Primary biliary cholangitis is a chronic cholestatic liver disease characterized by the presence of serum antimitochondrial antibodies and immune-mediated destruction of the small and medium-sized intrahepatic bile ducts. However, the pathophysiology of primary biliary cholangitis has not yet been completely elucidated. In recent years, proteomics has been comprehensively applied in many research fields, including the pathogenesis, prognosis, and diagnosis of disease. Among multiple methods, isobaric tag for relative and absolute quantitation is a powerful analytic method to characterize complex protein mixtures in combination with liquid chromatography-tandem mass spectrometry. In this chapter, we describe a strategy for using isobaric tag for relative and absolute quantitation to discover those differentially expressed proteins in primary biliary cholangitis. The goal is to identify the differences in protein expression between patients with primary biliary cholangitis and healthy controls for defining biomarkers and elucidating molecular mechanisms underlying disease states.