The mechanisms for most aspects of peptide fragment ion formation are well accepted. A high proportion of the fragment ion current corresponds to proton-directed cleavage at the amide bond. producing bn and yn ions. Other fragment ions can be produced from sequential cleavages of large fragment ions or by side-chain cleavages. However, understanding of the propensities for individual cleavages and of the stabilities of fragment ions is imperfect. Thus, the predictability of peptide product ion spectra remains poor. Investigating the fundamental aspects of peptide fragmentation may succeed in improving bioinformatics programs which interpret tandem mass spectra. Arginine residues have a significant effect on the collisionally activated decomposition (CAD) of peptide ions. The formation of y1 fragment ions during CAD of doubly protonated C-terminal arginine containing peptide ions is reliable. The consistent fragmentation is perhaps unexpected considering the requirement for an ionizing proton to promote peptide ion backbone cleavage proximal to a localised charge site. We propose the presence of an intraionic interaction between the arginine side-chain and the C-terminus acid moiety, providing cleavage of the peptide backbone adjacent to the arginine residue. Low energy CAD experiments of doubly protonated peptides containing C-terminal arginine residues have been undertaken to investigate the noted difference in dissociation. Evidence for the direction of peptide ion fragmentation by R/COOH intraionic interactions is provided by esterification of the peptide carboxylic acid and derivatization of the arginine residue to reduce the basicity of the guanidino side-chain involved. Energy resolved mass spectrometry experiments and molecular modelling studies support the conclusions of this work. Findings of the study are consistent with previous research detailing the importance of gas phase conformations in determining fragmentation pathways.