Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens

Franz F. Dressler*, Jana Schoenfeld, Olga Revyakina, Daniel Vogele, Selina Kiefer, Jutta Kirfel, Timo Gemoll, Sven Perner

*Corresponding author for this work
4 Citations (Scopus)


Objectives: Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins. Methods: Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS). Results: Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions: Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.

Original languageEnglish
Article number10
JournalClinical Proteomics
Issue number1
Publication statusPublished - 12.2022

Research Areas and Centers

  • Research Area: Luebeck Integrated Oncology Network (LION)


Dive into the research topics of 'Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens'. Together they form a unique fingerprint.

Cite this