Wu Yukun, Zhang Le
Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
J Bioinform Comput Biol. 2011 Dec;9(6):775-94. doi: 10.1142/s0219720011005665.
One of the key limitations for proteomic studies using two-dimensional (2D) gel is the lack of automatic, fast, robust, and reliable methods for detecting, matching, and quantifying protein spots. Although there are commercial software packages for 2D gel image analysis, extensive human intervention is still needed for spot detection and matching, which is time-consuming and error-prone. Moreover, the commercial software packages are usually expensive and non-open source. Thus, it is very beneficial for researchers to have free software that is fast, fully automatic, and robust. In this paper, we review and compare two recently developed and publicly available software packages, RegStatGel and Pinnacle, for analyzing 2D gel images. These two software packages share some common features and also have some fundamental difference in the aspects of spot detection and quantification. Based on our experience, RegStatGel is much better in terms of spot detection and matching. It also contains more advanced statistical tools and is more user-friendly. In contrast, Pinnacle is quite sensitive to background noise and relies on external statistical software packages for statistical analysis.
使用二维（2D）凝胶进行蛋白质组学研究的关键限制之一是缺乏用于检测、匹配和定量蛋白质斑点的自动、快速、稳健且可靠的方法。尽管有用于二维凝胶图像分析的商业软件包，但在斑点检测和匹配方面仍需要大量人工干预，这既耗时又容易出错。此外，商业软件包通常价格昂贵且不开源。因此，拥有快速、全自动且稳健的免费软件对研究人员非常有益。在本文中，我们回顾并比较了最近开发并公开可用的两个用于分析二维凝胶图像的软件包RegStatGel和Pinnacle。这两个软件包有一些共同特征，在斑点检测和定量方面也存在一些根本差异。根据我们的经验，RegStatGel在斑点检测和匹配方面要好得多。它还包含更先进的统计工具，并且对用户更友好。相比之下，Pinnacle对背景噪声相当敏感，并且依赖外部统计软件包进行统计分析。
