This study was undertaken to evaluate protein and lipid profiles of ovarian cancer tissue samples. Twenty-three frozen ovarian cancer samples and 6 adjacent normal samples were analyzed using histology-directed, matrix-assisted laser desorption/ionization mass spectrometry. Sinapinic acid and 2, 5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells to identify protein and lipid profiles respectively, and mass spectra were acquired using a matrix-assisted laser desorption/ionization-time of flight instrument. Protein and lipid profiles classify 11 cancer and 3 adjacent normal samples in 100 random test sets with 92.9% median accuracy. Phosphatidylcholines {32:3} [M + Na] (m/z = 750.66), {34:1} [M + K] (m/z = 798.60), and {36:2} [M + K] (m/z = 824.56) were found to be increased in ovarian cancer. Interestingly, breast cancer-associated changes in lipid and protein profiles were also found in ovarian cancer. Thus, protein and lipid profiles accurately distinguish ovarian cancer from adjacent normal tissue samples. Common cancer-associated alterations in lipid and protein profiles were identified between ovarian and breast cancers.