Analysis of protein-protein interactions is one of the mainstays of mass spectrometry-based proteomics and recent developments, which have simplified the methodology, have permitted non-specialised laboratories to adopt the approach. We introduce and review three complimentary methods which allow for the targeted, global and site-specific analysis of protein complexes. Co-precipitation of endogenous or ectopically expressed proteins and their complexes followed by proteomic analysis allows for the discovery and accurate quantification of specific protein interactions. Whereas complimentary methods, such as co-purification of entire complexes based on physico-chemical attributes, can give a snap-shot of the composition and dynamics of protein complexes on a global scale. Cross-linking on the other hand can pinpoint the amino acids involved in protein-protein interactions to such a resolution that the likely complex can be reconstructed computationally.
Keywords: Co-elution; Co-purification; Cross-linking; Interaction proteomics; Protein complex.