Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1002/pmic.200300737
Title (Primary) Web-accessible proteome databases for microbial research
Author Pleissner, K.P.; Eifert, T.; Buettner, S.; Schmidt, F.; Boehme, M.; Meyer, T.F.; Kaufmann, S.H.E.; Jungblut, P.R.
Source Titel Proteomics
Year 2004
Department PROTEOM
Volume 4
Issue 5
Page From 1305
Page To 1313
Language englisch
Keywords bioinformatics; databases; microorganisms; proteomics; two-dimensional gel electrophoresis
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 ( 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
Persistent UFZ Identifier
Pleissner, K.P., Eifert, T., Buettner, S., Schmidt, F., Boehme, M., Meyer, T.F., Kaufmann, S.H.E., Jungblut, P.R. (2004):
Web-accessible proteome databases for microbial research
Proteomics 4 (5), 1305 - 1313 10.1002/pmic.200300737