ProDB - Bioinformatics support for high throughput proteomics

Andreas Wilke1, Christian Rueckert2, Sebastian Kespoh , Martina Mahne, Andrea T. Hueser, Folker Meyer, UniversBielefeld University, Institute for Genome Research, Germany;, Int. NRW Grad. School in Bioinformatics Genome Research, Bielefeld Unive rsity, Germanyy

In the "post-genome" era, mass spectrometry has become an important method for the analysis of proteome data. The rapid advancement of this technique in combi nation with other methods used in proteomics, results in an increasing number of high-throughput projects. This leads to an increasing amount of data, that need s to be archived and analyzed. To cope with the need for automated data conversion, storage, and analysis in th e field of proteomics, the open source system ProDB was developed. The system ha ndles data conversion from different mass spectrometer software, automates data analysis, and will allow the annotation of MS spectra (e.g. assign gene names, s tore data on protein modifications, etc.).The system is based on an extensible r elational database to store the mass spectra together with the experimental setu p. It also provides a graphical user interface for managing the experimental ste ps led to the MS data. Furthermore, it allows the integration of genome and prot eome data.Data from an ongoing experiment was used to compare manual and automated analysis. First tests showed that the automation resulted in a significant saving of time. Furthermore the quality and interpretability of the results was improved in all cases.