Web-accessible proteome databases for microbial research.
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.
Pleissner
Klaus-Peter
KP
Max Planck Institute for Infection Biology, Berlin, Germany.
Eifert
Till
T
Buettner
Sven
S
Schmidt
Frank
F
Boehme
Martina
M
Meyer
Thomas F
TF
Kaufmann
Stefan H E
SH
Jungblut
Peter R
PR
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
D001426:Bacterial Proteins; D007554:Isotopes; D020543:Proteome