MS co-IP experiments are more powerful when combined with SILAC because this allows discrimination of true interactors from contaminants. Sometimes however, you may wish to analyse unlabelled co-IP samples. Our dedicated proteomics experts are happy to advise.
In MS analyses of co-IP samples, environmental contaminants and cell proteins that bind the beads usually make up most of the identifications.
SILAC co-IPs allow discrimination between true interactors and contaminants. If, however, SILAC labelling is not feasible in your particular case (for practical or budgetary reasons, or simply because you already have performed the experiment), we can still analyse your samples by MS.
Although unlabelled pair-wise comparison between target- and control IPs is difficult, contaminants identification can be improved based on known common bead proteomes and on predicted in-sample interactions.
We recommend using more stringent IP conditions for this than for SILAC co-IPs. Replicate experiments – as well as performing the IP again using a different type of beads – can greatly improve confidence in the results.
If you are interested in a protein’s interaction partners, also consider using BioID proximity-proteomics assay as a complementary approach to co-IPs.