Formation of diagnostic product ions from cyanobacterial cyclic peptides by the two-bond fission mechanism using ion trap liquid chromatography/multi-stage mass spectrometry

Product ions obtained by tandem mass spectrometry (MS/MS) are quite effective for the amino acid sequencing of linear peptides. However, in the case of cyclic peptides, the fragmentation pattern is complicated because the cleavages occur randomly and product ions are generated as an, bn, cn, xn, yn and zn series ions; therefore, the authors have never obtained sufficient sequence information. In order to overcome this problem, we applied ion trap liquid chromatography/multi‐stage mass spectrometry (LC/MSn) and characterized the product ions obtained from anabaenopeptins and aeruginopeptins as the cyclic peptides. For the anabaenopeptins, MS2 analysis did not provide sufficient sequence information on the cyclic structure, and MS3 analysis was applied to sequence the constituent amino acids. Diagnostic product ions were obtained by the MS3 analysis and were quite effective for obtaining the sequence information of the constituent amino acids. MS2 analysis was, however, sufficient to obtain the sequence information of the aeruginopeptins. In both cases, the resulting product ions obtained from the cyclic structures were formed by the two‐bond fission mechanism of the precursor ion, in which an initial fission of the cyclic structure to a linear one and subsequent fission(s) at the peptide bonds are included. The fragmentations were similar for the structurally related compounds, indicating that the cleavages occurred at definite peptide bonds. In addition, the resulting product ions are generated as bn series ions and the mass difference facilitates the amino acid sequencing. Thus, ion trap LC/MSn provides sequence information, and the resulting product ions are reproducible among the structurally related compounds and reliable for the sequencing of the constituent amino acids of the cyclic structure. Copyright © 2007 John Wiley & Sons, Ltd.