Mass spectrometers that rely on microchannel plate (MCP) detectors age when they are used intensively. The ageing process is due to a reduction of the MCP gain as ions repeatedly bombard the MCP, leading to a reduction of the secondary electron yield of an impacting ion and to a reduction of the electron amplification within the MCP pores. MCP gain therefore is both time- and position-dependent. This is particularly true for the Double Focusing Mass Spectrometer DFMS, part of the ROSINA instrument, embarked on the European Space Agency's Rosetta spacecraft that studied comet 67P/Churyumov-Gerasimenko continuously for over more than 2 years. A position-dependent gain correction technique is developed here. A detailed assessment of the technique demonstrates that improper treatment of this position-dependent gain can lead to misleading results and false conclusions, especially regarding less abundant species whose mass peak signature overlaps with peaks of abundant species. The correction technique presented here avoids such problems, especially in the situation where detector ageing is significant and uneven across the detector. It is also able to explain why all recorded mass peaks have a nearly symmetric double Gaussian shape, despite the strong variations in the position-dependent gain.