This dataset provides the mixing ratios of reactive nitrogen and halogen species measured by the NOAA Iodide Ion Time-of-Flight Chemical Ionization Mass Spectrometer (NOAA CIMS) during airborne campaigns conducted by NASA's Atmospheric Tomography (ATom) mission for ATom-3 and ATom-4 campaigns. The NOAA CIMS uses chemical ionization mass spectrometric detection of gas phase organic and inorganic analytes via I- adduct formation. Measurements for ATom include N2O5 (dinitrogen pentoxide), ClNO2 (chloro nitrite), Cl2 (Chlorine), HCOOH (formic acid), C2H4O3S (hydroperoxymethyl thioformate), BrCl (bromine monochloride), BrCN (cyanogen bromide), and BrO (bromine monoxide). ATom deploys an extensive gas and aerosol payload on the NASA DC-8 aircraft for systematic, global-scale sampling of the atmosphere, profiling continuously from 0.2-13 km altitude. This comprehensive dataset will be used to improve the representation of chemically reactive gases and short-lived climate forcers in global models of atmospheric chemistry and climate.