Methods for detecting the presence of nanoparticles or microparticles by cell mass spectrometry (CMS) are provided. CMS methods are provided for determining the number of nanoparticles or microparticles in each cell. Nanoparticles whose intracellular concentration can be determines by the CMS methods of the invention include polymeric nanoparticles (NPs), liposomes, viral-based NPs, carbon nanotubes, diamond NPs, polymeric micelles, nanocarriers, liposomes, and viral nanoparticles. Determination of the efficiency of drug delivery and intracellular titer of pathogens according to the invention is disclosed. Methods for determining intracellular uptake of virus particles are provided.