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

Alexander A Aksenov; Ivan Laponogov; Zheng Zhang; Sophie L F Doran; Ilaria Belluomo; Dennis Veselkov; Wout Bittremieux; Louis Felix Nothias; Mélissa Nothias-Esposito; Katherine N Maloney; Biswapriya B Misra; Alexey V Melnik; Aleksandr Smirnov; Xiuxia Du; Kenneth L Jones 2nd; Kathleen Dorrestein; Morgan Panitchpakdi; Madeleine Ernst; Justin J J van der Hooft; Mabel Gonzalez; Chiara Carazzone; Adolfo Amézquita; Chris Callewaert; James T Morton; Robert A Quinn; Amina Bouslimani; Andrea Albarracín Orio; Daniel Petras; Andrea M Smania; Sneha P Couvillion; Meagan C Burnet; Carrie D Nicora; Erika Zink; Thomas O Metz; Viatcheslav Artaev; Elizabeth Humston-Fulmer; Rachel Gregor; Michael M Meijler; Itzhak Mizrahi; Stav Eyal; Brooke Anderson; Rachel Dutton; Raphaël Lugan; Pauline Le Boulch; Yann Guitton; Stephanie Prevost; Audrey Poirier; Gaud Dervilly; Bruno Le Bizec; Aaron Fait; Noga Sikron Persi; Chao Song; Kelem Gashu; Roxana Coras; Monica Guma; Julia Manasson; Jose U Scher; Dinesh Kumar Barupal; Saleh Alseekh; Alisdair R Fernie; Reza Mirnezami; Vasilis Vasiliou; Robin Schmid; Roman S Borisov; Larisa N Kulikova; Rob Knight; Mingxun Wang; George B Hanna; Pieter C Dorrestein; Kirill Veselkov

doi:10.1038/s41587-020-0700-3

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

Nat Biotechnol. 2021 Feb;39(2):169-173. doi: 10.1038/s41587-020-0700-3. Epub 2020 Nov 9.

Authors

Alexander A Aksenov^#^{1

2}, Ivan Laponogov^#³, Zheng Zhang¹, Sophie L F Doran³, Ilaria Belluomo³, Dennis Veselkov^{4

5}, Wout Bittremieux^{1

2

6}, Louis Felix Nothias^{1

2}, Mélissa Nothias-Esposito^{1

2}, Katherine N Maloney^{1

7}, Biswapriya B Misra⁸, Alexey V Melnik¹, Aleksandr Smirnov⁹, Xiuxia Du⁹, Kenneth L Jones 2nd¹, Kathleen Dorrestein^{1

2}, Morgan Panitchpakdi¹, Madeleine Ernst^{1

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

11}, Mabel Gonzalez¹², Chiara Carazzone¹², Adolfo Amézquita¹³, Chris Callewaert^{14

15}, James T Morton^{15

16}, Robert A Quinn¹⁷, Amina Bouslimani^{1

2}, Andrea Albarracín Orio¹⁸, Daniel Petras^{1

2}, Andrea M Smania^{19

20}, Sneha P Couvillion²¹, Meagan C Burnet²¹, Carrie D Nicora²¹, Erika Zink²¹, Thomas O Metz²¹, Viatcheslav Artaev²², Elizabeth Humston-Fulmer²², Rachel Gregor²³, Michael M Meijler²³, Itzhak Mizrahi²⁴, Stav Eyal²⁴, Brooke Anderson²⁵, Rachel Dutton²⁵, Raphaël Lugan²⁶, Pauline Le Boulch²⁶, Yann Guitton²⁷, Stephanie Prevost²⁷, Audrey Poirier²⁷, Gaud Dervilly²⁷, Bruno Le Bizec²⁷, Aaron Fait²⁸, Noga Sikron Persi²⁸, Chao Song²⁸, Kelem Gashu²⁸, Roxana Coras²⁹, Monica Guma²⁹, Julia Manasson³⁰, Jose U Scher³⁰, Dinesh Kumar Barupal³¹, Saleh Alseekh^{32

33}, Alisdair R Fernie^{32

33}, Reza Mirnezami³⁴, Vasilis Vasiliou³⁵, Robin Schmid³⁶, Roman S Borisov³⁷, Larisa N Kulikova³⁸, Rob Knight^{15

39

40

41}, Mingxun Wang^{1

2}, George B Hanna³, Pieter C Dorrestein^{42

43

44

45}, Kirill Veselkov⁴⁶

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA.
³ Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK.
⁴ Intelligify Limited, London, UK.
⁵ Department of Computing, Imperial College, South Kensington Campus, London, UK.
⁶ Department of Computer Science, University of Antwerp, Antwerp, Belgium.
⁷ Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA.
⁸ Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
⁹ Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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, the 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, USA.
¹⁶ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
¹⁷ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
¹⁸ IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina.
¹⁹ Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina.
²⁰ CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina.
²¹ Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
²² LECO Corporation, St. Joseph, MI, USA.
²³ Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
²⁴ Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
²⁵ Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
²⁶ UMR Qualisud, Université d'Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France.
²⁷ Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France.
²⁸ 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.
²⁹ Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
³⁰ Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA.
³¹ Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
³² Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
³³ Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
³⁴ Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK.
³⁵ Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA.
³⁶ Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
³⁷ A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation.
³⁸ Рeoples' Friendship University of Russia (RUDN University), Moscow, Russian Federation.
³⁹ UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴⁰ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
⁴¹ Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA.
⁴² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴³ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴⁴ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴⁵ UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
⁴⁶ Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK. kirill.veselkov04@imperial.ac.uk.

^# Contributed equally.

Abstract

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.

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

Algorithms*
Animals
Anura
Gas Chromatography-Mass Spectrometry*
Humans
Metabolomics*

Abstract

Publication types

MeSH terms

Grants and funding