Protein Chemistry Research Group, Institute of Biotechnology, University of Helsinki, Finland.
J Proteome Res. 2010 Dec 3;9(12):6795-800. doi: 10.1021/pr100824w. Epub 2010 Nov 11.
Tandem mass spectrometry-based proteomics experiments produce large amounts of raw data, and different database search engines are needed to reliably identify all the proteins from this data. Here, we present Compid, an easy-to-use software tool that can be used to integrate and compare protein identification results from two search engines, Mascot and Paragon. Additionally, Compid enables extraction of information from large Mascot result files that cannot be opened via the Web interface and calculation of general statistical information about peptide and protein identifications in a data set. To demonstrate the usefulness of this tool, we used Compid to compare Mascot and Paragon database search results for mitochondrial proteome sample of human keratinocytes. The reports generated by Compid can be exported and opened as Excel documents or as text files using configurable delimiters, allowing the analysis and further processing of Compid output with a multitude of programs. Compid is freely available and can be downloaded from http://users.utu.fi/lanatr/compid. It is released under an open source license (GPL), enabling modification of the source code. Its modular architecture allows for creation of supplementary software components e.g. to enable support for additional input formats and report categories.
基于串联质谱的蛋白质组学实验会产生大量的原始数据，需要不同的数据库搜索引擎来可靠地识别这些数据中的所有蛋白质。在这里，我们介绍了 Compid，这是一个易于使用的软件工具，可以用于整合和比较来自两个搜索引擎（Mascot 和 Paragon）的蛋白质鉴定结果。此外，Compid 还可以从无法通过 Web 界面打开的大型 Mascot 结果文件中提取信息，并计算数据集中小肽和蛋白质鉴定的一般统计信息。为了证明这个工具的有用性，我们使用 Compid 比较了人角质形成细胞线粒体蛋白质组样品的 Mascot 和 Paragon 数据库搜索结果。Compid 生成的报告可以导出并以可配置分隔符的 Excel 文档或文本文件打开，允许使用多种程序对 Compid 输出进行分析和进一步处理。Compid 是免费提供的，可以从 http://users.utu.fi/lanatr/compid 下载。它是在开源许可证（GPL）下发布的，允许修改源代码。其模块化架构允许创建补充软件组件，例如支持其他输入格式和报告类别。
