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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and signal-to-noise ratio for the analyte. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.
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Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
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Updated: Sep 19, 2025

Whole-body Mass Spectrometry Imaging by Infrared Matrix-assisted Laser Desorption Electrospray Ionization IR-MALDESI
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MSI-Explorer: Napari-Powered Tool for Mass Spectrometry Imaging Data Analysis.

Nay Min Min Thaw Saw1, Lennart Kowitz1, Peter Lampen1

  • 1Leibniz-Institut für Analytische Wissenschaften─ISAS─e.V., Otto-Hahn-Str. 6b, Dortmund 44227, Germany.

Analytical Chemistry
|June 6, 2025
PubMed
Summary
This summary is machine-generated.

MSI-Explorer is a new napari plugin for mass spectrometry imaging (MSI) data analysis. It offers open-source tools for spatial omics research, improving data processing, visualization, and quantification.

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Area of Science:

  • Biomedical imaging
  • Spatial omics
  • Mass spectrometry imaging (MSI)

Background:

  • Mass spectrometry imaging (MSI) is crucial for label-free spatial localization of biomolecules in biological samples.
  • Limited open-source tools for MSI data analysis hinder its widespread adoption and integration with other imaging platforms.
  • Napari, a popular image analysis platform, lacks native support for MSI data, restricting its utility in spatial omics research.

Purpose of the Study:

  • To introduce MSI-Explorer, the first napari plugin designed for interactive mass spectrometry imaging data analysis.
  • To provide a user-friendly interface for MSI data processing, spectral analysis, molecular annotation, and quantification within the napari environment.
  • To bridge the gap between MSI data analysis and the broader bioimaging community by promoting open and accessible tools.

Main Methods:

  • Development of MSI-Explorer as a napari plugin.
  • Integration of MSI-specific functionalities with napari's visualization capabilities.
  • Implementation of interactive tools for image curation, multimodal analysis, and efficient data processing.

Main Results:

  • MSI-Explorer offers an interactive and user-friendly interface for MSI data analysis.
  • The plugin enables comprehensive processing, spectral analysis, molecular annotation, and quantification of MSI datasets.
  • It enhances image curation and facilitates multimodal analysis within napari.

Conclusions:

  • MSI-Explorer addresses the need for accessible, open-source tools in mass spectrometry imaging.
  • The plugin enhances the utility of napari for spatial omics and bioimaging research.
  • It promotes integrated and efficient analysis of complex MSI data.