8.2 Expasy proteomics tools

A proteome is the collection of all the proteins within a given organism, in the same way a genome is the collection of all the genes within a givenorganism. A proteome has some characteristics that are quite different from a genome, however. A principal difference is the fact that while a particularorganism will have the same set of identical DNA in any undamaged, healthy cell throughout its lifetime, the organism's proteins will differ greatly from onetissue to another, and from one life stage to another. Furthermore, proteins commonly incur a variety of chemical modifications after they are made.These modifications are critical for proper protein functioning and/or regulation, and moreover, these modifications cannot be determined withcertainty by looking at the DNA sequence alone. In a contempary high-throughput proteomics laboratory, the number of proteins identified and analyzed in oneday can be on the order of hundreds.

The term“proteome”was originally coined by an Australian scientist, Mark Wilkins (1), to describe the "PROTEin complement of the genOME". The term "proteomics" is used relatively loosely to describe any and all of thecollection of high throughput techniques that have emerged to enable the scientist to analyze all the proteins expressed under a certain set ofconditions within an individual cell or organism. The ExPASy (Expert Protein Analysis System) website (2), Swiss Institute of Bioinformatics, offers the definition that"proteomics can be defined as the qualitative and quantitative comparison of proteomes under different conditions to further unravel biological processes."

Common techniques for identifying the proteins within a proteome are 2D-PAGE (polyacrylamide gel electrophoresis) gels, amino acid (AA) composition analysis,peptide mass fingerprinting and other mass spectroscopy applications. A good starting point for becoming acquainted with 2D gels is the 2D PAGE tutorial offered by the Institute of Biological Sciences, University of Wales at Aberystwyth. ExPASy offers a good synopsis of peptide mass fingerprinting and AA composition analysis techniques, for those who are unfamiliar with these methods.

At the ExPASy Proteomics Tools server , the first category of tools are for protein identification and characterization. Take a look at the tools listedin this section. These tools are designed to identify the proteins that make up the proteome of study, using the data received from gels, AA analysis andmass spectroscopy experiments.