Cancer is one of the most frequent causes of death in Germany and worldwide. Despite great efforts during the last decades, there is still an urgent need for new diagnostic and therapeutic target molecules. Quantitative proteome analysis allows the discovery of novel proteins which are associated with malignancies. Pathophysiological mechanisms can be clarified and diagnostic tools (biomarkers) or therapeutic targets can be identified. In our group a main focus lies on the investigation of colorectal cancer, which is the second most frequent kind of cancer in Germany. Another emphasis is on the investigation of pancreatic cancer and malignancies of the liver. We make use of methods enabling the selective isolation of cell populations out of crude tissue in order to identify distinctive differences between tumor cells and the corresponding non-tumorous cells. Newly identified target proteins are investigated regarding their functional and diagnostic relevance by means of targeted mass spectrometry and antibody-based methods.