Strategies for analysis of electrophoretically separated proteins and peptides Review Article

Electrophoresis methodology is unsurpassed in separating individual proteins and peptides from a mixture and is regarded by the majority of protein biochemists as the methodology of choice. Proteins can be eluted into solution or electroblotted onto a membrane and subjected to direct sequencing, amino acid composition and post-translational modification analyses. Applications of highly reproducible 2D electrophoresis, “in-gel” and “on-blot” fragmentation procedures, high sensitivity N-terminal sequencing and a variety of mass spectrometric methods (post-source decay MALDI–MS, LC–ESI MS/MS and CE–MS) provide invaluable tools for characterisation of recombinant proteins and identification and characterisation of unknown proteins. In this article we overview strategies employed in recent years for analysis of proteins and peptides separated by various electrophoretic techniques. Methodological approach used in characterisation of proteins from a newly emerged virus is presented as an example of an effective strategy.