Why would I choose to biotinylate rather than immunoprecipitate to determine protein-protein interactions? I am trying to determine if two proteins in one cell interact in a pathway. Which process would provide higher specificity?
in your case, I personally prefer biotinylate. and would suggest chemical crosslinkage.
I think it depends on how good your antibody is and hopefully not too expensive. With immunoprecipitation, you can often retrieve your natively folded protein/antigen for downstream functional studies. Sometimes with crosslinking methods, you are covalently modifying your protein which may cause concern that binding to other proteins is imparied.