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Updated: Jan 28, 2026
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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
Published on: September 2, 2013
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Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis?
Malte Bayer1, Linus Angenendt2, Christoph Schliemann2
1Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty, University of Münster, Münster, Germany.
Journal of Mass Spectrometry : JMS
|March 5, 2019
Summary
Formalin-fixed and paraffin-embedded (FFPE) tissue proteomics offers valuable insights but faces limitations. FFPE processing causes protein modifications, hindering the identification of low-level proteins and specific modifications.
Area of Science:
- Proteomics
- Biochemistry
- Analytical Chemistry
Background:
- Formalin-fixed and paraffin-embedded (FFPE) tissues are crucial for long-term specimen archiving.
- FFPE processing preserves tissue structure but introduces significant protein modifications and cross-links.
Purpose of the Study:
- To evaluate published workflows for FFPE-tissue analysis using proteomics.
- To assess the impact of FFPE processing on protein identification and modification analysis.
Main Methods:
- Fit-for-purpose proteomics technologies were applied to FFPE-tissue samples.
- Several published FFPE-tissue workflows were evaluated.
Main Results:
- FFPE processing results in numerous irreversible protein modifications and cross-links.
- Analysis of abundant proteins in FFPE is feasible, but low-level protein and modification identification is challenging.
- High-quality spectra are essential for reliable peptide assignment, potentially reducing protein identification numbers.
Conclusions:
- Proteomics analysis of FFPE tissues is valuable but has inherent limitations due to chemical modifications.
- Careful consideration of FFPE-induced artifacts is necessary for accurate interpretation of proteomic data.
- Prioritizing data quality and analytical chemistry standards is critical for reliable FFPE proteomics.
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