Sample preparation is the most crucial step in the proteome research of
microbes. 2D gel electrophoresis (2-DGE) is a high throughput approach by which all
proteins imprint on the gel in the form of spots or dots. Various protocols for the
extraction of proteins exist in the literatures that are compatible with 2-DGE based
proteome analysis from different microbes. Analysis of low abundance proteins, the
solubility of proteins, and their resolution on the gel are some major issues observed
with sample preparation and 2-DGE. To combat these issues, researchers have
developed improved versions of the existing protocols using detergent/chaotropes for
the enrichment of proteins during extraction along with the compatible chemical
precipitation for better resolution of 2D gel pattern. In this chapter, we will discuss the
overview, challenges encountered during the protein sample preparation, and their
possible solutions in order to get a better 2-D gel of microbial proteins.
Keywords: 2-DGE, Detergents, Microbial proteins, Protein sample preparation.
