The mechanism of C-terminal fragmentations in alkali metal ion complexes of peptides

A combination of mass spectrometry and ab initio calculations (MP2/6-31 +G(d)//HF/6-31 +G(d)) has been used to study the mechanism of C-terminal residue cleavage in gas phase peptide/alkali metal ion complexes. Although previous workers had suggested a mechanism relying on a concerted cleavage of an oxazolidin-5-one intermediate, the present calculations indicate that this pathway has a high barrier and is not competitive. Instead, it appears that the mechanism involves a rearrangement to an anhydride intermediate that fragments to give the observed products. The computational data indicates that this mechanism has a much lower activation energy than a concerted pathway and should be viable. Moreover, compelling evidence for the mechanism is found in experiments involving the lithium complexes of dipeptides. In the proposed mechanism, the two amino acids of a dipeptide are in equivalent positions in the anhydride intermediate (i.e., sequence information is lost) and therefore, fragmentation of either sequence of a dipeptide should give the same result. This was confirmed for eight pairs of dipeptides by collision-induced dissociation (CID) of their lithium complexes in a quadrupole ion trap mass spectrometer. Although the CID spectra are not identical, the yields of the products that would pass through the anhydride intermediate are nearly equivalent, independent of the original sequence. Finally, additional computational work shows that the mechanism does not rely on the presence of a metal and is also viable as a charge-remote fragmentation pathway.