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Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 13, 2008
Briefings in Functional Genomics and Proteomics 2008 7(2):127-135; doi:10.1093/bfgp/eln007
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© The Author 2008. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Special Issue Papers

iTRAQPak: an R based analysis and visualization package for 8-plex isobaric protein expression data

Mark D'Ascenzo, Leila Choe and Kelvin H. Lee

Corresponding author. Kelvin H. Lee, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA. Tel: +1 302 831 0344; Fax: +1 302 831 4841; E-mail: KHL{at}udel.edu

The field of high throughput proteomics has spawned a number of mass spectrometry-based technologies, which enable the quantitative analysis of protein expression. One of these technologies is iTRAQ (trademarked by Applied Biosystems), which through the use of isobaric tags, enables the quantitation of up to eight complex protein samples in a single multiplexed analysis. Isobaric tagging methods are emerging as an important tool to study protein expression dynamics. In this report, we describe iTRAQPak, a free software package developed in the R statistical and visualization environment that can be applied to the analysis of 8-plex expression data. The utility of this package is demonstrated through its application to the analysis of 8-plex iTRAQ protein expression data obtained from cerebrospinal fluid samples from Alzheimer's disease subjects involved in a Phase I drug trial.

Keywords: iTRAQ, data analysis, shotgun proteomics, Alzheimer's disease, immunotherapy, cerebrospinal fluid


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