Recent technological developments and methodological advances of both liquid chromatography (LC) and mass spectrometry (MS) have allowed LC-MS-based plant metabolomics to become a common tool for investigating quantity, quality, and chemical diversity of plant metabolites. Targeted LC-MS metabolite analysis focuses on the detection and quantitation of the researcher's target metabolites. Whilst the word "target analysis" has been used for the analytical measurement to obtain the absolute concentrations evaluated by authentic and/or stable-isotope-labeled standards, over time the phrase came to be also used in a broad sense for the measurement of annotatable metabolites by structural information obtained from the combination of different strategies such as MS/MS analysis, reference extracts, mutant analysis and database search. Here, we describe a general protocol for targeted LC-MS metabolite profiling of plant secondary metabolites. Additionally, we introduce some examples of peak annotation using the combination approach.
Keywords: LC-MS/MS; Liquid chromatography–tandem mass spectrometry; Peak annotation; Peak identification; Plant secondary metabolites; Targeted analysis.