The mass fragmentation of potato glycoalkaloids, α-solanine and α-chaconine, and the aglycons, demissidine and solasodine were studied using the Orbitrap Fourier transform (FT) mass spectrometer. Using the linear ion trap (LIT) mass spectrometry, multistage collisional-induced dissociation (CID) experiments (MSn) on the [M + H]+ precursor ions were performed to aid the elucidation of the mass fragmentation pathways. In addition, higher energy collisional-induced dissociation (HCD) mass spectra were generated for these toxins at a high resolution setting [100 000 FWHM (full width at half maximum)] using the Orbitrap. This hybrid mass spectrometry instrumentation was exploited to produce MS3 spectra by selecting MS2 product ions, generated using LIT MS, and fragmentation using HCD. The accurate mass data in the MS3 spectra aided the confirmation of proposed product ion formulae. The precursor and product ions from glycoalkaloids lost up to four sugars from different regions during MSn experiments. Mass fragmentation of the six-ring aglycons were similar, generating major product ions that resulted from cleavages at the B-rings and E-rings. Copyright © 2010 John Wiley & Sons, Ltd.