Feature-based molecular networking in the GNPS analysis environment

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...

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Published inNature methods Vol. 17; no. 9; pp. 905 - 908
Main Authors Nothias, Louis-Félix, 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-Rodriguez, Andres Mauricio, Da Silva, Ricardo R., Dang, Tam, Garg, Neha, Gauglitz, Julia M., Gurevich, Alexey, Isaac, Giorgis, Jarmusch, Alan K., Kameník, Zdeněk, Kang, Kyo Bin, Kessler, Nikolas, Koester, Irina, Korf, Ansgar, Le Gouellec, Audrey, Ludwig, Marcus, Martin H., Christian, McCall, Laura-Isobel, McSayles, Jonathan, Meyer, Sven W., Mohimani, Hosein, Morsy, Mustafa, Moyne, Oriane, Neumann, Steffen, Neuweger, Heiko, Nguyen, Ngoc Hung, Nothias-Esposito, Melissa, Paolini, Julien, Phelan, Vanessa V., Pluskal, Tomáš, Quinn, Robert A., Rogers, Simon, Shrestha, Bindesh, Tripathi, Anupriya, van der Hooft, Justin J. J., Vargas, Fernando, Weldon, Kelly C., Witting, Michael, Yang, Heejung, Zhang, Zheng, Zubeil, Florian, Kohlbacher, Oliver, Böcker, Sebastian, Alexandrov, Theodore, Bandeira, Nuno, Wang, Mingxun, Dorrestein, Pieter C.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.09.2020
Nature Publishing Group
Subjects
631/114/2398
631/61/320
631/92/320
Analysis
Annotations
Biochemistry, Molecular Biology
Bioinformatics
Biological Microscopy
Biological Products - chemistry
Biological Techniques
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Brief Communication
Chromatography
Computational Biology - methods
Data analysis
Databases, Factual
Ethylenediaminetetraacetic acid
Feature recognition
Ionic mobility
Ions
Isomers
Life Sciences
Mass Spectrometry
Mass spectroscopy
Metabolomics - methods
Mobility
Natural products
Networking
Proteomics
Retention
Scientific imaging
Social organization
Software
Spectroscopy
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Summary: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. Feature-based molecular networking allows the generation of molecular networks for mass spectrometry data that can recognize isomers, incorporate relative quantification and integrate ion mobility data.
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PMCID: PMC7885687
J.R. and M.Wit. created the XCMS export tool.
A.K.J, L.F.N, and A.Tri. analyzed the results of the plasma samples.
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.
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.
H.T, M.W. and L.F.N. made possible the integration with MS-DIAL.
I.P., L.F.N., M.E., and T.A. created the FBMN prototype in Optimus.
L.F.N and A.S. created the OpenMS documentation.
D.P., L.F.N. and R.d.S. created the MZmine documentation.
A.A. performed the mass spectrometry for the American Gut Project samples.
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.
L.F.N, N.H.N., and T.D, created the MetaboScape documentation.
M.C., and L.-I. M. documented the FBMN interface workflow.
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.
M.W., G.I., B.S., S.W.M. and J.M. made possible the integration with Progenesis QI.
All authors have contributed to the final manuscript.
Author Contributions
M.W., L.F.N. D.P. and Z.Z. created the FBMN workflow on GNPS.
L.F.N. and M.W. created the FBMN documentation.
K.B.K., H.Y. created the MS-DIAL documentation.
L.F.N., A.B., H.N., F.Z. and T.D. made possible the integration with MetaboScape.
F.V. performed the mass spectrometry for the plasma and NIST1950SRM samples.
M.E., R.d.S., J.R., O.M., and S.N. created the XCMS documentation.
These authors contributed equally
L.F.N., D.P., M.W., and P.D. conceived the method and supervised its implementation and wrote the manuscript.
M.W., J.J.J.v.d.H, M.E. and S.R. made the integration with MS2LDA.
H.M, A.G., M.W. and L.F.N. made the integration with DEREPLICATOR.
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.
R.d.S made the integration with NAP.
J.R and L.F.N. performed the XCMS processing of the forensic dataset.
M.N.-E., I.K., and C.M created the Cytoscape documentation.
ISSN:1548-7091
1548-7105
DOI:10.1038/s41592-020-0933-6