Proper cellular functioning is dependent on the timely association of thousands of proteins in discrete complexes. A major challenge in the post genomic era is the elucidation of these diverse protein complexes and networks that govern mammalian cellular function and cell fate. Identification of the individual components of these arrangements is vital to the understanding of their function in biological processes. Currently, a widely used technique for the identification of protein complexes is a combinational approach of Tandem Affinity Purification coupled with Mass Spectrometry (TAP-MS). This technique was originally developed for the study of the yeast proteome but has since been adapted for studies of the mammalian system. This review discusses the applications of TAP-MS to the mammalian proteome. Our focus includes the technical improvements made in each step of the TAP-MS pipeline including vector design, delivery of the TAP construct into cells, expression of bait proteins, purification strategies and finally the identification of the protein complexes by mass spectrometry.