Premium
The microbial proteome database — an automated laboratory catalogue for monitoring protein expression in bacteria
Author(s) -
Cordwell Stuart J.,
Nouwens Amanda S.,
Verrills Nicole M.,
McPherson James C.,
Hains Peter G.,
Van Dyk Derek D.,
Walsh Bradley J.
Publication year - 1999
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/(sici)1522-2683(19991201)20:18<3580::aid-elps3580>3.0.co;2-2
Subject(s) - proteome , database , two dimensional gel electrophoresis , computational biology , gel electrophoresis , protein expression , biology , protein array analysis , proteomics , computer science , bioinformatics , biochemistry , gene expression , gene , dna microarray
Laboratories devoted to high‐throughput characterisation of purified proteins arrayed via two‐dimensional (2‐D) gel electrophoresis face an arduous task in maintaining a centralised and constantly evolving record of information relating to the characterisation of proteins and their responses following biological challenges. The Microbial Proteome Database (MPD) has been conceived as an in‐house resource for complementing the plethora of genomic databases available for such organisms. The database utilises commercially available software to provide an electronic ‘lab book’ of information obtained daily from 2‐D electrophoresis gels, image analysis packages, protein characterisation methodologies, and biological experimentation. The MPD begins from a single 2‐D gel image (a 2‐D ‘reference map’) with clickable spots that link to a ‘protein catalogue’ (ProtCat) with spot information including protein identity, changes in expression determined under experimental conditions, cellular location, mass, and p I . The entry for each protein then contains further links to gel images corresponding to the presence of the particular protein within different subproteomes (as defined by the pH of narrow‐ and wide‐range immobilised pH gradients or from differential extraction methods used to determine the location of the protein within a functional cell). The database currently contains information from strains of three microbial species ( Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus ) and 32 master gel images. The rapid accessibility of information obtained from microbial proteomes is an essential step towards the integrated analysis of these organisms at the gene, transcript, protein and functional levels and will aid in reducing turnaround times between sample preparation and the discovery of molecules of biological significance.