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

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Tonsil, Kidney

SUBMITTER: Melanie Christine Föll

LAB HEAD: Oliver Schilling

PROVIDER: PXD006401 | Pride | 2018-08-15

REPOSITORIES: Pride

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

Föll Melanie Christine MC Fahrner Matthias M Oria Victor Oginga VO Kühs Markus M Biniossek Martin Lothar ML Werner Martin M Bronsert Peter P Schilling Oliver O

Clinical proteomics 20180306

<h4>Background</h4>Proteomic analyses of clinical specimens often rely on human tissues preserved through formalin-fixation and paraffin embedding (FFPE). Minimal sample consumption is the key to preserve the integrity of pathological archives but also to deal with minimal invasive core biopsies. This has been achieved by using the acid-labile surfactant RapiGest in combination with a direct trypsinization (DTR) strategy. A critical comparison of the DTR protocol with the most commonly used filt ...[more]

PMID: 29527141

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