Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
OMICS. 2012 Sep;16(9):431-42. doi: 10.1089/omi.2012.0022. Epub 2012 Jul 17.
New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool ( http://www.proteosuite.org/?q=other_resources ) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology.
新的定量蛋白质组分析方法基于差异标记方案或无标记技术，几乎每月都有文献报道。与此同时，文献中也描述了大量用于定量蛋白质组学数据分析的软件工具，这些工具由私营公司开发。在本文中，我们重点回顾了该领域一些最流行的技术，并对可用于处理和分析所产生数据的几个软件包进行了评估。我们还描述了支持广泛软件的社区标准的重要性，这可能有助于研究人员使用不同的平台和协议分析数据。我们希望本综述既能为实验科学家提供有用的参考，也能为他们选择和使用不同的分析流程来进行定量蛋白质组数据分析提供指南。我们已经开发了一个基于网络的工具（http://www.proteosuite.org/?q=other_resources），帮助研究人员为他们的本地仪器、可用文件格式和定量方法找到合适的软件。
