Comparison of CID Versus ETD Based MS/MS Fragmentation for the Analysis of Protein Ubiquitination

53Citations
Citations of this article
141Readers
Mendeley users who have this article in their library.

Abstract

Ubiquitination has emerged as one of the major post-translational modifications that decide on protein fate, targeting, and regulation of protein function. Whereas the ubiquitination of proteins can be monitored with classic biochemical methods, the mapping of modified side chains proves to be challenging. More recently, mass spectrometry has been applied to identify ubiquitinated proteins and also their sites of modification. Typically, liquid chromatography tandem mass spectrometry (LC-MS/MS) based approaches, including collision-induced fragmentation (CID), have been successfully used in the past. However, a potential difficulty arises from the unstable nature of this modification, and also that the isopeptide bond linkage between C-terminal glycine and the N(ε) lysyl side chain is susceptible to fragmentation under these conditions. Here we investigate the utility of electron-transfer dissociation (ETD)-based fragmentation to detect ubiquitination sites in proteins. Our results indicate that ETD can provide alternative fragmentation patterns that allow detection of gly-gly-modified lysyl side chains, in particular z+1 fragment ions derived from triply charged precursor ions. We subsequently applied ETD fragmentation-based analysis and detected novel ubiquitination sites on DNA polymerase B1 that were not easily observed using CID. We conclude that ETD can provide significant alternative fragmentation information that complements CID-derived data to improve the coverage when mapping ubiquitination sites in proteins. © 2009 American Society for Mass Spectrometry.

Cite

CITATION STYLE

APA

Sobott, F., Watt, S. J., Smith, J., Edelmann, M. J., Kramer, H. B., & Kessler, B. M. (2009). Comparison of CID Versus ETD Based MS/MS Fragmentation for the Analysis of Protein Ubiquitination. Journal of the American Society for Mass Spectrometry, 20(9), 1652–1659. https://doi.org/10.1016/j.jasms.2009.04.023

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free