Probing the electron capture dissociation mass spectrometry of phosphopeptides with traveling wave ion mobility spectrometry and molecular dynamics simulations.

Doyong Kim,Pei-Jing Pai,Andrew J Creese,David H Russell,Andrew W Jones,Helen J Cooper

doi:10.1007/s13361-015-1094-1

Abstract

Electron capture dissociation mass spectrometry offers several advantages for the analysis of peptides, most notably that backbone c and z fragments typically retain labile modifications such as phosphorylation. We have shown previously that, in some cases, the presence of phosphorylation has a deleterious effect on peptide sequence coverage, and hypothesized that intramolecular interactions involving the phosphate group were preventing separation of backbone fragments. In the present work, we seek to rationalize the observed ECD behavior through a combination of ECD of model peptides, traveling wave ion mobility mass spectrometry and molecular dynamics simulations. The results suggest that for doubly protonated ions of phosphopeptide APLpSFRGSLPKSYVK a salt-bridge structure is favored, whereas for the doubly-protonated ions of APLSFRGSLPKpSYVK ionic hydrogen bonds predominate. Graphical ᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-015-1094-1) contains supplementary material, which is available to authorized users.

Highlights

Electron capture dissociation (ECD) is a tandem mass spectrometry technique in which trapped ions are irradiated with low energy electrons [1, 2]
We concluded that noncovalent interactions, either salt-bridges or ionic hydrogen bonds, were preventing the separation of any ECD fragments
Peptides were synthesized in which the arginine residue at position 6 was replaced with leucine and the ECD fragmentation recorded

Summary

Introduction

Electron capture dissociation (ECD) is a tandem mass spectrometry technique in which trapped ions are irradiated with low energy electrons [1, 2]. In order to address the question posed above, and to probe the nature of the noncovalent interactions (salt-bridges, ionic hydrogen bonds) in these phosphopeptides, we combined molecular dynamics simulations with traveling wave ion mobility spectrometry measurements to gain insight into the structures of the phosphopeptides.

Results

Conclusion