Background: Nowadays, the most conventional method to quantify physiological amino acids consists in ion exchange chromatography (IEC) followed by post-column ninhydrin derivatization and UV detection at two wavelengths. Unfortunately, the technique presents some drawbacks such as long run time, large sample volume, and specific costs associated to the maintenance of a dedicated instrument. Therefore, we aimed to switch towards a mass spectrometry approach.Methods: We have tested the aTRAQ kit for Amino Acid Analysis of Physiological Fluids (AB Sciex), affording the selective quantification of about 40 amino acids, and present here the results of our assessments.Results: Outlined accuracy profiles for each amino acid demonstrated very reliable data. A good linearity was observed from 1 to 1,000 mmol/L. Results comparison with IEC showed a right concordance. Reference intervals established were very similar to those obtained by IEC and patients suffering from inborn error of metabolism have been readily identified.