Nature Biotechnology

, volume 39 , issue 2 , pages 169-173

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

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-Félix 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

C. D. Nicora ²¹

E. C. 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

Raphael Lugan ²⁶

Pauline Le Boulch ²⁶

Yann Guitton ²⁷

Stephanie Prevost ²⁷

Audrey Poirier ²⁷

G. Dervilly-Pinel 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}

Eric Lam ^{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

Hide authors affiliations Show authors affiliations: 41 affiliations

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA |

Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California,San Diego, La Jolla, USA |

Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK |

⁴

Intelligify Limited, London, UK |

⁵

Department of Computing, Imperial College, South Kensington Campus, London, UK |

⁶

Department of Computer Science, University of Antwerp, Antwerp, Belgium |

⁷

Department of Chemistry, Point Loma Nazarene University, San Diego, USA |

⁸

Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, USA |

⁹

Department of Bioinformatics and Genomics, University of North Carolina At Charlotte, Charlotte, USA |

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, the 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, USA |

¹⁶

Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, USA |

¹⁷

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA |

¹⁸

IRNASUS, Universidad Católica de Córdoba, CONICET, Facultad de Ciencias Agropecuarias, Córdoba, Argentina |

¹⁹

Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina |

²⁰

CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina |

²¹

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, USA |

²²

LECO Corporation, St. Joseph, USA |

²³

Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel |

²⁴

Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel |

²⁵

Division of Biological Sciences, University of California, San Diego, La Jolla, USA |

²⁶

UMR Qualisud, Université d’Avignon et des Pays du Vaucluse, Agrosciences, Avignon, France |

²⁷

Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAe, Nantes, France |

²⁸

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 |

²⁹

Division of Rheumatology, Department of Medicine, University of California, San Diego, La Jolla, USA |

³⁰

Division of Rheumatology, Department of Medicine, New York University School of Medicine, New York, USA |

³¹

Department of Environmental Medicine and Public Health, Icahn School of Medicine At Mount Sinai, New York, USA |

³²

Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany |

³³

Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria |

³⁴

Department of Colorectal Surgery, Royal Free Hospital NHS Foundation Trust, Hampstead, UK |

³⁵

Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, USA |

³⁶

Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany |

³⁷

A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, Russian Federation |

³⁸

Рeoples’ Friendship University of Russia (RUDN University), Moscow, Russian Federation |

³⁹

UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, USA |

⁴⁰

Department of Bioengineering, University of California, San Diego, La Jolla, USA |

⁴¹

Department of Computer Science & Engineering, University of California, San Diego, La Jolla, USA |

Publication type: Journal Article

Publication date: 2020-11-09

Springer Nature

Nature Biotechnology

scimago Q1

wos Q1

SJR: 19.006

CiteScore: 58.8

Impact factor: 41.7

ISSN: 10870156, 15461696

DOI: 10.1038/s41587-020-0700-3

Copy DOI

PubMed ID: 33169034

Molecular Medicine

Applied Microbiology and Biotechnology

Biotechnology

Bioengineering

Biomedical Engineering

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. A machine learning workflow enables auto-deconvolution of gas chromatography–mass spectrometry data.

Found

1 citation

Borisov Roman

🤝

PhD in Chemistry

184 publications, 1 708 citations, 19 reviews

h-index: 20

A.V. Topchiev Institute of Petrochemical Synthesis RAS

Peoples' Friendship University of Russia

Research interests

Mass Spectrometry

1 citation

Tsymbarovich Petr

10 publications, 92 citations

h-index: 3

Dokuchaev Soil Science Institute

1 citation

Hu Xin

15 publications, 134 citations, 3 reviews

h-index: 5

Emory University

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Cite this

GOST |

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GOST Copy

Aksenov A. A. et al. Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data // Nature Biotechnology. 2020. Vol. 39. No. 2. pp. 169-173.

GOST all authors (up to 50) Copy

Aksenov A. A. et al. Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data // Nature Biotechnology. 2020. Vol. 39. No. 2. pp. 169-173.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1038/s41587-020-0700-3

UR - https://doi.org/10.1038/s41587-020-0700-3

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

T2 - Nature Biotechnology

AU - Aksenov, Alexander A

AU - Laponogov, Ivan

AU - Zhang, Zheng

AU - Doran, Sophie L. F.

AU - Belluomo, Ilaria

AU - Veselkov, Dennis

AU - Bittremieux, Wout

AU - Nothias, Louis-Félix

AU - Nothias Esposito, Mélissa

AU - Maloney, Katherine N

AU - Misra, Biswapriya B

AU - Melnik, Alexey V

AU - Smirnov, Aleksandr

AU - Du, Xiuxia

AU - JONES, KENNETH L.

AU - Dorrestein, Kathleen

AU - Panitchpakdi, Morgan

AU - Ernst, Madeleine

AU - van der Hooft, Justin J. J.

AU - Gonzalez, Mabel

AU - Carazzone, Chiara

AU - Amézquita, Adolfo

AU - Callewaert, Chris

AU - Morton, James T

AU - Quinn, Robert A.

AU - Bouslimani, Amina

AU - Orio, Andrea Albarracín

AU - Petras, Daniel

AU - SMANIA, Andrea M.

AU - Couvillion, Sneha P.

AU - Burnet, Meagan C

AU - Nicora, C. D.

AU - Zink, E. C.

AU - Metz, Thomas O.

AU - Artaev, Viatcheslav

AU - Humston Fulmer, Elizabeth

AU - Gregor, Rachel

AU - Meijler, Michael M.

AU - Mizrahi, Itzhak

AU - Eyal, Stav

AU - Anderson, Brooke

AU - Dutton, Rachel

AU - Lugan, Raphael

AU - Boulch, Pauline Le

AU - Guitton, Yann

AU - Prevost, Stephanie

AU - Poirier, Audrey

AU - Dervilly-Pinel, G.

AU - Le Bizec, Bruno

AU - Fait, Aaron

AU - Persi, Noga Sikron

AU - Song, Chao

AU - Gashu, Kelem

AU - Coras, Roxana

AU - Guma, Monica

AU - Manasson, Julia

AU - Scher, Jose U.

AU - Barupal, Dinesh Kumar

AU - Alseekh, Saleh

AU - Lam, Eric

AU - Mirnezami, Reza

AU - Vasiliou, Vasilis

AU - Schmid, Robin

AU - Borisov, Roman S

AU - Kulikova, Larisa N

AU - Knight, Rob

AU - Wang, Mingxun

AU - Hanna, George B.

AU - Dorrestein, Pieter C

AU - Veselkov, Kirill

PY - 2020

DA - 2020/11/09

PB - Springer Nature

SP - 169-173

IS - 2

VL - 39

PMID - 33169034

SN - 1087-0156

SN - 1546-1696

ER -

BibTex |

Cite this

BibTex (up to 50 authors) Copy

@article{2020_Aksenov,

author = {Alexander A Aksenov and Ivan Laponogov and Zheng Zhang and Sophie L. F. Doran and Ilaria Belluomo and Dennis Veselkov and Wout Bittremieux and Louis-Félix Nothias and Mélissa Nothias Esposito and Katherine N Maloney and Biswapriya B Misra and Alexey V Melnik and Aleksandr Smirnov and Xiuxia Du and KENNETH L. JONES and Kathleen Dorrestein and Morgan Panitchpakdi and Madeleine Ernst and Justin J. J. van der Hooft and Mabel Gonzalez and Chiara Carazzone and Adolfo Amézquita and Chris Callewaert and James T Morton and Robert A. Quinn and Amina Bouslimani and Andrea Albarracín Orio and Daniel Petras and Andrea M. SMANIA and Sneha P. Couvillion and Meagan C Burnet and C. D. Nicora and E. C. Zink and Thomas O. Metz and Viatcheslav Artaev and Elizabeth Humston Fulmer and Rachel Gregor and Michael M. Meijler and Itzhak Mizrahi and Stav Eyal and Brooke Anderson and Rachel Dutton and Raphael Lugan and Pauline Le Boulch and Yann Guitton and Stephanie Prevost and Audrey Poirier and G. Dervilly-Pinel and Bruno Le Bizec and Aaron Fait and others},

title = {Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data},

journal = {Nature Biotechnology},

year = {2020},

volume = {39},

publisher = {Springer Nature},

month = {nov},

url = {https://doi.org/10.1038/s41587-020-0700-3},

number = {2},

pages = {169--173},

doi = {10.1038/s41587-020-0700-3}

}

MLA

Cite this

MLA Copy

Aksenov, Alexander A., et al. “Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data.” Nature Biotechnology, vol. 39, no. 2, Nov. 2020, pp. 169-173. https://doi.org/10.1038/s41587-020-0700-3.

Publisher

Springer Nature

Journal

Nature Biotechnology

scimago Q1

wos Q1

SJR

19.006

CiteScore

58.8

Impact factor

41.7

ISSN

10870156 (Print)

15461696 (Electronic)

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