Cell-based proteome analysis: the first stage in the pipeline for biomarker discovery

The early detection of a distinct disease is crucial for a successful treatment and depends on a sensitive as well as specific diagnosis. In last years tremendous attempts were undertaken to identify new biomarker applying proteomics, but no relevant candidate has been identified for clinical application. Although proteomics is enabling quantitative and qualitative analysis of proteins within complex mixtures it could not significantly contribute to this field. Therefore, different proteomics approaches have been established focusing on the direct analysis of cell populations involved in pathogenic processes to identify candidate biomarkers even for in vitro diagnosis. Here, we will outline approaches applying cell- and tissue based proteome analysis as the first decisive step in the pipeline for the discovery of new diagnostic biomarkers. We will show examples for analysing precursor lesions of the pancreatic ductal adenocarcinoma (PDAC), nephron glomeruli and fibrotic and non-fibrotic liver tissue. This article provides also an overview about currently available techniques in the field of cell enrichment and quantitative proteome analysis of lowest amounts of sample.