<p>Chemical ionization mass spectrometers (CIMS) routinely detect hundreds of oxidized organic compounds in the atmosphere. A major limitation of these instruments is the uncertainty in their sensitivity to many of the detected ions. We describe the development of a new high-resolution time-of-flight chemical ionization mass spectrometer that operates in one of two ionization modes: using either ammonium ion ligand switching reactions as NH<sub>4</sub><sup>+</sup>-CIMS or proton transfer reactions as PTR-MS. Switching between the modes can be done within two minutes. The NH<sub>4</sub><sup>+</sup>-CIMS mode of the new instrument has sensitivities of up to 67 000 dcps ppbv<sup>−1</sup> (duty cycle corrected ion counts per second/parts per billion by volume) and detection limits between 1 and 60 pptv at 2σ for a 1s integration time for numerous oxygenated volatile organic compounds. We present a mass spectrometric voltage scanning procedure based on collision-induced dissociation that allows us to determine the stability of ammonium-organic ions detected by the NH<sub>4</sub><sup>+</sup>-CIMS. Using this procedure, we can effectively constrain the sensitivity of the ammonia chemical ionization mass-spectrometer to a wide range of detected oxidized volatile organic compounds for which no calibration standards exist. We demonstrate the application of this procedure by quantifying the composition of secondary organic aerosols in a series of laboratory experiments.</p>