Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a valuable tool for chemical imaging of surfaces and depth profiling. The main goal of the present work is to develop technique for chemical composition and structure characterization of core-shell quantum dots (QDs) by ToF-SIMS combined with sputter depth profiling. We report a method to acquire 6 nm CdSe/ZnS core-shell QDs depth profiles distinguishing core and shell layers. Obtained selenium and sulfur profiles correlate with core-shell structure characterized by transmission electron microscopy, X-ray diffraction and luminescence spectroscopy. Sample preparation for ToF-SIMS analysis involves accurate QDs deposition on thoroughly cleaned substrate surface, resulted in fairly flat topography and absence of significant aggregations verified by atomic force microscopy. We demonstrate capabilities of proposed technique for analysis of dopant atoms by establishing depth distribution of dopant atom inside Mn/ZnS/CdS quantum dots. Obtained results suggest that QDs do not melt under Cs+ or Bi3+ bombardment.