2DDB -: a bioinformatics solution for analysis of quantitative proteomics data
2DDB -: a bioinformatics solution for analysis of quantitative proteomics data
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DOI：
10.1186/1471-2105-7-158
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发表时间：
2006-03-20
影响因子：
3
通讯作者：
Malmström, J
中科院分区：
文献类型：
--
作者：
Malmström, L;Marko-Varga, G;Malmström, J
背景：我们提出了2DDB，一个用于存储、整合和分析定量蛋白质组学数据的生物信息学解决方案。随着蛋白质组学领域数据复杂性和生成速度的增加，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，该模型描述了实验描述和已鉴定的蛋白质等基本原理。扩展数据模型构建在核心数据模型之上，以捕获数据的更具体方面。一些公共数据库和生物信息学工具已被整合，使用户可以访问大量相关数据。统计和图形软件包R用于统计和图形分析。目前的实现处理来自2D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，从基于转化生长因子- β刺激的纤维母细胞的定量液相色谱-质谱分析到人宫颈活检的二维凝胶电泳/质谱分析。该软件可在SourceForge下载。
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.