Isobaric protein and peptide quantification: perspectives and issues

Abstract

An important challenge for proteomics is the ability to compare protein levels across biological samples. Since their introduction, isotopic and isobaric peptide labeling have played an important role in relative quantitative comparisons of proteomes. One important drawback of most of the isotopic-labeling techniques is an increase in sample complexity. This problem was successfully addressed with the construction of isobaric labeling strategies, such as isobaric tag for relative and absolute quantification (iTRAQ), tandem mass tagging, the cleavable isobaric affinity tag, dimethylated leucines and isobaric peptide termini labeling. Furthermore, numerous applications for multiplexing using iTRAQ and tandem mass tagging have been reported.

Keywords::

• IPTL
• isobaric peptide termini labeling
• isobaric tag for relative and absolute quantification
• isobaric tagging
• iTRAQ
• multiplexing
• quantitative proteomics
• tandem mass tagging
• TMT

Acknowledgements

The authors would like to thank the anonymous reviewers for providing excellent comments that have substantially improved the manuscript.

Financial & competing interests disclosure

This work was supported by the National Program for Research in Functional Genomics in Norway (FUGE, project no. 183418/S10) of the Norwegian Research Council to Bernd Thiede. Bernd Thiede is one of the inventors of ‘Quantitative proteomics using isobaric peptide termini labeling’, which was made as an employee of the University of Oslo and constitutes the basis for a patent application. Achim Treumann is working for NEPAF, a contract proteome-analysis facility (funded by the regional development agency ONE Northeast and by the European Regional Development Fund) that will offer IPTL-based protein quantification as a service. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.