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A system for fast ammonia (NH<sub>3</sub>) measurements with chemical ionisation mass spectrometry (CIMS) based on a commercial Proton Transfer Reaction-Mass Spectrometer (PTR-MS) is presented. It uses electron transfer reaction as ionisation pathway and features a drift tube of polyetheretherketone (PEEK) and silica-coated steel. Heating the instrumental inlet and the drift tube to 180 °C enabled an effective time resolution of ~1 s and made it possible to apply the instrument for eddy covariance (EC) measurements. EC fluxes of NH<sub>3</sub> were measured over two agricultural fields in Oensingen, Switzerland, following fertilisations with cattle slurry. Air was aspirated close to a sonic anemometer at a flow of 100 STP L min<sup>−1</sup> and was directed through a 23 m long 1/2" PFA tube heated to 150 °C to an air-conditioned trailer where the gas was sub-sampled from the large bypass stream. This setup minimised damping of fast NH<sub>3</sub> concentration changes between the sampling point and the actual measurement. High-frequency attenuation loss of the NH<sub>3</sub> fluxes of 20 to 40% was quantified and corrected for using an empirical ogive method. The instrumental NH<sub>3</sub> background signal showed a minor interference with H<sub>2</sub>O which was characterised in the laboratory. The resulting correction of the NH<sub>3</sub> flux after slurry spreading was less than 1‰. The flux detection limit of the EC system was about 5 ng m<sup>−2</sup> s<sup>−1</sup> while the accuracy of individual flux measurements was estimated 16% for the high-flux regime during these experiments. The NH<sub>3</sub> emissions after broad spreading of the slurry showed an initial maximum of 150 μg m<sup>−2</sup> s<sup>−1</sup> with a fast decline in the following hours.