My two proteins are membrane proteins, and I tagged them with myc and GFP, respectively. If I use total protein, I couldn't pull down each other. However, if I use membrane fraction and IP use the same condition, I can pull down the negative control as well. I already tried different systems like, GFP trap, Ab290 with Dynabeads, and the Miltenyi Biotec GFP, or Miltenyi Biotec myc. The results were the same.