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

DNA chip technologies are the most exiting genomic tools, which were develo ped within the last few years. It is, however, evident that knowledge of th e gene sequence or the quantity of gene expression is not sufficient to pre dict the biological nature and function of a protein. This can be particula rly important in cancer research where post-translational modifications of a protein can specifically contribute to the disease. To address this probl em, 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 resolutio n. As an alternative to 2-DE, a preliminary study using a new technique was employed to generate protein expression patterns from whole tissue extract s. Surface-enhanced laser desorption/ionization (SELDI) allows the retentio n of proteins on a solid-phase chromatographic surface (ProteinChip((R)) Ar ray) with direct detection of retained proteins by time of flight-mass spec trometry (TOF-MS). Using this system, we analyzed eight cases of renal cell carcinoma (RCC) including normal, peripheral and central tumor tissue as w ell 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 neoplast ic tissue, respectively. By applying this fast and powerful ProteinChip arr ay technology it becomes possible to investigate complex changes at the pro tein level in cancer associated with tumor development and progression.