Combinatorial Peptide Ligand Libraries as a “Trojan Horse” in Deep Discovery Proteomics

A review. The present review covers the latest developments of the combinatorial peptide ligand library (CPLL) methodol., a very useful tool for detection of low-​abundance proteins in proteomes of any origin. Originally available as a library of millions of hexa-​peptides, all terminating with a free amino group, it was further modified via succinylation to carry a terminal carboxyl, for a larger capture of species. Operating CPLLs at 3 different pH values also allows a better capture, since the ionic surface charge is modulated on both the baits and the ligand proteins. Elution of captured species in boiling 2-​4​% SDS also permits quant. recovery of bound material, whereas any other eluant is largely insufficient for this purpose. Finally, by performing the capture either at very low ionic strength (thus favoring ionic interactions) or in presence of lyotropic salts (up to 1 M, to force hydrophobic interactions)​, while maintaining the other two types of capture, namely at acidic and alk. pH values, one can use the CPLL technol. as a multi-​dimensional tool for max. coverage of proteomes.