The most effective methods of analysis of organic compounds in biological fluids are coupled chromatographic techniques. Capillary gas chromatography/mass spectrometry (GC-MS) allows the most efficient separation, identification and quantification of volatile metabolites in biological fluids. Liquid chromatography-mass spectrometry (LC-MS) is especially suitable for the analysis of non-volatile and/or thermally unstable compounds. A major drawback of liquid chromatography-mass spectrometry is that no standard spectral libraries such as NIST and Wiley for GC-MS are available to facilitate the identification of unknown compounds. Moreover, the identification of potential new compounds, especially new biomarkers in LC-MS, is much more challenging than in GC-MS. Capillary electrophoresis coupled with mass spectrometry (CE-MS) has been widely used to characterize metabolomes. Capillary electrophoresis is a powerful technique for the separation of charged metabolites, offering high analyte resolution. The advantages of CE-MS are applicability for hydrophilic metabolites, robust separation efficiency and short duration of analysis.
This review provides an overview of current chromatographic methods – gas chromatography – mass spectrometry, liquid chromatography – mass spectrometry and capillary electrophoresis-mass spectrometry – and their applications in current medical research. The focus is on the description of metabonomics research, strategies for biomarkers identification, medical diagnoses of diseases and research of drugs.

Keywords: Metabolic Diseases - metabolism, Mass Spectrometry - methods, Environmental Monitoring, Biomedical Research - methods, Metabolomics, Neoplasms - therapy