Rarefied vacuum flows are commonly applied in production processes for semiconductors, particle physics experiments, fundamental physics studies, space aerothermodynamics, and many more applications. Any flow is said to rarefied when the length or time scales of the flow become comparable to the molecular length and time scales. The continuum assumption breaks down and a particle level modelling of fluid flows is necessary. The operating pressure of these rarefied flow processes spans a wide range of rarefaction ranging from mild to strong rarefaction. For gas mixtures in rarefied flow regimes, the mass separation effect occurs because each species exhibits a flow behaviour independent of the other species which depends on the molecular mass of the gas species. This leads to a difference in composition of rarefied gas mixtures when transported through channels, orifices, or valves. In gas transport applications, the mass separation effect needs to be accounted for in the flow calculations and design process. While this effect has been studied in detail for the continuum and free-molecular regimes, its characterisation for the transition regime lacks in-depth investigation. This research characterises the mass separation effect in transition flow regime by investigating its variation with Knudsen number for short micro channels. The numerical model employed is based on the Direct Simulation Monte Carlo (DSMC) method with suitable physical interaction models chosen for accuracy in transition regime. It is accompanied by the design of validation experiments to test the accuracy of the numerical solver. The results of this research are used to make new recommendations for industrial practices to approximate the mass separation effect in rarefied gas mixture flows.