We provide an algorithm that introduces excited states into the molecular dynamics study of mass spectra. To decide the contributions of different electronic states, the ionization cross section associated with relevant molecular orbitals were calculated by the Binary-Encounter-Bethe (BEB) model. The effect of active space choice was evaluated with urocanic acid as an example, and larger active space sizes were shown to improve predictions of relative intensities in the mass spectrum, leading to overall better spectral accuracies. The 70 eV mass spectra of several intermediates from the histidine pathway were also calculated and these results indicate that excited state corrections can provide 75% more true positive ions(in both in-silico and experimental spectra) in average. The fast orthogonalization model/single and double state configuration interaction (OM2/CISD) method is used to implement these corrections. Overall, accounting for excited states in molecular dynamics simulations can supplement ground state simulations, leading to improved predictions to 726 dot product similarity score of 70eV electron ionization spectra of organic molecules.