Interaction Proteomics

Interaction Proteomics facilitates the study of protein-protein interactions (PPIs). Dysregulation and inappropriate activation of protein complexes are associated with several diseases, including cancer. These interactions play a vital role in cellular processes and fundamental biological insights can be gained by studying networks of interacting proteins rather than individual proteins.

We use the Affinity Purification-Mass Spectrometry (AP-MS) platform to study protein interactions and complexes. AP-MS combines the specificity of antibody based protein purification with the sensitivity of mass spectrometry to identify and quantify putative interacting proteins. Either native antibody or an epitope-tagging approach may be used to purify protein complexes. In the epitope-tagging approach, a recombinant epitope-tagged bait protein of interest is expressed in cultured cells, and then the bait protein and associated proteins are then retrieved using an antibody against the epitope, followed by identification of prey proteins using mass-spectrometry. The mass-spectrometry data is analyzed and scoring metrics applied to identify those proteins that are specific to the bait of interest. AP-MS enables protein networks and complexes to be studied at the proteomic scale and it can be anticipated that the knowledge gained from such projects will fuel drug target discovery and prove indispensable to the emerging field of systems biology.


  • Can provide functional information based on the function of proteins that are interacting with the bait
  • Provides information about protein molecular environment
  • Can help reconstruct pathways


  • Up-front effort in constructing epitope-tagged baits
  • Care must be taken to exclude non specific or promiscuously-binding proteins

Contact Person

Janna Kiselar, Ph.D.
Case Center for Proteomics and Bioinformatics
Case Western Reserve University
10900 Euclid Avenue, BRB 947 Cleveland, Ohio 44106
phone: 216-368-0979
fax: 216-368-6846

Interaction Proteomics Review

Berggård, T., et al. Methods for the detection and analysis of protein-protein interactions., Proteomics. 2007. 7:2833-2842. doi: 10.1002/pmic.200700131

Center Paper

Saha, S., et al. Computational Framework for Analysis of Prey-Prey Associations in Interaction Proteomics Identifies Novel Human Protein-Protein Interactions and Networks., J. Proteome Res. 2012. doi: 10.1021/pr300227y

Dazard J-E, Saha S., Ewing R.M. ROCS: A Reproducibility Index and Confidence Score for Interaction Proteomics Studies. BMC Bioinformatics (2012) 13(1):128.