Untargeted Metabolomics-Based Analysis of Metabolic Differences in Different Parts of Bidens bipinnata L

Bidens bipinnata L. is a medicinal plant widely used in traditional Chinese medicine, yet the metabolic differences among its aerial parts remain largely unexplored. In this study, untargeted metabolomics based on ultra‑performance liquid chromatography‑-mass spectrometry (UPLC‑-MS) was employed to comprehensively compare the metabolite profiles of stems, leaves, and fruits, with six biological replicates per tissue. A total of 1028 metabolites were putatively annotated. Multivariate analysis, including principal component analysis (PCA) and orthogonal partial least‑squares discriminant analysis (OPLS‑DA), revealed distinct tissue-specific metabolic profiles. Flavonoids such as luteolin, kaempferol-3-O-rutinoside, and quercetin were significantly enriched in leaves. Differential metabolites were primarily enriched in flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and aromatic amino acid metabolism pathways, with distinct enrichment patterns across the three pairwise comparisons. These findings elucidate the tissue-specific accumulation patterns of secondary metabolites in B. bipinnata, providing a theoretical basis for the targeted utilization of different plant parts and supporting its potential development as a functional feed additive in animal husbandry.