The “Invisible Proteome”: How to Capture the Low-Abundance Proteins Via Combinatorial Ligand Libraries

Pier   Giorgio   Righetti; Egisto      Boschetti; Bernard      Monsarrat

Abstract

Despite recent advances in pre-fractionation procedures and depletion methods via immuno-subtraction protocols of the most abundant species, the “low-abundance” proteome remains largely undetected. We report here a novel technology, called ProteoMiner, for bringing to the limelight this vast pool of low-abundance species, which could constitute > 50% of any proteome in any living organism. It consists of a combinatorial ligand library, composed of millions of diverse hexapeptide baits, able to capture and concentrate the “low-abundance” proteome, while drastically cutting the concentration of the most abundant compounds. Since no depletion of any species is contemplated by this methodology, but a drastic reduction of the sample dynamic range, the noxious phenomenon of co-depletion (especially troublesome in affinity depletion methods) does not occur. In addition to previously reported data on analysis of human sera and urines, we describe here novel applications for the detection of the low-abundance proteome in human blood cells, such as the red blood cells (RBC) and platelets and in biological fluids, such as cerebrospinal fluid. In particular, in the case of RBC, where hemoglobin alone constitutes ca. 98% of the total cytoplasmic proteome, the ProteoMiner technology allowed the detection of > 1500 proteins in the remaining 2% low-abundance cytoplasmic proteome, most of them not previously reported even in the most advanced investigations. The merits and limits of ProteMiner are discussed and evaluated.

Keywords: Ligand library, peptide ligands, rare proteome, platelets, red blood cells, cerebrospinal fluid, E. coli proteome, S.cerevisiae proteome