Metabolomics and polysaccharide fingerprinting reveal compositional differences between cultivated Fritillaria bulbs and flower by-products.

Although Fritillariae Cirrhosae Bulbus (FCB) is used in food-related product contexts and local botanical-infusion practices, co-produced flowers remain underutilized and poorly characterized. To support QC-oriented screening and consistency evaluation, we compared bulbs and flowers from two dominant cultivated sources, F. unibracteata var. wabuensis (FW) and F. unibracteata (F), across 36 batches. UHPLC-Q-TOF-MS metabolomics annotated 76 compounds and discriminated between cultivated source and tissue, yielding candidate markers. Targeted UHPLC-QQQ-MS quantified five alkaloids; peiminine differed significantly across four sample groups, whereas sipeimine showed a higher distributional tendency in FW flowers, indicating that flower by-products should be evaluated as compositionally distinct materials rather than simple bulb substitutes. GPC-RI-MALS indicated higher mean PDI in flower crude polysaccharides, and a validated UHPLC-QQQ-MS method quantified 12 monosaccharides, of which eight were higher in flowers. This framework provides integrated chemical evidence for FW/F discrimination and a compositional basis for future QC-oriented and food-related evaluation of flower by-products.