Metabolites are an important component 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, such 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 be either untargeted or more targeted, the choice depending on the analytical/biological questions posed and various other factors, including the classes, stability and other properties of metabolites of interest, whether or not the samples need to be purified, detection limits and required analytical accuracy.

Metabolomics methodology can be generally 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. 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.
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.

There are always drawbacks to using a more general and untargeted method rather than a more specific, targeted approach. The advantages of targeted approaches are their selectivity and greater accuracy. However, untargeted approaches cover many more classes of metabolites and thus provide broader information about the metabolic state of analysed samples. Another aspect to take into account when selecting analytical procedures is the efficiency of the analytical workflow for analysing large series of samples. General methods include fewer analytical steps, and thus are more efficient in terms of sample preparation.