Aerosol proteinaceous matter is comprised of a substantial fraction of bioaerosols. Its origins and interactions in the atmosphere remain poorly understood. We present observations of total proteins, combined, and free amino acids (CAAs and FAAs) in fine particulate matter (PM2.5) samples in urban Beijing before and during the 2014 Asia-Pacific Economic Cooperation (APEC) summit. The decreases in proteins, CAAs and FAAs levels were observed after the implementation of restrictive emission controls. Significant changes were observed for the composition profiles in FAAs with the predominance of valine before the APEC and glycine during the APEC, respectively. These variations could be attributed to the influence of sources, atmospheric processes, and meteorological conditions. FAAs (especially valine and glycine) were suggested to be released by the degradation of high molecular weight proteins/polypeptides by atmospheric oxidants (i.e., ozone and free radicals) and nitrogen dioxide. Besides daytime reactions, nighttime chemistry was found to play an important role in the atmospheric formation of valine during the nights, suggesting the possible influence of NO3 radicals. Our findings provide new insights into the significant impacts of atmospheric oxidation capacity on the occurrence and transformation of aerosol proteinaceous matter which may affect its environmental, climate and health effects.