Affinity Purification Combined with Mass Spectrometry-Based Proteomic Strategy to Study Mammalian Protein Complex and Protein-Protein Interactions

The versatile affinity purification techniques for isolating mammalian protein complex in combination with mass spectrometry-based proteomics are powerful to decipher the characters of the associated binding partners within a protein complex and protein-protein interactions. One single epitope-tag affinity purification for purifying protein complex is variable and limited in protein purity and specificity for a different individual bait protein. Recently, several newly developed tandem affinity purification (TAP) systems have been applied to isolate the native protein complexes with high purity and specificity at close to physiological levels in mammalian cells, furthermore a novel quantitative MAP (mixing after purification)-SILAC (stable isotope labeling with amino acids in cell culture)-based mass spectrometric technique integrated with affinity purification effectively investigates weak associated partners as well as deciphers specific and dynamic protein-protein interactions.