MS is the primary detection method for plant metabolomic analysis. GC-MS is applicable to detect volatile metabolites (e.g., alcohols, monoterpenes, esters), and also non-volatile polar metabolites (primary metabolites, e.g., amino acids, sugars, lipids, organic acids). Metabolites can be identified by comparing fragment peak patterns and retention indices with those of standard compounds in databases. LC-MS is a versatile technology to analyze non-volatile secondary metabolites. However, in contrast to GC-MS, few mass spectral databases

Fig. 11. Variation of tomato metabolites for molecular weights and polarities

are currently available for LC-MS. The lack of a searchable LC-MS database is a major obstacle in identifying metabolites by LC-MS.

Capillary electrophoresis MS (CE-MS) has been employed to analyze water-soluble metabolites (e.g., organic acids, nucleotides, amino acids, sugars, sugar phosphates). Although the application of CE-MS to the comprehensive profiling of plant metabolites has been limited to rice (Sato et al. 2004; Takahashi et al. 2006), CE-MS will likely be adopted more broadly due to its sensitivity, ease of sample preparation, and applicability to polar metabolites.

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