Affinity Proteomics covers all approaches where affinity reagents, such as antibodies and other capturing proteins are utilized within a proteomic perspective. This could for example be in a biomarker discovery context where various types of protein microarray setups are being utilized or where the affinity reagents are coupled to various mass spectrometric assays or being utilized for fractionation, depletion and purification purposes. As well as the impact of affinity proteomics technology on the biotech, biomedical and pharmaceutical industries. Two interacting molecules form the cognate groups of an affinity capture system One group is the protein of interest or an affinity tag appended to the protein of interest via genetic engineering, resulting in expression of a tagged fusion protein within a model organism. The other group is usually an antibody recognizing the target protein directly or through an affinity tag, although any molecule that exhibits high affinity and specificity for the target protein may be used; when that molecule is coupled to an insoluble medium, the resulting reagent (affinity medium) can bind and immobilize the target protein. Hence, for affinity capture an affinity medium is used to specifically enrich a target protein from bulk cell extract, and under appropriate conditions endogenous interacting partners are co-purified. Such samples can then be subjected to mass spectrometry (MS)-based analyses, forming the bases of physical and functional interactomic hypotheses.
A major benefit of the commonly used tags is the availability of high quality, high specificity, widely validated antibodies for affinity capture, independent of the target protein. Additionally, the epitope is usually known, providing the potential for competitive native elution of protein complexes from the affinity medium, and generally heterologous, so it is not involved in the target protein's interactome. Hence, tagging is often advantageous even when so-called IP-competent antibodies are available due to cost savings, practicality, improvement in the quality of obtained results, and consistency between different tagged proteins. However, antibodies against the native protein are useful for validating tagged expression constructs vs their endogenous counterparts.