A lab prototype CE-nanospray-MS platform with a high sensitivity porous sprayer was successfully applied in differential identification of Rhizoma coptidis in this paper. To obtain a stable and reliable nanospray, detailed optimizations about emitter geometry, buffer composition, emitter position, and spray voltage, as well as emitter cleanliness were discussed. Results showed that the reproducibility and sensitivity for separations of alkaloid standards were satisfactory using CE-nanospray-MS, which were also compared to ultra-HPLC (UHPLC)-MS. Their signal responds were at the same order of magnitude (intensities: 0.8 - 1.5 x 10(8) vs. 3.8 - 6.2 x 10(8)), even though a 2 nL injection for CE was 2500-fold lower than UHPLC (5 mu L injection). The absolute LOD results of CE-MS showed a remarkable superiority (18-24 fg), equal to 1000-fold lower than that of UHPLC-MS. Principal component analysis (PCA) of adulterated R. coptidis showed that this protocol had the ability to profile and qualify complex herb medicines, which also created a great potential for evaluation and qualification of rare and valuable Chinese medicines in future.