Pancreatic cancer (PC) is a devastating disease, with a mortality rate almost identical with its incidence. Biomarkers are desperately needed to improve earlier, more curable cancer diagnosis and to develop new effective therapeutic targets. In this study, differentially expressed proteins between PC and adjacent normal tissues from paired tissues of 9 patients were investigated by 2-DE coupled to MALDI-TOF/TOF mass spectrometry. 23 differentially expressed proteins were identified, 5 and 18 of which were up-regulated and down-regulated, respectively, including transcription regulators, signal transducers, antioxidant activity proteins, catalytic activity proteins and binding proteins. Carboxypeptidase B (CBPB1), trypsin-1 (TRY1) and peroxiredoxin-2 (PRDX2) were further confirmed by Western blot analysis. It is found that there is the significant difference for PRDX2 and TRY1 (p<0.05) compared with adjacent normal tissues. It should be noted that three proteins [lithostathine 1 beta (REG1B), serpin B6 (SPB6), glucagon (GLUC)] related to PC were first detected in this study, which may be potential biomarkers for the diagnosis and prognosis of patients with PC.