Research Of Identification Of Serum Biomarkers For Colorectal Cancer By Surface Enhanced Laser Desorption/Ionization-Time Of Flight-Mass Spectrometry And Empirical Proteomics Ontology Knowledge Base

ObjectiveThe incidence of colorectal cancer has become the third in all of the cancer nowdays in our country.about one third of these patients are in late stage when the colorectal cancer were diagnosised . there are still no effective serum marker to diagnosis the colorectal cancer. The development of proteomics opened a new window for tumor research. Tumor cell will certainly produce proteome which is different to health adults when it grows. If this proteome is found and analyzed correctly, a new method for carcinoma diagnosis will come into being. Surface enhanced laser desorption/ionization- time of flight- mass spectrometry (SELDI-TOF-MS), which emerged in the beginning of 1990, is a new kind of proteomic technology. The proteinchip has been exploited based on this technique, and the chip can bind all kinds of proteins in the sample. When the chip is bombarded by laser in the mass spectrometer, all the binded proteins will be stimulated and gasified into ions. Because ions have variant mass charge ratio(M/Z), they have variant time of flight. So the reception equipment can distinguish variant proteins by their mass charge ratio. It allows for protein profiling from a variety of complex biological materials such as serum, urine and cell lysates with limited sample preparation. But there are still some disadvantages in the technique of SELDI.the most important is that we couldn't get the protein directely ,what we get from the SELDI is only the mass charge ratio(M/Z). if we want to know which protein the mass charge ratio(M/Z) presents,wemust use two-dimensional electrophoresis , mass spectra and other techniques.The department of Biomedical Informatics in the University of Pittsburgh established the Empirical Proteomics Ontology Knowledge Base ,which make the will that find the protein only by the mass charge ratio(M/Z) comes true . the objective of this study is discover the serum protein marker by method of Surface Enhanced Laser Desorption/Ionization- Time of Flight- Mass Spectrometry combined with Empirical Proteomics Ontology Knowledge Base and estimated the feasibility of this method.MethodsProteomic spectra of 169 serum samples from colorectal carcinoma and 83 from health adults were generated by IMAC30 proteinchip array and SELDI-TOF-MS. The discriminatory profiling was analyzed by Biomarker Wizard software and Biomarker Pattern software. The classification tree mode was set up by cross-verification. Searching the protein with distinction in Empirical Proteomics Ontology Knowledge Base(http://www.dbmi.pitt.edu/EPO-KB) and verificated it with the method of ELISA .ResultsWe find the value of the protein in m/z 7778Da up-regulated in colorectal cancer patients. The sensitivity and specificity are 69.2% and 77.1% in the diagnosis of colorectal cancer. The protein is identified as PF4 by Searching of the Knowledge Base . The sensitivity and specificity are 61.1% and 76.9% in the diagnosis of colorectal cancer by ELISA with PF4 up-regulated in colorectal cancer patients.the result is familiar with what the SELDI-TOF-MS gets.ConclusionWith the up-regulation in colorectal cancer patients, PF4 chould become a new biomarker to identify the colorectal cancer. The method of Surface Enhanced Laser Desorption/Ionization-Time of Flight-Mass Spectrometry combined with Empirical Proteomics Ontology Knowledge Base is feasible.