title: Web-accessible proteome databases for microbial research.
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.
authors.affiliation: Max Planck Institute for Infection Biology, Berlin, Germany.
authors.forename: Klaus-Peter
authors.initials: KP
authors.lastname: Pleissner
authors.forename: Till
authors.initials: T
authors.lastname: Eifert
authors.forename: Sven
authors.initials: S
authors.lastname: Buettner
authors.forename: Frank
authors.initials: F
authors.lastname: Schmidt
authors.forename: Martina
authors.initials: M
authors.lastname: Boehme
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Meyer
authors.forename: Stefan H E
authors.initials: SH
authors.lastname: Kaufmann
authors.forename: Peter R
authors.initials: PR
authors.lastname: Jungblut
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D035843:Biomedical Research / Q000379:methods*; D002853:Chromatography, Liquid; D019295:Computational Biology; D016208:Databases, Factual; D015180:Electrophoresis, Gel, Two-Dimensional; D020407:Internet; D007554:Isotopes / Q000737:chemistry; D013058:Mass Spectrometry; D020543:Proteome
chemical_list: D001426:Bacterial Proteins; D007554:Isotopes; D020543:Proteome