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Updated: Aug 27, 2025
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
Published on: February 27, 2015
Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass
Carine Steiner1, Pierre Lescuyer2, Paul Cutler3
1Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland; BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland.
Liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) effectively quantifies proteins in formalin-fixed paraffin-embedded (FFPE) tissues. This advance aids biomarker discovery in breast cancer research using FFPE tumor samples.
Area of Science:
- Oncology
- Proteomics
- Biomarker Discovery
Background:
- Identifying clinically relevant biomarkers is crucial in oncology.
- Analyzing proteins in formalin-fixed paraffin-embedded (FFPE) tissues presents significant challenges.
- Biomarker discovery and verification studies often utilize FFPE tissues.
Purpose of the Study:
- To demonstrate the efficacy of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) for protein quantification in FFPE samples.
- To apply LC-MRM/MS for targeted measurement of proteins in various breast tumor subtypes.
- To validate LC-MRM/MS as a tool for biomarker discovery in FFPE tissues.
Main Methods:
- Development of an LC-MRM/MS method for simultaneous quantification of hundreds of peptides from FFPE samples.
- Targeted measurement of 200 proteins across 87 breast tumor samples (48 triple-negative, 19 HER2-overexpressing, 20 luminal A).
- Comparison of LC-MRM/MS results with immunohistochemistry and in situ hybridization data.
Main Results:
- Quantitative information obtained for 185 proteins, including known breast cancer markers (HER2, hormone receptors, Ki-67) and inflammation-related proteins.
- LC-MRM/MS data showed strong agreement with immunohistochemistry and chromogenic in situ hybridization.
- Identification of differentially expressed proteins in triple-negative breast cancer samples, suggesting potential novel biomarkers.
Conclusions:
- LC-MRM/MS assays reliably measure large sets of proteins from surrogate peptides in FFPE samples.
- This approach enables simultaneous quantification of target proteins across various pathways in tumor samples.
- LC-MRM/MS is a powerful tool for relative protein quantification in FFPE tissues and facilitates biomarker discovery.
