The structure and the dynamics of the isomerization of an ions, which are observed upon low-energy collision induced dissociation of protonated peptides in tandem mass spectrometry (MS/MS), are investigated using a combination of gas phase infrared spectroscopy and theory. IR spectra in the fingerprint region are discussed, but a particular emphasis is given to the NH stretching region which turns out to be highly structurally diagnostic. Overall, theory and infrared spectroscopy provide compelling evidence that an ions undergo cyclisation and/or rearrangement reactions. In the cases of the a2 and a3 ions of oligoglycine, the analysis of the NH stretching region is fully consistent with our previous conclusions based on the IR fingerprint spectra. In the case of the a4 ions of oligoglycine, a band observed near 3550 cm−1 provides a clear-cut signature of the permuted imine–amide structure, thus allowing for a better structural assignment. The dynamics of the rearrangement chemistry of the imine–amide structure is discussed in details, and a critical discussion on the influence of the experimental CID conditions is proposed in the case of the YG a2 ion.