Panax notoginseng inflorescences
(PNI) and leaves (PNL) are commonly used as folk medicine and food
supplements. In this study, an online two-dimensional hydrophilic
interaction × reversed-phase liquid chromatography coupled to
linear trap quadropole mass spectrometry method was developed to determine
24 ginsenosides, including two novel compounds, in PNI and PNL extracted
by water and methanol. Our data demonstrated that ginsenosides Rd,
Rc, Rb2, Rb3, Rb1, Ra2, Ra1, and Ra3 in both PNI and PNL extracted
by water rather than methanol can be transformed to ginsenoside F2,
notoginsenoside Fe, ginsenoside Rd2, notoginsenoside Fd, gypenoside
XVII, PN02, PN01, and PN03, respectively, by selectively cleaving
the β-(1→2)-glucosidic linkage at the C-3 position. Ginsenoside
transformation was further verified to be mediated by the proteins
isolated from samples. Additionally, the two newly discovered transformed
products, namely, PN02 and PN03, were prepared and identified as novel
compounds by nuclear magnetic resonance. Our findings provide new
insight into the importance of extraction solvents on the component
profile of natural products.