Scirpus triqueter has been reported to be an effective phytoremediation plant for pyrene dissipation. The study of S. triqueter in response to pyrene is crucial to understand the mechanism of phytoremediation. To gain a certain extent understanding of S. triqueter in response to pyrene, S. triqueter seedlings were exposed to 50 mg kg(-1) pyrene and a comparative proteomic analysis of total proteins was performed. 37 and 55 proteins were significantly differentially expressed in the shoot and root of S. triqueter upon exposure, respectively. 24 proteins (17 proteins in shoot and 7 proteins in root) were identified on the basis of the homology of their peptide profiles with existing protein sequences using mass spectrometry analysis. Analysis of protein expression patterns revealed that proteins in shoot associated with photosynthesis, defense, energy and matter metabolism, coenzyme metabolism and protein metabolism. Moreover, the proteins related photosynthesis accounted for more than 70% of the identified proteins. The proteins in root associated with stress, defense, energy metabolism, protein modification and carbohydrate metabolism. Pyrene appears to have an important deleterious effect on primary carbon metabolism, the synthesis of proteins and signal transduction. The present study demonstrates the use of proteomic approach to help us understand the phytoremediation mechanism of S. triqueter. (C) 2013 Elsevier B.V. All rights reserved.