Troubleshooting Table
PROBLEM	SOLUTION
Step 7 It is difficult to accurately and reproducibly pipet resin.	When pipetting resin from a stock tube to other tubes, keep a uniform slurry by frequently (but gently) flicking the bottom of the tube. Do not vortex the resin. In addition, because agarose-based beads will stick to the plastic pipet tip during transfer it is best to ‘precoat’ a pipet tip with resin before using the tip to transfer resin to multiple tubes. This is done by sucking up a desired volume of resin slurry from the stock tube into a pipet tip and ejecting the solution back into the same tube.
Step 12 We observe high background binding of target protein to control beads.	For some target proteins, background binding to beads can be decreased by increasing the NaCl or NP-40 concentration in the binding reaction or wash buffer.
Step 17 Immobilized bait protein and target protein are degraded during micrococcal nuclease treatment.	It is possible that proteases contaminating the protein preparations will degrade the bait and target proteins because of the higher temperature used for micrococcal nuclease treatment. If this occurs, additional protease inhibitors can be added to the TGMC(0.1) buffer.
Step 20 An anticipated interaction is not observed.	The amount of bait protein immobilized on the beads and the length of the incubation time can be increased to facilitate the detection of weak interactions.