Fragmentation of metastable anions of all deoxynucleosides and nucleosides constituting DNA and RNA has been studied experimentally and by computer simulations. The ions were formed through deprotonation in matrix assisted laser desorption/ionisation (MALDI). Clear difference in fragmentation patterns was obtained for nucleosides containing purinevs.pyrimidine bases. To elucidate the role of various potential deprotonation sites, systematic blocking by chemical modification was performed and this gave unambiguous correlation between deprotonation sites and fragments observed. Classical dynamics simulations of the fragmentation process, using density functional theory to describe the electronic degrees of freedom, were performed for the various deprotonation sites. These were found to reproduce the observed fragmentation patterns remarkably well.