Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Autor: Daniel Petras, Aldo Moreno Ulloa, Cristopher A. Boya P., Fernando Vargas, Randy Mojica-Flores, Alan K. Jarmusch, Kunyang Sun, Marcelino Gutiérrez, Kyo Bin Kang, Richard M. Tehan, Mingxun Wang, Robert A. Keyzers, Alexander A. Aksenov, Justin J. J. van der Hooft, Christine M. Aceves, Fidele Tugizimana, Andrew W. Truman, Martin H. Christian, Angela I. Calderón, Javier Andres Tejeda Mora, Johant Lakey-Beitia, Nicole Tayler, Nicole Sikora, Andrés Mauricio Caraballo-Rodríguez, Kelly C. Weldon, Julia M. Gauglitz, Emily C. Gentry, Pieter C. Dorrestein, Yilue Zhang, Nuno Bandeira, Louis-Félix Nothias, Mélissa Nothias-Esposito, Nombuso Ndlovu, Irina Koester, Samuel Bertrand, Allegra T. Aron, Victor Vásquez-Chaves, Robin Schmid, Kerry L. McPhail, Madeleine Ernst, Catherine Roullier, Amina Bouslimani
Přispěvatelé: Institut de recherche en cancérologie de Montpellier (IRCM - U896 Inserm - UM1), Université Montpellier 1 (UM1)-CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Süssmuth Institut für Chemie, Technische Universität Berlin (TU), University of Glasgow, Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN)
Rok vydání: 2020
Předmět:
Zdroj: Nature protocols, 15, 1954-1991
Nature protocols 15 (2020)
Nature Protocols
Nature Protocols, Nature Publishing Group, 2020, 15 (6), pp.1954-1991. ⟨10.1038/s41596-020-0317-5⟩
Nature Protocols volume 15, pages1954–1991(2020)
Kérwá
Universidad de Costa Rica
instacron:UCR
ISSN: 1750-2799
1754-2189
Popis: Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule–focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user’s underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking—one of the main analysis tools used within the GNPS platform—creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions. UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA) UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Química
Databáze: OpenAIRE
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