Abstract: The mass spectrometry method was established for analysis of differentially expressed protein in human serum after liver transplantation with immunosuppressive agent. The proteins in serum before and after liver transplantation were separated by two-dimensional gel electrophoresis with silver staining, the differentially expressed proteins on the gel were digested with surfactant Rapigest SF and trypsin and then identified by nanoUPLC-ESI-MS/MS. In the experiment, 9 differentially expressed protein spots were identified clearly, corresponding to 8 different proteins. It was found that differentially expressed proteins are mostly related to immune regulation and liver disease, and it may provide clues for the in-depth study the anti-rejection effect of immunosuppressive agent after liver transplantation.