Hi, I would suggest you to go on with the FLAG peptide based elution. It is usually very efficient and results in a cleaner elution, in the sense that you will only have your protein bait with the interactors, avoinding the presence of the contaminants, that will remain on the beads. I gentle shake the beads for 45 minutes at 4 °C with at least 3 beads volume of a eleution solution supplemented with 500 ng/ul of flag peptide. Then, if the volume is too much to be loaded on a SDS-PAGE gel, I concentrate the eluted proteins with amicon centrifugal filter till a convenient volume and then I add the loading buffer. If you have any further question, I'm glad to help you. Good luck.

i'm planning to do this as well. so far I can tell you that I tried to elute my FLAG tagged protein with 0,2% TFA (1h incubation on rotary wheel RT) and I was not successful as all the protein remained stuck to the beads. I will try other agents for elution, but if you manage to elute the protein by manipulating salt concentration, please share your experience;)

Thanks to Giuseppe and Malgorzata for sharing your experiences and advice. I think I will try both methods of elution. I will share my experience with either methods. I agree with Giuseppe that using the FLAG peptide would specifically release the tagged protein and its interactors.