Charge-separation reactions of doubly-protonated peptides: Effect of peptide chain length

The collision induced dissociation of doubly-protonated (Ala)_xHis (x=5, 6, 7, 8, 10) peptides have been studied. The major fragmentation reactions observed are symmetrical amide bond cleavages to give the complementary b_m and y_N-m ions, where N is the total number of residues in the peptide. Minor asymmetric cleavage to give doubly-protonated y ions also is observed, involving cleavage near the N-terminus. The shorter peptides (x=5, 6, 7) show major cleavage of the second amide bond to yield b₂ and y_N-2 ions, while (Ala)₁₀His shows major symmetrical cleavage at the fourth and fifth amide bonds. (Ala)₈His appears to be a transitional peptide in showing substantial symmetrical cleavage at the second, fourth, and fifth amide bonds. The results are in general agreement with the bifurcating nature of charge separation noted by Zubarev (J. Am. Soc. Mass Spectrom. 2008, 19, 1755–1763) from a statistical analysis of a large body of doubly-protonated tryptic peptide CID mass spectra. It is shown that the b₂ ion derived from doubly-protonated (Ala)₅His has a protonated oxazolone structure.