Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography–mass spectrometry (GC–MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC–MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

Authors

Aksenov A.A.^1, ² , Laponogov I.³ , Zhang Z.¹ , Doran S.L.F.³ , Belluomo I.³ , Veselkov D.^4, ⁵ , Bittremieux W.^1, ^2, ⁶ , Nothias L.F.^1, ² , Nothias-Esposito M.^1, ² , Maloney K.N.^1, ⁷ , Misra B.B.⁸ , Melnik A.V.¹ , Smirnov A. ⁹ , Du X.⁹ , Jones K.L.¹ , II , Panitchpakdi M.¹ , Ernst M.^1, ¹⁰ , Van Der Hooft J.J.J. , Gonzalez M.¹² , Carazzone C.¹² , Amézquita A.¹³ , Callewaert C.^14, ¹⁵ , Morton J.T.^15, ⁴¹ , Quinn R.A.¹⁶ , Bouslimani A.^1, ² , Orio A.A.¹⁷ , Petras D.^1, ² , Smania A.M.^18, ¹⁹ , Couvillion S.P.²⁰ , Burnet M.C.²⁰ , Nicora C.D.²⁰ , Zink E.²⁰ , Metz T.O.²⁰ , Artaev V.²¹ , Humston-Fulmer E.²¹ , Gregor R.²² , Meijler M.M.²² , Mizrahi I.²³ , Eyal S.²³ , Anderson B.²⁴ , Dutton R.²⁴ , Lugan R.²⁵ , Boulch P.L.²⁵ , Guitton Y.²⁶ , Prevost S.²⁶ , Poirier A.²⁶ , Dervilly G.²⁶ , Le Bizec B. , Fait A.²⁷ , Persi N.S.²⁷ , Song C.²⁷ , Gashu K.²⁷ , Coras R.²⁸ , Guma M.²⁸ , Manasson J.²⁹ , Scher J.U.²⁹ , Barupal D.K.³⁰ , Alseekh S.^31, ³² , Fernie A.R.^31, ³² , Mirnezami R.³³ , Vasiliou V.³⁴ , Schmid R.³⁵ , Borisov R.S. ³⁶ , Kulikova L.N. ³⁷ , Knight R.^15, ^38, ^39, ⁴⁰ , Wang M.^1, ² , Hanna G.B.³ , Dorrestein P.C.^1, ^2, ^15, ³⁸ , Veselkov K.³

Journal

Nature Biotechnology

Publisher

Nature Research

Number of issue

Language

English

Pages

169-173

Status

Published

Link

External link

DOI

10.1038/s41587-020-0700-3

Volume

Year

2021

Organizations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, United States
³ Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, United Kingdom
⁴ Intelligify Limited, London, United Kingdom
⁵ Department of Computing, Imperial College, South Kensington Campus, London, United Kingdom
⁶ Department of Computer Science, University of Antwerp, Antwerp, Belgium
⁷ Department of Chemistry, Point Loma Nazarene University, San Diego, CA, United States
⁸ Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, United States
⁹ Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States
¹⁰ Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
¹¹ Bioinformatics Group, Wageningen University, Wageningen, Netherlands
¹² Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
¹³ Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
¹⁴ Center for Microbial Ecology and Technology, Ghent, Belgium
¹⁵ Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
¹⁶ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
¹⁷ IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
¹⁸ Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
¹⁹ CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
²⁰ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
²¹ LECO Corporation, St. Joseph, MI, United States
²² Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
²³ Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
²⁴ Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
²⁵ UMR Qualisud, Université d’Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
²⁶ Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
²⁷ The French Associates Institute for Agriculture and Biotechnology of Dryland, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sede Boqer Campus, Beer Sheva, Israel
²⁸ Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
²⁹ Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, United States
³⁰ Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
³¹ Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
³² Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
³³ Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, United Kingdom
³⁴ Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, United States
³⁵ Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
³⁶ A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
³⁷ Рeoples’ Friendship University of Russia (RUDN University), Moscow, Russian Federation
³⁸ UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
³⁹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
⁴⁰ Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, United States
⁴¹ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States

Keywords

Drug products; Factorization; Mass spectrometry; Turing machines; Fragmentation patterns; Machine learning approaches; Mass spectrometry data; Natural products; Nonnegative matrix factorization; Reproducibilities; Work-flows; Gas chromatography; algorithm; animal; Anura; human; mass fragmentography; metabolomics; Algorithms; Animals; Anura; Gas Chromatography-Mass Spectrometry; Humans; Metabolomics

Date of creation

20.04.2021

Date of change

20.04.2021

Short link

https://repository.rudn.ru/en/records/article/record/71895/

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