Non-targeted metabolomic approach for authenticity differentiation of shallots and onions using UHPLC-HRMS/MS and chemometrics

Shallots ( Allium cepa var. aggregatum) and onions ( Allium cepa var. cepa) are subspecies of the Allium cepa that are marketed at different prices, the first being more valued for its more subtle flavor. However, authentication based on their morphological characteristics is often unreliable. The presented project aimed to design an analytical method applicable for distinguishing these two crops under routine inspection practice. Three sets of authentic shallots and onions, representing various cultivars, harvests (2022 and 2023), and storage conditions (short and long), were analysed by non-targeted metabolomic screening to identify authenticity markers and build classification models. Sample preparation and extraction were optimized for reverse phase ultra-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS). Advanced chemometrics were applied on the obtained metabolomic data, using Orthogonal Partial Least Squares discriminant analysis (OPLS-DA) to discriminate the two groups, with the models achieving excellent predictive values. The Variance in Projection (VIP) score was used to select statistically significant markers, which were tentatively identified and assessed for their stability during storage and variation across different harvests. The proposed identifications included derivatives of sugars and amino acids, oligopeptides, flavonoids, steroids, and a derivative of the organosulfur compound alliin, which is typical of the Allium species. The final classification model, built using the selected markers, achieved a 100% predictive performance upon external validation. Sugars and amino acids were determined to provide additional discrimination between shallots and onions, with sugars yielding a statistically significant screening value. Publication History Article published online: 05 March 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany