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

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...

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Bibliographic Details
Published in:Amino acids 2013-08, Vol.45 (2), p.205-218
Main Authors: Maes, Evelyne, Broeckx, Valérie, Mertens, Inge, Sagaert, Xavier, Prenen, Hans, Landuyt, Bart, Schoofs, Liliane
Format: Article
Language:English
Subjects:
Amino acids
Analytical Chemistry
analytical methods
Biochemical Engineering
Biochemistry
Biomedical and Life Sciences
Chromatography, Liquid
clinical trials
crosslinking
Fixatives
Formaldehyde
formalin
Hospitals
Human
Humans
Life Sciences
Mass Spectrometry
Mathematical analysis
Neurobiology
paraffin
Paraffin Embedding
Platforms
proteins
Proteins - analysis
proteome
Proteome - analysis
Proteomics
Retrospective Studies
Review Article
Strategy
tissue
Tissue Fixation
Tissue Preservation - methods
tissues
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Summary: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.
ISSN:0939-4451
1438-2199
DOI:10.1007/s00726-013-1494-0