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PubMed · 15188397

Web-accessible proteome databases for microbial research.

Klaus-Peter Pleissner·Till Eifert·Sven Buettner·Frank Schmidt·Martina Boehme·Thomas F Meyer·Stefan H E Kaufmann·Peter R Jungblut
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Abstract

The analysis of proteomes of biological organisms represents a major challenge of the post-genome era. Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib-berlin.mpg.de/2D-PAGE) for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly". The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.

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Bacterial ProteinsBiomedical ResearchChromatography, LiquidComputational BiologyDatabases, FactualElectrophoresis, Gel, Two-DimensionalInternetIsotopesMass SpectrometryProteomeJournal ArticleResearch Support, Non-U.S. Gov't

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Klaus-Peter Pleissner, Till Eifert, Sven Buettner, Frank Schmidt, Martina Boehme, Thomas F Meyer, Stefan H E Kaufmann, Peter R Jungblut. 2004. Web-accessible proteome databases for microbial research.. https://doi.org/10.1002/pmic.200300737

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