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- Title
OCAP: an open comprehensive analysis pipeline for iTRAQ.
- Authors
Wang, Penghao; Yang, Pengyi; Yang, Jean Yee Hwa
- Abstract
Motivation: Mass spectrometry-based iTRAQ protein quantification is a high-throughput assay for determining relative protein expressions and identifying disease biomarkers. Processing and analysis of these large and complex data involves a number of distinct components and it is desirable to have a pipeline to efficiently integrate these together. To date, there are limited public available comprehensive analysis pipelines for iTRAQ data and many of these existing pipelines have limited visualization tools and no convenient interfaces with downstream analyses. We have developed a new open source comprehensive iTRAQ analysis pipeline, OCAP, integrating a wavelet-based preprocessing algorithm which provides better peak picking, a new quantification algorithm and a suite of visualizsation tools. OCAP is mainly developed in C++ and is provided as a standalone version (OCAP_standalone) as well as an R package. The R package (OCAP) provides the necessary interfaces with downstream statistical analysis.Availability: OCAP is freely available and can be downloaded at http://www.maths.usyd.edu.au/u/penghaoContact: penghao.wang@sydney.edu.au
- Subjects
MASS spectrometry; PREDICATE calculus; PROTEINS; GENE expression; DATA visualization; ALGORITHMS; SOFTWARE development tools
- Publication
Bioinformatics, 2012, Vol 28, Issue 10, p1404
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bts150