Abstract: Objective: To screen differentially expressed proteins that relate to the invasive and metastatic potential. Methods: Nude mice were intraperitoneally injected with the human ovarian cancer cell line SKOV-3. The metastatic tumors were removed and cultured in vitro. When the cell lines were established they were transplanted intraperitoneally for several cycles. The invasive potential of cell lines was evaluated by cell electrophoresis and Matrigel invasion assay. The enhanced surface laser desorption ionizing-flight time-mass spectra (ELDI-TOF-MS) was applied to detect the cell disruption solution and the protein fingerprints were compared. Results: SKOV-3F3, a cell line established after repeated in vivo passage, showed more highly invasive capacity than the parental SKOV-3 line in cell electrophoresis and Matrigel invasion assays. Based on the proteomic fingerprint patterns, we found six differentially expressed proteins (6249, 14675, 15425, 15717, 17123 and 17660 at M/Z value) that were only expressed in SKOV-3. On the contrary, three distinct proteins (4355, 4823 and 5763 at M/Z value) were only expressed in SKOV-3F3. Furthermore, two differentially expressed proteins (1842 and 3145 at M/Z value) could only be detected in SKOV-3F1, SKOV-3F2 and SKOV-3F3. Five proteins (1242, 5465, 6899, 6568 and 14027 at M/Z value) were expressed in all SKOV-3, SKOV-3F1, SKOV-3F2 and SKOV-3F3 cell lines, but their abundance was different. Conclusion: These proteins expressed differentially between SKOV-3 and SKOV-3F3 are correlated with high invasive and metastatic potential. The identification of these proteins will help to clarify the invasion and metastasis mechanisms of ovarian cancer.