Indole alkaloids from Nauclea officinalis (Pierra ex Pitard) Merr are prospective agents for inflammation- related diseases. To speed up the process of discovering such bioactive compounds from natural origins, a mass spectrometry-based method was developed to screen N. officinalis for the presence of indole alkaloids. First, representative alkaloids were purified from herbs and analyzed using an ion trap (IT) mass spectrometer. Multi-stage mass spectra (MS(n))were utilized to establish the characteristic fragmentation pathways of indole alkaloids. It was shown that their fragmentation behaviors were correlated with the degree of unsaturation on ring-D of such alkaloids: if there is a double bond between C-3 and C-14, no fragments of ring cleavage are observed; otherwise, a fragment ion after reverse Diels-Alder cleavage of ring-D is observed as the base peak in their tandem mass spectrometry data. Then, herbal extracts of N. officinalis were analyzed using a combination of high- performance liquid chromatography (HPLC)/IT and HPLC/time-of-flight (ToF) systems. The structures of suspected alkaloids were deduced based on the accurate mass information from ToF and MS(n) from IT. Finally, a total of 10 indole and one indolizidine alkaloids were identified or tentatively characterized in extracts of N. officinalis. This work has demonstrated that the combination of MS(n) and ToF-MS can be used for rapid identification of monoterpenoid indole alkaloids in N. officinalis.