Method for removal of endotoxin from protein preparations using core-shell nanoparticles, which have the ability to selectively adsorb endotoxin molecules in a protein mixture. The method comprises the steps of (a) preparing a plurality of core-shell nanoparticles; (b) adding the core-shell nanoparticles into a protein preparation containing endotoxin; (c) incubating the core-shell nanoparticles with the protein preparation for a period of time; and (d) separating nanoparticles from the protein preparation.