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

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

Nature Biotechnology

Nature Research

2

Английский

169-173

Опубликовано

Внешняя ссылка

10.1038/S41587-020-0700-3

39

2021

• 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

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