Gas and ion transport in the capillary-skimmer subatmospheric interface of a mass spectrometer, which is typically utilized to separate unevaporated micro-droplets from ions, was studied numerically using a two-step approach spanning multiple gas dynamic regimes. The gas flow in the heated capillary and in the interface was determined by solving numerically the Navier-Stokes equation. The capillary-to-skimmer gas/ion flow was modeled through the solution of the full Boltzmann equation with a force term. The force term, together with calculated aerodynamic drag, determined the ion motion in the gap between the capillary and skimmer. Three-dimensional modeling of the impact of the voltage applied to the Einzel lens on the transmission of doubly charged peptide ions through the skimmer orifice was compared with experimental data obtained in the companion study. Good agreement between measured and computed signals was observed. The numerical results indicate that as many as 75% of the ions that exit from the capillary are lost on the conical surface of the skimmer or capillary outer surface because of the electrostatic force and plume divergence.
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