Abstract: Novel approaches for the qualitative and quantitative proteomics analysis by nanoscale LC/MS was applied to the study of protein expression respond in organ transplant. In this experiment nanoUPLC Q-TOF-based LC-MS/MS platforms was evaluated for shotgun proteomics by compare the protein level after the liver transplant between Sprague Dawley(SD) and Wistar. A brand new technology label-free LC/MS called MSe^TM from a nanoUPLC and Q-TOF (Waters) was applied attempt to establish a scientific model to for the liver transplant between Sprague Dawley(SD) and Wistar. The result is most of the protein found in the model are up-regulated between the 3 days sample and the 7 days sample after transplant. The novel LC/MS technology provides a fast and reliable research platform in the modeling of transplant proteomic research, provides the opportunities for discovery of new potential biomarkers.