Exercise is a powerful stimulus to increase energy metabolism, especially in the exercising muscles. If repeated, exercise training can treat and prevent numerous chronic conditions like obesity and metabolic disorders. When exercise is initiated, many biological processes are regulated, and a plethora of signaling pathways are affected, primarily via the rapid regulation of protein phosphorylation. Many factors contribute to the cellular response following exercise, including exercise intensity, but a thorough investigation of the regulated phosphoproteome following different exercise intensities has not been performed. In recovery from an acute bout of exercise, insulin sensitivity is enhanced in the previously active muscles. However, in the recovery period from whole-body exercise, the concentration of plasma FAs increases if no food is ingested, and the concomitant increase in plasma FA concentration may dampen the insulin-sensitizing effect post-exercise. This regulation is suggested to take place by the pyruvate dehydrogenase complex (PDC), which controls the conversion of pyruvate derived from glycolysis to acetyl-CoA. Dichloroacetate (DCA), a pharmacological activator of PDC, was used to elucidate whether PDC plays an important regulatory role in post-exercise insulin sensitivity. Thus, this thesis has a dual aim. First, to elucidate the phosphoproteome regulated following three different exercise modalities (endurance, sprint, and resistance). Second, to investigate the role of PDC in lipid-induced decreased insulin sensitivity post-exercise. In study I, a comparative analysis of the regulated phosphoproteome acutely after or three hours in recovery from endurance, sprint, or resistance exercise, identified modality-specific regulation, especially in recovery where 1, 2904, and 687 phosphorylation sites were regulated in endurance, sprint, and resistance, respectively. Immediately post-exercise, 420 phosphosites were regulated in all three modalities, which comprised the canonical exercise phosphoproteome. The phosphoproteins containing the most regulated phosphosites were implicated in acetyl-CoA and glycogen metabolism. However, only ~6% of the canonical phosphoproteome have been functionally characterized. In study II, one-legged knee extension exercise was used to investigate whether the exercise-induced increase in insulin-stimulated glucose uptake in skeletal muscle may be inhibited due to a high plasma FA concentration post-exercise and if so, to elucidate the mechanisms behind it. It was revealed that insulin sensitivity was decreased in a previously exercised leg when plasma FA concentration was raised to levels as observed following whole-body exercise. Furthermore, it was shown by the use of the pharmacological PDC-activator DCA that PDC plays an important regulatory role in post-exercise skeletal muscle insulin sensitivity. In conclusion, protein phosphorylation is regulated in a modality-specific and temporal manner, and only a small fraction of the molecular events have been characterized. By using a comparative approach of three different exercise modalities and pathway and kinome analysis, a ranking of important phosphorylation sites for future experiments has been performed. Further, PDC activation was shown to prevent lipid-induced insulin resistance post-exercise, presenting PDC as an important link between lipid and glucose metabolism and a regulator of skeletal muscle insulin sensitivity postexercise.