Quantification of bioactive compounds in the juices of 21 American elderberry cultivars

American elderberry ( Sambucus nigra subsp. canadensis ) is recognized as a rich source of bioactive compounds with nutritional and therapeutic potential. However, comprehensive quantification of its metabolites remains analytically challenging due to the structural complexity of phenolics and matrix interferences in juice extracts. In this study, a targeted ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC–MS/MS) workflow was developed and validated to quantify 22 bioactive metabolites, including anthocyanins, flavonoids, and phenolic acids, in juices from 21 American elderberry cultivars. An optimized UHPLC– MS/MS system demonstrated higher sensitivity, selectivity, and throughput than conventional high-performance liquid chromatography-tandem mass spectrometry (HPLC–MS/MS), achieving limits of detection and quantification below 0.1 ng/mL for most analytes. Matrix effects were effectively mitigated through sample dilution, enabling accurate and reproducible quantification across complex juice matrices. Quantification of metabolites showed that accession 1199 exhibited high levels of cyanidin-based anthocyanins, suggesting its utility as a natural food color source. Overall, high-throughput UHPLC–MS/MS method provides a robust analytical framework for metabolomic profiling for cultivar selection and the development of elderberry-derived functional products.