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Mass spectrometry has proven to be a key enabling technology for the quantification of changes in the proteome, surpassing the more traditional gel-based methods. Different methodologies have been applied, each with individual benefits and drawbacks. Broadly speaking, two experimental strategies currently prevail: label-based and label-free approaches. Chemical labelling using isobaric reagents (predominantly isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT)) is widely applied in relative quantification workflows. The key features of iTRAQ and TMT are their multiplexing capability (currently 4-plex and 8-plex for iTRAQ and 6-plex for TMT) and the simultaneous identification and relative quantification of peptides and proteins. Such features are attractive and contribute to their popularity. In this chapter we review the state-of-the-art in iTRAQ and TMT strategies for relative quantification. The merits and the drawbacks of the isobaric-tag workflows, developments in methodologies, hardware and software platforms, which are directed to improve precision and accuracy, are discussed. Applications of iTRAQ/TMT are shown in the areas of biological engineering and biomedical research.

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