This study presents the outstanding chromatographic selectivity of a porous graphitic carbon support for the separation of four isomeric tropane alkaloids from the stem-bark of Schizanthus grahamii (Solanaceae). Capillary liquid chromatography coupled to mass spectrometry was studied after the appropriate selection of mobile phase composition, temperature, nature and concentration of the acidic modifier. Fragmentation behaviour by in-source collision-induced dissociation (CID) on a single quadrupole mass spectrometer, or MSn with an ion-trap, was investigated for structural identification. The ability to differentiate the isomers by in-source CID was demonstrated and a fragmentation pathway, based on MSn sequences together with accurate mass experiments, was proposed.