A method of pulsing gas in a quadrupole ion trap to reduce excess internal energy of ions formed externally to the trap at high-vacuum conditions by laser desoprtion is disclosed. With pulsed gas introduction, pressures greater than those under which traps are normally operated can be achieved over a few milliseconds. Under these elevated pressure transients, the process of translational cooling is accelerated and ions undergo thermalized collisions before dissociation occurs. Minimization of uncontrolled fragmentation (thermalization) and enhanced sensitivity are observed at pressures exceeding a threshold of about 1 mTorr.