Background: Tissue amino acids are important markers to characterize (patho)physiology.
As neurotransmitters or their precursors, they have special significance in brain. However, mass spectrometry
(MS)-based quantifications of brain amino acids are rare and inconsistent.
Methods: To reveal efficient procedures optimal for brain research purposes, free amino acids in the
same extracts of rat cerebellum were quantified by published assays employing hybrid triple quadrupole-linear ion trap
(QTRAP) MS or amino acid analyzer with ninhydrin derivatization.
Results: Levels of four amino acids out of 14 quantified by the two methods were established to be perturbed in the
QTRAP MS assay, with the ninhydrin-based quantification agreeing well with the published values obtained by non-MS
approaches. The overestimation of Glu and Lys and underestimation of Gly and Tyr in brain extracts by QTRAP MS suggest
interference of the co-eluting compounds and ion suppression effects, correspondingly. The MS-inherent artifacts
presumably contribute to inconsistency of published MS data on the brain amino acid content, as our analysis of different
studies indicated that the variability of the MS data greatly exceeds the biological variability.
Conclusion: Evaluation of potential artifacts of the MS-based quantification of brain amino acids using the ninhydrin detection
as a reference method, provides a solution for reliable quantification of the artifact-resistant amino acids, pointing
to relatively good performance of the time- and cost-efficient QTRAP MS procedure employed.