Fragmentation of protonated molecular ions produced from catharanthine, tabersonine, ajmalicine and serpentine in a high‐performance liquid chromatography (HPLC) thermospray ion source was studied. Collision‐induced dissociation (CID) of the compounds was achieved by merely increasing the repeller potential; i.e. no discharge current was applied and filament was not on. Proportion of fragments to the protonated molecular ions increased with the potential at the 180–350 V range studied, but overall yield of detected ions decreased at the higher voltages in all cases. Comparison of fragments produced in the thermospray CID with those derived from the protonated molecular ions by colliding with argon in a triple‐stage quadrupole instrument showed that the fragmentation is very similar in both cases. An analytical application for identifying the alkaloids from plant cell culture material by HPLC/mass spectrometry using the thermospray CID is described.