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Mass spectrometry meets chip technology: A new proteomic tool in cancer research?

DNA chip technologies are the most exiting genomic tools, which were developed within the last few years. It is, however, evident that knowledge of the gene sequence or the quantity of gene expression is not sufficient to predict the biological nature and function of a protein. This can be particularly important in cancer research where post‐translational modifications of a protein can specifically contribute to the disease. To address this problem, several proteomic tools have been developed. Currently the most widely used proteomic tool is two‐dimensional protein gel electrophoresis (2‐DE), which can display protein expression patterns to a high degree of resolution. As an alternative to 2‐DE, a preliminary study using a new technique was employed to generate protein expression patterns from whole tissue extracts. Surface‐enhanced laser desorption/ionization (SELDI) allows the retention of proteins on a solid‐phase chromatographic surface (Protein Chip® Array) with direct detection of retained proteins by time of flight‐mass spectrometry (TOF‐MS). Using this system, we analyzed eight cases of renal cell carcinoma (RCC) including normal, peripheral and central tumor tissue as well as four microdissected cases of cervical intraepithelial neoplasia (CIN) and three microdissected cases of cervix uteri carcinoma. Differentially expressed proteins were found by comparing the protein expression patterns generated using SELDI‐based TOF‐MS of tumor tissue with normal and neoplastic tissue, respectively. By applying this fast and powerful Protein Chip array technology it becomes possible to investigate complex changes at the protein level in cancer associated with tumor development and progression.