Abstract: According to aspects of methods of characterizing a population of particles putatively containing recombinant nucleic acids in a fluid sample of the present disclosure, includes extracting nucleic acids from the particles, labeling the extracted recombinant nucleic acids, separating the labeled nucleic acids by size, and comparing the separated labeled nucleic acids with a standard to determine one or more of: 1) a ratio of full viral particles to empty viral particles in the fluid sample, 2) a ratio of full viral particles or empty viral particles to partially full viral particles, and 3) a ratio of viral particles containing an intact recombinant genome to viral particles containing an incomplete recombinant genome, thereby characterizing the population of particles in the fluid sample. Optionally included are extracting proteins from the particles, labeling the extracted proteins, separating the labeled proteins according to size, and comparing the separated labeled proteins with a standard.