Here we describe a chemical proteomics strategy using ATP acyl phosphates to measure the formation of a protein:protein complex between p38 alpha and mapkap kinases 2 and/or 3. Formation of the protein:protein complex results in a new probe labeling site on p38 alpha that can be used to quantify the extent of interaction in cell lysates and the equilibrium binding constant for the interaction in vitro. We demonstrate through RNA interference that the labeling site is dependent on formation of the protein:protein complex in cells. Further, we identify that active-site-directed, small-molecule inhibitors of MK2/3 selectively inhibit the heterodimer-dependent probe labeling, whereas p38 alpha inhibitors do not. These findings afford a new method to evaluate p38 alpha and MK2/3 inhibitors within native biological systems and a new tool for improved understanding of p38 alpha signaling pathways.