This journal is © The Royal Society of Chemistry 2000 Electronic Supplementary Information Chinese traditional medicine has been used in China for thousands of years for their low toxicity and less side effect. Nowadays, the constituent study of plant medicine becomes more and more important for the bioactive ingredients in them may provide model compounds for synthesizing some pharmaceuticals by chemical method. Capillary electrophoresis (CE) has become a powerful technique for determining some constituents in plant drugs. Chinese traditional medicine, Scutellariae Radix, is the root of Scutellaria baicalensis Georgi and can be use to clean away heat, purge fire and detoxify toxicosis. Astragali Radix is the root of Astragalus membranaceus (Fisch.) Bge. Var. mongholicus (Bge.) Hsiao or Astragalus membranaceus (Fisch.) Bge. It is mainly used to promote vital energy. However, the two crude drugs are usually confused for their shape, color, and the Chinese names are similar. For example, the Chinese names of Scutellariae Radix and Astragali Radix are “Huang-Qin” and “Huang-Qi”, respectively. It would bring about side effects if they were misused for their different therapeutical functions, so it is necessary to establish some simple and accurate methods for their differentiation. For many bioactive constituents such as flavonoids in plant drugs are electroactive, capillary electrophoresis with electrochemical detection (CE-ED) should become an alternative technique in the study of Chinese traditional medicines. A novel method for the differentiation of Scutellariae Radix from Astragali Radix based on CE-ED has been established in this paper, providing a reliable technique for pharmaceutical analysts. For Scutellariae Radix contains baicalin and baicalein that can not be found in Astragali Radix, this differentiation method for both the crude drugs was carried out by determining the baicalin and baicalein in them by CE-ED. The electrochemical detection used in this paper provided a high degree of selectivity and sensitivity to electroactive species. To our knowledge, no report on the application of CE on the differentiation of Chinese traditional medicines or plants has appeared. In order to improve the resolution and solubility of analytes, alkaline borate buffer This journal is © The Royal Society of Chemistry 2000 was employed in this study for baicalein and bacalin and can form negative-charged complex with boric acid in alkaline solution. 1 The adsorption of analytes on the surface of working electrode and inner surface of capillary can be inhibited by using alkaline borate buffer so that the reproducibility of peak current and migration time is improved. The effects of the acidity and concentration of running buffer, separation voltage and injection time on CE are illustrated as in Fig.1. Fig. 1 Effect of the acidity (A) and the concentration (B) of the running buffer and the separation voltage (C) on the migration time of baicalein (a) and baicalin (b), effect of injection time (D) on analyte peak current The effect of the running buffer pH on the migration time of the investigated analytes is shown in Fig. 1A. The running buffers were 100 mmol l1 BBs at five different pH values (8.0, 8.5, 9.0, 9.4 and 10.0). As shown in Fig. 1A, when the running buffer pH increases, the migration time increases with the resolution improved due to the dissociation of the hydroxyl group for the analytes. Meanwhile, the peak current is low and the peak shape becomes poor at pH value above 9.5. At pH 9.0, the analytes This journal is © The Royal Society of Chemistry 2000 can be well separated within a relatively short time. Fig. 1B indicates that the migration time and the resolution increases with increasing buffer concentration. However, higher buffer concentrations (100 mmol l1) also have a negative effect on the detection limits because the peak currents of both investigated analytes decrease and the effect of Joule heat is more pronounced. So 100 mmol l1 BB (pH 9.0) is chosen as the running buffer in this work in considering the peak current, resolution, analytical time and the buffer capacity. The influence of separation voltage on the migration time of the analytes is shown in Fig. 1C. Increasing the voltage gives shorter migration time for both compounds, but also increases the base line noise, resulting in poorer detection limits. It is found that higher separation voltages are not beneficial to the resolution. However, too lower separation voltage will increase the analysis time considerably, which in turn causes peak broadening. Based on experiments, 12 kV was chosen as the optimum voltage to accomplish a good compromise. The effect of injection time on CE separation was investigated by changing the sampling time (2, 4, 6, 8, 10 and 12 s at a voltage of 12 kV, as shown in Fig. 1D). The peak current increases with increasing sampling time, and the breadth of the peaks increases simultaneously. In this experiment, 6 s (at 12 kV) is selected as the optimum injection time. Through the above experiments, the optimum conditions for determining baicalein and baicalin are acquired. Reference 1 Ph. Morin, F. Villard, M. Dreux, J. Chromatogr., 1993, 628, 161