Loss of 45 Da from a2 ions and preferential loss of 48 Da from a2 ions containing methionine in peptide ion tandem mass spectra

While analyzing tandem mass spectra of tryptic tripeptides, intense unassigned peaks were observed, corresponding to neutral loss of 45 Da from a(2) ions. This process was confirmed by MS(3) experiments. Based on exact mass analysis, the loss was ascribed to (NH(3) + CO) or formamide. The proposed mechanism involves a cyclic form of the a(2) ions. The structure of the a(2) - 45 ions was confirmed by their fragmentation in MS(3) experiments. Loss of (NH(3) + CO) from the a(2) ions occurs in competition with other paths, such as the loss of H(2)O or the formation of immonium ions. However, if the a(2) ion contains methionine, a neutral loss of 48 Da (ascribed to CH(3)SH) predominates, and is followed by the loss of (NH(3) + CO). These processes were confirmed by MS(3) experiments. The intensity of the a(2) - 48 peak formed from XaaMet has a maximum value of 42% (of the total intensity of all ions) for Xaa=Gly, varies between 15% and 40% for most other Xaa residues, is lower for residues that can undergo loss of water or ammonia, and is very low for Lys or Arg. When the order of the residues is reversed to MetXaa, the loss of 48 Da is much smaller. This effect can be used to determine the sequence of b(2) ions containing Met in proteomic studies. Considerable loss of CH(3)SH is observed from doubly protonated tryptic tripeptides with N-terminal Met, but the loss is much less when they are singly protonated or when Met is in the center position.