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

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Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
Nature Biotechnology ( IF 33.1 ) Pub Date : 2020-11-09 , DOI: 10.1038/s41587-020-0700-3
Alexander A Aksenov _{1,

2} , Ivan Laponogov ₃ , Zheng Zhang ₁ , Sophie L F Doran ₃ , Ilaria Belluomo ₃ , 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 Misra ₈ , Alexey V Melnik ₁ , Aleksandr Smirnov ₉ , Xiuxia Du ₉ , Kenneth L Jones ₁ , Kathleen Dorrestein _{1,

2} , Morgan Panitchpakdi ₁ , Madeleine Ernst _{1,

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

11} , Mabel Gonzalez ₁₂ , Chiara Carazzone ₁₂ , Adolfo Amézquita ₁₃ , Chris Callewaert _{14,

15} , James T Morton _{15,

16} , Robert A Quinn ₁₇ , Amina Bouslimani _{1,

2} , Andrea Albarracín Orio ₁₈ , Daniel Petras _{1,

2} , Andrea M Smania _{19,

20} , Sneha P Couvillion ₂₁ , Meagan C Burnet ₂₁ , Carrie D Nicora ₂₁ , Erika Zink ₂₁ , Thomas O Metz ₂₁ , Viatcheslav Artaev ₂₂ , Elizabeth Humston-Fulmer ₂₂ , Rachel Gregor ₂₃ , Michael M Meijler ₂₃ , Itzhak Mizrahi ₂₄ , Stav Eyal ₂₄ , Brooke Anderson ₂₅ , Rachel Dutton ₂₅ , Raphaël Lugan ₂₆ , Pauline Le Boulch ₂₆ , Yann Guitton ₂₇ , Stephanie Prevost ₂₇ , Audrey Poirier ₂₇ , Gaud Dervilly ₂₇ , Bruno Le Bizec ₂₇ , Aaron Fait ₂₈ , Noga Sikron Persi ₂₈ , Chao Song ₂₈ , Kelem Gashu ₂₈ , Roxana Coras ₂₉ , Monica Guma ₂₉ , Julia Manasson ₃₀ , Jose U Scher ₃₀ , Dinesh Kumar Barupal ₃₁ , Saleh Alseekh _{32,

33} , Alisdair R Fernie _{32,

33} , Reza Mirnezami ₃₄ , Vasilis Vasiliou ₃₅ , Robin Schmid ₃₆ , Roman S Borisov ₃₇ , Larisa N Kulikova ₃₈ , Rob Knight _{15,

39,

40,

41} , Mingxun Wang _{1,

2} , George B Hanna ₃ , Pieter C Dorrestein _{1,

2,

15,

39} , Kirill Veselkov ₃

Affiliation

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
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.
Intelligify Limited, London, UK.
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.
Center for Microbial Ecology and Technology, Ghent, Belgium.
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.
Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, 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.
Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
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.
UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA.

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.

中文翻译：

气相色谱-质谱数据的自动解卷积和分子网络

我们设计了一种机器学习方法 MSHub，以实现气相色谱-质谱 (GC-MS) 数据的自动解卷积。然后，我们设计了工作流程，使社区能够在全球天然产物社交 (GNPS) 分子网络分析平台内存储、处理、共享、注释、比较和执行 GC-MS 数据的分子网络。MSHub/GNPS 通过无监督非负矩阵分解执行复合碎片模式的自动反卷积，并量化样本间碎片模式的再现性。

更新日期：2020-11-09

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