Enhance Proteomic Detection Limitation by Combinatorial Peptide and Nucleotide Library

Abstract

In most biological sample, the few high abundant proteins are usually composed to 95% of overall content. Although there are many methodologies for depletion of high abundant protein, unfortunately many defects still occur. For example, the immunodepletion method by antibody also removes other low abundant proteins that bind the depleted species simultaneously. Here, we provide a new method to reduce the dynamic range of complex biological samples by aptamer and peptide library. The heptapeptide library is composed of 7 random amino acids, and the aptamer library is also composed of 25 random sequences. Both libraries have sufficient diversity to match a ligand to every protein in complex biological sample. Therefore, according to the saturation-overloading principle, an abundant protein will saturate all its available ligands and leave the majority of the same protein unbound. After binding the library, the concentration range of complex sample will decrease and the low abundant proteins will be enriched by the library on the beads. In 1D and 2D PAGE experiments, we show that both peptide and aptamer libraries can remove high abundant protein, and consequently enrich low abundant protein. Following by the analysis of LTQ-Orbitrap mass spectrometry in the future, we may identify more low abundant proteins by the combinatorial peptide and nucleotide library depletion technology.