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Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data
- Source :
- 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
- Publication Year :
- 2020
- Publisher :
- Nature Research, 2020.
-
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.<br />Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Aksenov, Alexander A. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Laponogov, Ivan. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido<br />Fil: Zhang, Zheng. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Doran, Sophie L. F. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido<br />Fil: Belluomo, Ilaria. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido<br />Fil: Veselkov, Dennis. Intelligify Limited. Reino Unido. South Kensington Campus. Imperial College. Department of Computing; Reino Unido<br />Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Bittremieux, Wout. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Bittremieux, Wout. University of Antwerp. Department of Computer Science; Belgica<br />Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Nothias, Louis Felix. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Nothias-Esposito, Mélissa. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Maloney, Katherine N. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Maloney, Katherine N. Point Loma Nazarene University. Department of Chemistry; Estados Unidos<br />Fil: Misra, Biswapriya B. Wake Forest School of Medicine. Section of Molecular Medicine. Department of Internal Medicine. Center for Precision Medicine; Estados Unidos<br />Fil: Melnik, Alexey V. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Smirnov, Aleksandr. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos<br />Fil: Du, Xiuxia. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos<br />Fil: Jones, Kenneth L. University of North Carolina at Charlotte. Department of Bioinformatics and Genomics; Estados Unidos<br />Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Dorrestein, Kathleen. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Panitchpakdi, Morgan. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Ernst, Madeleine. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Ernst, Madeleine. Statens Serum Institut. Danish Center for Neonatal Screening. Department of Congenital Disorders. Section for Clinical Mass Spectrometry; Dinamarca<br />Fil: van der Hooft, Justin J. J. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: van der Hooft, Justin J. J. Wageningen University. Bioinformatics Group; Países Bajos<br />Fil: Gonzalez, Mabel. Universidad de los Andes. Department of Chemistry; Colombia<br />Fil: Carazzone, Chiara. Universidad de los Andes. Department of Chemistry; Colombia<br />Fil: Amézquita, Adolfo. Universidad de los Andes. Department of Biological Sciences; Colombia<br />Fil: Callewaert, Chris. Center for Microbial Ecology and Technology; Belgica<br />Fil: Callewaert, Chris. University of California. Department of Pediatrics; Estados Unidos<br />Fil: Morton, James T. University of California. Department of Pediatrics; Estados Unidos<br />Fil: Morton, James T. Simons Foundation. Flatiron Institute. Center for Computational Biology; Estados Unidos<br />Fil: Quinn, Robert A. Michigan State University. Department of Biochemistry and Molecular Biology; Estados Unidos<br />Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Bouslimani, Amina. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Orio, Andrea Albarracín. Universidad Católica de Córdoba. IRNASUS. CONICET. Facultad de Ciencias Agropecuarias; Argentina<br />Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Petras, Daniel. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Smania, Andrea M. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Biológica Ranwel Caputto; Argentina<br />Fil: Smania, Andrea M. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. CONICET; Argentina<br />Fil: Couvillion, Sneha P. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos<br />Fil: Burnet, Meagan C. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos<br />Fil: Nicora, Carrie D. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos<br />Fil: Zink, Erika. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos<br />Fil: Metz, Thomas O. Pacific Northwest National Laboratory. Biological Sciences Division; Estados Unidos<br />Fil: Artaev, Viatcheslav. LECO Corporation; Estados Unidos<br />Fil: Humston-Fulmer, Elizabeth. LECO Corporation; Estados Unidos<br />Fil: Gregor, Rachel. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel<br />Fil: Meijler, Michael M. Ben-Gurion University of the Negev. Department of Chemistry and the National Institute for Biotechnology in the Negev; Israel<br />Fil: Mizrahi, Itzhak. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel<br />Fil: Eyal, Stav. Ben-Gurion University of the Negev. Department of Life Sciences and the National Institute for Biotechnology in the Negev; Israel<br />Fil: Anderson, Brooke. University of California. Division of Biological Sciences; Estados Unidos<br />Fil: Dutton, Rachel. University of California. Division of Biological Sciences; Estados Unidos<br />Fil: Lugan, Raphaël. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia<br />Fil: Boulch, Pauline Le. Université d’Avignon et des Pays du Vaucluse, Agrosciences. UMR Qualisud; Francia<br />Fil: Guitton, Yann. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia<br />Fil: Prevost, Stephanie. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia<br />Fil: Poirier, Audrey. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia<br />Fil: Dervilly, Gaud. INRAe. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia<br />Fil: Le Bizec, Bruno. Oniris. Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA); Francia<br />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<br />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<br />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<br />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<br />Fil: Coras, Roxana. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos<br />Fil: Guma, Monica. University of California. Department of Medicine. Division of Rheumatology; Estados Unidos<br />Fil: Manasson, Julia. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos<br />Fil: Scher, Jose U. New York University School of Medicine. Department of Medicine. Division of Rheumatology; Estados Unidos<br />Fil: Barupal, Dinesh Kumar. Icahn School of Medicine at Mount Sinai. Department of Environmental Medicine and Public Health; Estados Unidos<br />Fil: Alseekh, Saleh. Max Planck Institute for Molecular Plant Physiology; Alemania<br />Fil: Alseekh, Saleh. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria<br />Fil: Fernie, Alisdair R. Max Planck Institute for Molecular Plant Physiology; Alemania<br />Fil: Fernie, Alisdair R. Center of Plant Systems Biology and Biotechnology (CPSBB); Bulgaria<br />Fil: Mirnezami, Reza. Royal Free Hospital NHS Foundation Trust. Department of Colorectal Surgery; Reino Unido<br />Fil: Vasiliou, Vasilis. Yale University. Yale School of Public Health. Department of Environmental Health Sciences; Estados Unidos<br />Fil: Schmid, Robin. University of Münster. Institute of Inorganic and Analytical Chemistry; Alemania<br />Fil: Borisov, Roman S. A.V. Topchiev Institute of Petrochemical Synthesis RAS; Rusia<br />Fil: Kulikova, Larisa N. Рeoples’ Friendship University of Russia (RUDN University); Rusia<br />Fil: Knight, Rob. University of California. Department of Pediatrics; Estados Unidos<br />Fil: Knight, Rob. University of California. UCSD Center for Microbiome Innovation; Estados Unidos<br />Fil: Knight, Rob. University of California. Department of Bioengineering; Estados Unidos<br />Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Wang, Mingxun. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Hanna, George B. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido<br />Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences; Estados Unidos<br />Fil: Dorrestein, Pieter C. University of California. Skaggs School of Pharmacy and Pharmaceutical Sciences. Collaborative Mass Spectrometry Innovation Center; Estados Unidos<br />Fil: Dorrestein, Pieter C. University of California. Department of Pediatrics; Estados Unidos<br />Fil: Veselkov, Kirill. South Kensington Campus. Imperial College London. Department of Surgery and Cancer; Reino Unido
- Subjects :
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 10870156
- Database :
- OpenAIRE
- Journal :
- 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
- Accession number :
- edsair.doi.dedup.....e1ff89483759269c68c13571b23db181