Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions

Published

February 25, 2011

Author(s)

Pedatsur Neta, Stephen E. Stein

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 y_n-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.

Citation

Journal of the American Society for Mass Spectrometry

Volume

22

Pub Type

Journals

Keywords

peptide ion, collision induced dissociation, y ions, charge distribution, proton affinity

Citation

Neta, P. and Stein, S. (2011), Charge States of y Ions in the Collision-Induced Dissociation of Doubly Charged Tryptic Peptide Ions, Journal of the American Society for Mass Spectrometry (Accessed December 15, 2024)