Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

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

Published

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 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.
Citation
Journal of the American Society for Mass Spectrometry
Volume
22

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 April 21, 2024)
Created February 25, 2011, Updated February 19, 2017