We have previously reported the identification of three ovarian cancer biomarker panels comprised of SELDI-TOF peaks representing fourteen differentially expressed serum proteins for the diagnosis of early ovarian cancer. We now report the identification and characterization of four of the proteins from the ovarian cancer biomarker panels. Using a variety of methods, including pI analysis, peak depletion studies, serum to pure protein comparisons, anion exchange fractionation, tryptic peptide analysis and LC-MS-MS, we confirmed the identity of two proteins that represent the m/z peaks 13.8 and 78.9 kDa in our original ovarian cancer biomarker panels. Furthermore, using western analyses and ELISA techniques (independent of SELDI), we confirmed the differential expression of transthyretin (13.8 kDa, prealbumin) and transferrin (78.9kDa) in a group of 44 test ovarian cancer serum samples. With the identification of these markers, we are now developing simple assays for improved clinical diagnosis and prognosis of ovarian cancer.