Skip Navigation

2D-PAGE


NAR Molecular Biology Database Collection entry number 606
Pleissner, K.-P., Eifert, T., Buettner, S., Knipper, J., Schmelzer, P., Stein, R., Schmidt, F., Mattow, J., Zimny-Arndt, U., Schmid, M., Jungblut, P.R.
Max Planck Institute for Infection Biology, Schumannstr.21-22, 10117 Berlin, Germany

Database Description

The publicly available Proteome Database System for Microbial Research 2D-PAGE has been established at the Max Planck Institute for Infection Biology and serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. The database system is centrally administrated, and investigators without specific bioinformatics competence in database construction can submit their data. The system comprises four heterogeneous but interconnected databases: (i) 2D-PAGE database for 2-D gel electrophoresis and mass spectrometry data, (ii) Isotope Coded Affinity Tag (ICAT)-LC/MS database, (iii) FUNC_CLASS database for functional classification of proteins, (iv) DIFF database for presentation of differentially regulated proteins detected by quantitative gel image analysis. The database system is hyperlinked with public databases such as SWISS-PROT; NCBI; PEDANT and KEGG. The current public release (May, 2004) contains proteomic information on 11 microorganisms such as Mycobacterium tuberculosis, Helicobacter pylori, Chlamydophila pneumoniae, Borrelia garinii, Francisella tularensis, Mycoplasma pneumoniae and information on Jurkat T-cells and mouse mammary gland. Proteomic data are presented in 18 two-dimensional gels with 2572 identified protein spots. For 254 of these spots peptide mass fingerprints are available. More than 1000 identified spots of further miroorganisms such as Mycobacterium bovis BCG, Salmonella SL-1344, Vibrio cholerae are stored in the internal release of 2D-PAGE which will be publicly accessible after paper submission. The annotated proteome data such as protein name, molecular weight Mr, isoelectric point pI, gene name, ORF, NCBI accession number, identification method, sequence coverage, protein spot number, class (antigen, gastric carcinoma associated antigen etc.) can be retrieved either by clicking on protein spots or by formulating complex queries. Specific data such as pI, Mr-values or codon usage for proteins can be visualized and analyzed on the fly using the statistical software environment R (http://www.r-project.org/) or can be downloaded as spread sheet files. The Proteome Database System for Microbial Research can be accessed from http://www.mpiib-berlin.mpg.de/2D-PAGE.

Acknowledgements

This work was partially funded by the German Federal Ministry for Eduction and Research (contract number: 031U107C/031U207C) and by the European Union (EBPnetwork - contract number: QLRT-1999-31536).

References

1. Jungblut, P. R., Schaible, U. E., Mollenkopf, H. J., Zimny-Arndt, U., et al., Mol. Microbiol. 1999,33(6), 1103-1117.

2. Mollenkopf, H. J., Jungblut, P. R., Raupach, B., Mattow, J. et al., Electrophoresis 1999, 20, 2172-2180.

3. Pleissner, K.-P., Eifert, T., Jungblut, P.R., Comp. Funct. Genom. 2002, 3, 97-100.

4. Mollenkopf, H. J., Mattow, J., Schaible,U. E. , Grode, L. et al., Methods Enzymol. 2002 358, 242-256.

5. Pleissner, K.-P., Eifert, T., S. Buettner, S., Schmidt, F., Boehme, M., T.F. Meyer, T. F., Kaufmann, S. H. E., Jungblut. P. R. Proteomics, 2004, 4, 1305-1313.


Oxford University Press is not responsible for the content of external internet sites