PNNL

Abstract

We present Monte Carlo simulations of collisionally activated dissociation of noncovalent protein complexes in the collision cell of a triple quadrupole mass spectrometer. These simulations account for the influence of the precursor ion mass-to-charge ration, acceleration potential, nature of the collision gas and the number of collisions experienced by the ion on the efficiency of ion dissociation. Evolution of the translational and internal energies of activated precursor ions along the collision cell was simulated using the hard-sphere and diffuse scattering models. Dissociation rate constants and ion survival probability were calculated based on the estimated internal energy content of the excited ion. It was found that dissociation of the precursor ion could occur anywhere in the collision cell provided there is enough gain of relative internal energy accumulated during collisions. Simulated dissociation curves are in a good agreement with experimental results obtained for different collision gases at different pressures. Monte Carlo simulations of collision events modeled by the hard-sphere and diffuse scattering approximations resulted in different dynamics of precursor ion dissociation. Comparison of Monte Carlo simulations with results obtained using the previously proposed collision model showed a good correlation between the integral results obtained using these two approaches over a variety of experimental parameters. However, in contrast to the collision model, Monte Carlo simulations allow to obtain detained information on the dynamics of ion dissociation in the collision cell. Moreover, Monte Carlo simulations provided a first insight into collisionally activated dissociation of the precursor ion under unfolding conditions including realistic increase in collision cross section during ion passage through the collision cell.