Abstract

European Journal of Mass Spectrometry
Volume 12 Issue 4, Pages 235–245 (2006)
doi: 10.1255/ejms.815

Multi-stage collisionally-activated decomposition in an ion trap for identification of sequences, structures and b_n→b_n–1 fragmentation pathways of protonated cyclic peptides

Chenxi Jia, Wei Qi,^* Zhimin He and Bin Qiao
Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. E-mail: qiwei@tju.edu.cn

Cyclic penta-, hexa- and heptapeptides have been designed, synthesized and their fragmentations induced by multistage tandem mass spectrometry have been studied. Under low-energy collisionally activated decomposition (CAD), the protonated cyclic peptides mainly dissociate via ring opening pathways and the corresponding b_n→b_n–1 pathways to form several sets of b ions as oxazolone rings (and b₁ ions as aziridinone rings). Through repeated observation of these b ions in multistep CAD experiments, accurate sequencing and head-to-tail ring structure of cyclic peptides can be determined. The mistaken assignments of these b ions can be avoided by this sequencing method. Semiempirical molecular orbital calculations have been utilized to provide insight into the proposed dissociation mechanism. In addition, for cyclic peptides that include an Asn residue, the nitrogen of the Asn side chain is observed to be preferentially protonated, which can induce a unique ring-opening pathway with a loss of ammonia that competes with the conventional ring opening pathway

Keywords: tandem mass spectrometry, cyclic peptides, fragmentation pathways, collisionally activated decomposition, sequencing

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