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Updated: Feb 5, 2026

Expanding the Comprehension of the Tumor Microenvironment using Mass Spectrometry Imaging of Formalin-Fixed and Paraffin-Embedded Tissue Samples
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In MALDI-Mass Spectrometry Imaging on Formalin-Fixed Paraffin-Embedded Tissue Specimen Section Thickness

Rémi Longuespée1, Katharina Kriegsmann2, Martin Cremer2

  • 1Institute of Pathology, University of Heidelberg, Heidelberg, Germany.

Proteomics. Clinical Applications
|September 15, 2018
PubMed
Abstract

Insights

Thinner tissue sections (1 μm) in matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) yield higher spectral intensities than thicker sections (5 μm). This emphasizes the need for standardized protocols in MALDI-MSI biomarker discovery.

Area of Science:

  • Biomolecular analysis
  • Mass spectrometry imaging
  • Tissue-based diagnostics

Background:

  • Standardized sample preparation is crucial for reliable matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) results.
  • Formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMAs) are used for comparative analyses in MSI.
  • The impact of tissue section thickness on spectral intensities in FFPE TMAs requires investigation.

Purpose of the Study:

  • To investigate the effect of tissue section thickness on spectral intensities in FFPE TMAs using MALDI-MSI.
  • To determine the optimal section thickness for maximizing spectral intensity and reliability in MALDI-MSI analyses.

Main Methods:

  • Tissue microarrays (TMAs) comprising ten different tissues from ten patients (n=200 cores) were prepared.
  • TMAs were sectioned at three different thicknesses: 1 μm, 3 μm, and 5 μm.
  • Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was performed, and spectral intensities were analyzed.

Main Results:

  • Thinner tissue sections (1 μm) consistently showed higher spectral intensities compared to thicker sections (5 μm).
  • A significant majority of peaks (98.6%) exhibited higher intensities in 1 μm sections versus 5 μm sections (p < 0.01).
  • 28.4% and 2.1% of m/z values showed at least two- and threefold intensity differences, respectively, between 1 μm and 5 μm sections (p < 0.01).

Conclusions:

  • A section thickness of 1 μm enhances spectral intensities in MALDI-MSI compared to 5 μm sections.
  • These findings underscore the importance of standardized protocols for identifying clinically relevant biomarkers using MSI.
  • TMAs are advantageous for comparative MSI analyses due to reduced variability in section thickness effects.
Keywords:
FFPEMALDI-mass spectrometry imagingproteomicssample preparationtissue section thickness

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