Exploring the role of p97 and its UBX-domain cofactors through identification of their interacting proteins.

The elucidation of protein-protein interaction networks can provide preliminary insights into the function of uncharacterized proteins based on the interactions they establish in the cell. Here, we describe a protein immunoprecipitation protocol that can be used in combination with mass spectrometry analysis to identify the p97 interactome as well as specific subgroups of proteins interacting with its UBX-domain adaptors. This approach aims to dissect the role played by individual UBX cofactors within the complex array of cellular functions performed by p97.