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2DDB - a bioinformatics solution for analysis of quantitative proteomics data.

Type Information
Nr 13 (Research article)
Authors Malmström, Lars; Marko-Varga, György; Westergren-Thorsson, Gunilla; Laurell, Thomas; Malmström, Johan
Title 2DDB - a bioinformatics solution for analysis of quantitative proteomics data.
Journal BMC Bioinformatics (2006) 7 158
DOI 10.1186/1471-2105-7-158
Citations 25 citations (journal impact: 3.78)
Abstract ABSTRACT 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 chromatographymass spectrometry experiments. Conclusions The software has successfully been employed in a number of projects ranging from quantitative liquidchromatography- mass spectrometry based analysis of transforming growth factor-beta stimulated fibroblasts to 2D gel electrophoresismass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge.