The Mars Organic Molecule Analyzer (MOMA) is a miniature ion trap mass spectrometer designed for the upcoming ExoMars Rover mission. The spectrometer uses laser desorption to ionize a Martian soil sample within an instrument internal clean zone maintained at ambient Martian pressure. A high-speed aperture valve transiently opens to allow ionized constituents, along with the ambient gas, to enter a vacuum cavity containing a linear ion trap mass spectrometer. The ambient clean zone and the vacuum cavity are connected via a few centimeter long aperture valve ion guide tube. In this paper, we present results from a recently completed numerical investigation of ion transport from the ion source across the ion guide. Specifically, we focus on collisional coupling between ions and the neutral molecules flowing into the vacuum cavity. The simulation domain contains the ambient region, and we consider the variation in ion conductance with ambient pressure. We also analyze the impact of a fixed potential bias applied to the aperture valve. Simulations are performed with a two-dimensional axisymmetric PIC / DSMC code Starfish. Numerical results are compared to experimental data.