Aspects of the disclosure relate to methods of purifying complexes comprising a protein (e.g., antibody) covalently linked to an oligonucleotide. In some embodiments, complexes comprising a protein covalently linked to an oligonucleotide are purified and isolated from unlinked oligonucleotide using an mixed-mode resin that comprises positively-charged metal sites and negatively charged ionic sites, e.g., hydroxyapatite resin. In some embodiments, complexes comprising a protein covalently linked to an oligonucleotide are purified from a mixture comprising the complexes, unlinked protein, and unlinked oligonucleotide using a purification step involving hydrophobic interaction chromatography resin followed by a purification step involving mixed-mode resin.