Related Experiment Video
Updated: Jun 4, 2026
09:00
A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
Published on: April 18, 2025
Protein mass spectrometry applications on FFPE tissue sections
Carol B Fowler1, Timothy J O'Leary, Jeffrey T Mason
1Armed Forces Institute of Pathology, Washington, DC, USA. carol.fowler1@us.army.mil
Methods in Molecular Biology (Clifton, N.J.)
|March 4, 2011
Summary
Formalin-fixed, paraffin-embedded (FFPE) tissue archives offer valuable proteomic data for disease research. New methods enable peptide recovery from FFPE tissues, allowing proteomic analysis of archival samples.
Area of Science:
- Biochemistry
- Pathology
- Analytical Chemistry
Background:
- Formalin-fixed, paraffin-embedded (FFPE) tissues are crucial archives for disease research, containing proteomic information linked to known patient outcomes.
- Advances in proteomic techniques now allow for the recovery of peptides from FFPE tissues, offering a representation of the original proteome.
- These methodologies are essential for studying diseases where fresh or frozen tissues are unavailable.
Purpose of the Study:
- To describe methods for proteomic analysis of FFPE tissues.
- To highlight the utility of FFPE archives for proteomic investigations.
- To detail the application of liquid chromatography and mass spectrometry for FFPE proteomic analysis.
Main Methods:
- Utilizing heat-induced antigen retrieval techniques, adapted from immunohistochemistry.
- Employing liquid chromatography (LC) for peptide separation.
- Applying mass spectrometry (MS) for peptide identification and quantification.
Main Results:
- Successful peptide recovery from FFPE tissues, providing a reasonable proteomic representation.
- Enabling qualitative proteomic analysis of archival FFPE specimens.
- Demonstrating the feasibility of LC-MS/MS for FFPE tissue proteome profiling.
Conclusions:
- Proteomic analysis of FFPE tissues is now feasible using advanced methodologies.
- FFPE archives are a valuable resource for retrospective proteomic studies in disease research.
- Liquid chromatography and mass spectrometry are key techniques for unlocking proteomic insights from FFPE samples.
Related Concept Videos
01:19MALDI-TOF Mass Spectrometry
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
01:33Peptide Identification Using Tandem Mass Spectrometry
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
01:21Mass Spectrometry: Complex Analysis
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...