2DDB – a bioinformatics solution for analysis of quantitative proteomics data

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.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.A typical proteomics experiment starts with separation of the biological material of interest. Popular separation technologies include two-dimensional gel electrophoresis (2DE) and liquid chromatography (LC). After separation, the proteins are commonly identified by mass spectrometry (MS) which identifies proteins by measuring the weight of protein fragments (for example peptides from a tryptic digestion) and subsequently search these fragment weights against sequence databases. This search is carried out by software such as SEQUEST [1] or MASCOT [2]. The usage of sequence databases for protein identification forces the user to choose between quality or quantity. Highly curated databases such as Swiss-Prot [3] (the curated protein sequence database of UniProt) ensure high-quality protein identifications and makes subsequent analysis less difficult. A protein or peptide cannot be identified unless the protein or peptide sequence is present in the searched database, and hence the relative small size of Swiss-Prot (about 172000 protein seq