School of Mathematics and Statistics, University of Sydney, Camperdown, NSW2006, Australia.
Bioinformatics. 2012 May 15;28(10):1404-5. doi: 10.1093/bioinformatics/bts150. Epub 2012 Mar 29.
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.
基于质谱的 iTRAQ 蛋白质定量是一种高通量测定相对蛋白质表达和鉴定疾病生物标志物的方法。这些大型复杂数据的处理和分析涉及许多不同的组件，最好有一个管道来有效地将它们集成在一起。迄今为止，用于 iTRAQ 数据的公共综合分析管道有限，并且其中许多现有管道具有有限的可视化工具，并且与下游分析没有方便的接口。我们开发了一个新的开源综合 iTRAQ 分析管道 OCAP，它集成了基于小波的预处理算法，该算法提供了更好的峰提取、新的定量算法和一套可视化工具。OCAP 主要用 C++开发，并提供独立版本（OCAP_standalone）和 R 包。R 包（OCAP）提供了与下游统计分析的必要接口。
