A comparison of positive and negative ion collision-induced dissociation for model heptapeptides with one basic residue.

The effects of the identity and position of basic residues on peptide dissociation were explored in the positive and negative modes. Low-energy collision-induced dissociation (CID) was performed on singly protonated and deprotonated heptapeptides of the type: XAAAAAA, AAAXAAA, AAAAAXA and AAAAAAX, where X is arginine (R), lysine (K) or histidine (H) residues and A is alanine. For [M + H](+), the CID spectra are dominated by cleavages adjacent to the basic residues and the majority of the product ions contain the basic residues. The order of a basic residue's influence on fragmentation of [M + H](+) is arginine > histidine approximately lysine, which is also the order of decreasing gas-phase basicity for these amino acids. These results are consistent with the side chains of basic residues being positive ion charge sites and with the more basic arginine residues having a higher retention (i.e. sequestering) of the positive charge. In contrast, for [M-H](-) the identity and position of basic residues has almost no effect on backbone fragmentation. This is consistent with basic residues not being negative mode charge sites. For these peptides, more complete series of backbone fragments, which are important in the sequencing of unknowns, can be found in the negative mode. Spectra at both polarities contain C-terminal y-ions, but y(n)''(+) has two more hydrogens than the corresponding y(n)(-). Another major difference is the production of the N-terminal backbone series b(n)(+) in the positive mode and c(n)(-) in the negative mode. Thus, comparison of positive and negative ion spectra with an emphasis on searching for pairs of ions that differ by 2 Da (y(n)''(+) vs y(n)(-)) and by 15 Da (b(n)(+) vs c(n)(-)) may be a useful method for determining whether a product ion is generated from the C-terminal or the N-terminal end of a peptide. In addition, a characteristic elimination of NH=C=NH from arginine residues is observed for deprotonated peptides. Copyright 2010 John Wiley & Sons, Ltd.