Collision-induced dissociation experiments of seven annonaceous acetogenins were carried out under high and low collision energy conditions. Each compound was studied as protonated or deprotonated and lithium- or sodium- cationized molecules, using ElectroSpray Ionisation (ESI) with a hybrid linear trap/orbitrap mass spectrometer (LTQ-Orbitrap®). The same ion species were studied with a Matrix-Assisted Laser Desorption Ionisation (MALDI) tandem mass spectrometer in a high collision energy regime (1 or 2 keV). Although each of the techniques showed some limitations in the detection of functional groups, unambiguous structural identification of the acetogenins was obtained. MALDI ToF-ToF has the advantage over ESI-based methods to provide mass spectra rich in informative fragments which allows the confirmation of some functional groups position. By contrast, ESI-LTQ-Orbitrap® analysis has the advantage over MALDI that the mass spectra are relatively simple with only fragments close to the functional groups. However, this technique needs to carry out experiments both in negative and positive ionization modes. Copyright © 2010 John Wiley & Sons, Ltd.