Tuberous sclerosis complex (TSC) is an autosomal dominant benign tumour syndrome caused by mutations to either the TSC1 or TSC2 tumour suppressor gene. The TSC1 and TSC2 gene products, TSC1 and TSC2, form a protein complex that integrates inputs from multiple signalling cascades to inactivate the small GTPase rheb, and thereby inhibit mTOR-dependent cell growth. We have used matrix-assisted laser desorption/ionisation time-of-flight and Fourier transform mass spectrometry to identify TSC1 and TSC2 phosphorylation sites and candidate TSC1 and TSC2 interacting proteins. We identified three sites of TSC2 phosphorylation and a novel site of TSC1 phosphorylation, and investigated the roles of these sites in regulating the activity of the TSC1-TSC2 complex. In addition, we identified three TSC1-TSC2 interacting proteins, including DOCK7 a putative rhebGEF.