A CE-MS method for metabolic profiling of amino acids was developed and used in an integrated functional genomics project to study the response of Medicago truncatula liquid suspension cell cultures to stress. This project required the analysis of more than 500 root cell culture extracts. The CE-MS method profiled 20 biologically important amino acids. The CE-MS method required no sample derivatization prior to injection and used minimal sample preparation. The method is described in terms of CE and MS operational parameters, reproducibility of migration times and response ratios, sample preparation, sample throughput, and reliability. This method was then compared with a previously published report that used GC-MS metabolic profiling for the same tissues. The data reveal a high level of similarity between the CE-MS and GC-MS amino acid profiling methods, thus supporting these as complementary technologies for metabolomics. We conclude that CE-MS is a valid alternative to GC-MS for targeted profiling of metabolites, such as amino acids, and possesses some significant advantages over GC-MS.