BACKGROUND: Pancreatic cancer is one of the most common malignant tumors. Early diagnosis of pancreatic cancer is difficult because of the latent onset and lack of good biomarkers. This study aimed to look for and identify differentially expressed proteins in tissues of pancreatic cancer and adjacent noncancerous tissues by proteomic approaches so as to provide information about possible pancreatic cancer markers and therapeutic targets. METHODS: Proteins extracted front 3 paired adjacent noncancerous and cancerous pancreatic tissue specimens were separated by two-dimensional gel electrophoresis (2-DE). The protein spots exhibiting statistical alternations between the two groups through computerized image analysis were then identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In addition, Western blotting and immunohistochemistry were performed to verify the expression of certain candidate proteins. RESULTS: Twelve proteins were significantly upregulated and 4 were downregulated between cancerous and paired adjacent noncancerous pancreatic tissues. Several proteins (S100A11, Ig gamma-l chain C region, GSTO1 and peroxiredoxin 4) were found for the first time to be associated with pancreatic cancer. Differential expression of some identified proteins was further confirmed by Western blotting analysis and/or immunohistochemical analysis. CONCLUSIONS: Comparative proteomic analysis using 2-DE and MALDI-TOF-MS is an effective method for identifying differentially expressed proteins that may be the potential diagnostic biomarkers and therapeutic targets for pancreatic cancer.