In this contribution the capabilities of laser ionization via resonant enhanced multi photon
ionization (ReMPI, MUPI) of molecules and molecular clusters are discussed with respect to the fragmentation and isomerisation processes observed in protonated di‐ and tripeptides. The measurements are supported by quantum mechanical calculations. It is shown that the formation of protonated peptides occur through the formation of biomolecular clusters from vanillic acid and different peptides. The use of the ReMPI technique allows detailed insight in the different elementary processes.