*Purpose: To a large extent the success of liver transplantation depends on quality of allografts. The molecular basis of the susceptibility of different liver allografts to transplant injury remains undefined. We investigated the proteomic alterations in liver grafts of different qualities by isobaric Tags for Relative and Absolute Quantification (iTRAQ).

*Methods: Transplanted liver samples were collected and divided into three groups: the optimal graft (OG) group, early allograft dysfunction (EAD) group, and primary nonfunction (PNF) group. Comparative quantitative proteomic analysis and multiple reaction monitoring (MRM) verification was performed. Samples from human IRI model were collected for further investigation at three different time points during liver transplantation.

*Results: A total of 6505 proteins were preliminarily identified in human liver. Specific proteins associated with IRI were identified by comparing the 3 groups at three different time points. In the IRI phase, more than 160 expressed differentially proteins were detected in the PNF group, compared to 54 and 36 proteins in the EAD and OG groups respectively. However, they are 56:52:22 at the cold preservation stage. There are 22 and 17 commonly differentially expressed proteins at IRI phase and cold preservation stage respectively in 3 groups. Among them Liver-type fatty acid-binding protein (L-FABP) and F10A1 are differentially expressed during two liver injury time points. The tissue expression of L-FABP is negatively correlated and the serum levels of L-FABP is positively correlated with the degree of IRI.

*Conclusions: The molecular basis of the susceptibility of different liver allografts to transplant injury is very complicated and we have made preliminary explorations and proved the biomarkers related to IRI.

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