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Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives

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Abstract

Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.

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Acknowledgments

The authors acknowledge the Flemish Institute for Technological Research (VITO), the Industrial Research Fund (KU Leuven) and the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Research Group of Functional Genomics and Proteomics, University of Leuven, Naamsestraat 59, Leuven, Belgium

    Evelyne Maes, Valérie Broeckx, Bart Landuyt & Liliane Schoofs

  2. Flemish Institute for Technological Research (VITO), Mol, Belgium

    Evelyne Maes & Inge Mertens

  3. CFP-CeProMa, University of Antwerp, Antwerp, Belgium

    Inge Mertens

  4. Centre for Translational Cell and Tissue Research, Leuven, Belgium

    Xavier Sagaert

  5. Department of Gastro-enterology, Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium

    Hans Prenen

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  1. Evelyne Maes
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Maes, E., Broeckx, V., Mertens, I. et al. Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 45, 205–218 (2013). https://doi.org/10.1007/s00726-013-1494-0

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