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Updated: Aug 30, 2025
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Sample Preparation for Metabolic Profiling using MALDI Mass Spectrometry Imaging
Published on: December 22, 2020
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Simultaneous metabolite MALDI-MSI, whole exome and transcriptome analysis from formalin-fixed paraffin-embedded
Lisa Kreutzer1,2, Peter Weber1,2, Theresa Heider1,2
1Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.
Summary
Simultaneous molecular profiling of formalin-fixed paraffin-embedded (FFPE) tissues using MALDI-MSI, whole-exome sequencing, and RNA sequencing is feasible. This integrated approach reliably analyzes FFPE tissues for genomic and transcriptomic insights.
Area of Science:
- Biomedical research
- Molecular pathology
- Genomics and transcriptomics
Background:
- Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enables spatial analysis of biomolecules in tissues.
- Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for clinical diagnostics but pose challenges for multi-omic analyses.
- Integrating various molecular data types from the same FFPE section is essential for comprehensive biological insights.
Purpose of the Study:
- To demonstrate the feasibility and reliability of simultaneous MALDI-MSI, whole-exome sequencing (WES), and RNA sequencing from the same FFPE tissue sections.
- To evaluate the impact of different FFPE tissue processing steps (untreated, HE staining, MALDI-MSI analysis) on subsequent genomic and transcriptomic data quality.
- To establish a workflow for multi-omic profiling of FFPE tissues.
Main Methods:
- Extraction of genomic DNA and total RNA from FFPE tissue sections subjected to different treatments (untreated, HE stained, MALDI-MSI analyzed).
- Generation of MALDI-MSI data using a time-of-flight analyzer.
- Whole-exome sequencing (WES) using a low-input protocol for variant detection and mutational burden analysis.
- 3'-RNA sequencing for transcriptome profiling.
Main Results:
- All generated data (MALDI-MSI, WES, RNA-seq) met quality criteria.
- Common single-nucleotide variants (SNVs) were identified across processing stages, alongside FFPE-specific artifactual variants.
- Tumor mutational burden and mutational signatures were consistent within patients and showed high overlap between processing groups.
- Transcriptome profiles exhibited high correlation across different processing stages.
Conclusions:
- Simultaneous multi-omic molecular profiling (MALDI-MSI, WES, RNA-seq) of FFPE tissue sections is achievable and dependable.
- The described workflow allows for integrated analysis of spatial, genomic, and transcriptomic information from a single FFPE sample.
- This approach enhances the utility of FFPE archives for comprehensive cancer research and biomarker discovery.
