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Pulsed high pressure source mass spectrometry has been used to investigate gas phase proton transfer reactions and the reactivity of gas phase protonated molecules. The mechanism of protonation of benzene has been studied using both pulsed high pressure source mass spectrometry and collision induced decomposition tandem mass spectrometry experiments. These experiments showed that at low temperature and high pressure a second new protonated isomer of benzene may exist, one in which the attaching proton is isolated from the other ring protons. An energy for this isomer was calculable. At high temperature the only isomer in existence was the well known σ, edge protonated species. The mechanisms of protonation at different sites on chlorobenzene has been studied in detail by tandem mass spectrometry/collision induced decomposition experiments. These experiments showed that under non-thermodynamic conditions the neutral molecule could be protonated upon the unfavoured Cl atom. The proton affinity of the substituent Cl was bracketed. At high pressure a clear temperature dependence was observed due to the equilibrium between ortho and para protonated isomers. From these experiments the energy difference between these two sites was calculable. The applicable of collision induced decomposition/tandem mass spectrometry experiments for the study of thermal isomerisation processes has been studied. Proton transfer reactions were surveyed to find suitable systems to study. Suitable systems were found to be protonation of chlorobenzene, fluorotoluenes and cyclohexane. It has been shown that studying a suitable system with this technique can demonstrate new isomeric forms of these protonated molecules and corresponding energies for the species.