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Updated: May 30, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

Peptide extraction from formalin-fixed paraffin-embedded tissue.

Katherine J Heaton¹, Stephen R Master

¹Phoenix S&T, Chester, Pennsylvania, USA.

Current Protocols in Protein Science

|August 16, 2011

Summary

This summary is machine-generated.

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This study details methods for extracting tryptic peptides from formalin-fixed, paraffin-embedded (FFPE) tissues. These peptides are prepared for nano-reverse-phase liquid chromatography/tandem mass spectrometry (nRPLC-MS/MS) analysis.

Area of Science:

Biochemistry
Proteomics
Analytical Chemistry

Background:

Formalin-fixed, paraffin-embedded (FFPE) tissues are a valuable resource for retrospective studies.
Extracting high-quality peptides from FFPE tissues is crucial for proteomic analysis.
Existing methods for FFPE tissue processing can be time-consuming and may lead to peptide degradation.

Purpose of the Study:

To describe optimized protocols for extracting tryptic peptides from FFPE tissues.
To prepare FFPE-derived peptides for nano-reverse-phase liquid chromatography/tandem mass spectrometry (nRPLC-MS/MS) analysis.
To offer alternative methods for efficient peptide extraction.

Main Methods:

Deparaffinization of FFPE tissues.
Cellular material isolation via needle dissection or laser capture microdissection (LCM).

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Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows

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Last Updated: May 30, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue

Published on: September 2, 2013

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

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Published on: March 26, 2011

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Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows

Published on: January 16, 2018

Heat-induced reversal of formalin cross-links.

Peptide extraction using filter-aided sample preparation (FASP) or commercial Liquid Tissue kits.

Preparation for nRPLC-MS/MS analysis.

Main Results:

Successful extraction of tryptic peptides from FFPE tissues.
Demonstrated compatibility of extracted peptides with nRPLC-MS/MS.
Provided two distinct protocols for peptide extraction, catering to different experimental needs.

Conclusions:

The described methods enable efficient tryptic peptide extraction from FFPE tissues.
These protocols facilitate downstream proteomic analysis using nRPLC-MS/MS.
The methods offer flexibility and reliability for FFPE sample processing in research.