Plasma free amino acids in Parkinson’s disease: An exploratory case–control study

INTRODUCTION: Objectives: Parkinson's disease (PD) is associated with systemic metabolic alterations; however, reproducibility and methodological standardization remain ongoing challenges in metabolomics research. This exploratory case–control study aimed to evaluate whether targeted plasma free amino acid profiling reveals statistically robust differences be-tween PD patients and healthy controls.
METHODS: Methods: Forty-three patients with PD and 43 age- and sex-matched healthy controls were included. Plasma free ami-no acids were quantified using a targeted triple quadrupole LC–MS/MS platform with Appendix 1 isotope-labeled inter-nal standards. Between-group comparisons were performed with appropriate statistical tests. False discovery rate (FDR) correction and effect size (Cohen’s d) calculations were applied. Compound-based KEGG pathway enrichment analysis was conducted using FDR-significant metabolites. ROC analyses were performed for signal strength assessment only.
RESULTS: Results: After FDR correction, alanine, arginine, aspartic acid, proline, taurine, threonine, and phenylalanine/tyro-sine-related ratios remained significant, with moderate-to-large effect sizes. Compound-based KEGG enrichment demonstrated significant clustering within interconnected amino acid metabolism pathways, including arginine and proline metabolism, taurine and hypotaurine metabolism, glycine, serine and threonine metabolism, and alanine, aspartate and glutamate metabolism (pathway-level FDR <0.05). Exploratory ROC analyses showed moderate signal strength for proline (AUC=0.794), taurine (AUC=0.792), and threonine (AUC=0.780).

DISCUSSION AND CONCLUSION: Conclusion: Targeted plasma amino acid profiling revealed coordinated systemic alterations in amino acid metabolism in PD within a statistically disciplined analytical framework. These findings reflect peripheral metabolic variation and should be interpreted as exploratory and hypothesis-generating. The study primarily contributes an analytically vali-dated and FDR-corrected dataset to the discussion on methodological rigor in PD metabolomics, rather than evidence of diagnostic or mechanistic inference. Validation in longitudinal, clinically well-characterized cohorts is required.

Keywords: Alanine, amino acids, arginine, aspartic acid, free amino acids, LC–MS/MS, phenylalanine, plasma, proline, targeted metabolomics, taurine, threonine