Extensive 15N labeling and multiple-stage tandem mass spectrometry were used to investigate the fragmentation pathways of the model peptide FGGFL during low-energy collision-induced-dissociation (CID) in an ion-trap mass spectrometer. Of particular interest was formation of a 4 from b 4 and a*4 (a 4-NH3) from a 4 ions correspondingly, and apparent rearrangement and scrambling of peptide sequence during CID. It is suggested that the original FGGFoxa b 4 structure undergoes b-type scrambling to form GGFFoxa. These two isomers fragment further by elimination of CO and 14NH3 or 15NH3 to form the corresponding a 4and a*4 isomers, respectively. For (15N-F)GGFL and FGG(15N-F)L the a*4 ion population appears as two distinct peaks separated by 1 mass unit. These two peaks could be separated and fragmented individually in subsequent CID stages to provide a useful tool for exploration of potential mechanisms along the a 4a*4 pathway reported previously in the literature (Vachet et al. J. Am. Chem. Soc. 1997, 119, 5481, and Cooper et al. J. Am. Soc. Mass Spectrom. 2006, 17, 1654). These mechanisms result in formally the same a*4 structures but differ in the position of the expelled nitrogen atom. Detailed analysis of the observed fragmentation patterns for the separated light and heavy a*4 ion fractions of (15N-F)GGFL indicates that the mechanism proposed by Cooper et al. is consistent with the experimental findings, while the mechanism proposed by Vachet et al. cannot account for the labeling data. In addition, a new rearrangement pathway is presented for a 4*-CO ions that effectively transfers the former C-terminal amino acid residue to the N-terminus.

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