Improved identification of O-linked glycopeptides from ETD data with optimized scoring for different charge states and cleavage specificities

Zsuzsa Darula, Robert J. Chalkley, Aenoch Lynn, Peter R. Baker, Katalin F. Medzihradszky

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

This article describes the effect of re-interrogation of electron-transfer dissociation (ETD) data with newly developed analytical tools. MS/MS-based characterization of O-linked glycopeptides is discussed using data acquired from a complex mixture of O-linked glycopeptides, featuring mucin core 1-type carbohydrates with and without sialic acid, as well as after partial deglycosylation to leave only the core GalNAc units (Darula and Medzihradszky in Mol Cell Proteomics 8:2515, 2009). Information content of collision-induced dissociation spectra generated in collision cell (in QqTOF instruments) and in ion traps is compared. Interpretation of the corresponding ETD data using Protein Prospector is also presented. Search results using scoring based on the frequency of different fragment ions occurring in ETD spectra of tryptic peptides are compared with results obtained after ion weightings were adjusted to accommodate differential ion frequencies in spectra of differing charge states or cleavage specificities. We show that the improved scoring is more than doubled the glycopeptide assignments under very strict acceptance criteria. This study illustrates that "old" proteomic data may yield significant new information when re-interrogated with new, improved tools.

Original languageEnglish
Pages (from-to)321-328
Number of pages8
JournalAmino Acids
Volume41
Issue number2
DOIs
Publication statusPublished - Jul 1 2011

Keywords

  • Collision-induced dissociation (CID)
  • Database search
  • Electron-transfer dissociation (ETD)
  • Mass spectrometry
  • O-glycosylation
  • O-linked glycopeptides

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry
  • Organic Chemistry

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