The diagnosis of inherited metabolic disorders of amino acid (AA) metabolism is based on the qualitative and/or the quantitative analysis of AAs, mainly in blood and urine. For years, the most widespread technique in use was ion-exchange chromatography followed by post-column derivatization with ninhydrin, a method which is the basis of numerous automated AA analyzers with a throughput of about eight samples/day. The emergence of tandem mass spectrometry (MS/MS) coupled to liquid chromatography (LC) has made possible the measurement of many metabolites for the diagnosis of inborn errors of metabolism. The LC-MS/MS method described here allows the clinical diagnosis of AA disorders by analysis of underivatized AAs and derivative molecules in various biological samples prepared by methanol precipitation. AAs are separated by ion-pairing reversed-phase LC, using perfluorocarboxylic acid as an ion-pairing agent. Each AA is detected in MS/MS-positive ionization mode by its specific transition. The method allows the analysis of about 40 biological samples/day.
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