The present disclosure provides methods of analyzing and/or purifying inorganic nanoparticles that may be functionalized with one or more dye group. Analyzing and/or purifying the inorganic nanoparticles includes utilizing liquid chromatography, such as, for example, high performance liquid chromatography (HPLC). Methods of the present disclosure may be used to determine the location of one or more dye groups on and/or in the inorganic nanoparticles. The present disclosure also provides methods of making inorganic nanoparticles and compositions of inorganic nanoparticles.