Surface-Enhanced Laser Desorption/Ionization (SELDI) ProteinChip® system is the new technology for the screening of biomarkers. This system is most fitting as an analysis system of sample obtained from patient since sample that it needs is very small amount.In the present experiment, we analyzed sera obtained from ovarian cancer patients in order to detect novel ovarian cancer markers and to establish the new diagnosis for ovarian caner. Sera of normal women and patients were analyzed by four types of chemical surfaces chip, which are hydrophobic (reverse phase chromatography), cationic (weak cation exchange), anionic (strong anion exchange) and IMAC (metal affinity chromatography) chip. In the preliminary protein differential display against two normal versus six patients, significant difference of protein expression were detected in analysis used three types of chemical chip, such as hydrophobic, cationic and IMAC chip. Therefore, we analyzed sera of sixty normal women and fifty two patients using these three chips. From the results of protein differential display in each chips, we detected many protein peaks that might be ovarian cancer marker. In the next step, four decision trees for diagnosis of ovarian cancer were constructed by the applied tree-based method by CART (Classification and Regression Trees) using the results of protein differential display in each chips. From results of the significant test for the decision tree constructed in the present experiment, it was suggested that each decision tree were the decision tree that did not pass over ovarian cancer patient.
