Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation

Saw Yen Ow, Malinda Salim, Josselin Noirel, Caroline Evans Evans, Phillip C. Wright

Research output: Contribution to journalArticleResearchpeer-review

95 Citations (Scopus)


Application of iTRAQ-based workflows for protein profiling has become widespread. Concomitantly, the idiosyncratic limitations of iTRAQ, such as its tendency to underestimate quantifications, have been studied and recognised. This report shows that the influence of ratio compression and limiting transmission in iTRAQ MS/MS in high-complexity mixtures (iTRAQ-labelled lysates) can be partly alleviated using high-resolution sample fractionation. Here, we also investigate in greater detail the dependency of iTRAQ quantification on the dynamics of online chromatography in low-complexity mixtures (iTRAQ-labelled standards). These findings will allow more efficient strategies to be designed for iTRAQ proteomics, alleviating iTRAQ underestimation and thus facilitating the detection of subtle abundance changes.

Original languageEnglish
Pages (from-to)2341-2346
Number of pages6
Issue number11
Publication statusPublished - Jun 2011
Externally publishedYes


  • ITRAQ proteomics
  • ITRAQ underestimation
  • MS/MS mixing
  • Quantitative proteomics
  • Technology

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