , Irina Koester ¹ ^, ² ^, ³ , Ansgar Korf ⁴ , Audrey Le Gouellec ²³ , Marcus Ludwig ⁵ , Christian Martin H. ²⁴ , Laura-Isobel McCall ²⁵ , Jonathan McSayles ²⁶ , Sven W. Meyer ¹⁴ , Hosein Mohimani ²⁷ , Mustafa Morsy ²⁸ , Oriane Moyne ²³ ^, ²⁹ , Steffen Neumann ³⁰ ^, ³¹ , Heiko Neuweger ¹⁴ , Ngoc Hung Nguyen ¹ ^, ² , Melissa Nothias-Esposito ¹ ^, ² , Julien Paolini ³² , Vanessa V. Phelan ³³ , Tomáš Pluskal ³⁴ , Robert A. Quinn ³⁵ , Simon Rogers ³⁶ , Bindesh Shrestha ¹⁹ , 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 Witting ⁴⁰ , Heejung Yang ⁴¹ , Zheng Zhang ¹ ^, ² , Florian Zubeil ¹⁴ , Oliver Kohlbacher ¹¹ ^, ¹² ^, ⁴² ^, ⁴³ , Sebastian Böcker ⁵ , Theodore Alexandrov ¹ ^, ² ^, ⁷ , Nuno Bandeira ¹ ^, ² ^, ⁴⁴ , Mingxun Wang ¹ ^, ² ^, ⁴⁴ ^, ^* , Pieter C. Dorrestein ¹ ^, ² ^, ²⁹ ^, ³⁹ ^, ^*

Publication date (Electronic): 24 August 2020

Journal: Nature methods

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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. The FBMN method brings quantitative analyses, isomeric resolution, including from ion-mobility spectrometry, into molecular networks.

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Most cited references 52

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Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Paul Shannon, Andrew Markiel, Owen Ozier … (2003)

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen, Jai Rideout, Matthew Dillon … (2019)

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Mingxun Wang, Jeremy J. Carver, Vanessa V Phelan … (2016)

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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Author and article information

Journal

Journal ID (nlm-journal-id): 101215604

Journal ID (pubmed-jr-id): 32338

Journal ID (nlm-ta): Nat Methods

Journal ID (iso-abbrev): Nat Methods

Title: Nature methods

ISSN (Print): 1548-7091

ISSN (Electronic): 1548-7105

Publication date Nihms-submitted: 9 January 2021

Publication date (Electronic): 24 August 2020

Publication date (Print): September 2020

Publication date PMC-release: 24 February 2021

Volume: 17

Issue: 9

Pages: 905-908

Affiliations

[1 ]Skaggs of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, San Diego, CA, USA

[2 ]Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, San Diego, 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, 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 ]Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark

[9 ]RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan

[10 ]RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan

[11 ]Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany

[12 ]Institute for Translational Bioinformatics, University Hospital 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 ]Technische Universität Berlin, Faculty II Mathematics and Natural Sciences, Institute of Chemistry, 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, 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, USA

[26 ]Nonlinear Dynamics, Milford, MA, USA

[27 ]Computational Biology Department, School of Computer Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

[28 ]Department of Biological and Environmental Sciences, University of West Alabama, Livingston, USA

[29 ]Department of Pediatrics, University of California San Diego, La Jolla, San Diego, 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, Germany

[32 ]Laboratoire de Chimie des Produits Naturels, UMR CNRS SPE, Université de Corse Pascal Paoli, 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, 48823, MI, USA

[36 ]School of Computing Science, University of Glasgow, Glasgow G12 8QQ, 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

[41 ]College of Pharmacy, Kangwon National University, Republic of Korea

[42 ]Institute for Bioinformatics and Medical Informatics, University of 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, CA, USA

Author notes

[#]

These authors contributed equally

Author Contributions

L.F.N., D.P., M.W., and P.D. conceived the method and supervised its implementation and wrote the manuscript.

I.P., L.F.N., M.E., and T.A. created the FBMN prototype in Optimus.

M.W., L.F.N. D.P. and Z.Z. created the FBMN workflow on GNPS.

R.S., L.F.N, M.W., D.P., A.K., M.F, Z.Z., A.S., and T.P. developed the GNPS Export module in MZmine.

K.D., A.K., M.L., and S.B. developed the spectral clustering algorithm and SIRIUS export in MZmine.

A.S., and L.F.N. created the GNPS Export tool in OpenMS, with the guidance from F.A, O.A., and O.K.

J.R. and M.Wit. created the XCMS export tool.

H.T, M.W. and L.F.N. made possible the integration with MS-DIAL.

L.F.N., A.B., H.N., F.Z. and T.D. made possible the integration with MetaboScape.

M.W., G.I., B.S., S.W.M. and J.M. made possible the integration with Progenesis QI.

F.V. performed the mass spectrometry for the plasma and NIST1950SRM samples.

A.A. performed the mass spectrometry for the American Gut Project samples.

A.K.J, L.F.N, and A.Tri. analyzed the results of the plasma samples.

J.R and L.F.N. performed the XCMS processing of the forensic dataset.

L.F.N. and M.W. created the FBMN documentation.

D.P., L.F.N. and R.d.S. created the MZmine documentation.

K.B.K., H.Y. created the MS-DIAL documentation.

F.V., J.M.G. K.W., and A.K.J. prepared the MS-DIAL video tutorial.

M.W., R.S., D.P. prepared the MZmine video tutorials.

M.E., R.d.S., J.R., O.M., and S.N. created the XCMS documentation.

L.F.N and A.S. created the OpenMS documentation.

L.F.N, N.H.N., and T.D, created the MetaboScape documentation.

M.C., and L.-I. M. documented the FBMN interface workflow.

M.N.-E., I.K., and C.M created the Cytoscape documentation.

H.M, A.G., M.W. and L.F.N. made the integration with DEREPLICATOR.

M.W., J.J.J.v.d.H, M.E. and S.R. made the integration with MS2LDA.

R.d.S made the integration with NAP.

M.M., N.B., X.C., J.P., N.G. R.A.Q, A.A., Z.K., and S.N. tested and provided suggestions on how to improve the methods.

J.J.J.v.d.H., T.A., A.K.J., T.P., V.V.P., A.L.G, L.-I.M., P.-M.A., S.B., and S.N. improved the manuscript.

All authors have contributed to the final manuscript.

[* ]Correspondence should be addressed to miw023@ 123456ucsd.edu and pdorrestein@ 123456ucsd.edu

Article

Manuscript ID: NIHMS1614324

DOI: 10.1038/s41592-020-0933-6

PMC ID: 7885687

PubMed ID: 32839597

SO-VID: ee573969-999d-49d1-bee9-1647274f50a0

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Feature-Based Molecular Networking in the GNPS Analysis Environment

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Most cited references 52

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

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