We have investigated the dissociation of alpha- and beta- alanine following impact of slow multicharged ions, namely He(+), He(2+), O(5+) and Xe(20+) at 10 keV per charge unit. The collision products were analyzed using a reflectron-type time-of-flight mass spectrometer. In general, for a given projectile, ionization of both alanine-isomers gives rise to similar fragmentation patterns. However, significantly different peak intensities are observed for fragments with mass over charge ratios (m/q) of 30 and 44 amu. These differences can be explained in terms of isomer geometry and fragment stability. By analyzing the fragment kinetic energies, we found that protons as well as ionic oxygen fragments are sufficiently energetic (up to 200 eV for Xe(20+)) to induce further damage in a biological environment.