Metabolites are important components of all living organisms. It is well known that disturbances in metabolic patterns cause metabolic diseases, which may have dramatic consequences for an organism’s survival. Besides screening of metabolic diseases, focused or general profiling of metabolites (metabolomics) or lipids is necessary in order to understand basic biological processes - processes as nitrogen uptake in plants, interactions between micro- and host organisms, and developmental biology of animals or plants.

A metabolomic analysis combines a number of steps from tissue extraction through the detection and measurement of metabolites to analysis, interpretation, and visualization of the results. All steps may either be untargeted or targeted. The choice depends on the analytical/biological questions posed and various other factors including the classes, stability, and other properties of the metabolites of interest. It also depends on whether or not the samples need to be purified, detection limits, and required analytical accuracy.

Metabolomics methodology can generally be divided into the following three analytical types:

1. Untargeted metabolite profiling
Up to 3000 putative metabolites can be detected using a combination of selected untargeted analytical techniques. Untargeted approaches can cover many classes of metabolites and thus provide broad information about the metabolic state of the analysed samples. However, only a fraction of the detected compounds will be automatically identified or annotated.
2. Targeted metabolite profiling
This refers to the analysis of specific compound classes, e.g. amino acids and amines, fatty acids, eicosanoids, and hormones. Using LC-QqQMSMS and GC-QqQMSMS in multiple-reaction-monitoring (MRM) mode up to 100 selected compounds can be detected and measured in a single analysis. The advantages of targeted approaches are their selectivity and accuracy.
3. Functional group-specific metabolite profiling
This refers to advanced chemical derivatisation and detection strategies to analyse compound-specific structures of both known and unknown compounds. Such strategies can profile, for example, primary and secondary amines, aldehydes, and carboxylic acids.