Gastrointestinal cancers are usually diagnosed at advanced stages, making a curative treatment difficult. Biomarkers can help to overcome this problem by allowing earlier diagnosis, and thus better therapy. Proteomics tools are novel technologies to identify such biomarkers. This review summarizes advances in biomarker detection using two-dimensional gel electrophoresis (2D-PAGE), chromatography and mass spectrometry technologies. 2D-PAGE combined with mass spectrometry has led to the identification of several differentially expressed proteins in cancer tissue. However, for serum analysis, 2D-PAGE has severe limitations. For serum-based cancer diagnosis, surface-enhanced laser desorption-ionization time-of-flight (SELDI-TOFTM) mass spectrometry is a promising new technology. The potential of proteins identified with this technology as novel cancer biomarkers still needs to be confirmed in clinical trials.

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