Related Experiment Video
Updated: Aug 8, 2025
09:00
A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
Published on: April 18, 2025
760
Targeted Quantitative Mass Spectrometry Analysis of Protein Biomarkers From Previously Stained Single Formalin-Fixed
Bradley L Ackermann1, Ryan D Morrison2, Salisha Hill2
1Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana.
Summary
This study introduces a mass spectrometry (MS) method to quantify proteins in stained formalin-fixed, paraffin-embedded tissue sections. This technique allows for deeper proteomic analysis of routinely processed clinical biopsy specimens.
Area of Science:
- Biochemistry
- Proteomics
- Histopathology
Background:
- Formalin-fixed, paraffin-embedded (FFPE) tissues are standard biopsy specimens.
- Mass spectrometry (MS) can quantify proteins in unstained FFPE sections.
- Staining and coverslips often preclude further analysis of FFPE tissues.
Purpose of the Study:
- To develop and validate an MS method for protein quantification in single, stained FFPE tissue sections.
- To assess the feasibility of analyzing proteins after routine histologic or immunohistochemical staining.
Main Methods:
- Proteins were analyzed from single 4-μm stained FFPE sections after coverslip removal.
- Tryptic digestion and targeted high-resolution liquid chromatography with tandem MS were employed.
- Stable isotope-labeled peptide standards were used for quantification.
Main Results:
- Proteins (PD-L1, RB1, CD73, HLA-DRA) were successfully quantified in stained sections.
- Low-abundance proteins RB1 and PD-L1 were detected in 31 and 35 of 50 sections, respectively.
- High-abundance proteins CD73 and HLA-DRA were detected in 49 and 50 sections, respectively, with low coefficients of variation.
Conclusions:
- Targeted MS protein quantification is feasible on stained FFPE tissue sections.
- This method adds a valuable proteomic data layer to routine clinical pathology specimens.
- The technique supports deeper insights into tissue biomarkers and disease mechanisms.
