Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS

Alexander Aksenov; Ivan Laponogov; Zheng Zhang; Sophie Lf Doran; Ilaria Belluomo; Dennis Veselkov; Wout Bittremieux; Louis Felix Nothias; Mélissa Nothias-Esposito; Katherine Maloney; Biswapriya Misra; Alexey Melnik; Kenneth Jones; Kathleen Dorrestein; Morgan Panitchpakdi; Madeleine Ernst; Justin J.J. van Der Hooft; Mabel Gonzalez; Chiara Carazzone; Adolfo Amézquita; Chris Callewaert; James Morton; Robert Quinn; Amina Bouslimani; Andrea Albarracín Orio; Daniel Petras; Andrea Smania; Sneha Couvillion; Meagan Burnet; Carrie Nicora; Erika Zink; Thomas Metz; Viatcheslav Artaev; Elizabeth Humston-Fulmer; Rachel Gregor; Michael Meijler; Itzhak Mizrahi; Stav Eyal; Brooke Anderson; Rachel Dutton; Raphaël Lugan; Pauline Le Boulch; Yann Guitton; Stéphanie Prévost; Audrey Poirier; Gaud Dervilly; Bruno Le Bizec; Aaron Fait; Noga Sikron Persi; Chao Song; Kelem Gashu; Roxana Coras; Monica Guma; Julia Manasson; Jose Scher; Dinesh Barupal; Saleh Alseekh; Alisdair Fernie; Reza Mirnezami; Vasilis Vasiliou; Robin Schmid; Roman Borisov; Larisa Kulikova; Rob Knight; Mingxun Wang; George Hanna; Pieter Dorrestein; Kirill Veselkov

doi:10.1101/2020.01.13.905091

Working paper

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS

Alexander Aksenov, Ivan Laponogov, Zheng Zhang, Sophie Lf Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Mélissa Nothias-Esposito, Katherine Maloney, …

DOI: https://doi.org/10.1101/2020.01.13.905091

Abstract

Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefore engineered a scalable machine learning workflow for the Global Natural Product Social Molecular Networking (GNPS) analysis platform to enable the mass spectrometry community to store, process, share, annotate, compare, and perform molecular networking of GC-MS data. The workflow performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization, using a Fast Fourier Transform-based strategy to overcome scalability limitations. We introduce a “balance score” that quantifies the reproducibility of fragmentation patterns across all samples. We demonstrate the utility of the platform with breathomics analysis applied to the early detection of oesophago-gastric cancer, and by creating the first molecular spatial map of the human volatilome.

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Title: Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS
Creators - without role: Alexander Aksenov - University of California, San Diego
Ivan Laponogov - Imperial College London
Zheng Zhang - University of California, San Diego
Sophie Lf Doran - Imperial College London
Ilaria Belluomo - Imperial College London
Dennis Veselkov - Intelligify
Wout Bittremieux - University of California, San Diego
Louis Felix Nothias - Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego]
Mélissa Nothias-Esposito - University of California, San Diego
Katherine Maloney - University of California, San Diego
Biswapriya Misra - Wake Forest University
Alexey Melnik - University of California, San Diego
Kenneth Jones - University of California, San Diego
Kathleen Dorrestein - University of California, San Diego
Morgan Panitchpakdi - University of California, San Diego
Madeleine Ernst - University of Montana
Justin J.J. van Der Hooft - University of Montana
Mabel Gonzalez - Universidad de Los Andes
Chiara Carazzone - Universidad de Los Andes
Adolfo Amézquita - Universidad de Los Andes
Chris Callewaert - University of California, San Diego
James Morton - University of California, San Diego
Robert Quinn - Michigan State University
Amina Bouslimani - University of Montana
Andrea Albarracín Orio - Universidad Católica de Córdoba
Daniel Petras - University of Montana
Andrea Smania - Universidad Nacional de Córdoba
Sneha Couvillion - Pacific Northwest National Laboratory
Meagan Burnet - Pacific Northwest National Laboratory
Carrie Nicora - Pacific Northwest National Laboratory
Erika Zink - Pacific Northwest National Laboratory
Thomas Metz - Pacific Northwest National Laboratory
Viatcheslav Artaev - Leco Corporation
Elizabeth Humston-Fulmer - Leco Corporation
Rachel Gregor - Ben-Gurion University of the Negev
Michael Meijler - Ben-Gurion University of the Negev
Itzhak Mizrahi - Ben-Gurion University of the Negev
Stav Eyal - Ben-Gurion University of the Negev
Brooke Anderson - University of San Diego
Rachel Dutton - University of San Diego
Raphaël Lugan - Université de Montpellier, Démarche intégrée pour l'obtention d'aliments de qualité - QUALISUD
Pauline Le Boulch - Université de Montpellier, Démarche intégrée pour l'obtention d'aliments de qualité - QUALISUD
Yann Guitton - Oniris
Stéphanie Prévost - Oniris
Audrey Poirier - Laboratoire D'étude des Résidus et Contaminants Dans les Aliments
Gaud Dervilly - Oniris
Bruno Le Bizec - Laboratoire D'étude des Résidus et Contaminants Dans les Aliments
Aaron Fait - Ben-Gurion University of the Negev
Noga Sikron Persi - Ben-Gurion University of the Negev
Chao Song - Ben-Gurion University of the Negev
Kelem Gashu - Ben-Gurion University of the Negev
Roxana Coras - University of California, San Diego
Monica Guma - University of California, San Diego
Julia Manasson - New York University
Jose Scher - New York University
Dinesh Barupal - University of California, Davis
Saleh Alseekh - Center of Plant Systems Biology and Biotechnology
Alisdair Fernie - Center of Plant Systems Biology and Biotechnology
Reza Mirnezami - Royal Free London NHS Foundation Trust
Vasilis Vasiliou - Yale University
Robin Schmid - Institute of Inorganic and Analytical chemistry [University of Freiburg] | Institut für Anorganische und Analytische Chemie [Albert-Ludwigs-Universität Freiburg]
Roman Borisov - A.V. Topchiev Institute of Petrochemical Synthesis
Larisa Kulikova - Amitie
Rob Knight - University of California, San Diego
Mingxun Wang - University of Montana
George Hanna - Imperial College London
Pieter Dorrestein - University of California, San Diego
Kirill Veselkov - Imperial College London
Identifiers: 9939528009311
Academic Unit: Démarche intégrée pour l'obtention d'aliments de qualité - QUALISUD
Language: English
Resource Type: Working paper
Local Fields: hal-03173091