Reporter ion-based mass spectrometry approaches for the detection of non-enzymatic protein modifications in biological samples

J Proteomics. 2013 Oct 30:92:71-9. doi: 10.1016/j.jprot.2013.03.033. Epub 2013 Apr 17.


Development of mass spectrometry techniques to detect protein oxidation, which contributes to signalling and inflammation, is important. Label-free approaches have the advantage of reduced sample manipulation, but are challenging in complex samples owing to undirected analysis of large data sets using statistical search engines. To identify oxidised proteins in biological samples, we previously developed a targeted approach involving precursor ion scanning for diagnostic MS(3) ions from oxidised residues. Here, we tested this approach for other oxidations, and compared it with an alternative approach involving the use of extracted ion chromatograms (XICs) generated from high-resolution MSMS data using very narrow mass windows. This accurate mass XIC data methodology was effective at identifying nitrotyrosine, chlorotyrosine, and oxidative deamination of lysine, and for tyrosine oxidations highlighted more modified peptide species than precursor ion scanning or statistical database searches. Although some false positive peaks still occurred in the XICs, these could be identified by comparative assessment of the peak intensities. The method has the advantage that a number of different modifications can be analysed simultaneously in a single LC-MSMS run.This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.

Biological significance: The use of accurate mass extracted product ion chromatograms to detect oxidised peptides could improve the identification of oxidatively damaged proteins in inflammatory conditions.

Keywords: 3-morpholinosydnonimine; Accurate mass XIC; Allysine; DTPA; HSA; Human serum albumin; PIS; Precursor ion scanning; SIN-1; TIC; Tyrosine chlorination; Tyrosine nitration; XIC; diethylene triamine pentaacetic acid; extracted ion chromatogram; human serum albumin; oxPTM; oxidative post-translational modification; precursor ion scanning; total ion chromatogram.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography / methods
  • Humans
  • Ions / chemistry*
  • Mass Spectrometry / methods*
  • Oxidation-Reduction
  • Protein Processing, Post-Translational*
  • Serum Albumin / chemistry*
  • Serum Albumin / metabolism*


  • Ions
  • Serum Albumin