The present thesis concerns the development of MS-based approaches for the analysis of amino acids in biological matrices. All amino acids have in common the presence of ionisable functions but the physico-chemical diversity introduced by the side chains may make it difficult the use of a single chromatographic approach. Capillary electrophoresis is the method of choice for the analysis of charged compounds. The latter may be hyphenated to triple quadrupole instrumentation for the detection of compound subset in complex biological matrices. However, CE suffers from several drawbacks that have impeded its widespread for bioanalysis. In the first part of this thesis, we introduced innovative approaches to fix these issues. In the second part of this thesis, we were interested in the growing need of stereoselective analysis for the comprehensive knowledge of amino acid relevance in stereoselective biological functions. Different calibration strategies were developed and validated for the simultaneous quantification of exo- and endogenous compound in plasma. Eventually, the potential of CE-MS for direct analysis of amino acid enantiomer is highlighted.