The ProteoMiner in the proteomic arena: A non-depleting tool for discovering low-abundance species

Combinatorial ligand libraries, composed by millions of hexapeptides, are here reviewed in terms of their ability of capturing the low-abundance proteome. First, the physico-chemical properties of such libraries are dealt with, especially in regard to the proper length of the bait. The capturing ability of single amino acids has been assessed demonstrating that there exist a protein adsorption capability dichotomy, by which 8 amino acids (Arg, Lys, His, Phe, Tyr, Trp, Val and Leu) are classified as interacting with a large number of proteins with all the remaining amino acids with limited capturing capabilities. The highest performance in capturing the largest possible population of proteins is offered by the three hydrophobic, aromatic amino acids, i.e. Phe, Tyr and Trp, suggesting that hydrophobic motifs are those responsible for the strongest, and most frequently occurring, interactions. By exploring baits ranging from single, individual amino acids, to di-, tri-, tetra- penta- and hexapeptides, it was demonstrated that the 6-mer baits are the ones with the most promising length for capturing the largest possible population of proteins and that probably longer lengths would hardly be needed. Some examples are given on the ability to explore the low-abundance proteome in two systems, notably chicken egg white and yolk. In both cases, by using the peptide library methodology, it is possible to detect at least twice as many protein species as compared to the best results obtained so far with the most advanced proteomics studies using highly sophisticated mass spectrometry tools.