On the dynamics of fragment isomerization in collision-induced dissociation of peptides.

The structures of peptide collision-induced dissociation (CID) product ions are investigated using ion mobility/mass spectrometry techniques combined with theoretical methods. The cross-section results are consistent with a mixture of linear and cyclic structures for both b4 and a4 fragment ions. Direct evidence for cyclic structures is essential in rationalizing the appearance of fragments with scrambled (i.e., permutated) primary structures, as the cycle may not open up where it was initially formed. It is demonstrated here that cyclic and linear a4 structures can interconvert freely as a result of collisional activation, implying that isomerization takes place prior to dissociation.