Comparative metabolomic profiling of tissue-specific Korean red pepper (Capsicum annuum L.) powders from Subicho and Bulcolor cultivars

Hot air-dried red peppers are consumed as spices worldwide for their color, flavor, and nutritional value. However, comprehensive metabolomic studies are limited. This study addresses this research gap by investigating metabolite profiles of two Korean red pepper cultivars (Subicho, landrace; and Bulcolor, virus-resistant cultivar) across three different tissues and two harvest time points. Comprehensive profiling using GC–QqQ MS, HPLC–DAD, and UHPLC–MS platforms identified 160 primary metabolites and multiple secondary metabolite classes including capsaicinoids, carotenoids, and polyphenols. The placenta of Subicho contained markedly higher levels of essential amino acids, whereas Bulcolor exhibited elevated sterols, tocopherols, and essential fatty acids associated with virus resistance. Capsaicinoid content was highest in the placenta tissues, especially in the Subicho at early harvest (16,879.5 ± 398.3 μg/g), whereas the pericarp tissues were the primary sites for carotenoid accumulation. Principal component analysis resolved clear separation (PC1: 58.9%, PC2: 30.8%) by cultivar, tissue, and harvest timing. The high-resolution cultivar-, tissue-, and harvest-specific metabolomic database established in this study provides a critical scientific reference for hot air-dried red peppers. This resource offers a foundation for optimized cultivar selection, targeted utilization of specific tissues, and rigorous quality assessment in breeding programs, industrial production, and evidence-based consumer decision making.