The Double Focusing Mass Spectrometer DFMS embarked on the European Space Agency’s Rosetta mission as part of the ROSINA instrument suite. It boasts a high mass resolution and a high sensitivity, which have guaranteed spectacular discoveries during Rosetta’s rendez-vous with comet 67P/Churyumov-Gerasimenko. This paper describes the DFMS data calibration procedure for determining the parent and fragment ion count rates in the neutral mode, which serve as the basis for retrieving the neutral gas densities. A new approach to computing secondary electron yields is presented. Attention is given to an analysis of the mass peak shapes, which change with magnet temperature. Discrete counting statistical effects also affect the peak shape at low counts. If not accounted for, changes of mass peak shape can induce errors of up to 20% on the determination of the ion fluxes. An assessment of the different sources of uncertainty on the obtained count rates and ratios of count rates is presented.