Organ‐Specific Profiling of Secondary Metabolites in <i>Gentiana scabra</i> Bunge via Molecular Networking‐based Liquid Chromatography/Mass Spectrometry

Gentiana scabra Bunge (G. scabra), a perennial herb of Gentianaceae, has long been valued in East Asian medicine for its dried roots used to treat various ailments. However, root-based utilization alone cannot meet the growing clinical demand. This study systematically investigated the diversity and organ-specific distribution of secondary metabolites in G. scabra to support the sustainable use of the non-medicinal parts. Six bioactive compounds were quantified in roots and rhizomes (R), stems (S), leaves (L), and flowers (F) by ultra-performance liquid chromatography (UPLC), while UPLC coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry enabled qualitative profiling. Significant organ-specific variations were observed: mangiferin was abundant in L, amarogentin was not detected in all parts of the organs, and other compounds were concentrated in R. In total, 33 metabolites were identified. Iridoids were primarily distributed in R, though a small proportion was also detected in S, while flavonoids, triterpenoids, and xanthones were mainly found in the aerial parts (S, L, and F, respectively). These findings reveal pronounced metabolic differentiation among the organs of G. scabra and provide a scientific basis for the rational exploitation of non-medicinal parts, supporting the broader application of whole-plant utilization in traditional medicine.