The TAP (Tandem Affinity Purification) method is an affinity purification method for the isolation of TAP-tagged proteins along with associated proteins. The TAP tag historically consists of a calmodulin binding peptide (CPB), a tobacco etch virus (TEV) protease cleavage site, and Protein A. However, additional tag combinations have been used with the TAP method including the combination of FLAG tags and HA tags. The TAP method permits the identification of proteins interacting with a particular target protein without any prior knowledge about the function, activity, or composition of the interacting proteins. The TAP tag has been especially useful and deployed with Yeast Tap-tagged ORF clones. These clones contain genomic fusions of the TAP construct and are extremely useful for determining natural protein interactions and expression level variations based on physiological changes.