The technique of combinatorial peptide ligand libraries (CPLL), for capturing and amplifying low-abundance proteins in r-DNA products as well as in a number of other biological systems, is here analyzed in depth and reviewed. This methodology is based on a creation of several millions of bio-specific ligands composed of hexapeptides produced in a combinatorial way. When acting on an overloading and saturation principle, high-abundance species are captured in limited amounts, whereas low-abundance ones keep being concentrated on their bio-specific ligand till substantial harvesting from solution (the capture process occurring in general from ca. 50% up to 90% efficiency). Examples are given on tracking host-cell impurities present in, e.g., recombinant albumin or monoclonal antibodies. Additionally, other examples of detecting traces of additives and fining agents in such beverages as white and red wines are presented. The unique mechanisms underlying the protein capture in the CPLL methodology, as opposed to capture by homogeneous beads, as represented by ion-exchangers and by hydrophobic resins, are discussed in depth.