Mass Spectrometry-Based Untargeted Plant Metabolomics

Q1 Agricultural and Biological Sciences Current protocols in plant biology Pub Date : 2019-11-19 DOI:10.1002/cppb.20100

Leonardo Perez de Souza, Saleh Alseekh, Thomas Naake, Alisdair Fernie

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引用次数: 48

Abstract

Metabolomics has grown into one of the major approaches for systems biology studies, in part driven by developments in mass spectrometry (MS), providing high sensitivity and coverage of the metabolome at high throughput. Untargeted metabolomics allows for the investigation of metabolic phenotypes involving several hundreds to thousands of metabolites. In this approach, all signals in a mass chromatogram are processed in an unbiased way, allowing for a deeper investigation of metabolic phenotypes, but also resulting in significantly more complex data processing and post-processing steps. In this article, we discuss all the intricacies involved in extracting and analyzing metabolites by chromatography coupled to MS, as well as the processing and analysis of such datasets. © 2019 The Authors.

Basic Protocol 1: Metabolite extraction for LC-MS

Alternate Protocol: Methyl tert-butyl ether (MTBE) extraction for multiple mass spectrometry platforms (GC-polar, LC-polar, LC-lipid)

Basic Protocol 2: LC-MS analysis

Support Protocol 1: GC-MS derivatization and analysis

Support Protocol 2: Lipid analysis

Basic Protocol 3: LC-MS data processing

Basic Protocol 4: Data analysis

Basic Protocol 5: Metabolite annotation

Support Protocol 3: Molecular networking using MetNet

Support Protocol 4: Co-injection of authentic standards

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基于质谱的非靶向植物代谢组学

代谢组学已经发展成为系统生物学研究的主要方法之一，部分原因是由于质谱(MS)的发展，它提供了高灵敏度和高通量代谢组学的覆盖范围。非靶向代谢组学允许研究涉及数百到数千种代谢物的代谢表型。在这种方法中，质谱中的所有信号都以无偏的方式进行处理，允许对代谢表型进行更深入的研究，但也导致更复杂的数据处理和后处理步骤。在这篇文章中，我们讨论了所有涉及到的复杂的提取和分析代谢物的色谱耦合质谱，以及处理和分析这些数据集。©2019作者。基本协议1:LC-MS代谢物提取替代协议:甲基叔丁基醚(MTBE)提取用于多个质谱平台(气相色谱-极性，lc -极性，lc -脂质)基本协议2:LC-MS分析支持协议1:GC-MS衍生化和分析支持协议2:脂质分析基本协议3:LC-MS数据处理基本协议4:数据分析基本协议5:代谢物注释支持协议3:使用metnetmolecular networking支持协议4:共同注入正品标准

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来源期刊

Current protocols in plant biology Agricultural and Biological Sciences-Plant Science

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期刊介绍： Sound and reproducible laboratory methods are the foundation of scientific discovery. Yet nuances that are critical for an experiment''s success are not captured in the primary literature but exist only as part of a lab''s oral tradition. Current Protocols in Plant Biology provides reproducible step-by-step instructions for protocols relevant to plant research. Furthermore, Current Protocols content is thoughtfully organized by topic for optimal usage and to maximize contextual knowledge. Quarterly issues allow Current Protocols in Plant Biology to constantly evolve to keep pace with the newest discoveries and developments. Current Protocols in Plant Biology is the comprehensive source for protocols in the multidisciplinary field of plant biology, providing an extensive range of protocols from basic to cutting edge. Coverage includes: Extraction and analysis of DNA, RNA, proteins Chromosome analysis Transcriptional analysis Protein expression Metabolites Plant enzymology Epigenetics Plant genetic transformation Mutagenesis Arabidopsis, Maize, Poplar, Rice, and Soybean, and more.