Integrated Untargeted Metabolomics and Antioxidant Profiling Reveal Tissue-Specific Chemical Differentiation Between Rhizomes and Leaves of Houttuynia cordata

Houttuynia cordata is used as food and medicine, yet integrated comparisons of the non-volatile chemical profiles and in vitro antioxidant capacities of its rhizomes and leaves remain limited. Ten rhizome (RZ) and ten leaf (LF) samples from 10 batches were compared using ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UHPLC–Q-TOF–MS)-based untargeted metabolomics, Functional Analysis of full peak tables, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, total phenolic and flavonoid content assays, and four antioxidant assays. Clear separation occurred in both modes. In the original exploratory Welch-based screening, variable importance in projection (VIP) > 1, absolute log2 fold change > 1, and Benjamini–Hochberg-adjusted q < 0.05 yielded 436 and 232 differential features with putative annotations in positive and negative modes, respectively, with LF-enriched features predominating. Sixty-four of 65 flavonoid-related features were LF-enriched. Functional and KEGG analyses suggested that differences may involve amino acid metabolism, flavone and flavonol biosynthesis, and lipid-related processes. LF had higher total phenolic and flavonoid contents and greater radical-scavenging and ferric-reducing capacities than RZ (all q < 0.001). Prioritization based on LF enrichment, chemical class, and annotation quality yielded 20 phenolic and flavonoid features assigned to nine candidate annotation groups. These findings support differentiated quality evaluation and utilization of RZ and LF.