Bioinformatics and In Silico 2D Gel Electrophoresis

Abstract

Proteins can be separated in a 2-D gel based on protein isoelectric point (pI) and molecular weight (MW), and the more abundant proteins will manifest themselves with a larger and darker dots in the gel than less abundant proteins. Because protein pI and MW can be easily calculated, and protein abundance can be approximated by predicted translation efficiency, we can do in silico 2-D gel and compare the separation pattern against that in the empirical 2-D gel. Differences between the two suggest post-translational modifications. The approach of in silico 2-D gel is detailed in this chapter.