2DBase: 2D-PAGE database of Escherichia coli

We present a web-based integrated proteome database, termed 2DBase of Escherichia coli which was designed to store, compare, analyse, and retrieve various information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry. The main objectives of this database are (1) to provide the...

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Bibliographic Details
Published in:Biochemical and biophysical research communications 2007-11, Vol.363 (3), p.822-827
Main Authors: Vijayendran, Chandran, Burgemeister, Sebastian, Friehs, Karl, Niehaus, Karsten, Flaschel, Erwin
Format: Article
Language:English
Subjects:
2D gels
2D-PAGE
Algorithms
Databases, Protein
E. coli
Electrophoresis, Gel, Two-Dimensional - methods
Escherichia coli
Escherichia coli Proteins - analysis
MG1655
Proteome - analysis
Proteomics
Proteomics - methods
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Summary:We present a web-based integrated proteome database, termed 2DBase of Escherichia coli which was designed to store, compare, analyse, and retrieve various information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry. The main objectives of this database are (1) to provide the features for query and data-mining applications to access the stored proteomics data (2) to efficiently compare the specific protein spots present in the comparable proteome maps and (3) to analyse the data with the integrated classification for cellular functions of gene products of E. coli. This database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins were identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analyzed, and compared in a tabular format based on various functional categories enabling quick and subsequent analyses. Our database satisfies the requirement to be a federated 2-DE database by accomplishing various tasks through a web interface providing access to a relational database system. The 2DBase of E. coli database can be accessed at http://2dbase.techfak.uni-bielefeld.de/.
ISSN:0006-291X
1090-2104
DOI:10.1016/j.bbrc.2007.09.050