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



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


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.
Journal of the American Society for Mass Spectrometry


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


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], (Accessed June 20, 2024)


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Created December 8, 2011, Updated September 4, 2018