Anti-HA affinity matrix contains a covalently immobilized anti-HA monoclonal antibody, so a protocol designed for use with it should also work with your anti-HA antibody, as long as it does not interfere with the non-covalent binding of the antibody to the beads.

It sounds like the worst of the denaturants (NaOH and TCA) are removed before the immunoprecipitation, leaving only 0.4% SDS. Try to find out from the manufacturer of the immunoprecipitation beads whether this much SDS interferes with antibody binding to the beads.

Thanks for your suggestion. My beads can be used in buffer containing 1% SDS according to manufacturer sheet. I will give a try then :)

You might be better off not having the commercial anti-HA resin since it usually doesn't work well due to low antibody density.  I'm not sure if you actually have the anti-HA antibody or plan to purchase it and then plan to either immobilize it or to do the antigen binding and then capture the complex with Protein A or G?