The Total Charge of Carbon and Nitrogen Atoms in the Amide Bonds Acts as a New Approach to Understand the Mobile Proton Model

Author： Xu Qifei

Publisher： Taylor & Francis Ltd

ISSN： 0038-7010

Source： Spectroscopy Letters, Vol.46, Iss.6, 2013-08, pp. : 408-414

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Abstract

The mobile proton model has been the main theory to describe peptide fragmentation in mass spectrometry (MS). In this study, Gly-Ala-Tyr (GAY) was used to research the mass spectrometry cleavage mechanism. The hydroxyl radical oxidation technique was applied to change the charge distribution of the peptide. We applied MS/MS technique to obtain the tandem mass spectrum of the peptide and then obtained fragmentation efficiency curves, which indicated that the cleavage of GAY became more and more difficult as more O atoms were added. The charge distribution was obtained from quantum chemical calculations at the B3LYP/6-31G(d) level using the Gaussian 03 W program. By analyzing the charge distribution around the amide bonds, we found that the total charge of C and N atoms (Q_C + Q_N) in the amide bonds provided a reasonable prediction of peptide fragmentation efficiency. A decrease of the Q_C + Q_N value in the amide bonds leads to a low fragmentation efficiency of GAY, and vice versa. Through comparing experimental data with calculation results to research the relationship between charge distribution and the mass spectrometry cleavage mechanism, this work provides a new way to understand the mobile proton model for peptide fragmentation.