Protein bioinformatics
Experiments done in a real laboratory need to be complemented by virtual experiments done on computer.
In addition to the software packages for analysing the electrophoretic separation, bioinformatic tools have been developed. Some of these are available via the internet with links to many provided from the ExPASy proteomics server (www.expasy.ch/www/tools.html).
These allow not only identification of proteins but further characterisation ranging from the calculation of basic physicochemical properties to the prediction of potential post-translational modifications and three-dimensional structures. Annotated protein and two-dimensional electrophoresis databases are the bioinformatic core of proteome research. SWISS-PROT is a typical example of such an annotated database.
Immersion in the proteomic world and its data flood...
Many proteome projects are now underway, resulting in the generation of two-dimensional electrophoresis databases that are accessible on the internet (many can be accessed via links from the ExPASy server at www.expasy.ch) and can be browsed with interactive software and integrated with in-house results. These databases include protein maps of human plasma, urine, cerebrospinal fluid, and tissues such as breast, heart, and bladder transitional-cell and squamous-cell carcinomas, as well as various microorganisms. Ultimately, given the dynamic nature of the proteome, complex experimental details and related results should be displayed with the relevant biochemical pathways or disease implications highlighted.
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Relative references
Sequences and topology- Genome and proteome informatics
Identifying the proteome- software tools
Database searching with mass-spectrometric information
Making predictions about the proteome
Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
Databases and knowledge resources for proteomics research
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