The molecular dynamics (MD) simulation technique has been applied to investigate fundamental aspects of matrix-assisted laser desorption. In this paper, we focus on direct comparisons of the results from the simulations with experimental data and on establishing links between the measured or calculated parameters and the basic mechanisms of molecular ejection. The results on the fluence dependence of the ablation/desorption yields and composition of the ejected plume are compared with mass spectrometry and trapping plate experiments. Implications of the prediction of a fluence threshold for ablation are discussed. The strongly forward-peaked velocity and angular distributions of matrix and analyte molecules, predicted in the simulations, are related to the experimental distributions. The shapes and amplitudes of the acoustic waves transmitted from the absorption region through the irradiated sample are compared to recent photoacoustic measurements and related to the ejection mechanisms. The conformational changes during plume evolution and the ejection velocities of analyte molecules are studied and the directions for future investigations are discussed. Finally, we demonstrate that the MD simulation technique can be used to model other processes relevant to mass spectrometry applications, such as laser disintegration of aerosol particles and laser ablation in the presence of photochemical reactions.