One of the fundamental challenges in proteome analysis is the fact that samples are often dominated by a relatively small number of high-abundance proteins whose presence can obscure less abundant proteins and limit the capacity and resolution of the separation technique employed. Samples are therefore often treated to remove high-abundance proteins. ProteoMiner™ protein enrichment is a novel technology which uses a bead-based library of combinatorial peptide ligands, which act as unique binders for proteins. When a complex sample is applied to the beads, high-abundance proteins will saturate their specific ligands and excess protein will be washed away. Low-abundance proteins will be concentrated on their specific ligands and following elution, the low-abundance proteins will be enriched relative to the high-abundance proteins.

ProteoMiner protein enrichment has been most extensively applied to serum and plasma, and the commercially available kit has been optimized for these samples. However, one of the main potential strengths of the ProteoMiner technique is its lack of intrinsic specificity for any particular sample type. ProteoMiner can in theory be used to decrease high-abundance proteins in any sample that could benefit from such a treatment. Cell- or tissue-derived samples can differ widely in protein concentration, protein abundance distribution and the presence of interfering substances. The basic method therefore needs to be tailored somewhat for each sample type. Progress in developing methods for applying ProteoMiner to diverse sample types will be presented.