Characterization of Highly Specific Protein Complexes
A major effort within the core service component of the Laboratory of Proteomics and Analytical Technologies (LPAT) is to identify protein-protein interactions using LC-MS/MS. Since any protein interaction identified using MS requires validation, it is imperative that the results provided by LPAT have a high probability of being validated. The success of any protein interaction study is highly dependent on the isolation of the protein complex. Leveraging the experience gained over the years, the LPAT instituted a program to:
i. Consult with NCI investigators who request assistance in isolating protein complexes.
ii. Develop technologies to decrease the number and abundance of non-specific proteins being isolated within a protein complex.
Previously the LPAT’s primary role in characterizing protein complexes was fractionation and MS analysis. While this model works well for some investigators, others required assistance in extracting specific protein complexes for MS analysis. The lab instituted a program to assist NCI investigators in protein complex isolation with the goal of maximizing the success rate of positive validation for proposed protein interactions. The LPAT also assists NCI investigators in validating the MS results through techniques such as co-IP or immunofluorescence.