Mass spectrometers are valuable tools for the in situ characterization of gaseous exo- and atmospheres and have been operated at various bodies in space. Typical measurements derive the elemental composition, relative abundances, and isotopic ratios of the examined environment. To sample tenuous gas environments around comets, icy moons, and the exosphere of Mercury, efficient instrument designs with high sensitivity are mandatory while the contamination by the spacecraft and the sensor itself should be kept as low as possible. With the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA), designed to characterize the coma of comet 67P/Churyumov-Gerasimenko, we were able to quantify the effects of spacecraft contamination on such measurements. By means of 3D computational modeling of a helium leak in the thruster pressurization tubing that was detected during the cruise phase we examine the physics involved leading to the measurements of contamination. 3 types of contamination can be distinguished: i) Compounds from the decomposition of the spacecraft material. ii) Contamination from thruster firing during maneuvers. iii) Adsorption and desorption of the sampled environment on and from the spacecraft. We show that even after more than ten years in space the effects of i) are still detectable by ROSINA and impose an important constraint on the lower limit of gas number densities one can examine by means of mass spectrometry. Effects from ii) act on much shorter time scales and can be avoided or minimized by proper mission planning and data analysis afterwards. iii) is the most difficult effect to quantify as it changes over time and finally carries the fingerprint of the sampled environment which makes prior calibration not possible. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.