This dataset provides mole fractions of atmospheric trace gases measured by the Programmable Flask Package (PFP) Whole Air Sampler during airborne campaigns conducted by NASA's Atmospheric Tomography (ATom) mission. The PFP whole air sampler provides a means of automated or manual filling of glass flasks. The sampler is designed to remove excess water vapor from the sampled air and compress it without contamination into ~1-liter volumes. These flasks are analyzed at the NOAA's Global Monitoring Division laboratory for trace gases and at the INSTAR's Staple Isotope Lab laboratory for isotopes of methane. Analysis of standardized PFP samples can measure more than 60 trace gases including N2O, SF6, H2, CS2, OCS, CO2, CH4, CO, CFCs, HCFCs, HFCs, Solvents, Methyl Halides, Hydrocarbons and Perfluorocarbons. The ATom mission deployed 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 to 12 km altitude. Flights occurred in each of 4 seasons from 2016 to 2018.