Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data
Alexander Aksenov
(1, 2)
,
Ivan Laponogov
(3)
,
Zheng Zhang
(1)
,
Sophie Doran
(3)
,
Ilaria Belluomo
(3)
,
Dennis Veselkov
(3)
,
Wout Bittremieux
(1, 2, 4)
,
Louis Felix Nothias
(1, 2)
,
Mélissa Nothias-Esposito
(1, 2)
,
Katherine Maloney
(1)
,
Biswapriya Misra
(5)
,
Alexey Melnik
(1)
,
Aleksandr Smirnov
(6)
,
Xiuxia Du
(6)
,
Kenneth Jones
(1)
,
Kathleen Dorrestein
(1, 2)
,
Morgan Panitchpakdi
(1)
,
Madeleine Ernst
(1, 7)
,
Justin van Der Hooft
(1, 8)
,
Mabel Gonzalez
(9)
,
Chiara Carazzone
(9)
,
Adolfo Amézquita
(9)
,
Chris Callewaert
(10, 11)
,
James Morton
(11, 12)
,
Robert Quinn
(13)
,
Amina Bouslimani
(1, 2)
,
Andrea Albarracín Orio
(14)
,
Daniel Petras
(1, 2)
,
Andrea Smania
(15)
,
Sneha Couvillion
(16)
,
Meagan Burnet
(16)
,
Carrie Nicora
(16)
,
Erika Zink
(16)
,
Thomas Metz
(16)
,
Viatcheslav Artaev
(17)
,
Elizabeth Humston-Fulmer
(17)
,
Rachel Gregor
(18)
,
Michael Meijler
(18)
,
Itzhak Mizrahi
(18)
,
Stav Eyal
(18)
,
Brooke Anderson
(11)
,
Rachel Dutton
(11)
,
Raphaël Lugan
(19)
,
Pauline Le Boulch
(19)
,
Yann Guitton
(20)
,
Stéphanie Prévost
(20)
,
Audrey Poirier
(20)
,
Gaud Dervilly
(20)
,
Bruno Le Bizec
(20)
,
Aaron Fait
(18)
,
Noga Sikron Persi
(18)
,
Chao Song
(18)
,
Kelem Gashu
(18)
,
Roxana Coras
(11)
,
Monica Guma
(11)
,
Julia Manasson
(21)
,
Jose Scher
(21)
,
Dinesh Kumar Barupal
(22)
,
Saleh Alseekh
(23, 24)
,
Alisdair Fernie
(23, 24)
,
Reza Mirnezami
(25)
,
Vasilis Vasiliou
(26)
,
Robin Schmid
(27)
,
Roman Borisov
(28)
,
Larisa Kulikova
(29)
,
Rob Knight
(11)
,
Mingxun Wang
(1, 2)
,
George Hanna
(3)
,
Pieter Dorrestein
(11)
,
Kirill Veselkov
(3)
1
Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego]
2 Collaborative Mass Spectrometry Innovation Center
3 Imperial College London
4 UA - University of Antwerp
5 Wake Forest School of Medicine [Winston-Salem]
6 UNC - University of North Carolina [Charlotte]
7 Statens Serum Institut [Copenhagen]
8 WUR - Wageningen University and Research [Wageningen]
9 UNIANDES - Universidad de los Andes [Bogota]
10 CMET - Center for Microbial Ecology and Technology
11 UC San Diego - University of California [San Diego]
12 Flatiron Institute
13 Michigan State University [East Lansing]
14 Universidad Católica de Córdoba
15 Universidad Nacional de Córdoba [Argentina]
16 PNNL - Pacific Northwest National Laboratory
17 LECO Corporation
18 BGU - Ben-Gurion University of the Negev
19 UMR QualiSud - Démarche intégrée pour l'obtention d'aliments de qualité
20 LABERCA - Laboratoire d'étude des Résidus et Contaminants dans les Aliments
21 NYU - New York University School of Medicine
22 MSSM - Icahn School of Medicine at Mount Sinai [New York]
23 CPSBB - Center of Plant Systems Biology and Biotechnology [Plovdiv]
24 MPI-MP - Max Planck Institute of Molecular Plant Physiology
25 NHS Foundation Trust [London]
26 YSPH - Yale School of Public Health
27 WWU - Westfälische Wilhelms-Universität Münster = University of Münster
28 TIPS - A.V. Topchiev Institute of Petrochemical Synthesis
29 RUDN University - People's Friendship University of Russia [Moscow] = Rossijskij universitet družby narodov [Moskva]
2 Collaborative Mass Spectrometry Innovation Center
3 Imperial College London
4 UA - University of Antwerp
5 Wake Forest School of Medicine [Winston-Salem]
6 UNC - University of North Carolina [Charlotte]
7 Statens Serum Institut [Copenhagen]
8 WUR - Wageningen University and Research [Wageningen]
9 UNIANDES - Universidad de los Andes [Bogota]
10 CMET - Center for Microbial Ecology and Technology
11 UC San Diego - University of California [San Diego]
12 Flatiron Institute
13 Michigan State University [East Lansing]
14 Universidad Católica de Córdoba
15 Universidad Nacional de Córdoba [Argentina]
16 PNNL - Pacific Northwest National Laboratory
17 LECO Corporation
18 BGU - Ben-Gurion University of the Negev
19 UMR QualiSud - Démarche intégrée pour l'obtention d'aliments de qualité
20 LABERCA - Laboratoire d'étude des Résidus et Contaminants dans les Aliments
21 NYU - New York University School of Medicine
22 MSSM - Icahn School of Medicine at Mount Sinai [New York]
23 CPSBB - Center of Plant Systems Biology and Biotechnology [Plovdiv]
24 MPI-MP - Max Planck Institute of Molecular Plant Physiology
25 NHS Foundation Trust [London]
26 YSPH - Yale School of Public Health
27 WWU - Westfälische Wilhelms-Universität Münster = University of Münster
28 TIPS - A.V. Topchiev Institute of Petrochemical Synthesis
29 RUDN University - People's Friendship University of Russia [Moscow] = Rossijskij universitet družby narodov [Moskva]
Zheng Zhang
- Fonction : Auteur
- PersonId : 770848
- IdRef : 176531688
Yann Guitton
- Fonction : Auteur
- PersonId : 1825
- IdHAL : yann-guitton
- ORCID : 0000-0002-4479-0636
- IdRef : 158912675
Gaud Dervilly
- Fonction : Auteur
- PersonId : 746756
- IdHAL : gaud-dervilly
- ORCID : 0000-0002-1867-0008
- IdRef : 18894821X
Bruno Le Bizec
- Fonction : Auteur
- PersonId : 748507
- IdHAL : bruno-le-bizec
- ORCID : 0000-0002-0600-5895
- IdRef : 077236483
Saleh Alseekh
- Fonction : Auteur
- PersonId : 775062
- ORCID : 0000-0003-2067-5235
Alisdair Fernie
- Fonction : Auteur
- PersonId : 776764
- ORCID : 0000-0001-9000-335X
Rob Knight
- Fonction : Auteur
- PersonId : 762535
- ORCID : 0000-0002-0975-9019
- IdRef : 192695541
Résumé
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.
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