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Predictive simulations of mixed plasma discharges, like deuterium-tritium plasmas, rely on self-consistent models for particle transport. These models have to be validated with interpretive analysis of existing experiments. Accounting for uncertainties in the particle balance equation is important for modelling of mixed-plasma discharges because simulation results are directly affected by plasma composition. JET deuterium and mixed hydrogen-deuterium plasma discharges heated by neutral beams only are analysed with the TRANSP code. Influence of prescribed quantities and terms entering into the particle balance equation is quantitatively assessed on the computed plasma parameters, in particular on the neutron rate and the plasma energy. Large uncertainties in the prescribed ion temperature, plasma rotation and impurity content might result in a noticeable over- or underestimate of the computed neutron rate. A significant difference in the time evolution of the measured and computed neutron rate is observed in the interpretive simulations if same diffusivity for electrons and thermal ions is assumed. Increased thermal deuterium ion transport is required to reach agreement with the plasma composition measured at the plasma edge and the measured neutron rate. Thermal ion density computed with the particle balance equation is mostly affected by the ion outflux term.