In a tandem mass spectrometer means are provided for molecular activation of ions prior to fragmentation. An embodiment of a tandem mass spectrometer comprises a first collision cell receiving analyte ions having an internal energy and a second collision cell situated downstream from the first collision cell wherein the first collision cell increases the internal energy of the analyte ions prior to entry of the ions into the second collision cell, the increase in internal energy imparted in the first collision cell alone being insufficient to fragment a substantial portion of the analyte ions. Another embodiment includes a collision cell with a heating device situated adjacent to the collision cell for controlling the temperature within the collision cell.