Here we describe the design and performance of a new water cluster chemical ionization-atmospheric pressure interface time-of-flight mass spectrometer (CI-APi-TOF). The instrument selectively measures trace gases with high proton affinity such as ammonia and dimethylamine, which are important for atmospheric new particle formation and growth. Following the instrument description and characterization, we demonstrate successful measurements at the CERN CLOUD (Cosmics Leaving OUtdoor Droplets) chamber where very low ammonia background levels of ∼4 pptv were achieved (at 278 K and 80 % RH). The limit of detection of the water cluster CI-APi-TOF is estimated to be ∼0.5 pptv for ammonia. Although no direct calibration was performed for dimethylamine (DMA), we estimate its detection limit is at least 3 times lower. Due to the short ion-molecule reaction time and high reagent ion concentrations, ammonia mixing ratios up to at least 10 ppbv can be measured with the instrument without significant reagent ion depletion. Besides the possibility to measure compounds like ammonia and amines (dimethylamine), we demonstrate that the ionization scheme is also suitable for the measurement of trace gases containing iodine. During CLOUD experiments to investigate the formation of new particles from I₂, many different iodine-containing species were identified with the water cluster CI-APi-TOF. The compounds included iodic acid and neutral molecular clusters containing up to four iodine atoms. However, the molecular structures of the iodine-containing clusters are ambiguous due to the presence of an unknown number of water molecules. The quantification of iodic acid (HIO₃) mixing ratios is performed from an intercomparison with a nitrate CI-APi-TOF. Using this method the detection limit for HIO₃ can be estimated as 0.007 pptv. In addition to presenting our measurements obtained at the CLOUD chamber, we discuss the applicability of the water cluster Ci-APi-TOF for atmospheric measurements.