Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 564691
Title Reproducible molecular networking of untargeted mass spectrometry data using GNPS
Author(s) Aron, Allegra T.; Gentry, Emily C.; McPhail, Kerry L.; Nothias, Louis Félix; Nothias-Esposito, Mélissa; Bouslimani, Amina; Petras, Daniel; Gauglitz, Julia M.; Sikora, Nicole; Vargas, Fernando; Hooft, Justin J.J. van der; Ernst, Madeleine; Kang, Kyo Bin; Aceves, Christine M.; Caraballo-Rodríguez, Andrés Mauricio; Koester, Irina; Weldon, Kelly C.; Bertrand, Samuel; Roullier, Catherine; Sun, Kunyang; Tehan, Richard M.; Boya P, Cristopher A.; Christian, Martin H.; Gutiérrez, Marcelino; Ulloa, Aldo Moreno; Tejeda Mora, Javier Andres; Mojica-Flores, Randy; Lakey-Beitia, Johant; Vásquez-Chaves, Victor; Zhang, Yilue; Calderón, Angela I.; Tayler, Nicole; Keyzers, Robert A.; Tugizimana, Fidele; Ndlovu, Nombuso; Aksenov, Alexander A.; Jarmusch, Alan K.; Schmid, Robin; Truman, Andrew W.; Bandeira, Nuno; Wang, Mingxun; Dorrestein, Pieter C.
Source Nature protocols 15 (2020). - ISSN 1754-2189 - p. 1954 - 1991.
DOI https://doi.org/10.1038/s41596-020-0317-5
Department(s) Bioinformatics
Publication type Refereed Article in a scientific journal
Publication year 2020
Abstract

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.

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