We describe the University of Colorado mobile Solar Occultation Flux instrument (CU mobile SOF). The instrument consists of a digital mobile solar tracker that is coupled to a Fourier Transform Spectrometer (FTS, 0.5 cm<sup>−1</sup> resolution), and a UV-Visible Spectrometer (UV-Vis, 0.55 nm resolution). The instrument is used to simultaneously measure the absorption of ammonia (NH<sub>3</sub>), ethane (C<sub>2</sub>H<sub>6</sub>), and nitrogen dioxide (NO<sub>2</sub>) along the direct solar beam from a moving laboratory. These direct sun observations provide high photon flux and enable measurements of vertical column densities (VCDs) with geometric air mass factors, high temporal (2 sec) and spatial (5–19 m) resolution. It is shown that the instrument line shape (ILS) of the FTS is independent of the azimuth and elevation angle pointing of the solar tracker. Further, collocated measurements next to a high resolution FTS at the National Center for Atmospheric Research (HR-NCAR-FTS) show that the CU mobile SOF measurements of NH<sub>3</sub> and C<sub>2</sub>H<sub>6</sub> are precise and accurate; the VCD error at high signal to noise is 2–7 %. During the Front Range Air Pollution and Photochemistry Experiment (FRAPPE, 21 July–3 September 2014) in Colorado, the CU mobile SOF instrument measured median (maximum, minimum) VCDs of 4.3 (45, 0.5) x 10<sup>16</sup> molecules/cm<sup>2</sup> NH<sub>3</sub>, 0.30 (2.23, 0.06) x 10<sup>16</sup> molecules/cm<sup>2</sup> NO<sub>2</sub>, and 3.5 (7.7, 1.5) x 10<sup>16</sup> molecules/cm<sup>2</sup> C<sub>2</sub>H<sub>6</sub>. All gases were detected in larger 95 % of the spectra recorded in urban, semi-polluted rural and remote rural areas of the Colorado Front Range. We calculate structure functions based on VCDs, which describe the variability of a gas column over distance, and find the largest variability for NH<sub>3</sub>. The structure functions suggest that currently available satellites resolve about 10 % of the observed NH<sub>3</sub> and NO<sub>2</sub> VCD variability in the study area. We further quantify the trace gas emission fluxes of NH<sub>3</sub> and C<sub>2</sub>H<sub>6</sub> and production rates of NO<sub>2</sub> from concentrated animal feeding operations (CAFO) using the mass balance method, i.e., the closed-loop vector integral of the VCD times wind speed along the drive track. Excellent reproducibility is found for NH<sub>3</sub> fluxes, and to a lesser extent also NO<sub>2</sub> production rates on two consecutive days; for C<sub>2</sub>H<sub>6</sub> the fluxes are affected by variable upwind conditions. Average emission factors were 12.0 and 11.4 gNH<sub>3</sub>/hr/head at 30 °C for feedlots with a combined capacity for ~ 54,000 cattle, and a dairy farm of ~ 7400 cattle; the pooled rate of 11.8 ± 2.0 gNH<sub>3</sub>/hr/head is compatible with the upper range of literature values. At this emission rate the NH<sub>3</sub> source from cattle in Weld County, CO (535,766 cattle) could be underestimated by a factor of 2–10. CAFO soils are found to be a significant source of NO<sub>x</sub>. The NO<sub>x</sub> source accounts for ~ 1.2 % of the N-flux in NH<sub>3</sub>, and has the potential to add ~ 10 % to the overall NO<sub>x</sub> emissions in Weld County, and double the NO<sub>x</sub> source in remote areas. This potential of CAFO to influence ambient NO<sub>x</sub> concentrations on the regional scale is relevant because O<sub>3</sub> formation is NO<sub>x</sub> sensitive in the Colorado Front Range. Emissions of NH<sub>3</sub> and NO<sub>x</sub> are relevant for the photochemical O<sub>3</sub> and secondary aerosol formation.