Aerosol time-of-flight mass spectrometry (ATOFMS) was used for characterizing the aerodynamic size and chemical composition of individual particles during the Atlanta Supersite Experiment in 1999. During certain time periods, increased numbers of particles scattered light but did not produce mass spectra. Upon comparison of the size-resolved unscaled particle counts from an aerosol time-of-flight mass spectrometer with those from a laser particle counter, the presence of a chemical bias became apparent in the single particle mass spectral measurements. Upon further analysis, it was determined that these events occurred during time periods of elevated ammonium and sulfate mass concentrations measured with semicontinuous particulate analysis instruments. The missed particle type occurred mostly in the smallest size range (0.35–0.54 μm) and correlated well with optical scattering measurements. As described herein, a scaling procedure is developed that allows one to account for the ATOFMS chemical bias. This procedure is tested by comparing the scaled ATOFMS data with multiple measurements from other techniques made during the 1999 Atlanta Supersite study. This is the second paper in a two-part series focusing on ATOFMS data collected during the Atlanta Supersite experiment in 1999 [Prather et al., 2002].