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Related Experiment Videos

Efficient method for the proteomic analysis of fixed and embedded tissues.

Darryl Erik Palmer-Toy1, Bryan Krastins, David A Sarracino

  • 1Harvard Partners Center for Genetics & Genomics, Cambridge, Massachusetts, USA.

Journal of Proteome Research
|December 13, 2005
PubMed
Summary

Formalin-fixed and paraffin-embedded (FFPE) tissues can now be analyzed for proteins. New methods efficiently extract peptides from FFPE tissues for liquid chromatography-mass spectrometry (LC-MS) analysis.

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Area of Science:

  • Biochemistry
  • Proteomics
  • Analytical Chemistry

Background:

  • Formalin-fixed and paraffin-embedded (FFPE) tissues are the most common form of archived clinical samples.
  • Proteomic analysis of FFPE tissues is challenging due to protein cross-linking and embedding medium interference.
  • Most global tissue archives are stored as FFPE, limiting their use in proteomic studies.

Purpose of the Study:

  • To develop and validate a method for effective proteomic analysis of FFPE tissues.
  • To enable the use of archived FFPE samples for large-scale proteomic investigations.
  • To demonstrate the utility of FFPE samples in LC-MS-based proteomic studies.

Main Methods:

  • Optimized conditions for removing embedding medium from FFPE tissues.

Related Experiment Videos

  • Established a robust protein digestion protocol to release tryptic peptides from fixed proteins.
  • Utilized liquid chromatography-mass spectrometry (LC-MS) for peptide identification and analysis.

    • Main Results:

    • Successfully extracted informative tryptic peptides from FFPE tissues.
    • Demonstrated that peptide identification from FFPE tissues favorably compares to matched fresh frozen tissues.
    • Achieved a high level of sequence coverage for target proteins from FFPE samples.

    Conclusions:

    • The developed method enables reliable proteomic analysis of FFPE tissues.
    • This approach significantly expands the utility of archived FFPE samples for research.
    • FFPE tissue analysis via LC-MS is a viable strategy for advancing proteomic discovery.