In principle, any technologies used for metabolomics can be used for exometabolomics. However, liquid chromatography–mass spectrometry (LC–MS) has been the most widely used. As with typical metabolomic measurements, metabolites are identified based on accurate mass, retention time, and their MS/MS fragmentation patterns, in comparison to authentic standards. Chromatographies typically used are hydrophilic interaction liquid chromatography for the measurement of polar metabolites, or reversed-phase (C18) chromatography for the measurement of non-polar compounds, lipids, and secondary metabolites. Gas chromatography–mass spectrometry can also be used to measure sugars and other carbohydrates, and to obtain complete metabolic profiles.
Because LC–MS does not give spatial data on metabolite localization, it can be complemented with mass spectrometry imaging (MSI).