Methods in Quantitative Proteomics: Setting iTRAQ on the Right Track

Josselin      Noirel; Caroline      Evans; Malinda      Salim; Joy      Mukherjee; Saw      Yen Ow; Jagroop      Pandhal; Trong      Khoa Pham; Catherine      A. Biggs; Phillip      C. Wright

Abstract

Isobaric tags for absolute and relative quantification (iTRAQ) provide the quantitative proteomics community with an easy-to-use tool to examine proteome changes. Five years after the launch of the technique, has the community become familiar with iTRAQ? In this review, we propose to answer this question by looking at two of its facets. On the one hand, we enquire whether iTRAQ is used ‘optimally’; in other words, whether the community is keeping up with the methods that have been devised and the requirements that have become recognised, in quantitative proteomics. On the other hand, there is the question of whether an iTRAQ paper is written in such a way as to allow other researchers to challenge or improve the results. To tackle these two problems, we have reviewed the iTRAQ literature and gathered data about the methods; in this study, we discuss the experimental designs, the use of biological and technical replicates, the confirmation through additional experiments, the strategies to identify differential expression and supplementary information. Our conclusions aim at giving recommendations in light of our statistics.

Keywords: Guidelines, iTRAQ, mass spectrometry, methods, publication standards, quantitative proteomics, review, statistics, Label-Free, SILAC, ICAT, Replicates, Enzymatic Digestion, SCX