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Briefings in Functional Genomics and Proteomics Advance Access published online on May 10, 2006
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/ell018
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© Oxford University Press, 2006, All rights reserved. For permissions please email: journals.permissions@oxfordjournals.org

Original Article

Shotgun proteomics using the iTRAQ isobaric tags

Kunal Aggarwal, Leila H. Choe, and Kelvin H. Lee *

* To whom correspondence should be addressed.
Kelvin H. Lee, E-mail: KHL9{at}cornell.edu


  Abstract

Shotgun proteomic methods involving isobaric tagging of peptides enable high-throughput proteomic analysis. iTRAQ reagents allow simultaneous identification and quantitation of proteins in four different samples using tandem mass spectrometry (MS). In this article, we provide a brief description of proteome analysis using iTRAQ reagents and review the current applications of these reagents in proteomic studies. We also compare different aspects of protein identification including protein sequence coverage and proteome coverage obtained using iTRAQ reagents with those using other shotgun proteomic techniques. We briefly discuss the issue of isotope purity correction in measured peak areas during protein quantitation using iTRAQ reagents. Finally, we conclude with some of the current challenges in MS-based proteomic analysis that are limiting protein identifications obtained by different shotgun proteomic methods.

Keywords: isobaric tag; iTRAQ; shotgun proteomics; tandem mass spectrometry.

Kunal Aggarwal is a graduate student in the School of Chemical and Biomolecular Engineering, Cornell University, NY, USA.

Leila H. Choe is a Research Support Specialist in the School of Chemical and Biomolecular Engineering, Cornell University, NY, USA.

Kelvin H. Lee is Associate Professor in the School of Chemical and Biomolecular Engineering, Cornell University and is the Director of the Cornell Institute for Biotechnology and Life Science Technologies, NY, USA.


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