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In clinical research, large cohorts of biological samples are required to search for diagnostic, prognostic and predictive markers. Markers are indicators of some biological state or condition. Since the concentration of low abundant proteins is significantly higher inside or within the vicinity of the affected tissue, freshly frozen clinical samples are in a high demand for biomarker studies. However, fresh tissues of sufficiently high quality are scarce, resulting in a poor availability for biomarker discovery research. On the other hand, formalin-fixed paraffin-embedded (FFPE) tissues have been routinely collected and archived for pathological investigation. As a consequence, there are millions of FFPE tissue clinical samples available worldwide. As formaldehyde enables long term stability of proteins and as this method preserves the architectural structure of the tissue, FFPE samples therefore represent a good alternative to fresh tissue samples. Unfortunately, formalin-induced protein cross-links and unknown protein modifications impede the analysis of FFPE-tissue-extracted proteins. Although several research groups tried to achieve an efficient FFPE proteomics workflow, there exists a general consensus that a successful standard operating procedure is still not available. In this project, we will therefore develop a reproducible FFPE proteomics procedure enabling an accurate and correct analysis of FFPE proteins. The technological challenges of this project: 1) formalin-induced protein cross-links impede the extraction of full-length proteins; 2) unknown and unexpected protein modifications impede unambiguous protein identification. Once the FFPE proteomics procedure is developed and optimized, it can be used in the search for answers to different clinical questions.