2DDB——一种用于定量蛋白质组学数据分析的生物信息学解决方案。
2DDB - a bioinformatics solution for analysis of quantitative proteomics data.
作者信息
Malmström Lars, Marko-Varga György, Westergren-Thorsson Gunilla, Laurell Thomas, Malmström Johan
机构信息
Department of Electrical Measurements, LTH, P,O Box 118, SE-221 00, Lund, Sweden.
出版信息
BMC Bioinformatics. 2006 Mar 20;7:158. doi: 10.1186/1471-2105-7-158.
BACKGROUND
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.
RESULTS
2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments.
CONCLUSION
The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge.
背景
我们展示了2DDB，这是一种用于定量蛋白质组学数据存储、整合和分析的生物信息学解决方案。随着蛋白质组学领域数据复杂性及其产生速度的增加，对灵活分析软件的需求也在增加。
结果
2DDB基于一个核心数据模型，该模型描述了诸如实验描述和已鉴定蛋白质等基本要素。扩展数据模型建立在核心数据模型之上，以捕获数据更具体的方面。整合了许多公共数据库和生物信息学工具，使用户能够访问大量相关数据。使用统计和图形软件包R进行统计和图形分析。当前版本处理来自二维凝胶电泳和多维液相色谱/质谱实验的定量数据。
结论
该软件已成功应用于多个项目，从基于定量液相色谱-质谱的转化生长因子-β刺激的成纤维细胞分析到人类宫颈活检的二维凝胶电泳/质谱分析。该软件可在SourceForge上下载。
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