Deciphering of the plant metabolome is one of the most difficult analytical tasks in functional genomic research. Studies directed at the gene or protein expression are well established, sequencing analyses of these kinds of biopolymers on genome or proteome level are possible. This is not the case for metabolites, where identification in single sample of many chemical entities of different elemental composition and structures and various physicochemical properties is necessary. Different instrumental methods are applied for identification of metabolites but none of them allows obtaining unambiguous structural information about more than 500 compounds in single mixture (metabolite profiling). This is a much smaller number of metabolites than is predicted for single plant metabolome. However, instrumental approaches were proposed (metabolite fingerprinting) in which biochemical phenotype of an organism may be estimated, but identification of individual compounds is not possible.
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