Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization

Four single consecutive murine kidney tissue specimens were prepared with the direct trypsinization with RapiGest (DTR) approach or with the filter aided sample preparation (FASP) protocol using both 10k and 30k filter devices and analyzed by label-free, quantitative liquid chromatography – tandem mass spectrometry (LC-MS/MS). Furthermore, we probed compatibility of the DTR protocol for the analysis of common histological stainings, namely hematoxylin & eosin (H&E), hematoxylin, and hemalaun. These were proteomically compared to an unstained control by analyzing four human tonsil FFPE tissues per condition.