Protocol for pull-down capture of ubiquitinated and NEDDylated liver proteins from transgenic biotinylated ubiquitin and NEDD8 mice

Ubiquitination and NEDDylation post-translational modifications (PTMs) are important regulatory mechanisms in liver disease. Here, we describe a protocol for capturing ubiquitinated and NEDDylated proteins by pull-down assay in liver samples from transgenic mouse models of whole-body biotinylated ubiquitin/NEDD8. We describe steps for sample preparation samples, protein immobilization, pull-down assay, and sample final elution. The identification of the hepatic ubiquitome and NEDDylome allows a better understanding of the pathophysiological mechanisms underlying liver disease. For complete details on the use and execution of this protocol, please refer to Gil-Pitarch et al.¹.