The identification of molecular changes underlying clinical pathogenic processes is often hampered by significant cellular diversity of the tissue. Pathogenic aberrant cells are surrounded by cells originating e.g., from stroma, the vascular system or other neighbouring cell types, which lead to under-representation of interesting cells when analysing whole tissue specimen. Therefore, selection of relevant cell types for detailed analysis is an absolute prerequisite for in depth elucidation of underlying biological processes. Microdissection offers the advantage to select for a biologically relevant cell type which is often in low abundance. Here, we present a proteomics approach allowing us to analyse 1,000 microdissected cells stemming from pancreatic carcinoma precursor lesions applying fluorescence dye saturation labeling.