Protein complexes can be isolated by several different approaches.  For example, a protein can be tagged with an epitope such as Flag or TAP and then overexpressed in a target cell, allowing the interacting proteins to be purified.  Similarly, epitope tags can be homologously recombined into the endogenous locus ("knocked-in"), allowing protein complexes containing the tagged proteins to be isolated at their natural expression level.

Protocol: Overview of Affinity Purification in Combination with Mass Spectrometry Protocol