As the field of proteomics expands, the need for functional annotation of the proteome increases to allow the rational choice of particular targets from amongst a bewildering and increasing set of candidates. Similarly, the description of the interactome will continue to generate a plethora of candidate interactions that will need to be validated in functional assays. Although knockout mice and RNAi knockdowns have proven to be invaluable as primary tools in functional genomics, it should be remembered that these techniques apply at the gene and transcript level respectively and are, therefore, not always suitable for true functional proteomics investigations. Protein levels do not always correlate with RNA levels, particularly where active protein levels are regulated by protein stability or post-translational modifications. Moreover, off-target regulation of genes by RNAi/siRNA can complicate the validation of targets using this approach. In recent years, a myriad of potential protein targets including complexes has been emerging from high-throughput proteomics. Thus, the dilemma facing many investigators is having too many potential targets and too few means of validating them. Therefore, there is an unmet need for the development of technologies which allow the targeted disruption of particular proteins. Intracellular antibodies (intrabodies) and peptide aptamers are beginning to be applied in this area. A new class of peptide, known as Phylomers^®, also has significant potential in the area of disruption of protein–protein interactions. Phylomers, which are derived from protein subdomains, are small enough to synthesise and are of a suitable size for delivery to tissues and even into cells, making them an ideal candidates for a next-generation tool for functional validation of the proteome.