I overexpressed a FLAG-tagged protein in HEK293T cells, performed co-IP with anti-FLAG M2 beads, and attempted elution with 3×FLAG peptide, but the yield was very low. I suspect oligomerization may cause avidity effects that make peptide elution inefficient. I am considering inserting a protease cleavage site to release the protein from the resin, but I also want to preserve its native conformation for downstream cross-linking reaction.