Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data
| Autor: | Ilaria Belluomo, Morgan Panitchpakdi, Aleksandr Smirnov, Mélissa Nothias-Esposito, Alexey V. Melnik, Gaud Dervilly, Rachel J. Dutton, Adolfo Amézquita, Vasilis Vasiliou, Zheng Zhang, Daniel Petras, Carrie D. Nicora, Audrey Poirier, James T. Morton, Ivan Laponogov, George B. Hanna, Sneha P. Couvillion, Biswapriya B. Misra, Robin Schmid, Wout Bittremieux, Raphaël Lugan, Brooke A. Anderson, Yann Guitton, Chris Callewaert, Kenneth L. Jones, Robert A. Quinn, Rob Knight, Larisa N. Kulikova, Itzhak Mizrahi, Erika M. Zink, Mabel Gonzalez, Sophie L. F. Doran, Rachel Gregor, Pauline Le Boulch, Kelem Gashu, Xiuxia Du, Michael M. Meijler, Kirill Veselkov, Chao Song, Elizabeth Humston-Fulmer, Noga Sikron Persi, Justin J. J. van der Hooft, Dennis Veselkov, Monica Guma, Kathleen Dorrestein, Saleh Alseekh, Roxana Coras, Chiara Carazzone, Thomas O. Metz, Aaron Fait, Andrea Georgina Albarracín Orio, Alexander A. Aksenov, Jose U. Scher, Andrea M. Smania, Bruno Le Bizec, Stav Eyal, Dinesh Kumar Barupal, Pieter C. Dorrestein, Alisdair R. Fernie, Reza Mirnezami, S. Prévost, Louis-Félix Nothias, Meagan C. Burnet, Viatcheslav B. Artaev, Mingxun Wang, Katherine N. Maloney, Julia Manasson, Madeleine Ernst, Roman S. Borisov, Amina Bouslimani |
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| Přispěvatelé: | The Vodafone Foundation, National Institutes of Health, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Collaborative Mass Spectrometry Innovation Center, Imperial College London, University of Antwerp (UA), Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, University of North Carolina [Charlotte] (UNC), University of North Carolina System (UNC), Statens Serum Institut [Copenhagen], Wageningen University and Research [Wageningen] (WUR), Universidad de los Andes [Bogota] (UNIANDES), Center for Microbial Ecology and Technology (CMET), Universiteit Gent = Ghent University [Belgium] (UGENT), University of California, Flatiron Institute, Simons Foundation, Michigan State University [East Lansing], Michigan State University System, Universidad Católica de Córdoba, Universidad Nacional de Córdoba [Argentina], Pacific Northwest National Laboratory (PNNL), LECO Corporation, Ben-Gurion University of the Negev (BGU), Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire d'étude des Résidus et Contaminants dans les Aliments (LABERCA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), New York University School of Medicine (NYU), New York University School of Medicine, NYU System (NYU)-NYU System (NYU), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Center of Plant Systems Biology and Biotechnology [Plovdiv] (CPSBB), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, NHS Foundation Trust [London], The Royal Marsden, Yale School of Public Health (YSPH), University of Münster, A.V. Topchiev Institute of Petrochemical Synthesis (TIPS), Russian Academy of Sciences [Moscow] (RAS), Peoples Friendship University of Russia [RUDN University] (RUDN) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Computer science
Bioinformatics [SDV]Life Sciences [q-bio] Biomedical Engineering MESH: Algorithms Bioengineering S Agricultura (General) Mass spectrometry computer.software_genre METABOLOMICS Applied Microbiology and Biotechnology Gas Chromatography-Mass Spectrometry Article Matrix decomposition 03 medical and health sciences 0302 clinical medicine [STAT.ML]Statistics [stat]/Machine Learning [stat.ML] [CHIM.ANAL]Chemical Sciences/Analytical chemistry Bioinformatica Metabolomics Life Science Animals Humans MESH: Metabolomics Biology 030304 developmental biology Q Ciencia (General) 0303 health sciences Science & Technology MESH: Gas Chromatography-Mass Spectrometry Workflow Biotechnology & Applied Microbiology Molecular networking Molecular Medicine Data mining Deconvolution Gas chromatography–mass spectrometry Anura computer Engineering sciences. Technology Life Sciences & Biomedicine 030217 neurology & neurosurgery Algorithms Biotechnology REPOSITORY STANDARDS |
| Zdroj: | Nat Biotechnol Nature biotechnology Aksenov, Alexander A., Laponogov, Ivan, Zhang, Zheng, Doran, Sophie L. F., Belluomo, Ilaria, Veselkov, Dennis, Bittremieux, Wout, Nothias, Louis Felix, Nothias-Esposito, Mélissa, Maloney, Katherine N., Misra, Biswapriya B., Melnik, Alexey V., Smirnov, Aleksandr, Du, Xiuxia, Jones, Kenneth L., Dorrestein, Kathleen, Panitchpakdi, Morgan, Ernst, Madeleine, van der Hooft, Justin J. J., Gonzalez, Mabel, Carazzone, Chiara, Amézquita, Adolfo, Callewaert, Chris, Morton, James T., Quinn, Robert A., Bouslimani, Amina, Orio, Andrea Albarracín, Petras, Daniel, Smania, Andrea M., Couvillion, Sneha P., Burnet, Meagan C., Nicora, Carrie D., Zink, Erika, Metz, Thomas O., Artaev, Viatcheslav, Humston-Fulmer, Elizabeth, Gregor, Rachel, Meijler, Michael M., Mizrahi, Itzhak, Eyal, Stav, Anderson, Brooke, Dutton, Rachel, Lugan, Raphaël, Boulch, Pauline Le, Guitton, Yann, Prevost, Stephanie, Poirier, Audrey, Dervilly, Gaud, Le Bizec, Bruno, Fait, Aaron, Persi, Noga Sikron, Song, Chao, Gashu, Kelem, Coras, Roxana, Guma, Monica, Manasson, Julia, Scher, Jose U., Barupal, Dinesh Kumar, Alseekh, Saleh, Fernie, Alisdair R., Mirnezami, Reza, Vasiliou, Vasilis, Schmid, Robin, Borisov, Roman S., Kulikova, Larisa N., Knight, Rob, Wang, Mingxun, Hanna, George B., Dorrestein, Pieter C. and Veselkov, Kirill (2021) Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data. Nature Biotechnology, 39 (2). ISSN 1087-0156 Nature Biotechnology Nature Biotechnology, 39(2), 169-173 Nature Biotechnology, Nature Publishing Group, 2021, 39 (2), pp.169-173. ⟨10.1038/s41587-020-0700-3⟩ Nature Biotechnology 39 (2021) 2 Nature biotechnology, vol 39, iss 2 |
| ISSN: | 1087-0156 |
| DOI: | 10.1038/s41587-020-0700-3⟩ |
| Popis: | 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. Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Laponogov, Ivan. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido Fil: Zhang, Zheng. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Doran, Sophie L. F. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido Fil: Belluomo, Ilaria. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido Fil: Veselkov, Dennis. Intelligify Limited. Reino Unido. South Kensington Campus. Imperial College. Department of Computing; Reino Unido Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Bittremieux, Wout. University of Antwerp. Department of Computer Science; Belgica Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Maloney, Katherine N. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Maloney, Katherine N. Point Loma Nazarene University. Department of Chemistry; Estados Unidos Fil: Misra, Biswapriya B. Wake Forest School of Medicine. Section of Molecular Medicine. Department of Internal Medicine. Center for Precision Medicine; Estados Unidos Fil: Melnik, Alexey V. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Smirnov, Aleksandr. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos Fil: Du, Xiuxia. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos Fil: Jones, Kenneth L. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Panitchpakdi, Morgan. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Ernst, Madeleine. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Ernst, Madeleine. Statens Serum Institut. Danish Center for Neonatal Screening. Department of Congenital Disorders. Section for Clinical Mass Spectrometry; Dinamarca Fil: van der Hooft, Justin J. J. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: van der Hooft, Justin J. J. Wageningen University. Bioinformatics Group; Países Bajos Fil: Gonzalez, Mabel. Universidad de los Andes. Department of Chemistry; Colombia Fil: Carazzone, Chiara. Universidad de los Andes. Department of Chemistry; Colombia Fil: Amézquita, Adolfo. Universidad de los Andes. Department of Biological Sciences; Colombia Fil: Callewaert, Chris. Center for Microbial Ecology and Technology; Belgica Fil: Callewaert, Chris. University of California. Department of Pediatrics; Estados Unidos Fil: Morton, James T. University of California. Department of Pediatrics; Estados Unidos Fil: Morton, James T. Simons Foundation. Flatiron Institute. Center for Computational Biology; Estados Unidos Fil: Quinn, Robert A. Michigan State University. Department of Biochemistry and Molecular Biology; Estados Unidos Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Orio, Andrea Albarracín. Universidad Católica de Córdoba. IRNASUS. CONICET. Facultad de Ciencias Agropecuarias; Argentina Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Smania, Andrea M. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto; Argentina Fil: Smania, Andrea M. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. CONICET; Argentina Fil: Couvillion, Sneha P. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos Fil: Burnet, Meagan C. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos Fil: Nicora, Carrie D. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos Fil: Zink, Erika. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos Fil: Metz, Thomas O. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos Fil: Artaev, Viatcheslav. LECO Corporation; Estados Unidos Fil: Humston-Fulmer, Elizabeth. LECO Corporation; Estados Unidos Fil: Gregor, Rachel. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel Fil: Meijler, Michael M. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel Fil: Mizrahi, Itzhak. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel Fil: Eyal, Stav. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel Fil: Anderson, Brooke. University of California. Division of Biological Sciences; Estados Unidos Fil: Dutton, Rachel. University of California. Division of Biological Sciences; Estados Unidos Fil: Lugan, Raphaël. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia Fil: Boulch, Pauline Le. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia Fil: Guitton, Yann. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia Fil: Prevost, Stephanie. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia Fil: Poirier, Audrey. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia Fil: Dervilly, Gaud. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia Fil: Le Bizec, Bruno. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia Fil: Fait, Aaron. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel Fil: Persi, Noga Sikron. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel Fil: Song, Chao. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel Fil: Gashu, Kelem. Ben Gurion University of the Negev. Sede Boqer Campus. The Jacob Blaustein Institutes for Desert Research. The French Associates Institute for Agriculture and Biotechnology of Dryland; Israel Fil: Coras, Roxana. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos Fil: Guma, Monica. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos Fil: Manasson, Julia. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos Fil: Scher, Jose U. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos Fil: Barupal, Dinesh Kumar. Icahn School of Medicine at Mount Sinai. Department of Environmental Medicine and Public Health; Estados Unidos Fil: Alseekh, Saleh. Max Planck Institute for Molecular Plant Physiology; Alemania Fil: Alseekh, Saleh. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria Fil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; Alemania Fil: Fernie, Alisdair R. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria Fil: Mirnezami, Reza. Royal Free Hospital NHS Foundation Trust. Department of Colorectal Surgery; Reino Unido Fil: Vasiliou, Vasilis. Yale University. Yale School of Public Health. Department of Environmental Health Sciences; Estados Unidos Fil: Schmid, Robin. University of Münster. Institute of Inorganic and Analytical Chemistry; Alemania Fil: Borisov, Roman S. A.V. Topchiev Institute of Petrochemical Synthesis RAS; Rusia Fil: Kulikova, Larisa N. Рeoples’ Friendship University of Russia (RUDN University); Rusia Fil: Knight, Rob. University of California. Department of Pediatrics; Estados Unidos Fil: Knight, Rob. University of California. UCSD Center for Microbiome Innovation; Estados Unidos Fil: Knight, Rob. University of California. Department of Bioengineering; Estados Unidos Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Hanna, George B. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos Fil: Dorrestein, Pieter C. University of California. Department of Pediatrics; Estados Unidos Fil: Veselkov, Kirill. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido |
| Databáze: | OpenAIRE |
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