A novel method for analyzing formalin-fixed paraffin embedded (FFPE) tissue sections by mass spectrometry imaging
Yutaka Aoki1, Atsuhiko Toyama1, Takashi Shimada1
1Life Science Laboratory, Shimadzu Corporation, Kyoto 604-8511, Japan . ; Division of Advanced Clinical Proteomics, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan .
Summary
This study introduces a new method for mass spectrometry imaging (MS imaging) on formalin-fixed paraffin-embedded (FFPE) tissues. This technique allows for molecular biomarker discovery in archived clinical samples.
Area of Science:
- Biomedical Sciences
- Analytical Chemistry
- Molecular Imaging
Background:
- Mass spectrometry imaging (MS imaging) is a powerful technique for detecting biological molecules in tissue sections.
- Current MS imaging primarily uses frozen tissue sections, which are impractical for clinical tumor samples.
- Formalin-fixed paraffin-embedded (FFPE) tissues are widely available in clinical archives but challenging for MS imaging.
Purpose of the Study:
- To develop a novel sample preparation technique for MS imaging of FFPE tissue sections.
- To enable retrospective analysis of archived clinical samples for molecular biomarker discovery.
Main Methods:
- Developed a new protocol for MS imaging on FFPE tissue sections.
- FFPE sections were dewaxed and enzymatically digested in nanoliter droplets to preserve analyte localization.
- Analyzed peptide peaks from ovarian cancer FFPE sections using MS/MS for protein identification.
Main Results:
- Successfully obtained MS images from FFPE tissue sections, including archives up to 11 years old.
- The quality of mass spectra from FFPE sections was comparable to those from frozen sections.
- Identified peptide peaks from several proteins in ovarian cancer FFPE samples.
Conclusions:
- The novel sample preparation technique facilitates MS imaging on FFPE tissues.
- This method opens possibilities for retrospective studies on archived clinical samples.
- Enables molecular biomarker discovery and pharmacokinetic studies using readily available FFPE tissues.
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