In conclusion, we identified the bile proteins that were elevated in the extrahepatic CCA more than in the control group, who did not have a biliary disease, and the significantly increased proteins were immunoglobulin kappa light chain, apolipoprotein E, albumin, apolipoprotein A-I, antithrombin-III, α1-antitrypsin, serotransferrin, immunoglobulin heavy constant mu, immunoglobulin J chain, complement C4-A, and complement C3. The gene discussed is APOE; the disease is cholangiocarcinoma.