Try immobilizing one protein of your interest (say CD99) on a polystyrene bead, and then incubate these beads with a fluorescently labeled second protein (CD88). You can also try other way round. Then run these beads for bead-associated fluorescence by flow cytometer for assessing protein-protein binding.

Alternatively, people have described FRET based techniques and you can look into couple of those

Article A Flow Cytometry-Based FRET Assay to Identify and Analyse Pr...

Article Automated nanoscale flow cytometry for assessing protein-pro...

Hi, the easy way is to fo the co-IP and run the native gel and western blot, the antibody works for flow should be OK for the western blot (since the protein is transferred from native gel).

You can go for flowcytometry for it. You will be able to find unbound single signal as well as interacted double signals. So you would be able to find % interaction.

I would go for flow cytometry. I would isolate the protein for which you do not have an antibody. U can purify using his tag. Just treat the cells with the isolated protein and immuno stain the protein on the membrane.. The protein that has bound to the target would appear as a low intensity population.. Make sure u have proper controls like cells stained with out ab treatment.

Hi,

As commented above, I also recommend using flow cytometry. There are differences in the signals of bound and unbound proteins. Remember to do a control experiment.

Flow is best ASSUMING that you have the appropriate negative controls and do titrations.