Advances in high-throughput untargeted LC-MS analysis for plant metabolomics

Plants produce an extensive chemical diversity of metabolites, estimated to be between 100,000 and 200,000 compounds. LC–MS provides a tool for dissecting this immense plant biodiversity due to this technique’s capability of analyzing a broad range of metabolites including secondary metabolites (e.g., alkaloids, benzoids, flavonoids, terpenes, isoprenes, glucosinolates and phenylpropanoids) and highly polar and/or higher molecular weight molecules (oligosaccharides and lipids). LC– MS is one of the major untargeted analytical techniques to determine global metabolite profiles, which aims at the identification and relative quantitation of all peaks in the chromatogram as ions that are initially defined by retention time and molecular mass. This chapter outlines the common untargeted metabolomics approaches based on LC–MS, focusing on applications in plants and including the latest software packages and bioinformatics tools capable of processing untargeted LC–MS datasets in a high throughput manner. It also discusses some challenges faced by untargeted metabolomics, as well as recent advancements to help address some of these challenges.