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.

Formation of y+10 and y+11 Ions in the Collision-Induced Dissociation of Peptide Ions

Published

Author(s)

Lisa E. Kilpatrick, Pedatsur Neta, Xiaoyu Yang, Yamil Simon, Yuxue Liang, Stephen E. Stein

Abstract

Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we report on a new class of fragment ions corresponding to yn-1+10 and yn-1+11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences are ascribed to the masses of [+CO –H2O] and [+CO –NH3], respectively, and were confirmed by accurate mass analysis. The mechanism is suggested to involve dissociation of the N terminal residue at the CH-CO bond along with, or following, loss of H2O or NH3. MS3 spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The yn-1+10 ion is most often found in peptides with N terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The yn-1+11 ion is observed predominantly with histidine and asparagine at the N terminus, but also occurs with asparagine in positions two through four. The intensities of the yn 1+10 ions decrease with increasing peptide length. These data for yn-1+10 and yn-1+11 ion formation may be used to improve peptide identification from MS/MS spectra.
Citation
Journal of the American Society for Mass Spectrometry

Keywords

peptide, MS/MS, y+10, y+11

Citation

Kilpatrick, L. , Neta, P. , Yang, X. , Simon, Y. , Liang, Y. and Stein, S. (2011), Formation of y+10 and y+11 Ions in the Collision-Induced Dissociation of Peptide Ions, Journal of the American Society for Mass Spectrometry, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=908709 (Accessed September 30, 2022)
Created December 8, 2011, Updated September 4, 2018