We are performing small and large scale 2-D gel electrophoresis (IEF coupled with SDS-PAGE) for protein separation and quantification of relative protein abundances.
2-D PAGE is particularly suitable for differentially displaying the protein complements (up to ca. 1500 protein spots per sample) of two or more related samples such as disease vs healthy, time course experiments etc. Absolute or quantitative differences between samples are usually excised from the gel and processed for mass spectrometric protein identification by MALDI-TOF/TOF-MS.
Proteins are usually visualise by in-gel detection either with fluorescent dyes or colloidal coomassie. Both staining methods are compatible with downstream mass spectrometric protein identification. Modified protocols for silver staining can also be used. However, silver staining is less compatible with downstream mass spectrometry.