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Effect of N-Terminal Glutamic Acid and Glutamine on Fragmentation of Peptide Ions



Bhaskar Godugu, Pedatsur Neta, Yamil Simon, Stephen Stein


A prominent dissociation path for electrospray generated tryptic peptide ions is the dissociation of the peptide bond linking the second and third residues from the amino-terminus. The formation of the resulting b2 and yn-2 fragments has been rationalized by specific facile mechanisms. An examination of spectral libraries shows that this path predominates in diprotonated peptides composed of 12 or fewer residues, with the notable exception of peptides containing glutamine or glutamic acid at the N-terminus. To elucidate the mechanism by which these amino acids affect peptide fragmentation, we synthesized peptides of varying size and composition and examined their MS/MS spectra as a function of collision voltage in a triple quadrupole mass spectrometer. Loss of water from N-terminal glutamic acid and glutamine is observed at a lower voltage than any other fragmentation, leading to cyclization of the terminal residue. This cyclization results in the conversion of the terminal amine group to an imide, which has a lower proton affinity. As a result, the second proton is not localized at the N-terminus but is readily transferred to various peptide bonds, leading to fragmentation at various sites near the center of the peptide. Further confirmation was obtained by examining peptides with N-terminal pyroglutamic acid and N-acetyl peptides. Peptides with N-terminal proline maintain the trend of forming b2 and yn-2 because their ring contains an imine rather than imide and has greater proton affinity.
Journal of the American Society for Mass Spectrometry


peptide ions, mass spectrometry, collision induced dissociation, glutamic acid, glutamine, neutral loss


Godugu, B. , Neta, P. , Simon, Y. and Stein, S. (2010), Effect of N-Terminal Glutamic Acid and Glutamine on Fragmentation of Peptide Ions, Journal of the American Society for Mass Spectrometry, [online], (Accessed July 22, 2024)


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Created March 26, 2010, Updated October 12, 2021