Exercise has enormous therapeutic benefits for individuals with a range of metabolic diseases. Understanding the mechanisms of these effects promises a range of novel therapeutic approaches for the treatment of these diseases. We recently performed a comprehensive analysis of the phosphoproteome in response to exercise in human muscle. This led to the identification of more than 1000 changes in protein phosphorylation in response to acute high intensity exercise. Only 10% of these phosphorylation sites had a predicted upstream kinase. As expected, AMPK was activated in response to exercise in human muscle, as indicated by phosphorylation of its known substrates including ACC and TBC1D1. We employed a number of additional mass spectrometry approaches in combination with machine learning to identify novel AMPK substrates. One such novel exercise regulated AMPK substrate was the mitochondrial scaffold protein AKAP1. We are currently investigating the role of AMPK dependent AKAP1 phosphorylation in vivo. This will likely reveal novel cross talk between the AMPK and PKA regulatory pathways in regulating mitochondrial metabolism.