AIM: To separate and identify differentially expressed nuclearmatrix proteins (NMPs) between the immortalized humanesophageal epithelial cell line (SHEE) and the malignantlytransformed esophageal carcinoma cell line (SHEEC), andto provide new ways for finding specific markers and thepathogenesis of esophageal carcinoma.METHODS: SHEE and SHEEC cell lines were used to extractNMPs. The quality of NMPs was monitored by Western blotanalysis including DNA topoisomerase II, proliferation cellnuclear antigen (PCNA) and histone. NMPs of SHEE andSHEEC were analyzed by two-dimensional electrophoresis(2-DE), silver staining and PDQuest6.2 image analysissoftware. Three spots in which the differentially expressedNMPs were more obvious, were selected and analyzed withmatrix-assisted laser desorption/ionization time of flying massspectrometry (MALDI- TOF-MS) and database search.RESULTS: Western blot analysis revealed that DNAtopoisomerase IIand PCNA were detected, and the majorityof histones were deleted in NMPs of SHEE and SHEEC. After2-DE image analysis by PDQuest6.2 software, the 2-DE mapswere detected with an average of 106±7.1 spots in SHEE and132±5.0 spots in SHEEC. Most of them were matched oneanother (r=0.72), only 16 protein spots were found differingin intensity. Three NMPs including cytoskeletal tropomyosin,FK506-binding protein 6, similar to retinoblastoma bindingprotein 8 were preliminarily identified by MALDI- TOF-MS.CONCLUSION: These differentially expressed NMPs mayplay an important role during malignant transformation fromSHEE to SHEEC. Their separation and identification willcontribute to searching for specific markers and probing intothe pathogenesis of esophageal carcinoma.