The dissociation kinetics of a small biological molecule, leucine enkephalin (LE), are examined using a Quadruple Ion Trap Mass Spectrometer in order to determine the effect of activation waveform on ion effective temperature (Teff). The effective temperature is found to have a linear relationship with the applied activation amplitude. The dissociation kinetics of LE are found to be greatly affected by pressure in the mass spectrometer, showing faster dissociation at lower pressures. The effects of other experimental parameters, including the temperature of the inlet capillary and sensitivity to the frequency of the activation waveform, are also explored. Calibration of Teff as a function of activation waveform will provide a way to obtain Arrhenius activation parameters (activation energy and frequency factor) for other biological
molecules and lead to better understand of their intrinsic properties.