The purpose of this study is to verify the inhibitory effect of a chemically standardized extract from Scutellariae radix in liver cancer cell lines (HepG2). The botanical extract was prepared using pressurized liquid extraction (PLE). A method using proteolytic digest with single dimensional and two-dimensional liquid chromatography with tandem mass spectrometry was used to characterize differential protein expression in mammalian cells in response to the botanical extract. The whole cell lysates were digested with trypsin, and the peptides were separated by one-dimensional (reversed phase) or by two-dimensional (cation exchange and reversed phase) solid-phase extraction (SPE) cleanup and separated by liquid chromatography with UV detection and mass spectrometry. In the presence of the botanical extracts, drug-induced apoptosis was not observed, and a number of proteins that played an important role in the metabolic pathways in HepG2 cell line had been affected. The data, as presented, suggest that the inhibitory effects of the standardized extracts from Scutellariae radix resulted from expression of heat shock protein and other proteins related to energy metabolism. The proposed platform had the potential to provide significant information about the particular proteome such as human hepatoma HepG2. At the molecular level, it was possible to study the proteins and how their levels and modifications change in response to the effects of the botanical extract.