Protein Fractionation and Enrichment Prior to Proteomics Sample Preparation

Proteins may be considered as polypeptides large enough to have a well-defined tertiary, or three-dimensional structure. In aqueous media, this structure is typically one in which polar and charged amino acid residues are on the surface while hydrophobic residues tend to be sequestered in the core and reasonably inaccessible to the aqueous environment. Proteins that are not normally found free in aqueous media, such as membrane proteins and apolipoproteins, can have tertiary structures that deviate from this model. In general, the biological activity of proteins requires the preservation of their tertiary structure, and this sets more limits upon the chromatography than is true of peptides. In proteomics, the concern is with which proteins are present and in what quantity rather than maintaining biological activity. Such applications are freer to use mobile and stationary phases that denature protein structure. However, considerations of solubility and recovery may still set more limits on the chromatography than is the case with peptides.