Publication Details

Reference Category Journals
DOI / URL link
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.;
Journal Proteomics
Year 2004
Department PROTEOM;
Volume 4
Issue 5
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 (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
ID 4435
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=4435
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