Tankyrase 1 (TNKS1) and tankyrase 2 (TNKS2) belong to the poly(ADP-ribose) polymerase (PARP) family of proteins, which use NAD+ to modify substrate proteins with ADP-ribose modifications. Tankyrases are implicated involving in multiple cellular functions, including the telomere length control, Wnt/b-catenin pathway regulation, glucose uptake and cell cycle regulation. Emerging evidences reveal the pathological relevance of tankyrase in diseases and propose these two key enzymes as potential drug targets. However, the cellular functions and regulatory machineries of tankyrases are still largely unknown. Through this proteomic analysis, we not only defined the protein-protein interaction map for the tankyrases which revealed 100~150 high confident interacting proteins for tankyrases in various cellular functions, but also uncovered the novel regulating function of tankyrase in peroxisome homeostasis.