Loss of 45 Da from a2 Ions and Preferential Loss of 48 Da from a2 Ions Containing Methionine in Peptide Ion Tandem Mass Spectra

Published

January 29, 2011

Author(s)

Yamil Simon, Pedatsur Neta, Xiaoyu Yang, Stephen E. Stein

Abstract

While analyzing tandem mass spectra of tryptic tripeptides, intense unassigned peaks were observed, which correspond to a neutral loss of 45 Da from a₂ ions. From exact mass analysis this loss is ascribed to formamide (or NH₃+CO). Elimination of formamide from a₂ ions requires that the ions cyclize. A mechanism for this elimination is proposed on the basis of theoretical calculations. The structure of the a₂-45 ions is confirmed by their fragmentation in MS³ experiments. Loss of formamide from a₂ ions occurs in competition with other neutral losses, such as H₂O. However, if the a₂ ion contains methionine, a neutral loss of 48 Da, ascribed to CH₃SH, predominates, and is followed by loss of formamide. The intensity of the a₂-48 peak formed from XaaMet has a maximum value of 42% (of the total intensities of all ions) for Xaa = Gly, varies between 15% and 40% for most other Xaa residues, is lower for residues that can undergo loss of water or ammonia, and very low for Lys or Arg. When the order of the residues is reversed to MetXaa the loss of 48 Da is much smaller. This effect can be used to determine the sequence of b₂ ions containing Met in proteomic studies. Direct loss of CH₃SH from b₂ ions is much less favorable than loss of CO to form a2 ions. Considerable loss of CH3SH is observed from doubly protonated tryptic tripeptides with N-terminal Met, but much less when singly protonated or when Met is in the center position.

Citation

Journal of the American Society for Mass Spectrometry

Volume

22

Issue

2

Pub Type

Journals

Keywords

tandem mass spectrometry, electrospray ionization, peptide fragmentation, tripeptides, loss of formamide, neutral losses

Citation

Simon, Y. , Neta, P. , Yang, X. and Stein, S. (2011), Loss of 45 Da from a2 Ions and Preferential Loss of 48 Da from a2 Ions Containing Methionine in Peptide Ion Tandem Mass Spectra, Journal of the American Society for Mass Spectrometry (Accessed April 18, 2024)