Author： Neta Pedatsur
Publisher： Springer Publishing Company
ISSN： 1044-0305
Source： Journal of The American Society for Mass Spectrometry, Vol.22, Iss.5, 2011-05, pp. : 898-905
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Abstract
Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative intensities of charge states of product y- and b-ions depend on the final location of that proton. This study examines y-ion charge distributions for dissociation of doubly charged peptide ions, using a large reference library of peptide ion fragmentation generated from ion-trap CID of peptide ions from tryptic digests. Trends in relative intensities of y2+ and y1+ ions are examined as a function of bond cleavage position, peptide length (n), residues on either side of the bond and effects of residues remote from the bond. It is found that yn-2/b2 dissociation is the most sensitive to adjacent amino acids, that y2+/y1+ steadily increase with increasing peptide length, that the N-terminal amino acid can have a major influence in all dissociations, and in some cases other residues remote from the bond cleavage exert significant effects. Good correlation is found between the values of y2+/y1+ for the peptide and the proton affinities of the amino acids present at the dissociating peptide bond. A few deviations from this correlation are rationalized by specific effects of the amino acid residues. These correlations can be used to estimate trends in y2+/y1+ ratios for peptide ions from amino acid proton affinities.
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