Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule. Unlike aliphatic amino acids, protonated tryptophan dissociates via NH3 elimination rather than the usual iminium ion formation by combined removal of H2O and CO molecules. Also, a major fragmentation pathway in the present work involves Cα-Cβ bond fission. Results of the chemical dynamics simulations reported here are in overall agreement with experiments, and detailed atomic level mechanisms are presented. © 2017 American Chemical Society.