Besides of the assignment of changes of peaks to changes of known metabolites by mapping metabolite spectra or by manual assignment with the help of databases, often peaks of unknown metabolites are significantly changed. The analytical setups used for metabolic profiling allow an efficient structure elucidation. Thereby analytical techniques like mass spectrometry or nuclear magnetic resonance spectroscopy and separation and concentration techniques like chromatography or solid phase extraction can be used (in most cases combinations of these techniques). If the concentration of the metabolite is high enough and the corresponding signals of this metabolite are not completely overlaid by other signals, a direct structure elucidation of this metabolite in the original biofluid is possible (for example by use of 2-D NMR experiments).
In this section two examples are shown for the structure elucidation of two unknown metabolites. The first example is the structure elucidation of a metabolite in the competitive study with the help of dedicated setups for separation and enrichement. The second example deals with an unknown metabolites in a ranking study, whereby the the structure elucidation is performed without special analytical separation or enrichement techniques.