I'm trying to precipitate my protein of interest from total cell lysate, along with interacting proteins, so that they are visible on silver stained gels. The problem is that I am getting a lot of nonspecific bands sticking to control IPs (beads alone or with nonrelated antibody).
I have tried preclearing, and using higher ultracentrifugation, which have improved the stain a bit, but still too many nonspecific bands. Any suggestions? I'm about to try washing with different salt concentrations (usually use lysis buffer with 1% triton and 150mM NaCl).