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Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues
Carine Steiner1,2,3, Pierre Lescuyer4,5, Jean-Christophe Tille6
1Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland. carine.steiner@roche.com.
Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2019
Summary
Developing a highly multiplexed assay using selected reaction monitoring (SRM) on formalin-fixed paraffin-embedded (FFPE) tissues enables efficient analysis of potential protein biomarkers in clinical samples.
Area of Science:
- Biochemistry
- Proteomics
- Clinical Chemistry
Background:
- Identifying clinically relevant biomarkers is a significant challenge.
- Mass spectrometry-based technologies are crucial for biomarker discovery.
- Formalin-fixed paraffin-embedded (FFPE) tissues offer valuable clinical data.
Purpose of the Study:
- To demonstrate a highly multiplexed assay for analyzing FFPE tissues.
- To develop an assay for 200 proteins in breast tumor FFPE samples.
- To identify and prioritize potential protein biomarkers.
Main Methods:
- Application of selected reaction monitoring (SRM) for high-throughput analysis.
- Analysis of formalin-fixed paraffin-embedded (FFPE) tissues.
- Selection of peptides suitable for FFPE analysis.
- Assay design biased towards measurable proteins in clinical samples.
Main Results:
- A detailed method for developing a 200-protein assay in breast tumor FFPE tissues.
- Identification of peptides specific to FFPE tissues.
- Demonstration of assay's potential for biomarker candidate prioritization.
Conclusions:
- Highly multiplexed SRM assays are effective for analyzing FFPE tissues.
- This approach facilitates the analysis of large sample collections for biomarker discovery.
- The developed assay aids in narrowing down potential biomarkers for clinical relevance.
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