Affinity pull-downs are one of the most common types of experiments performed in the laboratory. Combining such experiments with MS can be challenging but it is a very powerful approach for studying protein interactions.
Leverage the power of SILAC to discriminate real hits from
contaminants in your co-IP experiments.
Don’t have a good antibody to your protein? Express a GFP-tagged fusion, then perform a SILAC co-IP.
Proximity proteomics: complementary to co-IPs, detect proteins within a radius of your protein of interest.
Perform an unlabelled IP then compare with a list of common known contaminants to identify true hits.