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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-11-09

AUTHORS

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, 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

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. More... »

PAGES

169-173

Journal

TITLE

Nature Biotechnology

ISSUE

2

VOLUME

39

Author Affiliations

  • Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, CA, USA
  • Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
  • Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
  • Department of Computing, Imperial College, South Kensington Campus, London, UK
  • Department of Computer Science, University of Antwerp, Antwerp, Belgium
  • Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA
  • Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
  • Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
  • Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
  • Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
  • Department of Chemistry, Universidad de los Andes, Bogotá, Colombia
  • Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
  • Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
  • Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
  • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
  • IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina
  • CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
  • Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
  • LECO Corporation, St. Joseph, MI, USA
  • Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
  • Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
  • Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
  • UMR Qualisud, Université d’Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France
  • Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France
  • 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
  • Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
  • Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, NY, USA
  • Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
  • Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
  • Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, London, UK
  • Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
  • Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
  • A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation
  • Рeoples’ Friendship University of Russia (RUDN University), Moscow, Russian Federation
  • Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
  • UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41587-020-0700-3

    DOI

    http://dx.doi.org/10.1038/s41587-020-0700-3

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1132444124

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/33169034


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