This study sought to determine the primary components (isoquinoline alkaloids, diterpenoids and steroids) in crude extracts of the Chinese herb Jin-Guo-Lan, prepared from the roots of Tinospora sagittata and T. capillipes, by liquid chromatography/electrospray ionization multistage mass spectrometry coupled with diode-array detection (LC-DAD/ESI-MSn). After separation on a reversed-phase C18 column using gradient elution, positive and negative ESI-MS experiments were performed. In positive ion mode, the three types of compounds showed very different characteristic ions: strong [M]+ or [M+H]+ ions were observed for isoquinoline alkaloids; [M+NH4]+ and/or [M+H[BOND]CO2]+ for diterpenoids; [M+H[BOND]nH2O]+ (n=1–3) for steroids. These adduct ions and/or fragments were used to deduce the mass and categories of known and unknown components in crude extracts, and their structures were further confirmed by ESI-MSn in positive ion mode. Moreover, UV absorption peaks obtained from DAD provided useful functional group information to aid the MSn-based identification. As a result, 11 compounds were unambiguously identified by comparing with standard compounds and 13 compounds were tentatively identified or deduced according to their MSn data. Two of these compounds (13-hydroxycolumbamine and 13-hydroxyjatrorrhizine) were found to be new compounds and another one (13-hydroxypalmatine) was detected for the first time as a natural product. In addition, a [M[BOND]·CH3[BOND]H2O].+ ion in MS2 of [M]+ after in-source collision-induced dissociation was used to differentiate positional isomers of protoberberine alkaloids, columbamine and jatrorrhizine. Although the roots of T. sagittata and T. capillipes contain almost identical compounds, the content of the compounds in them is dramatically different, suggesting the necessity for further comparison of the bioactivities of the two species. Copyright © 2006 John Wiley & Sons, Ltd.