Integrated Metabolomics Reveals Chemical Differentiation among Andean Rubus Species and R. glaucus Genotypes

The metabolic diversity of Rubus fruits is relevant for authentication, nutritional assessment, and breeding, but biochemical information about Andean germplasm remains limited. This study aimed to characterize phytochemical variation at interspecific and intraspecific levels by integrating untargeted LC–QTOF-MS, targeted LC–QqQ-MS phenolic profiling, antioxidant assays, and molecular networking. Three Rubus materials and five Rubus glaucus genotypes were evaluated. Chemometric analysis revealed metabolic separation among the Rubus materials, with 63 differentially annotated metabolites in the untargeted analysis and 25 compounds significantly different in targeted profiling. Among R. glaucus genotypes, 79 differentially annotated metabolites and 12 targeted compounds showed differences. Discriminatory metabolites included phenylpropanoid-derived phenolics, organic acids, and glycerophospholipids. R. glaucus materials showed higher antioxidant capacity in several assays, with differences in phenolic composition. Correlation analysis revealed associations among phenolic, primary carbon, and lipid-related metabolism. The integrated approach characterized metabolic variation and identified metabolites associated with their chemical differentiation.