Reproducible molecular networking of untargeted mass spectrometry data using GNPS.,Nature Protocols

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Reproducible molecular networking of untargeted mass spectrometry data using GNPS.
Nature Protocols ( IF 13.1 ) Pub Date : 2020-05-13 , DOI: 10.1038/s41596-020-0317-5
Allegra T Aron ₁ , Emily C Gentry ₁ , Kerry L McPhail ₂ , Louis-Félix Nothias ₁ , Mélissa Nothias-Esposito ₁ , Amina Bouslimani ₁ , Daniel Petras _{1,

3} , Julia M Gauglitz ₁ , Nicole Sikora ₁ , Fernando Vargas _{1,

4} , Justin J J van der Hooft ₅ , Madeleine Ernst ₁ , Kyo Bin Kang ₆ , Christine M Aceves ₁ , Andrés Mauricio Caraballo-Rodríguez ₁ , Irina Koester _{1,

3} , Kelly C Weldon _{1,

7} , Samuel Bertrand _{8,

9} , Catherine Roullier _{6,

9} , Kunyang Sun ₁ , Richard M Tehan ₂ , Cristopher A Boya P _{10,

11} , Martin H Christian ₁₀ , Marcelino Gutiérrez ₁₀ , Aldo Moreno Ulloa ₁₂ , Javier Andres Tejeda Mora ₁₂ , Randy Mojica-Flores _{10,

13} , Johant Lakey-Beitia ₁₀ , Victor Vásquez-Chaves ₁₄ , Yilue Zhang ₁₅ , Angela I Calderón ₁₅ , Nicole Tayler _{10,

11} , Robert A Keyzers ₁₆ , Fidele Tugizimana _{17,

18} , Nombuso Ndlovu ₁₇ , Alexander A Aksenov ₁ , Alan K Jarmusch ₁ , Robin Schmid ₁₉ , Andrew W Truman ₂₀ , Nuno Bandeira ₂₁ , Mingxun Wang ₁ , Pieter C Dorrestein _{1,

22,

23,

24}

Affiliation

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
College of Pharmacy, Sookmyung Women's University, Seoul, Korea.
Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France.
ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France.
Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama.
Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India.
Biomedical Innovation Department, CICESE, Ensenada, Mexico.
Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama.
Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.
Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA.
School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand.
Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa.
International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa.
Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany.
Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

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.

中文翻译：

使用 GNPS 对非目标质谱数据进行可重复的分子网络。

全球天然产物社交分子网络 (GNPS) 是一个交互式在线小分子串联质谱 (MS2) 数据管理和分析基础设施。它旨在为非目标 MS2 数据集提供尽可能多的化学见解，并将这种化学见解与用户潜在的生物学问题联系起来。这可以在一次液相色谱 (LC)-MS2 实验中或以存储库规模进行。GNPS-MassIVE 是一个公共数据存储库，用于存储非目标 MS2 数据，其中包含样本信息（元数据）和带注释的 MS2 谱图。这些可公开访问的数据可以通过 GNPS 基础设施进行注释和更新，从而持续记录所有更改。这些知识在所有公共数据中传播；它是一个活的数据集。分子网络 - GNPS 平台中使用的主要分析工具之一 - 创建一个结构化数据表，通过计算 MS2 光谱的关系作为光谱相似性，反映串联质谱实验中捕获的分子多样性。该协议提供了创建可重复的高质量分子网络的分步说明。出于培训目的，读者将被引导完成 90 到 120 分钟的过程，首先回顾示例公共数据集及其样本信息，然后继续创建和解释分子网络。每个数据分析工作都可以共享或克隆，以传播所获得的知识，从而传播可以发现分子、代谢途径和生态系统/群落相互作用的信息。

更新日期：2020-05-13

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