Affinity-purification mass spectrometry (AP-MS) of serine/threonine phosphatases

Association of serine/threonine phosphatases with regulatory proteins is a key component of their specificity, and the identification of these binding partners is critical to understanding phosphatases function and regulation. Affinity-purification/mass spectrometry (AP-MS) approaches have been and continue to be instrumental in identifying these interactors. Here, we review the general principles of AP-MS, and present two affinity-purification protocols compatible with subsequent mass spectrometry, namely FLAG purification, and the tandem affinity purification (TAP). We have successfully used these protocols for the identification of binding partners for PP2A, PP4 and PP6, and they should be amenable to the analysis of interactors for other phosphatases.