Reproducible molecular networking of untargeted mass spectrometry data using GNPS

被引：473

作者：

Aron, Allegra T. ^{[1
]}

Gentry, Emily C. ^{[1
]}

McPhail, Kerry L. ^{[2
]}

Nothias, Louis-Felix ^{[1
]}

Nothias-Esposito, Melissa ^{[1
]}

Bouslimani, Amina ^{[1
]}

Petras, Daniel ^{[1
,3
]}

Gauglitz, Julia M. ^{[1
]}

Sikora, Nicole ^{[1
]}

Vargas, Fernando ^{[1
,4
]}

van Der Hooft, Justin J. J. ^{[5
]}

Ernst, Madeleine ^{[1
]}

Bin Kang, Kyo ^{[6
]}

Aceves, Christine M. ^{[1
]}

Caraballo-Rodriguez, Andres Mauricio ^{[1
]}

Koester, Irina ^{[1
,3
]}

Weldon, Kelly C. ^{[1
,7
]}

Bertrand, Samuel ^{[8
,9
]}

Roullier, Catherine ^{[6
,9
]}

Sun, Kunyang ^{[1
]}

Tehan, Richard M. ^{[2
]}

Boya P, Cristopher A. ^{[10
,11
]}

Christian, Martin H. ^{[10
]}

Gutierrez, Marcelino ^{[10
]}

Ulloa, Aldo Moreno ^{[12
]}

Mora, Javier Andres Tejeda ^{[12
]}

Mojica-Flores, Randy ^{[10
,13
]}

Lakey-Beitia, Johant ^{[10
]}

Vasquez-Chaves, Victor ^{[14
]}

Zhang, Yilue ^{[15
]}

Calderon, Angela, I ^{[15
]}

Tayler, Nicole ^{[10
,11
]}

Keyzers, Robert A. ^{[16
]}

Tugizimana, Fidele ^{[17
,18
]}

Ndlovu, Nombuso ^{[17
]}

Aksenov, Alexander A. ^{[1
]}

Jarmusch, Alan K. ^{[1
]}

Schmid, Robin ^{[19
]}

Truman, Andrew W. ^{[20
]}

Bandeira, Nuno ^{[21
]}

Wang, Mingxun ^{[1
]}

Dorrestein, Pieter C. ^{[1
,22
,23
,24
]}

机构：

[1] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[2] Oregon State Univ, Coll Pharm, Dept Pharmaceut Sci, Corvallis, OR 97331 USA

[3] Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Div Biol Sci, La Jolla, CA 92093 USA

[5] Wageningen Univ, Bioinformat Grp, Wageningen, Netherlands

[6] Sookmyung Womens Univ, Coll Pharm, Seoul, South Korea

[7] Univ Calif San Diego, Ctr Microbiome Innovat, La Jolla, CA 92093 USA

[8] Univ Nantes, UFR Sci Pharmaceut & Biol, Mol, Grp Mer,Sante EA 2160, Nantes, France

[9] Biogenouest, Plateforme Corsaire, ThalassOM Metabol Facil, Nantes, France

[10] Inst Invest Cient & Serv Alta Tecnol INDICASAT AI, Ctr Biodiversidad & Descubrimiento Drogas, Panama City, Panama

[11] Acharya Nagarjuna Univ, Dept Biotechnol, Nagarjuna Nagar, Andhra Pradesh, India

[12] CICESE, Biomed Innovat Dept, Ensenada, Baja California, Mexico

[13] Univ Autonoma Chiriqui UNACHI, Dept Quim, David, Chiriqui, Panama

[14] Univ Costa Rica, Ctr Invest Prod Nat CIPRONA, San Jose, Costa Rica

[15] Auburn Univ, Harrison Sch Pharm, Dept Drug Discovery & Dev, Auburn, AL 36849 USA

[16] Victoria Univ Wellington, Sch Chem & Phys Sci, Wellington, New Zealand

[17] Univ Johannesburg, Ctr Plant Metabol Res, Dept Biochem, Auckland Pk, South Africa

[18] Omnia Grp Pty Ltd, Int R&D Div, Johannesburg, South Africa

[19] Univ Munster, Inst Inorgan & Analyt Chem, Munster, Germany

[20] John Innes Ctr, Dept Mol Microbiol, Norwich, Norfolk, England

[21] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[22] Univ Calif San Diego, Ctr Computat Mass Spectrometry, La Jolla, CA 92093 USA

[23] Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA

[24] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

来源：

NATURE PROTOCOLS | 2020年 / 15卷 / 06期

基金：

美国国家科学基金会; 英国生物技术与生命科学研究理事会; 美国国家卫生研究院;

关键词：

PEPTIDIC NATURAL-PRODUCTS; SPECTRAL LIBRARY; SAMPLE PREPARATION; DARK-MATTER; METABOLOMICS; IDENTIFICATION; CHROMATOGRAPHY; ION; DEREPLICATION; CARTOGRAPHY;

D O I：

10.1038/s41596-020-0317-5

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Global Natural Product Social Molecular Networking (GNPS) is an online tandem mass spectrometry (MS2) data curation and analysis infrastructure. This protocol describes how to use GNPS to explore uploaded metabolomics data.

引用

页码：1954 / 1991

页数：38