The present invention provides a method for purifying a protein complex and the components comprising the complex from a cell, a cell or tissue lysate or a whole organism by employing a combined set of affinity tags of high affinity, specificity and ease of elution. The method involves using a protein or a peptide modified to contain one or more affinity tags separated by one or more specific protease cleavage sites to isolate any interacting proteins or fragments thereof. Specifically exemplified is a method employing a modified bait containing AviTag or GST and a removal tag of His6 hexapeptide positioned proximal to the bait such that any excess bait can be efficiently removed from the purified complex yielding enriched interacting proteins prior to subjecting the complex for further identification of individual components. The identification of the proteins or fragments thereof contained in the protein complex will provide new targets for the identification of new pharmaceuticals and diagnostic tools.