ANALYSIS OF PROSTATE CANCER BY PROTEOMICS USING TISSUE SPECIMENS

ABSTRACTPurpose: Prostate cancer cells differ from their normal counterpart in gene expression. Therefore, cancer and normal tissue/cells would show differences in their proteomes. From a diagnostic standpoint differences in the composition of secreted protein species are especially relevant. We used ProteinChip Array (Ciphergen Biosystems, Fremont, California) surface enhanced laser desorption/ionization (SELDI) time of flight mass spectrometry to profile prostate tissue samples to generate phenomic fingerprints. We used quantitative proteomics based on glycopeptide capture followed by tandem mass spectrometry to identify differentially expressed proteins.Materials and Methods: Patient matched cancer and noncancer specimens were digested by collagenase to single cells. After digestion the cells were pelleted and the cell-free supernatant was used for analysis. A reversed phase hydrophobic ProteinChip Array was used to generate SELDI patterns from 43 primary prostate tumors, including 26 with matched nonc...