Metabolite Annotation and Identification

Abstract Untargeted metabolomics has proven to be an excellent tool in biomarker discovery assays. It avoids the need for a priori specific hypotheses and measures a large number of signals potentially associated with metabolites from each sample. Currently, the process of metabolite identification, necessary for obtaining biological information, is still a significant bottleneck. In this chapter, we describe the different tools and strategies applied to identify metabolites detected in untargeted metabolomics studies that apply mass spectrometry (MS) platforms coupled to various separation techniques: liquid (LC) and gas chromatography (GC) or capillary electrophoresis (CE). Following a standard workflow in metabolite identification, the current limitations are highlighted, and the tools proposed to overcome those limitations are provided. These tools apply to both the identification of metabolites for which the structure can be obtained from database entries and to true unknowns.