Geographical differentiation of onions (Allium cepa) cultivated in South Korea revealed by untargeted metabolomics and chemometric analysis

Onions (Allium cepa) are widely cultivated in South Korea, yet region-specific metabolomic profiles remain underexplored. To address this gap, we conducted untargeted metabolomic profiling of ethanol extracts from onions collected at 56 cultivation sites using UPLC-TIMS-QTOF MS. The analysis detected 2339 (positive mode) and 1350 (negative mode) molecular features, among which 242 compounds were annotated through spectral library matching. To extend coverage beyond the limited annotated fraction, accurate mass-based formula prediction identified 1992 unique molecular formulas, which were subsequently used for molecular classification and index analysis. Multivariate clustering revealed consistent separation into Central–Southwestern (CSW) and Southeastern (SE) chemotypes, with SE onions enriched in lipid-like metabolites and higher H/C ratios, while CSW onions contained more indoles and organoheterocyclic compounds with elevated AI_mod and DBE values. Network analysis further highlighted region-specific enrichment of antioxidant and anti-inflammatory metabolites. Despite these regional differences, phenolic glycosides such as quercetin and kaempferol derivatives were consistently abundant across all samples. Collectively, these findings expand knowledge of onion metabolome diversity in South Korea and demonstrate the potential of metabolomic fingerprinting for both nutraceutical evaluation and geographical origin authentication.