Methods are described for producing non-immunogenic nanoparticles from protein sources by controlling the pH in a nanoprecipitation process. The nanoparticles that are produced by the disclosed methods range in diameter size from about 100 ran to about 400 nm, with a preferred diameter size of from approximately 100 nm to approximately 300 nm, thereby rendering them non-immunogenic. The invention further discloses methods for producing nanoconjugates that are suitable for a variety of therapeutic, diagnostic and other uses.