About
Affinity Purification Mass Spectrometry (AP-MS) is the method of choice to study protein-protein interactions (PPI) and complexes under near physiological conditions. A protein of interest – the bait – is purified by either a bait specific antibody or an affinity reagent specific for an epitope tag fused to the bait protein. Like in co-immunoprecipitation (co-IP) western blot experiments, AP-MS relies on the principle that under native lysis conditions, protein complexes remain largely intact and associated proteins (prey) purify together with the bait protein. The digested peptides of purified complexes are analyzed by shotgun LC-MS/MS and the compiled data of all purification experiments can be assembled to identify the specific interactors.
