Methods for making a site-specific modification of a glycoprotein are provided which preserve the charge and glycoform of the glycoprotein. One or more glycans are trimmed from the glycoprotein, while keeping a core glycan attached to the glycoprotein. The removal of the one or more glycans provides access to a targeted amino acid for a site-specific reaction. The attached core glycan can optionally be utilized for modulation of the glycoprotein, or one or more glycans or reagents can be attached to the core.